[med-svn] [cytoscape] 04/07: New upstream version 3.1.0
Andreas Tille
tille at debian.org
Sun Dec 3 18:13:51 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository cytoscape.
commit 83cb326fb46f8cda0c273f9f557de6ae32377a4c
Author: Andreas Tille <tille at debian.org>
Date: Sun Dec 3 19:08:54 2017 +0100
New upstream version 3.1.0
---
README.txt | 128 +
acceptance-testing/README | 4 +
acceptance-testing/pom.xml | 33 +
.../java/cytoscape/acceptance/FirstGUITest.java | 67 +
application/pom.xml | 465 +
application/src/main/java/cytoscape/CyEdge.java | 166 +
application/src/main/java/cytoscape/CyMain.java | 489 +
application/src/main/java/cytoscape/CyNetwork.java | 312 +
.../src/main/java/cytoscape/CyNetworkAdapter.java | 59 +
.../src/main/java/cytoscape/CyNetworkData.java | 45 +
.../src/main/java/cytoscape/CyNetworkEvent.java | 108 +
.../src/main/java/cytoscape/CyNetworkListener.java | 57 +
.../main/java/cytoscape/CyNetworkTitleChange.java | 32 +
application/src/main/java/cytoscape/CyNode.java | 305 +
.../src/main/java/cytoscape/CyStartupListener.java | 62 +
application/src/main/java/cytoscape/Cytoscape.java | 2023 +
.../src/main/java/cytoscape/CytoscapeInit.java | 680 +
.../cytoscape/CytoscapeModifiedNetworkManager.java | 138 +
.../src/main/java/cytoscape/CytoscapeVersion.java | 100 +
.../src/main/java/cytoscape/JavaVersion.java | 121 +
.../cytoscape/actions/AlignHorizontalAction.java | 98 +
.../cytoscape/actions/AlignVerticalAction.java | 99 +
.../actions/AlphabeticalSelectionAction.java | 143 +
.../cytoscape/actions/AnimatedLayoutAction.java | 169 +
.../java/cytoscape/actions/ApplyLayoutAction.java | 91 +
.../cytoscape/actions/ApplyVisualStyleAction.java | 71 +
.../main/java/cytoscape/actions/ArrangeAction.java | 127 +
.../cytoscape/actions/BackgroundColorAction.java | 119 +
.../cytoscape/actions/BendSelectedEdgesAction.java | 95 +
.../java/cytoscape/actions/BirdsEyeViewAction.java | 119 +
.../java/cytoscape/actions/BookmarkAction.java | 92 +
.../cytoscape/actions/CheckBoxFileChooser.java | 102 +
.../actions/CloneGraphInNewWindowAction.java | 139 +
.../cytoscape/actions/CreateNetworkViewAction.java | 196 +
.../java/cytoscape/actions/CytoPanelAction.java | 122 +
.../cytoscape/actions/DeSelectAllEdgesAction.java | 86 +
.../cytoscape/actions/DeSelectAllNodesAction.java | 86 +
.../main/java/cytoscape/actions/DeleteAction.java | 191 +
.../main/java/cytoscape/actions/DeleteEdit.java | 93 +
.../java/cytoscape/actions/DeselectAllAction.java | 85 +
.../cytoscape/actions/DestroyNetworkAction.java | 98 +
.../actions/DestroyNetworkViewAction.java | 101 +
.../cytoscape/actions/EdgeManipulationAction.java | 122 +
.../main/java/cytoscape/actions/ExitAction.java | 73 +
.../java/cytoscape/actions/ExpFileChooser.java | 113 +
.../main/java/cytoscape/actions/ExportAction.java | 100 +
.../java/cytoscape/actions/ExportAsGMLAction.java | 266 +
.../cytoscape/actions/ExportAsGraphicsAction.java | 277 +
.../actions/ExportAsInteractionsAction.java | 227 +
.../cytoscape/actions/ExportAsXGMMLAction.java | 286 +
.../actions/ExportEdgeAttributesAction.java | 68 +
.../actions/ExportNetworksAsNNFAction.java | 283 +
.../actions/ExportNodeAttributesAction.java | 68 +
.../java/cytoscape/actions/ExportVizmapAction.java | 156 +
.../java/cytoscape/actions/FitContentAction.java | 83 +
.../src/main/java/cytoscape/actions/GinyUtils.java | 383 +
.../actions/GraphObjectSelectionAction.java | 74 +
.../java/cytoscape/actions/HelpAboutAction.java | 113 +
.../actions/HelpContactHelpDeskAction.java | 69 +
.../java/cytoscape/actions/HelpContentsAction.java | 72 +
.../java/cytoscape/actions/HideSelectedAction.java | 104 +
.../cytoscape/actions/HideSelectedEdgesAction.java | 71 +
.../cytoscape/actions/HideSelectedNodesAction.java | 82 +
.../cytoscape/actions/HideSelectedNodesEdit.java | 91 +
.../actions/ImportEdgeAttributesAction.java | 105 +
.../actions/ImportExpressionMatrixAction.java | 194 +
.../cytoscape/actions/ImportGraphFileAction.java | 176 +
.../actions/ImportNodeAttributesAction.java | 197 +
.../java/cytoscape/actions/ImportVizmapAction.java | 149 +
.../actions/InvertSelectedEdgesAction.java | 90 +
.../actions/InvertSelectedNodesAction.java | 91 +
.../actions/ListFromFileSelectionAction.java | 147 +
.../java/cytoscape/actions/LoadNetworkTask.java | 366 +
.../main/java/cytoscape/actions/LoggerAction.java | 23 +
.../java/cytoscape/actions/MemoryUsageAction.java | 70 +
.../java/cytoscape/actions/NewNetworkAction.java | 43 +
.../java/cytoscape/actions/NewSessionAction.java | 88 +
.../actions/NewWindowSelectedNodesEdgesAction.java | 144 +
.../actions/NewWindowSelectedNodesOnlyAction.java | 153 +
.../java/cytoscape/actions/OpenSessionAction.java | 269 +
.../cytoscape/actions/PluginInstallAction.java | 93 +
.../cytoscape/actions/PluginManagerAction.java | 194 +
.../java/cytoscape/actions/PluginUpdateAction.java | 85 +
.../java/cytoscape/actions/PreferenceAction.java | 87 +
.../main/java/cytoscape/actions/PrintAction.java | 125 +
.../java/cytoscape/actions/ProxyServerAction.java | 86 +
.../actions/RotateSelectedNodesAction.java | 82 +
.../java/cytoscape/actions/SaveSessionAction.java | 217 +
.../cytoscape/actions/SaveSessionAsAction.java | 123 +
.../actions/SelectAdjacentEdgesAction.java | 111 +
.../java/cytoscape/actions/SelectAllAction.java | 90 +
.../cytoscape/actions/SelectAllEdgesAction.java | 85 +
.../cytoscape/actions/SelectAllNodesAction.java | 84 +
.../actions/SelectConnectedNodesAction.java | 92 +
.../actions/SelectFirstNeighborsAction.java | 98 +
.../cytoscape/actions/SelectionModeAction.java | 141 +
.../actions/SetVisualPropertiesAction.java | 114 +
.../main/java/cytoscape/actions/ShowAllAction.java | 77 +
.../actions/ShowCustomGraphicsManagerAction.java | 74 +
.../actions/ShowGraphicsDetailsAction.java | 119 +
.../actions/StraightenSelectedEdgesAction.java | 95 +
.../actions/ToggleVisualMapperAction.java | 97 +
.../cytoscape/actions/UnHideSelectedAction.java | 81 +
.../actions/UnHideSelectedEdgesAction.java | 84 +
.../actions/UnHideSelectedNodesAction.java | 85 +
.../actions/WebServiceNetworkImportAction.java | 25 +
.../main/java/cytoscape/actions/ZoomAction.java | 88 +
.../java/cytoscape/actions/ZoomSelectedAction.java | 88 +
.../src/main/java/cytoscape/actions/package.html | 14 +
.../cytoscape/command/AbstractCommandHandler.java | 382 +
.../java/cytoscape/command/CyCommandException.java | 106 +
.../java/cytoscape/command/CyCommandHandler.java | 199 +
.../java/cytoscape/command/CyCommandManager.java | 281 +
.../java/cytoscape/command/CyCommandNamespace.java | 63 +
.../java/cytoscape/command/CyCommandResult.java | 226 +
.../java/cytoscape/data/AttribTopoGraphNode.java | 68 +
.../main/java/cytoscape/data/AttributeFilter.java | 63 +
.../java/cytoscape/data/AttributeSaverDialog.java | 481 +
.../java/cytoscape/data/AttributeValueVisitor.java | 64 +
.../src/main/java/cytoscape/data/CyAttributes.java | 797 +
.../main/java/cytoscape/data/CyAttributesImpl.java | 1362 +
.../java/cytoscape/data/CyAttributesUtils.java | 880 +
.../java/cytoscape/data/CyNetworkUtilities.java | 245 +
.../main/java/cytoscape/data/ExpressionData.java | 1102 +
.../main/java/cytoscape/data/ImportHandler.java | 531 +
.../src/main/java/cytoscape/data/Interaction.java | 155 +
.../src/main/java/cytoscape/data/NetworkData.java | 834 +
.../src/main/java/cytoscape/data/SelectEvent.java | 211 +
.../java/cytoscape/data/SelectEventListener.java | 52 +
.../src/main/java/cytoscape/data/SelectFilter.java | 489 +
.../src/main/java/cytoscape/data/Semantics.java | 513 +
.../java/cytoscape/data/annotation/Annotation.java | 365 +
.../data/annotation/AnnotationDescription.java | 146 +
.../data/annotation/FlattenIntVectors.java | 95 +
.../java/cytoscape/data/annotation/Ontology.java | 296 +
.../data/annotation/OntologyDescription.java | 101 +
.../cytoscape/data/annotation/OntologyTerm.java | 377 +
.../java/cytoscape/data/annotation/package.html | 12 +
.../readers/AnnotationFlatFileReader.java | 270 +
.../annotation/readers/AnnotationXmlReader.java | 142 +
.../annotation/readers/OntologyFlatFileReader.java | 242 +
.../data/annotation/readers/OntologyXmlReader.java | 143 +
.../cytoscape/data/annotation/readers/package.html | 12 +
.../java/cytoscape/data/attr/CountedIterator.java | 51 +
.../java/cytoscape/data/attr/MultiHashMap.java | 226 +
.../data/attr/MultiHashMapDefinition.java | 172 +
.../data/attr/MultiHashMapDefinitionListener.java | 58 +
.../cytoscape/data/attr/MultiHashMapListener.java | 76 +
.../attr/util/ExtensibleMultiHashMapModel.java | 49 +
.../data/attr/util/MultiHashMapFactory.java | 59 +
.../data/attr/util/MultiHashMapHelpers.java | 333 +
.../data/attr/util/MultiHashMapModel.java | 1029 +
.../main/java/cytoscape/data/mRNAMeasurement.java | 122 +
.../cytoscape/data/ontology/DBCrossReferences.java | 113 +
.../java/cytoscape/data/ontology/DBReference.java | 158 +
.../main/java/cytoscape/data/ontology/GOTerm.java | 120 +
.../java/cytoscape/data/ontology/GeneOntology.java | 139 +
.../java/cytoscape/data/ontology/Ontology.java | 434 +
.../cytoscape/data/ontology/OntologyFactory.java | 113 +
.../java/cytoscape/data/ontology/OntologyTerm.java | 206 +
.../main/java/cytoscape/data/ontology/Triple.java | 196 +
.../ontology/readers/DBCrossReferenceReader.java | 183 +
.../data/ontology/readers/DBXrefKeywords.java | 61 +
.../data/ontology/readers/OBOFlatFileReader.java | 475 +
.../data/ontology/readers/OBOHeaderTags.java | 58 +
.../cytoscape/data/ontology/readers/OBOTags.java | 151 +
.../data/ontology/readers/OntologyReader.java | 75 +
.../src/main/java/cytoscape/data/package.html | 13 +
.../data/readers/AbstractGraphReader.java | 147 +
.../cytoscape/data/readers/BookmarkReader.java | 112 +
.../cytoscape/data/readers/CyAttributesReader.java | 404 +
.../data/readers/CytoscapeSessionReader.java | 1256 +
.../cytoscape/data/readers/EqnAttrTracker.java | 198 +
.../java/cytoscape/data/readers/GMLException.java | 54 +
.../main/java/cytoscape/data/readers/GMLNode.java | 225 +
.../java/cytoscape/data/readers/GMLParser.java | 323 +
.../java/cytoscape/data/readers/GMLReader.java | 1244 +
.../main/java/cytoscape/data/readers/GMLTag.java | 91 +
.../main/java/cytoscape/data/readers/GMLTree.java | 543 +
.../java/cytoscape/data/readers/GMLWriter.java | 615 +
.../java/cytoscape/data/readers/GraphReader.java | 91 +
.../cytoscape/data/readers/InteractionsReader.java | 362 +
.../main/java/cytoscape/data/readers/KeyValue.java | 60 +
.../cytoscape/data/readers/MetadataEntries.java | 69 +
.../cytoscape/data/readers/MetadataParser.java | 212 +
.../java/cytoscape/data/readers/NNFParser.java | 150 +
.../java/cytoscape/data/readers/NNFReader.java | 149 +
.../data/readers/NestedNetworkReader.java | 51 +
.../cytoscape/data/readers/TextFileReader.java | 135 +
.../cytoscape/data/readers/TextHttpReader.java | 173 +
.../java/cytoscape/data/readers/TextJarReader.java | 144 +
.../cytoscape/data/readers/VisualStyleBuilder.java | 314 +
.../cytoscape/data/readers/XGMMLException.java | 52 +
.../java/cytoscape/data/readers/XGMMLParser.java | 1755 +
.../java/cytoscape/data/readers/XGMMLReader.java | 879 +
.../main/java/cytoscape/data/readers/package.html | 12 +
.../java/cytoscape/data/servers/BioDataServer.java | 883 +
.../data/servers/BioDataServerInterface.java | 219 +
.../cytoscape/data/servers/BioDataServerRmi.java | 366 +
.../cytoscape/data/servers/OntologyServer.java | 221 +
.../main/java/cytoscape/data/servers/clear.java | 88 +
.../cytoscape/data/servers/getCanonicalName.java | 87 +
.../java/cytoscape/data/servers/getCommonName.java | 87 +
.../cytoscape/data/servers/loadAnnotation.java | 104 +
.../data/servers/loadAnnotationFromFlatFiles.java | 127 +
.../java/cytoscape/data/servers/loadThesaurus.java | 99 +
.../main/java/cytoscape/data/servers/package.html | 13 +
.../main/java/cytoscape/data/servers/status.java | 86 +
.../java/cytoscape/data/synonyms/AliasType.java | 50 +
.../main/java/cytoscape/data/synonyms/Aliases.java | 277 +
.../java/cytoscape/data/synonyms/Thesaurus.java | 306 +
.../main/java/cytoscape/data/synonyms/package.html | 13 +
.../synonyms/readers/ThesaurusFlatFileReader.java | 222 +
.../cytoscape/data/synonyms/readers/package.html | 12 +
.../data/webservice/AttributeImportQuery.java | 28 +
.../data/webservice/CyWebServiceEvent.java | 91 +
.../data/webservice/CyWebServiceEventListener.java | 54 +
.../data/webservice/CyWebServiceEventSupport.java | 84 +
.../data/webservice/CyWebServiceException.java | 69 +
.../data/webservice/DatabaseSearchResult.java | 27 +
.../webservice/NetworkImportWebServiceClient.java | 51 +
.../data/webservice/WebServiceClient.java | 155 +
.../data/webservice/WebServiceClientImpl.java | 270 +
.../webservice/WebServiceClientImplWithGUI.java | 125 +
.../data/webservice/WebServiceClientManager.java | 148 +
.../webservice/ui/UnifiedNetworkImportDialog.java | 776 +
.../data/webservice/ui/WSImportResultDialog.java | 171 +
.../data/webservice/ui/WebServiceClientGUI.java | 106 +
.../data/webservice/ui/WebServiceContextMenu.java | 138 +
.../ui/WebServiceContextMenuListener.java | 67 +
.../data/webservice/util/NetworkExpansionMenu.java | 200 +
.../webservice/util/WebServiceThemeInstall.java | 174 +
.../cytoscape/data/writers/CyAttributesWriter.java | 241 +
.../data/writers/CytoscapeSessionWriter.java | 1056 +
.../cytoscape/data/writers/InteractionWriter.java | 160 +
.../java/cytoscape/data/writers/XGMMLWriter.java | 1373 +
.../java/cytoscape/dialogs/ColorScaleTable.java | 170 +
.../dialogs/EdgeAttributesPopupDetails.java | 138 +
.../cytoscape/dialogs/EditNetworkTitleDialog.java | 167 +
.../dialogs/ExportAsGraphicsFileChooser.java | 410 +
.../dialogs/ExportBitmapOptionsDialog.java | 391 +
.../dialogs/ExpressionDataPopupTable.java | 366 +
.../cytoscape/dialogs/GinyEdgeControlDialog.java | 493 +
.../cytoscape/dialogs/GraphObjectSelection.java | 459 +
.../main/java/cytoscape/dialogs/GridBagGroup.java | 116 +
.../java/cytoscape/dialogs/IconPopupButton.java | 328 +
.../dialogs/ImportAttributeMatrixDialog.java | 255 +
.../cytoscape/dialogs/ImportNetworkDialog.java | 657 +
.../java/cytoscape/dialogs/IntegerEntryField.java | 200 +
.../java/cytoscape/dialogs/JointIntegerEntry.java | 255 +
.../java/cytoscape/dialogs/LabelTextPanel.java | 120 +
.../src/main/java/cytoscape/dialogs/MiscGB.java | 247 +
.../cytoscape/dialogs/NetworkMetaDataDialog.java | 267 +
.../dialogs/NetworkMetaDataTableModel.java | 182 +
.../src/main/java/cytoscape/dialogs/NewSlider.java | 308 +
.../cytoscape/dialogs/NewStringPopupDialog.java | 137 +
.../java/cytoscape/dialogs/PhoebeNodeControl.java | 611 +
.../main/java/cytoscape/dialogs/PopupTextArea.java | 138 +
.../cytoscape/dialogs/SetNestedNetworkDialog.java | 222 +
.../java/cytoscape/dialogs/ShrinkExpandGraph.java | 125 +
.../cytoscape/dialogs/ShrinkExpandGraphUI.java | 63 +
.../java/cytoscape/dialogs/VizChooser.java.old | 1014 +
.../cytoscape/dialogs/logger/LoggerDialog.java | 332 +
.../src/main/java/cytoscape/dialogs/package.html | 14 +
.../cytoscape/dialogs/plugins/LicenseDialog.java | 316 +
.../cytoscape/dialogs/plugins/ManagerModel.java | 301 +
.../cytoscape/dialogs/plugins/PluginIndex.java | 128 +
.../dialogs/plugins/PluginManageDialog.java | 1492 +
.../dialogs/plugins/PluginUpdateDialog.java | 447 +
.../cytoscape/dialogs/plugins/PluginUrlDialog.java | 414 +
.../dialogs/plugins/TreeCellRenderer.java | 57 +
.../java/cytoscape/dialogs/plugins/TreeNode.java | 347 +
.../dialogs/preferences/BookmarkDialog.java | 412 +
.../dialogs/preferences/EditBookmarkDialog.java | 267 +
.../dialogs/preferences/PluginsTableModel.java | 420 +
.../dialogs/preferences/PreferenceTableModel.java | 279 +
.../dialogs/preferences/PreferenceValueDialog.java | 219 +
.../dialogs/preferences/PreferencesDialog.java | 568 +
.../dialogs/preferences/ProxyServerDialog.java | 447 +
.../main/java/cytoscape/ding/CyGraphAllLOD.java | 66 +
.../src/main/java/cytoscape/ding/CyGraphLOD.java | 318 +
.../main/java/cytoscape/ding/DingNetworkView.java | 585 +
.../src/main/java/cytoscape/giny/CyEdgeDepot.java | 75 +
.../src/main/java/cytoscape/giny/CyNodeDepot.java | 75 +
.../cytoscape/giny/CytoscapeFingRootGraph.java | 204 +
.../java/cytoscape/giny/CytoscapeRootGraph.java | 108 +
.../main/java/cytoscape/giny/FingCyNetwork.java | 713 +
.../src/main/java/cytoscape/groups/CyGroup.java | 225 +
.../cytoscape/groups/CyGroupChangeListener.java | 52 +
.../main/java/cytoscape/groups/CyGroupImpl.java | 658 +
.../main/java/cytoscape/groups/CyGroupManager.java | 659 +
.../main/java/cytoscape/groups/CyGroupViewer.java | 102 +
.../groups/GroupPropertyChangeListener.java | 70 +
.../src/main/java/cytoscape/init/CyInitParams.java | 165 +
.../main/java/cytoscape/layout/AbstractLayout.java | 399 +
.../java/cytoscape/layout/CyLayoutAlgorithm.java | 212 +
.../layout/CyLayoutAlgorithmComparator.java | 57 +
.../src/main/java/cytoscape/layout/CyLayouts.java | 139 +
.../main/java/cytoscape/layout/LayoutAdapter.java | 215 +
.../java/cytoscape/layout/LayoutAlgorithm.java | 56 +
.../java/cytoscape/layout/LayoutProperties.java | 137 +
.../src/main/java/cytoscape/layout/LayoutTask.java | 131 +
.../src/main/java/cytoscape/layout/Tunable.java | 1322 +
.../java/cytoscape/layout/TunableListener.java | 23 +
.../layout/algorithms/GridNodeLayout.java | 190 +
.../src/main/java/cytoscape/layout/package.html | 12 +
.../cytoscape/layout/ui/DynamicLayoutMenu.java | 250 +
.../main/java/cytoscape/layout/ui/LayoutMenu.java | 161 +
.../cytoscape/layout/ui/LayoutMenuManager.java | 182 +
.../cytoscape/layout/ui/LayoutSettingsDialog.java | 324 +
.../java/cytoscape/layout/ui/SettingsAction.java | 62 +
.../java/cytoscape/layout/ui/StaticLayoutMenu.java | 86 +
.../main/java/cytoscape/logger/ConsoleLogger.java | 63 +
.../main/java/cytoscape/logger/CyLogHandler.java | 55 +
.../src/main/java/cytoscape/logger/CyLogger.java | 398 +
.../src/main/java/cytoscape/logger/LogLevel.java | 45 +
application/src/main/java/cytoscape/overview.html | 23 +
application/src/main/java/cytoscape/package.html | 49 +
.../src/main/java/cytoscape/plugin/Category.java | 27 +
.../java/cytoscape/plugin/CytoscapePlugin.java | 225 +
.../java/cytoscape/plugin/DownloadableInfo.java | 568 +
.../java/cytoscape/plugin/DownloadableType.java | 27 +
.../plugin/DuplicatePluginClassException.java | 21 +
.../main/java/cytoscape/plugin/Installable.java | 39 +
.../java/cytoscape/plugin/InstallablePlugin.java | 270 +
.../java/cytoscape/plugin/InstallableTheme.java | 204 +
.../java/cytoscape/plugin/InvalidDownloadable.java | 31 +
.../src/main/java/cytoscape/plugin/JarUtil.java | 147 +
.../java/cytoscape/plugin/ManagerException.java | 63 +
.../main/java/cytoscape/plugin/ManagerUtil.java | 193 +
.../java/cytoscape/plugin/NotAPluginException.java | 52 +
.../java/cytoscape/plugin/PluginException.java | 40 +
.../java/cytoscape/plugin/PluginFileReader.java | 407 +
.../src/main/java/cytoscape/plugin/PluginInfo.java | 327 +
.../java/cytoscape/plugin/PluginInquireAction.java | 77 +
.../main/java/cytoscape/plugin/PluginManager.java | 1054 +
.../cytoscape/plugin/PluginManagerInquireTask.java | 95 +
.../java/cytoscape/plugin/PluginProperties.java | 213 +
.../main/java/cytoscape/plugin/PluginStatus.java | 19 +
.../main/java/cytoscape/plugin/PluginTracker.java | 759 +
.../java/cytoscape/plugin/PluginVersionUtils.java | 67 +
.../src/main/java/cytoscape/plugin/PluginXml.java | 44 +
.../src/main/java/cytoscape/plugin/ThemeInfo.java | 140 +
.../java/cytoscape/plugin/TrackerException.java | 21 +
.../java/cytoscape/plugin/WebstartException.java | 24 +
.../src/main/java/cytoscape/plugin/package.html | 16 +
.../main/java/cytoscape/util/AbstractScaler.java | 85 +
.../java/cytoscape/util/BioDataServerUtil.java | 310 +
.../main/java/cytoscape/util/BookmarksUtil.java | 511 +
.../src/main/java/cytoscape/util/ColorUtil.java | 145 +
.../src/main/java/cytoscape/util/CreditScreen.java | 158 +
.../main/java/cytoscape/util/CyColorChooser.java | 82 +
.../src/main/java/cytoscape/util/CyFileFilter.java | 530 +
.../main/java/cytoscape/util/CyNetworkNaming.java | 154 +
.../main/java/cytoscape/util/CytoscapeAction.java | 381 +
.../main/java/cytoscape/util/CytoscapeMenuBar.java | 430 +
.../cytoscape/util/CytoscapeProgressMonitor.java | 193 +
.../main/java/cytoscape/util/CytoscapeToolBar.java | 169 +
application/src/main/java/cytoscape/util/Exec.java | 303 +
.../src/main/java/cytoscape/util/FileUtil.java | 544 +
.../main/java/cytoscape/util/GMLFileFilter.java | 106 +
.../main/java/cytoscape/util/GraphSetUtils.java | 528 +
.../cytoscape/util/IndeterminateProgressBar.java | 126 +
.../main/java/cytoscape/util/JnlpWriterUtil.java | 385 +
.../src/main/java/cytoscape/util/LinearScaler.java | 65 +
.../src/main/java/cytoscape/util/MacAppConfig.java | 189 +
.../src/main/java/cytoscape/util/MathUtil.java | 72 +
.../main/java/cytoscape/util/MemoryReporter.java | 64 +
.../src/main/java/cytoscape/util/MinMaxDouble.java | 110 +
.../src/main/java/cytoscape/util/MinMaxInt.java | 110 +
application/src/main/java/cytoscape/util/Misc.java | 181 +
.../main/java/cytoscape/util/ModuleProperties.java | 154 +
.../java/cytoscape/util/ModulePropertiesImpl.java | 277 +
.../main/java/cytoscape/util/MonitoredTask.java | 126 +
.../src/main/java/cytoscape/util/MutableBool.java | 80 +
.../src/main/java/cytoscape/util/MutableInt.java | 80 +
.../main/java/cytoscape/util/MutableString.java | 80 +
.../main/java/cytoscape/util/NNFFileFilter.java | 80 +
.../cytoscape/util/NestedNetworkViewUpdater.java | 134 +
.../src/main/java/cytoscape/util/OpenBrowser.java | 134 +
.../src/main/java/cytoscape/util/PercentUtil.java | 81 +
.../src/main/java/cytoscape/util/PropUtil.java | 127 +
.../src/main/java/cytoscape/util/ProxyHandler.java | 134 +
.../src/main/java/cytoscape/util/QuantileNorm.java | 184 +
.../src/main/java/cytoscape/util/RankScaler.java | 76 +
.../java/cytoscape/util/RecentlyOpenedTracker.java | 112 +
.../main/java/cytoscape/util/SIFFileFilter.java | 106 +
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application/src/main/resources/vizmap.props | 602 +
application/src/main/resources/xsd/bookmarks.xsd | 38 +
application/src/main/resources/xsd/cysession.xsd | 210 +
application/src/main/resources/xsd/xlinks-2001.xsd | 127 +
application/src/test/java/cytoscape/AllTests.java | 182 +
.../src/test/java/cytoscape/BugGetCyNodeTest.java | 70 +
.../java/cytoscape/BugHideNodeEventFiringTest.java | 111 +
application/src/test/java/cytoscape/BugTest1.java | 102 +
application/src/test/java/cytoscape/CoreSuite.java | 63 +
.../src/test/java/cytoscape/CyNodeTest.java | 143 +
.../src/test/java/cytoscape/CytoscapeTest.java | 288 +
.../test/java/cytoscape/data/CyAttributesTest.java | 440 +
.../java/cytoscape/data/CyAttributesUtilsTest.java | 436 +
.../java/cytoscape/data/CyNetworkEventTest.java | 139 +
.../test/java/cytoscape/data/CyNetworkTest.java | 369 +
.../java/cytoscape/data/ExpressionDataTest.java | 175 +
.../java/cytoscape/data/ImportHandlerTest.java | 374 +
.../test/java/cytoscape/data/InteractionTest.java | 155 +
.../test/java/cytoscape/data/NetworkDataTest.java | 227 +
.../test/java/cytoscape/data/SelectEventTest.java | 169 +
.../test/java/cytoscape/data/SelectFilterTest.java | 473 +
.../annotation/AnnotationAndOntologyFullTest.java | 149 +
.../data/annotation/AnnotationDescriptionTest.java | 129 +
.../cytoscape/data/annotation/AnnotationTest.java | 195 +
.../data/annotation/OntologyTermTest.java | 154 +
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.../test/java/cytoscape/data/annotation/Utils.java | 133 +
.../cytoscape/data/attr/util/MultiHashMapTest.java | 149 +
.../java/cytoscape/data/mRNAMeasurementTest.java | 100 +
.../test/java/cytoscape/data/networkProject.pro | 6 +
.../java/cytoscape/data/ontology/OntologyTest.java | 274 +
.../readers/DBCrossReferenceReaderTest.java | 175 +
.../ontology/readers/OBOFlatFileReaderTest.java | 151 +
.../cytoscape/data/readers/BookmarkReaderTest.java | 98 +
.../data/readers/CyAttributesReaderTest.java | 270 +
.../data/readers/CytoscapeSessionReaderTest.java | 184 +
.../cytoscape/data/readers/FileImporterTest.java | 150 +
.../java/cytoscape/data/readers/GMLReaderTest.java | 189 +
.../data/readers/InteractionsReaderTest.java | 279 +
.../cytoscape/data/readers/MetadataParserTest.java | 99 +
.../java/cytoscape/data/readers/NNFReaderTest.java | 195 +
.../cytoscape/data/readers/TextFileReaderTest.java | 112 +
.../cytoscape/data/readers/TextJarReaderTest.java | 140 +
.../cytoscape/data/readers/XGMMLReaderTest.java | 163 +
.../java/cytoscape/data/readers/degenerate.sif | 9 +
.../cytoscape/data/readers/multiWordProteins.sif | 30 +
.../multiWordProteinsFileTrailingSpaces.sif | 30 +
.../test/java/cytoscape/data/readers/sample.sif | 25 +
.../cytoscape/data/servers/BioDataServerTest.java | 377 +
.../java/cytoscape/data/synonyms/AliasesTest.java | 109 +
.../cytoscape/data/synonyms/ThesaurusTest.java | 263 +
.../readers/ThesaurusFlatFileReaderTest.java | 144 +
.../data/writers/CyAttributesWriterTest.java | 201 +
.../data/writers/CytoscapeSessionWriterTest.java | 70 +
.../data/writers/InteractionWriterTest.java | 160 +
.../cytoscape/data/writers/XGMMLWriterTest.java | 227 +
.../cytoscape/giny/CytoscapeFingRootGraphTest.java | 133 +
.../cytoscape/plugin/DownloadableInfoTest.java | 290 +
.../cytoscape/plugin/PluginFileReaderTest.java | 167 +
.../java/cytoscape/plugin/PluginIndexTest.java | 126 +
.../java/cytoscape/plugin/PluginManagerTest.java | 744 +
.../cytoscape/plugin/PluginPropertiesTest.java | 51 +
.../test/java/cytoscape/plugin/PluginTestXML.java | 84 +
.../java/cytoscape/plugin/PluginTrackerTest.java | 440 +
.../cytoscape/plugin/PluginVersionUtilsTest.java | 72 +
.../src/test/java/cytoscape/sampleProject.pro | 18 +
application/src/test/java/cytoscape/test1.cpr | 10 +
application/src/test/java/cytoscape/test2.cpr | 9 +
.../java/cytoscape/util/BookmarksUtilTest.java | 109 +
.../test/java/cytoscape/util/ColorUtilTest.java | 45 +
.../test/java/cytoscape/util/CyFileFilterTest.java | 312 +
.../src/test/java/cytoscape/util/FileUtilTest.java | 66 +
.../java/cytoscape/util/GMLFileFilterTest.java | 86 +
.../java/cytoscape/util/GraphSetUtilsTest.java | 254 +
.../test/java/cytoscape/util/LinearScalerTest.java | 26 +
.../src/test/java/cytoscape/util/MathUtilTest.java | 24 +
.../src/test/java/cytoscape/util/MinMaxTest.java | 146 +
.../src/test/java/cytoscape/util/MiscTest.java | 264 +
.../util/NestedNetworkImageManagerTest.java | 36 +
.../src/test/java/cytoscape/util/PropUtilTest.java | 147 +
.../test/java/cytoscape/util/RankScalerTest.java | 38 +
.../java/cytoscape/util/SIFFileFilterTest.java | 86 +
.../java/cytoscape/util/ScalerFactoryTest.java | 24 +
.../src/test/java/cytoscape/util/TestUtil.java | 20 +
.../java/cytoscape/util/TopologicalSortTest.java | 187 +
.../java/cytoscape/util/XGMMLFileFilterTest.java | 86 +
.../java/cytoscape/view/CytoscapeViewTest.java | 193 +
.../view/FlagAndSelectionHandlerTest.java | 217 +
.../java/cytoscape/visual/BypassHelperTest.java | 165 +
.../cytoscape/visual/CalculatorPropertiesTest.java | 203 +
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.../src/test/java/cytoscape/visual/TestLabel.java | 191 +
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.../test/java/cytoscape/visual/TestNodeView.java | 558 +
.../cytoscape/visual/VisualMappingManagerTest.java | 174 +
.../visual/VisualPropertyDependencyTest.java | 88 +
.../cytoscape/visual/VizMapPropertiesTest.java | 276 +
.../visual/mappings/BoundaryRangeValuesTest.java | 120 +
.../visual/mappings/FlatInterpolatorTest.java | 127 +
.../LinearNumberToColorInterpolatorTest.java | 126 +
.../LinearNumberToNumberInterpolatorTest.java | 117 +
.../cytoscape/visual/mappings/MappingUtilTest.java | 224 +
.../visual/mappings/PassthroughMappingTest.java | 97 +
.../TestContinuousColorRangeCalculator.java | 210 +
.../continuous/TestContinuousMappingReader.java | 141 +
.../continuous/TestContinuousMappingWriter.java | 104 +
.../discrete/DiscreteMappingReaderTest.java | 169 +
.../discrete/DiscreteMappingWriterTest.java | 184 +
.../testData/NNFData/1000SmallNetworks.nnf | 38139 ++++++++
.../testData/NNFData/100SmallNetworks.nnf | 3728 +
.../resources/testData/NNFData/10LargeNetworks.nnf | 87381 ++++++++++++++++++
.../testData/NNFData/300SmallNetworks.nnf | 6396 ++
.../test/resources/testData/NNFData/5Nested.nnf | 50 +
.../src/test/resources/testData/NNFData/bad1.nnf | 9 +
.../src/test/resources/testData/NNFData/bad2.nnf | 9 +
.../resources/testData/NNFData/calc_network_size | 47 +
.../testData/NNFData/generate_multi_level_networks | 117 +
.../resources/testData/NNFData/generate_networks | 78 +
.../src/test/resources/testData/NNFData/good1.nnf | 9 +
.../src/test/resources/testData/NNFData/good2.nnf | 9 +
.../src/test/resources/testData/NNFData/good3.nnf | 9 +
.../src/test/resources/testData/NNFData/good4.nnf | 18 +
.../src/test/resources/testData/NNFData/good5.nnf | 11 +
.../src/test/resources/testData/NNFData/good6.nnf | 2 +
.../resources/testData/NNFData/intermediate.nnf | 11195 +++
.../src/test/resources/testData/NNFData/large.nnf | 89514 +++++++++++++++++++
.../src/test/resources/testData/NNFData/loop.nnf | 2 +
.../src/test/resources/testData/NNFData/loop1.nnf | 2 +
.../src/test/resources/testData/NNFData/small.nnf | 5560 ++
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.../testData/XGMMLWriterTestFile01a.xgmml | 40 +
.../testData/XGMMLWriterTestFile01b.xgmml | 33 +
.../testData/XGMMLWriterTestFile02a.xgmml | 22 +
.../testData/XGMMLWriterTestFile02b.xgmml | 22 +
.../testData/XGMMLWriterTestFile02c.xgmml | 22 +
.../testData/XGMMLWriterTestFile02d.xgmml | 22 +
.../testData/annotation/goslim_generic.obo | 1754 +
.../src/test/resources/testData/broken_t.gml | 1031 +
.../src/test/resources/testData/bug1565.gml | 1639 +
.../src/test/resources/testData/bug_839.sif | 6 +
.../src/test/resources/testData/degenerate.sif | 9 +
.../src/test/resources/testData/directedGraph.sif | 5 +
.../resources/testData/explicitDouble.attribute | 4 +
application/src/test/resources/testData/gal.gml | 303 +
.../src/test/resources/testData/gal1.22x5.mRNA | 23 +
.../resources/testData/gal1.22x5.mRNA_wo_descript | 23 +
.../test/resources/testData/galFiltered.edgeAttrs2 | 354 +
.../test/resources/testData/galFiltered.nodeAttrs1 | 329 +
.../src/test/resources/testData/galFiltered.sif | 362 +
.../src/test/resources/testData/galFiltered2.xgmml | 17902 ++++
.../resources/testData/haloMetabolicPathway.xml | 4740 +
.../resources/testData/humanKeggAndGO/bioproc.anno | 40 +
.../testData/humanKeggAndGO/cellcomp.anno | 40 +
.../test/resources/testData/humanKeggAndGO/go.onto | 13108 +++
.../resources/testData/humanKeggAndGO/human.syno | 17 +
.../resources/testData/humanKeggAndGO/kegg.anno | 40 +
.../resources/testData/humanKeggAndGO/kegg.onto | 196 +
.../testData/humanKeggAndGO/manifest.both | 7 +
.../resources/testData/humanKeggAndGO/molfunc.anno | 40 +
.../testData/implicitStringArray.attribute | 6 +
.../testData/implicitStringArrayEnc.attribute | 6 +
.../testData/metabolicPathwayOntology.xml | 1174 +
.../test/resources/testData/multiWordProteins.sif | 30 +
.../multiWordProteinsFileTrailingSpaces.sif | 30 +
.../src/test/resources/testData/noLabels.gml | 8613 ++
.../src/test/resources/testData/old_vizmap.props | 436 +
.../test/resources/testData/plugins/BadPlugin.jar | Bin 0 -> 1780 bytes
.../test/resources/testData/plugins/GoodPlugin.jar | Bin 0 -> 1858 bytes
.../test/resources/testData/plugins/GoodPlugin.zip | Bin 0 -> 1214 bytes
.../resources/testData/plugins/MCODE_broken.jar | Bin 0 -> 1896 bytes
.../test/resources/testData/plugins/license.txt | 2 +
.../testData/plugins/partial_plugin_file.xml | 45 +
.../resources/testData/plugins/test_plugin.props | 34 +
.../resources/testData/plugins/test_plugin.xml | 390 +
.../testData/plugins/test_plugin_no_themes.xml | 183 +
.../resources/testData/plugins/test_plugins.xsl | 96 +
.../resources/testData/plugins/track_plugins.xml | 430 +
.../testData/plugins/track_plugins_c1.xml | 429 +
.../testData/plugins/track_plugins_c2.xml | 430 +
.../src/test/resources/testData/randomTextFile.txt | 6 +
application/src/test/resources/testData/sample.sif | 25 +
.../src/test/resources/testData/small.edgeAttr | 5 +
.../src/test/resources/testData/small.nodeAttr | 5 +
application/src/test/resources/testData/small.sif | 4 +
.../src/test/resources/testData/small.vizmap.props | 136 +
.../src/test/resources/testData/yeastSmall.txt | 10 +
archetypes/ant-sample-plugin/pom.xml | 36 +
.../ant-sample-plugin/src/main/assembly/src.xml | 14 +
.../ant-sample-plugin/src/main/resources/README | 11 +
.../ant-sample-plugin/src/main/resources/build.xml | 258 +
.../src/main/resources/resources/plugin.props | 26 +
.../src/main/resources/src/example/MyAction.java | 32 +
.../src/main/resources/src/example/MyPlugin.java | 23 +
.../main/resources/tests/example/MyActionTest.java | 17 +
archetypes/pom.xml | 55 +
archetypes/sample-plugin/pom.xml | 88 +
.../src/it/projects/firsttest/test.properties | 4 +
.../src/it/projects/firsttest/verify.bsh | 7 +
.../META-INF/maven/archetype-metadata.xml | 23 +
.../main/resources/META-INF/maven/archetype.xml | 13 +
.../src/main/resources/archetype-resources/pom.xml | 88 +
.../src/main/java/MyAction.java | 34 +
.../src/main/java/MyPlugin.java | 26 +
.../src/main/resources/plugin.props | 26 +
.../src/test/java/MyActionTest.java | 20 +
.../CYTOSCAPE_README | 11 +
.../commons-cli-1.x-cytocape-custom/LICENSE.txt | 202 +
.../commons-cli-1.x-cytocape-custom/NOTICE.txt | 2 +
.../commons-cli-1.x-cytocape-custom/README.txt | 42 +
.../RELEASE-NOTES.txt | 26 +
corelibs/commons-cli-1.x-cytocape-custom/pom.xml | 49 +
.../src/conf/MANIFEST.MF | 11 +
.../commons/cli/AlreadySelectedException.java | 36 +
.../java/org/apache/commons/cli/BasicParser.java | 44 +
.../java/org/apache/commons/cli/CommandLine.java | 295 +
.../org/apache/commons/cli/CommandLineParser.java | 86 +
.../java/org/apache/commons/cli/GnuParser.java | 134 +
.../java/org/apache/commons/cli/HelpFormatter.java | 801 +
.../commons/cli/MissingArgumentException.java | 36 +
.../apache/commons/cli/MissingOptionException.java | 35 +
.../main/java/org/apache/commons/cli/Option.java | 541 +
.../java/org/apache/commons/cli/OptionBuilder.java | 345 +
.../java/org/apache/commons/cli/OptionGroup.java | 144 +
.../org/apache/commons/cli/OptionValidator.java | 86 +
.../main/java/org/apache/commons/cli/Options.java | 266 +
.../org/apache/commons/cli/ParseException.java | 35 +
.../main/java/org/apache/commons/cli/Parser.java | 343 +
.../apache/commons/cli/PatternOptionBuilder.java | 180 +
.../java/org/apache/commons/cli/PosixParser.java | 265 +
.../java/org/apache/commons/cli/TypeHandler.java | 209 +
.../commons/cli/UnrecognizedOptionException.java | 36 +
.../src/main/java/org/apache/commons/cli/Util.java | 63 +
.../commons/cli/avalon/AbstractParserControl.java | 38 +
.../apache/commons/cli/avalon/CLArgsParser.java | 661 +
.../org/apache/commons/cli/avalon/CLOption.java | 158 +
.../commons/cli/avalon/CLOptionDescriptor.java | 208 +
.../java/org/apache/commons/cli/avalon/CLUtil.java | 106 +
.../apache/commons/cli/avalon/ParserControl.java | 36 +
.../java/org/apache/commons/cli/avalon/Token.java | 69 +
.../org/apache/commons/cli/avalon/package.html | 164 +
.../main/java/org/apache/commons/cli/overview.html | 28 +
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.../src/main/sampleData/galFiltered.nodeAttrs3 | 329 +
.../sampleData/galFiltered.select.from.file.txt | 10 +
distribution/src/main/sampleData/galFiltered.sif | 362 +
distribution/src/main/sampleData/galFiltered.txt | 362 +
distribution/src/main/sampleData/galFiltered.xgmml | 27388 ++++++
distribution/src/main/sampleData/galFiltered.xls | Bin 0 -> 59392 bytes
.../src/main/sampleData/galFiltered2.xgmml | 17902 ++++
distribution/src/main/sampleData/galFiltered25.cys | Bin 0 -> 168690 bytes
.../src/main/sampleData/galFilteredAnnotated.xgmml | 14663 +++
.../main/sampleData/galFiltered_int_edge_attr.ea | 363 +
.../main/sampleData/galFiltered_list_edge_attr.ea | 15 +
.../src/main/sampleData/galFilteredintAttr.xls | Bin 0 -> 38912 bytes
.../human_interactome_may07_small.tab.gz | Bin 0 -> 535386 bytes
.../src/main/sampleData/sampleStyles.props | 1063 +
.../src/main/sampleData/yeastHighQuality.sif | 6888 ++
javadoc/pom.xml | 177 +
legacy/build.xml | 1122 +
legacy/resources/Gene_Ontology_Wizard.html | 90 +
.../resources/cytoscape_jalopy_code_convention.xml | 434 +
legacy/resources/javax.imageio.spi.ImageWriterSpi | 1 +
.../org.freehep.util.export.ExportFileType | 5 +
.../resources/plugin_website/CyPluginDB_schema.sql | 135 +
.../plugin_website/generate_plugin_xml.pl | 501 +
.../resources/plugin_website/plugin.props.example | 43 +
legacy/resources/plugin_website/plugin.xml | 40 +
legacy/resources/schema/binding.xjb | 15 +
legacy/resources/schema/dcmes-xml-dtd.xsd | 200 +
legacy/resources/schema/plugins.xsd | 57 +
legacy/resources/schema/rdf.xsd | 29 +
legacy/resources/schema/readme.txt | 15 +
legacy/resources/schema/xgmml.xsd | 461 +
legacy/resources/schema/xml.xsd | 146 +
packaging/README.txt | 6 +
packaging/pom.xml | 140 +
packaging/src/main/images/cytoscape.icns | Bin 0 -> 46545 bytes
packaging/src/main/images/cytoscape_file.icns | Bin 0 -> 45977 bytes
packaging/src/main/images/gml.icns | Bin 0 -> 49342 bytes
packaging/src/main/images/icon16x16.png | Bin 0 -> 761 bytes
packaging/src/main/images/icon32x32.png | Bin 0 -> 2251 bytes
packaging/src/main/images/sif.icns | Bin 0 -> 48940 bytes
packaging/src/main/install4j/Cytoscape.install4j | 931 +
pom.xml | 225 +
webstart/README.txt | 17 +
webstart/pom.xml | 222 +
webstart/src/main/jnlp/template.vm | 57 +
3050 files changed, 1168151 insertions(+), 647 deletions(-)
diff --git a/README.txt b/README.txt
new file mode 100644
index 0000000..93f375c
--- /dev/null
+++ b/README.txt
@@ -0,0 +1,128 @@
+Welcome to the New Cytoscape Build Process
+--------------------------------------------
+
+I. Doing a Clean Checkout
+==========================
+
+If this is the first time reading this, make sure that you have done a clean checkout.
+You will need to have subversion installed (http://subversion.tigris.org).
+
+Then, do a clean check-out:
+
+ svn checkout file:///cellar/common/svn/cytoscape/trunk cytoscape
+
+or if you're remote:
+
+ svn checkout svn+ssh://grenache.ucsd.edu/cellar/common/svn/cytoscape/trunk cytoscape
+
+
+II. New Directory Structure
+============================
+
+Cytoscape now contains the following directory structure:
+
+cytoscape
+ +
+ +---corelibs/ This directoy contains all libraries written by the
+ + Cytoscape project and used in the Cytoscape Application.
+ +
+ +---application/ This directoy contains the code for the Cytoscape
+ + application.
+ +
+ +---coreplugins/ This directoy contains all plugins delivered as part
+ + of the Cytoscape Application.
+ +
+ +---distribution/ Contains a maven project that assembles the Cytoscape
+ + distribution based on the core plugins and the jar file
+ + built by application. This directory includes all shell
+ + scripts, sample data, and licenses for the distribution.
+ +
+ +---javadoc/ This directory contains a pom that creates a Javadoc jar
+ + file that only includes javadocs for corelibs and
+ + application, i.e. the public Cytoscape API.
+ +
+ +---packaging/ This directoy contains a maven pom file that creates
+ + Install4j release bundles and then puts the distribution
+ + zip file and javadocs in the same directory. Note that
+ + this packaging ONLY happens in the deploy phase.
+ +
+ +---webstart/ This directoy contains a maven pom file that creates
+ + a webstart (JNLP) distribution of Cytoscape. The webstart
+ + bundle is not created as part of the normal maven life
+ + cycle. See the README.txt in that directory for
+ + instructions on building a webstart distribution.
+ +
+ +---archetypes/ Contains maven archetypes to assist in the construction
+ + of Cytoscape plugins.
+ +
+ +---legacy/ Contains old and currently unused test data and resources.
+
+
+III. Build Process
+==================
+
+To build cytoscape:
+
+1. Download and install Apache Maven: http://maven.apache.org/
+
+2. To compile everything:
+ a. in the top level directory:
+
+ mvn install
+
+ Note: this may not work from within Eclipse; run on command line
+ Note: you may need to bump up your memory allocation:
+ export MAVEN_OPTS=-Xmx1024m
+
+ b. skip tests and javadocs for quick-and-dirty builds:
+
+ mvn install -Dmaven.javadoc.skip=true -Dmaven.test.skip=true
+
+ c. take advantage of multiple threads/cores:
+
+ mvn -T 4 (4 threads)
+ mvn -T 1C (1 thread per core)
+
+ d. to build for release, be sure to specify a profile that includes packaging, e.g.,
+
+ mvn install -Prelease
+
+3. To run cytoscape (assuming you've run mvn install):
+ a. you'll find the normal cytoscape distribution directory here:
+
+ cd distribution/target/distribution-${version}-null.dir/distribution-${version}
+
+
+IV. Release Process
+===================
+
+A release is created using the Maven Release plugin. So, incrementing the
+version numbers, tagging the release, incrementing the version numbers again,
+and then building the tagged version of the release and deploying properly
+versioned artifacts is accomplished as follows:
+
+ mvn release:prepare -Prelease
+ mvn release:perform -Prelease
+
+The next step is to copy the downloadable artifacts to the Cytoscape website.
+Everything to be copied over can be found in the packaging/target/install4j
+directory.
+
+V. To Build Installer
+=====================
+To build the installer bundles, cd to the packaging directory and edit
+pom.xml to change the <executable> for install4jc to where your install4j
+installation is. Then run:
+
+ mvn install4j:compile
+
+ Note: to package with plugins, first copy plugins into:
+ packaging/target/cytoscape-#.#.#/plugins/.
+
+ Note: to package with additional plugins, first copy plugins into:
+ distribution/target/cytoscape-#.#.#-null/cytoscape-#.#.#/plugins/.
+
+The installers will be created in the target/install4j subdirectory
+
+
+For questions, email Mike Smoot: msmoot at ucsd.edu
diff --git a/acceptance-testing/README b/acceptance-testing/README
new file mode 100644
index 0000000..247b12d
--- /dev/null
+++ b/acceptance-testing/README
@@ -0,0 +1,4 @@
+The intent of this directory is to contain a comprehensive set of
+AUTOMATED acceptance tests for Cytoscape. The tests should run
+the full Cytoscape application and exercise as much core functionality
+as possible.
diff --git a/acceptance-testing/pom.xml b/acceptance-testing/pom.xml
new file mode 100644
index 0000000..342f7f6
--- /dev/null
+++ b/acceptance-testing/pom.xml
@@ -0,0 +1,33 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>cytoscape</groupId>
+ <artifactId>parent</artifactId>
+ <version>2.8.0-beta3-SNAPSHOT</version>
+ </parent>
+
+ <groupId>cytoscape</groupId>
+ <artifactId>acceptance-testing</artifactId>
+ <packaging>jar</packaging>
+ <name>Cytoscape Acceptance Tests</name>
+
+ <dependencies>
+ <dependency>
+ <groupId>org.easytesting</groupId>
+ <artifactId>fest-swing</artifactId>
+ <version>1.2.1</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape</groupId>
+ <artifactId>application</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>junit</groupId>
+ <artifactId>junit</artifactId>
+ <version>4.8.1</version>
+ </dependency>
+ </dependencies>
+
+</project>
+
diff --git a/acceptance-testing/src/test/java/cytoscape/acceptance/FirstGUITest.java b/acceptance-testing/src/test/java/cytoscape/acceptance/FirstGUITest.java
new file mode 100644
index 0000000..7a63415
--- /dev/null
+++ b/acceptance-testing/src/test/java/cytoscape/acceptance/FirstGUITest.java
@@ -0,0 +1,67 @@
+package cytoscape.acceptance;
+
+import org.junit.Test;
+import org.junit.Before;
+import org.junit.After;
+import org.fest.swing.fixture.FrameFixture;
+import org.fest.swing.edt.*;
+import org.fest.swing.timing.*;
+import org.fest.swing.core.matcher.*;
+
+import cytoscape.CyMain;
+import cytoscape.Cytoscape;
+import cytoscape.view.CytoscapeDesktop;
+
+public class FirstGUITest {
+
+ private FrameFixture desktop;
+
+ public FirstGUITest() {
+ FailOnThreadViolationRepaintManager.install();
+ }
+
+ @Before public void setUp() {
+ CytoscapeDesktop frame = GuiActionRunner.execute(new GuiQuery<CytoscapeDesktop>() {
+ protected CytoscapeDesktop executeInEDT() {
+ try {
+ String[] args = new String[]{"-p","plugins"};
+ new CyMain(args);
+ return Cytoscape.getDesktop();
+ } catch (Exception e) {
+ e.printStackTrace();
+ return null;
+ }
+ }
+ });
+ desktop = new FrameFixture(frame);
+ desktop.show(); // shows the frame to test
+ }
+
+ @After
+ public void tearDown() {
+ desktop.cleanUp();
+ }
+
+ /**
+ * Since starting Cytoscape takes a while, it's probably best
+ * to run many different tests as a single test case. To maintain
+ * sanity, please add additional tests as separate method calls
+ * within this test case.
+ */
+ @Test
+ public void runTests() {
+ openAndClosePluginManager();
+ }
+
+
+ private void openAndClosePluginManager() {
+ desktop.menuItemWithPath("Plugins","Manage Plugins")
+ .click();
+ Pause.pause(5000);
+ desktop.dialog(DialogMatcher.withTitle("Manage Plugins"))
+ .show()
+ .button(JButtonMatcher.withText("Close"))
+ .click();
+ }
+}
+
diff --git a/application/pom.xml b/application/pom.xml
new file mode 100644
index 0000000..6d7043f
--- /dev/null
+++ b/application/pom.xml
@@ -0,0 +1,465 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>cytoscape</groupId>
+ <artifactId>parent</artifactId>
+ <version>2.8.4-SNAPSHOT</version>
+ </parent>
+
+ <groupId>cytoscape</groupId>
+ <artifactId>application</artifactId>
+ <packaging>jar</packaging>
+ <name>Cytoscape Application</name>
+
+
+ <build>
+
+ <!-- This block allows fields to be substituted into resource files,
+ such as the version number in cytoscape.props. -->
+ <resources>
+ <resource>
+ <directory>src/main/resources</directory>
+ <filtering>true</filtering>
+ </resource>
+ </resources>
+
+ <plugins>
+
+ <!-- this copies the javahelp files into place -->
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-dependency-plugin</artifactId>
+ <executions>
+ <execution>
+ <id>copy-javahelp</id>
+ <phase>generate-sources</phase>
+ <goals>
+ <goal>unpack</goal>
+ </goals>
+ <configuration>
+ <artifactItems>
+ <artifactItem>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>docs</artifactId>
+ <version>${project.version}</version>
+ <type>zip</type>
+ <classifier>javahelp</classifier>
+ <overWrite>true</overWrite>
+ <outputDirectory>${project.build.outputDirectory}/cytoscape/help</outputDirectory>
+ </artifactItem>
+ </artifactItems>
+ </configuration>
+ </execution>
+ </executions>
+ </plugin>
+ <!-- we might consider uncommenting this if we can get indexing to work!
+ <plugin>
+ <groupId>org.codehaus.mojo.javahelp</groupId>
+ <artifactId>maven-javahelp-plugin</artifactId>
+ <configuration>
+ <sourcePath>${project.build.outputDirectory}/cytoscape/help</sourcePath>
+ <dataBase>${project.build.outputDirectory}/cytoscape/help</dataBase>
+ </configuration>
+ <executions>
+ <execution>
+ <id>index-javahelp</id>
+ <phase>process-sources</phase>
+ <goals>
+ <goal>jhindex</goal>
+ </goals>
+ </execution>
+ </executions>
+ </plugin>
+ -->
+ <!-- generates classes for XML handling (bookmarks and sessions) -->
+ <plugin>
+ <groupId>org.jvnet.jaxb2.maven2</groupId>
+ <artifactId>maven-jaxb2-plugin</artifactId>
+ <version>0.7.4</version>
+ <executions>
+ <execution>
+ <id>session</id>
+ <goals>
+ <goal>generate</goal>
+ </goals>
+ <configuration>
+ <schemaDirectory>src/main/resources/xsd</schemaDirectory>
+ <schemaIncludes>
+ <include>cysession.xsd</include>
+ </schemaIncludes>
+ <generatePackage>cytoscape.generated</generatePackage>
+ <verbose>true</verbose>
+ <removeOldOutput>false</removeOldOutput>
+ <forceRegenerate>true</forceRegenerate>
+ </configuration>
+ </execution>
+ <execution>
+ <id>bookmarks</id>
+ <goals>
+ <goal>generate</goal>
+ </goals>
+ <configuration>
+ <schemaDirectory>src/main/resources/xsd</schemaDirectory>
+ <schemaIncludes>
+ <include>bookmarks.xsd</include>
+ </schemaIncludes>
+ <generatePackage>cytoscape.bookmarks</generatePackage>
+ <verbose>true</verbose>
+ <removeOldOutput>false</removeOldOutput>
+ <forceRegenerate>true</forceRegenerate>
+ </configuration>
+ </execution>
+ </executions>
+ </plugin>
+ <!-- creates the jar file -->
+ <plugin>
+ <artifactId>maven-assembly-plugin</artifactId>
+ <version>2.2-beta-5</version>
+ <configuration>
+ <descriptorRefs>
+ <descriptorRef>jar-with-dependencies</descriptorRef>
+ </descriptorRefs>
+ <archive>
+ <manifest>
+ <mainClass>cytoscape.CyMain</mainClass>
+ </manifest>
+ </archive>
+ </configuration>
+ <executions>
+ <execution>
+ <id>make-assembly</id>
+ <phase>package</phase>
+ <goals>
+ <goal>single</goal>
+ </goals>
+ </execution>
+ </executions>
+ </plugin>
+
+ <!-- Used to create the splash and credit screens.
+ The rasterizing needs to happen after the svg files
+ have been copied and filtered so that the version
+ number is correct. -->
+ <plugin>
+ <groupId>org.codehaus.mojo</groupId>
+ <artifactId>batik-maven-plugin</artifactId>
+ <version>1.0-beta-1</version>
+ <configuration>
+ <srcDir>${project.build.directory}/classes/cytoscape/images/versioned-svg</srcDir>
+ <destDir>${project.build.directory}/classes/cytoscape/images</destDir>
+ </configuration>
+ <executions>
+ <execution>
+ <!-- just needs to happen after resources are copied -->
+ <phase>compile</phase>
+ <goals>
+ <goal>rasterize</goal>
+ </goals>
+ </execution>
+ </executions>
+ <!-- We need to specify this so that we can exclude fop,
+ otherwise we get duplicate XML libs, which cause problems. -->
+ <dependencies>
+ <dependency>
+ <groupId>batik</groupId>
+ <artifactId>batik-rasterizer-ext</artifactId>
+ <version>1.6-1</version>
+ <scope>compile</scope>
+ <exclusions>
+ <exclusion>
+ <artifactId>fop</artifactId>
+ <groupId>fop</groupId>
+ </exclusion>
+ </exclusions>
+ </dependency>
+ </dependencies>
+ </plugin>
+ </plugins>
+ </build>
+
+ <!-- bootstrap for cytoscape dependencies, namely the parent POM snapshots -->
+ <repositories>
+ <repository>
+ <id>cytoscape_snapshots</id>
+ <snapshots>
+ <enabled>true</enabled>
+ </snapshots>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <name>Cytoscape Snapshots</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/</url>
+ </repository>
+ <repository>
+ <id>cytoscape_releases</id>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ <name>Cytoscape Releases</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/releases/</url>
+ </repository>
+ </repositories>
+
+ <pluginRepositories>
+ <pluginRepository>
+ <id>maven2-repository.dev.java.net</id>
+ <name>Java.net Maven 2 Repository</name>
+ <url>http://download.java.net/maven/2</url>
+ </pluginRepository>
+ </pluginRepositories>
+
+ <dependencies>
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>util-intr</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>graph-dynamic</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>graph-fixed</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>giny</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>render-immed</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>render-stateful</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>render-export</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>fing</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>phoebe-dnd</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>geom-spacial</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>geom-rtree</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>undo-support</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>equations</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>task</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>ding</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>obo</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>commons-cli-1-x-cytocape-custom</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>docs</artifactId>
+ <version>${project.version}</version>
+ <classifier>javahelp</classifier>
+ <type>zip</type>
+ </dependency>
+
+ <!-- swingx -->
+ <dependency>
+ <groupId>cytoscape-temp</groupId>
+ <artifactId>l2fprod-common-sheet</artifactId>
+ <version>7.3</version>
+ </dependency>
+ <dependency>
+ <groupId>org.swinglabs</groupId>
+ <artifactId>swingx</artifactId>
+ <version>1.6.1</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape-temp</groupId>
+ <artifactId>l2fprod-common-shared</artifactId>
+ <version>7.3</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape-temp</groupId>
+ <artifactId>l2fprod-common-fontchooser</artifactId>
+ <version>7.3</version>
+ </dependency>
+
+ <dependency>
+ <groupId>javax.help</groupId>
+ <artifactId>javahelp</artifactId>
+ <version>2.0.02</version>
+ </dependency>
+
+ <dependency>
+ <groupId>com.lowagie</groupId>
+ <artifactId>itext</artifactId>
+ <version>2.0.8</version>
+ </dependency>
+
+ <dependency>
+ <groupId>colt</groupId>
+ <artifactId>colt</artifactId>
+ <version>1.2.0</version>
+ </dependency>
+
+ <dependency>
+ <groupId>cytoscape-temp</groupId>
+ <artifactId>biojava</artifactId>
+ <version>1.4</version>
+ </dependency>
+
+ <dependency>
+ <groupId>org.jdom</groupId>
+ <artifactId>jdom</artifactId>
+ <version>1.1</version>
+ </dependency>
+
+ <dependency>
+ <groupId>org.swinglabs</groupId>
+ <artifactId>swing-layout</artifactId>
+ <version>1.0.3</version>
+ </dependency>
+
+ <dependency>
+ <groupId>com.jgoodies</groupId>
+ <artifactId>looks</artifactId>
+ <version>2.1.4</version>
+ </dependency>
+
+ <dependency>
+ <groupId>cytoscape-temp</groupId>
+ <artifactId>freehep-export</artifactId>
+ <version>2.1.1</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape-temp</groupId>
+ <artifactId>freehep-graphics2d</artifactId>
+ <version>2.1.1</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape-temp</groupId>
+ <artifactId>freehep-graphicsio</artifactId>
+ <version>2.1.1</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape-temp</groupId>
+ <artifactId>freehep-graphicsio-ps</artifactId>
+ <version>2.1.1</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape-temp</groupId>
+ <artifactId>freehep-graphicsio-svg</artifactId>
+ <version>2.1.1</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape-temp</groupId>
+ <artifactId>freehep-graphicsio-java</artifactId>
+ <version>2.1.1</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape-temp</groupId>
+ <artifactId>freehep-io</artifactId>
+ <version>2.0.2</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape-temp</groupId>
+ <artifactId>freehep-swing</artifactId>
+ <version>2.0.3</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape-temp</groupId>
+ <artifactId>freehep-util</artifactId>
+ <version>2.0.2</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape-temp</groupId>
+ <artifactId>freehep-xml</artifactId>
+ <version>2.1.1</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape-temp</groupId>
+ <artifactId>freehep-jas-plotter</artifactId>
+ <version>2.2</version>
+ </dependency>
+
+ <dependency>
+ <groupId>org.apache.lucene</groupId>
+ <artifactId>lucene-core</artifactId>
+ <version>3.0.1</version>
+ </dependency>
+
+ <dependency>
+ <groupId>cytoscape-temp</groupId>
+ <artifactId>tclib</artifactId>
+ <version>1.0</version>
+ </dependency>
+
+ <dependency>
+ <groupId>cytoscape-temp</groupId>
+ <artifactId>violinstrings</artifactId>
+ <version>1.0.2</version>
+ </dependency>
+
+ <dependency>
+ <groupId>cytoscape-temp</groupId>
+ <artifactId>install4j</artifactId>
+ <version>4.0</version>
+ </dependency>
+
+ <dependency>
+ <groupId>cytoscape-sun</groupId>
+ <artifactId>jaxb-api</artifactId>
+ <version>1.0</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape-sun</groupId>
+ <artifactId>jaxb-impl</artifactId>
+ <version>1.0</version>
+ </dependency>
+ </dependencies>
+
+</project>
+
diff --git a/application/src/main/java/cytoscape/CyEdge.java b/application/src/main/java/cytoscape/CyEdge.java
new file mode 100644
index 0000000..d6e01a2
--- /dev/null
+++ b/application/src/main/java/cytoscape/CyEdge.java
@@ -0,0 +1,166 @@
+/*
+ File: CyEdge.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape;
+
+import cytoscape.giny.CytoscapeFingRootGraph;
+
+import giny.model.*;
+
+
+/**
+ *
+ */
+public class CyEdge implements giny.model.Edge {
+ // Variables specific to public get/set methods.
+ CytoscapeFingRootGraph m_rootGraph = null;
+ int m_rootGraphIndex = 0;
+ String m_identifier = null;
+
+ /**
+ * Creates a new CyEdge object.
+ *
+ * @param root the RootGraph to put the edge into
+ * @param rootGraphIndex the index to assign to this edge
+ */
+ public CyEdge(RootGraph root, int rootGraphIndex) {
+ this.m_rootGraph = (CytoscapeFingRootGraph) root;
+ this.m_rootGraphIndex = rootGraphIndex;
+ this.m_identifier = new Integer(m_rootGraphIndex).toString();
+ }
+
+ /**
+ * Return the source node for this edge. All edges have a source
+ * Node and a target Node. For directed edges, the edge points from
+ * the source node to the target node, but for undirected edges, the
+ * definition of source and target is defined by the edge but
+ * which node is the source and which node is the target does not
+ * impact the behavior.
+ *
+ * @return The source Node for this edge. Note that this is returned as a Node
+ * rather than a CyNode. Generally, the Node may be safely cast to a CyNode.
+ */
+ public giny.model.Node getSource() {
+ return m_rootGraph.getNode(m_rootGraph.getEdgeSourceIndex(m_rootGraphIndex));
+ }
+
+ /**
+ * Return the target node for this edge. All edges have a source
+ * Node and a target Node. For directed edges, the edge points from
+ * the source node to the target node, but for undirected edges, the
+ * definition of source and target is defined by the edge but
+ * which node is the source and which node is the target does not
+ * impact the behavior.
+ *
+ * @return The target Node for this edge. Note that this is returned as a Node
+ * rather than a CyNode. Generally, the Node may be safely cast to a CyNode.
+ */
+ public giny.model.Node getTarget() {
+ return m_rootGraph.getNode(m_rootGraph.getEdgeTargetIndex(m_rootGraphIndex));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isDirected() {
+ return m_rootGraph.isEdgeDirected(m_rootGraphIndex);
+ }
+
+ /**
+ * Get the root graph for this edge.
+ *
+ * @return the root graph
+ */
+ public RootGraph getRootGraph() {
+ return m_rootGraph;
+ }
+
+ /**
+ * Get the root graph index for this edge
+ *
+ * @return the root graph index
+ */
+ public int getRootGraphIndex() {
+ return m_rootGraphIndex;
+ }
+
+ /**
+ * Return the "name" of an edge
+ *
+ * @return string representation of the edge
+ */
+ public String toString() {
+ return getIdentifier();
+ }
+
+ /**
+ * Return the edge identifier. Usually this is something of the
+ * form: "SourceNode (interaction) TargetNode".
+ *
+ * @return edge identifier
+ */
+ public String getIdentifier() {
+ return m_identifier;
+ }
+
+ /**
+ * Set the identifier for this edge
+ *
+ * @param new_id The new identifier
+ *
+ * @return always returns true
+ */
+ public boolean setIdentifier(String new_id) {
+ if (new_id == null) {
+ m_rootGraph.setEdgeIdentifier(m_identifier, 0);
+ } else {
+ m_rootGraph.setEdgeIdentifier(new_id, m_rootGraphIndex);
+ }
+
+ m_identifier = new_id;
+
+ return true;
+ }
+
+ /**
+ * A static method used to create edge identifiers.
+ */
+ public static String createIdentifier(String source, String attribute_value, String target) {
+ return source + " (" + attribute_value + ") " + target;
+ }
+}
diff --git a/application/src/main/java/cytoscape/CyMain.java b/application/src/main/java/cytoscape/CyMain.java
new file mode 100644
index 0000000..4931471
--- /dev/null
+++ b/application/src/main/java/cytoscape/CyMain.java
@@ -0,0 +1,489 @@
+/*
+ File: CyMain.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape;
+
+import java.awt.Dimension;
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Properties;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+import javax.swing.UIManager;
+
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.CommandLineParser;
+import org.apache.commons.cli.HelpFormatter;
+import org.apache.commons.cli.OptionBuilder;
+import org.apache.commons.cli.ParseException;
+import org.apache.commons.cli.PosixParser;
+
+import com.install4j.api.launcher.StartupNotification;
+import com.jgoodies.looks.LookUtils;
+import com.jgoodies.looks.Options;
+import com.jgoodies.looks.plastic.Plastic3DLookAndFeel;
+
+import cytoscape.init.CyInitParams;
+import cytoscape.logger.CyLogger;
+import cytoscape.util.FileUtil;
+import cytoscape.util.MathUtil;
+
+
+/**
+ * This is the main startup class for Cytoscape. This parses the command line
+ * and implements CyInitParams so that it can be used to initialize cytoscape.
+ *
+ * <p>
+ * Look and Feel is modified for jgoodies 2.1.4 by Kei Ono
+ * </p>
+ */
+public class CyMain implements CyInitParams {
+ protected String[] args;
+
+ protected Properties props;
+
+ protected String[] graphFiles;
+
+ protected String[] plugins;
+
+ protected Properties vizmapProps;
+
+ protected static String sessionFile;
+
+ protected String[] nodeAttrFiles;
+
+ protected String[] edgeAttrFiles;
+
+ protected String[] expressionFiles;
+
+ protected int mode;
+
+ protected org.apache.commons.cli.Options options;
+
+ protected CyLogger logger = null;
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args
+ * DOCUMENT ME!
+ *
+ * @throws Exception
+ * DOCUMENT ME!
+ */
+ public static void main(String[] args) throws Exception {
+ if (System.getProperty("os.name").startsWith("Mac")) {
+ System.setProperty("com.apple.mrj.application.apple.menu.about.name", "Cytoscape");
+ }
+
+ CyMain app = new CyMain(args);
+ }
+
+ /**
+ * Creates a new CyMain object.
+ *
+ * @param args
+ * DOCUMENT ME!
+ *
+ * @throws Exception
+ * DOCUMENT ME!
+ */
+ public CyMain(String[] args) throws Exception {
+ props = null;
+ graphFiles = null;
+ plugins = null;
+ vizmapProps = null;
+ sessionFile = null;
+ nodeAttrFiles = null;
+ edgeAttrFiles = null;
+ expressionFiles = null;
+ this.args = args;
+ mode = CyInitParams.ERROR;
+ options = new org.apache.commons.cli.Options();
+ logger = CyLogger.getLogger(CyMain.class);
+
+ // for (String asdf: args)
+ // logger.info("arg: '" + asdf + "'");
+ parseCommandLine(args);
+
+ // Register CyStartupListener to intercept arguments passed by file
+ // associations set by install4j for Mac OS
+ StartupNotification.registerStartupListener(new CyStartupListener());
+
+ CytoscapeInit initializer = new CytoscapeInit();
+
+ if (!initializer.init(this)) {
+ printHelp();
+ Cytoscape.exit(1);
+ }
+ }
+
+ protected void parseCommandLine(String[] args) {
+ // create the options
+ options.addOption("h", "help", false, "Print this message.");
+ options.addOption("v", "version", false, "Print the version number.");
+ // commented out until we actually support doing anything in headless
+ // mode
+ // options.addOption("H", "headless", false, "Run in headless (no gui)
+ // mode.");
+ options.addOption(OptionBuilder.withLongOpt("session").withDescription(
+ "Load a cytoscape session (.cys) file.").withValueSeparator(
+ '\0').withArgName("file").hasArg() // only allow one session!!!
+ .create("s"));
+
+ options.addOption(OptionBuilder.withLongOpt("network").withDescription(
+ "Load a network file (any format).").withValueSeparator('\0')
+ .withArgName("file").hasArgs().create("N"));
+
+ options
+ .addOption(OptionBuilder
+ .withLongOpt("edge-attrs")
+ .withDescription(
+ "Load an edge attributes file (edge attribute format).")
+ .withValueSeparator('\0').withArgName("file").hasArgs()
+ .create("e"));
+ options.addOption(OptionBuilder.withLongOpt("node-attrs")
+ .withDescription(
+ "Load a node attributes file (node attribute format).")
+ .withValueSeparator('\0').withArgName("file").hasArgs().create(
+ "n"));
+ options.addOption(OptionBuilder.withLongOpt("matrix").withDescription(
+ "Load a node attribute matrix file (table).")
+ .withValueSeparator('\0').withArgName("file").hasArgs().create(
+ "m"));
+
+ options
+ .addOption(OptionBuilder
+ .withLongOpt("plugin")
+ .withDescription(
+ "Load a plugin jar file, directory of jar files, plugin class name, or plugin jar URL.")
+ .withValueSeparator('\0').withArgName("file").hasArgs()
+ .create("p"));
+
+ options
+ .addOption(OptionBuilder
+ .withLongOpt("props")
+ .withDescription(
+ "Load cytoscape properties file (Java properties format) or individual property: -P name=value.")
+ .withValueSeparator('\0').withArgName("file").hasArgs()
+ .create("P"));
+ options.addOption(OptionBuilder.withLongOpt("vizmap").withDescription(
+ "Load vizmap properties file (Java properties format).")
+ .withValueSeparator('\0').withArgName("file").hasArgs().create(
+ "V"));
+
+ // try to parse the cmd line
+ CommandLineParser parser = new PosixParser();
+ CommandLine line = null;
+
+ try {
+ line = parser.parse(options, args);
+ } catch (ParseException e) {
+ System.err
+ .println("Parsing command line failed: " + e.getMessage());
+ printHelp();
+ System.exit(1);
+ }
+
+ // Read any argument containing ".cys" as session file.
+ // Allows session files to be passed in via MIME type settings.
+ // This imprecise method is overwritten by -s option, if specified.
+ for (String freeArg : args) {
+ if (freeArg.contains(".cys")) {
+ sessionFile = freeArg;
+ }
+ }
+
+ // use what is found on the command line to set values
+ if (line.hasOption("h")) {
+ printHelp();
+ System.exit(0);
+ }
+
+ if (line.hasOption("v")) {
+ CytoscapeVersion version = new CytoscapeVersion();
+ logger.info(version.getVersion());
+ System.exit(0);
+ }
+
+ if (line.hasOption("H")) {
+ mode = CyInitParams.TEXT;
+ } else {
+ mode = CyInitParams.GUI;
+ setupLookAndFeel();
+ }
+
+ if (line.hasOption("P"))
+ props = createProperties(line.getOptionValues("P"));
+ else
+ props = createProperties(new String[0]);
+
+ if (line.hasOption("N"))
+ graphFiles = line.getOptionValues("N");
+
+ if (line.hasOption("p"))
+ plugins = line.getOptionValues("p");
+
+ if (line.hasOption("V"))
+ vizmapProps = createProperties(line.getOptionValues("V"));
+ else
+ vizmapProps = createProperties(new String[0]);
+
+ if (line.hasOption("s"))
+ sessionFile = line.getOptionValue("s");
+
+ if (line.hasOption("n"))
+ nodeAttrFiles = line.getOptionValues("n");
+
+ if (line.hasOption("e"))
+ edgeAttrFiles = line.getOptionValues("e");
+
+ if (line.hasOption("m"))
+ expressionFiles = line.getOptionValues("m");
+ }
+
+ /**
+ * Provides access to the session file parsed from arguments intercepted by
+ * CyStartupListener
+ */
+ public static void setSessionFile(String sf) {
+ sessionFile = sf;
+ }
+
+ protected void setupLookAndFeel() {
+ try {
+ if (LookUtils.IS_OS_WINDOWS) {
+ /*
+ * For Windows: just use platform default look & feel.
+ */
+ UIManager.setLookAndFeel("com.sun.java.swing.plaf.windows.WindowsLookAndFeel");
+ } else if (LookUtils.IS_OS_MAC) {
+ /*
+ * For Mac: move menu bar to OS X default bar (next to Apple
+ * icon)
+ */
+ System.setProperty("apple.laf.useScreenMenuBar", "true");
+
+ } else {
+ final JavaVersion javaVersion = JavaVersion.getJavaVersion();
+ if (javaVersion.getMajor() >= 2 || javaVersion.getMinor() > 6
+ || (javaVersion.getMinor() == 6 && javaVersion.getUpdate() >= 10))
+ UIManager.setLookAndFeel("com.sun.java.swing.plaf.nimbus.NimbusLookAndFeel");
+ else {
+ /*
+ * For Unix platforms, use JGoodies Looks
+ */
+ UIManager.setLookAndFeel(new Plastic3DLookAndFeel());
+ Plastic3DLookAndFeel.set3DEnabled(true);
+ Plastic3DLookAndFeel
+ .setCurrentTheme(new com.jgoodies.looks.plastic.theme.SkyBluer());
+ Plastic3DLookAndFeel
+ .setTabStyle(Plastic3DLookAndFeel.TAB_STYLE_METAL_VALUE);
+ Plastic3DLookAndFeel.setHighContrastFocusColorsEnabled(true);
+
+ Options.setDefaultIconSize(new Dimension(18, 18));
+ Options.setHiResGrayFilterEnabled(true);
+ Options.setPopupDropShadowEnabled(true);
+ Options.setUseSystemFonts(true);
+
+ UIManager.put("Button.defaultButtonFollowsFocus", Boolean.TRUE);
+ UIManager.put(Options.USE_SYSTEM_FONTS_APP_KEY, Boolean.TRUE);
+ }
+ }
+ } catch (Exception e) {
+ logger.warn("Can't set look & feel:" + e.getMessage(), e);
+ }
+ }
+
+ protected void printHelp() {
+ HelpFormatter formatter = new HelpFormatter();
+ formatter.printHelp("java -Xmx512M -jar cytoscape.jar [OPTIONS]",
+ options);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Properties getProps() {
+ return props;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Properties getVizProps() {
+ return vizmapProps;
+ }
+
+ private Properties createProperties(String[] potentialProps) {
+ // for ( String asdf: potentialProps)
+ // logger.info("prop: '" + asdf + "'");
+ Properties props = new Properties();
+ Properties argProps = new Properties();
+
+ Matcher propPattern = Pattern.compile("^((\\w+\\.*)+)\\=(.+)$").matcher("");
+
+ for (int i = 0; i < potentialProps.length; i++) {
+ propPattern.reset(potentialProps[i]);
+
+ // check to see if the string is a key value pair
+ if (propPattern.matches()) {
+ argProps.setProperty(propPattern.group(1), propPattern.group(3));
+
+ // otherwise assume it's a file/url
+ } else {
+ try {
+ InputStream in = null;
+
+ try {
+ in = FileUtil.getInputStream(potentialProps[i]);
+ if (in != null)
+ props.load(in);
+ else
+ logger.info("Couldn't load property: "
+ + potentialProps[i]);
+ }
+ finally {
+ if (in != null) {
+ in.close();
+ }
+ }
+ } catch (IOException e) {
+ logger.warn("Couldn't load property '"+ potentialProps[i] + "' from file: "+e.getMessage(), e);
+ }
+ }
+ }
+
+ // Transfer argument properties into the full properties.
+ // We do this so that anything specified on the command line
+ // overrides anything specified in a file.
+ props.putAll(argProps);
+
+ addDefaultProps(props);
+
+ return props;
+ }
+
+ private void addDefaultProps(final Properties props) {
+ final String nestedNetworkImageScaleFactor = props.getProperty("nestedNetwork.imageScaleFactor");
+ if (nestedNetworkImageScaleFactor == null || !MathUtil.isValidDouble(nestedNetworkImageScaleFactor))
+ props.setProperty("nestedNetwork.imageScaleFactor", "1.0");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public List getGraphFiles() {
+ return createList(graphFiles);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public List getEdgeAttributeFiles() {
+ return createList(edgeAttrFiles);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public List getNodeAttributeFiles() {
+ return createList(nodeAttrFiles);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public List getExpressionFiles() {
+ return createList(expressionFiles);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public List getPlugins() {
+ return createList(plugins);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getSessionFile() {
+ return sessionFile;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getMode() {
+ return mode;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String[] getArgs() {
+ return args;
+ }
+
+ private List createList(String[] vals) {
+ if (vals == null)
+ return new ArrayList();
+
+ ArrayList a = new ArrayList(vals.length);
+
+ for (int i = 0; i < vals.length; i++)
+ a.add(i, vals[i]);
+
+ return a;
+ }
+}
diff --git a/application/src/main/java/cytoscape/CyNetwork.java b/application/src/main/java/cytoscape/CyNetwork.java
new file mode 100644
index 0000000..b98b0ea
--- /dev/null
+++ b/application/src/main/java/cytoscape/CyNetwork.java
@@ -0,0 +1,312 @@
+/*
+ File: CyNetwork.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape;
+
+import cytoscape.data.CyAttributes;
+import cytoscape.data.ExpressionData;
+import cytoscape.data.SelectEventListener;
+import cytoscape.data.SelectFilter;
+
+import giny.model.Edge;
+import giny.model.GraphPerspective;
+import giny.model.Node;
+
+import java.util.Collection;
+import java.util.Set;
+
+
+/**
+ * CyNetwork is the primary class for algorithm writing. All algorithms
+ * should take a CyNetwork as input, and do their best to only use the API of
+ * CyNetwork. Plugins that want to affect the display of a graph can look
+ * into using CyNetworkView as well.<br>
+ * <br>
+ * A CyNetwork can create Nodes or Edges. Any Nodes or Edges that wish to
+ * be added to a CyNetwork first need to be created in <span style="font-style:
+ * italic;">Cytoscape.</span> <br>
+ * <br>
+ * The methods that are defined by CyNetwork mostly deal with data integration
+ * and flagging of nodes/edges. All methods that deal with graph traversal
+ * are part of the inherited API of the GraphPerspective class. Links to
+ * which can be found at the bottom of the methods list. <br>
+ * <br>
+ * In general, all methods are supported for working with Nodes/Edges as
+ * objects, and as indices.<br>
+ */
+public interface CyNetwork extends GraphPerspective {
+ /**
+ * Can Change
+ */
+ public String getTitle();
+
+ /**
+ * Can Change
+ */
+ public void setTitle(String new_id);
+
+ /**
+ * Can't Change
+ */
+ public String getIdentifier();
+
+ /**
+ * Can't Change
+ */
+ public String setIdentifier(String new_id);
+
+ // ----------------------------------------//
+ // Network Methods
+ // ----------------------------------------//
+
+ /**
+ * Appends all of the nodes and edges in the given Network to this Network
+ */
+ public void appendNetwork(CyNetwork network);
+
+ // ------------------------------//
+ // Listener Methods
+ // ------------------------------//
+
+ /**
+ * Registers the argument as a listener to this object. Does nothing if the
+ * argument is already a listener.
+ */
+ public void addCyNetworkListener(CyNetworkListener listener);
+
+ /**
+ * Removes the argument from the set of listeners for this object. Returns
+ * true if the argument was a listener before this call, false otherwise.
+ */
+ public boolean removeCyNetworkListener(CyNetworkListener listener);
+
+ /**
+ * Returns the set of listeners registered with this object.
+ */
+ public Set getCyNetworkListeners();
+
+ /**
+ * Sets the selected state of all nodes in this CyNetwork to true
+ */
+ public void selectAllNodes();
+
+ /**
+ * Sets the selected state of all edges in this CyNetwork to true
+ */
+ public void selectAllEdges();
+
+ /**
+ * Sets the selected state of all nodes in this CyNetwork to false
+ */
+ public void unselectAllNodes();
+
+ /**
+ * Sets the selected state of all edges in this CyNetwork to false
+ */
+ public void unselectAllEdges();
+
+ /**
+ * Sets the selected state of a collection of nodes.
+ *
+ * @param nodes a Collection of Nodes
+ * @param selected_state the desired selection state for the nodes
+ */
+ public void setSelectedNodeState(Collection nodes, boolean selected_state);
+
+ /**
+ * Sets the selected state of a single node.
+ *
+ * @param node a single Node
+ * @param selected_state the desired selection state for the nodes
+ */
+ public void setSelectedNodeState(Node node, boolean selected_state);
+
+ /**
+ * Sets the selected state of a collection of edges.
+ *
+ * @param edges a Collection of Edges
+ * @param selected_state the desired selection state for the edges
+ */
+ public void setSelectedEdgeState(Collection edges, boolean selected_state);
+
+ /**
+ * Sets the selected state of a single edge.
+ *
+ * @param edge a single Edge
+ * @param selected_state the desired selection state for the edges
+ */
+ public void setSelectedEdgeState(Edge edge, boolean selected_state);
+
+ /**
+ * Returns the selected state of the given node.
+ *
+ * @param node the node
+ * @return true if selected, false otherwise
+ */
+ public boolean isSelected(Node node);
+
+ /**
+ * Returns the selected state of the given edge.
+ *
+ * @param edge the edge
+ * @return true if selected, false otherwise
+ */
+ public boolean isSelected(Edge edge);
+
+ /**
+ * Returns the set of selected nodes in this CyNetwork
+ *
+ * @return a Set of selected nodes
+ */
+ public Set getSelectedNodes();
+
+ /**
+ * Returns the set of selected edges in this CyNetwork
+ *
+ * @return a Set of selected edges
+ */
+ public Set getSelectedEdges();
+
+ /**
+ * Adds a listener for SelectEvents to this CyNetwork
+ *
+ * @param listener
+ */
+ public void addSelectEventListener(SelectEventListener listener);
+
+ /**
+ * Removes a listener for SelectEvents from this CyNetwork
+ * @param listener
+ */
+ public void removeSelectEventListener(SelectEventListener listener);
+
+ /**
+ *
+ * @return SelectFilter
+ */
+ public SelectFilter getSelectFilter();
+
+ // --------------------//
+ // Network Client Data
+
+ /**
+ * Networks can support client data.
+ *
+ * @deprecated Use {@link CyAttributes} directly. This method will be
+ * removed in May, 2007.
+ */
+ public void putClientData(String data_name, Object data);
+
+ /**
+ * Get a list of all currently available ClientData objects
+ *
+ * @deprecated Use {@link CyAttributes} directly. This method will be
+ * removed in May, 2007.
+ */
+ public Collection getClientDataNames();
+
+ /**
+ * Get Some client data
+ *
+ * @deprecated Use {@link CyAttributes} directly. This method will be
+ * removed in May, 2007.
+ */
+ public Object getClientData(String data_name);
+
+ // ----------------------------------------//
+ // Node and Edge creation/deletion
+ // ----------------------------------------//
+
+ // --------------------//
+ // Nodes
+
+ /**
+ * Add a node to this Network that already exists in Cytoscape
+ *
+ * @return the Network Index of this node
+ */
+ public int addNode(int cytoscape_node);
+
+ /**
+ * Add a node to this Network that already exists in Cytoscape
+ *
+ * @return the Network Index of this node
+ */
+ public CyNode addNode(Node cytoscape_node);
+
+ /**
+ * This will remove this node from the Network. However, unless forced, it
+ * will remain in Cytoscape to be possibly resused by another Network in the
+ * future.
+ *
+ * @param set_remove
+ * true removes this node from all of Cytoscape, false lets it be
+ * used by other CyNetworks
+ * @return true if the node is still present in Cytoscape ( i.e. in another
+ * Network )
+ */
+ public boolean removeNode(int node_index, boolean set_remove);
+
+ // --------------------//
+ // Edges
+
+ /**
+ * Add a edge to this Network that already exists in Cytoscape
+ *
+ * @return the Network Index of this edge
+ */
+ public int addEdge(int cytoscape_edge);
+
+ /**
+ * Add a edge to this Network that already exists in Cytoscape
+ *
+ * @return the Network Index of this edge
+ */
+ public CyEdge addEdge(Edge cytoscape_edge);
+
+ /**
+ * This will remove this edge from the Network. However, unless forced, it
+ * will remain in Cytoscape to be possibly resused by another Network in the
+ * future.
+ *
+ * @param set_remove
+ * true removes this edge from all of Cytoscape, false lets it be
+ * used by other CyNetworks
+ * @return true if the edge is still present in Cytoscape ( i.e. in another
+ * Network )
+ */
+ public boolean removeEdge(int edge_index, boolean set_remove);
+}
diff --git a/application/src/main/java/cytoscape/CyNetworkAdapter.java b/application/src/main/java/cytoscape/CyNetworkAdapter.java
new file mode 100644
index 0000000..8c0105c
--- /dev/null
+++ b/application/src/main/java/cytoscape/CyNetworkAdapter.java
@@ -0,0 +1,59 @@
+/*
+ File: CyNetworkAdapter.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+//-------------------------------------------------------------------------
+// $Revision: 9736 $
+// $Date: 2007-03-20 01:25:45 +0100 (Tue, 20 Mar 2007) $
+// $Author: mes $
+//-------------------------------------------------------------------------
+package cytoscape;
+
+
+//-------------------------------------------------------------------------
+/**
+ * Empty implementation of the CyNetworkListener interface, following the
+ * adapter pattern useful for defining anonymous inner classes.
+ */
+public class CyNetworkAdapter implements CyNetworkListener {
+ /**
+ * DOCUMENT ME!
+ *
+ * @param event DOCUMENT ME!
+ */
+ public void onCyNetworkEvent(CyNetworkEvent event) {
+ }
+}
diff --git a/application/src/main/java/cytoscape/CyNetworkData.java b/application/src/main/java/cytoscape/CyNetworkData.java
new file mode 100644
index 0000000..c3277e6
--- /dev/null
+++ b/application/src/main/java/cytoscape/CyNetworkData.java
@@ -0,0 +1,45 @@
+/*
+ File: CyNetworkData.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape;
+
+
+/**
+ * This will be the interface where things like multi-dimensional data
+ * are accessed.
+ */
+public interface CyNetworkData {
+}
diff --git a/application/src/main/java/cytoscape/CyNetworkEvent.java b/application/src/main/java/cytoscape/CyNetworkEvent.java
new file mode 100644
index 0000000..47158d2
--- /dev/null
+++ b/application/src/main/java/cytoscape/CyNetworkEvent.java
@@ -0,0 +1,108 @@
+/*
+ File: CyNetworkEvent.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+//-------------------------------------------------------------------------
+// $Revision: 9736 $
+// $Date: 2007-03-20 01:25:45 +0100 (Tue, 20 Mar 2007) $
+// $Author: mes $
+//-------------------------------------------------------------------------
+package cytoscape;
+
+
+//-------------------------------------------------------------------------
+/**
+ * Events of this class are fired from a CyNetwork object when something
+ * happens to the network. The event holds a reference to the network that
+ * is the source of the event, and an int flag identifying the type of event.
+ */
+public class CyNetworkEvent {
+ /**
+ * This type is used when the requested type is unknown to this class.
+ */
+ public static final int UNKNOWN = -1;
+
+ /**
+ * Indicates that someone is beginning to work with the network.
+ */
+ public static final int BEGIN = 0;
+
+ /**
+ * Indicates that someone is done working with the network.
+ */
+ public static final int END = 1;
+
+ /**
+ * Indicates that a new graph has been installed in the network.
+ */
+ public static final int GRAPH_REPLACED = 10;
+ private CyNetwork network;
+ private int type;
+
+ /**
+ * Creates a new CyNetworkEvent object.
+ *
+ * @param source DOCUMENT ME!
+ * @param type DOCUMENT ME!
+ */
+ public CyNetworkEvent(CyNetwork source, int type) {
+ network = source;
+
+ if ((type == this.BEGIN) || (type == this.END) || (type == this.GRAPH_REPLACED)) {
+ this.type = type;
+ } else {
+ this.type = this.UNKNOWN;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public CyNetwork getNetwork() {
+ return network;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getType() {
+ return type;
+ }
+}
diff --git a/application/src/main/java/cytoscape/CyNetworkListener.java b/application/src/main/java/cytoscape/CyNetworkListener.java
new file mode 100644
index 0000000..c7e99c6
--- /dev/null
+++ b/application/src/main/java/cytoscape/CyNetworkListener.java
@@ -0,0 +1,57 @@
+/*
+ File: CyNetworkListener.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+//-------------------------------------------------------------------------
+// $Revision: 9736 $
+// $Date: 2007-03-20 01:25:45 +0100 (Tue, 20 Mar 2007) $
+// $Author: mes $
+//-------------------------------------------------------------------------
+package cytoscape;
+
+
+//-------------------------------------------------------------------------
+/**
+ * Interface for listeners that respond to CyNetwork events.
+ */
+public interface CyNetworkListener {
+ /**
+ * This method is called when an event is fired by a CyNetwork. The
+ * argument contains a reference to the source network and the type
+ * of event.
+ */
+ void onCyNetworkEvent(CyNetworkEvent event);
+}
diff --git a/application/src/main/java/cytoscape/CyNetworkTitleChange.java b/application/src/main/java/cytoscape/CyNetworkTitleChange.java
new file mode 100644
index 0000000..73b1259
--- /dev/null
+++ b/application/src/main/java/cytoscape/CyNetworkTitleChange.java
@@ -0,0 +1,32 @@
+/**
+ *
+ */
+package cytoscape;
+
+/**
+ * Class used for passing along information about the network when the
+ * network title has changed (firing an event)
+ */
+public class CyNetworkTitleChange {
+ private String networkId;
+ private String networkName;
+
+ public CyNetworkTitleChange(String netId, String title) {
+ networkId = netId;
+ networkName = title;
+ }
+
+ public String getNetworkIdentifier() {
+ return networkId;
+ }
+
+ public String getNetworkTitle() {
+ return networkName;
+ }
+
+ public String toString() {
+ return networkName + ":" + networkId;
+ }
+
+
+}
diff --git a/application/src/main/java/cytoscape/CyNode.java b/application/src/main/java/cytoscape/CyNode.java
new file mode 100644
index 0000000..ee24466
--- /dev/null
+++ b/application/src/main/java/cytoscape/CyNode.java
@@ -0,0 +1,305 @@
+/*
+ File: CyNode.java
+
+ Copyright (c) 2006, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape;
+
+
+import giny.model.GraphPerspective;
+import giny.model.RootGraph;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import cytoscape.giny.CytoscapeFingRootGraph;
+import cytoscape.groups.CyGroup;
+import cytoscape.groups.CyGroupManager;
+
+
+public class CyNode implements giny.model.Node {
+ public static final String NESTED_NETWORK_ID_ATTR = "nested_network_id";
+ public static final String NESTED_NETWORK_IS_VISIBLE_ATTR = "nested_network_is_visible";
+ public static final String HAS_NESTED_NETWORK_ATTR = "has_nested_network";
+ public static final String PARENT_NODES_ATTR = "parent_nodes";
+
+ // Variables specific to public get/set methods.
+ CytoscapeFingRootGraph m_rootGraph = null;
+ int m_rootGraphIndex = 0;
+ String m_identifier = null;
+ ArrayList<CyGroup> groupList = null;
+
+ private GraphPerspective nestedNetwork;
+
+ /**
+ * Creates a new CyNode object.
+ *
+ * @param root DOCUMENT ME!
+ * @param rootGraphIndex DOCUMENT ME!
+ */
+ public CyNode(final RootGraph root, final int rootGraphIndex) {
+ this.m_rootGraph = (CytoscapeFingRootGraph) root;
+ this.m_rootGraphIndex = rootGraphIndex;
+ this.m_identifier = new Integer(m_rootGraphIndex).toString();
+ this.nestedNetwork = null;
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public GraphPerspective getGraphPerspective() {
+ return m_rootGraph.createGraphPerspective(m_rootGraph.getNodeMetaChildIndicesArray(m_rootGraphIndex),
+ m_rootGraph.getEdgeMetaChildIndicesArray(m_rootGraphIndex));
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param gp DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean setGraphPerspective(GraphPerspective gp) {
+ if (gp.getRootGraph() != m_rootGraph)
+ return false;
+
+ final int[] nodeInx = gp.getNodeIndicesArray();
+ final int[] edgeInx = gp.getEdgeIndicesArray();
+
+ for (int i = 0; i < nodeInx.length; i++)
+ m_rootGraph.addNodeMetaChild(m_rootGraphIndex, nodeInx[i]);
+
+ for (int i = 0; i < edgeInx.length; i++)
+ m_rootGraph.addEdgeMetaChild(m_rootGraphIndex, edgeInx[i]);
+
+ return true;
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public RootGraph getRootGraph() {
+ return m_rootGraph;
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getRootGraphIndex() {
+ return m_rootGraphIndex;
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getIdentifier() {
+ return m_identifier;
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param new_id DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean setIdentifier(final String new_id) {
+ if (new_id == null) {
+ m_rootGraph.setNodeIdentifier(m_identifier, 0);
+ } else {
+ m_rootGraph.setNodeIdentifier(new_id, m_rootGraphIndex);
+ }
+
+ m_identifier = new_id;
+
+ return true;
+ }
+
+
+ /**
+ * Add this node to the specified group.
+ *
+ * @param group CyGroup to add this group to
+ */
+ public void addToGroup(final CyGroup group) {
+ // We want to create this lazily to avoid any unnecessary performance/memory
+ // hits on CyNodes!
+ if (groupList == null)
+ groupList = new ArrayList<CyGroup>();
+
+ groupList.add(group);
+
+ if (!group.contains(this))
+ group.addNode(this);
+ }
+
+
+ /**
+ * Remove this node from the specified group.
+ *
+ * @param group CyGroup to remove this group from
+ */
+ public void removeFromGroup(final CyGroup group) {
+ if (groupList != null && groupList.size() > 0) {
+ groupList.remove(group);
+ groupList.trimToSize();
+ }
+
+ if (group.contains(this))
+ group.removeNode(this);
+ }
+
+
+ /**
+ * Return the list of groups this node is a member of
+ *
+ * @return list of CyGroups this group is a member of
+ */
+ public List<CyGroup> getGroups() {
+ return groupList;
+ }
+
+
+ /**
+ * Check to see if this node is a member of the requested group
+ *
+ * @param group the group to check
+ * @return 'true' if this node is in group
+ */
+ public boolean inGroup(CyGroup group) {
+ if (groupList == null)
+ return false;
+
+ return groupList.contains(group);
+ }
+
+
+ /**
+ * Check to see if this node is a group
+ *
+ * @return 'true' if this node is a group
+ */
+ public boolean isaGroup() {
+ return CyGroupManager.isaGroup(this);
+ }
+
+
+ /**
+ * Return the "name" of a node
+ *
+ * @return string representation of the node
+ */
+ public String toString() {
+ return getIdentifier();
+ }
+
+
+ /**
+ * Assign a graph perspective reference to this node.
+ */
+ public void setNestedNetwork(final GraphPerspective graphPerspective) {
+ // Sanity check.
+ if (graphPerspective == this.nestedNetwork)
+ return;
+
+ final GraphPerspective oldNestedNetwork = this.nestedNetwork;
+ final String nodeID = this.getIdentifier();
+
+ // create a Node Attribute "nested.network.id" for this Node
+ final String networkID = ((CyNetwork)(graphPerspective == null ? this.nestedNetwork : graphPerspective)).getIdentifier();
+ this.nestedNetwork = graphPerspective;
+
+ // create or update Network Attribute "parent.node.name.list" for the Network
+ final String[] attributeNames = Cytoscape.getNetworkAttributes().getAttributeNames();
+ boolean attrFound = false;
+ for (final String name : attributeNames) {
+ if (name.equals(PARENT_NODES_ATTR)) {
+ attrFound = true;
+ break;
+ }
+ }
+ List<String> parentNodeList;
+ if (!attrFound) {
+ parentNodeList = new ArrayList<String>();
+ parentNodeList.add(nodeID);
+ } else {
+ parentNodeList = (List<String>) Cytoscape.getNetworkAttributes().getListAttribute(networkID, PARENT_NODES_ATTR);
+ if (this.nestedNetwork != null) {
+ parentNodeList.add(nodeID);
+ } else {
+ parentNodeList.remove(nodeID);
+ }
+ }
+ Cytoscape.getNetworkAttributes().setListAttribute(networkID, PARENT_NODES_ATTR, parentNodeList);
+
+ // tag or untag the node as having a nested network
+ if (graphPerspective != null) {
+ Cytoscape.getNodeAttributes().setAttribute(nodeID, HAS_NESTED_NETWORK_ATTR, "yes");
+ Cytoscape.getNodeAttributes().setAttribute(nodeID, NESTED_NETWORK_IS_VISIBLE_ATTR, new Boolean(true));
+ Cytoscape.getNodeAttributes().setAttribute(nodeID, NESTED_NETWORK_ID_ATTR, networkID);
+ } else {
+ Cytoscape.getNodeAttributes().deleteAttribute(nodeID, HAS_NESTED_NETWORK_ATTR);
+ Cytoscape.getNodeAttributes().deleteAttribute(nodeID, NESTED_NETWORK_IS_VISIBLE_ATTR);
+ Cytoscape.getNodeAttributes().deleteAttribute(nodeID, NESTED_NETWORK_ID_ATTR);
+ }
+ Cytoscape.getPropertyChangeSupport().firePropertyChange(Cytoscape.ATTRIBUTES_CHANGED, this, oldNestedNetwork);
+
+ // Let listeners know that the previous nested network was removed
+ if (oldNestedNetwork != null)
+ Cytoscape.getPropertyChangeSupport().firePropertyChange(Cytoscape.NESTED_NETWORK_DESTROYED, this, oldNestedNetwork);
+
+ // Let listeners know nested network was assigned to this node.
+ if (this.nestedNetwork != null) {
+ Cytoscape.getPropertyChangeSupport().firePropertyChange(Cytoscape.NESTED_NETWORK_CREATED, this, graphPerspective);
+ }
+ }
+
+
+ /**
+ * Return the currently set graph perspective (may be null) associated with this node.
+ *
+ * @return a network reference or null.
+ */
+ public GraphPerspective getNestedNetwork() {
+ return nestedNetwork;
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/CyStartupListener.java b/application/src/main/java/cytoscape/CyStartupListener.java
new file mode 100644
index 0000000..955a3d6
--- /dev/null
+++ b/application/src/main/java/cytoscape/CyStartupListener.java
@@ -0,0 +1,62 @@
+/*
+ File: CyStartupListener.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape;
+
+import com.install4j.api.launcher.StartupNotification;
+
+/**
+ * Implementation of StartupListener interface in install4j API. Intercepts
+ * arguments passed from file assocations set by install4j for Mac OS.
+ *
+ * @author apico
+ *
+ */
+public class CyStartupListener implements StartupNotification.Listener {
+
+ /*
+ * (non-Javadoc)
+ *
+ * checks for '.cys' in argument string, then assigns to sessionFile
+ *
+ * @see com.exe4j.Controller$StartupListener#startupPerformed(java.lang.String)
+ *
+ */
+ public void startupPerformed(String arguments) {
+ CyMain.setSessionFile(arguments);
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/Cytoscape.java b/application/src/main/java/cytoscape/Cytoscape.java
new file mode 100644
index 0000000..19d9b4f
--- /dev/null
+++ b/application/src/main/java/cytoscape/Cytoscape.java
@@ -0,0 +1,2023 @@
+/*
+ File: Cytoscape.java
+
+ Copyright (c) 2006, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+//---------------------------------------------------------------------------
+package cytoscape;
+
+import giny.model.Edge;
+import giny.model.GraphPerspective;
+import giny.model.Node;
+import giny.view.GraphView;
+import giny.view.NodeView;
+
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeSupport;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import javax.swing.JOptionPane;
+import javax.swing.event.SwingPropertyChangeSupport;
+import javax.xml.bind.JAXBException;
+
+import cytoscape.actions.SaveSessionAction;
+import cytoscape.bookmarks.Bookmarks;
+import cytoscape.data.CyAttributes;
+import cytoscape.data.CyAttributesImpl;
+import cytoscape.data.ExpressionData;
+import cytoscape.data.ImportHandler;
+import cytoscape.data.Semantics;
+import cytoscape.data.readers.BookmarkReader;
+import cytoscape.data.readers.CyAttributesReader;
+import cytoscape.data.readers.EqnAttrTracker;
+import cytoscape.data.readers.GraphReader;
+import cytoscape.data.readers.NestedNetworkReader;
+import cytoscape.data.servers.BioDataServer;
+import cytoscape.data.servers.OntologyServer;
+import cytoscape.ding.CyGraphLOD;
+import cytoscape.ding.DingNetworkView;
+import cytoscape.giny.CytoscapeFingRootGraph;
+import cytoscape.giny.CytoscapeRootGraph;
+import cytoscape.groups.CyGroup;
+import cytoscape.groups.CyGroupManager;
+import cytoscape.init.CyInitParams;
+import cytoscape.layout.CyLayoutAlgorithm;
+import cytoscape.layout.CyLayouts;
+import cytoscape.util.FileUtil;
+import cytoscape.util.RecentlyOpenedTracker;
+import cytoscape.view.CyNetworkView;
+import cytoscape.view.CytoscapeDesktop;
+import cytoscape.visual.VisualMappingManager;
+import cytoscape.visual.VisualStyle;
+import cytoscape.logger.CyLogger;
+import ding.view.DGraphView;
+import ding.view.DNodeView;
+
+
+/**
+ * This class, Cytoscape is <i>the</i> primary class in the API.
+ *
+ * All Nodes and Edges must be created using the methods getCyNode and
+ * getCyEdge, available only in this class. Once A node or edge is created using
+ * these methods it can then be added to a CyNetwork, where it can be used
+ * algorithmically.<BR>
+ * <BR>
+ * The methods get/setNode/EdgeAttributeValue allow you to assocate data with
+ * nodes or edges. That data is then carried into all CyNetworks where that
+ * Node/Edge is present.
+ */
+public abstract class Cytoscape {
+ // All of these events should be reviewed and cleaned up in 3.0 using enum.
+
+ /**
+ * This signals when new attributes have been loaded and a few other
+ * large scale changes to attributes have been made. There is no
+ * equivalent in the CyAttributes events.
+ */
+ public static String ATTRIBUTES_CHANGED = "ATTRIBUTES_CHANGED";
+
+ /**
+ *
+ */
+ public static String NETWORK_CREATED = "NETWORK_CREATED";
+
+ /**
+ *
+ */
+ public static String DATASERVER_CHANGED = "DATASERVER_CHANGED";
+
+ /**
+ *
+ */
+ public static String EXPRESSION_DATA_LOADED = "EXPRESSION_DATA_LOADED";
+
+ /**
+ *
+ */
+ public static String NETWORK_DESTROYED = "NETWORK_DESTROYED";
+
+ /**
+ *
+ */
+ public static String CYTOSCAPE_INITIALIZED = "CYTOSCAPE_INITIALIZED";
+
+ /**
+ *
+ */
+ public static String CYTOSCAPE_EXIT = "CYTOSCAPE_EXIT";
+
+ // KONO: 03/10/2006 For vizmap saving and loading
+ /**
+ *
+ */
+ public static String SESSION_SAVED = "SESSION_SAVED";
+
+ /**
+ *
+ */
+ public static String SESSION_LOADED = "SESSION_LOADED";
+
+ /**
+ *
+ */
+ public static String VIZMAP_RESTORED = "VIZMAP_RESTORED";
+
+ /**
+ *
+ */
+ public static String SAVE_VIZMAP_PROPS = "SAVE_VIZMAP_PROPS";
+
+ /**
+ *
+ */
+ public static String VIZMAP_LOADED = "VIZMAP_LOADED";
+
+ // WANG: 11/14/2006 For plugin to save state
+ /**
+ *
+ */
+ public static final String SAVE_PLUGIN_STATE = "SAVE_PLUGIN_STATE";
+
+ /**
+ *
+ */
+ public static final String RESTORE_PLUGIN_STATE = "RESTORE_PLUGIN_STATE";
+
+ // events for network modification
+ /**
+ *
+ */
+ public static final String NETWORK_MODIFIED = "NETWORK_MODIFIED";
+
+ /**
+ *
+ */
+ public static final String NETWORK_TITLE_MODIFIED = "NETWORK_TITLE_MODIFIED";
+
+ /**
+ *
+ */
+ public static final String NETWORK_SAVED = "NETWORK_SAVED";
+
+ /**
+ *
+ */
+ public static final String NETWORK_LOADED = "NETWORK_LOADED";
+
+ // Root ontology network in the network panel
+ /**
+ *
+ */
+ public static final String ONTOLOGY_ROOT = "ONTOLOGY_ROOT";
+
+ // Events for Preference Dialog (properties).
+ /**
+ *
+ */
+ public static final String PREFERENCE_MODIFIED = "PREFERENCE_MODIFIED";
+
+ // Signals that CytoscapeInit properties have been updated.
+ /**
+ *
+ */
+ public static final String PREFERENCES_UPDATED = "PREFERENCES_UPDATED";
+
+ /**
+ * Specifies that the Proxy settings Cytoscape uses to connect to the
+ * internet have been changed.
+ */
+ public static final String PROXY_MODIFIED = "PROXY_MODIFIED";
+
+ /**
+ * Fired every time a nested network is assigned to a node.
+ * This event contains the following values:
+ * <ul>
+ * <li>oldValue - CyNode whose nested network was set.
+ * <li>newValue - The network assigned to the node above.
+ * </ul>
+ */
+ public static final String NESTED_NETWORK_CREATED = "NESTED_NETWORK_CREATED";
+
+ /**
+ * Fired every time a nested network is removed from a node.
+ */
+ public static final String NESTED_NETWORK_DESTROYED = "NESTED_NETWORK_DESTROYED";
+
+ /**
+ * Fired every time new attributes are loaded and provides the CyAttributes that was modified
+ * as well as a set of the new attribute names..
+ */
+ public static final String NEW_ATTRS_LOADED = "NEW_ATTRS_LOADED";
+
+ /**
+ * When creating a network, use one of the standard suffixes to have it
+ * parsed correctly<BR>
+ * <ul>
+ * <li> sif -- Simple Interaction File</li>
+ * <li> gml -- Graph Markup Languange</li>
+ * <li> sbml -- SBML</li>
+ * <li> xgmml -- XGMML</li>
+ * </ul>
+ */
+ public static int FILE_BY_SUFFIX = 0;
+
+ /**
+ *
+ */
+ public static int FILE_GML = 1;
+
+ /**
+ *
+ */
+ public static int FILE_SIF = 2;
+
+ /**
+ *
+ */
+ public static int FILE_SBML = 3;
+
+ /**
+ *
+ */
+ public static int FILE_XGMML = 4;
+
+ /**
+ *
+ */
+ public static int FILE_BIOPAX = 5;
+
+ /**
+ *
+ */
+ public static int FILE_PSI_MI = 6;
+
+ // constants for tracking selection mode globally
+ /**
+ *
+ */
+ public static final int SELECT_NODES_ONLY = 1;
+
+ /**
+ *
+ */
+ public static final int SELECT_EDGES_ONLY = 2;
+
+ /**
+ *
+ */
+ public static final int SELECT_NODES_AND_EDGES = 3;
+
+ // global to represent which selection mode is active
+ private static int currentSelectionMode = SELECT_NODES_ONLY;
+
+ // Value to manage session state
+ /**
+ *
+ */
+ public static final Integer SESSION_NEW = 0;
+
+ /**
+ *
+ */
+ public static final Integer SESSION_OPENED = 1;
+
+ /**
+ *
+ */
+ public static final Integer SESSION_CHANGED = 2;
+
+ /**
+ *
+ */
+ public static final int SESSION_CLOSED = 3;
+ private static int sessionState = SESSION_NEW;
+
+ /**
+ * New ontology server. This will replace BioDataServer.
+ */
+ private static OntologyServer ontologyServer;
+
+ /**
+ *
+ */
+ public static final String READER_CLIENT_KEY = "reader_client_key";
+
+
+ /**
+ * The shared RootGraph between all Networks
+ */
+ protected static CytoscapeRootGraph cytoscapeRootGraph;
+
+ /**
+ * Node CyAttributes.
+ */
+ private static CyAttributes nodeAttributes = new CyAttributesImpl();
+
+ /**
+ * Edge CyAttributes.
+ */
+ private static CyAttributes edgeAttributes = new CyAttributesImpl();
+
+ /**
+ * Network CyAttributes.
+ */
+ private static CyAttributes networkAttributes = new CyAttributesImpl();
+
+ /**
+ * Ontology Attributes
+ *
+ * Will be used to store annotations for ontology
+ *
+ */
+ private static CyAttributes ontologyAttributes = new CyAttributesImpl();
+ protected static ExpressionData expressionData;
+ protected static Object pcsO = new Object();
+ protected static SwingPropertyChangeSupport pcs = new SwingPropertyChangeSupport(pcsO);
+
+ // Test
+ protected static Object pcs2 = new Object();
+ protected static PropertyChangeSupport newPcs = new PropertyChangeSupport(pcs2);
+ protected static Map<String, CyNetworkView> networkViewMap;
+ protected static Map<String, CyNetwork> networkMap;
+ protected static CytoscapeDesktop defaultDesktop;
+ protected static String currentNetworkID;
+ protected static String currentNetworkViewID;
+ protected static String ontologyRootID;
+
+ /**
+ * Used by session writer. If this is null, session writer opens the file
+ * chooser. Otherwise, overwrite the file.
+ */
+ private static String currentSessionFileName;
+ private static Bookmarks bookmarks;
+
+ /**
+ * Used by session reader.
+ */
+ private static RecentlyOpenedTracker recentlyOpenedSessions = null;
+
+ /**
+ * A null CyNetwork to give when there is no Current Network
+ */
+ protected static CyNetwork nullNetwork = getRootGraph()
+ .createNetwork(new int[] { }, new int[] { });
+ private static ImportHandler importHandler = new ImportHandler();
+
+ /**
+ * The list analog to the currentNetworkViewID
+ */
+ protected static LinkedList<CyNetworkView> selectedNetworkViews = new LinkedList<CyNetworkView>();
+
+ /**
+ * The list analog to the currentNetworkID
+ */
+ protected static LinkedList<CyNetwork> selectedNetworks = new LinkedList<CyNetwork>();
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static ImportHandler getImportHandler() {
+ return importHandler;
+ }
+
+ /**
+ * A null CyNetworkView to give when there is no Current NetworkView
+ */
+ protected static final CyNetworkView nullNetworkView = new DingNetworkView(nullNetwork, "null");
+
+ /*
+ * VMM should be tied to Cytoscape, not to Desktop. Developers should call
+ * this from here.
+ * Don't initialize this until it is to be used.
+ */
+ protected static VisualMappingManager VMM = null;
+
+ protected static CyLogger logger = CyLogger.getLogger(Cytoscape.class);
+
+ /**
+ * @return a nullNetworkView object. This is NOT simply a null object.
+ */
+ public static CyNetworkView getNullNetworkView() {
+ return nullNetworkView;
+ }
+
+ /**
+ * @return the nullNetwork CyNetwork. This is NOT simply a null object.
+ */
+ public static CyNetwork getNullNetwork() {
+ return nullNetwork;
+ }
+
+ private static EqnAttrTracker eqnAttrTracker = null;
+
+ public static EqnAttrTracker getEqnAttrTracker() {
+ if (eqnAttrTracker == null)
+ eqnAttrTracker = new EqnAttrTracker();
+ return eqnAttrTracker;
+ }
+
+ /**
+ * Shuts down Cytoscape, after giving plugins time to react.
+ *
+ * @param returnVal
+ * The return value. Zero indicates success, non-zero otherwise.
+ */
+ public static void exit(int returnVal) {
+ int mode = CytoscapeInit.getCyInitParams().getMode();
+
+ if ((mode == CyInitParams.EMBEDDED_WINDOW) || (mode == CyInitParams.GUI)) {
+ // prompt the user about saving modified files before quitting
+ if (confirmQuit()) {
+ try {
+ firePropertyChange(CYTOSCAPE_EXIT, null, "now");
+ } catch (Exception e) {
+ logger.warn("Errors on close, closed anyways.", e);
+ }
+
+ logger.info("Cytoscape Exiting....");
+
+ if (mode == CyInitParams.EMBEDDED_WINDOW) {
+ // Don't system exit since we are running as part
+ // of a bigger application. We would like to just
+ // do getDesktop().dispose(), but then you cannot
+ // rerun Cytoscape, since Cytoscape is not designed
+ // to create a new Cytoscape while another is still
+ // alive. In other words, we can't just call 'CyMain.main
+ // (args)' and have a new Cytoscape that we can use.
+ // Many operations, like Cytoscape.getDesktop() just
+ // return a singleton instance that is already bound to
+ // the old desktop. To make matters worse, all the
+ // data content (mapping structures, nodes, networks)
+ // from previous usage is there. So our approach is to
+ // just make the existing desktop not visible and reset
+ // Cytoscape to a new session:
+ getDesktop().setVisible (false);
+ // get rid of existing data:
+ Cytoscape.createNewSession();
+ } else {
+ System.exit(returnVal);
+ }
+ } else {
+ return;
+ }
+ } else {
+ try {
+ getRecentlyOpenedSessionTracker().writeOut();
+ } catch (final IOException e) {
+ System.err.println("failed to save recent session URLs!");
+ }
+ logger.info("Cytoscape Exiting....");
+ System.exit(returnVal);
+ }
+ }
+
+ /**
+ * Prompt the user about saving modified files before quitting.
+ */
+ private static boolean confirmQuit() {
+ final String msg = "Do you want to save your session?";
+ int networkCount = Cytoscape.getNetworkSet().size();
+
+ // If there is no network, just quit.
+ if (networkCount == 0) {
+ return true;
+ }
+
+ //
+ // Confirm user to save current session or not.
+ //
+ Object[] options = { "Yes, save and quit", "No, just quit", "Cancel" };
+ int n = JOptionPane.showOptionDialog(Cytoscape.getDesktop(), msg,
+ "Save Networks Before Quitting?",
+ JOptionPane.YES_NO_OPTION,
+ JOptionPane.QUESTION_MESSAGE, null, options, options[0]);
+
+ if (n == JOptionPane.NO_OPTION) {
+ return true;
+ } else if (n == JOptionPane.YES_OPTION) {
+ SaveSessionAction saveAction = new SaveSessionAction();
+ saveAction.actionPerformed(null);
+
+ if (Cytoscape.getCurrentSessionFileName() == null) {
+ return confirmQuit();
+ } else {
+ return true;
+ }
+ } else {
+ return false; // default if dialog box is closed
+ }
+ }
+
+ // --------------------//
+ // Root Graph Methods
+ // --------------------//
+
+ /**
+ * Bound events are:
+ * <ol>
+ * <li>NETWORK_CREATED
+ * <li>NETWORK_DESTROYED
+ * <li>CYTOSCAPE_EXIT
+ * </ol>
+ */
+ public static SwingPropertyChangeSupport getSwingPropertyChangeSupport() {
+ return pcs;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static PropertyChangeSupport getPropertyChangeSupport() {
+ return newPcs;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static VisualMappingManager getVisualMappingManager() {
+ if ( VMM == null )
+ VMM = new VisualMappingManager(nullNetworkView);
+ return VMM;
+ }
+
+ /**
+ * Return the CytoscapeRootGraph
+ */
+ public static CytoscapeRootGraph getRootGraph() {
+ if (cytoscapeRootGraph == null)
+ cytoscapeRootGraph = new CytoscapeFingRootGraph();
+
+ return cytoscapeRootGraph;
+ }
+
+ /**
+ * Ensure the capacity of Cytoscapce. This is to prevent the inefficiency of
+ * adding nodes one at a time.
+ */
+ public static void ensureCapacity(int nodes, int edges) {
+ // getRootGraph().ensureCapacity( nodes, edges );
+ }
+
+ /**
+ * @return all CyNodes that are present in Cytoscape
+ */
+ public static List getCyNodesList() {
+ return getRootGraph().nodesList();
+ }
+
+ /**
+ * @return all CyEdges that are present in Cytoscape
+ */
+ public static List getCyEdgesList() {
+ return getRootGraph().edgesList();
+ }
+
+ /**
+ * @param alias
+ * an alias of a node
+ * @return will return a node, if one exists for the given alias
+ */
+ public static CyNode getCyNode(String alias) {
+ return getCyNode(alias, false);
+ }
+
+ /**
+ * @param nodeID
+ * an alias of a node
+ * @param create
+ * will create a node if one does not exist
+ * @return will always return a node, if <code>create</code> is true
+ *
+ */
+ public static CyNode getCyNode(String nodeID, boolean create) {
+ CyNode node = Cytoscape.getRootGraph().getNode(nodeID);
+
+ // If the node is already exists,return it.
+ if (node != null) {
+ return node;
+ }
+
+ // And if we do not have to create new one, just return null
+ if (!create) {
+ return null;
+ }
+
+ // Now, create a new node.
+ node = (CyNode) getRootGraph().getNode(Cytoscape.getRootGraph().createNode());
+ node.setIdentifier(nodeID);
+
+ // create the CANONICAL_NAME attribute
+ if (getNodeAttributes().getStringAttribute(nodeID, Semantics.CANONICAL_NAME) == null) {
+ getNodeAttributes().setAttribute(nodeID, Semantics.CANONICAL_NAME, nodeID);
+ }
+
+ return node;
+ }
+
+ /**
+ * Gets the first CyEdge found between the two nodes (direction does not
+ * matter) that has the given value for the given attribute. If the edge
+ * doesn't exist, then it creates an undirected edge.
+ *
+ * This method MIGHT be deprecated, or even removed, because Cytoscape
+ * shouldn't really be using undirected edges.
+ *
+ * @param node_1
+ * one end of the edge
+ * @param node_2
+ * the other end of the edge
+ * @param attribute
+ * the attribute of the edge to be searched, a common one is
+ * {@link Semantics#INTERACTION }
+ * @param attribute_value
+ * a value for the attribute, like "pp"
+ * @param create
+ * will create an edge if one does not exist and if attribute is
+ * {@link Semantics#INTERACTION}
+ * @return returns an existing CyEdge if present, or creates one if
+ * <code>create</code> is true and attribute is
+ * Semantics.INTERACTION, otherwise returns null.
+ */
+ public static CyEdge getCyEdge(Node node_1, Node node_2, String attribute,
+ Object attribute_value, boolean create) {
+ return getCyEdge(node_1, node_2, attribute, attribute_value, create, false);
+ }
+
+ /**
+ * Gets the first CyEdge found between the two nodes that has the given
+ * value for the given attribute. If direction flag is set, then direction
+ * is taken into account, A->B is NOT equivalent to B->A
+ *
+ * @param source
+ * one end of the edge
+ * @param target
+ * the other end of the edge
+ * @param attribute
+ * the attribute of the edge to be searched, a common one is
+ * {@link Semantics#INTERACTION }
+ * @param attribute_value
+ * a value for the attribute, like "pp"
+ * @param create
+ * will create an edge if one does not exist and if attribute is
+ * {@link Semantics#INTERACTION}
+ * @param directed
+ * take direction into account, source->target is NOT
+ * target->source
+ * @return returns an existing CyEdge if present, or creates one if
+ * <code>create</code> is true and attribute is
+ * Semantics.INTERACTION, otherwise returns null.
+ */
+ public static CyEdge getCyEdge(Node source, Node target, String attribute,
+ Object attribute_value, boolean create, boolean directed) {
+ if (Cytoscape.getRootGraph().getEdgeCount() != 0) {
+ int[] n1Edges = Cytoscape.getRootGraph()
+ .getAdjacentEdgeIndicesArray(source.getRootGraphIndex(), true,
+ true, true);
+
+ for (int i = 0; i < n1Edges.length; i++) {
+ CyEdge edge = (CyEdge) Cytoscape.getRootGraph().getEdge(n1Edges[i]);
+ Object attValue = private_getEdgeAttributeValue(edge, attribute);
+
+ if ((attValue != null) && attValue.equals(attribute_value)) {
+ // Despite the fact that we know the source node
+ // matches, the case of self edges dictates that
+ // we must check the source as well.
+ CyNode edgeTarget = (CyNode) edge.getTarget();
+ CyNode edgeSource = (CyNode) edge.getSource();
+
+ if ((edgeTarget.getRootGraphIndex() == target.getRootGraphIndex())
+ && (edgeSource.getRootGraphIndex() == source.getRootGraphIndex())) {
+ return edge;
+ }
+
+ if (!directed) {
+ // note that source and target are switched
+ if ((edgeTarget.getRootGraphIndex() == source.getRootGraphIndex())
+ && (edgeSource.getRootGraphIndex() == target.getRootGraphIndex())) {
+ return edge;
+ }
+ }
+ }
+ } // for i
+ }
+
+ if (create && attribute instanceof String && attribute.equals(Semantics.INTERACTION)) {
+ // create the edge
+ int rootEdge = Cytoscape.getRootGraph().createEdge(source, target);
+ CyEdge edge = (CyEdge) Cytoscape.getRootGraph().getEdge(rootEdge);
+
+ // create the edge id
+ String edge_name = CyEdge.createIdentifier(source.getIdentifier(),
+ (String) attribute_value,
+ target.getIdentifier());
+ edge.setIdentifier(edge_name);
+
+ edgeAttributes.setAttribute(edge_name, Semantics.INTERACTION, (String) attribute_value);
+ edgeAttributes.setAttribute(edge_name, Semantics.CANONICAL_NAME, edge_name);
+
+ return edge;
+ }
+
+ return null;
+ }
+
+ /**
+ * Returns and edge if it exists, otherwise creates a directed edge.
+ *
+ * @param source_alias
+ * an alias of a node
+ * @param edge_name
+ * the name of the node
+ * @param target_alias
+ * an alias of a node
+ * @return will always return an edge
+ */
+ public static CyEdge getCyEdge(String source_alias, String edge_name, String target_alias,
+ String interaction_type) {
+ CyEdge edge = Cytoscape.getRootGraph().getEdge(edge_name);
+
+ if (edge != null) {
+ return edge;
+ }
+
+ // edge does not exist, create one
+ if ( source_alias == null || source_alias.equals("") ) {
+ logger.warn("Attempting to get CyEdge with null or empty source node identifier.");
+ return null;
+ }
+
+ if ( target_alias == null || target_alias.equals("") ) {
+ logger.warn("Attempting to get CyEdge with null or empty target node identifier.");
+ return null;
+ }
+
+ CyNode source = getCyNode(source_alias,true);
+ CyNode target = getCyNode(target_alias,true);
+
+ return getCyEdge(source, target, Semantics.INTERACTION, interaction_type, true, true);
+ }
+
+ private static Object private_getEdgeAttributeValue(Edge edge, String attribute) {
+ final CyAttributes edgeAttrs = Cytoscape.getEdgeAttributes();
+ final String canonName = edge.getIdentifier();
+ final byte cyType = edgeAttrs.getType(attribute);
+
+ if (cyType == CyAttributes.TYPE_BOOLEAN) {
+ return edgeAttrs.getBooleanAttribute(canonName, attribute);
+ } else if (cyType == CyAttributes.TYPE_FLOATING) {
+ return edgeAttrs.getDoubleAttribute(canonName, attribute);
+ } else if (cyType == CyAttributes.TYPE_INTEGER) {
+ return edgeAttrs.getIntegerAttribute(canonName, attribute);
+ } else if (cyType == CyAttributes.TYPE_STRING) {
+ return edgeAttrs.getStringAttribute(canonName, attribute);
+ } else if (cyType == CyAttributes.TYPE_SIMPLE_LIST) {
+ return edgeAttrs.getListAttribute(canonName, attribute);
+ } else if (cyType == CyAttributes.TYPE_SIMPLE_MAP) {
+ return edgeAttrs.getMapAttribute(canonName, attribute);
+ } else {
+ return null;
+ }
+ }
+
+ // --------------------//
+ // Network Methods
+ // --------------------//
+
+ /**
+ * Return the Network that currently has the Focus. Can be different from
+ * getCurrentNetworkView
+ */
+ public static CyNetwork getCurrentNetwork() {
+ if ((currentNetworkID == null) || !(getNetworkMap().containsKey(currentNetworkID)))
+ return nullNetwork;
+
+ CyNetwork network = (CyNetwork) getNetworkMap().get(currentNetworkID);
+
+ return network;
+ }
+
+ /**
+ * Return a List of all available CyNetworks
+ */
+ public static Set<CyNetwork> getNetworkSet() {
+ return new java.util.LinkedHashSet(((HashMap) getNetworkMap()).values());
+ }
+
+ /**
+ * @return the CyNetwork that has the given identifier or the nullNetwork
+ * (see {@link #getNullNetwork()}) if there is no such network.
+ */
+ public static CyNetwork getNetwork(String id) {
+ if ((id != null) && getNetworkMap().containsKey(id))
+ return (CyNetwork) getNetworkMap().get(id);
+
+ return nullNetwork;
+ }
+
+ /**
+ * @return a CyNetworkView for the given ID, if one exists, otherwise
+ * returns NullNetworkView
+ */
+ public static CyNetworkView getNetworkView(String network_id) {
+ if ((network_id == null) || !(getNetworkViewMap().containsKey(network_id)))
+ return nullNetworkView;
+ return (CyNetworkView) getNetworkViewMap().get(network_id);
+ }
+
+ /**
+ * @return if a view exists for a given network id
+ */
+ public static boolean viewExists(String network_id) {
+ return getNetworkViewMap().containsKey(network_id);
+ }
+
+ /**
+ * Return the CyNetworkView that currently has the focus. Can be different
+ * from getCurrentNetwork
+ */
+ public static CyNetworkView getCurrentNetworkView() {
+ if ((currentNetworkViewID == null)
+ || !(getNetworkViewMap().containsKey(currentNetworkViewID)))
+ return nullNetworkView;
+
+ return getNetworkViewMap().get(currentNetworkViewID);
+ }
+
+ /**
+ * Returns the list of currently selected networks.
+ */
+ @SuppressWarnings("unchecked")
+ public static List<CyNetworkView> getSelectedNetworkViews() {
+ final CyNetworkView view = getCurrentNetworkView();
+
+ if (!selectedNetworkViews.contains(view))
+ selectedNetworkViews.add(view);
+
+ return (List<CyNetworkView>) selectedNetworkViews.clone();
+ }
+
+ /**
+ * Sets the selected network views.
+ */
+ public static void setSelectedNetworkViews(final List<String> viewIDs) {
+ selectedNetworkViews.clear();
+
+ if (viewIDs == null)
+ return;
+
+ CyNetworkView nview;
+ for (String id : viewIDs) {
+ nview = getNetworkViewMap().get(id);
+
+ if (nview != null && nview != nullNetworkView)
+ selectedNetworkViews.add(nview);
+ }
+
+ final CyNetworkView cv = getCurrentNetworkView();
+
+ if ((cv != nullNetworkView) && !selectedNetworkViews.contains(cv))
+ selectedNetworkViews.add(cv);
+ }
+
+
+ /**
+ * Returns the list of selected networks.
+ */
+ @SuppressWarnings("unchecked")
+ public static List<CyNetwork> getSelectedNetworks() {
+ final CyNetwork curNet = getCurrentNetwork();
+
+ if (!selectedNetworks.contains(curNet))
+ selectedNetworks.add(curNet);
+
+ return (List<CyNetwork>) selectedNetworks.clone();
+ }
+
+
+ /**
+ * Sets the list of selected networks.
+ */
+ public static void setSelectedNetworks(final List<String> ids) {
+ selectedNetworks.clear();
+
+ if (ids == null)
+ return;
+
+ for (String id : ids) {
+ final CyNetwork n = getNetworkMap().get(id);
+
+ if ((n != null) && (n != nullNetwork)) {
+ selectedNetworks.add(n);
+ }
+ }
+
+ final CyNetwork cn = getCurrentNetwork();
+
+ if (!selectedNetworks.contains(cn)) {
+ selectedNetworks.add(cn);
+ }
+ }
+
+ /**
+ * @return the reference to the One CytoscapeDesktop
+ */
+ public static CytoscapeDesktop getDesktop() {
+ if (defaultDesktop == null) {
+ defaultDesktop = new CytoscapeDesktop();
+ }
+
+ return defaultDesktop;
+ }
+
+ /**
+ */
+ public static void setCurrentNetwork(String id) {
+ //logger.info("- TRY setting current network" + id);
+ if (getNetworkMap().containsKey(id)) {
+ //logger.info("- SUCCEED setting current network " + id);
+ currentNetworkID = id;
+
+ // reset selected networks
+ selectedNetworks.clear();
+ selectedNetworks.add((CyNetwork) (getNetworkMap().get(id)));
+ }
+ }
+
+ /**
+ * @return true if there is network view, false if not
+ */
+ public static boolean setCurrentNetworkView(String id) {
+ //logger.info("= TRY setting current network VIEW " + id);
+ if (getNetworkViewMap().containsKey(id)) {
+ //logger.info("= SUCCEED setting current network VIEW " + id);
+ currentNetworkViewID = id;
+
+ // reset selected network views
+ selectedNetworkViews.clear();
+ selectedNetworkViews.add((CyNetworkView) (getNetworkViewMap().get(id)));
+
+ return true;
+ }
+
+ return false;
+ }
+
+ /**
+ * This Map has keys that are Strings ( network_ids ) and values that are
+ * networks.
+ */
+ protected static Map<String, CyNetwork> getNetworkMap() {
+ if (networkMap == null)
+ networkMap = new HashMap<String, CyNetwork>();
+
+ return networkMap;
+ }
+
+ /**
+ * This Map has keys that are Strings ( network_ids ) and values that are
+ * networkviews.
+ */
+ public static Map<String, CyNetworkView> getNetworkViewMap() {
+ if (networkViewMap == null)
+ networkViewMap = new HashMap<String, CyNetworkView>();
+
+ return networkViewMap;
+ }
+
+ /**
+ * destroys the given network
+ */
+ public static void destroyNetwork(String network_id) {
+ destroyNetwork((CyNetwork) getNetworkMap().get(network_id));
+ }
+
+ /**
+ * destroys the given network
+ */
+ public static void destroyNetwork(CyNetwork network) {
+ destroyNetwork(network, false);
+ }
+
+ /**
+ * destroys the given network
+ *
+ * @param network
+ * the network to be destroyed
+ * @param destroy_unique
+ * if this is true, then all Nodes and Edges that are in this
+ * network, but no other are also destroyed.
+ */
+ public static void destroyNetwork(CyNetwork network, boolean destroy_unique) {
+ if ((network == null) || (network == nullNetwork))
+ return;
+
+ getSelectedNetworks().remove(network);
+
+ final String networkId = network.getIdentifier();
+
+ firePropertyChange(NETWORK_DESTROYED, null, networkId);
+
+ network.unselectAllEdges();
+ network.unselectAllNodes();
+
+ final Map<String, CyNetwork> nmap = getNetworkMap();
+ nmap.remove(networkId);
+
+ if (networkId.equals(currentNetworkID)) {
+ if (nmap.size() <= 0) {
+ currentNetworkID = null;
+ } else {
+ // randomly pick a network to become the current network
+ for (String key : nmap.keySet()) {
+ currentNetworkID = key;
+
+ break;
+ }
+ }
+ }
+
+ if (viewExists(networkId))
+ destroyNetworkView(network);
+
+ if (destroy_unique) {
+ final List<Node> nodes = new ArrayList<Node>();
+ final List<Edge> edges = new ArrayList<Edge>();
+
+ final Collection<CyNetwork> networks = networkMap.values();
+
+ for (Node node : nodes) {
+ boolean add = true;
+
+ for (CyNetwork net : networks) {
+ if (net.containsNode(node)) {
+ add = false;
+
+ continue;
+ }
+ }
+
+ if (add)
+ nodes.add(node);
+ }
+
+ for (Edge edge : edges) {
+ boolean add = true;
+
+ for (CyNetwork net : networks) {
+ if (net.containsEdge(edge)) {
+ add = false;
+
+ continue;
+ }
+ }
+
+ if (add)
+ edges.add(edge);
+ }
+
+ for (Node node : nodes) {
+ getRootGraph().removeNode(node);
+ node = null;
+ }
+
+ for (Edge edge : edges) {
+ getRootGraph().removeEdge(edge);
+ edge = null;
+ }
+ }
+
+ updateNestedNetworkNodes(network);
+
+ // theoretically this should not be set to null till after the events
+ // firing is done
+ network = null;
+
+ // updates the desktop - but only if the view is null
+ // if a view exists, then the focus will have already been updated
+ // in destroyNetworkView
+ if ((currentNetworkID != null) && (currentNetworkViewID == null))
+ getDesktop().setFocus(currentNetworkID);
+ }
+
+
+ private static void updateNestedNetworkNodes(final GraphPerspective destroyedNetwork) {
+ for (final CyNode node: (List<CyNode>)Cytoscape.getRootGraph().nodesList()) {
+ if (node.getNestedNetwork() == destroyedNetwork) {
+ node.setNestedNetwork(null);
+ }
+ }
+ }
+
+ /**
+ * Destroys the network view.
+ */
+ public static void destroyNetworkView(CyNetworkView view) {
+ if ((view == null) || (view == nullNetworkView))
+ return;
+
+ getSelectedNetworkViews().remove(view);
+
+ final String viewID = view.getIdentifier();
+
+ if (viewID.equals(currentNetworkViewID)) {
+ if (getNetworkViewMap().size() <= 0)
+ currentNetworkViewID = null;
+ else {
+ // depending on which randomly chosen currentNetworkID we get,
+ // we may or may not have a view for it.
+ CyNetworkView newCurr = getNetworkViewMap().get(currentNetworkID);
+
+ if (newCurr != null)
+ currentNetworkViewID = newCurr.getIdentifier();
+ else
+ currentNetworkViewID = null;
+ }
+ }
+
+ firePropertyChange(CytoscapeDesktop.NETWORK_VIEW_DESTROYED, null, view);
+ // theoretically this should not be set to null till after the events
+ // firing is done
+ getNetworkViewMap().remove(viewID);
+ view = null;
+
+ // so that a network will be selected.
+ if (currentNetworkID != null)
+ getDesktop().setFocus(currentNetworkID);
+ }
+
+
+ /**
+ * destroys the networkview, including any layout information
+ */
+ public static void destroyNetworkView(final String networkViewID) {
+ destroyNetworkView(getNetworkViewMap().get(networkViewID));
+ }
+
+
+ /**
+ * destroys the networkview, including any layout information
+ */
+ public static void destroyNetworkView(final CyNetwork network) {
+ destroyNetworkView(getNetworkViewMap().get(network.getIdentifier()));
+ }
+
+
+ /**
+ * Add a network to Cytoscape's internal list of networks. This also fires the NETWORK_CREATED event
+ * and as a byproduct adds the network to the Network Panel.
+ *
+ * @param network the network to add
+ * @param title the title (name) of the network
+ * @param parent the parent of the network to be added
+ * @param create_view if <b>true</b> create the view for this network
+ */
+ public static void addNetwork(CyNetwork network, String title, CyNetwork parent, boolean create_view) {
+ getNetworkMap().put(network.getIdentifier(), network);
+ network.setTitle(title);
+
+ String parentID = (parent != null) ? parentID = parent.getIdentifier() : null;
+ firePropertyChange(NETWORK_CREATED, parentID, network.getIdentifier());
+
+ final String propVal = CytoscapeInit.getProperties().getProperty("viewThreshold");
+ if (create_view && propVal != null && (network.getNodeCount() < Integer.parseInt(propVal))) {
+ createNetworkView(network);
+ }
+ }
+
+
+ /**
+ * Creates a new, empty Network.
+ *
+ * @param title
+ * the title of the new network.
+ */
+ public static CyNetwork createNetwork(String title) {
+ return createNetwork(new int[] { }, new int[] { }, title, null, true);
+ }
+
+ /**
+ * Creates a new, empty Network.
+ *
+ * @param title
+ * the title of the new network.
+ * @param create_view
+ * if the size of the network is under the node limit, create a
+ * view
+ */
+ public static CyNetwork createNetwork(String title, boolean create_view) {
+ return createNetwork(new int[] { }, new int[] { }, title, null, create_view);
+ }
+
+ /**
+ * Creates a new, empty Network.
+ *
+ * @param title
+ * the title of the new network.
+ * @param create_view
+ * if the size of the network is under the node limit, create a
+ * view
+ */
+ public static CyNetwork createNetwork(String title, CyNetwork parent, boolean create_view) {
+ return createNetwork(new int[] { }, new int[] { }, title, parent, create_view);
+ }
+
+ /**
+ * Creates a new Network. A view will be created automatically.
+ *
+ * @param nodes
+ * the indeces of nodes
+ * @param edges
+ * the indeces of edges
+ * @param title
+ * the title of the new network.
+ */
+ public static CyNetwork createNetwork(int[] nodes, int[] edges, String title) {
+ return createNetwork(nodes, edges, title, null, true);
+ }
+
+ /**
+ * Creates a new Network. A view will be created automatically.
+ *
+ * @param nodes
+ * a collection of nodes
+ * @param edges
+ * a collection of edges
+ * @param title
+ * the title of the new network.
+ */
+ public static CyNetwork createNetwork(Collection nodes, Collection edges, String title) {
+ return createNetwork(nodes, edges, title, null, true);
+ }
+
+ /**
+ * Creates a new Network, that inherits from the given ParentNetwork. A view
+ * will be created automatically.
+ *
+ * @param nodes
+ * the indeces of nodes
+ * @param edges
+ * the indeces of edges
+ * @param child_title
+ * the title of the new network.
+ * @param parent
+ * the parent of the this Network
+ */
+ public static CyNetwork createNetwork(int[] nodes, int[] edges, String child_title,
+ CyNetwork parent) {
+ return createNetwork(nodes, edges, child_title, parent, true);
+ }
+
+ /**
+ * Creates a new Network, that inherits from the given ParentNetwork
+ *
+ * @param nodes
+ * the indeces of nodes
+ * @param edges
+ * the indeces of edges
+ * @param child_title
+ * the title of the new network.
+ * @param parent
+ * the parent of the this Network
+ * @param create_view
+ * whether or not a view will be created
+ */
+ public static CyNetwork createNetwork(int[] nodes, int[] edges, String child_title,
+ CyNetwork parent, boolean create_view) {
+ CyNetwork network = getRootGraph().createNetwork(nodes, edges);
+ addNetwork(network, child_title, parent, create_view);
+
+ return network;
+ }
+
+ /**
+ * Creates a new Network, that inherits from the given ParentNetwork. A view
+ * will be created automatically.
+ *
+ * @param nodes
+ * the indeces of nodes
+ * @param edges
+ * the indeces of edges
+ * @param parent
+ * the parent of the this Network
+ */
+ public static CyNetwork createNetwork(Collection nodes, Collection edges, String child_title,
+ CyNetwork parent) {
+ return createNetwork(nodes, edges, child_title, parent, true);
+ }
+
+ /**
+ * Creates a new Network, that inherits from the given ParentNetwork.
+ *
+ * @param nodes
+ * the indeces of nodes
+ * @param edges
+ * the indeces of edges
+ * @param parent
+ * the parent of the this Network
+ * @param create_view
+ * whether or not a view will be created
+ */
+ public static CyNetwork createNetwork(Collection nodes, Collection edges, String child_title,
+ CyNetwork parent, boolean create_view) {
+ CyNetwork network = getRootGraph().createNetwork(nodes, edges);
+ addNetwork(network, child_title, parent, create_view);
+
+ return network;
+ }
+
+ /**
+ * Creates a CyNetwork from a file. The file type is determined by the
+ * suffix of the file.* Uses the new ImportHandler and thus the passed in
+ * location should be a file of a recognized "Graph Nature". The "Nature" of
+ * a file is a new way to tell what a file is beyond it's filetype e.g.
+ * galFiltered.sif is, in addition to being a .sif file, the file is also of
+ * Graph "Nature". Other files of Graph Nature include GML and XGMML. Beyond
+ * Graph Nature there are Node, Edge, and Properties Nature.
+ *
+ * A view will be created automatically.
+ *
+ * @param location
+ * the location of the file
+ */
+ public static CyNetwork createNetworkFromFile(String location) {
+ return createNetworkFromFile(location, true);
+ }
+
+ /**
+ * Creates a CyNetwork from a file. The file type is determined by the
+ * suffix of the file.* Uses the new ImportHandler and thus the passed in
+ * location should be a file of a recognized "Graph Nature". The "Nature" of
+ * a file is a new way to tell what a file is beyond it's filetype e.g.
+ * galFiltered.sif is, in addition to being a .sif file, the file is also of
+ * Graph "Nature". Other files of Graph Nature include GML and XGMML. Beyond
+ * Graph Nature there are Node, Edge, and Properties Nature.
+ *
+ * @param loc
+ * location of importable file
+ * @param create_view
+ * whether or not a view will be created
+ * @return a network based on the specified file or null if the file type is
+ * supported but the file is not of Graph Nature.
+ */
+ public static CyNetwork createNetworkFromFile(String loc, boolean create_view) {
+ return createNetwork(importHandler.getReader(loc), create_view, null);
+ }
+
+ /**
+ * Creates a CyNetwork from a URL. The file type is determined by the
+ * suffix of the file or, if one does't exist, the contentType of the data.
+ * Uses the new ImportHandler and thus the passed in
+ * location should be a file of a recognized "Graph Nature". The "Nature" of
+ * a file is a new way to tell what a file is beyond it's filetype e.g.
+ * galFiltered.sif is, in addition to being a .sif file, the file is also of
+ * Graph "Nature". Other files of Graph Nature include GML and XGMML. Beyond
+ * Graph Nature there are Node, Edge, and Properties Nature.
+ *
+ * @param url
+ * url of importable file
+ * @param create_view
+ * whether or not a view will be created
+ * @return a network based on the specified file or null if the file type is
+ * supported but the file is not of Graph Nature.
+ */
+ public static CyNetwork createNetworkFromURL(URL url, boolean create_view) {
+ return createNetwork(importHandler.getReader(url), create_view, null);
+ }
+
+ /**
+ * Creates a cytoscape.data.CyNetwork from a reader. Neccesary with
+ * cesssions.
+ * <p>
+ * This operation may take a long time to complete. It is a good idea NOT to
+ * call this method from the AWT event handling thread. This operation
+ * assumes the reader is of type .xgmml since this should only be called by
+ * the cessions reader which opens .xgmml files from the zipped cytoscape
+ * session.
+ *
+ * @param reader
+ * the graphreader that will read in the network
+ * @param create_view
+ * whether or not a view will be created
+ */
+ public static CyNetwork createNetwork(final GraphReader reader, final boolean create_view, final CyNetwork parent) {
+ if (reader == null) {
+ throw new RuntimeException("Couldn't read specified file.");
+ }
+
+ // have the GraphReader read the given file
+
+ // Explanation for code below: the code below recasts an IOException
+ // into a RuntimeException, so that the exception can still be thrown
+ // without having to change the method signature. This is less than
+ // ideal, but the only sure way to ensure API stability for plugins.
+ try {
+ reader.read();
+ } catch (IOException e) {
+ throw new RuntimeException(e);
+ }
+
+ // Create the network if any nodes/edges exists in the file.
+ if (reader instanceof NestedNetworkReader) {
+ // This is a reader which creates multiple networks.
+ final List<CyNetwork> networks = ((NestedNetworkReader)reader).getNetworks();
+
+ // Turn views off for performance
+ Cytoscape.getDesktop().getNetworkViewManager().getDesktopPane().setVisible(false);
+ for (CyNetwork network : networks) {
+ getNetworkMap().put(network.getIdentifier(), network);
+ if (create_view && (network.getNodeCount() < Integer.parseInt(CytoscapeInit.getProperties() .getProperty("viewThreshold")))) {
+ createNetworkView(network);
+ }
+ }
+ Cytoscape.getDesktop().getNetworkViewManager().getDesktopPane().setVisible(true);
+
+ return networks.get(0); // Root network.
+ } else {
+ // get the RootGraph indices of the nodes and
+ // edges that were just created
+ final int[] nodes = reader.getNodeIndicesArray();
+ final int[] edges = reader.getEdgeIndicesArray();
+
+ if (nodes == null) {
+ logger.warn("Network reader didn't return any nodes");
+ }
+
+ if (edges == null) {
+ logger.warn("Network reader didn't return any edges");
+ }
+
+ // Change the identifier
+ final String title = reader.getNetworkName();
+ final CyNetwork network = getRootGraph().createNetwork(nodes, edges);
+ network.setIdentifier(title);
+
+ // network.putClientData(READER_CLIENT_KEY, reader);
+ addNetwork(network, title, parent, false);
+
+ if (create_view && (network.getNodeCount() < Integer.parseInt(CytoscapeInit.getProperties()
+ .getProperty("viewThreshold")))) {
+ createNetworkView(network, title, reader.getLayoutAlgorithm());
+ }
+
+ // Execute any necessary post-processing.
+ reader.doPostProcessing(network);
+
+ return network;
+ }
+ }
+
+ // --------------------//
+ // Network Data Methods
+ // --------------------//
+
+ /**
+ * Gets Global Node Attributes.
+ *
+ * @return CyAttributes Object.
+ */
+ public static CyAttributes getNodeAttributes() {
+ return nodeAttributes;
+ }
+
+ /**
+ * Gets Global Edge Attributes
+ *
+ * @return CyAttributes Object.
+ */
+ public static CyAttributes getEdgeAttributes() {
+ return edgeAttributes;
+ }
+
+ /**
+ * Gets Global Network Attributes.
+ *
+ * @return CyAttributes Object.
+ */
+ public static CyAttributes getNetworkAttributes() {
+ return networkAttributes;
+ }
+
+ /**
+ * Gets Global Network Attributes.
+ *
+ * @return CyAttributes Object.
+ */
+ public static CyAttributes getOntologyAttributes() {
+ return ontologyAttributes;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static ExpressionData getExpressionData() {
+ return expressionData;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param expData DOCUMENT ME!
+ */
+ public static void setExpressionData(ExpressionData expData) {
+ expressionData = expData;
+ }
+
+ /**
+ * Load Expression Data
+ */
+
+ // TODO: remove the JOption Pane stuff
+ public static boolean loadExpressionData(String filename, boolean copy_atts) {
+ try {
+ expressionData = new ExpressionData(filename);
+ } catch (Exception e) {
+ String errString = "Unable to load expression data from " + filename;
+ logger.warn(errString,e);
+ }
+
+ if (copy_atts) {
+ expressionData.copyToAttribs(getNodeAttributes(), null);
+ firePropertyChange(ATTRIBUTES_CHANGED, null, null);
+ }
+
+ // Fire off an EXPRESSION_DATA_LOADED event.
+ Cytoscape.firePropertyChange(Cytoscape.EXPRESSION_DATA_LOADED, null, expressionData);
+
+ return true;
+ }
+
+ /**
+ * Loads Node and Edge attribute data into Cytoscape from the given file
+ * locations. Currently, the only supported attribute types are of the type
+ * "name = value".
+ *
+ * @param nodeAttrLocations
+ * an array of node attribute file locations. May be null.
+ * @param edgeAttrLocations
+ * an array of edge attribute file locations. May be null.
+ */
+ public static void loadAttributes(String[] nodeAttrLocations, String[] edgeAttrLocations) {
+ // check to see if there are Node Attributes passed
+ if (nodeAttrLocations != null) {
+ final Set<String> oldNodeAttrNames = new HashSet<String>();
+ for (final String attrName : nodeAttributes.getAttributeNames())
+ oldNodeAttrNames.add(attrName);
+
+ boolean fireChange = false;
+ for (int i = 0; i < nodeAttrLocations.length; ++i) {
+ try {
+ InputStreamReader reader = null;
+ try {
+ reader = new InputStreamReader(FileUtil.getInputStream(nodeAttrLocations[i]));
+ CyAttributesReader.loadAttributes(nodeAttributes, reader);
+ }
+ finally {
+ if (reader != null) {
+ reader.close();
+ }
+ }
+ fireChange = true;
+ } catch (Exception e) {
+ // e.printStackTrace();
+ throw new IllegalArgumentException("Failure loading node attribute data: "
+ + nodeAttrLocations[i] + " because of:"
+ + e.getMessage());
+ }
+ }
+
+ if (fireChange) {
+ final Set<String> newNodeAttrNames = new HashSet<String>();
+ for (final String attrName : nodeAttributes.getAttributeNames()) {
+ if (!oldNodeAttrNames.contains(attrName))
+ newNodeAttrNames.add(attrName);
+ }
+
+ firePropertyChange(ATTRIBUTES_CHANGED, null, null);
+ firePropertyChange(NEW_ATTRS_LOADED, nodeAttributes, newNodeAttrNames);
+ }
+ }
+
+ // Check to see if there are Edge Attributes Passed
+ if (edgeAttrLocations != null) {
+ final Set<String> oldEdgeAttrNames = new HashSet<String>();
+ for (final String attrName : edgeAttributes.getAttributeNames())
+ oldEdgeAttrNames.add(attrName);
+
+ boolean fireChange = false;
+ for (int j = 0; j < edgeAttrLocations.length; ++j) {
+ try {
+ InputStreamReader reader = null;
+ try {
+ reader = new InputStreamReader(FileUtil.getInputStream(edgeAttrLocations[j]));
+ CyAttributesReader.loadAttributes(edgeAttributes, reader);
+ }
+ finally {
+ if (reader != null) {
+ reader.close();
+ }
+ }
+ fireChange = true;
+ } catch (Exception e) {
+ // e.printStackTrace();
+ throw new IllegalArgumentException("Failure loading edge attribute data: "
+ + edgeAttrLocations[j] + " because of:"
+ + e.getMessage());
+ }
+ }
+
+ if (fireChange) {
+ final Set<String> newEdgeAttrNames = new HashSet<String>();
+ for (final String attrName : edgeAttributes.getAttributeNames()) {
+ if (!oldEdgeAttrNames.contains(attrName))
+ newEdgeAttrNames.add(attrName);
+ }
+
+ firePropertyChange(ATTRIBUTES_CHANGED, null, null);
+ firePropertyChange(NEW_ATTRS_LOADED, edgeAttributes, newEdgeAttrNames);
+ }
+ }
+ }
+
+ /**
+ * This will replace the bioDataServer.
+ */
+ public static OntologyServer buildOntologyServer() {
+ try {
+ ontologyServer = new OntologyServer();
+ } catch (Exception e) {
+ logger.warn("Could not build OntologyServer.", e);
+ // e.printStackTrace();
+ throw new RuntimeException(e);
+
+ //return null;
+ }
+
+ return ontologyServer;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static OntologyServer getOntologyServer() {
+ return ontologyServer;
+ }
+
+ // ------------------------------//
+ // CyNetworkView Creation Methods
+ // ------------------------------//
+
+ /**
+ * Creates a CyNetworkView, but doesn't do anything with it. Ifnn's you want
+ * to use it
+ *
+ * @link {CytoscapeDesktop}
+ * @param network
+ * the network to create a view of
+ */
+ public static CyNetworkView createNetworkView(CyNetwork network) {
+ return createNetworkView(network, network.getTitle(), null, null);
+ }
+
+ /**
+ * Creates a CyNetworkView, but doesn't do anything with it. Ifnn's you want
+ * to use it
+ *
+ * @link {CytoscapeDesktop}
+ * @param network
+ * the network to create a view of
+ * @param title
+ * the title to use for the view
+ */
+ public static CyNetworkView createNetworkView(CyNetwork network, String title) {
+ return createNetworkView(network, title, null, null);
+ }
+
+ /**
+ * Creates a CyNetworkView, but doesn't do anything with it. Ifnn's you want
+ * to use it
+ *
+ * @link {CytoscapeDesktop}
+ * @param network
+ * the network to create a view of
+ * @param title
+ * the title to use for the view
+ * @param layout
+ * the CyLayoutAlgorithm to use to lay this out by default
+ */
+ public static CyNetworkView createNetworkView(CyNetwork network, String title, CyLayoutAlgorithm layout) {
+ return createNetworkView(network, title, layout, null);
+ }
+
+ /**
+ * Creates a CyNetworkView that is placed placed in a given visual style
+ * and rendered with a given layout algorithm.
+ * The CyNetworkView will become the current view and have focus.
+ *
+ * @param network
+ * the network to create a view of
+ * @param title
+ * the title to use for the view
+ * @param layout
+ * the CyLayoutAlgorithm to use for layout. If null, will
+ * use the default layout (CyLayouts.getDefaultLayout()).
+ * @param vs the VisualStyle in which to render this new network. If null,
+ * the default visual style will be used.
+ */
+ public static CyNetworkView createNetworkView(CyNetwork network, String title, CyLayoutAlgorithm layout, VisualStyle vs) {
+ if (network == nullNetwork) {
+ return nullNetworkView;
+ }
+
+ if (Cytoscape.viewExists(network.getIdentifier())) {
+ return getNetworkView(network.getIdentifier());
+ }
+
+ final DingNetworkView view = new DingNetworkView(network, title);
+ final VisualMappingManager vmm = Cytoscape.getVisualMappingManager();
+
+ view.setIdentifier(network.getIdentifier());
+ view.setTitle(network.getTitle());
+ getNetworkViewMap().put(network.getIdentifier(), view);
+ setSelectionMode(Cytoscape.getSelectionMode(), view);
+
+ if (vs != null) {
+ view.setVisualStyle(vs.getName());
+ vmm.setVisualStyle(vs);
+ } else {
+ view.setVisualStyle(vmm.getVisualStyle().getName());
+ }
+
+ if (layout == null) {
+ layout = CyLayouts.getDefaultLayout();
+ }
+
+ vmm.setNetworkView(view);
+ vmm.applyAppearances();
+ layout.doLayout(view);
+ view.setGraphLOD(new CyGraphLOD());
+ Cytoscape.firePropertyChange(cytoscape.view.CytoscapeDesktop.NETWORK_VIEW_CREATED, null, view);
+
+ return view;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param property_type DOCUMENT ME!
+ * @param old_value DOCUMENT ME!
+ * @param new_value DOCUMENT ME!
+ */
+ public static void firePropertyChange(String property_type, Object old_value, Object new_value) {
+ PropertyChangeEvent e = new PropertyChangeEvent(pcsO, property_type, old_value, new_value);
+ getSwingPropertyChangeSupport().firePropertyChange(e);
+ getPropertyChangeSupport().firePropertyChange(e);
+ }
+
+ /**
+ * Gets the selection mode value.
+ */
+ public static int getSelectionMode() {
+ return currentSelectionMode;
+ }
+
+ /**
+ * Sets the specified selection mode on all views.
+ *
+ * @param selectionMode
+ * SELECT_NODES_ONLY, SELECT_EDGES_ONLY, or
+ * SELECT_NODES_AND_EDGES.
+ */
+ public static void setSelectionMode(int selectionMode) {
+ // set the selection mode on all the views
+ GraphView view;
+ String network_id;
+ Map networkViewMap = getNetworkViewMap();
+
+ for (Iterator iter = networkViewMap.keySet().iterator(); iter.hasNext();) {
+ network_id = (String) iter.next();
+ view = (GraphView) networkViewMap.get(network_id);
+ setSelectionMode(selectionMode, view);
+ }
+
+ // update the global indicating the selection mode
+ currentSelectionMode = selectionMode;
+ }
+
+ /**
+ * Utility method to set the selection mode on the specified GraphView.
+ *
+ * @param selectionMode
+ * SELECT_NODES_ONLY, SELECT_EDGES_ONLY, or
+ * SELECT_NODES_AND_EDGES.
+ * @param view
+ * the GraphView to set the selection mode on.
+ */
+ public static void setSelectionMode(int selectionMode, GraphView view) {
+ switch (selectionMode) {
+ case SELECT_NODES_ONLY:
+ view.disableEdgeSelection();
+ view.enableNodeSelection();
+
+ break;
+
+ case SELECT_EDGES_ONLY:
+ view.disableNodeSelection();
+ view.enableEdgeSelection();
+
+ break;
+
+ case SELECT_NODES_AND_EDGES:
+ view.enableNodeSelection();
+ view.enableEdgeSelection();
+
+ break;
+ }
+ }
+
+ /**
+ * Get name of the current session file.
+ *
+ * @return current session file name
+ */
+ public static String getCurrentSessionFileName() {
+ return currentSessionFileName;
+ }
+
+ /**
+ * Set the current session name.
+ *
+ * @param newName
+ */
+ public static void setCurrentSessionFileName(String newName) {
+ currentSessionFileName = newName;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param state DOCUMENT ME!
+ */
+ public static void setSessionState(int state) {
+ sessionState = state;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static int getSessionstate() {
+ return sessionState;
+ }
+
+ /**
+ * Clear all networks and attributes and start a new session.
+ */
+ public static void createNewSession() {
+ // Clear groups
+ List<CyGroup>groups = CyGroupManager.getGroupList();
+ for (CyGroup group: groups) {
+ CyGroupManager.removeGroup(group);
+ }
+
+ // Destroy all networks
+ Set<CyNetwork> netSet = getNetworkSet();
+
+ for (CyNetwork net : netSet)
+ destroyNetwork(net, true);
+
+ // Clear node attributes
+ final String[] nodeAttrNames = nodeAttributes.getAttributeNames();
+ for (String name: nodeAttrNames)
+ nodeAttributes.deleteAttribute(name);
+
+ // Clear edge attributes
+ final String[] edgeAttrNames = edgeAttributes.getAttributeNames();
+ for (String name: edgeAttrNames)
+ edgeAttributes.deleteAttribute(name);
+
+ // Clear network attributes
+ final String[] networkAttrNames = networkAttributes.getAttributeNames();
+ for(String name: networkAttrNames)
+ networkAttributes.deleteAttribute(name);
+
+ // Reset Ontology Server
+ buildOntologyServer();
+ setOntologyRootID(null);
+
+ setCurrentSessionFileName(null);
+ firePropertyChange(ATTRIBUTES_CHANGED, null, null);
+ cytoscapeRootGraph = null;
+ cytoscapeRootGraph = new CytoscapeFingRootGraph();
+ // We need to fire SESSION_LOADED, but to avoid NPE, we'll provide
+ // a null network list
+ Cytoscape.firePropertyChange(Cytoscape.SESSION_LOADED, null, new ArrayList<CyNetwork>());
+ logger.info("Cytoscape Session Initialized.");
+ System.gc();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static String getOntologyRootID() {
+ return ontologyRootID;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param id DOCUMENT ME!
+ */
+ public static void setOntologyRootID(String id) {
+ ontologyRootID = id;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @throws JAXBException DOCUMENT ME!
+ * @throws IOException DOCUMENT ME!
+ */
+ public static Bookmarks getBookmarks() throws JAXBException, IOException {
+ if (bookmarks == null) {
+ BookmarkReader reader = new BookmarkReader();
+ reader.readBookmarks();
+ bookmarks = reader.getBookmarks();
+ }
+
+ return bookmarks;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param pBookmarks DOCUMENT ME!
+ */
+ public static void setBookmarks(Bookmarks pBookmarks) {
+ bookmarks = pBookmarks;
+ }
+
+ public synchronized static RecentlyOpenedTracker getRecentlyOpenedSessionTracker() {
+ if (recentlyOpenedSessions == null) {
+ final String trackerFileName = "sessions.tracker";
+ try {
+ recentlyOpenedSessions = new RecentlyOpenedTracker(trackerFileName);
+ } catch (final IOException e) {
+ System.err.println(e);
+ logger.warn("Failed to load \"" + trackerFileName + "\"!");
+ }
+ }
+
+ return recentlyOpenedSessions;
+ }
+}
diff --git a/application/src/main/java/cytoscape/CytoscapeInit.java b/application/src/main/java/cytoscape/CytoscapeInit.java
new file mode 100644
index 0000000..f38da8a
--- /dev/null
+++ b/application/src/main/java/cytoscape/CytoscapeInit.java
@@ -0,0 +1,680 @@
+/*
+ File: CytoscapeInit.java
+
+ Copyright (c) 2006, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape;
+
+import java.awt.Cursor;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Properties;
+
+import javax.swing.ImageIcon;
+
+import cytoscape.data.CyAttributes;
+import cytoscape.data.Semantics;
+import cytoscape.data.readers.CytoscapeSessionReader;
+import cytoscape.dialogs.logger.LoggerDialog;
+import cytoscape.init.CyInitParams;
+import cytoscape.logger.ConsoleLogger;
+import cytoscape.logger.CyLogger;
+import cytoscape.logger.LogLevel;
+import cytoscape.plugin.PluginManager;
+import cytoscape.plugin.DownloadableInfo;
+import cytoscape.plugin.PluginInfo;
+import cytoscape.plugin.ThemeInfo;
+import cytoscape.plugin.ManagerException;
+import cytoscape.plugin.Category;
+import cytoscape.plugin.PluginStatus;
+import cytoscape.util.FileUtil;
+import cytoscape.util.NestedNetworkViewUpdater;
+import cytoscape.util.shadegrown.WindowUtilities;
+import cytoscape.view.CyNetworkView;
+
+import org.cytoscape.equations.EqnParser;
+import org.cytoscape.equations.Parser;
+
+
+/**
+ * <p>
+ * Cytoscape Init is responsible for starting Cytoscape in a way that makes
+ * sense.
+ * </p>
+ * <p>
+ * The comments below are more hopeful than accurate. We currently do not
+ * support a "headless" mode (meaning there is no GUI). We do, however, hope to
+ * support this in the future.
+ * </p>
+ *
+ * <p>
+ * The two main modes of running Cytoscape are either in "headless" mode or in
+ * "script" mode. This class will use the command-line options to figure out
+ * which mode is desired, and run things accordingly.
+ * </p>
+ *
+ * The order for doing things will be the following:<br>
+ * <ol>
+ * <li>deterimine script mode, or headless mode</li>
+ * <li>get options from properties files</li>
+ * <li>get options from command line ( these overwrite properties )</li>
+ * <li>Load all Networks</li>
+ * <li>Load all data</li>
+ * <li>Load all Plugins</li>
+ * <li>Initialize all plugins, in order if specified.</li>
+ * <li>Start Desktop/Print Output exit.</li>
+ * </ol>
+ *
+ * @since Cytoscape 1.0
+ * @author Cytoscape Core Team
+ */
+public class CytoscapeInit implements PropertyChangeListener {
+ private static final String SPLASH_SCREEN_LOCATION = "/cytoscape/images/CytoscapeSplashScreen.png";
+ private static Properties properties;
+ private static Properties visualProperties;
+ private static CyLogger logger = null;
+ private static NestedNetworkViewUpdater nestedNetworkViewUpdater;
+
+ static {
+ logger = CyLogger.getLogger(CytoscapeInit.class);
+ logger.info("CytoscapeInit static initialization");
+
+ initProperties();
+
+ final String debug = properties.getProperty("cytoscape.debug", "false");
+ logger.setDebugging(Boolean.parseBoolean(debug));
+ }
+
+ private static CyInitParams initParams;
+
+ // Most-Recently-Used directories and files
+ private static Properties mrud;
+ private static File mruf;
+
+ // Error message
+ private static String ErrorMsg = "";
+
+ private PluginManager mgr;
+
+ /**
+ * Creates a new CytoscapeInit object.
+ */
+ public CytoscapeInit() {
+ Cytoscape.getPropertyChangeSupport().addPropertyChangeListener(Cytoscape.CYTOSCAPE_EXIT, this);
+ }
+
+ /**
+ * Cytoscape Init must be initialized using the command line arguments.
+ *
+ * @param params the arguments from the command line
+ * @return false, if we fail to initialize for some reason
+ */
+ public boolean init(CyInitParams params) {
+ long begintime = System.currentTimeMillis();
+ if (logger == null)
+ logger = CyLogger.getLogger(CytoscapeInit.class);
+
+ try {
+ initParams = params;
+
+ // setup properties
+ initProperties();
+
+ // Reinitialize so we can pick up the debug flag
+ logger = CyLogger.getLogger(CytoscapeInit.class);
+
+ properties.putAll(initParams.getProps());
+ visualProperties.putAll(initParams.getVizProps());
+
+ // Build the OntologyServer.
+ Cytoscape.buildOntologyServer();
+
+ // Instantiate a NestedNetworkViewUpdater
+ nestedNetworkViewUpdater = new NestedNetworkViewUpdater();
+
+ // AJK: 02/22/2010 make Semantics.INTERACTION not user Editable
+ CyAttributes edgeAttrs = Cytoscape.getEdgeAttributes();
+ edgeAttrs.setUserEditable(Semantics.INTERACTION, false);
+
+ initPluginManager();
+
+ // see if we are in headless mode
+ // show splash screen, if appropriate
+
+ // Initialize as GUI mode
+ if ((initParams.getMode() == CyInitParams.GUI)
+ || (initParams.getMode() == CyInitParams.EMBEDDED_WINDOW)) {
+ final ImageIcon image = new ImageIcon(Cytoscape.class
+ .getResource(SPLASH_SCREEN_LOCATION));
+ WindowUtilities.showSplash(image, 8000);
+
+ // Register the console logger, if we're not told not to
+ String consoleLogger = properties.getProperty("logger.console");
+ if (consoleLogger == null || Boolean.parseBoolean(consoleLogger)) {
+ logger.addLogHandler(ConsoleLogger.getLogger(), LogLevel.LOG_DEBUG);
+ } else {
+ logger.info("Log information can now be found in the Help->Error Console menu");
+ }
+
+ // Register the logger dialog as a log handler
+ logger.addLogHandler(LoggerDialog.getLoggerDialog(), LogLevel.LOG_DEBUG);
+
+ // Create Desktop. This includes Vizmapper GUI initialization.
+ Cytoscape.getDesktop();
+
+ // set the wait cursor
+ Cytoscape.getDesktop().setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR));
+
+ setUpAttributesChangedListener();
+ } else {
+ // Force logging to the console
+ logger.addLogHandler(ConsoleLogger.getLogger(), LogLevel.LOG_DEBUG);
+ }
+
+ logger.info("init mode: " + initParams.getMode());
+
+ logger.info("loading plugins....");
+ loadPlugins();
+
+ logger.info("loading session...");
+ boolean sessionLoaded = false;
+ if ((initParams.getMode() == CyInitParams.GUI)
+ || (initParams.getMode() == CyInitParams.EMBEDDED_WINDOW)) {
+ loadSessionFile();
+ sessionLoaded = true;
+ }
+
+ logger.info("loading networks...");
+ loadNetworks();
+
+ logger.info("loading attributes...");
+ loadAttributes();
+
+ logger.info("loading expression files...");
+ loadExpressionFiles();
+
+ if ((initParams.getMode() == CyInitParams.GUI)
+ || (initParams.getMode() == CyInitParams.EMBEDDED_WINDOW)) {
+ if(sessionLoaded == false) {
+ logger.info("Initializing VizMapper...");
+ initVizmapper();
+ }
+ }
+ } finally {
+ // Always restore the cursor and hide the splash, even there is
+ // exception
+ if ((initParams.getMode() == CyInitParams.GUI)
+ || (initParams.getMode() == CyInitParams.EMBEDDED_WINDOW)) {
+ WindowUtilities.hideSplash();
+ Cytoscape.getDesktop().setCursor(Cursor.getDefaultCursor());
+
+ // to clean up anything that the plugins have messed up
+ Cytoscape.getDesktop().repaint();
+ }
+ }
+
+ long endtime = System.currentTimeMillis() - begintime;
+ logger.info("Cytoscape initialized successfully in: " + endtime + " ms");
+ Cytoscape.firePropertyChange(Cytoscape.CYTOSCAPE_INITIALIZED, null, null);
+
+ return true;
+ }
+
+ /**
+ * Returns the CyInitParams object used to initialize Cytoscape.
+ */
+ public static CyInitParams getCyInitParams() {
+ return initParams;
+ }
+
+ /**
+ * Returns the properties used by Cytoscape, the result of cytoscape.props
+ * and command line options.
+ */
+ public static Properties getProperties() {
+ initProperties();
+ return properties;
+ }
+
+ /**
+ * @return the most recently used directory
+ */
+ public static File getMRUD() {
+ initMRUD();
+ return new File(mrud.getProperty("fileOpenLocation", System.getProperty("user.home")));
+ }
+
+ /**
+ * @return the most recently used file
+ */
+ public static File getMRUF() {
+ return mruf;
+ }
+
+ /**
+ * @param mrud_new the most recently used directory
+ */
+ public static void setMRUD(final File mrud_new) {
+ initMRUD();
+ mrud.setProperty("fileOpenLocation", mrud_new.toString());
+ }
+
+ /**
+ * @param mruf_new the most recently used file
+ */
+ public static void setMRUF(File mruf_new) {
+ mruf = mruf_new;
+ }
+
+ /**
+ * Within the .cytoscape directory create a version-specific directory
+ *
+ * @return the directory ".cytoscape/[cytoscape version]
+ */
+ public static File getConfigVersionDirectory() {
+ final File parent = getConfigDirectory();
+
+ File VersionDir = new File(parent, (new CytoscapeVersion()).getMajorVersion());
+ VersionDir.mkdir();
+
+ return VersionDir;
+ }
+
+ /**
+ * If .cytoscape directory does not exist, it creates it and returns it
+ *
+ * @return the directory ".cytoscape" in the users home directory.
+ */
+ public static File getConfigDirectory() {
+
+ try {
+ String dirName = System.getProperty("user.home");
+ File parent_dir = new File(dirName, ".cytoscape");
+
+ if (parent_dir.mkdir())
+ logger.info("Parent_Dir: " + parent_dir + " created.");
+
+ return parent_dir;
+ } catch (Exception e) {
+ logger.warn("error getting config directory", e);
+ }
+
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param file_name
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static File getConfigFile(String file_name) {
+ try {
+ File parent_dir = getConfigDirectory();
+ File file = new File(parent_dir, file_name);
+
+ if (file.createNewFile())
+ logger.info("Config file: " + file + " created.");
+
+ return file;
+ } catch (Exception e) {
+ logger.warn("error getting config file:" + file_name, e);
+ }
+
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static Properties getVisualProperties() {
+ return visualProperties;
+ }
+
+ /**
+ * Load the Properties found in a given given file into a given Properties object.
+ * @param defaultName the name of the properties file to use (.e.g., "cytoscape.props").
+ * @param props the Properties object in which to insert the
+ * property information found within defaultName.
+ */
+ public static void loadStaticProperties(String defaultName, Properties props) {
+ // TODO: This should probably be removed, since if
+ // props==null, then the props set here will be lost:
+ if (props == null) {
+ System.out.println("input props is null");
+ props = new Properties();
+ }
+
+ String tryName = "";
+
+ try {
+ // load the props from the jar file
+ tryName = "cytoscape.jar";
+
+ // This somewhat unusual way of getting the ClassLoader is because
+ // other methods don't work from WebStart.
+ ClassLoader cl = Thread.currentThread().getContextClassLoader();
+
+ URL vmu = null;
+
+ if (cl != null)
+ vmu = cl.getResource(defaultName);
+ else
+ System.err.println("ClassLoader for reading cytoscape.jar is null");
+
+ if (vmu != null)
+ // We'd like to use URLUtil.getBasicInputStream() to get
+ // InputStream, but it is too early in the initialization of
+ // Cytoscape and vmu is most likely out of a local resource, so
+ // get
+ // it directly:
+ props.load(vmu.openStream());
+ else
+ System.err.println("couldn't read " + defaultName + " from " + tryName);
+
+ // load the props file from $HOME/.cytoscape
+ tryName = "$HOME/.cytoscape";
+
+ File vmp = getConfigFile(defaultName);
+
+ if (vmp != null)
+ props.load(new FileInputStream(vmp));
+ else
+ System.err.println("couldn't read " + defaultName + " from " + tryName);
+ } catch (IOException ioe) {
+ System.err.println("couldn't open '" + tryName + " " + defaultName
+ + "' file: "+ioe.getMessage()+" - creating a hardcoded default"/*, ioe*/);
+ }
+ }
+
+ private static void loadExpressionFiles() {
+ // load expression data if specified
+ List ef = initParams.getExpressionFiles();
+
+ if ((ef != null) && (ef.size() > 0)) {
+ for (Iterator iter = ef.iterator(); iter.hasNext();) {
+ String expDataFilename = (String) iter.next();
+
+ if (expDataFilename != null) {
+ try {
+ Cytoscape.loadExpressionData(expDataFilename, true);
+ } catch (Exception e) {
+ logger.error("Couldn't open expression file: '"+expDataFilename+"': "+e.getMessage(), e);
+ }
+ }
+ }
+ }
+ }
+
+ private boolean loadSessionFile() {
+ String sessionFile = initParams.getSessionFile();
+
+ try {
+ String sessionName = "";
+
+ if (sessionFile != null) {
+
+ CytoscapeSessionReader reader = null;
+
+ if (sessionFile.matches(FileUtil.urlPattern)) {
+ URL u = new URL(sessionFile);
+ reader = new CytoscapeSessionReader(u);
+ sessionName = u.getFile();
+ } else {
+ Cytoscape.setCurrentSessionFileName(sessionFile);
+
+ final File shortName = new File(sessionFile);
+ sessionName = shortName.getName();
+ String absolutePath = shortName.getAbsolutePath();
+ if (absolutePath.startsWith("/"))
+ absolutePath = "/" + absolutePath;
+
+ final URL sessionURL = new URL("file:/" + absolutePath.replace("%", "%25"));
+
+ reader = new CytoscapeSessionReader(sessionURL);
+ }
+
+ if (reader != null) {
+ reader.read();
+ Cytoscape.getDesktop()
+ .setTitle("Cytoscape Desktop (Session Name: " + sessionName + ")");
+ return true;
+ }
+ }
+ } catch (Exception e) {
+ logger.error("couldn't create session from file '" + sessionFile + "': "+e.getMessage(), e);
+ } finally {
+ Cytoscape.getDesktop().getVizMapperUI().initVizmapperGUI();
+ System.gc();
+ }
+
+ return false;
+ }
+
+ private static void initProperties() {
+ if (properties == null) {
+ properties = new Properties();
+ loadStaticProperties("cytoscape.props", properties);
+ }
+
+ if (visualProperties == null) {
+ visualProperties = new Properties();
+ loadStaticProperties("vizmap.props", visualProperties);
+ }
+ }
+
+ private static void initMRUD() {
+ if (mrud == null) {
+ mrud = new Properties();
+ final File propsFile = new File(CytoscapeInit.getConfigVersionDirectory(), "mostRecentlyUsedDirectory.props");
+ if (propsFile != null) {
+ try {
+ final FileInputStream inputStream = new FileInputStream(propsFile);
+ mrud.load(inputStream);
+ } catch (final IOException e) {
+ // Intentionally empty!
+ }
+ }
+ }
+ }
+
+ private void setUpAttributesChangedListener() {
+ /*
+ * This cannot be done in CytoscapeDesktop construction (like the other
+ * menus) because we need CytoscapeDesktop created first. This is
+ * because CytoPanel menu item listeners need to register for CytoPanel
+ * events via a CytoPanel reference, and the only way to get a CytoPanel
+ * reference is via CytoscapeDeskop:
+ * Cytoscape.getDesktop().getCytoPanel(...)
+ * Cytoscape.getDesktop().getCyMenus().initCytoPanelMenus(); Add a
+ * listener that will apply vizmaps every time attributes change
+ */
+ final PropertyChangeListener attsChangeListener = new PropertyChangeListener() {
+ public void propertyChange(PropertyChangeEvent e) {
+ if (e.getPropertyName().equals(Cytoscape.ATTRIBUTES_CHANGED)) {
+ // apply vizmaps
+ final CyNetworkView currentView = Cytoscape.getCurrentNetworkView();
+ if (currentView != Cytoscape.getNullNetworkView())
+ Cytoscape.getCurrentNetworkView().redrawGraph(false, true);
+ }
+ }
+ };
+
+ Cytoscape.getSwingPropertyChangeSupport().addPropertyChangeListener(attsChangeListener);
+ }
+
+ // Load all requested networks
+ private void loadNetworks() {
+ for (Iterator i = initParams.getGraphFiles().iterator(); i.hasNext();) {
+ String net = (String) i.next();
+ logger.info("Load: " + net);
+
+ CyNetwork network = null;
+
+ boolean createView = false;
+
+ if ((initParams.getMode() == CyInitParams.GUI)
+ || (initParams.getMode() == CyInitParams.EMBEDDED_WINDOW))
+ createView = true;
+
+ if (net.matches(FileUtil.urlPattern)) {
+ try {
+ network = Cytoscape.createNetworkFromURL(new URL(net), createView);
+ } catch (Exception mue) {
+ logger.error("Couldn't load network from URL '"+net+"': " + mue.getMessage(), mue);
+ }
+ } else {
+ try {
+ network = Cytoscape.createNetworkFromFile(net, createView);
+ } catch (Exception mue) {
+ logger.error("Couldn't load network from file '"+net+"': " + mue.getMessage(), mue);
+ }
+ }
+
+ // This is for browser and other plugins.
+ Object[] ret_val = new Object[3];
+ ret_val[0] = network;
+ ret_val[1] = net;
+ ret_val[2] = new Integer(0);
+
+ Cytoscape.firePropertyChange(Cytoscape.NETWORK_LOADED, null, ret_val);
+ }
+ }
+
+ // load any specified data attribute files
+ private void loadAttributes() {
+ try {
+ Cytoscape.loadAttributes((String[]) initParams.getNodeAttributeFiles()
+ .toArray(new String[] { }),
+ (String[]) initParams.getEdgeAttributeFiles()
+ .toArray(new String[] { }));
+ } catch (Throwable ex) {
+ logger.error("failure loading specified attributes: "+ex.getMessage(), ex);
+ }
+ }
+
+ private void initVizmapper() {
+ Cytoscape.getDesktop().getVizMapperUI().initVizmapperGUI();
+ }
+
+ /**
+ * This is separated from the rest of the plugin manager because by getting
+ * the manager early, it can test for webstart before menus are created.
+ * This is a little hacky.
+ */
+ private void initPluginManager() {
+ try {
+ mgr = PluginManager.getPluginManager();
+ } catch (Throwable tp) {
+ logger.warn("Failed to start plugin manager.", tp);
+ }
+ }
+
+ private void loadPlugins() {
+ try {
+ try {
+ logger.info("Updating plugins...");
+ mgr.delete();
+ } catch (ManagerException me) {
+ logger.warn("Error updating plugins: "+me.getMessage(), me);
+ }
+
+ mgr.install();
+
+ //
+ // TODO smart plugin loading. If there are multiple of the same
+ // plugin (this will only work in the .cytoscape directory) load the
+ // newest version first. Should be able to examine the directories
+ // for this information. All installed plugins are named like
+ // 'MyPlugin-1.0' currently this isn't necessary as old version are
+ // not kept around
+ //
+ List<String> installedPlugins = new ArrayList<String>();
+
+ // load from those listed on the command line
+ installedPlugins.addAll(initParams.getPlugins());
+
+ // Get all directories where plugins have been installed
+ // going to have to be a little smart...themes contain their plugins
+ // in subdirectories
+ for (DownloadableInfo dInfo : mgr.getDownloadables(PluginStatus.CURRENT)) {
+ if (dInfo.getCategory().equals(Category.CORE.getCategoryText()))
+ continue;
+
+ // TODO get rid of switches
+ switch (dInfo.getType()) {
+ case PLUGIN:
+ installedPlugins.add(((PluginInfo) dInfo).getInstallLocation());
+
+ break;
+
+ case THEME:
+ ThemeInfo tInfo = (ThemeInfo) dInfo;
+ for (PluginInfo plugin : tInfo.getPlugins())
+ installedPlugins.add(plugin.getInstallLocation());
+
+ break;
+ }
+ }
+
+ mgr.loadPlugins(installedPlugins);
+
+ for (Throwable t : mgr.getLoadingErrors())
+ logger.warn("Plugin loading error: "+t.toString(),t);
+
+ mgr.clearErrorList();
+
+ } catch (Exception e) {
+ logger.error("Plugin system initialization error: "+e.toString(),e);
+ }
+ }
+
+ public void propertyChange(final PropertyChangeEvent e) {
+ if (e.getPropertyName().equals(Cytoscape.CYTOSCAPE_EXIT)) {
+ final File propsFile = new File(CytoscapeInit.getConfigVersionDirectory(), "mostRecentlyUsedDirectory.props");
+ initMRUD();
+ try {
+ mrud.store(new FileOutputStream(propsFile), "");
+ }
+ catch (final IOException ioe) {
+ System.err.println("Failed to save \"mostRecentlyUsedDirectory.props\"!");
+ }
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/CytoscapeModifiedNetworkManager.java b/application/src/main/java/cytoscape/CytoscapeModifiedNetworkManager.java
new file mode 100644
index 0000000..0773868
--- /dev/null
+++ b/application/src/main/java/cytoscape/CytoscapeModifiedNetworkManager.java
@@ -0,0 +1,138 @@
+/*
+ File: CytoscapeModifiedNetworkManager.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+/*
+ * Created on Sep 13, 2005
+ *
+ */
+package cytoscape;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+
+import java.util.HashMap;
+
+
+/**
+ *
+ * CytoscapeModifiedNetworkManager manages the modified state settings for the networks and listens for
+ * PropertyChangeEvents. This enables functionality such as prompting the user to save modified
+ * networks when exiting Cytoscape.
+ *
+ * @author Allan Kuchinsky
+ * @version 1.0
+ *
+ *
+ *
+ */
+public class CytoscapeModifiedNetworkManager implements PropertyChangeListener {
+ /**
+ *
+ */
+ public static final String MODIFIED = "Modified";
+
+ /**
+ *
+ */
+ public static final String CLEAN = "Clean";
+ private static HashMap networkStateMap = new HashMap();
+
+ /**
+ *
+ */
+ public CytoscapeModifiedNetworkManager() {
+ super();
+
+ Cytoscape.getDesktop().getSwingPropertyChangeSupport()
+ .addPropertyChangeListener(Cytoscape.NETWORK_MODIFIED, this);
+ Cytoscape.getDesktop().getSwingPropertyChangeSupport()
+ .addPropertyChangeListener(Cytoscape.NETWORK_SAVED, this);
+ Cytoscape.getDesktop().getSwingPropertyChangeSupport()
+ .addPropertyChangeListener(Cytoscape.NETWORK_CREATED, this);
+ Cytoscape.getSwingPropertyChangeSupport().addPropertyChangeListener(this);
+ }
+
+ public void propertyChange(PropertyChangeEvent e) {
+ // CyLogger.getLogger().info ("Property changed: " + e.getPropertyName());
+ // CyLogger.getLogger().info ("Old value = " + e.getOldValue());
+ // CyLogger.getLogger().info ("New value = " + e.getNewValue());
+ if (e.getPropertyName().equals(Cytoscape.NETWORK_MODIFIED)) {
+ CyNetwork net = (CyNetwork) e.getNewValue();
+
+ if (net instanceof CyNetwork) {
+ setModified(net, MODIFIED);
+ }
+ } else if (e.getPropertyName().equals(Cytoscape.NETWORK_SAVED)) {
+ // MLC 09/19/05 BEGIN:
+ // CyNetwork net = (CyNetwork) e.getNewValue();
+ CyNetwork net = (CyNetwork) (((Object[]) e.getNewValue())[0]);
+
+ // MLC 09/19/05 END.
+ if (net instanceof CyNetwork) {
+ setModified(net, CLEAN);
+ }
+ }
+ }
+
+ /**
+ * @param net
+ */
+ public static boolean isModified(CyNetwork net) {
+ Object modObj = networkStateMap.get(net);
+
+ if (modObj == null) // no network in table, so it can't be modified
+ {
+ return false;
+ } else if (modObj.toString().equals(MODIFIED)) {
+ return true;
+ } else {
+ return false;
+ }
+ }
+
+ /**
+ * set the state of the network
+ * @param net
+ * @param state values supported in this version: CLEAN, MODIFIED
+ */
+ public static void setModified(CyNetwork net, String state) {
+ networkStateMap.put(net, state);
+ }
+}
diff --git a/application/src/main/java/cytoscape/CytoscapeVersion.java b/application/src/main/java/cytoscape/CytoscapeVersion.java
new file mode 100644
index 0000000..05ff0bc
--- /dev/null
+++ b/application/src/main/java/cytoscape/CytoscapeVersion.java
@@ -0,0 +1,100 @@
+/*
+ * File: CytoscapeVersion.java Copyright (c) 2006, The Cytoscape Consortium
+ * (www.cytoscape.org) The Cytoscape Consortium is: - Institute for Systems
+ * Biology - University of California San Diego - Memorial Sloan-Kettering
+ * Cancer Center - Institut Pasteur - Agilent Technologies This library is free
+ * software; you can redistribute it and/or modify it under the terms of the GNU
+ * Lesser General Public License as published by the Free Software Foundation;
+ * either version 2.1 of the License, or any later version. This library is
+ * distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY,
+ * WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS FOR A
+ * PARTICULAR PURPOSE. The software and documentation provided hereunder is on
+ * an "as is" basis, and the Institute for Systems Biology and the Whitehead
+ * Institute have no obligations to provide maintenance, support, updates,
+ * enhancements or modifications. In no event shall the Institute for Systems
+ * Biology and the Whitehead Institute be liable to any party for direct,
+ * indirect, special, incidental or consequential damages, including lost
+ * profits, arising out of the use of this software and its documentation, even
+ * if the Institute for Systems Biology and the Whitehead Institute have been
+ * advised of the possibility of such damage. See the GNU Lesser General Public
+ * License for more details. You should have received a copy of the GNU Lesser
+ * General Public License along with this library; if not, write to the Free
+ * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ * USA.
+ */
+package cytoscape;
+
+/** CytoscapeVersion: identify (and describe) successive versions of cytoscape. */
+public class CytoscapeVersion {
+ /**
+ *
+ */
+ public static String version = CytoscapeInit.getProperties().getProperty(
+ "cytoscape.version.number");
+
+ private static String majorMinorVersion;
+
+ private static String bugFixVersion = "0";
+
+ public CytoscapeVersion() {
+ if (version.indexOf('-') > 0) {
+ // This is either a snapshot or a beta or something -- strip off that information
+ int indx = version.indexOf('-');
+ version = version.substring(0, indx);
+ }
+ String[] Versions = version.split("\\.");
+ majorMinorVersion = Versions[0] + "." + Versions[1];
+ if (Versions.length == 3) {
+ bugFixVersion = Versions[2];
+ }
+ }
+
+ /**
+ * Returns the string 'Cytoscape Version ' and the version number Do not use
+ * to just get a version.
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getVersion() {
+ return "Cytoscape Version " + version;
+ }
+
+ /**
+ * @return See getVersion()
+ */
+ public String toString() {
+ return getVersion();
+ }
+
+ /**
+ * This method gets the major and minor version for Cytsocape ignoring
+ * the bug fix version number. Example: If Cytoscape is currently at 2.4.6
+ * this method will return 2.4
+ *
+ * @return The major and minor version numbers of the currently running
+ * Cytoscape.
+ */
+ public String getMajorVersion() {
+ return majorMinorVersion;
+ }
+
+ /**
+ * This method gets the bug fix version for Cytsocape.
+ * Example: If Cytoscape is currently at 2.4.6 this method will return 6
+ * If there is no bug fix version the default is 0
+ *
+ * @return Just the bug fix version
+ */
+ public String getBugFixVersion() {
+ return bugFixVersion;
+ }
+
+ /**
+ *
+ * @return Full version number for currently running Cytoscape.
+ * Ex. 2.4.6
+ */
+ public String getFullVersion() {
+ return version;
+ }
+}
diff --git a/application/src/main/java/cytoscape/JavaVersion.java b/application/src/main/java/cytoscape/JavaVersion.java
new file mode 100644
index 0000000..7fbad09
--- /dev/null
+++ b/application/src/main/java/cytoscape/JavaVersion.java
@@ -0,0 +1,121 @@
+/*
+ File: CyMain.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape;
+
+
+import cytoscape.logger.CyLogger;
+
+
+/**
+ * A class that determines various components of the JVM version.
+ * Please <a href="http://java.sun.com/j2se/versioning_naming.html">see</a> for details.
+ */
+class JavaVersion {
+ private static JavaVersion theJavaVersion;
+
+ private final static CyLogger logger = CyLogger.getLogger(JavaVersion.class);
+
+ private int major;
+ private int minor;
+ private int maintenanceLevel;
+ private int update;
+
+ private JavaVersion() {
+ final String javaVersion = System.getProperty("java.version");
+
+ int nonDigitPos = 0;
+ while (Character.isDigit(javaVersion.charAt(nonDigitPos)))
+ ++nonDigitPos;
+ try {
+ major = Integer.parseInt(javaVersion.substring(0, nonDigitPos));
+ } catch (final NumberFormatException e) {
+ logger.error("Can't determine Java major version number from \"" + javaVersion + "\"!");
+ major = 0;
+ }
+
+ ++nonDigitPos;
+ int intStart = nonDigitPos;
+ while (Character.isDigit(javaVersion.charAt(nonDigitPos)))
+ ++nonDigitPos;
+ try {
+ minor = Integer.parseInt(javaVersion.substring(intStart, nonDigitPos));
+ } catch (final NumberFormatException e) {
+ logger.error("Can't determine Java major version number from \"" + javaVersion + "\"!");
+ minor = 0;
+ }
+
+ ++nonDigitPos;
+ intStart = nonDigitPos;
+ while (nonDigitPos < javaVersion.length() && Character.isDigit(javaVersion.charAt(nonDigitPos)))
+ ++nonDigitPos;
+ try {
+ maintenanceLevel = Integer.parseInt(javaVersion.substring(intStart, nonDigitPos));
+ } catch (final NumberFormatException e) {
+ logger.error("Can't determine Java maintenance level from \"" + javaVersion + "\"!");
+ maintenanceLevel = 0;
+ }
+
+ ++nonDigitPos;
+ intStart = nonDigitPos;
+ while (nonDigitPos < javaVersion.length() && Character.isDigit(javaVersion.charAt(nonDigitPos)))
+ ++nonDigitPos;
+ if (nonDigitPos > javaVersion.length())
+ update = 0;
+ else {
+ try {
+ update = Integer.parseInt(javaVersion.substring(intStart, nonDigitPos));
+ } catch (final NumberFormatException e) {
+ logger.error("Can't determine Java update version number from \"" + javaVersion + "\"!");
+ update = 0;
+ }
+ }
+ }
+
+ /**
+ * Factory method returning the singleton.
+ */
+ static synchronized JavaVersion getJavaVersion() {
+ if (theJavaVersion == null)
+ theJavaVersion = new JavaVersion();
+ return theJavaVersion;
+ }
+
+ /**
+ * We override clone() to prevent any callers from circumventing our singleton policy.
+ */
+ @Override public Object clone() throws CloneNotSupportedException {
+ throw new CloneNotSupportedException(); // That'll teach 'em!
+ }
+
+ int getMajor() { return major; }
+ int getMinor() { return minor; }
+ int getMaintenanceLevel() { return maintenanceLevel; }
+ int getUpdate() { return update; }
+}
diff --git a/application/src/main/java/cytoscape/actions/AlignHorizontalAction.java b/application/src/main/java/cytoscape/actions/AlignHorizontalAction.java
new file mode 100644
index 0000000..554057f
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/AlignHorizontalAction.java
@@ -0,0 +1,98 @@
+/*
+ File: AlignHorizontalAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+//-------------------------------------------------------------------------
+// $Revision: 9565 $
+// $Date: 2007-02-13 20:36:50 +0100 (Tue, 13 Feb 2007) $
+// $Author: mes $
+//-------------------------------------------------------------------------
+package cytoscape.actions;
+
+import cytoscape.view.CyNetworkView;
+
+import giny.view.*;
+
+//-------------------------------------------------------------------------
+import java.awt.event.ActionEvent;
+
+import java.util.*;
+
+import javax.swing.AbstractAction;
+
+
+//-------------------------------------------------------------------------
+/**
+ *
+ */
+public class AlignHorizontalAction extends AbstractAction {
+ CyNetworkView networkView;
+
+ /**
+ * Creates a new AlignHorizontalAction object.
+ *
+ * @param networkView DOCUMENT ME!
+ */
+ public AlignHorizontalAction(CyNetworkView networkView) {
+ super("Horizontal");
+ this.networkView = networkView;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ GraphView view = networkView.getView();
+ double avgYcoord = 0;
+
+ List selected_nodes = view.getSelectedNodes();
+ Iterator node_iterator;
+
+ node_iterator = selected_nodes.iterator();
+
+ while (node_iterator.hasNext()) {
+ avgYcoord += ((NodeView) node_iterator.next()).getYPosition();
+ }
+
+ node_iterator = selected_nodes.iterator();
+
+ while (node_iterator.hasNext()) {
+ ((NodeView) node_iterator.next()).setYPosition(avgYcoord);
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/AlignVerticalAction.java b/application/src/main/java/cytoscape/actions/AlignVerticalAction.java
new file mode 100644
index 0000000..896c6e7
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/AlignVerticalAction.java
@@ -0,0 +1,99 @@
+/*
+ File: AlignVerticalAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+//-------------------------------------------------------------------------
+// $Revision: 9565 $
+// $Date: 2007-02-13 20:36:50 +0100 (Tue, 13 Feb 2007) $
+// $Author: mes $
+//-------------------------------------------------------------------------
+package cytoscape.actions;
+
+import cytoscape.view.CyNetworkView;
+
+import giny.view.*;
+
+//-------------------------------------------------------------------------
+import java.awt.event.ActionEvent;
+
+import java.util.*;
+
+import javax.swing.AbstractAction;
+
+
+//-------------------------------------------------------------------------
+/**
+ *
+ */
+public class AlignVerticalAction extends AbstractAction {
+ CyNetworkView networkView;
+
+ /**
+ * Creates a new AlignVerticalAction object.
+ *
+ * @param networkView DOCUMENT ME!
+ */
+ public AlignVerticalAction(CyNetworkView networkView) {
+ super("Vertical");
+ this.networkView = networkView;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ GraphView view = networkView.getView();
+ double avgXcoord = 0;
+
+ List selected_nodes = view.getSelectedNodes();
+ Iterator node_iterator;
+
+ node_iterator = selected_nodes.iterator();
+
+ while (node_iterator.hasNext()) {
+ avgXcoord += ((NodeView) node_iterator.next()).getXPosition();
+ }
+
+ node_iterator = selected_nodes.iterator();
+
+ while (node_iterator.hasNext()) {
+ NodeView nv = (NodeView) node_iterator.next();
+ nv.setXPosition(avgXcoord);
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/AlphabeticalSelectionAction.java b/application/src/main/java/cytoscape/actions/AlphabeticalSelectionAction.java
new file mode 100644
index 0000000..9171379
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/AlphabeticalSelectionAction.java
@@ -0,0 +1,143 @@
+/*
+ File: AlphabeticalSelectionAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// $Revision: 11118 $
+// $Date: 2007-07-24 23:42:07 +0200 (Tue, 24 Jul 2007) $
+// $Author: mes $
+
+//-------------------------------------------------------------------------
+package cytoscape.actions;
+
+import ViolinStrings.Strings;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.data.CyNetworkUtilities;
+
+import cytoscape.util.CytoscapeAction;
+
+import cytoscape.view.CyNetworkView;
+
+import java.awt.*;
+
+//-------------------------------------------------------------------------
+import java.awt.event.*;
+
+import javax.swing.*;
+
+import javax.swing.event.MenuEvent;
+
+/**
+ *
+ */
+public class AlphabeticalSelectionAction extends CytoscapeAction implements ActionListener {
+ JDialog dialog;
+ JButton search;
+ JButton cancel;
+ JTextField searchField;
+
+ /**
+ * Creates a new AlphabeticalSelectionAction object.
+ */
+ public AlphabeticalSelectionAction() {
+ super("By Name...");
+ setPreferredMenu("Select.Nodes");
+ setAcceleratorCombo(java.awt.event.KeyEvent.VK_F, ActionEvent.CTRL_MASK);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ if (e.getSource() == cancel) {
+ dialog.setVisible(false);
+
+ return;
+ }
+
+ if ((e.getSource() == searchField) || (e.getSource() == search)) {
+ String search_string = searchField.getText();
+ CyNetworkUtilities.selectNodesStartingWith(Cytoscape.getCurrentNetwork(),
+ search_string,
+ Cytoscape.getCurrentNetworkView());
+ Cytoscape.getCurrentNetworkView().updateView();
+
+ return;
+ }
+
+ if (dialog == null)
+ createDialog();
+
+ dialog.setVisible(true);
+
+ Cytoscape.getCurrentNetworkView().updateView();
+ }
+
+ private JDialog createDialog() {
+ dialog = new JDialog(Cytoscape.getDesktop(), "Select Nodes By Name", false);
+
+ JPanel main_panel = new JPanel();
+ main_panel.setLayout(new BorderLayout());
+
+ JLabel label = new JLabel("<HTML>Select nodes whose <B>name or synonym</B> is like <small>(use \"*\" and \"?\" for wildcards)</small></HTML>");
+ main_panel.add(label, BorderLayout.NORTH);
+
+ searchField = new JTextField(30);
+ searchField.addActionListener(this);
+ main_panel.add(searchField, BorderLayout.CENTER);
+
+ JPanel button_panel = new JPanel();
+ search = new JButton("Search");
+ cancel = new JButton("Cancel");
+ search.addActionListener(this);
+ cancel.addActionListener(this);
+ button_panel.add(search);
+ button_panel.add(cancel);
+ main_panel.add(button_panel, BorderLayout.SOUTH);
+
+ dialog.setContentPane(main_panel);
+ dialog.pack();
+
+ return dialog;
+ }
+
+ public void menuSelected(MenuEvent e) {
+ enableForNetwork();
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/AnimatedLayoutAction.java b/application/src/main/java/cytoscape/actions/AnimatedLayoutAction.java
new file mode 100644
index 0000000..7425859
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/AnimatedLayoutAction.java
@@ -0,0 +1,169 @@
+/*
+ File: AnimatedLayoutAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.actions;
+
+import cytoscape.dialogs.GraphObjectSelection;
+
+//import giny.util.*;
+import cytoscape.ding.DingNetworkView;
+
+import cytoscape.view.CyNetworkView;
+
+import giny.model.*;
+
+import giny.view.*;
+
+import java.awt.event.ActionEvent;
+
+import java.util.*;
+
+import javax.swing.*;
+
+
+/**
+ * @deprecated Not apparently used. Shout if you are. Will be
+ * removed 5/2008.
+ */
+ at Deprecated
+public class AnimatedLayoutAction extends AbstractAction {
+ CyNetworkView networkView;
+ boolean bool = false;
+
+ /**
+ * Creates a new AnimatedLayoutAction object.
+ *
+ * @param networkView DOCUMENT ME!
+ */
+ public AnimatedLayoutAction(CyNetworkView networkView) {
+ super("Animate Layout");
+ this.networkView = networkView;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ JDialog dialog = new JDialog();
+ JPanel main = new JPanel();
+
+ main.add(new JButton(new AbstractAction("3D") {
+ public void actionPerformed(ActionEvent e) {
+ // Do this in the GUI Event Dispatch thread...
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ // PGrap*View gv = ( PGrap*View )networkView.getView();
+ // ISOM3DLayout isom = new ISOM3DLayout( gv );
+ // isom.doLayout();
+ }
+ });
+ }
+ }));
+
+ main.add(new JButton(new AbstractAction("Z Axis") {
+ public void actionPerformed(ActionEvent e) {
+ // Do this in the GUI Event Dispatch thread...
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ double maxZ = Double.MAX_VALUE;
+ double minZ = Double.MAX_VALUE;
+
+ DingNetworkView gv = (DingNetworkView) networkView
+ .getView();
+ Iterator nvi = gv.getNodeViewsIterator();
+
+ while (nvi.hasNext()) {
+ NodeView nv = (NodeView) nvi.next();
+
+ // CyLogger.getLogger().info( "Index: "+nv.getRootGraphIndex() );
+ // CyLogger.getLogger().info( "Index: "+nv.getRootGraphIndex() );
+ // CyLogger.getLogger().info( " X: "+gv.getNodeDoubleProperty( nv.getRootGraphIndex(), GraphView.NODE_X_POSITION ) );
+ // CyLogger.getLogger().info( " Y: "+gv.getNodeDoubleProperty( nv.getRootGraphIndex(), GraphView.NODE_Y_POSITION ) );
+ // CyLogger.getLogger().info( " Z: "+gv.getNodeDoubleProperty( nv.getRootGraphIndex(), GraphView.NODE_Z_POSITION ) );
+ if (maxZ == Double.MAX_VALUE) {
+ maxZ = gv.getNodeDoubleProperty(nv.getRootGraphIndex(),
+ GraphView.NODE_Z_POSITION);
+ minZ = gv.getNodeDoubleProperty(nv.getRootGraphIndex(),
+ GraphView.NODE_Z_POSITION);
+ }
+
+ if (maxZ < gv.getNodeDoubleProperty(nv.getRootGraphIndex(),
+ GraphView.NODE_Z_POSITION)) {
+ maxZ = gv.getNodeDoubleProperty(nv.getRootGraphIndex(),
+ GraphView.NODE_Z_POSITION);
+ }
+
+ if (minZ > gv.getNodeDoubleProperty(nv.getRootGraphIndex(),
+ GraphView.NODE_Z_POSITION)) {
+ minZ = gv.getNodeDoubleProperty(nv.getRootGraphIndex(),
+ GraphView.NODE_Z_POSITION);
+ }
+ }
+
+ // CyLogger.getLogger().info( "Z-RAnge: "+minZ+ " to "+maxZ );
+ nvi = gv.getNodeViewsIterator();
+
+ while (nvi.hasNext()) {
+ NodeView nv = (NodeView) nvi.next();
+
+ double scale = (gv.getNodeDoubleProperty(nv.getRootGraphIndex(),
+ GraphView.NODE_Z_POSITION)
+ - minZ) / (maxZ - minZ);
+
+ nv.setWidth(scale * 100);
+ nv.setHeight(scale * 100);
+ gv.setNodeDoubleProperty(nv.getRootGraphIndex(),
+ GraphView.NODE_Z_POSITION, scale * 100);
+ }
+
+ nvi = gv.getNodeViewsIterator();
+
+ while (nvi.hasNext()) {
+ NodeView nv = (NodeView) nvi.next();
+ gv.addNodeView("phoebe.util.P3DNode", nv.getRootGraphIndex());
+ }
+ }
+ });
+ }
+ }));
+
+ dialog.getContentPane().add(main);
+ dialog.pack();
+ dialog.setVisible(true);
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/ApplyLayoutAction.java b/application/src/main/java/cytoscape/actions/ApplyLayoutAction.java
new file mode 100644
index 0000000..89570c7
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/ApplyLayoutAction.java
@@ -0,0 +1,91 @@
+package cytoscape.actions;
+
+import java.awt.event.ActionEvent;
+import cytoscape.Cytoscape;
+import cytoscape.CytoscapeInit;
+import cytoscape.layout.CyLayoutAlgorithm;
+import cytoscape.layout.CyLayouts;
+import cytoscape.task.ui.JTaskConfig;
+import cytoscape.task.util.TaskManager;
+import cytoscape.util.CytoscapeAction;
+import cytoscape.view.CyNetworkView;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import javax.swing.JButton;
+import javax.swing.JOptionPane;
+import cytoscape.layout.LayoutTask;
+import java.util.List;
+import java.util.Iterator;
+
+public class ApplyLayoutAction extends CytoscapeAction implements PropertyChangeListener {
+
+ private static final long serialVersionUID = -576925581582912345L;
+
+ private String layoutName;
+ private CyLayoutAlgorithm alg;
+ private JButton applyLayoutButton;
+
+ public ApplyLayoutAction(){
+
+ layoutName = CytoscapeInit.getProperties().get("preferredLayoutAlgorithm").toString();
+ Cytoscape.getPropertyChangeSupport().addPropertyChangeListener(Cytoscape.PREFERENCES_UPDATED,this);
+ }
+
+
+ public void actionPerformed(ActionEvent ae) {
+
+ List<CyNetworkView> viewList = Cytoscape.getSelectedNetworkViews();
+ if (viewList.isEmpty()|| viewList.size() == 0 || Cytoscape.getCurrentNetworkView() == Cytoscape.getNullNetworkView()){
+ return;
+ }
+
+ alg = CyLayouts.getLayout(layoutName);
+
+ if (alg ==null){
+ // Can not find the layout algorithm specified
+ JOptionPane.showMessageDialog(Cytoscape.getDesktop(), "Unknown layout algorithm -- "+layoutName,"Warning", JOptionPane.ERROR_MESSAGE);
+ return;
+ }
+
+ Iterator<CyNetworkView> it = viewList.iterator();
+
+ while (it.hasNext()){
+ CyNetworkView view = it.next();
+
+ // Create Task
+ LayoutTask task = new LayoutTask(alg, view);
+
+ // Configure JTask Dialog Pop-Up Box
+ JTaskConfig jTaskConfig = new JTaskConfig();
+ jTaskConfig.setOwner(Cytoscape.getDesktop());
+ jTaskConfig.displayCloseButton(true);
+ jTaskConfig.displayStatus(true);
+ jTaskConfig.displayCancelButton(false);
+ jTaskConfig.setAutoDispose(true);
+
+ // Execute Task in New Thread; pop open JTask Dialog Box.
+ TaskManager.executeTask(task, jTaskConfig);
+ }
+ }
+
+ public void setButton(JButton button){
+ this.applyLayoutButton = button;
+ }
+
+ public boolean isInMenuBar(){
+ return false;
+ }
+
+ public void propertyChange(PropertyChangeEvent e) {
+
+ if (e.getPropertyName().equalsIgnoreCase(Cytoscape.PREFERENCES_UPDATED)){
+ String newLayoutName = CytoscapeInit.getProperties().get("preferredLayoutAlgorithm").toString();
+
+ if (!newLayoutName.equalsIgnoreCase(layoutName)){
+ layoutName = newLayoutName;
+ applyLayoutButton.setToolTipText("Apply "+layoutName+" layout");
+ }
+ }
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/actions/ApplyVisualStyleAction.java b/application/src/main/java/cytoscape/actions/ApplyVisualStyleAction.java
new file mode 100644
index 0000000..9bbb31a
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/ApplyVisualStyleAction.java
@@ -0,0 +1,71 @@
+package cytoscape.actions;
+
+import java.awt.event.ActionEvent;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import javax.swing.event.MenuEvent;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import cytoscape.util.CytoscapeAction;
+import cytoscape.view.CyNetworkView;
+
+/**
+ * Apply Visual Style for a set of selected networks.
+ * One action represents a
+ *
+ * @author kono
+ * @since Cytoscape 2.7.0
+ *
+ */
+public class ApplyVisualStyleAction extends CytoscapeAction {
+
+ private static final long serialVersionUID = 2435881456685787138L;
+
+ private final String styleName;
+
+
+ /**
+ * Create an action for the specified Visual Style.
+ *
+ * @param styleName - Name of the Visual Style
+ */
+ public ApplyVisualStyleAction(final String styleName) {
+ super(styleName);
+ this.styleName = styleName;
+ }
+
+
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ final List<CyNetwork> selected = Cytoscape.getSelectedNetworks();
+ final Set<CyNetworkView> views = new HashSet<CyNetworkView>();
+
+ for (final CyNetwork network: selected) {
+ final CyNetworkView targetView = Cytoscape.getNetworkView(network.getIdentifier());
+ if (targetView != Cytoscape.getNullNetworkView()) {
+ views.add(targetView);
+ }
+ }
+
+ applyStyle(views);
+ }
+
+ private void applyStyle(final Set<CyNetworkView> targetViews) {
+ // Switch current Visual Style
+ Cytoscape.getVisualMappingManager().setVisualStyle(styleName);
+
+ // Apply it for selected views.
+ for (CyNetworkView view: targetViews) {
+ view.setVisualStyle(styleName);
+ view.redrawGraph(false, true);
+ Cytoscape.getVisualMappingManager().setNetworkView(view);
+ }
+ }
+
+ public void menuSelected(MenuEvent e) {
+ this.enableForNetworkAndView();
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/ArrangeAction.java b/application/src/main/java/cytoscape/actions/ArrangeAction.java
new file mode 100644
index 0000000..01d1eff
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/ArrangeAction.java
@@ -0,0 +1,127 @@
+/*
+ File: PreferenceAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+//-------------------------------------------------------------------------
+// $Revision: 7760 $
+// $Date: 2006-06-26 09:28:49 -0700 (Mon, 26 Jun 2006) $
+// $Author: mes $
+//-------------------------------------------------------------------------
+package cytoscape.actions;
+
+import java.awt.event.ActionEvent;
+
+import javax.swing.AbstractAction;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.SwingUtilities;
+
+import cytoscape.view.CyDesktopManager;
+/**
+ *
+ */
+public class ArrangeAction extends JMenu {
+ /**
+ * .
+ */
+
+ private JMenuItem cascade;
+ private JMenuItem tiled;
+ private JMenuItem horizontal;
+ private JMenuItem vertical;
+ private JMenuItem bydefault;
+
+ public ArrangeAction() {
+ super("Arrange Network Windows");
+
+ cascade = new JMenuItem(new AbstractAction("Cascade") {
+ public void actionPerformed(ActionEvent e) {
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ CyDesktopManager.arrangeFrames(CyDesktopManager.Arrange.CASCADE);
+ }
+ });
+ }
+ });
+
+ tiled = new JMenuItem(new AbstractAction("Tiled") {
+ public void actionPerformed(ActionEvent e) {
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ CyDesktopManager.arrangeFrames(CyDesktopManager.Arrange.GRID);
+ }
+ });
+ }
+ });
+
+ horizontal = new JMenuItem(new AbstractAction("Horizontal") {
+ public void actionPerformed(ActionEvent e) {
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ CyDesktopManager.arrangeFrames(CyDesktopManager.Arrange.HORIZONTAL);
+ }
+ });
+ }
+ });
+
+ vertical = new JMenuItem(new AbstractAction("Vertical") {
+ public void actionPerformed(ActionEvent e) {
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ CyDesktopManager.arrangeFrames(CyDesktopManager.Arrange.VERTICAL);
+ }
+ });
+ }
+ });
+
+ bydefault = new JMenuItem(new AbstractAction("Default") {
+ public void actionPerformed(ActionEvent e) {
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ CyDesktopManager.arrangeFrames(CyDesktopManager.Arrange.DEFAULT);
+ }
+ });
+ }
+ });
+
+ this.add(cascade);
+ this.add(tiled);
+ this.add(horizontal);
+ this.add(vertical);
+ this.add(bydefault);
+ }
+}
+
diff --git a/application/src/main/java/cytoscape/actions/BackgroundColorAction.java b/application/src/main/java/cytoscape/actions/BackgroundColorAction.java
new file mode 100644
index 0000000..d46e853
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/BackgroundColorAction.java
@@ -0,0 +1,119 @@
+/*
+ File: BackgroundColorAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+//-------------------------------------------------------------------------
+// $Revision: 11413 $
+// $Date: 2007-08-16 19:54:49 +0200 (Thu, 16 Aug 2007) $
+// $Author: kono $
+//-------------------------------------------------------------------------
+package cytoscape.actions;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.util.CyColorChooser;
+import cytoscape.util.CytoscapeAction;
+
+import cytoscape.visual.GlobalAppearanceCalculator;
+import cytoscape.visual.VisualMappingManager;
+import cytoscape.visual.VisualStyle;
+
+import java.awt.Color;
+import java.awt.event.ActionEvent;
+
+import javax.swing.SwingUtilities;
+
+
+//-------------------------------------------------------------------------
+/**
+ * Prompts User for New Background Color.
+ *
+ * @deprecated Use vizmapper gui to edit background color.
+ * Will be removed 5/2008
+ */
+ at Deprecated
+public class BackgroundColorAction extends CytoscapeAction {
+ /**
+ * Constructor.
+ */
+ public BackgroundColorAction() {
+ super("Change Background Color");
+ setPreferredMenu("View");
+ setAcceleratorCombo(java.awt.event.KeyEvent.VK_B, ActionEvent.ALT_MASK);
+ }
+
+ /**
+ * Captures User Menu Selection.
+ * @param ev Action Event.
+ */
+ public void actionPerformed(ActionEvent ev) {
+ // Do this in the GUI Event Dispatch thread...
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ Color newPaint = CyColorChooser.showDialog(Cytoscape.getCurrentNetworkView()
+ .getComponent(),
+ "Choose a Background Color",
+ (java.awt.Color) Cytoscape.getCurrentNetworkView()
+ .getBackgroundPaint());
+
+ // Update the Current Background Color
+ // and Synchronize with current Visual Style
+ if (newPaint != null) {
+ Cytoscape.getCurrentNetworkView().setBackgroundPaint(newPaint);
+ synchronizeVisualStyle(newPaint);
+ }
+ }
+ });
+ } //action performed
+
+ /**
+ * Synchronizes the New Background Color with the Current Visual Style.
+ * @param newColor New Color
+ */
+ private void synchronizeVisualStyle(Color newColor) {
+ VisualMappingManager vmm = Cytoscape.getVisualMappingManager();
+
+ if (vmm != null) {
+ VisualStyle style = vmm.getVisualStyle();
+
+ if (style != null) {
+ GlobalAppearanceCalculator gCalc = style.getGlobalAppearanceCalculator();
+ gCalc.setDefaultBackgroundColor(newColor);
+ vmm.applyGlobalAppearances();
+ }
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/BendSelectedEdgesAction.java b/application/src/main/java/cytoscape/actions/BendSelectedEdgesAction.java
new file mode 100644
index 0000000..55765ff
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/BendSelectedEdgesAction.java
@@ -0,0 +1,95 @@
+/*
+ File: BendSelectedEdgesAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+//-------------------------------------------------------------------------
+// $Revision: 19327 $
+// $Date: 2010-02-12 23:01:44 +0100 (Fri, 12 Feb 2010) $
+// $Author: ruschein $
+//-------------------------------------------------------------------------
+package cytoscape.actions;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.util.CytoscapeAction;
+
+import cytoscape.view.CyNetworkView;
+
+import giny.view.EdgeView;
+
+//-------------------------------------------------------------------------
+import java.awt.event.ActionEvent;
+
+import javax.swing.AbstractAction;
+
+import javax.swing.event.MenuEvent;
+
+//-------------------------------------------------------------------------
+/**
+ *
+ */
+public class BendSelectedEdgesAction extends CytoscapeAction {
+ /**
+ * Creates a new BendSelectedEdgesAction object.
+ */
+ public BendSelectedEdgesAction() {
+ super("Smooth Selected Edges");
+ setPreferredMenu("Select.Edges");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ CyNetworkView view = Cytoscape.getCurrentNetworkView();
+ final int[] selectedEdges = view.getSelectedEdgeIndices();
+
+ if (selectedEdges != null) {
+ for (int i = 0; i < selectedEdges.length; i++) {
+ EdgeView ev = view.getEdgeView(selectedEdges[i]);
+ ev.setLineType(EdgeView.CURVED_LINES);
+ }
+
+ view.updateView();
+ }
+ }
+
+ public void menuSelected(MenuEvent e) {
+ enableForNetworkAndView();
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/BirdsEyeViewAction.java b/application/src/main/java/cytoscape/actions/BirdsEyeViewAction.java
new file mode 100644
index 0000000..45ed636
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/BirdsEyeViewAction.java
@@ -0,0 +1,119 @@
+/*
+ File: BirdsEyeViewAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.actions;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.util.CytoscapeAction;
+
+import cytoscape.view.CytoscapeDesktop;
+
+import ding.view.BirdsEyeView;
+import ding.view.DGraphView;
+
+import java.awt.Dimension;
+import java.awt.event.ActionEvent;
+
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+
+import javax.swing.Action;
+
+/**
+ * @deprecated This class is no longer used since the BirdsEyeView is now always part of
+ * the NetworkPanel. BirdsEyeView creation and event handling is done by the
+ * {@link cytoscape.view.BirdsEyeViewHandler} and initialized in {@link cytoscape.view.CytoscapeDesktop}
+ * This class will be removed 5/2008.
+ */
+public class BirdsEyeViewAction extends CytoscapeAction implements PropertyChangeListener {
+ BirdsEyeView bev;
+ boolean on = false;
+
+ /**
+ * Creates a new BirdsEyeViewAction object.
+ */
+ public BirdsEyeViewAction() {
+ super("Show/Hide Network Overview");
+ setPreferredMenu("View");
+ Cytoscape.getPropertyChangeSupport().addPropertyChangeListener(Cytoscape.CYTOSCAPE_INITIALIZED,this);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void propertyChange(PropertyChangeEvent e) {
+ if (CytoscapeDesktop.NETWORK_VIEW_FOCUSED.equals(e.getPropertyName())
+ || (CytoscapeDesktop.NETWORK_VIEW_FOCUS.equals(e.getPropertyName()))
+ || (CytoscapeDesktop.NETWORK_VIEW_DESTROYED.equals(e.getPropertyName()))) {
+ bev.changeView((DGraphView) Cytoscape.getCurrentNetworkView());
+ } else if (Cytoscape.CYTOSCAPE_INITIALIZED.equals(e.getPropertyName())) {
+ actionPerformed(null);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ if (!on) {
+ bev = new BirdsEyeView((DGraphView) Cytoscape.getCurrentNetworkView()) {
+ public Dimension getMinimumSize() {
+ return new Dimension(180, 180);
+ }
+ };
+ Cytoscape.getDesktop().getNetworkPanel().setNavigator(bev);
+ Cytoscape.getDesktop().getSwingPropertyChangeSupport().addPropertyChangeListener(this);
+ on = true;
+ putValue(Action.NAME, "Hide Network Overview");
+ } else {
+ if (bev != null) {
+ bev.destroy();
+ bev = null;
+ }
+
+ Cytoscape.getDesktop().getNetworkPanel()
+ .setNavigator(Cytoscape.getDesktop().getNetworkPanel().getNavigatorPanel());
+ Cytoscape.getDesktop().getSwingPropertyChangeSupport().removePropertyChangeListener(this);
+ on = false;
+ putValue(Action.NAME, "Show Network Overview");
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/BookmarkAction.java b/application/src/main/java/cytoscape/actions/BookmarkAction.java
new file mode 100644
index 0000000..cdf7591
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/BookmarkAction.java
@@ -0,0 +1,92 @@
+/*
+ File: PreferenceAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+//-------------------------------------------------------------------------
+// $Revision: 7760 $
+// $Date: 2006-06-26 09:28:49 -0700 (Mon, 26 Jun 2006) $
+// $Author: mes $
+//-------------------------------------------------------------------------
+package cytoscape.actions;
+
+import java.awt.event.ActionEvent;
+import java.io.IOException;
+
+import javax.swing.JFrame;
+import javax.xml.bind.JAXBException;
+
+import cytoscape.Cytoscape;
+import cytoscape.dialogs.preferences.BookmarkDialog;
+import cytoscape.logger.CyLogger;
+import cytoscape.util.CytoscapeAction;
+
+
+/**
+ *
+ */
+public class BookmarkAction extends CytoscapeAction {
+ /**
+ * Creates a new BookmarkAction object.
+ */
+ public BookmarkAction() {
+ super("Bookmarks...");
+
+ CyLogger.getLogger(BookmarkAction.class).info("BookmarkAction()...");
+ setPreferredMenu("Edit.Preferences");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ BookmarkDialog bookmarkDialog;
+
+ try {
+ bookmarkDialog = new BookmarkDialog((JFrame) Cytoscape.getDesktop());
+ bookmarkDialog.setVisible(true);
+ } catch (JAXBException e1) {
+ // TODO Auto-generated catch block
+ CyLogger.getLogger(BookmarkAction.class).error(null, e1);
+ } catch (IOException e1) {
+ // TODO Auto-generated catch block
+ CyLogger.getLogger(BookmarkAction.class).error(null, e1);
+ }
+
+ // bookmarkDialog.refresh();
+ } // actionPerformed
+}
diff --git a/application/src/main/java/cytoscape/actions/CheckBoxFileChooser.java b/application/src/main/java/cytoscape/actions/CheckBoxFileChooser.java
new file mode 100644
index 0000000..bdb4863
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/CheckBoxFileChooser.java
@@ -0,0 +1,102 @@
+/*
+ File: CheckBoxFileChooser.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.actions;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import java.io.File;
+
+import javax.swing.*;
+import javax.swing.event.*;
+import javax.swing.filechooser.FileSystemView;
+
+
+/**
+ * extends JFileChooser by adding a JCheckBox at the bottom of the chooser
+ * @deprecated This isn't apparently used anywhere. If you are using it,
+ * let us know! If you need a file use FileUtil.getFile(). Will be
+ * removed 5/2008.
+ */
+ at Deprecated
+public class CheckBoxFileChooser extends JFileChooser {
+ JCheckBox jcb;
+ boolean jcbFlag = false;
+ String jcbLabel;
+
+ /**
+ * Creates a new CheckBoxFileChooser object.
+ *
+ * @param currentDirectory DOCUMENT ME!
+ * @param checkBoxLabel DOCUMENT ME!
+ */
+ public CheckBoxFileChooser(File currentDirectory, String checkBoxLabel) {
+ super(currentDirectory, (FileSystemView) null);
+ jcbLabel = checkBoxLabel;
+ }
+
+ protected JDialog createDialog(Component parent) throws HeadlessException {
+ JDialog jd = super.createDialog(parent);
+ jcb = new JCheckBox(jcbLabel);
+ jcb.setSelected(jcbFlag);
+ jcb.addItemListener(new CheckBoxListener());
+
+ Container contentPane = jd.getContentPane();
+ contentPane.add(jcb, BorderLayout.SOUTH);
+ jd.pack();
+
+ return jd;
+ }
+
+ /** inner class for listening to the JCheckBox jcb
+ * and updating the boolean jcbFlag when appropriate
+ */
+ private class CheckBoxListener implements ItemListener {
+ public void itemStateChanged(ItemEvent e) {
+ if (e.getStateChange() == ItemEvent.SELECTED)
+ jcbFlag = true;
+ else if (e.getStateChange() == ItemEvent.DESELECTED)
+ jcbFlag = false;
+ }
+ }
+
+ /** method for accessing last state of JCheckBox jcb */
+ public boolean getCheckBoxState() {
+ return jcbFlag;
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/CloneGraphInNewWindowAction.java b/application/src/main/java/cytoscape/actions/CloneGraphInNewWindowAction.java
new file mode 100644
index 0000000..60dd617
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/CloneGraphInNewWindowAction.java
@@ -0,0 +1,139 @@
+/*
+ File: CloneGraphInNewWindowAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+//-------------------------------------------------------------------------
+// $Revision: 23990 $
+// $Date: 2011-02-01 18:44:08 +0100 (Tue, 01 Feb 2011) $
+// $Author: thully $
+//-------------------------------------------------------------------------
+package cytoscape.actions;
+
+import giny.model.Edge;
+import giny.model.Node;
+import giny.view.EdgeView;
+import giny.view.NodeView;
+
+import java.awt.event.ActionEvent;
+import java.awt.geom.Point2D;
+import java.util.Iterator;
+
+import javax.swing.event.MenuEvent;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import cytoscape.data.CyAttributesUtils;
+import cytoscape.util.CyNetworkNaming;
+import cytoscape.util.CytoscapeAction;
+import cytoscape.view.CyNetworkView;
+import cytoscape.visual.VisualStyle;
+import ding.view.DGraphView;
+
+/**
+ *
+ */
+public class CloneGraphInNewWindowAction extends CytoscapeAction {
+ /**
+ * Creates a new CloneGraphInNewWindowAction object.
+ */
+ public CloneGraphInNewWindowAction() {
+ super("Clone Current Network");
+ setPreferredMenu("File.New.Network");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ CyNetwork origNet = Cytoscape.getCurrentNetwork();
+ CyNetworkView origView = Cytoscape.getCurrentNetworkView();
+ VisualStyle vs = Cytoscape.getVisualMappingManager().getVisualStyle();
+ String newName = CyNetworkNaming.getSuggestedNetworkTitle(origNet.getTitle() + " copy");
+
+ CyNetwork new_network = Cytoscape.createNetwork(origNet.getNodeIndicesArray(),
+ origNet.getEdgeIndicesArray(),
+ newName, null, true);
+
+ // only clone the view if one actually exists
+ if ( origView == null || origView == Cytoscape.getNullNetworkView() )
+ return;
+
+ CyNetworkView newView = Cytoscape.getNetworkView(new_network.getIdentifier());
+ if ( newView != null || newView != Cytoscape.getNullNetworkView() ) {
+
+ // Use nodes as keys because they are less volatile than views...
+ Iterator ni = origView.getGraphPerspective().nodesIterator();
+ while (ni.hasNext()) {
+ Node n = (Node) ni.next();
+
+ NodeView onv = origView.getNodeView(n);
+ NodeView nnv = newView.getNodeView(n);
+
+ nnv.setXPosition(onv.getXPosition());
+ nnv.setYPosition(onv.getYPosition());
+ }
+
+ newView.setZoom(origView.getZoom());
+ Point2D origCenter = ((DGraphView)origView).getCenter();
+ ((DGraphView)newView).setCenter(origCenter.getX(), origCenter.getY());
+
+ // set edge anchors and bends
+ Iterator ei = origView.getGraphPerspective().edgesIterator();
+ while (ei.hasNext()) {
+ Edge ee = (Edge) ei.next();
+
+ EdgeView oev = origView.getEdgeView(ee);
+ EdgeView nev = newView.getEdgeView(ee);
+
+ nev.getBend().setHandles(oev.getBend().getHandles());
+ nev.getBend().setHandles(oev.getBend().getHandles());
+
+ nev.setLineType( oev.getLineType() );
+ }
+
+ Cytoscape.getVisualMappingManager().setVisualStyle(vs);
+ CyAttributesUtils.copyAttributes(origNet.getIdentifier(), new_network.getIdentifier(),
+ Cytoscape.getNetworkAttributes(), false);
+ Cytoscape.getPropertyChangeSupport().firePropertyChange(Cytoscape.ATTRIBUTES_CHANGED, null, null);
+ }
+ }
+
+ public void menuSelected(MenuEvent e) {
+ enableForNetwork();
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/CreateNetworkViewAction.java b/application/src/main/java/cytoscape/actions/CreateNetworkViewAction.java
new file mode 100644
index 0000000..651d4a9
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/CreateNetworkViewAction.java
@@ -0,0 +1,196 @@
+/*
+ File: CreateNetworkViewAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.actions;
+
+import java.awt.event.ActionEvent;
+import java.text.DecimalFormat;
+import java.text.NumberFormat;
+
+import javax.swing.JOptionPane;
+import javax.swing.event.MenuEvent;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import cytoscape.CytoscapeInit;
+import cytoscape.task.Task;
+import cytoscape.task.TaskMonitor;
+import cytoscape.task.ui.JTaskConfig;
+import cytoscape.task.util.TaskManager;
+import cytoscape.util.CytoscapeAction;
+import cytoscape.view.CyNetworkView;
+
+/**
+ *
+ */
+public class CreateNetworkViewAction extends CytoscapeAction {
+
+ private static final long serialVersionUID = 5033320941306310434L;
+
+ /**
+ * Creates a new CreateNetworkViewAction object.
+ */
+ public CreateNetworkViewAction() {
+ super("Create View");
+ setPreferredMenu("Edit");
+ setAcceleratorCombo(java.awt.event.KeyEvent.VK_V, ActionEvent.ALT_MASK);
+ }
+
+
+ /**
+ * Creates a new CreateNetworkViewAction object.
+ *
+ * @param label
+ * DOCUMENT ME!
+ */
+ public CreateNetworkViewAction(boolean label) {
+ super();
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ CyNetwork cyNetwork = Cytoscape.getCurrentNetwork();
+ createViewFromCurrentNetwork(cyNetwork);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param cyNetwork
+ * DOCUMENT ME!
+ */
+ public static void createViewFromCurrentNetwork(final CyNetwork cyNetwork) {
+ NumberFormat formatter = new DecimalFormat("#,###,###");
+
+ if (cyNetwork.getNodeCount() > Integer.parseInt(CytoscapeInit
+ .getProperties().getProperty("secondaryViewThreshold"))) {
+ int n = JOptionPane
+ .showConfirmDialog(
+ Cytoscape.getDesktop(),
+ "Network contains "
+ + formatter
+ .format(cyNetwork.getNodeCount())
+ + " nodes and "
+ + formatter
+ .format(cyNetwork.getEdgeCount())
+ + " edges. "
+ + "\nRendering a network this size may take several "
+ + "minutes.\n" + "Do you wish to proceed?",
+ "Rendering Large Network",
+ JOptionPane.YES_NO_OPTION);
+
+ if (n == JOptionPane.NO_OPTION)
+ return;
+ }
+
+ // Create Task
+ CreateNetworkViewTask task = new CreateNetworkViewTask(cyNetwork);
+
+ // Configure JTask Dialog Pop-Up Box
+ JTaskConfig jTaskConfig = new JTaskConfig();
+
+ jTaskConfig.displayCancelButton(false);
+ jTaskConfig.setOwner(Cytoscape.getDesktop());
+ jTaskConfig.displayCloseButton(false);
+ jTaskConfig.displayStatus(true);
+ jTaskConfig.setAutoDispose(true);
+
+ // Execute Task in New Thread; pop open JTask Dialog Box.
+ TaskManager.executeTask(task, jTaskConfig);
+ }
+
+ /**
+ * Sets the state of the action before rendering the menu.
+ */
+ public void menuSelected(MenuEvent e) {
+ CyNetwork currNet = Cytoscape.getCurrentNetwork();
+ if (currNet == null || currNet == Cytoscape.getNullNetwork()) {
+ setEnabled(false);
+ return;
+ }
+ CyNetworkView currView = Cytoscape.getNetworkView(currNet
+ .getIdentifier());
+ if (currView == null || currView == Cytoscape.getNullNetworkView())
+ setEnabled(true);
+ else
+ setEnabled(false);
+ }
+
+}
+
+class CreateNetworkViewTask implements Task {
+ private CyNetwork network;
+ private TaskMonitor taskMonitor;
+
+ CreateNetworkViewTask(CyNetwork network) {
+ this.network = network;
+ }
+
+ public void run() {
+ taskMonitor.setStatus("Creating network view ...");
+ taskMonitor.setPercentCompleted(-1);
+
+ try {
+ Cytoscape.createNetworkView(network);
+ } catch (Exception e) {
+ taskMonitor.setException(e,
+ "Could not create network view for network: "
+ + network.getTitle());
+ }
+
+ taskMonitor.setPercentCompleted(100);
+ taskMonitor.setStatus("Network view successfully create for: "
+ + network.getTitle());
+ }
+
+ public void halt() {
+ }
+
+ public void setTaskMonitor(TaskMonitor taskMonitor)
+ throws IllegalThreadStateException {
+ this.taskMonitor = taskMonitor;
+ }
+
+ public String getTitle() {
+ return "Creating Network View";
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/CytoPanelAction.java b/application/src/main/java/cytoscape/actions/CytoPanelAction.java
new file mode 100644
index 0000000..364533c
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/CytoPanelAction.java
@@ -0,0 +1,122 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.actions;
+
+import java.awt.event.ActionEvent;
+
+import javax.swing.Action;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.event.MenuEvent;
+
+import cytoscape.Cytoscape;
+import cytoscape.util.CytoscapeAction;
+import cytoscape.view.cytopanels.CytoPanel;
+import cytoscape.view.cytopanels.CytoPanelName;
+import cytoscape.view.cytopanels.CytoPanelState;
+
+/**
+ *
+ */
+public class CytoPanelAction extends CytoscapeAction {
+
+ private static final long serialVersionUID = 2069061664423847850L;
+
+ protected static final String SHOW = "Show";
+ protected static final String HIDE = "Hide";
+
+ protected String title;
+ protected int position;
+ protected CytoPanelName parent= null;
+
+ public CytoPanelAction(CytoPanelName cp, boolean show, CytoPanelName parent) {
+ this(cp.getTitle(), cp.getCompassDirection(), show);
+ this.parent = parent;
+ }
+
+ /**
+ * Base class for displaying cytopanel menu items.
+ *
+ * @param title The title that will be coupled with "show" and "hide" in the menu.
+ * @param position The SwingConstants.SOUTH,EAST,WEST,etc. position of the cyto panel.
+ * @param show Whether the cytopanel is initially shown at startup or not. Only used
+ * to define the initial title.
+ */
+ private CytoPanelAction(String title,int position, boolean show) {
+ super(show ? HIDE + " " + title : SHOW + " " + title);
+ this.title = title;
+ this.position = position;
+ setPreferredMenu("View");
+ }
+
+ /**
+ * Toggles the cytopanel state.
+ *
+ * @param ev Triggering event - not used.
+ */
+ public void actionPerformed(ActionEvent ev) {
+
+ CytoPanelState curState = Cytoscape.getDesktop().getCytoPanel(position).getState();
+
+ if (curState == CytoPanelState.HIDE) {
+ Cytoscape.getDesktop().getCytoPanel(position).setState(CytoPanelState.DOCK);
+
+ } else {
+ Cytoscape.getDesktop().getCytoPanel(position).setState(CytoPanelState.HIDE);
+ }
+ }
+
+ /**
+ * This dynamically sets the title of the menu based on the state of the CytoPanel.
+ */
+ public void menuSelected(MenuEvent me) {
+
+ if (parent != null){
+ CytoPanelState parentState = Cytoscape.getDesktop().getCytoPanel(parent.getCompassDirection()).getState();
+ if ( parentState == CytoPanelState.HIDE )
+ setEnabled(false);
+ else
+ setEnabled(true);
+ }
+
+ CytoPanelState curState = Cytoscape.getDesktop().getCytoPanel(position).getState();
+ if (curState == CytoPanelState.HIDE) {
+ putValue(Action.NAME, SHOW + " " + title);
+ } else {
+ putValue(Action.NAME, HIDE + " " + title);
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/DeSelectAllEdgesAction.java b/application/src/main/java/cytoscape/actions/DeSelectAllEdgesAction.java
new file mode 100644
index 0000000..0766403
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/DeSelectAllEdgesAction.java
@@ -0,0 +1,86 @@
+/*
+ File: DeSelectAllEdgesAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+//-------------------------------------------------------------------------
+// $Revision: 19327 $
+// $Date: 2010-02-12 23:01:44 +0100 (Fri, 12 Feb 2010) $
+// $Author: ruschein $
+//-------------------------------------------------------------------------
+package cytoscape.actions;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.util.CytoscapeAction;
+
+//-------------------------------------------------------------------------
+import java.awt.event.ActionEvent;
+
+import javax.swing.event.MenuEvent;
+
+//-------------------------------------------------------------------------
+/**
+ *
+ */
+public class DeSelectAllEdgesAction extends CytoscapeAction {
+ /**
+ * Creates a new DeSelectAllEdgesAction object.
+ */
+ public DeSelectAllEdgesAction() {
+ super("Deselect All Edges");
+ setPreferredMenu("Select.Edges");
+ setAcceleratorCombo(java.awt.event.KeyEvent.VK_A,
+ ActionEvent.ALT_MASK | ActionEvent.SHIFT_MASK);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ // GinyUtils.deselectAllEdges( Cytoscape.getCurrentNetworkView() );
+ Cytoscape.getCurrentNetwork().unselectAllEdges();
+
+ if (Cytoscape.getCurrentNetworkView() != null) {
+ Cytoscape.getCurrentNetworkView().updateView();
+ }
+ } // action performed
+
+ public void menuSelected(MenuEvent e) {
+ enableForNetwork();
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/DeSelectAllNodesAction.java b/application/src/main/java/cytoscape/actions/DeSelectAllNodesAction.java
new file mode 100644
index 0000000..acb45ca
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/DeSelectAllNodesAction.java
@@ -0,0 +1,86 @@
+/*
+ File: DeSelectAllNodesAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+//-------------------------------------------------------------------------
+// $Revision: 19327 $
+// $Date: 2010-02-12 23:01:44 +0100 (Fri, 12 Feb 2010) $
+// $Author: ruschein $
+//-------------------------------------------------------------------------
+package cytoscape.actions;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.util.CytoscapeAction;
+
+//-------------------------------------------------------------------------
+import java.awt.event.ActionEvent;
+
+import javax.swing.event.MenuEvent;
+
+//-------------------------------------------------------------------------
+/**
+ *
+ */
+public class DeSelectAllNodesAction extends CytoscapeAction {
+ /**
+ * Creates a new DeSelectAllNodesAction object.
+ */
+ public DeSelectAllNodesAction() {
+ super("Deselect All Nodes");
+ setPreferredMenu("Select.Nodes");
+ setAcceleratorCombo(java.awt.event.KeyEvent.VK_A,
+ ActionEvent.CTRL_MASK | ActionEvent.SHIFT_MASK);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ // GinyUtils.deselectAllNodes( Cytoscape.getCurrentNetworkView() );
+ Cytoscape.getCurrentNetwork().unselectAllNodes();
+
+ if (Cytoscape.getCurrentNetworkView() != null) {
+ Cytoscape.getCurrentNetworkView().updateView();
+ }
+ }
+
+ public void menuSelected(MenuEvent e) {
+ enableForNetwork();
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/DeleteAction.java b/application/src/main/java/cytoscape/actions/DeleteAction.java
new file mode 100644
index 0000000..21c718b
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/DeleteAction.java
@@ -0,0 +1,191 @@
+/*
+ File: DeleteAction.java
+
+ Copyright (c) 2006, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+//---------------------------------------------------------------------------
+package cytoscape.actions;
+
+import giny.model.GraphObject;
+import giny.view.EdgeView;
+import giny.view.NodeView;
+
+import java.awt.event.ActionEvent;
+import java.awt.event.KeyEvent;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import javax.swing.event.MenuEvent;
+
+import cytoscape.CyEdge;
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+import cytoscape.logger.CyLogger;
+import cytoscape.util.CytoscapeAction;
+import cytoscape.util.undo.CyUndo;
+import cytoscape.view.CyNetworkView;
+
+
+/**
+ *
+ * action for deleting selected Cytoscape nodes and edges
+ *
+ * @author Allan Kuchinsky, Agilent Technologies
+ * @version 1.0
+ *
+ */
+public class DeleteAction extends CytoscapeAction {
+ private static final long serialVersionUID = -5769255815829787466L;
+
+ /**
+ *
+ */
+ public static final String ACTION_TITLE = "Delete Selected Nodes and Edges";
+
+ private GraphObject graphObj = null;
+
+ /**
+ * action for deleting selected Cytoscape nodes and edges
+ */
+ public DeleteAction() {
+ this(null);
+ }
+
+ /**
+ * perform deletion on the input object. if object is a Node, then this will
+ * result in also deleting the edges adjacent to the node
+ *
+ * @param obj the object to be deleted
+ */
+
+ public DeleteAction(GraphObject obj) {
+ super(ACTION_TITLE);
+ CyLogger.getLogger().info("starting delete action");
+ setPreferredMenu("Edit");
+ setAcceleratorCombo(KeyEvent.VK_DELETE, 0);
+ graphObj = obj;
+ CyLogger.getLogger().info("ending delete action");
+ }
+
+
+ /**
+ * Delete all selected nodes, edges, edges adjacent to the selected nodes,
+ * and any nodes/edges passed as arguments.
+ */
+ public void actionPerformed(ActionEvent ae) {
+
+ CyNetworkView myView = Cytoscape.getCurrentNetworkView();
+ CyNetwork cyNet = myView.getNetwork();
+ List<EdgeView> edgeViews = myView.getSelectedEdges();
+ List<NodeView> nodeViews = myView.getSelectedNodes();
+ CyNode cyNode;
+ CyEdge cyEdge;
+ NodeView nv;
+ EdgeView ev;
+
+ // if an argument exists, add it to the appropriate list
+ if (graphObj != null ) {
+ if ( graphObj instanceof giny.model.Node) {
+ cyNode = (CyNode) graphObj;
+ nv = Cytoscape.getCurrentNetworkView().getNodeView(cyNode);
+ if ( !nodeViews.contains(nv) )
+ nodeViews.add(nv);
+ } else if ( graphObj instanceof giny.model.Edge) {
+ cyEdge = (CyEdge) graphObj;
+ ev = Cytoscape.getCurrentNetworkView().getEdgeView(cyEdge);
+ if ( !edgeViews.contains(ev) )
+ edgeViews.add(ev);
+ }
+ }
+
+ Set<Integer> edgeIndices = new HashSet<Integer>();
+ Set<Integer> nodeIndices = new HashSet<Integer>();
+
+ // add all node indices
+ for (int i = 0; i < nodeViews.size(); i++) {
+ nv = (NodeView) nodeViews.get(i);
+ cyNode = (CyNode) nv.getNode();
+ nodeIndices.add(cyNode.getRootGraphIndex());
+
+ // add adjacent edge indices for each node
+ int[] edgesList = cyNet.getAdjacentEdgeIndicesArray(cyNode.getRootGraphIndex(),true,true,true);
+ for ( int x = 0; x < edgesList.length; x++ )
+ edgeIndices.add(edgesList[x]);
+ }
+
+ // add all selected edge indices
+ for (int i = 0; i < edgeViews.size(); i++) {
+ ev = (EdgeView) edgeViews.get(i);
+ cyEdge = (CyEdge) ev.getEdge();
+ edgeIndices.add( cyEdge.getRootGraphIndex() );
+ }
+
+ // convert
+ int i = 0;
+ int[] edgeInd = new int[edgeIndices.size()];
+ for (Integer ei : edgeIndices)
+ edgeInd[i++] = ei.intValue();
+
+ i = 0;
+ int[] nodeInd = new int[nodeIndices.size()];
+ for (Integer ni : nodeIndices)
+ nodeInd[i++] = ni.intValue();
+
+ CyUndo.getUndoableEditSupport().postEdit( new DeleteEdit(cyNet,nodeInd,edgeInd, this) );
+
+ // delete the actual nodes and edges
+ cyNet.hideEdges(edgeInd);
+ cyNet.hideNodes(nodeInd);
+
+ Cytoscape.firePropertyChange(Cytoscape.NETWORK_MODIFIED, myView, cyNet);
+ }
+
+ public void menuSelected(MenuEvent me) {
+ CyNetwork n = Cytoscape.getCurrentNetwork();
+ if ( n == null || n == Cytoscape.getNullNetwork() ) {
+ setEnabled(false);
+ return;
+ }
+
+ java.util.Set nodes = n.getSelectedNodes();
+ java.util.Set edges = n.getSelectedEdges();
+
+ if ( ( nodes != null && nodes.size() > 0 ) ||
+ ( edges != null && edges.size() > 0 ) )
+ {
+
+ setEnabled(true);
+ }
+
+ else
+ setEnabled(false);
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/actions/DeleteEdit.java b/application/src/main/java/cytoscape/actions/DeleteEdit.java
new file mode 100644
index 0000000..ca019d0
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/DeleteEdit.java
@@ -0,0 +1,93 @@
+
+package cytoscape.actions;
+
+import java.awt.event.KeyEvent;
+
+import giny.view.NodeView;
+
+import javax.swing.event.MenuKeyListener;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import cytoscape.util.undo.CyAbstractEdit;
+import cytoscape.view.CyNetworkView;
+
+
+/**
+ * An undoable edit that will undo and redo deletion of nodes and edges.
+ */
+class DeleteEdit extends CyAbstractEdit {
+
+ private static final long serialVersionUID = -1164181258019250610L;
+ int[] nodes;
+ int[] edges;
+ double[] xPos;
+ double[] yPos;
+ CyNetwork net;
+ // AJK: 03082008 DeleteAction to be reenabled upon undo
+ DeleteAction deleteAction;
+
+
+ DeleteEdit(CyNetwork net, int[] nodeInd, int[] edgeInd) {
+ super("Delete");
+ if ( net == null )
+ throw new IllegalArgumentException("network is null");
+ this.net = net;
+
+ nodes = new int[nodeInd.length];
+ for ( int i = 0; i < nodeInd.length; i++ )
+ nodes[i] = nodeInd[i];
+
+ edges = new int[edgeInd.length];
+ for ( int i = 0; i < edgeInd.length; i++ )
+ edges[i] = edgeInd[i];
+
+ // save the positions of the nodes
+ xPos = new double[nodes.length];
+ yPos = new double[nodes.length];
+ CyNetworkView netView = Cytoscape.getNetworkView(net.getIdentifier());
+ if ( netView != null && netView != Cytoscape.getNullNetworkView() ) {
+ for ( int i = 0; i < nodes.length; i++ ) {
+ NodeView nv = netView.getNodeView(nodes[i]);
+ xPos[i] = nv.getXPosition();
+ yPos[i] = nv.getYPosition();
+ }
+ }
+
+ }
+
+ DeleteEdit(CyNetwork net, int[] nodeInd, int[] edgeInd, DeleteAction deleteAction) {
+ this (net, nodeInd, edgeInd);
+ this.deleteAction = deleteAction;
+ }
+
+
+ public void redo() {
+ super.redo();
+
+ net.hideEdges(edges);
+ net.hideNodes(nodes);
+ CyNetworkView netView = Cytoscape.getNetworkView(net.getIdentifier());
+ netView.redrawGraph(true, true);
+ Cytoscape.firePropertyChange(Cytoscape.NETWORK_MODIFIED, netView, net);
+ deleteAction.setEnabled(false);
+ }
+
+ public void undo() {
+ super.undo();
+
+ net.restoreNodes(nodes);
+ net.restoreEdges(edges);
+
+ CyNetworkView netView = Cytoscape.getNetworkView(net.getIdentifier());
+ if ( netView != null && netView != Cytoscape.getNullNetworkView() ) {
+ for ( int i = 0; i < nodes.length; i++ ) {
+ NodeView nv = netView.getNodeView(nodes[i]);
+ nv.setOffset( xPos[i], yPos[i] );
+ }
+ }
+ netView.redrawGraph(true, true);
+ Cytoscape.firePropertyChange(Cytoscape.NETWORK_MODIFIED, netView, net);
+ deleteAction.setEnabled(true);
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/DeselectAllAction.java b/application/src/main/java/cytoscape/actions/DeselectAllAction.java
new file mode 100644
index 0000000..5e3128e
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/DeselectAllAction.java
@@ -0,0 +1,85 @@
+/*
+ File: DeselectAllAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+//-------------------------------------------------------------------------
+// $Revision: 11118 $
+// $Date: 2007-07-24 23:42:07 +0200 (Tue, 24 Jul 2007) $
+// $Author: mes $
+//-------------------------------------------------------------------------
+package cytoscape.actions;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.util.CytoscapeAction;
+
+//-------------------------------------------------------------------------
+import java.awt.event.ActionEvent;
+
+import javax.swing.event.MenuEvent;
+
+//-------------------------------------------------------------------------
+/**
+ *
+ */
+public class DeselectAllAction extends CytoscapeAction {
+ /**
+ * Creates a new DeselectAllAction object.
+ */
+ public DeselectAllAction() {
+ super("Deselect All Nodes and Edges");
+ setPreferredMenu("Select");
+ setAcceleratorCombo(java.awt.event.KeyEvent.VK_A,
+ ActionEvent.CTRL_MASK | ActionEvent.SHIFT_MASK | ActionEvent.ALT_MASK);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ // GinyUtils.deselectAllNodes( Cytoscape.getCurrentNetworkView() );
+ // GinyUtils.deselectAllEdges( Cytoscape.getCurrentNetworkView() );
+ Cytoscape.getCurrentNetwork().unselectAllNodes();
+ Cytoscape.getCurrentNetwork().unselectAllEdges();
+ Cytoscape.getCurrentNetworkView().updateView();
+ }
+
+ public void menuSelected(MenuEvent e) {
+ enableForNetwork();
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/DestroyNetworkAction.java b/application/src/main/java/cytoscape/actions/DestroyNetworkAction.java
new file mode 100644
index 0000000..cdc2aa6
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/DestroyNetworkAction.java
@@ -0,0 +1,98 @@
+/*
+ File: DestroyNetworkAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.actions;
+
+import cytoscape.Cytoscape;
+import cytoscape.CyNetwork;
+
+import cytoscape.util.*;
+
+import java.awt.event.*;
+
+import javax.swing.event.MenuEvent;
+
+
+/**
+ *
+ */
+public class DestroyNetworkAction extends CytoscapeAction {
+ /**
+ * Creates a new DestroyNetworkAction object.
+ */
+ public DestroyNetworkAction() {
+ super("Destroy Network");
+ setPreferredMenu("Edit");
+ setAcceleratorCombo(java.awt.event.KeyEvent.VK_W,
+ ActionEvent.CTRL_MASK | ActionEvent.SHIFT_MASK);
+ }
+
+ /**
+ * Creates a new DestroyNetworkAction object.
+ *
+ * @param label DOCUMENT ME!
+ */
+ public DestroyNetworkAction(boolean label) {
+ super();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ java.util.List<CyNetwork> l = Cytoscape.getSelectedNetworks();
+ for ( CyNetwork n : l )
+ Cytoscape.destroyNetwork(n);
+ }
+
+ /**
+ * @deprecated Use Cytoscape.destroyNetwork(Cytoscape.getCurrentNetwork()) instead.
+ * Will be gone 11/2008.
+ */
+ @Deprecated
+ public static void destroyCurrentNetwork() {
+ Cytoscape.destroyNetwork(Cytoscape.getCurrentNetwork());
+ }
+
+ /**
+ * Sets the action state based on whether a current network exists.
+ */
+ public void menuSelected(MenuEvent e) {
+ enableForNetwork();
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/DestroyNetworkViewAction.java b/application/src/main/java/cytoscape/actions/DestroyNetworkViewAction.java
new file mode 100644
index 0000000..f1729e8
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/DestroyNetworkViewAction.java
@@ -0,0 +1,101 @@
+/*
+ File: DestroyNetworkViewAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.actions;
+
+import cytoscape.Cytoscape;
+import cytoscape.CyNetwork;
+
+import cytoscape.util.CytoscapeAction;
+
+import cytoscape.view.CyNetworkView;
+
+import java.awt.event.ActionEvent;
+import java.util.LinkedList;
+
+import javax.swing.event.MenuEvent;
+
+
+/**
+ *
+ */
+public class DestroyNetworkViewAction extends CytoscapeAction {
+ /**
+ * Creates a new DestroyNetworkViewAction object.
+ */
+ public DestroyNetworkViewAction() {
+ super("Destroy View");
+ setPreferredMenu("Edit");
+ setAcceleratorCombo(java.awt.event.KeyEvent.VK_W, ActionEvent.CTRL_MASK);
+ }
+
+ /**
+ * Creates a new DestroyNetworkViewAction object.
+ *
+ * @param label DOCUMENT ME!
+ */
+ public DestroyNetworkViewAction(boolean label) {
+ super();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ // Get the list first, then iterate. If you do this:
+ // for ( CyNetworkView cv : Cytoscape.getSelectedNetworkViews() )
+ // you will notice that the list of selected networks changes
+ // as you iterate through it. This is due to events getting fired
+ // as a result of the deletion.
+ java.util.List<CyNetworkView> l = Cytoscape.getSelectedNetworkViews();
+ for ( CyNetworkView cv : l )
+ Cytoscape.destroyNetworkView(cv);
+ }
+
+ /**
+ * @deprecated Use Cytoscape.destroyNetworkView() instead. Will go 11/2008.
+ */
+ @Deprecated
+ public static void destroyViewFromCurrentNetwork() {
+ Cytoscape.destroyNetworkView(Cytoscape.getCurrentNetwork());
+ }
+
+ public void menuSelected(MenuEvent e) {
+ enableForNetworkAndView();
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/EdgeManipulationAction.java b/application/src/main/java/cytoscape/actions/EdgeManipulationAction.java
new file mode 100644
index 0000000..e63c9db
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/EdgeManipulationAction.java
@@ -0,0 +1,122 @@
+/*
+ File: EdgeManipulationAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+//-------------------------------------------------------------------------
+// $Revision: 9565 $
+// $Date: 2007-02-13 20:36:50 +0100 (Tue, 13 Feb 2007) $
+// $Author: mes $
+//-------------------------------------------------------------------------
+package cytoscape.actions;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.data.CyAttributes;
+
+import cytoscape.dialogs.GinyEdgeControlDialog;
+
+import cytoscape.view.CyNetworkView;
+
+//-------------------------------------------------------------------------
+import java.awt.event.ActionEvent;
+
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Iterator;
+
+import javax.swing.AbstractAction;
+import javax.swing.JDialog;
+import javax.swing.JOptionPane;
+
+
+//-------------------------------------------------------------------------
+/**
+ *
+ */
+public class EdgeManipulationAction extends AbstractAction {
+ CyNetworkView networkView;
+
+ /**
+ * Creates a new EdgeManipulationAction object.
+ *
+ * @param networkView DOCUMENT ME!
+ */
+ public EdgeManipulationAction(CyNetworkView networkView) {
+ super("Edge select or hide by attributes...");
+ this.networkView = networkView;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ CyAttributes edgeAtts = Cytoscape.getEdgeAttributes();
+
+ String[] edgeAttributeNames = edgeAtts.getAttributeNames();
+ HashMap attributesTree = new HashMap();
+
+ for (int i = 0; i < edgeAttributeNames.length; i++) {
+ String att = edgeAttributeNames[i];
+
+ if (edgeAtts.getType(att) == CyAttributes.TYPE_STRING) {
+ // This iterator contains the edge uids that contain a value
+ // for this attribute
+ Iterator it = edgeAtts.getMultiHashMap().getObjectKeys(att);
+ HashSet nameSet = new HashSet();
+
+ while (it.hasNext()) {
+ String edgeId = (String) it.next();
+ nameSet.add(edgeAtts.getStringAttribute(edgeId, att));
+ }
+
+ attributesTree.put(att, (String[]) nameSet.toArray(new String[nameSet.size()]));
+ } // if a string attribute
+ } // for i
+
+ if (attributesTree.size() > 0) {
+ JDialog dialog = new GinyEdgeControlDialog(networkView, attributesTree,
+ "Edge Selection Control");
+ dialog.pack();
+ dialog.setLocationRelativeTo(networkView.getComponent());
+ dialog.setVisible(true);
+ } else {
+ JOptionPane.showMessageDialog(null,
+ "There are no String edge attributes suitable for controlling edge display");
+ }
+ } // actionPerformed
+}
diff --git a/application/src/main/java/cytoscape/actions/ExitAction.java b/application/src/main/java/cytoscape/actions/ExitAction.java
new file mode 100644
index 0000000..3de54f5
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/ExitAction.java
@@ -0,0 +1,73 @@
+/*
+ File: ExitAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// $Revision: 9565 $
+// $Date: 2007-02-13 20:36:50 +0100 (Tue, 13 Feb 2007) $
+// $Author: mes $
+package cytoscape.actions;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.util.CytoscapeAction;
+
+import java.awt.event.ActionEvent;
+
+
+/**
+ *
+ */
+public class ExitAction extends CytoscapeAction {
+ protected int returnVal;
+
+ /**
+ * Creates a new ExitAction object.
+ */
+ public ExitAction() {
+ super("Quit");
+ setPreferredMenu("File");
+ setAcceleratorCombo(java.awt.event.KeyEvent.VK_Q, ActionEvent.CTRL_MASK);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ Cytoscape.exit(returnVal);
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/ExpFileChooser.java b/application/src/main/java/cytoscape/actions/ExpFileChooser.java
new file mode 100644
index 0000000..9c948ab
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/ExpFileChooser.java
@@ -0,0 +1,113 @@
+/*
+ File: ExpFileChooser.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+//-------------------------------------------------------------------------
+// $Revision: 10373 $
+// $Date: 2007-06-01 23:07:29 +0200 (Fri, 01 Jun 2007) $
+// $Author: mes $
+//-------------------------------------------------------------------------
+package cytoscape.actions;
+
+import java.awt.*;
+import java.awt.event.*;
+
+//-------------------------------------------------------------------------
+import java.io.File;
+
+import javax.swing.*;
+import javax.swing.event.*;
+import javax.swing.filechooser.FileSystemView;
+
+
+//-------------------------------------------------------------------------
+/** extends JFileChooser in the following way:
+ * adds a JCheckBox at the bottom of the chooser, asking
+ * whether to copy expression data to attributes. The
+ * state of this box can be accessed using the method
+ * getWhetherToCopyExpToAttribs().
+ *
+ * @see #getWhetherToCopyExpToAttribs
+ * @deprecated Not apparently used anywhere. Shout if you are. Will be
+ * removed 5/2008.
+ */
+ at Deprecated
+public class ExpFileChooser extends JFileChooser {
+ JCheckBox jcb;
+ boolean copyToAttribs = true;
+
+ /**
+ * Creates a new ExpFileChooser object.
+ *
+ * @param currentDirectory DOCUMENT ME!
+ */
+ public ExpFileChooser(File currentDirectory) {
+ super(currentDirectory, (FileSystemView) null);
+ }
+
+ protected JDialog createDialog(Component parent) throws HeadlessException {
+ JDialog jd = super.createDialog(parent);
+ jcb = new JCheckBox("Copy Expression Data to Network Attributes?");
+ jcb.setSelected(copyToAttribs);
+ jcb.addItemListener(new CopyExpListener());
+
+ Container contentPane = jd.getContentPane();
+ contentPane.add(jcb, BorderLayout.SOUTH);
+ jd.pack();
+
+ return jd;
+ }
+
+ /** inner class for listening to the JCheckBox jcb
+ * and updating the boolean copyToAttribs when appropriate.
+ * {@link cytoscape.view.NetworkView.ExpFileChooser.copyToAttribs
+ * copyToAttribs} when appropriate.
+ */
+ private class CopyExpListener implements ItemListener {
+ public void itemStateChanged(ItemEvent e) {
+ if (e.getStateChange() == ItemEvent.SELECTED) {
+ copyToAttribs = true;
+ } else if (e.getStateChange() == ItemEvent.DESELECTED) {
+ copyToAttribs = false;
+ }
+ }
+ }
+
+ /** method for accessing last state of JCheckBox jcb */
+ public boolean getWhetherToCopyExpToAttribs() {
+ return copyToAttribs;
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/ExportAction.java b/application/src/main/java/cytoscape/actions/ExportAction.java
new file mode 100644
index 0000000..de25ab1
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/ExportAction.java
@@ -0,0 +1,100 @@
+/*
+ File: ExportAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+//-------------------------------------------------------------------------
+// $Revision: 19327 $
+// $Date: 2010-02-12 23:01:44 +0100 (Fri, 12 Feb 2010) $
+// $Author: ruschein $
+//-------------------------------------------------------------------------
+package cytoscape.actions;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.ding.DingNetworkView;
+
+import cytoscape.giny.*;
+
+import cytoscape.util.CytoscapeAction;
+
+import cytoscape.view.CyNetworkView;
+
+import org.freehep.util.export.ExportDialog;
+
+//-------------------------------------------------------------------------
+import java.awt.event.ActionEvent;
+import java.awt.print.PageFormat;
+import java.awt.print.PrinterJob;
+
+import javax.swing.AbstractAction;
+
+
+//-------------------------------------------------------------------------
+/**
+ *
+ */
+public class ExportAction extends CytoscapeAction {
+ /**
+ *
+ */
+ public final static String MENU_LABEL = "Export as...";
+
+ /**
+ * Creates a new ExportAction object.
+ */
+ public ExportAction() {
+ super(MENU_LABEL);
+ setPreferredMenu("File");
+ setAcceleratorCombo(java.awt.event.KeyEvent.VK_P,
+ ActionEvent.CTRL_MASK | ActionEvent.SHIFT_MASK);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ // ( (Phoeb*NetworkView)Cytoscape.getCurrentNetworkView() ).getCanvas().getCamera().addClientProperty( PrintingFixTextNode.PRINTING_CLIENT_PROPERTY_KEY, "true");
+ ExportDialog export = new ExportDialog();
+ export.showExportDialog(((DingNetworkView) Cytoscape.getCurrentNetworkView()).getComponent(),
+ "Export view as ...",
+ ((DingNetworkView) Cytoscape.getCurrentNetworkView()).getComponent(),
+ "export");
+
+ // ( (DingNetworkView)Cytoscape.getCurrentNetworkView() ).getCanvas().getCamera().addClientProperty( PrintingFixTextNode.PRINTING_CLIENT_PROPERTY_KEY, null);
+ } // actionPerformed
+}
diff --git a/application/src/main/java/cytoscape/actions/ExportAsGMLAction.java b/application/src/main/java/cytoscape/actions/ExportAsGMLAction.java
new file mode 100644
index 0000000..c1cad98
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/ExportAsGMLAction.java
@@ -0,0 +1,266 @@
+/*
+ File: ExportAsGMLAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// $Revision: 19168 $
+// $Date: 2010-02-04 00:14:58 +0100 (Thu, 04 Feb 2010) $
+// $Author: pwang $
+
+// $Revision: 19168 $
+// $Date: 2010-02-04 00:14:58 +0100 (Thu, 04 Feb 2010) $
+// $Author: pwang $
+package cytoscape.actions;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+
+import cytoscape.data.readers.GMLParser;
+import cytoscape.data.readers.GMLReader;
+import cytoscape.data.readers.GMLWriter;
+
+import cytoscape.task.Task;
+import cytoscape.task.TaskMonitor;
+
+import cytoscape.task.ui.JTaskConfig;
+
+import cytoscape.task.util.TaskManager;
+
+import cytoscape.util.CyFileFilter;
+import cytoscape.util.CytoscapeAction;
+import cytoscape.util.FileUtil;
+
+import cytoscape.view.CyNetworkView;
+
+import java.awt.event.ActionEvent;
+
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+
+import java.util.List;
+import java.util.Vector;
+
+import javax.swing.event.MenuEvent;
+
+/**
+ *
+ */
+public class ExportAsGMLAction extends CytoscapeAction {
+ /**
+ * Creates a new ExportAsGMLAction object.
+ */
+ public ExportAsGMLAction() {
+ super("Network as GML...");
+ setPreferredMenu("File.Export");
+ }
+
+ /**
+ * Creates a new ExportAsGMLAction object.
+ *
+ * @param label DOCUMENT ME!
+ */
+ public ExportAsGMLAction(boolean label) {
+ super();
+ }
+
+ /**
+ * User-initiated action to save the current network in GML format to a
+ * user-specified file. If successfully saved, fires a PropertyChange event
+ * with property=Cytoscape.NETWORK_SAVED, old_value=null, and new_value=a
+ * three element Object array containing:
+ * <OL>
+ * <LI>first element = CyNetwork saved
+ * <LI>second element = URI of the location where saved
+ * <LI>third element = an Integer representing the format in which the
+ * Network was saved (e.g., Cytoscape.FILE_GML).
+ * </OL>
+ *
+ * @param e
+ * ActionEvent Object.
+ */
+ public void actionPerformed(ActionEvent e) {
+ String name;
+
+ try {
+
+ CyFileFilter cyFileFilter = new CyFileFilter("gml");
+
+ String suggestedFileName = Cytoscape.getCurrentNetwork().getIdentifier();
+ if (!suggestedFileName.endsWith(".gml")){
+ suggestedFileName = suggestedFileName+ ".gml";
+ }
+
+ File suggestedFile = new File(suggestedFileName);
+
+ name = FileUtil.getFile("Export Network as GML", FileUtil.SAVE, cyFileFilter, suggestedFile)
+ .toString();
+ } catch (Exception exp) {
+ // this is because the selection was canceled
+ return;
+ }
+
+ if (!name.endsWith(".gml"))
+ name = name + ".gml";
+
+ // Get Current Network and View
+ CyNetwork network = Cytoscape.getCurrentNetwork();
+ CyNetworkView view = Cytoscape.getCurrentNetworkView();
+
+ // Create Task
+ ExportAsGMLTask task = new ExportAsGMLTask(name, network, view);
+
+ // Configure JTask Dialog Pop-Up Box
+ JTaskConfig jTaskConfig = new JTaskConfig();
+ jTaskConfig.setOwner(Cytoscape.getDesktop());
+ jTaskConfig.displayCloseButton(true);
+ jTaskConfig.displayStatus(true);
+ jTaskConfig.setAutoDispose(false);
+
+ // Execute Task in New Thread; pop open JTask Dialog Box.
+ TaskManager.executeTask(task, jTaskConfig);
+ }
+
+ public void menuSelected(MenuEvent e) {
+ enableForNetwork();
+ }
+
+}
+
+
+/**
+ * Task to Save Graph Data to GML Format.
+ */
+class ExportAsGMLTask implements Task {
+ private String fileName;
+ private CyNetwork network;
+ private CyNetworkView view;
+ private TaskMonitor taskMonitor;
+
+ /**
+ * Constructor.
+ *
+ * @param network
+ * Network Object.
+ * @param view
+ * Network View Object.
+ */
+ ExportAsGMLTask(String fileName, CyNetwork network, CyNetworkView view) {
+ this.fileName = fileName;
+ this.network = network;
+ this.view = view;
+ }
+
+ /**
+ * Executes Task
+ */
+ public void run() {
+ taskMonitor.setStatus("Saving Network...");
+ taskMonitor.setPercentCompleted(-1);
+
+ try {
+ int numNodes = network.getNodeCount();
+
+ if (numNodes == 0) {
+ throw new IllegalArgumentException("Network is empty.");
+ }
+
+ saveGraph();
+ taskMonitor.setPercentCompleted(100);
+ taskMonitor.setStatus("Network successfully saved to: " + fileName);
+ } catch (IllegalArgumentException e) {
+ taskMonitor.setException(e, "Network is Empty. Cannot be saved.");
+ } catch (IOException e) {
+ taskMonitor.setException(e, "Unable to save network.");
+ }
+ }
+
+ /**
+ * Halts the Task: Not Currently Implemented.
+ */
+ public void halt() {
+ // Task can not currently be halted.
+ }
+
+ /**
+ * Sets the Task Monitor.
+ *
+ * @param taskMonitor
+ * TaskMonitor Object.
+ */
+ public void setTaskMonitor(TaskMonitor taskMonitor) throws IllegalThreadStateException {
+ this.taskMonitor = taskMonitor;
+ }
+
+ /**
+ * Gets the Task Title.
+ *
+ * @return Task Title.
+ */
+ public String getTitle() {
+ return new String("Saving Network");
+ }
+
+ /**
+ * Saves Graph to File.
+ *
+ * @throws IOException
+ * Error Writing to File.
+ */
+ private void saveGraph() throws IOException {
+ FileWriter fileWriter = null;
+ List list = new Vector();
+
+ try {
+ fileWriter = new FileWriter(fileName);
+
+ GMLWriter gmlWriter = new GMLWriter();
+ gmlWriter.writeGML(network, view, list);
+ GMLParser.printList(list, fileWriter);
+ }
+ finally {
+ if (fileWriter != null) {
+ fileWriter.close();
+ }
+ }
+
+ Object[] ret_val = new Object[3];
+ ret_val[0] = network;
+ ret_val[1] = new File(fileName).toURI();
+ ret_val[2] = new Integer(Cytoscape.FILE_GML);
+ Cytoscape.firePropertyChange(Cytoscape.NETWORK_SAVED, null, ret_val);
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/actions/ExportAsGraphicsAction.java b/application/src/main/java/cytoscape/actions/ExportAsGraphicsAction.java
new file mode 100644
index 0000000..4c931fe
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/ExportAsGraphicsAction.java
@@ -0,0 +1,277 @@
+package cytoscape.actions;
+
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.KeyEvent;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.util.Set;
+
+import javax.swing.JOptionPane;
+import javax.swing.event.MenuEvent;
+
+import cytoscape.Cytoscape;
+import cytoscape.dialogs.ExportAsGraphicsFileChooser;
+import cytoscape.dialogs.ExportBitmapOptionsDialog;
+import cytoscape.logger.CyLogger;
+import cytoscape.task.Task;
+import cytoscape.task.TaskMonitor;
+import cytoscape.task.ui.JTaskConfig;
+import cytoscape.task.util.TaskManager;
+import cytoscape.util.CyFileFilter;
+import cytoscape.util.CytoscapeAction;
+import cytoscape.util.export.BitmapExporter;
+import cytoscape.util.export.Exporter;
+import cytoscape.util.export.PDFExporter;
+import cytoscape.util.export.PSExporter;
+import cytoscape.util.export.SVGExporter;
+import cytoscape.view.CyNetworkView;
+import cytoscape.view.InternalFrameComponent;
+
+/**
+ * Action for exporting a network view to bitmap or vector graphics.
+ *
+ * @author Samad Lotia
+ */
+public class ExportAsGraphicsAction extends CytoscapeAction {
+
+ private static final long serialVersionUID = -5887102279435784342L;
+
+ private static final ExportFilter BMP_FILTER = new BitmapExportFilter("bmp", "BMP");
+ private static final ExportFilter JPG_FILTER = new BitmapExportFilter("jpg", "JPEG");
+ private static final ExportFilter PDF_FILTER = new PDFExportFilter();
+ private static final ExportFilter PNG_FILTER = new BitmapExportFilter("png", "PNG");
+ private static final ExportFilter SVG_FILTER = new SVGExportFilter();
+ private static final ExportFilter EPS_FILTER = new PSExportFilter("eps","EPS");
+
+ private final static ExportFilter[] FILTERS = { PDF_FILTER, SVG_FILTER,
+ EPS_FILTER, JPG_FILTER, PNG_FILTER, BMP_FILTER };
+
+ static final CyLogger logger = CyLogger.getLogger(ExportAsGraphicsAction.class);
+
+ private static final String TITLE = "Current Network View as Graphics";
+
+ private ExportAsGraphicsFileChooser chooser;
+ private String defaultFileExt;
+
+ public ExportAsGraphicsAction() {
+ this("PDF");
+ }
+
+
+ public ExportAsGraphicsAction(final String fileExtension) {
+ super(TITLE + "...");
+ setPreferredMenu("File.Export");
+ setAcceleratorCombo(KeyEvent.VK_P, ActionEvent.CTRL_MASK
+ | ActionEvent.SHIFT_MASK);
+
+ this.defaultFileExt = fileExtension;
+ }
+
+
+ private ExportFilter getFilter(final String ext) {
+ for(ExportFilter filter: FILTERS) {
+ final Set<String> exts = filter.getExtensionSet();
+ for(String ex: exts) {
+ if(ex.equalsIgnoreCase(ext))
+ return filter;
+ }
+ }
+
+ return null;
+ }
+
+
+ public void menuSelected(MenuEvent e) {
+ enableForNetworkAndView();
+ }
+
+
+ public void actionPerformed(ActionEvent e) {
+
+ final CyNetworkView v = Cytoscape.getCurrentNetworkView();
+ if (v == null || v == Cytoscape.getNullNetworkView()) {
+ logger.error("No network view exists to export!");
+ return;
+ }
+
+ final ExportFilter filter = getFilter(defaultFileExt);
+ if(filter == null)
+ chooser = new ExportAsGraphicsFileChooser(FILTERS, PDF_FILTER);
+ else
+ chooser = new ExportAsGraphicsFileChooser(FILTERS, filter);
+
+
+ final ActionListener listener = new ActionListener() {
+ public void actionPerformed(ActionEvent event) {
+ ExportFilter filter = (ExportFilter) chooser.getSelectedFormat();
+ filter.setExportTextAsFont(chooser.getExportTextAsFont());
+
+ File file = chooser.getSelectedFile();
+
+ chooser.dispose();
+
+ FileOutputStream stream = null;
+ try {
+ stream = new FileOutputStream(file);
+ } catch (Exception exp) {
+ JOptionPane.showMessageDialog(Cytoscape.getDesktop(),
+ "Could not create file " + file.getName()
+ + "\n\nError: " + exp.getMessage());
+ return;
+ }
+ final CyNetworkView view = Cytoscape.getCurrentNetworkView();
+ filter.export(view, stream);
+ }
+ };
+ chooser.addActionListener(listener);
+ chooser.setVisible(true);
+ }
+}
+
+class ExportTask {
+ public static void run(final String title, final Exporter exporter,
+ final CyNetworkView view, final FileOutputStream stream) {
+ // Create the Task
+ Task task = new Task() {
+ TaskMonitor monitor;
+
+ public String getTitle() {
+ return title;
+ }
+
+ public void setTaskMonitor(TaskMonitor monitor) {
+ this.monitor = monitor;
+ }
+
+ public void halt() {
+ }
+
+ public void run() {
+ try {
+ try {
+ exporter.export(view, stream);
+ } catch (Exception e) {
+ monitor.setException(e,
+ "Could not complete export of network");
+ }
+ } finally {
+ if (stream != null) {
+ try {
+ stream.close();
+ } catch (IOException ioe) {
+ ExportAsGraphicsAction.logger.warn(
+ "Unable to close the stream: "
+ + ioe.getMessage(), ioe);
+ }
+ }
+ }
+ }
+ };
+
+ // Execute the task
+ final JTaskConfig jTaskConfig = new JTaskConfig();
+ jTaskConfig.displayCancelButton(false);
+ jTaskConfig.displayCloseButton(false);
+ jTaskConfig.displayStatus(false);
+ jTaskConfig.displayTimeElapsed(true);
+ jTaskConfig.displayTimeRemaining(false);
+ jTaskConfig.setAutoDispose(true);
+ jTaskConfig.setModal(true);
+ jTaskConfig.setOwner(Cytoscape.getDesktop());
+ TaskManager.executeTask(task, jTaskConfig);
+ }
+}
+
+abstract class ExportFilter extends CyFileFilter {
+
+ protected boolean exportTextAsFont = false;
+
+ public ExportFilter(String extension, String description) {
+ super(extension, description);
+ }
+
+ public boolean isExtensionListInDescription() {
+ return true;
+ }
+
+ public String toString() {
+ return getDescription();
+ }
+
+ public void setExportTextAsFont(boolean pExportTextAsFont) {
+ exportTextAsFont = pExportTextAsFont;
+ }
+
+ public boolean getExportTextAsFont() {
+ return exportTextAsFont;
+ }
+
+ public abstract void export(CyNetworkView view, FileOutputStream stream);
+}
+
+class PDFExportFilter extends ExportFilter {
+ public PDFExportFilter() {
+ super("pdf", "PDF");
+ }
+
+ public void export(final CyNetworkView view, final FileOutputStream stream) {
+ PDFExporter exporter = new PDFExporter();
+ exporter.setExportTextAsFont(this.getExportTextAsFont());
+ ExportTask.run("Exporting to PDF", exporter, view, stream);
+ }
+}
+
+class BitmapExportFilter extends ExportFilter {
+
+ private final String extension;
+
+ public BitmapExportFilter(String extension, String description) {
+ super(extension, description);
+ this.extension = extension;
+ }
+
+ public void export(final CyNetworkView view, final FileOutputStream stream) {
+
+
+ final InternalFrameComponent ifc = Cytoscape.getDesktop()
+ .getNetworkViewManager().getInternalFrameComponent(view);
+ final ExportBitmapOptionsDialog dialog = new ExportBitmapOptionsDialog(ifc.getWidth(), ifc.getHeight());
+
+ ActionListener listener = new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ BitmapExporter exporter = new BitmapExporter(extension, dialog.getZoom());
+ dialog.dispose();
+ ExportTask.run("Exporting to " + extension, exporter, view,
+ stream);
+ }
+ };
+ dialog.addActionListener(listener);
+ dialog.setVisible(true);
+ }
+}
+
+class SVGExportFilter extends ExportFilter {
+ public SVGExportFilter() {
+ super("svg", "SVG");
+ }
+
+ public void export(final CyNetworkView view, final FileOutputStream stream) {
+ final SVGExporter exporter = new SVGExporter();
+ exporter.setExportTextAsFont(this.getExportTextAsFont());
+ ExportTask.run("Exporting to SVG", exporter, view, stream);
+ }
+}
+
+class PSExportFilter extends ExportFilter {
+ public PSExportFilter(String extension, String description) {
+ super(extension, description);
+ }
+
+ public void export(final CyNetworkView view, final FileOutputStream stream) {
+ final PSExporter exporter = new PSExporter();
+ exporter.setExportTextAsFont(this.getExportTextAsFont());
+ ExportTask.run("Exporting to EPS", exporter, view, stream);
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/ExportAsInteractionsAction.java b/application/src/main/java/cytoscape/actions/ExportAsInteractionsAction.java
new file mode 100644
index 0000000..91536be
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/ExportAsInteractionsAction.java
@@ -0,0 +1,227 @@
+/*
+ File: ExportAsInteractionsAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// $Revision: 19167 $
+// $Date: 2010-02-03 23:58:10 +0100 (Wed, 03 Feb 2010) $
+// $Author: pwang $
+package cytoscape.actions;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+
+import cytoscape.data.CyAttributes;
+import cytoscape.data.Semantics;
+
+import cytoscape.data.writers.InteractionWriter;
+
+import cytoscape.task.Task;
+import cytoscape.task.TaskMonitor;
+
+import cytoscape.task.ui.JTaskConfig;
+
+import cytoscape.task.util.TaskManager;
+
+import cytoscape.util.CyFileFilter;
+import cytoscape.util.CytoscapeAction;
+import cytoscape.util.FileUtil;
+
+import java.awt.event.ActionEvent;
+
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+
+import java.util.Iterator;
+import java.util.List;
+
+import javax.swing.event.MenuEvent;
+
+
+/**
+ * write out the current graph to the specified file, using the standard
+ * interactions format: nodeA edgeType nodeB.
+ * for example: <code>
+ * <p/>
+ * YMR056C pp YLL013C
+ * YCR107W pp YBR265W
+ * <p/>
+ * </code>
+ */
+public class ExportAsInteractionsAction extends CytoscapeAction {
+ /**
+ * Constructor.
+ */
+ public ExportAsInteractionsAction() {
+ super("Network as SIF File...");
+ setPreferredMenu("File.Export");
+ }
+
+ // MLC 09/19/05 BEGIN:
+ /**
+ * User-initiated action to save the current network in SIF format
+ * to a user-specified file. If successfully saved, fires a
+ * PropertyChange event with property=Cytoscape.NETWORK_SAVED,
+ * old_value=null, and new_value=a three element Object array containing:
+ * <OL>
+ * <LI>first element = CyNetwork saved
+ * <LI>second element = URI of the location where saved
+ * <LI>third element = an Integer representing the format in which the
+ * Network was saved (e.g., Cytoscape.FILE_SIF).
+ * </OL>
+ * @param e ActionEvent Object.
+ */
+
+ // MLC 09/19/05 END.
+ public void actionPerformed(ActionEvent e) {
+
+ CyFileFilter cyFileFilter = new CyFileFilter("sif");
+
+ String suggestedFileName = Cytoscape.getCurrentNetwork().getIdentifier();
+ if (!suggestedFileName.endsWith(".sif")){
+ suggestedFileName = suggestedFileName+ ".sif";
+ }
+
+ File suggestedFile = new File(suggestedFileName);
+
+ // get the file name
+ File file = FileUtil.getFile("Save Network as Interactions", FileUtil.SAVE, cyFileFilter, suggestedFile);
+
+ if (file != null) {
+ String fileName = file.getAbsolutePath();
+
+ if (!fileName.endsWith(".sif"))
+ fileName = fileName + ".sif";
+
+ // Create LoadNetwork Task
+ SaveAsSifTask task = new SaveAsSifTask(fileName);
+
+ // Configure JTask Dialog Pop-Up Box
+ JTaskConfig jTaskConfig = new JTaskConfig();
+ jTaskConfig.setOwner(Cytoscape.getDesktop());
+ jTaskConfig.displayCloseButton(true);
+ jTaskConfig.displayStatus(true);
+ jTaskConfig.setAutoDispose(false);
+
+ // Execute Task in New Thread; pop open JTask Dialog Box.
+ TaskManager.executeTask(task, jTaskConfig);
+ }
+ }
+
+ public void menuSelected(MenuEvent e) {
+ enableForNetwork();
+ }
+}
+
+
+/**
+ * Task to Save Graph Data to SIF Format.
+ */
+class SaveAsSifTask implements Task {
+ private String fileName;
+ private TaskMonitor taskMonitor;
+
+ /**
+ * Constructor.
+ * @param fileName Filename to save to
+ */
+ SaveAsSifTask(String fileName) {
+ this.fileName = fileName;
+ }
+
+ /**
+ * Executes the Task.
+ */
+ public void run() {
+ taskMonitor.setStatus("Saving Interactions...");
+
+ try {
+ if (Cytoscape.getCurrentNetwork().getNodeCount() == 0) {
+ throw new IllegalArgumentException("Network is empty.");
+ }
+
+ CyNetwork netToSave = Cytoscape.getCurrentNetwork();
+ FileWriter f = null;
+ try {
+ f = new FileWriter(fileName);
+ InteractionWriter.writeInteractions(netToSave, f, taskMonitor);
+ }
+ finally {
+ if (f != null) {
+ f.close();
+ }
+ }
+
+ Object[] ret_val = new Object[3];
+ ret_val[0] = netToSave;
+ ret_val[1] = new File(fileName).toURI();
+ ret_val[2] = new Integer(Cytoscape.FILE_SIF);
+ Cytoscape.firePropertyChange(Cytoscape.NETWORK_SAVED, null, ret_val);
+
+ taskMonitor.setPercentCompleted(100);
+ taskMonitor.setStatus("Network successfully saved to: " + fileName);
+ } catch (IllegalArgumentException e) {
+ taskMonitor.setException(e, "Network is Empty. Cannot be saved.");
+ } catch (IOException e) {
+ taskMonitor.setException(e, "Unable to save network.");
+ }
+ }
+
+ /**
+ * Halts the Task: Not Currently Implemented.
+ */
+ public void halt() {
+ // Task can not currently be halted.
+ }
+
+ /**
+ * Sets the Task Monitor.
+ *
+ * @param taskMonitor TaskMonitor Object.
+ */
+ public void setTaskMonitor(TaskMonitor taskMonitor) throws IllegalThreadStateException {
+ this.taskMonitor = taskMonitor;
+ }
+
+ /**
+ * Gets the Task Title.
+ *
+ * @return Task Title.
+ */
+ public String getTitle() {
+ return new String("Saving Network");
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/ExportAsXGMMLAction.java b/application/src/main/java/cytoscape/actions/ExportAsXGMMLAction.java
new file mode 100644
index 0000000..5dd9787
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/ExportAsXGMMLAction.java
@@ -0,0 +1,286 @@
+/*
+ File: ExportAsXGMMLAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.actions;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import cytoscape.logger.CyLogger;
+
+import cytoscape.data.writers.XGMMLWriter;
+
+import cytoscape.task.Task;
+import cytoscape.task.TaskMonitor;
+
+import cytoscape.task.ui.JTaskConfig;
+
+import cytoscape.task.util.TaskManager;
+
+import cytoscape.util.CyFileFilter;
+import cytoscape.util.CytoscapeAction;
+import cytoscape.util.FileUtil;
+
+import cytoscape.view.CyNetworkView;
+
+import java.awt.event.ActionEvent;
+
+import java.io.File;
+import java.io.FileWriter;
+import java.io.FileOutputStream;
+import java.io.OutputStreamWriter;
+import java.io.IOException;
+
+import java.net.URISyntaxException;
+
+import java.util.Set;
+
+import javax.swing.JOptionPane;
+
+import javax.swing.event.MenuEvent;
+
+import javax.xml.bind.JAXBException;
+import javax.xml.stream.FactoryConfigurationError;
+import javax.xml.stream.XMLStreamException;
+
+
+/**
+ * This action is for exporting network and attributes in XGMML file.
+ *
+ * @author kono
+ *
+ */
+public class ExportAsXGMMLAction extends CytoscapeAction {
+ /**
+ * Creates a new ExportAsXGMMLAction object.
+ */
+ public ExportAsXGMMLAction() {
+ super("Network and Attributes as XGMML...");
+ setPreferredMenu("File.Export");
+ }
+
+ /**
+ * Creates a new ExportAsXGMMLAction object.
+ *
+ * @param label DOCUMENT ME!
+ */
+ public ExportAsXGMMLAction(boolean label) {
+ super();
+ }
+
+ protected boolean checkNetworkCount() {
+ Set networks = Cytoscape.getNetworkSet();
+
+ if (networks.size() == 0) {
+ JOptionPane.showMessageDialog(Cytoscape.getDesktop(), "No network in this session!",
+ "No network Error", JOptionPane.INFORMATION_MESSAGE);
+
+ return false;
+ } else {
+ return true;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ if (checkNetworkCount() == false)
+ return;
+
+ // Create FileFilters
+ CyFileFilter xgmmlFilter = new CyFileFilter();
+ CyFileFilter xmlFilter = new CyFileFilter();
+ CyFileFilter graphFilter = new CyFileFilter();
+ // Add accepted File Extensions
+ xgmmlFilter.addExtension("xgmml");
+ xgmmlFilter.setDescription("XGMML files");
+ xmlFilter.addExtension("xml");
+ xmlFilter.setDescription("XML files");
+ graphFilter.addExtension("xgmml");
+ graphFilter.addExtension("xml");
+ graphFilter.setDescription("All xml-based network files");
+
+ // XGMML file name
+ String name;
+
+ try {
+ name = FileUtil.getFile("Export Network and Attributes as XGMML", FileUtil.SAVE,
+ new CyFileFilter[] { xgmmlFilter, xmlFilter, graphFilter })
+ .toString();
+ } catch (Exception exp) {
+ // this is because the selection was canceled
+ return;
+ }
+
+ if (!name.endsWith(".xgmml"))
+ name = name + ".xgmml";
+
+ // Get Current Network and View
+ final CyNetwork network = Cytoscape.getCurrentNetwork();
+ final CyNetworkView view = Cytoscape.getNetworkView(network.getIdentifier());
+
+ // Create Task
+ final ExportAsXGMMLTask task = new ExportAsXGMMLTask(name, network, view);
+
+ // Configure JTask Dialog Pop-Up Box
+ final JTaskConfig jTaskConfig = new JTaskConfig();
+ jTaskConfig.setOwner(Cytoscape.getDesktop());
+ jTaskConfig.displayCloseButton(true);
+ jTaskConfig.displayStatus(true);
+ jTaskConfig.setAutoDispose(false);
+
+ // Execute Task in New Thread; pop open JTask Dialog Box.
+ TaskManager.executeTask(task, jTaskConfig);
+ }
+
+ public void menuSelected(MenuEvent e) {
+ enableForNetwork();
+ }
+}
+
+
+/**
+ * Task to Save Graph Data to XGMML Format.
+ */
+class ExportAsXGMMLTask implements Task {
+ private String fileName;
+ private CyNetwork network;
+ private CyNetworkView view;
+ private TaskMonitor taskMonitor;
+
+ /**
+ * Constructor.
+ *
+ * @param network
+ * Network Object.
+ * @param view
+ * Network View Object.
+ */
+ public ExportAsXGMMLTask(String fileName, CyNetwork network, CyNetworkView view) {
+ this.fileName = fileName;
+ this.network = network;
+ this.view = view;
+ }
+
+ /**
+ * Executes Task
+ *
+ * @throws Exception
+ */
+ public void run() {
+ taskMonitor.setStatus("Exporting Network and Attributes...");
+ taskMonitor.setPercentCompleted(-1);
+
+ int numNodes = network.getNodeCount();
+
+ // if (numNodes == 0) {
+ // throw new IllegalArgumentException("Network is empty.");
+ // }
+
+ try {
+ saveGraph();
+ } catch (Exception e) {
+ taskMonitor.setException(e, "Cannot export graph as XGMML.");
+ }
+
+ taskMonitor.setPercentCompleted(100);
+ taskMonitor.setStatus("Network and attributes are successfully saved to: " + fileName);
+
+ CyLogger.getLogger().info("Network and attributes are exported as an XGMML file: " + fileName);
+ }
+
+ /**
+ * Halts the Task: Not Currently Implemented.
+ */
+ public void halt() {
+ // Task can not currently be halted.
+ }
+
+ /**
+ * Sets the Task Monitor.
+ *
+ * @param taskMonitor
+ * TaskMonitor Object.
+ */
+ public void setTaskMonitor(TaskMonitor taskMonitor) throws IllegalThreadStateException {
+ this.taskMonitor = taskMonitor;
+ }
+
+ /**
+ * Gets the Task Title.
+ *
+ * @return Task Title.
+ */
+ public String getTitle() {
+ return new String("Exporting Network and Attributes");
+ }
+
+ /**
+ * Saves Graph to File.
+ *
+ * @throws IOException
+ * @throws JAXBException
+ * @throws URISyntaxException
+ * @throws FactoryConfigurationError
+ * @throws XMLStreamException
+ */
+ private void saveGraph()
+ throws IOException, JAXBException, URISyntaxException, XMLStreamException,
+ FactoryConfigurationError {
+ // final FileWriter fileWriter = new FileWriter(fileName);
+ OutputStreamWriter fileWriter = null;
+
+ try {
+ fileWriter = new OutputStreamWriter(new FileOutputStream(fileName), "UTF-8");
+ final XGMMLWriter writer = new XGMMLWriter(network, view);
+
+ writer.write(fileWriter);
+ } finally {
+ if (fileWriter != null) {
+ fileWriter.close();
+ }
+ }
+
+ final Object[] ret_val = new Object[3];
+ ret_val[0] = network;
+ ret_val[1] = new File(fileName).toURI();
+ ret_val[2] = new Integer(Cytoscape.FILE_XGMML);
+
+ Cytoscape.firePropertyChange(Cytoscape.NETWORK_SAVED, null, ret_val);
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/ExportEdgeAttributesAction.java b/application/src/main/java/cytoscape/actions/ExportEdgeAttributesAction.java
new file mode 100644
index 0000000..0f9a022
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/ExportEdgeAttributesAction.java
@@ -0,0 +1,68 @@
+/*
+ File: ExportEdgeAttributesAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.actions;
+
+import cytoscape.data.AttributeSaverDialog;
+
+import cytoscape.util.CytoscapeAction;
+
+// -------------------------------------------------------------------------
+import java.awt.event.ActionEvent;
+
+
+// -------------------------------------------------------------------------
+/**
+ *
+ */
+public class ExportEdgeAttributesAction extends CytoscapeAction {
+ /**
+ * Creates a new ExportEdgeAttributesAction object.
+ */
+ public ExportEdgeAttributesAction() {
+ super("Edge Attributes");
+ setPreferredMenu("File.Export");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ AttributeSaverDialog.showEdgeDialog();
+ }
+} // SaveAsGMLAction
diff --git a/application/src/main/java/cytoscape/actions/ExportNetworksAsNNFAction.java b/application/src/main/java/cytoscape/actions/ExportNetworksAsNNFAction.java
new file mode 100644
index 0000000..764a4dd
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/ExportNetworksAsNNFAction.java
@@ -0,0 +1,283 @@
+/*
+ File: ExportNetworksAsNNFAction.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.actions;
+
+
+import cytoscape.CyEdge;
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+import cytoscape.logger.CyLogger;
+
+import cytoscape.data.CyAttributes;
+import cytoscape.data.Semantics;
+import cytoscape.data.writers.XGMMLWriter;
+
+import cytoscape.task.Task;
+import cytoscape.task.TaskMonitor;
+
+import cytoscape.task.ui.JTaskConfig;
+
+import cytoscape.task.util.TaskManager;
+
+import cytoscape.util.CyFileFilter;
+import cytoscape.util.CytoscapeAction;
+import cytoscape.util.FileUtil;
+
+import java.awt.event.ActionEvent;
+
+import java.io.BufferedWriter;
+import java.io.FileWriter;
+import java.io.IOException;
+
+import java.net.URISyntaxException;
+
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import javax.swing.JOptionPane;
+
+import javax.swing.event.MenuEvent;
+
+
+/**
+ * This action is for exporting network and attributes in XGMML file.
+ *
+ * @author kono
+ *
+ */
+public class ExportNetworksAsNNFAction extends CytoscapeAction {
+ /**
+ * Creates a new ExportNetworksAsNNFAction object.
+ */
+ public ExportNetworksAsNNFAction() {
+ super("Networks as NNF File...");
+ setPreferredMenu("File.Export");
+ }
+
+ /**
+ * Creates a new ExportNetworksAsNNFAction object.
+ *
+ * @param label DOCUMENT ME!
+ */
+ public ExportNetworksAsNNFAction(boolean label) {
+ super();
+ }
+
+ protected boolean checkNetworkCount() {
+ final Set<CyNetwork> networks = Cytoscape.getNetworkSet();
+ if (networks.isEmpty()) {
+ JOptionPane.showMessageDialog(Cytoscape.getDesktop(), "No networks in this session!",
+ "No network Error", JOptionPane.INFORMATION_MESSAGE);
+ return false;
+ } else
+ return true;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ if (!checkNetworkCount())
+ return;
+
+ // Create FileFilters
+ CyFileFilter filter = new CyFileFilter("nnf");
+ filter.setDescription("All NNF network files");
+
+ String fileName;
+ try {
+ fileName = FileUtil.getFile("Export Networks as NNF", FileUtil.SAVE, new CyFileFilter[] { filter }).toString();
+ } catch (Exception exp) {
+ // this is because the selection was cancelled
+ return;
+ }
+
+ if (!fileName.endsWith(".nnf"))
+ fileName = fileName + ".nnf";
+
+ final BufferedWriter output;
+ try {
+ output = new BufferedWriter(new FileWriter(fileName));
+ } catch (final IOException ioe) {
+ JOptionPane.showMessageDialog(Cytoscape.getDesktop(), "Could not open file: " + ioe.getMessage(),
+ "Error", JOptionPane.ERROR_MESSAGE);
+ return;
+ }
+
+ // Create Task
+ final ExportAsNNFTask task = new ExportAsNNFTask(fileName, output);
+
+ // Configure JTask Dialog Pop-Up Box
+ final JTaskConfig jTaskConfig = new JTaskConfig();
+ jTaskConfig.setOwner(Cytoscape.getDesktop());
+ jTaskConfig.displayCloseButton(true);
+ jTaskConfig.displayStatus(true);
+ jTaskConfig.setAutoDispose(false);
+
+ // Execute Task in New Thread; pop open JTask Dialog Box.
+ TaskManager.executeTask(task, jTaskConfig);
+ }
+
+ public void menuSelected(MenuEvent e) {
+ enableForNetwork();
+ }
+}
+
+
+/**
+ * Task to Save Graph Data to NNF Format.
+ */
+class ExportAsNNFTask implements Task {
+ private final String fileName;
+ private final BufferedWriter output;
+ private TaskMonitor taskMonitor;
+
+ /**
+ * Constructor.
+ *
+ * @param network
+ * Network Object.
+ * @param view
+ * Network View Object.
+ */
+ public ExportAsNNFTask(final String fileName, final BufferedWriter output) {
+ this.fileName = fileName;
+ this.output = output;
+ }
+
+ /**
+ * Executes Task
+ *
+ * @throws Exception
+ */
+ public void run() {
+ taskMonitor.setStatus("Exporting Networks...");
+ taskMonitor.setPercentCompleted(0);
+
+ final Set<CyNetwork> networks = Cytoscape.getNetworkSet();
+ final float networkCount = networks.size();
+ try {
+ float writtenCount = 0.0f;
+ for (final CyNetwork network : networks) {
+ writeNetwork(network);
+ ++writtenCount;
+ taskMonitor.setPercentCompleted(Math.round(writtenCount / networkCount));
+ }
+ } catch (Exception e) {
+ taskMonitor.setException(e, "Cannot export networks as NNF.");
+ }
+
+ try {
+ output.close();
+ } catch (Exception e) {
+ // Intentionally empty!
+ }
+
+ taskMonitor.setPercentCompleted(100);
+ taskMonitor.setStatus("Networks have been successfully saved to: " + fileName);
+
+ CyLogger.getLogger().info("Networks have been exported as an NNF file: " + fileName);
+ }
+
+ /**
+ * Halts the Task: Not Currently Implemented.
+ */
+ public void halt() {
+ // Task can not currently be halted.
+ }
+
+ /**
+ * Sets the Task Monitor.
+ *
+ * @param taskMonitor
+ * TaskMonitor Object.
+ */
+ public void setTaskMonitor(TaskMonitor taskMonitor) throws IllegalThreadStateException {
+ this.taskMonitor = taskMonitor;
+ }
+
+ /**
+ * Gets the Task Title.
+ *
+ * @return Task Title.
+ */
+ public String getTitle() {
+ return new String("Exporting Networks");
+ }
+
+ private void writeNetwork(final CyNetwork network) throws IOException {
+ final String title = network.getTitle();
+
+ final CyAttributes edgeAttrs = Cytoscape.getEdgeAttributes();
+ final Set<String> encounteredNodes = new HashSet<String>();
+
+ final List<CyEdge> edges = (List<CyEdge>)network.edgesList();
+ for (final CyEdge edge : edges) {
+ output.write(escapeID(title) + " ");
+
+ final String sourceID = ((CyNode)edge.getSource()).getIdentifier();
+ encounteredNodes.add(sourceID);
+ output.write(escapeID(sourceID) + " ");
+
+ String interactionName = edgeAttrs.getStringAttribute(edge.getIdentifier(),
+ Semantics.INTERACTION);
+ if (interactionName == null)
+ interactionName = "xx";
+ output.write(escapeID(interactionName) + " ");
+
+ final String targetID = ((CyNode)edge.getTarget()).getIdentifier();
+ encounteredNodes.add(targetID);
+ output.write(escapeID(targetID) + "\n");
+ }
+
+ final List<CyNode> nodes = (List<CyNode>)network.nodesList();
+ for (final CyNode node : nodes) {
+ final String nodeID = node.getIdentifier();
+ if (!encounteredNodes.contains(nodeID))
+ output.write(escapeID(title) + " " + escapeID(nodeID) + "\n");
+ }
+ }
+
+ private String escapeID(final String ID) {
+ final StringBuilder builder = new StringBuilder(ID.length());
+ for (int i = 0; i < ID.length(); ++i) {
+ final char ch = ID.charAt(i);
+ if (ch == ' ' || ch == '\t' || ch == '\\')
+ builder.append('\\');
+ builder.append(ch);
+ }
+
+ return builder.toString();
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/ExportNodeAttributesAction.java b/application/src/main/java/cytoscape/actions/ExportNodeAttributesAction.java
new file mode 100644
index 0000000..b52c08e
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/ExportNodeAttributesAction.java
@@ -0,0 +1,68 @@
+/*
+ File: ExportNodeAttributesAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.actions;
+
+import cytoscape.data.AttributeSaverDialog;
+
+import cytoscape.util.CytoscapeAction;
+
+// -------------------------------------------------------------------------
+import java.awt.event.ActionEvent;
+
+
+// -------------------------------------------------------------------------
+/**
+ *
+ */
+public class ExportNodeAttributesAction extends CytoscapeAction {
+ /**
+ * Creates a new ExportNodeAttributesAction object.
+ */
+ public ExportNodeAttributesAction() {
+ super("Node Attributes");
+ setPreferredMenu("File.Export");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ AttributeSaverDialog.showNodeDialog();
+ }
+} // SaveAsGMLAction
diff --git a/application/src/main/java/cytoscape/actions/ExportVizmapAction.java b/application/src/main/java/cytoscape/actions/ExportVizmapAction.java
new file mode 100644
index 0000000..c21a4b0
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/ExportVizmapAction.java
@@ -0,0 +1,156 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.actions;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.task.Task;
+import cytoscape.task.TaskMonitor;
+
+import cytoscape.task.ui.JTaskConfig;
+
+import cytoscape.task.util.TaskManager;
+
+import cytoscape.util.CyFileFilter;
+import cytoscape.util.CytoscapeAction;
+import cytoscape.util.FileUtil;
+
+import java.awt.event.ActionEvent;
+
+
+/**
+ * Export visual styles as a vizmap.props file<br>
+ *
+ * @version 0.8
+ * @since 2.3
+ * @author kono
+ *
+ */
+public class ExportVizmapAction extends CytoscapeAction {
+ /**
+ * Creates a new ExportVizmapAction object.
+ */
+ public ExportVizmapAction() {
+ super("Vizmap Property File");
+ setPreferredMenu("File.Export");
+ }
+
+ /**
+ * Get file name and execute the saving task<br>
+ */
+ public void actionPerformed(ActionEvent e) {
+ String name;
+
+ try {
+ name = FileUtil.getFile("Export Vizmap property file", FileUtil.SAVE,
+ new CyFileFilter[] { }).toString();
+ } catch (Exception exp) {
+ // this is because the selection was canceled
+ return;
+ }
+
+ if (!name.endsWith(".props"))
+ name = name + ".props";
+
+ // Create Task
+ ExportVizmapTask task = new ExportVizmapTask(name);
+
+ // Configure JTask Dialog Pop-Up Box
+ JTaskConfig jTaskConfig = new JTaskConfig();
+ jTaskConfig.setOwner(Cytoscape.getDesktop());
+ jTaskConfig.displayCloseButton(true);
+ jTaskConfig.displayStatus(true);
+ jTaskConfig.displayCancelButton(false);
+ jTaskConfig.setAutoDispose(false);
+
+ // Execute Task in New Thread; pop open JTask Dialog Box.
+ TaskManager.executeTask(task, jTaskConfig);
+ }
+}
+
+
+/**
+ * Task to Save Graph Data to GML Format.
+ */
+class ExportVizmapTask implements Task {
+ private String fileName;
+ private TaskMonitor taskMonitor;
+
+ /**
+ * Constructor.
+ */
+ ExportVizmapTask(String fileName) {
+ this.fileName = fileName;
+ }
+
+ /**
+ * Executes Task
+ */
+ public void run() {
+ taskMonitor.setStatus("Saving Visual Styles...");
+ taskMonitor.setPercentCompleted(-1);
+
+ Cytoscape.firePropertyChange(Cytoscape.SAVE_VIZMAP_PROPS, null, fileName);
+
+ taskMonitor.setPercentCompleted(100);
+ taskMonitor.setStatus("Vizmaps successfully saved to: " + fileName);
+ }
+
+ /**
+ * Halts the Task: Not Currently Implemented.
+ */
+ public void halt() {
+ // Task can not currently be halted.
+ }
+
+ /**
+ * Sets the Task Monitor.
+ *
+ * @param taskMonitor
+ * TaskMonitor Object.
+ */
+ public void setTaskMonitor(TaskMonitor taskMonitor) throws IllegalThreadStateException {
+ this.taskMonitor = taskMonitor;
+ }
+
+ /**
+ * Gets the Task Title.
+ *
+ * @return Task Title.
+ */
+ public String getTitle() {
+ return new String("Saving Vizmap");
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/FitContentAction.java b/application/src/main/java/cytoscape/actions/FitContentAction.java
new file mode 100644
index 0000000..503c1c5
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/FitContentAction.java
@@ -0,0 +1,83 @@
+/*
+ File: FitContentAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+//-------------------------------------------------------------------------
+// $Revision: 9565 $
+// $Date: 2007-02-13 20:36:50 +0100 (Tue, 13 Feb 2007) $
+// $Author: mes $
+//-------------------------------------------------------------------------
+package cytoscape.actions;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+
+import cytoscape.ding.DingNetworkView;
+
+import cytoscape.util.CytoscapeAction;
+
+import cytoscape.view.CyNetworkView;
+
+//-------------------------------------------------------------------------
+import giny.view.*;
+
+// import cytoscape.giny.Phoeb*NetworkView;
+import java.awt.event.ActionEvent;
+
+import java.util.Iterator;
+
+
+//-------------------------------------------------------------------------
+/**
+ *
+ */
+public class FitContentAction extends CytoscapeAction {
+ /**
+ * Creates a new FitContentAction object.
+ */
+ public FitContentAction() {
+ super();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ Cytoscape.getCurrentNetworkView().fitContent();
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/GinyUtils.java b/application/src/main/java/cytoscape/actions/GinyUtils.java
new file mode 100644
index 0000000..abe8512
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/GinyUtils.java
@@ -0,0 +1,383 @@
+/*
+ File: GinyUtils.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+//-------------------------------------------------------------------------
+// $Revision: 21118 $
+// $Date: 2010-08-02 19:03:15 +0200 (Mon, 02 Aug 2010) $
+// $Author: ruschein $
+//-------------------------------------------------------------------------
+package cytoscape.actions;
+
+
+//-------------------------------------------------------------------------
+import giny.model.*;
+
+import giny.view.*;
+
+import java.util.*;
+
+
+/**
+ * Utility operations for selection and hiding/unhiding nodes and edges
+ * in a Giny GraphView. Most operations are self-explanatory.
+ */
+public class GinyUtils {
+ /**
+ * DOCUMENT ME!
+ *
+ * @param view DOCUMENT ME!
+ */
+ public static void hideSelectedNodes(GraphView view) {
+ //hides nodes and edges between them
+ if (view == null) {
+ return;
+ }
+
+ for (Iterator i = view.getSelectedNodes().iterator(); i.hasNext();) {
+ final NodeView nview = (NodeView) i.next();
+ view.hideGraphObject(nview);
+ }
+
+ view.updateView();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param view DOCUMENT ME!
+ */
+ public static void unHideSelectedNodes(GraphView view) {
+ if (view == null) {
+ return;
+ }
+
+ for (Iterator i = view.getSelectedNodes().iterator(); i.hasNext(); /* Empty! */) {
+ final NodeView nodeView = (NodeView)i.next();
+ view.showGraphObject(nodeView);
+
+ showEdges(view, nodeView);
+ }
+
+ view.updateView();
+ }
+
+ /**
+ * Shows all edges for "nodeView" found that are part of the network associated with "view".
+ */
+ public static void showEdges(final GraphView view, final NodeView nodeView) {
+ final int[] neighbours =
+ view.getGraphPerspective().neighborsArray(nodeView.getGraphPerspectiveIndex());
+
+ for (int n = 0; n < neighbours.length; ++n) {
+ final int[] edges =
+ view.getGraphPerspective().getEdgeIndicesArray(nodeView.getGraphPerspectiveIndex(),
+ neighbours[n], true, true);
+
+ for (int j = 0; j < edges.length; ++j)
+ view.showGraphObject(view.getEdgeView(edges[j]));
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param view DOCUMENT ME!
+ */
+ public static void unHideAll(GraphView view) {
+ if (view == null) {
+ return;
+ }
+
+ for (Iterator i = view.getNodeViewsIterator(); i.hasNext();) {
+ NodeView nview = (NodeView) i.next();
+ view.showGraphObject(nview);
+ }
+
+ for (Iterator ei = view.getEdgeViewsList().iterator(); ei.hasNext();) {
+ EdgeView eview = (EdgeView) ei.next();
+ view.showGraphObject(eview);
+ }
+
+ view.updateView();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param view DOCUMENT ME!
+ */
+ public static void unHideNodesAndInterconnectingEdges(GraphView view) {
+ if (view == null) {
+ return;
+ }
+
+ for (Iterator i = view.getNodeViewsIterator(); i.hasNext();) {
+ NodeView nview = (NodeView) i.next();
+ Node n = nview.getNode();
+
+ view.showGraphObject(nview);
+
+ int[] na = view.getGraphPerspective().neighborsArray(nview.getGraphPerspectiveIndex());
+
+ for (int i2 = 0; i2 < na.length; ++i2) {
+ int[] edges = view.getGraphPerspective()
+ .getEdgeIndicesArray(nview.getGraphPerspectiveIndex(), na[i2],
+ true);
+
+ if (edges != null)
+ for (int j = 0; j < edges.length; ++j) {
+ EdgeView ev = view.getEdgeView(edges[j]);
+ view.showGraphObject(ev);
+ }
+ }
+ }
+
+ view.updateView();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param view DOCUMENT ME!
+ */
+ public static void hideSelectedEdges(GraphView view) {
+ if (view == null) {
+ return;
+ }
+
+ for (Iterator i = view.getSelectedEdges().iterator(); i.hasNext();) {
+ EdgeView eview = (EdgeView) i.next();
+ view.hideGraphObject(eview);
+ }
+
+ view.updateView();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param view DOCUMENT ME!
+ */
+ public static void unHideSelectedEdges(GraphView view) {
+ if (view == null) {
+ return;
+ }
+
+ for (Iterator i = view.getSelectedEdges().iterator(); i.hasNext();) {
+ EdgeView eview = (EdgeView) i.next();
+ view.showGraphObject(eview);
+ }
+
+ view.updateView();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param view DOCUMENT ME!
+ */
+ public static void invertSelectedNodes(GraphView view) {
+ if (view == null) {
+ return;
+ }
+
+ for (Iterator i = view.getNodeViewsIterator(); i.hasNext();) {
+ NodeView nview = (NodeView) i.next();
+ nview.setSelected(!nview.isSelected());
+ }
+
+ view.updateView();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param view DOCUMENT ME!
+ */
+ public static void invertSelectedEdges(GraphView view) {
+ if (view == null) {
+ return;
+ }
+
+ for (Iterator i = view.getEdgeViewsList().iterator(); i.hasNext();) {
+ EdgeView eview = (EdgeView) i.next();
+ eview.setSelected(!eview.isSelected());
+ }
+
+ view.updateView();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param view DOCUMENT ME!
+ */
+ public static void selectFirstNeighbors(GraphView view) {
+ if (view == null) {
+ return;
+ }
+
+ GraphPerspective graphPerspective = view.getGraphPerspective();
+ Set nodeViewsToSelect = new HashSet();
+
+ for (Iterator i = view.getSelectedNodes().iterator(); i.hasNext();) {
+ NodeView nview = (NodeView) i.next();
+ Node n = nview.getNode();
+
+ for (Iterator ni = graphPerspective.neighborsList(n).iterator(); ni.hasNext();) {
+ Node neib = (Node) ni.next();
+ NodeView neibview = view.getNodeView(neib);
+ nodeViewsToSelect.add(neibview);
+ }
+ }
+
+ for (Iterator si = nodeViewsToSelect.iterator(); si.hasNext();) {
+ NodeView nview = (NodeView) si.next();
+ nview.setSelected(true);
+ }
+
+ view.updateView();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param view DOCUMENT ME!
+ */
+ public static void selectAllNodes(GraphView view) {
+ if (view == null) {
+ return;
+ }
+
+ for (Iterator i = view.getNodeViewsIterator(); i.hasNext();) {
+ NodeView nview = (NodeView) i.next();
+ nview.setSelected(true);
+ }
+
+ view.updateView();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param view DOCUMENT ME!
+ */
+ public static void deselectAllNodes(GraphView view) {
+ if (view == null) {
+ return;
+ }
+
+ for (Iterator i = view.getNodeViewsIterator(); i.hasNext();) {
+ NodeView nview = (NodeView) i.next();
+ nview.setSelected(false);
+ }
+
+ view.updateView();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param view DOCUMENT ME!
+ */
+ public static void selectAllEdges(GraphView view) {
+ if (view == null) {
+ return;
+ }
+
+ for (Iterator i = view.getEdgeViewsList().iterator(); i.hasNext();) {
+ EdgeView eview = (EdgeView) i.next();
+ eview.setSelected(true);
+ }
+
+ view.updateView();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param view DOCUMENT ME!
+ */
+ public static void deselectAllEdges(GraphView view) {
+ if (view == null) {
+ return;
+ }
+
+ for (Iterator i = view.getEdgeViewsList().iterator(); i.hasNext();) {
+ EdgeView eview = (EdgeView) i.next();
+ eview.setSelected(false);
+ }
+
+ view.updateView();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param view DOCUMENT ME!
+ */
+ public static void hideAllEdges(GraphView view) {
+ if (view == null) {
+ return;
+ }
+
+ for (Iterator i = view.getEdgeViewsList().iterator(); i.hasNext();) {
+ EdgeView eview = (EdgeView) i.next();
+ view.hideGraphObject(eview);
+ }
+
+ view.updateView();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param view DOCUMENT ME!
+ */
+ public static void unHideAllEdges(GraphView view) {
+ if (view == null) {
+ return;
+ }
+
+ for (Iterator i = view.getEdgeViewsList().iterator(); i.hasNext();) {
+ EdgeView eview = (EdgeView) i.next();
+ view.showGraphObject(eview);
+ }
+
+ view.updateView();
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/GraphObjectSelectionAction.java b/application/src/main/java/cytoscape/actions/GraphObjectSelectionAction.java
new file mode 100644
index 0000000..aa8b3bd
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/GraphObjectSelectionAction.java
@@ -0,0 +1,74 @@
+/*
+ File: GraphObjectSelectionAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.actions;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.dialogs.GraphObjectSelection;
+
+import cytoscape.util.CytoscapeAction;
+
+import java.awt.event.ActionEvent;
+
+import javax.swing.*;
+
+
+/**
+ *
+ */
+public class GraphObjectSelectionAction extends CytoscapeAction {
+ /**
+ * Creates a new GraphObjectSelectionAction object.
+ */
+ public GraphObjectSelectionAction() {
+ super("Node Selection based on Attributes");
+
+ setPreferredMenu("Data");
+ setAcceleratorCombo(java.awt.event.KeyEvent.VK_T,
+ ActionEvent.CTRL_MASK | ActionEvent.SHIFT_MASK);
+ }
+
+ /**
+ * This Should go away
+ **/
+ public void actionPerformed(ActionEvent e) {
+ JDialog dialog = new JDialog();
+ dialog.getContentPane().add(new GraphObjectSelection());
+ dialog.pack();
+ dialog.setVisible(true);
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/HelpAboutAction.java b/application/src/main/java/cytoscape/actions/HelpAboutAction.java
new file mode 100644
index 0000000..3e57a1d
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/HelpAboutAction.java
@@ -0,0 +1,113 @@
+/*
+ File: HelpAboutAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.actions;
+
+import cytoscape.Cytoscape;
+import cytoscape.util.CreditScreen;
+import cytoscape.util.CytoscapeAction;
+
+import java.awt.event.ActionEvent;
+
+import javax.swing.SwingUtilities;
+
+
+/**
+ *
+ */
+public class HelpAboutAction extends CytoscapeAction {
+ /**
+ * Creates a new HelpAboutAction object.
+ */
+ public HelpAboutAction() {
+ super("About...");
+ setPreferredMenu("Help");
+ }
+
+ /**
+ * Show about page.
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ // Normally, a StringBuffer would be more appropriate,
+ // but for some reason the newline chars don't get
+ // respected and thus we're unable to tokenize
+ // properly.
+ //
+ // If you've contributed, please add your name in the
+ // correct location.
+ //
+ String lines = "Cytoscape is a collaboration \n"
+ + "between the Institute for \n"
+ + "Systems Biology, University of \n"
+ + "California San Diego, Memorial \n"
+ + "Sloan-Kettering Cancer Center, \n"
+ + "Institut Pasteur, Agilent \n"
+ + "Technologies, University of \n"
+ + "California San Francisco,\n"
+ + "Unilever, University of Toronto,\n"
+ + "and the National Center for\n"
+ + "Integrative Biomedical Informatics\n"
+ + " \n"
+ + "For more information, please see: \n"
+ + " http://www.cytoscape.org\n" + " \n"
+ + "Cytosape Developers,\n" + " past and present,\n"
+ + " in alphabetical order: \n" + " \n" + " Annette Adler\n"
+ + " Nada Amin\n" + " Mark Anderson\n"
+ + " Iliana Avila-Campillo\n" + " Gary Bader\n"
+ + " Hamid Bolouri\n" + " Ethan Cerami\n" + " Rowan Christmas\n"
+ + " Melissa Cline\n" + " Mike Creech\n" + " Paul Edlefsen\n"
+ + " Stephanie Fan\n" + " Trey Ideker\n" + " Liz Kain\n"
+ + " Larissa Kamenkovich\n" + " Ryan Kelley\n"
+ + " Sarah Killcoyne\n" + " Brad Kohlenberg\n"
+ + " Allan Kuchinsky\n" + " Nerius Landys\n"
+ + " Willem Ligtenberg\n" + " Samad Lotia\n"
+ + " Andrew Markiel\n" + " James McIninch\n" + " Keiichiro Ono\n"
+ + " Owen Ozier\n" + " David Reiss\n" + "Johannes Ruscheinski\n" + " Chris Sander\n"
+ + " Paul Shannon\n" + " Robert Sheridan\n"
+ + " Benno Shwikowski\n" + " Mike Smoot\n" + " James Taylor\n"
+ + " Aditya Vailaya\n" + " Jonathan Wang\n" + "Peng-Liang Wang\n" + " Chris Workman\n";
+
+ CreditScreen.showCredits(Cytoscape.class
+ .getResource("images/CytoscapeCredits.png"),
+ lines);
+ }
+ });
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/HelpContactHelpDeskAction.java b/application/src/main/java/cytoscape/actions/HelpContactHelpDeskAction.java
new file mode 100644
index 0000000..0594ba4
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/HelpContactHelpDeskAction.java
@@ -0,0 +1,69 @@
+/*
+ File: HelpContactHelpDeskAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.actions;
+
+import cytoscape.util.CytoscapeAction;
+import cytoscape.view.CyHelpBroker;
+
+import java.awt.event.ActionEvent;
+
+import javax.swing.*;
+
+
+/**
+ *
+ */
+public class HelpContactHelpDeskAction extends CytoscapeAction {
+ private String helpDeskURL = "http://www.cytoscape.org/helpdesk.php";
+
+ /**
+ * Creates a new HelpContactHelpDeskAction object.
+ */
+ public HelpContactHelpDeskAction() {
+ super("Contact Help Desk");
+ setPreferredMenu("Help");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ cytoscape.util.OpenBrowser.openURL(helpDeskURL);
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/HelpContentsAction.java b/application/src/main/java/cytoscape/actions/HelpContentsAction.java
new file mode 100644
index 0000000..df1305d
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/HelpContentsAction.java
@@ -0,0 +1,72 @@
+/*
+ File: HelpContentsAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.actions;
+
+import cytoscape.util.CytoscapeAction;
+
+import java.awt.event.ActionListener;
+import java.awt.event.ActionEvent;
+import java.awt.event.KeyEvent;
+import javax.swing.JOptionPane;
+
+import cytoscape.view.CyHelpBroker;
+
+/**
+ * Really just a wrapper for the CSH.DisplayHelpFromSource action.
+ */
+public class HelpContentsAction extends CytoscapeAction {
+
+ private final ActionListener helpActionListener = CyHelpBroker.getHelpActionListener();
+
+ /**
+ * Creates a new HelpContentsAction object.
+ */
+ public HelpContentsAction() {
+ super("Contents...");
+ setPreferredMenu("Help");
+ setAcceleratorCombo(KeyEvent.VK_F1, 0);
+ }
+
+ /**
+ * Merely calls actionPerformed on the CSH.DisplayHelpFromSource object.
+ *
+ * @param e The triggering event - passed to CSH.DisplayHelpFromSource.actionPerformed(e)
+ */
+ public void actionPerformed(ActionEvent e) {
+ helpActionListener.actionPerformed(e);
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/HideSelectedAction.java b/application/src/main/java/cytoscape/actions/HideSelectedAction.java
new file mode 100644
index 0000000..af4cb51
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/HideSelectedAction.java
@@ -0,0 +1,104 @@
+/*
+ File: HideSelectedAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+//-------------------------------------------------------------------------
+// $Revision: 9565 $
+// $Date: 2007-02-13 20:36:50 +0100 (Tue, 13 Feb 2007) $
+// $Author: mes $
+//-------------------------------------------------------------------------
+package cytoscape.actions;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.util.CytoscapeAction;
+
+import giny.model.*;
+
+import giny.view.*;
+
+//-------------------------------------------------------------------------
+import java.awt.event.ActionEvent;
+
+import java.util.*;
+
+import javax.swing.AbstractAction;
+
+
+//-------------------------------------------------------------------------
+/**
+ *
+ */
+public class HideSelectedAction extends CytoscapeAction {
+ /**
+ * Creates a new HideSelectedAction object.
+ */
+ public HideSelectedAction() {
+ super("Hide Selected");
+ setPreferredMenu("Select.Edges");
+ }
+
+ /**
+ * Creates a new HideSelectedAction object.
+ *
+ * @param label DOCUMENT ME!
+ */
+ public HideSelectedAction(boolean label) {
+ super();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ // Get the selected nodes:
+ Set selectedNodes = Cytoscape.getCurrentNetwork().getSelectedNodes();
+ Set selectedEdges = Cytoscape.getCurrentNetwork().getSelectedEdges();
+ GinyUtils.hideSelectedNodes(Cytoscape.getCurrentNetworkView());
+ GinyUtils.hideSelectedEdges(Cytoscape.getCurrentNetworkView());
+
+ // unselect the nodes and edges
+ if (selectedNodes != null) {
+ Cytoscape.getCurrentNetwork().setSelectedNodeState(selectedNodes, false);
+ }
+
+ if (selectedEdges != null) {
+ Cytoscape.getCurrentNetwork().setSelectedEdgeState(selectedEdges, false);
+ }
+ } //action performed
+}
diff --git a/application/src/main/java/cytoscape/actions/HideSelectedEdgesAction.java b/application/src/main/java/cytoscape/actions/HideSelectedEdgesAction.java
new file mode 100644
index 0000000..f2dd64d
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/HideSelectedEdgesAction.java
@@ -0,0 +1,71 @@
+/*
+ File: HideSelectedEdgesAction.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.actions;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.util.CytoscapeAction;
+
+//-------------------------------------------------------------------------
+import java.awt.event.ActionEvent;
+
+import javax.swing.AbstractAction;
+
+import javax.swing.event.MenuEvent;
+
+//-------------------------------------------------------------------------
+/**
+ *
+ */
+public class HideSelectedEdgesAction extends CytoscapeAction {
+ public static final String MENU_LABEL = "Hide Edge Selection";
+
+ /**
+ * Creates a new HideSelectedEdgesAction object.
+ */
+ public HideSelectedEdgesAction() {
+ super(MENU_LABEL);
+ setPreferredMenu("Select.Edges");
+ setAcceleratorCombo(java.awt.event.KeyEvent.VK_H, ActionEvent.ALT_MASK);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ GinyUtils.hideSelectedEdges(Cytoscape.getCurrentNetworkView());
+ }
+
+ public void menuSelected(MenuEvent e) {
+ enableForNetworkAndView();
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/HideSelectedNodesAction.java b/application/src/main/java/cytoscape/actions/HideSelectedNodesAction.java
new file mode 100644
index 0000000..f4d27fb
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/HideSelectedNodesAction.java
@@ -0,0 +1,82 @@
+/*
+ File: HideSelectedNodesAction.java
+
+ Copyright (c) 2006, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.actions;
+
+
+import cytoscape.Cytoscape;
+import cytoscape.util.CytoscapeAction;
+import cytoscape.util.undo.CyUndo;
+import cytoscape.view.CyNetworkView;
+
+import giny.view.NodeView;
+
+import java.awt.event.ActionEvent;
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+
+import javax.swing.AbstractAction;
+import javax.swing.event.MenuEvent;
+
+
+public class HideSelectedNodesAction extends CytoscapeAction {
+ static public String MENU_LABEL = "Hide Node Selection";
+
+ /**
+ * Creates a new HideSelectedNodesAction object.
+ */
+ public HideSelectedNodesAction() {
+ super(MENU_LABEL);
+ setPreferredMenu("Select.Nodes");
+ setAcceleratorCombo(java.awt.event.KeyEvent.VK_H, ActionEvent.CTRL_MASK);
+ }
+
+ /**
+ * Creates a new HideSelectedNodesAction object.
+ */
+ public HideSelectedNodesAction(boolean label) {
+ super();
+ }
+
+ public void actionPerformed(final ActionEvent e) {
+ final CyNetworkView view = Cytoscape.getCurrentNetworkView();
+
+ final List<NodeView> hiddenNodeViews = new ArrayList<NodeView>();
+ for (Iterator i = view.getSelectedNodes().iterator(); i.hasNext(); /* Empty! */)
+ hiddenNodeViews.add((NodeView)i.next());
+ CyUndo.getUndoableEditSupport().postEdit(new HideSelectedNodesEdit(view, hiddenNodeViews, this));
+
+ GinyUtils.hideSelectedNodes(view);
+ }
+
+ public void menuSelected(MenuEvent e) {
+ enableForNetworkAndView();
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/HideSelectedNodesEdit.java b/application/src/main/java/cytoscape/actions/HideSelectedNodesEdit.java
new file mode 100644
index 0000000..4d0dfbe
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/HideSelectedNodesEdit.java
@@ -0,0 +1,91 @@
+/*
+ File: HideSelectedNodesEdit.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.actions;
+
+
+import java.awt.event.ActionEvent;
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+
+import giny.view.NodeView;
+
+import cytoscape.Cytoscape;
+import cytoscape.view.CyNetworkView;
+import cytoscape.util.undo.CyAbstractEdit;
+
+
+/**
+ * An undoable edit that will undo and redo hiding of selected nodes.
+ */
+class HideSelectedNodesEdit extends CyAbstractEdit {
+ private static final long serialVersionUID = -1146181528012954334L;
+
+ private final CyNetworkView networkView;
+ private final List<NodeView> hiddenNodeViews;
+ private final HideSelectedNodesAction hideSelectedNodesAction;
+
+ HideSelectedNodesEdit(final CyNetworkView networkView, final List<NodeView> hiddenNodeViews,
+ final HideSelectedNodesAction hideSelectedNodesAction)
+ {
+ super(HideSelectedNodesAction.MENU_LABEL);
+
+ this.networkView = networkView;
+ this.hiddenNodeViews = hiddenNodeViews;
+ this.hideSelectedNodesAction = hideSelectedNodesAction;
+ }
+
+ public void redo() {
+ super.redo();
+
+ final CyNetworkView view = Cytoscape.getCurrentNetworkView();
+ final List<NodeView> hiddenNodeViews = new ArrayList<NodeView>();
+ for (Iterator i = view.getSelectedNodes().iterator(); i.hasNext(); /* Empty! */)
+ hiddenNodeViews.add((NodeView)i.next());
+ GinyUtils.hideSelectedNodes(view);
+
+
+ hideSelectedNodesAction.setEnabled(false);
+ }
+
+ public void undo() {
+ super.undo();
+
+ for (final NodeView nodeView : hiddenNodeViews) {
+ networkView.showGraphObject(nodeView);
+ nodeView.setSelected(true);
+ GinyUtils.showEdges(networkView, nodeView);
+ }
+
+ networkView.updateView();
+
+ hideSelectedNodesAction.setEnabled(true);
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/ImportEdgeAttributesAction.java b/application/src/main/java/cytoscape/actions/ImportEdgeAttributesAction.java
new file mode 100644
index 0000000..9346d8a
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/ImportEdgeAttributesAction.java
@@ -0,0 +1,105 @@
+/*
+ File: ImportEdgeAttributesAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+// $Revision: 9736 $
+// $Date: 2007-03-20 01:25:45 +0100 (Tue, 20 Mar 2007) $
+// $Author: mes $
+package cytoscape.actions;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.task.ui.JTaskConfig;
+
+import cytoscape.task.util.TaskManager;
+
+import cytoscape.util.CyFileFilter;
+import cytoscape.util.CytoscapeAction;
+import cytoscape.util.FileUtil;
+
+import java.awt.event.ActionEvent;
+
+import java.io.File;
+
+
+/*
+ * Added by T. Ideker April 16, 2003
+ * to allow loading of edge / edge attributes from the GUI
+ */
+
+/**
+ *
+ */
+public class ImportEdgeAttributesAction extends CytoscapeAction {
+ /**
+ * Constructor.
+ */
+ public ImportEdgeAttributesAction() {
+ super("Edge Attributes...");
+ setPreferredMenu("File.Import");
+ }
+
+ /**
+ * User Initiated Request.
+ *
+ * @param e
+ * Action Event.
+ */
+ public void actionPerformed(ActionEvent e) {
+ // Use a Default CyFileFilter: enables user to select any file type.
+ CyFileFilter nf = new CyFileFilter();
+
+ // get the file name
+ File[] files = FileUtil.getFiles("Import Edge Attributes", FileUtil.LOAD,
+ new CyFileFilter[] { nf });
+
+ if (files != null) {
+ // Create Load Attributes Task
+ ImportAttributesTask task = new ImportAttributesTask(files,
+ ImportAttributesTask.EDGE_ATTRIBUTES);
+
+ // Configure JTask Dialog Pop-Up Box
+ JTaskConfig jTaskConfig = new JTaskConfig();
+ jTaskConfig.setOwner(Cytoscape.getDesktop());
+ jTaskConfig.displayCloseButton(true);
+ jTaskConfig.displayStatus(true);
+ jTaskConfig.setAutoDispose(false);
+
+ // Execute Task in New Thread; pop open JTask Dialog Box.
+ TaskManager.executeTask(task, jTaskConfig);
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/ImportExpressionMatrixAction.java b/application/src/main/java/cytoscape/actions/ImportExpressionMatrixAction.java
new file mode 100644
index 0000000..43074f1
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/ImportExpressionMatrixAction.java
@@ -0,0 +1,194 @@
+/*
+ File: ImportExpressionMatrixAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// $Revision: 19142 $
+// $Date: 2010-02-02 21:57:16 +0100 (Tue, 02 Feb 2010) $
+// $Author: mes $
+package cytoscape.actions;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.data.ExpressionData;
+
+import cytoscape.dialogs.ImportAttributeMatrixDialog;
+
+import cytoscape.task.Task;
+import cytoscape.task.TaskMonitor;
+
+import cytoscape.task.ui.JTaskConfig;
+
+import cytoscape.task.util.TaskManager;
+
+import cytoscape.util.CyFileFilter;
+import cytoscape.util.CytoscapeAction;
+import cytoscape.util.FileUtil;
+
+import cytoscape.view.CyMenus;
+
+import java.awt.event.ActionEvent;
+import java.awt.event.KeyEvent;
+
+import java.io.File;
+
+
+/**
+ * User has requested loading of an Expression Matrix File.
+ */
+public class ImportExpressionMatrixAction extends CytoscapeAction {
+ protected CyMenus windowMenu;
+
+ /**
+ * Constructor.
+ */
+ public ImportExpressionMatrixAction() {
+ super("Attribute/Expression Matrix...");
+ setPreferredMenu("File.Import");
+ setAcceleratorCombo(KeyEvent.VK_E, ActionEvent.CTRL_MASK);
+ setName("load");
+ }
+
+ /**
+ * User Initiated Request.
+ *
+ * @param e
+ * Action Event.
+ */
+ public void actionPerformed(ActionEvent e) {
+ // open new dialog
+ ImportAttributeMatrixDialog amd = new ImportAttributeMatrixDialog(Cytoscape.getDesktop(),
+ true);
+ amd.pack();
+ amd.setLocationRelativeTo(Cytoscape.getDesktop());
+ amd.setVisible(true);
+
+ if (amd.getStatus() == false) {
+ return;
+ }
+
+ String filename = amd.getFilename();
+ String keyAttributeName = amd.getKeyAttributeName();
+
+ if ((filename == null) || (keyAttributeName == null)) {
+ return;
+ } else {
+ // Create the LoadExpressionTask
+ ImportExpressionDataTask task = new ImportExpressionDataTask(filename, keyAttributeName);
+ JTaskConfig jTaskConfig = new JTaskConfig();
+ jTaskConfig.setOwner(Cytoscape.getDesktop());
+ jTaskConfig.displayCloseButton(true);
+ jTaskConfig.displayStatus(true);
+ jTaskConfig.setAutoDispose(false);
+
+ // Start Loading in a new Thread; and pop-open JTask Dialog Box.
+ TaskManager.executeTask(task, jTaskConfig);
+ }
+ }
+}
+
+
+/**
+ * Task to Load New Expression Data File.
+ */
+class ImportExpressionDataTask implements Task {
+ private TaskMonitor taskMonitor;
+ private String filename;
+ private String keyAttributeName;
+
+ /**
+ * Constructor.
+ *
+ * @param fileName
+ * File name containing expression data.
+ */
+ public ImportExpressionDataTask(String filename, String keyAttributeName) {
+ this.filename = filename;
+ this.keyAttributeName = keyAttributeName;
+ }
+
+ /**
+ * Executes the Task.
+ */
+ public void run() {
+ taskMonitor.setStatus("Analyzing Expression Data File...");
+
+ try {
+ // Read in Expression Data File
+ ExpressionData expressionData = new ExpressionData(filename, keyAttributeName,
+ taskMonitor);
+ Cytoscape.setExpressionData(expressionData);
+
+ // Copy Expression Data to Attributes
+ taskMonitor.setStatus("Mapping Expression Data to" + " Nodes according to "
+ + keyAttributeName);
+ expressionData.copyToAttribs(Cytoscape.getNodeAttributes(), taskMonitor);
+ Cytoscape.firePropertyChange(Cytoscape.ATTRIBUTES_CHANGED, null, null);
+ Cytoscape.firePropertyChange(Cytoscape.EXPRESSION_DATA_LOADED, null, expressionData);
+
+ // We are done; inform user of expression data details.
+ taskMonitor.setPercentCompleted(100);
+ taskMonitor.setStatus(expressionData.getDescription());
+ } catch (Exception e) {
+ taskMonitor.setException(e, "Unable to load expression matrix file.");
+ }
+ }
+
+ /**
+ * Halts the Task: Not Currently Implemented.
+ */
+ public void halt() {
+ // Task can not currently be halted.
+ }
+
+ /**
+ * Sets the Task Monitor.
+ *
+ * @param taskMonitor
+ * TaskMonitor Object.
+ */
+ public void setTaskMonitor(TaskMonitor taskMonitor) throws IllegalThreadStateException {
+ this.taskMonitor = taskMonitor;
+ }
+
+ /**
+ * Gets the Task Title.
+ *
+ * @return Task Title.
+ */
+ public String getTitle() {
+ return new String("Loading Gene Expression Data");
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/ImportGraphFileAction.java b/application/src/main/java/cytoscape/actions/ImportGraphFileAction.java
new file mode 100644
index 0000000..efffb8a
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/ImportGraphFileAction.java
@@ -0,0 +1,176 @@
+/*
+ File: ImportGraphFileAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+// $Revision: 19327 $
+// $Date: 2010-02-12 23:01:44 +0100 (Fri, 12 Feb 2010) $
+// $Author: ruschein $
+package cytoscape.actions;
+
+import java.awt.event.ActionEvent;
+import java.io.File;
+import java.io.IOException;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.swing.JOptionPane;
+import javax.xml.bind.JAXBException;
+
+import cytoscape.Cytoscape;
+import cytoscape.dialogs.ImportNetworkDialog;
+import cytoscape.logger.CyLogger;
+import cytoscape.util.CytoscapeAction;
+import cytoscape.view.CyMenus;
+
+
+/**
+ * Imports a graph of arbitrary type. The types of graphs allowed are defined by
+ * the ImportHandler.
+ */
+public class ImportGraphFileAction extends CytoscapeAction {
+ protected CyMenus windowMenu;
+ protected static CyLogger logger = CyLogger.getLogger(ImportGraphFileAction.class);
+
+ /**
+ * Constructor.
+ *
+ * @param windowMenu
+ * WindowMenu Object.
+ */
+ public ImportGraphFileAction(CyMenus windowMenu) {
+ super("Network (Multiple File Types)...");
+ setPreferredMenu("File.Import");
+ setAcceleratorCombo(java.awt.event.KeyEvent.VK_L, ActionEvent.CTRL_MASK);
+ this.windowMenu = windowMenu;
+
+ setName("load");
+ }
+
+ /**
+ * Constructor.
+ *
+ * @param windowMenu
+ * WindowMenu Object.
+ * @param label
+ * boolean label.
+ */
+ public ImportGraphFileAction(CyMenus windowMenu, boolean label) {
+ super();
+ this.windowMenu = windowMenu;
+ }
+
+ /**
+ * User-initiated action to load a CyNetwork into Cytoscape. If successfully
+ * loaded, fires a PropertyChange event with
+ * property=Cytoscape.NETWORK_LOADED, old_value=null, and new_value=a three
+ * element Object array containing:
+ * <OL>
+ * <LI>first element = CyNetwork loaded
+ * <LI>second element = URI of the location from which the network was
+ * loaded
+ * <LI>third element = an Integer representing the format in which the
+ * Network was loaded (e.g., Cytoscape.FILE_SIF).
+ * </OL>
+ *
+ * @param e
+ * ActionEvent Object.
+ */
+ public void actionPerformed(ActionEvent e) {
+ // open new dialog
+ ImportNetworkDialog fd = null;
+
+ try {
+ fd = new ImportNetworkDialog(Cytoscape.getDesktop(), true);
+ } catch (JAXBException e1) {
+ logger.error("Unable to parse the network: "+ e1.getMessage(), e1);
+ } catch (IOException e1) {
+ // TODO Auto-generated catch block
+ logger.error("Unable to read the network: "+e1.getMessage(), e1);
+ }
+
+ fd.pack();
+ fd.setLocationRelativeTo(Cytoscape.getDesktop());
+ fd.setVisible(true);
+
+ if (fd.getStatus() == false) {
+ return;
+ }
+
+ if (fd.isRemote()) {
+ String URLstr = fd.getURLStr();
+ logger.info("URL: "+URLstr);
+ try {
+ LoadNetworkTask.loadURL(new URL(URLstr), false);
+ } catch (MalformedURLException e3) {
+ JOptionPane.showMessageDialog(fd, "URL error!", "Warning",
+ JOptionPane.INFORMATION_MESSAGE);
+ }
+ } else {
+ final File[] files = fd.getFiles();
+ boolean skipMessage = false;
+
+ if ((files != null) && (files.length != 0)) {
+ if (files.length != 1) {
+ skipMessage = true;
+ }
+
+ List<String> messages = new ArrayList<String>();
+ messages.add("Successfully loaded the following files:");
+ messages.add(" ");
+
+ for (int i = 0; i < files.length; i++) {
+ if (fd.isRemote() == true) {
+ messages.add(fd.getURLStr());
+ } else {
+ messages.add(files[i].getName());
+ }
+
+ LoadNetworkTask.loadFile(files[i], skipMessage);
+ }
+
+ if (files.length != 1) {
+ JOptionPane messagePane = new JOptionPane();
+ messagePane.setLocation(Cytoscape.getDesktop().getLocationOnScreen());
+ messagePane.showMessageDialog(Cytoscape.getDesktop(), messages.toArray(),
+ "Multiple Network Files Loaded",
+ JOptionPane.INFORMATION_MESSAGE);
+ }
+ }
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/ImportNodeAttributesAction.java b/application/src/main/java/cytoscape/actions/ImportNodeAttributesAction.java
new file mode 100644
index 0000000..0dfaa90
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/ImportNodeAttributesAction.java
@@ -0,0 +1,197 @@
+/*
+ File: ImportNodeAttributesAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// $Revision: 9736 $
+// $Date: 2007-03-20 01:25:45 +0100 (Tue, 20 Mar 2007) $
+// $Author: mes $
+package cytoscape.actions;
+
+import cytoscape.Cytoscape;
+import cytoscape.CytoscapeInit;
+
+import cytoscape.data.servers.BioDataServer;
+
+import cytoscape.task.Task;
+import cytoscape.task.TaskMonitor;
+
+import cytoscape.task.ui.JTaskConfig;
+
+import cytoscape.task.util.TaskManager;
+
+import cytoscape.util.CyFileFilter;
+import cytoscape.util.CytoscapeAction;
+import cytoscape.util.FileUtil;
+
+import java.awt.event.ActionEvent;
+
+import java.io.File;
+
+
+/*
+ * Added by T. Ideker April 16, 2003
+ * to allow loading of node / edge attributes from the GUI
+ */
+
+/**
+ *
+ */
+public class ImportNodeAttributesAction extends CytoscapeAction {
+ /**
+ * Constructor.
+ */
+ public ImportNodeAttributesAction() {
+ super("Node Attributes...");
+ setPreferredMenu("File.Import");
+ }
+
+ /**
+ * User Initiated Request.
+ *
+ * @param e Action Event.
+ */
+ public void actionPerformed(ActionEvent e) {
+ // Use a Default CyFileFilter: enables user to select any file type.
+ CyFileFilter nf = new CyFileFilter();
+
+ // get the file name
+ File[] files = FileUtil.getFiles("Import Node Attributes", FileUtil.LOAD,
+ new CyFileFilter[] { nf });
+
+ if (files != null) {
+ // Create Load Attributes Task
+ ImportAttributesTask task = new ImportAttributesTask(files,
+ ImportAttributesTask.NODE_ATTRIBUTES);
+
+ // Configure JTask Dialog Pop-Up Box
+ JTaskConfig jTaskConfig = new JTaskConfig();
+ jTaskConfig.setOwner(Cytoscape.getDesktop());
+ jTaskConfig.displayCloseButton(true);
+ jTaskConfig.displayStatus(true);
+ jTaskConfig.setAutoDispose(false);
+
+ // Execute Task in New Thread; pop open JTask Dialog Box.
+ TaskManager.executeTask(task, jTaskConfig);
+ }
+ }
+}
+
+
+/**
+ * Task to Load New Node/Edge Attributes Data.
+ */
+class ImportAttributesTask implements Task {
+ private TaskMonitor taskMonitor;
+ private File[] files;
+ private int type;
+ static final int NODE_ATTRIBUTES = 0;
+ static final int EDGE_ATTRIBUTES = 1;
+
+ /**
+ * Constructor.
+ * @param file File Object.
+ * @param type NODE_ATTRIBUTES or EDGE_ATTRIBUTES
+ */
+ ImportAttributesTask(File[] files, int type) {
+ this.files = files;
+ this.type = type;
+ }
+
+ /**
+ * Executes Task.
+ */
+ public void run() {
+ try {
+ taskMonitor.setPercentCompleted(-1);
+ taskMonitor.setStatus("Reading in Attributes");
+
+ // Read in Data
+
+ // track progress. CyAttributes has separation between
+ // reading attributes and storing them
+ // so we need to find a different way of monitoring this task:
+ // attributes.setTaskMonitor(taskMonitor);
+ for (int i = 0; i < files.length; ++i) {
+ taskMonitor.setPercentCompleted((100 * i) / files.length);
+
+ if (type == NODE_ATTRIBUTES)
+ Cytoscape.loadAttributes(new String[] { files[i].getAbsolutePath() },
+ new String[] { });
+ else if (type == EDGE_ATTRIBUTES)
+ Cytoscape.loadAttributes(new String[] { },
+ new String[] { files[i].getAbsolutePath() });
+ else
+ throw new Exception("Unknown attribute type: " + Integer.toString(type));
+ }
+
+ // Inform others via property change event.
+ taskMonitor.setPercentCompleted(100);
+ Cytoscape.firePropertyChange(Cytoscape.ATTRIBUTES_CHANGED, null, null);
+ taskMonitor.setStatus("Done");
+ } catch (Exception e) {
+ taskMonitor.setException(e, e.getMessage());
+ }
+ }
+
+ /**
+ * Halts the Task: Not Currently Implemented.
+ */
+ public void halt() {
+ // Task can not currently be halted.
+ }
+
+ /**
+ * Sets the Task Monitor Object.
+ * @param taskMonitor
+ * @throws IllegalThreadStateException
+ */
+ public void setTaskMonitor(TaskMonitor taskMonitor) throws IllegalThreadStateException {
+ this.taskMonitor = taskMonitor;
+ }
+
+ /**
+ * Gets the Task Title.
+ *
+ * @return Task Title.
+ */
+ public String getTitle() {
+ if (type == NODE_ATTRIBUTES) {
+ return new String("Loading Node Attributes");
+ } else {
+ return new String("Loading Edge Attributes");
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/ImportVizmapAction.java b/application/src/main/java/cytoscape/actions/ImportVizmapAction.java
new file mode 100644
index 0000000..4c5727d
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/ImportVizmapAction.java
@@ -0,0 +1,149 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.actions;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.task.Task;
+import cytoscape.task.TaskMonitor;
+
+import cytoscape.task.ui.JTaskConfig;
+
+import cytoscape.task.util.TaskManager;
+
+import cytoscape.util.CyFileFilter;
+import cytoscape.util.CytoscapeAction;
+import cytoscape.util.FileUtil;
+
+import java.awt.event.ActionEvent;
+
+import java.io.File;
+
+
+/**
+ *
+ */
+public class ImportVizmapAction extends CytoscapeAction {
+ /**
+ * Creates a new ImportVizmapAction object.
+ */
+ public ImportVizmapAction() {
+ super("Vizmap Property File...");
+ setPreferredMenu("File.Import");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ final CyFileFilter propsFilter = new CyFileFilter();
+ propsFilter.addExtension("props");
+ propsFilter.setDescription("Property files");
+
+ // Get the file name
+ final File file = FileUtil.getFile("Import Vizmap Property File", FileUtil.LOAD,
+ new CyFileFilter[] { propsFilter });
+
+ // if the name is not null, then load
+ if (file != null) {
+ // Create LoadNetwork Task
+ LoadVizmapTask task = new LoadVizmapTask(file);
+
+ // Configure JTask Dialog Pop-Up Box
+ final JTaskConfig jTaskConfig = new JTaskConfig();
+ jTaskConfig.setOwner(Cytoscape.getDesktop());
+ jTaskConfig.displayCloseButton(true);
+ jTaskConfig.displayStatus(true);
+ jTaskConfig.setAutoDispose(false);
+
+ // Execute Task in New Thread; pops open JTask Dialog Box.
+ TaskManager.executeTask(task, jTaskConfig);
+ }
+ }
+}
+
+
+class LoadVizmapTask implements Task {
+ private File file;
+ private TaskMonitor taskMonitor;
+
+ /**
+ * Constructor.
+ *
+ */
+ public LoadVizmapTask(File file) {
+ this.file = file;
+ }
+
+ /**
+ * Executes Task.
+ */
+ public void run() {
+ taskMonitor.setStatus("Reading Vizmap File...");
+ taskMonitor.setPercentCompleted(-1);
+ // this even will load the file
+ Cytoscape.firePropertyChange(Cytoscape.VIZMAP_LOADED, null, file.getAbsolutePath());
+ taskMonitor.setStatus("Vizmapper updated by the file: " + file.getName());
+ taskMonitor.setPercentCompleted(100);
+ }
+
+ /**
+ * Halts the Task: Not Currently Implemented.
+ */
+ public void halt() {
+ // Task can not currently be halted.
+ }
+
+ /**
+ * Sets the Task Monitor.
+ *
+ * @param taskMonitor
+ * TaskMonitor Object.
+ */
+ public void setTaskMonitor(TaskMonitor taskMonitor) throws IllegalThreadStateException {
+ this.taskMonitor = taskMonitor;
+ }
+
+ /**
+ * Gets the Task Title.
+ *
+ * @return Task Title.
+ */
+ public String getTitle() {
+ return new String("Importing Vizmap");
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/InvertSelectedEdgesAction.java b/application/src/main/java/cytoscape/actions/InvertSelectedEdgesAction.java
new file mode 100644
index 0000000..208cfd3
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/InvertSelectedEdgesAction.java
@@ -0,0 +1,90 @@
+/*
+ File: InvertSelectedEdgesAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+//-------------------------------------------------------------------------
+// $Revision: 19327 $
+// $Date: 2010-02-12 23:01:44 +0100 (Fri, 12 Feb 2010) $
+// $Author: ruschein $
+//-------------------------------------------------------------------------
+package cytoscape.actions;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+
+import cytoscape.util.CytoscapeAction;
+
+//-------------------------------------------------------------------------
+import giny.model.Edge;
+
+import java.awt.event.ActionEvent;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.swing.event.MenuEvent;
+
+//-------------------------------------------------------------------------
+/**
+ *
+ */
+public class InvertSelectedEdgesAction extends CytoscapeAction {
+ /**
+ * Creates a new InvertSelectedEdgesAction object.
+ */
+ public InvertSelectedEdgesAction() {
+ super("Invert Edge Selection");
+ setPreferredMenu("Select.Edges");
+ setAcceleratorCombo(java.awt.event.KeyEvent.VK_I, ActionEvent.ALT_MASK);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ final CyNetwork cyNetwork = Cytoscape.getCurrentNetwork();
+ final List<Edge> selectedEdges = new ArrayList<Edge>(cyNetwork.getSelectedEdges());
+ cyNetwork.selectAllEdges();
+ cyNetwork.setSelectedEdgeState(selectedEdges, false);
+ Cytoscape.getCurrentNetworkView().updateView();
+ }
+
+ public void menuSelected(MenuEvent e) {
+ enableForNetwork();
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/InvertSelectedNodesAction.java b/application/src/main/java/cytoscape/actions/InvertSelectedNodesAction.java
new file mode 100644
index 0000000..e4ae957
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/InvertSelectedNodesAction.java
@@ -0,0 +1,91 @@
+/*
+ File: InvertSelectedNodesAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+//-------------------------------------------------------------------------
+// $Revision: 19327 $
+// $Date: 2010-02-12 23:01:44 +0100 (Fri, 12 Feb 2010) $
+// $Author: ruschein $
+//-------------------------------------------------------------------------
+package cytoscape.actions;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+
+import cytoscape.util.CytoscapeAction;
+
+//-------------------------------------------------------------------------
+import giny.model.Node;
+
+import java.awt.event.ActionEvent;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.swing.event.MenuEvent;
+
+
+//-------------------------------------------------------------------------
+/**
+ *
+ */
+public class InvertSelectedNodesAction extends CytoscapeAction {
+ /**
+ * Creates a new InvertSelectedNodesAction object.
+ */
+ public InvertSelectedNodesAction() {
+ super("Invert Node Selection");
+ setPreferredMenu("Select.Nodes");
+ setAcceleratorCombo(java.awt.event.KeyEvent.VK_I, ActionEvent.CTRL_MASK);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ final CyNetwork cyNetwork = Cytoscape.getCurrentNetwork();
+ final List<Node> selectedNodes = new ArrayList<Node>(cyNetwork.getSelectedNodes());
+ cyNetwork.selectAllNodes();
+ cyNetwork.setSelectedNodeState(selectedNodes, false);
+ Cytoscape.getCurrentNetworkView().updateView();
+ }
+
+ public void menuSelected(MenuEvent e) {
+ enableForNetwork();
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/ListFromFileSelectionAction.java b/application/src/main/java/cytoscape/actions/ListFromFileSelectionAction.java
new file mode 100644
index 0000000..7300603
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/ListFromFileSelectionAction.java
@@ -0,0 +1,147 @@
+/*
+ File: ListFromFileSelectionAction.java
+
+ Copyright (c) 2006, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.actions;
+
+
+import giny.model.Node;
+
+import java.awt.event.ActionEvent;
+import java.io.BufferedReader;
+import java.io.FileReader;
+import java.util.HashSet;
+import java.util.List;
+
+import javax.swing.JOptionPane;
+import javax.swing.event.MenuEvent;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import cytoscape.util.CytoscapeAction;
+import cytoscape.util.FileUtil;
+
+
+/**
+ * Select nodes from a text list of node IDs.
+ */
+public class ListFromFileSelectionAction extends CytoscapeAction {
+
+ private static final long serialVersionUID = 2309144834195371889L;
+
+ /**
+ * Creates a new ListFromFileSelectionAction object.
+ */
+ public ListFromFileSelectionAction() {
+ super("From ID List File...");
+ setPreferredMenu("Select.Nodes");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ selectFromFile();
+ Cytoscape.getCurrentNetworkView().updateView();
+ }
+
+ @SuppressWarnings("unchecked")
+ private boolean selectFromFile() {
+ final String fileName;
+
+ try {
+ fileName = FileUtil.getFile("Load ID List", FileUtil.LOAD).toString();
+ } catch (Exception exp) {
+ // this is because the selection was canceled
+ return false;
+ }
+
+ final CyNetwork network = Cytoscape.getCurrentNetwork();
+ final HashSet<String> fileNodes = new HashSet<String>();
+
+ try {
+ BufferedReader bin = null;
+
+ try {
+ bin = new BufferedReader(new FileReader(fileName));
+
+ String s;
+
+ while ((s = bin.readLine()) != null) {
+ final String trimedName = s.trim();
+
+ if (trimedName.length() > 0)
+ fileNodes.add(trimedName);
+ }
+ }
+ finally {
+ if (bin != null) {
+ bin.close();
+ bin = null;
+ }
+ }
+ } catch (Exception e) {
+ JOptionPane.showMessageDialog(null, e.toString(), "Error Reading \"" + fileName + "\"",
+ JOptionPane.ERROR_MESSAGE);
+ return false;
+ }
+
+ if (fileNodes.size() == 0) {
+ JOptionPane.showMessageDialog(null, "No nodes read from \"" + fileName + "\"!", "Warning!",
+ JOptionPane.WARNING_MESSAGE);
+ return false;
+ }
+
+ // loop through all the node of the graph
+ // selecting those in the file
+ final List<Node> nodeList = network.nodesList();
+
+ int selectCount = 0;
+ for (Node node: nodeList) {
+ if (fileNodes.contains(node.getIdentifier())) {
+ network.setSelectedNodeState(node, true);
+ selectCount++;
+ }
+ }
+
+ if (selectCount == 0) {
+ JOptionPane.showMessageDialog(null, "No nodes listed in \"" + fileName + "\" were found in the current network!",
+ "Information",
+ JOptionPane.INFORMATION_MESSAGE);
+ return false;
+ }
+
+ return true;
+ }
+
+ public void menuSelected(MenuEvent e) {
+ enableForNetwork();
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/LoadNetworkTask.java b/application/src/main/java/cytoscape/actions/LoadNetworkTask.java
new file mode 100644
index 0000000..6c43514
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/LoadNetworkTask.java
@@ -0,0 +1,366 @@
+/*
+ File: LoadNetworkTask.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+// $Revision: 8703 $
+// $Date: 2006-11-06 23:17:02 -0800 (Mon, 06 Nov 2006) $
+// $Author: pwang $
+package cytoscape.actions;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import cytoscape.CytoscapeInit;
+import cytoscape.logger.CyLogger;
+
+import cytoscape.data.readers.GraphReader;
+
+import cytoscape.init.CyInitParams;
+
+import cytoscape.layout.CyLayoutAlgorithm;
+
+import cytoscape.task.Task;
+import cytoscape.task.TaskMonitor;
+
+import cytoscape.task.ui.JTask;
+import cytoscape.task.ui.JTaskConfig;
+
+import cytoscape.task.util.TaskManager;
+
+import cytoscape.view.CyNetworkView;
+import cytoscape.view.CytoscapeDesktop;
+
+import java.io.File;
+import java.io.IOException;
+
+import java.net.URI;
+import java.net.URL;
+
+import java.text.DecimalFormat;
+import java.text.NumberFormat;
+
+import javax.swing.JOptionPane;
+import cytoscape.data.readers.NNFReader;
+
+/**
+ * Task to load a new network.
+ */
+public class LoadNetworkTask implements Task {
+ private static long taskLoadStart = 0; // "0" means that it has not bene initialised!
+
+ /**
+ * Load a network from a url. The reader code will attempt to determine
+ * the format of the network (GML, XGMML, SIF) from the HTTP content-type
+ * header. If it is unable to figure it out from there, it will try writing
+ * the HTTP stream to a file to look at the first couple of bytes. Note that
+ * the actual opening of the HTTP stream is postponed until the task is
+ * initiated to facility the ability of the user to abort the attempt.
+ *
+ * @param u the URL to load the network from
+ * @param skipMessage if true, dispose of the task monitor dialog immediately
+ */
+ public static void loadURL(URL u, boolean skipMessage) {
+ loadURL(u, skipMessage, null);
+ }
+
+ /**
+ * Load a network from a file. The reader code will attempt to determine
+ * the format of the network (GML, XGMML, SIF) from the file extension.
+ * If it is unable to figure it out from there, it will try reading
+ * the the first couple of bytes from the file.
+ *
+ * @param file the file to load the network from
+ * @param skipMessage if true, dispose of the task monitor dialog immediately
+ */
+ public static void loadFile(File file, boolean skipMessage) {
+ // Create LoadNetwork Task
+ loadFile(file, skipMessage, null);
+ }
+
+ /**
+ * Load a network from a url. The reader code will attempt to determine
+ * the format of the network (GML, XGMML, SIF) from the HTTP content-type
+ * header. If it is unable to figure it out from there, it will try writing
+ * the HTTP stream to a file to look at the first couple of bytes. Note that
+ * the actual opening of the HTTP stream is postponed until the task is
+ * initiated to facility the ability of the user to abort the attempt.
+ *
+ * @param u the URL to load the network from
+ * @param skipMessage if true, dispose of the task monitor dialog immediately
+ * @param layoutAlgorithm if this is non-null, use this algorithm to lay out the network
+ * after it has been read in (provided that a view was created).
+ */
+ public static void loadURL(URL u, boolean skipMessage, CyLayoutAlgorithm layoutAlgorithm) {
+ taskLoadStart = System.nanoTime();
+ LoadNetworkTask task = new LoadNetworkTask(u, layoutAlgorithm);
+ setupTask(task, skipMessage, true);
+ }
+
+ /**
+ * Load a network from a file. The reader code will attempt to determine
+ * the format of the network (GML, XGMML, SIF) from the file extension.
+ * If it is unable to figure it out from there, it will try reading
+ * the the first couple of bytes from the file.
+ *
+ * @param file the file to load the network from
+ * @param skipMessage if true, dispose of the task monitor dialog immediately
+ * @param layoutAlgorithm if this is non-null, use this algorithm to lay out the network
+ * after it has been read in (provided that a view was created).
+ */
+ public static void loadFile(File file, boolean skipMessage, CyLayoutAlgorithm layoutAlgorithm) {
+ taskLoadStart = System.nanoTime();
+ LoadNetworkTask task = new LoadNetworkTask(file, layoutAlgorithm);
+ setupTask(task, skipMessage, true);
+ }
+
+ private static void setupTask(LoadNetworkTask task, boolean skipMessage, boolean cancelable) {
+ // Configure JTask Dialog Pop-Up Box
+ JTaskConfig jTaskConfig = new JTaskConfig();
+ jTaskConfig.setOwner(Cytoscape.getDesktop());
+ jTaskConfig.displayCloseButton(true);
+
+ if (cancelable)
+ jTaskConfig.displayCancelButton(true);
+
+ jTaskConfig.displayStatus(true);
+ jTaskConfig.setAutoDispose(skipMessage);
+
+ // Execute Task in New Thread; pops open JTask Dialog Box.
+ TaskManager.executeTask(task, jTaskConfig);
+ }
+
+ private URI uri;
+ private TaskMonitor taskMonitor;
+ private GraphReader reader;
+ private String name;
+ private URL url;
+ private Thread myThread = null;
+ private boolean interrupted = false;
+ private CyLayoutAlgorithm layoutAlgorithm = null;
+
+ private LoadNetworkTask(URL u, CyLayoutAlgorithm layout) {
+ url = u;
+ name = u.toString();
+ reader = null;
+ layoutAlgorithm = layout;
+
+ // Postpone getting the reader since we want to do that in a thread
+ }
+
+ private LoadNetworkTask(File file, CyLayoutAlgorithm layout) {
+ reader = Cytoscape.getImportHandler().getReader(file.getAbsolutePath());
+ uri = file.toURI();
+ name = file.getName();
+ layoutAlgorithm = layout;
+
+ if (reader == null) {
+ uri = null;
+ url = null;
+ JOptionPane.showMessageDialog(Cytoscape.getDesktop(), "Unable to open file " + name,
+ "File Open Error", JOptionPane.ERROR_MESSAGE);
+ }
+ }
+
+ /**
+ * Executes Task.
+ */
+ public void run() {
+ if ((reader == null) && (url == null))
+ return;
+
+ myThread = Thread.currentThread();
+
+ if ((reader == null) && (url != null)) {
+ try {
+ taskMonitor.setStatus("Opening URL " + url);
+ reader = Cytoscape.getImportHandler().getReader(url);
+
+ if (interrupted)
+ return;
+
+ uri = url.toURI();
+ } catch (Exception e) {
+ uri = null;
+ taskMonitor.setException(e,
+ "Unable to connect to URL " + name + ": " + e.getMessage());
+
+ return;
+ }
+
+ if (reader == null) {
+ uri = null;
+ taskMonitor.setException(null, "Unable to connect to URL " + name);
+
+ return;
+ }
+
+ // URL is open, things will get very messy if the user cancels the actual
+ // network load, so prevent them from doing so
+ ((JTask) taskMonitor).setCancel(false);
+ }
+
+ taskMonitor.setStatus("Loading Network Data...");
+
+ // Remove unnecessary listeners:
+ if ((CytoscapeInit.getCyInitParams().getMode() == CyInitParams.GUI)
+ || (CytoscapeInit.getCyInitParams().getMode() == CyInitParams.EMBEDDED_WINDOW)) {
+ Cytoscape.getDesktop().getSwingPropertyChangeSupport()
+ .removePropertyChangeListener(Cytoscape.getDesktop().getBirdsEyeViewHandler());
+ }
+
+ try {
+ taskMonitor.setPercentCompleted(-1);
+
+ taskMonitor.setStatus("Creating Cytoscape Network...");
+
+ final CyNetwork cyNetwork = Cytoscape.createNetwork(reader, true, null);
+
+ Object[] ret_val = new Object[2];
+ ret_val[0] = cyNetwork;
+ ret_val[1] = uri;
+
+ if ((CytoscapeInit.getCyInitParams().getMode() == CyInitParams.GUI)
+ || (CytoscapeInit.getCyInitParams().getMode() == CyInitParams.EMBEDDED_WINDOW)) {
+ Cytoscape.getDesktop().getSwingPropertyChangeSupport()
+ .addPropertyChangeListener(Cytoscape.getDesktop().getBirdsEyeViewHandler());
+ Cytoscape.getDesktop().getNetworkViewManager()
+ .firePropertyChange(CytoscapeDesktop.NETWORK_VIEW_FOCUSED, null,
+ Cytoscape.getCurrentNetworkView().getNetwork()
+ .getIdentifier());
+ }
+
+ Cytoscape.firePropertyChange(Cytoscape.NETWORK_LOADED, null, ret_val);
+
+ if (cyNetwork != null) {
+ informUserOfGraphStats(cyNetwork);
+ } else {
+ StringBuffer sb = new StringBuffer();
+ sb.append("Could not read network from: ");
+ sb.append(name);
+ sb.append("\nThis file may not be a valid file format.");
+ taskMonitor.setException(new IOException(sb.toString()), sb.toString());
+ }
+
+ taskMonitor.setPercentCompleted(100);
+ } catch (Exception e) {
+ taskMonitor.setException(e, "Unable to load network.");
+
+ return;
+ } finally {
+ reader = null;
+ }
+ }
+
+ /**
+ * Inform User of Network Stats.
+ */
+ private void informUserOfGraphStats(CyNetwork newNetwork) {
+ NumberFormat formatter = new DecimalFormat("#,###,###");
+ StringBuffer sb = new StringBuffer();
+
+ String msg = "";
+ if (reader instanceof NNFReader){
+ final NNFReader theReader = (NNFReader) reader;
+ msg += "Successfully loaded "+ theReader.getNetworks().size() + " nested networks from " + name;
+
+ if (taskLoadStart != 0) // Display how long it took to load the NNs.
+ msg += " in " + (System.nanoTime() - taskLoadStart + 500000L) / 1000000L + "ms.";
+ else
+ msg += ".";
+
+ taskMonitor.setStatus(msg);
+ return;
+ }
+
+ // Give the user some confirmation
+ sb.append("Successfully loaded network from: ");
+ sb.append(name);
+ sb.append("\n\nNetwork contains " + formatter.format(newNetwork.getNodeCount()));
+ sb.append(" nodes and " + formatter.format(newNetwork.getEdgeCount()));
+ sb.append(" edges.\n\n");
+
+ if (newNetwork.getNodeCount() < Integer.parseInt(CytoscapeInit.getProperties()
+ .getProperty("viewThreshold"))) {
+ sb.append("Network is under "
+ + CytoscapeInit.getProperties().getProperty("viewThreshold")
+ + " nodes. A view has been created automatically.");
+ } else {
+ sb.append("Network is over "
+ + CytoscapeInit.getProperties().getProperty("viewThreshold")
+ + " nodes. A view has not been created."
+ + " If you wish to view this network, use "
+ + "\"Create View\" from the \"Edit\" menu.");
+ }
+
+ taskMonitor.setStatus(sb.toString());
+ }
+
+ /**
+ * Halts the Task: Not Currently Implemented.
+ */
+ public void halt() {
+ // Task can not currently be halted.
+ CyLogger.getLogger().info("Halt called");
+
+ if (myThread != null) {
+ myThread.interrupt();
+ this.interrupted = true;
+ ((JTask) taskMonitor).setDone();
+ }
+ }
+
+ /**
+ * Sets the Task Monitor.
+ *
+ * @param taskMonitor
+ * TaskMonitor Object.
+ */
+ public void setTaskMonitor(TaskMonitor taskMonitor) throws IllegalThreadStateException {
+ this.taskMonitor = taskMonitor;
+ }
+
+ /**
+ * Gets the Task Title.
+ *
+ * @return Task Title.
+ */
+ public String getTitle() {
+ if (reader instanceof NNFReader){
+ return new String("Loading Network(s)");
+ }
+
+ return new String("Loading Network");
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/LoggerAction.java b/application/src/main/java/cytoscape/actions/LoggerAction.java
new file mode 100644
index 0000000..8979db2
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/LoggerAction.java
@@ -0,0 +1,23 @@
+package cytoscape.actions;
+
+import cytoscape.util.CytoscapeAction;
+import cytoscape.dialogs.logger.LoggerDialog;
+
+import java.awt.event.ActionEvent;
+
+/**
+ * Created by IntelliJ IDEA. User: skillcoy Date: May 8, 2008 Time: 9:34:03 AM To change this template use File |
+ * Settings | File Templates.
+ */
+public class LoggerAction extends CytoscapeAction
+ {
+ public LoggerAction() {
+ super("Error Console");
+ this.setPreferredMenu("Help");
+ }
+
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ LoggerDialog.getLoggerDialog().setVisible(true);
+ }
+ }
diff --git a/application/src/main/java/cytoscape/actions/MemoryUsageAction.java b/application/src/main/java/cytoscape/actions/MemoryUsageAction.java
new file mode 100644
index 0000000..1cbc4e4
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/MemoryUsageAction.java
@@ -0,0 +1,70 @@
+/*
+ File: MemoryUsageAction.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.actions;
+
+
+import cytoscape.util.CytoscapeAction;
+import cytoscape.util.MemoryReporter;
+
+import java.awt.event.ActionEvent;
+
+import javax.swing.JOptionPane;
+
+
+public class MemoryUsageAction extends CytoscapeAction {
+ /**
+ * Creates a new MemoryUsageAction object and hooks it into the menu system.
+ */
+ public MemoryUsageAction() {
+ super("Memory Usage...");
+ setPreferredMenu("Help");
+ }
+
+ /**
+ * Show memory usage freport.
+ */
+ public void actionPerformed(final ActionEvent e) {
+ final StringBuilder msg =
+ new StringBuilder("used: " + roundToNearestMiB(MemoryReporter.getUsedMemory()) + "MiB\n");
+ final long maximum = MemoryReporter.getMaxMemory();
+ if (maximum == -1L)
+ msg.append("maximum: not available!");
+ else
+ msg.append("maximum: " + roundToNearestMiB(maximum) + "MiB\n");
+ msg.append("committed: " + roundToNearestMiB(MemoryReporter.getCommittedMemory()) + "MiB\n");
+
+ JOptionPane.showMessageDialog(null, msg.toString(), "Memory Usage",
+ JOptionPane.INFORMATION_MESSAGE);
+ }
+
+ private long roundToNearestMiB(final long noOfBytes) {
+ return (noOfBytes + 512L * 1024L) / (1024L * 1024L);
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/NewNetworkAction.java b/application/src/main/java/cytoscape/actions/NewNetworkAction.java
new file mode 100644
index 0000000..fa52e8f
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/NewNetworkAction.java
@@ -0,0 +1,43 @@
+/*
+ * Created on Jul 30, 2005
+ *
+ */
+package cytoscape.actions;
+
+import java.awt.event.ActionEvent;
+
+import javax.swing.JOptionPane;
+import javax.swing.SwingConstants;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import cytoscape.util.CytoscapeAction;
+import cytoscape.util.CyNetworkNaming;
+import cytoscape.view.CyNetworkView;
+
+
+/**
+ * creates a new network and associates an editor with it
+ * @author Allan Kuchinsky, Agilent Technologies
+ * @version 1.0
+ *
+ */
+public class NewNetworkAction extends CytoscapeAction {
+
+ private static final long serialVersionUID = -5729080768973677821L;
+
+ /**
+ * Creates a new NewNetworkAction object.
+ */
+ public NewNetworkAction() {
+ super("Empty Network");
+ setPreferredMenu("File.New.Network");
+ }
+
+ /**
+ * create the new network and view
+ */
+ public void actionPerformed(ActionEvent e) {
+ CyNetwork newNet = Cytoscape.createNetwork( CyNetworkNaming.getSuggestedNetworkTitle("Network") );
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/NewSessionAction.java b/application/src/main/java/cytoscape/actions/NewSessionAction.java
new file mode 100644
index 0000000..6d9e330
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/NewSessionAction.java
@@ -0,0 +1,88 @@
+/*
+ File: NewSessionAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.actions;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.util.CytoscapeAction;
+
+import java.awt.event.ActionEvent;
+
+import javax.swing.JOptionPane;
+
+
+/**
+ *
+ */
+public class NewSessionAction extends CytoscapeAction {
+ /**
+ * Creates a new NewSessionAction object.
+ */
+ public NewSessionAction() {
+ super("Session");
+ setPreferredMenu("File.New");
+ }
+
+ // Create dialog
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+
+ // Show warning
+ String warning = "Current session (all networks/attributes) will be lost.\nDo you want to continue?";
+
+ int result = JOptionPane.showConfirmDialog(Cytoscape.getDesktop(), warning, "Caution!",
+ JOptionPane.YES_NO_OPTION,
+ JOptionPane.WARNING_MESSAGE, null);
+
+ if (result == JOptionPane.YES_OPTION) {
+ Cytoscape.setSessionState(Cytoscape.SESSION_OPENED);
+ Cytoscape.createNewSession();
+ Cytoscape.getDesktop().setTitle("Cytoscape Desktop (New Session)");
+ Cytoscape.getDesktop().getNetworkPanel().repaint();
+ Cytoscape.getDesktop().repaint();
+ Cytoscape.setSessionState(Cytoscape.SESSION_NEW);
+
+ Cytoscape.getPropertyChangeSupport().firePropertyChange(Cytoscape.CYTOSCAPE_INITIALIZED, null, null);
+ } else {
+ return;
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/NewWindowSelectedNodesEdgesAction.java b/application/src/main/java/cytoscape/actions/NewWindowSelectedNodesEdgesAction.java
new file mode 100644
index 0000000..ae35180
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/NewWindowSelectedNodesEdgesAction.java
@@ -0,0 +1,144 @@
+/*
+ File: NewWindowSelectedNodesEdgesAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+//-------------------------------------------------------------------------
+// $Revision: 19327 $
+// $Date: 2010-02-12 23:01:44 +0100 (Fri, 12 Feb 2010) $
+// $Author: ruschein $
+//-------------------------------------------------------------------------
+package cytoscape.actions;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+
+import cytoscape.util.CyNetworkNaming;
+import cytoscape.util.CytoscapeAction;
+
+import cytoscape.view.CyNetworkView;
+import cytoscape.visual.VisualStyle;
+
+//-------------------------------------------------------------------------
+import giny.model.Node;
+import java.awt.event.ActionEvent;
+
+import java.util.Iterator;
+import java.util.Set;
+
+import javax.swing.event.MenuEvent;
+
+
+//-------------------------------------------------------------------------
+/**
+ *
+ */
+public class NewWindowSelectedNodesEdgesAction extends CytoscapeAction {
+ /**
+ * Creates a new NewWindowSelectedNodesEdgesAction object.
+ */
+ public NewWindowSelectedNodesEdgesAction() {
+ super("From Selected Nodes, Selected Edges");
+ setPreferredMenu("File.New.Network");
+ setAcceleratorCombo(java.awt.event.KeyEvent.VK_N,
+ ActionEvent.CTRL_MASK | ActionEvent.SHIFT_MASK);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ // keep ref to current state
+ CyNetwork current_network = Cytoscape.getCurrentNetwork();
+ CyNetworkView current_network_view = Cytoscape.getCurrentNetworkView();
+
+ if ((current_network == null) || (current_network == Cytoscape.getNullNetwork()))
+ return;
+
+ Set nodes = current_network.getSelectedNodes();
+ Set edges = current_network.getSelectedEdges();
+
+ CyNetwork new_network = Cytoscape.createNetwork(nodes, edges,
+ CyNetworkNaming.getSuggestedSubnetworkTitle(current_network),
+ current_network);
+
+ String title = " selection";
+ CyNetworkView new_network_view = Cytoscape.createNetworkView(new_network, title);
+
+ String vsName = "default";
+
+ // keep the node positions
+ if (current_network_view != Cytoscape.getNullNetworkView()) {
+ Iterator i = new_network.nodesIterator();
+
+ while (i.hasNext()) {
+ Node node = (Node) i.next();
+ new_network_view.getNodeView(node)
+ .setOffset(current_network_view.getNodeView(node).getXPosition(),
+ current_network_view.getNodeView(node).getYPosition());
+ }
+
+ new_network_view.fitContent();
+
+ // Set visual style
+ VisualStyle newVS = current_network_view.getVisualStyle();
+
+ if (newVS != null) {
+ vsName = newVS.getName();
+ }
+ }
+ Cytoscape.getVisualMappingManager().setVisualStyle(vsName);
+ }
+
+ public void menuSelected(MenuEvent e) {
+ CyNetwork n = Cytoscape.getCurrentNetwork();
+ if ( n == null || n == Cytoscape.getNullNetwork() ) {
+ setEnabled(false);
+ return;
+ }
+
+ java.util.Set edges = n.getSelectedEdges();
+ java.util.Set nodes = n.getSelectedNodes();
+
+ if ( ( nodes != null && nodes.size() > 0 ) ||
+ ( edges != null && edges.size() > 0 ) )
+ setEnabled(true);
+ else
+ setEnabled(false);
+
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/NewWindowSelectedNodesOnlyAction.java b/application/src/main/java/cytoscape/actions/NewWindowSelectedNodesOnlyAction.java
new file mode 100644
index 0000000..d0d28b8
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/NewWindowSelectedNodesOnlyAction.java
@@ -0,0 +1,153 @@
+/*
+ File: NewWindowSelectedNodesOnlyAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+//-------------------------------------------------------------------------
+// $Revision: 22311 $
+// $Date: 2010-10-20 19:47:14 +0200 (Wed, 20 Oct 2010) $
+// $Author: pwang $
+//-------------------------------------------------------------------------
+package cytoscape.actions;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+
+import cytoscape.util.CyNetworkNaming;
+import cytoscape.util.CytoscapeAction;
+
+import cytoscape.view.CyNetworkView;
+
+import cytoscape.visual.VisualStyle;
+
+//-------------------------------------------------------------------------
+import giny.model.Node;
+
+import java.awt.event.ActionEvent;
+
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.Set;
+
+import javax.swing.event.MenuEvent;
+
+/**
+ *
+ */
+public class NewWindowSelectedNodesOnlyAction extends CytoscapeAction {
+ /**
+ * Creates a new NewWindowSelectedNodesOnlyAction object.
+ */
+ public NewWindowSelectedNodesOnlyAction() {
+ super("From Selected Nodes, All Edges");
+ setPreferredMenu("File.New.Network");
+ setAcceleratorCombo(java.awt.event.KeyEvent.VK_N, ActionEvent.CTRL_MASK);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ // save the vizmapper catalog
+ CyNetwork current_network = Cytoscape.getCurrentNetwork();
+
+ if ((current_network == null) || (current_network == Cytoscape.getNullNetwork()))
+ return;
+
+ CyNetworkView current_network_view = null;
+
+ if (Cytoscape.viewExists(current_network.getIdentifier())) {
+ current_network_view = Cytoscape.getNetworkView(current_network.getIdentifier());
+ } // end of if ()
+
+ Set nodes = current_network.getSelectedNodes();
+
+ if (nodes == null || nodes.size() == 0){
+ return;
+ }
+
+ CyNetwork new_network = Cytoscape.createNetwork(nodes,
+ current_network.getConnectingEdges(new ArrayList(nodes)),
+ CyNetworkNaming.getSuggestedSubnetworkTitle(current_network),
+ current_network);
+
+ CyNetworkView new_view = Cytoscape.getNetworkView(new_network.getIdentifier());
+
+ if (new_view == Cytoscape.getNullNetworkView()) {
+ return;
+ }
+
+ String vsName = "default";
+
+ // keep the node positions
+ if (current_network_view != Cytoscape.getNullNetworkView()) {
+ Iterator i = new_network.nodesIterator();
+
+ while (i.hasNext()) {
+ Node node = (Node) i.next();
+ new_view.getNodeView(node)
+ .setOffset(current_network_view.getNodeView(node).getXPosition(),
+ current_network_view.getNodeView(node).getYPosition());
+ }
+
+ new_view.fitContent();
+
+ // Set visual style
+ VisualStyle newVS = current_network_view.getVisualStyle();
+
+ if (newVS != null) {
+ vsName = newVS.getName();
+ }
+ }
+ Cytoscape.getVisualMappingManager().setVisualStyle(vsName);
+ }
+
+ public void menuSelected(MenuEvent e) {
+ CyNetwork n = Cytoscape.getCurrentNetwork();
+ if ( n == null || n == Cytoscape.getNullNetwork() ) {
+ setEnabled(false);
+ return;
+ }
+
+ java.util.Set nodes = n.getSelectedNodes();
+
+ if ( nodes != null && nodes.size() > 0 )
+ setEnabled(true);
+ else
+ setEnabled(false);
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/OpenSessionAction.java b/application/src/main/java/cytoscape/actions/OpenSessionAction.java
new file mode 100644
index 0000000..a96b555
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/OpenSessionAction.java
@@ -0,0 +1,269 @@
+/*
+ File: OpenSessionAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.actions;
+
+import cytoscape.Cytoscape;
+import cytoscape.logger.CyLogger;
+
+import cytoscape.data.readers.CytoscapeSessionReader;
+import cytoscape.data.readers.XGMMLException;
+
+import cytoscape.task.Task;
+import cytoscape.task.TaskMonitor;
+
+import cytoscape.task.ui.JTaskConfig;
+
+import cytoscape.task.util.TaskManager;
+
+import cytoscape.util.CyFileFilter;
+import cytoscape.util.CytoscapeAction;
+import cytoscape.util.FileUtil;
+
+import cytoscape.view.CyMenus;
+
+import java.awt.event.ActionEvent;
+
+import java.io.File;
+import java.io.IOException;
+
+import javax.swing.JOptionPane;
+
+import javax.xml.bind.JAXBException;
+
+
+/**
+ * Call the session reader and read everything in the zip archive.<br>
+ *
+ * @version 1.0
+ * @since Cytoscape 2.3
+ * @see cytoscape.data.readers.CytoscapeSessionReader
+ * @author kono
+ *
+ */
+public class OpenSessionAction extends CytoscapeAction {
+ protected CyMenus windowMenu;
+ protected static CyLogger logger = CyLogger.getLogger(OpenSessionAction.class);
+
+ // Extension for the new cytoscape session file
+ /**
+ *
+ */
+ public static final String SESSION_EXT = "cys";
+
+ /**
+ * Constructor.<br>
+ * Add a menu item under "File" and set shortcut.
+ */
+ public OpenSessionAction() {
+ super("Open");
+ setPreferredMenu("File");
+ setAcceleratorCombo(java.awt.event.KeyEvent.VK_O, ActionEvent.CTRL_MASK);
+ this.windowMenu = null;
+ }
+
+ /**
+ * Constructor for the Icon button on the toolbar.<br>
+ *
+ * @param windowMenu
+ * @param label
+ */
+ public OpenSessionAction(CyMenus windowMenu, boolean label) {
+ super();
+ this.windowMenu = windowMenu;
+ }
+
+ /**
+ * Clear current session and open the cys file.
+ */
+ public void actionPerformed(ActionEvent e) {
+ String name; // Name of the file to be opened.
+ final boolean proceed = prepare();
+
+ if (proceed) {
+ // Create FileFilters
+ final CyFileFilter sessionFilter = new CyFileFilter();
+
+ // Add accepted File Extensions
+ sessionFilter.addExtension(SESSION_EXT);
+ sessionFilter.setDescription("Cytoscape Session files");
+
+ // Open Dialog to ask user the file name.
+ try {
+ name = FileUtil.getFile("Open a Session File", FileUtil.LOAD,
+ new CyFileFilter[] { sessionFilter }).toString();
+ } catch (Exception exp) {
+ // this is because the selection was canceled
+ return;
+ }
+
+ // Close all networks in the workspace.
+ Cytoscape.setSessionState(Cytoscape.SESSION_OPENED);
+ Cytoscape.createNewSession();
+ Cytoscape.setSessionState(Cytoscape.SESSION_NEW);
+
+ logger.info("Opening session file: " + name);
+
+ // Create Task
+ final OpenSessionTask task = new OpenSessionTask(name);
+
+ // Configure JTask Dialog Pop-Up Box
+ final JTaskConfig jTaskConfig = new JTaskConfig();
+ jTaskConfig.setOwner(Cytoscape.getDesktop());
+ jTaskConfig.displayCloseButton(true);
+ jTaskConfig.displayCancelButton(false);
+ jTaskConfig.displayStatus(true);
+ jTaskConfig.setAutoDispose(false);
+
+ // Execute Task in New Thread; pop open JTask Dialog Box.
+ TaskManager.executeTask(task, jTaskConfig);
+ }
+ }
+
+ /**
+ * Before loading the new session, we need to clean up current session.
+ *
+ */
+ private boolean prepare() {
+ final int currentNetworkCount = Cytoscape.getNetworkSet().size();
+
+ if (currentNetworkCount != 0) {
+ // Show warning
+ final String warning = "Current session will be lost.\nDo you want to continue?";
+
+ final int result = JOptionPane.showConfirmDialog(Cytoscape.getDesktop(), warning,
+ "Caution!", JOptionPane.YES_NO_OPTION,
+ JOptionPane.WARNING_MESSAGE, null);
+
+ if (result == JOptionPane.YES_OPTION) {
+ return true;
+ } else {
+ return false;
+ }
+ } else {
+ return true;
+ }
+ }
+} // SaveAsGMLAction
+
+
+class OpenSessionTask implements Task {
+ private String fileName;
+ private TaskMonitor taskMonitor;
+
+ /**
+ * Constructor.<br>
+ *
+ * @param fileName
+ * Session file name
+ */
+ OpenSessionTask(String fileName) {
+ this.fileName = fileName;
+ }
+
+ /**
+ * Executes Task
+ *
+ * @throws
+ * @throws Exception
+ */
+ public void run() {
+ taskMonitor.setStatus("Opening Session File.\n\nIt may take a while.\nPlease wait...");
+ taskMonitor.setPercentCompleted(0);
+
+ CytoscapeSessionReader sr;
+
+ try {
+ sr = new CytoscapeSessionReader(fileName, taskMonitor);
+ sr.read();
+ } catch (IOException e) {
+ taskMonitor.setException(e, "Cannot open the session file: " + e.getMessage());
+ OpenSessionAction.logger.error("Cannot open the session file: "+ e.getMessage(), e);
+ } catch (JAXBException e) {
+ taskMonitor.setException(e, "Cannot unmarshall document: " + e.getMessage());
+ OpenSessionAction.logger.error("Cannot unmarshall document: "+ e.getMessage(), e);
+ } catch (XGMMLException e) {
+ taskMonitor.setException(e, "XGMML format error in network: "+e.getMessage());
+ OpenSessionAction.logger.error("XGMML format error in network "+ e.getMessage(), e);
+ } catch (Exception e) { // catch any exception: the user should know something went wrong
+ taskMonitor.setException(e, "Error while loading session " + e.getMessage());
+ OpenSessionAction.logger.error("Error while loading session: "+ e.getMessage(), e);
+ } finally {
+ sr = null;
+ Cytoscape.getDesktop().getVizMapperUI().initVizmapperGUI();
+ System.gc();
+ }
+
+ taskMonitor.setPercentCompleted(100);
+ taskMonitor.setStatus("Session file " + fileName + " successfully loaded.");
+
+ Cytoscape.setCurrentSessionFileName(fileName);
+
+ final File sessionFile = new File(fileName);
+ Cytoscape.getDesktop().setTitle("Cytoscape Desktop (Session: " + sessionFile.getName()
+ + ")");
+ }
+
+ /**
+ * Halts the Task: Not Currently Implemented.
+ */
+ public void halt() {
+ // Task can not currently be halted.
+
+ OpenSessionAction.logger.info("HALT called!!!");
+ taskMonitor.setPercentCompleted(100);
+ taskMonitor.setStatus("Failed!!!");
+ }
+
+ /**
+ * Sets the Task Monitor.
+ *
+ * @param taskMonitor
+ * TaskMonitor Object.
+ */
+ public void setTaskMonitor(TaskMonitor taskMonitor) throws IllegalThreadStateException {
+ this.taskMonitor = taskMonitor;
+ }
+
+ /**
+ * Gets the Task Title.
+ *
+ * @return Task Title.
+ */
+ public String getTitle() {
+ return "Opening Session File";
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/PluginInstallAction.java b/application/src/main/java/cytoscape/actions/PluginInstallAction.java
new file mode 100644
index 0000000..9af9477
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/PluginInstallAction.java
@@ -0,0 +1,93 @@
+/**
+ *
+ */
+package cytoscape.actions;
+
+import java.awt.event.ActionEvent;
+
+import cytoscape.Cytoscape;
+import cytoscape.logger.CyLogger;
+
+import cytoscape.task.ui.JTaskConfig;
+import cytoscape.util.CyFileFilter;
+import cytoscape.util.CytoscapeAction;
+import cytoscape.util.FileUtil;
+
+import cytoscape.dialogs.plugins.PluginUpdateDialog;
+
+import cytoscape.plugin.DownloadableInfo;
+import cytoscape.plugin.PluginInfo;
+import cytoscape.plugin.PluginManager;
+import cytoscape.plugin.ManagerException;
+import cytoscape.plugin.PluginStatus;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStream;
+import java.net.MalformedURLException;
+import java.util.List;
+import java.util.ArrayList;
+
+import javax.swing.JOptionPane;
+
+public class PluginInstallAction extends CytoscapeAction {
+ protected static CyLogger logger = CyLogger.getLogger(PluginInstallAction.class);
+
+ public PluginInstallAction() {
+ super("Install Plugin from File");
+ setPreferredMenu("Plugins");
+
+ if (PluginManager.usingWebstartManager()) {
+ setEnabled(false);
+ }
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ if (PluginManager.usingWebstartManager())
+ return;
+
+ PluginManager manager = PluginManager.getPluginManager();
+
+ // Get the jar file
+ File[] jarFiles = FileUtil.getFiles("Select Plugin File", FileUtil.LOAD,
+ new CyFileFilter[] {new CyFileFilter("jar")});
+
+ if (jarFiles == null || jarFiles.length == 0) return;
+
+ File tempDir = manager.getPluginManageDirectory();
+
+ for (File file: jarFiles) {
+ // Copy the file into the temp directory
+ File outputFile = new File(tempDir, file.getName());
+ try {
+ copyfile(file, outputFile);
+
+ // Now we know what we want to load -- load it.
+ manager.loadPlugin(outputFile);
+ } catch (Exception ex) {
+ JOptionPane.showMessageDialog(Cytoscape.getDesktop(), "Unable to install plugin: "+ex,
+ "Plugin install error", JOptionPane.ERROR_MESSAGE);
+ logger.error("Unable to install plugin: "+ex.getMessage(), ex);
+ }
+ }
+ return;
+ }
+
+ private void copyfile(File src, File dest) throws FileNotFoundException, IOException {
+ InputStream in = new FileInputStream(src);
+ OutputStream out = new FileOutputStream(dest);
+
+ byte [] buf = new byte[4096];
+ int len;
+ while ((len = in.read(buf)) > 0) {
+ out.write(buf, 0, len);
+ }
+ in.close();
+ out.close();
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/actions/PluginManagerAction.java b/application/src/main/java/cytoscape/actions/PluginManagerAction.java
new file mode 100644
index 0000000..62d8dc3
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/PluginManagerAction.java
@@ -0,0 +1,194 @@
+/*
+ File: PluginManagerAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+// EdgeControlDialog
+//---------------------------------------------------------------------------------------
+// $Revision: 9565 $
+// $Date: 2007-02-13 11:36:50 -0800 (Tue, 13 Feb 2007) $
+// $Author: mes $
+//---------------------------------------------------------------------------------------
+package cytoscape.actions;
+
+import cytoscape.Cytoscape;
+import cytoscape.logger.CyLogger;
+//import cytoscape.CytoscapeInit;
+
+import cytoscape.bookmarks.Bookmarks;
+//import cytoscape.bookmarks.Category;
+import cytoscape.bookmarks.DataSource;
+
+import cytoscape.dialogs.plugins.PluginManageDialog;
+import cytoscape.dialogs.plugins.PluginManageDialog.PluginInstallStatus;
+
+import cytoscape.plugin.DownloadableInfo;
+//import cytoscape.plugin.PluginInfo;
+import cytoscape.plugin.PluginManager;
+import cytoscape.plugin.PluginInquireAction;
+import cytoscape.plugin.ManagerUtil;
+import cytoscape.plugin.PluginStatus;
+
+import cytoscape.task.ui.JTaskConfig;
+import cytoscape.task.util.TaskManager;
+import cytoscape.util.BookmarksUtil;
+import cytoscape.util.CytoscapeAction;
+
+import java.awt.event.ActionEvent;
+
+import java.util.List;
+import java.util.Map;
+
+public class PluginManagerAction extends CytoscapeAction {
+ private String bookmarkCategory = "plugins";
+ private CyLogger logger = CyLogger.getLogger(PluginManagerAction.class);
+
+ public PluginManagerAction() {
+ super("Manage Plugins");
+ setPreferredMenu("Plugins");
+ }
+
+ /**
+ * Gets the lists of plugins and creates the ManagerDialog for users.
+ *
+ * @param e
+ *
+ */
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ PluginManageDialog dialog = new PluginManageDialog(Cytoscape.getDesktop());
+
+ PluginManager Mgr = PluginManager.getPluginManager();
+
+ // this actually won't ever get called I think because the PM already has the trackign document in memory
+ // but in case it ever does get called...
+ if (Mgr.getLoadingErrors().size() > 0) {
+ String message = "";
+ for (Throwable t: Mgr.getLoadingErrors())
+ message += t.getMessage() + "\n";
+ javax.swing.JOptionPane.showMessageDialog(Cytoscape.getDesktop(), message,
+ "Plugin Manager Error", javax.swing.JOptionPane.ERROR_MESSAGE);
+ }
+
+ String DefaultUrl = cytoscape.CytoscapeInit.getProperties().getProperty("defaultPluginDownloadUrl");
+ String DefaultTitle = "Cytoscape";
+
+ try {
+ Bookmarks theBookmarks = Cytoscape.getBookmarks();
+ // Extract the URL entries
+ List<DataSource> DataSourceList = BookmarksUtil.getDataSourceList(
+ bookmarkCategory, theBookmarks.getCategory());
+
+ for (DataSource ds : DataSourceList) {
+ if (ds.getName().equals("Cytoscape")) {
+ DefaultUrl = ds.getHref();
+ DefaultTitle = ds.getName();
+ break;
+ }
+ }
+ } catch (Exception E) {
+ logger.warn("There was an error while reading the bookmarks file.", E);
+ }
+
+ List<DownloadableInfo> Current = Mgr.getDownloadables(PluginStatus.CURRENT);
+ Map<String, List<DownloadableInfo>> InstalledInfo = ManagerUtil.sortByCategory(Current);
+
+ for (String Category : InstalledInfo.keySet()) {
+ dialog.addCategory(Category, InstalledInfo.get(Category),
+ PluginInstallStatus.INSTALLED);
+ }
+
+ cytoscape.task.Task task = new cytoscape.plugin.PluginManagerInquireTask(DefaultUrl, new ManagerAction(dialog, DefaultTitle, DefaultUrl));
+
+ // Configure JTask Dialog Pop-Up Box
+ JTaskConfig jTaskConfig = new JTaskConfig();
+ jTaskConfig.setOwner(Cytoscape.getDesktop());
+ jTaskConfig.displayCloseButton(false);
+ jTaskConfig.displayStatus(true);
+ jTaskConfig.setAutoDispose(true);
+ jTaskConfig.displayCancelButton(false);
+ // Execute Task in New Thread; pop open JTask Dialog Box.
+ TaskManager.executeTask(task, jTaskConfig);
+ }
+
+
+ private class ManagerAction extends PluginInquireAction {
+ private CyLogger logger = CyLogger.getLogger(ManagerAction.class);
+
+ private PluginManageDialog dialog;
+ private String title;
+ private String url;
+
+ public ManagerAction(PluginManageDialog Dialog, String Title, String Url) {
+ dialog = Dialog;
+ title = Title;
+ url = Url;
+ }
+
+ public String getProgressBarMessage() {
+ return "Attempting to connect to " + url;
+ }
+
+ public void inquireAction(List<DownloadableInfo> Results) {
+ PluginManager Mgr = PluginManager.getPluginManager();
+ if (isExceptionThrown()) {
+ if (getIOException() != null) {
+ // failed to read the given url
+ logger.error(getIOException().getMessage(), getIOException());
+ dialog.setError(PluginManageDialog.CommonError.NOXML.toString());
+ } else if (getJDOMException() != null) {
+ // failed to parse the xml file at the url
+ logger.error(getJDOMException().getMessage(), getJDOMException());
+ dialog.setError(PluginManageDialog.CommonError.BADXML.toString());
+ } else {
+ logger.error(getException().getMessage(), getException());
+ dialog.setError(getException().getMessage());
+ }
+ } else {
+ List<DownloadableInfo> Unique = ManagerUtil.getUnique(Mgr.getDownloadables(PluginStatus.CURRENT), Results);
+ Map<String, List<DownloadableInfo>> AvailableInfo = ManagerUtil.sortByCategory(Unique);
+
+ for (String Category : AvailableInfo.keySet()) {
+ // get only the unique ones
+ dialog.addCategory(Category, AvailableInfo.get(Category),
+ PluginInstallStatus.AVAILABLE);
+ }
+ }
+ dialog.setSiteName(title);
+ dialog.setVisible(true);
+ }
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/actions/PluginUpdateAction.java b/application/src/main/java/cytoscape/actions/PluginUpdateAction.java
new file mode 100644
index 0000000..4a04570
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/PluginUpdateAction.java
@@ -0,0 +1,85 @@
+/**
+ *
+ */
+package cytoscape.actions;
+
+import java.awt.event.ActionEvent;
+
+import cytoscape.Cytoscape;
+import cytoscape.logger.CyLogger;
+
+import cytoscape.task.ui.JTaskConfig;
+import cytoscape.util.CytoscapeAction;
+
+import cytoscape.dialogs.plugins.PluginUpdateDialog;
+
+import cytoscape.plugin.DownloadableInfo;
+import cytoscape.plugin.PluginInfo;
+import cytoscape.plugin.PluginManager;
+import cytoscape.plugin.ManagerException;
+import cytoscape.plugin.PluginStatus;
+
+import java.util.List;
+import java.util.ArrayList;
+
+import javax.swing.JOptionPane;
+
+public class PluginUpdateAction extends CytoscapeAction {
+ protected static CyLogger logger = CyLogger.getLogger(PluginUpdateAction.class);
+
+ public PluginUpdateAction() {
+ super("Update Plugins");
+ setPreferredMenu("Plugins");
+
+ if (PluginManager.usingWebstartManager()) {
+ setEnabled(false);
+ }
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ PluginUpdateDialog dialog = new PluginUpdateDialog(Cytoscape.getDesktop());
+ dialog.setVisible(false);
+ ArrayList<String> xmlIncorrect = new ArrayList<String>();
+
+ if (!PluginManager.usingWebstartManager()) {
+ boolean updateFound = false;
+ PluginManager mgr = PluginManager.getPluginManager();
+ // Find updates
+ for (DownloadableInfo current : mgr.getDownloadables(PluginStatus.CURRENT)) {
+
+ try {
+ List<DownloadableInfo> updates = mgr.findUpdates(current);
+ if (updates.size() > 0) {
+ dialog.addCategory(current.getCategory(), current, updates);
+ updateFound = true;
+ }
+ } catch (org.jdom.JDOMException jde) {
+ logger.warn(jde.getMessage());
+ xmlIncorrect.add(current.toString());
+ } catch (java.io.IOException ioe) {
+ logger.warn("Failed to read XML file for "
+ + current.getName() + " at "
+ + current.getDownloadableURL(), ioe);
+ xmlIncorrect.add(current.toString());
+ }
+
+ }
+ if (xmlIncorrect.size() > 0) {
+ // show option pane warning message?
+ }
+
+ if (updateFound) {
+ dialog.setVisible(true);
+ } else {
+ JOptionPane.showMessageDialog(Cytoscape.getDesktop(),
+ "No updates available for currently installed plugins.",
+ "Plugin Updates", JOptionPane.INFORMATION_MESSAGE);
+ }
+ } else {
+ JOptionPane.showMessageDialog( Cytoscape.getDesktop(),
+ "Plugin updates are not available when using Cytoscape through webstart",
+ "Plugin Update", JOptionPane.INFORMATION_MESSAGE);
+ }
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/actions/PreferenceAction.java b/application/src/main/java/cytoscape/actions/PreferenceAction.java
new file mode 100644
index 0000000..4033d79
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/PreferenceAction.java
@@ -0,0 +1,87 @@
+/*
+ File: PreferenceAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+//-------------------------------------------------------------------------
+// $Revision: 14060 $
+// $Date: 2008-05-20 22:13:18 +0200 (Tue, 20 May 2008) $
+// $Author: skillcoyne $
+//-------------------------------------------------------------------------
+package cytoscape.actions;
+
+import cytoscape.Cytoscape;
+import cytoscape.logger.CyLogger;
+
+import cytoscape.dialogs.preferences.*;
+
+import cytoscape.giny.*;
+
+import cytoscape.util.*;
+import cytoscape.util.CytoscapeAction;
+
+import cytoscape.view.CyNetworkView;
+
+import java.awt.event.ActionEvent;
+
+import javax.swing.AbstractAction;
+import javax.swing.JFrame;
+
+
+/**
+ *
+ */
+public class PreferenceAction extends CytoscapeAction {
+ /**
+ * Creates a new PreferenceAction object.
+ */
+ public PreferenceAction() {
+ super("Properties...");
+
+ CyLogger.getLogger().info("PreferenceAction()...");
+ setPreferredMenu("Edit.Preferences");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ PreferencesDialog preferencesDialog = new PreferencesDialog((JFrame) Cytoscape.getDesktop());
+ preferencesDialog.refresh();
+ preferencesDialog.setVisible(true);
+ } // actionPerformed
+}
diff --git a/application/src/main/java/cytoscape/actions/PrintAction.java b/application/src/main/java/cytoscape/actions/PrintAction.java
new file mode 100644
index 0000000..eb48459
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/PrintAction.java
@@ -0,0 +1,125 @@
+/*
+ File: PrintAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+//-------------------------------------------------------------------------
+// $Revision: 14737 $
+// $Date: 2008-08-19 02:41:03 +0200 (Tue, 19 Aug 2008) $
+// $Author: scooter $
+//-------------------------------------------------------------------------
+package cytoscape.actions;
+
+import cytoscape.Cytoscape;
+import cytoscape.CytoscapeInit;
+
+import cytoscape.ding.DingNetworkView;
+import cytoscape.ding.DingNetworkView;
+
+import cytoscape.giny.*;
+
+import cytoscape.logger.CyLogger;
+
+import cytoscape.util.*;
+import cytoscape.util.CytoscapeAction;
+
+import cytoscape.view.CyNetworkView;
+import cytoscape.view.InternalFrameComponent;
+
+import ding.view.DGraphView;
+
+import java.awt.Component;
+import java.awt.Graphics;
+import java.awt.PrintJob;
+import java.awt.Toolkit;
+import java.awt.event.ActionEvent;
+import java.awt.print.PrinterJob;
+
+import javax.swing.AbstractAction;
+
+import javax.swing.event.MenuEvent;
+
+
+/**
+ *
+ */
+public class PrintAction extends CytoscapeAction {
+ /**
+ *
+ */
+ public final static String MENU_LABEL = "Print...";
+
+ /**
+ * Creates a new PrintAction object.
+ */
+ public PrintAction() {
+ super(MENU_LABEL);
+ setPreferredMenu("File");
+ setAcceleratorCombo(java.awt.event.KeyEvent.VK_P, ActionEvent.CTRL_MASK);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ CyNetworkView curr = Cytoscape.getCurrentNetworkView();
+ InternalFrameComponent ifc = Cytoscape.getDesktop().getNetworkViewManager()
+ .getInternalFrameComponent(curr);
+ PrinterJob printJob = PrinterJob.getPrinterJob();
+
+ // Export text as shape/font based on user's setting
+ DGraphView theViewToPrint = (DingNetworkView) Cytoscape.getCurrentNetworkView();
+ boolean exportTextAsShape = new Boolean(CytoscapeInit.getProperties()
+ .getProperty("exportTextAsShape"))
+ .booleanValue();
+ theViewToPrint.setPrintingTextAsShape(exportTextAsShape);
+
+ printJob.setPrintable(ifc);
+
+ if (printJob.printDialog()) {
+ try {
+ printJob.print();
+ } catch (Exception exc) {
+ CyLogger.getLogger(PrintAction.class).error("Print job failed", exc);
+ }
+ }
+ } // actionPerformed
+
+ public void menuSelected(MenuEvent e) {
+ enableForNetworkAndView();
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/ProxyServerAction.java b/application/src/main/java/cytoscape/actions/ProxyServerAction.java
new file mode 100644
index 0000000..549431a
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/ProxyServerAction.java
@@ -0,0 +1,86 @@
+/*
+ File: PreferenceAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+//-------------------------------------------------------------------------
+// $Revision: 7760 $
+// $Date: 2006-06-26 09:28:49 -0700 (Mon, 26 Jun 2006) $
+// $Author: mes $
+//-------------------------------------------------------------------------
+package cytoscape.actions;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.dialogs.preferences.*;
+import cytoscape.dialogs.preferences.ProxyServerDialog;
+
+import cytoscape.giny.*;
+
+import cytoscape.util.*;
+import cytoscape.util.CytoscapeAction;
+
+import cytoscape.view.CyNetworkView;
+
+import java.awt.event.ActionEvent;
+
+import javax.swing.AbstractAction;
+import javax.swing.JFrame;
+
+
+/**
+ *
+ */
+public class ProxyServerAction extends CytoscapeAction {
+ /**
+ * Creates a new ProxyServerAction object.
+ */
+ public ProxyServerAction() {
+ super("Proxy Server...");
+
+ setPreferredMenu("Edit.Preferences");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ ProxyServerDialog proxyServerDialog = new ProxyServerDialog((JFrame) Cytoscape.getDesktop());
+ //proxyServerDialog.refresh();
+ proxyServerDialog.setVisible(true);
+ } // actionPerformed
+}
diff --git a/application/src/main/java/cytoscape/actions/RotateSelectedNodesAction.java b/application/src/main/java/cytoscape/actions/RotateSelectedNodesAction.java
new file mode 100644
index 0000000..0f9a01a
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/RotateSelectedNodesAction.java
@@ -0,0 +1,82 @@
+/*
+ File: RotateSelectedNodesAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+//-------------------------------------------------------------------------
+// $Revision: 9565 $
+// $Date: 2007-02-13 20:36:50 +0100 (Tue, 13 Feb 2007) $
+// $Author: mes $
+//-------------------------------------------------------------------------
+package cytoscape.actions;
+
+import cytoscape.dialogs.PhoebeNodeControl;
+
+import cytoscape.view.CyNetworkView;
+
+//-------------------------------------------------------------------------
+import java.awt.event.ActionEvent;
+
+import javax.swing.AbstractAction;
+
+
+//-------------------------------------------------------------------------
+/**
+ * Rotates the given selection by the specified amount.
+ *
+ * added by dramage 2002-08-20
+ */
+public class RotateSelectedNodesAction extends AbstractAction {
+ CyNetworkView networkView;
+
+ /**
+ * Creates a new RotateSelectedNodesAction object.
+ *
+ * @param networkView DOCUMENT ME!
+ */
+ public RotateSelectedNodesAction(CyNetworkView networkView) {
+ super("Rotate Selected Nodes");
+ this.networkView = networkView;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ PhoebeNodeControl pnc = new PhoebeNodeControl(networkView.getView());
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/SaveSessionAction.java b/application/src/main/java/cytoscape/actions/SaveSessionAction.java
new file mode 100644
index 0000000..78d9f6a
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/SaveSessionAction.java
@@ -0,0 +1,217 @@
+/*
+ File: SaveSessionAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.actions;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.data.writers.CytoscapeSessionWriter;
+
+import cytoscape.task.Task;
+import cytoscape.task.TaskMonitor;
+
+import cytoscape.task.ui.JTaskConfig;
+
+import cytoscape.task.util.TaskManager;
+
+import cytoscape.util.CyFileFilter;
+import cytoscape.util.CytoscapeAction;
+import cytoscape.util.FileUtil;
+
+import java.awt.event.ActionEvent;
+import java.awt.event.KeyEvent;
+
+import java.io.File;
+
+
+/**
+ * Save Session action.<br>
+ * Write current states into a CYS file.<br>
+ *
+ * @version 1.0
+ * @since Cytoscape 2.3
+ * @see cytoscape.data.writers.CytoscapeSessionWriter
+ * @author kono
+ *
+ */
+public class SaveSessionAction extends CytoscapeAction {
+ // Extension for the new cytoscape session file
+ /**
+ *
+ */
+ public final static String SESSION_EXT = ".cys";
+
+ /**
+ * Constructor.
+ *
+ * @param label
+ * Label for the menu item.
+ */
+ public SaveSessionAction(String label) {
+ super(label);
+ setPreferredMenu("File");
+ setAcceleratorCombo(KeyEvent.VK_S, ActionEvent.CTRL_MASK);
+ }
+
+ /**
+ * Constructor.<br>
+ * This is mainly for the toolbar icon button.<br>
+ *
+ */
+ public SaveSessionAction() {
+ super();
+ }
+
+ /**
+ * If no current session file exists, open dialog box to ask user a new
+ * session file name, otherwise, overwrite the file.
+ */
+ public void actionPerformed(ActionEvent e) {
+ // Call file chooser only when the currentFileName is null.
+ String name = Cytoscape.getCurrentSessionFileName();
+
+ if (name == null) {
+ File file = FileUtil.getFile("Save Current Session as CYS File", FileUtil.SAVE,
+ new CyFileFilter[] { });
+
+ if (file == null) {
+ return;
+ }
+
+ name = file.getAbsolutePath();
+
+ if (!name.endsWith(SESSION_EXT))
+ name = name + SESSION_EXT;
+
+ Cytoscape.setCurrentSessionFileName(name);
+ }
+
+ // Create Task
+ SaveSessionTask task = new SaveSessionTask(name);
+
+ // Configure JTask Dialog Pop-Up Box
+ JTaskConfig jTaskConfig = new JTaskConfig();
+
+ jTaskConfig.displayCancelButton(false);
+ jTaskConfig.setOwner(Cytoscape.getDesktop());
+ jTaskConfig.displayCloseButton(true);
+ jTaskConfig.displayStatus(true);
+ jTaskConfig.setAutoDispose(true);
+
+ // Execute Task in New Thread; pop open JTask Dialog Box.
+ TaskManager.executeTask(task, jTaskConfig);
+ }
+} //End of SaveSessionAction
+
+
+/**
+ * Save Session Task.<br>
+ * Call the Session Writer to save the following:<br>
+ * <ul>
+ * <li>Networks with metadata</li>
+ * <li>All attributes (for nodes, edges, and network)</li>
+ * <li>Visual Styles</li>
+ * <li>Cytoscape Properties</li>
+ * </ul>
+ *
+ * @author kono
+ *
+ */
+class SaveSessionTask implements Task {
+ private String fileName;
+ private TaskMonitor taskMonitor;
+ CytoscapeSessionWriter sw;
+
+ /**
+ * Constructor.<br>
+ *
+ * @param fileName
+ * Absolute path to the Session file.
+ */
+ SaveSessionTask(String fileName) {
+ this.fileName = fileName;
+ // Create session writer object
+ sw = new CytoscapeSessionWriter(fileName);
+ }
+
+ /**
+ * Execute task.<br>
+ */
+ public void run() {
+ taskMonitor.setStatus("Saving Cytoscape Session.\n\nIt may take a while. Please wait...");
+ taskMonitor.setPercentCompleted(-1);
+
+ try {
+ sw.writeSessionToDisk();
+ } catch (Exception e) {
+ taskMonitor.setException(e, "Could not write session to the file: " + fileName);
+ }
+
+ taskMonitor.setPercentCompleted(100);
+ taskMonitor.setStatus("Session successfully saved to: " + fileName);
+
+ // Show the session Name as the window title.
+ File shortName = new File(fileName);
+ Cytoscape.setCurrentSessionFileName(fileName);
+ Cytoscape.getDesktop().setTitle("Cytoscape Desktop (Session: " + shortName.getName() + ")");
+ }
+
+ /**
+ * Halts the Task: Not Currently Implemented.
+ */
+ public void halt() {
+ // Task can not currently be halted.
+ }
+
+ /**
+ * Sets the Task Monitor.
+ *
+ * @param taskMonitor
+ * TaskMonitor Object.
+ */
+ public void setTaskMonitor(TaskMonitor taskMonitor) throws IllegalThreadStateException {
+ this.taskMonitor = taskMonitor;
+ }
+
+ /**
+ * Gets the Task Title.
+ *
+ * @return Task Title.
+ */
+ public String getTitle() {
+ return "Saving Cytoscape Session";
+ }
+} // End of SaveSessionTask
diff --git a/application/src/main/java/cytoscape/actions/SaveSessionAsAction.java b/application/src/main/java/cytoscape/actions/SaveSessionAsAction.java
new file mode 100644
index 0000000..6451ce4
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/SaveSessionAsAction.java
@@ -0,0 +1,123 @@
+/*
+ File: SaveSessionAsAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.actions;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.task.ui.JTaskConfig;
+
+import cytoscape.task.util.TaskManager;
+
+import cytoscape.util.CyFileFilter;
+import cytoscape.util.CytoscapeAction;
+import cytoscape.util.FileUtil;
+
+import java.awt.event.ActionEvent;
+
+
+/**
+ * Same as SaveSessionAction, but always opens file chooser.<br>
+ *
+ * @version 1.0
+ * @since 2.3
+ * @see cytoscape.actions.SaveSessionAction
+ * @see cytoscape.data.writers.CytoscapeSessionWriter
+ * @author kono
+ */
+public class SaveSessionAsAction extends CytoscapeAction {
+ // Extension for the new cytoscape session file
+ /**
+ *
+ */
+ public static String SESSION_EXT = ".cys";
+
+ /**
+ * Constructor.<br>
+ *
+ * @param label Label for menu item
+ */
+ public SaveSessionAsAction(String label) {
+ super(label);
+ setPreferredMenu("File");
+ setAcceleratorCombo(java.awt.event.KeyEvent.VK_S,
+ ActionEvent.CTRL_MASK | ActionEvent.SHIFT_MASK);
+ }
+
+ /**
+ * Creates a new SaveSessionAsAction object.
+ */
+ public SaveSessionAsAction() {
+ super();
+ }
+
+ /**
+ * If no current session file exists, open dialog box to save new session,
+ * and if it exists, overwrite the file.
+ *
+ */
+ public void actionPerformed(ActionEvent e) {
+ String name; // file name
+
+ // Open Dialog to ask user the file name.
+ try {
+ name = FileUtil.getFile("Save Current Session As CYS File", FileUtil.SAVE,
+ new CyFileFilter[] { }).toString();
+ } catch (Exception exp) {
+ // this is because the selection was canceled
+ return;
+ }
+
+ if (!name.endsWith(SESSION_EXT))
+ name = name + SESSION_EXT;
+
+ Cytoscape.setCurrentSessionFileName(name);
+
+ // Create Task
+ SaveSessionTask task = new SaveSessionTask(name);
+
+ // Configure JTask Dialog Pop-Up Box
+ JTaskConfig jTaskConfig = new JTaskConfig();
+ jTaskConfig.setOwner(Cytoscape.getDesktop());
+ jTaskConfig.displayCloseButton(true);
+ jTaskConfig.displayCancelButton(false);
+ jTaskConfig.displayStatus(true);
+ jTaskConfig.setAutoDispose(false);
+
+ // Execute Task in New Thread; pop open JTask Dialog Box.
+ TaskManager.executeTask(task, jTaskConfig);
+ }
+} // End of SaveSessionAsAction
diff --git a/application/src/main/java/cytoscape/actions/SelectAdjacentEdgesAction.java b/application/src/main/java/cytoscape/actions/SelectAdjacentEdgesAction.java
new file mode 100644
index 0000000..c2d7f68
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/SelectAdjacentEdgesAction.java
@@ -0,0 +1,111 @@
+/*
+ File: SelectAdjacentEdgesAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+//-------------------------------------------------------------------------
+// $Revision: 11118 $
+// $Date: 2007-07-24 14:42:07 -0700 (Tue, 24 Jul 2007) $
+// $Author: mes $
+//-------------------------------------------------------------------------
+package cytoscape.actions;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.CyNetwork;
+
+import cytoscape.CyNode;
+
+import cytoscape.CyEdge;
+
+import cytoscape.util.CytoscapeAction;
+
+//-------------------------------------------------------------------------
+import java.awt.event.ActionEvent;
+
+import java.util.Set;
+
+import java.util.HashMap;
+
+import javax.swing.event.MenuEvent;
+
+//-------------------------------------------------------------------------
+/**
+ *
+ */
+public class SelectAdjacentEdgesAction extends CytoscapeAction {
+ /**
+ * Creates a new SelectAdjacentEdgesAction object.
+ */
+ public SelectAdjacentEdgesAction() {
+ super("Select Adjacent Edges");
+ setPreferredMenu("Select.Edges");
+ setAcceleratorCombo(java.awt.event.KeyEvent.VK_E, ActionEvent.ALT_MASK);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ // GinyUtils.selectAllEdges( Cytoscape.getCurrentNetworkView() );
+ CyNetwork network = Cytoscape.getCurrentNetwork();
+ HashMap<CyEdge,CyEdge> edgeMap = new HashMap<CyEdge,CyEdge>();
+
+ // Get the list of selected nodes
+ for (CyNode node: (Set<CyNode>)network.getSelectedNodes()) {
+ // Get the list of edges connected to this node
+ int[] edgeIndices = network.getAdjacentEdgeIndicesArray(node.getRootGraphIndex(), true, true, true);
+ // For each node, select the appropriate edges
+ if (edgeIndices == null)
+ continue;
+
+ for (int i = 0; i < edgeIndices.length; i++) {
+ CyEdge edge = (CyEdge)network.getEdge(edgeIndices[i]);
+ edgeMap.put(edge,edge);
+ }
+ }
+ network.setSelectedEdgeState(edgeMap.keySet(), true);
+
+ if (Cytoscape.getCurrentNetworkView() != null) {
+ Cytoscape.getCurrentNetworkView().updateView();
+ }
+ } // action performed
+
+ public void menuSelected(MenuEvent e) {
+ enableForNetwork();
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/SelectAllAction.java b/application/src/main/java/cytoscape/actions/SelectAllAction.java
new file mode 100644
index 0000000..418e903
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/SelectAllAction.java
@@ -0,0 +1,90 @@
+/*
+ File: SelectAllAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+//-------------------------------------------------------------------------
+// $Revision: 19327 $
+// $Date: 2010-02-12 23:01:44 +0100 (Fri, 12 Feb 2010) $
+// $Author: ruschein $
+//-------------------------------------------------------------------------
+package cytoscape.actions;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.util.CytoscapeAction;
+
+import cytoscape.view.CytoscapeDesktop;
+
+//-------------------------------------------------------------------------
+import java.awt.event.ActionEvent;
+
+import javax.swing.event.MenuEvent;
+
+//-------------------------------------------------------------------------
+/**
+ *
+ */
+public class SelectAllAction extends CytoscapeAction {
+ /**
+ * Creates a new SelectAllAction object.
+ */
+ public SelectAllAction() {
+ super("Select All Nodes and Edges");
+ setPreferredMenu("Select");
+ setAcceleratorCombo(java.awt.event.KeyEvent.VK_A,
+ ActionEvent.CTRL_MASK | ActionEvent.ALT_MASK);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ // GinyUtils.selectAllNodes( Cytoscape.getCurrentNetworkView() );
+ // GinyUtils.selectAllEdges( Cytoscape.getCurrentNetworkView() );
+ Cytoscape.getCurrentNetwork().selectAllNodes();
+ Cytoscape.getCurrentNetwork().selectAllEdges();
+
+ if (Cytoscape.getCurrentNetworkView() != null) {
+ Cytoscape.getCurrentNetworkView().updateView();
+ }
+ } // action performed
+
+ public void menuSelected(MenuEvent e) {
+ enableForNetwork();
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/SelectAllEdgesAction.java b/application/src/main/java/cytoscape/actions/SelectAllEdgesAction.java
new file mode 100644
index 0000000..8312734
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/SelectAllEdgesAction.java
@@ -0,0 +1,85 @@
+/*
+ File: SelectAllEdgesAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+//-------------------------------------------------------------------------
+// $Revision: 19327 $
+// $Date: 2010-02-12 23:01:44 +0100 (Fri, 12 Feb 2010) $
+// $Author: ruschein $
+//-------------------------------------------------------------------------
+package cytoscape.actions;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.util.CytoscapeAction;
+
+//-------------------------------------------------------------------------
+import java.awt.event.ActionEvent;
+
+import javax.swing.event.MenuEvent;
+
+//-------------------------------------------------------------------------
+/**
+ *
+ */
+public class SelectAllEdgesAction extends CytoscapeAction {
+ /**
+ * Creates a new SelectAllEdgesAction object.
+ */
+ public SelectAllEdgesAction() {
+ super("Select All Edges");
+ setPreferredMenu("Select.Edges");
+ setAcceleratorCombo(java.awt.event.KeyEvent.VK_A, ActionEvent.ALT_MASK);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ // GinyUtils.selectAllEdges( Cytoscape.getCurrentNetworkView() );
+ Cytoscape.getCurrentNetwork().selectAllEdges();
+
+ if (Cytoscape.getCurrentNetworkView() != null) {
+ Cytoscape.getCurrentNetworkView().updateView();
+ }
+ } // action performed
+
+ public void menuSelected(MenuEvent e) {
+ enableForNetwork();
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/SelectAllNodesAction.java b/application/src/main/java/cytoscape/actions/SelectAllNodesAction.java
new file mode 100644
index 0000000..d69897c
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/SelectAllNodesAction.java
@@ -0,0 +1,84 @@
+/*
+ File: SelectAllNodesAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+//-------------------------------------------------------------------------
+// $Revision: 19327 $
+// $Date: 2010-02-12 23:01:44 +0100 (Fri, 12 Feb 2010) $
+// $Author: ruschein $
+//-------------------------------------------------------------------------
+package cytoscape.actions;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.util.CytoscapeAction;
+
+//-------------------------------------------------------------------------
+import java.awt.event.ActionEvent;
+
+import javax.swing.event.MenuEvent;
+
+//-------------------------------------------------------------------------
+/**
+ *
+ */
+public class SelectAllNodesAction extends CytoscapeAction {
+ /**
+ * Creates a new SelectAllNodesAction object.
+ */
+ public SelectAllNodesAction() {
+ super("Select All nodes");
+ setPreferredMenu("Select.Nodes");
+ setAcceleratorCombo(java.awt.event.KeyEvent.VK_A, ActionEvent.CTRL_MASK);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ Cytoscape.getCurrentNetwork().selectAllNodes();
+
+ if (Cytoscape.getCurrentNetworkView() != null) {
+ Cytoscape.getCurrentNetworkView().updateView();
+ }
+ }
+
+ public void menuSelected(MenuEvent e) {
+ enableForNetwork();
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/SelectConnectedNodesAction.java b/application/src/main/java/cytoscape/actions/SelectConnectedNodesAction.java
new file mode 100644
index 0000000..2fe1357
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/SelectConnectedNodesAction.java
@@ -0,0 +1,92 @@
+/*
+ File: SelectConnectedNodesAction.java
+
+ Copyright (c) 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+//-------------------------------------------------------------------------
+package cytoscape.actions;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import cytoscape.util.CytoscapeAction;
+import giny.model.Node;
+import giny.model.Edge;
+import java.awt.event.ActionEvent;
+import java.awt.event.KeyEvent;
+import java.util.ArrayList;
+import java.util.List;
+import javax.swing.event.MenuEvent;
+import java.util.Set;
+import java.util.HashSet;
+import cytoscape.CyEdge;
+
+//-------------------------------------------------------------------------
+/**
+ * select every node connected to the current selected edges.
+ */
+public class SelectConnectedNodesAction extends CytoscapeAction {
+ /**
+ * Creates a new SelectConnectedNodesAction object.
+ */
+ public SelectConnectedNodesAction() {
+ super("Nodes Connected by Selected Edges");
+ setPreferredMenu("Select.Nodes");
+ setAcceleratorCombo(KeyEvent.VK_7, ActionEvent.CTRL_MASK);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ final CyNetwork currentNetwork = Cytoscape.getCurrentNetwork();
+ Set<CyEdge> edgeSet = currentNetwork.getSelectedEdges();
+ final List<Edge> selectedEdges = new ArrayList<Edge>(edgeSet);
+
+ final Set<Node>nodesToSelect = new HashSet<Node>();
+ for (Edge edge: selectedEdges) {
+ nodesToSelect.add(edge.getSource());
+ nodesToSelect.add(edge.getTarget());
+ }
+ currentNetwork.setSelectedNodeState(nodesToSelect, true);
+ Cytoscape.getCurrentNetworkView().updateView();
+
+ } // actionPerformed
+
+ public void menuSelected(MenuEvent e) {
+ enableForNetwork();
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/SelectFirstNeighborsAction.java b/application/src/main/java/cytoscape/actions/SelectFirstNeighborsAction.java
new file mode 100644
index 0000000..1625509
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/SelectFirstNeighborsAction.java
@@ -0,0 +1,98 @@
+/*
+ File: SelectFirstNeighborsAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+//-------------------------------------------------------------------------
+// $Revision: 19327 $
+// $Date: 2010-02-12 23:01:44 +0100 (Fri, 12 Feb 2010) $
+// $Author: ruschein $
+//-------------------------------------------------------------------------
+package cytoscape.actions;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+
+import cytoscape.util.CytoscapeAction;
+
+//-------------------------------------------------------------------------
+import giny.model.Node;
+
+import java.awt.event.ActionEvent;
+import java.awt.event.KeyEvent;
+
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+
+import javax.swing.KeyStroke;
+
+import javax.swing.event.MenuEvent;
+
+//-------------------------------------------------------------------------
+/**
+ * select every first neighbor (directly connected nodes) of the currently
+ * selected nodes.
+ */
+public class SelectFirstNeighborsAction extends CytoscapeAction {
+ /**
+ * Creates a new SelectFirstNeighborsAction object.
+ */
+ public SelectFirstNeighborsAction() {
+ super("First Neighbors of Selected Nodes");
+ setPreferredMenu("Select.Nodes");
+ setAcceleratorCombo(KeyEvent.VK_6, ActionEvent.CTRL_MASK);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ final CyNetwork currentNetwork = Cytoscape.getCurrentNetwork();
+ final List<Node> selectedNodes = new ArrayList<Node>(currentNetwork.getSelectedNodes());
+
+ for (final Iterator it = selectedNodes.iterator(); it.hasNext();) {
+ currentNetwork.setSelectedNodeState(currentNetwork.neighborsList((Node) it.next()), true);
+ }
+
+ Cytoscape.getCurrentNetworkView().updateView();
+ } // actionPerformed
+
+ public void menuSelected(MenuEvent e) {
+ enableForNetwork();
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/SelectionModeAction.java b/application/src/main/java/cytoscape/actions/SelectionModeAction.java
new file mode 100644
index 0000000..cca8fc5
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/SelectionModeAction.java
@@ -0,0 +1,141 @@
+/*
+ File: SelectionModeAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.actions;
+
+import cytoscape.Cytoscape;
+import cytoscape.CyNetwork;
+
+import cytoscape.view.CyNetworkView;
+
+import giny.view.GraphView;
+
+import java.awt.event.ActionEvent;
+
+import javax.swing.*;
+import javax.swing.event.MenuEvent;
+import javax.swing.event.MenuListener;
+
+
+/**
+ *
+ */
+public class SelectionModeAction extends JMenu implements MenuListener {
+ /**
+ * Creates a new SelectionModeAction object.
+ */
+ JCheckBoxMenuItem nodes;
+ JCheckBoxMenuItem edges;
+ JCheckBoxMenuItem nodesAndEdges;
+
+ public SelectionModeAction() {
+ super("Mouse Drag Selects");
+
+ ButtonGroup modeGroup = new ButtonGroup();
+ nodes = new JCheckBoxMenuItem(new AbstractAction("Nodes Only") {
+ public void actionPerformed(ActionEvent e) {
+ // Do this in the GUI Event Dispatch thread...
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ Cytoscape.setSelectionMode(Cytoscape.SELECT_NODES_ONLY);
+ }
+ });
+ }
+ });
+ nodes.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_K,
+ ActionEvent.CTRL_MASK
+ | ActionEvent.SHIFT_MASK));
+
+ edges = new JCheckBoxMenuItem(new AbstractAction("Edges Only") {
+ public void actionPerformed(ActionEvent e) {
+ // Do this in the GUI Event Dispatch thread...
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ Cytoscape.setSelectionMode(Cytoscape.SELECT_EDGES_ONLY);
+ }
+ });
+ }
+ });
+ edges.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_K,
+ ActionEvent.CTRL_MASK
+ | ActionEvent.ALT_MASK));
+
+ nodesAndEdges = new JCheckBoxMenuItem(new AbstractAction("Nodes and Edges") {
+ public void actionPerformed(ActionEvent e) {
+ // Do this in the GUI Event Dispatch thread...
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ Cytoscape.setSelectionMode(Cytoscape.SELECT_NODES_AND_EDGES);
+ }
+ });
+ }
+ });
+ nodesAndEdges.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_K,
+ ActionEvent.CTRL_MASK));
+
+ modeGroup.add(nodes);
+ modeGroup.add(edges);
+ modeGroup.add(nodesAndEdges);
+
+ add(nodes);
+ add(edges);
+ add(nodesAndEdges);
+ // nodes.setSelected(true);
+ nodesAndEdges.setSelected(true);
+
+ GraphView view = Cytoscape.getCurrentNetworkView();
+ view.enableNodeSelection();
+ view.enableEdgeSelection();
+ Cytoscape.setSelectionMode(Cytoscape.SELECT_NODES_AND_EDGES);
+ }
+
+ public void menuCanceled(MenuEvent e) {}
+
+ public void menuDeselected(MenuEvent e) {}
+
+ public void menuSelected(MenuEvent e) {
+ CyNetwork n = Cytoscape.getCurrentNetwork();
+ if ( n == null || n == Cytoscape.getNullNetwork() ) {
+ nodes.setEnabled(false);
+ edges.setEnabled(false);
+ nodesAndEdges.setEnabled(false);
+ } else {
+ nodes.setEnabled(true);
+ edges.setEnabled(true);
+ nodesAndEdges.setEnabled(true);
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/SetVisualPropertiesAction.java b/application/src/main/java/cytoscape/actions/SetVisualPropertiesAction.java
new file mode 100644
index 0000000..e03a6f4
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/SetVisualPropertiesAction.java
@@ -0,0 +1,114 @@
+/*
+ File: SetVisualPropertiesAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+//-------------------------------------------------------------------------
+// $Revision: 18003 $
+// $Date: 2009-09-18 00:39:42 +0200 (Fri, 18 Sep 2009) $
+// $Author: kono $
+//------------------------------------------------------------------------------
+package cytoscape.actions;
+
+import java.awt.event.ActionEvent;
+
+import javax.swing.ImageIcon;
+import javax.swing.SwingConstants;
+
+import cytoscape.Cytoscape;
+import cytoscape.util.CytoscapeAction;
+import cytoscape.view.cytopanels.CytoPanel;
+import cytoscape.view.cytopanels.CytoPanelState;
+
+
+//------------------------------------------------------------------------------
+/**
+ *
+ */
+public class SetVisualPropertiesAction extends CytoscapeAction {
+
+ private static final long serialVersionUID = 3340562148562666874L;
+
+ private static final String title = "Open VizMapper\u2122";
+
+ /**
+ * Creates a new SetVisualPropertiesAction object.
+ */
+ public SetVisualPropertiesAction() {
+ super(title,
+ new ImageIcon(Cytoscape.class.getResource("images/ximian/stock_file-with-objects-16.png")));
+ setPreferredMenu("View");
+ setEnabled(true);
+ }
+
+ /**
+ * Creates a new SetVisualPropertiesAction object.
+ *
+ * @param icon DOCUMENT ME!
+ */
+ public SetVisualPropertiesAction(ImageIcon icon) {
+ super(title, icon);
+ setPreferredMenu("View");
+ setEnabled(true);
+ }
+
+ /**
+ * The constructor that takes a boolean shows no label, no matter what the
+ * value of the boolean actually is. This makes is appropriate for an icon,
+ * but inappropriate for the pulldown menu system.
+ */
+ public SetVisualPropertiesAction(boolean showLabel) {
+ super(); // no title here - this is for the toolbar
+ setPreferredMenu("View");
+ setEnabled(true);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ CytoPanel targetPanel = Cytoscape.getDesktop().getCytoPanel(SwingConstants.WEST);
+
+ targetPanel.setSelectedIndex(1);
+
+ // If Control Panel is hidden, display it.
+ CytoPanelState curState = targetPanel.getState();
+
+ if (curState == CytoPanelState.HIDE)
+ targetPanel.setState(CytoPanelState.DOCK);
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/ShowAllAction.java b/application/src/main/java/cytoscape/actions/ShowAllAction.java
new file mode 100644
index 0000000..db569d3
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/ShowAllAction.java
@@ -0,0 +1,77 @@
+/*
+ File: ShowAllAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+//-------------------------------------------------------------------------
+// $Revision: 9565 $
+// $Date: 2007-02-13 20:36:50 +0100 (Tue, 13 Feb 2007) $
+// $Author: mes $
+//-------------------------------------------------------------------------
+package cytoscape.actions;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.util.CytoscapeAction;
+
+//-------------------------------------------------------------------------
+import java.awt.event.ActionEvent;
+
+import javax.swing.AbstractAction;
+
+
+//-------------------------------------------------------------------------
+/**
+ *
+ */
+public class ShowAllAction extends CytoscapeAction {
+ /**
+ * Creates a new ShowAllAction object.
+ */
+ public ShowAllAction() {
+ super();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ GinyUtils.unHideAll(Cytoscape.getCurrentNetworkView());
+
+ //networkView.redrawGraph(false, true);
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/ShowCustomGraphicsManagerAction.java b/application/src/main/java/cytoscape/actions/ShowCustomGraphicsManagerAction.java
new file mode 100644
index 0000000..c13538f
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/ShowCustomGraphicsManagerAction.java
@@ -0,0 +1,74 @@
+package cytoscape.actions;
+
+import java.awt.event.ActionEvent;
+
+import javax.swing.Icon;
+import javax.swing.ImageIcon;
+
+import cytoscape.Cytoscape;
+import cytoscape.task.ui.JTaskConfig;
+import cytoscape.task.util.TaskManager;
+import cytoscape.util.CytoscapeAction;
+import cytoscape.visual.customgraphic.RestoreImageTask;
+import cytoscape.visual.customgraphic.ui.CustomGraphicsManagerDialog;
+
+/**
+ * Display Custom Graphics Manager GUI.
+ * First time user calls this function, manager loads image from .cytoscape/images directory.
+ *
+ * @author kono
+ *
+ */
+public class ShowCustomGraphicsManagerAction extends CytoscapeAction {
+
+ private static final long serialVersionUID = 5876533870116518191L;
+
+ private static final String TITLE = "Open Custom Graphics Manager";
+ private static final String ICON_LOCATION = "images/ximian/stock_symbol-selection-16.png";
+ private static final Icon ICON = new ImageIcon(Cytoscape.class.getResource(ICON_LOCATION));
+
+ private static final String MENU_NAME = "View";
+
+ private CustomGraphicsManagerDialog manager;
+
+ /**
+ * Creates a new SetVisualPropertiesAction object.
+ */
+ public ShowCustomGraphicsManagerAction() {
+ super(TITLE, ICON);
+ setPreferredMenu(MENU_NAME);
+ setEnabled(true);
+ }
+
+ /**
+ * Display custom graphics manager
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ // Add custom graphics manager
+
+ if (manager == null) {
+ // Create Task
+ final RestoreImageTask task = new RestoreImageTask();
+
+ // Configure JTask Dialog Pop-Up Box
+ final JTaskConfig jTaskConfig = new JTaskConfig();
+
+ jTaskConfig.displayCancelButton(false);
+ jTaskConfig.setOwner(Cytoscape.getDesktop());
+ jTaskConfig.displayCloseButton(false);
+ jTaskConfig.displayStatus(true);
+ jTaskConfig.setAutoDispose(true);
+
+ // Execute Task in New Thread; pop open JTask Dialog Box.
+ TaskManager.executeTask(task, jTaskConfig);
+
+ manager = new CustomGraphicsManagerDialog(Cytoscape.getDesktop(), false);
+ }
+
+ manager.setLocationRelativeTo(Cytoscape.getDesktop());
+ manager.setVisible(true);
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/ShowGraphicsDetailsAction.java b/application/src/main/java/cytoscape/actions/ShowGraphicsDetailsAction.java
new file mode 100644
index 0000000..4bdf6b1
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/ShowGraphicsDetailsAction.java
@@ -0,0 +1,119 @@
+/*
+ File: ShowGraphicsDetailsAction.java
+
+ Copyright (c) 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.actions;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import cytoscape.CytoscapeInit;
+
+import cytoscape.util.CytoscapeAction;
+
+import cytoscape.view.CytoscapeDesktop;
+import cytoscape.view.CyNetworkView;
+
+import cytoscape.ding.CyGraphLOD;
+import cytoscape.ding.CyGraphAllLOD;
+import cytoscape.ding.DingNetworkView;
+import cytoscape.render.stateful.GraphLOD;
+
+import java.awt.event.ActionEvent;
+
+import javax.swing.event.MenuEvent;
+import javax.swing.Action;
+
+
+/**
+ *
+ */
+public class ShowGraphicsDetailsAction extends CytoscapeAction {
+ boolean showFlag = true;
+
+ /**
+ * Creates a new ShowGraphicsDetailsAction object.
+ */
+ public ShowGraphicsDetailsAction() {
+ super("Show Graphics Details");
+ setPreferredMenu("View");
+ setAcceleratorCombo(java.awt.event.KeyEvent.VK_S, ActionEvent.ALT_MASK);
+ }
+
+ /**
+ * Creates a new ShowGraphicsDetailsAction object.
+ *
+ * @param label DOCUMENT ME!
+ */
+ public ShowGraphicsDetailsAction(boolean label) {
+ super();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ CyNetworkView currView = Cytoscape.getCurrentNetworkView();
+ if (!showFlag) {
+ ((DingNetworkView)currView).setGraphLOD(new CyGraphLOD());
+ } else {
+ ((DingNetworkView)currView).setGraphLOD(new CyGraphAllLOD());
+ }
+ currView.redrawGraph(true,false);
+ }
+
+ /**
+ * Sets the state of the action before rendering the menu.
+ */
+ public void menuSelected(MenuEvent e) {
+ CyNetworkView currView = Cytoscape.getCurrentNetworkView();
+ if ( currView == null || currView == Cytoscape.getNullNetworkView() )
+ setEnabled(false);
+ else {
+ setEnabled(true);
+ // Get the current graph LOD
+ GraphLOD lod = ((DingNetworkView)currView).getGraphLOD();
+ if (CyGraphLOD.class.isInstance(lod)) {
+ putValue(Action.NAME, "Show Graphics Details");
+ showFlag = true;
+ } else {
+ putValue(Action.NAME, "Hide Graphics Details");
+ showFlag = false;
+ }
+ }
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/actions/StraightenSelectedEdgesAction.java b/application/src/main/java/cytoscape/actions/StraightenSelectedEdgesAction.java
new file mode 100644
index 0000000..d8c6ec6
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/StraightenSelectedEdgesAction.java
@@ -0,0 +1,95 @@
+/*
+ File: StraightenSelectedEdgesAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+//-------------------------------------------------------------------------
+// $Revision: 19327 $
+// $Date: 2010-02-12 23:01:44 +0100 (Fri, 12 Feb 2010) $
+// $Author: ruschein $
+//-------------------------------------------------------------------------
+package cytoscape.actions;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.util.CytoscapeAction;
+
+import cytoscape.view.CyNetworkView;
+
+import giny.view.EdgeView;
+
+//-------------------------------------------------------------------------
+import java.awt.event.ActionEvent;
+
+import javax.swing.AbstractAction;
+
+import javax.swing.event.MenuEvent;
+
+//-------------------------------------------------------------------------
+/**
+ *
+ */
+public class StraightenSelectedEdgesAction extends CytoscapeAction {
+ /**
+ * Creates a new StraightenSelectedEdgesAction object.
+ */
+ public StraightenSelectedEdgesAction() {
+ super("Straighten Selected Edges");
+ setPreferredMenu("Select.Edges");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ CyNetworkView view = Cytoscape.getCurrentNetworkView();
+ final int[] selectedEdges = view.getSelectedEdgeIndices();
+
+ if (selectedEdges != null) {
+ for (int i = 0; i < selectedEdges.length; i++) {
+ EdgeView ev = view.getEdgeView(selectedEdges[i]);
+ ev.setLineType(EdgeView.STRAIGHT_LINES);
+ }
+
+ view.updateView();
+ }
+ }
+
+ public void menuSelected(MenuEvent e) {
+ enableForNetworkAndView();
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/ToggleVisualMapperAction.java b/application/src/main/java/cytoscape/actions/ToggleVisualMapperAction.java
new file mode 100644
index 0000000..6d695ff
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/ToggleVisualMapperAction.java
@@ -0,0 +1,97 @@
+/*
+ File: ToggleVisualMapperAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+//-------------------------------------------------------------------------
+// $Revision: 9827 $
+// $Date: 2007-03-30 01:24:05 +0200 (Fri, 30 Mar 2007) $
+// $Author: mes $
+//-------------------------------------------------------------------------
+package cytoscape.actions;
+
+import cytoscape.Cytoscape;
+import cytoscape.view.CyNetworkView;
+
+import cytoscape.util.CytoscapeAction;
+
+//-------------------------------------------------------------------------
+import java.awt.event.ActionEvent;
+import javax.swing.event.MenuEvent;
+import javax.swing.Action;
+
+
+/**
+ * This class implements two menu items that allow enabling and disabling the
+ * visual mapper.
+ */
+public class ToggleVisualMapperAction extends CytoscapeAction {
+
+ private static String LOCK = "Lock VizMapper\u2122";
+ private static String UNLOCK = "Unlock VizMapper\u2122";
+
+ /**
+ * Creates a new ToggleVisualMapperAction object.
+ */
+ public ToggleVisualMapperAction() {
+ super(LOCK);
+ setPreferredMenu("View");
+ setAcceleratorCombo(java.awt.event.KeyEvent.VK_M, ActionEvent.ALT_MASK);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ CyNetworkView cv = Cytoscape.getCurrentNetworkView();
+ if (cv != null && cv != Cytoscape.getNullNetworkView())
+ cv.toggleVisualMapperEnabled();
+ }
+
+ public void menuSelected(MenuEvent e) {
+ CyNetworkView cv = Cytoscape.getCurrentNetworkView();
+ if (cv != null && cv != Cytoscape.getNullNetworkView()) {
+ setEnabled(true);
+ if ( cv.getVisualMapperEnabled() )
+ putValue(Action.NAME, LOCK);
+ else
+ putValue(Action.NAME, UNLOCK);
+ } else {
+ setEnabled(false);
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/UnHideSelectedAction.java b/application/src/main/java/cytoscape/actions/UnHideSelectedAction.java
new file mode 100644
index 0000000..1583f68
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/UnHideSelectedAction.java
@@ -0,0 +1,81 @@
+/*
+ File: UnHideSelectedAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+//-------------------------------------------------------------------------
+// $Revision: 9565 $
+// $Date: 2007-02-13 20:36:50 +0100 (Tue, 13 Feb 2007) $
+// $Author: mes $
+//-------------------------------------------------------------------------
+package cytoscape.actions;
+
+import cytoscape.view.CyNetworkView;
+
+//-------------------------------------------------------------------------
+import java.awt.event.ActionEvent;
+
+import javax.swing.AbstractAction;
+
+
+//-------------------------------------------------------------------------
+/**
+ *
+ */
+public class UnHideSelectedAction extends AbstractAction {
+ CyNetworkView networkView;
+
+ /**
+ * Creates a new UnHideSelectedAction object.
+ *
+ * @param networkView DOCUMENT ME!
+ */
+ public UnHideSelectedAction(CyNetworkView networkView) {
+ super("Un Hide selection");
+ this.networkView = networkView;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ //GinyUtils.unHideSelectedNodes(networkView.getView());
+ //GinyUtils.unHideSelectedEdges(networkView.getView());
+ //networkView.redrawGraph(false, true);
+ GinyUtils.unHideAll(cytoscape.Cytoscape.getCurrentNetworkView());
+ } //action performed
+}
diff --git a/application/src/main/java/cytoscape/actions/UnHideSelectedEdgesAction.java b/application/src/main/java/cytoscape/actions/UnHideSelectedEdgesAction.java
new file mode 100644
index 0000000..a2a9543
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/UnHideSelectedEdgesAction.java
@@ -0,0 +1,84 @@
+/*
+ File: UnHideSelectedEdgesAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+//-------------------------------------------------------------------------
+// $Revision: 19327 $
+// $Date: 2010-02-12 23:01:44 +0100 (Fri, 12 Feb 2010) $
+// $Author: ruschein $
+//-------------------------------------------------------------------------
+package cytoscape.actions;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.util.CytoscapeAction;
+
+//-------------------------------------------------------------------------
+import java.awt.event.ActionEvent;
+
+import javax.swing.AbstractAction;
+
+import javax.swing.event.MenuEvent;
+
+//-------------------------------------------------------------------------
+/**
+ *
+ */
+public class UnHideSelectedEdgesAction extends CytoscapeAction {
+ /**
+ * Creates a new UnHideSelectedEdgesAction object.
+ */
+ public UnHideSelectedEdgesAction() {
+ super("Show All Edges");
+ setPreferredMenu("Select.Edges");
+ setAcceleratorCombo(java.awt.event.KeyEvent.VK_H,
+ ActionEvent.ALT_MASK | ActionEvent.SHIFT_MASK);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ //GinyUtils.unHideSelectedEdges( Cytoscape.getCurrentNetworkView() );
+ GinyUtils.unHideAll(cytoscape.Cytoscape.getCurrentNetworkView());
+ } //action performed
+
+ public void menuSelected(MenuEvent e) {
+ enableForNetworkAndView();
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/UnHideSelectedNodesAction.java b/application/src/main/java/cytoscape/actions/UnHideSelectedNodesAction.java
new file mode 100644
index 0000000..4169273
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/UnHideSelectedNodesAction.java
@@ -0,0 +1,85 @@
+/*
+ File: UnHideSelectedNodesAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+//-------------------------------------------------------------------------
+// $Revision: 19327 $
+// $Date: 2010-02-12 23:01:44 +0100 (Fri, 12 Feb 2010) $
+// $Author: ruschein $
+//-------------------------------------------------------------------------
+package cytoscape.actions;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.util.CytoscapeAction;
+
+//-------------------------------------------------------------------------
+import java.awt.event.ActionEvent;
+
+import javax.swing.AbstractAction;
+
+import javax.swing.event.MenuEvent;
+
+//-------------------------------------------------------------------------
+/**
+ *
+ */
+public class UnHideSelectedNodesAction extends CytoscapeAction {
+ /**
+ * Creates a new UnHideSelectedNodesAction object.
+ */
+ public UnHideSelectedNodesAction() {
+ super("Show All Nodes");
+ setPreferredMenu("Select.Nodes");
+ setAcceleratorCombo(java.awt.event.KeyEvent.VK_H,
+ ActionEvent.CTRL_MASK | ActionEvent.SHIFT_MASK);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ //GinyUtils.unHideSelectedNodes( Cytoscape.getCurrentNetworkView() );
+ //GinyUtils.unHideSelectedEdges( Cytoscape.getCurrentNetworkView() );
+ GinyUtils.unHideAll(cytoscape.Cytoscape.getCurrentNetworkView());
+ } //action performed
+
+ public void menuSelected(MenuEvent e) {
+ enableForNetworkAndView();
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/WebServiceNetworkImportAction.java b/application/src/main/java/cytoscape/actions/WebServiceNetworkImportAction.java
new file mode 100644
index 0000000..5ef39de
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/WebServiceNetworkImportAction.java
@@ -0,0 +1,25 @@
+package cytoscape.actions;
+
+import java.awt.event.ActionEvent;
+
+import cytoscape.data.webservice.ui.UnifiedNetworkImportDialog;
+import cytoscape.util.CytoscapeAction;
+
+public class WebServiceNetworkImportAction extends CytoscapeAction {
+ /**
+ * Creates a new FitContentAction object.
+ */
+ public WebServiceNetworkImportAction() {
+ super("Network from Web Services...");
+ setPreferredMenu("File.Import");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ UnifiedNetworkImportDialog.showDialog();
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/ZoomAction.java b/application/src/main/java/cytoscape/actions/ZoomAction.java
new file mode 100644
index 0000000..ce2acf6
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/ZoomAction.java
@@ -0,0 +1,88 @@
+/*
+ File: ZoomAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+//-------------------------------------------------------------------------
+// $Revision: 9565 $
+// $Date: 2007-02-13 20:36:50 +0100 (Tue, 13 Feb 2007) $
+// $Author: mes $
+//-------------------------------------------------------------------------
+package cytoscape.actions;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.util.CytoscapeAction;
+
+import cytoscape.view.CyNetworkView;
+
+import java.awt.event.ActionEvent;
+
+import javax.swing.AbstractAction;
+
+
+/**
+ *
+ */
+public class ZoomAction extends CytoscapeAction {
+ double factor;
+
+ /**
+ * Creates a new ZoomAction object.
+ *
+ * @param factor DOCUMENT ME!
+ */
+ public ZoomAction(double factor) {
+ super();
+ this.factor = factor;
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void zoom() {
+ Cytoscape.getCurrentNetworkView()
+ .setZoom(Cytoscape.getCurrentNetworkView().getZoom() * factor);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ Cytoscape.getCurrentNetworkView().setZoom(factor);
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/ZoomSelectedAction.java b/application/src/main/java/cytoscape/actions/ZoomSelectedAction.java
new file mode 100644
index 0000000..190a2ea
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/ZoomSelectedAction.java
@@ -0,0 +1,88 @@
+/*
+ File: ZoomSelectedAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+//-------------------------------------------------------------------------
+// $Revision: 9565 $
+// $Date: 2007-02-13 20:36:50 +0100 (Tue, 13 Feb 2007) $
+// $Author: mes $
+//-------------------------------------------------------------------------
+package cytoscape.actions;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.ding.DingNetworkView;
+
+import cytoscape.giny.*;
+
+import cytoscape.util.CytoscapeAction;
+
+import cytoscape.view.CyNetworkView;
+
+import giny.view.*;
+
+//-------------------------------------------------------------------------
+import java.awt.event.ActionEvent;
+import java.awt.geom.Rectangle2D;
+
+import java.util.Iterator;
+import java.util.List;
+
+import javax.swing.AbstractAction;
+
+
+//-------------------------------------------------------------------------
+/**
+ *
+ */
+public class ZoomSelectedAction extends CytoscapeAction {
+ /**
+ * Creates a new ZoomSelectedAction object.
+ */
+ public ZoomSelectedAction() {
+ super();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ ((DingNetworkView) Cytoscape.getCurrentNetworkView()).fitSelected();
+ Cytoscape.getCurrentNetworkView().updateView();
+ }
+}
diff --git a/application/src/main/java/cytoscape/actions/package.html b/application/src/main/java/cytoscape/actions/package.html
new file mode 100644
index 0000000..93a83e7
--- /dev/null
+++ b/application/src/main/java/cytoscape/actions/package.html
@@ -0,0 +1,14 @@
+<html>
+<head>
+ <!-- $Revision: 5801 $
+ $Date: 2004-04-20 01:53:47 +0200 (Tue, 20 Apr 2004) $
+ $Author: amarkiel $
+ -->
+</head>
+
+<body>
+UI classes that are attached to menu items in the menu or tool bar
+of the window. These classes are usually short and delegate to other
+objects to do the actual work.
+</body>
+</html>
diff --git a/application/src/main/java/cytoscape/command/AbstractCommandHandler.java b/application/src/main/java/cytoscape/command/AbstractCommandHandler.java
new file mode 100644
index 0000000..6607ac7
--- /dev/null
+++ b/application/src/main/java/cytoscape/command/AbstractCommandHandler.java
@@ -0,0 +1,382 @@
+/* vim: set ts=2: */
+/**
+ * Copyright (c) 2007 The Regents of the University of California.
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ * notice, this list of conditions, and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above
+ * copyright notice, this list of conditions, and the following
+ * disclaimer in the documentation and/or other materials provided
+ * with the distribution.
+ * 3. Redistributions must acknowledge that this software was
+ * originally developed by the UCSF Computer Graphics Laboratory
+ * under support by the NIH National Center for Research Resources,
+ * grant P41-RR01081.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY
+ * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+ * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+ * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
+ * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ */
+package cytoscape.command;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+import cytoscape.command.CyCommandException;
+import cytoscape.command.CyCommandHandler;
+import cytoscape.command.CyCommandManager;
+import cytoscape.command.CyCommandNamespace;
+import cytoscape.command.CyCommandResult;
+import cytoscape.data.CyAttributes;
+import cytoscape.layout.Tunable;
+
+/**
+ * This abstract class provides a convenient (but not necessary) base class
+ * for writing CyCommandHandlers. It may be used whether your handler handles
+ * a single command or multiple commands. The general use of this base class
+ * is to add a set of known arguments using the {@link AbstractCommandHandler#addArgument}() method
+ * and {@link AbstractCommandHandler#addDescription}() methods within the constructor of your
+ * command handler:
+ * <pre><code>
+ * public class MyCommandHandler extends AbstractCommandHandler {
+ * // Define our command name
+ * private static String COMMAND = "my command";
+ *
+ * // Settings
+ * private static String ARGKEY1 = "argkey1";
+ * private static String ARGKEY2 = "argkey2";
+ * private static String ARGKEY3 = "argkey3";
+ *
+ * public MyCommandHandler({@link CyCommandNamespace} ns) {
+ * super(ns);
+ * {@link AbstractCommandHandler#addDescription}(COMMAND, "This command does something really cool");
+ * {@link AbstractCommandHandler#addArgument}(COMMAND, ARGKEY1);
+ * {@link AbstractCommandHandler#addArgument}(COMMAND, ARGKEY2);
+ * {@link AbstractCommandHandler#addArgument}(COMMAND, ARGKEY3, "defaultValue");
+ * }
+ *
+ * public {@link CyCommandResult} execute(String command, Map<String, Object>args) throws {@link CyCommandException} {
+ * // Your execution code goes here....
+ * }
+ * ... or ...
+ * public {@link CyCommandResult} execute(String command, Collection<Tunable>args) throws {@link CyCommandException} {
+ * // Your execution code goes here....
+ * }
+ * }
+ * </code></pre>
+ * Note that both of the two {@link CyCommandHandler#execute} methods must be overridden, but only one of which must include
+ * your functionality. AbstractCommandHandler provides two additional methods to assist command authors with the conversion between
+ * the two execute methods. If your plugin uses {@link Tunable}s, to handle the Map version of the execute method, implement
+ * the following method:
+ * <code><pre>
+ * public class execute(String command, Map<String,Object> arguments) {
+ * return execute(command, createTunableCollection(arguments));
+ * }
+ * </pre></code>
+ * where the createTunableCollection method will create a list of {@link Tunable}s to call the Tunable version of execute. On
+ * the other hand, if your plugin does not use {@link Tunable}s, you can use:
+ * <code><pre>
+ * public CyCommandResult execute(String command, Collection<Tunable> arguments) {
+ * return execute(command, createKVMap(arguments));
+ * }
+ * </pre></code>
+ * where the createKVMap method will take a Collection of Tunables and create the corresponding Map to call your execute method.
+ *
+ * The {@link AbstractCommandHandler#addDescription}() method is used by the AbstractCommandHandler's {@link AbstractCommandHandler#getDescription}()
+ * method to produce a formatted description of the command, including the namespace, command name, description, and options
+ * (with default values). To avoid the formatting and provide your own full description, just override the getDescription() method
+ * and return your own description.
+ *
+ * Also note that the {@link CyCommandNamespace} must be reserved before the command handler is initialized.
+ *
+ *
+ */
+public abstract class AbstractCommandHandler implements CyCommandHandler {
+ protected Map<String, List<Tunable>> argumentMap = new HashMap();
+ protected Map<String, String> descriptionMap = new HashMap();
+ protected CyCommandNamespace namespace = null;
+
+ /**
+ * You do not need to call this constructor from you class, but if
+ * you don't, you will need to make sure you assign the namespace
+ * appropriately.
+ *
+ * @param ns the {@link CyCommandNamespace} for this command
+ */
+ public AbstractCommandHandler(CyCommandNamespace ns) { namespace = ns; }
+
+ /**
+ * Return the command or commands supported by this handler
+ *
+ * @return a list of strings with one or more commands
+ */
+ public List<String> getCommands() { return new ArrayList(argumentMap.keySet()); }
+
+ /**
+ * Return the arguments for a given command
+ *
+ * @param command the command to check for arguments
+ * @return the list of arguments this command will take
+ */
+ public List<String> getArguments(String command) {
+ if (!argumentMap.containsKey(command)) {
+ return null;
+ }
+
+ List<String> argList = new ArrayList();
+ for (Tunable t: argumentMap.get(command)) {
+ argList.add(t.getName());
+ }
+ return argList;
+ }
+
+ /**
+ * Return the current settings for a given command. At this point, for simplicity
+ * the only Object type supported as values are those that have "toString()" methods.
+ * This allows for simple mappings between textual input and settings without
+ * resorting to inspection of the object types. This signature is expected to be
+ * removed sometime in the 3.0 timeframe and only the getTunables version will remain.
+ *
+ * @param command the command we want the settings for
+ * @return the current settings as a map
+ */
+ public Map<String, Object> getSettings(String command) {
+ Map<String, Object> kvSettings = createKVSettings(command);
+ if (kvSettings != null)
+ return kvSettings;
+ return null;
+ }
+
+ /**
+ * Return the current settings for a given command as a map of setting name: tunable.
+ *
+ * @param command the command we want the settings for
+ * @return the current settings as a map of setting name: tunable.
+ */
+ public Map<String, Tunable> getTunables(String command) {
+ if (argumentMap.containsKey(command)) {
+ Map<String, Tunable> tunableMap = new HashMap();
+ for (Tunable t: argumentMap.get(command)) {
+ tunableMap.put(t.getName(), t);
+ }
+ return tunableMap;
+ }
+ return null;
+ }
+
+ /**
+ * This method returns a formatted description of the command, including
+ * the namespace, command name, plugin-provided description, and arguments.
+ * Override this to provide your own description.
+ *
+ * @param command the command we're inquiring about
+ * @return the description/documentation for this command
+ */
+ public String getDescription(String command) {
+ if (descriptionMap.containsKey(command)) {
+ return descriptionMap.get(command);
+ }
+ return null;
+ }
+
+ /**
+ * Execute a given command with a particular set of arguments. As with the
+
+ /**
+ * Use this method to support the Tunable version of the execute call if you don't
+ * support Tunables. This is actually pretty simple -- just add the following:
+ * <pre><code>
+ * public CyCommandResult execute(String command, Collection<Tunable>args) throws CyCommandException {
+ * return execute(command, createKVMap(args));
+ * }
+ * </code></pre>
+ * assuming that you've implemented the Map<String,Object> version of execute. Note that
+ * you <i>must</i> handle one version of execute at least.
+ *
+ * @param tList a Collection of Tunables
+ * @return a Map of String:Object pairs derived from tList
+ */
+ protected Map<String, Object> createKVMap(Collection<Tunable> tList) {
+ Map<String, Object> kvSettings = new HashMap();
+ for (Tunable t: tList) {
+ Object v = t.getValue();
+ if (v != null)
+ kvSettings.put(t.getName(), v.toString());
+ else
+ kvSettings.put(t.getName(), null);
+ }
+ return kvSettings;
+ }
+
+ /**
+ * Use this method to support the Map version of the execute call if you
+ * support Tunables. This is actually pretty simple -- just add the following:
+ * <pre><code>
+ * public CyCommandResult execute(String command, Map<String,Object>args) throws CyCommandException {
+ * return execute(command, createTunableCollection(args));
+ * }
+ * </code></pre>
+ * assuming that you've implemented the Collection<Tunable> version of execute. Note that
+ * you <i>must</i> handle one version of execute at least.
+ *
+ * @param args a Map of String,Object pairs
+ * @return a Collection of Tunables that correspond to the String,Object pairs
+ */
+ protected Collection<Tunable> createTunableCollection(Map<String, Object>args) {
+ List<Tunable> tCol = new ArrayList();
+ for (String key: args.keySet()) {
+ Tunable t = makeTunable(key, args.get(key));
+ if (t != null) tCol.add(t);
+ }
+ return tCol;
+ }
+
+ /**
+ * This method adds a new description for a command supported by this command
+ * handler. addDescription, in conjunction with the getDescription method
+ * provided by this class provide an easy way to get a formatted description,
+ * including available options. On the other hand, if a plugin want's to provide
+ * its own description, without any additional formatting, it should override
+ * getDescription and return the description directly
+ *
+ * @param command the name of the command to add the description to
+ * @param description the description to add
+ */
+ protected void addDescription(String command, String description) {
+ if (descriptionMap == null)
+ descriptionMap = new HashMap();
+ descriptionMap.put(command, description);
+ }
+
+ /**
+ * This method adds a new command to the list of command supported by this command
+ * handler. This assumes that this command has no arguments.
+ *
+ * @param command the name of the command to add
+ */
+ protected void addArgument(String command) {
+ if (argumentMap == null)
+ argumentMap = new HashMap();
+ if (!argumentMap.containsKey(command)) {
+ argumentMap.put(command, new ArrayList());
+ CyCommandManager.register(namespace, command, (CyCommandHandler)this);
+ }
+ }
+
+ /**
+ * Add a new argument key to a command supported by this command handler. If
+ * the command hasn't already been registered, register it.
+ *
+ * @param command the name of the command to add this argument key to
+ * @param vKey the key to add
+ */
+ protected void addArgument(String command, String vKey) {
+ addArgument(command, vKey, null);
+ }
+
+ /**
+ * Add a new argument key with a value to a command supported by this command
+ * handler. If the command hasn't already been registered, register it.
+ *
+ * @param command the name of the command to add this argument key to
+ * @param vKey the key to add
+ * @param value the value to associate with the key
+ */
+ protected void addArgument(String command, String vKey, String value) {
+ Tunable t = new Tunable(vKey, vKey, Tunable.STRING, value);
+ addArgument(command, t);
+ }
+
+ /**
+ * Add a new argument Tunable to a command supported by this command
+ * handler. If the command hasn't already been registered, register it.
+ *
+ * @param command the name of the command to add this argument key to
+ * @param t the Tunable to add
+ */
+ protected void addArgument(String command, Tunable t) {
+ if (argumentMap == null)
+ argumentMap = new HashMap();
+
+ if (!argumentMap.containsKey(command)) {
+ argumentMap.put(command, new ArrayList());
+ CyCommandManager.register(namespace, command, this);
+ }
+
+ List<Tunable> tList = argumentMap.get(command);
+ tList.add(t);
+ }
+
+ /**
+ * Return the string value of a specific argument from an args map.
+ *
+ * @param command the command we're getting the argument for
+ * @param key the argument we're interested in
+ * @param args the map of arguments that was passed to us
+ * @return the String value corresponding to the key
+ */
+ protected String getArg(String command, String key, Map<String,Object>args) {
+ // Do we have the key in our settings map?
+ String value = null;
+
+ if (argumentMap.containsKey(command)) {
+ List<Tunable> tL = argumentMap.get(command);
+ for (Tunable t: tL) {
+ if (t.getName().equals(key)) {
+ Object v = t.getValue();
+ if (v != null)
+ value = v.toString();
+ break;
+ }
+ }
+ }
+
+ if (args == null || args.size() == 0 || !args.containsKey(key))
+ return value;
+
+ return args.get(key).toString();
+ }
+
+ /**
+ * This method is useful for converting from Tunable lists to key-value settings
+ */
+ private Map<String, Object> createKVSettings(String command) {
+ if (!argumentMap.containsKey(command)) return null;
+ return createKVMap(argumentMap.get(command));
+ }
+
+ static public Tunable makeTunable(String name, Object value) {
+ Class vClass = value.getClass();
+ if (vClass == Double.class || vClass == Float.class) {
+ return new Tunable(name, name, Tunable.DOUBLE, value);
+ } else if (vClass == Integer.class) {
+ return new Tunable(name, name, Tunable.INTEGER, value);
+ } else if (vClass == Boolean.class) {
+ return new Tunable(name, name, Tunable.BOOLEAN, value);
+ } else if (vClass == String.class) {
+ return new Tunable(name, name, Tunable.STRING, value);
+ } else {
+ return new Tunable(name, name, Tunable.STRING, value.toString());
+ }
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/command/CyCommandException.java b/application/src/main/java/cytoscape/command/CyCommandException.java
new file mode 100644
index 0000000..08679d9
--- /dev/null
+++ b/application/src/main/java/cytoscape/command/CyCommandException.java
@@ -0,0 +1,106 @@
+/*
+ File: CyCommandException.java
+
+ Copyright (c) 2009, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+ - University of California San Francisco
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.command;
+
+/**
+ * The CyCommandException is thrown when a CyCommandHandler encounters an
+ * exception condition.
+ */
+public class CyCommandException extends Exception {
+ private CyCommandResult result;
+
+ /**
+ * Create a CyCommandException with a message, but no results
+ *
+ * @param message the message to include
+ */
+ public CyCommandException(String message) {
+ super(message);
+ result = new CyCommandResult();
+ result.addError(message);
+ }
+
+ /**
+ * Create a CyCommandException with a root cause but no results
+ *
+ * @param cause the cause of the exception
+ */
+ public CyCommandException(Throwable cause) {
+ super(cause);
+ result = new CyCommandResult();
+ result.addError(cause.getMessage());
+ }
+
+ /**
+ * Create a CyCommandException with a message and a root cause but no results
+ *
+ * @param message the message to include
+ * @param cause the cause of the exception
+ */
+ public CyCommandException(String message, Throwable cause) {
+ super(message, cause);
+ result = new CyCommandResult();
+ result.addError(message);
+ }
+
+ /**
+ * Create a CyCommandException with a message and a set of results
+ *
+ * @param message the message to include
+ * @param results the (possibly intermediate) results from this execution
+ */
+ public CyCommandException(String message, CyCommandResult results) {
+ super(message);
+ this.result = results;
+ this.result.addError(message);
+ }
+
+ /**
+ * Create a CyCommandException with a message, a cause, and a set of results
+ *
+ * @param message the message to include
+ * @param cause the cause of the exception
+ * @param results the (possibly intermediate) results from this execution
+ */
+ public CyCommandException(String message, Throwable cause, CyCommandResult results) {
+ super(message, cause);
+ this.result = results;
+ this.result.addError(message);
+ }
+}
diff --git a/application/src/main/java/cytoscape/command/CyCommandHandler.java b/application/src/main/java/cytoscape/command/CyCommandHandler.java
new file mode 100644
index 0000000..d10b37b
--- /dev/null
+++ b/application/src/main/java/cytoscape/command/CyCommandHandler.java
@@ -0,0 +1,199 @@
+ /*
+ File: CyCommandHandler.java
+
+ Copyright (c) 2009, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+ - University of California San Francisco
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.command;
+
+import java.util.Collection;
+import java.util.List;
+import java.util.Map;
+
+import cytoscape.layout.Tunable;
+
+/**
+ * The CyCommandHandler interface allows a Cytoscape plugin to make it's functions
+ * available to other plugins in a loosely-coupled manner (by passing command
+ * strings and arguments). It is intended as a stop-gap measure until the ability
+ * to directly call methods in other plugins (through OSGI services) is available
+ * in Cytoscape 3.0.
+ * <p>
+ * CyCommandHandler provide a simple method for a plugin to expose some functionality
+ * that can be used by other plugins. The idea is simple: a plugin registers
+ * one or more CyCommandHandlers with the {@link CyCommandManager}. In the simplest
+ * case, the plugin will directly implement CyCommandHandler:
+ * <pre><code>
+ * public class MyPlugin extend CytoscapePlugin implements CyCommandHandler {
+ * public MyPlugin() {
+ * // Plugin initialization
+ * try {
+ * // You must reserve your namespace first
+ * CyCommandNamespace ns = CyCommandManager.reserveNamespace("my namespace");
+ *
+ * // Now register this handler as handling "command"
+ * CyCommandManager.register(ns, command, this);
+ * } catch (RuntimeException e) {
+ * // Handle already registered exceptions
+ * }
+ * }
+ * }
+ * </code></pre>
+ * Alternatively, a plugin could implement multiple CyCommandHandlers, each one
+ * handling a single command string. This has the advantage of providing a clear
+ * separation where each class handles a single command, and is the recommended way
+ * to structure new plugins.
+ * <h3>Commands</h3>
+ * Each command handler can provide any number of commands.
+ * A command provides the actual functionality, and the passed arguments
+ * (name, value pairs) are specific to commands. Note that there aren't any
+ * restrictions about the number of words in a command handler name or command name. So, for
+ * example, the <i>view layout</i> command handler could provide a <i>get current</i> command.
+ * <h3>Arguments</h3>
+ * Arguments for commands may be specified either as name, value pairs
+ * (using a string, string map) or as a list of {@link Tunable}. It is recommended
+ * that whenever possible, plugins use Tunables as they provide type information
+ * that is useful to allow client plugins to perform some limited validation. In
+ * either case, both signatures (maps and Tunables) should be supported.
+ * <h3>Return Values</h3>
+ * CyCommandHandlers pass information about the execution of a command in a {@link CyCommandResult}. It is
+ * expected that a command will provide some limited information in the CyCommandResult
+ * message and the actual information in the results map.
+ * <h3>Exceptions</h3>
+ * A CyCommandHandler should always return a valid CyCommandResult to provide feedback to the user
+ * about the execution. If a processing error occurs, the CyCommandHandler should throw a
+ * CyCommandException with an appropriate message.
+ * <h3>Client Usage</h3>
+ * Using a CyCommandHandler from another plugin is relatively straightforward: get the CyCommandHandler,
+ * get the arguments for the desired command, set the arguments, and execute the
+ * the command:
+ * <pre><code>
+ * CyCommandHandler handler = CyCommandManager.getCommand("view layout", "force-directed");
+ * Map<String,Tunable> layoutTunables = handler.getTunables("force-directed");
+ * Tunable t = layoutTunables.get("iterations");
+ * t.setValue("100");
+ * try {
+ * CyCommandResult layoutResult = handler.execute("force-directed", layoutTunables);
+ * } catch (CyCommandException e) {
+ * }
+ * </code></pre>
+ * Alternatively....
+ * <pre><code>
+ * Map<String,Object> args = new HashMap();
+ * args.put("iterations", new Integer(100));
+ * try {
+ * CyCommandResult layoutResult = CyCommandManager.execute("view layout", "force-directed", args);
+ * } catch (CyCommandException e) {
+ * }
+ * </code></pre>
+ */
+public interface CyCommandHandler {
+ /**
+ * Return the list of commands supported by this CyCommandHandler. This
+ * implies that a single CyCommandHandler might support multiple commands, but
+ * it may also support only one, in which case, this is the same as the handler
+ * name;
+ *
+ * @return list of commands supported by this CyCommandHandler
+ */
+ public List<String> getCommands();
+
+ /**
+ * Return the list of arguments supported by a particular command. CyCommandHandler
+ * argument values are always Strings that can be converted to base types
+ * when passed. Internally, these are usually directly mapped to Tunables.
+ *
+ * @param command the command we're inquiring about
+ * @return list of arguments supported by that command
+ */
+ public List<String> getArguments(String command);
+
+ /**
+ * Get the current values for all of the arguments for a specific command.
+ * Argument values are always Strings that can be converted to base types
+ * when passed. Note that this interface is expected to be deprecated in
+ * Cytoscape 3.0 where everything is expected to be based on the new Tunable
+ * implementation.
+ *
+ * @param command the command we're inquiring about
+ * @return map of arguments supported by that command, where the key is the
+ * argument and the value is the String value for that argument.
+ */
+ public Map<String, Object> getSettings(String command);
+
+ /**
+ * Get the current Tunables for all of the arguments for a specific command.
+ * This is an alternative to getSettings for plugins that provide tunables,
+ * and is expected to be the standard approach for Cytoscape 3.0 and beyond.
+ *
+ * @param command the command we're inquiring about
+ * @return map of Tunables indexed by Tunable name supported by that command,
+ * or null if the plugin doesn't support tunables.
+ */
+ public Map<String,Tunable> getTunables(String command);
+
+ /**
+ * Get the description/documentation of the command. This could be used
+ * to describe the command's function or usage and is meant to be used
+ * by UI's that act as clients for the command.
+ *
+ * @param command the command we're inquiring about
+ * @return the description/documentation for this command
+ */
+ public String getDescription(String command);
+
+ /**
+ * Execute a given command with a particular set of arguments. As with the
+ * getSettings method above, this is expected to be retired in 3.0 when most
+ * things will use Tunables.
+ *
+ * @param command the command we're executing
+ * @param arguments to map of key, value pairs for the arguments we want to pass
+ * @return the results as a map of key, value pairs. If null, then the execution failed.
+ * @throws CyCommandException
+ */
+ public CyCommandResult execute(String command, Map<String, Object>arguments) throws CyCommandException;
+
+ /**
+ * Execute a given command with a particular set of arguments. This is the preferred
+ * method signature.
+ *
+ * @param command the command we're executing
+ * @param arguments the list of Tunables
+ * @return the results as a map of key, value pairs. If null, then the execution failed.
+ * @throws CyCommandException
+ */
+ public CyCommandResult execute(String command, Collection<Tunable>arguments) throws CyCommandException;
+}
diff --git a/application/src/main/java/cytoscape/command/CyCommandManager.java b/application/src/main/java/cytoscape/command/CyCommandManager.java
new file mode 100644
index 0000000..2ff32ff
--- /dev/null
+++ b/application/src/main/java/cytoscape/command/CyCommandManager.java
@@ -0,0 +1,281 @@
+/*
+File: CyCommandManager.java
+
+Copyright (c) 2009, The Cytoscape Consortium (www.cytoscape.org)
+
+The Cytoscape Consortium is:
+- Institute for Systems Biology
+- University of California San Diego
+- Memorial Sloan-Kettering Cancer Center
+- Institut Pasteur
+- Agilent Technologies
+- University of California San Francisco
+
+This library is free software; you can redistribute it and/or modify it
+under the terms of the GNU Lesser General Public License as published
+by the Free Software Foundation; either version 2.1 of the License, or
+any later version.
+
+This library is distributed in the hope that it will be useful, but
+WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+documentation provided hereunder is on an "as is" basis, and the
+Institute for Systems Biology and the Whitehead Institute
+have no obligations to provide maintenance, support,
+updates, enhancements or modifications. In no event shall the
+Institute for Systems Biology and the Whitehead Institute
+be liable to any party for direct, indirect, special,
+incidental or consequential damages, including lost profits, arising
+out of the use of this software and its documentation, even if the
+Institute for Systems Biology and the Whitehead Institute
+have been advised of the possibility of such damage. See
+the GNU Lesser General Public License for more details.
+
+You should have received a copy of the GNU Lesser General Public License
+along with this library; if not, write to the Free Software Foundation,
+Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.command;
+
+import java.io.StreamTokenizer;
+import java.io.StringReader;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+import cytoscape.layout.Tunable;
+
+/**
+ * CyCommandManager is a singleton Cytoscape class that provides a global registry
+ * of {@link CyCommand}s and {@link CyCommandNamespace}s. Each CyCommand is added to the registry through the register
+ * method. Commands may be accessed with a combination of command name and namespace.
+ */
+public class CyCommandManager {
+ private static Map<CyCommandNamespace, Map<String,CyCommandHandler>> comMap;
+ private static Map<String, CyCommandNamespace> nsMap;
+
+ static {
+ comMap = new HashMap<CyCommandNamespace, Map<String,CyCommandHandler>>();
+ nsMap = new HashMap<String, CyCommandNamespace>();
+ }
+
+
+ /**
+ * Reserve a namespace. In general, a namespace will map to a plugin and serve to reserve a command prefix
+ * to avoid conflict between plugins. A very rudimentary versioning system (minimum/maximum version numbers)
+ * provide for some version management.
+ *
+ * @param namespace the name of the namespace
+ * @param minVersion the minimum version this set of commands supports
+ * @param maxVersion the maximum version this set of commands supports
+ * @throws RuntimeException if a namespace by the requested name already exists
+ */
+ public static CyCommandNamespace reserveNamespace(String namespace,
+ double minVersion, double maxVersion) throws RuntimeException {
+ if (namespace == null || namespace.length() == 0) return null;
+
+ namespace = namespace.toLowerCase();
+ if (nsMap.containsKey(namespace))
+ throw new RuntimeException("Command namespace: "+namespace+" is already reserved");
+
+ CyCommandNamespace ns = new CyCommandNamespaceImpl(namespace, minVersion, maxVersion);
+ nsMap.put(namespace, ns);
+ comMap.put(ns, new HashMap());
+
+ return ns;
+ }
+
+ /**
+ * Reserve a namespace. In general, a namespace will map to a plugin and serve to reserve a command prefix
+ * to avoid conflict between plugins. This version of the call assumes a version of 0.0 for the min
+ * verison and 1.0 for the max version.
+ *
+ * @param namespace the name of the namespace
+ * @throws RuntimeException if a namespace by the requested name already exists
+ */
+ public static CyCommandNamespace reserveNamespace(String namespace) throws RuntimeException {
+ return reserveNamespace(namespace, 0.0, 1.0);
+ }
+
+ /**
+ * register a new CyCommandHandler.
+ *
+ * @param ns the namespace for this command
+ * @param command the command string that identified this command
+ * @param com the command handler for the command we want to register
+ * @throws RuntimeException if the command is already registered
+ */
+ public static void register(CyCommandNamespace ns, String command, CyCommandHandler com)
+ throws RuntimeException {
+ if (com == null)
+ return;
+
+ if (!comMap.containsKey(ns))
+ throw new RuntimeException("Command namespace: "+ns.getNamespaceName()+" is not yet registered");
+
+ Map<String,CyCommandHandler> subComMap = comMap.get(ns);
+
+ if ( subComMap.containsKey( command ) )
+ throw new RuntimeException("Command: " + ns.getNamespaceName() + " " +
+ command + " already exists!");
+
+ subComMap.put(command, com);
+ }
+
+ /**
+ * return a CyCommandHandler by either name or class name.
+ *
+ * @param name either the name of the class or command
+ * @return the command, or null if a command with name or class doesn't exist
+ */
+ public static CyCommandHandler getCommand(String namespace, String name) {
+ if ((namespace == null) || (namespace.length() == 0))
+ throw new RuntimeException("null or zero length namespace");
+
+ namespace = namespace.toLowerCase();
+
+ if ((name == null) || (name.length() == 0))
+ throw new RuntimeException("null or zero length command name");
+
+ CyCommandNamespace ns = nsMap.get(namespace);
+ if ( ns == null )
+ throw new RuntimeException("namespace '" + namespace + "' does not exist!");
+
+ Map<String,CyCommandHandler> subComMap = comMap.get(ns);
+ return subComMap.get(name);
+ }
+
+ /**
+ * Get the list of all of the currently registered namespaces. Note
+ * that only the <i>name</i> of the namespace is returned. Only the
+ * plugin that registered the namespace may have access to the namespace
+ * object itself.
+ *
+ * @return list of namespaces
+ */
+ public static List<String> getNamespaceList() {
+ List<String>list = new ArrayList();
+ list.addAll(nsMap.keySet());
+ return list;
+ }
+
+ /**
+ * Get the list of all commands that are currently registered,
+ * organized by namespaces
+ *
+ * @return the map of commands that are currently registered, with
+ * the namespaced used to register that command as a key
+ */
+ public static Map<String, List<CyCommandHandler>> getCommandMap() {
+ Map<String, List<CyCommandHandler>> map = new HashMap<String,List<CyCommandHandler>>();
+
+ for ( CyCommandNamespace namespace : comMap.keySet() ) {
+ List<CyCommandHandler> list = new ArrayList<CyCommandHandler>();
+ list.addAll( comMap.get(namespace).values() );
+ map.put(namespace.getNamespaceName(), list);
+ }
+
+ return map;
+ }
+
+ /**
+ * Get the list of all commands that are currently registered
+ * for the specified namespace.
+ *
+ * @param namespace the namespace of the commands to retrieve.
+ * @return the list of commands that are currently registered
+ */
+ public static List<String> getCommandList(String namespace) {
+ List<String> list = new ArrayList<String>();
+ if (!nsMap.containsKey(namespace))
+ return null;
+
+ CyCommandNamespace ns = nsMap.get(namespace.toLowerCase());
+
+ if ( comMap.containsKey( ns ) )
+ list.addAll( comMap.get(ns).keySet() );
+
+ return list;
+ }
+
+ /**
+ * Execute a command.
+ *
+ * @param namespace the namespace for this command
+ * @param command the command
+ * @param arguments the argument list to pass to the command
+ * @return the CyCommandResult
+ * @throws RuntimeException is the namespace or command is not yet registered
+ * @throws CyCommandException if there is an error with the execution
+ */
+ public static CyCommandResult execute(String namespace, String command, Map<String,Object>arguments)
+ throws CyCommandException, RuntimeException {
+ CyCommandHandler handler = getHandler(namespace, command);
+
+ return handler.execute(command, arguments);
+ }
+
+ /**
+ * Execute a command
+ *
+ * @param namespace the namespace for this command
+ * @param command the command
+ * @param arguments the argument list to pass to the command
+ * @return the CyCommandResult
+ * @throws RuntimeException is the namespace or command is not yet registered
+ * @throws CyCommandException if there is an error with the execution
+ */
+ public static CyCommandResult execute(String namespace, String command, List<Tunable>arguments)
+ throws CyCommandException, RuntimeException {
+ CyCommandHandler handler = getHandler(namespace, command);
+
+ return handler.execute(command, arguments);
+ }
+
+ /**
+ * Internal method to get a CyCommandHandler when given a namespace and a command.
+ *
+ * @param namespace the namespace of the command
+ * @param command the command itself
+ */
+ private static CyCommandHandler getHandler(String namespace, String command) {
+ if (!nsMap.containsKey(namespace))
+ throw new RuntimeException("The namespace "+namespace+" is unknown");
+
+ CyCommandNamespace ns = nsMap.get(namespace);
+ Map<String,CyCommandHandler> subComMap = comMap.get(ns);
+
+ if (!subComMap.containsKey(command))
+ throw new RuntimeException("The command "+namespace+" "+command+" isn't registered");
+
+ return subComMap.get(command);
+ }
+
+ /**
+ * Internal implementation for the CyCommandNamespace class.
+ */
+ private static class CyCommandNamespaceImpl implements CyCommandNamespace {
+ private String ns;
+ private int minVersion;
+ private int maxVersion;
+
+ protected CyCommandNamespaceImpl(String namespace, double minVersion, double maxVersion) {
+ this.ns = namespace;
+ this.minVersion = (int)(minVersion*100);
+ this.maxVersion = (int)(maxVersion*100);
+ }
+
+ public boolean supportsVersion(float version) {
+ int checkVersion = (int)(version*100);
+ if (minVersion <= checkVersion && maxVersion >= checkVersion)
+ return true;
+ return false;
+ }
+
+ public String getNamespaceName() { return ns; }
+ }
+}
diff --git a/application/src/main/java/cytoscape/command/CyCommandNamespace.java b/application/src/main/java/cytoscape/command/CyCommandNamespace.java
new file mode 100644
index 0000000..de447f1
--- /dev/null
+++ b/application/src/main/java/cytoscape/command/CyCommandNamespace.java
@@ -0,0 +1,63 @@
+/*
+File: CyCommandNamespace.java
+
+Copyright (c) 2009, The Cytoscape Consortium (www.cytoscape.org)
+
+The Cytoscape Consortium is:
+- Institute for Systems Biology
+- University of California San Diego
+- Memorial Sloan-Kettering Cancer Center
+- Institut Pasteur
+- Agilent Technologies
+- University of California San Francisco
+
+This library is free software; you can redistribute it and/or modify it
+under the terms of the GNU Lesser General Public License as published
+by the Free Software Foundation; either version 2.1 of the License, or
+any later version.
+
+This library is distributed in the hope that it will be useful, but
+WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+documentation provided hereunder is on an "as is" basis, and the
+Institute for Systems Biology and the Whitehead Institute
+have no obligations to provide maintenance, support,
+updates, enhancements or modifications. In no event shall the
+Institute for Systems Biology and the Whitehead Institute
+be liable to any party for direct, indirect, special,
+incidental or consequential damages, including lost profits, arising
+out of the use of this software and its documentation, even if the
+Institute for Systems Biology and the Whitehead Institute
+have been advised of the possibility of such damage. See
+the GNU Lesser General Public License for more details.
+
+You should have received a copy of the GNU Lesser General Public License
+along with this library; if not, write to the Free Software Foundation,
+Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.command;
+
+/**
+ * A CyCommandNamespace represents a reservation for a group of {@link CyCommand}s.
+ * A namespace reservation must be secured before a client can register commands
+ * to be executed.
+ */
+public interface CyCommandNamespace {
+ /**
+ * Return the string name that is held by this namespace.
+ *
+ * @return the name reserved by this namespace.
+ */
+ String getNamespaceName();
+
+ /**
+ * Check to see if this namespace supports a particular version of the command handlers.
+ * The version is a floating-point value of the form major.minor where minor is assumed to
+ * be two digits. So, a version of 1.1 should be thought of as 1.10, while version 1.01 is
+ * the first minor version of major version 1.
+ *
+ * @param version the version to check for support
+ * @return true if this namespace supports the requested version
+ */
+ boolean supportsVersion(float version);
+}
diff --git a/application/src/main/java/cytoscape/command/CyCommandResult.java b/application/src/main/java/cytoscape/command/CyCommandResult.java
new file mode 100644
index 0000000..43273ce
--- /dev/null
+++ b/application/src/main/java/cytoscape/command/CyCommandResult.java
@@ -0,0 +1,226 @@
+/*
+ File: CyCommandResult.java
+
+ Copyright (c) 2009, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+ - University of California San Francisco
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.command;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+/**
+ * CyCommandResult returns the results from the execution of a
+ * command. Generally, a command would create a CyCommandResult
+ * object at the beginning of the execute() method. A command should never
+ * return a <b>null</b> to indicate failure, and should throw {@link CyCommandException}
+ * instead. This will avoid a lot of redundant checking for null returns.
+ */
+public class CyCommandResult {
+ private boolean errors;
+ private List<String> messages;
+ private List<String> errorMessages;
+ private Map<String,Object> results;
+
+ /**
+ * Create a new empty CyCommandResult.
+ */
+ public CyCommandResult() {
+ messages = new ArrayList<String>();
+ results = null;
+ errorMessages = new ArrayList<String>();
+ errors = false;
+ }
+
+ /**
+ * Create a new CyCommandResult with an initial message and execution results.
+ *
+ * @param message a message to include in the result. Note that more messages
+ * may be added later.
+ * @param results a map of the results from the execution.
+ */
+ public CyCommandResult(String message, Map<String,Object> results) {
+ this();
+ messages.add(message);
+ this.results = results;
+ }
+
+ /**
+ * Add a message to the list of messages that results from this execution. This
+ * is an easy way to provide a record of the operation of a command that might
+ * be displayed to the user by a client plugin.
+ *
+ * @param message the message to add
+ */
+ public void addMessage(String message) {
+ messages.add(message);
+ }
+
+ /**
+ * Add an error message to the list of errors for this execution. As
+ * a byproduct, this will set the error flag.
+ *
+ * @param message the error message to add
+ */
+ public void addError(String message) {
+ errorMessages.add(message);
+ errors = true;
+ }
+
+ /**
+ * Add the result for this execution. Note that
+ * this version of the addResult method assumes
+ * there is only one result value. Subsequence
+ * calls to addResult(Object value) will overwrite
+ * this value.
+ *
+ * @param value the result value itself
+ */
+ public void addResult(Object value) {
+ if (results == null) results = new HashMap();
+ results.put("", value);
+ }
+
+ /**
+ * Add a result to the result set for this execution.
+ *
+ * @param key the result whose value we're setting
+ * @param value the result value itself
+ */
+ public void addResult(String key, Object value) {
+ if (results == null) results = new HashMap();
+ results.put(key, value);
+ }
+
+ /**
+ * Return true if the execution was successful, false
+ * if it failed.
+ *
+ * @return true if successful, false otherwise
+ */
+ public boolean successful() {
+ if (errors) return false;
+ return true;
+ }
+
+ /**
+ * Set all of the results for this execution.
+ *
+ * @param results the map of key, value pairs
+ */
+ public void setResults(Map<String, Object> results) {
+ this.results = results;
+ }
+
+ /**
+ * Return a particular result from an execution as
+ * a String. Internally, results are stored as name, value
+ * pairs where the value is an Object that can be converted
+ * to a Stirng. This method provides a short-hand to just
+ * calling toString on the Object-return signature.
+ *
+ * @param key the result value we're interested in
+ * @return the string equivilent of that value
+ */
+ public String getStringResult(String key) {
+ if (results != null && results.containsKey(key)) {
+ return results.get(key).toString();
+ }
+ return null;
+ }
+
+ /**
+ * Return the result from an execution, as a string.
+ *
+ * @return the execution result
+ */
+ public String getStringResult() {
+ return getStringResult("");
+ }
+
+ /**
+ * Return a particular result from an execution.
+ * Internally, results are stored as name, value
+ * pairs where the value is an Object that can be converted
+ * to a Stirng. This method returns the stored Object
+ * with no attempt to do any conversion.
+ *
+ * @param key the result value we're interested in
+ * @return the resulting value
+ */
+ public Object getResult(String key) {
+ if (results != null && results.containsKey(key)) return results.get(key);
+ return null;
+ }
+
+ /**
+ * Return the result from an execution.
+ *
+ * @return the execution result
+ */
+ public Object getResult() {
+ return getResult("");
+ }
+
+ /**
+ * Return all of the results from an execution as a map
+ * indexed by the result name.
+ *
+ * @return the map of key, value pairs
+ */
+ public Map<String, Object> getResults() {
+ return results;
+ }
+
+ /**
+ * Return all of the messages from an execution.
+ *
+ * @return list of message strings
+ */
+ public List<String> getMessages() {
+ return messages;
+ }
+
+ /**
+ * Return all of the erros from an execution.
+ *
+ * @return list of erros strings
+ */
+ public List<String> getErrors() {
+ return errorMessages;
+ }
+}
diff --git a/application/src/main/java/cytoscape/data/AttribTopoGraphNode.java b/application/src/main/java/cytoscape/data/AttribTopoGraphNode.java
new file mode 100644
index 0000000..546e919
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/AttribTopoGraphNode.java
@@ -0,0 +1,68 @@
+/*
+ File: AttribTopoGraphNode.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data;
+
+
+import java.util.Collection;
+import java.util.HashSet;
+import cytoscape.util.TopoGraphNode;
+
+
+/**
+ * Represents a node in a topological graph.
+ */
+public class AttribTopoGraphNode implements TopoGraphNode {
+ private final String nodeName;
+ private final Collection<TopoGraphNode> dependents;
+
+ public AttribTopoGraphNode(final String nodeName, final Collection<String> dependents) {
+ this.nodeName = nodeName;
+ this.dependents = new HashSet<TopoGraphNode>();
+
+ for (final String dependent : dependents)
+ this.dependents.add(new AttribTopoGraphNode(dependent));
+ }
+
+ private AttribTopoGraphNode(final String nodeName) {
+ this.nodeName = nodeName;
+ this.dependents = new HashSet<TopoGraphNode>();
+ }
+
+ public String getNodeName() { return nodeName; }
+ public Collection<TopoGraphNode> getDependents() { return dependents; }
+ @Override public int hashCode() { return nodeName.hashCode(); }
+ @Override public boolean equals(final Object o) {
+ if (!(o instanceof AttribTopoGraphNode))
+ return false;
+
+ final AttribTopoGraphNode other = (AttribTopoGraphNode)o;
+ return nodeName.equals(other.nodeName);
+ }
+}
diff --git a/application/src/main/java/cytoscape/data/AttributeFilter.java b/application/src/main/java/cytoscape/data/AttributeFilter.java
new file mode 100644
index 0000000..1d1aa4b
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/AttributeFilter.java
@@ -0,0 +1,63 @@
+/*
+ File: AttributeFilter.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data;
+
+
+/**
+ * Interface for defining CyEdge-based filters used for determining
+ * which Edges should be used for a particular operation, such as
+ * CyAttributesUtils.copyAttributes().
+ * @see cytoscape.data.CyAttributesUtils#copyAttributes
+ */
+public interface AttributeFilter {
+ /**
+ * Return true iff a given attribute should be included in
+ * some operation, such as {@link
+ * cytoscape.data.CyAttributesUtils#copyAttributes
+ * CyAttributesUtils.copyAttributes()}.
+ * @param CyAttributes attrs the CyAttributes where attrName
+ * is stored.
+ * @param objID the identifer of the object whose attrName attribute
+ * is stored in attrs.
+ * @param attrName the name of the Attribute to test.
+ * For example, if we were performing a CyAttributesUtils.copyAttributes(),
+ * returning true would mean to copy the attribute attrName
+ * for the object with key objID, within the CyAttributes attrs.
+ * @see cytoscape.data.CyAttributesUtils#copyAttributes
+ */
+ boolean includeAttribute(CyAttributes attrs, String objID, String attrName);
+}
diff --git a/application/src/main/java/cytoscape/data/AttributeSaverDialog.java b/application/src/main/java/cytoscape/data/AttributeSaverDialog.java
new file mode 100644
index 0000000..95a8d63
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/AttributeSaverDialog.java
@@ -0,0 +1,481 @@
+/*
+ File: AttributeSaverDialog.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.data;
+
+import cytoscape.Cytoscape;
+import cytoscape.CytoscapeInit;
+import cytoscape.logger.CyLogger;
+import cytoscape.data.writers.CyAttributesWriter;
+import java.awt.BorderLayout;
+import java.awt.Container;
+import java.awt.Dimension;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.util.Collections;
+import java.util.Iterator;
+import java.util.Vector;
+
+import javax.swing.BoxLayout;
+import javax.swing.JButton;
+import javax.swing.JDialog;
+import javax.swing.JFileChooser;
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTable;
+import javax.swing.event.TableModelListener;
+import javax.swing.event.TableModelEvent;
+import javax.swing.table.AbstractTableModel;
+
+
+/**
+ * Dialog box to save various attributes.<br>
+ *
+ * @version 1.1
+ */
+public class AttributeSaverDialog extends JDialog {
+ /**
+ * Default suffix for node attribute files
+ */
+ protected static final String NODE_SUFFIX = ".NA";
+
+ /**
+ * Default suffix for edge attribute files
+ */
+ protected static final String EDGE_SUFFIX = ".EA";
+
+ /**
+ * The max preferred size for the jscrollpane, will not let the jtable
+ * expand past this point
+ */
+ protected static final int MAX_PREFERRED_SIZE = 100;
+
+ /**
+ * Constant ot specify nodes
+ */
+ public static final int NODES = 0;
+
+ /**
+ * Constant to specify edges
+ */
+ public static final int EDGES = 1;
+
+ /**
+ * The state associated with the attribute table, keeps track of the
+ * attribute, filename and booleans. Edited through the jtable
+ */
+ private AttributeSaverState state;
+
+ /**
+ * JTable for displaying boolean, attribute and filename
+ */
+ private JTable attributeTable;
+
+ /**
+ * Show a dialog of hte specified type, see above constants
+ */
+ protected static void showDialog(final int type) {
+ final AttributeSaverDialog dialog = new AttributeSaverDialog(type);
+ dialog.setVisible(true);
+ }
+
+ /**
+ * Show a dialog box to save edge attributes
+ */
+ public static void showEdgeDialog() {
+ showDialog(EDGES);
+ }
+
+ /**
+ * Show a dialog box to save node attributes
+ */
+ public static void showNodeDialog() {
+ showDialog(NODES);
+ }
+
+ protected JButton saveButton = new JButton("Choose Directory and Save");
+ protected static CyLogger logger = CyLogger.getLogger(AttributeSaverDialog.class);
+
+ /**
+ * Create a dialog box of the specified type. Instead of constructor, use
+ * static methods to create dialog box
+ */
+ public AttributeSaverDialog(final int type) {
+ super(Cytoscape.getDesktop(), "Save Attributes", true);
+
+ final Container contentPane = getContentPane();
+ contentPane.setLayout(new BorderLayout());
+
+ // create the objects which will maintain the state of the dialog
+ final String suffix;
+ final String[] attributes;
+
+ if (type == NODES) {
+ suffix = NODE_SUFFIX;
+ attributes = Cytoscape.getNodeAttributes().getAttributeNames();
+ } // end of if ()
+ else {
+ suffix = EDGE_SUFFIX;
+ attributes = Cytoscape.getEdgeAttributes().getAttributeNames();
+ } // end of else
+
+ state = new AttributeSaverState(attributes, suffix, type);
+
+ // Add TableModelListener to syn the state of saveButton
+ TableModelListener tmListener = new TableModelListener() {
+ public void tableChanged(TableModelEvent e) {
+ if (state.saveChecked()){
+ AttributeSaverDialog.this.saveButton.setEnabled(true);
+ }
+ else {
+ AttributeSaverDialog.this.saveButton.setEnabled(false);
+ }
+ }
+ };
+ state.addTableModelListener(tmListener);
+
+ attributeTable = new JTable(state);
+ attributeTable.setToolTipText("Select multiple attributes to save. Modify \"Filename\" field to specify filename");
+ attributeTable.setCellSelectionEnabled(false);
+
+ // initialize the directory browser component
+ saveButton.setEnabled(false);
+ saveButton.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent ae) {
+ final JFileChooser myChooser = new JFileChooser(CytoscapeInit.getMRUD());
+ myChooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
+
+ if (myChooser.showSaveDialog(Cytoscape.getDesktop()) == JFileChooser.APPROVE_OPTION) {
+ state.setSaveDirectory(myChooser.getSelectedFile());
+ CytoscapeInit.setMRUD(myChooser.getSelectedFile());
+
+ int count = 0;
+
+ try {
+ count = state.writeState();
+ JOptionPane.showMessageDialog(Cytoscape.getDesktop(),
+ "Successfully saved " + count + " files");
+ } catch (IOException e) {
+ logger.warn("Unable to save attributes", e);
+ JOptionPane.showMessageDialog(Cytoscape.getDesktop(),
+ "Error saving attributes: "+e.getMessage(),
+ "Attribute Save Error", JOptionPane.WARNING_MESSAGE);
+ }
+
+ AttributeSaverDialog.this.dispose();
+ }
+ }
+ });
+
+ JPanel centerPanel = new JPanel();
+ JScrollPane scrollPane = new JScrollPane(attributeTable);
+ scrollPane.setPreferredSize(new Dimension(MAX_PREFERRED_SIZE, MAX_PREFERRED_SIZE));
+ centerPanel.setLayout(new BoxLayout(centerPanel, BoxLayout.Y_AXIS));
+ centerPanel.add(new JLabel("Select multiple attributes to save. Edit table to change filenames"));
+ centerPanel.add(scrollPane);
+
+ JPanel southPanel = new JPanel();
+ southPanel.add(saveButton);
+
+ contentPane.add(centerPanel, BorderLayout.CENTER);
+ contentPane.add(southPanel, BorderLayout.SOUTH);
+ pack();
+ }
+}
+
+
+/**
+ * Holds the state associated with the dialog.<br>
+ */
+class AttributeSaverState extends AbstractTableModel {
+ /**
+ *
+ */
+ public static String newline = System.getProperty("line.separator");
+
+ /**
+ * The default string to append for an attribute filename
+ */
+ protected final String suffix;
+
+ /**
+ * The directory in which to save the files
+ */
+ private File saveDirectory;
+
+ /**
+ * Type of graph object to save
+ */
+ private int type;
+
+ /**
+ * List of all attributes
+ */
+ private Vector<String> attributeNames;
+
+ /**
+ * List of all filenames
+ */
+ private Vector<String> filenames;
+
+ /**
+ * List of all booleans, tells whether to save
+ */
+ private Vector<Boolean> selectedAttributes;
+
+
+ /**
+ * Network to from which to read graph objects
+ */
+
+ // private CyNetwork cyNetwork;
+ // colum identities
+ protected static final int FILE_COLUMN = 2;
+ protected static final int ATTRIBUTE_COLUMN = 1;
+ protected static final int SAVE_COLUMN = 0;
+
+ /**
+ * Initialize the state
+ *
+ * @param nodeAttributes
+ * An array of strings containing all node attributes
+ * @param type
+ * operate on NODES or EDGES
+ * @param cyNetwork
+ * the network to save
+ */
+ public AttributeSaverState(final String[] nodeAttributes, final String suffix, int type) {
+ this.type = type;
+ this.suffix = suffix;
+ //this.listeners = new Vector();
+ this.attributeNames = new Vector<String>();
+ this.filenames = new Vector<String>();
+ this.selectedAttributes = new Vector<Boolean>();
+
+ for (int idx = 0; idx < nodeAttributes.length; idx++) {
+ attributeNames.add(nodeAttributes[idx]);
+ } // end of for ()
+
+ Collections.sort(attributeNames);
+
+ for (Iterator stringIt = attributeNames.iterator(); stringIt.hasNext();) {
+ String attribute = (String) stringIt.next();
+ filenames.add(attribute + suffix);
+ selectedAttributes.add(new Boolean(false));
+ } // end of for ()
+ }
+
+ /**
+ * Set the directory where the files will be saved to
+ */
+ public void setSaveDirectory(final File saveDirectory) {
+ this.saveDirectory = saveDirectory;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @throws IOException DOCUMENT ME!
+ */
+ public int writeState() throws IOException {
+ final CyAttributes cyAttributes;
+
+ if (type == AttributeSaverDialog.NODES) {
+ cyAttributes = Cytoscape.getNodeAttributes();
+ } else {
+ cyAttributes = Cytoscape.getEdgeAttributes();
+ }
+
+ int count = 0;
+
+ for (int idx = 0; idx < attributeNames.size(); idx++) {
+ if (selectedAttributes.get(idx)) {
+ final CyAttributesWriter writer = new CyAttributesWriter(cyAttributes,
+ attributeNames.get(idx),
+ new FileWriter(new File(saveDirectory,
+ filenames
+ .get(idx))));
+ writer.writeAttributes();
+ count++;
+ }
+ }
+
+ return count;
+ }
+
+ // Retrun true only if there are at least one checkbox is checked
+ public boolean saveChecked() {
+ for (int i=0; i<selectedAttributes.size(); i++) {
+ if (selectedAttributes.elementAt(i).booleanValue()) {
+ return true;
+ }
+ }
+ return false;
+ }
+
+ // below here is implementing the tableModel
+ /**
+ * DOCUMENT ME!
+ *
+ * @param columnIndex DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Class getColumnClass(int columnIndex) {
+ if (columnIndex == SAVE_COLUMN) {
+ return Boolean.class;
+ } // end of if ()
+ else {
+ return String.class;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getColumnCount() {
+ return 3;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getRowCount() {
+ return attributeNames.size();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param rowIndex DOCUMENT ME!
+ * @param columnIndex DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getValueAt(int rowIndex, int columnIndex) {
+ switch (columnIndex) {
+ case SAVE_COLUMN:
+ return selectedAttributes.get(rowIndex);
+
+ case ATTRIBUTE_COLUMN:
+ return attributeNames.get(rowIndex);
+
+ case FILE_COLUMN:
+ return filenames.get(rowIndex);
+
+ default:
+ throw new IllegalArgumentException();
+ } // end of switch ()
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param columnIndex DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getColumnName(int columnIndex) {
+ switch (columnIndex) {
+ case SAVE_COLUMN:
+ return "Save";
+
+ case ATTRIBUTE_COLUMN:
+ return "Attribute";
+
+ case FILE_COLUMN:
+ return "Filename";
+
+ default:
+ throw new IllegalArgumentException();
+ } // end of switch ()
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param rowIndex DOCUMENT ME!
+ * @param columnIndex DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isCellEditable(int rowIndex, int columnIndex) {
+ if (columnIndex != ATTRIBUTE_COLUMN) {
+ return true;
+ } // end of if ()
+
+ return false;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param aValue DOCUMENT ME!
+ * @param rowIndex DOCUMENT ME!
+ * @param columnIndex DOCUMENT ME!
+ */
+ public void setValueAt(final Object aValue, final int rowIndex, final int columnIndex) {
+ switch (columnIndex) {
+ case ATTRIBUTE_COLUMN:
+ throw new RuntimeException("Cell is not editable");
+
+ case SAVE_COLUMN:
+ selectedAttributes.set(rowIndex, (Boolean) aValue);
+ fireTableDataChanged();
+
+ break;
+
+ case FILE_COLUMN:
+ filenames.set(rowIndex, (String) aValue);
+
+ break;
+
+ default:
+ break;
+ } // end of switch ()
+ }
+}
diff --git a/application/src/main/java/cytoscape/data/AttributeValueVisitor.java b/application/src/main/java/cytoscape/data/AttributeValueVisitor.java
new file mode 100644
index 0000000..f7544d8
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/AttributeValueVisitor.java
@@ -0,0 +1,64 @@
+/*
+ File: AttributeValueVisitor.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data;
+
+
+/**
+ * Interface for defining attribute value visitors--operations to
+ * perform on each attribute value using {@link
+ * cytoscape.data.CyAttributesUtils#traverseAttributeValues
+ * CyAttributesUtils.traverseAttributeValues()}.
+ *
+ */
+public interface AttributeValueVisitor {
+ /**
+ * Perform whatever operations are desired on the given attribute value.
+ * @param objTraversedID the identifier of the object for which we have
+ * obtained an attribute value.
+ * @param attrName the attribute name for which this is a value.
+ * @param attrs the CyAttributes where this attribute value is stored.
+ * @param keySpace the key used to obtain this value. For complex
+ * values, this may consist of several elements (e.g., new
+ * Object[] {"url1", new Integer(1), new Integer(0)). Modification
+ * of this key may lead to unexpected traversal results or errors,
+ * so copy this key if you wish to make modifications.
+ * @param visitedValue the actual visited.
+ * @see cytoscape.data.CyAttributesUtils#traverseAttributeValues
+ */
+ void visitingAttributeValue(String objTraverseID, String attrName, CyAttributes attrs,
+ Object[] keySpace, Object visitedValue);
+}
diff --git a/application/src/main/java/cytoscape/data/CyAttributes.java b/application/src/main/java/cytoscape/data/CyAttributes.java
new file mode 100644
index 0000000..5a05076
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/CyAttributes.java
@@ -0,0 +1,797 @@
+/*
+ File: CyAttributes.java
+
+ Copyright (c) 2006, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data;
+
+import cytoscape.data.attr.MultiHashMap;
+import cytoscape.data.attr.MultiHashMapDefinition;
+import org.cytoscape.equations.Equation;
+
+import java.util.List;
+import java.util.Map;
+
+
+/**
+ * CyAttributes provides access to network, node, and edge attributes within Cytoscape.
+ * <P>
+ * CyAttributes is a replacement for {@link GraphObjAttributes}, which will be
+ * officially removed from the Cytoscape core in September, 2006.
+ * <h3>Basic Concepts:</h3>
+ * Each network, node, and edge within Cytoscape can be annotated with one or more
+ * attributes. For example, a node representing a protein could have
+ * attributes for description, species, NCBI Gene ID, UniProt ID, etc.
+ * These attributes are set and retrieved via the CyAttributes interface.
+ * <h3>Global Attributes:</h3>
+ * There are three sets of global attributes, one for networks, one for nodes, and one for edges.
+ * To access these global attributes, use:
+ * <UL>
+ * <LI>{@link cytoscape.Cytoscape#getNetworkAttributes()}
+ * <LI>{@link cytoscape.Cytoscape#getNodeAttributes()}
+ * <LI>{@link cytoscape.Cytoscape#getEdgeAttributes()}
+ * </UL>
+ * <h3>Unique Identifiers:</h3>
+ * CyAttributes uses unique identifiers to attach attributes to specific
+ * nodes and edges. The unique identifiers for nodes and edges are available
+ * via the <CODE>getIdentifier()</CODE> method:
+ * <UL>
+ * <LI>For networks, use {@link cytoscape.CyNetwork#getIdentifier()}.
+ * <LI>For nodes, use {@link cytoscape.CyNode#getIdentifier()}.
+ * <LI>For edges, use {@link cytoscape.CyEdge#getIdentifier()}.
+ * </UL>
+ * <h3>Data Type Restrictions:</h3>
+ * CyAttributes uses a {@link cytoscape.data.attr.MultiHashMap} data structure,
+ * which restricts attribute values to four data types: <CODE>Boolean</CODE>,
+ * <CODE>Integer</CODE>, <CODE>Double</CODE>, and <CODE>String</CODE>. It does
+ * not store arbitrary Java Objects. We do this for three reasons:
+ * <UL>
+ * <LI>We want to provide complete import/export of all attribute values,
+ * without having to rely on Java serialization.
+ * <LI>We want to enable inter-plugin communication, such that plugins can
+ * share attribute data without having to agree to use some predefined or
+ * custom data structure ahead of time.
+ * <LI>We want to build a universal network/node/edge attribute browser.
+ * </UL>
+ * <h3>Getting / Setting Attributes: An Overview</h3>
+ * There are three ways to get/set attributes. They are (in order
+ * of increasing complexity):
+ * <UL>
+ * <LI>Getting / setting individual values.</LI>
+ * <LI>Getting / setting 'simple' lists and 'simple' maps.</LI>
+ * <LI>Getting / setting arbitrarily complex data structures.</LI>
+ * </UL>
+ * Each of these approaches is detailed below.
+ * <h3>Getting / Setting Individual Values:</h3>
+ * This is the simplest option. Attributes are restricted to the following four
+ * types:
+ * <UL>
+ * <LI><CODE>Boolean</CODE>, <CODE>Integer</CODE>, <CODE>Double</CODE>,
+ * <CODE>String</CODE>
+ * </UL>
+ * There are getters and setters for each of these four types. For example,
+ * the following code snippet sets and gets an Integer attribute value:
+ * <PRE>
+ * cyAttributes.setAttribute (node.getIdentifier(),
+ * "Rank", new Integer(3));
+ * Integer value = cyAttributes.getIntegerAttribute
+ * (node.getIdentifier(), "Rank");
+ * </PRE>
+ * <h3>Getting / Setting Simple Lists:</h3>
+ * A 'simple' list is defined as follows:
+ * <UL>
+ * <LI>All items within the list are of the same type, and are chosen
+ * from one of the following: <CODE>Boolean</CODE>, <CODE>Integer</CODE>,
+ * <CODE>Double</CODE> or <CODE>String</CODE>.
+ * </UL>
+ * In other words, a list of three <CODE>Integer</CODE> Objects is a simple
+ * list, whereas a mix of two <CODE>Integer</CODE> and one <CODE>Boolean</CODE>
+ * Object is not.
+ * <P>
+ * The following code snippet illustrates how to set a simple list of three
+ * <CODE>Integer</CODE> Objects:
+ * <PRE>
+ * ArrayList list = new ArrayList();
+ * list.add (new Integer(1));
+ * list.add (new Integer(22));
+ * list.add (new Integer(5));
+ * cyAttributes.setList (node.getIdentifier(),
+ * "Rank List", list).
+ * </PRE>
+ * At run-time, the <CODE>setList</CODE> method will check that all items in
+ * the list are of the same type, and are chosen from the following list:
+ * <CODE>Boolean</CODE>, <CODE>Integer</CODE>, <CODE>Double</CODE>
+ * or <CODE>String</CODE>. If these criteria are not met, an
+ * <CODE>IllegalArgumentException</CODE> will be thrown.
+ * <P>
+ * To get a simple list, use the
+ * {@link CyAttributes#getListAttribute(String, String)} method.
+ * <h3>Getting / Setting Simple Maps:</h3>
+ * A 'simple' map is defined as follows:
+ * <UL>
+ * <LI>All keys within the map are of type: <CODE>String</CODE>.
+ * <LI>All values within the map are of the same type, and are chosen
+ * from one of the following: <CODE>Boolean</CODE>, <CODE>Integer</CODE>,
+ * <CODE>Double</CODE> or <CODE>String</CODE>.
+ * </UL>
+ * In other words, a map that contains three <CODE>Integer</CODE> values
+ * is a simple map, whereas a map that contains two <CODE>Integer</CODE>
+ * values and one <CODE>Boolean</CODE> value is not.
+ * <P>
+ * The following code snippet illustrates how to set a simple map
+ * of three <CODE>String</CODE> Objects:
+ * <PRE>
+ * Map map = new HashMap();
+ * map.put("name", "Reactome");
+ * map.put("url", "http://www.reactome.org");
+ * map.put("description", "Reactome - a knowledgebase of "
+ * + "biological processes");
+ * cyAttributes.setMapAttribute(node.getIdentifier(),
+ * "external_db", map);
+ * </PRE>
+ * To get a simple map, use the
+ * {@link CyAttributes#getMapAttribute(String, String)} method.
+ * <h3>Working with Fixed Attribute Types:</h3>
+ * Each attribute is bound to a specific data type, and this data type
+ * is set and fixed the first time the attribute is used. For example,
+ * in Plugin 1, the following code sets "RANK" to be of type
+ * <CODE>Integer</CODE>:
+ * <PRE>
+ * cyAttributes.setAttribute (node.getIdentifier(), "Rank", new Integer(3));
+ * </PRE>
+ * Later on, Plugin 2 executes the following code:
+ * <PRE>
+ * cyAttributes.setAttribute (node.getIdentifier(), "Rank",
+ * new String("Three"));
+ * </PRE>
+ * We are now attempting to set "RANK" to a String value, but "RANK" is already
+ * fixed as an <CODE>Integer</CODE> data type. Hence, the call is considered
+ * invalid, and an <CODE>IllegalArgumentException</CODE> will be thrown.
+ * <P>
+ * The same situation can occur with simple lists and simple maps. For example,
+ * if PlugIn 1 defines a simple list of all <CODE>Integer</CODE> values, and
+ * PlugIn 2 attempts to re-use this attribute with a list of <CODE>Double</CODE>
+ * values, the call is considered invalid, and an
+ * <CODE>IllegalArgumentException</CODE> will be thrown.
+ * <P>
+ * To prevent this type of problem, use
+ * {@link CyAttributes#getType(String)} to determine the attribute's data
+ * type <I>before</I> setting any new attributes.
+ * <P>
+ * To reset an attribute's data type, use
+ * {@link CyAttributes#deleteAttribute(String)}. Note that calling this method
+ * will delete all attributes with this name, preparing the way for a clean
+ * slate. Please use with caution!
+ * <h3>Working with Arbitrarily Complex Data Structures:</h3>
+ * CyAttributes uses a {@link cytoscape.data.attr.MultiHashMap} data structure
+ * to store attributes. This data structure enables you to store arbitrarily
+ * complex trees of data, but restricts the tree to Objects of type:
+ * <CODE>Boolean</CODE>, <CODE>Integer</CODE>, <CODE>Double</CODE> or
+ * <CODE>String</CODE>.
+ * <P>
+ * If you wish to store arbitarily complex data structures (e.g. anything
+ * more complicated than a simple list or a simple map), you can do so by
+ * obtaining the MultiHashMap via {@link CyAttributes#getMultiHashMap()},
+ * and {@link CyAttributes#getMultiHashMapDefinition()},
+ * and working on the data structure directly. Complete information is
+ * available in the {@link cytoscape.data.attr.MultiHashMap} javadocs.
+ * <h3>Listening for Attribute Events:</h3>
+ * As noted above, CyAttributes uses a {@link cytoscape.data.attr.MultiHashMap}
+ * data structure to store attributes. To listen to attribute events,
+ * first obtain the MultiHashMap via {@link CyAttributes#getMultiHashMap()},
+ * and then register a listener via
+ * {@link
+ * MultiHashMap#addDataListener(cytoscape.data.attr.MultiHashMapListener)}.
+ * <P>Note that calls to
+ * {@link CyAttributes#setListAttribute(String, String, java.util.List)}
+ * and
+ * {@link CyAttributes#setMapAttribute(String, String, java.util.Map)}
+ * result in many calls to the MultiHashMap object. For example, if you have
+ * five elements in a List, the implementation code makes five calls to
+ * the MultiHashMap, and you will therefore be notified of five separate
+ * events, rather than one global list event.
+ * <P>
+ * <h3>Setting attribute descriptions and user interaction flags:</h3>
+ * Starting in Cytoscape 2.4, you can add human readable text descriptions
+ * to attributes. These descriptions are automatically presented to the
+ * end user via various user interface elements, including the default
+ * node/edge attribute browser and via the QuickFind configuration panel.
+ * To set an attribute description, use the
+ * {@link CyAttributes#setAttributeDescription(String, String)} method.
+ * To retrieve an attribute description, use the
+ * {@link CyAttributes#getAttributeDescription(String)} method.
+ * <P>
+ * Starting in Cytoscape 2.4, you can also flag attributes as visible /
+ * hidden or editable / non-editable by the end user. User interface elements
+ * use these attribute flags to determine user interactivity. For example, the
+ * default attribute browser will hide all attributes marked as hidden, and
+ * will restrict users to edit only those attributes marked as editable.
+ * By default, all attributes are visible and editable. Therefore, you only
+ * need to interact with this portion of the API if you want to specifically
+ * hide certain attributes or mark certain attributes as non-editable.
+ * <P>
+ * To set an attribute as invisible, use the
+ * {@link CyAttributes#setUserVisible(String, boolean)} method and set
+ * to false.
+ * <P>
+ * To set an attribute as non-editable, use the
+ * {@link CyAttributes#setUserEditable(String, boolean)} method
+ * and set to false.
+ * <P>
+ * <B>Note:</B> CyAttributes does not enforce these user interfaction flags.
+ * Rather, relevant user interface (UI) element(s) must query CyAttributes,
+ * and enforce the interaction flags themselves.
+ *
+ * @author Cytoscape Development Team
+ */
+public interface CyAttributes {
+ /**
+ * This type corresponds to java.lang.Boolean.
+ */
+ public final byte TYPE_BOOLEAN = MultiHashMapDefinition.TYPE_BOOLEAN;
+
+ /**
+ * This type corresponds to java.lang.Double.
+ */
+ public final byte TYPE_FLOATING = MultiHashMapDefinition.TYPE_FLOATING_POINT;
+
+ /**
+ * This type corresponds to java.lang.Integer.
+ */
+ public final byte TYPE_INTEGER = MultiHashMapDefinition.TYPE_INTEGER;
+
+ /**
+ * This type corresponds to java.lang.String.
+ */
+ public final byte TYPE_STRING = MultiHashMapDefinition.TYPE_STRING;
+
+ /**
+ * This type corresponds to a 'simple' list.
+ * <P>
+ * A 'simple' list is defined as follows:
+ * <UL>
+ * <LI>All items within the list are of the same type, and are chosen
+ * from one of the following: <CODE>Boolean</CODE>, <CODE>Integer</CODE>,
+ * <CODE>Double</CODE> or <CODE>String</CODE>.
+ * </UL>
+ */
+ public final byte TYPE_SIMPLE_LIST = -2;
+
+ /**
+ * This type corresponds to a 'simple' hash map.
+ * <P>
+ * A 'simple' map is defined as follows:
+ * <UL>
+ * <LI>All keys within the map are of type: <CODE>String</CODE>.
+ * <LI>All values within the map are of the same type, and are chosen
+ * from one of the following: <CODE>Boolean</CODE>, <CODE>Integer</CODE>,
+ * <CODE>Double</CODE> or <CODE>String</CODE>.
+ * </UL>
+ */
+ public final byte TYPE_SIMPLE_MAP = -3;
+
+ /**
+ * This type corresponds to a data structure of arbitrary complexity,
+ * e.g. anything more complex than a 'simple' list or a 'simple' map.
+ * <P>
+ * For complete details, refer to the class comments, or
+ * {@link CyAttributes#getMultiHashMap()}.
+ */
+ public final byte TYPE_COMPLEX = -4;
+
+ /**
+ * This type corresponds to an attribute which has not been defined.
+ */
+ public final byte TYPE_UNDEFINED = -1;
+
+ /**
+ * Gets an array of all attribute names.
+ *
+ * @return an array of String Objects.
+ */
+ public String[] getAttributeNames();
+
+ /**
+ * Sets a human readable description of a specific attribute.
+ * @param attributeName attribute name.
+ * @param description human readable description of attribute.
+ * used for display to end-user.
+ */
+ public void setAttributeDescription(String attributeName, String description);
+
+ /**
+ * Gets the human readable description of a specific attribute.
+ * @param attributeName attribute name.
+ * @return human readable description of attribute or null (if no
+ * description has been specified).
+ */
+ public String getAttributeDescription(String attributeName);
+
+ /**
+ * Sets the specified boolean to indicate whether or not the specified
+ * attribute should be made visible to the end user.
+ * <P>
+ * By default, all attributes are visible.
+ * <P>
+ * <B>Note:</B> CyAttributes does not actually enforce user visibility.
+ * Rather, relevant user interface (UI) element(s) must query CyAttributes,
+ * and enforce the visibility flag themselves.
+ *
+ * @param attributeName Attribute name.
+ * @param value the boolean to be set. true indicates that the attribute
+ * should be made visible to the end user. false indicates that the
+ * attribute should not be made visible to the end user.
+ */
+ public void setUserVisible(String attributeName, boolean value);
+
+ /**
+ * Returns the boolean indicating whether the specified attribute should
+ * be made visible to the end user or not.
+ * <P>
+ * By default, all attributes are visible.
+ * <P>
+ * <B>Note:</B> CyAttributes does not actually enforce user visibility.
+ * Rather, relevant user interface (UI) element(s) must query CyAttributes,
+ * and enforce the visibility flag themselves.
+ *
+ * @param attributeName Attribute name.
+ * @return true indicates that the attribute should be made visible to the
+ * end user. false indicates that the attribute should not be made visible
+ * to the end user.
+ */
+ public boolean getUserVisible(String attributeName);
+
+ /**
+ * Sets the specified boolean to indicate whether or not the specified
+ * attribute should be editable by the end user.
+ * <P>
+ * By default, all attributes are editable.
+ * <P>
+ * <B>Note:</B> CyAttributes does not actually enforce restrictions
+ * on user editing of attributes. Rather, relevant user interface (UI)
+ * element(s) must query CyAttributes, and enforce the editing requirements
+ * themselves.
+ *
+ * @param attributeName Attribute name.
+ * @param value the boolean to be set. true indicates that the attribute
+ * should be editable by the end user. false indicates that the attribute
+ * should not be editable by the end user.
+ */
+ public void setUserEditable(String attributeName, boolean value);
+
+ /**
+ * Returns the boolean indicating whether this attribute should be editable
+ * by the end user or not.
+ * <P>
+ * By default, all attributes are editable.
+ * <P>
+ * <B>Note:</B> CyAttributes does not actually enforce restrictions
+ * on user editing of attributes. Rather, relevant user interface (UI)
+ * element(s) must query CyAttributes, and enforce the editing requirements
+ * themselves.
+ *
+ * @param attributeName Attribute name.
+ * @return true indicates that the attribute should be editable by the
+ * end user. false indicates that the attribute should not be editable
+ * by the end user.
+ */
+ public boolean getUserEditable(String attributeName);
+
+ /**
+ * Determines if the specified id/attributeName pair exists.
+ *
+ * @param id unique identifier.
+ * @param attributeName attribute name.
+ * @return true or false.
+ */
+ public boolean hasAttribute(String id, String attributeName);
+
+ /**
+ * Sets an id/attributeName pair of type Boolean.
+ *
+ * @param id unique identifier.
+ * @param attributeName attribute name.
+ * @param value boolean value.
+ * @throws IllegalArgumentException Indicates that this attribute has
+ * already been defined with a data type,
+ * and this data type is not of type:
+ * TYPE_BOOLEAN.
+ */
+ public void setAttribute(String id, String attributeName, Boolean value)
+ throws IllegalArgumentException;
+
+ /**
+ * Sets an id/attributeName pair of type Integer.
+ *
+ * @param id unique identifier.
+ * @param attributeName attribute name.
+ * @param value integer value.
+ * @throws IllegalArgumentException Indicates that this attribute has
+ * already been defined with a data type,
+ * and this data type is not of type:
+ * TYPE_INTEGER.
+ */
+ public void setAttribute(String id, String attributeName, Integer value)
+ throws IllegalArgumentException;
+
+ /**
+ * Sets an id/attributeName pair of type Double.
+ *
+ * @param id unique identifier.
+ * @param attributeName attribute name.
+ * @param value double value.
+ * @throws IllegalArgumentException Indicates that this attribute has
+ * already been defined with a data type,
+ * and this data type is not of type:
+ * TYPE_FLOATING.
+ */
+ public void setAttribute(String id, String attributeName, Double value)
+ throws IllegalArgumentException;
+
+ /**
+ * Sets an id/attributeName pair of type String.
+ *
+ * @param id unique identifier.
+ * @param attributeName attribute name.
+ * @param value string value.
+ * @throws IllegalArgumentException Indicates that this attribute has
+ * already been defined with a data type,
+ * and this data type is not of type:
+ * TYPE_STRING.
+ */
+ public void setAttribute(String id, String attributeName, String value)
+ throws IllegalArgumentException;
+
+ /**
+ * @param id unique identifier.
+ * @param attributeName attribute name.
+ * @param equation an attribute equation
+ */
+ public void setAttribute(final String id, final String attributeName, final Equation equation);
+
+ /**
+ * @param id unique identifier.
+ * @param attributeName attribute name.
+ * @param equation an attribute equation
+ * @param dataType must be one of MultiHashMapDefinition.TYPE_{BOOLEAN,STRING,INTEGER, or FLOATING_POINT}
+ */
+ public void setAttribute(final String id, final String attributeName, final Equation equation,
+ final byte dataType);
+
+ /**
+ * Gets a Boolean value at the specified id/attributeName.
+ *
+ * @param id unique identifier.
+ * @param attributeName attribute name.
+ * @return Boolean object, or null if no id/attributeName pair is found.
+ * @throws ClassCastException Indicates that the specified attribute
+ * is not of type: TYPE_BOOLEAN.
+ */
+ public Boolean getBooleanAttribute(String id, String attributeName) throws ClassCastException;
+
+ /**
+ * Gets an Integer value at the specified id/attributeName.
+ *
+ * @param id unique identifier.
+ * @param attributeName attribute name.
+ * @return Integer object, or null if no id/attributeName pair is found.
+ * @throws ClassCastException Indicates that the specified attribute
+ * is not of type: TYPE_INTEGER.
+ */
+ public Integer getIntegerAttribute(String id, String attributeName) throws ClassCastException;
+
+ /**
+ * Gets a Double value at the specified id/attributeName.
+ *
+ * @param id unique identifier.
+ * @param attributeName attribute name.
+ * @return Double object, or null if no id/attributeName pair is found..
+ * @throws ClassCastException Indicates that the specified attribute
+ * is not of type: TYPE_FLOATING.
+ */
+ public Double getDoubleAttribute(String id, String attributeName) throws ClassCastException;
+
+ /**
+ * Gets a String value at the specified id/attributeName.
+ *
+ * @param id unique identifier.
+ * @param attributeName attribute name.
+ * @return String object, or null if no id/attributeName pair is found.
+ * @throws ClassCastException Indicates that the specified attribute
+ * is not of type: TYPE_STRING.
+ */
+ public String getStringAttribute(String id, String attributeName) throws ClassCastException;
+
+ /**
+ * Gets an Object value at the specified id/attributeName. This is a convenience
+ * method for those situations when attribute type isn't relevant. You should
+ * NOT use this method and cast the result to the type of attribute. Instead,
+ * just call the appropriate get*Attribute method.
+ *
+ * @param id unique identifier.
+ * @param attributeName attribute name.
+ * @return Object, or null if no id/attributeName pair is found.
+ */
+ public Object getAttribute(String id, String attributeName);
+
+ /**
+ * Gets the data type of the specified attribute.
+ *
+ * @param attributeName Attribute Name.
+ * @return one of: TYPE_BOOLEAN, TYPE_INTEGER, TYPE_FLOATING,
+ * TYPE_STRING, TYPE_SIMPLE_LIST, TYPE_SIMPLE_MAP, TYPE_COMPLEX,
+ * TYPE_UNDEFINED.
+ */
+ public byte getType(String attributeName);
+
+ /**
+ * Gets the member data type of the specified simple list attribute.
+ *
+ * @param attributeName the name of a simple list attribute
+ * @return one of: TYPE_BOOLEAN, TYPE_INTEGER, TYPE_FLOATING, TYPE_STRING
+ */
+ public byte getListElementType(final String attributeName);
+
+ /**
+ * Deletes the id/attributeName pair.
+ *
+ * @param id unique identifier.
+ * @param attributeName attribute name.
+ * @return true indicates attribute was
+ * successfully removed.
+ */
+ public boolean deleteAttribute(String id, String attributeName);
+
+ /**
+ * Deletes the specified attribute.
+ * <P>
+ * Calling this method deletes all id/attributeName pairs with this
+ * attributeName, and resets the specified attribute data type to:
+ * TYPE_UNDEFINED. Please use with caution!
+ *
+ * @param attributeName attribute name.
+ * @return true indicates attribute was successfully reset.
+ */
+ public boolean deleteAttribute(String attributeName);
+
+ /**
+ * Sets a simple list of attributes.
+ * <p/>
+ * <P>A simple list is defined as follows:
+ * <UL>
+ * <LI>All items within the list are of the same type, and are chosen
+ * from one of the following: <CODE>Boolean</CODE>, <CODE>Integer</CODE>,
+ * <CODE>Double</CODE> or <CODE>String</CODE>.
+ * </UL>
+ * <P>
+ * If the above requirements are not met, an IllegalArgumentException
+ * will be thrown.
+ * <P>
+ * Implementation note: calling this method results in many calls to the
+ * MultiHashMap back-end data store. For example, if you have
+ * five elements in a List, the implementation code makes five calls to
+ * the MultiHashMap. Therefore, if you are listening to MultiHashMap
+ * events, you will be notified of five separate events, rather than one
+ * global list event.
+ *
+ * @param id unique identifier.
+ * @param list attribute name.
+ * @param list List Object.
+ * @throws IllegalArgumentException Simple List requirements have not
+ * been met, or this attribute has already
+ * been defined with a data type, and this
+ * data type is not of type:
+ * TYPE_SIMPLE_LIST.
+ */
+ public void setListAttribute(String id, String attributeName, List list)
+ throws IllegalArgumentException;
+
+ /**
+ * Sets a simple list of attributes.
+ * <p/>
+ * <P>A simple list is defined as follows:
+ * <UL>
+ * <LI>All items within the list are of the same type, and are chosen
+ * from one of the following: <CODE>Boolean</CODE>, <CODE>Integer</CODE>,
+ * <CODE>Double</CODE> or <CODE>String</CODE>.
+ * </UL>
+ * <P>
+ * If the above requirements are not met, an IllegalArgumentException
+ * will be thrown.
+ * <P>
+ * Implementation note: calling this method results in many calls to the
+ * MultiHashMap back-end data store. For example, if you have
+ * five elements in a List, the implementation code makes five calls to
+ * the MultiHashMap. Therefore, if you are listening to MultiHashMap
+ * events, you will be notified of five separate events, rather than one
+ * global list event.
+ *
+ * @param id unique identifier.
+ * @param list attribute name.
+ * @param list List Object.
+ * @param equation an attribute equation
+ * @throws IllegalArgumentException Simple List requirements have not
+ * been met, or this attribute has already
+ * been defined with a data type, and this
+ * data type is not of type:
+ * TYPE_SIMPLE_LIST.
+ */
+ public void setListAttribute(final String id, final String attributeName, final Equation equation)
+ throws IllegalArgumentException;
+
+ /**
+ * @deprecated Use {@link CyAttributes#getListAttribute getListAttribute()} instead. Will be removed 11/2007.
+ */
+ public List getAttributeList(String id, String attributeName) throws ClassCastException;
+
+ /**
+ * Gets a 'simple' list of attributes for the id/attributeName pair.
+ * <p/>
+ * <P>A 'simple' list is defined as follows:
+ * <UL>
+ * <LI>All items within the list are of the same type, and are chosen
+ * from one of the following: <CODE>Boolean</CODE>, <CODE>Integer</CODE>,
+ * <CODE>Double</CODE> or <CODE>String</CODE>.
+ * </UL>
+ * <P>
+ * <B>Note:</B> The returned List is useful for read operations only.
+ * If you add, edit, or delete elements within this list, these changes
+ * will not be stored, unless you explicitly call setListAttribute() again.
+ * For example:
+ *
+ * <PRE>
+ * List list = nodeAttributes.getListAttribute(id, attributeName);
+ *
+ * // Add new item
+ * list.add(new String("Hello, World");
+ *
+ * // Save modified list back
+ * nodeAttributes.setListAttribute(id, attributeName, list);
+ * </PRE>
+ *
+ * @param id unique identifier.
+ * @param attributeName attribute name.
+ * @return List object.
+ * @throws ClassCastException Indicates that the specified attribute
+ * is not of type: TYPE_SIMPLE_LIST.
+ */
+ public List getListAttribute(String id, String attributeName) throws ClassCastException;
+
+ /**
+ * Sets a 'simple' map of attribute values.
+ * <P>
+ * A 'simple' map is defined as follows:
+ * <UL>
+ * <LI>All keys within the map are of type: String.
+ * <LI>All values within the map are of the same type, and are chosen
+ * from one of the following: <CODE>Boolean</CODE>, <CODE>Integer</CODE>,
+ * <CODE>Double</CODE> or <CODE>String</CODE>.
+ * </UL>
+ * <P>
+ * If the above requirements are not met, an
+ * <CODE>IllegalArgumentException</CODE> will be thrown.
+ *
+ * <P>
+ * Implementation note: calling this method results in
+ * many calls to the MultiHashMap back-end data store. For example, if
+ * you have five elements in a Map, the implementation code makes five
+ * calls to the MultiHashMap. Therefore, if you are listening to
+ * MultiHashMap events, you will be notified of five separate events,
+ * rather than one global map event.
+ *
+ * @param id unique identifier.
+ * @param attributeName attribute name.
+ * @param map Map Object.
+ * @throws IllegalArgumentException Simple Map requirements have not
+ * been met or this attribute has already
+ * been defined with a data type, and this
+ * data type is not of type:
+ * TYPE_SIMPLE_MAP.
+ *
+ */
+ public void setMapAttribute(String id, String attributeName, Map map)
+ throws IllegalArgumentException;
+
+ /**
+ * @deprecated Use {@link CyAttributes#getMapAttribute getMapAttribute()} instead. Will be removed 11/2007.
+ */
+ public Map getAttributeMap(String id, String attributeName);
+
+ /**
+ * Gets a 'simple' map of attribute values.
+ * <p/>
+ * <P>A 'simple' map is defined as follows:
+ * <UL>
+ * <LI>All keys within the map are of type: String.
+ * <LI>All values within the map are of the same type, and are chosen
+ * from one of the following: <CODE>Boolean</CODE>, <CODE>Integer</CODE>,
+ * <CODE>Double</CODE> or <CODE>String</CODE>.
+ * </UL>
+ * <P>
+ * <B>Note:</B> The returned Map is useful for read operations only.
+ * If you add, edit, or delete elements within this Map, these changes
+ * will not be stored, unless you explicitly call setMapAttribute()
+ * again. For example:
+ *
+ * <PRE>
+ * Map map = nodeAttributes.getMapAttribute(id, attributeName);
+ *
+ * // Add new item
+ * map.put(new String("Message"), new String("Hello, World"));
+ *
+ * // Save modified map back
+ * nodeAttributes.setMapAttribute(id, attributeName, map);
+ * </PRE>
+ *
+ * @param id unique identifier.
+ * @param attributeName attribute name.
+ * @return Map Object.
+ * @throws ClassCastException Indicates that the specified attribute
+ * is not of type: TYPE_HASH_MAP.
+ */
+ public Map getMapAttribute(String id, String attributeName);
+
+ /**
+ * Gets the MultiHashMap Object, where we store attribute values.
+ * <p/>
+ * <P>By using MultiHashMap and MultiHashMapDefinition directly,
+ * you can store arbitrarily complex data structures.
+ * Recommended for advanced coders only.
+ * <p/>
+ *
+ * @return MultiHashMap Object.
+ */
+ public MultiHashMap getMultiHashMap();
+
+ /**
+ * Gets the MultiHashMapDefinition Object, where we store attribute
+ * definitions.
+ * <P>
+ * <P>By using MultiHashMap and MultiHashMapDefinition directly, you can
+ * store arbitrarily complex data structures (e.g. anything more
+ * complicated that 'simple' lists and 'simple' maps). Recommended for
+ * advanced coders only.
+ * <p/>
+ *
+ * @return MultiHashMapDefinition Object.
+ */
+ public MultiHashMapDefinition getMultiHashMapDefinition();
+
+ /**
+ * @return the equation associated with an attribute or null if there is no equation associated with it
+ */
+ public Equation getEquation(final String id, final String attributeName);
+
+ /**
+ * Returns any attribute-equation related error message after a call to getAttribute() or
+ * getXXXAttribute(). N.B., the last error message will be cached!
+ *
+ * @return an error message or null if the last call to getAttribute() did not result in an
+ * equation related error
+ */
+ public String getLastEquationError();
+}
diff --git a/application/src/main/java/cytoscape/data/CyAttributesImpl.java b/application/src/main/java/cytoscape/data/CyAttributesImpl.java
new file mode 100644
index 0000000..0226717
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/CyAttributesImpl.java
@@ -0,0 +1,1362 @@
+/*
+ File: CyAttributesImpl.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data;
+
+
+import cytoscape.Cytoscape;
+import cytoscape.data.attr.CountedIterator;
+import cytoscape.data.attr.MultiHashMap;
+import cytoscape.data.attr.MultiHashMapDefinition;
+import cytoscape.data.attr.util.MultiHashMapFactory;
+import cytoscape.logger.CyLogger;
+import cytoscape.util.TopoGraphNode;
+import cytoscape.util.TopologicalSort;
+
+import org.cytoscape.equations.Equation;
+import org.cytoscape.equations.DoubleList;
+import org.cytoscape.equations.LongList;
+import org.cytoscape.equations.StringList;
+import org.cytoscape.equations.BooleanList;
+import org.cytoscape.equations.interpreter.IdentDescriptor;
+import org.cytoscape.equations.interpreter.Interpreter;
+
+import java.util.*;
+
+
+public class CyAttributesImpl implements CyAttributes {
+ private final MultiHashMap mmap;
+ private final MultiHashMapDefinition mmapDef;
+
+ // used to store human readable descriptions of attributes.
+ private Map descriptionMap;
+
+ // used to store only those attributes, which should be hidden from
+ // the end user.
+ private Set userInvisibleSet;
+
+ // used to store only those attributes, which should not be editable
+ // by the end user.
+ private Set userNonEditableSet;
+
+ private String lastEquationError = null;
+ private Set<String> currentlyActiveAttributes = new TreeSet<String>();
+
+ protected static final CyLogger logger = CyLogger.getLogger(Cytoscape.class);
+
+ /**
+ * Creates a new CyAttributesImpl object.
+ */
+ public CyAttributesImpl() {
+ Object model = MultiHashMapFactory.instantiateDataModel();
+ mmap = (MultiHashMap) model;
+ mmapDef = (MultiHashMapDefinition) model;
+ descriptionMap = new HashMap();
+ userInvisibleSet = new HashSet();
+ userNonEditableSet = new HashSet();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param attributeName DOCUMENT ME!
+ * @param description DOCUMENT ME!
+ */
+ public void setAttributeDescription(String attributeName, String description) {
+ descriptionMap.put(attributeName, description);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param attributeName DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getAttributeDescription(String attributeName) {
+ return (String) descriptionMap.get(attributeName);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param attributeName DOCUMENT ME!
+ * @param value DOCUMENT ME!
+ */
+ public void setUserVisible(String attributeName, boolean value) {
+ if (value) {
+ if (userInvisibleSet.contains(attributeName)) {
+ userInvisibleSet.remove(attributeName);
+ }
+ } else {
+ if (!userInvisibleSet.contains(attributeName)) {
+ userInvisibleSet.add(attributeName);
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param attributeName DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean getUserVisible(String attributeName) {
+ // by default, all attributes are visible, return value = true
+ if (userInvisibleSet.contains(attributeName)) {
+ return false;
+ } else {
+ return true;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param attributeName DOCUMENT ME!
+ * @param value DOCUMENT ME!
+ */
+ public void setUserEditable(String attributeName, boolean value) {
+ if (value) {
+ if (userNonEditableSet.contains(attributeName)) {
+ userNonEditableSet.remove(attributeName);
+ }
+ } else {
+ if (!userNonEditableSet.contains(attributeName)) {
+ userNonEditableSet.add(attributeName);
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param attributeName DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean getUserEditable(String attributeName) {
+ // by default, all attributes are editable, return value = true
+ if (userNonEditableSet.contains(attributeName)) {
+ return false;
+ } else {
+ return true;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String[] getAttributeNames() {
+ final CountedIterator citer = mmapDef.getDefinedAttributes();
+ final String[] names = new String[citer.numRemaining()];
+ int inx = 0;
+
+ while (citer.hasNext()) {
+ names[inx++] = (String) citer.next();
+ }
+
+ return names;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param id DOCUMENT ME!
+ * @param attributeName DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean hasAttribute(String id, String attributeName) {
+ final byte valType = mmapDef.getAttributeValueType(attributeName);
+
+ if (valType < 0)
+ return false;
+
+ final byte[] dimTypes = mmapDef.getAttributeKeyspaceDimensionTypes(attributeName);
+
+ if (dimTypes.length == 0) {
+ return mmap.getAttributeValue(id, attributeName, null) != null;
+ } else {
+ return mmap.getAttributeKeyspan(id, attributeName, null).numRemaining() > 0;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param id DOCUMENT ME!
+ * @param attributeName DOCUMENT ME!
+ * @param value DOCUMENT ME!
+ */
+ public void setAttribute(final String id, final String attributeName, final Boolean value) {
+ if (id == null)
+ throw new IllegalArgumentException("id is null");
+
+ if (attributeName == null)
+ throw new IllegalArgumentException("attributeName is null");
+
+ final byte type = mmapDef.getAttributeValueType(attributeName);
+
+ if (type < 0) {
+ mmapDef.defineAttribute(attributeName, MultiHashMapDefinition.TYPE_BOOLEAN, null);
+ } else {
+ if (type != MultiHashMapDefinition.TYPE_BOOLEAN) {
+ throw new IllegalArgumentException("definition for attributeName '" + attributeName
+ + "' already exists and it is not of TYPE_BOOLEAN");
+ }
+
+ final byte[] dimTypes = mmapDef.getAttributeKeyspaceDimensionTypes(attributeName);
+
+ if (dimTypes.length != 0) {
+ throw new IllegalArgumentException("definition for attributeName '" + attributeName
+ + "' already exists and it is not of TYPE_BOOLEAN");
+ }
+ }
+
+ mmap.setAttributeValue(id, attributeName, value, null);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param id DOCUMENT ME!
+ * @param attributeName DOCUMENT ME!
+ * @param value DOCUMENT ME!
+ */
+ public void setAttribute(String id, String attributeName, Integer value) {
+ if (id == null)
+ throw new IllegalArgumentException("id is null");
+
+ if (attributeName == null)
+ throw new IllegalArgumentException("attributeName is null");
+
+ final byte type = mmapDef.getAttributeValueType(attributeName);
+
+ if (type < 0) {
+ mmapDef.defineAttribute(attributeName, MultiHashMapDefinition.TYPE_INTEGER, null);
+ } else {
+ if (type != MultiHashMapDefinition.TYPE_INTEGER) {
+ throw new IllegalArgumentException("definition for attributeName '" + attributeName
+ + "' already exists and it is not of TYPE_INTEGER");
+ }
+
+ final byte[] dimTypes = mmapDef.getAttributeKeyspaceDimensionTypes(attributeName);
+
+ if (dimTypes.length != 0) {
+ throw new IllegalArgumentException("definition for attributeName '" + attributeName
+ + "' already exists and it is not of TYPE_INTEGER");
+ }
+ }
+
+ mmap.setAttributeValue(id, attributeName, value, null);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param id DOCUMENT ME!
+ * @param attributeName DOCUMENT ME!
+ * @param value DOCUMENT ME!
+ */
+ public void setAttribute(String id, String attributeName, Double value) {
+ if (id == null)
+ throw new IllegalArgumentException("id is null");
+
+ if (attributeName == null)
+ throw new IllegalArgumentException("attributeName is null");
+
+ final byte type = mmapDef.getAttributeValueType(attributeName);
+
+ if (type < 0) {
+ mmapDef.defineAttribute(attributeName, MultiHashMapDefinition.TYPE_FLOATING_POINT, null);
+ } else {
+ if (type != MultiHashMapDefinition.TYPE_FLOATING_POINT) {
+ throw new IllegalArgumentException("definition for attributeName '" + attributeName
+ + "' already exists and it is not of TYPE_FLOATING");
+ }
+
+ final byte[] dimTypes = mmapDef.getAttributeKeyspaceDimensionTypes(attributeName);
+
+ if (dimTypes.length != 0) {
+ throw new IllegalArgumentException("definition for attributeName '" + attributeName
+ + "' already exists and it is not of TYPE_FLOATING");
+ }
+ }
+
+ mmap.setAttributeValue(id, attributeName, value, null);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param id DOCUMENT ME!
+ * @param attributeName DOCUMENT ME!
+ * @param value DOCUMENT ME!
+ */
+ public void setAttribute(String id, String attributeName, String value) {
+ if (id == null)
+ throw new IllegalArgumentException("id is null");
+
+ if (attributeName == null)
+ throw new IllegalArgumentException("attributeName is null");
+
+ final byte type = mmapDef.getAttributeValueType(attributeName);
+
+ if (type < 0) {
+ mmapDef.defineAttribute(attributeName, MultiHashMapDefinition.TYPE_STRING, null);
+ } else {
+ if (type != MultiHashMapDefinition.TYPE_STRING) {
+ throw new IllegalArgumentException("definition for attributeName '" + attributeName
+ + "' already exists and it is not of TYPE_STRING");
+ }
+
+ final byte[] dimTypes = mmapDef.getAttributeKeyspaceDimensionTypes(attributeName);
+
+ if (dimTypes.length != 0) {
+ throw new IllegalArgumentException("definition for attributeName '" + attributeName
+ + "' already exists and it is not of TYPE_STRING");
+ }
+ }
+
+ mmap.setAttributeValue(id, attributeName, value, null);
+ }
+
+ /**
+ * @param id unique identifier.
+ * @param attributeName attribute name.
+ * @param equation an attribute equation
+ */
+ public void setAttribute(final String id, final String attributeName, final Equation equation) {
+ if (id == null)
+ throw new IllegalArgumentException("id is null");
+
+ if (attributeName == null)
+ throw new IllegalArgumentException("attributeName is null");
+
+ final byte type = mmapDef.getAttributeValueType(attributeName);
+ final Class returnType = equation.getType();
+ if (type < 0) { // Attribute does not yet exist!
+ final byte mappedType;
+ if (returnType == Double.class)
+ mappedType = MultiHashMapDefinition.TYPE_FLOATING_POINT;
+ else if (returnType == String.class)
+ mappedType = MultiHashMapDefinition.TYPE_STRING;
+ else if (returnType == Boolean.class)
+ mappedType = MultiHashMapDefinition.TYPE_BOOLEAN;
+ else
+ throw new IllegalStateException("unknown equation return type: " + returnType + "!");
+ mmapDef.defineAttribute(attributeName, mappedType, null);
+ } else {
+ final byte[] dimTypes = mmapDef.getAttributeKeyspaceDimensionTypes(attributeName);
+ if (dimTypes.length != 0)
+ throw new IllegalArgumentException("definition for \"" + attributeName
+ + "\" already exists and it is not of a scalar type!");
+
+ if (type == MultiHashMapDefinition.TYPE_STRING)
+ /* Everything is compatible w/ this! */;
+ else if (type == MultiHashMapDefinition.TYPE_INTEGER) {
+ if (returnType != Long.class && returnType != Double.class && returnType != Boolean.class && returnType != Object.class)
+ throw new IllegalArgumentException("an equation of type " + returnType
+ + " is not compatible with TYPE_INTEGER for attribute \""
+ + attributeName + "\"!");
+ }
+ else if (type == MultiHashMapDefinition.TYPE_FLOATING_POINT) {
+ if (returnType != Double.class && returnType != Long.class && returnType != Boolean.class && returnType != Object.class)
+ throw new IllegalArgumentException("an equation of type " + returnType
+ + " is not compatible with TYPE_FLOATING_POINT for attribute \""
+ + attributeName + "\"!");
+ }
+ else if (type == MultiHashMapDefinition.TYPE_BOOLEAN) {
+ if (returnType != Boolean.class && returnType != Long.class && returnType != Double.class && returnType != Object.class)
+ throw new IllegalArgumentException("an equation of type " + returnType
+ + " is not compatible with TYPE_BOOLEAN for attribute \""
+ + attributeName + "\"!");
+ }
+ else
+ throw new IllegalArgumentException("an equation of type " + returnType
+ + " is not compatible with attribute \""
+ + attributeName + "\"!");
+ }
+
+ mmap.setAttributeValue(id, attributeName, equation, null);
+ }
+
+ /**
+ * @param id unique identifier.
+ * @param attributeName attribute name.
+ * @param equation an attribute equation
+ * @param dataType must be one of MultiHashMapDefinition.TYPE_{BOOLEAN,STRING,INTEGER, or FLOATING_POINT}
+ */
+ public void setAttribute(final String id, final String attributeName, final Equation equation,
+ final byte dataType)
+ {
+ if (id == null)
+ throw new IllegalArgumentException("id is null");
+
+ if (attributeName == null)
+ throw new IllegalArgumentException("attributeName is null");
+
+ final byte type = mmapDef.getAttributeValueType(attributeName);
+ final Class returnType = equation.getType();
+ if (type < 0) { // Attribute does not yet exist.
+ if (dataType == MultiHashMapDefinition.TYPE_STRING)
+ /* Everything is compatible w/ this! */;
+ else if (type == MultiHashMapDefinition.TYPE_INTEGER) {
+ if (returnType != Double.class && returnType != Boolean.class)
+ throw new IllegalArgumentException("an equation of type " + returnType
+ + " is not compatible with TYPE_INTEGER for attribute \""
+ + attributeName + "\"!");
+ }
+ else if (dataType == MultiHashMapDefinition.TYPE_FLOATING_POINT) {
+ if (returnType != Double.class && returnType != Boolean.class)
+ throw new IllegalArgumentException("an equation of type " + returnType
+ + " is not compatible with TYPE_FLOATING_POINT for attribute \""
+ + attributeName + "\"!");
+ }
+ mmapDef.defineAttribute(attributeName, dataType, null);
+ } else {
+ final byte[] dimTypes = mmapDef.getAttributeKeyspaceDimensionTypes(attributeName);
+ if (dimTypes.length != 0)
+ throw new IllegalArgumentException("definition for \"" + attributeName
+ + "\" already exists and it is not of a scalar type!");
+ if (type != dataType)
+ throw new IllegalArgumentException("incompatible data type!");
+
+ if (type == MultiHashMapDefinition.TYPE_STRING)
+ /* Everything is compatible w/ this! */;
+ else if (type == MultiHashMapDefinition.TYPE_INTEGER) {
+ if (returnType != Double.class && returnType != Boolean.class && returnType != Long.class)
+ throw new IllegalArgumentException("an equation of type " + returnType
+ + " is not compatible with TYPE_INTEGER for attribute \""
+ + attributeName + "\"!");
+ }
+ else if (type == MultiHashMapDefinition.TYPE_FLOATING_POINT) {
+ if (returnType != Double.class && returnType != Boolean.class)
+ throw new IllegalArgumentException("an equation of type " + returnType
+ + " is not compatible with TYPE_FLOATING_POINT for attribute \""
+ + attributeName + "\"!");
+ }
+ }
+
+ mmap.setAttributeValue(id, attributeName, equation, null);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param id DOCUMENT ME!
+ * @param attributeName DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Boolean getBooleanAttribute(final String id, final String attributeName) {
+ lastEquationError = null;
+
+ final byte type = mmapDef.getAttributeValueType(attributeName);
+ if (type < 0)
+ return null;
+
+ if (type != MultiHashMapDefinition.TYPE_BOOLEAN)
+ throw new ClassCastException("definition for attributeName '" + attributeName
+ + "' is not of TYPE_BOOLEAN");
+
+ final Object attribValue = mmap.getAttributeValue(id, attributeName, null);
+ if (attribValue == null)
+ return null;
+ if (attribValue instanceof Boolean)
+ return (Boolean)attribValue;
+
+ // Now we assume that we are dealing with an equation:
+ final StringBuilder errorMessage = new StringBuilder();
+ final Object equationValue = evalEquation(id, attributeName, (Equation)attribValue,
+ errorMessage);
+ if (equationValue == null) {
+ lastEquationError = errorMessage.toString();
+ return null;
+ }
+ return convertEqnRetValToBoolean(id, attributeName, equationValue);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param id DOCUMENT ME!
+ * @param attributeName DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Integer getIntegerAttribute(final String id, final String attributeName) {
+ lastEquationError = null;
+
+ final byte type = mmapDef.getAttributeValueType(attributeName);
+ if (type < 0)
+ return null;
+
+ if (type != MultiHashMapDefinition.TYPE_INTEGER)
+ throw new ClassCastException("definition for attributeName '" + attributeName
+ + "' is not of TYPE_INTEGER");
+
+ final Object attribValue = mmap.getAttributeValue(id, attributeName, null);
+ if (attribValue == null)
+ return null;
+ if (attribValue instanceof Integer)
+ return (Integer)attribValue;
+
+ // Now we assume that we are dealing with an equation:
+ final StringBuilder errorMessage = new StringBuilder();
+ final Object equationValue = evalEquation(id, attributeName, (Equation)attribValue,
+ errorMessage);
+ if (equationValue == null) {
+ lastEquationError = errorMessage.toString();
+ return null;
+ }
+ if (equationValue.getClass() == Long.class) {
+ final long valueAsLong = (Long)equationValue;
+ return (int)valueAsLong;
+ }
+ if (equationValue.getClass() == Boolean.class) {
+ final Boolean valueAsBoolean = (Boolean)equationValue;
+ return valueAsBoolean ? 1 : 0;
+ }
+ if (equationValue.getClass() == String.class) {
+ final String valueAsString = (String)equationValue;
+ try {
+ final double valueAsDouble = Double.parseDouble(valueAsString);
+ return (int)excelTrunc(valueAsDouble);
+ } catch (final NumberFormatException e) {
+ throw new IllegalStateException("\"" + valueAsString
+ + "\" cannot be interpreted as an integer value!");
+ }
+ }
+ if (equationValue.getClass() == Double.class) {
+ final double valueAsDouble = (Double)equationValue;
+ return (int)excelTrunc(valueAsDouble);
+ }
+
+ throw new IllegalStateException("an equation returned an unknown class type: "
+ + equationValue.getClass() + "!");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param id DOCUMENT ME!
+ * @param attributeName DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Double getDoubleAttribute(String id, String attributeName) {
+ lastEquationError = null;
+
+ final byte type = mmapDef.getAttributeValueType(attributeName);
+ if (type < 0)
+ return null;
+
+ if (type != MultiHashMapDefinition.TYPE_FLOATING_POINT)
+ throw new ClassCastException("definition for attributeName '" + attributeName
+ + "' is not of TYPE_FLOATING");
+
+ final Object attribValue = mmap.getAttributeValue(id, attributeName, null);
+ if (attribValue == null)
+ return null;
+ if (attribValue instanceof Double)
+ return (Double)attribValue;
+
+ // Now we assume that we are dealing with an equation:
+ final StringBuilder errorMessage = new StringBuilder();
+ final Object equationValue = evalEquation(id, attributeName, (Equation)attribValue,
+ errorMessage);
+ if (equationValue == null) {
+ lastEquationError = errorMessage.toString();
+ return null;
+ }
+ return convertEqnRetValToDouble(id, attributeName, equationValue);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param id DOCUMENT ME!
+ * @param attributeName DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getStringAttribute(final String id, final String attributeName) {
+ lastEquationError = null;
+
+ final byte type = mmapDef.getAttributeValueType(attributeName);
+ if (type < 0)
+ return null;
+
+ if (type != MultiHashMapDefinition.TYPE_STRING)
+ throw new ClassCastException("definition for attributeName '" + attributeName
+ + "' is not of TYPE_STRING");
+
+ final Object attribValue = mmap.getAttributeValue(id, attributeName, null);
+ if (attribValue == null)
+ return null;
+ if (attribValue instanceof String)
+ return (String)attribValue;
+
+ // Now we assume that we are dealing with an equation:
+ final StringBuilder errorMessage = new StringBuilder();
+ final Object equationValue = evalEquation(id, attributeName, (Equation)attribValue,
+ errorMessage);
+ if (equationValue == null) {
+ lastEquationError = errorMessage.toString();
+ return null;
+ }
+ return equationValue.toString();
+ }
+
+ /**
+ * Gets an Object value at the specified id/attributeName. This is a convenience
+ * method for those situations when attribute type isn't relevant. You should
+ * NOT use this method and cast the result to the type of attribute. Instead,
+ * just call the appropriate get*Attribute method.
+ *
+ * @param id unique identifier.
+ * @param attributeName attribute name.
+ * @return Object, or null if no id/attributeName pair is found.
+ */
+ public Object getAttribute(final String id, final String attributeName) {
+ lastEquationError = null;
+
+ final byte type = getType(attributeName);
+
+ if ( type == TYPE_SIMPLE_LIST )
+ return getListAttribute(id, attributeName);
+ else if ( type == TYPE_SIMPLE_MAP )
+ return getMapAttribute(id, attributeName);
+ else if ( type == TYPE_UNDEFINED || type == TYPE_COMPLEX )
+ return null;
+
+ final Object attribValue = mmap.getAttributeValue(id, attributeName, null);
+ if (attribValue == null)
+ return null;
+
+ if (attribValue instanceof Equation) {
+ final StringBuilder errorMessage = new StringBuilder();
+ final Object equationValue = evalEquation(id, attributeName, (Equation)attribValue,
+ errorMessage);
+ if (equationValue == null) {
+ lastEquationError = errorMessage.toString();
+ return null;
+ }
+
+ if (type == MultiHashMapDefinition.TYPE_INTEGER)
+ return convertEqnRetValToInteger(id, attributeName, equationValue);
+ if (type == MultiHashMapDefinition.TYPE_FLOATING_POINT)
+ return convertEqnRetValToDouble(id, attributeName, equationValue);
+ if (type == MultiHashMapDefinition.TYPE_BOOLEAN)
+ return convertEqnRetValToBoolean(id, attributeName, equationValue);
+ if (type == MultiHashMapDefinition.TYPE_STRING)
+ return equationValue.toString();
+ return equationValue;
+ }
+
+ return attribValue;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param attributeName DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public byte getType(final String attributeName) {
+ final byte valType = mmapDef.getAttributeValueType(attributeName);
+
+ if (valType < 0)
+ return TYPE_UNDEFINED;
+
+ final byte[] dimTypes = mmapDef.getAttributeKeyspaceDimensionTypes(attributeName);
+
+ if (dimTypes.length == 0) {
+ return valType;
+ }
+
+ if (dimTypes.length > 1) {
+ return TYPE_COMPLEX;
+ }
+
+ if (dimTypes[0] == MultiHashMapDefinition.TYPE_INTEGER) {
+ return TYPE_SIMPLE_LIST;
+ }
+
+ if (dimTypes[0] == MultiHashMapDefinition.TYPE_STRING) {
+ return TYPE_SIMPLE_MAP;
+ }
+
+ return TYPE_COMPLEX;
+ }
+
+ /**
+ * Gets the member data type of the specified simple list attribute.
+ *
+ * @param attributeName the name of a simple list attribute
+ * @return one of: TYPE_BOOLEAN, TYPE_INTEGER, TYPE_FLOATING, TYPE_STRING
+ */
+ public byte getListElementType(final String attributeName) {
+ final byte valType = mmapDef.getAttributeValueType(attributeName);
+ if (valType < 0)
+ throw new IllegalArgumentException("'" + attributeName + "' is not a simple list attribute!");
+
+ final byte[] dimTypes = mmapDef.getAttributeKeyspaceDimensionTypes(attributeName);
+ if (dimTypes.length != 1 || dimTypes[0] != MultiHashMapDefinition.TYPE_INTEGER)
+ throw new IllegalArgumentException("'" + attributeName + "' is not a simple list attribute!");
+
+ return valType;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param id DOCUMENT ME!
+ * @param attributeName DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean deleteAttribute(String id, String attributeName) {
+ boolean b = mmap.removeAllAttributeValues(id, attributeName);
+
+ return b;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param attributeName DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean deleteAttribute(String attributeName) {
+ boolean b = mmapDef.undefineAttribute(attributeName);
+
+ return b;
+ }
+
+ public void setListAttribute(String id, String attributeName, List list) {
+ if (id == null)
+ throw new IllegalArgumentException("id is null");
+
+ if (attributeName == null)
+ throw new IllegalArgumentException("attributeName is null");
+
+ if (list == null)
+ throw new IllegalArgumentException("list is null");
+
+ Iterator itor = list.iterator();
+
+ if (!itor.hasNext()) {
+ return;
+ }
+
+ final byte type;
+ Object obj = itor.next();
+
+ if (obj instanceof Double) {
+ type = TYPE_FLOATING;
+ } else if (obj instanceof Integer) {
+ type = TYPE_INTEGER;
+ } else if (obj instanceof Boolean) {
+ type = TYPE_BOOLEAN;
+ } else if (obj instanceof String) {
+ type = TYPE_STRING;
+ } else
+ throw new IllegalArgumentException("objects in list are of unrecognized type");
+
+ while (itor.hasNext()) {
+ obj = itor.next();
+
+ if (((type == TYPE_FLOATING) && (!(obj instanceof Double)))
+ || ((type == TYPE_INTEGER) && (!(obj instanceof Integer)))
+ || ((type == TYPE_BOOLEAN) && (!(obj instanceof Boolean)))
+ || ((type == TYPE_STRING) && (!(obj instanceof String))))
+ throw new IllegalArgumentException("items in list are not all of the same type");
+ }
+
+ final byte valType = mmapDef.getAttributeValueType(attributeName);
+
+ if (valType < 0) {
+ mmapDef.defineAttribute(attributeName, type,
+ new byte[] { MultiHashMapDefinition.TYPE_INTEGER });
+ } else {
+ if (valType != type) {
+ throw new IllegalArgumentException("existing definition for attributeName '"
+ + attributeName
+ + "' is a TYPE_SIMPLE_LIST that stores other value types");
+ }
+
+ final byte[] keyTypes = mmapDef.getAttributeKeyspaceDimensionTypes(attributeName);
+
+ if ((keyTypes.length != 1) || (keyTypes[0] != MultiHashMapDefinition.TYPE_INTEGER)) {
+ throw new IllegalArgumentException("existing definition for attributeName '"
+ + attributeName + "' is not of TYPE_SIMPLE_LIST");
+ }
+ }
+
+ mmap.removeAllAttributeValues(id, attributeName);
+ itor = list.iterator();
+
+ int inx = 0;
+ final Object[] key = new Object[1];
+
+ while (itor.hasNext()) {
+ key[0] = new Integer(inx++);
+ mmap.setAttributeValue(id, attributeName, itor.next(), key);
+ }
+ }
+
+ public void setListAttribute(final String id, final String attributeName, final Equation equation) {
+ if (id == null)
+ throw new IllegalArgumentException("id is null");
+
+ if (attributeName == null)
+ throw new IllegalArgumentException("attributeName is null");
+
+ if (equation == null)
+ throw new IllegalArgumentException("equation is null");
+
+ final byte type;
+ final Class returnType = equation.getType();
+ if (returnType == DoubleList.class)
+ type = TYPE_FLOATING;
+ else if (returnType == LongList.class)
+ type = TYPE_INTEGER;
+ else if (returnType == BooleanList.class)
+ type = TYPE_BOOLEAN;
+ else if (returnType == StringList.class)
+ type = TYPE_STRING;
+ else
+ throw new IllegalArgumentException("objects in list are of unrecognized type");
+
+ final byte valType = mmapDef.getAttributeValueType(attributeName);
+ if (valType < 0) {
+ mmapDef.defineAttribute(attributeName, type,
+ new byte[] { MultiHashMapDefinition.TYPE_INTEGER });
+ } else {
+ if (valType != type) {
+ throw new IllegalArgumentException("existing definition for attributeName '"
+ + attributeName
+ + "' is a TYPE_SIMPLE_LIST that stores other value types");
+ }
+
+ final byte[] keyTypes = mmapDef.getAttributeKeyspaceDimensionTypes(attributeName);
+
+ if ((keyTypes.length != 1) || (keyTypes[0] != MultiHashMapDefinition.TYPE_INTEGER)) {
+ throw new IllegalArgumentException("existing definition for attributeName '"
+ + attributeName + "' is not of TYPE_SIMPLE_LIST");
+ }
+ }
+
+ mmap.removeAllAttributeValues(id, attributeName);
+ final Object[] key = new Object[] { new Integer(-1) };
+ mmap.setAttributeValue(id, attributeName, equation, key);
+ }
+
+ // deprecated
+ public List getAttributeList(String id, String attributeName) {
+ return getListAttribute(id, attributeName);
+ }
+
+ public List getListAttribute(final String id, final String attributeName) {
+ lastEquationError = null;
+
+ if (mmapDef.getAttributeValueType(attributeName) < 0)
+ return null;
+
+ final byte[] keyTypes = mmapDef.getAttributeKeyspaceDimensionTypes(attributeName);
+ if ((keyTypes.length != 1) || (keyTypes[0] != MultiHashMapDefinition.TYPE_INTEGER))
+ throw new ClassCastException("attributeName '" + attributeName
+ + "' is not of TYPE_SIMPLE_LIST");
+
+ final Object equation = mmap.getAttributeValue(id, attributeName, new Object[] { new Integer(-1) });
+ if (equation != null) {
+ final StringBuilder errorMessage = new StringBuilder();
+ final Object equationValue = evalEquation(id, attributeName, (Equation)equation,
+ errorMessage);
+ if (equationValue == null) {
+ lastEquationError = errorMessage.toString();
+ return null;
+ }
+
+ // Map back to Integer from Long, if necessary:
+ if (equationValue instanceof LongList) {
+ final List<Integer> intList = new ArrayList<Integer>();
+ for (final Long l : (LongList)equationValue)
+ intList.add((int)(long)l);
+
+ return intList;
+ }
+
+ return (List)equationValue;
+ }
+
+ final ArrayList returnThis = new ArrayList();
+ final Object[] key = new Object[1];
+
+ for (int i = 0;; i++) {
+ key[0] = new Integer(i);
+
+ final Object val = mmap.getAttributeValue(id, attributeName, key);
+
+ if (val == null)
+ break;
+
+ returnThis.add(i, val);
+ }
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param id DOCUMENT ME!
+ * @param attributeName DOCUMENT ME!
+ * @param map DOCUMENT ME!
+ */
+ public void setMapAttribute(String id, String attributeName, Map map) {
+ if (id == null)
+ throw new IllegalArgumentException("id is null");
+
+ if (attributeName == null)
+ throw new IllegalArgumentException("attributeName is null");
+
+ final Set entrySet = map.entrySet();
+ Iterator itor = entrySet.iterator();
+
+ if (!itor.hasNext()) {
+ return;
+ }
+
+ final byte type;
+ Map.Entry entry = (Map.Entry) itor.next();
+
+ if (!(entry.getKey() instanceof String)) {
+ throw new IllegalArgumentException("keys in map are not all String");
+ }
+
+ Object val = entry.getValue();
+
+ if (val instanceof Double) {
+ type = TYPE_FLOATING;
+ } else if (val instanceof Integer) {
+ type = TYPE_INTEGER;
+ } else if (val instanceof Boolean) {
+ type = TYPE_BOOLEAN;
+ } else if (val instanceof String) {
+ type = TYPE_STRING;
+ } else
+ throw new IllegalArgumentException("values in map are of unrecognized type");
+
+ while (itor.hasNext()) {
+ entry = (Map.Entry) itor.next();
+
+ if (!(entry.getKey() instanceof String)) {
+ throw new IllegalArgumentException("keys in map are not all String");
+ }
+
+ val = entry.getValue();
+
+ if (((type == TYPE_FLOATING) && (!(val instanceof Double)))
+ || ((type == TYPE_INTEGER) && (!(val instanceof Integer)))
+ || ((type == TYPE_BOOLEAN) && (!(val instanceof Boolean)))
+ || ((type == TYPE_STRING) && (!(val instanceof String))))
+ throw new IllegalArgumentException("values in map are not all of the same type");
+ }
+
+ final byte valType = mmapDef.getAttributeValueType(attributeName);
+
+ if (valType < 0) {
+ mmapDef.defineAttribute(attributeName, type,
+ new byte[] { MultiHashMapDefinition.TYPE_STRING });
+ } else {
+ if (valType != type) {
+ throw new IllegalArgumentException("existing definition for attributeName '"
+ + attributeName
+ + "' is a TYPE_SIMPLE_MAP that stores other value types");
+ }
+
+ final byte[] keyTypes = mmapDef.getAttributeKeyspaceDimensionTypes(attributeName);
+
+ if ((keyTypes.length != 1) || (keyTypes[0] != MultiHashMapDefinition.TYPE_STRING)) {
+ throw new IllegalArgumentException("existing definition for attributeName '"
+ + attributeName + "' is not of TYPE_SIMPLE_MAP");
+ }
+ }
+
+ mmap.removeAllAttributeValues(id, attributeName);
+ itor = entrySet.iterator();
+
+ final Object[] key = new Object[1];
+
+ while (itor.hasNext()) {
+ entry = (Map.Entry) itor.next();
+ key[0] = entry.getKey();
+ mmap.setAttributeValue(id, attributeName, entry.getValue(), key);
+ }
+ }
+
+ // deprecated
+ /**
+ * DOCUMENT ME!
+ *
+ * @param id DOCUMENT ME!
+ * @param attributeName DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Map getAttributeMap(String id, String attributeName) {
+ return getMapAttribute(id, attributeName);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param id DOCUMENT ME!
+ * @param attributeName DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Map getMapAttribute(String id, String attributeName) {
+ lastEquationError = null;
+
+ if (mmapDef.getAttributeValueType(attributeName) < 0)
+ return null;
+
+ final byte[] keyTypes = mmapDef.getAttributeKeyspaceDimensionTypes(attributeName);
+ if ((keyTypes.length != 1) || (keyTypes[0] != MultiHashMapDefinition.TYPE_STRING)) {
+ throw new ClassCastException("attributeName '" + attributeName
+ + "' is not of TYPE_SIMPLE_MAP");
+ }
+
+ final Map returnThis = new HashMap();
+ final Iterator keyspan = mmap.getAttributeKeyspan(id, attributeName, null);
+ final Object[] key = new Object[1];
+
+ while (keyspan.hasNext()) {
+ key[0] = keyspan.next();
+ returnThis.put(key[0], mmap.getAttributeValue(id, attributeName, key));
+ }
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public MultiHashMap getMultiHashMap() {
+ return mmap;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public MultiHashMapDefinition getMultiHashMapDefinition() {
+ return mmapDef;
+ }
+
+ /**
+ * @return the equation associated with an attribute or null if there is no equation associated with it
+ */
+ public Equation getEquation(final String id, final String attributeName) {
+ // This check is necessary for when "attributeName" does not actually refer to an attribute!
+ final byte type = getType(attributeName);
+ if (type == TYPE_UNDEFINED)
+ return null;
+
+ if (type == TYPE_SIMPLE_LIST) {
+ final Object equation = mmap.getAttributeValue(id, attributeName, new Object[] { new Integer(-1) });
+ return (equation == null) ? null : (Equation)equation;
+ }
+
+ final byte[] dimTypes = mmapDef.getAttributeKeyspaceDimensionTypes(attributeName);
+ if (dimTypes.length > 0)
+ return null;
+
+ final Object attribValue = mmap.getAttributeValue(id, attributeName, null);
+ if (attribValue == null || !(attribValue instanceof Equation))
+ return null;
+
+ return (Equation)attribValue;
+ }
+
+ /**
+ * Returns any attribute-equation related error message after a call to getAttribute() or
+ * getXXXAttribute(). N.B., the last error message will be cached!
+ *
+ * @return an error message or null if the last call to getAttribute() did not result in an
+ * equation related error
+ */
+ public String getLastEquationError() { return lastEquationError; }
+
+ private Object evalEquation(final String id, final String attribName, final Equation equation,
+ final StringBuilder errorMessage)
+ {
+ if (currentlyActiveAttributes.contains(attribName)) {
+ currentlyActiveAttributes.clear();
+ errorMessage.append("Recursive equation evaluation of \"" + attribName + "\"!");
+ return null;
+ } else
+ currentlyActiveAttributes.add(attribName);
+
+ final Collection<String> attribReferences = equation.getAttribReferences();
+ final Map<String, Object> defaultValues = equation.getDefaultValues();
+
+ final Map<String, IdentDescriptor> nameToDescriptorMap = new TreeMap<String, IdentDescriptor>();
+ for (final String attribRef : attribReferences) {
+ if (attribRef.equals("ID")) {
+ nameToDescriptorMap.put("ID", new IdentDescriptor(id));
+ continue;
+ }
+
+ Object attribValue = getAttribute(id, attribRef);
+ if (attribValue == null) {
+ final Object defaultValue = defaultValues.get(attribRef);
+ if (defaultValue != null)
+ attribValue = defaultValue;
+ else {
+ currentlyActiveAttributes.clear();
+ errorMessage.append("Missing value for referenced attribute \"" + attribRef + "\"!");
+ logger.warn("Missing value for \"" + attribRef
+ + "\" while evaluating an equation (ID:" + id
+ + ", attribute name:" + attribName + ")");
+ return null;
+ }
+ }
+
+ try {
+ nameToDescriptorMap.put(attribRef, new IdentDescriptor(attribValue));
+ } catch (final Exception e) {
+ currentlyActiveAttributes.clear();
+ errorMessage.append("Bad attribute reference to \"" + attribRef + "\"!");
+ logger.warn("Bad attribute reference to \"" + attribRef
+ + "\" while evaluating an equation (ID:" + id
+ + ", attribute name:" + attribName + ")");
+ return null;
+ }
+ }
+
+ final Interpreter interpreter = new Interpreter(equation, nameToDescriptorMap);
+ try {
+ final Object result = interpreter.run();
+ currentlyActiveAttributes.remove(attribName);
+ return result;
+ } catch (final Exception e) {
+ currentlyActiveAttributes.clear();
+ errorMessage.append(e.getMessage());
+ logger.warn("Error while evaluating an equation: " + e.getMessage() + " (ID:"
+ + id + ", attribute name:" + attribName + ")");
+ return null;
+ }
+ }
+
+ /**
+ * @return an in-order list of attribute names that will have to be evaluated before "attribName" can be evaluated
+ */
+ private List<String> topoSortAttribReferences(final String id, final String attribName) {
+ final Object equationCandidate = mmap.getAttributeValue(id, attribName, null);
+ if (!(equationCandidate instanceof Equation))
+ return new ArrayList<String>();
+
+ final Equation equation = (Equation)equationCandidate;
+ final Set<String> attribReferences = equation.getAttribReferences();
+ if (attribReferences.size() == 0)
+ return new ArrayList<String>();
+
+ final Set<String> alreadyProcessed = new TreeSet<String>();
+ alreadyProcessed.add(attribName);
+ final List<TopoGraphNode> dependencies = new ArrayList<TopoGraphNode>();
+ for (final String attribReference : attribReferences)
+ followReferences(id, attribReference, alreadyProcessed, dependencies);
+
+
+ final List<TopoGraphNode> topoOrder = TopologicalSort.sort(dependencies);
+ final List<String> retVal = new ArrayList<String>();
+ for (final TopoGraphNode node : topoOrder) {
+ final AttribTopoGraphNode attribTopoGraphNode = (AttribTopoGraphNode)node;
+ final String nodeName = attribTopoGraphNode.getNodeName();
+ if (nodeName.equals(attribName))
+ return retVal;
+ else
+ retVal.add(nodeName);
+ }
+
+ // We should never get here because "attribName" should have been found in the for-loop above!
+ throw new IllegalStateException("\"" + attribName
+ + "\" was not found in the toplogical order, which should be impossible!");
+ }
+
+ /**
+ * Helper function for topoSortAttribReferences() performing a depth-first search of equation evaluation dependencies.
+ */
+ private void followReferences(final String id, final String attribName, final Collection<String> alreadyProcessed,
+ final Collection<TopoGraphNode> dependencies)
+ {
+ // Already visited this attribute?
+ if (alreadyProcessed.contains(attribName))
+ return;
+
+ alreadyProcessed.add(attribName);
+ final Object equationCandidate = mmap.getAttributeValue(id, attribName, null);
+ if (!(equationCandidate instanceof Equation))
+ return;
+
+ final Equation equation = (Equation)equationCandidate;
+ final Set<String> attribReferences = equation.getAttribReferences();
+ for (final String attribReference : attribReferences)
+ followReferences(id, attribReference, alreadyProcessed, dependencies);
+ }
+
+ /**
+ * @return "x" truncated using Excel's notion of truncation.
+ */
+ private static double excelTrunc(final double x) {
+ final boolean isNegative = x < 0.0;
+ return Math.round(x + (isNegative ? +0.5 : -0.5));
+ }
+
+ /**
+ * @return "d" converted to an Integer using Excel rules, should the number be outside the range of an int, null will be returned
+ */
+ private static Integer doubleToInteger(final double d) {
+ if (d > Integer.MAX_VALUE || d < Integer.MIN_VALUE)
+ return null;
+
+ double x = ((Double)d).intValue();
+ if (x != d && x < 0.0)
+ --x;
+
+ return (Integer)(int)x;
+ }
+
+ /**
+ * @return "l" converted to an Integer using Excel rules, should the number be outside the range of an int, null will be returned
+ */
+ private static Integer longToInteger(final double l) {
+ if (l >= Integer.MIN_VALUE && l <= Integer.MAX_VALUE)
+ return (Integer)(int)l;
+
+ return null;
+ }
+
+ /**
+ * @return "equationValue" interpreted according to Excel rules as an integer or null if that is not possible
+ */
+ private Integer convertEqnRetValToInteger(final String id, final String attribName, final Object equationValue) {
+ if (equationValue.getClass() == Double.class) {
+ final Integer retVal = doubleToInteger((Double)equationValue);
+ if (retVal == null)
+ logger.warn("Cannot convert a floating point value ("
+ + equationValue + ") to an integer! (ID:" + id
+ + ", attribute name:" + attribName + ")");
+ return retVal;
+ }
+ else if (equationValue.getClass() == Long.class) {
+ final Integer retVal = longToInteger((Long)equationValue);
+ if (retVal == null)
+ logger.warn("Cannot convert a large integer (long) value ("
+ + equationValue + ") to an integer! (ID:" + id
+ + ", attribute name:" + attribName + ")");
+ return retVal;
+ }
+ else if (equationValue.getClass() == Boolean.class) {
+ final Boolean boolValue = (Boolean)equationValue;
+ return (Integer)(boolValue ? 1 : 0);
+ }
+ else
+ throw new IllegalStateException("we should never get here!");
+ }
+
+ /**
+ * @return "equationValue" interpreted according to Excel rules as a double or null if that is not possible
+ */
+ private Double convertEqnRetValToDouble(final String id, final String attribName, final Object equationValue) {
+ if (equationValue.getClass() == Double.class)
+ return (Double)equationValue;
+ else if (equationValue.getClass() == Long.class)
+ return (double)(Long)(equationValue);
+ else if (equationValue.getClass() == Boolean.class) {
+ final Boolean boolValue = (Boolean)equationValue;
+ return boolValue ? 1.0 : 0.0;
+ }
+ else if (equationValue.getClass() == String.class) {
+ final String valueAsString = (String)equationValue;
+ try {
+ return Double.parseDouble(valueAsString);
+ } catch (final NumberFormatException e) {
+ logger.warn("Cannot convert a string (\"" + valueAsString
+ + "\") to a floating point value! (ID:" + id
+ + ", attribute name:" + attribName + ")");
+ return null;
+ }
+ }
+ else
+ throw new IllegalStateException("we should never get here!");
+ }
+
+ /**
+ * @return "equationValue" interpreted according to Excel rules as a boolean
+ */
+ private Boolean convertEqnRetValToBoolean(final String id, final String attribName, final Object equationValue) {
+ if (equationValue.getClass() == Double.class)
+ return (Double)equationValue != 0.0;
+ else if (equationValue.getClass() == Long.class)
+ return (Long)(equationValue) != 0L;
+ else if (equationValue.getClass() == Boolean.class) {
+ return (Boolean)equationValue;
+ }
+ else if (equationValue.getClass() == String.class) {
+ final String stringValue = (String)equationValue;
+ if (stringValue.compareToIgnoreCase("true") == 0)
+ return true;
+ else if (stringValue.compareToIgnoreCase("false") == 0)
+ return false;
+ else {
+ logger.warn("Cannot convert a string (\"" + stringValue
+ + "\") to a boolean value! (ID:" + id
+ + ", attribute name:" + attribName + ")");
+ return null;
+ }
+ }
+ else
+ throw new IllegalStateException("we should never get here!");
+ }
+}
diff --git a/application/src/main/java/cytoscape/data/CyAttributesUtils.java b/application/src/main/java/cytoscape/data/CyAttributesUtils.java
new file mode 100644
index 0000000..9b97840
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/CyAttributesUtils.java
@@ -0,0 +1,880 @@
+/*
+ File: CyAttributesUtils.java
+
+ Copyright (c) 2006, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.data.attr.CountedIterator;
+import cytoscape.data.attr.MultiHashMap;
+import cytoscape.data.attr.MultiHashMapDefinition;
+
+import giny.model.Edge;
+import giny.model.Node;
+
+import org.cytoscape.equations.Equation;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+
+
+/**
+ *
+ */
+public class CyAttributesUtils {
+ public static enum AttributeType {
+ NODE,
+ EDGE,
+ NETWORK;
+ }
+
+ /**
+ * An AttributeFilter that produces all attributes--none are filtered out.
+ */
+ public static final AttributeFilter ALL_ATTRIBUTES_FILTER = new AttributeFilter() {
+ public boolean includeAttribute(CyAttributes attr, String objID, String attrName) {
+ return true;
+ }
+ };
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param attributeName DOCUMENT ME!
+ * @param attrs DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static Map getAttribute(String attributeName, CyAttributes attrs) {
+ Map<String, Object> attrMap;
+
+ {
+ final HashMap<String, Object> returnThis = new HashMap<String, Object>();
+ final MultiHashMap mmap = attrs.getMultiHashMap();
+ final MultiHashMapDefinition mmapDef = attrs.getMultiHashMapDefinition();
+
+ if (mmapDef.getAttributeValueType(attributeName) != -1) {
+ final Iterator objs = mmap.getObjectKeys(attributeName);
+
+ while (objs.hasNext()) {
+ final String obj = (String) objs.next();
+ Object val;
+
+ switch (attrs.getType(attributeName)) {
+ case CyAttributes.TYPE_BOOLEAN:
+ val = attrs.getBooleanAttribute(obj, attributeName);
+
+ break;
+
+ case CyAttributes.TYPE_INTEGER:
+ val = attrs.getIntegerAttribute(obj, attributeName);
+
+ break;
+
+ case CyAttributes.TYPE_FLOATING:
+ val = attrs.getDoubleAttribute(obj, attributeName);
+
+ break;
+
+ case CyAttributes.TYPE_STRING:
+ val = attrs.getStringAttribute(obj, attributeName);
+
+ break;
+
+ case CyAttributes.TYPE_SIMPLE_LIST:
+
+ List l = attrs.getListAttribute(obj, attributeName);
+
+ if (l.size() > 0) {
+ // val = l.get(0);
+ val = l;
+ } else {
+ val = null;
+ }
+
+ break;
+
+ case CyAttributes.TYPE_SIMPLE_MAP:
+ val = attrs.getMapAttribute(obj, attributeName);
+
+ break;
+
+ default:
+ val = null;
+ }
+
+ returnThis.put(obj, val);
+ }
+ }
+
+ attrMap = (returnThis.size() == 0) ? null : returnThis;
+ }
+
+ return attrMap;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param canonicalName DOCUMENT ME!
+ * @param attrs DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static Map<String, Object> getAttributes(String canonicalName, CyAttributes attrs) {
+ Map<String, Object> returnThis = new HashMap<String, Object>();
+ final String[] attrNames = attrs.getAttributeNames();
+
+ for (int i = 0; i < attrNames.length; i++) {
+ final byte type = attrs.getType(attrNames[i]);
+
+ if (attrs.hasAttribute(canonicalName, attrNames[i])) {
+ if (type == CyAttributes.TYPE_SIMPLE_LIST) {
+ List l = attrs.getListAttribute(canonicalName, attrNames[i]);
+
+ if ((l != null) && (l.size() > 0)) {
+ // returnThis.put(attrNames[i], l.get(0));
+ returnThis.put(attrNames[i], l);
+ }
+ } else if (type == CyAttributes.TYPE_SIMPLE_MAP) {
+ Map m = attrs.getMapAttribute(canonicalName, attrNames[i]);
+
+ if ((m != null) && (m.size() > 0)) {
+ returnThis.put(attrNames[i], m);
+ }
+ } else if (type == CyAttributes.TYPE_BOOLEAN) {
+ returnThis.put(attrNames[i],
+ attrs.getBooleanAttribute(canonicalName, attrNames[i]));
+ } else if (type == CyAttributes.TYPE_INTEGER) {
+ returnThis.put(attrNames[i],
+ attrs.getIntegerAttribute(canonicalName, attrNames[i]));
+ } else if (type == CyAttributes.TYPE_FLOATING) {
+ returnThis.put(attrNames[i],
+ attrs.getDoubleAttribute(canonicalName, attrNames[i]));
+ } else if (type == CyAttributes.TYPE_STRING) {
+ returnThis.put(attrNames[i],
+ attrs.getStringAttribute(canonicalName, attrNames[i]));
+ }
+ }
+ }
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param attributeName DOCUMENT ME!
+ * @param attrs DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static Class getClass(String attributeName, CyAttributes attrs) {
+ Class cl = null;
+
+ switch (attrs.getType(attributeName)) {
+ case CyAttributes.TYPE_BOOLEAN:
+ cl = Boolean.class;
+
+ break;
+
+ case CyAttributes.TYPE_INTEGER:
+ cl = Integer.class;
+
+ break;
+
+ case CyAttributes.TYPE_FLOATING:
+ cl = Double.class;
+
+ break;
+
+ case CyAttributes.TYPE_STRING:
+ cl = String.class;
+
+ break;
+
+ case CyAttributes.TYPE_SIMPLE_LIST:
+ cl = List.class;
+
+ break;
+
+ case CyAttributes.TYPE_SIMPLE_MAP:
+ cl = Map.class;
+
+ break;
+
+ case CyAttributes.TYPE_COMPLEX:
+ cl = Object.class;
+
+ break;
+
+ default:
+ cl = null;
+ }
+
+ return cl;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param attrs DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static List<String> getVisibleAttributeNames(CyAttributes attrs) {
+ String[] allNames = attrs.getAttributeNames();
+ List<String> visibleNames = new ArrayList<String>();
+
+ for (String name : allNames)
+ if (attrs.getUserVisible(name)) {
+ visibleNames.add(name);
+ }
+
+ return visibleNames;
+ }
+
+ /**
+ * @param copyEquation if true, and the source contains an equation, the equation and not the value will be copied
+ * @param errorMessage will be set to an explanatory text should the copy operation fail
+ * @return true if the copy operation succeeded, else false
+ */
+ public static boolean copyAttribute(final CyAttributes attribs, final String sourceId, final String targetId,
+ final String attribName, final boolean copyEquation,
+ final StringBuilder errorMessage)
+ {
+ // Self-copy is a supported no-op!
+ if (sourceId.equals(targetId))
+ return true;
+
+ errorMessage.setLength(0);
+
+ if (copyEquation) {
+ final Equation equation = attribs.getEquation(sourceId, attribName);
+ if (equation == null)
+ attribs.deleteAttribute(targetId, attribName);
+ else
+ attribs.setAttribute(targetId, attribName, equation);
+
+ return true;
+ }
+
+ switch (attribs.getType(attribName)) {
+ case CyAttributes.TYPE_BOOLEAN:
+ final Boolean b = attribs.getBooleanAttribute(sourceId, attribName);
+ if (b == null)
+ attribs.deleteAttribute(targetId, attribName);
+ else
+ attribs.setAttribute(targetId, attribName, b);
+ return true;
+ case CyAttributes.TYPE_INTEGER:
+ final Integer i = attribs.getIntegerAttribute(sourceId, attribName);
+ if (i == null)
+ attribs.deleteAttribute(targetId, attribName);
+ else
+ attribs.setAttribute(targetId, attribName, i);
+ return true;
+ case CyAttributes.TYPE_FLOATING:
+ final Double d = attribs.getDoubleAttribute(sourceId, attribName);
+ if (d == null)
+ attribs.deleteAttribute(targetId, attribName);
+ else
+ attribs.setAttribute(targetId, attribName, d);
+ return true;
+ case CyAttributes.TYPE_STRING:
+ final String s = attribs.getStringAttribute(sourceId, attribName);
+ if (s == null)
+ attribs.deleteAttribute(targetId, attribName);
+ else
+ attribs.setAttribute(targetId, attribName, s);
+ return true;
+ case CyAttributes.TYPE_SIMPLE_LIST:
+ return copySimpleList(attribs, sourceId, targetId, attribName, errorMessage);
+ case CyAttributes.TYPE_SIMPLE_MAP:
+ return copySimpleMap(attribs, sourceId, targetId, attribName, errorMessage);
+ default:
+ final Object attribValue = attribs.getAttribute(sourceId, attribName);
+ if (attribValue == null) {
+ attribs.deleteAttribute(targetId, attribName);
+ return true;
+ }
+
+ errorMessage.append("can't copy an attribute of this type ("
+ + toString(attribs.getType(attribName)) + ")! (Source ID: "
+ + sourceId + ", Attribute name: " + attribName + ")");
+ return false;
+ }
+ }
+
+ /**
+ * Helper method used by copyAttribute().
+ */
+ private static boolean copySimpleList(final CyAttributes attribs, final String sourceId, final String targetId,
+ final String attribName, final StringBuilder errorMessage)
+ {
+ final List originalList = attribs.getListAttribute(sourceId, attribName);
+ if (originalList == null) {
+ attribs.deleteAttribute(targetId, attribName);
+ return true;
+ }
+
+ if (originalList.isEmpty()) {
+ attribs.setListAttribute(targetId, attribName, new ArrayList());
+ return true;
+ }
+
+ final Class entryType = originalList.get(0).getClass();
+ if (entryType != Boolean.class && entryType != Integer.class && entryType != Double.class
+ && entryType != String.class)
+ {
+ errorMessage.append("can't copy a list that has entries of a non-trivial type("
+ + toString(attribs.getType(attribName)) + ")! (Source ID: "
+ + sourceId + ", Attribute name: " + attribName + ")");
+ return false;
+ }
+
+ final List newList = new ArrayList(originalList.size());
+ for (final Object listEntry : originalList)
+ newList.add(listEntry);
+ attribs.setListAttribute(targetId, attribName, newList);
+ return true;
+ }
+
+ /**
+ * Helper method used by copyAttribute().
+ */
+ private static boolean copySimpleMap(final CyAttributes attribs, final String sourceId, final String targetId,
+ final String attribName, final StringBuilder errorMessage)
+ {
+ final Map originalMap = attribs.getMapAttribute(sourceId, attribName);
+ if (originalMap == null) {
+ attribs.deleteAttribute(targetId, attribName);
+ return true;
+ }
+
+ if (originalMap.isEmpty()) {
+ attribs.setMapAttribute(targetId, attribName, new HashMap());
+ return true;
+ }
+
+ final Map newMap = new HashMap();
+ newMap.putAll(originalMap);
+ attribs.setMapAttribute(targetId, attribName, newMap);
+ return true;
+ }
+
+ /**
+ * Copy all the attributes of a given object to another object.
+ * Equivalent to:
+ * <PRE>
+ * copyAttributes (originalID, copyID, attrs, ALL_ATTRIBUTES_FILTER, purge).
+ * </PRE>
+ * @see copyAttributes(String,String,CyAttributes,AttributeFilter,boolean)
+ */
+ static public void copyAttributes(String originalID, String copyID, CyAttributes attrs,
+ boolean purge) {
+ copyAttributes(originalID, copyID, attrs, ALL_ATTRIBUTES_FILTER, purge);
+ }
+
+ /**
+ * Copy all the attributes of a given object that pass a given filter to another
+ * object. This includes complex attributes.
+ * @param originalID the identifier of the object we are copying
+ * from (e.g, equivalent to CyNode.getIdentifier()).
+ * @param copyID the identifier of the object we are copying to.
+ * @param attrs the CyAttributes from which to copy and retrieve the attributes.
+ * @param filter an AttributeFilter that determines if a given attribute should
+ * be copied. The filter is applied to all attributes stored un originalID.
+ * An attribute will we copied iff filter.includeAttribute() returns true.
+ * To copy all attributes, use {@link
+ * CyAttributesUtils#ALL_ATTRIBUTES_FILTER ALL_ATTRIBUTES_FILTER}.
+ * @param purge true iff existing attribute values associated with
+ * the object represented by copyID are to be removed
+ * before copying the new attribute values from the
+ * object represented by originalID. This is useful
+ * when copying to an existing object that contained
+ * previous attribute values. This should be false
+ * for newly created, objects that have no previous
+ * attribute values.
+ * @throws IllegalArgumentException if originalID, copyID, attrs,
+ * or filter are null; or if originalID==copyID.
+ */
+ static public void copyAttributes(String originalID, String copyID, CyAttributes attrs,
+ AttributeFilter filter, boolean purge) {
+ // test filter separtely so that error message for copyAttributes() that doesn't
+ // have 'filter' argument will not be confusing:
+ if ((originalID == null) || (copyID == null) || (attrs == null)) {
+ throwIllegalArgumentException("copyAttributes(): 'original', 'copy', or 'attrs' was null.");
+ }
+
+ if (filter == null) {
+ throwIllegalArgumentException("copyAttributes(): 'filter' was null.");
+ }
+
+ if (originalID == copyID) {
+ throwIllegalArgumentException("copyAttributes(): 'original' must not be the same object as 'copy'.");
+ }
+
+ // String originalID = original.getIdentifier();
+ // String copyID = copy.getIdentifier();
+ MultiHashMapDefinition mmapDef = attrs.getMultiHashMapDefinition();
+
+ Iterator attIt = mmapDef.getDefinedAttributes();
+ String attrName;
+
+ AttributeValueVisitor copyVisitor = new CopyingAttributeValueVisitor(copyID);
+
+ while (attIt.hasNext()) {
+ attrName = (String) attIt.next();
+
+ if (filter.includeAttribute(attrs, originalID, attrName)) {
+ // primCopyAttribute(originalID, copyID, attrName, attrs, purge);
+ traverseAttributeValues(originalID, attrName, attrs, copyVisitor);
+ }
+ }
+ }
+
+ /**
+ * Copy a specific attribute of a given object to another
+ * object. This includes complex attributes.
+ * @param originalID the identifier of the object we are copying
+ * from (e.g, equivalent to CyNode.getIdentifier()).
+ * @param copyID the identifier of the object we are copying to.
+ * @param attrName the name of the attribute we wish to copy.
+ * @param attrs the CyAttributes from which to copy and retrieve the attribute.
+ * @param purge true iff existing attribute values associated with
+ * the object represented by copyID are to be removed
+ * before copying the new attribute values from the
+ * object represented by originalID. This is useful
+ * when copying to an existing object that contained
+ * previous attribute values. This should be false
+ * for newly created, objects that have no previous
+ * attribute values.
+ * @throws IllegalArgumentException if originalID, copyID,
+ * attrName, or attrs are null; or if originalID==copyID.
+ */
+ static public void copyAttribute(String originalID, String copyID, String attrName,
+ CyAttributes attrs, boolean purge) {
+ if ((originalID == null) || (copyID == null) || (attrName == null) || (attrs == null)) {
+ throwIllegalArgumentException("copyAttribute(): 'original', 'copy', 'attrName' or 'attrs' was null.");
+ }
+
+ if (originalID == copyID) {
+ throwIllegalArgumentException("copyAttribute(): 'original' must not be the same object as 'copy'.");
+ }
+
+ AttributeValueVisitor copyVisitor = new CopyingAttributeValueVisitor(copyID);
+
+ // String originalID = original.getIdentifier();
+ // String copyID = copy.getIdentifier();
+ traverseAttributeValues(originalID, attrName, attrs, copyVisitor);
+
+ // return primCopyAttribute(originalID, copyID, attrName, attrs, purge);
+ }
+
+ /**
+ * Traverse all the values of a given attribute applying an
+ * AttributeValueVisitor to each value. For simple attributes,
+ * such as those of type CyAttributes.TYPE_INTEGER or
+ * CyAttributes.TYPE_STRING, a single value is traversed. For
+ * Lists, Maps, and complex attribute types, all attribute values
+ * are traversed--applying the given AttributeValueVisitor to each
+ * value.
+ * @param objToTraverseID the identifier of the object containing
+ * the attribute of interest.
+ * @param attrName the name of the attribute for which we are to
+ * traverse values.
+ * @param attrs the CyAttributes that contains the attribute of interest.
+
+ * @param visitor an AttributeValueVisitor to be applied to each
+ * value of the attribute being traversed. For
+ * example, to print out all attribute values, we
+ * could perform:
+ * <PRE>
+ * traverseAttributeValues ("testObject",
+ * "testAttributeName",
+ * Cytoscape.getNodeAttributes(),
+ * new AttributeValueVisitor () {
+ * public void visitingAttributeValue (String objTraversedID,
+ * String attrName,
+ * CyAttributes attrs,
+ * Object[] keySpace,
+ * Object visitedValue) {
+ * CyLogger.getLogger().info ("traversing " + visitedValue);
+ * }});
+ * </PRE>
+ * No traversal is performed if objToTraverseID or attrName are null,
+ * or if objToTraverseID has no associated attrName attribute.
+ */
+ static public void traverseAttributeValues(String objToTraverseID, String attrName,
+ CyAttributes attrs, AttributeValueVisitor visitor) {
+ if ((objToTraverseID == null) || (attrName == null)) {
+ return;
+ }
+
+ // String visitID = objToTraverseID.getIdentifier();
+ if (!attrs.hasAttribute(objToTraverseID, attrName)) {
+ return;
+ }
+
+ // original has this attribute, now get it's value:
+ MultiHashMap mmap = attrs.getMultiHashMap();
+ MultiHashMapDefinition mmapDef = attrs.getMultiHashMapDefinition();
+ byte attrType = attrs.getType(attrName);
+
+ switch (attrType) {
+ case CyAttributes.TYPE_BOOLEAN:
+ case CyAttributes.TYPE_INTEGER:
+ case CyAttributes.TYPE_FLOATING:
+ case CyAttributes.TYPE_STRING:
+ visitor.visitingAttributeValue(objToTraverseID, attrName, attrs, null,
+ mmap.getAttributeValue(objToTraverseID, attrName,
+ null));
+
+ break;
+
+ case CyAttributes.TYPE_SIMPLE_LIST:
+ case CyAttributes.TYPE_SIMPLE_MAP:
+
+ Object[] key = new Object[1];
+ Iterator keyspan = mmap.getAttributeKeyspan(objToTraverseID, attrName, null);
+
+ while (keyspan.hasNext()) {
+ key[0] = keyspan.next();
+ visitor.visitingAttributeValue(objToTraverseID, attrName, attrs, key,
+ mmap.getAttributeValue(objToTraverseID,
+ attrName, key));
+ }
+
+ break;
+
+ case CyAttributes.TYPE_COMPLEX:
+
+ byte[] keyTypes = mmapDef.getAttributeKeyspaceDimensionTypes(attrName);
+ walkThruKeySpace(keyTypes.length, 0, new Object[0], objToTraverseID, attrName,
+ attrs, visitor);
+
+ break;
+ }
+ }
+
+ /**
+ * A recursive method that iterates through each set of keys at a
+ * particular dimension in the keyspace and then continues down to the
+ * next dimension. Once the final dimension is reached, the visitor
+ * is run passing it the stored attribute value and related info.
+ */
+ static private void walkThruKeySpace(int maxKeys, int keyTypesIndex,
+ Object[] currentDimensionKeys, String objToTraverseID,
+ String attrName, CyAttributes attrs,
+ AttributeValueVisitor visitor) {
+ CountedIterator dimIt = attrs.getMultiHashMap()
+ .getAttributeKeyspan(objToTraverseID, attrName,
+ currentDimensionKeys);
+ Object nextValue;
+ keyTypesIndex++;
+
+ Object[] nextDimensionKeys = null;
+
+ if (keyTypesIndex <= maxKeys) {
+ // we have another dimension to go down into (key to add).
+ // copy all the previous keys and then we'll add
+ // the last key during each iteration of dimIt:
+ nextDimensionKeys = new Object[keyTypesIndex];
+
+ for (int i = 0; i < (keyTypesIndex - 1); i++) {
+ nextDimensionKeys[i] = currentDimensionKeys[i];
+ }
+ }
+
+ while (dimIt.hasNext()) {
+ nextValue = dimIt.next();
+ // CyLogger.getLogger().info("dim " + keyTypesIndex + " value = " + nextValue);
+ nextDimensionKeys[keyTypesIndex - 1] = nextValue;
+
+ // have we reached the last dimension, or do we need to continue building
+ // the keys?
+ if (keyTypesIndex < maxKeys) {
+ // do next dimension:
+ walkThruKeySpace(maxKeys, keyTypesIndex, nextDimensionKeys, objToTraverseID,
+ attrName, attrs, visitor);
+ } else {
+ // we reached the final set of keys, now deal with the real values:
+ Object finalVal = attrs.getMultiHashMap()
+ .getAttributeValue(objToTraverseID, attrName,
+ nextDimensionKeys);
+ // CyLogger.getLogger().info("dim " + keyTypesIndex + " final value = " +
+ // finalVal);
+ visitor.visitingAttributeValue(objToTraverseID, attrName, attrs, nextDimensionKeys,
+ finalVal);
+ }
+ }
+ }
+
+ /**
+ * Return a non-null List of all the attribute names associated with
+ * a given identifier for a given CyAttributes. Will return
+ * an empty list if objID or attrs is null.
+ * @param objID the identifier of the object of interest.
+ * @param attrs the CyAttributes from which to check for attributes.
+ */
+ static public List<String> getAttributeNamesForObj(String objID, CyAttributes attrs) {
+ if ((objID == null) || (attrs == null)) {
+ return null;
+ }
+
+ CountedIterator nameIt = attrs.getMultiHashMapDefinition().getDefinedAttributes();
+ List<String> names = new ArrayList<String>();
+ String attrName;
+
+ while (nameIt.hasNext()) {
+ attrName = (String) nameIt.next();
+
+ if (attrs.hasAttribute(objID, attrName)) {
+ names.add(attrName);
+ }
+ }
+
+ return names;
+ }
+
+ /**
+ * Get list of IDs associated with a specific attribute value.
+ *
+ * @param attr DOCUMENT ME!
+ * @param attrName DOCUMENT ME!
+ * @param attrValue DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static List<String> getIDListFromAttributeValue(AttributeType type, String attrName,
+ Object attrValue) {
+ final CyAttributes attr;
+ final List<String> ids = new ArrayList<String>();
+ final List<String> result = new ArrayList<String>();
+
+ // Extract ids
+ if (type == AttributeType.NODE) {
+ attr = Cytoscape.getNodeAttributes();
+
+ final List<Node> nodes = Cytoscape.getRootGraph().nodesList();
+
+ for (Node node : nodes)
+ ids.add(node.getIdentifier());
+ } else if (type == AttributeType.EDGE) {
+ attr = Cytoscape.getEdgeAttributes();
+
+ final List<Edge> edges = Cytoscape.getRootGraph().edgesList();
+
+ for (Edge edge : edges) {
+ ids.add(edge.getIdentifier());
+ }
+ } else {
+ attr = Cytoscape.getNetworkAttributes();
+ }
+
+ final byte attrDataType = attr.getType(attrName);
+
+ String value;
+
+ List<Object> l = null;
+ if (attrDataType == CyAttributes.TYPE_SIMPLE_LIST) {
+ for (String id : ids) {
+ l = attr.getListAttribute(id, attrName);
+
+ if ((l != null) && (l.size() > 0)) {
+ for (Object obj : l) {
+ if ((obj != null) && obj.equals(attrValue)) {
+ result.add(id);
+
+ break;
+ }
+ }
+ }
+ }
+ } else if (attrDataType == CyAttributes.TYPE_STRING) {
+ for (String id : ids) {
+ // Extract attribute value from ID
+ value = attr.getStringAttribute(id, attrName);
+
+ if ((value != null) && value.equals(attrValue))
+ result.add(id);
+ }
+ }
+
+ return result;
+ }
+
+ /**
+ * Return a String representation of the various CyAttributes
+ * types returned by methods like CyAttributes.getType() and
+ * MultiHashMapDefinition.getAttributeKeysapceDimensionTypes().
+ * This is useful for "toString()" operations.
+ * @see cytoscape.data.CyAttributes#getType
+ * @see cytoscape.data.attr.MultiHashMapDefinition#getAttributeKeyspaceDimensionTypes
+ */
+ static public String toString(byte atype) {
+ switch (atype) {
+ case CyAttributes.TYPE_COMPLEX:
+ return "COMPLEX";
+
+ case CyAttributes.TYPE_SIMPLE_MAP:
+ return "SIMPLE_MAP";
+
+ case CyAttributes.TYPE_SIMPLE_LIST:
+ return "SIMPLE_LIST";
+
+ case CyAttributes.TYPE_UNDEFINED:
+ return "UNDEFINED";
+
+ case CyAttributes.TYPE_BOOLEAN:
+ return "BOOLEAN";
+
+ case CyAttributes.TYPE_INTEGER:
+ return "INTEGER";
+
+ case CyAttributes.TYPE_FLOATING:
+ return "FLOATING";
+
+ case CyAttributes.TYPE_STRING:
+ return "STRING";
+
+ default:
+ return "UNKNOWN:" + atype;
+ }
+ }
+
+ /**
+ * Return a byte representation of the various CyAttributes
+ * types returned by methods like CyAttributes.getType() and
+ * MultiHashMapDefinition.getAttributeKeysapceDimensionTypes().
+ * This is useful to return the byte when you have an Attribute String.
+ * @see cytoscape.data.CyAttributes#getType
+ * @see cytoscape.data.attr.MultiHashMapDefinition#getAttributeKeyspaceDimensionTypes
+ */
+ static public byte toByte(String attributeType) {
+ if (attributeType.equals("COMPLEX"))
+ return CyAttributes.TYPE_COMPLEX;
+
+ if (attributeType.equals("SIMPLE_MAP"))
+ return CyAttributes.TYPE_SIMPLE_MAP;
+
+ if (attributeType.equals("SIMPLE_LIST"))
+ return CyAttributes.TYPE_SIMPLE_LIST;
+
+ if (attributeType.equals("UNDEFINED"))
+ return CyAttributes.TYPE_UNDEFINED;
+
+ if (attributeType.equals("BOOLEAN"))
+ return CyAttributes.TYPE_BOOLEAN;
+
+ if (attributeType.equals("INTEGER"))
+ return CyAttributes.TYPE_INTEGER;
+
+ if (attributeType.equals("FLOATING"))
+ return CyAttributes.TYPE_FLOATING;
+
+ if (attributeType.equals("STRING"))
+ return CyAttributes.TYPE_STRING;
+
+ return CyAttributes.TYPE_UNDEFINED;
+ }
+
+ /**
+ * Convenience method for throwing an IllegalArgumentException given
+ * a message.
+ */
+ static private void throwIllegalArgumentException(String msg) throws IllegalArgumentException {
+ IllegalArgumentException ex = new IllegalArgumentException(msg);
+ ex.fillInStackTrace();
+
+ // ex.printStackTrace();
+ throw ex;
+ }
+
+ /**
+ * copy each attribute value from objTraversedID to an
+ * attribute value associated with objTraversedCopyID.
+ */
+ private static class CopyingAttributeValueVisitor implements AttributeValueVisitor {
+ private String copyID;
+
+ public CopyingAttributeValueVisitor(String objTraversedCopyID) {
+ copyID = objTraversedCopyID;
+ }
+
+ public void visitingAttributeValue(String objTraversedID, String attrName,
+ CyAttributes attrs, Object[] keySpace,
+ Object visitedValue) {
+ attrs.getMultiHashMap().setAttributeValue(copyID, attrName, visitedValue, keySpace);
+ }
+ }
+
+
+ /**
+ * Check if all the values for an attribute are NULL.
+ * @param attributeType "node" or "edge"
+ * @param attributeName attribute name.
+ */
+ public static boolean isNullAttribute(String attributeType, String attributeName){
+
+ boolean retValue = true;
+
+ CyAttributes attributes = null;
+ if (attributeType.equalsIgnoreCase("node")){
+ attributes = Cytoscape.getNodeAttributes();
+ int[] nodeIndices = Cytoscape.getCurrentNetwork().getNodeIndicesArray();
+ for (int i=0; i<nodeIndices.length; i++){
+ String nodeID = Cytoscape.getRootGraph().getNode(nodeIndices[i]).getIdentifier();
+ Object valueObj = attributes.getAttribute(nodeID, attributeName);
+ if (valueObj != null){
+ retValue = false;
+ break;
+ }
+ }
+ }
+ else {// edge
+ attributes = Cytoscape.getEdgeAttributes();
+ int[] edgeIndices = Cytoscape.getCurrentNetwork().getEdgeIndicesArray();
+ for (int i=0; i<edgeIndices.length; i++){
+ String edgeID = Cytoscape.getRootGraph().getEdge(edgeIndices[i]).getIdentifier();
+ Object valueObj = attributes.getAttribute(edgeID, attributeName);
+ if (valueObj != null){
+ retValue = false;
+ break;
+ }
+ }
+ }
+
+ return retValue;
+ }
+}
diff --git a/application/src/main/java/cytoscape/data/CyNetworkUtilities.java b/application/src/main/java/cytoscape/data/CyNetworkUtilities.java
new file mode 100644
index 0000000..359c412
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/CyNetworkUtilities.java
@@ -0,0 +1,245 @@
+/*
+ File: CyNetworkUtilities.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// $Revision: 18025 $
+// $Date: 2009-09-22 12:29:21 +0200 (Tue, 22 Sep 2009) $
+// $Author: noelr $
+package cytoscape.data;
+
+import ViolinStrings.Strings;
+
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+
+import cytoscape.data.Semantics;
+
+import cytoscape.view.CyNetworkView;
+
+import giny.model.GraphPerspective;
+import giny.model.Node;
+
+import giny.view.GraphView;
+import giny.view.NodeView;
+
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+
+import java.util.*;
+
+import javax.swing.JOptionPane;
+
+
+//-------------------------------------------------------------------------
+/**
+ * This class provides static methods that operate on a CyNetwork to perform
+ * various useful tasks. Many of these methods make assumptions about the data
+ * types that are available in the node and edge attributes of the network.
+ */
+public class CyNetworkUtilities {
+ // -------------------------------------------------------------------------
+ /**
+ * Saves all selected nodes in the current view to a file with the given
+ * name.
+ * TODO: The CyNetworkView is not a needed parameter
+ */
+ public static boolean saveSelectedNodeNames(CyNetworkView networkView, CyNetwork network,
+ String filename) {
+ if ((networkView == null) || (network == null) || (filename == null)) {
+ return false;
+ }
+
+ Set selectedNodes = network.getSelectedNodes();
+
+ if ((selectedNodes == null) || (selectedNodes.size() == 0)) {
+ JOptionPane.showMessageDialog(Cytoscape.getDesktop(), "No selected nodes.", "Message",
+ JOptionPane.INFORMATION_MESSAGE);
+
+ return false;
+ }
+
+ String lineSep = System.getProperty("line.separator");
+
+ try {
+ File file = new File(filename);
+ FileWriter fout = null;
+
+ try {
+ fout = new FileWriter(file);
+ for (Iterator i = selectedNodes.iterator(); i.hasNext();) {
+ CyNode node = (CyNode) i.next();
+ String nodeUID = node.getIdentifier();
+ fout.write(nodeUID + lineSep);
+ } // for i
+ }
+ finally {
+ if (fout != null) {
+ fout.close();
+ }
+ }
+
+ return true;
+ } catch (IOException e) {
+ JOptionPane.showMessageDialog(null, e.toString(),
+ "Error Writing to \"" + filename + "\"",
+ JOptionPane.ERROR_MESSAGE);
+
+ return false;
+ }
+ } // saveSelectedNodeNames
+
+ // -------------------------------------------------------------------------
+
+ /**
+ * Saves all nodes in the given network to a file with the given
+ * name.
+ */
+ public static boolean saveVisibleNodeNames(CyNetwork network, String filename) {
+ if ((network == null) || (filename == null)) {
+ return false;
+ }
+
+ String callerID = "CyNetworkUtilities.saveVisibleNodeNames";
+
+ //GraphPerspective theGraph = network.getGraphPerspective();
+ //CyAttributes nodeAttributes = Cytoscape.getNodeAttributes();
+ String lineSep = System.getProperty("line.separator");
+
+ try {
+ File file = new File(filename);
+ FileWriter fout = null;
+
+ try {
+ fout = new FileWriter(file);
+ for (Iterator i = network.nodesIterator(); i.hasNext();) {
+ CyNode node = (CyNode) i.next();
+ // String canonicalName = nodeAttributes.getCanonicalName(node);
+ //String canonicalName = nodeAttributes.getStringAttribute(node
+ // .getIdentifier(), "canonicalName");
+ fout.write(node.getIdentifier() + lineSep);
+ } // for i
+ }
+ finally {
+ if (fout != null) {
+ fout.close();
+ }
+ }
+
+ return true;
+ } catch (IOException e) {
+ JOptionPane.showMessageDialog(null, e.toString(),
+ "Error Writing to \"" + filename + "\"",
+ JOptionPane.ERROR_MESSAGE);
+
+ return false;
+ }
+ }
+
+ // -------------------------------------------------------------------------
+ /**
+ * Selects every node in the current view whose canonical name, label, or
+ * any known synonym starts with the string specified by the second
+ * argument. Note that synonyms are only available if a naming server is
+ * available.
+ *
+ * This method does not change the selection state of any node that doesn't
+ * match the given key, allowing multiple selection queries to be
+ * concatenated.
+ */
+ public static boolean selectNodesStartingWith(CyNetwork network, String key,
+ CyNetworkView networkView) {
+ if ((network == null) || (key == null) || (networkView == null)) {
+ return false;
+ }
+
+ key = key.toLowerCase();
+
+ boolean found = false;
+ String callerID = "CyNetworkUtilities.selectNodesStartingWith";
+
+ //GraphPerspective theGraph = network.getGraphPerspective();
+ //CyAttributes nodeAttributes = Cytoscape.getNodeAttributes();
+ int nodeFound = 0;
+ Vector matchedNodes = new Vector();
+
+ for (Iterator i = network.nodesIterator(); i.hasNext();) {
+ CyNode node = (CyNode) i.next();
+ String nodeUID = node.getIdentifier();
+
+ boolean matched = false;
+
+ if ((nodeUID != null) && Strings.isLike(nodeUID, key, 0, true)) {
+ matched = true;
+ found = true;
+ matchedNodes.add(node);
+ } else {
+ // this list always includes the canonical name itself
+ List synonyms = Semantics.getAllSynonyms(nodeUID, network);
+
+ for (Iterator synI = synonyms.iterator(); synI.hasNext();) {
+ String synonym = (String) synI.next();
+
+ if (Strings.isLike(synonym, key, 0, true)) {
+ matched = true;
+ found = true;
+ matchedNodes.add(node);
+
+ break;
+ }
+ } //inner for
+ } //else
+
+ if (matched)
+ nodeFound++;
+ } //for
+
+ if (nodeFound == 0) {
+ JOptionPane.showMessageDialog(null, "No match for the string \"" + key + "\"",
+ "Error: Node Not Found", JOptionPane.ERROR_MESSAGE);
+ }
+
+ if (nodeFound > 0) {
+ network.setSelectedNodeState(matchedNodes, true);
+ }
+
+ //CyLogger.getLogger().info("node found = " + nodeFound);
+ return found;
+ }
+
+ // -------------------------------------------------------------------------
+}
diff --git a/application/src/main/java/cytoscape/data/ExpressionData.java b/application/src/main/java/cytoscape/data/ExpressionData.java
new file mode 100644
index 0000000..63d4c6c
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/ExpressionData.java
@@ -0,0 +1,1102 @@
+/*
+ File: ExpressionData.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+//ExpressionData.java
+
+//--------------------------------------------------------------------
+// $Revision: 14391 $
+// $Date: 2008-07-09 22:14:37 +0200 (Wed, 09 Jul 2008) $
+// $Author: grossb $
+//--------------------------------------------------------------------
+package cytoscape.data;
+
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+
+//--------------------------------------------------------------------
+import cytoscape.data.readers.TextFileReader;
+import cytoscape.data.readers.TextJarReader;
+
+import cytoscape.task.TaskMonitor;
+
+import cytoscape.util.FileUtil;
+
+import java.io.*;
+
+import java.util.*;
+
+
+//--------------------------------------------------------------------
+
+/**
+ * This class provides a reader for the common file format for expression data
+ * and an interface to access the data.
+ * <P>
+ * <p/> <p/> There are variations in the file format used; the following
+ * assumptions about the file format are considered valid. Attempting to read a
+ * file that does not satisfy these assumptions is not guaranteed to work.
+ * <P>
+ * <p/> 1. A token is a consecutive sequence of alphanumeric characters
+ * separated by whitespace.<BR>
+ * 2. The file consists of an arbitrary number of lines, each of which contains
+ * the same number of tokens (except for possibly the first line) and has a
+ * total length less than 8193 characters.<BR>
+ * 3. The first line of the file is a header line with one of the following
+ * three formats:
+ * <P>
+ * <p/> <text> <text> cond1 cond2 ... condN cond1 cond2 ... condN NumSigConds
+ * <P>
+ * <p/> <text> <text> cond1 cond2 ... condN
+ * <P>
+ * <p/> <\t><\t>RATIOS<\t><\t>...LAMBDAS
+ * <P>
+ * <p/> Here cond1 through condN are the names of the conditions. In the first
+ * case, the two sequences of condition names must match exactly in order and
+ * lexicographically; each name among cond1 ... condN must be unique. In the
+ * second case, each name must be unique, but need only appear once. The last
+ * label, NumSigConds, is optional.<BR>
+ * The third case is the standard header for a MTX file. The numer of '\t'
+ * characters between the words "RATIOS" and "LAMBDAS" is equal to the number of
+ * ratio columns in the file (which must be equal to the number of lambda
+ * columns).
+ * <P>
+ * <p/> 4. Each successive line represents the measurements for a partcular
+ * gene, and has one of the following two formats, depending on the header:
+ * <P>
+ * <p/> <FNAME> <CNAME> E E ... E S S ... S I
+ * <P>
+ * <p/> <FNAME> <CNAME> E E ... E
+ * <P>
+ * <p/> where <FNAME> is the formal name of the gene, <CNAME> is the common
+ * name, the E's are tokens, parsable as doubles, representing the expression
+ * level change for each condition, the S's are tokens parsable as doubles
+ * representing the statistical significance of the expression level change, and
+ * I is an optional integer giving the number of conditions in which the
+ * expression level change was significant for this gene.
+ * <P>
+ * <p/> The first format is used in conjuction with the first or third header
+ * formats. The second format is used in conjunction with the second header
+ * format.
+ * <P>
+ * <p/> 5. An optional last line can be included with the following form:
+ * <P>
+ * <p/> NumSigGenes: I I ... I
+ * <P>
+ * <p/> where there are N I's, each an integer representing the number of
+ * significant genes in that condition.
+ * <P>
+ */
+public class ExpressionData implements Serializable {
+ private TaskMonitor taskMonitor;
+
+ /**
+ *
+ */
+ public static final int MAX_LINE_SIZE = 8192;
+
+ /**
+ * Significance value: PVAL.
+ */
+ public static final int PVAL = 0;
+
+ /**
+ * Significance value: LAMBA.
+ */
+ public static final int LAMBDA = 1;
+
+ /**
+ * Significance value: NONE.
+ */
+ public static final int NONE = 2;
+
+ /**
+ * Significance value: UNKNOWN.
+ */
+ public static final int UNKNOWN = 3;
+ private static final String DEFAULT_KEY_ATTRIBUTE = "ID";
+ protected int significanceType = 3;
+
+ /*
+ * the key attribute name is the attribute by which the expression data is
+ * matched to the node name. For instance, this might be a commercial
+ * probe set ID.
+ */
+ String keyAttributeName = DEFAULT_KEY_ATTRIBUTE;
+ private boolean mappingByAttribute = false;
+ String filename;
+ int numGenes;
+ int numConds;
+ int extraTokens;
+ boolean haveSigValues;
+ Vector geneNames;
+ Vector geneDescripts;
+ Vector condNames;
+ Hashtable geneNameToIndex;
+ Hashtable condNameToIndex;
+ double minExp;
+ double maxExp;
+ double minSig;
+ double maxSig;
+ Vector allMeasurements;
+
+ /**
+ * Constructor. Creates an empty Expression Data object with no data.
+ */
+ public ExpressionData() {
+ filename = null;
+ keyAttributeName = DEFAULT_KEY_ATTRIBUTE;
+ numGenes = 0;
+ numConds = 0;
+ extraTokens = 0;
+ haveSigValues = false;
+ this.initDataStructures();
+ }
+
+ /**
+ * Constructor. Loads the specified filename into memory.
+ *
+ * @param filename Name of Expression Data File.
+ * @throws IOException Error opening/parsing the expression data file.
+ */
+ public ExpressionData(String filename) throws IOException {
+ this.filename = null;
+ numGenes = 0;
+ numConds = 0;
+ extraTokens = 0;
+ haveSigValues = false;
+ this.initDataStructures();
+ this.loadData(filename, DEFAULT_KEY_ATTRIBUTE);
+ }
+
+ /**
+ * Constructor. Loads the specified filename into memory.
+ *
+ * @param filename Name of Expression Data File.
+ * @throws IOException Error opening/parsing the expression data file.
+ */
+ public ExpressionData(String filename, String keyAttributeName) throws IOException {
+ this.filename = null;
+ numGenes = 0;
+ numConds = 0;
+ extraTokens = 0;
+ haveSigValues = false;
+ this.initDataStructures();
+ this.loadData(filename, keyAttributeName);
+ }
+
+ /**
+ * Constructor. Loads the specified file into memory, and reports its
+ * progress to the specified TaskMonitor Object. This option is useful for
+ * displaying a progress bar to the end-user, while expression data is being
+ * parsed.
+ *
+ * @param filename Name of Expression Data File.
+ * @param taskMonitor TaskMonitor for reporting/monitoring progress.
+ * @throws IOException Error opening/parsing the expression data file.
+ */
+ public ExpressionData(String filename, TaskMonitor taskMonitor) throws IOException {
+ this.taskMonitor = taskMonitor;
+ this.filename = null;
+ numGenes = 0;
+ numConds = 0;
+ extraTokens = 0;
+ haveSigValues = false;
+ this.initDataStructures();
+ this.loadData(filename, DEFAULT_KEY_ATTRIBUTE);
+ }
+
+ /**
+ * Constructor. Loads the specified file into memory, and reports its
+ * progress to the specified TaskMonitor Object. This option is useful for
+ * displaying a progress bar to the end-user, while expression data is being
+ * parsed.
+ *
+ * @param filename Name of Expression Data File.
+ * @param keyAttributeName Identifies an attribute to use in mapping
+ * the data to the nodes.
+ * @param taskMonitor TaskMonitor for reporting/monitoring progress.
+ * @throws IOException Error opening/parsing the expression data file.
+ */
+ public ExpressionData(String filename, String keyAttributeName, TaskMonitor taskMonitor)
+ throws IOException {
+ this.taskMonitor = taskMonitor;
+ this.filename = null;
+ numGenes = 0;
+ numConds = 0;
+ extraTokens = 0;
+ haveSigValues = false;
+ this.initDataStructures();
+ this.loadData(filename, keyAttributeName);
+ }
+
+ /**
+ * Gets the Name of the Expression Data File.
+ *
+ * @return File String, as it was originally passed to the constructor, or
+ * null, if no filename is available.
+ */
+ public String getFileName() {
+ return filename;
+ }
+
+ /**
+ * Gets the File representation of the Expression Data Object. This File
+ * object can be queried for a full path to the file, etc.
+ *
+ * @return File Object.
+ */
+ public File getFullPath() {
+ File file = new File(filename);
+
+ return file.getAbsoluteFile();
+ }
+
+ /**
+ * Initializes all data structures.
+ */
+ private void initDataStructures() {
+ /*
+ * on overflow, capacity of vector will be increased by "expand"
+ * elements all at once; much more efficient when we don't know how many
+ * thousand genes are left in the file
+ */
+ int expand = 1000;
+
+ if (geneNames != null) {
+ geneNames.clear();
+ }
+
+ geneNames = new Vector(0, expand);
+
+ if (geneDescripts != null) {
+ geneDescripts.clear();
+ }
+
+ geneDescripts = new Vector(0, expand);
+
+ if (condNames != null) {
+ condNames.clear();
+ }
+
+ condNames = new Vector();
+
+ if (geneNameToIndex != null) {
+ geneNameToIndex.clear();
+ }
+
+ geneNameToIndex = new Hashtable();
+
+ if (condNameToIndex != null) {
+ condNameToIndex.clear();
+ }
+
+ condNameToIndex = new Hashtable();
+ minExp = Double.MAX_VALUE;
+ maxExp = Double.MIN_VALUE;
+ minSig = Double.MAX_VALUE;
+ maxSig = Double.MIN_VALUE;
+
+ if (allMeasurements != null) {
+ allMeasurements.clear();
+ }
+
+ allMeasurements = new Vector(0, expand);
+ }
+
+ /**
+ * Loads the Specified File into memory.
+ *
+ * @param filename Name of Expression Data File.
+ * @return always returns true, indicating succesful load.
+ * @throws IOException Error loading / parsing the Expression Data File.
+ */
+ public boolean loadData(String filename, String keyAttributeName) throws IOException {
+ Hashtable attributeToId = new Hashtable();
+
+ if (filename == null)
+ return false;
+
+ boolean mappingByKeyAttribute = false;
+
+ if (!keyAttributeName.equals(DEFAULT_KEY_ATTRIBUTE)) {
+ mappingByKeyAttribute = true;
+ attributeToId = getAttributeToIdList(keyAttributeName);
+ }
+
+ String rawText = FileUtil.getInputString(filename);
+ String[] lines = rawText.split(System.getProperty("line.separator"));
+
+ int lineCount = 0;
+
+ // allow file to start with an arbitrary number
+ // of comment lines starting with '#' symbol
+ while (lines[lineCount].startsWith("#")) ++lineCount;
+
+ String headerLine = lines[lineCount++];
+
+ if ((headerLine == null) || (headerLine.length() == 0)) {
+ throw new IOException("Missing header in data file.");
+ }
+
+ if (isHeaderLineMTXHeader(headerLine)) {
+ // for sure we know that the file contains lambdas
+ this.significanceType = this.LAMBDA;
+ headerLine = lines[lineCount++];
+ }
+
+ boolean hasCOMMON = doesHeaderLineHasCOMMON(headerLine);
+ boolean expectPvals = doesHeaderLineHaveDuplicates(headerLine, hasCOMMON);
+
+ if ((this.significanceType != this.LAMBDA) && !expectPvals) {
+ // we know that we don't have a lambda header and we don't
+ // have significance values
+ this.significanceType = this.NONE;
+ }
+
+ StringTokenizer headerTok = new StringTokenizer(headerLine);
+ int numTokens = headerTok.countTokens();
+
+ // if we don't expect p-values, 3 is the minimum number with COMMON column, 2 if without COMMON.
+ // if we expect p-values, 4 is the minimum number with COMMON column, 3 if without COMMON.
+ int minTokens = 2;
+ if (hasCOMMON) {
+ minTokens = 3;
+ }
+ if ((numTokens < minTokens) || ((numTokens < (minTokens+1)) && expectPvals)) {
+ StringBuffer msg = new StringBuffer("Invalid header format in data file.");
+ msg.append("\nNumber of tokens parsed: " + numTokens);
+
+ for (int i = 0; i < numTokens; i++) {
+ msg.append("\nToken " + i + ": " + headerTok.nextToken());
+ }
+
+ throw new IOException(msg.toString());
+ }
+
+ double tmpF = numTokens / 2.0;
+ int tmpI = (int) Math.rint(tmpF);
+ int numberOfConditions;
+ int haveExtraTokens = 0;
+
+ if (expectPvals) {
+ if (tmpI == tmpF) { // missing numSigConds field
+ numberOfConditions = (numTokens - 2) / 2;
+ haveExtraTokens = 0;
+ } else {
+ numberOfConditions = (numTokens - 3) / 2;
+ haveExtraTokens = 1;
+ } // else
+ } else {
+ numberOfConditions = numTokens - 2;
+ }
+
+ // Since COMMON is optional, it may not exist
+ if (!hasCOMMON) {
+ if (expectPvals) {
+ if (tmpI == tmpF) {
+ numberOfConditions = (numTokens - 2) / 2;
+ haveExtraTokens = 1;
+ } else {
+ numberOfConditions = (numTokens - 1) / 2;
+ haveExtraTokens = 0;
+ }
+ } else {
+ numberOfConditions = numTokens - 1;
+ }
+ }
+
+ /* eat the first two tokens from the header line */
+ headerTok.nextToken();
+ if (hasCOMMON) {
+ headerTok.nextToken();
+ }
+
+ /* the next numConds tokens are the condition names */
+ Vector cNames = new Vector(numberOfConditions);
+
+ for (int i = 0; i < numberOfConditions; i++)
+ cNames.add(headerTok.nextToken());
+
+ /*
+ * the next numConds tokens should duplicate the previous list of
+ * condition names
+ */
+ if (expectPvals) {
+ for (int i = 0; i < numberOfConditions; i++) {
+ String title = headerTok.nextToken();
+
+ if (!(title.equals(cNames.get(i)))) {
+ StringBuffer msg = new StringBuffer();
+ msg.append("Expecting both ratios and p-values.\n");
+ msg.append("Condition name mismatch in header line" + " of data file "
+ + filename + ": " + cNames.get(i) + " vs. " + title);
+ throw new IOException(msg.toString());
+ } // if !title
+ } // for i
+ } // if expectPvals
+
+ /* OK, we have a reasonable header; clobber all old information */
+ this.filename = filename;
+ this.numConds = numberOfConditions;
+ this.extraTokens = haveExtraTokens;
+ this.haveSigValues = expectPvals;
+ /* wipe old data */
+ initDataStructures();
+ /* store condition names */
+ condNames = cNames;
+
+ for (int i = 0; i < numConds; i++) {
+ condNameToIndex.put(condNames.get(i), new Integer(i));
+ }
+
+ /* parse rest of file line by line */
+ if (taskMonitor != null) {
+ taskMonitor.setStatus("Reading in Data...");
+ }
+
+ for (int ii = lineCount; ii < lines.length; ii++) {
+ if (taskMonitor != null) {
+ double percentComplete = ((double) ii / lines.length) * 100.0;
+ taskMonitor.setPercentCompleted((int) percentComplete);
+ }
+
+ parseOneLine(lines[ii], ii, expectPvals, mappingByKeyAttribute, attributeToId, hasCOMMON);
+ }
+
+ /* save numGenes and build hash of gene names to indices */
+ this.numGenes = geneNames.size();
+
+ for (int i = 0; i < geneNames.size(); i++) {
+ if (geneNames.get(i) != null) {
+ geneNameToIndex.put(geneNames.get(i), new Integer(i));
+ }
+ }
+
+ /* trim capacity of data structures for efficiency */
+ geneNames.trimToSize();
+ geneDescripts.trimToSize();
+ allMeasurements.trimToSize();
+
+ return true;
+ }
+
+ private Object getAttributeValue(byte type, String id, String att) {
+ if (type == CyAttributes.TYPE_INTEGER)
+ return Cytoscape.getNodeAttributes().getIntegerAttribute(id, att);
+ else if (type == CyAttributes.TYPE_FLOATING)
+ return Cytoscape.getNodeAttributes().getDoubleAttribute(id, att);
+ else if (type == CyAttributes.TYPE_BOOLEAN)
+ return Cytoscape.getNodeAttributes().getBooleanAttribute(id, att);
+ else if (type == CyAttributes.TYPE_STRING)
+ return Cytoscape.getNodeAttributes().getStringAttribute(id, att);
+ else if (type == CyAttributes.TYPE_SIMPLE_LIST)
+ return Cytoscape.getNodeAttributes().getListAttribute(id, att);
+ else if (type == CyAttributes.TYPE_SIMPLE_MAP)
+ return Cytoscape.getNodeAttributes().getMapAttribute(id, att);
+
+ return null;
+ }
+
+ private Hashtable getAttributeToIdList(String keyAttributeName) {
+ Hashtable attributeToIdList = new Hashtable();
+ List allNodes = Cytoscape.getCyNodesList();
+ byte attributeType = Cytoscape.getNodeAttributes().getType(keyAttributeName);
+
+ for (Iterator ii = allNodes.iterator(); ii.hasNext();) {
+ CyNode node = (CyNode) ii.next();
+ String nodeName = node.getIdentifier();
+ Object attrValue = getAttributeValue(attributeType, nodeName, keyAttributeName);
+
+ if (attrValue != null) {
+ String attributeValue = getAttributeValue(attributeType, nodeName, keyAttributeName)
+ .toString();
+
+ if (attributeValue != null) {
+ if (!attributeToIdList.contains(attributeValue)) {
+ ArrayList newGeneList = new ArrayList();
+ newGeneList.add(nodeName);
+ attributeToIdList.put(attributeValue, newGeneList);
+ } else {
+ ArrayList genesThisAttribute = (ArrayList) attributeToIdList.get(attributeValue);
+ genesThisAttribute.add(nodeName);
+ }
+ }
+ }
+ }
+
+ return (attributeToIdList);
+ }
+
+ // Check if the name of the second column is "COMMON" or "DESCRIPT"
+ private boolean doesHeaderLineHasCOMMON(String hline) {
+
+ StringTokenizer headerTok = new StringTokenizer(hline);
+
+ if (headerTok.countTokens() <2) {
+ return false;
+ }
+
+ headerTok.nextToken();
+ String secondColHeader = headerTok.nextToken();
+
+ if (secondColHeader.equalsIgnoreCase("COMMON")||secondColHeader.equalsIgnoreCase("DESCRIPT")) {
+ return true;
+ }
+ return false;
+ }
+
+
+ private boolean doesHeaderLineHaveDuplicates(String hline, boolean hasCOMMON) {
+ boolean retval = false;
+
+ StringTokenizer headerTok = new StringTokenizer(hline);
+ int numTokens = headerTok.countTokens();
+
+ int minTokens =2;
+ if (hasCOMMON) {
+ minTokens =3;
+ }
+ if (numTokens < minTokens) {
+ retval = false;
+ } else {
+ headerTok.nextToken();
+ if (hasCOMMON) {
+ headerTok.nextToken();
+ }
+
+ HashMap names = new HashMap();
+
+ while ((!retval) && headerTok.hasMoreTokens()) {
+ String title = headerTok.nextToken();
+ Object titleObject = (Object) title;
+
+ if (names.get(titleObject) == null) {
+ names.put(titleObject, titleObject);
+ } else {
+ retval = true;
+ }
+ }
+ }
+
+ return retval;
+ }
+
+ private boolean isHeaderLineNull(String hline, BufferedReader input, String filename)
+ throws IOException {
+ if (hline == null) {
+ throw new IOException("Could not read header line from data file: " + filename);
+ }
+
+ return false;
+ }
+
+ // added by iliana on 11.25.2002
+ // it is convenient for users to load their MTX files as they are
+ // the current code requires them to remove the first line
+ private boolean isHeaderLineMTXHeader(String hline) {
+ boolean b = false;
+ String pattern = "\t+RATIOS\t+LAMBDAS";
+ b = hline.matches(pattern);
+
+ return b;
+ }
+
+ private String readOneLine(BufferedReader f) {
+ String s = null;
+
+ try {
+ s = f.readLine();
+ } catch (IOException e) {
+ }
+
+ return s;
+ }
+
+ private void parseOneLine(String oneLine, int lineCount, boolean sig_vals,
+ boolean mappingByAttribute, Hashtable attributeToId, boolean hasCOMMON)
+ throws IOException {
+ //
+ // Step 1: divide the line into input tokens, and parse through
+ // the input tokens.
+ //
+ StringTokenizer strtok = new StringTokenizer(oneLine);
+ int numTokens = strtok.countTokens();
+
+ if (numTokens == 0) {
+ return;
+ }
+
+ /* first token is gene name (or identifying attribute), or NumSigGenes */
+ String firstToken = strtok.nextToken();
+
+ if (firstToken.startsWith("NumSigGenes")) {
+ return;
+ }
+
+ int numPreCols = 2; // Number of columns before data columns
+ if (!hasCOMMON) {
+ numPreCols = 1;
+ }
+ if ((sig_vals && (numTokens < ((2 * numConds) + numPreCols)))
+ || ((!sig_vals) && (numTokens < (numConds + numPreCols)))) {
+ throw new IOException("Warning: parse error on line " + lineCount + " tokens read: "
+ + numTokens);
+ }
+
+ String geneDescript = "";
+ if (hasCOMMON) {
+ geneDescript = strtok.nextToken();
+ }
+
+ String[] expData = new String[numConds];
+
+ for (int i = 0; i < numConds; i++) {
+ expData[i] = strtok.nextToken();
+ }
+
+ String[] sigData = new String[numConds];
+
+ if (sig_vals) {
+ for (int i = 0; i < numConds; i++) {
+ sigData[i] = strtok.nextToken();
+ }
+ } else {
+ for (int i = 0; i < numConds; i++) {
+ sigData[i] = expData[i];
+ }
+ }
+
+ ArrayList gNames = new ArrayList();
+
+ if (mappingByAttribute) {
+ if (attributeToId.containsKey(firstToken)) {
+ gNames = (ArrayList) attributeToId.get(firstToken);
+ }
+ } else {
+ gNames = new ArrayList();
+ gNames.add(firstToken);
+ }
+
+ for (int ii = 0; ii < gNames.size(); ii++) {
+ geneNames.add(gNames.get(ii));
+
+ /* store descriptor token */
+ geneDescripts.add(geneDescript);
+
+ Vector measurements = new Vector(numConds);
+
+ for (int jj = 0; jj < numConds; jj++) {
+ mRNAMeasurement m = new mRNAMeasurement(expData[jj], sigData[jj]);
+ measurements.add(m);
+
+ double ratio = m.getRatio();
+ double signif = m.getSignificance();
+
+ if (ratio < minExp) {
+ minExp = ratio;
+ }
+
+ if (ratio > maxExp) {
+ maxExp = ratio;
+ }
+
+ if (signif < minSig) {
+ minSig = signif;
+ }
+
+ if (signif > maxSig) {
+ maxSig = signif;
+
+ if ((this.significanceType != this.LAMBDA) && sig_vals && (maxSig > 1)) {
+ this.significanceType = this.LAMBDA;
+ }
+ }
+ }
+
+ if ((this.significanceType != this.LAMBDA) && sig_vals && (minSig > 0)) {
+ // We are probably not looking at lambdas, since no
+ // significance value was > 1
+ // and the header is not a LAMBDA header
+ this.significanceType = this.PVAL;
+ }
+
+ allMeasurements.add(measurements);
+ }
+ } // parseOneLine
+
+ /**
+ * Converts all lambdas to p-values. Lambdas are lost after this call.
+ */
+ public void convertLambdasToPvals() {
+ Iterator it = this.allMeasurements.iterator();
+
+ while (it.hasNext()) {
+ Vector v = (Vector) it.next();
+ Iterator it2 = v.iterator();
+
+ while (it2.hasNext()) {
+ mRNAMeasurement m = (mRNAMeasurement) it2.next();
+ double pval = ExpressionData.getPvalueFromLambda(m.getSignificance());
+ m.setSignificance(pval);
+ } // while it2
+ } // while it
+ } // convertPValsToLambdas
+
+ /**
+ * Gets a PValue of the specified lambda value.
+ *
+ * @return a very close approximation of the pvalue that corresponds to the
+ * given lambda value
+ */
+ static public double getPvalueFromLambda(double lambda) {
+ double x = StrictMath.sqrt(lambda) / 2.0;
+ double t = 1.0 / (1.0 + (0.3275911 * x));
+ double erfc = StrictMath.exp(-(x * x)) * ((0.254829592 * t)
+ + (-0.284496736 * StrictMath.pow(t, 2.0))
+ + (1.421413741 * StrictMath.pow(t, 3.0))
+ + (-1.453152027 * StrictMath.pow(t, 4.0))
+ + (1.061405429 * StrictMath.pow(t, 5.0)));
+ erfc = erfc / 2.0;
+
+ if ((erfc < 0) || (erfc > 1)) {
+ // P-value must be >= 0 and <= 1
+ throw new IllegalStateException("The calculated pvalue for lambda = " + lambda + " is "
+ + erfc);
+ }
+
+ return erfc;
+ } // getPvalueFromLambda
+
+ /**
+ * Gets the Significance Type.
+ *
+ * @return one of NONE, UNKNOWN, PVAL, LAMBDA
+ */
+ public int getSignificanceType() {
+ return this.significanceType;
+ }
+
+ /**
+ * Returns a text description of this data object.
+ *
+ * @return Text Decription of this Data Object.
+ */
+ public String getDescription() {
+ String lineSep = System.getProperty("line.separator");
+ StringBuffer sb = new StringBuffer();
+ File file = new File(filename);
+
+ sb.append("Data read from: " + file.getName() + lineSep);
+ sb.append(lineSep);
+ sb.append("Number of genes = " + getNumberOfGenes() + lineSep);
+ sb.append("Number of conditions = " + getNumberOfConditions() + lineSep);
+ sb.append("Significance values: ");
+
+ if (this.haveSigValues) {
+ sb.append("yes");
+ } else {
+ sb.append("no");
+ }
+
+ sb.append(lineSep).append(lineSep);
+ sb.append("MinExp: " + minExp + " MaxExp: " + maxExp + lineSep);
+
+ if (this.haveSigValues) {
+ sb.append("MinSig: " + minSig + " MaxSig: " + maxSig + lineSep);
+
+ String sigType = null;
+
+ if (this.significanceType == this.UNKNOWN) {
+ sigType = "unknown";
+ } else if (this.significanceType == this.LAMBDA) {
+ sigType = "lambda values";
+ } else if (this.significanceType == this.PVAL) {
+ sigType = "p-values";
+ } else if (this.significanceType == this.NONE) {
+ sigType = "none";
+ }
+
+ sb.append("Type of significance: " + sigType + lineSep);
+ }
+
+ return sb.toString();
+ }
+
+ /**
+ * Sets a List of Gene Names. This clobbers the old list of gene names, if
+ * it exists.
+ *
+ * @param newNames Vector of String Objects.
+ */
+ public void setGeneNames(Vector newNames) {
+ geneNames = newNames;
+ geneNameToIndex.clear();
+
+ for (int i = 0; i < geneNames.size(); i++) {
+ geneNameToIndex.put(geneNames.get(i), new Integer(i));
+ }
+ }
+
+ /**
+ * Gets an Array of GeneDescriptors.
+ *
+ * @return Array of String Objects.
+ */
+ public String[] getGeneDescriptors() {
+ return (String[]) geneDescripts.toArray(new String[0]);
+ }
+
+ /**
+ * Gets a Vector Gene Descriptors.
+ *
+ * @return Vector of String Objects.
+ */
+ public Vector getGeneDescriptorsVector() {
+ return geneDescripts;
+ }
+
+ /**
+ * Sets a List of Gene Descriptors. This clobbers the old list of gene
+ * descriptors, if it exists.
+ *
+ * @param newDescripts Vector of String Objects.
+ */
+ public void setGeneDescriptors(Vector newDescripts) {
+ geneDescripts = newDescripts;
+ }
+
+ /**
+ * Gets an Array of All Experimental Conditions.
+ *
+ * @return Array of String Objects.
+ */
+ public String[] getConditionNames() {
+ return (String[]) condNames.toArray(new String[0]);
+ }
+
+ /**
+ * Gets the index value of the specified experimenal conditon.
+ *
+ * @param condition Name of experimental condition.
+ * @return index value of the specified experimenal conditon.
+ */
+ public int getConditionIndex(String condition) {
+ return ((Integer) this.condNameToIndex.get(condition)).intValue();
+ }
+
+ /**
+ * Gets the Gene Descriptor for the specified gene.
+ *
+ * @param gene Gene Name.
+ * @return Gene Descriptor String.
+ */
+ public String getGeneDescriptor(String gene) {
+ Integer geneIndex = (Integer) geneNameToIndex.get(gene);
+
+ if (geneIndex == null) {
+ return null;
+ }
+
+ return (String) geneDescripts.get(geneIndex.intValue());
+ }
+
+ /**
+ * Indicates whether the expression data has significance values.
+ *
+ * @return true or false.
+ */
+ public boolean hasSignificanceValues() {
+ return haveSigValues;
+ }
+
+ /**
+ * Gets all Measurements.
+ *
+ * @return A Vector of Vectors. The embedded Vector contains mRNAMeasurement
+ * Objects.
+ */
+ public Vector getAllMeasurements() {
+ return allMeasurements;
+ }
+
+ /**
+ * Gets a List of All Gene Names. Same as getGeneNamesVector(), except this
+ * method returns an Array of String Objects.
+ *
+ * @return Array of Strings.
+ */
+ public String[] getGeneNames() {
+ return (String[]) geneNames.toArray(new String[0]);
+ }
+
+ /**
+ * Gets a List of All Gene Names. Same as getGeneNames(), except this method
+ * returns a Vector of String Objects.
+ *
+ * @return Vector of String Objects.
+ */
+ public Vector getGeneNamesVector() {
+ return geneNames;
+ }
+
+ /**
+ * Gets Total Number of Experimental Conditions. This corresponds to the
+ * number of condition columns in the original expression data file.
+ *
+ * @return total number of experimental conditions.
+ */
+ public int getNumberOfConditions() {
+ return numConds;
+ }
+
+ /**
+ * Gets Total Number of Genes. This corresponds to the number of rows of
+ * data in the original expression data file.
+ *
+ * @return total number of genes.
+ */
+ public int getNumberOfGenes() {
+ return numGenes;
+ }
+
+ /**
+ * Returns a 2D Matrix of Extreme Values. The matrix is set to the
+ * following:
+ * <p/>
+ * <PRE>
+ * <p/>
+ * maxVals[0][0] = minExp; maxVals[0][1] = maxExp; maxVals[1][0] = minSig;
+ * maxVals[0][1] = maxSig;
+ * <p/>
+ * </PRE>
+ *
+ * @return a 2D Matrix of double values.
+ */
+ public double[][] getExtremeValues() {
+ double[][] maxVals = new double[2][2];
+ maxVals[0][0] = minExp;
+ maxVals[0][1] = maxExp;
+ maxVals[1][0] = minSig;
+ maxVals[1][1] = maxSig;
+
+ return maxVals;
+ }
+
+ /**
+ * Gets a Vector of all Measurements associated with the specified gene.
+ *
+ * @param gene Gene Name.
+ * @return Vector of mRNAMeasurement Objects.
+ */
+ public Vector getMeasurements(String gene) {
+ if (gene == null) {
+ return null;
+ }
+
+ Integer geneIndex = (Integer) geneNameToIndex.get(gene);
+
+ if (geneIndex == null) {
+ return null;
+ }
+
+ Vector measurements = (Vector) (this.getAllMeasurements().get(geneIndex.intValue()));
+
+ return measurements;
+ }
+
+ /**
+ * Gets Single Measurement Value for the specified gene at the specified
+ * condition.
+ *
+ * @param gene Gene Name.
+ * @param condition Condition Name (corresponds to column heading in original
+ * expression data file.)
+ * @return an mRNAMeasurement Object.
+ */
+ public mRNAMeasurement getMeasurement(String gene, String condition) {
+ Integer condIndex = (Integer) condNameToIndex.get(condition);
+
+ if (condIndex == null) {
+ return null;
+ }
+
+ Vector measurements = this.getMeasurements(gene);
+
+ if (measurements == null) {
+ return null;
+ }
+
+ mRNAMeasurement returnVal = (mRNAMeasurement) measurements.get(condIndex.intValue());
+
+ return returnVal;
+ }
+
+ /**
+ * Copies ExpressionData data structure into CyAttributes data structure.
+ *
+ * @param nodeAttribs Node Attributes Object.
+ * @param taskMonitor Task Monitor. Can be null.
+ */
+ public void copyToAttribs(CyAttributes nodeAttribs, TaskMonitor taskMonitor) {
+ String[] condNames = getConditionNames();
+
+ for (int condNum = 0; condNum < condNames.length; condNum++) {
+ String condName = condNames[condNum];
+ String eStr = condName + "exp";
+ String sStr = condName + "sig";
+
+ for (int i = 0; i < geneNames.size(); i++) {
+ String canName = (String) geneNames.get(i);
+
+ mRNAMeasurement mm = getMeasurement(canName, condName);
+
+ if (mm != null) {
+ nodeAttribs.setAttribute(canName, eStr, new Double(mm.getRatio()));
+ nodeAttribs.setAttribute(canName, sStr, new Double(mm.getSignificance()));
+ }
+
+ // Report on Progress to the Task Monitor.
+ if (taskMonitor != null) {
+ int currentCoordinate = (condNum * geneNames.size()) + i;
+ int matrixSize = condNames.length * geneNames.size();
+ double percent = ((double) currentCoordinate / matrixSize) * 100.0;
+ taskMonitor.setPercentCompleted((int) percent);
+ }
+ }
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/data/ImportHandler.java b/application/src/main/java/cytoscape/data/ImportHandler.java
new file mode 100644
index 0000000..6393d24
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/ImportHandler.java
@@ -0,0 +1,531 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data;
+
+import cytoscape.data.readers.GraphReader;
+
+import cytoscape.logger.CyLogger;
+
+import cytoscape.task.TaskMonitor;
+
+import cytoscape.task.ui.JTask;
+
+import cytoscape.util.CyFileFilter;
+import cytoscape.util.GMLFileFilter;
+import cytoscape.util.NNFFileFilter;
+import cytoscape.util.ProxyHandler;
+import cytoscape.util.SIFFileFilter;
+import cytoscape.util.XGMMLFileFilter;
+
+import java.io.BufferedReader;
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.InputStreamReader;
+
+import java.net.Proxy;
+import java.net.URL;
+import java.net.URLConnection;
+
+import java.util.*;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+
+/**
+ * Central registry for all Cytoscape import classes.
+ *
+ * @author Cytoscape Development Team.
+ */
+public class ImportHandler {
+ /**
+ * Filter Type: NETWORK.
+ */
+ public static String GRAPH_NATURE = "NETWORK";
+
+ /**
+ * Filter Type: NODE.
+ */
+ public static String NODE_NATURE = "NODE";
+
+ /**
+ * Filter Type: EDGE.
+ */
+ public static String EDGE_NATURE = "EDGE";
+
+ /**
+ * Filer Type: PROPERTIES.
+ */
+ public static String PROPERTIES_NATURE = "PROPERTIES";
+
+ /**
+ * Set of all registered CyFileFilter Objects.
+ */
+ protected static Set<CyFileFilter> cyFileFilters = new HashSet<CyFileFilter>();
+
+ /**
+ * Constructor.
+ */
+ public ImportHandler() {
+ // By default, register SIF, XGMML, NNF, and GML File Filters
+ init();
+ }
+
+ /**
+ * Initialize ImportHandler.
+ */
+ private void init() {
+ addFilter(new SIFFileFilter());
+ addFilter(new XGMMLFileFilter());
+ addFilter(new GMLFileFilter());
+ addFilter(new NNFFileFilter());
+ }
+
+ /**
+ * Registers a new CyFileFilter.
+ *
+ * @param cff CyFileFilter.
+ * @return true indicates filter was added successfully.
+ */
+ public boolean addFilter(CyFileFilter cff) {
+ Set check = cff.getExtensionSet();
+
+ for (Iterator it = check.iterator(); it.hasNext();) {
+ String extension = (String) it.next();
+
+ if (getAllExtensions().contains(extension) && !extension.equals("xml")) {
+ return false;
+ }
+ }
+
+ cyFileFilters.add(cff);
+
+ return true;
+ }
+
+ /**
+ * Registers an Array of CyFileFilter Objects.
+ *
+ * @param cff Array of CyFileFilter Objects.
+ * @return true indicates all filters were added successfully.
+ */
+ public boolean addFilter(CyFileFilter[] cff) {
+ //first check if suffixes are unique
+ boolean flag = true;
+
+ for (int j = 0; (j < cff.length) && (flag == true); j++) {
+ flag = addFilter(cff[j]);
+ }
+
+ return flag;
+ }
+
+ /**
+ * Gets the GraphReader that is capable of reading the specified file.
+ *
+ * @param fileName File name or null if no reader is capable of reading the file.
+ * @return GraphReader capable of reading the specified file.
+ */
+ public GraphReader getReader(String fileName) {
+ // check if fileType is available
+ for (CyFileFilter cff : cyFileFilters) {
+ if (cff.accept(fileName))
+ return cff.getReader(fileName);
+ }
+ return null;
+ }
+
+ /**
+ * Gets the GraphReader that is capable of reading URL.
+ *
+ * @param url -- the URL string
+ * @return GraphReader capable of reading the specified URL.
+ */
+ public GraphReader getReader(URL url) {
+ // check if fileType is available
+
+ // Open up the connection
+ Proxy pProxyServer = ProxyHandler.getProxyServer();
+ URLConnection conn = null;
+
+ try {
+ if (pProxyServer == null)
+ conn = url.openConnection();
+ else
+ conn = url.openConnection(pProxyServer);
+ } catch (IOException ioe) {
+ CyLogger.getLogger().error("Unable to open " + url + ": " + ioe.getMessage(), ioe);
+
+ return null;
+ }
+
+ // Ensure we are reading the real content from url,
+ // and not some out-of-date cached content:
+ conn.setUseCaches(false);
+
+ // Get the content-type
+ String contentType = conn.getContentType();
+
+ if (contentType == null)
+ contentType = "";
+
+ // CyLogger.getLogger().info("Content-type: "+contentType);
+ int cend = contentType.indexOf(';');
+
+ if (cend >= 0)
+ contentType = contentType.substring(0, cend);
+
+ for (CyFileFilter cff: cyFileFilters) {
+ final boolean accept = cff.accept(url, contentType);
+ if (accept) {
+ // CyLogger.getLogger().info("Found reader: "+cff.getDescription());
+ final GraphReader reader = cff.getReader(url, conn);
+
+ // Does the reader support the url,connection constructor?
+ if (reader != null) {
+ // Yes, return it
+ return reader;
+ }
+
+ // No, see if we can find another one that does
+ }
+ }
+
+ // If the content type is text/plain or text/html or text/xml
+ // then write a temp file and handle things that way
+ if (contentType.contains("text/html") || contentType.contains("text/plain")
+ || contentType.contains("text/xml") || contentType.contains("application/rdf+xml")) {
+ File tmpFile = null;
+
+ try {
+ tmpFile = downloadFromURL(url, null);
+ } catch (Exception e) {
+ CyLogger.getLogger().error("Failed to download from URL: " + url, e);
+ }
+
+ if (tmpFile != null) {
+ return getReader(tmpFile.getAbsolutePath());
+ }
+ }
+
+ return null;
+ }
+
+ /**
+ * Gets descriptions for all registered filters, which are of the type: fileNature.
+ *
+ * @param fileNature type: GRAPH_NATURE, NODE_NATURE, EDGE_NATURE, etc.
+ * @return Collection of String descriptions, e.g. "XGMML files"
+ */
+ public Collection getAllTypes(String fileNature) {
+ Collection ans = new HashSet();
+ CyFileFilter cff;
+
+ for (Iterator it = cyFileFilters.iterator(); it.hasNext();) {
+ cff = (CyFileFilter) it.next();
+
+ //if statement to check if nature equals fileNature
+ if (cff.getFileNature().equals(fileNature)) {
+ cff.setExtensionListInDescription(false);
+ ans.add(cff.getDescription());
+ cff.setExtensionListInDescription(true);
+ }
+ }
+
+ return ans;
+ }
+
+ /**
+ * Gets a collection of all registered file extensions.
+ *
+ * @return Collection of Strings, e.g. "xgmml", "sif", etc.
+ */
+ public Collection getAllExtensions() {
+ Collection ans = new HashSet();
+
+ for (Iterator it = cyFileFilters.iterator(); it.hasNext();) {
+ ans.addAll(((CyFileFilter) (it.next())).getExtensionSet());
+ }
+
+ return ans;
+ }
+
+ /**
+ * Gets a collection of all registered filter descriptions.
+ * Descriptions are of the form: "{File Description} ({file extensions})".
+ * For example: "GML files (*.gml)"
+ *
+ * @return Collection of Strings, e.g. "GML files (*.gml)", etc.
+ */
+ public Collection getAllDescriptions() {
+ Collection ans = new HashSet();
+
+ for (Iterator it = cyFileFilters.iterator(); it.hasNext();) {
+ ans.add(((CyFileFilter) it.next()).getDescription());
+ }
+
+ return ans;
+ }
+
+ /**
+ * Gets the name of the filter which is capable of reading the specified file.
+ *
+ * @param fileName File Name.
+ * @return name of filter capable of reading the specified file.
+ */
+ public String getFileType(String fileName) {
+ CyFileFilter cff;
+ String ans = null;
+
+ for (Iterator it = cyFileFilters.iterator(); it.hasNext();) {
+ cff = (CyFileFilter) it.next();
+
+ if (cff.accept(fileName)) {
+ cff.setExtensionListInDescription(false);
+ ans = (cff.getDescription());
+ cff.setExtensionListInDescription(true);
+ }
+ }
+
+ return ans;
+ }
+
+ /**
+ * Gets a list of all registered filters plus a catch-all super set filter.
+ *
+ * @return List of CyFileFilter Objects.
+ */
+ public List getAllFilters() {
+ List ans = new ArrayList();
+
+ for (Iterator it = cyFileFilters.iterator(); it.hasNext();) {
+ ans.add((CyFileFilter) it.next());
+ }
+
+ if (ans.size() > 1) {
+ String[] allTypes = concatAllExtensions(ans);
+ ans.add(new CyFileFilter(allTypes, "All Natures"));
+ }
+
+ return ans;
+ }
+
+ /**
+ * Gets a list of all registered filters, which are of type: fileNature,
+ * plus a catch-all super set filter.
+ *
+ * @param fileNature type: GRAPH_NATURE, NODE_NATURE, EDGE_NATURE, etc.
+ * @return List of CyFileFilter Objects.
+ */
+ public List getAllFilters(String fileNature) {
+ List ans = new ArrayList();
+ CyFileFilter cff;
+
+ for (Iterator it = cyFileFilters.iterator(); it.hasNext();) {
+ cff = (CyFileFilter) it.next();
+
+ //if statement to check if nature equals fileNature
+ if (cff.getFileNature().equals(fileNature)) {
+ ans.add(cff);
+ }
+ }
+
+ if (ans.size() > 1) {
+ String[] allTypes = concatAllExtensions(ans);
+ ans.add(new CyFileFilter(allTypes, "All " + fileNature.toLowerCase() + " files",
+ fileNature));
+ }
+
+ return ans;
+ }
+
+ /**
+ * Unregisters all registered File Filters (except default file filters.)
+ * Resets everything with a clean slate.
+ */
+ public void resetImportHandler() {
+ cyFileFilters = new HashSet();
+ init();
+ }
+
+ /**
+ * Creates a String array of all extensions
+ */
+ private String[] concatAllExtensions(List cffs) {
+ Set ans = new HashSet();
+
+ for (Iterator it = cffs.iterator(); it.hasNext();) {
+ ans.addAll(((CyFileFilter) (it.next())).getExtensionSet());
+ }
+
+ String[] stringAns = (String[]) ans.toArray(new String[0]);
+
+ return stringAns;
+ }
+
+ private String extractExtensionFromContentType(String ct) {
+ Pattern p = Pattern.compile("^\\w+/([\\w|-]+);*.*");
+ Matcher m = p.matcher(ct);
+
+ if (m.matches())
+ return m.group(1);
+ else
+
+ return "txt";
+ }
+
+ // Create a temp file for URL download
+ private File createTempFile(URLConnection conn, URL url) throws IOException {
+ File tmpFile = null;
+ String tmpDir = System.getProperty("java.io.tmpdir");
+ String pURLstr = url.toString();
+
+ // Try if we can determine the network type from URLstr
+ // test the URL against the various file extensions,
+ // if one matches, then extract the basename
+ Collection theExts = getAllExtensions();
+
+ for (Iterator it = theExts.iterator(); it.hasNext();) {
+ String theExt = (String) it.next();
+
+ if (pURLstr.endsWith(theExt)) {
+ tmpFile = new File(tmpDir + System.getProperty("file.separator")
+ + pURLstr.substring(pURLstr.lastIndexOf("/") + 1));
+
+ break;
+ }
+ }
+
+ // if none of the extensions match, then use the the content type as
+ // a suffix and create a temp file.
+ if (tmpFile == null) {
+ String contentType = conn.getContentType();
+ if (contentType == null) contentType = "";
+ String ct = "." + extractExtensionFromContentType(contentType);
+ tmpFile = File.createTempFile("url.download.", ct, new File(tmpDir));
+ }
+
+ if (tmpFile == null)
+ return null;
+ else
+ tmpFile.deleteOnExit();
+
+ return tmpFile;
+ }
+
+ /**
+ * Download a temporary file from the given URL. The file will be saved in the
+ * temporary directory and will be deleted after Cytoscape exits.
+ * @param u -- the URL string, TaskMonitor if any
+ * @return -- a temporary file downloaded from the given URL.
+ */
+ public File downloadFromURL(URL url, TaskMonitor taskMonitor)
+ throws IOException, FileNotFoundException {
+ Proxy pProxyServer = ProxyHandler.getProxyServer();
+ URLConnection conn = null;
+
+ if (pProxyServer == null)
+ conn = url.openConnection();
+ else
+ conn = url.openConnection(pProxyServer);
+
+ // Ensure we are reading the real content from url,
+ // and not some out-of-date cached content:
+ conn.setUseCaches(false);
+
+ // create the temp file
+ File tmpFile = createTempFile(conn, url);
+
+ // This is needed for the progress monitor
+ int maxCount = conn.getContentLength(); // -1 if unknown
+ int progressCount = 0;
+
+ // now write the temp file
+ BufferedWriter out = null;
+ BufferedReader in = null;
+
+ out = new BufferedWriter(new FileWriter(tmpFile));
+ try {
+ in = new BufferedReader(new InputStreamReader(conn.getInputStream()));
+ try {
+ String inputLine = null;
+ double percent = 0.0d;
+
+ while ((inputLine = in.readLine()) != null) {
+ // Guard against leading blank lines...
+ if (progressCount == 0 && inputLine.length() == 0) continue;
+ progressCount += inputLine.length();
+
+ // Report on Progress
+ if (taskMonitor != null) {
+ percent = ((double) progressCount / maxCount) * 100.0;
+
+ if (maxCount == -1) { // file size unknown
+ percent = -1;
+ }
+
+ JTask jTask = (JTask) taskMonitor;
+
+ if (jTask.haltRequested()) { //abort
+ tmpFile = null;
+ taskMonitor.setStatus("Canceling the download task ...");
+ taskMonitor.setPercentCompleted(100);
+
+ break;
+ }
+
+ taskMonitor.setPercentCompleted((int) percent);
+ }
+ out.write(inputLine);
+ out.newLine();
+ }
+ }
+ finally {
+ if (in != null) {
+ in.close();
+ }
+ }
+ }
+ finally {
+ if (out != null) {
+ out.close();
+ }
+ }
+
+ return tmpFile;
+ } // End of downloadFromURL()
+}
diff --git a/application/src/main/java/cytoscape/data/Interaction.java b/application/src/main/java/cytoscape/data/Interaction.java
new file mode 100644
index 0000000..16314ff
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/Interaction.java
@@ -0,0 +1,155 @@
+/*
+ File: Interaction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.StringTokenizer;
+
+
+/**
+ * Interaction.java: protein-protein or protein-DNA: parse text file, encapsulate
+ */
+public class Interaction {
+ private String source;
+ private List<String> targets = new ArrayList<String>();
+ private String interactionType;
+
+ /**
+ * Creates a new Interaction object.
+ *
+ * @param source DOCUMENT ME!
+ * @param target DOCUMENT ME!
+ * @param interactionType DOCUMENT ME!
+ */
+ public Interaction(final String source, final String target, final String interactionType) {
+ this.source = source;
+ this.interactionType = interactionType;
+ this.targets.add(target);
+ } // ctor (3 args)
+
+ /**
+ * Creates a new Interaction object.
+ *
+ * @param rawText DOCUMENT ME!
+ */
+ public Interaction(String rawText) {
+ this(rawText, " ");
+ }
+
+ /**
+ * Creates a new Interaction object.
+ *
+ * @param rawText DOCUMENT ME!
+ * @param delimiter DOCUMENT ME!
+ */
+ public Interaction(String rawText, String delimiter) {
+ final StringTokenizer strtok = new StringTokenizer(rawText, delimiter);
+ int counter = 0;
+
+ while (strtok.hasMoreTokens()) {
+ if (counter == 0)
+ source = strtok.nextToken().trim();
+ else if (counter == 1)
+ interactionType = strtok.nextToken().trim();
+ else {
+ targets.add(strtok.nextToken().trim());
+ }
+
+ counter++;
+ }
+ } // ctor (String)
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getSource() {
+ return source;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getType() {
+ return interactionType;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int numberOfTargets() {
+ return targets.size();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String[] getTargets() {
+ return targets.toArray(new String[0]);
+ } // getTargets
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String toString() {
+ final StringBuilder sb = new StringBuilder();
+ sb.append(interactionType);
+ sb.append("::");
+ sb.append(source);
+ sb.append("::");
+
+ final int targetSize = targets.size();
+ for (int i = 0; i < targetSize; i++) {
+ sb.append(targets.get(i));
+
+ if (i < (targetSize - 1))
+ sb.append(",");
+ }
+
+ return sb.toString();
+ }
+} // Interaction
diff --git a/application/src/main/java/cytoscape/data/NetworkData.java b/application/src/main/java/cytoscape/data/NetworkData.java
new file mode 100755
index 0000000..c3752cd
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/NetworkData.java
@@ -0,0 +1,834 @@
+/*
+ File: NetworkData.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data;
+
+import cern.colt.list.*;
+
+// colt import
+import cern.colt.map.*;
+
+// tclib import
+import com.sosnoski.util.hashmap.*;
+
+// cytoscape import
+import cytoscape.*;
+import cytoscape.logger.CyLogger;
+
+// giny import
+import giny.model.*;
+
+// java import
+import java.util.*;
+
+import javax.swing.event.SwingPropertyChangeSupport;
+
+
+/**
+ * There is an event fired anytime that a value is modified, you need to be listener to the attribute name though.
+ */
+public abstract class NetworkData {
+ /**
+ *
+ */
+ public static String NODE_ATTRIBUTE_ADDED = "NODE_ATTRIBUTE_ADDED";
+
+ /**
+ *
+ */
+ public static String NODE_ATTRIBUTE_REMOVED = "NODE_ATTRIBUTE_REMOVED";
+
+ /**
+ *
+ */
+ public static String EDGE_ATTRIBUTE_ADDED = "EDGE_ATTRIBUTE_ADDED";
+
+ /**
+ *
+ */
+ public static String EDGE_ATTRIBUTE_REMOVED = "EDGE_ATTRIBUTE_REMOVED";
+
+ /**
+ *
+ */
+ public static int DOUBLE_TYPE = 0;
+
+ /**
+ *
+ */
+ public static int STRING_TYPE = 1;
+
+ /**
+ *
+ */
+ public static int OBJECT_TYPE = 2;
+
+ /**
+ *
+ */
+ public static int NO_SUCH_ATTRIBUTE = -1;
+
+ /**
+ *
+ */
+ public static int VALUE_NOT_A_DOUBLE = -2;
+
+ /**
+ *
+ */
+ public static int INSANE_ATTRIBUTE_TYPE = -4;
+
+ /**
+ *
+ */
+ public static int WRONG_ATTRIBUTE_TYPE = -8;
+
+ /**
+ *
+ */
+ public static int INSANE_ATTRIBUTE_ID = -16;
+
+ /**
+ *
+ */
+ public static int ATTRIBUTE_ALREADY_ASSIGNED = -32;
+ protected static Object pcsO = new Object();
+ private static SwingPropertyChangeSupport pcs = new SwingPropertyChangeSupport(pcsO);
+
+ //////////////////////////////
+ // Node Data Structures
+
+ /**
+ * Each Entry is also an IntObject Map, so that each attribute has itrs own entry,
+ * and each node has its own entry within each attribute.
+ */
+ private static OpenIntObjectHashMap nodeAttributeIDToAttributeValuesMap;
+
+ /**
+ * Keeps track of the map between an Attribute ID ( which is also
+ * the key for accessing the value of an attribute for a node).
+ */
+ private static StringIntHashMap nodeAttNameToAttIDMap;
+
+ /**
+ * reverse lookup of the attribute name for a given int.
+ */
+ private static OpenIntObjectHashMap nodeAttIDToAttNameMap;
+
+ /**
+ * Look up of attribute id to Data Type
+ */
+ private static OpenIntIntHashMap nodeAttIDToAttTypeMap;
+ private static OpenIntDoubleHashMap nodeAttIDToMinMap;
+ private static OpenIntDoubleHashMap nodeAttIDToMaxMap;
+ private static OpenIntDoubleHashMap nodeAttIDToMeanMap;
+ private static OpenIntDoubleHashMap nodeAttIDToMedianMap;
+ private static OpenIntDoubleHashMap nodeAttIDLastUpdate;
+
+ /**
+ * The functionality of this Map is largely replaceable by a BioDataServer,
+ * so this look-up will only be used when a BioDataServer is unavalible, or
+ * does not contain an alias.
+ */
+ private static StringIntHashMap nodeAliasToIDMap;
+
+ /**
+ * Each attribute is an int > 1.
+ */
+ private static int nodeAttributeCount = 1;
+
+ //////////////////////////////
+ // node data access methods
+
+ /**
+ * Attempts to add a new Attribute name, of Object type for nodes.
+ * @param attribute_name the name of the new attribute
+ * @return the ID of the attribute, if assinged, or -1 if already assigned/not a good name.
+ */
+ public static int addNodeAttribute(String attribute_name) {
+ return addNodeAttribute(attribute_name, OBJECT_TYPE);
+ }
+
+ /**
+ * Attempts to add a new Attribute name, of given type for nodes.
+ * Available types are: OBJECT_TYPE, DOUBLE_TYPE, and STRING_TYPE
+ * @param attribute_name the name of the new attribute
+ * @return the ID of the attribute, if assinged, or -1 if already assigned/not a good name.
+ */
+ public static int addNodeAttribute(String attribute_name, int attribute_type) {
+ StringIntHashMap a2id = getNodeAttNameToAttIDMap();
+
+ // return if already contained
+ if (a2id.containsKey(attribute_name)) {
+ return ATTRIBUTE_ALREADY_ASSIGNED;
+ }
+
+ // return if type is invalid
+ if ((attribute_type != OBJECT_TYPE) && (attribute_type != DOUBLE_TYPE)
+ && (attribute_type != STRING_TYPE)) {
+ return INSANE_ATTRIBUTE_TYPE;
+ }
+
+ // associate the attribute name with its id
+ int id = nodeAttributeCount++;
+ a2id.add(attribute_name, id);
+
+ // associate the id with the name
+ OpenIntObjectHashMap id2a = getNodeAttIDToAttNameMap();
+ id2a.put(id, attribute_name);
+
+ // associate the id with the type
+ OpenIntIntHashMap id2t = getNodeAttIDToAttTypeMap();
+ id2t.put(id, attribute_type);
+
+ // create the attribute map
+ OpenIntObjectHashMap a2v = getNodeAttributeIDToAttributeValuesMap();
+
+ if (attribute_type == DOUBLE_TYPE) {
+ // for doubles, put make the double hash map
+ OpenIntDoubleHashMap double_map = new OpenIntDoubleHashMap();
+ a2v.put(id, double_map);
+ } else if (attribute_type == STRING_TYPE) {
+ // for strings, make a string hash map
+ IntStringHashMap string_map = new IntStringHashMap();
+ a2v.put(id, string_map);
+ } else {
+ OpenIntObjectHashMap object_map = new OpenIntObjectHashMap();
+ a2v.put(id, object_map);
+ }
+
+ // everything should be normal, return the attribute id
+ return id;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param attribute DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static int getNodeAttributeType(String attribute) {
+ int att_id = getNodeAttNameToAttIDMap().get(attribute);
+
+ if (att_id == StringIntHashMap.DEFAULT_NOT_FOUND)
+ return NO_SUCH_ATTRIBUTE;
+
+ return getNodeAttIDToAttTypeMap().get(att_id);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param attribute DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static int getNodeAttributeID(String attribute) {
+ int att_id = getNodeAttNameToAttIDMap().get(attribute);
+
+ if (att_id == StringIntHashMap.DEFAULT_NOT_FOUND)
+ return NO_SUCH_ATTRIBUTE;
+
+ return att_id;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ * @param attribute DOCUMENT ME!
+ * @param value DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static int setNodeAttributeValue(Node node, String attribute, Object value) {
+ // todo: some sort of sanity check?
+ int node_index = node.getRootGraphIndex();
+
+ // make sure the attribute exists, if not, create it.
+ int att_id = getNodeAttNameToAttIDMap().get(attribute);
+
+ if (att_id == StringIntHashMap.DEFAULT_NOT_FOUND)
+ att_id = addNodeAttribute(attribute, OBJECT_TYPE);
+
+ return setNodeAttributeObjectValue(node_index, att_id, value);
+ }
+
+ /**
+ * Attempts to set the value for a node, for a given attribute. However, there a few checks that happen along the way. First the Node must be part of the CytoscapeRootGraph, also the value must match the attribute type, which must match the overall attribute type. No problem if the attribute is not initialized, but if has been initialized, and the types don't match, then you have a problem.
+ * @param node the node who should be part of Cytoscape
+ * @param attribute the name of this attribute
+ * @param value the value, which must match the attribute type
+ * @param attribute_type if this attribute has been previosly initialized, then this musht match that type. Otherwise the attribute will get initialized with this type.
+ * @return "1" or a positive value if all went well, otherwise a negative value that corresponds to the error. See the "throws" keeping in mind that these are not really exceptions...
+ * @throws {@link VALUE_NOT_A_DOUBLE} if the attribute_type was double and the value could be put into a Double.
+ * @throws {@link INSANE_ATTRIBUTE_TYPE} if the given attribute_type is not a supported one
+ * @throws {@link WRONG_ATTRIBUTE_TYPE} if the given attribute_type does not match the attribute_type of the attribute
+ * @throws {@link INSANE_ATTRIBUTE_ID} if the attribute does not exist
+ */
+ public static int setNodeAttributeValue(Node node, String attribute, Object value,
+ int attribute_type) {
+ // todo: some sort of sanity check?
+ int node_index = node.getRootGraphIndex();
+
+ // make sure the attribute exists, if not, create it.
+ int att_id = getNodeAttNameToAttIDMap().get(attribute);
+
+ if (att_id == StringIntHashMap.DEFAULT_NOT_FOUND) {
+ att_id = addNodeAttribute(attribute, attribute_type);
+ }
+
+ if (attribute_type == OBJECT_TYPE) {
+ return setNodeAttributeObjectValue(node_index, att_id, value);
+ } else if (attribute_type == DOUBLE_TYPE) {
+ Double dub = null;
+
+ if (value instanceof Double) {
+ dub = (Double) value;
+ } else if (value instanceof String) {
+ try {
+ dub = new Double((String) value);
+ } catch (NumberFormatException nfe) {
+ return VALUE_NOT_A_DOUBLE;
+ }
+ }
+
+ if (dub == null) {
+ return VALUE_NOT_A_DOUBLE;
+ } else {
+ return setNodeAttributeDoubleValue(node_index, att_id, dub.doubleValue());
+ }
+ } else if (attribute_type == STRING_TYPE) {
+ return setNodeAttributeStringValue(node_index, att_id, value.toString());
+ }
+
+ return INSANE_ATTRIBUTE_TYPE;
+ }
+
+ // node object set methods
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node_index DOCUMENT ME!
+ * @param attribute DOCUMENT ME!
+ * @param value DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static int setNodeAttributeObjectValue(int node_index, String attribute, Object value) {
+ // make sure the attribute exists, if not, create it.
+ int att_id = getNodeAttNameToAttIDMap().get(attribute);
+
+ if (att_id == StringIntHashMap.DEFAULT_NOT_FOUND)
+ att_id = addNodeAttribute(attribute, OBJECT_TYPE);
+
+ return setNodeAttributeObjectValue(node_index, att_id, value);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ * @param attribute DOCUMENT ME!
+ * @param value DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static int setNodeAttributeObjectValue(Node node, String attribute, Object value) {
+ // todo: some sort of sanity check?
+ int node_index = node.getRootGraphIndex();
+
+ // make sure the attribute exists, if not, create it.
+ int att_id = getNodeAttNameToAttIDMap().get(attribute);
+
+ if (att_id == StringIntHashMap.DEFAULT_NOT_FOUND)
+ att_id = addNodeAttribute(attribute, OBJECT_TYPE);
+
+ return setNodeAttributeObjectValue(node_index, att_id, value);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node_index DOCUMENT ME!
+ * @param att_id DOCUMENT ME!
+ * @param value DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static int setNodeAttributeObjectValue(int node_index, int att_id, Object value) {
+ // return if higher than the number of attributes
+ if (att_id > nodeAttributeCount)
+ return INSANE_ATTRIBUTE_ID;
+
+ // make sure that the attribute type is correct
+ if (getNodeAttIDToAttTypeMap().get(att_id) != OBJECT_TYPE)
+ return WRONG_ATTRIBUTE_TYPE;
+
+ OpenIntObjectHashMap object_map = (OpenIntObjectHashMap) getNodeAttributeIDToAttributeValuesMap()
+ .get(att_id);
+
+ object_map.put(node_index, value);
+
+ return 1;
+ }
+
+ // node double set methods
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node_index DOCUMENT ME!
+ * @param attribute DOCUMENT ME!
+ * @param value DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static int setNodeAttributeDoubleValue(int node_index, String attribute, double value) {
+ // make sure the attribute exists, if not, create it.
+ int att_id = getNodeAttNameToAttIDMap().get(attribute);
+
+ if (att_id == StringIntHashMap.DEFAULT_NOT_FOUND)
+ att_id = addNodeAttribute(attribute, DOUBLE_TYPE);
+
+ return setNodeAttributeDoubleValue(node_index, att_id, value);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ * @param attribute DOCUMENT ME!
+ * @param value DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static int setNodeAttributeDoubleValue(Node node, String attribute, double value) {
+ // todo: some sort of sanity check?
+ int node_index = node.getRootGraphIndex();
+
+ // make sure the attribute exists, if not, create it.
+ int att_id = getNodeAttNameToAttIDMap().get(attribute);
+
+ if (att_id == StringIntHashMap.DEFAULT_NOT_FOUND)
+ att_id = addNodeAttribute(attribute, DOUBLE_TYPE);
+
+ return setNodeAttributeDoubleValue(node_index, att_id, value);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node_index DOCUMENT ME!
+ * @param att_id DOCUMENT ME!
+ * @param value DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static int setNodeAttributeDoubleValue(int node_index, int att_id, double value) {
+ // return if higher than the number of attributes
+ if (att_id > nodeAttributeCount)
+ return INSANE_ATTRIBUTE_ID;
+
+ // make sure that the attribute type is correct
+ if (getNodeAttIDToAttTypeMap().get(att_id) != DOUBLE_TYPE)
+ return WRONG_ATTRIBUTE_TYPE;
+
+ OpenIntDoubleHashMap double_map = (OpenIntDoubleHashMap) getNodeAttributeIDToAttributeValuesMap()
+ .get(att_id);
+
+ double_map.put(node_index, value);
+
+ return 1;
+ }
+
+ // node String set methods
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node_index DOCUMENT ME!
+ * @param attribute DOCUMENT ME!
+ * @param value DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static int setNodeAttributeStringValue(int node_index, String attribute, String value) {
+ // make sure the attribute exists, if not, create it.
+ int att_id = getNodeAttNameToAttIDMap().get(attribute);
+
+ if (att_id == StringIntHashMap.DEFAULT_NOT_FOUND)
+ att_id = addNodeAttribute(attribute, STRING_TYPE);
+
+ return setNodeAttributeStringValue(node_index, att_id, value);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ * @param attribute DOCUMENT ME!
+ * @param value DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static int setNodeAttributeStringValue(Node node, String attribute, String value) {
+ // todo: some sort of sanity check?
+ int node_index = node.getRootGraphIndex();
+
+ // make sure the attribute exists, if not, create it.
+ int att_id = getNodeAttNameToAttIDMap().get(attribute);
+
+ if (att_id == StringIntHashMap.DEFAULT_NOT_FOUND)
+ att_id = addNodeAttribute(attribute, STRING_TYPE);
+
+ return setNodeAttributeStringValue(node_index, att_id, value);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node_index DOCUMENT ME!
+ * @param att_id DOCUMENT ME!
+ * @param value DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static int setNodeAttributeStringValue(int node_index, int att_id, String value) {
+ // return if higher than the number of attributes
+ if (att_id > nodeAttributeCount)
+ return INSANE_ATTRIBUTE_ID;
+
+ // make sure that the attribute type is correct
+ if (getNodeAttIDToAttTypeMap().get(att_id) != STRING_TYPE)
+ return WRONG_ATTRIBUTE_TYPE;
+
+ IntStringHashMap string_map = (IntStringHashMap) getNodeAttributeIDToAttributeValuesMap()
+ .get(att_id);
+
+ string_map.add(node_index, value);
+
+ return 1;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ * @param attribute DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static Object getNodeAttributeValue(Node node, String attribute) {
+ int att_id = getNodeAttributeID(attribute);
+
+ if (att_id < 0)
+ return null;
+
+ int node_index = node.getRootGraphIndex();
+
+ return (getNodeAttributeValue(node_index, att_id));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node_index DOCUMENT ME!
+ * @param att_id DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static Object getNodeAttributeValue(int node_index, int att_id) {
+ if (att_id > nodeAttributeCount)
+ return null;
+
+ int att_type = getNodeAttIDToAttTypeMap().get(att_id);
+
+ if (att_type == OBJECT_TYPE)
+ return ((OpenIntObjectHashMap) getNodeAttributeIDToAttributeValuesMap().get(att_id)).get(node_index);
+ else if (att_type == DOUBLE_TYPE) {
+ double result = getNodeAttributeDoubleValue(node_index,
+ (String) (getNodeAttIDToAttNameMap()
+ .get(att_id)));
+ if (Double.isNaN(result))
+ return Double.NaN;
+
+ return new Double(result);
+ } else if (att_type == STRING_TYPE) {
+ return ((IntStringHashMap) getNodeAttributeIDToAttributeValuesMap().get(att_id)).get(node_index);
+ }
+
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ * @param attribute DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static Object getNodeAttributeObjectValue(Node node, String attribute) {
+ int att_id = getNodeAttributeID(attribute);
+
+ if (att_id < 0)
+ return null;
+
+ int node_index = node.getRootGraphIndex();
+ int att_type = getNodeAttIDToAttTypeMap().get(att_id);
+
+ if (att_type == OBJECT_TYPE)
+ return ((OpenIntObjectHashMap) getNodeAttributeIDToAttributeValuesMap().get(att_id)).get(node_index);
+
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ * @param attribute DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static String getNodeAttributeStringValue(Node node, String attribute) {
+ int att_id = getNodeAttributeID(attribute);
+
+ if (att_id < 0)
+ return null;
+
+ int node_index = node.getRootGraphIndex();
+ int att_type = getNodeAttIDToAttTypeMap().get(att_id);
+
+ if (att_type == STRING_TYPE)
+ return ((IntStringHashMap) getNodeAttributeIDToAttributeValuesMap().get(att_id)).get(node_index);
+
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ * @param attribute DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static double getNodeAttributeDoubleValue(Node node, String attribute) {
+ int att_id = getNodeAttributeID(attribute);
+
+ if (att_id < 0)
+ return Double.NaN;
+
+ int node_index = node.getRootGraphIndex();
+ int att_type = getNodeAttIDToAttTypeMap().get(att_id);
+
+ if (att_type == DOUBLE_TYPE) {
+ OpenIntObjectHashMap a2v = getNodeAttributeIDToAttributeValuesMap();
+ OpenIntDoubleHashMap n2v = (OpenIntDoubleHashMap) getNodeAttributeIDToAttributeValuesMap()
+ .get(att_id);
+
+ if (n2v == null) {
+ CyLogger.getLogger().info("Internal error: Unable to get node attribute id map");
+
+ return Double.NaN;
+ }
+
+ if (n2v.containsKey(node_index))
+ return n2v.get(node_index);
+
+ // return ( ( OpenIntDoubleHashMap )getNodeAttributeIDToAttributeValuesMap().get( att_id )).get( node_index );
+ }
+
+ return Double.NaN;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node_index DOCUMENT ME!
+ * @param attribute DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static Object getNodeAttributeObjectValue(int node_index, String attribute) {
+ int att_id = getNodeAttributeID(attribute);
+
+ if (att_id < 0)
+ return null;
+
+ int att_type = getNodeAttIDToAttTypeMap().get(att_id);
+
+ if (att_type == OBJECT_TYPE)
+ return ((OpenIntObjectHashMap) getNodeAttributeIDToAttributeValuesMap().get(att_id)).get(node_index);
+
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node_index DOCUMENT ME!
+ * @param attribute DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static String getNodeAttributeStringValue(int node_index, String attribute) {
+ int att_id = getNodeAttributeID(attribute);
+
+ if (att_id < 0)
+ return null;
+
+ int att_type = getNodeAttIDToAttTypeMap().get(att_id);
+
+ if (att_type == STRING_TYPE)
+ return ((IntStringHashMap) getNodeAttributeIDToAttributeValuesMap().get(att_id)).get(node_index);
+
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node_index DOCUMENT ME!
+ * @param attribute DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static double getNodeAttributeDoubleValue(int node_index, String attribute) {
+ int att_id = getNodeAttributeID(attribute);
+
+ if (att_id < 0)
+ return Double.NaN;
+
+ int att_type = getNodeAttIDToAttTypeMap().get(att_id);
+
+ if (att_type == DOUBLE_TYPE) {
+ OpenIntObjectHashMap a2v = getNodeAttributeIDToAttributeValuesMap();
+ OpenIntDoubleHashMap n2v = (OpenIntDoubleHashMap) getNodeAttributeIDToAttributeValuesMap()
+ .get(att_id);
+
+ if (n2v == null) {
+ CyLogger.getLogger().info("Internal error: Unable to get node attribute id map");
+
+ return Double.NaN;
+ }
+
+ if (n2v.containsKey(node_index))
+ return n2v.get(node_index);
+
+ // return ( ( OpenIntDoubleHashMap )getNodeAttributeIDToAttributeValuesMap().get( att_id )).get( node_index );
+ }
+
+ return Double.NaN;
+ }
+
+ ////////////////////
+ // Node Double Attribute Useful Methods
+
+ /**
+ * Returns all Attributes that one or more of the given nodes have values for.
+ */
+ public static String[] getNodeAttributes(int[] node_indices) {
+ IntArrayList att_keys = new IntArrayList();
+ getNodeAttributeIDToAttributeValuesMap().keys(att_keys);
+
+ HashSet attributes = new HashSet();
+
+ for (int k = 0; k < att_keys.size(); ++k) {
+ for (int i = 0; i < node_indices.length; ++i) {
+ if (att_keys.get(k) == DOUBLE_TYPE) {
+ OpenIntDoubleHashMap n2v = (OpenIntDoubleHashMap) getNodeAttributeIDToAttributeValuesMap()
+ .get(att_keys.get(k));
+
+ if (n2v.containsKey(node_indices[i])) {
+ attributes.add(getNodeAttIDToAttNameMap().get(att_keys.get(k)));
+ // don't look at anymore nodes
+ i = node_indices.length;
+ }
+ } else {
+ OpenIntObjectHashMap n2v = (OpenIntObjectHashMap) getNodeAttributeIDToAttributeValuesMap()
+ .get(att_keys.get(k));
+
+ if (n2v.containsKey(node_indices[i])) {
+ attributes.add(getNodeAttIDToAttNameMap().get(att_keys.get(k)));
+ // don't look at anymore nodes
+ i = node_indices.length;
+ }
+ }
+ }
+ }
+
+ return (String[]) attributes.toArray(new String[] { });
+ }
+
+ //////////////////////////////
+ // node data structure access methods
+ private static OpenIntObjectHashMap getNodeAttributeIDToAttributeValuesMap() {
+ if (nodeAttributeIDToAttributeValuesMap == null)
+ nodeAttributeIDToAttributeValuesMap = new OpenIntObjectHashMap();
+
+ return nodeAttributeIDToAttributeValuesMap;
+ }
+
+ private static StringIntHashMap getNodeAttNameToAttIDMap() {
+ if (nodeAttNameToAttIDMap == null)
+ nodeAttNameToAttIDMap = new StringIntHashMap();
+
+ return nodeAttNameToAttIDMap;
+ }
+
+ private static OpenIntObjectHashMap getNodeAttIDToAttNameMap() {
+ if (nodeAttIDToAttNameMap == null)
+ nodeAttIDToAttNameMap = new OpenIntObjectHashMap();
+
+ return nodeAttIDToAttNameMap;
+ }
+
+ private static OpenIntIntHashMap getNodeAttIDToAttTypeMap() {
+ if (nodeAttIDToAttTypeMap == null)
+ nodeAttIDToAttTypeMap = new OpenIntIntHashMap();
+
+ return nodeAttIDToAttTypeMap;
+ }
+
+ private static StringIntHashMap getNodeAliasToIDMap() {
+ if (nodeAliasToIDMap == null)
+ nodeAliasToIDMap = new StringIntHashMap();
+
+ return nodeAliasToIDMap;
+ }
+}
diff --git a/application/src/main/java/cytoscape/data/SelectEvent.java b/application/src/main/java/cytoscape/data/SelectEvent.java
new file mode 100644
index 0000000..2ca3d01
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/SelectEvent.java
@@ -0,0 +1,211 @@
+/*
+ File: SelectEvent.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+//---------------------------------------------------------------------------
+// $Revision: 9565 $
+// $Date: 2007-02-13 20:36:50 +0100 (Tue, 13 Feb 2007) $
+// $Author: mes $
+//---------------------------------------------------------------------------
+package cytoscape.data;
+
+import giny.model.Edge;
+import giny.model.Node;
+
+//---------------------------------------------------------------------------
+import java.util.Set;
+
+
+//---------------------------------------------------------------------------
+/**
+ * Events that are fired when the selected state of a Node or Edge, or a group
+ * of Nodes or Edges, is changed.
+ */
+public class SelectEvent {
+ /**
+ * Static constant indicating a change to a single Node.
+ */
+ public static final int SINGLE_NODE = 0;
+
+ /**
+ * Static constant indicating a change to a single Edge.
+ */
+ public static final int SINGLE_EDGE = 1;
+
+ /**
+ * Static constant indicating a change to a group of Nodes.
+ */
+ public static final int NODE_SET = 2;
+
+ /**
+ * Static constant indicating a change to a group of Edges.
+ */
+ public static final int EDGE_SET = 3;
+ private SelectFilter source;
+ private Object target;
+ private int targetType;
+ private boolean selectOn = true;
+
+ /**
+ * Standard constructor.<P>
+ *
+ * The first argument is the object that fired this event.<P>
+ *
+ * The second argument decribes what objects were affected; it should be of
+ * type Node, Edge, a Set of Nodes, or a Set of Edges. If the argument is a
+ * Set, it should contain at least one element.
+ *
+ * The third argument is a boolean indicating the type of event. It should be true
+ * if the change is setting the selected state to true for the target objects, or false
+ * if the change is setting it to false.<P>
+ *
+ * @throws IllegalArgumentException if the target is null or an invalid type,
+ */
+ public SelectEvent(SelectFilter source, Object target, boolean selectOn) {
+ this.source = source;
+ this.target = target;
+ this.selectOn = selectOn;
+
+ if (target == null) {
+ throw new IllegalArgumentException("Unexpected null target");
+ } else if (target instanceof Node) {
+ this.targetType = this.SINGLE_NODE;
+ } else if (target instanceof Edge) {
+ this.targetType = this.SINGLE_EDGE;
+ } else if (target instanceof Set) {
+ Set targetSet = (Set) target;
+
+ if (targetSet.size() == 0) {
+ throw new IllegalArgumentException("Unexpected empty target set");
+ }
+
+ Object first = targetSet.iterator().next();
+
+ if (first instanceof Node) {
+ this.targetType = this.NODE_SET;
+ } else if (first instanceof Edge) {
+ this.targetType = this.EDGE_SET;
+ } else { //unknown object type
+ throw new IllegalArgumentException("Unknown object type in target set");
+ }
+ } else {
+ throw new IllegalArgumentException("Unexpected target type");
+ }
+ }
+
+ /**
+ * Returns the source of this event.
+ */
+ public SelectFilter getSource() {
+ return source;
+ }
+
+ /**
+ * Returns an object reference to the target that was changed. This should
+ * be a Node, an Edge, a Set of Nodes, or a Set of Edges. The return value
+ * of getTargetType determines which of the four cases applies.
+ */
+ public Object getTarget() {
+ return target;
+ }
+
+ /**
+ * Returns a static constant identifying the type of object; either SINGLE_NODE
+ * for a Node, SINGLE_EDGE for an Edge, NODE_SET for a Set of Nodes, or
+ * EDGE_SET for a Set of Edges.
+ */
+ public int getTargetType() {
+ return targetType;
+ }
+
+ /**
+ * Returns a boolean identifying the type of event, true the selectes state was set to true, false if it was set to false
+ */
+ public boolean getEventType() {
+ return selectOn;
+ }
+
+ /**
+ * Returns a String representation of this object's data.
+ */
+ public String toString() {
+ StringBuffer sb = new StringBuffer();
+ String lineSep = System.getProperty("line.separator");
+ sb.append("SelectEvent:" + lineSep);
+ sb.append(" target = " + getTarget() + lineSep);
+ sb.append(" target type = ");
+
+ switch (getTargetType()) {
+ case SINGLE_NODE:
+ sb.append("SINGLE_NODE");
+
+ break;
+
+ case SINGLE_EDGE:
+ sb.append("SINGLE_EDGE");
+
+ break;
+
+ case NODE_SET:
+ sb.append("NODE_SET");
+
+ break;
+
+ case EDGE_SET:
+ sb.append("EDGE_SET");
+
+ break;
+
+ default: //should never happen
+ sb.append(getTargetType());
+
+ break;
+ }
+
+ sb.append(lineSep);
+ sb.append(" event type = ");
+
+ if (getEventType()) {
+ sb.append("ON");
+ } else {
+ sb.append("OFF");
+ }
+
+ sb.append(lineSep);
+
+ return sb.toString();
+ }
+}
diff --git a/application/src/main/java/cytoscape/data/SelectEventListener.java b/application/src/main/java/cytoscape/data/SelectEventListener.java
new file mode 100644
index 0000000..941e9aa
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/SelectEventListener.java
@@ -0,0 +1,52 @@
+/*
+ File: SelectEventListener.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+//---------------------------------------------------------------------------
+// $Revision: 9736 $
+// $Date: 2007-03-20 01:25:45 +0100 (Tue, 20 Mar 2007) $
+// $Author: mes $
+//---------------------------------------------------------------------------
+package cytoscape.data;
+
+
+//---------------------------------------------------------------------------
+/**
+ * Listener for SelectEvents fired by a SelectFilter object.
+ */
+public interface SelectEventListener {
+ void onSelectEvent(SelectEvent event);
+}
diff --git a/application/src/main/java/cytoscape/data/SelectFilter.java b/application/src/main/java/cytoscape/data/SelectFilter.java
new file mode 100644
index 0000000..1e665f9
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/SelectFilter.java
@@ -0,0 +1,489 @@
+/*
+ File: SelectFilter.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+//---------------------------------------------------------------------------
+// $Revision: 10586 $
+// $Date: 2007-06-22 18:56:13 +0200 (Fri, 22 Jun 2007) $
+// $Author: kono $
+//---------------------------------------------------------------------------
+package cytoscape.data;
+
+
+//---------------------------------------------------------------------------
+import giny.filter.Filter;
+
+import giny.model.Edge;
+import giny.model.GraphPerspective;
+import giny.model.GraphPerspectiveChangeEvent;
+import giny.model.GraphPerspectiveChangeListener;
+import giny.model.Node;
+import giny.model.RootGraph;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Set;
+
+
+//---------------------------------------------------------------------------
+/**
+ * This class implements the ability to set the selected state of every node or
+ * edge in a GraphPerspective. The state can be either on or off. Methods are
+ * provided for inspecting the current state of any graph object, for setting
+ * the state, or getting the full set of states for nodes or edges. This
+ * functionality is often used to identify a set of interesting nodes or edges
+ * in the graph.
+ * <P>
+ *
+ * A non-null GraphPerspective reference is required to construct an instance of
+ * this class. This class will listen to the graph to respond to the removal of
+ * graph objects. A currently selected object that is removed from the graph
+ * will lose its selected state, even if it is later added back to the graph.
+ * <P>
+ *
+ * When the selected state of a node or edge is changed, a event of type
+ * SelectEvent is fired. When a group of nodes or edges are changed together in
+ * a single operation, one event will be fired for the whole group (but separate
+ * events for nodes and edges). Note: a listener should not be removed from this
+ * object in response to the firing of an event, as this may cause a
+ * ConcurrentModificationException.
+ * <P>
+ *
+ * WARNING: for performance reasons, the set of objects returned by the
+ * getSelectedXX methods is the actual data object, not a copy. Users should not
+ * directly modify these sets.
+ * <P>
+ *
+ * Performance note: the implementation is a HashSet of selected objects, so
+ * most methods are O(1). Operations on groups of nodes are O(N) where N is
+ * either the number of selected objects or the number of objects in the graph,
+ * as applicable.
+ * <P>
+ */
+public class SelectFilter implements Filter, GraphPerspectiveChangeListener {
+ private GraphPerspective graph;
+ private final Set<Node> selectedNodes = new HashSet<Node>();
+ private final Set<Edge> selectedEdges = new HashSet<Edge>();
+
+ private List listeners = new ArrayList();
+
+ /**
+ * Standard Constructor. The argument is the graph that this filter will
+ * apply to; it cannot be null.
+ *
+ * @throws NullPointerException
+ * if the argument is null.
+ */
+ public SelectFilter(final GraphPerspective graph) {
+ this.graph = graph;
+
+ // this throws a NullPointerException if the graph is null
+ graph.addGraphPerspectiveChangeListener(this);
+ }
+
+ /**
+ * Returns the set of all selected nodes in the referenced GraphPespective.
+ * <P>
+ *
+ * WARNING: the returned set is the actual data object, not a copy. Don't
+ * directly modify this set.
+ */
+ public Set getSelectedNodes() {
+ return selectedNodes;
+ }
+
+ /**
+ * Returns the set of all selected edges in the referenced GraphPespective.
+ * <P>
+ *
+ * WARNING: the returned set is the actual data object, not a copy. Don't
+ * directly modify this set.
+ */
+ public Set getSelectedEdges() {
+ return selectedEdges;
+ }
+
+ /**
+ * Returns true if the argument is a selected Node in the referenced
+ * GraphPerspective, false otherwise.
+ */
+ public boolean isSelected(Node node) {
+ return selectedNodes.contains(node);
+ }
+
+ /**
+ * Returns true if the argument is a selected Edge in the referenced
+ * GraphPerspective, false otherwise.
+ */
+ public boolean isSelected(Edge edge) {
+ return selectedEdges.contains(edge);
+ }
+
+ /**
+ * Implementation of the Filter interface. Returns true if the argument is a
+ * selected Node or Edge in the referenced GraphPerspective, false
+ * otherwise.
+ */
+ public boolean passesFilter(Object o) {
+ if (selectedNodes.contains(o) || selectedEdges.contains(o)) {
+ return true;
+ } else {
+ return false;
+ }
+ }
+
+ /**
+ * If the first argument is a Node in the referenced GraphPerspective, sets
+ * its selected state to the value of the second argument. An event will be
+ * fired iff the new state is different from the old state.
+ *
+ * @return true if an actual change was made, false otherwise
+ */
+ public boolean setSelected(final Node node, final boolean newState) {
+ boolean setChanged;
+
+ if (newState == true) { // set flag to on
+ // don't flag the node if it's not in the graph
+
+ if (!graph.containsNode(node)) {
+ return false;
+ }
+
+ setChanged = selectedNodes.add(node);
+
+ if (setChanged) {
+ fireEvent(node, true);
+ }
+ } else { // set flag to off
+ // a node can't be selected unless it's in the graph
+ setChanged = selectedNodes.remove(node);
+
+ if (setChanged) {
+ fireEvent(node, false);
+ }
+ }
+
+ return setChanged;
+ }
+
+ /**
+ * If the first argument is an Edge in the referenced GraphPerspective, sets
+ * its selected state to the value of the second argument. An event will be
+ * fired iff the new state is different from the old state.
+ *
+ * @return true if an actual change was made, false otherwise
+ */
+ public boolean setSelected(final Edge edge, final boolean newState) {
+ boolean setChanged;
+
+ if (newState == true) { // set flag to on
+ // don'tflagthe edge if it's not in the graph
+
+ if (!graph.containsEdge(edge)) {
+ return false;
+ }
+
+ setChanged = selectedEdges.add(edge);
+
+ if (setChanged) {
+ fireEvent(edge, true);
+ }
+ } else { // set flag to off
+ // an edge can't be selected unless it's in the graph
+ setChanged = selectedEdges.remove(edge);
+
+ if (setChanged) {
+ fireEvent(edge, false);
+ }
+ }
+
+ return setChanged;
+ }
+
+ /**
+ * Sets the selected state defined by the second argument for all Nodes
+ * contained in the first argument, which should be a Collection of Node
+ * objects contained in the referenced GraphPerspective. One event will be
+ * fired for the full set of changes. This method does nothing if the first
+ * argument is null.
+ *
+ * @return a Set containing the objects for which the selected state changed
+ * @throws ClassCastException
+ * if the first argument contains objects other than
+ * giny.model.Node objects
+ */
+ public Set<Node> setSelectedNodes(final Collection<Node> nodesToSet, final boolean newState) {
+ final Set<Node> returnSet = new HashSet<Node>();
+ if (nodesToSet == null || nodesToSet.size() == 0) {
+ return returnSet;
+ }
+
+
+ if (newState == true) {
+ for (Node node : nodesToSet) {
+ if (!graph.containsNode(node)) {
+ continue;
+ }
+
+ if (selectedNodes.add(node)) {
+ returnSet.add(node);
+ }
+ }
+
+ if (returnSet.size() > 0) {
+ fireEvent(returnSet, true);
+ }
+ } else {
+ for (Node node : nodesToSet) {
+ if (selectedNodes.remove(node)) {
+ returnSet.add(node);
+ }
+ }
+
+ if (returnSet.size() > 0) {
+ fireEvent(returnSet, false);
+ }
+ }
+ return returnSet;
+ }
+
+ /**
+ * Sets the selected state defined by the second argument for all Edges
+ * contained in the first argument, which should be a Collection of Edge
+ * objects contained in the referenced GraphPerspective. One event will be
+ * fired for the full set of changes. This method does nothing if the first
+ * argument is null.
+ *
+ * @return a Set containing the objects for which the selected state changed
+ * @throws ClassCastException
+ * if the first argument contains objects other than
+ * giny.model.Edge objects
+ */
+ public Set<Edge> setSelectedEdges(final Collection<Edge> edgesToSet, final boolean newState) {
+
+ final Set<Edge> edgeReturnSet = new HashSet<Edge>();
+
+ if (edgesToSet == null || edgesToSet.size() == 0) {
+ return edgeReturnSet;
+ }
+
+ if (newState == true) {
+ for (Edge edge : edgesToSet) {
+ if (!graph.containsEdge(edge)) {
+ continue;
+ }
+
+ if (selectedEdges.add(edge)) {
+ edgeReturnSet.add(edge);
+ }
+ }
+
+ if (edgeReturnSet.size() > 0) {
+ fireEvent(edgeReturnSet, true);
+ }
+ } else {
+ for (Edge edge : edgesToSet) {
+ if (selectedEdges.remove(edge)) {
+ edgeReturnSet.add(edge);
+ }
+ }
+
+ if (edgeReturnSet.size() > 0) {
+ fireEvent(edgeReturnSet, false);
+ }
+ }
+ return edgeReturnSet;
+ }
+
+ /**
+ * Sets the selected state to true for all Nodes in the GraphPerspective.
+ */
+ public Set selectAllNodes() {
+ return setSelectedNodes(graph.nodesList(), true);
+ }
+
+ /**
+ * Sets the selected state to true for all Edges in the GraphPerspective.
+ */
+ public Set selectAllEdges() {
+ return setSelectedEdges(graph.edgesList(), true);
+ }
+
+ /**
+ * Sets the selected state to false for all Nodes in the GraphPerspective.
+ */
+ public Set unselectAllNodes() {
+ return setSelectedNodes(graph.nodesList(), false);
+ }
+
+ /**
+ * Sets the selected state to false for all Edges in the GraphPerspective.
+ */
+ public Set unselectAllEdges() {
+ return setSelectedEdges(graph.edgesList(), false);
+ }
+
+ /**
+ * Implementation of the GraphPerspectiveChangeListener interface. Responds
+ * to the removal of nodes and edges by removing them from the set of
+ * selected graph objects if needed. Fires an event only if there was an
+ * actual change in the current selected set.
+ */
+ public void graphPerspectiveChanged(GraphPerspectiveChangeEvent event) {
+ // careful: this event can represent both hidden nodes and hidden edges
+ // if a hide node operation implicitly hid its incident edges
+ Set nodeChanges = null; // only create the set if we need it
+
+ if (event.isNodesHiddenType()) { // at least one node was hidden
+
+ Node[] hiddenNodes = event.getHiddenNodes();
+ final int hNodesCount = hiddenNodes.length;
+ Node node;
+ boolean setChanged;
+ for (int index = 0; index <hNodesCount; index++) {
+ node = hiddenNodes[index];
+ setChanged = selectedNodes.remove(node);
+
+ if (setChanged) { // the hidden node was actually selected
+
+ if (nodeChanges == null) {
+ nodeChanges = new HashSet();
+ }
+
+ nodeChanges.add(node); // save change for the event we'll
+ // fire
+ }
+ }
+ }
+
+ if ((nodeChanges != null) && (nodeChanges.size() > 0)) {
+ fireEvent(nodeChanges, false);
+ }
+
+ Set edgeChanges = null; // only create the set if we need it
+
+ if (event.isEdgesHiddenType()) { // at least one edge was hidden
+ // GINY bug: sometimes we get an event that has valid edge indices
+ // but the Edge array contains null objects
+ // for now, get around this by converting indices to edges ourselves
+
+ Object eventSource = event.getSource();
+ RootGraph root;
+
+ if (eventSource instanceof RootGraph)
+ root = (RootGraph) eventSource;
+ else
+ root = ((GraphPerspective) eventSource).getRootGraph();
+
+ int[] indices = event.getHiddenEdgeIndices();
+ final int eLength = indices.length;
+ Edge edge;
+ boolean setChanged;
+ for (int index = 0; index < eLength; index++) {
+ edge = root.getEdge(indices[index]);
+ setChanged = selectedEdges.remove(edge);
+
+ if (setChanged) { // the hidden edge was actually selected
+
+ if (edgeChanges == null) {
+ edgeChanges = new HashSet();
+ }
+
+ edgeChanges.add(edge); // save change for the event we'll
+ // fire
+ }
+ }
+
+ /*
+ * this is the code that sometimes doesn't work Edge[] hiddenEdges =
+ * event.getHiddenEdges(); for (int index=0; index<hiddenEdges.length;
+ * index++) { Edge edge = hiddenEdges[index]; boolean setChanged =
+ * selectedEdges.remove(edge); if (setChanged) { if (edgeChanges ==
+ * null) {edgeChanges = new HashSet();} edgeChanges.add(edge); } }
+ */
+ }
+
+ if ((edgeChanges != null) && (edgeChanges.size() > 0)) {
+ fireEvent(edgeChanges, false);
+ }
+ }
+
+ /**
+ * If the argument is not already a listener to this object, it is added.
+ * Does nothing if the argument is null.
+ */
+ public void addSelectEventListener(SelectEventListener listener) {
+ if (listener != null) {
+ listeners.add(listener);
+ }
+ }
+
+ /**
+ * If the argument is a listener to this object, removes it from the list of
+ * listeners.
+ */
+ public void removeSelectEventListener(SelectEventListener listener) {
+ listeners.remove(listener);
+ }
+
+ /**
+ * Gets a List of All Registered Listeners.
+ *
+ * @return
+ */
+ public List getSelectEventListeners() {
+ return listeners;
+ }
+
+ /**
+ * Fires an event to all registered listeners that represents the operation
+ * described by the arguments. The first argument should be the graph object
+ * whose selected state changed, or a Set of such objects. The second
+ * argument identifies the change; true for setting a flag and false for
+ * removing it. Creates a suitable event and passes it to all listeners.
+ */
+ protected void fireEvent(final Object target, final boolean selectOn) {
+ final SelectEvent event = new SelectEvent(this, target, selectOn);
+
+ for (Iterator i = this.listeners.iterator(); i.hasNext();) {
+ SelectEventListener listener = (SelectEventListener) i.next();
+ listener.onSelectEvent(event);
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/data/Semantics.java b/application/src/main/java/cytoscape/data/Semantics.java
new file mode 100644
index 0000000..c1beabb
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/Semantics.java
@@ -0,0 +1,513 @@
+/*
+ File: Semantics.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.data;
+
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+import cytoscape.CytoscapeInit;
+
+import cytoscape.data.attr.CountedIterator;
+import cytoscape.data.attr.MultiHashMap;
+
+import cytoscape.data.servers.BioDataServer;
+
+import giny.model.Edge;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Set;
+import java.util.TreeSet;
+
+
+/**
+ * This class defines names for certain data attributes that are commonly used
+ * within Cytoscape. The constants defined here are provided to enable different
+ * modules to use the same name when referring to the same conceptual attribute.
+ *
+ * This class also defines some static methods for assigning these attributes to
+ * a network, given the objects that serve as the source for this information.
+ *
+ * This is a logacy code. Use CANONICAL_NAME and INTERACTION only.
+ * Other values and functions are not in use Cytoscape.
+ *
+ */
+public class Semantics {
+
+ /**
+ * The name "CANONICAL_NAME" is an historical artifact. The <b>ONLY</b>
+ * purpose for this variable is to provide the name for an automatically
+ * created node attribute that is guaranteed to be created when the
+ * node is created. Any other purpose or function this value has supported
+ * in the past is officially no longer supported!
+ */
+ public static final String CANONICAL_NAME = "canonicalName";
+
+ /**
+ * Represents edge type attribute.
+ */
+ public static final String INTERACTION = "interaction";
+
+
+ /**
+ *
+ */
+ @Deprecated
+ public static final String GO_COMMON_NAME = "GO Common Name";
+
+ /**
+ *
+ */
+ @Deprecated
+ public static final String GO_ALIASES = "GO Aliases";
+
+ /**
+ *
+ */
+ @Deprecated
+ public static final String SPECIES = "species";
+
+
+
+ /**
+ *
+ */
+ @Deprecated
+ public static final String MOLECULE_TYPE = "molecule_type";
+
+ /**
+ *
+ */
+ @Deprecated
+ public static final String PROTEIN = "protein";
+
+ /**
+ *
+ */
+ @Deprecated
+ public static final String DNA = "DNA";
+
+ /**
+ *
+ */
+ @Deprecated
+ public static final String RNA = "RNA";
+
+ /**
+ *
+ */
+ @Deprecated
+ public static final String MOLECULAR_FUNCTION = "molecular_function";
+
+ /**
+ *
+ */
+ @Deprecated
+ public static final String BIOLOGICAL_PROCESS = "biological_process";
+
+ /**
+ *
+ */
+ @Deprecated
+ public static final String CELLULAR_COMPONENT = "cellular_component";
+
+ /**
+ * This method should be called in the process of creating a new network, or
+ * upon loading a new bioDataServer. This method will use the bioDataServer
+ * to assign common names to the network using the synonym utilities of the
+ * bioDataServer. In the process, it will assign a species attribute for any
+ * name that does not currently have one.
+ *
+ * Currently, this method calls assignSpecies and assignCommonNames. At some
+ * point it may be desirable to check the configuration to see what to do,
+ * or put up a UI to prompt the user for what services they would like.
+ *
+ * KONO: 04/19/2006 Since attribute cannonical name no longer exists, these
+ * names should be created node identifiers.
+ *
+ */
+ @Deprecated
+ public static void applyNamingServices(final CyNetwork network) {
+ assignSpecies(network);
+ //assignCommonNames(network, Cytoscape.getBioDataServer());
+ }
+
+ /**
+ * This method attempts to set a species attribute for every canonical name
+ * defined in the node attributes member of the supplied network. The value
+ * returned by getDefaultSpecies is used; if this return value is null, then
+ * this method exits without doing anything, as there is no species to set.
+ *
+ * If a canonical name already has an entry for the SPECIES attribute, then
+ * this method does not change that value. Otherwise, this method sets the
+ * value of that attribute to that returned by getDefaultSpecies.
+ *
+ * This method does nothing at all if either argument is null.
+ */
+ @Deprecated
+ public static void assignSpecies(final CyNetwork network) {
+ if (network == null) {
+ return;
+ }
+
+ final String defaultSpecies = CytoscapeInit.getProperties().getProperty("defaultSpeciesName");
+
+ if (defaultSpecies == null) {
+ return;
+ } // we have no value to set
+
+ final CyAttributes nodeAttributes = Cytoscape.getNodeAttributes();
+
+ final Iterator nodeIt = network.nodesIterator();
+
+ while (nodeIt.hasNext()) {
+ final String nodeLabel = ((CyNode) nodeIt.next()).getIdentifier();
+ final String species = nodeAttributes.getStringAttribute(nodeLabel, SPECIES);
+
+ if (species == null) { // only do something if no value exists
+ nodeAttributes.setAttribute(nodeLabel, SPECIES, defaultSpecies);
+ }
+ }
+ }
+
+ /**
+ * Returns every unique species defined in the supplied network. Searches
+ * the species attribute in the node attributes of the supplied network and
+ * returns a Set containing every unique value found.
+ */
+ @Deprecated
+ public static Set getSpeciesInNetwork(final CyNetwork network) {
+ final Set returnSet = new HashSet();
+
+ if (network == null) {
+ return returnSet;
+ }
+
+ final CyAttributes nodeAttributes = Cytoscape.getNodeAttributes();
+
+ // in the following map, keys are objects names and values are the
+ // species
+ final CountedIterator keys = nodeAttributes.getMultiHashMap().getObjectKeys(SPECIES);
+
+ while (keys.hasNext()) {
+ returnSet.add(nodeAttributes.getStringAttribute((String) keys.next(), SPECIES));
+ }
+
+ return returnSet;
+ }
+
+ /**
+ * Use the given BioDataServer to set all of the aliases for a node, given
+ * its species.<p>
+ *
+ * Note: This is only for GO data!
+ *
+ *
+ * @param node
+ * the Node that will be assigned names
+ * @param species
+ * the species of the Node ( NOTE: if null, there will be a check
+ * to see if the node has a species set for attribute
+ * Semantics.SPECIES, if not, then the general Cytoscape
+ * defaultSpecies ( settable with -s ) will be used. )
+ * @param bds
+ * the given BioDataServer ( NOTE: if null, then the general
+ * Cytoscape BioDataServer will be used ( settable with -b ) ).
+ */
+ @Deprecated
+ public static void assignNodeAliases(final CyNode node, String species, BioDataServer bds) {
+ final String nodeID = node.getIdentifier();
+ final CyAttributes nodeAttributes = Cytoscape.getNodeAttributes();
+
+ // can't have a null node
+ if (node == null) {
+ return;
+ }
+
+ // If species are null, use default species name
+ if (species == null) {
+ species = nodeAttributes.getStringAttribute(nodeID, SPECIES);
+
+ if (species == null) {
+ species = CytoscapeInit.getProperties().getProperty("defaultSpeciesName");
+ }
+ }
+
+ // Check for the case when we don't have a default species
+ if (species != null) {
+ nodeAttributes.setAttribute(nodeID, SPECIES, species);
+ }
+
+// // Get Gene Ontology Server
+// if (bds == null) {
+// bds = Cytoscape.getBioDataServer();
+// }
+
+ // return if no deafult BioDataServer
+ if (bds == null) {
+ return;
+ }
+
+ // now do the name assignment
+ // String nodeLabel = id;
+
+ // First, try to get aliases using the label.
+ final String[] synonyms = bds.getAllCommonNames(species, nodeID);
+
+ // Next,check the aliases, since nodeLabel can be a part of aliases.
+ final String canonicalFromAliases = bds.getCanonicalName(species, nodeID);
+ final String[] reverseSynonyms = bds.getAllCommonNames(species, canonicalFromAliases);
+
+ final Set synoSet = new TreeSet();
+
+ // StringBuffer concat = new StringBuffer();
+ String commonName = null;
+
+ /*
+ * Check the normal synonyms.
+ */
+ for (int j = 0; j < synonyms.length; ++j) {
+ if (!synonyms[j].equals(nodeID)) {
+ synoSet.add(synonyms[j]);
+ }
+ }
+
+ /*
+ * Check the reverse synonyms
+ */
+ for (int i = 0; i < reverseSynonyms.length; ++i) {
+ if (!reverseSynonyms[i].equals(nodeID)) {
+ synoSet.add(reverseSynonyms[i]);
+ }
+ }
+
+ /*
+ * Add canonical name obtained from alias.
+ * This should be in the GO Aliases.
+ */
+ if (!synoSet.contains(canonicalFromAliases)) {
+ synoSet.add(canonicalFromAliases);
+ }
+
+ /*
+ * Set common name.
+ * This choice is arbitrary.
+ */
+ if ((canonicalFromAliases != null) && !canonicalFromAliases.equals(nodeID)) {
+ commonName = canonicalFromAliases;
+ } else if (synonyms.length != 0) {
+ commonName = synonyms[0];
+ } else if (synoSet.size() == 0) {
+ commonName = nodeID;
+ synoSet.add(commonName);
+ } else {
+ commonName = nodeID;
+ }
+
+ nodeAttributes.setListAttribute(nodeID, GO_ALIASES, new ArrayList(synoSet));
+ nodeAttributes.setAttribute(nodeID, GO_COMMON_NAME, commonName);
+ }
+
+ /**
+ * This method takes every canonical name defines in the node attributes of
+ * the given network, and attempts to assign a common name by getting a list
+ * of synonyms for the canonical name from the bioDataServer and using the
+ * first synonym as the common name.
+ *
+ * This operation requires the SPECIES attribute to be defined for the
+ * canonical name, as input to the bioDataServer. Any canonicalName that
+ * does not have this attribute defined is skipped.
+ *
+ * This method does nothing if either argument is null. Also, for any
+ * canonical name, this method does nothing if no synonyms for that name can
+ * be provided by the bioDataServer.
+ */
+ @Deprecated
+ public static void assignCommonNames(final CyNetwork network, final BioDataServer bioDataServer) {
+ if ((network == null) || (bioDataServer == null)) {
+ return;
+ }
+
+ for (Iterator it = network.nodesIterator(); it.hasNext();) {
+ assignNodeAliases((CyNode) it.next(), null, bioDataServer);
+ }
+ }
+
+ /**
+ * Returns an array containing all of the unique interaction types present
+ * in the network. Formally, gets from the edge attributes all of the unique
+ * values for the "interaction" attribute.
+ *
+ * If the argument is null, returns an array of length 0.
+ */
+ public static String[] getInteractionTypes(final CyNetwork network) {
+ if (network == null) {
+ return new String[0];
+ }
+
+ final HashMap dupsFilter = new HashMap();
+ final CyAttributes attrs = Cytoscape.getEdgeAttributes();
+ final MultiHashMap mmap = attrs.getMultiHashMap();
+ final CountedIterator objs = mmap.getObjectKeys(Semantics.INTERACTION);
+
+ while (objs.hasNext()) {
+ final String obj = (String) objs.next();
+ final Object val = mmap.getAttributeValue(obj, Semantics.INTERACTION, null);
+ dupsFilter.put(val, val);
+ }
+
+ final String[] returnThis = new String[dupsFilter.size()];
+ final Iterator uniqueIter = dupsFilter.keySet().iterator();
+ int inx = 0;
+
+ while (uniqueIter.hasNext()) {
+ returnThis[inx++] = (String) uniqueIter.next();
+ }
+
+ return returnThis;
+ }
+
+ // -------------------------------------------------------------------------
+ /**
+ * Returns the interaction type of the given edge. Formally, gets from the
+ * edge attributes the value for the "interaction" attribute".
+ *
+ * If either argument is null, returns null.
+ */
+ public static String getInteractionType(final CyNetwork network, final Edge edge) {
+ if ((network == null) || (edge == null)) {
+ return null;
+ }
+
+ return Cytoscape.getEdgeAttributes()
+ .getStringAttribute(edge.getIdentifier(), Semantics.INTERACTION);
+ }
+
+ // -------------------------------------------------------------------------
+ /**
+ * This method is used to determine if two, potentially different names
+ * really refer to the same thing; that is, the two names are synonyms. The
+ * rules applied are as follows:
+ *
+ * 1) If either name is null, this method returns true if both are null,
+ * false otherwise. 2) If the names themselves match, this method returns
+ * true 3) The getAllSynonyms method is called for both names, to get all
+ * known synonyms. each possible pair of synonyms is compared, and this
+ * method returns true if any match is found, false otherwise.
+ *
+ * In all cases, comparisons are done with name1.equalsIgnoreCase(name2).
+ *
+ * The network and cytoscapeObj arguments may be null, which simply limits
+ * the tests that can be done to find synonyms.
+ */
+ @Deprecated
+ public static boolean areSynonyms(final String firstName, final String secondName,
+ final CyNetwork network) {
+ if ((firstName == null) || (secondName == null)) {
+ return ((firstName == null) && (secondName == null));
+ }
+
+ if (firstName.equalsIgnoreCase(secondName)) {
+ return true;
+ }
+
+ final List firstSynonyms = getAllSynonyms(firstName, network);
+ final List secondSynonyms = getAllSynonyms(secondName, network);
+
+ for (Iterator firstI = firstSynonyms.iterator(); firstI.hasNext();) {
+ for (Iterator secondI = secondSynonyms.iterator(); secondI.hasNext();) {
+ if (((String) firstI.next()).equalsIgnoreCase((String) secondI.next())) {
+ return true;
+ }
+ }
+ }
+
+ return false;
+ }
+
+ // -------------------------------------------------------------------------
+ /**
+ * This method returns a list of all names that are synonyms of the given
+ * name. The returned list will include the name argument itself, and thus
+ * will always be non-null and contain at least one member (unless the
+ * argument itself is null, in which case a list of size 0 is returned). The
+ * search for other names follows the following steps:
+ *
+ * First, if the network argument is non-null and the node attributes
+ * include the name argument as a canonical name, then add any entry for the
+ * COMMON_NAME attribute associated with the canonical name. Next, if a
+ * BioDataServer is available, try to get a species for the given name
+ * either from the SPECIES attribute associated with the canonicalName, or
+ * using the return value of getDefaultSpecies if needed. If a species can
+ * be determined, then use the BioDataServer to add all the synonyms that
+ * are registered for the name argument.
+ *
+ * @deprecated: Do not use this method. Synonym is no longer exist in Cytoscape.
+ *
+ */
+ @Deprecated
+ public static List getAllSynonyms(final String name, final CyNetwork network) {
+ final List returnList = new ArrayList();
+
+ if (name == null) {
+ return returnList;
+ }
+
+ returnList.add(name);
+
+ String species = null;
+
+ if (network != null) {
+ final String commonName = Cytoscape.getNodeAttributes()
+ .getStringAttribute(name, GO_COMMON_NAME);
+
+ if (commonName != null) {
+ returnList.add(commonName);
+ }
+
+ species = Cytoscape.getNodeAttributes().getStringAttribute(name, SPECIES);
+ }
+
+ species = CytoscapeInit.getProperties().getProperty("defaultSpeciesName");
+
+ return returnList;
+ }
+}
diff --git a/application/src/main/java/cytoscape/data/annotation/Annotation.java b/application/src/main/java/cytoscape/data/annotation/Annotation.java
new file mode 100755
index 0000000..8e196dd
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/annotation/Annotation.java
@@ -0,0 +1,365 @@
+/*
+ File: Annotation.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.data.annotation;
+
+import java.io.Serializable;
+
+import java.util.HashMap;
+import java.util.Vector;
+
+
+/**
+ * Store any number of classifications for named entities, each of which is from
+ * a specified species, and where the classifications are all terms from an
+ * ontology (a controlled vocabulary for some subject domain, expressed as a
+ * directed acyclic graph). For example:
+ * <p>
+ * <ul>
+ * <li> for the species Halobacterium
+ * <li> with respect to the KEGG metabolic pathways ontology
+ * <li> gene VNG0623G has been assigned into the following categories
+ * <ol>
+ * <li> Valine, leucine and isoleucine degradation
+ * <li> Propanoate metabolism
+ * </ol>
+ * </ul>
+ *
+ * This simple assignment of two classifications to one gene becomes richer when
+ * we refer to the ontology: in the KEGG ontology, these two terms belong to a
+ * tree, expressed linearly, and from the top (most general term) down as
+ * <ul>
+ * <li> metablolism -> amino acid metabolism -> valine, leucine and isoleucine
+ * degradation
+ * <li> metabolism -> carbohydrate metabolism -> propanoate metabolism
+ * <ul>
+ *
+ * Thus the combination of an annotation (the present class) with an ontology
+ * provides a means to richly and flexibly describe an object.
+ *
+ *
+ * @deprecated Use regular CyAttributes for annotation.
+ *
+ */
+ at Deprecated
+public class Annotation implements Serializable {
+ protected Ontology ontology;
+ protected String curator;
+ protected String species;
+ protected String type;
+ protected HashMap hash; // (name, Vector) pairs, the Vector contains Integers
+
+ /**
+ * Creates a new Annotation object.
+ *
+ * @param species DOCUMENT ME!
+ * @param type DOCUMENT ME!
+ * @param ontology DOCUMENT ME!
+ */
+ public Annotation(String species, String type, Ontology ontology) {
+ this.ontology = ontology;
+ this.species = species;
+ this.type = type;
+ this.curator = ontology.getCurator();
+ hash = new HashMap();
+ }
+
+ /**
+ * Creates a new Annotation object.
+ *
+ * @param species DOCUMENT ME!
+ * @param type DOCUMENT ME!
+ * @param curator DOCUMENT ME!
+ */
+ public Annotation(String species, String type, String curator) {
+ this.curator = curator;
+ this.species = species;
+ this.type = type;
+ hash = new HashMap();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public HashMap getMap() {
+ return hash;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param newValue DOCUMENT ME!
+ */
+ public void setOntology(Ontology newValue) {
+ ontology = newValue;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Ontology getOntology() {
+ return ontology;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getCurator() {
+ return curator;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getType() {
+ return type;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getOntologyType() {
+ if (ontology != null)
+ return ontology.getType();
+
+ return "unknown";
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getSpecies() {
+ return species;
+ }
+
+ /**
+ * create a new annotation for an entity (typically a gene) of the current
+ * species and with respect to the current ontology. an entity may have more
+ * than one classification.
+ *
+ * @param name
+ * usually an ORF name, a unique identifier for this species
+ * @param classificationID
+ * a pointer into the ontology hierarchy
+ */
+ public void add(String name, int classificationID) {
+ Vector classifications;
+
+ if (hash.containsKey(name))
+ classifications = (Vector) hash.get(name);
+ else {
+ classifications = new Vector();
+ hash.put(name, classifications);
+ }
+
+ Integer classificationInteger = new Integer(classificationID);
+
+ if (!classifications.contains(classificationInteger))
+ classifications.add(new Integer(classificationID));
+ }
+
+ /**
+ * returns an array of all the names (usually ORFs) currently annotated
+ */
+ public String[] getNames() {
+ return (String[]) hash.keySet().toArray(new String[0]);
+ }
+
+ /**
+ * returns an array of all the classifications in the current annotation
+ */
+ public int[] getClassifications() {
+ Vector[] arrayOfIntegerVectors = (Vector[]) hash.values().toArray(new Vector[0]);
+
+ Vector collector = new Vector();
+
+ for (int v = 0; v < arrayOfIntegerVectors.length; v++) {
+ Vector vec = arrayOfIntegerVectors[v];
+
+ for (int i = 0; i < vec.size(); i++)
+ collector.add(vec.get(i));
+ } // for v
+
+ int[] result = new int[collector.size()];
+
+ for (int i = 0; i < result.length; i++)
+ result[i] = ((Integer) collector.get(i)).intValue();
+
+ return result;
+ }
+
+ /**
+ * all of the ontology identifiers registered for the specified entity
+ */
+ public int[] getClassifications(String name) {
+ if (!hash.containsKey(name))
+ return new int[0];
+
+ Vector classifications = (Vector) hash.get(name);
+ int[] result = new int[classifications.size()];
+
+ for (int i = 0; i < result.length; i++)
+ result[i] = ((Integer) classifications.get(i)).intValue();
+
+ return result;
+ }
+
+ /**
+ * all of the ontology identifiers registered for the specified entity, as a
+ * Vector of Integers
+ */
+ public Vector getClassificationsVector(String name) {
+ if (!hash.containsKey(name))
+ return new Vector();
+ else
+
+ return (Vector) hash.get(name);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param name DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String[][] getAllHierarchyPathsAsNames(String name) {
+ if (ontology == null)
+ return new String[0][0];
+
+ int[] leafClassifications = getClassifications(name);
+ String[][] result;
+
+ if (leafClassifications.length == 0) {
+ result = new String[0][0];
+ }
+
+ Vector collector = new Vector();
+
+ for (int i = 0; i < leafClassifications.length; i++) {
+ String[][] paths = ontology.getAllHierarchyPathsAsNames(leafClassifications[i]);
+
+ for (int p = 0; p < paths.length; p++)
+ collector.add(paths[p]);
+ }
+
+ result = new String[collector.size()][];
+
+ for (int i = 0; i < collector.size(); i++) {
+ String[] path = (String[]) collector.get(i);
+ result[i] = path;
+ }
+
+ return result;
+ }
+
+ /**
+ * total number of entities, usually ORFs.
+ */
+ public int count() {
+ return hash.size();
+ }
+
+ /**
+ * total number of classifications. this will usually be larget than count
+ * (), since entities are frequently given two or more classifications,
+ * reflecting the multiple roles of many biological entities.
+ */
+ public int size() {
+ String[] names = getNames();
+ int total = 0;
+
+ for (int i = 0; i < names.length; i++) {
+ total += ((Vector) hash.get(names[i])).size();
+ }
+
+ return total;
+ }
+
+ /**
+ * get all of the full paths (as ints) from the ontology for all of the
+ * currently annotated entities. then traverse this (possibly large) list
+ * and return the longest path.
+ */
+ public int maxDepth() {
+ if (ontology == null)
+ return 0;
+
+ int[] classifications = getClassifications();
+ int max = 0;
+
+ for (int i = 0; i < classifications.length; i++) {
+ int[][] paths = ontology.getAllHierarchyPaths(classifications[i]);
+
+ for (int p = 0; p < paths.length; p++)
+ if (paths[p].length > max)
+ max = paths[p].length;
+ } // for i
+
+ return max;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String toString() {
+ StringBuffer sb = new StringBuffer();
+ sb.append("annotation: ");
+ sb.append(getCurator());
+ sb.append(", ");
+ sb.append(type);
+ sb.append(", ");
+ sb.append(species);
+ sb.append(" (" + count() + " entities) ");
+ sb.append(" (" + size() + " classifications) ");
+
+ return sb.toString();
+ }
+}
diff --git a/application/src/main/java/cytoscape/data/annotation/AnnotationDescription.java b/application/src/main/java/cytoscape/data/annotation/AnnotationDescription.java
new file mode 100755
index 0000000..59c96c9
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/annotation/AnnotationDescription.java
@@ -0,0 +1,146 @@
+/*
+ File: AnnotationDescription.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.data.annotation;
+
+import java.io.Serializable;
+
+
+/**
+ * Distinguish among different ontologies, by curator and type. For example,
+ * KEGG maintains two ontologies: metabolic pathways, and regulatory pathways.
+ * GO has three: biological process, molecular function, cellular component.
+ * This simple class captures these distinctions It will perhaps prove most
+ * useful when some data source (a biodata server, for example) contains a
+ * number of ontologies, and needs to communicate a summary of these to a
+ * client.
+ *
+ * @deprecated Use regular CyAttributes for annotation.
+ *
+ */
+ at Deprecated
+public class AnnotationDescription implements Serializable {
+ protected String species; // halopbacterium sp, saccharomyces cerevisiae, ...
+ protected String curator; // KEGG, GO, ...
+ protected String annotationType; // biological process, metabolic pathway, ...
+
+ /**
+ * @param species
+ * The formal Linnaean name (genus and species) is preferred
+ * @param curator
+ * The institute or group which maintains this annotation
+ * @param annotationType
+ * The nature of this annotation, eg, "metabolic pathway",
+ * "molecular function", or "cellular component"
+ */
+ public AnnotationDescription(String species, String curator, String annotationType) {
+ this.species = species;
+ this.curator = curator;
+ this.annotationType = annotationType;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getSpecies() {
+ return species;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getCurator() {
+ return curator;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getType() {
+ return annotationType;
+ }
+
+ /**
+ * redefine equals so that instances with the same contents are equal. this
+ * emulates the way that String equality is judged.
+ *
+ * @param obj DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean equals(Object obj) {
+ if (!obj.getClass().equals(this.getClass()))
+ return false;
+
+ AnnotationDescription other = (AnnotationDescription) obj;
+
+ if (species.equals(other.getSpecies()) && curator.equals(other.getCurator())
+ && annotationType.equals(other.getType()))
+ return true;
+
+ return false;
+ }
+
+ /**
+ * redefine hashCode so that instances with the same contents have the same
+ * hashCode. this will make them identical when used as the keys in
+ * HashMaps, the purpose for which they were invented.
+ *
+ * @return DOCUMENT ME!
+ */
+ public int hashCode() {
+ return species.hashCode() + curator.hashCode() + annotationType.hashCode();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String toString() {
+ StringBuffer sb = new StringBuffer();
+ sb.append("Data Source = " + curator + ", Type = " + annotationType + ", Species = "
+ + species);
+
+ return sb.toString();
+ }
+}
diff --git a/application/src/main/java/cytoscape/data/annotation/FlattenIntVectors.java b/application/src/main/java/cytoscape/data/annotation/FlattenIntVectors.java
new file mode 100755
index 0000000..ee3348a
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/annotation/FlattenIntVectors.java
@@ -0,0 +1,95 @@
+/*
+ File: FlattenIntVectors.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data.annotation;
+
+import java.util.Vector;
+
+
+/** given a vector which nests other vectors, each resolving
+ * eventually to a list of Integers, flatten it out into a simple 1-level-deep
+ * vector of Integer vectors.
+ * for example:
+ *
+ * ((1 2 3 (4 5 (6))), (7 (8) (9 10 11 (12))))
+ *
+ * becomes
+ *
+ * ((1 2 3 4 5 6), (7 8 9 10 11 12))
+ *
+ * @deprecated Use regular CyAttributes for annotation.
+ *
+ */
+ at Deprecated
+public class FlattenIntVectors {
+ Vector result = new Vector();
+
+ /**
+ * Creates a new FlattenIntVectors object.
+ *
+ * @param v DOCUMENT ME!
+ */
+ public FlattenIntVectors(Vector v) {
+ flatten(v);
+ }
+
+ private void flatten(Vector v) {
+ if (v == null)
+ return;
+
+ Object o = v.elementAt(0);
+ String className = o.getClass().getName();
+
+ if (!className.equalsIgnoreCase("java.util.Vector")) {
+ // CyLogger.getLogger().info (v);
+ result.addElement(v);
+ } else {
+ for (int i = 0; i < v.size(); i++) {
+ Vector w = (Vector) v.elementAt(i);
+ flatten(w);
+ } // for i
+ } // else
+ } // flatten
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Vector getResult() {
+ return result;
+ }
+} // FlattenIntVectors
diff --git a/application/src/main/java/cytoscape/data/annotation/Ontology.java b/application/src/main/java/cytoscape/data/annotation/Ontology.java
new file mode 100755
index 0000000..9817a56
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/annotation/Ontology.java
@@ -0,0 +1,296 @@
+/*
+ File: Ontology.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// Ontology.java
+package cytoscape.data.annotation;
+
+import java.io.Serializable;
+import java.util.HashMap;
+import java.util.Vector;
+
+
+/**
+ * Contains a collection of OntologyTerms, each of which may have pointers
+ * to other terms, creating a hierarchical controlled vocabulary. The pointers
+ * may express either "parent/child" relationships, or "container/contained"
+ * relationships. Objects of this class each aggregate a full set of
+ * related terms, creating a distinct ontology of a certain type, like KEGG's metabolic
+ * pathways, or GeneOntology's biological processes. Extensive navigational
+ * methods are provided so that, for instance, the full leaf-to-root biological
+ * process hierarchies which may exist for a given gene are conveniently
+ * returned.
+ *
+ * @deprecated Use regular CyAttributes for annotation.
+ *
+ */
+ at Deprecated
+public class Ontology implements Serializable {
+ protected String curator; // KEGG, GO, ...
+ protected String ontologyType; // biological process, metabolic pathway, ...
+ protected HashMap termHash;
+
+ /**
+ * @param curator The institute or group which maintains this ontology
+ * @param ontolotyType The nature of this ontology, eg, "metabolic pathway",
+ * "molecular function", or "cellular component"
+ */
+ public Ontology(String curator, String ontologyType) {
+ this.curator = curator;
+ this.ontologyType = ontologyType;
+ termHash = new HashMap();
+ } // ctor
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getCurator() {
+ return curator;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getType() {
+ return ontologyType;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param newTerm DOCUMENT ME!
+ */
+ public void add(OntologyTerm newTerm) {
+ termHash.put(new Integer(newTerm.getId()), newTerm);
+ } // add
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int size() {
+ return termHash.size();
+ } // size
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public HashMap getTerms() {
+ return termHash;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param id DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean containsTerm(int id) {
+ return termHash.containsKey(new Integer(id));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param id DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public OntologyTerm getTerm(int id) {
+ return (OntologyTerm) termHash.get(new Integer(id));
+ }
+
+ /**
+ * get all unique paths from the termID to the root of the ontology, in reverse
+ * order, with the most general classification first, and most specific last. for some
+ * terms, this will be a path, possibly with only one member. for other terms,
+ * which have be assigned to multiple categories, there will be multiple paths.
+ * furthermore, some categories belong to multiple pathways, further increasing
+ * the number of paths implicit in the termID.
+ *
+ */
+ public int[][] getAllHierarchyPaths(int termID) {
+ Vector flattenedList = getAllHierarchyPathsAsVector(termID);
+ int size = flattenedList.size();
+ int[][] result = new int[size][];
+
+ for (int i = 0; i < size; i++) {
+ Vector integerList = (Vector) flattenedList.get(i);
+ int max = integerList.size();
+ result[i] = new int[max];
+
+ for (int j = 0; j < max; j++) {
+ int indexForReversingOrder = max - j - 1;
+ result[i][j] = ((Integer) integerList.get(indexForReversingOrder)).intValue();
+ }
+ } // for i
+
+ return result;
+ } // getAllHierarchyPaths
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param termID DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String[][] getAllHierarchyPathsAsNames(int termID) {
+ int[][] hierarchy = getAllHierarchyPaths(termID);
+ String[][] result = new String[hierarchy.length][];
+
+ for (int i = 0; i < hierarchy.length; i++) {
+ int[] path = hierarchy[i];
+ int max = path.length;
+ result[i] = new String[max];
+
+ for (int j = 0; j < path.length; j++)
+ result[i][j] = getTerm(path[j]).getName();
+
+ //result [i][j] = getTerm (path [max-j-1]).getName ();
+ } // for i
+
+ return result;
+ } // getAllHierarchyPathsAsNames
+
+ protected Vector getAllHierarchyPathsAsVector(int termID) {
+ Vector nestedLists = recursiveGetPath(termID, new Vector());
+
+ if (nestedLists.size() == 0)
+ return nestedLists;
+
+ FlattenIntVectors flattener = new FlattenIntVectors(nestedLists);
+ Vector flattenedList = flattener.getResult();
+
+ return flattenedList;
+ } // getAllHierarchyPathsAsVector
+
+ protected Vector recursiveGetPath(int termID, Vector path) {
+ Integer ID = new Integer(termID);
+
+ if ((termHash != null) && termHash.containsKey(ID)) {
+ OntologyTerm term = (OntologyTerm) termHash.get(ID);
+ int parentCount = term.numberOfParentsAndContainers();
+ path.addElement(ID);
+
+ if (parentCount == 0)
+ return path;
+ else if (parentCount == 1) {
+ int parentID = term.getParentsAndContainers()[0];
+
+ return (recursiveGetPath(parentID, path));
+ } else { // assume for now: (parentCount == 2)
+
+ Vector newPath = new Vector();
+
+ for (int p = 0; p < parentCount; p++) {
+ Vector subPath = (Vector) path.clone();
+ int parent = term.getParentsAndContainers()[p];
+ newPath.addElement(recursiveGetPath(parent, subPath));
+ } // for p
+
+ return newPath;
+ } // else: 2 or more parents
+ } // if ID is in termHas
+
+ return path;
+ } // recursiveGetPath
+
+ protected Vector oldRecursiveGetPath(int termID, Vector path) {
+ Integer ID = new Integer(termID);
+
+ if ((termHash != null) && termHash.containsKey(ID)) {
+ OntologyTerm term = (OntologyTerm) termHash.get(ID);
+ int parentCount = term.numberOfParentsAndContainers();
+
+ if (parentCount == 0) {
+ path.addElement(ID);
+
+ return path;
+ } else if (parentCount == 1) {
+ path.addElement(ID);
+
+ int parentID = term.getParentsAndContainers()[0];
+
+ return (recursiveGetPath(parentID, path));
+ } else { // assume for now: (parentCount == 2)
+ path.addElement(ID);
+
+ Vector newPath = new Vector();
+ Vector path1 = (Vector) path.clone();
+ Vector path2 = (Vector) path.clone();
+ int parent1 = term.getParentsAndContainers()[0];
+ int parent2 = term.getParentsAndContainers()[1];
+ newPath.addElement(recursiveGetPath(parent1, path1));
+ newPath.addElement(recursiveGetPath(parent2, path2));
+
+ return newPath;
+ }
+ }
+
+ return path;
+ } // oldRecursiveGetPath
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public OntologyDescription getDescription() {
+ return new OntologyDescription(curator, ontologyType);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String toString() {
+ StringBuffer sb = new StringBuffer();
+ sb.append("ontology: " + ontologyType + "\n");
+ sb.append("curator: " + curator + "\n");
+
+ return sb.toString();
+ } // toString
+} // class Ontology
diff --git a/application/src/main/java/cytoscape/data/annotation/OntologyDescription.java b/application/src/main/java/cytoscape/data/annotation/OntologyDescription.java
new file mode 100755
index 0000000..f1a4a41
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/annotation/OntologyDescription.java
@@ -0,0 +1,101 @@
+/*
+ File: OntologyDescription.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// OntologyDescription.java
+package cytoscape.data.annotation;
+
+import java.io.Serializable;
+
+
+/**
+ * Distinguish among different ontologies, by curator and type.
+ * For example, KEGG maintains two ontologies: metabolic pathways,
+ * and regulatory pathways. GO has three: biological process, molecular
+ * function, cellular component.
+ * This simple class captures these distinctions
+ * It will perhaps prove most useful when some data source (a biodata server,
+ * for example) contains a number of ontologies, and needs to communicate
+ * a summary of these to a client.
+ *
+ * @deprecated Use regular CyAttributes for annotation.
+ *
+ */
+ at Deprecated
+public class OntologyDescription implements Serializable {
+ protected String curator; // KEGG, GO, ...
+ protected String ontologyType; // biological process, metabolic pathway, ...
+
+ /**
+ * @param curator The institute or group which maintains this ontology
+ * @param ontolotyType The nature of this ontology, eg, "metabolic pathway",
+ * "molecular function", or "cellular component"
+ */
+ public OntologyDescription(String curator, String ontologyType) {
+ this.curator = curator;
+ this.ontologyType = ontologyType;
+ } // ctor
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getCurator() {
+ return curator;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getType() {
+ return ontologyType;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String toString() {
+ StringBuffer sb = new StringBuffer();
+ sb.append("ontology: " + curator + ", " + ontologyType);
+
+ return sb.toString();
+ } // toString
+} // class OntologyDescription
diff --git a/application/src/main/java/cytoscape/data/annotation/OntologyTerm.java b/application/src/main/java/cytoscape/data/annotation/OntologyTerm.java
new file mode 100755
index 0000000..e00b3d9
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/annotation/OntologyTerm.java
@@ -0,0 +1,377 @@
+/*
+ File: OntologyTerm.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+// OntologyTerm.java
+package cytoscape.data.annotation;
+
+import java.io.*;
+
+import java.util.Vector;
+
+
+/**
+ * Represents one node in an ontology, which is a hierarchical classification of
+ * entities using a controlled vocabulary. Each term has a name, a unique
+ * integer identifier, a list of parent terms, and a list of containers. Parent
+ * terms capture the "is-child-of" relationship for this term. Container terms
+ * capture the "is-part-of" relationship. This data model was inspired by the
+ * three ontologies (biological process, molecular function, cellular component)
+ * of the Gene Ontology project. Other ontologies should work nicely with this
+ * class as well.
+ *
+ * @deprecated Use regular CyAttributes for annotation.
+ *
+ */
+ at Deprecated
+public class OntologyTerm implements Serializable {
+ String name;
+ int id;
+ Vector parents;
+ Vector containers;
+
+ /**
+ * Creates a new OntologyTerm object.
+ *
+ * @param name DOCUMENT ME!
+ * @param id DOCUMENT ME!
+ */
+ public OntologyTerm(String name, int id) {
+ this.name = name;
+ this.id = id;
+ parents = new Vector();
+ containers = new Vector();
+ } // ctor
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getId() {
+ return id;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param newParent DOCUMENT ME!
+ */
+ public void addParent(int newParent) {
+ parents.addElement(new Integer(newParent));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param newContainer DOCUMENT ME!
+ */
+ public void addContainer(int newContainer) {
+ containers.addElement(new Integer(newContainer));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int numberOfParentsAndContainers() {
+ return numberOfParents() + numberOfContainers();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int numberOfParents() {
+ return parents.size();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int numberOfContainers() {
+ return containers.size();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] getParents() {
+ int size = numberOfParents();
+ int[] result = new int[size];
+
+ for (int i = 0; i < size; i++) {
+ Integer tmp = (Integer) parents.elementAt(i);
+ result[i] = tmp.intValue();
+ }
+
+ return result;
+ } // getParents
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] getContainers() {
+ int size = numberOfContainers();
+ int[] result = new int[size];
+
+ for (int i = 0; i < size; i++) {
+ Integer tmp = (Integer) containers.elementAt(i);
+ result[i] = tmp.intValue();
+ }
+
+ return result;
+ } // getContainers
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] getParentsAndContainers() {
+ int size = numberOfParents() + numberOfContainers();
+
+ int[] result = new int[size];
+ int[] parents = getParents();
+ int[] containers = getContainers();
+
+ for (int i = 0; i < parents.length; i++)
+ result[i] = parents[i];
+
+ for (int i = 0; i < containers.length; i++)
+ result[i + parents.length] = containers[i];
+
+ return result;
+ } // getParentsAndContainers
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param other DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isParentOf(OntologyTerm other) {
+ int[] otherParents = other.getParents();
+
+ for (int i = 0; i < otherParents.length; i++) {
+ if (this.id == otherParents[i]) {
+ return true;
+ }
+ }
+
+ return false;
+ }
+
+ /**
+ * @param ontology
+ * the Ontology that contains the terms
+ * @return true if this OntologyTerm has a path to the other ontologyTerm
+ * via parent-child or container-contained relationships
+ */
+ public boolean isAncestorOf(Ontology ontology, OntologyTerm other) {
+ if (isParentOrContainerOf(other)) {
+ return true;
+ }
+
+ int[] myParents = getParentsAndContainers();
+
+ for (int i = 0; i < myParents.length; i++) {
+ OntologyTerm parentTerm = ontology.getTerm(myParents[i]);
+
+ if ((parentTerm != null) && parentTerm.isAncestorOf(ontology, other)) {
+ return true;
+ }
+ }
+
+ return false;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param other DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isChildOf(OntologyTerm other) {
+ int otherId = other.getId();
+ int[] myParents = getParents();
+
+ for (int i = 0; i < myParents.length; i++) {
+ if (myParents[i] == otherId) {
+ return true;
+ }
+ }
+
+ return false;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param other DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isContainerOf(OntologyTerm other) {
+ int[] otherContainers = other.getContainers();
+
+ for (int i = 0; i < otherContainers.length; i++) {
+ if (this.id == otherContainers[i]) {
+ return true;
+ }
+ }
+
+ return false;
+ } // isContainerOf
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param other DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isContainedIn(OntologyTerm other) {
+ int[] myContainers = getContainers();
+ int otherID = other.getId();
+
+ for (int i = 0; i < myContainers.length; i++) {
+ if (myContainers[i] == otherID) {
+ return true;
+ }
+ }
+
+ return false;
+ } // isContainedIn
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param other DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isChildOfOrContainedIn(OntologyTerm other) {
+ int otherID = other.getId();
+ int[] myParentsAndContainers = getParentsAndContainers();
+
+ for (int i = 0; i < myParentsAndContainers.length; i++) {
+ if (otherID == myParentsAndContainers[i]) {
+ return true;
+ }
+ }
+
+ return false;
+ } // isChildOfOrContainedIn
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param other DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isParentOrContainerOf(OntologyTerm other) {
+ int[] otherParentsAndContainers = other.getParentsAndContainers();
+
+ for (int i = 0; i < otherParentsAndContainers.length; i++) {
+ if (this.id == otherParentsAndContainers[i]) {
+ return true;
+ }
+ }
+
+ return false;
+ } // isParentOrContainerOf
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String toString() {
+ StringBuffer sb = new StringBuffer();
+ sb.append("name: ");
+ sb.append(name);
+ sb.append("\n");
+
+ sb.append("id: ");
+ sb.append(id);
+ sb.append("\n");
+
+ int[] parents = getParents();
+
+ sb.append("parents: ");
+
+ for (int i = 0; i < parents.length; i++) {
+ sb.append(parents[i]);
+ sb.append(" ");
+ }
+
+ sb.append("\n");
+
+ int[] containers = getContainers();
+
+ sb.append("containers: ");
+
+ for (int i = 0; i < containers.length; i++) {
+ sb.append(containers[i]);
+ sb.append(" ");
+ }
+
+ sb.append("\n");
+
+ return sb.toString();
+ } // toString
+} // OntologyTerm
diff --git a/application/src/main/java/cytoscape/data/annotation/package.html b/application/src/main/java/cytoscape/data/annotation/package.html
new file mode 100755
index 0000000..9c243e8
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/annotation/package.html
@@ -0,0 +1,12 @@
+<html>
+<head>
+ <!-- $Revision: 6563 $
+ $Date: 2005-08-17 20:59:44 +0200 (Wed, 17 Aug 2005) $
+ $Author: nlandys $
+ -->
+</head>
+
+<body>
+Classes used to represent generic annotation data in Cytoscape.
+</body>
+</html>
diff --git a/application/src/main/java/cytoscape/data/annotation/readers/AnnotationFlatFileReader.java b/application/src/main/java/cytoscape/data/annotation/readers/AnnotationFlatFileReader.java
new file mode 100755
index 0000000..eb14d7f
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/annotation/readers/AnnotationFlatFileReader.java
@@ -0,0 +1,270 @@
+/*
+ File: AnnotationFlatFileReader.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+// AnnotationFlatFileReader.java
+package cytoscape.data.annotation.readers;
+
+import cytoscape.data.annotation.Annotation;
+
+import cytoscape.data.readers.TextFileReader;
+import cytoscape.data.readers.TextHttpReader;
+import cytoscape.data.readers.TextJarReader;
+
+import cytoscape.data.synonyms.Thesaurus;
+import cytoscape.logger.CyLogger;
+
+import java.io.BufferedReader;
+import java.io.File;
+
+import java.util.Vector;
+
+
+/**
+ *
+ */
+public class AnnotationFlatFileReader {
+ Annotation annotation;
+ String annotationType;
+ String species;
+ String curator;
+ String filename;
+ File directoryAbsolute;
+ String fullText;
+ String[] lines;
+ Vector extractedLines;
+ boolean flip;
+ Thesaurus thr;
+
+ /**
+ * Creates a new AnnotationFlatFileReader object.
+ *
+ * @param file DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public AnnotationFlatFileReader(File file) throws Exception {
+ this(file.getPath(), null);
+ }
+
+ /*
+ * New const. written by Kei Ono (kono at uscd.edu) This accept new readers
+ * written by Nerius.
+ */
+
+ /**
+ * Creates a new AnnotationFlatFileReader object.
+ *
+ * @param rd DOCUMENT ME!
+ * @param th DOCUMENT ME!
+ * @param isFlip DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public AnnotationFlatFileReader(final BufferedReader rd, Thesaurus th, boolean isFlip)
+ throws Exception {
+ fullText = null;
+ extractedLines = new Vector();
+ this.thr = th;
+ this.flip = isFlip;
+
+ String curLine = null;
+
+ try {
+ while (null != (curLine = rd.readLine())) {
+ extractedLines.add(curLine);
+ }
+ }
+ finally {
+ if (rd != null) {
+ rd.close();
+ }
+ }
+
+ Object[] entireFile = extractedLines.toArray();
+ lines = new String[entireFile.length];
+
+ try {
+ System.arraycopy(entireFile, 0, lines, 0, lines.length);
+ } catch (Exception e) {
+ throw e;
+ }
+
+ parseHeader(lines[0]);
+ parse();
+ }
+
+ /**
+ * Creates a new AnnotationFlatFileReader object.
+ *
+ * @param filename DOCUMENT ME!
+ * @param th DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public AnnotationFlatFileReader(String filename, Thesaurus th) throws Exception {
+ // CyLogger.getLogger().info ("AnnotationFlatFileReader on " + filename);
+ this.filename = filename;
+ this.thr = th;
+
+ try {
+ if (filename.trim().startsWith("jar://")) {
+ TextJarReader reader = new TextJarReader(filename);
+ reader.read();
+ fullText = reader.getText();
+ } else if (filename.trim().startsWith("http://")) {
+ TextHttpReader reader = new TextHttpReader(filename);
+ reader.read();
+ fullText = reader.getText();
+ } else {
+ TextFileReader reader = new TextFileReader(filename);
+ reader.read();
+ fullText = reader.getText();
+ }
+ } catch (Exception e0) {
+ CyLogger.getLogger().warn("-- Exception while reading ontology flat file " + filename, e0);
+
+ return;
+ }
+
+ /***********************************************************************
+ * this.species = species; this.annotationType = annotationType;
+ * directoryAbsolute = file.getAbsoluteFile().getParentFile ();
+ * TextFileReader reader = new TextFileReader (file.getPath ());
+ * reader.read (); fullText = reader.getText ();
+ **********************************************************************/
+ lines = fullText.split("\n");
+ // CyLogger.getLogger().info ("number of lines: " + lines.length);
+ parseHeader(lines[0]);
+ parse();
+ }
+
+ private int stringToInt(String s) {
+ try {
+ return Integer.parseInt(s);
+ } catch (NumberFormatException nfe) {
+ return -1;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param firstLine DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ * @throws IllegalArgumentException DOCUMENT ME!
+ */
+ public void parseHeader(String firstLine) throws Exception {
+ String[] tokens = firstLine.trim().split("\\)");
+
+ String errorMsg = "error in AnnotationFlatFileReader.parseHeader ().\n";
+ errorMsg += ("First line of " + filename + " must have form:\n");
+ errorMsg += " (species=Homo sapiens) (type=Biological Process) (curator=GO)\n";
+ errorMsg += "instead found:\n";
+ errorMsg += (" " + firstLine + "\n");
+
+ if (tokens.length != 3)
+ throw new IllegalArgumentException(errorMsg);
+
+ for (int i = 0; i < tokens.length; i++) {
+ String[] subTokens = tokens[i].split("=");
+
+ if (subTokens.length != 2)
+ throw new IllegalArgumentException(errorMsg);
+
+ String name = subTokens[0].trim();
+ String value = subTokens[1].trim();
+
+ if (name.equalsIgnoreCase("(species"))
+ species = value;
+ else if (name.equalsIgnoreCase("(type"))
+ annotationType = value;
+ else if (name.equalsIgnoreCase("(curator"))
+ curator = value;
+ }
+ } // parseHeader
+
+ private void parse() throws Exception {
+ annotation = new Annotation(species, annotationType, curator);
+
+ String key = null;
+
+ for (int i = 1; i < lines.length; i++) {
+ String line = lines[i];
+
+ if (line.length() < 2)
+ continue;
+
+ String[] tokens = line.split("=");
+ String entityName = tokens[0].trim();
+ int id = stringToInt(tokens[1].trim());
+
+ // Swap first alias and label
+ if (flip == false) {
+ annotation.add(entityName, id);
+
+ String[] syno = thr.getAllCommonNames(entityName);
+
+ for (int idx = 0; idx < syno.length; idx++) {
+ annotation.add(syno[idx], id);
+ }
+ } else if (flip == true) {
+ // CyLogger.getLogger().info ( "EntityName is " + entityName );
+ key = thr.getNodeLabel(entityName);
+
+ if (key != null) {
+ // CyLogger.getLogger().info ("Found: Key is " + key );
+ annotation.add(key, id);
+ } else {
+ // annotation.add ( "Undef", id);
+ }
+ }
+
+ // CyLogger.getLogger().info ("Anno# Key = " + entityName + ", ID = " +
+ // id);
+ }
+ } // parse
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Annotation getAnnotation() {
+ return annotation;
+ }
+} // class AnnotationFlatFileReader
diff --git a/application/src/main/java/cytoscape/data/annotation/readers/AnnotationXmlReader.java b/application/src/main/java/cytoscape/data/annotation/readers/AnnotationXmlReader.java
new file mode 100755
index 0000000..0f57753
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/annotation/readers/AnnotationXmlReader.java
@@ -0,0 +1,142 @@
+/*
+ File: AnnotationXmlReader.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// AnnotationXmlReader.java
+package cytoscape.data.annotation.readers;
+
+import cytoscape.data.annotation.*;
+import cytoscape.logger.CyLogger;
+
+import org.jdom.*;
+
+import org.jdom.input.*;
+
+import org.jdom.output.*;
+
+import java.io.*;
+
+import java.util.List;
+import java.util.ListIterator;
+import java.util.Vector;
+
+
+/**
+ *
+ */
+public class AnnotationXmlReader {
+ File xmlFile;
+ Annotation annotation;
+ File directoryAbsolute;
+
+ /**
+ * Creates a new AnnotationXmlReader object.
+ *
+ * @param xmlFile DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public AnnotationXmlReader(File xmlFile) throws Exception {
+ if (!xmlFile.canRead()) {
+ CyLogger.getLogger().info("---- data.annotation.readers.AnnotationXmlReader error, cannot read\n " + xmlFile);
+ throw new Exception("cannot read input: " + xmlFile);
+ }
+
+ this.xmlFile = xmlFile;
+ directoryAbsolute = xmlFile.getAbsoluteFile().getParentFile();
+ read();
+ }
+
+ private void read() throws Exception {
+ SAXBuilder builder = new SAXBuilder();
+ InputStream is = null;
+ Document doc;
+ Element root;
+
+ try {
+ is = new FileInputStream(xmlFile);
+ doc = builder.build(is, xmlFile.toURI().toURL().toString());
+ }
+ finally {
+ if (is != null) {
+ is.close();
+ }
+ }
+
+ root = doc.getRootElement();
+
+ String species = root.getAttributeValue("species");
+ String ontologyXmlFileName = root.getAttributeValue("ontology");
+ String annotationType = root.getAttributeValue("type");
+
+ File ontologyXmlFileAbsolutePath = new File(directoryAbsolute, ontologyXmlFileName);
+
+ if (!ontologyXmlFileAbsolutePath.canRead()) {
+ String warn = "annotation xml file must name its associated ontology xml file ";
+ warn += "by giving its path relative to the actual location of the ";
+ warn += "annotation xml file.\n";
+ warn += "could not find:";
+ warn += " " + ontologyXmlFileAbsolutePath;
+ CyLogger.getLogger().warn(warn);
+ throw new FileNotFoundException(ontologyXmlFileAbsolutePath.getPath());
+ }
+
+ OntologyXmlReader oReader = new OntologyXmlReader(ontologyXmlFileAbsolutePath);
+ Ontology ontology = oReader.getOntology();
+
+ annotation = new Annotation(species, annotationType, ontology);
+
+ List children = root.getChildren();
+ ListIterator iterator = children.listIterator();
+
+ while (iterator.hasNext()) {
+ Element termElement = (Element) iterator.next();
+ String entityName = termElement.getChild("entity").getText().trim();
+ String tmp = termElement.getChild("id").getText().trim();
+ int id = Integer.parseInt(tmp);
+ annotation.add(entityName, id);
+ }
+ } // read
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Annotation getAnnotation() {
+ return annotation;
+ }
+} // class AnnotationXmlReader
diff --git a/application/src/main/java/cytoscape/data/annotation/readers/OntologyFlatFileReader.java b/application/src/main/java/cytoscape/data/annotation/readers/OntologyFlatFileReader.java
new file mode 100755
index 0000000..f35d39b
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/annotation/readers/OntologyFlatFileReader.java
@@ -0,0 +1,242 @@
+/*
+ File: OntologyFlatFileReader.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+// OntologyFlatFileReader.java
+package cytoscape.data.annotation.readers;
+
+import cytoscape.data.annotation.Ontology;
+import cytoscape.data.annotation.OntologyTerm;
+
+import cytoscape.data.readers.TextFileReader;
+import cytoscape.data.readers.TextHttpReader;
+import cytoscape.data.readers.TextJarReader;
+import cytoscape.logger.CyLogger;
+
+import java.io.BufferedReader;
+import java.io.File;
+
+import java.util.Vector;
+
+
+/**
+ *
+ */
+public class OntologyFlatFileReader {
+ Ontology ontology;
+ String curator = "unknown";
+ String ontologyType = "unknown";
+ String filename;
+ String fullText;
+ String[] lines;
+ Vector extractedLines;
+
+ /**
+ * Creates a new OntologyFlatFileReader object.
+ *
+ * @param file DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public OntologyFlatFileReader(File file) throws Exception {
+ this(file.getPath());
+ }
+
+ // Constructor to accept reader as the argument.
+ /**
+ * Creates a new OntologyFlatFileReader object.
+ *
+ * @param rd DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public OntologyFlatFileReader(final BufferedReader rd) throws Exception {
+ fullText = null;
+ extractedLines = new Vector();
+
+ String curLine = null;
+
+ try {
+ while ((curLine = rd.readLine()) != null) {
+ extractedLines.add(curLine);
+
+ // CyLogger.getLogger().info( curLine );
+ }
+ }
+ finally {
+ if (rd != null) {
+ rd.close();
+ }
+ }
+
+ Object[] entireFile = extractedLines.toArray();
+ lines = new String[entireFile.length];
+
+ try {
+ System.arraycopy(entireFile, 0, lines, 0, lines.length);
+ } catch (Exception e) {
+ throw e;
+ }
+
+ parseHeader();
+ parse();
+ }
+
+ /**
+ * Creates a new OntologyFlatFileReader object.
+ *
+ * @param filename DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public OntologyFlatFileReader(String filename) throws Exception {
+ this.filename = filename;
+
+ try {
+ if (filename.trim().startsWith("jar://")) {
+ TextJarReader reader = new TextJarReader(filename);
+ reader.read();
+ fullText = reader.getText();
+ } else if (filename.trim().startsWith("http://")) {
+ TextHttpReader reader = new TextHttpReader(filename);
+ reader.read();
+ fullText = reader.getText();
+ } else {
+ TextFileReader reader = new TextFileReader(filename);
+ reader.read();
+ fullText = reader.getText();
+ }
+ } catch (Exception e0) {
+ CyLogger.getLogger().warn("-- Exception while reading ontology flat file " + filename, e0);
+
+ return;
+ }
+
+ lines = fullText.split("\n");
+ parseHeader();
+ parse();
+ } // ctor
+
+ private int stringToInt(String s) {
+ try {
+ return Integer.parseInt(s);
+ } catch (NumberFormatException nfe) {
+ return -1;
+ }
+ }
+
+ private void parseHeader() throws Exception {
+ String firstLine = lines[0].trim();
+ String[] tokens = firstLine.split("\\)");
+
+ String errorMsg = "error in OntologyFlatFileReader.parseHeader ().\n";
+ errorMsg += ("First line of " + filename + " must have form:\n");
+ errorMsg += " (curator=GO) (type=all) \n";
+ errorMsg += "instead found:\n";
+ errorMsg += (" " + firstLine + "\n");
+
+ if (tokens.length != 2)
+ throw new IllegalArgumentException(errorMsg);
+
+ String[] curatorRaw = tokens[0].split("=");
+
+ if (curatorRaw.length != 2)
+ throw new IllegalArgumentException(errorMsg);
+
+ curator = curatorRaw[1].trim();
+
+ String[] typeRaw = tokens[1].split("=");
+
+ if (typeRaw.length != 2)
+ throw new IllegalArgumentException(errorMsg);
+
+ ontologyType = typeRaw[1].trim();
+ } // parseHeader
+
+ private void parse() throws Exception {
+ ontology = new Ontology(curator, ontologyType);
+
+ for (int i = 1; i < lines.length; i++) {
+ String line = lines[i];
+
+ int equals = line.indexOf("=");
+ String idString = line.substring(0, equals).trim();
+ int id = stringToInt(idString);
+ String value = line.substring(equals + 1);
+
+ int firstLeftBracket = value.indexOf("[");
+
+ if (firstLeftBracket < 0)
+ continue;
+
+ String name = value.substring(0, firstLeftBracket).trim();
+ OntologyTerm term = new OntologyTerm(name, id);
+
+ int isaStart = value.indexOf("[isa: ");
+
+ if (isaStart >= 0) {
+ int isaEnd = value.indexOf("]", isaStart);
+ String rawIsa = value.substring(isaStart + 6, isaEnd).trim();
+ String[] allIsas = rawIsa.split(" ");
+
+ for (int j = 0; j < allIsas.length; j++)
+ term.addParent(stringToInt(allIsas[j]));
+ } // found "[isa: "
+
+ int partofStart = value.indexOf("[partof: ");
+
+ if (partofStart >= 0) {
+ int partofEnd = value.indexOf("]", partofStart);
+ String rawPartof = value.substring(partofStart + 9, partofEnd).trim();
+ String[] allPartofs = rawPartof.split(" ");
+
+ for (int j = 0; j < allPartofs.length; j++)
+ term.addContainer(stringToInt(allPartofs[j]));
+ } // if
+
+ ontology.add(term);
+ } // for i
+ } // read
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Ontology getOntology() {
+ return ontology;
+ }
+} // class OntologyFlatFileReader
diff --git a/application/src/main/java/cytoscape/data/annotation/readers/OntologyXmlReader.java b/application/src/main/java/cytoscape/data/annotation/readers/OntologyXmlReader.java
new file mode 100755
index 0000000..fde2986
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/annotation/readers/OntologyXmlReader.java
@@ -0,0 +1,143 @@
+/*
+ File: OntologyXmlReader.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// OntologyXmlReader.java
+package cytoscape.data.annotation.readers;
+
+import cytoscape.data.annotation.Ontology;
+import cytoscape.data.annotation.OntologyTerm;
+
+import org.jdom.*;
+
+import org.jdom.input.*;
+
+import org.jdom.output.*;
+
+import java.io.*;
+
+import java.util.List;
+import java.util.ListIterator;
+import java.util.Vector;
+import org.xml.sax.InputSource;
+
+
+/**
+ *
+ */
+public class OntologyXmlReader {
+ File xmlFile;
+ Ontology ontology;
+
+ /**
+ * Creates a new OntologyXmlReader object.
+ *
+ * @param xmlFile DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public OntologyXmlReader(File xmlFile) throws Exception {
+ this.xmlFile = xmlFile;
+ read();
+ }
+
+ private void read() throws Exception {
+ SAXBuilder builder = new SAXBuilder();
+ InputStream is = null;
+ Document doc;
+ Element root;
+
+ try {
+ is = new FileInputStream(xmlFile);
+ doc = builder.build(is, xmlFile.toURI().toURL().toString());
+ }
+ finally {
+ if (is != null) {
+ is.close();
+ }
+ }
+
+ root = doc.getRootElement();
+
+ String curator = root.getAttributeValue("curator");
+ String ontologyType = root.getAttributeValue("type");
+
+ ontology = new Ontology(curator, ontologyType);
+
+ List children = root.getChildren();
+ ListIterator iterator = children.listIterator();
+
+ while (iterator.hasNext()) {
+ Element termElement = (Element) iterator.next();
+ String name = termElement.getChild("name").getText().trim();
+ String tmp = termElement.getChild("id").getText().trim();
+ int id = Integer.parseInt(tmp);
+
+ OntologyTerm term = new OntologyTerm(name, id);
+
+ List parents = termElement.getChildren("isa");
+ ListIterator parentIterator = parents.listIterator();
+
+ while (parentIterator.hasNext()) {
+ Element parentElement = (Element) parentIterator.next();
+ String parentTmp = parentElement.getText().trim();
+ int parent = Integer.parseInt(parentTmp);
+ term.addParent(parent);
+ }
+
+ List containers = termElement.getChildren("partof");
+ ListIterator containerIterator = containers.listIterator();
+
+ while (containerIterator.hasNext()) {
+ Element containerElement = (Element) containerIterator.next();
+ String containerTmp = containerElement.getText().trim();
+ int container = Integer.parseInt(containerTmp);
+ term.addContainer(container);
+ }
+
+ ontology.add(term);
+ }
+ } // read
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Ontology getOntology() {
+ return ontology;
+ }
+} // class OntologyXmlReader
diff --git a/application/src/main/java/cytoscape/data/annotation/readers/package.html b/application/src/main/java/cytoscape/data/annotation/readers/package.html
new file mode 100755
index 0000000..44d47a8
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/annotation/readers/package.html
@@ -0,0 +1,12 @@
+<html>
+<head>
+ <!-- $Revision: 6563 $
+ $Date: 2005-08-17 20:59:44 +0200 (Wed, 17 Aug 2005) $
+ $Author: nlandys $
+ -->
+</head>
+
+<body>
+Reader classes for generic annotation data.
+</body>
+</html>
diff --git a/application/src/main/java/cytoscape/data/attr/CountedIterator.java b/application/src/main/java/cytoscape/data/attr/CountedIterator.java
new file mode 100644
index 0000000..6855485
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/attr/CountedIterator.java
@@ -0,0 +1,51 @@
+/*
+ File: CountedIterator.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data.attr;
+
+import java.util.Iterator;
+
+
+/**
+ * A java.util.Iterator with knowledge of how many elements are remaining.
+ */
+public interface CountedIterator extends Iterator {
+ /**
+ * Returns a non-negative integer I such that next() will successfully
+ * return a value no more and no less than I times.
+ */
+ public int numRemaining();
+}
diff --git a/application/src/main/java/cytoscape/data/attr/MultiHashMap.java b/application/src/main/java/cytoscape/data/attr/MultiHashMap.java
new file mode 100644
index 0000000..56cb7b8
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/attr/MultiHashMap.java
@@ -0,0 +1,226 @@
+/*
+ File: MultiHashMap.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data.attr;
+
+
+/**
+ * This interface consists of the API specification to bind attribute
+ * values to objects. A sibling API is MultiHashMapDefinition, which is used
+ * to define attribute spaces in which attribute values can be bound
+ * to objects; attribute space definition is the first thing that happens.
+ */
+public interface MultiHashMap {
+ /**
+ * Binds an attribute value to an object.
+ * @param objectKey the object to which to bind a new attribute value.
+ * @param attributeName the attribute definition in which to assign an
+ * attribute value.
+ * @param attributeValue the attribute value to bind;
+ * the type of this object must be of the appropriate type based on
+ * the value type of specified attribute definition.
+ * @param keyIntoValue an array of length equal to the dimensionality of
+ * the key space of specified attribute definition; entry at index i
+ * is a "representative" from dimension i + 1 of the key space; if
+ * specified attribute definition has a zero-dimensional key space (this
+ * is perhaps the most common scenario) then
+ * this array may either be null or the empty array.
+ * @return previous attribute value bound at specified key sequence, or
+ * null if no attribute value was previously bound.
+ * @exception IllegalStateException if attributeName is not an existing
+ * attribute definition; see MultiHashMapDefinition.
+ * @exception NullPointerException if objectKey, attributeName, or
+ * attributeValue is null, or if keyIntoValue is [not null and]
+ * of positive length and any one of its entries is null.
+ * @exception ClassCastException if attributeValue is not of the
+ * appropriate object type or if any one of keyIntoValue's representatives
+ * is not of the appropriate object type; see MultiHashMapDefinition.
+ * @exception IllegalArgumentException if keyIntoValue's length does not
+ * match the key space dimensionality of attributeName.
+ */
+ public Object setAttributeValue(String objectKey, String attributeName, Object attributeValue,
+ Object[] keyIntoValue);
+
+ /**
+ * Retrieves a bound attribute value from an object.
+ * @param objectKey the object from which to retrieve a bound attribute
+ * value.
+ * @param attributeName the attribute definition in which assigned
+ * attribute value exists.
+ * @param keyIntoValue an array of length equal to the dimensionality of
+ * the key space of specified attribute definition; entry at index i
+ * is a "representative" from dimension i + 1 of the key space; if
+ * specified attribute definition has a zero-dimensional key space (this
+ * is perhaps the most commen scenario) then this array may either
+ * be null or the empty array.
+ * @return the same value that was set with setAttributeValue() with
+ * parameters specified or null if no such value is bound.
+ * @exception IllegalStateException if attributeName is not an existing
+ * attribute definition; see MultiHashMapDefinition.
+ * @exception NullPointerException if objectKey or attributeName is null,
+ * or if keyIntoValue is [not null and] of positive length and any one
+ * of its entries is null.
+ * @exception ClassCastException if any one of keyIntoValue's representatives
+ * is not of the appropriate object type; see MultiHashMapDefinition.
+ * @exception IllegalArgumentException if keyIntoValue's length does not
+ * match the key space dimensionality of attributeName.
+ */
+ public Object getAttributeValue(String objectKey, String attributeName, Object[] keyIntoValue);
+
+ /**
+ * This method is the same as getAttributeValue(), only the retrieved
+ * attribute value is also deleted.<p>
+ * @see #getAttributeValue(String, String, Object[])
+ */
+ public Object removeAttributeValue(String objectKey, String attributeName, Object[] keyIntoValue);
+
+ /**
+ * Removes all values bound to objectKey in attributeName. Most attribute
+ * definitions will have no key space, and such attribute definitions will
+ * bind at most one attribute value to any give objectKey; this method is
+ * useful with attribute definitions that have nonzero key spaces.
+ * @param objectKey the object from which to delete all bound attribute
+ * values.
+ * @param attributeName the attribute definition in which to delete
+ * attribute values.
+ * @return true if and only if objectKey had at least one attribute value
+ * bound in attributeName prior to this method invocation.
+ * @exception IllegalStateException if attributeName is not an existing
+ * attribute definition; see MultiHashMapDefinition.
+ * @exception NullPointerException if objectKey or attributeName is null.
+ */
+ public boolean removeAllAttributeValues(String objectKey, String attributeName);
+
+ /**
+ * For all key sequences, having specified prefix, that map into bound
+ * values on objectKey in attributeName, returns the [unique] representatives
+ * from dimension keyPrefix.length + 1. This method
+ * only makes sense for attributeNames that have nonzero key space
+ * dimensionality.<p>
+ * NOTE: The returned iterator does not support the remove() operation.<p>
+ * IMPORTANT: The returned iterator becomes invalid as soon as any
+ * attribute value is set or removed for some objectKey in attributeName.
+ * Calling methods on an invalid iterator will result in undefined
+ * behavior of that iterator.
+ * @param objectKey the object to query.
+ * @param attributeName the attribute definition to query.
+ * @param keyPrefix an array of length K, where K is strictly less than
+ * the dimensionality of key space of attributeName;
+ * entry at index i contains a "representative" from dimension i + 1 of
+ * the key space of attributeName; keyPrefix may
+ * be either null or the empty array, in which case the iterator
+ * returned consists of the representatives in the first dimension of
+ * key space.
+ * @return an iterator of key representatives in key space dimension K + 1
+ * along specified keyPrefix; the iterator returned is never null;
+ * the order of the returned keys is arbitrary.
+ * @exception IllegalStateException if attributeName is not an existing
+ * attribute definition; see MultiHashMapDefinition.
+ * @exception NullPointerException if objectKey or attributeName is null,
+ * or if keyPrefix is [not null and] of positive length and any one
+ * of its entries is null.
+ * @exception ClassCastException if any one of keyPrefix's representatives
+ * is not of the appropriate object type; see MultiHashMapDefinition.
+ * @exception IllegalArgumentException if keyPrefix's length is not
+ * strictly less than the dimensionality of attributeName's key space.
+ */
+ public CountedIterator getAttributeKeyspan(String objectKey, String attributeName,
+ Object[] keyPrefix);
+
+ /**
+ * Returns all objectKeys that have at least one attribute value assigned
+ * in attributeName.<p>
+ * NOTE: The returned iterator does not support the remove() operation.<p>
+ * NOTE: To quickly determine whether or not a given objectKey has at least
+ * one attribute value bound to it under attributeName, test for a null
+ * return value in getAttributeValue(objectKey, attributeName, null)
+ * if attributeName has zero key space dimensionality, or test for an empty
+ * iterator return value in
+ * getAttributeKeyspan(objectKey, attributeName, null) if attributeName has
+ * nonzero key space dimensionality.<p>
+ * IMPORTANT: The returned iterator becomes invalid as soon as any
+ * attribute value is set or removed for some objectKey in attributeName.
+ * Calling methods on an invalid iterator will result in undefined
+ * behavior of that iterator.
+ * @param attributeName the attribute definition to query.
+ * @return an iterator of objectKey strings (java.lang.String) that
+ * currently have value[s] assigned to them in the specified attribute
+ * definition; the order of the returned strings is arbitrary; null is
+ * never returned.
+ * @exception IllegalStateException if attributeName is not an existing
+ * attribute definition; to test whether or not attributeName is an
+ * existing attribute definition, use
+ * MultiHashMapDefinition.getAttributeValueType(attributeName).
+ * @exception NullPointerException if attributeName is null.
+ * @see MultiHashMapDefinition#getAttributeValueType(String)
+ */
+ public CountedIterator getObjectKeys(String attributeName);
+
+ /*
+ * I'm not including this method in the API for good reasons.
+ * For one, removal is the opposite of insertion, and even though
+ * we could potentially remove many entries at once for free, because
+ * we inserted them one-by-one, the time complexity for a complete
+ * insert-remove cycle of many elements is governed by the insertion
+ * time complexity. Therefore we don't lose in overall time complexity if
+ * we omit this removal optimization. Second, I want listeners to hear
+ * all removals that happen. If I include this method, I either have
+ * to iterate over all values that have been removed to fire appropriate
+ * listener events (which defeats the purpose of this optimization)
+ * or I have to define a separate listener method that
+ * says "hey I've removed a keyspan", but then the listener would not
+ * get a list of values (corresponding to all keys, recursively, in
+ * keyspan) that were removed.
+ */
+
+ // public int removeAttributeKeyspan(String objectKey,
+ // String attributeName,
+ // Object[] keyPrefix);
+
+ /**
+ * Registers a listener for receiving events having to do with
+ * attribute values being assigned and removed.
+ * @param listener the listener to register.
+ */
+ public void addDataListener(MultiHashMapListener listener);
+
+ /**
+ * Unregisters a listener; this method has the opposite effect as
+ * addDataListener(listener).
+ * @param listener the listener to unregister.
+ */
+ public void removeDataListener(MultiHashMapListener listener);
+}
diff --git a/application/src/main/java/cytoscape/data/attr/MultiHashMapDefinition.java b/application/src/main/java/cytoscape/data/attr/MultiHashMapDefinition.java
new file mode 100644
index 0000000..71e30c8
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/attr/MultiHashMapDefinition.java
@@ -0,0 +1,172 @@
+/*
+ File: MultiHashMapDefinition.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data.attr;
+
+
+/**
+ * This interface contains the API specification for creating
+ * attribute definitions.
+ */
+public interface MultiHashMapDefinition {
+ /**
+ * This type corresponds to java.lang.Boolean.
+ */
+ public final byte TYPE_BOOLEAN = 1;
+
+ /**
+ * This type corresponds to java.lang.Double.
+ */
+ public final byte TYPE_FLOATING_POINT = 2;
+
+ /**
+ * This type corresponds to java.lang.Integer.
+ */
+ public final byte TYPE_INTEGER = 3;
+
+ /**
+ * This type corresponds to java.lang.String.
+ */
+ public final byte TYPE_STRING = 4;
+
+ /**
+ * Creates an attribute definition. An attribute definition must be
+ * created before binding an attribute value to an object.<p>
+ * Perhaps the most common type of attribute definition is one where the
+ * key space has zero dimensions. For example, if I want to identify each
+ * object as having a color, I would create an attribute definition which
+ * stores values of TYPE_STRING (for storing "red", "blue", and so on)
+ * and has no key sequence mapping color
+ * values. By "no key sequence" I mean that the input parameter
+ * keyTypes would be either null or the empty array for my
+ * color attribute definition.<p>
+ * The more interesting case is where the key space in an attribute
+ * definition has one or more dimensions. For example, if I
+ * wanted to create an attribute that represents measured p-values for
+ * all objects over a set of experiments ("Ideker experiment",
+ * "Salk experiment", ...) I would define a one-dimensional key space
+ * of TYPE_STRING (to represent the experiment names) and a value of
+ * TYPE_FLOATING_POINT (to represent p-values).<p>
+ * NOTE: No constraints on attributeName are documented by this API. In
+ * other words, as far as this API is concerned, any attributeName is
+ * acceptable, including the empty string (""). The only necessary
+ * condition is that each attributeName be unique.
+ * @param attributeName an identifier for this attribute definition;
+ * this value must be unique from all existing attribute definitions;
+ * ideally, the choice of name would describe values being stored by this
+ * attribute definition.
+ * @param valueType one of the TYPE_* constants defining what type of
+ * values are bound to objects in this attribute definition.
+ * @param keyTypes defines the type (TYPE_*) of each dimension in the key
+ * space;
+ * the entry at index i defines the type of key space dimension i + 1;
+ * this parameter may either be null or the empty array if an attribute
+ * definition does not use a key space (this is perhaps the most common
+ * scenario).
+ * @exception IllegalStateException if attributeName is already the name
+ * of an existing attribute definition.
+ * @exception NullPointerException if attributeName is null.
+ * @exception IllegalArgumentException if valueType is not one of the
+ * TYPE_* constants, or if keyTypes is [not null and] of positive length
+ * and any one of its elements is not one of the TYPE_* constants.
+ */
+ public void defineAttribute(String attributeName, byte valueType, byte[] keyTypes);
+
+ /**
+ * Returns all defined attributeNames.<p>
+ * NOTE: The returned iterator does not support the remove() operation.<p>
+ * NOTE: To find out whether or not an attributeName is defined, use
+ * getAttributeValueType(attributeName) and test whether or not the
+ * return value is negative.<p>
+ * IMPORTANT: The returned iterator becomes invalid as soon as any
+ * attributeName is defined or undefined in this MultiHashMapDefinition.
+ * Calling methods on an invalid iterator will result in undefined
+ * behavior of that iterator.
+ * @return an iterator of java.lang.String; each returned string
+ * is an attributeName (an attribute definition name).
+ */
+ public CountedIterator getDefinedAttributes();
+
+ /**
+ * Returns the type of attribute values that exist in specified attribute
+ * space.
+ * @return the type (TYPE_*) of values bound to objects by this attribute
+ * definition, or -1 if specified attribute definition does not exist;
+ * note that all of the TYPE_* constants are positive.
+ * @exception NullPointerException if attributeName is null.
+ */
+ public byte getAttributeValueType(String attributeName);
+
+ /**
+ * Returns information about the dimensionality and types in the key space
+ * of specified attribute.
+ * @param attributeName the attribute definition whose key space
+ * we are querying.
+ * @return a carbon copy of the array that was used to initially define
+ * attributeName (see defineAttribute()); implementations are required
+ * to instantiate and return a new array on each call to this method;
+ * if attributeName has no key space defined, the empty array is returned;
+ * null is never returned.
+ * @exception IllegalStateException if attributeName is not an existing
+ * attribute definition.
+ * @exception NullPointerException if attributeName is null.
+ */
+ public byte[] getAttributeKeyspaceDimensionTypes(String attributeName);
+
+ /**
+ * WARNING: All bound attribute values on objects will go away in this
+ * attribute namespace when this method is called.
+ * @param attributeName the attribute definition to undefine.
+ * @return true if and only if attributeName was defined prior to this
+ * method invocation.
+ * @exception NullPointerException if attributeName is null.
+ */
+ public boolean undefineAttribute(String attributeName);
+
+ /**
+ * Registers a listener for receiving events having to do with
+ * attribute definitions being created and deleted.
+ * @param listener the listener to register.
+ */
+ public void addDataDefinitionListener(MultiHashMapDefinitionListener listener);
+
+ /**
+ * Unregisters a listener; this method has the opposite effect as
+ * addDataDefinitionListener(listener).
+ * @param listener the listener to unregister.
+ */
+ public void removeDataDefinitionListener(MultiHashMapDefinitionListener listener);
+}
diff --git a/application/src/main/java/cytoscape/data/attr/MultiHashMapDefinitionListener.java b/application/src/main/java/cytoscape/data/attr/MultiHashMapDefinitionListener.java
new file mode 100644
index 0000000..1128008
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/attr/MultiHashMapDefinitionListener.java
@@ -0,0 +1,58 @@
+/*
+ File: MultiHashMapDefinitionListener.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data.attr;
+
+
+/**
+ * A hook to receive notification when attribute definitions are created
+ * and destroyed.
+ */
+public interface MultiHashMapDefinitionListener {
+ /**
+ * This method is called by a MultiHashMapDefinition implementation as a
+ * result of a new attribute being defined
+ * (MultiHashMapDefinition.defineAttribute()).
+ */
+ public void attributeDefined(String attributeName);
+
+ /**
+ * This method is called by a MultiHashMapDefinition implementation as a
+ * result of an attribute being undefined
+ * (MultiHashMapDefinition.undefineAttribute()).
+ */
+ public void attributeUndefined(String attributeName);
+}
diff --git a/application/src/main/java/cytoscape/data/attr/MultiHashMapListener.java b/application/src/main/java/cytoscape/data/attr/MultiHashMapListener.java
new file mode 100644
index 0000000..3a9f0b2
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/attr/MultiHashMapListener.java
@@ -0,0 +1,76 @@
+/*
+ File: MultiHashMapListener.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data.attr;
+
+
+/**
+ * A hook to receive notification when attribute values are set and removed
+ * from objects.
+ */
+public interface MultiHashMapListener {
+ /**
+ * @param keyIntoValue don't modify this array; this array will be
+ * null if attributeName has a zero-dimensional keyspace.
+ * @param oldAttributeValue the previous attribute value that was bound
+ * at specified key sequence, or null if no previous attribute value was
+ * bound.
+ * @param newAttributeValue the new attribute value that is now bound
+ * at specified key sequence.
+ */
+ public void attributeValueAssigned(String objectKey, String attributeName,
+ Object[] keyIntoValue, Object oldAttributeValue,
+ Object newAttributeValue);
+
+ /**
+ * This listener method gets called as a result of
+ * MultiHashMap.removeAttributeValue(objectKey, attributeName, keyIntoValue),
+ * but only if an attribute value was found [and removed] for specified key.
+ * The parameter attributeValue in this listener method is the value that
+ * is returned by MultiHashMap.removeAttributeValue(), and it is never null.
+ * @param keyIntoValue don't modify this array; this array will be
+ * null if attributeName has a zero-dimensional keyspace.
+ */
+ public void attributeValueRemoved(String objectKey, String attributeName,
+ Object[] keyIntoValue, Object attributeValue);
+
+ /**
+ * This listener method gets called as a result of
+ * MultiHashMap.removeAllAttributeValues(objectKey, attributeName), but only
+ * if objectKey has at least one attribute value bound in attributeName.
+ */
+ public void allAttributeValuesRemoved(String objectKey, String attributeName);
+}
diff --git a/application/src/main/java/cytoscape/data/attr/util/ExtensibleMultiHashMapModel.java b/application/src/main/java/cytoscape/data/attr/util/ExtensibleMultiHashMapModel.java
new file mode 100644
index 0000000..3644069
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/attr/util/ExtensibleMultiHashMapModel.java
@@ -0,0 +1,49 @@
+/*
+ File: ExtensibleMultiHashMapModel.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data.attr.util;
+
+
+/**
+ * Please try to restrain from using this class. This class was created so
+ * that certain legacy applications would have an easier time integrating with
+ * the functionality provided by the MultiHashMap and MultiHashMapDefinition
+ * implementations.
+ * @deprecated Use MultiHashMapFactory instead.
+ * @see MultiHashMapFactory
+ **/
+public class ExtensibleMultiHashMapModel extends MultiHashMapModel {
+}
diff --git a/application/src/main/java/cytoscape/data/attr/util/MultiHashMapFactory.java b/application/src/main/java/cytoscape/data/attr/util/MultiHashMapFactory.java
new file mode 100644
index 0000000..3edbaa6
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/attr/util/MultiHashMapFactory.java
@@ -0,0 +1,59 @@
+/*
+ File: MultiHashMapFactory.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data.attr.util;
+
+
+/**
+ * This class provides access to implementations of MultiHashMap and
+ * MultiHashMapDefinition.
+ */
+public final class MultiHashMapFactory {
+ // "No constructor".
+ private MultiHashMapFactory() {
+ }
+
+ /**
+ * The return object implements both
+ * cytoscape.data.attr.MultiHashMapDefinition
+ * and cytoscape.data.attr.MultiHashMap.
+ * You will need to cast the return value to one of these to access the
+ * corresponding functionality.
+ */
+ public final static Object instantiateDataModel() {
+ return new MultiHashMapModel();
+ }
+}
diff --git a/application/src/main/java/cytoscape/data/attr/util/MultiHashMapHelpers.java b/application/src/main/java/cytoscape/data/attr/util/MultiHashMapHelpers.java
new file mode 100644
index 0000000..6718fb8
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/attr/util/MultiHashMapHelpers.java
@@ -0,0 +1,333 @@
+/*
+ File: MultiHashMapHelpers.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data.attr.util;
+
+import cytoscape.data.attr.CountedIterator;
+import cytoscape.data.attr.MultiHashMap;
+import cytoscape.data.attr.MultiHashMapDefinition;
+
+import java.util.ArrayList;
+import java.util.List;
+
+
+/**
+ * This class contains static utilitarian methods that return information
+ * pertaining to attributes. The reason why the methods here are defined
+ * in this helper class and not in MultiHashMap is that
+ * the return values in these
+ * methods are simply computed using the public API methods of MultiHashMap.
+ * MultiHashMapHelpers is an implementation layer on top of MultiHashMap,
+ * whereas MultiHashMap
+ * provides only those methods which are either essential to its API or are
+ * optimized by its implementation.
+ */
+public final class MultiHashMapHelpers {
+ // NOTE: This class resides in the same package as the MultiHashMapModel
+ // implementation of MultiHashMap for a good reason. We may want some
+ // of these helper methods to be more optimized than just calling
+ // MultiHashMapModel
+ // by its MultiHashMap interface. We could provide dual implementations for
+ // every method in this class, and choose the path of execution based on
+ // whether or not our input object is an instance of MultiHashMapModel.
+ // Right now, though, everything is implemented in terms of MultiHashMap
+ // interface methods.
+
+ // No constructor. Static methods only.
+ private MultiHashMapHelpers() {
+ }
+
+ /**
+ * Convenience method for discovering all attribute values on an object in
+ * a given attribute definition; this method is only useful with attribute
+ * definitions that have nonzero key spaces.
+ * @param objectKey the object whose attribute values to return.
+ * @param attributeName the attribute definition in which to find attribute
+ * values.
+ * @param cyData the data repository to use to dig for attribute values.
+ * @param cyDataDef the data definition registry to use to find out about
+ * the dimensionality of attributeName.
+ * @return a list of all bound values on objectKey in
+ * attributeName, with duplicate values included; the returned list
+ * is never null; elements in the returned list are ordered
+ * arbitrarily; subsequent operations on cyData or cyDataDef will have
+ * no effect on the returned list.
+ * @exception IllegalStateException if attributeName is not an existing
+ * attribute definition in cyData and cyDataDef.
+ * @exception NullPointerException if any one of the input parameters is
+ * null.
+ */
+ public static List getAllAttributeValues(final String objectKey, final String attributeName,
+ final MultiHashMap cyData,
+ final MultiHashMapDefinition cyDataDef) {
+ final ArrayList bucket = new ArrayList();
+ final int keyspaceDims = cyDataDef.getAttributeKeyspaceDimensionTypes(attributeName).length;
+
+ if (keyspaceDims < 1) { // It's either 0 or -1.
+
+ final Object attrVal = cyData.getAttributeValue(objectKey, attributeName, null); // May trigger exception; OK.
+
+ if (attrVal != null)
+ bucket.add(attrVal);
+ } else { // keyspaceDims > 0.
+ r_getAllAttributeValues(objectKey, attributeName, cyData, bucket, new Object[0],
+ keyspaceDims);
+ }
+
+ return bucket;
+ }
+
+ /**
+ * Convenience method for discovering attribute values along a specified
+ * key prefix; this method is only useful with attribute
+ * definitions that have nonzero key spaces.
+ * @param objectKey the object whose attribute values to return.
+ * @param attributeName the attribute definition in which to find attribute
+ * values.
+ * @param keyPrefix an array of length less than or equal to the
+ * dimensionality of key space of attributeName; entry at index i contains
+ * a "representative" from dimension i + 1 of the key space of
+ * attributeName; keyPrefix may be either null or the empty array, in
+ * which case all attribute values bound to objectKey in attributeName will
+ * be returned; if keyPrefix is not empty, all bound values having key
+ * sequences whose beginning matches the specified prefix will be returned.
+ * @param cyData the data repository to use to dig for attribute values.
+ * @param cyDataDef the data definition registry to use to find out about
+ * the dimensionality of attributeName.
+ * @return a list of all bound values on objectKey in attributeName
+ * along key space prefix keyPrefix, with duplicate values included; the
+ * returned list is never null; elements in the returned
+ * list are ordered arbitrarily; subsequent operations on cyData or
+ * cyDataDef will have no effect on the returned list.
+ * @exception IllegalStateException if attributeName is not an existing
+ * attribute definition in cyData and cyDataDef.
+ * @exception NullPointerException if any one of the input parameters except
+ * keyPrefix is null, or if keyPrefix is of positive length and any one
+ * of its entries is null.
+ * @exception ClassCastException if keyPrefix is of positive length and any
+ * one of its entries does not match the type of object specified
+ * by corresponding dimension type in attributeName's definition.
+ * @exception IllegalArgumentException if keyPrefix's length is
+ * greater than the dimensionality of attributeName's key space.
+ */
+ public static List getAllAttributeValuesAlongPrefix(final String objectKey,
+ final String attributeName,
+ final Object[] keyPrefix,
+ final MultiHashMap cyData,
+ final MultiHashMapDefinition cyDataDef) {
+ final ArrayList bucket = new ArrayList();
+ final int keyspaceDims = cyDataDef.getAttributeKeyspaceDimensionTypes(attributeName).length;
+ final int prefixDims = ((keyPrefix == null) ? 0 : keyPrefix.length);
+
+ if (keyspaceDims <= prefixDims) {
+ final Object attrVal = cyData.getAttributeValue(objectKey, attributeName, keyPrefix); // May trigger exception; OK.
+
+ if (attrVal != null)
+ bucket.add(attrVal);
+ } else {
+ final Object[] keyPrefixCopy = new Object[prefixDims];
+
+ for (int i = 0; i < prefixDims; i++)
+ keyPrefixCopy[i] = keyPrefix[i];
+
+ r_getAllAttributeValues(objectKey, attributeName, cyData, bucket, keyPrefixCopy,
+ keyspaceDims);
+ }
+
+ return bucket;
+ }
+
+ // Recursive helper for getAllAttributeValues() and
+ // getAllAttributeValuesAlongPrefix().
+ private static void r_getAllAttributeValues(final String objectKey, final String attributeName,
+ final MultiHashMap dataRegistry,
+ final ArrayList bucket, final Object[] prefixSoFar,
+ final int keyspaceDims) {
+ final CountedIterator currentKeyspan = dataRegistry.getAttributeKeyspan(objectKey,
+ attributeName,
+ prefixSoFar);
+ final Object[] newPrefix = new Object[prefixSoFar.length + 1];
+
+ for (int i = 0; i < prefixSoFar.length; i++)
+ newPrefix[i] = prefixSoFar[i];
+
+ while (currentKeyspan.hasNext()) {
+ newPrefix[newPrefix.length - 1] = currentKeyspan.next();
+
+ if (keyspaceDims == newPrefix.length) // The final dimension.
+ bucket.add(dataRegistry.getAttributeValue(objectKey, attributeName, newPrefix));
+ else // Not the final dimension.
+
+ r_getAllAttributeValues(objectKey, attributeName, dataRegistry, bucket, newPrefix,
+ keyspaceDims);
+ }
+ }
+
+ /**
+ * Convenience method for discovering all key sequnces that map into
+ * bound values; this method is primarily useful with attribute
+ * definitions that have nonzero key spaces.
+ * @param objectKey the object whose mapped attribute keys to return.
+ * @param attributeName the attribute definition in which to find
+ * attribute keys.
+ * @param cyData the data repository to use to discover attribute keys.
+ * @param cyDataDef the data definition registry to use to find out about
+ * the dimensionality of attributeName.
+ * @return a list of Object[]; each Object[] in the returned list is
+ * a unique key sequence into a bound value; the returned list is never
+ * null and always contains the full set of key sequences registered on
+ * objectKey in attributeName; subsequent operations on cyData or cyDataDef
+ * will have no effect on the returned list.
+ * @exception IllegalStateException if attributeName is not an existing
+ * attribute definition in cyData and cyDataDef.
+ * @exception NullPointerException if any one of the input parameters is
+ * null.
+ */
+ public static List getAllAttributeKeys(final String objectKey, final String attributeName,
+ final MultiHashMap cyData,
+ final MultiHashMapDefinition cyDataDef) {
+ final ArrayList bucket = new ArrayList();
+ final int keyspaceDims = cyDataDef.getAttributeKeyspaceDimensionTypes(attributeName).length;
+
+ if (keyspaceDims < 1) { // It's either 0 or -1.
+
+ final Object attrVal = cyData.getAttributeValue(objectKey, attributeName, null); // May trigger exception; OK.
+
+ if (attrVal != null)
+ bucket.add(new Object[0]);
+ } else { // keyspaceDims > 0.
+ r_getAllAttributeKeys(objectKey, attributeName, cyData, bucket, new Object[0],
+ keyspaceDims);
+ }
+
+ return bucket;
+ }
+
+ /**
+ * Convenience method for discovering all key sequences having a given
+ * prefix that map into bound values; this method is primarily useful with
+ * attribute definitions that have nonzero key spaces.
+ * @param objectKey the object whose mapped attribute keys to return.
+ * @param attributeName the attribute definition in which to find
+ * attribute keys.
+ * @param keyPrefix an array of length less than or equal to the
+ * dimensionality of key space of attributeName; entry at index i contains
+ * a "representative" from dimension i + 1 of the key space of
+ * attributeName; keyPrefix may be either null or the empty array, in which
+ * case all attribute key sequences mapped to attribute values for
+ * objectKey in attributeName will be returned; if keyPrefix is not empty,
+ * all mapped key sequences having prefix keyPrefix will be returned.
+ * @param cyData the data repository to use to discover attribute keys.
+ * @param cyDataDef the data definition registry to use to find out about
+ * the dimensionality of attributeName.
+ * @return a list of Object[]; each Object[] in the returned list is
+ * a unique key sequence whose beginning matches keyPrefix and which
+ * is mapped to a value; the returned list contains all such key sequences;
+ * the return value is never null; subsequent operations on cyData or
+ * cyDataDef will have no effect on the returned list.
+ * @exception IllegalStateException if attributeName is not an existing
+ * attribute definition in cyData and cyDataDef.
+ * @exception NullPointerException if any one of the input parameters except
+ * keyPrefix is null, or if keyPrefix is of positive length and any one
+ * of its entries is null.
+ * @exception ClassCastException if keyPrefix is of positive length and any
+ * one of its entries does not match the type of object specified
+ * by corresponding dimension type in attributeName's definition.
+ * @exception IllegalArgumentException if keyPrefix's length is
+ * greater than the dimensionality of attributeName's key space.
+ */
+ public static List getAllAttributeKeysAlongPrefix(final String objectKey,
+ final String attributeName,
+ final Object[] keyPrefix,
+ final MultiHashMap cyData,
+ final MultiHashMapDefinition cyDataDef) {
+ final ArrayList bucket = new ArrayList();
+ final int keyspaceDims = cyDataDef.getAttributeKeyspaceDimensionTypes(attributeName).length;
+ final int prefixDims = ((keyPrefix == null) ? 0 : keyPrefix.length);
+ final Object[] keyPrefixCopy = new Object[prefixDims];
+
+ for (int i = 0; i < prefixDims; i++)
+ keyPrefixCopy[i] = keyPrefix[i];
+
+ if (keyspaceDims <= prefixDims) {
+ final Object attrVal = cyData.getAttributeValue(objectKey, attributeName, keyPrefixCopy); // ? trigger exception; OK.
+
+ if (attrVal != null)
+ bucket.add(keyPrefixCopy);
+ } else {
+ r_getAllAttributeKeys(objectKey, attributeName, cyData, bucket, keyPrefixCopy,
+ keyspaceDims);
+ }
+
+ return bucket;
+ }
+
+ // Recursive helper for getAllAttributeKeys() and
+ // getAllAttributeKeysAlongPrefix().
+ private static void r_getAllAttributeKeys(final String objectKey, final String attributeName,
+ final MultiHashMap dataRegistry,
+ final ArrayList bucket, final Object[] prefixSoFar,
+ final int keyspaceDims) {
+ final CountedIterator currentKeyspan = dataRegistry.getAttributeKeyspan(objectKey,
+ attributeName,
+ prefixSoFar);
+
+ if (keyspaceDims == (prefixSoFar.length + 1)) { // The final dimension.
+
+ while (currentKeyspan.hasNext()) {
+ final Object[] newPrefix = new Object[prefixSoFar.length + 1];
+
+ for (int i = 0; i < prefixSoFar.length; i++)
+ newPrefix[i] = prefixSoFar[i];
+
+ newPrefix[newPrefix.length - 1] = currentKeyspan.next();
+ bucket.add(newPrefix);
+ }
+ } else { // Not the final dimension.
+
+ final Object[] newPrefix = new Object[prefixSoFar.length + 1];
+
+ for (int i = 0; i < prefixSoFar.length; i++)
+ newPrefix[i] = prefixSoFar[i];
+
+ while (currentKeyspan.hasNext()) {
+ newPrefix[newPrefix.length - 1] = currentKeyspan.next();
+ r_getAllAttributeKeys(objectKey, attributeName, dataRegistry, bucket, newPrefix,
+ keyspaceDims);
+ }
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/data/attr/util/MultiHashMapModel.java b/application/src/main/java/cytoscape/data/attr/util/MultiHashMapModel.java
new file mode 100644
index 0000000..373c017
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/attr/util/MultiHashMapModel.java
@@ -0,0 +1,1029 @@
+/*
+ File: MultiHashMapModel.java
+
+ Copyright (c) 2006, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data.attr.util;
+
+import cytoscape.data.attr.CountedIterator;
+import cytoscape.data.attr.MultiHashMap;
+import cytoscape.data.attr.MultiHashMapDefinition;
+import cytoscape.data.attr.MultiHashMapDefinitionListener;
+import cytoscape.data.attr.MultiHashMapListener;
+
+import org.cytoscape.equations.BooleanList;
+import org.cytoscape.equations.DoubleList;
+import org.cytoscape.equations.Equation;
+import org.cytoscape.equations.FunctionUtil;
+import org.cytoscape.equations.LongList;
+import org.cytoscape.equations.StringList;
+
+import java.util.HashMap;
+
+
+class MultiHashMapModel implements MultiHashMapDefinition, MultiHashMap {
+ private final static class AttrDefData {
+ private final HashMap objMap; // Keys are objectKey.
+ private final byte valueType;
+ private final byte[] keyTypes;
+
+ private AttrDefData(final HashMap objMap, final byte valueType, final byte[] keyTypes) {
+ this.objMap = objMap;
+ this.valueType = valueType;
+ this.keyTypes = keyTypes;
+ }
+ }
+
+ private final static class Iterator2Counted implements CountedIterator {
+ private final java.util.Iterator iter;
+ private int count;
+
+ private Iterator2Counted(final java.util.Iterator iter, final int count) {
+ this.iter = iter;
+ this.count = count;
+ }
+
+ public final boolean hasNext() {
+ return iter.hasNext();
+ }
+
+ public final Object next() {
+ if (iter.hasNext())
+ count--;
+
+ return iter.next();
+ }
+
+ public final int numRemaining() {
+ return count;
+ }
+
+ public final void remove() {
+ throw new UnsupportedOperationException("cannot remove from this iterator");
+ }
+ }
+
+ private final static class AttrDefLisChain implements MultiHashMapDefinitionListener {
+ // Use only the static methods from outside this inner class.
+ private final MultiHashMapDefinitionListener a;
+
+ // Use only the static methods from outside this inner class.
+ private final MultiHashMapDefinitionListener b;
+
+ private AttrDefLisChain(final MultiHashMapDefinitionListener a,
+ final MultiHashMapDefinitionListener b) {
+ this.a = a;
+ this.b = b;
+ }
+
+ public final void attributeDefined(final String attributeName) {
+ a.attributeDefined(attributeName);
+ b.attributeDefined(attributeName);
+ }
+
+ public final void attributeUndefined(final String attributeName) {
+ a.attributeUndefined(attributeName);
+ b.attributeUndefined(attributeName);
+ }
+
+ private final static MultiHashMapDefinitionListener add(final MultiHashMapDefinitionListener a,
+ final MultiHashMapDefinitionListener b) {
+ if (a == null)
+ return b;
+
+ if (b == null)
+ return a;
+
+ return new AttrDefLisChain(a, b);
+ }
+
+ private final static MultiHashMapDefinitionListener remove(final MultiHashMapDefinitionListener l,
+ final MultiHashMapDefinitionListener oldl) {
+ if ((l == oldl) || (l == null))
+ return null;
+ else if (l instanceof AttrDefLisChain)
+ return ((AttrDefLisChain) l).remove(oldl);
+ else
+
+ return l;
+ }
+
+ private final MultiHashMapDefinitionListener remove(final MultiHashMapDefinitionListener oldl) {
+ if (oldl == a)
+ return b;
+
+ if (oldl == b)
+ return a;
+
+ final MultiHashMapDefinitionListener a2 = remove(a, oldl);
+ final MultiHashMapDefinitionListener b2 = remove(b, oldl);
+
+ if ((a2 == a) && (b2 == b))
+ return this;
+
+ return add(a2, b2);
+ }
+ }
+
+ private final static class AttrLisChain implements MultiHashMapListener {
+ // Use only the static methods from outside this inner class.
+ private final MultiHashMapListener a;
+
+ // Use only the static methods from outside this inner class.
+ private final MultiHashMapListener b;
+
+ private AttrLisChain(final MultiHashMapListener a, final MultiHashMapListener b) {
+ this.a = a;
+ this.b = b;
+ }
+
+ public final void attributeValueAssigned(final String objectKey,
+ final String attributeName,
+ final Object[] keyIntoValue,
+ final Object oldAttrVal, final Object newAttrVal) {
+ a.attributeValueAssigned(objectKey, attributeName, keyIntoValue, oldAttrVal, newAttrVal);
+ b.attributeValueAssigned(objectKey, attributeName, keyIntoValue, oldAttrVal, newAttrVal);
+ }
+
+ public final void attributeValueRemoved(final String objectKey, final String attributeName,
+ final Object[] keyIntoValue,
+ final Object attributeValue) {
+ a.attributeValueRemoved(objectKey, attributeName, keyIntoValue, attributeValue);
+ b.attributeValueRemoved(objectKey, attributeName, keyIntoValue, attributeValue);
+ }
+
+ public final void allAttributeValuesRemoved(final String objectKey,
+ final String attributeName) {
+ a.allAttributeValuesRemoved(objectKey, attributeName);
+ b.allAttributeValuesRemoved(objectKey, attributeName);
+ }
+
+ private final static MultiHashMapListener add(final MultiHashMapListener a,
+ final MultiHashMapListener b) {
+ if (a == null)
+ return b;
+
+ if (b == null)
+ return a;
+
+ return new AttrLisChain(a, b);
+ }
+
+ private final static MultiHashMapListener remove(final MultiHashMapListener l,
+ final MultiHashMapListener oldl) {
+ if ((l == oldl) || (l == null))
+ return null;
+ else if (l instanceof AttrLisChain)
+ return ((AttrLisChain) l).remove(oldl);
+ else
+
+ return l;
+ }
+
+ private final MultiHashMapListener remove(final MultiHashMapListener oldl) {
+ if (oldl == a)
+ return b;
+
+ if (oldl == b)
+ return a;
+
+ final MultiHashMapListener a2 = remove(a, oldl);
+ final MultiHashMapListener b2 = remove(b, oldl);
+
+ if ((a2 == a) && (b2 == b))
+ return this;
+
+ return add(a2, b2);
+ }
+ }
+
+ private final static CountedIterator s_the_empty_iterator = new CountedIterator() {
+ public final int numRemaining() {
+ return 0;
+ }
+
+ public final boolean hasNext() {
+ return false;
+ }
+
+ public final Object next() {
+ throw new java.util.NoSuchElementException();
+ }
+
+ public final void remove() {
+ throw new UnsupportedOperationException("cannot remove from this iterator");
+ }
+ };
+
+ // Keys are attributeName, values are AttrDefData.
+ private final HashMap m_attrMap;
+ private MultiHashMapDefinitionListener m_dataDefListener;
+ private MultiHashMapListener m_dataListener;
+
+ MultiHashMapModel() {
+ m_attrMap = new HashMap();
+ m_dataDefListener = null;
+ m_dataListener = null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param attributeName DOCUMENT ME!
+ * @param valueType DOCUMENT ME!
+ * @param keyTypes DOCUMENT ME!
+ */
+ public final void defineAttribute(final String attributeName, final byte valueType,
+ final byte[] keyTypes) {
+ // Error-check attributeName. Unfortunately there are currently no
+ // constraints on the length or the contents of attributeName.
+ if (attributeName == null)
+ throw new NullPointerException("attributeName is null");
+
+ if (m_attrMap.containsKey(attributeName))
+ throw new IllegalStateException("attributeName '" + attributeName + "' already exists");
+
+ // Error-check valueType.
+ switch (valueType) {
+ case MultiHashMapDefinition.TYPE_BOOLEAN:
+ case MultiHashMapDefinition.TYPE_FLOATING_POINT:
+ case MultiHashMapDefinition.TYPE_INTEGER:
+ case MultiHashMapDefinition.TYPE_STRING:
+ break;
+
+ default:
+ throw new IllegalArgumentException("valueType is unrecognized");
+ }
+
+ // Make copy of keyTypes.
+ final int keyTypesLength = ((keyTypes == null) ? 0 : keyTypes.length);
+ final byte[] keyTypesCopy = new byte[keyTypesLength];
+
+ if (keyTypes != null)
+ for (int i = 0; i < keyTypesLength; i++)
+ keyTypesCopy[i] = keyTypes[i];
+
+ // Error-check keyTypesCopy.
+ for (int i = 0; i < keyTypesCopy.length; i++)
+ switch (keyTypesCopy[i]) {
+ case MultiHashMapDefinition.TYPE_BOOLEAN:
+ case MultiHashMapDefinition.TYPE_FLOATING_POINT:
+ case MultiHashMapDefinition.TYPE_INTEGER:
+ case MultiHashMapDefinition.TYPE_STRING:
+ break;
+
+ default:
+ throw new IllegalArgumentException("keyTypes[" + i + "] is unrecognized");
+ }
+
+ // Finally, create the definition.
+ final AttrDefData def = new AttrDefData(new HashMap(), valueType, keyTypesCopy);
+ m_attrMap.put(attributeName, def);
+
+ // Call listeners. Make sure this is done after we actually create def.
+ final MultiHashMapDefinitionListener l = m_dataDefListener;
+
+ if (l != null)
+ l.attributeDefined(attributeName);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final CountedIterator getDefinedAttributes() {
+ return new Iterator2Counted(m_attrMap.keySet().iterator(), m_attrMap.size());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param attributeName DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final byte getAttributeValueType(final String attributeName) {
+ if (attributeName == null)
+ throw new NullPointerException("attributeName is null");
+
+ final AttrDefData def = (AttrDefData) m_attrMap.get(attributeName);
+
+ if (def == null)
+ return -1;
+
+ return def.valueType;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param attributeName DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final byte[] getAttributeKeyspaceDimensionTypes(final String attributeName) {
+ if (attributeName == null)
+ throw new NullPointerException("attributeName is null");
+
+ final AttrDefData def = (AttrDefData) m_attrMap.get(attributeName);
+
+ if (def == null)
+ throw new IllegalStateException("no attributeName '" + attributeName + "' exists");
+
+ final byte[] returnThis = new byte[def.keyTypes.length];
+
+ for (int i = 0; i < returnThis.length; i++)
+ returnThis[i] = def.keyTypes[i];
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param attributeName DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final boolean undefineAttribute(final String attributeName) {
+ if (attributeName == null)
+ throw new NullPointerException("attributeName is null");
+
+ final Object o = m_attrMap.remove(attributeName);
+
+ if (o != null) { // attributeName was in fact deleted.
+
+ final MultiHashMapDefinitionListener l = m_dataDefListener;
+
+ if (l != null)
+ l.attributeUndefined(attributeName);
+
+ return true;
+ }
+
+ return false;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param listener DOCUMENT ME!
+ */
+ public final void addDataDefinitionListener(final MultiHashMapDefinitionListener listener) {
+ m_dataDefListener = AttrDefLisChain.add(m_dataDefListener, listener);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param listener DOCUMENT ME!
+ */
+ public final void removeDataDefinitionListener(final MultiHashMapDefinitionListener listener) {
+ m_dataDefListener = AttrDefLisChain.remove(m_dataDefListener, listener);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param objectKey DOCUMENT ME!
+ * @param attributeName DOCUMENT ME!
+ * @param attributeValue DOCUMENT ME!
+ * @param keyIntoValue DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final Object setAttributeValue(final String objectKey, final String attributeName,
+ final Object attributeValue, final Object[] keyIntoValue)
+ {
+ // Pull out the definition, error-checking attributeName in the process.
+ if (attributeName == null)
+ throw new NullPointerException("attributeName is null");
+
+ final AttrDefData def = (AttrDefData) m_attrMap.get(attributeName);
+ if (def == null)
+ throw new IllegalStateException("no attributeName '" + attributeName + "' exists");
+
+ // Error-check objectKey. Right now there are no constraints on the length
+ // or the contents of objectKey. In the future, consider having
+ // a "registry" of all objectKeys and permitting only assignment to those
+ // objectKeys.
+ if (objectKey == null)
+ throw new NullPointerException("objectKey is null");
+
+ // Error-check attributeValue. Note that the instanceof operation always
+ // returns false for null values, and does not throw an exception.
+ if (attributeValue == null)
+ throw new NullPointerException("cannot set null attributeValue - "
+ + "use removeAttributeValue() instead");
+
+ final Class actualType;
+ final boolean isEquation = attributeValue instanceof Equation;
+ if (isEquation)
+ actualType = ((Equation)attributeValue).getType();
+ else
+ actualType = attributeValue.getClass();
+
+ switch (def.valueType) { // I'm wondering what the most efficient way of doing this is.
+ case MultiHashMapDefinition.TYPE_BOOLEAN:
+ if (actualType == Boolean.class
+ || (isEquation && (actualType == Long.class || actualType == Double.class || actualType == BooleanList.class || actualType == Object.class)))
+ break;
+ throw new ClassCastException("found " + actualType + " for \"" + attributeName + "\", expected Boolean!");
+ case MultiHashMapDefinition.TYPE_FLOATING_POINT:
+ if (actualType == Double.class
+ || (isEquation && (actualType == Long.class || actualType == Boolean.class || actualType == DoubleList.class || actualType == Object.class)))
+ break;
+ throw new ClassCastException("found " + actualType + " for \"" + attributeName + "\", expected Double!");
+ case MultiHashMapDefinition.TYPE_INTEGER:
+ if (actualType == Integer.class
+ || (isEquation && (actualType == Double.class || actualType == Boolean.class
+ || actualType == Long.class || actualType == LongList.class || actualType == Object.class)))
+ break;
+ throw new ClassCastException("found " + actualType + " for \"" + attributeName + "\", expected Integer!");
+ case MultiHashMapDefinition.TYPE_STRING:
+ if (actualType == String.class || isEquation)
+ break;
+ throw new ClassCastException("found " + actualType + " for \"" + attributeName + "\", expected String!");
+ }
+
+ // Error-check keyIntoValue. Leave the type checks to the recursion.
+ if (def.keyTypes.length == 0) {
+ if ((keyIntoValue != null) && (keyIntoValue.length != 0)) {
+ throw new IllegalArgumentException("attributeName '" + attributeName
+ + "' has no keyspace"
+ + " defined, yet keyIntoValue is not empty");
+ }
+ if (FunctionUtil.isSomeKindOfList(actualType))
+ throw new ClassCastException("found " + actualType + " for \"" + attributeName + "\", expected String!");
+ } else { // Keyspace is not empty.
+ final int keyIntoValueLength = ((keyIntoValue == null) ? 0 : keyIntoValue.length);
+ if (def.keyTypes.length != keyIntoValueLength)
+ throw new IllegalArgumentException("keyIntoValue has incorrect dimensionality");
+ if (isEquation) {
+ switch (def.valueType) {
+ case MultiHashMapDefinition.TYPE_BOOLEAN:
+ if (actualType != BooleanList.class)
+ throw new ClassCastException("found " + actualType + " for \"" + attributeName + "\", expected String!");
+ break;
+ case MultiHashMapDefinition.TYPE_FLOATING_POINT:
+ if (actualType != DoubleList.class)
+ throw new ClassCastException("found " + actualType + " for \"" + attributeName + "\", expected String!");
+ break;
+ case MultiHashMapDefinition.TYPE_INTEGER:
+ if (actualType != LongList.class)
+ throw new ClassCastException("found " + actualType + " for \"" + attributeName + "\", expected String!");
+ break;
+ case MultiHashMapDefinition.TYPE_STRING:
+ if (actualType != StringList.class)
+ throw new ClassCastException("found " + actualType + " for \"" + attributeName + "\", expected String!");
+ break;
+ }
+ }
+ }
+
+ final MultiHashMapListener listener = m_dataListener;
+
+ if (def.keyTypes.length == 0) { // Don't even recurse.
+ final Object returnThis = def.objMap.put(objectKey, attributeValue);
+
+ if (listener != null)
+ listener.attributeValueAssigned(objectKey, attributeName, null, returnThis,
+ attributeValue);
+
+ return returnThis;
+ } else { // Recurse.
+
+ final Object o = def.objMap.get(objectKey);
+ final HashMap firstDim;
+
+ if (o == null)
+ firstDim = new HashMap();
+ else
+ firstDim = (HashMap) o;
+
+ final Object returnThis = r_setAttributeValue(firstDim, attributeValue, keyIntoValue,
+ def.keyTypes, 0);
+
+ // If firstDim is a new HashMap add it to the definition after the
+ // recursion completes so that if an exception is thrown, we can avoid
+ // cleanup.
+ if (o == null)
+ def.objMap.put(objectKey, firstDim);
+
+ if (listener != null)
+ listener.attributeValueAssigned(objectKey, attributeName, keyIntoValue, returnThis,
+ attributeValue);
+
+ return returnThis;
+ }
+ }
+
+ // Recursive helper method.
+ private final Object r_setAttributeValue(final HashMap hash, final Object attributeValue,
+ final Object[] keyIntoValue, final byte[] keyTypes,
+ final int currOffset) {
+ // Error check type of object keyIntoValue[currOffset].
+ final Object currKey = keyIntoValue[currOffset];
+
+ // Right now, key representatives cannot be null - that is the only
+ // constraint. This may or may not make sense; imagine a String key
+ // representative being "".
+ if (currKey == null)
+ throw new NullPointerException("keyIntoValue[" + currOffset + "] null");
+
+ boolean passed = false;
+
+ switch (keyTypes[currOffset]) {
+ case MultiHashMapDefinition.TYPE_BOOLEAN:
+ passed = (currKey instanceof java.lang.Boolean);
+
+ break;
+
+ case MultiHashMapDefinition.TYPE_FLOATING_POINT:
+ passed = (currKey instanceof java.lang.Double);
+
+ break;
+
+ case MultiHashMapDefinition.TYPE_INTEGER:
+ passed = (currKey instanceof java.lang.Integer);
+
+ break;
+
+ case MultiHashMapDefinition.TYPE_STRING:
+ passed = (currKey instanceof java.lang.String);
+
+ break;
+ }
+
+ if (!passed)
+ throw new ClassCastException("keyIntoValue[" + currOffset
+ + "] is of incorrect object type");
+
+ // Put something in.
+ if (currOffset == (keyIntoValue.length - 1)) { // The final dimension.
+
+ return hash.put(currKey, attributeValue);
+ } else { // Must recurse further.
+
+ final Object o = hash.get(currKey);
+ final HashMap dim;
+
+ if (o == null)
+ dim = new HashMap();
+ else
+ dim = (HashMap) o;
+
+ final Object returnThis = r_setAttributeValue(dim, attributeValue, keyIntoValue,
+ keyTypes, currOffset + 1);
+
+ // Put new HashMap in after recursive call to prevent the need for
+ // cleanup in case exception is thrown.
+ if (o == null)
+ hash.put(currKey, dim);
+
+ return returnThis;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param objectKey DOCUMENT ME!
+ * @param attributeName DOCUMENT ME!
+ * @param keyIntoValue DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final Object getAttributeValue(final String objectKey, final String attributeName,
+ final Object[] keyIntoValue)
+ {
+ // Pull out the definition, error-checking attributeName in the process.
+ if (attributeName == null)
+ throw new NullPointerException("attributeName is null");
+
+ final AttrDefData def = (AttrDefData) m_attrMap.get(attributeName);
+
+ if (def == null)
+ throw new IllegalStateException("no attributeName '" + attributeName + "' exists");
+
+ // Error-check objectKey.
+ if (objectKey == null)
+ throw new NullPointerException("objectKey is null");
+
+ // Error-check keyIntoValue. Leave the type checks to the recursion.
+ if (def.keyTypes.length == 0) {
+ if ((keyIntoValue != null) && (keyIntoValue.length != 0)) {
+ throw new IllegalArgumentException("attributeName '" + attributeName
+ + "' has no keyspace"
+ + " defined, yet keyIntoValue is not empty");
+ }
+ } else { // Keyspace is not empty.
+ final int keyIntoValueLength = ((keyIntoValue == null) ? 0 : keyIntoValue.length);
+ if (def.keyTypes.length != keyIntoValueLength)
+ throw new IllegalArgumentException("keyIntoValue has incorrect dimensionality for attribute \""
+ + attributeName + "\"(expected: "
+ + keyIntoValueLength + ", found: " + def.keyTypes.length + ")!");
+ }
+
+ if (def.keyTypes.length == 0) // Don't even recurse.
+ return def.objMap.get(objectKey);
+ else { // Recurse.
+
+ final Object o = def.objMap.get(objectKey);
+
+ if (o == null)
+ return null;
+
+ return r_getAttributeValue((HashMap) o, keyIntoValue, def.keyTypes, 0);
+ }
+ }
+
+ private final Object r_getAttributeValue(final HashMap hash, final Object[] keyIntoValue,
+ final byte[] keyTypes, final int currOffset) {
+ // Error-check type of object keyIntoValue[currOffset].
+ final Object currKey = keyIntoValue[currOffset];
+
+ if (currKey == null)
+ throw new NullPointerException("keyIntoValue[" + currOffset + "] null");
+
+ boolean passed = false;
+
+ switch (keyTypes[currOffset]) {
+ case MultiHashMapDefinition.TYPE_BOOLEAN:
+ passed = (currKey instanceof java.lang.Boolean);
+
+ break;
+
+ case MultiHashMapDefinition.TYPE_FLOATING_POINT:
+ passed = (currKey instanceof java.lang.Double);
+
+ break;
+
+ case MultiHashMapDefinition.TYPE_INTEGER:
+ passed = (currKey instanceof java.lang.Integer);
+
+ break;
+
+ case MultiHashMapDefinition.TYPE_STRING:
+ passed = (currKey instanceof java.lang.String);
+
+ break;
+ }
+
+ if (!passed)
+ throw new ClassCastException("keyIntoValue[" + currOffset
+ + "] is of incorrect object type");
+
+ // Retrieve the value.
+ if (currOffset == (keyIntoValue.length - 1)) { // The final dimension.
+
+ return hash.get(currKey);
+ } else { // Must recurse further.
+
+ final Object o = hash.get(currKey);
+
+ if (o == null)
+ return null;
+
+ return r_getAttributeValue((HashMap) o, keyIntoValue, keyTypes, currOffset + 1);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param objectKey DOCUMENT ME!
+ * @param attributeName DOCUMENT ME!
+ * @param keyIntoValue DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final Object removeAttributeValue(final String objectKey, final String attributeName,
+ final Object[] keyIntoValue) {
+ // Pull out the definition, error-checking attributeName in the process.
+ if (attributeName == null)
+ throw new NullPointerException("attributeName is null");
+
+ final AttrDefData def = (AttrDefData) m_attrMap.get(attributeName);
+
+ if (def == null)
+ throw new IllegalStateException("no attributeName '" + attributeName + "' exists");
+
+ // Error-check objectKey.
+ if (objectKey == null)
+ throw new NullPointerException("objectKey is null");
+
+ // Error-check keyIntoValue. Leave the type checks to the recursion.
+ if (def.keyTypes.length == 0) {
+ if ((keyIntoValue != null) && (keyIntoValue.length != 0)) {
+ throw new IllegalArgumentException("attributeName '" + attributeName
+ + "' has no keyspace"
+ + " defined, yet keyIntoValue is not empty");
+ }
+ } else { // Keyspace is not empty.
+
+ final int keyIntoValueLength = ((keyIntoValue == null) ? 0 : keyIntoValue.length);
+
+ if (def.keyTypes.length != keyIntoValueLength) {
+ throw new IllegalArgumentException("keyIntoValue has incorrect dimensionality");
+ }
+ }
+
+ final MultiHashMapListener listener = m_dataListener;
+
+ if (def.keyTypes.length == 0) { // Don't even recurse.
+
+ final Object returnThis = def.objMap.remove(objectKey);
+
+ if ((listener != null) && (returnThis != null))
+ listener.attributeValueRemoved(objectKey, attributeName, null, returnThis);
+
+ return returnThis;
+ } else { // Recurse.
+
+ final Object o = def.objMap.get(objectKey);
+
+ if (o == null)
+ return null;
+
+ final HashMap dim = (HashMap) o;
+ final Object returnThis = r_removeAttributeValue(dim, keyIntoValue, def.keyTypes, 0);
+
+ if (returnThis != null) {
+ if (dim.size() == 0)
+ def.objMap.remove(objectKey);
+
+ if (listener != null)
+ listener.attributeValueRemoved(objectKey, attributeName, keyIntoValue,
+ returnThis);
+ }
+
+ return returnThis;
+ }
+ }
+
+ private final Object r_removeAttributeValue(final HashMap hash, final Object[] keyIntoValue,
+ final byte[] keyTypes, final int currOffset) {
+ // Error check type of object keyIntoValue[currOffset].
+ final Object currKey = keyIntoValue[currOffset];
+
+ if (currKey == null)
+ throw new NullPointerException("keyIntoValue[" + currOffset + "] null");
+
+ boolean passed = false;
+
+ switch (keyTypes[currOffset]) {
+ case MultiHashMapDefinition.TYPE_BOOLEAN:
+ passed = (currKey instanceof java.lang.Boolean);
+
+ break;
+
+ case MultiHashMapDefinition.TYPE_FLOATING_POINT:
+ passed = (currKey instanceof java.lang.Double);
+
+ break;
+
+ case MultiHashMapDefinition.TYPE_INTEGER:
+ passed = (currKey instanceof java.lang.Integer);
+
+ break;
+
+ case MultiHashMapDefinition.TYPE_STRING:
+ passed = (currKey instanceof java.lang.String);
+
+ break;
+ }
+
+ if (!passed)
+ throw new ClassCastException("keyIntoValue[" + currOffset
+ + "] is of incorrect object type");
+
+ // Retrieve the value.
+ if (currOffset == (keyIntoValue.length - 1)) { // The final dimension.
+
+ return hash.remove(currKey);
+ } else { // Must recurse further.
+
+ final Object o = hash.get(currKey);
+
+ if (o == null)
+ return null;
+
+ final HashMap dim = (HashMap) o;
+ final Object returnThis = r_removeAttributeValue(dim, keyIntoValue, keyTypes,
+ currOffset + 1);
+
+ if (dim.size() == 0)
+ hash.remove(currKey);
+
+ return returnThis;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param objectKey DOCUMENT ME!
+ * @param attributeName DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final boolean removeAllAttributeValues(final String objectKey, final String attributeName) {
+ // Pull out the definition, error-checking attributeName in the process.
+ if (attributeName == null)
+ throw new NullPointerException("attributeName is null");
+
+ final AttrDefData def = (AttrDefData) m_attrMap.get(attributeName);
+
+ if (def == null)
+ throw new IllegalStateException("no attributeName '" + attributeName + "' exists");
+
+ // Error-check objectKey.
+ if (objectKey == null)
+ throw new NullPointerException("objectKey is null");
+
+ final boolean returnThis = (def.objMap.remove(objectKey) != null);
+
+ if (returnThis) {
+ final MultiHashMapListener listener = m_dataListener;
+
+ if (listener != null)
+ listener.allAttributeValuesRemoved(objectKey, attributeName);
+ }
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param objectKey DOCUMENT ME!
+ * @param attributeName DOCUMENT ME!
+ * @param keyPrefix DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final CountedIterator getAttributeKeyspan(final String objectKey,
+ final String attributeName,
+ final Object[] keyPrefix) {
+ // Pull out the definition, error-checking attributeName in the process.
+ if (attributeName == null)
+ throw new NullPointerException("attributeName is null");
+
+ final AttrDefData def = (AttrDefData) m_attrMap.get(attributeName);
+
+ if (def == null)
+ throw new IllegalStateException("no attributeName '" + attributeName + "' exists");
+
+ // Error-check objectKey.
+ if (objectKey == null)
+ throw new NullPointerException("objectKey is null");
+
+ // Error-check keyPrefix. Leave the type checks to the recursion.
+ if (def.keyTypes.length == 0)
+ throw new IllegalStateException("attributeName '" + attributeName
+ + "' has no keyspace, so"
+ + " calling this method makes no sense");
+
+ if ((keyPrefix != null) && (keyPrefix.length >= def.keyTypes.length))
+ throw new IllegalArgumentException("the length of keyPrefix must be strictly less than the"
+ + " dimensionality of keyspace");
+
+ if ((keyPrefix == null) || (keyPrefix.length == 0)) { // Don't even recurse.
+
+ final HashMap dim = (HashMap) def.objMap.get(objectKey);
+
+ if (dim == null)
+ return s_the_empty_iterator;
+
+ return new Iterator2Counted(dim.keySet().iterator(), dim.size());
+ } else { // Recurse.
+
+ final HashMap dim = (HashMap) def.objMap.get(objectKey);
+
+ if (dim == null)
+ return s_the_empty_iterator;
+
+ return r_getAttributeKeyspan(dim, keyPrefix, def.keyTypes, 0);
+ }
+ }
+
+ private final CountedIterator r_getAttributeKeyspan(final HashMap hash,
+ final Object[] keyPrefix,
+ final byte[] keyTypes, final int currOffset) {
+ // Error-check type of object keyPrefix[currOffset].
+ final Object currKey = keyPrefix[currOffset];
+
+ if (currKey == null)
+ throw new NullPointerException("keyPrefix[" + currOffset + "] is null");
+
+ boolean passed = false;
+
+ switch (keyTypes[currOffset]) {
+ case MultiHashMapDefinition.TYPE_BOOLEAN:
+ passed = (currKey instanceof java.lang.Boolean);
+
+ break;
+
+ case MultiHashMapDefinition.TYPE_FLOATING_POINT:
+ passed = (currKey instanceof java.lang.Double);
+
+ break;
+
+ case MultiHashMapDefinition.TYPE_INTEGER:
+ passed = (currKey instanceof java.lang.Integer);
+
+ break;
+
+ case MultiHashMapDefinition.TYPE_STRING:
+ passed = (currKey instanceof java.lang.String);
+
+ break;
+ }
+
+ if (!passed)
+ throw new ClassCastException("keyPrefix[" + currOffset
+ + "] is of incorrect object type");
+
+ if (currOffset == (keyPrefix.length - 1)) { // The dimension.
+
+ final HashMap dim = (HashMap) hash.get(currKey);
+
+ if (dim == null)
+ return s_the_empty_iterator;
+
+ return new Iterator2Counted(dim.keySet().iterator(), dim.size());
+ } else { // Recurse further.
+
+ final HashMap dim = (HashMap) hash.get(currKey);
+
+ if (dim == null)
+ return s_the_empty_iterator;
+
+ return r_getAttributeKeyspan(dim, keyPrefix, keyTypes, currOffset + 1);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param attributeName DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final CountedIterator getObjectKeys(final String attributeName) {
+ // Pull out the definition, error-checking attributeName in the process.
+ if (attributeName == null)
+ throw new NullPointerException("attributeName is null");
+
+ final AttrDefData def = (AttrDefData) m_attrMap.get(attributeName);
+
+ if (def == null)
+ throw new IllegalStateException("no attributeName '" + attributeName + "' exists");
+
+ return new Iterator2Counted(def.objMap.keySet().iterator(), def.objMap.size());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param listener DOCUMENT ME!
+ */
+ public final void addDataListener(final MultiHashMapListener listener) {
+ m_dataListener = AttrLisChain.add(m_dataListener, listener);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param listener DOCUMENT ME!
+ */
+ public final void removeDataListener(final MultiHashMapListener listener) {
+ m_dataListener = AttrLisChain.remove(m_dataListener, listener);
+ }
+}
diff --git a/application/src/main/java/cytoscape/data/mRNAMeasurement.java b/application/src/main/java/cytoscape/data/mRNAMeasurement.java
new file mode 100644
index 0000000..b2461fa
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/mRNAMeasurement.java
@@ -0,0 +1,122 @@
+/*
+ File: mRNAMeasurement.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// mRNAMeasurement: encapsulate the ratio/signficance pair
+package cytoscape.data;
+
+
+/**
+ *
+ */
+public class mRNAMeasurement implements java.io.Serializable {
+ private double expressionRatio;
+ private double significance;
+
+ /**
+ * Creates a new mRNAMeasurement object.
+ *
+ * @param ratioString DOCUMENT ME!
+ * @param significanceString DOCUMENT ME!
+ */
+ public mRNAMeasurement(String ratioString, String significanceString) {
+ expressionRatio = -99999.9;
+
+ try {
+ expressionRatio = Double.parseDouble(ratioString);
+ } catch (NumberFormatException ignore) {
+ ;
+ }
+
+ significance = -99999.9;
+
+ try {
+ significance = Double.parseDouble(significanceString);
+ } catch (NumberFormatException ignore) {
+ ;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public double getRatio() {
+ return expressionRatio;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public double getSignificance() {
+ return significance;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String toString() {
+ StringBuffer sb = new StringBuffer();
+ sb.append(expressionRatio);
+ sb.append(", ");
+ sb.append(significance);
+
+ return sb.toString();
+ } // toString
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param new_ratio DOCUMENT ME!
+ */
+ public void setRatio(double new_ratio) {
+ this.expressionRatio = new_ratio;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param new_significance DOCUMENT ME!
+ */
+ public void setSignificance(double new_significance) {
+ this.significance = new_significance;
+ }
+} // mRNAMeasurement
diff --git a/application/src/main/java/cytoscape/data/ontology/DBCrossReferences.java b/application/src/main/java/cytoscape/data/ontology/DBCrossReferences.java
new file mode 100644
index 0000000..3b9d2a9
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/ontology/DBCrossReferences.java
@@ -0,0 +1,113 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data.ontology;
+
+import cytoscape.data.ontology.readers.DBCrossReferenceReader;
+
+import java.io.IOException;
+
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Set;
+
+
+/**
+ * Database cress reference.<br>
+ * <p>
+ * This class manages the relationships between databases. The cross reference
+ * file is available at:<br>
+ *
+ * http://www.geneontology.org/doc/GO.xrf_abbs
+ *
+ * </p>
+ *
+ * @version 0.9
+ * @since Cytoscape 2.4
+ * @author kono
+ *
+ */
+public class DBCrossReferences {
+ /*
+ * Map to store the cross reference.
+ */
+ private Map<String, DBReference> crossRefMap;
+
+ /**
+ * Creates a new DBCrossReferences object.
+ */
+ public DBCrossReferences() {
+ this.crossRefMap = new HashMap<String, DBReference>();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws IOException DOCUMENT ME!
+ */
+ public void load() throws IOException {
+ DBCrossReferenceReader xrefReader = new DBCrossReferenceReader();
+ xrefReader.readResourceFile();
+ this.crossRefMap = xrefReader.getXrefMap();
+ }
+
+ /**
+ * Add a database reference object
+ *
+ * @param db
+ */
+ public void setDBReference(DBReference db) {
+ crossRefMap.put(db.getAbbreviation(), db);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Set getDBNames() {
+ return crossRefMap.keySet();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param abbreviation DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public DBReference getDBReference(String abbreviation) {
+ return crossRefMap.get(abbreviation);
+ }
+}
diff --git a/application/src/main/java/cytoscape/data/ontology/DBReference.java b/application/src/main/java/cytoscape/data/ontology/DBReference.java
new file mode 100644
index 0000000..0e1d4d6
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/ontology/DBReference.java
@@ -0,0 +1,158 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data.ontology;
+
+import java.net.MalformedURLException;
+import java.net.URL;
+
+import java.util.ArrayList;
+import java.util.List;
+
+
+/**
+ * Represents an entry in the database cross reference.<br>
+ *
+ * @author kono
+ *
+ */
+public class DBReference {
+ private String abbreviation;
+ private String name;
+ private String urlSyntax;
+ private String genericUrl;
+ private String object;
+ private List<String> synonyms;
+
+ /**
+ * Creates a new DBReference object.
+ *
+ * @param abbreviation DOCUMENT ME!
+ * @param name DOCUMENT ME!
+ * @param genericUrl DOCUMENT ME!
+ */
+ public DBReference(String abbreviation, String name, String genericUrl) {
+ this(abbreviation, name, null, genericUrl, null);
+ }
+
+ /**
+ * Creates a new DBReference object.
+ *
+ * @param abbreviation DOCUMENT ME!
+ * @param name DOCUMENT ME!
+ * @param urlSyntax DOCUMENT ME!
+ * @param genericUrl DOCUMENT ME!
+ * @param object DOCUMENT ME!
+ */
+ public DBReference(String abbreviation, String name, String urlSyntax, String genericUrl,
+ String object) {
+ this.abbreviation = abbreviation;
+ this.name = name;
+ this.urlSyntax = urlSyntax;
+ this.genericUrl = genericUrl;
+ this.synonyms = null;
+ this.object = object;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getAbbreviation() {
+ return abbreviation;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getFullName() {
+ return name;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @throws MalformedURLException DOCUMENT ME!
+ */
+ public URL getGenericURL() throws MalformedURLException {
+ return new URL(genericUrl);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getObject() {
+ return object;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public List<String> getSynonyms() {
+ return synonyms;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param entry DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @throws MalformedURLException DOCUMENT ME!
+ */
+ public URL getQueryURL(String entry) throws MalformedURLException {
+ final String queryURL = urlSyntax + entry;
+
+ return new URL(queryURL);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param synonym DOCUMENT ME!
+ */
+ public void setSynonym(List<String> synonym) {
+ this.synonyms = synonym;
+ }
+}
diff --git a/application/src/main/java/cytoscape/data/ontology/GOTerm.java b/application/src/main/java/cytoscape/data/ontology/GOTerm.java
new file mode 100644
index 0000000..f1387de
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/ontology/GOTerm.java
@@ -0,0 +1,120 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data.ontology;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.data.ontology.readers.OBOTags;
+
+import java.util.Map;
+
+
+/**
+ * A Gene Ontology term. This class is an extended version of normal ontology.
+ *
+ * @author kono
+ *
+ */
+public class GOTerm extends OntologyTerm {
+ /**
+ * Creates a new GOTerm object.
+ *
+ * @param id DOCUMENT ME!
+ * @param termName DOCUMENT ME!
+ * @param ontologyName DOCUMENT ME!
+ * @param description DOCUMENT ME!
+ */
+ public GOTerm(final String id, final String termName, final String ontologyName,
+ final String description) {
+ super(id, ontologyName, description);
+
+ if (termName != null) {
+ Cytoscape.getNodeAttributes()
+ .setAttribute(id, OBOTags.getPrefix() + "." + OBOTags.NAME.toString(), termName);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getNameSpace() {
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Map getCrossReferences() {
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getFullName() {
+ return Cytoscape.getNodeAttributes()
+ .getStringAttribute(super.getName(),
+ OBOTags.getPrefix() + "." + OBOTags.NAME.toString());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getDescription() {
+ return Cytoscape.getNodeAttributes()
+ .getStringAttribute(super.getName(),
+ OBOTags.getPrefix() + "." + OBOTags.DEF.toString());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getType() {
+ return Cytoscape.getNodeAttributes()
+ .getStringAttribute(super.getName(),
+ OBOTags.getPrefix() + "."
+ + OBOTags.NAMESPACE.toString());
+ }
+}
diff --git a/application/src/main/java/cytoscape/data/ontology/GeneOntology.java b/application/src/main/java/cytoscape/data/ontology/GeneOntology.java
new file mode 100644
index 0000000..28e7084
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/ontology/GeneOntology.java
@@ -0,0 +1,139 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data.ontology;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+
+import cytoscape.data.CyAttributes;
+
+import cytoscape.data.ontology.readers.OBOTags;
+import static cytoscape.data.ontology.readers.OBOTags.DEF;
+import static cytoscape.data.ontology.readers.OBOTags.NAME;
+import static cytoscape.data.ontology.readers.OBOTags.NAMESPACE;
+import static cytoscape.data.readers.MetadataEntries.SOURCE;
+
+import org.biojava.ontology.Term;
+
+import java.net.MalformedURLException;
+import java.net.URISyntaxException;
+
+import java.util.List;
+
+
+/**
+ * Gene Ontology object based on general Ontology.<br>
+ *
+ *
+ * @author kono
+ *
+ */
+public class GeneOntology extends Ontology {
+ private CyAttributes goTermAttributes = Cytoscape.getNodeAttributes();
+ public enum GOAspect {
+ BIOLOGICAL_PROCESS("P"),
+ CELLULAR_COMPONENT("C"),
+ MOLECULAR_FUNCTION("F");
+
+ private String aspect;
+
+ private GOAspect(String aspect) {
+ this.aspect = aspect;
+ }
+
+ public String toString() {
+ return aspect;
+ }
+ }
+ public GeneOntology(String name, String curator, String description, CyNetwork dag)
+ throws URISyntaxException, MalformedURLException {
+ super(name, curator, description, dag);
+
+ final DBReference reference = Cytoscape.getOntologyServer().getCrossReferences()
+ .getDBReference("GOC");
+ metaParser.setMetadata(SOURCE, reference.getGenericURL().toString());
+ }
+
+ /**
+ *
+ * @return Curator as string
+ */
+ public String getCurator() {
+ return null;
+ }
+
+ public List<Term> getTermsInNamespace(String namespace) {
+ return null;
+ }
+
+ public GOTerm getGOTerm(String goID) {
+ return new GOTerm(goID,
+ Cytoscape.getNodeAttributes()
+ .getStringAttribute(goID,
+ OBOTags.getPrefix() + "." + NAME.toString()),
+ name,
+ goTermAttributes.getStringAttribute(goID,
+ OBOTags.getPrefix() + "."
+ + DEF.toString()));
+ }
+
+ /**
+ * Returns Aspect/name space of the GO term.
+ *
+ * @param goID
+ * ID of the GO term (for example GO:000011)
+ *
+ * @return GOAspect of the given ID
+ */
+ public GOAspect getAspect(String goID) {
+ final String nameSpace = goTermAttributes.getStringAttribute(goID,
+ OBOTags.getPrefix() + "."
+ + NAMESPACE.toString());
+
+ if (nameSpace == null) {
+ return null;
+ }
+
+ if (nameSpace.equalsIgnoreCase(GOAspect.BIOLOGICAL_PROCESS.name())) {
+ return GOAspect.BIOLOGICAL_PROCESS;
+ } else if (nameSpace.equalsIgnoreCase(GOAspect.CELLULAR_COMPONENT.name())) {
+ return GOAspect.CELLULAR_COMPONENT;
+ } else if (nameSpace.equalsIgnoreCase(GOAspect.MOLECULAR_FUNCTION.name())) {
+ return GOAspect.MOLECULAR_FUNCTION;
+ }
+
+ return null;
+ }
+}
diff --git a/application/src/main/java/cytoscape/data/ontology/Ontology.java b/application/src/main/java/cytoscape/data/ontology/Ontology.java
new file mode 100644
index 0000000..b0d538e
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/ontology/Ontology.java
@@ -0,0 +1,434 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data.ontology;
+
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+
+import cytoscape.data.CyAttributes;
+import cytoscape.data.Semantics;
+
+import cytoscape.data.ontology.readers.OBOTags;
+import cytoscape.data.readers.MetadataEntries;
+import cytoscape.data.readers.MetadataParser;
+
+import giny.model.Node;
+
+import org.biojava.ontology.AlreadyExistsException;
+import org.biojava.ontology.OntologyOps;
+import org.biojava.ontology.Term;
+import org.biojava.ontology.Triple;
+import org.biojava.ontology.Variable;
+
+import org.biojava.utils.AbstractChangeable;
+import org.biojava.utils.ChangeVetoException;
+
+import java.net.URISyntaxException;
+
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.NoSuchElementException;
+import java.util.Set;
+
+
+/**
+ * General Ontology class which implements
+ * <ahref="http://www.biojava.org/docs/api14/org/biojava/ontology/Ontology.html">Ontology
+ * interface from BioJava project</a>.<br>
+ *
+ * This class representes a general and simple ontology class. This
+ * implementation uses <br>
+ * CyNetwork and CyAttributes for its actual data storage.
+ *
+ * @version 0.8
+ * @since Cytoscape 2.4
+ * @see org.biojava.ontology
+ *
+ * @author kono
+ *
+ */
+public class Ontology extends AbstractChangeable implements org.biojava.ontology.Ontology {
+ /*
+ * For metadata
+ */
+ private static final String CURATOR = "curator";
+ private static final String OBO_FORMAT = "OBO Flat File";
+ private static final String DATA_TYPE = "Ontology DAG";
+
+ // This network attribute indicates this is an ontology or not.
+ /**
+ *
+ */
+ public static final String IS_ONTOLOGY = "Is_Ontology";
+
+ /**
+ * Name of this ontorogy. This will be used as the ID of this ontology.
+ */
+ protected String name;
+ protected MetadataParser metaParser;
+
+ /*
+ * Currently not used.
+ */
+ private final OntologyOps ops;
+
+ /*
+ * Actual DAG of the Ontology
+ */
+ private CyNetwork ontologyGraph;
+ private CyAttributes ontologyAttr;
+ private CyAttributes termAttr;
+
+ /**
+ * Constructor.<br>
+ *
+ * <p>
+ * Creates null network for this ontology.
+ * </p>
+ *
+ * @param name
+ * Name of this ontology. Will be used as ID.
+ * @throws URISyntaxException
+ */
+ public Ontology(final String name) {
+ this(name, null, null, null);
+ }
+
+ /**
+ * Constructor.<br>
+ *
+ * <p>
+ * Takes CyNetwork as its DAG.
+ * </p>
+ *
+ * @param name
+ * @param curator
+ * @param description
+ * @param dag
+ * @throws URISyntaxException
+ * @throws URISyntaxException
+ */
+ public Ontology(final String name, final String curator, final String description,
+ final CyNetwork dag) {
+ ontologyAttr = Cytoscape.getNetworkAttributes();
+ termAttr = Cytoscape.getNodeAttributes();
+
+ this.name = name;
+
+ // Not yet implemented.
+ ops = new OntologyOps() {
+ public Set getRemoteTerms() {
+ // TODO Auto-generated method stub
+ return null;
+ }
+ };
+
+ if (dag == null) {
+ this.ontologyGraph = Cytoscape.createNetwork(this.name);
+ } else {
+ this.ontologyGraph = dag;
+ }
+
+ ontologyAttr.setAttribute(ontologyGraph.getIdentifier(), IS_ONTOLOGY, true);
+ ontologyAttr.setUserEditable(IS_ONTOLOGY, false);
+ ontologyAttr.setUserVisible(IS_ONTOLOGY, false);
+
+ /*
+ * Setup metadata & graph (network) attributes
+ */
+ metaParser = new MetadataParser(ontologyGraph);
+ metaParser.setMetadata(MetadataEntries.TITLE, name);
+ metaParser.setMetadata(MetadataEntries.FORMAT, OBO_FORMAT);
+ metaParser.setMetadata(MetadataEntries.TYPE, DATA_TYPE);
+
+ if (curator != null) {
+ ontologyAttr.setAttribute(ontologyGraph.getIdentifier(), CURATOR, curator);
+ }
+
+ if (description != null) {
+ metaParser.setMetadata(MetadataEntries.DESCRIPTION, description);
+ }
+ }
+
+ /**
+ * Returns name (actually, an ID).
+ *
+ * @return Name of the ontology as string
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ *
+ * @return Curator as string
+ */
+ public String getCurator() {
+ return ontologyAttr.getStringAttribute(ontologyGraph.getIdentifier(), CURATOR);
+ }
+
+ /**
+ * Add a new ontology term to the DAG.<br>
+ *
+ * @param newTerm
+ */
+ public void add(OntologyTerm newTerm) {
+ Node newOntologyTerm = Cytoscape.getCyNode(newTerm.getName(), true);
+ ontologyGraph.addNode(newOntologyTerm);
+ termAttr.setAttribute(newOntologyTerm.getIdentifier(), OBOTags.DEF.toString(),
+ newTerm.getDescription());
+ }
+
+ /**
+ *
+ * @return Number of ontology terms in this ontology.
+ */
+ public int size() {
+ return ontologyGraph.getNodeCount();
+ }
+
+ /**
+ * Return all the terms in this ontology.<br>
+ *
+ * @return All ontology terms as Set object.
+ */
+ public Set getTerms() {
+ Set<Term> terms = new HashSet<Term>();
+
+ Iterator nodeIt = ontologyGraph.nodesIterator();
+
+ while (nodeIt.hasNext()) {
+ final Node node = (Node) nodeIt.next();
+ final String id = node.getIdentifier();
+ final Term term = new OntologyTerm(node.getIdentifier(), this.name,
+ termAttr.getStringAttribute(id,
+ OBOTags.DEF.toString()));
+ terms.add(term);
+ }
+
+ return terms;
+ }
+
+ /**
+ * @return true if the term is in the DAG.
+ */
+ public boolean containsTerm(String id) {
+ CyNode testNode = Cytoscape.getCyNode(id, false);
+
+ if (testNode == null) {
+ return false;
+ } else {
+ return true;
+ }
+ }
+
+ /**
+ * Fetch the term with the specified name.
+ *
+ * @return The term named <code>name</code>
+ * @throws NoSuchElementException
+ * if no term exists with that name
+ */
+ public OntologyTerm getTerm(String id) {
+ final OntologyTerm term = new OntologyTerm(id, name,
+ termAttr.getStringAttribute(id,
+ OBOTags.DEF.toString()));
+
+ return term;
+ }
+
+ /**
+ *
+ */
+ public String toString() {
+ StringBuffer sb = new StringBuffer();
+ sb.append("Ontology Name: " + name + ", ");
+ sb.append("Curator: "
+ + ontologyAttr.getStringAttribute(ontologyGraph.getIdentifier(), CURATOR) + ", ");
+ sb.append("Description: " + this.getDescription());
+
+ return sb.toString();
+ }
+
+ /**
+ * See if a triple exists in this ontology.<br>
+ *
+ */
+ public boolean containsTriple(Term subject, Term object, Term predicate) {
+ Node source = Cytoscape.getCyNode(subject.getName());
+ Node target = Cytoscape.getCyNode(object.getName());
+
+ String interaction = predicate.getName();
+
+ if ((source == null) || (target == null)) {
+ return false;
+ }
+
+ if (Cytoscape.getCyEdge(source, target, Semantics.INTERACTION, interaction, false) != null) {
+ return true;
+ } else {
+ return false;
+ }
+ }
+
+ /**
+ * Create a new term in this ontology.
+ */
+ public Term createTerm(String name, String description)
+ throws AlreadyExistsException, ChangeVetoException, IllegalArgumentException {
+ Node newNode = Cytoscape.getCyNode(name, true);
+ ontologyGraph.addNode(newNode);
+ termAttr.setAttribute(name, MetadataEntries.DESCRIPTION.toString(), description);
+
+ Term newTerm = new OntologyTerm(name, this.name, description);
+
+ return newTerm;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param arg0 DOCUMENT ME!
+ * @param arg1 DOCUMENT ME!
+ * @param arg2 DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @throws AlreadyExistsException DOCUMENT ME!
+ * @throws ChangeVetoException DOCUMENT ME!
+ * @throws IllegalArgumentException DOCUMENT ME!
+ */
+ public Term createTerm(String arg0, String arg1, Object[] arg2)
+ throws AlreadyExistsException, ChangeVetoException, IllegalArgumentException {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param subject DOCUMENT ME!
+ * @param object DOCUMENT ME!
+ * @param predicate DOCUMENT ME!
+ * @param name DOCUMENT ME!
+ * @param description DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @throws AlreadyExistsException DOCUMENT ME!
+ * @throws ChangeVetoException DOCUMENT ME!
+ */
+ public Triple createTriple(Term subject, Term object, Term predicate, String name,
+ String description)
+ throws AlreadyExistsException, ChangeVetoException {
+ Triple newTriple = new cytoscape.data.ontology.Triple(subject, object, predicate, name,
+ description);
+
+ //Cytoscape.getCyEdge(subject.getName(), object.getName(), null, predicate.getName());
+ return newTriple;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param arg0 DOCUMENT ME!
+ * @param arg1 DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @throws AlreadyExistsException DOCUMENT ME!
+ * @throws ChangeVetoException DOCUMENT ME!
+ * @throws IllegalArgumentException DOCUMENT ME!
+ */
+ public Variable createVariable(String arg0, String arg1)
+ throws AlreadyExistsException, ChangeVetoException, IllegalArgumentException {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ /**
+ * Delete a term from DAG (CyNetwork)
+ */
+ public void deleteTerm(Term arg0) throws ChangeVetoException {
+ ontologyGraph.removeNode(Cytoscape.getRootGraph().getNode(arg0.getName()).getRootGraphIndex(),
+ true);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getDescription() {
+ return metaParser.getMetadataMap().get(MetadataEntries.DESCRIPTION.toString()).toString();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public OntologyOps getOps() {
+ return ops;
+ }
+
+ /**
+ * returns set of Triples.<br>
+ *
+ * This is an expensive operation!
+ */
+ public Set getTriples(Term arg0, Term arg1, Term arg2) {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param arg0 DOCUMENT ME!
+ * @param arg1 DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @throws ChangeVetoException DOCUMENT ME!
+ * @throws IllegalArgumentException DOCUMENT ME!
+ */
+ public Term importTerm(Term arg0, String arg1)
+ throws ChangeVetoException, IllegalArgumentException {
+ // TODO Auto-generated method stub
+ return null;
+ }
+}
diff --git a/application/src/main/java/cytoscape/data/ontology/OntologyFactory.java b/application/src/main/java/cytoscape/data/ontology/OntologyFactory.java
new file mode 100644
index 0000000..11b7450
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/ontology/OntologyFactory.java
@@ -0,0 +1,113 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data.ontology;
+
+import cytoscape.data.ontology.readers.OBOFlatFileReader;
+import static cytoscape.data.ontology.readers.OBOHeaderTags.*;
+
+import cytoscape.data.readers.MetadataEntries;
+import cytoscape.data.readers.MetadataParser;
+
+import java.io.IOException;
+
+import java.net.URISyntaxException;
+import java.net.URL;
+
+import java.util.Map;
+
+
+/**
+ *
+ */
+public class OntologyFactory {
+ private MetadataParser mdp;
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param dataSource DOCUMENT ME!
+ * @param name DOCUMENT ME!
+ * @param description DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @throws IOException DOCUMENT ME!
+ * @throws URISyntaxException DOCUMENT ME!
+ */
+ public Ontology createBasicOntology(URL dataSource, String name, String description)
+ throws IOException, URISyntaxException {
+ OBOFlatFileReader reader = new OBOFlatFileReader(dataSource, name);
+ reader.readOntology();
+
+ Ontology onto = new Ontology(name, "General Ontology", description, reader.getDag());
+
+ Map header = reader.getHeader();
+
+ if ((header != null) && (header.get(DATE.toString()) != null)) {
+ mdp = new MetadataParser(reader.getDag());
+
+ mdp.setMetadata(MetadataEntries.DATE, header.get(DATE.toString()).toString());
+ }
+
+ return onto;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param dataSource DOCUMENT ME!
+ * @param name DOCUMENT ME!
+ * @param description DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @throws IOException DOCUMENT ME!
+ * @throws URISyntaxException DOCUMENT ME!
+ */
+ public GeneOntology createGeneOntology(URL dataSource, String name, String description)
+ throws IOException, URISyntaxException {
+
+ OBOFlatFileReader reader = new OBOFlatFileReader(dataSource, name);
+ reader.readOntology();
+
+ final GeneOntology go = new GeneOntology(name, "GO", description, reader.getDag());
+ Map header = reader.getHeader();
+
+ mdp = new MetadataParser(reader.getDag());
+ mdp.setMetadata(MetadataEntries.DATE, header.get(DATE.toString()).toString());
+ reader = null;
+ return go;
+ }
+}
diff --git a/application/src/main/java/cytoscape/data/ontology/OntologyTerm.java b/application/src/main/java/cytoscape/data/ontology/OntologyTerm.java
new file mode 100644
index 0000000..399e7af
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/ontology/OntologyTerm.java
@@ -0,0 +1,206 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data.ontology;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.data.ontology.readers.OBOTags;
+
+import org.biojava.bio.Annotation;
+
+import org.biojava.ontology.Ontology;
+
+import org.biojava.utils.AbstractChangeable;
+
+import java.util.HashMap;
+import java.util.Map;
+
+
+/**
+ * Simple in-memory implementation of an ontology term based on BioJava's
+ * interface.<br>
+ *
+ * <p>
+ * This implementation uses CyNetwork and CyAttributes as its actual data
+ * storage. A term is equal to a CyNode and the node can have attributes like
+ * other regular nodes in CyNetwork. Synonyms, description, etc are stored in
+ * CyAttributes.
+ * </p>
+ *
+ * @since Cytoscape 2.4
+ * @version 0.8
+ * @author kono
+ *
+ */
+public class OntologyTerm extends AbstractChangeable implements org.biojava.ontology.OntologyTerm {
+ /*
+ * These constants will be used as the attribute names in CyAttributes.
+ */
+
+ //protected static final String DESCRIPTION = "description";
+ protected static final String SYNONYM = "synonym";
+
+ /*
+ * Type of Synonyms used in OBO
+ */
+ public enum SynonymType {
+ NORMAL("synonym"),
+ RELATED("related_synonym"),
+ EXACT("exact_synonym"),
+ BROAD("broad_synonym"),
+ NARROW("narrow_synonym");
+
+ private String typeText;
+
+ private SynonymType(String type) {
+ this.typeText = type;
+ }
+
+ public String toString() {
+ return typeText;
+ }
+ }
+
+ /**
+ * ID of this ontology term.
+ */
+ private String name;
+
+ /**
+ * Name (ID) of the ontology which contains this term.
+ */
+ private String ontologyName;
+
+ /**
+ * Constructor.<br>
+ *
+ * @param name ID of this term. SHOULD NOT BE NULL.
+ * @param ontologyName
+ * @param description
+ */
+ public OntologyTerm(String name, String ontologyName, String description) {
+ this.name = name;
+ this.ontologyName = ontologyName;
+
+ if (description != null) {
+ Cytoscape.getNodeAttributes()
+ .setAttribute(name, OBOTags.getPrefix() + "." + OBOTags.DEF.toString(),
+ description);
+ }
+ }
+
+ /**
+ * Return name (ID) of this term.<br>
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * Get ontology object which contains this term.<br>
+ */
+ public Ontology getOntology() {
+ return Cytoscape.getOntologyServer().getOntologies().get(ontologyName);
+ }
+
+ /**
+ * In this implementation, key is the synonym name, and value is the synonym
+ * type.
+ */
+ public void addSynonym(Object synonym) {
+ addSynonym(synonym, SynonymType.NORMAL);
+ }
+
+ /**
+ * In this implementation, key is the synonym name, and value is the synonym
+ * type.
+ */
+ public void addSynonym(Object synonym, SynonymType type) {
+ Map<Object, SynonymType> synoMap = Cytoscape.getNodeAttributes()
+ .getMapAttribute(name,
+ OBOTags.getPrefix() + "."
+ + SYNONYM);
+
+ if (synoMap == null) {
+ synoMap = new HashMap();
+ }
+
+ synoMap.put(synonym, type);
+ Cytoscape.getNodeAttributes()
+ .setMapAttribute(name, OBOTags.getPrefix() + "." + SYNONYM, synoMap);
+ }
+
+ /**
+ * Return a human-readable description of this term, or the empty string if
+ * none is available.
+ *
+ */
+ public String getDescription() {
+ return Cytoscape.getNodeAttributes()
+ .getStringAttribute(name, OBOTags.getPrefix() + "."
+ + OBOTags.DEF.toString());
+ }
+
+ /**
+ * Return sysnonym attributes for this term.
+ */
+ public Object[] getSynonyms() {
+ return Cytoscape.getNodeAttributes()
+ .getMapAttribute(name, OBOTags.getPrefix() + "." + SYNONYM).keySet()
+ .toArray();
+ }
+
+ /**
+ * Remove a synonym for this term.<br>
+ *
+ */
+ public void removeSynonym(Object synonym) {
+ Map synoMap = Cytoscape.getNodeAttributes().getMapAttribute(name, SYNONYM);
+
+ if (synoMap != null) {
+ synoMap.remove(synonym);
+ Cytoscape.getNodeAttributes()
+ .setMapAttribute(name, OBOTags.getPrefix() + "." + SYNONYM, synoMap);
+ }
+ }
+
+ /**
+ * Always return empty annotation object. Instead of using this, use normal
+ * Cyattributes API.
+ */
+ public Annotation getAnnotation() {
+ return Annotation.EMPTY_ANNOTATION;
+ }
+}
diff --git a/application/src/main/java/cytoscape/data/ontology/Triple.java b/application/src/main/java/cytoscape/data/ontology/Triple.java
new file mode 100644
index 0000000..8792546
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/ontology/Triple.java
@@ -0,0 +1,196 @@
+/**
+ *
+ */
+package cytoscape.data.ontology;
+
+import org.biojava.bio.Annotation;
+
+import org.biojava.ontology.Ontology;
+import org.biojava.ontology.Term;
+
+import org.biojava.utils.AbstractChangeable;
+
+import java.util.Collections;
+
+
+/**
+ *
+ * Extract partial graph structure.
+ *
+ * @since Cytoscape 2.4
+ * @version 0.5
+ * @author kono
+ *
+ */
+public class Triple extends AbstractChangeable implements org.biojava.ontology.Triple {
+ private final Term object;
+ private final Term subject;
+ private final Term predicate;
+ private final String name;
+ private final String description;
+
+ /**
+ * Creates a new Triple object.
+ *
+ * @param subject DOCUMENT ME!
+ * @param object DOCUMENT ME!
+ * @param predicate DOCUMENT ME!
+ * @param name DOCUMENT ME!
+ * @param description DOCUMENT ME!
+ */
+ public Triple(final Term subject, final Term object, final Term predicate, final String name,
+ final String description) {
+ this.object = object;
+ this.subject = subject;
+ this.predicate = predicate;
+
+ this.name = name;
+ this.description = description;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see org.biojava.ontology.Triple#getObject()
+ */
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Term getObject() {
+ return object;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see org.biojava.ontology.Triple#getPredicate()
+ */
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Term getPredicate() {
+ return predicate;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see org.biojava.ontology.Triple#getSubject()
+ */
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Term getSubject() {
+ return subject;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see org.biojava.ontology.Term#addSynonym(java.lang.Object)
+ */
+
+ /**
+ * Triple synonym is not supported.
+ */
+ public void addSynonym(Object arg0) {
+ throw new UnsupportedOperationException("Cytoscape does not know about triple synonyms.");
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see org.biojava.ontology.Term#getDescription()
+ */
+
+ /**
+ * Description for triple is not supported.
+ */
+ public String getDescription() {
+ return description;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see org.biojava.ontology.Term#getName()
+ */
+
+ /**
+ * Returns human-readable name of this triple.
+ */
+ public String getName() {
+ return name;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see org.biojava.ontology.Term#getOntology()
+ */
+
+ /**
+ * Returns ontology which this triple belongs to.
+ */
+ public Ontology getOntology() {
+ return object.getOntology();
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see org.biojava.ontology.Term#getSynonyms()
+ */
+
+ /**
+ * Synonym is not supported.
+ */
+ public Object[] getSynonyms() {
+ return Collections.EMPTY_LIST.toArray();
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see org.biojava.ontology.Term#removeSynonym(java.lang.Object)
+ */
+
+ /**
+ * Not supported.
+ */
+ public void removeSynonym(Object arg0) {
+ throw new UnsupportedOperationException("Cytoscape does not support triple synonyms.");
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see org.biojava.bio.Annotatable#getAnnotation()
+ */
+
+ /**
+ * Always return empty annotation object.
+ */
+ public Annotation getAnnotation() {
+ return Annotation.EMPTY_ANNOTATION;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String toString() {
+ return this.object.getOntology().getName() + ":" + this.predicate + "(" + this.subject
+ + "," + this.object + ")";
+ }
+}
diff --git a/application/src/main/java/cytoscape/data/ontology/readers/DBCrossReferenceReader.java b/application/src/main/java/cytoscape/data/ontology/readers/DBCrossReferenceReader.java
new file mode 100644
index 0000000..08b0918
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/ontology/readers/DBCrossReferenceReader.java
@@ -0,0 +1,183 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data.ontology.readers;
+
+import cytoscape.data.ontology.DBReference;
+import cytoscape.util.URLUtil;
+import static cytoscape.data.ontology.readers.DBXrefKeywords.ABBREVIATION;
+import static cytoscape.data.ontology.readers.DBXrefKeywords.DATABASE;
+import static cytoscape.data.ontology.readers.DBXrefKeywords.GENERIC_URL;
+import static cytoscape.data.ontology.readers.DBXrefKeywords.OBJECT;
+import static cytoscape.data.ontology.readers.DBXrefKeywords.SYNONYM;
+import static cytoscape.data.ontology.readers.DBXrefKeywords.URL_SYNTAX;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStreamReader;
+
+import java.net.URL;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+
+/**
+ * Reader for database cross reference file.<br>
+ *
+ * <p>
+ * The resource file location is hard-coded. This will be in the cytoscape.jar.
+ * </p>
+ *
+ * @version 0.9
+ * @since Cytoscape 2.4
+ * @author kono
+ *
+ */
+public class DBCrossReferenceReader {
+ private Map<String, DBReference> xref;
+
+ /*
+ * Resource file for DBXref.
+ *
+ * This is in the jar file.
+ */
+ private static final String DBXREF_RESOURCE_FILE = "/GO.xrf_abbs";
+
+ /**
+ * Constructor.<br>
+ *
+ * Create a new map for the DB references.
+ *
+ */
+ public DBCrossReferenceReader() {
+ xref = new HashMap<String, DBReference>();
+ }
+
+ /**
+ * Read the resource file in the jar.
+ *
+ * @throws IOException
+ */
+ public void readResourceFile() throws IOException {
+ URL resource = getClass().getResource(DBXREF_RESOURCE_FILE);
+ // BufferedReader bufRd = new BufferedReader(new InputStreamReader(resource.openStream()));
+ // Use URLUtil to get the InputStream since we might be using a proxy server and because pages may be cached:
+ BufferedReader bufRd = null;
+ String line;
+
+ try {
+ bufRd = new BufferedReader(new InputStreamReader(URLUtil.getBasicInputStream (resource)));
+ while ((line = bufRd.readLine()) != null) {
+ // Read header
+ if (line.startsWith(ABBREVIATION.toString())) {
+ int colonInx = line.indexOf(':');
+ String abb = line.substring(colonInx + 1).trim();
+ readEntry(abb, bufRd);
+ }
+ }
+ }
+ finally {
+ if (bufRd != null) {
+ bufRd.close();
+ }
+ }
+ }
+
+ /**
+ * Extract an entry.
+ *
+ * @param abbreviation
+ * @param rd
+ * @throws IOException
+ */
+ private void readEntry(final String abbreviation, final BufferedReader rd)
+ throws IOException {
+ String dbName = null;
+ String urlSyntax = null;
+ String genericUrl = null;
+ String object = null;
+ List<String> synonyms = new ArrayList<String>();
+
+ while (true) // Parse until blank line.
+ {
+ final String line = rd.readLine();
+
+ if (line == null) {
+ break;
+ }
+
+ if (line.trim().length() == 0)
+ break;
+
+ final int colonInx = line.indexOf(':');
+ final String key = line.substring(0, colonInx).trim();
+ final String val = line.substring(colonInx + 1).trim();
+
+ if (key.equals(SYNONYM.toString())) {
+ synonyms.add(val);
+ } else if (key.equals(DATABASE.toString())) {
+ dbName = val;
+ } else if (key.equals(GENERIC_URL.toString())) {
+ genericUrl = val;
+ } else if (key.equals(URL_SYNTAX.toString())) {
+ urlSyntax = val;
+ } else if (key.equals(OBJECT.toString())) {
+ object = val;
+ }
+ }
+
+ /*
+ * Create a new DBReference.
+ */
+ DBReference ref = new DBReference(abbreviation, dbName, urlSyntax, genericUrl, object);
+
+ if (synonyms.size() != 0) {
+ ref.setSynonym(synonyms);
+ }
+
+ xref.put(abbreviation, ref);
+ }
+
+ /**
+ * Get the references as a map.
+ *
+ * @return
+ */
+ public Map<String, DBReference> getXrefMap() {
+ return xref;
+ }
+}
diff --git a/application/src/main/java/cytoscape/data/ontology/readers/DBXrefKeywords.java b/application/src/main/java/cytoscape/data/ontology/readers/DBXrefKeywords.java
new file mode 100644
index 0000000..cc9bec6
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/ontology/readers/DBXrefKeywords.java
@@ -0,0 +1,61 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data.ontology.readers;
+
+public enum DBXrefKeywords {
+ ABBREVIATION("abbreviation"),
+ DATABASE("database"),
+ GENERIC_URL("generic_url"),
+ URL_SYNTAX("url_syntax"),
+ URL_EXAMPLE("url_example"),
+ OBJECT("object"),
+ EXAMPLE_ID("example_id"),
+ SYNONYM("synonym");
+
+ private String keyword;
+
+ private DBXrefKeywords(String keyword) {
+ this.keyword = keyword;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String toString() {
+ return keyword;
+ }
+}
diff --git a/application/src/main/java/cytoscape/data/ontology/readers/OBOFlatFileReader.java b/application/src/main/java/cytoscape/data/ontology/readers/OBOFlatFileReader.java
new file mode 100644
index 0000000..d40fb8a
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/ontology/readers/OBOFlatFileReader.java
@@ -0,0 +1,475 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data.ontology.readers;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+
+import cytoscape.data.CyAttributes;
+import cytoscape.data.Semantics;
+
+import cytoscape.data.ontology.Ontology;
+import static cytoscape.data.ontology.readers.OBOTags.*;
+import static cytoscape.data.ontology.readers.OBOTags.BROAD_SYNONYM;
+import static cytoscape.data.ontology.readers.OBOTags.DEF;
+import static cytoscape.data.ontology.readers.OBOTags.EXACT_SYNONYM;
+import static cytoscape.data.ontology.readers.OBOTags.ID;
+import static cytoscape.data.ontology.readers.OBOTags.IS_A;
+import static cytoscape.data.ontology.readers.OBOTags.IS_OBSOLETE;
+import static cytoscape.data.ontology.readers.OBOTags.NARROW_SYNONYM;
+import static cytoscape.data.ontology.readers.OBOTags.RELATED_SYNONYM;
+import static cytoscape.data.ontology.readers.OBOTags.RELATIONSHIP;
+import static cytoscape.data.ontology.readers.OBOTags.SYNONYM;
+import static cytoscape.data.ontology.readers.OBOTags.XREF;
+import static cytoscape.data.ontology.readers.OBOTags.XREF_ANALOG;
+
+import cytoscape.logger.CyLogger;
+
+import cytoscape.util.URLUtil;
+
+import giny.model.Edge;
+import giny.model.Node;
+
+import java.io.BufferedReader;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+
+import java.net.URL;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.TreeSet;
+
+
+/**
+ * OBO file reader.<br>
+ *
+ * <p>
+ * This is a general OBO (Open Biomedical Ontologies:
+ * http://obo.sourceforge.net/) flatfile reader.<br>
+ *
+ * In Cytoscape, This will be used mainly for reading gene ontology. However, it
+ * is compatible with all files written in OBO format.<br>
+ * </p>
+ *
+ * <p>
+ * OBO files are available at:<br>
+ * http://obo.sourceforge.net/cgi-bin/table.cgi
+ * </p>
+ *
+ * @since Cytoscape 2.4
+ * @version 0.7
+ * @author Keiichiro Ono
+ *
+ */
+public class OBOFlatFileReader implements OntologyReader {
+ /**
+ *
+ */
+ public static final String ONTOLOGY_DAG_ROOT = "Ontology DAGs";
+
+ /**
+ *
+ */
+ public static final String OBO_PREFIX = "ontology";
+ private static final String DEF_ORIGIN = "def_origin";
+ protected static final String TERM_TAG = "[Term]";
+ private static final String DEF_ONTOLOGY_NAME = "Ontology DAG";
+ private ArrayList<String[]> interactionList;
+ private CyNetwork ontologyDAG;
+
+ /*
+ * This is for attributes of nodes.
+ */
+ private CyAttributes termAttributes;
+
+ /*
+ * Attribute for the Ontology DAG.
+ */
+ private CyAttributes networkAttributes;
+ private Map<String, String> header;
+ private String name;
+ private InputStream inputStream;
+
+ /**
+ *
+ * @param fileName
+ * @throws FileNotFoundException
+ */
+ public OBOFlatFileReader(final String fileName, String name) throws FileNotFoundException {
+ this(new FileInputStream(fileName), name);
+ }
+
+ /**
+ *
+ * @param dataSource
+ * @throws IOException
+ */
+ public OBOFlatFileReader(URL dataSource, String name) throws IOException {
+ // this(dataSource.openStream(), name);
+ // Use URLUtil to get the InputStream since we might be using a proxy server
+ // and because pages may be cached:
+ this(URLUtil.getBasicInputStream(dataSource), name);
+ }
+
+ /**
+ *
+ * @param oboStream
+ * @param name
+ */
+ public OBOFlatFileReader(InputStream oboStream, String name) {
+ this.inputStream = oboStream;
+ this.name = name;
+ initialize();
+ }
+
+ private void initialize() {
+ interactionList = new ArrayList<String[]>();
+ header = new HashMap<String, String>();
+
+ networkAttributes = Cytoscape.getNetworkAttributes();
+ termAttributes = Cytoscape.getNodeAttributes();
+
+ if (name == null) {
+ name = DEF_ONTOLOGY_NAME;
+ }
+
+ /*
+ * Ontology DAGs will be distinguished by this attribute.
+ */
+ networkAttributes.setAttribute(name, Ontology.IS_ONTOLOGY, true);
+ networkAttributes.setUserVisible(Ontology.IS_ONTOLOGY, false);
+ networkAttributes.setUserEditable(Ontology.IS_ONTOLOGY, false);
+
+ String rootID = Cytoscape.getOntologyRootID();
+
+ if (rootID == null) {
+ Set<CyNetwork> networkSet = Cytoscape.getNetworkSet();
+
+ for (CyNetwork net : networkSet) {
+ if (net.getTitle().equals(ONTOLOGY_DAG_ROOT)) {
+ rootID = net.getIdentifier();
+ }
+ }
+
+ if (rootID == null) {
+ rootID = Cytoscape.createNetwork(ONTOLOGY_DAG_ROOT, false).getIdentifier();
+ Cytoscape.setOntologyRootID(rootID);
+ }
+ }
+
+ ontologyDAG = Cytoscape.createNetwork(name, Cytoscape.getNetwork(rootID), false);
+ }
+
+ /**
+ * @throws IOException
+ */
+ public void readOntology() throws IOException {
+ try {
+ try {
+ BufferedReader bufRd = null;
+ String line;
+
+ String key;
+ String val;
+ int colonInx;
+
+ try {
+ bufRd = new BufferedReader(new InputStreamReader(inputStream));
+ while ((line = bufRd.readLine()) != null) {
+ // Read header
+ if (line.startsWith(TERM_TAG)) {
+ readEntry(bufRd);
+
+ break;
+ } else if (line.length() != 0) {
+ colonInx = line.indexOf(':');
+
+ if (colonInx == -1)
+ continue;
+
+ key = line.substring(0, colonInx).trim();
+ val = line.substring(colonInx + 1).trim();
+ header.put(key, val);
+ }
+ }
+
+ while ((line = bufRd.readLine()) != null) {
+ // Read header
+ if (line.startsWith(TERM_TAG)) {
+ readEntry(bufRd);
+ }
+ }
+
+ }
+ finally {
+ if (bufRd != null) {
+ bufRd.close();
+ }
+ }
+ }
+ finally {
+ if (inputStream != null) {
+ inputStream.close();
+ }
+ }
+
+ buildDag();
+ setAttributeDescriptions();
+ }
+ catch (IOException ioe) {
+ }
+ finally {
+ inputStream = null;
+ }
+ }
+
+ /**
+ * Read one Ontology Term
+ *
+ * @param rd
+ * @throws IOException
+ */
+ private void readEntry(final BufferedReader rd) throws IOException {
+ String id = "";
+ String line = null;
+
+ String key;
+ String val;
+
+ int colonInx;
+
+ String[] definitionParts;
+ String[] synonymParts;
+ String[] entry;
+ String targetId;
+ List<String> listAttr;
+ Map<String, String> synoMap;
+
+ while (true) {
+ line = rd.readLine().trim();
+
+ if (line.length() == 0)
+ break;
+
+ colonInx = line.indexOf(':');
+ if (colonInx == -1) {
+ // Hmm.... this shouldn't happen, but if it does,
+ // just skip this line and try to recover
+ CyLogger.getLogger(OBOFlatFileReader.class).warn("Illegal format in ontology file for "+name+" ... continuing");
+ continue;
+ }
+
+ key = line.substring(0, colonInx).trim();
+ val = line.substring(colonInx + 1).trim();
+
+ Node source = null;
+
+ if (key.equals(ID.toString())) {
+ // There's only one id.
+ id = val;
+ } else if (key.equals(DEF.toString())) {
+ // CyLogger.getLogger().info("DEF: " + id + " = " + val);
+ definitionParts = val.split("\"");
+ termAttributes.setAttribute(id, OBO_PREFIX + "." + key, definitionParts[1]);
+
+ List<String> originList = getReferences(val.substring(definitionParts[1].length()
+ + 2));
+
+ if (originList != null)
+ termAttributes.setListAttribute(id, OBO_PREFIX + "." + DEF_ORIGIN, originList);
+ } else if (key.equals(EXACT_SYNONYM.toString())
+ || key.equals(RELATED_SYNONYM.toString())
+ || key.equals(BROAD_SYNONYM.toString())
+ || key.equals(NARROW_SYNONYM.toString()) || key.equals(SYNONYM.toString())) {
+ synonymParts = val.split("\"");
+
+ synoMap = termAttributes.getMapAttribute(id,
+ OBO_PREFIX + "."
+ + OBOTags.SYNONYM.toString());
+
+ if (synoMap == null)
+ synoMap = new HashMap<String, String>();
+
+ if (key.equals(SYNONYM.toString())) {
+ synoMap.put(synonymParts[1], synonymParts[2].trim());
+ } else
+ synoMap.put(synonymParts[1], key);
+
+ termAttributes.setMapAttribute(id, OBO_PREFIX + "." + SYNONYM.toString(), synoMap);
+ } else if (key.equals(RELATIONSHIP.toString())) {
+ if (source == null) {
+ source = Cytoscape.getCyNode(id, true);
+ ontologyDAG.addNode(source);
+ }
+
+ entry = val.split(" ");
+
+ final String[] itr = new String[3];
+ itr[0] = id;
+ itr[1] = entry[1];
+ itr[2] = entry[0];
+ interactionList.add(itr);
+ } else if (key.equals(IS_A.toString())) {
+ /*
+ * This is the keyword to create an edge. IS_A relationship
+ * means current node is the source, and target is the one
+ * written here.
+ */
+ final Node target;
+
+ if (source == null) {
+ source = Cytoscape.getCyNode(id, true);
+ ontologyDAG.addNode(source);
+ }
+
+ int colonidx = val.indexOf('!');
+
+ if (colonidx == -1)
+ targetId = val.trim();
+ else
+ targetId = val.substring(0, colonidx).trim();
+
+ target = Cytoscape.getCyNode(targetId, true);
+ ontologyDAG.addNode(target);
+
+ final String[] itr = new String[3];
+ itr[0] = id;
+ itr[1] = targetId;
+ itr[2] = "is_a";
+ interactionList.add(itr);
+ } else if (key.equals(IS_OBSOLETE.toString())) {
+ termAttributes.setAttribute(id, OBO_PREFIX + "." + key, Boolean.parseBoolean(val));
+ } else if (key.equals(XREF.toString()) || key.equals(XREF_ANALOG.toString())
+ || key.equals(ALT_ID.toString()) || key.equals(SUBSET.toString())
+ || key.equals(DISJOINT_FROM.toString())) {
+ listAttr = termAttributes.getListAttribute(id, OBO_PREFIX + "." + key);
+
+ if (listAttr == null)
+ listAttr = new ArrayList<String>();
+
+ if (val != null) {
+ if (key.equals(DISJOINT_FROM.toString())) {
+ listAttr.add(val.split("!")[0].trim());
+ } else
+ listAttr.add(val);
+ }
+
+ termAttributes.setListAttribute(id, OBO_PREFIX + "." + key, listAttr);
+ } else
+ termAttributes.setAttribute(id, OBO_PREFIX + "." + key, val);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Map<String, String> getHeader() {
+ return header;
+ }
+
+ private void buildDag() {
+ Iterator<String[]> it = interactionList.iterator();
+
+ while (it.hasNext()) {
+ String[] interaction = it.next();
+
+ Edge isA = Cytoscape.getCyEdge(Cytoscape.getCyNode(interaction[0], true),
+ Cytoscape.getCyNode(interaction[1], true),
+ Semantics.INTERACTION, interaction[2], true, true);
+ ontologyDAG.addEdge(isA);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public CyAttributes getTermsAttributes() {
+ return termAttributes;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public CyNetwork getDag() {
+ return ontologyDAG;
+ }
+
+ private List<String> getReferences(String list) {
+ String trimed = list.trim();
+ trimed = trimed.substring(trimed.indexOf("[") + 1, trimed.indexOf("]"));
+
+ if (trimed.length() == 0) {
+ return null;
+ } else {
+ List<String> entries = new ArrayList<String>();
+
+ for (String entry : trimed.split(",")) {
+ entries.add(entry.trim());
+ }
+
+ return entries;
+ }
+ }
+
+ private void setAttributeDescriptions() {
+ String[] attrNames = termAttributes.getAttributeNames();
+ Set<String> attrNameSet = new TreeSet<String>();
+
+ for (String name : attrNames) {
+ attrNameSet.add(name);
+ }
+
+ for (OBOTags tags : OBOTags.values()) {
+ if (attrNameSet.contains(OBOTags.getPrefix() + "." + tags.toString())) {
+ termAttributes.setAttributeDescription(OBOTags.getPrefix() + "." + tags.toString(),
+ tags.getDescription());
+ }
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/data/ontology/readers/OBOHeaderTags.java b/application/src/main/java/cytoscape/data/ontology/readers/OBOHeaderTags.java
new file mode 100644
index 0000000..50bc416
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/ontology/readers/OBOHeaderTags.java
@@ -0,0 +1,58 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data.ontology.readers;
+
+public enum OBOHeaderTags {
+ FORMAT_VERSION,
+ TYPEREF,
+ VERSION,
+ DATE,
+ SAVED_BY,
+ AUTO_GENERATED_BY,
+ DEFAULT_NAMESPACE,
+ REMARK,
+ SUBSETDEF;
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String toString() {
+ String name = name().toLowerCase();
+
+ return name.replace('_', '-');
+ }
+}
diff --git a/application/src/main/java/cytoscape/data/ontology/readers/OBOTags.java b/application/src/main/java/cytoscape/data/ontology/readers/OBOTags.java
new file mode 100644
index 0000000..7b3b279
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/ontology/readers/OBOTags.java
@@ -0,0 +1,151 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data.ontology.readers;
+
+
+/**
+ * Tags used in OBO file:<br>
+ * <a href="http://www.geneontology.org/GO.format.shtml#oboflat">OBO</a>
+ *
+ * <p>
+ * This requirs JavaSE 5
+ * </p>
+ *
+ * @author kono
+ *
+ */
+public enum OBOTags {
+
+ /*
+ * Descriptions for the tags.
+ */
+ ID("The unique id of the current term. This can be any string. This tag must always be the first tag in any term description."),
+ NAME("The term name. Any term may only have ONE name defined. If multiple term names are defined, it is a parse error."),
+ ALT_ID("Defines an alternate id for this term. A term may have any number of alternate ids."),
+ NAMESPACE("The namespace in which the term belongs. If this tag is not present, the term will be assigned to the "
+ + "'default-namespace' specified in the file header stanza."),
+ DEF("The definition of the current term. There must be zero or one instances of this tag per term description. "
+ + "More than one definition for a term generates a parse error. The value of this tag should be the quote "
+ + "enclosed definition text, followed by a dbxref list containing dbxrefs that describe the origin of this "
+ + "definition. The origine is stored in a separate attribute called def_origin."),
+ COMMENT("A comment for this term. There must be zero or one instances of this tag per term description. More than "
+ + "one comment for a term generates a parse error."),
+ SUBSET("This tag indicates a term subset to which this term belongs. The value of this tag must be a subset name as "
+ + "defined in a subsetdef tag in the file header. If the value of this tag is not mentioned in a subsetdef tag, "
+ + "a parse error will be generated. A term may belong to any number of subsets."),
+ SYNONYM("This tag gives a synonym for the term; whether the synonym is exact, broad, narrow, or otherwise related "
+ + "to the term is not specified. The value of this tag should be the quote enclosed synonym text, followed by "
+ + "an optional dbxref list containing dbxrefs that describe the origin of this synonym (see Dbxref Formatting "
+ + "for information on how dbxref lists are encoded). A term may have any number of synonyms."),
+ RELATED_SYNONYM("This tag gives a synonym for the term of the specified type."),
+ EXACT_SYNONYM("This tag gives a synonym for the term of the specified type."),
+ BROAD_SYNONYM("This tag gives a synonym for the term of the specified type."),
+ NARROW_SYNONYM("This tag gives a synonym for the term of the specified type."),
+ XREF("A dbxref that describes an analogous object in another vocabulary (see Dbxref Formatting for information "
+ + "about how the value of this tag must be formatted). A term may have any number of analogous xrefs. "),
+ XREF_ANALOG("A dbxref that describes an analogous object in another vocabulary (see Dbxref Formatting for information "
+ + "about how the value of this tag must be formatted). A term may have any number of analogous xrefs. "),
+ XREF_UNKNOWN("A dbxref with an unknown type."),
+ IS_A("This tag describes a subclassing relationship between one term and another. A term may have any number of is_a "
+ + "relationships. Terms with no is_a relationships are roots. A term with no is_a relationships may not specify "
+ + "any relationship tags."),
+ RELATIONSHIP("This tag describes a typed relationship between this term and another term. The value of this tag should "
+ + "be the relationship type id, and then the id of the target term. The relationship type name must be a "
+ + "relationship type name as defined in a typedef tag stanza. The [typedef] must either occur in a document in the "
+ + "current parse batch, or in a file imported via a typeref header tag. If the relationship type name is undefined, "
+ + "a parse error will be generated. If the id of the target term cannot be resolved by the end of parsing the current "
+ + "batch of files, this tag describes a \"dangling reference\"."),
+ IS_OBSOLETE("This tag indicates whether or not the term is obsolete. Allowable values are true and false (false is assumed "
+ + "if this tag is not present). Obsolete terms must have NO relationships, and no defined is_a tags."),
+ USE_TERM("This tag indicates which term to use instead of an obsolete term. The value of this tag is the id of another term. "
+ + "If the tag value refers to a term that is not specified in the current load batch, it is a \"dangling reference\" "
+ + "(see Parser Requirements). If this tag is specified and the \"is_obsolete\" value for the current term is not true, "
+ + "a parse error will be generated. This tag is not required for terms that specify the is_obsolete tag, but it is "
+ + "recommended (some parsers may choose to issue warnings about obsolete terms that do not specify a replacement term). "
+ + "An obsolete term may have any number of use_term tags."),
+ DOMAIN("This tag determines the children that can be assigned to relationships with this type. If the domain is set, term "
+ + "relationships with this type may only have children that are the same as, or subclasses of, the domain term."),
+ RANGE("This tag specifies the parents that can be assigned to relationships with this type. If the range is set, term "
+ + "relationships with this type may only have parents that are the same as, or subclasses of, the range term."),
+ IS_CYCLIC("This tag indicates that it is legal to create cycles out of this relationship."),
+ IS_TRANSITIVE("This tag indicates that the relationship is marked as transitive. This information is very useful to "
+ + "reasoners and other automatic traversals of the graph."),
+ IS_SYMMETRIC("This tag indicates that the relationship is marked as symmetric (meaning that if the relationship holds from "
+ + "the child to parent, it also holds from parent to child). This information is very useful to reasoners and other "
+ + "automatic traversals of the graph."),
+ DISJOINT_FROM("This tag indicates that a term is disjoint from another, meaning that the two terms have no instances or " +
+ "subclasses in common. The value is the id of the term from which the current term is disjoint. This tag may not be " +
+ "applied to relationship types."),
+
+ /*
+ * This is a local tag defined by Kei. This is a reference extracted from "DEF" tag.
+ */
+ DEF_ORIGIN("A dbxref list containing dbxrefs that describe the origin of this definition.");
+ /*
+ * Description String
+ */
+ private String description;
+
+ private OBOTags(String description) {
+ this.description = description;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getDescription() {
+ return description;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String toString() {
+ return name().toLowerCase();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static String getPrefix() {
+ return "ontology";
+ }
+}
diff --git a/application/src/main/java/cytoscape/data/ontology/readers/OntologyReader.java b/application/src/main/java/cytoscape/data/ontology/readers/OntologyReader.java
new file mode 100644
index 0000000..a48f81c
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/ontology/readers/OntologyReader.java
@@ -0,0 +1,75 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data.ontology.readers;
+
+import cytoscape.CyNetwork;
+
+import java.io.IOException;
+
+import java.util.Map;
+
+
+/**
+ * Interface for all ontology file readers.
+ *
+ * Basic function of the readers are build ontology DAG/Tree and its header.
+ *
+ * Actual data steructure is always CyNetwork and CyAttributes.
+ *
+ * @author kono
+ *
+ */
+public interface OntologyReader {
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws IOException DOCUMENT ME!
+ */
+ public void readOntology() throws IOException;
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public CyNetwork getDag();
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Map getHeader();
+}
diff --git a/application/src/main/java/cytoscape/data/package.html b/application/src/main/java/cytoscape/data/package.html
new file mode 100644
index 0000000..41f3bdc
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/package.html
@@ -0,0 +1,13 @@
+<html>
+<head>
+ <!-- $Revision: 5801 $
+ $Date: 2004-04-20 01:53:47 +0200 (Tue, 20 Apr 2004) $
+ $Author: amarkiel $
+ -->
+</head>
+
+<body>
+Basic data classes used by Cytoscape. This is also the superpackage
+for other packages that contain special types of data-related classes.
+</body>
+</html>
diff --git a/application/src/main/java/cytoscape/data/readers/AbstractGraphReader.java b/application/src/main/java/cytoscape/data/readers/AbstractGraphReader.java
new file mode 100644
index 0000000..00ebe04
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/readers/AbstractGraphReader.java
@@ -0,0 +1,147 @@
+/*
+ File: AbstractGraphReader.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data.readers;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.Set;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import cytoscape.layout.CyLayoutAlgorithm;
+import cytoscape.layout.CyLayouts;
+import cytoscape.task.TaskMonitor;
+import cytoscape.util.CyNetworkNaming;
+
+
+/**
+ *
+ */
+public abstract class AbstractGraphReader implements GraphReader {
+ protected String fileName;
+ protected String title=null; // network title
+
+ /**
+ * Creates a new AbstractGraphReader object.
+ *
+ * @param fileName DOCUMENT ME!
+ */
+ public AbstractGraphReader(String fileName) {
+ this.fileName = fileName;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws IOException DOCUMENT ME!
+ */
+ public abstract void read() throws IOException;
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] getNodeIndicesArray() {
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] getEdgeIndicesArray() {
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getNetworkName() {
+ String t = "";
+
+ if (title != null){
+ t = title;
+ }
+ else if (fileName != null) {
+ File tempFile = new File(fileName);
+ t = tempFile.getName();
+
+ // Remove the file extension '.sif' or '.gml' or '.xgmml' as network title
+ // 1. determine the extension of file
+ String ext = "";
+ int dotIndex = t.lastIndexOf(".");
+ if (dotIndex != -1){
+ ext = t.substring(dotIndex+1);
+ }
+
+ // 2. check if the file ext is one of the pre-defined exts
+ Set extSets = (Set) Cytoscape.getImportHandler().getAllExtensions();
+ if (extSets.contains(ext)){
+ // if the file ext is pre-defined, remove it from network title
+ t = t.substring(0, dotIndex);
+ }
+ }
+
+ return CyNetworkNaming.getSuggestedNetworkTitle(t);
+ }
+
+ /**
+ * Executes post-processing: no-op.
+ */
+ public void doPostProcessing(CyNetwork network) {
+ }
+
+ /**
+ * Return the CyLayoutAlgorithm used to layout the graph
+ */
+ public CyLayoutAlgorithm getLayoutAlgorithm() {
+ return CyLayouts.getDefaultLayout();
+ }
+
+ /**
+ * Set the task monitor to use for this reader
+ *
+ * @param monitor the TaskMonitor to use
+ */
+ public void setTaskMonitor(TaskMonitor monitor) {
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/data/readers/BookmarkReader.java b/application/src/main/java/cytoscape/data/readers/BookmarkReader.java
new file mode 100644
index 0000000..f72c8ca
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/readers/BookmarkReader.java
@@ -0,0 +1,112 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data.readers;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.bookmarks.Bookmarks;
+import cytoscape.util.URLUtil;
+
+import java.io.IOException;
+
+import java.net.URL;
+
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBException;
+import javax.xml.bind.Unmarshaller;
+
+
+/**
+ *
+ */
+public class BookmarkReader {
+ // Package name generated by JAXB based on XGMML schema file
+ private static final String BOOKMARK_PACKAGE = "cytoscape.bookmarks";
+
+ // Location of the default bookmark.
+ private static final String BOOKMARK_RESOURCE_FILE = "/bookmarks.xml";
+ private Bookmarks bookmarks;
+
+ /**
+ * Creates a new BookmarkReader object.
+ */
+ public BookmarkReader() {
+ }
+
+ /**
+ * Read bookmark from resource.
+ *
+ * @throws JAXBException
+ * @throws IOException
+ */
+ public void readBookmarks() throws JAXBException, IOException {
+ URL bookmarkSource = getClass().getResource(BOOKMARK_RESOURCE_FILE);
+ readBookmarks(bookmarkSource);
+ }
+
+ /**
+ * Read bookmarks from the specified location.
+ *
+ * @param bookmarkUrl location of bookmarks.xml as URL
+ *
+ * @throws JAXBException
+ * @throws IOException
+ */
+ public void readBookmarks(URL bookmarkUrl) throws JAXBException, IOException {
+ // Use JAXB-generated methods to create data structure
+ // final JAXBContext jaxbContext = JAXBContext.newInstance(
+ // BOOKMARK_PACKAGE, this.getClass().getClassLoader());
+ //
+ final JAXBContext jaxbContext = JAXBContext.newInstance(BOOKMARK_PACKAGE,
+ Cytoscape.class.getClassLoader());
+
+ // Unmarshall the XGMML file
+ final Unmarshaller unmarshaller = jaxbContext.createUnmarshaller();
+
+ // bookmarks = (Bookmarks) unmarshaller.unmarshal(bookmarkUrl.openStream());
+ // Use URLUtil to get the InputStream since we might be using a proxy server
+ // and because pages may be cached:
+ bookmarks = (Bookmarks) unmarshaller.unmarshal(URLUtil.getBasicInputStream (bookmarkUrl));
+ }
+
+ /**
+ * Get loaded bookmark.
+ *
+ * @return
+ */
+ public Bookmarks getBookmarks() {
+ return bookmarks;
+ }
+}
diff --git a/application/src/main/java/cytoscape/data/readers/CyAttributesReader.java b/application/src/main/java/cytoscape/data/readers/CyAttributesReader.java
new file mode 100644
index 0000000..578a8cb
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/readers/CyAttributesReader.java
@@ -0,0 +1,404 @@
+/*
+ File: CyAttributesReader.java
+
+ Copyright (c) 2006, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data.readers;
+
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.Reader;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.StringTokenizer;
+
+import cytoscape.Cytoscape;
+import cytoscape.data.CyAttributes;
+import cytoscape.data.attr.MultiHashMapDefinition;
+import cytoscape.data.writers.CyAttributesWriter;
+import cytoscape.logger.CyLogger;
+
+import org.cytoscape.equations.EqnCompiler;
+import org.cytoscape.equations.Equation;
+
+import java.net.URLDecoder;
+import java.text.MessageFormat;
+
+
+public class CyAttributesReader {
+ public static final String DECODE_PROPERTY = "cytoscape.decode.attributes";
+ private static final String badDecodeMessage =
+ "Trouble when decoding attribute value, first occurence line no. {0}" +
+ "\nIgnore if attributes file was created before 2.6.3 or wasn't creatad by Cytoscape." +
+ "\nUse -Dcytoscape.decode.attributes=false when starting Cytoscape to turn off decoding.";
+
+ private boolean badDecode;
+ private int lineNum;
+ private boolean doDecoding;
+ final Map<String, Map<String, Class>> idsToAttribNameToTypeMapMap;
+ private final CyLogger logger;
+
+
+ CyAttributesReader() {
+ logger = CyLogger.getLogger(CyAttributesReader.class);
+ lineNum = 0;
+ doDecoding = Boolean.valueOf(System.getProperty(DECODE_PROPERTY, "true"));
+ idsToAttribNameToTypeMapMap = new HashMap<String, Map<String, Class>>();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param cyAttrs DOCUMENT ME!
+ * @param fileIn DOCUMENT ME!
+ *
+ * @throws IOException DOCUMENT ME!
+ */
+ public static void loadAttributes(final CyAttributes cyAttrs, final Reader fileIn) throws IOException {
+ CyAttributesReader ar = new CyAttributesReader();
+ ar.loadAttributesInternal(cyAttrs, fileIn);
+ }
+
+ private Class mapCytoscapeAttribTypeToEqnType(final byte attribType) {
+ switch (attribType) {
+ case CyAttributes.TYPE_BOOLEAN:
+ return Boolean.class;
+ case CyAttributes.TYPE_INTEGER:
+ return Long.class;
+ case CyAttributes.TYPE_FLOATING:
+ return Double.class;
+ case CyAttributes.TYPE_STRING:
+ return String.class;
+ case CyAttributes.TYPE_SIMPLE_LIST:
+ return List.class;
+ default:
+ return null;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param cyAttrs DOCUMENT ME!
+ * @param fileIn DOCUMENT ME!
+ *
+ * @throws IOException DOCUMENT ME!
+ */
+ public void loadAttributesInternal(CyAttributes cyAttrs, Reader fileIn)
+ throws IOException
+ {
+ badDecode = false;
+ boolean guessedAttrType = false; // We later set this to true if we have to guess the attribute type.
+
+ try {
+ final BufferedReader reader;
+
+ if (fileIn instanceof BufferedReader) {
+ reader = (BufferedReader) fileIn;
+ } else {
+ reader = new BufferedReader(fileIn);
+ }
+
+ String attributeName;
+ byte type = -1;
+
+ {
+ final String firstLine = reader.readLine();
+ lineNum++;
+
+ if (firstLine == null) {
+ return;
+ }
+
+ final String searchStr = "class=";
+ final int inx = firstLine.indexOf(searchStr);
+
+ if (inx < 0) {
+ attributeName = firstLine.trim();
+ } else {
+ attributeName = firstLine.substring(0, inx - 1).trim();
+
+ String foo = firstLine.substring(inx);
+ final StringTokenizer tokens = new StringTokenizer(foo);
+ foo = tokens.nextToken();
+
+ String className = foo.substring(searchStr.length()).trim();
+
+ if (className.endsWith(")")) {
+ className = className.substring(0, className.length() - 1);
+ }
+
+ if (className.equalsIgnoreCase("java.lang.String")
+ || className.equalsIgnoreCase("String")) {
+ type = MultiHashMapDefinition.TYPE_STRING;
+ } else if (className.equalsIgnoreCase("java.lang.Boolean")
+ || className.equalsIgnoreCase("Boolean")) {
+ type = MultiHashMapDefinition.TYPE_BOOLEAN;
+ } else if (className.equalsIgnoreCase("java.lang.Integer")
+ || className.equalsIgnoreCase("Integer")) {
+ type = MultiHashMapDefinition.TYPE_INTEGER;
+ } else if (className.equalsIgnoreCase("java.lang.Double")
+ || className.equalsIgnoreCase("Double")
+ || className.equalsIgnoreCase("java.lang.Float")
+ || className.equalsIgnoreCase("Float")) {
+ type = MultiHashMapDefinition.TYPE_FLOATING_POINT;
+ }
+ }
+ }
+
+ if (attributeName.indexOf("(") >= 0) {
+ attributeName = attributeName.substring(0, attributeName.indexOf("(")).trim();
+ }
+
+ boolean firstLine = true;
+ boolean list = false;
+
+ while (true) {
+ final String line = reader.readLine();
+ lineNum++;
+
+ if (line == null)
+ break;
+
+ // Empty line?
+ if ("".equals(line.trim())) {
+ continue;
+ }
+
+ int inx = line.indexOf('=');
+ String key = line.substring(0, inx).trim();
+ String val = line.substring(inx + 1).trim();
+ final boolean equation = val.startsWith("=");
+
+ key = decodeString(key);
+
+ if (firstLine && val.startsWith("("))
+ list = true;
+
+ if (list) {
+ // Chop away leading '(' and trailing ')'.
+ val = val.substring(1).trim();
+ val = val.substring(0, val.length() - 1).trim();
+
+ String[] elms = val.split("::");
+ final ArrayList elmsBuff = new ArrayList();
+
+ for (String vs : elms) {
+ vs = decodeString(vs);
+ vs = decodeSlashEscapes(vs);
+ elmsBuff.add(vs);
+ }
+
+ if (firstLine) {
+ if (type < 0) {
+ guessedAttrType = true;
+ while (true) {
+ try {
+ new Integer((String) elmsBuff.get(0));
+ type = MultiHashMapDefinition.TYPE_INTEGER;
+ break;
+ } catch (Exception e) {
+ }
+
+ try {
+ new Double((String) elmsBuff.get(0));
+ type = MultiHashMapDefinition.TYPE_FLOATING_POINT;
+ break;
+ } catch (Exception e) {
+ }
+ type = MultiHashMapDefinition.TYPE_STRING;
+ break;
+ }
+ }
+
+ firstLine = false;
+ }
+
+ for (int i = 0; i < elmsBuff.size(); i++) {
+ if (type == MultiHashMapDefinition.TYPE_INTEGER) {
+ elmsBuff.set(i, new Integer((String) elmsBuff.get(i)));
+ } else if (type == MultiHashMapDefinition.TYPE_BOOLEAN) {
+ elmsBuff.set(i, new Boolean((String) elmsBuff.get(i)));
+ } else if (type == MultiHashMapDefinition.TYPE_FLOATING_POINT) {
+ elmsBuff.set(i, new Double((String) elmsBuff.get(i)));
+ } else {
+ // A string; do nothing.
+ }
+ }
+
+ cyAttrs.setListAttribute(key, attributeName, elmsBuff);
+ } else { // Not a list.
+ val = decodeString(val);
+ val = decodeSlashEscapes(val);
+
+ if (firstLine) {
+ if (type < 0) {
+ guessedAttrType = true;
+ while (true) {
+ try {
+ new Integer(val);
+ type = MultiHashMapDefinition.TYPE_INTEGER;
+ break;
+ } catch (Exception e) {
+ }
+
+ try {
+ new Double(val);
+ type = MultiHashMapDefinition.TYPE_FLOATING_POINT;
+ break;
+ } catch (Exception e) {
+ }
+
+ type = MultiHashMapDefinition.TYPE_STRING;
+ break;
+ }
+ }
+
+ firstLine = false;
+ }
+
+ if (equation) {
+ final Class eqnReturnType;
+ switch (type) {
+ case CyAttributes.TYPE_INTEGER:
+ eqnReturnType = Long.class;
+ break;
+ case CyAttributes.TYPE_FLOATING:
+ eqnReturnType = Double.class;
+ break;
+ case CyAttributes.TYPE_BOOLEAN:
+ eqnReturnType = Boolean.class;
+ break;
+ case CyAttributes.TYPE_STRING:
+ eqnReturnType = String.class;
+ break;
+ case CyAttributes.TYPE_SIMPLE_LIST:
+ eqnReturnType = List.class;
+ break;
+ default:
+ final String message = "don't know which equation return type to register on line " + lineNum + "!";
+ System.err.println(message);
+ logger.warn(message);
+ continue;
+ }
+ final EqnAttrTracker eqnAttrTracker = Cytoscape.getEqnAttrTracker();
+ eqnAttrTracker.recordEquation(cyAttrs, key, attributeName, val, eqnReturnType);
+ }
+ else if (type == MultiHashMapDefinition.TYPE_INTEGER)
+ cyAttrs.setAttribute(key, attributeName, new Integer(val));
+ else if (type == MultiHashMapDefinition.TYPE_BOOLEAN)
+ cyAttrs.setAttribute(key, attributeName, new Boolean(val));
+ else if (type == MultiHashMapDefinition.TYPE_FLOATING_POINT)
+ cyAttrs.setAttribute(key, attributeName, new Double(val));
+ else
+ cyAttrs.setAttribute(key, attributeName, val);
+ }
+ }
+ } catch (Exception e) {
+ String message;
+ if (guessedAttrType) {
+ message = "failed parsing attributes file at line: " + lineNum
+ + " with exception: " + e.getMessage()
+ + " This is most likely due to a missing attribute type on the first line.\n"
+ + "Attribute type should be one of the following: "
+ + "(class=String), (class=Boolean), (class=Integer), or (class=Double). "
+ + "(\"Double\" stands for a floating point a.k.a. \"decimal\" number.)"
+ + " This should be added to end of the first line.";
+ }
+ else
+ message = "failed parsing attributes file at line: " + lineNum
+ + " with exception: " + e.getMessage();
+ logger.warn(message, e);
+ throw new IOException(message);
+ }
+ }
+
+ private String decodeString(String in) throws IOException {
+ if (doDecoding) {
+ try {
+ in = URLDecoder.decode(in, CyAttributesWriter.ENCODING_SCHEME);
+ }
+ catch (IllegalArgumentException iae) {
+ if (!badDecode) {
+ logger.info(MessageFormat.format(badDecodeMessage, lineNum), iae);
+ badDecode = true;
+ }
+ }
+ }
+
+ return in;
+ }
+
+ private static String decodeSlashEscapes(String in) {
+ final StringBuilder elmBuff = new StringBuilder();
+ int inx2;
+
+ for (inx2 = 0; inx2 < in.length(); inx2++) {
+ char ch = in.charAt(inx2);
+
+ if (ch == '\\') {
+ if ((inx2 + 1) < in.length()) {
+ inx2++;
+
+ char ch2 = in.charAt(inx2);
+
+ if (ch2 == 'n') {
+ elmBuff.append('\n');
+ } else if (ch2 == 't') {
+ elmBuff.append('\t');
+ } else if (ch2 == 'b') {
+ elmBuff.append('\b');
+ } else if (ch2 == 'r') {
+ elmBuff.append('\r');
+ } else if (ch2 == 'f') {
+ elmBuff.append('\f');
+ } else {
+ elmBuff.append(ch2);
+ }
+ } else {
+ /* val ends in '\' - just ignore it. */ }
+ } else {
+ elmBuff.append(ch);
+ }
+ }
+
+ return elmBuff.toString();
+ }
+
+ public boolean isDoDecoding() {
+ return doDecoding;
+ }
+
+ public void setDoDecoding(boolean doDec) {
+ doDecoding = doDec;
+ }
+}
diff --git a/application/src/main/java/cytoscape/data/readers/CytoscapeSessionReader.java b/application/src/main/java/cytoscape/data/readers/CytoscapeSessionReader.java
new file mode 100644
index 0000000..6562381
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/readers/CytoscapeSessionReader.java
@@ -0,0 +1,1256 @@
+/*
+ File: CytoscapeSessionReader.java
+
+ Copyright (c) 2006, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.data.readers;
+
+import java.awt.Component;
+import java.io.BufferedReader;
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.net.JarURLConnection;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.net.URLConnection;
+import java.net.URLEncoder;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Properties;
+import java.util.Set;
+import java.util.TreeSet;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipInputStream;
+
+import javax.swing.JInternalFrame;
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBException;
+import javax.xml.bind.Unmarshaller;
+
+import cytoscape.CyEdge;
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+import cytoscape.CytoscapeInit;
+import cytoscape.bookmarks.Bookmarks;
+import cytoscape.data.CyAttributes;
+import cytoscape.data.Semantics;
+import cytoscape.generated.Child;
+import cytoscape.generated.Cysession;
+import cytoscape.generated.Edge;
+import cytoscape.generated.HiddenEdges;
+import cytoscape.generated.HiddenNodes;
+import cytoscape.generated.Network;
+import cytoscape.generated.NetworkFrame;
+import cytoscape.generated.Node;
+import cytoscape.generated.Ontology;
+import cytoscape.generated.SelectedEdges;
+import cytoscape.generated.SelectedNodes;
+import cytoscape.logger.CyLogger;
+import cytoscape.task.TaskMonitor;
+import cytoscape.util.PercentUtil;
+import cytoscape.util.RecentlyOpenedTracker;
+import cytoscape.util.URLUtil;
+import cytoscape.view.CyNetworkView;
+import cytoscape.visual.customgraphic.CustomGraphicsManager;
+import cytoscape.visual.customgraphic.CyCustomGraphics;
+import cytoscape.visual.customgraphic.IDGenerator;
+import cytoscape.visual.customgraphic.Taggable;
+import cytoscape.visual.customgraphic.impl.AbstractDCustomGraphics;
+import cytoscape.visual.customgraphic.impl.bitmap.URLImageCustomGraphics;
+import cytoscape.visual.parsers.GraphicsParser;
+
+/**
+ * Reader to load CYtoscape Session file (.cys).<br>
+ * This class unzip cys file and read all files in the archive.
+ * <p>
+ * This class accept input as URL only! If it is a file, use File.toURL() to get
+ * platform dependent file URL.
+ * </p>
+ *
+ * @version 1.0
+ * @since Cytoscape 2.3
+ * @see cytoscape.data.readers.XGMMLReader
+ * @author kono
+ *
+ */
+public class CytoscapeSessionReader {
+ /**
+ *
+ */
+ public static final String PACKAGE_NAME = "cytoscape.generated";
+
+ /**
+ *
+ */
+ public static final String BOOKMARK_PACKAGE_NAME = "cytoscape.bookmarks";
+
+ /**
+ *
+ */
+ public static final String CYSESSION = "cysession.xml";
+
+ /**
+ *
+ */
+ public static final String VIZMAP_PROPS = "vizmap.props";
+
+ /**
+ *
+ */
+ public static final String CY_PROPS = "cytoscape.props";
+
+ /**
+ *
+ */
+ public static final String XGMML_EXT = ".xgmml";
+ private static final String BOOKMARKS_FILE = "session_bookmarks.xml";
+ private static final String NETWORK_ROOT = "Network Root";
+ private URL sourceURL;
+ private Map networkURLs = null;
+ private URL cysessionFileURL = null;
+ private URL vizmapFileURL = null;
+ private URL cytoscapePropsURL = null;
+ private URL bookmarksFileURL = null;
+ private HashMap<String, Network> netMap;
+ private String sessionID;
+ private Cysession session;
+ private List networkList;
+ private Bookmarks bookmarks = null;
+ private HashMap<String, List<File>> pluginFileListMap;
+ private HashMap<String, List<String>> theURLstrMap = new HashMap<String, List<String>>();
+
+ private Map<String, URL> imageMap;
+ private URL imagePropsURL;
+
+ // Task monitor
+ private TaskMonitor taskMonitor = null;
+ private float networkCounter = 0;
+ private float netIndex = 0;
+ private long start;
+ private String lastVSName = null;
+
+ // Logging
+ private CyLogger logger = null;
+
+ /**
+ * Constructor for remote file (specified by an URL)<br>
+ *
+ * @param sourceName
+ * @throws IOException
+ *
+ * This is for remote session file (URL).
+ */
+ public CytoscapeSessionReader(final URL sourceName,
+ final TaskMonitor monitor) throws IOException {
+ this.sourceURL = sourceName;
+
+ if (sourceName.getProtocol().equals("file"))
+ this.sourceURL = sourceName;
+ else
+ this.sourceURL = temporaryLocalFileURL(sourceName);
+
+ networkList = new ArrayList();
+ bookmarks = new Bookmarks();
+ pluginFileListMap = new HashMap<String, List<File>>();
+ imageMap = new HashMap<String, URL>();
+
+ this.taskMonitor = monitor;
+
+ this.logger = CyLogger.getLogger(CytoscapeSessionReader.class);
+
+ final RecentlyOpenedTracker sessionTracker = Cytoscape
+ .getRecentlyOpenedSessionTracker();
+ if (sessionTracker != null)
+ sessionTracker.add(sourceName);
+ }
+
+ /**
+ * Creates a new CytoscapeSessionReader object.
+ *
+ * @param fileName
+ * DOCUMENT ME!
+ * @param monitor
+ * DOCUMENT ME!
+ *
+ * @throws IOException
+ * DOCUMENT ME!
+ */
+ public CytoscapeSessionReader(final String fileName,
+ final TaskMonitor monitor) throws IOException
+ {
+ this(new File(fileName.replace("%", "%25")).toURL(), monitor);
+ }
+
+ /**
+ * Constructor.<br>
+ * Create reader from file name.
+ *
+ * @param fileName
+ * @throws IOException
+ */
+ public CytoscapeSessionReader(final String fileName) throws IOException {
+ this(new File(fileName.replace("%", "%25")).toURL(), (TaskMonitor) null);
+ }
+
+ /**
+ * Creates a new CytoscapeSessionReader object.
+ *
+ * @param sourceName
+ * DOCUMENT ME!
+ *
+ * @throws IOException
+ * DOCUMENT ME!
+ */
+ public CytoscapeSessionReader(final URL sourceName) throws IOException {
+ this(sourceName, (TaskMonitor) null);
+ }
+
+ /**
+ * Extract Zip entries in the remote file
+ *
+ * @param sourceName
+ * @throws IOException
+ */
+ private void extractEntry() throws IOException {
+ /*
+ * This is an important part!
+ *
+ * We can create InputStream directly from URL, but it does not work
+ * always due to the cashing mechanism in URLConnection.
+ *
+ * By default, URLConnection creates a cash for session file name. This
+ * will be used even after we saved the session. Due to the conflict
+ * between cashed name and new saved session name (generated from system
+ * time), session reader cannot find the entry in the zip file. To avoid
+ * this problem, we shoud turn off the cashing mechanism by using:
+ *
+ * URLConnection.setDefaultUseCaches(false)
+ *
+ * This is a "sticky" parameter for all URLConnections and we have to
+ * set this only once.
+ */
+ final URLConnection juc = sourceURL.openConnection();
+ juc.setDefaultUseCaches(false);
+
+ ZipInputStream zis = null;
+
+ try {
+ zis = new ZipInputStream(juc.getInputStream());
+ networkURLs = new HashMap();
+
+ // Extract list of entries
+ ZipEntry zen = null;
+ String entryName = null;
+
+ while ((zen = zis.getNextEntry()) != null) {
+ entryName = zen.getName();
+
+ if (entryName.contains("/plugins/")) {
+ extractPluginEntry(entryName);
+ } else if (entryName.endsWith(CYSESSION)) {
+ cysessionFileURL = new URL("jar:" + sourceURL.toString()
+ + "!/" + entryName);
+ } else if (entryName.endsWith(VIZMAP_PROPS)) {
+ vizmapFileURL = new URL("jar:" + sourceURL.toString()
+ + "!/" + entryName);
+ } else if (entryName.endsWith(CY_PROPS)) {
+ cytoscapePropsURL = new URL("jar:" + sourceURL.toString()
+ + "!/" + entryName);
+ } else if (entryName.endsWith(XGMML_EXT)) {
+ // entryName should only contain one "/" character
+ // seperating the session directory from the file name
+ // All other "/" are eliminated by
+ // CytoscapeSessionWriter.getValidFileName
+ // URLEncoding the remainder of entryName makes sure the URL
+ // is valid
+ // without the need to eliminate additional characters when
+ // creating the filename.
+ // Spaces require special treatment, need to be encoded as
+ // "%20" not "+"
+ int sp;
+ String entryDir;
+ String entryRest;
+
+ entryDir = "";
+ entryRest = entryName;
+ sp = entryName.indexOf("/");
+ if (sp != -1) {
+ entryDir = entryRest.substring(0, sp + 1);
+ entryRest = entryRest.substring(sp + 1);
+ }
+
+ URL networkURL = new URL("jar:"
+ + sourceURL.toString()
+ + "!/"
+ + entryDir
+ + URLEncoder.encode(entryRest, "UTF-8").replace(
+ "+", "%20"));
+ networkURLs.put(entryName, networkURL);
+ networkCounter++;
+ } else if (entryName.endsWith(BOOKMARKS_FILE)) {
+ bookmarksFileURL = new URL("jar:" + sourceURL.toString()
+ + "!/" + entryName);
+ } else if (entryName.endsWith(".png")) {
+
+ // All bitmap images are saved as PNG files.
+ final URL imageURL = new URL("jar:" + sourceURL.toString()
+ + "!/" + entryName);
+ loadBitmapImageFiles(entryName, imageURL);
+ } else if (entryName.endsWith(CustomGraphicsManager.METADATA_FILE)) {
+ // This is the image property file.
+ imagePropsURL = new URL("jar:" + sourceURL.toString()
+ + "!/" + entryName);
+ } else
+ logger.warn("Unknown entry found in session zip file: "
+ + entryName);
+ } // while loop
+ } finally {
+ if (zis != null) {
+ zis.close();
+ }
+ }
+ }
+
+ private void extractPluginEntry(String entryName) {
+ String[] items = entryName.split("/");
+
+ if (items.length < 3) {
+ // It's a directory name, not a file name
+ return;
+ }
+
+ String pluginName = items[2];
+ String URLstr = "jar:" + sourceURL.toString() + "!/" + entryName;
+
+ if (theURLstrMap.containsKey(pluginName)) {
+ List<String> theURLstrList = theURLstrMap.get(pluginName);
+ theURLstrList.add(URLstr);
+ } else {
+ List<String> theURLstrList = new ArrayList<String>();
+ theURLstrList.add(URLstr);
+ theURLstrMap.put(pluginName, theURLstrList);
+ }
+ }
+
+ private void loadBitmapImageFiles(final String entryName,
+ final URL imageFileURL) throws IOException
+ {
+ final String rootName = extractFileName(entryName);
+
+ String displayName = rootName;
+ int i = 1;
+ while (imageMap.containsKey(displayName))
+ displayName = rootName + "-" + ++i;
+ imageMap.put(displayName, imageFileURL);
+ }
+
+ /**
+ * @return localFileName stripped of path prefix and extension
+ */
+ private String extractFileName(final String localFileName) {
+ // N.B., on Windows the file separator is a backslash and a nacked backslash is not a valid regex
+ // so we need to escape it with a leading slash. On UNIX on the other hand, having a slash
+ // escaped with a leading slash is innocuous.
+ final String[] components = localFileName.split("\\" + System.getProperty("file.separator"));
+ final String baseName = components[components.length - 1];
+ return baseName.split("\\.")[0];
+ }
+
+ private void restoreCustomGraphics() throws IOException {
+
+ // Restore metadata
+ final Properties imageProps = new Properties();
+ imageProps.load(URLUtil.getBasicInputStream(imagePropsURL));
+
+ // Remove all custom graphics from current session
+ final CustomGraphicsManager manager = Cytoscape.getVisualMappingManager()
+ .getCustomGraphicsManager();
+
+ // Remove all custom graphics before loading new images.
+ //manager.removeAll();
+
+ // First, restore image-based custom graphics
+ for (String id : imageMap.keySet()) {
+
+ String origId = id;
+
+ int lastSlashPos = id.lastIndexOf('/');
+ if (lastSlashPos != -1)
+ id = id.substring(lastSlashPos + 1);
+
+ // Create Custom Graphics with specified ID.
+ final CyCustomGraphics graphics = new URLImageCustomGraphics(Long.parseLong(id),
+ imageMap.get(origId).toString());
+
+ // This property contains display name and tags.
+ final String propEntry = imageProps.getProperty(id);
+ if(propEntry == null)
+ continue;
+
+ // Remove this prop.
+ imageProps.remove(id);
+
+ // Split string into blocks.
+ // This line should have: class Name, ID, name, tags.
+ final String[] parts = propEntry.split(",");
+ if(parts.length < 3)
+ continue;
+
+ String name = parts[parts.length - 2];
+ if (name.contains("___"))
+ name = name.replace("___", ",");
+
+ // Set display name
+ graphics.setDisplayName(name);
+
+ // Restore tags
+ String tagStr = null;
+ if (parts.length > 3 && graphics instanceof Taggable) {
+ tagStr = parts[3];
+ final Set<String> tags = new TreeSet<String>();
+ String[] tagParts = tagStr.split("\\"
+ + AbstractDCustomGraphics.LIST_DELIMITER);
+ for (String tag : tagParts)
+ tags.add(tag.trim());
+
+ // Add all restored tags.
+ ((Taggable) graphics).getTags().addAll(tags);
+ }
+
+
+ // If name is a valid URL, store as data source.
+ try {
+ final URL nameAsURL = new URL(name);
+ // The name is URL. Use as its source.
+ final CyCustomGraphics currentValue = manager.getBySourceURL(nameAsURL);
+
+ // Add only if the graphics does not exist in memory.
+ if(currentValue == null)
+ manager.addGraphics(graphics, nameAsURL);
+ } catch (MalformedURLException e) {
+ // Name is not an URL. These should be added always.
+ manager.addGraphics(graphics, null);
+ }
+ }
+
+ // Restore NON-image graphics
+ logger.debug("Need to restore non-image graphics: " + imageProps.size());
+
+ //TODO: Fix vector images
+ restoreNonImageGraphics(imageProps, manager);
+
+ // Reset the counter
+ final Long currentMax = manager.getIDSet().last();
+ IDGenerator.getIDGenerator().initCounter(currentMax+1);
+ }
+
+ private void restoreNonImageGraphics(final Properties imageProps, final CustomGraphicsManager manager) {
+
+
+ for(Object key:imageProps.keySet()) {
+ final String value = imageProps.getProperty(key.toString());
+
+ logger.debug("Key = " + key +", val = " + value);
+ final CyCustomGraphics cg = parser.parseStringValue(imageProps.getProperty(key.toString()));
+ logger.debug("CG result = " + cg);
+ if(cg != null)
+ manager.addGraphics(cg, null);
+ }
+ }
+
+ private final GraphicsParser parser = new GraphicsParser();
+
+
+ /**
+ * Read a session file.
+ *
+ * @throws IOException
+ * @throws JAXBException
+ */
+ public void read() throws IOException, JAXBException, Exception {
+ start = System.currentTimeMillis();
+
+ // All listeners should listen to this event to ignore unnecessary
+ // events!
+ Cytoscape.firePropertyChange(
+ Integer.toString(Cytoscape.SESSION_OPENED), null, true);
+
+ Cytoscape.getDesktop().getVizMapperUI().initializeTableState();
+
+ try {
+ final EqnAttrTracker eqnAttrTracker = Cytoscape.getEqnAttrTracker();
+ eqnAttrTracker.reset();
+ unzipSessionFromURL(true);
+ eqnAttrTracker.addAllEquations();
+ } catch (cytoscape.visual.DuplicateCalculatorNameException dcne) {
+ logger
+ .warn("Duplicate VS name found. It will be ignored...",
+ dcne);
+ }
+
+ // logger.debug("unzipSessionFromURL: " + (System.currentTimeMillis() -
+ // start) + " msec.");
+ if (session.getSessionState().getDesktop() != null) {
+ restoreDesktopState();
+
+ // logger.debug("restoreDesktopState: " +
+ // (System.currentTimeMillis() - start) + " msec.");
+ }
+
+ if (session.getSessionState().getServer() != null) {
+ restoreOntologyServerStatus();
+ // logger.debug("restoreOntologyServerStatus: " +
+ // (System.currentTimeMillis() - start) + " msec.");
+ }
+
+ // restoreNestedNetworkLinks();
+
+ // Send signal to others
+ Cytoscape.firePropertyChange(Cytoscape.ATTRIBUTES_CHANGED, null, null);
+ Cytoscape.firePropertyChange(Cytoscape.NETWORK_LOADED, null, null);
+ // logger.debug("fire attrs and network loaded: " +
+ // (System.currentTimeMillis() - start) + " msec.");
+
+ // Send signal to plugins
+ Cytoscape.firePropertyChange(Cytoscape.RESTORE_PLUGIN_STATE,
+ pluginFileListMap, null);
+ // logger.debug("fire restore_plugin_state: " +
+ // (System.currentTimeMillis() - start) + " msec.");
+ deleteTmpPluginFiles();
+ // logger.debug("deleteTmpPluginFiles: " + (System.currentTimeMillis() -
+ // start) + " msec.");
+
+ // Send message with list of loaded networks.
+ Cytoscape.firePropertyChange(Cytoscape.SESSION_LOADED, null,
+ networkList);
+
+ // Restore listener for VizMapper.
+ if (Cytoscape.getDesktop() != null) {
+
+ // Cleanup view
+ final CyNetworkView curView = Cytoscape.getCurrentNetworkView();
+
+ if ((curView != null)
+ && (curView.equals(Cytoscape.getNullNetworkView()) == false)) {
+ curView.setVisualStyle(lastVSName);
+ Cytoscape.getVisualMappingManager().setNetworkView(curView);
+ Cytoscape.getVisualMappingManager().setVisualStyle(
+ curView.getVisualStyle());
+ // TODO: is this necessary?
+ // curView.redrawGraph(false, true);
+ }
+
+ Cytoscape.getDesktop().getVizMapperUI().enableListeners(true);
+ }
+
+ logger.info("Session loaded in " + (System.currentTimeMillis() - start)
+ + " msec.");
+ }
+
+ /**
+ * Restore nested network references.
+ */
+ private void restoreNestedNetworkLinks() {
+ final CyAttributes nodeAttr = Cytoscape.getNodeAttributes();
+ final List<String> attrNames = Arrays.asList(nodeAttr
+ .getAttributeNames());
+ // Do nothing if nested network does not exists in this session.
+ if (!attrNames.contains(CyNode.NESTED_NETWORK_ID_ATTR))
+ return;
+
+ final Map<String, String> titleToIdMap = createNetworkTitleToIDMap();
+ for (final CyNetwork network : Cytoscape.getNetworkSet()) {
+ for (final CyNode node : (List<CyNode>) network.nodesList()) {
+ final String nestedNetworkTitle = nodeAttr.getStringAttribute(
+ node.getIdentifier(), CyNode.NESTED_NETWORK_ID_ATTR);
+ if (nestedNetworkTitle != null)
+ node.setNestedNetwork(Cytoscape.getNetwork(titleToIdMap
+ .get(nestedNetworkTitle)));
+ }
+ }
+ }
+
+ private Map<String, String> createNetworkTitleToIDMap() {
+ final Map<String, String> titleToIdMap = new HashMap<String, String>();
+
+ Set<CyNetwork> networks = Cytoscape.getNetworkSet();
+ for (CyNetwork network : networks) {
+ titleToIdMap.put(network.getTitle(), network.getIdentifier());
+ }
+ return titleToIdMap;
+ }
+
+ // Delete tmp files (the plugin state files) to cleanup
+ private void deleteTmpPluginFiles() {
+ if ((pluginFileListMap == null) || (pluginFileListMap.size() == 0))
+ return;
+
+ Set<String> pluginSet = pluginFileListMap.keySet();
+
+ for (String plugin : pluginSet) {
+ List<File> theFileList = pluginFileListMap.get(plugin);
+
+ for (File theFile : theFileList) {
+ if (theFile != null) {
+ theFile.delete();
+ }
+ }
+ }
+ }
+
+ /**
+ * Decompress session file
+ *
+ * @throws IOException
+ * @throws JAXBException
+ */
+ private void unzipSessionFromURL(final boolean loadVizmap)
+ throws IOException, JAXBException, Exception {
+ extractEntry();
+ logger.info("extractEntry: " + (System.currentTimeMillis() - start)
+ + " msec.");
+
+ /*
+ * Check the contents. If broken/invalid, throw exception.
+ */
+ if ((cysessionFileURL == null) || (vizmapFileURL == null)
+ || (cytoscapePropsURL == null)) {
+ IOException e = new IOException(
+ "Session file is broken or this is not a session file.");
+ throw e;
+ }
+
+ // Need to restore custom graphics BEFORE Visual Styles.
+ if (imagePropsURL != null)
+ restoreCustomGraphics();
+
+ if (loadVizmap) {
+ // restore vizmap.props
+ Cytoscape.firePropertyChange(Cytoscape.VIZMAP_RESTORED, null,
+ vizmapFileURL);
+ }
+ // Restore bookmarks
+ if (bookmarksFileURL != null) {
+ bookmarks = getBookmarksFromZip(bookmarksFileURL);
+ Cytoscape.setBookmarks(bookmarks);
+ }
+
+ /*
+ * Even though cytoscapePropsURL is probably a local URL, error on the
+ * side of caution and use URLUtil to get the input stream (which
+ * handles proxy servers and cached pages):
+ */
+ CytoscapeInit.getProperties().load(
+ URLUtil.getBasicInputStream(cytoscapePropsURL));
+ loadCySession();
+
+ // restore plugin state files
+ restorePlugnStateFilesFromZip();
+
+ // Restore Nested Networks
+ restoreNestedNetworkLinks();
+ }
+
+ private void restorePlugnStateFilesFromZip() {
+ if ((theURLstrMap == null) || (theURLstrMap.size() == 0)) {
+ return;
+ }
+
+ Set<String> pluginSet = theURLstrMap.keySet();
+
+ for (String pluginName : pluginSet) {
+ List<String> URLstrList = theURLstrMap.get(pluginName);
+
+ if ((URLstrList == null) || (URLstrList.size() == 0)) {
+ continue;
+ }
+
+ File theFile = null;
+
+ for (String URLstr : URLstrList) {
+ int index = URLstr.lastIndexOf("/");
+ String fileName = System.getProperty("java.io.tmpdir")
+ + File.separator + pluginName + "_"
+ + URLstr.substring(index + 1);
+
+ theFile = new File(fileName);
+
+ try {
+ // get inputstream from ZIP
+ URL theURL = new URL(URLstr);
+
+ // InputStream is = theURL.openStream();
+ // Even though theURL derives from a File, error on the
+ // side of caution and use URLUtil to get the input stream
+ // (which
+ // handles proxy servers and cached pages):
+ InputStream is = null;
+
+ try {
+ is = URLUtil.getBasicInputStream(theURL);
+
+ // Write input stream into tmp file
+ BufferedReader in = null;
+ BufferedWriter out = null;
+
+ in = new BufferedReader(new InputStreamReader(is));
+ try {
+ out = new BufferedWriter(new FileWriter(theFile));
+
+ try {
+ // Write to tmp file
+ String inputLine;
+
+ while ((inputLine = in.readLine()) != null) {
+ out.write(inputLine);
+ out.newLine();
+ }
+ } finally {
+ if (out != null) {
+ out.close();
+ }
+ }
+ } finally {
+ if (in != null) {
+ in.close();
+ }
+ }
+ } finally {
+ if (is != null) {
+ is.close();
+ }
+ }
+ } catch (IOException e) {
+ theFile = null;
+ logger.error("Error: reading from zip: " + URLstr, e);
+ }
+
+ if (theFile == null)
+ continue;
+
+ // Put the file into pluginFileListMap
+ if (!pluginFileListMap.containsKey(pluginName)) {
+ List<File> fileList = new ArrayList<File>();
+ fileList.add(theFile);
+ pluginFileListMap.put(pluginName, fileList);
+ } else {
+ List<File> fileList = pluginFileListMap.get(pluginName);
+ fileList.add(theFile);
+ }
+ }
+ }
+ }
+
+ private Bookmarks getBookmarksFromZip(URL pBookmarksFileURL) {
+ Bookmarks theBookmark = null;
+
+ try {
+ // InputStream is = pBookmarksFileURL.openStream();
+ // Use URLUtil to get the InputStream since we might be using a
+ // proxy server
+ // and because pages may be cached:
+ final JAXBContext jaxbContext = JAXBContext.newInstance(
+ BOOKMARK_PACKAGE_NAME, this.getClass().getClassLoader());
+ final Unmarshaller unmarshaller = jaxbContext.createUnmarshaller();
+
+ InputStream is = null;
+
+ try {
+ is = URLUtil.getBasicInputStream(pBookmarksFileURL);
+ theBookmark = (Bookmarks) unmarshaller.unmarshal(is);
+ } finally {
+ if (is != null) {
+ is.close();
+ }
+ }
+ } catch (FileNotFoundException e1) {
+ logger.warn("Can not find bookmark file in "
+ + pBookmarksFileURL.toString(), e1);
+ } catch (IOException e2) {
+ logger.warn("Can not read bookmark file from "
+ + pBookmarksFileURL.toString(), e2);
+ } catch (JAXBException e3) {
+ logger.warn("XML parse err in bookmark file in "
+ + pBookmarksFileURL.toString(), e3);
+ }
+
+ return theBookmark;
+ }
+
+ private void loadCySession() throws JAXBException, IOException, Exception {
+ // InputStream is = cysessionFileURL.openStream();
+ // Even though cytoscapeFileURL is probably a local URL, error on the
+ // side of caution and use URLUtil to get the input stream (which
+ // handles proxy servers and cached pages):
+ final JAXBContext jaxbContext = JAXBContext.newInstance(PACKAGE_NAME,
+ this.getClass().getClassLoader());
+ final Unmarshaller unmarshaller = jaxbContext.createUnmarshaller();
+ InputStream is = null;
+
+ try {
+ is = URLUtil.getBasicInputStream(cysessionFileURL);
+ session = (Cysession) unmarshaller.unmarshal(is);
+ } finally {
+ if (is != null)
+ is.close();
+ }
+
+ /*
+ * Session ID is the name of folder which contains everything for this
+ * session.
+ */
+ sessionID = session.getId();
+ netMap = new HashMap<String, Network>();
+
+ for (Network curNet : session.getNetworkTree().getNetwork())
+ netMap.put(curNet.getId(), curNet);
+
+ walkTree(netMap.get(NETWORK_ROOT), null, cysessionFileURL);
+ }
+
+ private void restoreDesktopState() {
+
+ final List<NetworkFrame> frames = session.getSessionState()
+ .getDesktop().getNetworkFrames().getNetworkFrame();
+ final Map<String, NetworkFrame> frameMap = new HashMap<String, NetworkFrame>();
+
+ for (NetworkFrame netFrame : frames)
+ frameMap.put(netFrame.getFrameID(), netFrame);
+
+ Component[] desktopFrames = Cytoscape.getDesktop()
+ .getNetworkViewManager().getDesktopPane().getComponents();
+
+ for (int i = 0; i < desktopFrames.length; i++) {
+ Component cmp;
+
+ cmp = desktopFrames[i];
+ if (cmp instanceof JInternalFrame) {
+ JInternalFrame frame = (JInternalFrame) cmp;
+ NetworkFrame nFrame = frameMap.get(frame.getTitle());
+
+ if (nFrame != null) {
+ frame.setSize(nFrame.getWidth().intValue(), nFrame
+ .getHeight().intValue());
+ frame.setLocation(nFrame.getX().intValue(), nFrame.getY()
+ .intValue());
+ }
+ }
+ }
+ }
+
+ /**
+ * Load the root network and then create its children.<br>
+ *
+ * @param currentNetwork
+ * @param parent
+ * @param sessionSource
+ * @throws JAXBException
+ * @throws IOException
+ */
+ private void walkTree(final Network currentNetwork, final CyNetwork parent,
+ final Object sessionSource) throws JAXBException, IOException {
+ // Get the list of children under this root
+ final List<Child> children = currentNetwork.getChild();
+
+ // Traverse using recursive call
+ final int numChildren = children.size();
+ Child child;
+ Network childNet;
+ URL targetNetworkURL;
+ CyNetworkView curNetView;
+
+ // Get the current state of the vsbSwitch
+ Properties prop = CytoscapeInit.getProperties();
+ String vsbSwitch = prop.getProperty("visualStyleBuilder");
+ // Since we're reading a session (which already has visual
+ // styles defined) force the vsbSwitch off
+ prop.setProperty("visualStyleBuilder", "off");
+
+ // Since we know what views the user want's created, let's disable
+ // the viewThreshold for now
+ String viewThreshold = prop.getProperty("viewThreshold");
+ prop.setProperty("viewThreshold", Integer.toString(Integer.MAX_VALUE));
+
+ for (int i = 0; i < numChildren; i++) {
+ child = children.get(i);
+ childNet = netMap.get(child.getId());
+
+ String targetNwUrlName = sessionID + "/" + childNet.getFilename();
+ targetNetworkURL = (URL) networkURLs.get(targetNwUrlName);
+
+ // handle the unlikely event that the stored network is corrupted
+ // with a bad filename (bug fix)
+ if (targetNetworkURL == null) {
+ logger
+ .error("Session file corrupt: Filename "
+ + childNet.getFilename()
+ + " does not correspond to a network of that name in session file");
+ continue;
+ }
+
+ CyNetwork new_network = null;
+ JarURLConnection jarConnection = null;
+ XGMMLReader reader = null;
+
+ jarConnection = (JarURLConnection) targetNetworkURL
+ .openConnection();
+ try {
+ InputStream networkStream = null;
+ try {
+ networkStream = (InputStream) jarConnection.getContent();
+
+ reader = new XGMMLReader(networkStream);
+ if (childNet.isViewAvailable()) {
+ new_network = Cytoscape.createNetwork(reader, true, parent);
+ curNetView = Cytoscape.getNetworkView(new_network.getIdentifier());
+ if (curNetView != null) {
+ // Set visual style
+ String vsName = childNet.getVisualStyle();
+ if (vsName == null) {
+ vsName = "default";
+ }
+ lastVSName = vsName;
+
+ // logger.debug("createNetworkView "+new_network.getIdentifier()+": "
+ // + (System.currentTimeMillis() - start) + " msec.");
+ curNetView.setVisualStyle(vsName);
+
+ Cytoscape.getVisualMappingManager().setNetworkView(curNetView);
+ Cytoscape.getVisualMappingManager().setVisualStyle(vsName);
+
+ // Set hidden nodes + edges
+ setHiddenNodes(curNetView, (HiddenNodes) childNet.getHiddenNodes());
+ setHiddenEdges(curNetView, (HiddenEdges) childNet.getHiddenEdges());
+ }
+ } else {
+ new_network = Cytoscape.createNetwork(reader, false, parent);
+ }
+ } finally {
+ if (networkStream != null)
+ networkStream.close();
+ }
+ } catch (final Exception e) {
+ final String message = "Unable to read XGMML file: "
+ + childNet.getFilename() + ". " + e.getMessage();
+ logger.error(message, e);
+ Cytoscape.destroyNetwork(new_network);
+ if (taskMonitor != null)
+ taskMonitor.setException(e, message);
+ // Load child networks, even if this network is bad
+ if (childNet.getChild().size() != 0)
+ walkTree(childNet, new_network, sessionSource);
+ continue;
+ }
+
+ if ((taskMonitor != null) && (networkCounter >= 20)) {
+ netIndex++;
+ taskMonitor
+ .setPercentCompleted(((Number) ((netIndex / networkCounter) * 100))
+ .intValue());
+ }
+
+ if (new_network != null) {
+ logger.info("XGMMLReader " + new_network.getIdentifier() + ": "
+ + (System.currentTimeMillis() - start) + " msec.");
+
+ networkList.add(new_network.getIdentifier());
+
+ }
+
+ setSelectedNodes(new_network, (SelectedNodes) childNet
+ .getSelectedNodes());
+ setSelectedEdges(new_network, (SelectedEdges) childNet
+ .getSelectedEdges());
+
+ // Load child networks
+ if (childNet.getChild().size() != 0)
+ walkTree(childNet, new_network, sessionSource);
+ }
+
+ // Restore the original state of the vsbSwitch
+ if (vsbSwitch != null)
+ prop.setProperty("visualStyleBuilder", vsbSwitch);
+ else
+ prop.remove("visualStyleBuilder");
+
+ // Restore the original state of the viewThreshold
+ if (viewThreshold != null)
+ prop.setProperty("viewThreshold", viewThreshold);
+ else
+ prop.remove("viewThreshold");
+ }
+
+ private void setSelectedNodes(final CyNetwork network,
+ final SelectedNodes selected) {
+ if (selected == null) {
+ return;
+ }
+
+ final List selectedNodeList = new ArrayList();
+ final Iterator it = selected.getNode().iterator();
+
+ while (it.hasNext()) {
+ final Node selectedNode = (Node) it.next();
+ selectedNodeList.add(Cytoscape.getCyNode(selectedNode.getId(),
+ false));
+ }
+
+ network.setSelectedNodeState(selectedNodeList, true);
+ }
+
+ private void setHiddenNodes(final CyNetworkView view,
+ final HiddenNodes hidden) {
+ if (hidden == null) {
+ return;
+ }
+
+ final Iterator it = hidden.getNode().iterator();
+
+ while (it.hasNext()) {
+ final Node hiddenNodeObject = (Node) it.next();
+ final CyNode hiddenNode = Cytoscape.getCyNode(hiddenNodeObject
+ .getId(), false);
+ view.hideGraphObject(view.getNodeView(hiddenNode));
+ }
+ }
+
+ private void setHiddenEdges(final CyNetworkView view,
+ final HiddenEdges hidden) {
+ if (hidden == null) {
+ return;
+ }
+
+ final Iterator it = hidden.getEdge().iterator();
+
+ while (it.hasNext()) {
+ final Edge hiddenEdgeObject = (Edge) it.next();
+ final CyEdge hiddenEdge = getCyEdge(hiddenEdgeObject);
+
+ if (hiddenEdge != null) {
+ view.hideGraphObject(view.getEdgeView(hiddenEdge));
+ }
+ }
+ }
+
+ private void setSelectedEdges(final CyNetwork network,
+ final SelectedEdges selected) {
+ if (selected == null) {
+ return;
+ }
+
+ CyEdge targetEdge = null;
+ final List selectedEdgeList = new ArrayList();
+ final Iterator it = selected.getEdge().iterator();
+
+ while (it.hasNext()) {
+ final cytoscape.generated.Edge selectedEdge = (cytoscape.generated.Edge) it
+ .next();
+ targetEdge = getCyEdge(selectedEdge);
+
+ if (targetEdge != null) {
+ selectedEdgeList.add(targetEdge);
+ }
+ }
+
+ network.setSelectedEdgeState(selectedEdgeList, true);
+ }
+
+ private CyEdge getCyEdge(final Edge edge) {
+ CyEdge targetEdge = null;
+
+ final String sourceString = edge.getSource();
+ final String targetString = edge.getTarget();
+ CyNode source = null;
+ CyNode target = null;
+ String interaction = edge.getInteraction();
+
+ // Try to get CyEdge by the source & target IDs
+ if ((sourceString != null) && (targetString != null)) {
+ source = Cytoscape.getCyNode(sourceString);
+ target = Cytoscape.getCyNode(targetString);
+ }
+
+ // If all 3 parameters are available, try to get CyEdge
+ if (((source != null) & (target != null)) && (interaction != null)) {
+ targetEdge = Cytoscape.getCyEdge(source, target,
+ Semantics.INTERACTION, interaction, false, true);
+ }
+
+ // If CyEdge is still null, try to get one from ID
+ if (targetEdge == null) {
+ final String[] parts = edge.getId().split(" ");
+
+ if (parts.length == 3) {
+ source = Cytoscape.getCyNode(parts[0], false);
+ target = Cytoscape.getCyNode(parts[2], false);
+ interaction = parts[1].substring(1, parts[1].length() - 1);
+
+ if ((source != null) && (target != null)
+ && (interaction != null)) {
+ targetEdge = Cytoscape.getCyEdge(source, target,
+ Semantics.INTERACTION, interaction, false, true);
+ }
+ }
+ }
+
+ return targetEdge;
+ }
+
+ /**
+ * Extract Session Note test field in cysession.xml
+ *
+ * @return Session Note
+ */
+ public String getCysessionNote() {
+ return session.getSessionNote();
+ }
+
+ /**
+ * Restore list of ontology servers
+ *
+ * @throws MalformedURLException
+ *
+ */
+ private void restoreOntologyServerStatus() throws MalformedURLException {
+ Map<String, URL> newMap = new HashMap<String, URL>();
+
+ List<Ontology> servers = session.getSessionState().getServer()
+ .getOntologyServer().getOntology();
+ String targetCyNetworkID = null;
+ String curator = null;
+ String description = null;
+
+ for (Ontology server : servers) {
+ newMap.put(server.getName(), new URL(server.getHref()));
+ targetCyNetworkID = getNetworkIdFromTitle(server.getName());
+
+ cytoscape.data.ontology.Ontology onto = new cytoscape.data.ontology.Ontology(
+ server.getName(), curator, description, Cytoscape
+ .getNetwork(targetCyNetworkID));
+ Cytoscape.getOntologyServer().addOntology(onto);
+ }
+
+ Cytoscape.getOntologyServer().setOntologySources(newMap);
+ }
+
+ private String getNetworkIdFromTitle(String title) {
+ Set<CyNetwork> networks = Cytoscape.getNetworkSet();
+
+ for (CyNetwork net : networks) {
+ if (net.getTitle().equals(title)) {
+ return net.getIdentifier();
+ }
+ }
+
+ // Not found
+ return null;
+ }
+
+ /**
+ * The CytoscapeSessionReader class reopens the session file each time it
+ * accesses or reads one of the files contained within the session file
+ * (which is just a zip container). This is fine for local files, but if you
+ * refer to a remote URL, it means that the session file is downloaded once
+ * for each file accessed -- that's 4-5 times on average, and performance
+ * suffers immensely.
+ *
+ * This method will attempt to create a local temporary file and copy the
+ * contents of the remote URL into the temporary file. It returns the URL
+ * for the local temporary file. Note that the file is marked
+ * "deleteOnExit", which means that if the JVM exits normally, it will be
+ * cleaned up automatically.
+ *
+ * The method returns either the local file URL, or the original remote URL
+ * if there was a problem in creating the local file.
+ *
+ * @param remoteURL
+ * @return
+ */
+ private URL temporaryLocalFileURL(final URL remoteURL) {
+ try {
+ // We need a unique local filename for the temporary file - which
+ // seems like a
+ // logical job for Java's UUID class...
+ File tempFile = File.createTempFile(java.util.UUID.randomUUID()
+ .toString(), ".cys");
+ tempFile.deleteOnExit();
+
+ byte[] buffer = new byte[100000];
+ java.io.OutputStream localContent = new java.io.FileOutputStream(
+ tempFile);
+
+ try {
+ // java.io.InputStream remoteContent = remoteURL.openStream();
+ // Use URLUtil to get the InputStream since we might be using a
+ // proxy server
+ // and because pages may be cached:
+ java.io.InputStream remoteContent = URLUtil
+ .getBasicInputStream(remoteURL);
+
+ try {
+ for (int nBytes = remoteContent.read(buffer); nBytes > 0; nBytes = remoteContent
+ .read(buffer)) {
+ localContent.write(buffer, 0, nBytes);
+ }
+ } finally {
+ if (remoteContent != null) {
+ remoteContent.close();
+ }
+ }
+ } finally {
+ if (localContent != null) {
+ localContent.close();
+ }
+ }
+
+ return tempFile.toURL();
+ } catch (FileNotFoundException e) {
+ // This could happen if the OS' temp directory doesn't exist
+ logger.error("Can't create a temporary file.", e);
+ } catch (MalformedURLException e) {
+ // If the provided URL is bad, this will happen
+ logger.error("Bad URL provided: " + remoteURL.toString(), e);
+ } catch (IOException e) {
+ // Any problem read or writing from either the remoteURL or the
+ // tempFile
+ logger.error("I/O error while cacheing URL data", e);
+ }
+
+ return remoteURL; // if we can't make a local copy for some reason, work
+ // with the remote.
+ }
+}
diff --git a/application/src/main/java/cytoscape/data/readers/EqnAttrTracker.java b/application/src/main/java/cytoscape/data/readers/EqnAttrTracker.java
new file mode 100644
index 0000000..93c25d3
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/readers/EqnAttrTracker.java
@@ -0,0 +1,198 @@
+/*
+ File: EqnAttrTracker.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data.readers;
+
+
+import cytoscape.Cytoscape;
+import cytoscape.data.CyAttributes;
+import cytoscape.logger.CyLogger;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.HashMap;
+import java.util.Map;
+
+import org.cytoscape.equations.EqnCompiler;
+import org.cytoscape.equations.Equation;
+
+
+public class EqnAttrTracker {
+ private enum AttrClass {
+ NODES(Cytoscape.getNodeAttributes()),
+ EDGES(Cytoscape.getEdgeAttributes()),
+ NETWORKS(Cytoscape.getNetworkAttributes());
+
+ private CyAttributes attribs;
+
+ AttrClass(final CyAttributes attribs) { this.attribs = attribs; }
+
+ CyAttributes getAttribs() { return attribs; }
+ };
+
+
+ private static class AttrInfo {
+ private String id;
+ private String attrName;
+ private String equation;
+ private Class returnType;
+
+ AttrInfo(final String id, final String attrName, final String equation, final Class returnType) {
+ this.id = id;
+ this.attrName = attrName;
+ this.equation = equation;
+ this.returnType = returnType;
+ }
+
+ String getID() { return id; }
+ String getAttrName() { return attrName; }
+ String getEquation() { return equation; }
+ Class getReturnType() { return returnType; }
+ }
+
+ private CyLogger logger;
+ private List<AttrInfo> nodeAttrs, edgeAttrs, networkAttrs;
+
+ public EqnAttrTracker() {
+ logger = CyLogger.getLogger(EqnAttrTracker.class);
+ nodeAttrs = new ArrayList<AttrInfo>();
+ edgeAttrs = new ArrayList<AttrInfo>();
+ networkAttrs = new ArrayList<AttrInfo>();
+ }
+
+ void reset() {
+ nodeAttrs.clear();
+ edgeAttrs.clear();
+ networkAttrs.clear();
+ }
+
+ void recordEquation(final CyAttributes attribs, final String id, final String attrName,
+ final String equation, final Class returnType)
+ {
+ if (attribs == AttrClass.NODES.getAttribs())
+ nodeAttrs.add(new AttrInfo(id, attrName, equation, returnType));
+ else if (attribs == AttrClass.EDGES.getAttribs())
+ edgeAttrs.add(new AttrInfo(id, attrName, equation, returnType));
+ else if (attribs == AttrClass.NETWORKS.getAttribs())
+ networkAttrs.add(new AttrInfo(id, attrName, equation, returnType));
+ else
+ throw new IllegalArgumentException("unkown CyAttributes!");
+
+ if (returnType == Double.class)
+ registerFloat(attribs, id, attrName);
+ else if (returnType == Long.class)
+ registerInteger(attribs, id, attrName);
+ else if (returnType == String.class)
+ registerString(attribs, id, attrName);
+ else if (returnType == Boolean.class)
+ registerBoolean(attribs, id, attrName);
+ else if (returnType == List.class)
+ registerList(attribs, id, attrName);
+ else
+ throw new IllegalArgumentException("unknown retuyrn type: " + returnType + "!");
+ }
+
+ void addAllEquations() {
+ addEquations(AttrClass.NODES.getAttribs(), nodeAttrs);
+ addEquations(AttrClass.EDGES.getAttribs(), edgeAttrs);
+ addEquations(AttrClass.NETWORKS.getAttribs(), networkAttrs);
+ }
+
+ private void addEquations(final CyAttributes attribs, final List<AttrInfo> attrInfos) {
+ final EqnCompiler compiler = new EqnCompiler();
+ final String[] allAttribNames = attribs.getAttributeNames();
+ final Class[] allTypes = new Class[allAttribNames.length];
+ final Map<String, Class> attribNameToTypeMap = new HashMap<String, Class>();
+ int index = 0;
+ for (final String attribName : allAttribNames) {
+ final byte type = attribs.getType(attribName);
+ final Class eqnType = mapCytoscapeAttribTypeToEqnType(type);
+ if (eqnType != null)
+ attribNameToTypeMap.put(attribName, eqnType);
+ }
+
+ for (final AttrInfo attrInfo : attrInfos) {
+ attribNameToTypeMap.remove(attrInfo.getAttrName());
+
+ if (compiler.compile(attrInfo.getEquation(), attribNameToTypeMap))
+ attribs.setAttribute(attrInfo.getID(), attrInfo.getAttrName(), compiler.getEquation());
+ else {
+ final String errorMessage = compiler.getLastErrorMsg();
+ logger.warn("bad equation on import: " + errorMessage);
+ final Equation errorEquation = Equation.getErrorEquation(attrInfo.getEquation(),
+ attrInfo.getReturnType(), errorMessage);
+ attribs.setAttribute(attrInfo.getID(), attrInfo.getAttrName(), errorEquation);
+ }
+
+ attribNameToTypeMap.put(attrInfo.getAttrName(), attrInfo.getReturnType());
+ }
+ }
+
+ private static Class mapCytoscapeAttribTypeToEqnType(final byte attribType) {
+ switch (attribType) {
+ case CyAttributes.TYPE_BOOLEAN:
+ return Boolean.class;
+ case CyAttributes.TYPE_INTEGER:
+ return Long.class;
+ case CyAttributes.TYPE_FLOATING:
+ return Double.class;
+ case CyAttributes.TYPE_STRING:
+ return String.class;
+ case CyAttributes.TYPE_SIMPLE_LIST:
+ return List.class;
+ default:
+ return null;
+ }
+ }
+
+ private static void registerFloat(final CyAttributes attrs, final String id, final String attrName) {
+ attrs.setAttribute(id, attrName, 0.0);
+ attrs.deleteAttribute(id, attrName);
+ }
+
+ private static void registerString(final CyAttributes attrs, final String id, final String attrName) {
+ attrs.setAttribute(id, attrName, "");
+ attrs.deleteAttribute(id, attrName);
+ }
+
+ private static void registerInteger(final CyAttributes attrs, final String id, final String attrName) {
+ attrs.setAttribute(id, attrName, 0);
+ attrs.deleteAttribute(id, attrName);
+ }
+
+ private static void registerBoolean(final CyAttributes attrs, final String id, final String attrName) {
+ attrs.setAttribute(id, attrName, true);
+ attrs.deleteAttribute(id, attrName);
+ }
+
+ private static void registerList(final CyAttributes attrs, final String id, final String attrName) {
+ attrs.setListAttribute(id, attrName, new ArrayList());
+ attrs.deleteAttribute(id, attrName);
+ }
+}
diff --git a/application/src/main/java/cytoscape/data/readers/GMLException.java b/application/src/main/java/cytoscape/data/readers/GMLException.java
new file mode 100644
index 0000000..e16b1de
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/readers/GMLException.java
@@ -0,0 +1,54 @@
+/*
+ File: GMLException.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.data.readers;
+
+
+/**
+ *
+ * Exception for GML Reader.
+ *
+ */
+public class GMLException extends RuntimeException {
+ /**
+ * Creates a new GMLException object.
+ *
+ * @param message DOCUMENT ME!
+ */
+ public GMLException(String message) {
+ super(message);
+ }
+}
diff --git a/application/src/main/java/cytoscape/data/readers/GMLNode.java b/application/src/main/java/cytoscape/data/readers/GMLNode.java
new file mode 100644
index 0000000..26f2e85
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/readers/GMLNode.java
@@ -0,0 +1,225 @@
+/*
+ File: GMLNode.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data.readers;
+
+import java.util.*;
+
+
+/**
+ * This class represents a GMLNode. A GMLNode can be either a
+ * GML terminal, or contain a mapping from string keys to other
+ * GMLNodes
+ **/
+public class GMLNode implements Comparator {
+ /**
+ * True if this node is a terminal. (A terminal node is one
+ * that just contains a piece of data (string,double,int) and
+ * not further mapping to GMLNodes
+ **/
+ public boolean terminal;
+
+ /**
+ * Remeber whether this data was initially quoted
+ */
+ private boolean quotes = false;
+
+ /**
+ * If this node is a terminal, this will contain
+ * the associated data in string form
+ */
+ private String string_value;
+
+ /**
+ * The string used in indenting the display
+ */
+ private static String TAB = "\t";
+
+ /**
+ * This will only be defined if the node is not a
+ * terminal. It contains a mapping from Strings to a vector
+ * of GMLNodes
+ */
+ private HashMap key2GMLNodeVec;
+ private HashMap key2Order;
+ private int order;
+
+ /**
+ * This constructor create a terminal GMLNode.
+ * @param string_value The terminal value of the GMLNode
+ */
+ public GMLNode(String string_value) {
+ if (string_value.startsWith("\"") && string_value.endsWith("\"")) {
+ quotes = true;
+ string_value = string_value.substring(1, string_value.length() - 1);
+ }
+
+ this.string_value = string_value;
+ terminal = true;
+ }
+
+ /**
+ * This constructor creates a non-terminal GMLNode.
+ * The mapping is initially empty. Mappings are added
+ * using addMapping
+ */
+ public GMLNode() {
+ terminal = false;
+ order = 1;
+ key2Order = new HashMap();
+ key2GMLNodeVec = new HashMap();
+ }
+
+ /**
+ * Return the string representation of this GMLNode. This will
+ * recursively print out all mapped subGMLNodes if present.
+ */
+ public String toString() {
+ return toString("");
+ }
+
+ /**
+ * Private recursive helper method to print out the contents of the
+ * node
+ * @param indent The indent to use when printing out this node
+ */
+ private String toString(String indent) {
+ String lineSep = System.getProperty("line.separator");
+ String result = "";
+
+ if (terminal) {
+ if (!quotes) {
+ return TAB + string_value;
+ } else {
+ return TAB + "\"" + string_value + "\"";
+ }
+ } else {
+ result += (lineSep + indent + "[" + lineSep);
+
+ //Iterator it = key2GMLNodeVec.keySet().iterator();
+ Vector sortedKeys = new Vector(key2GMLNodeVec.keySet());
+ Collections.sort(sortedKeys, this);
+
+ Iterator it = sortedKeys.iterator();
+
+ while (it.hasNext()) {
+ String key = (String) it.next();
+ Iterator mapIt = ((Vector) key2GMLNodeVec.get(key)).iterator();
+
+ while (mapIt.hasNext()) {
+ GMLNode next = (GMLNode) mapIt.next();
+ result += (indent + key + next.toString(indent + TAB) + lineSep);
+ }
+ }
+
+ result += (indent + "]");
+ }
+
+ return result;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param o1 DOCUMENT ME!
+ * @param o2 DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int compare(Object o1, Object o2) {
+ //get the integer orderings for these two objects
+ Integer int1 = (Integer) key2Order.get(o1);
+ Integer int2 = (Integer) key2Order.get(o2);
+
+ if ((int1 == null) || (int2 == null))
+ throw new RuntimeException("Forgot to add an order mapping for one of the keys");
+
+ return int1.compareTo(int2);
+ }
+
+ /**
+ * Get the value of this node as a Double
+ * @return The value of this node as a double
+ * @throws RuntimeException if the value of this node cannot be interpreted as a Double
+ */
+ public Double doubleValue() {
+ return new Double(string_value);
+ }
+
+ /**
+ * Get the value of this node as an Integer
+ * @return The value of this node as an Integer
+ * @throws RuntimeException if the value of this node cannot be interpreted as an Integer
+ */
+ public Integer integerValue() {
+ return new Integer(string_value);
+ }
+
+ /**
+ * Get the value of this node as a String
+ * @return The value of this node as a String
+ */
+ public String stringValue() {
+ return string_value;
+ }
+
+ /**
+ * Add a mapping from key to node
+ * @param key The key for the mapping
+ * @param node The node which will map to the key
+ */
+ public void addMapping(String key, GMLNode node) {
+ Vector values;
+ values = (Vector) key2GMLNodeVec.get(key);
+
+ if (values == null) {
+ values = new Vector();
+ key2GMLNodeVec.put(key, values);
+ key2Order.put(key, new Integer(order++));
+ }
+
+ values.add(node);
+ }
+
+ /**
+ * Return the data mapped by this key
+ * @param key The key to look up
+ * @return A vector of GMLNodes (may be null)
+ */
+ public Vector getMapping(String key) {
+ return (Vector) key2GMLNodeVec.get(key);
+ }
+}
diff --git a/application/src/main/java/cytoscape/data/readers/GMLParser.java b/application/src/main/java/cytoscape/data/readers/GMLParser.java
new file mode 100644
index 0000000..c91d87e
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/readers/GMLParser.java
@@ -0,0 +1,323 @@
+/*
+ File: GMLParser.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.data.readers;
+
+import java.io.FilterReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.Reader;
+import java.io.StreamTokenizer;
+import java.io.Writer;
+import java.text.ParseException;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.regex.Pattern;
+
+import cytoscape.util.FileUtil;
+
+/**
+ * The purpose of this class is to translate GML into an object tree, and print
+ * out an object tree into GML
+ */
+public class GMLParser {
+ /**
+ * This character begsin and ends a string literal in a GML file
+ */
+ private static final int QUOTE_CHAR = '"';
+
+ /**
+ * String versio of above
+ */
+ private static final String QUOTE_STRING = "\"";
+
+ /**
+ * This regex pattern will match a valid key
+ */
+ private static final Pattern keyPattern = Pattern.compile("\\w+");;
+
+ /**
+ * This regex pattern will match a valid integer
+ */
+ private static final Pattern integerPattern = Pattern.compile("(\\+|\\-){0,1}\\d+");;
+
+ /**
+ * This regex pattern will match a valid real (double)
+ */
+ private static final Pattern realPattern = Pattern
+ .compile("(\\+|\\-){0,1}\\d+\\.\\d+((E|e)(\\+|\\-){0,1}\\d+){0,1}");;
+
+ // opens a list
+ private static final String LIST_OPEN = "[";
+
+ // close a list
+ private static final String LIST_CLOSE = "]";
+
+ private StreamTokenizer tokenizer;
+
+ /**
+ * Constructor has to initialize the relevenat regular expression patterns
+ */
+ public GMLParser(final StreamTokenizer tokenizer) {
+ this.tokenizer = tokenizer;
+ }
+
+ /**
+ * Make a stream tokenizer out of the given this file and read in the file
+ */
+ public GMLParser(final String file) throws IOException, Exception {
+ this(FileUtil.getInputStream(file));
+ }
+
+ /**
+ * Make a stream tokenizer out of the given this file and read in the file
+ */
+ public GMLParser(final InputStream stream) throws IOException, Exception {
+ tokenizer = new StreamTokenizer(new FilterNewlineReader(
+ new InputStreamReader(stream)));
+
+ tokenizer.resetSyntax();
+ tokenizer.commentChar('#');
+ tokenizer.quoteChar('"');
+ tokenizer.eolIsSignificant(false);
+ /*
+ * Set up the relevant word and whitespace characters
+ */
+ tokenizer.wordChars(' ', '!');
+ tokenizer.wordChars('$', '~');
+ tokenizer.wordChars('\u00A0', '\u00FF');
+ tokenizer.whitespaceChars('\u0000', '\u0020');
+ tokenizer.nextToken();
+ }
+
+
+ /**
+ * Public method to print out a given object tree(list) using the supplied
+ * filewriter
+ */
+ public static void printList(final List<KeyValue> list, final Writer writer) throws IOException {
+ printList(list, "", writer);
+ }
+
+
+ /**
+ * Protected recurive helper method to print out an object tree
+ */
+ protected static void printList(final List<KeyValue> list, final String indent, final Writer writer)
+ throws IOException {
+ for (KeyValue keyVal: list) {
+ if (keyVal.value instanceof List<?>) {
+ // If the value is a list, print that list recursively
+ // surrounded by the list open and close characters
+ writer.write(indent + keyVal.key + "\t");
+ writer.write(LIST_OPEN + "\n");
+ printList((List<KeyValue>) keyVal.value, indent + "\t", writer);
+ writer.write(indent + LIST_CLOSE + "\n");
+ } else if (keyVal.value instanceof String) {
+ // Surround a string with the quote characters
+ writer.write(indent + keyVal.key + "\t");
+ writer.write(QUOTE_STRING + keyVal.value + QUOTE_STRING + "\n");
+ } else if (keyVal.value instanceof Double) {
+ // If the double contains a non-number, we will refuse to write
+ // it out because the result will be invalid gml
+ Double value = (Double) keyVal.value;
+
+ if (!(value.isNaN() || value.isInfinite())) {
+ writer.write(indent + keyVal.key + "\t");
+ writer.write(keyVal.value + "\n");
+ }
+ } else if (keyVal.value instanceof Integer) {
+ // Everything else (Integer, double) relies upon the default
+ // toString() method of the object
+ writer.write(indent + keyVal.key + "\t");
+ writer.write(keyVal.value + "\n");
+ }
+ }
+ }
+
+ /**
+ * A list consists of zero or more paris of keys and values
+ */
+ public List<KeyValue> parseList() throws IOException, ParseException {
+ final List<KeyValue> result = new ArrayList<KeyValue>();
+
+ String key;
+ Object value;
+ while (isKey()) {
+ key = parseKey();
+
+ if (key == null)
+ throw new ParseException("Bad key", tokenizer.lineno());
+
+ tokenizer.nextToken();
+
+ value = parseValue();
+
+ if (value == null) {
+ throw new ParseException(
+ "Bad value associated with key " + key, tokenizer
+ .lineno());
+ }
+
+ result.add(new KeyValue(key, value));
+ tokenizer.nextToken();
+ }
+
+ return result;
+ }
+
+ /**
+ * A key consists of one or more occurrences of lower/upper-case[A-Z][0-9]
+ */
+ private boolean isKey() {
+ /*
+ * A key must be some kind of word
+ */
+ if (tokenizer.ttype != StreamTokenizer.TT_WORD) {
+ return false;
+ }
+
+ return keyPattern.matcher(tokenizer.sval).matches();
+ }
+
+ /**
+ * An integer consists of hte characters [0-9] Assuming hte precondition
+ * that we have already checked for the end of file
+ */
+ private boolean isInteger() {
+ return integerPattern.matcher(tokenizer.sval).matches();
+ }
+
+ /**
+ * A real consists of 1 or more digits followed by a ., followed by one or
+ * more digits and an optional mantissa. Assuming the preconiditon that we
+ * have already checked for hte end of file
+ */
+ private boolean isReal() {
+ return realPattern.matcher(tokenizer.sval).matches();
+ }
+
+ /**
+ * A string consits of a string that begins and ends with the quote
+ * character The streamtokenizer will basically check for this for me, so I
+ * just have to check the token type and see if it is a quote char It's also
+ * not supposed ot have a couple things in it, but I don't really have a
+ * check for that.
+ */
+ private boolean isQuatedString() {
+ return tokenizer.ttype == QUOTE_CHAR;
+ }
+
+ /**
+ * A list starts with the list open character I'm assuming I get some white
+ * space before and after the list delimiter, that might not actually be
+ * true according to the spec
+ */
+ private boolean isList() {
+ return tokenizer.sval.equals(LIST_OPEN);
+ }
+
+ /**
+ * Verify that the current value is a key, and then return the key that is
+ * found
+ */
+ private String parseKey() {
+ if (isKey()) {
+ return tokenizer.sval;
+ } else {
+ return null;
+ }
+ }
+
+ /**
+ * Parse out a value, it can be a integer,real,string, or a list. Assume is
+ * has already been found to not be the end of file
+ */
+ private Object parseValue() throws IOException, ParseException {
+
+ if (tokenizer.ttype == StreamTokenizer.TT_EOL)
+ return null;
+
+ if (isQuatedString())
+ return tokenizer.sval;
+
+ if (isInteger())
+ return Integer.parseInt(tokenizer.sval);
+
+ if (isReal())
+ return Double.parseDouble(tokenizer.sval);
+
+ if (isList()) {
+ tokenizer.nextToken();
+
+ final List<KeyValue> list = parseList();
+
+ if (!tokenizer.sval.equals(LIST_CLOSE)) {
+ throw new ParseException("Unterminated list", tokenizer
+ .lineno());
+ }
+ return list;
+ }
+
+ // Treat as a regular string value.
+ return tokenizer.sval;
+ }
+
+ /**
+ * This misery exists to overcome a bug in the java.io.StreamTokenizer lib.
+ * the problem is that StreamTokenizer treats newlines as end-of-quotes,
+ * which means you can't have quoted strings over multiple lines. This,
+ * however, violates the GML grammar. So, since the grammar treats newlines
+ * and spaces the same, we just turn all newlines and carriage returns into
+ * spaces. Fortunately for us, StreamTokenizer only calls the read() method.
+ */
+ private class FilterNewlineReader extends FilterReader {
+ public FilterNewlineReader(Reader r) {
+ super(r);
+ }
+
+ public int read() throws IOException {
+ int c = super.read();
+
+ if ((c == '\n') || (c == '\r'))
+ return ' ';
+ else
+
+ return c;
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/data/readers/GMLReader.java b/application/src/main/java/cytoscape/data/readers/GMLReader.java
new file mode 100644
index 0000000..fc5eadf
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/readers/GMLReader.java
@@ -0,0 +1,1244 @@
+/*
+ File: GMLReader.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.data.readers;
+
+import giny.model.Edge;
+import giny.model.GraphObject;
+import giny.model.Node;
+import giny.view.EdgeView;
+import giny.view.GraphView;
+import giny.view.NodeView;
+
+import java.awt.Color;
+import java.awt.geom.Point2D;
+import java.io.InputStream;
+import java.io.StringWriter;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.Vector;
+
+import cern.colt.list.IntArrayList;
+import cern.colt.map.OpenIntIntHashMap;
+import cytoscape.CyEdge;
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import cytoscape.CytoscapeInit;
+import cytoscape.data.CyAttributes;
+import cytoscape.data.Semantics;
+import cytoscape.init.CyInitParams;
+import cytoscape.layout.CyLayoutAlgorithm;
+import cytoscape.layout.LayoutAdapter;
+import cytoscape.logger.CyLogger;
+import cytoscape.task.TaskMonitor;
+import cytoscape.util.FileUtil;
+import cytoscape.util.PercentUtil;
+import cytoscape.view.CyNetworkView;
+import cytoscape.visual.ArrowShape;
+import cytoscape.visual.NodeShape;
+import cytoscape.visual.VisualPropertyType;
+
+/**
+ * This class is responsible for converting a gml object tree into cytoscape
+ * objects New features to the current version: 1. Small bug fixes. 2. Translate
+ * all features in the GML file. This includes 3. New Visual Style will be
+ * generated when you call this class. The new style saves all visual features
+ * (like node shape) and will not be lost even after other style selected.
+ */
+public class GMLReader extends AbstractGraphReader {
+ /**
+ * The following are all taken to be reserved keywords for gml (note that
+ * not all of them are actually keywords according to the spec)
+ *
+ * Currently, only keywords below are supported by the Visual Style
+ * generation methods.
+ *
+ * (Maybe we need some documents on "cytoscape-style" GML format...)
+ */
+
+ // Global tags
+ protected static final String ID = "id";
+ protected static final String NAME = "name";
+ protected static final String LABEL = "label";
+ protected static final String COMMENT = "comment";
+ protected static final String VERSION = "Version";
+ protected static final String CREATOR = "Creator";
+ protected static final String TITLE = "Title";
+
+ // Graph Tags
+ protected static final String GRAPH = "graph";
+ protected static final String NODE = "node";
+ protected static final String EDGE = "edge";
+ protected static final String GRAPHICS = "graphics";
+ protected static final String SOURCE = "source";
+ protected static final String TARGET = "target";
+
+ // The following elements are in "graphics" section of GML
+ protected static final String X = "x";
+ protected static final String Y = "y";
+ protected static final String H = "h";
+ protected static final String W = "w";
+ protected static final String TYPE = "type";
+
+ protected static final String ROOT_INDEX = "root_index";
+
+ // Shapes used in Cytoscape (not GML standard)
+ // In GML, they are called "type"
+ protected static final String RECTANGLE = "rectangle";
+ protected static final String ELLIPSE = "ellipse";
+ protected static final String LINE = "Line"; // This is the Polyline object.
+ // no support for now...
+ protected static final String POINT = "point";
+ protected static final String DIAMOND = "diamond";
+ protected static final String HEXAGON = "hexagon";
+ protected static final String OCTAGON = "octagon";
+ protected static final String PARALELLOGRAM = "parallelogram";
+ protected static final String TRIANGLE = "triangle";
+
+ // Other GML "graphics" attributes
+ protected static final String FILL = "fill";
+ protected static final String WIDTH = "width";
+ protected static final String STRAIGHT_LINES = "line";
+ protected static final String CURVED_LINES = "curved";
+ protected static final String SOURCE_ARROW = "source_arrow";
+ protected static final String TARGET_ARROW = "target_arrow";
+
+ // Support for yEd GML dialect
+ protected static final String YED_SOURCE_ARROW = "sourceArrow";
+ protected static final String YED_TARGET_ARROW = "targetArrow";
+ protected static final String YED_DELTA = "delta";
+ protected static final String YED_STANDARD = "standard";
+ protected static final String YED_DIAMOND = "diamond";
+ protected static final String YED_SHORT = "short";
+ protected static final String YED_WHITE_DELTA = "white_delta";
+ protected static final String YED_WHITE_DIAMOND = "white_diamond";
+
+ // States of the ends of arrows
+ protected static final String ARROW = "arrow";
+ protected static final String ARROW_NONE = "none";
+ protected static final String ARROW_FIRST = "first";
+ protected static final String ARROW_LAST = "last";
+ protected static final String ARROW_BOTH = "both";
+ protected static final String OUTLINE = "outline";
+ protected static final String OUTLINE_WIDTH = "outline_width";
+ protected static final String DEFAULT_EDGE_INTERACTION = "pp";
+
+ private static final String VIZMAP_PREFIX = "vizmap:";
+
+ private static final Color DEF_COLOR = new Color(153, 153, 255);
+
+ private String vsbSwitch = CytoscapeInit.getProperties().getProperty(
+ "visualStyleBuilder");
+ private VisualStyleBuilder graphStyle = null;
+
+ private static CyLogger logger = CyLogger.getLogger(GMLReader.class);
+
+ // Entries in the file
+ private List<KeyValue> keyVals;
+
+ // Node ID's
+ OpenIntIntHashMap nodeIDMap;
+ IntArrayList nodes;
+ IntArrayList sources;
+ IntArrayList targets;
+
+ private List<String> nodeLabels;
+ private List<String> edgeLabels;
+
+ // Storage for CyAttributes
+ private List<Map<String, Object>> nodeAttributes;
+ private List<Map<String, Object>> edgeAttributes;
+
+ Vector edge_root_index_pairs;
+ Vector node_root_index_pairs;
+
+ private List<String> edgeNames;
+ private List<String> nodeNames;
+
+ IntArrayList giny_nodes;
+ IntArrayList giny_edges;
+ private TaskMonitor taskMonitor;
+ private PercentUtil percentUtil;
+
+ // Name for the new visual style
+ private String styleName;
+
+ // Hashes for node & edge attributes
+ HashMap nodeW;
+
+ // Hashes for node & edge attributes
+ HashMap nodeH;
+ // Hashes for node & edge attributes
+ HashMap<String, NodeShape> nodeShape;
+
+ // Hashes for node & edge attributes
+ HashMap nodeCol;
+ // Hashes for node & edge attributes
+ HashMap<String, Double> nodeBWidth;
+
+ // Hashes for node & edge attributes
+ HashMap nodeBCol;
+ HashMap edgeCol;
+ HashMap<String, Float> edgeWidth;
+ HashMap<String, String> edgeArrow;
+ HashMap edgeShape;
+
+ // The InputStream
+ InputStream inputStream = null;
+
+ /**
+ * Constructor.
+ *
+ * @param filename
+ * File name.
+ */
+ public GMLReader(final String filename) {
+ this(filename, null);
+ }
+
+ /**
+ * Constructor.<br>
+ * This is usually used for remote file loading.
+ *
+ * @param is
+ * Input stream of GML file,
+ *
+ */
+ public GMLReader(final InputStream is, final String name) {
+ super(name);
+
+ // Set new style name
+ styleName = createVSName();
+ initializeHash();
+ initStyle();
+
+ this.inputStream = is;
+ }
+
+ /**
+ * Constructor.
+ *
+ * @param filename
+ * File name.
+ * @param taskMonitor
+ * TaskMonitor Object.
+ */
+ public GMLReader(final String filename, final TaskMonitor taskMonitor) {
+ super(filename);
+ inputStream = FileUtil.getInputStream(filename);
+
+ // Set new style name
+ styleName = createVSName();
+ initializeHash();
+ initStyle();
+
+ if (taskMonitor != null) {
+ this.taskMonitor = taskMonitor;
+ percentUtil = new PercentUtil(5);
+ }
+ }
+
+ /**
+ * Sets the task monitor we want to use
+ *
+ * @param monitor
+ * the TaskMonitor to use
+ */
+ public void setTaskMonitor(TaskMonitor monitor) {
+ this.taskMonitor = monitor;
+ percentUtil = new PercentUtil(3);
+ }
+
+ private String createVSName() {
+ return getNetworkName();
+ }
+
+ private void initializeHash() {
+ edgeNames = new ArrayList<String>();
+ nodeNames = new ArrayList<String>();
+ nodeAttributes = new ArrayList<Map<String, Object>>();
+ edgeAttributes = new ArrayList<Map<String, Object>>();
+ }
+
+ // Initialize variables for the new style created from GML
+ private void initStyle() {
+ graphStyle = new VisualStyleBuilder(styleName, false);
+ graphStyle.setNodeSizeLocked(false);
+ }
+
+ /**
+ * Read GML file contents
+ */
+ public void read() {
+ try {
+ try {
+ keyVals = (new GMLParser(inputStream)).parseList();
+ } finally {
+ if (inputStream != null) {
+ inputStream.close();
+ }
+ }
+ } catch (Exception io) {
+ logger.warn("Error reading GML file: " + io.getMessage(), io);
+
+ if (taskMonitor != null)
+ taskMonitor.setException(io, io.getMessage());
+
+ throw new RuntimeException(io.getMessage());
+ }
+
+ initializeStructures();
+
+ readGML(keyVals); // read the GML file
+ createGraph(); // create the graph AND new visual style
+
+ //
+ // New features are called here:
+ // 1 Extract (virtually) all attributes from the GML file
+ // 2 Generate new VS
+ // 3 Apply the new VS to the current window of Cytoscape
+ //
+ extract();
+
+ releaseStructures();
+ }
+
+ /**
+ * Returns a list containing the gml object tree
+ */
+ public List<KeyValue> getList() {
+ return keyVals;
+ }
+
+ protected void initializeStructures() {
+ title = null;
+ nodes = new IntArrayList();
+ sources = new IntArrayList();
+ targets = new IntArrayList();
+ nodeLabels = new ArrayList<String>();
+ edgeLabels = new ArrayList<String>();
+ edge_root_index_pairs = new Vector();
+ node_root_index_pairs = new Vector();
+ }
+
+ protected void releaseStructures() {
+ nodes = null;
+ sources = null;
+ targets = null;
+ nodeLabels = null;
+ edgeLabels = null;
+ edge_root_index_pairs = null;
+ node_root_index_pairs = null;
+ }
+
+ private void mapAttributes(final GraphObject obj,
+ final CyAttributes attrs, final Map<String, Object> attrMap) {
+
+ for (String attrName : attrMap.keySet()) {
+ final Object attrVal = attrMap.get(attrName);
+ if (attrVal == null)
+ continue;
+
+ try {
+ if (attrVal instanceof Double) {
+ attrs.setAttribute(obj.getIdentifier(), attrName,
+ (Double) attrVal);
+ } else if (attrVal instanceof Integer) {
+ attrs.setAttribute(obj.getIdentifier(), attrName,
+ (Integer) attrVal);
+ } else {
+ attrs.setAttribute(obj.getIdentifier(), attrName,
+ attrVal.toString());
+ }
+ } catch (IllegalArgumentException e) {
+ continue;
+ }
+
+ }
+ }
+
+ /**
+ * This will create the graph model objects. This function expects node
+ * labels to be unique and edge labels to be unique between a particular
+ * source and target If this condition is not met, an error will be printed
+ * to the console, and the object will be skipped. That is, it is as though
+ * that particular object never existed in the gml file. If an edge depends
+ * on a node that was skipped, then that edge will be skipped as well.
+ */
+ protected void createGraph() {
+ Cytoscape.ensureCapacity(nodes.size(), sources.size());
+ nodeIDMap = new OpenIntIntHashMap(nodes.size());
+ giny_nodes = new IntArrayList(nodes.size());
+
+ OpenIntIntHashMap gml_id2order = new OpenIntIntHashMap(nodes.size());
+ Set<String> nodeNameSet = new HashSet<String>(nodes.size());
+
+ final CyAttributes nodeAttr = Cytoscape.getNodeAttributes();
+
+ // Add All Nodes to Network
+ for (int idx = 0; idx < nodes.size(); idx++) {
+ // Report Status Value
+ if (taskMonitor != null)
+ taskMonitor.setPercentCompleted(percentUtil.getGlobalPercent(2,
+ idx, nodes.size()));
+
+ final String label = nodeLabels.get(idx);
+
+ Node node;
+
+ if (nodeNameSet.add(label)) {
+ node = Cytoscape.getCyNode(label, true);
+ if (nodeLabels.get(idx) != null)
+ nodeAttr.setAttribute(node.getIdentifier(), LABEL,
+ nodeLabels.get(idx));
+ if (nodeNames.get(idx) != null)
+ nodeAttr.setAttribute(node.getIdentifier(), NAME, nodeNames
+ .get(idx));
+
+ // Map attributes
+ mapAttributes(node, nodeAttr, nodeAttributes.get(idx));
+
+ giny_nodes.add(node.getRootGraphIndex());
+ nodeIDMap.put(nodes.get(idx), node.getRootGraphIndex());
+ gml_id2order.put(nodes.get(idx), idx);
+ ((KeyValue) node_root_index_pairs.get(idx)).value = (new Integer(
+ node.getRootGraphIndex()));
+ } else {
+ throw new GMLException("GML id " + nodes.get(idx)
+ + " has a duplicated ID: " + label);
+ }
+ }
+
+ nodeNameSet = null;
+
+ giny_edges = new IntArrayList(sources.size());
+
+ Set edgeNameSet = new HashSet(sources.size());
+
+ final CyAttributes edgeAttr = Cytoscape.getEdgeAttributes();
+
+ // Add All Edges to Network
+ for (int idx = 0; idx < sources.size(); idx++) {
+ // Report Status Value
+ if (taskMonitor != null) {
+ taskMonitor.setPercentCompleted(percentUtil.getGlobalPercent(3,
+ idx, sources.size()));
+ }
+
+ if (gml_id2order.containsKey(sources.get(idx))
+ && gml_id2order.containsKey(targets.get(idx))) {
+ String label = (String) edgeLabels.get(idx);
+ String sourceName = (String) nodeLabels.get(gml_id2order
+ .get(sources.get(idx)));
+ String targetName = (String) nodeLabels.get(gml_id2order
+ .get(targets.get(idx)));
+ String edgeName = CyEdge.createIdentifier(sourceName, label,
+ targetName);
+
+ int duplicate_count = 1;
+
+ while (!edgeNameSet.add(edgeName)) {
+ edgeName = CyEdge.createIdentifier(sourceName, label,
+ targetName)
+ + "_" + duplicate_count;
+
+ duplicate_count += 1;
+ }
+
+ // String tempstr = "E name is :" + idx + "==" + edgeName;
+ edgeNames.add(idx, edgeName);
+
+ Edge edge = Cytoscape.getRootGraph().getEdge(edgeName);
+
+ if (edge == null) {
+ Node node_1 = Cytoscape.getCyNode(sourceName);
+ Node node_2 = Cytoscape.getCyNode(targetName);
+ // edge = (Edge) rootGraph.getEdge
+ // (rootGraph.createEdge(node_1, node_2));
+ edge = Cytoscape.getCyEdge(node_1, node_2,
+ Semantics.INTERACTION, label, true, true);
+ }
+
+ // Set correct ID, canonical name and interaction name
+ edge.setIdentifier(edgeName);
+ edgeAttr.setAttribute(edgeName, Semantics.INTERACTION, label);
+ mapAttributes(edge, edgeAttr, edgeAttributes.get(idx));
+
+ giny_edges.add(edge.getRootGraphIndex());
+ ((KeyValue) edge_root_index_pairs.get(idx)).value = (new Integer(
+ edge.getRootGraphIndex()));
+ } else {
+ throw new GMLException(
+ "Non-existant source/target node for edge with gml (source,target): "
+ + sources.get(idx) + "," + targets.get(idx));
+ }
+ }
+
+ edgeNameSet = null;
+ }
+
+ /**
+ * This function takes the root level list which defines a gml objec tree
+ */
+ @SuppressWarnings("unchecked")
+ protected void readGML(final List<KeyValue> list) {
+ // Report Progress Message
+ int counter = 0;
+ final int size = list.size();
+
+ for (KeyValue keyVal : list) {
+ // Report Progress Value
+ if (taskMonitor != null) {
+ taskMonitor.setPercentCompleted(percentUtil.getGlobalPercent(1,
+ counter, size));
+ counter++;
+ }
+
+ if (keyVal.key.equals(GRAPH))
+ readGraph((List<KeyValue>) keyVal.value);
+
+ if (keyVal.key.equals(TITLE))
+ title = (String)keyVal.value;
+ }
+ }
+
+ /**
+ * This function takes in a list which was given as the value to a "graph"
+ * key underneath the main gml list
+ */
+ @SuppressWarnings("unchecked")
+ protected void readGraph(final List<KeyValue> list) {
+ for (KeyValue keyVal : list) {
+ if (keyVal.key.equals(NODE))
+ readNode((List<KeyValue>) keyVal.value);
+
+ if (keyVal.key.equals(EDGE))
+ readEdge((List<KeyValue>) keyVal.value);
+ }
+ }
+
+ /**
+ * This will extract the model information from the list which is matched a
+ * "node" key
+ */
+ private void readNode(final List<KeyValue> list) {
+ String label = "";
+ String name = null;
+ final Map<String, Object> attr = new HashMap<String, Object>();
+
+ boolean contains_id = false;
+ int id = 0;
+ KeyValue root_index_pair = null;
+
+ for (final KeyValue keyVal : list) {
+ if (keyVal.key.equals(ID)) {
+ contains_id = true;
+ id = (Integer) keyVal.value;
+ } else if (keyVal.key.equals(LABEL)) {
+ label = keyVal.value.toString();
+ } else if (keyVal.key.equals(NAME)) {
+ name = keyVal.value.toString();
+ } else if (keyVal.key.equals(ROOT_INDEX)) {
+ root_index_pair = keyVal;
+ } else if (!keyVal.key.equals(GRAPHICS) && !keyVal.key.startsWith(VIZMAP_PREFIX)) {
+ // This is a regular attribute value
+ attr.put(keyVal.key, keyVal.value);
+ }
+ }
+
+ if (label.equals("") || label.matches("\\s+")) {
+ label = String.valueOf(id);
+ }
+
+ if (root_index_pair == null) {
+ root_index_pair = new KeyValue(ROOT_INDEX, null);
+ list.add(root_index_pair);
+ }
+
+ if (!contains_id) {
+ final StringWriter stringWriter = new StringWriter();
+
+ try {
+ GMLParser.printList(list, stringWriter);
+ } catch (Exception e) {
+ throw new RuntimeException(e.getMessage());
+ }
+
+ throw new GMLException("The node-associated list\n" + stringWriter
+ + "is missing an id field");
+ } else {
+ node_root_index_pairs.add(root_index_pair);
+ nodes.add(id);
+ nodeLabels.add(label);
+ nodeNames.add(name);
+
+ nodeAttributes.add(attr);
+ }
+ }
+
+ /**
+ * This will extract the model information from the list which is matched to
+ * an "edge" key.
+ */
+ protected void readEdge(final List<KeyValue> list) {
+ String label = DEFAULT_EDGE_INTERACTION;
+ boolean contains_source = false;
+ boolean contains_target = false;
+ int source = 0;
+ int target = 0;
+ KeyValue root_index_pair = null;
+ final Map<String, Object> attr = new HashMap<String, Object>();
+
+ for (final KeyValue keyVal: list) {
+ if (keyVal.key.equals(SOURCE)) {
+ contains_source = true;
+ source = ((Integer) keyVal.value).intValue();
+ } else if (keyVal.key.equals(TARGET)) {
+ contains_target = true;
+ target = ((Integer) keyVal.value).intValue();
+ } else if (keyVal.key.equals(LABEL)) {
+ label = (String) keyVal.value;
+ } else if (keyVal.key.equals(ROOT_INDEX)) {
+ root_index_pair = keyVal;
+ } else if (!keyVal.key.equals(GRAPHICS) && !keyVal.key.startsWith(VIZMAP_PREFIX)) {
+ attr.put(keyVal.key, keyVal.value);
+ }
+ }
+
+ if (root_index_pair == null) {
+ root_index_pair = new KeyValue(ROOT_INDEX, null);
+ list.add(root_index_pair);
+ }
+
+ if (!contains_source || !contains_target) {
+ StringWriter stringWriter = new StringWriter();
+
+ try {
+ GMLParser.printList(list, stringWriter);
+ } catch (Exception e) {
+ throw new RuntimeException(e.getMessage());
+ }
+
+ throw new GMLException("The edge-associated list\n" + stringWriter
+ + " is missing a source or target key");
+ } else {
+ sources.add(source);
+ targets.add(target);
+
+ edgeLabels.add(label);
+ edge_root_index_pairs.add(root_index_pair);
+
+ edgeAttributes.add(attr);
+ }
+ }
+
+ /**
+ * getLayoutAlgorithm is called to get the Layout Algorithm that will be
+ * used to layout the resulting graph. In our case, we just return a stub
+ * that will call our internal layout routine, which will just use the
+ * default layout, but with our task monitor
+ *
+ * @return the CyLayoutAlgorithm to use
+ */
+ public CyLayoutAlgorithm getLayoutAlgorithm() {
+ return new LayoutAdapter() {
+ public void doLayout(CyNetworkView networkView, TaskMonitor monitor) {
+ layout(networkView);
+ }
+ };
+ }
+
+ /**
+ * layout the graph based on the GML values we read
+ *
+ * @param myView
+ * the view of the network we want to layout
+ */
+ public void layout(CyNetworkView myView) {
+ if ((myView == null) || (myView.nodeCount() == 0)) {
+ return;
+ }
+
+ if (keyVals == null) {
+ throw new RuntimeException(
+ "Failed to read gml file on initialization");
+ }
+
+ for (Iterator it = keyVals.iterator(); it.hasNext();) {
+ KeyValue keyVal = (KeyValue) it.next();
+
+ if (keyVal.key.equals(GRAPH)) {
+ layoutGraph(myView, (List) keyVal.value);
+ }
+ }
+ }
+
+ //
+ /**
+ * DOCUMENT ME!
+ */
+ public void extract() {
+ if (keyVals == null) {
+ throw new RuntimeException(
+ "Failed to read gml file on initialization");
+ }
+
+ for (Iterator it = keyVals.iterator(); it.hasNext();) {
+ KeyValue keyVal = (KeyValue) it.next();
+
+ if (keyVal.key.equals(GRAPH)) {
+ extractGraph((List) keyVal.value);
+ }
+ }
+ }
+
+ protected void extractGraph(List list) {
+ String edgeName = null;
+
+ // Count the current edge
+ int ePtr = 0;
+
+ for (Iterator it = list.iterator(); it.hasNext();) {
+ final KeyValue keyVal = (KeyValue) it.next();
+
+ if (keyVal.key.equals(NODE)) {
+ extractNode((List) keyVal.value);
+ } else if (keyVal.key.equals(EDGE)) {
+ edgeName = (String) edgeNames.get(ePtr);
+ ePtr++;
+ extractEdge((List) keyVal.value, edgeName);
+ }
+ }
+ }
+
+ protected void extractNode(List list) {
+ List graphics_list = null;
+ String label = null;
+
+ int tempid = 0;
+
+ for (Iterator it = list.iterator(); it.hasNext();) {
+ KeyValue keyVal = (KeyValue) it.next();
+
+ if (keyVal.key.equals(ROOT_INDEX)) {
+ if (keyVal.value == null) {
+ return;
+ }
+ } else if (keyVal.key.equals(GRAPHICS)) {
+ graphics_list = (List) keyVal.value;
+ } else if (keyVal.key.equals(LABEL)) {
+ label = (String) keyVal.value;
+ } else if (keyVal.key.equals(ID)) {
+ tempid = ((Integer) keyVal.value).intValue();
+ }
+ }
+
+ if (graphics_list != null) {
+ if (label == null) {
+ label = "node" + tempid;
+ logger.info("Warning: node label is missing for node ID: "
+ + tempid);
+ }
+
+ extractNodeAttributes(graphics_list, label);
+ }
+ }
+
+ protected void extractEdge(List<KeyValue> list, String edgeName) {
+ List graphics_list = null;
+
+ for (KeyValue keyVal : list) {
+ if (keyVal.key.equals(ROOT_INDEX)) {
+ if (keyVal.value == null) {
+ return;
+ }
+ } else if (keyVal.key.equals(GRAPHICS)) {
+ graphics_list = (List) keyVal.value;
+ }
+ }
+
+ if (graphics_list != null)
+ extractEdgeAttributes(graphics_list, edgeName);
+ }
+
+ /**
+ * Lays Out the Graph, based on GML.
+ */
+ protected void layoutGraph(final GraphView myView, List list) {
+ String edgeName = null;
+
+ // Count the current edge
+ int ePtr = 0;
+
+ for (Iterator it = list.iterator(); it.hasNext();) {
+ final KeyValue keyVal = (KeyValue) it.next();
+
+ if (keyVal.key.equals(NODE))
+ layoutNode(myView, (List) keyVal.value);
+ }
+ }
+
+ /**
+ * Assign node properties based on the values in the list matched to the
+ * "node" key. Mostly just a wrapper around layoutNodeGraphics
+ */
+ protected void layoutNode(GraphView myView, List list) {
+ Integer root_index = null;
+ List graphics_list = null;
+ String label = null;
+ int tempid = 0;
+
+ NodeView view = null;
+
+ for (Iterator it = list.iterator(); it.hasNext();) {
+ KeyValue keyVal = (KeyValue) it.next();
+
+ if (keyVal.key.equals(ROOT_INDEX)) {
+ /*
+ * For some reason we didn't make an object for this node give
+ * up now
+ */
+ if (keyVal.value == null) {
+ return;
+ }
+
+ root_index = (Integer) keyVal.value;
+ } else if (keyVal.key.equals(GRAPHICS)) {
+ graphics_list = (List) keyVal.value;
+ } else if (keyVal.key.equals(LABEL)) {
+ label = (String) keyVal.value;
+ } else if (keyVal.key.equals(ID)) {
+ tempid = ((Integer) keyVal.value).intValue();
+ }
+ }
+
+ // logger.info( "In layout, Root index is: " + root_index );
+ // logger.info( " Checking label: " + label );
+ view = myView.getNodeView(root_index.intValue());
+
+ if (label != null) {
+ view.getLabel().setText(label);
+ } else {
+ view.getLabel().setText("node(" + tempid + ")");
+ }
+
+ if (graphics_list != null)
+ layoutNodeGraphics(myView, graphics_list, view);
+ }
+
+ /**
+ * This will assign node graphic properties based on the values in the list
+ * matches to the "graphics" key word
+ */
+ protected void layoutNodeGraphics(GraphView myView, List list,
+ NodeView nodeView) {
+ for (Iterator it = list.iterator(); it.hasNext();) {
+ KeyValue keyVal = (KeyValue) it.next();
+
+ if (keyVal.key.equals(X)) {
+ nodeView.setXPosition(((Number) keyVal.value).doubleValue());
+ } else if (keyVal.key.equals(Y)) {
+ nodeView.setYPosition(((Number) keyVal.value).doubleValue());
+ } else if (keyVal.key.equals(H)) {
+ nodeView.setHeight(((Number) keyVal.value).doubleValue());
+ } else if (keyVal.key.equals(W)) {
+ nodeView.setWidth(((Number) keyVal.value).doubleValue());
+ } else if (keyVal.key.equals(FILL)) {
+ nodeView.setUnselectedPaint(getColor((String) keyVal.value));
+ } else if (keyVal.key.equals(OUTLINE)) {
+ nodeView.setBorderPaint(getColor((String) keyVal.value));
+ } else if (keyVal.key.equals(OUTLINE_WIDTH)) {
+ nodeView.setBorderWidth(((Number) keyVal.value).floatValue());
+ } else if (keyVal.key.equals(TYPE)) {
+ String type = (String) keyVal.value;
+
+ if (type.equals(ELLIPSE)) {
+ nodeView.setShape(NodeView.ELLIPSE);
+ } else if (type.equals(RECTANGLE)) {
+ nodeView.setShape(NodeView.RECTANGLE);
+ } else if (type.equals(DIAMOND)) {
+ nodeView.setShape(NodeView.DIAMOND);
+ } else if (type.equals(HEXAGON)) {
+ nodeView.setShape(NodeView.HEXAGON);
+ } else if (type.equals(OCTAGON)) {
+ nodeView.setShape(NodeView.OCTAGON);
+ } else if (type.equals(PARALELLOGRAM)) {
+ nodeView.setShape(NodeView.PARALELLOGRAM);
+ } else if (type.equals(TRIANGLE)) {
+ nodeView.setShape(NodeView.TRIANGLE);
+ }
+ }
+ }
+ }
+
+ //
+ // Extract node attributes from GML file
+ protected void extractNodeAttributes(List list, String nodeName) {
+ // Put all attributes into hashes.
+ // Key is the node name
+ // (Assume we do not have duplicate node name.)
+ for (Iterator it = list.iterator(); it.hasNext();) {
+ KeyValue keyVal = (KeyValue) it.next();
+
+ if (keyVal.key.equals(X) || keyVal.key.equals(Y)) {
+ // Do nothing.
+ } else if (keyVal.key.equals(H)) {
+ graphStyle.addProperty(nodeName,
+ VisualPropertyType.NODE_HEIGHT, "" + keyVal.value);
+ } else if (keyVal.key.equals(W)) {
+ graphStyle.addProperty(nodeName, VisualPropertyType.NODE_WIDTH,
+ "" + keyVal.value);
+ } else if (keyVal.key.equals(FILL)) {
+ graphStyle.addProperty(nodeName,
+ VisualPropertyType.NODE_FILL_COLOR, "" + keyVal.value);
+ } else if (keyVal.key.equals(OUTLINE)) {
+ graphStyle
+ .addProperty(nodeName,
+ VisualPropertyType.NODE_BORDER_COLOR, ""
+ + keyVal.value);
+ } else if (keyVal.key.equals(WIDTH)) {
+ graphStyle.addProperty(nodeName,
+ VisualPropertyType.NODE_LINE_WIDTH, "" + keyVal.value);
+ } else if (keyVal.key.equals(TYPE)) {
+ String type = (String) keyVal.value;
+ graphStyle.addProperty(nodeName, VisualPropertyType.NODE_SHAPE,
+ type);
+ }
+ }
+ }
+
+ //
+ // Extract edge attributes from GML input
+ //
+ protected void extractEdgeAttributes(List<KeyValue> list, String edgeName) {
+ String value = null;
+
+ boolean isArrow = false;
+ String edgeFill = DEF_COLOR.toString();
+ String arrowShape = ARROW_NONE;
+
+ for (KeyValue keyVal : list) {
+ if (keyVal.key.equals(LINE)) {
+ // This represents "Polyline," which is a line (usually an edge)
+ // with arbitrary number of anchors.
+ // Current version of CS does not support this, so ignore this
+ // at this point of time...
+ } else if (keyVal.key.equals(WIDTH)) {
+ graphStyle.addProperty(edgeName,
+ VisualPropertyType.EDGE_LINE_WIDTH, new String(
+ keyVal.value.toString()));
+ } else if (keyVal.key.equals(FILL)) {
+ graphStyle.addProperty(edgeName, VisualPropertyType.EDGE_COLOR,
+ new String(keyVal.value.toString()));
+ edgeFill = keyVal.value.toString();
+ } else if (keyVal.key.equals(ARROW)) {
+ isArrow = true;
+
+ ArrowShape shape = ArrowShape.ARROW;
+ String arrowName = shape.getName();
+
+ if (keyVal.value.toString().equalsIgnoreCase(ARROW_FIRST)) {
+ arrowShape = ARROW_FIRST;
+ graphStyle.addProperty(edgeName,
+ VisualPropertyType.EDGE_SRCARROW_SHAPE, arrowName);
+ } else if (keyVal.value.toString().equalsIgnoreCase(ARROW_LAST)) {
+ arrowShape = ARROW_LAST;
+ graphStyle.addProperty(edgeName,
+ VisualPropertyType.EDGE_TGTARROW_SHAPE, arrowName);
+ } else if (keyVal.value.toString().equalsIgnoreCase(ARROW_BOTH)) {
+ arrowShape = ARROW_BOTH;
+ graphStyle.addProperty(edgeName,
+ VisualPropertyType.EDGE_SRCARROW_SHAPE, arrowName);
+ graphStyle.addProperty(edgeName,
+ VisualPropertyType.EDGE_TGTARROW_SHAPE, arrowName);
+ }
+ } else if (keyVal.key.equals(TYPE)) {
+ value = (String) keyVal.value;
+
+ if (value.equals(STRAIGHT_LINES)) {
+ // edgeShape.put(edgeName, (String) keyVal.value);
+ } else if (value.equals(CURVED_LINES)) {
+ // edgeView.setLineType(EdgeView.CURVED_LINES);
+ }
+ } else if (keyVal.key.equals(SOURCE_ARROW)) {
+ graphStyle.addProperty(edgeName,
+ VisualPropertyType.EDGE_SRCARROW_SHAPE, ArrowShape
+ .getArrowShape(
+ ((Number) keyVal.value).intValue())
+ .getName());
+ graphStyle.addProperty(edgeName,
+ VisualPropertyType.EDGE_SRCARROW_COLOR, edgeFill);
+ } else if (keyVal.key.equals(TARGET_ARROW)) {
+ graphStyle.addProperty(edgeName,
+ VisualPropertyType.EDGE_TGTARROW_SHAPE, ArrowShape
+ .getArrowShape(
+ ((Number) keyVal.value).intValue())
+ .getName());
+ graphStyle.addProperty(edgeName,
+ VisualPropertyType.EDGE_TGTARROW_COLOR, edgeFill);
+ } else if (keyVal.key.equals(YED_SOURCE_ARROW)) {
+ graphStyle.addProperty(edgeName,
+ VisualPropertyType.EDGE_SRCARROW_SHAPE,
+ convertYEDArrowShape(keyVal.value.toString()));
+ graphStyle.addProperty(edgeName,
+ VisualPropertyType.EDGE_SRCARROW_COLOR, edgeFill);
+ } else if (keyVal.key.equals(YED_TARGET_ARROW)) {
+ graphStyle.addProperty(edgeName,
+ VisualPropertyType.EDGE_TGTARROW_SHAPE,
+ convertYEDArrowShape(keyVal.value.toString()));
+ graphStyle.addProperty(edgeName,
+ VisualPropertyType.EDGE_TGTARROW_COLOR, edgeFill);
+ }
+ }
+
+ // make the arrow color the same as edge
+ if (isArrow) {
+ if (arrowShape.equals(ARROW_FIRST)) {
+ graphStyle.addProperty(edgeName,
+ VisualPropertyType.EDGE_SRCARROW_COLOR, edgeFill);
+ } else if (arrowShape.equals(ARROW_LAST)) {
+ graphStyle.addProperty(edgeName,
+ VisualPropertyType.EDGE_TGTARROW_COLOR, edgeFill);
+ } else if (arrowShape.equals(ARROW_BOTH)) {
+ graphStyle.addProperty(edgeName,
+ VisualPropertyType.EDGE_SRCARROW_COLOR, edgeFill);
+ graphStyle.addProperty(edgeName,
+ VisualPropertyType.EDGE_TGTARROW_COLOR, edgeFill);
+ }
+ }
+ }
+
+ private String convertYEDArrowShape(String yedArrow) {
+ String shape = ArrowShape.NONE.getName();
+
+ if (yedArrow.equals(YED_DELTA) || yedArrow.equals(YED_WHITE_DELTA))
+ shape = ArrowShape.DELTA.getName();
+ else if (yedArrow.equals(YED_DIAMOND)
+ || yedArrow.equals(YED_WHITE_DIAMOND))
+ shape = ArrowShape.DIAMOND.getName();
+ else if (yedArrow.equals(YED_STANDARD) || yedArrow.equals(YED_SHORT))
+ shape = ArrowShape.ARROW.getName();
+
+ return shape;
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void showMaps() {
+ String e = null;
+ String n = null;
+ String temp = null;
+
+ for (int i = 0; i < edgeNames.size(); i++) {
+ e = (String) edgeNames.get(i);
+ temp = e + ": ";
+ temp = temp + edgeCol.get(e) + ", ";
+ temp = temp + edgeWidth.get(e) + ", ";
+ temp = temp + edgeArrow.get(e) + ", ";
+ temp = temp + edgeShape.get(e) + ", ";
+ logger.info(temp);
+ temp = null;
+ }
+ }
+
+ /**
+ * Assign edge visual properties based on pairs in the list matched to the
+ * "edge" key world
+ */
+ protected void layoutEdge(GraphView myView, List list, String edgeName) {
+ EdgeView edgeView = null;
+ List graphics_list = null;
+
+ for (Iterator it = list.iterator(); it.hasNext();) {
+ KeyValue keyVal = (KeyValue) it.next();
+
+ if (keyVal.key.equals(ROOT_INDEX)) {
+ /*
+ * Previously, we didn't make an object for this edge for some
+ * reason. Don't try to go any further.
+ */
+ if (keyVal.value == null) {
+ return;
+ }
+
+ edgeView = myView.getEdgeView(((Integer) keyVal.value)
+ .intValue());
+ } else if (keyVal.key.equals(GRAPHICS)) {
+ graphics_list = (List) keyVal.value;
+ }
+ }
+
+ if ((edgeView != null) && (graphics_list != null))
+ layoutEdgeGraphics(myView, graphics_list, edgeView);
+ }
+
+ /**
+ * Assign edge graphics properties
+ */
+ protected void layoutEdgeGraphics(GraphView myView, List<KeyValue> list,
+ EdgeView edgeView) {
+ // Local vars.
+ String value = null;
+
+ // KeyValue keyVal = null;
+ for (KeyValue keyVal : list) {
+ // This is a polyline obj. However, it will be translated into
+ // straight line.
+ if (keyVal.key.equals(LINE)) {
+ layoutEdgeGraphicsLine(myView, (List) keyVal.value, edgeView);
+ } else if (keyVal.key.equals(WIDTH)) {
+ edgeView.setStrokeWidth(((Number) keyVal.value).floatValue());
+ } else if (keyVal.key.equals(FILL)) {
+ edgeView.setUnselectedPaint(getColor((String) keyVal.value));
+ } else if (keyVal.key.equals(TYPE)) {
+ value = (String) keyVal.value;
+
+ if (value.equals(STRAIGHT_LINES)) {
+ edgeView.setLineType(EdgeView.STRAIGHT_LINES);
+ } else if (value.equals(CURVED_LINES)) {
+ edgeView.setLineType(EdgeView.CURVED_LINES);
+ }
+ } else if (keyVal.key.equals(ARROW)) {
+ // The position of the arrow.
+ // There are 4 states: no arrows, both ends have arrows, source,
+ // or target.
+ //
+ // The arrow type below is hard-coded since GML does not
+ // support shape of the arrow.
+ if (keyVal.value.equals(ARROW_FIRST)) {
+ edgeView.setSourceEdgeEnd(2);
+ } else if (keyVal.value.equals(ARROW_LAST)) {
+ edgeView.setTargetEdgeEnd(2);
+ } else if (keyVal.value.equals(ARROW_BOTH)) {
+ edgeView.setSourceEdgeEnd(2);
+ edgeView.setTargetEdgeEnd(2);
+ } else if (keyVal.value.equals(ARROW_NONE)) {
+ // Do nothing. No arrows.
+ }
+ } else if (keyVal.key.equals(SOURCE_ARROW)) {
+ edgeView.setSourceEdgeEnd(((Number) keyVal.value).intValue());
+ } else if (keyVal.key.equals(TARGET_ARROW)) {
+ edgeView.setTargetEdgeEnd(((Number) keyVal.value).intValue());
+ }
+ }
+ }
+
+ /**
+ * Assign bend points based on the contents of the list associated with a
+ * "Line" key We make sure that there is both an x,y present in the
+ * underlying point list before trying to generate a bend point
+ */
+ protected void layoutEdgeGraphicsLine(GraphView myView, List list,
+ EdgeView edgeView) {
+ for (Iterator it = list.iterator(); it.hasNext();) {
+ KeyValue keyVal = (KeyValue) it.next();
+
+ if (keyVal.key.equals(POINT)) {
+ Number x = null;
+ Number y = null;
+
+ for (Iterator pointIt = ((List) keyVal.value).iterator(); pointIt
+ .hasNext();) {
+ KeyValue pointVal = (KeyValue) pointIt.next();
+
+ if (pointVal.key.equals(X)) {
+ x = (Number) pointVal.value;
+ } else if (pointVal.key.equals(Y)) {
+ y = (Number) pointVal.value;
+ }
+ }
+
+ if (!((x == null) || (y == null))) {
+ Point2D.Double pt = new Point2D.Double(x.doubleValue(), y
+ .doubleValue());
+ edgeView.getBend().addHandle(pt);
+ }
+ }
+ }
+ }
+
+ /**
+ * Part of interface contract
+ */
+ public int[] getNodeIndicesArray() {
+ giny_nodes.trimToSize();
+
+ return giny_nodes.elements();
+ }
+
+ /**
+ * Part of interace contract
+ */
+ public int[] getEdgeIndicesArray() {
+ giny_edges.trimToSize();
+
+ return giny_edges.elements();
+ }
+
+ /**
+ * Create a color object from the string like it is stored in a gml file
+ */
+ public Color getColor(String colorString) {
+ return new Color(Integer.parseInt(colorString.substring(1), 16));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param net
+ * DOCUMENT ME!
+ */
+ public void doPostProcessing(final CyNetwork net) {
+
+ CyInitParams init = CytoscapeInit.getCyInitParams();
+
+ if (init == null)
+ return;
+
+ if ((init.getMode() == CyInitParams.GUI)
+ || (init.getMode() == CyInitParams.EMBEDDED_WINDOW)) {
+ if (!((vsbSwitch != null) && vsbSwitch.equals("off"))) {
+ graphStyle.buildStyle();
+ }
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/data/readers/GMLTag.java b/application/src/main/java/cytoscape/data/readers/GMLTag.java
new file mode 100644
index 0000000..fd4b5a2
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/readers/GMLTag.java
@@ -0,0 +1,91 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data.readers;
+
+public enum GMLTag {
+ GRAPH("graph"),
+ NODE("node"),
+ EDGE("edge"),
+ GRAPHICS("graphics"),
+ LABEL("label"),
+ SOURCE("source"),
+ TARGET("target"),
+ X("x"),
+ Y("y"),
+ H("h"),
+ W("w"),
+ TYPE("type"),
+ ID("id"),
+ ROOT_INDEX("root_index"),
+ RECTANGLE("rectangle"),
+ ELLIPSE("ellipse"),
+ LINE("line"),
+ POINT("point"),
+ DIAMOND("diamond"),
+ HEXAGON("hexagon"),
+ OCTAGON("octagon"),
+ PARALLELOGRAM("parallelogram"),
+ TRIANGLE("triangle"),
+ FILL("fill"),
+ WIDTH("width"),
+ STRAIGHT_LINES("line"),
+ CURVED_LINES("curved"),
+ SOURCE_ARROW("source_arrow"),
+ TARGET_ARROW("target_arrow"),
+ ARROW("arrow"),
+ ARROW_NONE("none"),
+ ARROW_FIRST("first"),
+ ARROW_LAST("last"),
+ ARROW_BOTH("both"),
+ OUTLINE("outline"),
+ OUTLINE_WIDTH("outline_width"),
+ VERSION("Version"),
+ CREATOR("Creator");
+
+ private String tag;
+
+ private GMLTag(String tag) {
+ this.tag = tag;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String toString() {
+ return tag;
+ }
+}
diff --git a/application/src/main/java/cytoscape/data/readers/GMLTree.java b/application/src/main/java/cytoscape/data/readers/GMLTree.java
new file mode 100644
index 0000000..a3e03ed
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/readers/GMLTree.java
@@ -0,0 +1,543 @@
+/*
+ File: GMLTree.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data.readers;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.data.CyAttributes;
+import cytoscape.data.Semantics;
+
+import cytoscape.logger.CyLogger;
+import cytoscape.view.CyNetworkView;
+
+import giny.model.Edge;
+import giny.model.Node;
+
+import giny.view.EdgeView;
+import giny.view.GraphView;
+import giny.view.NodeView;
+
+import java.awt.Color;
+import java.awt.geom.Point2D;
+
+import java.text.DecimalFormat;
+import java.text.DecimalFormatSymbols;
+import java.util.Locale;
+
+import java.util.Iterator;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.StringTokenizer;
+import java.util.Vector;
+
+
+/**
+ * This class wraps around GMLNode and provides various methods for constructing
+ * a tree structure given other data.
+ */
+public class GMLTree {
+ /**
+ * The root node for this graph
+ */
+ GMLNode root;
+
+ /**
+ * The version of the GMLSpec parsed here
+ */
+ private static String VERSION = "1.0";
+
+ /**
+ * The string used to open a GMLNode declaration
+ */
+ private static String NODE_OPEN = "[";
+
+ /**
+ * The string used to close a GMLNode declaration
+ */
+ private static String NODE_CLOSE = "]";
+
+ /**
+ * When getting a vector, used to specify the type for the contained objects
+ */
+ public static int STRING = 0;
+
+ /**
+ * When getting a vector, used to specify the type for the contained objects
+ */
+ public static int DOUBLE = 1;
+
+ /**
+ * When getting a vector, used to specify the type for the contained objects
+ */
+ public static int INTEGER = 2;
+
+ /**
+ * When getting a vector, used to specify the type for the contained objects
+ */
+ public static int GMLTREE = 3;
+
+ private static CyLogger logger = CyLogger.getLogger(GMLTree.class);
+
+ /**
+ * Create an empty GMLTree
+ */
+ public GMLTree() {
+ root = new GMLNode();
+ }
+
+ /**
+ * Creates a new GMLTree object.
+ *
+ * @param init DOCUMENT ME!
+ */
+ public GMLTree(GMLNode init) {
+ root = init;
+ }
+
+ /**
+ * Create a GMLTree from the information contained in this GraphView.
+ * Currently this only concerns itself with x,y position information.
+ *
+ * @param myView
+ * the GraphView used to create the GMLTree
+ */
+ public GMLTree(CyNetworkView networkView) {
+ // force the locale to US so that we consistently serialize things
+ DecimalFormat df = new DecimalFormat("####0.0#", new DecimalFormatSymbols(Locale.US));
+ GraphView myView = networkView.getView();
+
+ // networkView.getNetwork().getNodeAttributes();
+ CyAttributes nodeAttributes = Cytoscape.getNodeAttributes();
+
+ // create a new root
+ root = new GMLNode();
+ // add the base level mappings
+ root.addMapping("Creator", new GMLNode("\"Cytoscape\""));
+ root.addMapping("Version", new GMLNode(VERSION));
+
+ // create hte subnode which will hold the grpah information
+ GMLNode graph = new GMLNode();
+ root.addMapping("graph", graph);
+
+ // for each node, add a mapping to the graph GMLNode
+ Iterator viewIt = myView.getNodeViewsIterator();
+
+ // Currently supported GML fields for "node"
+ // "id" node ID (integer from getRootGraphIndex())
+ // "label" node label
+ // "graphics" specify the following
+ // "x", "y" node x,y locations
+ // "h", "w" node height/width
+ // "fill" node fill color
+ // "type" node shape {"rectangle", "oval"}
+ //
+ while (viewIt.hasNext()) {
+ NodeView currentView = (NodeView) viewIt.next();
+ Node currentNode = currentView.getNode();
+
+ // create a new GMLNode to hold information about currentNode
+ GMLNode currentGML = new GMLNode();
+ // add the information about currentNode
+ currentGML.addMapping("id", new GMLNode("" + (-currentNode.getRootGraphIndex())));
+
+ // String name =
+ // nodeAttributes.getCanonicalName(currentView.getNode());
+ String name = currentView.getNode().getIdentifier();
+
+ if (name == null) {
+ name = "unknown";
+ } // end of if ()
+
+ String label = "\"" + name + "\"";
+ // brackets are reserved characters, let's replace them with parens
+ label.replaceAll("\\" + NODE_CLOSE, ")");
+ label.replaceAll("\\" + NODE_OPEN, "(");
+ currentGML.addMapping("label", new GMLNode(label));
+
+ GMLNode graphics = new GMLNode();
+ graphics.addMapping("x", new GMLNode("" + df.format(currentView.getXPosition())));
+ graphics.addMapping("y", new GMLNode("" + df.format(currentView.getYPosition())));
+ graphics.addMapping("h", new GMLNode("" + df.format(currentView.getHeight())));
+ graphics.addMapping("w", new GMLNode("" + df.format(currentView.getWidth())));
+
+ Color nodeColor = (Color) currentView.getUnselectedPaint();
+ graphics.addMapping("fill", new GMLNode("\"" + getColorHexString(nodeColor) + "\""));
+
+ switch (currentView.getShape()) {
+ case NodeView.RECTANGLE:
+ graphics.addMapping("type", new GMLNode("\"rectangle\""));
+
+ break;
+
+ case NodeView.ELLIPSE:
+ graphics.addMapping("type", new GMLNode("\"oval\""));
+
+ break;
+ }
+
+ currentGML.addMapping("graphics", graphics);
+ graph.addMapping("node", currentGML);
+ }
+
+ // Currently supported GML fields for "edge"
+ // "source" node ID from getRootGraphIndex()
+ // "target" node ID from getRootGraphIndex()
+ // "label" edge label from edgeAttributes.getCanonicalName
+ // "graphics"
+ // "width" edge line width
+ // "type" currently only "line"
+ // "fill" edge color
+ viewIt = myView.getEdgeViewsIterator();
+
+ CyAttributes edgeAttributes = Cytoscape.getEdgeAttributes();
+
+ while (viewIt.hasNext()) {
+ EdgeView currentView = (EdgeView) viewIt.next();
+ Edge currentEdge = currentView.getEdge();
+
+ // crate a new GMLNode to hold information about currentEdge
+ GMLNode currentGML = new GMLNode();
+ // add the information about currentEdge
+ currentGML.addMapping("source",
+ new GMLNode("" + (-currentEdge.getSource().getRootGraphIndex())));
+ currentGML.addMapping("target",
+ new GMLNode("" + (-currentEdge.getTarget().getRootGraphIndex())));
+
+ // label is a little bit different because I need to look it up from
+ // edgeattributes
+ // String interaction = (String) edgeAttributes.get("interaction",
+ // edgeAttributes.getCanonicalName(currentEdge));
+ String interaction = edgeAttributes.getStringAttribute(currentEdge.getIdentifier(),
+ Semantics.INTERACTION);
+
+ if (interaction != null) {
+ currentGML.addMapping("label", new GMLNode("\"" + interaction + "\""));
+ }
+
+ GMLNode graphics = new GMLNode();
+ graphics.addMapping("width", new GMLNode("" + df.format(currentView.getStrokeWidth())));
+
+ switch (currentView.getLineType()) {
+ case EdgeView.STRAIGHT_LINES: {
+ graphics.addMapping("type", new GMLNode("\"line\""));
+
+ Point2D[] pointsArray = currentView.getBend().getDrawPoints();
+
+ if (pointsArray.length > 2) {
+ GMLNode Line = new GMLNode();
+
+ for (int i = 0; i < pointsArray.length; i++) {
+ GMLNode point = new GMLNode();
+ point.addMapping("x", new GMLNode("" + df.format(pointsArray[i].getX())));
+ point.addMapping("y", new GMLNode("" + df.format(pointsArray[i].getY())));
+ Line.addMapping("point", point);
+ }
+
+ graphics.addMapping("Line", Line);
+ }
+ }
+
+ break;
+
+ // case EdgeView.CURVED_LINES: { // not implemented
+ // graphics.addMapping("type",new GMLNode("\"polygon\"")); // type
+ // "polygon" for splines
+ // GMLNode curvedLine = new GMLNode();
+ // } break;
+ }
+
+ Color edgeColor = (Color) currentView.getUnselectedPaint();
+ graphics.addMapping("fill", new GMLNode("\"" + getColorHexString(edgeColor) + "\""));
+ currentGML.addMapping("graphics", graphics);
+ graph.addMapping("edge", currentGML);
+ }
+ }
+
+ /**
+ * Create a GMLTree from data contained in a file
+ *
+ * @param filename
+ * The name of the file used to create this GMLTree
+ */
+ public GMLTree(String filename) {
+ StringTokenizer quotes = null;
+
+ if (filename.startsWith("jar://")) { // in a startup jar file
+
+ try {
+ TextJarReader reader = new TextJarReader(filename);
+ reader.read();
+ quotes = new StringTokenizer(reader.getText(), "\"", true);
+ } catch (Exception e) {
+ logger.warn("Error reading GML network from '"+filename+"': "+e.getMessage(),e);
+
+ return;
+ }
+ } else {
+ TextFileReader reader = new TextFileReader(filename);
+ reader.read();
+ quotes = new StringTokenizer(reader.getText(), "\"", true);
+ }
+
+ // note: no handling of error cases here
+ parse(quotes);
+ }
+
+ /**
+ * Creates a new GMLTree object.
+ *
+ * @param text DOCUMENT ME!
+ * @param zip_entry DOCUMENT ME!
+ */
+ public GMLTree(String text, boolean zip_entry) {
+ StringTokenizer quotes = new StringTokenizer(text, "\"", true);
+ parse(quotes);
+ }
+
+ protected void parse(StringTokenizer quotes) {
+ LinkedList tokenList = new LinkedList();
+
+ // handle the quotes -> build GMLToken list
+ // find the quoted strings first so we can preserve their white space
+ // @bug If the file starts with a quote this logic will fail.
+ while (quotes.hasMoreTokens()) {
+ StringTokenizer tokens = new StringTokenizer(quotes.nextToken());
+
+ while (tokens.hasMoreTokens()) {
+ tokenList.add(tokens.nextToken());
+ }
+
+ if (quotes.hasMoreTokens()) {
+ // clear the quote, this token must be "\""
+ String nextToken = quotes.nextToken();
+
+ // check to see if it is the empty string
+ if (quotes.hasMoreTokens()) {
+ nextToken = quotes.nextToken();
+
+ // check for empty string
+ if (!nextToken.equals("\"")) {
+ // this was the quoted empty string
+ tokenList.add("\"" + nextToken + "\"");
+
+ // now look for and clear the close quote
+ if (quotes.hasMoreTokens()) {
+ // since the last token was not a quote character
+ // this next token has to be the quote character,
+ // and we can clear it
+ quotes.nextToken();
+ } else {
+ throw new RuntimeException("Open quote with no end quote");
+ }
+ } else {
+ // add a token for the quoted empty string
+ tokenList.add("\"\"");
+ }
+ } else {
+ throw new RuntimeException("GMLFile ended with open quote");
+ }
+ }
+ }
+
+ root = initializeTree(tokenList);
+ }
+
+ /**
+ * Static helper method to build a tree from a list of tokens. Maybe I
+ * should change the GraphView constructor so that it can use this function.
+ */
+ private static GMLNode initializeTree(List tokens) {
+ GMLNode result = new GMLNode();
+
+ while (tokens.size() > 0) {
+ String current = (String) tokens.remove(0);
+
+ // expecting this be a key or a close node symbol
+ if (current.equals(NODE_OPEN)) {
+ throw new RuntimeException("Error parsing GML file");
+ }
+
+ if (current.equals(NODE_CLOSE)) {
+ return result;
+ }
+
+ // now find the thing we are trying to map
+ String key = current;
+
+ if (tokens.size() == 0) {
+ throw new RuntimeException("Error parsing GML file");
+ }
+
+ current = (String) tokens.remove(0);
+
+ if (current.equals(NODE_OPEN)) {
+ result.addMapping(key, initializeTree(tokens));
+ } else if (current.equals(NODE_CLOSE)) {
+ throw new RuntimeException("Error parsing GML file");
+ } else {
+ result.addMapping(key, new GMLNode(current));
+ }
+ }
+
+ return result;
+ }
+
+ /**
+ * Get string representation
+ *
+ * @return string representation
+ */
+ public String toString() {
+ // this function basically just calls toString on the root
+ String lineSep = System.getProperty("line.separator");
+ String result = root.toString();
+
+ return result.substring(3, result.length() - 2) + lineSep;
+ }
+
+ /**
+ * Get the String representation of the 6 character hexidecimal RGB values
+ * i.e. #ff000a
+ *
+ * @param Color
+ * The color to be converted
+ */
+ public String getColorHexString(Color c) {
+ return ("#" + Integer.toHexString(256 + c.getRed()).substring(1)
+ + Integer.toHexString(256 + c.getGreen()).substring(1)
+ + Integer.toHexString(256 + c.getBlue()).substring(1));
+ }
+
+ /**
+ * Return a vector of information stored in gmlNodes
+ *
+ * @param keys
+ * A vector of strings representing a sequence of keys down the
+ * tree
+ * @param type
+ * The type of vector to return. See public static values for
+ * specifying type
+ * @return A vector. The type of this vector is determined by type
+ */
+ private Vector getVector(Vector keys, int type) {
+ Vector result = new Vector();
+ GMLTree.getVector(root, keys, 0, type, result);
+
+ return result;
+ }
+
+ /**
+ * Return a vector of information stored in gmlNodes
+ *
+ * @param keys
+ * a string array containing the sequence of keys used to lookup
+ * the values in the tree
+ * @param type
+ * The type fo vector to return. See public static values for
+ * specifiying type
+ * @return A vector. The type of the objects in the vector is determined by
+ * type
+ */
+ public Vector getVector(String[] keys, int type) {
+ Vector keyVector = new Vector(keys.length);
+
+ for (int i = 0; i < keys.length; i++) {
+ keyVector.add(keys[i]);
+ } // end of for ()
+
+ return getVector(keyVector, type);
+ }
+
+ /**
+ * A recursive private static helper method to get a vector of values
+ *
+ * @param root
+ * The current GMLFile for which we are getting values
+ * @param keys
+ * A vector of strings representing a sequence of keys down the
+ * tree
+ * @param index
+ * The current position in the key vector (to find hte current
+ * key we need to look up)
+ * @param result
+ * The vector to which we add result data.
+ */
+ private static void getVector(GMLNode root, Vector keys, int index, int type, Vector result) {
+ Vector mapped = root.getMapping((String) keys.get(index));
+
+ if (mapped != null) {
+ Iterator it = mapped.iterator();
+
+ // logger.info("Level " + index + " " +
+ // (String)keys.get(index) + " has " + mapped.size());
+ if (index >= (keys.size() - 1)) {
+ while (it.hasNext()) {
+ GMLNode current = (GMLNode) it.next();
+
+ // if(current.terminal){
+ if (type == STRING) {
+ result.add(current.stringValue());
+ } else if (type == INTEGER) {
+ result.add(current.integerValue());
+ } else if (type == DOUBLE) {
+ result.add(current.doubleValue());
+ } else if (type == GMLTREE) {
+ // logger.info(current.toString());
+ result.add(new GMLTree(current));
+ } else {
+ throw new IllegalArgumentException("bad type");
+ }
+
+ // }
+ }
+ } else {
+ while (it.hasNext()) {
+ GMLNode current = (GMLNode) it.next();
+
+ if (!current.terminal) {
+ GMLTree.getVector(current, keys, index + 1, type, result);
+ }
+ }
+ }
+ } // may need to handle missing/empty values
+ // else {
+ // logger.info("ADDING NULL AT LEVEL " + index + " " +
+ // (String)keys.get(index));
+ // result.add(null);
+ // }
+ }
+}
diff --git a/application/src/main/java/cytoscape/data/readers/GMLWriter.java b/application/src/main/java/cytoscape/data/readers/GMLWriter.java
new file mode 100644
index 0000000..a93ccc5
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/readers/GMLWriter.java
@@ -0,0 +1,615 @@
+/*
+ File: GMLWriter.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.data.readers;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+
+import cytoscape.data.Semantics;
+
+import cytoscape.view.CyNetworkView;
+
+import giny.model.Edge;
+import giny.model.Node;
+
+import giny.view.EdgeView;
+import giny.view.NodeView;
+
+import java.awt.Color;
+import java.awt.geom.Point2D;
+
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Set;
+import java.util.Vector;
+
+
+/**
+ * The purpse of this class is to translate cytoscape data structures into a gml
+ * object tree, we can then use the gml parser to write this tree out into a
+ * file
+ */
+public class GMLWriter {
+ /**
+ * It is possible that nodes have been added to the graph since it was
+ * loaded. This set will keep track of nodes and edges that are currently in
+ * the perspective that have no corresponding entry in the object tree that
+ * was loaded with the netowrk
+ */
+ private Set<Integer> newNodes;
+
+ /**
+ * It is possible that nodes have been added to the graph since it was
+ * loaded. This set will keep track of nodes and edges that are currently in
+ * the perspective that have no corresponding entry in the object tree that
+ * was loaded with the netowrk
+ */
+ private Set<Integer> newEdges;
+
+ /**
+ * Given an object tree given in oldList, update it with the information
+ * provided in network and optional view (if view is not null). The GML
+ * spec requires that we remember all information provided in the original
+ * gml file. Therefore, we pass in the old object tree as oldList, as
+ * execute functions which will update that data structure. We would also
+ * like to save files that may not have been loaded from a gml file. This
+ * list is empty in that case. Those same update functions must be able to
+ * create all relevant key-value pairs as well then.
+ */
+ public void writeGML(final CyNetwork network, final CyNetworkView view, final List oldList) {
+ /*
+ * Initially all the nodes and edges have not been seen
+ */
+ newNodes = new HashSet<Integer>(network.getNodeCount());
+ newEdges = new HashSet<Integer>(network.getEdgeCount());
+
+ for (Iterator<Node> it = network.nodesIterator(); it.hasNext();) {
+ newNodes.add(new Integer((it.next()).getRootGraphIndex()));
+ }
+
+ for (Iterator<Edge> it = network.edgesIterator(); it.hasNext();) {
+ newEdges.add(new Integer((it.next()).getRootGraphIndex()));
+ }
+
+ /*
+ * We are going to make sure the keys graph,creator,and version are
+ * present and update them if they are already present
+ */
+ KeyValue graph = null;
+
+ /*
+ * We are going to make sure the keys graph,creator,and version are
+ * present and update them if they are already present
+ */
+ KeyValue creator = null;
+
+ /*
+ * We are going to make sure the keys graph,creator,and version are
+ * present and update them if they are already present
+ */
+ KeyValue version = null;
+ KeyValue keyVal = null;
+
+ /*
+ * Network title
+ */
+ KeyValue title = null;
+
+ for (Iterator<KeyValue> it = oldList.iterator(); it.hasNext();) {
+ keyVal = it.next();
+
+ if (keyVal.key.equals(GMLReader.GRAPH)) {
+ graph = keyVal;
+ } else if (keyVal.key.equals(GMLReader.CREATOR)) {
+ creator = keyVal;
+ } else if (keyVal.key.equals(GMLReader.VERSION)) {
+ version = keyVal;
+ }
+ }
+
+ if (creator == null) {
+ creator = new KeyValue(GMLReader.CREATOR, null);
+ oldList.add(creator);
+ }
+
+ if (version == null) {
+ version = new KeyValue(GMLReader.VERSION, null);
+ oldList.add(version);
+ }
+
+ if (graph == null) {
+ graph = new KeyValue(GMLReader.GRAPH, new Vector());
+ oldList.add(graph);
+ }
+
+ if (title == null) {
+ title = new KeyValue(GMLReader.TITLE, network.getTitle());
+ oldList.add(title);
+ }
+
+ /*
+ * Update the list associated with the graph pair
+ */
+ writeGraph(network, view, (List) graph.value);
+ creator.value = "Cytoscape";
+ version.value = new Double(1.0);
+
+ /*
+ * After update all of the graph objects that were already present in
+ * the object tree check and see if there are any objects in the current
+ * perspective that were not updated For these objects, create an empty
+ * key-value mapping and then update it
+ */
+ List graph_list = (List) graph.value;
+
+ while (!newNodes.isEmpty()) {
+ KeyValue nodePair = new KeyValue(GMLReader.NODE, new Vector());
+ graph_list.add(nodePair);
+ ((List) nodePair.value).add(new KeyValue(GMLReader.ROOT_INDEX,
+ newNodes.iterator().next()));
+ writeGraphNode(network, view, (List) nodePair.value);
+ }
+
+ while (!newEdges.isEmpty()) {
+ KeyValue edgePair = new KeyValue(GMLReader.EDGE, new Vector());
+ graph_list.add(edgePair);
+ ((List) edgePair.value).add(new KeyValue(GMLReader.ROOT_INDEX,
+ newEdges.iterator().next()));
+ writeGraphEdge(network, view, (List) edgePair.value);
+ }
+ }
+
+ /**
+ * Update the list associated with a graph key
+ */
+ private void writeGraph(final CyNetwork network, final CyNetworkView view, final List oldList) {
+ for (Iterator<KeyValue> it = oldList.iterator(); it.hasNext();) {
+ KeyValue keyVal = it.next();
+
+ /*
+ * For all nodes in the object tree, update the list that is
+ * associated with that key. If this node is no longer present in
+ * the perpsective, then we must remove it from the ojbect tree.
+ * Also do the same thing for the edges.
+ */
+ if (keyVal.key.equals(GMLReader.NODE)) {
+ if (!writeGraphNode(network, view, (List) keyVal.value)) {
+ it.remove();
+ }
+ } else if (keyVal.key.equals(GMLReader.EDGE)) {
+ if (!writeGraphEdge(network, view, (List) keyVal.value)) {
+ it.remove();
+ }
+ }
+ }
+ }
+
+ /**
+ * Update the list associated with a node key
+ */
+ private boolean writeGraphNode(final CyNetwork network, final CyNetworkView view,
+ final List oldList) {
+ /*
+ * We expect a list associated with node key to potentially have a
+ * graphic key, id key, and root_index key
+ */
+ Integer root_index = null;
+ KeyValue graphicsPair = null;
+ KeyValue labelPair = null;
+ KeyValue idPair = null;
+
+ for (Iterator it = oldList.iterator(); it.hasNext();) {
+ KeyValue keyVal = (KeyValue) it.next();
+
+ if (keyVal.key.equals(GMLReader.ROOT_INDEX)) {
+ root_index = (Integer) keyVal.value;
+ } else if (keyVal.key.equals(GMLReader.GRAPHICS)) {
+ graphicsPair = keyVal;
+ } else if (keyVal.key.equals(GMLReader.LABEL)) {
+ labelPair = keyVal;
+ } else if (keyVal.key.equals(GMLReader.ID)) {
+ idPair = keyVal;
+ }
+ }
+
+ /*
+ * Check to see if this nodes is still in the perspective
+ */
+ if (root_index == null) {
+ return false;
+ }
+
+ Node node = Cytoscape.getRootGraph().getNode(root_index.intValue());
+
+ if (!network.containsNode(node)) {
+ return false;
+ }
+
+ /*
+ * Mark this node as seen
+ */
+ newNodes.remove(root_index);
+
+ /*
+ * Update or create the id key-value pair for this list
+ */
+ if (idPair == null) {
+ idPair = new KeyValue(GMLReader.ID, null);
+ oldList.add(idPair);
+ }
+
+ idPair.value = root_index;
+
+ /*
+ * Optionall update/create the graphics key-value pair for this list if
+ * there is currently defined. NOte that if no view is defined, the
+ * previously loaded view information will remain intact
+ */
+ if (view != Cytoscape.getNullNetworkView()) {
+ if (graphicsPair == null) {
+ graphicsPair = new KeyValue(GMLReader.GRAPHICS, new Vector());
+ oldList.add(graphicsPair);
+ }
+
+ writeGraphNodeGraphics(network, view.getNodeView(node), (List) graphicsPair.value);
+ }
+
+ /*
+ * Update/create the label key-value pair. We have co-opted this field
+ * to mean the canoncial name
+ */
+ if (labelPair == null) {
+ labelPair = new KeyValue(GMLReader.LABEL, null);
+ oldList.add(labelPair);
+ }
+
+ labelPair.value = node.getIdentifier();
+
+ return true;
+ }
+
+ /**
+ * Update the list associated with an edge key
+ */
+ private boolean writeGraphEdge(final CyNetwork network, final CyNetworkView view,
+ final List oldList) {
+ /*
+ * An edge key will definitely have a root_index, labelPair (we enforce
+ * this on loading), source key, and a target key
+ */
+ Integer root_index = null;
+ KeyValue graphicsPair = null;
+ KeyValue labelPair = null;
+ KeyValue sourcePair = null;
+ KeyValue targetPair = null;
+
+ for (Iterator it = oldList.iterator(); it.hasNext();) {
+ KeyValue keyVal = (KeyValue) it.next();
+
+ if (keyVal.key.equals(GMLReader.GRAPHICS)) {
+ graphicsPair = keyVal;
+ } else if (keyVal.key.equals(GMLReader.LABEL)) {
+ labelPair = keyVal;
+ } else if (keyVal.key.equals(GMLReader.ROOT_INDEX)) {
+ root_index = (Integer) keyVal.value;
+ } else if (keyVal.key.equals(GMLReader.SOURCE)) {
+ sourcePair = keyVal;
+ } else if (keyVal.key.equals(GMLReader.TARGET)) {
+ targetPair = keyVal;
+ }
+ }
+
+ /*
+ * Make sure the edge is still present in this perspective
+ */
+ if (root_index == null) {
+ return false;
+ }
+
+ Edge edge = Cytoscape.getRootGraph().getEdge(root_index.intValue());
+
+ if (!network.containsEdge(edge)) {
+ return false;
+ }
+
+ newEdges.remove(root_index);
+
+ if (targetPair == null) {
+ targetPair = new KeyValue(GMLReader.TARGET, null);
+ oldList.add(targetPair);
+ }
+
+ targetPair.value = new Integer(edge.getTarget().getRootGraphIndex());
+
+ if (sourcePair == null) {
+ sourcePair = new KeyValue(GMLReader.SOURCE, null);
+ oldList.add(sourcePair);
+ }
+
+ sourcePair.value = new Integer(edge.getSource().getRootGraphIndex());
+
+ if (view != Cytoscape.getNullNetworkView()) {
+ if (graphicsPair == null) {
+ graphicsPair = new KeyValue(GMLReader.GRAPHICS, new Vector());
+ oldList.add(graphicsPair);
+ }
+
+ writeGraphEdgeGraphics(network, view.getEdgeView(edge), (List) graphicsPair.value);
+ }
+
+ if (labelPair == null) {
+ labelPair = new KeyValue(GMLReader.LABEL, null);
+ oldList.add(labelPair);
+ }
+
+ labelPair.value = Cytoscape.getEdgeAttributes()
+ .getStringAttribute(edge.getIdentifier(), Semantics.INTERACTION);
+
+ return true;
+ }
+
+ /**
+ * This writes all the graphical information for a particular node into an
+ * object tree
+ */
+ private void writeGraphNodeGraphics(final CyNetwork network, final NodeView nodeView,
+ final List oldList) {
+ KeyValue x = null;
+ KeyValue y = null;
+ KeyValue w = null;
+ KeyValue h = null;
+ KeyValue type = null;
+ KeyValue fill = null;
+ KeyValue outline = null;
+ KeyValue outline_width = null;
+
+ for (Iterator it = oldList.iterator(); it.hasNext();) {
+ KeyValue keyVal = (KeyValue) it.next();
+
+ if (keyVal.key.equals(GMLReader.X)) {
+ x = keyVal;
+ } else if (keyVal.key.equals(GMLReader.Y)) {
+ y = keyVal;
+ } else if (keyVal.key.equals(GMLReader.W)) {
+ w = keyVal;
+ } else if (keyVal.key.equals(GMLReader.H)) {
+ h = keyVal;
+ } else if (keyVal.key.equals(GMLReader.TYPE)) {
+ type = keyVal;
+ } else if (keyVal.key.equals(GMLReader.FILL)) {
+ fill = keyVal;
+ } else if (keyVal.key.equals(GMLReader.OUTLINE)) {
+ outline = keyVal;
+ } else if (keyVal.key.equals(GMLReader.OUTLINE_WIDTH)) {
+ outline_width = keyVal;
+ }
+ }
+
+ if (x == null) {
+ x = new KeyValue(GMLReader.X, null);
+ oldList.add(x);
+ }
+
+ if (y == null) {
+ y = new KeyValue(GMLReader.Y, null);
+ oldList.add(y);
+ }
+
+ if (w == null) {
+ w = new KeyValue(GMLReader.W, null);
+ oldList.add(w);
+ }
+
+ if (h == null) {
+ h = new KeyValue(GMLReader.H, null);
+ oldList.add(h);
+ }
+
+ if (fill == null) {
+ fill = new KeyValue(GMLReader.FILL, null);
+ oldList.add(fill);
+ }
+
+ if (type == null) {
+ type = new KeyValue(GMLReader.TYPE, null);
+ oldList.add(type);
+ }
+
+ if (outline == null) {
+ outline = new KeyValue(GMLReader.OUTLINE, null);
+ oldList.add(outline);
+ }
+
+ if (outline_width == null) {
+ outline_width = new KeyValue(GMLReader.OUTLINE_WIDTH, null);
+ oldList.add(outline_width);
+ }
+
+ x.value = new Double(nodeView.getXPosition());
+ y.value = new Double(nodeView.getYPosition());
+ w.value = new Double(nodeView.getWidth());
+ h.value = new Double(nodeView.getHeight());
+ fill.value = getColorHexString((Color) nodeView.getUnselectedPaint());
+ outline.value = getColorHexString((Color) nodeView.getBorderPaint());
+ outline_width.value = new Double(nodeView.getBorderWidth());
+
+ switch (nodeView.getShape()) {
+ case NodeView.RECTANGLE:
+ type.value = GMLReader.RECTANGLE;
+
+ break;
+
+ case NodeView.ELLIPSE:
+ type.value = GMLReader.ELLIPSE;
+
+ break;
+
+ case NodeView.DIAMOND:
+ type.value = GMLReader.DIAMOND;
+
+ break;
+
+ case NodeView.HEXAGON:
+ type.value = GMLReader.HEXAGON;
+
+ break;
+
+ case NodeView.OCTAGON:
+ type.value = GMLReader.OCTAGON;
+
+ break;
+
+ case NodeView.PARALELLOGRAM:
+ type.value = GMLReader.PARALELLOGRAM;
+
+ break;
+
+ case NodeView.TRIANGLE:
+ type.value = GMLReader.TRIANGLE;
+
+ break;
+ }
+ }
+
+ private void writeGraphEdgeGraphics(final CyNetwork network, final EdgeView edgeView,
+ final List oldList) {
+ KeyValue width = null;
+ KeyValue fill = null;
+ KeyValue line = null;
+ KeyValue type = null;
+ KeyValue source_arrow = null;
+ KeyValue target_arrow = null;
+
+ for (Iterator it = oldList.iterator(); it.hasNext();) {
+ KeyValue keyVal = (KeyValue) it.next();
+
+ if (keyVal.key.equals(GMLReader.WIDTH)) {
+ width = keyVal;
+ } else if (keyVal.key.equals(GMLReader.FILL)) {
+ fill = keyVal;
+ } else if (keyVal.key.equals(GMLReader.LINE)) {
+ line = keyVal;
+ } else if (keyVal.key.equals(GMLReader.TYPE)) {
+ type = keyVal;
+ } else if (keyVal.key.equals(GMLReader.SOURCE_ARROW)) {
+ source_arrow = keyVal;
+ } else if (keyVal.key.equals(GMLReader.TARGET_ARROW)) {
+ target_arrow = keyVal;
+ }
+ }
+
+ if (width == null) {
+ width = new KeyValue(GMLReader.WIDTH, null);
+ oldList.add(width);
+ }
+
+ width.value = new Double(edgeView.getStrokeWidth());
+
+ if (fill == null) {
+ fill = new KeyValue(GMLReader.FILL, null);
+ oldList.add(fill);
+ }
+
+ fill.value = getColorHexString((Color) edgeView.getUnselectedPaint());
+
+ if (type == null) {
+ type = new KeyValue(GMLReader.TYPE, null);
+ oldList.add(type);
+ }
+
+ switch (edgeView.getLineType()) {
+ case EdgeView.STRAIGHT_LINES:
+ type.value = GMLReader.STRAIGHT_LINES;
+
+ break;
+
+ case EdgeView.CURVED_LINES:
+ type.value = GMLReader.CURVED_LINES;
+
+ break;
+ }
+
+ if (line == null) {
+ line = new KeyValue(GMLReader.LINE, null);
+ oldList.add(line);
+ }
+
+ Point2D[] pointsArray = edgeView.getBend().getDrawPoints();
+ Vector points = new Vector(pointsArray.length);
+
+ // CTW funny thing with anchor points, need to trim off the first and
+ // last
+ // and reverse the order x
+ for (int idx = pointsArray.length - 2; idx > 0; idx--) {
+ Vector coords = new Vector(2);
+ coords.add(new KeyValue(GMLReader.X, new Double(pointsArray[idx].getX())));
+ coords.add(new KeyValue(GMLReader.Y, new Double(pointsArray[idx].getY())));
+ points.add(new KeyValue(GMLReader.POINT, coords));
+ }
+
+ line.value = points;
+
+ if (source_arrow == null) {
+ source_arrow = new KeyValue(GMLReader.SOURCE_ARROW, null);
+ oldList.add(source_arrow);
+ }
+
+ source_arrow.value = new Integer(edgeView.getSourceEdgeEnd());
+
+ if (target_arrow == null) {
+ target_arrow = new KeyValue(GMLReader.TARGET_ARROW, null);
+ oldList.add(target_arrow);
+ }
+
+ target_arrow.value = new Integer(edgeView.getTargetEdgeEnd());
+ }
+
+ /**
+ * Get the String representation of the 6 character hexidecimal RGB values
+ * i.e. #ff000a
+ *
+ * @param Color
+ * The color to be converted
+ */
+ private static String getColorHexString(final Color c) {
+ return ("#" // +Integer.toHexString(c.getRGB());
+ + Integer.toHexString(256 + c.getRed()).substring(1)
+ + Integer.toHexString(256 + c.getGreen()).substring(1)
+ + Integer.toHexString(256 + c.getBlue()).substring(1));
+ }
+}
diff --git a/application/src/main/java/cytoscape/data/readers/GraphReader.java b/application/src/main/java/cytoscape/data/readers/GraphReader.java
new file mode 100644
index 0000000..fba4c3c
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/readers/GraphReader.java
@@ -0,0 +1,91 @@
+/*
+ File: GraphReader.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data.readers;
+
+import giny.view.GraphView;
+
+import java.io.IOException;
+
+import cytoscape.CyNetwork;
+import cytoscape.layout.CyLayoutAlgorithm;
+
+
+/**
+ * Interface for Reading in Cytoscape Graphs.
+ *
+ * @author Cytoscape Development Group.
+ */
+public interface GraphReader {
+ /**
+ * Reads/imports the graph.
+ *
+ * @throws IOException IO Errors.
+ */
+ public void read() throws IOException;
+
+ /**
+ * Returns the CyLayoutAlgorithm used to layout the graph
+ *
+ * @param myView
+ */
+ public CyLayoutAlgorithm getLayoutAlgorithm();
+
+ /**
+ * Gets an array of node indices that participate in the newly created graph.
+ *
+ * @return array of node indices from the root graph.
+ */
+ public int[] getNodeIndicesArray();
+
+ /**
+ * Gets an array of edges indices that participate in the newly created graph.
+ *
+ * @return array of edges indices from the root graph.
+ */
+ public int[] getEdgeIndicesArray();
+
+ /**
+ * Execute whatever post-processing is required.
+ */
+ public void doPostProcessing(CyNetwork network);
+
+ /**
+ * Gets the name of the network.
+ * @return network name.
+ */
+ public String getNetworkName();
+}
diff --git a/application/src/main/java/cytoscape/data/readers/InteractionsReader.java b/application/src/main/java/cytoscape/data/readers/InteractionsReader.java
new file mode 100644
index 0000000..e0ab95b
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/readers/InteractionsReader.java
@@ -0,0 +1,362 @@
+/*
+ File: InteractionsReader.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+// InteractionsReader: from semi-structured text file, into an array of Interactions
+//------------------------------
+// $Revision: 20380 $
+// $Date: 2010-06-01 22:04:00 +0200 (Tue, 01 Jun 2010) $
+// $Author: kono $
+//------------------------------
+package cytoscape.data.readers;
+
+import cern.colt.list.IntArrayList;
+
+import cern.colt.map.OpenIntIntHashMap;
+
+import cytoscape.CyEdge;
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+
+import cytoscape.data.Interaction;
+
+import cytoscape.data.servers.BioDataServer;
+
+import cytoscape.task.TaskMonitor;
+
+import cytoscape.util.FileUtil;
+import cytoscape.util.PercentUtil;
+
+import cytoscape.view.CyNetworkView;
+
+import giny.model.Edge;
+import giny.model.Node;
+
+import java.io.IOException;
+import java.io.InputStream;
+
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+
+/**
+ * Reader for graphs in the interactions file format. Given the filename,
+ * provides the graph and attributes objects constructed from the file.
+ */
+public class InteractionsReader extends AbstractGraphReader {
+ private TaskMonitor taskMonitor;
+ private PercentUtil percentUtil;
+
+ /**
+ * A Vector that holds all of the Interactions
+ */
+ protected List<Interaction> allInteractions = new ArrayList<Interaction>();
+
+ private String zip_entry;
+ private boolean is_zip = false;
+ private IntArrayList node_indices;
+ private OpenIntIntHashMap edges;
+ private InputStream inputStream;
+
+ /**
+ * Creates an interaction reader based on a string consisting of data that has
+ * been read from a zip file.
+ * @param zip_entry The zip entry data.
+ * @param monitor An optional task monitor. May be null.
+ * @param is_zip Indicates that the data is from a zip file - Should almost
+ * always be true.
+ */
+ public InteractionsReader(String zip_entry, TaskMonitor monitor, boolean is_zip) {
+ super("zip_data");
+ this.zip_entry = zip_entry;
+ this.is_zip = is_zip;
+ this.taskMonitor = monitor;
+ }
+
+ /**
+ * Creates an interaction reader based on the string file name.
+ * @param filename The filename that contains the interaction data
+ * to be read.
+ */
+ public InteractionsReader(String filename) {
+ this(filename, null);
+ }
+
+ /**
+ * Creates an interaction reader based on the string file name.
+ * @param filename The filename that contains the interaction data
+ * to be read.
+ * @param monitor An optional task monitor. May be null.
+ */
+ public InteractionsReader(String filename, TaskMonitor monitor) {
+ this(FileUtil.getInputStream(filename), filename);
+ this.taskMonitor = monitor;
+ }
+
+ /**
+ * Constructor.<br>
+ * This is usually used for remote file loading.
+ *
+ * @param is
+ * Input stream of GML file,
+ *
+ */
+ public InteractionsReader(InputStream is, String name) {
+ super(name);
+
+ this.inputStream = is;
+ }
+
+ /**
+ * Sets the task monitor we want to use
+ *
+ * @param monitor the TaskMonitor to use
+ */
+ public void setTaskMonitor(TaskMonitor monitor) {
+ this.taskMonitor = monitor;
+ }
+
+
+ /**
+ * Calls read(false)
+ */
+ public void read() throws IOException {
+ String rawText;
+
+ if (!is_zip) {
+ try {
+ rawText = FileUtil.getInputString(inputStream);
+ }
+ finally {
+ if (inputStream != null) {
+ inputStream.close();
+ inputStream = null;
+ }
+ }
+ } else {
+ rawText = zip_entry;
+ }
+
+ String delimiter = " ";
+
+ if (rawText.indexOf("\t") >= 0)
+ delimiter = "\t";
+
+ final String[] lines = rawText.split(System.getProperty("line.separator"));
+
+ // There are a total of 6 steps to read in a complete SIF File
+ if (taskMonitor != null) {
+ percentUtil = new PercentUtil(6);
+ }
+
+ final int linesLength = lines.length;
+ String newLine;
+ Interaction newInteraction;
+
+ for (int i = 0; i < linesLength; i++) {
+ if (taskMonitor != null) {
+ taskMonitor.setPercentCompleted(percentUtil.getGlobalPercent(1, i, lines.length));
+ }
+
+ newLine = lines[i];
+
+ if (newLine.length() <= 0) {
+ continue;
+ }
+
+ newInteraction = new Interaction(newLine, delimiter);
+ allInteractions.add(newInteraction);
+ }
+
+ createRootGraphFromInteractionData();
+ } // readFromFile
+
+ // -------------------------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getCount() {
+ return allInteractions.size();
+ }
+
+ // -------------------------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Interaction[] getAllInteractions() {
+ return allInteractions.toArray(new Interaction[0]);
+ }
+
+
+
+ // -------------------------------------------------------------------------------------------
+ protected void createRootGraphFromInteractionData() {
+ final Interaction[] interactions = getAllInteractions();
+
+ // figure out how many nodes and edges we need before we create the
+ // graph;
+ // this improves performance for large graphs
+ final Set<String> nodeNameSet = new HashSet<String>();
+ int edgeCount = 0;
+ final int intSize = interactions.length;
+
+ Interaction interaction;
+ String sourceName;
+ String[] targets;
+ int targetLength;
+
+ for (int i = 0; i < intSize; i++) {
+ interaction = interactions[i];
+ sourceName = interaction.getSource();
+
+ nodeNameSet.add(sourceName); // does nothing if already there
+
+ targets = interaction.getTargets();
+ targetLength = targets.length;
+
+ for (int t = 0; t < targetLength; t++) {
+ nodeNameSet.add(targets[t]);
+ edgeCount++;
+ }
+
+ if (taskMonitor != null) {
+ taskMonitor.setPercentCompleted(percentUtil.getGlobalPercent(2, i,
+ interactions.length));
+ }
+ }
+
+ Cytoscape.ensureCapacity(nodeNameSet.size(), edgeCount);
+ node_indices = new IntArrayList(nodeNameSet.size());
+ edges = new OpenIntIntHashMap(edgeCount);
+
+ // now create all of the nodes, storing a hash from name to node
+ // Map nodes = new HashMap();
+ int counter = 0;
+ Node node;
+
+ for (String nodeName : nodeNameSet) {
+ if (taskMonitor != null) {
+ taskMonitor.setPercentCompleted(percentUtil.getGlobalPercent(3, counter,
+ nodeNameSet.size()));
+ counter++;
+ }
+
+ // use the static method
+ node = Cytoscape.getCyNode(nodeName, true);
+ node_indices.add(node.getRootGraphIndex());
+ }
+
+ // ---------------------------------------------------------------------------
+ // now loop over the interactions again, this time creating edges
+ // between
+ // all sources and each of their respective targets.
+ // for each edge, save the source-target pair, and their interaction
+ // type,
+ // in Cytoscape.getEdgeNetworkData() -- a hash of a hash of name-value
+ // pairs, like this:
+ // Cytoscape.getEdgeNetworkData() ["interaction"] = interactionHash
+ // interactionHash [sourceNode::targetNode] = "pd"
+ // ---------------------------------------------------------------------------
+ String targetNodeName;
+ String nodeName;
+ String interactionType;
+ String edgeName;
+ Edge edge;
+
+ for (int i = 0; i < interactions.length; i++) {
+ if (taskMonitor != null) {
+ taskMonitor.setPercentCompleted(percentUtil.getGlobalPercent(4, i,
+ interactions.length));
+ }
+
+ interaction = interactions[i];
+ nodeName = interaction.getSource();
+ interactionType = interaction.getType();
+ targets = interaction.getTargets();
+ targetLength = targets.length;
+
+ for (int t = 0; t < targetLength; t++) {
+ targetNodeName = targets[t];
+
+ edgeName = CyEdge.createIdentifier(nodeName, interactionType, targetNodeName);
+ edge = Cytoscape.getCyEdge(nodeName, edgeName, targetNodeName, interactionType);
+ edges.put(edge.getRootGraphIndex(), 0);
+ } // for t
+ } // for i
+ } // createRootGraphFromInteractionData
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] getNodeIndicesArray() {
+ node_indices.trimToSize();
+
+ return node_indices.elements();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] getEdgeIndicesArray() {
+ final IntArrayList edge_indices = new IntArrayList(edges.size());
+ edges.keys(edge_indices);
+ edge_indices.trimToSize();
+
+ return edge_indices.elements();
+ }
+
+ public void doPostProcessing(CyNetwork net) {
+
+ // Cleanup unnecessary references.
+ edges.clear();
+ node_indices.clear();
+ edges = null;
+ node_indices = null;
+
+ allInteractions.clear();
+ allInteractions = null;
+ }
+} // InteractionsReader
diff --git a/application/src/main/java/cytoscape/data/readers/KeyValue.java b/application/src/main/java/cytoscape/data/readers/KeyValue.java
new file mode 100644
index 0000000..8ee01ca
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/readers/KeyValue.java
@@ -0,0 +1,60 @@
+/*
+ File: KeyValue.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.data.readers;
+
+/**
+ * Key and Value pair in GML file.
+ */
+public class KeyValue {
+
+ // These are immutable.
+ public final String key;
+ public Object value;
+
+ /**
+ * Creates a new KeyValue object.
+ *
+ * @param key
+ * DOCUMENT ME!
+ * @param value
+ * DOCUMENT ME!
+ */
+ public KeyValue(final String key, final Object value) {
+ this.key = key;
+ this.value = value;
+ }
+}
diff --git a/application/src/main/java/cytoscape/data/readers/MetadataEntries.java b/application/src/main/java/cytoscape/data/readers/MetadataEntries.java
new file mode 100644
index 0000000..b3737fc
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/readers/MetadataEntries.java
@@ -0,0 +1,69 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data.readers;
+
+
+/**
+ * Entries in the network metadata.<br>
+ *
+ * This is the list of entries in the network metadata object.
+ *
+ * @author kono
+ *
+ */
+public enum MetadataEntries {
+ DATE("Date"),
+ TITLE("Title"),
+ IDENTIFIER("Identifier"),
+ DESCRIPTION("Description"),
+ SOURCE("Source"),
+ TYPE("Type"),
+ FORMAT("Format");
+
+ private String name;
+
+ private MetadataEntries(String name) {
+ this.name = name;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String toString() {
+ return name;
+ }
+}
diff --git a/application/src/main/java/cytoscape/data/readers/MetadataParser.java b/application/src/main/java/cytoscape/data/readers/MetadataParser.java
new file mode 100644
index 0000000..f41bc7a
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/readers/MetadataParser.java
@@ -0,0 +1,212 @@
+/*
+ File: MetadataParser.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.data.readers;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import cytoscape.CytoscapeInit;
+
+import cytoscape.data.CyAttributes;
+
+import java.net.URISyntaxException;
+
+import java.text.DateFormat;
+import java.text.SimpleDateFormat;
+
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.Map;
+import java.util.Set;
+
+/**
+ * Manipulates network metadata for loading and saving.<br>
+ *
+ * @author kono
+ *
+ */
+public class MetadataParser {
+ /*
+ * Actual CyAttribute name for the network metadata
+ */
+
+ /**
+ *
+ */
+ public static final String DEFAULT_NETWORK_METADATA_LABEL = "Network Metadata";
+
+ /*
+ * Default values for new meta data. Maybe changed later...
+ */
+ private static final String DEF_URI = "http://www.cytoscape.org/";
+ private static final String DEF_TYPE = "Protein-Protein Interaction";
+ private static final String DEF_FORMAT = "Cytoscape-XGMML";
+ private String metadataLabel;
+ private CyNetwork network;
+ private CyAttributes networkAttributes;
+ private Map rdfAsMap;
+
+ /**
+ * Constructor.
+ *
+ * @param network
+ * Target network for editing metadata.
+ */
+ public MetadataParser(CyNetwork network) {
+ this(network, DEFAULT_NETWORK_METADATA_LABEL);
+ }
+
+ /**
+ * Constructor.
+ *
+ * @param network
+ * Target network
+ * @param metadataLabel
+ * Label used as a tag for this attribute.
+ */
+ public MetadataParser(CyNetwork network, String metadataLabel) {
+ this.metadataLabel = metadataLabel;
+ this.network = network;
+ networkAttributes = Cytoscape.getNetworkAttributes();
+
+ // Extract Network Metadata from CyAttributes
+ rdfAsMap = networkAttributes.getMapAttribute(network.getIdentifier(), metadataLabel);
+ }
+
+ /**
+ * Build new metadata RDF structure based on given network information.
+ *
+ * Data items in "defaultLabels" will be created and inserted into RDF
+ * structure.
+ */
+ public Map<String, String> makeNewMetadataMap() {
+ Map<String, String> dataMap = new HashMap<String, String>();
+
+ // Extract default values from property
+ String defSource = CytoscapeInit.getProperties().getProperty("defaultMetadata.source");
+ String defType = CytoscapeInit.getProperties().getProperty("defaultMetadata.type");
+ String defFormat = CytoscapeInit.getProperties().getProperty("defaultMetadata.format");
+
+ MetadataEntries[] entries = MetadataEntries.values();
+
+ for (int i = 0; i < entries.length; i++) {
+ switch (entries[i]) {
+ case DATE:
+
+ java.util.Date now = new java.util.Date();
+ DateFormat df = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss");
+ dataMap.put(entries[i].toString(), df.format(now));
+
+ break;
+
+ case TITLE:
+ dataMap.put(entries[i].toString(), network.getTitle());
+
+ break;
+
+ case SOURCE:
+
+ if (defSource == null) {
+ dataMap.put(entries[i].toString(), DEF_URI);
+ } else {
+ dataMap.put(entries[i].toString(), defSource);
+ }
+
+ break;
+
+ case TYPE:
+
+ if (defType == null) {
+ dataMap.put(entries[i].toString(), DEF_TYPE);
+ } else {
+ dataMap.put(entries[i].toString(), defType);
+ }
+
+ break;
+
+ case FORMAT:
+
+ if (defFormat == null) {
+ dataMap.put(entries[i].toString(), DEF_FORMAT);
+ } else {
+ dataMap.put(entries[i].toString(), defFormat);
+ }
+
+ break;
+
+ default:
+ dataMap.put(entries[i].toString(), "N/A");
+
+ break;
+ }
+ }
+
+ return dataMap;
+ }
+
+ /**
+ * Get Network Metadata as Map object
+ *
+ * @return
+ * @throws URISyntaxException
+ */
+ public Map getMetadataMap() {
+ if ((rdfAsMap == null) || (rdfAsMap.keySet().size() == 0)) {
+ rdfAsMap = makeNewMetadataMap();
+ }
+
+ return rdfAsMap;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param entryName DOCUMENT ME!
+ * @param value DOCUMENT ME!
+ */
+ public void setMetadata(MetadataEntries entryName, String value) {
+ Map<String, String> metadata = networkAttributes.getMapAttribute(network.getIdentifier(),
+ metadataLabel);
+
+ if (metadata == null) {
+ metadata = makeNewMetadataMap();
+ }
+
+ metadata.put(entryName.toString(), value);
+ networkAttributes.setMapAttribute(network.getIdentifier(), metadataLabel, metadata);
+ rdfAsMap = metadata;
+ }
+}
diff --git a/application/src/main/java/cytoscape/data/readers/NNFParser.java b/application/src/main/java/cytoscape/data/readers/NNFParser.java
new file mode 100644
index 0000000..f99d0f6
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/readers/NNFParser.java
@@ -0,0 +1,150 @@
+package cytoscape.data.readers;
+
+import java.util.HashMap;
+import java.util.Map;
+import java.util.List;
+import java.util.ArrayList;
+import java.util.Set;
+
+import cytoscape.CyEdge;
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+import cytoscape.data.Semantics;
+
+
+/**
+ * Parser for NNF files.
+ *
+ * @author kono, ruschein
+ */
+public class NNFParser {
+ // For performance, these fields will be reused.
+ private String[] parts;
+ private int length;
+
+ // List of root network plus all nested networks.
+ private final List<CyNetwork> networks;
+
+ // Hash map from title to actual network
+ private Map<String, CyNetwork> networkMap;
+
+
+ public NNFParser() {
+ networkMap = new HashMap<String, CyNetwork>();
+ networks = new ArrayList<CyNetwork>();
+ }
+
+
+ /** Returns the first network with title "networkTitle" or null, if there is no network w/ this title.
+ */
+ private CyNetwork getNetworkByTitle(final String networkTitle) {
+ Set<CyNetwork> networks = Cytoscape.getNetworkSet();
+ for (final CyNetwork network : networks) {
+ if (network.getTitle().equals(networkTitle))
+ return network;
+ }
+
+ return null;
+ }
+
+
+ /**
+ * Parse an entry/line in an NNF file.
+ *
+ * @param line
+ */
+ public boolean parse(final String line) {
+ // Split with white space chars
+ parts = splitLine(line);
+ length = parts.length;
+
+ CyNetwork network = networkMap.get(parts[0]);
+ if (network == null) {
+ // Reuse existing networks, if possible:
+ network = getNetworkByTitle(parts[0]);
+ if (network == null) {
+ // Create network without view. View will be created later in class Cytoscape.
+ network = Cytoscape.createNetwork(parts[0], /* create_view = */false);
+ }
+
+ networkMap.put(parts[0], network);
+ networks.add(network);
+
+ // Attempt to nest network within the node with the same name
+ final CyNode parent = Cytoscape.getCyNode(parts[0]);
+ if (parent != null) {
+ parent.setNestedNetwork(network);
+ }
+ }
+
+ if (length == 2) {
+ final CyNode node = Cytoscape.getCyNode(parts[1], true);
+ network.addNode(node);
+ final CyNetwork nestedNetwork = networkMap.get(parts[1]);
+ if (nestedNetwork != null) {
+ node.setNestedNetwork(nestedNetwork);
+ }
+
+ } else if (length == 4) {
+ final CyNode source = Cytoscape.getCyNode(parts[1], true);
+ network.addNode(source);
+ CyNetwork nestedNetwork = networkMap.get(parts[1]);
+ if (nestedNetwork != null) {
+ source.setNestedNetwork(nestedNetwork);
+ }
+
+ final CyNode target = Cytoscape.getCyNode(parts[3], true);
+ network.addNode(target);
+ nestedNetwork = networkMap.get(parts[3]);
+ if (nestedNetwork != null) {
+ target.setNestedNetwork(nestedNetwork);
+ }
+
+ final CyEdge edge = Cytoscape.getCyEdge(source, target, Semantics.INTERACTION, parts[2], /* create = */true,
+ /* directed = */true);
+ network.addEdge(edge);
+ } else {
+ // Invalid number of columns.
+ return false;
+ }
+
+ return true;
+ }
+
+ private String[] splitLine(final String line) {
+ final List<String> parts = new ArrayList<String>();
+ boolean escaped = false;
+ StringBuilder part = null;
+ for (int i = 0; i < line.length(); ++i) {
+ final char ch = line.charAt(i);
+ if (escaped) {
+ escaped = false;
+ if (part == null)
+ part = new StringBuilder();
+ part.append(ch);
+ } else if (ch == '\\')
+ escaped = true;
+ else if (ch == ' ' || ch == '\t') {
+ if (part != null) {
+ parts.add(part.toString());
+ part = null;
+ }
+ } else {
+ if (part == null)
+ part = new StringBuilder();
+ part.append(ch);
+ }
+ }
+
+ if (part != null)
+ parts.add(part.toString());
+
+ final String[] array = new String[parts.size()];
+ return parts.toArray(array);
+ }
+
+ protected List<CyNetwork> getNetworks() {
+ return networks;
+ }
+}
diff --git a/application/src/main/java/cytoscape/data/readers/NNFReader.java b/application/src/main/java/cytoscape/data/readers/NNFReader.java
new file mode 100644
index 0000000..24f1359
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/readers/NNFReader.java
@@ -0,0 +1,149 @@
+package cytoscape.data.readers;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.util.List;
+
+import cytoscape.CyNetwork;
+import cytoscape.task.TaskMonitor;
+import cytoscape.util.FileUtil;
+import cytoscape.util.PercentUtil;
+
+
+/**
+ * Graph file reader for NNF files.
+ *
+ * @author kono, ruschein
+ * @since Cytoscape 2.7.0
+ *
+ */
+public class NNFReader extends AbstractGraphReader implements NestedNetworkReader {
+ // Optional comments start with this character and extend to the end of line.
+ private static final char COMMENT_CHAR = '#';
+
+ private final NNFParser parser;
+
+ // TODO: move to parent and remove from siblings
+ private final InputStream inputStream;
+ private TaskMonitor taskMonitor;
+ private PercentUtil percentUtil;
+
+
+ /**
+ * Creates an interaction reader based on the string file name.
+ *
+ * @param filename
+ * The filename that contains the interaction data to be read.
+ */
+ public NNFReader(String filename) {
+ this(filename, null);
+ }
+
+
+ /**
+ * Creates an interaction reader based on the string file name.
+ *
+ * @param filename
+ * The filename that contains the interaction data to be read.
+ * @param monitor
+ * An optional task monitor. May be null.
+ */
+ public NNFReader(String filename, TaskMonitor monitor) {
+ this(FileUtil.getInputStream(filename), filename);
+ this.taskMonitor = monitor;
+ }
+
+
+ /**
+ * Constructor.<br>
+ * This is usually used for remote file loading.
+ *
+ * @param is
+ * Input stream of GML file,
+ *
+ */
+ public NNFReader(final InputStream is, final String name) {
+ super(name);
+ this.inputStream = is;
+ this.parser = new NNFParser();
+ }
+
+
+ /**
+ * Sets the task monitor we want to use
+ *
+ * @param monitor
+ * the TaskMonitor to use
+ */
+ public void setTaskMonitor(TaskMonitor monitor) {
+ this.taskMonitor = monitor;
+ }
+
+
+ public void read() throws IOException {
+ // Create buffered reader from given InputStream
+ final BufferedReader in = new BufferedReader(new InputStreamReader(inputStream));
+
+ String line;
+ try {
+ for (int lineNumber = 1; (line = in.readLine()) != null; ++lineNumber) {
+ line = processComment(line);
+ if (line.length() == 0) {
+ continue;
+ }
+ if (!parser.parse(line)) {
+ throw new IOException("Malformed line in NNF file: " + lineNumber + " \"" + line + "\"");
+ }
+ }
+ } finally {
+ in.close();
+ }
+
+ if (parser.getNetworks().size() == 0) {
+ throw new IOException("Input NNF file is empty!");
+ }
+ }
+
+
+ public int[] getNodeIndicesArray() {
+ return null;
+ }
+
+
+ public int[] getEdgeIndicesArray() {
+ return null;
+ }
+
+
+ private String processComment(String line) {
+ final int hashPos = line.indexOf(COMMENT_CHAR);
+ if (hashPos != -1) {
+ line = line.substring(0, hashPos);
+ }
+ return line.trim();
+ }
+
+
+ /**
+ * Returns root network.
+ *
+ * <p>
+ * Usually used by the caller of reader.
+ *
+ */
+ public List<CyNetwork> getNetworks() {
+ return parser.getNetworks();
+ }
+
+
+ /**
+ * Always returns root network title.
+ *
+ */
+ @Override
+ public String getNetworkName() {
+ return "";
+ }
+}
diff --git a/application/src/main/java/cytoscape/data/readers/NestedNetworkReader.java b/application/src/main/java/cytoscape/data/readers/NestedNetworkReader.java
new file mode 100644
index 0000000..41bea45
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/readers/NestedNetworkReader.java
@@ -0,0 +1,51 @@
+/*
+ File: MultiGraphFileReader.java
+
+ Copyright (c) 2009, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.data.readers;
+
+import java.util.List;
+import cytoscape.CyNetwork;
+
+
+/**
+ * Special interface for Graph readers which read nested networks from a file.
+ *
+ * @author kono, ruschein
+ * @since Cytoscape 2.7.0
+ *
+ */
+public interface NestedNetworkReader {
+ /**
+ * Returns all networks, whether nested or not.
+ *
+ * @return A list of networks.
+ *
+ */
+ public List<CyNetwork> getNetworks();
+}
diff --git a/application/src/main/java/cytoscape/data/readers/TextFileReader.java b/application/src/main/java/cytoscape/data/readers/TextFileReader.java
new file mode 100644
index 0000000..63776de
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/readers/TextFileReader.java
@@ -0,0 +1,135 @@
+/*
+ File: TextFileReader.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// TextFileReader.java
+package cytoscape.data.readers;
+
+import cytoscape.logger.CyLogger;
+
+import java.io.*;
+
+
+/**
+ *
+ */
+public class TextFileReader {
+ String filename;
+ StringBuffer strbuf;
+ CyLogger logger = CyLogger.getLogger(TextFileReader.class);
+
+ /**
+ * Creates a new TextFileReader object.
+ *
+ * @param filename DOCUMENT ME!
+ */
+ public TextFileReader(String filename) {
+ this.filename = filename;
+ strbuf = new StringBuffer();
+ } // ctor
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int read() {
+ String newLineOfText;
+ BufferedReader bufferedReader = null;
+ int rv;
+
+ // Start with an empty StringBuffer in case this method is called more than once.
+ strbuf = new StringBuffer();
+ rv = -1;
+
+ try {
+ bufferedReader = new BufferedReader(new FileReader(filename));
+ try {
+ while ((newLineOfText = bufferedReader.readLine()) != null) {
+ strbuf.append(newLineOfText + "\n");
+ }
+ rv = strbuf.length();
+ } catch (IOException e) {
+ logger.warn("IO error reading from text file: "+e.getMessage(), e);
+
+ }
+ } catch (IOException e) {
+ logger.warn("Unable to open text file '"+filename+"': "+e.getMessage(), e);
+ }
+ finally {
+ if (bufferedReader != null) {
+ try {
+ bufferedReader.close();
+ }
+ catch (IOException e) {
+ logger.warn("Unable to close text file '"+filename+"': "+e.getMessage(), e);
+ }
+ }
+ }
+
+ return rv;
+ } // read
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getText() {
+ return (new String(strbuf));
+ } // read
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param argv DOCUMENT ME!
+ */
+ public static void main(String[] argv) {
+ String fileToRead;
+
+ int argCount = argv.length;
+
+ if (argCount == 0)
+ fileToRead = "TextFileReader.java";
+ else
+ fileToRead = argv[0];
+
+ TextFileReader reader = new TextFileReader(fileToRead);
+ int size = reader.read();
+ System.out.println("size of text block: " + size);
+ System.out.println(reader.getText());
+ } // main
+}
diff --git a/application/src/main/java/cytoscape/data/readers/TextHttpReader.java b/application/src/main/java/cytoscape/data/readers/TextHttpReader.java
new file mode 100644
index 0000000..df69ce6
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/readers/TextHttpReader.java
@@ -0,0 +1,173 @@
+/*
+ File: TextHttpReader.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// TextHttpReader.java
+package cytoscape.data.readers;
+
+import java.io.*;
+
+import java.net.*;
+
+
+/**
+ *
+ */
+public class TextHttpReader {
+ InputStreamReader reader;
+ StringBuffer sb;
+ String uri;
+
+ /**
+ * Creates a new TextHttpReader object.
+ *
+ * @param URI DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public TextHttpReader(String URI) throws Exception {
+ uri = URI;
+ sb = new StringBuffer();
+ } // ctor
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public int read() throws Exception {
+ // Start with an empty StringBuffer in case this method is called more than once.
+ sb = new StringBuffer(getPage(uri));
+
+ return sb.length();
+ } // read
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public String getText() throws Exception {
+ if (sb.length() <= 0)
+ read();
+
+ return sb.toString();
+ } // read
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param urlString DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ static public String getPage(String urlString) throws Exception {
+ return getPage(new URL(urlString));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param url DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ * @throws IOException DOCUMENT ME!
+ */
+ static public String getPage(URL url) throws Exception {
+ int characterCount = 0;
+ StringBuffer result = new StringBuffer();
+
+ HttpURLConnection urlConnection = null;
+
+ try {
+ urlConnection = (HttpURLConnection) url.openConnection();
+
+ // Ensure we are reading the real content from url,
+ // and not some out-of-date cached content:
+ urlConnection.setUseCaches(false);
+ int responseCode = urlConnection.getResponseCode();
+ String contentType = urlConnection.getContentType();
+
+ int contentLength = urlConnection.getContentLength();
+
+ String contentEncoding = urlConnection.getContentEncoding();
+
+ if (responseCode != HttpURLConnection.HTTP_OK)
+ throw new IOException("\nHTTP response code: " + responseCode);
+
+ String thisLine;
+ InputStream connStrm = null;
+
+ try {
+ BufferedReader theHTML = null;
+
+ connStrm = urlConnection.getInputStream();
+ try {
+ theHTML = new BufferedReader(new InputStreamReader(connStrm));
+ while ((thisLine = theHTML.readLine()) != null) {
+ result.append(thisLine);
+ result.append("\n");
+ }
+ }
+ finally {
+ if (theHTML != null) {
+ theHTML.close();
+ }
+ }
+ }
+ finally {
+ if (connStrm != null) {
+ connStrm.close();
+ }
+ }
+ }
+ finally {
+ if (urlConnection != null) {
+ urlConnection.disconnect();
+ }
+ }
+
+ return result.toString();
+ } // getPage
+} // TextReader
diff --git a/application/src/main/java/cytoscape/data/readers/TextJarReader.java b/application/src/main/java/cytoscape/data/readers/TextJarReader.java
new file mode 100644
index 0000000..c53b66a
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/readers/TextJarReader.java
@@ -0,0 +1,144 @@
+/*
+ File: TextJarReader.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data.readers;
+
+import cytoscape.*;
+import cytoscape.logger.CyLogger;
+import cytoscape.util.URLUtil;
+
+import java.io.*;
+
+import java.net.*;
+
+import java.util.*;
+import java.util.jar.*;
+
+
+/**
+ *
+ */
+public class TextJarReader {
+ String filename;
+ boolean oldStyle;
+ StringBuffer sb;
+
+ /**
+ * Creates a new TextJarReader object.
+ *
+ * @param urlString DOCUMENT ME!
+ *
+ * @throws IOException DOCUMENT ME!
+ */
+ public TextJarReader(String urlString) throws IOException {
+ if (!urlString.startsWith("jar"))
+ throw new IOException("Ok, so this isn't an IOException, but it's still a problem: "
+ + urlString + " This class only accepts JAR urls!!! "
+ + " See java.net.JarURLConnection for syntax");
+
+ sb = new StringBuffer();
+
+ oldStyle = urlString.matches("jar\\:\\/\\/.+");
+ if (oldStyle) {
+ // to support the old way of doing things
+ filename = urlString.substring(5);
+ } else {
+ // assume that we match proper jar url syntax
+ // jar:<url>!/{file}
+ // see JarURLConnection api for more details
+ filename = urlString;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @throws IOException DOCUMENT ME!
+ */
+ public int read() throws IOException {
+ CyLogger.getLogger().info("-- reading " + filename);
+
+ InputStream is = null;
+ char[] cBuffer = new char[1024];
+ int bytesRead;
+
+ // Start with an empty StringBuffer in case this method is called more than once.
+ sb = new StringBuffer();
+
+ try {
+ InputStreamReader reader = null;
+
+ if (oldStyle) {
+ is = getClass().getResourceAsStream(filename);
+ }
+ else {
+ URL url = new URL(filename);
+ // is = url.openStream();
+ // Use URLUtil to get the InputStream since we might be using a proxy server
+ // and because pages may be cached:
+ is = URLUtil.getBasicInputStream(url);
+ }
+ try {
+ reader = new InputStreamReader(is);
+ while ((bytesRead = reader.read(cBuffer, 0, 1024)) != -1)
+ sb.append(new String(cBuffer, 0, bytesRead));
+ }
+ finally {
+ if (reader != null) {
+ reader.close();
+ }
+ }
+ }
+ finally {
+ if (is != null) {
+ is.close();
+ }
+ }
+
+ return sb.length();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getText() {
+ return sb.toString();
+ }
+}
diff --git a/application/src/main/java/cytoscape/data/readers/VisualStyleBuilder.java b/application/src/main/java/cytoscape/data/readers/VisualStyleBuilder.java
new file mode 100644
index 0000000..45fb147
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/readers/VisualStyleBuilder.java
@@ -0,0 +1,314 @@
+
+/*
+ Copyright (c) 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.data.readers;
+
+import cytoscape.Cytoscape;
+import cytoscape.logger.CyLogger;
+import cytoscape.data.CyAttributes;
+import cytoscape.visual.*;
+import static cytoscape.visual.VisualPropertyDependency.Definition.NODE_SIZE_LOCKED;
+import cytoscape.visual.calculators.*;
+import cytoscape.visual.mappings.*;
+
+import java.util.*;
+import java.lang.Math;
+import java.awt.Color;
+
+/**
+ * Based on the graph/node/edge view information, build new Visual Style.
+ *
+ * This class accepts style properties and adds hidden Cytoscape attributes that
+ * will be used to actually create the style.
+ */
+public class VisualStyleBuilder {
+
+ Map<VisualPropertyType,Map<Object,Object>> valueMaps;
+ Map<VisualPropertyType,Map<Object,Integer>> counts;
+ String name;
+ private boolean nodeSizeLocked = true;
+
+ private int nodeMax;
+ private int edgeMax;
+ private Color backgroundColor;
+
+ /**
+ * Build a new VisualStyleBuilder object whose output style will be called "name".
+ *
+ * @param name the name of the visual style that will be created.
+ */
+ public VisualStyleBuilder(String name) {
+ // because visual style parsing breaks with '.' in the names
+ this.name = name.replaceAll("\\.","_");
+
+ valueMaps = new EnumMap<VisualPropertyType,Map<Object,Object>>(VisualPropertyType.class);
+ counts = new EnumMap<VisualPropertyType,Map<Object,Integer>>(VisualPropertyType.class);
+ this.backgroundColor = null;
+ }
+
+ /**
+ * Build a new VisualStyleBuilder object whose output style will be called "name" based
+ * on JAXB Graphics objects. This constructor is no longer used and is not supported.
+ *
+ * @param newName the name of the visual style that will be created.
+ * @param nodeGraphics the map of node to JAXB Graphics object
+ * @param edgeGraphics the map of edge to JAXB Graphics object
+ * @param globalGraphics the map of network to JAXB Graphics object
+ * @deprecated this should no longer be used and is not functional. Use VisualStyleBuilder(String)
+ * instead and then call addProperty for each value
+ */
+ public VisualStyleBuilder(String newName, Map nodeGraphics, Map edgeGraphics, Map globalGraphics) {
+ this(newName);
+ }
+
+ /**
+ * Build a new VisualStyleBuilder object whose output style will be called "name".
+ *
+ * @param name the name of the visual style that will be created.
+ * @param addOvAttr not used.
+ */
+ public VisualStyleBuilder(String name, boolean addOvAttr) {
+ this(name);
+ }
+
+ /**
+ * Set the background color for the style we build. We need to do this because
+ * our VisualStyleProperty stuff doesn't support global styles.
+ *
+ * @param backgroundColor the color
+ */
+ public void setBackgroundColor(Color backgroundColor) {
+ this.backgroundColor = backgroundColor;
+ }
+
+ /**
+ * Actually build the style using the provided properties
+ */
+ public void buildStyle() {
+ // First, get our current style information.
+ VisualMappingManager vm = Cytoscape.getVisualMappingManager();
+
+ String styleName = name + " style";
+
+ // Create the new style
+ final VisualStyle graphStyle = new VisualStyle(styleName);
+ final List<Calculator> calcs = new ArrayList<Calculator>(vm.getCalculatorCatalog()
+ .getCalculators());
+ final Calculator dummy = calcs.get(0);
+ graphStyle.getNodeAppearanceCalculator().setCalculator(dummy);
+
+ NodeAppearanceCalculator nac = graphStyle.getNodeAppearanceCalculator();
+ EdgeAppearanceCalculator eac = graphStyle.getEdgeAppearanceCalculator();
+ GlobalAppearanceCalculator gac = graphStyle.getGlobalAppearanceCalculator();
+
+ if (backgroundColor != null)
+ gac.setDefaultBackgroundColor(backgroundColor);
+
+ graphStyle.getDependency().set(NODE_SIZE_LOCKED, nodeSizeLocked);
+
+ processCounts();
+
+ for ( VisualPropertyType type : valueMaps.keySet() ) {
+
+ Map<Object,Object> valMap = valueMaps.get(type);
+
+ // If there is more than one value specified for a given
+ // visual property, or if only a subset of nodes/edges
+ // have a property then create a mapping and calculator.
+ if ( createMapping(type) ) {
+
+ DiscreteMapping dm = new DiscreteMapping( type.getVisualProperty().getDefaultAppearanceObject(),
+ getAttrName(type),
+ type.isNodeProp() ?
+ ObjectMapping.NODE_MAPPING :
+ ObjectMapping.EDGE_MAPPING );
+
+ CyLogger.getLogger().info( "ValueMaps size: " + valueMaps.get(type).size() );
+ dm.putAll( valMap );
+
+ Calculator calc = new BasicCalculator("VisualStyleBuilder-" + getAttrName(type), dm, type);
+
+ if ( type.isNodeProp() )
+ nac.setCalculator( calc );
+ else
+ eac.setCalculator( calc );
+
+ // Otherwise, set the default appearance value for the visual style
+ // and then remove the attribute that was created.
+ } else {
+ if ( type.isNodeProp() ) {
+ for ( Object key : valMap.keySet() ) {
+
+ // System.out.println("Node key = "+key);
+
+ nac.getDefaultAppearance().set( type, valMap.get(key) );
+ }
+ Cytoscape.getNodeAttributes().deleteAttribute(getAttrName(type));
+ } else {
+ for ( Object key : valMap.keySet() ) {
+ // System.out.println("Edge key = "+key);
+ eac.getDefaultAppearance().set( type, valMap.get(key) );
+ }
+ Cytoscape.getEdgeAttributes().deleteAttribute(getAttrName(type));
+ }
+ }
+ }
+
+ VisualMappingManager vizmapper = Cytoscape.getVisualMappingManager();
+ CalculatorCatalog catalog = vizmapper.getCalculatorCatalog();
+
+ // Remove this in case we've already loaded this network once
+ catalog.removeVisualStyle(styleName);
+
+ // Now, attempt to add it
+ catalog.addVisualStyle(graphStyle);
+ vizmapper.setVisualStyle(graphStyle);
+ }
+
+ private String getAttrName(VisualPropertyType type) {
+ return "vizmap:"+name + " " + type.toString();
+ }
+
+ /**
+ * This method actually adds a property to be considered for inclusion into
+ * the resulting style.
+ *
+ * @param id the id of the node or edge
+ * @param type the type of the property
+ * @param desc the property value
+ */
+ public void addProperty(String id, VisualPropertyType type, String desc) {
+ CyAttributes attrs;
+ Object value = type.getValueParser().parseStringValue(desc);
+ if (value == null)
+ return;
+ if ( type.isNodeProp() )
+ attrs = Cytoscape.getNodeAttributes();
+ else
+ attrs = Cytoscape.getEdgeAttributes();
+
+ attrs.setAttribute(id, getAttrName(type), value.toString());
+
+ String vString = value.toString();
+
+ // store the value
+ if ( !valueMaps.containsKey(type) )
+ valueMaps.put( type, new HashMap<Object,Object>() );
+ valueMaps.get(type).put( vString, value );
+
+ // store the count
+ if ( !counts.containsKey(type) )
+ counts.put( type, new HashMap<Object,Integer>() );
+
+ if ( !counts.get(type).containsKey(vString) )
+ counts.get(type).put( vString, 0 );
+
+ counts.get(type).put( vString, counts.get(type).get(vString) + 1 );
+ }
+
+ /**
+ * This method lock/unlock the size object (Node Width, Node Height) in NodeAppearanceCalculator
+ * If unlocked, we can modify both width and height of node
+ *
+ * @param pLock
+ */
+
+ public void setNodeSizeLocked(boolean pLock){
+ nodeSizeLocked = pLock;
+ }
+
+ /**
+ * Processes the counts for the various visual properties and establishes
+ * how many nodes and edges there are.
+ */
+ private void processCounts() {
+ Map<VisualPropertyType,Integer> cm = new EnumMap<VisualPropertyType,Integer>(VisualPropertyType.class);
+ for ( VisualPropertyType vpt : counts.keySet() ) {
+ int total = 0;
+ for ( Object o : counts.get(vpt).keySet() ) {
+ total += counts.get(vpt).get(o);
+ }
+ cm.put(vpt,total);
+ CyLogger.getLogger().info(vpt + " " + total);
+ }
+
+ nodeMax = 0;
+ edgeMax = 0;
+ for ( VisualPropertyType vpt : counts.keySet() ) {
+ if ( counts.get(vpt).size() == 1 ) {
+ for ( Object o : counts.get(vpt).keySet() ) {
+ if ( vpt.isNodeProp() )
+ nodeMax = Math.max( counts.get(vpt).get(o), nodeMax );
+ else
+ edgeMax = Math.max( counts.get(vpt).get(o), edgeMax );
+ }
+ }
+ }
+ }
+
+ /**
+ * This method determines whether or not to create a mapping for
+ * this visual property type. There are two times when you want
+ * to create a mapping: 1) when there is more than one key mapped
+ * to a value for type and 2) when only one key is mapped to a value,
+ * but only a subset of nodes or edges have that mapping (which is
+ * to say the property doesn't hold for all nodes or all edges).
+ */
+ private boolean createMapping(VisualPropertyType vpt) {
+ // if there is more than one mapping
+ if ( counts.get(vpt).size() > 1 )
+ return true;
+
+ // check the number of times the value is mapped
+ // relative to the number of nodes or edges
+ for ( Object o : counts.get(vpt).keySet() ) {
+ int ct = counts.get(vpt).get(o).intValue();
+ if ( vpt.isNodeProp() ) {
+ if ( ct < nodeMax )
+ return true;
+ else
+ return false;
+ } else {
+ if ( ct < edgeMax )
+ return true;
+ else
+ return false;
+ }
+ }
+
+ return false;
+ }
+}
diff --git a/application/src/main/java/cytoscape/data/readers/XGMMLException.java b/application/src/main/java/cytoscape/data/readers/XGMMLException.java
new file mode 100644
index 0000000..456f6c6
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/readers/XGMMLException.java
@@ -0,0 +1,52 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data.readers;
+
+
+/**
+ *
+ * Exception for XGMML Reader.
+ *
+ */
+public class XGMMLException extends RuntimeException {
+ /**
+ * Creates a new XGMMLException object.
+ *
+ * @param message DOCUMENT ME!
+ */
+ public XGMMLException(String message) {
+ super(message);
+ }
+}
diff --git a/application/src/main/java/cytoscape/data/readers/XGMMLParser.java b/application/src/main/java/cytoscape/data/readers/XGMMLParser.java
new file mode 100644
index 0000000..41f1db6
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/readers/XGMMLParser.java
@@ -0,0 +1,1755 @@
+/*
+ File: XGMMLParser.java
+
+ Copyright (c) 2007, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data.readers;
+
+import cytoscape.Cytoscape;
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.CyEdge;
+import cytoscape.groups.CyGroupManager;
+import cytoscape.groups.CyGroup;
+import cytoscape.data.CyAttributes;
+import cytoscape.data.Semantics;
+import cytoscape.data.attr.MultiHashMap;
+import cytoscape.data.attr.MultiHashMapDefinition;
+import cytoscape.util.intr.IntObjHash;
+import cytoscape.util.intr.IntEnumerator;
+import cytoscape.logger.CyLogger;
+
+import org.xml.sax.helpers.DefaultHandler;
+import org.xml.sax.helpers.AttributesImpl;
+import org.xml.sax.Attributes;
+import org.xml.sax.Locator;
+import org.xml.sax.SAXException;
+import org.xml.sax.SAXParseException;
+import java.util.Stack;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+import java.awt.Color;
+import java.awt.geom.Point2D;
+
+
+interface Handler {
+ public ParseState handle(String tag, Attributes atts, ParseState current) throws SAXException;
+}
+
+
+enum ParseState {
+ NONE("none"),
+ RDF("RDF"),
+ NETATT("Network Attribute"),
+ NODEATT("Node Attribute"),
+ EDGEATT("Edge Attribute"),
+ // Types of attributes that require special handling
+ LISTATT("List Attribute"),
+ LISTELEMENT("List Element"),
+ MAPATT("Map Attribute"),
+ MAPELEMENT("Map Element"),
+ COMPLEXATT("Complex Attribute"),
+ NODEGRAPHICS("Node Graphics"),
+ EDGEGRAPHICS("Edge Graphics"),
+ // Handle edge handles
+ EDGEBEND("Edge Bend"),
+ EDGEHANDLE("Edge Handle"),
+ EDGEHANDLEATT("Edge Handle Attribute"),
+ NODE("Node Element"),
+ EDGE("Edge Element"),
+ GROUP("Group"),
+ GRAPH("Graph Element"),
+ RDFDESC("RDF Description"),
+ ANY("any");
+
+ private String name;
+ private ParseState(String str) { name = str; }
+ public String toString() { return name; }
+};
+
+
+enum RDFTags { FORMAT, TYPE, DESC, DATE, SOURCE, IDENTIFIER};
+
+
+enum ObjectType {
+ NONE("none"),
+ STRING("string"),
+ BOOLEAN("boolean"),
+ REAL("real"),
+ INTEGER("integer"),
+ LIST("list"),
+ MAP("map"),
+ COMPLEX("complex");
+
+ private String name;
+ private ObjectType (String s) { name = s; }
+ public String toString() { return name; }
+};
+
+
+class XGMMLParser extends DefaultHandler {
+ final static String XLINK = "http://www.w3.org/1999/xlink";
+ final static String RDF = "http://www.w3.org/1999/02/22-rdf-syntax-ns#";
+ final static String DUBLINCORE = "http://purl.org/dc/elements/1.1/";
+
+ private static CyLogger logger = CyLogger.getLogger(XGMMLParser.class);
+
+ private Locator locator = null;
+ private ParseState parseState = ParseState.NONE;
+ private Stack<ParseState>stateStack = null;
+ private String networkName = null;
+ private String currentCData = null;
+ private String backgroundColor = null;
+ private double graphZoom = 1.0;
+ private double graphCenterX = 0.0;
+ private double graphCenterY = 0.0;
+ private boolean nodeSizeLocked = false;
+
+ //
+ private double documentVersion = 1.0;
+
+ /* RDF Data */
+ private String RDFDate = null;
+ private String RDFTitle = null;
+ private String RDFIdentifier = null;
+ private String RDFDescription = null;
+ private String RDFSource = null;
+ private String RDFType = null;
+ private String RDFFormat = null;
+
+ /* Internal lists of the created nodes and edges */
+ private List<CyNode> nodeList = null;
+ private List<CyEdge> edgeList = null;
+ /* Map of Groups to lists of node references that haven't been processed */
+ private HashMap<CyNode,List<String>> nodeLinks = null;
+ /* Map of XML ID's to nodes */
+ private HashMap<String,CyNode> idMap = null;
+ /* Map of group nodes to children */
+ private HashMap<CyNode,List<CyNode>> groupMap = null;
+ private HashMap<CyNode,List<CyEdge>> groupEdgeMap = null;
+ /* List of nodes we weren't able to resolve */
+ private HashMap<CyNode, CyEdge> unresolvedNodeMap = null;
+ /* List of edges we weren't able to resolve */
+ private HashMap<CyEdge, CyNode[]> unresolvedEdgeMap = null;
+
+ // Groups might actually recurse on us, so we need to
+ // maintain a stack
+ private Stack<CyNode> groupStack = null;
+
+ /* Map of nodes to graphics information */
+ private HashMap<CyNode, Attributes> nodeGraphicsMap = null;
+ /* Map of edges to graphics information */
+ private HashMap<CyEdge, Attributes> edgeGraphicsMap = null;
+
+ private CyNode currentNode = null;
+ private CyEdge currentEdge = null;
+ private CyNode currentGroupNode = null;
+
+ /* Attribute values */
+ private ParseState attState = ParseState.NONE;
+ private String currentAttributeID = null;
+ private CyAttributes currentAttributes = null;
+ private String objectTarget = null;
+
+ /* Complex attribute data */
+ private int level = 0;
+ private int numKeys = 0;
+ private Map complexMap[] = null;
+ private Object complexKey[] = null;
+ private byte[] attributeDefinition = null;
+ private byte valueType;
+ private boolean complexAttributeDefined = false;
+ private MultiHashMap mhm = null;
+
+ /* Edge handle list */
+ private List<String> handleList = null;
+
+ /* X handle */
+ private String edgeBendX = null;
+ /* Y handle */
+ private String edgeBendY = null;
+
+ private EqnAttrTracker eqnAttrTracker = null;
+
+ /**
+ * Main parse table. This table controls the state machine, and follows
+ * the standard format for a state machine:
+ * StartState, Tag, EndState, Method
+ */
+ final Object[][] startParseTable = {
+ // Initial state. It's all noise until we see our <graph> tag
+ {ParseState.NONE, "graph", ParseState.GRAPH, new HandleGraph()},
+ {ParseState.GRAPH, "att", ParseState.NETATT, new HandleNetworkAttribute()},
+ {ParseState.NETATT, "rdf", ParseState.RDF, null},
+ // RDF tags -- most of the data for the RDF tags comes from the CData
+ {ParseState.RDF, "description", ParseState.RDFDESC, new handleRDF()},
+ {ParseState.RDFDESC, "type", ParseState.RDFDESC, null},
+ {ParseState.RDFDESC, "description", ParseState.RDFDESC, null},
+ {ParseState.RDFDESC, "identifier", ParseState.RDFDESC, null},
+ {ParseState.RDFDESC, "date", ParseState.RDFDESC, null},
+ {ParseState.RDFDESC, "title", ParseState.RDFDESC, null},
+ {ParseState.RDFDESC, "source", ParseState.RDFDESC, null},
+ {ParseState.RDFDESC, "format", ParseState.RDFDESC, null},
+ // Handle our nodes
+ {ParseState.GRAPH, "node", ParseState.NODE, new handleNode()},
+ {ParseState.NODE, "graphics", ParseState.NODEGRAPHICS, new handleNodeGraphics()},
+ {ParseState.NODE, "att", ParseState.NODEATT, new handleNodeAttribute()},
+ {ParseState.NODEGRAPHICS, "att", ParseState.NODEGRAPHICS, new handleNodeGraphics()},
+ // Hanlde possible group
+ {ParseState.NODEATT, "graph", ParseState.GROUP, new handleGroup()},
+ {ParseState.GROUP, "node", ParseState.NODE, new handleGroupNode()},
+ {ParseState.GROUP, "edge", ParseState.EDGE, new handleEdge()},
+ // Handle our edges
+ {ParseState.GRAPH, "edge", ParseState.EDGE, new handleEdge()},
+ {ParseState.EDGE, "att", ParseState.EDGEATT, new handleEdgeAttribute()},
+ {ParseState.EDGE, "graphics", ParseState.EDGEGRAPHICS, new handleEdgeGraphics()},
+ {ParseState.EDGEGRAPHICS, "att", ParseState.EDGEGRAPHICS, new handleEdgeGraphics()},
+ {ParseState.EDGEBEND, "att", ParseState.EDGEHANDLE, new handleEdgeHandle()},
+ {ParseState.EDGEHANDLE, "att", ParseState.EDGEHANDLE, new handleEdgeHandle()},
+ {ParseState.LISTATT, "att", ParseState.LISTELEMENT, new handleListAttribute()},
+ {ParseState.LISTELEMENT, "att", ParseState.LISTELEMENT, new handleListAttribute()},
+ {ParseState.MAPATT, "att", ParseState.MAPELEMENT, new handleMapAttribute()},
+ {ParseState.MAPELEMENT, "att", ParseState.MAPELEMENT, new handleListAttribute()},
+ {ParseState.COMPLEXATT, "att", ParseState.COMPLEXATT, new handleComplexAttribute()},
+ };
+
+ /**
+ * End tag parse table. This table handles calling methods on end tags
+ * under those circumstances where the CData is used, or when it is
+ * important to take some sort of post-action (e.g. associating nodes to
+ * groups)
+ */
+ final Object[][] endParseTable = {
+ {ParseState.RDFDESC, "type", ParseState.RDFDESC, new handleRDFType()},
+ {ParseState.RDFDESC, "description", ParseState.RDFDESC, new handleRDFDescription()},
+ {ParseState.RDFDESC, "identifier", ParseState.RDFDESC, new handleRDFIdentifier()},
+ {ParseState.RDFDESC, "date", ParseState.RDFDESC, new handleRDFDate()},
+ {ParseState.RDFDESC, "title", ParseState.RDFDESC, new handleRDFTitle()},
+ {ParseState.RDFDESC, "source", ParseState.RDFDESC, new handleRDFSource()},
+ {ParseState.RDFDESC, "format", ParseState.RDFDESC, new handleRDFFormat()},
+ // Special handling for group completion
+ {ParseState.GROUP, "graph", ParseState.NONE, new handleGroupDone()},
+ // Special handling for edge handles
+ {ParseState.EDGEHANDLE, "att", ParseState.EDGEBEND, new handleEdgeHandleDone()},
+ {ParseState.EDGEBEND, "att", ParseState.EDGEBEND, new handleEdgeHandleList()},
+ // Special handling for complex attributes
+ {ParseState.COMPLEXATT, "att", ParseState.COMPLEXATT, new handleComplexAttributeDone()},
+ {ParseState.GRAPH, "graph", ParseState.NONE, new HandleGraphDone()},
+
+ {ParseState.LISTATT, "att", ParseState.NONE, new handleListAttributeDone()},
+ {ParseState.MAPATT, "att", ParseState.NONE, new handleMapAttributeDone()},
+ };
+
+
+ /********************************************************************
+ * Routines to handle attributes
+ *******************************************************************/
+
+ /**
+ * Return the string attribute value for the attribute indicated by "key". If
+ * no such attribute exists, return null. In particular, this routine looks
+ * for an attribute with a <b>name</b> or <b>label</b> of <i>key</i> and
+ * returns the <b>value</b> of that attribute.
+ *
+ * @param atts the attributes
+ * @param key the specific attribute to get
+ * @return the value for "key" or null if no such attribute exists
+ */
+ static String getAttributeValue(final Attributes atts, final String key) {
+ String name = atts.getValue("name");
+ if (name == null)
+ name = atts.getValue("label");
+
+ if (name != null && name.equals(key))
+ return atts.getValue("value");
+
+ return null;
+ }
+
+
+ /**
+ * Return the double attribute value for the attribute indicated by "key". If no such attribute exists, we throw a SAXParseException.
+ * In particular, this routine looks for an attribute with a <b>name</b> or <b>label</b> of <i>key</i> and returns the <b>value</b>
+ * of that attribute.
+ *
+ * @param atts the attributes
+ * @param key the specific attribute to get
+ * @return the value for "key."
+ * @throws SAXParseException if we either can't find the requested attribute or if its value cannot be converted to a double.
+ */
+ double getDoubleAttributeValue(final Attributes atts, final String key) throws SAXParseException {
+ final String attribute = getAttributeValue(atts, key);
+ if (attribute == null)
+ return 0.0;
+ try {
+ return Double.parseDouble(attribute);
+ } catch (final Exception e) {
+ throw new SAXParseException("Unable to convert '" + attribute + "' to a DOUBLE", locator);
+ }
+ }
+
+ /**
+ * Return the boolean attribute value for the attribute indicated by "key". If no such attribute exists, we throw a SAXParseException.
+ * In particular, this routine looks for an attribute with a <b>name</b> or <b>label</b> of <i>key</i> and returns the <b>value</b>
+ * of that attribute.
+ *
+ * @param atts the attributes
+ * @param key the specific attribute to get
+ * @return the value for "key."
+ * @throws SAXParseException if we either can't find the requested attribute or if its value cannot be converted to a double.
+ */
+ boolean getBooleanAttributeValue(final Attributes atts, final String key) throws SAXParseException {
+ final String attribute = getAttributeValue(atts, key);
+ if (attribute == null)
+ return false;
+ try {
+ return Boolean.parseBoolean(attribute);
+ } catch (final Exception e) {
+ throw new SAXParseException("Unable to convert '" + attribute + "' to a BOOLEAN", locator);
+ }
+ }
+
+
+ /**
+ * Return the typed attribute value for the passed attribute. In this case,
+ * the caller has already determined that this is the correct attribute and
+ * we just lookup the value. This routine is responsible for type conversion
+ * consistent with the passed argument.
+ *
+ * @param type the ObjectType of the value
+ * @param atts the attributes
+ * @return the value of the attribute in the appropriate type or a string if the value starts with an equal sign
+ */
+ Object getTypedAttributeValueOrEquation(final ObjectType type, final Attributes atts) throws SAXParseException {
+ final String value = atts.getValue("value");
+ if (value != null && value.length() >= 2 && value.charAt(0) == '=') // Must be an equation!
+ return value;
+ try {
+ return getTypedValue(type, value);
+ } catch (final Exception e) {
+ throw new SAXParseException("Unable to convert '" + value + "' to type " + type.toString(), locator);
+ }
+ }
+
+
+ /**
+ * Return the typed attribute value for the passed attribute. In this case,
+ * the caller has already determined that this is the correct attribute and
+ * we just lookup the value. This routine is responsible for type conversion
+ * consistent with the passed argument.
+ *
+ * @param type the ObjectType of the value
+ * @param atts the attributes
+ * @return the value of the attribute in the appropriate type
+ */
+ Object getTypedAttributeValue(final ObjectType type, final Attributes atts) throws SAXParseException {
+ final String value = atts.getValue("value");
+ try {
+ return getTypedValue(type, value);
+ } catch (final Exception e) {
+ throw new SAXParseException("Unable to convert '" + value + "' to type " + type.toString(), locator);
+ }
+ }
+
+
+ /**
+ * Return the typed value for the passed value.
+ *
+ * @param type the ObjectType of the value
+ * @param value the value to type
+ * @return the typed value
+ */
+ static Object getTypedValue(ObjectType type, String value) {
+ switch(type) {
+ case BOOLEAN:
+ if (value != null)
+ return new Boolean(value);
+ break;
+ case REAL:
+ if (value != null)
+ return new Double(value);
+ break;
+ case INTEGER:
+ if (value != null)
+ return new Integer(value);
+ break;
+ case STRING:
+ if (value != null) {
+ // Make sure we convert our newlines and tabs back
+ String sAttr = value.replace("\\t","\t");
+ sAttr = sAttr.replace("\\n","\n");
+ return sAttr;
+ }
+ break;
+ case LIST:
+ return new ArrayList();
+ case MAP:
+ return new HashMap();
+ }
+ return null;
+ }
+
+ /**
+ * Return the attribute value for the attribute indicated by "key". If
+ * no such attribute exists, return null.
+ *
+ * @param atts the attributes
+ * @param key the specific attribute to get
+ * @return the value for "key" or null if no such attribute exists
+ */
+ static String getAttribute(Attributes atts, String key) {
+ return atts.getValue(key);
+ }
+
+ /**
+ * Return the attribute value for the attribute indicated by "key". If
+ * no such attribute exists, return null.
+ *
+ * @param atts the attributes
+ * @param key the specific attribute to get
+ * @param ns the namespace for the attribute we're interested in
+ * @return the value for "key" or null if no such attribute exists
+ */
+ static String getAttributeNS(Attributes atts, String key, String ns) {
+ if (atts.getValue(ns, key) != null) {
+ return atts.getValue(ns, key);
+ } else {
+ return atts.getValue(key);
+ }
+ }
+
+ /**
+ * Return the integer attribute value for the attribute indicated by "key". If
+ * no such attribute exists, return null.
+ *
+ * @param atts the attributes
+ * @param key the specific attribute to get
+ * @return the value for "key" or null if no such attribute exists
+ */
+ static int getIntegerAttribute(Attributes atts, String key) {
+ String attribute = atts.getValue(key);
+ if (attribute == null)
+ return 0;
+ return (new Integer(attribute)).intValue();
+ }
+
+ /**
+ * Return the integer attribute value for the attribute indicated by "key". If
+ * no such attribute exists, return null.
+ *
+ * @param atts the attributes
+ * @param key the specific attribute to get
+ * @param ns the namespace for the attribute we're interested in
+ * @return the value for "key" or null if no such attribute exists
+ */
+ static int getIntegerAttributeNS(Attributes atts, String key, String ns) {
+ String attribute = atts.getValue(ns, key);
+ if (attribute == null)
+ return 0;
+ return (new Integer(attribute)).intValue();
+ }
+
+ /**
+ * Return the double attribute value for the attribute indicated by "key". If
+ * no such attribute exists, return null.
+ *
+ * @param atts the attributes
+ * @param key the specific attribute to get
+ * @return the value for "key" or null if no such attribute exists
+ */
+ static double getDoubleAttribute(Attributes atts, String key) {
+ String attribute = atts.getValue(key);
+ if (attribute == null)
+ return 0.0;
+ return (new Double(attribute)).doubleValue();
+ }
+
+ /**
+ * Return the double attribute value for the attribute indicated by "key". If
+ * no such attribute exists, return null.
+ *
+ * @param atts the attributes
+ * @param key the specific attribute to get
+ * @param ns the namespace for the attribute we're interested in
+ * @return the value for "key" or null if no such attribute exists
+ */
+ static double getDoubleAttributeNS(Attributes atts, String key, String ns) {
+ String attribute = atts.getValue(ns, key);
+ if (attribute == null)
+ return 0;
+ return (new Double(attribute)).doubleValue();
+ }
+
+ /**
+ * Return the Color attribute value for the attribute indicated by "key". If
+ * no such attribute exists, return null.
+ *
+ * @param atts the attributes
+ * @param key the specific attribute to get
+ * @return the value for "key" or null if no such attribute exists
+ */
+ static Color getColorAttribute(Attributes atts, String key) {
+ String attribute = atts.getValue(key);
+ if (attribute == null)
+ return null;
+ return new Color(Integer.parseInt(attribute.substring(1), 16));
+ }
+
+
+ /**
+ * Main constructor for our parser. Initialize any local arrays. Note that this
+ * parser is designed to be as memory efficient as possible. As a result, a minimum
+ * number of local data structures are created.
+ */
+ XGMMLParser() {
+ stateStack = new Stack<ParseState>();
+ groupStack = new Stack<CyNode>();
+ nodeList = new ArrayList<CyNode>();
+ edgeList = new ArrayList<CyEdge>();
+ nodeLinks = new HashMap<CyNode,List<String>>();
+ nodeGraphicsMap = new HashMap<CyNode, Attributes>();
+ edgeGraphicsMap = new HashMap<CyEdge, Attributes>();
+ idMap = new HashMap<String,CyNode>();
+ eqnAttrTracker = Cytoscape.getEqnAttrTracker();
+ unresolvedNodeMap = new HashMap<CyNode,CyEdge>();
+ unresolvedEdgeMap = new HashMap<CyEdge,CyNode[]>();
+ }
+
+
+ /********************************************************************
+ * Interface routines. These routines are called by the XGMMLReader
+ * to get the resulting data.
+ *******************************************************************/
+
+ int[] getNodeIndicesArray() {
+ int[] array = new int[nodeList.size()];
+ for (int i = 0; i < nodeList.size(); i++)
+ array[i] = nodeList.get(i).getRootGraphIndex();
+ return array;
+ }
+
+
+ int[] getEdgeIndicesArray() {
+ int[] array = new int[edgeList.size()];
+ for (int i = 0; i < edgeList.size(); i++)
+ array[i] = edgeList.get(i).getRootGraphIndex();
+ return array;
+ }
+
+
+ String getNetworkName() {
+ return networkName;
+ }
+
+
+ private Class mapCytoscapeAttribTypeToEqnType(final byte attribType) {
+ switch (attribType) {
+ case CyAttributes.TYPE_BOOLEAN:
+ return Boolean.class;
+ case CyAttributes.TYPE_INTEGER:
+ return Long.class;
+ case CyAttributes.TYPE_FLOATING:
+ return Double.class;
+ case CyAttributes.TYPE_STRING:
+ return String.class;
+ case CyAttributes.TYPE_SIMPLE_LIST:
+ return List.class;
+ default:
+ throw new IllegalStateException("can't map Cytoscape type " + attribType + " to equation return type!");
+ }
+ }
+
+
+ HashMap<CyNode, Attributes> getNodeGraphics() {
+ return nodeGraphicsMap;
+ }
+
+
+ HashMap<CyEdge, Attributes> getEdgeGraphics() {
+ return edgeGraphicsMap;
+ }
+
+
+ Color getBackgroundColor() {
+ if (backgroundColor == null)
+ return null;
+ return new Color(Integer.parseInt(backgroundColor.substring(1), 16));
+ }
+
+
+ double getGraphViewZoomLevel() {
+ return graphZoom;
+ }
+
+
+ boolean getNodeSizeLocked() {
+ return nodeSizeLocked;
+ }
+
+ Point2D getGraphViewCenter() {
+ if (graphCenterX == 0.0 && graphCenterY == 0.0)
+ return null;
+ return new Point2D.Double(graphCenterX, graphCenterY);
+ }
+
+
+ HashMap<CyNode, List<CyNode>> getGroupMap() {
+ return groupMap;
+ }
+
+ HashMap<CyNode, List<CyEdge>> getGroupEdgeMap() {
+ return groupEdgeMap;
+ }
+
+
+ void setMetaData(CyNetwork network) {
+ MetadataParser mdp = new MetadataParser(network);
+ if (RDFType != null)
+ mdp.setMetadata(MetadataEntries.TYPE, RDFType);
+ if (RDFDate != null)
+ mdp.setMetadata(MetadataEntries.DATE, RDFDate);
+ if (RDFTitle != null)
+ mdp.setMetadata(MetadataEntries.TITLE, RDFTitle);
+ if (RDFDescription != null)
+ mdp.setMetadata(MetadataEntries.DESCRIPTION, RDFDescription);
+ if (RDFSource != null)
+ mdp.setMetadata(MetadataEntries.SOURCE, RDFSource);
+ if (RDFFormat != null)
+ mdp.setMetadata(MetadataEntries.FORMAT, RDFFormat);
+ if (RDFIdentifier != null)
+ mdp.setMetadata(MetadataEntries.IDENTIFIER, RDFIdentifier);
+ }
+
+
+ /********************************************************************
+ * Handler routines. The following routines are called directly from
+ * the SAX parser.
+ *******************************************************************/
+
+ /**
+ * startElement is called whenever the SAX parser sees a start tag. We
+ * use this as the way to fire our state table.
+ *
+ * @param namespace the URL of the namespace (full spec)
+ * @param localName the tag itself, stripped of all namespace stuff
+ * @param qName the tag with the namespace prefix
+ * @param atts the Attributes list from the tag
+ */
+ public void startElement(String namespace, String localName, String qName, Attributes atts) throws SAXException {
+ /*
+ logger.debug("startElement("+namespace+", "+localName+", "+qName+", ");
+ for (int i = 0; i < atts.getLength(); i++) {
+ logger.debug(atts.getQName(i)+"="+atts.getValue(i)+" ");
+ }
+ logger.debug(")");
+ */
+
+ ParseState nextState = handleState(startParseTable, parseState, localName, atts);
+
+ stateStack.push(parseState);
+ parseState = nextState;
+ }
+
+
+ /**
+ * endElement is called whenever the SAX parser sees an end tag. We
+ * use this as the way to fire our state table.
+ *
+ * @param uri the URL of the namespace (full spec)
+ * @param localName the tag itself, stripped of all namespace stuff
+ * @param qName the tag with the namespace prefix
+ */
+ public void endElement(String uri, String localName, String qName) throws SAXException {
+ // logger.debug("endElement("+uri+", "+localName+", "+qName+")");
+
+ handleState(endParseTable, parseState, localName, null);
+
+ parseState = stateStack.pop();
+ }
+
+
+ /**
+ * characters is called to handle CData
+ *
+ * @param ch the character data
+ * @param start the start of the data for this tag
+ * @param length the number of bytes for this tag
+ */
+ public void characters(char[] ch, int start, int length) {
+ currentCData = new String(ch, start, length);
+ }
+
+
+ /**
+ * fatalError -- handle a fatal parsing error
+ *
+ * @param e the exception that generated the error
+ */
+ public void fatalError(SAXParseException e) throws SAXException {
+ String err = "Fatal parsing error on line "+e.getLineNumber()+" -- '"+e.getMessage()+"'";
+ throw new SAXException(err);
+ }
+
+
+ /**
+ * error -- handle a parsing error
+ *
+ * @param e the exception that generated the error
+ */
+ public void error(SAXParseException e) {
+ logger.warn("Parsing error on line "+e.getLineNumber()+" -- '"+e.getMessage()+"'. Attempting to recover");
+ }
+
+
+ /**
+ * Set the document locator to help us construct our own exceptions
+ *
+ * @param locator the document locator to set
+ */
+ public void setDocumentLocator(Locator locator) {
+ this.locator = locator;
+ }
+
+
+ /********************************************************************
+ * Private parser routines. The following routines are used to
+ * manage the state data.
+ *******************************************************************/
+
+ /**
+ * handleState takes as input a state table, the current state, and
+ * the tag. It then looks for a match in the state table of current
+ * state and tag, then it calls the appropriate handler.
+ *
+ * @param table the state table to use
+ * @param currentState the current state
+ * @param tag the element tag
+ * @param atts the Attributes associated with this tag. These will
+ * be passed to the handler
+ * @return the new state
+ */
+ private ParseState handleState(Object[][] table, ParseState currentState, String tag, Attributes atts) throws SAXException {
+ // If our element table ever gets long, we may want to make
+ // this more efficient with a hash or something
+ for (int i = 0; i < table.length; i++) {
+ if ((table[i][0] == currentState) && tag.equals(table[i][1])) {
+ Handler handler = (Handler)table[i][3];
+ if (handler != null)
+ return handler.handle(tag, atts, (ParseState)table[i][2]);
+ return (ParseState)table[i][2];
+ }
+ }
+ return currentState; // Throw an exception?
+ }
+
+
+ /********************************************************************
+ * Element handling routines. The following routines are the methods
+ * called by the state mechine.
+ *******************************************************************/
+
+ class HandleGraph implements Handler {
+ public ParseState handle(String tag, Attributes atts, ParseState current) throws SAXException {
+ String name = getLabel(atts);
+ if (name != null)
+ networkName = name;
+ return current;
+ }
+ }
+
+
+ /**
+ * HandleGraphDone is called when we finish parsing the entire XGMML file. This allows us to do
+ * deal with some cleanup line creating all of our groups, etc.
+ */
+ class HandleGraphDone implements Handler {
+ public ParseState handle(String tag, Attributes atts, ParseState current) throws SAXException {
+ // Resolve any unresolve node references
+ if (nodeLinks != null) {
+ for (CyNode groupNode : nodeLinks.keySet()) {
+ if (!groupMap.containsKey(groupNode)) {
+ groupMap.put(groupNode, new ArrayList<CyNode>());
+ }
+ List<CyNode>groupList = groupMap.get(groupNode);
+ for (String ref: nodeLinks.get(groupNode)) {
+ if (idMap.containsKey(ref)) {
+ groupList.add(idMap.get(ref));
+ }
+ }
+ }
+ }
+
+ // Finally, if we have any unresolved edges or nodes, remove them from the root graph
+ for (CyEdge edge: unresolvedEdgeMap.keySet()) {
+ logger.warning("Warning: one of the nodes for edge '"+edge.getIdentifier()+"' is missing: "+
+ "skipping this edge");
+ Cytoscape.getRootGraph().removeEdge(edge.getRootGraphIndex());
+ }
+ unresolvedEdgeMap.clear();
+
+ for (CyNode node: unresolvedNodeMap.keySet()) {
+ Cytoscape.getRootGraph().removeNode(node.getRootGraphIndex());
+ }
+ unresolvedNodeMap.clear();
+
+ return current;
+ }
+ }
+
+
+ class HandleNetworkAttribute implements Handler {
+ public ParseState handle(String tag, Attributes atts, ParseState current) throws SAXException {
+ currentAttributes = Cytoscape.getNetworkAttributes();
+ attState = current;
+ ParseState nextState = current;
+ // Look for "special" network attributes
+ if (getAttributeValue(atts, "backgroundColor") != null) {
+ backgroundColor = getAttributeValue(atts, "backgroundColor");
+ } else if (getAttributeValue(atts, "documentVersion") != null) {
+ documentVersion = getDoubleAttributeValue(atts, "documentVersion");
+ } else if (getAttributeValue(atts, "GRAPH_VIEW_ZOOM") != null) {
+ graphZoom = getDoubleAttributeValue(atts, "GRAPH_VIEW_ZOOM");
+ } else if (getAttributeValue(atts, "GRAPH_VIEW_CENTER_X") != null) {
+ graphCenterX = getDoubleAttributeValue(atts, "GRAPH_VIEW_CENTER_X");
+ } else if (getAttributeValue(atts, "GRAPH_VIEW_CENTER_Y") != null) {
+ graphCenterY = getDoubleAttributeValue(atts, "GRAPH_VIEW_CENTER_Y");
+ } else if (getAttributeValue(atts, "NODE_SIZE_LOCKED") != null) {
+ nodeSizeLocked = getBooleanAttributeValue(atts, "NODE_SIZE_LOCKED");
+ } else {
+ objectTarget = networkName;
+ nextState = handleAttribute(atts, currentAttributes, networkName);
+ }
+
+ // logger.debug("Network attribute: "+printAttribute(atts));
+ if (nextState != ParseState.NONE)
+ return nextState;
+
+ return current;
+ }
+ }
+
+
+ class handleNode implements Handler {
+ public ParseState handle(String tag, Attributes atts, ParseState current) throws SAXException {
+ String id = atts.getValue("id");
+ String label = atts.getValue("label");
+ if (label == null)
+ label = atts.getValue("name"); // For backwards compatibility
+ String href = atts.getValue(XLINK, "href");
+
+ if (href != null) {
+ // logger.debug(" href=\""+href+"\"");
+ throw new SAXException("Can't have a node reference outside of a group");
+ }
+ // Create the node
+ currentNode = createUniqueNode(label, id);
+
+ return current;
+ }
+ }
+
+
+ class handleNodeAttribute implements Handler {
+ public ParseState handle(String tag, Attributes atts, ParseState current) throws SAXException {
+ if (atts == null)
+ return current;
+
+ attState = current;
+ // logger.debug("Node attribute: "+printAttribute(atts));
+ // Is this a graphics override?
+ String name = atts.getValue("name");
+
+ // Check for blank attribute (e.g. surrounding a group)
+ if (name == null && atts.getValue("value") == null)
+ return current;
+
+ if (name.startsWith("node.")) {
+ // Yes, add it to our nodeGraphicsMap
+ name = atts.getValue("name").substring(5);
+ String value = atts.getValue("value");
+ if (!nodeGraphicsMap.containsKey(currentNode)) {
+ nodeGraphicsMap.put(currentNode, new AttributesImpl());
+ }
+ ((AttributesImpl)nodeGraphicsMap.get(currentNode)).addAttribute("", "", name, "string", value);
+ }
+
+ currentAttributes = Cytoscape.getNodeAttributes();
+ objectTarget = currentNode.getIdentifier();
+
+ ParseState nextState = handleAttribute(atts, currentAttributes, objectTarget);
+ if (nextState != ParseState.NONE)
+ return nextState;
+ return current;
+ }
+ }
+
+
+ /**
+ * handleNodeGraphics builds the objects that will remember the node graphic
+ * information until we do the actual layout. Unfortunately, the way the
+ * readers work, we can't apply the graphics information until we do the
+ * actual layout.
+ */
+ class handleNodeGraphics implements Handler {
+ public ParseState handle(String tag, Attributes atts, ParseState current) throws SAXException {
+ if (tag.equals("graphics")) {
+ if (nodeGraphicsMap.containsKey(currentNode)) {
+ addAttributes(nodeGraphicsMap.get(currentNode),atts);
+ } else {
+ nodeGraphicsMap.put(currentNode, new AttributesImpl(atts));
+ }
+ } else if (tag.equals("att")) {
+ // Handle special node graphics attributes
+ String name = atts.getValue("name");
+ if (name != null
+ && !name.equals("cytoscapeNodeGraphicsAttributes")) {
+ // Add this as a graphics attribute to the end of our list
+ ((AttributesImpl)nodeGraphicsMap.get(currentNode)).
+ addAttribute("", "", "cy:"+name, "string",atts.getValue("value"));
+ }
+ }
+ return current;
+ }
+ }
+
+
+ class handleEdge implements Handler {
+ public ParseState handle(String tag, Attributes atts, ParseState current) throws SAXException {
+ // Get the label, id, source and target
+ String label = atts.getValue("label");
+ String source = atts.getValue("source");
+ String target = atts.getValue("target");
+ String sourceAlias = null;
+ String targetAlias = null;
+ String interaction = "pp";
+
+ // XXX this is really fragile. Parens in labels will cause things to break in nasty ways....
+ //
+ // Parse out the interaction (if this is from Cytoscape)
+ // parts[0] = source alias
+ // parts[1] = interaction
+ // parts[2] = target alias
+ int interactionStart = label.indexOf(" (");
+ int interactionEnd = label.lastIndexOf(") ");
+ if (interactionStart != -1 && interactionEnd != -1) {
+ sourceAlias = label.substring(0, interactionStart);
+ if (sourceAlias.length() > 0) sourceAlias = sourceAlias.trim();
+
+ interaction = label.substring(interactionStart+2, interactionEnd);
+ if (interaction.length() > 0) interaction = interaction.trim();
+
+ targetAlias = label.substring(interactionEnd+2);
+ if (targetAlias.length() > 0) targetAlias = targetAlias.trim();
+ // logger.debug("Edge label parse: interaction = "+interaction);
+ }
+
+ if (idMap.containsKey(source) && idMap.containsKey(target)) {
+ CyNode sourceNode = idMap.get(source);
+ CyNode targetNode = idMap.get(target);
+ currentEdge = createEdge(sourceNode, targetNode, interaction, label);
+ } else if (sourceAlias != null && targetAlias != null) {
+ currentEdge = createEdge(sourceAlias, targetAlias, interaction, label);
+ }
+
+ // If we're part of a group, this edge needs to be remembered as (possibly) an
+ // inner or outer edge
+ if (currentGroupNode != null) {
+ List<CyEdge> groupEdges = groupEdgeMap.get(currentGroupNode);
+ groupEdges.add(currentEdge);
+ }
+
+ return current;
+ }
+ }
+
+
+ class handleEdgeAttribute implements Handler {
+ public ParseState handle(String tag, Attributes atts, ParseState current) throws SAXException {
+ attState = current;
+ currentAttributes = Cytoscape.getEdgeAttributes();
+ if (currentEdge != null)
+ objectTarget = currentEdge.getIdentifier();
+ else
+ objectTarget = null;
+
+ ParseState nextState = handleAttribute(atts, currentAttributes, objectTarget);
+ if (nextState != ParseState.NONE)
+ return nextState;
+ return current;
+ }
+ }
+
+
+ class handleEdgeGraphics implements Handler {
+ public ParseState handle(String tag, Attributes atts, ParseState current) throws SAXException {
+ if (tag.equals("graphics")) {
+ if (edgeGraphicsMap.containsKey(currentEdge)) {
+ addAttributes(edgeGraphicsMap.get(currentEdge),atts);
+ } else
+ edgeGraphicsMap.put(currentEdge, new AttributesImpl(atts));
+ } else if (tag.equals("att")) {
+ // Handle special edge graphics attributes
+ String name = atts.getValue("name");
+ if (name != null
+ && name.equals("edgeBend")) {
+ handleList = new ArrayList<String>();
+ return ParseState.EDGEBEND;
+ } else if (name != null
+ && !name.equals("cytoscapeEdgeGraphicsAttributes")) {
+ // Add this as a graphics attribute to the end of our list
+ ((AttributesImpl)edgeGraphicsMap.get(currentEdge)).
+ addAttribute("", "", "cy:"+name, "string",atts.getValue("value"));
+ }
+ }
+ return current;
+ }
+ }
+
+
+ class handleGroup implements Handler {
+ public ParseState handle(String tag, Attributes atts, ParseState current) throws SAXException {
+ if (groupMap == null) groupMap = new HashMap<CyNode, List<CyNode>>();
+ if (groupEdgeMap == null) groupEdgeMap = new HashMap<CyNode, List<CyEdge>>();
+ if (currentGroupNode != null) groupStack.push(currentGroupNode);
+ currentGroupNode = currentNode;
+ groupMap.put(currentGroupNode, new ArrayList<CyNode>());
+ groupEdgeMap.put(currentGroupNode, new ArrayList<CyEdge>());
+ // logger.debug("Found group: "+currentNode);
+ return current;
+ }
+ }
+
+
+ class handleGroupNode implements Handler {
+ public ParseState handle(String tag, Attributes atts, ParseState current) throws SAXException {
+ String id = atts.getValue("id");
+ String label = atts.getValue("label");
+ String href = atts.getValue(XLINK, "href");
+
+
+ // logger.debug("<node");
+ if (href == null) {
+ // Create the node
+ currentNode = createUniqueNode(label,id);
+ } else {
+ id = href.substring(1);
+ }
+
+ // Note that we don't want to add the node to the group until later,
+ // even if we know about it now, so that we can get the edges associated
+ // with the group when we add it.
+
+ // logger.debug(" href=\""+href+"\"");
+ // Add it to the list of nodes to be resolved for this group
+ if (currentGroupNode == null)
+ throw new SAXException("No group to add node reference to");
+
+ if (idMap.containsKey(id)) {
+ CyNode node = idMap.get(id);
+ List<CyNode>groupNodeList = groupMap.get(currentGroupNode);
+ groupNodeList.add(node);
+ } else {
+ // Remember it for later -- we'll fix this up in HandleGraphDone
+ if (!nodeLinks.containsKey(currentGroupNode)) {
+ nodeLinks.put(currentGroupNode, new ArrayList<String>());
+ }
+
+ List<String> links = nodeLinks.get(currentGroupNode);
+ links.add(id);
+ }
+ // logger.debug(">");
+ return current;
+ }
+ }
+
+
+ /**
+ * Routines to handle edge bends. There are two different formats for edge bends. The original
+ * XGMML code encoded edge bends as:
+ * <att name="edgeBend">
+ * <att name="handle">
+ * <att value="15277.6748046875" name="x"/>
+ * <att value="17113.919921875" name="y"/>
+ * </att>
+ * <att name="handle">
+ * <att value="15277.6748046875" name="x"/>
+ * <att value="17113.919921875" name="y"/>
+ * </att>
+ * </att>
+ *
+ * In version 1.1, which was simplified to:
+ * <att name="edgeBend">
+ * <att name="handle" x="15277.6748046875" y="17113.919921875" />
+ * <att name="handle" x="15277.6748046875" y="17113.919921875" />
+ * </att>
+ */
+
+ /**
+ * Handle the "handle" attribute. If this is an original format XGMML file (1.0) we just
+ * punt to the next level down. If this is a newer format file, we handle the attributes
+ * directly.
+ */
+ class handleEdgeHandle implements Handler {
+ public ParseState handle(String tag, Attributes atts, ParseState current) throws SAXException {
+ if (documentVersion == 1.0) {
+ // This is the outer "handle" attribute
+ if (!getAttribute(atts, "name").equals("handle")) {
+ // OK, this is one of our "data" attributes
+ if (getAttributeValue(atts, "x") != null) {
+ edgeBendX = getAttributeValue(atts, "x");
+ } else if (getAttributeValue(atts, "y") != null) {
+ edgeBendY = getAttributeValue(atts, "y");
+ } else {
+ throw new SAXException("expected x or y value for edgeBend handle - got "+atts.getValue("name"));
+ }
+ }
+ } else {
+ // New format -- get the x and y values directly
+ if (getAttribute(atts, "x") != null) {
+ edgeBendX = getAttribute(atts, "x");
+ }
+ if (getAttribute(atts, "y") != null) {
+ edgeBendY = getAttribute(atts, "y");
+ }
+ // logger.debug("x="+edgeBendX+" y="+edgeBendY);
+ if (edgeBendX != null && edgeBendY != null) {
+ if (handleList == null) handleList = new ArrayList();
+ handleList.add(edgeBendX+","+edgeBendY);
+ edgeBendX = null;
+ edgeBendY = null;
+ }
+ }
+ return current;
+ }
+ }
+
+
+ class handleEdgeHandleDone implements Handler {
+ public ParseState handle(String tag, Attributes atts, ParseState current) throws SAXException {
+ if (edgeBendX != null && edgeBendY != null && handleList != null) {
+ handleList.add(edgeBendX+","+edgeBendY);
+ edgeBendX = null;
+ edgeBendY = null;
+ }
+ return current;
+ }
+ }
+
+
+ class handleEdgeHandleList implements Handler {
+ public ParseState handle(String tag, Attributes atts, ParseState current) throws SAXException {
+ if (handleList != null) {
+ String list = "";
+ for (int i = 0; i < handleList.size(); i++) {
+ if (i != (handleList.size()-1)) {
+ list += handleList.get(i)+";";
+ } else {
+ list += handleList.get(i);
+ }
+ }
+ // logger.debug("Setting edgeHandleList to: "+list);
+ // Add this as a graphics attribute to the end of our list
+ ((AttributesImpl)edgeGraphicsMap.get(currentEdge)).addAttribute("", "", "edgeHandleList", "string", list);
+ handleList = null;
+ }
+ return current;
+ }
+ }
+
+
+ class handleGroupDone implements Handler {
+ public ParseState handle(String tag, Attributes atts, ParseState current) throws SAXException {
+ currentNode = currentGroupNode;
+ // logger.debug("Group "+currentNode+" done.");
+ if (!groupStack.empty())
+ currentGroupNode = groupStack.pop();
+ else
+ currentGroupNode = null;
+
+ return current;
+ }
+ }
+
+
+ private List listAttrHolder;
+
+
+ class handleListAttribute implements Handler {
+ public ParseState handle(String tag, Attributes atts, ParseState current) throws SAXException {
+ ObjectType objType = getType(atts.getValue("type"));
+ Object obj = getTypedAttributeValue(objType, atts);
+ String name = atts.getValue("name");
+
+ switch (objType) {
+ case BOOLEAN:
+ case REAL:
+ case INTEGER:
+ case STRING:
+ listAttrHolder.add(obj);
+ }
+ return current;
+ }
+ }
+
+
+ class handleListAttributeDone implements Handler {
+ public ParseState handle(String tag, Attributes atts, ParseState current) throws SAXException {
+ try {
+ if (listAttrHolder != null) {
+ currentAttributes.setListAttribute(objectTarget, currentAttributeID, listAttrHolder);
+ listAttrHolder = null;
+ }
+ } catch (final Exception e) {
+ String err = "XGMML attribute handling error for attribute '"+currentAttributeID+"' and object '"+objectTarget+"': "+e.getMessage();
+ throw new SAXException(err);
+ }
+ return current;
+ }
+ }
+
+
+ private Map mapAttrHolder;
+
+
+ class handleMapAttribute implements Handler {
+ public ParseState handle(String tag, Attributes atts, ParseState current) throws SAXException {
+ String name = atts.getValue("name");
+ ObjectType objType = getType(atts.getValue("type"));
+ Object obj = getTypedAttributeValue(objType, atts);
+
+ switch (objType) {
+ case BOOLEAN:
+ case REAL:
+ case INTEGER:
+ case STRING:
+ mapAttrHolder.put(name, obj);
+ }
+
+ return current;
+ }
+ }
+
+
+ class handleMapAttributeDone implements Handler {
+ public ParseState handle(String tag, Attributes atts, ParseState current) throws SAXException {
+
+ try {
+ if (mapAttrHolder != null) {
+ currentAttributes.setMapAttribute(objectTarget, currentAttributeID, mapAttrHolder);
+ mapAttrHolder = null;
+ }
+ } catch (Exception e) {
+ String err = "XGMML attribute handling error for attribute '"+currentAttributeID+"' and object '"+objectTarget+"': "+e.getMessage();
+ throw new SAXException(err);
+ }
+ return current;
+ }
+ }
+
+
+ /**
+ * handleComplexAttribute attempts to read an arbitrarily complex attribute
+ * map from the XGMML file. For our purposes, a complex attribute map is defined
+ * as a HashMap which has as its values Maps. For example, consider
+ * a pseudo hash with the following structure:
+ *
+ * {"externalref1"}->{"authors"}->{1}->"author1 name";
+ * {"externalref1"}->{"authors"}->{2}->"author2 name";
+ * {"externalref1"}->{"authors"}->{3}->"author3 name";
+ *
+ * where the keys externalref1 and authors are strings, and keys 1, 2, 3 are
+ * integers, and the values (author1 name, author2 name, author3 name) are
+ * strings, we would have the following attributes written to the xgmml
+ * file:
+ *
+ * <att type="complex" name="publication references" value="3">
+ * <att type="string" name="externalref1" value="1">
+ * <att type="string" name="authors" value="3">
+ * <att type="int" name="2" value="1">
+ * <att type="string" value="author2 name"/>
+ * </att>
+ * <att type="int" name="1" value="1">
+ * <att type="string" value="author1 name"/>
+ * </att>
+ * <att type="int" name="3" value="1">
+ * <att type="string" value="author3 name"/>
+ * </att>
+ * </att>
+ * </att>
+ * </att>
+ *
+ * Notes: - value attribute property for keys is assigned the number of
+ * sub-elements the key references - value attribute property for values is
+ * equal to the value - name attribute property for attributes is only set
+ * for keys, and the value of this property is the key name. - label
+ * attribute property is equal to the data type of the key or value. - name
+ * attribute properties are only set for keys
+ */
+ class handleComplexAttribute implements Handler {
+ public ParseState handle(String tag, Attributes atts, ParseState current) throws SAXException {
+ // We can't create the complex attribute until we know what the definition is, but
+ // since a complex attribute is really nothing more than a HashMap with a String
+ // key and Map values, we can create it on the fly.
+
+ // Get our attributes
+ ObjectType type = getType(atts.getValue("type"));
+ String value = atts.getValue("value");
+ // logger.debug("Complex attribute: "+currentAttributeID+" level "+level+" value="+atts.getValue("value"));
+
+ if (level == numKeys) {
+ complexMap[level-1].put(complexKey[level-1], getTypedValue(type, value));
+ valueType = getMultHashMapType(type);
+ // See if we've defined the attribute already
+ if (!multihashmapdefExists(currentAttributes, currentAttributeID)) {
+ defineComplexAttribute(currentAttributeID, currentAttributes, attributeDefinition);
+ }
+ // Now define set the attribute
+ if (objectTarget != null)
+ mhm.setAttributeValue(objectTarget, currentAttributeID,
+ getTypedValue(type, value), complexKey);
+ } else if (level == 0) {
+ if (complexMap[level] == null) {
+ complexMap[level] = new HashMap();
+ }
+ complexKey[level] = getTypedValue(type, atts.getValue("name"));
+ attributeDefinition[level] = getMultHashMapType(type);
+ } else {
+ if (complexMap[level] == null) {
+ complexMap[level] = new HashMap();
+ }
+ complexMap[level-1].put(complexKey[level-1], complexMap[level]);
+ complexKey[level] = getTypedValue(type, atts.getValue("name"));
+ attributeDefinition[level] = getMultHashMapType(type);
+ }
+ level++;
+
+ return current;
+ }
+ }
+
+
+ class handleComplexAttributeDone implements Handler {
+ public ParseState handle(String tag, Attributes atts, ParseState current) throws SAXException {
+ if (level == 0) {
+ // We are done, and have read in all of our attributes
+ // logger.debug("Complex attribute "+currentAttributeID+" ComplexMap["+level+"] = "+complexMap[level]);
+ } else if (level < numKeys) {
+ complexMap[level] = null;
+ complexKey[level] = null;
+ }
+ // Decrement our depth
+ level--;
+ return current;
+ }
+ }
+
+
+ /*
+ * The following routines all handle the RDF data. All of them
+ * except handleRDF are called by the endElement handler. At
+ * this point, while we carefully read in all of this metaData,
+ * it's not clear how it ever gets used...
+ */
+
+ class handleRDF implements Handler {
+ public ParseState handle(String tag, Attributes atts, ParseState current) throws SAXException {
+ return current;
+ }
+ }
+
+
+ class handleRDFType implements Handler {
+ public ParseState handle(String tag, Attributes atts, ParseState current) throws SAXException {
+ RDFType = currentCData;
+ return current;
+ }
+ }
+
+
+ class handleRDFDescription implements Handler {
+ public ParseState handle(String tag, Attributes atts, ParseState current) throws SAXException {
+ RDFDescription = currentCData;
+ return current;
+ }
+ }
+
+
+ class handleRDFIdentifier implements Handler {
+ public ParseState handle(String tag, Attributes atts, ParseState current) throws SAXException {
+ RDFIdentifier = currentCData;
+ return current;
+ }
+ }
+
+
+ class handleRDFDate implements Handler {
+ public ParseState handle(String tag, Attributes atts, ParseState current) throws SAXException {
+ RDFDate = currentCData;
+ return current;
+ }
+ }
+
+
+ class handleRDFTitle implements Handler {
+ public ParseState handle(String tag, Attributes atts, ParseState current) throws SAXException {
+ RDFTitle = currentCData;
+ return current;
+ }
+ }
+
+
+ class handleRDFSource implements Handler {
+ public ParseState handle(String tag, Attributes atts, ParseState current) throws SAXException {
+ RDFSource = currentCData;
+ return current;
+ }
+ }
+
+
+ class handleRDFFormat implements Handler {
+ public ParseState handle(String tag, Attributes atts, ParseState current) throws SAXException {
+ RDFFormat = currentCData;
+ return current;
+ }
+ }
+
+
+ public static String printAttributes(Attributes atts) {
+ String str = " ";
+ for (int i = 0; i < atts.getLength(); i++) {
+ str += atts.getLocalName(i)+": "+atts.getValue(i)+", ";
+ }
+ return str;
+ }
+
+
+ /********************************************************************
+ * Utility routines. The following routines are utilities that are
+ * used for internal purposes.
+ *******************************************************************/
+
+ private static String getLabel(Attributes att) {
+ String label = att.getValue("label");
+ if (label != null)
+ return label;
+
+ return att.getValue("id");
+ }
+
+
+ private ParseState handleAttribute(Attributes atts, CyAttributes cyAtts, String id) throws SAXException {
+ String name = atts.getValue("name");
+ ObjectType objType = getType(atts.getValue("type"));
+ Object obj = getTypedAttributeValueOrEquation(objType, atts);
+
+ // Set up defaults
+ boolean hidden = false;
+ boolean editable = true;
+ boolean equation = false;
+
+ String hString = atts.getValue("cy:hidden");
+ if (hString != null)
+ hidden = Boolean.parseBoolean(hString);
+
+ String eString = atts.getValue("cy:editable");
+ if (hString != null)
+ editable = Boolean.parseBoolean(hString);
+
+ String eqString = atts.getValue("cy:equation");
+ if (eqString != null)
+ equation = Boolean.parseBoolean(eqString);
+
+
+ switch (objType) {
+ case BOOLEAN:
+ if (obj != null && name != null && id != null) {
+ if (equation)
+ eqnAttrTracker.recordEquation(cyAtts, id, name, (String)obj, Boolean.class);
+ else
+ cyAtts.setAttribute(id, name, (Boolean)obj);
+ }
+ break;
+ case REAL:
+ if (obj != null && name != null && id != null) {
+ if (equation)
+ eqnAttrTracker.recordEquation(cyAtts, id, name, (String)obj, Double.class);
+ else
+ cyAtts.setAttribute(id, name, (Double)obj);
+ }
+ break;
+ case INTEGER:
+ if (obj != null && name != null && id != null) {
+ if (equation)
+ eqnAttrTracker.recordEquation(cyAtts, id, name, (String)obj, Long.class);
+ else
+ cyAtts.setAttribute(id, name, (Integer)obj);
+ }
+ break;
+ case STRING:
+ if (obj != null && name != null && id != null) {
+ if (equation)
+ eqnAttrTracker.recordEquation(cyAtts, id, name, (String)obj, String.class);
+ else
+ cyAtts.setAttribute(id, name, (String)obj);
+ }
+ break;
+
+ // We need to be *very* careful. Because we duplicate attributes for
+ // each network we write out, we wind up reading and processing each
+ // attribute multiple times, once for each network. This isn't a problem
+ // for "base" attributes, but is a significant problem for attributes
+ // like LIST and MAP where we add to the attribute as we parse. So, we
+ // must make sure to clear out any existing values before we parse.
+ case LIST:
+ currentAttributeID = name;
+ if (id != null && cyAtts.hasAttribute(id, name)) {
+ if (equation)
+ eqnAttrTracker.recordEquation(cyAtts, id, name, (String)obj, List.class);
+ else
+ cyAtts.deleteAttribute(id,name);
+ }
+
+ listAttrHolder = new ArrayList();
+
+ return ParseState.LISTATT;
+ case MAP:
+ currentAttributeID = name;
+ if (id != null && cyAtts.hasAttribute(id, name))
+ cyAtts.deleteAttribute(id,name);
+
+ mapAttrHolder = new HashMap();
+
+ return ParseState.MAPATT;
+ case COMPLEX:
+ currentAttributeID = name;
+ if (id != null && cyAtts.hasAttribute(id, name))
+ cyAtts.deleteAttribute(id, name);
+ // If this is a complex attribute, we know that the value attribute
+ // is an integer
+ numKeys = Integer.parseInt(atts.getValue("value"));
+ complexMap = new HashMap[numKeys];
+ complexKey = new Object[numKeys];
+ attributeDefinition = new byte[numKeys];
+ mhm = currentAttributes.getMultiHashMap();
+ level = 0;
+ return ParseState.COMPLEXATT;
+ }
+
+ if (hidden)
+ cyAtts.setUserVisible(name,false);
+ if (!editable)
+ cyAtts.setUserEditable(name,false);
+
+ return ParseState.NONE;
+ }
+
+
+ /**
+ * Determines if attribute name already exists in multihashmap def.
+ *
+ * @param attributes -
+ * CyAttributes ref
+ * @param attributeName -
+ * attribute name
+ *
+ * @return boolean
+ */
+ private boolean multihashmapdefExists(CyAttributes attributes, String attributeName) {
+ MultiHashMapDefinition mhmd = attributes.getMultiHashMapDefinition();
+
+ for (Iterator defIt = mhmd.getDefinedAttributes(); defIt.hasNext();) {
+ String thisDef = (String) defIt.next();
+
+ if ((thisDef != null) && thisDef.equals(attributeName)) {
+ return true;
+ }
+ }
+ return false;
+ }
+
+
+ /**
+ * Defines a cyattribute for the complex attribute based on its keyspace.
+ *
+ * @param attributeName -
+ * attribute name
+ * @param attributes -
+ * CyAttributes to load
+ * @param attributeDefinition -
+ * byte[] which stores attribute key space definition
+ * @param numKeys -
+ * the number of keys to discover
+ */
+ private void defineComplexAttribute(final String attributeName, final CyAttributes attributes, byte[] attributeDefinition) {
+ // if necessary, init attribute definition
+ MultiHashMapDefinition mhmd = attributes.getMultiHashMapDefinition();
+
+ mhmd.defineAttribute(attributeName, valueType, attributeDefinition);
+ }
+
+
+ /**
+ * Given an ObjectType, method returns a MultiHashMapDefinition byte
+ * corresponding to its type.
+ *
+ * @param objectType - the type
+ *
+ * @return - byte
+ */
+ private byte getMultHashMapType(final ObjectType objectType) {
+ switch(objectType) {
+ case BOOLEAN:
+ return MultiHashMapDefinition.TYPE_BOOLEAN;
+ case STRING:
+ return MultiHashMapDefinition.TYPE_STRING;
+ case INTEGER:
+ return MultiHashMapDefinition.TYPE_INTEGER;
+ case REAL:
+ return MultiHashMapDefinition.TYPE_FLOATING_POINT;
+ }
+
+ // outta here
+ return -1;
+ }
+
+
+ private CyNode createUniqueNode (String label, String id) throws SAXException {
+ if (label != null) {
+ if (id == null)
+ id = label;
+ // logger.debug(" label=\""+label+"\"");
+ }
+ // OK, now actually create it
+ CyNode node = Cytoscape.getCyNode(label, true);
+ // logger.debug("Created new node("+label+") id="+node.getRootGraphIndex());
+
+ // This may have already been created (for example for a group outer edge. If
+ // so, we want to remove it from the list. If both nodes for an edge have been
+ // removed from the list, add the edge to our edges list
+ if (unresolvedNodeMap.containsKey(node)) {
+ CyEdge edge = unresolvedNodeMap.get(node);
+ unresolvedNodeMap.remove(node);
+ CyNode nodes[] = unresolvedEdgeMap.get(edge);
+ if (!unresolvedNodeMap.containsKey(nodes[0]) &&
+ !unresolvedNodeMap.containsKey(nodes[1])) {
+ edgeList.add(edge);
+ unresolvedEdgeMap.remove(edge);
+ }
+ }
+
+ // Add it our indices
+ nodeList.add(node);
+ // logger.debug("Adding node "+node.getIdentifier()+"("+id+") to map");
+ idMap.put(id, node);
+ return node;
+ }
+
+
+ private CyEdge createEdge (CyNode source, CyNode target,
+ String interaction, String label) throws SAXException {
+ // OK create it
+ CyEdge edge = Cytoscape.getCyEdge(source, target, Semantics.INTERACTION, interaction, true, true);
+ edgeList.add(edge);
+ return edge;
+ }
+
+
+ private CyEdge createEdge (String source, String target, String interaction, String label) {
+ CyNode targetNode = Cytoscape.getCyNode(target, false);
+ CyNode sourceNode = Cytoscape.getCyNode(source, false);
+ boolean haveTarget = (targetNode != null);
+ boolean haveSource = (sourceNode != null);
+
+ // Make sure the target and destination nodes exist
+ if (!haveSource) {
+ // We don't have this node, yet, so go ahead and created it
+ sourceNode = Cytoscape.getCyNode(source, true);
+ }
+
+ if (!haveTarget) {
+ targetNode = Cytoscape.getCyNode(target, true);
+ }
+
+ // Create the edge
+ CyEdge edge = Cytoscape.getCyEdge(sourceNode, targetNode, Semantics.INTERACTION, interaction, true, true);
+ if (haveTarget && haveSource)
+ edgeList.add(edge);
+ else {
+ CyNode[] nodes = new CyNode[2];
+ if (!haveTarget)
+ unresolvedNodeMap.put(targetNode, edge);
+ if (!haveSource)
+ unresolvedNodeMap.put(sourceNode, edge);
+ nodes[0] = sourceNode;
+ nodes[1] = targetNode;
+ unresolvedEdgeMap.put(edge, nodes);
+ }
+ return edge;
+ }
+
+
+ private void addAttributes(Attributes attI, Attributes atts) {
+ String localName = null;
+ String qName = null;
+ String type = null;
+ String uri = null;
+ String value = null;
+ for (int i = 0; i < atts.getLength(); i++) {
+ localName = atts.getLocalName(i);
+ uri = atts.getURI(i);
+ value = atts.getValue(i);
+ type = atts.getType(i);
+ qName = atts.getQName(i);
+ ((AttributesImpl)attI).addAttribute(uri, localName, qName,type, value);
+ }
+ }
+
+
+ private ObjectType getType(String type) {
+ if (type == null)
+ return ObjectType.STRING;
+ else if (type.equals("string"))
+ return ObjectType.STRING;
+ else if (type.equals("boolean"))
+ return ObjectType.BOOLEAN;
+ else if (type.equals("real"))
+ return ObjectType.REAL;
+ else if (type.equals("integer"))
+ return ObjectType.INTEGER;
+ else if (type.equals("list"))
+ return ObjectType.LIST;
+ else if (type.equals("map"))
+ return ObjectType.MAP;
+ else if (type.equals("complex"))
+ return ObjectType.COMPLEX;
+
+ return ObjectType.NONE;
+ }
+}
diff --git a/application/src/main/java/cytoscape/data/readers/XGMMLReader.java b/application/src/main/java/cytoscape/data/readers/XGMMLReader.java
new file mode 100644
index 0000000..b6d035e
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/readers/XGMMLReader.java
@@ -0,0 +1,879 @@
+/*
+ File: XGMMLReader.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute of Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.data.readers;
+
+import giny.model.Edge;
+import giny.model.Node;
+import giny.view.EdgeView;
+import giny.view.GraphView;
+import giny.view.NodeView;
+
+import java.awt.Color;
+import java.awt.geom.Point2D;
+import java.io.BufferedInputStream;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Properties;
+import java.util.Set;
+
+import javax.xml.parsers.ParserConfigurationException;
+import javax.xml.stream.FactoryConfigurationError;
+import javax.xml.stream.XMLStreamException;
+
+import org.xml.sax.SAXException;
+import org.xml.sax.SAXParseException;
+import org.xml.sax.helpers.ParserAdapter;
+import org.xml.sax.InputSource;
+import org.xml.sax.Attributes;
+import javax.xml.parsers.SAXParser;
+import javax.xml.parsers.SAXParserFactory;
+
+import cytoscape.CyEdge;
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+import cytoscape.CytoscapeInit;
+import cytoscape.data.CyAttributes;
+import cytoscape.data.Semantics;
+import cytoscape.data.attr.MultiHashMap;
+import cytoscape.data.attr.MultiHashMapDefinition;
+import cytoscape.data.writers.XGMMLWriter;
+import cytoscape.groups.CyGroup;
+import cytoscape.groups.CyGroupManager;
+import cytoscape.groups.CyGroupViewer;
+import cytoscape.layout.LayoutAdapter;
+import cytoscape.layout.CyLayoutAlgorithm;
+import cytoscape.task.TaskMonitor;
+import cytoscape.util.FileUtil;
+import cytoscape.util.PercentUtil;
+import cytoscape.view.CyNetworkView;
+import cytoscape.visual.LineStyle;
+import cytoscape.visual.ArrowShape;
+import cytoscape.visual.VisualPropertyType;
+import cytoscape.visual.VisualMappingManager;
+import cytoscape.logger.CyLogger;
+import ding.view.DGraphView;
+
+import java.io.PushbackInputStream;
+import java.lang.management.ManagementFactory;
+import java.lang.management.MemoryMXBean;
+import java.lang.management.MemoryUsage;
+
+
+/**
+ * XGMML file reader.<br>
+ * This version is Metanode-compatible.
+ *
+ * @version 1.0
+ * @since Cytoscape 2.3
+ * @see cytoscape.data.writers.XGMMLWriter
+ * @author kono
+ *
+ */
+public class XGMMLReader extends AbstractGraphReader {
+ // Graph Tags
+ protected static final String GRAPH = "graph";
+ protected static final String NODE = "node";
+ protected static final String EDGE = "edge";
+ protected static final String GRAPHICS = "graphics";
+ protected static final String LABEL = "label";
+ protected static final String SOURCE = "source";
+ protected static final String TARGET = "target";
+
+ // Shapes used in Cytoscape (not GML standard)
+ // In GML, they are called "type"
+ protected static final String RECTANGLE = "rectangle";
+ protected static final String ELLIPSE = "ellipse";
+ protected static final String LINE = "Line"; // This is the Polyline
+ // object.
+ protected static final String POINT = "point";
+ protected static final String DIAMOND = "diamond";
+ protected static final String HEXAGON = "hexagon";
+ protected static final String OCTAGON = "octagon";
+ protected static final String PARALELLOGRAM = "parallelogram";
+ protected static final String TRIANGLE = "triangle";
+ protected static final String VEE = "vee";
+ protected static final String ROUNDED_RECTANGLE = "rounded_rectangle";
+
+ // XGMML shapes (these should be mapped to Cytoscape shapes
+ protected static final String BOX = "box"; // Map to rectangle
+ protected static final String CIRCLE = "circle"; // Map to ellipse
+ protected static final String VELLIPSIS = "ver_ellipsis";
+ protected static final String HELLIPSIS = "hor_ellipsis";
+ protected static final String RHOMBUS = "rhombus"; // Map to parallelogram
+ protected static final String PENTAGON = "pentagon"; // Map to hexagon
+
+ protected static final String CY_NAMESPACE = "http://www.cytoscape.org";
+
+ // XGMML file name to be loaded.
+ private String networkName = null;
+ private Double graphViewZoom;
+ private Double graphViewCenterX;
+ private Double graphViewCenterY;
+ private InputStream networkStream;
+ private XGMMLParser parser;
+ private boolean nodeSizeLocked = false;
+
+ private Properties prop = CytoscapeInit.getProperties();
+ private String vsbSwitch = prop.getProperty("visualStyleBuilder");
+
+ // For exception handling
+ private TaskMonitor taskMonitor;
+ private PercentUtil percentUtil;
+ private int nextID = 0; // Used to assign ID's to nodes that didn't have them
+ private CyLogger logger = null;
+
+
+ /**
+ * Constructor.<br>
+ * This is for local XGMML file.
+ *
+ * @param fileName File name of local XGMML file.
+ * @throws FileNotFoundException
+ *
+ */
+ public XGMMLReader(final String fileName) {
+ this(fileName, null);
+ }
+
+
+ /**
+ * Constructor.<br>
+ * This is usually used for remote file loading.
+ *
+ * @param is
+ * Input stream of XGMML file,
+ *
+ */
+ public XGMMLReader(InputStream is) {
+ super("InputStream");
+ this.networkStream = is;
+ initialize();
+ }
+
+
+ /**
+ * Constructor.<br>
+ * This is usually used for remote file loading.
+ *
+ * @param is
+ * Input stream of XGMML file,
+ *
+ */
+ public XGMMLReader(InputStream is, String name) {
+ super(name);
+
+ this.networkStream = is;
+ initialize();
+ }
+
+
+ /**
+ * Creates a new XGMMLReader object.
+ *
+ * @param fileName DOCUMENT ME!
+ * @param monitor DOCUMENT ME!
+ */
+ public XGMMLReader(final String fileName, final TaskMonitor monitor) {
+ super(fileName);
+ this.taskMonitor = monitor;
+ percentUtil = new PercentUtil(3);
+ networkStream = FileUtil.getInputStream(fileName, monitor);
+ initialize();
+ }
+
+
+ /**
+ * Sets the task monitor we want to use
+ *
+ * @param monitor the TaskMonitor to use
+ */
+ public void setTaskMonitor(TaskMonitor monitor) {
+ this.taskMonitor = monitor;
+ percentUtil = new PercentUtil(3);
+ }
+
+
+ private void initialize() {
+ logger = CyLogger.getLogger(XGMMLReader.class);
+
+ final boolean attemptRepair = Boolean.getBoolean("cytoscape.xgmml.repair.bare.ampersands");
+ if (attemptRepair) {
+ networkStream = new RepairBareAmpersandsInputStream(networkStream, 512);
+ }
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws IOException DOCUMENT ME!
+ */
+ public void read() throws IOException {
+ try {
+ this.readXGMML();
+ } catch (SAXException e) {
+ if (taskMonitor != null) {
+ taskMonitor.setException(e, e.getMessage());
+ }
+ // e.printStackTrace();
+ throw new IOException(e.getMessage());
+ }
+ }
+
+
+ /**
+ * Actual method to read XGMML documents.
+ *
+ * @throws IOException
+ * @throws IOException
+ * @throws SAXException
+ * @throws ParserConfigurationException
+ * @throws FactoryConfigurationError
+ * @throws XMLStreamException
+ */
+ private void readXGMML() throws SAXException, IOException {
+ // Performance check
+// final long start = System.currentTimeMillis();
+// final MemoryMXBean mbean = ManagementFactory.getMemoryMXBean();
+// MemoryUsage heapUsage = mbean.getHeapMemoryUsage();
+// MemoryUsage nonHeapUsage = mbean.getNonHeapMemoryUsage();
+
+// logger.debug("Heap Memory status (SAX): used = " + heapUsage.getUsed()/1000+"KB");
+// logger.debug("Heap Memory status (SAX): MAX = " + heapUsage.getMax()/1000+"KB");
+// logger.debug("Non-heap Memory status (SAX): used = " + nonHeapUsage.getUsed()/1000+"KB");
+// logger.debug("Non-heap Memory status (SAX): MAX = " + nonHeapUsage.getMax()/1000+"KB");
+
+ try {
+ try {
+ try {
+ /*
+ * Read the file and map the entire XML document into data
+ * structure.
+ */
+ if (taskMonitor != null) {
+ taskMonitor.setPercentCompleted(-1);
+ taskMonitor.setStatus("Reading XGMML data...");
+ }
+
+ // Get our parser
+ SAXParserFactory spf = SAXParserFactory.newInstance();
+ SAXParser sp = spf.newSAXParser();
+ ParserAdapter pa = new ParserAdapter(sp.getParser());
+ parser = new XGMMLParser();
+ pa.setContentHandler(parser);
+ pa.setErrorHandler(parser);
+ pa.parse(new InputSource(networkStream));
+ networkName = parser.getNetworkName();
+ } catch (OutOfMemoryError oe) {
+ /*
+ * It's not generally a good idea to catch OutOfMemoryErrors, but in
+ * this case, where we know the culprit (a file that is too large),
+ * we can at least try to degrade gracefully.
+ */
+ System.gc();
+ throw new XGMMLException("Out of memory error caught! The network being loaded is too large for the current memory allocation. Use the -Xmx flag for the java virtual machine to increase the amount of memory available, e.g. java -Xmx1G cytoscape.jar -p plugins ....");
+ } catch (ParserConfigurationException e) {
+ } catch (SAXParseException e) {
+ logger.error("XGMMLParser: fatal parsing error on line " + e.getLineNumber() + " -- '" + e.getMessage() + "'", e);
+ throw e;
+ }
+ } finally {
+ if (networkStream != null) {
+ networkStream.close();
+ }
+ }
+ }
+ finally {
+ networkStream = null;
+ }
+
+// heapUsage = mbean.getHeapMemoryUsage();
+// nonHeapUsage = mbean.getNonHeapMemoryUsage();
+// long memend = Runtime.getRuntime().freeMemory();
+
+// logger.debug("============= Total time for " + networkName + " = "
+// + (System.currentTimeMillis() - start));
+// logger.debug("Heap memory after parsing = " + (heapUsage.getUsed() / 1000)
+// + "KB");
+// logger.debug("Non-heap memory after parsing = " + (nonHeapUsage.getUsed() / 1000)
+// + "KB");
+ }
+
+
+ public int[] getNodeIndicesArray() {
+ return parser.getNodeIndicesArray();
+ }
+
+
+ public int[] getEdgeIndicesArray() {
+ return parser.getEdgeIndicesArray();
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getNetworkID() {
+ return networkName;
+ }
+
+
+ /**
+ * @return Returns the networkName.
+ * @uml.property name="networkName"
+ */
+ public String getNetworkName() {
+ return networkName;
+ }
+
+
+ /**
+ * getLayoutAlgorithm is called to get the Layout Algorithm that will be used
+ * to layout the resulting graph. In our case, we just return a stub that will
+ * call our internal layout routine, which will just use the default layout, but
+ * with our task monitor
+ *
+ * @return the CyLayoutAlgorithm to use
+ */
+ public CyLayoutAlgorithm getLayoutAlgorithm() {
+ return new LayoutAdapter() {
+ public void doLayout(CyNetworkView networkView, TaskMonitor monitor) {
+ // Set 'networkView' as currentView, so that
+ //the VisualStyle created for this view will be applied to this 'networkView' only
+ if (networkView != null && networkView.getIdentifier() != null){
+ Cytoscape.setCurrentNetworkView(networkView.getIdentifier());
+ }
+
+ layout(networkView);
+ }
+ };
+ }
+
+
+ /**
+ * layout the graph based on the graphic attributes
+ *
+ * @param myView the view of the network we want to layout
+ */
+ private void layout(CyNetworkView myView) {
+ // logger.debug("layout");
+ if ((myView == null) || (myView.nodeCount() == 0)) {
+ return;
+ }
+
+ // Create our visual style creator. We use the vsbSwitch to tell the style builder
+ // whether to create the override attributes or not
+ final boolean buildStyle = vsbSwitch == null || vsbSwitch.equals("on");
+
+ VisualStyleBuilder graphStyle = new VisualStyleBuilder(parser.getNetworkName(), false);
+ nodeSizeLocked = parser.getNodeSizeLocked();
+ graphStyle.setNodeSizeLocked(nodeSizeLocked); // False by default
+
+ // Set background color
+ if (parser.getBackgroundColor() != null) {
+ myView.setBackgroundPaint(parser.getBackgroundColor());
+ graphStyle.setBackgroundColor(parser.getBackgroundColor());
+ }
+
+ layoutNodes(myView, graphStyle, buildStyle);
+ layoutEdges(myView, graphStyle, buildStyle);
+
+ if (buildStyle)
+ graphStyle.buildStyle();
+ }
+
+
+ /**
+ * Layout nodes if view is available.
+ *
+ * @param myView
+ * GINY's graph view object for the current network.
+ * @param graphStyle the visual style creator object
+ * @param buildStyle if true, build the graphical style
+ */
+ private void layoutNodes(final GraphView myView, final VisualStyleBuilder graphStyle, boolean buildStyle) {
+ int tempid = 0;
+ NodeView view = null;
+ HashMap<CyNode, Attributes> nodeGraphicsMap = parser.getNodeGraphics();
+
+ for (CyNode node : nodeGraphicsMap.keySet()) {
+ view = myView.getNodeView(node.getRootGraphIndex());
+ String label = node.getIdentifier();
+
+ if (view != null) {
+ if (label != null) {
+ view.getLabel().setText(label);
+ } else {
+ view.getLabel().setText("node(" + tempid + ")");
+ tempid++;
+ }
+
+ if (nodeGraphicsMap != null) {
+ layoutNodeGraphics(nodeGraphicsMap.get(node), view, graphStyle, buildStyle);
+ }
+ }
+ }
+ }
+
+
+ /**
+ * Extract node graphics information from JAXB object.<br>
+ *
+ * @param graphics
+ * Graphics information for a node as JAXB object.
+ * @param nodeView
+ * Actual node view for the target node.
+ * @param graphStyle the visual style creator object
+ * @param buildStyle if true, build the graphical style
+ *
+ */
+ private void layoutNodeGraphics(final Attributes graphics, final NodeView nodeView, final VisualStyleBuilder graphStyle,
+ final boolean buildStyle) {
+ // The identifier of this node
+ String nodeID = nodeView.getNode().getIdentifier();
+
+ // Location and size of the node
+ double x;
+
+ // Location and size of the node
+ double y;
+
+ // Location and size of the node
+ double h;
+
+ // Location and size of the node
+ double w;
+
+ x = XGMMLParser.getDoubleAttribute(graphics,"x");
+ y = XGMMLParser.getDoubleAttribute(graphics,"y");
+ h = XGMMLParser.getDoubleAttribute(graphics,"h");
+ w = XGMMLParser.getDoubleAttribute(graphics,"w");
+
+ nodeView.setXPosition(x);
+ nodeView.setYPosition(y);
+
+ if (buildStyle) {
+ if (nodeSizeLocked && h != 0.0) {
+ graphStyle.addProperty(nodeID, VisualPropertyType.NODE_SIZE, ""+h);
+ } else {
+ if (h != 0.0)
+ graphStyle.addProperty(nodeID, VisualPropertyType.NODE_HEIGHT, ""+h);
+ if (w != 0.0)
+ graphStyle.addProperty(nodeID, VisualPropertyType.NODE_WIDTH, ""+w);
+ }
+ }
+
+ CyAttributes nodeAttributes = Cytoscape.getNodeAttributes();
+
+ // Set color
+ if (buildStyle && XGMMLParser.getAttribute(graphics,"fill") != null) {
+ String fillColor = XGMMLParser.getAttribute(graphics, "fill");
+ graphStyle.addProperty(nodeID, VisualPropertyType.NODE_FILL_COLOR, fillColor);
+ // nodeView.setUnselectedPaint(fillColor);
+ }
+
+ // Set border line color
+ if (buildStyle && XGMMLParser.getAttribute(graphics,"outline") != null) {
+ String outlineColor = XGMMLParser.getAttribute(graphics, "outline");
+ // nodeView.setBorderPaint(outlineColor);
+ graphStyle.addProperty(nodeID, VisualPropertyType.NODE_BORDER_COLOR, outlineColor);
+ }
+
+ // Set border line width
+ if (buildStyle && XGMMLParser.getAttribute(graphics,"width") != null) {
+ String lineWidth = XGMMLParser.getAttribute(graphics,"width");
+ // nodeView.setBorderWidth(lineWidth);
+ graphStyle.addProperty(nodeID, VisualPropertyType.NODE_LINE_WIDTH, lineWidth);
+ }
+
+ if (buildStyle && XGMMLParser.getAttributeNS(graphics,"nodeTransparency",CY_NAMESPACE) != null) {
+ String opString = XGMMLParser.getAttributeNS(graphics,"nodeTransparency", CY_NAMESPACE);
+ float opacity = (float)Double.parseDouble(opString)*255;
+ // Opacity is saved as a float from 0-1, but internally we use 0-255
+ // nodeView.setTransparency(opacity);
+ graphStyle.addProperty(nodeID, VisualPropertyType.NODE_OPACITY, ""+opacity);
+ }
+
+ if (buildStyle && XGMMLParser.getAttributeNS(graphics, "opacity", CY_NAMESPACE) != null) {
+ String opString = XGMMLParser.getAttributeNS(graphics,"opacity", CY_NAMESPACE);
+ float opacity = (float)Double.parseDouble(opString);
+ // nodeView.setTransparency(opacity);
+ graphStyle.addProperty(nodeID, VisualPropertyType.NODE_OPACITY, opString);
+ }
+
+ // These are saved in the exported XGMML, but it's not clear how they get set
+ if (buildStyle && XGMMLParser.getAttributeNS(graphics,"nodeLabel", CY_NAMESPACE) != null) {
+ String nodeLabel = XGMMLParser.getAttributeNS(graphics,"nodeLabel", CY_NAMESPACE);
+ graphStyle.addProperty(nodeID, VisualPropertyType.NODE_LABEL, nodeLabel);
+ }
+
+ if (buildStyle && XGMMLParser.getAttributeNS(graphics,"nodeLabelFont", CY_NAMESPACE) != null) {
+ String nodeLabelFont = XGMMLParser.getAttributeNS(graphics,"nodeLabelFont", CY_NAMESPACE);
+
+ String[] items = nodeLabelFont.split("-"); // e.g. nodeLabelFont = "Arial-0-24"
+ graphStyle.addProperty(nodeID, VisualPropertyType.NODE_FONT_SIZE, items[2]);
+ graphStyle.addProperty(nodeID, VisualPropertyType.NODE_FONT_FACE, items[0]);
+ }
+
+ if (buildStyle && XGMMLParser.getAttributeNS(graphics,"borderLineType", CY_NAMESPACE) != null) {
+ String borderLineType = XGMMLParser.getAttributeNS(graphics,"borderLineType", CY_NAMESPACE);
+ graphStyle.addProperty(nodeID, VisualPropertyType.NODE_LINETYPE, borderLineType);
+ }
+
+ String type = XGMMLParser.getAttribute(graphics,"type");
+ if (buildStyle && type != null) {
+ if (type.equals("rhombus"))
+ graphStyle.addProperty(nodeID, VisualPropertyType.NODE_SHAPE, "parallelogram");
+ else
+ graphStyle.addProperty(nodeID, VisualPropertyType.NODE_SHAPE, type);
+ }
+ }
+
+
+ /**
+ * Layout edges if view is available.
+ *
+ * @param myView GINY's graph view object for the current network.
+ * @param graphStyle the visual style creator object
+ * @param buildStyle if true, build the graphical style
+ */
+ private void layoutEdges(final GraphView myView, final VisualStyleBuilder graphStyle, final boolean buildStyle) {
+ int tempid = 0;
+ EdgeView view = null;
+ HashMap<CyEdge, Attributes> edgeGraphicsMap = parser.getEdgeGraphics();
+ if (edgeGraphicsMap == null) return;
+
+ for (CyEdge edge: edgeGraphicsMap.keySet()) {
+ view = myView.getEdgeView(edge.getRootGraphIndex());
+
+ if (view != null) {
+ layoutEdgeGraphics(edgeGraphicsMap.get(edge), view, graphStyle, buildStyle);
+ } else {
+ // If we don't have a view, assume that this is a hidden edge
+ myView.getGraphPerspective().hideEdge(edge);
+ }
+ }
+ }
+
+
+ /**
+ * Layout an edge using the stored graphics attributes
+ *
+ * @param graphics
+ * Graphics information for an edge as SAX attributes.
+ * @param edgeView
+ * Actual edge view for the target edge.
+ *
+ */
+ private void layoutEdgeGraphics(final Attributes graphics, final EdgeView edgeView, final VisualStyleBuilder graphStyle,
+ final boolean buildStyle) {
+ CyAttributes edgeAttributes = Cytoscape.getEdgeAttributes();
+ String edgeID = edgeView.getEdge().getIdentifier();
+
+ if (buildStyle && XGMMLParser.getAttribute(graphics, "width") != null) {
+ String lineWidth = XGMMLParser.getAttribute(graphics, "width");
+ // edgeView.setStrokeWidth(lineWidth);
+ graphStyle.addProperty(edgeID, VisualPropertyType.EDGE_LINE_WIDTH, lineWidth);
+ }
+
+ if (buildStyle && XGMMLParser.getAttribute(graphics, "fill") != null) {
+ String edgeColor = XGMMLParser.getAttribute(graphics, "fill");
+ // edgeView.setUnselectedPaint(edgeColor);
+ graphStyle.addProperty(edgeID, VisualPropertyType.EDGE_COLOR, edgeColor);
+ }
+
+ if (buildStyle && XGMMLParser.getAttributeNS(graphics, "sourceArrow", CY_NAMESPACE) != null) {
+ Integer arrowType = XGMMLParser.getIntegerAttributeNS(graphics, "sourceArrow", CY_NAMESPACE);
+ ArrowShape shape = ArrowShape.getArrowShape(arrowType);
+ String arrowName = shape.getName();
+ // edgeView.setSourceEdgeEnd(arrowType);
+ graphStyle.addProperty(edgeID, VisualPropertyType.EDGE_SRCARROW_SHAPE, arrowName);
+ }
+
+ if (buildStyle && XGMMLParser.getAttributeNS(graphics, "targetArrow", CY_NAMESPACE) != null) {
+ Integer arrowType = XGMMLParser.getIntegerAttributeNS(graphics, "targetArrow", CY_NAMESPACE);
+ ArrowShape shape = ArrowShape.getArrowShape(arrowType);
+ String arrowName = shape.getName();
+ // edgeView.setTargetEdgeEnd(arrowType);
+ graphStyle.addProperty(edgeID, VisualPropertyType.EDGE_TGTARROW_SHAPE, arrowName);
+ }
+
+ if (buildStyle && XGMMLParser.getAttributeNS(graphics, "sourceArrowColor", CY_NAMESPACE) != null) {
+ String arrowColor = XGMMLParser.getAttributeNS(graphics, "sourceArrowColor", CY_NAMESPACE);
+ // edgeView.setSourceEdgeEndPaint(arrowColor);
+ graphStyle.addProperty(edgeID, VisualPropertyType.EDGE_SRCARROW_COLOR, arrowColor);
+ }
+
+ if (buildStyle && XGMMLParser.getAttributeNS(graphics,"targetArrowColor", CY_NAMESPACE) != null) {
+ String arrowColor = XGMMLParser.getAttributeNS(graphics, "targetArrowColor", CY_NAMESPACE);
+ // edgeView.setTargetEdgeEndPaint(arrowColor);
+ graphStyle.addProperty(edgeID, VisualPropertyType.EDGE_TGTARROW_COLOR, arrowColor);
+ }
+
+ if (buildStyle && XGMMLParser.getAttributeNS(graphics, "edgeLineType", CY_NAMESPACE) != null) {
+ String value = XGMMLParser.getAttributeNS(graphics, "edgeLineType", CY_NAMESPACE);
+ graphStyle.addProperty(edgeID, VisualPropertyType.EDGE_LINE_STYLE, value);
+ }
+
+ if (XGMMLParser.getAttributeNS(graphics, "curved", CY_NAMESPACE) != null) {
+ String value = XGMMLParser.getAttributeNS(graphics, "curved", CY_NAMESPACE);
+ if (value.equals("STRAIGHT_LINES")) {
+ edgeView.setLineType(EdgeView.STRAIGHT_LINES);
+ } else if (value.equals("CURVED_LINES")) {
+ edgeView.setLineType(EdgeView.CURVED_LINES);
+ }
+ }
+
+ if (XGMMLParser.getAttribute(graphics,"edgeHandleList") != null) {
+ String handles[] = XGMMLParser.getAttribute(graphics, "edgeHandleList").split(";");
+ List<Point2D> bendPoints = new ArrayList<Point2D>();
+ for (int i = 0; i < handles.length; i++) {
+ String points[] = handles[i].split(",");
+ double x = (new Double(points[0])).doubleValue();
+ double y = (new Double(points[1])).doubleValue();
+ Point2D.Double point = new Point2D.Double();
+ point.setLocation(x,y);
+ bendPoints.add(point);
+ }
+ edgeView.getBend().setHandles(bendPoints);
+ }
+
+ // These are saved in the exported XGMML, but it's not clear how they get set
+ if (buildStyle && XGMMLParser.getAttributeNS(graphics,"edgeLabel", CY_NAMESPACE) != null) {
+ String nodeLabel = XGMMLParser.getAttributeNS(graphics,"edgeLabel", CY_NAMESPACE);
+ graphStyle.addProperty(edgeID, VisualPropertyType.EDGE_LABEL, nodeLabel);
+ }
+
+ if (buildStyle && XGMMLParser.getAttributeNS(graphics,"edgeLabelFont", CY_NAMESPACE) != null) {
+ String edgeLabelFont = XGMMLParser.getAttributeNS(graphics,"edgeLabelFont", CY_NAMESPACE);
+
+ String[] items = edgeLabelFont.split("-"); // e.g. edgeLabelFont = "Arial-0-24"
+ graphStyle.addProperty(edgeID, VisualPropertyType.EDGE_FONT_SIZE, items[2]);
+ graphStyle.addProperty(edgeID, VisualPropertyType.EDGE_FONT_FACE, items[0]);
+ }
+ }
+
+
+ /**
+ * This method does all of our postprocessing after reading and parsing the file
+ *
+ * @param network the network we've read in
+ */
+ public void doPostProcessing(final CyNetwork network) {
+ parser.setMetaData(network);
+
+ // Get the view. Note that for large networks this might be the null view
+ final CyNetworkView view = Cytoscape.getNetworkView(network.getIdentifier());
+
+ // Now that we have a network, handle the groups
+ // This is done here rather than in layout because layout is
+ // only called when we create a view. For large networks,
+ // we don't create views by default, but groups should still
+ // exist even when we don't create the view
+ Map<CyNode,List<CyNode>>groupMap = parser.getGroupMap();
+ Map<CyNode,List<CyEdge>>groupEdgeMap = parser.getGroupEdgeMap();
+ if (groupMap != null) {
+ CyAttributes nodeAttributes = Cytoscape.getNodeAttributes();
+
+ CyGroup newGroup = null;
+ String viewer = null;
+
+ for (CyNode groupNode : groupMap.keySet()) {
+ List<CyNode> childList = groupMap.get(groupNode);
+ List<CyEdge> edgeList = groupEdgeMap.get(groupNode);
+
+ viewer = nodeAttributes.getStringAttribute(groupNode.getIdentifier(), CyGroup.GROUP_VIEWER_ATTR);
+ CyGroupViewer groupViewer = CyGroupManager.getGroupViewer(viewer);
+ boolean isLocal = false;
+ if (nodeAttributes.hasAttribute(groupNode.getIdentifier(), CyGroup.GROUP_LOCAL_ATTR))
+ isLocal = nodeAttributes.getBooleanAttribute(groupNode.getIdentifier(), CyGroup.GROUP_LOCAL_ATTR);
+
+ CyNetwork groupNetwork = null;
+
+ if (isLocal)
+ groupNetwork = network;
+
+ // Note that we need to leave the group node in the network so that the saved
+ // location information (if there is any) can be utilized by the group viewer.
+ // This means that it will be the responsibility of the group viewer to remove
+ // the node if they don't want it to be visible
+
+ // Do we already have a view?
+ if (view == null || view == Cytoscape.getNullNetworkView()) {
+ // No, just create the group, but don't assign a viewer
+ newGroup = CyGroupManager.createGroup(groupNode, childList, null, groupNetwork);
+ network.hideNode(groupNode);
+ } else {
+ // Yes, see if the group already exists
+ newGroup = CyGroupManager.getCyGroup(groupNode);
+ if (newGroup == null) {
+ // No, OK so create it and pass down the viewer
+ newGroup = CyGroupManager.createGroup(groupNode, childList, viewer, groupNetwork);
+ } else {
+ // Either the group doesn't have a viewer or it has a different viewer -- change it
+ CyGroupManager.setGroupViewer(newGroup, viewer, view, false);
+ }
+ // If the group viewer isn't loaded, we need to hide the group node -- otherwise,
+ // we let the group viewer handle it
+ if (groupViewer == null)
+ network.hideNode(groupNode);
+ }
+
+ // OK, make sure we have all of our inner and outer edges added
+ for (CyEdge edge: edgeList) {
+ if (childList.contains(edge.getSource()) && childList.contains(edge.getTarget()))
+ newGroup.addInnerEdge(edge);
+ else
+ newGroup.addOuterEdge(edge);
+ }
+ }
+
+ // If we have a view, notify the group viewer
+ if (view != null && view != Cytoscape.getNullNetworkView()) {
+ CyGroupManager.setGroupViewer(newGroup, viewer, view, true);
+ }
+ }
+
+ if (view == null || view == Cytoscape.getNullNetworkView())
+ return;
+
+ // Apply visual style before updateView().
+ Cytoscape.getVisualMappingManager().applyAppearances();
+
+ // set view zoom
+ final Double zoomLevel = parser.getGraphViewZoomLevel();
+
+ if (zoomLevel != null)
+ view.setZoom(zoomLevel.doubleValue());
+
+ // set view center
+ final Point2D center = parser.getGraphViewCenter();
+
+ if (center != null)
+ ((DGraphView) view).setCenter(center.getX(), center.getY());
+ }
+
+
+ private class RepairBareAmpersandsInputStream extends PushbackInputStream {
+ private final byte[] encodedAmpersand = new byte[]{'a', 'm', 'p', ';'};
+ public RepairBareAmpersandsInputStream(InputStream in) {
+ super(in);
+ }
+
+ public RepairBareAmpersandsInputStream(InputStream in, int size) {
+ super(in, size);
+ }
+
+
+ @Override
+ public int read() throws IOException {
+ int c;
+
+ c = super.read();
+ if (c == (int)'&') {
+ byte[] b = new byte[7];
+ int cnt;
+
+ cnt = read(b);
+ if (cnt > 0) {
+ boolean isEntity;
+ int i;
+
+ isEntity = false;
+ i = 0;
+ while ((i < cnt) && (!isEntity)) {
+ isEntity = (b[i] == ';');
+ i++;
+ }
+
+ byte[] pb = new byte[cnt];
+ for (int p = 0; p < cnt; p++) {
+ pb[p] = b[p];
+ }
+ unread(pb);
+
+ if (!isEntity) {
+ unread(encodedAmpersand);
+ }
+ }
+ }
+
+ return c;
+ }
+
+
+ @Override
+ public int read(byte[] b, int off, int len) throws IOException {
+ if (b == null) {
+ throw new NullPointerException();
+ } else if (off < 0 || len < 0 || len > b.length - off) {
+ throw new IndexOutOfBoundsException();
+ } else if (len == 0) {
+ return 0;
+ }
+
+ int cnt;
+ int c = -1;
+
+ cnt = 0;
+ while (cnt < len) {
+ c = read();
+ if (c == -1) {
+ break;
+ }
+ b[off] = (byte)c;
+ off++;
+ cnt++;
+ }
+
+ if ((c == -1) && (cnt == 0)) {
+ cnt = -1;
+ }
+
+ return cnt;
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/data/readers/package.html b/application/src/main/java/cytoscape/data/readers/package.html
new file mode 100644
index 0000000..50eaf5e
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/readers/package.html
@@ -0,0 +1,12 @@
+<html>
+<head>
+ <!-- $Revision: 5801 $
+ $Date: 2004-04-20 01:53:47 +0200 (Tue, 20 Apr 2004) $
+ $Author: amarkiel $
+ -->
+</head>
+
+<body>
+Reader classes for the basic data types in cytoscape.data.
+</body>
+</html>
diff --git a/application/src/main/java/cytoscape/data/servers/BioDataServer.java b/application/src/main/java/cytoscape/data/servers/BioDataServer.java
new file mode 100755
index 0000000..16c31ff
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/servers/BioDataServer.java
@@ -0,0 +1,883 @@
+/*
+ File: BioDataServer.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+// BioDataServer
+// -----------------------------------------------------------------------------------------
+// $Revision: 18030 $
+// $Date: 2009-09-22 14:00:25 +0200 (Tue, 22 Sep 2009) $
+// $Author: noelr $
+// -----------------------------------------------------------------------------------------
+package cytoscape.data.servers;
+
+import cytoscape.CytoscapeInit;
+import cytoscape.logger.CyLogger;
+
+import cytoscape.cruft.obo.BiologicalProcessAnnotationReader;
+import cytoscape.cruft.obo.CellularComponentAnnotationReader;
+import cytoscape.cruft.obo.MolecularFunctionAnnotationReader;
+import cytoscape.cruft.obo.OboOntologyReader;
+import cytoscape.cruft.obo.OboOntologyReader2;
+import cytoscape.cruft.obo.SynonymReader;
+
+import cytoscape.data.annotation.Annotation;
+import cytoscape.data.annotation.AnnotationDescription;
+import cytoscape.data.annotation.Ontology;
+import cytoscape.data.annotation.readers.AnnotationFlatFileReader;
+import cytoscape.data.annotation.readers.AnnotationXmlReader;
+import cytoscape.data.annotation.readers.OntologyFlatFileReader;
+
+import cytoscape.data.readers.TextFileReader;
+import cytoscape.data.readers.TextHttpReader;
+import cytoscape.data.readers.TextJarReader;
+
+import cytoscape.data.synonyms.Thesaurus;
+import cytoscape.data.synonyms.readers.ThesaurusFlatFileReader;
+
+import cytoscape.util.BioDataServerUtil;
+import cytoscape.util.URLUtil;
+
+// -----------------------------------------------------------------------------------------
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.InputStreamReader;
+
+import java.net.URL;
+
+import java.rmi.Naming;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Vector;
+
+
+// ----------------------------------------------------------------------------------------
+/**
+ *
+ */
+public class BioDataServer {
+ private static String GENE_ASSOCIATION_FILE = "gene_association";
+ private static String OBO_FILE = "obo";
+ protected BioDataServerInterface server;
+ private static CyLogger logger = CyLogger.getLogger(BioDataServer.class);
+
+ // Flip the file content (names) or not.
+ private boolean flip;
+
+ // This is for taxon name-number conversion over the net
+ private static final String TAXON_RESOURCE_FILE = "/cytoscape/resources/tax_report.txt";
+ String taxonName;
+ String taxonNumber;
+ String absPath; // apparently not used for anything
+ String taxonFileName; // Filename of taxonomy table
+ File taxonFile; // Table for the NCBI Taxonomy number <-> Taxonomy Name
+ File start; // Start dir of the Cytoscape
+ Thesaurus thesaurus; // for flipping the names
+ HashMap attributeMap; // Manage which ontoligies are mapped as
+ // CyAttributes.
+ HashMap ontologyTypeMap;
+ BioDataServerUtil bdsu; // Utilities for the Biodataserver
+ BufferedReader taxonFileReader;
+
+ // ----------------------------------------------------------------------------------------
+ /**
+ * serverName is either an RMI URI, or a manifest file which says what files
+ * to load into an in-process server; the manifest, the annotations, and the
+ * ontologies, may be files on a filesystem, files in a jar, or files
+ * retrieved by HTTP
+ *
+ * Mod. by Kei (9/10/2005): 1. Read new obo file and gene_association file
+ * format. 2. Wrote a taxon number <-> taxon name converter. This function
+ * is based on the list in the file, users need to put the file in the dir.
+ *
+ * <New for Cytoscape 2.3> Bio Data Server manages ontologies mapped onto
+ * CyAttributes This can be managed through GO Mapper GUI. kono(4/12/2006)
+ */
+ public BioDataServer(String serverName) throws Exception {
+ attributeMap = new HashMap();
+ ontologyTypeMap = new HashMap();
+
+ bdsu = new BioDataServerUtil();
+
+ taxonFileReader = null;
+
+ // Flip the names or not. Will be given from the Wizard.
+ flip = false;
+
+ thesaurus = new Thesaurus(CytoscapeInit.getProperties().getProperty("defaultSpeciesName"));
+
+ taxonName = null;
+ taxonNumber = null;
+ start = CytoscapeInit.getMRUD();
+
+ if (serverName.indexOf("rmi://") >= 0)
+ server = (BioDataServerInterface) Naming.lookup(serverName);
+ else {
+ // look for a readable file
+ server = new BioDataServerRmi(); // actually runs in process
+
+ File fileTester = new File(serverName);
+
+ if ((serverName.startsWith("jar://")) || (serverName.startsWith("http://"))
+ || (!fileTester.isDirectory() && fileTester.canRead())) {
+ boolean fileFlag = false;
+
+ // Read manifest file. First, try to read new format manifest
+ // file which includes ".obo" and gene_association file.
+ BufferedReader manFileIn = null;
+
+ try {
+ manFileIn = new BufferedReader(new FileReader(serverName));
+ // Check file type.
+ // If the manifest contains obo or gene_association entry,
+ // handle it as a new manifest file format.
+ fileFlag = checkFileType(manFileIn);
+ }
+ finally {
+ if (manFileIn != null) {
+ manFileIn.close();
+ }
+ }
+
+ // New File Type found.
+ if (fileFlag) {
+ // Extract file names and flip state from the manifest file
+ String[] flags = parseLoadFile(serverName, "flip");
+
+ if (flags[0].endsWith("true")) {
+ flip = true;
+ logger.info("Cannonical and common names will be fliped...");
+ } else {
+ flip = false;
+ }
+
+ // Extract obo file name
+ String[] oboFile = parseLoadFile(serverName, OBO_FILE);
+
+ // Extract gene association file name
+ String[] geneAssociationFile = parseLoadFile(serverName, GENE_ASSOCIATION_FILE);
+
+ try {
+ loadObo(geneAssociationFile, oboFile);
+ } catch (Exception e) {
+ logger.warn("Unable to load OBO file: "+e.getMessage(), e);
+ throw e;
+ }
+ } else {
+ /*
+ * Load old-style manifest file (for backword
+ * compatibility).
+ */
+ String[] thesaurusFilenames = parseLoadFile(serverName, "synonyms");
+ loadThesaurusFiles(thesaurusFilenames);
+
+ String[] ontologyFiles = parseLoadFile(serverName, "ontology");
+ String[] annotationFilenames = parseLoadFile(serverName, "annotation");
+ loadAnnotationFiles(annotationFilenames, ontologyFiles);
+
+ // String[] thesaurusFilenames = parseLoadFile(serverName,
+ // "synonyms");
+ // loadThesaurusFiles(thesaurusFilenames);
+ }
+ } // if a plausible candidate load file
+ else {
+ logger.warn("Could not read BioDataServer load file '" + serverName + "'");
+ }
+ } // else: look for a readable file
+ } // ctor
+
+ //
+ // Determine whether given file is new format or old.
+ //
+ protected boolean checkFileType(final BufferedReader br) throws IOException {
+ String curLine = null;
+ boolean rv;
+
+ rv = false;
+ try {
+ while (!rv && (null != (curLine = br.readLine()))) {
+ if (curLine.startsWith(OBO_FILE) || curLine.startsWith(GENE_ASSOCIATION_FILE)) {
+ rv = true;
+ }
+ }
+ }
+ finally {
+ br.close();
+ }
+
+ return rv;
+ }
+
+ // ----------------------------------------------------------------------------------------
+
+ // Mod by Keiichiro Ono (09/09/2005)
+ // 1. support for the new manifest file
+ // 2. support for the internet files
+ //
+ // TODO:
+ // get rid of manifest file idea...
+ //
+ protected String[] parseLoadFile(String filename, String key) // todo (pshannon 2003/07/01): there is some ugly special casing here, as we
+ // figure
+ // todo: out if the manifest file path is jar, http, or a regular file
+ // system
+ // todo: file. this should be refactored.
+ {
+ String rawText;
+
+ // when annotation files are loaded from a filesystem, the manifest will
+ // probably
+ // use names which are relative to the manifest. so (for this case, but
+ // not when
+ // reading from jar files) get the absolute path to the manifest, and
+ // prepend
+ // that path to the names found in the manifest. somewhat clunkily,
+ // track that
+ // information with these next two variables
+ File absoluteDirectory = null;
+ String httpUrlPrefix = null;
+ boolean readingFromFileSystem = false;
+ boolean readingFromWeb = false;
+
+ try {
+ if (filename.trim().startsWith("jar://")) {
+ TextJarReader reader = new TextJarReader(filename);
+ reader.read();
+ rawText = reader.getText();
+ } // if
+ else if (filename.trim().startsWith("http://")) {
+ TextHttpReader reader = new TextHttpReader(filename);
+ reader.read();
+ rawText = reader.getText();
+ readingFromWeb = true;
+
+ try {
+ URL url = new URL(filename);
+ String fullUrlString = url.toString();
+ httpUrlPrefix = fullUrlString.substring(0, fullUrlString.lastIndexOf("/"));
+ } catch (Exception e) {
+ httpUrlPrefix = "url parsing error!";
+ }
+ } // else: http
+ else {
+ File file = new File(filename);
+ readingFromFileSystem = true;
+ absoluteDirectory = file.getAbsoluteFile().getParentFile();
+
+ TextFileReader reader = new TextFileReader(filename);
+ reader.read();
+ rawText = reader.getText();
+ } // else: regular filesystem file
+ } catch (Exception e0) {
+ logger.warn("-- Exception while reading annotation server load file " + filename, e0);
+
+ return new String[0];
+ }
+
+ String[] lines = rawText.split("\n");
+
+ List<String> list = new ArrayList<String>();
+
+ for (int i = 0; i < lines.length; i++) {
+ String line = lines[i].trim();
+
+ if (line.trim().startsWith("#"))
+ continue;
+
+ if (line.startsWith(key)) {
+ String fileToRead = line.substring(line.indexOf("=") + 1);
+
+ if (readingFromFileSystem)
+ fileToRead = (new File(absoluteDirectory, fileToRead)).getPath();
+ else if (readingFromWeb)
+ fileToRead = httpUrlPrefix + "/" + fileToRead;
+
+ list.add(fileToRead);
+ } // if
+ } // for i
+
+ if (list.size() == 0) {
+ return null;
+ } else
+
+ return (String[]) list.toArray(new String[0]);
+ } // parseLoadFile
+
+ // ----------------------------------------------------------------------------------------
+ /**
+ * Creates a new BioDataServer object.
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public BioDataServer() throws Exception {
+ server = new BioDataServerRmi();
+ } // ctor
+
+ // ----------------------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @param ontologyFilenames DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public Ontology[] readOntologyFlatFiles(String[] ontologyFilenames)
+ throws Exception // a quick hack. this is called only if annotation & ontology are each flat
+ // files,
+ // which means they must be read separately. and xml annotation file names
+ // its own
+ // ontology file, and the annotationXmlReader is responsible for loading its
+ // ontology.
+ {
+ Vector list = new Vector();
+
+ for (int i = 0; i < ontologyFilenames.length; i++) {
+ String filename = ontologyFilenames[i];
+
+ if (!filename.endsWith(".xml")) {
+ OntologyFlatFileReader reader = new OntologyFlatFileReader(filename);
+ list.add(reader.getOntology());
+ }
+ } // for i
+
+ return (Ontology[]) list.toArray(new Ontology[0]);
+ } // loadOntologyFiles
+
+ // Read new obo file format.
+ /**
+ * DOCUMENT ME!
+ *
+ * @param ontologyFilenames DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public Ontology[] readOntologyFlatFiles2(String[] ontologyFilenames) throws Exception {
+ // logger.info("Reading Ontology flat file...");
+ Vector list = new Vector();
+
+ for (int i = 0; i < ontologyFilenames.length; i++) {
+ String filename = ontologyFilenames[i];
+
+ // Reader for the ".obo" file
+ BufferedReader oboReader = null;
+ BufferedReader oboReader2 = null;
+
+ try {
+ oboReader = new BufferedReader(new OboOntologyReader(new FileReader(filename)));
+ OntologyFlatFileReader reader = new OntologyFlatFileReader(oboReader);
+ list.add(reader.getOntology());
+ }
+ finally {
+ if (oboReader != null) {
+ oboReader.close();
+ }
+ }
+
+ try {
+ oboReader2 = new BufferedReader(new OboOntologyReader2(new FileReader(filename)));
+ String line;
+ String[] parts = null;
+
+ while ((line = oboReader2.readLine()) != null) {
+ parts = line.split("=");
+
+ if (parts.length == 2) {
+ //logger.info("ID = " + parts[0] + ", " + parts[1]);
+ if (parts[1].equals("biological_process")) {
+ ontologyTypeMap.put(parts[0], "P");
+ } else if (parts[1].equals("molecular_function")) {
+ ontologyTypeMap.put(parts[0], "F");
+ } else if (parts[1].equals("cellular_component")) {
+ ontologyTypeMap.put(parts[0], "C");
+ }
+ }
+ }
+ }
+ finally {
+ if (oboReader2 != null) {
+ oboReader2.close();
+ }
+ }
+ }
+
+ return (Ontology[]) list.toArray(new Ontology[0]);
+ } // loadOntologyFiles
+
+ // ----------------------------------------------------------------------------------------
+ protected Ontology pickOntology(Ontology[] ontologies, Annotation annotation) {
+ for (int i = 0; i < ontologies.length; i++)
+ if (ontologies[i].getCurator().equalsIgnoreCase(annotation.getCurator()))
+ return ontologies[i];
+
+ return null;
+ } // pickOntology
+
+ // ----------------------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @param annotationFilenames DOCUMENT ME!
+ * @param ontologyFilenames DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void loadObo(String[] annotationFilenames, String[] ontologyFilenames)
+ throws Exception {
+ // logger.info("Loading OBO file...");
+//The following commented out code appears to replicate what's done in readOntologyFlatFiles2
+// BufferedReader[] oboReaders = new BufferedReader[ontologyFilenames.length];
+//
+// for (int i = 0; i < ontologyFilenames.length; i++) {
+// oboReaders[i] = new BufferedReader(new OboOntologyReader(new FileReader(ontologyFilenames[i])));
+// }
+
+ Ontology[] ontologies = readOntologyFlatFiles2(ontologyFilenames);
+
+ URL taxURL = getClass().getResource(TAXON_RESOURCE_FILE);
+ /*
+ * Since one Gene Association file is equal to the follwing:
+ *
+ * Biological Process Annotation Cellar Component Annotation Molecular
+ * Function Annotation
+ *
+ * we need 3 separate readers.
+ */
+ for (int i = 0; i < annotationFilenames.length; i++) {
+ Annotation bpAnnotation = null;
+ Annotation ccAnnotation = null;
+ Annotation mfAnnotation = null;
+ String filename = annotationFilenames[i];
+
+ String[] thFileName = new String[1];
+ thFileName[0] = annotationFilenames[i];
+
+ // Extract taxon name.
+ BufferedReader gaFileReader = null;
+ try {
+
+ gaFileReader = new BufferedReader(new FileReader(filename));
+
+ // Create tax_report file reader
+ // taxonFileReader = new BufferedReader(new InputStreamReader(taxURL.openStream()));
+ // Even though taxURL is probably a local URL, error on the
+ // side of caution and use URLUtil to get the input stream (which
+ // handles proxy servers and cached pages):
+ taxonFileReader = new BufferedReader(new InputStreamReader(URLUtil.getBasicInputStream(taxURL)));
+
+ // taxonName = checkSpecies(gaFileReader);
+ taxonName = bdsu.checkSpecies(gaFileReader, taxonFileReader);
+ }
+ finally {
+ if (gaFileReader != null) {
+ gaFileReader.close();
+ }
+ }
+
+ loadThesaurusFiles2(thFileName);
+
+ logger.info("Loading: " + annotationFilenames[i] + " (Species = " + taxonName + ")");
+
+ // Reader for the "gene_association" file
+ BufferedReader bpRd = null;
+ try {
+ bpRd = new BufferedReader(
+ new BiologicalProcessAnnotationReader(taxonName,
+ ontologyTypeMap,
+ new FileReader(filename)));
+ AnnotationFlatFileReader bpReader = new AnnotationFlatFileReader(bpRd, thesaurus, flip);
+ bpAnnotation = bpReader.getAnnotation();
+ }
+ finally {
+ if (bpRd != null) {
+ bpRd.close();
+ }
+ }
+
+ BufferedReader ccRd = null;
+ try {
+ ccRd = new BufferedReader(
+ new CellularComponentAnnotationReader(taxonName,
+ ontologyTypeMap,
+ new FileReader(filename)));
+ AnnotationFlatFileReader ccReader = new AnnotationFlatFileReader(ccRd, thesaurus, flip);
+ ccAnnotation = ccReader.getAnnotation();
+ }
+ finally {
+ if (ccRd != null) {
+ ccRd.close();
+ }
+ }
+
+ BufferedReader mfRd = null;
+
+ try {
+ mfRd = new BufferedReader(
+ new MolecularFunctionAnnotationReader(taxonName,
+ ontologyTypeMap,
+ new FileReader(filename)));
+ AnnotationFlatFileReader mfReader = new AnnotationFlatFileReader(mfRd, thesaurus, flip);
+ mfAnnotation = mfReader.getAnnotation();
+ }
+ finally {
+ if (mfRd != null) {
+ mfRd.close();
+ }
+ }
+
+ bpAnnotation.setOntology(pickOntology(ontologies, bpAnnotation));
+ ccAnnotation.setOntology(pickOntology(ontologies, ccAnnotation));
+ mfAnnotation.setOntology(pickOntology(ontologies, mfAnnotation));
+
+ server.addAnnotation(bpAnnotation);
+ server.addAnnotation(ccAnnotation);
+ server.addAnnotation(mfAnnotation);
+ }
+ } // loadAnnotationFiles2
+
+ // Read the content of the annotation and ontology file
+ /**
+ * DOCUMENT ME!
+ *
+ * @param annotationFilenames DOCUMENT ME!
+ * @param ontologyFilenames DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void loadAnnotationFiles(String[] annotationFilenames, String[] ontologyFilenames)
+ throws Exception {
+ Ontology[] ontologies = readOntologyFlatFiles(ontologyFilenames);
+
+ for (int i = 0; i < annotationFilenames.length; i++) {
+ Annotation annotation;
+ String filename = annotationFilenames[i];
+
+ if (!filename.endsWith(".xml")) {
+ AnnotationFlatFileReader reader = new AnnotationFlatFileReader(filename, thesaurus);
+ annotation = reader.getAnnotation();
+ annotation.setOntology(pickOntology(ontologies, annotation));
+ } else {
+ File xmlFile = new File(annotationFilenames[i]);
+ AnnotationXmlReader reader = new AnnotationXmlReader(xmlFile);
+ annotation = reader.getAnnotation();
+ }
+
+ server.addAnnotation(annotation);
+ } // for i
+ } // loadAnnotationFiles
+
+ // ----------------------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @param thesaurusFilenames DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void loadThesaurusFiles(String[] thesaurusFilenames) throws Exception {
+ for (int i = 0; i < thesaurusFilenames.length; i++) {
+ String filename = thesaurusFilenames[i];
+
+ ThesaurusFlatFileReader reader = new ThesaurusFlatFileReader(filename);
+ thesaurus = reader.getThesaurus();
+
+ //thesaurus.dump();
+ server.addThesaurus(thesaurus.getSpecies(), thesaurus);
+ }
+ } // loadThesaurusFiles
+
+ /*
+ * Accept new gene association file. And create Thesaurus file from it.
+ */
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param thesaurusFilenames DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void loadThesaurusFiles2(String[] thesaurusFilenames) throws Exception {
+ for (int i = 0; i < thesaurusFilenames.length; i++) {
+ String filename = thesaurusFilenames[i];
+
+ BufferedReader thRd = null;
+
+ try {
+ thRd = new BufferedReader(new SynonymReader(taxonName, new FileReader(filename)));
+ ThesaurusFlatFileReader reader = new ThesaurusFlatFileReader(thRd, flip);
+ thesaurus = reader.getThesaurus();
+
+ //thesaurus.dump();
+ server.addThesaurus(thesaurus.getSpecies(), thesaurus);
+ }
+ finally {
+ if (thRd != null) {
+ thRd.close();
+ }
+ }
+ }
+ } // loadThesaurusFiles
+
+ // ----------------------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ */
+ public void clear() {
+ try {
+ server.clear();
+ } catch (Exception e) {
+ logger.warn("Error! failed to clear", e);
+ }
+ }
+
+ // ----------------------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @param annotation DOCUMENT ME!
+ */
+ public void addAnnotation(Annotation annotation) {
+ try {
+ server.addAnnotation(annotation);
+ } catch (Exception e) {
+ logger.warn("Error! failed to add annotation " + annotation, e);
+ }
+ }
+
+ // ----------------------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getAnnotationCount() {
+ try {
+ int count = server.getAnnotationCount();
+
+ return count;
+ } catch (Exception e) {
+ return 0;
+ }
+ }
+
+ // ----------------------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public AnnotationDescription[] getAnnotationDescriptions() {
+ try {
+ return server.getAnnotationDescriptions();
+ } catch (Exception e) {
+ return null;
+ }
+ }
+
+ // ----------------------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @param species DOCUMENT ME!
+ * @param curator DOCUMENT ME!
+ * @param type DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Annotation getAnnotation(String species, String curator, String type) {
+ try {
+ return server.getAnnotation(species, curator, type);
+ } catch (Exception e) {
+ return null;
+ }
+ }
+
+ // ----------------------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @param description DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Annotation getAnnotation(AnnotationDescription description) {
+ try {
+ return server.getAnnotation(description);
+ } catch (Exception e) {
+ return null;
+ }
+ }
+
+ // ----------------------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @param species DOCUMENT ME!
+ * @param curator DOCUMENT ME!
+ * @param type DOCUMENT ME!
+ * @param entity DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] getClassifications(String species, String curator, String type, String entity) {
+ try {
+ return server.getClassifications(species, curator, type, entity);
+ } catch (Exception e) {
+ return null;
+ }
+ }
+
+ // ----------------------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @param description DOCUMENT ME!
+ * @param entity DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] getClassifications(AnnotationDescription description, String entity) {
+ try {
+ return server.getClassifications(description, entity);
+ } catch (Exception e) {
+ return null;
+ }
+ }
+
+ // ----------------------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @param description DOCUMENT ME!
+ * @param entity DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String[][] getAllAnnotations(AnnotationDescription description, String entity) {
+ try {
+ return server.getAllAnnotations(description, entity);
+ } catch (Exception e) {
+ return null;
+ }
+ }
+
+ // ----------------------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String describe() {
+ try {
+ return server.describe();
+ } catch (Exception e) {
+ return "error connecting to data server";
+ }
+ }
+
+ // ----------------------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @param species DOCUMENT ME!
+ * @param thesaurus DOCUMENT ME!
+ */
+ public void addThesaurus(String species, Thesaurus thesaurus) {
+ try {
+ server.addThesaurus(species, thesaurus);
+ } catch (Exception e) {
+ return;
+ }
+ }
+
+ // ----------------------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @param species DOCUMENT ME!
+ * @param commonName DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getCanonicalName(String species, String commonName) {
+ try {
+ return server.getCanonicalName(species, commonName);
+ } catch (Exception e) {
+ return null;
+ }
+ }
+
+ // ----------------------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @param species DOCUMENT ME!
+ * @param commonName DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String[] getAllCommonNames(String species, String commonName) {
+ try {
+ return server.getAllCommonNames(species, commonName);
+ } catch (Exception e) {
+ return null;
+ }
+ }
+
+ // ----------------------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @param species DOCUMENT ME!
+ * @param canonicalName DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getCommonName(String species, String canonicalName) {
+ try {
+ return server.getCommonName(species, canonicalName);
+ } catch (Exception e) {
+ return null;
+ }
+ }
+} // BioDataServer
diff --git a/application/src/main/java/cytoscape/data/servers/BioDataServerInterface.java b/application/src/main/java/cytoscape/data/servers/BioDataServerInterface.java
new file mode 100755
index 0000000..a836fea
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/servers/BioDataServerInterface.java
@@ -0,0 +1,219 @@
+/*
+ File: BioDataServerInterface.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+// BioDataServerInterface.java: define the interface
+
+//----------------------------------------------------------------------------------------
+// $Revision: 9736 $
+// $Date: 2007-03-20 01:25:45 +0100 (Tue, 20 Mar 2007) $
+// $Author: mes $
+//----------------------------------------------------------------------------------------
+package cytoscape.data.servers;
+
+import cytoscape.data.annotation.Annotation;
+import cytoscape.data.annotation.AnnotationDescription;
+
+import cytoscape.data.synonyms.Thesaurus;
+
+//----------------------------------------------------------------------------------------
+import java.rmi.Remote;
+
+
+//----------------------------------------------------------------------------------------
+/**
+ *
+ */
+public interface BioDataServerInterface extends Remote {
+ // annotations (typically of genes, but possibly of any entity whatsoever
+ /**
+ * DOCUMENT ME!
+ *
+ * @param annotation DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void addAnnotation(Annotation annotation) throws Exception;
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public int getAnnotationCount() throws Exception;
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public AnnotationDescription[] getAnnotationDescriptions() throws Exception;
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param species DOCUMENT ME!
+ * @param curator DOCUMENT ME!
+ * @param type DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public Annotation getAnnotation(String species, String curator, String type)
+ throws Exception;
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param description DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public Annotation getAnnotation(AnnotationDescription description) throws Exception;
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param species DOCUMENT ME!
+ * @param curator DOCUMENT ME!
+ * @param type DOCUMENT ME!
+ * @param entity DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public int[] getClassifications(String species, String curator, String type, String entity)
+ throws Exception;
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param description DOCUMENT ME!
+ * @param entity DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public int[] getClassifications(AnnotationDescription description, String entity)
+ throws Exception;
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param description DOCUMENT ME!
+ * @param entity DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public String[][] getAllAnnotations(AnnotationDescription description, String entity)
+ throws Exception;
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void clear() throws Exception;
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public String describe() throws Exception;
+
+ // names & synonyms, typically of genes, but possibly of any entity
+ /**
+ * DOCUMENT ME!
+ *
+ * @param species DOCUMENT ME!
+ * @param thesaurus DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void addThesaurus(String species, Thesaurus thesaurus) throws Exception;
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param species DOCUMENT ME!
+ * @param commonName DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public String getCanonicalName(String species, String commonName) throws Exception;
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param species DOCUMENT ME!
+ * @param commonName DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public String[] getAllCommonNames(String species, String commonName) throws Exception;
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param species DOCUMENT ME!
+ * @param canonicalName DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public String getCommonName(String species, String canonicalName) throws Exception;
+
+ // ----------------------------------------------------------------------------------------
+} // interface BioDataServerInterface
diff --git a/application/src/main/java/cytoscape/data/servers/BioDataServerRmi.java b/application/src/main/java/cytoscape/data/servers/BioDataServerRmi.java
new file mode 100755
index 0000000..af29949
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/servers/BioDataServerRmi.java
@@ -0,0 +1,366 @@
+/*
+ File: BioDataServerRmi.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+// BioDataServerRmi.java
+package cytoscape.data.servers;
+
+import cytoscape.data.annotation.Annotation;
+import cytoscape.data.annotation.AnnotationDescription;
+
+import cytoscape.data.synonyms.Thesaurus;
+import cytoscape.logger.CyLogger;
+
+import java.io.Serializable;
+
+import java.rmi.Naming;
+import java.rmi.RemoteException;
+import java.rmi.server.UnicastRemoteObject;
+
+import java.util.Date;
+import java.util.HashMap;
+
+
+/**
+ * This is the actual class which implements BioDataServer Methods.
+ *
+ * @author kono
+ *
+ * 04/19/2006: Old code removed (to resolve naming issue.)
+ */
+public class BioDataServerRmi extends UnicastRemoteObject implements BioDataServerInterface,
+ Serializable {
+ /*
+ * gene (or other biological entity) annotations are specific to - a species
+ * (i.e., halobacterium, or yeast) - a curator (i.e., KEGG or GO) - a type
+ * (i.e., GO's biological process, or KEGG's metabolic pathway) these three
+ * attributes are contained in an 'AttributeDescription', instances of which
+ * are used as keys in the following HashMap
+ */
+ protected HashMap annotations;
+ protected HashMap thesauri;
+ protected Date startTime;
+ protected Date lastAccessTime;
+
+ /**
+ * Creates a new BioDataServerRmi object.
+ *
+ * @throws RemoteException DOCUMENT ME!
+ */
+ public BioDataServerRmi() throws RemoteException {
+ super();
+ annotations = new HashMap();
+ thesauri = new HashMap();
+
+ startTime = new Date();
+ lastAccessTime = new Date();
+ }
+
+ /**
+ * if the new annotation is to an already annotated species, curator and
+ * type, then simply add (with possible overwriting for identical
+ */
+ public void addAnnotation(Annotation newAnnotation) {
+ lastAccessTime = new Date();
+
+ AnnotationDescription key = new AnnotationDescription(newAnnotation.getSpecies(),
+ newAnnotation.getCurator(),
+ newAnnotation.getType());
+
+ if (annotations.containsKey(key)) {
+ Annotation oldAnnotation = (Annotation) annotations.get(key);
+ String[] newNames = newAnnotation.getNames();
+
+ for (int i = 0; i < newNames.length; i++) {
+ int[] classificationIDs = newAnnotation.getClassifications(newNames[i]);
+
+ for (int c = 0; c < classificationIDs.length; c++)
+ oldAnnotation.add(newNames[i], classificationIDs[c]);
+ } // for i
+ } else {
+ annotations.put(key, newAnnotation);
+ }
+ } // addAnnotation (Annotation)
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void clear() {
+ annotations = new HashMap();
+ lastAccessTime = new Date();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getAnnotationCount() {
+ lastAccessTime = new Date();
+
+ return annotations.size();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public AnnotationDescription[] getAnnotationDescriptions() {
+ lastAccessTime = new Date();
+
+ AnnotationDescription[] result = (AnnotationDescription[]) annotations.keySet()
+ .toArray(new AnnotationDescription[0]);
+
+ return result;
+ } // getAnnotationDescriptions
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param species DOCUMENT ME!
+ * @param curator DOCUMENT ME!
+ * @param type DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Annotation getAnnotation(String species, String curator, String type) {
+ lastAccessTime = new Date();
+
+ AnnotationDescription description = new AnnotationDescription(species, curator, type);
+
+ return getAnnotation(description);
+ } // getAnnotations
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param description DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Annotation getAnnotation(AnnotationDescription description) {
+ lastAccessTime = new Date();
+
+ return (Annotation) annotations.get(description);
+ } // getAnnotations
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param species DOCUMENT ME!
+ * @param curator DOCUMENT ME!
+ * @param type DOCUMENT ME!
+ * @param entity DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] getClassifications(String species, String curator, String type, String entity) {
+ lastAccessTime = new Date();
+
+ AnnotationDescription description = new AnnotationDescription(species, curator, type);
+
+ return (getClassifications(description, entity));
+ } // getClassifications
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param description DOCUMENT ME!
+ * @param entity DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] getClassifications(AnnotationDescription description, String entity) {
+ lastAccessTime = new Date();
+
+ Annotation annotation = (Annotation) annotations.get(description);
+
+ return annotation.getClassifications(entity);
+ } // getClassifications
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param description DOCUMENT ME!
+ * @param entity DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String[][] getAllAnnotations(AnnotationDescription description, String entity) {
+ lastAccessTime = new Date();
+
+ Annotation annotation = (Annotation) annotations.get(description);
+
+ return annotation.getAllHierarchyPathsAsNames(entity);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String describe() {
+ StringBuffer sb = new StringBuffer();
+ Annotation[] tmp = (Annotation[]) annotations.values().toArray(new Annotation[0]);
+
+ for (int i = 0; i < tmp.length; i++) {
+ sb.append(tmp[i]);
+ sb.append("\n");
+ }
+
+ Thesaurus[] tmp2 = (Thesaurus[]) thesauri.values().toArray(new Thesaurus[0]);
+
+ for (int i = 0; i < tmp2.length; i++) {
+ sb.append(tmp2[i]);
+ sb.append("\n");
+ }
+
+ sb.append("\n");
+ sb.append(" started: " + startTime);
+ sb.append("\n");
+
+ sb.append("last access: " + lastAccessTime);
+ sb.append("\n");
+
+ return sb.toString();
+ } // describe
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param species DOCUMENT ME!
+ * @param thesaurus DOCUMENT ME!
+ */
+ public void addThesaurus(String species, Thesaurus thesaurus) {
+ thesauri.put(species, thesaurus);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param species DOCUMENT ME!
+ * @param commonName DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getCanonicalName(String species, String commonName) {
+ if (thesauri.containsKey(species)) {
+ Thesaurus t = (Thesaurus) thesauri.get(species);
+
+ if (t != null) {
+ String result = t.getNodeLabel(commonName);
+
+ if (result != null)
+ return result;
+ } // if thesaurus exists
+ } // if key
+
+ return commonName;
+ } // getCanonicalName
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param species DOCUMENT ME!
+ * @param commonName DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String[] getAllCommonNames(String species, String commonName) {
+ if (thesauri.containsKey(species)) {
+ Thesaurus t = (Thesaurus) thesauri.get(species);
+
+ if (t != null) {
+ String[] result = t.getAllCommonNames(commonName);
+
+ if (result != null)
+ return result;
+ } // if thesaurus exists
+ } // if key
+
+ String[] result = new String[1];
+ result[0] = commonName;
+
+ return result;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param species DOCUMENT ME!
+ * @param canonicalName DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getCommonName(String species, String canonicalName) {
+ if (thesauri.containsKey(species)) {
+ Thesaurus t = (Thesaurus) thesauri.get(species);
+
+ if (t != null) {
+ String result = t.getCommonName(canonicalName);
+
+ if (result != null)
+ return result;
+ } // if thesaurus exists
+ } // if key
+
+ return canonicalName;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ */
+ public static void main(String[] args) {
+ if (args.length != 1) {
+ System.out.println("usage: BioDataServerRmi <server name>");
+ System.exit(1);
+ }
+
+ String name = args[0];
+
+ try {
+ BioDataServerRmi rmiServer = new BioDataServerRmi();
+ Naming.rebind(name, rmiServer);
+ System.out.println("BioDataServer bound as '" + name + "'");
+ } catch (Exception e) {
+ System.out.println("BioDataServer exception: " + e.getMessage());
+ e.printStackTrace();
+ }
+ } // main
+} // class BioDataServerRmi
diff --git a/application/src/main/java/cytoscape/data/servers/OntologyServer.java b/application/src/main/java/cytoscape/data/servers/OntologyServer.java
new file mode 100644
index 0000000..3c80e19
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/servers/OntologyServer.java
@@ -0,0 +1,221 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data.servers;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+
+import cytoscape.bookmarks.Bookmarks;
+
+import cytoscape.data.ontology.DBCrossReferences;
+import cytoscape.data.ontology.Ontology;
+import cytoscape.data.ontology.OntologyFactory;
+
+import cytoscape.data.readers.BookmarkReader;
+
+import cytoscape.data.synonyms.AliasType;
+import cytoscape.data.synonyms.Aliases;
+
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.beans.PropertyChangeSupport;
+
+import java.io.IOException;
+
+import java.net.URISyntaxException;
+import java.net.URL;
+
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Set;
+
+import javax.xml.bind.JAXBException;
+
+
+/**
+ * Ontology Server which manages ontologies, aliases, and bookmarks.<br>
+ *
+ * @since Cytoscape 2.4
+ * @version 0.6
+ *
+ * @author kono
+ *
+ */
+public class OntologyServer implements PropertyChangeListener {
+ public static enum OntologyType {
+ BASIC,
+ GO;
+ }
+
+ /**
+ * Map of Ontologies.
+ */
+ private HashMap<String, Ontology> ontologies;
+
+ /*
+ * Aliases
+ */
+ private Aliases nodeAliases;
+ private Aliases edgeAliases;
+ private Aliases networkAliases;
+
+ /*
+ * Factory to create actual Ontology objects.
+ */
+ private OntologyFactory factory;
+
+ /*
+ * Bookmarks. This can be used not only for ontology stuff, but also network
+ * file locations, attributes, etc.
+ */
+
+ //private Bookmarks bookmarks;
+
+ /*
+ * URLs of ontology data in memory
+ */
+ private Map<String, URL> ontologySources;
+
+ /*
+ * Database cross references.
+ */
+ private DBCrossReferences xref;
+
+ /**
+ * Constructor.<br>
+ *
+ * Create hash map for ontologies.
+ *
+ * @throws ConfigurationException
+ * @throws IOException
+ * @throws JAXBException
+ */
+ public OntologyServer() throws IOException, JAXBException {
+ Cytoscape.getPropertyChangeSupport().addPropertyChangeListener(this);
+
+ factory = new OntologyFactory();
+ this.ontologies = new HashMap<String, Ontology>();
+ this.ontologySources = new HashMap<String, URL>();
+
+ xref = new DBCrossReferences();
+ xref.load();
+
+ //loadBookmarks();
+ nodeAliases = new Aliases(AliasType.NODE);
+ edgeAliases = new Aliases(AliasType.EDGE);
+ networkAliases = new Aliases(AliasType.NETWORK);
+ }
+
+ public DBCrossReferences getCrossReferences() {
+ return xref;
+ }
+
+ /**
+ * Getter of the property <tt>ontologies</tt>
+ *
+ * @return Returns the ontologies.
+ * @uml.property name="ontologies"
+ */
+ public HashMap<String, Ontology> getOntologies() {
+ return ontologies;
+ }
+
+ public void addOntology(Ontology onto) {
+ ontologies.put(onto.getName(), onto);
+ }
+
+ public void addOntology(URL dataSource, OntologyType type, String ontologyName,
+ String description) throws IOException, URISyntaxException {
+ Ontology onto;
+
+ switch (type) {
+ case BASIC:
+ onto = factory.createBasicOntology(dataSource, ontologyName, description);
+
+ break;
+
+ case GO:
+ onto = factory.createGeneOntology(dataSource, ontologyName, description);
+ break;
+
+ default:
+ onto = null;
+ }
+
+ ontologies.put(onto.getName(), onto);
+ ontologySources.put(onto.getName(), dataSource);
+ }
+
+ public int ontologyCount() {
+ return ontologies.size();
+ }
+
+ public void setOntology(Ontology onto) {
+ ontologies.put(onto.getName(), onto);
+ }
+
+ public Set<String> getOntologyNames() {
+ return ontologies.keySet();
+ }
+
+ public Map<String, URL> getOntologySources() {
+ return ontologySources;
+ }
+
+ public void setOntologySources(Map<String, URL> newMap) {
+ ontologySources = newMap;
+ }
+
+ public Aliases getNodeAliases() {
+ return nodeAliases;
+ }
+
+ public Aliases getEdgeAliases() {
+ return edgeAliases;
+ }
+
+ public Aliases getNetworkAliases() {
+ return networkAliases;
+ }
+
+ public void propertyChange(PropertyChangeEvent e) {
+ if (Cytoscape.NETWORK_DESTROYED.equals(e.getPropertyName())) {
+ /*
+ * Remove network name from ontology server.
+ */
+ ontologies.remove(Cytoscape.getNetwork((String) e.getNewValue()).getTitle());
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/data/servers/clear.java b/application/src/main/java/cytoscape/data/servers/clear.java
new file mode 100755
index 0000000..50548b6
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/servers/clear.java
@@ -0,0 +1,88 @@
+/*
+ File: clear.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// clear
+
+//------------------------------------------------------------------------------
+// $Revision: 14789 $
+// $Date: 2008-08-23 02:44:19 +0200 (Sat, 23 Aug 2008) $
+// $Author: scooter $
+//-----------------------------------------------------------------------------------
+package cytoscape.data.servers;
+
+import cytoscape.logger.CyLogger;
+
+import java.io.*;
+
+//-----------------------------------------------------------------------------------
+import java.rmi.*;
+
+import java.util.Vector;
+
+
+//------------------------------------------------------------------------------
+/**
+ *
+ */
+public class clear {
+ //------------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public static void main(String[] args) throws Exception {
+ if (args.length != 2) {
+ System.out.println("usage: clear <rmi host name> <rmi service name>");
+ System.exit(1);
+ }
+
+ String hostname = args[0];
+ String serviceName = args[1];
+
+ String serverName = "rmi://" + hostname + "/" + serviceName;
+ System.out.println("--- checking clear of " + serverName);
+
+ BioDataServer server = new BioDataServer(serverName);
+ System.out.println(server.describe());
+ server.clear();
+ System.out.println(server.describe());
+ } // main
+ //------------------------------------------------------------------------------
+} // clear
diff --git a/application/src/main/java/cytoscape/data/servers/getCanonicalName.java b/application/src/main/java/cytoscape/data/servers/getCanonicalName.java
new file mode 100755
index 0000000..2481fd3
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/servers/getCanonicalName.java
@@ -0,0 +1,87 @@
+/*
+ File: getCanonicalName.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// getCanonicalName
+
+//------------------------------------------------------------------------------
+// $Revision: 14789 $
+// $Date: 2008-08-23 02:44:19 +0200 (Sat, 23 Aug 2008) $
+// $Author: scooter $
+//-----------------------------------------------------------------------------------
+package cytoscape.data.servers;
+
+import cytoscape.data.annotation.*;
+import cytoscape.logger.CyLogger;
+
+import java.io.*;
+
+//-----------------------------------------------------------------------------------
+import java.rmi.*;
+
+import java.util.Vector;
+
+
+//------------------------------------------------------------------------------
+/**
+ *
+ */
+public class getCanonicalName {
+ //------------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public static void main(String[] args) throws Exception {
+ if (args.length != 4) {
+ CyLogger.getLogger().warn("usage: getCanonicalName <rmi host name> <rmi service name> \"<species>\" <canonicalName>");
+ System.exit(1);
+ }
+
+ String hostname = args[0];
+ String serviceName = args[1];
+ String species = args[2];
+ String canonicalName = args[3];
+
+ String serverName = "rmi://" + hostname + "/" + serviceName;
+ BioDataServer server = new BioDataServer(serverName);
+ CyLogger.getLogger().warn(canonicalName + " -> " + server.getCanonicalName(species, canonicalName));
+ } // main
+ //------------------------------------------------------------------------------
+} // getCanonicalName
diff --git a/application/src/main/java/cytoscape/data/servers/getCommonName.java b/application/src/main/java/cytoscape/data/servers/getCommonName.java
new file mode 100755
index 0000000..ed1ae46
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/servers/getCommonName.java
@@ -0,0 +1,87 @@
+/*
+ File: getCommonName.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// getCommonName
+
+//------------------------------------------------------------------------------
+// $Revision: 14060 $
+// $Date: 2008-05-20 22:13:18 +0200 (Tue, 20 May 2008) $
+// $Author: skillcoyne $
+//-----------------------------------------------------------------------------------
+package cytoscape.data.servers;
+
+import cytoscape.data.annotation.*;
+import cytoscape.logger.CyLogger;
+
+import java.io.*;
+
+//-----------------------------------------------------------------------------------
+import java.rmi.*;
+
+import java.util.Vector;
+
+
+//------------------------------------------------------------------------------
+/**
+ *
+ */
+public class getCommonName {
+ //------------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public static void main(String[] args) throws Exception {
+ if (args.length != 4) {
+ CyLogger.getLogger().warn("usage: getCommonName <rmi host name> <rmi service name> \"<species>\" <canonicalName>");
+ System.exit(1);
+ }
+
+ String hostname = args[0];
+ String serviceName = args[1];
+ String species = args[2];
+ String canonicalName = args[3];
+
+ String serverName = "rmi://" + hostname + "/" + serviceName;
+ BioDataServer server = new BioDataServer(serverName);
+ CyLogger.getLogger().info(canonicalName + " -> " + server.getCommonName(species, canonicalName));
+ } // main
+ //------------------------------------------------------------------------------
+} // getCommonName
diff --git a/application/src/main/java/cytoscape/data/servers/loadAnnotation.java b/application/src/main/java/cytoscape/data/servers/loadAnnotation.java
new file mode 100755
index 0000000..cf1a9c5
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/servers/loadAnnotation.java
@@ -0,0 +1,104 @@
+/*
+ File: loadAnnotation.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// loadAnnotation
+
+//------------------------------------------------------------------------------
+// $Revision: 14060 $
+// $Date: 2008-05-20 22:13:18 +0200 (Tue, 20 May 2008) $
+// $Author: skillcoyne $
+//-----------------------------------------------------------------------------------
+package cytoscape.data.servers;
+
+import cytoscape.data.annotation.*;
+import cytoscape.data.annotation.readers.*;
+import cytoscape.logger.CyLogger;
+
+import java.io.*;
+
+//-----------------------------------------------------------------------------------
+import java.rmi.*;
+
+import java.util.Vector;
+
+
+//------------------------------------------------------------------------------
+/**
+ * load an annotation into an rmi biodata server. an annotation -- necessarily
+ * accompanied by an ontology, whose location is specified in the annotation's xml
+ * file -- specifies the relationship of an entity (i.e., a gene) to one or more nodes
+ * (integers) in the ontology. from this assignment, the full ontological hierarchy
+ * can be deduced.
+ *
+ * @see cytoscape.data.annotation.Annotation
+ * @see cytoscape.data.annotation.Ontology
+ */
+public class loadAnnotation {
+ //------------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public static void main(String[] args) throws Exception {
+ if (args.length != 2) {
+ CyLogger.getLogger().warn("usage: loadAnnotation <server name> <annotation.xml>");
+ System.exit(1);
+ }
+
+ String serverName = args[0];
+ BioDataServer server = new BioDataServer(serverName);
+
+ String filename = args[1];
+
+ File xmlFile = new File(filename);
+
+ if (!xmlFile.canRead()) {
+ CyLogger.getLogger().warn("--- cytoscape.data.servers.loadAnnotation error: cannot read");
+ CyLogger.getLogger().warn(" " + filename);
+ System.exit(1);
+ }
+
+ AnnotationXmlReader reader = new AnnotationXmlReader(xmlFile);
+ server.addAnnotation(reader.getAnnotation());
+
+ CyLogger.getLogger().info(server.describe());
+ } // main
+ //------------------------------------------------------------------------------
+} // loadAnnotation
diff --git a/application/src/main/java/cytoscape/data/servers/loadAnnotationFromFlatFiles.java b/application/src/main/java/cytoscape/data/servers/loadAnnotationFromFlatFiles.java
new file mode 100755
index 0000000..a316137
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/servers/loadAnnotationFromFlatFiles.java
@@ -0,0 +1,127 @@
+/*
+ File: loadAnnotationFromFlatFiles.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// loadAnnotationFromFlatfiles
+
+//------------------------------------------------------------------------------
+// $Revision: 14060 $
+// $Date: 2008-05-20 22:13:18 +0200 (Tue, 20 May 2008) $
+// $Author: skillcoyne $
+//-----------------------------------------------------------------------------------
+package cytoscape.data.servers;
+
+import cytoscape.data.annotation.*;
+import cytoscape.data.annotation.readers.*;
+import cytoscape.logger.CyLogger;
+
+import java.io.*;
+
+//-----------------------------------------------------------------------------------
+import java.rmi.*;
+
+import java.util.Vector;
+
+
+//------------------------------------------------------------------------------
+/**
+ * load an annotation into an rmi biodata server. an annotation -- necessarily
+ * accompanied by an ontology, whose location is specified in the annotation's xml
+ * file -- specifies the relationship of an entity (i.e., a gene) to one or more nodes
+ * (integers) in the ontology. from this assignment, the full ontological hierarchy
+ * can be deduced.
+ *
+ * @see cytoscape.data.annotation.Annotation
+ * @see cytoscape.data.annotation.Ontology
+ */
+public class loadAnnotationFromFlatFiles {
+ //------------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public static void main(String[] args) throws Exception {
+ if (args.length != 3) {
+ CyLogger.getLogger().warn("usage: loadAnnotationFromFaltFile <server name> <annotation.txt> <ontology.txt>");
+ System.exit(1);
+ }
+
+ String serverName = args[0];
+ BioDataServer server = new BioDataServer(serverName);
+
+ String annotationFilename = args[1];
+ String ontologyFilename = args[2];
+
+ File annotationFile = new File(annotationFilename);
+
+ if (!annotationFile.canRead()) {
+ CyLogger.getLogger().warn("--- cytoscape.data.servers.loadAnnotationFromFlatfiles error: cannot read");
+ CyLogger.getLogger().warn(" " + annotationFilename);
+ System.exit(1);
+ }
+
+ File ontologyFile = new File(ontologyFilename);
+
+ if (!ontologyFile.canRead()) {
+ CyLogger.getLogger().warn("--- cytoscape.data.servers.loadAnnotationFromFlatfiles error: cannot read");
+ CyLogger.getLogger().warn(" " + ontologyFilename);
+ System.exit(1);
+ }
+
+ AnnotationFlatFileReader reader = new AnnotationFlatFileReader(annotationFile);
+ Annotation annotation = reader.getAnnotation();
+
+ OntologyFlatFileReader ontologyReader = new OntologyFlatFileReader(ontologyFile);
+ Ontology ontology = ontologyReader.getOntology();
+
+ if (!annotation.getCurator().equals(ontology.getCurator())) {
+ CyLogger.getLogger().warn("annotation is curated by " + annotation.getCurator());
+ CyLogger.getLogger().warn("ontology is curated by " + ontology.getCurator());
+ CyLogger.getLogger().warn(" --> these disagree. Exiting....");
+ System.exit(1);
+ }
+
+ annotation.setOntology(ontology);
+
+ server.addAnnotation(annotation);
+
+ CyLogger.getLogger().info(server.describe());
+ } // main
+ //------------------------------------------------------------------------------
+} // loadAnnotationFromFlatFiles
diff --git a/application/src/main/java/cytoscape/data/servers/loadThesaurus.java b/application/src/main/java/cytoscape/data/servers/loadThesaurus.java
new file mode 100755
index 0000000..3bbb42c
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/servers/loadThesaurus.java
@@ -0,0 +1,99 @@
+/*
+ File: loadThesaurus.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// loadThesaurus
+
+//------------------------------------------------------------------------------
+// $Revision: 14060 $
+// $Date: 2008-05-20 22:13:18 +0200 (Tue, 20 May 2008) $
+// $Author: skillcoyne $
+//-----------------------------------------------------------------------------------
+package cytoscape.data.servers;
+
+import cytoscape.data.annotation.*;
+import cytoscape.data.annotation.readers.*;
+import cytoscape.logger.CyLogger;
+
+import java.io.*;
+
+//-----------------------------------------------------------------------------------
+import java.rmi.*;
+
+import java.util.Vector;
+
+
+//------------------------------------------------------------------------------
+/**
+ * load an thesaurus into an rmi biodata server. an thesaurus -- necessarily
+ * accompanied by an ontology, whose location is specified in the thesaurus's xml
+ * file -- specifies the relationship of an entity (i.e., a gene) to one or more nodes
+ * (integers) in the ontology. from this assignment, the full ontological hierarchy
+ * can be deduced.
+ *
+ * @see cytoscape.data.synonyms.Thesaurus
+ * @see cytoscape.data.annotation.Ontology
+ */
+public class loadThesaurus {
+ //------------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public static void main(String[] args) throws Exception {
+ if (args.length != 2) {
+ CyLogger.getLogger().warn("usage: loadThesaurus <server name> <thesaurus flat file>");
+ System.exit(1);
+ }
+
+ String serverName = args[0];
+ BioDataServer server = new BioDataServer("rmi://localhost/" + serverName);
+
+ String[] filenames = new String[1];
+ filenames[0] = args[1];
+
+ CyLogger.getLogger().info("---------- server: " + server);
+ CyLogger.getLogger().info("---------- file: " + filenames[0]);
+
+ server.loadThesaurusFiles(filenames);
+
+ CyLogger.getLogger().info(server.describe());
+ } // main
+ //------------------------------------------------------------------------------
+} // loadThesaurus
diff --git a/application/src/main/java/cytoscape/data/servers/package.html b/application/src/main/java/cytoscape/data/servers/package.html
new file mode 100755
index 0000000..7f8d724
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/servers/package.html
@@ -0,0 +1,13 @@
+<html>
+<head>
+ <!-- $Revision: 6563 $
+ $Date: 2005-08-17 20:59:44 +0200 (Wed, 17 Aug 2005) $
+ $Author: nlandys $
+ -->
+</head>
+
+<body>
+An interface for annotation data providers and various implementations
+of that interface, including both remote and in-process implementations.
+</body>
+</html>
diff --git a/application/src/main/java/cytoscape/data/servers/status.java b/application/src/main/java/cytoscape/data/servers/status.java
new file mode 100755
index 0000000..086632d
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/servers/status.java
@@ -0,0 +1,86 @@
+/*
+ File: status.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// status
+
+//------------------------------------------------------------------------------
+// $Revision: 14060 $
+// $Date: 2008-05-20 22:13:18 +0200 (Tue, 20 May 2008) $
+// $Author: skillcoyne $
+//-----------------------------------------------------------------------------------
+package cytoscape.data.servers;
+
+import cytoscape.logger.CyLogger;
+
+import java.io.*;
+
+//-----------------------------------------------------------------------------------
+import java.rmi.*;
+
+import java.util.Vector;
+
+
+//------------------------------------------------------------------------------
+/**
+ *
+ */
+public class status {
+ //------------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public static void main(String[] args) throws Exception {
+ if (args.length != 2) {
+ CyLogger.getLogger().warn("usage: status <rmi host name> <rmi service name>");
+ System.exit(1);
+ }
+
+ String hostname = args[0];
+ String serviceName = args[1];
+
+ String serverName = "rmi://" + hostname + "/" + serviceName;
+ CyLogger.getLogger().info("--- checking status of " + serverName);
+
+ BioDataServer server = new BioDataServer(serverName);
+ CyLogger.getLogger().info(server.describe());
+ } // main
+ //------------------------------------------------------------------------------
+} // status
diff --git a/application/src/main/java/cytoscape/data/synonyms/AliasType.java b/application/src/main/java/cytoscape/data/synonyms/AliasType.java
new file mode 100644
index 0000000..ffc8464
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/synonyms/AliasType.java
@@ -0,0 +1,50 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data.synonyms;
+
+
+/**
+ * Type of Aliases.
+ *
+ * Aliases are always belongs to one of these types.
+ *
+ * @author kono
+ *
+ */
+public enum AliasType {
+ NODE,
+ EDGE,
+ NETWORK;
+}
diff --git a/application/src/main/java/cytoscape/data/synonyms/Aliases.java b/application/src/main/java/cytoscape/data/synonyms/Aliases.java
new file mode 100644
index 0000000..cb7ef66
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/synonyms/Aliases.java
@@ -0,0 +1,277 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data.synonyms;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.data.CyAttributes;
+
+import giny.model.Edge;
+import giny.model.Node;
+
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Set;
+import java.util.TreeSet;
+
+
+/**
+ *
+ * Simpler version of Thesaurus.<br>
+ *
+ * <p>
+ * Purpose of this class is providing simple aliasing without biological
+ * context. No species, commonname, nor canonical name are available. Just
+ * maintains keys (IDs) and their aliases in CyAttributes.<br>
+ * This will be used for importing attribute data.
+ * </p>
+ *
+ * <p>
+ * This class has no redundant data structure: everything will be stored in
+ * CyAttributes, and uses immutable special attributes called Alias
+ * </p>
+ *
+ * @since Cytoscape 2.4
+ * @version 0.6
+ *
+ * @author kono
+ *
+ */
+public class Aliases {
+ /**
+ * Name of the attribute for aliases
+ */
+ public static final String ALIAS = "cytoscape.alias.list";
+ private final AliasType objectType;
+ CyAttributes attributes;
+
+ /**
+ * Constructor for the aliases object.<br>
+ *
+ * @param type
+ * Type of alias: node, edge, or network.
+ */
+ public Aliases(AliasType type) {
+ this.objectType = type;
+
+ switch (objectType) {
+ case NODE:
+ attributes = Cytoscape.getNodeAttributes();
+
+ break;
+
+ case EDGE:
+ attributes = Cytoscape.getEdgeAttributes();
+
+ break;
+
+ case NETWORK:
+ attributes = Cytoscape.getNetworkAttributes();
+
+ break;
+
+ default:
+ // This should not happen
+ attributes = null;
+ }
+ }
+
+ /**
+ * Add new alias for an object.
+ *
+ * @param key
+ * ID of the object.
+ * @param alias
+ * New alias to be added.
+ */
+ public void add(String key, String alias) {
+ List<String> aliasList = attributes.getListAttribute(key, ALIAS);
+
+ /*
+ * If there is no alias attributes, create new one.
+ */
+ if (aliasList != null) {
+ aliasList.add(alias);
+
+ Set<String> aliasSet = new TreeSet<String>(aliasList);
+ attributes.setListAttribute(key, ALIAS, new ArrayList<String>(aliasSet));
+ } else {
+ aliasList = new ArrayList<String>();
+ aliasList.add(alias);
+ attributes.setListAttribute(key, ALIAS, aliasList);
+ }
+ }
+
+ /**
+ * Add list of aliases to the existing alias lists.<br>
+ *
+ * @param key
+ * @param aliaseList
+ */
+ public void add(String key, List<String> aliasList) {
+ List<String> curAliasList = attributes.getListAttribute(key, ALIAS);
+
+ /*
+ * If there is no alias attributes, add the given list as the new one.
+ */
+ if (curAliasList != null) {
+ curAliasList.addAll(aliasList);
+ }
+
+ /*
+ * Remove duplicates
+ */
+ Set<String> aliasSet = new TreeSet<String>(aliasList);
+ attributes.setListAttribute(key, ALIAS, new ArrayList<String>(aliasSet));
+ }
+
+ /**
+ * Remove an alias.<br>
+ *
+ * @param key
+ * ID of the object.
+ * @param alias
+ * Alias to be removed.
+ */
+ public void remove(String key, String alias) {
+ List<String> curAliasList = attributes.getListAttribute(key, ALIAS);
+
+ /*
+ * Need to remove the alias only when alias attributes exist.
+ */
+ if (curAliasList != null) {
+ curAliasList.remove(alias);
+ attributes.setListAttribute(key, ALIAS, curAliasList);
+ }
+ }
+
+ /**
+ *
+ * @param key
+ * @return
+ */
+ public List<String> getAliases(String key) {
+ return attributes.getListAttribute(key, ALIAS);
+ }
+
+ /**
+ *
+ * Returns true if the object with the alias wxists in the memory
+ * (rootGraph).
+ *
+ * This is an O(n) operation, which is expensive!
+ *
+ * @param key
+ * @param alias
+ * @return Key for this alias. If it does not exist, return null.
+ */
+ public String getKey(String alias) {
+ final Iterator it;
+ String id = null;
+
+ switch (objectType) {
+ case NODE:
+ it = Cytoscape.getRootGraph().nodesIterator();
+
+ while (it.hasNext()) {
+ id = ((Node) it.next()).getIdentifier();
+
+ final List aliases = attributes.getListAttribute(id, ALIAS);
+
+ if ((aliases != null) && aliases.contains(alias)) {
+ return id;
+ }
+ }
+
+ break;
+
+ case EDGE:
+ it = Cytoscape.getRootGraph().edgesIterator();
+
+ while (it.hasNext()) {
+ id = ((Edge) it.next()).getIdentifier();
+
+ final List aliases = attributes.getListAttribute(id, ALIAS);
+
+ if ((aliases != null) && aliases.contains(alias)) {
+ return id;
+ }
+ }
+
+ break;
+
+ case NETWORK:
+ it = Cytoscape.getNetworkSet().iterator();
+
+ while (it.hasNext()) {
+ id = ((Node) it.next()).getIdentifier();
+
+ final List aliases = attributes.getListAttribute(id, ALIAS);
+
+ if ((aliases != null) && aliases.contains(alias)) {
+ return id;
+ }
+ }
+
+ break;
+
+ default:
+
+ // This should not happen
+ }
+
+ return null;
+ }
+
+ /**
+ * Return set of all names for the key (including key itself.)
+ *
+ * @param key
+ * @return
+ */
+ public Set<String> getIdSet(String key) {
+ List<String> curAliases = attributes.getListAttribute(key, ALIAS);
+ Set<String> allNames = new TreeSet<String>();
+
+ if (curAliases != null) {
+ allNames.addAll(curAliases);
+ }
+
+ allNames.add(key);
+
+ return allNames;
+ }
+}
diff --git a/application/src/main/java/cytoscape/data/synonyms/Thesaurus.java b/application/src/main/java/cytoscape/data/synonyms/Thesaurus.java
new file mode 100755
index 0000000..dda361b
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/synonyms/Thesaurus.java
@@ -0,0 +1,306 @@
+/*
+ File: Thesaurus.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+// Thesaurus.java
+//-----------------------------------------------------------------------------
+// $Revision: 14060 $
+// $Date: 2008-05-20 22:13:18 +0200 (Tue, 20 May 2008) $
+// $Author: skillcoyne $
+//------------------------------------------------------------------------------
+package cytoscape.data.synonyms;
+
+
+//-----------------------------------------------------------------------------
+import cytoscape.logger.CyLogger;
+
+import java.io.Serializable;
+
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.Vector;
+
+
+//-----------------------------------------------------------------------------
+/**
+ * todo (pshannon, 25 oct 2002): there may be multiple canonicalNames for the
+ * same common name. a good example is from the d16s3098 marker region studied
+ * in the ISB's JDRF project:
+ *
+ * PHEMX -> NM_005705 PHEMX -> NM_139022 PHEMX -> NM_139023 PHEMX -> NM_139024
+ *
+ * these are (I believe) mRNA splice variants. what to do?
+ */
+public class Thesaurus implements Serializable {
+ String species;
+ HashMap labelToCommon; // String -> String
+ HashMap commonToLabel; // String -> String
+ HashMap aliasesToLabel; // String -> String
+ HashMap labelToAll; // String -> Vector of Strings
+
+ // -----------------------------------------------------------------------------
+ /**
+ * Creates a new Thesaurus object.
+ *
+ * @param species DOCUMENT ME!
+ */
+ public Thesaurus(String species) {
+ this.species = species;
+ labelToCommon = new HashMap();
+ commonToLabel = new HashMap();
+ aliasesToLabel = new HashMap();
+ labelToAll = new HashMap();
+ }
+
+ // -----------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getSpecies() {
+ return species;
+ }
+
+ // -----------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int nodeLabelCount() {
+ return labelToAll.size();
+ }
+
+ // -----------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @param canonicalName DOCUMENT ME!
+ * @param commonName DOCUMENT ME!
+ */
+ public void add(String canonicalName, String commonName) {
+ if (labelToCommon.containsKey(canonicalName)) {
+ addAlternateCommonName(canonicalName, commonName);
+ }
+
+ if (commonToLabel.containsKey(commonName)) {
+ // CyLogger.getLogger().info ("commonName " + commonName + " already has
+ // canonicalName " +
+ // commonToCanonical.get (commonName) + " skipping new map: " +
+ // commonName + " -> " + canonicalName);
+ } else
+ labelToCommon.put(canonicalName, commonName);
+
+ commonToLabel.put(commonName, canonicalName);
+ storeAmongAllCommonNames(commonName, canonicalName);
+ } // add
+
+ // -----------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @param canonicalName DOCUMENT ME!
+ * @param commonName DOCUMENT ME!
+ */
+ public void remove(String canonicalName, String commonName) {
+ labelToCommon.remove(canonicalName);
+ commonToLabel.remove(commonName);
+ labelToAll.remove(canonicalName);
+ }
+
+ // -----------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @param canonicalName DOCUMENT ME!
+ * @param alternateCommonName DOCUMENT ME!
+ */
+ public void addAlternateCommonName(String canonicalName, String alternateCommonName) {
+ aliasesToLabel.put(alternateCommonName, canonicalName);
+ storeAmongAllCommonNames(alternateCommonName, canonicalName);
+ }
+
+ // -----------------------------------------------------------------------------
+ protected void storeAmongAllCommonNames(String commonName, String canonicalName) {
+ Vector allCommonNames;
+
+ if (labelToAll.containsKey(canonicalName))
+ allCommonNames = (Vector) labelToAll.get(canonicalName);
+ else
+ allCommonNames = new Vector();
+
+ allCommonNames.add(commonName);
+ labelToAll.put(canonicalName, allCommonNames);
+ } // storeAmongAllCommonNames
+
+ // -----------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @param canonicalName DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getCommonName(String canonicalName) {
+ return (String) labelToCommon.get(canonicalName);
+ }
+
+ // -----------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @param commonName DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getNodeLabel(String commonName) {
+ if (commonToLabel.containsKey(commonName))
+ return (String) commonToLabel.get(commonName);
+ else if (aliasesToLabel.containsKey(commonName))
+ return (String) aliasesToLabel.get(commonName);
+ else
+
+ return null;
+ } // getCanonicalName
+
+ // -----------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @param canonicalName DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String[] getAllCommonNames(String canonicalName) {
+ if (labelToAll.containsKey(canonicalName)) {
+ Vector vector = (Vector) labelToAll.get(canonicalName);
+
+ return (String[]) vector.toArray(new String[0]);
+ } else
+
+ return new String[0];
+ } // getAllCommonNames
+
+ // -----------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @param canonicalName DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String[] getAlternateCommonNames(String canonicalName) {
+ if (labelToAll.containsKey(canonicalName)) {
+ Vector vector = (Vector) labelToAll.get(canonicalName);
+ vector.remove(getCommonName(canonicalName));
+
+ return (String[]) vector.toArray(new String[0]);
+ } else
+
+ return new String[0];
+ } // getAlternateCommonNames
+
+ /*
+ * This method returns all names including aliases and key.
+ */
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param key DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String[] getAllNamesInGroup(String key) {
+ if (labelToAll.containsKey(key)) {
+ Vector vector = (Vector) labelToAll.get(key);
+ vector.add(key);
+
+ return (String[]) vector.toArray(new String[0]);
+ } else if (aliasesToLabel.containsKey(key)) {
+ String label = (String) aliasesToLabel.get(key);
+ Vector vector = (Vector) labelToAll.get(label);
+
+ return (String[]) vector.toArray(new String[0]);
+ } else
+
+ return new String[0];
+ }
+
+ // -----------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String toString() {
+ int length = 0;
+
+ if (labelToCommon != null)
+ length = labelToCommon.size();
+
+ return species + ": " + length;
+ }
+
+ /*
+ * This is for debugging.
+ *
+ */
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void dump() {
+ Iterator it = labelToCommon.keySet().iterator();
+
+ while (it.hasNext()) {
+ String label = (String) it.next();
+
+ CyLogger.getLogger().info("Key is " + label + ", and commons are ");
+
+ String[] alias = this.getAllCommonNames(label);
+
+ for (int i = 0; i < alias.length; i++) {
+ CyLogger.getLogger().info(alias[i] + ", ");
+ }
+
+ CyLogger.getLogger().info("");
+ }
+ }
+
+ // -----------------------------------------------------------------------------
+} // Thesaurus
diff --git a/application/src/main/java/cytoscape/data/synonyms/package.html b/application/src/main/java/cytoscape/data/synonyms/package.html
new file mode 100755
index 0000000..6c7848b
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/synonyms/package.html
@@ -0,0 +1,13 @@
+<html>
+<head>
+ <!-- $Revision: 6563 $
+ $Date: 2005-08-17 20:59:44 +0200 (Wed, 17 Aug 2005) $
+ $Author: nlandys $
+ -->
+</head>
+
+<body>
+Classes providing synonym funcationality, that is identifying multiple
+names that refer to the same entity.
+</body>
+</html>
diff --git a/application/src/main/java/cytoscape/data/synonyms/readers/ThesaurusFlatFileReader.java b/application/src/main/java/cytoscape/data/synonyms/readers/ThesaurusFlatFileReader.java
new file mode 100755
index 0000000..c984216
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/synonyms/readers/ThesaurusFlatFileReader.java
@@ -0,0 +1,222 @@
+/*
+ File: ThesaurusFlatFileReader.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+// ThesaurusFlatFileReader.java
+
+// ------------------------------------------------------------------------------
+// $Revision: 17791 $
+// $Date: 2009-08-12 18:52:17 +0200 (Wed, 12 Aug 2009) $
+// $Author: noelr $
+// ------------------------------------------------------------------------------
+package cytoscape.data.synonyms.readers;
+
+import cytoscape.data.readers.TextFileReader;
+import cytoscape.data.readers.TextHttpReader;
+import cytoscape.data.readers.TextJarReader;
+
+import cytoscape.data.synonyms.Thesaurus;
+import cytoscape.logger.CyLogger;
+
+// ------------------------------------------------------------------------------
+import java.io.BufferedReader;
+
+import java.util.Vector;
+
+
+/**
+ * Read synonyms from flat file.
+ *
+ * @author kono
+ *
+ */
+public class ThesaurusFlatFileReader {
+ Thesaurus thesaurus;
+ String fullText;
+ String[] lines;
+ boolean flip;
+
+ // -------------------------------------------------------------------------
+ /**
+ * Creates a new ThesaurusFlatFileReader object.
+ *
+ * @param filename DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public ThesaurusFlatFileReader(String filename) throws Exception {
+ flip = false;
+
+ try {
+ if (filename.trim().startsWith("jar://")) {
+ TextJarReader reader = new TextJarReader(filename);
+ reader.read();
+ fullText = reader.getText();
+ } else if (filename.trim().startsWith("http://")) {
+ TextHttpReader reader = new TextHttpReader(filename);
+ reader.read();
+ fullText = reader.getText();
+ } else {
+ TextFileReader reader = new TextFileReader(filename);
+ reader.read();
+ fullText = reader.getText();
+ }
+ } catch (Exception e0) {
+ CyLogger.getLogger().warn("-- Exception while reading ontology flat file " + filename, e0);
+
+ return;
+ }
+
+ read();
+ }
+
+ /**
+ * Creates a new ThesaurusFlatFileReader object.
+ *
+ * @param rd DOCUMENT ME!
+ * @param isFlip DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public ThesaurusFlatFileReader(final BufferedReader rd, boolean isFlip)
+ throws Exception {
+ Vector extractedLines = null;
+
+ // Flip or not
+ flip = isFlip;
+
+ fullText = null;
+ extractedLines = new Vector();
+
+ String curLine = null;
+
+ try {
+ while (null != (curLine = rd.readLine())) {
+ extractedLines.add(curLine);
+
+ // CyLogger.getLogger().info( curLine );
+ }
+ }
+ finally {
+ if (rd != null) {
+ rd.close();
+ }
+ }
+
+ Object[] entireFile = extractedLines.toArray();
+ lines = new String[entireFile.length];
+
+ try {
+ System.arraycopy(entireFile, 0, lines, 0, lines.length);
+ } catch (Exception e) {
+ throw e;
+ }
+
+ read();
+ }
+
+ // -------------------------------------------------------------------------
+ private void read() throws Exception {
+ if (fullText != null) {
+ lines = fullText.split("\n");
+ }
+
+ String species = lines[0].trim();
+ thesaurus = new Thesaurus(species);
+
+ for (int i = 1; i < lines.length; i++) {
+ String line = lines[i].trim();
+
+ // If comment line or too short, just skip
+ if (line.startsWith("#"))
+ continue;
+
+ if (line.length() < 3)
+ continue;
+
+ String[] tokens = lines[i].split("\\s+", 0);
+
+ if (tokens.length < 2)
+ continue;
+
+ // Node label.
+ String canonicalName = tokens[0].trim();
+
+ // This is the first element in the Aliases
+ String commonName = tokens[1].trim();
+
+ if (canonicalName.length() == 0)
+ continue;
+
+ if (commonName.length() == 0)
+ continue;
+
+ // Flipping canonical and aliases.
+ if (flip == false) {
+ thesaurus.add(canonicalName, commonName);
+
+ // CyLogger.getLogger().info("Cannonical = " + canonicalName
+ // + " Common 1 = " + commonName);
+ for (int t = 2; t < tokens.length; t++) {
+ thesaurus.addAlternateCommonName(canonicalName, tokens[t].trim());
+
+ // CyLogger.getLogger().info(" Cannonical = " + canonicalName + "
+ // Common " + t + " = " + tokens [t].trim() );
+ } // for i
+ } else if (flip == true) {
+ // If flip is true, swap the fields.
+ thesaurus.add(commonName, canonicalName);
+
+ // Then, add Aliases
+ for (int t = 2; t < tokens.length; t++) {
+ thesaurus.addAlternateCommonName(commonName, tokens[t].trim());
+ }
+ }
+ }
+ } // read
+
+ // -------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Thesaurus getThesaurus() {
+ return thesaurus;
+ }
+
+ // -------------------------------------------------------------------------
+} // class ThesaurusFlatFileReader
diff --git a/application/src/main/java/cytoscape/data/synonyms/readers/package.html b/application/src/main/java/cytoscape/data/synonyms/readers/package.html
new file mode 100755
index 0000000..f82f4bd
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/synonyms/readers/package.html
@@ -0,0 +1,12 @@
+<html>
+<head>
+ <!-- $Revision: 6563 $
+ $Date: 2005-08-17 20:59:44 +0200 (Wed, 17 Aug 2005) $
+ $Author: nlandys $
+ -->
+</head>
+
+<body>
+Readers for classes in the cytoscape.data.synonyms package.
+</body>
+</html>
diff --git a/application/src/main/java/cytoscape/data/webservice/AttributeImportQuery.java b/application/src/main/java/cytoscape/data/webservice/AttributeImportQuery.java
new file mode 100644
index 0000000..7c486ca
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/webservice/AttributeImportQuery.java
@@ -0,0 +1,28 @@
+package cytoscape.data.webservice;
+
+public class AttributeImportQuery {
+
+ private final Object parameter;
+ private final String keyCyAttributeName;
+ private final String keyNameInWebService;
+
+ public AttributeImportQuery(Object parameter, String keyAttrName, String keyNameInWebService) {
+ this.parameter = parameter;
+ this.keyCyAttributeName = keyAttrName;
+ this.keyNameInWebService = keyNameInWebService;
+
+ }
+
+ public Object getParameter() {
+ return parameter;
+ }
+
+ public String getKeyCyAttrName() {
+ return this.keyCyAttributeName;
+ }
+
+ public String getKeyNameInWebService() {
+ return this.keyNameInWebService;
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/data/webservice/CyWebServiceEvent.java b/application/src/main/java/cytoscape/data/webservice/CyWebServiceEvent.java
new file mode 100644
index 0000000..befad4b
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/webservice/CyWebServiceEvent.java
@@ -0,0 +1,91 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data.webservice;
+
+import java.util.EventObject;
+
+
+/**
+ * Event object used by Web Service Clients and the core.
+ */
+public class CyWebServiceEvent<P> extends EventObject {
+
+ public enum WSEventType {
+ SEARCH_DATABASE,
+ IMPORT_NETWORK,
+ EXPAND_NETWORK,
+ IMPORT_ATTRIBUTE,
+ EXECUTE_ANALYSIS,
+ CANCEL;
+ }
+
+ /**
+ * Will be used to catch the signal from WS.
+ * Core will listen to this event to determine next move.
+ *
+ * @author kono
+ *
+ */
+ public enum WSResponseType {
+ SEARCH_FINISHED, DATA_IMPORT_FINISHED;
+ }
+
+ private final WSEventType type;
+ private final P parameter;
+ private final WSEventType nextMove;
+
+ public CyWebServiceEvent(String compatibleClient, WSEventType type, P parameter) {
+ this(compatibleClient, type, parameter, null);
+ }
+
+ public CyWebServiceEvent(String compatibleClient, WSEventType type, P parameter, WSEventType nextMove) {
+ super(compatibleClient);
+ this.type = type;
+ this.parameter = parameter;
+ this.nextMove = nextMove;
+ }
+
+ public WSEventType getEventType() {
+ return type;
+ }
+
+ public P getParameter() {
+ return parameter;
+ }
+
+ public WSEventType getNextMove() {
+ return nextMove;
+ }
+}
diff --git a/application/src/main/java/cytoscape/data/webservice/CyWebServiceEventListener.java b/application/src/main/java/cytoscape/data/webservice/CyWebServiceEventListener.java
new file mode 100644
index 0000000..9bc2584
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/webservice/CyWebServiceEventListener.java
@@ -0,0 +1,54 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.data.webservice;
+
+import java.util.EventListener;
+
+
+/**
+ * Listener for Web Service Event handling.
+ * Functions
+ */
+public interface CyWebServiceEventListener extends EventListener {
+
+ /**
+ * Execute the service specified in the event object.
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void executeService(CyWebServiceEvent e) throws CyWebServiceException;
+}
diff --git a/application/src/main/java/cytoscape/data/webservice/CyWebServiceEventSupport.java b/application/src/main/java/cytoscape/data/webservice/CyWebServiceEventSupport.java
new file mode 100644
index 0000000..a9e7841
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/webservice/CyWebServiceEventSupport.java
@@ -0,0 +1,84 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data.webservice;
+
+import java.util.Vector;
+
+
+/**
+ *
+ */
+public class CyWebServiceEventSupport {
+ private Vector<CyWebServiceEventListener> listenerVec;
+
+ /**
+ * Creates a new CyWebServiceEventSupport object.
+ */
+ public CyWebServiceEventSupport() {
+ listenerVec = new Vector<CyWebServiceEventListener>();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param listener DOCUMENT ME!
+ */
+ public void addCyWebServiceEventListener(CyWebServiceEventListener listener) {
+ listenerVec.addElement(listener);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param listener DOCUMENT ME!
+ */
+ public void removeCyWebServiceEventListener(CyWebServiceEventListener listener) {
+ listenerVec.removeElement(listener);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt DOCUMENT ME!
+ * @throws Exception
+ */
+ public void fireCyWebServiceEvent(CyWebServiceEvent evt) throws CyWebServiceException {
+ Vector<CyWebServiceEventListener> elements = (Vector<CyWebServiceEventListener>) listenerVec
+ .clone();
+
+ for (CyWebServiceEventListener lis : elements)
+ lis.executeService(evt);
+ }
+}
diff --git a/application/src/main/java/cytoscape/data/webservice/CyWebServiceException.java b/application/src/main/java/cytoscape/data/webservice/CyWebServiceException.java
new file mode 100644
index 0000000..8e9dd8c
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/webservice/CyWebServiceException.java
@@ -0,0 +1,69 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.data.webservice;
+
+/**
+ *
+ */
+public class CyWebServiceException extends Exception {
+ public enum WSErrorCode {
+ NO_RESULT("Service returned no result."),
+ REMOTE_EXEC_FAILED("Remote service failed."),
+ OPERATION_NOT_SUPPORTED("Operation is not supported by the service.");
+
+ private final String errorMessage;
+
+ private WSErrorCode(final String message) {
+ this.errorMessage = message;
+ }
+
+ public String getErrorMessage() {
+ return errorMessage;
+ }
+ }
+
+ private final WSErrorCode ec;
+
+ public CyWebServiceException(WSErrorCode ec) {
+ this.ec = ec;
+ }
+
+ public WSErrorCode getErrorCode() {
+ return ec;
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/data/webservice/DatabaseSearchResult.java b/application/src/main/java/cytoscape/data/webservice/DatabaseSearchResult.java
new file mode 100644
index 0000000..0acd669
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/webservice/DatabaseSearchResult.java
@@ -0,0 +1,27 @@
+package cytoscape.data.webservice;
+
+import cytoscape.data.webservice.CyWebServiceEvent.WSEventType;
+
+public class DatabaseSearchResult<R> {
+ private final Integer resultSize;
+ private final R searchResult;
+ private final WSEventType nextMove;
+
+ public DatabaseSearchResult(Integer resultSize, R searchResult, WSEventType nextMove) {
+ this.resultSize = resultSize;
+ this.searchResult = searchResult;
+ this.nextMove = nextMove;
+ }
+
+ public R getResult() {
+ return searchResult;
+ }
+
+ public Integer getResultSize() {
+ return resultSize;
+ }
+
+ public WSEventType getNextMove() {
+ return nextMove;
+ }
+}
diff --git a/application/src/main/java/cytoscape/data/webservice/NetworkImportWebServiceClient.java b/application/src/main/java/cytoscape/data/webservice/NetworkImportWebServiceClient.java
new file mode 100644
index 0000000..d51432a
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/webservice/NetworkImportWebServiceClient.java
@@ -0,0 +1,51 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data.webservice;
+
+import cytoscape.visual.VisualStyle;
+
+
+/**
+ *
+ */
+public interface NetworkImportWebServiceClient {
+ /**
+ * Return default vixual style for this network import client.
+ *
+ * @return default visual style.
+ */
+ public VisualStyle getDefaultVisualStyle();
+
+}
diff --git a/application/src/main/java/cytoscape/data/webservice/WebServiceClient.java b/application/src/main/java/cytoscape/data/webservice/WebServiceClient.java
new file mode 100644
index 0000000..76b634e
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/webservice/WebServiceClient.java
@@ -0,0 +1,155 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data.webservice;
+
+import cytoscape.data.webservice.WebServiceClientManager.ClientType;
+
+import cytoscape.util.ModuleProperties;
+
+import java.lang.reflect.Method;
+
+import java.util.Collection;
+
+
+/**
+ * Web service client wrapper for Cytoscape.
+ * <p>
+ * Usually, developers first use code generator to create Java code
+ * from WSDL. The generated code should be wrapped by this interface
+ * to be used in Cytoscape framework.
+ * </p>
+ * All web service clients <strong>must</strong> implement this method.
+ *
+ * @param <S> Client stub object. This is service dependent. For example, NCBI's eUtils
+ * stub has the class EUtilsServiceSoap.
+ *
+ * @author kono
+ * @version 0.5
+ * @since Cytoscape 2.6
+ */
+public interface WebServiceClient<S> {
+ /**
+ * Returns client ID.
+ * This ID should be unique.
+ *
+ * @return client ID as String.
+ */
+ public String getClientID();
+
+ /**
+ * Returns display name of this client.
+ * This is more human readable name for this client.
+ *
+ * @return display name for this client.
+ */
+ public String getDisplayName();
+
+ /**
+ * Returns client type.
+ * A client can have multiple types.
+ *
+ * For example, NCBI Client can be used as network import
+ * and attribute import, so this array contains both types.
+ *
+ * @see cytoscape.data.webservice.WebServiceClientManager.ClientType
+ *
+ * @return Array of client types.
+ */
+ public ClientType[] getClientType();
+
+ /**
+ * Return true if the given ClientType is compatible with this client.
+ *
+ * If a client is used as network importer, isCompatibleType(ClientType.NETWORK)
+ * returns true, but isCompatibleType(ClientType.ATTRIBUTE) returns false.
+ *
+ * @param ct Client type.
+ *
+ * @return true if compatible.
+ */
+ public boolean isCompatibleType(ClientType ct);
+
+ /**
+ * Get client stub object.
+ * All services available from this client will be
+ * accessed through this stub. This will be used when developer wants
+ * to access "raw" API of this service.
+ *
+ * @return Client stub. This object type depends on service.
+ */
+ public S getClientStub();
+
+ /**
+ * Set stub to this client.
+ *
+ * @param stub client stub used in this client.
+ */
+ public void setClientStub(S clientStub);
+
+ /**
+ * Get properties used by the Tunable.
+ *
+ * @return
+ */
+ public ModuleProperties getProps();
+
+ /**
+ * Set props used by Tunable.
+ *
+ * @param props Property.
+ */
+ public void setProps(ModuleProperties props);
+
+ /**
+ * Returns all available methods accessible through client stub.
+ *
+ * @return Collection of methods available through stub.
+ */
+ public Collection<Method> getAccessibleMethods();
+
+ /**
+ * Get description for this client.
+ *
+ * @return Description as a string. Users should write parser for this return value.
+ */
+ public String getDescription();
+
+ /**
+ * Set description for this service.
+ *
+ * @param description Description as a String.
+ */
+ public void setDescription(String description);
+}
diff --git a/application/src/main/java/cytoscape/data/webservice/WebServiceClientImpl.java b/application/src/main/java/cytoscape/data/webservice/WebServiceClientImpl.java
new file mode 100644
index 0000000..0424c87
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/webservice/WebServiceClientImpl.java
@@ -0,0 +1,270 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data.webservice;
+
+import cytoscape.data.webservice.WebServiceClientManager.ClientType;
+
+import cytoscape.util.ModuleProperties;
+
+import java.io.Serializable;
+
+import java.lang.reflect.Method;
+
+import java.util.ArrayList;
+import java.util.Collection;
+
+
+/**
+ * Abstract class for all web service clients.
+ * All clients MUST extend this class.
+ *
+ * @author Keiichiro Ono
+ * @since Cytoscape 2.6
+ * @version 0.5
+ *
+ * @param <S> Stub object type. This is service dependent.
+ */
+public abstract class WebServiceClientImpl<S> implements Serializable, WebServiceClient<S>,
+ CyWebServiceEventListener {
+ // Default ID
+ protected static final String DEF_NAME = "default";
+
+ // Default Display Name
+ protected static final String DEF_DISPLAY_NAME = "Default Web Service Cilent";
+
+ // Stub object.
+ protected S clientStub;
+
+ // Client ID. This should be unique.
+ protected String clientID;
+
+ // Display Name for this client.
+ protected String displayName;
+
+ // Compatible types.
+ protected ClientType[] type;
+
+ // Properties for this client. Will be used by Tunable.
+ protected ModuleProperties props;
+
+ // Methods available through the client stub.
+ protected Collection<Method> availableMethods = null;
+ protected String description = "Description for " + displayName + " is not available.";
+
+ /**
+ * Creates a new WebServiceClientImpl object.
+ */
+ public WebServiceClientImpl() {
+ this(DEF_NAME, DEF_DISPLAY_NAME);
+ }
+
+ /**
+ * Creates a new WebServiceClientImpl object.
+ *
+ * @param serviceName DOCUMENT ME!
+ * @param displayName DOCUMENT ME!
+ */
+ public WebServiceClientImpl(final String serviceName, final String displayName) {
+ this(serviceName, displayName, new ClientType[] { ClientType.ATTRIBUTE });
+ }
+
+ /**
+ * Creates a new WebServiceClientImpl object.
+ *
+ * @param serviceName DOCUMENT ME!
+ * @param displayName DOCUMENT ME!
+ * @param types DOCUMENT ME!
+ */
+ public WebServiceClientImpl(final String serviceName, final String displayName,
+ ClientType[] types) {
+ this(serviceName, displayName, types, null);
+ }
+
+ /**
+ * Creates a new WebServiceClientImpl object.
+ *
+ * @param serviceName DOCUMENT ME!
+ * @param displayName DOCUMENT ME!
+ * @param types DOCUMENT ME!
+ * @param props DOCUMENT ME!
+ */
+ public WebServiceClientImpl(final String serviceName, final String displayName,
+ final ClientType[] types, final ModuleProperties props) {
+ this(serviceName, displayName, types, props, null);
+ }
+
+ /**
+ * Creates a new WebServiceClientImpl object.
+ *
+ * @param serviceName DOCUMENT ME!
+ * @param displayName DOCUMENT ME!
+ * @param types DOCUMENT ME!
+ * @param props DOCUMENT ME!
+ */
+ public WebServiceClientImpl(final String serviceName, final String displayName,
+ final ClientType[] types, final ModuleProperties props,
+ final S clientStub) {
+ this.clientID = serviceName;
+ this.displayName = displayName;
+ this.type = types;
+ this.props = props;
+ this.clientStub = clientStub;
+
+ WebServiceClientManager.getCyWebServiceEventSupport().addCyWebServiceEventListener(this);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Collection<Method> getAccessibleMethods() {
+ if (availableMethods == null) {
+ availableMethods = new ArrayList<Method>();
+
+ final Class stubClass = clientStub.getClass();
+ final Method[] methods = stubClass.getMethods();
+
+ for (Method m : methods) {
+ if (m.toString().startsWith("public")) {
+ availableMethods.add(m);
+ }
+ }
+ }
+
+ return availableMethods;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getDisplayName() {
+ return displayName;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getClientID() {
+ return clientID;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public ClientType[] getClientType() {
+ return type;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param ct DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isCompatibleType(ClientType ct) {
+ for (ClientType t : type) {
+ if (t.equals(ct)) {
+ return true;
+ }
+ }
+
+ return false;
+ }
+
+ /**
+ * Client stub will be returned from this.
+ * All services are accessible thorough this stub.
+ *
+ * @return DOCUMENT ME!
+ */
+ public S getClientStub() {
+ return clientStub;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public ModuleProperties getProps() {
+ return props;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param props DOCUMENT ME!
+ */
+ public void setProps(ModuleProperties props) {
+ this.props = props;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getDescription() {
+ return description;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param description DOCUMENT ME!
+ */
+ public void setDescription(final String description) {
+ this.description = description;
+ }
+
+ public void setClientStub(S stub) {
+ this.clientStub = stub;
+ }
+
+ /**
+ * Execute the service through event handling system.
+ *
+ * @param e DOCUMENT ME!
+ */
+ public abstract void executeService(CyWebServiceEvent e) throws CyWebServiceException;
+}
diff --git a/application/src/main/java/cytoscape/data/webservice/WebServiceClientImplWithGUI.java b/application/src/main/java/cytoscape/data/webservice/WebServiceClientImplWithGUI.java
new file mode 100644
index 0000000..9ec5b53
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/webservice/WebServiceClientImplWithGUI.java
@@ -0,0 +1,125 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data.webservice;
+
+import cytoscape.data.webservice.WebServiceClientManager.ClientType;
+import cytoscape.data.webservice.ui.WebServiceClientGUI;
+
+import cytoscape.util.ModuleProperties;
+
+import giny.view.EdgeView;
+import giny.view.NodeView;
+
+import java.awt.Container;
+
+import java.util.List;
+
+import javax.swing.Icon;
+import javax.swing.JMenuItem;
+
+
+/**
+ * Client with GUI.
+ *
+ * @param <S> Client stub type.
+ * @param <U> User interface type.
+ */
+public abstract class WebServiceClientImplWithGUI<S, U extends Container>
+ extends WebServiceClientImpl<S> implements WebServiceClientGUI<U> {
+ // GUI for this client. This is optional and default is null.
+ protected U gui = null;
+
+ /**
+ * Creates a new WebServiceClientImpl object.
+ *
+ * @param serviceName DOCUMENT ME!
+ * @param displayName DOCUMENT ME!
+ * @param types DOCUMENT ME!
+ * @param props DOCUMENT ME!
+ */
+ public WebServiceClientImplWithGUI(final String serviceName, final String displayName,
+ final ClientType[] types, final ModuleProperties props,
+ final S clientStub, final U gui) {
+ super(serviceName, displayName, types, props, clientStub);
+ this.gui = gui;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public U getGUI() {
+ return gui;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param gui DOCUMENT ME!
+ */
+ public void setGUI(U gui) {
+ this.gui = gui;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param i DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Icon getIcon(WebServiceClientGUI.IconSize i) {
+ return null;
+ }
+
+ /**
+ * Returns client dependent context menu for nodes
+ *
+ * @return DOCUMENT ME!
+ */
+ public List<JMenuItem> getNodeContextMenuItems(NodeView nv) {
+ return null;
+ }
+
+ /**
+ * Returns client dependent context menu for edges
+ *
+ * @return DOCUMENT ME!
+ */
+ public List<JMenuItem> getEdgeContextMenuItems(EdgeView ev) {
+ return null;
+ }
+}
diff --git a/application/src/main/java/cytoscape/data/webservice/WebServiceClientManager.java b/application/src/main/java/cytoscape/data/webservice/WebServiceClientManager.java
new file mode 100644
index 0000000..a3c2f6a
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/webservice/WebServiceClientManager.java
@@ -0,0 +1,148 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data.webservice;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import javax.swing.tree.DefaultMutableTreeNode;
+import javax.swing.tree.DefaultTreeModel;
+import javax.swing.tree.TreeModel;
+
+
+/**
+ * Web Service Client Manager manages available web service
+ * clients in Cytoscape. All clients will be loaded & registered through
+ * Plugin Manager architecture.
+ *
+ * @author Keiichiro Ono
+ * @since Cytoscape 2.5
+ * @version 0.5
+ *
+ */
+public class WebServiceClientManager {
+
+ /**
+ * ClientType defines types/characteristics of
+ * the web service clients.
+ */
+ public enum ClientType {
+ ANALYSIS,
+ ATTRIBUTE,
+ NETWORK;
+ }
+
+ // List of loaded clients in Cytoscape.
+ // Key is
+ private static Map<String, WebServiceClient<?>> clients;
+ private static Map<String, WebServiceClient<?>> clientNameMap;
+
+ // Handles events between core and web service clients.
+ private static CyWebServiceEventSupport cwseSupport;
+
+ static {
+ new WebServiceClientManager();
+ }
+
+ private WebServiceClientManager() {
+ clients = new HashMap<String, WebServiceClient<?>>();
+ clientNameMap = new HashMap<String, WebServiceClient<?>>();
+
+ cwseSupport = new CyWebServiceEventSupport();
+ }
+
+ /**
+ * Register client to the manager.
+ *
+ * @param client DOCUMENT ME!
+ */
+ public static synchronized void registerClient(final WebServiceClient<?> client) {
+ if (client == null)
+ return;
+ clients.put(client.getDisplayName(), client);
+ clientNameMap.put(client.getClientID(), client);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static List<WebServiceClient<?>> getAllClients() {
+ final List<WebServiceClient<?>> clientList = new ArrayList<WebServiceClient<?>>();
+
+ for (String key : clients.keySet()) {
+ clientList.add(clients.get(key));
+ }
+
+ return clientList;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param clientID DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static WebServiceClient getClient(String clientID) {
+ return clientNameMap.get(clientID);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param serviceName DOCUMENT ME!
+ */
+ public static void removeClient(String serviceName) {
+ if (serviceName == null) {
+ return;
+ }
+
+ WebServiceClient cl = clientNameMap.get(serviceName);
+
+ if (cl != null) {
+ clientNameMap.remove(serviceName);
+ clients.remove(cl.getDisplayName());
+ cl = null;
+ }
+ }
+
+ public static CyWebServiceEventSupport getCyWebServiceEventSupport() {
+ return cwseSupport;
+ }
+}
diff --git a/application/src/main/java/cytoscape/data/webservice/ui/UnifiedNetworkImportDialog.java b/application/src/main/java/cytoscape/data/webservice/ui/UnifiedNetworkImportDialog.java
new file mode 100644
index 0000000..d72a55b
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/webservice/ui/UnifiedNetworkImportDialog.java
@@ -0,0 +1,776 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.data.webservice.ui;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Container;
+import java.awt.FlowLayout;
+import java.awt.Frame;
+import java.awt.GridLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import javax.swing.Box;
+import javax.swing.BoxLayout;
+import javax.swing.Icon;
+import javax.swing.ImageIcon;
+import javax.swing.JButton;
+import javax.swing.JDialog;
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTextArea;
+import javax.swing.border.EmptyBorder;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import cytoscape.data.webservice.CyWebServiceEvent;
+import cytoscape.data.webservice.CyWebServiceException;
+import cytoscape.data.webservice.DatabaseSearchResult;
+import cytoscape.data.webservice.NetworkImportWebServiceClient;
+import cytoscape.data.webservice.WebServiceClient;
+import cytoscape.data.webservice.WebServiceClientManager;
+import cytoscape.data.webservice.CyWebServiceEvent.WSEventType;
+import cytoscape.data.webservice.CyWebServiceEvent.WSResponseType;
+import cytoscape.data.webservice.ui.WebServiceClientGUI.IconSize;
+import cytoscape.layout.Tunable;
+import cytoscape.logger.CyLogger;
+import cytoscape.task.Task;
+import cytoscape.task.TaskMonitor;
+import cytoscape.task.ui.JTaskConfig;
+import cytoscape.task.util.TaskManager;
+import cytoscape.util.ModuleProperties;
+import cytoscape.util.swing.AboutDialog;
+import cytoscape.visual.VisualStyle;
+
+/**
+ * Default GUI component for network import web service clients.
+ *
+ * @author kono
+ */
+public class UnifiedNetworkImportDialog extends JDialog implements
+ PropertyChangeListener {
+
+ private static final long serialVersionUID = 3333726113970459078L;
+
+ // This is a singleton.
+ private static final UnifiedNetworkImportDialog dialog;
+
+ // Selected web service client ID
+ private String selectedClientID = null;
+
+ // Task to run in the separate thread.
+ private WSNetworkImportTask task;
+
+ // Key is display name, value is actual service name.
+ private Map<String, String> clientNames;
+
+ // Client-Dependent GUI panels
+ private Map<String, Container> serviceUIPanels = new HashMap<String, Container>();
+
+ // Default icon for about dialog
+ private static final Icon DEF_ICON = new javax.swing.ImageIcon(
+ Cytoscape.class.getResource("images/ximian/stock_internet-32.png"));
+
+ private static CyLogger logger = CyLogger
+ .getLogger(UnifiedNetworkImportDialog.class);
+
+ private int numDataSources = 0;
+ private int numClients = 0;
+
+ private boolean cancelFlag = false;
+
+ static {
+ dialog = new UnifiedNetworkImportDialog(Cytoscape.getDesktop(), false);
+ }
+
+ /**
+ * Display this standard GUI.
+ */
+ public static void showDialog() {
+ dialog.setLocationRelativeTo(Cytoscape.getDesktop());
+ dialog.setVisible(true);
+ }
+
+ /**
+ * Creates new form NetworkImportDialog
+ */
+ public UnifiedNetworkImportDialog(Frame parent, boolean modal) {
+ super(parent, modal);
+
+ // Register as listener.
+ Cytoscape.getPropertyChangeSupport().addPropertyChangeListener(this);
+
+ initGUI();
+ }
+
+ /**
+ * Resets the GUI w/ all new info.
+ */
+ public void resetGUI() {
+ this.getContentPane().removeAll();
+ initGUI();
+ }
+
+ private void initGUI() {
+ clientNames = new HashMap<String, String>();
+
+ List<WebServiceClient<?>> clients = WebServiceClientManager
+ .getAllClients();
+ for (WebServiceClient<?> client : clients) {
+ if (client instanceof NetworkImportWebServiceClient) {
+ numClients++;
+ }
+ }
+
+ initComponents();
+ setDatasource();
+
+ // If we have no data sources, show the install panel
+ getContentPane().setLayout(new BorderLayout());
+ if (numClients <= 1) {
+ this.getContentPane().add(installPanel, BorderLayout.SOUTH);
+ }
+ if (numClients > 0) {
+ this.getContentPane().add(queryPanel, BorderLayout.CENTER);
+ }
+
+ this.pack();
+ setProperty(clientNames.get(datasourceComboBox.getSelectedItem()));
+ selectedClientID = clientNames
+ .get(datasourceComboBox.getSelectedItem());
+
+ // Initialize GUI panel.
+ datasourceComboBoxActionPerformed(null);
+ }
+
+ /**
+ * This method is called from within the constructor to initialize the form.
+ * WARNING: Do NOT modify this code. The content of this method is always
+ * regenerated by the Form Editor.
+ */
+ private void initComponents() {
+ mainTabbedPane = new javax.swing.JTabbedPane();
+ searchTermScrollPane = new javax.swing.JScrollPane();
+ queryTextPane = new javax.swing.JTextPane();
+ propertyPanel = new javax.swing.JPanel();
+
+ queryTextPane.setFont(new java.awt.Font("SansSerif", 0, 12));
+ queryTextPane.setText("Please enter search terms...");
+ searchTermScrollPane.setViewportView(queryTextPane);
+
+ mainTabbedPane.addTab("Query", searchTermScrollPane);
+
+ org.jdesktop.layout.GroupLayout propertyPanelLayout = new org.jdesktop.layout.GroupLayout(
+ propertyPanel);
+ propertyPanel.setLayout(propertyPanelLayout);
+ propertyPanelLayout.setHorizontalGroup(propertyPanelLayout
+ .createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(0, 408, Short.MAX_VALUE));
+ propertyPanelLayout.setVerticalGroup(propertyPanelLayout
+ .createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(0, 303, Short.MAX_VALUE));
+
+ propertyScrollPane = new JScrollPane();
+ propertyScrollPane.setViewportView(propertyPanel);
+ mainTabbedPane.addTab("Search Property", propertyScrollPane);
+
+ titlePanel = new javax.swing.JPanel();
+ titleIconLabel = new javax.swing.JLabel();
+ datasourcePanel = new javax.swing.JPanel();
+ datasourceLabel = new javax.swing.JLabel();
+ datasourceComboBox = new javax.swing.JComboBox();
+ aboutButton = new javax.swing.JButton();
+ buttonPanel = new javax.swing.JPanel();
+ searchButton = new javax.swing.JButton();
+ cancelButton = new javax.swing.JButton();
+ clearButton = new javax.swing.JButton();
+ dataQueryPanel = new javax.swing.JPanel();
+
+ setTitle("Import Network from Database");
+
+ setDefaultCloseOperation(javax.swing.WindowConstants.DISPOSE_ON_CLOSE);
+
+ titlePanel.setBackground(new java.awt.Color(0, 0, 0));
+
+ titleIconLabel.setIcon(new javax.swing.ImageIcon(Cytoscape.class
+ .getResource("images/networkImportIcon.png"))); // NOI18N
+
+ org.jdesktop.layout.GroupLayout titlePanelLayout = new org.jdesktop.layout.GroupLayout(
+ titlePanel);
+ titlePanel.setLayout(titlePanelLayout);
+ titlePanelLayout.setHorizontalGroup(titlePanelLayout
+ .createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(titleIconLabel,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE, 461,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE));
+ titlePanelLayout.setVerticalGroup(titlePanelLayout.createParallelGroup(
+ org.jdesktop.layout.GroupLayout.LEADING).add(titleIconLabel));
+
+ datasourceLabel.setFont(new java.awt.Font("SansSerif", 0, 12));
+ datasourceLabel.setText("Data Source");
+
+ datasourceComboBox
+ .addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ datasourceComboBoxActionPerformed(evt);
+ }
+ });
+
+ aboutButton.setText("About");
+ aboutButton.setMargin(new java.awt.Insets(2, 5, 2, 5));
+ aboutButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ aboutButtonActionPerformed(evt);
+ }
+ });
+
+ org.jdesktop.layout.GroupLayout datasourcePanelLayout = new org.jdesktop.layout.GroupLayout(
+ datasourcePanel);
+ datasourcePanel.setLayout(datasourcePanelLayout);
+ datasourcePanelLayout
+ .setHorizontalGroup(datasourcePanelLayout
+ .createParallelGroup(
+ org.jdesktop.layout.GroupLayout.LEADING)
+ .add(
+ datasourcePanelLayout
+ .createSequentialGroup()
+ .addContainerGap()
+ .add(datasourceLabel)
+ .addPreferredGap(
+ org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(datasourceComboBox, 0, 301,
+ Short.MAX_VALUE)
+ .addPreferredGap(
+ org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(aboutButton).addContainerGap()));
+ datasourcePanelLayout
+ .setVerticalGroup(datasourcePanelLayout
+ .createParallelGroup(
+ org.jdesktop.layout.GroupLayout.LEADING)
+ .add(
+ datasourcePanelLayout
+ .createSequentialGroup()
+ .addContainerGap()
+ .add(
+ datasourcePanelLayout
+ .createParallelGroup(
+ org.jdesktop.layout.GroupLayout.BASELINE)
+ .add(datasourceLabel)
+ .add(aboutButton)
+ .add(
+ datasourceComboBox,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE))
+ .addContainerGap(
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE)));
+
+ buttonPanel.setBorder(javax.swing.BorderFactory.createEtchedBorder());
+
+ searchButton.setText("Search");
+ searchButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ searchButtonActionPerformed(evt);
+ }
+ });
+
+ cancelButton.setText("Cancel");
+ cancelButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ cancelButtonActionPerformed(evt);
+ }
+ });
+
+ clearButton.setText("Clear");
+ clearButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ clearButtonActionPerformed(evt);
+ }
+ });
+
+ org.jdesktop.layout.GroupLayout buttonPanelLayout = new org.jdesktop.layout.GroupLayout(
+ buttonPanel);
+ buttonPanel.setLayout(buttonPanelLayout);
+ buttonPanelLayout
+ .setHorizontalGroup(buttonPanelLayout
+ .createParallelGroup(
+ org.jdesktop.layout.GroupLayout.LEADING)
+ .add(
+ org.jdesktop.layout.GroupLayout.TRAILING,
+ buttonPanelLayout
+ .createSequentialGroup()
+ .addContainerGap()
+ .add(clearButton)
+ .addPreferredGap(
+ org.jdesktop.layout.LayoutStyle.RELATED,
+ 225, Short.MAX_VALUE)
+ .add(cancelButton)
+ .addPreferredGap(
+ org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(searchButton).addContainerGap()));
+ buttonPanelLayout
+ .setVerticalGroup(buttonPanelLayout
+ .createParallelGroup(
+ org.jdesktop.layout.GroupLayout.LEADING)
+ .add(
+ org.jdesktop.layout.GroupLayout.TRAILING,
+ buttonPanelLayout
+ .createSequentialGroup()
+ .addContainerGap(
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE)
+ .add(
+ buttonPanelLayout
+ .createParallelGroup(
+ org.jdesktop.layout.GroupLayout.BASELINE)
+ .add(searchButton).add(
+ cancelButton)
+ .add(clearButton))
+ .addContainerGap()));
+
+ org.jdesktop.layout.GroupLayout dataQueryPanelLayout = new org.jdesktop.layout.GroupLayout(
+ dataQueryPanel);
+ dataQueryPanel.setLayout(dataQueryPanelLayout);
+ dataQueryPanelLayout.setHorizontalGroup(dataQueryPanelLayout
+ .createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(0, 461, Short.MAX_VALUE));
+ dataQueryPanelLayout.setVerticalGroup(dataQueryPanelLayout
+ .createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(0, 247, Short.MAX_VALUE));
+
+ queryPanel = new JPanel();
+ org.jdesktop.layout.GroupLayout layout = new org.jdesktop.layout.GroupLayout(
+ queryPanel);
+ queryPanel.setLayout(layout);
+ layout.setHorizontalGroup(layout.createParallelGroup(
+ org.jdesktop.layout.GroupLayout.LEADING).add(titlePanel,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
+ .add(datasourcePanel,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE).add(buttonPanel,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE).add(dataQueryPanel,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE));
+ layout
+ .setVerticalGroup(layout
+ .createParallelGroup(
+ org.jdesktop.layout.GroupLayout.LEADING)
+ .add(
+ layout
+ .createSequentialGroup()
+ .add(
+ titlePanel,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(
+ org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(
+ datasourcePanel,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(
+ org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(
+ dataQueryPanel,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE)
+ .addPreferredGap(
+ org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(
+ buttonPanel,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)));
+
+ dataQueryPanel.setLayout(new BorderLayout());
+ createInstallPanel();
+ } // </editor-fold>
+
+ private void createInstallPanel() {
+ installPanel = new JPanel();
+ installPanel.setLayout(new BorderLayout());
+ JLabel titleIconLabel2 = new JLabel();
+ titleIconLabel2.setIcon(new ImageIcon(Cytoscape.class
+ .getResource("images/networkImportIcon.png")));
+ JPanel titlePanel2 = new JPanel();
+ titlePanel2.add(titleIconLabel2);
+ titlePanel2.setBackground(new Color(0, 0, 0));
+ titlePanel2.setLayout(new FlowLayout(FlowLayout.LEFT));
+ if (numClients == 0) {
+ installPanel.add(titlePanel2, BorderLayout.NORTH);
+ }
+
+ JPanel internalPanel = new JPanel();
+ internalPanel.setBorder(new EmptyBorder(10, 10, 10, 10));
+ internalPanel.setLayout(new BoxLayout(internalPanel,
+ BoxLayout.PAGE_AXIS));
+ JTextArea area = new JTextArea(1, 40);
+ area.setBorder(new EmptyBorder(0, 0, 0, 0));
+ if (numClients == 0) {
+ area
+ .setText("There are no network import web service clients installed.");
+ } else {
+ area.setText("To install additional web service clients, click the install button below.");
+ }
+ area.setEditable(false);
+ area.setOpaque(false);
+ area.setAlignmentX(Component.LEFT_ALIGNMENT);
+ internalPanel.add(area);
+ }
+
+
+ private void searchButtonActionPerformed(final ActionEvent evt) {
+ selectedClientID = clientNames
+ .get(datasourceComboBox.getSelectedItem());
+
+ final CyWebServiceEvent<String> event = buildEvent();
+ logger.info("Start importing network: " + evt.getActionCommand());
+
+ task = new WSNetworkImportTask(datasourceComboBox.getSelectedItem()
+ .toString(), event);
+
+ // Configure JTask Dialog Pop-Up Box
+ final JTaskConfig tConfig = new JTaskConfig();
+ tConfig.setOwner(Cytoscape.getDesktop());
+ tConfig.displayCloseButton(true);
+ tConfig.displayCancelButton(true);
+ tConfig.displayStatus(false);
+ tConfig.setAutoDispose(true);
+
+ // Execute Task in New Thread; pops open JTask Dialog Box.
+ TaskManager.executeTask(task, tConfig);
+
+ logger.info("Network Import from WS Success!");
+ }
+
+ private void aboutButtonActionPerformed(ActionEvent evt) {
+ final WebServiceClient<?> wsc = WebServiceClientManager
+ .getClient(selectedClientID);
+ final String clientName = wsc.getDisplayName();
+ final String description = wsc.getDescription();
+ Icon icon = null;
+ if (wsc instanceof WebServiceClientGUI) {
+ icon = ((WebServiceClientGUI) wsc).getIcon(IconSize.FULL);
+ }
+
+ if (icon == null) {
+ icon = DEF_ICON;
+ }
+ AboutDialog.showDialog(clientName, icon, description);
+ }
+
+ /**
+ * Clear query text field.
+ */
+ private void clearButtonActionPerformed(java.awt.event.ActionEvent evt) {
+ // Just set empty string for the field.
+ queryTextPane.setText("");
+ }
+
+ private void cancelButtonActionPerformed(java.awt.event.ActionEvent evt) {
+ // Do nothing. Just hide this window.
+ queryTextPane.setText("");
+ dispose();
+ }
+
+ private void datasourceComboBoxActionPerformed(
+ java.awt.event.ActionEvent evt) {
+
+ queryTextPane.setText("");
+ setProperty(clientNames.get(datasourceComboBox.getSelectedItem()));
+ selectedClientID = clientNames
+ .get(datasourceComboBox.getSelectedItem());
+
+ // Update Panel
+ dataQueryPanel.removeAll();
+
+ final Container gui = serviceUIPanels.get(selectedClientID);
+ if (gui != null) {
+ // This service has custom panel.
+ dataQueryPanel.add(gui, BorderLayout.CENTER);
+ // Hide button panel.
+ buttonPanel.setVisible(false);
+ } else {
+ // Otherwise, use the default panel.
+ logger.info("No custom GUI. Use default panel.");
+ dataQueryPanel.add(mainTabbedPane, BorderLayout.CENTER);
+ buttonPanel.setVisible(true);
+ }
+
+ pack();
+ repaint();
+ }
+
+ private void setProperty(String clientID) {
+ final WebServiceClient<?> client = WebServiceClientManager.getClient(clientID);
+
+ if (client == null)
+ return;
+
+ ModuleProperties props = client.getProps();
+ List<Tunable> tunables = props.getTunables();
+ propertyPanel = new JPanel(new GridLayout(0, 1));
+
+ for (Tunable tu : tunables) {
+ JPanel p = tu.getPanel();
+ p.setBackground(Color.white);
+
+ if (p != null)
+ propertyPanel.add(p);
+ }
+
+ propertyScrollPane.setViewportView(propertyPanel);
+ pack();
+ repaint();
+ }
+
+ private void setDatasource() {
+ List<WebServiceClient<?>> clients = WebServiceClientManager
+ .getAllClients();
+ for (WebServiceClient<?> client : clients) {
+ if (client instanceof NetworkImportWebServiceClient) {
+ this.datasourceComboBox.addItem(client.getDisplayName());
+ this.clientNames.put(client.getDisplayName(), client
+ .getClientID());
+
+ if (client instanceof WebServiceClientGUI
+ && (((WebServiceClientGUI) client).getGUI() != null)) {
+ serviceUIPanels.put(client.getClientID(),
+ ((WebServiceClientGUI) client).getGUI());
+ }
+ numDataSources++;
+ }
+ }
+ }
+
+ private CyWebServiceEvent<String> buildEvent() {
+ final String clientID = clientNames.get(datasourceComboBox
+ .getSelectedItem());
+
+ // Update props here.
+ WebServiceClientManager.getClient(clientID).getProps().updateValues();
+
+ return new CyWebServiceEvent<String>(clientID,
+ WSEventType.SEARCH_DATABASE, queryTextPane.getText(),
+ WSEventType.IMPORT_NETWORK);
+ }
+
+ // Variables declaration - do not modify
+ private javax.swing.JButton cancelButton;
+ private javax.swing.JComboBox datasourceComboBox;
+ private javax.swing.JLabel datasourceLabel;
+ private javax.swing.JTabbedPane mainTabbedPane;
+ private javax.swing.JPanel propertyPanel;
+ private JScrollPane propertyScrollPane;
+ private javax.swing.JButton searchButton;
+ private javax.swing.JScrollPane searchTermScrollPane;
+ private javax.swing.JTextPane queryTextPane;
+ private javax.swing.JButton aboutButton;
+ private javax.swing.JPanel buttonPanel;
+ private JPanel queryPanel;
+ private JPanel installPanel;
+ private javax.swing.JButton clearButton;
+ private javax.swing.JPanel dataQueryPanel;
+ private javax.swing.JPanel datasourcePanel;
+ private javax.swing.JLabel titleIconLabel;
+ private javax.swing.JPanel titlePanel;
+
+
+ /**
+ * Task to import network from web service.
+ *
+ * @author kono
+ *
+ */
+ private class WSNetworkImportTask implements Task {
+ private String serviceName;
+ private CyWebServiceEvent<String> evt;
+ private TaskMonitor taskMonitor;
+
+ public WSNetworkImportTask(final String serviceName,
+ final CyWebServiceEvent<String> evt) {
+ this.evt = evt;
+ this.serviceName = serviceName;
+ }
+
+ public String getTitle() {
+ return "Loading network from web service...";
+ }
+
+ public void halt() {
+
+ cancelFlag = true;
+ Thread.currentThread().interrupt();
+ taskMonitor.setPercentCompleted(100);
+
+ // Kill the import task.
+ CyWebServiceEvent<String> cancelEvent = new CyWebServiceEvent<String>(
+ serviceName, WSEventType.CANCEL, null, null);
+ try {
+ WebServiceClientManager.getCyWebServiceEventSupport()
+ .fireCyWebServiceEvent(cancelEvent);
+ } catch (CyWebServiceException e) {
+ taskMonitor.setException(e, "Cancel Failed.");
+ }
+ }
+
+ public void run() {
+ cancelFlag = false;
+ taskMonitor.setStatus("Loading network from " + serviceName);
+ taskMonitor.setPercentCompleted(-1);
+
+ try {
+ WebServiceClientManager.getCyWebServiceEventSupport()
+ .fireCyWebServiceEvent(evt);
+ } catch (Exception e) {
+ taskMonitor.setException(e,
+ "Failed to load network from web service.");
+ return;
+ }
+ taskMonitor.setPercentCompleted(100);
+ taskMonitor.setStatus("Network successfully loaded.");
+ }
+
+ public void setTaskMonitor(TaskMonitor arg0)
+ throws IllegalThreadStateException {
+ this.taskMonitor = arg0;
+ }
+
+ protected TaskMonitor getTaskMonitor() {
+ return taskMonitor;
+ }
+ }
+
+ /**
+ * Listening to events fired by service clients.
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ public void propertyChange(PropertyChangeEvent evt) {
+
+ if (cancelFlag)
+ return;
+
+ Object resultObject = evt.getNewValue();
+
+ if (evt.getPropertyName().equals(
+ WSResponseType.SEARCH_FINISHED.toString())
+ && (resultObject != null)
+ && resultObject instanceof DatabaseSearchResult) {
+ DatabaseSearchResult result = (DatabaseSearchResult) resultObject;
+
+ if (result.getNextMove().equals(WSEventType.IMPORT_NETWORK)) {
+ logger.info("Got search result from: " + evt.getSource()
+ + ", Num result = " + result.getResultSize()
+ + ", Source name = " + evt.getOldValue());
+
+ String[] message = {
+ result.getResultSize() + " records found in "
+ + selectedClientID,
+ "Do you want to create new network from the search result?" };
+ int value = JOptionPane.showConfirmDialog(Cytoscape
+ .getDesktop(), message, "Import network",
+ JOptionPane.YES_NO_OPTION);
+
+ if (value == JOptionPane.YES_OPTION) {
+ CyWebServiceEvent<Object> evt2 = new CyWebServiceEvent<Object>(
+ evt.getOldValue().toString(),
+ WSEventType.IMPORT_NETWORK, result.getResult());
+
+ try {
+ WebServiceClientManager.getCyWebServiceEventSupport()
+ .fireCyWebServiceEvent(evt2);
+ } catch (CyWebServiceException e) {
+ // TODO Auto-generated catch block
+ if (task.getTaskMonitor() != null) {
+ task.getTaskMonitor().setException(e,
+ "Database search failed.");
+ }
+ }
+ }
+ }
+ } else if (evt.getPropertyName().equals(
+ WSResponseType.DATA_IMPORT_FINISHED.toString())) {
+
+ // If result is empty, just ignore it.
+ if (evt.getNewValue() == null)
+ return;
+
+// VisualStyle style = ((NetworkImportWebServiceClient) WebServiceClientManager
+// .getClient(selectedClientID)).getDefaultVisualStyle();
+// if (style == null) {
+// style = Cytoscape.getVisualMappingManager().getVisualStyle();
+// }
+//
+// if (Cytoscape.getVisualMappingManager().getCalculatorCatalog()
+// .getVisualStyle(style.getName()) == null)
+// Cytoscape.getVisualMappingManager().getCalculatorCatalog()
+// .addVisualStyle(style);
+//
+// Cytoscape.getVisualMappingManager().setVisualStyle(style);
+
+ // Name the network
+ final String[] message = { "Network Loaded from " + selectedClientID,
+ "Please enter title for new network:" };
+ String value = JOptionPane.showInputDialog(Cytoscape.getDesktop(),
+ message, "Name new network", JOptionPane.QUESTION_MESSAGE);
+ if (value == null || value.length() == 0)
+ value = selectedClientID + " Network";
+
+ final CyNetwork cyNetwork = Cytoscape.getCurrentNetwork();
+ Cytoscape.getCurrentNetwork().setTitle(value);
+ Cytoscape.getDesktop().getNetworkPanel().updateTitle(cyNetwork);
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/data/webservice/ui/WSImportResultDialog.java b/application/src/main/java/cytoscape/data/webservice/ui/WSImportResultDialog.java
new file mode 100644
index 0000000..7d7566e
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/webservice/ui/WSImportResultDialog.java
@@ -0,0 +1,171 @@
+package cytoscape.data.webservice.ui;
+
+
+
+/**
+ *
+ * @author kono
+ */
+public class WSImportResultDialog extends javax.swing.JDialog {
+
+ public void showResult() {
+
+ }
+
+ /** Creates new form SearchResultDialog */
+ public WSImportResultDialog(java.awt.Frame parent, boolean modal) {
+ super(parent, modal);
+ initComponents();
+ }
+
+ /** This method is called from within the constructor to
+ * initialize the form.
+ * WARNING: Do NOT modify this code. The content of this method is
+ * always regenerated by the Form Editor.
+ */
+ // <editor-fold defaultstate="collapsed" desc=" Generated Code">
+ private void initComponents() {
+ basePanel = new javax.swing.JPanel();
+ titleLabel = new javax.swing.JLabel();
+ topSeparator = new javax.swing.JSeparator();
+ parameterPanel = new javax.swing.JPanel();
+ serviceLabel = new javax.swing.JLabel();
+ nameLabel = new javax.swing.JLabel();
+ parameterScrollPane = new javax.swing.JScrollPane();
+ parameterEditorPane = new javax.swing.JEditorPane();
+ resultPanel = new javax.swing.JPanel();
+ resultScrollPane = new javax.swing.JScrollPane();
+ okButton = new javax.swing.JButton();
+
+ setDefaultCloseOperation(javax.swing.WindowConstants.DISPOSE_ON_CLOSE);
+ setBackground(new java.awt.Color(255, 255, 255));
+ basePanel.setBackground(new java.awt.Color(255, 255, 255));
+ titleLabel.setFont(new java.awt.Font("SansSerif", 1, 14));
+ titleLabel.setText("Search Result");
+
+ parameterPanel.setBackground(new java.awt.Color(255, 255, 255));
+ parameterPanel.setBorder(javax.swing.BorderFactory.createTitledBorder("Search Parameters"));
+ serviceLabel.setText("Service Name:");
+
+ nameLabel.setText("Service Name will be here...");
+
+ parameterScrollPane.setBackground(new java.awt.Color(255, 255, 255));
+ parameterScrollPane.setViewportView(parameterEditorPane);
+
+ org.jdesktop.layout.GroupLayout parameterPanelLayout = new org.jdesktop.layout.GroupLayout(parameterPanel);
+ parameterPanel.setLayout(parameterPanelLayout);
+ parameterPanelLayout.setHorizontalGroup(
+ parameterPanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(parameterPanelLayout.createSequentialGroup()
+ .addContainerGap()
+ .add(parameterPanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(parameterScrollPane, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 542, Short.MAX_VALUE)
+ .add(parameterPanelLayout.createSequentialGroup()
+ .add(serviceLabel)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(nameLabel)))
+ .addContainerGap())
+ );
+ parameterPanelLayout.setVerticalGroup(
+ parameterPanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(parameterPanelLayout.createSequentialGroup()
+ .add(parameterPanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE)
+ .add(serviceLabel)
+ .add(nameLabel))
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(parameterScrollPane, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 154, Short.MAX_VALUE)
+ .addContainerGap())
+ );
+
+ resultPanel.setBackground(new java.awt.Color(255, 255, 255));
+ resultPanel.setBorder(javax.swing.BorderFactory.createTitledBorder("Result"));
+
+ org.jdesktop.layout.GroupLayout resultPanelLayout = new org.jdesktop.layout.GroupLayout(resultPanel);
+ resultPanel.setLayout(resultPanelLayout);
+ resultPanelLayout.setHorizontalGroup(
+ resultPanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(resultScrollPane, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 566, Short.MAX_VALUE)
+ );
+ resultPanelLayout.setVerticalGroup(
+ resultPanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(resultScrollPane, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 311, Short.MAX_VALUE)
+ );
+
+ okButton.setText("OK");
+ okButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ okButtonActionPerformed(evt);
+ }
+ });
+
+ org.jdesktop.layout.GroupLayout basePanelLayout = new org.jdesktop.layout.GroupLayout(basePanel);
+ basePanel.setLayout(basePanelLayout);
+ basePanelLayout.setHorizontalGroup(
+ basePanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(org.jdesktop.layout.GroupLayout.TRAILING, basePanelLayout.createSequentialGroup()
+ .add(basePanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.TRAILING)
+ .add(org.jdesktop.layout.GroupLayout.LEADING, basePanelLayout.createSequentialGroup()
+ .addContainerGap()
+ .add(titleLabel))
+ .add(basePanelLayout.createSequentialGroup()
+ .addContainerGap(535, Short.MAX_VALUE)
+ .add(okButton))
+ .add(org.jdesktop.layout.GroupLayout.LEADING, basePanelLayout.createSequentialGroup()
+ .addContainerGap()
+ .add(parameterPanel, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
+ .add(org.jdesktop.layout.GroupLayout.LEADING, basePanelLayout.createSequentialGroup()
+ .addContainerGap()
+ .add(resultPanel, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)))
+ .addContainerGap())
+ .add(topSeparator, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 600, Short.MAX_VALUE)
+ );
+ basePanelLayout.setVerticalGroup(
+ basePanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(basePanelLayout.createSequentialGroup()
+ .addContainerGap()
+ .add(titleLabel)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(topSeparator, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE, 2, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(parameterPanel, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(resultPanel, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(okButton)
+ .addContainerGap())
+ );
+
+ org.jdesktop.layout.GroupLayout layout = new org.jdesktop.layout.GroupLayout(getContentPane());
+ getContentPane().setLayout(layout);
+ layout.setHorizontalGroup(
+ layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(basePanel, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
+ );
+ layout.setVerticalGroup(
+ layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(basePanel, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
+ );
+ pack();
+ }// </editor-fold>
+
+ private void okButtonActionPerformed(java.awt.event.ActionEvent evt) {
+ dispose();
+ }
+
+
+
+ // Variables declaration - do not modify
+ private javax.swing.JPanel basePanel;
+ private javax.swing.JLabel nameLabel;
+ private javax.swing.JButton okButton;
+ private javax.swing.JEditorPane parameterEditorPane;
+ private javax.swing.JPanel parameterPanel;
+ private javax.swing.JScrollPane parameterScrollPane;
+ private javax.swing.JPanel resultPanel;
+ private javax.swing.JScrollPane resultScrollPane;
+ private javax.swing.JLabel serviceLabel;
+ private javax.swing.JLabel titleLabel;
+ private javax.swing.JSeparator topSeparator;
+ // End of variables declaration
+
+}
diff --git a/application/src/main/java/cytoscape/data/webservice/ui/WebServiceClientGUI.java b/application/src/main/java/cytoscape/data/webservice/ui/WebServiceClientGUI.java
new file mode 100644
index 0000000..ca11972
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/webservice/ui/WebServiceClientGUI.java
@@ -0,0 +1,106 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data.webservice.ui;
+
+import giny.view.EdgeView;
+import giny.view.NodeView;
+
+import java.awt.Container;
+import java.util.List;
+
+import javax.swing.Icon;
+import javax.swing.JMenuItem;
+
+
+/**
+ * Web service client which has custom component should implements this interface.
+ * Otherwise, default GUI will be used in the desktop.
+ * If this client will be used only through CLI or scripts, this is not required.
+ *
+ * @param <U> GUI component for this service.
+ */
+public interface WebServiceClientGUI<U extends Container> {
+ /**
+ * Defines icon type.
+ *
+ * @author kono
+ *
+ */
+ public enum IconSize {
+ SMALL,
+ MEDIUM,
+ FULL;
+ }
+
+ /**
+ * Returns GUI for this client.
+ * Will be used only with Cytoscape Desktop.
+ *
+ * U is the Component for GUI. In many cases, this is a JPanel.
+ *
+ *
+ * @return GUI for this service.
+ */
+ public U getGUI();
+
+ /**
+ * Set GUI for this service.
+ *
+ * @param gui GUI for this service.
+ */
+ public void setGUI(U gui);
+
+ /**
+ * Returns icon for the GUI. May be used for about page.
+ *
+ * @param t
+ * @return
+ */
+ public Icon getIcon(IconSize t);
+
+ /**
+ * Return node context menu item if available.
+ *
+ * @return Custom context menu.
+ *
+ */
+ public List<JMenuItem> getNodeContextMenuItems(NodeView nv);
+
+ /**
+ * Return edge context menu if available.
+ * @return
+ */
+ public List<JMenuItem> getEdgeContextMenuItems(EdgeView ev);
+}
diff --git a/application/src/main/java/cytoscape/data/webservice/ui/WebServiceContextMenu.java b/application/src/main/java/cytoscape/data/webservice/ui/WebServiceContextMenu.java
new file mode 100644
index 0000000..9c019d9
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/webservice/ui/WebServiceContextMenu.java
@@ -0,0 +1,138 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data.webservice.ui;
+
+import cytoscape.data.webservice.WebServiceClient;
+import cytoscape.data.webservice.WebServiceClientManager;
+
+import ding.view.EdgeContextMenuListener;
+import ding.view.NodeContextMenuListener;
+
+import giny.view.EdgeView;
+import giny.view.NodeView;
+
+import java.util.HashMap;
+import java.util.List;
+
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JPopupMenu;
+
+
+/**
+ * Context menu for web service clients.
+ *
+ * @author kono
+ * @since Cytoscape 2.6
+ * @version 0.5
+ *
+ */
+public class WebServiceContextMenu implements NodeContextMenuListener, EdgeContextMenuListener {
+ private HashMap<String, String> clientMap;
+ private JMenu nodeRootMenu;
+ private JMenu edgeRootMenu;
+
+ /**
+ * Creates a new WebServiceContextMenu object.
+ */
+ public WebServiceContextMenu() {
+ clientMap = new HashMap<String, String>();
+ nodeRootMenu = new JMenu("Use Web Services");
+ edgeRootMenu = new JMenu("Use Web Services");
+ }
+
+ /**
+ * Add this menu to the node context menu.
+ *
+ * @param nodeView DOCUMENT ME!
+ * @param menu DOCUMENT ME!
+ */
+ public void addNodeContextMenuItems(NodeView nodeView, JPopupMenu menu) {
+ addMenu(nodeView, menu);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edgeView DOCUMENT ME!
+ * @param menu DOCUMENT ME!
+ */
+ public void addEdgeContextMenuItems(EdgeView edgeView, JPopupMenu menu) {
+ addMenu(edgeView, menu);
+ }
+
+ private void addMenu(Object view, JPopupMenu menu) {
+ if (menu == null)
+ menu = new JPopupMenu();
+ else {
+ // Clean up menu
+ nodeRootMenu.removeAll();
+ edgeRootMenu.removeAll();
+ }
+
+ List<JMenuItem> context = null;
+ final List<WebServiceClient<?>> clients = WebServiceClientManager.getAllClients();
+
+ for (WebServiceClient<?> client : clients) {
+ if (client instanceof WebServiceClientGUI) {
+ if (view instanceof NodeView)
+ context = ((WebServiceClientGUI) client).getNodeContextMenuItems((NodeView) view);
+ else if (view instanceof EdgeView)
+ context = ((WebServiceClientGUI) client).getEdgeContextMenuItems((EdgeView) view);
+
+ if (context != null) {
+ JMenu cMenu = new JMenu(client.getDisplayName());
+
+ for (JMenuItem menuItem : context) {
+ cMenu.add(menuItem);
+ }
+
+ nodeRootMenu.add(cMenu);
+ clientMap.put(client.getDisplayName(), client.getClientID());
+ }
+ }
+ }
+
+ if(view instanceof NodeView) {
+ menu.add(this.nodeRootMenu);
+ if(nodeRootMenu.getItemCount() == 0)
+ nodeRootMenu.setEnabled(false);
+ } else {
+ menu.add(this.edgeRootMenu);
+ if(edgeRootMenu.getItemCount() == 0)
+ edgeRootMenu.setEnabled(false);
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/data/webservice/ui/WebServiceContextMenuListener.java b/application/src/main/java/cytoscape/data/webservice/ui/WebServiceContextMenuListener.java
new file mode 100644
index 0000000..6f81482
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/webservice/ui/WebServiceContextMenuListener.java
@@ -0,0 +1,67 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.data.webservice.ui;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.view.CytoscapeDesktop;
+
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+
+
+/**
+ *
+ */
+public class WebServiceContextMenuListener implements PropertyChangeListener {
+ private WebServiceContextMenu cMenu = null;
+
+ /**
+ * Add expander.
+ *
+ * @param evt DOCUMENT ME!
+ */
+ public void propertyChange(PropertyChangeEvent evt) {
+ if (CytoscapeDesktop.NETWORK_VIEW_CREATED.equals(evt.getPropertyName())) {
+ if (cMenu == null)
+ cMenu = new WebServiceContextMenu();
+
+ Cytoscape.getCurrentNetworkView().addNodeContextMenuListener(cMenu);
+ Cytoscape.getCurrentNetworkView().addEdgeContextMenuListener(cMenu);
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/data/webservice/util/NetworkExpansionMenu.java b/application/src/main/java/cytoscape/data/webservice/util/NetworkExpansionMenu.java
new file mode 100644
index 0000000..cb7ef67
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/webservice/util/NetworkExpansionMenu.java
@@ -0,0 +1,200 @@
+package cytoscape.data.webservice.util;
+
+import giny.model.Node;
+
+import java.awt.event.ActionEvent;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.util.Set;
+
+import javax.swing.AbstractAction;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+
+import cytoscape.Cytoscape;
+import cytoscape.CytoscapeInit;
+import cytoscape.logger.CyLogger;
+import cytoscape.data.webservice.CyWebServiceEvent;
+import cytoscape.data.webservice.DatabaseSearchResult;
+import cytoscape.data.webservice.NetworkImportWebServiceClient;
+import cytoscape.data.webservice.WebServiceClient;
+import cytoscape.data.webservice.WebServiceClientManager;
+import cytoscape.data.webservice.CyWebServiceEvent.WSEventType;
+import cytoscape.layout.CyLayouts;
+import cytoscape.task.Task;
+import cytoscape.task.TaskMonitor;
+import cytoscape.task.ui.JTaskConfig;
+import cytoscape.task.util.TaskManager;
+
+public class NetworkExpansionMenu implements PropertyChangeListener {
+
+ // Default layout algorithm name in property.
+ private static final String LAYOUT_PROP = "expanderDefaultLayout";
+ private static final String DEF_LAYOUT = "force-directed";
+
+ private static NetworkExpansionMenu expander;
+
+ private static CyLogger logger = CyLogger.getLogger(NetworkExpansionMenu.class);
+
+ static {
+ expander = new NetworkExpansionMenu();
+ }
+
+ public static JMenuItem getExpander(WebServiceClient client) {
+ return expander.getMenuItem(client);
+
+ }
+
+ private String defLayout;
+
+ public NetworkExpansionMenu() {
+ // Listening to event from core.
+ Cytoscape.getPropertyChangeSupport().addPropertyChangeListener(this);
+
+ // Set layout algorithm
+ defLayout = CytoscapeInit.getProperties().getProperty(LAYOUT_PROP);
+
+ if (defLayout == null)
+ defLayout = DEF_LAYOUT;
+
+ }
+
+ private JMenuItem getMenuItem(final WebServiceClient client) {
+ final JMenuItem expandMenu = new JMenuItem(new AbstractAction("Get neighbours by ID(s)") {
+ public void actionPerformed(ActionEvent e) {
+ logger.info("Start expanding network: " + e.getActionCommand());
+
+ final CyWebServiceEvent evt = new CyWebServiceEvent(client.getClientID(),
+ WSEventType.SEARCH_DATABASE,
+ buildStringQuery(),
+ WSEventType.EXPAND_NETWORK);
+
+ SearchTask task = new SearchTask(evt);
+
+ // Configure JTask Dialog Pop-Up Box
+ final JTaskConfig jTaskConfig = new JTaskConfig();
+ jTaskConfig.setOwner(Cytoscape.getDesktop());
+ jTaskConfig.displayCloseButton(true);
+ jTaskConfig.displayStatus(true);
+ jTaskConfig.setAutoDispose(true);
+
+ // Execute Task in New Thread; pops open JTask Dialog Box.
+ TaskManager.executeTask(task, jTaskConfig);
+ }
+ });
+
+ return expandMenu;
+ }
+
+ private String buildStringQuery() {
+ final StringBuilder builder = new StringBuilder();
+ final Set<Node> selectedNodes = Cytoscape.getCurrentNetwork().getSelectedNodes();
+
+ for (Node node : selectedNodes) {
+ builder.append(node.getIdentifier() + " ");
+ }
+
+ return builder.toString();
+ }
+
+ /**
+ * Catch result from the service.
+ *
+ * @param evt DOCUMENT ME!
+ */
+ public void propertyChange(PropertyChangeEvent evt) {
+ Object resultObj = evt.getNewValue();
+
+ if (evt.getPropertyName().equals(CyWebServiceEvent.WSResponseType.SEARCH_FINISHED.toString())
+ && ((DatabaseSearchResult) resultObj).getNextMove().equals(WSEventType.EXPAND_NETWORK)) {
+ logger.info("Search result from " + evt.getSource() + ", Number of result = "
+ + evt.getNewValue() + ", Source name = " + evt.getOldValue());
+
+ String[] message = {
+ ((DatabaseSearchResult) resultObj).getResultSize()
+ + " interactions found.",
+
+ "Do you want to add new nodes and edges to " + Cytoscape.getCurrentNetwork().getTitle()
+ + "?"
+ };
+ int value = JOptionPane.showConfirmDialog(Cytoscape.getDesktop(), message,
+ "Expand network", JOptionPane.YES_NO_OPTION);
+
+ if (value == JOptionPane.YES_OPTION) {
+
+ CyWebServiceEvent evt2 = new CyWebServiceEvent(evt.getOldValue().toString(),
+ WSEventType.EXPAND_NETWORK,
+ ((DatabaseSearchResult) resultObj).getResult());
+
+ try {
+ WebServiceClientManager.getCyWebServiceEventSupport().fireCyWebServiceEvent(evt2);
+ } catch (Exception e) {
+ logger.warn("Exception handling web service event '"+evt2.toString()+"': ",e);
+ }
+ }
+ } else if (evt.getPropertyName().equals(Cytoscape.NETWORK_MODIFIED)
+ && evt.getSource() instanceof NetworkImportWebServiceClient) {
+ String[] message = { "Neighbours loaded.", "Do you want to layout the network now?" };
+ int value = JOptionPane.showConfirmDialog(Cytoscape.getDesktop(), message,
+ "Expansion complete",
+ JOptionPane.YES_NO_OPTION);
+
+ if (value == JOptionPane.YES_OPTION) {
+ CyLayouts.getLayout(defLayout).doLayout();
+ }
+ } else if (evt.getPropertyName().equals(Cytoscape.PREFERENCES_UPDATED)) {
+ defLayout = CytoscapeInit.getProperties().getProperty("expanderDefaultLayout");
+
+ if (defLayout == null) {
+ defLayout = "force-directed";
+ }
+ }
+ }
+
+
+ class SearchTask implements Task {
+ private CyWebServiceEvent evt;
+ private TaskMonitor taskMonitor;
+
+ public SearchTask(CyWebServiceEvent evt) {
+ this.evt = evt;
+ }
+
+ public String getTitle() {
+ // TODO Auto-generated method stub
+ return "Expanding Network";
+ }
+
+ public void halt() {
+ // TODO Auto-generated method stub
+ }
+
+ public void run() {
+ taskMonitor.setStatus("Loading neighbours...");
+ taskMonitor.setPercentCompleted(-1);
+
+ // this even will load the file
+ try {
+ WebServiceClientManager.getCyWebServiceEventSupport().fireCyWebServiceEvent(evt);
+ } catch (Exception e) {
+ taskMonitor.setException(e, "Failed to load neighbours.");
+
+ return;
+ }
+
+ taskMonitor.setPercentCompleted(100);
+
+ Cytoscape.getDesktop().setFocus(Cytoscape.getCurrentNetwork().getIdentifier());
+
+ String curNetID = Cytoscape.getCurrentNetwork().getIdentifier();
+
+ Cytoscape.getNetworkView(curNetID)
+ .setVisualStyle(Cytoscape.getVisualMappingManager().getVisualStyle().getName());
+ Cytoscape.getNetworkView(curNetID).redrawGraph(false, true);
+ }
+
+ public void setTaskMonitor(TaskMonitor arg0) throws IllegalThreadStateException {
+ this.taskMonitor = arg0;
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/data/webservice/util/WebServiceThemeInstall.java b/application/src/main/java/cytoscape/data/webservice/util/WebServiceThemeInstall.java
new file mode 100644
index 0000000..4834f8a
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/webservice/util/WebServiceThemeInstall.java
@@ -0,0 +1,174 @@
+package cytoscape.data.webservice.util;
+
+import cytoscape.Cytoscape;
+import cytoscape.data.webservice.ui.UnifiedNetworkImportDialog;
+import cytoscape.logger.CyLogger;
+import cytoscape.plugin.PluginManager;
+import cytoscape.plugin.DownloadableInfo;
+import cytoscape.plugin.ManagerUtil;
+import cytoscape.plugin.Category;
+
+import cytoscape.task.TaskMonitor;
+import cytoscape.task.ui.JTaskConfig;
+import cytoscape.task.util.TaskManager;
+
+import javax.swing.*;
+import java.util.*;
+
+public class WebServiceThemeInstall {
+
+ public final static String WEBSERVICE_THEME = "WebServiceClientPack";
+ private static CyLogger logger = CyLogger.getLogger(WebServiceThemeInstall.class);
+
+ private PluginManager mgr;
+ private UnifiedNetworkImportDialog unifiedNetworkImportDialog;
+
+ public WebServiceThemeInstall(UnifiedNetworkImportDialog dialog) {
+ super();
+ unifiedNetworkImportDialog = dialog;
+ mgr = PluginManager.getPluginManager();
+ }
+
+ // for test purposes so a manager pointing at the tmp directory can be used
+ protected WebServiceThemeInstall(PluginManager manager) {
+ super();
+ mgr = manager;
+ }
+
+ public DownloadableInfo installTheme() throws org.jdom.JDOMException, java.io.IOException {
+ Map<String, List<DownloadableInfo>> DownloadableByCategory =
+ ManagerUtil.sortByCategory( mgr.inquire(cytoscape.CytoscapeInit.getProperties().getProperty("defaultPluginDownloadUrl")) );
+
+ DownloadableInfo WSTheme = null;
+ for (DownloadableInfo Theme: DownloadableByCategory.get( Category.THEME.toString() )) {
+ if (Theme.getName().equals(WEBSERVICE_THEME) && Theme.isPluginCompatibleWithCurrent()) {
+ //if (Theme.getName().equals(WEBSERVICE_THEME) && Theme.isCytoscapeVersionCurrent() ) {
+ if (WSTheme == null)
+ WSTheme = Theme;
+
+ if (Theme.isNewerObjectVersion(WSTheme))
+ WSTheme = Theme;
+ }
+ }
+ return this.runInstallTask(WSTheme);
+ }
+
+
+ private DownloadableInfo runInstallTask(DownloadableInfo obj) {
+ // Create Task
+ InstallTask task = new InstallTask(obj);
+
+ // Configure JTask Dialog Pop-Up Box
+ JTaskConfig jTaskConfig = new JTaskConfig();
+ jTaskConfig.setOwner(Cytoscape.getDesktop());
+ jTaskConfig.displayCloseButton(false);
+ jTaskConfig.displayStatus(true);
+ jTaskConfig.setAutoDispose(true);
+ jTaskConfig.displayCancelButton(true);
+ // Execute Task in New Thread; pop open JTask Dialog Box.
+ TaskManager.executeTask(task, jTaskConfig);
+ DownloadableInfo info = task.getDownloadedPlugin();
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ unifiedNetworkImportDialog.resetGUI();
+ JOptionPane.showMessageDialog(Cytoscape.getDesktop(),
+ "Web Services Pack Successfully Installed.",
+ "Installation Successfull", JOptionPane.INFORMATION_MESSAGE);
+ }
+ });
+ return info;
+ }
+
+ private class InstallTask implements cytoscape.task.Task {
+ private cytoscape.task.TaskMonitor taskMonitor;
+ private DownloadableInfo infoObj;
+ private String errorMsg;
+
+ public InstallTask(DownloadableInfo Info)
+ throws java.lang.IllegalArgumentException {
+ String ErrorMsg = null;
+ if (Info == null) {
+ ErrorMsg = "DownloadableInfo object cannot be null\n";
+ throw new java.lang.IllegalArgumentException(ErrorMsg);
+ }
+ infoObj = Info;
+ }
+
+ public void run() {
+ if (taskMonitor == null) {
+ throw new IllegalStateException("Task Monitor is not set.");
+ }
+ taskMonitor.setStatus("Installing " + infoObj.getName() + " v"
+ + infoObj.getObjectVersion());
+ taskMonitor.setPercentCompleted(-1);
+
+ PluginManager Mgr = PluginManager.getPluginManager();
+ try {
+ infoObj = Mgr.download(infoObj, taskMonitor);
+ taskMonitor.setStatus(infoObj.getName() + " v"
+ + infoObj.getObjectVersion() + " complete.");
+
+ taskMonitor.setStatus(infoObj.getName() + " v"
+ + infoObj.getObjectVersion() + " loading...");
+
+ Mgr.install(infoObj);
+ Mgr.loadPlugin(infoObj);
+ } catch (java.io.IOException ioe) {
+ taskMonitor
+ .setException(ioe, "Failed to download "
+ + infoObj.getName() + " from "
+ + infoObj.getObjectUrl());
+ infoObj = null;
+ logger.warn("Failed to download "
+ + infoObj.getName() + " from "
+ + infoObj.getObjectUrl(), ioe);
+ } catch (cytoscape.plugin.ManagerException me) {
+ this.setErrorMessage("Failed to install " + infoObj.toString());
+ taskMonitor.setException(me, me.getMessage());
+ infoObj = null;
+ logger.warn("Failed to install " + infoObj.toString(), me);
+ } catch (cytoscape.plugin.PluginException pe) {
+ this.setErrorMessage("Failed to install " + infoObj.toString());
+ infoObj = null;
+ taskMonitor.setException(pe, pe.getMessage());
+ logger.warn("Failed to install " + infoObj.toString(), pe);
+ } catch (ClassNotFoundException cne) {
+ taskMonitor.setException(cne, cne.getMessage());
+ this.setErrorMessage("Failed to install " + infoObj.toString());
+ infoObj = null;
+ logger.warn("Failed to install " + infoObj.toString(), cne);
+ } finally {
+ taskMonitor.setPercentCompleted(100);
+ }
+ }
+
+ private void setErrorMessage(String em) {
+ errorMsg = em;
+ }
+
+ public String getErrorMessage() {
+ return errorMsg;
+ }
+
+ public DownloadableInfo getDownloadedPlugin() {
+ return infoObj;
+ }
+
+ public void halt() {
+ // not haltable
+ }
+
+ public void setTaskMonitor(TaskMonitor monitor)
+ throws IllegalThreadStateException {
+ this.taskMonitor = monitor;
+ }
+
+ public String getTitle() {
+ return "Installing Cytoscape Theme: '" + infoObj.getName() + "'"; }
+
+ }
+
+
+
+
+}
diff --git a/application/src/main/java/cytoscape/data/writers/CyAttributesWriter.java b/application/src/main/java/cytoscape/data/writers/CyAttributesWriter.java
new file mode 100644
index 0000000..cc9757e
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/writers/CyAttributesWriter.java
@@ -0,0 +1,241 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data.writers;
+
+import cytoscape.data.CyAttributes;
+
+import cytoscape.data.attr.MultiHashMap;
+import cytoscape.data.attr.MultiHashMapDefinition;
+
+import java.io.IOException;
+import java.io.UnsupportedEncodingException;
+import java.io.Writer;
+
+import java.net.URLEncoder;
+import java.util.Collection;
+import java.util.Iterator;
+import java.util.List;
+
+
+/**
+ * CyAttributeWriter extracted from AttributeSaverDialog.
+ *
+ */
+public class CyAttributesWriter {
+ /**
+ *
+ */
+ public static String newline = System.getProperty("line.separator");
+ public static final String ENCODE_PROPERTY = "cytoscape.encode.attributes";
+
+ public static final String ENCODING_SCHEME = "UTF-8";
+ private final CyAttributes cyAttributes;
+ private final String attributeName;
+ private Writer fileWriter;
+ private boolean doEncoding;
+
+ /**
+ * Creates a new CyAttributesWriter2 object.
+ *
+ * @param attributes DOCUMENT ME!
+ * @param attributeName DOCUMENT ME!
+ * @param fileWriter DOCUMENT ME!
+ */
+ public CyAttributesWriter(final CyAttributes attributes, final String attributeName,
+ final Writer fileWriter) {
+ this.cyAttributes = attributes;
+ this.attributeName = attributeName;
+ this.fileWriter = fileWriter;
+ doEncoding = Boolean.valueOf(System.getProperty(ENCODE_PROPERTY, "true"));
+ }
+
+ /**
+ * Write out the state for the given attributes
+ *
+ * @param selectedRows
+ *
+ * @return number of files successfully saved, the better way to do this
+ * would just be to throw the error and display a specific message
+ * for each failure, but oh well.
+ * @throws IOException
+ *
+ */
+ public void writeAttributes() throws IOException {
+ final String className;
+ final byte dataType = cyAttributes.getMultiHashMapDefinition()
+ .getAttributeValueType(attributeName);
+
+ if ((dataType == CyAttributes.TYPE_COMPLEX) || (dataType == CyAttributes.TYPE_SIMPLE_MAP)
+ || (dataType == CyAttributes.TYPE_UNDEFINED))
+ throw new IOException("Unsupported Datatype.");
+
+ if (dataType == MultiHashMapDefinition.TYPE_BOOLEAN)
+ className = "java.lang.Boolean";
+ else if (dataType == MultiHashMapDefinition.TYPE_INTEGER)
+ className = "java.lang.Integer";
+ else if (dataType == MultiHashMapDefinition.TYPE_FLOATING_POINT)
+ className = "java.lang.Double";
+ else
+ className = "java.lang.String";
+
+ try {
+ fileWriter.write(attributeName + " (class=" + className + ")" + newline);
+
+ final MultiHashMap attributeMap = cyAttributes.getMultiHashMap();
+
+ if (attributeMap != null) {
+ final Iterator<String> keys = cyAttributes.getMultiHashMap().getObjectKeys(attributeName);
+
+ String key;
+ Object value;
+ Iterator objIt;
+ String vs;
+ StringBuilder result = new StringBuilder();
+
+ while (keys.hasNext()) {
+ key = keys.next();
+
+ if (cyAttributes.getType(attributeName) == CyAttributes.TYPE_SIMPLE_LIST)
+ value = cyAttributes.getListAttribute(key, attributeName);
+ else
+ value = cyAttributes.getAttribute(key, attributeName);
+
+ key = encodeString(key);
+
+ if (value != null) {
+ if (value instanceof List) {
+ result.append(key + " = ");
+
+ if (((Collection) value).size() > 0) {
+ Object o;
+
+ objIt = ((Collection) value).iterator();
+ result.append("(");
+ o = objIt.next();
+ vs = o.toString();
+ vs = slashEncodeString(vs);
+ vs = encodeString(vs);
+ result.append(vs);
+
+ while (objIt.hasNext()) {
+
+ o = objIt.next();
+ vs = o.toString();
+ vs = slashEncodeString(vs);
+ vs = encodeString(vs);
+ result.append("::" + vs);
+ }
+ result.append(")" + newline);
+ fileWriter.write(result.toString());
+ result = new StringBuilder();
+ }
+ } else {
+ vs = value.toString();
+ vs = slashEncodeString(vs);
+ vs = encodeString(vs);
+ fileWriter.write(key + " = " + vs + newline);
+ }
+ }
+ }
+
+ fileWriter.flush();
+ }
+ }
+ finally {
+ if (fileWriter != null) {
+ fileWriter.close();
+ }
+ }
+ }
+
+ private String encodeString(String in) throws UnsupportedEncodingException {
+ if (doEncoding) {
+ in = URLEncoder.encode(in, ENCODING_SCHEME);
+ }
+
+ return in;
+ }
+
+ private static String slashEncodeString(String in) {
+ StringBuilder sb;
+
+ sb = new StringBuilder(in.length());
+ for (int i = 0; i < in.length(); i++) {
+ char c;
+
+ c = in.charAt(i);
+ switch (c) {
+ case '\n': {
+ sb.append("\\n");
+ break;
+ }
+ case '\t': {
+ sb.append("\\t");
+ break;
+ }
+ case '\b': {
+ sb.append("\\b");
+ break;
+ }
+ case '\r': {
+ sb.append("\\r");
+ break;
+ }
+ case '\f': {
+ sb.append("\\f");
+ break;
+ }
+ case '\\': {
+ sb.append("\\\\");
+ break;
+ }
+ default : {
+ sb.append(c);
+ break;
+ }
+ }
+ }
+
+ return sb.toString();
+ }
+
+ public boolean isDoEncoding() {
+ return doEncoding;
+ }
+
+ public void setDoEncoding(boolean doEnc) {
+ doEncoding = doEnc;
+ }
+}
diff --git a/application/src/main/java/cytoscape/data/writers/CytoscapeSessionWriter.java b/application/src/main/java/cytoscape/data/writers/CytoscapeSessionWriter.java
new file mode 100644
index 0000000..e7a0a9e
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/writers/CytoscapeSessionWriter.java
@@ -0,0 +1,1056 @@
+/*
+ File: CytoscapeSessionWriter.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.data.writers;
+
+import giny.view.EdgeView;
+import giny.view.NodeView;
+
+import java.awt.Component;
+import java.awt.Image;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.OutputStreamWriter;
+import java.io.Writer;
+import java.math.BigInteger;
+import java.net.URISyntaxException;
+import java.net.URL;
+import java.text.DateFormat;
+import java.text.SimpleDateFormat;
+import java.util.Collection;
+import java.util.Date;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Properties;
+import java.util.Set;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipOutputStream;
+
+import javax.imageio.ImageIO;
+import javax.swing.JInternalFrame;
+import javax.swing.SwingConstants;
+import javax.swing.tree.DefaultMutableTreeNode;
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBException;
+import javax.xml.bind.Marshaller;
+import javax.xml.stream.XMLStreamException;
+
+import com.sun.xml.bind.marshaller.NamespacePrefixMapper;
+
+import cytoscape.CyEdge;
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+import cytoscape.CytoscapeInit;
+import cytoscape.bookmarks.Bookmarks;
+import cytoscape.data.Semantics;
+import cytoscape.generated.Child;
+import cytoscape.generated.Cysession;
+import cytoscape.generated.Cytopanel;
+import cytoscape.generated.Cytopanels;
+import cytoscape.generated.Desktop;
+import cytoscape.generated.DesktopSize;
+import cytoscape.generated.HiddenEdges;
+import cytoscape.generated.HiddenNodes;
+import cytoscape.generated.Network;
+import cytoscape.generated.NetworkFrame;
+import cytoscape.generated.NetworkFrames;
+import cytoscape.generated.NetworkTree;
+import cytoscape.generated.Node;
+import cytoscape.generated.ObjectFactory;
+import cytoscape.generated.Ontology;
+import cytoscape.generated.OntologyServer;
+import cytoscape.generated.Panel;
+import cytoscape.generated.Panels;
+import cytoscape.generated.Parent;
+import cytoscape.generated.Plugins;
+import cytoscape.generated.SelectedEdges;
+import cytoscape.generated.SelectedNodes;
+import cytoscape.generated.Server;
+import cytoscape.generated.SessionState;
+import cytoscape.util.BookmarksUtil;
+import cytoscape.util.RecentlyOpenedTracker;
+import cytoscape.util.swing.JTreeTable;
+import cytoscape.view.CyNetworkView;
+import cytoscape.view.CytoscapeDesktop;
+import cytoscape.view.NetworkPanel;
+import cytoscape.visual.CalculatorCatalog;
+import cytoscape.visual.CalculatorIO;
+import cytoscape.visual.VisualMappingManager;
+import cytoscape.visual.VisualStyle;
+import cytoscape.visual.customgraphic.CustomGraphicsManager;
+import cytoscape.visual.customgraphic.CyCustomGraphics;
+import cytoscape.visual.customgraphic.ImageUtil;
+import cytoscape.visual.customgraphic.NullCustomGraphics;
+import cytoscape.visual.customgraphic.impl.bitmap.URLImageCustomGraphics;
+
+
+/**
+ * Write session states into files.<br>
+ * Basic functions of this class are:<br>
+ * <ul>
+ * <li> 1. Create network files</li>
+ * <li> 2. Create session state file</li>
+ * <li> 3. Get properties file locations</li>
+ * <li> 4. Zip them into one session file "*.cys" </li>
+ * </ul>
+ *
+ * @version 1.0
+ * @since 2.3
+ * @see cytoscape.data.readers.XGMMLReader
+ * @author kono
+ *
+ */
+public class CytoscapeSessionWriter {
+
+ // These values will be replaced.
+ private static final char[] INVALID_CHAR = {'[', '\\', '/', ':', '*', '?', '"', '<', '>', '|', ']'};
+
+ // cysession.xml document version
+ private static final String cysessionVersion = "0.9";
+
+ // Enumerate types (node & edge)
+ /**
+ *
+ */
+ public static final int NODE = 1;
+
+ /**
+ *
+ */
+ public static final int EDGE = 2;
+ private static final String DEFAULT_VS_NAME = "default";
+
+ // Number of Cytopanels. Currently, we have 3 panels.
+ private static final int CYTOPANEL_COUNT = 3;
+
+ // Name of CySession file.
+ private static final String CYSESSION_FILE_NAME = "cysession.xml";
+ private static final String VIZMAP_FILE = "session_vizmap.props";
+ private static final String CYPROP_FILE = "session_cytoscape.props";
+ private static final String BOOKMARKS_FILE = "session_bookmarks.xml";
+
+ // Extension for the xgmml file
+ private static final String XGMML_EXT = ".xgmml";
+
+ // Package name generated by JAXB.
+ // This file was created from "cysession.schema"
+ private final String packageName = "cytoscape.generated";
+
+ // Property files
+ Properties prop;
+
+ // Root of the network tree
+ private static final String TREE_ROOT = "root";
+
+ // File name for the session
+ private String sessionFileName = null;
+ private Bookmarks bookmarks;
+ private Set<CyNetwork> networks;
+ private HashMap networkMap;
+ private String sessionNote = "You can add note for this session here.";
+
+ //
+ // The following JAXB-generated objects are for CySession.xml file.
+ //
+ private ObjectFactory factory;
+ private Cysession session;
+ private NetworkTree tree;
+ private SessionState sState;
+ private List netList;
+ private Cytopanels cps;
+ private Plugins plugins;
+ private String sessionDirName;
+ private String sessionDir;
+ private Map viewMap = Cytoscape.getNetworkViewMap();
+ private ZipOutputStream zos;
+
+ /**
+ * Constructor.
+ *
+ * @param sessionName
+ * Filename of the session.
+ */
+ public CytoscapeSessionWriter(String sessionName) {
+ this.sessionFileName = sessionName;
+
+ // For now, session ID is time and date
+ final DateFormat df = new SimpleDateFormat("yyyy_MM_dd-HH_mm");
+ sessionDirName = "CytoscapeSession-" + df.format(new Date());
+ sessionDir = sessionDirName + "/";
+
+ // Get all networks in the session
+ networks = Cytoscape.getNetworkSet();
+ networkMap = new HashMap();
+ }
+
+ /**
+ * Write current session to a local .cys file.
+ *
+ * @throws Exception
+ *
+ */
+ public void writeSessionToDisk() throws Exception {
+ FileOutputStream fos = null;
+
+ try {
+ fos = new FileOutputStream(sessionFileName);
+
+ final RecentlyOpenedTracker sessionTracker =
+ Cytoscape.getRecentlyOpenedSessionTracker();
+ if (sessionTracker != null) {
+ final URL sessionFileNameAsURL;
+ try {
+ sessionFileNameAsURL = new URL("file://" + sessionFileName);
+ sessionTracker.add(sessionFileNameAsURL);
+ } catch (final Exception e) {
+ System.err.println("Could not convert \"file://" + sessionFileName + "\" to a URL!");
+ }
+ }
+
+ try {
+ zos = new ZipOutputStream(fos);
+
+ for (CyNetwork network : networks)
+ zipNetwork(network);
+ zipCySession();
+ zipVizmapProps();
+ zipCytoscapeProps();
+ zipBookmarks();
+ zipFileListMap();
+ zipCustomGraphics();
+ }
+ finally {
+ if (zos != null) {
+ zos.close();
+ }
+ }
+ }
+ finally {
+ if (fos != null) {
+ fos.close();
+ }
+ }
+
+ Cytoscape.firePropertyChange(Cytoscape.SESSION_SAVED, null, null);
+ }
+
+
+ /**
+ * Utility to replace invalid chars in the XGMML file name.<br>
+ *
+ * @param fileName
+ * Original file name directly taken from the title.
+ * @return Modified file name without invalid chars.
+ *
+ */
+ private String getValidFileName(String fileName) {
+
+ String newFileName = fileName;
+ Integer i = 0;
+ for(Character ch : INVALID_CHAR)
+ newFileName = newFileName.replace(ch.toString(), (i++).toString());
+
+ return newFileName;
+ }
+
+ /**
+ * Initialize objects for the marshaller.
+ *
+ * @throws JAXBException
+ */
+ private void initObjectsForDataBinding() throws JAXBException {
+ factory = new ObjectFactory();
+
+ session = factory.createCysession();
+ session.setSessionNote(sessionNote);
+
+ tree = factory.createNetworkTree();
+ sState = factory.createSessionState();
+ setDesktopStates();
+ session.setSessionState(sState);
+ cps = getCytoPanelStates();
+ netList = tree.getNetwork();
+ sState.setPlugins(plugins);
+ sState.setCytopanels(cps);
+ sState.setServer(getServerState());
+ }
+
+ private void setDesktopStates() throws JAXBException {
+ DesktopSize dSize = factory.createDesktopSize();
+ NetworkFrames frames = factory.createNetworkFrames();
+ Component[] networkFrames = Cytoscape.getDesktop().getNetworkViewManager().getDesktopPane()
+ .getComponents();
+
+ for (int i = 0; i < networkFrames.length; i++) {
+ if(networkFrames[i] instanceof JInternalFrame) {
+ JInternalFrame networkFrame = (JInternalFrame) networkFrames[i];
+ NetworkFrame frame = factory.createNetworkFrame();
+ frame.setFrameID(networkFrame.getTitle());
+ frame.setWidth(BigInteger.valueOf(networkFrame.getWidth()));
+ frame.setHeight(BigInteger.valueOf(networkFrame.getHeight()));
+ frame.setX(BigInteger.valueOf(networkFrame.getX()));
+ frame.setY(BigInteger.valueOf(networkFrame.getY()));
+ frames.getNetworkFrame().add(frame);
+ }
+ }
+
+ dSize.setHeight(BigInteger.valueOf(Cytoscape.getDesktop().getSize().height));
+ dSize.setWidth(BigInteger.valueOf(Cytoscape.getDesktop().getSize().width));
+
+ Desktop desktop = factory.createDesktop();
+ desktop.setDesktopSize(dSize);
+ desktop.setNetworkFrames(frames);
+ sState.setDesktop(desktop);
+ }
+
+ /**
+ * Writes the vizmap.props file to the session zip.
+ */
+ private void zipVizmapProps() throws IOException {
+
+ VisualMappingManager vizmapper = Cytoscape.getVisualMappingManager();
+ CalculatorCatalog catalog = vizmapper.getCalculatorCatalog();
+
+ zos.putNextEntry(new ZipEntry(sessionDir + VIZMAP_FILE) );
+
+ Writer writer = new OutputStreamWriter( zos );
+ CalculatorIO.storeCatalog(catalog, writer);
+ }
+
+ /**
+ * Writes the cytoscape.props file to the session zip.
+ */
+ private void zipCytoscapeProps() throws IOException {
+
+ zos.putNextEntry(new ZipEntry(sessionDir + CYPROP_FILE) );
+
+ CytoscapeInit.getProperties().store(zos, "Cytoscape Property File");
+ }
+
+ /**
+ * Writes the bookmarks.xml file to the session zip.
+ */
+ private void zipBookmarks() throws IOException, JAXBException {
+
+ zos.putNextEntry(new ZipEntry(sessionDir + BOOKMARKS_FILE) );
+
+ bookmarks = Cytoscape.getBookmarks();
+ BookmarksUtil.saveBookmark(bookmarks, zos);
+ }
+
+
+ /**
+ * Create archive of Custom Graphics.
+ *
+ * @throws IOException
+ * @throws InterruptedException
+ */
+ private void zipCustomGraphics() throws IOException, InterruptedException {
+
+ final CustomGraphicsManager pool = Cytoscape.getVisualMappingManager().getCustomGraphicsManager();
+
+ // Collect all custom graphics
+ final Collection<CyCustomGraphics> customGraphics = pool.getAll();
+
+ final Properties graphicsProps = new Properties();
+ for(CyCustomGraphics cg: customGraphics) {
+ // Save only images used in current session.
+ if(pool.isUsedInCurrentSession(cg) == false)
+ continue;
+ else
+ graphicsProps.setProperty(cg.getIdentifier().toString(), cg.toString());
+
+ final Image img = cg.getRenderedImage();
+ // For now, save URLImage only.
+ // TODO: how can we handle Dynamic Images?
+ if(img != null && cg instanceof NullCustomGraphics == false && cg instanceof URLImageCustomGraphics) {
+ final Long id= cg.getIdentifier();
+ zos.putNextEntry(new ZipEntry(sessionDir + "images/" + id + ".png"));
+ ImageIO.write(ImageUtil.toBufferedImage(img), "PNG", zos);
+ }
+ }
+
+ // Add metadata file to the session file
+ zos.putNextEntry(new ZipEntry(sessionDir + "images/" + CustomGraphicsManager.METADATA_FILE));
+ graphicsProps.store(zos, "Image Metadata");
+ }
+
+
+ /**
+ * Writes a network file to the session zip.
+ *
+ * @throws URISyntaxException
+ * @throws JAXBException
+ * @throws XMLStreamException
+ */
+ private void zipNetwork(final CyNetwork network)
+ throws IOException, JAXBException, URISyntaxException {
+
+ String xgmmlFile = getValidFileName( network.getTitle() + XGMML_EXT );
+ CyNetworkView view = Cytoscape.getNetworkView(network.getIdentifier());
+
+ zos.putNextEntry(new ZipEntry(sessionDir + xgmmlFile));
+
+ Writer writer = new OutputStreamWriter(zos, "UTF-8");
+ // Write the XGMML file *without* our graphics attributes
+ // We'll let the Vizmapper handle those
+ XGMMLWriter xgmmlWriter = new XGMMLWriter(network, view, true);
+ xgmmlWriter.write(writer);
+ }
+
+ /**
+ * Create cysession.xml file.
+ *
+ * @throws Exception
+ */
+ private void zipCySession() throws Exception {
+ final JAXBContext jc = JAXBContext.newInstance(packageName, this.getClass().getClassLoader());
+
+ initObjectsForDataBinding();
+ session.setId(sessionDirName);
+
+ // Document version. Maybe used in the future.
+ session.setDocumentVersion(cysessionVersion);
+
+ getNetworkTree();
+ session.setNetworkTree(tree);
+
+ Marshaller m = jc.createMarshaller();
+ m.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, Boolean.TRUE);
+ m.setProperty("com.sun.xml.bind.namespacePrefixMapper",
+ new NamespacePrefixMapperForCysession());
+
+ zos.putNextEntry(new ZipEntry(sessionDir + CYSESSION_FILE_NAME) );
+
+ m.marshal(session, zos);
+ session = null;
+ }
+
+ /**
+ * Writes any files from plugins to the session file.
+ *
+ * @throws IOException
+ */
+ private void zipFileListMap() throws IOException {
+
+ // fire an event to tell plugins we're ready to save!
+ Map<String, List<File>> pluginFileMap = new HashMap<String, List<File>>();
+ Cytoscape.firePropertyChange(Cytoscape.SAVE_PLUGIN_STATE, pluginFileMap, null);
+
+ // now write any files to the zip files
+ if ((pluginFileMap != null) && (pluginFileMap.size() > 0)) {
+ byte[] buf = new byte[5000];
+ Set<String> pluginSet = pluginFileMap.keySet();
+
+ for (String pluginName : pluginSet) {
+ List<File> theFileList = (List<File>) pluginFileMap.get(pluginName);
+
+ if ((theFileList == null) || (theFileList.size() == 0))
+ continue;
+
+ for (File theFile : theFileList) {
+ if ((theFile == null) || (!theFile.exists()))
+ continue;
+
+ zos.putNextEntry(new ZipEntry( sessionDir + "plugins/" + pluginName +
+ "/" + theFile.getName() ) );
+
+ // copy the file contents to the zip output stream
+ FileInputStream fileIS = null;
+ try {
+ fileIS = new FileInputStream(theFile);
+ int numRead = 0;
+ while ((numRead = fileIS.read(buf)) > -1) {
+ zos.write(buf, 0, numRead);
+ }
+ }
+ finally {
+ if (fileIS != null) {
+ fileIS.close();
+ }
+ }
+ }
+ }
+ }
+ }
+
+ /**
+ * Get information about the current session status.
+ *
+ * This includes the following: 1. List of networks opened/created by the
+ * user. 2. Status of the network. 3. relationship between
+ * network-attributes Build GML file into xml
+ *
+ * Extract current NetworkPanel state for saving.
+ */
+ private void getNetworkTree() throws Exception {
+ // Tree table storeed in the Network Panel
+ JTreeTable treeTable;
+
+ // Get network panel
+ CytoscapeDesktop cyDesktop = Cytoscape.getDesktop();
+ NetworkPanel netPanel = cyDesktop.getNetworkPanel();
+
+ // Get list of networks
+ treeTable = netPanel.getTreeTable();
+
+ Iterator itr = networks.iterator();
+
+ // Visit each node in the tree
+ while (itr.hasNext()) {
+ CyNetwork network = (CyNetwork) itr.next();
+ String networkID = network.getIdentifier();
+ String networkName = network.getTitle();
+
+ networkMap.put(networkName, networkID);
+ }
+
+ if (treeTable != null) {
+ // Extract root node in the tree
+ DefaultMutableTreeNode root = (DefaultMutableTreeNode) netPanel.getNetworkNode(TREE_ROOT);
+
+ walkTree(root);
+ }
+ }
+
+ /**
+ * Visit all tree node and save the status in the model.
+ *
+ * @param node
+ * @throws JAXBException
+ */
+ private void walkTree(DefaultMutableTreeNode node) throws JAXBException {
+ // Check number of children for this node.
+ int childCount = node.getChildCount();
+
+ // Create Network object for this node.
+ String fileName = node.getUserObject().toString() + XGMML_EXT;
+ Network curNode = factory.createNetwork();
+ curNode.setFilename(getValidFileName(fileName));
+ curNode.setId(node.getUserObject().toString());
+
+ CyNetwork curNet = Cytoscape.getNetwork((String) networkMap.get(node.getUserObject()
+ .toString()));
+ CyNetworkView curView = (CyNetworkView) viewMap.get(curNet.getIdentifier());
+
+ if (!node.getUserObject().toString().equals("Network Root")) {
+ String visualStyleName = null;
+
+ if (curView != null) {
+ VisualStyle curVS = curView.getVisualStyle();
+
+ if (curVS != null) {
+ visualStyleName = curVS.getName();
+ }
+ }
+
+ if (visualStyleName == null) {
+ visualStyleName = DEFAULT_VS_NAME;
+ }
+
+ curNode.setVisualStyle(visualStyleName);
+ } else {
+ curNode.setVisualStyle(DEFAULT_VS_NAME);
+ }
+
+ if (Cytoscape.getNetworkView((String) networkMap.get(node.getUserObject().toString())) == Cytoscape
+ .getNullNetworkView()) {
+ curNode.setViewAvailable(false);
+ } else {
+ curNode.setViewAvailable(true);
+ }
+
+ Parent parent = null;
+ parent = factory.createParent();
+
+ if (node.getParent() == null) {
+ parent.setId("NULL");
+ curNode.setParent(parent);
+ } else {
+ // Set current network as the parent of child networks.
+ DefaultMutableTreeNode curParent = (DefaultMutableTreeNode) node.getParent();
+ parent.setId(curParent.getUserObject().toString());
+ curNode.setParent(parent);
+ }
+
+ List children = curNode.getChild();
+
+ for (int i = 0; i < childCount; i++) {
+ // Exctract a network from the Network Panel.
+ DefaultMutableTreeNode child = (DefaultMutableTreeNode) node.getChildAt(i);
+
+ // Create Child object
+ Child childNetwork = factory.createChild();
+ childNetwork.setId(child.getUserObject().toString());
+ children.add(childNetwork);
+
+ if (child.isLeaf()) {
+ // Reached to the leaf of network tree.
+ // Need to create leaf node here.
+ Network leaf = factory.createNetwork();
+ String childFileName = child.getUserObject().toString() + XGMML_EXT;
+ leaf.setFilename(getValidFileName(childFileName));
+ leaf.setId(child.getUserObject().toString());
+
+ CyNetworkView leafView = Cytoscape.getNetworkView((String) networkMap.get(child.getUserObject()
+ .toString()));
+
+ String leafVisualStyleName = null;
+
+ if (leafView != Cytoscape.getNullNetworkView()) {
+ VisualStyle leafVS = leafView.getVisualStyle();
+
+ if (leafVS != null) {
+ leafVisualStyleName = leafVS.getName();
+ }
+ }
+
+ if (leafVisualStyleName == null) {
+ leafVisualStyleName = DEFAULT_VS_NAME;
+ }
+
+ leaf.setVisualStyle(leafVisualStyleName);
+
+ String targetID = (String) networkMap.get(child.getUserObject().toString());
+
+ Parent tempParent = factory.createParent();
+ tempParent.setId(curNode.getId());
+ leaf.setParent(tempParent);
+
+ CyNetwork targetNetwork = Cytoscape.getNetwork(targetID);
+ CyNetworkView curNetworkView = Cytoscape.getNetworkView(targetID);
+
+ if (curNetworkView == Cytoscape.getNullNetworkView()) {
+ leaf.setViewAvailable(false);
+ } else {
+ leaf.setViewAvailable(true);
+ }
+
+ /*
+ * This is for Metanode. Will be used in the future...
+ *
+ * Iterator it = targetNetwork.nodesIterator(); ViewableNodes vn =
+ * factory.createViewableNodes(); while (it.hasNext()) { String
+ * viewableID = ((CyNode) it.next()) .getIdentifier(); Node
+ * viewableNode = factory.createNode();
+ * viewableNode.setId(viewableID);
+ * vn.getNode().add(viewableNode); } leaf.setViewableNodes(vn);
+ */
+
+ /*
+ * Add selected & hidden nodes/edges foe leaf nodes.
+ */
+ SelectedNodes sn = (SelectedNodes) getSelectedObjects(NODE, targetNetwork);
+
+ if (sn != null) {
+ leaf.setSelectedNodes(sn);
+ }
+
+ SelectedEdges se = (SelectedEdges) getSelectedObjects(EDGE, targetNetwork);
+
+ if (se != null) {
+ leaf.setSelectedEdges(se);
+ }
+
+ HiddenNodes hn = (HiddenNodes) getHiddenObjects(NODE, curNetworkView);
+ HiddenEdges he = (HiddenEdges) getHiddenObjects(EDGE, curNetworkView);
+
+ if (hn != null) {
+ leaf.setHiddenNodes(hn);
+ }
+
+ if (he != null) {
+ leaf.setHiddenEdges(he);
+ }
+
+ netList.add(leaf);
+ } else {
+ walkTree(child);
+ }
+ }
+
+ //
+ // Add hidden/selected nodes and edges
+ //
+ String targetID = (String) networkMap.get(node.getUserObject().toString());
+ CyNetwork targetNetwork = Cytoscape.getNetwork(targetID);
+
+ /*
+ * This is for metanode. will be used in the future.
+ *
+ * if (curNode.getId() != "Network Root") { Iterator it =
+ * targetNetwork.nodesIterator(); ViewableNodes vn =
+ * factory.createViewableNodes(); while (it.hasNext()) {
+ *
+ * String viewableID = ((CyNode) it.next()).getIdentifier(); Node
+ * viewableNode = factory.createNode(); viewableNode.setId(viewableID);
+ * vn.getNode().add(viewableNode); } curNode.setViewableNodes(vn); }
+ */
+ SelectedNodes sn = (SelectedNodes) getSelectedObjects(NODE, targetNetwork);
+
+ if (sn != null) {
+ curNode.setSelectedNodes(sn);
+ }
+
+ SelectedEdges se = (SelectedEdges) getSelectedObjects(EDGE, targetNetwork);
+
+ if (se != null) {
+ curNode.setSelectedEdges(se);
+ }
+
+ // Extract hidden nodes and edges
+ CyNetworkView curNetworkView = Cytoscape.getNetworkView(targetID);
+
+ if (curNetworkView != Cytoscape.getNullNetworkView()) {
+ HiddenNodes hn = (HiddenNodes) getHiddenObjects(NODE, curNetworkView);
+ HiddenEdges he = (HiddenEdges) getHiddenObjects(EDGE, curNetworkView);
+
+ if (hn != null) {
+ curNode.setHiddenNodes(hn);
+ }
+
+ if (he != null) {
+ curNode.setHiddenEdges(he);
+ }
+ }
+
+ // Add current network to the list.
+ netList.add(curNode);
+ }
+
+ /**
+ *
+ * @param type
+ * Type of the object (node or edge)
+ * @param view
+ * Current network view.
+ * @return JAXB object (HiddenNodes or HiddenEdges)
+ * @throws JAXBException
+ */
+ private Object getHiddenObjects(int type, CyNetworkView view) throws JAXBException {
+ // List-up all hidden nodes
+ if (type == NODE) {
+ HiddenNodes hn = factory.createHiddenNodes();
+ List hNodeList = hn.getNode();
+
+ CyNode targetNode = null;
+ String curNodeName = null;
+
+ for (Iterator i = view.getNodeViewsIterator(); i.hasNext();) {
+ NodeView nview = (NodeView) i.next();
+
+ // Check if the node is hidden or not.
+ // If it's hidden, store in the session file.
+ if (view.showGraphObject(nview)) {
+ targetNode = (CyNode) nview.getNode();
+ curNodeName = targetNode.getIdentifier();
+
+ Node tempNode = factory.createNode();
+ tempNode.setId(curNodeName);
+
+ hNodeList.add(tempNode);
+
+ // Keep them hidden...
+ view.hideGraphObject(nview);
+ }
+ }
+
+ if (hn.getNode().size() != 0) {
+ return hn;
+ } else {
+ return null;
+ }
+ } else if (type == EDGE) {
+ HiddenEdges he = factory.createHiddenEdges();
+ List hEdgeList = he.getEdge();
+
+ CyEdge targetEdge = null;
+ String curEdgeName = null;
+
+ for (Iterator i = view.getEdgeViewsIterator(); i.hasNext();) {
+ EdgeView eview = (EdgeView) i.next();
+
+ // Check if the edge is hidden or not.
+ // If it's hidden, store in the session file.
+ if (view.showGraphObject(eview)) {
+ targetEdge = (CyEdge) eview.getEdge();
+ curEdgeName = targetEdge.getIdentifier();
+
+ cytoscape.generated.Edge tempEdge = factory.createEdge();
+ tempEdge.setId(curEdgeName);
+ tempEdge.setSource(targetEdge.getSource().getIdentifier());
+ tempEdge.setTarget(targetEdge.getTarget().getIdentifier());
+ tempEdge.setInteraction(Cytoscape.getEdgeAttributes()
+ .getStringAttribute(targetEdge.getIdentifier(),
+ Semantics.INTERACTION));
+ hEdgeList.add(tempEdge);
+ // Keep them hidden...
+ view.hideGraphObject(eview);
+ }
+ }
+
+ if (he.getEdge().size() != 0) {
+ return he;
+ } else {
+ return null;
+ }
+ }
+
+ return null;
+ }
+
+ /**
+ * List all selected nodes and edges in the session file.
+ *
+ * @param type
+ * Tyoe if object (node or edge)
+ * @param curNet
+ * Current network
+ * @return
+ * @throws JAXBException
+ */
+ private Object getSelectedObjects(int type, CyNetwork curNet) throws JAXBException {
+ if (type == NODE) {
+ SelectedNodes sn = factory.createSelectedNodes();
+ List sNodeList = sn.getNode();
+
+ Set selectedNodes = curNet.getSelectedNodes();
+
+ if (selectedNodes.size() != 0) {
+ Iterator iterator = selectedNodes.iterator();
+ CyNode targetNode = null;
+
+ while (iterator.hasNext()) {
+ targetNode = (CyNode) iterator.next();
+
+ String curNodeName = targetNode.getIdentifier();
+ Node tempNode = factory.createNode();
+ tempNode.setId(curNodeName);
+
+ sNodeList.add(tempNode);
+ }
+
+ return sn;
+ } else {
+ return null;
+ }
+ } else if (type == EDGE) {
+ SelectedEdges se = factory.createSelectedEdges();
+ List sEdgeList = se.getEdge();
+
+ Set selectedEdges = curNet.getSelectedEdges();
+
+ if (selectedEdges.size() != 0) {
+ Iterator iterator = selectedEdges.iterator();
+ CyEdge targetEdge = null;
+
+ while (iterator.hasNext()) {
+ targetEdge = (CyEdge) iterator.next();
+
+ String curEdgeName = targetEdge.getIdentifier();
+ cytoscape.generated.Edge tempEdge = factory.createEdge();
+ tempEdge.setId(curEdgeName);
+ tempEdge.setSource(targetEdge.getSource().getIdentifier());
+ tempEdge.setTarget(targetEdge.getTarget().getIdentifier());
+ tempEdge.setInteraction(Cytoscape.getEdgeAttributes()
+ .getStringAttribute(targetEdge.getIdentifier(),
+ Semantics.INTERACTION));
+ sEdgeList.add(tempEdge);
+ }
+
+ return se;
+ } else {
+ return null;
+ }
+ }
+
+ return null;
+ }
+
+ /**
+ * Extract states of the 3 Cytopanels.
+ *
+ * @return
+ * @throws JAXBException
+ *
+ * Note: We will store the states of plugins near future. The location of
+ * those states will be stored here.
+ */
+ private Cytopanels getCytoPanelStates() throws JAXBException {
+ Cytopanels cps = factory.createCytopanels();
+ List cytoPanelList = cps.getCytopanel();
+
+ String[] cytopanelStates = new String[CYTOPANEL_COUNT + 1];
+ int[] selectedPanels = new int[CYTOPANEL_COUNT + 1];
+
+ // Extract states of 3 panels.
+ cytopanelStates[1] = Cytoscape.getDesktop().getCytoPanel(SwingConstants.WEST).getState()
+ .toString();
+ selectedPanels[1] = Cytoscape.getDesktop().getCytoPanel(SwingConstants.WEST)
+ .getSelectedIndex();
+
+ cytopanelStates[2] = Cytoscape.getDesktop().getCytoPanel(SwingConstants.SOUTH).getState()
+ .toString();
+ selectedPanels[2] = Cytoscape.getDesktop().getCytoPanel(SwingConstants.SOUTH)
+ .getSelectedIndex();
+
+ cytopanelStates[3] = Cytoscape.getDesktop().getCytoPanel(SwingConstants.EAST).getState()
+ .toString();
+ selectedPanels[3] = Cytoscape.getDesktop().getCytoPanel(SwingConstants.EAST)
+ .getSelectedIndex();
+
+ for (int i = 1; i < (CYTOPANEL_COUNT + 1); i++) {
+ Panels internalPanels = factory.createPanels();
+ List iPanelList = internalPanels.getPanel();
+ Panel iPanel = factory.createPanel();
+ iPanel.setId("test");
+
+ iPanelList.add(iPanel);
+
+ Cytopanel curCp = factory.createCytopanel();
+ curCp.setId("CytoPanel" + i);
+ curCp.setPanelState(cytopanelStates[i]);
+ curCp.setSelectedPanel(Integer.toString(selectedPanels[i]));
+ curCp.setPanels(internalPanels);
+ cytoPanelList.add(curCp);
+ }
+
+ return cps;
+ }
+
+ /**
+ * Set session note.<br>
+ * Session note can be anything, it is just like a memo pad for the session.
+ * NOTE: session note should be set before calling writeSessionToDisk().
+ *
+ * @param note
+ * Session note string.
+ * @uml.property name="sessionNote"
+ */
+ public void setSessionNote(String note) {
+ this.sessionNote = note;
+ }
+
+ /**
+ * Check loaded ontologies and save those states in cysession.xml.
+ *
+ * @return Server object
+ */
+ private Server getServerState() {
+ Server server = factory.createServer();
+ OntologyServer os = factory.createOntologyServer();
+
+ Set<String> ontoNames = Cytoscape.getOntologyServer().getOntologyNames();
+ Map<String, URL> sources = Cytoscape.getOntologyServer().getOntologySources();
+
+ for (String name : ontoNames) {
+ Ontology onto = factory.createOntology();
+ onto.setName(name);
+ onto.setHref(sources.get(name).toString());
+ os.getOntology().add(onto);
+ }
+
+ server.setOntologyServer(os);
+
+ return server;
+ }
+}
+
+
+class NamespacePrefixMapperForCysession extends NamespacePrefixMapper {
+ /**
+ * Returns a preferred prefix for the given namespace URI.
+ *
+ * This method is intended to be overrided by a derived class.
+ *
+ * @param namespaceUri
+ * The namespace URI for which the prefix needs to be found.
+ * Never be null. "" is used to denote the default namespace.
+ * @param suggestion
+ * When the content tree has a suggestion for the prefix to the
+ * given namespaceUri, that suggestion is passed as a parameter.
+ * Typicall this value comes from the QName.getPrefix to show the
+ * preference of the content tree. This parameter may be null,
+ * and this parameter may represent an already occupied prefix.
+ * @param requirePrefix
+ * If this method is expected to return non-empty prefix. When
+ * this flag is true, it means that the given namespace URI
+ * cannot be set as the default namespace.
+ *
+ * @return null if there's no prefered prefix for the namespace URI. In this
+ * case, the system will generate a prefix for you.
+ *
+ * Otherwise the system will try to use the returned prefix, but generally
+ * there's no guarantee if the prefix will be actually used or not.
+ *
+ * return "" to map this namespace URI to the default namespace. Again,
+ * there's no guarantee that this preference will be honored.
+ *
+ * If this method returns "" when requirePrefix=true, the return value will
+ * be ignored and the system will generate one.
+ */
+ public String getPreferredPrefix(final String namespaceUri, final String suggestion,
+ boolean requirePrefix) {
+ // I want this namespace to be mapped to "xsi"
+ if ("http://www.w3.org/2001/XMLSchema-instance".equals(namespaceUri))
+ return "xsi";
+
+ // Xlink
+ if ("http://www.w3.org/1999/xlink".equals(namespaceUri)) {
+ return "xlink";
+ }
+
+ // otherwise I don't care. Just use the default suggestion, whatever it
+ // may be.
+ return suggestion;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String[] getPreDeclaredNamespaceUris() {
+ return new String[] {
+ "http://www.w3.org/2001/XMLSchema-instance", "http://www.w3.org/1999/xlink",
+ };
+ }
+}
diff --git a/application/src/main/java/cytoscape/data/writers/InteractionWriter.java b/application/src/main/java/cytoscape/data/writers/InteractionWriter.java
new file mode 100644
index 0000000..d8abe0e
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/writers/InteractionWriter.java
@@ -0,0 +1,160 @@
+/*
+ File: InteractionWriter.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data.writers;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+
+import cytoscape.data.CyAttributes;
+import cytoscape.data.Semantics;
+
+import cytoscape.task.TaskMonitor;
+
+import giny.model.Node;
+
+import java.io.IOException;
+import java.io.Writer;
+
+import java.util.Iterator;
+import java.util.List;
+
+
+/**
+ * A few utility methods to assist in writing SIF files.
+ */
+public class InteractionWriter {
+ /**
+ * Writes a SIF formatted string of the specified network to the specified writer.
+ * @param network The network to be written.
+ * @param writer The writer the network should be written to.
+ * @param taskMonitor An optional task monitor.
+ */
+ public static void writeInteractions(CyNetwork network, Writer writer, TaskMonitor taskMonitor)
+ throws IOException {
+ String sif = getInteractionString(network, taskMonitor);
+ writer.write(sif);
+ }
+
+ /**
+ * Writes a SIF formatted string of the specified network to the specified writer.
+ * @param network The network to be written.
+ * @param writer The writer the network should be written to.
+ */
+ public static void writeInteractions(CyNetwork network, Writer writer)
+ throws IOException {
+ writeInteractions(network, writer, null);
+ }
+
+ /**
+ * Returns a SIF formatted string of the specified network.
+ * @param network The network to be formatted as a SIF string.
+ * @return A string of a CyNetwork in SIF format.
+ */
+ public static String getInteractionString(CyNetwork network) {
+ return getInteractionString(network, null);
+ }
+
+ /**
+ * Returns a SIF formatted string of the specified network.
+ * @param network The network to be formatted as a SIF string.
+ * @param taskMonitor An optional taskMonitor in case you want to
+ * use one. Use null otherwise.
+ * @return A string of a CyNetwork in SIF format.
+ */
+ public static String getInteractionString(CyNetwork network, TaskMonitor taskMonitor) {
+ if (network == null) {
+ return "";
+ }
+
+ final StringBuilder sb = new StringBuilder();
+
+ final String lineSep = System.getProperty("line.separator");
+ final List<Node> nodeList = network.nodesList();
+
+ final CyAttributes edgeAtts = Cytoscape.getEdgeAttributes();
+ final Node[] nodes = (giny.model.Node[]) nodeList.toArray(new giny.model.Node[0]);
+
+ final int nodeCount = nodes.length;
+
+ for (int i = 0; i < nodeCount; i++) {
+ if (taskMonitor != null) {
+ // Report on Progress
+ double percent = ((double) i / nodes.length) * 100.0;
+ taskMonitor.setPercentCompleted((int) percent);
+ }
+
+ Node node = nodes[i];
+ String canonicalName = node.getIdentifier();
+ List edges = network.getAdjacentEdgesList(node, true, true, true);
+
+ if (edges.size() == 0) {
+ sb.append(canonicalName + lineSep);
+ } else {
+ Iterator it = edges.iterator();
+
+ while (it.hasNext()) {
+ giny.model.Edge edge = (giny.model.Edge) it.next();
+
+ if (node == edge.getSource()) { //do only for outgoing edges
+
+ giny.model.Node target = edge.getTarget();
+
+ String canonicalTargetName = target.getIdentifier();
+
+ String edgeName = edge.getIdentifier();
+
+ String interactionName = edgeAtts.getStringAttribute(edge.getIdentifier(),
+ Semantics.INTERACTION);
+
+ if (interactionName == null) {
+ interactionName = "xx";
+ }
+
+ sb.append(canonicalName);
+ sb.append("\t");
+ sb.append(interactionName);
+ sb.append("\t");
+ sb.append(canonicalTargetName);
+ sb.append(lineSep);
+ }
+ } // while
+ } // else: this node has edges, write out one line for every
+ } // for i
+
+ return sb.toString();
+ }
+}
diff --git a/application/src/main/java/cytoscape/data/writers/XGMMLWriter.java b/application/src/main/java/cytoscape/data/writers/XGMMLWriter.java
new file mode 100644
index 0000000..4950b10
--- /dev/null
+++ b/application/src/main/java/cytoscape/data/writers/XGMMLWriter.java
@@ -0,0 +1,1373 @@
+/*
+ File: XGMMLWriter.java
+
+ Copyright (c) 2006, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.data.writers;
+
+import giny.view.Bend;
+import giny.view.EdgeView;
+import giny.view.NodeView;
+
+import java.awt.BasicStroke;
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.Paint;
+import java.awt.geom.Point2D;
+import java.io.IOException;
+import java.io.Writer;
+import java.net.URISyntaxException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+
+import javax.xml.bind.JAXBException;
+
+import cytoscape.CyEdge;
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+import cytoscape.data.CyAttributes;
+import cytoscape.data.attr.MultiHashMap;
+import cytoscape.data.attr.MultiHashMapDefinition;
+import cytoscape.groups.CyGroup;
+import cytoscape.groups.CyGroupManager;
+import cytoscape.logger.CyLogger;
+import cytoscape.view.CyNetworkView;
+import cytoscape.visual.LineStyle;
+import cytoscape.visual.VisualPropertyDependency;
+import cytoscape.visual.VisualPropertyDependency.Definition;
+import cytoscape.visual.VisualStyle;
+
+import ding.view.DGraphView;
+import ding.view.DingCanvas;
+
+import org.cytoscape.equations.Equation;
+
+
+enum GraphicsType {
+ ARC("arc"),
+ BITMAP("bitmap"),
+ IMAGE("image"),
+ LINE("line"),
+ OVAL("oval"),
+ POLYGON("polygon"),
+ RECTANGLE("rectangle"),
+ TEXT("text"),
+ BOX("box"),
+ CIRCLE("circle"),
+ VER_ELLIPSIS("ver_ellipsis"),
+ HOR_ELLIPSIS("hor_ellipsis"),
+ RHOMBUS("rhombus"),
+ TRIANGLE("triangle"),
+ PENTAGON("pentagon"),
+ HEXAGON("hexagon"),
+ OCTAGON("octagon"),
+ ELLIPSE("ellipse"),
+ DIAMOND("diamond"),
+ PARALLELOGRAM("parallelogram"),
+ ROUNDED_RECTANGLE("rounded_rectangle"),
+ VEE("vee"),
+ ;
+
+ private final String value;
+
+ private GraphicsType(String v) {
+ value = v;
+ }
+
+ public String value() {
+ return value;
+ }
+}
+
+enum ObjectType {
+ LIST("list"),
+ STRING("string"),
+ REAL("real"),
+ INTEGER("integer"),
+ BOOLEAN("boolean"),
+ MAP("map"),
+ COMPLEX("complex");
+
+ private final String value;
+
+ ObjectType(String v) {
+ value = v;
+ }
+
+ String value() {
+ return value;
+ }
+
+ static ObjectType fromValue(String v) {
+ for (ObjectType c: ObjectType.values()) {
+ if (c.value.equals(v)) {
+ return c;
+ }
+ }
+ throw new IllegalArgumentException(v.toString());
+ }
+
+ public String toString() {
+ return value;
+ }
+}
+
+
+/**
+ *
+ * Write network and attributes in XGMML format and <br>
+ * marshall it in a streme.<br>
+ *
+ * @version 1.2
+ * @since Cytoscape 2.6
+ * @see cytoscape.data.readers.XGMMLReader
+ * @author kono
+ * @author scooter
+ *
+ */
+public class XGMMLWriter {
+ // XML preamble information
+ public static final String ENCODING = "UTF-8";
+ private static final String XML_STRING = "<?xml version=\"1.0\" encoding=\"" + ENCODING + "\" standalone=\"yes\"?>";
+
+ private static final String[] NAMESPACES = {
+ "xmlns:dc=\"http://purl.org/dc/elements/1.1/\"",
+ "xmlns:xlink=\"http://www.w3.org/1999/xlink\"",
+ "xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\"",
+ "xmlns:cy=\"http://www.cytoscape.org\"",
+ "xmlns=\"http://www.cs.rpi.edu/XGMML\""
+ };
+
+ // File format version. For compatibility.
+ private static final String FORMAT_VERSION = "documentVersion";
+ private static final float VERSION = (float) 1.1;
+ private static final String METADATA_NAME = "networkMetadata";
+ private static final String METADATA_ATTR_NAME = "Network Metadata";
+
+ // Node types
+ protected static final String NORMAL = "normal";
+ protected static final String METANODE = "group";
+ protected static final String REFERENCE = "reference";
+
+ // Object types
+ protected static final int NODE = 1;
+ protected static final int EDGE = 2;
+ protected static final int NETWORK = 3;
+
+ /**
+ *
+ */
+ public static final String BACKGROUND = "backgroundColor";
+
+ /**
+ *
+ */
+ public static final String GRAPH_VIEW_ZOOM = "GRAPH_VIEW_ZOOM";
+
+ /**
+ *
+ */
+ public static final String GRAPH_VIEW_CENTER_X = "GRAPH_VIEW_CENTER_X";
+
+ /**
+ *
+ */
+ public static final String GRAPH_VIEW_CENTER_Y = "GRAPH_VIEW_CENTER_Y";
+
+ /**
+ *
+ */
+ public static final String NODE_SIZE_LOCKED = "NODE_SIZE_LOCKED";
+
+ /**
+ *
+ */
+ public static final String ENCODE_PROPERTY = "cytoscape.encode.xgmml.attributes";
+
+ private CyAttributes nodeAttributes;
+ private CyAttributes edgeAttributes;
+ private CyAttributes networkAttributes;
+ private String[] nodeAttNames = null;
+ private String[] edgeAttNames = null;
+ private String[] networkAttNames = null;
+ private CyNetwork network;
+ private CyNetworkView networkView;
+ private HashMap <CyNode, CyNode>nodeMap;
+ private HashMap <CyEdge, CyEdge>edgeMap;
+ private boolean noCytoscapeGraphics = false;
+
+ private int depth = 0; // XML depth
+ private String indentString = "";
+ private Writer writer = null;
+ private CyLogger logger = CyLogger.getLogger(XGMMLWriter.class);
+
+ private boolean doFullEncoding;
+
+ /**
+ * Constructor.<br>
+ * Initialize data objects to be saved in XGMML file.<br>
+ *
+ * @param network
+ * CyNetwork object to be saved.
+ * @param view
+ * CyNetworkView for the network.
+ * @throws URISyntaxException
+ * @throws JAXBException
+ */
+ public XGMMLWriter(final CyNetwork network, final CyNetworkView view)
+ throws IOException, URISyntaxException {
+ this.network = network;
+ this.networkView = view;
+
+ nodeAttributes = Cytoscape.getNodeAttributes();
+ edgeAttributes = Cytoscape.getEdgeAttributes();
+ networkAttributes = Cytoscape.getNetworkAttributes();
+
+ nodeMap = new HashMap<CyNode, CyNode>();
+ edgeMap = new HashMap<CyEdge, CyEdge>();
+
+ nodeAttNames = nodeAttributes.getAttributeNames();
+ edgeAttNames = edgeAttributes.getAttributeNames();
+ networkAttNames = networkAttributes.getAttributeNames();
+
+ Arrays.sort(nodeAttNames);
+ Arrays.sort(edgeAttNames);
+ Arrays.sort(networkAttNames);
+
+ // Create our indent string (480 blanks);
+ for (int i = 0; i < 20; i++)
+ indentString += " ";
+
+ doFullEncoding = Boolean.valueOf(System.getProperty(ENCODE_PROPERTY, "true"));
+ }
+
+ /**
+ * Constructor.<br>
+ * Initialize data objects to be saved in XGMML file.<br>
+ *
+ * @param network
+ * CyNetwork object to be saved.
+ * @param view
+ * CyNetworkView for the network.
+ * @param noCytoscapeGraphics
+ * boolean to indicate whether cytoscape graphics
+ * attributes should be written
+ * @throws URISyntaxException
+ * @throws JAXBException
+ */
+ public XGMMLWriter(final CyNetwork network, final CyNetworkView view,
+ boolean noCytoscapeGraphics) throws IOException, URISyntaxException {
+ this(network, view);
+ this.noCytoscapeGraphics = noCytoscapeGraphics;
+ }
+
+ /**
+ * Write the XGMML file.<br>
+ * This method creates all JAXB objects from Cytoscape internal<br>
+ * data structure, and them marshall it into an XML (XGMML) document.<br>
+ *
+ * @param writer
+ * Witer to create XGMML file
+ * @throws IOException
+ */
+ public void write(final Writer writer) throws IOException {
+ this.writer = writer;
+
+ // write out the XGMML preamble
+ writePreamble();
+ depth++;
+
+ // write out our metadata
+ writeMetadata();
+
+ // write out network attributes
+ writeNetworkAttributes();
+
+ // Output our nodes
+ writeNodes();
+
+ // Output any global groups
+ writeGroups(null);
+
+ // Now, output our groups
+ // Output any global groups
+ writeGroups(network);
+
+ // Create edge objects
+ writeEdges();
+
+ depth--;
+ // Wwrite final tag
+ writeElement("</graph>\n");
+
+ writer.flush();
+ }
+
+ /**
+ * Output the XML preamble. This includes the XML line as well as the initial
+ * <graph> element, along with all of our namespaces.
+ *
+ * @throws IOException
+ */
+ private void writePreamble() throws IOException {
+ writeElement(XML_STRING+"\n");
+ writeElement("<graph label="+quote(network.getTitle())+" ");
+ for (int ns = 0; ns < NAMESPACES.length; ns++)
+ writer.write(NAMESPACES[ns]+" ");
+ writer.write(" directed=\"1\">\n");
+ }
+
+ /**
+ * Output the network metadata. This includes our format version and our RDF
+ * data.
+ *
+ * @throws IOException
+ */
+ private void writeMetadata() throws IOException {
+ writeElement("<att name=\""+FORMAT_VERSION+"\" value=\""+VERSION+"\"/>\n");
+ writeElement("<att name=\"networkMetadata\">\n");
+ depth++;
+ writeRDF();
+ depth--;
+ writeElement("</att>\n");
+ }
+
+ /**
+ * Output the RDF information for this network.
+ * <rdf:RDF>
+ * <rdf:Description rdf:about="http://www.cytoscape.org/">
+ * <dc:type>Protein-Protein Interaction</dc:type>
+ * <dc:description>N/A</dc:description>
+ * <dc:identifier>N/A</dc:identifier>
+ * <dc:date>2007-01-16 13:29:50</dc:date>
+ * <dc:title>Amidohydrolase Superfamily--child</dc:title>
+ * <dc:source>http://www.cytoscape.org/</dc:source>
+ * <dc:format>Cytoscape-XGMML</dc:format>
+ * </rdf:Description>
+ * </rdf:RDF>
+ *
+ * @throws IOException
+ */
+ private void writeRDF() throws IOException {
+ writeElement("<rdf:RDF>\n");
+ depth++;
+ writeElement("<rdf:Description rdf:about=\"http://www.cytoscape.org/\">\n");
+ depth++;
+ writeElement("<dc:type>Protein-Protein Interaction</dc:type>\n");
+ writeElement("<dc:description>N/A</dc:description>\n");
+ writeElement("<dc:identifier>N/A</dc:identifier>\n");
+ java.util.Date now = new java.util.Date();
+ java.text.DateFormat df = new java.text.SimpleDateFormat("yyyy-MM-dd HH:mm:ss");
+ writeElement("<dc:date>"+df.format(now)+"</dc:date>\n");
+ writeElement("<dc:title>"+encode(network.getTitle())+"</dc:title>\n");
+ writeElement("<dc:source>http://www.cytoscape.org/</dc:source>\n");
+ writeElement("<dc:format>Cytoscape-XGMML</dc:format>\n");
+ depth--;
+ writeElement("</rdf:Description>\n");
+ depth--;
+ writeElement("</rdf:RDF>\n");
+ }
+
+ /**
+ * Output any network attributes we have defined, including
+ * the network graphics information we encode as attributes:
+ * backgroundColor, zoom, and the graph center.
+ *
+ * @throws IOException
+ */
+ private void writeNetworkAttributes() throws IOException {
+ if (networkView != null) {
+ // Get our background color
+ DingCanvas backgroundCanvas =
+ ((DGraphView)Cytoscape.getCurrentNetworkView()).
+ getCanvas(DGraphView.Canvas.BACKGROUND_CANVAS);
+ writeAttributeXML(BACKGROUND, ObjectType.STRING, paint2string(backgroundCanvas.getBackground()), true);
+
+ // lets also write the zoom
+ final Double dAttr = new Double(networkView.getZoom());
+ writeAttributeXML(GRAPH_VIEW_ZOOM, ObjectType.REAL, dAttr ,true);
+
+ final Point2D center = ((DGraphView) networkView).getCenter();
+ writeAttributeXML(GRAPH_VIEW_CENTER_X, ObjectType.REAL, new Double(center.getX()) ,true);
+ writeAttributeXML(GRAPH_VIEW_CENTER_Y, ObjectType.REAL, new Double(center.getY()) ,true);
+
+ // Figure out if our node height and width is locked
+ VisualStyle networkStyle = Cytoscape.getCurrentNetworkView().getVisualStyle();
+ VisualPropertyDependency vpd = networkStyle.getDependency();
+ if (vpd.check(VisualPropertyDependency.Definition.NODE_SIZE_LOCKED))
+ writeAttributeXML(NODE_SIZE_LOCKED, ObjectType.BOOLEAN, Boolean.TRUE ,true);
+
+ }
+
+ // Now handle all of the other network attributes
+ for (int att = 0; att < networkAttNames.length; att++) {
+ if (networkAttributes.hasAttribute(network.getIdentifier(), networkAttNames[att]))
+ writeAttribute(network.getIdentifier(), networkAttributes, networkAttNames[att]);
+ }
+ }
+
+ /**
+ * Output Cytoscape nodes as XGMML
+ *
+ * @throws IOException
+ */
+ private void writeNodes() throws IOException {
+ for (CyNode curNode: (List<CyNode>)network.nodesList()) {
+ if (!curNode.isaGroup())
+ writeNode(curNode, null);
+ }
+ }
+
+ /**
+ * Output a single CyNode as XGMML
+ *
+ * @param node the node to output
+ * @throws IOException
+ */
+ private void writeNode(CyNode node, CyGroup group) throws IOException {
+ // Make sure this node is in this network
+ // if (!node.isaGroup() && !network.containsNode(node))
+ // return;
+
+ // Remember that we've seen this node
+ nodeMap.put(node, node);
+
+ // Output the node
+ writeElement("<node label="+quote(node.getIdentifier()));
+ writer.write(" id="+quote(Integer.toString(node.getRootGraphIndex()))+">\n");
+ depth++;
+
+ // Output the node attributes
+ for (int att = 0; att < nodeAttNames.length; att++) {
+ if (nodeAttributes.hasAttribute(node.getIdentifier(), nodeAttNames[att]))
+ writeAttribute(node.getIdentifier(), nodeAttributes, nodeAttNames[att]);
+ }
+
+ if (group != null) {
+ writeGroup(group);
+ }
+
+ if (networkView != null) {
+ // Output the node graphics if we have a view
+ writeNodeGraphics(node, (NodeView)networkView.getNodeView(node));
+ }
+
+ depth--;
+ writeElement("</node>\n");
+ }
+
+ /**
+ * Output the node graphics
+ * <graphics y="17276.9" x="15552.7" width="5" outline="#000000" fill="#44f687" type="diamond" w="35.0" h="35.0">
+ * <att name="cytoscapeNodeGraphicsAttributes">
+ * <att value="1.0" name="nodeTransparency"/>
+ * <att value="Arial Bold-0-6" name="nodeLabelFont"/>
+ * <att value="solid" name="borderLineType"/>
+ * </att>
+ * </graphics>
+ *
+ * @param node the node whose graphics we're outputting
+ * @param nodeView the view for this node
+ *
+ * @throws IOException
+ */
+ private void writeNodeGraphics(CyNode node, NodeView nodeView) throws IOException {
+
+
+ if (nodeView == null) return;
+
+ // In case node is hidden, we temporarily show the node view
+ // and then hide it later on.
+ boolean rehideNode = false;
+ if (nodeView.getWidth() == -1) {
+ networkView.showGraphObject(nodeView);
+ rehideNode = true;
+ }
+
+ writeElement("<graphics");
+ // Node shape
+ GraphicsType shape = number2shape(nodeView.getShape());
+ if (shape == GraphicsType.PARALLELOGRAM)
+ writeAttributePair("type",GraphicsType.RHOMBUS);
+ else
+ writeAttributePair("type",shape);
+
+ // Node size and position
+ writeAttributePair("h",Double.toString(nodeView.getHeight()));
+ writeAttributePair("w",Double.toString(nodeView.getWidth()));
+ writeAttributePair("x",Double.toString(nodeView.getXPosition()));
+ writeAttributePair("y",Double.toString(nodeView.getYPosition()));
+
+ // Node color
+ writeAttributePair("fill", paint2string(nodeView.getUnselectedPaint()));
+
+ // Node border basic info.
+ final BasicStroke borderType = (BasicStroke) nodeView.getBorder();
+ writeAttributePair("width", Integer.toString(((int)borderType.getLineWidth())));
+ writeAttributePair("outline", paint2string(nodeView.getBorderPaint()));
+
+ // Write out the Cytoscape-specific attributes
+ if (!noCytoscapeGraphics) {
+ // Get the opacity
+ Integer tp = ((Color) nodeView.getUnselectedPaint()).getAlpha();
+ double transparency = 1.0;
+ if (tp != null && tp.intValue() != 255)
+ transparency = tp.doubleValue()/255.0;
+
+ writeAttributePair("cy:nodeTransparency", Double.toString(transparency));
+ writeAttributePair("cy:nodeLabelFont", encodeFont(nodeView.getLabel().getFont()));
+ writeAttributePair("cy:nodeLabel", nodeView.getLabel().getText());
+
+ // Where should we store line-type info???
+ final float[] dash = borderType.getDashArray();
+
+ if (dash == null) {
+ // CyLogger.getLogger().info("##Border is NORMAL LINE");
+ writeAttributePair("cy:borderLineType", "solid");
+ } else {
+ // CyLogger.getLogger().info("##Border is DASHED LINE");
+ String dashArray = null;
+ final StringBuilder dashBuf = new StringBuilder();
+
+ for (int i = 0; i < dash.length; i++) {
+ dashBuf.append(Double.toString(dash[i]));
+
+ if (i < (dash.length - 1)) {
+ dashBuf.append(",");
+ }
+ }
+
+ dashArray = dashBuf.toString();
+ writeAttributePair("cy:borderLineType", dashArray);
+ }
+ }
+
+ writer.write("/>\n");
+
+ if ( rehideNode )
+ networkView.hideGraphObject(nodeView);
+ }
+
+ private void writeGroups(CyNetwork groupNetwork) throws IOException {
+ // Two pass approach. First, walk through the list
+ // and see if any of the children of a group are
+ // themselves a group. If so, remove them from
+ // the list & will pick them up on recursion, but only
+ // if all of the non-group node members are in
+ // this graph perspective
+
+ List <CyGroup> groupList = (ArrayList) CyGroupManager.getGroupList(groupNetwork);
+
+ if ((groupList == null) || groupList.isEmpty()) {
+ return;
+ }
+
+ HashMap<CyGroup,CyGroup> embeddedGroupList = new HashMap();
+ List<CyGroup> groupsToWrite = new ArrayList();
+
+ for (CyGroup group: groupList) {
+ List<CyNode> childList = group.getNodes();
+
+ if ((childList == null) || (childList.size() == 0))
+ continue;
+
+ boolean allNodesVisible = true;
+ for (CyNode childNode: childList) {
+ if (CyGroupManager.isaGroup(childNode)) {
+ // Get the actual group
+ CyGroup embGroup = CyGroupManager.getCyGroup(childNode);
+ embeddedGroupList.put(embGroup, embGroup);
+ } else if (!network.containsNode(childNode)) {
+ allNodesVisible = false;
+ }
+ }
+ if (allNodesVisible || network.containsNode(group.getGroupNode())) {
+ groupsToWrite.add(group);
+ }
+ }
+
+ for (CyGroup group: groupsToWrite) {
+ // Is this an embedded group?
+ if (embeddedGroupList.containsKey(group))
+ continue; // Yes, skip it
+
+ writeNode(group.getGroupNode(), group);
+ }
+ }
+
+ /**
+ * Write out a group
+ *
+ * @param group the group to output
+ * @throws IOException
+ */
+ private void writeGroup(CyGroup group) throws IOException {
+
+ logger.debug("Writing group "+group+" "+group.getNodes().size()+" nodes, "+
+ group.getInnerEdges().size()+" inner edges, and "+group.getOuterEdges().size()+
+ " outer edges");
+ List<CyNode> groupList = group.getNodes();
+ if (groupList != null && groupList.size() > 0) {
+ // If we're a group, output the graph attribute now
+ writeElement("<att>\n");
+ depth++;
+ writeElement("<graph>\n");
+ depth++;
+ for (CyNode childNode: groupList) {
+ if (childNode.isaGroup()) {
+ // We have an embedded group -- recurse
+ CyGroup childGroup = CyGroupManager.getCyGroup(childNode);
+ writeNode(childGroup.getGroupNode(), childGroup);
+ } else {
+ if (nodeMap.containsKey(childNode))
+ writeElement("<node xlink:href=\"#"+childNode.getRootGraphIndex()+"\"/>\n");
+ else
+ writeNode(childNode, null);
+ }
+ }
+
+ // Now, output the edges for this group
+ for (CyEdge edge: group.getInnerEdges()) {
+ logger.debug("Writing inner edge "+edge.getIdentifier()+" for group "+group);
+ if (!edgeMap.containsKey(edge)) {
+ edgeMap.put(edge,edge);
+ writeEdge(edge, false);
+ }
+ }
+ for (CyEdge edge: group.getOuterEdges()) {
+ logger.debug("Writing outer edge "+edge.getIdentifier()+" for group "+group);
+ // if (!edgeMap.containsKey(edge)) {
+ edgeMap.put(edge,edge);
+ writeEdge(edge, false);
+ // }
+ }
+
+ depth--; writeElement("</graph>\n");
+ depth--; writeElement("</att>\n");
+ }
+ }
+
+ /**
+ * Output Cytoscape edges as XGMML
+ *
+ * @throws IOException
+ */
+ private void writeEdges() throws IOException {
+ for (CyEdge curEdge: (List<CyEdge>)network.edgesList()) {
+ edgeMap.put(curEdge,curEdge);
+ writeEdge(curEdge, true);
+ }
+ }
+
+ /**
+ * Output a Cytoscape edge as XGMML
+ *
+ * @param curEdge the edge to output
+ *
+ * @throws IOException
+ */
+ private void writeEdge(CyEdge curEdge, boolean checkNodes) throws IOException {
+ // Write the edge
+ String target = quote(Integer.toString(curEdge.getTarget().getRootGraphIndex()));
+ String source = quote(Integer.toString(curEdge.getSource().getRootGraphIndex()));
+
+ if (checkNodes) {
+ // Make sure these nodes exist
+ if (!nodeMap.containsKey(curEdge.getTarget()) || !nodeMap.containsKey(curEdge.getSource()))
+ return;
+ }
+
+ writeElement("<edge label="+quote(curEdge.getIdentifier())+" source="+source+" target="+target+">\n");
+ depth++;
+
+ // Write the edge attributes
+ for (int att = 0; att < edgeAttNames.length; att++) {
+ if (edgeAttributes.hasAttribute(curEdge.getIdentifier(), edgeAttNames[att]))
+ writeAttribute(curEdge.getIdentifier(), edgeAttributes, edgeAttNames[att]);
+ }
+
+ if (networkView != null) {
+ // Write the edge graphics
+ writeEdgeGraphics(curEdge, (EdgeView)networkView.getEdgeView(curEdge));
+ }
+
+ depth--;
+ writeElement("</edge>\n");
+ }
+
+ /**
+ * Output the edge graphics
+ *
+ * @param edge the edge whose graphics we're outputting
+ * @param edgeView the view for this edge
+ *
+ * @throws IOException
+ */
+ private void writeEdgeGraphics(CyEdge edge, EdgeView edgeView) throws IOException {
+ if (edgeView == null)
+ return;
+
+ writeElement("<graphics");
+ // Width
+ writeAttributePair("width", Integer.toString((int) edgeView.getStrokeWidth()));
+ // Color
+ writeAttributePair("fill", paint2string(edgeView.getUnselectedPaint()));
+
+ // Store Cytoscape-local graphical attributes
+ if (!noCytoscapeGraphics) {
+ writeAttributePair("cy:sourceArrow", Integer.toString(edgeView.getSourceEdgeEnd()));
+ writeAttributePair("cy:targetArrow", Integer.toString(edgeView.getTargetEdgeEnd()));
+ writeAttributePair("cy:sourceArrowColor", paint2string(edgeView.getSourceEdgeEndPaint()));
+ writeAttributePair("cy:targetArrowColor", paint2string(edgeView.getTargetEdgeEndPaint()));
+
+ writeAttributePair("cy:edgeLabelFont", encodeFont(edgeView.getLabel().getFont()));
+ writeAttributePair("cy:edgeLabel", edgeView.getLabel().getText());
+ writeAttributePair("cy:edgeLineType", LineStyle.extractLineStyle(edgeView.getStroke()).toString());
+ // Set curved or not
+ if (edgeView.getLineType() == EdgeView.CURVED_LINES) {
+ writeAttributePair("cy:curved", "CURVED_LINES");
+ } else if (edgeView.getLineType() == EdgeView.STRAIGHT_LINES) {
+ writeAttributePair("cy:curved", "STRAIGHT_LINES");
+ }
+ }
+
+
+ // Handle bends
+ final Bend bendData = edgeView.getBend();
+ final List<Point2D> handles = bendData.getHandles();
+
+ if (handles.size() == 0) {
+ writer.write("/>\n");
+ return;
+ } else {
+ writer.write(">\n");
+ }
+
+ depth++;
+ writeElement("<att name=\"edgeBend\">\n");
+ depth++;
+ for (Point2D handle: handles) {
+ String x = Double.toString(handle.getX());
+ String y = Double.toString(handle.getY());
+ writeElement("<att name=\"handle\" x=\""+x+"\" y=\""+y+"\" />\n");
+ }
+ depth--;
+ writeElement("</att>\n");
+ depth--;
+ writeElement("</graphics>\n");
+ }
+
+
+ /**
+ * Creates an attribute to write into XGMML file.
+ *
+ * @param id -
+ * id of node, edge or network
+ * @param attributes -
+ * CyAttributes to load
+ * @param attributeName -
+ * attribute name
+ * @return att - Att to return (gets written into xgmml file - CAN BE NULL)
+ *
+ * @throws IOException
+ */
+ private void writeAttribute(final String id, final CyAttributes attributes,
+ final String attributeName) throws IOException
+ {
+ // create an attribute and its type
+ final byte attType = attributes.getType(attributeName);
+ String value = null;
+ String type = null;
+ final boolean editable = attributes.getUserEditable(attributeName);
+ final boolean hidden = !attributes.getUserVisible(attributeName);
+ final Equation equation = attributes.getEquation(id, attributeName);
+
+ // process float
+ if (attType == CyAttributes.TYPE_FLOATING) {
+ if (equation != null)
+ writeEquationAttributeXML(attributeName, ObjectType.REAL, equation.toString(),
+ true, hidden, editable);
+ else {
+ final Double dAttr = attributes.getDoubleAttribute(id, attributeName);
+ writeAttributeXML(attributeName, ObjectType.REAL, dAttr, true, hidden, editable);
+ }
+ }
+ // process integer
+ else if (attType == CyAttributes.TYPE_INTEGER) {
+ if (equation != null)
+ writeEquationAttributeXML(attributeName, ObjectType.INTEGER, equation.toString(),
+ true, hidden, editable);
+ else {
+ final Integer iAttr = attributes.getIntegerAttribute(id, attributeName);
+ writeAttributeXML(attributeName, ObjectType.INTEGER, iAttr, true, hidden, editable);
+ }
+ }
+ // process string
+ else if (attType == CyAttributes.TYPE_STRING) {
+ if (equation != null)
+ writeEquationAttributeXML(attributeName, ObjectType.STRING, equation.toString(),
+ true, hidden, editable);
+ else {
+ String sAttr = attributes.getStringAttribute(id, attributeName);
+ // Protect tabs and returns
+ if (sAttr != null) {
+ sAttr = sAttr.replace("\n", "\\n");
+ sAttr = sAttr.replace("\t", "\\t");
+ }
+ if (attributeName.equals(CyNode.NESTED_NETWORK_ID_ATTR)) {
+ // This is a special attribute for nested network.
+ sAttr = Cytoscape.getNetwork(sAttr).getTitle();
+ }
+ writeAttributeXML(attributeName, ObjectType.STRING, sAttr, true, hidden, editable);
+ }
+ }
+ // process boolean
+ else if (attType == CyAttributes.TYPE_BOOLEAN) {
+ if (equation != null)
+ writeEquationAttributeXML(attributeName, ObjectType.BOOLEAN, equation.toString(),
+ true, hidden, editable);
+ else {
+ final Boolean bAttr = attributes.getBooleanAttribute(id, attributeName);
+ writeAttributeXML(attributeName, ObjectType.BOOLEAN, bAttr, true, hidden, editable);
+ }
+ }
+ // process simple list
+ else if (attType == CyAttributes.TYPE_SIMPLE_LIST) {
+ // get the attribute list
+ final List listAttr = attributes.getListAttribute(id, attributeName);
+ writeAttributeXML(attributeName, ObjectType.LIST, null, false, hidden, editable);
+
+ depth++;
+ // interate through the list
+ for (Object obj: listAttr) {
+ // Protect tabs and returns (if necessary)
+ String sAttr = obj.toString();
+ if (sAttr != null) {
+ sAttr = sAttr.replace("\n", "\\n");
+ sAttr = sAttr.replace("\t", "\\t");
+ }
+ // set child attribute value & label
+ writeAttributeXML(attributeName, checkType(obj), sAttr, true);
+ }
+ depth--;
+ writeAttributeXML(null, null, null, true);
+ }
+ // process simple map
+ else if (attType == CyAttributes.TYPE_SIMPLE_MAP) {
+ // get the attribute map
+ final Map mapAttr = attributes.getMapAttribute(id, attributeName);
+ writeAttributeXML(attributeName, ObjectType.MAP, null, false, hidden, editable);
+
+ depth++;
+ // interate through the map
+ for (Object obj: mapAttr.keySet()) {
+ // get the attribute from the map
+ String key = (String) obj;
+ Object val = mapAttr.get(key);
+ String sAttr = val.toString();
+ if (sAttr != null) {
+ sAttr = sAttr.replace("\n", "\\n");
+ sAttr = sAttr.replace("\t", "\\t");
+ }
+
+ writeAttributeXML(key, checkType(val), sAttr, true);
+ }
+ depth--;
+ writeAttributeXML(null, null, null, true);
+ }
+ // process complex map
+ else if (attType == CyAttributes.TYPE_COMPLEX) {
+ MultiHashMap mmap = attributes.getMultiHashMap();
+ MultiHashMapDefinition mmapDef = attributes.getMultiHashMapDefinition();
+
+ // get the number & types of dimensions
+ byte[] dimTypes = mmapDef.getAttributeKeyspaceDimensionTypes(attributeName);
+
+ // Check to see if id has value assigned to attribute
+ if (!objectHasKey(id, attributes, attributeName)) {
+ return;
+ }
+ // Output the first <att>
+ writeAttributeXML(attributeName, ObjectType.COMPLEX, String.valueOf(dimTypes.length), false, hidden, editable);
+
+ // grab the complex attribute structure
+ Map complexAttributeStructure = getComplexAttributeStructure(mmap, id, attributeName, null,
+ 0, dimTypes.length);
+
+ // determine val type, get its string equivalent to store in XGMML
+ ObjectType valType = getType(mmapDef.getAttributeValueType(attributeName));
+
+ depth++;
+ // walk the structure
+ writeComplexAttribute(complexAttributeStructure, valType, dimTypes, 0);
+ depth--;
+ // Close
+ writeAttributeXML(null, null, null, true);
+ }
+ }
+
+ /**
+ * Returns a map where the key(s) are each key in the attribute key space,
+ * and the value is another map or the attribute value.
+ *
+ * For example, if the following key:
+ *
+ * {externalref1}{authors}{1} pointed to the following value:
+ *
+ * "author 1 name",
+ *
+ * Then we would have a Map where the key is externalref1, the value is a
+ * Map where the key is {authors}, the value is a Map where the key is {1},
+ * the value is "author 1 name".
+ *
+ * @param mmap -
+ * reference to MultiHashMap used by CyAttributes
+ * @param id -
+ * id of node, edge or network
+ * @param attributeName -
+ * name of attribute
+ * @param keys -
+ * array of objects which store attribute keys
+ * @param keysIndex -
+ * index into keys array we should add the next key
+ * @param numKeyDimensions -
+ * the number of keys used for given attribute name
+ * @return Map - ref to Map interface
+ */
+ private Map getComplexAttributeStructure(MultiHashMap mmap, String id, String attributeName,
+ Object[] keys, int keysIndex, int numKeyDimensions) {
+ // are we done?
+ if (keysIndex == numKeyDimensions)
+ return null;
+
+ // the hashmap to return
+ Map keyHashMap = new HashMap();
+
+ // create a new object array to store keys for this interation
+ // copy all existing keys into it
+ Object[] newKeys = new Object[keysIndex + 1];
+
+ for (int lc = 0; lc < keysIndex; lc++) {
+ newKeys[lc] = keys[lc];
+ }
+
+ // get the key span
+ Iterator keyspan = mmap.getAttributeKeyspan(id, attributeName, keys);
+
+ while (keyspan.hasNext()) {
+ Object newKey = keyspan.next();
+ newKeys[keysIndex] = newKey;
+
+ Map nextLevelMap = getComplexAttributeStructure(mmap, id, attributeName, newKeys,
+ keysIndex + 1, numKeyDimensions);
+ Object objectToStore = (nextLevelMap == null)
+ ? mmap.getAttributeValue(id, attributeName, newKeys) : nextLevelMap;
+ keyHashMap.put(newKey, objectToStore);
+ }
+ return keyHashMap;
+ }
+
+
+ /**
+ * This method is a recursive routine to output a complex attribute.
+ *
+ * @param complexAttributeStructure the structure of the attribute
+ * @param type the type of the attribute
+ * @param dimTypes the array of dimension types
+ * @param dimTypesIndex which dimType we're working on
+ */
+ private void writeComplexAttribute(Map complexAttributeStructure, ObjectType type,
+ byte[] dimTypes, int dimTypesIndex) throws IOException {
+ for (Object key: complexAttributeStructure.keySet()) {
+ Object possibleAttributeValue = complexAttributeStructure.get(key);
+
+ // Is this a leaf or are we still dealing with maps?
+ if (possibleAttributeValue instanceof Map) {
+ // Another map
+ writeAttributeXML(key.toString(), getType(dimTypes[dimTypesIndex]),
+ String.valueOf(((Map) possibleAttributeValue).size()), false);
+ // Recurse
+ depth++;
+ writeComplexAttribute((Map)possibleAttributeValue, type, dimTypes, dimTypesIndex+1);
+ depth--;
+ // Close
+ writeAttributeXML(null, null, null, true);
+ } else {
+ // Final key
+ writeAttributeXML(key.toString(), getType(dimTypes[dimTypesIndex]),
+ String.valueOf(1), false);
+ depth++;
+ writeAttributeXML(null, type, possibleAttributeValue.toString(), true);
+ depth--;
+ writeAttributeXML(null, null, null, true);
+ }
+ }
+ }
+
+ /**
+ * writeAttributeXML outputs an XGMML attribute
+ *
+ * @param name is the name of the attribute we are outputting
+ * @param type is the XGMML type of the attribute
+ * @param value is the value of the attribute we're outputting
+ * @param end is a flag to tell us if the attribute should include a tag end
+ *
+ * @throws IOException
+ */
+ private void writeAttributeXML(final String name, final ObjectType type, final Object value,
+ final boolean end) throws IOException
+ {
+ if (name == null && type == null)
+ writeElement("</att>\n");
+ else {
+ writeElement("<att type=" + quote(type.toString()));
+ if (name != null)
+ writer.write(" name=" + quote(name));
+ if (value != null)
+ writer.write(" value=" + quote(value.toString()));
+ if (end)
+ writer.write("/>\n");
+ else
+ writer.write(">\n");
+ }
+ }
+
+ /**
+ * writeAttributeXML outputs an XGMML attribute
+ *
+ * @param name is the name of the attribute we are outputting
+ * @param type is the XGMML type of the attribute
+ * @param value is the value of the attribute we're outputting
+ * @param end is a flag to tell us if the attribute should include a tag end
+ * @param hidden is a flag to tell us if the attribute should be hidden
+ * @param editable is a flag to tell us if the attribute should be user editable
+ *
+ * @throws IOException
+ */
+ private void writeAttributeXML(final String name, final ObjectType type,
+ final Object value, final boolean end,
+ final boolean hidden, final boolean editable) throws IOException
+ {
+ if (name == null && type == null)
+ writeElement("</att>\n");
+ else {
+ writeElement("<att type=" + quote(type.toString()));
+ if (name != null)
+ writer.write(" name=" + quote(name));
+ if (value != null)
+ writer.write(" value=" + quote(value.toString()));
+
+ // Only output hidden and editable if they differ from the default.
+ if (hidden)
+ writer.write(" cy:hidden=\"true\"");
+ if (!editable)
+ writer.write(" cy:editable=\"false\"");
+
+ if (end)
+ writer.write("/>\n");
+ else
+ writer.write(">\n");
+ }
+ }
+
+ /**
+ * writeEquationAttributeXML outputs an XGMML attribute
+ *
+ * @param name is the name of the attribute we are outputting
+ * @param type is the XGMML type of the attribute
+ * @param equation is the textual representation of the formula we're outputting
+ * @param end is a flag to tell us if the attribute should include a tag end
+ * @param hidden is a flag to tell us if the attribute should be hidden
+ * @param editable is a flag to tell us if the attribute should be user editable
+ *
+ * @throws IOException
+ */
+ private void writeEquationAttributeXML(final String name, final ObjectType type,
+ final String equation, final boolean end,
+ final boolean hidden, final boolean editable) throws IOException
+ {
+ if (name == null && type == null)
+ writeElement("</att>\n");
+ else {
+ writeElement("<att type=" + quote(type.toString()));
+ if (name != null)
+ writer.write(" name=" + quote(name));
+ writer.write(" value=" + quote(equation));
+ writer.write(" cy:equation=\"true\"");
+
+ // Only output hidden and editable if they differ from the default.
+ if (hidden)
+ writer.write(" cy:hidden=\"true\"");
+ if (!editable)
+ writer.write(" cy:editable=\"false\"");
+
+ if (end)
+ writer.write("/>\n");
+ else
+ writer.write(">\n");
+ }
+ }
+
+ /**
+ * writeAttributePair outputs the name,value pairs for an attribute
+ *
+ * @param name is the name of the attribute we are outputting
+ * @param value is the value of the attribute we're outputting
+ *
+ * @throws IOException
+ */
+ private void writeAttributePair(String name, Object value) throws IOException {
+ writer.write(" "+name+"="+quote(value.toString()));
+ }
+
+ /**
+ * writeElement outputs the name,value pairs for an attribute
+ *
+ * @param line is the element string to output
+ *
+ * @throws IOException
+ */
+ private void writeElement(String line) throws IOException {
+ while ( depth*2 > indentString.length()-1 )
+ indentString = indentString + " ";
+ writer.write(indentString,0,depth*2);
+ writer.write(line);
+ }
+
+ /**
+ * Convert enumerated shapes into human-readable string.<br>
+ *
+ * @param type
+ * Enumerated node shape.
+ * @return Shape in string.
+ */
+ private GraphicsType number2shape(final int type) {
+ switch (type) {
+ case NodeView.ELLIPSE:
+ return GraphicsType.ELLIPSE;
+
+ case NodeView.RECTANGLE:
+ return GraphicsType.RECTANGLE;
+
+ case NodeView.ROUNDED_RECTANGLE:
+ return GraphicsType.ROUNDED_RECTANGLE;
+
+ case NodeView.DIAMOND:
+ return GraphicsType.DIAMOND;
+
+ case NodeView.HEXAGON:
+ return GraphicsType.HEXAGON;
+
+ case NodeView.OCTAGON:
+ return GraphicsType.OCTAGON;
+
+ case NodeView.PARALELLOGRAM:
+ return GraphicsType.PARALLELOGRAM;
+
+ case NodeView.TRIANGLE:
+ return GraphicsType.TRIANGLE;
+
+ case NodeView.VEE:
+ return GraphicsType.VEE;
+
+ default:
+ return null;
+ }
+ }
+
+ /**
+ * Convert color (paint) to RGB string.<br>
+ *
+ * @param p
+ * Paint object to be converted.
+ * @return Color in RGB string.
+ */
+ private String paint2string(final Paint p) {
+ final Color c = (Color) p;
+
+ return ("#" // +Integer.toHexString(c.getRGB());
+ + Integer.toHexString(256 + c.getRed()).substring(1)
+ + Integer.toHexString(256 + c.getGreen()).substring(1)
+ + Integer.toHexString(256 + c.getBlue()).substring(1));
+ }
+
+ /**
+ * Encode font into a human-readable string.<br>
+ *
+ * @param font
+ * Font object.
+ * @return String extracted from the given Font object.
+ */
+ private String encodeFont(final Font font) {
+ // Encode font into "fontname-style-pointsize" string
+ return font.getName() + "-" + font.getStyle() + "-" + font.getSize();
+ }
+
+ /**
+ * Check the type of Attributes.
+ *
+ * @param obj
+ * @return Attribute type in string.
+ *
+ */
+ private ObjectType checkType(final Object obj) {
+ if (obj.getClass() == String.class) {
+ return ObjectType.STRING;
+ } else if (obj.getClass() == Integer.class) {
+ return ObjectType.INTEGER;
+ } else if ((obj.getClass() == Double.class) || (obj.getClass() == Float.class)) {
+ return ObjectType.REAL;
+ } else if (obj.getClass() == Boolean.class) {
+ return ObjectType.BOOLEAN;
+ } else
+ return null;
+ }
+
+ /**
+ * Given a byte describing a MultiHashMapDefinition TYPE_*, return the
+ * proper XGMMLWriter type.
+ *
+ * @param dimType -
+ * byte as described in MultiHashMapDefinition
+ * @return the type pointed to by this dim
+ */
+ private ObjectType getType(final byte dimType) {
+ if (dimType == MultiHashMapDefinition.TYPE_BOOLEAN)
+ return ObjectType.BOOLEAN;
+
+ if (dimType == MultiHashMapDefinition.TYPE_FLOATING_POINT)
+ return ObjectType.REAL;
+
+ if (dimType == MultiHashMapDefinition.TYPE_INTEGER)
+ return ObjectType.INTEGER;
+
+ if (dimType == MultiHashMapDefinition.TYPE_STRING)
+ return ObjectType.STRING;
+
+ // houston we have a problem
+ return null;
+ }
+
+ /**
+ * encode returns a quoted string appropriate for use as an XML attribute
+ *
+ * @param str the string to encode
+ * @return the encoded string
+ */
+ private String encode(String str) {
+ // Find and replace any "magic", control, non-printable etc. characters
+ // For maximum safety, everything other than printable ASCII (0x20 thru 0x7E) is converted into a character entity
+
+ StringBuilder sb;
+
+ sb = new StringBuilder(str.length());
+ for (int i = 0; i < str.length(); i++) {
+ char c;
+
+ c = str.charAt(i);
+ if ((c < ' ') || (c > '~'))
+ {
+ if (doFullEncoding) {
+ sb.append("&#x");
+ sb.append(Integer.toHexString((int)c));
+ sb.append(";");
+ }
+ else {
+ sb.append(c);
+ }
+ }
+ else if (c == '"') {
+ sb.append(""");
+ }
+ else if (c == '\'') {
+ sb.append("'");
+ }
+ else if (c == '&') {
+ sb.append("&");
+ }
+ else if (c == '<') {
+ sb.append("<");
+ }
+ else if (c == '>') {
+ sb.append(">");
+ }
+ else {
+ sb.append(c);
+ }
+ }
+
+ return sb.toString();
+ }
+
+ /**
+ * quote returns a quoted string appropriate for use as an XML attribute
+ *
+ * @param str the string to quote
+ * @return the quoted string
+ */
+ private String quote(String str) {
+ return '"' + encode(str) + '"';
+ }
+
+ public boolean isDoFullEncoding() {
+ return doFullEncoding;
+ }
+
+ public void setDoFullEncoding(boolean doFullEnc) {
+ doFullEncoding = doFullEnc;
+ }
+
+ /**
+ * Determines if object has key in multihashmap
+ *
+ * @param id -
+ * node, edge, network id
+ * @param attributes -
+ * CyAttributes ref
+ * @param attributeName -
+ * attribute name
+ *
+ * @return boolean
+ */
+ private boolean objectHasKey(String id, CyAttributes attributes, String attributeName) {
+ MultiHashMap mmap = attributes.getMultiHashMap();
+
+ for (Iterator keysIt = mmap.getObjectKeys(attributeName); keysIt.hasNext();) {
+ String thisKey = (String) keysIt.next();
+
+ if ((thisKey != null) && thisKey.equals(id)) {
+ return true;
+ }
+ }
+ return false;
+ }
+}
diff --git a/application/src/main/java/cytoscape/dialogs/ColorScaleTable.java b/application/src/main/java/cytoscape/dialogs/ColorScaleTable.java
new file mode 100644
index 0000000..e0b3954
--- /dev/null
+++ b/application/src/main/java/cytoscape/dialogs/ColorScaleTable.java
@@ -0,0 +1,170 @@
+/*
+ File: ColorScaleTable.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// ColorScaleTable.java
+
+//---------------------------------------------------------------------------------------
+// $Revision: 9736 $
+// $Date: 2007-03-20 01:25:45 +0100 (Tue, 20 Mar 2007) $
+// $Author: mes $
+//---------------------------------------------------------------------------------------
+package cytoscape.dialogs;
+
+
+//---------------------------------------------------------------------------------------
+import java.awt.*;
+import java.awt.event.*;
+
+import javax.swing.*;
+import javax.swing.DefaultCellEditor;
+import javax.swing.border.Border;
+import javax.swing.table.AbstractTableModel;
+import javax.swing.table.TableCellRenderer;
+
+
+/**
+ *
+ */
+public class ColorScaleTable extends JPanel {
+ /**
+ * Creates a new ColorScaleTable object.
+ *
+ * @param width DOCUMENT ME!
+ * @param height DOCUMENT ME!
+ * @param bins DOCUMENT ME!
+ */
+ public ColorScaleTable(int width, int height, double[][] bins) {
+ MyTableModel myModel = new MyTableModel(bins);
+ JTable table = new JTable(myModel);
+
+ table.setPreferredScrollableViewportSize(new Dimension(width, height));
+
+ //Create the scroll pane and add the table to it.
+ JScrollPane scrollPane = new JScrollPane(table);
+
+ //Set up renderer and editor for the Favorite Color column.
+ setUpColorRenderer(table);
+
+ //Add the scroll pane to this window.
+ this.add(scrollPane);
+ }
+
+ class ColorRenderer extends JLabel implements TableCellRenderer {
+ Border unselectedBorder = null;
+ Border selectedBorder = null;
+ boolean isBordered = true;
+
+ public ColorRenderer(boolean isBordered) {
+ super();
+ this.isBordered = isBordered;
+ setOpaque(true); //MUST do this for background to show up.
+ }
+
+ public Component getTableCellRendererComponent(JTable table, Object color,
+ boolean isSelected, boolean hasFocus,
+ int row, int column) {
+ setBackground((Color) color);
+
+ if (isBordered) {
+ if (isSelected) {
+ if (selectedBorder == null) {
+ selectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5,
+ table
+ .getSelectionBackground());
+ }
+
+ setBorder(selectedBorder);
+ } else {
+ if (unselectedBorder == null) {
+ unselectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5,
+ table.getBackground());
+ }
+
+ setBorder(unselectedBorder);
+ }
+ }
+
+ return this;
+ }
+ }
+
+ private void setUpColorRenderer(JTable table) {
+ table.setDefaultRenderer(Color.class, new ColorRenderer(false));
+ }
+
+ class MyTableModel extends AbstractTableModel {
+ final String[] columnNames = { "Value", "Color" };
+ final Object[][] data;
+
+ MyTableModel(double[][] bins) {
+ int binCount = bins.length;
+ data = new Object[binCount][2];
+
+ for (int i = 0; i < binCount; i++) {
+ data[i][0] = new Double(bins[i][0]);
+
+ Color tempColor = new Color((int) bins[i][1], (int) bins[i][2], (int) bins[i][3]);
+ data[i][1] = tempColor;
+ }
+ }
+
+ public int getColumnCount() {
+ return columnNames.length;
+ }
+
+ public int getRowCount() {
+ return data.length;
+ }
+
+ public String getColumnName(int col) {
+ return columnNames[col];
+ }
+
+ public Object getValueAt(int row, int col) {
+ return data[row][col];
+ }
+
+ public void setValueAt(Object value, int row, int col) {
+ data[row][col] = value;
+ fireTableCellUpdated(row, col);
+ }
+
+ public Class getColumnClass(int c) {
+ return getValueAt(0, c).getClass();
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/dialogs/EdgeAttributesPopupDetails.java b/application/src/main/java/cytoscape/dialogs/EdgeAttributesPopupDetails.java
new file mode 100644
index 0000000..79d381b
--- /dev/null
+++ b/application/src/main/java/cytoscape/dialogs/EdgeAttributesPopupDetails.java
@@ -0,0 +1,138 @@
+/*
+ File: EdgeAttributesPopupDetails.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+//
+
+// EdgeAttributesPopupDetails.java
+//
+// $Revision: 9565 $
+// $Date: 2007-02-13 20:36:50 +0100 (Tue, 13 Feb 2007) $
+// $Author: mes $
+//
+package cytoscape.dialogs;
+
+import cytoscape.data.CyAttributes;
+
+import java.awt.BorderLayout;
+import java.awt.Component;
+import java.awt.Frame;
+import java.awt.event.ActionEvent;
+
+import javax.swing.AbstractAction;
+import javax.swing.JButton;
+import javax.swing.JDialog;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTextArea;
+
+
+/**
+ * This class provides a detailed list of attribute information for a given
+ * edge.
+ */
+public class EdgeAttributesPopupDetails extends JDialog {
+ /**
+ * Creates a new EdgeAttributesPopupDetails object.
+ *
+ * @param parentFrame DOCUMENT ME!
+ * @param name DOCUMENT ME!
+ * @param edgeAttributes DOCUMENT ME!
+ */
+ public EdgeAttributesPopupDetails(Frame parentFrame, String name, CyAttributes edgeAttributes) {
+ super(parentFrame, "Edge Attributes - " + name, false);
+
+ JScrollPane scrollPanel = new JScrollPane(getContentComponent(edgeAttributes, name));
+
+ JPanel buttonPanel = new JPanel();
+ JButton okButton = new JButton("OK");
+ okButton.addActionListener(new OKAction(this));
+ buttonPanel.add(okButton, BorderLayout.CENTER);
+
+ JPanel panel = new JPanel();
+ panel.setLayout(new BorderLayout());
+ panel.add(scrollPanel, BorderLayout.CENTER);
+ panel.add(buttonPanel, BorderLayout.SOUTH);
+
+ setContentPane(panel);
+ }
+
+ protected Component getContentComponent(CyAttributes edgeAttributes, String name) {
+ String contents = name;
+
+ if (name.length() == 0) {
+ contents = "Unable to locate attributes for selected edge";
+ } else {
+ String[] attributes = edgeAttributes.getAttributeNames();
+
+ for (int i = 0; i < attributes.length; i++) {
+ // Object value = edgeAttributes.getValue(attributes[i], name);
+ Object value = null;
+ byte attrType = edgeAttributes.getType(attributes[i]);
+
+ if (attrType == CyAttributes.TYPE_BOOLEAN) {
+ value = edgeAttributes.getBooleanAttribute(attributes[i], name);
+ } else if (attrType == CyAttributes.TYPE_FLOATING) {
+ value = edgeAttributes.getDoubleAttribute(attributes[i], name);
+ } else if (attrType == CyAttributes.TYPE_INTEGER) {
+ value = edgeAttributes.getIntegerAttribute(attributes[i], name);
+ } else if (attrType == CyAttributes.TYPE_STRING) {
+ value = edgeAttributes.getStringAttribute(attributes[i], name);
+ }
+
+ if (value != null)
+ contents += ("\n\n" + attributes[i] + ":\n" + value);
+ }
+ }
+
+ JTextArea textArea = new JTextArea(contents, 8, 40);
+
+ return textArea;
+ }
+
+ protected class OKAction extends AbstractAction {
+ private JDialog dialog;
+
+ OKAction(JDialog dialog) {
+ super("");
+ this.dialog = dialog;
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ dialog.dispose();
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/dialogs/EditNetworkTitleDialog.java b/application/src/main/java/cytoscape/dialogs/EditNetworkTitleDialog.java
new file mode 100644
index 0000000..17fb2b2
--- /dev/null
+++ b/application/src/main/java/cytoscape/dialogs/EditNetworkTitleDialog.java
@@ -0,0 +1,167 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.dialogs;
+
+import java.awt.Component;
+import java.awt.Dimension;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.Insets;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import javax.swing.JButton;
+import javax.swing.JDialog;
+import javax.swing.JFrame;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JTextField;
+
+
+/**
+ *
+ */
+public class EditNetworkTitleDialog extends JDialog implements ActionListener {
+ /**
+ * Creates a new EditNetworkTitleDialog object.
+ *
+ * @param parent DOCUMENT ME!
+ * @param modal DOCUMENT ME!
+ * @param pName DOCUMENT ME!
+ */
+ public EditNetworkTitleDialog(Component parent, boolean modal, String pName) {
+ super((JFrame) parent, modal);
+ initComponents();
+ tfNetworkTitle.setText(pName);
+ tfNetworkTitle.setSelectionStart(0);
+ tfNetworkTitle.setSelectionEnd(pName.length());
+
+ setSize(new java.awt.Dimension(300, 170));
+ }
+
+ /** This method is called from within the constructor to
+ * initialize the form.
+ * WARNING: Do NOT modify this code. The content of this method is
+ * always regenerated by the Form Editor.
+ */
+
+ // <editor-fold defaultstate="collapsed" desc=" Generated Code ">
+ private void initComponents() {
+ GridBagConstraints gridBagConstraints;
+
+ jLabel1 = new JLabel();
+ tfNetworkTitle = new JTextField();
+ jPanel1 = new JPanel();
+ btnOK = new JButton();
+ btnCancel = new JButton();
+
+ btnOK.addActionListener(this);
+ btnCancel.addActionListener(this);
+
+ getContentPane().setLayout(new GridBagLayout());
+
+ setDefaultCloseOperation(javax.swing.WindowConstants.DISPOSE_ON_CLOSE);
+ setTitle("Edit Network Title");
+ jLabel1.setText("Please enter new network title:");
+ gridBagConstraints = new GridBagConstraints();
+ gridBagConstraints.anchor = GridBagConstraints.WEST;
+ gridBagConstraints.insets = new Insets(15, 10, 0, 0);
+ getContentPane().add(jLabel1, gridBagConstraints);
+
+ gridBagConstraints = new GridBagConstraints();
+ gridBagConstraints.gridy = 1;
+ gridBagConstraints.fill = GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.weightx = 1.0;
+ gridBagConstraints.insets = new Insets(10, 10, 10, 10);
+ getContentPane().add(tfNetworkTitle, gridBagConstraints);
+
+ btnOK.setText("OK");
+ btnOK.setPreferredSize(new Dimension(65, 23));
+ btnCancel.setPreferredSize(new Dimension(65, 23));
+
+ jPanel1.add(btnOK);
+
+ btnCancel.setText("Cancel");
+ jPanel1.add(btnCancel);
+
+ gridBagConstraints = new GridBagConstraints();
+ gridBagConstraints.gridy = 2;
+ gridBagConstraints.insets = new Insets(10, 0, 10, 0);
+ getContentPane().add(jPanel1, gridBagConstraints);
+
+ pack();
+ } // </editor-fold>
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ Object _actionObject = e.getSource();
+
+ // handle Button events
+ if (_actionObject instanceof JButton) {
+ JButton _btn = (JButton) _actionObject;
+
+ if (_btn == btnOK) {
+ networkTitle = tfNetworkTitle.getText();
+ this.dispose();
+ } else if (_btn == btnCancel) {
+ this.dispose();
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getNewNetworkTitle() {
+ return networkTitle;
+ }
+
+ private String networkTitle = "";
+
+ // Variables declaration - do not modify
+ private JButton btnCancel;
+ private JButton btnOK;
+ private JLabel jLabel1;
+ private JPanel jPanel1;
+ private JTextField tfNetworkTitle;
+
+ // End of variables declaration
+}
diff --git a/application/src/main/java/cytoscape/dialogs/ExportAsGraphicsFileChooser.java b/application/src/main/java/cytoscape/dialogs/ExportAsGraphicsFileChooser.java
new file mode 100644
index 0000000..5bad07c
--- /dev/null
+++ b/application/src/main/java/cytoscape/dialogs/ExportAsGraphicsFileChooser.java
@@ -0,0 +1,410 @@
+package cytoscape.dialogs;
+
+import java.awt.Dimension;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.io.File;
+import java.util.Enumeration;
+import java.util.List;
+import java.util.Properties;
+
+import javax.swing.DefaultComboBoxModel;
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JComboBox;
+import javax.swing.JDialog;
+import javax.swing.JOptionPane;
+
+import com.lowagie.text.Font;
+
+import cytoscape.Cytoscape;
+import cytoscape.CytoscapeInit;
+import cytoscape.util.CyFileFilter;
+import cytoscape.util.FileUtil;
+import cytoscape.view.CyNetworkView;
+import cytoscape.visual.VisualStyle;
+import cytoscape.visual.calculators.Calculator;
+
+/**
+ * Dialog that chooses file to export to.
+ * @author Samad Lotia
+ */
+public class ExportAsGraphicsFileChooser extends JDialog implements ActionListener {
+
+ private static final long serialVersionUID = 4895622023575071394L;
+
+ private final String SEPARATOR = System.getProperty("file.separator");
+
+ private static final Dimension DIALOG_SIZE = new Dimension(650, 165);
+
+ private File selectedFile;
+ private CyFileFilter selectedFilter;
+
+ private boolean exportTextAsFont = !(Boolean.getBoolean(CytoscapeInit.getProperties().getProperty("exportTextAsShape")));
+
+ @Deprecated
+ public ExportAsGraphicsFileChooser(final CyFileFilter[] formats) {
+ this(formats, null);
+ }
+
+ public ExportAsGraphicsFileChooser(final CyFileFilter[] formats, final CyFileFilter defaultFilter) {
+
+ super(Cytoscape.getDesktop(), "Export Network View as Graphics");
+ setDefaultCloseOperation(JDialog.DISPOSE_ON_CLOSE);
+
+ this.selectedFilter = defaultFilter;
+
+ initComponents();
+
+ setModal(true);
+
+ chooseFileButton.addActionListener(this);
+ cancelButton.addActionListener(this);
+ formatComboBox.addActionListener(this);
+ chkExportTextAsFont.addActionListener(this);
+
+ // Set the init value based on Cytoscape property "exportTextAsShape"
+ chkExportTextAsFont.setSelected(exportTextAsFont);
+
+ formatComboBox.setModel(new DefaultComboBoxModel(formats));
+
+ if(selectedFilter == null) {
+ formatComboBox.setSelectedIndex(0);
+ this.selectedFilter = (CyFileFilter) formatComboBox.getSelectedItem();
+ } else
+ formatComboBox.setSelectedItem(defaultFilter);
+
+ formatComboBox.addItemListener(new FormatItemListener());
+
+ removeFile();
+
+ setDefaultFileName();
+
+ setLocationRelativeTo(Cytoscape.getDesktop());
+ pack();
+ okButton.requestFocusInWindow();
+ }
+
+
+ private void setDefaultFileName() {
+ final File recentDir = CytoscapeInit.getMRUD();
+ final CyNetworkView view = Cytoscape.getCurrentNetworkView();
+
+ final String title = view.getTitle();
+
+ this.selectedFile = new File(recentDir.toString() + SEPARATOR + title);
+ this.updateExtension();
+ this.filePathField.setText(selectedFile.toString());
+ }
+
+
+ // This is a work-around, because ItemEvent is received twice in MyItemListener.
+ private static int eventCount =0;
+
+ private class FormatItemListener implements ItemListener {
+ public void itemStateChanged(ItemEvent e) {
+ // Ignore double event
+ eventCount++;
+ if (eventCount%2 == 0) {
+ eventCount =0;
+ return;
+ }
+
+ if (formatComboBox.getSelectedItem().toString().equalsIgnoreCase("EPS (*.eps)") && useTransparency()) {
+ JOptionPane.showMessageDialog( Cytoscape.getDesktop(),
+ "Could not export in EPS format, because transparency is used in the Visual Style!");
+ okButton.setEnabled(false);
+ chooseFileButton.setEnabled(false);
+ }
+ else {
+ if (selectedFile !=null)
+ okButton.setEnabled(true);
+ else
+ okButton.setEnabled(false);
+
+ chooseFileButton.setEnabled(true);
+ }
+ }
+ }
+
+ // Check if transparency is used in the visual style
+ private boolean useTransparency(){
+
+ VisualStyle vs = Cytoscape.getVisualMappingManager().getVisualStyle();
+
+ // Check opacity in default setting
+ Properties node_default_props = vs.getNodeAppearanceCalculator().getDefaultAppearance().getDefaultProperties("");
+ Properties edge_default_props = vs.getEdgeAppearanceCalculator().getDefaultAppearance().getDefaultProperties("");
+
+ Enumeration nodePropNames = node_default_props.propertyNames();
+ Enumeration edgePropNames = edge_default_props.propertyNames();
+
+ while (nodePropNames.hasMoreElements()) {
+ String tmp = (String) nodePropNames.nextElement();
+ if (tmp.contains("Opacity")) {
+ if ((new Float(node_default_props.getProperty(tmp))).floatValue() != 255) {
+ return true;
+ }
+ }
+ }
+
+ while (edgePropNames.hasMoreElements()) {
+ String tmp = (String) edgePropNames.nextElement();
+ if (tmp.contains("Opacity")) {
+ if ((new Float(edge_default_props.getProperty(tmp))).floatValue() != 255) {
+ return true;
+ }
+ }
+ }
+
+ //Check opacity in calculators
+ List<Calculator> node_calculators = vs.getNodeAppearanceCalculator().getCalculators();
+ for (Calculator cal: node_calculators) {
+ if (cal.getVisualPropertyType() == cytoscape.visual.VisualPropertyType.NODE_OPACITY ||
+ cal.getVisualPropertyType() == cytoscape.visual.VisualPropertyType.NODE_BORDER_OPACITY ||
+ (cal.getVisualPropertyType() == cytoscape.visual.VisualPropertyType.NODE_LABEL_OPACITY))
+ {
+ return true;
+ }
+ }
+
+ List<Calculator> edge_calculators = vs.getEdgeAppearanceCalculator().getCalculators();
+ for (Calculator cal: edge_calculators) {
+ if (cal.getVisualPropertyType()== cytoscape.visual.VisualPropertyType.EDGE_OPACITY ||
+ cal.getVisualPropertyType()== cytoscape.visual.VisualPropertyType.EDGE_LABEL_OPACITY ||
+ cal.getVisualPropertyType()== cytoscape.visual.VisualPropertyType.EDGE_TGTARROW_OPACITY ||
+ cal.getVisualPropertyType()== cytoscape.visual.VisualPropertyType.EDGE_SRCARROW_OPACITY
+ ) {
+ return true;
+ }
+ }
+
+ return false;
+ }
+
+ public CyFileFilter getSelectedFormat() {
+ return (CyFileFilter) formatComboBox.getSelectedItem();
+ }
+
+
+ public File getSelectedFile() {
+ return selectedFile;
+ }
+
+
+ public void addActionListener(ActionListener l) {
+ okButton.addActionListener(l);
+ }
+
+
+ protected void assignFile(File file) {
+ selectedFile = file;
+ filePathField.setText(selectedFile.getPath());
+ okButton.setEnabled(true);
+ if (formatComboBox.getSelectedItem().toString().equalsIgnoreCase("EPS (*.eps)") && useTransparency()) {
+ okButton.setEnabled(false);
+ }
+ }
+
+
+ protected void removeFile() {
+ selectedFile = null;
+ filePathField.setText("");
+ okButton.setEnabled(false);
+ }
+
+
+ private void updateExtension() {
+ if (selectedFile == null)
+ return;
+
+ // Strip away the extension
+ String name = selectedFile.getName();
+ int extensionIndex = name.lastIndexOf('.');
+ if (extensionIndex != -1)
+ name = name.substring(0, extensionIndex);
+
+ // Figure out what extension to append
+ CyFileFilter filter = (CyFileFilter) formatComboBox.getSelectedItem();
+ String newExtension = (String) filter.getExtensionSet().iterator().next();
+
+ selectedFile = new File(selectedFile.getParent(), name + "." + newExtension);
+ filePathField.setText(selectedFile.getPath());
+ okButton.setEnabled(true);
+ if (formatComboBox.getSelectedItem().toString().equalsIgnoreCase("EPS (*.eps)") && useTransparency()) {
+ okButton.setEnabled(false);
+ }
+ }
+
+
+ public void actionPerformed(ActionEvent e) {
+ Object obj = e.getSource();
+ if (obj instanceof JButton) {
+ JButton btn = (JButton) obj;
+ if (btn == okButton) {
+ //handle in ExportAsGraphicsAction
+ }
+ else if (btn == cancelButton) {
+ this.dispose();
+ }
+ else if (btn == chooseFileButton) {
+ final CyFileFilter filter = getSelectedFormat();
+ String extension = "." + (String) filter.getExtensionSet().iterator().next();
+ CyFileFilter[] filters = new CyFileFilter[1];
+ filters[0] = filter;
+ File[] files = FileUtil.getFiles("Export Network View as Graphics", FileUtil.SAVE, filters, null, null, false);
+ if (files != null && files.length != 0 && files[0] != null)
+ {
+ File file = files[0];
+ if (!file.getName().endsWith(extension))
+ file = new File(file.getPath() + extension);
+ assignFile(file);
+ }
+ }
+ }
+ if (obj instanceof JComboBox) {
+ updateExtension();
+ CyFileFilter filter = (CyFileFilter) formatComboBox.getSelectedItem();
+
+ if (filter.getClass().getName().equalsIgnoreCase("cytoscape.actions.PDFExportFilter") ||
+ filter.getClass().getName().equalsIgnoreCase("cytoscape.actions.SVGExportFilter") ||
+ filter.getClass().getName().equalsIgnoreCase("cytoscape.actions.PSExportFilter")) {
+ this.chkExportTextAsFont.setEnabled(true);
+ }
+ else {
+ this.chkExportTextAsFont.setEnabled(false);
+ }
+ }
+ if (obj instanceof JCheckBox) {
+ exportTextAsFont = chkExportTextAsFont.isSelected();
+ // Update Cytoscape property "exportTextAsShape"
+ String exportTextAsShape = "false";
+ if (!exportTextAsFont) {
+ exportTextAsShape = "true";
+ }
+ CytoscapeInit.getProperties().setProperty("exportTextAsShape", exportTextAsShape);
+ }
+ }
+
+
+ public boolean getExportTextAsFont() {
+ return exportTextAsFont;
+ }
+
+
+ /** This method is called from within the constructor to
+ * initialize the form.
+ * WARNING: Do NOT modify this code. The content of this method is
+ * always regenerated by the Form Editor.
+ */
+ // <editor-fold defaultstate="collapsed" desc=" Generated Code ">
+ private void initComponents() {
+ this.setMinimumSize(DIALOG_SIZE);
+ this.setPreferredSize(DIALOG_SIZE);
+
+ java.awt.GridBagConstraints gridBagConstraints;
+
+ selectFileLabel = new javax.swing.JLabel();
+ filePathField = new javax.swing.JTextField();
+ chooseFileButton = new javax.swing.JButton();
+ formatLabel = new javax.swing.JLabel();
+ formatComboBox = new javax.swing.JComboBox();
+ btnPanel = new javax.swing.JPanel();
+ cancelButton = new javax.swing.JButton();
+ okButton = new javax.swing.JButton();
+ jSeparator1 = new javax.swing.JSeparator();
+ chkExportTextAsFont = new javax.swing.JCheckBox();
+
+ getContentPane().setLayout(new java.awt.GridBagLayout());
+
+ setDefaultCloseOperation(javax.swing.WindowConstants.DISPOSE_ON_CLOSE);
+ selectFileLabel.setText("File to export to:");
+ selectFileLabel.setFont(new java.awt.Font("SansSerif", Font.BOLD, 12));
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridwidth = 2;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
+ gridBagConstraints.insets = new java.awt.Insets(20, 10, 10, 0);
+ getContentPane().add(selectFileLabel, gridBagConstraints);
+
+ filePathField.setEditable(false);
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 0;
+ gridBagConstraints.gridy = 1;
+ gridBagConstraints.gridwidth = 3;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.weightx = 1.0;
+ gridBagConstraints.insets = new java.awt.Insets(0, 10, 10, 0);
+ getContentPane().add(filePathField, gridBagConstraints);
+
+ chooseFileButton.setText("Choose...");
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 3;
+ gridBagConstraints.gridy = 1;
+ gridBagConstraints.insets = new java.awt.Insets(0, 10, 10, 10);
+ getContentPane().add(chooseFileButton, gridBagConstraints);
+
+ formatLabel.setText("Format:");
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = 2;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
+ gridBagConstraints.insets = new java.awt.Insets(0, 10, 0, 10);
+ getContentPane().add(formatLabel, gridBagConstraints);
+
+ formatComboBox.setPreferredSize(new java.awt.Dimension(120, 22));
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = 2;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
+ gridBagConstraints.insets = new java.awt.Insets(0, 0, 0, 10);
+ getContentPane().add(formatComboBox, gridBagConstraints);
+
+ final Dimension buttonSize = new Dimension(100, 25);
+ okButton.setText("OK");
+ okButton.setPreferredSize(buttonSize);
+ btnPanel.add(okButton);
+
+ cancelButton.setText("Cancel");
+ cancelButton.setPreferredSize(buttonSize);
+ btnPanel.add(cancelButton);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 1;
+ gridBagConstraints.gridy = 4;
+ gridBagConstraints.gridwidth = 3;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.insets = new java.awt.Insets(0, 350, 15, 0);
+ getContentPane().add(btnPanel, gridBagConstraints);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = 3;
+ gridBagConstraints.gridwidth = 4;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.insets = new java.awt.Insets(0, 10, 0, 10);
+ getContentPane().add(jSeparator1, gridBagConstraints);
+
+ chkExportTextAsFont.setText("Export text as font");
+ chkExportTextAsFont.setBorder(javax.swing.BorderFactory.createEmptyBorder(0, 0, 0, 0));
+ chkExportTextAsFont.setMargin(new java.awt.Insets(0, 0, 0, 0));
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 2;
+ gridBagConstraints.gridy = 2;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
+ gridBagConstraints.insets = new java.awt.Insets(0, 20, 0, 0);
+ getContentPane().add(chkExportTextAsFont, gridBagConstraints);
+
+ }// </editor-fold>
+
+ // Variables declaration - do not modify
+ private javax.swing.JPanel btnPanel;
+ private javax.swing.JButton cancelButton;
+ private javax.swing.JCheckBox chkExportTextAsFont;
+ private javax.swing.JButton chooseFileButton;
+ private javax.swing.JTextField filePathField;
+ private javax.swing.JComboBox formatComboBox;
+ private javax.swing.JLabel formatLabel;
+ private javax.swing.JSeparator jSeparator1;
+ private javax.swing.JButton okButton;
+ private javax.swing.JLabel selectFileLabel;
+ // End of variables declaration
+}
diff --git a/application/src/main/java/cytoscape/dialogs/ExportBitmapOptionsDialog.java b/application/src/main/java/cytoscape/dialogs/ExportBitmapOptionsDialog.java
new file mode 100644
index 0000000..79b96f4
--- /dev/null
+++ b/application/src/main/java/cytoscape/dialogs/ExportBitmapOptionsDialog.java
@@ -0,0 +1,391 @@
+package cytoscape.dialogs;
+
+import javax.swing.*;
+import javax.swing.border.*;
+import java.awt.*;
+import java.awt.event.*;
+import java.text.*;
+
+import cytoscape.Cytoscape;
+
+/**
+ * Options dialog for exporting to bitmap images.
+ * @author Samad Lotia
+ */
+public class ExportBitmapOptionsDialog extends JDialog {
+
+ private static final long serialVersionUID = 5333484131669731753L;
+ private JFormattedTextField zoomField;
+ private JFormattedTextField widthInPixelsField;
+ private JFormattedTextField heightInPixelsField;
+ private JFormattedTextField widthInInchesField;
+ private JFormattedTextField heightInInchesField;
+ private JComboBox resolutionComboBox;
+ private JButton okButton;
+
+ private int originalWidth;
+ private int originalHeight;
+
+ /**
+ * Creates the options dialog.
+ * This dialog disposes itself when it is closed.
+ * @param imageWidth The image width to be exported
+ * @param imageHeight The image height to be exported
+ * @param listener The action will be called when the "OK" button is clicked
+ */
+ public ExportBitmapOptionsDialog(int imageWidth, int imageHeight) {
+ super(Cytoscape.getDesktop(), "Export Bitmap Options");
+
+ this.originalWidth = imageWidth;
+ this.originalHeight = imageHeight;
+
+ setDefaultCloseOperation(JDialog.DISPOSE_ON_CLOSE);
+ Container content = getContentPane();
+
+ JPanel sizePanel = new JPanel();
+ sizePanel.setBorder(new TitledBorder(new EtchedBorder(), "Image Size"));
+ sizePanel.setLayout(new GridBagLayout());
+ GridBagConstraints c = new GridBagConstraints();
+ c.anchor = GridBagConstraints.WEST;
+ c.insets = new Insets(5,5,5,5);
+
+ JLabel zoomLabel = new JLabel("Zoom: ");
+ c.gridx = 0; c.gridy = 0;
+ c.gridwidth = 1; c.gridheight = 1;
+ c.weightx = 0.0; c.weighty = 0.0;
+ c.fill = GridBagConstraints.NONE;
+ sizePanel.add(zoomLabel, c);
+
+ zoomField = new JFormattedTextField(new DecimalFormat());
+ zoomField.setColumns(3);
+ ZoomListener zoomListener = new ZoomListener(zoomField);
+ c.gridx = 1; c.gridy = 0;
+ c.gridwidth = 1; c.gridheight = 1;
+ c.weightx = 1.0; c.weighty = 0.0;
+ c.fill = GridBagConstraints.HORIZONTAL;
+ sizePanel.add(zoomField, c);
+
+ JLabel zoomPercentLabel = new JLabel("%");
+ c.gridx = 2; c.gridy = 0;
+ c.gridwidth = 1; c.gridheight = 1;
+ c.weightx = 0.0; c.weighty = 0.0;
+ c.fill = GridBagConstraints.NONE;
+ sizePanel.add(zoomPercentLabel, c);
+
+ JSeparator separator0 = new JSeparator();
+ c.gridx = 0; c.gridy = 1;
+ c.gridwidth = 3; c.gridheight = 1;
+ c.weightx = 1.0; c.weighty = 0.0;
+ c.fill = GridBagConstraints.HORIZONTAL;
+ sizePanel.add(separator0, c);
+
+ JLabel widthInPixelsLabel = new JLabel("Width: ");
+ c.gridx = 0; c.gridy = 2;
+ c.gridwidth = 1; c.gridheight = 1;
+ c.weightx = 0.0; c.weighty = 0.0;
+ c.fill = GridBagConstraints.NONE;
+ sizePanel.add(widthInPixelsLabel, c);
+
+ widthInPixelsField = new JFormattedTextField(NumberFormat.getIntegerInstance());
+ widthInPixelsField.setColumns(4);
+ new WidthInPixelsListener(widthInPixelsField);
+ c.gridx = 1; c.gridy = 2;
+ c.gridwidth = 1; c.gridheight = 1;
+ c.weightx = 1.0; c.weighty = 0.0;
+ c.fill = GridBagConstraints.HORIZONTAL;
+ sizePanel.add(widthInPixelsField, c);
+
+ JLabel widthPixelsLabel = new JLabel("pixels");
+ c.gridx = 2; c.gridy = 2;
+ c.gridwidth = 1; c.gridheight = 1;
+ c.weightx = 0.0; c.weighty = 0.0;
+ c.fill = GridBagConstraints.NONE;
+ sizePanel.add(widthPixelsLabel, c);
+
+ JLabel heightInPixelsLabel = new JLabel("Height:");
+ c.gridx = 0; c.gridy = 3;
+ c.gridwidth = 1; c.gridheight = 1;
+ c.weightx = 0.0; c.weighty = 0.0;
+ c.fill = GridBagConstraints.NONE;
+ sizePanel.add(heightInPixelsLabel, c);
+
+ heightInPixelsField = new JFormattedTextField(NumberFormat.getIntegerInstance());
+ heightInPixelsField.setColumns(4);
+ new HeightInPixelsListener(heightInPixelsField);
+ c.gridx = 1; c.gridy = 3;
+ c.gridwidth = 1; c.gridheight = 1;
+ c.weightx = 1.0; c.weighty = 0.0;
+ c.fill = GridBagConstraints.HORIZONTAL;
+ sizePanel.add(heightInPixelsField, c);
+
+ JLabel heightPixelsLabel = new JLabel("pixels");
+ c.gridx = 2; c.gridy = 3;
+ c.gridwidth = 1; c.gridheight = 1;
+ c.weightx = 0.0; c.weighty = 0.0;
+ c.fill = GridBagConstraints.NONE;
+ sizePanel.add(heightPixelsLabel, c);
+
+ JSeparator separator1 = new JSeparator();
+ c.gridx = 0; c.gridy = 4;
+ c.gridwidth = 3; c.gridheight = 1;
+ c.weightx = 1.0; c.weighty = 0.0;
+ c.fill = GridBagConstraints.HORIZONTAL;
+ sizePanel.add(separator1, c);
+
+ JLabel widthInInchesLabel = new JLabel("Width: ");
+ c.gridx = 0; c.gridy = 5;
+ c.gridwidth = 1; c.gridheight = 1;
+ c.weightx = 0.0; c.weighty = 0.0;
+ c.fill = GridBagConstraints.NONE;
+ sizePanel.add(widthInInchesLabel, c);
+
+ widthInInchesField = new JFormattedTextField(new DecimalFormat());
+ widthInInchesField.setColumns(4);
+ new WidthInInchesListener(widthInInchesField);
+ c.gridx = 1; c.gridy = 5;
+ c.gridwidth = 1; c.gridheight = 1;
+ c.weightx = 1.0; c.weighty = 0.0;
+ c.fill = GridBagConstraints.HORIZONTAL;
+ sizePanel.add(widthInInchesField, c);
+
+ JLabel widthInchesLabel = new JLabel("inches");
+ c.gridx = 2; c.gridy = 5;
+ c.gridwidth = 1; c.gridheight = 1;
+ c.weightx = 0.0; c.weighty = 0.0;
+ c.fill = GridBagConstraints.NONE;
+ sizePanel.add(widthInchesLabel, c);
+
+ JLabel heightInInchesLabel = new JLabel("Height:");
+ c.gridx = 0; c.gridy = 6;
+ c.gridwidth = 1; c.gridheight = 1;
+ c.weightx = 0.0; c.weighty = 0.0;
+ c.fill = GridBagConstraints.NONE;
+ sizePanel.add(heightInInchesLabel, c);
+
+ heightInInchesField = new JFormattedTextField(new DecimalFormat());
+ heightInInchesField.setColumns(4);
+ new HeightInInchesListener(heightInInchesField);
+ c.gridx = 1; c.gridy = 6;
+ c.gridwidth = 1; c.gridheight = 1;
+ c.weightx = 1.0; c.weighty = 0.0;
+ c.fill = GridBagConstraints.HORIZONTAL;
+ sizePanel.add(heightInInchesField, c);
+
+ JLabel heightInchesLabel = new JLabel("inches");
+ c.gridx = 2; c.gridy = 6;
+ c.gridwidth = 1; c.gridheight = 1;
+ c.weightx = 0.0; c.weighty = 0.0;
+ c.fill = GridBagConstraints.NONE;
+ sizePanel.add(heightInchesLabel, c);
+
+ JLabel resolutionLabel = new JLabel("Resolution:");
+ c.gridx = 0; c.gridy = 7;
+ c.gridwidth = 1; c.gridheight = 1;
+ c.weightx = 0.0; c.weighty = 0.0;
+ c.fill = GridBagConstraints.NONE;
+ sizePanel.add(resolutionLabel, c);
+
+ final Integer[] resolutions = { 72, 100, 150, 300, 600 };
+ resolutionComboBox = new JComboBox(resolutions);
+ resolutionComboBox.addActionListener(zoomListener);
+ c.gridx = 1; c.gridy = 7;
+ c.gridwidth = 1; c.gridheight = 1;
+ c.weightx = 1.0; c.weighty = 0.0;
+ c.fill = GridBagConstraints.HORIZONTAL;
+ sizePanel.add(resolutionComboBox, c);
+
+ JLabel dpiLabel = new JLabel("DPI");
+ c.gridx = 2; c.gridy = 7;
+ c.gridwidth = 1; c.gridheight = 1;
+ c.weightx = 0.0; c.weighty = 0.0;
+ c.fill = GridBagConstraints.NONE;
+ sizePanel.add(dpiLabel, c);
+
+ okButton = new JButton(" OK ");
+ okButton.setDefaultCapable(true);
+ JButton cancelButton = new JButton("Cancel");
+ cancelButton.addActionListener(new CancelListener());
+
+ JPanel buttonsPanel = new JPanel();
+ buttonsPanel.add(cancelButton);
+ buttonsPanel.add(okButton);
+
+ content.setLayout(new GridBagLayout());
+ c.gridx = 0; c.gridy = 0;
+ c.weightx = 1.0; c.weighty = 0.0;
+ c.fill = GridBagConstraints.HORIZONTAL;
+ content.add(sizePanel, c);
+ c.gridx = 0; c.gridy = 1;
+ c.weightx = 1.0; c.weighty = 1.0;
+ c.fill = GridBagConstraints.NONE;
+ c.anchor = GridBagConstraints.SOUTHEAST;
+ content.add(buttonsPanel, c);
+
+ updateOnZoom(1.0);
+
+ setLocationRelativeTo(Cytoscape.getDesktop());
+ pack();
+ }
+
+
+ public double getZoom()
+ {
+ return ((Number) zoomField.getValue()).doubleValue() / 100.0;
+ }
+
+ /**
+ * Add an action for when the "OK" button is pressed.
+ */
+ public void addActionListener(ActionListener l)
+ {
+ okButton.addActionListener(l);
+ }
+
+ private void updateOnZoom(double newZoom)
+ {
+ zoomField.setValue(new Double(newZoom * 100.0));
+ int newWidth = (int) (newZoom * originalWidth);
+ int newHeight = (int) (newZoom * originalHeight);
+ widthInPixelsField.setValue(new Integer(newWidth));
+ heightInPixelsField.setValue(new Integer(newHeight));
+ final double dpi = ((Number) resolutionComboBox.getSelectedItem()).doubleValue();
+ final double newWidthInches = newWidth / dpi;
+ final double newHeightInches = newHeight / dpi;
+ widthInInchesField.setValue(new Double(newWidthInches));
+ heightInInchesField.setValue(new Double(newHeightInches));
+ }
+
+ private void updateOnWidthPixels(int newWidthPixels)
+ {
+ double newZoom = ((double) newWidthPixels) / ((double) originalWidth);
+ updateOnZoom(newZoom);
+ }
+
+ private void updateOnHeightPixels(int newHeightPixels)
+ {
+ double newZoom = ((double) newHeightPixels) / ((double) originalHeight);
+ updateOnZoom(newZoom);
+ }
+
+ private void updateOnWidthInches(double newWidthInches)
+ {
+ double dpi = ((Number) resolutionComboBox.getSelectedItem()).doubleValue();
+ updateOnWidthPixels((int) (newWidthInches * dpi));
+ }
+
+ private void updateOnHeightInches(double newHeightInches)
+ {
+ double dpi = ((Number) resolutionComboBox.getSelectedItem()).doubleValue();
+ updateOnHeightPixels((int) (newHeightInches * dpi));
+ }
+
+ private abstract class FormattedFieldListener extends FocusAdapter implements ActionListener
+ {
+ public abstract void update();
+
+ private JFormattedTextField field;
+ public FormattedFieldListener(JFormattedTextField field)
+ {
+ this.field = field;
+ field.addActionListener(this);
+ field.addFocusListener(this);
+ }
+
+ public void actionPerformed(ActionEvent e)
+ {
+ update();
+ }
+
+ public void focusLost(FocusEvent l)
+ {
+ try
+ {
+ field.commitEdit();
+ }
+ catch (ParseException exp)
+ {
+ return;
+ }
+ update();
+ }
+ }
+
+ private class ZoomListener extends FormattedFieldListener
+ {
+ public ZoomListener(JFormattedTextField field)
+ {
+ super(field);
+ }
+
+ public void update()
+ {
+ double zoom = ((Number) zoomField.getValue()).doubleValue();
+ zoom /= 100.0;
+ updateOnZoom(zoom);
+ }
+ }
+
+ private class WidthInPixelsListener extends FormattedFieldListener
+ {
+ public WidthInPixelsListener(JFormattedTextField field)
+ {
+ super(field);
+ }
+
+ public void update()
+ {
+ int width = ((Number) widthInPixelsField.getValue()).intValue();
+ updateOnWidthPixels(width);
+ }
+ }
+
+ private class HeightInPixelsListener extends FormattedFieldListener
+ {
+ public HeightInPixelsListener(JFormattedTextField field)
+ {
+ super(field);
+ }
+
+ public void update()
+ {
+ int height = ((Number) heightInPixelsField.getValue()).intValue();
+ updateOnHeightPixels(height);
+ }
+ }
+
+ private class WidthInInchesListener extends FormattedFieldListener
+ {
+ public WidthInInchesListener(JFormattedTextField field)
+ {
+ super(field);
+ }
+
+ public void update()
+ {
+ double width = ((Number) widthInInchesField.getValue()).doubleValue();
+ updateOnWidthInches(width);
+ }
+ }
+
+ private class HeightInInchesListener extends FormattedFieldListener
+ {
+ public HeightInInchesListener(JFormattedTextField field)
+ {
+ super(field);
+ }
+
+ public void update()
+ {
+ double height = ((Number) heightInInchesField.getValue()).doubleValue();
+ updateOnHeightInches(height);
+ }
+ }
+
+ private class CancelListener implements ActionListener
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ ExportBitmapOptionsDialog.this.dispose();
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/dialogs/ExpressionDataPopupTable.java b/application/src/main/java/cytoscape/dialogs/ExpressionDataPopupTable.java
new file mode 100644
index 0000000..7df46d8
--- /dev/null
+++ b/application/src/main/java/cytoscape/dialogs/ExpressionDataPopupTable.java
@@ -0,0 +1,366 @@
+/*
+ File: ExpressionDataPopupTable.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// ExpressionDataPopupTable
+package cytoscape.dialogs;
+
+import cytoscape.data.ExpressionData;
+import cytoscape.data.mRNAMeasurement;
+
+import java.awt.*;
+import java.awt.BorderLayout;
+import java.awt.event.*;
+
+import java.util.Vector;
+
+import javax.swing.AbstractAction;
+import javax.swing.DefaultCellEditor;
+import javax.swing.JButton;
+import javax.swing.JComboBox;
+import javax.swing.JDialog;
+import javax.swing.JFrame;
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTable;
+import javax.swing.SwingUtilities;
+import javax.swing.table.AbstractTableModel;
+import javax.swing.table.DefaultTableCellRenderer;
+import javax.swing.table.TableCellRenderer;
+import javax.swing.table.TableColumn;
+import javax.swing.table.TableColumnModel;
+
+
+/**
+ *
+ */
+public class ExpressionDataPopupTable extends JDialog {
+ Frame mainFrame;
+ ExpressionDataPopupTable popupTable;
+ private JTable table;
+ ExpressionData geneExpressionInfo = null;
+
+ /**
+ * Creates a new ExpressionDataPopupTable object.
+ *
+ * @param parentFrame DOCUMENT ME!
+ * @param geneNames DOCUMENT ME!
+ * @param conditionName DOCUMENT ME!
+ * @param geneExpressionInfo DOCUMENT ME!
+ */
+ public ExpressionDataPopupTable(Frame parentFrame, String[] geneNames, String conditionName,
+ ExpressionData geneExpressionInfo) {
+ super(parentFrame, false);
+ mainFrame = parentFrame;
+ setTitle(conditionName);
+ this.geneExpressionInfo = geneExpressionInfo;
+ popupTable = this;
+
+ JPanel panel = new JPanel();
+ panel.setLayout(new BorderLayout());
+
+ table = new JTable(new MultipleGenesTableModel(geneNames, conditionName));
+ // table.setPreferredScrollableViewportSize (new Dimension (400, 100));
+ table.setDefaultRenderer(JButton.class,
+ new ButtonCellRenderer(table.getDefaultRenderer(JButton.class)));
+ table.addMouseListener(new MyMouseListener(table));
+
+ //table.getColumnModel().getColumn(2).setPreferredWidth (6);
+ //table.getColumnModel().getColumn(3).setPreferredWidth (8);
+ JScrollPane scrollPane = new JScrollPane(table);
+ panel.add(scrollPane, BorderLayout.CENTER);
+
+ JPanel buttonPanel = new JPanel();
+ JButton okButton = new JButton("OK");
+ okButton.addActionListener(new OKAction(this));
+ buttonPanel.add(okButton, BorderLayout.CENTER);
+ pack();
+ panel.add(buttonPanel, BorderLayout.SOUTH);
+
+ setContentPane(panel);
+ } // ExpressionDataPopupTable ctor
+
+ /**
+ * Creates a new ExpressionDataPopupTable object.
+ *
+ * @param parentFrame DOCUMENT ME!
+ * @param geneName DOCUMENT ME!
+ * @param conditionNames DOCUMENT ME!
+ * @param geneExpressionInfo DOCUMENT ME!
+ */
+ public ExpressionDataPopupTable(Frame parentFrame, String geneName, String[] conditionNames,
+ ExpressionData geneExpressionInfo) {
+ super(parentFrame, false);
+ setTitle(geneName);
+ this.geneExpressionInfo = geneExpressionInfo;
+ popupTable = this;
+
+ JPanel panel = new JPanel();
+ panel.setLayout(new BorderLayout());
+
+ table = new JTable(new MultipleConditionsTableModel(geneName, conditionNames));
+ table.setPreferredScrollableViewportSize(new Dimension(400, 400));
+ table.setDefaultRenderer(JButton.class,
+ new ButtonCellRenderer(table.getDefaultRenderer(JButton.class)));
+ table.addMouseListener(new MyMouseListener(table));
+
+ JScrollPane scrollPane = new JScrollPane(table);
+ panel.add(scrollPane, BorderLayout.CENTER);
+
+ JPanel buttonPanel = new JPanel();
+ JButton okButton = new JButton("OK");
+ okButton.addActionListener(new OKAction(this));
+ buttonPanel.add(okButton, BorderLayout.CENTER);
+ panel.add(buttonPanel, BorderLayout.SOUTH);
+
+ setContentPane(panel);
+ } // ExpressionDataPopupTable ctor
+
+ public class OKAction extends AbstractAction {
+ private JDialog dialog;
+
+ OKAction(JDialog popup) {
+ super("");
+ this.dialog = popup;
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ dialog.dispose();
+ }
+ } // QuitAction
+
+ class MultipleGenesTableModel extends AbstractTableModel {
+ String[] columnNames;
+ Object[][] data;
+
+ public MultipleGenesTableModel(String[] geneNames, String conditionName) {
+ columnNames = new String[3];
+ columnNames[0] = "GENE";
+ columnNames[1] = "RATIO";
+ columnNames[2] = "LAMBDA";
+
+ int geneCount = geneNames.length;
+ data = new Object[geneCount][3];
+
+ for (int i = 0; i < geneNames.length; i++) {
+ mRNAMeasurement measurement = geneExpressionInfo.getMeasurement(geneNames[i],
+ conditionName);
+ final String condition = conditionName;
+ final String name = geneNames[i];
+
+ if (measurement != null) {
+ data[i][1] = new Double(measurement.getRatio());
+ data[i][2] = new Double(measurement.getSignificance());
+ }
+
+ JButton button = new JButton(geneNames[i]);
+ button.setToolTipText("display expression values for all conditions");
+ data[i][0] = button;
+ ((JButton) data[i][0]).addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ //PopupTextArea text = new PopupTextArea (popupTable, name, name);
+ //text.setLocationRelativeTo (popupTable);
+ String[] conditions = geneExpressionInfo.getConditionNames();
+ ExpressionDataPopupTable crossConditionsTable = new ExpressionDataPopupTable(mainFrame,
+ name,
+ conditions,
+ geneExpressionInfo);
+ crossConditionsTable.pack();
+ crossConditionsTable.setLocationRelativeTo(mainFrame);
+ crossConditionsTable.setVisible(true);
+ }
+ });
+ } // for i
+ } // ctor
+
+ public String getColumnName(int col) {
+ return columnNames[col];
+ }
+
+ public int getColumnCount() {
+ return columnNames.length;
+ }
+
+ public int getRowCount() {
+ return data.length;
+ }
+
+ public Object getValueAt(int row, int col) {
+ return data[row][col];
+ }
+
+ public boolean isCellEditable(int row, int col) {
+ return false;
+ }
+
+ public Class getColumnClass(int column) {
+ return getValueAt(0, column).getClass();
+ }
+ } // inner class MultipleGenesTableModel
+
+ class MultipleConditionsTableModel extends AbstractTableModel {
+ String[] columnNames;
+ Object[][] data;
+
+ public MultipleConditionsTableModel(String geneName, String[] conditionNames) {
+ columnNames = new String[3];
+ columnNames[0] = "CONDITION";
+ columnNames[1] = "RATIO";
+ columnNames[2] = "LAMBDA";
+
+ int conditionCount = conditionNames.length;
+ data = new Object[conditionCount][3];
+
+ for (int i = 0; i < conditionNames.length; i++) {
+ mRNAMeasurement measurement = geneExpressionInfo.getMeasurement(geneName,
+ conditionNames[i]);
+ final String condition = conditionNames[i];
+ data[i][0] = condition;
+
+ if (measurement == null) {
+ data[i][1] = new Double(-999999.99);
+ data[i][2] = new Double(-999999.99);
+ } else {
+ data[i][1] = new Double(measurement.getRatio());
+ data[i][2] = new Double(measurement.getSignificance());
+ }
+
+ //JButton button = new JButton (geneNames [i]);
+ //data [i][0] = button;
+ //((JButton)data[i][0]).addActionListener (new ActionListener () {
+ // public void actionPerformed (ActionEvent e) {
+ // PopupTextArea text = new PopupTextArea (popupTable, name, name);
+ // text.setLocationRelativeTo (popupTable);
+ // }});
+ } // for i
+ } // ctor
+
+ public String getColumnName(int col) {
+ return columnNames[col];
+ }
+
+ public int getColumnCount() {
+ return columnNames.length;
+ }
+
+ public int getRowCount() {
+ return data.length;
+ }
+
+ public Object getValueAt(int row, int col) {
+ return data[row][col];
+ }
+
+ public boolean isCellEditable(int row, int col) {
+ return false;
+ }
+
+ public Class getColumnClass(int column) {
+ return getValueAt(0, column).getClass();
+ }
+ } // inner class MultipleConditionsTableModel
+
+ class ButtonCellRenderer implements TableCellRenderer {
+ private TableCellRenderer defaultRenderer;
+
+ public ButtonCellRenderer(TableCellRenderer renderer) {
+ defaultRenderer = renderer;
+ }
+
+ public Component getTableCellRendererComponent(JTable table, Object value,
+ boolean isSelected, boolean hasFocus,
+ int row, int column) {
+ if (value instanceof Component)
+ return (Component) value;
+ else
+
+ return defaultRenderer.getTableCellRendererComponent(table, value, isSelected,
+ hasFocus, row, column);
+ }
+ } // inner class ButtonCellRenderer
+
+ class MyMouseListener implements MouseListener {
+ private JTable table;
+
+ public MyMouseListener(JTable table) {
+ this.table = table;
+ }
+
+ private void forwardEventToButton(MouseEvent e) {
+ TableColumnModel columnModel = table.getColumnModel();
+ int column = columnModel.getColumnIndexAtX(e.getX());
+ int row = e.getY() / table.getRowHeight();
+ Object value;
+ JButton button;
+ MouseEvent buttonEvent;
+
+ if ((row >= table.getRowCount()) || (row < 0) || (column >= table.getColumnCount())
+ || (column < 0))
+ return;
+
+ value = table.getValueAt(row, column);
+
+ boolean isButton = value instanceof JButton;
+
+ if (!isButton)
+ return;
+
+ button = (JButton) value;
+ buttonEvent = (MouseEvent) SwingUtilities.convertMouseEvent(table, e, button);
+ // button.dispatchEvent (buttonEvent);
+ button.doClick();
+ table.repaint();
+ }
+
+ public void mouseClicked(MouseEvent e) {
+ forwardEventToButton(e);
+ }
+
+ public void mouseEntered(MouseEvent e) {
+ }
+
+ public void mouseExited(MouseEvent e) {
+ }
+
+ public void mousePressed(MouseEvent e) {
+ }
+
+ public void mouseReleased(MouseEvent e) {
+ }
+ } // inner class MyMouseListener
+} // class ExpressionDataPopupTable
diff --git a/application/src/main/java/cytoscape/dialogs/GinyEdgeControlDialog.java b/application/src/main/java/cytoscape/dialogs/GinyEdgeControlDialog.java
new file mode 100644
index 0000000..ccd4bed
--- /dev/null
+++ b/application/src/main/java/cytoscape/dialogs/GinyEdgeControlDialog.java
@@ -0,0 +1,493 @@
+/*
+ File: GinyEdgeControlDialog.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// EdgeControlDialog
+
+//---------------------------------------------------------------------------------------
+// $Revision: 9565 $
+// $Date: 2007-02-13 20:36:50 +0100 (Tue, 13 Feb 2007) $
+// $Author: mes $
+//---------------------------------------------------------------------------------------
+package cytoscape.dialogs;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.actions.GinyUtils;
+
+import cytoscape.data.CyAttributes;
+
+import cytoscape.view.CyNetworkView;
+
+import giny.model.*;
+
+import giny.view.*;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import java.util.*;
+
+//---------------------------------------------------------------------------------------
+import javax.swing.*;
+import javax.swing.border.*;
+import javax.swing.event.*;
+import javax.swing.tree.*;
+
+
+//--------------------------------------------------------------------------------------
+/**
+ * present a JTree with edge attributes names as top level nodes, and attribute values
+ * as child nodes; any node/s, once selected, are operated on by buttons in the bottom
+ * of the dialog box.
+ */
+public class GinyEdgeControlDialog extends JDialog {
+ CyNetworkView networkView;
+ GraphView view;
+ String[] edgeNames;
+ HashMap edgeNamesHash;
+ TreePath[] selectedTreePaths;
+ CyAttributes edgeAttributes;
+ JTree tree;
+
+ //--------------------------------------------------------------------------------------
+ /**
+ * Creates a new GinyEdgeControlDialog object.
+ *
+ * @param networkView DOCUMENT ME!
+ * @param edgeNamesHash DOCUMENT ME!
+ * @param title DOCUMENT ME!
+ */
+ public GinyEdgeControlDialog(CyNetworkView networkView, HashMap edgeNamesHash, String title) {
+ super();
+ this.networkView = networkView;
+ this.edgeNamesHash = edgeNamesHash;
+ this.view = networkView.getView();
+ //this.graphHider = networkView.getGraphHider ();
+ this.edgeAttributes = Cytoscape.getEdgeAttributes();
+ setTitle(title);
+ setContentPane(createTreeViewGui());
+ } // EdgeControlDialog ctor
+ //--------------------------------------------------------------------------------------
+
+ JPanel createTreeViewGui() {
+ JPanel contentPane = new JPanel();
+ contentPane.setLayout(new BorderLayout());
+
+ JScrollPane scrollPane = new JScrollPane(createTreeView(edgeNamesHash));
+
+ contentPane.add(scrollPane, BorderLayout.CENTER);
+
+ JPanel actionButtonPanel = new JPanel();
+ actionButtonPanel.setLayout(new GridLayout(4, 2));
+
+ JButton hideButton = new JButton("Hide");
+ JButton hideOthersButton = new JButton("Hide Others");
+ JButton hideAllButton = new JButton("Hide All");
+ JButton showAllButton = new JButton("Show All");
+
+ JButton selectButton = new JButton("Select");
+ JButton selectOthersButton = new JButton("Select Others");
+ JButton selectAllButton = new JButton("Select All");
+ JButton deselectAllButton = new JButton("Deselect All");
+
+ JButton okButton = new JButton("OK");
+
+ actionButtonPanel.add(selectButton);
+ actionButtonPanel.add(hideButton);
+
+ actionButtonPanel.add(selectOthersButton);
+ actionButtonPanel.add(hideOthersButton);
+
+ actionButtonPanel.add(selectAllButton);
+ actionButtonPanel.add(hideAllButton);
+
+ actionButtonPanel.add(deselectAllButton);
+ actionButtonPanel.add(showAllButton);
+
+ hideButton.addActionListener(new HideAction());
+ hideOthersButton.addActionListener(new HideOthersAction());
+ hideAllButton.addActionListener(new HideAllAction());
+ showAllButton.addActionListener(new ShowAllAction());
+
+ selectButton.addActionListener(new SelectAction());
+ selectAllButton.addActionListener(new SelectAllAction());
+ deselectAllButton.addActionListener(new DeselectAllAction());
+ selectOthersButton.addActionListener(new SelectOthersAction());
+
+ okButton.addActionListener(new OKAction());
+
+ JPanel allButtonsPanel = new JPanel();
+ allButtonsPanel.setLayout(new BorderLayout());
+ allButtonsPanel.add(actionButtonPanel, BorderLayout.CENTER);
+ allButtonsPanel.add(okButton, BorderLayout.SOUTH);
+
+ contentPane.add(allButtonsPanel, BorderLayout.SOUTH);
+
+ return contentPane;
+ } // createTreeViewGui
+ //--------------------------------------------------------------------------------------
+
+ protected JTree createTreeView(HashMap edgeNamesHash) {
+ DefaultMutableTreeNode root = new DefaultMutableTreeNode("Edge Attributes");
+ createTreeNodes(root, edgeNamesHash);
+ tree = new JTree(root);
+ tree.addTreeSelectionListener(new MyTreeSelectionListener());
+
+ return tree;
+ } // createTreeView
+ //--------------------------------------------------------------------------------------
+
+ class MyTreeSelectionListener implements TreeSelectionListener {
+ public void valueChanged(TreeSelectionEvent e) {
+ DefaultMutableTreeNode node = (DefaultMutableTreeNode) tree.getLastSelectedPathComponent();
+ selectedTreePaths = tree.getSelectionPaths();
+ } // valueChanged
+ } // inner class MyTreeSelectionListener
+ //-----------------------------------------------------------------------------------
+
+ protected void createTreeNodes(DefaultMutableTreeNode root, HashMap edgeNamesHash) {
+ DefaultMutableTreeNode branch = null;
+ DefaultMutableTreeNode leaf = null;
+ String[] topLevelNames = (String[]) edgeNamesHash.keySet().toArray(new String[0]);
+ java.util.Arrays.sort(topLevelNames, String.CASE_INSENSITIVE_ORDER);
+
+ for (int i = 0; i < topLevelNames.length; i++) {
+ branch = new DefaultMutableTreeNode(topLevelNames[i]);
+
+ String[] children = (String[]) edgeNamesHash.get(topLevelNames[i]);
+ java.util.Arrays.sort(children, String.CASE_INSENSITIVE_ORDER);
+
+ for (int j = 0; j < children.length; j++)
+ branch.add(new DefaultMutableTreeNode(children[j]));
+
+ root.add(branch);
+ } // for i
+ } // createTreeNodes
+ //-----------------------------------------------------------------------------------
+
+ class SelectAction extends AbstractAction {
+ SelectAction() {
+ super("");
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ if ((selectedTreePaths == null) || (selectedTreePaths.length == 0)) {
+ GinyEdgeControlDialog.this.getToolkit().beep();
+
+ return;
+ }
+
+ GinyUtils.deselectAllEdges(view);
+
+ for (int i = 0; i < selectedTreePaths.length; i++)
+ selectEdgesByName(selectedTreePaths[i]);
+
+ networkView.redrawGraph(false, true);
+ } // actionPerformed
+ } // SelectAction
+ //------------------------------------------------------------------------------
+
+ class HideAction extends AbstractAction {
+ HideAction() {
+ super("");
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ if ((selectedTreePaths == null) || (selectedTreePaths.length == 0)) {
+ GinyEdgeControlDialog.this.getToolkit().beep();
+
+ return;
+ }
+
+ GinyUtils.unHideAllEdges(view);
+
+ String action = e.getActionCommand();
+
+ for (int i = 0; i < selectedTreePaths.length; i++)
+ hideEdgesByName(selectedTreePaths[i]);
+
+ networkView.redrawGraph(false, true);
+ } // actionPerformed
+ } // HideButtonAction
+ //------------------------------------------------------------------------------
+
+ boolean pathMatchesEdge(String edgeName, TreePath treePath, CyAttributes edgeAttributes) {
+ Object[] objPath = treePath.getPath();
+ String[] pathNames = new String[objPath.length];
+
+ for (int i = 0; i < pathNames.length; i++)
+ pathNames[i] = objPath[i].toString();
+
+ int pathLength = pathNames.length;
+
+ if (pathLength < 2)
+ return false;
+
+ if (!edgeAttributes.hasAttribute(edgeName, pathNames[1]))
+ return false;
+
+ if (pathLength == 2)
+ return true;
+
+ if (pathLength == 3) {
+ java.util.List l = edgeAttributes.getListAttribute(edgeName, pathNames[1]);
+ String[] values = (String[]) l.toArray(new String[0]);
+
+ for (int i = 0; i < values.length; i++)
+ if (values[i].equalsIgnoreCase(pathNames[2]))
+ return true;
+ } // pathLength == 3
+
+ return false;
+ } // pathMatchesEdge
+ //------------------------------------------------------------------------------
+
+ protected void hideEdgesByName(TreePath treePath) {
+ java.util.List list = view.getEdgeViewsList();
+
+ for (Iterator i = list.iterator(); i.hasNext();) {
+ EdgeView ev = (EdgeView) i.next();
+
+ String edgeName = ev.getEdge().getIdentifier();
+
+ if (pathMatchesEdge(edgeName, treePath, edgeAttributes))
+ view.hideGraphObject(ev);
+ } // for ec
+ } // hideEdgesByName
+ //------------------------------------------------------------------------------
+
+ protected void hideOtherEdges() {
+ Vector keepVisibleList = new Vector();
+
+ if (selectedTreePaths == null)
+ return;
+
+ java.util.List list = view.getEdgeViewsList();
+
+ for (Iterator i = list.iterator(); i.hasNext();) {
+ EdgeView ev = (EdgeView) i.next();
+
+ String canonicalName = ev.getEdge().getIdentifier();
+
+ for (int p = 0; p < selectedTreePaths.length; p++) {
+ TreePath treePath = selectedTreePaths[p];
+
+ if (pathMatchesEdge(canonicalName, treePath, edgeAttributes))
+ keepVisibleList.add(ev);
+ } // for p
+ } // for ec
+
+ list = view.getEdgeViewsList();
+
+ for (Iterator i = list.iterator(); i.hasNext();) {
+ EdgeView ev = (EdgeView) i.next();
+
+ if (!keepVisibleList.contains(ev))
+ view.hideGraphObject(ev);
+ }
+ } // hideOtherEdges
+ //------------------------------------------------------------------------------
+
+ protected void inverseHideEdgesByName(TreePath treePath) { // this is the same as hideEdgesByName action ... Bug?
+
+ java.util.List list = view.getEdgeViewsList();
+
+ for (Iterator i = list.iterator(); i.hasNext();) {
+ EdgeView ev = (EdgeView) i.next();
+
+ String edgeName = ev.getEdge().getIdentifier();
+
+ if (!pathMatchesEdge(edgeName, treePath, edgeAttributes))
+ view.hideGraphObject(ev);
+ } // for ec
+ } // inverseHideEdgesByName
+ //------------------------------------------------------------------------------
+
+ protected void selectEdgesByName(TreePath treePath) {
+ java.util.List list = view.getEdgeViewsList();
+ Vector vector = new Vector();
+
+ for (Iterator i = list.iterator(); i.hasNext();) {
+ EdgeView ev = (EdgeView) i.next();
+ String canonicalName = ev.getEdge().getIdentifier();
+
+ if (pathMatchesEdge(canonicalName, treePath, edgeAttributes))
+ vector.add(ev);
+ } // for ec
+
+ for (Iterator vi = vector.iterator(); vi.hasNext();) {
+ EdgeView edge = (EdgeView) vi.next();
+ edge.setSelected(true);
+ }
+ } // selectEdgesByName
+ //------------------------------------------------------------------------------
+
+ class SelectOthersAction extends AbstractAction {
+ SelectOthersAction() {
+ super("");
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ selectOtherEdges();
+ networkView.redrawGraph(false, true);
+ }
+ } // SelectOthersAction
+ //------------------------------------------------------------------------------
+
+ class DeselectAllAction extends AbstractAction {
+ DeselectAllAction() {
+ super("");
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ deselectAllEdges();
+ networkView.redrawGraph(false, true);
+ }
+ } // DeselectAllAction
+ //------------------------------------------------------------------------------
+
+ class HideOthersAction extends AbstractAction {
+ HideOthersAction() {
+ super("");
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ GinyUtils.unHideAllEdges(view);
+ hideOtherEdges();
+ networkView.redrawGraph(false, true);
+ }
+ } // HideOthersAction
+ //------------------------------------------------------------------------------
+
+ class HideAllAction extends AbstractAction {
+ HideAllAction() {
+ super("");
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ GinyUtils.hideAllEdges(view);
+ }
+ } // HideAllAction
+ //------------------------------------------------------------------------------
+
+ class SelectAllAction extends AbstractAction {
+ SelectAllAction() {
+ super("");
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ selectAllEdges();
+ networkView.redrawGraph(false, true);
+ }
+ } // HideAllAction
+ //------------------------------------------------------------------------------
+
+ class ShowAllAction extends AbstractAction {
+ ShowAllAction() {
+ super("");
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ GinyUtils.unHideAllEdges(view);
+ }
+ } // ShowAllAction
+ //------------------------------------------------------------------------------
+
+ protected void selectAllEdges() {
+ GinyUtils.selectAllEdges(view);
+ }
+
+ //------------------------------------------------------------------------------
+ protected void invertEdgeSelection() {
+ GinyUtils.invertSelectedEdges(view);
+ }
+
+ //------------------------------------------------------------------------------
+ protected void selectOtherEdges() {
+ Vector keepUnselectedList = new Vector();
+
+ java.util.List list = view.getEdgeViewsList();
+
+ for (Iterator i = list.iterator(); i.hasNext();) {
+ EdgeView ev = (EdgeView) i.next();
+ String canonicalName = ev.getEdge().getIdentifier();
+
+ for (int p = 0; p < selectedTreePaths.length; p++) {
+ TreePath treePath = selectedTreePaths[p];
+
+ if (pathMatchesEdge(canonicalName, treePath, edgeAttributes))
+ keepUnselectedList.add(ev);
+ } // for p
+ } // for ec
+
+ Vector selectList = new Vector();
+ list = view.getEdgeViewsList();
+
+ for (Iterator i = list.iterator(); i.hasNext();) {
+ EdgeView ev = (EdgeView) i.next();
+
+ ev.setSelected(!keepUnselectedList.contains(ev));
+ }
+ } // selectOtherEdges
+ //------------------------------------------------------------------------------
+
+ protected void deselectAllEdges() {
+ GinyUtils.deselectAllEdges(view);
+ }
+
+ //------------------------------------------------------------------------------
+ private void placeInCenter() {
+ GraphicsConfiguration gc = getGraphicsConfiguration();
+ int screenHeight = (int) gc.getBounds().getHeight();
+ int screenWidth = (int) gc.getBounds().getWidth();
+ int windowWidth = getWidth();
+ int windowHeight = getHeight();
+ setLocation((screenWidth - windowWidth) / 2, (screenHeight - windowHeight) / 2);
+ } // placeInCenter
+ //------------------------------------------------------------------------------
+
+ public class OKAction extends AbstractAction {
+ OKAction() {
+ super("");
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ GinyEdgeControlDialog.this.dispose();
+ }
+ } // OKAction
+ //-----------------------------------------------------------------------------
+} // class EdgeControlDialog
diff --git a/application/src/main/java/cytoscape/dialogs/GraphObjectSelection.java b/application/src/main/java/cytoscape/dialogs/GraphObjectSelection.java
new file mode 100644
index 0000000..68ff929
--- /dev/null
+++ b/application/src/main/java/cytoscape/dialogs/GraphObjectSelection.java
@@ -0,0 +1,459 @@
+/*
+ File: GraphObjectSelection.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.dialogs;
+
+import ViolinStrings.Strings;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import cytoscape.logger.CyLogger;
+
+import cytoscape.data.CyAttributes;
+
+import cytoscape.ding.DingNetworkView;
+
+import cytoscape.view.CyNetworkView;
+
+import giny.model.Node;
+
+import java.awt.GridLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import java.lang.reflect.Constructor;
+
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.Set;
+import java.util.TreeSet;
+
+import javax.swing.AbstractAction;
+import javax.swing.ButtonGroup;
+import javax.swing.DefaultListModel;
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JLabel;
+import javax.swing.JList;
+import javax.swing.JPanel;
+import javax.swing.JRadioButton;
+import javax.swing.JScrollPane;
+import javax.swing.JSplitPane;
+import javax.swing.JTextField;
+import javax.swing.SwingUtilities;
+import javax.swing.border.TitledBorder;
+
+
+/**
+ *
+ */
+public class GraphObjectSelection extends JPanel implements ActionListener {
+ JTextField searchField;
+ JCheckBox regexpSearch;
+ JCheckBox clearSelection;
+ JRadioButton hideFailed;
+ JRadioButton grayFailed;
+ JRadioButton selectPassed;
+ JList selectedAttributes;
+ JList allAttributes;
+ CyNetwork cyNetwork;
+ CyAttributes nodeAttributes;
+ CyAttributes edgeAttributes;
+ DingNetworkView graphView;
+ CyNetworkView networkView;
+
+ /**
+ * Creates a new GraphObjectSelection object.
+ */
+ public GraphObjectSelection() {
+ initialize();
+ }
+
+ protected void initialize() {
+ networkView = Cytoscape.getCurrentNetworkView();
+ cyNetwork = networkView.getNetwork();
+ nodeAttributes = Cytoscape.getNodeAttributes();
+ edgeAttributes = Cytoscape.getEdgeAttributes();
+
+ // Create the Node Selection Panel
+ JPanel searchPanel = new JPanel();
+ searchPanel.setBorder(new TitledBorder("Describe Filter"));
+ searchPanel.add(new JLabel("Filter: "));
+ searchField = new JTextField(30);
+ searchField.addActionListener(this);
+ searchPanel.add(searchField);
+ regexpSearch = new JCheckBox("Regexp?");
+ searchPanel.add(regexpSearch);
+ searchPanel.add(new JButton(new AbstractAction("Go!") {
+ public void actionPerformed(ActionEvent e) {
+ // Do this in the GUI Event Dispatch thread...
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ // do the search
+ performSearch();
+ }
+ });
+ }
+ }));
+
+ // Create the All Attributes List Panel
+ JPanel allAttributesPanel = new JPanel();
+ allAttributesPanel.setBorder(new TitledBorder("All Available String Attributes"));
+
+ String[] node_attribute_names = nodeAttributes.getAttributeNames();
+ ArrayList string_attributes = new ArrayList(node_attribute_names.length);
+ ArrayList number_attributes = new ArrayList(node_attribute_names.length);
+ ArrayList other_attributes = new ArrayList(node_attribute_names.length);
+
+ for (int i = 0; i < node_attribute_names.length; ++i) {
+ Class type = deduceClass(node_attribute_names[i]);
+ CyLogger.getLogger().info("Attr: " + node_attribute_names[i] + " Class: " + type.getName());
+
+ if (type.getName().equals(String.class.getName())) {
+ string_attributes.add(node_attribute_names[i]);
+ } else if (type.getName().equals(Double.class.getName())) {
+ number_attributes.add(node_attribute_names[i]);
+ } else {
+ other_attributes.add(node_attribute_names[i]);
+ }
+ }
+
+ DefaultListModel model_nodes = new DefaultListModel();
+ Iterator string_atts = string_attributes.iterator();
+
+ for (int i = 0; string_atts.hasNext(); ++i) {
+ model_nodes.add(i, (String) string_atts.next());
+ }
+
+ allAttributes = new JList(model_nodes);
+
+ JScrollPane scrollPaneAll = new JScrollPane();
+ scrollPaneAll.getViewport().setView(allAttributes);
+ allAttributesPanel.add(scrollPaneAll);
+
+ // Create the Selection Panel
+ JPanel selectedAttributesPanel = new JPanel();
+ selectedAttributesPanel.setBorder(new TitledBorder("Selected Attributes"));
+ selectedAttributes = new JList(new DefaultListModel());
+
+ JScrollPane scrollPaneSel = new JScrollPane();
+ scrollPaneSel.getViewport().setView(selectedAttributes);
+ allAttributesPanel.add(scrollPaneSel);
+ selectedAttributesPanel.add(scrollPaneSel);
+
+ // Create the Center Panel
+ JPanel centerPanel = new JPanel();
+ centerPanel.setLayout(new GridLayout(0, 1));
+
+ JPanel controlPanel = new JPanel();
+ controlPanel.setBorder(new TitledBorder("Control"));
+ controlPanel.add(new JButton(new AbstractAction("+") {
+ public void actionPerformed(ActionEvent e) {
+ // Do this in the GUI Event Dispatch thread...
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ // Add the Attributes selected in the all attributes
+ // list to the selectionlist
+
+ // get the selected attributes
+ Object[] attributes = allAttributes.getSelectedValues();
+
+ // add them to the selection list
+ Set current_selection = new TreeSet(java.util.Arrays.asList(((DefaultListModel) selectedAttributes
+ .getModel())
+ .toArray()));
+ current_selection.addAll(java.util.Arrays.asList(attributes));
+
+ DefaultListModel new_model = new DefaultListModel();
+ Iterator sel = current_selection.iterator();
+
+ while (sel.hasNext()) {
+ new_model.addElement(sel.next());
+ }
+
+ selectedAttributes.setModel(new_model);
+ }
+ });
+ }
+ }));
+ controlPanel.add(new JButton(new AbstractAction("-") {
+ public void actionPerformed(ActionEvent e) {
+ // Do this in the GUI Event Dispatch thread...
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ // Remove all Selected Attributes in the Selection List
+ Object[] attributes = selectedAttributes.getSelectedValues();
+ DefaultListModel dlm = (DefaultListModel) selectedAttributes
+ .getModel();
+
+ for (int i = 0; i < attributes.length; ++i) {
+ dlm.removeElement(attributes[i]);
+ }
+ }
+ });
+ }
+ }));
+ controlPanel.add(new JButton(new AbstractAction("Update") {
+ public void actionPerformed(ActionEvent e) {
+ // Do this in the GUI Event Dispatch thread...
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ // update the integration view
+ // integration.updateView();
+ }
+ });
+ }
+ }));
+
+ clearSelection = new JCheckBox("Clear", false);
+ controlPanel.add(clearSelection);
+ centerPanel.add(controlPanel);
+
+ JPanel actionPanel = new JPanel();
+ ButtonGroup actionGroup = new ButtonGroup();
+ actionPanel.setBorder(new TitledBorder("Action to Take"));
+
+ hideFailed = new JRadioButton("Hide Failed", true);
+ actionGroup.add(hideFailed);
+ actionPanel.add(hideFailed);
+
+ grayFailed = new JRadioButton("Gray Failed", false);
+ actionGroup.add(grayFailed);
+ actionPanel.add(grayFailed);
+
+ selectPassed = new JRadioButton("Select Passed", false);
+ actionGroup.add(selectPassed);
+ actionPanel.add(selectPassed);
+
+ centerPanel.add(actionPanel);
+
+ JSplitPane all_center_1 = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT, true, centerPanel,
+ allAttributesPanel);
+ JSplitPane sel = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT, true, selectedAttributesPanel,
+ all_center_1);
+ JSplitPane all = new JSplitPane(JSplitPane.VERTICAL_SPLIT, true, searchPanel, sel);
+ add(all);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object[] getSelectionList() {
+ return ((DefaultListModel) selectedAttributes.getModel()).toArray();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param event DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent event) {
+ // when ENTER is pressed do a search
+ this.graphView = (DingNetworkView) networkView.getView();
+ performSearch();
+
+ // update the view
+ } // actionPerformed
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void performSearch() {
+ ArrayList passes = new ArrayList();
+ Object[] selected_attributes_o = getSelectionList();
+ String[] selected_attributes = new String[selected_attributes_o.length];
+
+ for (int i = 0; i < selected_attributes_o.length; ++i) {
+ selected_attributes[i] = (String) selected_attributes_o[i];
+ }
+
+ if (regexpSearch.isSelected()) {
+ CyLogger.getLogger().info("not Implemented");
+ } else {
+ String[] pattern = searchField.getText().split("\\s");
+ String[] nodes_with_attribute;
+
+ for (int i = 0; i < selected_attributes.length; ++i) {
+ // nodes_with_attribute = nodeAttributes.getObjectNames(
+ // selected_attributes[i] );
+ nodes_with_attribute = nodeAttributes.getAttributeNames();
+
+ for (int j = 0; j < nodes_with_attribute.length; ++j) {
+ // get the String Value for the node for the given attribute
+ String value = nodeAttributes.getStringAttribute(selected_attributes[i],
+ nodes_with_attribute[j]);
+
+ for (int p = 0; p < pattern.length; ++p)
+ if (Strings.isLike(value, pattern[p], 0, true)) {
+ // this means that:
+ // the value, which is associated with a given
+ // selected attribute
+ // and a node name is like one of the strings in the
+ // search
+ // box, which includes wildcards.
+ // passes.add( graphView.getNodeView(
+ // nodes_with_attribute[j] ) );
+ // CyLogger.getLogger().info( nodes_with_attribute[j]+"
+ // Matches Pattern: "+pattern[p]+" on Attribute:
+ // "+selected_attributes[i]+" and the object is a:
+ // "+ ( nodeAttributes.getGraphObject(
+ // nodes_with_attribute[j]) ).getClass().getName()
+ // );
+ // passes.add( graphView.getNodeView( ( Node
+ // )nodeAttributes.getGraphObject(
+ // nodes_with_attribute[j]) ) );
+ // CyLogger.getLogger().info( "This got added to Passed:
+ // "+graphView.getNodeView( ( Node
+ // )nodeAttributes.getGraphObject(
+ // nodes_with_attribute[j]) ) );
+ passes.add(nodes_with_attribute[j]);
+ }
+ }
+ }
+ }
+
+ // Iterator views = networkView.getView().getNodeViewsList().iterator();
+ // while ( views.hasNext() ) {
+ // CyLogger.getLogger().info( "On Crack: "+views.next() );
+ // }
+
+ // Hide the Failed Nodes
+ if (hideFailed.isSelected()) {
+ // restore all EdgeViews prior to hiding
+ graphView.showGraphObjects(graphView.getEdgeViewsList());
+
+ Iterator all_nodes = networkView.getView().getGraphPerspective().nodesList().iterator();
+
+ while (all_nodes.hasNext()) {
+ Node node = (Node) all_nodes.next();
+
+ if (passes.contains(node.getIdentifier())) {
+ graphView.showGraphObject(graphView.getNodeView(node));
+ } else {
+ graphView.hideGraphObject(graphView.getNodeView(node));
+ }
+ }
+ }
+ // gray the Failed
+ else if (grayFailed.isSelected()) {
+ graphView.showGraphObjects(graphView.getEdgeViewsList());
+ graphView.showGraphObjects(graphView.getNodeViewsList());
+
+ Iterator all_nodes = graphView.getGraphPerspective().nodesList().iterator();
+
+ while (all_nodes.hasNext()) {
+ Node node = (Node) all_nodes.next();
+
+ if (passes.contains(node.getIdentifier())) {
+ graphView.getNodeView(node).setTransparency(1f);
+ } else {
+ graphView.getNodeView(node).setTransparency(0.5f);
+ }
+ }
+ }
+ // select those who passed
+ else if (selectPassed.isSelected()) {
+ graphView.showGraphObjects(graphView.getEdgeViewsList());
+ graphView.showGraphObjects(graphView.getNodeViewsList());
+
+ Iterator all_nodes = graphView.getGraphPerspective().nodesList().iterator();
+
+ while (all_nodes.hasNext()) {
+ Node node = (Node) all_nodes.next();
+
+ if (passes.contains(node.getIdentifier())) {
+ graphView.getNodeView(node).setSelected(true);
+ } else {
+ graphView.getNodeView(node).setSelected(false);
+ }
+ }
+ }
+ }
+
+ /**
+ * determine (heuristically) the most-specialized class instance which can
+ * be constructed from the supplied string.
+ */
+ static private Class deduceClass(String string) {
+ String[] classNames = {
+ "java.net.URL", "java.lang.Integer", // using
+ // this
+ // breaks
+ // the
+ // vizmapper,
+ // see
+ // below
+ "java.lang.Double", "java.lang.String"
+ };
+
+ /**
+ * vizmapper error: Exception in thread "main"
+ * java.lang.ClassCastException: java.lang.Double at
+ * java.lang.Integer.compareTo(Integer.java:913) at
+ * cytoscape.vizmap.ContinuousMapper.getRangeValue(ContinuousMapper.java:78)
+ */
+ for (int i = 0; i < classNames.length; i++) {
+ try {
+ Object obj = createInstanceFromString(Class.forName(classNames[i]), string);
+
+ return obj.getClass();
+ } catch (Exception e) {
+ ; // try the next class
+ }
+ } // for i
+
+ return null;
+ } // deduceClass
+
+ /**
+ * given a string and a class, dynamically create an instance of that class
+ * from the string
+ */
+ static private Object createInstanceFromString(Class requestedClass, String ctorArg)
+ throws Exception {
+ Class[] ctorArgsClasses = new Class[1];
+ ctorArgsClasses[0] = Class.forName("java.lang.String");
+
+ Object[] ctorArgs = new Object[1];
+ ctorArgs[0] = new String(ctorArg);
+
+ Constructor ctor = requestedClass.getConstructor(ctorArgsClasses);
+
+ return ctor.newInstance(ctorArgs);
+ }
+}
diff --git a/application/src/main/java/cytoscape/dialogs/GridBagGroup.java b/application/src/main/java/cytoscape/dialogs/GridBagGroup.java
new file mode 100644
index 0000000..ebe779c
--- /dev/null
+++ b/application/src/main/java/cytoscape/dialogs/GridBagGroup.java
@@ -0,0 +1,116 @@
+/*
+ File: GridBagGroup.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// GridBagGroup.java: more GridBagLayout utilities
+
+//--------------------------------------------------------------------------------------
+// $Revision: 9736 $
+// $Date: 2007-03-20 01:25:45 +0100 (Tue, 20 Mar 2007) $
+// $Author: mes $
+//--------------------------------------------------------------------------------------
+package cytoscape.dialogs;
+
+import java.awt.*;
+
+//--------------------------------------------------------------------------------------
+import java.io.*;
+
+import java.util.*;
+
+import javax.swing.*;
+import javax.swing.border.*;
+
+
+//------------------------------------------------------------------------------
+/**
+ *
+ */
+public class GridBagGroup {
+ /**
+ *
+ */
+ public JPanel panel;
+
+ /**
+ *
+ */
+ public GridBagLayout gridbag;
+
+ /**
+ *
+ */
+ public GridBagConstraints constraints;
+
+ /**
+ * Creates a new GridBagGroup object.
+ */
+ public GridBagGroup() {
+ panel = new JPanel();
+ init();
+ }
+
+ /**
+ * Creates a new GridBagGroup object.
+ *
+ * @param panel DOCUMENT ME!
+ */
+ public GridBagGroup(JPanel panel) {
+ this.panel = panel;
+ init();
+ }
+
+ private void init() {
+ gridbag = new GridBagLayout();
+ constraints = new GridBagConstraints();
+ panel.setLayout(gridbag);
+ }
+
+ /**
+ * Creates a new GridBagGroup object.
+ *
+ * @param title DOCUMENT ME!
+ */
+ public GridBagGroup(String title) {
+ panel = new JPanel();
+ init();
+
+ Border border = BorderFactory.createLineBorder(Color.black);
+ Border titledBorder = BorderFactory.createTitledBorder(border, title, TitledBorder.CENTER,
+ TitledBorder.DEFAULT_POSITION);
+ panel.setBorder(titledBorder);
+ }
+}
diff --git a/application/src/main/java/cytoscape/dialogs/IconPopupButton.java b/application/src/main/java/cytoscape/dialogs/IconPopupButton.java
new file mode 100644
index 0000000..8a8e1e6
--- /dev/null
+++ b/application/src/main/java/cytoscape/dialogs/IconPopupButton.java
@@ -0,0 +1,328 @@
+/*
+ File: IconPopupButton.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// IconPopupButton.java
+
+//---------------------------------------------------------------------------------------
+// $Revision: 14060 $
+// $Date: 2008-05-20 22:13:18 +0200 (Tue, 20 May 2008) $
+// $Author: skillcoyne $
+//---------------------------------------------------------------------------------------
+package cytoscape.dialogs;
+
+
+//---------------------------------------------------------------------------------------
+import cytoscape.logger.CyLogger;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.GridLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+
+import java.util.HashMap;
+
+import javax.swing.AbstractAction;
+import javax.swing.BorderFactory;
+import javax.swing.Box;
+import javax.swing.BoxLayout;
+import javax.swing.ImageIcon;
+import javax.swing.JButton;
+import javax.swing.JDialog;
+import javax.swing.JFrame;
+import javax.swing.JLabel;
+import javax.swing.JList;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.ListModel;
+import javax.swing.ListSelectionModel;
+
+
+//---------------------------------------------------------------------------------------
+/**
+ *
+ */
+public class IconPopupButton extends JPanel
+ implements ActionListener {
+ String title; // title of the button
+ String objectName;
+ String currentIconName; // internal storage of node icon type
+ Object currentIcon; // and here as a icon byte
+ JButton iconButton; // the button on the left
+ JLabel iconSelectionForPanel; // the icon type displayed on the right
+ JFrame mainFrame;
+ JDialog mainDialog;
+ JPanel mainPanel;
+ HashMap iconObjectToString;
+ HashMap stringToIconObject;
+ JList iconList; // ... and the equivalent list for display
+ JDialog parentDialog;
+ boolean alreadyConstructed;
+
+ /**
+ * Creates a new IconPopupButton object.
+ *
+ * @param title DOCUMENT ME!
+ * @param objectName DOCUMENT ME!
+ * @param iconObjectToString DOCUMENT ME!
+ * @param stringToIconObject DOCUMENT ME!
+ * @param icons DOCUMENT ME!
+ * @param startIconObject DOCUMENT ME!
+ * @param parentDialog DOCUMENT ME!
+ */
+ public IconPopupButton(String title, String objectName,
+ HashMap iconObjectToString, HashMap stringToIconObject,
+ ImageIcon[] icons, Object startIconObject, JDialog parentDialog) {
+ this.title = title;
+
+ if (icons.length == 0) {
+ setupErrorWindow();
+
+ return;
+ }
+
+ if ((icons[0] == null) || (icons[0].getIconWidth() < 0)) {
+ CyLogger.getLogger().info("Icon width: " + icons[0].getImage().getWidth(parentDialog));
+ setupErrorWindow();
+
+ return;
+ }
+
+ alreadyConstructed = false;
+ this.objectName = objectName;
+ this.iconObjectToString = iconObjectToString;
+ this.stringToIconObject = stringToIconObject;
+ this.parentDialog = parentDialog;
+ iconList = new JList(icons);
+
+ if (startIconObject != null)
+ this.setIconObject(startIconObject);
+ else {
+ CyLogger.getLogger().info("starticon null " + title);
+
+ ImageIcon icon = (ImageIcon) iconList.getModel()
+ .getElementAt(0); // default icon
+ setIconName(icon.getDescription());
+ }
+
+ setupWindow();
+ }
+
+ private void setupWindow() {
+ // find the right icon
+ ListModel theModel = iconList.getModel();
+ ImageIcon icon = (ImageIcon) theModel.getElementAt(0); // default icon
+ int modelSize = theModel.getSize();
+
+ for (int modelIndex = 0; modelIndex < modelSize; modelIndex++) {
+ ImageIcon indexedIcon = (ImageIcon) theModel.getElementAt(modelIndex);
+
+ if (currentIconName == indexedIcon.getDescription()) {
+ icon = indexedIcon;
+ iconList.setSelectedValue(icon, true);
+ }
+ }
+
+ iconButton = new JButton(title);
+ iconButton.addActionListener(this);
+ mainPanel = new JPanel(new GridLayout(0, 1));
+ iconSelectionForPanel = new JLabel(icon);
+ add(iconButton);
+ add(iconSelectionForPanel);
+ }
+
+ private void setupErrorWindow() {
+ iconButton = new JButton(title + ": CYTOSCAPE_HOME error");
+ iconSelectionForPanel = new JLabel(" X ");
+
+ JLabel errorLabel = new JLabel(
+ "ERROR: No CYTOSCAPE_HOME specified on java command line.");
+ add(errorLabel);
+ }
+
+ // if button is pressed, launch window with list of choices
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ if (!alreadyConstructed) {
+ mainDialog = new JDialog(parentDialog, this.title);
+
+ // create buttons
+ final JButton setButton = new JButton("Apply");
+ JButton cancelButton = new JButton("Cancel");
+ setButton.addActionListener(new ApplyIconAction());
+ cancelButton.addActionListener(new CancelIconAction());
+
+ // create list
+ iconList.setLayoutOrientation(JList.HORIZONTAL_WRAP);
+ iconList.setVisibleRowCount(1);
+ //iconList.setFixedCellHeight(35);
+ //iconList.setFixedCellWidth(35);
+ iconList.setBackground(Color.WHITE);
+ iconList.setSelectionBackground(Color.RED);
+ iconList.setSelectionForeground(Color.RED);
+ iconList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
+ iconList.addMouseListener(
+ new MouseAdapter() {
+ public void mouseClicked(MouseEvent e) {
+ if (e.getClickCount() == 2)
+ setButton.doClick();
+ }
+ });
+
+ JScrollPane listScroller = new JScrollPane(iconList);
+ listScroller.setPreferredSize(new Dimension(150, 50));
+ listScroller.setMinimumSize(new Dimension(150, 50));
+ listScroller.setAlignmentX(LEFT_ALIGNMENT);
+ listScroller.setAlignmentY(BOTTOM_ALIGNMENT);
+ iconList.ensureIndexIsVisible(iconList.getSelectedIndex());
+
+ // Create a container so that we can add a title around the scroll pane
+ JPanel listPane = new JPanel();
+ listPane.setLayout(new BoxLayout(listPane, BoxLayout.Y_AXIS));
+
+ JLabel label = new JLabel("Set " + objectName);
+ label.setLabelFor(iconList);
+ listPane.add(label);
+ listPane.add(Box.createRigidArea(new Dimension(0, 5)));
+ listPane.add(listScroller);
+ listPane.setBorder(BorderFactory.createEmptyBorder(10, 10, 10, 10));
+
+ // Lay out the buttons from left to right.
+ JPanel buttonPane = new JPanel();
+ buttonPane.setLayout(new BoxLayout(buttonPane, BoxLayout.X_AXIS));
+ buttonPane.setBorder(
+ BorderFactory.createEmptyBorder(0, 10, 10, 10));
+ buttonPane.add(Box.createHorizontalGlue());
+ buttonPane.add(Box.createRigidArea(new Dimension(10, 0)));
+ buttonPane.add(setButton);
+ buttonPane.add(cancelButton);
+
+ // add everything
+ mainPanel.add(listPane, BorderLayout.CENTER);
+ mainPanel.add(buttonPane, BorderLayout.SOUTH);
+ mainDialog.setContentPane(mainPanel);
+ alreadyConstructed = true;
+ }
+
+ mainDialog.pack();
+ mainDialog.setLocationRelativeTo(parentDialog);
+ mainDialog.setVisible(true);
+ }
+
+ public class ApplyIconAction extends AbstractAction {
+ public void actionPerformed(ActionEvent e) {
+ //setIcon((String) iconList.getSelectedValue());
+ ImageIcon icon = (ImageIcon) iconList.getSelectedValue();
+ setIconName(icon.getDescription());
+ iconSelectionForPanel.setIcon(icon);
+ mainDialog.dispose();
+ }
+ }
+
+ public class CancelIconAction extends AbstractAction {
+ CancelIconAction() {
+ super("");
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ mainDialog.dispose();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getIconName() {
+ return currentIconName;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getIconObject() {
+ return currentIcon;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param iconName DOCUMENT ME!
+ */
+ public void setIconName(String iconName) {
+ currentIconName = iconName;
+ currentIcon = (Object) stringToIconObject.get(iconName);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param iconObject DOCUMENT ME!
+ */
+ public void setIconObject(Object iconObject) {
+ currentIcon = iconObject;
+ currentIconName = (String) iconObjectToString.get(iconObject);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public JLabel getLabel() {
+ return iconSelectionForPanel;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public JButton getButton() {
+ return iconButton;
+ }
+} //class IconPopupButton
diff --git a/application/src/main/java/cytoscape/dialogs/ImportAttributeMatrixDialog.java b/application/src/main/java/cytoscape/dialogs/ImportAttributeMatrixDialog.java
new file mode 100644
index 0000000..0954e20
--- /dev/null
+++ b/application/src/main/java/cytoscape/dialogs/ImportAttributeMatrixDialog.java
@@ -0,0 +1,255 @@
+/*
+ * AttributeMatrixImportDialog.java
+ *
+ * Created on 2006/05/08, 11:33
+ */
+package cytoscape.dialogs;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.util.CyFileFilter;
+import cytoscape.util.FileUtil;
+
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+
+import java.io.File;
+
+import java.util.Iterator;
+
+import javax.swing.DefaultComboBoxModel;
+import javax.swing.JComboBox;
+import javax.swing.JDialog;
+
+
+/**
+ *
+ * This class prompts the user for data for entry of the attribute matrix,
+ * which includes expression data as a use case. The user supplies two
+ * things: a filename, and a "key attribute name". This key attribute
+ * establishes the correspondence between nodes in the network and data
+ * in the attribute matrix. For example, when inputting expression data,
+ * the data might be listed by probe set. The user might enter a "probe set"
+ * attribute for relating the expression data to nodes on the graph.
+ *
+ * The key attribute name defaults to "ID".
+ *
+ * @author cline
+ */
+public class ImportAttributeMatrixDialog extends javax.swing.JDialog {
+ private boolean status;
+ private String currentKeyAttributeName = "ID";
+ private DefaultComboBoxModel keyAttributeModel = new DefaultComboBoxModel();
+ private JComboBox keyAttributeBox = new JComboBox(keyAttributeModel);
+
+ protected class KeyAttributeListener implements ItemListener {
+ public void itemStateChanged(ItemEvent event) {
+ currentKeyAttributeName = (String) keyAttributeBox.getSelectedItem();
+ }
+ }
+
+ /** Creates new form AttributeMatrixImportDialog */
+ public ImportAttributeMatrixDialog(java.awt.Frame parent, boolean modal) {
+ super(parent, modal);
+ initComponents();
+ status = false;
+ pack();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getKeyAttributeName() {
+ return currentKeyAttributeName;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getFilename() {
+ String attributeMatrixFilename = attributeMatrixFileNameTextField.getText();
+
+ return attributeMatrixFilename;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean getStatus() {
+ return status;
+ }
+
+ /**
+ * This method is called from within the constructor to initialize the form.
+ * WARNING: Do NOT modify this code. The content of this method is always
+ * regenerated by the Form Editor.
+ */
+
+ // <editor-fold defaultstate="collapsed" desc=" Generated Code ">
+ private void initComponents() {
+ this.setTitle("Import an Attribute/Expression Matrix");
+
+ titleLabel = new javax.swing.JLabel();
+ attributeMatrixFileNameTextField = new javax.swing.JTextField();
+ selectAttributeMatrixFileButton = new javax.swing.JButton();
+ jSeparator1 = new javax.swing.JSeparator();
+ cancelButton = new javax.swing.JButton();
+ importButton = new javax.swing.JButton();
+
+ setDefaultCloseOperation(javax.swing.WindowConstants.DISPOSE_ON_CLOSE);
+ titleLabel.setFont(new java.awt.Font("Dialog", 1, 14));
+ titleLabel.setText("Import Attribute/Expression Matrix File");
+
+ attributeMatrixFileNameTextField.setText("Please select an attribute or expression matrix file...");
+ attributeSelectionSliderLabel = new javax.swing.JLabel();
+ attributeSelectionSliderLabel.setText("Assign values to nodes using...");
+
+ selectAttributeMatrixFileButton.setText("Select");
+ selectAttributeMatrixFileButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ selectAttributeMatrixFileButtonActionPerformed(evt);
+ }
+ });
+
+ cancelButton.setText("Cancel");
+ cancelButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ cancelButtonActionPerformed(evt);
+ }
+ });
+
+ importButton.setText("Import");
+ importButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ importButtonActionPerformed(evt);
+ }
+ });
+ importButton.setEnabled(false);
+
+ keyAttributeBox = new JComboBox(keyAttributeModel);
+ keyAttributeBox.setBounds(10, 75, 260, 20);
+
+ String[] attribs = Cytoscape.getNodeAttributes().getAttributeNames();
+ boolean hasCanonicalNameAttribute = false;
+ this.keyAttributeModel.addElement("ID");
+
+ for (int ii = 0; ii < attribs.length; ++ii) {
+ this.keyAttributeModel.addElement(attribs[ii]);
+ }
+
+ keyAttributeBox.setEditable(true);
+ keyAttributeBox.setSelectedItem("ID");
+
+ KeyAttributeListener listen = new KeyAttributeListener();
+ keyAttributeBox.addItemListener(listen);
+ keyAttributeBox.setVisible(true);
+
+ org.jdesktop.layout.GroupLayout layout = new org.jdesktop.layout.GroupLayout(getContentPane());
+ getContentPane().setLayout(layout);
+ layout.setHorizontalGroup(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(layout.createSequentialGroup().addContainerGap()
+ .add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(jSeparator1,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 379, Short.MAX_VALUE)
+ .add(titleLabel,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ 367,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .add(layout.createSequentialGroup()
+ .add(attributeMatrixFileNameTextField,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 302, Short.MAX_VALUE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(selectAttributeMatrixFileButton)
+ .add(1, 1, 1))
+ .add(keyAttributeBox)
+ .add(attributeSelectionSliderLabel,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 312, Short.MAX_VALUE)
+ .add(org.jdesktop.layout.GroupLayout.TRAILING,
+ layout.createSequentialGroup()
+ .add(importButton)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(cancelButton)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)))
+ .addContainerGap()));
+ layout.setVerticalGroup(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(layout.createSequentialGroup().addContainerGap()
+ .add(titleLabel)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(jSeparator1,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE)
+ .add(attributeMatrixFileNameTextField,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ 23,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .add(selectAttributeMatrixFileButton))
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(attributeSelectionSliderLabel)
+ .add(keyAttributeBox)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(29, 29, 29)
+ .add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE)
+ .add(importButton).add(cancelButton))
+ .addContainerGap(org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE)));
+ pack();
+ } // </editor-fold>
+
+ private void cancelButtonActionPerformed(java.awt.event.ActionEvent evt) {
+ // TODO add your handling code here:
+ status = false;
+ this.dispose();
+ }
+
+ private void importButtonActionPerformed(java.awt.event.ActionEvent evt) {
+ // TODO add your handling code here:
+ status = true;
+ this.dispose();
+ }
+
+ private void selectAttributeMatrixFileButtonActionPerformed(java.awt.event.ActionEvent evt) {
+ // TODO add your handling code here:
+
+ // Create FileFilter
+ CyFileFilter filter = new CyFileFilter();
+
+ // Add accepted File Extensions
+ filter.addExtension("mrna");
+ filter.addExtension("mRNA");
+ filter.addExtension("pvals");
+ filter.setDescription("All Attribute Matrix files");
+
+ // Get the file name
+ File file = FileUtil.getFile("Import AttributeMatrix File", FileUtil.LOAD,
+ new CyFileFilter[] { filter });
+
+ if (file != null) {
+ attributeMatrixFileNameTextField.setText(file.getAbsolutePath());
+ attributeMatrixFileNameTextField.setToolTipText(file.getAbsolutePath());
+ importButton.setEnabled(true);
+ }
+ }
+
+ // Variables declaration - do not modify
+ private javax.swing.JButton cancelButton;
+ private javax.swing.JButton importButton;
+ private javax.swing.JSeparator jSeparator1;
+ private javax.swing.JTextField attributeMatrixFileNameTextField;
+ private javax.swing.JLabel attributeSelectionSliderLabel;
+ private javax.swing.JButton selectAttributeMatrixFileButton;
+ private javax.swing.JLabel titleLabel;
+
+ // End of variables declaration
+}
diff --git a/application/src/main/java/cytoscape/dialogs/ImportNetworkDialog.java b/application/src/main/java/cytoscape/dialogs/ImportNetworkDialog.java
new file mode 100644
index 0000000..a904b7b
--- /dev/null
+++ b/application/src/main/java/cytoscape/dialogs/ImportNetworkDialog.java
@@ -0,0 +1,657 @@
+/*
+ * NetworkImportDialog.java
+ *
+ * Created on 2006/05/08, 11:33
+ */
+package cytoscape.dialogs;
+
+import java.awt.Component;
+import java.awt.Font;
+import java.awt.event.ActionListener;
+import java.awt.event.KeyListener;
+import java.awt.event.FocusListener;
+import java.awt.event.FocusEvent;
+import java.awt.event.ActionEvent;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.List;
+import java.lang.reflect.Method;
+import java.awt.event.ItemListener;
+import java.awt.event.ItemEvent;
+import javax.swing.DefaultComboBoxModel;
+import javax.swing.JButton;
+import javax.swing.JDialog;
+import javax.swing.JLabel;
+import javax.swing.JList;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JRadioButton;
+import javax.swing.JTextField;
+import javax.swing.ListCellRenderer;
+import javax.swing.ToolTipManager;
+import javax.xml.bind.JAXBException;
+
+import cytoscape.Cytoscape;
+import cytoscape.bookmarks.Bookmarks;
+import cytoscape.bookmarks.Category;
+import cytoscape.bookmarks.DataSource;
+import cytoscape.data.ImportHandler;
+import cytoscape.task.Task;
+import cytoscape.task.TaskMonitor;
+import cytoscape.task.ui.JTaskConfig;
+import cytoscape.task.util.TaskManager;
+import cytoscape.util.BookmarksUtil;
+import cytoscape.util.CyFileFilter;
+import cytoscape.util.FileUtil;
+
+
+/**
+ *
+ * @author kono
+ */
+public class ImportNetworkDialog extends JDialog
+ implements ActionListener,FocusListener {
+ private boolean status;
+ private File[] networkFiles;
+ private Bookmarks theBookmarks = null; // get it from session
+ private String bookmarkCategory = "network";
+ private String URLstr;
+ private BookmarkComboBoxEditor bookmarkEditor = new BookmarkComboBoxEditor();
+ private String pleaseMessage = "Please provide URL or select from list";
+
+ private static final String URL_TOOLTIP = "<html>Enter URL or <strong><font color=\"red\">Drag and Drop local/remote files.</font></strong></html>";
+ private static final String LOCAL_TOOLTIP = "<html>Specify path to local files.</html>";
+
+
+ /** Creates new form NetworkImportDialog
+ * @throws IOException
+ * @throws JAXBException */
+ public ImportNetworkDialog(java.awt.Frame parent, boolean modal)
+ throws JAXBException, IOException {
+ super(parent, modal);
+
+ setTitle("Import Network");
+ initComponents();
+ addListeners();
+
+ // By default, import from local
+ switchImportView("Local");
+
+ status = false;
+ networkFiles = null;
+
+ theBookmarks = Cytoscape.getBookmarks();
+
+ // if theBookmarks doesnot exist, create an empty one
+ if (theBookmarks == null) {
+ theBookmarks = new Bookmarks();
+ Cytoscape.setBookmarks(theBookmarks);
+ }
+
+ // if bookmarkCategory "network" does not exist, create a "network" with
+ // empty DataSource
+ Category theCategory = BookmarksUtil.getCategory(bookmarkCategory,
+ theBookmarks.getCategory());
+
+ if (theCategory == null) {
+ theCategory = new Category();
+ theCategory.setName(bookmarkCategory);
+
+ List<Category> theCategoryList = theBookmarks.getCategory();
+ theCategoryList.add(theCategory);
+ }
+
+
+ }
+
+ /**
+ * Get first file only.
+ *
+ * @return
+ */
+ public File getFile() {
+ if ((networkFiles != null) && (networkFiles.length > 0)) {
+ return networkFiles[0];
+ } else {
+ return null;
+ }
+ }
+
+ /**
+ * Get all files selected.
+ *
+ * @return
+ */
+ public File[] getFiles() {
+ return networkFiles;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean getStatus() {
+ return status;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isRemote() {
+ return remoteRadioButton.isSelected();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getURLStr() {
+ return URLstr;
+ }
+
+ /**
+ * This method is called from within the constructor to initialize the form.
+ * WARNING: Do NOT modify this code. The content of this method is always
+ * regenerated by the Form Editor.
+ */
+
+ // <editor-fold defaultstate="collapsed" desc=" Generated Code ">
+ private void initComponents() {
+
+
+ buttonGroup1 = new javax.swing.ButtonGroup();
+ titleLabel = new javax.swing.JLabel();
+ localRadioButton = new javax.swing.JRadioButton();
+ remoteRadioButton = new javax.swing.JRadioButton();
+ networkFileTextField = new javax.swing.JTextField();
+ networkFileComboBox = new javax.swing.JComboBox();
+ selectButton = new javax.swing.JButton();
+ importButton = new javax.swing.JButton();
+ cancelButton = new javax.swing.JButton();
+ titleSeparator = new javax.swing.JSeparator();
+ radioButtonPanel = new javax.swing.JPanel();
+
+ setDefaultCloseOperation(javax.swing.WindowConstants.DISPOSE_ON_CLOSE);
+ titleLabel.setFont(new java.awt.Font("Sans-Serif", Font.BOLD, 14));
+ titleLabel.setText("Import Network File");
+
+ radioButtonPanel.setBorder(javax.swing.BorderFactory.createTitledBorder("Data Source Type"));
+ buttonGroup1.add(localRadioButton);
+ localRadioButton.setSelected(true);
+ localRadioButton.setText("Local");
+ localRadioButton.setBorder(javax.swing.BorderFactory.createEmptyBorder(0, 0, 0, 0));
+ localRadioButton.setMargin(new java.awt.Insets(0, 0, 0, 0));
+ localRadioButton.setToolTipText(LOCAL_TOOLTIP);
+
+ buttonGroup1.add(remoteRadioButton);
+ remoteRadioButton.setText("Remote/URL");
+ remoteRadioButton.setBorder(javax.swing.BorderFactory.createEmptyBorder(0, 0, 0, 0));
+ remoteRadioButton.setMargin(new java.awt.Insets(0, 0, 0, 0));
+ remoteRadioButton.setToolTipText(URL_TOOLTIP);
+
+ networkFileTextField.setText("Please select a network file...");
+ networkFileTextField.setName("networkFileTextField");
+ networkFileTextField.addFocusListener(this);
+
+ selectButton.setText("Select");
+
+ importButton.setText("Import");
+ importButton.setName("btnImport");
+ importButton.setEnabled(false);
+
+ cancelButton.setText("Cancel");
+ cancelButton.setName("btnCancel");
+
+ networkFileComboBox.setRenderer(new MyCellRenderer());
+ networkFileComboBox.setEditor(bookmarkEditor);
+ networkFileComboBox.setEditable(true);
+ networkFileComboBox.setName("networkFileComboBox");
+ networkFileComboBox.setToolTipText("<html><body>You can specify URL by the following:<ul><li>Type URL</li><li>Select from pull down menu</li><li>Drag & Drop URL from Web Browser</li></ul></body><html>");
+ final ToolTipManager tp = ToolTipManager.sharedInstance();
+ tp.setInitialDelay(1);
+ tp.setDismissDelay(7500);
+
+
+ org.jdesktop.layout.GroupLayout radioButtonPanelLayout = new org.jdesktop.layout.GroupLayout(radioButtonPanel);
+ radioButtonPanel.setLayout(radioButtonPanelLayout);
+ radioButtonPanelLayout.setHorizontalGroup(radioButtonPanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(radioButtonPanelLayout.createSequentialGroup()
+ .addContainerGap()
+ .add(localRadioButton)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(remoteRadioButton)
+ .addContainerGap(250,
+ Short.MAX_VALUE)));
+ radioButtonPanelLayout.setVerticalGroup(radioButtonPanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(radioButtonPanelLayout.createSequentialGroup()
+ .add(radioButtonPanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE)
+ .add(localRadioButton)
+ .add(remoteRadioButton))));
+
+ org.jdesktop.layout.GroupLayout layout = new org.jdesktop.layout.GroupLayout(getContentPane());
+ getContentPane().setLayout(layout);
+ layout.setHorizontalGroup(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(layout.createSequentialGroup().addContainerGap()
+ .add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(networkFileComboBox, 0, 350,
+ Short.MAX_VALUE)
+ .add(titleLabel,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ 350,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .add(titleSeparator,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 350, Short.MAX_VALUE)
+ .add(radioButtonPanel,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE)
+ .add(layout.createSequentialGroup()
+ .add(networkFileTextField,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 350, Short.MAX_VALUE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(selectButton))
+ .add(org.jdesktop.layout.GroupLayout.TRAILING,
+ layout.createSequentialGroup()
+ .add(importButton)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(cancelButton)))
+ .addContainerGap()));
+ layout.setVerticalGroup(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(layout.createSequentialGroup().addContainerGap()
+ .add(titleLabel).add(8, 8, 8)
+ .add(titleSeparator,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .add(7, 7, 7)
+ .add(radioButtonPanel,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE)
+ .add(selectButton)
+ .add(networkFileTextField))
+ .add(networkFileComboBox,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED,
+ 3, Short.MAX_VALUE)
+ .add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE)
+ .add(cancelButton).add(importButton))
+ .addContainerGap()));
+ pack();
+ } // </editor-fold>
+
+ private void addListeners() {
+ LocalRemoteListener l = new LocalRemoteListener();
+ localRadioButton.addActionListener(l);
+ remoteRadioButton.addActionListener(l);
+
+ // ButtonActionListener btnActionListener = new ButtonActionListener();
+ selectButton.addActionListener(this);
+ cancelButton.addActionListener(this);
+ importButton.addActionListener(this);
+
+ bookmarkEditor.addActionListener(this);
+ }
+
+ private void switchImportView(String pLocation) {
+ if (pLocation.equalsIgnoreCase("Local")) {
+ // for the case of local import
+ networkFileComboBox.setVisible(false);
+
+ networkFileTextField.setVisible(true);
+ selectButton.setVisible(true);
+ } else { // Remote
+ networkFileComboBox.setVisible(true);
+
+ networkFileTextField.setVisible(false);
+ selectButton.setVisible(false);
+
+ loadBookmarkCMBox();
+ }
+ }
+
+ private void loadBookmarkCMBox() {
+ networkFileComboBox.removeAllItems();
+
+ DefaultComboBoxModel theModel = new DefaultComboBoxModel();
+
+ DataSource firstDataSource = new DataSource();
+ firstDataSource.setName("");
+ firstDataSource.setHref(null);
+
+ theModel.addElement(firstDataSource);
+
+ // Extract the URL entries
+ List<DataSource> theDataSourceList = BookmarksUtil.getDataSourceList(bookmarkCategory,
+ theBookmarks
+ .getCategory());
+
+ if (theDataSourceList != null) {
+ for (int i = 0; i < theDataSourceList.size(); i++) {
+ theModel.addElement(theDataSourceList.get(i));
+ }
+ }
+
+ networkFileComboBox.setModel(theModel);
+ }
+
+ private void cancelButtonActionPerformed(java.awt.event.ActionEvent evt) {
+ status = false;
+ this.dispose();
+ }
+
+ private void importButtonActionPerformed(java.awt.event.ActionEvent evt) {
+ // See if the user just typed in the desired file
+ if (!isRemote() && networkFiles == null && networkFileTextField.getText() != null) {
+ networkFiles = new File[1];
+ networkFiles[0] = new File(networkFileTextField.getText());
+ }
+
+ status = true;
+ this.dispose();
+ }
+
+ private void selectNetworkFileButtonActionPerformed(java.awt.event.ActionEvent evt) {
+ CyFileFilter[] tempCFF = (CyFileFilter[]) Cytoscape.getImportHandler()
+ .getAllFilters(ImportHandler.GRAPH_NATURE)
+ .toArray(new CyFileFilter[0]);
+
+ networkFiles = FileUtil.getFiles("Import Network Files", FileUtil.LOAD, tempCFF);
+
+ if (networkFiles != null) {
+ /*
+ * Accept multiple files
+ */
+ StringBuffer fileNameSB = new StringBuffer();
+ StringBuffer tooltip = new StringBuffer();
+ tooltip.append("<html><body><strong><font color=RED>The following files will be loaded:</font></strong><br>");
+
+ for (int i = 0; i < networkFiles.length; i++) {
+ fileNameSB.append(networkFiles[i].getAbsolutePath() + ", ");
+ tooltip.append("<p>" + networkFiles[i].getAbsolutePath() + "</p>");
+ }
+
+ tooltip.append("</body></html>");
+ networkFileTextField.setText(fileNameSB.toString());
+ networkFileTextField.setToolTipText(tooltip.toString());
+
+ importButton.setEnabled(true);
+ importButton.requestFocusInWindow();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(java.awt.event.ActionEvent e) {
+ Object _actionObject = e.getSource();
+
+ // handle Button events
+ if (_actionObject instanceof JButton) {
+ JButton _btn = (JButton) _actionObject;
+
+ // process radio button events
+ if (_btn == selectButton) {
+ selectNetworkFileButtonActionPerformed(e);
+ } else if (_btn == importButton) {
+ if (localRadioButton.isSelected()) // local import
+ {
+ importButtonActionPerformed(e);
+ } else // case for remote import
+ {
+ //doURLimport(e);
+ //createURLimportTask(e);
+ URLstr = bookmarkEditor.getURLstr().trim();
+ importButtonActionPerformed(e);
+ }
+ } else if (_btn == cancelButton) {
+ cancelButtonActionPerformed(e);
+ }
+ }
+
+ if (_actionObject instanceof JTextField) {
+ // createURLimportTask(e);
+ URLstr = bookmarkEditor.getURLstr().trim();
+ importButtonActionPerformed(e);
+ }
+ }
+
+ /**
+ * Listen for focus events in the text field. Mostly, this is used to
+ * clear the text field for alternative input, but we only want to do
+ * this when the content of the text field is our instruction text
+ *
+ * @param e the FocusEvent
+ */
+ public void focusGained(FocusEvent e) {
+ // Get get the text from the text field
+ String text = networkFileTextField.getText();
+ // If it's our initial text, erase it.
+ if (text.equals("Please select a network file...")) {
+ networkFileTextField.setText("");
+ // We assume that the user is going to type in a filename. If so,
+ // we want to set the import button to be the default
+ getRootPane().setDefaultButton(importButton);
+ importButton.setEnabled(true);
+ }
+ }
+
+ /**
+ * Listen for focus lost events in the text field. These are ignored.
+ *
+ * @param e the FocusEvent
+ */
+ public void focusLost(FocusEvent e) { };
+
+ private void createURLimportTask(java.awt.event.ActionEvent e) {
+ String theURLstr = bookmarkEditor.getURLstr().trim();
+ URL theURL = null;
+
+ try {
+ theURL = new URL(theURLstr);
+ } catch (MalformedURLException e1) {
+ JOptionPane.showMessageDialog(this, "URL error!", "Warning",
+ JOptionPane.INFORMATION_MESSAGE);
+
+ return;
+ }
+
+ // Create Task
+ Task task = new URLdownloadTask(theURL, e);
+
+ // Configure JTask Dialog Pop-Up Box
+ JTaskConfig jTaskConfig = new JTaskConfig();
+ jTaskConfig.setOwner(Cytoscape.getDesktop());
+ jTaskConfig.displayCloseButton(false);
+ jTaskConfig.displayStatus(true);
+ jTaskConfig.setAutoDispose(true);
+ jTaskConfig.displayCancelButton(true);
+
+ // Execute Task in New Thread; pop open JTask Dialog Box.
+ TaskManager.executeTask(task, jTaskConfig);
+ }
+
+ private class URLdownloadTask implements Task {
+ private TaskMonitor taskMonitor;
+ URL url;
+ java.awt.event.ActionEvent e;
+
+ public URLdownloadTask(URL url, java.awt.event.ActionEvent e) {
+ this.url = url;
+ this.e = e;
+ }
+
+ public void run() {
+ taskMonitor.setStatus("Downloading ...");
+ taskMonitor.setPercentCompleted(-1);
+
+ doURLimport(url, e, taskMonitor);
+
+ taskMonitor.setPercentCompleted(100);
+ taskMonitor.setStatus("Downloading successfully from " + url.toString());
+ }
+
+ public void halt() {
+ }
+
+ public void setTaskMonitor(TaskMonitor monitor) throws IllegalThreadStateException {
+ this.taskMonitor = monitor;
+ }
+
+ public String getTitle() {
+ return "URL downloading";
+ }
+ }
+
+ private void doURLimport(URL url, java.awt.event.ActionEvent e, TaskMonitor taskMonitor) {
+ cytoscape.data.ImportHandler theHandler = Cytoscape.getImportHandler();
+ cytoscape.data.readers.GraphReader reader = null;
+
+ try {
+ reader = theHandler.getReader(url);
+ if (reader == null )
+ return;
+
+ // See if the reader supports setTaskMonitor. We need to use reflection
+ // to provide backwards comptibility for those readers that do not inherit
+ // from AbstractGraphReader
+ Method[] mlist = reader.getClass().getDeclaredMethods();
+ for (int i = 0; i < mlist.length; i++) {
+ Method m = mlist[i];
+ if (m.getName().equals("setTaskMonitor")) {
+ m.invoke(reader, taskMonitor);
+ break;
+ }
+ }
+ reader.read();
+
+ } catch (MalformedURLException e1) {
+ JOptionPane.showMessageDialog(this, "URL error!", "Warning",
+ JOptionPane.INFORMATION_MESSAGE);
+ } catch (FileNotFoundException e2) {
+ JOptionPane.showMessageDialog(this,
+ "File was not found! Please make sure the URL is correct!",
+ "Warning", JOptionPane.INFORMATION_MESSAGE);
+ } catch (IOException e3) {
+ JOptionPane.showMessageDialog(this,
+ "IO error! May caused by server-name, proxy, write-permission.",
+ "Warning", JOptionPane.INFORMATION_MESSAGE);
+ } catch (Exception e4) {
+ JOptionPane.showMessageDialog(this, "Failed to download from URL!", "Warning",
+ JOptionPane.INFORMATION_MESSAGE);
+ }
+ }
+
+ class LocalRemoteListener implements java.awt.event.ActionListener {
+ public void actionPerformed(java.awt.event.ActionEvent e) {
+ Object _actionObject = e.getSource();
+
+ // handle radioButton events
+ if (_actionObject instanceof JRadioButton) {
+ JRadioButton _rbt = (JRadioButton) _actionObject;
+
+ // process radio button events
+ if (_rbt == localRadioButton) {
+ switchImportView("Local");
+ } else { // from rbtRemote
+ switchImportView("Remote");
+ importButton.setEnabled(true);
+ }
+
+ pack();
+ }
+ } // actionPerformed()
+ }
+
+ class MyCellRenderer extends JLabel implements ListCellRenderer {
+ public MyCellRenderer() {
+ setOpaque(true);
+ }
+
+ public Component getListCellRendererComponent(JList list, Object value, int index,
+ boolean isSelected, boolean cellHasFocus) {
+ DataSource dataSource = (DataSource) value;
+ setText(dataSource.getName());
+
+ if (isSelected) {
+ if (0 < index) {
+ list.setToolTipText(dataSource.getHref());
+ }
+ }
+
+ return this;
+ }
+ } // MyCellRenderer
+
+ class BookmarkComboBoxEditor implements javax.swing.ComboBoxEditor {
+ DataSource theDataSource = new DataSource();
+ JTextField tfInput = new JTextField(pleaseMessage);
+
+ public String getURLstr() {
+ return tfInput.getText();
+ }
+
+ public void addActionListener(ActionListener l) {
+ tfInput.addActionListener(l);
+ }
+
+ public void addKeyListener(KeyListener l) {
+ tfInput.addKeyListener(l);
+ }
+
+ public Component getEditorComponent() {
+ return tfInput;
+ }
+
+ public Object getItem() {
+ return theDataSource;
+ }
+
+ public void removeActionListener(ActionListener l) {
+ }
+
+ public void selectAll() {
+ }
+
+ public void setItem(Object anObject) {
+ if (anObject == null) {
+ return;
+ }
+
+ if (anObject instanceof DataSource) {
+ theDataSource = (DataSource) anObject;
+ tfInput.setText(theDataSource.getHref());
+ }
+ }
+ } // BookmarkComboBoxEditor
+
+ // Variables declaration - do not modify
+ private javax.swing.JButton cancelButton;
+ private javax.swing.JButton importButton;
+ private JPanel radioButtonPanel;
+ private javax.swing.JButton selectButton;
+ private javax.swing.ButtonGroup buttonGroup1;
+ private javax.swing.JComboBox networkFileComboBox;
+ private javax.swing.JLabel titleLabel;
+ private javax.swing.JRadioButton remoteRadioButton;
+ private javax.swing.JRadioButton localRadioButton;
+ private javax.swing.JTextField networkFileTextField;
+ private javax.swing.JSeparator titleSeparator;
+
+ // End of variables declaration
+}
diff --git a/application/src/main/java/cytoscape/dialogs/IntegerEntryField.java b/application/src/main/java/cytoscape/dialogs/IntegerEntryField.java
new file mode 100644
index 0000000..27756fc
--- /dev/null
+++ b/application/src/main/java/cytoscape/dialogs/IntegerEntryField.java
@@ -0,0 +1,200 @@
+/*
+ File: IntegerEntryField.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// IntegerEntryField.java
+
+//---------------------------------------------------------------------------------------
+// $Revision: 14790 $
+// $Date: 2008-08-23 02:50:50 +0200 (Sat, 23 Aug 2008) $
+// $Author: scooter $
+//---------------------------------------------------------------------------------------
+package cytoscape.dialogs;
+
+
+//---------------------------------------------------------------------------------------
+import cytoscape.logger.CyLogger;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import java.text.*;
+
+import java.util.*;
+
+import javax.swing.*;
+import javax.swing.event.*;
+
+
+//---------------------------------------------------------------------------------------
+/**
+ *
+ */
+public class IntegerEntryField extends JPanel {
+ JTextField sizeField;
+ JLabel sizeLabel;
+ JFrame mainFrame;
+ JPanel mainPanel;
+
+ /**
+ * Creates a new IntegerEntryField object.
+ *
+ * @param fieldName DOCUMENT ME!
+ * @param defaultValue DOCUMENT ME!
+ * @param maxValue DOCUMENT ME!
+ */
+ public IntegerEntryField(String fieldName, int defaultValue, int maxValue) {
+ super(new GridLayout(1, 2, 10, 10));
+
+ sizeLabel = new JLabel(fieldName);
+ sizeField = new JTextField(Integer.toString(defaultValue));
+ sizeField.addFocusListener(new PositiveIntegerListener(defaultValue, maxValue));
+
+ add(sizeLabel);
+ add(sizeField);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Integer getInteger() {
+ return new Integer(sizeField.getText());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param newVal DOCUMENT ME!
+ */
+ public void setInteger(Integer newVal) {
+ sizeField.setText(newVal.toString());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getInt() {
+ return Integer.parseInt(sizeField.getText());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param newVal DOCUMENT ME!
+ */
+ public void setInt(int newVal) {
+ sizeField.setText(Integer.toString(newVal));
+ }
+
+ public class PositiveIntegerListener implements FocusListener {
+ private int digits;
+ private int maxval;
+ private int defaultVal;
+ private String maxvalString;
+ private String defaultString;
+
+ public PositiveIntegerListener(int defaultVal, int maxval) {
+ super();
+ this.maxval = maxval;
+ this.defaultVal = defaultVal;
+ this.maxvalString = Integer.toString(maxval);
+ this.defaultString = Integer.toString(defaultVal);
+ this.digits = this.maxvalString.length();
+ }
+
+ public void focusGained(FocusEvent e) {
+ //CyLogger.getLogger().info("gained");
+ validate((JTextField) e.getSource());
+ }
+
+ public void focusLost(FocusEvent e) {
+ //CyLogger.getLogger().info("lost");
+ validate((JTextField) e.getSource());
+ }
+
+ private void validate(JTextField field) {
+ String fieldStr = field.getText();
+ fieldStr = fieldStr.replaceAll("[^0-9]", ""); // ditch all non-numeric
+
+ if (fieldStr.length() > 0) {
+ if (fieldStr.length() > digits) {
+ field.setText(maxvalString);
+ } else {
+ //CyLogger.getLogger().info(" length " + fieldStr.length());
+ try {
+ int val = Integer.parseInt(fieldStr);
+
+ if (val <= 0) {
+ field.setText(defaultString);
+ } else if (val > maxval) {
+ field.setText(maxvalString);
+ } else {
+ field.setText(fieldStr);
+ }
+ } catch (NumberFormatException nfe) {
+ CyLogger.getLogger().info("Not an integer: " + fieldStr, nfe);
+ field.setText(defaultString);
+ }
+ }
+ } // if gt 0
+ else {
+ field.setText(defaultString);
+ } // if gt 0 (else)
+ }
+ } // PositiveIntegerListener
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public JTextField getField() {
+ return sizeField;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public JLabel getLabel() {
+ return sizeLabel;
+ }
+} //class IntegerEntryField
diff --git a/application/src/main/java/cytoscape/dialogs/JointIntegerEntry.java b/application/src/main/java/cytoscape/dialogs/JointIntegerEntry.java
new file mode 100644
index 0000000..1236c69
--- /dev/null
+++ b/application/src/main/java/cytoscape/dialogs/JointIntegerEntry.java
@@ -0,0 +1,255 @@
+/*
+ File: JointIntegerEntry.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// JointIntegerEntry.java
+
+//---------------------------------------------------------------------------------------
+// $Revision: 9565 $
+// $Date: 2007-02-13 20:36:50 +0100 (Tue, 13 Feb 2007) $
+// $Author: mes $
+//---------------------------------------------------------------------------------------
+package cytoscape.dialogs;
+
+import cytoscape.dialogs.IntegerEntryField;
+
+//---------------------------------------------------------------------------------------
+import java.awt.*;
+import java.awt.event.*;
+
+import java.text.*;
+
+import java.util.*;
+
+import javax.swing.*;
+import javax.swing.event.*;
+
+
+//---------------------------------------------------------------------------------------
+/**
+ *
+ */
+public class JointIntegerEntry extends JPanel {
+ IntegerEntryField field1;
+ IntegerEntryField field2;
+ JLabel constraintLabel;
+ JCheckBox constraintBox;
+ JFrame mainFrame;
+ JPanel mainPanel;
+ String field1Name;
+ String field2Name;
+ String fieldName;
+ boolean locked;
+
+ /**
+ * Creates a new JointIntegerEntry object.
+ *
+ * @param fieldName DOCUMENT ME!
+ * @param field1Name DOCUMENT ME!
+ * @param field2Name DOCUMENT ME!
+ * @param defaultValue1 DOCUMENT ME!
+ * @param defaultValue2 DOCUMENT ME!
+ * @param maxValue1 DOCUMENT ME!
+ * @param maxValue2 DOCUMENT ME!
+ */
+ public JointIntegerEntry(String fieldName, String field1Name, String field2Name,
+ int defaultValue1, int defaultValue2, int maxValue1, int maxValue2) {
+ super(new GridLayout(1, 2, 10, 10));
+
+ this.field1Name = field1Name;
+ this.field2Name = field2Name;
+ this.fieldName = fieldName;
+
+ String fullName1 = fieldName + " " + field1Name;
+ field1 = new IntegerEntryField(fullName1, defaultValue1, maxValue1);
+
+ String fullName2 = fieldName + " " + field2Name;
+ field2 = new IntegerEntryField(fullName2, defaultValue2, maxValue2);
+
+ String constrString = "Lock " + fullName1 + " to " + field2Name + "?";
+ constraintLabel = new JLabel(constrString);
+ locked = false;
+
+ if (defaultValue1 == defaultValue2)
+ locked = true;
+
+ constraintBox = new JCheckBox("", locked);
+ constraintBox.addItemListener(new LockedItemListener());
+
+ field1.getField().addFocusListener(new CopyField1To2Listener());
+ whetherField2IsEnabled();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param whichField DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Integer getInteger(String whichField) {
+ if (whichField.equalsIgnoreCase(field1Name))
+ return field1.getInteger();
+ else
+
+ return field2.getInteger();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param whichField DOCUMENT ME!
+ * @param newVal DOCUMENT ME!
+ */
+ public void setInteger(String whichField, Integer newVal) {
+ if (whichField.equalsIgnoreCase(field1Name))
+ field1.setInteger(newVal);
+ else
+ field2.setInteger(newVal);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param whichField DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getInt(String whichField) {
+ if (whichField.equalsIgnoreCase(field1Name))
+ return field1.getInt();
+ else
+
+ return field2.getInt();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param whichField DOCUMENT ME!
+ * @param newVal DOCUMENT ME!
+ */
+ public void setInt(String whichField, int newVal) {
+ if (whichField.equalsIgnoreCase(field1Name))
+ field1.setInt(newVal);
+ else
+ field2.setInt(newVal);
+ }
+
+ public class LockedItemListener implements ItemListener {
+ public void itemStateChanged(ItemEvent e) {
+ JCheckBox jcb = (JCheckBox) e.getItem();
+ locked = jcb.isSelected();
+
+ if (locked)
+ copy1to2();
+
+ whetherField2IsEnabled();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void whetherField2IsEnabled() {
+ field2.getLabel().setEnabled(!locked);
+ field2.getField().setEnabled(!locked);
+ }
+
+ public class CopyField1To2Listener implements FocusListener {
+ public void focusGained(FocusEvent e) {
+ if (locked)
+ copy1to2();
+ }
+
+ public void focusLost(FocusEvent e) {
+ if (locked)
+ copy1to2();
+ }
+ }
+
+ private void copy1to2() {
+ field2.setInt(field1.getInt());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param whichField DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public JTextField getField(String whichField) {
+ if (whichField.equalsIgnoreCase(field1Name))
+ return field1.getField();
+ else
+
+ return field2.getField();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param whichField DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public JLabel getLabel(String whichField) {
+ if (whichField.equalsIgnoreCase(field1Name))
+ return field1.getLabel();
+ else
+
+ return field2.getLabel();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public JCheckBox getConstraintBox() {
+ return constraintBox;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public JLabel getConstraintLabel() {
+ return constraintLabel;
+ }
+} //class JointIntegerEntry
diff --git a/application/src/main/java/cytoscape/dialogs/LabelTextPanel.java b/application/src/main/java/cytoscape/dialogs/LabelTextPanel.java
new file mode 100644
index 0000000..595e08d
--- /dev/null
+++ b/application/src/main/java/cytoscape/dialogs/LabelTextPanel.java
@@ -0,0 +1,120 @@
+/*
+ File: LabelTextPanel.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// LabelTextPanel.java
+
+// ---------------------------------------------------------------------------------------
+// $Revision: 9565 $
+// $Date: 2007-02-13 20:36:50 +0100 (Tue, 13 Feb 2007) $
+// $Author: mes $
+// ---------------------------------------------------------------------------------------
+package cytoscape.dialogs;
+
+import cytoscape.data.CyAttributes;
+import cytoscape.data.Semantics;
+
+import cytoscape.util.MutableString;
+
+import cytoscape.visual.calculators.AbstractCalculator;
+
+// ---------------------------------------------------------------------------------------
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.event.ActionEvent;
+
+import javax.swing.AbstractAction;
+import javax.swing.DefaultComboBoxModel;
+import javax.swing.JComboBox;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+
+
+// --------------------------------------------------------------------------------------
+/**
+ *
+ */
+public class LabelTextPanel extends JPanel {
+ String[] attributeNames;
+ MutableString nodeLabelKey;
+ JComboBox theBox;
+
+ // --------------------------------------------------------------------------------------
+ /**
+ * Creates a new LabelTextPanel object.
+ *
+ * @param nodeAttribs DOCUMENT ME!
+ * @param writeHere DOCUMENT ME!
+ */
+ public LabelTextPanel(CyAttributes nodeAttribs, MutableString writeHere) {
+ super();
+ attributeNames = nodeAttribs.getAttributeNames();
+ nodeLabelKey = writeHere;
+
+ GridBagLayout gridbag = new GridBagLayout();
+ GridBagConstraints c = new GridBagConstraints();
+ this.setLayout(gridbag);
+
+ // using Model so we can manually add "canonicalName" at the end.
+ DefaultComboBoxModel boxModel = new DefaultComboBoxModel();
+
+ for (int i = 0; i < attributeNames.length; i++)
+ boxModel.addElement(new String(attributeNames[i]));
+
+ //boxModel.addElement(new String("canonicalName"));
+ boxModel.addElement(AbstractCalculator.ID);
+ theBox = new JComboBox(boxModel);
+ theBox.setSelectedItem(nodeLabelKey.getString());
+ theBox.addActionListener(new BoxAction());
+
+ JLabel label = new JLabel("Node Label: ");
+ c.gridx = 0;
+ c.gridy = 0;
+ gridbag.setConstraints(label, c);
+ this.add(label);
+ c.gridx = 1;
+ c.gridy = 0;
+ gridbag.setConstraints(theBox, c);
+ this.add(theBox);
+ } // LabelTextPanel ctor
+
+ public class BoxAction extends AbstractAction {
+ public void actionPerformed(ActionEvent e) {
+ JComboBox jcb = (JComboBox) e.getSource();
+ nodeLabelKey.setString((String) jcb.getSelectedItem());
+ }
+ }
+} // class LabelTextPanel
diff --git a/application/src/main/java/cytoscape/dialogs/MiscGB.java b/application/src/main/java/cytoscape/dialogs/MiscGB.java
new file mode 100644
index 0000000..783e3a5
--- /dev/null
+++ b/application/src/main/java/cytoscape/dialogs/MiscGB.java
@@ -0,0 +1,247 @@
+/*
+ File: MiscGB.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+
+package cytoscape.dialogs;
+
+
+import cytoscape.logger.CyLogger;
+
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.Insets;
+
+import javax.swing.JButton;
+import javax.swing.JDialog;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+
+
+/**
+ * We DO need to replace this with swing-layout!
+ * Miscellaneous static GridBagLayout utilities
+ */
+public class MiscGB {
+ // sets GridBagConstraints.
+ /**
+ * DOCUMENT ME!
+ *
+ * @param c DOCUMENT ME!
+ * @param padx DOCUMENT ME!
+ * @param pady DOCUMENT ME!
+ */
+ public static void pad(GridBagConstraints c, int padx, int pady) {
+ c.ipadx = padx;
+ c.ipady = pady;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param c DOCUMENT ME!
+ * @param b DOCUMENT ME!
+ * @param l DOCUMENT ME!
+ * @param r DOCUMENT ME!
+ * @param t DOCUMENT ME!
+ */
+ public static void inset(GridBagConstraints c, int b, int l, int r, int t) {
+ c.insets = new Insets(b, l, r, t);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param c DOCUMENT ME!
+ * @param s DOCUMENT ME!
+ */
+ public static void inset(GridBagConstraints c, int s) {
+ inset(c, s, s, s, s);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param c DOCUMENT ME!
+ * @param x DOCUMENT ME!
+ * @param y DOCUMENT ME!
+ * @param w DOCUMENT ME!
+ * @param h DOCUMENT ME!
+ * @param weightx DOCUMENT ME!
+ * @param weighty DOCUMENT ME!
+ * @param f DOCUMENT ME!
+ */
+ public static void set(GridBagConstraints c, int x, int y, int w, int h, int weightx,
+ int weighty, int f) {
+ c.gridx = x;
+ c.gridy = y;
+ c.gridwidth = w;
+ c.gridheight = h;
+ c.weightx = weightx;
+ c.weighty = weighty;
+ c.fill = f;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param c DOCUMENT ME!
+ * @param x DOCUMENT ME!
+ * @param y DOCUMENT ME!
+ * @param w DOCUMENT ME!
+ * @param h DOCUMENT ME!
+ */
+ public static void set(GridBagConstraints c, int x, int y, int w, int h) {
+ set(c, x, y, w, h, 0, 0, GridBagConstraints.NONE);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param c DOCUMENT ME!
+ * @param x DOCUMENT ME!
+ * @param y DOCUMENT ME!
+ */
+ public static void set(GridBagConstraints c, int x, int y) {
+ set(c, x, y, 1, 1, 0, 0, GridBagConstraints.NONE);
+ }
+
+ // inserts a component into a panel with a GridBagLayout.
+ /**
+ * DOCUMENT ME!
+ *
+ * @param panel DOCUMENT ME!
+ * @param comp DOCUMENT ME!
+ * @param bag DOCUMENT ME!
+ * @param c DOCUMENT ME!
+ */
+ public static void insert(JPanel panel, Component comp, GridBagLayout bag, GridBagConstraints c) {
+ if (bag == null)
+ CyLogger.getLogger().info("bag is null");
+
+ if (comp == null)
+ CyLogger.getLogger().info("comp is null");
+
+ if (c == null)
+ CyLogger.getLogger().info("c is null");
+
+ if (panel == null)
+ CyLogger.getLogger().info("panel is null");
+
+ bag.setConstraints(comp, c);
+ panel.add(comp);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param gbg DOCUMENT ME!
+ * @param comp DOCUMENT ME!
+ * @param x DOCUMENT ME!
+ * @param y DOCUMENT ME!
+ */
+ public static void insert(GridBagGroup gbg, Component comp, int x, int y) {
+ set(gbg.constraints, x, y);
+ insert(gbg.panel, comp, gbg.gridbag, gbg.constraints);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param gbg DOCUMENT ME!
+ * @param comp DOCUMENT ME!
+ * @param x DOCUMENT ME!
+ * @param y DOCUMENT ME!
+ * @param w DOCUMENT ME!
+ * @param h DOCUMENT ME!
+ */
+ public static void insert(GridBagGroup gbg, Component comp, int x, int y, int w, int h) {
+ set(gbg.constraints, x, y, w, h);
+ insert(gbg.panel, comp, gbg.gridbag, gbg.constraints);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param gbg DOCUMENT ME!
+ * @param comp DOCUMENT ME!
+ * @param x DOCUMENT ME!
+ * @param y DOCUMENT ME!
+ * @param w DOCUMENT ME!
+ * @param h DOCUMENT ME!
+ * @param f DOCUMENT ME!
+ */
+ public static void insert(GridBagGroup gbg, Component comp, int x, int y, int w, int h, int f) {
+ set(gbg.constraints, x, y, w, h, 0, 0, f);
+ insert(gbg.panel, comp, gbg.gridbag, gbg.constraints);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param gbg DOCUMENT ME!
+ * @param comp DOCUMENT ME!
+ * @param x DOCUMENT ME!
+ * @param y DOCUMENT ME!
+ * @param w DOCUMENT ME!
+ * @param h DOCUMENT ME!
+ * @param weightx DOCUMENT ME!
+ * @param weighty DOCUMENT ME!
+ * @param f DOCUMENT ME!
+ */
+ public static void insert(GridBagGroup gbg, Component comp, int x, int y, int w, int h,
+ int weightx, int weighty, int f) {
+ set(gbg.constraints, x, y, w, h, weightx, weighty, f);
+ insert(gbg.panel, comp, gbg.gridbag, gbg.constraints);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param c DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static JLabel createColorLabel(Color c) {
+ JLabel label = new JLabel(" ");
+ label.setOpaque(true);
+ label.setBackground(c);
+
+ return label;
+ }
+}
diff --git a/application/src/main/java/cytoscape/dialogs/NetworkMetaDataDialog.java b/application/src/main/java/cytoscape/dialogs/NetworkMetaDataDialog.java
new file mode 100644
index 0000000..5aefddb
--- /dev/null
+++ b/application/src/main/java/cytoscape/dialogs/NetworkMetaDataDialog.java
@@ -0,0 +1,267 @@
+/*
+ * MetadataDialog.java
+ *
+ * Created on 2006/03/22, 12:39
+ */
+package cytoscape.dialogs;
+
+import cytoscape.CyNetwork;
+
+import cytoscape.data.readers.MetadataEntries;
+import cytoscape.data.readers.MetadataParser;
+
+import cytoscape.logger.CyLogger;
+
+import java.awt.Color;
+import java.awt.Font;
+
+import java.net.URISyntaxException;
+
+import java.util.Iterator;
+import java.util.Vector;
+
+import javax.swing.JDialog;
+import javax.swing.JScrollPane;
+import javax.swing.JTable;
+import javax.swing.event.TableModelEvent;
+import javax.swing.event.TableModelListener;
+
+import javax.xml.bind.JAXBException;
+
+
+/**
+ * Dialog for editing network metadata in RDF.<br>
+ *
+ * @version 1.0
+ * @since 2.3
+ * @see cytoscape.dialogs.NetworkMetaDataTableModel
+ * @author kono
+ *
+ */
+public class NetworkMetaDataDialog extends JDialog implements TableModelListener {
+ private NetworkMetaDataTableModel metaTM;
+ private MetadataParser mdp;
+ private CyNetwork network;
+ private String description;
+ private CyLogger logger = CyLogger.getLogger(NetworkMetaDataDialog.class);
+
+ /**
+ * Creates new form MetadataDialog
+ *
+ * @throws URISyntaxException
+ */
+ public NetworkMetaDataDialog(java.awt.Frame parent, boolean modal, CyNetwork network) {
+ super(parent, modal);
+ this.network = network;
+ this.mdp = new MetadataParser(network);
+ metaTM = new NetworkMetaDataTableModel(network);
+
+ try {
+ metaTM.setTable();
+ } catch (URISyntaxException e) {
+ // TODO Auto-generated catch block
+ logger.warn("Unable to parse some of the network meta-data", e);
+ }
+
+ description = metaTM.getDescription();
+
+ initComponents();
+ }
+
+ /**
+ * This method is called from within the constructor to initialize the form.
+ * WARNING: Do NOT modify this code. The content of this method is always
+ * regenerated by the Form Editor.
+ */
+
+ // <editor-fold defaultstate="collapsed" desc=" Generated Code ">
+ private void initComponents() {
+ Font titleFont = new Font("SansSerif", Font.BOLD, 14);
+
+ this.setTitle("Network Metadata Editor");
+
+ okButton = new javax.swing.JButton();
+ cancelButton = new javax.swing.JButton();
+ jPanel1 = new javax.swing.JPanel();
+ titleLabel = new javax.swing.JLabel();
+ mainSplitPane = new javax.swing.JSplitPane();
+ metadataTableScrollPane = new javax.swing.JScrollPane();
+ descriptionScrollPane = new javax.swing.JScrollPane();
+ descriptionTextArea = new javax.swing.JTextArea();
+
+ setDefaultCloseOperation(javax.swing.WindowConstants.DISPOSE_ON_CLOSE);
+ okButton.setText("Update");
+ okButton.addMouseListener(new java.awt.event.MouseAdapter() {
+ public void mouseClicked(java.awt.event.MouseEvent evt) {
+ okButtonMouseClicked(evt);
+ }
+ });
+
+ cancelButton.setText("Cancel");
+ cancelButton.addMouseListener(new java.awt.event.MouseAdapter() {
+ public void mouseClicked(java.awt.event.MouseEvent evt) {
+ cancelButtonMouseClicked(evt);
+ }
+ });
+
+ titleLabel.setText("Network Metadata for " + network.getTitle());
+ titleLabel.setFont(titleFont);
+ titleLabel.setForeground(Color.BLUE);
+
+ org.jdesktop.layout.GroupLayout jPanel1Layout = new org.jdesktop.layout.GroupLayout(jPanel1);
+ jPanel1.setLayout(jPanel1Layout);
+ jPanel1Layout.setHorizontalGroup(jPanel1Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(jPanel1Layout.createSequentialGroup()
+ .addContainerGap()
+ .add(titleLabel,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ 500,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .addContainerGap(5,
+ Short.MAX_VALUE)));
+ jPanel1Layout.setVerticalGroup(jPanel1Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(jPanel1Layout.createSequentialGroup()
+ .addContainerGap(org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE)
+ .add(titleLabel)));
+
+ mainSplitPane.setDividerLocation(120);
+ mainSplitPane.setDividerSize(5);
+ mainSplitPane.setOrientation(javax.swing.JSplitPane.VERTICAL_SPLIT);
+
+ metadataTableScrollPane.setViewportView(getMetadataTable());
+
+ mainSplitPane.setTopComponent(metadataTableScrollPane);
+
+ descriptionScrollPane.setBorder(null);
+ descriptionScrollPane.setBorder(javax.swing.BorderFactory.createTitledBorder("Description"));
+
+ descriptionTextArea.setText(description);
+ descriptionTextArea.setLineWrap(true);
+ descriptionTextArea.setWrapStyleWord(false);
+ descriptionTextArea.setTabSize(4);
+ descriptionTextArea.setEditable(true);
+
+ descriptionScrollPane.setViewportView(descriptionTextArea);
+ descriptionScrollPane.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
+
+ mainSplitPane.setRightComponent(descriptionScrollPane);
+
+ org.jdesktop.layout.GroupLayout layout = new org.jdesktop.layout.GroupLayout(getContentPane());
+ getContentPane().setLayout(layout);
+ layout.setHorizontalGroup(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(org.jdesktop.layout.GroupLayout.TRAILING,
+ layout.createSequentialGroup()
+ .addContainerGap(201, Short.MAX_VALUE)
+ .add(okButton)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(cancelButton).addContainerGap())
+ .add(jPanel1, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE)
+ .add(mainSplitPane,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 343,
+ Short.MAX_VALUE));
+ layout.setVerticalGroup(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(layout.createSequentialGroup()
+ .add(jPanel1,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(mainSplitPane,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 339, Short.MAX_VALUE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE)
+ .add(okButton).add(cancelButton))
+ .addContainerGap()));
+ pack();
+ } // </editor-fold>
+
+ private void cancelButtonMouseClicked(java.awt.event.MouseEvent evt) {
+ // TODO add your handling code here:
+ this.dispose();
+ }
+
+ private void okButtonMouseClicked(java.awt.event.MouseEvent evt) {
+ // TODO add your handling code here:
+ try {
+ update();
+ } catch (JAXBException e1) {
+ logger.warn("Unable to update network metadata", e1);
+ }
+
+ // Cytoscape.firePropertyChange(Cytoscape.ATTRIBUTES_CHANGED, null,
+ // null);
+ this.dispose();
+ }
+
+ private void update() throws JAXBException {
+ Vector dataVector = metaTM.getDataVector();
+ Iterator it = dataVector.iterator();
+
+ while (it.hasNext()) {
+ Vector row = (Vector) it.next();
+ String label = (String) row.get(0);
+ Object value = row.get(1);
+
+ if (label != null) {
+ if (value == null) {
+ mdp.setMetadata(MetadataEntries.valueOf(label.toUpperCase()), "N/A");
+ } else {
+ mdp.setMetadata(MetadataEntries.valueOf(label.toUpperCase()), value.toString());
+ }
+ }
+ }
+
+ mdp.setMetadata(MetadataEntries.DESCRIPTION, descriptionTextArea.getText());
+ }
+
+ /**
+ * @return Returns the metadataTable.
+ */
+ private JTable getMetadataTable() {
+ if (metadataTable == null) {
+ metaTM.addTableModelListener(new metadataTableListener());
+
+ metadataTable = new JTable(metaTM);
+ metadataTable.setRowSelectionAllowed(true);
+ }
+
+ return metadataTable;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param arg0 DOCUMENT ME!
+ */
+ public void tableChanged(TableModelEvent arg0) {
+ // TODO Auto-generated method stub
+ }
+
+ /**
+ * table listener.
+ *
+ * @author kono
+ *
+ */
+ class metadataTableListener implements TableModelListener {
+ public void tableChanged(TableModelEvent arg0) {
+ }
+ }
+
+ // Variables declaration - do not modify
+ private javax.swing.JButton okButton;
+ private javax.swing.JButton cancelButton;
+ private javax.swing.JTextArea descriptionTextArea;
+ private javax.swing.JLabel titleLabel;
+ private javax.swing.JPanel jPanel1;
+ private javax.swing.JScrollPane metadataTableScrollPane;
+ private javax.swing.JScrollPane descriptionScrollPane;
+ private javax.swing.JSplitPane mainSplitPane;
+ private JTable metadataTable;
+
+ // End of variables declaration
+}
diff --git a/application/src/main/java/cytoscape/dialogs/NetworkMetaDataTableModel.java b/application/src/main/java/cytoscape/dialogs/NetworkMetaDataTableModel.java
new file mode 100644
index 0000000..7dd7e72
--- /dev/null
+++ b/application/src/main/java/cytoscape/dialogs/NetworkMetaDataTableModel.java
@@ -0,0 +1,182 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.dialogs;
+
+import cytoscape.CyNetwork;
+
+import cytoscape.data.readers.MetadataParser;
+
+import java.net.URISyntaxException;
+
+import java.util.Map;
+
+import javax.swing.table.DefaultTableModel;
+
+
+/**
+ *
+ * Table model for the Network Metadata Dialog.
+ *
+ * @version 1.0
+ * @since 2.3
+ * @see cytoscape.dialogs.NetworkMetaDataDialog
+ * @author kono
+ *
+ */
+public class NetworkMetaDataTableModel extends DefaultTableModel {
+ private CyNetwork network;
+ private Object[][] dataArray;
+ private Map data;
+ private String description;
+
+ // Define Column names
+ private static String[] columnHeader = new String[] { "Data Label", "Value" };
+
+ // Define default entries. This determins the order in the table.
+ private static String[] defaultEntries = {
+ "Title", "Identifier", "Source", "Type", "Format",
+ "Date"
+ };
+ private MetadataParser mdp;
+
+ /**
+ * Constructor for the network metadata table model.
+ *
+ * @param network
+ * Metadata for this network will be edited.
+ */
+ public NetworkMetaDataTableModel(CyNetwork network) {
+ super();
+ this.network = network;
+ description = null;
+ mdp = new MetadataParser(this.network);
+ }
+
+ /**
+ * Set table data based on the Map object returned by the data
+ * parser.
+ *
+ * @throws URISyntaxException
+ */
+ protected void setTable() throws URISyntaxException {
+ // Always 2 columns --- Data label and value.
+ Object[] column_names = new Object[2];
+ column_names[0] = "Data Label";
+ column_names[1] = "Value";
+
+ data = mdp.getMetadataMap();
+ description = (String) data.get("Description");
+ dataArray = new Object[defaultEntries.length][2];
+
+ // Order vector based on the labels
+ for (int i = 0; i < defaultEntries.length; i++) {
+ String key = defaultEntries[i];
+ dataArray[i][0] = key;
+ dataArray[i][1] = data.get(key);
+ }
+
+ setDataVector(dataArray, columnHeader);
+ }
+
+ /**
+ * Get Desctiption entry, which will not be included in the table.
+ *
+ * @return
+ * Long string of description.
+ *
+ */
+ public String getDescription() {
+ return description;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getColumnCount() {
+ // TODO Auto-generated method stub
+ return columnHeader.length;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getRowCount() {
+ return defaultEntries.length;
+ }
+
+ /**
+ * Determine which cell is editible or not.
+ */
+ public boolean isCellEditable(int row, int column) {
+ if (column == 0) {
+ // Do not allow to edit data names.
+ return false;
+ } else if (row == 0) {
+ return false;
+ } else {
+ return true;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param arg0 DOCUMENT ME!
+ * @param arg1 DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getValueAt(int arg0, int arg1) {
+ // TODO Auto-generated method stub
+ return dataArray[arg0][arg1];
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param obj DOCUMENT ME!
+ * @param row DOCUMENT ME!
+ * @param col DOCUMENT ME!
+ */
+ public void setValueAt(Object obj, int row, int col) {
+ dataArray[row][col] = obj;
+ setDataVector(dataArray, columnHeader);
+ fireTableCellUpdated(row, col);
+ }
+}
diff --git a/application/src/main/java/cytoscape/dialogs/NewSlider.java b/application/src/main/java/cytoscape/dialogs/NewSlider.java
new file mode 100644
index 0000000..b1c2fcc
--- /dev/null
+++ b/application/src/main/java/cytoscape/dialogs/NewSlider.java
@@ -0,0 +1,308 @@
+/*
+ File: NewSlider.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// NewSlider.java
+
+//---------------------------------------------------------------------------------------
+// $Revision: 9736 $
+// $Date: 2007-03-20 01:25:45 +0100 (Tue, 20 Mar 2007) $
+// $Author: mes $
+//---------------------------------------------------------------------------------------
+package cytoscape.dialogs;
+
+
+//---------------------------------------------------------------------------------------
+import java.awt.*;
+import java.awt.event.*;
+
+import java.lang.Math;
+
+import java.text.*;
+
+import javax.swing.*;
+import javax.swing.event.*;
+
+
+/**
+ *
+ */
+public class NewSlider extends JPanel {
+ private int minimum;
+ private int maximum;
+ private int current;
+ private int sigFigs;
+ private JLabel myTitle;
+ private JLabel myMin;
+ private JLabel myMax;
+ private MJTextField myTextbox;
+ private String title;
+ private MJSlider mySlider;
+ String attributeName;
+
+ /**
+ * Creates a new NewSlider object.
+ */
+ public NewSlider() {
+ sigFigs = 0;
+ minimum = returnInt(0);
+ maximum = returnInt(100);
+ current = returnInt(50);
+ title = new String(" ");
+ attributeName = "";
+ setup();
+ }
+
+ /**
+ * Creates a new NewSlider object.
+ *
+ * @param id DOCUMENT ME!
+ * @param min DOCUMENT ME!
+ * @param max DOCUMENT ME!
+ * @param cur DOCUMENT ME!
+ */
+ public NewSlider(String id, double min, double max, double cur) {
+ sigFigs = 0; //ORDER IS IMPORTANT
+ title = new String(id);
+ minimum = returnInt(min);
+ maximum = returnInt(max);
+ current = returnInt(cur);
+ setup();
+ }
+
+ /**
+ * Creates a new NewSlider object.
+ *
+ * @param id DOCUMENT ME!
+ * @param min DOCUMENT ME!
+ * @param max DOCUMENT ME!
+ * @param cur DOCUMENT ME!
+ * @param decimal DOCUMENT ME!
+ */
+ public NewSlider(String id, double min, double max, double cur, int decimal) {
+ sigFigs = decimal;
+ title = new String(id);
+ minimum = returnInt(min);
+ maximum = returnInt(max);
+ current = returnInt(cur);
+ setup();
+ }
+
+ /**
+ * Creates a new NewSlider object.
+ *
+ * @param attribute DOCUMENT ME!
+ * @param id DOCUMENT ME!
+ * @param min DOCUMENT ME!
+ * @param max DOCUMENT ME!
+ * @param cur DOCUMENT ME!
+ */
+ public NewSlider(String attribute, String id, double min, double max, double cur) {
+ sigFigs = 0; //ORDER IS IMPORTANT
+ title = new String(id);
+ minimum = returnInt(min);
+ maximum = returnInt(max);
+ current = returnInt(cur);
+ attributeName = attribute;
+ setup();
+ }
+
+ /**
+ * Creates a new NewSlider object.
+ *
+ * @param attribute DOCUMENT ME!
+ * @param id DOCUMENT ME!
+ * @param min DOCUMENT ME!
+ * @param max DOCUMENT ME!
+ * @param cur DOCUMENT ME!
+ * @param decimal DOCUMENT ME!
+ */
+ public NewSlider(String attribute, String id, double min, double max, double cur, int decimal) {
+ sigFigs = decimal;
+ title = new String(id);
+ minimum = returnInt(min);
+ maximum = returnInt(max);
+ current = returnInt(cur);
+ attributeName = attribute;
+ setup();
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void setup() {
+ //order is important! the slider uses integers, the textboxes
+ //use doubles
+ // safeguards that ought not to be needed, but nonetheless are
+ // (pshannon, 2002/02/26)
+ if (current < minimum)
+ current = minimum;
+
+ if (current > maximum)
+ current = maximum;
+
+ mySlider = new MJSlider(minimum, maximum, current);
+
+ if (sigFigs == 0)
+ myTextbox = new MJTextField((int) returnDouble(current).doubleValue(), 6);
+ else
+ myTextbox = new MJTextField(returnDouble(current).doubleValue(), 6);
+
+ if (sigFigs == 0) {
+ myMin = new JLabel(String.valueOf((int) returnDouble(minimum).doubleValue()),
+ JLabel.LEFT);
+ myMax = new JLabel(String.valueOf((int) returnDouble(maximum).doubleValue()),
+ JLabel.RIGHT);
+ } else {
+ myMin = new JLabel(String.valueOf(returnDouble(minimum)), JLabel.LEFT);
+ myMax = new JLabel(String.valueOf(returnDouble(maximum)), JLabel.RIGHT);
+ }
+
+ myTitle = new JLabel(title);
+
+ JLabel myFiller = new JLabel(" ");
+
+ //holds the title and slider value
+ JPanel firstSubPanel = new JPanel();
+ firstSubPanel.add(myTitle, BorderLayout.CENTER);
+ firstSubPanel.add(myTextbox);
+
+ //mixes text box with max/min boxes
+ JPanel secondSubPanel = new JPanel();
+ secondSubPanel.setLayout(new GridLayout(0, 2));
+ secondSubPanel.add(myMin);
+ secondSubPanel.add(myMax);
+
+ //integrates both previous panels
+ JPanel sumOneTwoPanel = new JPanel();
+ sumOneTwoPanel.setLayout(new GridLayout(0, 1));
+ sumOneTwoPanel.add(firstSubPanel);
+ sumOneTwoPanel.add(mySlider);
+ sumOneTwoPanel.add(secondSubPanel);
+
+ this.add(sumOneTwoPanel);
+
+ Dimension tempDim = this.getPreferredSize();
+ //commented out 1-15-02: setting preferred size seemed to mess up the look on one cpu,
+ // whereas it was fine on another.
+ // this.setPreferredSize(new Dimension((int)(tempDim.getWidth()-10), (int)(tempDim.getHeight()-17)));
+ this.setAlignmentX(CENTER_ALIGNMENT);
+ this.setAlignmentY(CENTER_ALIGNMENT);
+
+ // this.setBorder(BorderFactory.createLineBorder(Color.black));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public double getDoubleValue() {
+ return (returnDouble(current).doubleValue());
+ }
+
+ //getIntegerValue requires the programmer to know if he's dealing
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getIntegerValue() {
+ return ((int) (returnDouble(current).doubleValue()));
+ }
+
+ private int returnInt(double original) {
+ return (int) (original * (Math.pow(10.0, (double) sigFigs)));
+ }
+
+ private Double returnDouble(int original) {
+ Double returnVal = new Double(original / Math.pow(10.0, (double) sigFigs));
+
+ return returnVal;
+ }
+
+ //*******************************************//
+ public class MJTextField extends JTextField implements ActionListener {
+ MJTextField(double dub, int columns) {
+ super(String.valueOf(dub), columns);
+ addActionListener(this);
+ }
+
+ MJTextField(int tempInt, int columns) {
+ super(String.valueOf(tempInt), columns);
+ addActionListener(this);
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ String str = this.getText();
+ Double temp = new Double(str);
+ int test = returnInt(temp.doubleValue());
+
+ if ((minimum <= test) && (test <= maximum)) {
+ mySlider.setValue(test);
+ } else {
+ this.setText(String.valueOf(returnDouble(mySlider.getValue())));
+ }
+ }
+ }
+
+ //*******************************************//
+ public class MJSlider extends JSlider implements ChangeListener {
+ String test;
+
+ MJSlider(double x, double y, double currentValue) {
+ super((int) x, (int) y, (int) currentValue);
+ setMajorTickSpacing((maximum - minimum) / 4);
+ setPaintTicks(true);
+ addChangeListener(this);
+ }
+
+ public void stateChanged(ChangeEvent e) {
+ JSlider source = (JSlider) e.getSource();
+ current = source.getValue();
+
+ String test = myTitle.getText();
+
+ if (sigFigs == 0) {
+ int tempInt = returnInt(source.getValue());
+ myTextbox.setText(String.valueOf(tempInt));
+ } else {
+ Double tempDub = returnDouble(source.getValue());
+ myTextbox.setText(String.valueOf(tempDub));
+ }
+ }
+ }
+} //class NewSlider
diff --git a/application/src/main/java/cytoscape/dialogs/NewStringPopupDialog.java b/application/src/main/java/cytoscape/dialogs/NewStringPopupDialog.java
new file mode 100644
index 0000000..93e9abc
--- /dev/null
+++ b/application/src/main/java/cytoscape/dialogs/NewStringPopupDialog.java
@@ -0,0 +1,137 @@
+/*
+ File: NewStringPopupDialog.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// NewStringPopupDialog.java: the name says it all.
+
+//--------------------------------------------------------------------------------------
+// $Revision: 9565 $
+// $Date: 2007-02-13 20:36:50 +0100 (Tue, 13 Feb 2007) $
+// $Author: mes $
+//--------------------------------------------------------------------------------------
+package cytoscape.dialogs;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import javax.swing.*;
+
+
+/**
+ * NewStringPopupDialog: a dialog that is used for creating a
+ * new string. Use the getString() method to retrieve the string.
+ *
+ */
+public class NewStringPopupDialog extends JDialog {
+ private String theString;
+ JTextField textField;
+
+ /**
+ * Creates a new NewStringPopupDialog object.
+ *
+ * @param parent DOCUMENT ME!
+ * @param title DOCUMENT ME!
+ */
+ public NewStringPopupDialog(Frame parent, String title) {
+ super(parent, true);
+ setTitle(title);
+ textField = new JTextField();
+ textField.setPreferredSize(new Dimension(200, 25));
+ theString = null;
+
+ JButton okButton = new JButton("OK");
+ JButton cancelButton = new JButton("Cancel");
+ okButton.addActionListener(new OkAction());
+ cancelButton.addActionListener(new CancelAction());
+
+ JPanel panel = new JPanel();
+ GridBagLayout gridbag = new GridBagLayout();
+ GridBagConstraints c = new GridBagConstraints();
+ panel.setLayout(gridbag);
+ c.gridx = 0;
+ c.gridy = 0;
+ c.gridwidth = 2;
+ gridbag.setConstraints(textField, c);
+ panel.add(textField);
+ c.gridx = 0;
+ c.gridy = 1;
+ c.gridwidth = 1;
+ gridbag.setConstraints(okButton, c);
+ panel.add(okButton);
+ c.gridx = 1;
+ c.gridy = 1;
+ gridbag.setConstraints(cancelButton, c);
+ panel.add(cancelButton);
+ setContentPane(panel);
+ pack();
+ setLocationRelativeTo(parent);
+ setVisible(true);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getString() {
+ if (theString != null)
+ return theString.trim();
+ else
+
+ return null;
+ }
+
+ public class OkAction extends AbstractAction {
+ OkAction() {
+ super("");
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ theString = textField.getText();
+ NewStringPopupDialog.this.dispose();
+ }
+ }
+
+ public class CancelAction extends AbstractAction {
+ CancelAction() {
+ super("");
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ NewStringPopupDialog.this.dispose();
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/dialogs/PhoebeNodeControl.java b/application/src/main/java/cytoscape/dialogs/PhoebeNodeControl.java
new file mode 100644
index 0000000..c790481
--- /dev/null
+++ b/application/src/main/java/cytoscape/dialogs/PhoebeNodeControl.java
@@ -0,0 +1,611 @@
+/*
+ File: PhoebeNodeControl.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.dialogs;
+
+import giny.model.*;
+
+import giny.view.*;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import java.util.*;
+import java.util.List;
+
+import javax.swing.*;
+import javax.swing.border.*;
+import javax.swing.colorchooser.*;
+import javax.swing.event.*;
+
+
+/**
+ * An Adobe style node organizer.
+ * Thanks KK!
+ */
+public class PhoebeNodeControl {
+ GraphView view;
+ double Xmin;
+ double Ymin;
+ double Xmax;
+ double Ymax;
+ boolean setToCircle;
+ double side;
+ JSlider radius;
+ JSlider rotation;
+ JSlider twist;
+
+ /**
+ * Creates a new PhoebeNodeControl object.
+ *
+ * @param view DOCUMENT ME!
+ */
+ public PhoebeNodeControl(GraphView view) {
+ JFrame frame = new JFrame("Node Control");
+ JTabbedPane tabbed = new JTabbedPane();
+
+ this.view = view;
+
+ //Add Control tabs
+ tabbed.addTab("Align", createAlignTab());
+ tabbed.addTab("Circular", createCircularTab());
+
+ frame.getContentPane().add(tabbed);
+ frame.pack();
+ frame.setVisible(true);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public JComponent createAlignTab() {
+ JPanel panel = new JPanel();
+ panel.setLayout(new GridLayout(0, 1));
+
+ JPanel align = new JPanel();
+ align.setBorder(new TitledBorder("Alignment"));
+
+ JPanel dist = new JPanel();
+ dist.setBorder(new TitledBorder("Distribution"));
+
+ align.setLayout(new BorderLayout());
+ dist.setLayout(new BorderLayout());
+
+ JPanel aButtons = new JPanel();
+ JPanel bButtons = new JPanel();
+ JPanel dButtons = new JPanel();
+
+ aButtons.add(createHorizontalAlignLeft());
+ aButtons.add(createHorizontalAlignCenter());
+ aButtons.add(createHorizontalAlignRight());
+ bButtons.add(createVerticalAlignTop());
+ bButtons.add(createVerticalAlignCenter());
+ bButtons.add(createVerticalAlignBottom());
+
+ align.add(aButtons, BorderLayout.NORTH);
+ align.add(bButtons, BorderLayout.SOUTH);
+
+ dButtons.add(createHorizontalDistributeCenter());
+ dButtons.add(createVerticalDistributeCenter());
+
+ dist.add(dButtons);
+
+ panel.add(align);
+ panel.add(dist);
+
+ return panel;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public JButton createHorizontalAlignLeft() {
+ return new JButton(new AbstractAction("HorizontalAlignLeft") {
+ public void actionPerformed(ActionEvent e) {
+ // Do this in the GUI Event Dispatch thread...
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ // do it.
+ double h;
+ NodeView node_view;
+ Node node;
+ Iterator sel_nodes;
+ sel_nodes = view.getSelectedNodes().iterator();
+ h = ((NodeView) sel_nodes.next()).getXPosition();
+
+ while (sel_nodes.hasNext()) {
+ node_view = (NodeView) sel_nodes.next();
+
+ if (node_view.getXPosition() < h) {
+ h = node_view.getXPosition();
+ }
+ }
+
+ sel_nodes = view.getSelectedNodes().iterator();
+
+ while (sel_nodes.hasNext()) {
+ ((NodeView) sel_nodes.next()).setXPosition(h);
+ }
+
+ // done doing it
+ }
+ });
+ }
+ });
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public JButton createHorizontalAlignRight() {
+ return new JButton(new AbstractAction("HorizontalAlignRight") {
+ public void actionPerformed(ActionEvent e) {
+ // Do this in the GUI Event Dispatch thread...
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ // do it.
+ double h;
+ NodeView node_view;
+ Node node;
+ Iterator sel_nodes;
+ sel_nodes = view.getSelectedNodes().iterator();
+ h = ((NodeView) sel_nodes.next()).getXPosition();
+
+ while (sel_nodes.hasNext()) {
+ node_view = (NodeView) sel_nodes.next();
+
+ if (node_view.getXPosition() > h) {
+ h = node_view.getXPosition();
+ }
+ }
+
+ sel_nodes = view.getSelectedNodes().iterator();
+
+ while (sel_nodes.hasNext()) {
+ ((NodeView) sel_nodes.next()).setXPosition(h);
+ }
+
+ // done doing it
+ }
+ });
+ }
+ });
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public JButton createHorizontalAlignCenter() {
+ return new JButton(new AbstractAction("HorizontalAlignCenter") {
+ public void actionPerformed(ActionEvent e) {
+ // Do this in the GUI Event Dispatch thread...
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ // do it.
+ double min;
+ double max;
+ NodeView node_view;
+ Iterator sel_nodes;
+ sel_nodes = view.getSelectedNodes().iterator();
+ min = ((NodeView) sel_nodes.next()).getXPosition();
+ max = min;
+
+ while (sel_nodes.hasNext()) {
+ node_view = (NodeView) sel_nodes.next();
+
+ if (node_view.getXPosition() > max) {
+ max = node_view.getXPosition();
+ }
+
+ if (node_view.getXPosition() < min) {
+ min = node_view.getXPosition();
+ }
+ }
+
+ min = (min + ((max - min) / 2));
+ sel_nodes = view.getSelectedNodes().iterator();
+
+ while (sel_nodes.hasNext()) {
+ ((NodeView) sel_nodes.next()).setXPosition(min);
+ }
+ }
+
+ // done doing it
+ });
+ }
+ });
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public JButton createVerticalAlignBottom() {
+ return new JButton(new AbstractAction("VerticalAlignBottom") {
+ public void actionPerformed(ActionEvent e) {
+ // Do this in the GUI Event Dispatch thread...
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ // do it.
+ double h;
+ NodeView node_view;
+ Node node;
+ Iterator sel_nodes;
+ sel_nodes = view.getSelectedNodes().iterator();
+ h = ((NodeView) sel_nodes.next()).getYPosition();
+
+ while (sel_nodes.hasNext()) {
+ node_view = (NodeView) sel_nodes.next();
+
+ if (node_view.getYPosition() > h) {
+ h = node_view.getYPosition();
+ }
+ }
+
+ sel_nodes = view.getSelectedNodes().iterator();
+
+ while (sel_nodes.hasNext()) {
+ ((NodeView) sel_nodes.next()).setYPosition(h);
+ }
+
+ // done doing it
+ }
+ });
+ }
+ });
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public JButton createVerticalAlignCenter() {
+ return new JButton(new AbstractAction("VerticalAlignCenter") {
+ public void actionPerformed(ActionEvent e) {
+ // Do this in the GUI Event Dispatch thread...
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ // do it.
+ double min;
+ double max;
+ NodeView node_view;
+ Iterator sel_nodes;
+ sel_nodes = view.getSelectedNodes().iterator();
+ min = ((NodeView) sel_nodes.next()).getYPosition();
+ max = min;
+
+ while (sel_nodes.hasNext()) {
+ node_view = (NodeView) sel_nodes.next();
+
+ if (node_view.getYPosition() > max) {
+ max = node_view.getYPosition();
+ }
+
+ if (node_view.getYPosition() < min) {
+ min = node_view.getYPosition();
+ }
+ }
+
+ min = (min + ((max - min) / 2));
+ sel_nodes = view.getSelectedNodes().iterator();
+
+ while (sel_nodes.hasNext()) {
+ ((NodeView) sel_nodes.next()).setYPosition(min);
+ }
+
+ // done doing it
+ }
+ });
+ }
+ });
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public JButton createVerticalAlignTop() {
+ return new JButton(new AbstractAction("VerticalAlignTop") {
+ public void actionPerformed(ActionEvent e) {
+ // Do this in the GUI Event Dispatch thread...
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ // do it.
+ double h;
+ NodeView node_view;
+ Node node;
+ Iterator sel_nodes;
+ sel_nodes = view.getSelectedNodes().iterator();
+ h = ((NodeView) sel_nodes.next()).getYPosition();
+
+ while (sel_nodes.hasNext()) {
+ node_view = (NodeView) sel_nodes.next();
+
+ if (node_view.getYPosition() < h) {
+ h = node_view.getYPosition();
+ }
+ }
+
+ sel_nodes = view.getSelectedNodes().iterator();
+
+ while (sel_nodes.hasNext()) {
+ ((NodeView) sel_nodes.next()).setYPosition(h);
+ }
+
+ // done doing it
+ }
+ });
+ }
+ });
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public JButton createVerticalDistributeCenter() {
+ return new JButton(new AbstractAction("VerticalDistributeBottom") {
+ public void actionPerformed(ActionEvent e) {
+ // Do this in the GUI Event Dispatch thread...
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ // do it.
+ double min = 0;
+ double max = 0;
+ NodeView node_view = null;
+ List sel_nodes_list = view.getSelectedNodes();
+
+ if (sel_nodes_list.size() == 0)
+ return;
+
+ Iterator sel_nodes;
+ sel_nodes = sel_nodes_list.iterator();
+ min = ((NodeView) sel_nodes.next()).getYPosition();
+ max = min;
+
+ while (sel_nodes.hasNext()) {
+ node_view = (NodeView) sel_nodes.next();
+
+ if (node_view.getYPosition() > max) {
+ max = node_view.getYPosition();
+ }
+
+ if (node_view.getYPosition() < min) {
+ min = node_view.getYPosition();
+ }
+ }
+
+ double diff = ((min + ((max - min) / 2)) / sel_nodes_list.size())
+ + node_view.getHeight();
+ double loc = min + ((max - min) / 2);
+
+ sel_nodes = sel_nodes_list.iterator();
+
+ while (sel_nodes.hasNext()) {
+ node_view = (NodeView) sel_nodes.next();
+ node_view.setYPosition(loc);
+ loc += diff;
+ }
+
+ // done doing it
+ }
+ });
+ }
+ });
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public JButton createHorizontalDistributeCenter() {
+ return new JButton(new AbstractAction("HorizontalDistributeCenter") {
+ public void actionPerformed(ActionEvent e) {
+ // Do this in the GUI Event Dispatch thread...
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ // do it.
+ double min = 0;
+ double max = 0;
+ NodeView node_view = null;
+ List sel_nodes_list = view.getSelectedNodes();
+
+ if (sel_nodes_list.size() == 0)
+ return;
+
+ Iterator sel_nodes;
+ sel_nodes = sel_nodes_list.iterator();
+ min = ((NodeView) sel_nodes.next()).getXPosition();
+ max = min;
+
+ while (sel_nodes.hasNext()) {
+ node_view = (NodeView) sel_nodes.next();
+
+ if (node_view.getXPosition() > max) {
+ max = node_view.getXPosition();
+ }
+
+ if (node_view.getXPosition() < min) {
+ min = node_view.getXPosition();
+ }
+ }
+
+ double diff = ((min + ((max - min) / 2)) / sel_nodes_list.size())
+ + node_view.getWidth();
+ double loc = min + ((max - min) / 2);
+
+ sel_nodes = sel_nodes_list.iterator();
+
+ while (sel_nodes.hasNext()) {
+ node_view = (NodeView) sel_nodes.next();
+ node_view.setXPosition(loc);
+ loc += diff;
+ }
+
+ // done doing it
+ }
+ });
+ }
+ });
+ }
+
+ protected JComponent createCircularTab() {
+ radius = new JSlider(0, 2000);
+ radius.addChangeListener(new SliderListener());
+
+ rotation = new JSlider(0, 360);
+ rotation.addChangeListener(new SliderListener());
+
+ twist = new JSlider(0, 50000);
+ twist.addChangeListener(new SliderListener());
+
+ rotation.setValue(90);
+ radius.setValue(100);
+ twist.setValue(0);
+
+ JPanel panel = new JPanel();
+ panel.setLayout(new GridLayout(0, 1));
+
+ JPanel rad = new JPanel();
+ rad.setLayout(new BorderLayout());
+ rad.setBorder(new TitledBorder("Radius"));
+ rad.add(radius);
+
+ JPanel rot = new JPanel();
+ rot.setBorder(new TitledBorder("Rotation"));
+ rot.add(rotation);
+
+ JPanel twt = new JPanel();
+ twt.setBorder(new TitledBorder("Twist"));
+ twt.add(twist);
+
+ panel.add(rad);
+ panel.add(rot);
+ panel.add(twt);
+
+ return panel;
+ }
+
+ protected void updateSliders() {
+ double theta;
+ double thetaIncr;
+
+ int ra = radius.getValue();
+ int ro = rotation.getValue();
+ int tw = twist.getValue();
+ double radius = (new Integer(ra)).doubleValue();
+ double rotation = (new Integer(ro)).doubleValue();
+ double radians = Math.toRadians(tw);
+ NodeView node_view;
+
+ List sel_nodes_list = view.getSelectedNodes();
+
+ if (sel_nodes_list.size() == 0) {
+ return;
+ }
+
+ Iterator sel_nodes;
+ sel_nodes = sel_nodes_list.iterator();
+
+ double maxX;
+ double maxY;
+ double minX;
+ double minY;
+ node_view = (NodeView) sel_nodes.next();
+ maxY = node_view.getYPosition();
+ minY = maxY;
+ maxX = node_view.getXPosition();
+ minX = maxX;
+
+ while (sel_nodes.hasNext()) {
+ node_view = (NodeView) sel_nodes.next();
+
+ if (node_view.getXPosition() > maxX) {
+ maxX = node_view.getXPosition();
+ }
+
+ if (node_view.getXPosition() < minX) {
+ minX = node_view.getXPosition();
+ }
+
+ if (node_view.getYPosition() > maxY) {
+ maxY = node_view.getYPosition();
+ }
+
+ if (node_view.getYPosition() < minY) {
+ minY = node_view.getYPosition();
+ }
+ }
+
+ double midX = minX + ((maxX - minX) / 2);
+ double midY = minY + ((maxY - minY) / 2);
+
+ theta = Math.acos(((maxX - minX) / 2) / radius);
+ theta += Math.toRadians(rotation);
+ thetaIncr = (Math.PI - (2 * theta)) / sel_nodes_list.size();
+
+ sel_nodes = sel_nodes_list.iterator();
+
+ while (sel_nodes.hasNext()) {
+ node_view = (NodeView) sel_nodes.next();
+ node_view.setXPosition((Math.cos(theta + Math.toRadians(radians)) * radius) + midX);
+ node_view.setYPosition((Math.sin(theta + Math.toRadians(radians)) * radius) + midY);
+ theta += thetaIncr;
+ }
+ }
+
+ public class SliderListener implements ChangeListener {
+ public SliderListener() {
+ }
+
+ public void stateChanged(ChangeEvent e) {
+ updateSliders();
+ }
+ } // class SliderListener
+}
diff --git a/application/src/main/java/cytoscape/dialogs/PopupTextArea.java b/application/src/main/java/cytoscape/dialogs/PopupTextArea.java
new file mode 100644
index 0000000..aa8cf5e
--- /dev/null
+++ b/application/src/main/java/cytoscape/dialogs/PopupTextArea.java
@@ -0,0 +1,138 @@
+/*
+ File: PopupTextArea.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// PopupTextArea
+
+//----------------------------------------------------------------------------------------
+// $Revision: 9565 $
+// $Date: 2007-02-13 20:36:50 +0100 (Tue, 13 Feb 2007) $
+// $Author: mes $
+//---------------------------------------------------------------------------------------
+package cytoscape.dialogs;
+
+import java.awt.*;
+import java.awt.BorderLayout;
+import java.awt.event.*;
+
+import javax.swing.AbstractAction;
+import javax.swing.JButton;
+import javax.swing.JDialog;
+import javax.swing.JLabel;
+
+//---------------------------------------------------------------------------------------
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTextArea;
+
+
+//-------------------------------------------------------------------------------------
+/**
+ *
+ */
+public class PopupTextArea extends JDialog {
+ PopupTextArea popupTextArea;
+ Point location;
+
+ //-------------------------------------------------------------------------------------
+ /**
+ * Creates a new PopupTextArea object.
+ *
+ * @param parent DOCUMENT ME!
+ * @param title DOCUMENT ME!
+ * @param text DOCUMENT ME!
+ */
+ public PopupTextArea(JDialog parent, String title, String text) {
+ super(parent, false);
+ location = parent.getLocationOnScreen();
+ init(title, text);
+ }
+
+ //-------------------------------------------------------------------------------------
+ /**
+ * Creates a new PopupTextArea object.
+ *
+ * @param parent DOCUMENT ME!
+ * @param title DOCUMENT ME!
+ * @param text DOCUMENT ME!
+ */
+ public PopupTextArea(Frame parent, String title, String text) {
+ super(parent, false);
+ location = parent.getLocationOnScreen();
+ init(title, text);
+ }
+
+ //-------------------------------------------------------------------------------------
+ private void init(String title, String text) {
+ setTitle(title);
+ popupTextArea = this;
+
+ JPanel panel = new JPanel();
+ panel.setLayout(new BorderLayout());
+
+ final JTextArea textArea = new JTextArea(text);
+ textArea.setEditable(false);
+
+ JScrollPane scrollPane = new JScrollPane(textArea);
+ //textArea.setPreferredSize (new Dimension (600, 400));
+ //scrollPane.setPreferredSize (new Dimension (600, 400));
+ panel.setPreferredSize(new Dimension(600, 400));
+ panel.add(scrollPane, BorderLayout.CENTER);
+
+ JPanel buttonPanel = new JPanel();
+ JButton okButton = new JButton("OK");
+ okButton.addActionListener(new OKAction());
+ buttonPanel.add(okButton, BorderLayout.CENTER);
+ panel.add(buttonPanel, BorderLayout.SOUTH);
+ setContentPane(panel);
+ setLocation(location);
+ pack();
+ setVisible(true);
+ } // PopupTextArea ctor
+ //------------------------------------------------------------------------------------
+
+ public class OKAction extends AbstractAction {
+ OKAction() {
+ super("");
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ popupTextArea.dispose();
+ }
+ } // QuitAction
+ //-----------------------------------------------------------------------------------
+} // class PopupTextArea
diff --git a/application/src/main/java/cytoscape/dialogs/SetNestedNetworkDialog.java b/application/src/main/java/cytoscape/dialogs/SetNestedNetworkDialog.java
new file mode 100644
index 0000000..7e5e1ad
--- /dev/null
+++ b/application/src/main/java/cytoscape/dialogs/SetNestedNetworkDialog.java
@@ -0,0 +1,222 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.dialogs;
+
+import giny.view.NodeView;
+import javax.swing.JDialog;
+import javax.swing.JFrame;
+import javax.swing.event.ListSelectionListener;
+import javax.swing.event.ListSelectionEvent;
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import java.util.Set;
+import java.util.ArrayList;
+import javax.swing.ListCellRenderer;
+import java.awt.Color;
+/**
+ *
+ */
+public class SetNestedNetworkDialog extends JDialog implements ListSelectionListener {
+ /**
+ * Creates a new EditNetworkTitleDialog object.
+ *
+ * @param parent DOCUMENT ME!
+ * @param modal DOCUMENT ME!
+ * @param pName DOCUMENT ME!
+ */
+ NodeView nodeView;
+
+ public SetNestedNetworkDialog(JFrame parent, boolean modal, NodeView nodeView) {
+ super(parent, "Set Nested Network for " + nodeView.getNode().getIdentifier(), modal);
+ init(nodeView);
+ }
+
+ public SetNestedNetworkDialog(JFrame parent, boolean modal) {
+ super(parent, "Set Nested Network for new node", modal);
+ init(null);
+ }
+
+ private void init(NodeView nodeView){
+ this.nodeView = nodeView;
+
+ initComponents();
+ this.lstNetwork.addListSelectionListener(this);
+ this.lstNetwork.setCellRenderer(new MyCellRenderer());
+ this.btnOK.setEnabled(false);
+
+ Set<CyNetwork> networkSet = Cytoscape.getNetworkSet();
+
+ Object[] objs = networkSet.toArray();
+
+ CyNetwork[] networkArray = new CyNetwork[objs.length];
+ for (int i=0; i< networkArray.length; i++){
+ networkArray[i] = (CyNetwork) objs[i];
+ }
+
+ this.lstNetwork.setListData(networkArray);
+
+ setSize(new java.awt.Dimension(500, 300));
+ }
+
+
+ /** This method is called from within the constructor to
+ * initialize the form.
+ * WARNING: Do NOT modify this code. The content of this method is
+ * always regenerated by the Form Editor.
+ */
+ // <editor-fold defaultstate="collapsed" desc=" Generated Code ">
+ private void initComponents() {
+ java.awt.GridBagConstraints gridBagConstraints;
+
+ lbTitle = new javax.swing.JLabel();
+ jScrollPane1 = new javax.swing.JScrollPane();
+ lstNetwork = new javax.swing.JList();
+ pnlButtons = new javax.swing.JPanel();
+ btnOK = new javax.swing.JButton();
+ btnCancel = new javax.swing.JButton();
+
+ getContentPane().setLayout(new java.awt.GridBagLayout());
+
+ setDefaultCloseOperation(javax.swing.WindowConstants.DISPOSE_ON_CLOSE);
+ lbTitle.setFont(new java.awt.Font("Tahoma", 1, 14));
+ lbTitle.setText("Please choose a network");
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
+ getContentPane().add(lbTitle, gridBagConstraints);
+
+ lstNetwork.setModel(new javax.swing.AbstractListModel() {
+ String[] strings = { "Item 1", "Item 2", "Item 3", "Item 4", "Item 5" };
+ public int getSize() { return strings.length; }
+ public Object getElementAt(int i) { return strings[i]; }
+ });
+ lstNetwork.setSelectionMode(javax.swing.ListSelectionModel.SINGLE_SELECTION);
+ jScrollPane1.setViewportView(lstNetwork);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = 1;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.BOTH;
+ gridBagConstraints.weightx = 1.0;
+ gridBagConstraints.weighty = 1.0;
+ gridBagConstraints.insets = new java.awt.Insets(0, 10, 0, 10);
+ getContentPane().add(jScrollPane1, gridBagConstraints);
+
+ btnOK.setText("OK");
+ btnOK.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ btnOKActionPerformed(evt);
+ }
+ });
+
+ pnlButtons.add(btnOK);
+
+ btnCancel.setText("Cancel");
+ btnCancel.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ btnCancelActionPerformed(evt);
+ }
+ });
+
+ pnlButtons.add(btnCancel);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = 2;
+ gridBagConstraints.insets = new java.awt.Insets(10, 0, 10, 0);
+ getContentPane().add(pnlButtons, gridBagConstraints);
+
+ pack();
+ }// </editor-fold>
+
+
+ // Variables declaration - do not modify
+ private javax.swing.JButton btnCancel;
+ private javax.swing.JButton btnOK;
+ private javax.swing.JScrollPane jScrollPane1;
+ private javax.swing.JLabel lbTitle;
+ private javax.swing.JList lstNetwork;
+ private javax.swing.JPanel pnlButtons;
+ // End of variables declaration
+
+ private CyNetwork selectedNetwork = null;
+
+ public CyNetwork getSelectedNetwork(){
+ return selectedNetwork;
+ }
+
+ private void btnOKActionPerformed(java.awt.event.ActionEvent evt) {
+ selectedNetwork = (CyNetwork) this.lstNetwork.getSelectedValue();
+ if (this.nodeView != null) {
+ this.nodeView.getNode().setNestedNetwork(selectedNetwork);
+ }
+ this.dispose();
+ }
+
+ private void btnCancelActionPerformed(java.awt.event.ActionEvent evt) {
+ this.dispose();
+ }
+
+
+ public void valueChanged(ListSelectionEvent e) {
+ // DIsable the OK button if no row is selected in the list
+ if (this.lstNetwork.getSelectedIndex() == -1){
+ this.btnOK.setEnabled(false);
+ }
+ else {
+ this.btnOK.setEnabled(true);
+ }
+ }
+
+
+ class MyCellRenderer extends javax.swing.JLabel implements ListCellRenderer {
+
+ public MyCellRenderer() {
+ setOpaque(true);
+ }
+ public java.awt.Component getListCellRendererComponent(
+ javax.swing.JList list,
+ Object value,
+ int index,
+ boolean isSelected,
+ boolean cellHasFocus)
+ {
+ CyNetwork cyNetwork = (CyNetwork) value;
+ setText(cyNetwork.getTitle());
+ setBackground(isSelected ? SELECTED_CELL_COLOR: Color.white);
+ setForeground(isSelected ? Color.BLACK : Color.black);
+ return this;
+ }
+ }
+
+ private static final Color SELECTED_CELL_COLOR = new Color(0, 100, 255, 40);
+}
diff --git a/application/src/main/java/cytoscape/dialogs/ShrinkExpandGraph.java b/application/src/main/java/cytoscape/dialogs/ShrinkExpandGraph.java
new file mode 100644
index 0000000..5168bdc
--- /dev/null
+++ b/application/src/main/java/cytoscape/dialogs/ShrinkExpandGraph.java
@@ -0,0 +1,125 @@
+/*
+ File: ShrinkExpandGraph.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// ShrinkExpandGraph plugin
+
+//--------------------------------------------------------------------------
+// $Revision: 9565 $
+// $Date: 2007-02-13 20:36:50 +0100 (Tue, 13 Feb 2007) $
+// $Author: mes $
+//--------------------------------------------------------------------------
+package cytoscape.dialogs;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.util.CytoscapeAction;
+
+import cytoscape.view.CyNetworkView;
+
+import giny.view.*;
+
+//--------------------------------------------------------------------------
+import java.awt.event.ActionEvent;
+
+import java.util.*;
+
+import javax.swing.AbstractAction;
+
+
+/**
+ * This class shifts the nodes to shrink or expand the graph:
+ * it averages the coordinates of all the nodes to find the center
+ * it translates the graph to a center at (0,0)
+ * it multiplies each node coordinate by a factor m
+ * it translates the graph back to the original center
+ */
+public class ShrinkExpandGraph extends CytoscapeAction {
+ protected double m;
+
+ ShrinkExpandGraph(String change, double m) {
+ super(change);
+ setPreferredMenu("Layout");
+ this.m = m;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ // sum of coordinates
+ double sx = 0;
+ double sy = 0;
+
+ // coordinates of center of graph
+ double cx = 0;
+ double cy = 0;
+
+ // coordinates with graph centered at (0,0)
+ double nx;
+ double ny;
+
+ CyNetworkView parent = Cytoscape.getCurrentNetworkView();
+
+ //loop through each node to add up all x and all y coordinates
+ for (Iterator i = parent.getNodeViewsIterator(); i.hasNext();) {
+ NodeView nodeView = (NodeView) i.next();
+
+ // get coordinates of node
+ double ax = nodeView.getXPosition();
+ double ay = nodeView.getYPosition();
+ // sum up coordinates of all the nodes
+ sx += ax;
+ sy += ay;
+ }
+
+ // set new coordinates of each node at center (0,0), shrink, then return to
+ // original center at (cx, cy)
+ for (Iterator i = parent.getNodeViewsIterator(); i.hasNext();) {
+ NodeView nodeView = (NodeView) i.next();
+ nodeView.setXPosition((m * ((nodeView.getXPosition()) - cx)) + cx);
+ nodeView.setYPosition((m * ((nodeView.getYPosition()) - cy)) + cy);
+ }
+
+ // remove bends
+ for (Iterator i = parent.getEdgeViewsIterator(); i.hasNext();) {
+ EdgeView edgeView = (EdgeView) i.next();
+ edgeView.getBend().removeAllHandles();
+ }
+ } //Action Performed
+} //ShrinkExpandGraph class
diff --git a/application/src/main/java/cytoscape/dialogs/ShrinkExpandGraphUI.java b/application/src/main/java/cytoscape/dialogs/ShrinkExpandGraphUI.java
new file mode 100644
index 0000000..ea3868b
--- /dev/null
+++ b/application/src/main/java/cytoscape/dialogs/ShrinkExpandGraphUI.java
@@ -0,0 +1,63 @@
+/*
+ File: ShrinkExpandGraphUI.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// ShrinkExpandGraphUI
+
+//--------------------------------------------------------------------------
+// $Revision: 9565 $
+// $Date: 2007-02-13 20:36:50 +0100 (Tue, 13 Feb 2007) $
+// $Author: mes $
+//--------------------------------------------------------------------------
+package cytoscape.dialogs;
+
+import cytoscape.view.CyMenus;
+
+
+/**
+ *
+ */
+public class ShrinkExpandGraphUI {
+ /**
+ * DOCUMENT ME!
+ *
+ * @param cymenus DOCUMENT ME!
+ */
+ public static void makeShrinkExpandGraphUI(CyMenus cymenus) {
+ cymenus.addAction(new ShrinkExpandGraph("Shrink Network", 0.8));
+ cymenus.addAction(new ShrinkExpandGraph("Expand Network", 1.25));
+ }
+} // class
diff --git a/application/src/main/java/cytoscape/dialogs/VizChooser.java.old b/application/src/main/java/cytoscape/dialogs/VizChooser.java.old
new file mode 100644
index 0000000..4be865a
--- /dev/null
+++ b/application/src/main/java/cytoscape/dialogs/VizChooser.java.old
@@ -0,0 +1,1014 @@
+// VizChooser
+//----------------------------------------------------------------------------------------
+// $Revision: 4706 $
+// $Date: 2002-04-12 23:41:10 +0200 (Fri, 12 Apr 2002) $
+// $Author: isb $
+//----------------------------------------------------------------------------------------
+package cytoscape.dialogs;
+//----------------------------------------------------------------------------------------
+import javax.swing.*;
+import javax.swing.event.*;
+import java.awt.*;
+import java.awt.event.*;
+
+import java.util.HashMap;
+
+import cytoscape.vizmap.*;
+import cytoscape.VizChooserClient;
+import cytoscape.GraphObjAttributes;
+import cytoscape.data.*;
+//-------------------------------------------------------------------------------------
+public class VizChooser extends JDialog {
+ VizChooserClient theClient;
+ VizChooser thisChooser;
+ NodeViz nodeViz;
+ GraphObjAttributes nodeAttributes;
+ //GraphObjAttributes edgeAttributes;
+ ExpressionData expressionData;
+ JColorChooser colorChooser;
+ JTabbedPane tabbedPane;
+ Frame parent;
+ final String MINCOLOR = " Minimum Color...";
+ final String MAXCOLOR = " Maximum Color...";
+ final String ZEROCOLOR = "Threshold Color...";
+ final String BINID = "Bins per Color Scale";
+ final String MAXID = "Max Value";
+ final String MINID = "Min Value";
+ final String EDGEID = "Edge Thickness";
+ final String THRESHOLDID = "Threshold";
+
+
+//-------------------------------------------------------------------------------------
+public VizChooser(){super();}
+
+public VizChooser (VizChooserClient theClient, Frame parent,
+ NodeViz nodeViz,
+ GraphObjAttributes nodeAttributes,
+ //GraphObjAttributes edgeAttributes,
+ ExpressionData expressionData)
+{
+ super (parent, false);
+ setTitle ("VizChooser");
+ thisChooser = this;
+ this.parent = parent;
+ this.theClient = theClient;
+ this.nodeViz = nodeViz;
+ this.nodeAttributes = nodeAttributes;
+ //this.edgeAttributes = edgeAttributes;
+ this.expressionData = expressionData;
+
+ JPanel panel = new JPanel ();
+ panel.setLayout (new BorderLayout ());
+ tabbedPane = new JTabbedPane ();
+
+ panel.add (tabbedPane);
+
+ if (expressionData!=null)
+ tabbedPane.addTab("Summary", createSummaryPanel("expression"));
+ else
+ tabbedPane.addTab("Summary", createSummaryPanel("default"));
+
+ if(expressionData != null)
+ tabbedPane.addTab("Expression Settings", createExpressionSettingsPanel());
+
+ for (int i=0; i < nodeAttributes.size (); i++) {
+ String attributeName = nodeAttributes.getAttributeNames()[i];
+ HashMap attributeMap = nodeAttributes.getAttribute (attributeName);
+ tabbedPane.addTab (attributeName, createAttributeRenderingChooser (
+ attributeName, attributeMap));
+ }
+
+ /****************
+ for (int i=0; i<edgeAttributes.size();i++) {
+ String edgeAttributeName = edgeAttributes.getAttributeNames()[i];
+ HashMap edgeAttributeMap = edgeAttributes.getAttribute(edgeAttributeName);
+ Class attributeClass = getAttributeValueClass (edgeAttributeMap);
+ try {
+ boolean numericalData = (attributeClass == (Class.forName ("java.lang.Double")) ||
+ attributeClass == (Class.forName ("java.lang.Integer")));
+ if (numericalData)
+ tabbedPane.addTab(edgeAttributeName, createEdgeAttributeRenderingChooser(
+ edgeAttributeName, edgeAttributeMap));
+ }
+ catch (ClassNotFoundException ignore) {}
+ // todo (pshannon, 22 feb 2002): with signficant refactoring along the way,
+ // create an edgeAttribute controller for non-numerical data.
+ }
+ ****************/
+
+ tabbedPane.addTab ("Default Settings", createDefaultSettingsPanel());
+ setContentPane (panel);
+ pack();
+ Dimension originalDimension = tabbedPane.getPreferredSize();
+ int heightTotal = tabbedPane.getHeight();
+ tabbedPane.setPreferredSize(new Dimension(2000,1000));//larger than necessary
+ pack();
+ int tabCounter = tabbedPane.getTabCount();
+ int widthTotal = 0;
+ for (int i=0;i<tabCounter;i++){
+ Rectangle tempRect = tabbedPane.getBoundsAt(i);
+ widthTotal += tempRect.width;
+ }
+ if (originalDimension.getWidth()<widthTotal&&widthTotal<1000){
+ tabbedPane.setPreferredSize(new Dimension(widthTotal+10, heightTotal));//added 10 to make the width big enough to fit on one line
+ }
+ else{
+ tabbedPane.setPreferredSize(originalDimension);
+ }
+ this.setLocation(parent.getLocationOnScreen());
+ pack();
+ setVisible (true);
+} // ctor
+//-------------------------------------------------------------------------------------
+private JPanel createAttributeRenderingChooser (String attribute, HashMap attributeMap)
+{
+ final JPanel mainPanel = new JPanel ();
+ mainPanel.setLayout (new BorderLayout ());
+
+ JTabbedPane tabPane = new JTabbedPane ();
+ mainPanel.add (tabPane, BorderLayout.CENTER);
+
+ String attributeName = attribute;
+ double minSliderValue, zeroSliderValue, maxSliderValue, binSliderValue;
+
+ double [] minMax = findMinMax (attributeMap);
+
+
+ String valueRangeMessage = attributeName + " values range from " + minMax [0] +
+ " to " + minMax [1] + ".";
+ JLabel textValues = new JLabel(valueRangeMessage);
+ mainPanel.add(textValues, BorderLayout.NORTH);
+
+
+ JPanel colorPanel = new JPanel ();
+ colorPanel.setLayout (new BorderLayout ());
+
+ //-----------------------------------------------------
+ // add Node Color tab
+ //-----------------------------------------------------
+
+ tabPane.addTab ("Node Color", colorPanel);
+ JPanel binPanel = new JPanel();
+ JPanel minPanel = new JPanel();
+ JPanel zeroPanel = new JPanel();
+ JPanel maxPanel = new JPanel();
+
+ JPanel sliderPanel = new JPanel ();
+ sliderPanel.setLayout(new GridLayout(0,1));
+ NewSlider binSlider = new NewSlider(attributeName,BINID, 2, 40, 20);
+ binPanel.add(binSlider);
+ ColorPopupButton minButton = new ColorPopupButton(attributeName,MINCOLOR, Color.red);
+ NewSlider lowSlider = new NewSlider(attributeName,MINID, minMax[0], minMax[1], minMax[0], 4);
+ minPanel.add(minButton);
+ minPanel.add(lowSlider);
+
+ ColorPopupButton zeroButton = new ColorPopupButton(attributeName,ZEROCOLOR, Color.white);
+
+ int dataRange = (int)(minMax[1]-minMax[0]);
+ int currentValue= (int)(minMax[0]+(dataRange/4));
+ NewSlider zeroSlider= new NewSlider (attributeName,THRESHOLDID, minMax[0], minMax[1],
+ currentValue, 4);
+ zeroPanel.add(zeroButton);
+ zeroPanel.add(zeroSlider);
+
+ ColorPopupButton maxButton = new ColorPopupButton(attributeName,MAXCOLOR, Color.green);
+ NewSlider highSlider = new NewSlider(attributeName,MAXID,minMax[0], minMax[1], minMax[1], 4);
+ maxPanel.add(maxButton);
+ maxPanel.add(highSlider);
+
+ sliderPanel.add(binPanel);
+ sliderPanel.add(minPanel);
+ sliderPanel.add(zeroPanel);
+ sliderPanel.add(maxPanel);
+
+ colorPanel.add (sliderPanel, BorderLayout.CENTER);
+
+ JPanel buttonPanel = new JPanel ();
+ JButton applyButton = new JButton ("Apply");
+ JButton dismissButton = new JButton ("Dismiss");
+ applyButton.addActionListener (new ApplyNodeColorAction (attributeName,
+ minMax [0], minMax [1],
+ binSlider,
+ lowSlider, minButton,
+ zeroSlider, zeroButton,
+ highSlider, maxButton));
+ dismissButton.addActionListener (new DismissAction ());
+ buttonPanel.add (applyButton, BorderLayout.CENTER);
+ buttonPanel.add (dismissButton, BorderLayout.SOUTH);//make this EAST?
+ colorPanel.add (buttonPanel, BorderLayout.SOUTH);
+
+ //-----------------------------------------------------
+ // add Border Color/Thickness tab
+ //-----------------------------------------------------
+
+ JPanel borderPanel = new JPanel ();
+ borderPanel.setLayout(new BorderLayout());
+
+ tabPane.addTab ("Node Border Thickness", borderPanel);
+
+ JPanel borderBinPanel = new JPanel();
+ JPanel borderThickPanel = new JPanel();
+ JPanel borderMinPanel = new JPanel();
+ JPanel borderZeroPanel = new JPanel();
+ JPanel borderMaxPanel = new JPanel();
+
+ JPanel borderSliderPanel = new JPanel();
+ borderSliderPanel.setLayout(new GridLayout(0,1));
+ NewSlider borderBinSlider = new NewSlider(attributeName, BINID, 2, 40, 20);
+ borderBinPanel.add(borderBinSlider);
+ NewSlider borderThickSlider = new NewSlider(attributeName, EDGEID, 1,7,2);
+ borderThickPanel.add(borderThickSlider);
+
+ ColorPopupButton borderMinColor = new ColorPopupButton(attributeName,MINCOLOR, nodeViz.getDefaultBorderColor());
+ NewSlider borderLowSlider = new NewSlider(attributeName,MINID, minMax[0], minMax[1], minMax[0], 4);
+ borderMinPanel.add(borderMinColor);
+ borderMinPanel.add(borderLowSlider);
+
+ ColorPopupButton borderMaxColor = new ColorPopupButton(attributeName,MAXCOLOR, nodeViz.getDefaultBorderColor());
+ NewSlider borderHighSlider = new NewSlider(attributeName,MAXID,minMax[0], minMax[1], minMax[1], 4);
+ borderMaxPanel.add(borderMaxColor);
+ borderMaxPanel.add(borderHighSlider);
+
+ ColorPopupButton borderZeroColor = new ColorPopupButton(attributeName,ZEROCOLOR, nodeViz.getDefaultBorderColor());
+
+ int borderCurrentValue = (int)(minMax[0]+((minMax[1]-minMax[0])/4));
+ NewSlider borderZeroSlider= new NewSlider(attributeName,THRESHOLDID, minMax[0], minMax[1],borderCurrentValue, 4);
+ borderZeroPanel.add(borderZeroColor);
+ borderZeroPanel.add(borderZeroSlider);
+
+ borderSliderPanel.add(borderBinPanel);
+ borderSliderPanel.add(borderThickPanel);
+ borderSliderPanel.add(borderMinPanel);
+ borderSliderPanel.add(borderZeroPanel);
+ borderSliderPanel.add(borderMaxPanel);
+
+ borderPanel.add (borderSliderPanel, BorderLayout.CENTER);
+
+ JPanel borderButtonPanel = new JPanel ();
+ JButton borderApplyButton = new JButton ("Apply");
+ JButton borderDismissButton = new JButton ("Dismiss");
+ borderApplyButton.addActionListener (new ApplyBorderColorAction (attributeName, minMax[0], minMax[1],
+ borderBinSlider, borderThickSlider,
+ borderLowSlider, borderMinColor,
+ borderZeroSlider,borderZeroColor,
+ borderHighSlider,borderMaxColor));
+ borderDismissButton.addActionListener (new DismissAction ());
+ borderButtonPanel.add (borderApplyButton, BorderLayout.CENTER);
+ borderButtonPanel.add (borderDismissButton, BorderLayout.EAST);//is EAST correct?
+ borderPanel.add (borderButtonPanel, BorderLayout.SOUTH);
+
+ return mainPanel;
+
+} // createAttributeRenderingChooser
+//------------------------------------------------------------------------------------
+/****************
+private JPanel createEdgeAttributeRenderingChooser (String attributeName, HashMap attributeMap)
+{
+ final JPanel mainPanel = new JPanel ();
+ mainPanel.setLayout (new BorderLayout ());
+
+ JTabbedPane tabPane = new JTabbedPane ();
+ mainPanel.add (tabPane, BorderLayout.CENTER);
+
+ double minSliderValue, zeroSliderValue, maxSliderValue, binSliderValue;
+
+ double [] minMax = findMinMax (attributeMap);
+ String valueRangeMessage = attributeName + " values range from " + minMax [0] +
+ " to " + minMax [1] + ".";
+ JLabel textValues = new JLabel(valueRangeMessage);
+ mainPanel.add(textValues, BorderLayout.NORTH);
+
+
+ JPanel colorPanel = new JPanel ();
+ colorPanel.setLayout (new BorderLayout ());
+
+ //-----------------------------------------------------
+ // add Edge Tab
+ //-----------------------------------------------------
+
+ JPanel edgePanel = new JPanel ();
+ edgePanel.setLayout(new BorderLayout());
+
+ tabPane.addTab ("Edge Properties", edgePanel);
+
+ JPanel edgeBinPanel = new JPanel();
+ JPanel edgeThickPanel = new JPanel();
+ JPanel edgeMinPanel = new JPanel();
+ JPanel edgeZeroPanel = new JPanel();
+ JPanel edgeMaxPanel = new JPanel();
+
+ JPanel edgeSliderPanel = new JPanel();
+ edgeSliderPanel.setLayout(new GridLayout(0,1));
+ NewSlider edgeBinSlider = new NewSlider(attributeName, BINID, 2, 40, 20);
+ edgeBinPanel.add(edgeBinSlider);
+
+ NewSlider edgeThickSlider = new NewSlider(attributeName, EDGEID, 1,7,2);
+ edgeThickPanel.add(edgeThickSlider);
+
+ ColorPopupButton edgeMinColor = new ColorPopupButton(attributeName,MINCOLOR, Color.red);
+ NewSlider edgeLowSlider = new NewSlider(attributeName,MINID, minMax[0], minMax[1], minMax[0], 4);
+ edgeMinPanel.add(edgeMinColor);
+ edgeMinPanel.add(edgeLowSlider);
+
+ ColorPopupButton edgeZeroColor = new ColorPopupButton(attributeName,ZEROCOLOR, Color.white);
+ NewSlider edgeZeroSlider= new NewSlider(attributeName,THRESHOLDID, minMax[0], minMax[1],(minMax[0]+minMax[1])/4, 4);
+ edgeZeroPanel.add(edgeZeroColor);
+ edgeZeroPanel.add(edgeZeroSlider);
+
+ ColorPopupButton edgeMaxColor = new ColorPopupButton(attributeName,MAXCOLOR, Color.green);
+ NewSlider edgeHighSlider = new NewSlider(attributeName,MAXID,minMax[0], minMax[1], minMax[1], 4);
+ edgeMaxPanel.add(edgeMaxColor);
+ edgeMaxPanel.add(edgeHighSlider);
+
+ edgeSliderPanel.add(edgeBinPanel);
+ edgeSliderPanel.add(edgeThickPanel);
+ edgeSliderPanel.add(edgeMinPanel);
+ edgeSliderPanel.add(edgeZeroPanel);
+ edgeSliderPanel.add(edgeMaxPanel);
+
+ edgePanel.add (edgeSliderPanel, BorderLayout.CENTER);
+
+ JPanel edgeButtonPanel = new JPanel ();
+ JButton edgeApplyButton = new JButton ("Apply");
+ JButton edgeDismissButton = new JButton ("Dismiss");
+ edgeApplyButton.addActionListener (new ApplyEdgeColorAction (attributeName, minMax[0], minMax[1],
+ edgeBinSlider, edgeThickSlider,
+ edgeLowSlider, edgeMinColor,
+ edgeZeroSlider,edgeZeroColor,
+ edgeHighSlider,edgeMaxColor));
+ edgeDismissButton.addActionListener (new DismissAction ());
+ edgeButtonPanel.add (edgeApplyButton, BorderLayout.CENTER);
+ edgeButtonPanel.add (edgeDismissButton, BorderLayout.EAST);//is EAST correct?
+ edgePanel.add (edgeButtonPanel, BorderLayout.SOUTH);
+
+ return mainPanel;
+
+} // createEdgeAttributeRenderingChooser
+****************/
+//------------------------------------------------------------------------------------
+private JPanel createSummaryPanel(String controller){
+ String controlString = controller;
+ String nodeTitle = nodeViz.getNodeAttributeWhichControlsFillColor();
+ String borderTitle = nodeViz.getBorderAttributeWhichControlsFillColor();
+ //String edgeTitle = nodeViz.getEdgeAttributeWhichControlsFillColor();
+ Color nodeMinColor, nodeZeroColor, nodeMaxColor;
+ Color borderMinColor, borderZeroColor, borderMaxColor;
+ //Color edgeMinColor, edgeZeroColor, edgeMaxColor;
+ double [][] nodeBins;
+ double [][] borderBins;
+ //double [][] edgeBins;
+ if (controlString == "expression"){
+ nodeBins = nodeViz.getExpressionColorBins();
+ nodeMinColor = nodeViz.getExpressionRatioMinColor();
+ nodeZeroColor = nodeViz.getExpressionRatioZeroColor();
+ nodeMaxColor = nodeViz.getExpressionRatioMaxColor();
+ borderBins = nodeViz.getSignificanceColorBins();
+ borderMinColor = nodeViz.getExpressionSigMinColor();
+ borderZeroColor = nodeViz.getExpressionSigZeroColor();
+ borderMaxColor = nodeViz.getExpressionSigMaxColor();
+ //edgeBins = nodeViz.getDefaultEdgeColorBins();
+ //edgeMinColor = nodeViz.getDefaultEdgeColor();
+ //edgeZeroColor = nodeViz.getDefaultEdgeColor();
+ //edgeMaxColor = nodeViz.getDefaultEdgeColor();
+ }
+ else if (controlString == "default"){
+ nodeBins = nodeViz.getDefaultNodeColorBins();
+ nodeMinColor = nodeViz.getDefaultNodeColor();
+ nodeZeroColor = nodeViz.getDefaultNodeColor();
+ nodeMaxColor = nodeViz.getDefaultNodeColor();
+ borderBins = nodeViz.getDefaultBorderColorBins();
+ borderMinColor = nodeViz.getDefaultBorderColor();
+ borderZeroColor = nodeViz.getDefaultBorderColor();
+ borderMaxColor = nodeViz.getDefaultBorderColor();
+ //edgeBins = nodeViz.getDefaultEdgeColorBins();
+ //edgeMinColor = nodeViz.getDefaultEdgeColor();
+ //edgeZeroColor = nodeViz.getDefaultEdgeColor();
+ //edgeMaxColor = nodeViz.getDefaultEdgeColor();
+ }
+ else{
+ nodeBins = nodeViz.getNodeColorBins();
+ nodeMinColor = nodeViz.getNodeMinColor();
+ nodeZeroColor = nodeViz.getNodeZeroColor();
+ nodeMaxColor = nodeViz.getNodeMaxColor();
+ borderBins = nodeViz.getBorderColorBins();
+ borderMinColor = nodeViz.getBorderMinColor();
+ borderZeroColor = nodeViz.getBorderZeroColor();
+ borderMaxColor = nodeViz.getBorderMaxColor();
+ //edgeBins = nodeViz.getEdgeColorBins();
+ //edgeMinColor = nodeViz.getEdgeMinColor();
+ //edgeZeroColor = nodeViz.getEdgeZeroColor();
+ //edgeMaxColor = nodeViz.getEdgeMaxColor();
+ }
+
+ JPanel mainPanel = new JPanel();
+ mainPanel.setLayout(new BorderLayout());
+
+ JPanel subPanel = new JPanel();
+ subPanel.setLayout(new GridLayout(0,1));
+
+ JPanel nodeColorPanel = createSummarySubPanel("Node",
+ nodeTitle,
+ nodeMinColor,
+ nodeZeroColor,
+ nodeMaxColor,
+ nodeBins);
+ JPanel borderColorPanel = createSummarySubPanel("Node Border",
+ borderTitle,
+ borderMinColor,
+ borderZeroColor,
+ borderMaxColor,
+ borderBins);
+ //JPanel edgeColorPanel = createSummarySubPanel("Edge",
+ // edgeTitle,
+ // edgeMinColor,
+ // edgeZeroColor,
+ // edgeMaxColor,
+ // edgeBins);
+ subPanel.add(nodeColorPanel);
+ subPanel.add(borderColorPanel);
+ // subPanel.add(edgeColorPanel);
+ mainPanel.add(subPanel, BorderLayout.CENTER);
+
+ JPanel buttonPanel = new JPanel ();
+ JButton dismissButton = new JButton ("Dismiss");
+ dismissButton.addActionListener (new DismissAction ());
+ buttonPanel.add (dismissButton);
+ mainPanel.add (buttonPanel, BorderLayout.SOUTH);
+
+ return mainPanel;
+}
+
+private JPanel createSummarySubPanel(String idTitle,String attribute,
+ Color minC,Color zeroC, Color maxC,
+ double[][] bins){
+ JPanel returnPanel = new JPanel();
+ returnPanel.setLayout(new BorderLayout());
+
+ JPanel returnSubPanel = new JPanel();
+
+ String criteria = new String(idTitle+" Color Determined by: ");
+ criteria += attribute;
+ JLabel criteriaLabel = new JLabel(criteria);
+
+ JPanel extremePanel = new JPanel();
+ extremePanel.setLayout(new GridLayout(0,1));
+
+ JPanel minSubPanel = new JPanel();
+ JPanel zeroSubPanel = new JPanel();
+ JPanel maxSubPanel = new JPanel();
+
+ JLabel minTitle = new JLabel(" Minimum Color: ");
+ JLabel zeroTitle= new JLabel("Threshold Color: ");
+ JLabel maxTitle = new JLabel(" Maximum Color: ");
+ JLabel minColor = new JLabel(" ");
+ JLabel zeroColor= new JLabel(" ");
+ JLabel maxColor = new JLabel(" ");
+ minColor.setBackground(minC);
+ zeroColor.setBackground(zeroC);
+ maxColor.setBackground(maxC);
+ minColor.setOpaque(true);
+ zeroColor.setOpaque(true);
+ maxColor.setOpaque(true);
+
+ minSubPanel.add(minTitle);
+ minSubPanel.add(minColor);
+
+ zeroSubPanel.add(zeroTitle);
+ zeroSubPanel.add(zeroColor);
+
+ maxSubPanel.add(maxTitle);
+ maxSubPanel.add(maxColor);
+
+ extremePanel.add(minSubPanel);
+ extremePanel.add(zeroSubPanel);
+ extremePanel.add(maxSubPanel);
+ ColorScaleTable myColorScaleTable = new ColorScaleTable(100,100, bins);
+
+ returnSubPanel.add(extremePanel);
+ returnSubPanel.add(myColorScaleTable);
+ returnPanel.add(criteriaLabel, BorderLayout.NORTH);
+ returnPanel.add(returnSubPanel, BorderLayout.CENTER);
+ return returnPanel;
+}
+
+//------------------------------------------------------------------------------------
+private JPanel createExpressionSettingsPanel(){
+ double [][] extremeValues = nodeViz.getExtremeValues();
+ double ratioMin, ratioMax, sigMin, sigMax;
+ ratioMin = extremeValues[0][0];
+ ratioMax = extremeValues[0][1];
+ sigMin = extremeValues[1][0];
+ sigMax = extremeValues[1][1];
+
+
+ JPanel mainPanel = new JPanel();
+ mainPanel.setLayout(new BorderLayout());
+
+ String instructionString = new String("Specify Settings for Displaying Data:");
+ instructionString += "\n"+ "Each time a new data set is viewed, these settings will be applied.";
+ JTextArea instructions = new JTextArea(instructionString);
+ mainPanel.add(instructions, BorderLayout.NORTH);
+
+ JTabbedPane tabs = new JTabbedPane();
+ JPanel ratioSubPanel = new JPanel();
+ JPanel sigSubPanel = new JPanel();
+
+ JPanel ratioMinPanel = new JPanel();
+ JPanel ratioZeroPanel = new JPanel();
+ JPanel ratioMaxPanel = new JPanel();
+
+ JPanel sigMinPanel = new JPanel();
+ JPanel sigZeroPanel = new JPanel();
+ JPanel sigMaxPanel = new JPanel();
+
+ ratioSubPanel.setLayout(new GridLayout(0,1));
+ sigSubPanel.setLayout(new GridLayout(0,1));
+ NewSlider ratioBinSlider = new NewSlider("Bins", 2, 40,nodeViz.getExpressionRatioBinValue());
+ NewSlider sigBinSlider = new NewSlider("Bins", 2, 40,nodeViz.getExpressionSigBinValue());
+
+
+
+ NewSlider thicknessSlider = new NewSlider("Border Thickness", 2,7,nodeViz.getDefaultBorderThickness());
+
+ NewSlider ratioMinSlider = new NewSlider(MINID,ratioMin,ratioMax,nodeViz.getExpressionRatioMinValue(),4);
+ NewSlider sigMinSlider = new NewSlider(MINID,sigMin ,sigMax ,nodeViz.getExpressionSigMinValue() ,4);
+ ColorPopupButton ratioMinColor = new ColorPopupButton(MINCOLOR,nodeViz.getExpressionRatioMinColor());
+ ColorPopupButton sigMinColor = new ColorPopupButton(MINCOLOR,nodeViz.getExpressionSigMinColor());
+ ratioMinPanel.add(ratioMinColor);
+ ratioMinPanel.add(ratioMinSlider);
+ sigMinPanel.add(sigMinColor);
+ sigMinPanel.add(sigMinSlider);
+
+ NewSlider ratioZeroSlider = new NewSlider(THRESHOLDID,ratioMin,ratioMax,nodeViz.getExpressionRatioZeroValue(),4);
+ NewSlider sigZeroSlider = new NewSlider(THRESHOLDID,sigMin ,sigMax ,nodeViz.getExpressionSigZeroValue(),4);
+ ColorPopupButton ratioZeroColor = new ColorPopupButton(ZEROCOLOR,nodeViz.getExpressionRatioZeroColor());
+ ColorPopupButton sigZeroColor = new ColorPopupButton(ZEROCOLOR,nodeViz.getExpressionSigZeroColor());
+ ratioZeroPanel.add(ratioZeroColor);
+ ratioZeroPanel.add(ratioZeroSlider);
+ sigZeroPanel.add(sigZeroColor);
+ sigZeroPanel.add(sigZeroSlider);
+
+ NewSlider ratioMaxSlider = new NewSlider(MAXID,ratioMin,ratioMax,nodeViz.getExpressionRatioMaxValue(),4);
+ NewSlider sigMaxSlider = new NewSlider(MAXID,sigMin ,sigMax ,nodeViz.getExpressionSigMaxValue(),4);
+ ColorPopupButton ratioMaxColor = new ColorPopupButton(MAXCOLOR,nodeViz.getExpressionRatioMaxColor());
+ ColorPopupButton sigMaxColor = new ColorPopupButton(MAXCOLOR,nodeViz.getExpressionSigMaxColor());
+ ratioMaxPanel.add(ratioMaxColor);
+ ratioMaxPanel.add(ratioMaxSlider);
+ sigMaxPanel.add(sigMaxColor);
+ sigMaxPanel.add(sigMaxSlider);
+
+
+ ratioSubPanel.add(ratioBinSlider);
+ ratioSubPanel.add(ratioMinPanel);
+ ratioSubPanel.add(ratioZeroPanel);
+ ratioSubPanel.add(ratioMaxPanel);
+
+ sigSubPanel.add(sigBinSlider);
+ sigSubPanel.add(thicknessSlider);
+ sigSubPanel.add(sigMinPanel);
+ sigSubPanel.add(sigZeroPanel);
+ sigSubPanel.add(sigMaxPanel);
+
+ tabs.addTab("Ratio/Node Color", ratioSubPanel);
+ tabs.addTab("Significance/Border Color", sigSubPanel);
+
+ mainPanel.add(tabs, BorderLayout.CENTER);
+
+ JPanel buttonPanel = new JPanel ();
+ JButton applyButton = new JButton ("Apply");
+ JButton dismissButton = new JButton ("Dismiss");
+
+ applyButton.addActionListener (new ApplyExpressionColorAction (ratioBinSlider,
+ ratioMinSlider, ratioMinColor,
+ ratioZeroSlider, ratioZeroColor,
+ ratioMaxSlider, ratioMaxColor,
+ sigBinSlider,
+ sigMinSlider, sigMinColor,
+ sigZeroSlider, sigZeroColor,
+ sigMaxSlider, sigMaxColor,
+ thicknessSlider));
+ buttonPanel.add (applyButton, BorderLayout.CENTER);
+ dismissButton.addActionListener (new DismissAction ());
+ buttonPanel.add (dismissButton, BorderLayout.SOUTH);
+ mainPanel.add (buttonPanel, BorderLayout.SOUTH);
+
+ return mainPanel;
+}//createExpressionSettingsPanel
+//------------------------------------------------------------------------------------
+/**
+ * present choosers for the default color of node, node border, edge, and background.
+ * the apply button causes all current values to be passed to the VizChooserClient.
+ * <br>
+ * <b> todo: </b> <i>(pshannon, 26 feb 2002)</i>: allow user to assign and apply
+ * any one value (for instance, a new background color) without causing the
+ * VizChooserClient to apply the other defaults (node color, node border color, edge
+ * color).
+ * @see VizChooserClient
+ */
+private JPanel createDefaultSettingsPanel()
+{
+ JPanel mainPanel = new JPanel();
+ mainPanel.setLayout(new GridLayout(0,1));
+
+ String tempString = new String("Default Settings:");
+ tempString += "\n"+"Click on desired default setting to change its color.";
+ JTextArea instructions = new JTextArea(tempString);
+
+ ColorPopupButton nodeDefault =
+ new ColorPopupButton("Default Node Color...", nodeViz.getDefaultNodeColor());
+ ColorPopupButton borderDefault =
+ new ColorPopupButton("Default Border Color...", nodeViz.getDefaultBorderColor());
+ //ColorPopupButton edgeDefault =
+ // new ColorPopupButton("Default Edge Color...", nodeViz.getDefaultEdgeColor());
+ ColorPopupButton backDefault =
+ new ColorPopupButton("Background Color...", nodeViz.getDefaultBackgroundColor());
+
+ JPanel buttonPanel = new JPanel();
+ JButton applyButton = new JButton ("Apply");
+ JButton dismissButton = new JButton ("Dismiss");
+ applyButton.addActionListener (new ApplyAllDefaultColorsAction (nodeDefault,
+ borderDefault,
+ // edgeDefault,
+ backDefault));
+ dismissButton.addActionListener (new DismissAction ());
+ buttonPanel.add (applyButton, BorderLayout.EAST);
+ buttonPanel.add (dismissButton, BorderLayout.WEST);
+
+ mainPanel.add(instructions);
+ mainPanel.add(nodeDefault);
+ mainPanel.add(borderDefault);
+ // mainPanel.add(edgeDefault);
+ mainPanel.add(backDefault);
+ mainPanel.add(buttonPanel);
+ return mainPanel;
+
+} // createDefaultSettingsPanel
+//------------------------------------------------------------------------------------
+public class ApplyExpressionColorAction extends AbstractAction
+{
+ NewSlider ratioBin,ratioMin,ratioZero,ratioMax;
+ NewSlider sigBin, sigMin, sigZero, sigMax, thickSlider;
+ ColorPopupButton ratioMinColor,ratioZeroColor,ratioMaxColor;
+ ColorPopupButton sigMinColor, sigZeroColor, sigMaxColor;
+ ApplyExpressionColorAction (NewSlider rBin,
+ NewSlider rMin, ColorPopupButton rMinC,
+ NewSlider rZero, ColorPopupButton rZeroC,
+ NewSlider rMax, ColorPopupButton rMaxC,
+ NewSlider sBin,
+ NewSlider sMin, ColorPopupButton sMinC,
+ NewSlider sZero, ColorPopupButton sZeroC,
+ NewSlider sMax, ColorPopupButton sMaxC,
+ NewSlider thickness)
+{
+ ratioBin = rBin;
+ ratioMin = rMin;
+ ratioZero = rZero;
+ ratioMax = rMax;
+
+ sigBin = sBin;
+ sigMin = sMin;
+ sigZero = sZero;
+ sigMax = sMax;
+ thickSlider = thickness;
+
+ ratioMinColor = rMinC;
+ ratioZeroColor = rZeroC;
+ ratioMaxColor = rMaxC;
+
+ sigMinColor = sMinC;
+ sigZeroColor = sZeroC;
+ sigMaxColor = sMaxC;
+
+} // inner class ApplyExpressionColorAction ctor
+//--------------------------------------------------------------------------------
+public void actionPerformed(ActionEvent e)
+{
+ if (ratioMin.getDoubleValue() >ratioZero.getDoubleValue()||
+ ratioZero.getDoubleValue()>ratioMax.getDoubleValue()){
+ JFrame errorFrame = new JFrame();
+ String errorMessage = "\n"+"Error: Threshold Value"+"\n"
+ +"must be between Min Value"+"\n"
+ +"and Max Value" +"\n";
+ JOptionPane.showMessageDialog (errorFrame, errorMessage, "Threshold Error for Ratio",
+ JOptionPane.ERROR_MESSAGE);
+ errorFrame.setVisible(true);
+ return;
+ } // if
+
+ if (sigMin.getDoubleValue() >sigZero.getDoubleValue()||
+ sigZero.getDoubleValue()>sigMax.getDoubleValue()) {
+ JFrame errorFrame = new JFrame();
+ String errorMessage = "\n"+"Error: Threshold Value"+"\n"
+ +"must be between Min Value"+"\n"
+ +"and Max Value" +"\n";
+ JOptionPane.showMessageDialog (errorFrame, errorMessage, "Threshold Error for Signficance",
+ JOptionPane.ERROR_MESSAGE);
+ errorFrame.setVisible(true);
+ return;
+ } // if
+
+ nodeViz.setExpressionInformation (ratioBin.getIntegerValue(),
+ ratioMin.getDoubleValue(),
+ ratioZero.getDoubleValue(),
+ ratioMax.getDoubleValue(),
+ ratioMinColor.getColor(),
+ ratioZeroColor.getColor(),
+ ratioMaxColor.getColor(),
+ sigBin.getIntegerValue(),
+ sigMin.getDoubleValue(),
+ sigZero.getDoubleValue(),
+ sigMax.getDoubleValue(),
+ sigMinColor.getColor(),
+ sigZeroColor.getColor(),
+ sigMaxColor.getColor(),
+ thickSlider.getIntegerValue());
+ updateSummaryPanel("expression");
+ theClient.applyExpressionVizMappings (nodeViz);
+
+} // inner class ApplyExpresionColorAction.actionPerfomred
+//-----------------------------------------------------------------------------------
+} // inner class ApplyExpressionSettingsAction
+//------------------------------------------------------------------------------------
+public void updateSummaryPanel(String control)
+{
+ int index = tabbedPane.getSelectedIndex();
+ tabbedPane.remove(0);
+ JPanel tempPanel = createSummaryPanel(control);
+ tabbedPane.add(tempPanel, 0);
+ tabbedPane.setTitleAt(0, "Summary");
+ tabbedPane.setSelectedIndex(index);
+}
+//------------------------------------------------------------------------------------
+public class ApplyAllDefaultColorsAction extends AbstractAction
+{
+ ColorPopupButton node, border,edge, background;
+ ApplyAllDefaultColorsAction (ColorPopupButton nodeDefault,
+ ColorPopupButton borderDefault,
+ //ColorPopupButton edgeDefault,
+ ColorPopupButton backDefault){
+ node = nodeDefault;
+ border = borderDefault;
+ //edge = edgeDefault;
+ background = backDefault;
+ }
+ public void actionPerformed (ActionEvent e) {
+ nodeViz.setDefaultSettings(node.getColor(), border.getColor(),
+ // edge.getColor(),
+ background.getColor());
+ updateSummaryPanel("default");
+ //theClient.applyDefaultNodeViz(nodeViz);
+ theClient.applyAllVizMappings (nodeViz);
+ }
+}// ApplyAllDefaultColorsAction
+//------------------------------------------------------------------------------------
+/**
+ *
+ */
+public class ApplyNodeColorAction extends AbstractAction
+{
+ String attributeName;
+ double min, max, minColorValue, zeroColorValue, maxColorValue;
+ NewSlider binSlider, minSlider, zeroSlider, maxSlider;
+ ColorPopupButton minColor,zeroColor, maxColor;
+
+ ApplyNodeColorAction (String tabName, double min, double max,
+ NewSlider binSlide,
+ NewSlider minSlide, ColorPopupButton minC,
+ NewSlider zeroSlide, ColorPopupButton zeroC,
+ NewSlider maxSlide, ColorPopupButton maxC) {
+ super ("");
+ attributeName = tabName;
+ this.min = min;
+ this.max = max;
+ binSlider = binSlide;
+ minSlider = minSlide;
+ zeroSlider= zeroSlide;
+ maxSlider = maxSlide;
+ minColor = minC;
+ zeroColor = zeroC;
+ maxColor = maxC;
+ }
+
+ public void actionPerformed (ActionEvent e) {
+ minColorValue = minSlider.getDoubleValue();
+ zeroColorValue = zeroSlider.getDoubleValue();
+ maxColorValue = maxSlider.getDoubleValue();
+ if (minColorValue>zeroColorValue || zeroColorValue>maxColorValue){
+ JFrame errorFrame = new JFrame();
+ String errorMessage = "\n"+"Error: Threshold Value"+"\n"
+ +"must be between Min Value"+"\n"
+ +"and Max Value" +"\n";
+ JOptionPane.showMessageDialog(errorFrame, errorMessage, "Threshold Error",
+ JOptionPane.ERROR_MESSAGE);
+ errorFrame.setVisible(true);
+ return;
+ }
+ nodeViz.setNodeAttributeWhichControlsFillColor(attributeName);
+ nodeViz.setNodeColorCalculationFactors (attributeName,
+ minColor.getColor(),
+ zeroColor.getColor(),
+ maxColor.getColor(),
+ binSlider.getIntegerValue(),
+ min,
+ max,
+ minColorValue,
+ zeroColorValue,
+ maxColorValue);
+ updateSummaryPanel(attributeName);
+ //theClient.applyNodeNodeViz (nodeViz);
+ theClient.applyAllVizMappings (nodeViz);
+ } // actionPerformed
+
+} // ApplyNodeColorAction
+//------------------------------------------------------------------------------------
+/************************
+public class ApplyEdgeColorAction extends AbstractAction
+{
+ String attributeName;
+ double min, max, minColorValue, zeroColorValue, maxColorValue;
+ NewSlider binSlider, minSlider, zeroSlider, maxSlider, thickSlider;
+ ColorPopupButton minColor,zeroColor, maxColor;
+
+ ApplyEdgeColorAction (String tabName, double min, double max,
+ NewSlider binSlide, NewSlider thickSlide,
+ NewSlider minSlide, ColorPopupButton minC,
+ NewSlider zeroSlide, ColorPopupButton zeroC,
+ NewSlider maxSlide, ColorPopupButton maxC) {
+ super ("");
+ attributeName = tabName;
+ this.min = min;
+ this.max = max;
+ binSlider = binSlide;
+ thickSlider = thickSlide;
+ minSlider = minSlide;
+ zeroSlider = zeroSlide;
+ maxSlider = maxSlide;
+ minColor = minC;
+ zeroColor = zeroC;
+ maxColor = maxC;
+ }
+
+ public void actionPerformed (ActionEvent e) {
+ minColorValue = minSlider.getDoubleValue();
+ zeroColorValue = zeroSlider.getDoubleValue();
+ maxColorValue = maxSlider.getDoubleValue();
+
+ if (minColorValue>zeroColorValue || zeroColorValue>maxColorValue){
+ JFrame errorFrame = new JFrame();
+ String errorMessage = "\n"+"Error: Threshold Value"+"\n"
+ +"must be between Min Value"+"\n"
+ +"and Max Value" +"\n";
+ JOptionPane.showMessageDialog (errorFrame, errorMessage, "Threshold Error",
+ JOptionPane.ERROR_MESSAGE);
+ errorFrame.setVisible(true);
+ return;
+ }
+ nodeViz.setEdgeAttributeWhichControlsFillColor(attributeName);
+ nodeViz.setEdgeColorCalculationFactors (attributeName,
+ minColor.getColor(),
+ zeroColor.getColor(),
+ maxColor.getColor(),
+ binSlider.getIntegerValue(),
+ min,
+ max,
+ minColorValue,
+ zeroColorValue,
+ maxColorValue,
+ thickSlider.getIntegerValue());
+ updateSummaryPanel(attributeName);
+ //theClient.applyEdgeNodeViz (nodeViz);
+ theClient.applyAllVizMappings (nodeViz);
+ }
+} // ApplyEdgeColorAction
+************************/
+//------------------------------------------------------------------------------------
+public class ApplyBorderColorAction extends AbstractAction
+{
+ String attributeName;
+ double min, max;
+ NewSlider tempBinSlider, tempThickSlider;
+ NewSlider tempMinSlider, tempZeroSlider, tempMaxSlider;
+ ColorPopupButton tempMinC, tempZeroC, tempMaxC;
+ ApplyBorderColorAction (String tabName, double min, double max,
+ NewSlider binSlider, NewSlider thickSlider,
+ NewSlider minSlider, ColorPopupButton minC,
+ NewSlider zeroSlider,ColorPopupButton zeroC,
+ NewSlider maxSlider, ColorPopupButton maxC) {
+ super ("");
+ attributeName = tabName;
+ this.min = min;
+ this.max = max;
+
+ tempBinSlider = binSlider;
+ tempThickSlider=thickSlider;
+ tempMinSlider = minSlider;
+ tempZeroSlider= zeroSlider;
+ tempMaxSlider = maxSlider;
+ tempMinC = minC;
+ tempZeroC= zeroC;
+ tempMaxC = maxC;
+ }
+ public void actionPerformed (ActionEvent e) {
+ double minColorValue = tempMinSlider.getDoubleValue();
+ double zeroColorValue= tempZeroSlider.getDoubleValue();
+ double maxColorValue = tempMaxSlider.getDoubleValue();
+ //error checking step to ensure min<=zero<=max
+ if (minColorValue>zeroColorValue || zeroColorValue>maxColorValue){
+ JFrame error = new JFrame("Error");
+ String errorMessage = "\n"+"Error: Threshold Value"+"\n"
+ +"must be between Min Value"+"\n"
+ +"and Max Value" +"\n";
+ JTextArea message = new JTextArea(errorMessage);
+ JLabel filler = new JLabel (" ");
+ message.setBackground (Color.red);
+ message.setOpaque(true);
+ error.getContentPane().add(message);
+ error.pack();
+ error.setVisible(true);
+ return;
+ }
+ nodeViz.setBorderAttributeWhichControlsFillColor(attributeName);
+ nodeViz.setBorderColorCalculationFactors(attributeName,
+ tempMinC.getColor(),
+ tempZeroC.getColor(),
+ tempMaxC.getColor(),
+ tempBinSlider.getIntegerValue(),
+ min,
+ max,
+ minColorValue,
+ zeroColorValue,
+ maxColorValue,
+ tempThickSlider.getIntegerValue());
+ updateSummaryPanel(attributeName);
+ //theClient.applyBorderNodeViz (nodeViz);
+ theClient.applyAllVizMappings (nodeViz);
+ }
+
+} // ApplyBorderColorAction
+
+//------------------------------------------------------------------------------------
+public class DismissAction extends AbstractAction
+{
+
+ DismissAction () {super ("");}
+
+ public void actionPerformed (ActionEvent e) {
+ thisChooser.dispose ();
+ }
+
+} // DismissAction
+//-----------------------------------------------------------------------------------
+double [] findMinMax (HashMap attributeMap)
+{
+ String [] keys = (String []) attributeMap.keySet().toArray (new String [0]);
+ //for (int i=0; i < keys.length; i++)
+ // System.out.println ("key " + i + ": " + keys [i]);
+
+ Object [] oValues = attributeMap.values().toArray ();
+ //System.out.println ("number of object values in attributeMap: " + oValues.length);
+ //System.out.println ("class type: " + oValues [0].getClass ());
+ try {
+ Class expectedClass = Class.forName ("java.lang.Double");
+ Class actualClass = oValues [0].getClass ();
+ if (!actualClass.equals (expectedClass)) {
+ double result [] = new double [2];
+ result [0] = 0.0;
+ result [1] = 1.0;
+ return result;
+ }
+ }
+ catch (ClassNotFoundException e) {
+ double result [] = new double [2];
+ result [0] = 0.0;
+ result [1] = 1.0;
+ return result;
+ }
+
+ Double [] values = (Double []) attributeMap.values ().toArray (new Double [0]);
+
+ double min = Double.MAX_VALUE;
+ double max = Double.MIN_VALUE;
+
+ for (int i=0; i < values.length; i++) {
+ double current = values [i].doubleValue ();
+ if (current < min) min = current;
+ if (current > max) max = current;
+ }
+
+ double result [] = new double [2];
+ result [0] = min;
+ result [1] = max;
+
+ return result;
+
+}// findMinMax
+//-----------------------------------------------------------------------------------
+private Class getAttributeValueClass (HashMap attributeMap)
+{
+ Object [] oValues = attributeMap.values().toArray ();
+ // System.out.println ("class type: " + oValues [0].getClass ());
+ return oValues [0].getClass();
+
+}// getAttributeValueClass
+//-----------------------------------------------------------------------------------
+} // class VizChooserPopup
diff --git a/application/src/main/java/cytoscape/dialogs/logger/LoggerDialog.java b/application/src/main/java/cytoscape/dialogs/logger/LoggerDialog.java
new file mode 100644
index 0000000..42815fe
--- /dev/null
+++ b/application/src/main/java/cytoscape/dialogs/logger/LoggerDialog.java
@@ -0,0 +1,332 @@
+package cytoscape.dialogs.logger;
+
+import cytoscape.Cytoscape;
+import cytoscape.logger.CyLogHandler;
+import cytoscape.logger.LogLevel;
+import cytoscape.logger.CyLogger;
+import cytoscape.util.CyFileFilter;
+import cytoscape.util.FileUtil;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import javax.swing.*;
+
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.PrintWriter;
+
+/** Singleton dialog */
+public class LoggerDialog extends javax.swing.JDialog implements CyLogHandler {
+ private static LoggerDialog dialog;
+ private Map<LogLevel, List<String>> messageMap;
+ private Map<LogLevel, JScrollPane> logTabMap;
+ private boolean messageAdded = false;
+
+ // Variables declaration - do not modify
+ private javax.swing.JButton clearButton;
+ private javax.swing.JButton closeButton;
+ private javax.swing.JButton saveButton;
+ private javax.swing.JTabbedPane logTabs;
+
+ // aware no one can currently create the console with an owner, gotta see how headless mode works
+ protected LoggerDialog(JFrame owner) {
+ super(owner, false);
+ init();
+ }
+
+ public static LoggerDialog getLoggerDialog() {
+ if (dialog == null) {
+ dialog = new LoggerDialog(Cytoscape.getDesktop());
+ dialog.setTitle("Cytoscape Error Console");
+ }
+
+ return dialog;
+ }
+
+ public String getAllMessages() {
+ String allMessages = "";
+
+ //set prioritized order for logs
+ List<LogLevel> orderedLevels = new ArrayList<LogLevel>();
+ orderedLevels.add(LogLevel.LOG_FATAL);
+ orderedLevels.add(LogLevel.LOG_ERROR);
+ orderedLevels.add(LogLevel.LOG_WARN);
+ orderedLevels.add(LogLevel.LOG_INFO);
+ orderedLevels.add(LogLevel.LOG_DEBUG);
+
+ //set colors for log titles
+ Map<LogLevel, String> logColors = new HashMap<LogLevel, String>();
+ logColors.put(LogLevel.LOG_FATAL, "red");
+ logColors.put(LogLevel.LOG_ERROR, "red");
+ logColors.put(LogLevel.LOG_WARN, "orange");
+ logColors.put(LogLevel.LOG_INFO, "green");
+ logColors.put(LogLevel.LOG_DEBUG, "blue");
+
+ for (LogLevel logLevel : orderedLevels){
+ if (this.logTabMap.containsKey(logLevel)) {
+ allMessages += "<H1><font color='"+logColors.get(logLevel)+"'>"+logLevel.getPrettyName()+"</font></H1>";
+ String msg = ((JEditorPane) this.logTabMap.get(logLevel).getViewport().getView()).getText();
+ allMessages += msg ;
+ }
+ }
+ return allMessages;
+ }
+
+ private void init() {
+ messageMap = new HashMap<LogLevel, List<String>>();
+ logTabMap = new HashMap<LogLevel, JScrollPane>();
+ initComponents();
+ this.setSize(this.getWidth()*2, this.getHeight()*2);
+ }
+
+
+ private void initComponents() {
+ closeButton = new javax.swing.JButton();
+ clearButton = new javax.swing.JButton();
+ saveButton = new javax.swing.JButton();
+ logTabs = new javax.swing.JTabbedPane();
+
+ setDefaultCloseOperation(javax.swing.WindowConstants.DISPOSE_ON_CLOSE);
+ closeButton.setText("Close");
+ closeButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ closeButtonActionPerformed(evt);
+ }
+ });
+
+ clearButton.setText("Clear All");
+ clearButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ clearButtonActionPerformed(evt);
+ }
+ });
+
+ saveButton.setText("Save All");
+ saveButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ saveButtonActionPerformed(evt);
+ }
+ });
+
+ logTabs.setAutoscrolls(true);
+
+ org.jdesktop.layout.GroupLayout layout = new org.jdesktop.layout.GroupLayout(getContentPane());
+ getContentPane().setLayout(layout);
+ layout.setHorizontalGroup(layout.createParallelGroup(
+ org.jdesktop.layout.GroupLayout.LEADING)
+ .add(layout.createSequentialGroup()
+ .addContainerGap()
+ .add(layout.createParallelGroup(
+ org.jdesktop.layout.GroupLayout.LEADING)
+ .add(logTabs,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 380,
+ Short.MAX_VALUE)
+ .add(org.jdesktop.layout.GroupLayout.TRAILING,
+ layout.createSequentialGroup().add(saveButton)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(clearButton)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(closeButton))).addContainerGap()));
+ layout.setVerticalGroup(layout.createParallelGroup(
+ org.jdesktop.layout.GroupLayout.LEADING)
+ .add(org.jdesktop.layout.GroupLayout.TRAILING,
+ layout.createSequentialGroup().addContainerGap()
+ .add(logTabs,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 263,
+ Short.MAX_VALUE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(layout.createParallelGroup(
+ org.jdesktop.layout.GroupLayout.BASELINE)
+ .add(closeButton).add(clearButton).add(saveButton))
+ .addContainerGap()));
+ pack();
+ }
+
+ private void clearButtonActionPerformed(java.awt.event.ActionEvent evt) {
+ for (LogLevel key : this.messageMap.keySet()) {
+ this.messageMap.get(key).clear();
+ if (this.logTabMap.containsKey(key))
+ ((JEditorPane) this.logTabMap.get(key).getViewport().getView()).setText("");
+ }
+ }
+
+ private void closeButtonActionPerformed(java.awt.event.ActionEvent evt) {
+ this.dispose();
+ }
+
+ private void saveButtonActionPerformed(java.awt.event.ActionEvent evt) {
+ File file = null;
+ try {
+
+ CyFileFilter cyFileFilter = new CyFileFilter("html");
+ String suggestedFileName = "Cytoscape_error_console.html";
+
+ File suggestedFile = new File(suggestedFileName);
+
+ file = FileUtil.getFile("Save all to file", FileUtil.SAVE, cyFileFilter, suggestedFile);
+ }
+ catch (Exception e){
+ // canceled dialog
+ }
+
+ if (file != null) {
+ String filename = file.toString();
+ if (!filename.endsWith(".html")){
+ filename = filename + ".html";
+ file.renameTo(new File(filename));
+ }
+
+ try{
+ PrintWriter out = new PrintWriter(new FileWriter(file));
+ out.print(getAllMessages());
+ out.close();
+ } catch (IOException e) {
+ CyLogger.getLogger().info(
+ "Didn't write error console messages to file: " + e);
+ }
+ }
+ }
+
+
+ public void handleLog(LogLevel level, String msg) {
+ if (level.getLevel() > 3) {
+ return; // not adding messages for "fatal" errors
+ }
+
+ if (level.equals(LogLevel.LOG_DEBUG)) {
+ // check for a "debugging" mode, if false do not add a tab
+ }
+
+ // get or create list of messages
+ List<String> Messages = (this.messageMap.get(level) != null)
+ ? this.messageMap.get(level) : new ArrayList<String>();
+
+ // Do whatever formatting we need
+ msg = msg.replace("\n", "<br>");
+ msg = msg.replace("\t", " ");
+
+ Messages.add(msg);
+ // Make sure it gets added back in
+ this.messageMap.put(level, Messages);
+
+ messageAdded = true;
+
+ if (isVisible()) {
+ JEditorPane MessagePane = addTab(level);
+ StringBuffer sb = createMessages(level);
+
+ MessagePane.setText("");
+ MessagePane.setText(sb.toString());
+ messageAdded = false;
+ } else if (level.equals(LogLevel.LOG_ERROR)) {
+ setVisible(true);
+ }
+
+ if (((level == LogLevel.LOG_ERROR) || (level == LogLevel.LOG_WARN)) &&
+ isVisible()) {
+ logTabs.setSelectedComponent(logTabMap.get(level));
+ }
+ }
+
+ private JEditorPane addTab(LogLevel level) {
+ JEditorPane MessagesPane = null;
+
+ if (this.logTabMap.get(level) != null) {
+ JScrollPane ScrollPane = this.logTabMap.get(level);
+ MessagesPane = (JEditorPane) ScrollPane.getViewport().getView();
+ } else {
+ JScrollPane ScrollPane = new JScrollPane();
+ this.logTabMap.put(level, ScrollPane);
+ logTabs.addTab(level.getPrettyName(), ScrollPane);
+ MessagesPane = new JEditorPane();
+ ScrollPane.setViewportView(MessagesPane);
+ MessagesPane.setEditable(false);
+ MessagesPane.setContentType("text/html");
+ }
+
+ return MessagesPane;
+ }
+
+ private void addEmptyMessage() {
+ this.addTab(LogLevel.LOG_ERROR);
+ }
+
+ private StringBuffer createMessages(LogLevel level) {
+ StringBuffer sb = new StringBuffer();
+ String color = "#333333";
+
+ if (level.equals(LogLevel.LOG_ERROR)) {
+ color = "#ff0000";
+ } else if (level.equals(LogLevel.LOG_WARN)) {
+ color = "#ff4500";
+ }
+
+ sb.append("<html><style type='text/css'>");
+ sb.append("body,th,td,div,p,h1,h2,li,dt,dd ");
+ sb.append("{ font-family: Tahoma, \"Gill Sans\", Arial, sans-serif; }");
+ sb.append("body { margin: 0px; color: " + color +
+ "; background-color: #ffffff; }");
+ sb.append("#indent { padding-left: 30px; }");
+ sb.append("ul {list-style-type: none}");
+ sb.append("</style><body>");
+
+ sb.append("<table width='100%' cellspacing='5'>");
+
+ // show the message in order, i.e. most recent message on bottom
+ for (int i = 0; i < messageMap.get(level).size(); i++) {
+ sb.append("<tr><td width='5%'>" + i + "</td><td width='95%'>");
+ sb.append(messageMap.get(level).get(i));
+ sb.append("</td></tr>");
+ sb.append("<tr><td colspan='2'><hr></td></tr>");
+ }
+
+ sb.append("</table></body></html>");
+
+ return sb;
+ }
+
+ public void setVisible(boolean vis) {
+ if (this.messageMap.size() <= 0) {
+ this.addEmptyMessage();
+ }
+
+ // Have we updated any messages?
+ if (messageAdded) {
+ Set<LogLevel> levels = this.messageMap.keySet();
+
+ for (LogLevel level : levels) {
+ JEditorPane MessagePane = addTab(level);
+ StringBuffer sb = createMessages(level);
+
+ MessagePane.setContentType("text/html");
+ MessagePane.setText(sb.toString());
+ }
+
+ messageAdded = false;
+ }
+
+ // Yes, rebuild the list
+ super.setVisible(vis);
+ }
+
+ /* -------------------------------------- */
+ public static void main(String[] args) {
+ LoggerDialog dialog = LoggerDialog.getLoggerDialog();
+ dialog.setVisible(true);
+
+ dialog.handleLog(LogLevel.LOG_ERROR, "Error, error!");
+ dialog.handleLog(LogLevel.LOG_ERROR, "It's gonna blow!!!");
+
+ dialog.handleLog(LogLevel.LOG_WARN, "Canna take much more Cap'n!");
+ dialog.handleLog(LogLevel.LOG_WARN, "Foobared");
+
+ dialog.handleLog(LogLevel.LOG_INFO, "Just sayin'...");
+ }
+
+ // End of variables declaration
+}
diff --git a/application/src/main/java/cytoscape/dialogs/package.html b/application/src/main/java/cytoscape/dialogs/package.html
new file mode 100644
index 0000000..25a3dce
--- /dev/null
+++ b/application/src/main/java/cytoscape/dialogs/package.html
@@ -0,0 +1,14 @@
+<html>
+<head>
+ <!-- $Revision: 5801 $
+ $Date: 2004-04-20 01:53:47 +0200 (Tue, 20 Apr 2004) $
+ $Author: amarkiel $
+ -->
+</head>
+
+<body>
+UI classes for performing some action, generally more complicated than
+those contained in the cytoscape.actions package. Some provide a
+persistent dialog for manipulating the view and core data structures.
+</body>
+</html>
diff --git a/application/src/main/java/cytoscape/dialogs/plugins/LicenseDialog.java b/application/src/main/java/cytoscape/dialogs/plugins/LicenseDialog.java
new file mode 100644
index 0000000..c097e35
--- /dev/null
+++ b/application/src/main/java/cytoscape/dialogs/plugins/LicenseDialog.java
@@ -0,0 +1,316 @@
+package cytoscape.dialogs.plugins;
+
+import cytoscape.plugin.DownloadableInfo;
+import cytoscape.logger.CyLogger;
+
+import java.awt.Color;
+import java.awt.Component;
+
+import javax.swing.JLabel;
+import javax.swing.JList;
+import javax.swing.ListCellRenderer;
+
+public class LicenseDialog extends javax.swing.JDialog {
+ private static String title = "Plugin License Agreement";
+
+ /** Creates new form LicenseDialog */
+ public LicenseDialog() {
+ setModal(true);
+ setTitle(title);
+ setLocationRelativeTo(this);
+ initComponents();
+ listSetup();
+ }
+
+ public LicenseDialog(javax.swing.JDialog owner) {
+ super(owner, title, true);
+ setLocationRelativeTo(owner);
+ initComponents();
+ listSetup();
+ }
+
+ public LicenseDialog(javax.swing.JFrame owner) {
+ super(owner, title, true);
+ setLocationRelativeTo(owner);
+ initComponents();
+ listSetup();
+ }
+
+ private void listSetup() {
+ listModel = new LicenseListModel();
+ pluginList.setCellRenderer(new LicenseListCellRenderer());
+ pluginList.setModel(listModel);
+ pluginList.setSelectionMode(javax.swing.ListSelectionModel.SINGLE_SELECTION);
+ acceptRadio.setEnabled(false);
+ declineRadio.setEnabled(false);
+ }
+
+ public void addPlugin(DownloadableInfo obj) {
+ listModel.addElement(obj);
+ }
+
+ public void selectDefault() {
+ pluginList.setSelectedIndex(0);
+ DownloadableInfo infoObj = (DownloadableInfo) pluginList.getSelectedValue();
+ setLicenseText(infoObj.getLicenseText());
+ }
+
+ /** This method is called from within the constructor to
+ * initialize the form.
+ * WARNING: Do NOT modify this code. The content of this method is
+ * always regenerated by the Form Editor.
+ */
+ // <editor-fold defaultstate="collapsed" desc=" Generated Code ">
+ private void initComponents() {
+ licenseSplitPane = new javax.swing.JSplitPane();
+ pluginListScrollPane = new javax.swing.JScrollPane();
+ pluginList = new javax.swing.JList();
+ licenseScrollPane = new javax.swing.JScrollPane();
+ licensePanel = new javax.swing.JEditorPane();
+ buttonPane = new javax.swing.JPanel();
+ cancelButton = new javax.swing.JButton();
+ okButton = new javax.swing.JButton();
+ acceptRadio = new javax.swing.JRadioButton();
+ declineRadio = new javax.swing.JRadioButton();
+ licenseLabel = new javax.swing.JLabel();
+
+ setDefaultCloseOperation(javax.swing.WindowConstants.DISPOSE_ON_CLOSE);
+ licenseSplitPane.setDividerLocation(150);
+ pluginList.addListSelectionListener(new javax.swing.event.ListSelectionListener() {
+ public void valueChanged(javax.swing.event.ListSelectionEvent evt) {
+ pluginListValueChanged(evt);
+ }
+ });
+
+ pluginListScrollPane.setViewportView(pluginList);
+
+ licenseSplitPane.setLeftComponent(pluginListScrollPane);
+
+ licenseScrollPane.setViewportView(licensePanel);
+
+ licenseSplitPane.setRightComponent(licenseScrollPane);
+
+ cancelButton.setText("Cancel");
+ cancelButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ cancelButtonActionPerformed(evt);
+ }
+ });
+
+ okButton.setText("Ok");
+ okButton.setEnabled(false);
+ okButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ okButtonActionPerformed(evt);
+ }
+ });
+
+ acceptRadio.setText("Accept All");
+ acceptRadio.setBorder(javax.swing.BorderFactory.createEmptyBorder(0, 0, 0, 0));
+ acceptRadio.setMargin(new java.awt.Insets(0, 0, 0, 0));
+ acceptRadio.addActionListener( new java.awt.event.ActionListener () {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ radioAcceptEvent(evt);
+ }
+ });
+
+ declineRadio.setText("Decline All");
+ declineRadio.setBorder(javax.swing.BorderFactory.createEmptyBorder(0, 0, 0, 0));
+ declineRadio.setMargin(new java.awt.Insets(0, 0, 0, 0));
+ declineRadio.addActionListener( new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ radioDeclineEvent(evt);
+ }
+ });
+
+ org.jdesktop.layout.GroupLayout buttonPaneLayout = new org.jdesktop.layout.GroupLayout(buttonPane);
+ buttonPane.setLayout(buttonPaneLayout);
+ buttonPaneLayout.setHorizontalGroup(
+ buttonPaneLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(org.jdesktop.layout.GroupLayout.TRAILING, buttonPaneLayout.createSequentialGroup()
+ .addContainerGap()
+ .add(acceptRadio)
+ .add(17, 17, 17)
+ .add(declineRadio)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED, 221, Short.MAX_VALUE)
+ .add(okButton)
+ .add(20, 20, 20)
+ .add(cancelButton)
+ .addContainerGap())
+ );
+ buttonPaneLayout.setVerticalGroup(
+ buttonPaneLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(buttonPaneLayout.createSequentialGroup()
+ .addContainerGap(org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
+ .add(buttonPaneLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE)
+ .add(acceptRadio)
+ .add(declineRadio)
+ .add(cancelButton)
+ .add(okButton)))
+ );
+
+ licenseLabel.setText("Cytoscape Plugin License Agreements");
+
+ org.jdesktop.layout.GroupLayout layout = new org.jdesktop.layout.GroupLayout(getContentPane());
+ getContentPane().setLayout(layout);
+ layout.setHorizontalGroup(
+ layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(org.jdesktop.layout.GroupLayout.TRAILING, layout.createSequentialGroup()
+ .addContainerGap()
+ .add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.TRAILING)
+ .add(org.jdesktop.layout.GroupLayout.LEADING, licenseLabel, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 595, Short.MAX_VALUE)
+ .add(buttonPane, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
+ .add(licenseSplitPane, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 595, Short.MAX_VALUE))
+ .addContainerGap())
+ );
+ layout.setVerticalGroup(
+ layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(org.jdesktop.layout.GroupLayout.TRAILING, layout.createSequentialGroup()
+ .addContainerGap()
+ .add(licenseLabel, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE, 16, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .add(14, 14, 14)
+ .add(licenseSplitPane, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 356, Short.MAX_VALUE)
+ .add(9, 9, 9)
+ .add(buttonPane, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .addContainerGap())
+ );
+ pack();
+ }// </editor-fold>
+
+ private void radioAcceptEvent(java.awt.event.ActionEvent evt) {
+ acceptRadio.setSelected(true);
+ declineRadio.setSelected(false);
+ okButton.setEnabled(true);
+ }
+
+ private void radioDeclineEvent(java.awt.event.ActionEvent evt) {
+ declineRadio.setSelected(true);
+ acceptRadio.setSelected(false);
+ okButton.setEnabled(false);
+ }
+
+ // a listener has to be added in order to decide what to do after 'ok'
+ public void addListenerToOk(java.awt.event.ActionListener listener) {
+ okButton.addActionListener(listener);
+ }
+
+
+ private void okButtonActionPerformed(java.awt.event.ActionEvent evt) {
+ CyLogger.getLogger().info("FINISHED");
+ dispose();
+ }
+
+ private void cancelButtonActionPerformed(java.awt.event.ActionEvent evt) {
+ this.dispose();
+ }
+
+ private void pluginListValueChanged(javax.swing.event.ListSelectionEvent evt) {
+ if (pluginList.getSelectedIndex() < 0) { // nothing selected, use the top license
+ pluginList.setSelectedIndex(0);
+ }
+ DownloadableInfo infoObj = (DownloadableInfo) pluginList.getSelectedValue();
+ setLicenseText(infoObj.getLicenseText());
+
+ acceptRadio.setEnabled(true);
+ declineRadio.setEnabled(true);
+ }
+
+ private void setLicenseText(String licenseText) {
+ licensePanel.setContentType("text/html");
+ String Html = "<html><style type='text/css'>";
+ Html += "body,th,td,div,p,h1,h2,li,dt,dd ";
+ Html += "{ font-family: Tahoma, \"Gill Sans\", Arial, sans-serif; }";
+ Html += "body { margin: 0px; color: #333333; background-color: #ffffff; }";
+ Html += "#indent { padding-left: 30px; }";
+ Html += "ul {list-style-type: none}";
+ Html += "</style><body>";
+ Html += licenseText;
+ Html += "</body></html>";
+ licensePanel.setText(Html);
+ licensePanel.setEditable(false);
+ licensePanel.setCaretPosition(0);
+ }
+
+
+
+ // Variables declaration - do not modify
+ private javax.swing.JRadioButton acceptRadio;
+ private javax.swing.JPanel buttonPane;
+ private javax.swing.JButton cancelButton;
+ private javax.swing.JRadioButton declineRadio;
+ private javax.swing.JLabel licenseLabel;
+ private javax.swing.JEditorPane licensePanel;
+ private javax.swing.JScrollPane licenseScrollPane;
+ private javax.swing.JSplitPane licenseSplitPane;
+ private javax.swing.JButton okButton;
+ private javax.swing.JList pluginList;
+ private javax.swing.JScrollPane pluginListScrollPane;
+ private LicenseListModel listModel;
+ // End of variables declaration
+
+ // class LicenseListModel
+ class LicenseListModel extends javax.swing.AbstractListModel {
+
+ private java.util.List<DownloadableInfo> licenseObjs;
+ public LicenseListModel() {
+ super();
+ licenseObjs = new java.util.ArrayList<DownloadableInfo>();
+ }
+
+ public void addElement(DownloadableInfo obj) {
+ licenseObjs.add(obj);
+ }
+
+ public void removeElement(int index) {
+ licenseObjs.remove(index);
+ fireContentsChanged(this, index, index);
+ }
+
+ public int getSize() {
+ return licenseObjs.size();
+ }
+
+ public Object getElementAt(int index) {
+ return licenseObjs.get(index);
+ }
+ }
+
+ // class LicenseListCellRenderer
+ class LicenseListCellRenderer extends JLabel implements ListCellRenderer {
+ public LicenseListCellRenderer() {
+ setOpaque(true);
+ }
+
+ public Component getListCellRendererComponent(JList list, Object value, int index,
+ boolean isSelected, boolean cellHasFocus) {
+ DownloadableInfo dInfo = (DownloadableInfo) value;
+ setText(dInfo.getName());
+ setToolTipText(dInfo.toString());
+ setBackground(isSelected ? Color.gray : Color.white);
+ setForeground(isSelected ? Color.white : Color.black);
+ return this;
+ }
+ }
+/*
+ public static void main(String[] args) {
+ LicenseDialog ld = new LicenseDialog();
+
+ DownloadableInfo di_a = new cytoscape.plugin.PluginInfo();
+ di_a.setName("Foobar");
+ di_a.addCytoscapeVersion("2.6");
+ di_a.setLicense("This is just some text", true);
+
+ DownloadableInfo di_b = new cytoscape.plugin.PluginInfo();
+ di_b.setName("Booya");
+ di_b.addCytoscapeVersion("2.6");
+ di_b.setLicense("Hi there!", true);
+
+
+ ld.addPlugin(di_a);
+ ld.addPlugin(di_b);
+ ld.selectDefault();
+ ld.setVisible(true);
+ }
+*/
+
+}
diff --git a/application/src/main/java/cytoscape/dialogs/plugins/ManagerModel.java b/application/src/main/java/cytoscape/dialogs/plugins/ManagerModel.java
new file mode 100644
index 0000000..81daf19
--- /dev/null
+++ b/application/src/main/java/cytoscape/dialogs/plugins/ManagerModel.java
@@ -0,0 +1,301 @@
+/*
+ File: ManagerModel.java
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.dialogs.plugins;
+
+import cytoscape.logger.CyLogger;
+
+import javax.swing.event.TreeModelListener;
+import javax.swing.event.EventListenerList;
+import javax.swing.event.TreeModelEvent;
+import javax.swing.tree.TreeModel;
+import javax.swing.tree.TreePath;
+
+/**
+ * Fairly similar to DefaultTreeModel but I wanted to add some extra
+ * functionality to removing/adding nodes and use my own node objects
+ */
+public class ManagerModel implements TreeModel {
+ private TreeNode root;
+
+ protected EventListenerList listenerList = new EventListenerList();
+
+ public ManagerModel(TreeNode Root) {
+ root = Root;
+ }
+
+
+ public void removeNodesFromParent(java.util.List<TreeNode> children) {
+ for (TreeNode child: children)
+ recursiveRemoveNodeFromParent(child);
+ }
+
+ /**
+ * Removes given node from it's parent.
+ *
+ * @param child
+ */
+ public void removeNodeFromParent(TreeNode child) {
+ recursiveRemoveNodeFromParent(child);
+ }
+
+ // not recursive anymore
+ private void recursiveRemoveNodeFromParent(TreeNode child) {
+ TreeNode Parent = child.getParent();
+ TreeNode[] Children = new TreeNode[] { child };
+ int[] ChildIndicies = new int[] { getIndexOfChild(Parent, child) };
+ Parent.removeChild(child);
+ nodesRemoved(Parent, ChildIndicies, Children);
+
+ // parent is empty, remove it from it's parent
+// if (Parent.getChildCount() == 0 && !Parent.equals(root)) {
+// recursiveRemoveNodeFromParent(Parent);
+// }
+ }
+
+ /**
+ * Adds node to given parent, fires event
+ *
+ * @param parent
+ * @param child
+ */
+ public void addNodeToParent(TreeNode parent, TreeNode child) {
+ parent.addChild(child);
+ TreeNode[] Children = new TreeNode[] { child };
+ int[] ChildIndicies = new int[] { getIndexOfChild(parent, child) };
+ nodesAdded(parent, ChildIndicies, Children);
+ }
+
+ /**
+ * Fires necessary event, use addNodeToParent
+ *
+ * @param parent
+ * @param childIndicies
+ * @param addedChildren
+ */
+ protected void nodesAdded(TreeNode parent, int[] childIndicies,
+ TreeNode[] addedChildren) {
+ fireTreeNodesAdded(parent, getPathToRoot(parent), childIndicies,
+ addedChildren);
+ }
+
+ /**
+ * Fires necessary event, use removeNodeFromParent
+ *
+ * @param parent
+ * @param childIndicies
+ * @param removedChildren
+ */
+ protected void nodesRemoved(TreeNode parent, int[] childIndicies,
+ TreeNode[] removedChildren) {
+ fireTreeNodesRemoved(parent, getPathToRoot(parent), childIndicies,
+ removedChildren);
+ }
+
+ /**
+ * Gets child TreeNode from given parent at given index.
+ *
+ * @param parent
+ * @param index
+ */
+ public Object getChild(Object parent, int index) {
+ TreeNode treeNode = (TreeNode) parent;
+ return treeNode.getChildAt(index);
+ }
+
+ /**
+ * Gets count of all children under given parent (not including leaves)
+ *
+ * @param parent
+ */
+ public int getChildCount(Object parent) {
+ TreeNode treeNode = (TreeNode) parent;
+ return treeNode.getChildCount();
+ }
+
+ /**
+ * Gets the index of the given child node from the given parent node.
+ *
+ * @param parent
+ * @param child
+ */
+ public int getIndexOfChild(Object parent, Object child) {
+ TreeNode treeNode = (TreeNode) parent;
+ return treeNode.getIndexOfChild((TreeNode) child);
+ }
+
+ /**
+ * Gets root TreeNode
+ *
+ * @return root
+ */
+ public Object getRoot() {
+ return root;
+ }
+
+ /**
+ * Checks if given node is a leaf. True if it either has no children or is
+ * {@link TreeNode#isLeaf()} return true;
+ *
+ * @param node
+ */
+ public boolean isLeaf(Object node) {
+ TreeNode treeNode = (TreeNode) node;
+ return (treeNode.getChildCount() == 0 || treeNode.isLeaf());
+ }
+
+ /**
+ * Removes given listener
+ *
+ * @param l
+ */
+ public void removeTreeModelListener(TreeModelListener l) {
+ listenerList.remove(TreeModelListener.class, l);
+ }
+
+ /**
+ * Adds given listener
+ *
+ * @param l
+ */
+ public void addTreeModelListener(TreeModelListener l) {
+ listenerList.add(TreeModelListener.class, l);
+ }
+
+ /**
+ *
+ * @return TreeModelListener[]
+ */
+ public TreeModelListener[] getTreeModelListeners() {
+ return (TreeModelListener[]) listenerList
+ .getListeners(TreeModelListener.class);
+ }
+
+ protected void fireTreeNodesRemoved(Object source, Object[] path,
+ int[] childIndicies, Object[] children) {
+ TreeModelEvent Event = new TreeModelEvent(source, path, childIndicies,
+ children);
+ TreeModelListener[] listeners = getTreeModelListeners();
+ for (int i = listeners.length - 1; i >= 0; i--) {
+ listeners[i].treeNodesRemoved(Event);
+ }
+ }
+
+ protected void fireTreeNodesAdded(Object source, Object[] path,
+ int[] childIndicies, Object[] children) {
+ TreeModelEvent Event = new TreeModelEvent(source, path, childIndicies,
+ children);
+ TreeModelListener[] listeners = getTreeModelListeners();
+ for (int i = listeners.length - 1; i >= 0; i--) {
+ listeners[i].treeNodesInserted(Event);
+ }
+ }
+
+ // this will reset entire tree
+ protected void fireTreeStructureChanged(Object source, Object[] path,
+ int[] childIndicies, Object[] children) {
+ TreeModelEvent Event = new TreeModelEvent(source, path, childIndicies,
+ children);
+ TreeModelListener[] listeners = getTreeModelListeners();
+ for (int i = listeners.length - 1; i >= 0; i--) {
+ listeners[i].treeStructureChanged(Event);
+ }
+ }
+
+ /**
+ *
+ * @param node
+ * @return
+ */
+ public TreeNode[] getPathToRoot(TreeNode node) {
+ return getPathToRoot(node, 0);
+ }
+
+ // copied from DefaultTreeModel
+ protected TreeNode[] getPathToRoot(TreeNode node, int depth) {
+ if (node == null) {
+ if (depth == 0) {
+ return null;
+ }
+ return new TreeNode[depth];
+ }
+
+ TreeNode[] path = getPathToRoot(node.getParent(), depth + 1);
+ path[path.length - depth - 1] = node;
+ return path;
+ }
+
+ /**
+ * Reloads entire tree, fires event
+ */
+ public void reload() {
+ int n = getChildCount(root);
+ int[] ChildIndex = new int[n];
+ Object[] Children = new Object[n];
+
+ for (int i = 0; i < n; i++) {
+ ChildIndex[i] = i;
+ Children[i] = getChild(root, i);
+ }
+ fireTreeStructureChanged(this, new Object[] { root }, ChildIndex,
+ Children);
+ }
+
+ /**
+ * Reloads given node, fires event.
+ *
+ * @param node
+ */
+ public void reload(TreeNode node) {
+ int n = getChildCount(node);
+ int[] ChildIndex = new int[n];
+ Object[] Children = new Object[n];
+
+ for (int i = 0; i < n; i++) {
+ ChildIndex[i] = i;
+ Children[i] = getChild(node, i);
+ }
+ fireTreeStructureChanged(this, new Object[] { node }, ChildIndex,
+ Children);
+ }
+
+ /**
+ * NOT IMPLEMENTED
+ */
+ public void valueForPathChanged(TreePath path, Object newValue) {
+ CyLogger.getLogger().warn("valueForPathChanged NOT IMPLEMENTED");
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/dialogs/plugins/PluginIndex.java b/application/src/main/java/cytoscape/dialogs/plugins/PluginIndex.java
new file mode 100644
index 0000000..233eed4
--- /dev/null
+++ b/application/src/main/java/cytoscape/dialogs/plugins/PluginIndex.java
@@ -0,0 +1,128 @@
+package cytoscape.dialogs.plugins;
+
+import java.io.IOException;
+import java.util.Vector;
+import java.util.HashMap;
+
+import org.apache.lucene.analysis.standard.StandardAnalyzer;
+import org.apache.lucene.document.Document;
+import org.apache.lucene.document.Field;
+import org.apache.lucene.index.IndexWriter;
+import org.apache.lucene.queryParser.ParseException;
+import org.apache.lucene.queryParser.QueryParser;
+import org.apache.lucene.search.*;
+import org.apache.lucene.store.Directory;
+import org.apache.lucene.store.RAMDirectory;
+import org.apache.lucene.util.Version;
+import cytoscape.plugin.DownloadableInfo;
+import cytoscape.plugin.PluginInfo;
+import cytoscape.plugin.ThemeInfo;
+import java.util.List;
+
+public class PluginIndex {
+
+ private static StandardAnalyzer analyzer = new StandardAnalyzer(Version.LUCENE_30);
+
+ private static Vector indices = new Vector();
+ private static HashMap<String,Directory> indexTracker = new HashMap<String,Directory>();
+ private static HashMap<String,Vector> pluginVectTracker = new HashMap<String,Vector>();
+
+ private static Vector allPluginVect;
+
+ public static void setAllPluginVector( Vector allPluginVect, boolean versionCheck, String downloadLocText ) throws Exception {
+
+ String index_id = downloadLocText.trim() + Boolean.toString(versionCheck);
+
+ pluginVectTracker.put(index_id, allPluginVect);
+
+ // build an index for this id
+ Directory index = new RAMDirectory();
+
+ // the boolean arg in the IndexWriter ctor means to
+ // create a new index, overwriting any existing index
+ IndexWriter w = new IndexWriter(index, analyzer, true, IndexWriter.MaxFieldLength.UNLIMITED);
+
+ for (int i=0; i<allPluginVect.size(); i++ ){
+ Vector aPlugin = (Vector) allPluginVect.elementAt(i);
+
+ if (aPlugin.elementAt(2) instanceof PluginInfo){
+ PluginInfo info = (PluginInfo) aPlugin.elementAt(2);
+
+ List<PluginInfo.AuthorInfo> authorInfo = info.getAuthors();
+ String authorNames = "";
+ String institutionNames = "";
+ for (int j=0; j<authorInfo.size(); j++){
+ PluginInfo.AuthorInfo oneAuthor = authorInfo.get(j);
+ authorNames += " " + oneAuthor.getAuthor();
+ institutionNames += " " + oneAuthor.getInstitution();
+ }
+ String wholeText = info.getName() + " " + info.getDescription() + " "+ authorNames + " "+ institutionNames;
+
+ addDoc(w, wholeText, "default");
+ }
+ else {
+ // This could be a themeInfo
+ DownloadableInfo downloadableInfo = (DownloadableInfo) aPlugin.elementAt(2);
+ addDoc(w, downloadableInfo.getDescription(), "default");
+ }
+ }
+
+ w.close();
+
+ indexTracker.put(index_id, index);
+
+ }
+
+ private static void addDoc(IndexWriter w, String value, String title) throws IOException {
+ Document doc = new Document();
+ doc.add(new Field(title, value, Field.Store.YES, Field.Index.ANALYZED));
+ w.addDocument(doc);
+ }
+
+
+ public static Vector getSearchResult(String querystr, boolean versionCheck, String downloadLocText ) throws Exception {
+
+ String index_id = downloadLocText.trim() + Boolean.toString(versionCheck);
+
+ // Check if the index for this case already existed
+ if (!indexTracker.containsKey(index_id)){
+ // The index does not exist, so we can not do search, just return null
+ return null;
+ }
+
+ // Add wildcard characters to queryStr at beginning and end
+ querystr = querystr.trim();
+ if (!querystr.startsWith("*")){
+ querystr = "*"+querystr;
+ }
+ if (!querystr.endsWith("*")){
+ querystr = querystr+ "*";
+ }
+
+ // The index does exist, do the search now
+ Directory index = (Directory) indexTracker.get(index_id);
+ QueryParser qp = new QueryParser(Version.LUCENE_30, "default", analyzer);
+ qp.setAllowLeadingWildcard(true);
+ Query q = qp.parse(querystr);
+
+ // search
+ int hitsPerPage = 1000;
+ IndexSearcher searcher = new IndexSearcher(index, true);
+ TopScoreDocCollector collector = TopScoreDocCollector.create(hitsPerPage, true);
+ searcher.search(q, collector);
+ ScoreDoc[] hits = collector.topDocs().scoreDocs;
+
+ // Retrive all the plugins for this situation
+ Vector pluginVect = pluginVectTracker.get(index_id);
+
+ // This will hold the filered set of plugins
+ Vector filteredPluginVector = new Vector();
+
+ for(int i=0;i<hits.length;++i) {
+ int docId = hits[i].doc;
+ filteredPluginVector.add(pluginVect.elementAt(docId));
+ }
+
+ return filteredPluginVector;
+ }
+}
diff --git a/application/src/main/java/cytoscape/dialogs/plugins/PluginManageDialog.java b/application/src/main/java/cytoscape/dialogs/plugins/PluginManageDialog.java
new file mode 100644
index 0000000..3800d95
--- /dev/null
+++ b/application/src/main/java/cytoscape/dialogs/plugins/PluginManageDialog.java
@@ -0,0 +1,1492 @@
+/*
+ File: PluginManageDialog.java
+ Copyright (c) 2006, 2007, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.dialogs.plugins;
+
+import cytoscape.Cytoscape;
+import cytoscape.CytoscapeVersion;
+import cytoscape.bookmarks.Bookmarks;
+import cytoscape.bookmarks.DataSource;
+import cytoscape.dialogs.preferences.BookmarkDialog;
+import cytoscape.dialogs.preferences.EditBookmarkDialog;
+import cytoscape.logger.CyLogger;
+
+import cytoscape.plugin.DownloadableInfo;
+import cytoscape.plugin.ManagerUtil;
+import cytoscape.plugin.PluginInquireAction;
+import cytoscape.plugin.PluginManagerInquireTask;
+import cytoscape.plugin.PluginStatus;
+import cytoscape.plugin.ThemeInfo;
+import cytoscape.plugin.PluginInfo;
+import cytoscape.plugin.PluginManager;
+import cytoscape.plugin.PluginException;
+import cytoscape.plugin.ManagerException;
+
+import cytoscape.task.TaskMonitor;
+import cytoscape.task.ui.JTaskConfig;
+import cytoscape.task.util.TaskManager;
+import cytoscape.util.BookmarksUtil;
+import cytoscape.util.OpenBrowser;
+
+import java.awt.Component;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+
+import java.util.List;
+import java.util.Map;
+import java.util.Vector;
+import javax.swing.*;
+import javax.swing.event.TreeSelectionEvent;
+import javax.swing.event.TreeSelectionListener;
+import javax.swing.tree.TreePath;
+import java.util.ArrayList;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+import java.awt.Color;
+import javax.swing.event.ListSelectionEvent;
+import javax.swing.event.ListSelectionListener;
+
+public class PluginManageDialog extends javax.swing.JDialog implements
+ TreeSelectionListener, ActionListener {
+ private static CyLogger logger = CyLogger.getLogger(PluginManageDialog.class);
+
+ public static String CURRENTLY_INSTALLED = "Currently Installed";
+ public static String AVAILABLE_FOR_INSTALL = "Available for Install";
+
+ public static String defaultPluginSiteUrl = cytoscape.CytoscapeInit.getProperties().getProperty("defaultPluginDownloadUrl");
+ public static String DefaultPluginSiteTitle = "Cytoscape";
+
+ //private boolean hasPluginSiteURLChanged = false;
+ private String currentPluginSiteURL = defaultPluginSiteUrl;
+
+ private String HOWTOSEARCH = "You can use wildcard * or ? in your search words";
+
+ public enum PluginInstallStatus {
+ INSTALLED(CURRENTLY_INSTALLED), AVAILABLE(AVAILABLE_FOR_INSTALL);
+ private String typeText;
+
+ private PluginInstallStatus(String type) {
+ typeText = type;
+ }
+
+ public String toString() {
+ return typeText;
+ }
+ }
+
+ public enum CommonError {
+ NOXML("ERROR: Failed to read XML file "), BADXML(
+ "ERROR: XML file may be incorrectly formatted, unable to read ");
+
+ private String errorText;
+
+ private CommonError(String error) {
+ errorText = error;
+ }
+
+ public String toString() {
+ return errorText;
+ }
+ }
+
+ private String baseSiteLabel = "Plugins available for download from: ";
+
+ public PluginManageDialog() {
+ this.setTitle("Manage Plugins");
+ initComponents();
+ initTree();
+ this.setSize(600, 500);
+ }
+
+ public PluginManageDialog(javax.swing.JDialog owner) {
+ super(owner, "Manage Plugins");
+ setLocationRelativeTo(owner);
+ initComponents();
+ initTree();
+ this.setSize(600, 500);
+ }
+
+ public PluginManageDialog(javax.swing.JFrame owner) {
+ super(owner, "Manage Plugins");
+ setLocationRelativeTo(owner);
+ initComponents();
+ initTree();
+ this.setSize(600, 500);
+ this.btnSearch.setEnabled(false);
+ this.availablePluginsLabel.setVisible(false);
+ this.downloadLocText.setVisible(false);
+ //this.sitePanel2.setVisible(false);
+ //this.changeSiteButton.setVisible(false);
+ this.btnClear.setEnabled(false);
+
+ bookmarksSetUp();
+
+ this.lstDownloadSites.setCellRenderer(new BookmarkCellRenderer());
+ this.lstDownloadSites.addListSelectionListener(new MyListSelectionListener());
+ this.lstDownloadSites.getSelectionModel().setSelectionMode(javax.swing.ListSelectionModel.SINGLE_SELECTION);
+ loadBookmarkCMBox(true);
+
+ //this.lbSiteURL.setText(((DataSource)this.cmbDownloadSites.getSelectedItem()).getHref());
+ //this.jTabbedPane1.setSelectedIndex(1);
+
+ this.jTabbedPane1.addChangeListener(new MyChangeListener());
+ this.tfSearch.setToolTipText(HOWTOSEARCH);
+
+ // by default, show all the plugins
+ this.versionCheck.setSelected(false);
+
+ this.btnEditSite.setEnabled(false);
+ this.btnDeleteSite.setEnabled(false);
+ }
+
+
+ class MyChangeListener implements ChangeListener {
+ public void stateChanged(ChangeEvent e){
+ int width = PluginManageDialog.this.jTabbedPane1.getSize().width;
+
+ if (PluginManageDialog.this.jTabbedPane1.getSelectedIndex() == 0){
+
+ //PluginManageDialog.this.jTabbedPane1.setMinimumSize(new Dimension(width, 50));
+ //PluginManageDialog.this.jTabbedPane1.setPreferredSize(new Dimension(width, 50));
+ //PluginManageDialog.this.pnlSearch.setPreferredSize(new Dimension(width, 50));
+ //PluginManageDialog.this.pnlSettings.setPreferredSize(new Dimension(width, 50));
+ }
+ else {
+ //PluginManageDialog.this.jTabbedPane1.setMinimumSize(new Dimension(width, 150));
+ //PluginManageDialog.this.jTabbedPane1.setPreferredSize(new Dimension(width, 150));
+ //PluginManageDialog.this.pnlSearch.setPreferredSize(new Dimension(width, 150));
+ //PluginManageDialog.this.pnlSettings.setPreferredSize(new Dimension(width, 150));
+
+ }
+ //PluginManageDialog.this.pack();
+ }
+ }
+
+ // Refresh the plugin-tree after the change of Plugin site URL
+ private void refreshPluginTree(){
+ switchDownloadSites();
+ cytoscape.task.Task task = new PluginManagerInquireTask
+ (this.currentPluginSiteURL, new UrlAction(this, this.currentPluginSiteURL));
+ // Configure JTask Dialog Pop-Up Box
+ JTaskConfig jTaskConfig = new JTaskConfig();
+ jTaskConfig.setOwner(Cytoscape.getDesktop());
+ jTaskConfig.displayCloseButton(false);
+ jTaskConfig.displayStatus(true);
+ jTaskConfig.setAutoDispose(true);
+ jTaskConfig.displayCancelButton(true);
+ // Execute Task in New Thread; pop open JTask Dialog Box.
+ TaskManager.executeTask(task, jTaskConfig);
+ }
+
+
+ private class UrlAction extends PluginInquireAction {
+
+ private PluginManageDialog dialog;
+ private String url;
+
+ public UrlAction(PluginManageDialog Dialog, String Url) {
+ dialog = Dialog;
+ url = Url;
+ }
+
+ public boolean displayProgressBar() {
+ return true;
+ }
+
+ public String getProgressBarMessage() {
+ return "Attempting to connect...";
+ }
+
+ public void inquireAction(List<DownloadableInfo> Results) {
+
+ if (isExceptionThrown()) {
+ if (getIOException() != null) {
+ // failed to read the given url
+ logger.warn(PluginManageDialog.CommonError.NOXML + url, getIOException());
+ dialog.setError(PluginManageDialog.CommonError.NOXML + url);
+ } else if (getJDOMException() != null) {
+ // failed to parse the xml file at the url
+ logger.warn(PluginManageDialog.CommonError.BADXML + url, getJDOMException());
+ dialog.setError(PluginManageDialog.CommonError.BADXML + url);
+ }
+ } else {
+
+ PluginManager Mgr = PluginManager.getPluginManager();
+ List<DownloadableInfo> UniqueAvailable = ManagerUtil.getUnique(Mgr
+ .getDownloadables(PluginStatus.CURRENT), Results);
+
+ Map<String, List<DownloadableInfo>> NewPlugins = ManagerUtil
+ .sortByCategory(UniqueAvailable);
+
+ if (NewPlugins.size() <= 0) {
+ dialog.setError("No plugins compatible with "
+ + new CytoscapeVersion().getFullVersion()
+ + " available from this site.");
+ } else {
+ dialog.setMessage("");
+ }
+
+ for (String Category : NewPlugins.keySet()) {
+ dialog.addCategory(Category, NewPlugins.get(Category),
+ PluginManageDialog.PluginInstallStatus.AVAILABLE);
+ }
+ }
+
+ }
+
+ }
+
+
+ // trying to listen to events in the Url dialog
+ public void actionPerformed(ActionEvent evt) {
+ logger.info("URL DIALOG: " + evt.getSource().toString());
+ }
+
+ /**
+ * Enables the delete/install buttons when the correct leaf node is selected
+ */
+ public void valueChanged(TreeSelectionEvent e) {
+ TreeNode Node = (TreeNode) pluginTree.getLastSelectedPathComponent();
+ if (Node == null) {
+ return;
+ }
+
+ if (Node.isLeaf()) {
+ // display any object selected
+ infoTextPane.setContentType("text/html");
+ infoTextPane.setText(((DownloadableInfo) Node.getObject()).htmlOutput());
+ infoTextPane.setCaretPosition(0);
+ infoTextPane.setEditable(false);
+ infoTextPane.addHyperlinkListener(new javax.swing.event.HyperlinkListener() {
+ public void hyperlinkUpdate(javax.swing.event.HyperlinkEvent evt) {
+ if (evt.getEventType() == javax.swing.event.HyperlinkEvent.EventType.ACTIVATED) {
+ // call open browser on the link
+ OpenBrowser.openURL(evt.getURL().toString());
+ }
+
+ }
+ });
+ if (Node.getParent().getParent().getTitle().equalsIgnoreCase(CURRENTLY_INSTALLED)) {
+ installDeleteButton.setText("Delete");
+ if (PluginManager.usingWebstartManager()) {
+ installDeleteButton.setEnabled(false);
+ setMessage("Delete is unavailable when using Web Start");
+ } else {
+ installDeleteButton.setEnabled(true);
+ }
+ } else if (Node.getParent().getParent().getTitle().equalsIgnoreCase(AVAILABLE_FOR_INSTALL)) {
+
+ installDeleteButton.setText("Install");
+ installDeleteButton.setEnabled(true);
+ }
+ } else {
+ installDeleteButton.setEnabled(false);
+ }
+ }
+
+ /**
+ * Sets a message to be shown to the user regarding the plugin management
+ * actions.
+ *
+ * @param Msg
+ */
+ public void setMessage(String Msg) {
+ msgPanel.setForeground(java.awt.Color.BLACK);
+ msgPanel.setText(Msg);
+ }
+
+ public void setError(String Msg) {
+ msgPanel.setForeground(new java.awt.Color(204, 0, 51));
+ msgPanel.setText(Msg);
+ }
+
+ /**
+ * Set the name of the site the available plugins are from.
+ *
+ * @param SiteName
+ */
+ public void setSiteName(String SiteName) {
+ downloadLocText.setText(SiteName);
+ }
+
+ /**
+ * Call this when changing download sites to clear out the old available
+ * list in order to create a new one.
+ */
+ public void switchDownloadSites() {
+ hiddenNodes.clear();
+ java.util.Vector<TreeNode> AvailableNodes = new java.util.Vector<TreeNode>(
+ availableNode.getChildren());
+ for (TreeNode child : AvailableNodes) {
+ treeModel.removeNodeFromParent(child);
+ }
+ }
+
+ /**
+ * Adds a category and it's list of plugins to the appropriate tree (based
+ * on Status) in the dialog.
+ *
+ * @param CategoryName
+ * String category for this list of plugins
+ * @param Plugins
+ * List of DownloadableInfo objects to be shown in the given
+ * category
+ * @param Status
+ * PluginInstallStatus (currently installed or available for
+ * install)
+ */
+ public void addCategory(String CategoryName,
+ List<DownloadableInfo> Plugins, PluginInstallStatus Status) {
+ switch (Status) {
+ case INSTALLED:
+ addCategory(CategoryName, Plugins, installedNode);
+ break;
+
+ case AVAILABLE:
+ addCategory(CategoryName, Plugins, availableNode);
+ if (treeModel.getIndexOfChild(rootTreeNode, availableNode) < 0) {
+ treeModel.addNodeToParent(rootTreeNode, availableNode);
+ }
+ break;
+ }
+
+ javax.swing.ToolTipManager.sharedInstance().registerComponent(
+ pluginTree);
+ javax.swing.ImageIcon warningIcon = createImageIcon(
+ "/cytoscape/images/misc/alert-red2.gif", "Warning");
+ javax.swing.ImageIcon okIcon = createImageIcon(
+ "/cytoscape/images/misc/check-mark.gif", "Ok");
+ if (warningIcon != null) {
+ treeRenderer = new TreeCellRenderer(warningIcon, okIcon);
+ pluginTree.setCellRenderer(treeRenderer);
+ }
+
+ pluginTree.expandPath( new TreePath(availableNode.getPath()) );
+ pluginTree.expandPath( new TreePath(installedNode.getPath()) );
+ }
+
+ // add category to the set of plugins under given node
+ private void addCategory(String CategoryName,
+ List<DownloadableInfo> Plugins, TreeNode node) {
+ TreeNode Category = new TreeNode(CategoryName, true);
+
+ for (DownloadableInfo CurrentPlugin : Plugins) {
+ TreeNode PluginNode = new TreeNode(CurrentPlugin);
+
+ if (node.equals(availableNode)
+ && !CurrentPlugin.isPluginCompatibleWithCurrent()) {
+ java.util.List<TreeNode> hiddenCat = hiddenNodes.get(Category);
+ if (hiddenCat == null)
+ hiddenCat = new java.util.ArrayList<TreeNode>();
+
+ hiddenCat.add(PluginNode);
+ hiddenNodes.put(Category, hiddenCat);
+ if (!versionCheck.isSelected())
+ treeModel.addNodeToParent(Category, PluginNode);
+ } else {
+ treeModel.addNodeToParent(Category, PluginNode);
+ }
+ }
+ if (Category.getChildCount() > 0)
+ treeModel.addNodeToParent(node, Category);
+ }
+
+
+ // allow for outdated versions
+ private void versionCheckItemStateChanged(java.awt.event.ItemEvent evt) {
+ TreePath[] SelectedPaths = pluginTree.getSelectionPaths();
+ if (evt.getStateChange() == ItemEvent.DESELECTED) {
+ pluginTree.collapsePath( new TreePath(availableNode.getPath()) );
+ availableNode.removeChildren();
+ for (TreeNode Category : hiddenNodes.keySet()) {
+ for (TreeNode Plugin : hiddenNodes.get(Category)) {
+ treeModel.addNodeToParent(Category, Plugin);
+ }
+ treeModel.addNodeToParent(availableNode, Category);
+ }
+ } else if (evt.getStateChange() == ItemEvent.SELECTED) {
+
+ for (TreeNode Category : hiddenNodes.keySet()) {
+ for (TreeNode Plugin: hiddenNodes.get(Category)) {
+ hiddenNodes.get(Category);
+ treeModel.removeNodesFromParent(hiddenNodes.get(Category));
+ if (Category.getChildCount() <= 0) {
+ availableNode.removeChild(Category);
+ treeModel.reload();
+ }
+ }
+ }
+ }
+ if (SelectedPaths != null) {
+ for (TreePath Path: SelectedPaths) {
+ pluginTree.expandPath(Path);
+ pluginTree.setSelectionPath(Path);
+ }
+ } else {
+ pluginTree.expandPath( new TreePath(availableNode.getPath()) );
+ pluginTree.expandPath( new TreePath(installedNode.getPath()) );
+ }
+ }
+
+ private void installDeleteButtonActionPerformed(ActionEvent evt) {
+ if (installDeleteButton.getText().equals("Delete")) {
+ deleteButtonActionPerformed(evt);
+ } else if (installDeleteButton.getText().equals("Install")) {
+ installButtonActionPerformed(evt);
+ }
+ }
+
+ // delete event
+ private void deleteButtonActionPerformed(ActionEvent evt) {
+ TreeNode Node = (TreeNode) pluginTree.getLastSelectedPathComponent();
+
+ if (Node == null) {
+ return;
+ }
+ DownloadableInfo NodeInfo = Node.getObject();
+ String ChangeMsg = "Changes will not take effect until you have restarted Cytoscape.";
+ String VerifyMsg = "";
+ if (NodeInfo.getCategory().equalsIgnoreCase("core")) {
+ VerifyMsg = "This is a 'core' plugin and other plugins may depend on it, "
+ + "are you sure you want to delete it?\n" + ChangeMsg;
+ } else {
+ VerifyMsg = "Are you sure you want to delete the plugin '"
+ + NodeInfo.getName() + "'?\n" + ChangeMsg;
+ }
+ if (JOptionPane.YES_OPTION == JOptionPane.showConfirmDialog(this,
+ VerifyMsg, "Verify Delete Plugin", JOptionPane.YES_NO_OPTION,
+ JOptionPane.QUESTION_MESSAGE)) {
+ try {
+ PluginManager.getPluginManager().delete(NodeInfo);
+ treeModel.removeNodeFromParent(Node);
+ setMessage(NodeInfo.getName()
+ + " will be removed when you restart Cytoscape.");
+ } catch (cytoscape.plugin.WebstartException we) {
+ logger.warn("Unable to remove '"+NodeInfo.getName()+"': "+we.getMessage(), we);
+ }
+ }
+ }
+
+ // install new downloadable obj
+ private void installButtonActionPerformed(java.awt.event.ActionEvent evt) {
+ final TreeNode node = (TreeNode) pluginTree
+ .getLastSelectedPathComponent();
+
+ if (node == null) { // error
+ return;
+ }
+ Object nodeInfo = node.getObject();
+ if (node.isLeaf()) {
+ boolean licenseRequired = false;
+ final LicenseDialog License = new LicenseDialog(this);
+ final DownloadableInfo infoObj = (DownloadableInfo) nodeInfo;
+
+ switch (infoObj.getType()) {
+ case PLUGIN:
+ if (infoObj.getLicenseText() != null) {
+ License.addPlugin(infoObj);
+ licenseRequired = true;
+ }
+ break;
+ case THEME:
+ ThemeInfo themeInfo = (ThemeInfo) infoObj;
+ for (PluginInfo pInfo : themeInfo.getPlugins()) {
+ if (pInfo.getLicenseText() != null) {
+ License.addPlugin(pInfo);
+ licenseRequired = true;
+ }
+ }
+ break;
+ case FILE: // currently nothing, there are no FileInfo objects
+ // right now
+ break;
+ }
+
+ if (licenseRequired) {
+ License.addListenerToOk(new ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ License.dispose();
+ createInstallTask(infoObj, node);
+ }
+ });
+ License.selectDefault();
+ License.setVisible(true);
+ } else {
+ createInstallTask(infoObj, node);
+ }
+ }
+ }
+
+ private void updateCurrent(DownloadableInfo info) {
+ boolean categoryMatched = false;
+
+ for (TreeNode Child : installedNode.getChildren()) {
+ if (Child.getTitle().equals(info.getCategory())) {
+ Child.addChild(new TreeNode(info));
+ categoryMatched = true;
+ }
+ }
+
+ if (!categoryMatched) {
+ List<DownloadableInfo> NewPlugin = new java.util.ArrayList<DownloadableInfo>();
+ NewPlugin.add(info);
+ addCategory(info.getCategory(), NewPlugin,
+ PluginInstallStatus.INSTALLED);
+ }
+ }
+
+ // close button
+ private void closeButtonActionPerformed(java.awt.event.ActionEvent evt) {
+ dispose();
+ }
+
+ // initialize the JTree and base nodes
+ private void initTree() {
+ pluginTree.setRootVisible(false);
+ pluginTree.addTreeSelectionListener(this);
+
+ pluginTree.getSelectionModel().setSelectionMode(
+ javax.swing.tree.TreeSelectionModel.SINGLE_TREE_SELECTION);
+
+ rootTreeNode = new TreeNode("Plugins", true);
+ installedNode = new TreeNode(PluginInstallStatus.INSTALLED.toString(),
+ true);
+ availableNode = new TreeNode(PluginInstallStatus.AVAILABLE.toString(),
+ true);
+
+ treeModel = new ManagerModel(rootTreeNode);
+ treeModel.addNodeToParent(rootTreeNode, installedNode);
+ treeModel.addNodeToParent(rootTreeNode, availableNode);
+
+ pluginTree.setModel(treeModel);
+
+ hiddenNodes = new java.util.HashMap<TreeNode, java.util.List<TreeNode>>();
+ }
+
+
+ private Vector getAllPluginVector(){
+
+ Vector<Vector> allPluginVect = new Vector<Vector>();
+
+ TreeNode root = (TreeNode) this.treeModel.getRoot();
+ for (int i=0; i< root.getChildCount(); i++){
+ TreeNode n = root.getChildAt(i);
+ Vector<TreeNode> categories = n.getChildren();
+ for (int j=0; j<categories.size(); j++){
+ TreeNode category = categories.elementAt(j);
+ for (int k=0; k<category.getChildCount(); k++){
+ TreeNode leaf = category.getChildAt(k);
+ Vector aPluginVect = new Vector();
+ aPluginVect.add(n.getTitle());
+ aPluginVect.add(category.getTitle());
+ aPluginVect.add(leaf.getObject());
+ allPluginVect.add(aPluginVect);
+ }
+ }
+ }
+
+ return allPluginVect;
+ }
+
+
+ // Update tree model based on the search result
+ private void updateTreeModel(Vector filteredPluginVector) {
+
+ TreeNode newRootTreeNode = new TreeNode("Plugins", true);
+ ManagerModel newTreeModel = new ManagerModel(newRootTreeNode);
+
+ TreeNode newInstalledNode = new TreeNode(PluginInstallStatus.INSTALLED.toString());
+ TreeNode newAvailableNode = new TreeNode(PluginInstallStatus.AVAILABLE.toString());
+ //
+ newTreeModel.addNodeToParent(newRootTreeNode, newInstalledNode);
+ newTreeModel.addNodeToParent(newRootTreeNode, newAvailableNode);
+
+ if (filteredPluginVector != null){
+ // Add the filtered plugins to the new Tree Model
+ for (int i=0; i < filteredPluginVector.size(); i++ ){
+
+ Vector aPlugin = (Vector) filteredPluginVector.elementAt(i);
+
+ if (aPlugin.elementAt(0).toString().equalsIgnoreCase(CURRENTLY_INSTALLED)){
+ //add to branch of newInstalledNode
+ String category = aPlugin.elementAt(1).toString();
+ TreeNode leafNode = new TreeNode((DownloadableInfo) aPlugin.elementAt(2));
+ // get the category TreeNode
+ TreeNode categoryNode = null;
+ for (int j=0; j<newInstalledNode.getChildCount();j++ ){
+ TreeNode node = newInstalledNode.getChildAt(j);
+ if (node.getTitle().equalsIgnoreCase(category)){
+ categoryNode = node;
+ newTreeModel.addNodeToParent(categoryNode, leafNode);
+ break;
+ }
+ }
+ if (categoryNode == null){
+ categoryNode = new TreeNode(category, true);
+ newTreeModel.addNodeToParent(categoryNode, leafNode);
+ newTreeModel.addNodeToParent(newInstalledNode,categoryNode);
+ }
+ }
+ else if (aPlugin.elementAt(0).toString().equalsIgnoreCase(AVAILABLE_FOR_INSTALL)){
+ //add to the branch of newAvailableNode
+ String category = aPlugin.elementAt(1).toString();
+ TreeNode leafNode = new TreeNode((DownloadableInfo) aPlugin.elementAt(2));
+ // get the category TreeNode
+ TreeNode categoryNode = null;
+ for (int j=0; j<newAvailableNode.getChildCount();j++ ){
+ TreeNode node = newAvailableNode.getChildAt(j);
+ if (node.getTitle().equalsIgnoreCase(category)){
+ categoryNode = node;
+ newTreeModel.addNodeToParent(categoryNode, leafNode);
+ break;
+ }
+ }
+ if (categoryNode == null){
+ categoryNode = new TreeNode(category, true);
+ newTreeModel.addNodeToParent(categoryNode, leafNode);
+ newTreeModel.addNodeToParent(newAvailableNode,categoryNode);
+ }
+ }
+ }
+ }
+
+ pluginTree.setModel(newTreeModel);
+
+ pluginTree.expandPath( new TreePath(newAvailableNode.getPath()) );
+ pluginTree.expandPath( new TreePath(newInstalledNode.getPath()) );
+ }
+
+
+ private void switchToMainDialog() {
+ // switch to the main treeModel
+ pluginTree.setModel(treeModel);
+ TreeNode root = (TreeNode) treeModel.getRoot();
+
+ // Expand the tree to level 1
+ Vector<TreeNode> treeNodeVect = root.getChildren();
+ for (int i=0; i< treeNodeVect.size(); i++){
+ TreeNode n = treeNodeVect.elementAt(i);
+ pluginTree.expandPath(new TreePath(treeModel.getPathToRoot(n)));
+ }
+
+ // switch the sitePanel
+ this.sitePanel.setVisible(true);
+ //this.sitePanel2.setVisible(false);
+ }
+
+
+ /** This method is called from within the constructor to
+ * initialize the form.
+ * WARNING: Do NOT modify this code. The content of this method is
+ * always regenerated by the Form Editor.
+ */
+ // <editor-fold defaultstate="collapsed" desc=" Generated Code ">
+ private void initComponents() {
+ java.awt.GridBagConstraints gridBagConstraints;
+
+ jSplitPane2 = new javax.swing.JSplitPane();
+ jTabbedPane1 = new javax.swing.JTabbedPane();
+ pnlSearch = new javax.swing.JPanel();
+ topPane = new javax.swing.JPanel();
+ sitePanel = new javax.swing.JPanel();
+ tfSearch = new javax.swing.JTextField();
+ btnSearch = new javax.swing.JButton();
+ btnClear = new javax.swing.JButton();
+ downloadLocText = new javax.swing.JLabel();
+ lbSearchTitle = new javax.swing.JLabel();
+ pnlSettings = new javax.swing.JPanel();
+ jLabel3 = new javax.swing.JLabel();
+ jPanel2 = new javax.swing.JPanel();
+ btnAddSite = new javax.swing.JButton();
+ btnEditSite = new javax.swing.JButton();
+ btnDeleteSite = new javax.swing.JButton();
+ jScrollPane1 = new javax.swing.JScrollPane();
+ lstDownloadSites = new javax.swing.JList();
+ jPanel3 = new javax.swing.JPanel();
+ availablePluginsLabel = new javax.swing.JLabel();
+ versionCheck = new javax.swing.JCheckBox();
+ jSplitPane1 = new javax.swing.JSplitPane();
+ treeScrollPane = new javax.swing.JScrollPane();
+ pluginTree = new javax.swing.JTree();
+ infoScrollPane = new javax.swing.JScrollPane();
+ infoTextPane = new javax.swing.JEditorPane();
+ msgLabel = new javax.swing.JLabel();
+ msgPanel = new javax.swing.JTextArea();
+ bottomPane = new javax.swing.JPanel();
+ buttonPanel = new javax.swing.JPanel();
+ installDeleteButton = new javax.swing.JButton();
+ closeButton = new javax.swing.JButton();
+
+ getContentPane().setLayout(new java.awt.GridBagLayout());
+
+ setDefaultCloseOperation(javax.swing.WindowConstants.DISPOSE_ON_CLOSE);
+ jSplitPane2.setOrientation(javax.swing.JSplitPane.VERTICAL_SPLIT);
+ pnlSearch.setLayout(new java.awt.GridBagLayout());
+
+ topPane.setLayout(new java.awt.GridBagLayout());
+
+ sitePanel.setLayout(new java.awt.GridBagLayout());
+
+ tfSearch.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ tfSearchActionPerformed(evt);
+ }
+ });
+ tfSearch.addKeyListener(new java.awt.event.KeyAdapter() {
+ public void keyTyped(java.awt.event.KeyEvent evt) {
+ tfSearchKeyTyped(evt);
+ }
+ });
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = 3;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.weightx = 1.0;
+ sitePanel.add(tfSearch, gridBagConstraints);
+
+ btnSearch.setText("Search");
+ btnSearch.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ btnSearchActionPerformed(evt);
+ }
+ });
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 1;
+ gridBagConstraints.gridy = 3;
+ gridBagConstraints.insets = new java.awt.Insets(5, 10, 5, 10);
+ sitePanel.add(btnSearch, gridBagConstraints);
+
+ btnClear.setText("Clear");
+ btnClear.setPreferredSize(new java.awt.Dimension(67, 23));
+ btnClear.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ btnClearActionPerformed(evt);
+ }
+ });
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 2;
+ gridBagConstraints.gridy = 3;
+ gridBagConstraints.insets = new java.awt.Insets(0, 0, 0, 10);
+ sitePanel.add(btnClear, gridBagConstraints);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = 1;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.weightx = 0.2;
+ gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 0);
+ topPane.add(sitePanel, gridBagConstraints);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 0;
+ gridBagConstraints.gridy = 1;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.EAST;
+ gridBagConstraints.weightx = 1.0;
+ gridBagConstraints.insets = new java.awt.Insets(0, 0, 10, 0);
+ pnlSearch.add(topPane, gridBagConstraints);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 0;
+ gridBagConstraints.gridy = 2;
+ pnlSearch.add(downloadLocText, gridBagConstraints);
+
+ lbSearchTitle.setText("Enter key words to search");
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
+ gridBagConstraints.insets = new java.awt.Insets(0, 10, 0, 0);
+ pnlSearch.add(lbSearchTitle, gridBagConstraints);
+
+ jTabbedPane1.addTab("Search", pnlSearch);
+
+ pnlSettings.setLayout(new java.awt.GridBagLayout());
+
+ jLabel3.setText("Download sites");
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
+ gridBagConstraints.insets = new java.awt.Insets(10, 10, 5, 0);
+ pnlSettings.add(jLabel3, gridBagConstraints);
+
+ jPanel2.setLayout(new java.awt.GridBagLayout());
+
+ btnAddSite.setText("Add");
+ btnAddSite.setPreferredSize(new java.awt.Dimension(65, 23));
+ btnAddSite.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ btnAddSiteActionPerformed(evt);
+ }
+ });
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 0;
+ gridBagConstraints.gridy = 0;
+ gridBagConstraints.insets = new java.awt.Insets(5, 0, 0, 20);
+ jPanel2.add(btnAddSite, gridBagConstraints);
+
+ btnEditSite.setText("Edit");
+ btnEditSite.setPreferredSize(new java.awt.Dimension(65, 23));
+ btnEditSite.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ btnEditSiteActionPerformed(evt);
+ }
+ });
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 1;
+ gridBagConstraints.gridy = 0;
+ gridBagConstraints.insets = new java.awt.Insets(5, 0, 0, 20);
+ jPanel2.add(btnEditSite, gridBagConstraints);
+
+ btnDeleteSite.setText("Delete");
+ btnDeleteSite.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ btnDeleteSiteActionPerformed(evt);
+ }
+ });
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 2;
+ gridBagConstraints.gridy = 0;
+ gridBagConstraints.insets = new java.awt.Insets(5, 0, 0, 20);
+ jPanel2.add(btnDeleteSite, gridBagConstraints);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 0;
+ gridBagConstraints.gridy = 2;
+ gridBagConstraints.insets = new java.awt.Insets(0, 0, 5, 0);
+ pnlSettings.add(jPanel2, gridBagConstraints);
+
+ lstDownloadSites.setModel(new javax.swing.AbstractListModel() {
+ String[] strings = { "Item 1", "Item 2" };
+ public int getSize() { return strings.length; }
+ public Object getElementAt(int i) { return strings[i]; }
+ });
+ jScrollPane1.setViewportView(lstDownloadSites);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 0;
+ gridBagConstraints.gridy = 1;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.BOTH;
+ gridBagConstraints.weightx = 1.0;
+ gridBagConstraints.weighty = 1.0;
+ gridBagConstraints.insets = new java.awt.Insets(0, 10, 5, 10);
+ pnlSettings.add(jScrollPane1, gridBagConstraints);
+
+ jTabbedPane1.addTab("Settings", pnlSettings);
+
+ jSplitPane2.setLeftComponent(jTabbedPane1);
+
+ jPanel3.setLayout(new java.awt.GridBagLayout());
+
+ availablePluginsLabel.setText("Plugins available for download from:");
+ availablePluginsLabel.setEnabled(false);
+ availablePluginsLabel.setFocusable(false);
+ availablePluginsLabel.setInheritsPopupMenu(false);
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
+ gridBagConstraints.insets = new java.awt.Insets(10, 10, 5, 0);
+ jPanel3.add(availablePluginsLabel, gridBagConstraints);
+
+ versionCheck.setText("Show only plugins verified to work in this release");
+
+ versionCheck.setBorder(javax.swing.BorderFactory.createEmptyBorder(0, 0, 0, 0));
+ versionCheck.setMargin(new java.awt.Insets(0, 0, 0, 0));
+ versionCheck.addItemListener(new java.awt.event.ItemListener() {
+ public void itemStateChanged(java.awt.event.ItemEvent evt) {
+ versionCheckItemStateChanged(evt);
+ }
+ });
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 0;
+ gridBagConstraints.gridy = 1;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
+ gridBagConstraints.insets = new java.awt.Insets(5, 10, 5, 0);
+ jPanel3.add(versionCheck, gridBagConstraints);
+
+ jSplitPane1.setDividerLocation(250);
+ jSplitPane1.setPreferredSize(new java.awt.Dimension(400, 326));
+ treeScrollPane.setViewportView(pluginTree);
+
+ jSplitPane1.setLeftComponent(treeScrollPane);
+
+ infoScrollPane.setViewportView(infoTextPane);
+
+ jSplitPane1.setRightComponent(infoScrollPane);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = 2;
+ gridBagConstraints.gridwidth = 2;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.BOTH;
+ gridBagConstraints.weightx = 1.0;
+ gridBagConstraints.weighty = 1.0;
+ gridBagConstraints.insets = new java.awt.Insets(0, 10, 0, 10);
+ jPanel3.add(jSplitPane1, gridBagConstraints);
+
+ msgLabel.setText("Messages:");
+ msgLabel.setEnabled(false);
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 0;
+ gridBagConstraints.gridy = 3;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
+ gridBagConstraints.insets = new java.awt.Insets(10, 10, 5, 0);
+ jPanel3.add(msgLabel, gridBagConstraints);
+
+ msgPanel.setBackground(new java.awt.Color(230, 230, 230));
+ msgPanel.setColumns(20);
+ msgPanel.setEditable(false);
+ msgPanel.setLineWrap(true);
+ msgPanel.setRows(5);
+ msgPanel.setWrapStyleWord(true);
+ msgPanel.setMinimumSize(new java.awt.Dimension(30, 50));
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = 4;
+ gridBagConstraints.gridheight = 2;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.weightx = 1.0;
+ gridBagConstraints.insets = new java.awt.Insets(0, 10, 10, 20);
+ jPanel3.add(msgPanel, gridBagConstraints);
+
+ bottomPane.setLayout(new java.awt.GridBagLayout());
+
+ buttonPanel.setLayout(new java.awt.GridBagLayout());
+
+ installDeleteButton.setText("Install");
+ installDeleteButton.setEnabled(false);
+ installDeleteButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ installDeleteButtonActionPerformed(evt);
+ }
+ });
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.insets = new java.awt.Insets(10, 0, 10, 10);
+ buttonPanel.add(installDeleteButton, gridBagConstraints);
+
+ closeButton.setText("Close");
+ closeButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ closeButtonActionPerformed(evt);
+ }
+ });
+
+ buttonPanel.add(closeButton, new java.awt.GridBagConstraints());
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 1;
+ gridBagConstraints.gridy = 1;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.EAST;
+ gridBagConstraints.insets = new java.awt.Insets(0, 20, 0, 20);
+ bottomPane.add(buttonPanel, gridBagConstraints);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = 4;
+ jPanel3.add(bottomPane, gridBagConstraints);
+
+ jSplitPane2.setRightComponent(jPanel3);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.fill = java.awt.GridBagConstraints.BOTH;
+ gridBagConstraints.weightx = 1.0;
+ gridBagConstraints.weighty = 1.0;
+ getContentPane().add(jSplitPane2, gridBagConstraints);
+
+ pack();
+ }// </editor-fold>
+
+
+
+ private void btnDeleteSiteActionPerformed(java.awt.event.ActionEvent evt) {
+
+ DataSource theDataSource = (DataSource)this.lstDownloadSites.getSelectedValue();
+
+ if (theDataSource.getName().equalsIgnoreCase("Cytoscape")){
+ JOptionPane.showMessageDialog(this, "Your can not delete default Cytoscape site", "Warning", JOptionPane.WARNING_MESSAGE);
+ return;
+ }
+
+ int confirm = JOptionPane.showConfirmDialog(this,"Are you sure you want to " +
+ "delete this site","Delete Confirm",JOptionPane.OK_CANCEL_OPTION);
+
+ if (confirm == JOptionPane.OK_OPTION){
+ BookmarksUtil.deleteBookmark(theBookmarks, bookmarkCategory, theDataSource);
+ loadBookmarkCMBox(true); // reload is required to update the GUI
+ }
+
+ }
+
+ private void btnEditSiteActionPerformed(java.awt.event.ActionEvent evt) {
+
+ DataSource theDataSource = (DataSource) this.lstDownloadSites.getSelectedValue();
+ EditBookmarkDialog theEditDialog = new EditBookmarkDialog(this, true, theBookmarks,
+ bookmarkCategory, "edit", theDataSource);
+ theEditDialog.setLocationRelativeTo(this);
+
+ theEditDialog.setVisible(true);
+ loadBookmarkCMBox(true);
+
+ }
+
+ private void btnAddSiteActionPerformed(java.awt.event.ActionEvent evt) {
+ EditBookmarkDialog theNewDialog = new EditBookmarkDialog(this, true, theBookmarks,
+ bookmarkCategory, "new", null);
+ theNewDialog.setLocationRelativeTo(this);
+ theNewDialog.setVisible(true);
+ theNewDialog.getDataSource();
+ loadBookmarkCMBox(true); // reload is required to update the GUI
+ }
+
+
+ private void btnClearActionPerformed(java.awt.event.ActionEvent evt) {
+ this.switchToMainDialog();
+ this.tfSearch.setText("");
+ this.btnSearch.setEnabled(false);
+ this.versionCheck.setEnabled(true);
+ }
+
+ private void btnBackMainActionPerformed(java.awt.event.ActionEvent evt) {
+ // TODO add your handling code here:
+ }
+
+
+ // Disable btnSearch if there is no text in the Search textfield
+ private void tfSearchKeyTyped(java.awt.event.KeyEvent evt) {
+ if (this.tfSearch.getText().trim().equals("")){
+ this.btnSearch.setEnabled(false);
+ this.switchToMainDialog();
+ this.btnClear.setEnabled(false);
+ this.versionCheck.setEnabled(true);
+ }
+ else {
+ this.btnSearch.setEnabled(true);
+ this.btnClear.setEnabled(true);
+ this.versionCheck.setEnabled(false);
+ }
+ }
+
+ private void tfSearchActionPerformed(java.awt.event.ActionEvent evt) {
+ // Perform the same effect as the click of btnSearch
+ //System.out.println("Entered is pressed in search textField");
+ btnSearchActionPerformed(null);
+ }
+
+ private void btnSearchActionPerformed(java.awt.event.ActionEvent evt) {
+
+ try {
+ Vector filteredPluginVector = PluginIndex.getSearchResult(this.tfSearch.getText().trim(),!this.versionCheck.isSelected(), downloadLocText.getText());
+
+ if (filteredPluginVector == null){
+ // The index does not exist, build it now
+
+ //This will create new index for the AllPluginVector
+ PluginIndex.setAllPluginVector(this.getAllPluginVector(), !this.versionCheck.isSelected(), downloadLocText.getText());
+ // After the index is created, we can do searching against the index
+ filteredPluginVector = PluginIndex.getSearchResult(this.tfSearch.getText().trim(),!this.versionCheck.isSelected(), downloadLocText.getText());
+ }
+
+ updateTreeModel(filteredPluginVector);
+
+ //this.sitePanel.setVisible(false);
+ //this.sitePanel2.setVisible(true);
+ }
+ catch (Exception e){
+ e.printStackTrace();
+ JOptionPane.showMessageDialog(this, "Error in build index for PluginManager!");
+ }
+ }
+
+
+ /*
+ * --- create the tasks and task monitors to show the user what's going on
+ * during download/install ---
+ */
+
+ private void createInstallTask(DownloadableInfo obj, TreeNode node) {
+ // Create Task
+ InstallTask task = new InstallTask(obj, node);
+
+ // Configure JTask Dialog Pop-Up Box
+ JTaskConfig jTaskConfig = new JTaskConfig();
+ jTaskConfig.setOwner(Cytoscape.getDesktop());
+ jTaskConfig.displayCloseButton(false);
+ jTaskConfig.displayStatus(true);
+ jTaskConfig.setAutoDispose(true);
+ jTaskConfig.displayCancelButton(true);
+ // Execute Task in New Thread; pop open JTask Dialog Box.
+ TaskManager.executeTask(task, jTaskConfig);
+ DownloadableInfo info = task.getDownloadedPlugin();
+ if (info != null) {
+ updateCurrent(info);
+ cleanTree(node);
+ } else {
+ // TODO somehow disable the node??
+ }
+ }
+
+ private void cleanTree(TreeNode node) {
+ DownloadableInfo info = (DownloadableInfo) node.getObject();
+ List<TreeNode> RemovableNodes = new java.util.ArrayList<TreeNode>();
+
+ for (int i = 0; i < node.getParent().getChildCount(); i++) {
+ TreeNode Child = (TreeNode) node.getParent().getChildAt(i);
+ DownloadableInfo childInfo = (DownloadableInfo) Child.getObject();
+
+ if (childInfo.getID().equals(info.getID())
+ && childInfo.getName().equals(info.getName())) {
+ RemovableNodes.add(Child);
+ }
+ }
+
+ for (TreeNode treeNode : RemovableNodes) {
+ treeModel.removeNodeFromParent(treeNode);
+ }
+ }
+
+
+ /** Returns an ImageIcon, or null if the path was invalid. */
+ private javax.swing.ImageIcon createImageIcon(String path,
+ String description) {
+ java.net.URL imgURL = getClass().getResource(path);
+ if (imgURL != null) {
+ return new javax.swing.ImageIcon(imgURL, description);
+ } else {
+ CyLogger.getLogger().warn("Couldn't find file: " + path);
+ return null;
+ }
+ }
+
+ private class InstallTask implements cytoscape.task.Task {
+ private cytoscape.task.TaskMonitor taskMonitor;
+
+ private DownloadableInfo infoObj;
+
+ private TreeNode node;
+
+ public InstallTask(DownloadableInfo Info, TreeNode Node)
+ throws java.lang.IllegalArgumentException {
+ String ErrorMsg = null;
+ if (Info == null) {
+ ErrorMsg = "DownloadableInfo object cannot be null\n";
+ throw new java.lang.IllegalArgumentException(ErrorMsg);
+ }
+ infoObj = Info;
+ node = Node;
+ }
+
+ public void run() {
+ if (taskMonitor == null) {
+ throw new IllegalStateException("Task Monitor is not set.");
+ }
+ taskMonitor.setStatus("Installing " + infoObj.getName() + " v"
+ + infoObj.getObjectVersion());
+ taskMonitor.setPercentCompleted(-1);
+
+ PluginManager Mgr = PluginManager.getPluginManager();
+ cytoscape.plugin.Installable ins = infoObj.getInstallable();
+ try {
+ infoObj = Mgr.download(infoObj, taskMonitor);
+ taskMonitor.setStatus(infoObj.getName() + " v"
+ + infoObj.getObjectVersion() + " download complete.");
+
+ PluginManageDialog.this.setMessage(infoObj.toString()
+ + " download complete.");
+
+ taskMonitor.setStatus(infoObj.toString() + " installing...");
+
+ Mgr.install(infoObj);
+ Mgr.loadPlugin(infoObj);
+
+ if ( Mgr.getLoadingErrors().size() > 0 ) {
+ // since we're only loading one plugin, presumably there will only
+ // be one throwable...
+ Throwable t = Mgr.getLoadingErrors().get(0);
+ Mgr.clearErrorList();
+ throw new PluginException("Failed to load plugin: " + infoObj.toString(),t);
+ }
+
+ taskMonitor.setStatus(infoObj.toString() + " install complete.");
+
+ } catch (java.io.IOException ioe) {
+ taskMonitor.setException(ioe, "Failed to download "
+ + infoObj.getName() + " from "
+ + infoObj.getObjectUrl());
+ logger.warn("Failed to download "
+ + infoObj.getName() + " from "
+ + infoObj.getObjectUrl(), ioe);
+ infoObj = null;
+ } catch (ManagerException me) {
+ PluginManageDialog.this.setError("Failed to install " + infoObj.toString());
+ logger.warn("Failed to install " + infoObj.toString(), me);
+ taskMonitor.setException(me, me.getMessage());
+ infoObj = null;
+ } catch (PluginException pe) {
+ PluginManageDialog.this.setError("Failed to install " + infoObj.toString());
+ logger.warn("Failed to install " + infoObj.toString(), pe);
+ taskMonitor.setException(pe, pe.getMessage());
+ infoObj = null;
+ } catch (ClassNotFoundException cne) {
+ PluginManageDialog.this.setError("Failed to install " + infoObj.toString());
+ logger.warn("Failed to install " + infoObj.toString(), cne);
+ taskMonitor.setException(cne, cne.getMessage());
+ infoObj = null;
+ } finally {
+ taskMonitor.setPercentCompleted(100);
+ }
+
+ try {
+ if (infoObj == null)
+ ins.uninstall();
+ } catch (ManagerException me) {
+ logger.warn("Failed to cleanup after installation failure", me);
+ }
+
+ }
+
+ public DownloadableInfo getDownloadedPlugin() {
+ return infoObj;
+ }
+
+ public void halt() {
+ // not haltable
+ }
+
+ public void setTaskMonitor(TaskMonitor monitor)
+ throws IllegalThreadStateException {
+ this.taskMonitor = monitor;
+ }
+
+ public String getTitle() {
+ return "Installing Cytoscape " + infoObj.getType().name() + " '" + infoObj.getName() + "'";
+ }
+
+ }
+
+ // Variables declaration - do not modify
+ private javax.swing.JLabel availablePluginsLabel;
+ private javax.swing.JPanel bottomPane;
+ private javax.swing.JButton btnAddSite;
+ private javax.swing.JButton btnClear;
+ private javax.swing.JButton btnDeleteSite;
+ private javax.swing.JButton btnEditSite;
+ private javax.swing.JButton btnSearch;
+ private javax.swing.JPanel buttonPanel;
+ private javax.swing.JButton closeButton;
+ private javax.swing.JLabel downloadLocText;
+ private javax.swing.JScrollPane infoScrollPane;
+ private javax.swing.JEditorPane infoTextPane;
+ private javax.swing.JButton installDeleteButton;
+ private javax.swing.JLabel jLabel3;
+ private javax.swing.JPanel jPanel2;
+ private javax.swing.JPanel jPanel3;
+ private javax.swing.JScrollPane jScrollPane1;
+ private javax.swing.JSplitPane jSplitPane1;
+ private javax.swing.JSplitPane jSplitPane2;
+ private javax.swing.JTabbedPane jTabbedPane1;
+ private javax.swing.JLabel lbSearchTitle;
+ private javax.swing.JList lstDownloadSites;
+ private javax.swing.JLabel msgLabel;
+ private javax.swing.JTextArea msgPanel;
+ private javax.swing.JTree pluginTree;
+ private javax.swing.JPanel pnlSearch;
+ private javax.swing.JPanel pnlSettings;
+ private javax.swing.JPanel sitePanel;
+ private javax.swing.JTextField tfSearch;
+ private javax.swing.JPanel topPane;
+ private javax.swing.JScrollPane treeScrollPane;
+ private javax.swing.JCheckBox versionCheck;
+ // End of variables declaration
+
+ private TreeNode rootTreeNode;
+ private TreeNode installedNode;
+ private TreeNode availableNode;
+ private ManagerModel treeModel;
+ private TreeCellRenderer treeRenderer;
+ private java.util.HashMap<TreeNode, java.util.List<TreeNode>> hiddenNodes;
+
+
+ // loads the combo box for bookmarks
+ private void loadBookmarkCMBox(boolean selectLast) {
+ DefaultComboBoxModel theModel = new DefaultComboBoxModel();
+
+ // Extract the URL entries
+ List<DataSource> theDataSourceList = BookmarksUtil.getDataSourceList(
+ bookmarkCategory, theBookmarks.getCategory());
+
+ if (theDataSourceList != null) {
+ for (DataSource Current : theDataSourceList) {
+ theModel.addElement(Current);
+ if (selectLast)
+ theModel.setSelectedItem(Current);
+ }
+ }
+
+ this.lstDownloadSites.setModel(theModel);
+ }
+
+ private String bookmarkCategory = "plugins";
+ private Bookmarks theBookmarks;
+ /*
+ * Sets up the bookmarks for plugin download sites
+ */
+ private void bookmarksSetUp() {
+ try {
+ theBookmarks = Cytoscape.getBookmarks();
+ } catch (Exception E) {
+ JOptionPane.showMessageDialog(Cytoscape.getDesktop(),
+ "Failed to retrieve bookmarks for plugin download sites.",
+ "Error", JOptionPane.ERROR_MESSAGE);
+ logger.warn("Failed to retrieve bookmarks for plugin download sites.", E);
+
+ return;
+ }
+
+ // if theBookmarks does not exist, create an empty one
+ if (theBookmarks == null) {
+ theBookmarks = new Bookmarks();
+ Cytoscape.setBookmarks(theBookmarks);
+ }
+
+ }
+
+ private static final Color HIGHLIGHT_COLOR = new Color(0, 0, 128);
+
+ // required to make the text of the data source show up correctly in the
+ // combo box
+ private class BookmarkCellRenderer extends JLabel implements
+ ListCellRenderer {
+
+ public BookmarkCellRenderer() {
+ setOpaque(true);
+ }
+
+ public Component getListCellRendererComponent(JList list, Object value,
+ int index, boolean isSelected, boolean cellHasFocus) {
+ DataSource dataSource = (DataSource) value;
+ setText(dataSource.getName());
+
+ setToolTipText(dataSource.getHref());
+
+ if (isSelected) {
+ setBackground(HIGHLIGHT_COLOR);
+ setForeground(Color.white);
+ } else {
+ setBackground(Color.white);
+ setForeground(Color.black);
+ }
+
+ return this;
+ }
+ }
+
+
+ private class MyListSelectionListener implements ListSelectionListener {
+
+ private int clickCount =0;
+
+ public void valueChanged(ListSelectionEvent ev){
+ clickCount++;
+
+ JList list = (JList) ev.getSource();
+ if (list.getSelectedIndices().length == 0){
+ // If nothing is selected, disable Edit/Delete button
+ PluginManageDialog.this.btnEditSite.setEnabled(false);
+ PluginManageDialog.this.btnDeleteSite.setEnabled(false);
+ return;
+ }
+
+ if (clickCount % 2 == 0){
+ //This is a work-around to handle two events -- from mouse press and mouse release
+ // Reset the click counter
+ clickCount = 0;
+ return;
+ }
+
+ DataSource dataSource = (DataSource) list.getSelectedValue();
+
+ if (dataSource.getName().equalsIgnoreCase("Cytoscape")){
+ // Cytoscape is the default site, user should never edit/delete it
+ PluginManageDialog.this.btnEditSite.setEnabled(false);
+ PluginManageDialog.this.btnDeleteSite.setEnabled(false);
+ }
+ else {
+ PluginManageDialog.this.btnEditSite.setEnabled(true);
+ PluginManageDialog.this.btnDeleteSite.setEnabled(true);
+ }
+
+ //If download site is changed, update the plugin tree
+ String urlStr = dataSource.getHref();
+ if (!PluginManageDialog.this.currentPluginSiteURL.equalsIgnoreCase(urlStr)){
+ PluginManageDialog.this.currentPluginSiteURL = urlStr;
+ PluginManageDialog.this.refreshPluginTree();
+ }
+ }
+ }
+
+
+ public static void main(String[] args) {
+ PluginManageDialog pd = new PluginManageDialog();
+ //pd.setSiteName("Testing");
+ List<DownloadableInfo> Plugins = new java.util.ArrayList<DownloadableInfo>();
+
+ PluginInfo infoC = new PluginInfo("1", "A Plugin");
+ infoC.addCytoscapeVersion(cytoscape.CytoscapeVersion.version);
+ Plugins.add(infoC);
+
+ infoC = new PluginInfo("2", "B Plugin");
+ infoC.addCytoscapeVersion(cytoscape.CytoscapeVersion.version);
+ Plugins.add(infoC);
+
+ infoC = new PluginInfo("3", "C");
+ infoC.addCytoscapeVersion(cytoscape.CytoscapeVersion.version);
+ Plugins.add(infoC);
+
+ pd.addCategory(cytoscape.plugin.Category.NONE.toString(), Plugins,
+ PluginInstallStatus.AVAILABLE);
+
+ List<DownloadableInfo> Outdated = new java.util.ArrayList<DownloadableInfo>();
+
+ PluginInfo infoOD = new PluginInfo("11", "CyGoose");
+ infoOD.addCytoscapeVersion("2.3");
+ Outdated.add(infoOD);
+
+ infoOD = new PluginInfo("12", "Y");
+ infoOD.addCytoscapeVersion("2.3");
+ Outdated.add(infoOD);
+
+ pd.addCategory("Outdated", Outdated, PluginInstallStatus.AVAILABLE);
+
+ pd.setMessage("Foo bar");
+
+ pd.setVisible(true);
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/dialogs/plugins/PluginUpdateDialog.java b/application/src/main/java/cytoscape/dialogs/plugins/PluginUpdateDialog.java
new file mode 100644
index 0000000..966019e
--- /dev/null
+++ b/application/src/main/java/cytoscape/dialogs/plugins/PluginUpdateDialog.java
@@ -0,0 +1,447 @@
+package cytoscape.dialogs.plugins;
+
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import javax.swing.JDialog;
+import javax.swing.JOptionPane;
+import javax.swing.tree.TreeSelectionModel;
+import javax.swing.event.TreeSelectionEvent;
+import javax.swing.event.TreeSelectionListener;
+
+import cytoscape.Cytoscape;
+import cytoscape.logger.CyLogger;
+import cytoscape.plugin.DownloadableInfo;
+import cytoscape.plugin.PluginInfo;
+import cytoscape.plugin.ThemeInfo;
+import cytoscape.plugin.PluginManager;
+
+import cytoscape.task.Task;
+import cytoscape.task.TaskMonitor;
+import cytoscape.task.ui.JTaskConfig;
+import cytoscape.task.util.TaskManager;
+
+// TODO clean out the tree for each updated plugin
+
+public class PluginUpdateDialog extends JDialog implements
+ TreeSelectionListener {
+ private static String title = "Update Plugins";
+ private static CyLogger logger = CyLogger.getLogger(PluginUpdateDialog.class);
+
+ public PluginUpdateDialog(javax.swing.JDialog owner) {
+ super(owner, title);
+ setLocationRelativeTo(owner);
+ initComponents();
+ initTree();
+ }
+
+ public PluginUpdateDialog(javax.swing.JFrame owner) {
+ super(owner, title);
+ setLocationRelativeTo(owner);
+ initComponents();
+ initTree();
+ }
+
+ /**
+ * Enables the delete/install buttons when the correct leaf node is selected
+ */
+ public void valueChanged(TreeSelectionEvent e) {
+ infoTextPane.setContentType("text/html");
+ javax.swing.tree.TreePath[] Paths = pluginTree.getSelectionPaths();
+ if (Paths == null) {
+ updateSelectedButton.setEnabled(false);
+ return;
+ }
+
+ if (Paths.length == 0) {
+ updateSelectedButton.setEnabled(false);
+ }
+
+ for (int i = 0; i < Paths.length; i++) {
+ TreeNode LastSelectedNode = (TreeNode) Paths[i]
+ .getLastPathComponent();
+
+ if (LastSelectedNode.isLeaf()) {
+ PluginInfo New = (PluginInfo) LastSelectedNode.getObject();
+
+ infoTextPane.setText(New.htmlOutput());
+ updateSelectedButton.setEnabled(true);
+ } else if (LastSelectedNode.getObject() != null
+ && LastSelectedNode.getObject().getClass().equals(
+ PluginInfo.class)) {
+ PluginInfo NodeInfo = (PluginInfo) LastSelectedNode.getObject();
+ infoTextPane.setText(NodeInfo.htmlOutput());
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME
+ *
+ * @param CategoryName
+ * @param Plugins
+ * @param Status
+ */
+ public void addCategory(String CategoryName, DownloadableInfo CurrentPlugin,
+ List<DownloadableInfo> NewPlugins) {
+ TreeNode Category = new TreeNode(CategoryName, true);
+ treeModel.addNodeToParent(rootTreeNode, Category);
+
+ TreeNode CurrentPluginNode = new TreeNode(CurrentPlugin, true);
+ treeModel.addNodeToParent(Category, CurrentPluginNode);
+
+ for (DownloadableInfo New : NewPlugins) {
+ treeModel.addNodeToParent(CurrentPluginNode, new TreeNode(New));
+ }
+ }
+
+ /**
+ *
+ * @param Msg
+ */
+ public void setMessage(String Msg) {
+ msgLabel.setText(Msg);
+ }
+
+ // update for single selections
+ private void updateSelectedButtonActionPerformed(
+ java.awt.event.ActionEvent evt) {
+ Set<TreeNode> AllParents = new java.util.HashSet<TreeNode>();
+
+ javax.swing.tree.TreePath[] Paths = pluginTree.getSelectionPaths();
+ Map<DownloadableInfo, DownloadableInfo> UpdatableObjs = new java.util.HashMap<DownloadableInfo, DownloadableInfo>();
+
+ // first make sure each node only has one option picked
+ String Msg = "Please choose just one update option for the following plugins:\n";
+ boolean TooManyChildren = false;
+ for (javax.swing.tree.TreePath Path : Paths) {
+ TreeNode Node = (TreeNode) Path.getLastPathComponent();
+ TreeNode Parent = Node.getParent();
+
+ if (AllParents.contains(Parent)) {
+ Msg += Parent.toString() + "\n";
+ TooManyChildren = true;
+ } else {
+ AllParents.add(Parent);
+ UpdatableObjs.put(Parent.getObject(), Node.getObject());
+ treeModel.removeNodeFromParent(Node);
+ }
+ }
+ if (TooManyChildren) {
+ JOptionPane.showMessageDialog(this, Msg,
+ "Warning: Too many updates selected",
+ JOptionPane.WARNING_MESSAGE);
+ return;
+ }
+
+ // run the update
+ List<DownloadableInfo[]> Updatable = getUpdateList(UpdatableObjs);
+ createUpdateTask(Updatable);
+
+ setMessage("Update will complete when Cytoscape is restarted.");
+ }
+
+ // close dialog
+ private void closeButtonActionPerformed(java.awt.event.ActionEvent evt) {
+ dispose();
+ }
+
+ private void updateAllButtonActionPerformed(java.awt.event.ActionEvent evt) {
+ if (JOptionPane
+ .showConfirmDialog(
+ this,
+ "All plugins will be updated to the newest available version.\n"
+ + "If you wish to choose a different version please press \"No\" then\n"
+ + "choose each version and \"Update Selected Plugins\"",
+ "Warning", JOptionPane.YES_NO_OPTION) == JOptionPane.NO_OPTION) {
+ return;
+ }
+
+ Map<DownloadableInfo, DownloadableInfo> UpdateableObjs = new java.util.HashMap<DownloadableInfo, DownloadableInfo>();
+ Set<TreeNode> RemovableNodes = new java.util.HashSet<TreeNode>();
+
+ List<TreeNode> Leaves = recursiveReadTree(rootTreeNode);
+ for (TreeNode Node : Leaves) {
+ TreeNode Parent = Node.getParent();
+
+ if (Parent.getChildCount() > 1) { // multiple possible updates
+ DownloadableInfo LastInfoObj = null;
+ for (TreeNode Sib : Parent.getChildren()) {
+ DownloadableInfo CurrentInfoObj = Sib.getObject();
+ if (LastInfoObj == null
+ || LastInfoObj.isNewerObjectVersion(CurrentInfoObj))
+ UpdateableObjs.put(Parent.getObject(), CurrentInfoObj);
+ LastInfoObj = CurrentInfoObj;
+ }
+ } else {
+ UpdateableObjs.put(Parent.getObject(), Node.getObject());
+ }
+ RemovableNodes.add(Parent);
+ }
+ List<DownloadableInfo[]> ObjToUpdate = getUpdateList(UpdateableObjs);
+ createUpdateTask(ObjToUpdate);
+
+ for (TreeNode Node : RemovableNodes) {
+ treeModel.removeNodeFromParent(Node);
+ }
+
+ setMessage("Update will complete when Cytoscape is restarted.");
+ }
+
+ /**
+ * Show licenses if required, add all plugins to be updated to list.
+ *
+ * @param PotentialUpdates
+ * Key: Current plugin, Value: New plugin
+ * @return List <PluginInfo[]{Old, New}>
+ */
+ private List<DownloadableInfo[]> getUpdateList(
+ java.util.Map<DownloadableInfo, DownloadableInfo> PotentialUpdates) {
+ final List<DownloadableInfo[]> Updates = new java.util.ArrayList<DownloadableInfo[]>();
+
+ // display licenses, set up the list of objects to be updated
+ for (DownloadableInfo Original : PotentialUpdates.keySet()) {
+ final DownloadableInfo Old = (DownloadableInfo) Original;
+ final DownloadableInfo New = (DownloadableInfo) PotentialUpdates.get(Old);
+ final LicenseDialog ld = new LicenseDialog();
+ boolean showLicense = false;
+ // display only if always required at update
+ switch (New.getType()) {
+ case PLUGIN:
+ if (New.isLicenseRequired() && New.getLicenseText() != null) {
+ ld.addPlugin(New);
+ showLicense = true;
+ }
+ break;
+ case THEME:
+ ThemeInfo themeInfo = (ThemeInfo) New;
+ for (PluginInfo pInfo: themeInfo.getPlugins()) {
+ if (pInfo.isLicenseRequired() && pInfo.getLicenseText() != null) {
+ ld.addPlugin(pInfo);
+ showLicense = true;
+ }
+ }
+ break;
+ case FILE: // there is currently not a FileInfo object
+ break;
+ }
+
+ if (showLicense) {
+ ld.addListenerToOk(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ Updates.add(new DownloadableInfo[] { Old, New });
+ ld.dispose();
+ }
+ });
+ ld.selectDefault();
+ ld.setVisible(true);
+ } else {
+ Updates.add(new DownloadableInfo[] { Old, New });
+ }
+ }
+ return Updates;
+ }
+
+ private List<TreeNode> recursiveReadTree(TreeNode Node) {
+ List<TreeNode> LeafNodes = new java.util.ArrayList<TreeNode>();
+ for (TreeNode Child : Node.getChildren()) {
+ if (!Child.isLeaf()) {
+ List<TreeNode> DeeperNodes = recursiveReadTree(Child);
+ LeafNodes.addAll(DeeperNodes);
+ } else {
+ LeafNodes.add(Child);
+ }
+ }
+ return LeafNodes;
+ }
+
+ // sets up the swing stuff
+ private void initTree() {
+ rootTreeNode = new TreeNode("Updatable Plugins", true);
+
+ pluginTree.addTreeSelectionListener(this);
+ pluginTree.getSelectionModel().setSelectionMode(
+ TreeSelectionModel.DISCONTIGUOUS_TREE_SELECTION);
+
+ treeModel = new ManagerModel(rootTreeNode);
+ pluginTree.setModel(treeModel);
+ }
+
+ /** This method is called from within the constructor to
+ * initialize the form.
+ * WARNING: Do NOT modify this code. The content of this method is
+ * always regenerated by the Form Editor.
+ */
+ // <editor-fold defaultstate="collapsed" desc=" Generated Code ">
+ private void initComponents() {
+ jSplitPane1 = new javax.swing.JSplitPane();
+ infoScrollPane = new javax.swing.JScrollPane();
+ infoTextPane = new javax.swing.JEditorPane();
+ treeScrollPane = new javax.swing.JScrollPane();
+ pluginTree = new javax.swing.JTree();
+ updateLabel = new javax.swing.JLabel();
+ updateAllButton = new javax.swing.JButton();
+ updateSelectedButton = new javax.swing.JButton();
+ closeButton = new javax.swing.JButton();
+ msgLabel = new javax.swing.JLabel();
+
+ setDefaultCloseOperation(javax.swing.WindowConstants.DISPOSE_ON_CLOSE);
+ jSplitPane1.setDividerLocation(250);
+ infoScrollPane.setViewportView(infoTextPane);
+
+ jSplitPane1.setRightComponent(infoScrollPane);
+
+ treeScrollPane.setViewportView(pluginTree);
+
+ jSplitPane1.setLeftComponent(treeScrollPane);
+
+ updateLabel.setLabelFor(jSplitPane1);
+ updateLabel.setText("Listed are updates available for currently installed plugins");
+ updateLabel.setVerticalAlignment(javax.swing.SwingConstants.TOP);
+
+ updateAllButton.setText("Update All");
+ updateAllButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ updateAllButtonActionPerformed(evt);
+ }
+ });
+
+ updateSelectedButton.setText("Update Selected");
+ updateSelectedButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ updateSelectedButtonActionPerformed(evt);
+ }
+ });
+
+ closeButton.setText("Close");
+ closeButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ closeButtonActionPerformed(evt);
+ }
+ });
+
+ msgLabel.setForeground(java.awt.Color.BLACK);
+ //msgLabel.setForeground(new java.awt.Color(204, 0, 51));
+ msgLabel.setVerticalAlignment(javax.swing.SwingConstants.TOP);
+
+ org.jdesktop.layout.GroupLayout layout = new org.jdesktop.layout.GroupLayout(getContentPane());
+ getContentPane().setLayout(layout);
+ layout.setHorizontalGroup(
+ layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(layout.createSequentialGroup()
+ .add(43, 43, 43)
+ .add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.TRAILING)
+ .add(org.jdesktop.layout.GroupLayout.LEADING, updateLabel, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 574, Short.MAX_VALUE)
+ .add(org.jdesktop.layout.GroupLayout.LEADING, jSplitPane1, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 574, Short.MAX_VALUE)
+ .add(org.jdesktop.layout.GroupLayout.LEADING, msgLabel, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 574, Short.MAX_VALUE))
+ .add(41, 41, 41))
+ .add(org.jdesktop.layout.GroupLayout.TRAILING, layout.createSequentialGroup()
+ .addContainerGap(272, Short.MAX_VALUE)
+ .add(updateAllButton)
+ .add(18, 18, 18)
+ .add(updateSelectedButton)
+ .add(22, 22, 22)
+ .add(closeButton)
+ .add(50, 50, 50))
+ );
+ layout.setVerticalGroup(
+ layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(layout.createSequentialGroup()
+ .addContainerGap()
+ .add(updateLabel, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE, 32, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(jSplitPane1, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 324, Short.MAX_VALUE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(msgLabel, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 33, Short.MAX_VALUE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE)
+ .add(updateAllButton)
+ .add(updateSelectedButton)
+ .add(closeButton))
+ .addContainerGap())
+ );
+ pack();
+ }// </editor-fold>
+
+ private void createUpdateTask(List<DownloadableInfo[]> UpdateObjs) {
+ // Create Task
+ Task task = new PluginUpdateTask(UpdateObjs);
+
+ // Configure JTask Dialog Pop-Up Box
+ JTaskConfig jTaskConfig = new JTaskConfig();
+ jTaskConfig.setOwner(Cytoscape.getDesktop());
+ jTaskConfig.displayCloseButton(false);
+ jTaskConfig.displayStatus(true);
+ jTaskConfig.setAutoDispose(true);
+ jTaskConfig.displayCancelButton(true);
+ // Execute Task in New Thread; pop open JTask Dialog Box.
+ TaskManager.executeTask(task, jTaskConfig);
+ }
+
+ private class PluginUpdateTask implements cytoscape.task.Task {
+ private cytoscape.task.TaskMonitor taskMonitor;
+
+ private List<DownloadableInfo[]> toUpdate;
+
+ public PluginUpdateTask(List<DownloadableInfo[]> Updates) {
+ toUpdate = Updates;
+ }
+
+ public void run() {
+ if (taskMonitor == null) {
+ throw new IllegalStateException("Task Monitor is not set.");
+ }
+ taskMonitor.setStatus("Updating...");
+ taskMonitor.setPercentCompleted(-1);
+
+ PluginManager Mgr = PluginManager.getPluginManager();
+
+ for (DownloadableInfo[] UpdatePair : toUpdate) {
+ taskMonitor.setStatus("Updating " + UpdatePair[0].getName()
+ + " to version " + UpdatePair[1].getObjectVersion());
+ try {
+ Mgr.update(UpdatePair[0], UpdatePair[1], taskMonitor);
+ } catch (java.io.IOException ioe) {
+ taskMonitor.setException(ioe, "Failed to download "
+ + UpdatePair[1].getName());
+ } catch (cytoscape.plugin.ManagerException me) {
+ JOptionPane.showMessageDialog(PluginUpdateDialog.this, me
+ .getMessage(), "Error", JOptionPane.ERROR_MESSAGE);
+ } catch (cytoscape.plugin.WebstartException we) {
+ logger.warn("Unable to update '"+UpdatePair[1].getName()+"': "+we.getMessage(), we);
+ }
+ }
+ taskMonitor.setPercentCompleted(100);
+ }
+
+ public void halt() {
+ // not haltable
+ }
+
+ public void setTaskMonitor(TaskMonitor monitor)
+ throws IllegalThreadStateException {
+ this.taskMonitor = monitor;
+ }
+
+ public String getTitle() {
+ return "Updating Plugins";
+ }
+
+ }
+
+ // Variables declaration - do not modify
+ private javax.swing.JButton closeButton;
+ private javax.swing.JScrollPane infoScrollPane;
+ private javax.swing.JEditorPane infoTextPane;
+ private javax.swing.JSplitPane jSplitPane1;
+ private javax.swing.JLabel msgLabel;
+ private javax.swing.JTree pluginTree;
+ private javax.swing.JScrollPane treeScrollPane;
+ private javax.swing.JButton updateAllButton;
+ private javax.swing.JLabel updateLabel;
+ private javax.swing.JButton updateSelectedButton;
+ private TreeNode rootTreeNode;
+ private ManagerModel treeModel;
+ // End of variables declaration
+}
diff --git a/application/src/main/java/cytoscape/dialogs/plugins/PluginUrlDialog.java b/application/src/main/java/cytoscape/dialogs/plugins/PluginUrlDialog.java
new file mode 100644
index 0000000..81c188e
--- /dev/null
+++ b/application/src/main/java/cytoscape/dialogs/plugins/PluginUrlDialog.java
@@ -0,0 +1,414 @@
+/**
+ *
+ */
+package cytoscape.dialogs.plugins;
+
+import cytoscape.*;
+
+import cytoscape.bookmarks.Bookmarks;
+//import cytoscape.bookmarks.Category;
+import cytoscape.bookmarks.DataSource;
+
+import cytoscape.dialogs.preferences.BookmarkDialog;
+
+import cytoscape.logger.CyLogger;
+import cytoscape.plugin.DownloadableInfo;
+//import cytoscape.plugin.DownloadableType;
+//import cytoscape.plugin.ManagerException;
+import cytoscape.plugin.ManagerUtil;
+//import cytoscape.plugin.PluginInfo;
+import cytoscape.plugin.PluginManager;
+import cytoscape.plugin.PluginInquireAction;
+import cytoscape.plugin.PluginStatus;
+import cytoscape.plugin.PluginManagerInquireTask;
+
+import cytoscape.task.ui.JTaskConfig;
+import cytoscape.task.util.TaskManager;
+import cytoscape.util.BookmarksUtil;
+
+import org.jdesktop.layout.GroupLayout;
+import org.jdesktop.layout.LayoutStyle;
+
+import java.awt.Component;
+//import java.awt.Dimension;
+
+import java.util.List;
+import java.util.Map;
+
+import javax.swing.DefaultComboBoxModel;
+import javax.swing.JButton;
+import javax.swing.JComboBox;
+import javax.swing.JDialog;
+//import javax.swing.JFrame;
+import javax.swing.JLabel;
+import javax.swing.JList;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.ListCellRenderer;
+import javax.swing.WindowConstants;
+
+/**
+ * @author skillcoy
+ */
+public class PluginUrlDialog extends JDialog {
+ private String bookmarkCategory = "plugins";
+
+ private Bookmarks theBookmarks;
+
+ private PluginManageDialog parentDialog;
+
+ private static CyLogger logger = CyLogger.getLogger(PluginUrlDialog.class);
+
+ /**
+ * Creates a new PluginUrlDialog object.
+ */
+ public PluginUrlDialog(JDialog owner) {
+ super(owner, "Plugin Download Sites");
+ parentDialog = (PluginManageDialog) owner;
+ setLocationRelativeTo(owner);
+ bookmarksSetUp();
+ initComponents();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param Items
+ * DOCUMENT ME!
+ */
+ public void addItems(String[] Items) {
+ urlComboBox.setModel(new javax.swing.DefaultComboBoxModel(Items));
+ }
+
+ /*
+ * Sets up the bookmarks for plugin dowload sites
+ */
+ private void bookmarksSetUp() {
+ try {
+ theBookmarks = Cytoscape.getBookmarks();
+ } catch (Exception E) {
+ JOptionPane.showMessageDialog(Cytoscape.getDesktop(),
+ "Failed to retrieve bookmarks for plugin download sites.",
+ "Error", JOptionPane.ERROR_MESSAGE);
+ logger.warn("Failed to retrieve bookmarks for plugin download sites.", E);
+
+ return;
+ }
+
+ // if theBookmarks does not exist, create an empty one
+ if (theBookmarks == null) {
+ theBookmarks = new Bookmarks();
+ Cytoscape.setBookmarks(theBookmarks);
+ }
+
+ }
+
+ // ok - chooses a site. Needs to reopen the InstallDialog using new url for
+ // the manager inquiry
+ private void okHandler(java.awt.event.ActionEvent evt) {
+ DataSource SelectedSite = (DataSource) urlComboBox.getSelectedItem();
+ parentDialog.switchDownloadSites();
+ dispose();
+
+ cytoscape.task.Task task = new PluginManagerInquireTask
+ (SelectedSite.getHref(), new UrlAction(parentDialog, SelectedSite.getHref()));
+ // Configure JTask Dialog Pop-Up Box
+ JTaskConfig jTaskConfig = new JTaskConfig();
+ jTaskConfig.setOwner(Cytoscape.getDesktop());
+ jTaskConfig.displayCloseButton(false);
+ jTaskConfig.displayStatus(true);
+ jTaskConfig.setAutoDispose(true);
+ jTaskConfig.displayCancelButton(true);
+ // Execute Task in New Thread; pop open JTask Dialog Box.
+ TaskManager.executeTask(task, jTaskConfig);
+
+
+ parentDialog.setSiteName(SelectedSite.getName());
+ }
+
+ // add - opens the bookmarks dialog to add a new download site
+ private void addSiteHandler(java.awt.event.ActionEvent evt) {
+ try {
+ final int preEdit = BookmarksUtil.getDataSourceList(
+ bookmarkCategory, theBookmarks.getCategory()).size();
+
+ BookmarkDialog bDialog = new BookmarkDialog(Cytoscape.getDesktop(), "plugins");
+
+ /* for some reason the windowStateListener wasn't getting the event
+ so I have to use this one this allows me to update the combo
+ box when the user is done adding */
+ bDialog.addWindowListener(new java.awt.event.WindowListener() {
+ public void windowClosed(java.awt.event.WindowEvent evt) {
+ int postEdit = BookmarksUtil.getDataSourceList(
+ bookmarkCategory, theBookmarks.getCategory()).size();
+
+ if (preEdit >= postEdit)
+ loadBookmarkCMBox(false);
+ else loadBookmarkCMBox(true);
+ }
+
+ public void windowOpened(java.awt.event.WindowEvent evt) {
+ }
+
+ public void windowDeiconified(java.awt.event.WindowEvent evt) {
+ }
+
+ public void windowIconified(java.awt.event.WindowEvent evt) {
+ }
+
+ public void windowClosing(java.awt.event.WindowEvent evt) {
+ }
+
+ public void windowDeactivated(java.awt.event.WindowEvent evt) {
+ }
+
+ public void windowActivated(java.awt.event.WindowEvent evt) {
+ }
+ });
+ bDialog.pack();
+ bDialog.setVisible(true);
+ } catch (Exception E) {
+ JOptionPane
+ .showMessageDialog(
+ Cytoscape.getDesktop(),
+ "Failed to get bookmarks. Go to Edit->Preferences->Bookmarks to edit your plugin download sites.",
+ "Error", JOptionPane.ERROR_MESSAGE);
+ logger.warn("Failed to get bookmarks from plugin download sites: "+E.getMessage(), E);
+ }
+ }
+
+ // loads the combo box for bookmars
+ private void loadBookmarkCMBox(boolean selectLast) {
+ DefaultComboBoxModel theModel = new DefaultComboBoxModel();
+
+ // Extract the URL entries
+ List<DataSource> theDataSourceList = BookmarksUtil.getDataSourceList(
+ bookmarkCategory, theBookmarks.getCategory());
+
+ if (theDataSourceList != null) {
+ for (DataSource Current : theDataSourceList) {
+ theModel.addElement(Current);
+ if (selectLast)
+ theModel.setSelectedItem(Current);
+ }
+ }
+
+ urlComboBox.setModel(theModel);
+ }
+
+ private void initComponents() {
+ labelPanel = new JPanel();
+ label = new JLabel();
+ urlComboBox = new JComboBox();
+ urlComboBox.setRenderer(new BookmarkCellRenderer());
+ urlComboBox.setEditable(false);
+
+ jPanel1 = new JPanel();
+ okButton = new JButton();
+ editSiteButton = new JButton();
+ cancelButton = new JButton();
+ setDefaultCloseOperation(WindowConstants.DISPOSE_ON_CLOSE);
+ label.setText("Choose a plugin download site");
+
+ GroupLayout labelPanelLayout = new GroupLayout(labelPanel);
+ labelPanel.setLayout(labelPanelLayout);
+ labelPanelLayout.setHorizontalGroup(labelPanelLayout
+ .createParallelGroup(GroupLayout.LEADING).add(
+ labelPanelLayout.createSequentialGroup()
+ .addContainerGap().add(label,
+ GroupLayout.DEFAULT_SIZE, 239,
+ Short.MAX_VALUE).addContainerGap()));
+ labelPanelLayout.setVerticalGroup(labelPanelLayout.createParallelGroup(
+ GroupLayout.LEADING).add(
+ labelPanelLayout.createSequentialGroup().addContainerGap().add(
+ label, GroupLayout.DEFAULT_SIZE, 16, Short.MAX_VALUE)
+ .addContainerGap()));
+ okButton.setText("Ok");
+ okButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ okHandler(evt);
+ }
+ });
+ editSiteButton.setText("Edit Sites");
+ editSiteButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ addSiteHandler(evt);
+ }
+ });
+ cancelButton.setText("Cancel");
+ cancelButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ PluginUrlDialog.this.dispose();
+ }
+ });
+
+ GroupLayout jPanel1Layout = new GroupLayout(jPanel1);
+ jPanel1.setLayout(jPanel1Layout);
+ jPanel1Layout.setHorizontalGroup(jPanel1Layout.createParallelGroup(
+ GroupLayout.LEADING).add(
+ jPanel1Layout.createSequentialGroup().add(8, 8, 8)
+ .add(okButton).addPreferredGap(LayoutStyle.RELATED)
+ .add(editSiteButton)
+ .addPreferredGap(LayoutStyle.RELATED).add(cancelButton)
+ .addContainerGap(46, Short.MAX_VALUE)));
+ jPanel1Layout.setVerticalGroup(jPanel1Layout.createParallelGroup(
+ GroupLayout.LEADING).add(
+ jPanel1Layout.createSequentialGroup().addContainerGap().add(
+ jPanel1Layout.createParallelGroup(GroupLayout.BASELINE)
+ .add(okButton).add(editSiteButton).add(
+ cancelButton)).addContainerGap(
+ GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)));
+
+ GroupLayout layout = new GroupLayout(getContentPane());
+ getContentPane().setLayout(layout);
+ layout
+ .setHorizontalGroup(layout
+ .createParallelGroup(GroupLayout.LEADING)
+ .add(
+ layout
+ .createSequentialGroup()
+ .add(
+ layout
+ .createParallelGroup(
+ GroupLayout.LEADING)
+ .add(
+ labelPanel,
+ GroupLayout.PREFERRED_SIZE,
+ GroupLayout.DEFAULT_SIZE,
+ GroupLayout.PREFERRED_SIZE)
+ .add(
+ layout
+ .createSequentialGroup()
+ .add(
+ 21,
+ 21,
+ 21)
+ .add(
+ layout
+ .createParallelGroup(
+ GroupLayout.LEADING)
+ .add(
+ urlComboBox,
+ 0,
+ 296,
+ Short.MAX_VALUE)
+ .add(
+ jPanel1,
+ GroupLayout.DEFAULT_SIZE,
+ GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE))))
+ .addContainerGap()));
+ layout.setVerticalGroup(layout.createParallelGroup(GroupLayout.LEADING)
+ .add(
+ layout.createSequentialGroup().add(labelPanel,
+ GroupLayout.PREFERRED_SIZE,
+ GroupLayout.DEFAULT_SIZE,
+ GroupLayout.PREFERRED_SIZE).addPreferredGap(
+ LayoutStyle.RELATED).add(urlComboBox,
+ GroupLayout.PREFERRED_SIZE,
+ GroupLayout.DEFAULT_SIZE,
+ GroupLayout.PREFERRED_SIZE).addPreferredGap(
+ LayoutStyle.RELATED).add(jPanel1,
+ GroupLayout.PREFERRED_SIZE,
+ GroupLayout.DEFAULT_SIZE,
+ GroupLayout.PREFERRED_SIZE)));
+ loadBookmarkCMBox(false);
+ pack();
+ }
+
+ // required to make the text of the data source show up correctly in the
+ // combo box
+ private class BookmarkCellRenderer extends JLabel implements
+ ListCellRenderer {
+
+ public BookmarkCellRenderer() {
+ setOpaque(true);
+ }
+
+ public Component getListCellRendererComponent(JList list, Object value,
+ int index, boolean isSelected, boolean cellHasFocus) {
+ DataSource dataSource = (DataSource) value;
+ setText(dataSource.getName());
+
+ if (isSelected) {
+ if (0 < index) {
+ list.setToolTipText(dataSource.getHref());
+ }
+ }
+
+ return this;
+ }
+ }
+
+ private class UrlAction extends PluginInquireAction {
+
+ private PluginManageDialog dialog;
+ private String url;
+
+ public UrlAction(PluginManageDialog Dialog, String Url) {
+ dialog = Dialog;
+ url = Url;
+
+ }
+
+ public boolean displayProgressBar() {
+ return true;
+ }
+
+ public String getProgressBarMessage() {
+ return "Attempting to connect...";
+ }
+
+ public void inquireAction(List<DownloadableInfo> Results) {
+
+ if (isExceptionThrown()) {
+ if (getIOException() != null) {
+ // failed to read the given url
+ logger.warn(PluginManageDialog.CommonError.NOXML + url, getIOException());
+ dialog.setError(PluginManageDialog.CommonError.NOXML + url);
+ } else if (getJDOMException() != null) {
+ // failed to parse the xml file at the url
+ logger.warn(PluginManageDialog.CommonError.BADXML + url, getJDOMException());
+ dialog.setError(PluginManageDialog.CommonError.BADXML + url);
+ }
+ } else {
+
+ PluginManager Mgr = PluginManager.getPluginManager();
+ List<DownloadableInfo> UniqueAvailable = ManagerUtil.getUnique(Mgr
+ .getDownloadables(PluginStatus.CURRENT), Results);
+
+ Map<String, List<DownloadableInfo>> NewPlugins = ManagerUtil
+ .sortByCategory(UniqueAvailable);
+
+ if (NewPlugins.size() <= 0) {
+ dialog.setError("No plugins compatible with "
+ + new CytoscapeVersion().getFullVersion()
+ + " available from this site.");
+ } else {
+ dialog.setMessage("");
+ }
+
+ for (String Category : NewPlugins.keySet()) {
+ dialog.addCategory(Category, NewPlugins.get(Category),
+ PluginManageDialog.PluginInstallStatus.AVAILABLE);
+ }
+ }
+
+ }
+
+ }
+
+ private JButton editSiteButton;
+
+ private JButton cancelButton;
+
+ private JPanel jPanel1;
+
+ private JLabel label;
+
+ private JPanel labelPanel;
+
+ private JButton okButton;
+
+ private JComboBox urlComboBox;
+}
diff --git a/application/src/main/java/cytoscape/dialogs/plugins/TreeCellRenderer.java b/application/src/main/java/cytoscape/dialogs/plugins/TreeCellRenderer.java
new file mode 100644
index 0000000..37e5bc2
--- /dev/null
+++ b/application/src/main/java/cytoscape/dialogs/plugins/TreeCellRenderer.java
@@ -0,0 +1,57 @@
+/**
+ *
+ */
+package cytoscape.dialogs.plugins;
+
+import javax.swing.tree.DefaultTreeCellRenderer;
+
+import cytoscape.plugin.DownloadableInfo;
+
+/**
+ * @author skillcoy
+ *
+ */
+public class TreeCellRenderer extends DefaultTreeCellRenderer {
+
+ javax.swing.Icon warningIcon;
+
+ javax.swing.Icon okIcon;
+
+ public TreeCellRenderer(javax.swing.Icon warningLeafIcon,
+ javax.swing.Icon okLeafIcon) {
+ warningIcon = warningLeafIcon;
+ okIcon = okLeafIcon;
+ }
+
+ public java.awt.Component getTreeCellRendererComponent(
+ javax.swing.JTree tree, Object value, boolean sel,
+ boolean expanded, boolean leaf, int row, boolean hasFocus) {
+
+ super.getTreeCellRendererComponent(tree, value, sel, expanded, leaf,
+ row, hasFocus);
+
+ if (((TreeNode) value).getObject() != null) {
+ if (leaf && isOutdated(value)) {
+ setIcon(warningIcon);
+ setToolTipText("This plugin is not verified to work with the current version of Cytoscape.");
+ } else if (leaf && !isOutdated(value)) {
+ setIcon(okIcon);
+ setToolTipText("Verified to work in "
+ + cytoscape.CytoscapeVersion.version);
+ } else {
+ setToolTipText(null); // no tool tip
+ }
+ }
+ return this;
+ }
+
+ private boolean isOutdated(Object value) {
+ TreeNode node = (TreeNode) value;
+ DownloadableInfo infoObj = node.getObject();
+ if (infoObj != null && !infoObj.isPluginCompatibleWithCurrent()) {
+ return true;
+ }
+ return false;
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/dialogs/plugins/TreeNode.java b/application/src/main/java/cytoscape/dialogs/plugins/TreeNode.java
new file mode 100644
index 0000000..ca8edfd
--- /dev/null
+++ b/application/src/main/java/cytoscape/dialogs/plugins/TreeNode.java
@@ -0,0 +1,347 @@
+/*
+ File: TreeNode.java
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.dialogs.plugins;
+
+import cytoscape.plugin.DownloadableInfo;
+
+import java.util.Vector;
+import javax.swing.tree.DefaultMutableTreeNode;
+import javax.swing.tree.TreePath;
+
+public class TreeNode extends DefaultMutableTreeNode {
+ private Vector<TreeNode> children;
+
+ private DownloadableInfo infoObj;
+
+ private String title;
+
+ private TreeNode parent;
+
+ private boolean childAllowed;
+
+ private boolean visible;
+
+ /**
+ * Creates a TreeNode with given title, no parent and allows children.
+ *
+ * @param Title
+ */
+ public TreeNode(String Title) {
+ init(Title, true);
+ }
+
+ /**
+ * Creates a TreeNode with given title, no parent and allows children if
+ * specified.
+ *
+ * @param Title
+ * @param allowsChildren
+ */
+ public TreeNode(String Title, boolean allowsChildren) {
+ init(Title, allowsChildren);
+ }
+
+ /**
+ * Creates a TreeNode with given PluginInfo object, no parent and does not
+ * allow children.
+ *
+ * @param obj
+ */
+ public TreeNode(DownloadableInfo obj) {
+ init(obj.getName(), false);
+ addObject(obj);
+ }
+
+ /**
+ * Creates a TreeNode with given PluginInfo object, no parent and allows
+ * children if specified.
+ *
+ * @param obj
+ * @param allowsChildren
+ */
+ public TreeNode(DownloadableInfo obj, boolean allowsChildren) {
+ init(obj.getName(), allowsChildren);
+ addObject(obj);
+ }
+
+ private void init(String Title, boolean childrenOk) {
+ children = new Vector<TreeNode>();
+ this.title = Title;
+ childAllowed = childrenOk;
+ }
+
+ public void setVisible(boolean vis) {
+ visible = vis;
+ }
+
+ public boolean isVisible() {
+ return visible;
+ }
+
+ /**
+ * Returns true if this node has no children or does not allow them.
+ *
+ * @return
+ */
+ public boolean isLeaf() {
+ if (childAllowed)
+ return false;
+ else
+ return true;
+ }
+
+ /**
+ * Returns true if otherNode is an ancestor of this node.
+ *
+ * @param otherNode
+ * @return
+ */
+ public boolean isNodeAncestor(TreeNode otherNode) {
+ return recursiveParentLookup(this, otherNode);
+ }
+
+ /**
+ * Sets this nodes parent to newParent, child list does not change.
+ *
+ * @param newParent
+ */
+ public void setParent(TreeNode newParent) {
+ parent = newParent;
+ }
+
+ /**
+ * Gets the parent of this node
+ *
+ * @return TreeNode
+ */
+ public TreeNode getParent() {
+ return parent;
+ }
+
+ /**
+ * Adds a PluginInfo object to this node.
+ *
+ * @param info
+ */
+ public void addObject(DownloadableInfo info) {
+ infoObj = info;
+ }
+
+ /**
+ * Adds newChild to this node if children are allowed.
+ *
+ * @param newChild
+ */
+ public void addChild(TreeNode newChild) {
+ if (!childAllowed)
+ throw new IllegalStateException();
+ if (newChild == null)
+ throw new IllegalArgumentException();
+ if (isNodeAncestor(newChild))
+ throw new IllegalArgumentException("Cannot add ancestor node.");
+ children.add(newChild);
+ newChild.setParent(this);
+ }
+
+ /**
+ * Removes child from this node.
+ *
+ * @param child
+ */
+ public void removeChild(TreeNode child) {
+ children.remove(child);
+ }
+
+ /**
+ * Clears the list of children for this node.
+ */
+ public void removeChildren() {
+ children.clear();
+ }
+
+ /**
+ * Adds all children to the child list of this node if children are allowed.
+ *
+ * @param children
+ */
+ public void addChildren(TreeNode[] children) {
+ for (TreeNode c : children) {
+ if (c.isVisible())
+ addChild(c);
+ }
+ }
+
+ /**
+ * Gets the list of children for this node
+ *
+ * @return Vector<TreeNode>
+ */
+ public Vector<TreeNode> getChildren() {
+ return children;
+ }
+
+ /**
+ * Get total number of children for this node
+ *
+ * @return int
+ */
+ public int getChildCount() {
+ return children.size();
+ }
+
+ /**
+ * Get child from this node's child list at given index.
+ *
+ * @param index
+ * @return TreeNode
+ */
+ public TreeNode getChildAt(int index) {
+ return children.get(index);
+ }
+
+ /**
+ * Gets the index of child from this node's child list.
+ *
+ * @param child
+ * @return int
+ */
+ public int getIndexOfChild(TreeNode child) {
+ return children.indexOf(child);
+ }
+
+ /**
+ * Gets the total (recursively) of all child nodes that are not leaves.
+ *
+ * @return int
+ */
+ public int getTreeCount() {
+ return recursiveTotalSubCategorySize(this);
+ }
+
+ /**
+ * Gets the total (recursively) of all leaves under this node.
+ *
+ * @return
+ */
+ public int getLeafCount() {
+ if (this.getChildCount() <= 0)
+ return 0;
+ return recursiveTotalLeafSize(this);
+ }
+
+ /**
+ * Gets the title of this node.
+ *
+ * @return String
+ */
+ public String getTitle() {
+ return this.title;
+ }
+
+ /**
+ * Gets the PluginInfo object of this node.
+ *
+ * @return PluginInfo
+ */
+ public DownloadableInfo getObject() {
+ return this.infoObj;
+ }
+
+ /**
+ * Gets string representation of this node as 'title: total leaves'
+ */
+ public String toString() {
+ if (this.infoObj != null)
+ return this.infoObj.toString();
+ else
+ return getTitle() + ": " + getLeafCount();
+ }
+
+
+// public TreePath getPath(TreeNode node) {
+// return node.getPath(node);
+// }
+
+// public javax.swing.tree.TreePath getPath(TreeNode node) {
+// // Get node depth
+// int depth = 0;
+// for(TreeNode node = current; node != null; node.getParent())
+// depth++;
+// // Construct node path
+// // First scan helped us, now we can directly allocate array of exact
+// // size => no extra objects created (be kind to your local gc, it has
+// // hard job cleaning that mess already), no collection reverse.
+// // Price is doubling path construction time.
+// // But in many situations you know the depth already. In such case
+// // Only code below applies and time complexity is O(depth) not
+// // O(2*depth)
+// TreeNode[] path = new TreeNode[depth];
+// for(TreeNode node = current; node != null; node.getParent())
+// path[--depth] = node; // reverse fill array
+// return new TreePath(path);
+
+
+ private int recursiveTotalSubCategorySize(TreeNode node) {
+ int n = 0;
+ n += node.getChildCount();
+ for (TreeNode c : node.getChildren()) {
+ n += recursiveTotalSubCategorySize(c);
+ }
+ return n;
+ }
+
+ private int recursiveTotalLeafSize(TreeNode node) {
+ int n = 0;
+ if (node.getChildCount() == 0) {
+ n = 1;
+ }
+ for (TreeNode c : node.getChildren()) {
+ n += recursiveTotalLeafSize(c);
+ }
+ return n;
+ }
+
+ private boolean recursiveParentLookup(TreeNode node, TreeNode ancestor) {
+ boolean lookup = false;
+ if (node.getParent() != null) {
+ if (node.getParent().equals(ancestor))
+ lookup = true;
+ else
+ lookup = recursiveParentLookup(node.getParent(), ancestor);
+ }
+ return lookup;
+ }
+}
diff --git a/application/src/main/java/cytoscape/dialogs/preferences/BookmarkDialog.java b/application/src/main/java/cytoscape/dialogs/preferences/BookmarkDialog.java
new file mode 100644
index 0000000..2d26f48
--- /dev/null
+++ b/application/src/main/java/cytoscape/dialogs/preferences/BookmarkDialog.java
@@ -0,0 +1,412 @@
+/*
+ Copyright (c) 2006, 2007, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.dialogs.preferences;
+
+import cytoscape.Cytoscape;
+import cytoscape.logger.CyLogger;
+
+import cytoscape.bookmarks.Bookmarks;
+import cytoscape.bookmarks.DataSource;
+
+import cytoscape.util.BookmarksUtil;
+
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Dimension;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+
+import java.io.IOException;
+
+import java.net.URL;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.swing.JButton;
+import javax.swing.JDialog;
+import javax.swing.JFrame;
+import javax.swing.JLabel;
+import javax.swing.JList;
+import javax.swing.JOptionPane;
+import javax.swing.ListCellRenderer;
+import javax.swing.ListSelectionModel;
+import javax.swing.event.ListSelectionEvent;
+import javax.swing.event.ListSelectionListener;
+
+import javax.xml.bind.JAXBException;
+
+
+/**
+ *
+ */
+public class BookmarkDialog extends JDialog implements ActionListener, ListSelectionListener,
+ ItemListener {
+ private String bookmarkCategory;
+ private Bookmarks theBookmarks = null;
+
+ // private Category theCategory = new Category();;
+ private String[] bookmarkCategories = { "network", "annotation", "plugins" };
+
+ // private URL bookmarkURL;
+
+ /**
+ * Creates new BookmarkDialog
+ *
+ * @throws IOException
+ * @throws JAXBException
+ */
+ public BookmarkDialog(JFrame pParent) throws JAXBException, IOException {
+ super(pParent, true);
+ this.setTitle("Bookmark manager");
+
+ initComponents();
+ bookmarkCategory = cmbCategory.getSelectedItem().toString();
+ theBookmarks = Cytoscape.getBookmarks();
+ loadBookmarks();
+
+ setSize(new Dimension(500, 250));
+ this.setLocationRelativeTo(pParent);
+ }
+
+ /**
+ * Creates new BookmarkDialog, set the selection on the given category
+ *
+ * @throws IOException
+ * @throws JAXBException
+ */
+ public BookmarkDialog(JFrame pParent, String pCategoryName) throws JAXBException, IOException {
+ this(pParent);
+
+ Dimension winSize = this.getSize();
+
+ // Set the given category the selected item in comboBox
+ for (int i=0; i< cmbCategory.getItemCount(); i++) {
+ if (cmbCategory.getItemAt(i).toString().equalsIgnoreCase(pCategoryName)) {
+ cmbCategory.setSelectedIndex(i);
+ this.setPreferredSize(winSize);
+ this.pack();
+ break;
+ }
+ }
+ }
+
+
+ // Variables declaration - do not modify
+ private javax.swing.JButton btnAddBookmark;
+ private javax.swing.JButton btnDeleteBookmark;
+ private javax.swing.JButton btnEditBookmark;
+ private javax.swing.JButton btnOK;
+ private javax.swing.JComboBox cmbCategory;
+ private javax.swing.JPanel jPanel1;
+ private javax.swing.JScrollPane jScrollPane1;
+
+ // private javax.swing.JLabel lbTitle;
+ private javax.swing.JList listBookmark;
+
+ // End of variables declaration
+ private void initComponents() {
+ java.awt.GridBagConstraints gridBagConstraints;
+
+ // lbTitle = new javax.swing.JLabel();
+ cmbCategory = new javax.swing.JComboBox();
+ jScrollPane1 = new javax.swing.JScrollPane();
+ listBookmark = new javax.swing.JList();
+ jPanel1 = new javax.swing.JPanel();
+ btnAddBookmark = new javax.swing.JButton();
+ btnEditBookmark = new javax.swing.JButton();
+ btnDeleteBookmark = new javax.swing.JButton();
+ btnOK = new javax.swing.JButton();
+
+ getContentPane().setLayout(new java.awt.GridBagLayout());
+
+ setDefaultCloseOperation(javax.swing.WindowConstants.DISPOSE_ON_CLOSE);
+ // lbTitle.setText("Title");
+ // getContentPane().add(lbTitle, new java.awt.GridBagConstraints());
+ cmbCategory.setToolTipText("Bookmark category");
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = 1;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.weightx = 1.0;
+ gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 0);
+ getContentPane().add(cmbCategory, gridBagConstraints);
+
+ jScrollPane1.setViewportView(listBookmark);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = 2;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.BOTH;
+ gridBagConstraints.weighty = 1.0;
+ gridBagConstraints.insets = new java.awt.Insets(0, 10, 0, 0);
+ getContentPane().add(jScrollPane1, gridBagConstraints);
+
+ jPanel1.setLayout(new java.awt.GridBagLayout());
+
+ btnAddBookmark.setText("Add");
+ btnAddBookmark.setToolTipText("Add a new bookmark");
+ //btnAddBookmark.setPreferredSize(new java.awt.Dimension(75, 25));
+ jPanel1.add(btnAddBookmark, new java.awt.GridBagConstraints());
+
+ btnEditBookmark.setText("Edit");
+ btnEditBookmark.setToolTipText("Edit a bookmark");
+/*
+ btnEditBookmark.setMaximumSize(new java.awt.Dimension(75, 25));
+ btnEditBookmark.setMinimumSize(new java.awt.Dimension(75, 25));
+ btnEditBookmark.setPreferredSize(new java.awt.Dimension(75, 25));
+*/
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = 1;
+ gridBagConstraints.insets = new java.awt.Insets(10, 0, 10, 0);
+ jPanel1.add(btnEditBookmark, gridBagConstraints);
+
+ btnDeleteBookmark.setText("Delete");
+ btnDeleteBookmark.setToolTipText("Delete a bookmark");
+ // btnDeleteBookmark.setMaximumSize(new java.awt.Dimension(63, 25));
+ // btnDeleteBookmark.setMinimumSize(new java.awt.Dimension(63, 25));
+ //btnDeleteBookmark.setPreferredSize(new java.awt.Dimension(, 25));
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = 2;
+ jPanel1.add(btnDeleteBookmark, gridBagConstraints);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 1;
+ gridBagConstraints.gridy = 2;
+ gridBagConstraints.insets = new java.awt.Insets(0, 10, 0, 10);
+ getContentPane().add(jPanel1, gridBagConstraints);
+
+ btnOK.setText("OK");
+ btnOK.setToolTipText("Close Bookmark dialog");
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = 3;
+ gridBagConstraints.insets = new java.awt.Insets(20, 0, 20, 0);
+ getContentPane().add(btnOK, gridBagConstraints);
+
+ for (String AnItem : bookmarkCategories) {
+ cmbCategory.addItem(AnItem);
+ }
+
+ cmbCategory.addItemListener(this);
+
+ btnEditBookmark.setEnabled(false);
+ btnDeleteBookmark.setEnabled(false);
+
+ // add event listeners
+ btnOK.addActionListener(this);
+ btnAddBookmark.addActionListener(this);
+ btnEditBookmark.addActionListener(this);
+ btnDeleteBookmark.addActionListener(this);
+
+ listBookmark.addListSelectionListener(this);
+
+ listBookmark.setCellRenderer(new MyListCellRenderer());
+ listBookmark.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
+
+ // pack();
+ } // </editor-fold>
+
+ private void loadBookmarks() {
+ List<DataSource> theDataSourceList = BookmarksUtil.getDataSourceList(bookmarkCategory,
+ theBookmarks
+ .getCategory());
+
+ MyListModel theModel = new MyListModel(theDataSourceList);
+ listBookmark.setModel(theModel);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void itemStateChanged(ItemEvent e) {
+ bookmarkCategory = cmbCategory.getSelectedItem().toString();
+ loadBookmarks();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ Object _actionObject = e.getSource();
+
+ // handle Button events
+ if (_actionObject instanceof JButton) {
+ JButton _btn = (JButton) _actionObject;
+
+ if (_btn == btnOK) {
+ this.dispose();
+ } else if (_btn == btnAddBookmark) {
+ EditBookmarkDialog theNewDialog = new EditBookmarkDialog(this, true, theBookmarks,
+ bookmarkCategory, "new",
+ null);
+ theNewDialog.setLocationRelativeTo(this);
+
+ theNewDialog.setVisible(true);
+ loadBookmarks(); // reload is required to update the GUI
+ } else if (_btn == btnEditBookmark) {
+ DataSource theDataSource = (DataSource) listBookmark.getSelectedValue();
+ EditBookmarkDialog theEditDialog = new EditBookmarkDialog(this, true, theBookmarks,
+ bookmarkCategory, "edit",
+ theDataSource);
+ theEditDialog.setLocationRelativeTo(this);
+
+ theEditDialog.setVisible(true);
+ loadBookmarks(); // reload is required to update the GUI
+ } else if (_btn == btnDeleteBookmark) {
+ DataSource theDataSource = (DataSource) listBookmark.getSelectedValue();
+
+ MyListModel theModel = (MyListModel) listBookmark.getModel();
+ theModel.removeElement(listBookmark.getSelectedIndex());
+
+ BookmarksUtil.deleteBookmark(theBookmarks, bookmarkCategory, theDataSource);
+
+ if (theModel.getSize() == 0) {
+ btnEditBookmark.setEnabled(false);
+ btnDeleteBookmark.setEnabled(false);
+ }
+ }
+ }
+ }
+
+ /**
+ * Called by ListSelectionListener interface when a table item is selected.
+ *
+ * @param pListSelectionEvent
+ */
+ public void valueChanged(ListSelectionEvent pListSelectionEvent) {
+ if (listBookmark.getSelectedIndex() == -1) { // nothing is selected
+ btnEditBookmark.setEnabled(false);
+ btnDeleteBookmark.setEnabled(false);
+ } else {
+ // enable buttons
+ btnEditBookmark.setEnabled(true);
+ btnDeleteBookmark.setEnabled(true);
+ }
+ }
+
+ class MyListModel extends javax.swing.AbstractListModel {
+ List<DataSource> theDataSourceList = new ArrayList<DataSource>(0);
+
+ public MyListModel(List<DataSource> pDataSourceList) {
+ theDataSourceList = pDataSourceList;
+ }
+
+ public int getSize() {
+ if (theDataSourceList == null) {
+ return 0;
+ }
+
+ return theDataSourceList.size();
+ }
+
+ public Object getElementAt(int i) {
+ if (theDataSourceList == null) {
+ return null;
+ }
+
+ return theDataSourceList.get(i);
+ }
+
+ public void addElement(DataSource pDataSource) {
+ theDataSourceList.add(pDataSource);
+ }
+
+ public void removeElement(int pIndex) {
+ theDataSourceList.remove(pIndex);
+ fireContentsChanged(this, pIndex, pIndex);
+ }
+ } // MyListModel
+
+ // class MyListCellrenderer
+ class MyListCellRenderer extends JLabel implements ListCellRenderer {
+ public MyListCellRenderer() {
+ setOpaque(true);
+ }
+
+ public Component getListCellRendererComponent(JList list, Object value, int index,
+ boolean isSelected, boolean cellHasFocus) {
+ DataSource theDataSource = (DataSource) value;
+ setText(theDataSource.getName());
+ setToolTipText(theDataSource.getHref());
+ setBackground(isSelected ? Color.red : Color.white);
+ setForeground(isSelected ? Color.white : Color.black);
+
+ return this;
+ }
+ }
+
+
+ /**
+ * @param args
+ */
+ public static void main(String[] args) {
+ JDialog theDialog = new BookmarkDialog();
+ theDialog.setPreferredSize(new Dimension(350, 400));
+ theDialog.pack();
+ theDialog.setVisible(true);
+ }
+
+ // for test only
+ /**
+ * Creates a new BookmarkDialog object.
+ */
+ public BookmarkDialog() {
+ this.setTitle("Bookmark manager");
+
+ theBookmarks = getTestBookmarks();
+ initComponents();
+ bookmarkCategory = cmbCategory.getSelectedItem().toString();
+ // theBookmarks = Cytoscape.getBookmarks();
+ loadBookmarks();
+ }
+
+ // For test only, remove after test pass
+ private Bookmarks getTestBookmarks() {
+ Bookmarks tmpBookmarks = null;
+
+ java.io.File tmpBookmarkFile = new java.io.File("bookmarks_kei.xml");
+ CyLogger.getLogger().info("tmpBookmarkFile =" + tmpBookmarkFile.getAbsolutePath());
+
+ // Load the Bookmarks object from given xml file
+ try {
+ tmpBookmarks = BookmarksUtil.getBookmarks(tmpBookmarkFile.toURL());
+ } catch (IOException e) {
+ CyLogger.getLogger().info("IOException -- bookmarkSource");
+ } catch (JAXBException e) {
+ CyLogger.getLogger().info("JAXBException -- bookmarkSource");
+ } catch (Exception e) {
+ CyLogger.getLogger().info("Can not read the bookmark file, the bookmark file may not exist!");
+ }
+
+ return tmpBookmarks;
+ }
+}
diff --git a/application/src/main/java/cytoscape/dialogs/preferences/EditBookmarkDialog.java b/application/src/main/java/cytoscape/dialogs/preferences/EditBookmarkDialog.java
new file mode 100644
index 0000000..262f007
--- /dev/null
+++ b/application/src/main/java/cytoscape/dialogs/preferences/EditBookmarkDialog.java
@@ -0,0 +1,267 @@
+package cytoscape.dialogs.preferences;
+
+
+import cytoscape.bookmarks.Bookmarks;
+import cytoscape.bookmarks.DataSource;
+import cytoscape.util.BookmarksUtil;
+import cytoscape.util.URLUtil;
+
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.net.MalformedURLException;
+import java.net.URL;
+import javax.swing.JButton;
+import javax.swing.JDialog;
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+import javax.swing.JTextField;
+import javax.swing.WindowConstants;
+
+
+/**
+ * @author ruschein
+ */
+public class EditBookmarkDialog extends JDialog {
+ private JButton cancelButton;
+ private JLabel categoryLabel;
+ private JLabel jLabel1;
+ private JLabel jLabel3;
+ private JLabel jLabel4;
+ private JTextField nameTextField;
+ private JButton okButton;
+ private JTextField urlTextField;
+
+ private final JDialog parent;
+ private final Bookmarks bookmarks;
+ private final String categoryName;
+ private final String mode;
+ private DataSource dataSource;
+
+ /** Creates new form EditBookmarkDialog */
+ public EditBookmarkDialog(final JDialog parent, final boolean modal, final Bookmarks bookmarks,
+ final String categoryName, final String mode, final DataSource dataSource)
+ {
+ super(parent, modal);
+
+ this.parent = parent;
+ this.bookmarks = bookmarks;
+ this.categoryName = categoryName;
+ this.mode = mode;
+ this.dataSource = dataSource;
+
+ initComponents();
+ categoryLabel.setText(categoryName);
+
+ if (mode.equalsIgnoreCase("new"))
+ setTitle("Add New Bookmark");
+ else {
+ setTitle("Edit Bookmark");
+ nameTextField.setText(dataSource.getName());
+ urlTextField.setText(dataSource.getHref());
+ }
+ }
+
+ public DataSource getDataSource(){
+ return dataSource;
+ }
+
+ /** This method is called from within the constructor to
+ * initialize the form.
+ * WARNING: Do NOT modify this code. The content of this method is
+ * always regenerated by the Form Editor.
+ */
+ @SuppressWarnings("unchecked")
+ private void initComponents() {
+
+ jLabel1 = new JLabel();
+ categoryLabel = new JLabel();
+ jLabel3 = new JLabel();
+ jLabel4 = new JLabel();
+ nameTextField = new JTextField();
+ urlTextField = new JTextField();
+ okButton = new JButton();
+ cancelButton = new JButton();
+
+ setDefaultCloseOperation(WindowConstants.DISPOSE_ON_CLOSE);
+ setTitle("Edit Bookmark");
+
+ jLabel1.setText("Category:");
+
+ categoryLabel.setText("******************");
+
+ jLabel3.setText("Name:");
+
+ jLabel4.setText("URL:");
+
+ okButton.setText("Ok");
+ okButton.setSelected(true);
+ okButton.addActionListener(new ActionListener() {
+ public void actionPerformed(final ActionEvent evt) {
+ if (mode.equalsIgnoreCase("new"))
+ okButtonNewActionPerformed(evt);
+ else
+ okButtonEditActionPerformed(evt);
+ }
+ });
+
+ cancelButton.setText("Cancel");
+ cancelButton.addActionListener(new ActionListener() {
+ public void actionPerformed(final ActionEvent evt) {
+ cancelButtonActionPerformed(evt);
+ }
+ });
+
+ org.jdesktop.layout.GroupLayout layout = new org.jdesktop.layout.GroupLayout(getContentPane());
+ getContentPane().setLayout(layout);
+ layout.setHorizontalGroup(
+ layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(layout.createSequentialGroup()
+ .add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING, false)
+ .add(layout.createSequentialGroup()
+ .add(32, 32, 32)
+ .add(jLabel1)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED))
+ .add(org.jdesktop.layout.GroupLayout.TRAILING, layout.createSequentialGroup()
+ .addContainerGap(42, Short.MAX_VALUE)
+ .add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.TRAILING)
+ .add(jLabel4)
+ .add(jLabel3))
+ .add(20, 20, 20)))
+ .add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(categoryLabel, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE, 112, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.TRAILING, false)
+ .add(org.jdesktop.layout.GroupLayout.LEADING, urlTextField)
+ .add(org.jdesktop.layout.GroupLayout.LEADING, nameTextField, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 608, Short.MAX_VALUE)
+ .add(layout.createSequentialGroup()
+ .add(441, 441, 441)
+ .add(okButton)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(cancelButton))))
+ .addContainerGap())
+ );
+ layout.setVerticalGroup(
+ layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(layout.createSequentialGroup()
+ .add(22, 22, 22)
+ .add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE)
+ .add(jLabel1, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE, 16, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .add(categoryLabel))
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.UNRELATED)
+ .add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE)
+ .add(nameTextField, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .add(jLabel3))
+ .add(28, 28, 28)
+ .add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE)
+ .add(jLabel4)
+ .add(urlTextField, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE))
+ .add(18, 18, 18)
+ .add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE)
+ .add(cancelButton)
+ .add(okButton))
+ .addContainerGap(org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
+ );
+
+ pack();
+ }
+
+ private void okButtonNewActionPerformed(final ActionEvent evt) {
+ final String name = nameTextField.getText().trim();
+ final String urlCandidate = urlTextField.getText().trim();
+
+ if (name.equals("") || urlCandidate.equals("")) {
+ JOptionPane.showMessageDialog(parent, "Please provide a name and URL!", "Warning",
+ JOptionPane.INFORMATION_MESSAGE);
+ return;
+ }
+
+ final URL url;
+ if (URLUtil.isValid(urlCandidate)) {
+ try {
+ url = new URL(urlCandidate);
+ } catch (final MalformedURLException e) {
+ throw new IllegalStateException("We should never get here!");
+ }
+ } else {
+ JOptionPane.showMessageDialog(parent, "Invalid URL!", "Warning",
+ JOptionPane.INFORMATION_MESSAGE);
+ return;
+ }
+
+ final DataSource theDataSource = new DataSource();
+ theDataSource.setName(name);
+ theDataSource.setHref(urlCandidate);
+
+
+ if (BookmarksUtil.isInBookmarks(url, categoryName, theDataSource)) {
+ JOptionPane.showMessageDialog(parent, "Duplicate bookmark!", "Warning",
+ JOptionPane.INFORMATION_MESSAGE);
+
+ return;
+ }
+
+ BookmarksUtil.saveBookmark(bookmarks, categoryName, theDataSource);
+ dataSource = theDataSource;
+
+ dispose();
+ }
+
+ private void okButtonEditActionPerformed(final ActionEvent evt) {
+ final String name = nameTextField.getText().trim();
+ final String url = urlTextField.getText().trim();
+
+ if (name.equals("") || url.equals("")) {
+ JOptionPane.showMessageDialog(parent, "Please provide a name and URL!", "Warning",
+ JOptionPane.INFORMATION_MESSAGE);
+ return;
+ }
+
+ if (!URLUtil.isValid(url)){
+ JOptionPane.showMessageDialog(parent, "Invalid URL!", "Warning",
+ JOptionPane.INFORMATION_MESSAGE);
+ return;
+ }
+
+ // There is no change, do nothing
+ if (dataSource.getName().equalsIgnoreCase(name) && this.dataSource.getHref().equalsIgnoreCase(url)){
+ dispose();
+ return;
+ }
+
+ if (!URLUtil.isValid(url)){
+ JOptionPane.showMessageDialog(parent, "Invalid URL", "Warning",
+ JOptionPane.INFORMATION_MESSAGE);
+ return;
+ }
+
+ if (!name.equalsIgnoreCase(dataSource.getName())) {
+ // The bookmark name has been changed
+ DataSource newDataSource = new DataSource();
+ newDataSource.setName(name);
+ newDataSource.setHref(url);
+
+ if (BookmarksUtil.isInBookmarks(bookmarks, categoryName, newDataSource)){
+ // The bookmark name must be unique
+ JOptionPane.showMessageDialog(parent, "Bookmark with this name already existed!", "Warning",
+ JOptionPane.INFORMATION_MESSAGE);
+ return;
+ }
+
+ // first delete the old one, then add (note: name is key of DataSource)
+ BookmarksUtil.deleteBookmark(bookmarks, categoryName, dataSource);
+ BookmarksUtil.saveBookmark(bookmarks, categoryName, newDataSource);
+ }
+ else { // The bookmark name has not been changed
+ // first delete the old one, then add (note: name is key of DataSource)
+ BookmarksUtil.deleteBookmark(bookmarks, categoryName, dataSource);
+
+ dataSource.setHref(url);
+ BookmarksUtil.saveBookmark(bookmarks, categoryName, dataSource);
+ }
+
+ dispose();
+ }
+
+ private void cancelButtonActionPerformed(final ActionEvent evt) {
+ dispose();
+ }
+}
diff --git a/application/src/main/java/cytoscape/dialogs/preferences/PluginsTableModel.java b/application/src/main/java/cytoscape/dialogs/preferences/PluginsTableModel.java
new file mode 100644
index 0000000..b99c2c6
--- /dev/null
+++ b/application/src/main/java/cytoscape/dialogs/preferences/PluginsTableModel.java
@@ -0,0 +1,420 @@
+/*
+ File: PluginsTableModel.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.dialogs.preferences;
+
+import cytoscape.*;
+import cytoscape.logger.CyLogger;
+
+import java.io.*;
+
+import java.net.URL;
+
+import java.util.*;
+
+import javax.swing.*;
+import javax.swing.table.*;
+
+
+/**
+ * @deprecated This class is no longer used in cytoscape. If you are using it,
+ * let us know and we'll figure something out. Otherwise, this will be
+ * removed December 2007.
+ */
+public class PluginsTableModel extends AbstractTableModel {
+ static int[] columnWidth = new int[] { 400 };
+ static int[] alignment = new int[] { JLabel.LEFT };
+ private Properties properties;
+ TreeSet pluginsSet = new TreeSet();
+ static String[] columnHeader = new String[] { "Plugin Location" };
+ boolean pluginsFromCommandLineLoadedAndSaved;
+ private static CyLogger logger = CyLogger.getLogger(PluginsTableModel.class);
+
+ /**
+ * Creates a new PluginsTableModel object.
+ */
+ public PluginsTableModel() {
+ super();
+ pluginsFromCommandLineLoadedAndSaved = false;
+ // get only one entry from properties: key=plugins
+ properties = new Properties();
+
+ if (CytoscapeInit.getProperties().get("plugins") != null) {
+ properties.put("plugins", CytoscapeInit.getProperties().get("plugins"));
+ }
+
+ loadProperties();
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void loadProperties() {
+ pluginsSet.clear();
+
+ if (getProperty("plugins") != null) {
+ String[] pargs = getProperty("plugins", "").split(",");
+
+ for (int i = 0; i < pargs.length; i++) {
+ addPlugin(pargs[i]);
+ }
+ }
+
+ // now (non-redundantly) include plugins specified on the command line
+ if (!pluginsFromCommandLineLoadedAndSaved) {
+ Set plugins = new HashSet(cytoscape.plugin.PluginManager.getPluginURLs());
+ Iterator iterator = plugins.iterator();
+
+ while (iterator.hasNext()) {
+ URL url = (URL) iterator.next();
+ addPlugin(url);
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param key DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getProperty(String key) {
+ return properties.getProperty(key);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param key DOCUMENT ME!
+ * @param defaultValue DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getProperty(String key, String defaultValue) {
+ return properties.getProperty(key, defaultValue);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param key DOCUMENT ME!
+ * @param value DOCUMENT ME!
+ */
+ public void setProperty(String key, String value) {
+ properties.setProperty(key, value);
+ }
+
+ // Add plugin to plugins=... String in private Properties object for
+ /**
+ * DOCUMENT ME!
+ *
+ * @param newPlugin DOCUMENT ME!
+ */
+ public void addPluginToPropertyString(String newPlugin) {
+ String tempPlugins = properties.getProperty("plugins");
+
+ if (tempPlugins != null) {
+ //cull out duplicate entries, since single entries and directory adds
+ // can result in duplicates not specified strictly at UI level
+ properties.setProperty("plugins", cullDuplicates(tempPlugins + "," + newPlugin));
+ } else {
+ properties.setProperty("plugins", newPlugin);
+ }
+ }
+
+ /*
+ * cull duplicate entries in comma-separated tokens in String
+ */
+ String cullDuplicates(String s) {
+ StringTokenizer st = new StringTokenizer(s, ",");
+ HashSet hashSet = new HashSet();
+
+ while (st.hasMoreTokens()) {
+ hashSet.add(st.nextToken());
+ }
+
+ String newString = new String();
+ Iterator it = hashSet.iterator();
+ StringBuffer sb = new StringBuffer();
+
+ while (it.hasNext()) {
+ sb.append((String) it.next());
+ sb.append(",");
+ }
+
+ sb.deleteCharAt(sb.length() - 1);
+
+ return sb.toString();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param deletedPlugins DOCUMENT ME!
+ */
+ public void deletePlugins(String[] deletedPlugins) {
+ // deletion a little weird - multiple selection deletes not working
+ // right - restricting via setting Tables to use single selection
+
+ // remove deleted plugin from plugins=... property
+ String tempPlugins = properties.getProperty("plugins");
+
+ for (int k = 0; k < deletedPlugins.length; k++) {
+ String value = deletedPlugins[k];
+
+ if (value.startsWith("file:"))
+ value = value.substring(5);
+ else if (value.startsWith("jar:"))
+ value = value.substring(4);
+ else if (value.startsWith("http\\:")) // don't want the backslash
+ value = value.substring(0, 3) + value.substring(5);
+
+ // NB: \\ is escaped "\"
+ if (tempPlugins != null) {
+ String[] plugins = tempPlugins.split(",");
+ String returnString = null;
+
+ for (int i = 0; i < plugins.length; i++) {
+ if (value.compareTo(plugins[i]) == 0) {
+ } else {
+ if (returnString == null) {
+ returnString = new String(plugins[i]);
+ } else {
+ returnString = new String(returnString + "," + plugins[i]);
+ }
+ }
+ }
+
+ if (returnString == null) {
+ properties.remove("plugins");
+ } else {
+ properties.setProperty("plugins", returnString);
+ }
+ }
+
+ // and remove deleted plugins from TreeSet for model and table
+ pluginsSet.remove(value);
+ }
+ }
+
+ // add plugin to table and properties object
+ /**
+ * DOCUMENT ME!
+ *
+ * @param pluginString DOCUMENT ME!
+ */
+ public void addPlugin(String pluginString) {
+ String[] plugin = pluginString.split(",");
+
+ for (int i = 0; i < plugin.length; i++) {
+ URL url;
+
+ try {
+ if (plugin[i].startsWith("http")) {
+ plugin[i] = "jar:" + plugin[i] + "!/";
+ url = new URL(plugin[i]);
+ } else if (plugin[i].startsWith("file") || plugin[i].startsWith("jar")) {
+ // do no massaging of string, just create URL
+ url = new URL(plugin[i]);
+ } else {
+ url = new URL("file", "", plugin[i]);
+ }
+
+ addPlugin(url);
+ } catch (Exception ue) {
+ logger.warn("Error: cannot construct URL from: " + plugin[i]);
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param u DOCUMENT ME!
+ */
+ public void addPlugin(URL u) {
+ if (u != null) {
+ // get string info (no protocol) for insertion into table
+ // and plugins=... property
+ String path = u.getPath();
+
+ // strip off trailing "!/" for JAR URLs
+ if (path.endsWith("!/"))
+ path = path.substring(0, path.length() - 2);
+
+ pluginsSet.add(path); // add to TreeSet for model and table
+ addPluginToPropertyString(path); // also add to plugins=... string
+ // in private properties object
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param col DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getColumnName(int col) {
+ return columnHeader[col];
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param saveToProps DOCUMENT ME!
+ */
+ public void save(Properties saveToProps) {
+ // save local property values to passed-in Properties
+ saveToProps.putAll(properties);
+ // mark these plugins loaded from the command line as loaded
+ // and saved, so no need to reparse, etc.
+ pluginsFromCommandLineLoadedAndSaved = true;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param restoreFromProps DOCUMENT ME!
+ */
+ public void restore(Properties restoreFromProps) {
+ properties.clear();
+
+ if (restoreFromProps.getProperty("plugins") != null) {
+ properties.put("plugins", restoreFromProps.getProperty("plugins"));
+ loadProperties(); // now get pluginsSet populated from properties
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getColumnCount() {
+ return columnHeader.length;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param row DOCUMENT ME!
+ * @param col DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getValueAt(int row, int col) {
+ Object retVal = new String("");
+ int index = 0;
+
+ for (Iterator it = pluginsSet.iterator(); it.hasNext();) {
+ retVal = it.next();
+
+ if (index == row)
+ break;
+
+ index++;
+ }
+
+ return retVal;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getRowCount() {
+ return pluginsSet.size();
+ }
+
+ /*
+ * check for presence of name/value pair in table/table model
+ */
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param value DOCUMENT ME!
+ * @param listOfDuplicates DOCUMENT ME!
+ * @param listOfNew DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean validateNewPlugins(String value, Vector listOfDuplicates, Vector listOfNew) {
+ listOfDuplicates.clear();
+ listOfNew.clear();
+
+ try {
+ // handle comma separated list of paths, or single path
+ String[] path = value.split(",");
+
+ for (int i = 0; i < path.length; i++) {
+ File newFile = new File(path[i]);
+ int numRows = getRowCount();
+ boolean isDuplicate = false;
+
+ for (int j = 0; j < numRows; j++) {
+ String currentFileStr = (String) getValueAt(j, 0);
+
+ // test for simple string match - path[i] already in list
+ if (currentFileStr.equals(path[i])) {
+ listOfDuplicates.add(path[i]);
+ isDuplicate = true;
+ } else {
+ // not textually in list, but must test for File equivalence
+ // - are the two file paths the same file?
+ File currentFile = new File(currentFileStr);
+
+ if ((currentFile.getCanonicalPath()).equals(newFile.getCanonicalPath())) {
+ listOfDuplicates.add(path[i]);
+ isDuplicate = true;
+ }
+ }
+ }
+
+ if (!isDuplicate) {
+ listOfNew.add(path[i]);
+ }
+ }
+ } catch (IOException ioe) {
+ logger.warn("Failed to validate new plugins: "+ioe.getMessage(), ioe);
+ }
+
+ return ((listOfDuplicates.size() > 0) ? true : false);
+ }
+}
diff --git a/application/src/main/java/cytoscape/dialogs/preferences/PreferenceTableModel.java b/application/src/main/java/cytoscape/dialogs/preferences/PreferenceTableModel.java
new file mode 100644
index 0000000..5fc7704
--- /dev/null
+++ b/application/src/main/java/cytoscape/dialogs/preferences/PreferenceTableModel.java
@@ -0,0 +1,279 @@
+/*
+ File: PreferenceTableModel.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.dialogs.preferences;
+
+import cytoscape.CytoscapeInit;
+
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.Enumeration;
+import java.util.Iterator;
+import java.util.Properties;
+import java.util.Vector;
+
+import javax.swing.table.AbstractTableModel;
+
+
+/**
+ *
+ */
+public class PreferenceTableModel extends AbstractTableModel {
+ protected static String[] columnHeader = new String[] { "Property Name", "Value" };
+
+ private Properties properties;
+ private Vector<String[]> propertiesList = new Vector<String[]>();
+
+ /**
+ * Creates a new PreferenceTableModel object.
+ */
+ public PreferenceTableModel() {
+ super();
+ // use clone of CytoscapeInit properties
+ properties = (Properties) (CytoscapeInit.getProperties().clone());
+ loadProperties();
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void loadProperties() {
+ clearVector();
+
+ String name;
+
+ for (Enumeration names = properties.propertyNames(); names.hasMoreElements();) {
+ name = (String) names.nextElement();
+ addProperty(new String[] { name, properties.getProperty(name) });
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param key DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getProperty(String key) {
+ return properties.getProperty(key);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param key DOCUMENT ME!
+ * @param defaultValue DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getProperty(String key, String defaultValue) {
+ return properties.getProperty(key, defaultValue);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param key DOCUMENT ME!
+ * @param value DOCUMENT ME!
+ */
+ public void setProperty(String key, String value) {
+ // update property object
+ properties.setProperty(key, value);
+
+ // update table model (propertiesList)
+ for (String[] prop : propertiesList) {
+ if (prop[0].equals(key)) {
+ prop[1] = value;
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param key DOCUMENT ME!
+ */
+ public void deleteProperty(String key) {
+ // remove property from property object
+ properties.remove(key);
+
+ // remove property from table model (propertiesList)
+ for (String[] prop : propertiesList) {
+ if (prop[0].equals(key)) {
+ propertiesList.remove(prop);
+
+ return;
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param val DOCUMENT ME!
+ */
+ public void addProperty(String[] val) {
+ if ((val.length < 0) || (val.length > columnHeader.length))
+ return;
+
+ // add to table model (propertiesList vector) if not present,
+ // otherwise replace existing entry
+ boolean found = false;
+
+ for (Iterator it = propertiesList.iterator(); it.hasNext();) {
+ String[] prop = (String[]) it.next();
+
+ if (prop[0].equals(val[0])) {
+ prop[1] = val[1];
+ found = true;
+ }
+ }
+
+ if (!found)
+ propertiesList.add(val);
+
+ sort();
+ // also add to local properties object for saving
+ properties.setProperty(val[0], val[1]);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param col DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getColumnName(int col) {
+ return columnHeader[col];
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void clearVector() {
+ propertiesList.clear();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param saveToProps DOCUMENT ME!
+ */
+ public void save(Properties saveToProps) {
+ // save local property values to passed-in Properties
+ saveToProps.putAll(properties);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param restoreFromProps DOCUMENT ME!
+ */
+ public void restore(Properties restoreFromProps) {
+ properties.clear();
+ properties.putAll(restoreFromProps);
+ loadProperties();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getColumnCount() {
+ return columnHeader.length;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param row DOCUMENT ME!
+ * @param col DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getValueAt(int row, int col) {
+ String[] rowData = (String[]) propertiesList.get(row);
+
+ return rowData[col];
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getRowCount() {
+ return propertiesList.size();
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void sort() {
+ Collections.sort(propertiesList, new StringComparator());
+ }
+}
+
+
+class StringComparator implements Comparator {
+ /**
+ * DOCUMENT ME!
+ *
+ * @param o1 DOCUMENT ME!
+ * @param o2 DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int compare(Object o1, Object o2) {
+ int result = 0;
+
+ String[] str1 = ((String[]) o1);
+ String[] str2 = ((String[]) o2);
+
+ for (int i = 0; i < str1.length; i++) {
+ result = str1[i].compareTo(str2[i]);
+
+ if (result != 0) {
+ return result;
+ }
+ }
+
+ return 0;
+ }
+}
diff --git a/application/src/main/java/cytoscape/dialogs/preferences/PreferenceValueDialog.java b/application/src/main/java/cytoscape/dialogs/preferences/PreferenceValueDialog.java
new file mode 100644
index 0000000..82ef838
--- /dev/null
+++ b/application/src/main/java/cytoscape/dialogs/preferences/PreferenceValueDialog.java
@@ -0,0 +1,219 @@
+/*
+ File: PreferenceValueDialog.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.dialogs.preferences;
+
+import cytoscape.*;
+
+import cytoscape.util.CyFileFilter;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import java.io.*;
+
+import javax.swing.*;
+import javax.swing.event.*;
+import javax.swing.table.*;
+
+
+/**
+ *
+ */
+public class PreferenceValueDialog extends JDialog {
+ String preferenceName = null;
+ String preferenceValue = null;
+ String title = null;
+ JLabel preferenceNameL = null;
+ JTextField value = null;
+ JButton okButton = null;
+ JButton cancelButton = null;
+ TableModel tableModel = null;
+ PreferencesDialog callerRef = null;
+
+ /**
+ * Creates a new PreferenceValueDialog object.
+ *
+ * @param owner DOCUMENT ME!
+ * @param name DOCUMENT ME!
+ * @param value DOCUMENT ME!
+ * @param caller DOCUMENT ME!
+ * @param tm DOCUMENT ME!
+ * @param title DOCUMENT ME!
+ * @param includeBrowse DOCUMENT ME!
+ *
+ * @deprecated includeBrowse is not longer supported. Use the other constructor instead.
+ * Will be removed 5/2008.
+ */
+ @Deprecated
+ public PreferenceValueDialog(Dialog owner, String name, String value, PreferencesDialog caller,
+ TableModel tm, String title, boolean includeBrowse) {
+ this(owner,name,value,caller,tm,title);
+ }
+
+ /**
+ * Creates a new PreferenceValueDialog object.
+ *
+ * @param owner DOCUMENT ME!
+ * @param name DOCUMENT ME!
+ * @param value DOCUMENT ME!
+ * @param caller DOCUMENT ME!
+ * @param tm DOCUMENT ME!
+ * @param title DOCUMENT ME!
+ */
+ public PreferenceValueDialog(Dialog owner, String name, String value, PreferencesDialog caller,
+ TableModel tm, String title) {
+ super(owner, true);
+ callerRef = caller;
+ tableModel = tm;
+ this.title = title;
+
+ preferenceName = new String(name);
+ preferenceValue = new String(value);
+
+ showDialog(owner);
+ }
+
+ protected void showDialog(Dialog owner) {
+ preferenceNameL = new JLabel(preferenceName);
+ value = new JTextField(preferenceValue, 32);
+ okButton = new JButton("OK");
+ cancelButton = new JButton("Cancel");
+
+ okButton.addActionListener(new OkButtonListener(this, callerRef));
+ cancelButton.addActionListener(new CancelButtonListener(this, callerRef));
+
+ JPanel outerPanel = new JPanel(new BorderLayout());
+ JPanel valuePanel = new JPanel(new FlowLayout());
+ JPanel buttonPanel = new JPanel(new FlowLayout());
+ valuePanel.add(preferenceNameL);
+ valuePanel.add(value);
+
+ buttonPanel.add(okButton);
+ buttonPanel.add(cancelButton);
+ outerPanel.add(valuePanel, BorderLayout.NORTH);
+ outerPanel.add(buttonPanel, BorderLayout.SOUTH);
+
+ this.getContentPane().add(outerPanel, BorderLayout.CENTER);
+ pack();
+
+ this.setTitle(title);
+ // popup relative to owner/parent
+ this.setLocationRelativeTo(owner);
+ this.setVisible(true);
+ }
+
+
+ /** @deprecated no longer used by anyting. Will leave this world Dec 2007. */
+ public String validatedPluginData(Component comp, String selection) {
+ String validatedData = null;
+ File file = new File(selection);
+
+ // directory was specified
+ if (file.isDirectory()) {
+ // must expand as list of files, as the autoloading tries to
+ // use the specified values as JAR files.
+ String[] fileList = file.list(); // could use FileFilter
+ String pluginFiles = new String("");
+
+ for (int j = 0; j < fileList.length; j++) {
+ String jarString = file.getAbsolutePath() + File.separator + fileList[j];
+
+ if (jarString.endsWith(".jar")) {
+ if (pluginFiles.length() > 0) {
+ pluginFiles = pluginFiles + "," + jarString;
+ } else {
+ pluginFiles = new String(jarString);
+ }
+ }
+ }
+
+ if (pluginFiles.length() == 0) {
+ // no *.jar files found in directory, popup info dialog
+ JOptionPane.showMessageDialog(comp, "No plugins (*.jar files) found.",
+ "Information", JOptionPane.INFORMATION_MESSAGE);
+ } else {
+ validatedData = pluginFiles;
+ }
+ } else {
+ // ordinary file was specified
+ if (!selection.endsWith(".jar")) {
+ // no *.jar files found in input string, popup info
+ // dialog
+ JOptionPane.showMessageDialog(comp, "No plugins (*.jar files) found.",
+ "Information", JOptionPane.INFORMATION_MESSAGE);
+ } else {
+ validatedData = selection;
+ }
+ }
+
+ return validatedData;
+ }
+
+ class OkButtonListener implements ActionListener {
+ PreferenceValueDialog motherRef = null;
+ PreferencesDialog grandmotherRef = null;
+
+ public OkButtonListener(PreferenceValueDialog mother, PreferencesDialog grandmother) {
+ super();
+ motherRef = mother;
+ grandmotherRef = grandmother;
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ // properties
+ motherRef.preferenceValue = motherRef.value.getText();
+ grandmotherRef.setParameter(tableModel, motherRef.preferenceName,
+ motherRef.preferenceValue);
+ motherRef.dispose();
+ }
+ }
+
+ class CancelButtonListener implements ActionListener {
+ PreferenceValueDialog motherRef = null;
+ PreferencesDialog grandmotherRef = null;
+
+ public CancelButtonListener(PreferenceValueDialog mother, PreferencesDialog grandmother) {
+ super();
+ motherRef = mother;
+ grandmotherRef = grandmother;
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ motherRef.dispose();
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/dialogs/preferences/PreferencesDialog.java b/application/src/main/java/cytoscape/dialogs/preferences/PreferencesDialog.java
new file mode 100644
index 0000000..dc14958
--- /dev/null
+++ b/application/src/main/java/cytoscape/dialogs/preferences/PreferencesDialog.java
@@ -0,0 +1,568 @@
+/*
+ File: PreferencesDialog.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.dialogs.preferences;
+
+import cytoscape.Cytoscape;
+import cytoscape.CytoscapeInit;
+
+import cytoscape.logger.CyLogger;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Dimension;
+import java.awt.FlowLayout;
+import java.awt.Font;
+import java.awt.Frame;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+
+import java.io.File;
+import java.io.FileOutputStream;
+
+import java.util.Properties;
+
+import javax.swing.BorderFactory;
+import javax.swing.Box;
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JDialog;
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTable;
+import javax.swing.JTextArea;
+import javax.swing.ListSelectionModel;
+import javax.swing.SwingConstants;
+import javax.swing.event.ListSelectionEvent;
+import javax.swing.event.ListSelectionListener;
+import javax.swing.table.DefaultTableCellRenderer;
+import javax.swing.table.TableCellRenderer;
+import javax.swing.table.TableColumn;
+import javax.swing.table.TableModel;
+
+
+/**
+ *
+ */
+public class PreferencesDialog extends JDialog implements PropertyChangeListener {
+ private static final int[] alignment = new int[] { JLabel.LEFT, JLabel.LEFT };
+ private static final int[] columnWidth = new int[] { 200, 350 };
+
+ private static final Color SELECTED_CELL_COLOR = new Color(0, 100, 255, 40);
+ private static CyLogger logger = CyLogger.getLogger(PreferencesDialog.class);
+
+ int[] selection = null;
+ JScrollPane propsTablePane = new JScrollPane();
+ JTable prefsTable = new JTable();
+ JPanel propBtnPane = new JPanel(new FlowLayout());
+ JPanel okButtonPane = new JPanel(new FlowLayout());
+ JPanel vizmapPane = new JPanel(new FlowLayout());
+ JPanel cyPropsPane = new JPanel(new FlowLayout());
+ JCheckBox saveVizmapBtn = new JCheckBox("Make Current Visual Styles Default", false);
+ JCheckBox saveCyPropsBtn = new JCheckBox("Make Current Cytoscape Properties Default", false);
+ JTextArea vizmapText = new JTextArea("Only check this option if you want the current visual styles to be defaults in ALL future cytoscape sessions. Your current visual styles are automatically saved in your Cytoscape session file and won't be lost.");
+ JTextArea cyPropsText = new JTextArea("Only check this option if you want the current Cytoscape properties to be defaults in ALL future cytoscape sessions. Your current Cytoscape properties are automatically saved in your Cytoscape session file and won't be lost.");
+ JButton addPropBtn = new JButton("Add");
+ JButton deletePropBtn = new JButton("Delete");
+ JButton modifyPropBtn = new JButton("Modify");
+ JButton okButton = new JButton("OK");
+ JButton cancelButton = new JButton("Cancel");
+
+ /**
+ *
+ */
+ public PreferenceTableModel prefsTM = null;
+ private ListSelectionModel lsm = null;
+ private boolean saveCyPropsAsDefault = false;
+ private boolean saveVizmapAsDefault = false;
+
+ // When properties are changed, it will be processed here.
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void propertyChange(PropertyChangeEvent e) {
+ if (e.getPropertyName().equals(Cytoscape.PREFERENCE_MODIFIED)) {
+ String info = "Cytoscape Prop. has changed: \n";
+ info += " - Old value is " + e.getOldValue()+"\n";
+ info += " - New value is " + e.getNewValue();
+ logger.info(info);
+
+ String propName = null;
+
+ if ((CytoscapeInit.getProperties().getProperty("defaultSpeciesName") == e.getOldValue())
+ || (CytoscapeInit.getProperties().getProperty("defaultSpeciesName") == e.getNewValue())) {
+ propName = "defaultSpeciesName";
+ } else if ((CytoscapeInit.getProperties().getProperty("defaultWebBrowser") == e.getOldValue())
+ || (CytoscapeInit.getProperties().getProperty("defaultWebBrowser") == e.getNewValue())) {
+ propName = "defaultWebBrowser";
+ }
+
+ if (propName != null) {
+ // Set to new val
+ CytoscapeInit.getProperties().setProperty(propName, (String) e.getNewValue());
+ prefsTM.setProperty(propName, (String) e.getNewValue());
+ // refresh();
+ logger.info(propName + " updated to "
+ + CytoscapeInit.getProperties().getProperty(propName));
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param tm DOCUMENT ME!
+ * @param preferenceName DOCUMENT ME!
+ * @param preferenceValue DOCUMENT ME!
+ */
+ public void setParameter(TableModel tm, String preferenceName, String preferenceValue) {
+ // preferences/properties
+ if (tm == prefsTM) {
+ Cytoscape.firePropertyChange(Cytoscape.PREFERENCE_MODIFIED,
+ prefsTM.getProperty(preferenceName), preferenceValue);
+ prefsTM.setProperty(preferenceName, preferenceValue);
+ }
+
+ refresh();
+
+ // reset state of Modify and Delete buttons to inactive
+ // since update of parameter will clear any selections
+ modifyPropBtn.setEnabled(false);
+ deletePropBtn.setEnabled(false);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void refresh() {
+ // refresh the view
+ prefsTable.setModel(prefsTM);
+
+ prefsTable.clearSelection();
+ prefsTable.revalidate();
+ prefsTable.repaint();
+ }
+
+ private void initButtonPane() {
+ propBtnPane.add(addPropBtn);
+ propBtnPane.add(modifyPropBtn);
+ propBtnPane.add(deletePropBtn);
+
+ okButtonPane.add(okButton);
+ okButtonPane.add(cancelButton);
+
+ modifyPropBtn.setEnabled(false);
+ deletePropBtn.setEnabled(false);
+ addPropBtn.addActionListener(new AddPropertyListener(this));
+ modifyPropBtn.addActionListener(new ModifyPropertyListener(this));
+ deletePropBtn.addActionListener(new DeletePropertyListener(this));
+ okButton.addActionListener(new OkButtonListener(this));
+ cancelButton.addActionListener(new CancelButtonListener(this));
+ saveVizmapBtn.addItemListener(new CheckBoxListener());
+ saveCyPropsBtn.addItemListener(new CheckBoxListener());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public PreferenceTableModel getPTM() {
+ return prefsTM;
+ }
+
+ private void initTable() {
+ prefsTM = new PreferenceTableModel();
+
+ prefsTable.setAutoCreateColumnsFromModel(false);
+ prefsTable.setRowSelectionAllowed(true);
+ lsm = prefsTable.getSelectionModel();
+ lsm.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
+ lsm.addListSelectionListener(new TableListener(this, lsm));
+
+ prefsTable.setModel(prefsTM);
+
+ prefsTable.setRowHeight(16);
+ TableColumn column;
+ DefaultTableCellRenderer renderer = new DefaultTableCellRenderer() {
+
+ public Component getTableCellRendererComponent(JTable table,
+ Object value, boolean isSelected, boolean hasFocus,
+ int row, int column) {
+
+ setFont(new Font("SansSerif", Font.PLAIN, 12));
+ setVerticalTextPosition(SwingConstants.CENTER);
+ if(isSelected)
+ setBackground(SELECTED_CELL_COLOR);
+ else
+ setBackground(Color.WHITE);
+
+ if(value != null) {
+ setToolTipText(value.toString());
+ setText(value.toString());
+ } else
+ setText("");
+ return this;
+ }};
+
+ for (int i = 0; i < PreferenceTableModel.columnHeader.length; i++) {
+ renderer.setHorizontalAlignment(alignment[i]);
+ column = new TableColumn(i, columnWidth[i], renderer, null);
+ column.setIdentifier(PreferenceTableModel.columnHeader[i]);
+ prefsTable.addColumn(column);
+ }
+ }
+
+ /**
+ * Creates a new PreferencesDialog object.
+ *
+ * @param owner DOCUMENT ME!
+ */
+ public PreferencesDialog(Frame owner) {
+ super(owner);
+
+ Cytoscape.getSwingPropertyChangeSupport().addPropertyChangeListener(this);
+
+ initButtonPane();
+ initTable();
+
+ try {
+ prefPopupInit();
+ } catch (Exception e) {
+ logger.warn("Unable to initialize preferences popup: "+e.getMessage(), e);
+ }
+
+ this.setTitle("Cytoscape Preferences Editor");
+ pack();
+ // set location relative to owner/parent
+ this.setLocationRelativeTo(owner);
+ this.setVisible(true);
+ }
+
+ private void prefPopupInit() throws Exception {
+ java.awt.GridBagConstraints gridBagConstraints;
+
+ JPanel outerPanel = new JPanel(new java.awt.GridBagLayout());
+
+ JPanel propsTablePanel = new JPanel(new java.awt.GridBagLayout());
+ propsTablePanel.setBorder(BorderFactory.createTitledBorder("Properties"));
+
+ propsTablePane.setBorder(BorderFactory.createEmptyBorder(2, 9, 4, 9));
+ propsTablePane.getViewport().add(prefsTable, null);
+ prefsTable.setPreferredScrollableViewportSize(new Dimension(500, 300));
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.fill = java.awt.GridBagConstraints.BOTH;
+ gridBagConstraints.weightx = 1.0;
+ gridBagConstraints.weighty = 1.0;
+ propsTablePanel.add(propsTablePane, gridBagConstraints);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = 1;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.insets = new java.awt.Insets(10, 0, 0, 0);
+ propsTablePanel.add(propBtnPane, gridBagConstraints);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.fill = java.awt.GridBagConstraints.BOTH;
+ gridBagConstraints.weightx = 1.0;
+ gridBagConstraints.weighty = 1.0;
+ gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
+ outerPanel.add(propsTablePanel, gridBagConstraints);
+
+ JTextArea textArea = new JTextArea("NOTE: Changes to these properties are used in the current session ONLY unless otherwise specified below.");
+
+ textArea.setBackground(outerPanel.getBackground());
+ textArea.setEditable(false);
+ textArea.setDragEnabled(false);
+ textArea.setLineWrap(true);
+ textArea.setWrapStyleWord(true);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = 1;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.insets = new java.awt.Insets(0, 10, 10, 10);
+ outerPanel.add(textArea, gridBagConstraints);
+
+ Box vizmapBox = Box.createVerticalBox();
+ vizmapBox.setBorder(BorderFactory.createTitledBorder("Default Visual Styles"));
+ vizmapText.setBackground(outerPanel.getBackground());
+ vizmapText.setEditable(false);
+ vizmapText.setDragEnabled(false);
+ vizmapText.setLineWrap(true);
+ vizmapText.setWrapStyleWord(true);
+ vizmapBox.add(vizmapText);
+ vizmapBox.add(Box.createVerticalStrut(5));
+ vizmapPane.add(saveVizmapBtn);
+ vizmapBox.add(vizmapPane);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = 2;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.insets = new java.awt.Insets(0, 10, 10, 10);
+ outerPanel.add(vizmapBox, gridBagConstraints);
+
+ Box cyPropsBox = Box.createVerticalBox();
+ cyPropsBox.setBorder(BorderFactory.createTitledBorder("Default Cytoscape Properties"));
+ cyPropsText.setBackground(outerPanel.getBackground());
+ cyPropsText.setEditable(false);
+ cyPropsText.setDragEnabled(false);
+ cyPropsText.setLineWrap(true);
+ cyPropsText.setWrapStyleWord(true);
+ cyPropsBox.add(cyPropsText);
+ cyPropsBox.add(Box.createVerticalStrut(5));
+ cyPropsPane.add(saveCyPropsBtn);
+ cyPropsBox.add(cyPropsPane);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = 3;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.insets = new java.awt.Insets(0, 10, 10, 10);
+ outerPanel.add(cyPropsBox, gridBagConstraints);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = 4;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.insets = new java.awt.Insets(0, 10, 10, 10);
+ outerPanel.add(okButtonPane, gridBagConstraints);
+
+ this.getContentPane().add(outerPanel, BorderLayout.CENTER);
+ }
+
+ class AddPropertyListener implements ActionListener {
+ PreferencesDialog callerRef = null;
+
+ public AddPropertyListener(PreferencesDialog caller) {
+ super();
+ callerRef = caller;
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ String key = JOptionPane.showInputDialog(addPropBtn, "Enter property name:",
+ "Add Property", JOptionPane.QUESTION_MESSAGE);
+
+ if (key != null) {
+ String value = JOptionPane.showInputDialog(addPropBtn,
+ "Enter value for property " + key + ":",
+ "Add Property Value",
+ JOptionPane.QUESTION_MESSAGE);
+
+ if (value != null) {
+ String[] vals = { key, value };
+ prefsTM.addProperty(vals);
+ refresh(); // refresh view in table
+ }
+ }
+ }
+ }
+
+ class ModifyPropertyListener implements ActionListener {
+ PreferencesDialog callerRef = null;
+
+ public ModifyPropertyListener(PreferencesDialog caller) {
+ super();
+ callerRef = caller;
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ for (int i = 0; i < selection.length; i++) {
+ String name = new String((String) (prefsTM.getValueAt(selection[i], 0)));
+ String value = new String((String) (prefsTM.getValueAt(selection[i], 1)));
+
+ PreferenceValueDialog pd = new PreferenceValueDialog(PreferencesDialog.this, name,
+ value, callerRef, prefsTM,
+ "Modify value...");
+ }
+ }
+ }
+
+ class DeletePropertyListener implements ActionListener {
+ PreferencesDialog callerRef = null;
+
+ public DeletePropertyListener(PreferencesDialog caller) {
+ super();
+ callerRef = caller;
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ for (int i = 0; i < selection.length; i++) {
+ String name = new String((String) (prefsTM.getValueAt(selection[i], 0)));
+ prefsTM.deleteProperty(name);
+ }
+
+ refresh();
+ }
+ }
+
+ class OkButtonListener implements ActionListener {
+ PreferencesDialog callerRef = null;
+
+ public OkButtonListener(PreferencesDialog caller) {
+ super();
+ callerRef = caller;
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ // just saving via putAll() doesn't handle deletes...
+ // therefore use TableModel's putAll() into new Properties obj
+ // then clear Cytoscape's properties and
+ Properties newProps = new Properties();
+ callerRef.prefsTM.save(newProps);
+ CytoscapeInit.getProperties().clear();
+ CytoscapeInit.getProperties().putAll(newProps);
+ callerRef.setVisible(false);
+
+ if (saveVizmapAsDefault) {
+ Cytoscape.firePropertyChange(Cytoscape.SAVE_VIZMAP_PROPS, null, null);
+ saveVizmapAsDefault = false;
+ saveVizmapBtn.setSelected(false);
+ }
+
+ if (saveCyPropsAsDefault) {
+ try {
+ File file = CytoscapeInit.getConfigFile("cytoscape.props");
+ FileOutputStream output = null;
+ try {
+ output = new FileOutputStream(file);
+ CytoscapeInit.getProperties().store(output, "Cytoscape Property File");
+ logger.info("wrote Cytoscape properties file to: " + file.getAbsolutePath());
+ }
+ finally {
+ if (output != null) {
+ output.close();
+ }
+ }
+ } catch (Exception ex) {
+ logger.error("Could not write cytoscape.props file!", ex);
+ }
+
+ saveCyPropsAsDefault = false;
+ saveCyPropsBtn.setSelected(false);
+ }
+
+ Cytoscape.firePropertyChange(Cytoscape.PREFERENCES_UPDATED, null, null);
+ }
+ }
+
+ class CheckBoxListener implements ItemListener {
+ public CheckBoxListener() {
+ super();
+ }
+
+ public void itemStateChanged(ItemEvent e) {
+ Object source = e.getItemSelectable();
+
+ if (e.getStateChange() == ItemEvent.SELECTED) {
+ if (source == saveVizmapBtn)
+ saveVizmapAsDefault = true;
+
+ if (source == saveCyPropsBtn)
+ saveCyPropsAsDefault = true;
+ }
+ }
+ }
+
+ class CancelButtonListener implements ActionListener {
+ PreferencesDialog callerRef = null;
+
+ public CancelButtonListener(PreferencesDialog caller) {
+ super();
+ callerRef = caller;
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ Properties oldProps = CytoscapeInit.getProperties();
+ callerRef.prefsTM.restore(oldProps);
+ callerRef.setVisible(false);
+ }
+ }
+
+ class TableListener implements ListSelectionListener {
+ private ListSelectionModel model = null;
+ private PreferencesDialog motherRef = null;
+
+ public TableListener(PreferencesDialog mother, ListSelectionModel lsm) {
+ motherRef = mother;
+ model = lsm;
+ }
+
+ public void valueChanged(ListSelectionEvent lse) {
+ if (!lse.getValueIsAdjusting()) {
+ selection = getSelectedIndices(model.getMinSelectionIndex(),
+ model.getMaxSelectionIndex());
+
+ if (selection.length == 0) {
+ } else {
+ modifyPropBtn.setEnabled(true);
+ deletePropBtn.setEnabled(true);
+ }
+ }
+ }
+
+ protected int[] getSelectedIndices(int start, int stop) {
+ if ((start == -1) || (stop == -1)) {
+ return new int[0];
+ }
+
+ int[] guesses = new int[stop - start + 1];
+ int index = 0;
+
+ for (int i = start; i <= stop; i++) {
+ if (model.isSelectedIndex(i)) {
+ guesses[index++] = i;
+ }
+ }
+
+ int[] realthing = new int[index];
+ System.arraycopy(guesses, 0, realthing, 0, index);
+
+ return realthing;
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/dialogs/preferences/ProxyServerDialog.java b/application/src/main/java/cytoscape/dialogs/preferences/ProxyServerDialog.java
new file mode 100644
index 0000000..c827ec1
--- /dev/null
+++ b/application/src/main/java/cytoscape/dialogs/preferences/ProxyServerDialog.java
@@ -0,0 +1,447 @@
+/*
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.dialogs.preferences;
+
+import java.awt.Dimension;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.Insets;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.net.InetSocketAddress;
+import java.net.Proxy;
+import java.net.URL;
+import java.net.URLConnection;
+import java.util.Properties;
+
+import javax.swing.BorderFactory;
+import javax.swing.DefaultComboBoxModel;
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JComboBox;
+import javax.swing.JDialog;
+import javax.swing.JFrame;
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JTextField;
+import javax.swing.WindowConstants;
+
+import cytoscape.Cytoscape;
+import cytoscape.CytoscapeInit;
+import cytoscape.logger.CyLogger;
+import cytoscape.util.ProxyHandler;
+
+
+/**
+ *
+ */
+public class ProxyServerDialog extends JDialog implements ActionListener, ItemListener {
+
+ private static final long serialVersionUID = -2693844068486336199L;
+ private static final String WELL_KNOWN_URL = "http://google.com";
+ private static final String PROPERTIES_FILE_NAME = "cytoscape.props";
+
+ /** Creates new form URLimportAdvancedDialog */
+ public ProxyServerDialog(JFrame pParent) {
+ super(pParent, true);
+ this.setTitle("Proxy Server Settings");
+ this.setLocationRelativeTo(pParent);
+
+ initComponents();
+ initValues();
+ }
+
+ private JButton btnCancel;
+ // TODO: Change the update button only be enabled when there has
+ // been a change that needs updating.
+ private JButton btnUpdate;
+ private JCheckBox chbUseProxy;
+ private JComboBox cmbType;
+ private JPanel jPanel1;
+ private JPanel jPanel2;
+ private JPanel jPanel3;
+ private JLabel lbHost;
+ private JLabel lbPort;
+ private JLabel lbType;
+ private JLabel lbUseProxy;
+ private JTextField tfHost;
+ private JTextField tfPort;
+ private boolean _lastUseProxy;
+ private String _lastProxyHost;
+ private String _lastProxyPort;
+ private String _lastProxyType;
+
+ private void initComponents() {
+
+ GridBagConstraints gridBagConstraints;
+
+ jPanel3 = new JPanel();
+ lbUseProxy = new JLabel();
+ chbUseProxy = new JCheckBox();
+ jPanel1 = new JPanel();
+ btnUpdate = new JButton();
+ btnCancel = new JButton();
+ jPanel2 = new JPanel();
+ lbType = new JLabel();
+ lbHost = new JLabel();
+ lbPort = new JLabel();
+ cmbType = new JComboBox();
+ tfHost = new JTextField();
+ tfPort = new JTextField();
+
+ getContentPane().setLayout(new GridBagLayout());
+
+ setDefaultCloseOperation(WindowConstants.DISPOSE_ON_CLOSE);
+ lbUseProxy.setText("Use Proxy");
+ jPanel3.add(lbUseProxy);
+
+ chbUseProxy.setBorder(BorderFactory.createEmptyBorder(0, 0, 0, 0));
+ chbUseProxy.setMargin(new Insets(0, 0, 0, 0));
+ jPanel3.add(chbUseProxy);
+
+ gridBagConstraints = new GridBagConstraints();
+ gridBagConstraints.gridx = 0;
+ gridBagConstraints.anchor = GridBagConstraints.WEST;
+ gridBagConstraints.insets = new Insets(5, 5, 5, 5);
+ getContentPane().add(jPanel3, gridBagConstraints);
+
+ btnUpdate.setText("Update");
+ jPanel1.add(btnUpdate);
+
+ btnCancel.setText("Cancel");
+ jPanel1.add(btnCancel);
+
+ gridBagConstraints = new GridBagConstraints();
+ gridBagConstraints.gridy = 3;
+ gridBagConstraints.gridwidth = GridBagConstraints.REMAINDER;
+ gridBagConstraints.insets = new Insets(10, 0, 0, 0);
+ getContentPane().add(jPanel1, gridBagConstraints);
+
+ jPanel2.setLayout(new GridBagLayout());
+
+ jPanel2.setBorder(BorderFactory.createTitledBorder("Proxy Settings"));
+ lbType.setText("Type");
+ gridBagConstraints = new GridBagConstraints();
+ gridBagConstraints.gridy = 1;
+ jPanel2.add(lbType, gridBagConstraints);
+
+ lbHost.setText("Host name");
+ gridBagConstraints = new GridBagConstraints();
+ gridBagConstraints.gridy = 1;
+ jPanel2.add(lbHost, gridBagConstraints);
+
+ lbPort.setText("Port");
+ gridBagConstraints = new GridBagConstraints();
+ gridBagConstraints.gridy = 1;
+ jPanel2.add(lbPort, gridBagConstraints);
+
+ cmbType.setModel(new DefaultComboBoxModel(new String[] { "HTTP", "SOCKS" }));
+ cmbType.setMinimumSize(new Dimension(61, 18));
+ gridBagConstraints = new GridBagConstraints();
+ gridBagConstraints.gridy = 2;
+ gridBagConstraints.insets = new Insets(5, 10, 10, 5);
+ jPanel2.add(cmbType, gridBagConstraints);
+
+ gridBagConstraints = new GridBagConstraints();
+ gridBagConstraints.gridy = 2;
+ gridBagConstraints.fill = GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.weightx = 1.0;
+ gridBagConstraints.insets = new Insets(5, 5, 10, 5);
+ jPanel2.add(tfHost, gridBagConstraints);
+
+ final int tfPortHeight = (int)tfHost.getMinimumSize().getHeight();
+ tfPort.setMinimumSize(new Dimension(43, tfPortHeight));
+ tfPort.setPreferredSize(new Dimension(43, tfPortHeight));
+ gridBagConstraints = new GridBagConstraints();
+ gridBagConstraints.gridy = 2;
+ gridBagConstraints.insets = new Insets(5, 5, 10, 10);
+ jPanel2.add(tfPort, gridBagConstraints);
+
+ gridBagConstraints = new GridBagConstraints();
+ gridBagConstraints.gridx = 0;
+ gridBagConstraints.gridy = 1;
+ gridBagConstraints.fill = GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.weightx = 1.0;
+ getContentPane().add(jPanel2, gridBagConstraints);
+
+ // add event listeners
+ btnUpdate.addActionListener(this);
+ btnCancel.addActionListener(this);
+ //cmbType.addItemListener(this);
+ chbUseProxy.addItemListener(this);
+
+ pack();
+ setSize(new Dimension(400, 210));
+ } // </editor-fold>
+
+ private void initValues() {
+ // initially set the last values as they are read from the
+ // ProxyHandler. We will compare these to the final values
+ // to see if anything changed.
+ _lastUseProxy = false;
+ _lastProxyHost = "";
+ _lastProxyPort = "";
+ _lastProxyType = "";
+
+ Proxy p = ProxyHandler.getProxyServer();
+ chbUseProxy.setSelected(true);
+ cmbType.setEnabled(true);
+ tfHost.setEnabled(true);
+ tfPort.setEnabled(true);
+
+ if ((p != null) && (p.type() != Proxy.Type.DIRECT)) {
+ _lastUseProxy = true;
+ if (p.type() == Proxy.Type.HTTP) {
+ _lastProxyType = "HTTP";
+ cmbType.setSelectedItem(_lastProxyType);
+ } else if (p.type() == Proxy.Type.SOCKS) {
+ _lastProxyType = "SOCKS";
+ cmbType.setSelectedItem(_lastProxyType);
+ }
+
+ InetSocketAddress address = (InetSocketAddress) p.address();
+ _lastProxyHost = address.getHostName();
+ _lastProxyPort = new Integer(address.getPort()).toString();
+ } else {
+ chbUseProxy.setSelected(false);
+ cmbType.setEnabled(false);
+ tfHost.setEnabled(false);
+ tfPort.setEnabled(false);
+ }
+ tfHost.setText(_lastProxyHost);
+ tfPort.setText(_lastProxyPort);
+
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void itemStateChanged(ItemEvent e) {
+
+ Object _actionObject = e.getSource();
+
+ if (_actionObject instanceof JCheckBox)
+ {
+ if (chbUseProxy.isSelected()) { // UseProxy is checked
+ // enable the setting panel
+ cmbType.setEnabled(true);
+ tfHost.setEnabled(true);
+ tfPort.setEnabled(true);
+ }
+ else
+ {// UseProxy is unchecked
+ // disable the setting panel
+ cmbType.setEnabled(false);
+ tfHost.setEnabled(false);
+ tfPort.setEnabled(false);
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ // TODO: Split each action into a separate private class so _btn and _actionObject are not needed:
+ public void actionPerformed(ActionEvent e) {
+ Object _actionObject = e.getSource();
+
+ // handle Button events
+ if (_actionObject instanceof JButton) {
+ JButton _btn = (JButton) _actionObject;
+
+ if (_btn == btnCancel) {
+ this.dispose();
+ } else if (_btn == btnUpdate) {
+ if (!updateProxyServer())
+ return;
+
+ this.dispose();
+ }
+ }
+ }
+
+ private boolean updateProxyServer() {
+ Proxy.Type proxyType = Proxy.Type.valueOf(cmbType.getSelectedItem().toString());
+
+ // If UseProxy is unchecked, that means NULL proxy sever
+ if (!chbUseProxy.isSelected()) {
+ tfHost.setText("");
+ tfPort.setText("");
+ // If Host or Port is empty, ProxyServer will be set to NULL
+ }
+ else { //UseProxy is checked
+ // Try if we can create a proxyServer, if not, report error
+ if (tfHost.getText().trim().equals("")) {
+ JOptionPane.showMessageDialog(this, "Host name is empty!", "Warning",
+ JOptionPane.INFORMATION_MESSAGE);
+ return false;
+ }
+
+ int thePort;
+
+ try {
+ Integer tmpInteger = new Integer(tfPort.getText().trim());
+ thePort = tmpInteger.intValue();
+ } catch (Exception exp) {
+ JOptionPane.showMessageDialog(this, "Port error!", "Warning",
+ JOptionPane.INFORMATION_MESSAGE);
+ return false;
+ }
+
+ InetSocketAddress theAddress = new InetSocketAddress(tfHost.getText().trim(), thePort);
+
+ try {
+ new Proxy(proxyType, theAddress);
+ } catch (Exception expProxy) {
+ JOptionPane.showMessageDialog(this, "Proxy server error!", "Warning",
+ JOptionPane.INFORMATION_MESSAGE);
+ return false;
+ }
+ //Yes, got valid input for a proxy server
+ }
+
+ // Update the proxy server info
+ CytoscapeInit.getProperties().setProperty(ProxyHandler.PROXY_HOST_PROPERTY_NAME, tfHost.getText().trim());
+ CytoscapeInit.getProperties().setProperty(ProxyHandler.PROXY_PORT_PROPERTY_NAME, tfPort.getText());
+ CytoscapeInit.getProperties()
+ .setProperty(ProxyHandler.PROXY_TYPE_PROPERTY_NAME, cmbType.getSelectedItem().toString());
+ return saveProxyChangesAndTestWhenNeeded ();
+ }
+
+ // Return true iff something with the proxy settings has changes
+ // since this dialog was constructed:
+ private boolean hasProxyValuesChanged () {
+ return ((_lastUseProxy != chbUseProxy.isSelected()) ||
+ (!_lastProxyType.equals (cmbType.getSelectedItem().toString())) ||
+ (!_lastProxyPort.equals (tfPort.getText())) ||
+ (!_lastProxyHost.equals (tfHost.getText().trim())));
+ }
+
+
+ // TODO: This method is using knowledge of how properties are loaded
+ // and saved. A better approach is to add some property management
+ // classes or methods that encapsulate this behavior. This also
+ // applies to the PreferencesDialog.
+
+ private boolean saveProxyChangesAndTestWhenNeeded () {
+
+ if (!hasProxyValuesChanged ()) {
+ // nothing requires saving, but test the Proxy:
+ return performProxyTest();
+ }
+ // To avoid saving potentially unwanted, temporary properties,
+ // we can't just save the existing in-memory
+ // properties. Instead, we must read the last saved properties
+ // into a new Properties object, add the proxy values, and
+ // save the Properties back out. If the user saved the in-memory
+ // properties, that will be fine also, since the proxy info
+ // has been updated there.
+
+ Properties inMemoryProps = CytoscapeInit.getProperties();
+ Properties propsToSave = new Properties();
+ // fill in propsToSave with the last read properties (NOT the
+ // existing in-memory properties):
+ CytoscapeInit.loadStaticProperties (PROPERTIES_FILE_NAME, propsToSave);
+ // Now add in-memory values to our Properties to save:
+ propsToSave.setProperty (ProxyHandler.PROXY_HOST_PROPERTY_NAME,
+ inMemoryProps.getProperty(ProxyHandler.PROXY_HOST_PROPERTY_NAME,null));
+ propsToSave.setProperty (ProxyHandler.PROXY_PORT_PROPERTY_NAME,
+ inMemoryProps.getProperty(ProxyHandler.PROXY_PORT_PROPERTY_NAME,null));
+ propsToSave.setProperty (ProxyHandler.PROXY_TYPE_PROPERTY_NAME,
+ inMemoryProps.getProperty(ProxyHandler.PROXY_TYPE_PROPERTY_NAME,null));
+ // Now save the updated properties back out:
+ try {
+ File file = CytoscapeInit.getConfigFile(PROPERTIES_FILE_NAME);
+ FileOutputStream output = null;
+ try {
+ output = new FileOutputStream(file);
+ propsToSave.store(output, "Cytoscape Property File");
+ CyLogger.getLogger().info("wrote Cytoscape properties file to: " + file.getAbsolutePath());
+ }
+ finally {
+ if (output != null) {
+ output.close();
+ }
+ }
+ } catch (Exception ex) {
+ CyLogger.getLogger().error("Could not write the " + PROPERTIES_FILE_NAME + " file!", ex);
+ }
+ // Even if the properties were not sucessfully written, signal
+ // they changed in memory. The ProxyHandler will use this
+ // event to update the real Proxy:
+ Cytoscape.firePropertyChange(Cytoscape.PREFERENCES_UPDATED, null, null);
+ return performProxyTest ();
+ }
+
+ private boolean performProxyTest () {
+ if (testNetConnection (ProxyHandler.getProxyServer(), 2000)) {
+ JOptionPane.showMessageDialog (this,
+ "We successfully connected to " + WELL_KNOWN_URL + " using your new settings!");
+ return true;
+ } else {
+ JOptionPane.showMessageDialog (this,
+ "<HTML>We could <STRONG>not connect</STRONG> to " + WELL_KNOWN_URL + " using your new settings.");
+ return false;
+ }
+ }
+
+ // Attempt to connect to a well known site (e.g., google.com):
+ // return true if we successfully connected to the Internet to
+ // a well know site. Return false otherwise.
+ private boolean testNetConnection(final Proxy proxy, final int ms_timeout) {
+ try {
+ final URL u = new URL(WELL_KNOWN_URL);
+ URLConnection uc = null;
+ if (proxy != null) {
+ uc = u.openConnection(proxy);
+ } else {
+ uc = u.openConnection();
+ }
+ uc.setAllowUserInteraction(false);
+ uc.setUseCaches(false); // don't use a cached page
+ uc.setConnectTimeout(ms_timeout);
+ uc.connect();
+ return true;
+ } catch (IOException e) {
+ // we couldn't connect:
+ return false;
+ }
+ }
+
+
+}
diff --git a/application/src/main/java/cytoscape/ding/CyGraphAllLOD.java b/application/src/main/java/cytoscape/ding/CyGraphAllLOD.java
new file mode 100644
index 0000000..93ae67d
--- /dev/null
+++ b/application/src/main/java/cytoscape/ding/CyGraphAllLOD.java
@@ -0,0 +1,66 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.ding;
+
+import cytoscape.render.stateful.GraphLOD;
+import ding.view.PrintLOD;
+
+
+/**
+ * CyGraphAllLOD is the level of detail (LOD) class used
+ * for the "Show Graphics Details" menu item. It should
+ * be thought of as a "preview" for printing or exporting
+ * a network to some high-resolution graphical format (PDF,
+ * SVG, etc.). Essentially, this extends PrintLOD, but to
+ * preserve some efficiency we override the textAsShape method
+ * to allow us to continue to use fonts.
+ */
+public class CyGraphAllLOD extends PrintLOD {
+ /**
+ * textAsShape is called to determine if the text
+ * labels should be converted from fonts to text
+ *
+ * @param renderNodeCount the number of nodes
+ * @param renderEdgeCount the number of edges
+ *
+ * @return true if text should be converted to shapes, false otherwise
+ */
+ public boolean textAsShape(int renderNodeCount, int renderEdgeCount) {
+ return false;
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/ding/CyGraphLOD.java b/application/src/main/java/cytoscape/ding/CyGraphLOD.java
new file mode 100644
index 0000000..819bc31
--- /dev/null
+++ b/application/src/main/java/cytoscape/ding/CyGraphLOD.java
@@ -0,0 +1,318 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.ding;
+
+import cytoscape.Cytoscape;
+import cytoscape.CytoscapeInit;
+import cytoscape.util.PropUtil;
+
+import cytoscape.render.stateful.GraphLOD;
+
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+
+import java.util.Properties;
+
+
+/**
+ * An instance of this class defines the level of detail that goes into
+ * a single rendering of a graph. This class is meant to be subclassed; its
+ * methods are meant to be overridden; nonetheless, sane defaults are
+ * used in the default method implementations.<p>
+ * To understand the significance of each method's return value, it makes
+ * sense to become familiar with the API cytoscape.render.immed.GraphGraphics.
+ */
+public class CyGraphLOD extends GraphLOD implements PropertyChangeListener {
+ protected int coarseDetailThreshold;
+ protected int nodeBorderThreshold;
+ protected int nodeLabelThreshold;
+ protected int edgeArrowThreshold;
+ protected int edgeLabelThreshold;
+
+ /**
+ * Creates a new CyGraphLOD object.
+ */
+ public CyGraphLOD() {
+ init();
+ Cytoscape.getSwingPropertyChangeSupport().addPropertyChangeListener(this);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void propertyChange(PropertyChangeEvent e) {
+ if (Cytoscape.PREFERENCES_UPDATED.equals(e.getPropertyName())) {
+ init();
+
+ java.util.Map networkViewMap = cytoscape.Cytoscape.getNetworkViewMap();
+ java.util.Iterator foo = networkViewMap.values().iterator();
+
+ while (foo.hasNext()) {
+ ((ding.view.DGraphView) foo.next()).setGraphLOD(this);
+ }
+ }
+ }
+
+ protected void init() {
+ Properties p = CytoscapeInit.getProperties();
+ coarseDetailThreshold = PropUtil.getInt(p,"render.coarseDetailThreshold", 2000);
+ nodeBorderThreshold = PropUtil.getInt(p,"render.nodeBorderThreshold", 200);
+ nodeLabelThreshold = PropUtil.getInt(p,"render.nodeLabelThreshold", 100);
+ edgeArrowThreshold = PropUtil.getInt(p,"render.edgeArrowThreshold", 300);
+ edgeLabelThreshold = PropUtil.getInt(p,"render.edgeLabelThreshold", 120);
+ }
+
+ /**
+ * @deprecated Use PropUtil.getInt(..) instead. Leaving Feb 2011.
+ */
+ @Deprecated
+ protected int getInt(String key, int defaultValue) {
+ return PropUtil.getInt(CytoscapeInit.getProperties(),key,defaultValue);
+ }
+
+ /**
+ * @deprecated Use PropUtil.getBoolean(..) instead. Leaving Feb 2011.
+ */
+ @Deprecated
+ protected boolean getBoolean(String key, boolean defaultValue) {
+ return PropUtil.getBoolean(CytoscapeInit.getProperties(),key,defaultValue);
+ }
+
+ /**
+ * Determines whether or not to render all edges in a graph, no edges, or
+ * only those edges which touch a visible node. By default
+ * this method returns zero, which leads the rendering engine to render
+ * only those edges that touch at least one visible node. If a positive
+ * value is returned, all edges in the graph will be rendered. If a negative
+ * value is returned, no edges will be rendered. This is the first
+ * method called on an instance of GraphLOD by the rendering engine;
+ * the renderEdgeCount parameter passed to other methods
+ * will have a value which reflects the decision made by the return value
+ * of this method call.<p>
+ * Note that rendering all edges leads to a dramatic performance decrease
+ * when rendering large graphs.
+ * @param visibleNodeCount the number of nodes visible in the current
+ * viewport; note that a visible node is not necessarily a rendered node,
+ * because visible nodes with zero width or height are not rendered.
+ * @param totalNodeCount the total number of nodes in the graph that is
+ * being rendered.
+ * @param totalEdgeCount the total number of edges in the graph that is
+ * being rendered.
+ * @return zero if only edges touching a visible node are to be rendered,
+ * positive if all edges are to be rendered, or negative if no edges
+ * are to be rendered.
+ */
+ public byte renderEdges(final int visibleNodeCount, final int totalNodeCount,
+ final int totalEdgeCount) {
+ if (totalEdgeCount >= Math.min(edgeArrowThreshold, edgeLabelThreshold)) {
+ return (byte) 0;
+ } else {
+ return (byte) 1;
+ }
+ }
+
+ /**
+ * Determines whether or not to render a graph at full detail.
+ * By default this method returns true if and only if the sum of rendered
+ * nodes and rendered edges is less than 1200.<p>
+ * The following table describes the difference between full and low
+ * rendering detail in terms of what methods on an instance of
+ * GraphGraphics get called:
+ * <blockquote><table border="1" cellpadding="5" cellspacing="0">
+ * <tr> <td></td>
+ * <th>full detail</th>
+ * <th>low detail</th> </tr>
+ * <tr> <th>nodes</th>
+ * <td>drawNodeFull()</td>
+ * <td>drawNodeLow()</td> </tr>
+ * <tr> <th>edges</th>
+ * <td>drawEdgeFull()</td>
+ * <td>drawEdgeLow()</td> </tr>
+ * <tr> <th>node labels</th>
+ * <td>drawTextFull()</td>
+ * <td>not rendered</td> </tr>
+ * <tr> <th>edge labels</th>
+ * <td>drawTextFull()</td>
+ * <td>not rendered</td> </tr>
+ * <tr> <th>custom node graphics</th>
+ * <td>drawCustomGraphicFull()</td>
+ * <td>not rendered</td> </tr>
+ * </table></blockquote>
+ * @param renderNodeCount the number of nodes that are about to be rendered.
+ * @param renderEdgeCount the number of edges that are about to be rendered.
+ * @return true for full detail, false for low detail.
+ */
+ public boolean detail(final int renderNodeCount, final int renderEdgeCount) {
+ return (renderNodeCount + renderEdgeCount) < coarseDetailThreshold;
+ }
+
+ /**
+ * Determines whether or not to render node borders. By default this
+ * method returns true if and only if the number of rendered nodes
+ * is less than 200.<p>
+ * It is only possible to draw node borders at the full detail
+ * level. If low detail is chosen, the output of this method is ignored.
+ * @param renderNodeCount the number of nodes that are about to be rendered.
+ * @param renderEdgeCount the number of edges that are about to be rendered.
+ * @return true if and only if node borders are to be rendered.
+ * @see #detail(int, int)
+ */
+ public boolean nodeBorders(final int renderNodeCount, final int renderEdgeCount) {
+ return renderNodeCount < nodeBorderThreshold;
+ }
+
+ /**
+ * Determines whether or not to render node labels. By default this method
+ * returns true if and only if the number of rendered nodes is less than
+ * 60.<p>
+ * Node labels are only rendered at the full detail level. If low detail is
+ * chosen, the output of this method is ignored.
+ * @param renderNodeCount the number of nodes that are about to be rendered.
+ * @param renderEdgeCount the number of edges that are about to be rendered.
+ * @return true if and only if node labels are to be rendered.
+ * @see #detail(int, int)
+ */
+ public boolean nodeLabels(final int renderNodeCount, final int renderEdgeCount) {
+ return renderNodeCount < nodeLabelThreshold;
+ }
+
+ /**
+ * Determines whether or not to render custom graphics on nodes.
+ * By default this method returns true if and only if the number of rendered
+ * nodes is less than 60.<p>
+ * Custom node graphics are only rendered at the full detail level. If low
+ * detail is chosen, the output of this method is ignored.
+ * @param renderNodeCount the number of nodes that are about to be rendered.
+ * @param renderEdgeCount the number of edges that are about to be rendered.
+ * @return true if and only if custom node graphics are to be rendered.
+ * @see #detail(int, int)
+ */
+ public boolean customGraphics(final int renderNodeCount, final int renderEdgeCount) {
+ return renderNodeCount < nodeBorderThreshold;
+ }
+
+ /**
+ * Determines whether or not to render edge arrows. By default this
+ * method returns true if and only if the number of rendered edges is less
+ * than 300.<p>
+ * It is only possible to draw edge arrows at the full detail
+ * level. If low detail is chosen, the output of this method is ignored.
+ * @param renderNodeCount the number of nodes that are about to be rendered.
+ * @param renderEdgeCount the number of edges that are about to be rendered.
+ * @return true if and only if edge arrows are to be rendered.
+ * @see #detail(int, int)
+ */
+ public boolean edgeArrows(final int renderNodeCount, final int renderEdgeCount) {
+ return renderEdgeCount < edgeArrowThreshold;
+ }
+
+ /**
+ * Determines whether or not to honor dashed edges. By default this
+ * method always returns true. If false is returned, edges that
+ * claim to be dashed will be rendered as solid.<p>
+ * It is only possible to draw dashed edges at the full detail
+ * level. If low detail is chosen, the output of this method is ignored.
+ * Note that drawing dashed edges is computationally expensive;
+ * the default implementation of this method does not make a very
+ * performance-minded decision if a lot of edges happen to be dashed.
+ * @param renderNodeCount the number of nodes that are about to be rendered.
+ * @param renderEdgeCount the number of edges that are about to be rendered.
+ * @return true if and only if dashed edges are to be honored.
+ * @see #detail(int, int)
+ */
+ public boolean dashedEdges(final int renderNodeCount, final int renderEdgeCount) {
+ return true;
+ }
+
+ /**
+ * Determines whether or not to honor edge anchors. By default this
+ * method always returns true. If false is returned, edges that
+ * claim to have edge anchors will be rendered as simple straight
+ * edges.<p>
+ * It is only possible to draw poly-edges at the full detail
+ * level. If low detail is chosen, the output of this method is ignored.
+ * @param renderNodeCount the number of nodes that are about to be rendered.
+ * @param renderEdgeCount the number of edges that are about to be rendered.
+ * @return true if and only if edge anchors are to be honored.
+ * @see #detail(int, int)
+ */
+ public boolean edgeAnchors(final int renderNodeCount, final int renderEdgeCount) {
+ return true;
+ }
+
+ /**
+ * Determines whether or not to render edge labels. By default this method
+ * returns true if and only if the number of rendered edges is less than
+ * 80.<p>
+ * Edge labels are only rendered at the full detail level. If low detail is
+ * chosen, the output of this method is ignored.
+ * @param renderNodeCount the number of nodes that are about to be rendered.
+ * @param renderEdgeCount the number of edges that are about to be rendered.
+ * @return true if and only if edge labels are to be rendered.
+ * @see #detail(int, int)
+ */
+ public boolean edgeLabels(final int renderNodeCount, final int renderEdgeCount) {
+ return renderEdgeCount < edgeLabelThreshold;
+ }
+
+ /**
+ * Determines whether or not to draw text as shape when rendering node and
+ * edge labels. By default this method always returns false.<p>
+ * This method affects the boolean parameter drawTextAsShape in the method
+ * call GraphGraphics.drawTextFull(). If neither node nor edge labels are
+ * rendered then the output of this method is ignored.
+ * @param renderNodeCount the number of nodes that are about to be rendered.
+ * @param renderEdgeCount the number of edges that are about to be rendered.
+ * @return true if and only if rendered label text should be drawn as
+ * primitive shapes.
+ * @see #nodeLabels(int, int)
+ * @see #edgeLabels(int, int)
+ */
+ public boolean textAsShape(final int renderNodeCount, final int renderEdgeCount) {
+ return false;
+ }
+
+ public double getNestedNetworkImageScaleFactor() {
+ final String scaleFactor = CytoscapeInit.getProperties().getProperty("nestedNetwork.imageScaleFactor", "1.0");
+ try {
+ final double d = Double.valueOf(scaleFactor);
+ return d <= 0.0 ? 1.0 : d;
+ } catch (final Exception e) {
+ return 1.0;
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/ding/DingNetworkView.java b/application/src/main/java/cytoscape/ding/DingNetworkView.java
new file mode 100644
index 0000000..fbee0f9
--- /dev/null
+++ b/application/src/main/java/cytoscape/ding/DingNetworkView.java
@@ -0,0 +1,585 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.ding;
+
+import giny.view.EdgeView;
+import giny.view.NodeView;
+
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+
+import cytoscape.CyEdge;
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+import cytoscape.CytoscapeInit;
+import cytoscape.layout.CyLayoutAlgorithm;
+import cytoscape.util.PropUtil;
+import cytoscape.view.CyEdgeView;
+import cytoscape.view.CyNetworkView;
+import cytoscape.view.CyNodeView;
+import cytoscape.view.CytoscapeDesktop;
+import cytoscape.view.FlagAndSelectionHandler;
+import cytoscape.visual.VisualMappingManager;
+import cytoscape.visual.VisualStyle;
+import ding.view.DGraphView;
+
+
+/**
+ * Extended version of DGraphView defined in Ding.
+ *
+ */
+public class DingNetworkView extends DGraphView implements CyNetworkView, PropertyChangeListener {
+
+ private String title;
+ private boolean vizmapEnabled = true;
+ private HashMap clientData = new HashMap();
+ private VisualStyle vs;
+ private final FlagAndSelectionHandler flagHandler;
+
+ /**
+ * A string used to specify the number of pixels wide and high the nested
+ * network image should be.
+ */
+ public static final String NESTED_NETWORK_SNAPSHOT_SIZE_PROP = "nestedNetworkSnapshotSize";
+
+ /**
+ * Creates a new DingNetworkView object.
+ *
+ * @param network DOCUMENT ME!
+ * @param title DOCUMENT ME!
+ */
+ public DingNetworkView(CyNetwork network, String title) {
+ super(network);
+ this.title = title;
+
+ final int[] nodes = network.getNodeIndicesArray();
+ final int[] edges = network.getEdgeIndicesArray();
+
+ final int nodeCount = nodes.length;
+ final int edgeCount = edges.length;
+
+ for (int i = 0; i < nodeCount; i++)
+ addNodeView(nodes[i]);
+
+ for (int i = 0; i < edgeCount; i++)
+ addEdgeView(edges[i]);
+
+ flagHandler = new FlagAndSelectionHandler(getNetwork().getSelectFilter(), this);
+
+ // Allows us to update the nested network snapshot size based on
+ // a property.
+ Cytoscape.getSwingPropertyChangeSupport().addPropertyChangeListener(this);
+ checkSnapshotSize();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param vsName DOCUMENT ME!
+ */
+ public void setVisualStyle(String vsName) {
+ vs = Cytoscape.getVisualMappingManager().getCalculatorCatalog().getVisualStyle(vsName);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public VisualStyle getVisualStyle() {
+ if (vs == null) {
+ String defaultStyle = CytoscapeInit.getProperties().getProperty("defaultVisualStyle");
+
+ if (defaultStyle == null)
+ defaultStyle = "default";
+
+ setVisualStyle(defaultStyle);
+ }
+
+ return vs;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public CyNetwork getNetwork() {
+ return (CyNetwork) getGraphPerspective();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param title DOCUMENT ME!
+ */
+ public void setTitle(String title) {
+ this.title = title;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getTitle() {
+ return title;
+ }
+
+ /**
+ * Apply visual style and redraw graph.
+ *
+ * @param layout Always ignored!
+ * @param vizmap Always ignored!
+ */
+ public void redrawGraph(boolean layout, boolean vizmap) {
+ final VisualMappingManager vmm = Cytoscape.getVisualMappingManager();
+ vmm.setNetworkView(this);
+ vmm.applyAppearances();
+ // This simply repaints the canvas.
+ updateView();
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public CyNetworkView getView() {
+ return this;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public VisualMappingManager getVizMapManager() {
+ // Believe it or not, this is the correct f***ing implementation.
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void toggleVisualMapperEnabled() {
+ vizmapEnabled = !vizmapEnabled;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param state DOCUMENT ME!
+ */
+ public void setVisualMapperEnabled(boolean state) {
+ vizmapEnabled = state;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean getVisualMapperEnabled() {
+ return vizmapEnabled;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param data_name DOCUMENT ME!
+ * @param data DOCUMENT ME!
+ */
+ public void putClientData(String data_name, Object data) {
+ clientData.put(data_name, data);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Collection getClientDataNames() {
+ return clientData.keySet();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param data_name DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getClientData(String data_name) {
+ return clientData.get(data_name);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nodes DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean setSelected(CyNode[] nodes) {
+ return setSelected(convertToViews(nodes));
+ }
+
+ private NodeView[] convertToViews(CyNode[] nodes) {
+ NodeView[] views = new NodeView[nodes.length];
+
+ for (int i = 0; i < nodes.length; i++) {
+ views[i] = getNodeView(nodes[i]);
+ }
+
+ return views;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node_views DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean setSelected(NodeView[] node_views) {
+ for (int i = 0; i < node_views.length; i++) {
+ node_views[i].select();
+ }
+
+ return true;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edge DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean applyVizMap(CyEdge edge) {
+ return applyVizMap(getEdgeView(edge));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edge_view DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean applyVizMap(EdgeView edge_view) {
+ return applyVizMap(edge_view, (VisualStyle) getClientData(CytoscapeDesktop.VISUAL_STYLE));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean applyVizMap(CyNode node) {
+ return applyVizMap(getNodeView(node));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node_view DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean applyVizMap(NodeView node_view) {
+ return applyVizMap(node_view, (VisualStyle) getClientData(CytoscapeDesktop.VISUAL_STYLE));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edge DOCUMENT ME!
+ * @param style DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean applyVizMap(CyEdge edge, VisualStyle style) {
+ return applyVizMap(getEdgeView(edge), style);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edge_view DOCUMENT ME!
+ * @param style DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean applyVizMap(EdgeView edge_view, VisualStyle style) {
+ VisualStyle old_style = Cytoscape.getDesktop().setVisualStyle(style);
+ Cytoscape.getVisualMappingManager().vizmapEdge(edge_view, this);
+ Cytoscape.getDesktop().setVisualStyle(old_style);
+
+ return true;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ * @param style DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean applyVizMap(CyNode node, VisualStyle style) {
+ return applyVizMap(getNodeView(node), style);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node_view DOCUMENT ME!
+ * @param style DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean applyVizMap(NodeView node_view, VisualStyle style) {
+ VisualStyle old_style = Cytoscape.getDesktop().setVisualStyle(style);
+ Cytoscape.getVisualMappingManager().vizmapNode(node_view, this);
+ Cytoscape.getDesktop().setVisualStyle(old_style);
+
+ return true;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edges DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean setSelected(CyEdge[] edges) {
+ return setSelected(convertToViews(edges));
+ }
+
+ private EdgeView[] convertToViews(CyEdge[] edges) {
+ EdgeView[] views = new EdgeView[edges.length];
+
+ for (int i = 0; i < edges.length; i++) {
+ views[i] = getEdgeView(edges[i]);
+ }
+
+ return views;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edge_views DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean setSelected(EdgeView[] edge_views) {
+ for (int i = 0; i < edge_views.length; i++) {
+ edge_views[i].select();
+ }
+
+ return true;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param style DOCUMENT ME!
+ */
+ public void applyVizmapper(VisualStyle style) {
+ final VisualStyle old_style = Cytoscape.getDesktop().setVisualStyle(style);
+ redrawGraph(false, true);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param layout DOCUMENT ME!
+ */
+ public void applyLayout(CyLayoutAlgorithm layout) {
+ layout.doLayout(this);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param layout DOCUMENT ME!
+ * @param nodes DOCUMENT ME!
+ * @param edges DOCUMENT ME!
+ */
+ public void applyLockedLayout(CyLayoutAlgorithm layout, CyNode[] nodes, CyEdge[] edges) {
+ layout.lockNodes(convertToViews(nodes));
+ layout.setSelectedOnly(true);
+ layout.doLayout(this);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param layout DOCUMENT ME!
+ * @param nodes DOCUMENT ME!
+ * @param edges DOCUMENT ME!
+ */
+ public void applyLayout(CyLayoutAlgorithm layout, CyNode[] nodes, CyEdge[] edges) {
+ layout.lockNodes(getInverseViews(convertToViews(nodes)));
+ layout.setSelectedOnly(true);
+ layout.doLayout(this);
+ }
+
+ private NodeView[] getInverseViews(NodeView[] given) {
+ // This code, like most all of the code in this class, is copied from
+ // PhoebeNetworkView. Zum kotzen.
+ final NodeView[] inverse = new NodeView[getNodeViewCount() - given.length];
+ final List<NodeView> node_views = getNodeViewsList();
+
+ int count = 0;
+ // Arrays.sort(given);
+ HashSet<NodeView>viewSet = new HashSet();
+ for (int g = 0; g < given.length; g++)
+ viewSet.add(given[g]);
+
+ for (NodeView view : node_views) {
+ if (!viewSet.contains(view)) {
+ inverse[count] = view;
+ count++;
+ }
+ }
+ return inverse;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public List getNodeViewsList() {
+ final List<NodeView> list = new ArrayList<NodeView>(getNodeViewCount());
+ final int[] gp_indices = getGraphPerspective().getNodeIndicesArray();
+ final int gpSize = gp_indices.length;
+
+ for (int i = 0; i < gpSize; i++)
+ list.add(getNodeView(gp_indices[i]));
+
+ return list;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param layout DOCUMENT ME!
+ * @param nodes DOCUMENT ME!
+ * @param edges DOCUMENT ME!
+ */
+ public void applyLockedLayout(CyLayoutAlgorithm layout, CyNodeView[] nodes, CyEdgeView[] edges) {
+ layout.lockNodes(nodes);
+ layout.setSelectedOnly(true);
+ layout.doLayout();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param layout DOCUMENT ME!
+ * @param nodes DOCUMENT ME!
+ * @param edges DOCUMENT ME!
+ */
+ public void applyLayout(CyLayoutAlgorithm layout, CyNodeView[] nodes, CyEdgeView[] edges) {
+ layout.lockNodes(getInverseViews(nodes));
+ layout.setSelectedOnly(true);
+ layout.doLayout(this);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param layout DOCUMENT ME!
+ * @param nodes DOCUMENT ME!
+ * @param edges DOCUMENT ME!
+ */
+ public void applyLockedLayout(CyLayoutAlgorithm layout, int[] nodes, int[] edges) {
+ layout.lockNodes(convertToNodeViews(nodes));
+ layout.setSelectedOnly(true);
+ layout.doLayout(this);
+ }
+
+ private NodeView[] convertToNodeViews(int[] nodes) {
+ final NodeView[] views = new NodeView[nodes.length];
+ final int size = views.length;
+
+ for (int i = 0; i < size; i++)
+ views[i] = getNodeView(nodes[i]);
+
+ return views;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param layout DOCUMENT ME!
+ * @param nodes DOCUMENT ME!
+ * @param edges DOCUMENT ME!
+ */
+ public void applyLayout(CyLayoutAlgorithm layout, int[] nodes, int[] edges) {
+ layout.lockNodes(getInverseViews(convertToNodeViews(nodes)));
+ layout.setSelectedOnly(true);
+ layout.doLayout(this);
+ }
+
+ public void propertyChange(PropertyChangeEvent e) {
+ if (Cytoscape.PREFERENCES_UPDATED.equals(e.getPropertyName())) {
+ checkSnapshotSize();
+ }
+ }
+
+ private void checkSnapshotSize() {
+ final int newSize = PropUtil.getInt(CytoscapeInit.getProperties(),
+ NESTED_NETWORK_SNAPSHOT_SIZE_PROP,
+ DEF_SNAPSHOT_SIZE);
+ if ( newSize > 0 )
+ DEF_SNAPSHOT_SIZE = newSize;
+ }
+}
diff --git a/application/src/main/java/cytoscape/giny/CyEdgeDepot.java b/application/src/main/java/cytoscape/giny/CyEdgeDepot.java
new file mode 100755
index 0000000..be39192
--- /dev/null
+++ b/application/src/main/java/cytoscape/giny/CyEdgeDepot.java
@@ -0,0 +1,75 @@
+/*
+ File: CyEdgeDepot.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.giny;
+
+import cytoscape.CyEdge;
+
+import fing.model.*;
+
+import giny.model.Edge;
+import giny.model.RootGraph;
+
+
+final class CyEdgeDepot implements FingEdgeDepot {
+ CyEdgeDepot() {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param root DOCUMENT ME!
+ * @param index DOCUMENT ME!
+ * @param id DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Edge getEdge(RootGraph root, int index, String id) {
+ final CyEdge returnThis = new CyEdge(root, index);
+
+ // returnThis.setIdentifier(id);
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edge DOCUMENT ME!
+ */
+ public void recycleEdge(Edge edge) {
+ edge.setIdentifier(null);
+ }
+}
diff --git a/application/src/main/java/cytoscape/giny/CyNodeDepot.java b/application/src/main/java/cytoscape/giny/CyNodeDepot.java
new file mode 100755
index 0000000..e51dd78
--- /dev/null
+++ b/application/src/main/java/cytoscape/giny/CyNodeDepot.java
@@ -0,0 +1,75 @@
+/*
+ File: CyNodeDepot.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.giny;
+
+import cytoscape.CyNode;
+
+import fing.model.*;
+
+import giny.model.Node;
+import giny.model.RootGraph;
+
+
+final class CyNodeDepot implements FingNodeDepot {
+ CyNodeDepot() {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param root DOCUMENT ME!
+ * @param index DOCUMENT ME!
+ * @param id DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Node getNode(RootGraph root, int index, String id) {
+ final CyNode returnThis = new CyNode(root, index);
+
+ // returnThis.setIdentifier(id);
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ */
+ public void recycleNode(Node node) {
+ node.setIdentifier(null);
+ }
+}
diff --git a/application/src/main/java/cytoscape/giny/CytoscapeFingRootGraph.java b/application/src/main/java/cytoscape/giny/CytoscapeFingRootGraph.java
new file mode 100755
index 0000000..4a71359
--- /dev/null
+++ b/application/src/main/java/cytoscape/giny/CytoscapeFingRootGraph.java
@@ -0,0 +1,204 @@
+/*
+ File: CytoscapeFingRootGraph.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.giny;
+
+import cytoscape.*;
+
+import cytoscape.util.intr.*;
+
+import fing.model.*;
+
+import giny.model.*;
+import giny.model.Edge;
+import giny.model.Node;
+
+import java.util.Collection;
+import java.util.Map;
+import java.util.HashMap;
+
+
+/**
+ *
+ */
+public class CytoscapeFingRootGraph extends FingExtensibleRootGraph implements CytoscapeRootGraph {
+ Map<String,Integer> node_name_index_map;
+ Map<String,Integer> edge_name_index_map;
+
+ /**
+ * Creates a new CytoscapeFingRootGraph object.
+ */
+ public CytoscapeFingRootGraph() {
+ super(new CyNodeDepot(), new CyEdgeDepot());
+
+ node_name_index_map = new HashMap<String,Integer>();
+ edge_name_index_map = new HashMap<String,Integer>();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nodes DOCUMENT ME!
+ * @param edges DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public CyNetwork createNetwork(Collection nodes, Collection edges) {
+ Node[] node = (Node[]) nodes.toArray(new Node[] { });
+ Edge[] edge = (Edge[]) edges.toArray(new Edge[] { });
+
+ return createNetwork(node, edge);
+ }
+
+ /**
+ * Creates a new Network
+ */
+ public CyNetwork createNetwork(Node[] nodes, Edge[] edges) {
+ final Node[] nodeArr = ((nodes != null) ? nodes : new Node[0]);
+ final Edge[] edgeArr = ((edges != null) ? edges : new Edge[0]);
+ final RootGraph root = this;
+
+ try {
+ return new FingCyNetwork(this,
+ new IntIterator() {
+ private int index = 0;
+
+ public boolean hasNext() {
+ return index < nodeArr.length;
+ }
+
+ public int nextInt() {
+ if ((nodeArr[index] == null) || (nodeArr[index].getRootGraph() != root))
+ throw new IllegalArgumentException();
+
+ return nodeArr[index++].getRootGraphIndex();
+ }
+ },
+ new IntIterator() {
+ private int index = 0;
+
+ public boolean hasNext() {
+ return index < edgeArr.length;
+ }
+
+ public int nextInt() {
+ if ((edgeArr[index] == null) || (edgeArr[index].getRootGraph() != root))
+ throw new IllegalArgumentException();
+
+ return edgeArr[index++].getRootGraphIndex();
+ }
+ });
+ } catch (IllegalArgumentException exc) {
+ return null;
+ }
+ }
+
+ /**
+ * Uses Code copied from ColtRootGraph to create a new Network.
+ */
+ public CyNetwork createNetwork(int[] nodeInx, int[] edgeInx) {
+ if (nodeInx == null)
+ nodeInx = new int[0];
+
+ if (edgeInx == null)
+ edgeInx = new int[0];
+
+ try {
+ return new FingCyNetwork(this, new ArrayIntIterator(nodeInx, 0, nodeInx.length),
+ new ArrayIntIterator(edgeInx, 0, edgeInx.length));
+ } catch (IllegalArgumentException exc) {
+ return null;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param identifier DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public CyNode getNode(String identifier) {
+ Integer nodeId = node_name_index_map.get(identifier);
+ if ( nodeId != null )
+ return (CyNode) getNode(nodeId.intValue());
+ else
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param identifier DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public CyEdge getEdge(String identifier) {
+ Integer edgeId = edge_name_index_map.get(identifier);
+ if ( edgeId != null )
+ return (CyEdge) getEdge(edgeId.intValue());
+ else
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param identifier DOCUMENT ME!
+ * @param index DOCUMENT ME!
+ */
+ public void setNodeIdentifier(String identifier, int index) {
+ if (index == 0) {
+ node_name_index_map.remove(identifier);
+ } else {
+ node_name_index_map.put(identifier, index);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param identifier DOCUMENT ME!
+ * @param index DOCUMENT ME!
+ */
+ public void setEdgeIdentifier(String identifier, int index) {
+ if (index == 0) {
+ edge_name_index_map.remove(identifier);
+ } else {
+ edge_name_index_map.put(identifier, index);
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/giny/CytoscapeRootGraph.java b/application/src/main/java/cytoscape/giny/CytoscapeRootGraph.java
new file mode 100644
index 0000000..be082c0
--- /dev/null
+++ b/application/src/main/java/cytoscape/giny/CytoscapeRootGraph.java
@@ -0,0 +1,108 @@
+/*
+ File: CytoscapeRootGraph.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.giny;
+
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+
+import giny.model.Edge;
+import giny.model.Node;
+import giny.model.RootGraph;
+
+import java.util.Collection;
+
+
+/**
+ *
+ */
+public interface CytoscapeRootGraph extends RootGraph {
+ //public int createNode ( CyNetwork network ) ;
+
+ /**
+ * Uses Code copied from ColtRootGraph to create a new CyNetwork.
+ */
+ public CyNetwork createNetwork(giny.model.Node[] nodes, giny.model.Edge[] edges);
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nodes DOCUMENT ME!
+ * @param edges DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public CyNetwork createNetwork(Collection nodes, Collection edges);
+
+ /**
+ * Uses Code copied from ColtRootGraph to create a new Network.
+ */
+ public CyNetwork createNetwork(int[] node_indices, int[] edge_indices);
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param identifier DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public cytoscape.CyNode getNode(String identifier);
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param identifier DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public cytoscape.CyEdge getEdge(String identifier);
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param identifier DOCUMENT ME!
+ * @param index DOCUMENT ME!
+ */
+ public void setNodeIdentifier(String identifier, int index);
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param identifier DOCUMENT ME!
+ * @param index DOCUMENT ME!
+ */
+ public void setEdgeIdentifier(String identifier, int index);
+}
diff --git a/application/src/main/java/cytoscape/giny/FingCyNetwork.java b/application/src/main/java/cytoscape/giny/FingCyNetwork.java
new file mode 100755
index 0000000..e7f0804
--- /dev/null
+++ b/application/src/main/java/cytoscape/giny/FingCyNetwork.java
@@ -0,0 +1,713 @@
+/*
+ File: FingCyNetwork.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.giny;
+
+import cytoscape.*;
+
+import cytoscape.data.*;
+
+import cytoscape.giny.*;
+
+import cytoscape.util.intr.*;
+
+import fing.model.*;
+
+import giny.model.Edge;
+import giny.model.GraphPerspective;
+import giny.model.Node;
+import giny.model.RootGraph;
+
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeSupport;
+import java.util.*;
+
+import javax.swing.event.SwingPropertyChangeSupport;
+
+
+/**
+ *
+ * FinhCyNetwork provides an implementation of the CyNetwork interface,
+ * as well as the GraphPerspective inteface, and also provides the
+ * functionality formally provided by GraphObjAttributes.
+ *
+ * The Network will notify listeners when nodes/edges are added/removed
+ * and when relavant data changes.
+ */
+public class FingCyNetwork extends FingExtensibleGraphPerspective implements CyNetwork,
+ GraphPerspective {
+ private static int uid_counter = 0;
+ private String identifier;
+ protected String title;
+
+ /**
+ * The Network Listeners Set
+ */
+
+ //TODO: implement the bean accepted way
+ protected Set listeners = new HashSet();
+
+ /**
+ * The ClientData map
+ */
+ protected Map clientData;
+
+ /**
+ * The default object to set the selected state of nodes and edges
+ */
+ protected final SelectFilter selectFilter;
+
+ //TODO: remove
+ int activityCount = 0;
+
+ //----------------------------------------//
+ // Constructors
+ //----------------------------------------//
+
+ /**
+ * rootGraphNodeInx need not contain all endpoint nodes corresponding to
+ * edges in rootGraphEdgeInx - this is calculated automatically by this
+ * constructor. If any index does not correspond to an existing node or
+ * edge, an IllegalArgumentException is thrown. The indices lists need not
+ * be non-repeating - the logic in this constructor handles duplicate
+ * filtering.
+ **/
+ public FingCyNetwork(FingExtensibleRootGraph root, IntIterator rootGraphNodeInx,
+ IntIterator rootGraphEdgeInx) {
+ super(root, rootGraphNodeInx, rootGraphEdgeInx);
+ initialize();
+ selectFilter = new SelectFilter(this);
+ }
+
+ protected void initialize() {
+ // TODO: get a better naming system in place
+ Integer i = new Integer(uid_counter);
+ identifier = i.toString();
+ uid_counter++;
+ clientData = new HashMap();
+ }
+
+ /**
+ * Can Change
+ */
+ public String getTitle() {
+ if (title == null)
+ return identifier;
+
+ return title;
+ }
+
+ /**
+ * Can Change
+ * Throws a PropertyChangeEvent if the title has changed with a CyNetworkTitleChange object that contains the network id and the name.
+ */
+ public void setTitle(String new_id) {
+ if (title == null) {
+ title = new_id;
+ } else if (!title.equals(new_id)) { // new title is different from the old one
+ CyNetworkTitleChange OldTitle = new CyNetworkTitleChange(this.getIdentifier(), title);
+ title = new_id;
+ Cytoscape.firePropertyChange(Cytoscape.NETWORK_TITLE_MODIFIED, OldTitle, new CyNetworkTitleChange(this.getIdentifier(), new_id) );
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getIdentifier() {
+ return identifier;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param new_id DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String setIdentifier(String new_id) {
+ identifier = new_id;
+
+ return identifier;
+ }
+
+ //-------------------------------------//
+ // Client Data - Deprecated April 2006
+ //-------------------------------------//
+
+ /**
+ * @deprecated
+ *
+ * Networks can support client data.
+ * @param data_name the name of this client data
+ */
+ public void putClientData(String data_name, Object data) {
+ clientData.put(data_name, data);
+ }
+
+ /**
+ * @deprecated
+ *
+ * Get a list of all currently available ClientData objects
+ */
+ public Collection getClientDataNames() {
+ return clientData.keySet();
+ }
+
+ /**
+ * @deprecated
+ *
+ * Get Some client data
+ * @param data_name the data to get
+ */
+ public Object getClientData(String data_name) {
+ return clientData.get(data_name);
+ }
+
+ /**
+ * Appends all of the nodes and edges in teh given Network to
+ * this Network
+ */
+ public void appendNetwork(CyNetwork network) {
+ int[] nodes = network.getNodeIndicesArray();
+ int[] edges = network.getEdgeIndicesArray();
+ restoreNodes(nodes);
+ restoreEdges(edges);
+ }
+
+ /**
+ * Sets the selected state of all nodes in this CyNetwork to true
+ */
+ public void selectAllNodes() {
+ this.selectFilter.selectAllNodes();
+ }
+
+ /**
+ * Sets the selected state of all edges in this CyNetwork to true
+ */
+ public void selectAllEdges() {
+ this.selectFilter.selectAllEdges();
+ }
+
+ /**
+ * Sets the selected state of all nodes in this CyNetwork to false
+ */
+ public void unselectAllNodes() {
+ this.selectFilter.unselectAllNodes();
+ }
+
+ /**
+ * Sets the selected state of all edges in this CyNetwork to false
+ */
+ public void unselectAllEdges() {
+ this.selectFilter.unselectAllEdges();
+ }
+
+ /**
+ * Sets the selected state of a collection of nodes.
+ *
+ * @param nodes a Collection of Nodes
+ * @param selected_state the desired selection state for the nodes
+ */
+ public void setSelectedNodeState(Collection nodes, boolean selected_state) {
+ this.selectFilter.setSelectedNodes(nodes, selected_state);
+ }
+
+ /**
+ * Sets the selected state of a node.
+ *
+ * @param nodes a Node
+ * @param selected_state the desired selection state for the node
+ */
+ public void setSelectedNodeState(Node node, boolean selected_state) {
+ this.selectFilter.setSelected(node, selected_state);
+ }
+
+ /**
+ * Sets the selected state of a collection of edges.
+ *
+ * @param edges a Collection of Edges
+ * @param selected_state the desired selection state for the edges
+ */
+ public void setSelectedEdgeState(Collection edges, boolean selected_state) {
+ this.selectFilter.setSelectedEdges(edges, selected_state);
+ }
+
+ /**
+ * Sets the selected state of an edge.
+ *
+ * @param edges an Edge
+ * @param selected_state the desired selection state for the edge
+ */
+ public void setSelectedEdgeState(Edge edge, boolean selected_state) {
+ this.selectFilter.setSelected(edge, selected_state);
+ }
+
+ /**
+ * Returns the selected state of the given node.
+ *
+ * @param node the node
+ * @return true if selected, false otherwise
+ */
+ public boolean isSelected(Node node) {
+ return this.selectFilter.isSelected(node);
+ }
+
+ /**
+ * Returns the selected state of the given edge.
+ *
+ * @param edge the edge
+ * @return true if selected, false otherwise
+ */
+ public boolean isSelected(Edge edge) {
+ return this.selectFilter.isSelected(edge);
+ }
+
+ /**
+ * Returns the set of selected nodes in this CyNetwork
+ *
+ * @return a Set of selected nodes
+ */
+ public Set getSelectedNodes() {
+ return this.selectFilter.getSelectedNodes();
+ }
+
+ /**
+ * Returns the set of selected edges in this CyNetwork
+ *
+ * @return a Set of selected edges
+ */
+ public Set getSelectedEdges() {
+ return this.selectFilter.getSelectedEdges();
+ }
+
+ /**
+ * Adds a listener for SelectEvents to this CyNetwork
+ *
+ * @param listener
+ */
+ public void addSelectEventListener(SelectEventListener listener) {
+ this.selectFilter.addSelectEventListener(listener);
+ }
+
+ /**
+ * Removes a listener for SelectEvents from this CyNetwork
+ * @param listener
+ */
+ public void removeSelectEventListener(SelectEventListener listener) {
+ this.selectFilter.removeSelectEventListener(listener);
+ }
+
+ /**
+ *
+ * @return SelectFilter
+ */
+ public SelectFilter getSelectFilter() {
+ return this.selectFilter;
+ }
+
+ //----------------------------------------//
+ // Data Access Methods
+ //----------------------------------------//
+
+ //--------------------//
+ // Member Data
+
+ // get
+
+ /**
+ * Return the requested Attribute for the given Node
+ * @param node the given CyNode
+ * @param attribute the name of the requested attribute
+ * @return the value for the give node, for the given attribute
+ */
+ public Object getNodeAttributeValue(Node node, String attribute) {
+ return getNodeAttributeValue(node.getRootGraphIndex(), attribute);
+ }
+
+ /**
+ * Return the requested Attribute for the given Node
+ */
+ public Object getNodeAttributeValue(int node, String attribute) {
+ final String canonName = getNode(node).getIdentifier();
+ final CyAttributes attrs = Cytoscape.getNodeAttributes();
+ final byte cyType = attrs.getType(attribute);
+
+ if (cyType == CyAttributes.TYPE_BOOLEAN) {
+ return attrs.getBooleanAttribute(canonName, attribute);
+ } else if (cyType == CyAttributes.TYPE_FLOATING) {
+ return attrs.getDoubleAttribute(canonName, attribute);
+ } else if (cyType == CyAttributes.TYPE_INTEGER) {
+ return attrs.getIntegerAttribute(canonName, attribute);
+ } else if (cyType == CyAttributes.TYPE_STRING) {
+ return attrs.getStringAttribute(canonName, attribute);
+ } else if (cyType == CyAttributes.TYPE_SIMPLE_LIST) {
+ return attrs.getListAttribute(canonName, attribute);
+ } else if (cyType == CyAttributes.TYPE_SIMPLE_MAP) {
+ return attrs.getMapAttribute(canonName, attribute);
+ } else {
+ return null;
+ }
+ }
+
+ /**
+ * Return the requested Attribute for the given Edge
+ */
+ public Object getEdgeAttributeValue(Edge edge, String attribute) {
+ return getEdgeAttributeValue(edge.getRootGraphIndex(), attribute);
+ }
+
+ /**
+ * Return the requested Attribute for the given Edge
+ */
+ public Object getEdgeAttributeValue(int edge, String attribute) {
+ final String canonName = getEdge(edge).getIdentifier();
+ final CyAttributes attrs = Cytoscape.getEdgeAttributes();
+ final byte cyType = attrs.getType(attribute);
+
+ if (cyType == CyAttributes.TYPE_BOOLEAN) {
+ return attrs.getBooleanAttribute(canonName, attribute);
+ } else if (cyType == CyAttributes.TYPE_FLOATING) {
+ return attrs.getDoubleAttribute(canonName, attribute);
+ } else if (cyType == CyAttributes.TYPE_INTEGER) {
+ return attrs.getIntegerAttribute(canonName, attribute);
+ } else if (cyType == CyAttributes.TYPE_STRING) {
+ return attrs.getStringAttribute(canonName, attribute);
+ } else if (cyType == CyAttributes.TYPE_SIMPLE_LIST) {
+ return attrs.getListAttribute(canonName, attribute);
+ } else if (cyType == CyAttributes.TYPE_SIMPLE_MAP) {
+ return attrs.getMapAttribute(canonName, attribute);
+ } else {
+ return null;
+ }
+ }
+
+ /**
+ * Return all availble Attributes for the Nodes in this CyNetwork
+ */
+ public String[] getNodeAttributesList() {
+ return Cytoscape.getNodeAttributes().getAttributeNames();
+ }
+
+ /**
+ * Return all available Attributes for the given Nodes
+ */
+ public String[] getNodeAttributesList(Node[] nodes) {
+ return Cytoscape.getNodeAttributes().getAttributeNames();
+ }
+
+ /**
+ * Return all availble Attributes for the Edges in this CyNetwork
+ */
+ public String[] getEdgeAttributesList() {
+ return Cytoscape.getEdgeAttributes().getAttributeNames();
+ }
+
+ /**
+ * Return all available Attributes for the given Edges
+ */
+ public String[] getNodeAttributesList(Edge[] edges) {
+ return Cytoscape.getEdgeAttributes().getAttributeNames();
+ }
+
+ /**
+ * Return the requested Attribute for the given Node
+ * @param node the given CyNode
+ * @param attribute the name of the requested attribute
+ * @param value the value to be set
+ * @return if it overwrites a previous value
+ */
+ public boolean setNodeAttributeValue(Node node, String attribute, Object value) {
+ return setNodeAttributeValue(node.getRootGraphIndex(), attribute, value);
+ }
+
+ /**
+ * Return the requested Attribute for the given Node
+ */
+ public boolean setNodeAttributeValue(int node, String attribute, Object value) {
+ final String canonName = getNode(node).getIdentifier();
+ final CyAttributes attrs = Cytoscape.getNodeAttributes();
+
+ if (value instanceof Boolean) {
+ attrs.setAttribute(canonName, attribute, (Boolean) value);
+
+ return true;
+ } else if (value instanceof Integer) {
+ attrs.setAttribute(canonName, attribute, (Integer) value);
+
+ return true;
+ } else if (value instanceof Double) {
+ attrs.setAttribute(canonName, attribute, (Double) value);
+
+ return true;
+ } else if (value instanceof String) {
+ attrs.setAttribute(canonName, attribute, (String) value);
+
+ return true;
+ } else if (value instanceof List) {
+ attrs.setListAttribute(canonName, attribute, (List) value);
+
+ return true;
+ } else if (value instanceof Map) {
+ attrs.setMapAttribute(canonName, attribute, (Map) value);
+
+ return true;
+ } else {
+ return false;
+ }
+ }
+
+ /**
+ * Return the requested Attribute for the given Edge
+ */
+ public boolean setEdgeAttributeValue(Edge edge, String attribute, Object value) {
+ return setEdgeAttributeValue(edge.getRootGraphIndex(), attribute, value);
+ }
+
+ /**
+ * Return the requested Attribute for the given Edge
+ */
+ public boolean setEdgeAttributeValue(int edge, String attribute, Object value) {
+ final String canonName = getEdge(edge).getIdentifier();
+ final CyAttributes attrs = Cytoscape.getEdgeAttributes();
+
+ if (value instanceof Boolean) {
+ attrs.setAttribute(canonName, attribute, (Boolean) value);
+
+ return true;
+ } else if (value instanceof Integer) {
+ attrs.setAttribute(canonName, attribute, (Integer) value);
+
+ return true;
+ } else if (value instanceof Double) {
+ attrs.setAttribute(canonName, attribute, (Double) value);
+
+ return true;
+ } else if (value instanceof String) {
+ attrs.setAttribute(canonName, attribute, (String) value);
+
+ return true;
+ } else if (value instanceof List) {
+ attrs.setListAttribute(canonName, attribute, (List) value);
+
+ return true;
+ } else if (value instanceof Map) {
+ attrs.setMapAttribute(canonName, attribute, (Map) value);
+
+ return true;
+ } else {
+ return false;
+ }
+ }
+
+ /**
+ * Deletes the attribute with the given name from node attributes
+ */
+ public void deleteNodeAttribute(String attribute) {
+ Cytoscape.getNodeAttributes().deleteAttribute(attribute);
+ }
+
+ /**
+ * Deletes the attribute with the given name from edge attributes
+ */
+ public void deleteEdgeAttribute(String attribute) {
+ Cytoscape.getEdgeAttributes().deleteAttribute(attribute);
+ }
+
+ //------------------------------//
+ // Listener Methods
+ //------------------------------//
+
+ /**
+ * Registers the argument as a listener to this object. Does nothing if
+ * the argument is already a listener.
+ */
+ public void addCyNetworkListener(CyNetworkListener listener) {
+ listeners.add(listener);
+ }
+
+ /**
+ * Removes the argument from the set of listeners for this object. Returns
+ * true if the argument was a listener before this call, false otherwise.
+ */
+ public boolean removeCyNetworkListener(CyNetworkListener listener) {
+ return listeners.remove(listener);
+ }
+
+ /**
+ * Returns the set of listeners registered with this object.
+ */
+ public Set getCyNetworkListeners() {
+ return new HashSet(listeners);
+ }
+
+ //--------------------//
+ // Event Firing
+ //--------------------//
+
+ /**
+ * Fires an event to all listeners registered with this object. The argument
+ * should be a constant from the CyNetworkEvent class identifying the type
+ * of the event.
+ */
+ protected void fireEvent(int type) {
+ CyNetworkEvent event = new CyNetworkEvent(this, type);
+
+ for (Iterator i = listeners.iterator(); i.hasNext();) {
+ CyNetworkListener listener = (CyNetworkListener) i.next();
+ listener.onCyNetworkEvent(event);
+ }
+ }
+
+ //----------------------------------------//
+ // Implements Network
+ //----------------------------------------//
+
+ //----------------------------------------//
+ // Node and Edge creation/deletion
+ //----------------------------------------//
+
+ //--------------------//
+ // Nodes
+
+ /**
+ * This method will create a new node.
+ * @return the Cytoscape index of the created node
+ */
+ public int createNode() {
+ return restoreNode(Cytoscape.getRootGraph().createNode());
+ }
+
+ /**
+ * Add a node to this Network that already exists in
+ * Cytoscape
+ * @return the Network Index of this node
+ */
+ public int addNode(int cytoscape_node) {
+ return restoreNode(cytoscape_node);
+ }
+
+ /**
+ * Add a node to this Network that already exists in
+ * Cytoscape
+ * @return the Network Index of this node
+ */
+ public CyNode addNode(Node cytoscape_node) {
+ return (CyNode) restoreNode(cytoscape_node);
+ }
+
+ /**
+ * Adds a node to this Network, by looking it up via the
+ * given attribute and value
+ * @return the Network Index of this node
+ */
+ public int addNode(String attribute, Object value) {
+ return 0;
+ }
+
+ /**
+ * This will remove this node from the Network. However,
+ * unless forced, it will remain in Cytoscape to be possibly
+ * resused by another Network in the future.
+ * @param force force this node to be removed from all Networks
+ * @return true if the node is still present in Cytoscape
+ * ( i.e. in another Network )
+ */
+ public boolean removeNode(int node_index, boolean force) {
+ hideNode(node_index);
+
+ return true;
+ }
+
+ //--------------------//
+ // Edges
+
+ /**
+ * This method will create a new edge.
+ * @param source the source node
+ * @param target the target node
+ * @param directed weather the edge should be directed
+ * @return the Cytoscape index of the created edge
+ */
+ public int createEdge(int source, int target, boolean directed) {
+ return restoreEdge(Cytoscape.getRootGraph().createEdge(source, target, directed));
+ }
+
+ /**
+ * Add a edge to this Network that already exists in
+ * Cytoscape
+ * @return the Network Index of this edge
+ */
+ public int addEdge(int cytoscape_edge) {
+ return restoreEdge(cytoscape_edge);
+ }
+
+ /**
+ * Add a edge to this Network that already exists in
+ * Cytoscape
+ * @return the Network Index of this edge
+ */
+ public CyEdge addEdge(Edge cytoscape_edge) {
+ return (CyEdge) restoreEdge(cytoscape_edge);
+ }
+
+ /**
+ * Adds a edge to this Network, by looking it up via the
+ * given attribute and value
+ * @return the Network Index of this edge
+ */
+ public int addEdge(String attribute, Object value) {
+ return 0;
+ }
+
+ /**
+ * This will remove this edge from the Network. However,
+ * unless forced, it will remain in Cytoscape to be possibly
+ * resused by another Network in the future.
+ * @param force force this edge to be removed from all Networks
+ * @return true if the edge is still present in Cytoscape
+ * ( i.e. in another Network )
+ */
+ public boolean removeEdge(int edge_index, boolean force) {
+ super.hideEdge(edge_index);
+
+ return true;
+ }
+
+
+}
diff --git a/application/src/main/java/cytoscape/groups/CyGroup.java b/application/src/main/java/cytoscape/groups/CyGroup.java
new file mode 100644
index 0000000..6ca668b
--- /dev/null
+++ b/application/src/main/java/cytoscape/groups/CyGroup.java
@@ -0,0 +1,225 @@
+/* vim :set ts=2: */
+/*
+ File: CyGroup.java
+
+ Copyright (c) 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.groups;
+
+import java.util.Iterator;
+import java.util.List;
+
+import cytoscape.CyEdge;
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+
+
+/**
+ * The CyGroup interface provides the methods for a group model that
+ * maintains the list of nodes belonging to a group, the parent of a particular
+ * group, and the node that represents the group. Group information is stored
+ * in the CyGroup itself, as well as in special group attributes that are associated
+ * with the network, nodes, and edges involved. These attributes provide a natural
+ * mechanism for the saving and restoration of groups. There are also opaque flags
+ */
+public interface CyGroup {
+ // Static data
+
+ /**
+ * The attribute key to use for group membership
+ */
+ public static final String MEMBER_LIST_ATTR = "__groupMembers";
+
+ /**
+ * The attribute key to use for group viewer
+ */
+ public static final String GROUP_VIEWER_ATTR = "__groupViewer";
+
+ /**
+ * The attribute key to use for group state
+ */
+ public static final String GROUP_STATE_ATTR = "__groupState";
+
+ /**
+ * The attribute that indicates that this is a local group
+ */
+ public static final String GROUP_LOCAL_ATTR = "__groupIsLocal";
+
+ // Public methods
+
+ /**
+ * Return the name of this group
+ */
+ public String getGroupName();
+
+ /**
+ * Get all of the nodes in this group
+ *
+ * @return list of nodes in the group
+ */
+ public List<CyNode> getNodes();
+
+ /**
+ * Get the CyNode that represents this group
+ *
+ * @return CyNode representing the group
+ */
+ public CyNode getGroupNode();
+
+ /**
+ * Get an iterator over all of the nodes in this group
+ *
+ * @return node iterator
+ */
+ public Iterator<CyNode> getNodeIterator();
+
+ /**
+ * Get all of the edges completely contained within this group
+ *
+ * @return list of edges in the group
+ */
+ public List<CyEdge> getInnerEdges();
+
+ /**
+ * Get all of the edges partially contained within this group
+ *
+ * @return list of edges in the group
+ */
+ public List<CyEdge> getOuterEdges();
+
+ /**
+ * Get the network for this group
+ *
+ * @return network for this group or "null" if this is a global group
+ */
+ public CyNetwork getNetwork();
+
+ /**
+ * Get the graph (network) that represents this network
+ *
+ * @return graph perspective (in the form of a CyNetwork) for this network
+ */
+ public CyNetwork getGraphPerspective();
+
+ /**
+ * Set the network for this group
+ *
+ * @param network the network for this group or "null" if this is a global group
+ * @param notify notify listeners of the change
+ */
+ public void setNetwork(CyNetwork network, boolean notify);
+
+ /**
+ * Add an outer edge to the map. Some viewers may need to do this
+ * if they add and remove edges, for example.
+ *
+ * @param edge the CyEdge to add to the outer edge map
+ */
+ public void addOuterEdge(CyEdge edge);
+
+ /**
+ * Remove an outer edge from the map. Some viewers may need to do this
+ * if they add and remove edges, for example.
+ *
+ * @param edge the CyEdge to add to the outer edge map
+ */
+ public void removeOuterEdge(CyEdge edge);
+
+ /**
+ * Add an inner edge to the map. Some viewers may need to do this
+ * if they add and remove edges, for example.
+ *
+ * @param edge the CyEdge to add to the innter edge map
+ */
+ public void addInnerEdge(CyEdge edge);
+
+ /**
+ * Remove an inner edge from the map. Some viewers may need to do this
+ * if they add and remove edges, for example.
+ *
+ * @param edge the CyEdge to add to the innter edge map
+ */
+ public void removeInnerEdge(CyEdge edge);
+
+ /**
+ * Determine if a node is a member of this group
+ *
+ * @param node the CyNode to test
+ * @return true if node is a member of the group
+ */
+ public boolean contains(CyNode node);
+
+ /**
+ * Set the state of the group
+ *
+ * @param state the state to set
+ */
+ public void setState(int state);
+
+ /**
+ * Get the state of the group
+ *
+ * @return group state
+ */
+ public int getState();
+
+ /**
+ * Provide the default toString method
+ *
+ * @return group name
+ */
+ public String toString();
+
+ /**
+ * Get the name of the viewer for this group
+ *
+ * @return viewer for this group
+ */
+ public String getViewer();
+
+ /**
+ * Add a new node to this group
+ *
+ * @param node the node to add
+ */
+ public void addNode ( CyNode node );
+
+
+ /**
+ * Remove a node from a group
+ *
+ * @param node the node to remove
+ */
+ public void removeNode ( CyNode node );
+}
diff --git a/application/src/main/java/cytoscape/groups/CyGroupChangeListener.java b/application/src/main/java/cytoscape/groups/CyGroupChangeListener.java
new file mode 100644
index 0000000..f74bbba
--- /dev/null
+++ b/application/src/main/java/cytoscape/groups/CyGroupChangeListener.java
@@ -0,0 +1,52 @@
+/* vim :set ts=2: */
+/*
+ File: CyGroupChangeListener.java
+
+ Copyright (c) 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.groups;
+
+/**
+ * The CyGroupChangeListener interface provides a mechanism for plugins that track
+ * group-related events to get notified of global group changes (new groups, etc.).
+ */
+public interface CyGroupChangeListener {
+ public enum ChangeType { GROUP_CREATED, GROUP_DELETED, GROUP_MODIFIED }
+
+ /**
+ * This method will be called by the CyGroupManager when a group is created, deleted,
+ * or modified.
+ */
+ public void groupChanged(CyGroup group, ChangeType change);
+}
diff --git a/application/src/main/java/cytoscape/groups/CyGroupImpl.java b/application/src/main/java/cytoscape/groups/CyGroupImpl.java
new file mode 100644
index 0000000..6e5487d
--- /dev/null
+++ b/application/src/main/java/cytoscape/groups/CyGroupImpl.java
@@ -0,0 +1,658 @@
+/* vim :set ts=2: */
+/*
+ File: CyGroupImpl.java
+
+ Copyright (c) 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.groups;
+
+import cytoscape.Cytoscape;
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.CyEdge;
+
+import cytoscape.data.CyAttributes;
+import cytoscape.giny.CytoscapeRootGraph;
+
+import cytoscape.groups.CyGroupViewer.ChangeType;
+
+import giny.model.Edge;
+import giny.model.GraphObject;
+import giny.model.GraphPerspective;
+import giny.model.Node;
+import giny.model.RootGraph;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+
+
+/**
+ * The CyGroup class provides the implementation for a group model that
+ * maintains the list of nodes belonging to a group, the parent of a particular
+ * group, and the node that represents the group. Group information is stored
+ * in the CyGroup itself, as well as in special group attributes that are associated
+ * with the network, nodes, and edges involved. These attributes provide a natural
+ * mechanism for the saving and restoration of groups. There are also opaque flags
+ */
+public class CyGroupImpl implements CyGroup {
+ // Instance data
+
+ /**
+ * A map storing the list of edges for a node at the time it was
+ * added to the group
+ */
+ private HashMap<CyNode,List<CyEdge>> nodeToEdgeMap;
+
+ /**
+ * The edges in this group that involve members outside of this group
+ */
+ private HashMap<CyEdge, CyEdge> outerEdgeMap;
+
+ /**
+ * This is the network that this group is part of. If this
+ * is null, it's a global group.
+ */
+ private CyNetwork network = null;
+
+ /**
+ * The node that represents this group
+ */
+ private CyNode groupNode = null;
+
+ /**
+ * The group name
+ */
+ private String groupName = null;
+
+ /**
+ * Group state. This is used by the view components to set the current
+ * state of the group (collapsed, expanded, etc.)
+ */
+ private int groupState = 0;
+
+ /**
+ * viewValue is an opaque type for use by view compoenents to "remember"
+ * information about the group
+ */
+ private Object viewValue = null;
+
+ /**
+ * viewer is the viewer that this group is managed by
+ */
+ private String viewer = null;
+
+ /**
+ * the internal graph that represents this network
+ */
+ private CyNetwork myGraph = null;
+
+ // Public methods
+
+ /**
+ * Empty constructor
+ */
+ protected CyGroupImpl() {
+ this.nodeToEdgeMap = new HashMap<CyNode, List<CyEdge>>();
+ this.outerEdgeMap = new HashMap<CyEdge,CyEdge>();
+ this.network = null;
+ }
+
+ /**
+ * Constructor to create an empty group.
+ *
+ * @param groupNode the CyNode to use for this group
+ * @param nodeList the initial set of nodes for this group
+ * @param internalEdges the initial set of internal edges for this group
+ * @param externalEdges the initial set of external edges for this group
+ * @param network the network this group is part of
+ *
+ */
+ protected CyGroupImpl(CyNode groupNode, List<CyNode> nodeList, List<CyEdge> internalEdges,
+ List<CyEdge> externalEdges, CyNetwork network) {
+
+ // System.out.println("Creating group "+groupNode);
+
+ this.nodeToEdgeMap = new HashMap<CyNode, List<CyEdge>>();
+ this.outerEdgeMap = new HashMap<CyEdge,CyEdge>();
+ this.network = network;
+
+ this.groupNode = groupNode;
+ this.groupName = this.groupNode.getIdentifier();
+
+ if (nodeList == null && internalEdges == null && externalEdges == null) {
+ CytoscapeRootGraph rootGraph = Cytoscape.getRootGraph();
+ Node[] nodeArray = null;
+ Edge[] edgeArray = null;
+ myGraph = rootGraph.createNetwork(nodeArray, edgeArray);
+ return;
+ }
+
+ // System.out.println(" Group "+groupNode+" has "+nodeList.size()+" nodes");
+
+ CyNetwork thisNetwork = network;
+ if (network == null)
+ thisNetwork = Cytoscape.getCurrentNetwork();
+
+ // If we aren't provided with any inner or outer edges, we need to get them
+ if (internalEdges == null) {
+ // Get our list of internal edges
+ internalEdges = (List<CyEdge>) thisNetwork.getConnectingEdges(nodeList);
+ }
+
+ // At this point, we've got a list of nodes and a list of edges. We
+ // could now create a CyNetwork that contains the internal components
+ // of this group.
+ {
+ CytoscapeRootGraph rootGraph = Cytoscape.getRootGraph();
+
+ Node[] nodeArray = null;
+ Edge[] edgeArray = null;
+ if (nodeList != null && nodeList.size() > 0)
+ nodeArray = nodeList.toArray(new Node[0]);
+ if (internalEdges != null && internalEdges.size() > 0)
+ edgeArray = internalEdges.toArray(new Edge[0]);
+ myGraph = rootGraph.createNetwork(nodeArray, edgeArray);
+ }
+
+ // Create our node and edge map
+ for (CyNode node: nodeList) {
+ List<CyEdge> adjacentEdges = (List<CyEdge>)thisNetwork.getAdjacentEdgesList(node, true, true, true);
+ nodeToEdgeMap.put(node, adjacentEdges);
+ // If we don't have external edges, add them now
+ if (externalEdges == null && adjacentEdges != null) {
+ for (CyEdge edge: adjacentEdges) {
+ if (!myGraph.containsEdge(edge))
+ outerEdgeMap.put(edge, edge);
+ }
+ }
+ node.addToGroup(this);
+ }
+
+ // If we were provided with an external edge list, create our map now.
+ if (externalEdges != null) {
+ for (CyEdge edge: externalEdges)
+ outerEdgeMap.put(edge, edge);
+ }
+ }
+
+ /**
+ * Constructor to create an empty group
+ *
+ * @param groupName the identifier to use for this group -- should be unique!
+ */
+ protected CyGroupImpl(String groupName) {
+ this(Cytoscape.getCyNode(groupName, true), null, null, null, null);
+ }
+
+ /**
+ * Constructor to create an empty group when the group node is specified.
+ *
+ * @param groupNode the CyNode to use for this group
+ */
+ protected CyGroupImpl(CyNode groupNode) {
+ this(groupNode, null, null, null, null);
+ }
+
+ /**
+ * Constructor to create a group with the listed nodes as initial members, and a predetermined
+ * CyNode to act as the group Node.
+ *
+ * @param groupNode the group node to use for this group
+ * @param nodeList the initial set of nodes for this group
+ */
+ protected CyGroupImpl(CyNode groupNode, List<CyNode> nodeList) {
+ this(groupNode, nodeList, null, null, null);
+ }
+
+ /**
+ * Constructor to create a group with the listed nodes as initial members.
+ *
+ * @param groupName the identifier to use for this group -- should be unique!
+ * @param nodeList the initial set of nodes for this group
+ */
+ protected CyGroupImpl(String groupName, List<CyNode> nodeList) {
+ this(Cytoscape.getCyNode(groupName, true), nodeList, null, null, null);
+ }
+
+ /**
+ * Return the name of this group
+ */
+ public String getGroupName() {
+ return groupName;
+ }
+
+ /**
+ * Set the name of this group
+ */
+ public void setGroupName(String name) {
+ this.groupName = name;
+ }
+
+ /**
+ * Get all of the nodes in this group
+ *
+ * @return list of nodes in the group
+ */
+ public List<CyNode> getNodes() {
+ return (List<CyNode>)myGraph.nodesList();
+ }
+
+ /**
+ * Get the CyNode that represents this group
+ *
+ * @return CyNode representing the group
+ */
+ public CyNode getGroupNode() {
+ return this.groupNode;
+ }
+
+ /**
+ * Get an iterator over all of the nodes in this group
+ *
+ * @return node iterator
+ */
+ public Iterator<CyNode> getNodeIterator() {
+ return (Iterator<CyNode>)myGraph.nodesIterator();
+ }
+
+ /**
+ * Get all of the edges completely contained within this group
+ *
+ * @return list of edges in the group
+ */
+ public List<CyEdge> getInnerEdges() {
+ return (List<CyEdge>)myGraph.edgesList();
+ }
+
+ /**
+ * Get all of the edges partially contained within this group
+ *
+ * @return list of edges in the group
+ */
+ public List<CyEdge> getOuterEdges() {
+ Collection<CyEdge> v = outerEdgeMap.values();
+
+ return new ArrayList<CyEdge>(v);
+ }
+
+ /**
+ * Add an outer edge to the map. Some viewers may need to do this
+ * if they add and remove edges, for example.
+ *
+ * @param edge the CyEdge to add to the outer edge map
+ */
+ public void addOuterEdge(CyEdge edge) {
+ if (edge == null) return;
+ outerEdgeMap.put(edge, edge);
+
+ notifyViewer(edge, ChangeType.OUTER_EDGE_ADDED);
+ }
+
+ /**
+ * Remove an outer edge from the map. Some viewers may need to do this
+ * if they add and remove edges, for example.
+ *
+ * @param edge the CyEdge to add to the outer edge map
+ */
+ public void removeOuterEdge(CyEdge edge) {
+ if (edge == null) return;
+ outerEdgeMap.remove(edge);
+
+ notifyViewer(edge, ChangeType.OUTER_EDGE_REMOVED);
+ }
+
+ /**
+ * Add an inner edge to the map. Some viewers may need to do this
+ * if they add and remove edges, for example.
+ *
+ * @param edge the CyEdge to add to the innter edge map
+ */
+ public void addInnerEdge(CyEdge edge) {
+ if (edge == null) return;
+ myGraph.addEdge(edge);
+
+ notifyViewer(edge, ChangeType.INNER_EDGE_ADDED);
+
+ }
+
+ /**
+ * Remove an inner edge from the map. Some viewers may need to do this
+ * if they add and remove edges, for example.
+ *
+ * @param edge the CyEdge to add to the innter edge map
+ */
+ public void removeInnerEdge(CyEdge edge) {
+ if (edge == null) return;
+ myGraph.removeEdge(edge.getRootGraphIndex(), false);
+
+ notifyViewer(edge, ChangeType.INNER_EDGE_REMOVED);
+ }
+
+ /**
+ * Get the network this group is a member of
+ *
+ * @return the network, or null if this is a global group
+ */
+ public CyNetwork getNetwork() {
+ return network;
+ }
+
+ /**
+ * Set (or change) the network fro this group
+ *
+ * @param network the network to change this group to
+ * @param notify whether to notify any viewers
+ */
+ public void setNetwork(CyNetwork network, boolean notify) {
+
+ // Change our attribute
+ CyAttributes nodeAttributes = Cytoscape.getNodeAttributes();
+ if (network != null)
+ nodeAttributes.setAttribute(groupNode.getIdentifier(), CyGroup.GROUP_LOCAL_ATTR, Boolean.TRUE);
+ else
+ nodeAttributes.setAttribute(groupNode.getIdentifier(), CyGroup.GROUP_LOCAL_ATTR, Boolean.FALSE);
+
+ if (notify && this.network != network) {
+ notifyViewer(null, ChangeType.NETWORK_CHANGED);
+ }
+ this.network = network;
+ }
+
+ /**
+ * Determine if a node is a member of this group
+ *
+ * @param node the CyNode to test
+ * @return true if node is a member of the group
+ */
+ public boolean contains(CyNode node) {
+ if (myGraph.containsNode(node))
+ return true;
+
+ return false;
+ }
+
+ /**
+ * Return a CyNetwork that represents
+ * the internal components of this group
+ *
+ * @return the CyNetwork
+ */
+ public CyNetwork getGraphPerspective() {
+ return myGraph;
+ }
+
+ /**
+ * Set the state of the group. Setting the state of a group has
+ * two byproducts. First, the attribute "__groupState" is set to
+ * the state value to allow persistance across saves and restores.
+ * Second, if there is a viewer for this group, it is informed that
+ * the state has changed. This is used by the metaNode viewer, for
+ * example to provide programmatic control of whether the group is
+ * expanded or collapsed.
+ *
+ * @param state the state to set
+ */
+ public void setState(int state) {
+ CyAttributes attributes = Cytoscape.getNodeAttributes();
+ this.groupState = state;
+ attributes.setUserVisible(GROUP_STATE_ATTR, false);
+ attributes.setAttribute(this.groupName, GROUP_STATE_ATTR, this.groupState);
+
+ notifyViewer(null, ChangeType.STATE_CHANGED);
+ }
+
+ /**
+ * Get the state of the group
+ *
+ * @return group state
+ */
+ public int getState() {
+ return this.groupState;
+ }
+
+ /**
+ * Set the viewValue for the group
+ *
+ * @param viewValue the view value to set
+ */
+ public void setViewValue(Object viewValue) {
+ this.viewValue = viewValue;
+ }
+
+ /**
+ * Get the viewValue for the group
+ *
+ * @return the view value
+ */
+ public Object getViewValue() {
+ return this.viewValue;
+ }
+
+ /**
+ * Provide the default toString method
+ *
+ * @return group name
+ */
+ public String toString() {
+ return this.groupName;
+ }
+
+ /**
+ * Set the viewer for this group. In order to maintain the
+ * static tables correctly, this method is protected and
+ * CyGroup.setGroupViewer(group, viewer, notify) should be used
+ * instead.
+ *
+ * @param viewerName name of the viewer for the group
+ */
+ protected void setViewer(String viewerName) {
+ CyAttributes attributes = Cytoscape.getNodeAttributes();
+ this.viewer = viewerName;
+
+ if (this.viewer != null) {
+ attributes.setUserVisible(GROUP_VIEWER_ATTR, false);
+ attributes.setAttribute(this.groupName, GROUP_VIEWER_ATTR, this.viewer);
+ }
+ }
+
+ /**
+ * Get the name of the viewer for this group
+ *
+ * @return viewer for this group
+ */
+ public String getViewer() {
+ return this.viewer;
+ }
+
+ /**
+ * Add a new node to this group
+ *
+ * @param node the node to add
+ */
+ public void addNode ( CyNode node ) {
+ addNode(node, true);
+ }
+
+ /**
+ * Add a new node to this group
+ *
+ * @param node the node to add
+ */
+ public void addNode ( CyNode node, boolean addEdges ) {
+ // First see if this node is already in this group
+ if (myGraph.containsNode(node))
+ return;
+
+ myGraph.addNode(node);
+
+ if (!addEdges)
+ return;
+
+ // We need to go throught our outerEdgeMap first to see if this
+ // node has outer edges and proactively move them to inner edges.
+ // this needs to be done here because some viewers might have
+ // hidden edges on us, so the the call to getAdjacentEdgeIndices in
+ // addNodeToGroup won't return all of the edges.
+ List <CyEdge> eMove = new ArrayList<CyEdge>();
+ for (CyEdge edge: outerEdgeMap.keySet()) {
+ if (edge.getTarget() == node || edge.getSource() == node) {
+ eMove.add(edge);
+ }
+ }
+ for (CyEdge edge: eMove) {
+ outerEdgeMap.remove(edge);
+ myGraph.addEdge(edge);
+ }
+
+ // Note the cute little trick we play -- making sure these
+ // are added to the edgeMap
+ nodeToEdgeMap.put(node, eMove);
+
+ addNodeToGroup(node);
+
+ notifyViewer(node, ChangeType.NODE_ADDED);
+ }
+
+
+ /**
+ * Remove a node from a group
+ *
+ * @param node the node to remove
+ */
+ public void removeNode ( CyNode node ) {
+ removeNodeFromGroup(node);
+
+ notifyViewer(node, ChangeType.NODE_REMOVED);
+
+ }
+
+ /**
+ * Add a new node to this group
+ *
+ * @param node the node to add
+ */
+ private void addNodeToGroup ( CyNode node ) {
+ CyNetwork groupNetwork = this.network;
+
+ if (groupNetwork == null)
+ groupNetwork = Cytoscape.getCurrentNetwork();
+
+ List <CyEdge>edgeList = null;
+
+ if (nodeToEdgeMap.containsKey(node)) {
+ edgeList = nodeToEdgeMap.get(node);
+ } else {
+ edgeList = new ArrayList<CyEdge>();
+ }
+
+ // Add all of the edges
+ List<CyEdge> adjacentEdges = (List<CyEdge>)groupNetwork.getAdjacentEdgesList(node, true, true, true);
+ if (adjacentEdges != null) {
+ for (CyEdge edge: adjacentEdges) {
+ // Not sure if this is faster or slower than going through the entire loop
+ if (myGraph.containsEdge(edge))
+ continue;
+
+ edgeList.add(edge);
+ CyNode target = (CyNode)edge.getTarget();
+ CyNode source = (CyNode)edge.getSource();
+
+ // Check to see if this edge is one of our own metaEdges
+ if (source == groupNode || target == groupNode) {
+ // It is -- skip it
+ continue;
+ }
+
+ if (outerEdgeMap.containsKey(edge)) {
+ outerEdgeMap.remove(edge);
+ myGraph.addEdge(edge);
+ } else if (myGraph.containsNode(target) && myGraph.containsNode(source)) {
+ myGraph.addEdge(edge);
+ } else if (myGraph.containsNode(target) || myGraph.containsNode(source)) {
+ outerEdgeMap.put(edge,edge);
+ }
+ }
+ }
+ nodeToEdgeMap.put(node, edgeList);
+
+ // Tell the node about it (if necessary)
+ if (!node.inGroup(this))
+ node.addToGroup(this);
+ }
+
+ /**
+ * Remove a node from a group
+ *
+ * @param node the node to remove
+ */
+ private void removeNodeFromGroup ( CyNode node ) {
+ // Get the list of edges
+ List <CyEdge>edgeArray = nodeToEdgeMap.get(node);
+
+ // Do we have any edges at all?
+ if (edgeArray != null) {
+ for (CyEdge edge: edgeArray) {
+ if (myGraph.containsEdge(edge)) {
+ outerEdgeMap.put(edge,edge);
+ } else if (outerEdgeMap.containsKey(edge)) {
+ outerEdgeMap.remove(edge);
+ }
+ }
+ }
+ nodeToEdgeMap.remove(node);
+
+ // Remove the node from our map
+ myGraph.removeNode(node.getRootGraphIndex(), false);
+
+ // Tell the node about it (if necessary)
+ if (node.inGroup(this))
+ node.removeFromGroup(this);
+ }
+
+ /**
+ * Notify our viewer that something has changed
+ *
+ */
+ private void notifyViewer(GraphObject object, CyGroupViewer.ChangeType change) {
+ // Get our viewer
+ CyGroupViewer v = CyGroupManager.getGroupViewer(this.viewer);
+ if (v != null) {
+ // Tell the viewer that something has changed
+ v.groupChanged(this, object, change);
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/groups/CyGroupManager.java b/application/src/main/java/cytoscape/groups/CyGroupManager.java
new file mode 100644
index 0000000..238009f
--- /dev/null
+++ b/application/src/main/java/cytoscape/groups/CyGroupManager.java
@@ -0,0 +1,659 @@
+/* vim :set ts=2: */
+/*
+ File: CyGroup.java
+
+ Copyright (c) 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.groups;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import giny.model.RootGraph;
+
+import cytoscape.CyEdge;
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+import cytoscape.view.CyNetworkView;
+import cytoscape.data.CyAttributes;
+
+/**
+ * The CyGroup class provides the implementation for a group model that
+ * maintains the list of nodes belonging to a group, the parent of a particular
+ * group, and the node that represents the group. Group information is stored
+ * in the CyGroup itself, as well as in special group attributes that are associated
+ * with the network, nodes, and edges involved. These attributes provide a natural
+ * mechanism for the saving and restoration of groups. There are also opaque flags
+ */
+public class CyGroupManager {
+ // Static data
+
+ /**
+ * The list of groups, indexed by the CyNode that represents the group. The values
+ * are the CyGroup itself.
+ */
+ private static Map<CyNode, CyGroup> groupMap = new HashMap<CyNode, CyGroup>();
+
+ /**
+ * The list of group viewers currently registered.
+ */
+ private static Map<String, CyGroupViewer> viewerMap = new HashMap<String, CyGroupViewer>();
+
+ /**
+ * The list of groups, indexed by the managing viewer
+ */
+ private static Map<String, List<CyGroup>> groupViewerMap = new HashMap<String, List<CyGroup>>();
+
+ /**
+ * The list of groups, indexed by the network
+ */
+ private static Map<CyNetwork, List<CyGroup>> networkGroupMap = new HashMap<CyNetwork, List<CyGroup>>();
+
+ /**
+ * The list of group change listeners
+ */
+ private static List<CyGroupChangeListener> changeListeners = new ArrayList<CyGroupChangeListener>();
+
+ /**
+ * The internal group map for global groups
+ */
+ private static CyNetwork GLOBAL_GROUPS = Cytoscape.getNullNetwork();
+
+ /**
+ * Initialize our property change listener
+ */
+ private static GroupPropertyChangeListener gpcl = new GroupPropertyChangeListener();
+
+ // Static methods
+ /**
+ * getCyGroup is a static method that returns a CyGroup structure when
+ * given the CyNode that represents this group.
+ *
+ * @param groupNode the CyNode that represents this group
+ * @return the associated CyGroup structure
+ */
+ public static CyGroup getCyGroup(CyNode groupNode) {
+ if ((groupMap == null) || !groupMap.containsKey(groupNode))
+ return null;
+
+ return groupMap.get(groupNode);
+ }
+
+ /**
+ * getGroup is a static method that returns a CyGroup structure when
+ * given a CyNode that is a member of a group.
+ *
+ * @param memberNode a CyNode whose group membership we're looking for
+ * @return a list of CyGroups this node is a member of
+ */
+ public static List<CyGroup> getGroup(CyNode memberNode) {
+ List<CyGroup> groupList = new ArrayList<CyGroup>();
+
+ for (CyGroup group: groupMap.values()) {
+ if (group.contains(memberNode))
+ groupList.add(group);
+ }
+
+ if (groupList.size() == 0)
+ return null;
+
+ return groupList;
+ }
+
+ /**
+ * Return the list of all groups
+ *
+ * @return the list of groups
+ */
+ public static List<CyGroup> getGroupList() {
+ Collection<CyGroup> c = groupMap.values();
+
+ return new ArrayList<CyGroup>(c);
+ }
+
+ /**
+ * Return the list of all groups for this network
+ *
+ * @param network the network we're interested in. If network is null, return
+ * the list of global groups
+ * @return the list of groups
+ */
+ public static List<CyGroup> getGroupList(CyNetwork network) {
+ if (network == null) {
+ network = GLOBAL_GROUPS;
+ }
+
+ if (networkGroupMap.containsKey(network))
+ return networkGroupMap.get(network);
+
+ return new ArrayList();
+ }
+
+ /**
+ * Return the list of all groups managed by a particular viewer
+ *
+ * @param viewer the CyGroupViewer
+ * @return the list of groups
+ */
+ public static List<CyGroup> getGroupList(CyGroupViewer viewer) {
+ if (viewer == null) return getGroupList();
+ String viewerName = viewer.getViewerName();
+ if (!groupViewerMap.containsKey(viewerName))
+ return null;
+ List<CyGroup> groupList = groupViewerMap.get(viewerName);
+
+ return groupList;
+ }
+
+ /**
+ * Search all groups for the group named 'groupName'
+ *
+ * @param groupName the name of the group to find
+ * @return the group, or null if no such group exists
+ */
+ public static CyGroup findGroup(String groupName) {
+ for (CyGroup group: getGroupList()) {
+ if (group.getGroupName().equals(groupName)) {
+ return group;
+ } else if (group.getGroupNode().getIdentifier().equals(groupName)) {
+ // This means that someone changed the name of our groupNode, but
+ // not the name of the group. Update our name and return
+ ((CyGroupImpl)group).setGroupName(group.getGroupNode().getIdentifier());
+ return group;
+ }
+ }
+ return null;
+ }
+
+ /**
+ * Create a copy of a group, potentially in a new network, and name the
+ * copy automatically. The copy name is simply formed by placing an integer
+ * in brackets after the name of the current group.
+ *
+ * @param group the group to make a copy of
+ * @param network the network the copy is to be part of
+ * @return the new group, or null if we can't find a suitable name
+ */
+ public static CyGroup copyGroup(CyGroup group, CyNetwork network) {
+ // First, create a new (unique) name for the group
+ String currentName = group.getGroupNode().getIdentifier();
+ for (int i = 0; i < 1000; i++) {
+ String newName = currentName+"["+i+"]";
+ if (Cytoscape.getCyNode(newName, false) == null) {
+ return copyGroup(newName, group, network);
+ }
+ }
+ return null;
+ }
+
+ /**
+ * Create a copy of a group, potentially in a new network, and name the
+ * copy with the provided new name.
+ *
+ * @param newName the name of the copied group
+ * @param group the group to make a copy of
+ * @param network the network the copy is to be part of
+ * @return the new group, or null if a node of 'newName' already exists
+ */
+ public static CyGroup copyGroup(String newName, CyGroup group, CyNetwork network) {
+ // If the new name already exists, return null
+ if (Cytoscape.getCyNode(newName, false) != null) { return null; }
+
+ // Great, now create the new group
+ CyGroup newGroup = createGroup(newName, group.getNodes(), group.getInnerEdges(),
+ group.getOuterEdges(), group.getViewer(), network);
+ return newGroup;
+ }
+
+ /**
+ * Create a new group by specifying all components. Use this to get a new group.
+ * This constructor allows the caller to provide all of the components required
+ * to create a group. This is the most efficient of all of the constructors in
+ * that no additional processing is done to find internal and external edges,
+ * etc. If innerEdgeList and outerEdgeList are both null, the underlying implementation
+ * will find all internal and external edges.
+ *
+ * @param groupName the identifier to use for this group -- should be unique!
+ * @param nodeList the initial set of nodes for this group
+ * @param innerEdgeList the initial set of internal edges for this group
+ * @param outerEdgeList the initial set of external edges for this group
+ * @param viewer the name of the viewer to manage this group
+ * @param network the network that this group is in
+ * @return the newly created group
+ */
+ public static CyGroup createGroup(String groupName, List<CyNode> nodeList,
+ List<CyEdge> innerEdgeList, List<CyEdge> outerEdgeList,
+ String viewer, CyNetwork network) {
+ // Do we already have a group by this name?
+ if (findGroup(groupName) != null) return null;
+ // Create a node for the group
+ CyNode groupNode = Cytoscape.getCyNode(groupName, true);
+ // Create the group itself
+ CyGroup group = new CyGroupImpl(groupNode, nodeList, innerEdgeList, outerEdgeList, network);
+ groupMap.put(group.getGroupNode(), group);
+ setGroupNetwork(group, network);
+ notifyListeners(group, CyGroupChangeListener.ChangeType.GROUP_CREATED);
+ if (viewer != null)
+ setGroupViewer(group, viewer, null, true);
+ return group;
+ }
+
+ /**
+ * Create a new, empty group. Use this to get a new group. In particular,
+ * this form should be used by internal routines (as opposed to view
+ * implementations) as this form will cause the viewer to be notified of
+ * the group creation. Viewers should use createGroup(String, List, String)
+ * as defined below.
+ *
+ * @param groupName the identifier to use for this group -- should be unique!
+ * @param viewer the name of the viewer to manage this group
+ * @param network the network that this group is in
+ * @return the newly created group
+ */
+ public static CyGroup createGroup(String groupName, String viewer, CyNetwork network) {
+ // Do we already have a group by this name?
+ if (findGroup(groupName) != null) return null;
+ // Create the group
+ CyGroup group = new CyGroupImpl(groupName);
+ groupMap.put(group.getGroupNode(), group);
+ setGroupNetwork(group, network);
+ notifyListeners(group, CyGroupChangeListener.ChangeType.GROUP_CREATED);
+ setGroupViewer(group, viewer, null, true);
+ return group;
+ }
+
+ /**
+ * Create a new group with a list of nodes as initial members. Note that this
+ * method is the prefered method to be used by viewers. Using this method,
+ * once the group is created the viewer is *not* notified (since it is assumed
+ * they are doing the creation).
+ *
+ * @param groupName the identifier to use for this group -- should be unique!
+ * @param nodeList the initial set of nodes for this group
+ * @param viewer the name of the viewer to manage this group
+ * @param network the network that this group is in
+ */
+ public static CyGroup createGroup(String groupName, List<CyNode> nodeList, String viewer,
+ CyNetwork network) {
+ // Do we already have a group by this name?
+ if (findGroup(groupName) != null) return null;
+ // Create the group
+ CyGroup group = new CyGroupImpl(groupName, nodeList);
+ groupMap.put(group.getGroupNode(), group);
+ setGroupNetwork(group, network);
+ notifyListeners(group, CyGroupChangeListener.ChangeType.GROUP_CREATED);
+ setGroupViewer(group, viewer, null, false);
+ return group;
+ }
+
+ /**
+ * Create a new group with a list of nodes as initial members, and a precreated
+ * group node. This is usually used by the XGMML reader since the group node
+ * may need to alread be created with its associated "extra" edges. Note that
+ * the node will be created, but *not* added to the network. That is the
+ * responsibility of the appropriate viewer.
+ *
+ * @param groupNode the groupNode to use for this group
+ * @param nodeList the initial set of nodes for this group
+ * @param viewer the name of the viewer to manage this group
+ * @param network the network that this group is in
+ */
+ public static CyGroup createGroup(CyNode groupNode, List<CyNode> nodeList, String viewer,
+ CyNetwork network) {
+ // Do we already have a group by this name?
+ if (findGroup(groupNode.getIdentifier()) != null) return null;
+ // Create the group
+ CyGroup group = null;
+ if (nodeList != null)
+ group = new CyGroupImpl(groupNode, nodeList);
+ else
+ group = new CyGroupImpl(groupNode);
+
+ groupMap.put(group.getGroupNode(), group);
+
+ // See if this groupNode has a state attribute
+ CyAttributes nodeAttributes = Cytoscape.getNodeAttributes();
+ try {
+ int state = nodeAttributes.getIntegerAttribute(groupNode.getIdentifier(), CyGroup.GROUP_STATE_ATTR);
+ group.setState(state);
+ } catch (Exception e) {}
+
+ setGroupNetwork(group, network);
+
+ notifyListeners(group, CyGroupChangeListener.ChangeType.GROUP_CREATED);
+
+ if (viewer != null)
+ setGroupViewer(group, viewer, null, true);
+ return group;
+ }
+
+ /**
+ * Create a new, empty group. Use this to get a new group. In particular,
+ * this form should be used by internal routines (as opposed to view
+ * implementations) as this form will cause the viewer to be notified of
+ * the group creation. Viewers should use createGroup(String, List, String)
+ * as defined below.
+ *
+ * @param groupName the identifier to use for this group -- should be unique!
+ * @param viewer the name of the viewer to manage this group
+ * @return the newly created group
+ */
+ public static CyGroup createGroup(String groupName, String viewer) {
+ return createGroup(groupName, viewer, null);
+ }
+
+ /**
+ * Create a new, empty group. Use this to get a new group. In particular,
+ * this form should be used by internal routines (as opposed to view
+ * implementations) as this form will cause the viewer to be notified of
+ * the group creation. Viewers should use createGroup(String, List, String)
+ * as defined below.
+ *
+ * @param groupName the identifier to use for this group -- should be unique!
+ * @param nodeList the initial set of nodes for this group
+ * @param viewer the name of the viewer to manage this group
+ * @return the newly created group
+ */
+ public static CyGroup createGroup(String groupName, List<CyNode>nodeList, String viewer) {
+ return createGroup(groupName, nodeList, viewer, null);
+ }
+
+ /**
+ * Create a new group with a list of nodes as initial members, and a precreated
+ * group node. This is usually used by the XGMML reader since the group node
+ * may need to alread be created with its associated "extra" edges. Note that
+ * the node will be created, but *not* added to the network. That is the
+ * responsibility of the appropriate viewer.
+ *
+ * @param groupNode the groupNode to use for this group
+ * @param nodeList the initial set of nodes for this group
+ * @param viewer the name of the viewer to manage this group
+ */
+ public static CyGroup createGroup(CyNode groupNode, List<CyNode> nodeList, String viewer) {
+ return createGroup(groupNode, nodeList, viewer, null);
+ }
+
+ /**
+ * Remove (delete) a group
+ *
+ * @param group the group to remove
+ */
+ public static void removeGroup(CyGroup group) {
+ removeGroup(group.getGroupNode());
+ }
+
+ /**
+ * Remove (delete) a group
+ *
+ * @param groupNode the group node of the group to remove
+ */
+ public static void removeGroup(CyNode groupNode) {
+ if (groupMap.containsKey(groupNode)) {
+ notifyRemoveGroup(groupMap.get(groupNode));
+
+ // Now, remove this group's node from any groups
+ // it might be a member of
+ List<CyGroup> groupList = groupNode.getGroups();
+ if (groupList != null && groupList.size() > 0) {
+ for (CyGroup group: new ArrayList<CyGroup>(groupList)) {
+ group.removeNode(groupNode);
+ }
+ }
+
+ // Remove this from the viewer's list
+ CyGroup group = groupMap.get(groupNode);
+ String viewerName = group.getViewer();
+ CyNetwork network = group.getNetwork();
+
+ if ((viewerName != null) && groupViewerMap.containsKey(viewerName)) {
+ List<CyGroup> gList = groupViewerMap.get(viewerName);
+ gList.remove(group);
+ }
+
+ if ((network != null) && networkGroupMap.containsKey(network)) {
+ List<CyGroup> gList = networkGroupMap.get(network);
+ gList.remove(group);
+
+ if (gList.size() == 0)
+ networkGroupMap.remove(network);
+ }
+
+ // Remove it from the groupMap
+ groupMap.remove(groupNode);
+
+ // Remove this group from all the nodes
+ List<CyNode> nodeList = group.getNodes();
+ for (CyNode node: nodeList) {
+ node.removeFromGroup(group);
+ }
+
+ // Remove the group node from the network
+ if (network == null)
+ network = Cytoscape.getCurrentNetwork();
+ network.removeNode(groupNode.getRootGraphIndex(), false);
+
+ // Remove it from the root graph
+ RootGraph rg = groupNode.getRootGraph();
+ rg.removeNode(groupNode);
+
+ notifyListeners(group, CyGroupChangeListener.ChangeType.GROUP_DELETED);
+ }
+ }
+
+ /**
+ * See if this CyNode represents a group
+ *
+ * @param groupNode the node we want to test
+ * @return 'true' if groupNode is a group
+ */
+ public static boolean isaGroup(CyNode groupNode) {
+ return groupMap.containsKey(groupNode);
+ }
+
+ // Viewer methods
+ /**
+ * Register a viewer.
+ *
+ * @param viewer the viewer we're registering
+ */
+ public static void registerGroupViewer(CyGroupViewer viewer) {
+ viewerMap.put(viewer.getViewerName(), viewer);
+ }
+
+ /**
+ * Return a list of all registered viewers
+ *
+ * @return list of registered group viewers
+ */
+ public static Collection<CyGroupViewer> getGroupViewers() {
+ return viewerMap.values();
+ }
+
+ /**
+ * Set the viewer for a group
+ *
+ * @param group the group we're associating with a viewer
+ * @param viewer the viewer
+ * @param myView the network view that this is being operated on
+ * @param notify if 'true' the viewer will be notified of the creation
+ */
+ public static void setGroupViewer(CyGroup group, String viewer, CyNetworkView myView, boolean notify) {
+ if (group == null) return;
+
+ // System.out.println("Setting group viewer for "+group+" to "+viewer);
+
+ // See if we need to remove the current viewer first
+ if (group.getViewer() != null && !group.getViewer().equals(viewer)) {
+ // get the viewer
+ String oldViewer = group.getViewer();
+
+ CyGroupViewer v = null;
+ if (viewerMap.containsKey(oldViewer))
+ v = viewerMap.get(oldViewer);
+
+ if (groupViewerMap.containsKey(oldViewer)) {
+ groupViewerMap.get(oldViewer).remove(group);
+ if (notify && v != null)
+ v.groupWillBeRemoved(group);
+ }
+ ((CyGroupImpl)group).setViewer(null);
+ }
+
+ if ((viewer != null) && viewerMap.containsKey(viewer)) {
+ // The viewer might already be set (this could just be a notify)
+ if (!viewer.equals(group.getViewer())) {
+ // create the list if necessary
+ if (!groupViewerMap.containsKey(viewer))
+ groupViewerMap.put(viewer, new ArrayList<CyGroup>());
+
+ // Add this group to the list
+ groupViewerMap.get(viewer).add(group);
+ }
+
+ if (notify) {
+ // get the viewer
+ CyGroupViewer v = viewerMap.get(viewer);
+
+ // Make sure we have a view before we notify
+ CyNetworkView currentView = Cytoscape.getCurrentNetworkView();
+ if (myView != null) {
+ v.groupCreated(group, myView);
+ } else if (currentView != null) {
+ v.groupCreated(group, currentView);
+ }
+ notifyListeners(group, CyGroupChangeListener.ChangeType.GROUP_MODIFIED);
+ }
+ }
+
+ ((CyGroupImpl)group).setViewer(viewer);
+ }
+
+ /**
+ * Return the viewer object for a named viewer
+ *
+ * @param viewerName the name of the viewer
+ * @return the viewer object
+ */
+ public static CyGroupViewer getGroupViewer(String viewerName) {
+ if ((viewerName != null) && viewerMap.containsKey(viewerName))
+ return viewerMap.get(viewerName);
+ return null;
+ }
+
+ /**
+ * Notify a viewer that a group has been created for them to manage.
+ *
+ * @param group the group that was just created
+ */
+ public static void notifyCreateGroup(CyGroup group) {
+ String viewer = group.getViewer();
+
+ if ((viewer != null) && viewerMap.containsKey(viewer)) {
+ CyGroupViewer v = viewerMap.get(viewer);
+ v.groupCreated(group);
+ }
+ }
+
+ /**
+ * Notify a viewer the a group of interest is going to be removed.
+ *
+ * @param group the group to be removed
+ */
+ public static void notifyRemoveGroup(CyGroup group) {
+ String viewer = group.getViewer();
+
+ if ((viewer != null) && viewerMap.containsKey(viewer)) {
+ CyGroupViewer v = viewerMap.get(viewer);
+ v.groupWillBeRemoved(group);
+ }
+ }
+
+ /**
+ * Add a new change listener to our list of listeners
+ *
+ * @param listener the listener to add
+ */
+ public static void addGroupChangeListener(CyGroupChangeListener listener) {
+ changeListeners.add(listener);
+ }
+
+ /**
+ * Remove a change listener from our list of listeners
+ *
+ * @param listener the listener to remove
+ */
+ public static void removeGroupChangeListener(CyGroupChangeListener listener) {
+ changeListeners.remove(listener);
+ }
+
+ /**
+ * Notify a listener that something has happened
+ *
+ * @param group the group that has changed
+ * @param whatChanged the thing that has changed about the group
+ */
+ private static void notifyListeners(CyGroup group, CyGroupChangeListener.ChangeType whatChanged) {
+ for (CyGroupChangeListener listener: changeListeners) {
+ listener.groupChanged(group, whatChanged);
+ }
+ }
+
+
+ /**
+ * Maintain the network group map
+ *
+ * @param group the group we're adding to the map
+ * @param network the network -- if it's null, we're adding it to the global map
+ */
+ private static void setGroupNetwork(CyGroup group, CyNetwork network) {
+ group.setNetwork(network, false);
+ if (network == null)
+ network = GLOBAL_GROUPS;
+
+ List<CyGroup> groupList = null;
+
+ if (!networkGroupMap.containsKey(network)) {
+ groupList = new ArrayList<CyGroup>();
+ } else {
+ groupList = networkGroupMap.get(network);
+ }
+ groupList.add(group);
+ networkGroupMap.put(network, groupList);
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/groups/CyGroupViewer.java b/application/src/main/java/cytoscape/groups/CyGroupViewer.java
new file mode 100644
index 0000000..fe7b531
--- /dev/null
+++ b/application/src/main/java/cytoscape/groups/CyGroupViewer.java
@@ -0,0 +1,102 @@
+/* vim :set ts=2: */
+/*
+ File: CyGroupViewer.java
+
+ Copyright (c) 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.groups;
+
+import cytoscape.CyNode;
+import cytoscape.view.CyNetworkView;
+
+import giny.model.GraphObject;
+
+/**
+ * The CyGroupViewer interface provides a mechanism for group view implementations
+ * to register themselves and get notified of group creation and deletion. The
+ * primary goals of this mechanism are to allow multiple group viewers to maintain
+ * different groups at the same time, and to provide a mechanism to retain view
+ * mechanism across session save and restore.
+ */
+public interface CyGroupViewer {
+ /**
+ * The change values
+ */
+ public static enum ChangeType { NODE_ADDED, NODE_REMOVED, STATE_CHANGED, NETWORK_CHANGED,
+ INNER_EDGE_ADDED, INNER_EDGE_REMOVED,
+ OUTER_EDGE_ADDED, OUTER_EDGE_REMOVED }
+
+ /**
+ * Provide the string name of this viewer. This will be used to reassociate
+ * this viewer with its groups upon session restoration.
+ *
+ * @return String name of the viewer
+ */
+ public String getViewerName();
+
+ /**
+ * Provide viewer-specific initialization after the creation of a group.
+ * This method will be called when a group is created from outside of the
+ * viewer mechanism. For example, when a session is restored. This allows
+ * the appropriate viewer to "take ownership" of the group, setting appropriate
+ * node attributes, or even adding the group node to the view, if appropriate.
+ * Note that this is called *after* the group creation has happened.
+ *
+ * @param group the CyGroup that was just created.
+ */
+ public void groupCreated(CyGroup group);
+ public void groupCreated(CyGroup group, CyNetworkView myView);
+
+ /**
+ * Provide viewer-specific hooks to deletion of a group. Most of the time
+ * group deletion would happen completely within the context of the viewer,
+ * but there might be occaisions where alternative mechanisms would be provided.
+ * Note that this is called *before* the group deletion actually occurs.
+ *
+ * @param group the CyGroup that will be deleted.
+ */
+ public void groupWillBeRemoved(CyGroup group);
+
+ /**
+ * Provide viewer-specific hooks to the change of a group. At this point,
+ * group change will be either the addition or deletion of a node, but
+ * it could be imagined in a future implementation where we might want to
+ * notify viewers of changes in group edges, state, or viewObject information.
+ *
+ * @param group the CyGroup that will be deleted.
+ * @param changedObject the node or edge that triggered the change
+ * @param change the change that was made (see CyGroup defines)
+ */
+ public void groupChanged(CyGroup group, GraphObject changedObject, ChangeType change);
+}
diff --git a/application/src/main/java/cytoscape/groups/GroupPropertyChangeListener.java b/application/src/main/java/cytoscape/groups/GroupPropertyChangeListener.java
new file mode 100644
index 0000000..8190e4b
--- /dev/null
+++ b/application/src/main/java/cytoscape/groups/GroupPropertyChangeListener.java
@@ -0,0 +1,70 @@
+/* vim :set ts=2: */
+/*
+ File: GroupPropertyChangeListener.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.groups;
+
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+
+/**
+ * This inner class listens for network destroyed events and deletes
+ * any groups in that network
+ */
+class GroupPropertyChangeListener implements PropertyChangeListener {
+ public void propertyChange(PropertyChangeEvent e) {
+ if (Cytoscape.NETWORK_DESTROYED.equals(e.getPropertyName())) {
+ String networkId = (String) e.getNewValue();
+ if (networkId == null)
+ return;
+
+ CyNetwork network = Cytoscape.getNetwork(networkId);
+ if (network == null || network.equals(Cytoscape.getNullNetwork()))
+ return;
+
+ List<CyGroup> groupList = CyGroupManager.getGroupList(network);
+ for (CyGroup group: groupList) {
+ CyGroupManager.removeGroup(group);
+ }
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/init/CyInitParams.java b/application/src/main/java/cytoscape/init/CyInitParams.java
new file mode 100644
index 0000000..0756688
--- /dev/null
+++ b/application/src/main/java/cytoscape/init/CyInitParams.java
@@ -0,0 +1,165 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.init;
+
+import java.util.List;
+import java.util.Properties;
+
+
+/**
+ * An interface that describes the initialization parameters needed
+ * by cytoscape. Anything initialing Cytoscape should implement this
+ * interface and pass that object into CytoscapeInit. By setting the
+ * mode you can control how Cytoscape is initialized.
+ */
+public interface CyInitParams {
+ /**
+ * Returns the properties that were defined at initialization.
+ *
+ * @return A Properties object containing whatever property values
+ * that were defined at initialization.
+ */
+ public Properties getProps();
+
+ /**
+ * Returns properties specific to the VizMapper. These properties
+ * aren't necessarily intended for human consumption.
+ *
+ * @return A Properties object containing VizMapper specific properties.
+ */
+ public Properties getVizProps();
+
+ /**
+ * A list of Strings that describe graph file locations. The strings may
+ * represent URLs.
+ *
+ * @return A list of Strings representing graph file locations.
+ */
+ public List getGraphFiles();
+
+ /**
+ * A list of Strings that describe edge attribute file locations.
+ *
+ * @return A list of Strings representing edge attribute file locations.
+ */
+ public List getEdgeAttributeFiles();
+
+ /**
+ * A list of Strings that describe node attribute file locations.
+ *
+ * @return A list of Strings representing node attribute file locations.
+ */
+ public List getNodeAttributeFiles();
+
+ /**
+ * A list of Strings that describe expression matrix file locations.
+ *
+ * @return A list of Strings representing expression matrixfile locations.
+ */
+ public List getExpressionFiles();
+
+ /**
+ * A list of Strings that describe plugins. The descriptions can be any of the following:
+ * <ul>
+ * <li>A jar file location, file or URL </li>
+ * <li>A directory name </li>
+ * <li>A plugin class name </li>
+ * <li>A local file location where the file lists one plugin jar per line</li>
+ * </ul>
+ *
+ * @return A list of strings describing the plugin locations.
+ */
+ public List getPlugins();
+
+ /**
+ * A single string describing the session file location.
+ *
+ * @return A string describing the session file locaton.
+ */
+ public String getSessionFile();
+
+ /**
+ * Returns and int representing the mode cytoscape runs in. The possible
+ * modes are:
+ * <ul>
+ * <li>ERROR </li>
+ * <li>GUI - normal operation as a gui </li>
+ * <li>TEXT - headless mode where cytoscape acts as a command line app </li>
+ * <li>LIBRARY - headless mode wehre cytoscape acts as a server or daemon</li>
+ * <li>EMBEDDED_WINDOW - gui mode where cytoscape is embedded in another app</li>
+ * </ul>
+ *
+ * @return the int representing the mode
+ */
+ public int getMode();
+
+ /**
+ * Returns the arguments used to trigger the initialization. While args are
+ * appropriate for the command line, they're not really appropriate for other modes.
+ * Therefore, to pass initialization information to cytoscape, it's better to
+ * use getProperties().
+ *
+ * @return An array of strings representing arguments used to intialize cytoscape.
+ */
+ public String[] getArgs();
+
+ /**
+ * Error. Something is wrong.
+ */
+ public static final int ERROR = 0;
+
+ /**
+ * Normal gui mode.
+ */
+ public static final int GUI = 1;
+
+ /**
+ * Headless mode (no gui) were cytoscape acts like a normal command line app and exits
+ * once finished processing.
+ */
+ public static final int TEXT = 2;
+
+ /**
+ * Another headless mode (no gui), but meant for a server or daemon that runs in the
+ * background without exiting.
+ */
+ public static final int LIBRARY = 3;
+
+ /**
+ * A gui mode, but where cytoscape is embedded within a different application
+ * meaning the usual menus and/or toolbars may not be present.
+ */
+ public static final int EMBEDDED_WINDOW = 4;
+}
diff --git a/application/src/main/java/cytoscape/layout/AbstractLayout.java b/application/src/main/java/cytoscape/layout/AbstractLayout.java
new file mode 100644
index 0000000..f9bce08
--- /dev/null
+++ b/application/src/main/java/cytoscape/layout/AbstractLayout.java
@@ -0,0 +1,399 @@
+/* vim :set ts=2:
+ File: AbstractLayout.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Pasteur Institute
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.layout;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import cytoscape.CyNode;
+
+import cytoscape.task.TaskMonitor;
+
+import cytoscape.view.CyNetworkView;
+import cytoscape.data.CyAttributes;
+
+import ding.view.DGraphView;
+import ding.view.ViewChangeEdit;
+
+import giny.view.NodeView;
+
+import java.awt.Dimension;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+import java.util.Collection;
+
+import javax.swing.JPanel;
+
+
+/**
+ * The AbstractLayout provides nice starting point for Layouts
+ * written for Cytoscape.
+ */
+abstract public class AbstractLayout implements CyLayoutAlgorithm {
+ // Graph Objects and Views
+ protected Set<NodeView> staticNodes;
+ protected CyNetworkView networkView;
+ protected CyNetwork network;
+
+ //
+ protected boolean selectedOnly = false;
+ protected String edgeAttribute = null;
+ protected String nodeAttribute = null;
+ protected boolean canceled = false;
+ protected Dimension currentSize = new Dimension(20, 20);
+ protected HashMap propertyMap = null;
+ protected HashMap savedPropertyMap = null;
+ private ViewChangeEdit undoableEdit;
+
+ // Monitor
+ protected TaskMonitor taskMonitor;
+
+ protected static TaskMonitor nullTaskMonitor = new TaskMonitor() {
+ public void setPercentCompleted(int percent) {
+ }
+
+ public void setEstimatedTimeRemaining(long time) throws IllegalThreadStateException {
+ }
+
+ public void setException(Throwable t, String userErrorMessage) {
+ }
+
+ public void setException(Throwable t, String userErrorMessage, String recoveryTip) {
+ }
+
+ public void setStatus(String message)
+ throws IllegalThreadStateException, NullPointerException {
+ }
+ };
+
+ // Should definitely be overridden!
+ protected String propertyPrefix = "abstract";
+
+ /**
+ * The Constructor is null
+ */
+ public AbstractLayout() {
+ this.staticNodes = new HashSet();
+ }
+
+ /**
+ * These abstract methods must be overridden.
+ */
+ public abstract void construct();
+
+ /**
+ * getName is used to construct property strings
+ * for this layout.
+ */
+ public abstract String getName();
+
+ /**
+ * toString is used to get the user-visible name
+ * of the layout
+ */
+ public abstract String toString();
+
+ /**
+ * These methods should be overridden
+ */
+ public boolean supportsSelectedOnly() {
+ return false;
+ }
+
+ /**
+ * Set the flag that indicates that this algorithm
+ * should only operate on the currently selected nodes.
+ *
+ * @param selectedOnly set to "true" if the algorithm should
+ * only apply to selected nodes only
+ */
+ public void setSelectedOnly(boolean selectedOnly) {
+ this.selectedOnly = selectedOnly;
+ }
+
+ /**
+ * Returns the types of node attributes supported by
+ * this algorithm. This should be overloaded by the
+ * specific algorithm
+ *
+ * @return the list of supported attribute types, or null
+ * if node attributes are not supported
+ */
+ public byte[] supportsNodeAttributes() {
+ return null;
+ }
+
+ /**
+ * Returns the types of edge attributes supported by
+ * this algorithm. This should be overloaded by the
+ * specific algorithm
+ *
+ * @return the list of supported attribute types, or null
+ * if edge attributes are not supported
+ */
+ public byte[] supportsEdgeAttributes() {
+ return null;
+ }
+
+ /**
+ * Set the name of the attribute to use for attribute
+ * dependent layout algorithms.
+ *
+ * @param attributeName The name of the attribute
+ */
+ public void setLayoutAttribute(String attributeName) {
+ if (supportsNodeAttributes() != null) {
+ nodeAttribute = attributeName;
+ } else if (supportsEdgeAttributes() != null) {
+ edgeAttribute = attributeName;
+ }
+ }
+
+ /*
+ * Override this if you want to provide a custom attribute
+ */
+
+ /**
+ * This returns the list of "attributes" that are provided
+ * by an algorithm for internal purposes. For example,
+ * an edge-weighted algorithmn might seed the list of
+ * attributes with "unweighted". This should be overloaded
+ * by algorithms that intend to return custom attributes.
+ *
+ * @return A (possibly empty) list of attributes
+ */
+ public List<String> getInitialAttributeList() {
+ return new ArrayList();
+ }
+
+ /**
+ * Returns a JPanel to be used as part of the Settings dialog for this layout
+ * algorithm.
+ *
+ */
+ public JPanel getSettingsPanel() {
+ return null;
+ }
+
+ /**
+ * Property handling -- these must be overridden by any algorithms
+ * that want to use properties or have a settings UI.
+ */
+ public void revertSettings() {
+ }
+
+ /**
+ * Property handling -- these must be overridden by any algorithms
+ * that want to use properties or have a settings UI.
+ */
+ public void updateSettings() {
+ }
+
+ /**
+ * Property handling -- these must be overridden by any algorithms
+ * that want to use properties or have a settings UI.
+ */
+ public LayoutProperties getSettings() {
+ return null;
+ }
+
+ /**
+ * doLayout on current network view.
+ */
+ public void doLayout() {
+ doLayout(Cytoscape.getCurrentNetworkView(), nullTaskMonitor);
+ }
+
+ /**
+ * doLayout on specified network view.
+ */
+ public void doLayout(CyNetworkView nview) {
+ doLayout(nview, nullTaskMonitor);
+ }
+
+ /**
+ * doLayout on specified network view with specified monitor.
+ */
+ public void doLayout(CyNetworkView nview, TaskMonitor monitor) {
+ canceled = false;
+
+ networkView = nview;
+
+ // do some sanity checking
+ if ((networkView == null) || (networkView == Cytoscape.getNullNetworkView()))
+ return;
+
+ this.network = networkView.getNetwork();
+
+ if ((network == null) || (network == Cytoscape.getNullNetwork()))
+ return;
+
+ if (network.getNodeCount() <= 0)
+ return;
+
+ if (monitor == null)
+ monitor = nullTaskMonitor;
+
+ taskMonitor = monitor;
+
+ // set up the edit
+ undoableEdit = new ViewChangeEdit((DGraphView) networkView, toString() + " Layout");
+
+ // reset label positions
+ resetLabelPositions();
+
+ // this is overridden by children and does the actual layout
+ construct();
+
+ // update the view
+ if (!selectedOnly)
+ networkView.fitContent();
+ else
+ networkView.updateView();
+
+ // post the edit
+ undoableEdit.post();
+
+ // update the __layoutAlgorithm attribute
+ final CyAttributes networkAttributes = Cytoscape.getNetworkAttributes();
+ networkAttributes.setAttribute(network.getIdentifier(), "__layoutAlgorithm", getName());
+ networkAttributes.setUserVisible("__layoutAlgorithm", false);
+
+ this.network = null;
+ this.networkView = null;
+ }
+
+ /**
+ * Initializer, calls <tt>intialize_local</tt> to
+ * start construction process.
+ */
+ public void initialize() {
+ double node_count = (double) network.getNodeCount();
+ node_count = Math.sqrt(node_count);
+ node_count *= 100;
+ currentSize = new Dimension((int) node_count, (int) node_count);
+ initialize_local();
+ }
+
+ /**
+ * Initializes all local information, and is called immediately
+ * within the <tt>initialize()</tt> process.
+ * The user is responsible for overriding this method
+ * to do any construction that may be necessary:
+ * for example, to initialize local per-edge or
+ * graph-wide data.
+ */
+ protected void initialize_local() {
+ }
+
+ /**
+ * Lock these nodes (i.e. prevent them from moving).
+ *
+ * @param nodes An array of NodeView's to lock
+ */
+ public void lockNodes(NodeView[] nodes) {
+ for (int i = 0; i < nodes.length; ++i) {
+ staticNodes.add(nodes[i]);
+ }
+ }
+
+ /**
+ * Lock this node (i.e. prevent it from moving).
+ *
+ * @param v A NodeView to lock
+ */
+ public void lockNode(NodeView v) {
+ staticNodes.add(v);
+ }
+
+ /**
+ * Unlock this node
+ *
+ * @param v A NodeView to unlock
+ */
+ public void unlockNode(NodeView v) {
+ staticNodes.remove(v);
+ }
+
+ protected boolean isLocked(NodeView v) {
+ return (staticNodes.contains(v));
+ }
+
+ /**
+ * Unlock all nodes
+ */
+ public void unlockAllNodes() {
+ staticNodes.clear();
+ }
+
+ /**
+ * Halt the algorithm.
+ */
+ public void halt() {
+ canceled = true;
+ }
+
+ /**
+ * Deletes labelPosition attribute of selected nodes (if selectedOnly) or all nodes
+ * This has the effect of moving labels back to their parent nodes position
+ */
+ protected void resetLabelPositions() {
+
+ // logger.info("Reseting labels position");
+
+ CyAttributes nodeAtts = Cytoscape.getNodeAttributes();
+ Collection<CyNode> selectedNodes = (Collection<CyNode>)network.getSelectedNodes();
+
+ // Go through all nodes deleting the label position attribute
+ for (CyNode node: (List<CyNode>)network.nodesList()) {
+ if (!supportsSelectedOnly() || !selectedOnly || selectedNodes.contains(node) )
+ if (nodeAtts.hasAttribute(node.getIdentifier(), "node.labelPosition")) {
+ nodeAtts.deleteAttribute(node.getIdentifier(), "node.labelPosition");
+ // logger.info("Deleted label position attribute of node: " + node.toString() );
+ }
+ }
+
+ // redraw the network so that the new label positions are visible
+ networkView.updateView();
+ networkView.redrawGraph(true, true);
+ }
+
+
+}
diff --git a/application/src/main/java/cytoscape/layout/CyLayoutAlgorithm.java b/application/src/main/java/cytoscape/layout/CyLayoutAlgorithm.java
new file mode 100644
index 0000000..d519d22
--- /dev/null
+++ b/application/src/main/java/cytoscape/layout/CyLayoutAlgorithm.java
@@ -0,0 +1,212 @@
+/* vim: set ts=2:
+ File: CyLayoutAlgorithm.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.layout;
+
+import cytoscape.task.TaskMonitor;
+
+import cytoscape.util.*;
+
+import cytoscape.view.CyNetworkView;
+
+import giny.view.NodeView;
+
+import java.util.List;
+
+import javax.swing.JPanel;
+
+
+/**
+ *
+ */
+public interface CyLayoutAlgorithm {
+ /**
+ * This method performs the layout on the current network using the
+ * current network view.
+ *
+ */
+ public void doLayout();
+
+ /**
+ * This method performs the layout on the current network.
+ *
+ * @param networkView the CyNetworkView on which to perform the layout
+ */
+ public void doLayout(CyNetworkView networkView);
+
+ /**
+ * This method performs the layout on the current network, but assumes
+ * that the layout is part of an existing monitored task
+ *
+ * @param networkView the CyNetworkView on which to perform the layout
+ * @param monitor the task monitor to use
+ */
+ public void doLayout(CyNetworkView networkView, TaskMonitor monitor);
+
+ /**
+ * Tests to see if this layout supports doing a layout on a subset of the
+ * nodes in this network view.
+ *
+ * @return true if layout supports layouts on a subset of the nodes
+ */
+ public boolean supportsSelectedOnly();
+
+ /**
+ * Sets the "selectedOnly" flag
+ *
+ * @param selectedOnly boolean value that tells the layout algorithm whether to
+ * only layout the selected nodes
+ */
+ public void setSelectedOnly(boolean selectedOnly);
+
+ /**
+ * Tests to see if this layout supports doing a layout based on node attributes.
+ *
+ * @return byte array of allowable attribute types or "null" if not supported. If the
+ * first type is "-1", all types are supported
+ */
+ public byte[] supportsNodeAttributes();
+
+ /**
+ * Tests to see if this layout supports doing a layout based on edge attributes.
+ *
+ * @return type array of allowable attribute types or "null" if not supported. If the
+ * first type is "-1", all types are supported
+ */
+ public byte[] supportsEdgeAttributes();
+
+ /**
+ * Sets the attribute to use for node- or edge- based attribute layouts
+ *
+ * @param attributeName String with the name of the attribute to use
+ */
+ public void setLayoutAttribute(String attributeName);
+
+ /**
+ * This returns a (possibly empty) List of Strings that is used for
+ * the attribute list in the menu for attribute-based layouts. This
+ * allows layout algorithms to provide "special" attributes. For example,
+ * a force directed layout might want to set the list to ["(unweighted)"]
+ * to allow the user to perform an unweighted layout. Note that this value
+ * will be set using setLayoutAttribute() just like other attributes, so the
+ * layout algorithm will need to check for it.
+ *
+ * @return List of Strings
+ */
+ public List<String> getInitialAttributeList();
+
+ /**
+ * This method should return a JPanel that implements the UI to set
+ * the tuneable parameters for the algorithm.
+ *
+ * @return JPanel that will be used in the LayoutSettingsDialog. If
+ * this algorithm does not support a UI for settings,
+ * it should return null
+ */
+ public JPanel getSettingsPanel();
+
+ /**
+ * This method is used to ask the algorithm to revert its settings
+ * to some previous state. It is called from the settings dialog
+ * when the user presses the "Cancel" button.
+ *
+ * NOTE: AbstractLayout implements this on behalf of all its subclasses
+ * by using Java Preferences.
+ */
+ public void revertSettings();
+
+ /**
+ * This method is used to ask the algorithm to get its settings
+ * from the settings dialog. It is called from the settings dialog
+ * when the user presses the "Done" or the "Execute" buttons.
+ *
+ * NOTE: AbstractLayout implements this on behalf of all its subclasses
+ * by using Java Preferences.
+ */
+ public void updateSettings();
+
+ /**
+ * This method is used to ask the algorithm to get all of its tunables
+ * and return them to the caller.
+ *
+ * @return the layout properties for this algorithm
+ *
+ */
+ public LayoutProperties getSettings();
+
+ /**
+ * Get the name of this layout.
+ *
+ * @return String representing the name of the layout.
+ */
+ public String getName();
+
+ /**
+ * Lock this array of nodes. Locking a node prevents the node
+ * from being moved by layout algorithmes.
+ *
+ * @param nodes the array of nodes to lock
+ */
+ public void lockNodes(NodeView[] nodes);
+
+ /**
+ * Lock this node. Locking a node prevents the node
+ * from being moved by layout algorithmes.
+ *
+ * @param v the NodeView of the node to lock
+ */
+ public void lockNode(NodeView v);
+
+ /**
+ * Unlock this node. Unlocking a node allows the node
+ * to be moved by a layout algorithmes.
+ *
+ * @param v the node to unlock
+ */
+ public void unlockNode(NodeView v);
+
+ /**
+ * Unlock all of the nodes. Unlocking a node allows the node
+ * to be moved by a layout algorithmes.
+ *
+ */
+ public void unlockAllNodes();
+
+ /**
+ * Can be used to stop the layout from running.
+ */
+ public void halt();
+}
diff --git a/application/src/main/java/cytoscape/layout/CyLayoutAlgorithmComparator.java b/application/src/main/java/cytoscape/layout/CyLayoutAlgorithmComparator.java
new file mode 100644
index 0000000..40242cd
--- /dev/null
+++ b/application/src/main/java/cytoscape/layout/CyLayoutAlgorithmComparator.java
@@ -0,0 +1,57 @@
+/* vim: set ts=2:
+ File: CyLayoutAlgorithm.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.layout;
+
+import java.util.Comparator;
+
+import cytoscape.layout.CyLayoutAlgorithm;
+
+
+/**
+ *
+ */
+public class CyLayoutAlgorithmComparator <CyLayoutAlgorithm> implements Comparator {
+
+ public int compare(Object o1, Object o2) {
+ return o1.toString().compareToIgnoreCase(o2.toString());
+ }
+
+ public boolean equals(Object o1, Object o2) {
+ return o1.toString().equalsIgnoreCase(o2.toString());
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/layout/CyLayouts.java b/application/src/main/java/cytoscape/layout/CyLayouts.java
new file mode 100644
index 0000000..773f593
--- /dev/null
+++ b/application/src/main/java/cytoscape/layout/CyLayouts.java
@@ -0,0 +1,139 @@
+/*
+ File: CyLayouts.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.layout;
+
+import java.util.Collection;
+import java.util.HashMap;
+
+import cytoscape.CytoscapeInit;
+import cytoscape.layout.algorithms.GridNodeLayout;
+
+
+/**
+ * CyLayouts is a singleton class that is used to register all available
+ * layout algorithms.
+ */
+public class CyLayouts {
+ private static HashMap<String, CyLayoutAlgorithm> layoutMap;
+ private static HashMap<CyLayoutAlgorithm, String> menuNameMap;
+
+ private static final String DEFAULT_LAYOUT_PROP = "layout.default";
+
+ static {
+ new CyLayouts();
+ }
+
+ private CyLayouts() {
+ layoutMap = new HashMap<String,CyLayoutAlgorithm>();
+ menuNameMap = new HashMap<CyLayoutAlgorithm,String>();
+
+ addLayout(new GridNodeLayout(), "Cytoscape Layouts");
+ }
+
+ /**
+ * Add a layout to the layout manager's list. If menu is "null"
+ * it will be assigned to the "none" menu, which is not displayed.
+ * This can be used to register layouts that are to be used for
+ * specific algorithmic purposes, but not, in general, supposed
+ * to be for direct user use.
+ *
+ * @param layout The layout to be added
+ * @param menu The menu that this should appear under
+ */
+ public static void addLayout(CyLayoutAlgorithm layout, String menu) {
+ layoutMap.put(layout.getName(),layout);
+ menuNameMap.put(layout,menu);
+ }
+
+ /**
+ * Remove a layout from the layout maanger's list.
+ *
+ * @param layout The layout to remove
+ */
+ public static void removeLayout(CyLayoutAlgorithm layout) {
+ layoutMap.remove(layout.getName());
+ menuNameMap.remove(layout);
+ }
+
+ /**
+ * Get the layout named "name". If "name" does
+ * not exist, this will return null
+ *
+ * @param name String representing the name of the layout
+ * @return the layout of that name or null if it is not reigstered
+ */
+ public static CyLayoutAlgorithm getLayout(String name) {
+ if (layoutMap.containsKey(name))
+ return layoutMap.get(name);
+ return null;
+ }
+
+ /**
+ * Get all of the available layouts.
+ *
+ * @return a Collection of all the available layouts
+ */
+ public static Collection<CyLayoutAlgorithm> getAllLayouts() {
+ return layoutMap.values();
+ }
+
+ /**
+ * Get the default layout. This is either the grid layout or a layout
+ * chosen by the user via the setting of the "layout.default" property.
+ *
+ * @return CyLayoutAlgorithm to use as the default layout algorithm
+ */
+ public static CyLayoutAlgorithm getDefaultLayout() {
+ // See if the user has set the layout.default property
+ String defaultLayout = CytoscapeInit.getProperties().getProperty(DEFAULT_LAYOUT_PROP);
+
+ if ((defaultLayout == null) || !layoutMap.containsKey(defaultLayout)) {
+ defaultLayout = "grid";
+ }
+
+ CyLayoutAlgorithm l = layoutMap.get(defaultLayout);
+ // CyLogger.getLogger().info("getDefaultLayout returning " + l);
+
+ // Nope, so return the grid layout
+ return l;
+ }
+
+ // Ack.
+ public static String getMenuName(CyLayoutAlgorithm layout) {
+ return menuNameMap.get(layout);
+ }
+}
diff --git a/application/src/main/java/cytoscape/layout/LayoutAdapter.java b/application/src/main/java/cytoscape/layout/LayoutAdapter.java
new file mode 100644
index 0000000..8e5e989
--- /dev/null
+++ b/application/src/main/java/cytoscape/layout/LayoutAdapter.java
@@ -0,0 +1,215 @@
+/* vim :set ts=2:
+ File: LayoutAdapter.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Pasteur Institute
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.layout;
+
+import java.lang.String;
+import java.util.List;
+import java.util.ArrayList;
+
+import cytoscape.Cytoscape;
+import cytoscape.view.CyNetworkView;
+
+import cytoscape.task.TaskMonitor;
+
+import giny.view.EdgeView;
+import giny.view.NodeView;
+
+import javax.swing.JPanel;
+
+/**
+ * LayoutAdapter provides a *very* minimal interface to implement a layout
+ * algorithm. It is meant to be used by graph readers and plugins that provide
+ * their own node placement and whose layout approach should not be made
+ * available outside of the reader or plugin's context.
+ */
+abstract public class LayoutAdapter implements CyLayoutAlgorithm {
+ /**
+ * This method performs the layout on the current network using the
+ * current network view.
+ *
+ */
+ public void doLayout() {
+ doLayout(Cytoscape.getCurrentNetworkView(), null);
+ }
+
+ /**
+ * This method performs the layout on the current network.
+ *
+ * @param networkView the CyNetworkView on which to perform the layout
+ */
+ public void doLayout(CyNetworkView networkView) {
+ doLayout(networkView, null);
+ }
+
+ /**
+ * This method performs the layout on the current network, but assumes
+ * that the layout is part of an existing monitored task
+ *
+ * @param networkView the CyNetworkView on which to perform the layout
+ * @param monitor the task monitor to use
+ */
+ public abstract void doLayout(CyNetworkView networkView, TaskMonitor monitor);
+
+ /**
+ * Get the name of this layout.
+ *
+ * @return String representing the name of the layout.
+ */
+ public String getName() {return "LayoutAdaptor";}
+
+ /**
+ * Tests to see if this layout supports doing a layout on a subset of the
+ * nodes in this network view.
+ *
+ * @return true if layout supports layouts on a subset of the nodes
+ */
+ public boolean supportsSelectedOnly() {return false;}
+
+ /**
+ * Sets the "selectedOnly" flag
+ *
+ * @param selectedOnly boolean value that tells the layout algorithm whether to
+ * only layout the selected nodes
+ */
+ public void setSelectedOnly(boolean selectedOnly) {}
+
+ /**
+ * Tests to see if this layout supports doing a layout based on node attributes.
+ *
+ * @return byte array of allowable attribute types or "null" if not supported. If the
+ * first type is "-1", all types are supported
+ */
+ public byte[] supportsNodeAttributes() { return null; }
+
+ /**
+ * Tests to see if this layout supports doing a layout based on edge attributes.
+ *
+ * @return type array of allowable attribute types or "null" if not supported. If the
+ * first type is "-1", all types are supported
+ */
+ public byte[] supportsEdgeAttributes() { return null; }
+
+ /**
+ * Sets the attribute to use for node- or edge- based attribute layouts
+ *
+ * @param attributeName String with the name of the attribute to use
+ */
+ public void setLayoutAttribute(String attributeName) {}
+
+ /**
+ * This returns a (possibly empty) List of Strings that is used for
+ * the attribute list in the menu for attribute-based layouts. This
+ * allows layout algorithms to provide "special" attributes. For example,
+ * a force directed layout might want to set the list to ["(unweighted)"]
+ * to allow the user to perform an unweighted layout. Note that this value
+ * will be set using setLayoutAttribute() just like other attributes, so the
+ * layout algorithm will need to check for it.
+ *
+ * @return List of Strings
+ */
+ public List<String> getInitialAttributeList() {return new ArrayList<String>();}
+
+ /**
+ * This method should return a JPanel that implements the UI to set
+ * the tuneable parameters for the algorithm.
+ *
+ * @return JPanel that will be used in the LayoutSettingsDialog. If
+ * this algorithm does not support a UI for settings,
+ * it should return null
+ */
+ public JPanel getSettingsPanel() {return null;}
+
+ /**
+ * This method is used to ask the algorithm to revert its settings
+ * to some previous state. It is called from the settings dialog
+ * when the user presses the "Cancel" button.
+ *
+ * NOTE: AbstractLayout implements this on behalf of all its subclasses
+ * by using Java Preferences.
+ */
+ public void revertSettings() {}
+
+ /**
+ * This method is used to ask the algorithm to get its settings
+ * from the seetings dialog. It is called from the settings dialog
+ * when the user presses the "Done" or the "Execute" buttons.
+ *
+ * NOTE: AbstractLayout implements this on behalf of all its subclasses
+ * by using Java Preferences.
+ */
+ public void updateSettings() {}
+
+ /**
+ * This method is used to ask the algorithm to get all of its tunables
+ * and return them to the caller.
+ *
+ * @return the layout properties for this algorithm
+ *
+ */
+ public LayoutProperties getSettings() {return null;}
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nodes DOCUMENT ME!
+ */
+ public void lockNodes(NodeView[] nodes) {}
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param v DOCUMENT ME!
+ */
+ public void lockNode(NodeView v) {}
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param v DOCUMENT ME!
+ */
+ public void unlockNode(NodeView v) {}
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void unlockAllNodes() {}
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void halt() {}
+}
diff --git a/application/src/main/java/cytoscape/layout/LayoutAlgorithm.java b/application/src/main/java/cytoscape/layout/LayoutAlgorithm.java
new file mode 100644
index 0000000..b855781
--- /dev/null
+++ b/application/src/main/java/cytoscape/layout/LayoutAlgorithm.java
@@ -0,0 +1,56 @@
+
+/*
+ File: LayoutAlgorithm.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.layout;
+
+import cytoscape.util.*;
+import giny.view.NodeView;
+
+/** @deprecated Use CyLayoutAlgorithm instead. Will be removed June, 2008 **/
+
+public interface LayoutAlgorithm extends MonitoredTask {
+
+ public abstract void doLayout ();
+
+ public void lockNodes ( NodeView[] nodes );
+
+ public void lockNode ( NodeView v );
+
+ public void unlockNode( NodeView v );
+
+}
diff --git a/application/src/main/java/cytoscape/layout/LayoutProperties.java b/application/src/main/java/cytoscape/layout/LayoutProperties.java
new file mode 100644
index 0000000..dc76de9
--- /dev/null
+++ b/application/src/main/java/cytoscape/layout/LayoutProperties.java
@@ -0,0 +1,137 @@
+// vim: set ts=2: */
+package cytoscape.layout;
+
+import cytoscape.CytoscapeInit;
+import cytoscape.util.ModulePropertiesImpl;
+
+import java.awt.event.ComponentEvent;
+import java.awt.event.ComponentListener;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.Map;
+
+import javax.swing.JPanel;
+import javax.swing.BoxLayout;
+
+
+/**
+ * The LayoutProperties class is a helper class to support the management
+ * of settings and properties for layout algorithms that implement
+ * CyLayoutAlgorithm or extend AbstractLayout. LayoutProperties objects
+ * maintain a list of Tunables that are supplied by the individual
+ * algorithms. Each Tunable represents a value that should be loaded
+ * from the Cytoscape properties file, and made available as a setting
+ * in the LayoutSettingsDialog. Tunables are added to the LayoutProperties
+ * using the <tt>add</tt> method and are retrieved with the <tt>get</tt>
+ * method.
+ */
+public class LayoutProperties extends ModulePropertiesImpl implements TunableListener {
+ JPanel tunablesPanel = null;
+
+ /**
+ * Constructor.
+ *
+ * @param propertyPrefix String representing the prefix to be used
+ * when pulling properties from the property
+ * list.
+ */
+ public LayoutProperties(String propertyPrefix) {
+ super(propertyPrefix, "layout");
+ }
+
+
+ /**
+ * This method returns a JPanel that represents the all of the Tunables
+ * associated with this LayoutProperties object.
+ *
+ * @return JPanel that contains all of the Tunable widgets
+ */
+ public JPanel getTunablePanel() {
+ if (tunablesPanel != null) return tunablesPanel;
+
+ tunablesPanel = new JPanel();
+ BoxLayout box = new BoxLayout(tunablesPanel, BoxLayout.Y_AXIS);
+ tunablesPanel.setLayout(box);
+
+ addSubPanels(tunablesPanel, tunablesList.iterator(), new Integer(100000), this);
+
+ tunablesPanel.validate();
+ return tunablesPanel;
+ }
+
+ /**
+ * This method is called to update the panel for this property sheet.
+ */
+ public void updateTunablePanel() {
+ if (tunablesPanel == null) return;
+
+ tunablesPanel.removeAll();
+
+ addSubPanels(tunablesPanel, tunablesList.iterator(), new Integer(100000), null);
+
+ tunablesPanel.doLayout();
+ tunablesPanel.validate();
+ // now signal any listeners that we've resized
+ ComponentListener[] resizeListeners = tunablesPanel.getComponentListeners();
+ if (resizeListeners == null) return;
+
+ for (int i = 0; i < resizeListeners.length; i++) {
+ resizeListeners[i].componentResized(new ComponentEvent(tunablesPanel, ComponentEvent.COMPONENT_RESIZED));
+ }
+ }
+
+ private void addSubPanels(JPanel panel, Iterator<Tunable>iter, Object count, TunableListener listener) {
+ int groupCount = ((Integer)count).intValue();
+ for (int n = 0; n < groupCount; n++) {
+ if (!iter.hasNext()) {
+ return;
+ }
+ // Get the next tunable
+ Tunable tunable = iter.next();
+
+ JPanel p = tunable.getPanel();
+ if (panel == null)
+ p = null;
+
+ if (tunable.getType() == Tunable.GROUP) {
+ if (!tunable.checkFlag(Tunable.COLLAPSABLE)) {
+ addSubPanels(p, iter, tunable.getValue(), listener);
+ } else {
+ tunable.addTunableValueListener(listener); // We need to listen to collapse/expand changes
+ Boolean collapsed = (Boolean)tunable.getLowerBound();
+ if (!collapsed.booleanValue())
+ addSubPanels(p, iter, tunable.getValue(), listener);
+ else
+ addSubPanels(null, iter, tunable.getValue(), listener);
+ }
+ }
+ if (p != null)
+ panel.add(p);
+ }
+ }
+
+ public void tunableChanged(Tunable tunable) {
+/*
+ Map<Tunable,Object> values = new HashMap<Tunable, Object>();
+ for (Tunable t: tunablesList) {
+ if (t.getType() == Tunable.GROUP)
+ continue;
+ if (t.getValue() != null) {
+ System.out.println("Saving value for tunable "+t.getName()+" = "+t.getValue().toString());
+ values.put(t, t.getValue());
+ }
+ }
+*/
+
+ // In our case, we just update our display
+ updateTunablePanel();
+
+/*
+ // Now, update all of the values
+ for (Tunable t: values.keySet()) {
+ System.out.println("Setting value for tunable "+t.getName()+" = "+values.get(t).toString());
+ t.setValue(values.get(t));
+ }
+*/
+ }
+}
diff --git a/application/src/main/java/cytoscape/layout/LayoutTask.java b/application/src/main/java/cytoscape/layout/LayoutTask.java
new file mode 100644
index 0000000..b5cf6d1
--- /dev/null
+++ b/application/src/main/java/cytoscape/layout/LayoutTask.java
@@ -0,0 +1,131 @@
+/*
+ File: LayoutTask.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Pasteur Institute
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.layout;
+
+import cytoscape.Cytoscape;
+import cytoscape.layout.CyLayoutAlgorithm;
+import cytoscape.logger.CyLogger;
+import cytoscape.view.CyNetworkView;
+
+import cytoscape.task.Task;
+import cytoscape.task.TaskMonitor;
+
+import cytoscape.task.ui.JTaskConfig;
+
+/**
+ * A wrapper for applying a layout in a task. Use it something like
+ * this:
+ * <p>TaskManager.executeTask( new LayoutTask(layout, view), LayoutTask.getDefaultTaskConfig() );
+
+ */
+public class LayoutTask implements Task {
+
+ CyLayoutAlgorithm layout;
+ CyNetworkView view;
+ TaskMonitor monitor;
+ CyLogger logger = CyLogger.getLogger(LayoutTask.class);
+
+ /**
+ * Creates the task.
+ *
+ * @param layout The CyLayoutAlgorithm to apply.
+ * @param view The view the algorithm should be applied to.
+ */
+ public LayoutTask(CyLayoutAlgorithm layout,CyNetworkView view) {
+ this.layout = layout;
+ this.view = view;
+ }
+
+ /**
+ * Sets the task monitor to be used for the layout.
+ */
+ public void setTaskMonitor(TaskMonitor monitor) {
+ this.monitor = monitor;
+ }
+
+ /**
+ * Run the algorithm.
+ */
+ public void run() {
+ try {
+ layout.doLayout(view,monitor);
+ } catch (Exception e) {
+ String message = "Execution of "+layout.getName()+" did not complete! Error: "+e.getMessage();
+ // Update our monitor, if we have one
+ if (monitor != null) {
+ monitor.setException(e, message);
+ logger.warn(message, e);
+ } else {
+ logger.error(message, e); // Send to error so the user is sure to see it
+ }
+ }
+ }
+
+ /**
+ * Halt the algorithm if the CyLayoutAlgorithm supports it.
+ */
+ public void halt() {
+ layout.halt();
+ }
+
+ /**
+ * Get the "nice" title of this algorithm
+ *
+ * @return algorithm title
+ */
+ public String getTitle() {
+ return "Performing " + layout.toString();
+ }
+
+ /**
+ * This method returns a default TaskConfig object.
+ * @return a default JTaskConfig object.
+ */
+ public static JTaskConfig getDefaultTaskConfig() {
+ JTaskConfig result = new JTaskConfig();
+
+ result.displayCancelButton(true);
+ result.displayCloseButton(false);
+ result.displayStatus(true);
+ result.displayTimeElapsed(false);
+ result.setAutoDispose(true);
+ result.setModal(true);
+ result.setOwner(Cytoscape.getDesktop());
+
+ return result;
+ }
+}
diff --git a/application/src/main/java/cytoscape/layout/Tunable.java b/application/src/main/java/cytoscape/layout/Tunable.java
new file mode 100644
index 0000000..f3385a0
--- /dev/null
+++ b/application/src/main/java/cytoscape/layout/Tunable.java
@@ -0,0 +1,1322 @@
+// vim: set ts=2: */
+package cytoscape.layout;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.data.CyAttributes;
+
+import java.awt.BorderLayout;
+import java.awt.GridLayout;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.FocusEvent;
+import java.awt.event.FocusListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+
+import javax.swing.BorderFactory;
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JComboBox;
+import javax.swing.JComponent;
+import javax.swing.JLabel;
+import javax.swing.JList;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JSlider;
+import javax.swing.JTextField;
+import javax.swing.UIManager;
+
+import javax.swing.BoxLayout;
+import javax.swing.border.Border;
+import javax.swing.border.EtchedBorder;
+import javax.swing.border.TitledBorder;
+
+import javax.swing.event.ChangeListener;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ListSelectionListener;
+import javax.swing.event.ListSelectionEvent;
+
+
+/**
+ * Tunables are typed objects that maintain properties and an
+ * easy way to generate a settings panel to allow user manipulation
+ * of them.
+ * <p>
+ * A Tunable is a utility that serves two important functions:
+ * <ol><li>It provides a convenient way to read, set, and save
+ * properties that can be used to influence algorithms or presentation</li>
+ * <li>It provides a quick way to present an interface to the user
+ * to allow them to update and change those properties.</li></ol>
+ * <p>Tunables were originally written to support the needs of users
+ * of Cytoscape's various layout algorithms (see {@link CyLayoutAlgorithm})
+ * to access the various tunable parameters in the algorithms. In general,
+ * Tunables are collected together by the {@link cytoscape.util.ModuleProperties} system.
+ * See {@link LayoutProperties} as a good example.
+ * <h3>Basic Concepts</h3>
+ * A Tunable can be thought of as a typed variable that knowns how
+ * to initialize and save itself as a Cytoscape property, and present
+ * itself to the user for input. All tunables have the following
+ * information:
+ * <ul><li><b>name</b>: the name of the tunable, which is used to access
+ * the tunable and to save it as a property.</li>
+ * <li><b>description</b>: the description of the tunable, which is displayed
+ * to the user for input.</li>
+ * <li><b>type</b>: the type of the tunable, which must be one of
+ * {@link #INTEGER}, {@link #DOUBLE}, {@link #BOOLEAN}, {@link #STRING},
+ * {@link #NODEATTRIBUTE}, {@link #EDGEATTRIBUTE}, {@link #LIST}, {@link #GROUP},
+ * or {@link #BUTTON}.</li>
+ * <li><b>value</b>: this is set in construction as the initial value, but is
+ * also maintained as the value loaded from the Cytoscape properties or entered
+ * by the user. The type of this value depends on the <b>type</b> of the
+ * Tunable:
+ * <ul>
+ * <li>{@link #INTEGER}: {@link Integer}</li>
+ * <li>{@link #DOUBLE}: {@link Double}</li>
+ * <li>{@link #BOOLEAN}: {@link Boolean}</li>
+ * <li>{@link #STRING}: {@link String}</li>
+ * <li>{@link #NODEATTRIBUTE}: {@link String}, or if {@link #MULTISELECT}, comma-separated list of Strings representing the selected attributes</li>
+ * <li>{@link #EDGEATTRIBUTE}: {@link String}, or if {@link #MULTISELECT}, comma-separated list of Strings representing the selected attributes</li>
+ * <li>{@link #LIST}: {@link Integer}, or if {@link #MULTISELECT}, comma-separated list of integers representing the selected attributes</li>
+ * </ul></li>
+ * <li><b>lowerBound</b>: for {@link #INTEGER} or {@link #DOUBLE} tunables,
+ * the lowerBound is an optional {@link Integer} or {@link Double} value representing
+ * the smallest integer or double that constitutes a legal
+ * input. For {@link #LIST} tunables, the lowerBound is an array of Objects representing the list to choose from, and for
+ * {@link #NODEATTRIBUTE}, and {@link #EDGEATTRIBUTE} tunables, lowerBound is an optional array of {@link String}s that will
+ * prefix the list of attributes. This allows users to provide their own overrides into the list. For {@link #GROUP} tunables,
+ * that have the {@link #COLLAPSABLE} flag set, this is a Boolean value that indicates whether the group is collapsed or expanded.</li>
+ * <li><b>upperBound</b>: for {@link #INTEGER} or {@link #DOUBLE} tunables,
+ * the upperBound is an optional {@link Integer} or {@link Double} value representing
+ * the larget integer or double that constitutes a legal
+ * input. </li>
+ * <li><b>flag</b>: Flags provide hints as to the desired presentation of the Tunable or restrictions on the values. Currently, the flags
+ * include: {@link #IMMUTABLE}, which prevents user entry; {@link #MULTISELECT}, which presents lists as a {@link javax.swing.JList} rather
+ * than {@link javax.swing.JComboBox}; {@link #NOINPUT}, which indicates that this tunable should not be
+ * presented to the user; {@link #NUMERICATTRIBUTE}, which indicates for attribute lists that only numeric attributes
+ * should be used; and {@link #USESLIDER}, which suggests to the UI to use a slider to present this value.</li>
+ *
+ * </ul>
+ * <h3>Common Usage</h3>
+ * <p>
+ * The most common usage of Tunables is to provide a list of values that influences the presentation or calculation of
+ * a layout, clustering algorithm, etc. When combined with {@link LayoutProperties}, tunables provide a very quick way
+ * to put together a user interface and get the results from it. A common approach would be for the algorithm to
+ * include a section of code that creates all of the Tunables associated with the algorithm's parameters. For example
+ * this section from {@link csplugins.layout.algorithms.force#ForceDirectedLayout}:
+ *
+ * <pre><code>
+ * layoutProperties = new LayoutProperties("my_module");
+ * layoutProperties.add(new Tunable("standard", "Standard settings",
+ * Tunable.GROUP, new Integer(2)));
+ *
+ * layoutProperties.add(new Tunable("partition", "Partition graph before layout",
+ * Tunable.BOOLEAN, new Boolean(true)));
+ *
+ * layoutProperties.add(new Tunable("selected_only", "Only layout selected nodes",
+ * Tunable.BOOLEAN, new Boolean(false)));
+ *
+ * layoutProperties.add(new Tunable("force_alg_settings", "Algorithm settings",
+ * Tunable.GROUP, new Integer(5), new Boolean(true), null, Tunable.COLLAPSABLE));
+ *
+ * layoutProperties.add(new Tunable("defaultSpringCoefficient", "Default Spring Coefficient",
+ * Tunable.DOUBLE, new Double(defaultSpringCoefficient)));
+ *
+ * layoutProperties.add(new Tunable("defaultSpringLength", "Default Spring Length",
+ * Tunable.DOUBLE, new Double(defaultSpringLength)));
+ *
+ * layoutProperties.add(new Tunable("defaultNodeMass", "Default Node Mass",
+ * Tunable.DOUBLE, new Double(defaultNodeMass)));
+ *
+ * layoutProperties.add(new Tunable("numIterations", "Number of Iterations",
+ * Tunable.INTEGER, new Integer(numIterations)));
+ *
+ * layoutProperties.add(new Tunable("integrator", "Integration algorithm to use",
+ * Tunable.LIST, new Integer(0),
+ * (Object) integratorArray, (Object) null, 0));
+ *
+ * </code></pre>
+ *
+ * The values are read in an update method:
+ * <pre><code>
+ * Tunable t = layoutProperties.get("selected_only");
+ * if ((t != null) && (t.valueChanged() || force))
+ * selectedOnly = ((Boolean) t.getValue()).booleanValue();
+ *
+ * t = layoutProperties.get("partition");
+ * if ((t != null) && (t.valueChanged() || force))
+ * setPartition(t.getValue().toString());
+ *
+ * t = layoutProperties.get("defaultSpringCoefficient");
+ * if ((t != null) && (t.valueChanged() || force))
+ * defaultSpringCoefficient = ((Double) t.getValue()).doubleValue();
+ *
+ * t = layoutProperties.get("defaultSpringLength");
+ * if ((t != null) && (t.valueChanged() || force))
+ * defaultSpringLength = ((Double) t.getValue()).doubleValue();
+ *
+ * t = layoutProperties.get("defaultNodeMass");
+ * if ((t != null) && (t.valueChanged() || force))
+ * defaultNodeMass = ((Double) t.getValue()).doubleValue();
+ *
+ * t = layoutProperties.get("numIterations");
+ * if ((t != null) && (t.valueChanged() || force))
+ * numIterations = ((Integer) t.getValue()).intValue();
+ *
+ * t = layoutProperties.get("integrator");
+ * if ((t != null) && (t.valueChanged() || force)) {
+ * if (((Integer) t.getValue()).intValue() == 0)
+ * integrator = new RungeKuttaIntegrator();
+ * else if (((Integer) t.getValue()).intValue() == 1)
+ * integrator = new EulerIntegrator();
+ * else
+ * return;
+ * }
+ * </code></pre>
+ *
+ * {@link LayoutProperties} has a method {@link LayoutProperties#getTunablePanel()} that can be called to
+ * return a {@link javax.swing.JPanel} that contains all of the Tunable panels. These are combined into
+ * a dialog to allow users to set and update the values. By using {@link #addTunableValueListener(cytoscape.layout.TunableListener)} a
+ * caller can be notified when a user changes a value.
+ *
+ */
+public class Tunable implements FocusListener,ChangeListener,ActionListener,ItemListener,ListSelectionListener {
+ private String name;
+ private String desc;
+ private int type = STRING;
+ private int flag = 0;
+ private Object value;
+ private Object lowerBound;
+ private Object upperBound;
+ private JComponent inputField = null;
+ private JSlider slider = null;
+ private boolean valueChanged = true;
+ private String savedValue = null;
+ private boolean usingSlider = false;
+ private boolean collapsed = false;
+ private List<String>attributeList = null;
+ private List<TunableListener>listenerList = null;
+
+ /****************************************************
+ * Types
+ ***************************************************/
+
+ /**
+ * Tunables of type INTEGER allow data entry of integer
+ * values, possibly bounded between lowerBound and
+ * upperBound: if the flag {@link #USESLIDER} is set,
+ * and the caller provides both lower and upper bounds,
+ * the user is presented with a slider interface.
+ */
+ final public static int INTEGER = 0;
+
+ /**
+ * Tunables of type DOUBLE allow data entry of double
+ * values, possibly bounded between lowerBound and
+ * upperBound: if the flag {@link #USESLIDER} is set,
+ * and the caller provides both lower and upper bounds,
+ * the user is presented with a slider interface.
+ */
+ final public static int DOUBLE = 1;
+
+ /**
+ * Tunables of type BOOLEAN allow data entry of a
+ * boolean value: this is presented to the user
+ * as a simple check box.
+ */
+ final public static int BOOLEAN = 2;
+
+ /**
+ * Tunables of type STRING allow data entry of
+ * text.
+ */
+ final public static int STRING = 3;
+
+ /**
+ * Tunables of type NODEATTRIBUTE present a
+ * user with a list of the currently defined
+ * node attributes for selection: if the
+ * flag {@link #NUMERICATTRIBUTE} is set, only
+ * integer or double attributes are shown, and if
+ * the {@link #MULTISELECT} flag is set, the user
+ * is presented with a list from which multiple
+ * values can be selected, otherwise, the user
+ * is presented with a combo box.
+ */
+ final public static int NODEATTRIBUTE = 4;
+
+ /**
+ * Tunables of type EDGEATTRIBUTE present a
+ * user with a list of the currently defined
+ * edge attributes for selection: if the
+ * flag {@link #NUMERICATTRIBUTE} is set, only
+ * integer or double attributes are shown, and if
+ * the {@link #MULTISELECT} flag is set, the user
+ * is presented with a list from which multiple
+ * values can be selected, otherwise, the user
+ * is presented with a combo box.
+ */
+ final public static int EDGEATTRIBUTE = 5;
+
+ /**
+ * Tunables of type LIST present a
+ * user with a list of values to select
+ * from: if the {@link #MULTISELECT} flag is
+ * set, the user is presented with a list
+ * from which multiple values can be selected,
+ * otherwise, the user is presented with a
+ * combo box.
+ */
+ final public static int LIST = 6;
+
+ /**
+ * The GROUP Tunable provides a mechanism to
+ * improve the asthetics of the interface:
+ * the value of the GROUP Tunable indicates the
+ * number of the subsequent tunables that should
+ * be grouped together.
+ */
+ final public static int GROUP = 7;
+
+ /**
+ * The BUTTON Tunable provides a simple button
+ * to be presented to the user: the caller can
+ * provide an ActionListener to be called when
+ * the button is selected.
+ */
+ final public static int BUTTON = 8;
+
+ /****************************************************
+ * Flags
+ ***************************************************/
+
+ /**
+ * When the NOINPUT flag is set, this Tunable is not
+ * presented to the user, it is only used for property
+ * settings.
+ */
+ final public static int NOINPUT = 0x1;
+
+ /**
+ * For attributes, indicate that the list should be restricted to integer
+ * or float attributes.
+ */
+ final public static int NUMERICATTRIBUTE = 0x2;
+
+ /**
+ * For LIST, NODEATTRIBUTE, or EDGEATTRIBUTE types, use a list widget that
+ * supports multiselect rather than a combo box.
+ */
+ final public static int MULTISELECT = 0x4;
+
+ /**
+ * For INTEGER or DOUBLE tunables, preferentially use a slider widget -- this
+ * will *only* take effect if the upper and lower bounds are provided.
+ */
+ final public static int USESLIDER = 0x8;
+
+ /**
+ * If the IMMUTABLE flag is set, then the Tunable is presented as usual,
+ * with both label and user widget, but the user widget is disabled.
+ */
+ final public static int IMMUTABLE =0x10;
+
+ /**
+ * If the COLLAPSABLE flag is set for a GROUP Tunable, then this Group of Tunables
+ * should be collapsable, and will be rendered with a button to allow
+ * collapse/expand.
+ */
+ final public static int COLLAPSABLE =0x20;
+
+ /**
+ * Constructor to create a Tunable with no bounds
+ * information, and no flag.
+ *
+ * @param name The name of the Tunable
+ * @param desc The description of the Tunable
+ * @param type Integer value that represents the type of
+ * the Tunable. The type not only impact the
+ * way that the value is interpreted, but also
+ * the component used for the LayoutSettingsDialog
+ * @param value The initial (default) value of the Tunable
+ */
+ public Tunable(String name, String desc, int type, Object value) {
+ this(name, desc, type, value, null, null, 0);
+ }
+
+ /**
+ * Constructor to create a Tunable with no bounds
+ * information, but with a flag.
+ *
+ * @param name The name of the Tunable
+ * @param desc The description of the Tunable
+ * @param type Integer value that represents the type of
+ * the Tunable. The type not only impact the
+ * way that the value is interpreted, but also
+ * the component used for the LayoutSettingsDialog
+ * @param value The initial (default) value of the Tunable
+ * @param flag The initial value of the flag. This can be
+ * used to indicate that this tunable is not user
+ * changeable (e.g. debug), or to indicate if there
+ * is a specific type for the attributes.
+ */
+ public Tunable(String name, String desc, int type, Object value, int flag) {
+ this(name, desc, type, value, null, null, flag);
+ }
+
+ /**
+ * Constructor to create a Tunable with bounds
+ * information as well as a flag.
+ *
+ * @param name The name of the Tunable
+ * @param desc The description of the Tunable
+ * @param type Integer value that represents the type of
+ * the Tunable. The type not only impact the
+ * way that the value is interpreted, but also
+ * the component used for the LayoutSettingsDialog
+ * @param value The initial (default) value of the Tunable. This
+ * is a String in the case of an EDGEATTRIBUTE or
+ * NODEATTRIBUTE tunable, it is an Integer index
+ * a LIST tunable.
+ * @param lowerBound An Object that either represents the lower
+ * bounds of a numeric Tunable or an array of values
+ * for an attribute (or other type of) list.
+ * @param upperBound An Object that represents the upper bounds
+ * of a numeric Tunable.
+ * @param flag The initial value of the flag. This can be
+ * used to indicate that this tunable is not user
+ * changeable (e.g. debug), or to indicate if there
+ * is a specific type for the attributes.
+ */
+ public Tunable(String name, String desc, int type, Object value, Object lowerBound,
+ Object upperBound, int flag) {
+ this.name = name;
+ this.desc = desc;
+ this.type = type;
+ this.value = value;
+ this.upperBound = upperBound;
+ this.lowerBound = lowerBound;
+ this.flag = flag;
+ }
+
+ /**
+ * Constructor to create a Tunable with bounds
+ * information as well as a flag.
+ *
+ * @param name The name of the Tunable
+ * @param desc The description of the Tunable
+ * @param type Integer value that represents the type of
+ * the Tunable. The type not only impact the
+ * way that the value is interpreted, but also
+ * the component used for the LayoutSettingsDialog
+ * @param value The initial (default) value of the Tunable. This
+ * is a String in the case of an EDGEATTRIBUTE or
+ * NODEATTRIBUTE tunable, it is an Integer index
+ * a LIST tunable.
+ * @param lowerBound An Object that either represents the lower
+ * bounds of a numeric Tunable or an array of values
+ * for an attribute (or other type of) list.
+ * @param upperBound An Object that represents the upper bounds
+ * of a numeric Tunable.
+ * @param flag The initial value of the flag. This can be
+ * used to indicate that this tunable is not user
+ * changeable (e.g. debug), or to indicate if there
+ * is a specific type for the attributes.
+ * @param immutable If 'true', this Tunable is immutable
+ *
+ * @deprecated Use the <b>IMMUTABLE</b> flag directly rather than this special constructor.
+ */
+ public Tunable(String name, String desc, int type, Object value, Object lowerBound,
+ Object upperBound, int flag, boolean immutable) {
+ this(name, desc, type, value, lowerBound, upperBound, flag);
+ if (immutable)
+ setFlag(IMMUTABLE);
+ // CyLogger.getLogger().info("Tunable "+desc+" has value "+value);
+ }
+
+ /**
+ * This method can be used to set a flag for this Tunable
+ *
+ * @param flag integer value the contains the flag to set.
+ */
+ public void setFlag(int flag) {
+ this.flag |= flag;
+ }
+
+ /**
+ * This method can be used to clear a flag for this Tunable
+ *
+ * @param flag integer value the contains the flag to be cleared.
+ */
+ public void clearFlag(int flag) {
+ this.flag &= ~flag;
+ }
+
+ /**
+ * This method is used to check the value of a flag. It
+ * returns <b>true</b> if the flag is set, <b>false</b>
+ * otherwise.
+ *
+ * @param flag integer value the contains the flag to be checked.
+ * @return true if the flag is set.
+ */
+ public boolean checkFlag(int flag) {
+ return ( (this.flag & flag) != 0 );
+ }
+
+ /**
+ * This method can be used to set the "immutable" boolean,
+ * which essentially get's mapped to the appropriate mechanism
+ * for allowing a value to be editted.
+ *
+ * @param immutable 'true' if this is an immutable value
+ */
+ public void setImmutable(boolean immutable) {
+ if (immutable)
+ setFlag(IMMUTABLE);
+ else
+ clearFlag(IMMUTABLE);
+ if (inputField != null) {
+ inputField.setEnabled(!checkFlag(IMMUTABLE));
+ if (checkFlag(USESLIDER) && slider != null) {
+ slider.setEnabled(!checkFlag(IMMUTABLE));
+ }
+ }
+ }
+
+ /**
+ * This method is used to set the value for this Tunable. If
+ * this is an INTEGER, DOUBLE, or BOOLEAN Tunable, then value
+ * is assumed to be a String. This also sets the "changed" state
+ * of the value to "true".
+ *
+ * @param value Object (usually String) containing the value to be set
+ */
+ public void setValue(Object value) {
+
+ switch (type) {
+ case INTEGER:
+ // CyLogger.getLogger().info("Setting Integer tunable "+desc+" value to "+value);
+ if (value.getClass() == String.class)
+ this.value = new Integer((String) value);
+ else
+ this.value = value;
+
+ if ((slider != null) && checkFlag(USESLIDER)) {
+ slider.setValue(sliderScale(this.value));
+ ((JTextField)inputField).setText(this.value.toString());
+ } else if (inputField != null) {
+ ((JTextField)inputField).setText(this.value.toString());
+ }
+ break;
+
+ case DOUBLE:
+ // CyLogger.getLogger().info("Setting Double tunable "+desc+" value to "+value);
+ if (value.getClass() == String.class)
+ this.value = new Double((String) value);
+ else
+ this.value = value;
+ if ((slider != null) && checkFlag(USESLIDER)) {
+ slider.setValue(sliderScale(this.value));
+ ((JTextField)inputField).setText(this.value.toString());
+ } else if (inputField != null) {
+ ((JTextField)inputField).setText(this.value.toString());
+ }
+ break;
+
+ case BOOLEAN:
+ // CyLogger.getLogger().info("Setting Boolean tunable "+desc+" value to "+value);
+ if (value.getClass() == String.class)
+ this.value = new Boolean((String) value);
+ else
+ this.value = value;
+ if (inputField != null)
+ ((JCheckBox)inputField).setSelected(((Boolean)this.value).booleanValue());
+ break;
+
+ case LIST:
+ // CyLogger.getLogger().info("Setting List tunable "+desc+" value to "+value);
+ if (checkFlag(MULTISELECT)) {
+ // Multiselect LIST -- value is a List of Integers, or String values
+ this.value = value;
+ if (inputField != null && value != null) {
+ int[] intArray = decodeIntegerArray((String)value);
+ if (intArray != null)
+ ((JList)inputField).setSelectedIndices(intArray);
+ }
+ } else {
+ // Two possibilities -- could be an Integer, or could be a string that matches something
+ // in the list. We need to check both
+ if (value.getClass() == String.class)
+ try {
+ this.value = new Integer((String) value);
+ } catch (NumberFormatException e) {
+ // OK, probably a string that we need to match (if possible)
+ if (lowerBound == null || value == null)
+ return;
+ this.value = getSelectedValue((Object [])lowerBound,(String)value);
+ }
+ else
+ this.value = value;
+
+ if (inputField != null)
+ ((JComboBox)inputField).setSelectedIndex(((Integer)this.value).intValue());
+ }
+ break;
+
+ case NODEATTRIBUTE:
+ case EDGEATTRIBUTE:
+ // CyLogger.getLogger().info("Setting List tunable "+desc+" value to "+value);
+ if (checkFlag(MULTISELECT)) {
+ // Multiselect LIST -- value is a List of Integers, or String values
+ this.value = value;
+ if (inputField != null) {
+ ((JList)inputField).setSelectedIndices(getSelectedValues(attributeList, decodeArray((String)value)));
+ }
+ } else {
+ this.value = value;
+
+ if (inputField != null)
+ ((JComboBox)inputField).setSelectedItem(this.value);
+ }
+ break;
+
+ case GROUP:
+ // CyLogger.getLogger().info("Setting Group tunable "+desc+" value to "+value);
+ if (value.getClass() == String.class)
+ this.value = new Integer((String) value);
+ else
+ this.value = value;
+ return;
+
+ case STRING:
+ // CyLogger.getLogger().info("Setting String tunable "+desc+" value to "+value);
+ this.value = value;
+ if (inputField != null)
+ ((JTextField)inputField).setText((String)value);
+ break;
+
+ case BUTTON:
+ // CyLogger.getLogger().info("Setting String tunable "+desc+" value to "+value);
+ this.value = value;
+ if (inputField != null)
+ ((JButton)inputField).setText((String)value);
+ break;
+ }
+
+ if (inputField != null)
+ inputField.validate();
+
+ valueChanged = true;
+ }
+
+ /**
+ * This method returns the current value. This method
+ * also resets the state of the value to indicate that
+ * it has not been changed since the last "get".
+ *
+ * @return Object that contains the value for this Tunable
+ */
+ public Object getValue() {
+ valueChanged = false;
+
+ return value;
+ }
+
+ /**
+ * Returns the changed state of the value. If true,
+ * the value has been changed since it was last retrieved.
+ *
+ * @return boolean value of the changed state.
+ */
+ public boolean valueChanged() {
+ return valueChanged;
+ }
+
+ /**
+ * Method to set the lowerBound for this Tunable. This might be used to change a Tunable
+ * based on changes in the plugin environment.
+ *
+ * @param lowerBound the new lowerBound for the tunable
+ */
+ public void setLowerBound(Object lowerBound) {
+ this.lowerBound = lowerBound;
+ if (inputField == null)
+ return;
+
+ // If we're a slider or a list, this might require us to reset things...
+ if (type == LIST) {
+ Object[] listData = (Object[])lowerBound;
+ if (checkFlag(MULTISELECT)) {
+ JList list = (JList)inputField;
+ list.setListData(listData);
+ // Get the scroll pane
+ JScrollPane listScroller = (JScrollPane)list.getParent().getParent();
+ listScroller.setPreferredSize(getPreferredSize((Object[])lowerBound));
+ } else {
+ JComboBox cbox = (JComboBox)inputField;
+ cbox.removeAllItems();
+ for (int i = 0; i < listData.length; i++)
+ cbox.addItem(listData[i]);
+ }
+ } else if (type == NODEATTRIBUTE) {
+ } else if (type == EDGEATTRIBUTE) {
+ } else if (checkFlag(USESLIDER)) {
+ slider.setMinimum(sliderScale(lowerBound));
+ slider.setLabelTable(createLabels(slider));
+ } else if (type == GROUP) {
+ // This indicates whether this GROUP is collapsed
+ // or not
+ if (!checkFlag(COLLAPSABLE))
+ return;
+ // Update presentation
+ updateValueListeners();
+ }
+ }
+
+ /**
+ * Method to get the lowerBound for this Tunable.
+ *
+ * @return the lowerBound the tunable
+ */
+ public Object getLowerBound() {
+ return this.lowerBound;
+ }
+
+ /**
+ * Method to set the upperBound for this Tunable. This might be used to change a Tunable
+ * based on changes in the plugin environment.
+ *
+ * @param upperBound the new upperBound for the tunable
+ */
+ public void setUpperBound(Object upperBound) {
+ this.upperBound = upperBound;
+ if (inputField == null)
+ return;
+
+ // If we're a slider, this might require us to reset things
+ if (checkFlag(USESLIDER)) {
+ slider.setMaximum(sliderScale(upperBound));
+ slider.setLabelTable(createLabels(slider));
+ }
+ }
+
+ /**
+ * Method to get the upperBound for this Tunable.
+ *
+ * @return the upperBound the tunable
+ */
+ public Object getUpperBound() {
+ return this.upperBound;
+ }
+
+ /**
+ * Method to return a string representation of this Tunable,
+ * which is essentially its name.
+ *
+ * @return String value of the name of the Tunable.
+ */
+ public String toString() {
+ return name;
+ }
+
+ /**
+ * Method to return a string representation of this Tunable,
+ * which is essentially its name.
+ *
+ * @return String value of the name of the Tunable.
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * Method to return the type of this Tunable.
+ *
+ * @return Tunable type
+ */
+ public int getType() {
+ return type;
+ }
+
+ /**
+ * Method to return the description for this Tunable.
+ *
+ * @return Tunable description
+ */
+ public String getDescription() {
+ return desc;
+ }
+
+
+ /**
+ * Method to add a value listener to this Tunable. A value
+ * listener is called whenever a tunable value is updated
+ * by the user (as opposed to programmatically). This can
+ * be used to change the UI based on certain inputs.
+ *
+ * @param listener the TunableListener to add
+ */
+ public void addTunableValueListener(TunableListener listener) {
+ if (listenerList == null)
+ listenerList = new ArrayList();
+
+ if (listener == null || listenerList.contains(listener))
+ return;
+
+ listenerList.add(listener);
+ }
+
+ /**
+ * Method to remove a value listener from this Tunable. A value
+ * listener is called whenever a tunable value is updated
+ * by the user (as opposed to programmatically). This can
+ * be used to change the UI based on certain inputs.
+ *
+ * @param listener the TunableListener to remove
+ */
+ public void removeTunableValueListener(TunableListener listener) {
+ if (listener == null || listenerList == null)
+ return;
+
+ listenerList.remove(listener);
+ }
+
+ /**
+ * Method to call all of the value listeners.
+ */
+ public void updateValueListeners() {
+ updateValue();
+
+ if (listenerList == null)
+ return;
+
+ for (TunableListener listener: listenerList)
+ listener.tunableChanged(this);
+ }
+
+ /**
+ * This method returns a JPanel suitable for inclusion in the
+ * LayoutSettingsDialog to represent this Tunable. Note that
+ * while the type of the widgets used to represent the Tunable
+ * are customized to represent the type, no ActionListeners are
+ * included. The dialog must call updateSettings to set the
+ * value of the Tunable from the user input data.
+ *
+ * @return JPanel that can be used to enter values for this Tunable
+ */
+ public JPanel getPanel() {
+ if (checkFlag(NOINPUT))
+ return null;
+
+ if (type == GROUP) {
+ JPanel tunablesPanel = new JPanel();
+ BoxLayout box = new BoxLayout(tunablesPanel, BoxLayout.Y_AXIS);
+ tunablesPanel.setLayout(box);
+
+ // Special case for groups
+ Border refBorder = BorderFactory.createEtchedBorder(EtchedBorder.LOWERED);
+ TitledBorder titleBorder = BorderFactory.createTitledBorder(refBorder, this.desc);
+ titleBorder.setTitlePosition(TitledBorder.LEFT);
+ titleBorder.setTitlePosition(TitledBorder.TOP);
+ tunablesPanel.setBorder(titleBorder);
+ if (checkFlag(COLLAPSABLE)) {
+ String label = "<html><b><i> Hide "+desc+"</i></b></html>";
+ // Update the internal collapsed flag
+ this.collapsed = ((Boolean)lowerBound).booleanValue();
+ if (collapsed)
+ label = "<html><b><i> Show "+desc+"</i></b></html>";
+ // Add collapse/expand button
+ JPanel collapsePanel = new JPanel(new BorderLayout(0, 2));
+ JButton collapseButton = null;
+ if (collapsed)
+ collapseButton = new JButton(UIManager.getIcon("Tree.collapsedIcon"));
+ else
+ collapseButton = new JButton(UIManager.getIcon("Tree.expandedIcon"));
+ collapseButton.setActionCommand("collapse");
+ collapseButton.addActionListener(this);
+ collapsePanel.add(collapseButton, BorderLayout.LINE_START);
+ collapsePanel.add(new JLabel(label), BorderLayout.CENTER);
+ tunablesPanel.add(collapsePanel);
+ }
+
+ return tunablesPanel;
+ }
+
+ JPanel tunablePanel = new JPanel(new BorderLayout(0, 3));
+ JLabel tunableLabel = new JLabel(desc);
+ String labelLocation = BorderLayout.LINE_START;
+ String fieldLocation = BorderLayout.LINE_END;
+
+ if ((type == DOUBLE) || (type == INTEGER)) {
+ if ( (checkFlag(USESLIDER)) && (lowerBound != null) && (upperBound != null)) {
+ // We're going to use a slider, We need to be somewhat intelligent about the bounds and
+ // labels. It would also be nice to provide feedback, which we do by providing a text field
+ // in addition to the slider. The text field can also be used to enter the desired value
+ // directly.
+
+ slider = new JSlider(JSlider.HORIZONTAL,
+ sliderScale(lowerBound),
+ sliderScale(upperBound),
+ sliderScale(value));
+
+ slider.setLabelTable(createLabels(slider));
+ slider.setPaintLabels(true);
+ slider.addChangeListener(this);
+ tunablePanel.add(tunableLabel, BorderLayout.NORTH);
+ tunablePanel.add(slider, BorderLayout.CENTER);
+
+ JTextField textField = new JTextField(value.toString(), 4);
+ textField.addFocusListener(this);
+ inputField = textField;
+ tunablePanel.add(textField, BorderLayout.EAST);
+ textField.setBackground(Color.white);
+ if(checkFlag(IMMUTABLE)) {
+ inputField.setEnabled(false);
+ slider.setEnabled(false);
+ }
+ return tunablePanel;
+
+ } else {
+ // We can't use a slider, so turn off the flag
+ clearFlag(USESLIDER);
+ JTextField field = new JTextField(value.toString(), 8);
+ field.setHorizontalAlignment(JTextField.RIGHT);
+ // If we have an upper and/or lower bounds, we want to "listen" for changes
+ field.addFocusListener(this);
+ inputField = field;
+ }
+ } else if (type == BOOLEAN) {
+ JCheckBox box = new JCheckBox();
+ box.setSelected(((Boolean) value).booleanValue());
+ box.addItemListener(this);
+ inputField = box;
+ } else if (type == NODEATTRIBUTE) {
+ CyAttributes nodeAttributes = Cytoscape.getNodeAttributes();
+ inputField = getAttributePanel(nodeAttributes);
+ } else if (type == EDGEATTRIBUTE) {
+ CyAttributes edgeAttributes = Cytoscape.getEdgeAttributes();
+ inputField = getAttributePanel(edgeAttributes);
+ } else if (type == LIST) {
+ inputField = getListPanel((Object[]) lowerBound);
+ } else if (type == STRING) {
+ JTextField field = new JTextField(value.toString(), 20);
+ field.addFocusListener(this);
+ field.setHorizontalAlignment(JTextField.RIGHT);
+ inputField = field;
+ } else if (type == BUTTON) {
+ JButton button = new JButton((String)value);
+ button.addActionListener((ActionListener)lowerBound);
+ button.setActionCommand(name);
+ inputField = button;
+ }
+
+ // Added by kono
+ // This allow immutable value.
+ if(checkFlag(IMMUTABLE)) {
+ inputField.setEnabled(false);
+ }
+ inputField.setBackground(Color.white);
+
+ tunablePanel.add(tunableLabel, labelLocation);
+ // Add a spacer
+ tunablePanel.add(new JLabel(" "), BorderLayout.CENTER);
+
+ // Special case for MULTISELECT lists
+ if ((type == LIST || type == NODEATTRIBUTE || type == EDGEATTRIBUTE)
+ && checkFlag(MULTISELECT)) {
+ JScrollPane listScroller = new JScrollPane(inputField);
+ listScroller.setPreferredSize(getPreferredSize((Object[])lowerBound));
+ tunablePanel.add(listScroller, fieldLocation);
+ } else {
+ tunablePanel.add(inputField, fieldLocation);
+ }
+ return tunablePanel;
+ }
+
+ /**
+ * This method is used by getPanel to construct a JComboBox that
+ * contains a list of node or edge attributes that the user can
+ * choose from for doing attribute-dependent layouts.
+ *
+ * @param attributes CyAttributes of the appropriate (edge or node) type
+ * @return a JComponent with an entry for each attribute
+ */
+ private JComponent getAttributePanel(CyAttributes attributes) {
+ final String[] attList = attributes.getAttributeNames();
+ final List<String> list = new ArrayList<String>();
+
+ // See if we have any initial attributes (mapped into lowerBound)
+ if (lowerBound != null) {
+ list.addAll((List) lowerBound);
+ }
+
+ for (int i = 0; i < attList.length; i++) {
+ // Is this attribute user visible?
+ if (!attributes.getUserVisible(attList[i]))
+ continue;
+
+ byte type = attributes.getType(attList[i]);
+
+ if (((flag & NUMERICATTRIBUTE) == 0)
+ || ((type == CyAttributes.TYPE_FLOATING)
+ || (type == CyAttributes.TYPE_INTEGER))) {
+ list.add(attList[i]);
+ }
+ }
+
+ attributeList = list;
+
+ if (checkFlag(MULTISELECT)) {
+ // Set our current value as selected
+ JList jList = new JList(list.toArray());
+ int [] indices = getSelectedValues(attributeList, decodeArray((String)value));
+ if (indices != null && indices.length > 0)
+ jList.setSelectedIndices(indices);
+ jList.addListSelectionListener(this);
+ return jList;
+ } else {
+ // Set our current value as selected
+ JComboBox box = new JComboBox(attributeList.toArray());
+ box.setSelectedItem((String) value);
+ box.addActionListener(this);
+ return box;
+ }
+ }
+
+ /**
+ * This method is used by getPanel to construct a JComboBox that
+ * contains a list of values the user can choose from.
+ *
+ * @param list Array of Objects containing the list
+ * @return a JComboBox with an entry for each item on the list
+ */
+ private JComponent getListPanel(Object[] list) {
+ if (checkFlag(MULTISELECT)) {
+ JList jList = new JList(list);
+ if (value != null && ((String)value).length() > 0) {
+ int[] intArray = decodeIntegerArray((String)value);
+ if (intArray != null)
+ jList.setSelectedIndices(intArray);
+ }
+ jList.addListSelectionListener(this);
+ return jList;
+ } else {
+ // Set our current value as selected
+ JComboBox box = new JComboBox(list);
+ box.setSelectedIndex(((Integer) value).intValue());
+ box.addActionListener(this);
+ return box;
+ }
+ }
+
+ private Dimension getPreferredSize(Object[] list) {
+ Dimension dim = new Dimension(300, 200);
+ if (list == null)
+ return dim;
+
+ dim.height = Math.min(list.length * 12, 300);
+ int maxString = 0;
+ for (int i = 0; i < list.length; i++)
+ if (list[i].toString() != null)
+ maxString = Math.max(list[i].toString().length(), maxString);
+ dim.width = Math.min(maxString*12, 400);
+
+ return dim;
+ }
+
+ /**
+ * Return an array of indices suitable for selection. The passed
+ * String value is an encoded list of entries of the form [attr1,attr2,...]
+ *
+ * @param attrs the list of attributes to choose from
+ * @param values the list of values
+ * @return array of integers to use to select values
+ */
+ private int[] getSelectedValues(List<String>attrs, String[] values) {
+ if (values == null) return null;
+ int[] selVals = new int[values.length];
+ for (int i = 0; i < values.length; i++) {
+ selVals[i] = attrs.indexOf(values[i]);
+ }
+ return selVals;
+ }
+
+ private Integer getSelectedValue(Object []valueList, String value) {
+ if (valueList == null || value == null) return null;
+ for (int i = 0; i < valueList.length; i++) {
+ if (value.equals(valueList[i].toString()))
+ return new Integer(i);
+ }
+ return null;
+ }
+
+ private int[] decodeIntegerArray(String value) {
+ if(value == null || value.length() == 0) {
+ return null;
+ }
+ String[] valArray = value.split(",");
+ int[] intArray = new int[valArray.length];
+ for (int i = 0; i < valArray.length; i++) {
+ intArray[i] = Integer.valueOf(valArray[i]).intValue();
+ }
+ return intArray;
+ }
+
+ private String[] decodeArray(String value) {
+ if(value == null || value.length() == 0) {
+ return null;
+ }
+ return value.split(",");
+ }
+
+ /**
+ * This method is called to extract the user-entered data from the
+ * JPanel and store it as our value.
+ */
+ public void updateValue() {
+ Object newValue;
+
+ if (inputField == null || type == GROUP || type == BUTTON)
+ return;
+
+ if (type == DOUBLE) {
+ if (usingSlider) {
+ newValue = new Double(((JSlider) inputField).getValue());
+ } else {
+ newValue = new Double(((JTextField) inputField).getText());
+ }
+ } else if (type == INTEGER) {
+ if (usingSlider) {
+ newValue = new Integer(((JSlider) inputField).getValue());
+ } else {
+ newValue = new Integer(((JTextField) inputField).getText());
+ }
+ } else if (type == BOOLEAN) {
+ newValue = new Boolean(((JCheckBox) inputField).isSelected());
+ } else if (type == LIST) {
+ if (checkFlag(MULTISELECT)) {
+ int [] selVals = ((JList) inputField).getSelectedIndices();
+ String newString = "";
+ for (int i = 0; i < selVals.length; i++) {
+ newString += Integer.toString(selVals[i]);
+ if (i < selVals.length-1) newString+= ",";
+ }
+ newValue = (Object) newString;
+ } else {
+ newValue = new Integer(((JComboBox) inputField).getSelectedIndex());
+ }
+ } else if ((type == NODEATTRIBUTE) || (type == EDGEATTRIBUTE)) {
+ if (checkFlag(MULTISELECT)) {
+ Object [] selVals = ((JList) inputField).getSelectedValues();
+ String newString = "";
+ for (int i = 0; i < selVals.length; i++) {
+ newString += selVals[i];
+ if (i < selVals.length) newString+= ",";
+ }
+ newValue = (Object) newString;
+ } else {
+ newValue = (String) ((JComboBox) inputField).getSelectedItem();
+ }
+ } else {
+ newValue = ((JTextField) inputField).getText();
+ }
+
+ if (value == null || !value.equals(newValue)) {
+ valueChanged = true;
+ }
+
+ value = newValue;
+ }
+
+ /**
+ * Document listener routines to handle bounds checking
+ */
+ public void focusLost(FocusEvent ev) {
+ Object value = null;
+ // Check the bounds
+ if (type == DOUBLE) {
+ Double newValue = null;
+ try {
+ newValue = new Double(((JTextField) inputField).getText());
+ } catch (NumberFormatException e) {
+ displayBoundsError("a floating point");
+ return;
+ }
+ if ((upperBound != null && newValue > (Double)upperBound) ||
+ (lowerBound != null && newValue < (Double)lowerBound)) {
+ displayBoundsError("a floating point");
+ return;
+ }
+ value = (Object)newValue;
+ } else if (type == INTEGER) {
+ Integer newValue = null;
+ try {
+ newValue = new Integer(((JTextField) inputField).getText());
+ } catch (NumberFormatException e) {
+ displayBoundsError("an integer");
+ return;
+ }
+ if ((upperBound != null && newValue > (Integer)upperBound) ||
+ (lowerBound != null && newValue < (Integer)lowerBound)) {
+ displayBoundsError("an integer");
+ return;
+ }
+ value = (Object)newValue;
+ }
+
+ if (checkFlag(USESLIDER)) {
+ // Update the slider with this new value
+ slider.removeChangeListener(this);
+ slider.setValue(sliderScale(value));
+ slider.addChangeListener(this);
+ }
+ updateValueListeners();
+ }
+
+ /**
+ * This method is public as a byproduct of the implementation.
+ */
+ public void focusGained(FocusEvent ev) {
+ // Save the current value
+ savedValue = ((JTextField) inputField).getText();
+ }
+
+ /**
+ * This method is public as a byproduct of the implementation.
+ */
+ public void stateChanged(ChangeEvent e) {
+ if (((type == DOUBLE) || (type == INTEGER)) && (checkFlag(USESLIDER))) {
+ // Get the widget
+ JSlider slider = (JSlider) e.getSource();
+
+ // Get the value
+ int value = slider.getValue();
+
+ // Update the text box
+ ((JTextField) inputField).setText(sliderScale(value).toString());
+ }
+ updateValueListeners();
+ }
+
+ /**
+ * This method is public as a byproduct of the implementation.
+ */
+ public void actionPerformed(ActionEvent e) {
+ if (type == GROUP && checkFlag(COLLAPSABLE)) {
+ if (collapsed)
+ collapsed = false;
+ else
+ collapsed = true;
+ lowerBound = Boolean.valueOf(collapsed);
+ }
+ updateValueListeners();
+ }
+
+ /**
+ * This method is public as a byproduct of the implementation.
+ */
+ public void itemStateChanged(ItemEvent e) {
+ updateValueListeners();
+ }
+
+ /**
+ * This method is public as a byproduct of the implementation.
+ */
+ public void valueChanged(ListSelectionEvent e) {
+ updateValueListeners();
+ }
+
+ private void displayBoundsError(String typeString) {
+ if (lowerBound != null && upperBound != null) {
+ JOptionPane.showMessageDialog(null, "Value must be "+typeString+" between "+lowerBound+" and "+upperBound,
+ "Bounds Error", JOptionPane.ERROR_MESSAGE);
+ } else if (lowerBound != null) {
+ JOptionPane.showMessageDialog(null, "Value must be "+typeString+" greater than "+lowerBound,
+ "Bounds Error", JOptionPane.ERROR_MESSAGE);
+ } else if (upperBound != null) {
+ JOptionPane.showMessageDialog(null, "Value must be "+typeString+" less than "+upperBound,
+ "Bounds Error", JOptionPane.ERROR_MESSAGE);
+ } else {
+ JOptionPane.showMessageDialog(null, "Value must be "+typeString+" number",
+ "Type Error", JOptionPane.ERROR_MESSAGE);
+ }
+ ((JTextField) inputField).setText(savedValue);
+ }
+
+ private int getIntValue(Object v) {
+ if (type == DOUBLE) {
+ Double d = (Double)v;
+ return d.intValue();
+ } else if (type == INTEGER) {
+ Integer d = (Integer)v;
+ return d.intValue();
+ }
+ return 0;
+ }
+
+ private int sliderScale(Object value) {
+ if (type == INTEGER) {
+ // Don't mess with Integer values
+ return ((Integer)value).intValue();
+ }
+ double minimum = ((Double)lowerBound).doubleValue();
+ double maximum = ((Double)upperBound).doubleValue();
+ double input = ((Double)value).doubleValue();
+ double extent = maximum-minimum;
+
+ // Use a scale from 0-100 with 0 = minimum and 100 = maximum
+ return (int)(((input-minimum)/extent)*100.0);
+ }
+
+ private Object sliderScale(int value) {
+ if (type == INTEGER) {
+ // Don't mess with Integer values
+ return Integer.valueOf(value);
+ }
+ double minimum = ((Double)lowerBound).doubleValue();
+ double maximum = ((Double)upperBound).doubleValue();
+ double extent = maximum-minimum;
+ double dvalue = (double)value/100.0;
+ double scaledValue = (dvalue*extent)+minimum;
+ int places = 2;
+ if (extent < 1.0)
+ places = (int)Math.round(-Math.log10(extent)) + 1;
+ return new Double(round(scaledValue, places));
+
+ }
+
+ private Hashtable createLabels(JSlider slider) {
+ if (type == INTEGER) {
+ int increment = (getIntValue(upperBound)-getIntValue(lowerBound))/5;
+ if (increment > 1)
+ return slider.createStandardLabels(increment);
+ else
+ return slider.createStandardLabels(1);
+ }
+ Hashtable<Integer,JComponent>table = new Hashtable();
+ // Create our table in 5 steps from lowerBound to upperBound
+ // This could obviously be much fancier, but it's probably sufficient for now.
+ for (int label = 0; label < 6; label++) {
+ Double v = (Double)sliderScale(label*20);
+ table.put(label*20, new JLabel(v.toString()));
+ }
+ return table;
+ }
+
+ private double round(double val, int places) {
+ long factor = (long)Math.pow(10, places);
+ val = val * factor;
+
+ long tmp = Math.round(val);
+
+ return (double)tmp / factor;
+ }
+}
diff --git a/application/src/main/java/cytoscape/layout/TunableListener.java b/application/src/main/java/cytoscape/layout/TunableListener.java
new file mode 100644
index 0000000..62fe09d
--- /dev/null
+++ b/application/src/main/java/cytoscape/layout/TunableListener.java
@@ -0,0 +1,23 @@
+// vim: set ts=2: */
+package cytoscape.layout;
+
+/**
+ * The TunableListener interface provides a way to encapsulate
+ * CyLayoutAlgorithm property and settings values. Each Tunable
+ * has a name, which corresponds to the property name, a description,
+ * which is used as the label in the settings dialog, a type, a
+ * value, and information about the value, such as a list of options
+ * or the lower and upper bounds for the value. These are meant
+ * to be used as part of the LayoutSettingsDialog (see getPanel).
+ */
+public interface TunableListener {
+ /**
+ * The tunableChanged method is called whenever a tunable value
+ * has been changed by the user (as opposed to programmatically).
+ * It can be used by systems to react to user input to improve
+ * interactivity or user feedback.
+ *
+ * @param tunable the Tunable that was changed
+ */
+ public void tunableChanged(Tunable tunable);
+}
diff --git a/application/src/main/java/cytoscape/layout/algorithms/GridNodeLayout.java b/application/src/main/java/cytoscape/layout/algorithms/GridNodeLayout.java
new file mode 100644
index 0000000..6062e3b
--- /dev/null
+++ b/application/src/main/java/cytoscape/layout/algorithms/GridNodeLayout.java
@@ -0,0 +1,190 @@
+/*
+ File: GridNodeLayout.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Pasteur Institute
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.layout.algorithms;
+
+import giny.view.EdgeView;
+import giny.view.NodeView;
+
+import java.util.Iterator;
+import java.util.List;
+
+import javax.swing.JPanel;
+
+import cytoscape.CyEdge;
+import cytoscape.layout.AbstractLayout;
+
+
+/**
+ * The GridNodeLayout provides a very simple layout, suitable as
+ * the default layout for Cytoscape data readers.
+ */
+public class GridNodeLayout extends AbstractLayout {
+ /**
+ * Creates a new GridNodeLayout object.
+ */
+ public GridNodeLayout() {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getName() {
+ return "grid";
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String toString() {
+ return "Grid Layout";
+ }
+
+ // We do support selected only
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean supportsSelectedOnly() {
+ return true;
+ }
+
+ // We dont support node or edge attribute-based layouts
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public byte[] supportsNodeAttributes() {
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public byte[] supportsEdgeAttributes() {
+ return null;
+ }
+
+ /**
+ * Returns a JPanel to be used as part of the Settings dialog for this layout
+ * algorithm.
+ *
+ */
+ public JPanel createSettings() {
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void construct() {
+ // This creates the default square layout.
+ double distanceBetweenNodes = 80.0d;
+ double currX = 0.0d;
+ double currY = 0.0d;
+ double initialX = 0.0d;
+ double initialY = 0.0d;
+ int columns;
+
+ NodeView nView = null;
+
+ // Selected only?
+ if (selectedOnly) {
+ // Yes, our size and starting points need to be different
+ int nodeCount = networkView.nodeCount() - staticNodes.size();
+ columns = (int) Math.sqrt(nodeCount);
+
+ // Calculate our starting point as the geographical center of the
+ // selected nodes.
+ Iterator<NodeView> nodeViews = networkView.getNodeViewsIterator();
+
+
+ while (nodeViews.hasNext()) {
+ nView = nodeViews.next();
+
+ if (!isLocked(nView)) {
+ initialX += (nView.getXPosition() / nodeCount);
+ initialY += (nView.getYPosition() / nodeCount);
+ }
+ }
+
+ // initialX and initialY reflect the center of our grid, so we
+ // need to offset by distance*columns/2 in each direction
+ initialX = initialX - ((distanceBetweenNodes * (columns - 1)) / 2);
+ initialY = initialY - ((distanceBetweenNodes * (columns - 1)) / 2);
+ currX = initialX;
+ currY = initialY;
+ } else
+ columns = (int) Math.sqrt(networkView.nodeCount());
+
+
+ Iterator<NodeView> nodeViews = networkView.getNodeViewsIterator();
+ int count = 0;
+
+ List<CyEdge> edgeList;
+ EdgeView ev;
+ while (nodeViews.hasNext()) {
+ nView = nodeViews.next();
+ edgeList = network.getAdjacentEdgesList(nView.getNode(),true,true,true);
+ for (CyEdge edge: edgeList) {
+ ev = networkView.getEdgeView(edge);
+ ev.clearBends();
+ }
+
+ if (isLocked(nView))
+ continue;
+
+ nView.setOffset(currX, currY);
+ count++;
+
+ if (count == columns) {
+ count = 0;
+ currX = initialX;
+ currY += distanceBetweenNodes;
+ } else {
+ currX += distanceBetweenNodes;
+ }
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/layout/package.html b/application/src/main/java/cytoscape/layout/package.html
new file mode 100644
index 0000000..2bf2238
--- /dev/null
+++ b/application/src/main/java/cytoscape/layout/package.html
@@ -0,0 +1,12 @@
+<html>
+<head>
+ <!-- $Revision: 5801 $
+ $Date: 2004-04-20 01:53:47 +0200 (Tue, 20 Apr 2004) $
+ $Author: amarkiel $
+ -->
+</head>
+
+<body>
+Classes providing some kind of graph layout functionality.
+</body>
+</html>
diff --git a/application/src/main/java/cytoscape/layout/ui/DynamicLayoutMenu.java b/application/src/main/java/cytoscape/layout/ui/DynamicLayoutMenu.java
new file mode 100644
index 0000000..d13284c
--- /dev/null
+++ b/application/src/main/java/cytoscape/layout/ui/DynamicLayoutMenu.java
@@ -0,0 +1,250 @@
+/*
+ File: DynamicLayoutMenu.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.layout.ui;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+
+import cytoscape.data.CyAttributes;
+
+import cytoscape.layout.CyLayoutAlgorithm;
+import cytoscape.layout.LayoutTask;
+
+import cytoscape.view.CyNetworkView;
+
+import cytoscape.task.util.TaskManager;
+
+import giny.model.Node;
+
+import giny.view.NodeView;
+
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Set;
+
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.event.MenuEvent;
+import javax.swing.event.MenuListener;
+
+
+/**
+ *
+ * A DynamicLayoutMenu is a more complicated layout menu that constructs layout menu
+ * items on-the-fly based on the capabilities of the layout algorithm and environment
+ * factors such as whether or not nodes are selected, the presence of node or edge
+ * attributes, etc.
+ */
+public class DynamicLayoutMenu extends JMenu implements MenuListener {
+ private CyLayoutAlgorithm layout;
+ private static final String NOATTRIBUTE = "(none)";
+ private Set<Node> selectedNodes;
+
+ /**
+ * Creates a new DynamicLayoutMenu object.
+ *
+ * @param layout DOCUMENT ME!
+ */
+ public DynamicLayoutMenu(CyLayoutAlgorithm layout, boolean enabled) {
+ super(layout.toString());
+ addMenuListener(this);
+ this.layout = layout;
+ selectedNodes = new HashSet();
+ setEnabled(enabled);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void menuCanceled(MenuEvent e) {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void menuDeselected(MenuEvent e) {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void menuSelected(MenuEvent e) {
+ // Clear any previous entries
+ this.removeAll();
+
+ // Base the menu structure only on the current network.
+ CyNetwork network = Cytoscape.getCurrentNetwork();
+
+ // First, do we support selectedOnly?
+ selectedNodes = network.getSelectedNodes();
+
+ if (layout.supportsSelectedOnly() && (selectedNodes.size() > 0)) {
+ // Add selected node/all nodes menu
+ addSelectedOnlyMenus();
+ } else if (layout.supportsNodeAttributes() != null) {
+ // Add node attributes menus
+ addNodeAttributeMenus(this, false);
+ } else if (layout.supportsEdgeAttributes() != null) {
+ // Add edge attributes menus
+ addEdgeAttributeMenus(this, false);
+ } else {
+
+ // No special menus, so make sure we layout all selected
+ List<CyNetworkView> views = Cytoscape.getSelectedNetworkViews();
+ for ( CyNetworkView view: views ) {
+ layout.setSelectedOnly(false);
+ layout.setLayoutAttribute(null);
+ TaskManager.executeTask( new LayoutTask(layout, view),
+ LayoutTask.getDefaultTaskConfig() );
+ }
+ }
+ }
+
+ private void addNodeAttributeMenus(JMenu parent, boolean selectedOnly) {
+ // Get the node attributes
+ CyAttributes nodeAttributes = Cytoscape.getNodeAttributes();
+ addAttributeMenus(parent, nodeAttributes, layout.supportsNodeAttributes(), selectedOnly);
+ }
+
+ private void addEdgeAttributeMenus(JMenu parent, boolean selectedOnly) {
+ // Get the edge attributes
+ CyAttributes edgeAttributes = Cytoscape.getEdgeAttributes();
+ addAttributeMenus(parent, edgeAttributes, layout.supportsEdgeAttributes(), selectedOnly);
+ }
+
+ private void addAttributeMenus(JMenu parent, CyAttributes attributes, byte[] typeList,
+ boolean selectedOnly) {
+ // Add any special attributes
+ List specialList = layout.getInitialAttributeList();
+
+ if (specialList != null) {
+ for (Iterator iter = specialList.iterator(); iter.hasNext();) {
+ parent.add(new LayoutAttributeMenuItem((String) iter.next(), selectedOnly));
+ }
+ }
+
+ String[] attList = attributes.getAttributeNames();
+
+ for (int i = 0; i < attList.length; i++) {
+ if (!attributes.getUserVisible(attList[i]))
+ continue;
+ byte type = attributes.getType(attList[i]);
+
+ for (int t = 0; t < typeList.length; t++) {
+ if ((typeList[t] == -1) || (typeList[t] == type))
+ parent.add(new LayoutAttributeMenuItem(attList[i], selectedOnly));
+ }
+ }
+ }
+
+ private void addSelectedOnlyMenus() {
+ JMenuItem allNodes;
+ JMenuItem selNodes;
+
+ if ((layout.supportsNodeAttributes() != null) || (layout.supportsEdgeAttributes() != null)) {
+ allNodes = new JMenu("All Nodes");
+ selNodes = new JMenu("Selected Nodes Only");
+
+ if (layout.supportsNodeAttributes() != null) {
+ addNodeAttributeMenus((JMenu) allNodes, false);
+ addNodeAttributeMenus((JMenu) selNodes, true);
+ } else {
+ addEdgeAttributeMenus((JMenu) allNodes, false);
+ addEdgeAttributeMenus((JMenu) selNodes, true);
+ }
+ } else {
+ allNodes = new LayoutAttributeMenuItem("All Nodes", false);
+ selNodes = new LayoutAttributeMenuItem("Selected Nodes Only", true);
+ }
+
+ this.add(allNodes);
+ this.add(selNodes);
+ }
+
+ protected class LayoutAttributeMenuItem extends JMenuItem implements ActionListener {
+ boolean selectedOnly = false;
+
+ public LayoutAttributeMenuItem(String label, boolean selectedOnly) {
+ super(label);
+ addActionListener(this);
+ this.selectedOnly = selectedOnly;
+ }
+
+ public void actionPerformed(ActionEvent e) {
+
+ List<CyNetworkView> views = Cytoscape.getSelectedNetworkViews();
+
+ for ( CyNetworkView netView : views ) {
+
+ if (layout.supportsSelectedOnly()) {
+ layout.setSelectedOnly(selectedOnly);
+
+ if (selectedOnly && (selectedNodes.size() > 0)) {
+ // Lock all unselected nodes
+ Iterator nodeViews = netView.getNodeViewsIterator();
+
+ while (nodeViews.hasNext()) {
+ NodeView nv = (NodeView) nodeViews.next();
+ Node node = nv.getNode();
+
+ if (!selectedNodes.contains(node))
+ layout.lockNode(nv);
+ }
+ }
+ }
+
+ if ((layout.supportsNodeAttributes() != null)
+ || (layout.supportsEdgeAttributes() != null)) {
+ layout.setLayoutAttribute(e.getActionCommand());
+ }
+
+ TaskManager.executeTask( new LayoutTask(layout, netView),
+ LayoutTask.getDefaultTaskConfig() );
+ }
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/layout/ui/LayoutMenu.java b/application/src/main/java/cytoscape/layout/ui/LayoutMenu.java
new file mode 100644
index 0000000..4bcec41
--- /dev/null
+++ b/application/src/main/java/cytoscape/layout/ui/LayoutMenu.java
@@ -0,0 +1,161 @@
+/*
+ File: LayoutMenu.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.layout.ui;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+
+import cytoscape.data.CyAttributes;
+
+import cytoscape.layout.CyLayoutAlgorithm;
+
+import cytoscape.view.CyNetworkView;
+
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.Set;
+import java.util.List;
+
+import javax.swing.JMenu;
+import javax.swing.event.MenuEvent;
+import javax.swing.event.MenuListener;
+
+
+/**
+ *
+ * A DynamicLayoutMenu is a more complicated layout menu that constructs layout menu
+ * items on-the-fly based on the capabilities of the layout algorithm and environment
+ * factors such as whether or not nodes are selected, the presence of node or edge
+ * attributes, etc.
+ */
+public class LayoutMenu extends JMenu implements MenuListener {
+ List<CyLayoutAlgorithm> subMenuList;
+
+ /**
+ * Creates a new LayoutMenu object.
+ *
+ * @param menuName DOCUMENT ME!
+ */
+ public LayoutMenu(String menuName) {
+ super(menuName);
+ addMenuListener(this);
+ subMenuList = new ArrayList<CyLayoutAlgorithm>();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param layout DOCUMENT ME!
+ */
+ public void add(CyLayoutAlgorithm layout) {
+ subMenuList.add(layout);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param layout DOCUMENT ME!
+ */
+ public void remove(CyLayoutAlgorithm layout) {
+ subMenuList.remove(layout);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getItemCount() {
+ return subMenuList.size();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void menuCanceled(MenuEvent e) { } ;
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void menuDeselected(MenuEvent e) { } ;
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void menuSelected(MenuEvent e) {
+ // Clear any previous entries
+ this.removeAll();
+
+ // Figure out if we have anything selected
+ CyNetwork network = Cytoscape.getCurrentNetwork();
+ Set selectedNodes = network.getSelectedNodes();
+ boolean enableMenuItem = checkEnabled();
+
+ // Now, add each layout, as appropriate
+ for (CyLayoutAlgorithm layout: LayoutMenuManager.getLayoutsInMenu(getText())) {
+ // Make sure we don't have any lingering locked nodes
+ layout.unlockAllNodes();
+
+ if ((layout.supportsNodeAttributes() != null)
+ || (layout.supportsEdgeAttributes() != null)) {
+ super.add(new DynamicLayoutMenu(layout,enableMenuItem));
+ } else if (layout.supportsSelectedOnly() && (selectedNodes.size() > 0)) {
+ super.add(new DynamicLayoutMenu(layout,enableMenuItem));
+ } else {
+ super.add(new StaticLayoutMenu(layout,enableMenuItem));
+ }
+ }
+ }
+
+ private boolean checkEnabled() {
+ CyNetwork network = Cytoscape.getCurrentNetwork();
+ if ( network == null || network == Cytoscape.getNullNetwork() )
+ return false;
+
+ CyNetworkView view = Cytoscape.getCurrentNetworkView();
+ if ( view == null || view == Cytoscape.getNullNetworkView() )
+ return false;
+ else
+ return true;
+ }
+}
diff --git a/application/src/main/java/cytoscape/layout/ui/LayoutMenuManager.java b/application/src/main/java/cytoscape/layout/ui/LayoutMenuManager.java
new file mode 100644
index 0000000..d60b80d
--- /dev/null
+++ b/application/src/main/java/cytoscape/layout/ui/LayoutMenuManager.java
@@ -0,0 +1,182 @@
+/*
+ File: LayoutMenuManager.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.layout.ui;
+
+import cytoscape.Cytoscape;
+import cytoscape.CytoscapeInit;
+import cytoscape.init.CyInitParams;
+
+import cytoscape.layout.CyLayoutAlgorithm;
+import cytoscape.layout.CyLayoutAlgorithmComparator;
+import cytoscape.layout.CyLayouts;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.TreeSet;
+
+import javax.swing.JMenu;
+import javax.swing.event.MenuEvent;
+import javax.swing.event.MenuListener;
+
+
+public class LayoutMenuManager implements MenuListener {
+
+ private static Map<String, List<CyLayoutAlgorithm>> menuAlgorithmMap;
+ private static Map<String, LayoutMenu> menuMap;
+ private static Set<CyLayoutAlgorithm> existingLayouts;
+
+ static {
+ menuAlgorithmMap = new HashMap<String,List<CyLayoutAlgorithm>>();
+ menuMap = new HashMap<String,LayoutMenu>();
+ existingLayouts = new HashSet<CyLayoutAlgorithm>();
+ }
+
+ public void menuCanceled(MenuEvent e) { };
+
+ public void menuDeselected(MenuEvent e) { };
+
+ public void menuSelected(MenuEvent e) {
+ Object o = e.getSource();
+ if ( o instanceof JMenu )
+ updateMenus((JMenu)o);
+ }
+
+ private void updateMenus(JMenu parentMenu) {
+
+ // first add all layouts from cylayouts if they're not already there
+ for ( CyLayoutAlgorithm la : CyLayouts.getAllLayouts() )
+ if ( !existingLayouts.contains(la) )
+ addLayout(la);
+
+ // now remove any existing layouts that are no longer in cylayouts
+ Set<CyLayoutAlgorithm> newLayouts = new HashSet<CyLayoutAlgorithm>(CyLayouts.getAllLayouts());
+ for ( CyLayoutAlgorithm la : existingLayouts )
+ if ( !newLayouts.contains(la) )
+ removeLayout(la);
+
+ // now update the menus if necessary
+ for ( String name : menuMap.keySet() ) {
+ LayoutMenu lm = menuMap.get(name);
+ int size = menuAlgorithmMap.get(name).size();
+
+ // if the menu is not already there and
+ // actually contains layouts, add it
+ if ( !parentMenu.isMenuComponent(lm) && size > 0 )
+ parentMenu.add(lm);
+
+ // remove any menus that don't contain any layouts
+ else if ( parentMenu.isMenuComponent(lm) && size <= 0 )
+ parentMenu.remove(lm);
+ }
+ }
+
+ private void addLayout(CyLayoutAlgorithm layout) {
+
+ String menuName = CyLayouts.getMenuName(layout);
+ if (menuName == null )
+ return;
+
+ existingLayouts.add(layout);
+
+ // make sure the list is set up for this name
+ if ( !menuAlgorithmMap.containsKey(menuName) ) {
+ List<CyLayoutAlgorithm> menuList = new ArrayList<CyLayoutAlgorithm>();
+ menuAlgorithmMap.put(menuName, menuList);
+ }
+
+ // add layout to the list of layouts for this name
+ menuAlgorithmMap.get(menuName).add(layout);
+
+ // make sure the menu is set up
+ if ( !menuMap.containsKey(menuName) ) {
+ LayoutMenu menu = new LayoutMenu(menuName);
+ menuMap.put(menuName, menu);
+ }
+
+ // add layout to the menu for this name
+ menuMap.get(menuName).add(layout);
+ }
+
+ private void removeLayout(CyLayoutAlgorithm layout) {
+
+ for (String menu : menuAlgorithmMap.keySet()) {
+
+ List<CyLayoutAlgorithm> menuList = menuAlgorithmMap.get(menu);
+
+ if (menuList.indexOf(layout) >= 0) {
+ menuList.remove(layout);
+ menuMap.get(menu).remove(layout);
+ existingLayouts.remove(layout);
+ return;
+ }
+ }
+ }
+
+ /**
+ * Get all of the layouts associated with a specific
+ * menu.
+ *
+ * @param menu The name of the menu
+ * @return a List of all layouts associated with this menu (could be null)
+ */
+ static List<CyLayoutAlgorithm> getLayoutsInMenu(String menu) {
+ List<CyLayoutAlgorithm> unsorted = menuAlgorithmMap.get(menu);
+
+ return sortLayoutList(unsorted);
+ }
+
+ /**
+ * Get all of the menus (categories of layouts) currently defined.
+ *
+ * @return a Collection of Strings representing each of the menus
+ */
+ static Set<String> getLayoutMenuNames() {
+ return new TreeSet<String>(menuAlgorithmMap.keySet());
+ }
+
+ protected static List<CyLayoutAlgorithm> sortLayoutList(List<CyLayoutAlgorithm> unsorted) {
+ CyLayoutAlgorithm[] sorted = unsorted.toArray(new CyLayoutAlgorithm[1]);
+ Arrays.sort(sorted, new CyLayoutAlgorithmComparator());
+ return Arrays.asList(sorted);
+ }
+}
diff --git a/application/src/main/java/cytoscape/layout/ui/LayoutSettingsDialog.java b/application/src/main/java/cytoscape/layout/ui/LayoutSettingsDialog.java
new file mode 100644
index 0000000..a90545a
--- /dev/null
+++ b/application/src/main/java/cytoscape/layout/ui/LayoutSettingsDialog.java
@@ -0,0 +1,324 @@
+/* vim: set ts=2:
+
+ File: LayoutSettingsDialog.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ Dout of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.layout.ui;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.layout.CyLayouts;
+import cytoscape.layout.CyLayoutAlgorithm;
+import cytoscape.layout.LayoutProperties;
+import cytoscape.layout.LayoutTask;
+
+import cytoscape.task.util.TaskManager;
+
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Font;
+import java.awt.GridLayout;
+import java.awt.event.*;
+
+import java.util.Collection;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Set;
+
+import javax.swing.BorderFactory;
+import javax.swing.BoxLayout;
+import javax.swing.JButton;
+import javax.swing.JComboBox;
+import javax.swing.JDialog;
+import javax.swing.JLabel;
+import javax.swing.JList;
+import javax.swing.JPanel;
+import javax.swing.ListCellRenderer;
+import javax.swing.WindowConstants.*;
+import javax.swing.border.*;
+import javax.swing.text.Position;
+
+
+/**
+ *
+ * The LayoutSettingsDialog is a dialog that provides an interface into all of the
+ * various settings for layout algorithms. Each CyLayoutAlgorithm must return a single
+ * JPanel that provides all of its settings.
+ */
+public class LayoutSettingsDialog extends JDialog implements ActionListener {
+ private CyLayoutAlgorithm currentLayout = null;
+
+ private static Object defaultLayout = null;
+
+ // Dialog components
+ private JLabel titleLabel; // Our title
+ private JPanel mainPanel; // The main content pane
+ private JPanel buttonBox; // Our action buttons (Save Settings, Cancel, Execute, Done)
+ private JComboBox algorithmSelector; // Which algorithm we're using
+ private JPanel algorithmPanel; // The panel this algorithm uses
+
+ /**
+ * Creates a new LayoutSettingsDialog object.
+ */
+ public LayoutSettingsDialog() {
+ super(Cytoscape.getDesktop(), "Layout Settings", false);
+ initializeOnce(); // Initialize the components we only do once
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ // Are we the source of the event?
+ String command = e.getActionCommand();
+
+ if (command.equals("done")) {
+ updateAllSettings();
+ setVisible(false);
+ } else if (command.equals("save")) {
+ updateAllSettings();
+ saveAllProperties();
+ } else if (command.equals("execute")) {
+ // Layout using the current layout
+ updateAllSettings();
+ TaskManager.executeTask( new LayoutTask(currentLayout,Cytoscape.getCurrentNetworkView()),
+ LayoutTask.getDefaultTaskConfig() );
+ } else if (command.equals("cancel")) {
+ // Call revertSettings for each layout
+ revertAllSettings();
+ setVisible(false);
+ } else {
+ // OK, initialize and display
+ initialize();
+ pack();
+ setLocationRelativeTo(Cytoscape.getDesktop());
+ setVisible(true);
+ }
+ }
+
+ private void initializeOnce() {
+ setDefaultCloseOperation(HIDE_ON_CLOSE);
+
+ // Create our main panel
+ mainPanel = new JPanel();
+ mainPanel.setLayout(new BoxLayout(mainPanel, BoxLayout.PAGE_AXIS));
+
+ // Create a panel for the list of algorithms
+ JPanel algorithmSelectorPanel = new JPanel();
+ algorithmSelector = new JComboBox();
+ algorithmSelectorPanel.add(algorithmSelector);
+
+ Border selBorder = BorderFactory.createEtchedBorder(EtchedBorder.LOWERED);
+ TitledBorder titleBorder = BorderFactory.createTitledBorder(selBorder, "Layout Algorithm");
+ titleBorder.setTitlePosition(TitledBorder.LEFT);
+ titleBorder.setTitlePosition(TitledBorder.TOP);
+ algorithmSelectorPanel.setBorder(titleBorder);
+ mainPanel.add(algorithmSelectorPanel);
+
+ // Create a panel for algorithm's content
+ this.algorithmPanel = new JPanel();
+ mainPanel.add(algorithmPanel);
+
+ // Create a panel for our button box
+ this.buttonBox = new JPanel();
+
+ JButton doneButton = new JButton("Done");
+ doneButton.setActionCommand("done");
+ doneButton.addActionListener(this);
+
+ JButton saveButton = new JButton("Save Settings");
+ saveButton.setActionCommand("save");
+ saveButton.addActionListener(this);
+
+ JButton executeButton = new JButton("Execute Layout");
+ executeButton.setActionCommand("execute");
+ executeButton.addActionListener(this);
+
+ JButton cancelButton = new JButton("Cancel");
+ cancelButton.setActionCommand("cancel");
+ cancelButton.addActionListener(this);
+ buttonBox.add(executeButton);
+ buttonBox.add(saveButton);
+ buttonBox.add(cancelButton);
+ buttonBox.add(doneButton);
+ buttonBox.setBorder(BorderFactory.createEtchedBorder(EtchedBorder.LOWERED));
+ mainPanel.add(buttonBox);
+ setContentPane(mainPanel);
+ }
+
+ private void initialize() {
+ // Populate the algorithm selector
+ algorithmSelector.removeAllItems();
+
+ // Add the "instructions"
+ algorithmSelector.setRenderer(new MyItemRenderer());
+ algorithmSelector.addItem("Select algorithm to view settings");
+
+ // Get the list of known layout menus
+ Set<String> menus = LayoutMenuManager.getLayoutMenuNames();
+
+ for (String menu : menus) {
+
+ if (menus.size() > 1) {
+ algorithmSelector.addItem(menu);
+ }
+
+ for (CyLayoutAlgorithm algo : LayoutMenuManager.getLayoutsInMenu(menu)) {
+ if (algo.getSettingsPanel() != null) {
+ algorithmSelector.addItem(algo);
+ }
+ }
+ }
+
+ algorithmSelector.addItemListener(new AlgorithmItemListener());
+
+ // Do we already have a defaultLayout?
+ if (LayoutSettingsDialog.defaultLayout != null) {
+ algorithmSelector.setSelectedItem(defaultLayout);
+ }
+ }
+
+ private void updateAllSettings() {
+ for ( CyLayoutAlgorithm algo : CyLayouts.getAllLayouts() ) {
+ algo.updateSettings();
+ }
+ }
+
+ private void saveAllProperties() {
+ for ( CyLayoutAlgorithm algo : CyLayouts.getAllLayouts() ) {
+ LayoutProperties props = algo.getSettings();
+ if (props != null)
+ props.saveProperties();
+ }
+ }
+
+ private void revertAllSettings() {
+ for ( CyLayoutAlgorithm algo : CyLayouts.getAllLayouts() ) {
+ algo.revertSettings();
+ }
+ }
+
+ private class AlgorithmItemListener implements ItemListener, ComponentListener {
+ public AlgorithmItemListener() {
+ }
+
+ public void itemStateChanged(ItemEvent e) {
+ if (e.getStateChange() == ItemEvent.SELECTED) {
+ algorithmPanel.removeAll();
+
+ if (e.getItem().getClass() == String.class) {
+ currentLayout = null;
+ LayoutSettingsDialog.defaultLayout = null;
+ algorithmPanel.setBorder(null);
+ } else {
+ CyLayoutAlgorithm newLayout = (CyLayoutAlgorithm) e.getItem();
+ LayoutSettingsDialog.defaultLayout = newLayout;
+
+ // Replace the previous settings panel with a new one
+ JPanel panel = newLayout.getSettingsPanel();
+ algorithmPanel.removeAll();
+ algorithmPanel.add(panel);
+
+ // Add a component listener to the panel in case it gets dynamically updated
+ panel.addComponentListener(this);
+
+ Border selBorder = BorderFactory.createEtchedBorder(EtchedBorder.LOWERED);
+ TitledBorder titleBorder = BorderFactory.createTitledBorder(selBorder,
+ newLayout.toString()
+ + " Settings");
+ titleBorder.setTitlePosition(TitledBorder.LEFT);
+ titleBorder.setTitlePosition(TitledBorder.TOP);
+ algorithmPanel.setBorder(titleBorder);
+ currentLayout = newLayout; // Remember which one is set
+ }
+
+ validate();
+ pack();
+ }
+ }
+
+ public void componentHidden(ComponentEvent e) { }
+
+ public void componentMoved(ComponentEvent e) { }
+
+ // This gets called by the Tunable mechanism is one of our
+ // Tunable GUI's changes size. This allows us to dynamically
+ // repaint our layout in response
+ public void componentResized(ComponentEvent e) {
+ validate();
+ doLayout();
+ pack();
+ }
+
+ public void componentShown(ComponentEvent e) { }
+
+ }
+
+ private class MyItemRenderer extends JLabel implements ListCellRenderer {
+ public MyItemRenderer() {
+ }
+
+ public Component getListCellRendererComponent(JList list, Object value, int index,
+ boolean isSelected, boolean cellHasFocus) {
+ // If this is a String, we don't want to allow selection. If this is
+ // index 0, we want to set the font
+ Font f = getFont();
+
+ if (value.getClass() == String.class) {
+ setFont(f.deriveFont(Font.PLAIN));
+ setText((String) value);
+ setHorizontalAlignment(CENTER);
+ setForeground(Color.GRAY);
+ setEnabled(false);
+ } else {
+ setForeground(list.getForeground());
+ setHorizontalAlignment(LEFT);
+ setEnabled(true);
+
+ if (isSelected) {
+ setFont(f.deriveFont(Font.BOLD));
+ } else {
+ setFont(f.deriveFont(Font.PLAIN));
+ }
+
+ setText(value.toString());
+ }
+
+ return this;
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/layout/ui/SettingsAction.java b/application/src/main/java/cytoscape/layout/ui/SettingsAction.java
new file mode 100644
index 0000000..1fb202e
--- /dev/null
+++ b/application/src/main/java/cytoscape/layout/ui/SettingsAction.java
@@ -0,0 +1,62 @@
+/*
+ File: SettingsAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.layout.ui;
+
+import cytoscape.util.CytoscapeAction;
+import cytoscape.layout.ui.LayoutSettingsDialog;
+import java.awt.event.ActionEvent;
+import javax.swing.event.MenuEvent;
+
+/**
+ */
+public class SettingsAction extends CytoscapeAction {
+
+
+ public SettingsAction() {
+ super("Settings...");
+ setPreferredMenu("Layout");
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ LayoutSettingsDialog settingsDialog = new LayoutSettingsDialog();
+ settingsDialog.actionPerformed(e);
+ }
+
+ public void menuSelected(MenuEvent e) {
+ enableForNetworkAndView();
+ }
+}
diff --git a/application/src/main/java/cytoscape/layout/ui/StaticLayoutMenu.java b/application/src/main/java/cytoscape/layout/ui/StaticLayoutMenu.java
new file mode 100644
index 0000000..219f9ec
--- /dev/null
+++ b/application/src/main/java/cytoscape/layout/ui/StaticLayoutMenu.java
@@ -0,0 +1,86 @@
+/*
+ File: StaticLayoutMenu.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.layout.ui;
+
+import cytoscape.Cytoscape;
+import cytoscape.view.CyNetworkView;
+
+import cytoscape.layout.CyLayoutAlgorithm;
+import cytoscape.layout.LayoutTask;
+
+import cytoscape.task.util.TaskManager;
+
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import javax.swing.JMenuItem;
+import java.util.List;
+
+
+/**
+ * StaticLayoutMenu provides a simple menu item to be added to a layout
+ * menu.
+ */
+public class StaticLayoutMenu extends JMenuItem implements ActionListener {
+ private CyLayoutAlgorithm layout;
+
+ /**
+ * Creates a new StaticLayoutMenu object.
+ *
+ * @param layout DOCUMENT ME!
+ */
+ public StaticLayoutMenu(CyLayoutAlgorithm layout,boolean enabled) {
+ super(layout.toString());
+ addActionListener(this);
+ this.layout = layout;
+ setEnabled(enabled);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ List<CyNetworkView> views = Cytoscape.getSelectedNetworkViews();
+ for ( CyNetworkView view: views ) {
+ layout.setSelectedOnly(false);
+ TaskManager.executeTask( new LayoutTask(layout, view),
+ LayoutTask.getDefaultTaskConfig() );
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/logger/ConsoleLogger.java b/application/src/main/java/cytoscape/logger/ConsoleLogger.java
new file mode 100644
index 0000000..4b4a54f
--- /dev/null
+++ b/application/src/main/java/cytoscape/logger/ConsoleLogger.java
@@ -0,0 +1,63 @@
+/*
+ File: ConsoleLogger.java
+
+ Copyright (c) 2008, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+ - University of California San Francisco
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.logger;
+
+/**
+ * The ConsoleLogger is the default log handler for Cytoscape and does nothing
+ * much more than issue messages to System.out or System.err, as appropriate.
+ */
+public class ConsoleLogger implements CyLogHandler {
+ private static ConsoleLogger logger = null;
+
+ protected ConsoleLogger() {}
+
+ public void handleLog(LogLevel level, String logMessage) {
+ if (level == LogLevel.LOG_ERROR || level == LogLevel.LOG_FATAL)
+ System.err.println(logMessage);
+ else
+ System.out.println(logMessage);
+ }
+
+ public static ConsoleLogger getLogger() {
+ if (logger == null)
+ logger = new ConsoleLogger();
+
+ return logger;
+ }
+}
diff --git a/application/src/main/java/cytoscape/logger/CyLogHandler.java b/application/src/main/java/cytoscape/logger/CyLogHandler.java
new file mode 100644
index 0000000..136e196
--- /dev/null
+++ b/application/src/main/java/cytoscape/logger/CyLogHandler.java
@@ -0,0 +1,55 @@
+/*
+ File: CyLogHandler.java
+
+ Copyright (c) 2008, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+ - University of California San Francisco
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.logger;
+
+/**
+ * The CyLogHandler interface must be implemented by log handlers for plugins
+ * that wish to handle their own logging.
+ */
+public interface CyLogHandler {
+ /**
+ * The only method required is handleLog, which is called whenever the
+ * logging mechanism detects that a message appropriate for this handler
+ * has been logged.
+ *
+ * @param level the level of the message
+ * @param logMessage the message itself
+ */
+ public void handleLog(LogLevel level, String logMessage);
+}
diff --git a/application/src/main/java/cytoscape/logger/CyLogger.java b/application/src/main/java/cytoscape/logger/CyLogger.java
new file mode 100644
index 0000000..3018c9e
--- /dev/null
+++ b/application/src/main/java/cytoscape/logger/CyLogger.java
@@ -0,0 +1,398 @@
+ /*
+ File: CyLogger.java
+
+ Copyright (c) 2008, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+/**
+ * The CyLogger class is meant to be a wrapper around a general logging
+ * mechanism. The idea is to provide a simple interface that can be used
+ * to alert/inform users about various events that occur during the processing
+ * within Cytoscape or within a Cytoscape plugin. Currently, this class provides
+ * it's own logging buffers -- in the 3.0 time frame, this will probably be replaced
+ * by a more general mechanism such as log4j or java's own logging. Of note to
+ * developers is the <i>cytoscape.debug</i> property, which when set to <b>true</b>
+ * will enable the LOG_DEBUG level of logging. Otherwise, no debug level logging
+ * will be done.
+ */
+package cytoscape.logger;
+
+
+import cytoscape.CytoscapeInit;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+
+
+public class CyLogger {
+ private static HashMap<String,CyLogger> logMap = new HashMap();
+ private static HashMap<LogLevel,List<CyLogHandler>> globalHandlerMap = new HashMap();
+ private HashMap<LogLevel, List<CyLogHandler>> handlerMap = new HashMap();
+ private String loggerName = null;
+ private static boolean debugging = false;
+
+ /**
+ * Get a logger with the specified name
+ *
+ * @param name the name of the logger
+ * @return the logger to use
+ */
+ public static CyLogger getLogger(String name) {
+ CyLogger logger = null;
+ if (logMap.containsKey(name)) {
+ logger = logMap.get(name);
+ } else {
+ logger = new CyLogger(name);
+ }
+ return logger;
+ }
+
+ /**
+ * Get a logger for the specified class
+ *
+ * @param logClass the class this logger logs for
+ * @return the logger to use
+ */
+ public static CyLogger getLogger(Class logClass) {
+ return CyLogger.getLogger(logClass.getName());
+ }
+
+ /**
+ * Get the default ("cytoscape") logger
+ *
+ * @return the logger to use
+ */
+ public static CyLogger getLogger() {
+ return getLogger("cytoscape");
+ }
+
+ /**
+ * The constructor to create a CyLogger. This should
+ * not be used, use getLogger instead.
+ */
+ protected CyLogger(String name) {
+ loggerName = name;
+ logMap.put(name,this);
+ }
+
+ public static void setDebugging(final boolean on) {
+ debugging = on;
+ }
+
+ /**
+ * Log a debug message.
+ *
+ * @param message the message to be logged
+ */
+ public void debug(String message) { log(message,LogLevel.LOG_DEBUG); }
+
+ /**
+ * Log a debug message.
+ *
+ * @param message the message to be logged
+ * @param exception the exception to be logged
+ */
+ public void debug(String message, Throwable exception) { log(message,LogLevel.LOG_DEBUG,exception); }
+
+ /**
+ * Log an informational message.
+ *
+ * @param message the message to be logged
+ */
+ public void info(String message) { log(message,LogLevel.LOG_INFO); }
+
+ /**
+ * Log an informational message.
+ *
+ * @param message the message to be logged
+ * @param exception the exception to be logged
+ */
+ public void info(String message, Throwable exception) { log(message,LogLevel.LOG_INFO,exception); }
+
+ /**
+ * Log a warning message.
+ *
+ * @param message the message to be logged
+ */
+ public void warn(String message) { log(message,LogLevel.LOG_WARN); }
+
+ /**
+ * Log a warning message.
+ *
+ * @param message the message to be logged
+ * @param exception the exception to be logged
+ */
+ public void warn(String message, Throwable exception) { log(message,LogLevel.LOG_WARN,exception); }
+
+ /**
+ * Log a warning message.
+ *
+ * @param message the message to be logged
+ */
+ public void warning(String message) { log(message,LogLevel.LOG_WARN); }
+
+ /**
+ * Log a warning message.
+ *
+ * @param message the message to be logged
+ * @param exception the exception to be logged
+ */
+ public void warning(String message, Throwable exception) { log(message,LogLevel.LOG_WARN,exception); }
+
+ /**
+ * Log an error message.
+ *
+ * @param message the message to be logged
+ */
+ public void error(String message) { log(message,LogLevel.LOG_ERROR); }
+
+ /**
+ * Log an error exception message.
+ *
+ * @param message the message to be printed
+ * @param exception the exception to be logged
+ */
+ public void error(String message, Throwable exception) { log(message, LogLevel.LOG_ERROR, exception); }
+
+ /**
+ * Log a fatal error message.
+ *
+ * @param message the message to be logged
+ */
+ public void fatal(String message) { log(message,LogLevel.LOG_FATAL); }
+
+ /**
+ * Log a fatal exception message.
+ *
+ * @param message the message to be printed
+ * @param exception the exception to be logged
+ */
+ public void fatal(String message, Throwable exception) { log(message,LogLevel.LOG_FATAL, exception); }
+
+ /**
+ * Set the debug status. This will override the default debug setting
+ * from cytoscape.debug for this logger only.
+ *
+ * @param debug boolean setting for debugging state.
+ */
+ public void setDebug(boolean debug) {
+ this.debugging = debug;
+ }
+
+ /**
+ * Get the debug status.
+ *
+ * @return 'true' if the debug flag is enabled.
+ */
+ public boolean isDebugging() {
+ return this.debugging;
+ }
+
+ /**
+ * Log a message at the specified log level.
+ *
+ * @param message the message to be logged
+ * @param level the LogLevel to log the message at
+ * @param t a throwable to use to get a stack trace
+ */
+ public void log(String message, LogLevel level, Throwable t) {
+ if (message != null && message.length() > 0)
+ message += "\n";
+ if (t != null) {
+ message += getStack(t);
+ }
+ log(message,level);
+ }
+
+ /**
+ * Log a message at the specified log level.
+ *
+ * @param message the message to be logged
+ * @param level the LogLevel to log the message at
+ */
+ public void log(String message, LogLevel level) {
+ // Is this a DEBUG message?
+ if (level == LogLevel.LOG_DEBUG && !debugging) {
+ return;
+ }
+ // Format the message
+ String formattedMessage = loggerName+"["+level+"]: "+message;
+ // See if there are any handlers at all
+ if (globalHandlerMap.size() == 0 && handlerMap.size() == 0) {
+ // No, just print the message to the console
+ System.out.println(formattedMessage);
+ return;
+ }
+
+ // Send it to all interested global handlers
+ List<CyLogHandler> handlerList = getHandlers(globalHandlerMap, level);
+ handlerList.addAll(getHandlers(handlerMap, level));
+
+ for (CyLogHandler handler: handlerList) {
+ handler.handleLog(level, formattedMessage);
+ }
+ }
+
+ /**
+ * Add a new log handler for specific messages
+ *
+ * @param handler the CyLogHandler that will handle the messages
+ * @param loggerName a String that indicates which messages this handler handles
+ * @param level the minimum LogLevel this handler is interested in
+ */
+ public void addLogHandler(CyLogHandler handler, String loggerName, LogLevel level) {
+ List<CyLogHandler>list = null;
+ HashMap<LogLevel,List<CyLogHandler>> map = null;
+
+ // Is this a global handler?
+ if (loggerName == null) {
+ map = globalHandlerMap;
+ } else {
+ map = handlerMap;
+ }
+
+ if (map.containsKey(level)) {
+ list = map.get(level);
+ } else {
+ list = new ArrayList();
+ }
+ list.add(handler);
+ map.put(level, list);
+ }
+
+ /**
+ * Add a new general log handler for all messages
+ *
+ * @param handler the CyLogHandler that will handle the messages
+ * @param level the minimum LogLevel this handler is interested in
+ */
+ public void addLogHandler(CyLogHandler handler, LogLevel level) {
+ addLogHandler(handler, null, level);
+ }
+
+ /**
+ * Returns the current list of log handlers for the specified logger at
+ * the suggested minimum level.
+ *
+ * @param loggerName a String that indicates which messages the handlers handle
+ * @param level the minimum LogLevel the handlers are interested in
+ * @return a List of CyLogHandlers the meet the criteria
+ */
+ public List<CyLogHandler> getLogHandlers(String loggerName, LogLevel level) {
+ HashMap<LogLevel,List<CyLogHandler>> map = null;
+
+ // Is this a global handler?
+ if (loggerName == null) {
+ map = globalHandlerMap;
+ } else {
+ map = handlerMap;
+ }
+
+ if (map.containsKey(level)) {
+ return map.get(level);
+ }
+ return null;
+ }
+
+ /**
+ * Returns the current list of log handlers for the specified
+ * minimum level.
+ *
+ * @param level the minimum LogLevel the handlers are interested in
+ * @return a List of CyLogHandlers the meet the criteria
+ */
+ public List<CyLogHandler> getLogHandlers(LogLevel level) {
+ return getLogHandlers(null, level);
+ }
+
+ /**
+ * Remove a log handler for specific messages
+ *
+ * @param handler the CyLogHandler to remove
+ * @param loggerName a String that indicates which messages this handler handles
+ * @param level the minimum LogLevel this handler is interested in
+ */
+ public CyLogHandler removeLogHandler(CyLogHandler handler, String loggerName, LogLevel level) {
+ HashMap<LogLevel,List<CyLogHandler>> map = null;
+
+ // Is this a global handler?
+ if (loggerName == null) {
+ map = globalHandlerMap;
+ } else {
+ map = handlerMap;
+ }
+
+ if (!map.containsKey(level)) {
+ return null;
+ }
+
+ // Get the list
+ List<CyLogHandler>list = map.get(level);
+ if (list.contains(handler)) {
+ list.remove(handler);
+ map.put(level, list);
+ return handler;
+ }
+ return null;
+ }
+
+ /**
+ * Remove a general log handler
+ *
+ * @param handler the CyLogHandler to remove
+ * @param level the minimum LogLevel this handler is interested in
+ */
+ public CyLogHandler removeLogHandler(CyLogHandler handler, LogLevel level) {
+ return removeLogHandler(handler, null, level);
+ }
+
+ private List<CyLogHandler> getHandlers(HashMap<LogLevel,List<CyLogHandler>> map, LogLevel targetLevel) {
+ // Find all of the handlers in this map that apply to this level
+ List<CyLogHandler> list = new ArrayList();
+ for (LogLevel level: map.keySet()) {
+ if (targetLevel.applies(level))
+ list.addAll(map.get(level));
+ }
+ return list;
+ }
+
+ private String getStack(Throwable t) {
+ if ( t == null )
+ return "";
+ String message = "\nCaused by:\n";
+ if (t.getMessage() != null)
+ message += t.getMessage();
+ else
+ message += t.toString();
+ StackTraceElement[] stackArray = t.getStackTrace();
+ for (int i = 0; stackArray != null && i < stackArray.length; i++) {
+ message += "\n at "+stackArray[i].toString();
+ }
+ return message + "\n" + getStack(t.getCause());
+ }
+}
diff --git a/application/src/main/java/cytoscape/logger/LogLevel.java b/application/src/main/java/cytoscape/logger/LogLevel.java
new file mode 100644
index 0000000..628ae83
--- /dev/null
+++ b/application/src/main/java/cytoscape/logger/LogLevel.java
@@ -0,0 +1,45 @@
+package cytoscape.logger;
+
+/**
+ * The levels of logged messages
+ */
+public enum LogLevel {
+ /**
+ * LOG_DEBUG should be used only for low-level debugging
+ */
+ LOG_DEBUG("DEBUG",0, "Debugging"),
+ /**
+ * LOG_INFO should be used for general, informational messagse
+ */
+ LOG_INFO("INFO",1, "Information"),
+ /**
+ * LOG_WARN should be used to warn the user of some event or issue
+ */
+ LOG_WARN("WARN",2, "Warnings"),
+ /**
+ * LOG_ERROR indicates an error of some sort
+ */
+ LOG_ERROR("ERROR",3, "Errors"),
+ /**
+ * LOG_FATAL is a fatal error
+ */
+ LOG_FATAL("FATAL",4, null);
+
+ private String prettyName;
+ private String name;
+ protected int level;
+ private LogLevel(String str, int level, String pretty) {
+ this.level = level;
+ this.name = str;
+ this.prettyName = pretty;
+ }
+ public int getLevel() { return this.level; }
+ public String getPrettyName() { return this.prettyName; }
+ public String toString() { return name; }
+ public boolean applies(LogLevel target) { return (this.level >= target.level); }
+ }
+
+
+
+
+
diff --git a/application/src/main/java/cytoscape/overview.html b/application/src/main/java/cytoscape/overview.html
new file mode 100644
index 0000000..439a6ae
--- /dev/null
+++ b/application/src/main/java/cytoscape/overview.html
@@ -0,0 +1,23 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+<html>
+<head>
+<!-- $Revision: 4826 $ -->
+<!-- $Date: 2002-05-13 22:03:40 +0200 (Mon, 13 May 2002) $ -->
+</head>
+<body bgcolor="white">
+
+A software platform for visualizing and analyzing biological networks.
+
+Please note that -- the above description notwithstanding -- <b> no </b> biological
+semantics should appear in any cytoscape package. All biological semantics
+shall be implemented in cytoscape plugins, for which see the separately-archived
+<b><i>csplugins</i></b> package.
+
+
+<h2>Package Specification</h2>
+
+<!-- Put @see and @since tags down here. -->
+
+</body>
+</html>
+
diff --git a/application/src/main/java/cytoscape/package.html b/application/src/main/java/cytoscape/package.html
new file mode 100644
index 0000000..545e06c
--- /dev/null
+++ b/application/src/main/java/cytoscape/package.html
@@ -0,0 +1,49 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html>
+<head>
+<!-- $Revision: 6462 $
+ $Date: 2005-02-24 17:04:38 +0100 (Thu, 24 Feb 2005) $
+ $Author: cerami $
+ -->
+</head>
+<body>
+Core Cytoscape Classes.
+</P>
+Cytoscape is a software pacakge designed to enable the vizualization
+and analysis of networks. While commonly used for biological
+networks, it is designed to be able to accomodate any field which
+requires a junction between graph theory and associated data.<br>
+<br>
+The Cytoscape API is designed to be easy to use, and intuitive.
+Which means that most method names are fairly boring, and follow Java
+standards, so there are a lot of get/set methods. More
+information on using the classes can be found at
+http://www.cytoscape.org/alpha.html . <br>
+<br>
+In general, the most commonly used classes will be found in the <span
+ style="font-style: italic;">cytoscape</span> package. So:<br>
+<span style="font-style: italic;"><br>
+import cytoscape.*;<br>
+<span style="font-style: italic;"><br>
+</span></span><span style="font-weight: bold;"></span>will be sufficent
+for many of your classes. The class <span
+ style="font-style: italic;">cytoscape.Cytoscape</span> is where <span
+ style="font-style: italic;">CyNodes </span>and <span
+ style="font-style: italic;">CyEdges</span> are created. This is
+done via the <span style="font-style: italic;">getCyNode </span>and
+<span style="font-style: italic;">getCyEdge</span> methods. Note
+that Cytoscape does its best to not create duplicate nodes and
+edges. All of the nodes and edges are then accessable from <span
+ style="font-style: italic;">Cytoscape. </span>To actually do
+things like run algorithms a <span style="font-style: italic;">CyNetwork
+</span>is required. The <span style="font-style: italic;">createNetwork
+</span>series of methods will get you started in that directions.<br>
+<br>
+Generally, working with <span style="font-style: italic;">CyNetworks</span>
+is the preffered method of interacting with Cytoscape. <span
+ style="font-style: italic;">CyNetwork</span> contains many methods for
+easily writing Graph algoroithms, and for the smooth integration of
+data. More information can be found in the Developer
+documentation.<br>
+</body>
+</html>
diff --git a/application/src/main/java/cytoscape/plugin/Category.java b/application/src/main/java/cytoscape/plugin/Category.java
new file mode 100644
index 0000000..82fee82
--- /dev/null
+++ b/application/src/main/java/cytoscape/plugin/Category.java
@@ -0,0 +1,27 @@
+package cytoscape.plugin;
+
+public enum Category {
+ CORE("Core"), ANALYSIS("Analysis"), NETWORK_ATTRIBUTE_IO(
+ "Network and Attribute I/O"), NETWORK_INFERENCE(
+ "Network Inference"), FUNCTIONAL_ENRICHMENT(
+ "Functional Enrichment"), COMMUNICATION_SCRIPTING(
+ "Communication/Scripting"), THEME("Theme"),
+ NONE("Uncategorized"), OUTDATED("Outdated")
+ ;
+
+ private String catText;
+
+ private Category(String type) {
+ catText = type;
+ }
+
+ public String toString() {
+ return catText;
+ }
+
+ public String getCategoryText() {
+ return toString();
+ }
+}
+
+
diff --git a/application/src/main/java/cytoscape/plugin/CytoscapePlugin.java b/application/src/main/java/cytoscape/plugin/CytoscapePlugin.java
new file mode 100644
index 0000000..e0a04c4
--- /dev/null
+++ b/application/src/main/java/cytoscape/plugin/CytoscapePlugin.java
@@ -0,0 +1,225 @@
+/*
+ File: CytoscapePlugin.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.plugin;
+
+import cytoscape.*;
+import cytoscape.logger.CyLogger;
+
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+
+import java.io.File;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+
+/**
+ * A CytoscapePlugin is the new "Global" plugin. A CytoscapePlugin constructor
+ * does not have any arguments, since it is Network agnostic. Instead all access
+ * to the Cytoscape Data Structures is handled throught the static methods
+ * provided by cytoscape.Cytoscape.
+ *
+ * It is encouraged, but not mandatory, for plugins to override the
+ * {@link #describe describe} method to state what the plugin does and how it
+ * should be used.
+ */
+public abstract class CytoscapePlugin implements PropertyChangeListener {
+
+ /**
+ * There are no arguments required or allowed in a CytoscapePlugin
+ * constructor.
+ */
+ public CytoscapePlugin() {
+ Cytoscape.getPropertyChangeSupport().addPropertyChangeListener(
+ Cytoscape.SAVE_PLUGIN_STATE, this);
+ Cytoscape.getPropertyChangeSupport().addPropertyChangeListener(
+ Cytoscape.RESTORE_PLUGIN_STATE, this);
+ Cytoscape.getPropertyChangeSupport().addPropertyChangeListener(
+ Cytoscape.CYTOSCAPE_EXIT, this);
+ }
+
+ /**
+ * If true, this plugin is capable if accepting scripts, and we will find
+ * out what its script name is
+ */
+ public boolean isScriptable() {
+ return false;
+ }
+
+ /**
+ * If this plugin is scriptable, then this will return a unique script name,
+ * that will come after the colon like: :name
+ */
+ public String getScriptName() {
+ return "default";
+ }
+
+ /**
+ * Take a CyNetwork as input along with some arguments, and return a
+ * CyNetwork, which can be the same, or different, it doesn't really matter,
+ * and is up to the individual plugin.
+ */
+ public CyNetwork interpretScript(String[] args, CyNetwork network) {
+ return null;
+ }
+
+ /**
+ * If implemented, then this plugin will be activated after being
+ * initialized
+ */
+ public void activate() {
+ }
+
+ /**
+ * If implemented then this plugin can remove itself from the Menu system,
+ * and anything else, when the user decides to deactivate it.
+ */
+ public void deactivate() {
+ }
+
+ /**
+ * Attempts to instantiate a plugin of the class argument.
+ *
+ * @return The object, if it was not successfully constructed object will be
+ * null
+ * @return true if the plugin was successfulyl constructed, false otherwise
+ */
+ public static Object loadPlugin(Class pluginClass)
+ //throws InstantiationException, IllegalAccessException,
+ throws PluginException {
+ CyLogger logger = CyLogger.getLogger(pluginClass);
+
+ if (pluginClass == null) {
+ return false;
+ }
+
+ Object object = null;
+
+ try {
+ object = pluginClass.newInstance();
+ // We want to catch everything possible. Errors will cause the
+ // entire
+ // cytoscape app to crash, which a plugin should not do.
+ } catch (Throwable e) {
+ object = null;
+ // logger.error("Instantiation has failed for");
+ // Here's a bit of Java strangeness: newInstance() throws
+ // two exceptions (above) -- however, it also propagates any
+ // exception that occurs during the creation of that new instance.
+ // Here, we need to catch whatever other exceptions might be thrown --
+ // for example, attempting to load an older plugin that looks
+ // for the class cytoscape.CyWindow, which is no longer defined,
+ // propagates a ClassNotFoundException (which, if we don't
+ // catch causes the application to crash).
+ String ErrorMsg = "Unchecked '" + e.getClass().getName() + "'exception while attempting to load plugin " + pluginClass.getName() + ".\n"
+ + "This may happen when loading a plugin written for a different \n"
+ + "version of Cytoscape than this one, or if the plugin is dependent \n"
+ + "on another plugin that isn't available. Consult the documentation \n"
+ + "for the plugin or contact the plugin author for more information.";
+
+ //CyLogger.getLogger().warn(ErrorMsg);
+ // CyLogger.getLogger().warn(e);
+ // e.printStackTrace();
+ throw new PluginException(ErrorMsg, e);
+ }
+ logger.info("Plugin successfully loaded");
+ return object;
+ }
+
+ private HashMap<String, List<File>> pluginFileListMap;
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void propertyChange(PropertyChangeEvent e) {
+ String pluginName = this.getClass().getName();
+ int index = pluginName.lastIndexOf(".");
+ pluginName = pluginName.substring(index + 1);
+
+ if (e.getPropertyName().equalsIgnoreCase(Cytoscape.SAVE_PLUGIN_STATE)) {
+ pluginFileListMap = (HashMap<String, List<File>>) e.getOldValue();
+
+ List<File> newfiles = new ArrayList<File>();
+ saveSessionStateFiles(newfiles);
+
+ if (newfiles.size() > 0) {
+ pluginFileListMap.put(pluginName, newfiles);
+ }
+ } else if (e.getPropertyName().equalsIgnoreCase(
+ Cytoscape.RESTORE_PLUGIN_STATE)) {
+ pluginFileListMap = (HashMap<String, List<File>>) e.getOldValue();
+
+ if (pluginFileListMap.containsKey(pluginName)) {
+ List<File> theFileList = pluginFileListMap.get(pluginName);
+
+ if ((theFileList != null) && (theFileList.size() > 0)) {
+ restoreSessionState(theFileList);
+ }
+ }
+ } else if (e.getPropertyName().equalsIgnoreCase(
+ Cytoscape.CYTOSCAPE_EXIT)) {
+ onCytoscapeExit();
+ }
+ }
+
+ public void onCytoscapeExit() {
+
+ }
+
+ // override the following two methods to save state.
+ /**
+ * DOCUMENT ME!
+ *
+ * @param pStateFileList
+ * DOCUMENT ME!
+ */
+ public void restoreSessionState(List<File> pStateFileList) {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param pFileList
+ * DOCUMENT ME!
+ */
+ public void saveSessionStateFiles(List<File> pFileList) {
+ }
+}
diff --git a/application/src/main/java/cytoscape/plugin/DownloadableInfo.java b/application/src/main/java/cytoscape/plugin/DownloadableInfo.java
new file mode 100644
index 0000000..54c3136
--- /dev/null
+++ b/application/src/main/java/cytoscape/plugin/DownloadableInfo.java
@@ -0,0 +1,568 @@
+/*
+ File: DownloadableInfo.java
+ Copyright (c) 2006, 2007, 2011 The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.plugin;
+
+
+import java.net.URL;
+import java.io.IOException;
+
+import cytoscape.util.URLUtil;
+import cytoscape.logger.CyLogger;
+import cytoscape.CytoscapeVersion;
+
+import static cytoscape.plugin.PluginVersionUtils.versionOk;
+import static cytoscape.plugin.PluginVersionUtils.getNewerVersion;
+
+import java.util.Set;
+import java.util.HashSet;
+import java.util.List;
+import java.util.ArrayList;
+import java.util.Arrays;
+
+
+public abstract class DownloadableInfo {
+ private static CyLogger logger = CyLogger.getLogger(DownloadableInfo.class);
+
+ private String releaseDate;
+
+ private String uniqueID;
+
+ private String name = "";
+
+ private String description;
+
+ private String objVersion;
+
+ private String downloadURL = "";
+
+ private String objURL = "";
+
+ private String category;
+
+ private License license;
+
+ private boolean licenseRequired = false;
+
+ private Set<String> compatibleCyVersions;
+
+ private DownloadableInfo parentObj;
+
+ public DownloadableInfo() {
+ this(null,null);
+ }
+
+ public DownloadableInfo(String id) {
+ this(id, null);
+ }
+
+ public DownloadableInfo(String id, DownloadableInfo parentObj) {
+ this.uniqueID = id;
+ this.parentObj = parentObj;
+ this.compatibleCyVersions = new HashSet<String>();
+ }
+
+ /**
+ * Sets the license information for the plugin. Not required.
+ *
+ * @param url
+ * object where license can be downloaded from.
+ */
+ public void setLicense(URL url) {
+ license = new License(url);
+ }
+
+ /**
+ * Sets the license information for the plugin. Not required.
+ *
+ * @param licenseText
+ * string of license.
+ * @param alwaysRequired
+ * If the user expects the license to be required for both
+ * install and update at all times (true) or only at install
+ * (false)
+ */
+ public void setLicense(String licenseText, boolean alwaysRequired) {
+ license = new License(licenseText);
+ licenseRequired = alwaysRequired;
+ }
+
+ /**
+ * @param Category
+ * Sets the category of the downloadable object.
+ */
+ public void setCategory(String Category) {
+ this.category = Category;
+ }
+
+ public void setCategory(Category cat) {
+ this.category = cat.toString();
+ }
+
+ public void setParent(DownloadableInfo parentObj) {
+ this.parentObj = parentObj;
+ }
+
+ /**
+ * @param name
+ * Sets the name of the downloadable object.
+ */
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ /**
+ * @param description
+ * Sets the descriptoin of the downloadable object.
+ */
+ public void setDescription(String description) {
+ this.description = description;
+ }
+
+ /**
+ * @param url
+ * Sets the URL for the xml file describing all downloadable
+ * objects from any given project. (ex.
+ * http://cytoscape.org/plugins/plugin.xml)
+ */
+ public void setDownloadableURL(String url) {
+ this.downloadURL = url;
+ }
+
+ /**
+ * @param url
+ * Set the URL where this object can be downloaded from.
+ */
+ public void setObjectUrl(String url) {
+ this.objURL = url;
+ }
+
+ /**
+ * Contains a list of all the Cytoscape versions this object is compatible
+ * with.
+ *
+ * @param cyVersion
+ * @throws NumberFormatException
+ */
+ public void addCytoscapeVersion(final String cyVersion) throws NumberFormatException {
+ if (versionOk(cyVersion, false))
+ compatibleCyVersions.add(cyVersion);
+ else {
+ throw new NumberFormatException(
+ "Cytoscape version numbers must be in the format: \""
+ + PluginVersionUtils.VALID_CYTOSCAPE_VERSION_PATTERN + "\"!"
+ + " (Bad version is \"" + cyVersion + "\".)");
+ }
+ }
+
+ /**
+ * @param objVersion
+ * Sets the version of this object.
+ */
+ public void setObjectVersion(String Version) {
+ if (versionOk(Version, true)) {
+ this.objVersion = Version;
+ } else {
+ throw new NumberFormatException("Bad version '" + Version + "'."
+ + this
+ + " version numbers must be in the format: \\d+.\\d+");
+ }
+ }
+
+ /**
+ * TODO - would probably be better to use a date object
+ *
+ * @param date
+ * Sets the release date of this object.
+ */
+ public void setReleaseDate(String date) {
+ this.releaseDate = date;
+ }
+
+ /* --- GET --- */
+
+ /**
+ * @return The text of the license for this plugin if available.
+ */
+ public String getLicenseText() {
+ if (license != null)
+ return license.getLicense();
+ else
+ return null;
+ }
+
+ /**
+ * @return If the license is always required to be accepted for installs and
+ * updates this returns true. If it only is required at install time
+ * (never at update) returns false.
+ */
+ public boolean isLicenseRequired() {
+ return licenseRequired;
+ }
+
+ public abstract Installable getInstallable();
+
+ /**
+ * Return the downloadable type of this object.
+ */
+ public abstract DownloadableType getType();
+
+ /**
+ * @return The parent DownloadableInfo object for this object if it has one.
+ */
+ public DownloadableInfo getParent() {
+ return this.parentObj;
+ }
+
+ /**
+ * @return The URL this object can be downloaded from.
+ */
+ public String getObjectUrl() {
+ return this.objURL;
+ }
+
+ /**
+ * @return Category that describes this downloadable object.
+ */
+ public String getCategory() {
+ return this.category;
+ }
+
+ /**
+ * @return Url that returns the document of available downloadable objects
+ * this object came from. Example
+ * http://cytoscape.org/plugins/plugins.xml
+ */
+ public String getDownloadableURL() {
+ return this.downloadURL;
+ }
+
+ /**
+ * @return Version of the downloadable object.
+ */
+ public String getObjectVersion() {
+ return this.objVersion;
+ }
+
+ /**
+ * @return Name of the downloadable object.
+ */
+ public String getName() {
+ return this.name;
+ }
+
+ /**
+ * @return Description of the downloadable object.
+ */
+ public String getDescription() {
+ return this.description;
+ }
+
+ /**
+ * @return Compatible Cytocape version of this object.
+ *
+ * BUG: THIS IS WRONG, I need to be getting the version that MATCHES the current version
+ * not the one that is newest!!
+ *
+ */
+ public String getCytoscapeVersion() {
+
+ //Bug fix, if currentVersion matches one of compatible versions of Cytosape, just return current version
+ for (String v : this.compatibleCyVersions) {
+ if (isCytoscapeVersionCurrent(v)){
+ return v;
+ }
+ }
+
+ String currentPluginVersion = null;
+ String all = "";
+ for (String v : this.compatibleCyVersions) {
+ all += v + " ";
+
+ if (currentPluginVersion != null) {
+ currentPluginVersion = getNewerVersion(v, currentPluginVersion);
+ // compare to cytoscape version
+ if ( isCytoscapeVersionCurrent(currentPluginVersion) )
+ return currentPluginVersion;
+ }
+ else {
+ currentPluginVersion = v;
+ }
+ }
+
+ logger.debug(getName() +": Compatible: " + all + " cyvers: " + currentPluginVersion
+ + "(cyversion " + cytoscape.CytoscapeVersion.version +")");
+ return currentPluginVersion;
+ }
+
+ /**
+ * @return All compatible Cytoscape versions.
+ */
+ public List<String> getCytoscapeVersions() {
+ return new ArrayList<String>(this.compatibleCyVersions);
+ }
+
+ protected boolean containsVersion(String cyVersion) {
+ return compatibleCyVersions.contains(cyVersion);
+ }
+
+ /**
+ * @return Release date for this object.
+ */
+ public String getReleaseDate() {
+ return this.releaseDate;
+ }
+
+ /**
+ * @return Unique identifier for the downloadable object.
+ */
+ public String getID() {
+ return this.uniqueID;
+ }
+
+ /**
+ * Compare the version of the object to the given object.
+ *
+ * @param New
+ * Potentially newer DownloadableInfo object
+ * @return true if given version is newer
+ */
+ public boolean isNewerObjectVersion(DownloadableInfo New) {
+ String[] CurrentVersion = this.getObjectVersion().split(PluginVersionUtils.VERSION_SEPARATOR);
+ String[] NewVersion = New.getObjectVersion().split(PluginVersionUtils.VERSION_SEPARATOR);
+
+ // make sure it's the same object first
+ if (!(this.getID().equals(New.getID()) && this.getDownloadableURL()
+ .equals(New.getDownloadableURL()))) {
+ return false;
+ }
+
+ int CurrentMajor = Integer.valueOf(CurrentVersion[0]).intValue();
+ int NewMajor = Integer.valueOf(NewVersion[0]).intValue();
+
+ int CurrentMinor = Integer.valueOf(CurrentVersion[1]).intValue();
+ int NewMinor = Integer.valueOf(NewVersion[1]).intValue();
+
+ if ((CurrentMajor > NewMajor || (CurrentMajor == NewMajor && CurrentMinor >= NewMinor))) {
+ return false;
+ }
+
+ return true;
+ }
+
+ /**
+ * @param pluginVersion
+ * @return true if the given version is compatible with the current Cytoscape
+ * version major.minor (bugfix is only checked if the plugin
+ * specifies a bugfix version)
+ */
+ private boolean isCytoscapeVersionCurrent(String pluginVersion) {
+ if (pluginVersion == null )
+ return false;
+
+ String[] cyVersion = new CytoscapeVersion().getFullVersion().split(PluginVersionUtils.VERSION_SEPARATOR);
+ String[] plVersion = pluginVersion.split(PluginVersionUtils.VERSION_SEPARATOR);
+
+ if ( cyVersion.length < plVersion.length )
+ return false;
+
+ for (int i = 0; i < plVersion.length; i++)
+ if (Integer.valueOf(cyVersion[i]).intValue() != Integer.valueOf(plVersion[i]).intValue())
+ return false;
+
+ return true;
+ }
+
+
+ private boolean compareVersions(String[] v1, String[] v2) {
+ if (v1.length != v2.length) return false;
+
+ for (int i = 0; i < v1.length; i++) {
+ // Remove ".SNAPSHOT in versiopn number if any
+ v1[i] = v1[i].toUpperCase();
+ int idx = v1[i].indexOf("SNAPSHOT");
+ if (idx >0){
+ v1[i] = v1[i].substring(0, idx-1);
+ }
+
+ if (Integer.valueOf(v1[i]).intValue() != Integer.valueOf(
+ v2[i]).intValue())
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ * @return true if the plugin is compatible with the current version of Cytoscape.
+ * NOTE: It is assumed that if a plugin is listed as being compatible with the minor version number
+ * it is compatible with all bug fix versions.
+ */
+ public boolean isPluginCompatibleWithCurrent() {
+
+ if (this.getCategory() != null && this.getCategory().equalsIgnoreCase("Core")){
+ // core plugins already compatible with current version
+ return true;
+ }
+
+ boolean compatible = false;
+ CytoscapeVersion cv = new CytoscapeVersion();
+ for (String pluginVersion: compatibleCyVersions) {
+ String[] cyVersion = cv.getFullVersion().split(PluginVersionUtils.VERSION_SEPARATOR);
+ String[] plVersion = pluginVersion.split(PluginVersionUtils.VERSION_SEPARATOR);
+ if ( PluginVersionUtils.isVersion(pluginVersion, PluginVersionUtils.MINOR) ) {
+ cyVersion = new String[]{cyVersion[0], cyVersion[1]};
+ }
+ logger.debug("Comparing versions: " + Arrays.toString(cyVersion) + " : " + Arrays.toString(plVersion));
+
+ if (compareVersions(cyVersion, plVersion)) {
+ compatible = true;
+ break;
+ }
+ }
+ return compatible;
+ }
+
+ /**
+ * Compare the two info objects. If the ID, downloadable url and object
+ * version are the same they are considered to be the same object.
+ *
+ * Careful, this overwrites the Object.equals method
+ */
+ public boolean equals(Object Obj) {
+ DownloadableInfo obj = (DownloadableInfo) Obj;
+
+ if ( this.getType().equals(obj.getType()) ) {
+ if ( (this.getID() != null && obj.getID() != null) ) {
+ if (this.getID().equals(obj.getID()) &&
+ this.getDownloadableURL().equals(obj.getDownloadableURL()) &&
+ this.getObjectVersion().equals(obj.getObjectVersion()))
+ return true;
+ } else if (this.getDownloadableURL().equals(obj.getDownloadableURL()) &&
+ this.getObjectVersion().equals(obj.getObjectVersion())) {
+ // should I do this?? Without an id there is no other good way to
+ // tell I suppose
+ return true;
+ }
+ }
+ return false;
+ }
+
+ /**
+ * Compares the ID and download URL of the two objects. If they are the same
+ * the objects are considered to be equal regardless of version.
+ *
+ * @param Obj
+ * @return
+ */
+ public boolean equalsDifferentObjectVersion(Object Obj) {
+ DownloadableInfo obj = (DownloadableInfo) Obj;
+ if (this.getID().equals(obj.getID())
+ && this.getType().equals(obj.getType())
+ && this.getDownloadableURL().equals(obj.getDownloadableURL()))
+ return true;
+
+ return false;
+ }
+
+ /**
+ * @return Returns String of downloadable name and version ex. MyPlugin
+ * v.1.0
+ */
+ public String toString() {
+ return getName() + " v." + getObjectVersion();
+ }
+
+ public abstract String htmlOutput();
+
+ // yea, it's ugly...styles taken from cytoscape website
+ protected String basicHtmlOutput() {
+ String Html = "<html><style type='text/css'>";
+ Html += "body,th,td,div,p,h1,h2,li,dt,dd ";
+ Html += "{ font-family: Tahoma, \"Gill Sans\", Arial, sans-serif; }";
+ Html += "body { margin: 0px; color: #333333; background-color: #ffffff; }";
+ Html += "#indent { padding-left: 30px; }";
+ Html += "ul {list-style-type: none}";
+ Html += "</style><body>";
+
+ Html += "<b>" + getName() + "</b><p>";
+ Html += "<b>Version:</b> " + getObjectVersion() + "<p>";
+ Html += "<b>Category:</b> " + getCategory() + "<p>";
+ Html += "<b>Description:</b><br>" + getDescription();
+
+ if (!isPluginCompatibleWithCurrent()) {
+ Html += "<br><b>Verified with the following Cytoscape versions:</b> "
+ + getCytoscapeVersions().toString() + "<br>";
+ Html += "<font color='red'><i>" + toString()
+ + " is not verfied to work in the current version ("
+ + cytoscape.CytoscapeVersion.version
+ + ") of Cytoscape.</i></font>";
+ }
+ Html += "<p>";
+
+ if (getReleaseDate() != null && getReleaseDate().length() > 0) {
+ Html += "<b>Release Date:</b> " + getReleaseDate() + "<p>";
+ }
+
+ return Html;
+ }
+
+
+ /**
+ * Fetches and keeps a plugin license if one is available.
+ */
+ protected class License {
+ private URL url;
+ private String text;
+
+ public License(URL url) {
+ this.url = url;
+ }
+
+ public License(String licenseText) {
+ text = licenseText;
+ }
+
+ /**
+ * Get the license text as a string. Will download from url if License
+ * was not initialized with text string.
+ *
+ * @return String
+ */
+ public String getLicense() {
+ if (text == null) {
+ try {
+ text = URLUtil.download(url);
+ } catch (Exception e) {
+ DownloadableInfo.logger.warn("Unable to get license: "+e.toString());
+ text = "No license found";
+ }
+ }
+ return text;
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/plugin/DownloadableType.java b/application/src/main/java/cytoscape/plugin/DownloadableType.java
new file mode 100644
index 0000000..9696e65
--- /dev/null
+++ b/application/src/main/java/cytoscape/plugin/DownloadableType.java
@@ -0,0 +1,27 @@
+/**
+ *
+ */
+package cytoscape.plugin;
+
+public enum DownloadableType {
+ PLUGIN("plugin"), THEME("theme"), FILE("file");
+
+ private String type;
+
+ private DownloadableType(String Type) {
+ type = Type;
+ }
+
+ public String value() {
+ return type;
+ }
+
+ public static DownloadableType getStatus(String value)
+ throws InvalidDownloadable {
+ for (DownloadableType type : values()) {
+ if (type.value().equals(value)) return type;
+ }
+ throw new InvalidDownloadable("'" + value + "' is not a valid downloadable object.");
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/plugin/DuplicatePluginClassException.java b/application/src/main/java/cytoscape/plugin/DuplicatePluginClassException.java
new file mode 100644
index 0000000..030dd59
--- /dev/null
+++ b/application/src/main/java/cytoscape/plugin/DuplicatePluginClassException.java
@@ -0,0 +1,21 @@
+package cytoscape.plugin;
+
+public class DuplicatePluginClassException extends PluginException {
+
+ public DuplicatePluginClassException() {
+ super("Failed to load duplicate plugin class");
+ }
+
+ public DuplicatePluginClassException(String arg0) {
+ super(arg0);
+ }
+
+ public DuplicatePluginClassException(Throwable arg0) {
+ super("Failed to load duplicate plugin class", arg0);
+ }
+
+ public DuplicatePluginClassException(String arg0, Throwable arg1) {
+ super(arg0, arg1);
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/plugin/Installable.java b/application/src/main/java/cytoscape/plugin/Installable.java
new file mode 100644
index 0000000..f1d330a
--- /dev/null
+++ b/application/src/main/java/cytoscape/plugin/Installable.java
@@ -0,0 +1,39 @@
+/**
+ *
+ */
+package cytoscape.plugin;
+
+
+
+
+/**
+ * @author skillcoy
+ *
+ */
+public interface Installable {
+
+ public DownloadableInfo getInfoObj();
+
+ public boolean install() throws java.io.IOException, cytoscape.plugin.ManagerException;
+
+ public boolean install(cytoscape.task.TaskMonitor taskMonitor)
+ throws java.io.IOException, cytoscape.plugin.ManagerException;
+
+ public boolean installToDir(java.io.File dir) throws java.io.IOException, cytoscape.plugin.ManagerException;
+
+ public boolean installToDir(java.io.File dir, cytoscape.task.TaskMonitor taskMonitor)
+ throws java.io.IOException, cytoscape.plugin.ManagerException;
+
+ public boolean uninstall() throws cytoscape.plugin.ManagerException;
+
+ public boolean update(cytoscape.plugin.DownloadableInfo newObj)
+ throws java.io.IOException, cytoscape.plugin.ManagerException;
+
+ public boolean update(cytoscape.plugin.DownloadableInfo newObj, cytoscape.task.TaskMonitor taskMonitor)
+ throws java.io.IOException, cytoscape.plugin.ManagerException;
+
+ public java.util.List<cytoscape.plugin.DownloadableInfo> findUpdates()
+ throws java.io.IOException, org.jdom.JDOMException;
+
+
+}
diff --git a/application/src/main/java/cytoscape/plugin/InstallablePlugin.java b/application/src/main/java/cytoscape/plugin/InstallablePlugin.java
new file mode 100644
index 0000000..152a74e
--- /dev/null
+++ b/application/src/main/java/cytoscape/plugin/InstallablePlugin.java
@@ -0,0 +1,270 @@
+/**
+ *
+ */
+package cytoscape.plugin;
+
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+import java.util.jar.JarFile;
+import java.util.jar.JarInputStream;
+import java.util.jar.Manifest;
+import java.util.zip.ZipEntry;
+
+import cytoscape.task.util.TaskManager;
+import cytoscape.util.URLUtil;
+import cytoscape.util.ZipUtil;
+import cytoscape.logger.CyLogger;
+import java.util.zip.ZipFile;
+
+/**
+ * @author skillcoy
+ *
+ */
+public class InstallablePlugin implements Installable {
+
+ /**
+ * @deprecated This was only ever used internally, so now it is package
+ * protected and part of JarUtil. Use that one as an alternative.
+ * Will be removed Jan 2010.
+ */
+ @Deprecated
+ public static final String MATCH_JAR_REGEXP = JarUtil.MATCH_JAR_REGEXP;
+
+ private static CyLogger logger = CyLogger.getLogger(InstallablePlugin.class);
+
+ private PluginInfo infoObj;
+
+ public InstallablePlugin(PluginInfo obj) {
+ this.infoObj = obj;
+ }
+
+ public PluginInfo getInfoObj() {
+ return this.infoObj;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see cytoscape.plugin.Installable#install()
+ */
+ public boolean install() throws java.io.IOException,
+ cytoscape.plugin.ManagerException {
+ return installToDir(null, null);
+ }
+
+ public boolean installToDir(File dir) throws java.io.IOException,
+ cytoscape.plugin.ManagerException {
+ return installToDir(dir, null);
+ }
+
+ public boolean installToDir(File dir, cytoscape.task.TaskMonitor taskMonitor)
+ throws java.io.IOException,cytoscape.plugin.ManagerException {
+
+
+ File PluginDir = dir;
+ if (PluginDir == null)
+ PluginDir = infoObj.getPluginDirectory();
+ else
+ PluginDir = new File(PluginDir, getInfoObj().getName() + "-" + getInfoObj().getObjectVersion());
+
+ if (!PluginDir.exists()) {
+ PluginDir.mkdirs();
+ }
+
+ File Download = new File(PluginDir, createFileName(infoObj));
+ if (taskMonitor != null)
+ taskMonitor.setStatus(infoObj.toString() + " loading...");
+ URLUtil.download(infoObj.getObjectUrl(), Download, taskMonitor);
+
+ try {
+ String ClassName = JarUtil.getPluginClass(Download.getAbsolutePath(),
+ infoObj.getFileType());
+
+ if (ClassName != null) {
+ infoObj.setPluginClassName(ClassName);
+ } else { // no class name so delete the plugin
+ Download.delete();
+ Download.getParentFile().delete();
+ ManagerException E = new ManagerException(
+ infoObj.getName()
+ + " does not define the attribute 'Cytoscape-Plugin' in the jar manifest file.\n"
+ + "This plugin cannot be auto-installed. Please install manually or contact the plugin author.");
+ throw E;
+ }
+ } catch (IOException ioe) {
+ Download.delete();
+ Download.getParentFile().delete();
+ throw ioe;
+ }
+
+ switch (infoObj.getFileType()) {
+ case JAR: // do nothing, it's installed
+ break;
+ case ZIP:
+ try {
+ List<String> UnzippedFiles = ZipUtil.unzip(Download
+ .getAbsolutePath(), Download.getParent(), taskMonitor);
+ infoObj.setFileList(UnzippedFiles);
+ } catch (IOException ioe) {
+ Download.delete();
+ throw ioe;
+ }
+ break;
+ }
+
+ infoObj.setInstallLocation(PluginDir.getAbsolutePath());
+ infoObj.addFileName(Download.getAbsolutePath());
+
+ return true;
+ }
+
+ public boolean install(cytoscape.task.TaskMonitor taskMonitor)
+ throws java.io.IOException, cytoscape.plugin.ManagerException {
+
+ return installToDir(null, taskMonitor);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see cytoscape.plugin.Installable#uninstall()
+ */
+ public boolean uninstall() throws cytoscape.plugin.ManagerException {
+ boolean Deleted = false;
+ if (infoObj.getInstallLocation() != null
+ && infoObj.getInstallLocation().length() > 0) {
+ File Installed = new File(infoObj.getInstallLocation());
+ Deleted = PluginManager.recursiveDeleteFiles(Installed);
+ } else {
+ for (String f : infoObj.getFileList()) {
+ Deleted = (new File(f)).delete();
+ }
+ }
+ return Deleted;
+ }
+
+ public java.util.List<cytoscape.plugin.DownloadableInfo> findUpdates()
+ throws java.io.IOException, org.jdom.JDOMException {
+
+ final List<DownloadableInfo> UpdatablePlugins = new ArrayList<DownloadableInfo>();
+ final Set<DownloadableInfo> Seen = new HashSet<DownloadableInfo>();
+
+ Seen.add(this.infoObj);
+
+ if (this.infoObj.getDownloadableURL() == null
+ || this.infoObj.getDownloadableURL().length() <= 0) {
+ return UpdatablePlugins;
+ }
+
+ final PluginInfo InfoToUpdate = this.infoObj;
+ final List<Exception> Exceptions = new ArrayList<Exception>();
+
+ PluginManagerInquireTask task = new PluginManagerInquireTask(
+ this.infoObj.getDownloadableURL(), new PluginInquireAction() {
+
+ public String getProgressBarMessage() {
+ return "Connecting to "
+ + InfoToUpdate.getDownloadableURL()
+ + " to search for updates...";
+ }
+
+ public void inquireAction(List<DownloadableInfo> Results) {
+
+ if (isExceptionThrown()) {
+ Exceptions.add(0, getIOException());
+ Exceptions.add(1, getJDOMException());
+ }
+
+ for (DownloadableInfo NewInfo : Results) {
+ if (!InfoToUpdate.getType().equals(
+ NewInfo.getType()))
+ continue;
+
+ PluginInfo New = (PluginInfo) NewInfo;
+ // ID or classname are unique
+ boolean newer = InfoToUpdate
+ .isNewerObjectVersion(New);
+ if ((New.getID().equals(InfoToUpdate.getID()) || New
+ .getPluginClassName().equals(
+ InfoToUpdate.getPluginClassName()))
+ && newer) {
+
+ if (!Seen.contains(New) && newer) {
+ UpdatablePlugins.add(New);
+ } else {
+ Seen.add(New);
+ }
+ }
+ }
+ }
+ });
+
+ // Execute Task in New Thread; pop open JTask Dialog Box.
+ TaskManager.executeTask(task, null);
+
+ if (Exceptions.size() > 0) {
+ if (Exceptions.get(0) != null) {
+ throw (java.io.IOException) Exceptions.get(0);
+ }
+ if (Exceptions.size() > 1 && Exceptions.get(1) != null) {
+ throw (org.jdom.JDOMException) Exceptions.get(1);
+ }
+ }
+
+ return UpdatablePlugins;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see cytoscape.plugin.Installable#update()
+ */
+ public boolean update(DownloadableInfo newObj) throws java.io.IOException,
+ cytoscape.plugin.ManagerException {
+ return update(newObj, null);
+ }
+
+ public boolean update(DownloadableInfo newInfoObj,
+ cytoscape.task.TaskMonitor taskMonitor) throws java.io.IOException,
+ cytoscape.plugin.ManagerException {
+
+ PluginInfo newObj = (PluginInfo) newInfoObj;
+
+ if (infoObj.getDownloadableURL() == null) {
+ throw new ManagerException(
+ infoObj.getName()
+ + " does not have a project url.\nCannot auto-update this plugin.");
+ }
+ // ID or classname
+ if ((infoObj.getID().equals(newObj.getID()) || infoObj
+ .getPluginClassName().equals(newObj.getPluginClassName()))
+ && infoObj.getDownloadableURL().equals(
+ newObj.getDownloadableURL())
+ && infoObj.isNewerObjectVersion(newObj)) {
+
+ this.infoObj = newObj;
+ this.install(taskMonitor);
+
+ } else {
+ throw new ManagerException(
+ "Failed to update '"
+ + infoObj.getName()
+ + "', the new plugin did not match what is currently installed\n"
+ + "or the version was not newer than what is currently installed.");
+ }
+
+ return true;
+ }
+
+ /*
+ * Standard name for the plugin install file <Plugin Name>.jar|zip
+ */
+ private String createFileName(PluginInfo Obj) {
+ return Obj.getName() + "." + Obj.getFileType().toString();
+ }
+}
diff --git a/application/src/main/java/cytoscape/plugin/InstallableTheme.java b/application/src/main/java/cytoscape/plugin/InstallableTheme.java
new file mode 100644
index 0000000..7c17d7b
--- /dev/null
+++ b/application/src/main/java/cytoscape/plugin/InstallableTheme.java
@@ -0,0 +1,204 @@
+/**
+ *
+ */
+package cytoscape.plugin;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import org.jdom.JDOMException;
+
+import cytoscape.task.TaskMonitor;
+import cytoscape.task.util.TaskManager;
+
+/**
+ * @author skillcoy
+ *
+ */
+public class InstallableTheme implements Installable {
+
+ private ThemeInfo infoObj;
+
+ public InstallableTheme(ThemeInfo obj) {
+ this.infoObj = obj;
+ }
+
+ /* (non-Javadoc)
+ * @see cytoscape.plugin.Installable#getInfoObj()
+ */
+ public DownloadableInfo getInfoObj() {
+ return this.infoObj;
+ }
+
+ /* (non-Javadoc)
+ * @see cytoscape.plugin.Installable#install()
+ */
+ public boolean install() throws IOException, ManagerException {
+ return installToDir(null, null);
+ }
+
+ public boolean installToDir(File dir) throws IOException, ManagerException {
+ return installToDir(dir, null);
+ }
+
+ public boolean installToDir(File dir, TaskMonitor taskMonitor) throws IOException, ManagerException {
+ File InstallDir = dir;
+ if (InstallDir == null)
+ InstallDir = new File(this.infoObj.getInstallLocation());
+
+ if (!InstallDir.exists())
+ InstallDir.mkdirs();
+
+ for (PluginInfo plugin: this.infoObj.getPlugins()) {
+ InstallablePlugin pi = new InstallablePlugin(plugin);
+ try {
+ pi.installToDir(InstallDir, taskMonitor);
+ this.infoObj.replacePlugin(plugin, pi.getInfoObj());
+ } catch (Exception me) {
+ // failed to install a plugin stop now and remove all of them
+ // throw exception that theme failed to install due to bad plugin
+ for (PluginInfo pInfo: infoObj.getPlugins()) {
+ if (pInfo.equals(plugin))
+ continue;
+ InstallablePlugin ipDelete = new InstallablePlugin(pInfo);
+ ipDelete.uninstall();
+ }
+ throw new ManagerException("Failed to install the theme '" + this.infoObj.toString() + "'", me);
+ }
+
+ }
+ return true;
+ }
+
+ /* (non-Javadoc)
+ * @see cytoscape.plugin.Installable#install(cytoscape.task.TaskMonitor)
+ */
+ public boolean install(TaskMonitor taskMonitor) throws IOException,
+ ManagerException {
+ return installToDir(null, taskMonitor);
+ }
+
+ /* (non-Javadoc)
+ * @see cytoscape.plugin.Installable#uninstall()
+ */
+ public boolean uninstall() throws cytoscape.plugin.ManagerException {
+ boolean deleteOk = true;
+ for (PluginInfo plugin: this.infoObj.getPlugins()) {
+ InstallablePlugin ins = new InstallablePlugin(plugin);
+ if (!ins.uninstall())
+ deleteOk = false;
+ }
+ deleteOk = new File(infoObj.getInstallLocation()).delete();
+ return deleteOk;
+ }
+
+ /* (non-Javadoc)
+ * @see cytoscape.plugin.Installable#findUpdates()
+ */
+ public List<DownloadableInfo> findUpdates() throws IOException, JDOMException {
+ final List<DownloadableInfo> UpdatableThemes = new ArrayList<DownloadableInfo>();
+ final Set<DownloadableInfo> Seen = new HashSet<DownloadableInfo>();
+
+ Seen.add(this.infoObj);
+
+ if (this.infoObj.getDownloadableURL() == null
+ || this.infoObj.getDownloadableURL().length() <= 0) {
+ return UpdatableThemes;
+ }
+
+ final ThemeInfo InfoToUpdate = this.infoObj;
+ final List<Exception> Exceptions = new ArrayList<Exception>();
+
+
+ PluginManagerInquireTask task = new PluginManagerInquireTask(this.infoObj.getDownloadableURL(),
+ new PluginInquireAction() {
+
+ public String getProgressBarMessage() {
+ return "Connecting to "
+ + InfoToUpdate.getDownloadableURL()
+ + " to search for updates...";
+ }
+
+ public void inquireAction(List<DownloadableInfo> Results) {
+
+ if (isExceptionThrown()) {
+ Exceptions.add(0, getIOException());
+ Exceptions.add(1, getJDOMException());
+ }
+
+ for (DownloadableInfo New : Results) {
+ DownloadableInfo temp = InfoToUpdate;
+ if (!InfoToUpdate.getType().equals(New.getType()))
+ continue;
+ // ID or classname are unique
+ boolean newer = InfoToUpdate.isNewerObjectVersion(New);
+ if ( New.getID().equals(InfoToUpdate.getID()) && newer ) {
+ if (!Seen.contains(New) && newer) {
+ UpdatableThemes.add(New);
+ } else {
+ Seen.add(New);
+ }
+ }
+ }
+ }
+ });
+
+ // Execute Task in New Thread; pop open JTask Dialog Box.
+ TaskManager.executeTask(task, null);
+
+ if (Exceptions.size() > 0) {
+ if (Exceptions.get(0) != null) {
+ throw (java.io.IOException) Exceptions.get(0);
+ }
+ if (Exceptions.size() > 1 && Exceptions.get(1) != null) {
+ throw (org.jdom.JDOMException) Exceptions.get(1);
+ }
+ }
+
+ return UpdatableThemes;
+ }
+
+ /* (non-Javadoc)
+ * @see cytoscape.plugin.Installable#update(cytoscape.plugin.DownloadableInfo, cytoscape.task.TaskMonitor)
+ */
+ public boolean update(DownloadableInfo newInfoObj, TaskMonitor taskMonitor) throws IOException, ManagerException {
+
+ ThemeInfo newObj = (ThemeInfo) newInfoObj;
+
+ if (infoObj.getDownloadableURL() == null) {
+ throw new ManagerException(
+ infoObj.getName()
+ + " does not have a project url.\nCannot auto-update this plugin.");
+ }
+ // ID or classname
+ if ( infoObj.getID().equals(newObj.getID())
+ && infoObj.getDownloadableURL().equals(newObj.getDownloadableURL())
+ && infoObj.isNewerObjectVersion(newObj)) {
+
+ this.infoObj = newObj;
+ this.install(taskMonitor);
+
+ } else {
+ throw new ManagerException(
+ "Failed to update '"
+ + infoObj.getName()
+ + "', the new plugin did not match what is currently installed\n"
+ + "or the version was not newer than what is currently installed.");
+ }
+
+ return true;
+ }
+
+ /* (non-Javadoc)
+ * @see cytoscape.plugin.Installable#update(cytoscape.plugin.DownloadableInfo)
+ */
+ public boolean update(DownloadableInfo newInfoObj) throws IOException, ManagerException {
+ return update(newInfoObj, null);
+ }
+
+
+}
diff --git a/application/src/main/java/cytoscape/plugin/InvalidDownloadable.java b/application/src/main/java/cytoscape/plugin/InvalidDownloadable.java
new file mode 100644
index 0000000..b8c6d90
--- /dev/null
+++ b/application/src/main/java/cytoscape/plugin/InvalidDownloadable.java
@@ -0,0 +1,31 @@
+/**
+ *
+ */
+package cytoscape.plugin;
+
+
+/**
+ * @author skillcoy
+ *
+ */
+public class InvalidDownloadable extends PluginException
+ {
+
+ /**
+ * @param arg0
+ */
+ public InvalidDownloadable(String arg0)
+ {
+ super(arg0);
+ }
+
+ /**
+ * @param arg0
+ * @param arg1
+ */
+ public InvalidDownloadable(String arg0, Throwable arg1)
+ {
+ super(arg0, arg1);
+ }
+
+ }
diff --git a/application/src/main/java/cytoscape/plugin/JarUtil.java b/application/src/main/java/cytoscape/plugin/JarUtil.java
new file mode 100644
index 0000000..d939b98
--- /dev/null
+++ b/application/src/main/java/cytoscape/plugin/JarUtil.java
@@ -0,0 +1,147 @@
+package cytoscape.plugin;
+
+/*
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+import java.util.jar.JarFile;
+import java.util.jar.JarInputStream;
+import java.util.jar.Manifest;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipFile;
+
+import cytoscape.util.URLUtil;
+import cytoscape.util.ZipUtil;
+import cytoscape.logger.CyLogger;
+
+/**
+ * A utility class designed to capture methods used by multiple classes.
+ */
+class JarUtil {
+
+ /**
+ * Bug 2055 changing regexp used to match jars
+ * Was "\\w+\\.jar", which seemed unecessarily restrictive
+ */
+ static final String MATCH_JAR_REGEXP = ".*\\.jar$";
+
+ /**
+ * Iterate through all class files, return the subclass of CytoscapePlugin.
+ * Similar to CytoscapeInit, however only plugins with manifest files that
+ * describe the class of the CytoscapePlugin are valid.
+ */
+ static String getPluginClass(String fileName, PluginInfo.FileType type) throws IOException {
+
+ String pluginClassName = null;
+
+ try {
+
+ switch (type) {
+ case JAR:
+ JarFile jar = new JarFile(fileName);
+ try {
+ pluginClassName = getManifestAttribute(jar.getManifest());
+ } finally {
+ if (jar != null)
+ jar.close();
+ }
+ break;
+
+ case ZIP:
+ List<ZipEntry> Entries = ZipUtil.getAllFiles(fileName, MATCH_JAR_REGEXP);
+ if (Entries.size() <= 0) {
+ String[] filePath = fileName.split("/");
+ fileName = filePath[filePath.length - 1];
+ throw new IOException( fileName +
+ " does not contain any jar files or is not a zip file.");
+ }
+
+ ZipFile zf = null;
+
+ try {
+ zf = new ZipFile(fileName);
+ for (ZipEntry entry : Entries) {
+ String entryName = entry.getName();
+
+ InputStream is = null;
+
+ try {
+ JarInputStream jis = null;
+
+ is = ZipUtil.readFile(zf, entryName);
+ try {
+ jis = new JarInputStream(is);
+ pluginClassName = getManifestAttribute(jis.getManifest());
+ } finally {
+ if (jis != null)
+ jis.close();
+ }
+ } finally {
+ if (is != null)
+ is.close();
+ }
+ }
+ } finally {
+ if (zf != null)
+ zf.close();
+ }
+ }
+
+ } catch (Exception e) {
+ CyLogger.getLogger().debug("Problem getting plugin class name for " +
+ fileName + " " + type, e);
+ throw new IOException(e.toString());
+ }
+
+ return pluginClassName;
+ }
+
+ /*
+ * Gets the manifest file value for the Cytoscape-Plugin attribute
+ */
+ static String getManifestAttribute(Manifest m) {
+ String value = null;
+ if (m != null) {
+ value = m.getMainAttributes().getValue("Cytoscape-Plugin");
+ }
+ return value;
+ }
+}
diff --git a/application/src/main/java/cytoscape/plugin/ManagerException.java b/application/src/main/java/cytoscape/plugin/ManagerException.java
new file mode 100644
index 0000000..177f957
--- /dev/null
+++ b/application/src/main/java/cytoscape/plugin/ManagerException.java
@@ -0,0 +1,63 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.plugin;
+
+
+/**
+ * Thrown to indicate PluginManager errors
+ * @author skillcoyne
+ */
+public class ManagerException extends PluginException {
+ /**
+ * Creates a new ManagerError object.
+ *
+ * @param arg0 DOCUMENT ME!
+ */
+ public ManagerException(String arg0) {
+ super(arg0);
+ }
+
+ /**
+ * Creates a new ManagerError object.
+ *
+ * @param arg0 DOCUMENT ME!
+ * @param arg1 DOCUMENT ME!
+ */
+ public ManagerException(String arg0, Throwable arg1) {
+ super(arg0, arg1);
+ }
+}
diff --git a/application/src/main/java/cytoscape/plugin/ManagerUtil.java b/application/src/main/java/cytoscape/plugin/ManagerUtil.java
new file mode 100644
index 0000000..a602e98
--- /dev/null
+++ b/application/src/main/java/cytoscape/plugin/ManagerUtil.java
@@ -0,0 +1,193 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+package cytoscape.plugin;
+
+import java.util.List;
+import java.util.ArrayList;
+import java.util.Map;
+import java.util.Collections;
+import java.util.Comparator;
+import cytoscape.plugin.PluginStatus;
+
+/**
+ *
+ */
+public class ManagerUtil {
+ // get the list sorted the way we want to display it, I'd like to do these
+ // in one method somehow
+ // where you just give it the PluginInfo method to sort by. I'm sure there's
+ // a way, I just don't know it yet
+ /**
+ * DOCUMENT ME!
+ *
+ * @param Plugins
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static Map<String, List<DownloadableInfo>> sortByCategory(
+ List<DownloadableInfo> Plugins) {
+ Map<String, List<DownloadableInfo>> Categories = new java.util.HashMap<String, List<DownloadableInfo>>();
+
+ for (DownloadableInfo Current : Plugins) {
+ if (Categories.containsKey(Current.getCategory())) {
+ Categories.get(Current.getCategory()).add(Current);
+ } else {
+ List<DownloadableInfo> List = new java.util.ArrayList<DownloadableInfo>();
+ List.add(Current);
+ Collections.sort(List, NAME_ORDER);
+ Categories.put(Current.getCategory(), List);
+ }
+ }
+
+ return Categories;
+ }
+
+ // cheap and hacky I know....
+ public static Map<String, List<PluginInfo>> sortByClass(
+ List<PluginInfo> Plugins) {
+ Map<String, List<PluginInfo>> Classes = new java.util.HashMap<String, List<PluginInfo>>();
+
+ for (PluginInfo Current : Plugins) {
+ if (Classes.containsKey(Current.getPluginClassName())) {
+ Classes.get(Current.getPluginClassName()).add(Current);
+ } else {
+ List<PluginInfo> List = new java.util.ArrayList<PluginInfo>();
+ List.add(Current);
+ Classes.put(Current.getPluginClassName(), List);
+ }
+ }
+ return Classes;
+ }
+
+ public static Map<String, List<PluginInfo>> sortByID(
+ List<PluginInfo> Plugins) {
+ Map<String, List<PluginInfo>> Ids = new java.util.HashMap<String, List<PluginInfo>>();
+
+ for (PluginInfo Current : Plugins) {
+ if (Ids.containsKey(Current.getID())) {
+ Ids.get(Current.getID()).add(Current);
+ } else {
+ List<PluginInfo> List = new java.util.ArrayList<PluginInfo>();
+ List.add(Current);
+ Ids.put(Current.getID(), List);
+ }
+ }
+ return Ids;
+ }
+
+ /**
+ * Returns a list of available plugins minus any currently installed
+ *
+ * @param Current
+ * @param Available
+ */
+ public static List<DownloadableInfo> getUnique(
+ List<DownloadableInfo> Current, List<DownloadableInfo> Available) {
+ java.util.Set<DownloadableInfo> CurrentSet = new java.util.HashSet<DownloadableInfo>(Current);
+
+ List<DownloadableInfo> UniqueAvail = new java.util.ArrayList<DownloadableInfo>(
+ Available);
+
+ if (Current == null) {
+ return Available;
+ }
+
+ for (DownloadableInfo infoAvail : Available) {
+ for (DownloadableInfo infoCur : Current) {
+ if (!PluginManager.getPluginManager().usingWebstartManager()) {
+ if (infoCur.getType().equals(infoAvail.getType()) && infoCur.equalsDifferentObjectVersion(infoAvail)) {
+ UniqueAvail.remove(infoAvail);
+ }
+ } else { // in webstart
+ if ( infoCur.equalsDifferentObjectVersion(infoAvail) ||
+ infoCur.getName().equals(infoAvail.getName()) ) {
+ infoAvail.setDescription( infoCur.getDescription() +
+ "<p><font color='red'><i><b>Webstart Warning:</b><br>This plugin may be the same as a plugin loaded with the webstart bundle '" +
+ infoCur.toString() + "' </i></font>");
+ }
+
+ }
+
+ }
+ }
+ return UniqueAvail;
+ }
+
+ /**
+ * Takes a Class object for a CytoscapePlugin and returns the DownloadableInfo
+ * object associated
+ *
+ * @param pluginClass
+ * @return DownloadableInfo object
+ */
+ public static DownloadableInfo getInfoObject(Class pluginClass) {
+ PluginManager mgr = PluginManager.getPluginManager();
+
+ List<DownloadableInfo> Downloadables = mgr.getDownloadables(PluginStatus.CURRENT);
+
+ for (DownloadableInfo Current : Downloadables) {
+
+ if (Current.getType().equals(DownloadableType.THEME)) {
+ ThemeInfo t = (ThemeInfo) Current;
+ for (PluginInfo p: t.getPlugins()) {
+ if (p.getPluginClassName().equals(pluginClass.getName()))
+ return t; // return the theme that contains the plugin
+ }
+ } else {
+ PluginInfo p = (PluginInfo) Current;
+ if (p.getPluginClassName().equals(pluginClass.getName()))
+ return p;
+ }
+ }
+ return null;
+ }
+
+ public static List sort(List toSort) {
+
+ return null;
+ }
+
+ // this doesn't appear to work as I would expect
+ private static final Comparator<DownloadableInfo> NAME_ORDER = new Comparator<DownloadableInfo>() {
+ public int compare(DownloadableInfo p1, DownloadableInfo p2) {
+ int nameCmp = p2.getName().toLowerCase().compareTo(
+ p1.getName().toLowerCase());
+ return nameCmp;
+ }
+ };
+
+}
diff --git a/application/src/main/java/cytoscape/plugin/NotAPluginException.java b/application/src/main/java/cytoscape/plugin/NotAPluginException.java
new file mode 100644
index 0000000..9ab59a4
--- /dev/null
+++ b/application/src/main/java/cytoscape/plugin/NotAPluginException.java
@@ -0,0 +1,52 @@
+/*
+ File: NotAPluginException.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.plugin;
+
+
+/**
+ * Thrown to indicate that a class cannot be used as a plugin
+ * becuase it does not extend CytoscapePlugin.
+ */
+public class NotAPluginException extends PluginException {
+ /**
+ * constructor.
+ * @param msg
+ */
+ public NotAPluginException(String msg) {
+ super(msg);
+ }
+}
diff --git a/application/src/main/java/cytoscape/plugin/PluginException.java b/application/src/main/java/cytoscape/plugin/PluginException.java
new file mode 100644
index 0000000..4a594e1
--- /dev/null
+++ b/application/src/main/java/cytoscape/plugin/PluginException.java
@@ -0,0 +1,40 @@
+/**
+ *
+ */
+package cytoscape.plugin;
+
+/**
+ * @author skillcoy
+ *
+ */
+public class PluginException extends Exception {
+
+ /**
+ * For all plugin exceptions
+ */
+ public PluginException() {
+ }
+
+ /**
+ * @param arg0
+ */
+ public PluginException(String arg0) {
+ super(arg0);
+ }
+
+ /**
+ * @param arg0
+ */
+ public PluginException(Throwable arg0) {
+ super(arg0);
+ }
+
+ /**
+ * @param arg0
+ * @param arg1
+ */
+ public PluginException(String arg0, Throwable arg1) {
+ super(arg0, arg1);
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/plugin/PluginFileReader.java b/application/src/main/java/cytoscape/plugin/PluginFileReader.java
new file mode 100644
index 0000000..0177971
--- /dev/null
+++ b/application/src/main/java/cytoscape/plugin/PluginFileReader.java
@@ -0,0 +1,407 @@
+/**
+ *
+ */
+package cytoscape.plugin;
+
+import org.jdom.Document;
+import org.jdom.Element;
+import org.jdom.JDOMException;
+
+import org.jdom.input.SAXBuilder;
+
+import cytoscape.util.URLUtil;
+import cytoscape.logger.CyLogger;
+
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+
+import java.net.URL;
+
+import java.io.InputStream;
+
+/**
+ * @author skillcoy
+ *
+ */
+public class PluginFileReader {
+ private static CyLogger logger = CyLogger.getLogger(PluginFileReader.class);
+
+ private Document document;
+
+ private String downloadUrl;
+
+ /**
+ * Creates a new PluginFileReader object.
+ *
+ * @param Url
+ * DOCUMENT ME!
+ *
+ */
+ protected PluginFileReader(String Url) throws java.io.IOException,
+ JDOMException {
+ downloadUrl = Url;
+
+ InputStream is = null;
+
+ try {
+ URL dlUrl = new URL(downloadUrl);
+ is = URLUtil.getInputStream(dlUrl);
+ // would be nice to validate later
+ SAXBuilder Builder = new SAXBuilder(false);
+ document = Builder.build(is, dlUrl.toString());
+ }
+ finally {
+ if (is != null) {
+ is.close();
+ }
+ }
+
+ // don't use this xsd it's no longer valid
+ // InputStream is = URLUtil.getInputStream( new URL(downloadUrl) );
+ // BufferedReader xsdReader = new BufferedReader( new
+ // InputStreamReader(PluginFileReader.class.getResourceAsStream("plugins.xsd"))
+ // );
+ // String line = null;
+ // String Xsd = "";
+ // while ( (line = xsdReader.readLine()) != null)
+ // Xsd += line;
+ //
+ // // validate
+ // SAXBuilder Builder = new
+ // SAXBuilder("org.apache.xerces.parsers.SAXParser", true);
+ // Builder.setFeature("http://apache.org/xml/features/validation/schema",
+ // true);
+ // Builder.setProperty(
+ // "http://apache.org/xml/properties/schema"
+ // + "/external-noNamespaceSchemaLocation",
+ // Xsd );
+ // document = Builder.build(is);
+
+ }
+
+ /**
+ * @return The global project name given by the xml document. NOT CURRENTLY
+ * USED
+ */
+ protected String getProjectName() {
+ return document.getRootElement().getChild(nameTag).getTextTrim();
+ }
+
+ /**
+ * @return The global project description given by the xml document. NOT
+ * CURRENTLY USED
+ */
+ protected String getProjectDescription() {
+ return document.getRootElement().getChild(descTag).getTextTrim();
+ }
+
+ /**
+ * @return The global project url given by the xml document. NOT CURRENTLY
+ * USED
+ */
+ protected String getProjectUrl() {
+ return document.getRootElement().getChild(urlTag).getTextTrim();
+ }
+
+ /**
+ * Retrieves the full list of all downloadable objects in the xml file.
+ *
+ * @return
+ */
+ protected List<DownloadableInfo> getDownloadables() {
+ List<DownloadableInfo> downloadableObjs = new ArrayList<DownloadableInfo>();
+ downloadableObjs.addAll(getPlugins());
+ downloadableObjs.addAll(getThemes());
+ return downloadableObjs;
+ }
+
+ /**
+ * Use getDownloadables() Gets the ThemeInfo objects as set up in the xml
+ * document.
+ *
+ * @return
+ */
+ protected List<ThemeInfo> getThemes() {
+ List<ThemeInfo> Themes = new ArrayList<ThemeInfo>();
+
+ Element ThemeList = document.getRootElement().getChild(
+ PluginXml.THEME_LIST.getTag());
+
+ if (ThemeList != null) {
+ logger.debug("Theme list from xml: " + ThemeList.getChildren().size());
+ Iterator<Element> themeI = ThemeList.getChildren(
+ PluginXml.THEME.getTag()).iterator();
+
+ while (themeI.hasNext()) {
+ Element CurrentTheme = themeI.next();
+ ThemeInfo Info = createThemeObject(CurrentTheme);
+ if (Info == null)
+ continue;
+ Themes.add(Info);
+ }
+ }
+ return Themes;
+ }
+
+ /**
+ * Use getDownloadables() This gets the PluginInfo objects as
+ * set up in the xml document.
+ *
+ * @return The list of PluginInfo objects specified by the xml document.
+ */
+ protected List<PluginInfo> getPlugins() {
+ List<PluginInfo> Plugins = new ArrayList<PluginInfo>();
+
+ Element PluginList = document.getRootElement().getChild(pluginListTag);
+ if (PluginList != null) {
+ Iterator<Element> pluginI = PluginList.getChildren(pluginTag)
+ .iterator();
+
+ while (pluginI.hasNext()) {
+ Element CurrentPlugin = pluginI.next();
+ PluginInfo Info = createPluginObject(CurrentPlugin);
+ if (Info == null)
+ continue;
+ Plugins.add(Info);
+ }
+ }
+ return Plugins;
+ }
+
+ protected ThemeInfo createThemeObject(Element CurrentTheme) {
+ ThemeInfo Info = (ThemeInfo) this.createBasicInfoObject(CurrentTheme,
+ DownloadableType.THEME);
+ logger.debug("Creating Theme: " + Info.getName() + " " + Info.getID());
+ if (Info != null) {
+ /*
+ * add plugins this is plugins from the current download location
+ * only (others not yet supported)
+ */
+ java.util.Map<String, List<PluginInfo>> Plugins = ManagerUtil
+ .sortByID(getPlugins());
+
+ Iterator<Element> themePluginI = CurrentTheme.getChild(
+ PluginXml.PLUGIN_LIST.getTag()).getChildren(
+ PluginXml.PLUGIN.getTag()).iterator();
+
+ // two ways to specify a plugin in a theme
+ while (themePluginI.hasNext()) {
+ Element ThemePlugin = themePluginI.next();
+
+ if (ThemePlugin.getChildren().size() == 2) {
+ logger.debug("Theme plugins defined shorthand");
+ for (PluginInfo pluginInfo : Plugins.get(ThemePlugin.getChildTextTrim(PluginXml.UNIQUE_ID.getTag()))) {
+ String version = Double.valueOf(ThemePlugin.getChildTextTrim(PluginXml.PLUGIN_VERSION.getTag())).toString();
+ if (pluginInfo.getObjectVersion().equals(version)) {
+ pluginInfo.setParent(Info);
+ Info.addPlugin(pluginInfo);
+ }
+ }
+ } else {
+ PluginInfo pluginInfo = this.createPluginObject(ThemePlugin);
+ pluginInfo.setParent(Info);
+ Info.addPlugin(pluginInfo);
+ }
+ }
+ }
+ return Info;
+ }
+
+ private DownloadableInfo createBasicInfoObject(Element E,
+ DownloadableType Type) {
+
+ DownloadableInfo Info = null;
+ String Id = E.getChildTextTrim(uniqueID);
+ switch (Type) { // TODO sort this type stuff out (no more switches)
+ case PLUGIN:
+ Info = new PluginInfo(Id);
+ Info.setObjectUrl(E.getChildTextTrim(urlTag));
+ break;
+ case THEME:
+ Info = new ThemeInfo(Id);
+ break;
+ }
+
+ Info.setName(E.getChildTextTrim(nameTag));
+ Info.setDescription(E.getChildTextTrim(descTag));
+ Info.setDownloadableURL(downloadUrl);
+
+ // category
+ if (Info.getCategory().equals(Category.NONE.getCategoryText())) {
+ if (E.getChild(categoryTag) != null) {
+ Info.setCategory(E.getChildTextTrim(categoryTag));
+ } else {
+ Info.setCategory(Category.NONE);
+ }
+ }
+ // object version
+ Info = addVersion(Info, E, Type);
+
+
+ // cytoscape version
+ Iterator<Element> versionI = E.getChild(
+ PluginXml.CYTOSCAPE_VERSIONS.getTag()).getChildren(
+ PluginXml.VERSION.getTag()).iterator();
+ while (versionI.hasNext()) {
+ Element Version = versionI.next();
+ Info.addCytoscapeVersion(Version.getTextTrim());
+ }
+ return Info;
+ }
+
+ /**
+ * Creates the PluginInfo object from the xml <plugin> element. This could
+ * be useful to the PluginTracker.
+ *
+ * @param CurrentPlugin
+ * Element
+ * @return PluginInfo object
+ */
+ protected PluginInfo createPluginObject(Element CurrentPlugin) {
+ PluginInfo Info = (PluginInfo) createBasicInfoObject(CurrentPlugin,
+ DownloadableType.PLUGIN);
+ if (Info != null) {
+ Info.setProjectUrl(CurrentPlugin.getChildTextTrim(projUrlTag));
+ Info.setInstallLocation(CurrentPlugin.getChildTextTrim(installLocTag));
+
+ // file type
+ PluginInfo.FileType Type = getType(CurrentPlugin);
+ if (Type == null) { // unknown type error and move on
+ logger.warn("Unknown plugin file type '" + Type
+ + " skipping plugin " + Info.getName());
+ return null;
+ } else {
+ Info.setFiletype(Type);
+ }
+ // authors
+ Info = addAuthors(Info, CurrentPlugin);
+ // license
+ Info = addLicense(Info, CurrentPlugin);
+ }
+ return Info;
+ }
+
+ protected DownloadableInfo addVersion(DownloadableInfo obj, Element e,
+ DownloadableType Type) {
+ String Version = null;
+ switch (Type) {
+ case PLUGIN:
+ Version = e.getChildTextTrim(pluginVersTag);
+ break;
+ case THEME:
+ Version = e.getChildTextTrim(PluginXml.THEME_VERSION.getTag());
+ break;
+ }
+
+ try {
+ obj.setObjectVersion(Version);
+ return obj;
+ } catch (NumberFormatException ie) { // is there a better way to let
+ // people know it's a bad
+ // version? This will just skip
+ // past bad version numbers
+ // ie.printStackTrace();
+ logger.warn("Version number format error: "+Version);
+ return null;
+ }
+ }
+
+ // get license text, add to info object
+ protected static PluginInfo addLicense(PluginInfo obj, Element Plugin) {
+ Element License = Plugin.getChild(licenseTag);
+
+ if (License != null) {
+ boolean RequireAlways = false;
+ if (License.getChild("license_required") != null) {
+ RequireAlways = true;
+ }
+ if (License.getChild(licenseText) != null) {
+ obj.setLicense(License.getChildTextTrim(licenseText),
+ RequireAlways);
+ } else if (License.getChild(urlTag) != null) {
+ try {
+ String LicenseText = URLUtil.download(new URL(License
+ .getChildTextTrim(urlTag)));
+ obj.setLicense(LicenseText, RequireAlways);
+ } catch (Exception E) {
+ logger.warn("Unable to add license: "+E.toString(), E);
+ }
+ }
+ }
+ return obj;
+ }
+
+ // get the authors, add to info object
+ private PluginInfo addAuthors(PluginInfo obj, Element Plugin) {
+ if (Plugin.getChild(authorListTag) != null) {
+ List<Element> Authors = Plugin.getChild(authorListTag).getChildren(authorTag);
+ //Iterator<Element> authI = Plugin.getChild(authorListTag).getChildren(authorTag).iterator();
+ for (Element CurrentAuthor: Authors) {
+ //while (authI.hasNext()) {
+ //Element CurrentAuthor = authI.next();
+ obj.addAuthor(CurrentAuthor.getChildTextTrim(nameTag),
+ CurrentAuthor.getChildTextTrim(instTag));
+ }
+ }
+ return obj;
+ }
+
+ // get the type from the plugin element
+ private PluginInfo.FileType getType(Element Plugin) {
+ PluginInfo.FileType Type = null;
+
+ String GivenType = Plugin.getChild(fileType).getTextTrim();
+
+ if (GivenType.equalsIgnoreCase(PluginInfo.FileType.JAR.toString())) {
+ Type = PluginInfo.FileType.JAR;
+ } else if (GivenType.equalsIgnoreCase(PluginInfo.FileType.ZIP
+ .toString())) {
+ Type = PluginInfo.FileType.ZIP;
+ }
+ return Type;
+ }
+
+ // XML Tags PluginTracker uses the same tags
+ private static String nameTag = PluginXml.NAME.getTag();
+
+ private static String descTag = PluginXml.DESCRIPTION.getTag();
+
+ private static String classTag = PluginXml.CLASS_NAME.getTag();
+
+ private static String pluginVersTag = PluginXml.PLUGIN_VERSION.getTag();
+
+ private static String cytoVersTag = "cytoscapeVersion";
+
+ private static String urlTag = PluginXml.URL.getTag();
+
+ private static String projUrlTag = PluginXml.PROJECT_URL.getTag();
+
+ private static String downloadUrlTag = PluginXml.DOWNLOAD_URL.getTag();
+
+ private static String categoryTag = PluginXml.CATEGORY.getTag();
+
+ private static String fileListTag = PluginXml.FILE_LIST.getTag();
+
+ private static String fileTag = PluginXml.FILE.getTag();
+
+ private static String pluginListTag = PluginXml.PLUGIN_LIST.getTag();
+
+ private static String pluginTag = PluginXml.PLUGIN.getTag();
+
+ private static String authorListTag = PluginXml.AUTHOR_LIST.getTag();
+
+ private static String authorTag = PluginXml.AUTHOR.getTag();
+
+ private static String instTag = PluginXml.INSTITUTION.getTag();
+
+ private static String fileType = PluginXml.FILE_TYPE.getTag();
+
+ private static String uniqueID = PluginXml.UNIQUE_ID.getTag();
+
+ private static String licenseTag = PluginXml.LICENSE.getTag();
+
+ private static String licenseText = PluginXml.LICENSE_TEXT.getTag();
+
+ private static String installLocTag = PluginXml.INSTALL_LOCATION.getTag();
+}
diff --git a/application/src/main/java/cytoscape/plugin/PluginInfo.java b/application/src/main/java/cytoscape/plugin/PluginInfo.java
new file mode 100644
index 0000000..9b29a79
--- /dev/null
+++ b/application/src/main/java/cytoscape/plugin/PluginInfo.java
@@ -0,0 +1,327 @@
+/*
+ File: PluginInfo.java
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.plugin;
+
+import cytoscape.util.URLUtil;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import java.net.URL;
+
+/**
+ * Object describes a plugin
+ */
+public class PluginInfo extends DownloadableInfo {
+ /**
+ * Jar and Zip files currently supported
+ *
+ * @author skillcoy
+ *
+ */
+ public enum FileType {
+ JAR("jar"), ZIP("zip");
+
+ private String typeText;
+
+ private FileType(String type) {
+ typeText = type;
+ }
+
+ public String toString() {
+ return typeText;
+ }
+ }
+
+ private FileType fileType;
+
+ private String pluginClassName;
+
+ private List<AuthorInfo> authors;
+
+ private String projectUrl;
+
+ private List<String> pluginFiles;
+
+ protected String enclosingJar;
+
+ protected String installLocation;
+
+
+ /**
+ * See {@link DownloadableInfo#DownloadableInfo()}
+ *
+ * Initializes a PluginInfo object with the following defaults:
+ * setName("Unknown"); setDescription("No description");
+ * setObjectVersion("0.1"); setCytoscapeVersion(
+ * cytoscape.cytoscapeVersion.version ); setCategory("Uncategorized");
+ *
+ */
+ public PluginInfo() {
+ init();
+ }
+
+ /**
+ * See {@link DownloadableInfo#DownloadableInfo(String)}
+ *
+ * @param UniqueID
+ * Additionally this sets the unique identifier that will be used
+ * to find a new version of the plugin at the given download url.
+ */
+ public PluginInfo(String UniqueID) {
+ super(UniqueID);
+ init();
+ }
+
+ public PluginInfo(String UniqueID, String Name) {
+ super(UniqueID);
+ init();
+ this.setName(Name);
+ }
+
+ /**
+ * See {@link DownloadableInfo#DownloadableInfo(String)}
+ *
+ * @param UniqueID
+ * @param ParentObj
+ * Additionally this sets the unique identifier that will be used
+ * to find a new version of the plugin at the given download url and
+ * sets the parent downloadable object.
+ */
+ public PluginInfo(String UniqueID, DownloadableInfo ParentObj) {
+ super(UniqueID, ParentObj);
+ init();
+ }
+
+ /*
+ * Sets all the fields that are required to a default value in case it is
+ * not called
+ */
+ private void init() {
+ pluginFiles = new ArrayList<String>();
+ authors = new ArrayList<AuthorInfo>();
+ setName("Unknown");
+ setDescription("No description");
+ setObjectVersion("0.1");
+ setCategory(Category.NONE);
+ setPluginClassName("");
+ }
+
+ /**
+ * Sets the plugin class name. Used for tracking plugins.
+ *
+ * @param className
+ */
+ public void setPluginClassName(String className) {
+ pluginClassName = className;
+ }
+
+
+ /**
+ * Sets the url of a site describing this plugin project
+ * @param url
+ */
+ public void setProjectUrl(String url) {
+ projectUrl = url;
+ }
+
+ /**
+ * Jar or Zip are currently supported. Use PluginInfo.JAR or PluginInfo.ZIP.
+ * This will only be set by the PluginManager generally and can only be set once
+ * as an object's file type will not change.
+ * @param type
+ */
+ protected void setFiletype(FileType type) {
+ if (fileType == null)
+ fileType = type;
+ }
+
+ /**
+ * Sets a list of files (prefer full paths) installed with this plugin.
+ * Includes the jar file.
+ * @param list
+ */
+ protected void setFileList(List<String> list) {
+ pluginFiles = list;
+ }
+
+ /**
+ * Adds a file to the list of installed files.
+ *
+ * @param fileName
+ */
+ protected void addFileName(String fileName) {
+ if (!pluginFiles.contains(fileName))
+ pluginFiles.add(fileName);
+ }
+
+ /**
+ * Adds an author to the list of authors.
+ *
+ * @param authorName
+ * @param institution
+ */
+ public void addAuthor(String authorName, String institution) {
+ authors.add(new AuthorInfo(authorName, institution));
+ }
+
+ /**
+ * Clears author list.
+ */
+ public void clearAuthorList() {
+ authors.clear();
+ }
+
+
+ /**
+ * This is meant to only get set by the PluginManager. It can only
+ * be set once as the install location can't move.
+ *
+ * @param Loc
+ */
+ protected void setInstallLocation(String Loc) {
+ if (installLocation == null)
+ installLocation = Loc;
+ }
+
+ /* GET */
+ /**
+ * Gets the full install path for this plugin. Should look like
+ * <HOME_DIR>/.cytoscape/<cytoscape_version>/plugins/<pluginName-pluginVersion>
+ */
+ public java.io.File getPluginDirectory() {
+ java.io.File PluginDir = new java.io.File(
+ PluginManager.getPluginManager().getPluginManageDirectory(),
+ this.getName()+"-"+this.getObjectVersion());
+ return PluginDir;
+ }
+
+ /**
+ * @return String of the installation location for the plugin and all of it's files.
+ * Generally this is .cytoscape/[cytoscape version]/plugins/PluginName-version
+ */
+ public String getInstallLocation() {
+ return installLocation;
+ }
+
+ /**
+ * @return FileType of file type for plugin. PluginInfo.JAR or
+ * PluginInfo.ZIP
+ */
+ public FileType getFileType() {
+ return fileType;
+ }
+
+ /**
+ * @return Java class name
+ */
+ public String getPluginClassName() {
+ return pluginClassName;
+ }
+
+ /**
+ * @return List of authors.
+ */
+ public List<AuthorInfo> getAuthors() {
+ return authors;
+ }
+
+ /**
+ *
+ * @return Url that points to a site describing this plugin project
+ */
+ public String getProjectUrl() {
+ return projectUrl;
+ }
+
+ public Installable getInstallable() {
+ return new InstallablePlugin(this);
+ }
+
+ /**
+ * {@link DownloadableInfo#getType()}
+ */
+ public DownloadableType getType() {
+ return DownloadableType.PLUGIN;
+ }
+
+ /**
+ * @return List of files installed with this plugin (includes plugin jar
+ * file).
+ */
+ public List<String> getFileList() {
+ return pluginFiles;
+ }
+
+ public String htmlOutput() {
+
+ String Html = this.basicHtmlOutput();
+ Html += "<b>Released By:</b><br><ul>";
+ for (AuthorInfo ai : getAuthors()) {
+ Html += "<li>" + ai.getAuthor() + ", " + ai.getInstitution()
+ + "<br>";
+ }
+ Html += "</ul>";
+
+ Html += "</font></body></html>";
+ return Html;
+ }
+
+ /**
+ * Describes an author for a given plugin.
+ *
+ */
+ public class AuthorInfo {
+ private String authorName;
+
+ private String institutionName;
+
+ public AuthorInfo(String Name, String Institution) {
+ authorName = Name;
+ institutionName = Institution;
+ }
+
+ public String getAuthor() {
+ return authorName;
+ }
+
+ public String getInstitution() {
+ return institutionName;
+ }
+ }
+
+
+}
diff --git a/application/src/main/java/cytoscape/plugin/PluginInquireAction.java b/application/src/main/java/cytoscape/plugin/PluginInquireAction.java
new file mode 100644
index 0000000..a623e30
--- /dev/null
+++ b/application/src/main/java/cytoscape/plugin/PluginInquireAction.java
@@ -0,0 +1,77 @@
+/**
+ *
+ */
+package cytoscape.plugin;
+
+import java.util.List;
+
+import cytoscape.util.IndeterminateProgressBar;
+
+/**
+ * Object should be implmeneted by anyone using the {@link PluginManager#inquireThread(String, PluginInquireAction)}
+ * method to get plugins from a given site.
+ */
+public abstract class PluginInquireAction {
+
+ private Exception threadE;
+ private java.io.IOException ioe;
+ private org.jdom.JDOMException jde;
+
+
+ public boolean isExceptionThrown() {
+ if (threadE != null || ioe != null || jde != null) return true;
+ else return false;
+ }
+
+
+ public Exception getException() {
+ return threadE;
+ }
+
+ public org.jdom.JDOMException getJDOMException() {
+ return jde;
+ }
+
+
+ public java.io.IOException getIOException() {
+ return ioe;
+ }
+
+ /**
+ * If the thread has thrown an exception while running {@link PluginManager#inquireThread(String, PluginInquireAction)}
+ * it will be set here.
+ */
+ protected void setExceptionThrown(Exception e) {
+
+ if (java.io.IOException.class.isAssignableFrom(e.getClass())) {
+ ioe = (java.io.IOException) e;
+ } else if (org.jdom.JDOMException.class.isAssignableFrom(e.getClass())) {
+ jde = (org.jdom.JDOMException) e;
+ } else {
+ threadE = e;
+ }
+ }
+
+
+ /**
+ *
+ * @return Message to display in progress bar
+ */
+ public abstract String getProgressBarMessage();
+
+ /**
+ *
+ * @return True to display the IndeterminateProgressBar while running
+ * {@link PluginManager#inquireThread(String, PluginInquireAction)}
+ */
+
+
+ /**
+ * Does some work on the list that results from a successful inquire query.
+ * @param
+ * @throws Exception
+ */
+ public abstract void inquireAction(List<DownloadableInfo> results);
+
+
+}
diff --git a/application/src/main/java/cytoscape/plugin/PluginManager.java b/application/src/main/java/cytoscape/plugin/PluginManager.java
new file mode 100644
index 0000000..fed9cb1
--- /dev/null
+++ b/application/src/main/java/cytoscape/plugin/PluginManager.java
@@ -0,0 +1,1054 @@
+/*
+ File: PluginManager.java
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+package cytoscape.plugin;
+
+import cytoscape.*;
+
+import cytoscape.util.FileUtil;
+import cytoscape.util.ZipUtil;
+import cytoscape.task.TaskMonitor;
+import cytoscape.logger.CyLogger;
+
+import java.io.File;
+import java.io.InputStream;
+import java.io.IOException;
+import java.lang.reflect.InvocationTargetException;
+import java.lang.reflect.Method;
+import java.net.JarURLConnection;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.net.URLClassLoader;
+
+import java.util.Enumeration;
+import java.util.HashSet;
+import java.util.List;
+import java.util.ArrayList; // import java.util.Map;
+import java.util.HashMap;
+import java.util.Set;
+
+import java.util.jar.JarFile;
+import java.util.jar.JarInputStream;
+import java.util.jar.Manifest;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipFile;
+
+/**
+ * @author skillcoy
+ *
+ */
+public class PluginManager {
+ protected PluginTracker pluginTracker;
+
+ private boolean duplicateLoadError;
+
+ private List<String> duplicateClasses;
+
+ private static PluginManager pluginMgr = null;
+
+ private static File tempDir;
+
+ private static List<java.net.URL> pluginURLs;
+
+ private static List<String> resourcePlugins;
+
+ private static Set<String> loadedPlugins;
+
+ private static Set<Throwable> loadingErrors;
+
+ private static HashMap<String, PluginInfo> initializedPlugins;
+
+ private static URLClassLoader classLoader;
+
+ private static boolean usingWebstart;
+
+ private static String cyVersion = new CytoscapeVersion().getMajorVersion();
+
+ private static CyLogger logger = CyLogger.getLogger(PluginManager.class);
+
+ /**
+ /**
+ * Returns list of loading exceptions.
+ */
+ public List<Throwable> getLoadingErrors() {
+ if (pluginTracker.hasCorruptedElements()) {
+ loadingErrors
+ .add(new TrackerException(
+ "Corrupted elements removed from the Plugin Tracker. Some plugins may need to be reinstalled."));
+ }
+ return new ArrayList<Throwable>(loadingErrors);
+ }
+
+ /**
+ * Clears the loading error list. Ideally this should be called after
+ * checking the list each time.
+ */
+ public void clearErrorList() {
+ pluginTracker.clearCorruptedElements();
+ loadingErrors.clear();
+ }
+
+ /**
+ * @return URLClassLoader used to load plugins at startup.
+ */
+ public static URLClassLoader getClassLoader() {
+ return classLoader;
+ }
+
+ /**
+ * @return Set<String> of resource plugins from startup
+ */
+ public static List<String> getResourcePlugins() {
+ return resourcePlugins;
+ }
+
+ /**
+ * @return Set<URL> of plugin URL's from startup
+ */
+ public static List<java.net.URL> getPluginURLs() {
+ return pluginURLs;
+ }
+
+ /**
+ * Returns true/false based on the System property. This is what is checked
+ * to find out if install/delete/download methods are permitted.
+ *
+ * @return true if Cytoscape is in webstart
+ */
+ public static boolean usingWebstartManager() {
+ return usingWebstart;
+ }
+
+ /**
+ * Deletes everything under the webstart install directory. Nothing in here
+ * should stick around.
+ *
+ * @return True if all files deleted successfully
+ */
+ protected boolean removeWebstartInstalls() {
+ if (tempDir == null) {
+ logger.warn("Directory not yet set up, can't delete");
+ return false;
+ }
+ return recursiveDeleteFiles(tempDir.getParentFile());
+ }
+
+ /**
+ * Get the PluginManager object.
+ *
+ * @return PluginManager
+ */
+ public static PluginManager getPluginManager() {
+ if (pluginMgr == null) {
+ pluginMgr = new PluginManager(null);
+ }
+ return pluginMgr;
+ }
+
+ /**
+ * @param loc
+ * Location of plugin download/install directory. If this method
+ * is not called the default is .cytoscape/[cytoscape
+ * version]/plugins
+ */
+ public static void setPluginManageDirectory(String loc) {
+ tempDir = new File(loc);
+ if (!tempDir.getAbsolutePath().contains(cyVersion)) {
+ tempDir = new File(tempDir, cyVersion);
+ }
+ }
+
+ /**
+ *
+ * @return The current version directory under .cytoscape that includes the
+ * plugins/ directory.
+ *
+ * Ex. /<user dir>/.cytoscape/2.6/plugins
+ */
+ public File getPluginManageDirectory() {
+ return tempDir;
+ }
+
+ /*
+ * Just checks the system property 'javawebstart.version' which is only set
+ * when running as a webstart.
+ */
+ private static void setWebstart() {
+ if (System.getProperty("javawebstart.version") != null
+ && System.getProperty("javawebstart.version").length() > 0) {
+ logger.info("USING WEBSTART: "
+ + System.getProperty("javawebstart.version"));
+ usingWebstart = true;
+ } else {
+ usingWebstart = false;
+ }
+ }
+
+ /**
+ * This should ONLY be used by tests!!
+ *
+ * @param Tracker
+ * @return
+ */
+ protected static PluginManager getPluginManager(PluginTracker Tracker) {
+ if (pluginMgr == null) {
+ pluginMgr = new PluginManager(Tracker);
+ }
+ return pluginMgr;
+ }
+
+ /**
+ * This is used in testing to isolate each test case. DO NOT USE THIS IN
+ * CYTOSCAPE RUNTIME CODE
+ */
+ protected void resetManager() {
+ if (pluginTracker != null && pluginMgr != null) {
+ pluginTracker.delete();
+ pluginTracker = null;
+ recursiveDeleteFiles(tempDir);
+ pluginMgr = null;
+ }
+ }
+
+ // create plugin manager
+ private PluginManager(PluginTracker Tracker) {
+ // XXX is this needed anymore?
+ loadingErrors = new HashSet<Throwable>();
+
+ setWebstart();
+ String trackerFileName = "track_plugins.xml";
+
+ if (tempDir == null) {
+ if (usingWebstartManager()) {
+ tempDir = new File(CytoscapeInit.getConfigDirectory(),
+ "webstart" + File.separator
+ + (new CytoscapeVersion()).getMajorVersion()
+ + File.separator + "plugins");
+ removeWebstartInstalls();
+ trackerFileName = "track_webstart_plugins.xml";
+ } else {
+ tempDir = new File(CytoscapeInit.getConfigVersionDirectory(), "plugins");
+ }
+ } else if (!tempDir.getAbsolutePath().endsWith("/plugins")) {
+ tempDir = new File(tempDir, "plugins");
+ }
+
+ if (!tempDir.exists()) {
+ logger.info("Creating directories for "
+ + tempDir.getAbsolutePath());
+ if (!tempDir.mkdirs()) {
+ Cytoscape.exit(-1);
+ }
+ }
+
+ if (Tracker != null) {
+ pluginTracker = Tracker;
+ } else {
+ try {
+ pluginTracker = new PluginTracker(tempDir.getParentFile(),
+ trackerFileName);
+ } catch (IOException ioe) {
+ // ioe.printStackTrace();
+ loadingErrors.add(ioe);
+ } catch (TrackerException te) {
+ // te.printStackTrace();
+ loadingErrors.add(te);
+ } finally { // document should be cleaned out by now
+ try {
+ pluginTracker = new PluginTracker(tempDir.getParentFile(),
+ trackerFileName);
+ } catch (Exception e) {
+ logger.warn("Unable to read plugin tracking file", e);
+ // this could go on forever, surely there's a better way!
+ }
+ }
+ }
+ pluginURLs = new ArrayList<java.net.URL>();
+ loadedPlugins = new HashSet<String>();
+ initializedPlugins = new HashMap<String, PluginInfo>();
+ resourcePlugins = new ArrayList<String>();
+ }
+
+ /**
+ * Get a list of downloadable objects by status. CURRENT: currently
+ * installed INSTALL: objects to be installed DELETE: objects to be deleted
+ *
+ * @param Status
+ * @return
+ */
+ public List<DownloadableInfo> getDownloadables(PluginStatus Status) {
+ return pluginTracker.getDownloadableListByStatus(Status);
+ }
+
+ /**
+ * Calls the given url, expects document describing plugins available for
+ * download
+ *
+ * @param Url
+ * @return List of PluginInfo objects
+ */
+ public List<DownloadableInfo> inquire(String Url) throws IOException,
+ org.jdom.JDOMException {
+ List<DownloadableInfo> infoObjs = null;
+ PluginFileReader Reader = new PluginFileReader(Url);
+ infoObjs = Reader.getDownloadables();
+ return infoObjs;
+ }
+
+ /**
+ * Registers a currently installed plugin with tracking object. Only useful
+ * if the plugin was not installed via the install process.
+ *
+ * @param Plugin
+ * @param JarFileName
+ */
+ protected void register(CytoscapePlugin Plugin, JarFile Jar) {
+ logger.info("Registering " + Plugin.toString());
+
+ DownloadableInfo InfoObj = ManagerUtil.getInfoObject(Plugin.getClass());
+ if (InfoObj != null && InfoObj.getType().equals(DownloadableType.THEME)) {
+ this.registerTheme(Plugin, Jar, (ThemeInfo) InfoObj);
+ } else {
+ this.registerPlugin(Plugin, Jar, (PluginInfo) InfoObj, true);
+ }
+ }
+
+ private PluginInfo registerPlugin(CytoscapePlugin Plugin, JarFile Jar,
+ PluginInfo PluginObj, boolean addToTracker) {
+ // try to get it from the file
+ // XXX PROBLEM: what to do about a plugin that attempts to register
+ // itself and is not compatible with the current version?
+ logger.info(" Registering " + Plugin.getClass().getName());
+ try {
+ PluginProperties pp = new PluginProperties(Plugin);
+ PluginObj = pp.fillPluginInfoObject(PluginObj);
+
+ } catch (IOException ioe) {
+ logger.warn("ERROR registering plugin: " + ioe.getMessage(), ioe);
+ logger.warn(Plugin.getClass().getName()
+ + " loaded but not registered, this will not affect the operation of the plugin");
+ } catch (Exception e) {
+ logger.warn("ERROR registering plugin: ", e);
+ } finally {
+ if (PluginObj == null) { // still null, create a default one
+ PluginObj = new PluginInfo();
+ PluginObj.addCytoscapeVersion(cyVersion);
+ PluginObj.setName(Plugin.getClass().getName());
+ PluginObj.setObjectVersion("0.1");
+ }
+
+ PluginObj.setPluginClassName(Plugin.getClass().getName());
+ if (!usingWebstart && Jar != null) {
+ PluginObj.setInstallLocation(Jar.getName());
+ PluginObj.addFileName(Jar.getName());
+ }
+ PluginObj.setFiletype(PluginInfo.FileType.JAR);
+
+ initializedPlugins.put(PluginObj.getPluginClassName(), PluginObj);
+ // TODO This causes a bug where theme plugins essentially get added
+ // to the current list twice
+ logger.info("Track plugin: " + addToTracker);
+ if (addToTracker) {
+ pluginTracker.addDownloadable(PluginObj, PluginStatus.CURRENT);
+ }
+ }
+ return PluginObj;
+ }
+
+ private void registerTheme(CytoscapePlugin Plugin, JarFile Jar,
+ ThemeInfo ThemeObj) {
+ logger.info("--- Registering THEME " + ThemeObj.getName());
+ for (PluginInfo plugin : ThemeObj.getPlugins()) {
+ if (plugin.getPluginClassName().equals(Plugin.getClass().getName())) {
+ logger.info(plugin.getName());
+ PluginInfo updatedPlugin = registerPlugin(Plugin, Jar, plugin,
+ false);
+ ThemeObj.replacePlugin(plugin, updatedPlugin);
+ }
+ }
+ pluginTracker.addDownloadable(ThemeObj, PluginStatus.CURRENT);
+ }
+
+ // TODO would be better to fix how initializedPlugins are tracked...
+ private void cleanCurrentList() {
+ List<DownloadableInfo> CurrentList = getDownloadables(PluginStatus.CURRENT);
+ for (DownloadableInfo info : CurrentList) {
+ if (info.getType().equals(DownloadableType.PLUGIN)) {
+ PluginInfo pInfo = (PluginInfo) info;
+ if (!initializedPlugins.containsKey(pInfo.getPluginClassName())) {
+ pluginTracker.removeDownloadable(info, PluginStatus.CURRENT);
+ }
+ }
+ }
+ }
+
+ /**
+ * Sets all plugins on the "install" list to "current"
+ */
+ public void install() {
+ for (DownloadableInfo info : getDownloadables(PluginStatus.INSTALL)) {
+ install(info);
+ }
+ }
+
+ /**
+ * Change the given downloadable object from "install" to "current" status
+ *
+ * @param obj
+ */
+ public void install(DownloadableInfo obj) {
+ pluginTracker.removeDownloadable(obj, PluginStatus.INSTALL);
+ pluginTracker.addDownloadable(obj, PluginStatus.CURRENT);
+
+ // mark all webstart-installed plugins for deletion
+ if (usingWebstartManager()) {
+ pluginTracker.addDownloadable(obj, PluginStatus.DELETE);
+ }
+ }
+
+ /**
+ * Marks the given object for deletion the next time Cytoscape is restarted.
+ *
+ * @param Obj
+ */
+ public void delete(DownloadableInfo Obj) throws WebstartException {
+ checkWebstart();
+ pluginTracker.addDownloadable(Obj, PluginStatus.DELETE);
+ }
+
+ /**
+ * Takes all objects on the "to-delete" list and deletes them. This can only
+ * occur at start up.
+ *
+ * @throws ManagerException
+ * If all files fail to delete
+ * @throws WebstartException
+ * If this method is called from a webstart instance
+ */
+ public void delete() throws ManagerException {
+ List<DownloadableInfo> toDelete = pluginTracker.getDownloadableListByStatus(
+ PluginStatus.DELETE);
+
+ for (DownloadableInfo infoObj : toDelete) {
+ Installable ins = infoObj.getInstallable();
+
+ try {
+ if (ins.uninstall()) {
+ pluginTracker.removeDownloadable(infoObj, PluginStatus.DELETE);
+ pluginTracker.removeDownloadable(infoObj, PluginStatus.CURRENT);
+ } // TODO um.....XXXX
+ } catch (Exception me) {
+ throw new ManagerException(
+ "Failed to completely delete the following installed components:\n" +
+ infoObj.getName() + " v" + infoObj.getObjectVersion() + "\n", me);
+ }
+ }
+ }
+
+ protected static boolean recursiveDeleteFiles(File file) {
+ if (file.isDirectory())
+ for (File f : file.listFiles())
+ recursiveDeleteFiles(f);
+
+ boolean del = file.delete();
+ // Utterly f*#king retarded, but apparently necessary since sometimes
+ // directories don't realize they're empty...
+ if (!del) {
+ for (int i = 0; i < 1000 && file.exists(); i++) {
+ System.gc();
+ del = file.delete();
+ }
+ }
+
+ return del;
+ }
+
+ private void checkWebstart() throws WebstartException {
+ if (usingWebstart) {
+ throw new WebstartException();
+ }
+ }
+
+ /**
+ * Get list of plugins that would update the given plugin.
+ *
+ * @param Info
+ * @return List<PluginInfo>
+ * @throws ManagerException
+ */
+ public List<DownloadableInfo> findUpdates(DownloadableInfo Info)
+ throws IOException, org.jdom.JDOMException {
+ return Info.getInstallable().findUpdates();
+ }
+
+ /**
+ * Finds the given version of the new object, sets the old object for
+ * deletion and downloads new object to temporary directory
+ *
+ * @param Current
+ * DownloadableInfo object currently installed
+ * @param New
+ * DownloadableInfo object to install
+ * @throws IOException
+ * Fails to download the file.
+ * @throws ManagerException
+ * If the objects don't match or the new one is not a newer
+ * version.
+ */
+ public void update(DownloadableInfo Current, DownloadableInfo New)
+ throws IOException, ManagerException, WebstartException {
+ update(Current, New, null);
+ }
+
+ /**
+ * Finds the given version of the new object, sets the old object for
+ * deletion and downloads new object to temporary directory
+ *
+ * @param Current
+ * PluginInfo object currently installed
+ * @param New
+ * PluginInfo object to install
+ * @param taskMonitor
+ * TaskMonitor for downloads
+ * @throws IOException
+ * Fails to download the file.
+ * @throws ManagerException
+ * If the plugins don't match or the new one is not a newer
+ * version.
+ */
+ public void update(DownloadableInfo currentObj, DownloadableInfo newObj,
+ cytoscape.task.TaskMonitor taskMonitor) throws IOException,
+ ManagerException, WebstartException {
+
+ if (!currentObj.getType().equals(newObj.getType())) {
+ throw new ManagerException(
+ "Cannot update an object of one download type to an object of a different download type");
+ }
+ currentObj.getInstallable().update(newObj, taskMonitor);
+
+ pluginTracker.addDownloadable(currentObj, PluginStatus.DELETE);
+ pluginTracker.addDownloadable(newObj, PluginStatus.INSTALL);
+ }
+
+ /**
+ * Downloads given object to the temporary directory.
+ *
+ * @param Obj
+ * PluginInfo object to be downloaded
+ * @return File downloaded
+ */
+ public DownloadableInfo download(DownloadableInfo Obj) throws IOException,
+ ManagerException {
+ return this.download(Obj, null);
+ }
+
+ /**
+ * Downloads given object to the temporary directory. Uses a task monitor if
+ * available.
+ *
+ * @param Obj
+ * PluginInfo object to be downloaded
+ * @param taskMonitor
+ * TaskMonitor
+ * @param tempDirectory
+ * Download to a different temporary directory. Default is
+ * .cytoscape/plugins/[cytoscape version number]
+ * @return File downloaded
+ */
+ public DownloadableInfo download(DownloadableInfo Obj,
+ TaskMonitor taskMonitor) throws IOException, ManagerException {
+ // run a check for plugins
+ List<DownloadableInfo> CurrentAndInstalled = new ArrayList<DownloadableInfo>();
+ CurrentAndInstalled.addAll(this.getDownloadables(PluginStatus.CURRENT));
+ CurrentAndInstalled.addAll(this.getDownloadables(PluginStatus.INSTALL));
+
+ List<DownloadableInfo> FlattenedList = this.flattenDownloadableList(CurrentAndInstalled);
+
+ for (DownloadableInfo currentlyInstalled : FlattenedList) {
+ DownloadableInfo CurrentlyInstalled = null;
+ if (currentlyInstalled.getParent() != null) {
+ CurrentlyInstalled = currentlyInstalled.getParent();
+ } else {
+ CurrentlyInstalled = currentlyInstalled;
+ }
+
+ if (Obj.equals(currentlyInstalled) || Obj.equalsDifferentObjectVersion(currentlyInstalled)) {
+ throw new ManagerException(Obj.toString() + " cannot be installed, it is already loaded in: " + CurrentlyInstalled.toString());
+ }
+
+ if (Obj.getType().equals(DownloadableType.THEME)) {
+ for (PluginInfo themePlugin: ((ThemeInfo) Obj).getPlugins()) {
+ if (themePlugin.equalsDifferentObjectVersion(currentlyInstalled)) {
+ throw new ManagerException(Obj.toString() + " cannot be installed a plugin contained within the theme is already present: "
+ + CurrentlyInstalled.toString());
+ }
+ }
+ }
+ }
+
+ Installable installable = Obj.getInstallable();
+ installable.install(taskMonitor);
+ pluginTracker.addDownloadable(Obj, PluginStatus.INSTALL);
+ return installable.getInfoObj();
+ }
+
+ private List<DownloadableInfo> flattenDownloadableList(List<DownloadableInfo> list) {
+ List<DownloadableInfo> FlattenedList = new ArrayList<DownloadableInfo>();
+ for (DownloadableInfo info: list) {
+ switch (info.getType()) {
+ case THEME:
+ FlattenedList.addAll(((ThemeInfo) info).getPlugins());
+ case PLUGIN:
+ FlattenedList.add(info);
+ }
+ }
+ return FlattenedList;
+ }
+
+ /*
+ * Methods for loading plugins when Cytoscape starts up.
+ */
+ public void loadPlugin(DownloadableInfo i) throws MalformedURLException,
+ IOException, ClassNotFoundException, PluginException {
+ switch (i.getType()) {
+ case PLUGIN:
+ loadPlugin((PluginInfo) i);
+ break;
+ case THEME:
+ ThemeInfo Info = (ThemeInfo) i;
+ for (PluginInfo p : Info.getPlugins())
+ loadPlugin(p);
+ break;
+ case FILE: // currently there is no FileInfo type
+ break;
+ }
+ }
+
+ /**
+ * Load a single plugin based on the PluginInfo object given
+ *
+ * @param PluginInfo
+ * The plugin to load
+ * @throws ManagerException
+ */
+ public void loadPlugin(PluginInfo p) throws ManagerException {
+ List<URL> ToLoad = new ArrayList<URL>();
+
+ for (String FileName : p.getFileList()) {
+ if (FileName.endsWith(".jar")) {
+ try {
+ ToLoad.add(jarURL(FileName));
+ } catch (MalformedURLException mue) {
+ // mue.printStackTrace();
+ loadingErrors.add(mue);
+ }
+ }
+ }
+ // don't need to register if we have the info object
+ InstallablePlugin insp = new InstallablePlugin(p);
+ loadURLPlugins(ToLoad, false);
+
+ if (duplicateLoadError) {
+ insp.uninstall();
+ pluginTracker.removeDownloadable(p, PluginStatus.CURRENT);
+ addDuplicateError();
+ }
+
+ }
+
+ /**
+ * Load a single plugin based on the File object given
+ *
+ * @param plugin
+ * The plugin to load
+ * @throws MalformedURLException
+ */
+ public void loadPlugin(File plugin) throws MalformedURLException, PluginException {
+ String fileName = plugin.getAbsolutePath();
+ if (fileName.endsWith(".jar")) {
+ try {
+ String className = JarUtil.getPluginClass(fileName,
+ PluginInfo.FileType.JAR);
+
+ // See if we already have this className registered
+ try {
+ Class pluginClass = getPluginClass(className); // Get the plugin class
+ // If this succeeded, we're in trouble -- this class is already
+ // registered
+ throw new PluginException("Duplicate class name: "+className+". \n"+
+ "You may need to delete a previously installed plugin.");
+ } catch (ClassNotFoundException cnfe1) {
+ // This is what we want....
+ }
+
+ // We don't want to register because we're going to play a little
+ // fast and loose with the uniqueID, so we need to contruct things
+ // ourselves
+
+ try {
+ addClassPath(jarURL(fileName));
+
+ // OK, now hand-craft the registration
+ Class pluginClass = getPluginClass(className); // Get the plugin class
+ Object obj = CytoscapePlugin.loadPlugin(pluginClass);
+ PluginInfo base = new PluginInfo(plugin.getName(), className);
+ registerPlugin((CytoscapePlugin)obj, new JarFile(plugin), base, true);
+ } catch (Throwable t) {
+ throw new PluginException("Classloader Error: " + jarURL(fileName), t);
+ }
+ } catch (IOException ioe) {
+ throw new PluginException("Unable to read plugin jar: "+ioe.getMessage(), ioe);
+ }
+
+ }
+
+ if (duplicateLoadError) {
+ addDuplicateError();
+ }
+ }
+
+ /**
+ * Parses the plugin input strings and transforms them into the appropriate
+ * URLs or resource names. The method first checks to see if the
+ */
+ public void loadPlugins(List<String> p) {
+ Set<String> PluginsSeen = new HashSet<String>();
+
+ // Parse the plugin strings and determine whether they're urls,
+ // files, directories, class names, or manifest file names.
+ for (String currentPlugin : p) {
+ try {
+ if (PluginsSeen.contains(currentPlugin))
+ continue;
+
+ if (currentPlugin.contains(".cytoscape")) {
+ logger.info(currentPlugin);
+ }
+
+ File f = new File(currentPlugin);
+
+ // If the file name ends with .jar add it to the list as a url.
+ if (currentPlugin.endsWith(".jar")) {
+ PluginsSeen.add(f.getAbsolutePath());
+
+ // If the name doesn't match a url, turn it into one.
+ if (!currentPlugin.matches(FileUtil.urlPattern)) {
+ logger.info(" - file: " + f.getAbsolutePath());
+ pluginURLs.add(jarURL(f.getAbsolutePath()));
+ } else {
+ logger.info(" - url: " + f.getAbsolutePath());
+ pluginURLs.add(jarURL(currentPlugin));
+ }
+ } else if (!f.exists()) {
+ // If the file doesn't exists, assume
+ // that it's a resource plugin.
+ logger.info(" - classpath: " + currentPlugin);
+ resourcePlugins.add(currentPlugin);
+ } else if (f.isDirectory()) {
+ // If the file is a directory, load
+ // all of the jars in the directory.
+ logger.info(" - directory: " + f.getAbsolutePath());
+
+ for (String fileName : f.list()) {
+ if (!fileName.endsWith(".jar")) {
+ continue;
+ }
+ PluginsSeen.add(f.getAbsolutePath()
+ + System.getProperty("file.separator")
+ + fileName);
+ pluginURLs.add(jarURL(f.getAbsolutePath()
+ + System.getProperty("file.separator")
+ + fileName));
+ }
+ } else {
+ // Assume the file is a manifest (i.e. list of jar names)
+ // and make urls out of them.
+ logger.info(" - file manifest: "
+ + f.getAbsolutePath());
+
+ String text = FileUtil.getInputString(currentPlugin);
+
+ String[] allLines = text.split(System
+ .getProperty("line.separator"));
+ for (String pluginLoc : allLines) {
+ if (pluginLoc.endsWith(".jar")) {
+ PluginsSeen.add(pluginLoc);
+ if (pluginLoc.matches(FileUtil.urlPattern)) {
+ pluginURLs.add(jarURL(pluginLoc));
+ } else {
+ // TODO this should have a better error
+ // perhaps, throw an exception??
+ logger.warn("Plugin location specified in "
+ + currentPlugin
+ + " is not a valid url: "
+ + pluginLoc
+ + " -- NOT adding it.");
+ loadingErrors.add(new PluginException(
+ "Plugin location specified in "
+ + currentPlugin
+ + " is not a valid url: "
+ + pluginLoc
+ + " -- NOT adding it."));
+ }
+ }
+ }
+ }
+ // Catching Throwable because Errors (e.g. NoClassDefFoundError) could
+ // cause Cytoscape to crash, which plugins should definitely not do.
+ } catch (Throwable t) {
+ loadingErrors.add(new PluginException("problem loading plugin: "+currentPlugin,t));
+ t.printStackTrace();
+ }
+ }
+ // now load the plugins in the appropriate manner
+ loadURLPlugins(pluginURLs, true);
+ loadResourcePlugins(resourcePlugins);
+
+ cleanCurrentList();
+ if (duplicateLoadError)
+ addDuplicateError();
+ }
+
+ private void addDuplicateError() {
+ String Msg = "The following plugins were not loaded due to duplicate class definitions:\n";
+ for (String dup : duplicateClasses)
+ Msg += "\t" + dup + "\n";
+ logger.warn(Msg);
+ loadingErrors.add(new DuplicatePluginClassException(Msg));
+ }
+
+ /**
+ * Load all plugins by using the given URLs loading them all on one
+ * URLClassLoader, then interating through each Jar file looking for classes
+ * that are CytoscapePlugins
+ */
+ private void loadURLPlugins(List<URL> pluginUrls, boolean register) {
+ URL[] urls = new URL[pluginUrls.size()];
+ pluginUrls.toArray(urls);
+
+ duplicateClasses = new ArrayList<String>();
+ duplicateLoadError = false;
+
+ for (URL url : urls) {
+ try {
+ addClassPath(url);
+ // Catching Throwable because Errors (e.g. NoClassDefFoundError) could
+ // cause Cytoscape to crash, which plugins should definitely not do.
+ } catch (Throwable t) {
+ loadingErrors.add(new PluginException("Classloader Error: " + url, t));
+ }
+ }
+
+ // the creation of the class loader automatically loads the plugins
+ if ( usingWebstartManager() )
+ // Note: For the case of websatart, we should use the following statement to get classLoader
+ // The URLs will be a list of URLs pointed to the jars at source website. This may solve the
+ //Class not found exception, because webstart does not have access to the local jar files
+ // in the class path.
+ classLoader = (URLClassLoader)this.getClass().getClassLoader();
+ //classLoader = (URLClassLoader) Thread.currentThread().getContextClassLoader();
+ else
+ classLoader = (URLClassLoader) ClassLoader.getSystemClassLoader();
+
+
+ // iterate through the given jar files and find classes that are
+ // assignable from CytoscapePlugin
+ for (int i = 0; i < urls.length; ++i) {
+
+ try {
+ logger.info("attempting to load plugin url: "+urls[i]);
+
+ JarURLConnection jc = (JarURLConnection) urls[i]
+ .openConnection();
+ // Ensure we are reading the real content from urls[i],
+ // and not some out-of-date cached content:
+ jc.setUseCaches(false);
+ JarFile jar = jc.getJarFile();
+
+ // if the jar file is null, do nothing
+ if (jar == null) {
+ continue;
+ }
+
+ // try to get class name from the manifest file
+ String className = JarUtil.getManifestAttribute(jar.getManifest());
+
+ if (className != null) {
+ Class pc = getPluginClass(className);
+
+ if (pc != null) {
+ logger.info("Loading from manifest");
+ loadPlugin(pc, jar, register);
+ continue;
+ }
+ }
+
+ // new-school failed, so revert to old school. Search through
+ // the jar entries
+ Enumeration entries = jar.entries();
+
+ if (entries == null) {
+ loadingErrors.add(new PluginException("Jar file "
+ + jar.getName()
+ + " has no entries, skipped loading."));
+ logger.warn("Jar file "
+ + jar.getName()
+ + " has no entries, skipped loading.");
+ continue;
+ }
+
+ int totalPlugins = 0;
+ while (entries.hasMoreElements()) {
+ // get the entry
+ String entry = entries.nextElement().toString();
+
+ if (entry.endsWith("class")) {
+ // convert the entry to an assignable class name
+ entry = entry.replaceAll("\\.class$", "");
+ // A regex to match the two known types of file
+ // separators. We can't use File.separator because
+ // the system the jar was created on is not
+ // necessarily the same is the one it is running on.
+ entry = entry.replaceAll("/|\\\\", ".");
+
+ Class pc = getPluginClass(entry);
+ if (pc == null) {
+ continue;
+ }
+ totalPlugins++;
+ loadPlugin(pc, jar, register);
+ break;
+ }
+ }
+ if (totalPlugins == 0) {
+ logger.info("No plugin found in specified jar - assuming it's a library.");
+ }
+ // Catching Throwable because Errors (e.g. NoClassDefFoundError) could
+ // cause Cytoscape to crash, which plugins should definitely not do.
+ } catch (Throwable t) {
+ loadingErrors.add(new PluginException("problem loading plugin URL: " + urls[i], t));
+ t.printStackTrace();
+ }
+ }
+ }
+
+ // these are jars that *may or may not* extend CytoscapePlugin but may be
+ // used by jars that do
+ private void loadResourcePlugins(List<String> resourcePlugins) {
+ // attempt to load resource plugins
+ for (String resource : resourcePlugins) {
+ logger.info("attempting to load plugin resourse: " + resource);
+
+ // try to get the class
+ try {
+ Class rclass = Class.forName(resource);
+ loadPlugin(rclass, null, true);
+ // Catching Throwable because Errors (e.g. NoClassDefFoundError) could
+ // cause Cytoscape to crash, which plugins should definitely not do.
+ } catch (Throwable t) {
+ loadingErrors.add(new PluginException("problem loading plugin resource: " + resource, t));
+ }
+ }
+ }
+
+ private void loadPlugin(Class plugin, JarFile jar, boolean register)
+ throws PluginException {
+ if (CytoscapePlugin.class.isAssignableFrom(plugin)
+ && !loadedPlugins.contains(plugin.getName())) {
+
+ Object obj = CytoscapePlugin.loadPlugin(plugin);
+ if (obj != null) {
+ loadedPlugins.add(plugin.getName());
+ if (register) {
+ register((CytoscapePlugin) obj, jar);
+ }
+ }
+
+ } else if (loadedPlugins.contains(plugin.getName())) {
+ duplicateClasses.add(plugin.getName());
+ duplicateLoadError = true;
+ }
+ }
+
+ /**
+ * Determines whether the class with a particular name extends
+ * CytoscapePlugin by attempting to load the class first.
+ *
+ * @param name
+ * the name of the putative plugin class
+ */
+ private Class getPluginClass(String name) throws ClassNotFoundException,
+ NoClassDefFoundError {
+ Class c;
+ if ( usingWebstartManager() )
+ c = Class.forName(name,false,classLoader);
+ else
+ c = classLoader.loadClass(name);
+
+ if (CytoscapePlugin.class.isAssignableFrom(c))
+ return c;
+ else
+ return null;
+ }
+
+ // creates a URL object from a jar file name
+ private static URL jarURL(String urlString) throws MalformedURLException {
+ String uString;
+ if (urlString.matches(FileUtil.urlPattern)) {
+ uString = "jar:" + urlString + "!/";
+ } else {
+ uString = "jar:file:" + urlString + "!/";
+ }
+ return new URL(uString);
+ }
+
+ /**
+ * This will be used to add plugin jars' URL to the System Loader's
+ * classpath.
+ *
+ * @param url
+ * @throws NoSuchMethodException
+ * @throws IllegalAccessException
+ * @throws InvocationTargetException
+ */
+ private void addClassPath(URL url) throws NoSuchMethodException,
+ IllegalAccessException, InvocationTargetException {
+ Method method = URLClassLoader.class.getDeclaredMethod("addURL",
+ new Class[] { URL.class });
+ method.setAccessible(true);
+ method.invoke(ClassLoader.getSystemClassLoader(), new Object[] { url });
+ }
+}
diff --git a/application/src/main/java/cytoscape/plugin/PluginManagerInquireTask.java b/application/src/main/java/cytoscape/plugin/PluginManagerInquireTask.java
new file mode 100644
index 0000000..11c66a6
--- /dev/null
+++ b/application/src/main/java/cytoscape/plugin/PluginManagerInquireTask.java
@@ -0,0 +1,95 @@
+/*
+ File: PluginManagerInquireTask.java
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.plugin;
+
+import java.util.List;
+
+import cytoscape.task.Task;
+import cytoscape.task.TaskMonitor;
+
+public class PluginManagerInquireTask implements Task {
+
+
+ private String url;
+
+ private PluginInquireAction actionObj;
+
+ private cytoscape.task.TaskMonitor taskMonitor;
+
+ public PluginManagerInquireTask(String Url, PluginInquireAction Obj) {
+ url = Url;
+ actionObj = Obj;
+ }
+
+ public void setTaskMonitor(TaskMonitor monitor)
+ throws IllegalThreadStateException {
+ taskMonitor = monitor;
+ }
+
+ public void halt() {
+ // not implemented
+ }
+
+ public String getTitle() {
+ return "Attempting to connect to " + url;
+ }
+
+ public void run() {
+ List<DownloadableInfo> Results = null;
+
+ taskMonitor.setStatus(actionObj.getProgressBarMessage());
+ taskMonitor.setPercentCompleted(-1);
+
+ try {
+ Results = PluginManager.getPluginManager().inquire(url);
+ } catch (org.jdom.JDOMException jde) {
+ actionObj.setExceptionThrown(jde);
+ } catch (java.io.IOException ioe) {
+ actionObj.setExceptionThrown(ioe);
+ } catch (Exception e) {
+
+ if (e.getClass().equals(java.lang.NullPointerException.class)) {
+ e = new org.jdom.JDOMException(
+ "XML was incorrectly formed", e);
+ }
+ actionObj.setExceptionThrown(e);
+ } finally {
+ taskMonitor.setPercentCompleted(100);
+ actionObj.inquireAction(Results);
+ }
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/plugin/PluginProperties.java b/application/src/main/java/cytoscape/plugin/PluginProperties.java
new file mode 100644
index 0000000..b0b0724
--- /dev/null
+++ b/application/src/main/java/cytoscape/plugin/PluginProperties.java
@@ -0,0 +1,213 @@
+/**
+ *
+ */
+package cytoscape.plugin;
+import cytoscape.logger.CyLogger;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.InputStream;
+import java.io.IOException;
+import java.util.Properties;
+
+
+/**
+ * This class reads the plugin.props file that is expected to be in
+ * each plugin jar file and turns it into a PluginInfo object for
+ * the PluginManager
+ */
+public class PluginProperties extends Properties {
+ private String configFileName = "plugin.props";
+ private String packageName;
+ private String errorMsg;
+
+ /**
+ * Properties in the plugin.props file
+ */
+ public enum PluginProperty {
+ NAME("pluginName", true), DESCRIPTION("pluginDescription", true),
+ VERSION("pluginVersion", true), CYTOSCAPE_VERSION("cytoscapeVersion", true),
+ CATEGORY("pluginCategory", true),
+ PROJECT_URL("projectURL", false), AUTHORS("pluginAuthorsInstitutions", false),
+ RELEASE_DATE("releaseDate", false), UNIQUE_ID("uniqueID", false),
+ DOWNLOAD_URL("downloadURL", false);
+
+ private String propText;
+ private boolean requiredProp;
+
+ private PluginProperty(String prop, boolean required) {
+ propText = prop;
+ requiredProp = required;
+ }
+
+ public String toString() {
+ return propText + ":" + requiredProp;
+ }
+
+ public String getPropertyKey() {
+ return propText;
+ }
+
+ public boolean isRequired() {
+ return requiredProp;
+ }
+
+ }
+
+ /**
+ * Used in testing only.
+ * @param fileName
+ */
+ PluginProperties(String fileName) throws IOException {
+ FileInputStream fis = null;
+ try {
+ fis = new FileInputStream(new File(fileName));
+ readPluginProperties(fis);
+ }
+ finally {
+ if (fis != null) {
+ fis.close();
+ }
+ }
+ }
+
+ /**
+ * The plugin.props file is expected to be in the jar file under the package directory.
+ * It will not be found if it is anywhere else.
+ * @param Plugin
+ * @throws IOException
+ */
+ public PluginProperties(CytoscapePlugin Plugin) throws IOException {
+ if (Plugin.getClass().getPackage() == null) {
+ throw new IOException(Plugin.getClass().getName() + " is not part of a package, cannot read " + configFileName);
+ }
+ packageName = Plugin.getClass().getPackage().getName();
+ packageName = packageName.replace('.', '/'); // the package name has to be in the directory structure form with unix slashes
+ readPluginProperties(Plugin.getClass().getClassLoader().getResourceAsStream(packageName + "/" + configFileName));
+ }
+
+ private void readPluginProperties(InputStream is) throws IOException {
+ if (is == null || is.available() == 0) {
+ // throw an error!
+ String Msg = "";
+ if (is == null) {
+ Msg = "File is not in the expected location: " + packageName;
+ } else if (is.available() == 0) {
+ Msg = "0 bytes in input stream";
+ }
+
+ IOException Error = new IOException("Unable to load " + packageName
+ + "/" + configFileName + ". " + Msg);
+ throw Error;
+ } else {
+ load(is);
+ }
+ }
+
+ /**
+ * Takes a PluginInfo object (can be null) and fills it in with information that would not come from
+ * a properties file like the unique identifier and download url.
+ * @param info
+ * @return
+ * @throws ManagerException
+ */
+ public PluginInfo fillPluginInfoObject(DownloadableInfo info) throws ManagerException {
+ if (!expectedPropertiesPresent()) {
+ throw new ManagerException("Required properties are missing from plugins.props file: " + errorMsg);
+ }
+
+
+ PluginInfo pi;
+ if (containsKey(PluginProperty.UNIQUE_ID.getPropertyKey())) {
+ pi = new PluginInfo(getProperty(PluginProperty.UNIQUE_ID.getPropertyKey()));
+ if (info != null) {
+ pi.setObjectUrl(info.getObjectUrl());
+ pi.setDownloadableURL(info.getDownloadableURL());
+ }
+ } else if (info != null) { // ????
+ CyLogger.getLogger().info(info.toString());
+ pi = (PluginInfo) info;
+ pi.clearAuthorList();
+ } else {
+ pi = new PluginInfo();
+ }
+
+ // required parameters
+ pi.setName(getProperty(PluginProperty.NAME.getPropertyKey()));
+
+ try {
+ pi.setObjectVersion( getProperty(PluginProperty.VERSION.getPropertyKey()) );
+ } catch (java.lang.NumberFormatException ne) { // skip it or set it to a default value??
+ CyLogger.getLogger().warn(pi.getName() + " version is incorrectly formatted, format is: \\d+.\\d+. Version set to 0.1 to allow plugin to load");
+ // ne.printStackTrace();
+ pi.setObjectVersion("0.1");
+ }
+
+ pi.setDescription(getProperty(PluginProperty.DESCRIPTION.getPropertyKey()));
+ pi.setCategory(getProperty(PluginProperty.CATEGORY.getPropertyKey()));
+
+
+ // optional parameters
+ if (containsKey(PluginProperty.PROJECT_URL.getPropertyKey())) {
+ pi.setProjectUrl(getProperty(PluginProperty.PROJECT_URL.getPropertyKey()));
+ }
+
+ if (containsKey(PluginProperty.DOWNLOAD_URL.getPropertyKey())) {
+ pi.setDownloadableURL(getProperty(PluginProperty.DOWNLOAD_URL.getPropertyKey()));
+ }
+
+ if (containsKey(PluginProperty.AUTHORS.getPropertyKey()) || containsKey("pluginAuthorsIntsitutions")) {
+ // split up the value and add each
+ String AuthorProp = getProperty(PluginProperty.AUTHORS.getPropertyKey());
+
+ // bug fix, misspelled the property file key but need to be sure anyone who used the
+ // misspelling is taken care of for now
+ if (AuthorProp == null)
+ AuthorProp = getProperty("pluginAuthorsIntsitutions");
+
+ String[] AuthInst = AuthorProp.split(";");
+
+ for (String ai: AuthInst) {
+ String[] CurrentAI = ai.split(":");
+ if (CurrentAI.length != 2) {
+ CyLogger.getLogger().warn("Author line '" + ai + "' incorrectly formatted. Please enter authors as 'Name1, Name2 and Name3: Institution");
+ continue;
+ }
+ pi.addAuthor(CurrentAI[0], CurrentAI[1]);
+ }
+ }
+
+ if (containsKey(PluginProperty.RELEASE_DATE.getPropertyKey())) {
+ pi.setReleaseDate(getProperty(PluginProperty.RELEASE_DATE.getPropertyKey()));
+ }
+
+ // on the off chance that someone did not install this via the PM this should be null if the version is not current
+ String [] AllCytoscapeVersions = getProperty(PluginProperty.CYTOSCAPE_VERSION.getPropertyKey()).split(",");
+
+ for (String v: AllCytoscapeVersions) {
+ v = v.trim();
+ pi.addCytoscapeVersion(v);
+ }
+ /*
+ * The only current usage of this method is in the PluginManager.register() method. By
+ * the time it gets to that point a plugin is already loaded (or has failed to load) and
+ * we can't unload it. Instead we'll add notes and change the category to make it clear
+ * this may not be a good plugin.
+ */
+
+ return pi;
+ }
+
+
+ private boolean expectedPropertiesPresent() {
+ for (PluginProperty pp : PluginProperty.values()) {
+ if (pp.isRequired() && !containsKey(pp.getPropertyKey())) {
+ errorMsg = pp.getPropertyKey();
+ return false;
+ }
+ }
+ return true;
+ }
+
+
+}
diff --git a/application/src/main/java/cytoscape/plugin/PluginStatus.java b/application/src/main/java/cytoscape/plugin/PluginStatus.java
new file mode 100644
index 0000000..2fa9b85
--- /dev/null
+++ b/application/src/main/java/cytoscape/plugin/PluginStatus.java
@@ -0,0 +1,19 @@
+package cytoscape.plugin;
+
+public enum PluginStatus {
+ CURRENT("CurrentPlugins"),
+ DELETE("DeletePlugins"),
+ INSTALL("InstallPlugins");
+
+ private String statusText;
+
+ private PluginStatus(String status) {
+ statusText = status;
+ }
+
+ public String getTagName() {
+ return statusText;
+ }
+}
+
+
diff --git a/application/src/main/java/cytoscape/plugin/PluginTracker.java b/application/src/main/java/cytoscape/plugin/PluginTracker.java
new file mode 100644
index 0000000..06deb70
--- /dev/null
+++ b/application/src/main/java/cytoscape/plugin/PluginTracker.java
@@ -0,0 +1,759 @@
+/*
+ File: PluginTracker.java
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.plugin;
+
+import cytoscape.plugin.PluginInfo.AuthorInfo;
+import cytoscape.logger.CyLogger;
+
+import org.jdom.Document;
+import org.jdom.Element;
+import org.jdom.JDOMException;
+
+import org.jdom.input.SAXBuilder;
+
+import org.jdom.output.Format;
+import org.jdom.output.XMLOutputter;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileWriter;
+import java.io.IOException;
+
+import java.util.*;
+
+
+public class PluginTracker {
+ private static CyLogger logger = CyLogger.getLogger(PluginTracker.class);
+ private Document trackerDoc;
+ private File installFile;
+ private HashMap<String, Element> infoObjMap;
+ private Set<Element> corruptedElements;
+ private boolean corruptedElementsFound = false;
+
+ /**
+ * Used for testing
+ *
+ * @param FileName
+ * Xml file name
+ * @param Dir
+ * directory to to write xml file
+ * @throws IOException
+ */
+ protected PluginTracker(File Dir, String FileName) throws IOException, TrackerException {
+ installFile = new File(Dir, FileName);
+ init();
+ }
+
+ protected PluginTracker(File file) throws IOException, TrackerException {
+ installFile = file;
+ init();
+ }
+
+ /*
+ * Used for tests.
+ */
+ protected File getTrackerFile() {
+ return installFile;
+ }
+
+ /*
+ * Sets up the xml doc for tracking.
+ */
+ private void init() throws IOException, TrackerException {
+ corruptedElements = new HashSet<Element>();
+
+ if (PluginManager.usingWebstartManager()) {
+ // we don't want the old webstart file
+ installFile.delete();
+ }
+
+ if (installFile.exists() && installFile.length() > 0) {
+ SAXBuilder Builder = new SAXBuilder(false);
+ try {
+ FileInputStream is = null;
+
+ try {
+ is = new FileInputStream(installFile);
+ trackerDoc = Builder.build(is, installFile.toURI().toURL().toString());
+ } finally {
+ if (is != null) {
+ is.close();
+ }
+ }
+ removeMissingIdEntries();
+ write();
+ validateTrackerDoc();
+ } catch (Exception jde) {
+ installFile.delete();
+ createCleanDoc();
+ throw new TrackerException("Plugin tracking file is corrupted. Please reinstall your plugins. Deleting " + installFile.getAbsolutePath(), jde);
+ } finally {
+ createPluginTable();
+ }
+ } else {
+ createCleanDoc();
+ createPluginTable();
+ }
+ }
+
+ /**
+ * Will throw an exception if the tracker document doesn't contain the necessary
+ * elements. The goal is to force a dummy plugin table to be created.
+ */
+ private void validateTrackerDoc() {
+ for (PluginStatus ps: PluginStatus.values()) {
+ // several of these calls could also produce an NPE
+ Iterator<Element> iter = trackerDoc.getRootElement().getChild(ps.getTagName()).getChildren().iterator();
+ if ( iter == null )
+ throw new NullPointerException("corrupted tracker file");
+
+ }
+ }
+
+ private void createCleanDoc() {
+ logger.warn("Plugin tracker file: " + installFile.getAbsolutePath());
+ trackerDoc = new Document();
+ trackerDoc.setRootElement(new Element("CytoscapePlugin"));
+ trackerDoc.getRootElement().addContent(new Element(PluginStatus.CURRENT.getTagName()));
+ trackerDoc.getRootElement().addContent(new Element(PluginStatus.INSTALL.getTagName()));
+ trackerDoc.getRootElement().addContent(new Element(PluginStatus.DELETE.getTagName()));
+ write();
+ }
+
+ /* In order to maintain a list of plugins that does not duplicate entries due to lack of a unique identifier
+ * all entries that lack an unique id will be purged and expected to re-register. User will see no difference.
+ */
+ private void removeMissingIdEntries() {
+ List<Element> Plugins = trackerDoc.getRootElement().getChild(PluginStatus.CURRENT.getTagName()).getChildren(pluginTag);
+ List<Element> PluginsToRemove = new ArrayList<Element>();
+
+ for (Element plugin: Plugins) {
+ if (plugin.getChild(uniqueIdTag) == null ||
+ plugin.getChild(uniqueIdTag).getTextTrim().length() <= 0)
+ PluginsToRemove.add(plugin);
+ }
+
+ for (Element child: PluginsToRemove)
+ trackerDoc.getRootElement().getChild(PluginStatus.CURRENT.getTagName()).removeContent(child);
+
+ }
+
+ /**
+ * Gets a list of plugins by their status. CURRENT: currently installed
+ * DELETED: to be deleted INSTALL: to be installed
+ *
+ * @param Status
+ * @return List of PluginInfo objects
+ */
+ protected List<PluginInfo> getPluginListByStatus(PluginStatus Status) {
+ return getPluginContent(trackerDoc.getRootElement().getChild(Status.getTagName()));
+ }
+
+ /**
+ * Get the list of all downloadable object by their status.
+ * CURRENT: currently installed
+ * DELETED: to be deleted
+ * INSTALLED: to be installed
+ *
+ * @param Status
+ * @return
+ */
+ protected List<DownloadableInfo> getDownloadableListByStatus(PluginStatus Status) {
+ return this.getDownloadableContent(trackerDoc.getRootElement().getChild(Status.getTagName()));
+ }
+
+ /**
+ *
+ * Gets a list of themes by their status. CURRENT: currently installed
+ * DELETED: to be deleted INSTALL: to be installed
+ *
+ * @param Status
+ * @return List of ThemeInfo objects
+ */
+ protected List<ThemeInfo> getThemeListByStatus(PluginStatus Status) {
+ return getThemeContent(trackerDoc.getRootElement().getChild(Status.getTagName()));
+ }
+
+ protected void addDownloadable(DownloadableInfo obj, PluginStatus Status) {
+ Element Parent = trackerDoc.getRootElement().getChild(Status.getTagName());
+
+ switch (obj.getType()) {
+ case PLUGIN:
+ addPlugin((PluginInfo) obj, Status);
+ break;
+ case THEME:
+ addTheme((ThemeInfo) obj, Status);
+ break;
+ }
+ }
+
+ /**
+ * Adds the given ThemeInof object to the list of themes sharing the given
+ * status.
+ *
+ * @param obj
+ * @param Status
+ */
+ private void addTheme(ThemeInfo obj, PluginStatus Status) {
+ Element ThemeParent = trackerDoc.getRootElement().getChild(Status.getTagName());
+ Element Theme = getMatchingInfoObj(obj, Status);
+
+ if (Theme != null) {
+ Theme = updateBasicElement(obj, Theme);
+ Theme.getChild(PluginXml.PLUGIN_LIST.getTag()).removeChildren(PluginXml.PLUGIN.getTag());
+
+ for (PluginInfo plugin: obj.getPlugins()) {
+ Element ThemePlugin = getMatchingInfoObj(plugin, Status); // XXX not sure this will get the right element
+ ThemePlugin = updatePluginElement(plugin, ThemePlugin);
+ Theme.getChild(PluginXml.PLUGIN_LIST.getTag()).addContent(ThemePlugin);
+ }
+ } else {
+ Theme = createThemeContent(obj);
+ ThemeParent.addContent(Theme);
+ this.infoObjMap.put(infoMapKey(obj, Status), Theme);
+ logger.info("Adding theme " + obj.getName() + " status " + Status.name());
+ }
+ write();
+ }
+
+ private Element updateBasicElement(DownloadableInfo obj, Element element) {
+ if (!obj.getCategory().equals(Category.NONE.getCategoryText())) {
+ element.getChild(categoryTag).setText(obj.getCategory());
+ }
+ element.getChild(cytoVersTag).setText(obj.getCytoscapeVersion());
+ element.getChild(descTag).setText(obj.getDescription());
+
+ if (element.getChild(pluginVersTag) != null) {
+ element.getChild(pluginVersTag).setText(obj.getObjectVersion());
+ } else {
+ Element PluginVersion = new Element(pluginVersTag);
+ element.addContent( PluginVersion.setText(obj.getObjectVersion()) );
+ }
+
+ if (element.getChild(PluginXml.RELEASE_DATE.getTag()) != null) {
+ element.getChild(PluginXml.RELEASE_DATE.getTag()).setText(obj.getReleaseDate());
+ } else {
+ Element ReleaseDate = new Element(PluginXml.RELEASE_DATE.getTag());
+ element.addContent( ReleaseDate.setText(obj.getReleaseDate()) );
+ }
+ return element;
+ }
+
+
+ private Element updatePluginElement(PluginInfo obj, Element Plugin) {
+ if (!obj.getName().equals(obj.getPluginClassName())) {
+ Plugin.getChild(nameTag).setText(obj.getName());
+ }
+ Plugin = updateBasicElement(obj, Plugin);
+ Plugin.getChild(installLocTag).setText(obj.getInstallLocation());
+
+ if (obj.getPluginClassName() != null) {
+ Plugin.getChild(classTag).setText(obj.getPluginClassName());
+ }
+
+ Plugin.removeChild(authorListTag);
+ Element Authors = new Element(authorListTag);
+ for(AuthorInfo ai: obj.getAuthors()) {
+ Element Author = new Element(authorTag);
+ Author.addContent( new Element(nameTag).setText(ai.getAuthor()) );
+ Author.addContent( new Element(instTag).setText(ai.getInstitution()) );
+ Authors.addContent(Author);
+ }
+ Plugin.addContent(Authors);
+
+ return Plugin;
+ }
+
+ /**
+ * Adds the given PluginInfo object to the list of plugins sharing the given
+ * status.
+ *
+ * @param obj
+ * @param Status
+ */
+ private void addPlugin(PluginInfo obj, PluginStatus Status) {
+ Element PluginParent = trackerDoc.getRootElement().getChild(Status.getTagName());
+
+ Element PluginEl = getMatchingInfoObj(obj, Status);
+ if (PluginEl != null) {
+ updatePluginElement(obj, PluginEl);
+ infoObjMap.put(this.infoMapKey(obj, Status), PluginEl);
+ } else {
+ Element NewPlugin = createPluginContent(obj);
+ PluginParent.addContent(NewPlugin);
+ infoObjMap.put(this.infoMapKey(obj, Status), NewPlugin);
+ logger.info("Adding plugin " + obj.getName() + " status " + Status.name());
+ }
+ write();
+ }
+
+ /**
+ * Removes the given DownloadableInfo object from the list of plugins/themes sharing the
+ * given status.
+ *
+ * @param obj
+ * @param Status
+ */
+ protected void removeDownloadable(DownloadableInfo obj, PluginStatus Status) {
+ Element Parent = trackerDoc.getRootElement().getChild(Status.getTagName());
+ Element InfoObj = this.getMatchingInfoObj(obj, Status);
+ if (InfoObj != null) {
+ Parent.removeContent(InfoObj);
+ infoObjMap.remove( this.infoMapKey(obj, Status) );
+
+ if (obj.getType().equals(DownloadableType.THEME)) {
+ ThemeInfo theme = (ThemeInfo) obj;
+ for (PluginInfo themePlugin: theme.getPlugins()) {
+ infoObjMap.remove( this.infoMapKey(themePlugin, Status) );
+ }
+ }
+ logger.info("Removing plugin/theme " + obj.getName() + " status " + Status.name());
+ write();
+ }
+ }
+
+
+ /**
+ * Matches one of the following rule: 1. Plugin class name 2. uniqueID &&
+ * projUrl 3. Plugin specific Url (on the assumption that no two plugins can
+ * be downloaded from the same url)
+ *
+ * @param Obj
+ * @param Tag
+ * @return
+ */
+ // TODO this needs to go through both the pluginlist and the theme pluginlist
+ // may need different method or two different lists as the first list will actually
+ // contain elements of the second (which is why there is an error)
+ protected Element getMatchingInfoObj(DownloadableInfo Obj, PluginStatus Status) {
+ String Key = this.infoMapKey(Obj, Status);
+ if (Key != null) { // actually kinda ugly but easiest way to handle plugins w/o ids
+ return this.infoObjMap.get(Key);
+ } else {
+ return null;
+ }
+ }
+
+ private void createPluginTable() {
+ this.infoObjMap = new HashMap<String, Element>();
+ for (PluginStatus ps: PluginStatus.values()) {
+ // A missing status tag should probably not happen because we check for that in
+ // validateTrackerDoc(). Only if createCleanDoc() fails to produce something usable
+ // will we run into problems here.
+ Iterator<Element> iter = trackerDoc.getRootElement().getChild(ps.getTagName()).getChildren().iterator();
+
+ while (iter.hasNext()) {
+ Element el = iter.next();
+ if (el.getName().equals(PluginXml.THEME.getTag())) {
+ // make sure the theme gets added
+ infoObjMap.put(infoMapKey(el, ps), el);
+
+ Iterator<Element> ptIter = el.getChild(PluginXml.PLUGIN_LIST.getTag()).getChildren(PluginXml.PLUGIN.getTag()).iterator();
+ while (ptIter.hasNext()) {
+ Element pEl = ptIter.next();
+ String key = this.infoMapKey(pEl, ps);
+ // all theme plugins should be added too
+ infoObjMap.put(key, pEl);
+ }
+ } else if (el.getName().equals(PluginXml.PLUGIN.getTag())) {
+ String key = this.infoMapKey(el, ps);
+ infoObjMap.put(key, el);
+ } else {
+ logger.warn("Unknown tag in plugin tracker file: "+el.getName());
+ }
+ }
+ }
+ }
+
+ // important to have the type in this key or a plugin and theme with the same id will appear to be the same object
+ private String infoMapKey(DownloadableInfo Obj, PluginStatus Status) {
+ return (Obj.getID() != null)? Obj.getID() + "_" + Obj.getType().value() + "_" + Obj.getDownloadableURL() + "_" + Status.getTagName(): null;
+ }
+ private String infoMapKey(Element el, PluginStatus Status) {
+ return el.getChildTextTrim(uniqueIdTag) + "_" + el.getName() + "_" + el.getChildTextTrim(downloadUrlTag) + "_" + Status.getTagName();
+ }
+
+
+ /**
+ * Writes doc to file
+ */
+ protected void write() {
+ // before writing remove all corrupted elements
+ for (Element e: corruptedElements) {
+ e.detach();
+ }
+
+ try {
+ XMLOutputter out = new XMLOutputter(Format.getPrettyFormat());
+ FileWriter writer = null;
+ try {
+ writer = new FileWriter(installFile);
+ out.output(trackerDoc, writer);
+ }
+ finally {
+ if (writer != null) {
+ writer.close();
+ }
+ }
+ } catch (IOException E) {
+ logger.warn("Error writing plugin status file "+E.toString());
+ }
+ }
+
+ /**
+ * @return True if one or more corrupted elements were found.
+ */
+ public boolean hasCorruptedElements() {
+ return this.corruptedElementsFound;
+ }
+
+ /**
+ * @return Total number of corrupted elements found in the file.
+ */
+ public int getTotalCorruptedElements() {
+ return corruptedElements.size();
+ }
+
+ /**
+ * Clears the list of elements and sets the found flag to false.
+ * This should only be called after checking the hadCorruptedElements()
+ * or getTotalCorruptedElements();
+ */
+ public void clearCorruptedElements() {
+ corruptedElementsFound = false;
+ corruptedElements.clear();
+ }
+
+ private void addCorruptedElement(Element e) {
+ logger.warn("** Adding corrupted element **");
+ corruptedElements.add(e);
+ corruptedElementsFound = true;
+ }
+
+
+ public String toString() {
+ XMLOutputter out = new XMLOutputter(Format.getPrettyFormat());
+ return out.outputString(trackerDoc);
+ }
+
+
+ /**
+ * Deletes the tracker file. This is currently never used outside of tests.
+ */
+ protected void delete() {
+ if (installFile.exists())
+ installFile.delete();
+ }
+
+ /*
+ * Set up the object with all the basic fields filled in
+ */
+ private DownloadableInfo createBasicObject(Element e, DownloadableType Type) {
+ DownloadableInfo Info = null;
+
+ if (e.getChildren().size() > 0 && e.getChild(uniqueIdTag) != null) {
+ switch (Type) {
+ case PLUGIN:
+ Info = new PluginInfo(e.getChildTextTrim(uniqueIdTag));
+ break;
+ case THEME:
+ Info = new ThemeInfo(e.getChildTextTrim(uniqueIdTag));
+ break;
+ }
+
+ if (e.getChild(nameTag) == null ||
+ e.getChild(descTag) == null ||
+ e.getChild(cytoVersTag) == null ||
+ e.getChild(urlTag) == null ||
+ e.getChild(downloadUrlTag) == null) {
+ return null;
+ }
+
+ Info.setName(e.getChildTextTrim(nameTag));
+ Info.setDescription(e.getChildTextTrim(descTag));
+ Info.addCytoscapeVersion(e.getChildTextTrim(cytoVersTag));
+ Info.setObjectUrl(e.getChildTextTrim(urlTag));
+ Info.setDownloadableURL(e.getChildTextTrim(downloadUrlTag));
+
+ if (e.getChild(categoryTag) != null)
+ Info.setCategory(e.getChildTextTrim(categoryTag));
+ if (e.getChild(PluginXml.RELEASE_DATE.getTag()) != null)
+ Info.setReleaseDate(e.getChildTextTrim(PluginXml.RELEASE_DATE.getTag()));
+ }
+
+ return Info;
+ }
+
+
+ // Not sure this is the right way to do this but for now...
+ private List<ThemeInfo> getThemeContent(Element ThemeParentTag) {
+ List<ThemeInfo> Content = new ArrayList<ThemeInfo>();
+ List<Element> Themes = ThemeParentTag.getChildren(PluginXml.THEME.getTag());
+
+ for (Element CurrentTheme: Themes) {
+ ThemeInfo themeInfo = (ThemeInfo) createBasicObject(CurrentTheme, DownloadableType.THEME);
+ if (themeInfo == null ||
+ CurrentTheme.getChild(PluginXml.THEME_VERSION.getTag()) == null ||
+ CurrentTheme.getChild(PluginXml.PLUGIN_LIST.getTag()) == null ||
+ CurrentTheme.getChild(PluginXml.PLUGIN_LIST.getTag()).getChildren(PluginXml.PLUGIN.getTag()).size() <= 0) {
+ this.addCorruptedElement(CurrentTheme);
+ continue;
+ }
+
+ themeInfo.setObjectVersion( CurrentTheme.getChildTextTrim(PluginXml.THEME_VERSION.getTag()) );
+ // add plugins
+ Iterator<Element> pluginI = CurrentTheme.getChild(PluginXml.PLUGIN_LIST.getTag()).getChildren(PluginXml.PLUGIN.getTag()).iterator();
+ while (pluginI.hasNext()) {
+ PluginInfo pluginInfo = createPluginObject(pluginI.next());
+ if (pluginInfo == null) {
+ this.addCorruptedElement(CurrentTheme);
+ break;
+ }
+ pluginInfo.setParent(themeInfo);
+ themeInfo.addPlugin(pluginInfo);
+ }
+ // if it wasn't corrupted
+ if (!corruptedElements.contains(CurrentTheme)) {
+ Content.add(themeInfo);
+ }
+ }
+ return Content;
+ }
+
+ // TODO PluginFileReader does much the same stuff, need to merge the two (??
+ // maybe)
+ /*
+ * Takes a list of elemnts, creates the PluginInfo object for each and
+ * returns list of objects
+ */
+ private List<PluginInfo> getPluginContent(Element PluginParentTag) {
+ List<PluginInfo> Content = new ArrayList<PluginInfo>();
+
+ List<Element> Plugins = PluginParentTag.getChildren(pluginTag);
+
+ for (Element CurrentPlugin : Plugins) {
+ PluginInfo Info = createPluginObject(CurrentPlugin);
+ if (Info == null) {
+ // remove the Element and move on
+ this.addCorruptedElement(CurrentPlugin);
+ continue;
+ }
+ Content.add(Info);
+ }
+ return Content;
+ }
+
+ /**
+ * Gets all downloadable objects currently available.
+ * @param Parent
+ * @return
+ */
+ private List<DownloadableInfo> getDownloadableContent(Element Parent) {
+ List<DownloadableInfo> Content = new ArrayList<DownloadableInfo>();
+
+ Content.addAll( getPluginContent(Parent) );
+ Content.addAll( getThemeContent(Parent) );
+
+ return Content;
+ }
+
+
+
+ /*
+ * Create the PluginInfo object from a <plugin>...</plugin> tree
+ */
+ private PluginInfo createPluginObject(Element PluginElement) {
+ PluginInfo Info = (PluginInfo) createBasicObject(PluginElement, DownloadableType.PLUGIN);
+
+ if (Info == null ||
+ PluginElement.getChildren().size() <= 0 ||
+ PluginElement.getChild(classTag) == null ||
+ PluginElement.getChild(installLocTag) == null ||
+ PluginElement.getChild(pluginVersTag) == null ||
+ PluginElement.getChild(fileTypeTag) == null ||
+ PluginElement.getChild(fileListTag) == null) {
+ // bad xml, remove it and return null
+ //PluginElement.getParent().removeContent(PluginElement);
+ return null;
+ }
+
+ Info.setPluginClassName(PluginElement.getChildTextTrim(classTag));
+ Info.setInstallLocation(PluginElement.getChildTextTrim(installLocTag));
+ Info.setObjectVersion(PluginElement.getChildTextTrim(pluginVersTag));
+ Info.setProjectUrl(PluginElement.getChildTextTrim(projUrlTag));
+
+
+ // set file type
+ String FileType = PluginElement.getChildTextTrim(fileTypeTag);
+ if (FileType.equalsIgnoreCase(PluginInfo.FileType.JAR.toString())) {
+ Info.setFiletype(PluginInfo.FileType.JAR);
+ } else if (FileType.equalsIgnoreCase(PluginInfo.FileType.ZIP.toString())) {
+ Info.setFiletype(PluginInfo.FileType.ZIP);
+ }
+
+ // add plugin files
+ List<Element> Files = PluginElement.getChild(fileListTag).getChildren(fileTag);
+ for (Element File : Files) {
+ Info.addFileName(File.getTextTrim());
+ }
+
+ // add plugin authors
+ if (PluginElement.getChild(authorListTag) != null) {
+ List<Element> Authors = PluginElement.getChild(authorListTag)
+ .getChildren(authorTag);
+ for (Element Author : Authors) {
+ Info.addAuthor(Author.getChildTextTrim(nameTag),
+ Author.getChildTextTrim(instTag));
+ }
+ }
+
+ Info = PluginFileReader.addLicense(Info, PluginElement);
+
+ return Info;
+ }
+
+
+ private Element createBasicContent(DownloadableInfo obj, Element e) {
+ e.addContent(new Element(uniqueIdTag).setText(obj.getID()));
+ e.addContent(new Element(nameTag).setText(obj.getName()));
+ e.addContent(new Element(descTag).setText(obj.getDescription()));
+ e.addContent(new Element(cytoVersTag).setText(obj.getCytoscapeVersion()));
+ e.addContent(new Element(urlTag).setText(obj.getObjectUrl()));
+ e.addContent(new Element(downloadUrlTag).setText(obj.getDownloadableURL()));
+ e.addContent(new Element(categoryTag).setText(obj.getCategory()));
+ e.addContent(new Element(PluginXml.RELEASE_DATE.getTag()).setText(obj.getReleaseDate()));
+
+ return e;
+ }
+
+ private Element createThemeContent(ThemeInfo obj) {
+ Element Theme = new Element(PluginXml.THEME.getTag());
+
+ Theme = createBasicContent(obj, Theme);
+ Theme.addContent(new Element(PluginXml.THEME_VERSION.getTag()).setText(obj.getObjectVersion()));
+
+ Element PluginList = new Element(PluginXml.PLUGIN_LIST.getTag());
+ for (PluginInfo plugin: obj.getPlugins()) {
+ PluginList.addContent(createPluginContent(plugin));
+ }
+ Theme.addContent(PluginList);
+
+ return Theme;
+ }
+
+ /*
+ * Create the plugin tag with all the appropriate tags for the PluginInfo
+ * object
+ */
+ private Element createPluginContent(PluginInfo obj) {
+ Element Plugin = new Element(pluginTag);
+
+ Plugin = createBasicContent(obj, Plugin);
+
+ Plugin.addContent(new Element(pluginVersTag).setText(obj.getObjectVersion()));
+ Plugin.addContent(new Element(classTag).setText(obj.getPluginClassName()));
+ Plugin.addContent(new Element(projUrlTag).setText(obj.getProjectUrl()));
+ Plugin.addContent(new Element(fileTypeTag).setText(obj.getFileType().toString()));
+ Plugin.addContent(new Element(installLocTag).setText(obj.getInstallLocation()));
+
+ // license
+ Element License = new Element(licenseTag);
+ License.addContent( new Element("text").setText(obj.getLicenseText()) );
+ Plugin.addContent(License);
+
+ // authors
+ Element AuthorList = new Element(authorListTag);
+ for (AuthorInfo CurrentAuthor : obj.getAuthors()) {
+ Element Author = new Element(authorTag);
+ Author.addContent(new Element(nameTag).setText(CurrentAuthor.getAuthor()));
+ Author.addContent(new Element(instTag).setText(CurrentAuthor.getInstitution()));
+ AuthorList.addContent(Author);
+ }
+ Plugin.addContent(AuthorList);
+
+ // files
+ Element FileList = new Element(fileListTag);
+ for (String FileName : obj.getFileList()) {
+ FileList.addContent(new Element(fileTag).setText(FileName));
+ }
+ Plugin.addContent(FileList);
+
+ return Plugin;
+ }
+
+ // XML Tags to prevent misspelling issues, PluginFileReader uses most of the
+ // same tags, the xml needs to stay consistent
+ private String cytoVersTag = "cytoscapeVersion";
+
+ private String nameTag = PluginXml.NAME.getTag();
+
+ private String descTag = PluginXml.DESCRIPTION.getTag();
+
+ private String classTag = PluginXml.CLASS_NAME.getTag();
+
+ private String pluginVersTag = PluginXml.PLUGIN_VERSION.getTag();
+
+ private String urlTag = PluginXml.URL.getTag();
+
+ private String projUrlTag = PluginXml.PROJECT_URL.getTag();
+
+ private String downloadUrlTag = PluginXml.DOWNLOAD_URL.getTag();
+
+ private String categoryTag = PluginXml.CATEGORY.getTag();
+
+ private String fileListTag = PluginXml.FILE_LIST.getTag();
+
+ private String fileTag = PluginXml.FILE.getTag();
+
+ private String pluginListTag = PluginXml.PLUGIN_LIST.getTag();
+
+ private String pluginTag = PluginXml.PLUGIN.getTag();
+
+ private String authorListTag = PluginXml.AUTHOR_LIST.getTag();
+
+ private String authorTag = PluginXml.AUTHOR.getTag();
+
+ private String instTag = PluginXml.INSTITUTION.getTag();
+
+ private String uniqueIdTag = PluginXml.UNIQUE_ID.getTag();
+
+ private String fileTypeTag = PluginXml.FILE_TYPE.getTag();
+
+ private String licenseTag = PluginXml.LICENSE.getTag();
+
+ private String installLocTag = PluginXml.INSTALL_LOCATION.getTag();
+}
diff --git a/application/src/main/java/cytoscape/plugin/PluginVersionUtils.java b/application/src/main/java/cytoscape/plugin/PluginVersionUtils.java
new file mode 100644
index 0000000..71dd130
--- /dev/null
+++ b/application/src/main/java/cytoscape/plugin/PluginVersionUtils.java
@@ -0,0 +1,67 @@
+package cytoscape.plugin;
+
+
+import cytoscape.logger.CyLogger;
+
+
+public final class PluginVersionUtils {
+ public static final String VALID_CYTOSCAPE_VERSION_PATTERN = "^\\d+\\.\\d+(\\.\\d+(-[a-zA-Z]+)?)?$";
+ public static final int MINOR = 2;
+ public static final String VERSION_SEPARATOR = "\\.";
+ private static final CyLogger logger = CyLogger.getLogger(PluginVersionUtils.class);
+
+ public static boolean isVersion(String vers, int vt) {
+ String[] version = vers.split("\\.");
+ if (version.length == 2 && version[1].equals("0"))
+ version = new String[]{version[0]};
+
+ return vt == version.length;
+ }
+
+ /**
+ * Return the newer of the two versions.
+ *
+ * @param arg0
+ * @param arg1
+ * @return
+ */
+ public static String getNewerVersion(String arg0, String arg1) {
+ String MostRecentVersion = null;
+ int max = 3;
+
+ String[] SplitVersionA = arg0.split("\\.");
+ String[] SplitVersionB = arg1.split("\\.");
+
+ for (int i = 0; i < max; i++) {
+ int a = 0;
+ int b = 0;
+
+ if (i == (max - 1)) {
+ logger.debug("A length: " + SplitVersionA.length + " B length: " + SplitVersionB.length);
+ a = (SplitVersionA.length == max) ? Integer
+ .valueOf(SplitVersionA[i]) : 0;
+ b = (SplitVersionB.length == max) ? Integer
+ .valueOf(SplitVersionB[i]) : 0;
+ } else {
+ a = Integer.valueOf(SplitVersionA[i]);
+ b = Integer.valueOf(SplitVersionB[i]);
+ }
+
+ if (a != b) {
+ MostRecentVersion = (a > b) ? arg0 : arg1;
+ break;
+ }
+ }
+ return MostRecentVersion;
+ }
+
+ // this just checks the downloadable object version and the cytoscape version
+ public static boolean versionOk(String version, final boolean downloadObj) {
+ final String pattern = downloadObj ? "^\\d+\\.\\d+$" : VALID_CYTOSCAPE_VERSION_PATTERN;
+
+ // Check to see if we've got a subversion number
+ if (version.indexOf('.') < 0)
+ version = version+".0"; // No, give it one
+ return version.matches(pattern);
+ }
+}
diff --git a/application/src/main/java/cytoscape/plugin/PluginXml.java b/application/src/main/java/cytoscape/plugin/PluginXml.java
new file mode 100644
index 0000000..6a56457
--- /dev/null
+++ b/application/src/main/java/cytoscape/plugin/PluginXml.java
@@ -0,0 +1,44 @@
+/**
+ *
+ */
+package cytoscape.plugin;
+
+/**
+ * @author skillcoy
+ *
+ */
+public enum PluginXml {
+ // basic tags
+ NAME("name"), DESCRIPTION("description"),
+ CLASS_NAME("classname"), UNIQUE_ID("uniqueID"),
+ CATEGORY("category"), FILE_TYPE("filetype"),
+ INSTALL_LOCATION("installLocation"),
+ RELEASE_DATE("releaseDate"),
+ // versions
+ PLUGIN_VERSION("pluginVersion"),
+ THEME_VERSION("themeVersion"),
+ CYTOSCAPE_VERSIONS("cytoscapeVersions"),
+ VERSION("version"),
+ // url tags
+ URL("url"),
+ PROJECT_URL("projectUrl"),
+ DOWNLOAD_URL("downloadUrl"),
+ // more specific tags for the lists
+ FILE_LIST("filelist"), FILE("file"),
+ THEME_LIST("themes"), THEME("theme"),
+ PLUGIN_LIST("pluginlist"), PLUGIN("plugin"),
+ AUTHOR_LIST("authorlist"), AUTHOR("author"), INSTITUTION("institution"),
+ // license
+ LICENSE("license"), LICENSE_TEXT("text"), LICENSE_REQUIRED("license_required");
+
+ private String tagName;
+
+ private PluginXml(String Name) {
+ tagName = Name;
+ }
+
+ public String getTag() {
+ return tagName;
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/plugin/ThemeInfo.java b/application/src/main/java/cytoscape/plugin/ThemeInfo.java
new file mode 100644
index 0000000..e6411c0
--- /dev/null
+++ b/application/src/main/java/cytoscape/plugin/ThemeInfo.java
@@ -0,0 +1,140 @@
+/*
+ File: ThemeInfo.java
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.plugin;
+
+import java.util.*;
+
+import cytoscape.plugin.PluginInfo.AuthorInfo;
+
+public class ThemeInfo extends DownloadableInfo {
+ private Set<PluginInfo> themePlugins;
+
+ /**
+ * See {@link DownloadableInfo#DownloadableInfo()}
+ *
+ * Initializes a ThemeInfo object with the following defaults:
+ * setName("Unknown"); setDescription("No description");
+ * setObjectVersion("0.1"); setCytoscapeVersion(
+ * cytoscape.cytoscapeVersion.version ); setCategory("Theme");
+ */
+ public ThemeInfo() {
+ init();
+ }
+
+ /**
+ * See {@link DownloadableInfo#DownloadableInfo(String)}
+ *
+ * @param UniqueID
+ * Additionally this sets the unique identifier that will be used
+ * to find a new version of the theme at the given download url.
+ */
+ public ThemeInfo(String ID) {
+ super(ID);
+ init();
+ }
+
+ private void init() {
+ setName("Unknown");
+ setDescription("No description");
+ setObjectVersion("0.1");
+ setCategory(Category.THEME);
+ themePlugins = new HashSet<PluginInfo>();
+ }
+
+ public Installable getInstallable() {
+ return new InstallableTheme(this);
+ }
+
+ /**
+ * See {@link DownloadableInfo#getType()}
+ */
+ public DownloadableType getType() {
+ return DownloadableType.THEME;
+ }
+
+ public void replacePlugin(PluginInfo oldPlugin, PluginInfo newPlugin) {
+ themePlugins.remove(oldPlugin);
+ themePlugins.add(newPlugin);
+ }
+
+ /**
+ * @param plugin
+ * Add a plugin object to this theme.
+ */
+ public void addPlugin(PluginInfo plugin) {
+ themePlugins.add(plugin);
+ }
+
+ /**
+ * @return All plugins that make up this theme.
+ */
+ public List<PluginInfo> getPlugins() {
+ return new ArrayList<PluginInfo>(themePlugins);
+ }
+
+ public boolean containsPlugin(PluginInfo plugin) {
+ for (PluginInfo pi: themePlugins) {
+ if (pi.equalsDifferentObjectVersion(plugin))
+ return true;
+ }
+ return false;
+ }
+
+ public void clearPluginList() {
+ this.themePlugins.clear();
+ }
+
+ public String getInstallLocation() {
+ java.io.File Dir = new java.io.File(
+ PluginManager.getPluginManager().getPluginManageDirectory(),
+ this.getName()+"-"+this.getObjectVersion());
+ return Dir.getAbsolutePath();
+ }
+
+ public String htmlOutput() {
+ String Html = this.basicHtmlOutput();
+
+ Html += "<b>Plugins Included</b>:<br><ul>";
+ for (PluginInfo i: getPlugins()) {
+ Html += "<li>" + i.toString();
+ }
+ Html += "</ul>";
+
+ Html += "</font></body></html>";
+ return Html;
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/plugin/TrackerException.java b/application/src/main/java/cytoscape/plugin/TrackerException.java
new file mode 100644
index 0000000..e3664bf
--- /dev/null
+++ b/application/src/main/java/cytoscape/plugin/TrackerException.java
@@ -0,0 +1,21 @@
+package cytoscape.plugin;
+
+public class TrackerException extends PluginException {
+
+ public TrackerException() {
+ super();
+ }
+
+ public TrackerException(String arg0) {
+ super(arg0);
+ }
+
+ public TrackerException(Throwable arg0) {
+ super(arg0);
+ }
+
+ public TrackerException(String arg0, Throwable arg1) {
+ super(arg0, arg1);
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/plugin/WebstartException.java b/application/src/main/java/cytoscape/plugin/WebstartException.java
new file mode 100644
index 0000000..77bdf2c
--- /dev/null
+++ b/application/src/main/java/cytoscape/plugin/WebstartException.java
@@ -0,0 +1,24 @@
+/**
+ *
+ */
+package cytoscape.plugin;
+
+/**
+ * This exception is used when methods that can't be used from the PluginManager if
+ * webstart is running are called.
+ */
+public class WebstartException extends PluginException {
+
+ public WebstartException() {
+ super("Method unavailable in webstart");
+ }
+
+ /**
+ * @param arg0
+ */
+ public WebstartException(String arg0) {
+ super(arg0);
+ }
+
+
+}
diff --git a/application/src/main/java/cytoscape/plugin/package.html b/application/src/main/java/cytoscape/plugin/package.html
new file mode 100644
index 0000000..0d94feb
--- /dev/null
+++ b/application/src/main/java/cytoscape/plugin/package.html
@@ -0,0 +1,16 @@
+<html>
+<head>
+ <!-- $Revision: 5801 $
+ $Date: 2004-04-20 01:53:47 +0200 (Tue, 20 Apr 2004) $
+ $Author: amarkiel $
+ -->
+</head>
+
+<body>
+Classes related to Cytoscape plugins.
+Enables loading of plugins from jar files;
+from the command-line, or while Cytoscape is running.
+Central PluginRegistry for multiple windows.
+</body>
+</html>
+
diff --git a/application/src/main/java/cytoscape/util/AbstractScaler.java b/application/src/main/java/cytoscape/util/AbstractScaler.java
new file mode 100644
index 0000000..fd1f350
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/AbstractScaler.java
@@ -0,0 +1,85 @@
+/*
+ File: AbstractScaler.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.util;
+
+
+import java.util.Collection;
+
+
+/**
+ * Used to scale a list of values to [a,b]
+ */
+public abstract class AbstractScaler implements Scaler {
+ public abstract double[] scale(final double values[], final double a, final double b) throws IllegalArgumentException;
+
+ public final double[] scale(final Collection<Double> values, final double a,
+ final double b) throws IllegalArgumentException
+ {
+ // Convert the collection to an array:
+ final double[] array = new double[values.size()];
+ int i = 0;
+ for (final Double d : values)
+ array[i++] = d;
+
+ return scale(array, a, b);
+ }
+
+ public final float[] scale(final float values[], final float a, final float b) throws IllegalArgumentException {
+ return doubleToFloatArray(scale(floatToDoubleArray(values), (double)a, (double)b));
+ }
+
+ public final float[] scale(final Collection<Float> values, final float a,
+ final float b) throws IllegalArgumentException
+ {
+ // Convert the collection to an array:
+ final float[] array = new float[values.size()];
+ int i = 0;
+ for (final Float f : values)
+ array[i++] = f;
+
+ return scale(array, a, b);
+ }
+
+ private double[] floatToDoubleArray(final float[] floatArray) {
+ final double[] doubleArray = new double[floatArray.length];
+ for (int i = 0; i < floatArray.length; ++i)
+ doubleArray[i] = floatArray[i];
+
+ return doubleArray;
+ }
+
+ private float[] doubleToFloatArray(final double[] doubleArray) {
+ final float[] floatArray = new float[doubleArray.length];
+ for (int i = 0; i < doubleArray.length; ++i)
+ floatArray[i] = (float)doubleArray[i];
+
+ return floatArray;
+ }
+}
diff --git a/application/src/main/java/cytoscape/util/BioDataServerUtil.java b/application/src/main/java/cytoscape/util/BioDataServerUtil.java
new file mode 100644
index 0000000..1ec2470
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/BioDataServerUtil.java
@@ -0,0 +1,310 @@
+/*
+ File: BioDataServerUtil.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.util;
+
+import cytoscape.CytoscapeInit;
+import cytoscape.logger.CyLogger;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.InputStreamReader;
+
+import java.net.MalformedURLException;
+import java.net.URL;
+
+import java.util.HashMap;
+import java.util.StringTokenizer;
+
+
+// Provides some utility methods for the BDS classes.
+/**
+ *
+ */
+public class BioDataServerUtil {
+ private static final String NCBI_TAXON_SERVER = "http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=";
+ private static final String TAXON_RESOURCE_FILE = "/cytoscape/resources/tax_report.txt";
+ private static final String TAXON_FILE = "tax_report.txt";
+
+ private static CyLogger logger = CyLogger.getLogger(BioDataServerUtil.class);
+
+ /*
+ * Takes readers (for tax_report and gene_association) and returns species
+ * name in the GA file.
+ */
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param taxRd DOCUMENT ME!
+ * @param gaRd DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @throws IOException DOCUMENT ME!
+ */
+ public String getSpecies(final BufferedReader taxRd, final BufferedReader gaRd)
+ throws IOException {
+ String sp = null;
+ String curLine = null;
+
+ while ((sp == null) && (null != (curLine = gaRd.readLine()))) {
+ curLine.trim();
+
+ // Skip comment
+ if (curLine.startsWith("!")) {
+ // do nothing
+ // logger.info("Comment: " + curLine);
+ } else {
+ StringTokenizer st = new StringTokenizer(curLine, "\t");
+
+ while ((sp == null) && (st.hasMoreTokens())) {
+ String curToken = st.nextToken();
+
+ if (curToken.startsWith("taxon") || curToken.startsWith("Taxon")) {
+ st = new StringTokenizer(curToken, ":");
+ st.nextToken();
+ curToken = st.nextToken();
+ st = new StringTokenizer(curToken, "|");
+ curToken = st.nextToken();
+ // logger.info("Taxon ID found: " + curToken);
+ sp = curToken;
+ sp = taxIdToName(sp, taxRd);
+ }
+ }
+ }
+ }
+
+ return sp;
+ }
+
+ // Convert taxonomy ID number to species name.
+ /**
+ * DOCUMENT ME!
+ *
+ * @param taxId DOCUMENT ME!
+ * @param taxRd DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @throws IOException DOCUMENT ME!
+ */
+ public String taxIdToName(String taxId, final BufferedReader taxRd) throws IOException {
+ String name = null;
+ String curLine = null;
+
+ taxRd.readLine();
+
+ while (null != (curLine = taxRd.readLine())) {
+ curLine.trim();
+
+ StringTokenizer st = new StringTokenizer(curLine, "|");
+ String[] oneEntry = new String[st.countTokens()];
+ int counter = 0;
+
+ while (st.hasMoreTokens()) {
+ String curToken = st.nextToken().trim();
+ oneEntry[counter] = curToken;
+ counter++;
+
+ if (curToken.equals(taxId)) {
+ name = oneEntry[1];
+
+ return name;
+ }
+ }
+ }
+
+ return name;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param gaReader DOCUMENT ME!
+ * @param taxonFileReader DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @throws IOException DOCUMENT ME!
+ */
+ public String checkSpecies(BufferedReader gaReader, BufferedReader taxonFileReader)
+ throws IOException {
+ String txName = null;
+ // Get taxon name
+ txName = getSpecies(taxonFileReader, gaReader);
+
+ if (txName == null) {
+ txName = CytoscapeInit.getProperties().getProperty("defaultSpeciesName");
+ logger.info("Warning: Cannot recognize species. Species field is set to defaultSpeciesName ("
+ + txName + ")");
+ logger.info("Warning: Please check your tax_report.txt file.");
+ }
+
+ return txName;
+ }
+
+ // Returns taxon Map
+ /**
+ * DOCUMENT ME!
+ *
+ * @param taxonFile DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @throws IOException DOCUMENT ME!
+ */
+ public HashMap getTaxonMap(File taxonFile) throws IOException {
+ HashMap taxonMap = null;
+
+ String name = null;
+ String curLine = null;
+
+ if (taxonFile.canRead() == true) {
+ BufferedReader taxonFileRd = null;
+
+ try {
+ taxonFileRd = new BufferedReader(new FileReader(taxonFile));
+ taxonFileRd.readLine();
+
+ while (null != (curLine = taxonFileRd.readLine())) {
+ curLine.trim();
+
+ StringTokenizer st = new StringTokenizer(curLine, "|");
+ String[] oneEntry = new String[st.countTokens()];
+ int counter = 0;
+
+ while (st.hasMoreTokens()) {
+ String curToken = st.nextToken().trim();
+ oneEntry[counter] = curToken;
+ counter++;
+ name = oneEntry[1];
+ taxonMap.put(curToken, name);
+ }
+ }
+ }
+ finally {
+ if (taxonFileRd != null) {
+ taxonFileRd.close();
+ }
+ }
+ }
+
+ return taxonMap;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param taxonFileReader DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @throws IOException DOCUMENT ME!
+ */
+ public HashMap getTaxonMap(BufferedReader taxonFileReader) throws IOException {
+ HashMap taxonMap = new HashMap();
+
+ String curLine = null;
+
+ taxonFileReader.readLine();
+
+ while ((curLine = taxonFileReader.readLine()) != null) {
+ // logger.info("===========Line: " + curLine + "
+ // ===============");
+ String[] parts = curLine.split("\\|");
+
+ // logger.info("####ID = " + parts[3].trim() + ", Name = "
+ // + parts[1].trim());
+ taxonMap.put(parts[3].trim(), parts[1].trim());
+ }
+
+ return taxonMap;
+ }
+
+ /*
+ * For a given taxon ID, returns species name. This method connects to
+ * NCBI's Taxonomy server, so Internet connection is required.
+ *
+ * Kei
+ */
+ protected String getTaxonFromNCBI(String id) throws MalformedURLException {
+ String txName = null;
+ URL taxonURL = null;
+ BufferedReader htmlPageReader = null;
+ String curLine = null;
+
+ String targetId = id + "&lvl=0";
+
+ taxonURL = new URL(NCBI_TAXON_SERVER + targetId);
+
+ try {
+ // htmlPageReader = new BufferedReader(new InputStreamReader(taxonURL.openStream()));
+ // Use URLUtil to get the InputStream since we might be using a proxy server
+ // and because pages may be cached:
+ try {
+ htmlPageReader = new BufferedReader(new InputStreamReader(URLUtil.getBasicInputStream(taxonURL)));
+
+ while ((txName == null) && ((curLine = htmlPageReader.readLine()) != null)) {
+ curLine.trim();
+
+ // logger.info("HTML:" + curLine);
+ if (curLine.startsWith("<title>Taxonomy")) {
+ logger.info("HTML:" + curLine);
+
+ StringTokenizer st = new StringTokenizer(curLine, "(");
+ st.nextToken();
+ curLine = st.nextToken();
+ st = new StringTokenizer(curLine, ")");
+ txName = st.nextToken().trim();
+ logger.info("Fetch result: NCBI code " + id + " is " + txName);
+ }
+ }
+ }
+ finally {
+ if (htmlPageReader != null) {
+ htmlPageReader.close();
+ }
+ }
+ } catch (IOException e) {
+ logger.error("Unable to get taxonomy "+id+" from NCBI: "+e.getMessage());
+ }
+
+ return txName;
+ }
+}
diff --git a/application/src/main/java/cytoscape/util/BookmarksUtil.java b/application/src/main/java/cytoscape/util/BookmarksUtil.java
new file mode 100644
index 0000000..8f4d6e3
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/BookmarksUtil.java
@@ -0,0 +1,511 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.util;
+
+import cytoscape.bookmarks.Attribute;
+import cytoscape.bookmarks.Bookmarks;
+import cytoscape.bookmarks.Category;
+import cytoscape.bookmarks.DataSource;
+
+import cytoscape.data.readers.BookmarkReader;
+import cytoscape.logger.CyLogger;
+
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.OutputStream;
+
+import java.net.URL;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBException;
+import javax.xml.bind.Marshaller;
+
+
+/**
+ * Utility methods for getting entries in the bookmark object.
+ *
+ * @author kono
+ *
+ */
+public abstract class BookmarksUtil {
+ protected static CyLogger logger = CyLogger.getLogger(BookmarksUtil.class);
+ /**
+ * Traverse bookmark tree and get a list of data sources from the specified category.
+ *
+ * @param categoryName
+ * @return
+ */
+ public static List<DataSource> getDataSourceList(String categoryName,
+ List<Category> categoryList) {
+ Category targetCat = getCategory(categoryName, categoryList);
+
+ if (targetCat != null) {
+ return extractDataSources(targetCat);
+ } else {
+ return null;
+ }
+ }
+
+ /**
+ * Select specific category from a list of categories.
+ *
+ * @param categoryName
+ * @param categoryList
+ * @return
+ */
+ public static Category getCategory(String categoryName, List<Category> categoryList) {
+ Category result = null;
+
+ for (Category cat : categoryList) {
+ if (cat.getName().equals(categoryName)) {
+ result = cat;
+
+ break;
+ } else {
+ List<Category> subCategories = extractCategory(cat);
+
+ if ((subCategories.size() != 0) && (result == null)) {
+ result = getCategory(categoryName, subCategories);
+ }
+ }
+
+ if (result != null) {
+ break;
+ }
+ }
+
+ return result;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param source DOCUMENT ME!
+ * @param attrName DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static String getAttribute(DataSource source, String attrName) {
+ List<Attribute> attrs = source.getAttribute();
+
+ for (Attribute attr : attrs) {
+ if (attrName.equals(attr.getName())) {
+ return attr.getContent();
+ }
+ }
+
+ return null;
+ }
+
+ private static List<DataSource> extractDataSources(Category cat) {
+ final List<Object> entries = cat.getCategoryOrDataSource();
+ final List<DataSource> datasourceList = new ArrayList<DataSource>();
+
+ for (Object obj : entries) {
+ if (obj.getClass() == DataSource.class) {
+ datasourceList.add((DataSource) obj);
+ }
+ }
+
+ return datasourceList;
+ }
+
+ private static List<Category> extractCategory(Category cat) {
+ final List<Object> entries = cat.getCategoryOrDataSource();
+ final List<Category> categoryList = new ArrayList<Category>();
+
+ for (Object obj : entries) {
+ if (obj.getClass() == Category.class) {
+ categoryList.add((Category) obj);
+ }
+ }
+
+ return categoryList;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param bookmarkUrl DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @throws JAXBException DOCUMENT ME!
+ * @throws IOException DOCUMENT ME!
+ */
+ public static Bookmarks getBookmarks(URL bookmarkUrl) throws JAXBException, IOException {
+ BookmarkReader reader = new BookmarkReader();
+ reader.readBookmarks(bookmarkUrl);
+
+ return reader.getBookmarks();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param pBookmarkFile DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static Bookmarks getBookmarks(java.io.File pBookmarkFile) {
+ Bookmarks theBookmarks = null;
+
+ // Load the Bookmarks object from given xml file
+ try {
+ theBookmarks = BookmarksUtil.getBookmarks(pBookmarkFile.toURL());
+ } catch (IOException e) {
+ CyLogger.getLogger().warn("Can not read the bookmark file, the bookmark file may not exist!");
+ } catch (JAXBException e) {
+ CyLogger.getLogger().warn("JAXBException -- bookmarkSource");
+ }
+
+ return theBookmarks;
+ }
+
+ private static String bookmarkPackageName = "cytoscape.bookmarks";
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param pBookmarks DOCUMENT ME!
+ * @param pCategoryName DOCUMENT ME!
+ * @param pDataSource DOCUMENT ME!
+ * @param pFos DOCUMENT ME!
+ *
+ * @throws JAXBException DOCUMENT ME!
+ * @throws IOException DOCUMENT ME!
+ */
+ public static void saveBookmark(Bookmarks pBookmarks, String pCategoryName,
+ DataSource pDataSource, FileOutputStream pFos)
+ throws JAXBException, IOException {
+ List<Category> theCategoryList = pBookmarks.getCategory();
+
+ // if the category does not exist, create it
+ if (theCategoryList.size() == 0) {
+ Category theCategory = new Category();
+ theCategory.setName(pCategoryName);
+ theCategoryList.add(theCategory);
+ }
+
+ Category theCategory = getCategory(pCategoryName, theCategoryList);
+
+ List<Object> theObjList = theCategory.getCategoryOrDataSource();
+
+ theObjList.add(pDataSource);
+
+ // Write the bookmarks objects back into a file
+ JAXBContext jc = JAXBContext.newInstance(bookmarkPackageName);
+ Marshaller m = jc.createMarshaller();
+ m.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, Boolean.TRUE);
+
+ m.marshal(pBookmarks, pFos);
+ }
+
+ // Save one bookmark (DataSource object) belonged to specified category into a XML file
+ /**
+ * DOCUMENT ME!
+ *
+ * @param pBookmarkURL DOCUMENT ME!
+ * @param pCategoryName DOCUMENT ME!
+ * @param pDataSource DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static boolean saveBookmark(URL pBookmarkURL, String pCategoryName,
+ DataSource pDataSource) {
+ Bookmarks theBookmarks = null;
+
+ try {
+ theBookmarks = BookmarksUtil.getBookmarks(pBookmarkURL);
+ } catch (Exception e) {
+ theBookmarks = new Bookmarks();
+ }
+
+ java.io.File tmpFile = new java.io.File(pBookmarkURL.getFile());
+
+ if (!tmpFile.exists()) {
+ try {
+ tmpFile.createNewFile();
+ } catch (Exception ex) {
+ logger.info("Bookmark file may not exist, failed to create new one.");
+ }
+ }
+
+ try {
+ FileOutputStream fos = null;
+ try {
+ fos = new FileOutputStream(pBookmarkURL.getFile());
+ saveBookmark(theBookmarks, pCategoryName, pDataSource, fos);
+ }
+ finally {
+ if (fos != null) {
+ fos.close();
+ }
+ }
+ } catch (JAXBException e) {
+ logger.error("Error converting bookmark: "+e.getMessage());
+ return false;
+ } catch (Exception e) {
+ logger.error("Unable to save bookmark: "+e.getMessage());
+ return false;
+ }
+
+ return true;
+ }
+
+ /**
+ * Write the bookmarks object into a file
+ *
+ * @param pBookmarks DOCUMENT ME!
+ * @param pFile DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static boolean saveBookmark(Bookmarks pBookmarks, File pFile) {
+ FileOutputStream fos = null;
+
+ try {
+ fos = new FileOutputStream(pFile);
+ saveBookmark(pBookmarks,fos);
+
+ } catch (Exception e) {
+ logger.error("Unable to save bookmark: "+e.getMessage());
+ return false;
+ } finally {
+ if (fos != null) {
+ try {
+ fos.close();
+ } catch (IOException e) {
+ logger.warn("Unable to close bookmark file: "+e.getMessage());
+ }
+ }
+ }
+
+ return true;
+ }
+
+ /**
+ * Write the bookmarks object into an outputstream
+ *
+ * @param pBookmarks DOCUMENT ME!
+ * @param os DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static boolean saveBookmark(Bookmarks pBookmarks, OutputStream os) {
+ try {
+ JAXBContext jc = JAXBContext.newInstance(bookmarkPackageName);
+ Marshaller m = jc.createMarshaller();
+ m.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, Boolean.TRUE);
+ m.marshal(pBookmarks, os);
+ } catch (Exception e) {
+ logger.error("Unable to save bookmark: "+e.getMessage());
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param pBookmarks DOCUMENT ME!
+ * @param pCategoryName DOCUMENT ME!
+ * @param pDataSource DOCUMENT ME!
+ */
+ public static void saveBookmark(Bookmarks pBookmarks, String pCategoryName,
+ DataSource pDataSource) {
+ if (pBookmarks == null) {
+ pBookmarks = new Bookmarks();
+ }
+
+ List<Category> theCategoryList = pBookmarks.getCategory();
+
+ // if the category does not exist, create it
+ if (theCategoryList.size() == 0) {
+ Category theCategory = new Category();
+ theCategory.setName(pCategoryName);
+ theCategoryList.add(theCategory);
+ }
+
+ Category theCategory = getCategory(pCategoryName, theCategoryList);
+
+ if (theCategory == null) {
+ Category newCategory = new Category();
+ newCategory.setName(pCategoryName);
+ theCategoryList.add(newCategory);
+ theCategory = newCategory;
+ }
+
+ List<Object> theObjList = theCategory.getCategoryOrDataSource();
+
+ theObjList.add(pDataSource);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param filename DOCUMENT ME!
+ * @param pBookmarks DOCUMENT ME!
+ * @param pCategoryName DOCUMENT ME!
+ * @param pDataSource DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static boolean deleteBookmark(String filename, Bookmarks pBookmarks,
+ String pCategoryName, DataSource pDataSource) {
+ List<Category> theCategoryList = pBookmarks.getCategory();
+ Category theCategory = getCategory(pCategoryName, theCategoryList);
+
+ List<Object> theObjList = theCategory.getCategoryOrDataSource();
+
+ for (int i = 0; i < theObjList.size(); i++) {
+ Object obj = theObjList.get(i);
+
+ if (obj instanceof DataSource) {
+ DataSource theDataSource = (DataSource) obj;
+
+ if (theDataSource.getName().equalsIgnoreCase(pDataSource.getName())) {
+ theObjList.remove(i);
+
+ try {
+ // Write the bookmarks objects back into a file
+ JAXBContext jc = JAXBContext.newInstance(bookmarkPackageName);
+ Marshaller m = jc.createMarshaller();
+ m.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, Boolean.TRUE);
+
+ m.marshal(pBookmarks, new FileOutputStream(filename));
+ } catch (Exception e) {
+ logger.error("Unable to update bookmark file after delete: "+e.getMessage());
+ }
+
+ return true;
+ }
+ }
+ }
+
+ return false;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param pBookmarks DOCUMENT ME!
+ * @param pCategoryName DOCUMENT ME!
+ * @param pDataSource DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static boolean deleteBookmark(Bookmarks pBookmarks, String pCategoryName,
+ DataSource pDataSource) {
+ if (!isInBookmarks(pBookmarks, pCategoryName, pDataSource)) {
+ return false;
+ }
+
+ List<Category> theCategoryList = pBookmarks.getCategory();
+ Category theCategory = getCategory(pCategoryName, theCategoryList);
+
+ List<Object> theObjList = theCategory.getCategoryOrDataSource();
+
+ for (int i = 0; i < theObjList.size(); i++) {
+ Object obj = theObjList.get(i);
+
+ if (obj instanceof DataSource) {
+ DataSource theDataSource = (DataSource) obj;
+
+ if (theDataSource.getName().equalsIgnoreCase(pDataSource.getName())) {
+ theObjList.remove(i);
+ }
+ }
+ }
+
+ return true;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param pBookmarks DOCUMENT ME!
+ * @param pCategoryName DOCUMENT ME!
+ * @param pDataSource DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static boolean isInBookmarks(Bookmarks pBookmarks, String pCategoryName,
+ DataSource pDataSource) {
+ if (pBookmarks == null) {
+ return false;
+ }
+
+ List<DataSource> theDataSources = getDataSourceList(pCategoryName, pBookmarks.getCategory());
+
+ if ((theDataSources == null) || (theDataSources.size() == 0)) {
+ return false;
+ }
+
+ for (DataSource theDataSource : theDataSources) {
+ if (theDataSource.getName().equalsIgnoreCase(pDataSource.getName())) {
+ return true;
+ }
+ }
+
+ return false;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param pBookmarkURL DOCUMENT ME!
+ * @param pCategoryName DOCUMENT ME!
+ * @param pDataSource DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static boolean isInBookmarks(URL pBookmarkURL, String pCategoryName,
+ DataSource pDataSource) {
+ Bookmarks theBookmarks = null;
+
+ try {
+ theBookmarks = getBookmarks(pBookmarkURL);
+ } catch (Exception e) {
+ return false;
+ }
+
+ return isInBookmarks(theBookmarks, pCategoryName, pDataSource);
+ }
+}
diff --git a/application/src/main/java/cytoscape/util/ColorUtil.java b/application/src/main/java/cytoscape/util/ColorUtil.java
new file mode 100644
index 0000000..ae1c5d4
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/ColorUtil.java
@@ -0,0 +1,145 @@
+package cytoscape.util;
+
+import java.awt.Color;
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.net.URL;
+import java.util.HashMap;
+import java.util.Map;
+
+import cytoscape.Cytoscape;
+
+/**
+ * Color utility class to convert Java color object to string and vice versa.
+ *
+ * @author kono
+ * @since Cytoscape 2.8.0
+ *
+ */
+public class ColorUtil {
+
+ private static final int COLOR_RANGE_MAX = 255;
+
+ private static final Map<String, String> COLOR_MAP = new HashMap<String, String>();
+ private static final String COLOR_CODE_RESOURCE = "/cross_browser_color_code.txt";
+
+ static {
+ buildColorCodeTable(Cytoscape.class.getResource(COLOR_CODE_RESOURCE));
+ }
+
+ private static void buildColorCodeTable(final URL resourceURL) {
+ BufferedReader bufRd = null;
+ String line;
+
+ try {
+ bufRd = new BufferedReader(new InputStreamReader(URLUtil
+ .getBasicInputStream(resourceURL)));
+ while ((line = bufRd.readLine()) != null) {
+ String[] parts = line.split("\\t");
+ COLOR_MAP.put(parts[0].trim().toUpperCase(), parts[1].trim());
+ }
+ } catch (IOException e) {
+ e.printStackTrace();
+ } finally {
+ if (bufRd != null) {
+ try {
+ bufRd.close();
+ } catch (IOException e) {
+ e.printStackTrace();
+ } finally {
+ bufRd = null;
+ }
+ }
+ }
+ }
+
+ /**
+ * Convert text representation of color into Color object.
+ *
+ * <p>
+ * This parser cupports the following test representation of color:
+ *
+ * <ul>
+ * <li>Hex representation of color (e.g. #6677FF)</li>
+ * <li>RGB numbers (float or integer, e.g. (255, 10, 100))</li>
+ * <li>Java standard colors text representations (all lower case. e.g.
+ * "black")</li>
+ * </ul>
+ *
+ * @param colorAsText
+ * @return Color object
+ */
+ public static Color parseColorText(final String colorAsText) {
+ if (colorAsText == null)
+ return null;
+
+ final String trimed = colorAsText.trim();
+ final String[] parts = trimed.split(",");
+
+ // Start by seeing if this is a hex representation
+ if (parts.length == 1) {
+ try {
+ // Chech this is a cross-browser standard color name
+ final String upper = trimed.toUpperCase();
+ if (COLOR_MAP.containsKey(upper))
+ return Color.decode(COLOR_MAP.get(upper));
+
+ // Otherwise, treat as a hex notation.
+ return Color.decode(trimed);
+ } catch (Exception e) {
+ return null;
+ }
+ }
+
+ if (parts.length != 3)
+ return null;
+
+ final String red = parts[0].trim();
+ final String green = parts[1].trim();
+ final String blue = parts[2].trim();
+
+ try {
+ if (red.contains(".") || green.contains(".") || blue.contains(".")) {
+ float r = Float.parseFloat(red);
+ float g = Float.parseFloat(green);
+ float b = Float.parseFloat(blue);
+ return new Color(r, g, b);
+ } else {
+ int r = Integer.parseInt(red);
+ int g = Integer.parseInt(green);
+ int b = Integer.parseInt(blue);
+ return new Color(r, g, b);
+ }
+
+ } catch (Exception e) {
+ return null;
+ }
+ }
+
+ /**
+ * Convert Color object into RGB String (e.g., (200,100,120))
+ *
+ * @param color
+ * @return
+ */
+ public static String getColorAsText(Color color) {
+ return color.getRed() + "," + color.getGreen() + "," + color.getBlue();
+ }
+
+ public static Color getComplementaryColor(final Color color1) {
+ final Color complement = new Color(COLOR_RANGE_MAX - color1.getRed(),
+ COLOR_RANGE_MAX - color1.getGreen(), COLOR_RANGE_MAX
+ - color1.getBlue());
+ final float[] hsb = Color.RGBtoHSB(color1.getRed(), color1.getGreen(),
+ color1.getBlue(), null);
+ final float[] cHSB = Color.RGBtoHSB(complement.getRed(), complement
+ .getGreen(), complement.getBlue(), null);
+
+ if (hsb[2] > 0.7f)
+ return Color.getHSBColor(cHSB[0], 1.0f - hsb[1], 0f);
+ else
+ return Color.getHSBColor(cHSB[0], 1.0f - hsb[1], 1.0f);
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/util/CreditScreen.java b/application/src/main/java/cytoscape/util/CreditScreen.java
new file mode 100644
index 0000000..793221d
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/CreditScreen.java
@@ -0,0 +1,158 @@
+/*
+ File: CreditScreen.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.util;
+
+import cytoscape.util.shadegrown.WindowUtilities;
+
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.event.ActionEvent;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+
+import java.net.URL;
+
+import javax.swing.AbstractAction;
+import javax.swing.Action;
+import javax.swing.ImageIcon;
+import javax.swing.JPanel;
+import javax.swing.JWindow;
+import javax.swing.Timer;
+
+
+/**
+ *
+ */
+public abstract class CreditScreen {
+ /**
+ * DOCUMENT ME!
+ *
+ * @param url DOCUMENT ME!
+ * @param lines DOCUMENT ME!
+ */
+ public static void showCredits(URL url, String lines) {
+ final JWindow window = new JWindow();
+ final ScrollingLinesPanel panel = new ScrollingLinesPanel(url, lines);
+ window.add(panel);
+ window.pack();
+ window.validate();
+ window.setPreferredSize(panel.getPreferredSize());
+ window.requestFocusInWindow();
+ WindowUtilities.centerWindowLocation(window);
+ window.setAlwaysOnTop(true);
+ window.setVisible(true);
+
+ Action scrollText = new AbstractAction() {
+ boolean shouldDraw = false;
+
+ public void actionPerformed(ActionEvent e) {
+ panel.incrementYPos();
+ window.repaint();
+ }
+ };
+
+ final javax.swing.Timer timer = new javax.swing.Timer(100, scrollText);
+
+ window.addMouseListener(new MouseListener() {
+ public void mouseClicked(MouseEvent e) {
+ window.dispose();
+ timer.stop();
+ }
+
+ public void mouseEntered(MouseEvent e) {
+ }
+
+ public void mouseExited(MouseEvent e) {
+ }
+
+ public void mousePressed(MouseEvent e) {
+ }
+
+ public void mouseReleased(MouseEvent e) {
+ }
+ });
+
+ timer.start();
+ }
+
+ private static class ScrollingLinesPanel extends JPanel {
+ int yPos;
+ int xPos;
+ ImageIcon background;
+ String lines;
+
+ public ScrollingLinesPanel(URL url, String lines) {
+ super();
+ background = new ImageIcon(url);
+ this.lines = lines;
+ yPos = background.getIconHeight();
+ xPos = (int) ((float) background.getIconWidth() / 2.0f);
+ setOpaque(false);
+ setPreferredSize(new Dimension(background.getIconWidth(), background.getIconHeight()));
+ }
+
+ protected void paintComponent(Graphics g) {
+ g.drawImage(background.getImage(), 0, 0, null);
+ ((Graphics2D) g).setPaint(Color.white);
+
+ int end = lines.indexOf("\n");
+ int begin = 0;
+ int i = 1;
+ int y = yPos;
+
+ while (end > 0) {
+ String sub = lines.substring(begin, end);
+ y = yPos + (12 * i);
+
+ if (y > 80)
+ g.drawString(sub, xPos, y);
+
+ begin = end + 1;
+ end = lines.indexOf("\n", begin);
+ i++;
+ }
+
+ super.paintComponent(g);
+ }
+
+ public void incrementYPos() {
+ yPos -= 2;
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/util/CyColorChooser.java b/application/src/main/java/cytoscape/util/CyColorChooser.java
new file mode 100644
index 0000000..0458e59
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/CyColorChooser.java
@@ -0,0 +1,82 @@
+/*
+ File: CyColorChooser.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.util;
+
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import javax.swing.JColorChooser;
+import javax.swing.JDialog;
+import javax.swing.JDialog;
+
+
+/**
+ * This is an annoying re-implementation of JColorChooser.showDialog() that remembers
+ * recently used colors between invocations of the chooser dialog.
+ */
+public class CyColorChooser {
+ protected static JColorChooser chooser = new JColorChooser();
+ protected static ColorListener listener = new ColorListener();
+ protected static Color color;
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param component DOCUMENT ME!
+ * @param title DOCUMENT ME!
+ * @param initialColor DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static Color showDialog(Component component, String title, Color initialColor) {
+ if (initialColor != null)
+ chooser.setColor(initialColor);
+
+ JDialog dialog = JColorChooser.createDialog(component, title, true, chooser, listener, null);
+ dialog.setVisible(true);
+
+ return color;
+ }
+
+ static class ColorListener implements ActionListener {
+ public void actionPerformed(ActionEvent e) {
+ color = chooser.getColor();
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/util/CyFileFilter.java b/application/src/main/java/cytoscape/util/CyFileFilter.java
new file mode 100644
index 0000000..8ef8fd8
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/CyFileFilter.java
@@ -0,0 +1,530 @@
+/*
+ File: CyFileFilter.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.util;
+
+import cytoscape.data.readers.GraphReader;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileReader;
+import java.io.FilenameFilter;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.Reader;
+
+import java.net.URL;
+import java.net.URLConnection;
+
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.Set;
+
+import javax.swing.filechooser.FileFilter;
+
+
+/**
+ * A convenience implementation of FileFilter that filters out
+ * all files except for those type extensions that it knows about.
+ * <p/>
+ * Extensions are of the type ".foo", which is typically found on
+ * Windows and Unix boxes, but not on Macinthosh. Case is ignored.
+ *
+ * @author Larissa Kamenkovich
+ * @author Brad Kohlenberg
+ */
+public class CyFileFilter extends FileFilter implements FilenameFilter {
+ private Hashtable filters = null;
+ private String description = null;
+ private String fullDescription = null;
+ private boolean useExtensionsInDescription = true;
+ protected Hashtable contentTypes = null;
+ protected GraphReader reader = null;
+ protected String fileNature = "UNKNOWN";
+
+ /**
+ * Creates a file filter. If no filters are added, then all
+ * files are accepted.
+ *
+ * @see #addExtension
+ */
+ public CyFileFilter() {
+ this.filters = new Hashtable();
+ }
+
+ /**
+ * Creates a file filter that accepts files with the given extension.
+ * Example: new ExampleFileFilter("jpg");
+ *
+ * @see #addExtension
+ */
+ public CyFileFilter(String extension) {
+ this(extension, null, null);
+ }
+
+ /**
+ * Creates a file filter that accepts the given file type.
+ * Example: new ExampleFileFilter("jpg", "JPEG Image Images");
+ * <p/>
+ * Note that the "." before the extension is not needed. If
+ * provided, it will be ignored.
+ *
+ * @see #addExtension
+ */
+ public CyFileFilter(String extension, String description) {
+ this(extension, description, null);
+ }
+
+ /**
+ * Creates a file filter from the given string array.
+ * Example: new ExampleFileFilter(String {"gif", "jpg"});
+ * <p/>
+ * Note that the "." before the extension is not needed adn
+ * will be ignored.
+ *
+ * @see #addExtension
+ */
+ public CyFileFilter(String[] filters) {
+ this(filters, null, null);
+ }
+
+ /**
+ * Creates a file filter from the given string array and description.
+ * Example: new ExampleFileFilter(String {"gif", "jpg"}, "Gif and JPG Images");
+ * <p/>
+ * Note that the "." before the extension is not needed and will be ignored.
+ *
+ * @see #addExtension
+ */
+ public CyFileFilter(String[] filters, String description) {
+ this(filters, description, null);
+ }
+
+ /**
+ * Creates a file filter that accepts the given file type.
+ * Example: new ExampleFileFilter("jpg", "JPEG Image Images");
+ * <p/>
+ * Note that the "." before the extension is not needed. If
+ * provided, it will be ignored.
+ *
+ * @see #addExtension
+ */
+ public CyFileFilter(String extension, String description, String nature) {
+ this.filters = new Hashtable();
+
+ if (extension != null) {
+ addExtension(extension);
+ }
+
+ if (description != null) {
+ setDescription(description);
+ }
+
+ if (nature != null) {
+ setFileNature(nature);
+ }
+ }
+
+ /**
+ * Creates a file filter from the given string array and description.
+ * Example: new ExampleFileFilter(String {"gif", "jpg"}, "Gif and JPG Images");
+ * <p/>
+ * Note that the "." before the extension is not needed and will be ignored.
+ *
+ * @see #addExtension
+ */
+ public CyFileFilter(String[] filters, String description, String nature) {
+ this.filters = new Hashtable();
+
+ for (int i = 0; i < filters.length; i++) {
+ // add filters one by one
+ addExtension(filters[i]);
+ }
+
+ if (description != null) {
+ setDescription(description);
+ }
+
+ if (nature != null) {
+ setFileNature(nature);
+ }
+ }
+
+ /**
+ * Returns true if this class is capable of processing the specified file.
+ *
+ * @param f File
+ */
+ public boolean accept(File f) {
+ if (f != null) {
+ // If there are no filters, always accept
+ if (filters.size() == 0)
+ return true;
+
+ if (f.isDirectory()) {
+ return true;
+ }
+
+ String extension = getExtension(f);
+
+ if ((extension != null) && (filters.get(extension) != null)) {
+ return true;
+ }
+ }
+
+ return false;
+ }
+
+ /**
+ * Returns true if this class is capable of processing the specified file.
+ *
+ * @param dir Directory.
+ * @param fileName File name.
+ *
+ */
+ public boolean accept(File dir, String fileName) {
+ return accept(new File(fileName));
+ }
+
+ /**
+ * Returns true if this class is capable of processing the specified file.
+ *
+ * @param fileName File name.
+ */
+ public boolean accept(String fileName) {
+ return accept(new File(fileName));
+ }
+
+ /**
+ * Returns true if this class is capable of processing the specified URL
+ *
+ * @param url the URL
+ * @param contentType the content-type of the URL
+ *
+ */
+ public boolean accept(URL url, String contentType) {
+ // Check for matching content type
+ if ((contentType != null) && (contentTypes != null)
+ && (contentTypes.get(contentType) != null)) {
+ return true;
+ }
+
+ // No content-type match -- try for an extnsion match
+ String extension = getExtension(url.getFile());
+
+ if ((extension != null) && (filters.get(extension) != null)) {
+ return true;
+ }
+
+ return false;
+ }
+
+ /**
+ * Return the extension portion of the file's name.
+ *
+ * @see #getExtension
+ * @see FileFilter#accept
+ */
+ public String getExtension(File f) {
+ if (f != null) {
+ return getExtension(f.getName());
+ } else {
+ return null;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param filename DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getExtension(String filename) {
+ if (filename != null) {
+ int i = filename.lastIndexOf('.');
+
+ if ((i > 0) && (i < (filename.length() - 1))) {
+ return filename.substring(i + 1).toLowerCase();
+ }
+
+ ;
+ }
+
+ return null;
+ }
+
+ /**
+ * Adds a filetype "dot" extension to filter against.
+ * <p/>
+ * For example: the following code will create a filter that filters
+ * out all files except those that end in ".jpg" and ".tif":
+ * <p/>
+ * ExampleFileFilter filter = new ExampleFileFilter();
+ * filter.addExtension("jpg");
+ * filter.addExtension("tif");
+ * <p/>
+ * Note that the "." before the extension is not needed and will be ignored.
+ */
+ public void addExtension(String extension) {
+ if (filters == null) {
+ filters = new Hashtable(5);
+ }
+
+ filters.put(extension.toLowerCase(), this);
+ fullDescription = null;
+ }
+
+ /**
+ * Adds a content-type to filter against.
+ * <p/>
+ * For example: the following code will create a filter that filters
+ * out all streams except those that are of type "text/xgmml+xml"
+ * and "text/xgmml":
+ * <p/>
+ * ExampleFileFilter filter = new ExampleFileFilter();
+ * filter.addContentType("text/xgmml+xml");
+ * filter.addContentType("text/xgmml");
+ * <p/>
+ */
+ public void addContentType(String type) {
+ if (contentTypes == null) {
+ contentTypes = new Hashtable(5);
+ }
+
+ contentTypes.put(type.toLowerCase(), this);
+ }
+
+ /**
+ * Returns the human readable description of this filter. For
+ * example: "JPEG and GIF Image Files (*.jpg, *.gif)"
+ *
+ * @see setDescription
+ * @see setExtensionListInDescription
+ * @see isExtensionListInDescription
+ * @see FileFilter#getDescription
+ */
+ public String getDescription() {
+ if (fullDescription == null) {
+ if ((description == null) || isExtensionListInDescription()) {
+ fullDescription = (description == null) ? "(" : (description + " (");
+
+ // build the description from the extension list
+ Enumeration extensions = filters.keys();
+
+ if (extensions != null) {
+ fullDescription += ("*."
+ + (String) (extensions.hasMoreElements()
+ ? extensions.nextElement() : "*"));
+
+ while (extensions.hasMoreElements()) {
+ fullDescription += (", *." + (String) extensions.nextElement());
+ }
+ }
+
+ fullDescription += ")";
+ } else {
+ fullDescription = description;
+ }
+ }
+
+ return fullDescription;
+ }
+
+ /**
+ * Sets the human readable description of this filter. For
+ * example: filter.setDescription("Gif and JPG Images");
+ *
+ * @see setDescription
+ * @see setExtensionListInDescription
+ * @see isExtensionListInDescription
+ */
+ public void setDescription(String description) {
+ this.description = description;
+ fullDescription = null;
+ }
+
+ /**
+ * Determines whether the extension list (.jpg, .gif, etc) should
+ * show up in the human readable description.
+ * <p/>
+ * Only relevent if a description was provided in the constructor
+ * or using setDescription();
+ *
+ * @see getDescription
+ * @see setDescription
+ * @see isExtensionListInDescription
+ */
+ public void setExtensionListInDescription(boolean b) {
+ useExtensionsInDescription = b;
+ fullDescription = null;
+ }
+
+ /**
+ * Returns whether the extension list (.jpg, .gif, etc) should
+ * show up in the human readable description.
+ * <p/>
+ * Only relevent if a description was provided in the constructor
+ * or using setDescription();
+ *
+ * @see getDescription
+ * @see setDescription
+ * @see setExtensionListInDescription
+ */
+ public boolean isExtensionListInDescription() {
+ return useExtensionsInDescription;
+ }
+
+ /**
+ * Returns the Set of file extension names.
+ */
+ public Set<String> getExtensionSet() {
+ return filters.keySet();
+ }
+
+ //
+ // The following code is an extension of the CyFileFilter duties.
+ // It provides extra functionality that allows a reader to be
+ // associated with a file type, which allows us to disassociate
+ // the checking of file type and file loading. Simply ask the
+ // file filter for the reader and you'll automatically get the
+ // correct one.
+ //
+
+ /**
+ * Returns the reader. This should be overridden by file type subclasses.
+ */
+ public GraphReader getReader(String fileName) {
+ return null;
+ }
+
+ /**
+ * Returns the reader. This should be overridden by file type subclasses.
+ */
+ public GraphReader getReader(URL url, URLConnection conn) {
+ return null;
+ }
+
+ /**
+ * Returns the nature of the file. "Nature" refers to a grouping
+ * of file types. For instance, GML, XGMML, and SIF are all file formats
+ * that contain graphs, therefore they belong to the GRAPH_NATURE. This
+ * allows the ImportHandler to return all file types with the same nature.
+ */
+ public String getFileNature() {
+ if (fileNature == null) {
+ return null;
+ }
+
+ return fileNature;
+ }
+
+ /**
+ * Sets the nature of the files for this filter.
+ * The files can be of the nature: Node, Edge, Graph, or Vizmap;
+ *
+ * @see setDescription
+ * @see setExtensionListInDescription
+ * @see isExtensionListInDescription
+ */
+ public void setFileNature(String nature) {
+ fileNature = nature;
+ }
+
+ /**
+ * Gets header of specified file.
+ */
+ protected String getHeader(File file) throws IOException {
+ BufferedReader bufferedReader = null;
+ String header = null;
+
+ try {
+ bufferedReader = new BufferedReader(new FileReader(file));
+
+ header = parseHeader(bufferedReader);
+ }
+ finally {
+ if (bufferedReader != null) {
+ bufferedReader.close();
+ }
+ }
+
+ return header;
+ }
+
+ protected String getHeader(URL url) throws IOException {
+ String header = null;
+ InputStream is = null;
+
+ try {
+ BufferedReader br = null;
+ final URLConnection connection = url.openConnection();
+ is = connection.getInputStream();
+ try {
+ br = new BufferedReader(new InputStreamReader(is));
+ header = parseHeader(br);
+ } finally {
+ if(br != null) {
+ br.close();
+ }
+ }
+ }
+ finally {
+ if (is != null) {
+ is.close();
+ }
+ }
+
+ return header;
+ }
+
+ private String parseHeader(BufferedReader bufferedReader) throws IOException {
+ StringBuffer header = new StringBuffer();
+
+ String line = bufferedReader.readLine();
+
+ int numLines = 0;
+
+ while ((line != null) && (numLines < 20)) {
+ header.append(line + "\n");
+ line = bufferedReader.readLine();
+ numLines++;
+ }
+
+ return header.toString();
+ }
+}
diff --git a/application/src/main/java/cytoscape/util/CyNetworkNaming.java b/application/src/main/java/cytoscape/util/CyNetworkNaming.java
new file mode 100644
index 0000000..8158c59
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/CyNetworkNaming.java
@@ -0,0 +1,154 @@
+/*
+ File: CyNetworkNaming.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.util;
+
+import java.awt.Component;
+import java.util.Set;
+
+import javax.swing.JOptionPane;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import cytoscape.CyNetworkTitleChange;
+
+
+/**
+ *
+ */
+public class CyNetworkNaming {
+ /**
+ * DOCUMENT ME!
+ *
+ * @param parentNetwork DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static String getSuggestedSubnetworkTitle(CyNetwork parentNetwork) {
+ for (int i = 0; true; i++) {
+ String nameCandidate = parentNetwork.getTitle() + "--child"
+ + ((i == 0) ? "" : ("." + i));
+
+ if (!isNetworkTitleTaken(nameCandidate))
+ return nameCandidate;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param desiredTitle DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static String getSuggestedNetworkTitle(String desiredTitle) {
+ for (int i = 0; true; i++) {
+ String titleCandidate = desiredTitle + ((i == 0) ? "" : ("." + i));
+
+ if (!isNetworkTitleTaken(titleCandidate))
+ return titleCandidate;
+ }
+ }
+
+ private static boolean isNetworkTitleTaken(String titleCandidate) {
+ final Set<CyNetwork> existingNetworks = Cytoscape.getNetworkSet();
+
+ for (CyNetwork existingNetwork: existingNetworks) {
+ if (existingNetwork.getTitle().equals(titleCandidate))
+ return true;
+ }
+
+ return false;
+ }
+
+ /**
+ * This will prompt the user to edit the title of a given CyNetork,
+ * and after ensuring that the network title is not already in use,
+ * this will assign that title to the given CyNetwork
+ * @para network is the CyNetwork whose title is to be changed
+ */
+ public static void editNetworkTitle(CyNetwork network) {
+ Component parent = Cytoscape.getDesktop();
+ String pname = network.getTitle();
+ String name = null;
+ String sname = "";
+ Object[] options = { "Try Again", "Cancel", "Use Suggestion" };
+ int value = JOptionPane.NO_OPTION;
+
+ while (true) {
+ cytoscape.dialogs.EditNetworkTitleDialog theDialog = new cytoscape.dialogs.EditNetworkTitleDialog(parent,
+ true,
+ pname);
+ theDialog.setLocationRelativeTo(parent);
+ theDialog.setVisible(true);
+ name = theDialog.getNewNetworkTitle();
+
+ //name = JOptionPane.showInputDialog(parent,
+ // "Please enter new network title: ", "Edit Network Title",
+ // JOptionPane.QUESTION_MESSAGE);
+ if (name == pname)
+ break;
+ else if ((name == null) || name.trim().equals("")) {
+ name = pname;
+
+ break;
+ } else if (isNetworkTitleTaken(name)) {
+ sname = getSuggestedNetworkTitle(name);
+ value = JOptionPane.showOptionDialog(parent,
+ "That network title already exists, try again or use \""
+ + sname + "\" instead: ",
+ "Duplicate Network Title",
+ JOptionPane.WARNING_MESSAGE,
+ JOptionPane.YES_NO_CANCEL_OPTION, null,
+ options, options[2]);
+
+ if (value == JOptionPane.NO_OPTION) {
+ name = pname;
+
+ break;
+ } else if (value == JOptionPane.CANCEL_OPTION) {
+ name = sname;
+
+ break;
+ }
+ } else
+
+ break;
+ }
+
+ network.setTitle(name);
+ }
+}
diff --git a/application/src/main/java/cytoscape/util/CytoscapeAction.java b/application/src/main/java/cytoscape/util/CytoscapeAction.java
new file mode 100644
index 0000000..e3682f2
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/CytoscapeAction.java
@@ -0,0 +1,381 @@
+/*
+ File: CytoscapeAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.util;
+
+import java.awt.event.ActionEvent;
+
+import java.util.LinkedList;
+import java.util.List;
+
+import javax.swing.AbstractAction;
+import javax.swing.event.MenuListener;
+import javax.swing.event.MenuEvent;
+
+import cytoscape.Cytoscape;
+import cytoscape.CyNetwork;
+import cytoscape.view.CyNetworkView;
+
+/**
+ *
+ */
+public abstract class CytoscapeAction extends AbstractAction implements MenuListener {
+ protected String preferredMenu = null;
+ protected String preferredButtonGroup = null;
+ protected Integer menuIndex = new Integer(-1);
+ protected boolean acceleratorSet = false;
+ protected int keyModifiers;
+ protected int keyCode;
+ protected String consoleName;
+ private static List actionList = new LinkedList();
+ protected boolean useCheckBoxMenuItem = false;
+
+ /**
+ * @beaninfo (rwb)
+ */
+ public CytoscapeAction() {
+ super();
+ initialize();
+ }
+
+ /**
+ * Creates a new CytoscapeAction object.
+ *
+ * @param name DOCUMENT ME!
+ */
+ public CytoscapeAction(String name) {
+ super(name);
+ this.consoleName = name;
+ consoleName = consoleName.replaceAll(":. \'", "");
+ actionList.add(this);
+ initialize();
+ }
+
+ /**
+ * Creates a new CytoscapeAction object.
+ *
+ * @param name DOCUMENT ME!
+ * @param icon DOCUMENT ME!
+ */
+ public CytoscapeAction(String name, javax.swing.Icon icon) {
+ super(name, icon);
+ this.consoleName = name;
+ consoleName = consoleName.replaceAll(" ", "");
+ actionList.add(this);
+ initialize();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static List getActionList() {
+ return actionList;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param name DOCUMENT ME!
+ */
+ public void setName(String name) {
+ this.consoleName = name;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getName() {
+ return consoleName;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String actionHelp() {
+ return "";
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String[] completions() {
+ return new String[] { };
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param argv DOCUMENT ME!
+ */
+ public void takeArgs(String[] argv) {
+ }
+
+ // implements AbstractAction
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public abstract void actionPerformed(ActionEvent e);
+
+ /**
+ * Initialization method called by all constructors. Envelop if you wish.
+ */
+ protected void initialize() {
+ // Do nothing.
+ }
+
+ /**
+ * The default clone() implementation delegates to the create() method of
+ * DataTypeUtilities.getDataTypeFactory( this.getClass() ). Override if your
+ * CytoscapeAction maintains state that must be transmitted to the clone.
+ */
+
+ // implements Cloneable
+ public Object clone() {
+ return this;
+ } // clone()
+
+ /**
+ * By default all CytoscapeActions wish to be included in CommunityMenuBars,
+ * but you may override if you wish.
+ *
+ * @return true If this Action should be included in a CommunityMenuBar.
+ * @see #getPrefferedMenu();
+ * @beaninfo (ri)
+ */
+ public boolean isInMenuBar() {
+ return true;
+ }
+
+ /**
+ * By default no CytoscapeActions wish to be included in CommunityToolBars,
+ * but you may override if you wish.
+ *
+ * @return true If this Action should be included in a CommunityMenuBar.
+ * @see #getPrefferedButtonGroup();
+ * @beaninfo (ri)
+ */
+ public boolean isInToolBar() {
+ return false;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param index DOCUMENT ME!
+ */
+ public void setPreferredIndex(int index) {
+ menuIndex = new Integer(index);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Integer getPrefferedIndex() {
+ return menuIndex;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param key_code DOCUMENT ME!
+ * @param key_mods DOCUMENT ME!
+ */
+ public void setAcceleratorCombo(int key_code, int key_mods) {
+ acceleratorSet = true;
+ keyCode = key_code;
+ keyModifiers = key_mods;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isAccelerated() {
+ return acceleratorSet;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getKeyCode() {
+ return keyCode;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getKeyModifiers() {
+ return keyModifiers;
+ }
+
+ /**
+ * This method returns a Menu specification string. Submenus are preceeded
+ * by dots in this string, so the result "File.Import" specifies the submenu
+ * "Import" of the menu "File". If the result is null, the menu will be
+ * placed in a default location.
+ *
+ * @return a Menu specification string, or null if this Action should be
+ * placed in a default Menu.
+ * @see #inMenuBar()
+ */
+ public String getPreferredMenu() {
+ return preferredMenu;
+ }
+
+ /**
+ * @beaninfo (rwb)
+ */
+ public void setPreferredMenu(String new_preferred) {
+ if ((preferredMenu == new_preferred)
+ || ((preferredMenu != null) && preferredMenu.equals(new_preferred))) {
+ return;
+ }
+
+ String old_preferred = preferredMenu;
+ preferredMenu = new_preferred;
+ firePropertyChange("preferredMenu", old_preferred, new_preferred);
+ } // setPreferredMenu( String )
+
+ /**
+ * This method returns a ButtonGroup specification string. Subgroups are
+ * preceeded by dots in this string, so the result "Edit.Selection Modes"
+ * specifies the subgroup "Selection Modes" of the group "Edit". If the
+ * result is null, the button will be placed in a default location.
+ *
+ * @return a ButtonGroup specification string, or null if the button for
+ * this Action should be placed in a default ButtonGroup.
+ * @see #inToolBar()
+ */
+ public String getPreferredButtonGroup() {
+ return preferredButtonGroup;
+ }
+
+ /**
+ * @beaninfo (rwb)
+ */
+ public void setPreferredButtonGroup(String new_preferred) {
+ if (preferredButtonGroup.equals(new_preferred)) {
+ return;
+ }
+
+ String old_preferred = preferredButtonGroup;
+ preferredButtonGroup = new_preferred;
+ firePropertyChange("preferredButtonGroup", old_preferred, new_preferred);
+ } // setPreferredButtonGroup( String )
+
+ /**
+ * Indicates whether a check box menu item should be used instead of a normal one.
+ */
+ boolean useCheckBoxMenuItem() {
+ return useCheckBoxMenuItem;
+ }
+
+ /**
+ * This method can be used at your discretion, but otherwise does nothing. It exists
+ * primarily to have access to menuSelected().
+ * @param e The triggering event.
+ */
+ public void menuCanceled(MenuEvent e) {}
+
+ /**
+ * This method can be used at your discretion, but otherwise does nothing. It exists
+ * primarily to have access to menuSelected().
+ * @param e The triggering event.
+ */
+ public void menuDeselected(MenuEvent e) {}
+
+ /**
+ * This method can be overridden by individual actions to set the state of menu items
+ * based on whatever unique circumstances that menu option cares about. If not overridden,
+ * this method does nothing.
+ * @param e The triggering event.
+ */
+ public void menuSelected(MenuEvent e) {}
+
+ //
+ // The following methods are utility methods that that enable or disable
+ // the action based on the state of Cytoscape. These methods are meant to
+ // reduce duplicate code since many actions demand the same state to be
+ // functional (e.g. a network and network view must exist). These methods
+ // are generally called from within implementations of {@link #menuSelected},
+ // but can be called from anywhere.
+ //
+
+ /**
+ * Enable the action if the current network exists and is not null.
+ */
+ protected void enableForNetwork() {
+ CyNetwork n = Cytoscape.getCurrentNetwork();
+ if ( n == null || n == Cytoscape.getNullNetwork() )
+ setEnabled(false);
+ else
+ setEnabled(true);
+ }
+
+ /**
+ * Enable the action if the current network and view exist and are not null.
+ */
+ protected void enableForNetworkAndView() {
+ CyNetwork n = Cytoscape.getCurrentNetwork();
+ if ( n == null || n == Cytoscape.getNullNetwork() ) {
+ setEnabled(false);
+ return;
+ }
+
+ CyNetworkView v = Cytoscape.getCurrentNetworkView();
+ if ( v == null || v == Cytoscape.getNullNetworkView() )
+ setEnabled(false);
+ else
+ setEnabled(true);
+ }
+}
diff --git a/application/src/main/java/cytoscape/util/CytoscapeMenuBar.java b/application/src/main/java/cytoscape/util/CytoscapeMenuBar.java
new file mode 100644
index 0000000..cb5ebba
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/CytoscapeMenuBar.java
@@ -0,0 +1,430 @@
+/*
+ File: CytoscapeMenuBar.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.util;
+
+
+import cytoscape.logger.CyLogger;
+
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Set;
+import java.util.StringTokenizer;
+
+import javax.swing.Action;
+import javax.swing.JMenu;
+import javax.swing.JMenuBar;
+import javax.swing.JMenuItem;
+import javax.swing.JCheckBoxMenuItem;
+
+
+/**
+ *
+ */
+public class CytoscapeMenuBar extends JMenuBar {
+ /**
+ *
+ */
+ public static final String DEFAULT_MENU_SPECIFIER = "Tools";
+ protected static final int NO_INDEX = -2;
+ protected String defaultMenuSpecifier = DEFAULT_MENU_SPECIFIER;
+ protected Set actionMembersSet = null;
+ protected Map actionMenuItemMap = null;
+ protected Map menuMap = null;
+
+
+ /**
+ * The Menu->Integer "effective last index"
+ * Map for Menus with menu items that want to be at the end.
+ */
+ protected Map menuEffectiveLastIndexMap = null;
+
+ /**
+ * @beaninfo (rwb)
+ */
+ private String identifier;
+
+ /**
+ * Default constructor.
+ */
+ public CytoscapeMenuBar() {
+ menuEffectiveLastIndexMap = new HashMap();
+ menuMap = new HashMap();
+ actionMenuItemMap = new HashMap();
+
+ // Load the first menu, just to please the layouter. Also make sure the
+ // menu bar doesn't get too small.
+ // "File" is always first
+ setMinimumSize(getMenu("File").getPreferredSize());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param menu_name DOCUMENT ME!
+ */
+ public void setDefaultMenuSpecifier(String menu_name) {
+ // TODO: If the existing menu exists, should we rename it?
+ defaultMenuSpecifier = menu_name;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getDefaultMenuSpecifier() {
+ return defaultMenuSpecifier;
+ }
+
+ /**
+ * If the given Action has a present and false inMenuBar property, return;
+ * otherwise delegate to addAction( String, Action ) with the value of its
+ * preferredMenu property, or null if it does not have that property.
+ */
+ public boolean addAction(Action action) {
+ return addAction(action, NO_INDEX);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param action DOCUMENT ME!
+ * @param index DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean addAction(Action action, int index) {
+ String menu_name = null;
+
+ if (action instanceof CytoscapeAction) {
+ if (((CytoscapeAction) action).isInMenuBar()) {
+ menu_name = ((CytoscapeAction) action).getPreferredMenu();
+ } else {
+ return false;
+ }
+ } else {
+ menu_name = DEFAULT_MENU_SPECIFIER;
+ }
+
+ if (index != NO_INDEX) {
+ ((CytoscapeAction) action).setPreferredIndex(index);
+ }
+
+ return addAction(menu_name, action);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param menu_name DOCUMENT ME!
+ * @param action DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean addAction(String menu_name, Action action) {
+ // At present we allow an Action to be in this menu bar only once.
+ JMenuItem menu_item = null;
+
+ if (actionMenuItemMap != null) {
+ menu_item = (JMenuItem) actionMenuItemMap.get(action);
+ }
+
+ if (menu_item != null) {
+ return false;
+ }
+
+ JMenu menu = getMenu(menu_name);
+ menu_item = createJMenuItem(action);
+
+ // Add an Accelerator Key, if wanted
+
+ // If it wants to be anywhere in particular, try to put it there..
+ Object index_object = new Integer(-1);
+
+ if (action instanceof CytoscapeAction) {
+ index_object = ((CytoscapeAction) action).getPrefferedIndex();
+
+ if (((CytoscapeAction) action).isAccelerated()) {
+ menu_item.setAccelerator(javax.swing.KeyStroke.getKeyStroke(((CytoscapeAction) action)
+ .getKeyCode(),
+ ((CytoscapeAction) action)
+ .getKeyModifiers()));
+ }
+
+ menu.addMenuListener((CytoscapeAction)action);
+ }
+
+ if (index_object != null) {
+ int index = -1;
+
+ if (index_object instanceof Integer) {
+ index = ((Integer) index_object).intValue();
+ } else if (index_object instanceof String) {
+ try {
+ index = Integer.parseInt((String) index_object);
+ } catch (NumberFormatException e) {
+ CyLogger.getLogger().warn("WARNING: The action " + action
+ + " has an \"index\" property but its String value"
+ + " cannot be converted to an int. Ignoring.");
+ index_object = null;
+ }
+ } else {
+ CyLogger.getLogger().warn("WARNING: The action " + action
+ + " has an \"index\" property but its value is neither"
+ + " an Integer nor a String. Ignoring.");
+ index_object = null;
+ }
+
+ if (index_object != null) {
+ if (index < 0) {
+ index = (menu.getItemCount() + (index + 1));
+
+ if (index < 0) {
+ index = 0;
+ } else {
+ Integer effective_last_index = (Integer) menuEffectiveLastIndexMap.get(menu);
+
+ if (effective_last_index == null) {
+ menuEffectiveLastIndexMap.put(menu, new Integer(index));
+ index += 1;
+ } else if (effective_last_index.intValue() >= index) {
+ menuEffectiveLastIndexMap.put(menu, new Integer(index));
+ }
+ }
+ }
+
+ menu.insert(menu_item, index);
+ }
+ }
+
+ if (index_object == null) {
+ boolean added_it = false;
+
+ Integer effective_last_index = (Integer) menuEffectiveLastIndexMap.get(menu);
+
+ if (effective_last_index != null) {
+ menu.insert(menu_item, effective_last_index.intValue());
+ menuEffectiveLastIndexMap.put(menu, new Integer(effective_last_index.intValue() + 1));
+ added_it = true;
+ }
+
+ if (!added_it) {
+ menu.add(menu_item);
+ }
+ }
+
+ actionMenuItemMap.put(action, menu_item);
+
+ return true;
+ }
+
+ /**
+ * If the given Action has a present and false inMenuBar property, return;
+ * otherwise if there's a menu item for the action, remove it. Its menu is
+ * determined my its preferredMenu property if it is present; otherwise by
+ * defaultMenuSpecifier.
+ */
+ public boolean removeAction(Action action) {
+ if (actionMenuItemMap == null) {
+ return false;
+ }
+
+ JMenuItem menu_item = (JMenuItem) actionMenuItemMap.remove(action);
+
+ if (menu_item == null) {
+ return false;
+ }
+
+ String menu_name = null;
+
+ if (action instanceof CytoscapeAction) {
+ if (((CytoscapeAction) action).isInMenuBar()) {
+ menu_name = ((CytoscapeAction) action).getPreferredMenu();
+ } else {
+ return false;
+ }
+ } else {
+ menu_name = DEFAULT_MENU_SPECIFIER;
+ }
+
+ if (menu_name == null) {
+ menu_name = defaultMenuSpecifier;
+ }
+
+ getMenu(menu_name).remove(menu_item);
+
+ return true;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param menu_string DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public JMenu getMenu(String menu_string) {
+ return getMenu(menu_string, -1);
+ }
+
+ /**
+ * @return the menu named in the given String. The String may contain
+ * multiple menu names, separated by dots ('.'). If any contained
+ * menu name does not correspond to an existing menu, then that menu
+ * will be created as a child of the menu preceeding the most recent
+ * dot or, if there is none, then as a child of this MenuBar.
+ */
+ public JMenu getMenu(String menu_string, int parentPosition) {
+ if (menu_string == null) {
+ menu_string = getDefaultMenuSpecifier();
+ }
+
+ StringTokenizer st = new StringTokenizer(menu_string, ".");
+ String menu_token;
+ JMenu parent_menu = null;
+ JMenu menu = null;
+
+ // The menu_key is introduced to find the correct submenu relative
+ // to the specified top-level menus, this is necessary in order to
+ // have submenus with equal names in different top-level menus,
+ // e.g. mymenu.export, file.export, xxx.yyy.export, ... . previously,
+ // the string in "menu_token" was used and the first occurence of a
+ // particular menu was used.
+ String menu_key = null;
+
+ while (st.hasMoreTokens()) {
+ menu_token = (String) st.nextToken();
+ menu_key = menu_key == null ? menu_token : menu_key + "." + menu_token;
+
+ if (menuMap.containsKey(menu_key)) {
+ parent_menu = (JMenu) menuMap.get(menu_key);
+ } else {
+ menu = createJMenu(menu_token);
+
+ if (parent_menu == null) {
+ this.add(menu);
+ invalidate();
+ } else {
+ parent_menu.add(menu, parentPosition);
+ }
+
+ menuMap.put(menu_key, menu);
+ parent_menu = menu;
+ }
+ }
+
+ if (menu == null) {
+ return parent_menu;
+ }
+
+ return menu;
+ }
+
+ /**
+ * CytoscapeMenuBars are unique -- this equals() method returns true iff the
+ * other object == this.
+ */
+ public boolean equals(Object other_object) {
+ return (this == other_object);
+ }
+
+ /**
+ * implements CommunityMember
+ *
+ * @return identifier
+ */
+ public String getIdentifier() {
+ return identifier;
+ }
+
+ /**
+ * imlements Reidentifiable
+ * @beaninfo (rwb)
+ */
+ public void setIdentifier(String new_identifier) {
+ if (identifier == null) {
+ if (new_identifier == null) {
+ return;
+ }
+ } else if (new_identifier != null) {
+ if (identifier.equals(new_identifier)) {
+ return;
+ }
+ }
+
+ String old_identifier = identifier;
+ identifier = new_identifier;
+ firePropertyChange("identifier", old_identifier, new_identifier);
+ }
+
+ /**
+ * imlements Reidentifiable
+ * @return true (always)
+ */
+ public boolean isReidentificationEnabled() {
+ return true;
+ }
+
+ /**
+ * Delegates to {@link #getIdentifier()}.
+ */
+ public String toString() {
+ return getIdentifier();
+ }
+
+ /**
+ * Factory method for instantiating objects of type JMenu
+ */
+ public JMenu createJMenu(String title) {
+ JMenu menu = new JMenu(title);
+ revalidate();
+ repaint();
+
+ return menu;
+ }
+
+ /**
+ * Factory method for instantiating the menuItems in the menu.
+ */
+ protected JMenuItem createJMenuItem(Action action) {
+ if ( action instanceof CytoscapeAction )
+ if ( ((CytoscapeAction)action).useCheckBoxMenuItem() )
+ return new JCheckBoxMenuItem(action);
+
+ return new JMenuItem(action);
+ }
+}
diff --git a/application/src/main/java/cytoscape/util/CytoscapeProgressMonitor.java b/application/src/main/java/cytoscape/util/CytoscapeProgressMonitor.java
new file mode 100644
index 0000000..6cf742e
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/CytoscapeProgressMonitor.java
@@ -0,0 +1,193 @@
+/*
+ File: CytoscapeProgressMonitor.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+//----------------------------------------------------------------------
+// CytoscapeProgressMonitor
+//----------------------------------------------------------------------
+/**
+ * $Revision: 14060 $
+ * $Date: 2008-05-20 22:13:18 +0200 (Tue, 20 May 2008) $
+ * @author iliana iavila at systemsbiology.org
+ */
+
+//----------------------------------------------------------------------
+package cytoscape.util;
+
+
+//----------------------------------------------------------------------
+import cytoscape.logger.CyLogger;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import java.lang.*;
+
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+import java.util.Timer;
+import java.util.TimerTask;
+
+import javax.swing.*;
+
+
+//---------------------------------------------------------------------------------------
+/**
+ * CytoscapeProgressMonitor. A progress monitor for cytoscape. It is recommended
+ * to run the monitor in a different Thread, specially if the user class wants
+ * to wait until the task is done running to resume.
+ */
+public class CytoscapeProgressMonitor extends JFrame implements Runnable {
+ /**
+ *
+ */
+ public final static int ONE_SECOND = 1000;
+ private ProgressMonitor pMonitor;
+ private Timer timer;
+ private Component parentComponent;
+ private MonitoredTask monitoredTask;
+
+ /**
+ * Construtor.
+ * @param monitored_task the task to be monitored
+ */
+ public CytoscapeProgressMonitor(MonitoredTask monitored_task) {
+ this(monitored_task, (Component) null);
+ }
+
+ /**
+ * Constructor.
+ * @param monitored_task the task to be monitored
+ * @param parent_component the component with respect to which we will draw the monitor dialog
+ */
+ public CytoscapeProgressMonitor(MonitoredTask monitored_task, Component parent_component) {
+ this.monitoredTask = monitored_task;
+ this.parentComponent = parent_component;
+ } //CytoscapeProgressMonitor
+
+ /**
+ * Implementes Runnable.run()
+ */
+ public void run() {
+ startMonitor(true);
+ } //run ()
+
+ /**
+ * Starts the monitor by running the monitoredTask.
+ * @param wait_for_task whether or not we should wait for the task to be done before we return
+ * from this method
+ */
+ public void startMonitor(boolean wait_for_task) {
+ if (this.parentComponent != null) {
+ this.parentComponent.setEnabled(false);
+ }
+
+ Thread monitoringThread = new MonitoringThread();
+ // run in separate thread so that monitor can get updated
+ initializeMonitor();
+ monitoringThread.start();
+ // If wait_for_task is true,
+ // the current thread will return from go() only when the task is done running
+ monitoredTask.go(wait_for_task);
+ } // startMonitor()
+
+ class MonitoringThread extends Thread {
+ MonitoringThread() {
+ super();
+ } //cons
+
+ public void run() {
+ java.util.Timer mytimer = new java.util.Timer(false);
+ mytimer.scheduleAtFixedRate(new UpdateProgressMonitor(mytimer), 0, ONE_SECOND);
+ } //run
+
+ class UpdateProgressMonitor extends TimerTask {
+ private boolean firstTick = true;
+ private java.util.Timer myTimer;
+
+ UpdateProgressMonitor(java.util.Timer timer) {
+ super();
+ this.myTimer = timer;
+ } //cons
+
+ public void run() {
+ // if(firstTick){
+ //CyLogger.getLogger().info("UpdateProgressMonitor: " + Thread.currentThread());
+ //firstTick = false;
+ //System.out.flush();
+ //}
+ if (pMonitor.isCanceled()) {
+ //CyLogger.getLogger().info("pMonitor.isCanceled() == " + pMonitor.isCanceled());
+ pMonitor.close();
+ monitoredTask.cancel();
+ myTimer.cancel();
+
+ if (parentComponent != null) {
+ parentComponent.setEnabled(true);
+ }
+ } else if (monitoredTask.done()) {
+ //CyLogger.getLogger().info(monitoredTask.getTaskName() + " monitoredTask.done() == " + monitoredTask.done());
+ pMonitor.close();
+ monitoredTask.stop();
+ myTimer.cancel();
+
+ if (parentComponent != null) {
+ parentComponent.setEnabled(true);
+ }
+ } else {
+ pMonitor.setNote(monitoredTask.getMessage());
+ pMonitor.setProgress(monitoredTask.getCurrent());
+ }
+ } //run
+ } //internal class UpdateProgressMonitor
+ } //internal class MonitoringThread
+
+ /**
+ * It creates and initializes a progress monitor.
+ */
+ protected void initializeMonitor() {
+ String message = monitoredTask.getTaskName();
+ pMonitor = new ProgressMonitor(this.parentComponent, new Object[] { message }, null, 0,
+ monitoredTask.getLengthOfTask());
+
+ CyLogger.getLogger().info("Task length: " + monitoredTask.getLengthOfTask());
+ CyLogger.getLogger().info("About to Popup");
+ pMonitor.setProgress(0);
+ pMonitor.setMillisToDecideToPopup(0);
+ pMonitor.setMillisToPopup(0);
+ } //initializeMonitor
+} //CytoscapeProgressMonitor class
diff --git a/application/src/main/java/cytoscape/util/CytoscapeToolBar.java b/application/src/main/java/cytoscape/util/CytoscapeToolBar.java
new file mode 100644
index 0000000..a358bcc
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/CytoscapeToolBar.java
@@ -0,0 +1,169 @@
+/*
+ File: CytoscapeToolBar.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.util;
+
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Set;
+
+import javax.swing.Action;
+import javax.swing.JButton;
+import javax.swing.JToolBar;
+
+
+/**
+ *
+ */
+public class CytoscapeToolBar extends JToolBar {
+ protected Map actionButtonMap = null;
+ protected Set actionMembersSet;
+
+ /**
+ * Default constructor delegates to the superclass void constructor and then
+ * calls {@link #initializeCytoscapeToolBar()}.
+ */
+ public CytoscapeToolBar() {
+ super("Cytoscape Tools");
+ initializeCytoscapeToolBar();
+ }
+
+ /**
+ * Envelop if you wish. Presently does nothing.
+ */
+ protected void initializeCytoscapeToolBar() {
+ }
+
+ /**
+ * If the given Action has an absent or false inToolBar property, return;
+ * otherwise delegate to addAction( String, Action ) with the value of its
+ * preferredButtonGroup property, or null if it does not have that property.
+ */
+ public boolean addAction(Action action) {
+ String button_group_name = null;
+
+ if (action instanceof CytoscapeAction) {
+ if (((CytoscapeAction) action).isInToolBar()) {
+ button_group_name = ((CytoscapeAction) action).getPreferredButtonGroup();
+ } else {
+ return false;
+ }
+ }
+
+ return addAction(button_group_name, action);
+ } // addAction( action )
+
+ /**
+ * Note that this presently ignores the button group name.
+ */
+ public boolean addAction(String button_group_name, Action action) {
+ // At present we allow an Action to be in this tool bar only once.
+ JButton button = null;
+
+ if (actionButtonMap != null) {
+ button = (JButton) actionButtonMap.get(action);
+ }
+
+ if (button != null) {
+ return false;
+ }
+
+ button = createJButton(action);
+ button.setBorderPainted(false);
+ button.setRolloverEnabled(true);
+
+ // If SHORT_DESCRIPTION exists, use this as tool-tip
+ String shortDescription = (String) action.getValue(Action.SHORT_DESCRIPTION);
+
+ if (shortDescription != null) {
+ button.setToolTipText(shortDescription);
+ }
+
+ // TODO: Do something with the preferred button group.
+ add(button);
+
+ //add( action );
+ if (actionButtonMap == null) {
+ actionButtonMap = createActionButtonMap();
+ }
+
+ actionButtonMap.put(action, button);
+
+ return true;
+ } // addAction( button_group_name, action )
+
+ /**
+ * If the given Action has an absent or false inToolBar property, return;
+ * otherwise if there's a button for the action, remove it.
+ */
+ public boolean removeAction(Action action) {
+ if (actionButtonMap == null) {
+ return false;
+ }
+
+ JButton button = (JButton) actionButtonMap.remove(action);
+
+ if (button == null) {
+ return false;
+ }
+
+ remove(button);
+
+ return true;
+ } // removeAction( action )
+
+ /**
+ * CytoscapeToolBars are unique -- this equals() method returns true
+ * iff the other object == this.
+ */
+ public boolean equals(Object other_object) {
+ return (this == other_object);
+ } // equals( Object )
+
+ /**
+ * Factory method for instantiating the buttons in the toolbar.
+ */
+ protected JButton createJButton(Action action) {
+ return new JButton(action);
+ }
+
+ /**
+ * Factory method for instantiating the action->button map.
+ */
+ protected Map createActionButtonMap() {
+ return new HashMap();
+ }
+} // class CytoscapeToolBar
diff --git a/application/src/main/java/cytoscape/util/Exec.java b/application/src/main/java/cytoscape/util/Exec.java
new file mode 100644
index 0000000..10a05a7
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/Exec.java
@@ -0,0 +1,303 @@
+/*
+ File: Exec.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// Exec.java
+
+// exec a child process, and get its stdout & stderr
+package cytoscape.util;
+
+import cytoscape.logger.CyLogger;
+
+import java.io.*;
+import java.io.IOException;
+import java.io.InputStreamReader;
+
+import java.util.Enumeration;
+import java.util.Vector;
+
+
+/**
+ *
+ */
+public class Exec {
+ String[] cmd;
+ Vector stdoutResults;
+ Vector stderrResults;
+ String stringToSendToStandardInput;
+ boolean runInBackground = false;
+ String stdout;
+ String stderr;
+ static CyLogger logger = CyLogger.getLogger(Exec.class);
+
+ /**
+ * Creates a new Exec object.
+ */
+ public Exec() {
+ this(null);
+ }
+
+ /**
+ * Creates a new Exec object.
+ *
+ * @param cmd DOCUMENT ME!
+ */
+ public Exec(String[] cmd) {
+ this.cmd = cmd;
+ stdoutResults = new Vector(100); // just guessing...
+ stderrResults = new Vector(10);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param input DOCUMENT ME!
+ */
+ public void setStandardInput(String input) {
+ stringToSendToStandardInput = input;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param newValue DOCUMENT ME!
+ */
+ public void setRunInBackground(boolean newValue) {
+ runInBackground = newValue;
+
+ int length = cmd.length;
+ String[] revisedCmd = new String[length + 1];
+
+ for (int i = 0; i < length; i++)
+ revisedCmd[i] = cmd[i];
+
+ revisedCmd[length] = " &";
+
+ cmd = revisedCmd;
+ } // setRunInBackground
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getCmd() {
+ StringBuffer sb = new StringBuffer();
+
+ for (int i = 0; i < cmd.length; i++) {
+ sb.append(cmd[i]);
+ sb.append(" ");
+ }
+
+ return sb.toString();
+ } // getCmd
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int run() {
+ int execExitValue = -1; // be pessimistic
+
+ StringBuffer cmdSB = new StringBuffer();
+
+ for (int i = 0; i < cmd.length; i++) {
+ cmdSB.append(cmd[i]);
+ cmdSB.append(" ");
+ }
+
+ try {
+ Runtime runtime = Runtime.getRuntime();
+
+ // logger.info (" --> just before exec: \n\t" + getCmd ());
+ //Process process = runtime.exec (cmd);
+ Process process = runtime.exec(cmdSB.toString());
+ BufferedReader stdoutReader = new BufferedReader(new InputStreamReader(process.getInputStream()));
+ BufferedReader stderrReader = new BufferedReader(new InputStreamReader(process.getErrorStream()));
+
+ if (stringToSendToStandardInput != null) {
+ // A PrintStream adds functionality to another output stream, namely the
+ // ability to print representations of various data values
+ // conveniently. Two other features are provided as well. Unlike other
+ // output streams, a PrintStream never throws an IOException; instead,
+ // exceptional situations merely set an internal flag that can be tested
+ // via the checkError method. Optionally, a PrintStream can be created so
+ // as to flush automatically; this means that the flush method is
+ // automatically invoked after a byte array is written, one of
+ // the println methods is invoked, or a newline character or
+ // byte ('\n') is written.
+ PrintStream stdinWriter = null;
+ try {
+ stdinWriter = new PrintStream(process.getOutputStream(), true);
+ stdinWriter.print(stringToSendToStandardInput);
+ }
+ finally {
+ if (stdinWriter != null)
+ {
+ stdinWriter.close();
+ }
+ }
+ }
+
+ try {
+ execExitValue = process.waitFor();
+ } catch (InterruptedException e) {
+ logger.warn("Interrupted waiting for child process: "+e.getMessage());
+ }
+
+ String stdoutResult;
+
+ while ((stdoutResult = stdoutReader.readLine()) != null) {
+ stdoutResults.addElement(stdoutResult);
+ }
+
+ String stderrResult;
+
+ while ((stderrResult = stderrReader.readLine()) != null) {
+ stderrResults.addElement(stderrResult);
+ }
+ } // try
+ catch (IOException e) {
+ logger.warn("I/O error while communicating with child process: "+e.getMessage());
+ }
+
+ return execExitValue;
+ } // run
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public int runThreaded() throws Exception {
+ int execExitValue = -1; // be pessimistic
+
+ StringBuffer cmdSB = new StringBuffer();
+
+ for (int i = 0; i < cmd.length; i++) {
+ cmdSB.append(cmd[i]);
+ cmdSB.append(" ");
+ }
+
+ Runtime runtime = Runtime.getRuntime();
+ Process process = runtime.exec(cmdSB.toString());
+
+ final BufferedReader stdoutReader = new BufferedReader(new InputStreamReader(process.getInputStream()));
+ final BufferedReader stderrReader = new BufferedReader(new InputStreamReader(process.getErrorStream()));
+ final StringBuffer stdoutSB = new StringBuffer();
+ final StringBuffer stderrSB = new StringBuffer();
+
+ Thread stdoutReadingThread = new Thread() {
+ public void run() {
+ String s;
+
+ try {
+ while ((s = stdoutReader.readLine()) != null) {
+ stdoutSB.append(s + "\n");
+ } // while
+ } // trey
+ catch (Exception exc0) {
+ logger.warn("error reading output from command '"+getCmd()+"': "+ exc0.toString());
+ } // catch
+ }
+ ; // run
+ }; // thread
+
+ Thread stderrReadingThread = new Thread() {
+ public void run() {
+ String s;
+
+ try {
+ while ((s = stderrReader.readLine()) != null) {
+ stderrSB.append(s + "\n");
+ } // while
+ } // try
+ catch (Exception exc1) {
+ logger.warn("error reading errors from command '"+getCmd()+"': "+ exc1.toString());
+ } // catch
+ }
+ ; // run
+ }; // thread
+
+ stdoutReadingThread.start();
+ stderrReadingThread.start();
+ execExitValue = process.waitFor();
+
+ stdout = stdoutSB.toString();
+ stderr = stderrSB.toString();
+
+ return execExitValue;
+ } // runThreaded
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Vector getStdout() {
+ return stdoutResults;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Vector getStderr() {
+ return stderrResults;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getStdoutAsString() {
+ return stdout;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getStderrAsString() {
+ return stderr;
+ }
+} // Exec.java
diff --git a/application/src/main/java/cytoscape/util/FileUtil.java b/application/src/main/java/cytoscape/util/FileUtil.java
new file mode 100644
index 0000000..a8f2f8e
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/FileUtil.java
@@ -0,0 +1,544 @@
+/*
+ File: FileUtil.java
+
+ Copyright (c) 2006, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.util;
+
+import cytoscape.Cytoscape;
+import cytoscape.CytoscapeInit;
+import cytoscape.logger.CyLogger;
+
+import cytoscape.task.TaskMonitor;
+
+import java.awt.Component;
+import java.awt.Container;
+import java.awt.FileDialog;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+
+import java.net.URL;
+
+import java.util.Iterator;
+
+import javax.swing.JFileChooser;
+import javax.swing.JList;
+import javax.swing.JOptionPane;
+
+
+/**
+ * Provides a platform-dependent way to open files. Mainly
+ * because Mac would prefer that you use java.awt.FileDialog
+ * instead of the Swing FileChooser.
+ */
+public abstract class FileUtil {
+ /**
+ * This class exists to work around a bug in JFileChooser that will allow editing of
+ * file and directory names even when LOAD has been specified.
+ */
+ static class NoEditFileChooser extends JFileChooser {
+ public NoEditFileChooser(final File start) {
+ super(start);
+
+ final JList list = findFileList(this);
+ if (list == null)
+ return;
+
+ for (MouseListener l : list.getMouseListeners()) {
+ if (l.getClass().getName().indexOf("FilePane") >= 0) {
+ list.removeMouseListener(l);
+ list.addMouseListener(new MyMouseListener(l));
+ }
+ }
+ }
+
+ private JList findFileList(final Component comp) {
+ if (comp instanceof JList)
+ return (JList)comp;
+
+ if (comp instanceof Container) {
+ for (Component child : ((Container)comp).getComponents()) {
+ JList list = findFileList(child);
+ if (list != null)
+ return list;
+ }
+ }
+
+ return null;
+ }
+
+ private class MyMouseListener extends MouseAdapter {
+ MyMouseListener(final MouseListener listenerChain) {
+ m_listenerChain = listenerChain;
+ }
+
+ public void mouseClicked(final MouseEvent event) {
+ if (event.getClickCount() > 1)
+ m_listenerChain.mouseClicked(event);
+ }
+
+ private MouseListener m_listenerChain;
+ }
+ }
+
+ protected static CyLogger logger = CyLogger.getLogger(FileUtil.class);
+
+ /**
+ *
+ */
+ public static int LOAD = FileDialog.LOAD;
+
+ /**
+ *
+ */
+ public static int SAVE = FileDialog.SAVE;
+
+ /**
+ *
+ */
+ public static int CUSTOM = LOAD + SAVE;
+
+ /**
+ * A string that defines a simplified java regular expression for a URL.
+ * This may need to be updated to be more precise.
+ */
+ public static final String urlPattern =
+ "^(jar\\:)?((http|https|ftp|file)+\\:\\/+\\S+)(\\!\\/\\S*)?$";
+
+ /**
+ * Returns a File object, this method should be used instead
+ * of rolling your own JFileChooser.
+ *
+ * @return the location of the selcted file
+ * @param title the title of the dialog box
+ * @param load_save_custom a flag for the type of file dialog
+ */
+ public static File getFile(String title, int load_save_custom) {
+ return getFile(title, load_save_custom, new CyFileFilter[] { }, null, null);
+ }
+
+ /**
+ * Returns a File object, this method should be used instead
+ * of rolling your own JFileChooser.
+ *
+ * @return the location of the selected file
+ * @param title the title of the dialog box
+ * @param load_save_custom a flag for the type of file dialog
+ * @param filters an array of CyFileFilters that let you filter
+ * based on extension
+ */
+ public static File getFile(String title, int load_save_custom, CyFileFilter[] filters) {
+ return getFile(title, load_save_custom, filters, null, null);
+ }
+
+ /**
+ * Returns a File object, this method should be used instead
+ * of rolling your own JFileChooser.
+ *
+ * @return the location of the selected file
+ * @param title the title of the dialog box
+ * @param load_save_custom a flag for the type of file dialog
+ * @param filters an array of CyFileFilters that let you filter
+ * based on extension
+ * @param selectedFile selectedFile
+ */
+ public static File getFile(String title, int load_save_custom, CyFileFilter filter, File selectedFile) {
+ CyFileFilter[] filters = new CyFileFilter[1];
+ filters[0] = filter;
+ File[] selectedFiles = new File[1];
+ selectedFiles[0] = selectedFile;
+
+ File[] result = getFiles(null, title, load_save_custom, filters, null, null, false, selectedFiles);
+
+ return ((result == null) || (result.length <= 0)) ? null : result[0];
+
+ }
+
+
+ /**
+ * Returns a File object, this method should be used instead
+ * of rolling your own JFileChooser.
+ *
+ * @return the location of the selcted file
+ * @param title the title of the dialog box
+ * @param load_save_custom a flag for the type of file dialog
+ * @param filters an array of CyFileFilters that let you filter
+ * based on extension
+ * @param start_dir an alternate start dir, if null the default
+ * cytoscape MUD will be used
+ * @param custom_approve_text if this is a custom dialog, then
+ * custom text should be on the approve
+ * button.
+ */
+ public static File getFile(String title, int load_save_custom, CyFileFilter[] filters,
+ String start_dir, String custom_approve_text) {
+ File[] result = getFiles(title, load_save_custom, filters, start_dir, custom_approve_text,
+ false);
+
+ return ((result == null) || (result.length <= 0)) ? null : result[0];
+ }
+
+ /**
+ * Returns an array of File objects, this method should be used instead
+ * of rolling your own JFileChooser.
+ *
+ * @return the location of the selcted file
+ * @param title the title of the dialog box
+ * @param load_save_custom a flag for the type of file dialog
+ * @param filters an array of CyFileFilters that let you filter
+ * based on extension
+ */
+ public static File[] getFiles(String title, int load_save_custom, CyFileFilter[] filters) {
+ return getFiles(null,title, load_save_custom, filters, null, null, true);
+ }
+
+ /**
+ * Returns an array of File objects, this method should be used instead
+ * of rolling your own JFileChooser.
+ * @return the location of the selcted file
+ * @param parent the parent component of the JFileChooser dialog
+ * @param title the title of the dialog box
+ * @param load_save_custom a flag for the type of file dialog
+ * @param filters an array of CyFileFilters that let you filter
+ * based on extension
+ */
+ public static File[] getFiles(Component parent, String title, int load_save_custom, CyFileFilter[] filters) {
+ return getFiles(parent,title, load_save_custom, filters, null, null, true);
+ }
+
+
+ /**
+ * Returns a list of File objects, this method should be used instead
+ * of rolling your own JFileChooser.
+ *
+ * @return and array of selected files, or null if none are selected
+ * @param title the title of the dialog box
+ * @param load_save_custom a flag for the type of file dialog
+ * @param filters an array of CyFileFilters that let you filter
+ * based on extension
+ * @param start_dir an alternate start dir, if null the default
+ * cytoscape MUD will be used
+ * @param custom_approve_text if this is a custom dialog, then
+ * custom text should be on the approve
+ * button.
+ */
+ public static File[] getFiles(String title, int load_save_custom, CyFileFilter[] filters,
+ String start_dir, String custom_approve_text) {
+ return getFiles(null,title, load_save_custom, filters, start_dir, custom_approve_text, true);
+ }
+
+
+ /**
+ * Returns a list of File objects, this method should be used instead
+ * of rolling your own JFileChooser.
+ *
+ * @return and array of selected files, or null if none are selected
+ * @param title the title of the dialog box
+ * @param load_save_custom a flag for the type of file dialog
+ * @param filters an array of CyFileFilters that let you filter
+ * based on extension
+ * @param start_dir an alternate start dir, if null the default
+ * cytoscape MUD will be used
+ * @param custom_approve_text if this is a custom dialog, then
+ * custom text should be on the approve
+ * button.
+ * @param multiselect Enable selection of multiple files (Macs are
+ * still limited to a single file because we use
+ * FileDialog there -- is this fixed in Java 1.5?)
+ */
+ public static File[] getFiles(String title, int load_save_custom, CyFileFilter[] filters,
+ String start_dir, String custom_approve_text, boolean multiselect) {
+ return getFiles(null, title, load_save_custom, filters, start_dir, custom_approve_text, multiselect);
+ }
+
+ /**
+ * Returns a list of File objects, this method should be used instead
+ * of rolling your own JFileChooser.
+ *
+ * @return and array of selected files, or null if none are selected
+ * @param parent the parent of the JFileChooser dialog
+ * @param title the title of the dialog box
+ * @param load_save_custom a flag for the type of file dialog
+ * @param filters an array of CyFileFilters that let you filter
+ * based on extension
+ * @param start_dir an alternate start dir, if null the default
+ * cytoscape MUD will be used
+ * @param custom_approve_text if this is a custom dialog, then
+ * custom text should be on the approve
+ * button.
+ * @param multiselect Enable selection of multiple files (Macs are
+ * still limited to a single file because we use
+ * FileDialog there -- is this fixed in Java 1.5?)
+ */
+ public static File[] getFiles(Component parent, String title, int load_save_custom, CyFileFilter[] filters,
+ String start_dir, String custom_approve_text, boolean multiselect) {
+ return getFiles(parent, title, load_save_custom, filters, start_dir, custom_approve_text, multiselect, null);
+ }
+
+
+ /**
+ * Returns a list of File objects, this method should be used instead
+ * of rolling your own JFileChooser.
+ *
+ * @return and array of selected files, or null if none are selected
+ * @param parent the parent of the JFileChooser dialog
+ * @param title the title of the dialog box
+ * @param load_save_custom a flag for the type of file dialog
+ * @param filters an array of CyFileFilters that let you filter
+ * based on extension
+ * @param start_dir an alternate start dir, if null the default
+ * cytoscape MUD will be used
+ * @param custom_approve_text if this is a custom dialog, then
+ * custom text should be on the approve
+ * button.
+ * @param multiselect Enable selection of multiple files (Macs are
+ * still limited to a single file because we use
+ * FileDialog there -- is this fixed in Java 1.5?)
+ * @param selectedFiles The list of selected files
+ */
+ public static File[] getFiles(Component parent, String title, int load_save_custom, CyFileFilter[] filters,
+ String start_dir, String custom_approve_text, boolean multiselect, File[] selectedFiles) {
+
+ if (parent == null) {
+ parent = Cytoscape.getDesktop();
+ }
+
+ File start = null;
+
+ if (start_dir == null) {
+ start = CytoscapeInit.getMRUD();
+ } else {
+ start = new File(start_dir);
+ }
+
+ String osName = System.getProperty("os.name");
+
+ //logger.info( "Os name: "+osName );
+ if (osName.startsWith("Mac")) {
+ // this is a Macintosh, use the AWT style file dialog
+ FileDialog chooser = new FileDialog(Cytoscape.getDesktop(), title, load_save_custom);
+
+ final File mostRecentlyUsedDirectory = CytoscapeInit.getMRUD();
+ if (mostRecentlyUsedDirectory != null)
+ chooser.setDirectory(mostRecentlyUsedDirectory.toString());
+
+ if (!multiselect && selectedFiles != null)
+ chooser.setFile(selectedFiles[0].toString());
+
+ // we can only set the one filter; therefore, create a special
+ // version of CyFileFilter that contains all extensions
+ CyFileFilter fileFilter = new CyFileFilter();
+
+ for (int i = 0; i < filters.length; i++) {
+ Iterator iter;
+ for (iter = filters[i].getExtensionSet().iterator(); iter.hasNext(); /* Empty! */)
+ fileFilter.addExtension((String) iter.next());
+ }
+
+ fileFilter.setDescription("All network files");
+ chooser.setFilenameFilter(fileFilter);
+
+ chooser.setVisible(true);
+
+ if (chooser.getFile() != null) {
+ File[] result = new File[1];
+ result[0] = new File(chooser.getDirectory() + "/" + chooser.getFile());
+
+ if (chooser.getDirectory() != null)
+ CytoscapeInit.setMRUD(new File(chooser.getDirectory()));
+
+ return result;
+ }
+
+ return null;
+ } else {
+ // this is not a mac, use the Swing based file dialog
+ final JFileChooser chooser = (load_save_custom == LOAD) ? new NoEditFileChooser(start) : new JFileChooser(start);
+
+ if (multiselect && selectedFiles != null){
+ chooser.setSelectedFiles(selectedFiles);
+ }
+ if (!multiselect && selectedFiles != null){
+ chooser.setSelectedFile(selectedFiles[0]);
+ }
+
+ // set multiple selection, if applicable
+ chooser.setMultiSelectionEnabled(multiselect);
+
+ // set the dialog title
+ chooser.setDialogTitle(title);
+
+ // add filters
+ for (int i = 0; i < filters.length; ++i) {
+ chooser.addChoosableFileFilter(filters[i]);
+ }
+
+ File[] result = null;
+ File tmp = null;
+
+ // set the dialog type
+ if (load_save_custom == LOAD) {
+ if (chooser.showOpenDialog(parent) == JFileChooser.APPROVE_OPTION) {
+ if (multiselect)
+ result = chooser.getSelectedFiles();
+ else if ((tmp = chooser.getSelectedFile()) != null) {
+ result = new File[1];
+ result[0] = tmp;
+ }
+ }
+ } else if (load_save_custom == SAVE) {
+ if (chooser.showSaveDialog(parent) == JFileChooser.APPROVE_OPTION) {
+ if (multiselect)
+ result = chooser.getSelectedFiles();
+ else if ((tmp = chooser.getSelectedFile()) != null) {
+ result = new File[1];
+ result[0] = tmp;
+ }
+ // FileDialog checks for overwrte, but JFileChooser does not, so we need to do
+ // so ourselves
+ for (int i = 0; i < result.length; i++) {
+ if (result[i].exists()) {
+ int answer = JOptionPane.showConfirmDialog(chooser,
+ "The file '"+result[i].getName()+"' already exists, are you sure you want to overwrite it?",
+ "File exists", JOptionPane.YES_NO_OPTION, JOptionPane.WARNING_MESSAGE);
+ if (answer == 1)
+ return null;
+ }
+ }
+ }
+ } else {
+ if (chooser.showDialog(parent, custom_approve_text) == JFileChooser.APPROVE_OPTION) {
+ if (multiselect)
+ result = chooser.getSelectedFiles();
+ else if ((tmp = chooser.getSelectedFile()) != null) {
+ result = new File[1];
+ result[0] = tmp;
+ }
+ }
+ }
+
+ if ((result != null) && (start_dir == null))
+ CytoscapeInit.setMRUD(chooser.getCurrentDirectory());
+
+ return result;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param name DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static InputStream getInputStream(String name) {
+ return getInputStream(name, null);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param name DOCUMENT ME!
+ * @param monitor DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static InputStream getInputStream(String name, TaskMonitor monitor) {
+ InputStream in = null;
+
+ try {
+ if (name.matches(urlPattern)) {
+ URL u = new URL(name);
+ // in = u.openStream();
+ // Use URLUtil to get the InputStream since we might be using a proxy server
+ // and because pages may be cached:
+ in = URLUtil.getBasicInputStream(u);
+ } else
+ in = new FileInputStream(name);
+ } catch (IOException ioe) {
+ logger.error("Unable to open file '"+name+"': "+ioe.getMessage());
+
+ if (monitor != null)
+ monitor.setException(ioe, ioe.getMessage());
+ }
+
+ return in;
+ }
+
+ /**
+ *
+ * @param filename
+ * File to read in
+ *
+ * @return The contents of the given file as a string.
+ */
+ public static String getInputString(String filename) {
+ try {
+ InputStream stream = getInputStream(filename);
+ return getInputString(stream);
+ } catch (IOException ioe) {
+ logger.warn("Couldn't create string from '"+filename+"': "+ioe.getMessage());
+ }
+
+ return null;
+ }
+
+ /**
+ *
+ * @param inputStream
+ * An InputStream
+ *
+ * @return The contents of the given file as a string.
+ */
+ public static String getInputString(InputStream inputStream) throws IOException {
+ String lineSep = System.getProperty("line.separator");
+ StringBuffer sb = new StringBuffer();
+ String line = null;
+ BufferedReader br = null;
+
+ try {
+ br = new BufferedReader(new InputStreamReader(inputStream));
+ while ((line = br.readLine()) != null)
+ sb.append(line + lineSep);
+ }
+ finally {
+ if (br != null) {
+ br.close();
+ }
+ }
+
+ return sb.toString();
+ }
+}
diff --git a/application/src/main/java/cytoscape/util/GMLFileFilter.java b/application/src/main/java/cytoscape/util/GMLFileFilter.java
new file mode 100644
index 0000000..d982f40
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/GMLFileFilter.java
@@ -0,0 +1,106 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.util;
+
+import cytoscape.data.ImportHandler;
+
+import cytoscape.data.readers.GMLReader;
+import cytoscape.data.readers.GraphReader;
+
+import cytoscape.logger.CyLogger;
+
+import java.net.URL;
+import java.net.URLConnection;
+
+/**
+ * FileFilter for Reading in GML Files.
+ *
+ * @author Cytoscape Development Team.
+ */
+public class GMLFileFilter extends CyFileFilter {
+ /**
+ * GML Files are Graphs.
+ */
+ private static String fileNature = ImportHandler.GRAPH_NATURE;
+
+ /**
+ * File Extensions.
+ */
+ private static String fileExtension = "gml";
+
+ /**
+ * Content Types
+ */
+ private static String[] contentTypes = { "text/gml", "text/gml+xml" };
+
+ /**
+ * Filter Description.
+ */
+ private static String description = "GML files";
+
+ /**
+ * Constructor.
+ */
+ public GMLFileFilter() {
+ super(fileExtension, description, fileNature);
+ }
+
+ /**
+ * Gets GraphReader.
+ * @param fileName File Name.
+ * @return GraphReader Object.
+ */
+ public GraphReader getReader(String fileName) {
+ reader = new GMLReader(fileName);
+
+ return reader;
+ }
+
+ /**
+ * Gets Graph Reader.
+ * @param fileName File name.
+ * @return GraphReader Object.
+ */
+ public GraphReader getReader(URL url, URLConnection conn) {
+ try {
+ // Get the input stream
+ reader = new GMLReader(conn.getInputStream(), url.toString());
+ } catch (Exception e) {
+ CyLogger.getLogger(GMLFileFilter.class).error("Unable to get GML reader: "+e.getMessage());
+ reader = null;
+ }
+ return reader;
+ }
+}
diff --git a/application/src/main/java/cytoscape/util/GraphSetUtils.java b/application/src/main/java/cytoscape/util/GraphSetUtils.java
new file mode 100644
index 0000000..a1d3796
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/GraphSetUtils.java
@@ -0,0 +1,528 @@
+/*
+ File: GraphSetUtils.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.util;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import cytoscape.logger.CyLogger;
+
+import cytoscape.plugin.CytoscapePlugin;
+
+import cytoscape.view.CyNetworkView;
+import cytoscape.visual.VisualStyle;
+
+import giny.model.Edge;
+import giny.model.Node;
+
+import giny.view.EdgeView;
+import giny.view.Label;
+import giny.view.NodeView;
+
+import java.util.*;
+
+
+/**
+ * Class contains various static methods to perform set-like operations on
+ * graph.
+ *
+ * @author Ryan Kelley
+ *
+ */
+public class GraphSetUtils {
+ /**
+ * The different types of network graph operations
+ */
+ protected static final int UNION = 0;
+ protected static final int INTERSECTION = 1;
+ protected static final int DIFFERENCE = 2;
+ protected static final int DIFFERENCE2 = 3;
+
+ /**
+ * Create a new graph which is the union of multiple graphs. The union graph
+ * is created by applying the set union on both the edges and the nodes.
+ *
+ * @param networkList
+ * A list containing all of the networks.
+ * @param copyView
+ * This argument is ignored.
+ * @param title
+ * The title of the new network
+ * @return A cyNetwork which is the union of the input graphs
+ */
+ public static CyNetwork createUnionGraph(List networkList, boolean copyView, String title) {
+ return performNetworkOperation(networkList, UNION, copyView, title);
+ }
+
+ /**
+ * Create a new graph which is the intersection of multiple graphs. The
+ * intersection graph is created by applying the set intersection on both
+ * the edges and the nodes.
+ *
+ * @param networkList
+ * A list containing all of the networks.
+ * @param copyView
+ * This argument is ignored.
+ * @param title
+ * The title of the new network
+ * @return A cyNetwork which is the intersection of the input graphs
+ */
+ public static CyNetwork createIntersectionGraph(List networkList, boolean copyView, String title) {
+ return performNetworkOperation(networkList, INTERSECTION, copyView, title);
+ }
+
+ /**
+ * Create a new graph which is the difference of multiple graphs. Note that
+ * this is not the symmetric difference. The second graph in the list (and
+ * the third and the fourth ... ) are subtracted from the first graph. Here,
+ * we can not directly apply the set difference on the nodes and edge sets
+ * and get a valid graph. Therefore, we apply the difference operation on
+ * the edge sets firsts and add those nodes in the node difference set which
+ * are required for those edges to exist.
+ *
+ * @param networkList
+ * A list containing all of the networks.
+ * @param copyView
+ * This argument is ignored.
+ * @param title
+ * The title of the new network
+ * @return A cyNetwork which is the difference of the input graphs
+ */
+ public static CyNetwork createDifferenceGraph(List networkList, boolean copyView, String title) {
+ return performNetworkOperation(networkList, DIFFERENCE, copyView, title);
+ }
+
+ /**
+ * The way this works is that the 2nd and optional additional networks will be subtracted
+ * from the 1st network. The way this works is that all the nodes and edges in the 2nd and
+ * consecutive networks will be removed from the 1st network.
+ *
+ * @param networkList
+ * A list containing all of the networks.
+ * @param copyView
+ * This argument is ignored.
+ * @param title
+ * The title of the resulting, new network
+ * @return A cyNetwork which is the difference of the input graphs
+ */
+ public static CyNetwork createDifferenceGraph2(List networkList, boolean copyView, String title) {
+ return performNetworkOperation(networkList, DIFFERENCE2, copyView, title);
+ }
+
+ /**
+ * Protected helper function that actually does the heavy lifting to perform
+ * the set operations. For explantion of the input parameters, see any of
+ * the public methods.
+ *
+ * @return cyNetwork created from applying this set operation
+ */
+ protected static CyNetwork performNetworkOperation(List networkList, int operation,
+ boolean copyView, String title) {
+ /*
+ * We require at least one network for this operation This should be
+ * enforced by hte GUI, bujt we will check it here as well
+ */
+ if (networkList.size() == 0) {
+ throw new IllegalArgumentException("Must have at least one network in the list");
+ }
+
+ /*
+ * Just handle each type of operation independently, this will cause
+ * some potential duplications of code, but it should be a little bit
+ * more readable
+ */
+ int[] new_nodes = null;
+ int[] new_edges = null;
+
+ switch (operation) {
+ case UNION:
+ new_nodes = GraphSetUtils.unionizeNodes(networkList);
+ new_edges = GraphSetUtils.unionizeEdges(networkList);
+ break;
+ case INTERSECTION:
+ new_nodes = GraphSetUtils.intersectNodes(networkList);
+ new_edges = GraphSetUtils.intersectEdges(networkList);
+ CyLogger.getLogger().warn("number of intersecting nodes is " + new_nodes.length);
+ break;
+ case DIFFERENCE:
+ new_edges = GraphSetUtils.differenceEdges(networkList);
+ new_nodes = GraphSetUtils.differenceNodes(networkList, new_edges);
+ break;
+ case DIFFERENCE2:
+ new_nodes = GraphSetUtils.differenceNodes2(networkList);
+ new_edges = GraphSetUtils.differenceEdges2(networkList, new_nodes);
+ break;
+ default:
+ throw new IllegalArgumentException("Specified invalid graph set operation");
+ }
+
+ // create the new network
+ CyNetwork newNetwork = Cytoscape.createNetwork(new_nodes, new_edges, title);
+
+ // get the visual style for the first network in the list and try to apply
+ // it to the new network.
+ CyNetwork firstNetwork = (CyNetwork)networkList.get(0);
+ CyNetworkView firstView = Cytoscape.getNetworkView( firstNetwork.getIdentifier() );
+ if ( firstView != null && firstView != Cytoscape.getNullNetworkView() ) {
+ VisualStyle firstVS = firstView.getVisualStyle();
+
+ CyNetworkView newView = Cytoscape.getNetworkView( newNetwork.getIdentifier() );
+ if ( newView != null && newView != Cytoscape.getNullNetworkView() && firstVS != null ) {
+ newView.setVisualStyle(firstVS.getName());
+ Cytoscape.getVisualMappingManager().setVisualStyle(firstVS);
+ newView.redrawGraph(true,true);
+ }
+ }
+
+ return newNetwork;
+ }
+
+ /**
+ * Determine the set of difference edges. This apply a straight set difference
+ * operation to the edge sets.
+ * @param networkList A lists containing cyNetworks
+ * @return an integer array containing the set of edges in the difference
+ */
+ protected static int[] differenceEdges(List networkList) {
+ final List<Edge> edges = new Vector<Edge>();
+
+ /*
+ * For each node in the first network, chech to make sure that it is not
+ * present in all the other networks, add it to the list if this is the
+ * case
+ */
+ CyNetwork firstNetwork = (CyNetwork) networkList.get(0);
+EDGE_LOOP:
+ for (Iterator edgeIt = firstNetwork.edgesIterator(); edgeIt.hasNext();) {
+ Edge currentEdge = (Edge) edgeIt.next();
+
+ for (int idx = 1; idx < networkList.size(); idx++) {
+ CyNetwork currentNetwork = (CyNetwork) networkList.get(idx);
+
+ if (currentNetwork.containsEdge(currentEdge)) {
+ continue EDGE_LOOP;
+ }
+ }
+
+ edges.add(currentEdge);
+ }
+
+ int[] result = new int[edges.size()];
+ int idx = 0;
+
+ for (Iterator edgeIt = edges.iterator(); edgeIt.hasNext(); idx++) {
+ Edge currentEdge = (Edge) edgeIt.next();
+ result[idx] = currentEdge.getRootGraphIndex();
+ }
+
+ return result;
+ }
+
+ /**
+ * Returns the nodes of the 1st network that are not contained in any of the other networks.
+ * @param networkList A lists containing cyNetworks
+ * @return an integer array containing the set of nodes in the difference
+ */
+ protected static int[] differenceNodes2(List networkList) {
+ final List<Node> nodes = new Vector<Node>();
+ final CyNetwork firstNetwork = (CyNetwork)networkList.get(0);
+NODE_LOOP:
+ for (Iterator nodeIt = firstNetwork.nodesIterator(); nodeIt.hasNext(); /* Empty! */)
+ {
+ Node currentNode = (Node) nodeIt.next();
+
+ for (int idx = 1; idx < networkList.size(); idx++) {
+ CyNetwork currentNetwork = (CyNetwork) networkList.get(idx);
+
+ if (currentNetwork.containsNode(currentNode))
+ continue NODE_LOOP;
+ }
+
+ nodes.add(currentNode);
+ }
+
+ final int[] result = new int[nodes.size()];
+ int idx = 0;
+ for (Iterator nodeIt = nodes.iterator(); nodeIt.hasNext(); idx++) {
+ Node currentNode = (Node) nodeIt.next();
+ result[idx] = currentNode.getRootGraphIndex();
+ }
+
+ return result;
+ }
+
+ /**
+ * Determine the set of difference nodes. In order to perform this operation
+ * we also have to know the set of edges in the edge difference, so that we
+ * can make sure that any nodes are present that are required by those
+ * edges
+ * @param networkList A lists containing cyNetworks
+ * @param edges The difference set of edges
+ * @return an integer array containing the set of edges in the difference
+ */
+ protected static int[] differenceNodes(List networkList, int[] edges) {
+ final HashSet<Node> nodes = new HashSet<Node>();
+
+ /*
+ * For each node in the first network, check to see if it is not present
+ * in any of the other networks, add it to the list if this is the case
+ */
+ CyNetwork firstNetwork = (CyNetwork) networkList.get(0);
+NODE_LOOP:
+ for (Iterator nodeIt = firstNetwork.nodesIterator(); nodeIt.hasNext();) {
+ Node currentNode = (Node) nodeIt.next();
+
+ for (int idx = 1; idx < networkList.size(); idx++) {
+ CyNetwork currentNetwork = (CyNetwork) networkList.get(idx);
+
+ if (currentNetwork.containsNode(currentNode)) {
+ continue NODE_LOOP;
+ }
+ }
+
+ nodes.add(currentNode);
+ }
+
+ /*
+ * Now we need to make sure that any nodes required to be present are
+ * included (if these nodes connect an edge in the difference set)
+ */
+ for (int idx = 0; idx < edges.length; idx++) {
+ nodes.add(firstNetwork.getNode(firstNetwork.getEdgeSourceIndex(edges[idx])));
+ nodes.add(firstNetwork.getNode(firstNetwork.getEdgeTargetIndex(edges[idx])));
+ }
+
+ int[] result = new int[nodes.size()];
+ int idx = 0;
+
+ for (Iterator nodeIt = nodes.iterator(); nodeIt.hasNext(); idx++) {
+ Node currentNode = (Node) nodeIt.next();
+ result[idx] = currentNode.getRootGraphIndex();
+ }
+
+ return result;
+ }
+
+ /**
+ * Determine the set of difference edges. In order to perform this operation
+ * we also have to know the set of nodes in the node difference, so that we
+ * can make sure that any edges are present that are required by those
+ * nodes
+ * @param networkList A lists containing cyNetworks
+ * @param nodes The difference set of nodes
+ * @return an integer array containing the set of nodes in the difference
+ */
+ protected static int[] differenceEdges2(List networkList, int[] nodes) {
+ final HashSet<Edge> edges = new HashSet<Edge>();
+
+ /*
+ * For each edge in the first network, check to see if it is not present
+ * in any of the other networks, add it to the list if this is the case
+ */
+ CyNetwork firstNetwork = (CyNetwork) networkList.get(0);
+EDGE_LOOP:
+ for (Iterator edgeIt = firstNetwork.edgesIterator(); edgeIt.hasNext(); /* Empty! */)
+ {
+ Edge currentEdge = (Edge) edgeIt.next();
+
+ for (int idx = 1; idx < networkList.size(); idx++) {
+ final CyNetwork currentNetwork = (CyNetwork) networkList.get(idx);
+ if (currentNetwork.containsEdge(currentEdge))
+ continue EDGE_LOOP;
+ }
+
+ edges.add(currentEdge);
+ }
+
+ /*
+ * Now we need to make sure that we do not keep edges if either source or target
+ * nodes are not in "nodes."
+ */
+
+ final Set<Integer> knownNodes = new HashSet<Integer>(nodes.length);
+ for (final int nodeIndex : nodes)
+ knownNodes.add(nodeIndex);
+
+ final ArrayList<Integer> acceptableEdges = new ArrayList<Integer>(edges.size());
+ for (final Edge edgeCandidate : edges) {
+ if (knownNodes.contains(edgeCandidate.getSource())
+ && knownNodes.contains(edgeCandidate.getTarget()))
+ acceptableEdges.add(edgeCandidate.getRootGraphIndex());
+ }
+
+ final int[] result = new int[acceptableEdges.size()];
+ int index = 0;
+ for (final int edgeIndex : acceptableEdges)
+ result[index++] = edgeIndex;
+ return result;
+ }
+
+ /**
+ * Apply a simple intersection operation to the node sets
+ * @param networkList A list of cyNetworks
+ * @return an integer array which contains the indices of nodes in the intersection
+ */
+ protected static int[] intersectNodes(List networkList) {
+ final List<Node> nodes = new Vector<Node>();
+
+ /*
+ * For each node in the first network, check to see if it is present in
+ * all of the other networks, add it to the list if this is the case
+ */
+ CyNetwork firstNetwork = (CyNetwork) networkList.get(0);
+NODE_LOOP:
+ for (Iterator nodeIt = firstNetwork.nodesIterator(); nodeIt.hasNext();) {
+ Node currentNode = (Node) nodeIt.next();
+
+ for (int idx = 1; idx < networkList.size(); idx++) {
+ CyNetwork currentNetwork = (CyNetwork) networkList.get(idx);
+
+ if (!currentNetwork.containsNode(currentNode)) {
+ continue NODE_LOOP;
+ }
+ }
+
+ nodes.add(currentNode);
+ }
+
+ int[] result = new int[nodes.size()];
+ int idx = 0;
+
+ for (Iterator nodeIt = nodes.iterator(); nodeIt.hasNext(); idx++) {
+ Node currentNode = (Node) nodeIt.next();
+ result[idx] = currentNode.getRootGraphIndex();
+ }
+
+ return result;
+ }
+
+ /**
+ * Apply a simple intersection operation to the edge sets
+ * @param networkList A list of cyNetworks
+ * @return an integer array which contains the indices of edges in the intersection
+ */
+ protected static int[] intersectEdges(List networkList) {
+ final List<Edge> edges = new Vector<Edge>();
+
+ /*
+ * For each node in the first network, check to see if it is present in
+ * all of the other networks, add it to the list if this is the case
+ */
+ CyNetwork firstNetwork = (CyNetwork) networkList.get(0);
+EDGE_LOOP:
+ for (Iterator edgeIt = firstNetwork.edgesIterator(); edgeIt.hasNext();) {
+ Edge currentEdge = (Edge) edgeIt.next();
+
+ for (int idx = 1; idx < networkList.size(); idx++) {
+ CyNetwork currentNetwork = (CyNetwork) networkList.get(idx);
+
+ if (!currentNetwork.containsEdge(currentEdge)) {
+ continue EDGE_LOOP;
+ }
+ }
+
+ edges.add(currentEdge);
+ }
+
+ int[] result = new int[edges.size()];
+ int idx = 0;
+
+ for (Iterator edgeIt = edges.iterator(); edgeIt.hasNext(); idx++) {
+ Edge currentEdge = (Edge) edgeIt.next();
+ result[idx] = currentEdge.getRootGraphIndex();
+ }
+
+ return result;
+ }
+
+ /**
+ * Makes nodes request overtime pay.
+ * @param networkList a list of cyNetworks
+ * @return an integer array containing the indices of nodes in the union
+ */
+ protected static int[] unionizeNodes(List networkList) {
+ /*
+ * This is the set of nodes that will be in the final merged network
+ */
+ Set<Integer> nodes = new HashSet<Integer>();
+
+ for (Iterator it = networkList.iterator(); it.hasNext();) {
+ CyNetwork currentNetwork = (CyNetwork) it.next();
+
+ for (Iterator nodeIt = currentNetwork.nodesIterator(); nodeIt.hasNext();) {
+ nodes.add(new Integer(((Node) nodeIt.next()).getRootGraphIndex()));
+ }
+ }
+
+ int[] result = new int[nodes.size()];
+ int idx = 0;
+
+ for (Iterator nodeIt = nodes.iterator(); nodeIt.hasNext(); idx++) {
+ result[idx] = ((Integer) nodeIt.next()).intValue();
+ }
+
+ return result;
+ }
+
+ /**
+ * Perform a simple set union on the sets of nodes
+ * @param networkList a list of cyNetworks
+ * @return an integer array containing the indices of edges in the union
+ */
+ protected static int[] unionizeEdges(List networkList) {
+ /*
+ * This is the set of edges that will be in the final network
+ */
+ Set<Integer> edges = new HashSet<Integer>();
+
+ for (Iterator it = networkList.iterator(); it.hasNext();) {
+ CyNetwork currentNetwork = (CyNetwork) it.next();
+
+ for (Iterator edgeIt = currentNetwork.edgesIterator(); edgeIt.hasNext();) {
+ edges.add(new Integer(((Edge) edgeIt.next()).getRootGraphIndex()));
+ }
+ }
+
+ int[] result = new int[edges.size()];
+ int idx = 0;
+
+ for (Iterator edgeIt = edges.iterator(); edgeIt.hasNext(); idx++) {
+ result[idx] = ((Integer) edgeIt.next()).intValue();
+ }
+
+ return result;
+ }
+}
diff --git a/application/src/main/java/cytoscape/util/IndeterminateProgressBar.java b/application/src/main/java/cytoscape/util/IndeterminateProgressBar.java
new file mode 100644
index 0000000..1ef1691
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/IndeterminateProgressBar.java
@@ -0,0 +1,126 @@
+/*
+ File: IndeterminateProgressBar.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// IndeterminateProgressBar.java
+//-----------------------------------------------------------------
+// $Date: 2007-03-20 01:25:45 +0100 (Tue, 20 Mar 2007) $
+// $Author: iliana
+//-----------------------------------------------------------------
+package cytoscape.util;
+
+
+//-----------------------------------------------------------------
+import java.awt.Dialog;
+import java.awt.Frame;
+
+import javax.swing.BoxLayout;
+import javax.swing.JDialog;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JProgressBar;
+import javax.swing.border.*;
+
+
+//-----------------------------------------------------------------
+/**
+ * This class creates a dialog with a JProgressBar in indeterminate state.
+ * Showing a bar in indeterminate state is useful when a long task is running,
+ * the task's running time can't be approximated (if it can, then it is
+ * better to use csplugins.util.CytoscapeProgressMonitor), and the client
+ * wants to let the user know that something is happening (instead of giving the
+ * impression of a frozen program).
+ */
+public class IndeterminateProgressBar extends JDialog {
+ JPanel mainPanel;
+ JPanel labelPanel;
+ JPanel barPanel;
+ JLabel label;
+ String labelText;
+ JProgressBar pBar;
+
+ /**
+ * Constructs an initially invisible, non-modal Dialog with no owner, the given title and label.
+ */
+ public IndeterminateProgressBar(String title, String label) {
+ super();
+ labelText = label;
+ setTitle(title);
+ } //cons
+
+ /**
+ * Constructs an initially invisible, non-modal Dialog with the specified owner dialog, title and label.
+ */
+ public IndeterminateProgressBar(Dialog owner, String title, String label) {
+ super(owner, title);
+ labelText = label;
+ create();
+ } //cons
+
+ /**
+ * Constructs an initially invisible, non-modal Dialog with the specified owner frame, title and label.
+ */
+ public IndeterminateProgressBar(Frame owner, String title, String label) {
+ super(owner, title);
+ labelText = label;
+ create();
+ } //cons
+
+ protected void create() {
+ mainPanel = new JPanel();
+ mainPanel.setLayout(new BoxLayout(mainPanel, BoxLayout.Y_AXIS));
+ labelPanel = new JPanel();
+ label = new JLabel(labelText);
+ labelPanel.add(label);
+ mainPanel.add(labelPanel);
+ barPanel = new JPanel();
+ pBar = new JProgressBar(JProgressBar.HORIZONTAL);
+ pBar.setIndeterminate(true);
+ barPanel.add(pBar);
+ mainPanel.add(barPanel);
+ getContentPane().add(mainPanel);
+ } //create
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param label_text DOCUMENT ME!
+ */
+ public void setLabelText(String label_text) {
+ labelText = label_text;
+ label.setText(labelText);
+ } //setLabelText
+} //IndeterminateProgressBar
diff --git a/application/src/main/java/cytoscape/util/JnlpWriterUtil.java b/application/src/main/java/cytoscape/util/JnlpWriterUtil.java
new file mode 100644
index 0000000..789da75
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/JnlpWriterUtil.java
@@ -0,0 +1,385 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.util;
+
+import org.jdom.Comment;
+
+/**
+ * Utility script to create an up-to-date jnlp file for Cytoscape webstart.
+ *
+ * It uses the plugin manifest files to figure out the CytoscapePlugin classes
+ * or attempts to guess by looking for a class in the jar file with "Plugin" in the name.
+ *
+ * Meant to use as a standalone script through an ant bulidfile.
+ */
+import org.jdom.Document;
+import org.jdom.Element;
+
+import org.jdom.output.XMLOutputter;
+
+import java.io.File;
+import java.io.FileWriter;
+
+import java.util.ArrayList;
+
+//import org.jdom.output.Format; //jdom vs 1.0, currently on 0.9
+import java.util.HashMap;
+import java.util.jar.JarFile;
+import java.util.jar.Manifest;
+
+import cytoscape.logger.CyLogger;
+
+
+/**
+ *
+ */
+public class JnlpWriterUtil {
+ /**
+ *
+ */
+ public Document document;
+
+ /**
+ *
+ */
+ public Element rootTag;
+
+ /**
+ *
+ */
+ public XMLOutputter out;
+ protected String fileName;
+ protected String cytoDir;
+ protected String url = "http://your.jnlp.location";
+ protected String saveDir;
+
+ /**
+ *
+ */
+ public String libDir;
+
+ /**
+ *
+ */
+ public String pluginDir;
+ protected HashMap<String, String> options;
+
+ /**
+ * Creates a new JnlpWriterUtil object.
+ *
+ * @param args DOCUMENT ME!
+ */
+ public JnlpWriterUtil(String[] args) {
+ options = getOptions(args);
+ fileName = options.get("filename");
+ cytoDir = options.get("cyto_dir");
+ saveDir = options.get("save_dir");
+
+ if (options.containsKey("url"))
+ url = options.get("url");
+
+ libDir = cytoDir + "/lib";
+ pluginDir = cytoDir + "/plugins";
+
+ setupDoc();
+ }
+
+ private void setupDoc() {
+ document = new Document();
+ rootTag = new Element("jnlp");
+ document.setRootElement(rootTag);
+
+ if (!options.containsKey("url")) {
+ Comment Codebase = new Comment("Replace the codebase URL with your own");
+ rootTag.addContent(Codebase);
+ }
+
+ rootTag.setAttribute("codebase", url);
+ rootTag.setAttribute("href", fileName);
+
+ out = new XMLOutputter(org.jdom.output.Format.getPrettyFormat());
+ }
+
+ private static void print(String s) {
+ System.out.println(s);
+ }
+
+ /*
+ * Creates jnlp file,
+ *
+ */
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public static void main(String[] args) throws Exception {
+ JnlpWriterUtil jutil = new JnlpWriterUtil(args);
+
+ ArrayList<String> MainLibs = jutil.getLibJars();
+ print("Adding " + MainLibs.size() + " total main jars");
+
+ ArrayList<String> PluginLibs = jutil.getPluginJars();
+ ArrayList<String> PluginClasses = jutil.getMainClass(PluginLibs, jutil.pluginDir);
+ print("Adding " + PluginLibs.size() + " total plugin jars");
+
+ jutil.createInfoTag();
+ jutil.createResourcesTag();
+ jutil.addJars("lib/", MainLibs, null);
+ jutil.addJars("plugins/", PluginLibs,
+ "These are the plugins you wish to load, edit as necessary.");
+
+ jutil.addArguments(PluginClasses);
+
+ jutil.writeToFile();
+ }
+
+ /**
+ * @return jdom.Document as a string
+ */
+ public String getString() {
+ return out.outputString(document);
+ }
+
+ /**
+ *
+ * @param Loc - directory to write xml file
+ * @throws java.io.IOException
+ */
+ public void writeToFile() throws java.io.IOException {
+ File SaveDirCheck = new File(saveDir);
+
+ if (!SaveDirCheck.exists())
+ SaveDirCheck.mkdir();
+
+ FileWriter writer = new FileWriter(saveDir + "/" + fileName);
+ out.output(document, writer);
+ }
+
+ /*
+ * Adding the <information> tag
+ */
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void createInfoTag() {
+ Element Info = new Element("information");
+ Info.addContent(new Element("title").setText("Cytoscape Webstart"));
+ Info.addContent(new Element("vendor").setText("Cytoscape Collaboration"));
+ Info.addContent(new Element("homepage").setAttribute("href", "http://cytoscape.org"));
+ Info.addContent(new Element("offline-allowed"));
+
+ rootTag.addContent(new Element("security").addContent(new Element("all-permissions")));
+
+ rootTag.addContent(Info);
+ }
+
+ /*
+ * Adding the <resource> tag
+ */
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void createResourcesTag() {
+ Element Resources = new Element("resources");
+ Element JSE = new Element("j2se");
+ JSE.setAttribute("version", "1.5+");
+ JSE.setAttribute("max-heap-size", "1024M");
+ Resources.addContent(JSE);
+ Resources.addContent(new Comment("All lib jars that cytoscape requires to run should be in this list"));
+ Resources.addContent(new Element("jar").setAttribute("href", "cytoscape.jar"));
+
+ rootTag.addContent(Resources);
+ }
+
+ /**
+ *
+ * @param Prefix (append to beginning of jar file name)
+ * @param Jars
+ * @param Comment
+ */
+ public void addJars(String Prefix, ArrayList<String> Jars, String Comment) {
+ Element Resources = rootTag.getChild("resources");
+
+ if (Comment != null)
+ Resources.addContent(new Comment(Comment));
+
+ for (int i = 0; i < Jars.size(); i++) {
+ Resources.addContent(new Element("jar").setAttribute("href", Prefix + Jars.get(i)));
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public ArrayList<String> getLibJars() {
+ return getJarList(libDir);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public ArrayList<String> getPluginJars() {
+ return getJarList(pluginDir);
+ }
+
+ /**
+ * @param Dir
+ * @return ArrayList<String> of jars listed in given directory
+ */
+ private ArrayList<String> getJarList(String Dir) {
+ File JarDir = new File(Dir);
+
+ if (!JarDir.exists()) {
+ CyLogger.getLogger().warn("Required directory '" + JarDir.getAbsolutePath()
+ + "' does not exist");
+ System.exit(-1);
+ }
+
+ ArrayList<String> JarFiles = new ArrayList<String>();
+
+ for (File Current : JarDir.listFiles()) {
+ if (Current.isFile() && Current.getName().endsWith(".jar")) {
+ JarFiles.add(Current.getName());
+ }
+ }
+
+ return JarFiles;
+ }
+
+ /**
+ * @param JarFiles
+ * @param JarDir
+ * @return ArrayList<String> of the CytoscapePlugin classes that could be determined from each plugin
+ */
+ public ArrayList<String> getMainClass(ArrayList<String> JarFiles, String JarDir) {
+ ArrayList<String> PluginMainClass = new ArrayList<String>();
+
+ for (int i = 0; i < JarFiles.size(); i++) {
+ try {
+ JarFile jf = new JarFile(JarDir + "/" + JarFiles.get(i));
+ Manifest m = jf.getManifest();
+
+ if (m != null) {
+ String className = m.getMainAttributes().getValue("Cytoscape-Plugin");
+
+ if (className != null) {
+ // add to list
+ PluginMainClass.add(className);
+
+ continue;
+ }
+ }
+ } catch (Exception E) {
+ E.printStackTrace();
+ }
+ }
+
+ return PluginMainClass;
+ }
+
+ /**
+ * @param args
+ * @return HashMap<String, String> of the command line options
+ */
+ private HashMap<String, String> getOptions(String[] args) {
+ String Usage = "Usage: java " + this + " [parameters]\n"
+ + "Option : Description Required\n"
+ + "-filename : Name of jnlp file yes\n"
+ + "-cyto_dir : Cytoscape directory yes\n"
+ + "-url : Webstart url no\n"
+ + "-save_dir : Save to dir yes\n";
+
+ HashMap<String, String> Opts = new HashMap<String, String>();
+
+ if (args.length < 2) {
+ CyLogger.getLogger().warn("Too few arguments (" + args.length + "). " + Usage);
+ System.exit(-1);
+ }
+
+ for (int i = 0; i < args.length; i++) {
+ if (args[i].equals("-filename"))
+ Opts.put("filename", args[i + 1]);
+
+ if (args[i].equals("-cyto_dir"))
+ Opts.put("cyto_dir", args[i + 1]);
+
+ if (args[i].equals("-url"))
+ Opts.put("url", args[i + 1]);
+
+ if (args[i].equals("-save_dir"))
+ Opts.put("save_dir", args[i + 1]);
+ }
+
+ if (!Opts.containsKey("filename") || !Opts.containsKey("cyto_dir")
+ || !Opts.containsKey("save_dir")) {
+ CyLogger.getLogger().warn("Required arguments missing. " + Usage);
+ System.exit(-1);
+ }
+
+ return Opts;
+ }
+
+ /**
+ *
+ * @param Args
+ * These are all plugin arguments at the moment, only specifies the -p tag between each.
+ */
+ public void addArguments(ArrayList<String> Args) {
+ Element Application = rootTag.getChild("application-desc");
+
+ if (Application == null) {
+ rootTag.addContent(new Comment("This starts-up Cytoscape, specify your plugins to load, and other command line arguments. Plugins not specified here will not be loaded."));
+
+ Application = new Element("application-desc").setAttribute("main-class",
+ "cytoscape.CyMain");
+ rootTag.addContent(Application);
+ }
+
+ for (int i = 0; i < Args.size(); i++) {
+ Application.addContent(new Element("argument").setText("-p"));
+ Application.addContent(new Element("argument").setText(Args.get(i)));
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/util/LinearScaler.java b/application/src/main/java/cytoscape/util/LinearScaler.java
new file mode 100644
index 0000000..c909dc3
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/LinearScaler.java
@@ -0,0 +1,65 @@
+/*
+ File: LinearScaler.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.util;
+
+
+/**
+ * Used to scale a list of values to [a,b]
+ */
+class LinearScaler extends AbstractScaler {
+ public double[] scale(final double values[], final double a, final double b) throws IllegalArgumentException
+ {
+ if (values.length < 2)
+ throw new IllegalArgumentException("need at least 2 values for scaling!");
+ if (a >= b)
+ throw new IllegalArgumentException("bad bounds!");
+
+ double min = Double.POSITIVE_INFINITY;
+ double max = Double.NEGATIVE_INFINITY;
+ for (final double d : values) {
+ if (d < min)
+ min = d;
+ if (d > max)
+ max = d;
+ }
+
+ if (min == max)
+ throw new IllegalArgumentException("input values are all identical!");
+
+ final double c = (a - b) / (min - max);
+ final double d = a - c * min;
+
+ final double[] scaledValues = new double[values.length];
+ for (int i = 0; i < values.length; ++i)
+ scaledValues[i] = c * values[i] + d;
+
+ return scaledValues;
+ }
+}
diff --git a/application/src/main/java/cytoscape/util/MacAppConfig.java b/application/src/main/java/cytoscape/util/MacAppConfig.java
new file mode 100644
index 0000000..074dc99
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/MacAppConfig.java
@@ -0,0 +1,189 @@
+/*
+ File: MacAppConfig.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.util;
+
+import cytoscape.Cytoscape;
+import cytoscape.logger.CyLogger;
+
+import org.jdom.Document;
+import org.jdom.Element;
+import org.jdom.JDOMException;
+
+import org.jdom.input.SAXBuilder;
+
+import org.jdom.output.XMLOutputter;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.FileWriter;
+import java.io.IOException;
+
+
+/**
+ * Configures the Mac OS X Info.plist file associated with Cytoscape.
+ * This enables us to run a "Macified" version of Cytoscape, with its
+ * own icon, integrated menus, etc. The plist file is part of the package
+ * contents automatically generated by the Mac OS X Jar Bundler application.
+ *
+ * The existing Info.plist file checked into CVS provides preset
+ * configuration settings. This class modified the existing file by adding
+ * all JAR files in cytoscape/lib to the plist file. It does so be replacing
+ * the JAR_ARRAY element with the correct array element, and then adding
+ * all the correct JAR files. By automating this task, we can easily
+ * update the Mac OS X application as part of our regular build process.
+ *
+ * Full documentation on the Mac OS X Jar Bundler is available at:
+ * http://developer.apple.com/documentation/Java/Conceptual/Jar_Bundler
+ *
+ * @author Ethan Cerami
+ */
+public class MacAppConfig {
+ /**
+ * Name of Jar Bundler Configuration File.
+ */
+ private String configFile = "Cytoscape.app/Contents/Info.plist";
+
+ /**
+ * Configures the Info.plist list with all cytoscape/*.jar files.
+ * @throws IOException Error Reading Document.
+ * @throws JDOMException Error Processing XML Document.
+ */
+ public void configure() throws IOException, JDOMException {
+ // Parse Info.plist file
+ Document doc = getConfiguration();
+
+ // Get all files in cytocape/lib
+ String[] files = getJarList();
+
+ // Get the Correct JAR_ARRAY Element Placeholder.
+ Element root = doc.getRootElement();
+ Element dict = root.getChild("dict");
+ dict = dict.getChild("dict");
+
+ Element array = dict.getChild("JAR_ARRAY");
+ array.setName("array");
+ addJars(files, array);
+
+ // Overwrite existing Info.plist file.
+ // jdom 0.9
+ //XMLOutputter outputter = new XMLOutputter(" ", false);
+ // jdom 1.0
+ XMLOutputter outputter = new XMLOutputter(org.jdom.output.Format.getPrettyFormat());
+
+ FileWriter writer = null;
+ try {
+ writer = new FileWriter(configFile);
+ outputter.output(doc, writer);
+ }
+ finally {
+ if (writer != null) {
+ writer.close();
+ }
+ }
+ CyLogger.getLogger().info("File is now updated with correct JARs: " + configFile);
+ }
+
+ /**
+ * Add all JAR Files to Info.plist
+ * @param files Array of Files in cytocape/lib.
+ * @param array Array Element in Info.plist.
+ */
+ private void addJars(String[] files, Element array) {
+ for (int i = 0; i < files.length; i++) {
+ String file = files[i];
+
+ if (file.endsWith("jar")) {
+ Element jar = new Element("string");
+ jar.setText("$JAVAROOT/" + file);
+ array.addContent(jar);
+ array.addContent("\n");
+ }
+ }
+ }
+
+ /**
+ * Gets all Files in cytoscape/lib
+ * @return Array of File Strings.
+ */
+ private String[] getJarList() {
+ File dir = new File("lib");
+ String[] files = dir.list();
+
+ return files;
+ }
+
+ /**
+ * Parses Info.Plist file into JDOM Document object.
+ * @return JDOM Document Object.
+ * @throws IOException Error Reading Document.
+ * @throws JDOMException Error Processing XML Document.
+ */
+ private Document getConfiguration() throws IOException, JDOMException {
+ Document doc = null;
+
+ try {
+ FileReader reader = null;
+ try {
+ reader = new FileReader(configFile);
+ SAXBuilder saxBuilder = new SAXBuilder();
+ doc = saxBuilder.build(reader, new File(configFile).toURI().toURL().toString());
+ }
+ finally {
+ if (reader != null) {
+ reader.close();
+ }
+ }
+ } catch (FileNotFoundException e) {
+ CyLogger.getLogger().info("Cannot find: " + configFile);
+ CyLogger.getLogger().info("Try running: 'ant mac' first.");
+ Cytoscape.exit(-1);
+ }
+
+ return doc;
+ }
+
+ /**
+ * Main Method.
+ * @param args Command Line Arguments.
+ * @throws Exception All Exceptions.
+ */
+ public static void main(String[] args) throws Exception {
+ MacAppConfig mac = new MacAppConfig();
+ mac.configure();
+ }
+}
diff --git a/application/src/main/java/cytoscape/util/MathUtil.java b/application/src/main/java/cytoscape/util/MathUtil.java
new file mode 100644
index 0000000..1143f68
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/MathUtil.java
@@ -0,0 +1,72 @@
+package cytoscape.util;
+
+
+public class MathUtil {
+ /**
+ * @returns the unbiased exponent of a single-precision IEEE floating point number
+ */
+ static public int getExponent(final float f) {
+ final int EXPONENT_MASK = 0x7f800000;
+ final int bits = Float.floatToIntBits(f) & EXPONENT_MASK;
+ final int BIAS = 127;
+ final int BIT_OFFSET = 23;
+ return (bits >> BIT_OFFSET) - BIAS;
+ }
+ /**
+ * @returns the unbiased exponent of a double-precision IEEE floating point number
+ */
+ static public long getExponent(final double f) {
+ final long EXPONENT_MASK = 0x7FFFF00000000000L;
+ final long bits = Double.doubleToLongBits(f) & EXPONENT_MASK;
+ final int BIAS = 1023;
+ final int BIT_OFFSET = 52;
+ return (bits >> BIT_OFFSET) - BIAS;
+ }
+
+ static public boolean almostEqual(final float x1, final float x2) {
+ if (x1 == x2)
+ return true;
+
+ if (Math.signum(x1) != Math.signum(x2))
+ return false;
+
+ if (MathUtil.getExponent(x1) != MathUtil.getExponent(x2))
+ return false;
+
+ final float absX1 = Math.abs(x1);
+ final float absX2 = Math.abs(x2);
+
+ if (x1 != 0.0f)
+ return Math.abs(x1 - x2) / Math.abs(x1) < 1.0e-6f;
+ else
+ return Math.abs(x1 - x2) / Math.abs(x2) < 1.0e-6f;
+ }
+
+ static public boolean almostEqual(final double x1, final double x2) {
+ if (x1 == x2)
+ return true;
+
+ if (Math.signum(x1) != Math.signum(x2))
+ return false;
+
+ if (MathUtil.getExponent(x1) != MathUtil.getExponent(x2))
+ return false;
+
+ final double absX1 = Math.abs(x1);
+ final double absX2 = Math.abs(x2);
+
+ if (x1 != 0.0)
+ return Math.abs(x1 - x2) / Math.abs(x1) < 1.0e-12;
+ else
+ return Math.abs(x1 - x2) / Math.abs(x2) < 1.0e-12;
+ }
+
+ static public boolean isValidDouble(final String s) {
+ try {
+ double d = Double.valueOf(s);
+ return true;
+ } catch (final Exception e) {
+ return false;
+ }
+ }
+}
\ No newline at end of file
diff --git a/application/src/main/java/cytoscape/util/MemoryReporter.java b/application/src/main/java/cytoscape/util/MemoryReporter.java
new file mode 100644
index 0000000..731d304
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/MemoryReporter.java
@@ -0,0 +1,64 @@
+/**
+ * @author Johannes Ruscheinski
+ */
+package cytoscape.util;
+
+
+import java.lang.management.ManagementFactory;
+import java.lang.management.MemoryPoolMXBean;
+import java.util.List;
+
+
+
+/**
+ * A class used to track JVM memory usage.
+ */
+public class MemoryReporter {
+ /**
+ * @return the actually used memory in bytes
+ */
+ public static long getUsedMemory() {
+ final List<MemoryPoolMXBean> beans = ManagementFactory.getMemoryPoolMXBeans();
+ long used = 0;
+ for (final MemoryPoolMXBean bean : beans)
+ used += bean.getUsage().getUsed();
+
+ return used;
+ }
+
+ /**
+ * @return the maximum amount of memory in bytes that can be used for memory management.
+ * If not available, -1 will be returned instead
+ *
+ * "This amount of memory is not guaranteed to be available for memory management if it is
+ * greater than the amount of committed memory. The Java virtual machine may fail to
+ * allocate memory even if the amount of used memory does not exceed this maximum size."
+ */
+ public static long getMaxMemory() {
+ final List<MemoryPoolMXBean> beans = ManagementFactory.getMemoryPoolMXBeans();
+ long max = 0;
+ for (final MemoryPoolMXBean bean : beans) {
+ final long beanMax = bean.getUsage().getMax();
+ if (beanMax == -1L)
+ return -1L;
+
+ max += beanMax;
+ }
+
+ return max;
+ }
+
+ /**
+ * @return the "committed" amount of memory for the current JVM instance in bytes
+ *
+ * "This amount of memory is guaranteed for the Java virtual machine to use."
+ */
+ public static long getCommittedMemory() {
+ final List<MemoryPoolMXBean> beans = ManagementFactory.getMemoryPoolMXBeans();
+ long committed = 0;
+ for (final MemoryPoolMXBean bean : beans)
+ committed += bean.getUsage().getCommitted();
+
+ return committed;
+ }
+}
diff --git a/application/src/main/java/cytoscape/util/MinMaxDouble.java b/application/src/main/java/cytoscape/util/MinMaxDouble.java
new file mode 100644
index 0000000..430a07d
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/MinMaxDouble.java
@@ -0,0 +1,110 @@
+/*
+ File: MinMaxDouble.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// MinMaxDouble
+package cytoscape.util;
+
+
+/**
+ * find the min and max of a 1- or 2-d aarray of doubles.
+ */
+public class MinMaxDouble {
+ double min = new Double(Double.MAX_VALUE).doubleValue();
+ double max = new Double(Double.MIN_VALUE).doubleValue();
+
+ /**
+ * Creates a new MinMaxDouble object.
+ *
+ * @param array DOCUMENT ME!
+ */
+ public MinMaxDouble(double[] array) {
+ for (int i = 0; i < array.length; i++) {
+ double val = array[i];
+
+ if (val > max)
+ max = val;
+
+ if (val < min)
+ min = val;
+ } // for i
+ } // ctor
+
+ /**
+ * Creates a new MinMaxDouble object.
+ *
+ * @param array DOCUMENT ME!
+ */
+ public MinMaxDouble(double[][] array) {
+ for (int i = 0; i < array.length; i++)
+ for (int j = 0; j < array[0].length; j++) {
+ double val = array[i][j];
+
+ if (val > max)
+ max = val;
+
+ if (val < min)
+ min = val;
+ } // for j
+ } // ctor
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public double getMin() {
+ return min;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public double getMax() {
+ return max;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String toString() {
+ return min + " -> " + max;
+ }
+} // class MinMaxDouble
diff --git a/application/src/main/java/cytoscape/util/MinMaxInt.java b/application/src/main/java/cytoscape/util/MinMaxInt.java
new file mode 100644
index 0000000..d3cb6f9
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/MinMaxInt.java
@@ -0,0 +1,110 @@
+/*
+ File: MinMaxInt.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// MinMaxInt
+package cytoscape.util;
+
+
+/**
+ * find the min and max of a 1- or 2-d array of ints.
+ */
+public class MinMaxInt {
+ int min = new Integer(Integer.MAX_VALUE).intValue();
+ int max = new Integer(Integer.MIN_VALUE).intValue();
+
+ /**
+ * Creates a new MinMaxInt object.
+ *
+ * @param array DOCUMENT ME!
+ */
+ public MinMaxInt(int[] array) {
+ for (int i = 0; i < array.length; i++) {
+ int val = array[i];
+
+ if (val > max)
+ max = val;
+
+ if (val < min)
+ min = val;
+ } // for i
+ } // ctor
+
+ /**
+ * Creates a new MinMaxInt object.
+ *
+ * @param array DOCUMENT ME!
+ */
+ public MinMaxInt(int[][] array) {
+ for (int i = 0; i < array.length; i++)
+ for (int j = 0; j < array[0].length; j++) {
+ int val = array[i][j];
+
+ if (val > max)
+ max = val;
+
+ if (val < min)
+ min = val;
+ } // for i
+ } // ctor
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getMin() {
+ return min;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getMax() {
+ return max;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String toString() {
+ return min + " -> " + max;
+ }
+} // class MinMaxInt
diff --git a/application/src/main/java/cytoscape/util/Misc.java b/application/src/main/java/cytoscape/util/Misc.java
new file mode 100644
index 0000000..f63665d
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/Misc.java
@@ -0,0 +1,181 @@
+/*
+ File: Misc.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+// Misc.java: miscellaneous static utilities
+package cytoscape.util;
+
+import java.awt.Color;
+import java.util.Properties;
+import java.util.Vector;
+
+/**
+ *
+ */
+public class Misc {
+
+ /**
+ * Convert string to color object.
+ *
+ * @param text
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @deprecated will be removed in April, 2011. use ColorUtil.parseColorText
+ * instead.
+ */
+ @Deprecated
+ public static Color parseRGBText(final String colorAsText) {
+ return ColorUtil.parseColorText(colorAsText);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param color
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @deprecated Will be removed April, 2011. Use ColorUtil.getColorAsText
+ * instead.
+ *
+ */
+ @Deprecated
+ public static String getRGBText(Color color) {
+ return ColorUtil.getColorAsText(color);
+ }
+
+ /**
+ * return the (possibly multiple) value of the specified property as a
+ * vector. property values (which typically come from cytoscape.prop files)
+ * are usually scalar strings, but may be a list of such strings, surrounded
+ * by parentheses, and delimited by the value of a property called
+ * 'property.delimiter' (whose value is usually "::") get the property
+ * value; check to see if it is a list; parse it if necessary
+ */
+ static public Vector getPropertyValues(Properties props, String propName) {
+ String propertyDelimiterName = "property.token.delimiter";
+ String delimiter = props.getProperty(propertyDelimiterName, "::");
+
+ String listStartTokenName = "list.startToken";
+ String listStartToken = props.getProperty(listStartTokenName, "(");
+
+ String listEndTokenName = "list.endToken";
+ String listEndToken = props.getProperty(listEndTokenName, ")");
+
+ Vector result = new Vector();
+ String propString = props.getProperty(propName);
+
+ if (propString == null)
+ return result;
+
+ String propStringTrimmed = propString.trim();
+ String[] tokens = Misc.parseList(propStringTrimmed, listStartToken,
+ listEndToken, delimiter);
+
+ for (int i = 0; i < tokens.length; i++)
+ result.add(tokens[i]);
+
+ return result;
+ } // getPropertyValues
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param listString
+ * DOCUMENT ME!
+ * @param startToken
+ * DOCUMENT ME!
+ * @param endToken
+ * DOCUMENT ME!
+ * @param delimiter
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ static public boolean isList(String listString, String startToken,
+ String endToken, String delimiter) {
+ String s = listString.trim();
+ Vector list = new Vector();
+
+ if (s.startsWith(startToken) && s.endsWith(endToken))
+ return true;
+ else
+
+ return false;
+ } // isList
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param listString
+ * DOCUMENT ME!
+ * @param startToken
+ * DOCUMENT ME!
+ * @param endToken
+ * DOCUMENT ME!
+ * @param delimiter
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ static public String[] parseList(String listString, String startToken,
+ String endToken, String delimiter) {
+ String s = listString.trim();
+
+ if (s.startsWith(startToken) && s.endsWith(endToken)) {
+ s = s.substring(1, s.length() - 1);
+
+ return s.split(delimiter);
+ } else {
+ String[] unparseableResult = new String[1];
+ unparseableResult[0] = listString;
+
+ return unparseableResult;
+ }
+
+ /*********************
+ * StringTokenizer strtok = new StringTokenizer (deparenthesizedString,
+ * delimiter); int count = strtok.countTokens (); for (int i=0; i <
+ * count; i++) list.add (strtok.nextToken ()); } else list.add
+ * (listString);
+ *
+ * return (String []) list.toArray (new String [0]);
+ **********************/
+ } // parseList
+} // class Misc
diff --git a/application/src/main/java/cytoscape/util/ModuleProperties.java b/application/src/main/java/cytoscape/util/ModuleProperties.java
new file mode 100644
index 0000000..992d6db
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/ModuleProperties.java
@@ -0,0 +1,154 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.util;
+
+import java.util.HashMap;
+import java.util.List;
+
+import cytoscape.layout.Tunable;
+
+
+/**
+ *
+ */
+public interface ModuleProperties {
+ /**
+ * This method is used to add a new Tunable to the LayoutProperties
+ * list. The Tunable can later be retrieved by name using the
+ * <tt>get</tt> method.
+ *
+ * @param tunable The Tunable to add to this LayoutProperties
+ */
+ public void add(Tunable tunable);
+
+ /**
+ * This method is used to get the Tunable named <tt>name</tt>
+ * from this LayoutProperties. In general, the name of a
+ * Tunable should correspond to the last component of the
+ * property that it is associated with.
+ *
+ * @param name The name of the Tunable to retrieve.
+ * @return Tunable associated with <tt>name</tt> or null if
+ * there is no Tunable with that name.
+ */
+ public Tunable get(String name);
+
+ /**
+ * This method is used to get the list of available Tunables for
+ * this algorithm.
+ *
+ * @return the list of the names of Tunables for this algorithm
+ */
+ public List<String> getTunableList();
+
+ /**
+ * This method is used to get the value from the Tunable
+ * named <tt>name</tt> from this LayoutProperties. The
+ * value is always returned as a String.
+ *
+ * @param name The name of the Tunable whose value you
+ * want to retrieve.
+ * @return String value from the Tunable or null if
+ * there is no Tunable with that name.
+ */
+ public String getValue(String name);
+
+ /**
+ * This method calls the <tt>updateValues</tt> method of each
+ * Tunable that is part of this LayoutProperty.
+ */
+ public void updateValues();
+
+ /**
+ * These methods provide some simple convenience methods for property
+ * handling. They are intended to be used as a mechanism to track
+ * settings and tuneables.
+ */
+
+ /**
+ * getProperties is used to extract properties from the Cytoscape properties
+ * file. getProperties should always be called first to initialize the property
+ * maps.
+ *
+ * @return HashMap containing the resulting properties
+ */
+ public HashMap getProperties();
+
+ /**
+ * saveProperties is used to add modified properties to the Cytoscape properties
+ * so they can be saved in the properties file.
+ *
+ */
+ public void saveProperties();
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param property DOCUMENT ME!
+ * @param value DOCUMENT ME!
+ */
+ public void setProperty(String property, String value);
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param property DOCUMENT ME!
+ * @param value DOCUMENT ME!
+ */
+ public void setSavedProperty(String property, String value);
+
+ /**
+ * revertProperties is used primarily by the settings dialog mechanism when
+ * the user does a "Cancel".
+ */
+ public void revertProperties();
+
+ /**
+ * This method is used to read the properties from the Cytoscape properties
+ * file and set the values for that property in the appropriate Tunable. If
+ * there is no value for the property, then the default value in the Tunable
+ * is used to initialize the property.
+ */
+ public void initializeProperties();
+
+ /**
+ * This method returns list of tunables.
+ *
+ * @return JPanel that contains all of the Tunable widgets
+ */
+ public List<Tunable> getTunables();
+}
diff --git a/application/src/main/java/cytoscape/util/ModulePropertiesImpl.java b/application/src/main/java/cytoscape/util/ModulePropertiesImpl.java
new file mode 100644
index 0000000..17e8c66
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/ModulePropertiesImpl.java
@@ -0,0 +1,277 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.util;
+
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Properties;
+import java.util.Set;
+
+import cytoscape.CytoscapeInit;
+import cytoscape.layout.Tunable;
+
+
+/**
+ *
+ */
+public class ModulePropertiesImpl implements ModuleProperties {
+ protected HashMap<String, String> propertyMap = null;
+ protected HashMap<String, String> savedPropertyMap = null;
+ protected HashMap<String, Tunable> tunablesMap = null;
+ protected List<Tunable> tunablesList = null;
+ protected String propertyPrefix = null;
+
+ protected String moduleType;
+
+ /**
+ * Constructor.
+ *
+ * @param propertyPrefix String representing the prefix to be used
+ * when pulling properties from the property
+ * list.
+ */
+ public ModulePropertiesImpl(String propertyPrefix, String moduleType) {
+ this.moduleType = moduleType;
+ this.propertyPrefix = propertyPrefix;
+ this.tunablesMap = new HashMap<String, Tunable>();
+ this.tunablesList = new ArrayList<Tunable>();
+ }
+
+ /**
+ * This method is used to add a new Tunable to the LayoutProperties
+ * list. The Tunable can later be retrieved by name using the
+ * <tt>get</tt> method.
+ *
+ * @param tunable The Tunable to add to this LayoutProperties
+ */
+ public void add(Tunable tunable) {
+ tunablesMap.put(tunable.getName(), tunable);
+ tunablesList.add(tunable);
+ }
+
+ /**
+ * This method is used to get the Tunable named <tt>name</tt>
+ * from this LayoutProperties. In general, the name of a
+ * Tunable should correspond to the last component of the
+ * property that it is associated with.
+ *
+ * @param name The name of the Tunable to retrieve.
+ * @return Tunable associated with <tt>name</tt> or null if
+ * there is no Tunable with that name.
+ */
+ public Tunable get(String name) {
+ if (tunablesMap.containsKey(name))
+ return (Tunable) tunablesMap.get(name);
+
+ return null;
+ }
+
+ /**
+ * This method is used to get the list of available Tunables for
+ * this algorithm.
+ *
+ * @return the list of the names of Tunables for this algorithm
+ */
+ public List<String> getTunableList() {
+ return new ArrayList<String>(tunablesMap.keySet());
+ }
+
+ /**
+ * This method is used to get the value from the Tunable
+ * named <tt>name</tt> from this LayoutProperties. The
+ * value is always returned as a String.
+ *
+ * @param name The name of the Tunable whose value you
+ * want to retrieve.
+ * @return String value from the Tunable or null if
+ * there is no Tunable with that name.
+ */
+ public String getValue(String name) {
+ if (tunablesMap.containsKey(name)) {
+ Tunable t = (Tunable) tunablesMap.get(name);
+
+ return t.getValue().toString();
+ }
+
+ return null;
+ }
+
+ /**
+ * This method calls the <tt>updateValues</tt> method of each
+ * Tunable that is part of this LayoutProperty.
+ */
+ public void updateValues() {
+ for (Tunable tunable : tunablesList)
+ tunable.updateValue();
+ }
+
+ /**
+ * These methods provide some simple convenience methods for property
+ * handling. They are intended to be used as a mechanism to track
+ * settings and tuneables.
+ */
+
+ /**
+ * getProperties is used to extract properties from the Cytoscape properties
+ * file. getProperties should always be called first to initialize the property
+ * maps.
+ *
+ * @return HashMap containing the resulting properties
+ */
+ public HashMap getProperties() {
+ String prefix = getPrefix();
+ Properties props = CytoscapeInit.getProperties();
+ propertyMap = new HashMap();
+ savedPropertyMap = new HashMap();
+
+ // Find all properties with this prefix
+ Enumeration iter = props.propertyNames();
+
+ while (iter.hasMoreElements()) {
+ String property = (String) iter.nextElement();
+
+ if (property.startsWith(prefix)) {
+ int start = prefix.length();
+ propertyMap.put(property.substring(start), props.getProperty(property));
+ savedPropertyMap.put(property.substring(start), props.getProperty(property));
+ }
+ }
+
+ return propertyMap;
+ }
+
+ /**
+ * saveProperties is used to add modified properties to the Cytoscape properties
+ * so they can be saved in the properties file.
+ *
+ */
+ public void saveProperties() {
+ String prefix = getPrefix();
+ Properties props = CytoscapeInit.getProperties();
+
+ for (String key : propertyMap.keySet()) {
+ props.setProperty(prefix + key, propertyMap.get(key));
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param property DOCUMENT ME!
+ * @param value DOCUMENT ME!
+ */
+ public void setProperty(String property, String value) {
+ propertyMap.put(property, value);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param property DOCUMENT ME!
+ * @param value DOCUMENT ME!
+ */
+ public void setSavedProperty(String property, String value) {
+ savedPropertyMap.put(property, value);
+ }
+
+ /**
+ * revertProperties is used primarily by the settings dialog mechanism when
+ * the user does a "Cancel".
+ */
+ public void revertProperties() {
+ propertyMap = new HashMap();
+ if (savedPropertyMap == null)
+ return;
+
+ Set keys = savedPropertyMap.keySet();
+
+ for (Iterator iter = keys.iterator(); iter.hasNext();) {
+ String key = (String) iter.next();
+ propertyMap.put(new String(key), new String((String) savedPropertyMap.get(key)));
+
+ Tunable t = (Tunable) tunablesMap.get(key);
+
+ if (t != null)
+ t.setValue((String) savedPropertyMap.get(key));
+ }
+ }
+
+ /**
+ * This method is used to read the properties from the Cytoscape properties
+ * file and set the values for that property in the appropriate Tunable. If
+ * there is no value for the property, then the default value in the Tunable
+ * is used to initialize the property.
+ */
+ public void initializeProperties() {
+ getProperties();
+
+ for (Iterator iter = tunablesList.iterator(); iter.hasNext();) {
+ Tunable tunable = (Tunable) iter.next();
+ String property = tunable.getName();
+
+ // Do we have this property?
+ if (propertyMap.containsKey(property)) {
+ // Yes -- set it in our array
+ tunable.setValue(propertyMap.get(property));
+ } else {
+ // No, set the default
+ setProperty(property, tunable.getValue().toString());
+ setSavedProperty(property, tunable.getValue().toString());
+ }
+ }
+ }
+
+ public List<Tunable> getTunables() {
+ return tunablesList;
+ }
+
+ protected void setModuleType(String type) {
+ moduleType = type;
+ }
+
+ protected String getPrefix() {
+ String prefix = moduleType + "." + propertyPrefix;
+
+ if (prefix.lastIndexOf('.') != prefix.length())
+ prefix = prefix + ".";
+
+ return prefix;
+ }
+}
diff --git a/application/src/main/java/cytoscape/util/MonitoredTask.java b/application/src/main/java/cytoscape/util/MonitoredTask.java
new file mode 100644
index 0000000..6381013
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/MonitoredTask.java
@@ -0,0 +1,126 @@
+/*
+ File: MonitoredTask.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// MonitoredTask. An interface for classes for which progress will be monitored
+// (for example, using a progress bar UI)
+//----------------------------------------------------------------------------------------
+// $Revision: 9736 $
+// $Date: 2007-03-20 01:25:45 +0100 (Tue, 20 Mar 2007) $
+// $Author: iliana
+//----------------------------------------------------------------------------------------
+package cytoscape.util;
+
+
+//----------------------------------------------------------------------------------------
+import java.lang.String;
+
+
+/**
+ *
+ */
+public interface MonitoredTask {
+ // ------ Classes that implement this interface must have the following members:
+
+ //int lenghtOfTask; // estimate of how long the task will take to complete
+ //int currentProgress; // how much work has been done so far
+ //String statMessage; // if using a dialog, this message may be displayed to show progress
+ // for example:"Completed 55%"
+ //String taskName // if using a dialog, this message may be displayed to show what task is being
+ // performed, example: "Calculating APSP"
+
+ // ------------ Methods in alphabetical order --------------
+
+ /**
+ * Returns true if the task is done. Otherwise false.
+ * This can be done by either returning (currentProgress == lengthOfTask)
+ * or having a boolean "done" variable that is set to true in the code
+ * whenever the task is done, and returning it here.
+ */
+ public boolean done();
+
+ /**
+ * Returns the currentProgress parameter.
+ */
+ public int getCurrent();
+
+ /**
+ * Returns the lenghtOfTask parameter.
+ */
+ public int getLengthOfTask();
+
+ /**
+ * Returns a String, possibly the message to be printed on a dialog.
+ * Example: "Completed 12%"
+ */
+ public String getMessage();
+
+ /**
+ * Returns a String, possibly the message that describes the task being performed.
+ * Example: "Calculating connecting paths."
+ */
+ public String getTaskName();
+
+ /**
+ * Initializes currentProgress (generally to zero) and then spawns a SwingWorker
+ * to start doing the work.
+ * @param wait whether or not the method should wait for the task to be done before returning
+ * if true, should call SwingWorker.get() before returning
+ */
+ public void go(boolean wait);
+
+ /**
+ * Increments the progress by one
+ */
+ public void incrementProgress();
+
+ /**
+ * Stops the task by simply setting currentProgress to lengthOfTask,
+ * or if a boolean "done" variable is used, setting it to true.
+ */
+ public void stop();
+
+ /**
+ * Gets called by the <code>CytoscapeProgressMonitor</code> when the user
+ * click on the Cancel button.
+ */
+ public void cancel();
+
+ /**
+ * @return whether the task was canceled while running or not.
+ */
+ public boolean wasCanceled();
+} // MonitoredTask class
diff --git a/application/src/main/java/cytoscape/util/MutableBool.java b/application/src/main/java/cytoscape/util/MutableBool.java
new file mode 100644
index 0000000..908e259
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/MutableBool.java
@@ -0,0 +1,80 @@
+/*
+ File: MutableBool.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// MutableBool.java: mutable boolean for listeners
+
+//-------------------------------------------------------------------------
+// $Revision: 9736 $
+// $Date: 2007-03-20 01:25:45 +0100 (Tue, 20 Mar 2007) $
+// $Author: mes $
+//-------------------------------------------------------------------------
+package cytoscape.util;
+
+
+/**
+ *
+ */
+public class MutableBool {
+ private boolean b;
+
+ /**
+ * Creates a new MutableBool object.
+ *
+ * @param b DOCUMENT ME!
+ */
+ public MutableBool(boolean b) {
+ this.b = b;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean getBool() {
+ return this.b;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param b DOCUMENT ME!
+ */
+ public void setBool(boolean b) {
+ this.b = b;
+ }
+}
diff --git a/application/src/main/java/cytoscape/util/MutableInt.java b/application/src/main/java/cytoscape/util/MutableInt.java
new file mode 100644
index 0000000..a1e153f
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/MutableInt.java
@@ -0,0 +1,80 @@
+/*
+ File: MutableInt.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// MutableInt.java: mutable int for listeners
+
+//--------------------------------------------------------------------------------------
+// $Revision: 9736 $
+// $Date: 2007-03-20 01:25:45 +0100 (Tue, 20 Mar 2007) $
+// $Author: mes $
+//--------------------------------------------------------------------------------------
+package cytoscape.util;
+
+
+/**
+ *
+ */
+public class MutableInt {
+ private int i;
+
+ /**
+ * Creates a new MutableInt object.
+ *
+ * @param i DOCUMENT ME!
+ */
+ public MutableInt(int i) {
+ this.i = i;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getInt() {
+ return this.i;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param i DOCUMENT ME!
+ */
+ public void setInt(int i) {
+ this.i = i;
+ }
+}
diff --git a/application/src/main/java/cytoscape/util/MutableString.java b/application/src/main/java/cytoscape/util/MutableString.java
new file mode 100644
index 0000000..b165c8b
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/MutableString.java
@@ -0,0 +1,80 @@
+/*
+ File: MutableString.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// MutableString.java: mutable string for listeners
+
+//--------------------------------------------------------------------------------------
+// $Revision: 9736 $
+// $Date: 2007-03-20 01:25:45 +0100 (Tue, 20 Mar 2007) $
+// $Author: mes $
+//--------------------------------------------------------------------------------------
+package cytoscape.util;
+
+
+/**
+ *
+ */
+public class MutableString {
+ private String str;
+
+ /**
+ * Creates a new MutableString object.
+ *
+ * @param str DOCUMENT ME!
+ */
+ public MutableString(String str) {
+ this.str = str;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getString() {
+ return this.str;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param str DOCUMENT ME!
+ */
+ public void setString(String str) {
+ this.str = str;
+ }
+}
diff --git a/application/src/main/java/cytoscape/util/NNFFileFilter.java b/application/src/main/java/cytoscape/util/NNFFileFilter.java
new file mode 100644
index 0000000..f55d71c
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/NNFFileFilter.java
@@ -0,0 +1,80 @@
+package cytoscape.util;
+
+import java.net.URL;
+import java.net.URLConnection;
+
+import cytoscape.data.ImportHandler;
+import cytoscape.data.readers.GraphReader;
+import cytoscape.data.readers.NNFReader;
+import cytoscape.logger.CyLogger;
+
+/**
+ * File filter for Nested Network Format (NNF).
+ *
+ * @author kono, ruschein
+ * @since Cytoscape 2.7.0
+ */
+public class NNFFileFilter extends CyFileFilter {
+ /**
+ * NNF Files are Graphs.
+ */
+ private static String fileNature = ImportHandler.GRAPH_NATURE;
+
+
+ /**
+ * File Extension.
+ */
+ private static String fileExtension = "nnf";
+
+
+ /**
+ * Content Types
+ */
+ private static String[] contentTypes = { "text/nnf" };
+
+
+ /**
+ * Filter Description.
+ */
+ private static String description = "NNF files";
+
+
+ /**
+ * Constructor.
+ */
+ public NNFFileFilter() {
+ super(fileExtension, description, fileNature);
+ }
+
+
+ /**
+ * Gets Graph Reader.
+ *
+ * @param fileName
+ * File name.
+ * @return GraphReader Object.
+ */
+ public GraphReader getReader(String fileName) {
+ reader = new NNFReader(fileName);
+
+ return reader;
+ }
+
+ /**
+ * Gets Graph Reader.
+ *
+ * @param fileName
+ * File name.
+ * @return GraphReader Object.
+ */
+ public GraphReader getReader(URL url, URLConnection conn) {
+ try {
+ // Get the input stream
+ reader = new NNFReader(conn.getInputStream(), url.toString());
+ } catch (Exception e) {
+ CyLogger.getLogger(NNFFileFilter.class).error("Unable to get NNF reader: " + e.getMessage());
+ reader = null;
+ }
+ return reader;
+ }
+}
diff --git a/application/src/main/java/cytoscape/util/NestedNetworkViewUpdater.java b/application/src/main/java/cytoscape/util/NestedNetworkViewUpdater.java
new file mode 100644
index 0000000..1bb7c29
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/NestedNetworkViewUpdater.java
@@ -0,0 +1,134 @@
+package cytoscape.util;
+
+import giny.view.NodeView;
+
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+import cytoscape.view.CyNetworkView;
+import cytoscape.view.CytoscapeDesktop;
+import cytoscape.visual.VisualMappingManager;
+import cytoscape.visual.VisualStyle;
+import ding.view.DGraphView;
+import ding.view.DNodeView;
+
+
+/**
+ * This class manages images that represent nested networks. This "management" includes creation,
+ * updating and destruction of such images as well as updating network views when any of their
+ * nodes nested networks have changed.
+ *
+ * @since Cytoscape 2.7.0
+ * @author kono, ruschein
+ */
+public class NestedNetworkViewUpdater implements PropertyChangeListener {
+
+ private static final String NESTED_NETWORK_VS_NAME = "Nested Network Style";
+
+ private final VisualMappingManager vmm = Cytoscape.getVisualMappingManager();
+
+ private boolean ignoreNextEvent = false;
+
+ public NestedNetworkViewUpdater() {
+ Cytoscape.getPropertyChangeSupport().addPropertyChangeListener(this);
+ Cytoscape.getSwingPropertyChangeSupport().addPropertyChangeListener(this);
+ }
+
+ public void propertyChange(final PropertyChangeEvent evt) {
+ if (evt.getPropertyName().equals(CytoscapeDesktop.NETWORK_VIEW_CREATED) ||
+ evt.getPropertyName().equals(CytoscapeDesktop.NETWORK_VIEW_DESTROYED)) {
+ if (ignoreNextEvent) {
+ ignoreNextEvent = false;
+ return;
+ } else {
+ ignoreNextEvent = true;
+ }
+ final boolean created = evt.getPropertyName().equals(CytoscapeDesktop.NETWORK_VIEW_CREATED);
+
+ // "New value" always contains newly created/destroyed CyNetworkView.
+ final CyNetworkView view = (CyNetworkView) evt.getNewValue();
+ if (created) {
+ updateNodeViews(view.getNetwork(), view);
+ }
+
+ final List<String> parents = Cytoscape.getNetworkAttributes().getListAttribute(view.getNetwork().getIdentifier(),
+ CyNode.PARENT_NODES_ATTR);
+ if (parents == null || parents.isEmpty()) {
+ return; // Not a nested network.
+ }
+ setNestedNetworkViews(parents, created);
+
+ } else if (evt.getPropertyName().equals(Cytoscape.NESTED_NETWORK_CREATED)) {
+ final CyNode parentNode = (CyNode) evt.getOldValue();
+ final List<String> parents = new ArrayList<String>();
+ parents.add(parentNode.getIdentifier());
+ setNestedNetworkViews(parents, /* created = */ true);
+ } else if (evt.getPropertyName().equals(Cytoscape.NESTED_NETWORK_DESTROYED)) {
+ final CyNode parentNode = (CyNode) evt.getOldValue();
+ final List<String> parents = new ArrayList<String>();
+ parents.add(parentNode.getIdentifier());
+ setNestedNetworkViews(parents, /* created = */ false);
+ }
+ }
+
+
+ private void setNestedNetworkViews(final List<String> parents, final boolean created) {
+ final Collection<CyNetworkView> networkViews = Cytoscape.getNetworkViewMap().values();
+ for (final CyNetworkView networkView: networkViews) {
+ boolean applyStyle = false;
+ for (final String parentNode: parents) {
+ // If this view contains a parentNode, then update its nested network view.
+ final CyNode node = Cytoscape.getCyNode(parentNode);
+ if (node == null) {
+ continue;
+ }
+ final NodeView nodeView = networkView.getNodeView(node);
+
+ if (nodeView != null) {
+ final CyNetwork nestedNetwork = (CyNetwork)nodeView.getNode().getNestedNetwork();
+ if (nestedNetwork != null) {
+ CyNetworkView nestedNetworkView = Cytoscape.getNetworkView(nestedNetwork.getIdentifier());
+ if (nestedNetworkView == Cytoscape.getNullNetworkView()) {
+ nestedNetworkView = null;
+ }
+ ((DNodeView)nodeView).setNestedNetworkView(created ? (DGraphView) nestedNetworkView : null);
+ }
+ applyStyle = true;
+ }
+ }
+
+ // Apply visual style if necessary
+ if (applyStyle) {
+ final VisualStyle currentStyle = vmm.getVisualStyle();
+ if(!currentStyle.equals(networkView.getVisualStyle())) {
+ vmm.setVisualStyle(networkView.getVisualStyle());
+ networkView.redrawGraph(/* do layout = */ false, /* apply visual style = */ true);
+ vmm.setVisualStyle(currentStyle);
+ } else {
+ networkView.redrawGraph(/* do layout = */ false, /* apply visual style = */ true);
+ }
+
+ }
+ }
+ }
+
+
+ private void updateNodeViews(final CyNetwork currentNetwork, final CyNetworkView currentNetworkView) {
+ for (final CyNode node: (List<CyNode>)currentNetwork.nodesList()) {
+ final CyNetwork nestedNetwork = (CyNetwork) node.getNestedNetwork();
+ if (nestedNetwork != null) {
+ final CyNetworkView nestedNetworkView = Cytoscape.getNetworkView(nestedNetwork.getIdentifier());
+ if (!nestedNetworkView.equals(Cytoscape.getNullNetworkView())) {
+ final NodeView nodeView = currentNetworkView.getNodeView(node);
+ ((DNodeView)nodeView).setNestedNetworkView((DGraphView) nestedNetworkView);
+ }
+ }
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/util/OpenBrowser.java b/application/src/main/java/cytoscape/util/OpenBrowser.java
new file mode 100644
index 0000000..75199da
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/OpenBrowser.java
@@ -0,0 +1,134 @@
+/*
+ File: OpenBrowser.java
+
+ Copyright (c) 2006-2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+//-------------------------------------------------------------------------
+// $Revision: 19546 $
+// $Date: 2010-03-09 22:25:15 +0100 (Tue, 09 Mar 2010) $
+// $Author: mes $
+//-------------------------------------------------------------------------
+package cytoscape.util;
+
+import cytoscape.CytoscapeInit;
+import cytoscape.logger.CyLogger;
+
+import java.io.IOException;
+import java.util.Properties;
+
+
+public abstract class OpenBrowser {
+ static String[] LINUX_BROWSERS =
+ { "xdg-open", "htmlview", "firefox", "mozilla", "konqueror", "chrome", "chromium" };
+
+ static String MAC_PATH = "open";
+
+ private static final String WIN_PATH = "rundll32";
+ private static final String WIN_FLAG = "url.dll,FileProtocolHandler";
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param url DOCUMENT ME!
+ */
+ public static void openURL(final String url) {
+ final Properties prop = CytoscapeInit.getProperties();
+ String defBrowser = prop.getProperty("defaultWebBrowser");
+ if (defBrowser != null && defBrowser.equals(""))
+ defBrowser = null;
+ final String osName = System.getProperty("os.name");
+
+ boolean succeeded;
+ if (osName.startsWith("Windows"))
+ succeeded = openURLOnWindows(url, defBrowser);
+ else if (osName.startsWith("Mac"))
+ succeeded = openURLOnMac(url, defBrowser);
+ else // Assume Linux
+ succeeded = openURLOnLinux(url, defBrowser);
+
+ if (!succeeded)
+ CyLogger.getLogger().error("failed to launch browser!");
+ }
+
+ private static boolean openURLOnWindows(final String url, final String defBrowser) {
+ final String cmd = (defBrowser != null) ? defBrowser + " " + url
+ : WIN_PATH + " " + WIN_FLAG + " " + url;
+ CyLogger.getLogger().info("Opening URL by command \"" + cmd + "\"");
+ return tryExecute(cmd) == 0;
+ }
+
+ private static boolean openURLOnMac(final String url, final String defBrowser) {
+ final String cmd = (defBrowser != null) ? defBrowser + " " + url
+ : MAC_PATH + " " + " " + url;
+ CyLogger.getLogger().info("Opening URL by command \"" + cmd + "\"");
+ return tryExecute(cmd) == 0;
+ }
+
+ private static boolean openURLOnLinux(final String url, final String defBrowser)
+ {
+ String cmd;
+ if (defBrowser != null) {
+ cmd = defBrowser + " " + url;
+ CyLogger.getLogger().info("Opening URL by command \"" + cmd + "\"");
+ if (tryExecute(cmd) == 0)
+ return true;
+ }
+
+ for (final String browser : LINUX_BROWSERS) {
+ cmd = browser + " " + url;
+ CyLogger.getLogger().info("Opening URL by command \"" + cmd + "\"");
+ if (tryExecute(cmd) == 0)
+ return true;
+ }
+
+ return false;
+ }
+
+ /**
+ * @return the command's exit code
+ */
+ private static int tryExecute(final String cmd) {
+ try {
+ final Process p = Runtime.getRuntime().exec(cmd);
+ return p.waitFor();
+ } catch (final InterruptedException e) {
+ CyLogger.getLogger().error("failed to execute browser command: '" + cmd + "'", e );
+ return -1;
+ } catch (final IOException e) {
+ CyLogger.getLogger().error("failed to execute browser command: '" + cmd + "'", e );
+ return -1;
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/util/PercentUtil.java b/application/src/main/java/cytoscape/util/PercentUtil.java
new file mode 100644
index 0000000..5ee05ce
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/PercentUtil.java
@@ -0,0 +1,81 @@
+/*
+ File: PercentUtil.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.util;
+
+
+/**
+ * Helper Class for Calculating Percentage of Multi-Step Processes.
+ */
+public class PercentUtil {
+ private double stepMultiple;
+
+ /**
+ * Constructor.
+ *
+ * @param numSteps Number of Steps in Process.
+ */
+ public PercentUtil(int numSteps) {
+ this.stepMultiple = 100.0 / numSteps;
+ }
+
+ /**
+ * Calculates Global Percent Based on Current Step, Current Value,
+ * and MaxValue.
+ *
+ * @param currentStep Current Step Number.
+ * @param currentValue Current Value Number.
+ * @param maxValue Max Value Number.
+ * @return an integer value between 0..100.
+ */
+ public int getGlobalPercent(int currentStep, int currentValue, int maxValue) {
+ double currentPercent = calcCurrentPercent(currentValue, maxValue);
+ double value = (stepMultiple * currentStep) + currentPercent;
+
+ return (int) value;
+ }
+
+ /**
+ * Calculates Current Local Percentage.
+ *
+ * @param currentValue Current Value Number.
+ * @param maxValue Max Value Number.
+ * @return an integer value between 0..100.
+ */
+ private double calcCurrentPercent(int currentValue, int maxValue) {
+ return (currentValue * stepMultiple) / maxValue;
+ }
+}
diff --git a/application/src/main/java/cytoscape/util/PropUtil.java b/application/src/main/java/cytoscape/util/PropUtil.java
new file mode 100644
index 0000000..2a01110
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/PropUtil.java
@@ -0,0 +1,127 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.util;
+
+import cytoscape.logger.CyLogger;
+import java.util.regex.Pattern;
+import java.util.Properties;
+
+/**
+ * A stateless utility class that makes it easy to parse int and boolean values
+ * from a Properties object.
+ */
+public class PropUtil {
+
+ private PropUtil() {}
+
+ private static CyLogger logger = CyLogger.getLogger(PropUtil.class);
+
+ private static Pattern truePattern = Pattern.compile("^\\s*true\\s*$", Pattern.CASE_INSENSITIVE);
+ private static Pattern falsePattern = Pattern.compile("^\\s*false\\s*$", Pattern.CASE_INSENSITIVE);
+ private static Pattern yesPattern = Pattern.compile("^\\s*yes\\s*$", Pattern.CASE_INSENSITIVE);
+ private static Pattern noPattern = Pattern.compile("^\\s*no\\s*$", Pattern.CASE_INSENSITIVE);
+
+ /**
+ * Will return an integer for the specified property key only if the
+ * value exists and is properly formatted as an integer. Otherwise
+ * it will return the defaultValue.
+ */
+ public static int getInt(Properties props, String key, int defaultValue) {
+ String val = props.getProperty(key);
+
+ if (val == null)
+ return defaultValue;
+
+ int ret = defaultValue;
+
+ try {
+ ret = Integer.parseInt(val);
+ } catch (Exception e) {
+ logger.warn("Property value for "+key+" must be an integer");
+ }
+
+ return ret;
+ }
+
+ /**
+ * Will return a float for the specified property key only if the
+ * value exists and is properly formatted as an float. Otherwise
+ * it will return the defaultValue.
+ */
+ public static float getFloat(Properties props, String key, float defaultValue) {
+ String val = props.getProperty(key);
+
+ if (val == null)
+ return defaultValue;
+
+ float ret = defaultValue;
+
+ try {
+ ret = Float.parseFloat(val);
+ } catch (Exception e) {
+ logger.warn("Property value for "+key+" must be a float");
+ }
+
+ return ret;
+ }
+
+ /**
+ * Will return a boolean for the specified property key only if the
+ * value exists and if the string matches "true", "false", "yes", or "no"
+ * in a case insensitive manner. Otherwise it will return the defaultValue.
+ */
+ public static boolean getBoolean(Properties props, String key, boolean defaultValue) {
+ String val = props.getProperty(key);
+
+ if (val == null)
+ return defaultValue;
+
+ boolean ret = defaultValue;
+
+ try {
+ if (truePattern.matcher(val).matches() || yesPattern.matcher(val).matches())
+ ret = true;
+ else if (falsePattern.matcher(val).matches() || noPattern.matcher(val).matches())
+ ret = false;
+ else
+ ret = defaultValue;
+ } catch (Exception e) {
+ logger.warn("Property value for "+key+" must be a boolean");
+ }
+
+ return ret;
+ }
+}
diff --git a/application/src/main/java/cytoscape/util/ProxyHandler.java b/application/src/main/java/cytoscape/util/ProxyHandler.java
new file mode 100644
index 0000000..4724978
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/ProxyHandler.java
@@ -0,0 +1,134 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.util;
+
+import cytoscape.Cytoscape;
+import cytoscape.CytoscapeInit;
+
+import java.beans.*;
+
+import java.net.InetSocketAddress;
+import java.net.Proxy;
+
+
+/**
+ *
+ */
+public class ProxyHandler implements PropertyChangeListener {
+ public static final String PROXY_HOST_PROPERTY_NAME = "proxy.server";
+ public static final String PROXY_TYPE_PROPERTY_NAME = "proxy.server.type";
+ public static final String PROXY_PORT_PROPERTY_NAME = "proxy.server.port";
+ private static Proxy proxyServer = null;
+
+ static {
+ new ProxyHandler();
+ }
+
+ private ProxyHandler() {
+ Cytoscape.getPropertyChangeSupport().addPropertyChangeListener(this);
+ }
+
+ /**
+ * Return the Proxy representing the proxy server to use
+ * when reading and writing URLs. If no proxy server is being
+ * used, return null.
+ */
+ // TODO: Change this to *always* return a Proxy (no null value).
+ // For a null proxy, return Proxy.NO_PROXY instead.
+ public static Proxy getProxyServer() {
+ if (proxyServer == null) {
+ loadProxyServer();
+ }
+ return proxyServer;
+ }
+
+ // TODO: Change to always setup proxyServer to a non-null value
+ // using Proxy.NO_PROXY for direct connections. Also, change to
+ // not produce a new Proxy if the proxy is the same as previous
+ // Proxy.
+ private static void loadProxyServer() {
+ String proxyName = CytoscapeInit.getProperties()
+ .getProperty(PROXY_HOST_PROPERTY_NAME);
+
+ if ((proxyName == null) || proxyName.equals("")) {
+ proxyServer = null;
+
+ return;
+ }
+
+ String proxyT = CytoscapeInit.getProperties()
+ .getProperty(PROXY_TYPE_PROPERTY_NAME);
+
+ if ((proxyT == null) || proxyT.equals("")) {
+ proxyServer = null;
+
+ return;
+ }
+
+ Proxy.Type proxyType = Proxy.Type.valueOf(proxyT);
+ String proxyP = CytoscapeInit.getProperties()
+ .getProperty(PROXY_PORT_PROPERTY_NAME);
+
+ if ((proxyP == null) || proxyP.equals("")) {
+ proxyServer = null;
+
+ return;
+ }
+
+ int proxyPort = Integer.parseInt(proxyP);
+
+ proxyServer = new Proxy(proxyType,
+ new InetSocketAddress(proxyName, proxyPort));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void propertyChange(PropertyChangeEvent e) {
+ if (Cytoscape.PREFERENCES_UPDATED.equals(e.getPropertyName())) {
+ Proxy savedProxy = proxyServer;
+ loadProxyServer();
+
+ // Only fire event if the proxy changed:
+ if (((proxyServer == null) && (savedProxy != null)) ||
+ ((proxyServer != null) && (!proxyServer.equals(savedProxy)))) {
+ Cytoscape.firePropertyChange(Cytoscape.PROXY_MODIFIED,
+ savedProxy, proxyServer);
+ }
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/util/QuantileNorm.java b/application/src/main/java/cytoscape/util/QuantileNorm.java
new file mode 100644
index 0000000..9afac90
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/QuantileNorm.java
@@ -0,0 +1,184 @@
+package cytoscape.util;
+
+
+/**
+ * A self-contained module for performing quantile normalization.
+ * Handles ties by assigning each the average value.
+ * @author ghannum 5/4/10
+ */
+class QuantileNorm
+{
+ public static float[] quantileNorm(float[] v)
+ {
+ float[] rank = rankWTies(v);
+
+ return divideBy(subtract(rank, .5f),v.length);
+ }
+
+ private static int[] sort_I(float[] v)
+ {
+ return Sort_I(copy(v));
+ }
+
+ private static float[] rankWTies(float[] v)
+ {
+ int[] order = sort_I(v);
+
+ float[] out = new float[order.length];
+
+ for (int i=0;i<order.length;i++)
+ {
+ int j;
+ for (j=i+1;j<order.length && v[order[i]]==v[order[j]];j++);
+ j--;
+
+ if (i==j)
+ out[order[i]] = i+1;
+ else
+ {
+ long rsum = 0;
+ for (int k=i;k<=j;k++)
+ rsum += k+1;
+
+ float r = rsum / (float) (j-i+1);
+
+ for (int k=i;k<=j;k++)
+ out[order[k]] = r;
+ }
+
+ i = j;
+ }
+
+ return out;
+ }
+
+ private static float[] divideBy(float[] v, int val)
+ {
+ float[] out = new float[v.length];
+
+ for (int i=0;i<v.length;i++)
+ out[i] = v[i]/val;
+
+ return out;
+ }
+
+ private static float[] subtract(float[] v, float val)
+ {
+ float[] out = new float[v.length];
+
+ for (int i=0;i<v.length;i++)
+ out[i] = v[i]-val;
+
+ return out;
+ }
+
+ public static float[] copy(float[] vec)
+ {
+ float[] out = new float[vec.length];
+
+ for (int i=0;i<vec.length;i++)
+ out[i] = vec[i];
+
+ return out;
+ }
+
+ public static int[] Sort_I(float[] dv)
+ {
+ int[] index = new int[dv.length];
+ for (int i=0;i<dv.length;i++)
+ index[i]=i;
+
+ sortwI(dv,0,dv.length,index);
+
+ return index;
+ }
+
+ /**
+ * Sorts the specified sub-array of floats into ascending order.
+ * Adapted from Array.sort() source.
+ */
+ private static void sortwI(float x[], int off, int len, int[] index) {
+
+ // Insertion sort on smallest arrays
+ if (len < 7) {
+ for (int i=off; i<len+off; i++)
+ for (int j=i; j>off && x[j-1]>x[j]; j--)
+ swap(x, j, j-1, index);
+ return;
+ }
+
+ // Choose a partition element, v
+ int m = off + (len >> 1); // Small arrays, middle element
+ if (len > 7) {
+ int l = off;
+ int n = off + len - 1;
+ if (len > 40) { // Big arrays, pseudomedian of 9
+ int s = len/8;
+ l = med3(x, l, l+s, l+2*s);
+ m = med3(x, m-s, m, m+s);
+ n = med3(x, n-2*s, n-s, n);
+ }
+ m = med3(x, l, m, n); // Mid-size, med of 3
+ }
+ float v = x[m];
+
+ // Establish Invariant: v* (<v)* (>v)* v*
+ int a = off, b = a, c = off + len - 1, d = c;
+ while(true) {
+ while (b <= c && x[b] <= v) {
+ if (x[b]==v)
+ swap(x, a++, b, index);
+ b++;
+ }
+ while (c >= b && x[c] >= v) {
+ if (x[c]==v)
+ swap(x, c, d--, index);
+ c--;
+ }
+ if (b > c)
+ break;
+ swap(x, b++, c--, index);
+ }
+
+ // Swap partition elements back to middle
+ int s, n = off + len;
+ s = Math.min(a-off, b-a ); vecswap(x, off, b-s, s, index);
+ s = Math.min(d-c, n-d-1); vecswap(x, b, n-s, s, index);
+
+ // Recursively sort non-partition-elements
+ if ((s = b-a) > 1)
+ sortwI(x, off, s,index);
+ if ((s = d-c) > 1)
+ sortwI(x, n-s, s,index);
+ }
+
+ /**
+ * Swaps x[a] with x[b].
+ */
+ private static void swap(float x[], int a, int b, int[] index) {
+ float t = x[a];
+ x[a] = x[b];
+ x[b] = t;
+
+ int ti = index[a];
+ index[a] = index[b];
+ index[b] = ti;
+ }
+
+ /**
+ * Swaps x[a .. (a+n-1)] with x[b .. (b+n-1)].
+ */
+ private static void vecswap(float x[], int a, int b, int n, int[] index) {
+ for (int i=0; i<n; i++, a++, b++)
+ swap(x, a, b, index);
+ }
+
+ /**
+ * Returns the index of the median of the three indexed floats.
+ */
+ private static int med3(float x[], int a, int b, int c) {
+ return (x[a] < x[b] ?
+ (x[b] < x[c] ? b : x[a] < x[c] ? c : a) :
+ (x[b] > x[c] ? b : x[a] > x[c] ? c : a));
+ }
+}
diff --git a/application/src/main/java/cytoscape/util/RankScaler.java b/application/src/main/java/cytoscape/util/RankScaler.java
new file mode 100644
index 0000000..9a9186d
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/RankScaler.java
@@ -0,0 +1,76 @@
+/*
+ File: RankScaler.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.util;
+
+
+import java.util.Arrays;
+import java.util.HashMap;
+
+
+/**
+ * Used to scale a list of values to [a,b]
+ */
+class RankScaler extends AbstractScaler {
+ public double[] scale(final double values[], final double a, final double b) throws IllegalArgumentException
+ {
+ if (values.length < 2)
+ throw new IllegalArgumentException("need at least 2 values for scaling!");
+ if (a >= b)
+ throw new IllegalArgumentException("bad bounds!");
+
+ final double sortedValues[] = values.clone();
+ Arrays.sort(sortedValues);
+
+ final HashMap<Double, Double> origValueToRankValueMap = new HashMap<Double, Double>();
+ final double stepSize = (b - a) / values.length;
+ double currentValue = sortedValues[0];
+ double sum = stepSize / 2.0;
+ double count = 1.0;
+ for (int i = 1; i < values.length; ++i) {
+ final double currentRankValue = stepSize * (0.5 + i);
+ if (sortedValues[i] == currentValue) {
+ ++count;
+ sum += currentRankValue;
+ } else {
+ origValueToRankValueMap.put(currentValue, sum / count);
+ currentValue = sortedValues[i];
+ sum = currentRankValue;
+ count = 1.0;
+ }
+ }
+ origValueToRankValueMap.put(sortedValues[values.length - 1], sum / count);
+
+ final double[] scaledValues = new double[values.length];
+ for (int i = 0; i < values.length; ++i)
+ scaledValues[i] = origValueToRankValueMap.get(values[i]);
+
+ return scaledValues;
+ }
+}
diff --git a/application/src/main/java/cytoscape/util/RecentlyOpenedTracker.java b/application/src/main/java/cytoscape/util/RecentlyOpenedTracker.java
new file mode 100644
index 0000000..22f96cb
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/RecentlyOpenedTracker.java
@@ -0,0 +1,112 @@
+/*
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.util;
+
+
+import cytoscape.CytoscapeInit;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.net.URL;
+import java.util.List;
+import java.util.LinkedList;
+
+
+/**
+ * A class to keep track of a short list of recently opened URLs.
+ */
+public class RecentlyOpenedTracker {
+ private static final int MAX_TRACK_COUNT = 5;
+ private final String trackerFileName;
+ private final LinkedList<URL> trackerURLs;
+
+ /**
+ * Creates a "recently opened" file tracker.
+ *
+ * @param trackerFileName the name of the file in the Cytoscape config directory to read
+ * saved file names from.
+ */
+ public RecentlyOpenedTracker(final String trackerFileName) throws IOException {
+ this.trackerFileName = trackerFileName;
+ trackerURLs = new LinkedList<URL>();
+
+ final File input = new File(CytoscapeInit.getConfigVersionDirectory(), trackerFileName);
+ if (!input.exists())
+ input.createNewFile();
+
+ final BufferedReader reader = new BufferedReader(new FileReader(input));
+ String line;
+ while ((line = reader.readLine()) != null && trackerURLs.size() < MAX_TRACK_COUNT) {
+ final String newURL = line.trim();
+ if (newURL.length() > 0)
+ trackerURLs.addLast(new URL(newURL));
+ }
+ }
+
+ /**
+ * @returns the current list of recently opened file names
+ */
+ @SuppressWarnings("unchecked") public synchronized List<URL> getRecentlyOpenedURLs() {
+ return (List<URL>)trackerURLs.clone();
+ }
+
+ /**
+ * Adds "newURL" to the list of recently opened file names and trims the list if it has
+ * exceeded its maximum length.
+ */
+ public synchronized void add(final URL newURL) {
+ trackerURLs.remove(newURL);
+ if (trackerURLs.size() == MAX_TRACK_COUNT)
+ trackerURLs.removeLast();
+ trackerURLs.addFirst(newURL);
+ }
+
+ /**
+ * Writes the list of recently opened files to the file specified by the constructor argument.
+ */
+ public void writeOut() throws FileNotFoundException {
+ final PrintWriter writer = new PrintWriter(new File(CytoscapeInit.getConfigVersionDirectory(), trackerFileName));
+ for (final URL trackerURL : trackerURLs)
+ writer.println(trackerURL.toString());
+ writer.close();
+ }
+
+ /**
+ * @return the last addition or null if there are no URLs
+ */
+ public synchronized URL getMostRecentAddition() {
+ if (trackerURLs.isEmpty())
+ return null;
+ else
+ return trackerURLs.getFirst();
+ }
+}
\ No newline at end of file
diff --git a/application/src/main/java/cytoscape/util/SIFFileFilter.java b/application/src/main/java/cytoscape/util/SIFFileFilter.java
new file mode 100644
index 0000000..40f7a22
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/SIFFileFilter.java
@@ -0,0 +1,106 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.util;
+
+import cytoscape.data.ImportHandler;
+
+import cytoscape.data.readers.GraphReader;
+import cytoscape.data.readers.InteractionsReader;
+
+import cytoscape.logger.CyLogger;
+
+import java.net.URL;
+import java.net.URLConnection;
+
+/**
+ * FileFilter for Reading in Cytoscape SIF Files.
+ *
+ * @author Cytoscape Development Team.
+ */
+public class SIFFileFilter extends CyFileFilter {
+ /**
+ * SIF Files are Graphs.
+ */
+ private static String fileNature = ImportHandler.GRAPH_NATURE;
+
+ /**
+ * File Extension.
+ */
+ private static String fileExtension = "sif";
+
+ /**
+ * Content Types
+ */
+ private static String[] contentTypes = { "text/sif" };
+
+ /**
+ * Filter Description.
+ */
+ private static String description = "SIF files";
+
+ /**
+ * Constructor.
+ */
+ public SIFFileFilter() {
+ super(fileExtension, description, fileNature);
+ }
+
+ /**
+ * Gets Graph Reader.
+ * @param fileName File name.
+ * @return GraphReader Object.
+ */
+ public GraphReader getReader(String fileName) {
+ reader = new InteractionsReader(fileName);
+
+ return reader;
+ }
+
+ /**
+ * Gets Graph Reader.
+ * @param fileName File name.
+ * @return GraphReader Object.
+ */
+ public GraphReader getReader(URL url, URLConnection conn) {
+ try {
+ // Get the input stream
+ reader = new InteractionsReader(conn.getInputStream(), url.toString());
+ } catch (Exception e) {
+ CyLogger.getLogger(SIFFileFilter.class).error("Unable to get SIF reader: "+e.getMessage());
+ reader = null;
+ }
+ return reader;
+ }
+}
diff --git a/application/src/main/java/cytoscape/util/Scaler.java b/application/src/main/java/cytoscape/util/Scaler.java
new file mode 100644
index 0000000..b41a642
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/Scaler.java
@@ -0,0 +1,48 @@
+/*
+ File: Scaler.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.util;
+
+
+import java.util.Collection;
+
+
+/**
+ * Used to scale a list of values to [a,b]
+ */
+public interface Scaler {
+ double[] scale(final double values[], final double a, final double b) throws IllegalArgumentException;
+ double[] scale(final Collection<Double> values, final double a, final double b) throws IllegalArgumentException;
+
+ float[] scale(final float values[], final float a, final float b) throws IllegalArgumentException;
+ float[] scale(final Collection<Float> values, final float a, final float b) throws IllegalArgumentException;
+}
+
+
+
diff --git a/application/src/main/java/cytoscape/util/ScalerFactory.java b/application/src/main/java/cytoscape/util/ScalerFactory.java
new file mode 100644
index 0000000..a16e1e3
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/ScalerFactory.java
@@ -0,0 +1,72 @@
+/*
+ File: ScalerFactory.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.util;
+
+
+import java.util.Map;
+import java.util.TreeMap;
+
+
+public class ScalerFactory {
+ private static Map<String, Scaler> typeToScalerMap = null;
+
+ /**
+ * @return one of the registered Scaler types. Preregistered are "linear" and "rank".
+ */
+ public static synchronized Scaler getScaler(final String type) throws IllegalArgumentException {
+ if (typeToScalerMap == null)
+ init();
+
+ final Scaler scaler = typeToScalerMap.get(type);
+ if (scaler == null)
+ throw new IllegalArgumentException("unknown type \"" + type + "\"!");
+
+ return scaler;
+ }
+
+ public static synchronized void registerScaler(final String type, final Scaler newScaler) {
+ if (typeToScalerMap == null)
+ init();
+
+ if (typeToScalerMap.containsKey(type))
+ throw new IllegalArgumentException("trying to register a duplicate type \"" + type + "\"!");
+
+ typeToScalerMap.put(type, newScaler);
+ }
+
+ private static void init() {
+ if (typeToScalerMap != null)
+ throw new IllegalStateException("already initialised!");
+ typeToScalerMap = new TreeMap<String, Scaler>();
+
+ typeToScalerMap.put("linear", new LinearScaler());
+ typeToScalerMap.put("rank", new RankScaler());
+ }
+}
diff --git a/application/src/main/java/cytoscape/util/ScalingMethod.java b/application/src/main/java/cytoscape/util/ScalingMethod.java
new file mode 100644
index 0000000..16eb263
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/ScalingMethod.java
@@ -0,0 +1,25 @@
+package cytoscape.util;
+
+
+public enum ScalingMethod {
+ NONE("none (prescaled)"),
+ LINEAR_LOWER("linear/lower"),
+ LINEAR_UPPER("linear/upper"),
+ RANK_LOWER("rank/lower"),
+ RANK_UPPER("rank/upper");
+
+ private String displayString;
+
+ ScalingMethod(final String displayString) { this.displayString = displayString; }
+
+ public String getDisplayString() { return displayString; }
+
+ static public ScalingMethod getEnumValue(final String displayString) {
+ for (final ScalingMethod method : ScalingMethod.values()) {
+ if (method.getDisplayString().equals(displayString))
+ return method;
+ }
+
+ throw new IllegalStateException("unknown string representation: \"" + displayString + "\"!");
+ }
+}
diff --git a/application/src/main/java/cytoscape/util/SwingWorker.java b/application/src/main/java/cytoscape/util/SwingWorker.java
new file mode 100644
index 0000000..712c3ec
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/SwingWorker.java
@@ -0,0 +1,184 @@
+/*
+ File: SwingWorker.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.util;
+
+import javax.swing.SwingUtilities;
+
+
+/**
+ * This is the 3rd version of SwingWorker (also known as
+ * SwingWorker 3), an abstract class that you subclass to
+ * perform GUI-related work in a dedicated thread. For
+ * instructions on using this class, see:
+ *
+ * http://java.sun.com/docs/books/tutorial/uiswing/misc/threads.html
+ *
+ * Note that the API changed slightly in the 3rd version:
+ * You must now invoke start() on the SwingWorker after
+ * creating it.
+ */
+public abstract class SwingWorker {
+ private Object value; // see getValue(), setValue()
+ private Thread thread;
+
+ /**
+ * Class to maintain reference to current worker thread
+ * under separate synchronization control.
+ */
+ private static class ThreadVar {
+ private Thread thread;
+
+ ThreadVar(Thread t) {
+ thread = t;
+ }
+
+ synchronized Thread get() {
+ return thread;
+ }
+
+ synchronized void clear() {
+ thread = null;
+ }
+ }
+
+ private ThreadVar threadVar;
+
+ /**
+ * Get the value produced by the worker thread, or null if it
+ * hasn't been constructed yet.
+ */
+ protected synchronized Object getValue() {
+ return value;
+ }
+
+ /**
+ * Set the value produced by worker thread
+ */
+ private synchronized void setValue(Object x) {
+ value = x;
+ }
+
+ /**
+ * Compute the value to be returned by the <code>get</code> method.
+ */
+ public abstract Object construct();
+
+ /**
+ * Called on the event dispatching thread (not on the worker thread)
+ * after the <code>construct</code> method has returned.
+ */
+ public void finished() {
+ }
+
+ /**
+ * A new method that interrupts the worker thread. Call this method
+ * to force the worker to stop what it's doing.
+ */
+ public void interrupt() {
+ Thread t = threadVar.get();
+
+ if (t != null) {
+ t.interrupt();
+ }
+
+ threadVar.clear();
+ }
+
+ /**
+ * Return the value created by the <code>construct</code> method.
+ * Returns null if either the constructing thread or the current
+ * thread was interrupted before a value was produced.
+ *
+ * @return the value created by the <code>construct</code> method
+ */
+ public Object get() {
+ while (true) {
+ Thread t = threadVar.get();
+
+ if (t == null) {
+ return getValue();
+ }
+
+ try {
+ t.join();
+ } catch (InterruptedException e) {
+ Thread.currentThread().interrupt(); // propagate
+
+ return null;
+ }
+ }
+ }
+
+ /**
+ * Start a thread that will call the <code>construct</code> method
+ * and then exit.
+ */
+ public SwingWorker() {
+ final Runnable doFinished = new Runnable() {
+ public void run() {
+ finished();
+ }
+ };
+
+ Runnable doConstruct = new Runnable() {
+ public void run() {
+ try {
+ setValue(construct());
+ } finally {
+ threadVar.clear();
+ }
+
+ SwingUtilities.invokeLater(doFinished);
+ }
+ };
+
+ Thread t = new Thread(doConstruct);
+
+ threadVar = new ThreadVar(t);
+ }
+
+ /**
+ * Start the worker thread.
+ */
+ public void start() {
+ Thread t = threadVar.get();
+
+ if (t != null) {
+ t.start();
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/util/TopoGraphNode.java b/application/src/main/java/cytoscape/util/TopoGraphNode.java
new file mode 100644
index 0000000..1952e63
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/TopoGraphNode.java
@@ -0,0 +1,42 @@
+/*
+ File: TopoGraphNode.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.util;
+
+
+import java.util.Collection;
+
+
+/**
+ * Represents a node in a topological graph.
+ */
+public interface TopoGraphNode {
+ public Collection<TopoGraphNode> getDependents();
+}
+
diff --git a/application/src/main/java/cytoscape/util/TopologicalSort.java b/application/src/main/java/cytoscape/util/TopologicalSort.java
new file mode 100644
index 0000000..2213c94
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/TopologicalSort.java
@@ -0,0 +1,86 @@
+/*
+ File: TopologicalSort.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.util;
+
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+import java.util.Stack;
+
+
+/**
+ * Implements topological sorting of nodes in a graph.
+ * See for example http://en.wikipedia.org/wiki/Topological_sorting (the Tarjan algorithm)
+ */
+public class TopologicalSort {
+ /**
+ * @param nodes the list of all nodes
+ * @param edges the edges that connect the nodes that need to be sorted.
+ * @return the topological order
+ * @throws IllegalStateException if a cycle has been detected
+ * N.B. it might be a good idea to make sure that whatever the concrete type of the nodes in
+ * "nodes" are has a toString() method that returns the name of a node since this method
+ * will be used if a cycle has been detected to report one of the nodes in the cycle.
+ */
+ public static List<TopoGraphNode> sort(final Collection<TopoGraphNode> nodes)
+ throws IllegalStateException
+ {
+ final List<TopoGraphNode> order = new ArrayList<TopoGraphNode>();
+ final Set<TopoGraphNode> visited = new HashSet<TopoGraphNode>();
+
+ final Set<TopoGraphNode> alreadySeen = new HashSet<TopoGraphNode>();
+ for (final TopoGraphNode n : nodes) {
+ alreadySeen.clear();
+ visit(n, alreadySeen, visited, order);
+ }
+
+ return order;
+ }
+
+ private static void visit(final TopoGraphNode n, final Set<TopoGraphNode> alreadySeen,
+ final Set<TopoGraphNode> visited, final List<TopoGraphNode> order)
+ {
+ if (alreadySeen.contains(n))
+ throw new IllegalStateException("cycle containing " + n + " found!");
+ alreadySeen.add(n);
+
+ if (!visited.contains(n)) {
+ visited.add(n);
+ for (final TopoGraphNode m : n.getDependents())
+ visit(m, alreadySeen, visited, order);
+ order.add(n);
+ }
+
+ alreadySeen.remove(n);
+ }
+}
diff --git a/application/src/main/java/cytoscape/util/Transform.java b/application/src/main/java/cytoscape/util/Transform.java
new file mode 100644
index 0000000..ac7b571
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/Transform.java
@@ -0,0 +1,108 @@
+/*
+ File: Transform.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.util;
+
+import cytoscape.logger.CyLogger;
+
+import java.io.File;
+
+import javax.xml.transform.Transformer;
+import javax.xml.transform.TransformerException;
+import javax.xml.transform.TransformerFactory;
+import javax.xml.transform.stream.StreamResult;
+import javax.xml.transform.stream.StreamSource;
+
+
+/**
+ * Apply XSLT to an XML document
+ *
+ * @author kono
+ *
+ */
+public class Transform {
+ private File input;
+ private File xslt;
+ private File output;
+
+ /**
+ * Creates a new Transform object.
+ *
+ * @param document DOCUMENT ME!
+ * @param template DOCUMENT ME!
+ * @param output DOCUMENT ME!
+ */
+ public Transform(String document, String template, String output) {
+ input = new File(document);
+ xslt = new File(template);
+ this.output = new File(output);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws TransformerException DOCUMENT ME!
+ */
+ public void convert() throws TransformerException {
+ StreamSource in = new StreamSource(input);
+ StreamSource ss = new StreamSource(xslt);
+ StreamResult out = new StreamResult(output);
+
+ TransformerFactory tff = TransformerFactory.newInstance();
+ Transformer tf = tff.newTransformer(ss);
+ tf.transform(in, out);
+
+ CyLogger.getLogger().info("File conversion done!: " + output.getName());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public static void main(String[] args) throws Exception {
+ StreamSource in = new StreamSource(new File(args[0]));
+ StreamSource ss = new StreamSource(new File(args[1]));
+ StreamResult out = new StreamResult(new File(args[2]));
+
+ TransformerFactory tff = TransformerFactory.newInstance();
+ Transformer tf = tff.newTransformer(ss);
+ tf.transform(in, out);
+ CyLogger.getLogger().info("Done: " + args[2]);
+ }
+}
diff --git a/application/src/main/java/cytoscape/util/URLUtil.java b/application/src/main/java/cytoscape/util/URLUtil.java
new file mode 100644
index 0000000..8c75a3e
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/URLUtil.java
@@ -0,0 +1,252 @@
+/*
+ * Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org) The
+ * Cytoscape Consortium is: - Institute for Systems Biology - University of
+ * California San Diego - Memorial Sloan-Kettering Cancer Center - Institut
+ * Pasteur - Agilent Technologies This library is free software; you can
+ * redistribute it and/or modify it under the terms of the GNU Lesser General
+ * Public License as published by the Free Software Foundation; either version
+ * 2.1 of the License, or any later version. This library is distributed in the
+ * hope that it will be useful, but WITHOUT ANY WARRANTY, WITHOUT EVEN THE
+ * IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The
+ * software and documentation provided hereunder is on an "as is" basis, and the
+ * Institute for Systems Biology and the Whitehead Institute have no obligations
+ * to provide maintenance, support, updates, enhancements or modifications. In
+ * no event shall the Institute for Systems Biology and the Whitehead Institute
+ * be liable to any party for direct, indirect, special, incidental or
+ * consequential damages, including lost profits, arising out of the use of this
+ * software and its documentation, even if the Institute for Systems Biology and
+ * the Whitehead Institute have been advised of the possibility of such damage.
+ * See the GNU Lesser General Public License for more details. You should have
+ * received a copy of the GNU Lesser General Public License along with this
+ * library; if not, write to the Free Software Foundation, Inc., 59 Temple
+ * Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.util;
+
+import cytoscape.task.TaskMonitor;
+
+import cytoscape.task.ui.JTask;
+
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+
+import java.net.MalformedURLException;
+import java.net.Proxy;
+import java.net.URL;
+import java.net.URLConnection;
+
+import java.util.jar.JarInputStream;
+import java.util.zip.GZIPInputStream;
+import java.util.zip.ZipInputStream;
+
+/**
+ *
+ */
+public class URLUtil {
+ private static final String GZIP = ".gz";
+
+ private static final String ZIP = ".zip";
+
+ private static final String JAR = ".jar";
+
+ private static int msConnectionTimeout = 2000;
+
+ /**
+ * Gets the an input stream given a URL.
+ *
+ * @param source
+ * URL source for a zip or jar file.
+ * @return InputStream for given URL
+ * @throws IOException
+ *
+ */
+ public static InputStream getInputStream(URL source) throws IOException {
+ final InputStream newIs;
+ final InputStream proxyIs;
+ proxyIs = getBasicInputStream(source);
+ if (source.toString().toLowerCase().endsWith(GZIP)) {
+ newIs = new GZIPInputStream(proxyIs);
+ } else if (source.toString().toLowerCase().endsWith(ZIP)) {
+ // CyLogger.getLogger().warn(source.toString() + " ZIP ");
+ newIs = new ZipInputStream(proxyIs);
+ } else if (source.toString().toLowerCase().endsWith(JAR)) {
+ newIs = new JarInputStream(proxyIs);
+ } else {
+ newIs = proxyIs;
+ }
+ return newIs;
+ }
+
+ /**
+ * Obtain an InputStream for a given URL. Ensure proxy servers and an input
+ * stream to the real URL source is created--not a locally cached and out of
+ * date source. Proxy servers and other characteristics can cause pages to
+ * be cached.
+ *
+ * @param source
+ * the non-null URL from which to obtain an InputStream.
+ * @return InputStream from the source URL.
+ * @throws IllegalStateException
+ * if source is null.
+ * @throws IOException
+ * if a connection to the URL can't be opened or a problem
+ * occurs with the InputStream.
+ */
+ public static InputStream getBasicInputStream(URL source)
+ throws IOException {
+ if (source == null) {
+ throw new IllegalStateException(
+ "getBasicInputStream was given a null 'source' argument.");
+ }
+ URLConnection uc = getURLConnection(source);
+
+ final InputStream is;
+ try {
+ is = uc.getInputStream();
+ } catch (final Exception e) {
+ throw new IllegalStateException("Failed to get input stream for \"" + source + "\"!");
+ }
+ return is;
+ }
+
+ /**
+ * Obtain a URLConnection for a given URL. Ensure proxy servers are
+ * considered and page caching is ignored.
+ *
+ * @param source
+ * the non-null URL from which to obtain a URLConnection.
+ * @return URLConnection to the source URL.
+ * @throws IllegalStateException
+ * if source is null.
+ * @throws IOException
+ * if a connection to the URL can't be opened.
+ */
+ public static URLConnection getURLConnection(URL source) throws IOException {
+ if (source == null) {
+ throw new IllegalStateException(
+ "getURLConnection was given a null 'source' argument.");
+ }
+ Proxy cytoProxy = ProxyHandler.getProxyServer();
+ URLConnection uc = null;
+ if (cytoProxy == null) {
+ uc = source.openConnection();
+ } else {
+ try {
+ uc = source.openConnection(cytoProxy);
+ } catch (UnsupportedOperationException e) {
+ // This happens when we have a URL whose
+ // protocol handler doesn't take a proxy
+ // argument (such as a URL referring to inside
+ // a jar file). In this case, just use the
+ // normal way to open a connection:
+ uc = source.openConnection();
+ }
+ }
+ uc.setUseCaches(false); // don't use a cached page
+ uc.setConnectTimeout(msConnectionTimeout); // set timeout for connection
+ return uc;
+ }
+
+ /**
+ * Download the file specified by the url string to the given File object
+ *
+ * @param urlString
+ * @param downloadFile
+ * @param taskMonitor
+ * @return
+ * @throws IOException
+ */
+ public static void download(String urlString, File downloadFile,
+ TaskMonitor taskMonitor) throws IOException
+ {
+ boolean stop = false;
+
+ try {
+ URL url = new URL(urlString);
+ InputStream is = null;
+
+ try {
+ int maxCount = 0; // -1 if unknown
+ int progressCount = 0;
+ URLConnection conn = getURLConnection(url);
+ maxCount = conn.getContentLength();
+ is = conn.getInputStream();
+ FileOutputStream os = null;
+ try {
+ os = new FileOutputStream(downloadFile);
+ double percent = 0.0d;
+ byte[] buffer = new byte[1];
+ while (((is.read(buffer)) != -1) && !stop) {
+ progressCount += buffer.length;
+ // Report on Progress
+ if (taskMonitor != null) {
+ percent = ((double) progressCount / maxCount) * 100.0;
+ if (maxCount == -1) { // file size unknown
+ percent = -1;
+ }
+ JTask jTask = (JTask) taskMonitor;
+ if (jTask.haltRequested()) { // abort
+ stop = true;
+ taskMonitor.setStatus("Canceling the download ...");
+ taskMonitor.setPercentCompleted(100);
+ break;
+ }
+ taskMonitor.setPercentCompleted((int) percent);
+ }
+ os.write(buffer);
+ }
+ os.flush();
+ }
+ finally {
+ if (os != null) {
+ os.close();
+ }
+ }
+ } finally {
+ if (is != null)
+ is.close();
+ }
+ } finally {
+ if (stop)
+ downloadFile.delete();
+ }
+ }
+
+ /**
+ * Get the the contents of the given URL as a string.
+ *
+ * @param source
+ * @return String
+ * @throws IOException
+ */
+ public static String download(URL source) throws IOException {
+ InputStream is = null;
+ StringBuffer buffer = new StringBuffer();
+ int c;
+
+ try {
+ is = getInputStream(source);
+ while ((c = is.read()) != -1) {
+ buffer.append((char) c);
+ }
+ }
+ finally {
+ if (is != null) {
+ is.close();
+ }
+ }
+
+ return buffer.toString();
+ }
+
+ public static boolean isValid(final String urlCandidate) {
+ try {
+ new URL(urlCandidate);
+ return true;
+ } catch (final MalformedURLException e) {
+ return false;
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/util/XGMMLFileFilter.java b/application/src/main/java/cytoscape/util/XGMMLFileFilter.java
new file mode 100644
index 0000000..6534fcd
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/XGMMLFileFilter.java
@@ -0,0 +1,166 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.util;
+
+import java.io.File;
+import java.io.IOException;
+import java.net.URL;
+import java.net.URLConnection;
+
+import cytoscape.data.ImportHandler;
+import cytoscape.data.readers.GraphReader;
+import cytoscape.data.readers.XGMMLReader;
+import cytoscape.logger.CyLogger;
+
+/**
+ * FileFilter for Reading in XGMML Files.
+ *
+ * @author Cytoscape Development Team.
+ */
+public class XGMMLFileFilter extends CyFileFilter {
+ /**
+ * XGMML Files are Graphs.
+ */
+ private static String fileNature = ImportHandler.GRAPH_NATURE;
+
+ /**
+ * File Extensions.
+ */
+ private static String[] fileExtensions = { "xgmml", "xml" };
+
+ /**
+ * Content Types
+ */
+ private static String[] xgmmlContentTypes = { "text/xgmml", "text/xgmml+xml" };
+
+ /**
+ * Filter Description.
+ */
+ private static String description = "XGMML files";
+
+ /**
+ * Constructor.
+ */
+ public XGMMLFileFilter() {
+ super(fileExtensions, description, fileNature);
+
+ // Add our content types
+ for (int i = 0; i < xgmmlContentTypes.length; i++)
+ addContentType(xgmmlContentTypes[i]);
+ }
+
+ /**
+ * Gets Graph Reader.
+ * @param fileName File name.
+ * @return GraphReader Object.
+ */
+ public GraphReader getReader(String fileName) {
+ reader = new XGMMLReader(fileName);
+
+ return reader;
+ }
+
+ /**
+ * Gets Graph Reader.
+ * @param fileName File name.
+ * @return GraphReader Object.
+ */
+ public GraphReader getReader(URL url, URLConnection conn) {
+ try {
+ // Get the input stream
+ reader = new XGMMLReader(conn.getInputStream(), url.toString());
+ } catch (Exception e) {
+ CyLogger.getLogger(XGMMLFileFilter.class).error("Unable to get XGMML reader: "+e.getMessage());
+ reader = null;
+ }
+ return reader;
+ }
+
+ /**
+ * Indicates which files the XGMMLFileFilter accepts.
+ *
+ * This method will return true only if:
+ * <UL>
+ * <LI>File ends in .xml or .xgmml; and
+ * <LI>File headers includes the www.cs.rpi.edu/XGMML namespace declaration.
+ * </UL>
+ *
+ * @param file File
+ * @return true or false.
+ */
+ public boolean accept(File file) {
+ String fileName = file.getName();
+ boolean firstPass = false;
+
+ // First test: file must end with one of the registered file extensions.
+ for (int i = 0; i < fileExtensions.length; i++) {
+ if (fileName.endsWith(fileExtensions[i])) {
+ firstPass = true;
+ }
+ }
+
+ if (firstPass) {
+ // Second test: file header must contain the xgmml declaration
+ try {
+ String header = getHeader(file).toLowerCase();
+
+ if (header.indexOf("www.cs.rpi.edu/xgmml") > 0) {
+ return true;
+ }
+ } catch (IOException e) {
+ }
+ }
+
+ return false;
+ }
+
+ public boolean accept(URL url, String contentType) {
+ // Check for matching content type
+ if ((contentType != null) && (contentTypes != null) &&
+ (contentTypes.get(contentType) != null)) {
+ return true;
+ }
+
+ try {
+ final String header = getHeader(url).toLowerCase();
+ if (header.indexOf("www.cs.rpi.edu/xgmml") > 0)
+ return true;
+ } catch (IOException e) {
+ e.printStackTrace();
+ return false;
+ }
+ return false;
+ }
+}
diff --git a/application/src/main/java/cytoscape/util/ZipUtil.java b/application/src/main/java/cytoscape/util/ZipUtil.java
new file mode 100644
index 0000000..39b6133
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/ZipUtil.java
@@ -0,0 +1,529 @@
+/*
+ File: ZipMultipleFiles.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.util;
+
+import java.io.BufferedOutputStream;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Set;
+import java.util.zip.CRC32;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipFile;
+import java.util.zip.ZipInputStream;
+import java.util.zip.ZipOutputStream;
+
+import cytoscape.task.TaskMonitor;
+import cytoscape.task.Task;
+import cytoscape.task.ui.JTask;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+/**
+ * Compression-related methods mainly for Session Writer.<br>
+ * The created zip files can be decompressed by any zip utilities.
+ *
+ * @version 0.9
+ * @since Cytoscape 2.3
+ * @see cytoscape.data.writers.CytoscapeSessionWriter
+ * @author kono
+ *
+ */
+public class ZipUtil {
+ /*
+ * Default Compression Level. Range is 0-9. Basically, 0 is no compression,
+ * and 9 will make the most space-efficeint zip file. However, it takes
+ * long!
+ */
+
+ /**
+ *
+ */
+ public static final int DEF_COMPRESSION_LEVEL = 1;
+ private String zipArchiveName;
+ private String[] inputFiles;
+ private String inputFileDir;
+ private int fileCount;
+ private String sessionDirName;
+ private HashMap pluginFileMap = null;
+
+ /**
+ * For zip file, file separator is always "/" in all platforms inclding Win,
+ * Mac, and Unix.
+ */
+ private static final String FS = "/";
+
+ /**
+ * Constructor.<br>
+ *
+ * @param zipFile
+ * Output zip file name.
+ * @param fileNameList
+ * List of file names to be compressed.
+ * @param sessionDir
+ * Root dir created in the zip archive.
+ *
+ */
+ public ZipUtil(final String zipFile, final String[] fileNameList, final String sessionDir) {
+ this(zipFile, fileNameList, sessionDir, "");
+ }
+
+ /**
+ * Constructor.<br>
+ *
+ * @param zipFile
+ * Output zip file name.
+ * @param fileNameList
+ * List of file names to be compressed.
+ * @param sessionDir
+ * Root dir created in the zip archive.
+ * @param fileDir
+ * root directory of files in fileList.
+ *
+ */
+ public ZipUtil(final String zipFile, final String[] fileNameList, final String sessionDir,
+ final String fileDir) {
+ this.zipArchiveName = zipFile;
+ this.fileCount = fileNameList.length;
+ this.inputFiles = new String[fileCount];
+ this.sessionDirName = sessionDir;
+ this.inputFileDir = fileDir;
+
+ System.arraycopy(fileNameList, 0, inputFiles, 0, fileCount);
+ }
+
+ /**
+ * Delete input files.
+ *
+ */
+ private void clean() {
+ for (int i = 0; i < fileCount; i++) {
+ final File tempFile = new File(inputFileDir + inputFiles[i]);
+ tempFile.delete();
+ }
+ }
+
+ /**
+ * Faster version of compression method.<br>
+ *
+ * @param compressionLevel
+ * Level of compression. Range = 0-9. 0 is no-compression, and 9
+ * is most space-efficeint. However, 9 is slow.
+ * @param cleanFlag
+ * If true, remove all imput files.
+ * @throws IOException
+ */
+ public void compressFast(final int compressionLevel, final boolean cleanFlag)
+ throws IOException {
+ // For time measurement
+ // final double start = System.currentTimeMillis();
+
+ // FileInputStream fileIS;
+ final CRC32 crc32 = new CRC32();
+ final byte[] rgb = new byte[5000];
+ BufferedOutputStream bos = null;
+
+ try {
+ ZipOutputStream zipOS = null;
+
+ bos = new BufferedOutputStream(new FileOutputStream(zipArchiveName));
+ try {
+ zipOS = new ZipOutputStream(bos);
+ // Tuning performance
+ zipOS.setMethod(ZipOutputStream.DEFLATED);
+
+ if ((compressionLevel >= 0) && (compressionLevel <= 9)) {
+ zipOS.setLevel(compressionLevel);
+ } else {
+ zipOS.setLevel(DEF_COMPRESSION_LEVEL);
+ }
+
+ String targetName = "";
+
+ for (int i = 0; i < fileCount; i++) {
+ final File file = new File(inputFileDir + inputFiles[i]);
+ targetName = sessionDirName + FS + inputFiles[i];
+ addEntryToZip(file, targetName, zipOS, crc32, rgb);
+ }
+
+ if ((pluginFileMap != null) && (pluginFileMap.size() > 0)) {
+ Set<String> pluginSet = pluginFileMap.keySet();
+
+ for (String pluginName : pluginSet) {
+ List<File> theFileList = (List<File>) pluginFileMap.get(pluginName);
+
+ if ((theFileList == null) || (theFileList.size() == 0))
+ continue;
+
+ for (File theFile : theFileList) {
+ if ((theFile == null) || (!theFile.exists()))
+ continue;
+
+ targetName = sessionDirName + FS + "plugins" + FS + pluginName + FS
+ + theFile.getName();
+ addEntryToZip(theFile, targetName, zipOS, crc32, rgb);
+ }
+ }
+ }
+ }
+ finally {
+ if (zipOS != null) {
+ zipOS.close();
+ }
+ }
+ }
+ finally {
+ if (bos != null) {
+ bos.close();
+ }
+ }
+
+ // final double stop = System.currentTimeMillis();
+ // final double diff = stop - start;
+ // CyLogger.getLogger().info("Compression time 3 = " + diff / 1000 + " sec.");
+ if (cleanFlag) {
+ clean();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param pMap DOCUMENT ME!
+ */
+ public void setPluginFileMap(HashMap pMap) {
+ pluginFileMap = pMap;
+ }
+
+ private void addEntryToZip(File srcFile, String targetName, ZipOutputStream zipOS, CRC32 crc32,
+ byte[] rgb) throws IOException {
+ int numRead;
+
+ // Set CRC
+ FileInputStream fileIS = null;
+
+ try {
+ fileIS = new FileInputStream(srcFile);
+ while ((numRead = fileIS.read(rgb)) > -1) {
+ crc32.update(rgb, 0, numRead);
+ }
+ }
+ finally {
+ if (fileIS != null) {
+ fileIS.close();
+ }
+ }
+
+ fileIS = null;
+ try {
+ final ZipEntry zipEntry = new ZipEntry(targetName);
+ zipEntry.setSize(srcFile.length());
+ zipEntry.setTime(srcFile.lastModified());
+ zipEntry.setCrc(crc32.getValue());
+ zipOS.putNextEntry(zipEntry);
+
+ // Write the file
+ try {
+ fileIS = new FileInputStream(srcFile);
+
+ while ((numRead = fileIS.read(rgb)) > -1) {
+ zipOS.write(rgb, 0, numRead);
+ }
+ }
+ finally {
+ if (fileIS != null) {
+ fileIS.close();
+ }
+ }
+ }
+ finally {
+ if (zipOS != null) {
+ zipOS.closeEntry();
+ }
+ }
+ }
+
+ /**
+ * Reads a file contained within a zip file and returns an InputStream for the
+ * specific file you want from within the zip file.
+ *
+ * @param zipName
+ * The name of the zip file to read.
+ * @param fileNameRegEx
+ * A regular expression that identifies the file to be read. In
+ * general this should just be the file name you're looking for.
+ * If more than one file matches the regular expression, only the
+ * first will be returned. If you're looking for a specific file
+ * remeber to build your regular expression correctly. For
+ * example, if you're looking for the file 'vizmap.props', make
+ * your regular expression '.*vizmap.props' to accomodate any
+ * clutter from the zip file.
+ * @return An InputStream of the zip entry identified by the regular
+ * expression or null if nothing matches.
+ * @throws IOexception
+ * @deprecated
+ */
+ @Deprecated
+ public static InputStream readFile(String zipName, String fileNameRegEx)
+ throws IOException {
+ final ZipFile sessionZipFile = new ZipFile(zipName);
+ final Enumeration zipEntries = sessionZipFile.entries();
+
+ try {
+ while (zipEntries.hasMoreElements()) {
+ final ZipEntry zent = (ZipEntry) zipEntries.nextElement();
+
+ if (zent.getName().matches(fileNameRegEx)) {
+ return sessionZipFile.getInputStream(zent);
+ }
+ }
+ }
+ catch (Exception e) {
+ // This is not an ideal way to address bug 1988 for this method,
+ // as sessionZipFile must remain open for the stream on the entry
+ // to be usable.
+ // Therefore sessionZipFile can only be closed explicitly when an
+ // exception has occured.
+ // More importantly sessionZipFile cannot otherwise be closed and
+ // so will remain open until the finalize is called on it.
+ // This is the reason for deprecating this method for one that
+ // allows the enclosing method to timely close the ZipFile object
+ // and otherwise properly manage it's lifetime.
+ if (sessionZipFile != null) {
+ sessionZipFile.close();
+ }
+ if (e instanceof RuntimeException) {
+ throw (RuntimeException)e;
+ }
+ else if (e instanceof IOException) {
+ throw (IOException)e;
+ }
+ else {
+ throw new RuntimeException(e);
+ }
+ }
+
+ return null;
+ }
+
+ /**
+ * Reads a file contained within a zip file and returns an InputStream for the
+ * specific file you want from within the zip file.
+ *
+ * @param sessionZipFile
+ * The ZipFile in which to look for an entry matching
+ * fileNameRegEx.
+ * @param fileNameRegEx
+ * A regular expression that identifies the file to be read. In
+ * general this should just be the file name you're looking for.
+ * If more than one file matches the regular expression, only the
+ * first will be returned. If you're looking for a specific file
+ * remeber to build your regular expression correctly. For
+ * example, if you're looking for the file 'vizmap.props', make
+ * your regular expression '.*vizmap.props' to accomodate any
+ * clutter from the zip file.
+ * @return An InputStream of the zip entry identified by the regular
+ * expression or null if nothing matches.
+ * @throws IOexception
+ */
+ public static InputStream readFile(ZipFile sessionZipFile, String fileNameRegEx)
+ throws IOException {
+ //final ZipFile sessionZipFile = new ZipFile(zipName);
+ final Enumeration zipEntries = sessionZipFile.entries();
+
+ while (zipEntries.hasMoreElements()) {
+ final ZipEntry zent = (ZipEntry) zipEntries.nextElement();
+
+ if (zent.getName().matches(fileNameRegEx)) {
+ return sessionZipFile.getInputStream(zent);
+ }
+ }
+
+ return null;
+ }
+
+ /**
+ * Reads zip file, returns a list of all entries that match the given
+ * regular expression
+ * @param zipName
+ * @param fileNameRegEx
+ * @return
+ * @throws IOException
+ */
+ public static List<ZipEntry> getAllFiles(String zipName, String fileNameRegEx) throws IOException {
+ List<ZipEntry> Matching = new ArrayList<ZipEntry>();
+ Pattern p;
+ Matcher m;
+
+ p = Pattern.compile(fileNameRegEx);
+ m = p.matcher("");
+
+ ZipFile Zip = null;
+ try {
+ Zip = new ZipFile(zipName);
+ Enumeration Entries = Zip.entries();
+
+ while (Entries.hasMoreElements()) {
+ ZipEntry CurrentEntry = (ZipEntry) Entries.nextElement();
+ m.reset(CurrentEntry.getName());
+ if (m.matches()) {
+ Matching.add(CurrentEntry);
+ }
+ }
+ }
+ finally {
+ if (Zip != null) {
+ Zip.close();
+ }
+ }
+
+ return Matching;
+ }
+
+
+
+ /**
+ * Unzips the given zip file and returns a list of all files unzipped
+ * @param is
+ * InputStream for a zip file
+ */
+ public static List<String> unzip(String zipName, String unzipDir, TaskMonitor taskMonitor) throws java.io.IOException {
+ ArrayList<String> UnzippedFiles = new ArrayList<String>();
+
+ if (unzipDir != null) {
+ unzipDir = unzipDir + File.separator;
+ } else {
+ unzipDir = "";
+ }
+
+ int maxCount = 0; // -1 if unknown
+ int progressCount = 0;
+ double percent = 0.0d;
+
+ ZipFile Zip = null;
+ try {
+ Zip = new ZipFile(zipName);
+ Enumeration Entries = Zip.entries();
+ int BUFFER = 2048;
+
+ while(Entries.hasMoreElements()) {
+ ZipEntry CurrentEntry = (ZipEntry)Entries.nextElement();
+ File ZipFile = new File(unzipDir + CurrentEntry.getName());
+ if (!CurrentEntry.isDirectory()) {
+ if (ZipFile.getParent() != null) {
+ File ParentDirs = new File(ZipFile.getParent());
+
+ if (!ParentDirs.exists()) {
+ ParentDirs.mkdirs();
+ }
+ }
+ } else { // entry is directory, create and move on
+ if (!ZipFile.exists()) {
+ ZipFile.mkdirs();
+ }
+ continue;
+ }
+
+ InputStream zis = null;
+ try {
+ zis = Zip.getInputStream(CurrentEntry);
+ maxCount = zis.available();
+
+ BufferedOutputStream dest = null;
+
+ try {
+ dest = new BufferedOutputStream(new FileOutputStream(ZipFile), BUFFER);
+ // write the files to the disk
+ int count;
+ byte[] data = new byte[BUFFER];
+
+ while ((count = zis.read(data, 0, BUFFER)) != -1) {
+ dest.write(data, 0, count);
+ // Report on Progress
+ if (taskMonitor != null) {
+ percent = ((double) progressCount / maxCount) * 100.0;
+ if (maxCount == -1) { // file size unknown
+ percent = -1;
+ }
+
+ JTask jTask = (JTask) taskMonitor;
+ // TODO erm...how?
+ if (jTask.haltRequested()) { //abort
+ taskMonitor.setStatus("Canceling the unzip ...");
+ taskMonitor.setPercentCompleted(100);
+ break;
+ }
+ taskMonitor.setPercentCompleted((int) percent);
+ }
+ }
+
+ dest.flush();
+ }
+ finally {
+ if (dest != null) {
+ dest.close();
+ }
+ }
+ }
+ finally {
+ if (zis != null) {
+ zis.close();
+ }
+ }
+
+ UnzippedFiles.add(ZipFile.getAbsolutePath());
+ }
+ }
+ finally {
+ if (Zip != null) {
+ Zip.close();
+ }
+ }
+
+ return UnzippedFiles;
+ }
+
+
+
+}
diff --git a/application/src/main/java/cytoscape/util/export/BitmapExporter.java b/application/src/main/java/cytoscape/util/export/BitmapExporter.java
new file mode 100644
index 0000000..22b0cb6
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/export/BitmapExporter.java
@@ -0,0 +1,56 @@
+package cytoscape.util.export;
+
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.awt.Graphics2D;
+import java.awt.image.BufferedImage;
+import javax.imageio.ImageIO;
+
+import cytoscape.Cytoscape;
+import cytoscape.view.CyNetworkView;
+import cytoscape.view.InternalFrameComponent;
+
+/**
+ * Bitmap exporter by the ImageIO class.
+ * @author Samad Lotia
+ */
+public class BitmapExporter implements Exporter {
+
+ private String extension;
+ private double scale;
+
+ public BitmapExporter(String extension, double scale) {
+ this.extension = extension;
+ this.scale = scale;
+
+ boolean match = false;
+ String[] formats = ImageIO.getWriterFormatNames();
+ for (int i = 0; i < formats.length; i++)
+ {
+ if (formats[i].equals(extension))
+ {
+ match = true;
+ break;
+ }
+ }
+ if (!match)
+ throw new IllegalArgumentException("Format " + extension + " is not supported by the ImageIO class");
+ }
+
+ public void export(CyNetworkView view, FileOutputStream stream) throws IOException
+ {
+ InternalFrameComponent ifc = Cytoscape.getDesktop().getNetworkViewManager().getInternalFrameComponent(view);
+ int width = (int) (ifc.getWidth() * scale);
+ int height = (int) (ifc.getHeight() * scale);
+
+ // CyLogger.getLogger().info("Exporting "+width+"X"+height+" image");
+
+ BufferedImage image = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB);
+ Graphics2D g = (Graphics2D) image.getGraphics();
+ g.scale(scale, scale);
+ ifc.print(g);
+ g.dispose();
+
+ ImageIO.write(image, extension, stream);
+ }
+}
diff --git a/application/src/main/java/cytoscape/util/export/Exporter.java b/application/src/main/java/cytoscape/util/export/Exporter.java
new file mode 100644
index 0000000..bcaa9f5
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/export/Exporter.java
@@ -0,0 +1,20 @@
+package cytoscape.util.export;
+
+import java.io.FileOutputStream;
+import java.io.IOException;
+import cytoscape.view.CyNetworkView;
+
+/**
+ * Interface for exporting a network view to a graphics file.
+ */
+public interface Exporter
+{
+ /**
+ * Export a view as graphics to a stream.
+ * @param view The view to export
+ * @param stream The stream to write the graphics to;
+ * the stream is not closed when exporting
+ * is finished.
+ */
+ public void export(CyNetworkView view, FileOutputStream stream) throws IOException;
+}
diff --git a/application/src/main/java/cytoscape/util/export/PDFExporter.java b/application/src/main/java/cytoscape/util/export/PDFExporter.java
new file mode 100644
index 0000000..9902b5b
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/export/PDFExporter.java
@@ -0,0 +1,75 @@
+package cytoscape.util.export;
+
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.awt.Graphics2D;
+
+import cytoscape.Cytoscape;
+import cytoscape.view.CyNetworkView;
+import cytoscape.view.InternalFrameComponent;
+
+import com.lowagie.text.Document;
+import com.lowagie.text.DocumentException;
+import com.lowagie.text.PageSize;
+import com.lowagie.text.Rectangle;
+import com.lowagie.text.pdf.PdfContentByte;
+import com.lowagie.text.pdf.PdfWriter;
+import com.lowagie.text.pdf.DefaultFontMapper;
+import cytoscape.ding.DingNetworkView;
+
+/**
+ * PDF exporter by the iText library.
+ *
+ * @author Samad Lotia
+ */
+public class PDFExporter implements Exporter {
+ private boolean exportTextAsFont = true;
+
+ public void export(final CyNetworkView view, final FileOutputStream stream)
+ throws IOException {
+
+ final DingNetworkView dView = (DingNetworkView) view;
+ dView.setPrintingTextAsShape(!exportTextAsFont);
+
+ final InternalFrameComponent ifc = Cytoscape.getDesktop()
+ .getNetworkViewManager().getInternalFrameComponent(view);
+ Rectangle pageSize = PageSize.LETTER;
+ Document document = new Document(pageSize);
+ try {
+ PdfWriter writer = PdfWriter.getInstance(document, stream);
+ try {
+ document.open();
+ PdfContentByte cb = writer.getDirectContent();
+ Graphics2D g = null;
+ if (exportTextAsFont) {
+ g = cb.createGraphics(pageSize.getWidth(), pageSize
+ .getHeight(), new DefaultFontMapper());
+ } else {
+ g = cb.createGraphicsShapes(pageSize.getWidth(), pageSize
+ .getHeight());
+ }
+
+ double imageScale = Math.min(pageSize.getWidth()
+ / ((double) ifc.getWidth()), pageSize.getHeight()
+ / ((double) ifc.getHeight()));
+ g.scale(imageScale, imageScale);
+
+ ifc.print(g);
+ g.dispose();
+ } finally {
+ if (document != null) {
+ document.close();
+ }
+ if (writer != null) {
+ writer.close();
+ }
+ }
+ } catch (DocumentException exp) {
+ throw new IOException(exp.getMessage());
+ }
+ }
+
+ public void setExportTextAsFont(boolean pExportTextAsFont) {
+ exportTextAsFont = pExportTextAsFont;
+ }
+}
diff --git a/application/src/main/java/cytoscape/util/export/PSExporter.java b/application/src/main/java/cytoscape/util/export/PSExporter.java
new file mode 100644
index 0000000..6b25eb7
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/export/PSExporter.java
@@ -0,0 +1,72 @@
+/*
+ File: PSExporter.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.util.export;
+
+
+import java.io.FileOutputStream;
+import java.io.IOException;
+import cytoscape.Cytoscape;
+import cytoscape.ding.DingNetworkView;
+import cytoscape.view.CyNetworkView;
+import cytoscape.view.InternalFrameComponent;
+import org.freehep.graphicsio.ps.PSGraphics2D;
+import java.util.Properties;
+
+
+public class PSExporter implements Exporter {
+ private boolean exportTextAsFont = true;
+
+ public PSExporter() {
+ }
+
+ public void export(CyNetworkView view, FileOutputStream stream) throws IOException {
+ DingNetworkView theView = (DingNetworkView) view;
+ theView.setPrintingTextAsShape(!exportTextAsFont);
+
+ InternalFrameComponent ifc = Cytoscape.getDesktop().getNetworkViewManager().getInternalFrameComponent(view);
+
+ Properties p = new Properties();
+ p.setProperty(PSGraphics2D.PAGE_SIZE,"Letter");
+ p.setProperty("org.freehep.graphicsio.AbstractVectorGraphicsIO.TEXT_AS_SHAPES",
+ Boolean.toString(!exportTextAsFont));
+
+ PSGraphics2D g = new PSGraphics2D(stream,ifc);
+ g.setMultiPage(false);
+ g.setProperties(p);
+
+ g.startExport();
+ ifc.printWithoutForeground(g);
+ g.endExport();
+ }
+
+ public void setExportTextAsFont(boolean pExportTextAsFont) {
+ exportTextAsFont = pExportTextAsFont;
+ }
+}
diff --git a/application/src/main/java/cytoscape/util/export/SVGExporter.java b/application/src/main/java/cytoscape/util/export/SVGExporter.java
new file mode 100644
index 0000000..a5b4776
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/export/SVGExporter.java
@@ -0,0 +1,50 @@
+package cytoscape.util.export;
+
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.OutputStreamWriter;
+
+import cytoscape.Cytoscape;
+import cytoscape.ding.DingNetworkView;
+import cytoscape.view.CyNetworkView;
+import cytoscape.view.InternalFrameComponent;
+
+import org.freehep.graphicsio.svg.SVGGraphics2D;
+import org.freehep.graphics2d.VectorGraphics;
+
+/**
+ * SVG exporter by the batik library.
+ * @author Samad Lotia
+ */
+public class SVGExporter implements Exporter
+{
+ private boolean exportTextAsFont = true;
+
+ public SVGExporter()
+ {
+ }
+
+ public void export(CyNetworkView view, FileOutputStream stream) throws IOException
+ {
+ DingNetworkView theView = (DingNetworkView) view;
+ theView.setPrintingTextAsShape(!exportTextAsFont);
+
+ InternalFrameComponent ifc = Cytoscape.getDesktop().getNetworkViewManager().getInternalFrameComponent(view);
+ SVGGraphics2D g = new SVGGraphics2D(stream, ifc);
+
+ // this sets text as shape
+ java.util.Properties p = new java.util.Properties();
+ p.setProperty("org.freehep.graphicsio.AbstractVectorGraphicsIO.TEXT_AS_SHAPES",
+ Boolean.toString(!exportTextAsFont));
+ g.setProperties(p);
+
+ g.startExport();
+ ifc.print(g);
+ g.endExport();
+ }
+
+ public void setExportTextAsFont(boolean pExportTextAsFont) {
+ exportTextAsFont = pExportTextAsFont;
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/util/package.html b/application/src/main/java/cytoscape/util/package.html
new file mode 100644
index 0000000..197ce51
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/package.html
@@ -0,0 +1,16 @@
+<html>
+
+<head>
+ <!-- $Revision: 4812 $
+ $Date: 2002-05-07 19:02:23 +0200 (Tue, 07 May 2002) $
+ $Author: isb $
+ -->
+</head>
+
+<body>
+This package contains utility classes which are deemed generally useful,
+but which do not clearly belong to any other package. For the most
+part they are short and simple.
+</body>
+</html>
+
diff --git a/application/src/main/java/cytoscape/util/shadegrown/WindowUtilities.java b/application/src/main/java/cytoscape/util/shadegrown/WindowUtilities.java
new file mode 100644
index 0000000..5bceaa5
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/shadegrown/WindowUtilities.java
@@ -0,0 +1,207 @@
+/*
+ File: WindowUtilities.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.util.shadegrown;
+
+import java.awt.Dimension;
+import java.awt.GraphicsConfiguration;
+import java.awt.GraphicsEnvironment;
+import java.awt.Insets;
+import java.awt.Toolkit;
+import java.awt.Window;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+
+import javax.swing.ImageIcon;
+import javax.swing.JComponent;
+import javax.swing.JLabel;
+import javax.swing.JWindow;
+import javax.swing.WindowConstants;
+
+
+/**
+ * WindowUtilities keeps track of open windows and may close down the JVM when
+ * all primary windows are closed (see {@link #setExitJVMWhenAllWindowsClose}
+ * and {@link #addPrimaryWindow( Window )}).
+ */
+
+// TODO: add createDialog stuff...
+public abstract class WindowUtilities implements WindowConstants {
+ protected static JWindow splashWindow = null;
+ protected static JComponent splashContent = null;
+
+ // protected static javax.swing.Timer splashTimer = null;
+ /**
+ * DOCUMENT ME!
+ *
+ * @param window DOCUMENT ME!
+ */
+ public static void centerWindowOnScreen(Window window) {
+ centerWindowSize(window);
+ centerWindowLocation(window);
+ window.setVisible(true);
+ } // static centerWindowOnScreen( Window )
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param window DOCUMENT ME!
+ */
+ public static void centerWindowSize(Window window) {
+ Dimension screen_size = Toolkit.getDefaultToolkit().getScreenSize();
+ GraphicsConfiguration configuration = GraphicsEnvironment.getLocalGraphicsEnvironment()
+ .getDefaultScreenDevice()
+ .getDefaultConfiguration();
+ Insets screen_insets = Toolkit.getDefaultToolkit().getScreenInsets(configuration);
+
+ screen_size.width -= screen_insets.left;
+ screen_size.width -= screen_insets.right;
+ screen_size.height -= screen_insets.top;
+ screen_size.height -= screen_insets.bottom;
+
+ Dimension frame_size = window.getSize();
+ frame_size.width = (int) (screen_size.width * .75);
+ frame_size.height = (int) (screen_size.height * .75);
+ window.setSize(frame_size);
+ } // static centerWindowSize( Window )
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param window DOCUMENT ME!
+ */
+ public static void centerWindowLocation(Window window) {
+ Dimension screen_size = Toolkit.getDefaultToolkit().getScreenSize();
+ GraphicsConfiguration configuration = GraphicsEnvironment.getLocalGraphicsEnvironment()
+ .getDefaultScreenDevice()
+ .getDefaultConfiguration();
+ Insets screen_insets = Toolkit.getDefaultToolkit().getScreenInsets(configuration);
+
+ screen_size.width -= screen_insets.left;
+ screen_size.width -= screen_insets.right;
+ screen_size.height -= screen_insets.top;
+ screen_size.height -= screen_insets.bottom;
+
+ Dimension frame_size = window.getSize();
+ window.setLocation(((screen_size.width / 2) - (frame_size.width / 2)) + screen_insets.left,
+ ((screen_size.height / 2) - (frame_size.height / 2)) + screen_insets.top);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param image DOCUMENT ME!
+ * @param milliseconds DOCUMENT ME!
+ */
+ public static void showSplash(ImageIcon image, int milliseconds) {
+ showSplash(image, milliseconds, true);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param image DOCUMENT ME!
+ * @param milliseconds DOCUMENT ME!
+ * @param start_timer DOCUMENT ME!
+ */
+ public static void showSplash(ImageIcon image, int milliseconds, boolean start_timer) {
+ showSplash(new JLabel(image), milliseconds, start_timer);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param content DOCUMENT ME!
+ * @param milliseconds DOCUMENT ME!
+ */
+ public static void showSplash(JComponent content, int milliseconds) {
+ showSplash(content, milliseconds, true);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param content DOCUMENT ME!
+ * @param milliseconds DOCUMENT ME!
+ * @param start_timer DOCUMENT ME!
+ */
+ public static void showSplash(JComponent content, int milliseconds, boolean start_timer) {
+ hideSplash();
+
+ if (splashWindow == null) {
+ splashWindow = new JWindow();
+ }
+
+ splashContent = content;
+ splashWindow.getContentPane().add(splashContent);
+ splashWindow.pack();
+ centerWindowLocation(splashWindow);
+ splashWindow.setVisible(true);
+ splashWindow.setAlwaysOnTop(true);
+
+ splashContent.addMouseListener(new MouseListener() {
+ public void mouseClicked(MouseEvent e) {
+ hideSplash();
+ }
+
+ public void mouseEntered(MouseEvent e) {
+ }
+
+ public void mouseExited(MouseEvent e) {
+ }
+
+ public void mousePressed(MouseEvent e) {
+ }
+
+ public void mouseReleased(MouseEvent e) {
+ }
+ });
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public static void hideSplash() {
+ if ((splashWindow != null) && splashWindow.isVisible()) {
+ splashWindow.setVisible(false);
+
+ if (splashContent != null) {
+ splashWindow.getContentPane().remove(splashContent);
+ splashContent = null;
+ }
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/util/swing/AboutDialog.java b/application/src/main/java/cytoscape/util/swing/AboutDialog.java
new file mode 100644
index 0000000..c774b6a
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/swing/AboutDialog.java
@@ -0,0 +1,249 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.util.swing;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.logger.CyLogger;
+import cytoscape.util.OpenBrowser;
+
+import java.io.IOException;
+
+import java.net.MalformedURLException;
+import java.net.URL;
+
+import javax.swing.*;
+import javax.swing.event.HyperlinkEvent;
+import javax.swing.event.HyperlinkListener;
+
+
+/**
+ * About page for web service clients or other plugins.
+ * Accepts HTML as the argument.
+ *
+ * @author kono
+ */
+public class AboutDialog extends javax.swing.JDialog implements HyperlinkListener {
+ // Singleton.
+ private static final AboutDialog about;
+ private static CyLogger logger = CyLogger.getLogger(AboutDialog.class);
+
+ static {
+ about = new AboutDialog(Cytoscape.getDesktop(), true);
+ }
+
+ // Show method with full parameter set.
+ /**
+ * DOCUMENT ME!
+ *
+ * @param title DOCUMENT ME!
+ * @param icon DOCUMENT ME!
+ * @param description DOCUMENT ME!
+ */
+ public static void showDialog(String title, Icon icon, String description) {
+ about.titleLabel.setText(title);
+ about.titleLabel.setIcon(icon);
+
+ URL target = null;
+ about.mainEditorPane.putClientProperty(JEditorPane.HONOR_DISPLAY_PROPERTIES,
+ Boolean.TRUE);
+ try {
+ target = new URL(description);
+ } catch (MalformedURLException e) {
+ about.mainEditorPane.setContentType("text/html");
+ about.mainEditorPane.setText(description);
+ about.repaint();
+ about.setVisible(true);
+ return;
+ }
+
+ try {
+ about.mainEditorPane.setPage(target);
+ about.pack();
+ about.repaint();
+ about.setVisible(true);
+ } catch (IOException e) {
+ about.mainEditorPane.setText("Could not connect to " + target.toString());
+ logger.warn("Could not connect to " + target.toString(), e);
+ about.pack();
+ about.repaint();
+ about.setVisible(true);
+ }
+ }
+
+ /** Creates new form WSAboutDialog */
+ public AboutDialog(java.awt.Frame parent, boolean modal) {
+ super(parent, modal);
+ initComponents();
+ mainEditorPane.setEditable(false);
+ mainEditorPane.addHyperlinkListener(this);
+ setLocationRelativeTo(Cytoscape.getDesktop());
+ setAlwaysOnTop(true);
+ }
+
+ /**
+ * Creates a new AboutDialog object.
+ *
+ * @param parent DOCUMENT ME!
+ * @param modal DOCUMENT ME!
+ * @param title DOCUMENT ME!
+ * @param icon DOCUMENT ME!
+ * @param contentURL DOCUMENT ME!
+ */
+ public AboutDialog(java.awt.Frame parent, boolean modal, String title, Icon icon, URL contentURL) {
+ super(parent, modal);
+ initComponents();
+ mainEditorPane.setContentType("text/html");
+ }
+
+ /** This method is called from within the constructor to
+ * initialize the form.
+ * WARNING: Do NOT modify this code. The content of this method is
+ * always regenerated by the Form Editor.
+ */
+
+ // <editor-fold defaultstate="collapsed" desc="Generated Code">
+ private void initComponents() {
+ titlePanel = new javax.swing.JPanel();
+ titleLabel = new javax.swing.JLabel();
+ mainPanel = new javax.swing.JPanel();
+ mainScrollPane = new javax.swing.JScrollPane();
+ mainEditorPane = new javax.swing.JEditorPane();
+
+ setDefaultCloseOperation(javax.swing.WindowConstants.DISPOSE_ON_CLOSE);
+ setTitle("About");
+ setAlwaysOnTop(true);
+
+ titlePanel.setBackground(new java.awt.Color(255, 255, 255));
+
+ titleLabel.setFont(new java.awt.Font("SansSerif", 0, 18));
+ titleLabel.setText("Client Name Here");
+
+ org.jdesktop.layout.GroupLayout titlePanelLayout = new org.jdesktop.layout.GroupLayout(titlePanel);
+ titlePanel.setLayout(titlePanelLayout);
+ titlePanelLayout.setHorizontalGroup(titlePanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(titlePanelLayout.createSequentialGroup()
+ .addContainerGap()
+ .add(titleLabel,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 339,
+ Short.MAX_VALUE)
+ .addContainerGap()));
+ titlePanelLayout.setVerticalGroup(titlePanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(titlePanelLayout.createSequentialGroup()
+ .addContainerGap()
+ .add(titleLabel,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 32,
+ Short.MAX_VALUE)
+ .addContainerGap()));
+
+ mainPanel.setBackground(new java.awt.Color(255, 255, 255));
+
+ mainScrollPane.setHorizontalScrollBarPolicy(javax.swing.ScrollPaneConstants.HORIZONTAL_SCROLLBAR_NEVER);
+ mainScrollPane.setFont(new java.awt.Font("SansSerif", 0, 12));
+
+ mainEditorPane.setEditable(false);
+ mainScrollPane.setViewportView(mainEditorPane);
+
+ org.jdesktop.layout.GroupLayout mainPanelLayout = new org.jdesktop.layout.GroupLayout(mainPanel);
+ mainPanel.setLayout(mainPanelLayout);
+ mainPanelLayout.setHorizontalGroup(mainPanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(mainPanelLayout.createSequentialGroup()
+ .addContainerGap()
+ .add(mainScrollPane)
+ .addContainerGap()));
+ mainPanelLayout.setVerticalGroup(mainPanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(mainPanelLayout.createSequentialGroup()
+ .addContainerGap()
+ .add(mainScrollPane,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 215,
+ Short.MAX_VALUE)
+ .addContainerGap()));
+
+ org.jdesktop.layout.GroupLayout layout = new org.jdesktop.layout.GroupLayout(getContentPane());
+ getContentPane().setLayout(layout);
+ layout.setHorizontalGroup(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(titlePanel,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE)
+ .add(org.jdesktop.layout.GroupLayout.TRAILING, mainPanel,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE));
+ layout.setVerticalGroup(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(layout.createSequentialGroup()
+ .add(titlePanel,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(mainPanel,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE)));
+
+ pack();
+ } // </editor-fold>
+
+ // Variables declaration - do not modify
+ private javax.swing.JEditorPane mainEditorPane;
+ private javax.swing.JScrollPane mainScrollPane;
+ private javax.swing.JLabel titleLabel;
+ private javax.swing.JPanel titlePanel;
+ private javax.swing.JPanel mainPanel;
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void hyperlinkUpdate(HyperlinkEvent e) {
+ if (e.getEventType() != HyperlinkEvent.EventType.ACTIVATED)
+ return;
+
+ String url = e.getURL().toString();
+
+ try {
+ OpenBrowser.openURL(url);
+ } catch (Exception err) {
+ logger.warn("Unable to open browser for "+url.toString(), err);
+ }
+ }
+
+ // End of variables declaration
+}
diff --git a/application/src/main/java/cytoscape/util/swing/AbstractCellEditor.java b/application/src/main/java/cytoscape/util/swing/AbstractCellEditor.java
new file mode 100644
index 0000000..1bbc38b
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/swing/AbstractCellEditor.java
@@ -0,0 +1,132 @@
+/*
+ * The contents of this file are subject to the Sapient Public License
+ * Version 1.0 (the "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ * http://carbon.sf.net/License.html.
+ *
+ * Software distributed under the License is distributed on an "AS IS" basis,
+ * WITHOUT WARRANTY OF ANY KIND, either express or implied. See the License for
+ * the specific language governing rights and limitations under the License.
+ *
+ * The Original Code is The Carbon Component Framework.
+ *
+ * The Initial Developer of the Original Code is Sapient Corporation
+ *
+ * Copyright (C) 2003 Sapient Corporation. All Rights Reserved.
+ */
+package cytoscape.util.swing;
+
+import java.util.EventObject;
+
+import javax.swing.CellEditor;
+import javax.swing.event.CellEditorListener;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.EventListenerList;
+
+
+/**
+ *
+ */
+public class AbstractCellEditor implements CellEditor {
+ protected EventListenerList listenerList = new EventListenerList();
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getCellEditorValue() {
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isCellEditable(EventObject e) {
+ return true;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param anEvent DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean shouldSelectCell(EventObject anEvent) {
+ return false;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean stopCellEditing() {
+ return true;
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void cancelCellEditing() {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param l DOCUMENT ME!
+ */
+ public void addCellEditorListener(CellEditorListener l) {
+ listenerList.add(CellEditorListener.class, l);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param l DOCUMENT ME!
+ */
+ public void removeCellEditorListener(CellEditorListener l) {
+ listenerList.remove(CellEditorListener.class, l);
+ }
+
+ /*
+ * Notify all listeners that have registered interest for
+ * notification on this event type.
+ * @see EventListenerList
+ */
+ protected void fireEditingStopped() {
+ // Guaranteed to return a non-null array
+ Object[] listeners = listenerList.getListenerList();
+
+ // Process the listeners last to first, notifying
+ // those that are interested in this event
+ for (int i = listeners.length - 2; i >= 0; i -= 2) {
+ if (listeners[i] == CellEditorListener.class) {
+ ((CellEditorListener) listeners[i + 1]).editingStopped(new ChangeEvent(this));
+ }
+ }
+ }
+
+ /*
+ * Notify all listeners that have registered interest for
+ * notification on this event type.
+ * @see EventListenerList
+ */
+ protected void fireEditingCanceled() {
+ // Guaranteed to return a non-null array
+ Object[] listeners = listenerList.getListenerList();
+
+ // Process the listeners last to first, notifying
+ // those that are interested in this event
+ for (int i = listeners.length - 2; i >= 0; i -= 2) {
+ if (listeners[i] == CellEditorListener.class) {
+ ((CellEditorListener) listeners[i + 1]).editingCanceled(new ChangeEvent(this));
+ }
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/util/swing/AbstractTreeTableModel.java b/application/src/main/java/cytoscape/util/swing/AbstractTreeTableModel.java
new file mode 100644
index 0000000..0cf6930
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/swing/AbstractTreeTableModel.java
@@ -0,0 +1,269 @@
+/*
+ * The contents of this file are subject to the Sapient Public License
+ * Version 1.0 (the "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ * http://carbon.sf.net/License.html.
+ *
+ * Software distributed under the License is distributed on an "AS IS" basis,
+ * WITHOUT WARRANTY OF ANY KIND, either express or implied. See the License for
+ * the specific language governing rights and limitations under the License.
+ *
+ * The Original Code is The Carbon Component Framework.
+ *
+ * The Initial Developer of the Original Code is Sapient Corporation
+ *
+ * Copyright (C) 2003 Sapient Corporation. All Rights Reserved.
+ */
+package cytoscape.util.swing;
+
+
+/*
+ * @(#)AbstractTreeTableModel.java 1.2 98/10/27
+ *
+ * Copyright 1997, 1998 by Sun Microsystems, Inc.,
+ * 901 San Antonio Road, Palo Alto, California, 94303, U.S.A.
+ * All rights reserved.
+ *
+ * This software is the confidential and proprietary information
+ * of Sun Microsystems, Inc. ("Confidential Information"). You
+ * shall not disclose such Confidential Information and shall use
+ * it only in accordance with the terms of the license agreement
+ * you entered into with Sun.
+ */
+import javax.swing.event.EventListenerList;
+import javax.swing.event.TreeModelEvent;
+import javax.swing.event.TreeModelListener;
+import javax.swing.tree.TreePath;
+
+
+/**
+ * @version 1.2 10/27/98
+ * An abstract implementation of the TreeTableModel interface, handling the list
+ * of listeners.
+ * @author Philip Milne
+ */
+public abstract class AbstractTreeTableModel implements TreeTableModel {
+
+ protected Object root;
+ protected EventListenerList listenerList = new EventListenerList();
+
+ /**
+ * Creates a new AbstractTreeTableModel object.
+ *
+ * @param root DOCUMENT ME!
+ */
+ public AbstractTreeTableModel(Object root) {
+ this.root = root;
+ }
+
+ //
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getRoot() {
+ return root;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isLeaf(Object node) {
+ return getChildCount(node) == 0;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param path DOCUMENT ME!
+ * @param newValue DOCUMENT ME!
+ */
+ public void valueForPathChanged(TreePath path, Object newValue) {
+ }
+
+ // This is not called in the JTree's default mode: use a naive implementation.
+ /**
+ * DOCUMENT ME!
+ *
+ * @param parent DOCUMENT ME!
+ * @param child DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getIndexOfChild(Object parent, Object child) {
+ for (int i = 0; i < getChildCount(parent); i++) {
+ if (getChild(parent, i).equals(child)) {
+ return i;
+ }
+ }
+
+ return -1;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param l DOCUMENT ME!
+ */
+ public void addTreeModelListener(TreeModelListener l) {
+ listenerList.add(TreeModelListener.class, l);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param l DOCUMENT ME!
+ */
+ public void removeTreeModelListener(TreeModelListener l) {
+ listenerList.remove(TreeModelListener.class, l);
+ }
+
+ /*
+ * Notify all listeners that have registered interest for
+ * notification on this event type. The event instance
+ * is lazily created using the parameters passed into
+ * the fire method.
+ * @see EventListenerList
+ */
+ protected void fireTreeNodesChanged(Object source, Object[] path, int[] childIndices,
+ Object[] children) {
+ // Guaranteed to return a non-null array
+ Object[] listeners = listenerList.getListenerList();
+ TreeModelEvent e = null;
+
+ // Process the listeners last to first, notifying
+ // those that are interested in this event
+ for (int i = listeners.length - 2; i >= 0; i -= 2) {
+ if (listeners[i] == TreeModelListener.class) {
+ // Lazily create the event:
+ if (e == null)
+ e = new TreeModelEvent(source, path, childIndices, children);
+
+ ((TreeModelListener) listeners[i + 1]).treeNodesChanged(e);
+ }
+ }
+ }
+
+ /*
+ * Notify all listeners that have registered interest for
+ * notification on this event type. The event instance
+ * is lazily created using the parameters passed into
+ * the fire method.
+ * @see EventListenerList
+ */
+ protected void fireTreeNodesInserted(Object source, Object[] path, int[] childIndices,
+ Object[] children) {
+ // Guaranteed to return a non-null array
+ Object[] listeners = listenerList.getListenerList();
+ TreeModelEvent e = null;
+
+ // Process the listeners last to first, notifying
+ // those that are interested in this event
+ for (int i = listeners.length - 2; i >= 0; i -= 2) {
+ if (listeners[i] == TreeModelListener.class) {
+ // Lazily create the event:
+ if (e == null)
+ e = new TreeModelEvent(source, path, childIndices, children);
+
+ ((TreeModelListener) listeners[i + 1]).treeNodesInserted(e);
+ }
+ }
+ }
+
+ /*
+ * Notify all listeners that have registered interest for
+ * notification on this event type. The event instance
+ * is lazily created using the parameters passed into
+ * the fire method.
+ * @see EventListenerList
+ */
+ protected void fireTreeNodesRemoved(Object source, Object[] path, int[] childIndices,
+ Object[] children) {
+ // Guaranteed to return a non-null array
+ Object[] listeners = listenerList.getListenerList();
+ TreeModelEvent e = null;
+
+ // Process the listeners last to first, notifying
+ // those that are interested in this event
+ for (int i = listeners.length - 2; i >= 0; i -= 2) {
+ if (listeners[i] == TreeModelListener.class) {
+ // Lazily create the event:
+ if (e == null)
+ e = new TreeModelEvent(source, path, childIndices, children);
+
+ ((TreeModelListener) listeners[i + 1]).treeNodesRemoved(e);
+ }
+ }
+ }
+
+ /*
+ * Notify all listeners that have registered interest for
+ * notification on this event type. The event instance
+ * is lazily created using the parameters passed into
+ * the fire method.
+ * @see EventListenerList
+ */
+ protected void fireTreeStructureChanged(Object source, Object[] path, int[] childIndices,
+ Object[] children) {
+ // Guaranteed to return a non-null array
+ Object[] listeners = listenerList.getListenerList();
+ TreeModelEvent e = null;
+
+ // Process the listeners last to first, notifying
+ // those that are interested in this event
+ for (int i = listeners.length - 2; i >= 0; i -= 2) {
+ if (listeners[i] == TreeModelListener.class) {
+ // Lazily create the event:
+ if (e == null)
+ e = new TreeModelEvent(source, path, childIndices, children);
+
+ ((TreeModelListener) listeners[i + 1]).treeStructureChanged(e);
+ }
+ }
+ }
+
+ //
+ /**
+ * DOCUMENT ME!
+ *
+ * @param column DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Class getColumnClass(int column) {
+ return Object.class;
+ }
+
+ /** By default, make the column with the Tree in it the only editable one.
+ * Making this column editable causes the JTable to forward mouse
+ * and keyboard events in the Tree column to the underlying JTree.
+ */
+ public boolean isCellEditable(Object node, int column) {
+ return getColumnClass(column) == TreeTableModel.class;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param aValue DOCUMENT ME!
+ * @param node DOCUMENT ME!
+ * @param column DOCUMENT ME!
+ */
+ public void setValueAt(Object aValue, Object node, int column) {
+ }
+
+ // Left to be implemented in the subclass:
+
+ /*
+ * public Object getChild(Object parent, int index)
+ * public int getChildCount(Object parent)
+ * public int getColumnCount()
+ * public String getColumnName(Object node, int column)
+ * public Object getValueAt(Object node, int column)
+ */
+}
diff --git a/application/src/main/java/cytoscape/util/swing/AttributeImportPanel.java b/application/src/main/java/cytoscape/util/swing/AttributeImportPanel.java
new file mode 100644
index 0000000..3e57b1c
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/swing/AttributeImportPanel.java
@@ -0,0 +1,382 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.util.swing;
+
+import java.awt.Color;
+import java.awt.event.ActionEvent;
+import java.util.Arrays;
+
+import javax.swing.DefaultListModel;
+import javax.swing.Icon;
+import javax.swing.JPanel;
+
+import cytoscape.Cytoscape;
+import cytoscape.data.CyAttributes;
+import cytoscape.data.attr.MultiHashMapDefinitionListener;
+
+
+/**
+ * General GUI component for importing attributes.<br>
+ * Maybe used by Web Service Clients to import attributes.
+ *
+ * This UI accepts title and icon. Usually, those are from source database.
+ *
+ * @author kono
+ * @since Cytoscape 2.6
+ * @version 0.5
+ *
+ */
+public abstract class AttributeImportPanel extends JPanel implements MultiHashMapDefinitionListener {
+
+ private static final long serialVersionUID = 876173290119736978L;
+
+ /**
+ * Will be caught by parent object (usually a dialog.)
+ */
+ public static final String CLOSE_EVENT = "CLOSE";
+
+ // Default title of this panel.
+ private static final String DEF_TITLE = "Attribute Import Utility";
+
+ // Labels for the sub-panels.
+ private static final String DATASOURCE = "Data Source";
+ private static final String KEY_ATTR = "Key Attribute in Cytoscape";
+ private static final String ATTR_PANEL_TITLE = "Available Annotations";
+
+ // Title of the panel.
+ protected String panelTitle;
+
+ // Icon for this panel title.
+ protected Icon logo;
+
+ // Attribute panel border title
+ protected String attributePanelTitle;
+
+ protected AttributeImportPanel() {
+ this(null, DEF_TITLE, ATTR_PANEL_TITLE);
+ }
+
+ protected AttributeImportPanel(Icon logo, String title, String attrPanelTitle) {
+ this.logo = logo;
+ this.panelTitle = title;
+ this.attributePanelTitle = attrPanelTitle;
+
+ initComponents();
+ setAttributes(null);
+
+ // Listening to the changes in Node Attributes.
+ Cytoscape.getNodeAttributes().getMultiHashMapDefinition().addDataDefinitionListener(this);
+ }
+
+ protected void initComponents() {
+ attrList = new CheckBoxJList();
+ model = new DefaultListModel();
+ attrList.setModel(model);
+
+ titleLabel = new javax.swing.JLabel();
+ databasePanel = new javax.swing.JPanel();
+ databaseComboBox = new javax.swing.JComboBox();
+ attributePanel = new javax.swing.JPanel();
+ attributeLabel = new javax.swing.JLabel();
+ attributeComboBox = new javax.swing.JComboBox();
+ attributeTypeLabel = new javax.swing.JLabel();
+ attributeTypeComboBox = new javax.swing.JComboBox();
+ availableAttrPanel = new javax.swing.JPanel();
+ availableAttrScrollPane = new javax.swing.JScrollPane();
+ attrListPanel = new javax.swing.JPanel();
+ importButton = new javax.swing.JButton();
+ cancelButton = new javax.swing.JButton();
+ resetButton = new javax.swing.JButton();
+
+ setBackground(new java.awt.Color(255, 255, 255));
+ titleLabel.setBackground(new java.awt.Color(255, 255, 255));
+ titleLabel.setIcon(logo);
+ titleLabel.setText(panelTitle);
+
+ databasePanel.setBackground(new java.awt.Color(255, 255, 255));
+ databasePanel.setBorder(javax.swing.BorderFactory.createTitledBorder(DATASOURCE));
+
+ attributeComboBox.setBackground(Color.white);
+
+ databaseComboBox.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ databaseComboBoxActionPerformed(evt);
+ }
+ });
+ databaseComboBox.setBackground(Color.white);
+
+ org.jdesktop.layout.GroupLayout databasePanelLayout = new org.jdesktop.layout.GroupLayout(databasePanel);
+ databasePanel.setLayout(databasePanelLayout);
+ databasePanelLayout.setHorizontalGroup(databasePanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(databasePanelLayout.createSequentialGroup()
+ .addContainerGap()
+ .add(databaseComboBox,
+ 0,
+ 350,
+ Short.MAX_VALUE)
+ .addContainerGap()));
+ databasePanelLayout.setVerticalGroup(databasePanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(databasePanelLayout.createSequentialGroup()
+ .add(databaseComboBox,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .addContainerGap(14,
+ Short.MAX_VALUE)));
+
+ attributePanel.setBackground(new java.awt.Color(255, 255, 255));
+ attributePanel.setBorder(javax.swing.BorderFactory.createTitledBorder(KEY_ATTR));
+ attributeLabel.setText("Attribute:");
+
+ attributeTypeLabel.setText("Data Type:");
+
+ attributeTypeComboBox.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ attributeTypeComboBoxActionPerformed(evt);
+ }
+ });
+ attributeTypeComboBox.setBackground(Color.white);
+
+ org.jdesktop.layout.GroupLayout attributePanelLayout = new org.jdesktop.layout.GroupLayout(attributePanel);
+ attributePanel.setLayout(attributePanelLayout);
+ attributePanelLayout.setHorizontalGroup(attributePanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(attributePanelLayout.createSequentialGroup()
+ .addContainerGap()
+ .add(attributePanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(attributeLabel)
+ .add(attributeTypeLabel))
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(attributePanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(attributeTypeComboBox,
+ 0,
+ 350,
+ Short.MAX_VALUE)
+ .add(attributeComboBox,
+ 0,
+ 350,
+ Short.MAX_VALUE))
+ .addContainerGap()));
+ attributePanelLayout.setVerticalGroup(attributePanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(attributePanelLayout.createSequentialGroup()
+ .add(attributePanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE)
+ .add(attributeLabel)
+ .add(attributeComboBox,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE))
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(attributePanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE)
+ .add(attributeTypeLabel)
+ .add(attributeTypeComboBox,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE))
+ .addContainerGap(13,
+ Short.MAX_VALUE)));
+
+ availableAttrPanel.setBackground(new java.awt.Color(255, 255, 255));
+ availableAttrPanel.setBorder(javax.swing.BorderFactory.createTitledBorder(attributePanelTitle));
+ availableAttrScrollPane.setHorizontalScrollBarPolicy(javax.swing.ScrollPaneConstants.HORIZONTAL_SCROLLBAR_NEVER);
+ availableAttrScrollPane.setViewportView(attrList);
+
+ org.jdesktop.layout.GroupLayout availableAttrPanelLayout = new org.jdesktop.layout.GroupLayout(availableAttrPanel);
+ availableAttrPanel.setLayout(availableAttrPanelLayout);
+ availableAttrPanelLayout.setHorizontalGroup(availableAttrPanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(availableAttrPanelLayout.createSequentialGroup()
+ .addContainerGap()
+ .add(availableAttrScrollPane,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 350,
+ Short.MAX_VALUE)
+ .addContainerGap()));
+ availableAttrPanelLayout.setVerticalGroup(availableAttrPanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(org.jdesktop.layout.GroupLayout.TRAILING,
+ availableAttrPanelLayout.createSequentialGroup()
+ .add(availableAttrScrollPane,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 362,
+ Short.MAX_VALUE)
+ .addContainerGap()));
+
+ importButton.setText("Import");
+ importButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ importButtonActionPerformed(evt);
+ }
+ });
+ importButton.setBackground(Color.white);
+
+ cancelButton.setText("Cancel");
+ cancelButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ cancelButtonActionPerformed(evt);
+ }
+ });
+ cancelButton.setBackground(Color.white);
+
+ resetButton.setText("Reset");
+ resetButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ resetButtonActionPerformed(evt);
+ }
+ });
+ resetButton.setBackground(Color.white);
+
+ org.jdesktop.layout.GroupLayout layout = new org.jdesktop.layout.GroupLayout(this);
+ this.setLayout(layout);
+ layout.setHorizontalGroup(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(org.jdesktop.layout.GroupLayout.TRAILING,
+ layout.createSequentialGroup().addContainerGap()
+ .add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.TRAILING)
+ .add(org.jdesktop.layout.GroupLayout.LEADING,
+ availableAttrPanel,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE)
+ .add(org.jdesktop.layout.GroupLayout.LEADING,
+ attributePanel,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE)
+ .add(org.jdesktop.layout.GroupLayout.LEADING,
+ databasePanel,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE)
+ .add(org.jdesktop.layout.GroupLayout.LEADING,
+ titleLabel)
+ .add(layout.createSequentialGroup()
+ .add(resetButton)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED,
+ 343,
+ Short.MAX_VALUE)
+ .add(cancelButton)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(importButton)))
+ .addContainerGap()));
+ layout.setVerticalGroup(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(layout.createSequentialGroup().addContainerGap()
+ .add(titleLabel)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(databasePanel,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(attributePanel,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(availableAttrPanel,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE)
+ .add(importButton).add(cancelButton)
+ .add(resetButton)).addContainerGap()));
+ } // </editor-fold>
+
+ protected void resetButtonActionPerformed(ActionEvent evt) {
+ // TODO Auto-generated method stub
+ }
+
+ protected void importButtonActionPerformed(ActionEvent evt) {
+ importAttributes();
+ }
+
+ protected void cancelButtonActionPerformed(java.awt.event.ActionEvent evt) {
+ firePropertyChange(CLOSE_EVENT, null, null);
+ }
+
+ private void attributeTypeComboBoxActionPerformed(java.awt.event.ActionEvent evt) {
+ // TODO add your handling code here:
+ }
+
+ abstract protected void databaseComboBoxActionPerformed(java.awt.event.ActionEvent evt);
+
+ protected abstract void importAttributes();
+
+ /**
+ * Set list of attributes currently available for Cytoscape.
+ */
+ protected void setAttributes(final String attributeName) {
+ if (attributeName != null) {
+ attributeComboBox.removeItem(attributeName);
+ return;
+ }
+
+ final CyAttributes nodeAttr = Cytoscape.getNodeAttributes();
+ final String[] names = nodeAttr.getAttributeNames();
+ Arrays.sort(names);
+
+ attributeComboBox.removeAllItems();
+ attributeComboBox.addItem("ID");
+
+ for (String name : names) {
+ if (nodeAttr.getUserVisible(name)) {
+ attributeComboBox.addItem(name);
+ }
+ }
+ }
+
+ public void attributeDefined(String attributeName) {
+ setAttributes(null);
+ }
+
+
+ public void attributeUndefined(String attributeName) {
+ setAttributes(attributeName);
+ }
+
+ // Swing components. Maybe accessed from child classes.
+ protected javax.swing.JComboBox attributeComboBox;
+ protected javax.swing.JLabel attributeLabel;
+ protected javax.swing.JPanel attributePanel;
+ protected javax.swing.JComboBox attributeTypeComboBox;
+ protected javax.swing.JLabel attributeTypeLabel;
+ protected javax.swing.JButton cancelButton;
+ protected javax.swing.JComboBox databaseComboBox;
+ protected javax.swing.JPanel databasePanel;
+ protected javax.swing.JPanel attrListPanel;
+ protected javax.swing.JPanel availableAttrPanel;
+ protected javax.swing.JScrollPane availableAttrScrollPane;
+ protected javax.swing.JButton importButton;
+ protected javax.swing.JLabel titleLabel;
+ protected javax.swing.JButton resetButton;
+ protected CheckBoxJList attrList;
+ protected DefaultListModel model;
+}
diff --git a/application/src/main/java/cytoscape/util/swing/CheckBoxJList.java b/application/src/main/java/cytoscape/util/swing/CheckBoxJList.java
new file mode 100644
index 0000000..1dfe593
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/swing/CheckBoxJList.java
@@ -0,0 +1,202 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.util.swing;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Font;
+
+import java.util.HashSet;
+import java.util.List;
+
+import javax.swing.DefaultListCellRenderer;
+import javax.swing.JCheckBox;
+import javax.swing.JComponent;
+import javax.swing.JList;
+import javax.swing.ListCellRenderer;
+import javax.swing.UIDefaults;
+import javax.swing.UIManager;
+import javax.swing.event.ListSelectionEvent;
+import javax.swing.event.ListSelectionListener;
+
+
+/**
+ * <p>
+ * This class is based on CheckBoxJList: from SWING HACKS
+ * ISBN: 0-596-00907-0
+ * By Joshua Marinacci, Chris Adamson
+ * </p>
+ *
+ * <p>
+ * Customized by Keiichiro Ono
+ * </p>
+ */
+public class CheckBoxJList extends JList implements ListSelectionListener {
+ private static final Color SELECTED_COLOR = new Color(0, 100, 250, 250);
+ private static final Color NORMAL_COLOR = new Color(100, 100, 100, 170);
+
+ private static Color listBackground;
+ private static final Font NORMAL_FONT = new Font("SansSerif", Font.PLAIN, 12);
+ private static final Font SELECTED_FONT = new Font("SansSerif", Font.BOLD, 12);
+
+ public static final String LIST_UPDATED = "LIST_UPDATED";
+
+ static {
+ UIDefaults uid = UIManager.getLookAndFeel().getDefaults();
+ listBackground = uid.getColor("List.background");
+ }
+
+ private HashSet<Integer> selectionCache = new HashSet<Integer>();
+
+ /**
+ * Creates a new CheckBoxJList object.
+ */
+ public CheckBoxJList() {
+ super();
+ setCellRenderer(new CheckBoxListCellRenderer());
+ addListSelectionListener(this);
+ }
+
+ public void setSelectedItems(final List<String> selected) {
+ final ListSelectionListener[] listeners = this.getListSelectionListeners();
+ for(ListSelectionListener l :listeners)
+ removeListSelectionListener(l);
+
+ getSelectionModel().clearSelection();
+ selectionCache.clear();
+
+ for(int i=0; i<this.getModel().getSize(); i++) {
+ if(selected.contains(getModel().getElementAt(i))) {
+ getSelectionModel().addSelectionInterval(i, i);
+ selectionCache.add(i);
+ }
+ }
+
+ for(ListSelectionListener l :listeners) {
+ addListSelectionListener(l);
+ }
+ }
+
+ // ListSelectionListener implementation
+ /**
+ * Update the list items.
+ *
+ * @param lse DOCUMENT ME!
+ */
+ public void valueChanged(ListSelectionEvent lse) {
+
+ if (!lse.getValueIsAdjusting()) {
+ removeListSelectionListener(this);
+
+ // remember everything selected as a result of this action
+ final HashSet<Integer> newSelections = new HashSet<Integer>();
+ final int size = getModel().getSize();
+
+ for (int i = 0; i < size; i++) {
+ if (getSelectionModel().isSelectedIndex(i)) {
+ newSelections.add(i);
+ }
+ }
+
+ // turn on everything that was previously selected
+ for (Integer index : selectionCache) {
+ getSelectionModel().addSelectionInterval(index, index);
+ }
+
+ // add or remove the delta
+ for (Integer index : newSelections) {
+ if (selectionCache.contains(index))
+ getSelectionModel().removeSelectionInterval(index, index);
+ else
+ getSelectionModel().addSelectionInterval(index, index);
+ }
+
+ // save selections for next time
+ selectionCache.clear();
+
+ for (int i = 0; i < size; i++) {
+ if (getSelectionModel().isSelectedIndex(i)) {
+ selectionCache.add(i);
+ }
+ }
+
+ addListSelectionListener(this);
+ firePropertyChange(LIST_UPDATED, null, null);
+ }
+ }
+
+ class CheckBoxListCellRenderer extends JComponent implements ListCellRenderer {
+ private final DefaultListCellRenderer defaultComp;
+ private final JCheckBox checkbox;
+ private final BorderLayout layout = new BorderLayout();
+
+ public CheckBoxListCellRenderer() {
+ setLayout(layout);
+ defaultComp = new DefaultListCellRenderer();
+ checkbox = new JCheckBox();
+ add(checkbox, BorderLayout.WEST);
+ add(defaultComp, BorderLayout.CENTER);
+ }
+
+ public Component getListCellRendererComponent(JList list, Object value, int index,
+ boolean isSelected, boolean cellHasFocus) {
+ defaultComp.getListCellRendererComponent(list, value, index, isSelected, cellHasFocus);
+
+ checkbox.setSelected(isSelected);
+
+ if (isSelected) {
+ checkbox.setFont(SELECTED_FONT);
+ defaultComp.setFont(SELECTED_FONT);
+ checkbox.setForeground(SELECTED_COLOR);
+ defaultComp.setForeground(SELECTED_COLOR);
+ } else {
+ checkbox.setFont(NORMAL_FONT);
+ defaultComp.setFont(NORMAL_FONT);
+ checkbox.setForeground(NORMAL_COLOR);
+ defaultComp.setForeground(NORMAL_COLOR);
+ }
+
+ final Component[] comps = getComponents();
+ final int length = comps.length;
+
+ for (int i = 0; i < length; i++) {
+ comps[i].setBackground(listBackground);
+ }
+
+ return this;
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/util/swing/ColumnResizer.java b/application/src/main/java/cytoscape/util/swing/ColumnResizer.java
new file mode 100644
index 0000000..c4196e8
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/swing/ColumnResizer.java
@@ -0,0 +1,164 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.util.swing;
+
+import java.awt.Component;
+
+import javax.swing.JTable;
+import javax.swing.table.TableCellRenderer;
+import javax.swing.table.TableColumn;
+import javax.swing.table.TableColumnModel;
+import java.util.HashMap;
+
+
+/**
+ *
+ * Automatically resize column based on the objects in the cell.<br>
+ *
+ * <p>
+ * From <i>Swing Hacks</i> by Joshua Marinacci and Chris Adamson.<br>
+ * 2005 Oreilly & Associates Inc. ISBN: 0-596-00907-0<br>
+ * </p>
+ * Customized by Keiichiro Ono
+ *
+ * @since Cytoscape 2.4
+ * @version 1.0
+ * @author Joshua Marinacci, Chris Adamson, Keiichiro Ono
+ *
+ */
+public class ColumnResizer {
+ private static final int DEFLMAX_WIDTH = 280;
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param table DOCUMENT ME!
+ */
+ public static void adjustColumnPreferredWidths(JTable table) {
+ // strategy - get max width for cells in column and
+ // make that the preferred width
+ TableColumnModel columnModel = table.getColumnModel();
+
+ for (int col = 0; col < table.getColumnCount(); col++) {
+ int maxwidth = 0;
+
+ for (int row = 0; row < table.getRowCount(); row++) {
+ TableCellRenderer rend = table.getCellRenderer(row, col);
+ Object value = table.getValueAt(row, col);
+ Component comp = rend.getTableCellRendererComponent(table, value, false, false,
+ row, col);
+ maxwidth = Math.max(comp.getPreferredSize().width, maxwidth);
+ } // for row
+
+ /*
+ * this version of the width set considers the column header's
+ * preferred width too
+ */
+ TableColumn column = columnModel.getColumn(col);
+ TableCellRenderer headerRenderer = column.getHeaderRenderer();
+
+ if (headerRenderer == null)
+ headerRenderer = table.getTableHeader().getDefaultRenderer();
+
+ Object headerValue = column.getHeaderValue();
+ Component headerComp = headerRenderer.getTableCellRendererComponent(table, headerValue,
+ false, false, 0, col);
+ maxwidth = Math.max(maxwidth, headerComp.getPreferredSize().width);
+
+ /*
+ * If the value is too big, adjust to fixed maximum val.
+ */
+ if (DEFLMAX_WIDTH < maxwidth) {
+ maxwidth = DEFLMAX_WIDTH;
+ }
+
+ column.setPreferredWidth(maxwidth + 20);
+ } // for col
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param table DOCUMENT ME!
+ */
+ public static HashMap<String, Integer> getColumnPreferredWidths(JTable table) {
+
+ HashMap<String, Integer> retMap = new HashMap<String, Integer>();
+
+ // strategy - get max width for cells in column and
+ // make that the preferred width
+ TableColumnModel columnModel = table.getColumnModel();
+
+ for (int col = 0; col < table.getColumnCount(); col++) {
+ int maxwidth = 0;
+
+ for (int row = 0; row < table.getRowCount(); row++) {
+ TableCellRenderer rend = table.getCellRenderer(row, col);
+ Object value = table.getValueAt(row, col);
+ Component comp = rend.getTableCellRendererComponent(table, value, false, false,
+ row, col);
+ maxwidth = Math.max(comp.getPreferredSize().width, maxwidth);
+ } // for row
+
+ /*
+ * this version of the width set considers the column header's
+ * preferred width too
+ */
+ TableColumn column = columnModel.getColumn(col);
+ TableCellRenderer headerRenderer = column.getHeaderRenderer();
+
+ if (headerRenderer == null)
+ headerRenderer = table.getTableHeader().getDefaultRenderer();
+
+ Object headerValue = column.getHeaderValue();
+ Component headerComp = headerRenderer.getTableCellRendererComponent(table, headerValue,
+ false, false, 0, col);
+ maxwidth = Math.max(maxwidth, headerComp.getPreferredSize().width);
+
+ /*
+ * If the value is too big, adjust to fixed maximum val.
+ */
+ if (DEFLMAX_WIDTH < maxwidth) {
+ maxwidth = DEFLMAX_WIDTH;
+ }
+
+ retMap.put(headerValue.toString(), new Integer(maxwidth + 20));
+ } // for col
+
+ return retMap;
+ }
+
+
+}
diff --git a/application/src/main/java/cytoscape/util/swing/CyCollapsiblePanel.java b/application/src/main/java/cytoscape/util/swing/CyCollapsiblePanel.java
new file mode 100644
index 0000000..7a3d624
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/swing/CyCollapsiblePanel.java
@@ -0,0 +1,402 @@
+package cytoscape.util.swing;
+
+import javax.swing.*;
+import javax.swing.border.Border;
+import javax.swing.border.TitledBorder;
+
+import java.awt.*;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.net.URL;
+
+/**
+ * * Copyright (c) 2004 Memorial Sloan-Kettering Cancer Center
+ * *
+ * * Code written by: Gary Bader
+ * * Authors: Gary Bader, Ethan Cerami, Chris Sander
+ * *
+ * * This library is free software; you can redistribute it and/or modify it
+ * * under the terms of the GNU Lesser General Public License as published
+ * * by the Free Software Foundation; either version 2.1 of the License, or
+ * * any later version.
+ * *
+ * * This library is distributed in the hope that it will be useful, but
+ * * WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ * * MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ * * documentation provided hereunder is on an "as is" basis, and
+ * * Memorial Sloan-Kettering Cancer Center
+ * * has no obligations to provide maintenance, support,
+ * * updates, enhancements or modifications. In no event shall the
+ * * Memorial Sloan-Kettering Cancer Center
+ * * be liable to any party for direct, indirect, special,
+ * * incidental or consequential damages, including lost profits, arising
+ * * out of the use of this software and its documentation, even if
+ * * Memorial Sloan-Kettering Cancer Center
+ * * has been advised of the possibility of such damage. See
+ * * the GNU Lesser General Public License for more details.
+ * *
+ * * You should have received a copy of the GNU Lesser General Public License
+ * * along with this library; if not, write to the Free Software Foundation,
+ * * Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ *
+ * User: Vuk Pavlovic
+ * Date: Nov 29, 2006
+ * Time: 5:34:46 PM
+ * Description: The user-triggered collapsable panel containing the component (trigger) in the titled border
+ */
+
+/**
+ * The user-triggered collapsable panel containing the component (trigger) in the titled border
+ */
+public class CyCollapsiblePanel extends JPanel {
+ //Border
+ CollapsableTitledBorder border; // includes upper left component and line type
+ Border collapsedBorderLine = BorderFactory.createEmptyBorder(2, 2, 2, 2); // no border
+ Border expandedBorderLine = null; // because this is null, default is used, etched lowered border on MAC
+
+ //Title
+ AbstractButton titleComponent; // displayed in the titled border
+
+ //Expand/Collapse button
+ final static int COLLAPSED = 0, EXPANDED = 1; // image States
+ ImageIcon[] iconArrow = createExpandAndCollapseIcon();
+ JButton arrow = createArrowButton();
+
+ //Content Pane
+ JPanel panel;
+
+ //Container State
+ boolean collapsed; // stores curent state of the collapsable panel
+
+ /**
+ * Constructor for an option button controlled collapsable panel.
+ * This is useful when a group of options each have unique sub contents. The radio buttons should be created,
+ * grouped, and then used to construct their own collapsable panels. This way choosing a different option in
+ * the same option group will collapse all unselected options. Expanded panels draw a border around the
+ * contents and through the radio button in the fashion of a titled border.
+ *
+ * @param component Radio button that expands and collapses the panel based on if it is selected or not
+ */
+ public CyCollapsiblePanel(JRadioButton component) {
+ component.addItemListener(new CyCollapsiblePanel.ExpandAndCollapseAction());
+ titleComponent = component;
+ collapsed = !component.isSelected();
+ commonConstructor();
+ }
+
+ /**
+ * Constructor for a label/button controlled collapsable panel. Displays a clickable title that resembles a
+ * native titled border except for an arrow on the right side indicating an expandable panel. The actual border
+ * only appears when the panel is expanded.
+ *
+ * @param text Title of the collapsable panel in string format, used to create a button with text and an arrow icon
+ */
+ public CyCollapsiblePanel(String text) {
+ arrow.setText(text);
+ titleComponent = arrow;
+ collapsed = true;
+ commonConstructor();
+ }
+
+ /**
+ * Sets layout, creates the content panel and adds it and the title component to the container,
+ * all constructors have this procedure in common.
+ */
+ private void commonConstructor () {
+ setLayout(new BorderLayout());
+
+ panel = new JPanel();
+ panel.setLayout(new BorderLayout());
+
+ add(titleComponent, BorderLayout.CENTER);
+ add(panel, BorderLayout.CENTER);
+ setCollapsed(collapsed);
+
+ placeTitleComponent();
+ }
+
+ /**
+ * Sets the bounds of the border title component so that it is properly positioned.
+ */
+ private void placeTitleComponent() {
+ Insets insets = this.getInsets();
+ Rectangle containerRectangle = this.getBounds();
+ Rectangle componentRectangle = border.getComponentRect(containerRectangle, insets);
+ titleComponent.setBounds(componentRectangle);
+ }
+
+ public void setTitleComponentText(String text) {
+ if (titleComponent instanceof JButton) {
+ titleComponent.setText(text);
+ }
+ placeTitleComponent();
+ }
+
+ /**
+ * This class requires that all content be placed within a designated panel, this method returns that panel.
+ *
+ * @return panel The content panel
+ */
+ public JPanel getContentPane() {
+ return panel;
+ }
+
+ /**
+ * Collapses or expands the panel. This is done by adding or removing the content pane,
+ * alternating between a frame and empty border, and changing the title arrow.
+ * Also, the current state is stored in the collapsed boolean.
+ *
+ * @param collapse When set to true, the panel is collapsed, else it is expanded
+ */
+ public void setCollapsed(boolean collapse) {
+ if (collapse) {
+ //collapse the panel, remove content and set border to empty border
+ remove(panel);
+ arrow.setIcon(iconArrow[COLLAPSED]);
+ border = new CollapsableTitledBorder(collapsedBorderLine, titleComponent);
+ } else {
+ //expand the panel, add content and set border to titled border
+ add(panel, BorderLayout.NORTH);
+ arrow.setIcon(iconArrow[EXPANDED]);
+ border = new CollapsableTitledBorder(expandedBorderLine, titleComponent);
+ }
+ setBorder(border);
+ collapsed = collapse;
+ updateUI();
+ }
+
+ /**
+ * Returns the current state of the panel, collapsed (true) or expanded (false).
+ *
+ * @return collapsed Returns true if the panel is collapsed and false if it is expanded
+ */
+ public boolean isCollapsed() {
+ return collapsed;
+ }
+
+ /**
+ * Returns an ImageIcon array with arrow images used for the different states of the panel.
+ *
+ * @return iconArrow An ImageIcon array holding the collapse and expanded versions of the right hand side arrow
+ */
+ private ImageIcon[] createExpandAndCollapseIcon () {
+ ImageIcon[] iconArrow = new ImageIcon[2];
+ URL iconURL;
+
+ iconURL = getClass().getResource("/cytoscape/images/arrow_collapsed.gif");
+ if (iconURL != null) {
+ iconArrow[COLLAPSED] = new ImageIcon(iconURL);
+ }
+ iconURL = getClass().getResource("/cytoscape/images/arrow_expanded.gif");
+ if (iconURL != null) {
+ iconArrow[EXPANDED] = new ImageIcon(iconURL);
+ }
+ return iconArrow;
+ }
+
+ /**
+ * Returns a button with an arrow icon and a collapse/expand action listener.
+ *
+ * @return button Button which is used in the titled border component
+ */
+ private JButton createArrowButton () {
+ JButton button = new JButton("arrow", iconArrow[COLLAPSED]);
+ button.setBorder(BorderFactory.createEmptyBorder(0,1,5,1));
+ button.setVerticalTextPosition(AbstractButton.CENTER);
+ button.setHorizontalTextPosition(AbstractButton.LEFT);
+ button.setMargin(new Insets(0,0,3,0));
+
+ //We want to use the same font as those in the titled border font
+ Font font = BorderFactory.createTitledBorder("Sample").getTitleFont();
+ Color color = BorderFactory.createTitledBorder("Sample").getTitleColor();
+ button.setFont(font);
+ button.setForeground(color);
+ button.setFocusable(false);
+ button.setContentAreaFilled(false);
+
+ button.addActionListener(new CyCollapsiblePanel.ExpandAndCollapseAction());
+
+ return button;
+ }
+
+ /**
+ * Handles expanding and collapsing of extra content on the user's click of the titledBorder component.
+ */
+ private class ExpandAndCollapseAction extends AbstractAction implements ActionListener, ItemListener {
+ public void actionPerformed(ActionEvent e) {
+ setCollapsed(!isCollapsed());
+ }
+ public void itemStateChanged(ItemEvent e) {
+ setCollapsed(!isCollapsed());
+ }
+ }
+
+ /**
+ * Special titled border that includes a component in the title area
+ */
+ private class CollapsableTitledBorder extends TitledBorder {
+ JComponent component;
+ //Border border;
+
+ public CollapsableTitledBorder(JComponent component) {
+ this(null, component, LEFT, TOP);
+ }
+
+ public CollapsableTitledBorder(Border border) {
+ this(border, null, LEFT, TOP);
+ }
+
+ public CollapsableTitledBorder(Border border, JComponent component) {
+ this(border, component, LEFT, TOP);
+ }
+
+ public CollapsableTitledBorder(Border border, JComponent component, int titleJustification, int titlePosition) {
+ //TitledBorder needs border, title, justification, position, font, and color
+ super(border, null, titleJustification, titlePosition, null, null);
+ this.component = component;
+ if (border == null) {
+ this.border = super.getBorder();
+ }
+ }
+
+ public void paintBorder(Component c, Graphics g, int x, int y, int width, int height) {
+ Rectangle borderR = new Rectangle(x + EDGE_SPACING, y + EDGE_SPACING, width - (EDGE_SPACING * 2), height - (EDGE_SPACING * 2));
+ Insets borderInsets;
+ if (border != null) {
+ borderInsets = border.getBorderInsets(c);
+ } else {
+ borderInsets = new Insets(0, 0, 0, 0);
+ }
+
+ Rectangle rect = new Rectangle(x, y, width, height);
+ Insets insets = getBorderInsets(c);
+ Rectangle compR = getComponentRect(rect, insets);
+ int diff;
+ switch (titlePosition) {
+ case ABOVE_TOP:
+ diff = compR.height + TEXT_SPACING;
+ borderR.y += diff;
+ borderR.height -= diff;
+ break;
+ case TOP:
+ case DEFAULT_POSITION:
+ diff = insets.top / 2 - borderInsets.top - EDGE_SPACING;
+ borderR.y += diff;
+ borderR.height -= diff;
+ break;
+ case BELOW_TOP:
+ case ABOVE_BOTTOM:
+ break;
+ case BOTTOM:
+ diff = insets.bottom / 2 - borderInsets.bottom - EDGE_SPACING;
+ borderR.height -= diff;
+ break;
+ case BELOW_BOTTOM:
+ diff = compR.height + TEXT_SPACING;
+ borderR.height -= diff;
+ break;
+ }
+ border.paintBorder(c, g, borderR.x, borderR.y, borderR.width, borderR.height);
+ Color col = g.getColor();
+ g.setColor(c.getBackground());
+ g.fillRect(compR.x, compR.y, compR.width, compR.height);
+ g.setColor(col);
+ }
+
+ public Insets getBorderInsets(Component c, Insets insets) {
+ Insets borderInsets;
+ if (border != null) {
+ borderInsets = border.getBorderInsets(c);
+ } else {
+ borderInsets = new Insets(0, 0, 0, 0);
+ }
+ insets.top = EDGE_SPACING + TEXT_SPACING + borderInsets.top;
+ insets.right = EDGE_SPACING + TEXT_SPACING + borderInsets.right;
+ insets.bottom = EDGE_SPACING + TEXT_SPACING + borderInsets.bottom;
+ insets.left = EDGE_SPACING + TEXT_SPACING + borderInsets.left;
+
+ if (c == null || component == null) {
+ return insets;
+ }
+
+ int compHeight = component.getPreferredSize().height;
+
+ switch (titlePosition) {
+ case ABOVE_TOP:
+ insets.top += compHeight + TEXT_SPACING;
+ break;
+ case TOP:
+ case DEFAULT_POSITION:
+ insets.top += Math.max(compHeight, borderInsets.top) - borderInsets.top;
+ break;
+ case BELOW_TOP:
+ insets.top += compHeight + TEXT_SPACING;
+ break;
+ case ABOVE_BOTTOM:
+ insets.bottom += compHeight + TEXT_SPACING;
+ break;
+ case BOTTOM:
+ insets.bottom += Math.max(compHeight, borderInsets.bottom) - borderInsets.bottom;
+ break;
+ case BELOW_BOTTOM:
+ insets.bottom += compHeight + TEXT_SPACING;
+ break;
+ }
+ return insets;
+ }
+
+ public JComponent getTitleComponent() {
+ return component;
+ }
+
+ public void setTitleComponent(JComponent component) {
+ this.component = component;
+ }
+
+ public Rectangle getComponentRect(Rectangle rect, Insets borderInsets) {
+ Dimension compD = component.getPreferredSize();
+ Rectangle compR = new Rectangle(0, 0, compD.width, compD.height);
+ switch (titlePosition) {
+ case ABOVE_TOP:
+ compR.y = EDGE_SPACING;
+ break;
+ case TOP:
+ case DEFAULT_POSITION:
+ if (titleComponent instanceof JButton) {
+ compR.y = EDGE_SPACING + (borderInsets.top - EDGE_SPACING - TEXT_SPACING - compD.height) / 2;
+ } else if (titleComponent instanceof JRadioButton) {
+ compR.y = (borderInsets.top - EDGE_SPACING - TEXT_SPACING - compD.height) / 2;
+ }
+ break;
+ case BELOW_TOP:
+ compR.y = borderInsets.top - compD.height - TEXT_SPACING;
+ break;
+ case ABOVE_BOTTOM:
+ compR.y = rect.height - borderInsets.bottom + TEXT_SPACING;
+ break;
+ case BOTTOM:
+ compR.y = rect.height - borderInsets.bottom + TEXT_SPACING + (borderInsets.bottom - EDGE_SPACING - TEXT_SPACING - compD.height) / 2;
+ break;
+ case BELOW_BOTTOM:
+ compR.y = rect.height - compD.height - EDGE_SPACING;
+ break;
+ }
+ switch (titleJustification) {
+ case LEFT:
+ case DEFAULT_JUSTIFICATION:
+ //compR.x = TEXT_INSET_H + borderInsets.left;
+ compR.x = TEXT_INSET_H + borderInsets.left - EDGE_SPACING;
+ break;
+ case RIGHT:
+ compR.x = rect.width - borderInsets.right - TEXT_INSET_H - compR.width;
+ break;
+ case CENTER:
+ compR.x = (rect.width - compR.width) / 2;
+ break;
+ }
+ return compR;
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/util/swing/DropDownMenuButton.java b/application/src/main/java/cytoscape/util/swing/DropDownMenuButton.java
new file mode 100644
index 0000000..4d61864
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/swing/DropDownMenuButton.java
@@ -0,0 +1,81 @@
+package cytoscape.util.swing;
+
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Dimension;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.Insets;
+import java.awt.RenderingHints;
+
+import javax.swing.AbstractAction;
+import javax.swing.BorderFactory;
+import javax.swing.Icon;
+import javax.swing.JButton;
+
+
+/**
+ * Button with drop down menu.
+ *
+ * @version 0.7
+ * @since Cytoscape 2.5
+ * @author kono
+ */
+public class DropDownMenuButton extends JButton {
+ private final Icon buttonIcon = new MenuArrowIcon();
+
+ /**
+ * Creates a new DropDownMenuButton object.
+ *
+ * @param action DOCUMENT ME!
+ */
+ public DropDownMenuButton(final AbstractAction action) {
+ super(action);
+ this.setFocusPainted(false);
+
+ this.setBorder(
+ BorderFactory.createEmptyBorder(4, 4, 4,
+ 4 + buttonIcon.getIconWidth()));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g DOCUMENT ME!
+ */
+ public void paintComponent(Graphics g) {
+ super.paintComponent(g);
+
+ Dimension dim = getSize();
+ Insets ins = getInsets();
+ int x = dim.width - ins.right;
+ int y = ins.top +
+ ((dim.height - ins.top - ins.bottom - buttonIcon.getIconHeight()) / 2);
+ buttonIcon.paintIcon(this, g, x, y);
+ }
+
+ class MenuArrowIcon
+ implements Icon {
+ public void paintIcon(Component c, Graphics g, int x, int y) {
+ Graphics2D g2 = (Graphics2D) g;
+ // Turn AA on
+ g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+ RenderingHints.VALUE_ANTIALIAS_ON);
+
+ g2.setColor(Color.black);
+ g2.translate(x, y);
+ g2.drawLine(2, 3, 6, 3);
+ g2.drawLine(3, 4, 5, 4);
+ g2.drawLine(4, 5, 4, 5);
+ g2.translate(-x, -y);
+ }
+
+ public int getIconWidth() {
+ return 9;
+ }
+
+ public int getIconHeight() {
+ return 9;
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/util/swing/FilterHistoryJList.java b/application/src/main/java/cytoscape/util/swing/FilterHistoryJList.java
new file mode 100644
index 0000000..6b52363
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/swing/FilterHistoryJList.java
@@ -0,0 +1,236 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.util.swing;
+
+import cytoscape.Cytoscape;
+
+import java.awt.BorderLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.LinkedList;
+
+import javax.swing.AbstractAction;
+import javax.swing.AbstractListModel;
+import javax.swing.Action;
+import javax.swing.ImageIcon;
+import javax.swing.JButton;
+import javax.swing.JComponent;
+import javax.swing.JList;
+import javax.swing.JPopupMenu;
+import javax.swing.JTextField;
+import javax.swing.ListModel;
+import javax.swing.event.DocumentEvent;
+import javax.swing.event.DocumentListener;
+
+
+/**
+ * JList with incremntal search & search history.<br>
+ *
+ * <p>
+ * From <i>Swing Hacks</i> by Joshua Marinacci and Chris Adamson.
+ * </p>
+ * Customized by Keiichiro Ono
+ *
+ */
+public class FilterHistoryJList extends JList {
+ private FilterField filterField;
+ private int DEFAULT_FIELD_WIDTH = 20;
+
+ /**
+ * Creates a new FilterHistoryJList object.
+ */
+ public FilterHistoryJList() {
+ super();
+ setModel(new FilterModel());
+ filterField = new FilterField(DEFAULT_FIELD_WIDTH);
+ filterField.textField.requestFocus();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param m DOCUMENT ME!
+ */
+ public void setModel(ListModel m) {
+ if (!(m instanceof FilterModel))
+ throw new IllegalArgumentException();
+
+ super.setModel(m);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param o DOCUMENT ME!
+ */
+ public void addItem(Object o) {
+ ((FilterModel) getModel()).addElement(o);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public FilterField getFilterField() {
+ return filterField;
+ }
+
+ // inner class to provide filtered model
+ class FilterModel extends AbstractListModel {
+ ArrayList items;
+ ArrayList filterItems;
+
+ public FilterModel() {
+ super();
+ items = new ArrayList();
+ filterItems = new ArrayList();
+ }
+
+ public Object getElementAt(int index) {
+ if (index < filterItems.size())
+ return filterItems.get(index);
+ else
+
+ return null;
+ }
+
+ public int getSize() {
+ return filterItems.size();
+ }
+
+ public void addElement(Object o) {
+ items.add(o);
+ refilter();
+ }
+
+ private void refilter() {
+ filterItems.clear();
+
+ String term = getFilterField().textField.getText();
+
+ for (int i = 0; i < items.size(); i++)
+ if (items.get(i).toString().indexOf(term, 0) != -1)
+ filterItems.add(items.get(i));
+
+ fireContentsChanged(this, 0, getSize());
+ }
+ }
+
+ // inner class provides filter-by-keystroke field
+ class FilterField extends JComponent implements DocumentListener, ActionListener {
+ LinkedList prevSearches;
+ JTextField textField;
+ JButton prevSearchButton;
+ JPopupMenu prevSearchMenu;
+
+ public FilterField(int width) {
+ super();
+ setLayout(new BorderLayout());
+ textField = new JTextField(width);
+ textField.getDocument().addDocumentListener(this);
+ textField.addActionListener(this);
+ prevSearchButton = new JButton(new ImageIcon(Cytoscape.class.getResource("images/ximian/stock_search.png")));
+ prevSearchButton.setBorder(null);
+ prevSearchButton.addMouseListener(new MouseAdapter() {
+ public void mousePressed(MouseEvent me) {
+ popMenu(me.getX(), me.getY());
+ }
+ });
+ add(prevSearchButton, BorderLayout.WEST);
+ add(textField, BorderLayout.CENTER);
+ prevSearches = new LinkedList();
+ }
+
+ public void popMenu(int x, int y) {
+ prevSearchMenu = new JPopupMenu();
+
+ Iterator it = prevSearches.iterator();
+
+ while (it.hasNext())
+ prevSearchMenu.add(new PrevSearchAction(it.next().toString()));
+
+ prevSearchMenu.show(prevSearchButton, x, y);
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ // called on return/enter, adds term to prevSearches
+ if (e.getSource() == textField) {
+ prevSearches.addFirst(textField.getText());
+
+ if (prevSearches.size() > 10)
+ prevSearches.removeLast();
+ }
+ }
+
+ public void changedUpdate(DocumentEvent e) {
+ ((FilterModel) getModel()).refilter();
+ }
+
+ public void insertUpdate(DocumentEvent e) {
+ ((FilterModel) getModel()).refilter();
+ }
+
+ public void removeUpdate(DocumentEvent e) {
+ ((FilterModel) getModel()).refilter();
+ }
+ }
+
+ class PrevSearchAction extends AbstractAction {
+ String term;
+
+ public PrevSearchAction(String s) {
+ term = s;
+ putValue(Action.NAME, term);
+ }
+
+ public String toString() {
+ return term;
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ getFilterField().textField.setText(term);
+
+ // don't need this - setText fires a DocumentEvent
+ // that FilterField handles
+ // ((FilterModel)getModel()).refilter();
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/util/swing/JStatusBar.java b/application/src/main/java/cytoscape/util/swing/JStatusBar.java
new file mode 100644
index 0000000..1f8dc09
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/swing/JStatusBar.java
@@ -0,0 +1,183 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.util.swing;
+
+import java.awt.Dimension;
+import java.awt.Font;
+
+import javax.swing.JPanel;
+
+
+/**
+ * Simple status bar with 3 fields.<br>
+ *
+ * @author kono
+ *
+ */
+public class JStatusBar extends JPanel {
+ /**
+ * Creates a new JStatusBar object.
+ */
+ public JStatusBar() {
+ initComponents();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param text DOCUMENT ME!
+ */
+ public void setLeftLabel(String text) {
+ leftLabel.setText(text);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param text DOCUMENT ME!
+ */
+ public void setCenterLabel(String text) {
+ centerLabel.setText(text);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param text DOCUMENT ME!
+ */
+ public void setRightLabel(String text) {
+ rightLabel.setText(text);
+ }
+
+ private void initComponents() {
+ leftPanel = new javax.swing.JPanel();
+ leftLabel = new javax.swing.JLabel();
+ centerPanel = new javax.swing.JPanel();
+ centerLabel = new javax.swing.JLabel();
+ rightPanel = new javax.swing.JPanel();
+ rightLabel = new javax.swing.JLabel();
+
+ leftPanel.setBorder(javax.swing.BorderFactory.createEtchedBorder());
+ leftPanel.setPreferredSize(new Dimension(40, 40));
+ leftLabel.setFont(new Font("Sans-Serif", Font.PLAIN, 10));
+ leftLabel.setPreferredSize(new Dimension(20, 20));
+
+ org.jdesktop.layout.GroupLayout jPanel1Layout = new org.jdesktop.layout.GroupLayout(leftPanel);
+ leftPanel.setLayout(jPanel1Layout);
+ jPanel1Layout.setHorizontalGroup(jPanel1Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(org.jdesktop.layout.GroupLayout.TRAILING,
+ jPanel1Layout.createSequentialGroup()
+ .addContainerGap()
+ .add(leftLabel,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 300, Short.MAX_VALUE)
+ .addContainerGap()));
+ jPanel1Layout.setVerticalGroup(jPanel1Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(jPanel1Layout.createSequentialGroup()
+ .add(leftLabel)
+ .addContainerGap(2,
+ Short.MAX_VALUE)));
+
+ centerPanel.setBorder(javax.swing.BorderFactory.createEtchedBorder());
+ centerLabel.setText("jLabel2");
+
+ org.jdesktop.layout.GroupLayout jPanel2Layout = new org.jdesktop.layout.GroupLayout(centerPanel);
+ centerPanel.setLayout(jPanel2Layout);
+ jPanel2Layout.setHorizontalGroup(jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(jPanel2Layout.createSequentialGroup()
+ .addContainerGap()
+ .add(centerLabel,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 100, Short.MAX_VALUE)
+ .addContainerGap()));
+ jPanel2Layout.setVerticalGroup(jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(centerLabel,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 17, Short.MAX_VALUE));
+
+ rightPanel.setBorder(javax.swing.BorderFactory.createEtchedBorder());
+ rightLabel.setText("jLabel3");
+
+ org.jdesktop.layout.GroupLayout jPanel3Layout = new org.jdesktop.layout.GroupLayout(rightPanel);
+ rightPanel.setLayout(jPanel3Layout);
+ jPanel3Layout.setHorizontalGroup(jPanel3Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(jPanel3Layout.createSequentialGroup()
+ .addContainerGap()
+ .add(rightLabel,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 130, Short.MAX_VALUE)
+ .addContainerGap()));
+ jPanel3Layout.setVerticalGroup(jPanel3Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(jPanel3Layout.createSequentialGroup()
+ .add(rightLabel)
+ .addContainerGap(2,
+ Short.MAX_VALUE)));
+
+ org.jdesktop.layout.GroupLayout layout = new org.jdesktop.layout.GroupLayout(this);
+ this.setLayout(layout);
+ layout.setHorizontalGroup(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(layout.createSequentialGroup()
+ .add(leftPanel,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(centerPanel,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(rightPanel,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE)));
+ layout.setVerticalGroup(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(leftPanel, 0, 21, Short.MAX_VALUE)
+ .add(centerPanel,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE).add(rightPanel, 0, 21, Short.MAX_VALUE));
+ } // </editor-fold>
+
+ // Variables declaration - do not modify
+ private javax.swing.JLabel leftLabel;
+ private javax.swing.JLabel centerLabel;
+ private javax.swing.JLabel rightLabel;
+ private javax.swing.JPanel leftPanel;
+ private javax.swing.JPanel centerPanel;
+ private javax.swing.JPanel rightPanel;
+
+ // End of variables declaration
+}
diff --git a/application/src/main/java/cytoscape/util/swing/JTreeTable.java b/application/src/main/java/cytoscape/util/swing/JTreeTable.java
new file mode 100644
index 0000000..d20b87e
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/swing/JTreeTable.java
@@ -0,0 +1,440 @@
+/*
+ * The contents of this file are subject to the Sapient Public License
+ * Version 1.0 (the "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ * http://carbon.sf.net/License.html.
+ *
+ * Software distributed under the License is distributed on an "AS IS" basis,
+ * WITHOUT WARRANTY OF ANY KIND, either express or implied. See the License for
+ * the specific language governing rights and limitations under the License.
+ *
+ * The Original Code is The Carbon Component Framework.
+ *
+ * The Initial Developer of the Original Code is Sapient Corporation
+ *
+ * Copyright (C) 2003 Sapient Corporation. All Rights Reserved.
+ */
+package cytoscape.util.swing;
+
+
+/*
+ * @(#)JTreeTable.java 1.2 98/10/27
+ *
+ * Copyright 1997, 1998 by Sun Microsystems, Inc., 901 San Antonio Road, Palo
+ * Alto, California, 94303, U.S.A. All rights reserved.
+ *
+ * This software is the confidential and proprietary information of Sun
+ * Microsystems, Inc. ("Confidential Information"). You shall not disclose such
+ * Confidential Information and shall use it only in accordance with the terms
+ * of the license agreement you entered into with Sun.
+ */
+import java.awt.Component;
+import java.awt.Dimension;
+import java.awt.Graphics;
+import java.awt.Point;
+import java.awt.Rectangle;
+import java.awt.event.MouseEvent;
+import java.util.EventObject;
+
+import javax.swing.JComponent;
+import javax.swing.JTable;
+import javax.swing.JTree;
+import javax.swing.ListSelectionModel;
+import javax.swing.LookAndFeel;
+import javax.swing.UIManager;
+import javax.swing.event.ListSelectionEvent;
+import javax.swing.event.ListSelectionListener;
+import javax.swing.table.TableCellEditor;
+import javax.swing.table.TableCellRenderer;
+import javax.swing.tree.DefaultTreeCellRenderer;
+import javax.swing.tree.DefaultTreeSelectionModel;
+import javax.swing.tree.TreeCellRenderer;
+import javax.swing.tree.TreeModel;
+import javax.swing.tree.TreePath;
+
+
+/**
+ * This example shows how to create a simple JTreeTable component, by using a
+ * JTree as a renderer (and editor) for the cells in a particular column in the
+ * JTable.
+ *
+ * @version 1.2 10/27/98
+ *
+ * @author Philip Milne
+ * @author Scott Violet
+ */
+public class JTreeTable extends JTable {
+
+ private static final long serialVersionUID = -505249707913524363L;
+
+ /** A subclass of JTree. */
+ protected TreeTableCellRenderer tree;
+
+ /**
+ * Creates a new JTreeTable object.
+ *
+ * @param treeTableModel DOCUMENT ME!
+ */
+ public JTreeTable(TreeTableModel treeTableModel) {
+ super();
+
+ // Create the tree. It will be used as a renderer and editor.
+ tree = new TreeTableCellRenderer(treeTableModel);
+
+ // Install a tableModel representing the visible rows in the tree.
+ super.setModel(new TreeTableModelAdapter(treeTableModel, tree));
+
+ // Force the JTable and JTree to share their row selection models.
+ ListToTreeSelectionModelWrapper selectionWrapper = new ListToTreeSelectionModelWrapper();
+ tree.setSelectionModel(selectionWrapper);
+ setSelectionModel(selectionWrapper.getListSelectionModel());
+
+ // Install the tree editor renderer and editor.
+ setDefaultRenderer(TreeTableModel.class, tree);
+ setDefaultEditor(TreeTableModel.class, new TreeTableCellEditor());
+
+ // No grid.
+ setShowGrid(false);
+
+ // No intercell spacing
+ setIntercellSpacing(new Dimension(0, 0));
+
+ // And update the height of the trees row to match that of
+ // the table.
+ if (tree.getRowHeight() < 1) {
+ // Metal looks better like this.
+ setRowHeight(18);
+ }
+ }
+
+ /**
+ * The code in this method is copy and pasted from source code to the same
+ * method in javax.swing.JTable, except for one value change on one line. If
+ * you'd like to see the change, please read the source code below.
+ */
+ public String getToolTipText(MouseEvent event) {
+ String tip = null;
+ Point p = event.getPoint();
+
+ // Locate the renderer under the event location
+ int hitColumnIndex = columnAtPoint(p);
+ int hitRowIndex = rowAtPoint(p);
+
+ if ((hitColumnIndex != -1) && (hitRowIndex != -1)) {
+ TableCellRenderer renderer = getCellRenderer(hitRowIndex, hitColumnIndex);
+ Component component = prepareRenderer(renderer, hitRowIndex, hitColumnIndex);
+
+ // Now have to see if the component is a JComponent before
+ // getting the tip
+ if (component instanceof JComponent) {
+ // Convert the event to the renderer's coordinate system
+ Rectangle cellRect = getCellRect(hitRowIndex, hitColumnIndex, false);
+ // HERE IS THE MODIFICATION FROM javax.swing.JTable:
+ // p.translate(-cellRect.x, -cellRect.y);
+ p.translate(-cellRect.x, 0);
+
+ // END OF MODIFICATION
+ MouseEvent newEvent = new MouseEvent(component, event.getID(), event.getWhen(),
+ event.getModifiers(), p.x, p.y,
+ event.getClickCount(), event.isPopupTrigger());
+
+ tip = ((JComponent) component).getToolTipText(newEvent);
+ }
+ }
+
+ // No tip from the renderer get our own tip
+ if (tip == null)
+ tip = getToolTipText();
+
+ return tip;
+ }
+
+ /**
+ * Overridden to message super and forward the method to the tree. Since the
+ * tree is not actually in the component hieachy it will never receive this
+ * unless we forward it in this manner.
+ */
+ public void updateUI() {
+ super.updateUI();
+
+ if (tree != null) {
+ tree.updateUI();
+ }
+
+ // Use the tree's default foreground and background colors in the
+ // table.
+ LookAndFeel.installColorsAndFont(this, "Tree.background", "Tree.foreground", "Tree.font");
+ }
+
+ /*
+ * Workaround for BasicTableUI anomaly. Make sure the UI never tries to
+ * paint the editor. The UI currently uses different techniques to paint the
+ * renderers and editors and overriding setBounds() below is not the right
+ * thing to do for an editor. Returning -1 for the editing row in this case,
+ * ensures the editor is never painted.
+ */
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getEditingRow() {
+ return (getColumnClass(editingColumn) == TreeTableModel.class) ? (-1) : editingRow;
+ }
+
+ /**
+ * Overridden to pass the new rowHeight to the tree.
+ */
+ public void setRowHeight(int rowHeight) {
+ super.setRowHeight(rowHeight);
+
+ if ((tree != null) && (tree.getRowHeight() != rowHeight)) {
+ tree.setRowHeight(getRowHeight());
+ }
+ }
+
+ /**
+ * Returns the tree that is being shared between the model.
+ */
+ public JTree getTree() {
+ return tree;
+ }
+
+ /**
+ * A TreeCellRenderer that displays a JTree.
+ */
+ public class TreeTableCellRenderer extends JTree implements TableCellRenderer {
+ /** Last table/tree row asked to renderer. */
+ protected int visibleRow;
+
+ public TreeTableCellRenderer(TreeModel model) {
+ super(model);
+ }
+
+ /**
+ * updateUI is overridden to set the colors of the Tree's renderer to
+ * match that of the table.
+ */
+ public void updateUI() {
+ super.updateUI();
+
+ // Make the tree's cell renderer use the table's cell selection
+ // colors.
+ TreeCellRenderer tcr = getCellRenderer();
+
+ if (tcr instanceof DefaultTreeCellRenderer) {
+ DefaultTreeCellRenderer dtcr = ((DefaultTreeCellRenderer) tcr);
+ // For 1.1 uncomment this, 1.2 has a bug that will cause an
+ // exception to be thrown if the border selection color is
+ // null.
+ // dtcr.setBorderSelectionColor(null);
+ dtcr.setTextSelectionColor(UIManager.getColor("Table.selectionForeground"));
+ dtcr.setBackgroundSelectionColor(UIManager.getColor("Table.selectionBackground"));
+ }
+ }
+
+ /**
+ * Sets the row height of the tree, and forwards the row height to the
+ * table.
+ */
+ public void setRowHeight(int rowHeight) {
+ if (rowHeight > 0) {
+ super.setRowHeight(rowHeight);
+
+ if ((JTreeTable.this != null) && (JTreeTable.this.getRowHeight() != rowHeight)) {
+ JTreeTable.this.setRowHeight(getRowHeight());
+ }
+ }
+ }
+
+ /**
+ * This is overridden to set the height to match that of the JTable.
+ */
+ public void setBounds(int x, int y, int w, int h) {
+ super.setBounds(x, 0, w, JTreeTable.this.getHeight());
+ }
+
+ /**
+ * Sublcassed to translate the graphics such that the last visible row
+ * will be drawn at 0,0.
+ */
+ public void paint(Graphics g) {
+ if (g == null)
+ return;
+
+ g.translate(0, -visibleRow * getRowHeight());
+
+ try {
+ super.paint(g);
+ } catch (Exception e) {
+ //CyLogger.getLogger().warn("********************");
+ }
+ }
+
+ /**
+ * TreeCellRenderer method. Overridden to update the visible row.
+ */
+ public Component getTableCellRendererComponent(JTable table, Object value,
+ boolean isSelected, boolean hasFocus,
+ int row, int column) {
+ if (isSelected)
+ setBackground(table.getSelectionBackground());
+ else
+ setBackground(table.getBackground());
+
+ visibleRow = row;
+
+ return this;
+ }
+ }
+
+ /**
+ * TreeTableCellEditor implementation. Component returned is the JTree.
+ */
+ public class TreeTableCellEditor extends AbstractCellEditor implements TableCellEditor {
+ public Component getTableCellEditorComponent(JTable table, Object value,
+ boolean isSelected, int r, int c) {
+ return tree;
+ }
+
+ /**
+ * Overridden to return false, and if the event is a mouse event it is
+ * forwarded to the tree.
+ * <p>
+ * The behavior for this is debatable, and should really be offered as a
+ * property. By returning false, all keyboard actions are implemented in
+ * terms of the table. By returning true, the tree would get a chance to
+ * do something with the keyboard events. For the most part this is ok.
+ * But for certain keys, such as left/right, the tree will
+ * expand/collapse where as the table focus should really move to a
+ * different column. Page up/down should also be implemented in terms of
+ * the table. By returning false this also has the added benefit that
+ * clicking outside of the bounds of the tree node, but still in the
+ * tree column will select the row, whereas if this returned true that
+ * wouldn't be the case.
+ * <p>
+ * By returning false we are also enforcing the policy that the tree
+ * will never be editable (at least by a key sequence).
+ */
+ public boolean isCellEditable(EventObject e) {
+ if (e instanceof MouseEvent) {
+ for (int counter = getColumnCount() - 1; counter >= 0; counter--) {
+ if (getColumnClass(counter) == TreeTableModel.class) {
+ MouseEvent me = (MouseEvent) e;
+ MouseEvent newME = new MouseEvent(tree, me.getID(), me.getWhen(),
+ me.getModifiers(),
+ me.getX()
+ - getCellRect(0, counter, true).x,
+ me.getY(), me.getClickCount(),
+ me.isPopupTrigger());
+ tree.dispatchEvent(newME);
+
+ break;
+ }
+ }
+ }
+
+ return false;
+ }
+ }
+
+ /**
+ * ListToTreeSelectionModelWrapper extends DefaultTreeSelectionModel to
+ * listen for changes in the ListSelectionModel it maintains. Once a change
+ * in the ListSelectionModel happens, the paths are updated in the
+ * DefaultTreeSelectionModel.
+ */
+ class ListToTreeSelectionModelWrapper extends DefaultTreeSelectionModel {
+ /** Set to true when we are updating the ListSelectionModel. */
+ protected boolean updatingListSelectionModel;
+
+ public ListToTreeSelectionModelWrapper() {
+ super();
+ getListSelectionModel().addListSelectionListener(createListSelectionListener());
+ }
+
+ /**
+ * Returns the list selection model. ListToTreeSelectionModelWrapper
+ * listens for changes to this model and updates the selected paths
+ * accordingly.
+ */
+ ListSelectionModel getListSelectionModel() {
+ return listSelectionModel;
+ }
+
+ /**
+ * This is overridden to set <code>updatingListSelectionModel</code>
+ * and message super. This is the only place DefaultTreeSelectionModel
+ * alters the ListSelectionModel.
+ */
+ public void resetRowSelection() {
+ if (!updatingListSelectionModel) {
+ updatingListSelectionModel = true;
+
+ try {
+ super.resetRowSelection();
+ } finally {
+ updatingListSelectionModel = false;
+ }
+ }
+
+ // Notice how we don't message super if
+ // updatingListSelectionModel is true. If
+ // updatingListSelectionModel is true, it implies the
+ // ListSelectionModel has already been updated and the
+ // paths are the only thing that needs to be updated.
+ }
+
+ /**
+ * Creates and returns an instance of ListSelectionHandler.
+ */
+ protected ListSelectionListener createListSelectionListener() {
+ return new ListSelectionHandler();
+ }
+
+ /**
+ * If <code>updatingListSelectionModel</code> is false, this will
+ * reset the selected paths from the selected rows in the list selection
+ * model.
+ */
+ protected void updateSelectedPathsFromSelectedRows() {
+ if (!updatingListSelectionModel) {
+ updatingListSelectionModel = true;
+
+ try {
+ // This is way expensive, ListSelectionModel needs an
+ // enumerator for iterating.
+ int min = listSelectionModel.getMinSelectionIndex();
+ int max = listSelectionModel.getMaxSelectionIndex();
+
+ clearSelection();
+
+ if ((min != -1) && (max != -1)) {
+ for (int counter = min; counter <= max; counter++) {
+ if (listSelectionModel.isSelectedIndex(counter)) {
+ TreePath selPath = tree.getPathForRow(counter);
+
+ if (selPath != null) {
+ addSelectionPath(selPath);
+ }
+ }
+ }
+ }
+ } finally {
+ updatingListSelectionModel = false;
+ }
+ }
+ }
+
+ /**
+ * Class responsible for calling updateSelectedPathsFromSelectedRows
+ * when the selection of the list changse.
+ */
+ class ListSelectionHandler implements ListSelectionListener {
+ public void valueChanged(ListSelectionEvent e) {
+ updateSelectedPathsFromSelectedRows();
+ }
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/util/swing/NetworkSelectorPanel.java b/application/src/main/java/cytoscape/util/swing/NetworkSelectorPanel.java
new file mode 100644
index 0000000..d594644
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/swing/NetworkSelectorPanel.java
@@ -0,0 +1,90 @@
+package cytoscape.util.swing;
+
+
+import java.awt.BorderLayout;
+import java.awt.event.ItemListener;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.util.Set;
+import java.util.SortedSet;
+import java.util.TreeSet;
+
+import javax.swing.JComboBox;
+import javax.swing.JPanel;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+
+
+public class NetworkSelectorPanel extends JPanel implements
+ PropertyChangeListener
+{
+ private static final long serialVersionUID = 8694272457769377810L;
+
+ protected final JComboBox networkComboBox;
+
+ public NetworkSelectorPanel() {
+ super();
+ this.setLayout(new BorderLayout());
+ networkComboBox = new JComboBox();
+
+ //This should help to limit the length of combobox if the network name is too long
+ networkComboBox.setPreferredSize(new java.awt.Dimension(networkComboBox.getPreferredSize().width,
+ networkComboBox.getPreferredSize().height));
+
+ add(networkComboBox, BorderLayout.CENTER);
+ updateNetworkList();
+
+ Cytoscape.getPropertyChangeSupport().addPropertyChangeListener(this);
+ }
+
+ /**
+ * If selected, return selected network.
+ * Otherwise, return null.
+ *
+ * @return
+ */
+ public CyNetwork getSelectedNetwork() {
+ for (CyNetwork net : Cytoscape.getNetworkSet()) {
+ if (net.getTitle().equals(networkComboBox.getSelectedItem()))
+ return net;
+ }
+
+ return null;
+ }
+
+ private void updateNetworkList() {
+ final Set<CyNetwork> networks = Cytoscape.getNetworkSet();
+ final SortedSet<String> networkNames = new TreeSet<String>();
+
+ for (CyNetwork net : networks)
+ networkNames.add(net.getTitle());
+
+ networkComboBox.removeAllItems();
+ for (String name : networkNames)
+ networkComboBox.addItem(name);
+
+ networkComboBox.setSelectedItem(Cytoscape.getCurrentNetwork()
+ .getTitle());
+ }
+
+ public void propertyChange(PropertyChangeEvent evt) {
+
+ final String propName = evt.getPropertyName();
+
+ if (propName.equals(Cytoscape.NETWORK_CREATED)||propName.equals(Cytoscape.NETWORK_TITLE_MODIFIED)){
+ updateNetworkList();
+ }
+ else if (propName.equals(Cytoscape.NETWORK_DESTROYED))
+ networkComboBox.removeItem(Cytoscape.getNetwork(
+ (String) evt.getNewValue()).getTitle());
+
+ }
+
+ /**
+ * Installs a new item listener for the embedded combo box.
+ */
+ public void addItemListener(final ItemListener newListener) {
+ networkComboBox.addItemListener(newListener);
+ }
+}
diff --git a/application/src/main/java/cytoscape/util/swing/SwingMenuSorter.java b/application/src/main/java/cytoscape/util/swing/SwingMenuSorter.java
new file mode 100644
index 0000000..1694a6a
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/swing/SwingMenuSorter.java
@@ -0,0 +1,101 @@
+/*
+ File: PluginMenuListener.java
+
+ Copyright (c) 2011, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.util.swing;
+
+import java.util.Arrays;
+import java.util.Comparator;
+
+import java.awt.Component;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JSeparator;
+import javax.swing.event.MenuEvent;
+import javax.swing.event.MenuListener;
+
+/**
+ * This class is called from CyMenus to sort the plugins menu to make it
+ * easier to find a particular plugin from a long list.
+ */
+public class SwingMenuSorter implements MenuListener {
+ JMenu pluginMenu;
+ int sepCount = 0;
+
+ public SwingMenuSorter(JMenu p, int sepCount) {
+ pluginMenu = p;
+ this.sepCount = sepCount;
+ }
+
+ public void menuCanceled(MenuEvent e) {}
+ public void menuDeselected(MenuEvent e) {}
+ public void menuSelected(MenuEvent e) {
+ // Get the list of Components
+ Component[] components = pluginMenu.getMenuComponents();
+ int sepFound = 0;
+ int userMenuStart = 0;
+ for (int i = 0; (i < components.length) && (sepFound < sepCount); i++) {
+ if (components[i] instanceof JSeparator) {
+ sepFound++;
+ userMenuStart = i+1;
+ }
+ }
+
+ JMenuItem[] userMenus = new JMenuItem[components.length-userMenuStart];
+ int j = 0;
+ for (int i = userMenuStart; i < components.length; i++) {
+ userMenus[j++] = (JMenuItem)components[i];
+ }
+
+ // OK, now sort and put back in
+ Arrays.sort(userMenus, new MenuComparator());
+ j = 0;
+ for (int i = userMenuStart; i < components.length; i++) {
+ pluginMenu.add(userMenus[j++],i);
+ }
+
+ }
+
+ class MenuComparator implements Comparator {
+ public int compare(Object o1, Object o2) {
+ JMenuItem j1 = (JMenuItem)o1;
+ JMenuItem j2 = (JMenuItem)o2;
+ return j1.getText().compareTo(j2.getText());
+ }
+
+ public boolean equals(Object o1, Object o2) {
+ JMenuItem j1 = (JMenuItem)o1;
+ JMenuItem j2 = (JMenuItem)o2;
+ return j1.getText().equals(j2.getText());
+ }
+ }
+}
+
+
+
diff --git a/application/src/main/java/cytoscape/util/swing/TreeTableModel.java b/application/src/main/java/cytoscape/util/swing/TreeTableModel.java
new file mode 100644
index 0000000..6d613c7
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/swing/TreeTableModel.java
@@ -0,0 +1,86 @@
+/*
+ * The contents of this file are subject to the Sapient Public License
+ * Version 1.0 (the "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ * http://carbon.sf.net/License.html.
+ *
+ * Software distributed under the License is distributed on an "AS IS" basis,
+ * WITHOUT WARRANTY OF ANY KIND, either express or implied. See the License for
+ * the specific language governing rights and limitations under the License.
+ *
+ * The Original Code is The Carbon Component Framework.
+ *
+ * The Initial Developer of the Original Code is Sapient Corporation
+ *
+ * Copyright (C) 2003 Sapient Corporation. All Rights Reserved.
+ */
+package cytoscape.util.swing;
+
+
+/*
+ * TreeTableModel.java
+ *
+ * Copyright (c) 1998 Sun Microsystems, Inc. All Rights Reserved.
+ *
+ * This software is the confidential and proprietary information of Sun
+ * Microsystems, Inc. ("Confidential Information"). You shall not
+ * disclose such Confidential Information and shall use it only in
+ * accordance with the terms of the license agreement you entered into
+ * with Sun.
+ *
+ * SUN MAKES NO REPRESENTATIONS OR WARRANTIES ABOUT THE SUITABILITY OF THE
+ * SOFTWARE, EITHER EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR
+ * PURPOSE, OR NON-INFRINGEMENT. SUN SHALL NOT BE LIABLE FOR ANY DAMAGES
+ * SUFFERED BY LICENSEE AS A RESULT OF USING, MODIFYING OR DISTRIBUTING
+ * THIS SOFTWARE OR ITS DERIVATIVES.
+ *
+ */
+import javax.swing.tree.TreeModel;
+
+
+/**
+ * TreeTableModel is the model used by a JTreeTable. It extends TreeModel
+ * to add methods for getting inforamtion about the set of columns each
+ * node in the TreeTableModel may have. Each column, like a column in
+ * a TableModel, has a name and a type associated with it. Each node in
+ * the TreeTableModel can return a value for each of the columns and
+ * set that value if isCellEditable() returns true.
+ *
+ * @author Philip Milne
+ * @author Scott Violet
+ */
+public interface TreeTableModel extends TreeModel {
+ /**
+ * Returns the number of availible columns.
+ */
+ public int getColumnCount();
+
+ /**
+ * Returns the name for column number <code>column</code>.
+ */
+ public String getColumnName(int column);
+
+ /**
+ * Returns the type for column number <code>column</code>.
+ */
+ public Class getColumnClass(int column);
+
+ /**
+ * Returns the value to be displayed for node <code>node</code>,
+ * at column number <code>column</code>.
+ */
+ public Object getValueAt(Object node, int column);
+
+ /**
+ * Indicates whether the the value for node <code>node</code>,
+ * at column number <code>column</code> is editable.
+ */
+ public boolean isCellEditable(Object node, int column);
+
+ /**
+ * Sets the value for node <code>node</code>,
+ * at column number <code>column</code>.
+ */
+ public void setValueAt(Object aValue, Object node, int column);
+}
diff --git a/application/src/main/java/cytoscape/util/swing/TreeTableModelAdapter.java b/application/src/main/java/cytoscape/util/swing/TreeTableModelAdapter.java
new file mode 100644
index 0000000..7d09e44
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/swing/TreeTableModelAdapter.java
@@ -0,0 +1,209 @@
+/*
+ * The contents of this file are subject to the Sapient Public License
+ * Version 1.0 (the "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ * http://carbon.sf.net/License.html.
+ *
+ * Software distributed under the License is distributed on an "AS IS" basis,
+ * WITHOUT WARRANTY OF ANY KIND, either express or implied. See the License for
+ * the specific language governing rights and limitations under the License.
+ *
+ * The Original Code is The Carbon Component Framework.
+ *
+ * The Initial Developer of the Original Code is Sapient Corporation
+ *
+ * Copyright (C) 2003 Sapient Corporation. All Rights Reserved.
+ */
+package cytoscape.util.swing;
+
+
+/*
+ * @(#)TreeTableModelAdapter.java 1.2 98/10/27
+ *
+ * Copyright 1997, 1998 by Sun Microsystems, Inc.,
+ * 901 San Antonio Road, Palo Alto, California, 94303, U.S.A.
+ * All rights reserved.
+ *
+ * This software is the confidential and proprietary information
+ * of Sun Microsystems, Inc. ("Confidential Information"). You
+ * shall not disclose such Confidential Information and shall use
+ * it only in accordance with the terms of the license agreement
+ * you entered into with Sun.
+ */
+import javax.swing.JTree;
+import javax.swing.SwingUtilities;
+import javax.swing.event.TreeExpansionEvent;
+import javax.swing.event.TreeExpansionListener;
+import javax.swing.event.TreeModelEvent;
+import javax.swing.event.TreeModelListener;
+import javax.swing.table.AbstractTableModel;
+import javax.swing.tree.TreePath;
+
+
+/**
+ * This is a wrapper class takes a TreeTableModel and implements
+ * the table model interface. The implementation is trivial, with
+ * all of the event dispatching support provided by the superclass:
+ * the AbstractTableModel.
+ *
+ * @version 1.2 10/27/98
+ *
+ * @author Philip Milne
+ * @author Scott Violet
+ */
+public class TreeTableModelAdapter extends AbstractTableModel {
+
+ private static final long serialVersionUID = 4492106324533343342L;
+
+ private JTree tree;
+ private TreeTableModel treeTableModel;
+
+ /**
+ * Creates a new TreeTableModelAdapter object.
+ *
+ * @param treeTableModel DOCUMENT ME!
+ * @param tree DOCUMENT ME!
+ */
+ public TreeTableModelAdapter(TreeTableModel treeTableModel, JTree tree) {
+ this.tree = tree;
+ this.treeTableModel = treeTableModel;
+
+ tree.addTreeExpansionListener(new TreeExpansionListener() {
+ // Don't use fireTableRowsInserted() here; the selection model
+ // would get updated twice.
+ public void treeExpanded(TreeExpansionEvent event) {
+ fireTableDataChanged();
+ }
+
+ public void treeCollapsed(TreeExpansionEvent event) {
+ fireTableDataChanged();
+ }
+ });
+
+ // Install a TreeModelListener that can update the table when
+ // tree changes. We use delayedFireTableDataChanged as we can
+ // not be guaranteed the tree will have finished processing
+ // the event before us.
+ treeTableModel.addTreeModelListener(new TreeModelListener() {
+ public void treeNodesChanged(TreeModelEvent e) {
+ delayedFireTableDataChanged();
+ }
+
+ public void treeNodesInserted(TreeModelEvent e) {
+ delayedFireTableDataChanged();
+ }
+
+ public void treeNodesRemoved(TreeModelEvent e) {
+ delayedFireTableDataChanged();
+ }
+
+ public void treeStructureChanged(TreeModelEvent e) {
+ delayedFireTableDataChanged();
+ }
+ });
+ }
+
+ // Wrappers, implementing TableModel interface.
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getColumnCount() {
+ return treeTableModel.getColumnCount();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param column DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getColumnName(int column) {
+ return treeTableModel.getColumnName(column);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param column DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Class getColumnClass(int column) {
+ return treeTableModel.getColumnClass(column);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getRowCount() {
+ return tree.getRowCount();
+ }
+
+ protected Object nodeForRow(int row) {
+ TreePath treePath = tree.getPathForRow(row);
+
+ if (treePath != null) {
+ return treePath.getLastPathComponent();
+ } else
+
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param row DOCUMENT ME!
+ * @param column DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getValueAt(int row, int column) {
+ Object tempObj = nodeForRow(row);
+
+ if (tempObj != null) {
+ return treeTableModel.getValueAt(tempObj, column);
+ } else {
+ return null;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param row DOCUMENT ME!
+ * @param column DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isCellEditable(int row, int column) {
+ return treeTableModel.isCellEditable(nodeForRow(row), column);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param value DOCUMENT ME!
+ * @param row DOCUMENT ME!
+ * @param column DOCUMENT ME!
+ */
+ public void setValueAt(Object value, int row, int column) {
+ treeTableModel.setValueAt(value, nodeForRow(row), column);
+ }
+
+ /**
+ * Invokes fireTableDataChanged after all the pending events have been
+ * processed. SwingUtilities.invokeLater is used to handle this.
+ */
+ protected void delayedFireTableDataChanged() {
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ fireTableDataChanged();
+ }
+ });
+ }
+}
diff --git a/application/src/main/java/cytoscape/util/swing/WidestStringComboBoxModel.java b/application/src/main/java/cytoscape/util/swing/WidestStringComboBoxModel.java
new file mode 100644
index 0000000..f18de36
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/swing/WidestStringComboBoxModel.java
@@ -0,0 +1,221 @@
+/*
+ Copyright (c) 2009, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.util.swing;
+
+import java.util.Vector;
+import javax.swing.DefaultComboBoxModel;
+
+/**
+ * @author Noel Ruddock
+ * This ComboBoxModel tracks the widest string
+ * getLabel(Object anObject) should be overridden to derive the String from
+ * an Object in the model when getString() doesn't provide what will be
+ * displayed.
+ */
+public class WidestStringComboBoxModel extends DefaultComboBoxModel implements WidestStringProvider {
+ private String widest = null;
+ private boolean widestValid = false;
+
+ /**
+ * Class Constructor.
+ */
+ public WidestStringComboBoxModel() {
+ super();
+ }
+
+ /**
+ * Class Constructor specifying an array of Objects to form the model.
+ *
+ * @param items
+ */
+ public WidestStringComboBoxModel(Object[] items) {
+ super(items);
+ }
+
+ /**
+ * Class Constructor specifying a vector of Objects to form the model.
+ *
+ * @param v
+ */
+ public WidestStringComboBoxModel(Vector<?> v) {
+ super(v);
+ }
+
+ /**
+ * Adds the given object to the model.
+ * Additionally updates cached longest String.
+ *
+ * @param anObject the object to be added to the model
+ */
+ @Override
+ public void addElement(Object anObject) {
+ updateWidest(anObject, true);
+ super.addElement(anObject);
+ }
+
+ /**
+ * Inserts an object into the model at the given index.
+ * Additionally updates cached longest String.
+ *
+ * @param anObject the object to be added to the model
+ * @param index the index at which the given object is to be added
+ */
+ @Override
+ public void insertElementAt(Object anObject, int index) {
+ updateWidest(anObject, true);
+ super.insertElementAt(anObject, index);
+ }
+
+ /**
+ * Removes all objects from the model.
+ * Additionally updates cached longest String.
+ */
+ @Override
+ public void removeAllElements() {
+ resetWidest();
+ super.removeAllElements();
+ }
+
+ /**
+ * Removes the given object from the model.
+ * Additionally updates cached longest String.
+ *
+ * @param anObject the object to be removed from the model
+ */
+ @Override
+ public void removeElement(Object anObject) {
+ updateWidest(anObject, false);
+ super.removeElement(anObject);
+ }
+
+ /**
+ * Removes the object at the specified index from the model.
+ * Additionally updates cached longest String.
+ */
+ @Override
+ public void removeElementAt(int index) {
+ updateWidest(getElementAt(index), false);
+ super.removeElementAt(index);
+ }
+
+ /**
+ * Invalidates the cached longest String.
+ */
+ public void resetWidest() {
+ widest = null;
+ widestValid = false;
+ }
+
+ /**
+ * Returns the longest display String for the objects in this model.
+ * If the cached longest String is not valid, the longest String is
+ * determined and cached.
+ * @return the longest display String for the objects in this model
+ */
+ public String getWidest() {
+ if (!widestValid) {
+ findWidest();
+ }
+
+ return widest;
+ }
+
+ /**
+ * Update the cached longest String if required when a new object is added
+ * to the model, or invalidate it when removing.
+ *
+ * @param anObject the Object being added or removed
+ * @param adding true if the anObject is being added to the model, false if
+ * it is being removed
+ */
+ private void updateWidest(Object anObject, boolean adding) {
+ String label;
+
+ label = getLabel(anObject);
+ if (widestValid) {
+ if (adding) {
+ if (label.length() > widest.length()) {
+ widest = label;
+ }
+ }
+ else {
+ if (widest.equals(label)) {
+ resetWidest();
+ }
+ }
+ }
+ else {
+ if (adding) {
+ widest = label;
+ widestValid = true;
+ }
+ }
+ }
+
+ /**
+ * Find which display string for the objects in the model is the longest.
+ */
+ private void findWidest() {
+ int size;
+
+ size = getSize();
+ widest = "";
+ for (int i = 0; i < size; i++) {
+ String label;
+
+ label = getLabel(getElementAt(i));
+ if (label.length() > widest.length()) {
+ widest = label;
+ }
+ }
+ widestValid = true;
+ }
+
+ /**
+ * Returns the String corresponding to the parameter object for use in
+ * calculating the width of popup required.
+ * This method should be overridden when the toString method of whatever
+ * objects are stored in the model, doesn't return a suitable String.
+ * Should return an empty string when anObject == null.
+ *
+ * @param anObject
+ * @return the string that will be displayed for anObject. "" is returned
+ * when the passed object is null
+ */
+ protected String getLabel(Object anObject) {
+ return (anObject != null) ? anObject.toString() : "";
+ }
+}
diff --git a/application/src/main/java/cytoscape/util/swing/WidestStringComboBoxPopupMenuListener.java b/application/src/main/java/cytoscape/util/swing/WidestStringComboBoxPopupMenuListener.java
new file mode 100644
index 0000000..8dda7da
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/swing/WidestStringComboBoxPopupMenuListener.java
@@ -0,0 +1,118 @@
+/*
+ Copyright (c) 2009, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.util.swing;
+
+import java.awt.Dimension;
+import java.awt.FontMetrics;
+import javax.swing.ComboBoxModel;
+import javax.swing.JComboBox;
+import javax.swing.JComponent;
+import javax.swing.JPopupMenu;
+import javax.swing.JScrollPane;
+import javax.swing.event.PopupMenuEvent;
+import javax.swing.event.PopupMenuListener;
+
+/**
+ * @author Noel Ruddock
+ *
+ * Listener that can be attached to a JComboBox.
+ * When the JComboBox to which it is attached uses a ComboBoxModel that
+ * implements WidestStringProvider, the popup list will be resized so that the
+ * longest String will be completely visible.
+ */
+public class WidestStringComboBoxPopupMenuListener implements PopupMenuListener {
+ /**
+ * Resize the popup list based on the longest display string for objects in
+ * the model of the JComboBox being listened to.
+ * The model must implement WidestStringProvider for the popup to be sized.
+ *
+ * @param e
+ */
+ public void popupMenuWillBecomeVisible(PopupMenuEvent e) {
+ ComboBoxModel cbm;
+ WidestStringProvider wsp;
+ int w, h;
+ Dimension d;
+
+ JComboBox box = (JComboBox)e.getSource();
+ cbm = box.getModel();
+
+ if (!(cbm instanceof WidestStringProvider)) {
+ // Silently ignore if not listening to a JComboBox with a suitable model object
+ return;
+ }
+ wsp = (WidestStringProvider)cbm;
+
+ Object comp = box.getUI().getAccessibleChild(box, 0);
+
+ if (!(comp instanceof JPopupMenu)) {
+ return;
+ }
+
+ Object scrollObject = ((JComponent)comp).getComponent(0);
+
+ if (!(scrollObject instanceof JScrollPane)) {
+ return;
+ }
+
+ JScrollPane scrollPane = (JScrollPane)scrollObject;
+
+ FontMetrics fm = box.getFontMetrics(scrollPane.getFont());
+ w = (int)fm.stringWidth(wsp.getWidest());
+ h = (int)scrollPane.getMinimumSize().getHeight();
+ d = new Dimension(Math.max((int)((double)w + scrollPane.getVerticalScrollBar().getMinimumSize().getWidth()), box.getWidth()), h);
+ scrollPane.setPreferredSize(d);
+ scrollPane.setMaximumSize(d);
+ }
+
+ /**
+ * Not interested in this event.
+ *
+ * @param e
+ */
+ public void popupMenuWillBecomeInvisible(PopupMenuEvent e) {
+ return;
+ }
+
+ /**
+ * Not interested in this event.
+ *
+ * @param e
+ */
+ public void popupMenuCanceled(PopupMenuEvent e) {
+ return;
+ }
+}
diff --git a/application/src/main/java/cytoscape/util/swing/WidestStringProvider.java b/application/src/main/java/cytoscape/util/swing/WidestStringProvider.java
new file mode 100644
index 0000000..7e75615
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/swing/WidestStringProvider.java
@@ -0,0 +1,56 @@
+/*
+ Copyright (c) 2009, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.util.swing;
+
+/**
+ * @author Noel Ruddock
+ *
+ * Marker interface to decouple WidestStringComboBoxPopupMenuListener from
+ * WidestStringComboBoxModel.
+ */
+public interface WidestStringProvider {
+ /**
+ * Return the longest display String
+ *
+ * @return
+ */
+ public String getWidest();
+
+ /**
+ * Invalidate any cached longest String.
+ */
+ public void resetWidest();
+}
diff --git a/application/src/main/java/cytoscape/util/undo/CyAbstractEdit.java b/application/src/main/java/cytoscape/util/undo/CyAbstractEdit.java
new file mode 100644
index 0000000..ccc2909
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/undo/CyAbstractEdit.java
@@ -0,0 +1,75 @@
+
+/*
+ File: CyAbstractEdit.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.util.undo;
+
+import javax.swing.undo.AbstractUndoableEdit;
+
+/**
+ * A small convenience class that can be used to create new edits. All
+ * you should have to do is implement the undo() and redo() methods. The
+ * benefit is that you don't need to worry about setting up names.
+ */
+public abstract class CyAbstractEdit extends AbstractUndoableEdit {
+
+ protected String desc;
+
+ public CyAbstractEdit(String desc) {
+ this.desc = desc;
+ }
+
+ public String getPresentationName() {
+ return desc;
+ }
+
+ public String getRedoPresentationName() {
+ return "Redo: " + desc;
+ }
+
+ public String getUndoPresentationName() {
+ return "Undo: " + desc;
+ }
+
+ public void undo() {
+ super.undo();
+ }
+
+ public void redo() {
+ super.redo();
+ }
+}
diff --git a/application/src/main/java/cytoscape/util/undo/CyUndo.java b/application/src/main/java/cytoscape/util/undo/CyUndo.java
new file mode 100644
index 0000000..2db861b
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/undo/CyUndo.java
@@ -0,0 +1,86 @@
+/*
+ File: CyUndo.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.util.undo;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import javax.swing.*;
+import javax.swing.event.*;
+import javax.swing.undo.*;
+
+import cytoscape.Cytoscape;
+import cytoscape.CytoscapeInit;
+import cytoscape.logger.CyLogger;
+import cytoscape.view.CytoscapeDesktop;
+
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+
+import undo.Undo;
+
+/**
+ * A tiny class for supporting undo in the Cytoscape context. If you
+ * want to post an edit, use CyUndo.getUndoableEditSupport().postEdit(yourEdit).
+ */
+public class CyUndo extends Undo {
+
+ protected static UndoManager undoManager;
+ protected static CyLogger logger = CyLogger.getLogger(CyUndo.class);
+
+ static {
+ undoManager = getUndoManager();
+ undoManager.setLimit(getLimit());
+ new UndoMonitor();
+ }
+
+ private static int getLimit() {
+ int lim;
+ try {
+ lim = Integer.parseInt( CytoscapeInit.getProperties().getProperty("undo.limit") );
+ } catch ( Exception e ) {
+ logger.warn("Non-integer value for property 'undo.limit'", e);
+ lim = 10;
+ }
+
+ if ( lim < 0 )
+ lim = 10;
+
+ return lim;
+ }
+}
+
diff --git a/application/src/main/java/cytoscape/util/undo/RedoAction.java b/application/src/main/java/cytoscape/util/undo/RedoAction.java
new file mode 100644
index 0000000..c8c9ea4
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/undo/RedoAction.java
@@ -0,0 +1,102 @@
+/*
+ File: RedoAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.util.undo;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import javax.swing.*;
+import javax.swing.event.*;
+import javax.swing.undo.*;
+
+import cytoscape.util.CytoscapeAction;
+import cytoscape.logger.CyLogger;
+
+/**
+ * An action that calls redo for the most recent edit in the
+ * undoable edit stack.
+ */
+public class RedoAction extends CytoscapeAction {
+ private static CyLogger logger = CyLogger.getLogger(RedoAction.class);
+
+ /**
+ * Constructs the action.
+ */
+ public RedoAction() {
+ super("Redo");
+ setAcceleratorCombo(KeyEvent.VK_Y, ActionEvent.CTRL_MASK);
+ setPreferredMenu("Edit");
+ setEnabled(true);
+ }
+
+ /**
+ * Tries to run redo() on the top edit of the edit stack.
+ * @param e The action event that triggers this method call.
+ */
+ public void actionPerformed(ActionEvent e) {
+ try {
+ if ( CyUndo.undoManager.canRedo() )
+ CyUndo.undoManager.redo();
+ } catch (CannotUndoException ex) {
+ logger.warn("Unable to redo: " + ex.getMessage(), ex);
+ }
+ }
+
+ /**
+ * Called when the menu that contains this action is clicked on.
+ * @param e The menu event that triggers this method call.
+ */
+ public void menuSelected(MenuEvent e) {
+ if (CyUndo.undoManager.canRedo()) {
+ setEnabled(true);
+ putValue(Action.NAME, CyUndo.undoManager.getRedoPresentationName());
+ } else {
+ setEnabled(false);
+ putValue(Action.NAME, "Redo");
+ }
+ }
+
+ /**
+ * Called when a menu is hidden once you click on a menu item or elsewhere.
+ * This is a hack to make sure that redo is available via the accelerator
+ * keys at all times.
+ * @param e The menu event that triggers this method call.
+ */
+ public void menuDeselected(MenuEvent e) {
+ setEnabled(true);
+ }
+}
diff --git a/application/src/main/java/cytoscape/util/undo/UndoAction.java b/application/src/main/java/cytoscape/util/undo/UndoAction.java
new file mode 100644
index 0000000..44794a1
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/undo/UndoAction.java
@@ -0,0 +1,102 @@
+/*
+ File: UndoAction.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.util.undo;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import javax.swing.*;
+import javax.swing.event.*;
+import javax.swing.undo.*;
+
+import cytoscape.util.CytoscapeAction;
+import cytoscape.logger.CyLogger;
+
+/**
+ * An action that calls undo for the most recent edit in the
+ * undoable edit stack.
+ */
+public class UndoAction extends CytoscapeAction {
+ private static CyLogger logger = CyLogger.getLogger(UndoAction.class);
+
+ /**
+ * Constructs the action.
+ */
+ public UndoAction() {
+ super("Undo");
+ setAcceleratorCombo(KeyEvent.VK_Z, ActionEvent.CTRL_MASK);
+ setPreferredMenu("Edit");
+ setEnabled(true);
+ }
+
+ /**
+ * Tries to run undo() on the top edit of the edit stack.
+ * @param e The action event that triggers this method call.
+ */
+ public void actionPerformed(ActionEvent e) {
+ try {
+ if ( CyUndo.undoManager.canUndo() )
+ CyUndo.undoManager.undo();
+ } catch (CannotUndoException ex) {
+ logger.warn("Unable to undo: " + ex.getMessage(), ex);
+ }
+ }
+
+ /**
+ * Called when the menu that contains this action is clicked on.
+ * @param e The menu event that triggers this method call.
+ */
+ public void menuSelected(MenuEvent e) {
+ if (CyUndo.undoManager.canUndo()) {
+ setEnabled(true);
+ putValue(Action.NAME, CyUndo.undoManager.getUndoPresentationName());
+ } else {
+ setEnabled(false);
+ putValue(Action.NAME, "Undo");
+ }
+ }
+
+ /**
+ * Called when a menu is hidden once you click on a menu item or elsewhere.
+ * This is a hack to make sure that undo is available via the accelerator
+ * keys at all times.
+ * @param e The menu event that triggers this method call.
+ */
+ public void menuDeselected(MenuEvent e) {
+ setEnabled(true);
+ }
+}
diff --git a/application/src/main/java/cytoscape/util/undo/UndoMonitor.java b/application/src/main/java/cytoscape/util/undo/UndoMonitor.java
new file mode 100644
index 0000000..93d0623
--- /dev/null
+++ b/application/src/main/java/cytoscape/util/undo/UndoMonitor.java
@@ -0,0 +1,78 @@
+/*
+ File: UndoMonitor.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.util.undo;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import javax.swing.*;
+import javax.swing.event.*;
+import javax.swing.undo.*;
+
+import cytoscape.Cytoscape;
+import cytoscape.view.CytoscapeDesktop;
+
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+
+
+/**
+ * This class monitors the undoable edit stack and implements whatever
+ * discard policy we might have. Currently, we discard all edits if
+ * the network view focus changes.
+ */
+class UndoMonitor implements PropertyChangeListener {
+
+ UndoMonitor() {
+ Cytoscape.getDesktop().getSwingPropertyChangeSupport().addPropertyChangeListener(
+ CytoscapeDesktop.NETWORK_VIEW_FOCUSED,this);
+ }
+
+
+ /**
+ * This method listens for property change events and discards all edits
+ * if it hears are NETWORK_VIEW_FOCUSED event.
+ *
+ * @param e The change event.
+ */
+ public void propertyChange(PropertyChangeEvent e) {
+ if (e.getPropertyName().equals(CytoscapeDesktop.NETWORK_VIEW_FOCUSED)) {
+ CyUndo.undoManager.discardAllEdits();
+ }
+ }
+}
+
diff --git a/application/src/main/java/cytoscape/view/BasicGraphViewHandler.java b/application/src/main/java/cytoscape/view/BasicGraphViewHandler.java
new file mode 100644
index 0000000..ec22115
--- /dev/null
+++ b/application/src/main/java/cytoscape/view/BasicGraphViewHandler.java
@@ -0,0 +1,743 @@
+/*
+ File: BasicGraphViewHandler.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+/**
+ * @author Iliana Avila-Campillo <iavila at systemsbiology.org>
+ * @version %I%, %G%
+ * @since 2.0
+ */
+package cytoscape.view;
+
+import cern.colt.list.IntArrayList;
+
+import giny.model.Edge;
+import giny.model.GraphPerspective;
+import giny.model.GraphPerspectiveChangeEvent;
+import giny.model.Node;
+
+import giny.view.EdgeView;
+import giny.view.GraphView;
+import giny.view.NodeView;
+
+import java.util.*;
+
+import cytoscape.logger.CyLogger;
+
+
+/**
+ * A basic <code>GraphViewHandler</code> that simply reflects <code>GraphPerspective</code>
+ * changes on a given <code>GraphView</code>
+ */
+public class BasicGraphViewHandler implements GraphViewHandler {
+ /**
+ * Constructor
+ */
+ public BasicGraphViewHandler() {
+ } //BasicGraphViewHandler
+
+ /**
+ * Handles the event as desired by updating the given <code>giny.view.GraphView</code>.
+ *
+ * @param event the event to handle
+ * @param graph_view the <code>giny.view.GraphView</code> that views the
+ * <code>giny.model.GraphPerspective</code> that generated the event and that should
+ * be updated as necessary
+ */
+ public void handleGraphPerspectiveEvent(GraphPerspectiveChangeEvent event, GraphView graph_view) {
+ //TODO: Remove
+ //CyLogger.getLogger().info("In BasicGraphViewHandler.handleGraphPerspectiveEvent().");
+ int numTypes = 0; // An event may have more than one type
+
+ // Node Events:
+ if (event.isNodesHiddenType()) {
+ //TODO: Remove
+ //CyLogger.getLogger().info("isNodesHiddenType == " + event.isNodesHiddenType());
+ removeGraphViewNodes(graph_view, event.getHiddenNodeIndices());
+ numTypes++;
+ }
+
+ if (event.isNodesRestoredType()) {
+ //TODO: Remove
+ //CyLogger.getLogger().info("isNodesRestoredType == " + event.isNodesRestoredType());
+ restoreGraphViewNodes(graph_view, event.getRestoredNodeIndices(), true);
+ numTypes++;
+ }
+
+ // A GraphPerspective cannot have selected graph objects (Rowan told me)
+ //if(event.isNodesSelectedType()){
+ //selectGraphViewNodes(graph_view, event.getSelectedNodes());
+ //numTypes++;
+ //}
+
+ // Same as above
+ //if(event.isNodesUnselectedType()){
+ //unselectGraphViewNodes(graph_view, event.getUnselectedNodes());
+ //numTypes++;
+ //}
+
+ // Edge events:
+ if (event.isEdgesHiddenType()) {
+ //TODO: Remove
+ //CyLogger.getLogger().info("isEdgesHiddenType == " + event.isEdgesHiddenType());
+ removeGraphViewEdges(graph_view, event.getHiddenEdgeIndices());
+ numTypes++;
+ }
+
+ if (event.isEdgesRestoredType()) {
+ //TODO: Remove
+ //CyLogger.getLogger().info("isEdgesRestoredType == " + event.isEdgesRestoredType());
+ restoreGraphViewEdges(graph_view, event.getRestoredEdgeIndices());
+ numTypes++;
+ }
+
+ // A GraphPerspective cannot have selected graph objects (Rowan told me)
+ //if(event.isEdgesSelectedType()){
+ //selectGraphViewEdges(graph_view, event.getSelectedEdges());
+ //numTypes++;
+ //}
+
+ // Same as above
+ //if(event.isEdgesUnselectedType()){
+ //unselectGraphViewEdges(graph_view, event.getUnselectedEdges());
+ //numTypes++;
+ //}
+ if (numTypes == 0) {
+ //CyLogger.getLogger().warn("In BasicGraphViewHandler.handleGraphPerspectiveEvent, "
+ //+ "unrecognized event type");
+ return;
+ }
+
+ graph_view.updateView();
+
+ // if ( graph_view instanceof cytoscape.giny.Phoeb*NetworkView ) {
+ // ( ( cytoscape.giny.Phoeb*NetworkView )graph_view ).redrawGraph();
+ // }
+
+ //TODO: Remove
+ //CyLogger.getLogger().info("Leaving BasicGraphViewHandler.handleGraphPerspectiveEvent()." +
+ //" numTypes caught = " + numTypes);
+ } //handleGraphPerspectiveEvent
+
+ /**
+ * It removes the views of the edges in the array from the given <code>giny.view.GraphView</code>
+ * object.
+ *
+ * @param graph_view the <code>giny.view.GraphView</code> object from which edges will be removed
+ * @param edges the edges whose views will be removed
+ * @return an array of edges that were removed
+ */
+
+ // TESTED: Gets an exception because the edges array has references to null.
+ // USE INSTEAD: removeGraphViewEdges(GraphView, int [])
+ static public Edge[] removeGraphViewEdges(GraphView graph_view, Edge[] edges) {
+ //TODO: Remove
+ //CyLogger.getLogger().info("In BasicGraphViewHandler.removeGraphViewEdges()");
+ Set removedEdges = new HashSet();
+
+ for (int i = 0; i < edges.length; i++) {
+ EdgeView edgeView = graph_view.removeEdgeView(edges[i]);
+
+ if (edgeView != null) {
+ removedEdges.add(edges[i]);
+ }
+ } //for i
+ //TODO: Remove
+ //CyLogger.getLogger().info("Leaving BasicGraphViewHandler.removeGraphViewEdges()," + "num removed edges = " + removedEdges.size());
+
+ return (Edge[]) removedEdges.toArray(new Edge[removedEdges.size()]);
+ } //removeGraphViewEdges
+
+ /**
+ * It removes the views of the edges in the array from the given <code>giny.view.GraphView</code>
+ * object.
+ *
+ * @param graph_view the <code>giny.view.GraphView</code> object from which edges will be removed
+ * @param edge_indices the indices of the edges that will be removed
+ * @return an array of edge indices that were removed
+ */
+
+ // TESTED
+ // NOTE: USE THIS INSTEAD OF removeGraphViewEdges (GraphView,Edge[])
+ static public int[] removeGraphViewEdges(GraphView graph_view, int[] edge_indices) {
+ //TODO: Remove
+ //CyLogger.getLogger().info("In BasicGraphViewHandler.removeGraphViewEdges()");
+ IntArrayList removedEdges = new IntArrayList(edge_indices.length);
+
+ for (int i = 0; i < edge_indices.length; i++) {
+ EdgeView edgeView = graph_view.removeEdgeView(edge_indices[i]);
+
+ if (edgeView != null) {
+ removedEdges.add(edge_indices[i]);
+ }
+ } //for i
+
+ removedEdges.trimToSize();
+
+ //TODO: Remove
+ //CyLogger.getLogger().info("Leaving BasicGraphViewHandler.removeGraphViewEdges()," + "num removed edges = " + removedEdges.size());
+ return removedEdges.elements();
+ } //removeGraphViewEdges
+
+ /**
+ * It restores the views of the edges in the array in the given <code>giny.view.GraphView</code>
+ * object
+ *
+ * @param graph_view the <code>giny.view.GraphView</code> object in which edges will be restored
+ * @param edges the edges that will be restored
+ * @return an array of edges that were restored
+ */
+
+ // TESTED
+ static public Edge[] restoreGraphViewEdges(GraphView graph_view, Edge[] edges) {
+ //TODO: Remove
+ //CyLogger.getLogger().info("In BasicGraphViewHandler.restoreGraphViewEdges()");
+ Set restoredEdges = new HashSet();
+
+ for (int i = 0; i < edges.length; i++) {
+ EdgeView edgeView = graph_view.getEdgeView(edges[i]);
+ boolean restored = false;
+
+ if (edgeView == null) {
+ // This means that the restored edge had not been viewed before
+ // by graph_view
+ edgeView = graph_view.addEdgeView(edges[i].getRootGraphIndex());
+
+ if (edgeView != null) {
+ restored = true;
+ }
+ } else {
+ // This means that the restored edge had been viewed by the graph_view
+ // before, so all we need to do is tell the graph_view to re-show it
+ restored = graph_view.showGraphObject(edgeView);
+ }
+
+ if (restored) {
+ restoredEdges.add(edgeView.getEdge());
+ }
+ } //for i
+ //TODO: Remove
+ //CyLogger.getLogger().info("Leaving BasicGraphViewHandler.restoreGraphViewEdges(), "+"num restored edges = " + restoredEdges.size() );
+
+ return (Edge[]) restoredEdges.toArray(new Edge[restoredEdges.size()]);
+ } //restoreGraphViewEdges
+
+ /**
+ * It restores the views of the edges with the given indices in the given
+ * <code>giny.view.GraphView</code> object
+ *
+ * @param graph_view the <code>giny.view.GraphView</code> object in which edges' views
+ * will be restored
+ * @param edge_indices the indices of the edges that will be restored
+ * @return an array of indices of edges that were restored
+ */
+
+ // TODO: What if a connected node is not in the graph view or graph perspective?
+ static public int[] restoreGraphViewEdges(GraphView graph_view, int[] edge_indices) {
+ //TODO: Remove
+ //CyLogger.getLogger().info("In BasicGraphViewHandler.restoreGraphViewEdges()");
+ IntArrayList restoredEdgeIndices = new IntArrayList(edge_indices.length);
+
+ for (int i = 0; i < edge_indices.length; i++) {
+ // TEST: See if the NodeViews of the connected Nodes are in graph_view
+ // TODO: What to do in this case? I would say throw exception.
+ //GraphPerspective graphPerspective = graph_view.getGraphPerspective();
+ //int sourceRootIndex =
+ // graphPerspective.getRootGraphNodeIndex(graphPerspective.getEdgeSourceIndex(edge_indices[i]));
+ //int targetRootIndex =
+ //graphPerspective.getRootGraphNodeIndex(graphPerspective.getEdgeTargetIndex(edge_indices[i]));
+ //NodeView sourceNodeView = graph_view.getNodeView(sourceRootIndex);
+ //NodeView targetNodeView = graph_view.getNodeView(targetRootIndex);
+ //if(sourceNodeView == null){
+ //CyLogger.getLogger().warn("ERROR: Source NodeView for edge "+edge_indices[i]+" is null");
+ //}
+ //if(targetNodeView == null){
+ //CyLogger.getLogger().warn("ERROR: Target NodeView for edge "+edge_indices[i]+" is null");
+ //}
+
+ // The given index can be either RootGraph index or GraphPerspective index
+ EdgeView edgeView = graph_view.getEdgeView(edge_indices[i]);
+ boolean restored = false;
+
+ if (edgeView == null) {
+ // This means that the restored edge had not been viewed before
+ // by graph_view
+ edgeView = graph_view.addEdgeView(edge_indices[i]);
+
+ if (edgeView != null) {
+ restored = true;
+ }
+ } else {
+ // This means that the restored edge had been viewed by the graph_view
+ // before, so all we need to do is tell the graph_view to re-show it
+ restored = graph_view.showGraphObject(edgeView);
+ }
+
+ if (restored) {
+ restoredEdgeIndices.add(edge_indices[i]);
+ }
+ } //for i
+
+ restoredEdgeIndices.trimToSize();
+
+ //TODO: Remove
+ //CyLogger.getLogger().info("Leaving BasicGraphViewHandler.restoreGraphViewEdges(), "+"num restored edges = " + restoredEdgeIndices.size() );
+ return restoredEdgeIndices.elements();
+ } //restoreGraphViewEdges
+
+ /**
+ * It selects the edges in the array in the given <code>giny.view.GraphView</code> object.
+ *
+ * @param graph_view the <code>giny.view.GraphView</code> object in which edges will be selected
+ * @param edges the edges in <code>graph_view</code> that will be selected
+ * @return the edges that were selected
+ */
+ static public Edge[] selectGraphViewEdges(GraphView graph_view, Edge[] edges) {
+ //TODO: Remove
+ //CyLogger.getLogger().info("In BasicGraphViewHandler.selectGraphViewEdges()");
+ Set selectedEdges = new HashSet();
+
+ for (int i = 0; i < edges.length; i++) {
+ EdgeView edgeView = graph_view.getEdgeView(edges[i]);
+
+ if (edgeView != null) {
+ edgeView.setSelected(true);
+ selectedEdges.add(edges[i]);
+ }
+ } //for i
+ //TODO: Remove
+ //CyLogger.getLogger().info("Leaving BasicGraphViewHandler.selectGraphViewEdges()," +"num selected edges = " + selectedEdges.size());
+
+ return (Edge[]) selectedEdges.toArray(new Edge[selectedEdges.size()]);
+ } //selectGraphViewEdges
+
+ /**
+ * It unselects the edges in the array in the given <code>giny.view.GraphView</code> object
+ *
+ * @param graph_view the <code>giny.view.GraphView</code> object in which edges will be unselected
+ * @param edges the edges that will be unselected in <code>graph_view</code>
+ * @return an array of edges that were unselected
+ */
+ static public Edge[] unselectGraphViewEdges(GraphView graph_view, Edge[] edges) {
+ //TODO: Remove
+ //CyLogger.getLogger().info("In BasicGraphViewHandler.unselectGraphViewEdges()");
+ Set unselectedEdges = new HashSet();
+
+ for (int i = 0; i < edges.length; i++) {
+ EdgeView edgeView = graph_view.getEdgeView(edges[i]);
+
+ if (edgeView != null) {
+ edgeView.setSelected(false);
+ unselectedEdges.add(edges[i]);
+ }
+ } //for i
+ //TODO: Remove
+ //CyLogger.getLogger().info("Leaving BasicGraphViewHandler.unselectGraphViewEdges()," +"num unselected edges = " + unselectedEdges.size());
+
+ return (Edge[]) unselectedEdges.toArray(new Edge[unselectedEdges.size()]);
+ } //unselectGraphViewEdges
+
+ /**
+ * It removes the nodes in the array from the given <code>giny.view.GraphView</code> object,
+ * it also removes the connected edges to these nodes (an edge without a connecting node makes
+ * no mathematical sense).
+ *
+ * @param graph_view the <code>giny.view.GraphView</code> object from which nodes will be removed
+ * @param nodes the nodes whose views will be removed from <code>graph_view</code>
+ * @return an array of nodes that were removed
+ */
+
+ // NOTE: GINY automatically hides the edges connected to the nodes in the GraphPerspective
+ // and this hiding fires a hideEdgesEvent, so removeGraphViewEdges will get called on those
+ // edges and we don't need to hide them in this method
+ // TESTED
+ static public Node[] removeGraphViewNodes(GraphView graph_view, Node[] nodes) {
+ //TODO: Remove
+ //CyLogger.getLogger().info("In BasicGraphViewHandler.removeGraphViewNodes()");
+ Set removedNodes = new HashSet();
+
+ for (int i = 0; i < nodes.length; i++) {
+ NodeView nodeView = graph_view.removeNodeView(nodes[i]);
+
+ if (nodeView != null) {
+ removedNodes.add(nodes[i]);
+ }
+ } //for i
+ //TODO: Remove
+ //CyLogger.getLogger().info("Leaving BasicGraphViewHandler.removeGraphViewNodes(), " +"num removed nodes = " + removedNodes.size());
+
+ return (Node[]) removedNodes.toArray(new Node[removedNodes.size()]);
+ } //removeGraphViewNodes
+
+ /**
+ * It removes the views of the nodes with the given indices that are contained in the given
+ * <code>giny.view.GraphView</code> object, it also removes the connected edges to
+ * these nodes (an edge without a connecting node makes no mathematical sense).
+ *
+ * @param graph_view the <code>giny.view.GraphView</code> object from which nodes will be removed
+ * @param node_indices the indices of the nodes that will be removed
+ * @return an array of indices of nodes that were removed
+ */
+
+ // NOTE: GINY automatically hides the edges connected to the nodes in the GraphPerspective
+ // and this hiding fires a hideEdgesEvent, so removeGraphViewEdges will get called on those
+ // edges and we don't need to remove them in this method
+ static public int[] removeGraphViewNodes(GraphView graph_view, int[] node_indices) {
+ //TODO: Remove
+ //CyLogger.getLogger().info("In BasicGraphViewHandler.removeGraphViewNodes()");
+ IntArrayList removedNodesIndices = new IntArrayList(node_indices.length);
+
+ for (int i = 0; i < node_indices.length; i++) {
+ NodeView nodeView = graph_view.removeNodeView(node_indices[i]);
+
+ if (nodeView != null) {
+ removedNodesIndices.add(node_indices[i]);
+ }
+ } //for i
+
+ removedNodesIndices.trimToSize();
+
+ //TODO: Remove
+ //CyLogger.getLogger().info("Leaving BasicGraphViewHandler.removeGraphViewNodes(), " +"num removed nodes = " + removedNodesIndices.size());
+ return removedNodesIndices.elements();
+ } //removeGraphViewNodes
+
+ /**
+ * It restores the views of the nodes in the array in the given
+ * <code>giny.view.GraphView</code> object
+ *
+ * @param graph_view the <code>giny.view.GraphView</code> object in which nodes will be restored
+ * @param nodes the nodes whose views will be restored in <code>graph_view</code>
+ * @param restore_connected_edges whether or not the connected edges to the restored nodes
+ * should also be restored or not (for now this argument is ignored)
+ * @return an array of nodes that were restored
+ */
+
+ // TODO: Depending on restore_connected_edges, restore connected edges or not.
+ // TESTED
+ static public Node[] restoreGraphViewNodes(GraphView graph_view, Node[] nodes,
+ boolean restore_connected_edges) {
+ //TODO: Remove
+ //CyLogger.getLogger().info("In BasicGraphViewHandler.restoreGraphViewNodes()");
+ Set restoredNodes = new HashSet();
+
+ for (int i = 0; i < nodes.length; i++) {
+ NodeView nodeView = graph_view.getNodeView(nodes[i]);
+ boolean restored = false;
+
+ if (nodeView == null) {
+ // This means that the nodes that were restored had never been viewed by
+ // the graph_view, so we need to create a new NodeView.
+ nodeView = graph_view.addNodeView(nodes[i].getRootGraphIndex());
+
+ if (nodeView != null) {
+ restored = true;
+ }
+ } else {
+ // This means that the nodes that were restored had been viewed by the graph_view
+ // before, so all we need to do is tell the graph_view to re-show them
+ restored = graph_view.showGraphObject(nodeView);
+ }
+
+ if (restored) {
+ //TODO: Remove
+ //CyLogger.getLogger().warn("Restored node w/index " + nodes[i].getRootGraphIndex());
+ positionToBarycenter(nodeView);
+ restoredNodes.add(nodeView.getNode());
+ }
+ } //for i
+ //TODO: Remove
+ //CyLogger.getLogger().info("Leaving BasicGraphViewHandler.restoreGraphViewNodes()." +"Total restored nodes == " + restoredNodes.size());
+
+ return (Node[]) restoredNodes.toArray(new Node[restoredNodes.size()]);
+ } //restoreGraphViewNodes
+
+ /**
+ * It restores the views of the nodes with the given indices in the given
+ * <code>giny.view.GraphView</code> object
+ *
+ * @param graph_view the <code>giny.view.GraphView</code> object in which node views will be restored
+ * @param node_indices the indices of the nodes whose views will be restored
+ * @param restore_connected_edges whether or not the connected edges to the restored nodes
+ * should also be restored or not (for now this argument is ignored)
+ * @return an array of indices of the nodes whose views were restored
+ */
+
+ //TODO: Depending on restore_connected_edges, restore connected edges or not.
+ static public int[] restoreGraphViewNodes(GraphView graph_view, int[] node_indices,
+ boolean restore_connected_edges) {
+ //TODO: Remove
+ //CyLogger.getLogger().info("In BasicGraphViewHandler.restoreGraphViewNodes()");
+ IntArrayList restoredNodeIndices = new IntArrayList(node_indices.length);
+
+ for (int i = 0; i < node_indices.length; i++) {
+ NodeView nodeView = graph_view.getNodeView(node_indices[i]);
+ boolean restored = false;
+
+ if (nodeView == null) {
+ // This means that the nodes that were restored had never been viewed by
+ // the graph_view, so we need to create a new NodeView.
+ nodeView = graph_view.addNodeView(node_indices[i]);
+
+ if (nodeView != null) {
+ restored = true;
+ }
+ } else {
+ // This means that the nodes that were restored had been viewed by the graph_view
+ // before, so all we need to do is tell the graph_view to re-show them
+ restored = graph_view.showGraphObject(nodeView);
+ }
+
+ if (restored) {
+ restoredNodeIndices.add(node_indices[i]);
+ positionToBarycenter(nodeView);
+
+ //TODO: Remove
+ //CyLogger.getLogger().warn("NodeView for node index " + node_indices[i] + " was added to graph_view");
+ } else {
+ //TODO: Remove
+ //CyLogger.getLogger().warn("ERROR: NodeView for node index " + node_indices[i] +" was NOT added to graph_view");
+ }
+ } //for i
+
+ restoredNodeIndices.trimToSize();
+
+ //TODO: Remove
+ //CyLogger.getLogger().info("Leaving BasicGraphViewHandler.restoreGraphViewNodes()." +"Showed in graph_view/Restored in GP == " + restoredNodeIndices.size() +"/" + node_indices.length);
+ return restoredNodeIndices.elements();
+ } //restoreGraphViewNodes
+
+ /**
+ * It selects the nodes in the array in the given <code>giny.view.GraphView</code> object.
+ *
+ * @param graph_view the <code>giny.view.GraphView</code> object in which nodes will be selected
+ * @param nodes the nodes in <code>graph_view</code> that will be selected
+ * @return the nodes that were selected
+ */
+ static public Node[] selectGraphViewNodes(GraphView graph_view, Node[] nodes) {
+ //TODO: Remove
+ ////CyLogger.getLogger().info("In BasicGraphViewHandler.selectGraphViewNodes()");
+ Set selectedNodes = new HashSet();
+
+ for (int i = 0; i < nodes.length; i++) {
+ NodeView nodeView = graph_view.getNodeView(nodes[i]);
+
+ if (nodeView != null) {
+ nodeView.setSelected(true);
+ selectedNodes.add(nodes[i]);
+ }
+ } //for i
+ //TODO: Remove
+ //CyLogger.getLogger().info("Leaving BasicGraphViewHandler.selectGraphViewNodes(),"+"num selected nodes = " + selectedNodes.size());
+
+ return (Node[]) selectedNodes.toArray(new Node[selectedNodes.size()]);
+ } //selectGraphViewNodes
+
+ /**
+ * It unselects the nodes in the array in the given <code>giny.view.GraphView</code> object
+ *
+ * @param graph_view the <code>giny.view.GraphView</code> object in which nodes will be unselected
+ * @param nodes the nodes that will be unselected in <code>graph_view</code>
+ * @return an array of nodes that were unselected
+ */
+ static public Node[] unselectGraphViewNodes(GraphView graph_view, Node[] nodes) {
+ //TODO: Remove
+ //CyLogger.getLogger().info("In BasicGraphViewHandler.unselectGraphViewNodes()");
+ Set unselectedNodes = new HashSet();
+
+ for (int i = 0; i < nodes.length; i++) {
+ NodeView nodeView = graph_view.getNodeView(nodes[i]);
+
+ if (nodeView != null) {
+ nodeView.setSelected(false);
+ unselectedNodes.add(nodes[i]);
+ }
+ } //for i
+ //TODO: Remove
+ //CyLogger.getLogger().info("Leaving BasicGraphViewHandler.unselectGraphViewNodes()," +"num unselected nodes = " + unselectedNodes.size());
+
+ return (Node[]) unselectedNodes.toArray(new Node[unselectedNodes.size()]);
+ } //unselectGraphViewNodes
+
+ /**
+ * If the node that node_view represents is a meta-node, then it
+ * positions it at the barycenter of its viewable children nodes.
+ *
+ * @param node_view the <code>giny.view.NodeView</code> that will be positioned
+ * to the barycenter of its children
+ */
+ static public void positionToBarycenter(NodeView node_view) {
+ Node node = node_view.getNode();
+ int rootIndex = node.getRootGraphIndex();
+ GraphView graphView = node_view.getGraphView();
+ GraphPerspective gp = graphView.getGraphPerspective();
+
+ int[] childrenNodeIndices = gp.getNodeMetaChildIndicesArray(rootIndex);
+
+ if ((childrenNodeIndices == null) || (childrenNodeIndices.length == 0)) {
+ return;
+ }
+
+ GraphPerspective childGP = node.getGraphPerspective();
+
+ if ((childGP == null) || (childGP.getNodeCount() == 0)) {
+ throw new IllegalStateException("Node " + node.getIdentifier()
+ + " has a non-empty array "
+ + " of children-node indices, but, it has no child GraphPerspective");
+ }
+
+ List childrenNodeList = childGP.nodesList();
+ Iterator it = childrenNodeList.iterator();
+ double x = 0.0;
+ double y = 0.0;
+ double viewableChildren = 0;
+
+ while (it.hasNext()) {
+ Node childNode = (Node) it.next();
+
+ if (gp.containsNode(childNode, false)) {
+ NodeView childNV = graphView.getNodeView(childNode.getRootGraphIndex());
+
+ if (childNV != null) {
+ x += childNV.getXPosition();
+ y += childNV.getYPosition();
+ viewableChildren++;
+ }
+ }
+ } //while it
+
+ if (viewableChildren != 0) {
+ x /= viewableChildren;
+ y /= viewableChildren;
+ node_view.setXPosition(x);
+ node_view.setYPosition(y);
+ }
+ } //positionToBarycenter
+
+ /**
+ * Updates the given graph_view to contain node and edge visual representations
+ * of only nodes and edges that are in its <code>GraphPerspective</code>
+ *
+ * @see GraphViewController#resumeListening()
+ * @see GraphViewController#resumeListening(GraphView)
+ */
+ public void updateGraphView(GraphView graph_view) {
+ GraphPerspective graphPerspective = graph_view.getGraphPerspective();
+
+ IntArrayList gpNodeIndices = new IntArrayList(graphPerspective.getNodeIndicesArray());
+ IntArrayList gpEdgeIndices = new IntArrayList(graphPerspective.getEdgeIndicesArray());
+
+ IntArrayList gvNodeIndices = new IntArrayList(graph_view.getNodeViewCount());
+ IntArrayList gvEdgeIndices = new IntArrayList(graph_view.getEdgeViewCount());
+
+ // Obtain a list of nodes' root indices that are represented in graph_view
+ Iterator it = graph_view.getNodeViewsIterator();
+
+ while (it.hasNext()) {
+ NodeView nodeView = (NodeView) it.next();
+ Node gvNode = nodeView.getNode();
+
+ if (gvNode == null) {
+ CyLogger.getLogger().warn("Node for nodeView is null (nodeView = " + nodeView + ")");
+
+ continue;
+ }
+
+ int nodeIndex = gvNode.getRootGraphIndex();
+ gvNodeIndices.add(nodeIndex);
+ } // while there are more graph view nodes
+
+ // Obtain a list of edges that are represented in graph_view,
+ // and remove EdgeViews that are no longer in graph_perspective
+ it = graph_view.getEdgeViewsIterator();
+
+ while (it.hasNext()) {
+ EdgeView edgeView = (EdgeView) it.next();
+ Edge gvEdge = edgeView.getEdge();
+
+ if (gvEdge == null) {
+ CyLogger.getLogger().warn("Edge for edgeView is null (edgeView = " + edgeView + ")");
+
+ continue;
+ }
+
+ int edgeIndex = gvEdge.getRootGraphIndex();
+ gvEdgeIndices.add(edgeIndex);
+ } // while there are more graph view edges
+
+ // Make sure that graph_view represents all nodes that are
+ // currently in graphPerspective
+ for (int i = 0; i < gpNodeIndices.size(); i++) {
+ int nodeIndex = gpNodeIndices.getQuick(i);
+ NodeView nodeView = graph_view.getNodeView(nodeIndex);
+
+ if (nodeView == null) {
+ graph_view.addNodeView(nodeIndex);
+ } else {
+ graph_view.showGraphObject(nodeView);
+ }
+ } // for each graphPerspective node
+
+ // Make sure that graph_view represents all edges that are
+ // currently in graphPerspective
+ for (int i = 0; i < gpEdgeIndices.size(); i++) {
+ int edgeIndex = gpEdgeIndices.getQuick(i);
+ EdgeView edgeView = graph_view.getEdgeView(edgeIndex);
+
+ if (edgeView == null) {
+ graph_view.addEdgeView(edgeIndex);
+ } else {
+ graph_view.showGraphObject(edgeView);
+ }
+ } // for each GraphPerspective edge
+
+ // Remove from graph_view all edge representations that are not in graphPerspective
+ gvEdgeIndices.removeAll(gpEdgeIndices);
+ gvEdgeIndices.trimToSize();
+
+ for (int i = 0; i < gvEdgeIndices.size(); i++) {
+ graph_view.removeEdgeView(gvEdgeIndices.getQuick(i));
+ } // for each edge that is in graph_view but that is not in graphPerspective
+
+ // Remove from graph_view all node representations that are not in graphPerspective
+ gvNodeIndices.removeAll(gpNodeIndices);
+ gvNodeIndices.trimToSize();
+
+ for (int i = 0; i < gvNodeIndices.size(); i++) {
+ graph_view.removeNodeView(gvNodeIndices.getQuick(i));
+ } // for each node that is in graph_view but that is not in graphPerspective
+ } //updateGraphview
+} //classs BasicGraphViewHandler
diff --git a/application/src/main/java/cytoscape/view/BirdsEyeViewHandler.java b/application/src/main/java/cytoscape/view/BirdsEyeViewHandler.java
new file mode 100644
index 0000000..d40b66f
--- /dev/null
+++ b/application/src/main/java/cytoscape/view/BirdsEyeViewHandler.java
@@ -0,0 +1,149 @@
+/*
+ File: BirdsEyeViewHandler.java
+
+ Copyright (c) 2006, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.view;
+
+import java.awt.Component;
+import java.awt.Dimension;
+import java.awt.event.ComponentEvent;
+import java.awt.event.ComponentListener;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+
+import javax.swing.JDesktopPane;
+import javax.swing.JInternalFrame;
+
+import cytoscape.Cytoscape;
+import ding.view.BirdsEyeView;
+import ding.view.DGraphView;
+
+/**
+ * This class handles the creation of the BirdsEyeView navigation object
+ * and handles the events which change view seen.
+ */
+class BirdsEyeViewHandler implements PropertyChangeListener {
+ final BirdsEyeView bev;
+ FrameListener frameListener = new FrameListener();
+
+ /**
+ * Creates a new BirdsEyeViewHandler object.
+ * @param desktopPane The JDesktopPane of the NetworkViewManager. Can be null.
+ */
+ BirdsEyeViewHandler(Component desktopPane) {
+ bev = new BirdsEyeView((DGraphView) Cytoscape.getCurrentNetworkView(), desktopPane) {
+ public Dimension getMinimumSize() {
+ return new Dimension(180, 180);
+ }
+
+ public Dimension getMaximumSize() {
+ return new Dimension(180, 180);
+ }
+
+ public Dimension getPreferredSize() {
+ return new Dimension(180, 180);
+ }
+ };
+
+ if (desktopPane != null)
+ desktopPane.addComponentListener(new DesktopListener());
+ }
+
+ /**
+ * Listens for NETWORK_VIEW_FOCUSED, NETWORK_VIEW_FOCUS, NETWORK_VIEW_DESTROYED,
+ * and CYTOSCAPE_INITIALIZED events and changes the network view accordingly.
+ *
+ * @param e The event triggering this method.
+ */
+ public void propertyChange(PropertyChangeEvent e) {
+ if (CytoscapeDesktop.NETWORK_VIEW_FOCUSED.equals(e.getPropertyName())
+ || (CytoscapeDesktop.NETWORK_VIEW_FOCUS.equals(e.getPropertyName()))
+ || (CytoscapeDesktop.NETWORK_VIEW_DESTROYED.equals(e.getPropertyName()))
+ || (Cytoscape.CYTOSCAPE_INITIALIZED.equals(e.getPropertyName()))) {
+ bev.changeView((DGraphView) Cytoscape.getCurrentNetworkView());
+ }
+
+ // Add the frameListener to the currently focused view if it
+ // doesn't already have one.
+ if (CytoscapeDesktop.NETWORK_VIEW_FOCUSED.equals(e.getPropertyName()))
+ {
+ JDesktopPane desktopPane = Cytoscape.getDesktop().getNetworkViewManager().getDesktopPane();
+ if (desktopPane == null)
+ return;
+
+ JInternalFrame frame = desktopPane.getSelectedFrame();
+ if (frame == null)
+ return;
+
+ boolean hasListener = false;
+ ComponentListener[] listeners = frame.getComponentListeners();
+ for(int i = 0; i < listeners.length; i++)
+ if (listeners[i] == frameListener)
+ hasListener = true;
+
+ if (!hasListener)
+ frame.addComponentListener(frameListener);
+ }
+ }
+
+ /**
+ * Returns a birds eye view component.
+ * @return The component that contains the birds eye view.
+ */
+ Component getBirdsEyeView() {
+ return bev;
+ }
+
+ /**
+ * Repaint a JInternalFrame whenever it is moved.
+ */
+ class FrameListener implements ComponentListener
+ {
+ public void componentHidden(ComponentEvent e) {}
+ public void componentMoved(ComponentEvent e)
+ {
+ bev.repaint();
+ }
+ public void componentResized(ComponentEvent e) {}
+ public void componentShown(java.awt.event.ComponentEvent e) {}
+ }
+
+ /**
+ * Repaint the JDesktopPane whenever its size has changed.
+ */
+ class DesktopListener implements ComponentListener
+ {
+ public void componentHidden(ComponentEvent e) {}
+ public void componentMoved(ComponentEvent e) {}
+ public void componentResized(ComponentEvent e)
+ {
+ bev.repaint();
+ }
+ public void componentShown(java.awt.event.ComponentEvent e) {}
+ }
+}
diff --git a/application/src/main/java/cytoscape/view/ColumnTypes.java b/application/src/main/java/cytoscape/view/ColumnTypes.java
new file mode 100644
index 0000000..9d84156
--- /dev/null
+++ b/application/src/main/java/cytoscape/view/ColumnTypes.java
@@ -0,0 +1,27 @@
+package cytoscape.view;
+
+import javax.swing.Icon;
+
+import cytoscape.util.swing.TreeTableModel;
+
+public enum ColumnTypes {
+ NETWORK("Network", TreeTableModel.class), NETWORK_ICONS("Overview",
+ Icon.class), NODES("Nodes", String.class), EDGES("Edges",
+ String.class);
+
+ private final String displayName;
+ private final Class<?> type;
+
+ private ColumnTypes(final String displayName, final Class<?> type) {
+ this.displayName = displayName;
+ this.type = type;
+ }
+
+ public Class<?> getType() {
+ return type;
+ }
+
+ public String getDisplayName() {
+ return displayName;
+ }
+}
diff --git a/application/src/main/java/cytoscape/view/CyDesktopManager.java b/application/src/main/java/cytoscape/view/CyDesktopManager.java
new file mode 100644
index 0000000..065e71e
--- /dev/null
+++ b/application/src/main/java/cytoscape/view/CyDesktopManager.java
@@ -0,0 +1,323 @@
+/*
+ File: CyNodeView.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.view;
+
+import javax.swing.JDesktopPane;
+import javax.swing.JInternalFrame;
+import cytoscape.Cytoscape;
+import java.awt.Dimension;
+
+/**
+ *
+ */
+public class CyDesktopManager {
+
+ public static enum Arrange {
+ GRID,CASCADE,HORIZONTAL,VERTICAL,DEFAULT
+ }
+ public static int MINIMUM_WIN_WIDTH = 200;
+ public static int MINIMUM_WIN_HEIGHT = 200;
+
+ public static int DEFAULT_WIN_WIDTH = 400;
+ public static int DEFAULT_WIN_HEIGHT = 400;
+
+ protected static JDesktopPane desktop;
+ private CyDesktopManager() {
+ desktop = Cytoscape.getDesktop().getNetworkViewManager().getDesktopPane();
+ }
+
+ //Closes all open windows
+ public void closeAllWindows() {
+ JInternalFrame[] allFrames = desktop.getAllFrames();
+ for (int i= allFrames.length -1; i>=0; i--) {
+ allFrames[i].dispose();
+ }
+ }
+
+ // Implementation of grid layout algorithm
+ // gridLayout -- an int array-- int[i] holds the number of row for column i
+ private static void getGridLayout(final int pTotal, final int pCol, final int pRow, int[] gridLayout) {
+ if (pTotal > pRow) {
+ int row = -1;
+ if (pTotal%pCol == 0) {
+ row = pTotal/pCol;
+ gridLayout[pCol-1] = row;
+ }
+ else {
+ row = pRow;
+ gridLayout[pCol-1] = pRow;
+ }
+ getGridLayout(pTotal-row, pCol-1,row, gridLayout);
+ }
+ else {
+ gridLayout[0] = pTotal;
+ }
+ }
+
+
+ // Arrange all windows in the desktop according to the given style
+ public static void arrangeFrames(Arrange pStyle) {
+ if (desktop == null)
+ new CyDesktopManager();
+
+ final Dimension desktopSize = desktop.getSize();
+
+ final JInternalFrame[] allFrames = desktop.getAllFrames();
+
+ int frameCount = allFrames.length;
+ if ( frameCount == 0)
+ return;
+
+ if (pStyle == Arrange.CASCADE) {
+ int delta_x = 20;
+ int delta_y = 20;
+ int delta_block = 50;
+
+ int[] x = new int[frameCount];
+ int[] y = new int[frameCount];
+ int[] w = new int[frameCount];
+ int[] h = new int[frameCount];
+ x[0] = 0; y[0] = 0; w[0] = 0; h[0] =0;
+ int width = 0;
+ int height = 0;
+
+ boolean multiBlock = false;
+ int blockSize =0;
+ for (int i=1; i<frameCount; i++) {
+ blockSize++;
+ x[i] = x[i-1] + delta_x;
+ y[i] = y[i-1] + delta_y;
+
+ if (desktopSize.height - y[i]<MINIMUM_WIN_HEIGHT) {
+ y[i] =0;
+ multiBlock = true;
+ }
+ if (desktopSize.width - x[i]<MINIMUM_WIN_WIDTH) {
+ x[i] = x[i-1];
+ }
+
+ // Determine the w,h for the previous block and start of another block
+ if (y[i]==0 && multiBlock) {
+ // The first block
+ if (i == blockSize) {
+ width = desktopSize.width - x[i-1];
+ height = desktopSize.height - y[i-1];
+ }
+
+ // The blocks other than the first (i.e. 2nd, 3rd, 4th, ...)
+ if (i > blockSize) {
+ //try to use the same (w, h) as previous block
+ width = w[i-blockSize -1];
+ height = h[i-blockSize -1];
+
+ if (desktopSize.width - x[i-1] < width) {
+ width = desktopSize.width - x[i-1];
+ if (width < MINIMUM_WIN_WIDTH) {
+ width = MINIMUM_WIN_WIDTH;
+ }
+ }
+ if (desktopSize.height - y[i-1]<MINIMUM_WIN_HEIGHT) {
+ height = MINIMUM_WIN_HEIGHT;
+ }
+ }
+
+ // Set width the same for the whole block
+ for (int j=0; j< blockSize; j++) {
+ w[i-j-1] = width;
+ h[i-j-1] = height;
+ }
+
+ //start of another block
+ x[i] = x[i-blockSize] + delta_block;
+ if (x[i] > (desktopSize.width - delta_x * blockSize - MINIMUM_WIN_WIDTH)) {
+ x[i] = x[i-blockSize];
+ }
+ blockSize =0;
+ }
+ }
+
+ // Handle the last block
+ if (!multiBlock) { // single block
+ for (int i = 0; i < frameCount; i++) {
+ w[frameCount-1-i] = desktopSize.width - x[frameCount - 1];
+ h[frameCount-1-i] = desktopSize.height - y[frameCount - 1];
+
+ if (desktopSize.width - x[frameCount-1-i]<MINIMUM_WIN_WIDTH) {
+ w[frameCount-1-i] = MINIMUM_WIN_WIDTH;
+ }
+ if (desktopSize.height - y[frameCount-1-i]<MINIMUM_WIN_HEIGHT) {
+ h[frameCount-1-i] = MINIMUM_WIN_HEIGHT;
+ }
+ }
+ }
+ else { //case for multiBlock
+ //try to use the same (w, h) as previous block
+ width = w[frameCount-blockSize -1];
+ height = h[frameCount-blockSize -1];
+
+ if (desktopSize.width - x[frameCount-1] < width) {
+ width = desktopSize.width - x[frameCount-1];
+ if (width < MINIMUM_WIN_WIDTH) {
+ width = MINIMUM_WIN_WIDTH;
+ }
+ }
+ if (desktopSize.height - y[frameCount-1]<MINIMUM_WIN_HEIGHT) {
+ height = MINIMUM_WIN_HEIGHT;
+ }
+
+ for (int i = 0; i < blockSize; i++) {
+ w[frameCount-1-i] = width;
+ h[frameCount-1-i] = height;
+ }
+ }
+
+ if (desktopSize.height - MINIMUM_WIN_HEIGHT < delta_y ) { // WinHeight is too small, This is a special case
+ double delta_x1 = ((double)(desktopSize.width - MINIMUM_WIN_WIDTH))/(frameCount-1);
+ for (int i = 0; i < frameCount; i++) {
+ x[i] = (int) Math.ceil( i * delta_x1);
+ y[i] =0;
+ w[i] = MINIMUM_WIN_WIDTH;
+ h[i] = MINIMUM_WIN_HEIGHT;
+ }
+ }
+
+ //Arrange all frames on the screen
+ for (int i=0; i<frameCount; i++) {
+ allFrames[frameCount-1-i].setBounds(x[i], y[i], w[i], h[i]);
+ }
+ }
+ else if (pStyle == Arrange.GRID) {
+ // Determine the max_col and max_row for grid layout
+ int maxCol = (new Double(Math.ceil(Math.sqrt(frameCount)))).intValue();
+ int maxRow = maxCol;
+ while (true) {
+ if (frameCount <= maxCol*(maxRow -1)) {
+ maxRow--;
+ continue;
+ }
+ break;
+ }
+
+ // Calculate frame layout on the screen, i.e. the number of frames for each column
+ int[] gridLayout = new int[maxCol];
+ getGridLayout(frameCount, maxCol, maxRow, gridLayout);
+
+ // Apply the layout on screen
+ int w = desktopSize.width/maxCol;
+ int curFrame = frameCount -1;
+ for (int col=maxCol-1; col>=0; col--) {
+ int h = desktopSize.height/gridLayout[col];
+
+ for (int i=0; i< gridLayout[col]; i++) {
+ int x = col * w;
+ int y = (gridLayout[col]-i-1)* h;
+ allFrames[curFrame--].setBounds(x, y, w, h);
+ }
+ }
+ }
+ else if (pStyle == Arrange.HORIZONTAL) {
+ int x = 0;
+ int y = 0;
+ int w = desktopSize.width;
+ int h = desktopSize.height/frameCount;
+ if (h < MINIMUM_WIN_HEIGHT ) {
+ h = MINIMUM_WIN_HEIGHT;
+ }
+
+ double delta_y = 0;
+ if (frameCount > 1) {
+ if (h < MINIMUM_WIN_HEIGHT) {
+ delta_y = ((double)(desktopSize.height - MINIMUM_WIN_HEIGHT))/(frameCount-1);
+ }
+ else {
+ delta_y = ((double)(desktopSize.height))/(frameCount);
+ }
+ }
+
+ for (int i=0; i< frameCount; i++) {
+ y = (int)(delta_y * i);
+ if (y> desktopSize.height - MINIMUM_WIN_HEIGHT) {
+ y = desktopSize.height - MINIMUM_WIN_HEIGHT;
+ }
+ allFrames[frameCount-i-1].setBounds(x, y, w, h);
+ }
+ }
+ else if (pStyle == Arrange.VERTICAL) {
+ int x = 0;
+ int y = 0;
+ int w = desktopSize.width/frameCount;
+ int h = desktopSize.height;
+
+ if (w < MINIMUM_WIN_WIDTH) {
+ w = MINIMUM_WIN_WIDTH;
+ }
+
+ double delta_x = 0;
+ if (frameCount > 1) {
+ if (w < MINIMUM_WIN_WIDTH) {
+ delta_x = ((double)(desktopSize.width - MINIMUM_WIN_WIDTH))/(frameCount-1);
+ }
+ else {
+ delta_x = ((double)desktopSize.width)/frameCount;
+ }
+ }
+
+ for (int i=0; i< frameCount; i++) {
+ x = (int)(delta_x * i);
+ if (x > desktopSize.width - MINIMUM_WIN_WIDTH) {
+ x = desktopSize.width - MINIMUM_WIN_WIDTH;
+ }
+ allFrames[frameCount-i-1].setBounds(x, y, w, h);
+ }
+ }
+ else if (pStyle == Arrange.DEFAULT) {
+ int x = 0;
+ int y = 0;
+ int w = DEFAULT_WIN_WIDTH;
+ int h = DEFAULT_WIN_HEIGHT;
+
+ for (int i=0; i< frameCount; i++) {
+ allFrames[frameCount-i-1].setBounds(x, y, w, h);
+ }
+ }
+
+ // Clean up.
+ System.gc();
+ }
+
+}
+
diff --git a/application/src/main/java/cytoscape/view/CyEdgeView.java b/application/src/main/java/cytoscape/view/CyEdgeView.java
new file mode 100644
index 0000000..786d65c
--- /dev/null
+++ b/application/src/main/java/cytoscape/view/CyEdgeView.java
@@ -0,0 +1,44 @@
+/*
+ File: CyEdgeView.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.view;
+
+
+/**
+ *
+ */
+public interface CyEdgeView extends giny.view.EdgeView {
+}
diff --git a/application/src/main/java/cytoscape/view/CyHelpBroker.java b/application/src/main/java/cytoscape/view/CyHelpBroker.java
new file mode 100644
index 0000000..4429e27
--- /dev/null
+++ b/application/src/main/java/cytoscape/view/CyHelpBroker.java
@@ -0,0 +1,159 @@
+/*
+ File: CyHelpBroker.java
+
+ Copyright (c) 2006, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.view;
+
+
+import cytoscape.logger.CyLogger;
+import cytoscape.Cytoscape;
+
+import java.net.URL;
+import java.net.URLClassLoader;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.StringTokenizer;
+
+import javax.help.HelpBroker;
+import javax.help.HelpSet;
+
+import java.awt.Component;
+import java.awt.event.ActionListener;
+import java.awt.event.ActionEvent;
+import javax.swing.JOptionPane;
+
+import javax.help.CSH;
+
+
+/**
+ * This class creates the Cytoscape Help Broker for managing the JavaHelp system
+ * and help set access
+ */
+public class CyHelpBroker {
+ private static HelpBroker hb;
+ private static HelpSet masterHelpSet;
+ private static CSH.DisplayHelpFromFocus csh;
+ private static ActionListener actionListener;
+ private static final String HELP_RESOURCE = "/cytoscape/help/jhelpset.hs";
+ private static final CyLogger logger = CyLogger.getLogger(CyHelpBroker.class);
+
+ static {
+ try {
+ masterHelpSet = new HelpSet(null, CyHelpBroker.class.getResource(HELP_RESOURCE));
+ hb = masterHelpSet.createHelpBroker();
+ hb.setCurrentID("Cytoscape User Manual");
+ csh = new CSH.DisplayHelpFromFocus(hb);
+ actionListener = new SensibleActionListener();
+ } catch (Exception e) {
+ logger.warning("HelpSet " + HELP_RESOURCE + " not loaded.", e);
+ }
+ }
+
+ /**
+ * Creates a new CyHelpBroker object.
+ */
+ private CyHelpBroker() { }
+
+ /**
+ * Returns the HelpBroker.
+ *
+ * @return the HelpBroker.
+ */
+ public static HelpBroker getHelpBroker() {
+ return hb;
+ }
+
+ /**
+ * Returns the HelpSet.
+ *
+ * @return the HelpSet.
+ */
+ public static HelpSet getHelpSet() {
+ return masterHelpSet;
+ }
+
+ /**
+ * @return true if we successfully added the help set, else false
+ */
+ public static boolean addHelpSet(final HelpSet newHelpSet) {
+ try {
+ masterHelpSet.add(newHelpSet);
+ return true;
+ } catch (final Exception e) {
+ return false;
+ }
+ }
+
+ /**
+ * Removes a help set that was previously added with addHelpSet().
+ *
+ * @return true if "hs" has been successfully removed, false otherwise
+ */
+ public static boolean removeHelpSet(final HelpSet hs) {
+ return masterHelpSet.remove(hs);
+ }
+
+
+ /**
+ * Provides access to an ActionListener that pops up a help dialog. To enable,
+ * for example, a help button, you would simple add the available action as a
+ * ActionListener to the button.
+ * <br/>
+ * <pre>
+ * JButton helpButton = new JButton("Help");
+ * helpButton.addActionListener( CyHelpBroker.getHelpActionListener() );
+ * </pre>
+ */
+ public static ActionListener getHelpActionListener() {
+ return actionListener;
+ }
+
+ /**
+ * An ActionListener that wraps the available CSH ActionListener and tries
+ * to gracefully handle exceptions.
+ */
+ private static class SensibleActionListener implements ActionListener {
+ public void actionPerformed(ActionEvent ae) {
+ try {
+ csh.actionPerformed(ae);
+ } catch (Exception e) {
+ logger.warn("Couldn't display help for event: " + ae.toString(), e);
+ // Try again with a fake action with a different source, a source
+ // that has help defined for it.
+ try {
+ csh.actionPerformed( new ActionEvent( Cytoscape.getDesktop(),
+ ae.getID(), ae.getActionCommand(),
+ ae.getWhen(), ae.getModifiers() ) );
+ } catch (Exception ex) {
+ logger.error("REALLY Couldn't display help for previous event", ex);
+ }
+ }
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/view/CyMenus.java b/application/src/main/java/cytoscape/view/CyMenus.java
new file mode 100644
index 0000000..f867a0f
--- /dev/null
+++ b/application/src/main/java/cytoscape/view/CyMenus.java
@@ -0,0 +1,690 @@
+/*
+ File: CyMenus.java
+
+ Copyright (c) 2006, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.view;
+
+
+import giny.view.GraphViewChangeEvent;
+import giny.view.GraphViewChangeListener;
+
+import java.awt.Component;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseWheelEvent;
+import java.awt.event.MouseWheelListener;
+import java.awt.event.ActionListener;
+import java.awt.event.ActionEvent;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.net.URL;
+import java.util.List;
+
+import javax.swing.Action;
+import javax.swing.ImageIcon;
+import javax.swing.JButton;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JSeparator;
+
+import org.jdesktop.swingx.JXTitledSeparator;
+
+import cytoscape.Cytoscape;
+import cytoscape.CytoscapeInit;
+import cytoscape.actions.*;
+import cytoscape.layout.ui.LayoutMenuManager;
+import cytoscape.layout.ui.SettingsAction;
+import cytoscape.util.CytoscapeAction;
+import cytoscape.util.CytoscapeMenuBar;
+import cytoscape.util.CytoscapeToolBar;
+import cytoscape.util.RecentlyOpenedTracker;
+import cytoscape.util.undo.RedoAction;
+import cytoscape.util.undo.UndoAction;
+import cytoscape.util.swing.SwingMenuSorter;
+import cytoscape.view.cytopanels.CytoPanelName;
+import cytoscape.layout.CyLayoutAlgorithm;
+import cytoscape.layout.CyLayouts;
+
+
+/**
+ * Creates the menu and tool bars for a Cytoscape window object. It
+ * also provides access to individual menus and items.<BR>
+ * <p>
+ * AddAction takes one more optional argument to specify index. Plugin
+ * writers can use this function to specify the location of the menu item.
+ * </p>
+ */
+public class CyMenus implements GraphViewChangeListener, PropertyChangeListener {
+ boolean menusInitialized = false;
+
+ CytoscapeMenuBar menuBar;
+ CytoscapeToolBar toolBar;
+
+ JMenu fileMenu;
+ JMenu loadSubMenu;
+ JMenu saveSubMenu;
+ JMenu newSubMenu;
+ JMenu newSubMenu2;
+ JMenu editMenu;
+ JMenu viewMenu;
+ JMenu viewSubMenu;
+ JMenu selectMenu;
+ JMenu layoutMenu;
+ JMenu vizMenu;
+ JMenu helpMenu;
+ JMenu opsMenu;
+ JMenu recentlyOpenedSubMenu;
+
+ JButton openSessionButton;
+ JButton saveButton;
+ JButton zoomInButton;
+ JButton zoomOutButton;
+ JButton zoomSelectedButton;
+ JButton zoomDisplayAllButton;
+ JButton snapshotButton;
+ JButton showAllButton;
+ JButton hideSelectedButton;
+ JButton annotationButton;
+ JButton helpButton;
+ JButton vizButton;
+ JButton applyLayoutButton;
+ JButton createNewNetworkButton;
+ /**
+ * Creates a new CyMenus object. This will construct the basic bar objects,
+ * but won't fill them with menu items and associated action listeners.
+ */
+ public CyMenus() {
+ Cytoscape.getPropertyChangeSupport().addPropertyChangeListener(this);
+
+ toolBar = new CytoscapeToolBar();
+
+ menuBar = new CytoscapeMenuBar();
+
+ fileMenu = menuBar.getMenu("File");
+ newSubMenu = menuBar.getMenu("File.New", 0);
+ newSubMenu2 = menuBar.getMenu("File.New.Network");
+ loadSubMenu = menuBar.getMenu("File.Import", 1);
+ saveSubMenu = menuBar.getMenu("File.Export", 2);
+ recentlyOpenedSubMenu = menuBar.getMenu("File.Recently Opened", 3);
+ initRecentlyOpenedSubMenu();
+ editMenu = menuBar.getMenu("Edit");
+ viewMenu = menuBar.getMenu("View");
+ selectMenu = menuBar.getMenu("Select");
+ layoutMenu = menuBar.getMenu("Layout");
+ opsMenu = menuBar.getMenu("Plugins");
+ helpMenu = menuBar.getMenu("Help");
+
+ // Add a listener to sort the Layout and Plugins menus after the separator
+ opsMenu.addMenuListener(new SwingMenuSorter(opsMenu, 1));
+ layoutMenu.addMenuListener(new SwingMenuSorter(layoutMenu, 2));
+
+ }
+
+ private void initRecentlyOpenedSubMenu() {
+ final RecentlyOpenedTracker sessionTracker = Cytoscape.getRecentlyOpenedSessionTracker();
+ if (sessionTracker == null)
+ return;
+
+ final List<URL> recentlyOpenedSessions = sessionTracker.getRecentlyOpenedURLs();
+ for (final URL url : recentlyOpenedSessions)
+ recentlyOpenedSubMenu.add(new JMenuItem(new OpenRecentAction(url)));
+ }
+
+ /**
+ * Returns the main menu bar constructed by this object.
+ */
+ public CytoscapeMenuBar getMenuBar() {
+ return menuBar;
+ }
+
+ /**
+ * Returns the menu with items related to file operations.
+ */
+ public JMenu getFileMenu() {
+ return fileMenu;
+ }
+
+ /**
+ * Returns the submenu with items related to loading objects.
+ */
+ public JMenu getLoadSubMenu() {
+ return loadSubMenu;
+ }
+
+ /**
+ * Returns the submenu with items related to saving objects.
+ */
+ public JMenu getSaveSubMenu() {
+ return saveSubMenu;
+ }
+
+ /**
+ * returns the menu with items related to editing the graph.
+ */
+ public JMenu getEditMenu() {
+ return editMenu;
+ }
+
+ /**
+ * Returns the menu with items related to data operations.
+ */
+ public JMenu getViewMenu() {
+ return viewMenu;
+ }
+
+ /**
+ * Returns the menu with items related to selecting nodes and edges in the
+ * graph.
+ */
+ public JMenu getSelectMenu() {
+ return selectMenu;
+ }
+
+ /**
+ * Returns the menu with items realted to layout actions.
+ */
+ public JMenu getLayoutMenu() {
+ return layoutMenu;
+ }
+
+ /**
+ * Returns the menu with items related to visualiation.
+ */
+ public JMenu getVizMenu() {
+ return vizMenu;
+ }
+
+ /**
+ * Returns the help menu.
+ */
+ public JMenu getHelpMenu() {
+ return helpMenu;
+ }
+
+ /**
+ * Returns the menu with items associated with plugins. Most plugins grab
+ * this menu and add their menu option.
+ */
+ public JMenu getOperationsMenu() {
+ return opsMenu;
+ }
+
+ /**
+ * Returns the File.New.Network menu.
+ */
+ public JMenu getNewNetworkMenu() {
+ return newSubMenu2;
+ }
+
+ /**
+ * Returns the toolbar object constructed by this class.
+ */
+ public CytoscapeToolBar getToolBar() {
+ return toolBar;
+ }
+
+ /**
+ * Add the menu item.
+ *
+ * @param action
+ */
+ public void addAction(CytoscapeAction action) {
+ addCytoscapeAction(action);
+ }
+
+ /**
+ * Add the menu item in a specific position
+ *
+ * @param action
+ * @param index
+ */
+ public void addAction(CytoscapeAction action, int index) {
+ addCytoscapeAction(action, index);
+ }
+
+ /**
+ * Takes a CytoscapeAction and will add it to the MenuBar or the Toolbar as
+ * is appropriate.
+ */
+ public void addCytoscapeAction(CytoscapeAction action) {
+ if (action.isInMenuBar()) {
+ getMenuBar().addAction(action);
+ }
+
+ if (action.isInToolBar()) {
+ getToolBar().addAction(action);
+ }
+ }
+
+ /**
+ * Add the menu item in a specific position
+ *
+ * @param action
+ * @param index
+ */
+ public void addCytoscapeAction(CytoscapeAction action, int index) {
+ if (action.isInMenuBar()) {
+ getMenuBar().addAction(action, index);
+ }
+
+ if (action.isInToolBar()) {
+ getToolBar().addAction(action);
+ }
+ }
+
+ /**
+ * @deprecated Will be removed April 2008. Item state is now handled by Actions directly. Don't use this.
+ */
+ public void setVisualMapperItemsEnabled(boolean newState) { }
+
+ /**
+ * @deprecated Will be removed April 2008. Item state is now handled by Actions directly. Don't use this.
+ */
+ public void setOverviewEnabled(boolean newState) { }
+
+ /**
+ * @deprecated Will be removed April 2008. Item state is now handled by Actions directly. Don't use this.
+ */
+ public void setNodesRequiredItemsEnabled() { }
+
+ /**
+ * We are not listening for any GraphViewChangeEvents. MenuItems are responsible for
+ * updating their own state, which is generally accomplished by implementing the menuSelected()
+ * method.
+ *
+ * @param e
+ */
+ public void graphViewChanged(GraphViewChangeEvent e) { }
+
+ /**
+ * Used to return the cytopanels menu.
+ * @deprecated Will be removed April 2008. Cytopanels no longer have a separate menu (they're in View).
+ */
+ public JMenu getCytoPanelMenu() {
+ return null;
+ }
+
+ /**
+ * Used to set up the CytoPanelMenu items.
+ * @deprecated Will be removed April 2008. Cytopanels are initialized in the Display* actions. Do not use.
+ */
+ public void initCytoPanelMenus() { }
+
+ /**
+ * This method should be called by the creator of this object after the
+ * constructor has finished. It fills the previously created menu and tool
+ * bars with items and action listeners that respond when those items are
+ * activated. This needs to come after the constructor is done, because some
+ * of the listeners try to access this object in their constructors.
+ *
+ * Any calls to this method after the first will do nothing.
+ */
+ public void initializeMenus() {
+ if (!menusInitialized) {
+ menusInitialized = true;
+ fillMenuBar();
+ fillToolBar();
+ }
+ }
+
+ /**
+ * Fills the previously created menu bar with a large number of items with
+ * attached action listener objects.
+ */
+ private void fillMenuBar() {
+
+ //
+ // File menu
+ //
+
+ // New submenu
+ addAction(new NewSessionAction());
+ addAction(new NewWindowSelectedNodesOnlyAction());
+ addAction(new NewWindowSelectedNodesEdgesAction());
+ addAction(new CloneGraphInNewWindowAction());
+ addAction(new NewNetworkAction());
+
+ addAction(new OpenSessionAction(),1);
+
+ addAction(new SaveSessionAction("Save"),2);
+ addAction(new SaveSessionAsAction("Save as..."),3);
+
+ fileMenu.add(new JSeparator(), 2);
+ fileMenu.add(new JSeparator(), 5);
+
+
+ // Import sub menu
+ addAction(new ImportGraphFileAction(this));
+ addAction(new WebServiceNetworkImportAction());
+
+ loadSubMenu.add(new JSeparator());
+
+ addAction(new ImportNodeAttributesAction());
+ addAction(new ImportEdgeAttributesAction());
+ addAction(new ImportExpressionMatrixAction());
+
+ addAction(new ImportVizmapAction());
+
+ loadSubMenu.add(new JSeparator());
+
+ // Save submenu
+ addAction(new ExportAsXGMMLAction());
+ addAction(new ExportAsGMLAction());
+ addAction(new ExportAsInteractionsAction());
+ addAction(new ExportNetworksAsNNFAction());
+ addAction(new ExportNodeAttributesAction());
+ addAction(new ExportEdgeAttributesAction());
+ addAction(new ExportVizmapAction());
+ addAction(new ExportAsGraphicsAction("PDF"));
+
+ fileMenu.add(new JSeparator());
+ addAction(new PrintAction());
+ fileMenu.add(new JSeparator());
+ addAction(new ExitAction());
+
+ //
+ // Edit menu
+ //
+ addAction(new UndoAction());
+ addAction(new RedoAction());
+
+ editMenu.add(new JSeparator());
+
+ addAction(new CreateNetworkViewAction());
+ addAction(new DestroyNetworkViewAction());
+ addAction(new DestroyNetworkAction());
+
+ editMenu.add(new JSeparator());
+
+ addAction(new DeleteAction());
+
+ editMenu.add(new JSeparator());
+
+ addAction(new PreferenceAction());
+ addAction(new BookmarkAction());
+ addAction(new ProxyServerAction());
+
+ //
+ // Select menu
+ //
+ SelectionModeAction sma = new SelectionModeAction();
+ selectMenu.add(sma);
+ selectMenu.addMenuListener(sma);
+
+ addAction(new InvertSelectedNodesAction());
+ addAction(new HideSelectedNodesAction());
+ addAction(new UnHideSelectedNodesAction());
+
+ addAction(new SelectAllNodesAction());
+ addAction(new DeSelectAllNodesAction());
+ addAction(new SelectFirstNeighborsAction());
+ addAction(new SelectConnectedNodesAction());
+ addAction(new AlphabeticalSelectionAction());
+ addAction(new ListFromFileSelectionAction());
+
+ addAction(new InvertSelectedEdgesAction());
+ addAction(new HideSelectedEdgesAction());
+ addAction(new UnHideSelectedEdgesAction());
+ addAction(new SelectAllEdgesAction());
+ addAction(new SelectAdjacentEdgesAction());
+ addAction(new DeSelectAllEdgesAction());
+ addAction(new BendSelectedEdgesAction());
+ addAction(new StraightenSelectedEdgesAction());
+
+ selectMenu.addSeparator();
+
+ addAction(new SelectAllAction());
+ addAction(new DeselectAllAction());
+
+ selectMenu.addSeparator();
+
+ //
+ // View menu
+ //
+ addAction(new CytoPanelAction(CytoPanelName.WEST,true,null));
+ addAction(new CytoPanelAction(CytoPanelName.SOUTH,true,null));
+ addAction(new CytoPanelAction(CytoPanelName.EAST,false,null));
+ addAction(new CytoPanelAction(CytoPanelName.SOUTH_WEST,false, CytoPanelName.WEST));
+
+ viewMenu.add(new JSeparator());
+
+ addAction(new ShowGraphicsDetailsAction());
+
+ viewMenu.add(new JSeparator());
+ addAction(new SetVisualPropertiesAction());
+ addAction(new ShowCustomGraphicsManagerAction());
+ viewMenu.add(new JSeparator());
+
+ viewMenu.add(new ArrangeAction());
+
+ //
+ // Layout menu
+ //
+ layoutMenu.addSeparator();
+ addAction(new SettingsAction() );
+ layoutMenu.addSeparator();
+ layoutMenu.addMenuListener( new LayoutMenuManager() );
+
+ //
+ // Plugin menu
+ //
+ addAction(new PluginManagerAction());
+ addAction(new PluginUpdateAction());
+ addAction(new PluginInstallAction());
+
+ opsMenu.addSeparator();
+
+ //
+ // Help menu
+ //
+ addAction(new HelpContentsAction());
+ addAction(new HelpContactHelpDeskAction());
+
+ helpMenu.addSeparator();
+
+ addAction(new HelpAboutAction());
+ addAction(new LoggerAction());
+ addAction(new MemoryUsageAction());
+ }
+
+ /**
+ * Fills the toolbar for easy access to commonly used actions.
+ */
+ private void fillToolBar() {
+ openSessionButton = toolBar.add(new OpenSessionAction(this, false));
+ openSessionButton.setToolTipText("Open Session File...");
+ openSessionButton.setIcon(new ImageIcon(Cytoscape.class
+ .getResource("images/ximian/stock_open.png")));
+ openSessionButton.setBorderPainted(false);
+ openSessionButton.setRolloverEnabled(true);
+
+ saveButton = toolBar.add(new SaveSessionAction());
+ saveButton.setToolTipText("Save Current Session as...");
+ saveButton.setIcon(new ImageIcon(Cytoscape.class.getResource("images/ximian/stock_save.png")));
+
+ saveButton.setBorderPainted(false);
+ saveButton.setRolloverEnabled(true);
+
+ toolBar.addSeparator();
+
+ final ZoomAction zoom_in = new ZoomAction(1.1);
+ zoomInButton = new JButton();
+ zoomInButton.setIcon(new ImageIcon(Cytoscape.class.getResource("images/ximian/stock_zoom-in.png")));
+ zoomInButton.setToolTipText("Zoom In");
+ zoomInButton.setBorderPainted(false);
+ zoomInButton.setRolloverEnabled(true);
+ zoomInButton.addMouseListener(new MouseListener() {
+ public void mouseClicked(MouseEvent e) {
+ zoom_in.zoom();
+ }
+
+ public void mouseEntered(MouseEvent e) {
+ }
+
+ public void mouseExited(MouseEvent e) {
+ }
+
+ public void mousePressed(MouseEvent e) {
+ zoomInButton.setSelected(true);
+ }
+
+ public void mouseReleased(MouseEvent e) {
+ zoomInButton.setSelected(false);
+ }
+ });
+
+ final ZoomAction zoom_out = new ZoomAction(0.9);
+ zoomOutButton = new JButton();
+ zoomOutButton.setIcon(new ImageIcon(Cytoscape.class
+ .getResource("images/ximian/stock_zoom-out.png")));
+ zoomOutButton.setToolTipText("Zoom Out");
+ zoomOutButton.setBorderPainted(false);
+ zoomOutButton.setRolloverEnabled(true);
+ zoomOutButton.addMouseListener(new MouseListener() {
+ public void mouseClicked(MouseEvent e) {
+ zoom_out.zoom();
+ }
+
+ public void mouseEntered(MouseEvent e) {
+ }
+
+ public void mouseExited(MouseEvent e) {
+ }
+
+ public void mousePressed(MouseEvent e) {
+ zoomOutButton.setSelected(true);
+ }
+
+ public void mouseReleased(MouseEvent e) {
+ zoomOutButton.setSelected(false);
+ }
+ });
+
+ zoomOutButton.addMouseWheelListener(new MouseWheelListener() {
+ public void mouseWheelMoved(MouseWheelEvent e) {
+ if (e.getWheelRotation() < 0) {
+ zoom_in.zoom();
+ } else {
+ zoom_out.zoom();
+ }
+ }
+ });
+ zoomInButton.addMouseWheelListener(new MouseWheelListener() {
+ public void mouseWheelMoved(MouseWheelEvent e) {
+ if (e.getWheelRotation() < 0) {
+ zoom_in.zoom();
+ } else {
+ zoom_out.zoom();
+ }
+ }
+ });
+
+ toolBar.add(zoomOutButton);
+ toolBar.add(zoomInButton);
+
+ zoomSelectedButton = toolBar.add(new ZoomSelectedAction());
+ zoomSelectedButton.setIcon(new ImageIcon(Cytoscape.class
+ .getResource("images/ximian/stock_zoom-object.png")));
+ zoomSelectedButton.setToolTipText("Zoom Selected Region");
+ zoomSelectedButton.setBorderPainted(false);
+
+ zoomDisplayAllButton = toolBar.add(new FitContentAction());
+ zoomDisplayAllButton.setIcon(new ImageIcon(Cytoscape.class
+ .getResource("images/ximian/stock_zoom-1.png")));
+ zoomDisplayAllButton.setToolTipText("Zoom out to display all of current Network");
+ zoomDisplayAllButton.setBorderPainted(false);
+
+ toolBar.addSeparator();
+
+ final ExportAsGraphicsAction eag = new ExportAsGraphicsAction("PNG");
+ eag.putValue(Action.NAME, null);
+ snapshotButton = toolBar.add(eag);
+ snapshotButton.setToolTipText("Export current network view as graphics");
+ snapshotButton.setIcon(new ImageIcon(Cytoscape.class.getResource("images/ximian/tango-32-camera-photo.png")));
+
+ snapshotButton.setBorderPainted(false);
+ snapshotButton.setRolloverEnabled(true);
+
+ toolBar.addSeparator();
+
+ helpButton = new JButton();
+ helpButton.addActionListener( CyHelpBroker.getHelpActionListener() );
+ helpButton.setIcon(new ImageIcon(Cytoscape.class.getResource("images/ximian/stock_help.png")));
+ helpButton.setToolTipText("Help");
+ helpButton.setBorderPainted(false);
+
+ toolBar.add(helpButton);
+
+ toolBar.addSeparator();
+
+ vizButton = toolBar.add(new SetVisualPropertiesAction(false));
+ vizButton.setIcon(new ImageIcon(Cytoscape.class
+ .getResource("images/ximian/stock_file-with-objects.png")));
+ vizButton.setToolTipText("Open VizMapper\u2122");
+ vizButton.setBorderPainted(false);
+
+ ///Add a button -- apply layout, 'force-directed' by default
+ String layoutName = CytoscapeInit.getProperties().get("preferredLayoutAlgorithm").toString();
+ final ApplyLayoutAction layoutAction = new ApplyLayoutAction();
+ layoutAction.putValue(Action.NAME, null);
+ applyLayoutButton = toolBar.add(layoutAction);
+ layoutAction.setButton(applyLayoutButton);
+ applyLayoutButton.setIcon(new ImageIcon(Cytoscape.class
+ .getResource("images/apply-force-directed-layout-32.png")));
+ applyLayoutButton.setToolTipText("Apply "+layoutName + " layout");
+ applyLayoutButton.setBorderPainted(false);
+ applyLayoutButton.setRolloverEnabled(true);
+
+ /////Add a button -- Create new network from selected nodes, all edges
+ final NewWindowSelectedNodesOnlyAction newWindowSelectedNodesOnlyAction = new NewWindowSelectedNodesOnlyAction();
+ newWindowSelectedNodesOnlyAction.putValue(Action.NAME, null);
+ createNewNetworkButton = toolBar.add(newWindowSelectedNodesOnlyAction);
+ createNewNetworkButton.setIcon(new ImageIcon(Cytoscape.class
+ .getResource("images/new-network-from-selected-nodes-32.png")));
+ createNewNetworkButton.setToolTipText("Create new network from selected nodes, all edges");
+ createNewNetworkButton.setBorderPainted(false);
+ createNewNetworkButton.setRolloverEnabled(true);
+ }
+
+ public void propertyChange(PropertyChangeEvent e) {
+ if (!e.getPropertyName().equals(Integer.toString(Cytoscape.SESSION_OPENED)))
+ return;
+
+ final RecentlyOpenedTracker sessionTracker = Cytoscape.getRecentlyOpenedSessionTracker();
+ if (sessionTracker == null)
+ return;
+
+ final URL mostRecentlyAddedSession = sessionTracker.getMostRecentAddition();
+ if (mostRecentlyAddedSession == null)
+ return;
+
+ recentlyOpenedSubMenu.add(new JMenuItem(new OpenRecentAction(mostRecentlyAddedSession)));
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/view/CyNetworkView.java b/application/src/main/java/cytoscape/view/CyNetworkView.java
new file mode 100644
index 0000000..246bd41
--- /dev/null
+++ b/application/src/main/java/cytoscape/view/CyNetworkView.java
@@ -0,0 +1,340 @@
+/*
+ File: CyNetworkView.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.view;
+
+import cytoscape.*;
+
+import cytoscape.layout.*;
+
+import cytoscape.visual.*;
+
+import ding.view.EdgeContextMenuListener;
+
+// AJK: 05/19/06 BEGIN
+// for context menus
+import ding.view.NodeContextMenuListener;
+
+import giny.view.*;
+
+import java.util.*;
+
+
+/**
+ * CyNetworkView is responsible for actually getting a graph to show up on the screen.<br><br>
+ * Cytoscape does not currently define specific classes for NodeViews and EdgeViews, the defaults from the GINY graph library
+ * (namely phoebe.PNodeView and phoebe.PEdgeView) are most commonly used. Making custom nodes is easy and fun. One must implement the
+ * giny.view.NodeView interface and inherit from edu.umd.cs.piccolo.PNode. The Piccolo project is what all of the painting is based on, and is very
+ * fast, flexible and powerful. Becoming acquainted with Piccolo is essential for build custom nodes.<br><br>
+ * Fortunately, if you just want basic shapes and colors, it's all built into the UI already, and you really need never even use this class. Just
+ * learn how to use the VizMapper to accomplish your data to view mappings. The manual is a good place to start.
+ */
+public interface CyNetworkView extends GraphView {
+ /**
+ * Returns the network displayed by this object.
+ */
+ public CyNetwork getNetwork();
+
+
+ /**
+ * Sets the Title of this View
+ */
+ public void setTitle(String title);
+
+
+ /**
+ * Returns the Title of this View
+ */
+ public String getTitle();
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param layout DOCUMENT ME!
+ * @param vizmap DOCUMENT ME!
+ */
+ public void redrawGraph(boolean layout, boolean vizmap);
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public CyNetworkView getView();
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public VisualMappingManager getVizMapManager();
+
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void toggleVisualMapperEnabled();
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param state DOCUMENT ME!
+ */
+ public void setVisualMapperEnabled(boolean state);
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean getVisualMapperEnabled();
+
+
+ //--------------------//
+ // Network Client Data
+
+ /**
+ * Networks can support client data.
+ * @param data_name the name of this client data
+ */
+ public void putClientData(String data_name, Object data);
+
+
+ /**
+ * Get a list of all currently available ClientData objects
+ */
+ public Collection getClientDataNames();
+
+
+ /**
+ * Get Some client data
+ * @param data_name the data to get
+ */
+ public Object getClientData(String data_name);
+
+
+ /**
+ * Sets the Given nodes Selected<br>
+ * @deprecated this method is not working, use {@link Cytoscape.CyNetwork#setSelectedNodeState(Collection, boolean)}
+ *
+ */
+ public boolean setSelected(CyNode[] nodes);
+
+
+ /**
+ * Sets the Given nodes Selected<br>
+ * @deprecated this method is not working, use {@link Cytoscape.CyNetwork#setSelectedNodeState(Collection, boolean)}
+ */
+ public boolean setSelected(NodeView[] node_views);
+
+
+ /**
+ * Applies the given edge to the given vizmapper
+ */
+ public boolean applyVizMap(CyEdge edge);
+
+
+ /**
+ * Applies the given edge to the given vizmapper
+ */
+ public boolean applyVizMap(EdgeView edge_view);
+
+
+ /**
+ * Applies the given node to the given vizmapper
+ */
+ public boolean applyVizMap(CyNode node);
+
+
+ /**
+ * Applies the given node to the given vizmapper
+ */
+ public boolean applyVizMap(NodeView node_view);
+
+
+ /**
+ * Applies the given edge to the given vizmapper
+ */
+ public boolean applyVizMap(CyEdge edge, VisualStyle style);
+
+
+ /**
+ * Applies the given edge to the given vizmapper
+ */
+ public boolean applyVizMap(EdgeView edge_view, VisualStyle style);
+
+
+ /**
+ * Applies the given node to the given vizmapper
+ */
+ public boolean applyVizMap(CyNode node, VisualStyle style);
+
+
+ /**
+ * Applies the given node to the given vizmapper
+ */
+ public boolean applyVizMap(NodeView node_view, VisualStyle style);
+
+
+ /**
+ * Sets the Given edges Selected<br>
+ * @deprecated this method is not working, use {@link cytoscape.CyNetwork#setSelectedEdgeState(Collection, boolean)}
+ */
+ public boolean setSelected(CyEdge[] edges);
+
+
+ /**
+ * Sets the Given edges Selected<br>
+ * @deprecated this method is not working, use {@link cytoscape.CyNetwork#setSelectedEdgeState(Collection, boolean)}
+ */
+ public boolean setSelected(EdgeView[] edge_views);
+
+
+ /**
+ * @param applyAppearances if true, the vizmapper will recalculate the node and edge appearances
+ */
+ public void applyVizmapper(VisualStyle style);
+
+
+ /**
+ * Applies the given layout to the entire CyNetworkView
+ */
+ public void applyLayout(CyLayoutAlgorithm layout);
+
+
+ /**
+ * Applies the given layout to the entire CyNetworkView,
+ * but locks the given Nodes and Edges in place.
+ * NOTE: currently, none of the layout algorithms support edge-locked layouts, so
+ * the edges argument is ignored.
+ */
+ public void applyLockedLayout(CyLayoutAlgorithm layout, CyNode[] nodes, CyEdge[] edges);
+
+
+ /**
+ * Applies the given layout to only the given Nodes and Edges.
+ * NOTE: currently, none of the layout algorithms support edge-locked layouts, so
+ * the edges argument is ignored.
+ */
+ public void applyLayout(CyLayoutAlgorithm layout, CyNode[] nodes, CyEdge[] edges);
+
+
+ /**
+ * Applies the given layout to the entire CyNetworkView,
+ * but locks the given NodeViews and EdgeViews in place.
+ * NOTE: currently, none of the layout algorithms support edge-locked layouts, so
+ * the edges argument is ignored.
+ */
+ public void applyLockedLayout(CyLayoutAlgorithm layout, CyNodeView[] nodes, CyEdgeView[] edges);
+
+
+ /**
+ * Applies the given layout to only the given NodeViews and EdgeViews.
+ * NOTE: currently, none of the layout algorithms support edge-locked layouts, so
+ * the edges argument is ignored.
+ */
+ public void applyLayout(CyLayoutAlgorithm layout, CyNodeView[] nodes, CyEdgeView[] edges);
+
+
+ /**
+ * Applies the given layout to the entire CyNetworkView,
+ * but locks the given Nodes and Edges in place.
+ * NOTE: currently, none of the layout algorithms support edge-locked layouts, so
+ * the edges argument is ignored.
+ */
+ public void applyLockedLayout(CyLayoutAlgorithm layout, int[] nodes, int[] edges);
+
+
+ /**
+ * Applies the given layout to only the given Nodes and Edges.
+ * NOTE: currently, none of the layout algorithms support edge-locked layouts, so
+ * the edges argument is ignored.
+ */
+ public void applyLayout(CyLayoutAlgorithm layout, int[] nodes, int[] edges);
+
+
+ // This is necessary since we should save the association between VS
+ /**
+ * DOCUMENT ME!
+ *
+ * @param VSName DOCUMENT ME!
+ */
+ public void setVisualStyle(String VSName);
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public VisualStyle getVisualStyle();
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param l DOCUMENT ME!
+ */
+ public void addNodeContextMenuListener(NodeContextMenuListener l);
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param l DOCUMENT ME!
+ */
+ public void removeNodeContextMenuListener(NodeContextMenuListener l);
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param l DOCUMENT ME!
+ */
+ public void addEdgeContextMenuListener(EdgeContextMenuListener l);
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param l DOCUMENT ME!
+ */
+ public void removeEdgeContextMenuListener(EdgeContextMenuListener l);
+}
diff --git a/application/src/main/java/cytoscape/view/CyNodeView.java b/application/src/main/java/cytoscape/view/CyNodeView.java
new file mode 100644
index 0000000..2be7b97
--- /dev/null
+++ b/application/src/main/java/cytoscape/view/CyNodeView.java
@@ -0,0 +1,44 @@
+/*
+ File: CyNodeView.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.view;
+
+
+/**
+ *
+ */
+public interface CyNodeView extends giny.view.NodeView {
+}
diff --git a/application/src/main/java/cytoscape/view/CytoscapeDesktop.java b/application/src/main/java/cytoscape/view/CytoscapeDesktop.java
new file mode 100644
index 0000000..580bd59
--- /dev/null
+++ b/application/src/main/java/cytoscape/view/CytoscapeDesktop.java
@@ -0,0 +1,813 @@
+/*
+ File: CytoscapeDesktop.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.view;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.Toolkit;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.util.List;
+import java.util.Properties;
+
+import javax.help.CSH;
+import javax.swing.ImageIcon;
+import javax.swing.JFrame;
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JSplitPane;
+import javax.swing.JTabbedPane;
+import javax.swing.SwingConstants;
+import javax.swing.WindowConstants;
+import javax.swing.border.EmptyBorder;
+import javax.swing.event.SwingPropertyChangeSupport;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import cytoscape.CytoscapeInit;
+import cytoscape.CytoscapeVersion;
+import cytoscape.data.webservice.ui.WebServiceContextMenuListener;
+import cytoscape.util.undo.CyUndo;
+import cytoscape.view.cytopanels.BiModalJSplitPane;
+import cytoscape.view.cytopanels.CytoPanel;
+import cytoscape.view.cytopanels.CytoPanelImp;
+import cytoscape.view.cytopanels.CytoPanelState;
+import cytoscape.visual.VisualMappingManager;
+import cytoscape.visual.VisualStyle;
+import cytoscape.visual.ui.HideEdgeListener;
+import cytoscape.visual.ui.HideNodeListener;
+import cytoscape.visual.ui.NestedNetworkListener;
+import cytoscape.visual.ui.VizMapBypassNetworkListener;
+import cytoscape.visual.ui.VizMapperMainPanel;
+
+/**
+ * The CytoscapeDesktop is the central Window for working with Cytoscape
+ */
+public class CytoscapeDesktop extends JFrame implements PropertyChangeListener {
+
+ private static final long serialVersionUID = 2986320083629749014L;
+
+ private static final String MAC_OS_ID = "mac";
+
+ protected long lastPluginRegistryUpdate;
+ protected int returnVal;
+
+ // Default sizes of components
+ private static final Dimension DEF_DESKTOP_SIZE = new Dimension(1000, 720);
+ private static final int DEF_CONTROL_PANEL_WIDTH = 400;
+ private static final int DEF_DATAPANEL_HEIGHT = 300;
+
+ private static final int DEVIDER_SIZE = 4;
+
+ /**
+ *
+ */
+ public static final String NETWORK_VIEWS_SELECTED = "NETWORK_VIEWS_SELECTED";
+
+ /**
+ *
+ */
+ public static final String NETWORK_VIEW_FOCUSED = "NETWORK_VIEW_FOCUSED";
+
+ /**
+ *
+ */
+ public static final String NETWORK_VIEW_FOCUS = "NETWORK_VIEW_FOCUS";
+
+ /**
+ *
+ */
+ public static final String NETWORK_VIEW_CREATED = "NETWORK_VIEW_CREATED";
+
+ /**
+ *
+ */
+ public static final String NETWORK_VIEW_DESTROYED = "NETWORK_VIEW_DESTROYED";
+
+ // state variables
+ /**
+ *
+ */
+ public static final String VISUAL_STYLE = "VISUAL_STYLE";
+
+ /**
+ *
+ */
+ public static final String VIZMAP_ENABLED = "VIZMAP_ENABLED";
+
+ private static final String SMALL_ICON = "images/c16.png";
+
+ protected VisualStyle defaultVisualStyle;
+
+ /**
+ * The network panel that sends out events when a network is selected from
+ * the Tree that it contains.
+ */
+ protected NetworkPanel networkPanel;
+
+ /**
+ * The CyMenus object provides access to the all of the menus and toolbars
+ * that will be needed.
+ */
+ protected CyMenus cyMenus;
+
+ /**
+ * The NetworkViewManager can support three types of interfaces.
+ * Tabbed/InternalFrame/ExternalFrame
+ */
+ protected NetworkViewManager networkViewManager;
+
+
+ /**
+ * provides support for property change events
+ */
+ protected final SwingPropertyChangeSupport pcs = new SwingPropertyChangeSupport(this);
+
+ /**
+ * The GraphViewController for all NetworkViews that we know about
+ */
+ protected GraphViewController graphViewController;
+
+ /**
+ * Provides Operations for Mapping Data Attributes of CyNetworks to
+ * CyNetworkViews
+ */
+ protected VisualMappingManager vmm;
+
+ /**
+ * New VizMapper UI
+ */
+ protected VizMapperMainPanel vizmapperUI;
+
+ /**
+ * Current network and view.
+ */
+ protected String currentNetworkID;
+ protected String currentNetworkViewID;
+
+ // CytoPanels
+ protected CytoPanelImp cytoPanelWest;
+ protected CytoPanelImp cytoPanelEast;
+ protected CytoPanelImp cytoPanelSouth;
+ protected CytoPanelImp cytoPanelSouthWest;
+
+ // Status Bar
+ protected JLabel statusBar;
+
+ protected final JPanel main_panel;
+
+ // This is used to keep track of the visual style combo box.
+ // This is the index of the box in the toolbar. We use this so that we can
+ // add and remove the stylebox from the same place.
+ protected int styleBoxIndex = -1;
+
+ // Overview Window;
+ private BirdsEyeViewHandler bevh;
+
+ // These values will be calculated based on start-up window size.
+ private int defaultControlPanelWidth;
+ private int defaultDataPanelHeight;
+
+ // Desktop and Result Panel
+ private BiModalJSplitPane topRightPane;
+
+ // Desktop and Data Panel
+ private BiModalJSplitPane rightPane;
+
+ // Network Panel and Desktop
+ private BiModalJSplitPane masterPane;
+
+
+ /**
+ * Creates a new CytoscapeDesktop object.
+ */
+ public CytoscapeDesktop() {
+ super("Cytoscape Desktop (New Session)");
+
+ setIconImage(Toolkit.getDefaultToolkit().getImage(Cytoscape.class.getResource(SMALL_ICON)));
+
+ main_panel = new JPanel();
+ main_panel.setLayout(new BorderLayout());
+
+ // ------------------------------//
+ // Set up the Panels, Menus, and Event Firing
+ networkViewManager = new NetworkViewManager(this);
+
+ getBirdsEyeViewHandler();
+
+ getSwingPropertyChangeSupport().addPropertyChangeListener(bevh);
+ Cytoscape.getPropertyChangeSupport().addPropertyChangeListener(bevh);
+
+ networkPanel = new NetworkPanel(this);
+ networkPanel.setNavigator(bevh.getBirdsEyeView());
+
+ cyMenus = new CyMenus();
+
+ // Listener Setup
+ // ----------------------------------------
+ // |----------|
+ // | CyMenus |
+ // |----------|
+ // |
+ // |
+ // |-----| |---------| |------| |-------|
+ // | N P |------| Desktop |----| NVM |--| Views |
+ // |-----| |---------| |------| |-------|
+ // |
+ // |
+ // |-----------|
+ // | Cytoscape |
+ // |-----------|
+
+ // The CytoscapeDesktop listens to NETWORK_VIEW_CREATED events,
+ // and passes them on, The NetworkPanel listens for them
+ // The Desktop also keeps Cytoscape up2date, but NOT via events
+ Cytoscape.getSwingPropertyChangeSupport().addPropertyChangeListener(this);
+
+ // The Networkviewmanager listens to the CytoscapeDesktop to know when
+ // to
+ // put new NetworkViews in the userspace and to get passed focus events
+ // from
+ // the NetworkPanel. The CytoscapeDesktop also listens to the NVM
+ this.getSwingPropertyChangeSupport().addPropertyChangeListener(networkViewManager);
+ networkViewManager.getSwingPropertyChangeSupport().addPropertyChangeListener(this);
+
+ // The NetworkPanel listens to the CytoscapeDesktop for
+ // NETWORK_CREATED_EVENTS a
+ // as well as for passing focused events from the Networkviewmanager.
+ // The
+ // CytoscapeDesktop also listens to the NetworkPanel
+ this.getSwingPropertyChangeSupport().addPropertyChangeListener(networkPanel);
+ networkPanel.getSwingPropertyChangeSupport().addPropertyChangeListener(this);
+
+ // add a listener for node bypass
+ Cytoscape.getSwingPropertyChangeSupport()
+ .addPropertyChangeListener(new VizMapBypassNetworkListener());
+
+ // add a listener for nestedNetwork
+ Cytoscape.getSwingPropertyChangeSupport()
+ .addPropertyChangeListener(new NestedNetworkListener());
+
+ // Web Service Client context menu.
+ Cytoscape.getSwingPropertyChangeSupport()
+ .addPropertyChangeListener(new WebServiceContextMenuListener());
+
+ Cytoscape.getSwingPropertyChangeSupport().addPropertyChangeListener(new HideNodeListener());
+ Cytoscape.getSwingPropertyChangeSupport().addPropertyChangeListener(new HideEdgeListener());
+
+ // initialize Menus
+ cyMenus.initializeMenus();
+
+ // create the CytoscapeDesktop
+ masterPane = setupCytoPanels(networkPanel, networkViewManager);
+
+ // note - proper networkViewManager has been properly selected in
+ // setupCytoPanels()
+ main_panel.add(masterPane, BorderLayout.CENTER);
+ main_panel.add(cyMenus.getToolBar(), BorderLayout.NORTH);
+
+ // Remove status bar.
+ initStatusBar(main_panel);
+ setJMenuBar(cyMenus.getMenuBar());
+
+ // Set up the VizMapper
+ //setupVizMapper();
+ getVizMapperUI();
+
+ // don't automatically close window. Let Cytoscape.exit(returnVal)
+ // handle this,
+ // based upon user confirmation.
+ setDefaultCloseOperation(WindowConstants.DO_NOTHING_ON_CLOSE);
+
+ addWindowListener(new WindowAdapter() {
+ public void windowClosing(WindowEvent we) {
+ Cytoscape.exit(returnVal);
+ }
+ });
+
+ setContentPane(main_panel);
+
+ setSize(DEF_DESKTOP_SIZE);
+ pack();
+
+ // Calculate panel sizes based on current window size.
+ calculateProperPanelSize();
+
+ /* Set the width of Cytopanel West
+ * ...now handled in CytoPanelImpl
+ * masterPane.setDividerLocation(defaultControlPanelWidth);
+ */
+ rightPane.setDividerLocation(getSize().height - defaultDataPanelHeight);
+ masterPane.setDividerSize(DEVIDER_SIZE);
+
+ // Set desktop location
+ setDesktopLocation();
+
+ // show the Desktop
+ setVisible(true);
+ toFront();
+
+ // a trick to force macs to bring the window to the front
+ setAlwaysOnTop(true);
+ setAlwaysOnTop(false);
+
+ // sets the top level identifier for java help
+ CSH.setHelpIDString(this,"Cytoscape User Manual");
+ }
+
+
+ private void calculateProperPanelSize() {
+ final Dimension windowSize = this.getSize();
+
+ this.defaultControlPanelWidth = (int)(windowSize.width * 0.4);
+ if (defaultControlPanelWidth>DEF_CONTROL_PANEL_WIDTH)
+ defaultControlPanelWidth = DEF_CONTROL_PANEL_WIDTH;
+
+ this.defaultDataPanelHeight = (int)(windowSize.getHeight() * 0.3);
+ if(defaultDataPanelHeight > DEF_DATAPANEL_HEIGHT)
+ defaultControlPanelWidth = DEF_DATAPANEL_HEIGHT;
+ }
+
+ private void setDesktopLocation(){
+ //restore desktop to previous location
+ try {
+ Properties props = new Properties();
+ File desktop_prop_file = new File(CytoscapeInit.getConfigVersionDirectory(), "desktop.props");
+ props.load(new FileInputStream(desktop_prop_file));
+ this.setLocation(new Integer(props.get("x").toString()).intValue(),
+ new Integer(props.get("y").toString()).intValue());
+ this.setSize(new Integer(props.get("w").toString()).intValue(),
+ new Integer(props.get("h").toString()).intValue());
+ }
+ catch (Exception e){
+ setLocationRelativeTo(null);
+ this.setSize(800, 600);
+ }
+ }
+
+ private void initStatusBar(JPanel panel) {
+ statusBar = new JLabel();
+ statusBar.setFont(new Font("SansSerif", Font.PLAIN, 10));
+ statusBar.setBorder(new EmptyBorder(0, 7, 0, 7));
+ statusBar.setForeground(new Color(40, 40, 40));
+ panel.add(statusBar, BorderLayout.SOUTH);
+ if(isMacOS())
+ setStatusBarMsg("Welcome to Cytoscape " + CytoscapeVersion.version
+ + " Right-click + drag or Control-Click + drag to ZOOM Command-Click + drag to PAN");
+ else
+ setStatusBarMsg("Welcome to Cytoscape " + CytoscapeVersion.version
+ + " Right-click + drag to ZOOM Middle-click + drag to PAN");
+ }
+
+ private boolean isMacOS() {
+ String os = System.getProperty("os.name");
+ return os.regionMatches(true, 0, MAC_OS_ID, 0, MAC_OS_ID.length());
+ }
+
+ /**
+ * Sets the Status Bar Message.
+ *
+ * @param msg
+ * Status Bar Message.
+ */
+ public void setStatusBarMsg(String msg) {
+ statusBar.setText(msg);
+ }
+
+ /**
+ * Clears the Status Bar Message.
+ */
+ public void clearStatusBar() {
+ // By using mutiple white spaces, layout for the statusBar is preserved.
+ statusBar.setText(" ");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public NetworkPanel getNetworkPanel() {
+ return networkPanel;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public CyMenus getCyMenus() {
+ return cyMenus;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param newNetwork DOCUMENT ME!
+ */
+ public void setNewNetwork(CyNetwork newNetwork) {
+ }
+
+ /**
+ * Returns new vizmapper GUI.
+ *
+ * @return DOCUMENT ME!
+ */
+ public VizMapperMainPanel getVizMapperUI() {
+ if (vizmapperUI == null) {
+ this.vmm = Cytoscape.getVisualMappingManager();
+ vizmapperUI = VizMapperMainPanel.getVizMapperUI();
+ getCytoPanel(SwingConstants.WEST).add("VizMapper\u2122", vizmapperUI);
+ this.getSwingPropertyChangeSupport().addPropertyChangeListener(vizmapperUI);
+
+ }
+
+ return vizmapperUI;
+ }
+
+ /**
+ * @param style the NEW VisualStyle
+ * @return the OLD VisualStyle
+ *
+ * @deprecated use VisualMappingManager.setVisualStyle(VisualStyle style) instead.
+ */
+ @Deprecated
+ public VisualStyle setVisualStyle(VisualStyle style) {
+ vmm.setVisualStyle(style);
+ return null;
+ }
+
+ protected void updateFocus(String network_id) {
+ final VisualStyle old_style = vmm.getVisualStyle();
+ final CyNetworkView old_view = Cytoscape.getCurrentNetworkView();
+
+ if (old_view != null) {
+ old_view.putClientData(VISUAL_STYLE, old_style);
+ old_view.putClientData(VIZMAP_ENABLED, new Boolean(old_view.getVisualMapperEnabled()));
+ }
+
+ // set the current Network/View
+ Cytoscape.setCurrentNetwork(network_id);
+
+ if (Cytoscape.setCurrentNetworkView(network_id)) {
+ // deal with the new Network
+ final CyNetworkView new_view = Cytoscape.getCurrentNetworkView();
+
+ // VisualStyle new_style = (VisualStyle) new_view.getClientData(VISUAL_STYLE);
+ VisualStyle new_style = new_view.getVisualStyle();
+
+ Boolean vizmap_enabled = ((Boolean) new_view.getClientData(VIZMAP_ENABLED));
+
+ if (new_style == null)
+ new_style = vmm.getCalculatorCatalog().getVisualStyle("default");
+
+ if (vizmap_enabled == null)
+ vizmap_enabled = true;
+
+ vmm.setNetworkView(new_view);
+
+ if (new_style.getName().equals(old_style.getName()) == false) {
+ vmm.setVisualStyle(new_style);
+
+ // Redraw Graph only when current network view's style is not equal to the selected style.
+ final CyNetworkView curView = Cytoscape.getCurrentNetworkView();
+ final VisualStyle curViewStyle = curView.getVisualStyle();
+ if (curView != Cytoscape.getNullNetworkView() && curViewStyle != null) {
+ if (new_style.getName().equals(curViewStyle.getName()) == false)
+ Cytoscape.getCurrentNetworkView().redrawGraph(false, true);
+ }
+ }
+ }
+ }
+
+ /**
+ * TODO: We should remove one of this event!
+ *
+ * @param network_id DOCUMENT ME!
+ */
+ public void setFocus(String network_id) {
+ pcs.firePropertyChange(new PropertyChangeEvent(this, NETWORK_VIEW_FOCUSED, null, network_id));
+ pcs.firePropertyChange(new PropertyChangeEvent(this, NETWORK_VIEW_FOCUS, null, network_id));
+ }
+
+ /**
+ * TO keep things clearer there is one GraphView Controller per
+ * CytoscapeDesktop
+ */
+ public GraphViewController getGraphViewController() {
+ if (graphViewController == null)
+ graphViewController = new GraphViewController();
+
+ return graphViewController;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public SwingPropertyChangeSupport getSwingPropertyChangeSupport() {
+ return pcs;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void propertyChange(PropertyChangeEvent e) {
+ if (NETWORK_VIEW_CREATED.equals(e.getPropertyName())) {
+ // add the new view to the GraphViewController
+ getGraphViewController().addGraphView((CyNetworkView) e.getNewValue());
+ // pass on the event
+ pcs.firePropertyChange(e);
+ } else if (NETWORK_VIEW_FOCUSED.equals(e.getPropertyName())) {
+ // get focus event from NetworkViewManager
+ updateFocus(e.getNewValue().toString());
+ pcs.firePropertyChange(e);
+ } else if (NETWORK_VIEW_FOCUS.equals(e.getPropertyName())) {
+ // get Focus from NetworkPanel
+ updateFocus(e.getNewValue().toString());
+ pcs.firePropertyChange(e);
+ } else if (NETWORK_VIEWS_SELECTED.equals(e.getPropertyName())) {
+ Cytoscape.setSelectedNetworkViews( (List<String>)(e.getNewValue()) );
+ Cytoscape.setSelectedNetworks( (List<String>)(e.getNewValue()) );
+ pcs.firePropertyChange(e);
+ } else if (Cytoscape.NETWORK_CREATED.equals(e.getPropertyName())) {
+ // fire the event so that the NetworkPanel can catch it
+ pcs.firePropertyChange(e);
+ } else if (Cytoscape.NETWORK_DESTROYED.equals(e.getPropertyName())) {
+ // fire the event so that the NetworkPanel can catch it
+ pcs.firePropertyChange(e);
+
+ // Check new session or not
+ if ((Cytoscape.getNetworkSet().size() == 0)
+ && (Cytoscape.getSessionstate() != Cytoscape.SESSION_OPENED)) {
+ String message = "Do you want to create a new session?.\n(All attributes will be lost!)";
+
+ int result = JOptionPane.showConfirmDialog(this, message, "Create New Session?",
+ JOptionPane.YES_NO_OPTION,
+ JOptionPane.WARNING_MESSAGE, null);
+
+ if (result == JOptionPane.YES_OPTION)
+ Cytoscape.createNewSession();
+ }
+ } else if (NETWORK_VIEW_DESTROYED.equals(e.getPropertyName())) {
+ // remove the view from the GraphViewController
+ getGraphViewController().removeGraphView((CyNetworkView) e.getNewValue());
+ // pass on the event
+ pcs.firePropertyChange(e);
+ }
+ else if (e.getPropertyName().equalsIgnoreCase(Cytoscape.CYTOSCAPE_EXIT)){
+ // save Desktop location into property file "desktop.prop"
+ File desktop_prop_file = new File(CytoscapeInit.getConfigVersionDirectory(), "desktop.props");
+ Properties props = new Properties();
+ props.setProperty("x", new Integer(this.getX()).toString());
+ props.setProperty("y", new Integer(this.getY()).toString());
+ props.setProperty("w", new Integer(this.getWidth()).toString());
+ props.setProperty("h", new Integer(this.getHeight()).toString());
+ try {
+ props.store(new FileOutputStream(desktop_prop_file), "Remember desktop frame location");
+ }
+ catch (IOException ioe){
+ }
+
+ try {
+ Cytoscape.getRecentlyOpenedSessionTracker().writeOut();
+ } catch (final IOException ioe) {
+ System.err.println("failed to save recent session URLs!");
+ }
+ }
+ }
+
+ // ---------------------------------------------------------------------------//
+ // Cytopanels - Public and Protected methods
+
+ /**
+ * Gets a cytoPanel given a Compass direction.
+ *
+ * @param compassDirection
+ * Compass Direction (SwingConstants.{SOUTH,EAST,WEST}).
+ * @return CytoPanel The CytoPanel that lives in the region specified by
+ * compass direction.
+ */
+ public CytoPanel getCytoPanel(int compassDirection) {
+ // return appropriate cytoPanel based on compass direction
+ switch (compassDirection) {
+ case SwingConstants.SOUTH:
+ return (CytoPanel) cytoPanelSouth;
+ case SwingConstants.EAST:
+ return (CytoPanel) cytoPanelEast;
+ case SwingConstants.WEST:
+ return (CytoPanel) cytoPanelWest;
+ case SwingConstants.SOUTH_WEST:
+ return (CytoPanel) cytoPanelSouthWest;
+ }
+
+ // Houston we have a problem!
+ throw new IllegalArgumentException("Illegal Argument: " + compassDirection
+ + ". Must be one of: SwingConstants.{SOUTH,EAST,WEST,SOUTH_WEST}.");
+ }
+
+ /**
+ * Create the CytoPanels UI.
+ *
+ * @param networkPanel
+ * to load on left side of right bimodal.
+ * @param networkViewManager
+ * to load on left side (CytoPanel West).
+ * @return BiModalJSplitPane Object.
+ */
+ private BiModalJSplitPane setupCytoPanels(NetworkPanel networkPanel,
+ NetworkViewManager networkViewManager) {
+ // bimodals that our Cytopanels Live within
+ topRightPane = createTopRightPane(networkViewManager);
+ rightPane = createRightPane(topRightPane);
+ masterPane = createMasterPane(networkPanel, rightPane);
+ createBottomLeft();
+
+ return masterPane;
+ }
+
+ protected void createBottomLeft() {
+ cytoPanelSouthWest = new CytoPanelImp(SwingConstants.SOUTH_WEST, JTabbedPane.TOP,
+ CytoPanelState.HIDE);
+
+ final BiModalJSplitPane split = new BiModalJSplitPane(this, JSplitPane.VERTICAL_SPLIT,
+ BiModalJSplitPane.MODE_HIDE_SPLIT, new JPanel(),
+ cytoPanelSouthWest);
+ split.setResizeWeight(0);
+ cytoPanelSouthWest.setCytoPanelContainer(split);
+ cytoPanelSouthWest.setMinimumSize(new Dimension(180, 330));
+ cytoPanelSouthWest.setMaximumSize(new Dimension(180, 330));
+ cytoPanelSouthWest.setPreferredSize(new Dimension(180, 330));
+
+ split.setDividerSize(DEVIDER_SIZE);
+
+ new ToolCytoPanelListener( split, (CytoPanelImp)cytoPanelWest, cytoPanelSouthWest );
+ }
+
+ /**
+ * Creates the TopRight Pane.
+ *
+ * @param networkViewManager
+ * to load on left side of top right bimodal.
+ * @return BiModalJSplitPane Object.
+ */
+ protected BiModalJSplitPane createTopRightPane(NetworkViewManager networkViewManager) {
+ // create cytopanel with tabs along the top
+ cytoPanelEast = new CytoPanelImp(SwingConstants.EAST, JTabbedPane.TOP, CytoPanelState.HIDE);
+
+ // create the split pane - we show this on startup
+ final BiModalJSplitPane splitPane = new BiModalJSplitPane(this, JSplitPane.HORIZONTAL_SPLIT,
+ BiModalJSplitPane.MODE_HIDE_SPLIT,
+ networkViewManager.getDesktopPane(), cytoPanelEast);
+
+ // set the cytopanelcontainer
+ cytoPanelEast.setCytoPanelContainer(splitPane);
+
+ // set the resize weight - left component gets extra space
+ splitPane.setResizeWeight(1.0);
+
+ // outta here
+ return splitPane;
+ }
+
+ /**
+ * Creates the Right Panel.
+ *
+ * @param topRightPane
+ * TopRightPane Object.
+ * @return BiModalJSplitPane Object
+ */
+ protected BiModalJSplitPane createRightPane(BiModalJSplitPane topRightPane) {
+ // create cytopanel with tabs along the bottom
+ cytoPanelSouth = new CytoPanelImp(SwingConstants.SOUTH, JTabbedPane.BOTTOM,
+ CytoPanelState.HIDE);
+
+ // create the split pane - hidden by default
+ final BiModalJSplitPane splitPane = new BiModalJSplitPane(this, JSplitPane.VERTICAL_SPLIT,
+ BiModalJSplitPane.MODE_HIDE_SPLIT,
+ topRightPane, cytoPanelSouth);
+
+ // set the cytopanel container
+ cytoPanelSouth.setCytoPanelContainer(splitPane);
+
+ splitPane.setDividerSize(DEVIDER_SIZE);
+
+ // set resize weight - top component gets all the extra space.
+ splitPane.setResizeWeight(1.0);
+
+ // outta here
+ return splitPane;
+ }
+
+ /**
+ * Creates the Master Split Pane.
+ *
+ * @param networkPanel
+ * to load on left side of CytoPanel (cytoPanelWest).
+ * @param rightPane
+ * BiModalJSplitPane Object.
+ * @return BiModalJSplitPane Object.
+ */
+ protected BiModalJSplitPane createMasterPane(NetworkPanel networkPanel,
+ BiModalJSplitPane rightPane) {
+ // create cytopanel with tabs along the top
+ cytoPanelWest = new CytoPanelImp(SwingConstants.WEST, JTabbedPane.TOP, CytoPanelState.DOCK);
+
+ // add the network panel to our tab
+ String tab1Name = new String("Network");
+ cytoPanelWest.add(tab1Name, new ImageIcon(Cytoscape.class.getResource("images/class_hi.gif")),
+ networkPanel, "Cytoscape Network List");
+
+ // create the split pane - hidden by default
+ final BiModalJSplitPane splitPane = new BiModalJSplitPane(this, JSplitPane.HORIZONTAL_SPLIT,
+ BiModalJSplitPane.MODE_SHOW_SPLIT,
+ cytoPanelWest, rightPane);
+ splitPane.setDividerSize(DEVIDER_SIZE);
+
+ // set the cytopanel container
+ cytoPanelWest.setCytoPanelContainer(splitPane);
+
+ // We want to make sure that the networkPanel is selected (and resized)
+ int index = cytoPanelWest.indexOfComponent(networkPanel);
+ cytoPanelWest.setSelectedIndex(index);
+
+ // outta here
+ return splitPane;
+ }
+
+ // End Cytopanels - Public and Protected methods
+ // ---------------------------------------------------------------------------//
+
+ /**
+ * Gets the NetworkView Manager.
+ *
+ * @return NetworkViewManager Object.
+ */
+ public NetworkViewManager getNetworkViewManager() {
+ return this.networkViewManager;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public BirdsEyeViewHandler getBirdsEyeViewHandler() {
+ if (bevh == null)
+ bevh = new BirdsEyeViewHandler(networkViewManager.getDesktopPane());
+
+ return bevh;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param vt DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ * @deprecated View types are no longer support so stop using this. Will be removed August 2008.
+ */
+ public static int parseViewType(String vt) {
+ return 1; // What was internal
+ }
+}
diff --git a/application/src/main/java/cytoscape/view/FlagAndSelectionHandler.java b/application/src/main/java/cytoscape/view/FlagAndSelectionHandler.java
new file mode 100644
index 0000000..623269c
--- /dev/null
+++ b/application/src/main/java/cytoscape/view/FlagAndSelectionHandler.java
@@ -0,0 +1,276 @@
+/*
+ File: FlagAndSelectionHandler.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+//---------------------------------------------------------------------------
+// $Revision: 9920 $
+// $Date: 2007-04-09 23:17:52 +0200 (Mon, 09 Apr 2007) $
+// $Author: mes $
+//---------------------------------------------------------------------------
+package cytoscape.view;
+
+import cytoscape.data.SelectEvent;
+import cytoscape.data.SelectEventListener;
+import cytoscape.data.SelectFilter;
+
+//---------------------------------------------------------------------------
+import giny.model.Edge;
+import giny.model.Node;
+import giny.model.RootGraph;
+
+import giny.view.EdgeView;
+import giny.view.GraphView;
+import giny.view.GraphViewChangeEvent;
+import giny.view.GraphViewChangeListener;
+import giny.view.NodeView;
+
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Set;
+
+
+//---------------------------------------------------------------------------
+/**
+ * This class synchronizes the flagged status of nodes and edges as held by a
+ * SelectFilter object of a network with the selection status of the corresponding
+ * node and edge views in a GraphView. An object will be selected in the view
+ * iff the matching object is flagged in the SelectFilter. This class is only used
+ * by PhoebeNetworkView, which no longer used anywhere.
+ */
+public class FlagAndSelectionHandler implements SelectEventListener, GraphViewChangeListener {
+ private SelectFilter selectFilter;
+ private GraphView view;
+
+ /**
+ * Standard constructor takes the flag filter and the view that should be
+ * synchronized. On construction, this object will synchronize the filter
+ * and view by turning on flags or selections that are currently on in one
+ * of the two objects.
+ */
+ public FlagAndSelectionHandler(SelectFilter selectFilter, GraphView view) {
+ this.selectFilter = selectFilter;
+ this.view = view;
+ syncFilterAndView();
+ selectFilter.addSelectEventListener(this);
+ view.addGraphViewChangeListener(this);
+ }
+
+ /**
+ * Synchronizes the filter and view of this object by selecting every object
+ * that is currently flagged and vice versa.
+ */
+ private void syncFilterAndView() {
+ final Set<Node> flaggedNodes = selectFilter.getSelectedNodes();
+ final Set<Edge> flaggedEdges = selectFilter.getSelectedEdges();
+
+ final List<Node> selectedNodes = view.getSelectedNodes();
+ final List<Edge> selectedEdges = view.getSelectedEdges();
+
+ // select all nodes that are flagged but not currently selected
+ for (Iterator iter = flaggedNodes.iterator(); iter.hasNext();) {
+ Node node = (Node) iter.next();
+ NodeView nv = view.getNodeView(node);
+
+ if ((nv == null) || nv.isSelected()) {
+ continue;
+ }
+
+ nv.setSelected(true);
+ }
+
+ // select all edges that are flagged but not currently selected
+ for (Iterator iter = flaggedEdges.iterator(); iter.hasNext();) {
+ Edge edge = (Edge) iter.next();
+ EdgeView ev = view.getEdgeView(edge);
+
+ if ((ev == null) || ev.isSelected()) {
+ continue;
+ }
+
+ ev.setSelected(true);
+ }
+
+ // flag all nodes that are selected but not currently flagged
+ for (Iterator iter = selectedNodes.iterator(); iter.hasNext();) {
+ NodeView nv = (NodeView) iter.next();
+ Node node = nv.getNode();
+ selectFilter.setSelected(node, true); // does nothing if already
+ // flagged
+ }
+
+ // flag all edges that are selected but not currently flagged
+ for (Iterator iter = selectedEdges.iterator(); iter.hasNext();) {
+ EdgeView ev = (EdgeView) iter.next();
+ Edge edge = ev.getEdge();
+ selectFilter.setSelected(edge, true); // does nothing if already
+ // flagged
+ }
+ }
+
+ /**
+ * Responds to selection events from the view by setting the matching
+ * flagged state in the SelectFilter object.
+ */
+ public void graphViewChanged(GraphViewChangeEvent event) {
+ // GINY bug: the event we get frequently has the correct indices
+ // but incorrect Node and Edge objects. For now we get around this
+ // by converting indices to graph objects ourselves
+ final GraphView source = (GraphView) event.getSource();
+ final RootGraph rootGraph = source.getGraphPerspective().getRootGraph();
+
+ int[] objIndecies;
+
+ if (event.isNodesSelectedType()) {
+ objIndecies = event.getSelectedNodeIndices();
+
+ final List<Node> selList = new ArrayList<Node>();
+
+ for (int index = 0; index < objIndecies.length; index++) {
+ selList.add(rootGraph.getNode(objIndecies[index]));
+ }
+
+ selectFilter.setSelectedNodes(selList, true);
+ } else if (event.isNodesUnselectedType() || event.isNodesHiddenType()) {
+ if (event.isNodesUnselectedType()) {
+ objIndecies = event.getUnselectedNodeIndices();
+ } else {
+ objIndecies = event.getHiddenNodeIndices();
+ }
+
+ final List<Node> unselList = new ArrayList<Node>();
+
+ for (int index = 0; index < objIndecies.length; index++) {
+ unselList.add(rootGraph.getNode(objIndecies[index]));
+ }
+
+ selectFilter.setSelectedNodes(unselList, false);
+ } else if (event.isEdgesSelectedType()) {
+ objIndecies = event.getSelectedEdgeIndices();
+
+ final List<Edge> selList = new ArrayList<Edge>();
+
+ for (int index = 0; index < objIndecies.length; index++) {
+ selList.add(rootGraph.getEdge(objIndecies[index]));
+ }
+
+ selectFilter.setSelectedEdges(selList, true);
+ } else if (event.isEdgesUnselectedType() || event.isEdgesHiddenType()) {
+ if (event.isEdgesUnselectedType()) {
+ objIndecies = event.getUnselectedEdgeIndices();
+ } else {
+ objIndecies = event.getHiddenEdgeIndices();
+ }
+
+ final List<Edge> unselList = new ArrayList<Edge>();
+
+ for (int index = 0; index < objIndecies.length; index++) {
+ unselList.add(rootGraph.getEdge(objIndecies[index]));
+ }
+
+ selectFilter.setSelectedEdges(unselList, false);
+ }
+ }
+
+ /**
+ * Responds to events indicating a change in the flagged state of one or
+ * more nodes or edges. Sets the corresponding selection state for views of
+ * those objects in the graph view.
+ */
+ public void onSelectEvent(SelectEvent event) {
+ if (event.getTargetType() == SelectEvent.SINGLE_NODE) { // single node
+ setNodeSelected((Node) event.getTarget(), event.getEventType());
+ } else if (event.getTargetType() == SelectEvent.SINGLE_EDGE) { // single
+ // edge
+ setEdgeSelected((Edge) event.getTarget(), event.getEventType());
+ } else if (event.getTargetType() == SelectEvent.NODE_SET) { // multiple
+ // nodes
+
+ Set nodeSet = (Set) event.getTarget();
+
+ for (Iterator iter = nodeSet.iterator(); iter.hasNext();) {
+ Node node = (Node) iter.next();
+ setNodeSelected(node, event.getEventType());
+ }
+ } else if (event.getTargetType() == SelectEvent.EDGE_SET) { // multiple
+ // edges
+
+ Set edgeSet = (Set) event.getTarget();
+
+ for (Iterator iter = edgeSet.iterator(); iter.hasNext();) {
+ Edge edge = (Edge) iter.next();
+ setEdgeSelected(edge, event.getEventType());
+ }
+ } else { // unexpected target type
+
+ return;
+ }
+ }
+
+ /**
+ * Helper method to set selection for a node view.
+ */
+ private void setNodeSelected(Node node, boolean selectOn) {
+ NodeView nodeView = view.getNodeView(node);
+
+ if (nodeView == null) {
+ return;
+ } // sanity check
+ // Giny fires a selection event even if there's no change in state
+ // we trap this by only requesting a selection if there's a change
+
+ if (nodeView.isSelected() != selectOn) {
+ nodeView.setSelected(selectOn);
+ }
+ }
+
+ /**
+ * Helper method to set selection for an edge view.
+ */
+ private void setEdgeSelected(Edge edge, boolean selectOn) {
+ EdgeView edgeView = view.getEdgeView(edge);
+
+ if (edgeView == null) {
+ return;
+ } // sanity check
+ // Giny fires a selection event even if there's no change in state
+ // we trap this by only requesting a selection if there's a change
+
+ if (edgeView.isSelected() != selectOn) {
+ edgeView.setSelected(selectOn);
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/view/GraphViewController.java b/application/src/main/java/cytoscape/view/GraphViewController.java
new file mode 100644
index 0000000..566ab6a
--- /dev/null
+++ b/application/src/main/java/cytoscape/view/GraphViewController.java
@@ -0,0 +1,450 @@
+/*
+ File: GraphViewController.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+/**
+ * @author Iliana Avila-Campillo
+ * @version %I%, %G%
+ * @since 2.0
+ */
+package cytoscape.view;
+
+import cern.colt.list.IntArrayList;
+
+import giny.model.GraphPerspective;
+import giny.model.GraphPerspectiveChangeEvent;
+import giny.model.GraphPerspectiveChangeListener;
+
+import giny.view.GraphView;
+
+import java.util.*;
+
+import cytoscape.logger.CyLogger;
+
+
+/**
+ *
+ */
+public class GraphViewController implements giny.model.GraphPerspectiveChangeListener {
+ protected Map graphViewToHandler; // a map of GraphViews to GraphViewHandlers
+ protected Map gpToGv; // a map of GraphPerspectives to GraphViews
+
+ /**
+ *
+ */
+ public static final GraphViewHandler DEFAULT_GRAPH_VIEW_HANDLER = new BasicGraphViewHandler();
+
+ /**
+ * Empty constructor, initializes class members to empty HashMaps.
+ */
+ public GraphViewController() {
+ this.graphViewToHandler = new HashMap();
+ this.gpToGv = new HashMap();
+ } //GraphViewController
+
+ /**
+ * Constructor, assigns <code>GraphViewController.DEFAULT_GRAPH_VIEW_HANDLER</code>
+ * to all the given <code>giny.view.GraphView</code> objects in the array.
+ *
+ * @param graph_views an array of <code>giny.view.GraphView</code> objects
+ * that this <code>GraphViewController</code> will keep synchronized to
+ * their corresponding <code>giny.model.GraphPerspective</code> objects
+ * available through their <code>getGraphPerspective()</code> method.
+ */
+ public GraphViewController(GraphView[] graph_views) {
+ this.graphViewToHandler = new HashMap();
+ this.gpToGv = new HashMap();
+ setGraphViews(graph_views);
+ } //GraphViewController
+
+ /**
+ * Constructor, specifies the <code>cytoscape.view.GraphViewHandler</code> objects
+ * for the given <code>giny.view.GraphView</code> objects in the arrays.
+ *
+ * @param graph_views an array of <code>giny.view.GraphView</code> objects
+ * that this <code>GraphViewController</code> will keep synchronized to
+ * their corresponding <code>giny.model.GraphPerspective</code> objects
+ * available through their <code>getGraphPerspective()</code> method
+ * @param gv_to_handler a <code>Map</code> with <code>giny.view.GraphView</code>
+ * objects as keys, and <code>cytoscape.view.GraphViewHandler</code> objects
+ * as values, two or more different keys can share the same value, the
+ * DEFAULT_GRAPH_VIEW_HANDLER will be set for <code>giny.view.GraphView</code>
+ * objects that are not keys in the given <code>Map</code>
+ */
+ public GraphViewController(GraphView[] graph_views, Map gv_to_handler) {
+ this.graphViewToHandler = new HashMap();
+ this.gpToGv = new HashMap();
+ setGraphViews(graph_views, gv_to_handler);
+ } //GraphViewController
+
+ /**
+ * Sets the array of <code>giny.view.GraphView</code> objects
+ * that this <code>GraphViewController</code> will keep synchronized with
+ * their corresponding <code>giny.model.GraphPerspective</code> objects
+ * available through their <code>getGraphPerspective()</code> method, the
+ * DEFAULT_GRAPH_VIEW_HANDLER is set for all the views. Any previous <code>GraphView</code>
+ * objects are removed from this listener
+ *
+ * @param graph_views an array of <code>giny.view.GraphView</code> objects
+ */
+ public void setGraphViews(GraphView[] graph_views) {
+ removeAllGraphViews();
+
+ for (int i = 0; i < graph_views.length; i++) {
+ GraphPerspective graphPerspective = graph_views[i].getGraphPerspective();
+ graphPerspective.addGraphPerspectiveChangeListener(this);
+ this.gpToGv.put(graphPerspective, graph_views[i]);
+ this.graphViewToHandler.put(graph_views[i], DEFAULT_GRAPH_VIEW_HANDLER);
+ } //for i
+ } //setGraphViews
+
+ /**
+ * Sets the array of <code>giny.view.GraphView</code> objects
+ * that this <code>GraphViewController</code> will keep synchronized with
+ * their corresponding <code>giny.model.GraphPerspective</code> objects
+ * available through their <code>getGraphPerspective()</code> method, the
+ * <code>cytoscape.view.GraphViewHandler</code> objects for the
+ * <code>GraphView</code>s are obtained from the given <code>Map</code>,
+ * if a <code>GraphView</code> in the array is not a key in the <code>Map</code>
+ * then DEFAULT_GRAPH_VIEW_HANDLER is used. Any previous <code>GraphView</code>
+ * objects are removed from this listener
+ *
+ * @param graph_views an array of <code>giny.view.GraphView</code> objects
+ * @param gv_to_handler a <code>Map</code> with <code>giny.view.GraphView</code>
+ * for keys and <code>cytoscape.view.GraphViewHandler</code> objects for values
+ */
+ public void setGraphViews(GraphView[] graph_views, Map gv_to_handler) {
+ removeAllGraphViews();
+
+ for (int i = 0; i < graph_views.length; i++) {
+ GraphPerspective graphPerspective = graph_views[i].getGraphPerspective();
+ graphPerspective.addGraphPerspectiveChangeListener(this);
+ this.gpToGv.put(graphPerspective, graph_views[i]);
+
+ GraphViewHandler handler = (GraphViewHandler) gv_to_handler.get(graph_views[i]);
+
+ if (handler == null) {
+ this.graphViewToHandler.put(graph_views[i], DEFAULT_GRAPH_VIEW_HANDLER);
+ } else {
+ this.graphViewToHandler.put(graph_views[i], handler);
+ }
+ } //for i
+ } //setGraphViews
+
+ /**
+ * Gets an array of <code>giny.view.GraphView</code> objects
+ * that this <code>GraphViewController</code> will keep synchronized with
+ * their corresponding <code>giny.model.GraphPerspective</code> objects
+ * available through their <code>getGraphPerspective()</code> method
+ *
+ * @return an array of <code>giny.view.GraphView</code> objects
+ */
+ public GraphView[] getGraphViews() {
+ Set keySet = this.graphViewToHandler.keySet();
+
+ return (GraphView[]) keySet.toArray(new GraphView[keySet.size()]);
+ } //getGraphViews
+
+ /**
+ * Gets a <code>Map</code> with <code>giny.view.GraphView</code>
+ * objects as keys, and <code>cytoscape.view.GraphViewHandler</code> objects
+ * as values, two or more different keys can share the same value.
+ *
+ * @return the <code>Map</code> that specifies what <code>cytoscape.view.GraphViewHandler</code>
+ * objects handle the <code>giny.view.GraphView</code> objects in this controller.
+ */
+ public Map getGraphViewHandlersMap() {
+ return this.graphViewToHandler;
+ } //getGraphViewHandlersMap
+
+ /**
+ * Gets the <code>cytoscape.view.GraphViewHandler</code> for the given
+ * <code>giny.view.GraphView</code>
+ *
+ * @return a <code>cytoscape.view.GraphViewHandler</code>, or null if this
+ * <code>GraphViewController</code> does not control the given
+ * <code>giny.view.GraphView</code>
+ */
+ public GraphViewHandler getGraphViewHandler(GraphView graph_view) {
+ return (GraphViewHandler) this.graphViewToHandler.get(graph_view);
+ } //getGraphViewHandler
+
+ /**
+ * If this <code>GraphViewController</code> contains the given
+ * <code>giny.view.GraphView</code>, then it is removed from it, and it no longer listens
+ * for change events from the removed <code>giny.view.GraphView</code>'s
+ * <code>giny.model.GraphPerspective</code>.
+ *
+ * @param graph_view the <code>giny.view.GraphView</code> that will be removed
+ * @return the removed <code>giny.view.GraphView</code>'s
+ * <code>cytoscape.view.GraphViewHandler</code>, or null if it is not in this
+ * <code>GraphViewController</code>
+ */
+ public GraphViewHandler removeGraphView(GraphView graph_view) {
+ if (this.graphViewToHandler.containsKey(graph_view)) {
+ GraphPerspective graphPerspective = graph_view.getGraphPerspective();
+ graphPerspective.removeGraphPerspectiveChangeListener(this);
+ this.gpToGv.remove(graphPerspective);
+
+ GraphViewHandler gvHandler = (GraphViewHandler) this.graphViewToHandler.remove(graph_view);
+
+ return gvHandler;
+ } // if containsKey
+
+ return null;
+ } //removeGraphView
+
+ /**
+ * Adds to the set of <code>giny.view.GraphView</code> objects that this
+ * <code>GraphViewController</code> keeps synchronized with their
+ * <code>giny.model.GraphPerspective</code> objects.
+ * DEFAULT_GRAPH_VIEW_HANDLER is used for the given <code>giny.view.GraphView</code>
+ *
+ * @param graph_view the <code>giny.view.GraphView</code> to be added
+ * @return true if succesfully added, false otherwise (if it was already added)
+ * @see GraphViewController.setGraphViewHandler
+ */
+ public boolean addGraphView(GraphView graph_view) {
+ if (this.graphViewToHandler.containsKey(graph_view)) {
+ // already contained in this controller
+ return false;
+ }
+
+ GraphPerspective graphPerspective = graph_view.getGraphPerspective();
+ graphPerspective.addGraphPerspectiveChangeListener(this);
+ this.gpToGv.put(graphPerspective, graph_view);
+ this.graphViewToHandler.put(graph_view, DEFAULT_GRAPH_VIEW_HANDLER);
+
+ return true;
+ } //addGraphView
+
+ /**
+ * Adds to the set of <code>giny.view.GraphView</code> objects that this
+ * <code>GraphViewController</code> keeps synchronized to their
+ * <code>giny.model.GraphPerspective</code> objects. The given <code>GraphViewHandler</code>
+ * is used for the given <code>giny.view.GraphView</code> object.
+ *
+ * @param graph_view the <code>giny.view.GraphView</code> to be added
+ * @param gv_to_handler the <code>GraphViewHandler</code> that will handle
+ * change events from <code>graph_view</code>'s <code>giny.model.GraphPerspective</code> member
+ * @return true if succesfully added, false otherwise (if <code>graph_view</code> is
+ * already in this controller)
+ * @see #setGraphViewHandler(GraphView, GraphViewHandler) setGraphViewHandler
+ */
+ public boolean addGraphView(GraphView graph_view, GraphViewHandler gv_handler) {
+ if (this.graphViewToHandler.containsKey(graph_view)) {
+ // already contained
+ return false;
+ }
+
+ GraphPerspective graphPerspective = graph_view.getGraphPerspective();
+ graphPerspective.addGraphPerspectiveChangeListener(this);
+ this.gpToGv.put(graphPerspective, graph_view);
+ this.graphViewToHandler.put(graph_view, gv_handler);
+
+ return true;
+ } //addGraphView
+
+ /**
+ * If the given <code>giny.view.GraphView</code> object belongs to this
+ * <code>GraphViewController</code>, then its <code>GraphViewHandler</code>
+ * is set to the given one.
+ *
+ * @param graph_view the <code>giny.view.GraphView</code> to be updated
+ * @param gv_handler the <code>GraphViewHandler</code> that will handle
+ * change events from <code>graph_view</code>'s <code>giny.model.GraphPerspective</code>
+ * @return true if the method was successful, false otherwise (if <code>graph_view</code>
+ * is not in this controller)
+ */
+ public boolean setGraphViewHandler(GraphView graph_view, GraphViewHandler gv_handler) {
+ if (this.graphViewToHandler.containsKey(graph_view)) {
+ this.graphViewToHandler.put(graph_view, gv_handler);
+
+ return true;
+ }
+
+ return false;
+ } //setGraphViewHandler
+
+ /**
+ * Removes all of the current <code>giny.view.GraphView</code> objects that this
+ * <code>GraphViewController</code> keeps synchronized to their corresponding
+ * <code>giny.model.GraphPerspective</code> members. This <code>GraphViewController</code>
+ * will no longer receive events from <code>giny.model.GraphPerspective</code>s after
+ * this call.
+ *
+ * @return the array of removed <code>giny.view.GraphView</code> objects
+ */
+ public GraphView[] removeAllGraphViews() {
+ GraphView[] gViews = getGraphViews();
+
+ for (int i = 0; i < gViews.length; i++) {
+ GraphPerspective graphPerspective = gViews[i].getGraphPerspective();
+ graphPerspective.removeGraphPerspectiveChangeListener(this);
+ } //for i
+
+ this.gpToGv.clear();
+ this.graphViewToHandler.clear();
+
+ return gViews;
+ } //removeAllGraphViews
+
+ /**
+ * Whether or not the given <code>giny.view.GraphView</code> is kept synchronized
+ * with its <code>giny.model.GraphPerspective</code> member by this
+ * <code>GraphViewController</code>.
+ *
+ * @param graph_view the <code>giny.view.GraphView</code> object to test
+ */
+ public boolean containsGraphView(GraphView graph_view) {
+ return this.graphViewToHandler.containsKey(graph_view);
+ } //containsGraphView
+
+ /**
+ * It temporarily removes this <code>GraphViewController</code> as a listener for
+ * all <code>giny.model.GraphPerspective</code> objects that it currently
+ * listens to
+ *
+ * @see #resumeListening() resumeListening
+ */
+ public void stopListening() {
+ GraphView[] graphViews = getGraphViews();
+
+ for (int i = 0; i < graphViews.length; i++) {
+ GraphPerspective graphPerspective = graphViews[i].getGraphPerspective();
+ graphPerspective.removeGraphPerspectiveChangeListener(this);
+ } //for i
+ } //stopListening
+
+ /**
+ * It temporarily removes this <code>GraphViewController</code> listener
+ * from the <code>giny.model.GraphPerspective</code> object that the given
+ * <code>giny.view.GraphView</code> views.
+ *
+ * @see #resumeListening(GraphView)
+ */
+
+ // TODO: Catch all change events even of stopListening has been called, and when
+ // listening is resumed, update the graph view
+ public void stopListening(GraphView graph_view) {
+ GraphPerspective graphPerspective = graph_view.getGraphPerspective();
+ graphPerspective.removeGraphPerspectiveChangeListener(this);
+ } //stopListening
+
+ /**
+ * It adds this <code>GraphViewController</code> as a listener for
+ * all <code>giny.model.GraphPerspective</code> that were temporarily
+ * "removed" by calling <code>stopListening()</code>, it updates the <code>GraphViews</code>
+ * of the <code>GraphPerspectives</code> so that they are synchronized to reflect changes that
+ * may have occured while not listening.
+ *
+ * @see #stopListening() stopListening
+ */
+ public void resumeListening() {
+ GraphView[] graphViews = getGraphViews();
+
+ for (int i = 0; i < graphViews.length; i++) {
+ GraphPerspective graphPerspective = graphViews[i].getGraphPerspective();
+ GraphViewHandler handler = (GraphViewHandler) this.graphViewToHandler.get(graphViews[i]);
+ handler.updateGraphView(graphViews[i]);
+ graphPerspective.addGraphPerspectiveChangeListener(this);
+ } //for i
+ } //resumeListening
+
+ /**
+ * It adds this <code>GraphViewController</code> listener to the
+ * <code>giny.model.GraphPerspective</code> of the given <code>giny.view.GraphView</code>
+ * that was temporarily "removed" by a call to <code>stopListening(GraphView)</code>, it updates
+ * <code>graph_view</code> so that it's synchronized to its <code>GraphPerspective</code>
+ * due to changes that may have occured while not listening.
+ *
+ * @see #stopListening(GraphView)
+ */
+ public void resumeListening(GraphView graph_view) {
+ GraphViewHandler handler = (GraphViewHandler) this.graphViewToHandler.get(graph_view);
+ handler.updateGraphView(graph_view);
+
+ GraphPerspective graphPerspective = graph_view.getGraphPerspective();
+ graphPerspective.addGraphPerspectiveChangeListener(this);
+ } //resumeListening
+
+ /**
+ * Invoked when a graph change to any of the <code>giny.model.GraphPerspective</code>
+ * objects accessed through <code>giny.view.GraphView.getGraphPerspective()</code> of
+ * this object's graphViews is made.
+ *
+ * @param event the event that was generated, contains the source
+ * <code>giny.model.GraphPerspective</code>
+ */
+ public void graphPerspectiveChanged(GraphPerspectiveChangeEvent event) {
+ //TODO: Remove
+ //CyLogger.getLogger().info("In GraphViewController.graphPerspectiveChanged()");
+ Object source = event.getSource();
+
+ if (!(source instanceof GraphPerspective)) {
+ // TODO: What to do? There was a change in the RootGraph, do we propagate it
+ // to all the GraphPerspectives????
+ return;
+ }
+
+ GraphPerspective changedGraphPers = (GraphPerspective) source;
+ GraphView graphView = (GraphView) this.gpToGv.get(changedGraphPers);
+
+ if (graphView == null) {
+ // Somehow, we are listening to events of a GraphPerspective that
+ // no GraphView in our data structures views
+ CyLogger.getLogger().warn("Oops! the GraphPerspective " + changedGraphPers
+ + " does not have a corresponding GraphView in the GraphViewController!!!");
+
+ return;
+ } // if graphView == null
+
+ GraphViewHandler gvHandler = (GraphViewHandler) this.graphViewToHandler.get(graphView);
+
+ if (gvHandler == null) {
+ // Somehow, we have a graphView with no handler!
+ CyLogger.getLogger().warn("Oops! the GraphView " + graphView
+ + " has no GraphViewHandler in the GraphViewController!!!");
+
+ return;
+ } //if gvHandler == null
+
+ gvHandler.handleGraphPerspectiveEvent(event, graphView);
+
+ // if ( graphView instanceof PhoebeNetworkView )
+ // ( ( PhoebeNetworkView )graphView).updateStatusLabel();
+ } //graphPerspectiveChanged
+} //class GraphViewController
diff --git a/application/src/main/java/cytoscape/view/GraphViewHandler.java b/application/src/main/java/cytoscape/view/GraphViewHandler.java
new file mode 100644
index 0000000..2c6691a
--- /dev/null
+++ b/application/src/main/java/cytoscape/view/GraphViewHandler.java
@@ -0,0 +1,75 @@
+/*
+ File: GraphViewHandler.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+/**
+ * @author Iliana Avila-Campillo
+ * @version %I%, %G%
+ * @since 2.0
+ */
+package cytoscape.view;
+
+import giny.model.GraphPerspectiveChangeEvent;
+
+import giny.view.GraphView;
+
+
+/**
+ * This interface represents an object that handles a change in a
+ * <code>giny.mode.GraphPerspective</code> by updating one of its
+ * <code>giny.view.GraphView</code>s.
+ */
+public interface GraphViewHandler {
+ /**
+ * Handles the event as desired by updating the given <code>giny.view.GraphView</code>.
+ *
+ * @param event the event to handle
+ * @param graph_view the <code>giny.view.GraphView</code> that views the
+ * <code>giny.model.GraphPerspective</code> that generated the event and that should
+ * be updated as necessary
+ */
+ public void handleGraphPerspectiveEvent(GraphPerspectiveChangeEvent event, GraphView graph_view);
+
+ /**
+ * Updates graph_view so that it is synchronized with its <code>giny.model.GraphPerspective</code>
+ * Useful if <code>GraphPerspectiveChangeEvents</code> haven't been handled,
+ * and a <code>graph_view</code> must be made synchronized with its GraphPerspective.
+ *
+ * @param graph_view the <code>giny.view.GraphView</code> that views the should
+ * be updated as necessary
+ */
+ public void updateGraphView(GraphView graph_view);
+} //GraphViewHandler
diff --git a/application/src/main/java/cytoscape/view/IconTableCellRenderer.java b/application/src/main/java/cytoscape/view/IconTableCellRenderer.java
new file mode 100644
index 0000000..dcb0f5e
--- /dev/null
+++ b/application/src/main/java/cytoscape/view/IconTableCellRenderer.java
@@ -0,0 +1,39 @@
+package cytoscape.view;
+
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Font;
+
+import javax.swing.BorderFactory;
+import javax.swing.Icon;
+import javax.swing.JLabel;
+import javax.swing.JTable;
+import javax.swing.SwingConstants;
+import javax.swing.table.TableCellRenderer;
+
+public class IconTableCellRenderer implements TableCellRenderer {
+
+ private static final Font ICON_FONT = new Font("SansSerif", Font.BOLD, 20);
+
+ public Component getTableCellRendererComponent(JTable table, Object value,
+ boolean isSelected, boolean hasFocus, int row, int column) {
+
+ final JLabel label = new JLabel();
+ label.setBorder(BorderFactory.createLineBorder(Color.DARK_GRAY, 1));
+ label.setHorizontalTextPosition(SwingConstants.CENTER);
+ label.setHorizontalAlignment(SwingConstants.CENTER);
+ label.setVerticalAlignment(SwingConstants.CENTER);
+ label.setVerticalTextPosition(SwingConstants.CENTER);
+
+ if (value != null && value instanceof Icon) {
+ label.setIcon((Icon) value);
+ } else {
+
+ label.setFont(ICON_FONT);
+ label.setText("?");
+ }
+
+ return label;
+ }
+
+}
\ No newline at end of file
diff --git a/application/src/main/java/cytoscape/view/InternalFrameComponent.java b/application/src/main/java/cytoscape/view/InternalFrameComponent.java
new file mode 100644
index 0000000..19ac810
--- /dev/null
+++ b/application/src/main/java/cytoscape/view/InternalFrameComponent.java
@@ -0,0 +1,208 @@
+/*
+ File: InternalFrameComponent.java
+
+ Copyright (c) 2006, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.view;
+
+
+// imports
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.print.PageFormat;
+import java.awt.print.Printable;
+import java.awt.print.PrinterException;
+
+import javax.swing.JComponent;
+import javax.swing.JLayeredPane;
+
+import ding.view.DGraphView;
+import ding.view.DingCanvas;
+
+
+/**
+ * This class manages the JLayeredPane that resides in
+ * each internal frame of cytoscape. Its intended to be the
+ * class which encapsulates the multiple canvases that are created
+ * by the DGraphView class.
+ */
+public class InternalFrameComponent extends JComponent implements Printable {
+
+ private static final long serialVersionUID = -6037450600865410121L;
+
+ /**
+ * z-order enumeration
+ *
+ * TODO: this breaks resize-handle on Mac OS X.
+ * Need to do some research on this layring order.
+ *
+ */
+ private static enum ZOrder {
+ BACKGROUND_PANE,
+ NETWORK_PANE,
+ FOREGROUND_PANE;
+ int layer() {
+ if (this == BACKGROUND_PANE)
+ return 10;
+
+ if (this == NETWORK_PANE)
+ return 20;
+
+ if (this == FOREGROUND_PANE)
+ return 30;
+
+ return 0;
+ }
+ }
+
+ /**
+ * ref to the JInternalFrame's JLayeredPane
+ */
+ private JLayeredPane layeredPane;
+
+ /**
+ * ref to background canvas
+ */
+ private DingCanvas backgroundCanvas;
+
+ /**
+ * ref to network canvas
+ */
+ private DingCanvas networkCanvas;
+
+ /**
+ * ref to foreground canvas
+ */
+ private DingCanvas foregroundCanvas;
+
+ /**
+ * Constructor.
+ *
+ * @param layeredPane JLayedPane
+ * @param dGraphView dGraphView
+ */
+ public InternalFrameComponent(JLayeredPane layeredPane, DGraphView dGraphView) {
+ // init members
+ this.layeredPane = layeredPane;
+ this.backgroundCanvas = dGraphView.getCanvas(DGraphView.Canvas.BACKGROUND_CANVAS);
+ this.networkCanvas = dGraphView.getCanvas(DGraphView.Canvas.NETWORK_CANVAS);
+ this.foregroundCanvas = dGraphView.getCanvas(DGraphView.Canvas.FOREGROUND_CANVAS);
+
+ // set default ordering
+ initLayeredPane();
+ }
+
+ /**
+ * Our implementation of Component setBounds(). If we don't do this, the
+ * individual canvasses do not get rendered.
+ *
+ * @param x int
+ * @param y int
+ * @param width int
+ * @param height int
+ */
+ public void setBounds(int x, int y, int width, int height) {
+ super.setBounds(x, y, width, height);
+ // call reshape on each innercanvas
+ backgroundCanvas.setBounds(x, y, width, height);
+ networkCanvas.setBounds(x, y, width, height);
+ foregroundCanvas.setBounds(x, y, width, height);
+ }
+
+ /**
+ * Our implementation of the Printable interface.
+ *
+ * @param graphics Graphics (context into which the page is drawn)
+ * @param pageFormat PageFormat (size and orientation of the page being drawn)
+ * @param pageIndex int (the zero based index of the page being drawn)
+ *
+ * @return PAGE_EXISTS if the page is rendered or NO_SUCH_PAGE if pageIndex specifies non-existent page
+ * @throws PrinterException
+ */
+ public int print(Graphics graphics, PageFormat pageFormat, int pageIndex) throws PrinterException
+ {
+ if (pageIndex == 0) {
+ ((Graphics2D) graphics).translate(pageFormat.getImageableX(), pageFormat.getImageableY());
+
+ // Apply a scale factor to the image to make sure the whole image on the screen
+ // will fit to the printable area of the paper
+ double image_scale = Math.min(pageFormat.getImageableWidth() / this.getWidth(),
+ pageFormat.getImageableHeight() / this.getHeight());
+
+ if (image_scale < 1.0d) {
+ ((Graphics2D) graphics).scale(image_scale, image_scale);
+ }
+
+ //TODO look at whether we should be clipping like this
+ graphics.clipRect(0, 0, backgroundCanvas.getWidth(), backgroundCanvas.getHeight());
+ backgroundCanvas.print(graphics);
+ networkCanvas.print(graphics);
+ foregroundCanvas.print(graphics);
+
+ return PAGE_EXISTS;
+ } else
+
+ return NO_SUCH_PAGE;
+ }
+
+ /**
+ * This method is used by image export libraries.
+ */
+ public void print(Graphics g) {
+ backgroundCanvas.print(g);
+
+ // This is a work-around, otherwise we lose backgroundCanvas color
+ networkCanvas.setBackground(backgroundCanvas.getBackground());
+
+ networkCanvas.print(g);
+ foregroundCanvas.print(g);
+ }
+
+ /**
+ * This method is used by image export libraries. This method is required for export formats that
+ * do not support transparency because otherwise the foreground layer will obscure a network.
+ */
+ public void printWithoutForeground(Graphics g) {
+ backgroundCanvas.print(g);
+
+ // This is a work-around, otherwise we lose backgroundCanvas color
+ networkCanvas.setBackground(backgroundCanvas.getBackground());
+
+ networkCanvas.print(g);
+ }
+
+ /**
+ * Places the canvas on the layeredPane in the following manner:
+ * top - bottom: foreground, network, background
+ */
+ private void initLayeredPane() {
+ // foreground followed by network followed by background
+ layeredPane.add(backgroundCanvas, new Integer(ZOrder.BACKGROUND_PANE.layer()));
+ layeredPane.add(networkCanvas, new Integer(ZOrder.NETWORK_PANE.layer()));
+ layeredPane.add(foregroundCanvas, new Integer(ZOrder.FOREGROUND_PANE.layer()));
+ }
+}
diff --git a/application/src/main/java/cytoscape/view/NetworkPanel.java b/application/src/main/java/cytoscape/view/NetworkPanel.java
new file mode 100644
index 0000000..82091cf
--- /dev/null
+++ b/application/src/main/java/cytoscape/view/NetworkPanel.java
@@ -0,0 +1,666 @@
+/*
+ File: NetworkPanel.java
+
+ Copyright (c) 2006, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.view;
+
+import java.awt.BorderLayout;
+import java.awt.Component;
+import java.awt.Dimension;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.Iterator;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Set;
+import java.util.TreeSet;
+
+import javax.swing.BoxLayout;
+import javax.swing.InputMap;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JPanel;
+import javax.swing.JPopupMenu;
+import javax.swing.JScrollPane;
+import javax.swing.JSplitPane;
+import javax.swing.JTree;
+import javax.swing.KeyStroke;
+import javax.swing.ListSelectionModel;
+import javax.swing.ToolTipManager;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+import javax.swing.event.SwingPropertyChangeSupport;
+import javax.swing.event.TreeSelectionEvent;
+import javax.swing.event.TreeSelectionListener;
+import javax.swing.tree.DefaultMutableTreeNode;
+import javax.swing.tree.TreeNode;
+import javax.swing.tree.TreePath;
+
+import cytoscape.CyNetwork;
+import cytoscape.CyNetworkTitleChange;
+import cytoscape.Cytoscape;
+import cytoscape.actions.ApplyVisualStyleAction;
+import cytoscape.actions.CreateNetworkViewAction;
+import cytoscape.data.SelectEvent;
+import cytoscape.data.SelectEventListener;
+import cytoscape.logger.CyLogger;
+import cytoscape.util.CyNetworkNaming;
+import cytoscape.util.swing.JTreeTable;
+import cytoscape.view.cytopanels.BiModalJSplitPane;
+
+import giny.model.Node;
+
+
+/**
+ * GUI component for managing network list in current session.
+ */
+public class NetworkPanel extends JPanel implements PropertyChangeListener, TreeSelectionListener,
+ SelectEventListener, ChangeListener
+{
+ private static final long serialVersionUID = -7102083850894612840L;
+
+ private static final int DEF_DEVIDER_LOCATION = 280;
+ private static final int PANEL_PREFFERED_WIDTH = 250;
+
+ private static final int DEF_ROW_HEIGHT = 20;
+
+ // Make this panel as a source of events.
+ private final SwingPropertyChangeSupport pcs;
+
+ private final JTreeTable treeTable;
+ private final NetworkTreeNode root;
+
+ private JPanel navigatorPanel;
+
+ private JPanel networkTreePanel;
+
+ private JPopupMenu popup;
+ private PopupActionListener popupActionListener;
+
+ private JMenuItem createViewItem;
+ private JMenuItem destroyViewItem;
+ private JMenuItem destroyNetworkItem;
+ private JMenuItem editNetworkTitle;
+ private JMenuItem applyVisualStyleMenu;
+
+ private BiModalJSplitPane split;
+
+ private final NetworkTreeTableModel treeTableModel;
+ private final CytoscapeDesktop cytoscapeDesktop;
+
+ private boolean doNotEnterValueChanged = false;
+
+ /**
+ * Constructor for the Network Panel.
+ *
+ * @param desktop
+ */
+ public NetworkPanel(final CytoscapeDesktop desktop) {
+ super();
+ this.cytoscapeDesktop = desktop;
+
+ root = new NetworkTreeNode("Network Root", "root");
+ treeTableModel = new NetworkTreeTableModel(root);
+
+ treeTable = new JTreeTable(treeTableModel);
+ treeTable.setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION);
+ initialize();
+
+ /*
+ * Remove CTR-A for enabling select all function in the main window.
+ */
+ for (KeyStroke listener : treeTable.getRegisteredKeyStrokes()) {
+ if (listener.toString().equals("ctrl pressed A")) {
+ final InputMap map = treeTable.getInputMap();
+ map.remove(listener);
+ treeTable.setInputMap(WHEN_FOCUSED, map);
+ treeTable.setInputMap(WHEN_ANCESTOR_OF_FOCUSED_COMPONENT, map);
+ }
+ }
+
+ pcs = new SwingPropertyChangeSupport(this);
+
+ // Make this a prop change listener for Cytoscape global events.
+ Cytoscape.getPropertyChangeSupport().addPropertyChangeListener(this);
+
+ // For listening to adding/removing Visual Style events.
+ Cytoscape.getVisualMappingManager().addChangeListener(this);
+ }
+
+ /**
+ * Initialize GUI components
+ */
+ private void initialize() {
+ setLayout(new BorderLayout());
+ setPreferredSize(new Dimension(PANEL_PREFFERED_WIDTH, 700));
+ setMinimumSize(new Dimension(PANEL_PREFFERED_WIDTH, PANEL_PREFFERED_WIDTH));
+
+ networkTreePanel = new JPanel();
+ networkTreePanel.setLayout(new BoxLayout(networkTreePanel, BoxLayout.Y_AXIS));
+
+ treeTable.getTree().addTreeSelectionListener(this);
+ treeTable.getTree().setRootVisible(false);
+
+ ToolTipManager.sharedInstance().registerComponent(treeTable);
+
+ treeTable.getTree().setCellRenderer(new TreeCellRenderer());
+
+ resetTable();
+
+ navigatorPanel = new JPanel();
+ navigatorPanel.setMinimumSize(new Dimension(180, 180));
+ navigatorPanel.setMaximumSize(new Dimension(180, 180));
+ navigatorPanel.setPreferredSize(new Dimension(180, 180));
+
+ final JScrollPane scroll = new JScrollPane(treeTable);
+
+ networkTreePanel.add(scroll);
+ split = new BiModalJSplitPane(cytoscapeDesktop, JSplitPane.VERTICAL_SPLIT,
+ BiModalJSplitPane.MODE_SHOW_SPLIT, networkTreePanel, navigatorPanel);
+ split.setResizeWeight(1);
+ split.setDividerLocation(DEF_DEVIDER_LOCATION);
+ add(split);
+
+ // this mouse listener listens for the right-click event and will show
+ // the pop-up
+ // window when that occurrs
+ treeTable.addMouseListener(new PopupListener());
+
+ // create and populate the popup window
+ popup = new JPopupMenu();
+ editNetworkTitle = new JMenuItem(PopupActionListener.EDIT_TITLE);
+ createViewItem = new JMenuItem(PopupActionListener.CREATE_VIEW);
+ destroyViewItem = new JMenuItem(PopupActionListener.DESTROY_VIEW);
+ destroyNetworkItem = new JMenuItem(PopupActionListener.DESTROY_NETWORK);
+ applyVisualStyleMenu = new JMenu(PopupActionListener.APPLY_VISUAL_STYLE);
+
+ // action listener which performs the tasks associated with the popup
+ // listener
+ popupActionListener = new PopupActionListener();
+ editNetworkTitle.addActionListener(popupActionListener);
+ createViewItem.addActionListener(popupActionListener);
+ destroyViewItem.addActionListener(popupActionListener);
+ destroyNetworkItem.addActionListener(popupActionListener);
+ applyVisualStyleMenu.addActionListener(popupActionListener);
+ popup.add(editNetworkTitle);
+ popup.add(createViewItem);
+ popup.add(destroyViewItem);
+ popup.add(destroyNetworkItem);
+ popup.addSeparator();
+ popup.add(applyVisualStyleMenu);
+ }
+
+
+ private void resetTable() {
+ treeTable.getColumn(ColumnTypes.NETWORK.getDisplayName()).setPreferredWidth(170);
+ treeTable.getColumn(ColumnTypes.NODES.getDisplayName()).setPreferredWidth(45);
+ treeTable.getColumn(ColumnTypes.EDGES.getDisplayName()).setPreferredWidth(45);
+ treeTable.setRowHeight(DEF_ROW_HEIGHT);
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param comp DOCUMENT ME!
+ */
+ public void setNavigator(final Component comp) {
+ split.setRightComponent(comp);
+ split.validate();
+ }
+
+ /**
+ * This is used by Session writer.
+ *
+ * @return
+ */
+ public JTreeTable getTreeTable() {
+ return treeTable;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public JPanel getNavigatorPanel() {
+ return navigatorPanel;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public SwingPropertyChangeSupport getSwingPropertyChangeSupport() {
+ return pcs;
+ }
+
+ /**
+ * Remove a network from the panel.
+ *
+ * @param network_id
+ */
+ public void removeNetwork(final String network_id) {
+ final NetworkTreeNode node = getNetworkNode(network_id);
+ if (node == null) return;
+
+ final Enumeration<NetworkTreeNode> children = node.children();
+ NetworkTreeNode child = null;
+ final List removed_children = new ArrayList();
+
+ while (children.hasMoreElements()) {
+ removed_children.add(children.nextElement());
+ }
+
+ for (Iterator i = removed_children.iterator(); i.hasNext();) {
+ child = (NetworkTreeNode) i.next();
+ child.removeFromParent();
+ root.add(child);
+ }
+
+ Cytoscape.getNetwork(network_id).removeSelectEventListener(this);
+ node.removeFromParent();
+ treeTable.getTree().updateUI();
+ treeTable.doLayout();
+ }
+
+
+ /**
+ * update a network title
+ */
+ public void updateTitle(final CyNetwork network) {
+ // updates the title in the network panel
+ if (treeTable.getTree().getSelectionPath() != null) { // user has selected something
+ treeTableModel.setValueAt(network.getTitle(),
+ treeTable.getTree().getSelectionPath().getLastPathComponent(), 0);
+ } else { // no selection, means the title has been changed programmatically
+ NetworkTreeNode node = getNetworkNode(network.getIdentifier());
+ treeTableModel.setValueAt(network.getTitle(), node, 0);
+ }
+ treeTable.getTree().updateUI();
+ treeTable.doLayout();
+ // updates the title in the networkViewMap
+ Cytoscape.getDesktop().getNetworkViewManager().updateNetworkTitle(network);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param event DOCUMENT ME!
+ */
+ public void onSelectEvent(final SelectEvent event) {
+ if (event.getTargetType() == SelectEvent.SINGLE_NODE || event.getTargetType() == SelectEvent.NODE_SET) {
+ final Set<Node> selectedNodes = (Set<Node>)Cytoscape.getCurrentNetwork().getSelectedNodes();
+ final List<String> selectedNestedNetworkIDs = new ArrayList<String>();
+ for (final Node node : selectedNodes) {
+ final CyNetwork nestedNetwork = (CyNetwork)node.getNestedNetwork();
+ if (nestedNetwork != null)
+ selectedNestedNetworkIDs.add(nestedNetwork.getIdentifier());
+ }
+
+ doNotEnterValueChanged = true;
+ try {
+ final TreePath[] treePaths = new TreePath[selectedNestedNetworkIDs.size() + 1];
+ int index = 0;
+ final String currentNetworkID = Cytoscape.getCurrentNetwork().getIdentifier();
+ TreePath currentPath = null;
+ final JTree tree = treeTable.getTree();
+ for (int row = 0; row < tree.getRowCount(); ++row) {
+ final TreePath path = tree.getPathForRow(row);
+ final String ID = ((NetworkTreeNode)path.getLastPathComponent()).getNetworkID();
+ if (ID.equals(currentNetworkID))
+ currentPath = path;
+ else if (selectedNestedNetworkIDs.contains(ID))
+ treePaths[index++] = path;
+ }
+
+ Cytoscape.setSelectedNetworks(selectedNestedNetworkIDs);
+
+ treePaths[index] = currentPath;
+ tree.getSelectionModel().setSelectionPaths(treePaths);
+ tree.scrollPathToVisible(currentPath);
+ } finally {
+ doNotEnterValueChanged = false;
+ }
+ }
+
+ treeTable.getTree().updateUI();
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param network_id DOCUMENT ME!
+ * @param parent_id DOCUMENT ME!
+ */
+ public void addNetwork(String network_id, String parent_id) {
+ // first see if it exists
+ if (getNetworkNode(network_id) == null) {
+ //logger.info("NetworkPanel: addNetwork " + network_id);
+ NetworkTreeNode dmtn = new NetworkTreeNode(Cytoscape.getNetwork(network_id).getTitle(),
+ network_id);
+ Cytoscape.getNetwork(network_id).addSelectEventListener(this);
+
+ if (parent_id != null && getNetworkNode(parent_id) != null) {
+ getNetworkNode(parent_id).add(dmtn);
+ } else {
+ root.add(dmtn);
+ }
+
+ // apparently this doesn't fire valueChanged
+ treeTable.getTree().collapsePath(new TreePath(new TreeNode[] { root }));
+
+ treeTable.getTree().updateUI();
+ TreePath path = new TreePath(dmtn.getPath());
+ treeTable.getTree().expandPath(path);
+ treeTable.getTree().scrollPathToVisible(path);
+ treeTable.doLayout();
+
+ // this is necessary because valueChanged is not fired above
+ focusNetworkNode(network_id);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param network_id DOCUMENT ME!
+ */
+ public void focusNetworkNode(String network_id) {
+ //logger.info("NetworkPanel: focus network node");
+ DefaultMutableTreeNode node = getNetworkNode(network_id);
+
+ if (node != null) {
+ // fires valueChanged if the network isn't already selected
+ treeTable.getTree().getSelectionModel().setSelectionPath(new TreePath(node.getPath()));
+ treeTable.getTree().scrollPathToVisible(new TreePath(node.getPath()));
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param network_id DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public NetworkTreeNode getNetworkNode(String network_id) {
+ Enumeration tree_node_enum = root.breadthFirstEnumeration();
+
+ while (tree_node_enum.hasMoreElements()) {
+ NetworkTreeNode node = (NetworkTreeNode) tree_node_enum.nextElement();
+
+ if ((String) node.getNetworkID() == network_id) {
+ return node;
+ }
+ }
+
+ return null;
+ }
+
+ /**
+ * This method highlights a network in the NetworkPanel.
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void valueChanged(TreeSelectionEvent e) {
+ // TODO: Every time user select a network name, this method will be called 3 times!
+ if (doNotEnterValueChanged)
+ return;
+
+ final JTree mtree = treeTable.getTree();
+
+ // sets the "current" network based on last node in the tree selected
+ final NetworkTreeNode node = (NetworkTreeNode) mtree.getLastSelectedPathComponent();
+ if ( node == null || node.getUserObject() == null )
+ return;
+
+ pcs.firePropertyChange(new PropertyChangeEvent(this, CytoscapeDesktop.NETWORK_VIEW_FOCUS,
+ null, (String) node.getNetworkID()));
+
+ // creates a list of all selected networks
+ final List<String> networkList = new LinkedList<String>();
+ try {
+ for ( int i = mtree.getMinSelectionRow(); i <= mtree.getMaxSelectionRow(); i++ ) {
+ NetworkTreeNode n = (NetworkTreeNode) mtree.getPathForRow(i).getLastPathComponent();
+ if ( n != null && n.getUserObject() != null && mtree.isRowSelected(i) )
+ networkList.add( n.getNetworkID() );
+ }
+ } catch (Exception ex) {
+ CyLogger.getLogger().warn("Exception handling network panel change: "+ex.getMessage());
+ ex.printStackTrace();
+ }
+
+ if ( networkList.size() > 0 ) {
+ Cytoscape.setSelectedNetworks(networkList);
+ Cytoscape.setSelectedNetworkViews(networkList);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void propertyChange(PropertyChangeEvent e) {
+ if (Cytoscape.NETWORK_CREATED.equals(e.getPropertyName())) {
+ addNetwork((String) e.getNewValue(), (String) e.getOldValue());
+ } else if (Cytoscape.NETWORK_DESTROYED.equals(e.getPropertyName())) {
+ removeNetwork((String) e.getNewValue());
+ } else if (CytoscapeDesktop.NETWORK_VIEW_FOCUSED.equals(e.getPropertyName())) {
+ if ( e.getSource() != this )
+ focusNetworkNode((String) e.getNewValue());
+ } else if (Cytoscape.NETWORK_TITLE_MODIFIED.equals(e.getPropertyName())) {
+ CyNetworkTitleChange cyNetworkTitleChange = (CyNetworkTitleChange) e.getNewValue();
+ String newID = cyNetworkTitleChange.getNetworkIdentifier();
+ //String newTitle = cyNetworkTitleChange.getNetworkTitle();
+ CyNetwork _network = Cytoscape.getNetwork(newID);
+ // Network "0" is the default and does not appear in the netowrk panel
+ if (_network != null && !_network.getIdentifier().equals("0"))
+ updateTitle(_network);
+ } else if(Cytoscape.CYTOSCAPE_INITIALIZED.equals(e.getPropertyName())) {
+ updateVSMenu();
+ }
+ }
+
+
+ /**
+ * This class listens to mouse events from the TreeTable, if the mouse event
+ * is one that is canonically associated with a popup menu (ie, a right
+ * click) it will pop up the menu with option for destroying view, creating
+ * view, and destroying network (this is platform specific apparently)
+ */
+ protected class PopupListener extends MouseAdapter {
+ /**
+ * Don't know why you need both of these, but this is how they did it in
+ * the example
+ */
+ public void mousePressed(MouseEvent e) {
+ maybeShowPopup(e);
+ }
+
+ /*
+ * On windows, popup is triggered by this method, not the above one
+ */
+ public void mouseReleased(MouseEvent e) {
+ maybeShowPopup(e);
+ }
+
+ /**
+ * if the mouse press is of the correct type, this function will maybe
+ * display the popup
+ */
+ private void maybeShowPopup(MouseEvent e) {
+ // check for the popup type
+ if (e.isPopupTrigger()) {
+ // get the row where the mouse-click originated
+ final int[] selected = treeTable.getSelectedRows();
+
+ if (selected != null && selected.length != 0) {
+ boolean enableViewRelatedMenu = false;
+ final int selectedItemCount = selected.length;
+ CyNetwork cyNetwork = null;
+ final JTree tree = treeTable.getTree();
+ for (int i = 0; i<selectedItemCount; i++) {
+
+ final TreePath treePath = tree.getPathForRow(selected[i]);
+ final String networkID = (String) ((NetworkTreeNode) treePath.getLastPathComponent())
+ .getNetworkID();
+
+ cyNetwork = Cytoscape.getNetwork(networkID);
+ if(Cytoscape.viewExists(networkID)) {
+ enableViewRelatedMenu = true;
+ }
+ }
+
+ // Edit title command will be enabled only when ONE network is selected.
+ if (selectedItemCount == 1) {
+ editNetworkTitle.setEnabled(true);
+ popupActionListener.setActiveNetwork(cyNetwork);
+ } else
+ editNetworkTitle.setEnabled(false);
+
+ if (enableViewRelatedMenu) {
+ // At least one selected network has a view.
+ createViewItem.setEnabled(true);
+ destroyViewItem.setEnabled(true);
+ applyVisualStyleMenu.setEnabled(true);
+ } else {
+ // None of the selected networks has view.
+ createViewItem.setEnabled(true);
+ destroyViewItem.setEnabled(false);
+ applyVisualStyleMenu.setEnabled(false);
+ }
+
+ popup.show(e.getComponent(), e.getX(), e.getY());
+ }
+ }
+ }
+ }
+
+ public void stateChanged(ChangeEvent e) {
+ updateVSMenu();
+ }
+
+ private void updateVSMenu() {
+ applyVisualStyleMenu.removeAll();
+
+ final Set<String> vsNames = new TreeSet<String>(Cytoscape.getVisualMappingManager().getCalculatorCatalog().getVisualStyleNames());
+ for (String name: vsNames) {
+ final JMenuItem styleMenu = new JMenuItem(name);
+ styleMenu.setAction(new ApplyVisualStyleAction(name));
+ applyVisualStyleMenu.add(styleMenu);
+ }
+ }
+}
+
+
+/**
+ * This class listens for actions from the popup menu, it is responsible for
+ * performing actions related to destroying and creating views, and destroying
+ * the network.
+ */
+class PopupActionListener implements ActionListener {
+ /**
+ * Constants for JMenuItem labels
+ */
+ public static final String DESTROY_VIEW = "Destroy View";
+
+ /**
+ *
+ */
+ public static final String CREATE_VIEW = "Create View";
+
+ /**
+ *
+ */
+ public static final String DESTROY_NETWORK = "Destroy Network";
+
+ /**
+ *
+ */
+ public static final String EDIT_TITLE = "Edit Network Title";
+
+ public static final String APPLY_VISUAL_STYLE = "Apply Visual Style";
+
+ /**
+ * This is the network which originated the mouse-click event (more
+ * appropriately, the network associated with the ID associated with the row
+ * associated with the JTable that originated the popup event
+ */
+ protected CyNetwork cyNetwork;
+
+ /**
+ * Based on the action event, destroy or create a view, or destroy a network
+ */
+ public void actionPerformed(ActionEvent ae) {
+ final String label = ((JMenuItem) ae.getSource()).getText();
+
+ if (DESTROY_VIEW.equals(label)) {
+ final List<CyNetwork> selected = Cytoscape.getSelectedNetworks();
+ for (final CyNetwork network: selected) {
+ final CyNetworkView targetView = Cytoscape.getNetworkView(network.getIdentifier());
+ if (targetView != Cytoscape.getNullNetworkView()) {
+ Cytoscape.destroyNetworkView(targetView);
+ }
+ }
+ } else if (CREATE_VIEW.equals(label)) {
+ final List<CyNetwork> selected = Cytoscape.getSelectedNetworks();
+
+ for(CyNetwork network: selected) {
+ if (!Cytoscape.viewExists(network.getIdentifier()))
+ CreateNetworkViewAction.createViewFromCurrentNetwork(network);
+ }
+ } else if (DESTROY_NETWORK.equals(label)) {
+ final List<CyNetwork> selected = Cytoscape.getSelectedNetworks();
+ for (CyNetwork network: selected)
+ Cytoscape.destroyNetwork(network);
+ } else if (EDIT_TITLE.equals(label)) {
+ CyNetworkNaming.editNetworkTitle(cyNetwork);
+ Cytoscape.getDesktop().getNetworkPanel().updateTitle(cyNetwork);
+ } else {
+ CyLogger.getLogger().warn("Unexpected network panel popup option");
+ }
+ }
+
+ /**
+ * Right before the popup menu is displayed, this function is called so we
+ * know which network the user is clicking on to call for the popup menu
+ */
+ public void setActiveNetwork(final CyNetwork cyNetwork) {
+ this.cyNetwork = cyNetwork;
+ }
+}
diff --git a/application/src/main/java/cytoscape/view/NetworkTreeNode.java b/application/src/main/java/cytoscape/view/NetworkTreeNode.java
new file mode 100644
index 0000000..44327fe
--- /dev/null
+++ b/application/src/main/java/cytoscape/view/NetworkTreeNode.java
@@ -0,0 +1,23 @@
+package cytoscape.view;
+
+import javax.swing.tree.DefaultMutableTreeNode;
+
+public class NetworkTreeNode extends DefaultMutableTreeNode {
+
+ private static final long serialVersionUID = -1504239724666254584L;
+
+ private String network_uid;
+
+ public NetworkTreeNode(Object userobj, String id) {
+ super(userobj.toString());
+ network_uid = id;
+ }
+
+ protected void setNetworkID(String id) {
+ network_uid = id;
+ }
+
+ protected String getNetworkID() {
+ return network_uid;
+ }
+}
diff --git a/application/src/main/java/cytoscape/view/NetworkTreeTableModel.java b/application/src/main/java/cytoscape/view/NetworkTreeTableModel.java
new file mode 100644
index 0000000..5585211
--- /dev/null
+++ b/application/src/main/java/cytoscape/view/NetworkTreeTableModel.java
@@ -0,0 +1,120 @@
+package cytoscape.view;
+
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import javax.swing.Icon;
+import javax.swing.tree.DefaultMutableTreeNode;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import cytoscape.util.swing.AbstractTreeTableModel;
+
+/**
+ * Inner class that extends the AbstractTreeTableModel
+ */
+public final class NetworkTreeTableModel extends AbstractTreeTableModel {
+
+ private List<ColumnTypes> columnNames;
+ private final Map<String, Icon> networkIcons;
+
+ public NetworkTreeTableModel(Object root) {
+ super(root);
+ columnNames = new ArrayList<ColumnTypes>();
+ columnNames.add(ColumnTypes.NETWORK);
+ columnNames.add(ColumnTypes.NODES);
+ columnNames.add(ColumnTypes.EDGES);
+
+ networkIcons = new HashMap<String, Icon>();
+ }
+
+ public void addColumn(final ColumnTypes model, final int idx) {
+ columnNames.add(idx, model);
+ }
+
+ public void removeColumn(final int idx) {
+ columnNames.remove(idx);
+ }
+
+ public Object getChild(Object parent, int index) {
+ final Enumeration<?> tree_node_enum = ((DefaultMutableTreeNode) getRoot())
+ .breadthFirstEnumeration();
+
+ while (tree_node_enum.hasMoreElements()) {
+ DefaultMutableTreeNode node = (DefaultMutableTreeNode) tree_node_enum
+ .nextElement();
+
+ if (node == parent) {
+ return node.getChildAt(index);
+ }
+ }
+
+ return null;
+ }
+
+ public int getChildCount(Object parent) {
+ Enumeration<?> tree_node_enum = ((DefaultMutableTreeNode) getRoot())
+ .breadthFirstEnumeration();
+
+ while (tree_node_enum.hasMoreElements()) {
+ DefaultMutableTreeNode node = (DefaultMutableTreeNode) tree_node_enum
+ .nextElement();
+
+ if (node == parent) {
+ return node.getChildCount();
+ }
+ }
+
+ return 0;
+ }
+
+ public int getColumnCount() {
+ return columnNames.size();
+ }
+
+ public String getColumnName(int column) {
+ return columnNames.get(column).getDisplayName();
+ }
+
+ public Class<?> getColumnClass(int column) {
+ return columnNames.get(column).getType();
+ }
+
+ public Object getValueAt(Object node, int column) {
+ if (columnNames.get(column).equals(ColumnTypes.NETWORK))
+ return ((DefaultMutableTreeNode) node).getUserObject();
+ else if (columnNames.get(column).equals(ColumnTypes.NODES)) {
+ CyNetwork cyNetwork = Cytoscape.getNetwork(((NetworkTreeNode) node)
+ .getNetworkID());
+
+ return "" + cyNetwork.getNodeCount() + "("
+ + cyNetwork.getSelectedNodes().size() + ")";
+ } else if (columnNames.get(column).equals(ColumnTypes.EDGES)) {
+ CyNetwork cyNetwork = Cytoscape.getNetwork(((NetworkTreeNode) node)
+ .getNetworkID());
+
+ return "" + cyNetwork.getEdgeCount() + "("
+ + cyNetwork.getSelectedEdges().size() + ")";
+ } else if (columnNames.get(column).equals(ColumnTypes.NETWORK_ICONS)) {
+
+ return networkIcons.get(((NetworkTreeNode) node).getNetworkID());
+ }
+
+ return "";
+ }
+
+ public void setValueAt(Object aValue, Object node, int column) {
+ if (columnNames.get(column).equals(ColumnTypes.NETWORK)) {
+ ((DefaultMutableTreeNode) node).setUserObject(aValue);
+ } else if (columnNames.get(column).equals(ColumnTypes.NETWORK_ICONS)) {
+ if(aValue == null)
+ networkIcons.put(((NetworkTreeNode) node).getNetworkID(), null);
+ else
+ networkIcons.put(((NetworkTreeNode) node).getNetworkID(),
+ (Icon) aValue);
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/view/NetworkViewManager.java b/application/src/main/java/cytoscape/view/NetworkViewManager.java
new file mode 100644
index 0000000..682374a
--- /dev/null
+++ b/application/src/main/java/cytoscape/view/NetworkViewManager.java
@@ -0,0 +1,472 @@
+/*
+ File: NetworkViewManager.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.view;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import cytoscape.CytoscapeInit;
+import cytoscape.logger.CyLogger;
+
+import ding.view.DGraphView;
+import ding.view.InnerCanvas;
+
+import java.awt.Color;
+import java.awt.event.WindowEvent;
+import java.awt.event.WindowFocusListener;
+
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.beans.PropertyVetoException;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import javax.swing.JDesktopPane;
+import javax.swing.JInternalFrame;
+import javax.swing.JLabel;
+import javax.swing.JLayeredPane;
+import javax.swing.JPanel;
+import javax.swing.JTabbedPane;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+import javax.swing.event.InternalFrameAdapter;
+import javax.swing.event.InternalFrameEvent;
+import javax.swing.event.InternalFrameListener;
+import javax.swing.event.SwingPropertyChangeSupport;
+
+
+/**
+ *
+ */
+public class NetworkViewManager implements PropertyChangeListener, InternalFrameListener,
+ WindowFocusListener, ChangeListener {
+ private static CyLogger logger = CyLogger.getLogger(NetworkViewManager.class);
+ private JDesktopPane desktopPane;
+ private Map<String, JInternalFrame> networkViewMap;
+ private Map<JInternalFrame, String> componentMap;
+ private Map<String, InternalFrameComponent> internalFrameComponentMap;
+ protected final CytoscapeDesktop cytoscapeDesktop;
+ protected final SwingPropertyChangeSupport pcs;
+ protected int MINIMUM_WIN_WIDTH = 200;
+ protected int MINIMUM_WIN_HEIGHT = 200;
+
+ /**
+ * @deprecated view_type is no longer used. Use the other constructor. Will
+ * be removed Aug 2008.
+ */
+ public NetworkViewManager(CytoscapeDesktop desktop, int view_type) {
+ this(desktop);
+ }
+
+ /**
+ * Creates a new NetworkViewManager object.
+ *
+ * @param desktop
+ * DOCUMENT ME!
+ */
+ public NetworkViewManager(CytoscapeDesktop desktop) {
+ this.cytoscapeDesktop = desktop;
+ desktopPane = new JDesktopPane();
+ pcs = new SwingPropertyChangeSupport(this);
+
+ Cytoscape.getPropertyChangeSupport().addPropertyChangeListener(this);
+
+ networkViewMap = new HashMap<String, JInternalFrame>();
+ componentMap = new HashMap<JInternalFrame, String>();
+ internalFrameComponentMap = new HashMap<String, InternalFrameComponent>();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public SwingPropertyChangeSupport getSwingPropertyChangeSupport() {
+ return pcs;
+ }
+
+ /**
+ * @deprecated Tabbed view is no longer used. Will be removed Aug 2008.
+ */
+ public JTabbedPane getTabbedPane() {
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public JDesktopPane getDesktopPane() {
+ return desktopPane;
+ }
+
+ /**
+ * Given a CyNetworkView, returns the InternalFrameComponent that wraps it.
+ *
+ * @param view
+ * CyNetworkView
+ * @return InternalFrameComponent
+ * @throws IllegalArgumentException
+ */
+ public InternalFrameComponent getInternalFrameComponent(CyNetworkView view)
+ throws IllegalArgumentException {
+ // check args
+ if (view == null) {
+ throw new IllegalArgumentException("NetworkViewManager.getInternalFrameComponent(), argument is null");
+ }
+
+ // outta here
+ return internalFrameComponentMap.get(view.getIdentifier());
+ }
+
+ /**
+ * Given a CyNetworkView, returns the internal frame.
+ *
+ * @param view
+ * CyNetworkView
+ * @return InternalFrameComponent
+ * @throws IllegalArgumentException
+ */
+ public JInternalFrame getInternalFrame(CyNetworkView view) throws IllegalArgumentException {
+ // check args
+ if (view == null) {
+ throw new IllegalArgumentException("NetworkViewManager.getInternalFrame(), argument is null");
+ }
+
+ // outta here
+ return networkViewMap.get(view.getIdentifier());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param network
+ * DOCUMENT ME!
+ */
+ public void updateNetworkTitle(CyNetwork network) {
+ final JInternalFrame frame = networkViewMap.get(network.getIdentifier());
+
+ if (frame != null) {
+ frame.setTitle(network.getTitle());
+ frame.repaint();
+ }
+ }
+
+ /**
+ * Method to update the network title on the JInternalFrame, but not in the network panel.
+ *
+ * @param network CyNetwork
+ * @param title String
+ */
+ public void updateNetworkTitle(CyNetwork network, String title) {
+ final JInternalFrame frame = networkViewMap.get(network.getIdentifier());
+
+ if (frame != null) {
+ frame.setTitle(title);
+ frame.repaint();
+ }
+ }
+
+ /**
+ * @deprecated Will no longer support ChangeListener. Will be removed August
+ * 2008.
+ */
+ public void stateChanged(ChangeEvent e) {
+ }
+
+ /**
+ * Fire Events when a Managed Network View gets the Focus.
+ */
+ public void internalFrameActivated(InternalFrameEvent e) {
+ String network_id = componentMap.get(e.getInternalFrame());
+
+ if (network_id == null) {
+ return;
+ }
+
+ //logger.info("NetworkViewManager: firing NETWORK_VIEW_FOCUSED (intenalFrameActivate)");
+ firePropertyChange(CytoscapeDesktop.NETWORK_VIEW_FOCUSED, null, network_id);
+ }
+
+ /**
+ * Fire Events when a Managed Network View gets the Focus.
+ */
+ public void internalFrameOpened(InternalFrameEvent e) {
+ internalFrameActivated(e);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void internalFrameClosed(InternalFrameEvent e) {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void internalFrameClosing(InternalFrameEvent e) {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void internalFrameDeactivated(InternalFrameEvent e) {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void internalFrameDeiconified(InternalFrameEvent e) {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void internalFrameIconified(InternalFrameEvent e) {
+ }
+
+ /**
+ * @deprecated Will no longer support WindowFocusListener. Will be removed
+ * August 2008.
+ */
+ public void windowGainedFocus(WindowEvent e) {
+ }
+
+ /**
+ * @deprecated Will no longer support WindowFocusListener. Will be removed
+ * August 2008.
+ */
+ public void windowLostFocus(WindowEvent e) {
+ }
+
+ /**
+ * This handles all of the incoming PropertyChangeEvents. If you are going
+ * to have multiple NetworkViewManagers, then this method should be extended
+ * such that the desired behaviour is achieved, assuming of course that you
+ * want your NetworkViewManagers to behave differently.
+ */
+ public void propertyChange(PropertyChangeEvent e) {
+ // handle focus event
+ if (CytoscapeDesktop.NETWORK_VIEW_FOCUS.equals(e.getPropertyName())) {
+ //logger.info("NetworkViewManager got NETWORK_VIEW_FOCUS " + e.getSource().getClass().getName());
+ String network_id = (String) e.getNewValue();
+ e = null;
+ unsetFocus(); // in case the newly focused network doesn't have a
+ // view
+
+ setFocus(network_id);
+
+ // hack to add transfer handlers to canvas
+ InnerCanvas canvas = ((DGraphView) Cytoscape.getCurrentNetworkView()).getCanvas();
+
+ if (this.getDesktopPane() != null) {
+ canvas.addTransferComponent(this.getDesktopPane());
+ }
+ }
+ // handle putting a newly created CyNetworkView into a Container
+ else if (CytoscapeDesktop.NETWORK_VIEW_CREATED.equals(e.getPropertyName())) {
+ CyNetworkView new_view = (CyNetworkView) e.getNewValue();
+ //logger.info("NetworkViewManager got NETWORK_VIEW_CREATED " + e.getSource().getClass().getName() + ", view = " + new_view);
+ createContainer(new_view);
+ e = null;
+ } else if (CytoscapeDesktop.NETWORK_VIEW_DESTROYED.equals(e.getPropertyName())) {
+ //logger.info("NetworkViewManager got NETWORK_VIEW_DEST");
+ CyNetworkView view = (CyNetworkView) e.getNewValue();
+ removeView(view);
+ e = null;
+ }
+ }
+
+ /**
+ * Fires a PropertyChangeEvent
+ */
+ public void firePropertyChange(String property_type, Object old_value, Object new_value) {
+ pcs.firePropertyChange(new PropertyChangeEvent(this, property_type, old_value, new_value));
+ }
+
+ /**
+ * Used to unset the focus of all the views. This is for the situation when
+ * a network is focused but the network doesn't have a view.
+ */
+ protected void unsetFocus() {
+ for (JInternalFrame f : networkViewMap.values()) {
+ try {
+ f.setSelected(false);
+ } catch (PropertyVetoException pve) {
+ logger.info("NetworkViewManager: Couldn't unset focus for internal frame.");
+ }
+ }
+ }
+
+ /**
+ * Sets the focus of the passed network, if possible The Network ID
+ * corresponds to the CyNetworkView.getNetwork().getIdentifier()
+ */
+ protected void setFocus(String network_id) {
+ if (networkViewMap.containsKey(network_id)) {
+ try {
+ networkViewMap.get(network_id).setIcon(false);
+ networkViewMap.get(network_id).show();
+ // fires internalFrameActivated
+ networkViewMap.get(network_id).setSelected(true);
+ } catch (Exception e) {
+ logger.warn("Network View unable to be focused");
+ }
+ }
+ }
+
+ protected void removeView(CyNetworkView view) {
+ try {
+ final String targetID = view.getIdentifier();
+
+ if ((targetID != null) && (networkViewMap.get(targetID) != null)) {
+ networkViewMap.get(targetID).dispose();
+
+ JInternalFrame target = networkViewMap.remove(targetID);
+ target.removeAll();
+ target = null;
+ }
+ } catch (Exception e) {
+ logger.warn("Network View unable to be killed: " + view.getIdentifier(), e);
+ }
+
+ view = null;
+ }
+
+ /**
+ * Contains a CyNetworkView.
+ */
+ protected void createContainer(final CyNetworkView view) {
+ if (networkViewMap.containsKey(view.getNetwork().getIdentifier()))
+ return;
+
+ // create a new InternalFrame and put the CyNetworkViews Component into
+ // it
+ final JInternalFrame iframe = new JInternalFrame(view.getTitle(), true, true, true, true);
+ iframe.addInternalFrameListener(new InternalFrameAdapter() {
+ public void internalFrameClosing(InternalFrameEvent e) {
+ Cytoscape.destroyNetworkView(view);
+ }
+ });
+ desktopPane.add(iframe);
+
+ // code added to support layered canvas for each CyNetworkView
+ if (view instanceof DGraphView) {
+ final InternalFrameComponent internalFrameComp =
+ new InternalFrameComponent(iframe.getLayeredPane(), (DGraphView) view);
+
+ iframe.getContentPane().add(internalFrameComp);
+ internalFrameComponentMap.put(view.getNetwork().getIdentifier(), internalFrameComp);
+ } else {
+ logger.info("NetworkViewManager.createContainer() - DGraphView not found!");
+ iframe.getContentPane().add(view.getComponent());
+ }
+
+ iframe.pack();
+
+ int x = 0;
+ int y = 0;
+ JInternalFrame refFrame = null;
+ JInternalFrame[] allFrames = desktopPane.getAllFrames();
+
+ if (allFrames.length > 1) {
+ refFrame = allFrames[0];
+ }
+
+ if (refFrame != null) {
+ x = refFrame.getLocation().x + 20;
+ y = refFrame.getLocation().y + 20;
+ }
+
+ if (x > (desktopPane.getWidth() - MINIMUM_WIN_WIDTH)) {
+ x = desktopPane.getWidth() - MINIMUM_WIN_WIDTH;
+ }
+
+ if (y > (desktopPane.getHeight() - MINIMUM_WIN_HEIGHT)) {
+ y = desktopPane.getHeight() - MINIMUM_WIN_HEIGHT;
+ }
+
+ if (x < 0) {
+ x = 0;
+ }
+
+ if (y < 0) {
+ y = 0;
+ }
+
+ iframe.setBounds(x, y, 400, 400);
+
+ // maximize the frame if the specified property is set
+ try {
+ String max = CytoscapeInit.getProperties().getProperty("maximizeViewOnCreate");
+
+ if ((max != null) && Boolean.parseBoolean(max))
+ iframe.setMaximum(true);
+ } catch (PropertyVetoException pve) {
+ logger.warn("Unable to maximize internal frame: "+pve.getMessage());
+ }
+
+ iframe.setVisible(true);
+ iframe.addInternalFrameListener(this);
+ iframe.setResizable(true);
+
+ networkViewMap.put(view.getNetwork().getIdentifier(), iframe);
+ componentMap.put(iframe, view.getNetwork().getIdentifier());
+
+ firePropertyChange(CytoscapeDesktop.NETWORK_VIEW_FOCUSED, null,
+ view.getNetwork().getIdentifier());
+ }
+}
diff --git a/application/src/main/java/cytoscape/view/OpenRecentAction.java b/application/src/main/java/cytoscape/view/OpenRecentAction.java
new file mode 100644
index 0000000..8f1a824
--- /dev/null
+++ b/application/src/main/java/cytoscape/view/OpenRecentAction.java
@@ -0,0 +1,77 @@
+/*
+ File: OpenRecentAction.java
+
+ Copyright (c) 2006, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.view;
+
+
+import cytoscape.Cytoscape;
+import cytoscape.data.readers.CytoscapeSessionReader;
+import cytoscape.logger.CyLogger;
+
+import java.awt.event.ActionEvent;
+import java.io.IOException;
+import java.net.URL;
+import javax.swing.AbstractAction;
+
+
+class OpenRecentAction extends AbstractAction {
+ private URL sessionFileURL;
+ private CyLogger logger;
+
+ OpenRecentAction(final URL sessionFileURL) {
+ super(sessionFileURL.toString());
+
+ this.sessionFileURL = sessionFileURL;
+ this.logger = CyLogger.getLogger(OpenRecentAction.class);
+ }
+
+ public void actionPerformed(final ActionEvent e) {
+ try {
+ final CytoscapeSessionReader reader = new CytoscapeSessionReader(sessionFileURL);
+ if (reader == null) {
+ logger.warn("Failed to load: " + sessionFileURL);
+ return;
+ }
+ try {
+ reader.read();
+ } catch (final Exception ex1) {
+ logger.warn("Failed to load: " + sessionFileURL);
+ return;
+ }
+
+ final String sessionName = sessionFileURL.toString();
+ Cytoscape.setCurrentSessionFileName(sessionName);
+ Cytoscape.getDesktop().setTitle("Cytoscape Desktop (Session Name: " + sessionName + ")");
+
+ } catch (final IOException ex2) {
+ logger.warn("Failed to open session: " + sessionFileURL);
+ System.err.println(ex2);
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/view/ToolCytoPanelListener.java b/application/src/main/java/cytoscape/view/ToolCytoPanelListener.java
new file mode 100644
index 0000000..a87eade
--- /dev/null
+++ b/application/src/main/java/cytoscape/view/ToolCytoPanelListener.java
@@ -0,0 +1,83 @@
+
+/*
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.view;
+
+import cytoscape.view.cytopanels.BiModalJSplitPane;
+import cytoscape.view.cytopanels.CytoPanelListener;
+import cytoscape.view.cytopanels.CytoPanelState;
+import cytoscape.view.cytopanels.CytoPanel;
+import cytoscape.view.cytopanels.CytoPanelImp;
+
+import javax.swing.JLabel;
+
+
+/**
+ * This class handles the embedding of the Tools CytoPanel within the Control
+ * CytoPanel. For all other cytopanels this is handled by CytoPanelAction,
+ * but because tools panel is within another cytopanel, we have to handle things
+ * separately.
+ */
+class ToolCytoPanelListener implements CytoPanelListener {
+
+ BiModalJSplitPane split;
+ CytoPanel southWest;
+ CytoPanelImp west;
+
+ ToolCytoPanelListener(BiModalJSplitPane split, CytoPanelImp west, CytoPanel southWest) {
+ this.split = split;
+ this.west = west;
+ this.southWest = southWest;
+
+ southWest.addCytoPanelListener(this);
+ }
+
+
+ public void onStateChange(CytoPanelState newState) {
+
+ if (newState == CytoPanelState.DOCK)
+ west.addComponentToSouth(split);
+ else
+ // removeComponentAtSouth() doesn't work properly, so we do this...
+ west.addComponentToSouth(new JLabel());
+
+ west.validate();
+ }
+
+ public void onComponentSelected(int componentIndex) {}
+ public void onComponentAdded(int count) {}
+ public void onComponentRemoved(int count) {}
+}
diff --git a/application/src/main/java/cytoscape/view/TreeCellRenderer.java b/application/src/main/java/cytoscape/view/TreeCellRenderer.java
new file mode 100644
index 0000000..199aceb
--- /dev/null
+++ b/application/src/main/java/cytoscape/view/TreeCellRenderer.java
@@ -0,0 +1,37 @@
+package cytoscape.view;
+
+import java.awt.Component;
+
+import javax.swing.JTree;
+import javax.swing.tree.DefaultTreeCellRenderer;
+
+import cytoscape.Cytoscape;
+
+public class TreeCellRenderer extends DefaultTreeCellRenderer {
+
+ private static final long serialVersionUID = -678559990857492912L;
+
+ public Component getTreeCellRendererComponent(JTree tree, Object value,
+ boolean sel, boolean expanded, boolean leaf, int row,
+ boolean hasFocus) {
+ super.getTreeCellRendererComponent(tree, value, sel, expanded, leaf,
+ row, hasFocus);
+
+ if (hasView(value)) {
+ setBackgroundNonSelectionColor(java.awt.Color.green.brighter());
+ setBackgroundSelectionColor(java.awt.Color.green.darker());
+ } else {
+ setBackgroundNonSelectionColor(java.awt.Color.red.brighter());
+ setBackgroundSelectionColor(java.awt.Color.red.darker());
+ }
+
+ return this;
+ }
+
+ private boolean hasView(Object value) {
+ NetworkTreeNode node = (NetworkTreeNode) value;
+ setToolTipText(Cytoscape.getNetwork(node.getNetworkID()).getTitle());
+
+ return Cytoscape.viewExists(node.getNetworkID());
+ }
+}
diff --git a/application/src/main/java/cytoscape/view/cytopanels/BiModalJSplitPane.java b/application/src/main/java/cytoscape/view/cytopanels/BiModalJSplitPane.java
new file mode 100644
index 0000000..0c88e6a
--- /dev/null
+++ b/application/src/main/java/cytoscape/view/cytopanels/BiModalJSplitPane.java
@@ -0,0 +1,316 @@
+/*
+ File: BiModalJSplitPane.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+//
+// $Id: BiModalJSplitPane.java 9736 2007-03-20 00:25:45Z mes $
+//------------------------------------------------------------------------------
+
+// our package
+package cytoscape.view.cytopanels;
+
+import java.awt.Component;
+import java.awt.Container;
+
+// imports
+import java.awt.Point;
+import java.awt.Rectangle;
+import java.awt.event.ComponentAdapter;
+import java.awt.event.ComponentEvent;
+
+import javax.swing.JFrame;
+import javax.swing.JSplitPane;
+import javax.swing.SwingConstants;
+
+
+/**
+ * The BiModalJSplitPane class extends JSplitPane to provide two modes:
+ * <UL>
+ * <LI>MODE_SHOW_SPLIT: The split in the split pane appears as it normally
+ * would, and the user can resize the split pane as
+ * needed.
+ * <LI>MODE_HIDE_SPLIT: The split in the split pane is hidden, and the
+ * user cannot resize the split pane.
+ * </UL>
+ *
+ * BIModalJSplitPane also implements the CytoPanelContainer interface.
+ *
+ * @author Ethan Cerami, Ben Gross
+ */
+public class BiModalJSplitPane extends JSplitPane implements CytoPanelContainer {
+ /**
+ * Reference application frame.
+ */
+ private JFrame frame;
+
+ /**
+ * Available modes of the BiModalJSplitPane.
+ */
+ public static final int MODE_SHOW_SPLIT = 1;
+
+ /**
+ *
+ */
+ public static final int MODE_HIDE_SPLIT = 2;
+
+ /**
+ * Property listener modes.
+ */
+ public static final String MODE_PROPERTY = "MODE_PROPERTY";
+
+ /**
+ * The current mode.
+ */
+ private int currentMode;
+
+ /**
+ * The default divider size.
+ */
+ private int defaultDividerSize;
+
+ /**
+ * The saved divider location.
+ */
+ private int dividerLocation;
+
+ /**
+ * Constructor.
+ *
+ * @param orientation JSplitPane Orientation.
+ * JSplitPane.HORIZONTAL_SPLIT or
+ * JSplitPane.VERTICAL_SPLIT.
+ * @param initialMode Initial Mode.
+ * MODE_SHOW_SPLIT or
+ * MODE_HIDE_SPLIT.
+ * @param leftComponent Left/Top Component.
+ * @param rightComponent Right/Bottom Component.
+ */
+ public BiModalJSplitPane(JFrame f, int orientation, int initialMode, Component leftComponent,
+ Component rightComponent) {
+ super(orientation, leftComponent, rightComponent);
+
+ // init some member vars
+ currentMode = initialMode;
+ frame = f;
+
+ // add component listener to get resize events
+ addComponentListener();
+
+ // remove the border
+ setBorder(null);
+ setOneTouchExpandable(false);
+
+ // store the default divider size
+ defaultDividerSize = this.getDividerSize();
+
+ // hide split
+ if (initialMode == MODE_HIDE_SPLIT) {
+ this.setDividerSize(0);
+ }
+ }
+
+ /**
+ * Inserts CytoPanel at desired compass direction.
+ *
+ * @param cytoPanel CytoPanel reference.
+ * @param compassDirection SwingConstants integer value.
+ */
+ public void insertCytoPanel(CytoPanelImp cytoPanel, int compassDirection) {
+ boolean success = false;
+
+ switch (compassDirection) {
+ case SwingConstants.NORTH:
+ this.setTopComponent(cytoPanel);
+ success = true;
+
+ break;
+
+ case SwingConstants.SOUTH:
+ this.setBottomComponent(cytoPanel);
+ success = true;
+
+ break;
+
+ case SwingConstants.EAST:
+ this.setRightComponent(cytoPanel);
+ success = true;
+
+ break;
+
+ case SwingConstants.WEST:
+ this.setLeftComponent(cytoPanel);
+ success = true;
+
+ break;
+
+ case SwingConstants.SOUTH_WEST:
+ this.setBottomComponent(cytoPanel);
+ success = true;
+
+ break;
+ }
+
+ // houston we have a problem
+ if (!success) {
+ // made it here, houston, we have a problem
+ throw new IllegalArgumentException("Illegal Argument: " + compassDirection
+ + ". Must be one of: SwingConstants.{NORTH,SOUTH,EAST,WEST.");
+ }
+
+ // hack to set divider size back to what it should be
+ setDividerSize(defaultDividerSize);
+
+ // hack to set divider location back to what it was
+ if (dividerLocation != -1) {
+ setDividerLocation(dividerLocation);
+ }
+ }
+
+ /**
+ * Gets the location of the applications mainframe.
+ *
+ * @return Point object.
+ */
+ public Point getLocationOnScreen() {
+ return frame.getLocationOnScreen();
+ }
+
+ /**
+ * Gets the bounds of the applications mainframe.
+ *
+ * @return Rectangle Object.
+ */
+ public Rectangle getBounds() {
+ return frame.getBounds();
+ }
+
+ /**
+ * Sets the BiModalJSplitframe mode.
+ *
+ * @param newMode MODE_SHOW_SPLIT or MODE_HIDE_SPLIT.
+ */
+ public void setMode(CytoPanelState cytoPanelState, int newMode) {
+ // check args
+ if ((newMode != MODE_SHOW_SPLIT) && (newMode != MODE_HIDE_SPLIT)) {
+ throw new IllegalArgumentException("Illegal Argument: " + newMode
+ + ". Must be one of: MODE_SHOW_SPLIT or "
+ + " MODE_HIDE_SPLIT.");
+ }
+
+ int oldMode = currentMode;
+
+ // only process if the mode has changed
+ if (newMode != currentMode) {
+ if (newMode == MODE_HIDE_SPLIT) {
+ hideSplit();
+ } else if (newMode == MODE_SHOW_SPLIT) {
+ showSplit();
+ }
+
+ this.currentMode = newMode;
+
+ // fire a property change
+ this.firePropertyChange(MODE_PROPERTY, oldMode, newMode);
+ }
+
+ // hack to make sure divider is zero when we go from dock to float
+ // and divider location is set properly when we go back to dock
+ if (cytoPanelState == cytoPanelState.FLOAT) {
+ setDividerSize(0);
+ dividerLocation = getDividerLocation();
+ }
+ }
+
+ /**
+ * Gets the current mode.
+ *
+ * @return MODE_SHOW_SPLIT or MODE_HIDE_SPLIT.
+ */
+ public int getMode() {
+ return currentMode;
+ }
+
+ /**
+ * Shows the split.
+ */
+ private void showSplit() {
+ setDividerSize(defaultDividerSize);
+
+ if (dividerLocation != -1) {
+ setDividerLocation(dividerLocation);
+ }
+
+ resetToPreferredSizes();
+ validateParent();
+ }
+
+ /**
+ * Hides the split.
+ */
+ private void hideSplit() {
+ setDividerSize(0);
+ dividerLocation = getDividerLocation();
+ resetToPreferredSizes();
+ validateParent();
+ }
+
+ /**
+ * Validates the parent container.
+ */
+ private void validateParent() {
+ Container container = this.getParent();
+
+ if (container != null) {
+ container.validate();
+ }
+ }
+
+ /**
+ * Add a component listener to the app frame to get windows resize events.
+ */
+ private void addComponentListener() {
+ frame.addComponentListener(new ComponentAdapter() {
+ /**
+ * Frame is resized.
+ *
+ * @param e Component Event.
+ */
+ public void componentResized(ComponentEvent e) {
+ dividerLocation = -1;
+ }
+ });
+ }
+}
diff --git a/application/src/main/java/cytoscape/view/cytopanels/CytoPanel.java b/application/src/main/java/cytoscape/view/cytopanels/CytoPanel.java
new file mode 100644
index 0000000..91baa7c
--- /dev/null
+++ b/application/src/main/java/cytoscape/view/cytopanels/CytoPanel.java
@@ -0,0 +1,225 @@
+/*
+ File: CytoPanel.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+//
+// $Id: CytoPanel.java 21857 2010-09-14 23:42:44Z apico $
+//------------------------------------------------------------------------------
+
+// our package
+package cytoscape.view.cytopanels;
+
+
+// imports
+import java.awt.Component;
+
+import javax.swing.Icon;
+
+
+/**
+ * Interface to a CytoPanel.
+ *
+ * @author Ben Gross.
+ */
+public interface CytoPanel {
+ /**
+ * Adds a component to the CytoPanel.
+ *
+ * @param component Component reference.
+ * @return component Component reference.
+ */
+ public Component add(Component component);
+
+ /**
+ * Adds a component to the CytoPanel at specified index.
+ *
+ * @param component Component reference.
+ * @param index Component index.
+ * @return component Component reference.
+ */
+ public Component add(Component component, int index);
+
+ /**
+ * Adds a component to the CytoPanel with a specified title.
+ *
+ * @param title Component title.
+ * @param component Component reference.
+ * @return component Component reference.
+ */
+ public Component add(String title, Component component);
+
+ /**
+ * Adds a component to the CytoPanel with specified title and icon.
+ *
+ * @param title Component title (can be null).
+ * @param icon Component icon (can be null).
+ * @param component Component reference.
+ */
+ public void add(String title, Icon icon, Component component);
+
+ /**
+ * Adds a component to the CytoPanel with specified title, icon, and tool tip.
+ *
+ * @param title Component title (can be null).
+ * @param icon Component icon (can be null).
+ * @param component Component reference.
+ * @param tip Component Tool tip text.
+ */
+ public void add(String title, Icon icon, Component component, String tip);
+
+ /**
+ * Adds a component to the CytoPanel with specified title, icon, and tool tip at specified index.
+ *
+ * @param title Component title (can be null).
+ * @param icon Component icon (can be null).
+ * @param component Component reference.
+ * @param tip Component Tool tip text.
+ * @param index Component index.
+ */
+ public void add(String title, Icon icon, Component component, String tip, int index);
+
+ /**
+ * Returns the title of the CytoPanel.
+ *
+ * @return String Title.
+ */
+ public String getTitle();
+
+ /**
+ * Returns the number of components in the CytoPanel.
+ *
+ * @return int Number of components.
+ */
+ public int getCytoPanelComponentCount();
+
+ /**
+ * Returns the currently selected component.
+ *
+ * @return component Currently selected Component reference.
+ */
+ public Component getSelectedComponent();
+
+ /**
+ * Returns the currently selected index.
+ *
+ * @return index Currently selected index.
+ */
+ public int getSelectedIndex();
+
+ /**
+ * Returns the component at index.
+ *
+ * @return component at the given index.
+ */
+ public Component getComponentAt(int index);
+
+ /**
+ * Gets the state of the CytoPanel.
+ *
+ * @return A CytoPanelState.
+ */
+ public CytoPanelState getState();
+
+ /**
+ * Returns the index for the specified component.
+ *
+ * @param component Component reference.
+ * @return int Index of the Component or -1 if not found.
+ */
+ public int indexOfComponent(Component component);
+
+ /**
+ * Returns the first Component index with given title.
+ *
+ * @param title Component title.
+ * @return int Component index with given title or -1 if not found.
+ */
+ public int indexOfComponent(String title);
+
+ /**
+ * Removes specified component from the CytoPanel.
+ *
+ * @param component Component reference.
+ */
+ public void remove(Component component);
+
+ /**
+ * Removes the component from the CytoPanel at the specified index.
+ *
+ * @param index Component index.
+ */
+ public void remove(int index);
+
+ /**
+ * Removes all the components from the CytoPanel.
+ */
+ public void removeAll();
+
+ /**
+ * Sets the selected index on the CytoPanel.
+ *
+ * @param index The desired index.
+ */
+ public void setSelectedIndex(int index);
+
+ /**
+ * Sets the state of the CytoPanel.
+ *
+ * @param cytoPanelState A CytoPanelState.
+ */
+ public void setState(CytoPanelState cytoPanelState);
+
+ /**
+ * Adds a CytoPanel listener.
+ *
+ * @param cytoPanelListener Reference to a CytoPanelListener.
+ */
+ public void addCytoPanelListener(CytoPanelListener cytoPanelListener);
+
+ /**
+ * Removes a CytoPanel listener.
+ *
+ * @param cytoPanelListener Reference to a CytoPanelListener.
+ */
+ public void removeCytoPanelListener(CytoPanelListener cytoPanelListener);
+
+ /**
+ * Returns the int indicating the position in the layout.
+ *
+ * @return The int indicating the position in the layout.
+ */
+ public int getCompassDirection();
+}
diff --git a/application/src/main/java/cytoscape/view/cytopanels/CytoPanelContainer.java b/application/src/main/java/cytoscape/view/cytopanels/CytoPanelContainer.java
new file mode 100644
index 0000000..ce57639
--- /dev/null
+++ b/application/src/main/java/cytoscape/view/cytopanels/CytoPanelContainer.java
@@ -0,0 +1,78 @@
+/*
+ File: CytoPanelContainer.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+//
+// $Id: CytoPanelContainer.java 9565 2007-02-13 19:36:50Z mes $
+//------------------------------------------------------------------------------
+
+// our package
+package cytoscape.view.cytopanels;
+
+
+// imports
+import java.awt.Point;
+import java.awt.Rectangle;
+
+
+/**
+ * Interface for Container of CytoPanel Objects.
+ *
+ * @author Ethan Cerami
+ */
+public interface CytoPanelContainer {
+ /**
+ * Inserts CytoPanel at Specified Compass Direction.
+ *
+ * @param cytoPanel CytoPanel Object.
+ * @param compassDirection SwingConstants integer value.
+ */
+ void insertCytoPanel(CytoPanelImp cytoPanel, int compassDirection);
+
+ /**
+ * Gets Location of Container, in screen coordinates.
+ *
+ * @return Point Object.
+ */
+ Point getLocationOnScreen();
+
+ /**
+ * Gets Bounds of Container, relative to parent component.
+ *
+ * @return Rectangle Object.
+ */
+ Rectangle getBounds();
+}
diff --git a/application/src/main/java/cytoscape/view/cytopanels/CytoPanelImp.java b/application/src/main/java/cytoscape/view/cytopanels/CytoPanelImp.java
new file mode 100644
index 0000000..277ac2f
--- /dev/null
+++ b/application/src/main/java/cytoscape/view/cytopanels/CytoPanelImp.java
@@ -0,0 +1,1051 @@
+/*
+ File: CytoPanelImp.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+//
+// $Id: CytoPanelImp.java 26563 2011-08-15 23:39:00Z scooter $
+//------------------------------------------------------------------------------
+
+// our package
+package cytoscape.view.cytopanels;
+
+import cytoscape.Cytoscape;
+import cytoscape.logger.CyLogger;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Container;
+import java.awt.Dimension;
+
+// imports
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Insets;
+import java.awt.Point;
+import java.awt.Rectangle;
+import java.awt.Toolkit;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
+
+import java.util.ArrayList;
+
+import javax.swing.Icon;
+import javax.swing.ImageIcon;
+import javax.swing.JButton;
+import javax.swing.JDialog;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JSplitPane;
+import javax.swing.JTabbedPane;
+import javax.swing.SwingConstants;
+import javax.swing.border.EmptyBorder;
+import javax.swing.border.LineBorder;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+
+
+/**
+ * The CytoPanel class extends JPanel to provide the following functionality:
+ * <UL>
+ * <LI> Floating/Docking of Panel.
+ * <UL>
+ *
+ * CytoPanel also implements CytoPanel interface.
+ *
+ * @author Ethan Cerami, Benjamin Gross
+ */
+public class CytoPanelImp extends JPanel implements CytoPanel, ChangeListener {
+
+ private static final long serialVersionUID = 8431678873343221338L;
+
+ /**
+ * Minimum standards for CytoPanels.
+ */
+ private static final int WEST_MIN_WIDTH = 100;
+ private static final int WEST_MAX_WIDTH = 400;
+ private static final int WEST_MIN_HEIGHT = 500;
+ private static final int SOUTH_MIN_WIDTH = 500;
+ private static final int SOUTH_MIN_HEIGHT = 50;
+ private static final int EAST_MIN_WIDTH = 100;
+ private static final int EAST_MAX_WIDTH = 500;
+ private static final int EAST_MIN_HEIGHT = 100;
+
+ /**
+ * The JTabbedPane we hide.
+ */
+ private final JTabbedPane tabbedPane;
+
+ /**
+ * Our state.
+ */
+ private CytoPanelState cytoPanelState;
+
+ /**
+ * Our compass direction.
+ */
+ private int compassDirection;
+
+ /**
+ * An array of CytoPanelListeners
+ */
+ private ArrayList cytoPanelListenerList;
+
+ /**
+ * Notification state change.
+ */
+ private final int NOTIFICATION_STATE_CHANGE = 0;
+
+ /**
+ * Notification component selected.
+ */
+ private final int NOTIFICATION_COMPONENT_SELECTED = 1;
+
+ /**
+ * Notification component added.
+ */
+ private final int NOTIFICATION_COMPONENT_ADDED = 2;
+
+ /**
+ * Notification component removed.
+ */
+ private final int NOTIFICATION_COMPONENT_REMOVED = 3;
+
+ /**
+ * Reference to CytoPanelContainer we live in.
+ */
+ private CytoPanelContainer cytoPanelContainer;
+
+ /**
+ * External window used to hold the floating CytoPanel.
+ */
+ private JDialog externalFrame;
+
+ /**
+ * The float icon.
+ */
+ private ImageIcon floatIcon;
+
+ /**
+ * The dock icon.
+ */
+ private ImageIcon dockIcon;
+
+ /**
+ * The label which contains the tab title - not sure if its needed.
+ */
+ private JLabel floatLabel;
+
+ /**
+ * The float/dock button.
+ */
+ private JButton floatButton;
+
+ /**
+ * The float/dock button.
+ */
+ private final int FLOAT_PANEL_SCALE_FACTOR = 2;
+
+ /**
+ * Color of the dock/float button panel.
+ */
+ private Color FLOAT_PANEL_COLOR = new Color(204, 204, 204);
+
+ /* the following constants should probably move into common constants class */
+
+ /**
+ * The float button tool tip.
+ */
+ private static final String TOOL_TIP_FLOAT = "Float Window";
+
+ /**
+ * The dock button tool tip.
+ */
+ private static final String TOOL_TIP_DOCK = "Dock Window";
+
+ /**
+ * Location of our icons.
+ */
+ private static final String RESOURCE_DIR = "/cytoscape/images/";
+
+ /**
+ * The float icon gif filename.
+ */
+ private static final String FLOAT_GIF = "float.gif";
+
+ /**
+ * The dock icon gif filename.
+ */
+ private static final String DOCK_GIF = "pin.gif";
+
+ /**
+ * The file separator character.
+ */
+ private static final String FILE_SEPARATOR = "/";
+
+ /**
+ * Constructor.
+ *
+ * @param compassDirection Compass direction of this CytoPanel.
+ * @param tabPlacement Tab placement of this CytoPanel.
+ * @param cytoPanelState The starting CytoPanel state.
+ */
+ public CytoPanelImp(int compassDirection, int tabPlacement, CytoPanelState cytoPanelState) {
+ // setup our tabbed pane
+ tabbedPane = new JTabbedPane(tabPlacement);
+ tabbedPane.setTabLayoutPolicy(JTabbedPane.SCROLL_TAB_LAYOUT);
+ tabbedPane.addChangeListener(this);
+
+ // set our compass direction - limit to n,s,e,w
+ if ((compassDirection == SwingConstants.NORTH) || (compassDirection == SwingConstants.EAST)
+ || (compassDirection == SwingConstants.WEST)
+ || (compassDirection == SwingConstants.SOUTH_WEST)
+ || (compassDirection == SwingConstants.SOUTH)) {
+ this.compassDirection = compassDirection;
+ } else {
+ throw new IllegalArgumentException("Illegal Argument: " + compassDirection
+ + ". Must be one of: SwingConstants.{NORTH,SOUTH,EAST,WEST,SOUTH_WEST}.");
+ }
+
+ // init listener list
+ cytoPanelListenerList = new ArrayList();
+
+ // init the icons
+ initIcons();
+
+ // construct our panel
+ constructPanel();
+
+ // to hidden by default
+ setState(cytoPanelState);
+ }
+
+ /**
+ * Sets CytoPanelContainer interface reference.
+ *
+ * @param cytoPanelContainer Reference to CytoPanelContainer
+ */
+ public void setCytoPanelContainer(CytoPanelContainer cytoPanelContainer) {
+ // set our cytoPanelContainerReference
+ this.cytoPanelContainer = cytoPanelContainer;
+ }
+
+ /**
+ * Returns the proper title based on our compass direction.
+ *
+ * @return A title string
+ */
+ public String getTitle() {
+ return CytoPanelName.getTitle(compassDirection);
+ }
+
+ /**
+ * Adds a component to the CytoPanel.
+ *
+ * @param component Component reference.
+ * @return component Component reference.
+ */
+ public Component add(Component component) {
+ // override minSize to keep panels sane
+ if (compassDirection == SwingConstants.WEST)
+ component.setMinimumSize(new Dimension(
+ WEST_MIN_WIDTH,
+ WEST_MIN_HEIGHT));
+ else if (compassDirection == SwingConstants.SOUTH)
+ component.setMinimumSize(new Dimension(
+ SOUTH_MIN_WIDTH,
+ SOUTH_MIN_HEIGHT));
+ else if (compassDirection == SwingConstants.EAST)
+ component.setMinimumSize(new Dimension(
+ EAST_MIN_WIDTH,
+ EAST_MIN_HEIGHT));
+
+ // add tab to JTabbedPane (component)
+ Component c = tabbedPane.add(component);
+
+ // send out a notification
+ notifyListeners(NOTIFICATION_COMPONENT_ADDED);
+
+ // outta here
+ return c;
+ }
+
+ /**
+ * Adds a component to the CytoPanel at specified index.
+ *
+ * @param component Component reference.
+ * @param index Component index.
+ * @return component Component reference.
+ */
+ public Component add(Component component, int index) {
+ // override minSize to keep panels sane
+ if (compassDirection == SwingConstants.WEST)
+ component.setMinimumSize(new Dimension(
+ WEST_MIN_WIDTH,
+ WEST_MIN_HEIGHT));
+ else if (compassDirection == SwingConstants.SOUTH)
+ component.setMinimumSize(new Dimension(
+ SOUTH_MIN_WIDTH,
+ SOUTH_MIN_HEIGHT));
+ else if (compassDirection == SwingConstants.EAST)
+ component.setMinimumSize(new Dimension(
+ EAST_MIN_WIDTH,
+ EAST_MIN_HEIGHT));
+
+ // add tab to JTabbedPane (component, index)
+ Component c = tabbedPane.add(component, index);
+
+ // send out a notification
+ notifyListeners(NOTIFICATION_COMPONENT_ADDED);
+
+ // outta here
+ return c;
+ }
+
+ /**
+ * Adds a component to the CytoPanel with a specified title.
+ *
+ * @param title Component title.
+ * @param component Component reference.
+ * @return component Component reference.
+ */
+ public Component add(String title, Component component) {
+ // override minSize to keep panels sane
+ if (compassDirection == SwingConstants.WEST)
+ component.setMinimumSize(new Dimension(
+ WEST_MIN_WIDTH,
+ WEST_MIN_HEIGHT));
+ else if (compassDirection == SwingConstants.SOUTH)
+ component.setMinimumSize(new Dimension(
+ SOUTH_MIN_WIDTH,
+ SOUTH_MIN_HEIGHT));
+ else if (compassDirection == SwingConstants.EAST)
+ component.setMinimumSize(new Dimension(
+ EAST_MIN_WIDTH,
+ EAST_MIN_HEIGHT));
+
+ // add tab to JTabbedPane (title, component)
+ Component c = tabbedPane.add(title, component);
+
+ // send out a notification
+ notifyListeners(NOTIFICATION_COMPONENT_ADDED);
+
+ // outta here
+ return c;
+ }
+
+ /**
+ * Adds a component to the CytoPanel with specified title and icon.
+ *
+ * @param title Component title (can be null).
+ * @param icon Component icon (can be null).
+ * @param component Component reference.
+ */
+ public void add(String title, Icon icon, Component component) {
+ // override minSize to keep panels sane
+ if (compassDirection == SwingConstants.WEST)
+ component.setMinimumSize(new Dimension(
+ WEST_MIN_WIDTH,
+ WEST_MIN_HEIGHT));
+ else if (compassDirection == SwingConstants.SOUTH)
+ component.setMinimumSize(new Dimension(
+ SOUTH_MIN_WIDTH,
+ SOUTH_MIN_HEIGHT));
+ else if (compassDirection == SwingConstants.EAST)
+ component.setMinimumSize(new Dimension(
+ EAST_MIN_WIDTH,
+ EAST_MIN_HEIGHT));
+
+ // add tab to JTabbedPane (title, icon, component)
+ tabbedPane.addTab(title, icon, component);
+
+ // send out a notification
+ notifyListeners(NOTIFICATION_COMPONENT_ADDED);
+ }
+
+ /**
+ * Adds a component to the CytoPanel with specified title, icon, and tool tip.
+ *
+ * @param title Component title (can be null).
+ * @param icon Component icon (can be null).
+ * @param component Component reference.
+ * @param tip Component Tool tip text.
+ */
+ public void add(String title, Icon icon, Component component, String tip) {
+ // override minSize to keep panels sane
+ if (compassDirection == SwingConstants.WEST)
+ component.setMinimumSize(new Dimension(
+ WEST_MIN_WIDTH,
+ WEST_MIN_HEIGHT));
+ else if (compassDirection == SwingConstants.SOUTH)
+ component.setMinimumSize(new Dimension(
+ SOUTH_MIN_WIDTH,
+ SOUTH_MIN_HEIGHT));
+ else if (compassDirection == SwingConstants.EAST)
+ component.setMinimumSize(new Dimension(
+ EAST_MIN_WIDTH,
+ EAST_MIN_HEIGHT));
+
+ // add tab to JTabbedPane (string, icon, component, tip)
+ tabbedPane.addTab(title, icon, component, tip);
+
+ // send out a notification
+ notifyListeners(NOTIFICATION_COMPONENT_ADDED);
+ }
+
+ /**
+ * Adds a component to the CytoPanel with specified title, icon, and tool tip at specified index.
+ *
+ * @param title Component title (can be null).
+ * @param icon Component icon (can be null).
+ * @param component Component reference.
+ * @param tip Component Tool tip text.
+ * @param index Component index.
+ */
+ public void add(String title, Icon icon, Component component, String tip, int index) {
+ // override minSize to keep panels sane
+ if (compassDirection == SwingConstants.WEST)
+ component.setMinimumSize(new Dimension(
+ WEST_MIN_WIDTH,
+ WEST_MIN_HEIGHT));
+ else if (compassDirection == SwingConstants.SOUTH)
+ component.setMinimumSize(new Dimension(
+ SOUTH_MIN_WIDTH,
+ SOUTH_MIN_HEIGHT));
+ else if (compassDirection == SwingConstants.EAST)
+ component.setMinimumSize(new Dimension(
+ EAST_MIN_WIDTH,
+ EAST_MIN_HEIGHT));
+
+ // insert tab into JTabbedPane (string, icon, component, tip, index)
+ tabbedPane.insertTab(title, icon, component, tip, index);
+
+ // send out a notification
+ notifyListeners(NOTIFICATION_COMPONENT_ADDED);
+ }
+
+ /**
+ * Returns the number of components in the CytoPanel.
+ *
+ * @return int Number of components.
+ */
+ public int getCytoPanelComponentCount() {
+ // return the number of tabs in the JTabbedPane.
+ return tabbedPane.getTabCount();
+ }
+
+ /**
+ * Returns the currently selected component.
+ *
+ * @return component Currently selected Component reference.
+ */
+ public Component getSelectedComponent() {
+ // get currently selected component in the JTabbedPane.
+ return tabbedPane.getSelectedComponent();
+ }
+
+ /**
+ * Returns the component at index.
+ *
+ * @return component at the given index.
+ */
+ public Component getComponentAt(int index) {
+ return tabbedPane.getComponentAt(index);
+ }
+
+ /**
+ * Returns the currently selected index.
+ *
+ * @return index Currently selected index.
+ */
+ public int getSelectedIndex() {
+ // get currently selected component in the JTabbedPane.
+ return tabbedPane.getSelectedIndex();
+ }
+
+ /**
+ * Returns the index for the specified component.
+ *
+ * @param component Component reference.
+ * @return int Index of the Component or -1 if not found.
+ */
+ public int indexOfComponent(Component component) {
+ // get the index from JTabbedPane
+ return tabbedPane.indexOfComponent(component);
+ }
+
+ /**
+ * Returns the first Component index with given title.
+ *
+ * @param title Component title.
+ * @return int Component index with given title or -1 if not found.
+ */
+ public int indexOfComponent(String title) {
+ // get the index from JTabbedPane
+ return tabbedPane.indexOfTab(title);
+ }
+
+ /**
+ * Removes specified component from the CytoPanel.
+ *
+ * @param component Component reference.
+ */
+ public void remove(Component component) {
+ // remove tab from JTabbedPane (component)
+ tabbedPane.remove(component);
+
+ // send out a notification
+ notifyListeners(NOTIFICATION_COMPONENT_REMOVED);
+ }
+
+ /**
+ * Removes the component from the CytoPanel at the specified index.
+ *
+ * @param index Component index.
+ */
+ public void remove(int index) {
+ // remove tab from JTabbedPane (index)
+ tabbedPane.remove(index);
+
+ // send out a notification
+ notifyListeners(NOTIFICATION_COMPONENT_REMOVED);
+ }
+
+ /**
+ * Removes all the components from the CytoPanel.
+ */
+ public void removeAll() {
+ // remove all tabs and components from JTabbedPane
+ tabbedPane.removeAll();
+
+ // send out a notification
+ notifyListeners(NOTIFICATION_COMPONENT_REMOVED);
+ }
+
+ /**
+ * Sets the selected index on the CytoPanel.
+ *
+ * @param index The desired index.
+ */
+ public void setSelectedIndex(int index) {
+ // set selected index
+ tabbedPane.setSelectedIndex(index);
+ resizeSelectedComponent();
+
+ // do not have to sent out notification - the tabbedPane will let us know.
+ }
+
+ /**
+ * Sets the state of the CytoPanel.
+ *
+ * @param cytoPanelState A CytoPanelState.
+ */
+ public void setState(CytoPanelState cytoPanelState) {
+ boolean success = false;
+
+ // 'switch' on the state
+ if (cytoPanelState == CytoPanelState.HIDE) {
+ hideCytoPanel(cytoPanelState);
+ success = true;
+ } else if (cytoPanelState == CytoPanelState.FLOAT) {
+ FloatCytoPanel();
+ success = true;
+ } else if (cytoPanelState == CytoPanelState.DOCK) {
+ DockCytoPanel();
+ success = true;
+ }
+
+ // houston we have a problem
+ if (!success) {
+ // made it here, houston, we have a problem
+ throw new IllegalArgumentException("Illegal Argument: " + cytoPanelState
+ + ". is unknown. Please see CytoPanelState class.");
+ }
+
+ // set our new state
+ this.cytoPanelState = cytoPanelState;
+
+ // let our listeners know
+ notifyListeners(NOTIFICATION_STATE_CHANGE);
+ }
+
+ /**
+ * Gets the state of the CytoPanel.
+ *
+ * @return A CytoPanelState.
+ */
+ public CytoPanelState getState() {
+ return cytoPanelState;
+ }
+
+ /**
+ * Adds a CytoPanel listener.
+ *
+ * @param cytoPanelListener Reference to a CytoPanelListener.
+ */
+ public void addCytoPanelListener(CytoPanelListener cytoPanelListener) {
+ // nothing to do if listener is already in our list
+ if (cytoPanelListenerList.contains(cytoPanelListener)) {
+ return;
+ }
+
+ // add listener to our list
+ cytoPanelListenerList.add(cytoPanelListener);
+ }
+
+ /**
+ * Removes a CytoPanel listener.
+ *
+ * @param cytoPanelListener Reference to a CytoPanelListener.
+ */
+ public void removeCytoPanelListener(CytoPanelListener cytoPanelListener) {
+ // remove listener if they exist in our list
+ if (cytoPanelListenerList.contains(cytoPanelListener)) {
+ cytoPanelListenerList.remove(cytoPanelListenerList.indexOf(cytoPanelListener));
+ }
+ }
+
+ /**
+ * Our implementation of the ChangeListener interface,
+ * to determine when new tab has been selected
+ */
+ public void stateChanged(ChangeEvent e) {
+ // Handle the resize
+ resizeSelectedComponent();
+
+ // let our listeners know
+ notifyListeners(NOTIFICATION_COMPONENT_SELECTED);
+ }
+
+ /**
+ * Initialize all Icons.
+ */
+ private void initIcons() {
+ // icon strings
+ String floatIconStr = new String(RESOURCE_DIR + FLOAT_GIF);
+ String dockIconStr = new String(RESOURCE_DIR + DOCK_GIF);
+
+ // create our icon objects
+ floatIcon = new ImageIcon(getClass().getResource(floatIconStr));
+ dockIcon = new ImageIcon(getClass().getResource(dockIconStr));
+ }
+
+ /**
+ * Shows the CytoPanel.
+ */
+ private void showCytoPanel(CytoPanelState cytoPanelState) {
+ // make ourselves visible
+ setVisible(true);
+
+ // if our parent is a BiModalSplitPane, show the split
+ Container parent = this.getParent();
+
+ if (parent instanceof BiModalJSplitPane) {
+ BiModalJSplitPane biModalSplitPane = (BiModalJSplitPane) parent;
+ biModalSplitPane.setMode(cytoPanelState, BiModalJSplitPane.MODE_SHOW_SPLIT);
+ }
+ }
+
+ /**
+ * Hides the CytoPanel.
+ */
+ private void hideCytoPanel(CytoPanelState cytoPanelState) {
+ // dock ourselves
+ if (isFloating()) {
+ DockCytoPanel();
+ }
+
+ // hide ourselves
+ setVisible(false);
+
+ // if our Parent Container is a BiModalSplitPane, hide the split
+ Container parent = this.getParent();
+
+ if (parent instanceof BiModalJSplitPane) {
+ BiModalJSplitPane biModalSplitPane = (BiModalJSplitPane) parent;
+ biModalSplitPane.setMode(cytoPanelState, BiModalJSplitPane.MODE_HIDE_SPLIT);
+ }
+ }
+
+ /**
+ * Constructs this CytoPanel.
+ */
+ void constructPanel() {
+ // init our components
+ initLabel();
+ initButton();
+
+ // add label and button components to yet another panel,
+ // so we can layout properly
+ final JPanel floatDockPanel = new JPanel(new BorderLayout());
+
+ // set float dock panel attributes
+ floatDockPanel.add(floatLabel, BorderLayout.WEST);
+ floatDockPanel.add(floatButton, BorderLayout.EAST);
+ floatDockPanel.setBorder(new EmptyBorder(0, 1, 0, 1));
+ floatDockPanel.setBackground(FLOAT_PANEL_COLOR);
+
+ // set preferred size - we can use float or dock icon diminsions - they are the same
+ FontMetrics fm = floatLabel.getFontMetrics(floatLabel.getFont());
+ floatDockPanel.setMinimumSize(new Dimension((int) ((fm.stringWidth(getTitle())
+ + floatIcon.getIconWidth()) * FLOAT_PANEL_SCALE_FACTOR),
+ floatIcon.getIconHeight()));
+ floatDockPanel.setPreferredSize(new Dimension((int) ((fm.stringWidth(getTitle())
+ + floatIcon.getIconWidth()) * FLOAT_PANEL_SCALE_FACTOR),
+ floatIcon.getIconHeight() + 2));
+
+ // use the border layout for this CytoPanel
+ setLayout(new BorderLayout());
+ tabbedPane.setBorder(new EmptyBorder(0, 0, 0, 0));
+ add(floatDockPanel, BorderLayout.NORTH);
+ add(tabbedPane, BorderLayout.CENTER);
+ }
+
+ /**
+ * Add a component to the CytoPanel just below the TabbedPane.
+ *
+ * @param pComponent the component to be added.
+ */
+ public void addComponentToSouth(Component pComponent) {
+ add(pComponent, BorderLayout.SOUTH);
+ }
+
+ /**
+ * Remove a component from the CytoPanel just below the TabbedPane.
+ *
+ * @param pComponent the component to be removed.
+ */
+ public void removeComponentAtSouth(Component pComponent) {
+ remove(pComponent);
+ }
+
+ /**
+ * Initializes the label.
+ */
+ private void initLabel() {
+ floatLabel = new JLabel(getTitle());
+ floatLabel.setFont(new Font("SansSerif", Font.PLAIN, 12));
+ floatLabel.setBackground(FLOAT_PANEL_COLOR);
+ floatLabel.setBorder(new EmptyBorder(0, 5, 0, 0));
+ }
+
+ /**
+ * Initializes the button.
+ */
+ private void initButton() {
+ // Create Float / Dock Button
+ floatButton = new JButton();
+ floatButton.setIcon(floatIcon);
+ floatButton.setToolTipText(TOOL_TIP_FLOAT);
+ floatButton.setRolloverEnabled(true);
+
+ // Set 0 Margin All-Around and setBorderPainted to false
+ // so that button appears as small as possible
+ floatButton.setMargin(new Insets(0, 0, 0, 0));
+ floatButton.setBorder(new EmptyBorder(1, 1, 1, 1));
+ floatButton.setBorderPainted(false);
+ floatButton.setSelected(false);
+ floatButton.setBackground(FLOAT_PANEL_COLOR);
+
+ // When User Hovers Over Button, highlight it with a gray box
+ floatButton.addMouseListener(new MouseAdapter() {
+ public void mouseEntered(MouseEvent e) {
+ floatButton.setBorder(new LineBorder(Color.GRAY, 1));
+ floatButton.setBorderPainted(true);
+ floatButton.setBackground(Color.LIGHT_GRAY);
+ }
+
+ public void mouseExited(MouseEvent e) {
+ floatButton.setBorder(new EmptyBorder(1, 1, 1, 1));
+ floatButton.setBorderPainted(false);
+ floatButton.setBackground(FLOAT_PANEL_COLOR);
+ }
+ });
+
+ floatButton.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ if (isFloating()) {
+ DockCytoPanel();
+ } else {
+ FloatCytoPanel();
+ }
+
+ notifyListeners(NOTIFICATION_STATE_CHANGE);
+ }
+ });
+ }
+
+ /**
+ * Float cytoPanel
+ */
+ private void FloatCytoPanel() {
+ // show ourselves
+ showCytoPanel(CytoPanelState.FLOAT);
+
+ if (!isFloating()) {
+ // new frame to place this CytoPanel
+ externalFrame = new JDialog(Cytoscape.getDesktop());
+
+ // When floating, Cytopanel is always on top.
+ externalFrame.setAlwaysOnTop(true);
+
+ // add listener to handle when window is closed
+ addWindowListener();
+
+ // Add CytoPanel to the New External Frame
+ Container contentPane = externalFrame.getContentPane();
+ contentPane.add(this, BorderLayout.CENTER);
+ externalFrame.setSize(this.getSize());
+ externalFrame.validate();
+
+ // set proper title of frame
+ externalFrame.setTitle(getTitle());
+
+ // set proper button icon/text
+ floatButton.setIcon(dockIcon);
+ floatButton.setToolTipText(TOOL_TIP_DOCK);
+
+ // set float label text
+ floatLabel.setText("");
+
+ // set location of external frame
+ setLocationOfExternalFrame(externalFrame);
+ // lets show it
+ externalFrame.setVisible(true);
+
+ // set our new state
+ this.cytoPanelState = CytoPanelState.FLOAT;
+
+ // turn off the border
+ floatButton.setBorderPainted(false);
+
+ // re-layout
+ this.validate();
+
+ // SOUTH_WEST is used for manualLayout, it is nested in cytoPanel_1
+ if (compassDirection == SwingConstants.SOUTH_WEST) {
+ ((CytoPanelImp) Cytoscape.getDesktop().getCytoPanel(SwingConstants.WEST)).validate();
+ }
+ }
+ }
+
+ /**
+ * Dock cytoPanel
+ */
+ private void DockCytoPanel() {
+ // show ourselves
+ showCytoPanel(CytoPanelState.DOCK);
+
+ if (isFloating()) {
+ // remove cytopanel from external view
+ externalFrame.remove(this);
+
+ // add this cytopanel back to cytopanel container
+ if (cytoPanelContainer == null) {
+ CyLogger.getLogger().info("CytoPanel::DockCytoPanel() -"
+ + "cytoPanelContainer reference has not been set!");
+ Cytoscape.exit(1);
+ }
+
+ cytoPanelContainer.insertCytoPanel(this, compassDirection);
+
+ // dispose of the external frame
+ externalFrame.dispose();
+
+ // set proper button icon/text
+ floatButton.setIcon(floatIcon);
+ floatButton.setToolTipText(TOOL_TIP_FLOAT);
+
+ // set float label text
+ floatLabel.setText(getTitle());
+
+ // set our new state
+ this.cytoPanelState = CytoPanelState.DOCK;
+
+ // turn off the border
+ floatButton.setBorderPainted(false);
+
+ // re-layout
+ this.validate();
+
+ // SOUTH_WEST is used for manualLayout, it is nested in cytoPanel_1
+ if (compassDirection == SwingConstants.SOUTH_WEST) {
+ try {
+ this.getParent().getParent().validate();
+ } catch (Exception e) {
+ }
+ }
+ }
+ }
+
+ /**
+ * Are we floating ?
+ */
+ private boolean isFloating() {
+ return (cytoPanelState == CytoPanelState.FLOAT);
+ }
+
+ /**
+ * Are we hidden ?
+ */
+ private boolean isHidden() {
+ return (cytoPanelState == CytoPanelState.HIDE);
+ }
+
+ /**
+ * Adds the listener to the floating window.
+ */
+ private void addWindowListener() {
+ externalFrame.addWindowListener(new WindowAdapter() {
+ /**
+ * Window is Closing.
+ *
+ * @param e Window Event.
+ */
+ public void windowClosing(WindowEvent e) {
+ DockCytoPanel();
+ notifyListeners(NOTIFICATION_STATE_CHANGE);
+ }
+ });
+ }
+
+ /**
+ * Sets the Location of the External Frame.
+ *
+ * @param externalWindow ExternalFrame Object.
+ */
+ private void setLocationOfExternalFrame(JDialog externalWindow) {
+ Toolkit tk = Toolkit.getDefaultToolkit();
+ Dimension screenDimension = tk.getScreenSize();
+
+ // Get Absolute Location and Bounds, relative to Screen
+ Rectangle containerBounds = cytoPanelContainer.getBounds();
+ containerBounds.setLocation(cytoPanelContainer.getLocationOnScreen());
+
+ Point p = CytoPanelUtil.getLocationOfExternalFrame(screenDimension, containerBounds,
+ externalWindow.getSize(),
+ compassDirection, false);
+
+ externalWindow.setLocation(p);
+ externalWindow.setVisible(true);
+ }
+
+ /**
+ * Code to notify our listeners of some particular event.
+ *
+ * @param notificationType What type of notification to perform.
+ */
+ private void notifyListeners(int notificationType) {
+ // interate through all our listeners
+ for (int lc = 0; lc < cytoPanelListenerList.size(); lc++) {
+ CytoPanelListener cytoPanelListener = (CytoPanelListener) cytoPanelListenerList.get(lc);
+
+ // determine what event to fire
+ switch (notificationType) {
+ case NOTIFICATION_STATE_CHANGE:
+ cytoPanelListener.onStateChange(cytoPanelState);
+
+ break;
+
+ case NOTIFICATION_COMPONENT_SELECTED:
+
+ int selectedIndex = tabbedPane.getSelectedIndex();
+ cytoPanelListener.onComponentSelected(selectedIndex);
+
+ break;
+
+ case NOTIFICATION_COMPONENT_ADDED:
+ cytoPanelListener.onComponentAdded(getCytoPanelComponentCount());
+
+ break;
+
+ case NOTIFICATION_COMPONENT_REMOVED:
+ cytoPanelListener.onComponentRemoved(getCytoPanelComponentCount());
+
+ break;
+ }
+ }
+ }
+
+ /**
+ * Size the divider to the currently selected panel's preferredSize
+ */
+ private void resizeSelectedComponent() {
+ /*
+ * Set default resize behavior based on the currently
+ * selected panel's preferredSize setting
+ *
+ */
+ Component panel = tabbedPane.getSelectedComponent();
+ // Make sure we're not being notified that we've deleted
+ // the last panel
+ if (panel != null && cytoPanelContainer instanceof JSplitPane) {
+ int width = panel.getPreferredSize().width;
+ JSplitPane jsp = (JSplitPane)cytoPanelContainer;
+ if (compassDirection == SwingConstants.WEST) {
+ if (width > WEST_MAX_WIDTH)
+ width = WEST_MAX_WIDTH;
+ else if (width < WEST_MIN_WIDTH)
+ width = WEST_MIN_WIDTH;
+ jsp.setDividerLocation(width+jsp.getInsets().left+jsp.getInsets().right+5);
+ } else if (compassDirection == SwingConstants.EAST) {
+ if (width > EAST_MAX_WIDTH)
+ width = EAST_MAX_WIDTH;
+ else if (width < EAST_MIN_WIDTH)
+ width = EAST_MIN_WIDTH;
+ jsp.setDividerLocation(jsp.getSize().width
+ -jsp.getInsets().right
+ -jsp.getInsets().left
+ -jsp.getDividerSize()
+ -width-5);
+ }
+ // TODO: What's the right thing to do with SOUTH?
+ }
+ }
+
+ /**
+ * Returns the int indicating the location within the layout.
+ *
+ * @return The int indicating the location within the layout.
+ */
+ public int getCompassDirection() {
+ return compassDirection;
+ }
+}
diff --git a/application/src/main/java/cytoscape/view/cytopanels/CytoPanelListener.java b/application/src/main/java/cytoscape/view/cytopanels/CytoPanelListener.java
new file mode 100644
index 0000000..c14b9bb
--- /dev/null
+++ b/application/src/main/java/cytoscape/view/cytopanels/CytoPanelListener.java
@@ -0,0 +1,84 @@
+/*
+ File: CytoPanelListener.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+//
+// $Id: CytoPanelListener.java 9565 2007-02-13 19:36:50Z mes $
+//------------------------------------------------------------------------------
+
+// our package
+package cytoscape.view.cytopanels;
+
+
+// imports
+import java.util.EventListener;
+
+
+/**
+ * This listener interface provides the
+ * mechanism to respond to CytoPanel Events.
+ *
+ * @author Ben Gross
+ */
+public interface CytoPanelListener extends EventListener {
+ /**
+ * Notifies the listener on a change in the CytoPanel state.
+ *
+ * @param newState The new CytoPanel state - see CytoPanelState class.
+ */
+ public void onStateChange(CytoPanelState newState);
+
+ /**
+ * Notifies the listener when a new component on the CytoPanel is selected.
+ *
+ * @param componentIndex The index of the component selected.
+ */
+ public void onComponentSelected(int componentIndex);
+
+ /**
+ * Notifies the listener when a component is added to the CytoPanel.
+ *
+ * @param count The number of components on the CytoPanel after the add.
+ */
+ public void onComponentAdded(int count);
+
+ /**
+ * Notifies the listener when a component is removed from the CytoPanel.
+ *
+ * @param count The number of components on the CytoPanel after the remove.
+ */
+ public void onComponentRemoved(int count);
+}
diff --git a/application/src/main/java/cytoscape/view/cytopanels/CytoPanelName.java b/application/src/main/java/cytoscape/view/cytopanels/CytoPanelName.java
new file mode 100644
index 0000000..0d88d4f
--- /dev/null
+++ b/application/src/main/java/cytoscape/view/cytopanels/CytoPanelName.java
@@ -0,0 +1,77 @@
+
+/*
+ File: CytoPanelName.java
+
+ Copyright (c) 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+
+package cytoscape.view.cytopanels;
+
+import javax.swing.SwingConstants;
+
+/**
+ * An enum that maps names to compass directions.
+ */
+public enum CytoPanelName {
+ NORTH("Top Panel",SwingConstants.NORTH),
+ SOUTH("Data Panel",SwingConstants.SOUTH),
+ EAST("Results Panel",SwingConstants.EAST),
+ WEST("Control Panel",SwingConstants.WEST),
+ SOUTH_WEST("Tool Panel",SwingConstants.SOUTH_WEST),
+ ;
+
+ private String title;
+ private int compassDirection;
+
+ private CytoPanelName(String title, int compassDirection) {
+ this.title = title;
+ this.compassDirection = compassDirection;
+ }
+
+ public String getTitle() {
+ return title;
+ }
+
+ public int getCompassDirection() {
+ return compassDirection;
+ }
+
+ public static String getTitle(int dir) {
+ for (CytoPanelName cpn : values())
+ if ( dir == cpn.getCompassDirection() )
+ return cpn.getTitle();
+ return null;
+ }
+}
diff --git a/application/src/main/java/cytoscape/view/cytopanels/CytoPanelState.java b/application/src/main/java/cytoscape/view/cytopanels/CytoPanelState.java
new file mode 100644
index 0000000..13e6a5f
--- /dev/null
+++ b/application/src/main/java/cytoscape/view/cytopanels/CytoPanelState.java
@@ -0,0 +1,96 @@
+/*
+ File: CytoPanelState.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+//
+// $Id: CytoPanelState.java 9736 2007-03-20 00:25:45Z mes $
+//------------------------------------------------------------------------------
+
+// our package
+package cytoscape.view.cytopanels;
+
+
+/**
+ * CytoPanelState Class. The following States are supported:
+ * <UL>
+ * <LI>CytoPanelState.HIDE: Hide the CytoPanel.
+ * <LI>CytoPanelState.FLOAT: Float the CytoPanel.
+ * <LI>CytoPanelState.DOCK: Dock the CytoPanel.
+ * </UL>
+ *
+ * @author Ben Gross
+ */
+public class CytoPanelState {
+ /*
+ * The state name.
+ */
+ private final String name;
+
+ /*
+ * Private constructor.
+ */
+ private CytoPanelState(String name) {
+ this.name = name;
+ }
+
+ /*
+ * In case a someone wants to translated a state into printable strings
+ */
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String toString() {
+ return name;
+ }
+
+ /**
+ * Hide state of a CytoPanel.
+ */
+ public static final CytoPanelState HIDE = new CytoPanelState("hide");
+
+ /**
+ * Float state of a CytoPanel.
+ */
+ public static final CytoPanelState FLOAT = new CytoPanelState("float");
+
+ /**
+ * Dock state of a CytoPanel.
+ */
+ public static final CytoPanelState DOCK = new CytoPanelState("dock");
+}
diff --git a/application/src/main/java/cytoscape/view/cytopanels/CytoPanelUtil.java b/application/src/main/java/cytoscape/view/cytopanels/CytoPanelUtil.java
new file mode 100644
index 0000000..30fa4a9
--- /dev/null
+++ b/application/src/main/java/cytoscape/view/cytopanels/CytoPanelUtil.java
@@ -0,0 +1,148 @@
+/*
+ File: CytoPanelUtil.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+//
+// $Id: CytoPanelUtil.java 14060 2008-05-20 20:13:18Z skillcoyne $
+//------------------------------------------------------------------------------
+
+// our package
+package cytoscape.view.cytopanels;
+
+import cytoscape.logger.CyLogger;
+
+import java.awt.Dimension;
+
+// imports
+import java.awt.Point;
+import java.awt.Rectangle;
+
+import javax.swing.SwingConstants;
+
+
+/**
+ * Contains methods to assist with various
+ * tasks performed by the CytoPanel API.
+ *
+ * @author Ethan Cerami, Ben Gross
+ */
+public class CytoPanelUtil {
+ /**
+ * String used to compare against os.name System property -
+ * to determine if we are running on Windows platform.
+ */
+ static final String WINDOWS = "windows";
+
+ /**
+ * Inset between owner frame and floating window.
+ */
+ private static final int INSET = 5;
+
+ /**
+ * Gets Location of External Frame, based on current UI Dimensions.
+ *
+ * @param screenDimension Current Screen Dimensions.
+ * @param containerBounds Container Bounds Rectangle.
+ * @param frameDimension Current Frame Dimensions.
+ * @param compassDirection Compass Direction, SwingConstants.
+ * @return Point Object.
+ */
+ public static Point getLocationOfExternalFrame(Dimension screenDimension,
+ Rectangle containerBounds,
+ Dimension frameDimension, int compassDirection,
+ boolean outputDiagnostics) {
+ if (outputDiagnostics) {
+ outputDiagnostics(screenDimension, containerBounds, frameDimension, compassDirection);
+ }
+
+ // Get Location and Dimension of Container
+ Point containerLocation = containerBounds.getLocation();
+ int containerWidth = (int) containerBounds.getWidth();
+ int containerHeight = (int) containerBounds.getHeight();
+
+ // Get Screen Dimensions
+ int screenWidth = (int) screenDimension.getWidth();
+ int screenHeight = (int) screenDimension.getHeight();
+
+ // Initialize Point
+ Point p = new Point(containerLocation.x, containerLocation.y);
+
+ // Set Point Based on Compass Direction
+ if (compassDirection == SwingConstants.WEST) {
+ p.x = containerLocation.x - INSET - (int) frameDimension.getWidth();
+ } else if (compassDirection == SwingConstants.EAST) {
+ p.x = containerLocation.x + INSET + (int) containerWidth;
+ } else if (compassDirection == SwingConstants.SOUTH) {
+ p.y = containerLocation.y + INSET + (int) containerHeight;
+ }
+
+ // Remove any negative coordinates
+ p.x = Math.max(0, p.x);
+ p.y = Math.max(0, p.y);
+
+ if ((p.x + frameDimension.getWidth()) > screenWidth) {
+ // Adjust for right most case
+ p.x = screenWidth - (int) frameDimension.getWidth();
+ }
+
+ if ((p.y + frameDimension.getHeight()) > screenHeight) {
+ // Adjust for bottom-most case
+ p.y = screenHeight - (int) frameDimension.getHeight();
+ }
+
+ return p;
+ }
+
+ /**
+ * Determines if we are running on Windows platform.
+ */
+ public boolean isWindows() {
+ String os = System.getProperty("os.name");
+
+ return os.regionMatches(true, 0, WINDOWS, 0, WINDOWS.length());
+ }
+
+ /**
+ * Outputs Diagnostics Related to Screen/Frame Dimensions.
+ */
+ private static void outputDiagnostics(Dimension screenDimension, Rectangle containerBounds,
+ Dimension preferredSizeOfPanel, int compassDirection) {
+ CyLogger.getLogger().warn("Compass Direction: " + compassDirection);
+ CyLogger.getLogger().warn("Screen Dimension: " + screenDimension);
+ CyLogger.getLogger().warn("Container Bounds: " + containerBounds.toString());
+ CyLogger.getLogger().warn("Preferred Size of Panel: " + preferredSizeOfPanel.toString());
+ }
+}
diff --git a/application/src/main/java/cytoscape/view/cytopanels/package.html b/application/src/main/java/cytoscape/view/cytopanels/package.html
new file mode 100644
index 0000000..f22a645
--- /dev/null
+++ b/application/src/main/java/cytoscape/view/cytopanels/package.html
@@ -0,0 +1,143 @@
+<html>
+<body>
+CytoPanels Framework.
+<P>
+<UL>
+<LI><A HREF="#whatarecytopanels">What are CytoPanels ?</A></LI>
+<LI><A HREF="#basicusage">Basic Usage</A></LI>
+<LI><A HREF="#workingwith">Working with the CytoPanel API</A></LI>
+<LI><A HREF="#events">CytoPanel Events</A></LI>
+</UL>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+1">
+<B><A NAME="whatarecytopanels">What are CytoPanels ?</A></B></FONT></TD>
+</TR>
+</TABLE>
+<P>
+CytoPanels are floatable / dockable panels, which will be available in Cytoscape 2.2. We built the CytoPanel API to cut down on the number of pop-up windows within Cytoscape, and create a more unified user experience. For example, in Cytoscape 2.1, the cPath Plugin enables users to click on a node and immediately view node details in a pop-up window. Using the CytoPanel API, we can now show these node details in an embedded CytoPanel, and present a more integrated experience to the user. [...]
+
+<P>
+<IMG SRC="http://cbio.mskcc.org/~cerami/biopax/bp_plugin1.png" BORDER=0/>
+<P>
+The user can then chose to resize, hide or float the left CytoPanel. For example, in the screenshot below, the user has chosen to float it:
+<P>
+<IMG SRC="http://cbio.mskcc.org/~cerami/biopax/bp_plugin2.png" BORDER=0/>
+<P>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+1">
+<B><A NAME="basicusage">Basic Usage</A></B></FONT></TD>
+</TR>
+</TABLE>
+<P>
+Cytoscape 2.2 now includes three CytoPanels: CytoPanel 1 (appears on the left), CytoPanel 2 (appears on the bottom), and CytoPanel 3 (appears on the right). By default, only CytoPanel 1 will appear, and it will automatically contain the network list and bird's eye view component. The other panels will be hidden.
+
+The end-user can show / hide any panel via the new CytoPanel menu, or via the keyboard accelerator short-cuts.
+<P>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+1">
+<B><A NAME="workingwith">Working with the CytoPanel API</A></B></FONT></TD>
+</TR>
+</TABLE>
+<P>
+The CytoPanel API is straightforward and fully documented. If you are a core Cytoscape coder or a Plugin writer, here are a few tips to get started.
+<P>
+<h2>Step 1: Obtain a CytoPanel</h2>
+<P>
+As noted above, the Cytoscape Desktop contains three default CytoPanels. To obtain one, use the CytoscapeDesktop.getCytoPanel() method. This method takes a SwingConstants integer value, indicating a compass direction (this enables us to add additional CytoPanels in the future, if we decide that's necessary.) Here is sample code for accessing the left CytoPanel:
+<P>
+<TABLE WIDTH="100%" CELLPADDING="3" CELLSPACING="0">
+<TR BGCOLOR="#EEEEEE">
+<TD>CytoscapeDesktop desktop = Cytoscape.getDesktop();<br>
+CytoPanel cytoPanel = desktop.getCytoPanel (SwingConstants.WEST);
+</TD>
+</TR>
+</TABLE>
+<P>
+<h2>Step 2: Add your Component</h2>
+<P>
+You can place any Swing <tt>Component</tt> object in a CytoPanel, and it will automatically get its own tab. For example, in the code below, I create a BioPAX component, and add it the left CytoPanel. The code also adds an icon and a tooltip:
+<P>
+<TABLE WIDTH="100%" CELLPADDING="3" CELLSPACING="0">
+<TR BGCOLOR="#EEEEEE">
+<TD>BioPaxContainer bpContainer = BioPaxContainer.getInstance();<br>
+CytoscapeDesktop desktop = Cytoscape.getDesktop();<br>
+CytoPanel cytoPanel = desktop.getCytoPanel (SwingConstants.WEST);<br>
+URL url = BioPaxDetailsPanel.class.getResource("resources/read_obj.gif");<br>
+Icon icon = new ImageIcon(url);<br>
+cytoPanel.add("BioPax PlugIn", icon, bpContainer, "BioPax PlugIn");
+</TD>
+</TR>
+</TABLE>
+<P>
+<h2>Step 3: Set the CytoPanel State</h2>
+<P>
+You can also (optionally) set the CytoPanel state. Each CytoPanel exists in one of three states:
+<ul>
+<li><p> <tt>CytoPanelState.HIDE</tt>: The panel is hidden from the user's view. </p>
+</li>
+<li><p> <tt>CytoPanelState.FLOAT</tt>: The panel is floating in a separate, external window frame. </p>
+</li>
+<li><p> <tt>CytoPanelState.DOCK</tt>: The panel is docked in the main Cytoscape window, and visible to the user. </p>
+</li>
+</ul>
+<p>Here is sample code for setting the current state: </p>
+<P>
+<TABLE WIDTH="100%" CELLPADDING="3" CELLSPACING="0">
+<TR BGCOLOR="#EEEEEE">
+<TD>cytoPanel.setState(CytoPanelState.DOCK);</TD>
+</TR>
+</TABLE>
+<P>
+If you want, you can also activate your tab within a CytoPanel. To do so, first determine the index value of your component. Then, call setSelectedIndex(). For example:
+<P>
+<TABLE WIDTH="100%" CELLPADDING="3" CELLSPACING="0">
+<TR BGCOLOR="#EEEEEE">
+<TD>int index = cytoPanel.indexOfComponent(myComponent);<br>
+cytoPanel.setSelectedIndex(index);</TD>
+</TR>
+</TABLE>
+<P>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+1">
+<B><A NAME="events">CytoPanel Events</A></B></FONT></TD>
+</TR>
+</TABLE>
+<P>
+You can also (optionally) register to receive CytoPanel Events. In order to do so, you must implement the <A HREF="../../../cytoscape/view/cytopanels/CytoPanelListener.html" title="interface in cytoscape.view.cytopanels">CytoPanelListener</A> interface and make the following call:
+<P>
+<TABLE WIDTH="100%" CELLPADDING="3" CELLSPACING="0">
+<TR BGCOLOR="#EEEEEE">
+<TD>addCytoPanelListener(CytoPanelListener cytoPanelListener);</TD>
+</TR>
+</TABLE>
+<P>
+Once you are registered to receive CytoPanel events, you will be notified of the following:
+<ul>
+<li><p> <tt>a CytoPanel State has changed.</tt> </p>
+</li>
+<li><p> <tt>a Component has been added to a CytoPanel.</tt> </p>
+</li>
+<li><p> <tt>a Component has been removed from a CytoPanel.</tt> </p>
+</li>
+<li><p> <tt>a Component on a CytoPanel has been selected.</tt> </p>
+</li>
+</ul>
+<P>
+A CytoPanel Listener can choose to stop receiving CytoPanel Events. To do so, call:
+<P>
+<TABLE WIDTH="100%" CELLPADDING="3" CELLSPACING="0">
+<TR BGCOLOR="#EEEEEE">
+<TD>removeCytoPanelListener(CytoPanelListener cytoPanelListener);</TD>
+</TR>
+</TABLE>
+<P>
+See <A HREF="../../../cytoscape/view/cytopanels/CytoPanelListener.html" title="interface in cytoscape.view.cytopanels">CytoPanelListener</A> for more information.
+</body>
+</html>
\ No newline at end of file
diff --git a/application/src/main/java/cytoscape/view/package.html b/application/src/main/java/cytoscape/view/package.html
new file mode 100644
index 0000000..c58a5dc
--- /dev/null
+++ b/application/src/main/java/cytoscape/view/package.html
@@ -0,0 +1,13 @@
+<html>
+<head>
+ <!-- $Revision: 5801 $
+ $Date: 2004-04-20 01:53:47 +0200 (Tue, 20 Apr 2004) $
+ $Author: amarkiel $
+ -->
+</head>
+
+<body>
+Classes that provide a window to display a graph and UI components
+connected to that window, such as the menus.
+</body>
+</html>
diff --git a/application/src/main/java/cytoscape/visual/Appearance.java b/application/src/main/java/cytoscape/visual/Appearance.java
new file mode 100644
index 0000000..77810fa
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/Appearance.java
@@ -0,0 +1,291 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.visual;
+
+import giny.model.Edge;
+import giny.model.GraphObject;
+import giny.model.Node;
+import giny.view.EdgeView;
+import giny.view.NodeView;
+
+import java.awt.Color;
+import java.util.EnumMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Properties;
+
+import cytoscape.Cytoscape;
+import cytoscape.data.CyAttributes;
+import cytoscape.visual.converter.ValueToStringConverterManager;
+import cytoscape.visual.parsers.ValueParser;
+
+
+/**
+ * A class that holds the appearance information for NodeViews and EdgeViews.
+ * The class is indexed on {@link VisualPropertyType}, so to access the node
+ * shape you would use the VisualPropertyType.NODE_SHAPE enum to get and set
+ * node shape values for this Appearance.
+ */
+public class Appearance {
+
+ protected Map<VisualPropertyType, Object> vizProps;
+
+ /**
+ * Creates a new Appearance object.
+ */
+ public Appearance() {
+ vizProps = new EnumMap<VisualPropertyType,Object>(VisualPropertyType.class);
+
+ for (VisualPropertyType type : VisualPropertyType.values())
+ vizProps.put(type, type.getVisualProperty().getDefaultAppearanceObject());
+ }
+
+ /**
+ * Sets the appearance for the specified VisualPropertyType.
+ *
+ * @param p The VisualPropertyType that identifies which aspect of the appearance
+ * this particular object should be applied to.
+ * @param o The object the defines the appearance for the aspect of the appearance
+ * defined by parameter p.
+ */
+ public void set(VisualPropertyType p, Object o) {
+ if (o != null)
+ vizProps.put(p, o);
+ }
+
+ /**
+ * Gets the appearance for the specified VisualPropertyType.
+ *
+ * @param p The VisualPropertyType that identifies which aspect of the appearance to get.
+ *
+ * @return An Object of varying type depending on the VisualPropertyType. The
+ * VisualPropertyType enum defines what the type of this object will be.
+ */
+ public Object get(VisualPropertyType p) {
+ return vizProps.get(p);
+ }
+
+ /**
+ * Applies this appearance to the specified NodeView.
+ *
+ * @param nodeView The NodeView that this appearance will be applied to.
+ */
+ public void applyAppearance(final NodeView nodeView, final VisualPropertyDependency fdeps) {
+ for ( VisualPropertyType type : VisualPropertyType.values() )
+ if ( type.isNodeProp() )
+ type.getVisualProperty().applyToNodeView(nodeView, vizProps.get(type), fdeps);
+ }
+
+ /**
+ * Applies this appearance to the specified EdgeView.
+ *
+ * @param edgeView The EdgeView that this appearance will be applied to.
+ */
+ public void applyAppearance(final EdgeView edgeView, final VisualPropertyDependency fdeps) {
+ for (VisualPropertyType type : VisualPropertyType.values())
+ if ( !type.isNodeProp() )
+ type.getVisualProperty().applyToEdgeView(edgeView, vizProps.get(type),fdeps);
+ }
+
+ /**
+ * Applies the specified properties as default values for this appearance.
+ *
+ * @param nacProps The properties used to specify the default appearance.
+ * @param baseKey A string identifying which specific properties should be
+ * used for the appearance.
+ */
+ public void applyDefaultProperties(final Properties nacProps, String baseKey) {
+ for (VisualPropertyType type : VisualPropertyType.values()) {
+ Object o = type.getVisualProperty().parseProperty(nacProps, baseKey);
+
+ if (o != null && type.getVisualProperty().isValidValue(o))
+ vizProps.put(type,o);
+ }
+ }
+
+ /**
+ * Returns a Properties object that defines this appearance.
+ *
+ * @param baseKey The key to use to identify the specific properties for this appearance.
+ *
+ * @return A Properties object that defines this appearance.
+ */
+ public Properties getDefaultProperties(String baseKey) {
+ Properties props = new Properties();
+
+ for (VisualPropertyType type : VisualPropertyType.values()) {
+ String key = type.getDefaultPropertyKey(baseKey);
+ String value = ValueToStringConverterManager.manager.toString(vizProps.get(type));
+ if ( key != null && value != null ) {
+ props.setProperty(key,value);
+ }
+ }
+
+ return props;
+ }
+
+ /**
+ * Returns a string describing this appearance.
+ *
+ * @param prefix Can be used to apply an identifying prefix to the output strings.
+ *
+ * @return A string describing the appearance.
+ */
+ public String getDescription(String prefix) {
+ if (prefix == null)
+ prefix = "";
+
+ final String lineSep = System.getProperty("line.separator");
+ final StringBuilder sb = new StringBuilder();
+
+ for (VisualPropertyType type : VisualPropertyType.values()) {
+ if (vizProps.get(type) != null) {
+ sb.append(prefix);
+ sb.append(type.getName());
+ sb.append(" = ");
+ sb.append(ValueToStringConverterManager.manager.toString(vizProps.get(type)));
+ sb.append(lineSep);
+ }
+ }
+
+ return sb.toString();
+ }
+
+ /**
+ * Returns a string describing this appearance with no identifying prefix.
+ *
+ * @return A string describing the appearance.
+ */
+ public String getDescription() {
+ return getDescription(null);
+ }
+
+ /**
+ * Copies the specified Appearance into <i>this</i> Appearance object.
+ *
+ * @param na The Appearance object that will be copied into <i>this</i> Appearance object.
+ */
+ public void copy(final Appearance na) {
+ for (VisualPropertyType type : VisualPropertyType.values())
+ this.vizProps.put(type, na.get(type));
+ }
+
+ /**
+ * Returns a clone of this Appearance.
+ *
+ * @return A clone of this Appearance.
+ */
+ public Object clone() {
+ Appearance ga = new Appearance();
+ ga.copy(this);
+
+ return ga;
+ }
+
+ /**
+ * Applies the visual bypass values specified in the node (edge) attributes
+ * for the specified node (edge) to the node (edge).
+ *
+ * @param n The {@link Node} or {@link Edge} object that the visual bypass
+ * should be applied to.
+ */
+ public void applyBypass(final GraphObject n, List<VisualPropertyType> bypassedVPs) {
+ if (n == null)
+ return;
+
+ if ( bypassedVPs == null || bypassedVPs.size() <= 0 )
+ return;
+
+ final String id = n.getIdentifier();
+ CyAttributes attrs = null;
+
+ if (n instanceof Node)
+ attrs = Cytoscape.getNodeAttributes();
+ else if (n instanceof Edge)
+ attrs = Cytoscape.getEdgeAttributes();
+ else
+ return;
+
+ for (VisualPropertyType type : bypassedVPs) {
+ Object bypass = getBypass(attrs, id, type);
+
+ if (bypass != null)
+ vizProps.put(type,bypass);
+ }
+ }
+
+ /**
+ * A helper method that returns the specified bypass object if one happens to exist for
+ * this node/edge and property type.
+ *
+ * This method has default scope only to help with unit testing.
+ *
+ * You really shouldn't have any reason to use this method!
+ */
+ static Object getBypass( CyAttributes attrs, String id, VisualPropertyType type ) {
+ String attrName = type.getBypassAttrName();
+
+ final String value = attrs.getStringAttribute(id, attrName);
+
+ if (value == null)
+ return null;
+
+ ValueParser p = type.getValueParser();
+
+ Object ret = null;
+ if (p != null)
+ ret = p.parseStringValue(value);
+ else
+ return null;
+
+ // now do color...
+ if ( ret == null || !(ret instanceof Color) || !(ret.equals(Color.black)))
+ return ret;
+
+ // now check to see that the attribute actually specifies black,
+ // and isn't returning black by default
+ final String v = attrs.getStringAttribute(id, attrName);
+
+ if (v == null)
+ return null;
+
+ if (v.equals("0,0,0"))
+ return ret;
+ else
+ return null;
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/AppearanceCalculator.java b/application/src/main/java/cytoscape/visual/AppearanceCalculator.java
new file mode 100644
index 0000000..b043bbf
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/AppearanceCalculator.java
@@ -0,0 +1,266 @@
+/*
+ File: AppearanceCalculator.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual;
+
+import cytoscape.visual.calculators.BasicCalculator;
+import cytoscape.visual.calculators.Calculator;
+import cytoscape.visual.mappings.ObjectMapping;
+import cytoscape.logger.CyLogger;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Properties;
+
+
+/**
+ * This class calculates the appearance of a Node. It holds a default value and
+ * a (possibly null) calculator for each visual attribute.
+ */
+abstract class AppearanceCalculator implements Cloneable {
+
+ protected static final String CLONE_SUFFIX = "-clone-";
+
+ protected final List<Calculator> calcs = new ArrayList<Calculator>();
+
+ protected Appearance tmpDefaultAppearance;
+
+ protected VisualPropertyDependency deps;
+
+ /**
+ * Creates a new AppearanceCalculator object.
+ */
+ public AppearanceCalculator(VisualPropertyDependency deps) {
+ this.deps = deps;
+ }
+
+ /**
+ * Creates a new AppearanceCalculator and immediately customizes it by
+ * calling applyProperties with the supplied arguments.
+ */
+ public AppearanceCalculator(String name, Properties nacProps, String baseKey,
+ CalculatorCatalog catalog, Appearance appr, VisualPropertyDependency deps) {
+ this(deps);
+ tmpDefaultAppearance = appr;
+ applyProperties(appr, name, nacProps, baseKey, catalog);
+ }
+
+ /**
+ * Creates a new AppearanceCalculator object.
+ *
+ * @param toCopy DOCUMENT ME!
+ */
+ public AppearanceCalculator(AppearanceCalculator toCopy) {
+ if (toCopy == null)
+ return;
+
+ for (Calculator c : toCopy.getCalculators())
+ setCalculator(c);
+
+ if (deps != null)
+ deps.copy( toCopy.deps );
+
+ copyDefaultAppearance(toCopy);
+ }
+
+ /**
+ * Make shallow copy of this object
+ */
+ public Object clone() {
+ Object copy = null;
+
+ try {
+ copy = super.clone();
+ } catch (CloneNotSupportedException e) {
+ CyLogger.getLogger().warn("Error cloning!");
+ }
+
+ return copy;
+ }
+
+ /**
+ * Make deep copy of this object
+ */
+ public Object clone(String vsName) {
+ Object copy = null;
+
+ CyLogger.getLogger().info("====Cloning: " + this.toString());
+
+ try {
+ copy = super.clone();
+ } catch (CloneNotSupportedException e) {
+ CyLogger.getLogger().warn("Error cloning!");
+ }
+
+ return copy;
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param type DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Calculator getCalculator(final VisualPropertyType type) {
+ for (Calculator nc : calcs) {
+ if (nc.getVisualPropertyType() == type)
+ return nc;
+ }
+
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public List<Calculator> getCalculators() {
+ return calcs;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param type DOCUMENT ME!
+ */
+ public void removeCalculator(final VisualPropertyType type) {
+ Calculator toBeRemoved = null;
+
+ for (Calculator c : calcs) {
+ if (c.getVisualPropertyType() == type) {
+ toBeRemoved = c;
+
+ break;
+ }
+ }
+
+ calcs.remove(toBeRemoved);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param c DOCUMENT ME!
+ */
+ public void setCalculator(Calculator c) {
+ if (c == null)
+ return;
+
+ Calculator toReplace = null;
+
+ for (Calculator nc : calcs)
+ if (nc.getVisualPropertyType() == c.getVisualPropertyType()) {
+ toReplace = nc;
+
+ break;
+ }
+
+ if (toReplace != null)
+ calcs.remove(toReplace);
+
+ calcs.add(c);
+ }
+
+ protected String getDescription(String name, Appearance defaultAppr) {
+ final String lineSep = System.getProperty("line.separator");
+ final StringBuilder sb = new StringBuilder();
+
+ sb.append(name + ":" + lineSep);
+ sb.append(defaultAppr.getDescription("default")).append(lineSep);
+
+ for (Calculator c : calcs)
+ sb.append(c.toString()).append(lineSep);
+
+ return sb.toString();
+ }
+
+ protected void applyProperties(Appearance appr, String name, Properties nacProps,
+ String baseKey, CalculatorCatalog catalog) {
+ String value = null;
+
+ appr.applyDefaultProperties(nacProps, baseKey);
+ deps.applyDefaultProperties(nacProps, baseKey);
+
+ Calculator newCalc;
+
+ for (VisualPropertyType type : catalog.getCalculatorTypes()) {
+ for (Calculator c : catalog.getCalculators(type)) {
+ value = nacProps.getProperty(baseKey + "."
+ + c.getVisualPropertyType().getPropertyLabel());
+ newCalc = catalog.getCalculator(c.getVisualPropertyType(), value);
+ setCalculator(newCalc);
+ }
+ }
+ }
+
+ protected Properties getProperties(Appearance appr, String baseKey) {
+ String key = null;
+ String value = null;
+ Properties newProps = appr.getDefaultProperties(baseKey);
+ Properties depProps = deps.getDefaultProperties(baseKey);
+ newProps.putAll(depProps);
+
+ for (Calculator c : calcs) {
+ // do actual
+ key = baseKey + "." + c.getVisualPropertyType().getPropertyLabel();
+ value = c.toString();
+ newProps.setProperty(key, value);
+ }
+
+ return newProps;
+ }
+
+ protected abstract void copyDefaultAppearance(AppearanceCalculator toCopy);
+
+ protected void copyCalculators(AppearanceCalculator copy) {
+ // Copy individual calculators
+ for(Calculator cal : this.calcs) {
+ final ObjectMapping mCopy = (ObjectMapping) cal.getMapping(0).clone();
+ final String originalName = cal.toString();
+ String copyName;
+ if(originalName.contains(CLONE_SUFFIX))
+ copyName = originalName.split(CLONE_SUFFIX)[0] + CLONE_SUFFIX + System.currentTimeMillis();
+ else
+ copyName = originalName + CLONE_SUFFIX + System.currentTimeMillis();
+
+ final Calculator bCalc = new BasicCalculator(copyName, mCopy, cal.getVisualPropertyType());
+ copy.setCalculator(bCalc);
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/Arrow.java b/application/src/main/java/cytoscape/visual/Arrow.java
new file mode 100644
index 0000000..4e582d8
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/Arrow.java
@@ -0,0 +1,208 @@
+/*
+ File: Arrow.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+//----------------------------------------------------------------------------
+// $Revision: 18694 $
+// $Date: 2009-12-08 00:35:57 +0100 (Tue, 08 Dec 2009) $
+// $Author: mes $
+//----------------------------------------------------------------------------
+package cytoscape.visual;
+
+import giny.view.EdgeView;
+
+import java.awt.Color;
+
+import java.io.Serializable;
+
+
+/**
+ * This class is a replacement for the yFiles Arrow class.
+ */
+public class Arrow
+ implements Serializable {
+ private static final Color DEFAULT_ARROW_COLOR = Color.BLACK;
+
+ /**
+ * DOCUMENT ME!
+ */
+ public static final Arrow NONE = new Arrow(ArrowShape.NONE,
+ DEFAULT_ARROW_COLOR);
+
+ /**
+ * DOCUMENT ME!
+ */
+ public static final Arrow DIAMOND = new Arrow(ArrowShape.DIAMOND,
+ DEFAULT_ARROW_COLOR);
+
+ /**
+ * DOCUMENT ME!
+ */
+ public static final Arrow DELTA = new Arrow(ArrowShape.DELTA,
+ DEFAULT_ARROW_COLOR);
+
+ /**
+ * DOCUMENT ME!
+ */
+ public static final Arrow ARROW = new Arrow(ArrowShape.ARROW,
+ DEFAULT_ARROW_COLOR);
+
+ /**
+ * DOCUMENT ME!
+ */
+ public static final Arrow T = new Arrow(ArrowShape.T, DEFAULT_ARROW_COLOR);
+
+ /**
+ * DOCUMENT ME!
+ */
+ public static final Arrow CIRCLE = new Arrow(ArrowShape.CIRCLE,
+ DEFAULT_ARROW_COLOR);
+
+ /*
+ * New in 2.5: Arrow can have arbitrary color. This can be different from
+ */
+ private Color arrowColor;
+ private ArrowShape shape;
+
+ // Maybe supported in future.
+ private int size;
+
+ /**
+ * New constructor for 2.5 and later:<br>
+ *
+ * @param shape
+ * @param arrowColor
+ */
+ public Arrow(ArrowShape shape, Color arrowColor) {
+ this.shape = shape;
+ this.arrowColor = arrowColor;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public ArrowShape getShape() {
+ return shape;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param newShape DOCUMENT ME!
+ */
+ public void setShape(ArrowShape newShape) {
+ this.shape = newShape;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Color getColor() {
+ return arrowColor;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param newColor DOCUMENT ME!
+ */
+ public void setColor(Color newColor) {
+ this.arrowColor = newColor;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String toString() {
+ return shape.getGinyName();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param text DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static Arrow parseArrowText(String text) {
+ String arrowtext = text.trim();
+
+ if (arrowtext.equals("WHITE_DIAMOND"))
+ return new Arrow(ArrowShape.DIAMOND, Color.white);
+ else if (arrowtext.equals("BLACK_DIAMOND"))
+ return DIAMOND;
+ else if (arrowtext.equals("COLOR_DIAMOND"))
+ return DIAMOND;
+
+ else if (arrowtext.equals("WHITE_DELTA"))
+ return new Arrow(ArrowShape.DELTA, Color.white);
+ else if (arrowtext.equals("BLACK_DELTA"))
+ return DELTA;
+ else if (arrowtext.equals("COLOR_DELTA"))
+ return DELTA;
+
+ else if (arrowtext.equals("WHITE_ARROW"))
+ return new Arrow(ArrowShape.ARROW, Color.white);
+ else if (arrowtext.equals("BLACK_ARROW"))
+ return ARROW;
+ else if (arrowtext.equals("COLOR_ARROW"))
+ return ARROW;
+
+ else if (arrowtext.equals("WHITE_T"))
+ return new Arrow(ArrowShape.T, Color.white);
+ else if (arrowtext.equals("BLACK_T"))
+ return T;
+ else if (arrowtext.equals("COLOR_T"))
+ return T;
+
+ else if (arrowtext.equals("WHITE_CIRCLE"))
+ return new Arrow(ArrowShape.CIRCLE, Color.white);
+ else if (arrowtext.equals("BLACK_CIRCLE"))
+ return CIRCLE;
+ else if (arrowtext.equals("COLOR_CIRCLE"))
+ return CIRCLE;
+
+ else
+
+ return Arrow.NONE;
+ } // parseArrowText
+}
diff --git a/application/src/main/java/cytoscape/visual/ArrowShape.java b/application/src/main/java/cytoscape/visual/ArrowShape.java
new file mode 100644
index 0000000..1039b92
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ArrowShape.java
@@ -0,0 +1,218 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.visual;
+
+import giny.view.EdgeView;
+import ding.view.DGraphView;
+import javax.swing.Icon;
+import java.util.Map;
+import java.util.HashMap;
+import java.awt.Shape;
+import cytoscape.visual.ui.icon.*;
+
+/**
+ * Defines arrow shapes.<br>
+ * This replaces constants defined in Arrow.java.
+ *
+ * @since Cytoscape 2.5
+ * @author kono
+ *
+ */
+public enum ArrowShape {
+ NONE("No Arrow", "NONE", EdgeView.NO_END,
+ new int[]{EdgeView.NO_END},
+ new String[]{"NO_END"}, true),
+ DIAMOND("Diamond", "COLOR_DIAMOND", EdgeView.EDGE_COLOR_DIAMOND,
+ new int[]{EdgeView.EDGE_COLOR_DIAMOND, EdgeView.WHITE_DIAMOND,EdgeView.BLACK_DIAMOND},
+ new String[]{"EDGE_COLOR_DIAMOND", "WHITE_DIAMOND","BLACK_DIAMOND"}, true),
+ DELTA("Delta", "COLOR_DELTA", EdgeView.EDGE_COLOR_DELTA,
+ new int[]{ EdgeView.EDGE_COLOR_DELTA, EdgeView.WHITE_DELTA,EdgeView.BLACK_DELTA},
+ new String[]{ "EDGE_COLOR_DELTA", "WHITE_DELTA","BLACK_DELTA"}, true),
+ ARROW("Arrow", "COLOR_ARROW", EdgeView.EDGE_COLOR_ARROW,
+ new int[]{EdgeView.EDGE_COLOR_ARROW, EdgeView.WHITE_ARROW,EdgeView.BLACK_ARROW },
+ new String[]{"EDGE_COLOR_ARROW", "WHITE_ARROW","BLACK_ARROW"}, true),
+ T("T", "COLOR_T", EdgeView.EDGE_COLOR_T,
+ new int[]{EdgeView.EDGE_COLOR_T, EdgeView.WHITE_T,EdgeView.BLACK_T},
+ new String[]{"EDGE_COLOR_T", "WHITE_T","BLACK_T"}, true),
+ CIRCLE("Circle", "COLOR_CIRCLE", EdgeView.EDGE_COLOR_CIRCLE,
+ new int[]{EdgeView.EDGE_COLOR_CIRCLE, EdgeView.WHITE_CIRCLE,EdgeView.BLACK_CIRCLE},
+ new String[]{"EDGE_COLOR_CIRCLE", "WHITE_CIRCLE","BLACK_CIRCLE"}, true),
+ HALF_ARROW_TOP("Half Arrow Top", "HALF_ARROW_TOP", EdgeView.EDGE_HALF_ARROW_TOP,
+ new int[]{EdgeView.EDGE_HALF_ARROW_TOP}, new String[]{"HALF_ARROW_TOP"}, false),
+ HALF_ARROW_BOTTOM("Half Arrow Bottom", "HALF_ARROW_BOTTOM", EdgeView.EDGE_HALF_ARROW_BOTTOM,
+ new int[]{EdgeView.EDGE_HALF_ARROW_BOTTOM}, new String[]{"HALF_ARROW_BOTTOM"}, false),
+
+ ;
+
+ private static Map<Integer,Shape> arrowShapes = DGraphView.getArrowShapes();
+
+ private String shapeName;
+ private String ginyShapeName;
+ private int ginyType;
+ private int[] possibleGinyTypes;
+ private String[] possibleGinyNames;
+ private boolean renderEdgeWithArrow;
+
+ private ArrowShape(String shapeName, String ginyShapeName, int ginyType, int[] possibleGinyTypes,
+ String[] possibleGinyNames, boolean renderEdgeWithArrow) {
+ this.shapeName = shapeName;
+ this.ginyShapeName = ginyShapeName;
+ this.ginyType = ginyType;
+ this.possibleGinyTypes = possibleGinyTypes;
+ this.possibleGinyNames = possibleGinyNames;
+ this.renderEdgeWithArrow = renderEdgeWithArrow;
+ }
+
+ /**
+ * Returns arrow type in GINY.
+ *
+ * @return
+ */
+ public int getGinyArrow() {
+ return ginyType;
+ }
+
+ /**
+ * Returns name of arrow shape.
+ *
+ * @return
+ */
+ public String getGinyName() {
+ return ginyShapeName;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getName() {
+ return shapeName;
+ }
+
+ /**
+ *
+ * @param text
+ * @return
+ */
+ public static ArrowShape parseArrowText(String text) {
+ try {
+ ArrowShape val = valueOf(text);
+ return val;
+ // brilliant flow control
+ // this isn't a problem, we just don't match
+ } catch (IllegalArgumentException e) { }
+
+ // if string doesn't match, then try other possible GINY names
+ for (ArrowShape shape : values()) {
+ if (shape.shapeName.equals(text) || shape.ginyShapeName.equals(text))
+ return shape;
+ for (String possibleName : shape.getPossibleGinyNames()) {
+ if ( possibleName.equals(text) )
+ return shape;
+ }
+ }
+
+ return NONE;
+ }
+
+ public String[] getPossibleGinyNames() {
+ return possibleGinyNames;
+ }
+
+ public int[] getPossibleGinyTypes() {
+ return possibleGinyTypes;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param ginyType
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static ArrowShape getArrowShape(int ginyType) {
+ // first try for an exact match
+ for (ArrowShape shape : values()) {
+ if (shape.getGinyArrow() == ginyType)
+ return shape;
+ }
+
+ // if no exact match is found, then try the possible ginyTypes
+ for (ArrowShape shape : values()) {
+ for ( int possible : shape.getPossibleGinyTypes() ) {
+ if ( possible == ginyType )
+ return shape;
+ }
+ }
+
+ // if we can't match anything, just return NONE.
+ return NONE;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Shape getShape() {
+ return arrowShapes.get(ginyType);
+ }
+
+ /**
+ * A method that helps render the arrow shape icon properly.
+ */
+ public boolean renderEdgeWithArrow() {
+ return renderEdgeWithArrow;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param size DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static Map<Object, Icon> getIconSet() {
+ Map<Object, Icon> arrowShapeIcons = new HashMap<Object, Icon>();
+
+ for (ArrowShape arrow : values()) {
+ arrowShapeIcons.put(arrow, new ArrowIcon(arrow, VisualPropertyIcon.DEFAULT_ICON_SIZE) );
+ }
+
+ return arrowShapeIcons;
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/CalculatorCatalog.java b/application/src/main/java/cytoscape/visual/CalculatorCatalog.java
new file mode 100644
index 0000000..0a5bb91
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/CalculatorCatalog.java
@@ -0,0 +1,558 @@
+/*
+ File: CalculatorCatalog.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+package cytoscape.visual;
+
+import static cytoscape.visual.VisualPropertyType.NODE_LABEL;
+
+import cytoscape.visual.calculators.*;
+
+import cytoscape.visual.mappings.ObjectMapping;
+import cytoscape.visual.mappings.PassThroughMapping;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.EnumMap;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Properties;
+import java.util.Set;
+
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+
+
+//----------------------------------------------------------------------------
+/**
+ * Stores various types of Calculators from data attributes to an attribute of a
+ * specified type. Also keeps track of available mappings. Notifies interested
+ * classes of changes to the underlying datasets.
+ */
+public class CalculatorCatalog {
+ private static final String label = "label";
+ private Map<VisualPropertyType, Map<String, Calculator>> calculators;
+ private Map<VisualPropertyType, List<?>> listeners;
+ private Map<String, VisualStyle> visualStyles;
+ private Map<String, Class<?>> mappers;
+
+ /**
+ * Only one <code>ChangeEvent</code> is needed per catalog instance since
+ * the event's only state is the source property. The source of events
+ * generated is always "this".
+ */
+ protected transient ChangeEvent changeEvent;
+
+ /**
+ * Creates a new CalculatorCatalog object.
+ */
+ public CalculatorCatalog() {
+ clear();
+ }
+
+ /**
+ * Creates a new CalculatorCatalog object.
+ *
+ * @param props DOCUMENT ME!
+ */
+ public CalculatorCatalog(Properties props) {
+ clear();
+
+ // should read calculators from their description in the properties
+ // object
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void clear() {
+ calculators = new EnumMap<VisualPropertyType, Map<String, Calculator>>(VisualPropertyType.class);
+ listeners = new EnumMap<VisualPropertyType, List<?>>(VisualPropertyType.class);
+
+ visualStyles = new HashMap<String, VisualStyle>();
+
+ // mapping database
+ mappers = new HashMap<String, Class<?>>();
+ }
+
+
+ protected List getListenerList(final VisualPropertyType type) throws IllegalArgumentException {
+ List l = listeners.get(type);
+
+ if (l == null) {
+ l = new ArrayList();
+ listeners.put(type, l);
+ }
+
+ return l;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param l DOCUMENT ME!
+ * @param type DOCUMENT ME!
+ *
+ * @throws IllegalArgumentException DOCUMENT ME!
+ */
+ public void addChangeListener(ChangeListener l, VisualPropertyType type)
+ throws IllegalArgumentException {
+ List theListeners = getListenerList(type);
+ theListeners.add(l);
+ }
+
+ protected void fireStateChanged(final VisualPropertyType type) throws IllegalArgumentException {
+ List notifyEvents = getListenerList(type);
+
+ ChangeListener listener;
+
+ for (int i = notifyEvents.size() - 1; i >= 0; i--) {
+ listener = (ChangeListener) notifyEvents.get(i);
+
+ // Lazily create the event:
+ if (changeEvent == null)
+ changeEvent = new ChangeEvent(this);
+
+ listener.stateChanged(changeEvent);
+ }
+ }
+
+
+ /**
+ * Given a known byte identifier, returns the matching Map structure holding
+ * calculators of that type.
+ *
+ * @param VisualPropertyType
+ * a known type identifier
+ * @return Map the matching Map structure
+ */
+ protected Map<String, Calculator> getCalculatorMap(final VisualPropertyType type) {
+ Map<String, Calculator> m = calculators.get(type);
+
+ if (m == null) {
+ m = new HashMap<String, Calculator>();
+
+ if (type == null)
+ return m;
+
+ calculators.put(type, m);
+ }
+
+ return m;
+ }
+
+ /**
+ * Add any calculator to the catalog. Automatically checks type. Calculator
+ * is added according to its name as reported by the toString() method.
+ *
+ * @param dupe
+ * Calculator to add
+ * @throws DuplicateCalculatorNameException
+ * if calculator's name is a duplicate with valid name as detail
+ * message
+ * @throws IllegalArgumentException
+ * if calculator is of an unknown type
+ */
+ public void addCalculator(Calculator dupe)
+ throws DuplicateCalculatorNameException, IllegalArgumentException {
+ final VisualPropertyType calcType = dupe.getVisualPropertyType();
+ Map<String, Calculator> theMap = getCalculatorMap(calcType);
+ addCalculator(dupe, theMap);
+
+ // throw event listeners
+ fireStateChanged(calcType);
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param calcName DOCUMENT ME!
+ * @param calcType DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String checkCalculatorName(String calcName, VisualPropertyType calcType) {
+ Map<String, Calculator> theMap = getCalculatorMap(calcType);
+
+ return checkName(calcName, theMap);
+ }
+
+ /**
+ * Renames a calculator.
+ *
+ * @param c
+ * Calculator to rename
+ * @param name
+ * New name for calculator
+ * @throws DuplicateCalculatorNameException
+ * if name is a duplicate with valid name as detail message
+ * @throws IllegalArgumentException
+ * if c is of an unknown type
+ */
+ public void renameCalculator(Calculator c, String name)
+ throws DuplicateCalculatorNameException, IllegalArgumentException {
+ final VisualPropertyType calcType = c.getVisualPropertyType();
+ final Map<String, Calculator> theMap = getCalculatorMap(calcType);
+ final String newName = checkName(name, theMap);
+
+ if (newName.equals(name)) { // given name is unique
+ theMap.remove(c.toString());
+ c.setName(name);
+ theMap.put(name, c);
+ fireStateChanged(calcType);
+ } else
+ throw new DuplicateCalculatorNameException(newName);
+ }
+
+ /**
+ * Remove a calculator.
+ *
+ * @param c
+ * Calculator to remove
+ * @throws IllegalArgumentException
+ * if c is of an unknown calculator type
+ */
+ public void removeCalculator(Calculator c) throws IllegalArgumentException {
+ final VisualPropertyType calcType = c.getVisualPropertyType();
+ final Map<String, Calculator> theMap = getCalculatorMap(calcType);
+
+ theMap.remove(c.toString());
+
+ // fire event
+ fireStateChanged(calcType);
+ }
+
+ /**
+ * Returns the HashMap of mappers
+ */
+ public Set<String> getMappingNames() {
+ return mappers.keySet();
+ }
+
+ /**
+ * Add a mapping to the database of available mappings. Because mappings are
+ * instantiated for each calculator, only class types are stored.
+ *
+ * @param name
+ * Name of the mapping
+ * @param m
+ * Class of the mapping
+ * @throws DuplicateCalculatorNameException
+ * if the given name is already taken
+ * @throws IllegalArgumentException
+ * if the given class is not in the mapping hierarchy
+ */
+ public void addMapping(String name, Class m)
+ throws DuplicateCalculatorNameException, IllegalArgumentException {
+ // verify that the class is in the mapping hierarchy
+ if (!ObjectMapping.class.isAssignableFrom(m))
+ throw new IllegalArgumentException("Class " + m.getName() + " is not an ObjectMapper!");
+
+ // check for duplicate names
+ if (mappers.keySet().contains(name))
+ throw new DuplicateCalculatorNameException("Duplicate mapper name " + name);
+
+ mappers.put(name, m);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param name DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Class removeMapping(String name) {
+ return mappers.remove(name);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param name DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Class getMapping(String name) {
+ return mappers.get(name);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param name DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String checkMappingName(String name) {
+ String newName = name;
+ int nameApp = 2;
+
+ while (mappers.keySet().contains(newName)) {
+ newName = name + nameApp;
+ nameApp++;
+ }
+
+ return newName;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Set<String> getVisualStyleNames() {
+ return visualStyles.keySet();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Collection<VisualStyle> getVisualStyles() {
+ return visualStyles.values();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param vs DOCUMENT ME!
+ */
+ public void addVisualStyle(final VisualStyle vs) {
+ if (vs == null)
+ return;
+
+ final String name = vs.toString();
+
+ // check for duplicate names
+ if (visualStyles.keySet().contains(name)) {
+ String s = "Duplicate visual style name " + name;
+ throw new DuplicateCalculatorNameException(s);
+ }
+
+ visualStyles.put(name, vs);
+
+ // store the individual attribute calculators via helper methods
+ addNodeAppearanceCalculator(vs.getNodeAppearanceCalculator());
+ addEdgeAppearanceCalculator(vs.getEdgeAppearanceCalculator());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param name DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public VisualStyle removeVisualStyle(String name) {
+ return visualStyles.remove(name);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param name DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public VisualStyle getVisualStyle(String name) {
+ if ((name != null) && name.equals("default") && !visualStyles.containsKey(name))
+ createDefaultVisualStyle();
+
+ return visualStyles.get(name);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param name DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String checkVisualStyleName(String name) {
+ return checkName(name, visualStyles);
+ }
+
+ private void addNodeAppearanceCalculator(NodeAppearanceCalculator c) {
+ for (Calculator cc : c.getCalculators()) {
+ Map m = getCalculatorMap(cc.getVisualPropertyType());
+
+ if (!m.values().contains(cc))
+ m.put(cc.toString(), cc);
+ }
+ }
+
+ private void addEdgeAppearanceCalculator(EdgeAppearanceCalculator c) {
+ for (Calculator cc : c.getCalculators()) {
+ Map m = getCalculatorMap(cc.getVisualPropertyType());
+
+ if (!m.values().contains(cc))
+ m.put(cc.toString(), cc);
+ }
+ }
+
+ protected void addCalculator(Calculator c, Map m) throws DuplicateCalculatorNameException {
+ if (c == null)
+ return;
+
+ final String name = c.toString();
+
+ // check for duplicate names
+ if (m.keySet().contains(name)) {
+ String s = "Duplicate calculator name " + name;
+ throw new DuplicateCalculatorNameException(s);
+ }
+
+ m.put(name, c);
+ }
+
+ protected String checkName(String name, Map m) {
+ if (name == null)
+ return null;
+
+ String newName = name;
+ int nameApp = 2;
+
+ while (m.keySet().contains(newName)) {
+ newName = name + nameApp;
+ nameApp++;
+ }
+
+ return newName;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Collection<Calculator> getCalculators() {
+ final List<Calculator> calcList = new ArrayList<Calculator>();
+
+ for (VisualPropertyType type : calculators.keySet()) {
+ for (String s : calculators.get(type).keySet())
+ calcList.add(calculators.get(type).get(s));
+ }
+
+ return calcList;
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param type DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Collection<Calculator> getCalculators(VisualPropertyType type) {
+ Map<String, Calculator> m = getCalculatorMap(type);
+
+ return m.values();
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param type DOCUMENT ME!
+ * @param name DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Calculator getCalculator(VisualPropertyType type, String name) {
+ Map<String, Calculator> m = getCalculatorMap(type);
+
+ return m.get(name);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param type DOCUMENT ME!
+ * @param name DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String checkCalculatorName(VisualPropertyType type, String name) {
+ return checkName(name, getCalculatorMap(type));
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param type DOCUMENT ME!
+ * @param name DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Calculator removeCalculator(VisualPropertyType type, String name) {
+ Map<String, Calculator> m = getCalculatorMap(type);
+
+ return m.remove(name);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Collection<VisualPropertyType> getCalculatorTypes() {
+ return calculators.keySet();
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void createDefaultVisualStyle() {
+ final VisualStyle defaultVS = new VisualStyle("default");
+
+ Calculator nlc = getCalculator(NODE_LABEL, label);
+
+ if (nlc == null) {
+ final PassThroughMapping m = new PassThroughMapping(String.class, AbstractCalculator.ID);
+ nlc = new BasicCalculator(label, m, NODE_LABEL);
+ }
+
+ defaultVS.getNodeAppearanceCalculator().setCalculator(nlc);
+ addVisualStyle(defaultVS);
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/visual/CalculatorCatalogFactory.java b/application/src/main/java/cytoscape/visual/CalculatorCatalogFactory.java
new file mode 100644
index 0000000..59697f5
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/CalculatorCatalogFactory.java
@@ -0,0 +1,288 @@
+/*
+ File: CalculatorCatalogFactory.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+//----------------------------------------------------------------------------
+// $Revision: 21067 $
+// $Date: 2010-07-29 01:52:44 +0200 (Thu, 29 Jul 2010) $
+// $Author: kono $
+//----------------------------------------------------------------------------
+package cytoscape.visual;
+
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.io.InputStream;
+import java.net.URL;
+import java.util.Iterator;
+import java.util.Properties;
+import java.util.Set;
+import java.util.zip.ZipFile;
+
+import cytoscape.Cytoscape;
+import cytoscape.CytoscapeInit;
+import cytoscape.logger.CyLogger;
+import cytoscape.util.FileUtil;
+import cytoscape.util.URLUtil;
+import cytoscape.util.ZipUtil;
+import cytoscape.visual.mappings.ContinuousMapping;
+import cytoscape.visual.mappings.DiscreteMapping;
+import cytoscape.visual.mappings.PassThroughMapping;
+
+
+/**
+ * This class provides a static method for reading a CalculatorCatalog object
+ * from file, using parameters specified in a supplied CytoscapeConfig. What's
+ * provided here is the set of files from which to read the calculator
+ * information, as well as the construction of a suitable default visual style
+ * if one does not already exist.
+ */
+public abstract class CalculatorCatalogFactory {
+
+ protected static CyLogger logger = CyLogger.getLogger(CalculatorCatalogFactory.class);
+
+ private enum MapperNames {DISCRETE("Discrete Mapper"),
+ CONTINUOUS("Continuous Mapper"), PASSTHROUGH("Passthrough Mapper");
+ private String name;
+
+ private MapperNames(String name) {
+ this.name = name;
+ }
+
+ @Override
+ public String toString() {
+ return name;
+ }
+ }
+
+ private static final String VIZMAP_PROPS_FILE_NAME = "vizmap.props";
+
+ // static File propertiesFile;
+ static Properties vizmapProps;
+ static CalculatorCatalog calculatorCatalog = new CalculatorCatalog();
+
+ public static CalculatorCatalog loadCalculatorCatalog() {
+ return loadCalculatorCatalog(null);
+ }
+
+ /**
+ * Loads a CalculatorCatalog object from the various properties files
+ * specified by the options in the supplied CytoscapeConfig object. The
+ * catalog will be properly initialized with known mapping types and a
+ * default visual style (named "default").
+ *
+ * @deprecated The vmName parameter is no longer used - just use
+ * loadCalculatorCatalog(). Will be removed 10/06.
+ */
+ public static CalculatorCatalog loadCalculatorCatalog(String vmName) {
+ vizmapProps = CytoscapeInit.getVisualProperties();
+
+ initCatalog();
+
+ Cytoscape.getSwingPropertyChangeSupport()
+ .addPropertyChangeListener(new VizMapListener());
+
+ return calculatorCatalog;
+ }
+
+ private static void initCatalog() {
+ calculatorCatalog.clear();
+
+ calculatorCatalog.addMapping(
+ MapperNames.DISCRETE.toString(),
+ DiscreteMapping.class);
+ calculatorCatalog.addMapping(
+ MapperNames.CONTINUOUS.toString(),
+ ContinuousMapping.class);
+ calculatorCatalog.addMapping(
+ MapperNames.PASSTHROUGH.toString(),
+ PassThroughMapping.class);
+
+ CalculatorIO.loadCalculators(vizmapProps, calculatorCatalog);
+ }
+
+ /**
+ * Catch the signal and save/load VS.
+ *
+ */
+ private static class VizMapListener
+ implements PropertyChangeListener {
+ public void propertyChange(PropertyChangeEvent e) {
+ String pn = null;
+
+ if (e != null) {
+ pn = e.getPropertyName();
+ }
+
+ if (Cytoscape.SAVE_VIZMAP_PROPS.equals(pn)) {
+ /*
+ * This section is for saving VS in a vizmap.props file.
+ *
+ * If signal contains no new value, Cytoscape consider it as a
+ * default file. Otherwise, save it as a user file.
+ */
+ File propertiesFile = null;
+
+ if (e.getNewValue() == null)
+ propertiesFile = CytoscapeInit.getConfigFile(VIZMAP_PROPS_FILE_NAME);
+ else
+ propertiesFile = new File((String) e.getNewValue());
+
+ if (propertiesFile != null) {
+ Set test = calculatorCatalog.getVisualStyleNames();
+ Iterator it = test.iterator();
+ String styles = "Saving the following Visual Styles: ";
+
+ while (it.hasNext())
+ styles += "\n - " + it.next().toString();
+
+ logger.info(styles);
+ try {
+ CalculatorIO.storeCatalog(calculatorCatalog, propertiesFile);
+ logger.info("Vizmap saved to: " + propertiesFile);
+ } catch (IOException e1) {
+ logger.error("Unable to save vizmap to: " + propertiesFile, e1);
+ }
+ }
+ } else if ((Cytoscape.VIZMAP_RESTORED.equals(pn)) ||
+ (Cytoscape.VIZMAP_LOADED.equals(pn))) {
+ /*
+ * This section is for restoring VS from a file.
+ */
+
+ // only clear the existing vizmap.props if we're restoring
+ // from a session file
+ if (Cytoscape.VIZMAP_RESTORED.equals(pn))
+ vizmapProps.clear();
+
+ // get the new vizmap.props and apply it the existing properties
+ Object vizmapSource = e.getNewValue();
+ logger.info("vizmapSource: '" + vizmapSource.toString() +
+ "'");
+
+ try {
+ InputStream is = null;
+ ZipFile zf = null;
+
+ if (vizmapSource.getClass() == URL.class)
+ // is = ((URL) vizmapSource).openStream();
+ // Use URLUtil to get the InputStream since we might be using a proxy server
+ // and because pages may be cached:
+ is = URLUtil.getBasicInputStream((URL) vizmapSource);
+ else if (vizmapSource.getClass() == String.class) {
+ // if its a RESTORED event the vizmap
+ // file will be in a zip file.
+ if (Cytoscape.VIZMAP_RESTORED.equals(pn)) {
+ zf = new ZipFile((String) vizmapSource);
+ is = ZipUtil.readFile(zf,
+ ".*vizmap.props");
+
+ // if its a LOADED event the vizmap file
+ // will be a normal file.
+ } else
+ is = FileUtil.getInputStream((String) vizmapSource);
+ }
+
+ if (is != null) {
+ try {
+ vizmapProps.load(is);
+ }
+ finally {
+ try {
+ if (zf != null) {
+ zf.close();
+ }
+ }
+ finally {
+ is.close();
+ }
+ }
+ }
+ } catch (FileNotFoundException e1) {
+ logger.error("Unable to open visual mapper file: "+e1.getMessage());
+ // e1.printStackTrace();
+ } catch (IOException e1) {
+ logger.error("Unable to read visual mapper file: "+e1.getMessage());
+ // e1.printStackTrace();
+ }
+
+ initCatalog();
+
+ /*
+ * TODO: Mechanism to apply VS is too complicated. Should be
+ * something like
+ * Cytoscape.getDesktop.getVisualMappingManger.apply(VS_NAME);
+ */
+ logger.info("Applying visual styles from: " +
+ vizmapSource.toString());
+ // Always re-create the vizmapper, otherwise things won't
+ // initialize correctly... or figure out how to reinitialize
+ // things, in particular the various VizMapAttrTabs.
+// Cytoscape.getDesktop()
+// .setupVizMapper();
+// Cytoscape.getDesktop()
+// .getVizMapUI()
+// .getStyleSelector()
+// .resetStyles();
+// Cytoscape.getDesktop()
+// .getVizMapUI()
+// .getStyleSelector()
+// .repaint();
+// Cytoscape.getDesktop()
+// .getVizMapUI()
+// .refreshUI();
+
+ // In the situation where the old visual style has been
+ // overwritten
+ // with a new visual style of the same name, then make sure it
+ // is
+ // reapplied.
+ final VisualMappingManager vmm = Cytoscape.getVisualMappingManager();
+ vmm.setVisualStyle(vmm.getVisualStyle().getName());
+ Cytoscape.getCurrentNetworkView()
+ .setVisualStyle(vmm.getVisualStyle().getName());
+ Cytoscape.getCurrentNetworkView()
+ .redrawGraph(false, true);
+
+ // Since the toolbar tends to get messed up, repaint it.
+ Cytoscape.getDesktop()
+ .repaint();
+ }
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/CalculatorIO.java b/application/src/main/java/cytoscape/visual/CalculatorIO.java
new file mode 100644
index 0000000..a698a4c
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/CalculatorIO.java
@@ -0,0 +1,722 @@
+/*
+ File: CalculatorIO.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+
+package cytoscape.visual;
+
+
+import static cytoscape.visual.VisualPropertyType.EDGE_LINETYPE;
+import static cytoscape.visual.VisualPropertyType.EDGE_LINE_STYLE;
+import static cytoscape.visual.VisualPropertyType.EDGE_LINE_WIDTH;
+import static cytoscape.visual.VisualPropertyType.EDGE_SRCARROW;
+import static cytoscape.visual.VisualPropertyType.EDGE_SRCARROW_COLOR;
+import static cytoscape.visual.VisualPropertyType.EDGE_SRCARROW_SHAPE;
+import static cytoscape.visual.VisualPropertyType.EDGE_TGTARROW;
+import static cytoscape.visual.VisualPropertyType.EDGE_TGTARROW_COLOR;
+import static cytoscape.visual.VisualPropertyType.EDGE_TGTARROW_SHAPE;
+import static cytoscape.visual.VisualPropertyType.NODE_BORDER_COLOR;
+import static cytoscape.visual.VisualPropertyType.NODE_FILL_COLOR;
+import static cytoscape.visual.VisualPropertyType.NODE_HEIGHT;
+import static cytoscape.visual.VisualPropertyType.NODE_LINETYPE;
+import static cytoscape.visual.VisualPropertyType.NODE_LINE_STYLE;
+import static cytoscape.visual.VisualPropertyType.NODE_LINE_WIDTH;
+import static cytoscape.visual.VisualPropertyType.NODE_SIZE;
+import static cytoscape.visual.VisualPropertyType.NODE_WIDTH;
+
+import java.io.BufferedReader;
+import java.io.ByteArrayOutputStream;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.StringReader;
+import java.io.Writer;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Enumeration;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Properties;
+import java.util.Set;
+
+import cytoscape.logger.CyLogger;
+import cytoscape.visual.calculators.Calculator;
+import cytoscape.visual.calculators.CalculatorFactory;
+
+
+/**
+ * This class defines static methods for reading calculator definitions from a
+ * properties object and installing them into a CalculatorCatalog, and for
+ * constructing a properties object that describes all the calculators in a
+ * CalculatorCatalog.
+ */
+public class CalculatorIO {
+ private static final List<String> OLD_CALC_KEYS;
+ private static CyLogger logger = CyLogger.getLogger(CalculatorIO.class);
+
+ static {
+ OLD_CALC_KEYS = new ArrayList<String>();
+ OLD_CALC_KEYS.add("EDGELINETYPE");
+ OLD_CALC_KEYS.add("NODELINETYPE");
+ OLD_CALC_KEYS.add(VisualPropertyType.EDGE_SRCARROW.getDefaultPropertyLabel().toUpperCase()
+ + "=");
+ OLD_CALC_KEYS.add(VisualPropertyType.EDGE_TGTARROW.getDefaultPropertyLabel().toUpperCase()
+ + "=");
+ }
+
+ private static final String nodeColorBaseKey = "nodeColorCalculator";
+ private static final String nodeSizeBaseKey = "nodeSizeCalculator";
+ private static final String edgeArrowBaseKey = "edgeArrowCalculator";
+
+ // appearance labels
+ private static final String nodeAppearanceBaseKey = "nodeAppearanceCalculator";
+ private static final String edgeAppearanceBaseKey = "edgeAppearanceCalculator";
+ private static final String globalAppearanceBaseKey = "globalAppearanceCalculator";
+
+ /**
+ * Writes the contents of a CalculatorCatalog to the specified file as a
+ * properties file. This method sorts the lines of text produced by the
+ * store method of Properties, so that the properties descriptions of the
+ * calculators are reasonably human-readable.
+ */
+ public static void storeCatalog(CalculatorCatalog catalog, File outFile) throws IOException {
+ Writer writer = null;
+ try {
+ writer = new FileWriter(outFile);
+ storeCatalog(catalog, writer);
+ }
+ finally {
+ if (writer != null) {
+ writer.close();
+ }
+ }
+ }
+
+ /**
+ * Writes the contents of a CalculatorCatalog to the specified writer as a
+ * properties file. This method sorts the lines of text produced by the
+ * store method of Properties, so that the properties descriptions of the
+ * calculators are reasonably human-readable.
+ */
+ public static void storeCatalog(CalculatorCatalog catalog, Writer writer) throws IOException {
+ // construct the header comment for the file
+ final String lineSep = System.getProperty("line.separator");
+ final StringBuffer header = new StringBuffer();
+ header.append("This file specifies visual mappings for Cytoscape");
+ header.append(" and has been automatically generated.").append(lineSep);
+ header.append("# WARNING: any changes you make to this file while");
+ header.append(" Cytoscape is running may be overwritten.").append(lineSep);
+ header.append("# Any changes may make these visual mappings unreadable.");
+ header.append(lineSep);
+ header.append("# Please make sure you know what you are doing before");
+ header.append(" modifying this file by hand.").append(lineSep);
+
+ final BufferedReader reader;
+ final ByteArrayOutputStream buffer;
+
+ // get a Properties description of the catalog
+ final Properties props = getProperties(catalog);
+
+ // read all the lines and store them in a container object
+ // store the header lines separately so they don't get sorted
+ final List<String> headerLines = new ArrayList<String>();
+ final List<String> lines = new ArrayList<String>();
+
+ // and dump it to a buffer of bytes
+ buffer = new ByteArrayOutputStream();
+ props.store(buffer, header.toString());
+ buffer.close();
+
+ // convert the bytes to a String we can read from
+ reader = new BufferedReader(new StringReader(buffer.toString()));
+ String oneLine = reader.readLine();
+
+ while (oneLine != null) {
+ if (oneLine.startsWith("#"))
+ headerLines.add(oneLine);
+ else {
+ boolean test = true;
+ for (String key : OLD_CALC_KEYS) {
+ if (oneLine.toUpperCase().contains(key) == false)
+ continue;
+ else {
+ test = false;
+ break;
+ }
+ }
+
+ if (test)
+ lines.add(oneLine);
+ }
+
+ oneLine = reader.readLine();
+ }
+ reader.close();
+
+ // now sort all the non-header lines
+ Collections.sort(lines);
+
+ // and write to file
+ for (String theLine : headerLines) {
+ writer.write(theLine, 0, theLine.length());
+ writer.write(lineSep);
+ }
+
+ for (String theLine : lines) {
+ writer.write(theLine, 0, theLine.length());
+ writer.write(lineSep);
+ }
+
+ writer.flush();
+ }
+
+ /**
+ * Given a CalculatorCatalog, assembles a Properties object representing all
+ * of the calculators contained in the catalog. The resulting Properties
+ * object, if passed to the loadCalculators method, would reconstruct all
+ * the calculators. This method works by getting each set of calculators
+ * from the catalog and calling the getProperties method on each calculator
+ * with the proper header for the property key.
+ */
+ public static Properties getProperties(CalculatorCatalog catalog) {
+ final Properties newProps = new Properties();
+
+ for (Calculator c : catalog.getCalculators())
+ newProps.putAll(c.getProperties());
+
+ // visual styles
+ final Set<String> visualStyleNames = catalog.getVisualStyleNames();
+
+ VisualStyle vs;
+ Properties styleProps;
+
+ for (String name : visualStyleNames) {
+ vs = catalog.getVisualStyle(name);
+ styleProps = new Properties();
+
+ try {
+ styleProps.putAll(vs.getNodeAppearanceCalculator()
+ .getProperties(nodeAppearanceBaseKey + "." + name));
+ styleProps.putAll(vs.getEdgeAppearanceCalculator()
+ .getProperties(edgeAppearanceBaseKey + "." + name));
+ styleProps.putAll(vs.getGlobalAppearanceCalculator()
+ .getProperties(globalAppearanceBaseKey + "." + name));
+
+ // now that we've constructed all the properties for this visual
+ // style without Exceptions, store in the global properties
+ // object
+ newProps.putAll(styleProps);
+ } catch (Exception e) {
+ logger.info("Exception while saving visual style '" + name + "': "+e.getMessage());
+ // e.printStackTrace();
+ }
+ }
+
+ return newProps;
+ }
+
+ /**
+ * Equivalent to loadCalculators(props, catalog, true);
+ */
+ public static void loadCalculators(Properties props, CalculatorCatalog catalog) {
+ loadCalculators(props, catalog, true);
+ }
+
+ /**
+ * Loads calculators from their description in a Properties object into a
+ * supplied CalculatorCatalog object. This method searches the Properties
+ * object for known keys identifying calculators, then delegates to other
+ * methods that use the preprocessed properties to construct valid
+ * calculator objects. For any calculator defined by the Properties, it is
+ * possible for the catalog to already hold a calculator with the same name
+ * and interface type (especially if this method has already been run with
+ * the same Properties object and catalog). If the overWrite argument is
+ * true, this method will remove any such duplicate calculator before adding
+ * the new one to prevent duplicate name exceptions. If overwrite is false,
+ * this method will get a unique name from the catalog and change the name
+ * of the installed calculator as needed.
+ */
+ public static void loadCalculators(Properties props, CalculatorCatalog catalog,
+ boolean overWrite) {
+ // The supplied Properties object may contain any kinds of properties.
+ // We look for keys that start with a name we recognize, identifying a
+ // particular type of calculator. The second field of the key should
+ // then be an identifying name. For example,
+ // nodeFillColorCalculator.mySpecialCalculator.{anything else}
+ //
+ // We begin by creating a map of calculator types
+ // (nodeFillColorCalculator) to a map of names (mySpecialCalculator) to
+ // properties. Note that this will create maps for _any_ "calculator"
+ // that appears, even if it isn't a Calculator. This is OK, because the
+ // CalculatorFactory won't create anything that isn't actually a
+ // Calculator.
+ //
+ // Note that we need separate constructs for each type of calculator,
+ // because calculators of different types are allowed to share the same
+ // name.
+ final Map<String, Map<String, Properties>> calcNames = new HashMap<String, Map<String, Properties>>();
+
+ // use the propertyNames() method instead of the generic Map iterator,
+ // because the former method recognizes layered properties objects.
+ // see the Properties javadoc for details
+ String key;
+
+ for (Enumeration eI = props.propertyNames(); eI.hasMoreElements();) {
+ key = (String) eI.nextElement();
+
+ // handle legacy names In these cases the old calculator base key
+ // was applicable to more than one calculator. In the new system
+ // it's one key to one calculator, so we simply apply the old
+ // calculator to all of the new types of calculators that the old
+ // calculator mapped to.
+
+ // separate color into fill color and border color
+ if (key.startsWith(nodeColorBaseKey + ".")) {
+ key = updateLegacyKey(key, props, nodeColorBaseKey,
+ NODE_FILL_COLOR.getPropertyLabel(),
+ "cytoscape.visual.calculators.GenericNodeFillColorCalculator");
+ storeKey(key, props, calcNames);
+
+ key = updateLegacyKey(key, props, NODE_FILL_COLOR.getPropertyLabel(),
+ NODE_BORDER_COLOR.getPropertyLabel(),
+ "cytoscape.visual.calculators.GenericNodeBorderColorCalculator");
+ storeKey(key, props, calcNames);
+
+ // separate size into uniform, width, and height
+ } else if (key.startsWith(nodeSizeBaseKey + ".")) {
+ key = updateLegacyKey(key, props, nodeSizeBaseKey, NODE_SIZE.getPropertyLabel(),
+ "cytoscape.visual.calculators.GenericNodeUniformSizeCalculator");
+ storeKey(key, props, calcNames);
+
+ key = updateLegacyKey(key, props, NODE_SIZE.getPropertyLabel(),
+ NODE_WIDTH.getPropertyLabel(),
+ "cytoscape.visual.calculators.GenericNodeWidthCalculator");
+ storeKey(key, props, calcNames);
+
+ key = updateLegacyKey(key, props, NODE_WIDTH.getPropertyLabel(),
+ NODE_HEIGHT.getPropertyLabel(),
+ "cytoscape.visual.calculators.GenericNodeHeightCalculator");
+ storeKey(key, props, calcNames);
+
+ // separate arrow into source shape, source color, target shape, target color
+ } else if (key.startsWith(edgeArrowBaseKey + ".")) {
+ // the first two separations are to support the
+ // deprecated EDGE_SRCARROW and EDGE_TGTARROW
+ key = updateLegacyKey(key, props, edgeArrowBaseKey,
+ EDGE_SRCARROW.getPropertyLabel(),
+ "cytoscape.visual.calculators.GenericEdgeSourceArrowCalculator");
+ storeKey(key, props, calcNames);
+
+ key = updateLegacyKey(key, props, EDGE_SRCARROW.getPropertyLabel(),
+ EDGE_TGTARROW.getPropertyLabel(),
+ "cytoscape.visual.calculators.GenericEdgeTargetArrowCalculator");
+ storeKey(key, props, calcNames);
+
+ // eventually (4/2008), these should be the only separations
+ key = updateLegacyKey(key, props, EDGE_TGTARROW.getPropertyLabel(),
+ EDGE_SRCARROW_COLOR.getPropertyLabel(),
+ "cytoscape.visual.calculators.GenericEdgeSourceArrowColorCalculator");
+ storeKey(key, props, calcNames);
+
+ key = updateLegacyKey(key, props, EDGE_SRCARROW_COLOR.getPropertyLabel(),
+ EDGE_SRCARROW_SHAPE.getPropertyLabel(),
+ "cytoscape.visual.calculators.GenericEdgeSourceArrowShapeCalculator");
+ storeKey(key, props, calcNames);
+
+ key = updateLegacyKey(key, props, EDGE_SRCARROW_SHAPE.getPropertyLabel(),
+ EDGE_TGTARROW_COLOR.getPropertyLabel(),
+ "cytoscape.visual.calculators.GenericEdgeTargetArrowColorCalculator");
+ storeKey(key, props, calcNames);
+
+ key = updateLegacyKey(key, props, EDGE_TGTARROW_COLOR.getPropertyLabel(),
+ EDGE_TGTARROW_SHAPE.getPropertyLabel(),
+ "cytoscape.visual.calculators.GenericEdgeTargetArrowShapeCalculator");
+ storeKey(key, props, calcNames);
+
+ // separated source arrow into source color and source shape
+ } else if (key.startsWith(EDGE_SRCARROW.getPropertyLabel() + ".")) {
+ // this first store is to support deprecated EDGE_SRCARROW
+ //storeKey(key, props, calcNames);
+
+ // eventually, these should be the only separations
+ key = updateLegacyKey(key, props, EDGE_SRCARROW.getPropertyLabel(),
+ EDGE_SRCARROW_COLOR.getPropertyLabel(),
+ "cytoscape.visual.calculators.GenericEdgeSourceArrowColorCalculator");
+ storeKey(key, props, calcNames);
+
+ key = updateLegacyKey(key, props, EDGE_SRCARROW_COLOR.getPropertyLabel(),
+ EDGE_SRCARROW_SHAPE.getPropertyLabel(),
+ "cytoscape.visual.calculators.GenericEdgeSourceArrowShapeCalculator");
+
+ storeKey(key, props, calcNames);
+
+ // separated target arrow into target color and target shape
+ } else if (key.startsWith(EDGE_TGTARROW.getPropertyLabel() + ".")) {
+ // this first store is to support deprecated EDGE_TGTARROW
+ //storeKey(key, props, calcNames);
+
+ // eventually, these should be the only separations
+ key = updateLegacyKey(key, props, EDGE_TGTARROW.getPropertyLabel(),
+ EDGE_TGTARROW_COLOR.getPropertyLabel(),
+ "cytoscape.visual.calculators.GenericEdgeTargetArrowColorCalculator");
+ storeKey(key, props, calcNames);
+
+ key = updateLegacyKey(key, props, EDGE_TGTARROW_COLOR.getPropertyLabel(),
+ EDGE_TGTARROW_SHAPE.getPropertyLabel(),
+ "cytoscape.visual.calculators.GenericEdgeTargetArrowShapeCalculator");
+
+ storeKey(key, props, calcNames);
+
+ // handle normal names
+ // This is how all "modern" properties files should work.
+ } else if (key.startsWith(EDGE_LINETYPE.getPropertyLabel() + ".")) {
+ // This first store is to support deprecated EDGE_LINETYPE.
+ // This should be replaced with line style and line width.
+ //storeKey(key, props, calcNames);
+
+ // eventually, these should be the only separations
+ key = updateLegacyKey(key, props, EDGE_LINETYPE.getPropertyLabel(),
+ EDGE_LINE_STYLE.getPropertyLabel(),
+ "cytoscape.visual.calculators.GenericEdgeLineStyleCalculator");
+ storeKey(key, props, calcNames);
+
+ key = updateLegacyKey(key, props, EDGE_LINE_STYLE.getPropertyLabel(),
+ EDGE_LINE_WIDTH.getPropertyLabel(),
+ "cytoscape.visual.calculators.GenericEdgeLineWidthCalculator");
+ storeKey(key, props, calcNames);
+ } else if (key.startsWith(NODE_LINETYPE.getPropertyLabel() + ".")) {
+ // This first store is to support deprecated EDGE_LINETYPE.
+ // This should be replaced with line style and line width.
+ //storeKey(key, props, calcNames);
+
+ // eventually, these should be the only separations
+ key = updateLegacyKey(key, props, NODE_LINETYPE.getPropertyLabel(),
+ NODE_LINE_STYLE.getPropertyLabel(),
+ "cytoscape.visual.calculators.GenericNodeLineStyleCalculator");
+ storeKey(key, props, calcNames);
+
+ key = updateLegacyKey(key, props, NODE_LINE_STYLE.getPropertyLabel(),
+ NODE_LINE_WIDTH.getPropertyLabel(),
+ "cytoscape.visual.calculators.GenericNodeLineWidthCalculator");
+ storeKey(key, props, calcNames);
+
+ // These change the visual styles (rather than calculators) so that the
+ // visual style, instead of mapping a TGTARROW, now maps a TGTARROW_SHAPE.
+ } else if (key.endsWith(EDGE_TGTARROW.getPropertyLabel())) {
+ key = updateLegacyKey(key, props, EDGE_TGTARROW.getPropertyLabel(),
+ EDGE_TGTARROW_SHAPE.getPropertyLabel(),
+ "cytoscape.visual.calculators.GenericEdgeTargetArrowShapeCalculator");
+ storeKey(key, props, calcNames);
+ } else if (key.endsWith(EDGE_SRCARROW.getPropertyLabel())) {
+ key = updateLegacyKey(key, props, EDGE_SRCARROW.getPropertyLabel(),
+ EDGE_SRCARROW_SHAPE.getPropertyLabel(),
+ "cytoscape.visual.calculators.GenericEdgeSourceArrowShapeCalculator");
+ storeKey(key, props, calcNames);
+ } else if (key.endsWith(EDGE_LINETYPE.getPropertyLabel())) {
+ key = updateLegacyKey(key, props, EDGE_LINETYPE.getPropertyLabel(),
+ EDGE_LINE_STYLE.getPropertyLabel(),
+ "cytoscape.visual.calculators.GenericEdgeLineStyleCalculator");
+ storeKey(key, props, calcNames);
+ } else if (key.endsWith(NODE_LINETYPE.getPropertyLabel())) {
+ key = updateLegacyKey(key, props, NODE_LINETYPE.getPropertyLabel(),
+ NODE_LINE_STYLE.getPropertyLabel(),
+ "cytoscape.visual.calculators.GenericNodeLineStyleCalculator");
+ storeKey(key, props, calcNames);
+
+ // Likewise, these change the default values of visual styles to so that
+ // the default LINETYPE gets turned into the default LINE_STYLE.
+ } else if (key.endsWith(NODE_LINETYPE.getDefaultPropertyLabel())) {
+ key = updateLegacyKey(key, props, NODE_LINETYPE.getDefaultPropertyLabel(),
+ NODE_LINE_STYLE.getDefaultPropertyLabel(),
+ "cytoscape.visual.calculators.GenericNodeLineStyleCalculator");
+ storeKey(key, props, calcNames);
+ } else if (key.endsWith(EDGE_LINETYPE.getDefaultPropertyLabel())) {
+ key = updateLegacyKey(key, props, EDGE_LINETYPE.getDefaultPropertyLabel(),
+ EDGE_LINE_STYLE.getDefaultPropertyLabel(),
+ "cytoscape.visual.calculators.GenericEdgeLineStyleCalculator");
+ storeKey(key, props, calcNames);
+ } else if (key.endsWith(EDGE_TGTARROW.getDefaultPropertyLabel())) {
+ key = updateLegacyKey(key, props, EDGE_TGTARROW.getDefaultPropertyLabel(),
+ EDGE_TGTARROW_SHAPE.getDefaultPropertyLabel(),
+ "cytoscape.visual.calculators.GenericEdgeTargetArrowShapeCalculator");
+ storeKey(key, props, calcNames);
+ } else if (key.endsWith(EDGE_SRCARROW.getDefaultPropertyLabel())) {
+ key = updateLegacyKey(key, props, EDGE_SRCARROW.getDefaultPropertyLabel(),
+ EDGE_SRCARROW_SHAPE.getDefaultPropertyLabel(),
+ "cytoscape.visual.calculators.GenericEdgeSourceArrowShapeCalculator");
+ storeKey(key, props, calcNames);
+
+ // Store the key as is.
+ } else
+ storeKey(key, props, calcNames);
+ }
+
+ // Now that we have all the properties in groups, we pass each Map of
+ // names and Properties objects to a helper function that creates a
+ // calculator for each entry and stores the calculators in the catalog.
+ // Before storing the calculator, we either remove any existing
+ // calculator with the same name, or get a unique name from the
+ // calculator, depending on the value of the overWrite argument.
+ for (String calcTypeKey : calcNames.keySet())
+ handleCalculators(calcNames.get(calcTypeKey), catalog, overWrite, calcTypeKey);
+
+ // Map structure to hold visual styles that we build here
+ final Map<String, VisualStyle> visualStyles = new HashMap<String, VisualStyle>();
+
+ // now that all the individual calculators are loaded, load the
+ // Node/Edge/Global appearance calculators
+ final Map<String, Properties> nacNames = calcNames.get(nodeAppearanceBaseKey);
+
+ VisualStyle vs;
+
+ for (String name : nacNames.keySet()) {
+ // store in the matching visual style, creating as needed
+ vs = visualStyles.get(name);
+
+ if (vs == null) {
+ vs = new VisualStyle(name);
+ visualStyles.put(name, vs);
+ }
+
+ vs.getNodeAppearanceCalculator().applyProperties(name, nacNames.get(name),
+ nodeAppearanceBaseKey + "."
+ + name, catalog);
+
+ }
+
+ Map<String, Properties> eacNames = calcNames.get(edgeAppearanceBaseKey);
+
+ for (String name : eacNames.keySet()) {
+ // store in the matching visual style, creating as needed
+ vs = visualStyles.get(name);
+
+ if (vs == null) {
+ vs = new VisualStyle(name);
+ visualStyles.put(name, vs);
+ }
+
+ vs.getEdgeAppearanceCalculator().applyProperties(name, eacNames.get(name),
+ edgeAppearanceBaseKey + "."
+ + name, catalog);
+ }
+
+ Map<String, Properties> gacNames = calcNames.get(globalAppearanceBaseKey);
+
+ for (String name : gacNames.keySet()) {
+ // store in the matching visual style, creating as needed
+ vs = visualStyles.get(name);
+
+ if (vs == null) {
+ vs = new VisualStyle(name);
+ visualStyles.put(name, vs);
+ }
+
+ vs.getGlobalAppearanceCalculator().applyProperties(name, gacNames.get(name),
+ globalAppearanceBaseKey
+ + "." + name, catalog);
+ }
+
+ // now store the visual styles in the catalog
+ for (VisualStyle visualStyle : visualStyles.values())
+ catalog.addVisualStyle(visualStyle);
+ }
+
+ /**
+ * The supplied Map m maps calculator types to a map of names to Properties
+ * objects that hold all the properties entries associated with that name.
+ * Given a new key, this method first extract the calculator type, and then
+ * finds the name to prop map for that calc type. It then extracts the name
+ * field from the key, gets the matching Properties object from the name to
+ * props map (creating a new map entry if needed) and stores the (key,
+ * value) property pair in that Properties object).
+ */
+ private static void storeKey(String key, Properties props,
+ Map<String, Map<String, Properties>> calcNames) {
+ // get the name->props map for the given calculator type, as
+ // defined by the key.
+ final String calcTypeKey = extractCalcType(key);
+
+ if (calcTypeKey == null) {
+ logger.warn("couldn't parse calcTypeKey from '" + key + "'");
+
+ return;
+ }
+
+ Map<String, Properties> name2props = calcNames.get(calcTypeKey);
+
+ // if the props don't yet exist, create them
+ if (name2props == null) {
+ name2props = new HashMap<String, Properties>();
+ calcNames.put(calcTypeKey, name2props);
+ }
+
+ // now the get the props from the name->props map
+ final String name = extractName(key);
+
+ if (name != null) {
+ // calcProps contains all of the properties for this calculator,
+ // e.g. the mappings, the controller, etc.
+ Properties calcProps = name2props.get(name);
+
+ // create a new entry for this name if it doesn't already exist
+ if (calcProps == null) {
+ calcProps = new Properties();
+ name2props.put(name, calcProps);
+ }
+
+ calcProps.setProperty(key, props.getProperty(key));
+ } // should report parse errors if we can't get a name
+ }
+
+ /**
+ * Given the key of a property entry, extract the second field (i.e.,
+ * between the first and second period) and return it.
+ */
+ private static String extractName(final String key) {
+ if (key == null)
+ return null;
+
+ // find index of first period character
+ final int dot1 = key.indexOf(".");
+
+ // return null if not found, or found at end of string
+ if ((dot1 == -1) || (dot1 >= (key.length() - 1)))
+ return null;
+
+ // find the second period character
+ final int dot2 = key.indexOf(".", dot1 + 1);
+
+ if (dot2 == -1) {
+ return null;
+ } // return null if not found
+ // return substring between the periods
+
+ return key.substring(dot1 + 1, dot2);
+ }
+
+ /**
+ * Extracts the base key from the string.
+ */
+ private static String extractCalcType(final String key) {
+ if (key == null)
+ return null;
+
+ // find index of first period character
+ final int dot1 = key.indexOf(".");
+
+ // return null if not found, or found at end of string
+ if ((dot1 == -1) || (dot1 >= (key.length() - 1)))
+ return null;
+
+ // return substring between the periods
+ return key.substring(0, dot1);
+ }
+
+ /**
+ * Construct and store Calculators. Ensures that there will be no name
+ * collision by either removing an existing duplicate or renaming the new
+ * calculator as needed.
+ */
+ private static void handleCalculators(Map<String, Properties> nameMap,
+ CalculatorCatalog catalog, boolean overWrite,
+ String calcTypeKey) {
+ // for each calculator name
+ for (String name : nameMap.keySet()) {
+ // get the properties object that contains all info for
+ // that particular calculator
+
+ // create a calculator based on the calculator name and type
+ final Calculator c = CalculatorFactory.newCalculator(name, nameMap.get(name),
+ calcTypeKey + "." + name);
+
+ if (c != null) {
+ // remove any existing calculator of same name and type
+ if (overWrite) {
+ catalog.removeCalculator(c);
+
+ // otherwise ensure a unique name
+ } else
+ renameAsNeeded(c, catalog);
+
+ catalog.addCalculator(c);
+ }
+ }
+ }
+
+ /**
+ * Given a Calculator of a given type and a CalculatorCatalog, checks for an
+ * existing catalog with the same name and type. If one exists, gets a new
+ * unique name from the catalog and applied it to the calculator argument.
+ */
+ public static void renameAsNeeded(Calculator c, CalculatorCatalog catalog) {
+ final String name = c.toString();
+ final String newName = catalog.checkCalculatorName(c.getVisualPropertyType(), name);
+
+ if (!newName.equals(name))
+ c.setName(newName);
+ }
+
+ /**
+ * Used for updating calculator names from old style to new style. Only used
+ * in a few cases where the old and new don't align.
+ */
+ private static String updateLegacyKey(String key, Properties props, String oldKey,
+ String newKey, String newClass) {
+ String value = props.getProperty(key);
+
+ // Update arrow
+ if ((key.endsWith("equal") || key.endsWith("greater") || key.endsWith("lesser"))
+ && (key.startsWith(EDGE_TGTARROW.getPropertyLabel() + ".")
+ || key.startsWith(EDGE_SRCARROW.getPropertyLabel() + "."))) {
+ value = Arrow.parseArrowText(value).getShape().toString();
+ }
+
+ if (key.endsWith(EDGE_TGTARROW.getDefaultPropertyLabel())
+ || key.endsWith(EDGE_SRCARROW.getDefaultPropertyLabel())) {
+ value = Arrow.parseArrowText(value).getShape().toString();
+ }
+
+ key = key.replace(oldKey, newKey);
+
+ if (key.endsWith(".class"))
+ props.setProperty(key, newClass);
+ else
+ props.setProperty(key, value);
+
+ return key;
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/DuplicateCalculatorNameException.java b/application/src/main/java/cytoscape/visual/DuplicateCalculatorNameException.java
new file mode 100644
index 0000000..45183b2
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/DuplicateCalculatorNameException.java
@@ -0,0 +1,61 @@
+/*
+ File: DuplicateCalculatorNameException.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+//------------------------------------------------------------------------------
+// $Revision: 9565 $
+// $Date: 2007-02-13 20:36:50 +0100 (Tue, 13 Feb 2007) $
+// $Author: mes $
+//------------------------------------------------------------------------------
+package cytoscape.visual;
+
+
+//------------------------------------------------------------------------------
+/**
+ * This Exception is thrown when one attempts to add a Calculator to a
+ * CalculatorCatalog that already has a Calculator of the same name and
+ * interface type.
+ */
+public class DuplicateCalculatorNameException extends RuntimeException {
+ /**
+ * Creates a new DuplicateCalculatorNameException object.
+ *
+ * @param s DOCUMENT ME!
+ */
+ public DuplicateCalculatorNameException(String s) {
+ super(s);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/EdgeAppearance.java b/application/src/main/java/cytoscape/visual/EdgeAppearance.java
new file mode 100644
index 0000000..203de9e
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/EdgeAppearance.java
@@ -0,0 +1,80 @@
+/*
+ File: EdgeAppearance.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+package cytoscape.visual;
+
+import java.util.Properties;
+
+import cytoscape.visual.converter.ValueToStringConverterManager;
+
+/**
+ * Objects of this class hold data describing the appearance of an Edge.
+ */
+public class EdgeAppearance extends Appearance {
+
+ /**
+ * Creates a new EdgeAppearance object.
+ */
+ public EdgeAppearance() {
+ super();
+ }
+
+ public Object clone() {
+ EdgeAppearance ga = new EdgeAppearance();
+ ga.copy(this);
+ return ga;
+ }
+
+ public Properties getDefaultProperties(final String baseKey) {
+
+ Properties props = new Properties();
+
+ for (VisualPropertyType type : VisualPropertyType.values()) {
+ if(type.isNodeProp())
+ continue;
+
+ String key = type.getDefaultPropertyKey(baseKey);
+ String value = ValueToStringConverterManager.manager
+ .toString(vizProps.get(type));
+ if (key != null && value != null) {
+ props.setProperty(key, value);
+ }
+ }
+
+ return props;
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/EdgeAppearanceCalculator.java b/application/src/main/java/cytoscape/visual/EdgeAppearanceCalculator.java
new file mode 100644
index 0000000..6bcae43
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/EdgeAppearanceCalculator.java
@@ -0,0 +1,195 @@
+/*
+ File: EdgeAppearanceCalculator.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+package cytoscape.visual;
+
+import giny.model.Edge;
+
+import java.util.List;
+import java.util.Properties;
+
+import cytoscape.CyNetwork;
+import cytoscape.visual.calculators.BasicCalculator;
+import cytoscape.visual.calculators.Calculator;
+import cytoscape.visual.mappings.ObjectMapping;
+
+
+/**
+ * This class calculates the appearance of an Edge. It holds a default value and
+ * a (possibly null) calculator for each visual attribute.
+ */
+public class EdgeAppearanceCalculator extends AppearanceCalculator {
+ private EdgeAppearance defaultAppearance = new EdgeAppearance();
+
+ /**
+ * @deprecated Use VisualStyle.getEdgeAppearanceCalculator() or new EdgeAppearanceCalculator( VisualStyle.getDependency() ); Will be removed Jan 2010.
+ */
+ @Deprecated
+ public EdgeAppearanceCalculator() {
+ super(new VisualPropertyDependencyImpl());
+ }
+ /**
+ * Creates a new EdgeAppearanceCalculator object.
+ */
+ public EdgeAppearanceCalculator(VisualPropertyDependency deps) {
+ super(deps);
+ }
+
+ /**
+ * Copy constructor. Returns a default object if the argument is null.
+ */
+ public EdgeAppearanceCalculator(EdgeAppearanceCalculator toCopy) {
+ super(toCopy);
+ }
+
+ /**
+ * Creates a new EdgeAppearanceCalculator and immediately customizes it by
+ * calling applyProperties with the supplied arguments.
+ */
+ public EdgeAppearanceCalculator(String name, Properties eacProps, String baseKey,
+ CalculatorCatalog catalog, VisualPropertyDependency deps) {
+ super(name, eacProps, baseKey, catalog, new EdgeAppearance(), deps);
+ defaultAppearance = (EdgeAppearance) tmpDefaultAppearance;
+ }
+
+ /**
+ * Create deep copy of the object.
+ */
+ public Object clone() {
+ final EdgeAppearanceCalculator copy = new EdgeAppearanceCalculator(deps);
+
+ // Copy defaults
+ final EdgeAppearance defAppr = new EdgeAppearance();
+
+ for (VisualPropertyType type : VisualPropertyType.getEdgeVisualPropertyList()) {
+ defAppr.set(type, defaultAppearance.get(type));
+ }
+
+ copy.setDefaultAppearance(defAppr);
+ copyCalculators(copy);
+
+ return copy;
+ }
+
+ /**
+ * Using the rules defined by the default values and calculators in this
+ * object, compute an appearance for the requested Edge in the supplied
+ * CyNetwork. A new EdgeApperance object will be created.
+ */
+ public EdgeAppearance calculateEdgeAppearance(Edge edge, CyNetwork network) {
+ EdgeAppearance appr = (EdgeAppearance) defaultAppearance.clone();
+ calculateEdgeAppearance(appr,edge,network,VisualPropertyType.getEdgeVisualPropertyList());
+
+ return appr;
+ }
+
+ /**
+ * Using the rules defined by the default values and calculators in this
+ * object, compute an appearance for the requested Edge in the supplied
+ * CyNetwork. The supplied EdgeAppearance object will be changed to hold the
+ * new values.
+ */
+ public void calculateEdgeAppearance(EdgeAppearance appr, Edge edge, CyNetwork network) {
+ calculateEdgeAppearance(appr,edge,network,VisualPropertyType.getEdgeVisualPropertyList());
+ }
+
+ void calculateEdgeAppearance(EdgeAppearance appr, Edge edge, CyNetwork network, List<VisualPropertyType> bypassedVPs) {
+ appr.copy(defaultAppearance); // set default values
+
+ for (Calculator c : calcs)
+ c.apply(appr, edge, network);
+
+ appr.applyBypass(edge,bypassedVPs);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public EdgeAppearance getDefaultAppearance() {
+ return defaultAppearance;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param appr DOCUMENT ME!
+ */
+ public void setDefaultAppearance(EdgeAppearance appr) {
+ defaultAppearance = appr;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getDescription() {
+ return getDescription("EdgeAppearanceCalculator", defaultAppearance);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param name DOCUMENT ME!
+ * @param eacProps DOCUMENT ME!
+ * @param baseKey DOCUMENT ME!
+ * @param catalog DOCUMENT ME!
+ */
+ public void applyProperties(String name, Properties eacProps, String baseKey,
+ CalculatorCatalog catalog) {
+ applyProperties(defaultAppearance, name, eacProps, baseKey, catalog);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param baseKey DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Properties getProperties(String baseKey) {
+ return getProperties(defaultAppearance, baseKey);
+ }
+
+ protected void copyDefaultAppearance(AppearanceCalculator toCopy) {
+ defaultAppearance = (EdgeAppearance) (((EdgeAppearanceCalculator) toCopy).getDefaultAppearance()
+ .clone());
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/visual/GlobalAppearance.java b/application/src/main/java/cytoscape/visual/GlobalAppearance.java
new file mode 100644
index 0000000..3ad1589
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/GlobalAppearance.java
@@ -0,0 +1,191 @@
+/*
+ File: GlobalAppearance.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+//----------------------------------------------------------------------------
+// $Revision: 18674 $
+// $Date: 2009-12-05 02:49:26 +0100 (Sat, 05 Dec 2009) $
+// $Author: mes $
+//----------------------------------------------------------------------------
+package cytoscape.visual;
+
+import java.awt.Color;
+
+
+/**
+ * Objects of this class hold data describing global appearance attributes of
+ * the graph window.
+ */
+public class GlobalAppearance {
+
+ private enum GlobalAppearenceName {
+ BACKGROUND_COLOR("Background Color"),
+ NODE_SELECTION_COLOR("Node Selection Color"),
+ NODE_REVERSE_SELECTION_COLOR("Node Reverse Selection Color"),
+ EDGE_SELECTION_COLOR("Edge Selection Color"),
+ EDGE_REVERSE_SELECTION_COLOR("Edge Reverse Selection Color");
+
+ private String name;
+ private static String[] names;
+
+ static {
+ names = new String[GlobalAppearenceName.values().length];
+ int i = 0;
+ for(GlobalAppearenceName ganame: GlobalAppearenceName.values()) {
+ names[i] = ganame.getName();
+ i++;
+ }
+ }
+
+ private GlobalAppearenceName(String name) {
+ this.name = name;
+ }
+
+ public String getName() {
+ return name;
+ }
+
+ public static String[] getAllNames() {
+ return names;
+ }
+ }
+
+ private Color backgroundColor;
+ private Color nodeSelectionColor;
+ private Color nodeReverseSelectionColor;
+ private Color edgeSelectionColor;
+ private Color edgeReverseSelectionColor;
+
+ /**
+ * Creates a new GlobalAppearance object.
+ */
+ public GlobalAppearance() {
+ }
+
+ protected static String[] getCalculatorNames() {
+ return GlobalAppearenceName.getAllNames();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Color getBackgroundColor() {
+ return backgroundColor;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param c DOCUMENT ME!
+ */
+ public void setBackgroundColor(Color c) {
+ backgroundColor = c;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Color getNodeSelectionColor() {
+ return nodeSelectionColor;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param c DOCUMENT ME!
+ */
+ public void setNodeSelectionColor(Color c) {
+ nodeSelectionColor = c;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Color getNodeReverseSelectionColor() {
+ return nodeReverseSelectionColor;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param c DOCUMENT ME!
+ */
+ public void setNodeReverseSelectionColor(Color c) {
+ nodeReverseSelectionColor = c;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Color getEdgeSelectionColor() {
+ return edgeSelectionColor;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param c DOCUMENT ME!
+ */
+ public void setEdgeSelectionColor(Color c) {
+ edgeSelectionColor = c;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Color getEdgeReverseSelectionColor() {
+ return edgeReverseSelectionColor;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param c DOCUMENT ME!
+ */
+ public void setEdgeReverseSelectionColor(Color c) {
+ edgeReverseSelectionColor = c;
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/GlobalAppearanceCalculator.java b/application/src/main/java/cytoscape/visual/GlobalAppearanceCalculator.java
new file mode 100644
index 0000000..4091ccb
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/GlobalAppearanceCalculator.java
@@ -0,0 +1,454 @@
+/*
+ File: GlobalAppearanceCalculator.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+package cytoscape.visual;
+
+import java.awt.Color;
+import java.lang.reflect.Method;
+import java.util.Properties;
+
+import cytoscape.CyNetwork;
+import cytoscape.visual.converter.ValueToStringConverterManager;
+import cytoscape.visual.parsers.ColorParser;
+
+
+//----------------------------------------------------------------------------
+/**
+ * This class calculates global visual attributes such as the background color
+ * of the graph window. Currently dynamic calculators for these values are not
+ * supported, only default values.
+ */
+public class GlobalAppearanceCalculator extends SubjectBase implements Cloneable {
+ /*
+ * Set default colors
+ */
+ private Color defaultBackgroundColor = Color.WHITE;
+ private Color defaultNodeSelectionColor = Color.YELLOW;
+ private Color defaultNodeReverseSelectionColor = Color.GREEN;
+ private Color defaultEdgeSelectionColor = Color.RED;
+ private Color defaultEdgeReverseSelectionColor = Color.GREEN;
+
+// /**
+// * Make shallow copy of this object
+// */
+// public Object clone() throws CloneNotSupportedException {
+// Object copy = null;
+// copy = super.clone();
+//
+// return copy;
+// }
+//
+ /**
+ * Make deep copy of this object
+ */
+ public Object clone() throws CloneNotSupportedException {
+ final GlobalAppearanceCalculator copy = new GlobalAppearanceCalculator();
+ copy.setDefaultBackgroundColor(this.defaultBackgroundColor);
+ copy.setDefaultNodeSelectionColor(this.defaultNodeSelectionColor);
+ copy.setDefaultEdgeSelectionColor(this.defaultEdgeSelectionColor);
+ copy.setDefaultNodeReverseSelectionColor(this.defaultNodeReverseSelectionColor);
+ copy.setDefaultEdgeReverseSelectionColor(this.defaultEdgeReverseSelectionColor);
+ return copy;
+ }
+
+ /**
+ * Creates a new GlobalAppearanceCalculator object.
+ */
+ public GlobalAppearanceCalculator() {
+ }
+
+ /**
+ * Get default color for the given parameter name.
+ * Should be used names in GlobalAppearenceNames enum.
+ *
+ * @param name DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public Color getDefaultColor(final String name) throws Exception {
+ final Class cls = this.getClass();
+ final String newName = name.replace(" ", "");
+ final Method method = cls.getMethod("getDefault" + newName, new Class[] {});
+ final Object obj = method.invoke(this, new Object[] {});
+
+ if ((obj != null) && obj instanceof Color) {
+ return (Color) obj;
+ } else
+
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param name DOCUMENT ME!
+ * @param newColor DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void setDefaultColor(final String name, final Color newColor) throws Exception {
+ final Class cls = this.getClass();
+ final String newName = name.replace(" ", "");
+ final Method method = cls.getMethod("setDefault" + newName, new Class[] { Color.class });
+ method.invoke(this, new Object[] { newColor });
+ }
+
+ /**
+ * Get name of global appearances.
+ *
+ * @return DOCUMENT ME!
+ */
+ public static String[] getGlobalAppearanceNames() {
+ return GlobalAppearance.getCalculatorNames();
+ }
+
+ /**
+ * Copy constructor. Returns a default object if the argument is null.
+ */
+ public GlobalAppearanceCalculator(GlobalAppearanceCalculator toCopy) {
+ if (toCopy == null) {
+ return;
+ }
+
+ setDefaultBackgroundColor(toCopy.getDefaultBackgroundColor());
+ setDefaultNodeSelectionColor(toCopy.getDefaultNodeSelectionColor());
+ setDefaultNodeReverseSelectionColor(toCopy.getDefaultNodeReverseSelectionColor());
+ setDefaultEdgeSelectionColor(toCopy.getDefaultEdgeSelectionColor());
+ setDefaultEdgeReverseSelectionColor(toCopy.getDefaultEdgeReverseSelectionColor());
+ }
+
+ /**
+ * Creates a new GlobalAppearanceCalculator and immediately customizes it by
+ * calling applyProperties with the supplied arguments.
+ */
+ public GlobalAppearanceCalculator(String name, Properties gProps, String baseKey,
+ CalculatorCatalog catalog) {
+ applyProperties(name, gProps, baseKey, catalog);
+ }
+
+ /**
+ * Constructs a new GlobalAppearance object containing the values for the
+ * known global visual attributes.
+ */
+ public GlobalAppearance calculateGlobalAppearance(CyNetwork network) {
+ GlobalAppearance appr = new GlobalAppearance();
+ calculateGlobalAppearance(appr, network);
+
+ return appr;
+ }
+
+ /**
+ * The supplied GlobalAppearance object will be changed to hold new values
+ * for the known global visual attributes.
+ */
+ public void calculateGlobalAppearance(GlobalAppearance appr, CyNetwork network) {
+ appr.setBackgroundColor(calculateBackgroundColor(network));
+ appr.setNodeSelectionColor(calculateNodeSelectionColor(network));
+ appr.setNodeReverseSelectionColor(calculateNodeReverseSelectionColor(network));
+ appr.setEdgeSelectionColor(calculateEdgeSelectionColor(network));
+ appr.setEdgeReverseSelectionColor(calculateEdgeReverseSelectionColor(network));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Color getDefaultBackgroundColor() {
+ return defaultBackgroundColor;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param c DOCUMENT ME!
+ */
+ public void setDefaultBackgroundColor(Color c) {
+ if (c != null) {
+ defaultBackgroundColor = c;
+ this.fireStateChanged();
+ }
+ }
+
+ /**
+ * Currently no calculators are supported for global visual attributes, so
+ * this method simply returns the default background color.
+ */
+ public Color calculateBackgroundColor(CyNetwork network) {
+ return defaultBackgroundColor;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Color getDefaultNodeSelectionColor() {
+ return defaultNodeSelectionColor;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param c DOCUMENT ME!
+ */
+ public void setDefaultNodeSelectionColor(Color c) {
+ if (c != null) {
+ defaultNodeSelectionColor = c;
+ this.fireStateChanged();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Color getDefaultNodeReverseSelectionColor() {
+ return defaultNodeReverseSelectionColor;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param c DOCUMENT ME!
+ */
+ public void setDefaultNodeReverseSelectionColor(Color c) {
+ if (c != null) {
+ defaultNodeReverseSelectionColor = c;
+ this.fireStateChanged();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Color getDefaultEdgeSelectionColor() {
+ return defaultEdgeSelectionColor;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param c DOCUMENT ME!
+ */
+ public void setDefaultEdgeSelectionColor(Color c) {
+ if (c != null) {
+ defaultEdgeSelectionColor = c;
+ this.fireStateChanged();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Color getDefaultEdgeReverseSelectionColor() {
+ return defaultEdgeReverseSelectionColor;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param c DOCUMENT ME!
+ */
+ public void setDefaultEdgeReverseSelectionColor(Color c) {
+ if (c != null) {
+ defaultEdgeReverseSelectionColor = c;
+ this.fireStateChanged();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param network DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Color calculateNodeSelectionColor(CyNetwork network) {
+ return defaultNodeSelectionColor;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param network DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Color calculateNodeReverseSelectionColor(CyNetwork network) {
+ return defaultNodeReverseSelectionColor;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param network DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Color calculateEdgeSelectionColor(CyNetwork network) {
+ return defaultEdgeSelectionColor;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param network DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Color calculateEdgeReverseSelectionColor(CyNetwork network) {
+ return defaultEdgeReverseSelectionColor;
+ }
+
+ /**
+ * Returns a text description of this object's current state.
+ */
+ public String getDescription() {
+ String lineSep = System.getProperty("line.separator");
+ StringBuffer sb = new StringBuffer();
+ sb.append("GlobalAppearanceCalculator:" + lineSep);
+ sb.append("defaultBackgroundColor = ");
+ sb.append(defaultBackgroundColor).append(lineSep);
+ return sb.toString();
+ }
+
+ /**
+ * This method customizes this object by searching the supplied properties
+ * object for keys identifying default values and calculators. Recognized
+ * keys are of the form "globalAppearanceCalculator." + name + ident, where
+ * name is a supplied argument and ident is a String indicating a default
+ * value for a specific visual attribute. Since calculators are not
+ * supported for global visual attributes, the catalog argument is currently
+ * ignored.
+ */
+ public void applyProperties(String name, Properties nacProps, String baseKey,
+ CalculatorCatalog catalog) {
+ String value = null;
+
+ // look for default values
+ value = nacProps.getProperty(baseKey + ".defaultBackgroundColor");
+
+ if (value != null) {
+ Color c = (new ColorParser()).parseColor(value);
+
+ if (c != null) {
+ setDefaultBackgroundColor(c);
+ }
+ }
+
+ value = nacProps.getProperty(baseKey + ".defaultNodeSelectionColor");
+
+ if (value != null) {
+ Color c = (new ColorParser()).parseColor(value);
+
+ if (c != null) {
+ setDefaultNodeSelectionColor(c);
+ }
+ }
+
+ value = nacProps.getProperty(baseKey + ".defaultNodeReverseSelectionColor");
+
+ if (value != null) {
+ Color c = (new ColorParser()).parseColor(value);
+
+ if (c != null) {
+ setDefaultNodeReverseSelectionColor(c);
+ }
+ }
+
+ value = nacProps.getProperty(baseKey + ".defaultEdgeSelectionColor");
+
+ if (value != null) {
+ Color c = (new ColorParser()).parseColor(value);
+
+ if (c != null) {
+ setDefaultEdgeSelectionColor(c);
+ }
+ }
+
+ value = nacProps.getProperty(baseKey + ".defaultEdgeReverseSelectionColor");
+
+ if (value != null) {
+ Color c = (new ColorParser()).parseColor(value);
+
+ if (c != null) {
+ setDefaultEdgeReverseSelectionColor(c);
+ }
+ }
+ }
+
+ /**
+ * Returns a Properties description of this object, suitable for
+ * customization by the applyProperties method.
+ */
+ public Properties getProperties(String baseKey) {
+ String key = null;
+ String value = null;
+ Properties newProps = new Properties();
+
+ // save default values
+ key = baseKey + ".defaultBackgroundColor";
+ value = ValueToStringConverterManager.manager.toString(getDefaultBackgroundColor());
+ newProps.setProperty(key, value);
+
+ key = baseKey + ".defaultNodeSelectionColor";
+ value = ValueToStringConverterManager.manager.toString(getDefaultNodeSelectionColor());
+ newProps.setProperty(key, value);
+
+ key = baseKey + ".defaultNodeReverseSelectionColor";
+ value = ValueToStringConverterManager.manager.toString(getDefaultNodeReverseSelectionColor());
+ newProps.setProperty(key, value);
+
+ key = baseKey + ".defaultEdgeSelectionColor";
+ value = ValueToStringConverterManager.manager.toString(getDefaultEdgeSelectionColor());
+ newProps.setProperty(key, value);
+
+ key = baseKey + ".defaultEdgeReverseSelectionColor";
+ value = ValueToStringConverterManager.manager.toString(getDefaultEdgeReverseSelectionColor());
+ newProps.setProperty(key, value);
+
+ return newProps;
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/LabelPosition.java b/application/src/main/java/cytoscape/visual/LabelPosition.java
new file mode 100644
index 0000000..d2f2923
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/LabelPosition.java
@@ -0,0 +1,558 @@
+/*
+ File: LabelPosition.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual;
+
+import giny.view.Label;
+
+import java.text.DecimalFormat;
+import java.text.DecimalFormatSymbols;
+import java.util.Locale;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+import cytoscape.logger.CyLogger;
+
+/**
+ * Deprecated. Use ObjectPosition instead. Will be removed 03/2011
+ *
+ * @deprecated
+ */
+ at Deprecated
+public class LabelPosition {
+ /**
+ *
+ */
+ public static final String northWestName = "Northwest";
+
+ /**
+ *
+ */
+ public static final String northName = "North";
+
+ /**
+ *
+ */
+ public static final String northEastName = "Northeast";
+
+ /**
+ *
+ */
+ public static final String westName = "West";
+
+ /**
+ *
+ */
+ public static final String centerName = "Center";
+
+ /**
+ *
+ */
+ public static final String eastName = "East";
+
+ /**
+ *
+ */
+ public static final String southWestName = "Southwest";
+
+ /**
+ *
+ */
+ public static final String southName = "South";
+
+ /**
+ *
+ */
+ public static final String southEastName = "Southeast";
+ protected static final String nwName = "NW";
+ protected static final String nName = "N";
+ protected static final String neName = "NE";
+ protected static final String wName = "W";
+ protected static final String cName = "C";
+ protected static final String eName = "E";
+ protected static final String swName = "SW";
+ protected static final String sName = "S";
+ protected static final String seName = "SE";
+
+ /**
+ *
+ */
+ public static final String noName = "none";
+
+ /**
+ *
+ */
+ public static final String justifyCenterName = "Center Justified";
+
+ /**
+ *
+ */
+ public static final String justifyLeftName = "Left Justified";
+
+ /**
+ *
+ */
+ public static final String justifyRightName = "Right Justified";
+ protected static final String justifyCName = "c";
+ protected static final String justifyLName = "l";
+ protected static final String justifyRName = "r";
+ protected int labelAnchor;
+ protected int targetAnchor;
+ protected int justify;
+ protected double xOffset;
+ protected double yOffset;
+
+ /**
+ * Creates a new LabelPosition object.
+ */
+ public LabelPosition() {
+ this(Label.CENTER, Label.CENTER, Label.JUSTIFY_CENTER, 0.0, 0.0);
+ }
+
+ /**
+ * Creates a new LabelPosition object.
+ *
+ * @param lp
+ * DOCUMENT ME!
+ */
+ public LabelPosition(LabelPosition lp) {
+ targetAnchor = lp.getTargetAnchor();
+ labelAnchor = lp.getLabelAnchor();
+ xOffset = lp.getOffsetX();
+ yOffset = lp.getOffsetY();
+ justify = lp.getJustify();
+ }
+
+ /**
+ * Creates a new LabelPosition object.
+ *
+ * @param targ
+ * DOCUMENT ME!
+ * @param lab
+ * DOCUMENT ME!
+ * @param just
+ * DOCUMENT ME!
+ * @param x
+ * DOCUMENT ME!
+ * @param y
+ * DOCUMENT ME!
+ */
+ public LabelPosition(int targ, int lab, int just, double x, double y) {
+ targetAnchor = targ;
+ labelAnchor = lab;
+ justify = just;
+ xOffset = x;
+ yOffset = y;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getLabelAnchor() {
+ return labelAnchor;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getTargetAnchor() {
+ return targetAnchor;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getJustify() {
+ return justify;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public double getOffsetX() {
+ return xOffset;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public double getOffsetY() {
+ return yOffset;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param b
+ * DOCUMENT ME!
+ */
+ public void setLabelAnchor(int b) {
+ labelAnchor = b;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param b
+ * DOCUMENT ME!
+ */
+ public void setTargetAnchor(int b) {
+ targetAnchor = b;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param b
+ * DOCUMENT ME!
+ */
+ public void setJustify(int b) {
+ justify = b;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param d
+ * DOCUMENT ME!
+ */
+ public void setOffsetX(double d) {
+ xOffset = d;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param d
+ * DOCUMENT ME!
+ */
+ public void setOffsetY(double d) {
+ yOffset = d;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param lp
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean equals(Object lp) {
+ if (lp == null)
+ return false;
+
+ if (lp instanceof LabelPosition) {
+ LabelPosition LP = (LabelPosition) lp;
+
+ if (Math.abs(LP.getOffsetX() - xOffset) > 0.0000001) {
+ CyLogger.getLogger().info("xoff");
+
+ return false;
+ }
+
+ if (Math.abs(LP.getOffsetY() - yOffset) > 0.0000001) {
+ CyLogger.getLogger().info("yoff");
+
+ return false;
+ }
+
+ if (LP.getLabelAnchor() != labelAnchor) {
+ CyLogger.getLogger().info("label");
+
+ return false;
+ }
+
+ if (LP.getTargetAnchor() != targetAnchor) {
+ CyLogger.getLogger().info("taret");
+
+ return false;
+ }
+
+ if (LP.getJustify() != justify) {
+ CyLogger.getLogger().info("justify");
+
+ return false;
+ }
+
+ return true;
+ } else {
+ return false;
+ }
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param b
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static String convert(int b) {
+ switch (b) {
+ case (Label.NORTH):
+ return northName;
+
+ case (Label.SOUTH):
+ return southName;
+
+ case (Label.EAST):
+ return eastName;
+
+ case (Label.WEST):
+ return westName;
+
+ case (Label.NORTHWEST):
+ return northWestName;
+
+ case (Label.NORTHEAST):
+ return northEastName;
+
+ case (Label.SOUTHWEST):
+ return southWestName;
+
+ case (Label.SOUTHEAST):
+ return southEastName;
+
+ case (Label.CENTER):
+ return centerName;
+
+ case (Label.NONE):
+ return noName;
+
+ case (Label.JUSTIFY_CENTER):
+ return justifyCenterName;
+
+ case (Label.JUSTIFY_LEFT):
+ return justifyLeftName;
+
+ case (Label.JUSTIFY_RIGHT):
+ return justifyRightName;
+
+ default:
+ return null;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param s
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static int convert(String s) {
+ if (northName.equals(s) || nName.equals(s))
+ return Label.NORTH;
+ else if (southName.equals(s) || sName.equals(s))
+ return Label.SOUTH;
+ else if (eastName.equals(s) || eName.equals(s))
+ return Label.EAST;
+ else if (westName.equals(s) || wName.equals(s))
+ return Label.WEST;
+ else if (northWestName.equals(s) || nwName.equals(s))
+ return Label.NORTHWEST;
+ else if (northEastName.equals(s) || neName.equals(s))
+ return Label.NORTHEAST;
+ else if (southWestName.equals(s) || swName.equals(s))
+ return Label.SOUTHWEST;
+ else if (southEastName.equals(s) || seName.equals(s))
+ return Label.SOUTHEAST;
+ else if (centerName.equals(s) || cName.equals(s))
+ return Label.CENTER;
+ else if (justifyCenterName.equals(s) || justifyCName.equals(s))
+ return Label.JUSTIFY_CENTER;
+ else if (justifyLeftName.equals(s) || justifyLName.equals(s))
+ return Label.JUSTIFY_LEFT;
+ else if (justifyRightName.equals(s) || justifyRName.equals(s))
+ return Label.JUSTIFY_RIGHT;
+ else
+
+ return -1;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static String[] getJustifyNames() {
+ String[] s = { justifyLeftName, justifyCenterName, justifyRightName };
+
+ return s;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static String[] getAnchorNames() {
+ String[] s = { northWestName, northName, northEastName, westName,
+ centerName, eastName, southWestName, southName, southEastName };
+
+ return s;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String toString() {
+ StringBuffer sb = new StringBuffer();
+ sb.append("target: ").append(convert(targetAnchor));
+ sb.append(" label: ").append(convert(labelAnchor));
+ sb.append(" justify: ").append(convert(justify));
+ sb.append(" X offset: ").append(Double.toString(xOffset));
+ sb.append(" Y offset: ").append(Double.toString(yOffset));
+
+ return sb.toString();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String shortString() {
+ // force the locale to US so that we consistently serialize
+ DecimalFormat df = new DecimalFormat("#0.00;-#0.00", new DecimalFormatSymbols(Locale.US));
+
+ StringBuffer sb = new StringBuffer();
+ sb.append(getShortName(targetAnchor));
+ sb.append(",");
+ sb.append(getShortName(labelAnchor));
+ sb.append(",");
+ sb.append(getShortName(justify));
+ sb.append(",");
+ sb.append(df.format(xOffset));
+ sb.append(",");
+ sb.append(df.format(yOffset));
+
+ return sb.toString();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param value
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static LabelPosition parse(String value) {
+ Pattern p = Pattern
+ .compile("^([NSEWC]{1,2}+),([NSEWC]{1,2}+),([clr]{1}+),(-?\\d+(.\\d+)?),(-?\\d+(.\\d+)?)$");
+ Matcher m = p.matcher(value);
+
+ if (m.matches()) {
+ LabelPosition lp = new LabelPosition();
+ lp.setTargetAnchor(convert(m.group(1)));
+ lp.setLabelAnchor(convert(m.group(2)));
+ lp.setJustify(convert(m.group(3)));
+ lp.setOffsetX(Double.parseDouble(m.group(4)));
+ lp.setOffsetY(Double.parseDouble(m.group(6)));
+
+ return lp;
+ }
+
+ return null;
+ }
+
+ protected static String getShortName(int x) {
+ switch (x) {
+ case (Label.NORTH):
+ return nName;
+
+ case (Label.SOUTH):
+ return sName;
+
+ case (Label.EAST):
+ return eName;
+
+ case (Label.WEST):
+ return wName;
+
+ case (Label.NORTHWEST):
+ return nwName;
+
+ case (Label.NORTHEAST):
+ return neName;
+
+ case (Label.SOUTHWEST):
+ return swName;
+
+ case (Label.SOUTHEAST):
+ return seName;
+
+ case (Label.CENTER):
+ return cName;
+
+ case (Label.JUSTIFY_CENTER):
+ return justifyCName;
+
+ case (Label.JUSTIFY_LEFT):
+ return justifyLName;
+
+ case (Label.JUSTIFY_RIGHT):
+ return justifyRName;
+
+ default:
+ CyLogger.getLogger().info("don't recognize type: " + x);
+
+ return "x";
+ }
+ }
+
+ /**
+ *
+ */
+ public static final LabelPosition DEFAULT = new LabelPosition();
+}
diff --git a/application/src/main/java/cytoscape/visual/LineStyle.java b/application/src/main/java/cytoscape/visual/LineStyle.java
new file mode 100644
index 0000000..fb1a333
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/LineStyle.java
@@ -0,0 +1,151 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.visual;
+
+import java.awt.BasicStroke;
+import java.awt.Stroke;
+import java.awt.Shape;
+import java.awt.geom.Ellipse2D;
+import javax.swing.Icon;
+import java.util.Map;
+import java.util.HashMap;
+import java.util.regex.Pattern;
+import java.util.regex.Matcher;
+import cytoscape.visual.ui.icon.*;
+import cytoscape.visual.strokes.*;
+
+/**
+ * Define line stroke.
+ *
+ * @author kono
+ */
+public enum LineStyle {
+ // note that "line" and "dash" regexs are legacy, so don't change them!
+ SOLID("line", new SolidStroke(1.0f)),
+ LONG_DASH( "dash", new LongDashStroke(1.0f)),
+ EQUAL_DASH( "equal_dash", new EqualDashStroke(1.0f)),
+ DASH_DOT( "dash_dot", new DashDotStroke(1.0f)),
+ DOT("dot_dot", new DotStroke(1.0f)),
+ ZIGZAG("zigzag", new ZigzagStroke(1.0f)),
+ SINEWAVE("sinewave", new SineWaveStroke(1.0f)),
+ VERTICAL_SLASH("vertical_slash",new VerticalSlashStroke(1.0f,PipeStroke.Type.VERTICAL)),
+ FORWARD_SLASH("forward_slash",new ForwardSlashStroke(1.0f,PipeStroke.Type.FORWARD)),
+ BACKWARD_SLASH("backward_slash",new BackwardSlashStroke(1.0f,PipeStroke.Type.BACKWARD)),
+ PARALLEL_LINES("parallel_lines", new ParallelStroke(1.0f)),
+ CONTIGUOUS_ARROW("contiguous_arrow", new ContiguousArrowStroke(1.0f)),
+ SEPARATE_ARROW("separate_arrow", new SeparateArrowStroke(1.0f)),
+ ;
+
+ private String regex;
+ private WidthStroke stroke;
+
+ private LineStyle(String regex, WidthStroke stroke) {
+ this.regex = regex;
+ this.stroke = stroke;
+ }
+
+ private String getRegex() {
+ return regex;
+ }
+
+ /**
+ * Attempts to parse a LineStyle object from a string. If the string does
+ * not match any LineStyle.toString() value exactly, then it attempts a regular
+ * expression match on regex pattern defined in this Enum. The regex support
+ * exists primarily to support legacy file formats.
+ */
+ public static LineStyle parse(String val) {
+ // First check the style names.
+ for ( LineStyle ls : values() ) {
+ if ( ls.toString().equals(val) )
+ return ls;
+ }
+
+ // Then try regex matching. This is for legacy line types and
+ // should really only either match "line" or "dash".
+ for ( LineStyle ls : values() ) {
+ Pattern p = Pattern.compile(ls.getRegex(),Pattern.CASE_INSENSITIVE);
+ Matcher m = p.matcher(val);
+ if ( m.matches() ) {
+ return ls;
+ }
+ }
+
+ // default
+ return SOLID;
+ }
+
+ /**
+ * Will attempt to find the LineStyle based on the type of stroke.
+ * If it doesn't match a known stroke, it will return SOLID.
+ * @return the LineStyle guessed from the stroke.
+ */
+ public static LineStyle extractLineStyle(Stroke s) {
+ if ( s instanceof WidthStroke ) {
+ return ((WidthStroke)s).getLineStyle();
+ }
+
+ return SOLID;
+ }
+
+ /**
+ * Creates a new stroke of this LineStyle with the specified width.
+ */
+ public Stroke getStroke(float width) {
+ if ( width <= 0 )
+ return new ZeroStroke(stroke);
+ else
+ return stroke.newInstanceForWidth( width );
+ }
+
+ /**
+ * Returns a map of Icons that can be used for user interfaces.
+ */
+ public static Map<Object,Icon> getIconSet() {
+ Map<Object,Icon> icons = new HashMap<Object,Icon>();
+
+ for (LineStyle def : values()) {
+ LineTypeIcon icon = new LineTypeIcon(def.getStroke(5.0f),
+ VisualPropertyIcon.DEFAULT_ICON_SIZE * 4,
+ VisualPropertyIcon.DEFAULT_ICON_SIZE,
+ def.name());
+ icons.put(def, icon);
+ }
+
+ return icons;
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/NodeAppearance.java b/application/src/main/java/cytoscape/visual/NodeAppearance.java
new file mode 100644
index 0000000..1825d15
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/NodeAppearance.java
@@ -0,0 +1,118 @@
+/*
+ File: NodeAppearance.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+package cytoscape.visual;
+
+import java.util.Properties;
+
+import cytoscape.visual.converter.ValueToStringConverterManager;
+
+/**
+ * Objects of this class hold data describing the appearance of a Node.
+ */
+public class NodeAppearance extends Appearance {
+
+ /**
+ * Constructor.
+ */
+ public NodeAppearance() {
+ super();
+ }
+
+ private VisualPropertyDependency dep;
+
+ public Object clone() {
+ NodeAppearance ga = new NodeAppearance();
+ ga.copy(this);
+ return ga;
+ }
+
+ public Properties getDefaultProperties(final String baseKey) {
+
+ Properties props = new Properties();
+
+ for (VisualPropertyType type : VisualPropertyType.values()) {
+ if(!type.isNodeProp())
+ continue;
+
+ String key = type.getDefaultPropertyKey(baseKey);
+ String value = ValueToStringConverterManager.manager
+ .toString(vizProps.get(type));
+ if (key != null && value != null) {
+ props.setProperty(key, value);
+ }
+ }
+
+ return props;
+ }
+
+ /**
+ * @deprecated This exists only for backwards compatibility. Do not use it!
+ * Will be removed Jan 2011.
+ */
+ @Deprecated
+ NodeAppearance(VisualPropertyDependency dep) {
+ super();
+ this.dep = dep;
+ }
+
+ /**
+ * Returns whether or not the node height and width are locked.
+ *
+ * @return Whether or not the node height and width are locked.
+ * @deprecated Use
+ * VisualStyle.getDependency().check(VisualPropertyDependency
+ * .Definition.NODE_SIZE_LOCKED) instead. Will be removed Jan
+ * 2011.
+ */
+ @Deprecated
+ public boolean getNodeSizeLocked() {
+ return dep.check(VisualPropertyDependency.Definition.NODE_SIZE_LOCKED);
+ }
+
+ /**
+ * Sets whether or not the node height and width are locked.
+ *
+ * @deprecated Use
+ * VisualStyle.getDependency().set(VisualPropertyDependency.Definition
+ * .NODE_SIZE_LOCKED,b) instead. Will be removed Jan 2011.
+ */
+ @Deprecated
+ public void setNodeSizeLocked(boolean b) {
+ dep.set(VisualPropertyDependency.Definition.NODE_SIZE_LOCKED, b);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/NodeAppearanceCalculator.java b/application/src/main/java/cytoscape/visual/NodeAppearanceCalculator.java
new file mode 100644
index 0000000..f31f8a0
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/NodeAppearanceCalculator.java
@@ -0,0 +1,213 @@
+/*
+ File: NodeAppearanceCalculator.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual;
+
+import giny.model.Node;
+
+import java.util.List;
+import java.util.Properties;
+
+import cytoscape.CyNetwork;
+import cytoscape.visual.calculators.BasicCalculator;
+import cytoscape.visual.calculators.Calculator;
+import cytoscape.visual.mappings.ObjectMapping;
+
+
+/**
+ * This class calculates the appearance of a Node. It holds a default value and
+ * a (possibly null) calculator for each visual attribute.
+ */
+public class NodeAppearanceCalculator extends AppearanceCalculator {
+
+ private NodeAppearance defaultAppearance = new NodeAppearance();
+
+ /**
+ * @deprecated Use VisualStyle.getNodeAppearanceCalculator() or new NodeAppearancCalculator( VisualStyle.getDependency() ) instead. Will be removed
+ * January 2011.
+ */
+ @Deprecated
+ public NodeAppearanceCalculator() {
+ super(new VisualPropertyDependencyImpl());
+ }
+
+ /**
+ * Creates a new NodeAppearanceCalculator object.
+ */
+ public NodeAppearanceCalculator(VisualPropertyDependency deps) {
+ super(deps);
+ }
+
+ /**
+ * Creates a new NodeAppearanceCalculator and immediately customizes it by
+ * calling applyProperties with the supplied arguments.
+ */
+ public NodeAppearanceCalculator(String name, Properties nacProps,
+ String baseKey, CalculatorCatalog catalog, VisualPropertyDependency deps) {
+ super(name, nacProps, baseKey, catalog, new NodeAppearance(), deps);
+ defaultAppearance = (NodeAppearance) tmpDefaultAppearance;
+ }
+
+ /**
+ * Copy constructor. Returns a default object if the argument is null.
+ */
+ public NodeAppearanceCalculator(NodeAppearanceCalculator toCopy) {
+ super(toCopy);
+ }
+
+ /**
+ * Using the rules defined by the default values and calculators in this
+ * object, compute an appearance for the requested Node in the supplied
+ * CyNetwork. A new NodeApperance object will be created.
+ */
+ public NodeAppearance calculateNodeAppearance(Node node, CyNetwork network) {
+ NodeAppearance appr = new NodeAppearance(deps);
+ calculateNodeAppearance(appr,node,network,VisualPropertyType.getNodeVisualPropertyList());
+
+ return appr;
+ }
+
+ /**
+ * Create deep copy of the object.
+ */
+ public Object clone() {
+
+ final NodeAppearanceCalculator copy = new NodeAppearanceCalculator(deps);
+
+ // Copy defaults
+ final NodeAppearance defAppr = new NodeAppearance();
+ for(VisualPropertyType type : VisualPropertyType.getNodeVisualPropertyList()) {
+ defAppr.set(type, defaultAppearance.get(type));
+ }
+ copy.setDefaultAppearance(defAppr);
+
+ this.copyCalculators(copy);
+
+ return copy;
+ }
+
+ /**
+ * Using the rules defined by the default values and calculators in this
+ * object, compute an appearance for the requested Node in the supplied
+ * CyNetwork. The supplied NodeAppearance object will be changed to hold the
+ * new values.
+ */
+ public void calculateNodeAppearance(NodeAppearance appr, Node node, CyNetwork network) {
+ calculateNodeAppearance(appr,node,network,VisualPropertyType.getNodeVisualPropertyList());
+ }
+
+
+ void calculateNodeAppearance(NodeAppearance appr, Node node,
+ CyNetwork network, List<VisualPropertyType> bypassedVPs) {
+ appr.copy(defaultAppearance); // set defaults and node lock state
+
+ for (Calculator nc : calcs)
+ nc.apply(appr, node, network);
+
+ appr.applyBypass(node,bypassedVPs);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public NodeAppearance getDefaultAppearance() {
+ return defaultAppearance;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param n DOCUMENT ME!
+ */
+ public void setDefaultAppearance(NodeAppearance n) {
+ defaultAppearance = n;
+ }
+
+ /**
+ * Returns a text description of the current default values and calculator
+ * names.
+ */
+ public String getDescription() {
+ return getDescription("NodeAppearanceCalculator", defaultAppearance);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param name DOCUMENT ME!
+ * @param nacProps DOCUMENT ME!
+ * @param baseKey DOCUMENT ME!
+ * @param catalog DOCUMENT ME!
+ */
+ public void applyProperties(String name, Properties nacProps,
+ String baseKey, CalculatorCatalog catalog) {
+ applyProperties(defaultAppearance, name, nacProps, baseKey, catalog);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param baseKey DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Properties getProperties(String baseKey) {
+ return getProperties(defaultAppearance, baseKey);
+ }
+
+ protected void copyDefaultAppearance(AppearanceCalculator toCopy) {
+ defaultAppearance = (NodeAppearance) (((NodeAppearanceCalculator) toCopy).getDefaultAppearance().clone());
+ }
+
+
+ /**
+ * @deprecated Use VisualStyle.getDependency().check(VisualPropertyDependency.Definition.NODE_SIZE_LOCKED) instead.
+ * Will be removed Jan 2011.
+ */
+ public boolean getNodeSizeLocked() {
+ return deps.check(VisualPropertyDependency.Definition.NODE_SIZE_LOCKED);
+ }
+
+ /**
+ * @deprecated Use VisualStyle.getDependency().set(VisualPropertyDependency.Definition.NODE_SIZE_LOCKED,b) instead.
+ * Will be removed Jan 2011.
+ */
+ public void setNodeSizeLocked(boolean b) {
+ deps.set(VisualPropertyDependency.Definition.NODE_SIZE_LOCKED,b);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/NodeShape.java b/application/src/main/java/cytoscape/visual/NodeShape.java
new file mode 100644
index 0000000..a6e7a88
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/NodeShape.java
@@ -0,0 +1,217 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.visual;
+
+import cytoscape.visual.ui.icon.NodeIcon;
+import cytoscape.visual.ui.icon.VisualPropertyIcon;
+
+import ding.view.DGraphView;
+
+import giny.view.NodeView;
+
+import java.awt.Shape;
+
+import java.util.HashMap;
+import java.util.Map;
+
+import javax.swing.Icon;
+
+/**
+ *
+ * @since Cytoscape 2.5
+ * @version 0.7
+ * @author kono
+ *
+ */
+public enum NodeShape {
+ RECT(NodeView.RECTANGLE, "Rectangle", true),
+ ROUND_RECT(NodeView.ROUNDED_RECTANGLE, "Round Rectangle", true),
+ RECT_3D(NodeView.RECTANGLE, "3D Rectabgle", false),
+ TRAPEZOID(NodeView.RECTANGLE, "Trapezoid", false),
+ TRAPEZOID_2(NodeView.RECTANGLE, "Trapezoid 2", false),
+ TRIANGLE(NodeView.TRIANGLE, "Triangle", true),
+ PARALLELOGRAM(NodeView.PARALELLOGRAM, "Parallelogram", true),
+ DIAMOND(NodeView.DIAMOND, "Diamond", true),
+ ELLIPSE(NodeView.ELLIPSE, "Ellipse", true),
+ HEXAGON(NodeView.HEXAGON, "Hexagon", true),
+ OCTAGON(NodeView.OCTAGON, "Octagon", true),
+ VEE(NodeView.VEE, "V", true),
+ ;
+
+ private int ginyShape;
+ private String name;
+ private boolean isSupported;
+ private static Map<Integer, Shape> nodeShapes = DGraphView.getNodeShapes();
+
+ private NodeShape(int ginyShape, String name, boolean isSupported) {
+ this.ginyShape = ginyShape;
+ this.name = name;
+ this.isSupported = isSupported;
+ }
+
+ /**
+ * If the shape is supported by rendering engine, return true.<br>
+ * Otherwise, return false.
+ * @return
+ */
+ public boolean isSupported() {
+ return isSupported;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param text DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static NodeShape parseNodeShapeText(String text) {
+ String trimed = text.trim();
+
+ for (NodeShape shape : values()) {
+ if (getNodeShapeText(shape).equalsIgnoreCase(trimed))
+ return shape;
+ }
+
+ // Unknown shape: return rectangle.
+ return NodeShape.RECT;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static String[] valuesAsString() {
+ final int length = values().length;
+ final String[] nameArray = new String[length];
+
+ for (int i = 0; i < length; i++)
+ nameArray[i] = values()[i].getShapeName();
+
+ return nameArray;
+ }
+
+ /**
+ * Get name of the shape.
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getShapeName() {
+ return name;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param type
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static boolean isValidShape(NodeShape type) {
+ for (NodeShape curType : values()) {
+ if (type == curType)
+ return true;
+ }
+
+ return false;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param shape
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static String getNodeShapeText(NodeShape shape) {
+ String nstext = shape.name();
+ nstext = nstext.replaceAll("_", "");
+
+ return nstext.toLowerCase();
+ }
+
+ /**
+ * Get GINY shape as integer.
+ *
+ * @return Giny shape as integer.
+ */
+ public int getGinyShape() {
+ return ginyShape;
+ }
+
+ /**
+ * Convert from Giny shape to Cytoscape NodeShape enum.
+ *
+ * @param ginyShape
+ * @return
+ */
+ public static NodeShape getNodeShape(int ginyShape) {
+ for (NodeShape shape : values()) {
+ if (shape.ginyShape == ginyShape)
+ return shape;
+ }
+
+ // Unknown. Return rectangle as the def val.
+ return NodeShape.RECT;
+ }
+
+ /**
+ * Returns a Shape object for the NodeShape in question.
+ */
+ public Shape getShape() {
+ return nodeShapes.get(ginyShape);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static Map<Object, Icon> getIconSet() {
+ Map<Object, Icon> nodeShapeIcons = new HashMap<Object, Icon>();
+
+ for (NodeShape shape : values()) {
+ NodeIcon icon = new NodeIcon(shape.getShape(),
+ VisualPropertyIcon.DEFAULT_ICON_SIZE,
+ VisualPropertyIcon.DEFAULT_ICON_SIZE, shape.getShapeName());
+ nodeShapeIcons.put(shape, icon);
+ }
+
+ return nodeShapeIcons;
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/SubjectBase.java b/application/src/main/java/cytoscape/visual/SubjectBase.java
new file mode 100644
index 0000000..bb17338
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/SubjectBase.java
@@ -0,0 +1,96 @@
+/*
+ File: SubjectBase.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+
+
+/**
+ * Abstract Base Class for Subject in the Subject / Observer Pattern. Also Known
+ * as Publisher / Subscriber Pattern.
+ *
+ * A Subject class notifies all its subscribers whenever its state changes.
+ *
+ * Note that this code duplicates some code in the AbstractCalculator class. May
+ * be a good place to refactor in the future.
+ */
+public abstract class SubjectBase {
+ /**
+ * An Array List of All Observers who want to be notified of changes.
+ */
+ protected final List<ChangeListener> observers = new ArrayList<ChangeListener>();
+
+ /**
+ * Add a ChangeListener. When the state underlying the calculator changes,
+ * all ChangeListeners will be notified.
+ *
+ * @param listener
+ * ChangeListener to add
+ */
+ public void addChangeListener(ChangeListener listener) {
+ observers.add(listener);
+ }
+
+ /**
+ * Remove a ChangeListener from the calcaultor. When the state underlying
+ * the calculator changes, all ChangeListeners will be notified.
+ *
+ * @param listener
+ * ChangeListener to add
+ */
+ public void removeChangeListener(ChangeListener listener) {
+ observers.remove(listener);
+ }
+
+ /**
+ * Notifies all listeners that have registered interest for notification on
+ * this event type.
+ */
+ public void fireStateChanged() {
+ // Process the listeners last to first, notifying
+ // those that are interested in this event
+ for (int i = observers.size() - 1; i >= 0; i--) {
+ final ChangeListener listener = observers.get(i);
+ final ChangeEvent changeEvent = new ChangeEvent(this);
+ listener.stateChanged(changeEvent);
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/VisualMappingManager.java b/application/src/main/java/cytoscape/visual/VisualMappingManager.java
new file mode 100644
index 0000000..b4ffe52
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/VisualMappingManager.java
@@ -0,0 +1,573 @@
+/*
+ File: VisualMappingManager.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual;
+
+import giny.model.Node;
+import giny.view.EdgeView;
+import giny.view.NodeView;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import cytoscape.CyEdge;
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+import cytoscape.CytoscapeInit;
+import cytoscape.data.CyAttributes;
+import cytoscape.data.CyAttributesUtils;
+import cytoscape.data.attr.CountedIterator;
+import cytoscape.data.attr.MultiHashMapDefinition;
+import cytoscape.logger.CyLogger;
+import cytoscape.view.CyNetworkView;
+import cytoscape.visual.NodeAppearance;
+import cytoscape.visual.calculators.AbstractCalculator;
+import cytoscape.visual.calculators.Calculator;
+import cytoscape.visual.calculators.GenericNodeCustomGraphicCalculator;
+import cytoscape.visual.customgraphic.CustomGraphicsManager;
+import cytoscape.visual.customgraphic.CyCustomGraphics;
+import cytoscape.visual.mappings.ContinuousMapping;
+import cytoscape.visual.mappings.DiscreteMapping;
+import cytoscape.visual.mappings.ObjectMapping;
+import cytoscape.visual.mappings.PassThroughMapping;
+import cytoscape.visual.mappings.RangeValueCalculator;
+import cytoscape.visual.mappings.RangeValueCalculatorFactory;
+import cytoscape.visual.mappings.RangeValueCalculatorFactoryImpl;
+import cytoscape.visual.mappings.continuous.ContinuousMappingPoint;
+import cytoscape.visual.mappings.rangecalculators.ColorRangeValueCalculator;
+import cytoscape.visual.mappings.rangecalculators.CustomGraphicsRangeValueCalculator;
+import cytoscape.visual.mappings.rangecalculators.DoubleRangeValueCalculator;
+import cytoscape.visual.mappings.rangecalculators.FloatRangeValueCalculator;
+import cytoscape.visual.mappings.rangecalculators.NodeShapeRangeValueCalculator;
+import cytoscape.visual.mappings.rangecalculators.StringRangeValueCalculator;
+import ding.view.DGraphView;
+import ding.view.DingCanvas;
+
+/**
+ * Top-level class for controlling the visual appearance of nodes and edges
+ * according to data attributes, as well as some global visual attributes. This
+ * class holds a reference to a NetworkView that displays the network, a
+ * CalculatorCatalog that holds the set of known visual styles and calculators,
+ * and a current VisualStyle that is used to determine the values of the visual
+ * attributes. A Logger is also supplied to report errors.
+ * <P>
+ *
+ * Note that a null VisualStyle is not allowed; this class always provides at
+ * least a default object.
+ * <P>
+ *
+ * The key methods are the apply* methods. These methods first recalculate the
+ * visual appearances by delegating to the calculators contained in the current
+ * visual style. The usual return value of these methods is an Appearance object
+ * that contains the visual attribute values; these values are then applied to
+ * the network by calling the appropriate set methods in the graph view API.
+ * <P>
+ */
+public class VisualMappingManager extends SubjectBase {
+
+ // Catalog of visual styles and calculators.
+ // This is the actual object to store styles.
+ private CalculatorCatalog catalog;
+
+ private CyNetworkView networkView; // the object displaying the network
+ private VisualStyle activeVS; // the currently active visual style
+
+ // reusable appearance objects
+ private final NodeAppearance myNodeApp = new NodeAppearance();
+ private final EdgeAppearance myEdgeApp = new EdgeAppearance();
+ private final GlobalAppearance myGlobalApp = new GlobalAppearance();
+
+ // Default VS name. This one cannot be removed.
+ private static final String DEF_STYLE_NAME = "default";
+
+ // New in Cytoscape 2.8: Pool of available custom graphics
+ private final CustomGraphicsManager manager;
+
+ // New in 2.8: Dynamically manage mappings
+ private final RangeValueCalculatorFactory rvcFactory;
+
+ /**
+ * Creates a new VisualMappingManager object.
+ *
+ * @param networkView
+ * DOCUMENT ME!
+ */
+ public VisualMappingManager(final CyNetworkView networkView) {
+
+ //TODO: Why this parameter is required to instantiate this manager?
+ this.networkView = networkView;
+
+ // Creates a repository of static images.
+ manager = new CustomGraphicsManager();
+
+ // New in 2.8: dynamically manages object mappings.
+ rvcFactory = new RangeValueCalculatorFactoryImpl();
+ registerDefaultRangeValueCalculators();
+
+ loadCalculatorCatalog();
+
+ // Try to find default style name from prop.
+ String defStyle = CytoscapeInit.getProperties().getProperty(
+ "defaultVisualStyle");
+
+ if (defStyle == null)
+ defStyle = DEF_STYLE_NAME;
+
+ VisualStyle vs = catalog.getVisualStyle(defStyle);
+
+ if (vs == null)
+ vs = catalog.getVisualStyle(DEF_STYLE_NAME);
+
+ setVisualStyle(vs);
+ }
+
+
+ /**
+ * Attempts to load a CalculatorCatalog object, using the information from
+ * the CytoscapeConfig object.
+ *
+ * Does nothing if a catalog has already been loaded.
+ *
+ * @see CalculatorCatalog
+ * @see CalculatorCatalogFactory
+ */
+ public void loadCalculatorCatalog() {
+ loadCalculatorCatalog(null);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param vizmapLocation
+ * DOCUMENT ME!
+ */
+ public void loadCalculatorCatalog(final String vizmapLocation) {
+ if (catalog == null)
+ catalog = CalculatorCatalogFactory.loadCalculatorCatalog();
+ else if (vizmapLocation != null)
+ catalog = CalculatorCatalogFactory.loadCalculatorCatalog();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param new_view
+ * DOCUMENT ME!
+ */
+ public void setNetworkView(final CyNetworkView new_view) {
+ this.networkView = new_view;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public CyNetworkView getNetworkView() {
+ return networkView;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public CyNetwork getNetwork() {
+ return networkView.getNetwork();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public CalculatorCatalog getCalculatorCatalog() {
+ return catalog;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public VisualStyle getVisualStyle() {
+ return activeVS;
+ }
+
+ /**
+ * Sets a new visual style, and returns the old style. Also fires an event
+ * to attached listeners only if the visual style changes.
+ *
+ * If the argument is null, the previous visual style is simply returned.
+ */
+ public VisualStyle setVisualStyle(final VisualStyle vs) {
+
+ if ((vs != null) && (vs != activeVS)) {
+ VisualStyle tmp = activeVS;
+ activeVS = vs;
+ fireStateChanged();
+
+ return tmp;
+ } else
+ return activeVS;
+ }
+
+ /**
+ * Sets a new visual style. Attempts to get the style with the given name
+ * from the catalog and pass that to setVisualStyle(VisualStyle). The return
+ * value is the old style.
+ *
+ * If no visual style with the given name is found, no change is made, an
+ * error message is passed to the logger, and null is returned.
+ */
+ public VisualStyle setVisualStyle(final String newVSName) {
+ final VisualStyle vs = catalog.getVisualStyle(newVSName);
+
+ if (vs != null)
+ return setVisualStyle(vs);
+ else
+ return activeVS;
+ }
+
+ /**
+ * Recalculates and reapplies all of the node appearances. The visual
+ * attributes are calculated by delegating to the NodeAppearanceCalculator
+ * member of the current visual style.
+ */
+ public void applyNodeAppearances() {
+ applyNodeAppearances(getNetwork(), getNetworkView());
+ }
+
+ /**
+ * Recalculates and reapplies all of the node appearances. The visual
+ * attributes are calculated by delegating to the NodeAppearanceCalculator
+ * member of the current visual style.
+ */
+ public void applyNodeAppearances(final CyNetwork network, final CyNetworkView network_view) {
+ final NodeAppearanceCalculator nodeAppearanceCalculator = activeVS
+ .getNodeAppearanceCalculator();
+
+ List<VisualPropertyType> bypassedVPs = getBypassedVPs("NODE", Cytoscape
+ .getNodeAttributes());
+
+ final Set<CyCustomGraphics> byPassedCustomGraphics = new HashSet<CyCustomGraphics>();
+ final Iterator<NodeView> itr = network_view.getNodeViewsIterator();
+ while (itr.hasNext()) {
+ final NodeView nodeView = itr.next();
+ final Node node = nodeView.getNode();
+
+ // Identify and collect the bypassed custom graphics:
+ final List<Object> bypassedProps =
+ getByPassedVisProps(nodeView, bypassedVPs);
+ for (final Object bypassedProp : bypassedProps) {
+ if (bypassedProp instanceof CyCustomGraphics)
+ byPassedCustomGraphics.add((CyCustomGraphics)bypassedProp);
+ }
+
+ nodeAppearanceCalculator.calculateNodeAppearance(myNodeApp, node,
+ network, bypassedVPs);
+ myNodeApp.applyAppearance(nodeView, activeVS.getDependency());
+ }
+
+ checkCustomGraphicsInUse(byPassedCustomGraphics);
+ }
+
+ private static final List<Object> getByPassedVisProps(final NodeView nv,
+ final List<VisualPropertyType> bypassedVPs)
+ {
+ final List<Object> bypassedProps = new ArrayList<Object>();
+ final CyAttributes nodeAttrs = Cytoscape.getNodeAttributes();
+ final String id = nv.getNode().getIdentifier();
+ for (final VisualPropertyType propType : bypassedVPs) {
+ final Object bypass = Appearance.getBypass(nodeAttrs, id, propType);
+ if (bypass != null)
+ bypassedProps.add(bypass);
+ }
+ return bypassedProps;
+ }
+
+ /**
+ * Reset status of used Custom Graphics
+ */
+ private void checkCustomGraphicsInUse(final Set<CyCustomGraphics> byPassedCustomGraphics) {
+
+ // Set everything unused.
+ final Collection<CyCustomGraphics> allCG = manager.getAll();
+ for(CyCustomGraphics cg: allCG)
+ manager.setUsedInCurrentSession(cg, false);
+
+ final NodeAppearanceCalculator nac = activeVS.getNodeAppearanceCalculator();
+ final VisualPropertyType[] allCustomGraphicsPropType = VisualPropertyType.getAllCustomGraphicsType();
+ for(VisualPropertyType cgType: allCustomGraphicsPropType) {
+ // First, check default mapping values.
+ final Object value = nac.getDefaultAppearance().get(cgType);
+ if(value instanceof CyCustomGraphics) {
+ manager.setUsedInCurrentSession((CyCustomGraphics) value, true);
+ }
+
+ // Next, check mapping values.
+ final Calculator cgCalc = nac.getCalculator(cgType);
+ if(cgCalc == null)
+ continue;
+
+ final ObjectMapping cgMapping = cgCalc.getMapping(0);
+ if(cgMapping == null)
+ continue;
+
+ if(cgMapping instanceof DiscreteMapping) {
+ final Map allMapping = ((DiscreteMapping) cgMapping).getAll();
+ Collection cgSet = allMapping.values();
+ for(Object cg: cgSet) {
+ if(cg != null)
+ manager.setUsedInCurrentSession((CyCustomGraphics) cg, true);
+ }
+ } else if(cgMapping instanceof ContinuousMapping) {
+ final List<ContinuousMappingPoint> points = ((ContinuousMapping) cgMapping).getAllPoints();
+ for(ContinuousMappingPoint point: points) {
+ manager.setUsedInCurrentSession((CyCustomGraphics) point.getRange().equalValue, true);
+ manager.setUsedInCurrentSession((CyCustomGraphics) point.getRange().greaterValue, true);
+ manager.setUsedInCurrentSession((CyCustomGraphics) point.getRange().lesserValue, true);
+ }
+ } else if(cgMapping instanceof PassThroughMapping) {
+ final RangeValueCalculator<?> rangeValueCalculator = ((PassThroughMapping) cgMapping).getRangeValueCalculator();
+ if(rangeValueCalculator == null)
+ return;
+
+ final CyAttributes nodeAttr = Cytoscape.getNodeAttributes();
+ final String attrName = cgMapping.getControllingAttributeName();
+ CountedIterator keys = nodeAttr.getMultiHashMap().getObjectKeys(attrName);
+ while(keys.hasNext()) {
+ Object key = keys.next();
+ String attrValue = nodeAttr.getStringAttribute(key.toString(), attrName);
+ Object cg = rangeValueCalculator.getRange(attrValue);
+ if(cg instanceof CyCustomGraphics) {
+ manager.setUsedInCurrentSession((CyCustomGraphics) cg, true);
+ }
+ }
+ CyAttributesUtils.getAttributes(attrName, Cytoscape.getNodeAttributes());
+ }
+
+ }
+
+ for (final CyCustomGraphics cg : byPassedCustomGraphics)
+ manager.setUsedInCurrentSession(cg, true);
+ }
+
+ /**
+ * Recalculates and reapplies all of the edge appearances. The visual
+ * attributes are calculated by delegating to the EdgeAppearanceCalculator
+ * member of the current visual style.
+ */
+ public void applyEdgeAppearances() {
+ applyEdgeAppearances(getNetwork(), getNetworkView());
+ }
+
+ /**
+ * Recalculates and reapplies all of the edge appearances. The visual
+ * attributes are calculated by delegating to the EdgeAppearanceCalculator
+ * member of the current visual style.
+ */
+ public void applyEdgeAppearances(final CyNetwork network,
+ final CyNetworkView network_view) {
+ final EdgeAppearanceCalculator edgeAppearanceCalculator = activeVS
+ .getEdgeAppearanceCalculator();
+
+ EdgeView edgeView;
+
+ List<VisualPropertyType> bypassedVPs = getBypassedVPs("EDGE", Cytoscape
+ .getEdgeAttributes());
+
+ for (Iterator i = network_view.getEdgeViewsIterator(); i.hasNext();) {
+ edgeView = (EdgeView) i.next();
+
+ if (edgeView == null)
+
+ // WARNING: This is a hack, edgeView should not be null, but
+ // for now do this! (iliana)
+ continue;
+
+ edgeAppearanceCalculator.calculateEdgeAppearance(myEdgeApp,
+ edgeView.getEdge(), network, bypassedVPs);
+ myEdgeApp.applyAppearance(edgeView, activeVS.getDependency());
+ }
+ }
+
+ private List<VisualPropertyType> getBypassedVPs(final String prefix,
+ final CyAttributes attrs) {
+ MultiHashMapDefinition mhmd = attrs.getMultiHashMapDefinition();
+ List<VisualPropertyType> bypassAttrs = new ArrayList<VisualPropertyType>();
+ for (VisualPropertyType vp : VisualPropertyType.values())
+ if (vp.toString().startsWith(prefix)
+ && mhmd.getAttributeValueType(vp.getBypassAttrName()) >= 0)
+ bypassAttrs.add(vp);
+
+ return bypassAttrs;
+ }
+
+ /**
+ * Recalculates and reapplies the global visual attributes. The
+ * recalculation is done by delegating to the GlobalAppearanceCalculator
+ * member of the current visual style.
+ */
+ public void applyGlobalAppearances() {
+ applyGlobalAppearances(getNetwork(), getNetworkView());
+ }
+
+ /**
+ * Recalculates and reapplies the global visual attributes. The
+ * recalculation is done by delegating to the GlobalAppearanceCalculator
+ * member of the current visual style.
+ *
+ * @param network
+ * the network to apply to
+ * @param network_view
+ * the view to apply to
+ */
+ public void applyGlobalAppearances(CyNetwork network,
+ CyNetworkView network_view) {
+ GlobalAppearanceCalculator globalAppearanceCalculator = activeVS
+ .getGlobalAppearanceCalculator();
+ globalAppearanceCalculator.calculateGlobalAppearance(myGlobalApp,
+ network);
+
+ // setup proper background colors
+ if (network_view instanceof DGraphView) {
+ DingCanvas backgroundCanvas = ((DGraphView) network_view)
+ .getCanvas(DGraphView.Canvas.BACKGROUND_CANVAS);
+ backgroundCanvas.setBackground(myGlobalApp.getBackgroundColor());
+ } else {
+ CyLogger
+ .getLogger()
+ .info(
+ "VisualMappingManager.applyGlobalAppearances() - DGraphView not found!");
+ network_view.setBackgroundPaint(myGlobalApp.getBackgroundColor());
+ }
+
+ // will ignore sloppy & reverse selection color for now
+
+ // Set selection colors
+ Iterator nodeIt = network.nodesIterator();
+
+ while (nodeIt.hasNext()) {
+ network_view.getNodeView((CyNode) nodeIt.next()).setSelectedPaint(
+ myGlobalApp.getNodeSelectionColor());
+ }
+
+ Iterator edgeIt = network.edgesIterator();
+
+ while (edgeIt.hasNext())
+ network_view.getEdgeView((CyEdge) edgeIt.next()).setSelectedPaint(
+ myGlobalApp.getEdgeSelectionColor());
+ }
+
+ /**
+ * Recalculates and reapplies all of the node, edge, and global visual
+ * attributes. This method delegates to, in order, applyNodeAppearances,
+ * applyEdgeAppearances, and applyGlobalAppearances.
+ */
+ public void applyAppearances() {
+ /** first apply the node appearance to all nodes */
+ applyNodeAppearances();
+ /** then apply the edge appearance to all edges */
+ applyEdgeAppearances();
+ /** now apply global appearances */
+ applyGlobalAppearances();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nodeView
+ * DOCUMENT ME!
+ * @param network_view
+ * DOCUMENT ME!
+ */
+ public void vizmapNode(NodeView nodeView, CyNetworkView network_view) {
+ CyNode node = (CyNode) nodeView.getNode();
+ List<VisualPropertyType> bypassedVPs = getBypassedVPs("NODE", Cytoscape
+ .getNodeAttributes());
+ NodeAppearanceCalculator nodeAppearanceCalculator = activeVS
+ .getNodeAppearanceCalculator();
+ nodeAppearanceCalculator.calculateNodeAppearance(myNodeApp, node,
+ network_view.getNetwork(), bypassedVPs);
+ myNodeApp.applyAppearance(nodeView, activeVS.getDependency());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edgeView
+ * DOCUMENT ME!
+ * @param network_view
+ * DOCUMENT ME!
+ */
+ public void vizmapEdge(EdgeView edgeView, CyNetworkView network_view) {
+ CyEdge edge = (CyEdge) edgeView.getEdge();
+ List<VisualPropertyType> bypassedVPs = getBypassedVPs("EDGE", Cytoscape
+ .getEdgeAttributes());
+ EdgeAppearanceCalculator edgeAppearanceCalculator = activeVS
+ .getEdgeAppearanceCalculator();
+ edgeAppearanceCalculator.calculateEdgeAppearance(myEdgeApp, edge,
+ network_view.getNetwork(), bypassedVPs);
+ myEdgeApp.applyAppearance(edgeView, activeVS.getDependency());
+ }
+
+ public CustomGraphicsManager getCustomGraphicsManager() {
+ return manager;
+ }
+
+
+ public RangeValueCalculatorFactory getRangeValueCalculatorFactory() {
+ return rvcFactory;
+ }
+
+ private void registerDefaultRangeValueCalculators() {
+ this.rvcFactory.registerRVC(new StringRangeValueCalculator());
+ this.rvcFactory.registerRVC(new DoubleRangeValueCalculator());
+ this.rvcFactory.registerRVC(new ColorRangeValueCalculator());
+ this.rvcFactory.registerRVC(new NodeShapeRangeValueCalculator());
+ this.rvcFactory.registerRVC(new CustomGraphicsRangeValueCalculator());
+ this.rvcFactory.registerRVC(new FloatRangeValueCalculator());
+ }
+
+
+}
diff --git a/application/src/main/java/cytoscape/visual/VisualProperty.java b/application/src/main/java/cytoscape/visual/VisualProperty.java
new file mode 100644
index 0000000..3481d12
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/VisualProperty.java
@@ -0,0 +1,115 @@
+/*
+ Copyright (c) 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual;
+
+import java.awt.Graphics2D;
+
+import java.util.Map;
+
+import javax.swing.Icon;
+import java.util.Properties;
+import giny.view.EdgeView;
+import giny.view.NodeView;
+
+
+/**
+ * Represents a visual property. All vp should implement this interface.
+ *
+ */
+public interface VisualProperty {
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public VisualPropertyType getType();
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void showDiscreteEditor();
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void showContinousEditor();
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Map<Object, Icon> getIconSet();
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g2 DOCUMENT ME!
+ */
+ public void paintIcon(Graphics2D g2);
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Icon getDefaultIcon();
+ public Icon getIcon(final Object value);
+
+ /**
+ * @deprecated Use other the applyToNodeView method with the
+ * VisualPropertyDependency arg as null. Will be removed Jan 2011.
+ */
+ @Deprecated
+ public void applyToNodeView(NodeView nv, Object o);
+
+ public void applyToNodeView(NodeView nv, Object o, VisualPropertyDependency dep);
+
+ /**
+ * @deprecated Use other the applyToNodeView method with the
+ * VisualPropertyDependency arg as null. Will be removed Jan 2011.
+ */
+ @Deprecated
+ public void applyToEdgeView(EdgeView nv, Object o);
+
+ public void applyToEdgeView(EdgeView nv, Object o, VisualPropertyDependency dep);
+
+ public Object parseProperty(Properties props, String baseKey);
+ public Object getDefaultAppearanceObject();
+
+ public boolean constrained(VisualPropertyDependency dep);
+
+ boolean isValidValue(Object value);
+}
diff --git a/application/src/main/java/cytoscape/visual/VisualPropertyDependency.java b/application/src/main/java/cytoscape/visual/VisualPropertyDependency.java
new file mode 100644
index 0000000..bd2f193
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/VisualPropertyDependency.java
@@ -0,0 +1,125 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+package cytoscape.visual;
+
+import java.util.Properties;
+
+/**
+ * Define dependency of visual properties.
+ *
+ *
+ * @author mes
+ *
+ */
+public interface VisualPropertyDependency {
+
+ /**
+ * An enum that lists the possible dependencies.
+ */
+ public enum Definition {
+ NODE_SIZE_LOCKED("nodeSizeLocked",true, "Lock Node Width/Height"),
+ ARROW_COLOR_MATCHES_EDGE("arrowColorMatchesEdge",false,"Make Arrow Color Match Edge Color"),
+
+ // From Cytoscape 2.8: Synchronize node size to custom cgraphics size.
+ NODE_CUSTOM_GRAPHICS_SIZE_SYNC("nodeCustomGraphicsSizeSync", true, "Synchronize Custom Graphics Size to Node Size"),
+
+ // From Cytoscape 2.8: Create new color based on label background.
+ NODE_LABLE_COLOR_FROM_NODE_COLOR("nodeLabelColorFromNodeColor", false, "Create Node Label Color from Node Color");
+
+ private final String propKey;
+ private final boolean defaultValue;
+ private final String title;
+
+ private Definition(String propKey, boolean defaultValue, String title) {
+ this.propKey = propKey;
+ this.defaultValue = defaultValue;
+ this.title = title;
+ }
+
+ /**
+ * Will return the key used to identify this Definition for use in Properties objects.
+ */
+ public String getDefaultPropertyKey() {
+ return propKey;
+ }
+
+ /**
+ * Will return the default state for this Definition.
+ */
+ public boolean getDefault() {
+ return defaultValue;
+ }
+
+ /**
+ * Will return a human readable title suitable for use in a user interface.
+ */
+ public String getTitle() {
+ return title;
+ }
+ }
+
+ /**
+ * Checks the state of the specified dependency definition. If a value has not
+ * been explicitly set for the specified definition then the default value for
+ * that definition will be returned.
+ */
+ boolean check(final Definition s);
+
+ /**
+ * Sets the state of the specified definition to the specified value.
+ */
+ void set(final Definition s, final boolean b);
+
+ /**
+ * Clears the current object and copies the state of the specified VisualPropertyDependency
+ * into this object. Once complete this object should have the identical settings to
+ * the specified object.
+ */
+ void copy(VisualPropertyDependency v);
+
+ /**
+ * Will search the specified Properties using the specified basedKey for
+ * each dependency definition and will update this object according
+ * to any properties found.
+ */
+ void applyDefaultProperties(final Properties props, final String baseKey);
+
+ /**
+ * Will return a new Properties object with properties set based on the
+ * specified baseKey and any dependency definitions set in this object.
+ */
+ Properties getDefaultProperties(final String baseKey);
+}
diff --git a/application/src/main/java/cytoscape/visual/VisualPropertyDependencyImpl.java b/application/src/main/java/cytoscape/visual/VisualPropertyDependencyImpl.java
new file mode 100644
index 0000000..3da04e7
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/VisualPropertyDependencyImpl.java
@@ -0,0 +1,110 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+package cytoscape.visual;
+
+import java.util.Map;
+import java.util.EnumMap;
+import java.util.Properties;
+
+class VisualPropertyDependencyImpl implements VisualPropertyDependency {
+
+ private final Map<Definition,Boolean> state;
+
+ VisualPropertyDependencyImpl() {
+ state = new EnumMap<Definition,Boolean>(VisualPropertyDependency.Definition.class);
+ }
+
+ public boolean check(final Definition s) {
+ if ( state.containsKey(s) )
+ return state.get(s);
+ else
+ return s.getDefault();
+ }
+
+ public void set(final Definition s, final boolean b) {
+ if ( s != null )
+ state.put(s,b);
+ }
+
+ public void applyDefaultProperties(final Properties props, final String baseKey) {
+ for ( Definition d : Definition.values() ) {
+ final String lockKey = baseKey + "." + d.getDefaultPropertyKey();
+ final String lockVal = props.getProperty(lockKey);
+ // Don't set any value if we don't explicitly match something (rely on default).
+ if (lockVal != null) {
+ if ( lockVal.equalsIgnoreCase("true") )
+ set(d,true);
+ else if ( lockVal.equalsIgnoreCase("false") )
+ set(d,false);
+ }
+ }
+ }
+
+ public Properties getDefaultProperties(final String baseKey) {
+ Properties props = new Properties();
+ // only set properties that have been explicitly set
+ for ( Definition d : state.keySet() ) {
+ final String lockKey = baseKey + "." + d.getDefaultPropertyKey();
+ props.setProperty(lockKey, Boolean.valueOf(check(d)).toString());
+ }
+ return props;
+ }
+
+ /**
+ * First clear this VisualPropertyDependency and the copy the provided
+ * VisualPropertyDependency settings into this one.
+ */
+ public void copy(VisualPropertyDependency d) {
+ if ( this == d )
+ return;
+ state.clear();
+ for ( Definition def : Definition.values() ) {
+ final boolean b = d.check(def);
+ if ( b != def.getDefault() )
+ state.put( def, b );
+ }
+ }
+
+
+ @Override
+ public String toString() {
+ String ret = "dependency state (" + hashCode() + "): ";
+ for ( Definition d : state.keySet() )
+ ret += " [" + d + " " + state.get(d) + "]";
+
+ return ret;
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/VisualPropertyType.java b/application/src/main/java/cytoscape/visual/VisualPropertyType.java
new file mode 100644
index 0000000..4e8ce6a
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/VisualPropertyType.java
@@ -0,0 +1,714 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual;
+
+import giny.view.ObjectPosition;
+
+import java.awt.Color;
+import java.awt.Font;
+import java.lang.reflect.InvocationTargetException;
+import java.lang.reflect.Method;
+import java.util.ArrayList;
+import java.util.List;
+
+import cytoscape.Cytoscape;
+import cytoscape.logger.CyLogger;
+import cytoscape.visual.calculators.Calculator;
+import cytoscape.visual.converter.ValueToStringConverterManager;
+import cytoscape.visual.customgraphic.CyCustomGraphics;
+import cytoscape.visual.parsers.ArrowShapeParser;
+import cytoscape.visual.parsers.BooleanParser;
+import cytoscape.visual.parsers.ColorParser;
+import cytoscape.visual.parsers.DoubleParser;
+import cytoscape.visual.parsers.FloatParser;
+import cytoscape.visual.parsers.FontParser;
+import cytoscape.visual.parsers.GraphicsParser;
+import cytoscape.visual.parsers.LineStyleParser;
+import cytoscape.visual.parsers.NodeShapeParser;
+import cytoscape.visual.parsers.ObjectPositionParser;
+import cytoscape.visual.parsers.StringParser;
+import cytoscape.visual.parsers.ValueParser;
+import cytoscape.visual.properties.EdgeColorProp;
+import cytoscape.visual.properties.EdgeFontFaceProp;
+import cytoscape.visual.properties.EdgeFontSizeProp;
+import cytoscape.visual.properties.EdgeLabelColorProp;
+import cytoscape.visual.properties.EdgeLabelOpacityProp;
+import cytoscape.visual.properties.EdgeLabelPositionProp;
+import cytoscape.visual.properties.EdgeLabelProp;
+import cytoscape.visual.properties.EdgeLabelWidthProp;
+import cytoscape.visual.properties.EdgeLineStyleProp;
+import cytoscape.visual.properties.EdgeLineWidthProp;
+import cytoscape.visual.properties.EdgeOpacityProp;
+import cytoscape.visual.properties.EdgeSourceArrowColorProp;
+import cytoscape.visual.properties.EdgeSourceArrowOpacityProp;
+import cytoscape.visual.properties.EdgeSourceArrowShapeProp;
+import cytoscape.visual.properties.EdgeTargetArrowColorProp;
+import cytoscape.visual.properties.EdgeTargetArrowOpacityProp;
+import cytoscape.visual.properties.EdgeTargetArrowShapeProp;
+import cytoscape.visual.properties.EdgeToolTipProp;
+import cytoscape.visual.properties.NodeBorderColorProp;
+import cytoscape.visual.properties.NodeBorderOpacityProp;
+import cytoscape.visual.properties.NodeCustomGraphicsPositionProp;
+import cytoscape.visual.properties.NodeCustomGraphicsProp;
+import cytoscape.visual.properties.NodeFillColorProp;
+import cytoscape.visual.properties.NodeFontFaceProp;
+import cytoscape.visual.properties.NodeFontSizeProp;
+import cytoscape.visual.properties.NodeHeightProp;
+import cytoscape.visual.properties.NodeLabelColorProp;
+import cytoscape.visual.properties.NodeLabelOpacityProp;
+import cytoscape.visual.properties.NodeLabelPositionProp;
+import cytoscape.visual.properties.NodeLabelProp;
+import cytoscape.visual.properties.NodeLabelWidthProp;
+import cytoscape.visual.properties.NodeLineStyleProp;
+import cytoscape.visual.properties.NodeLineWidthProp;
+import cytoscape.visual.properties.NodeOpacityProp;
+import cytoscape.visual.properties.NodeShapeProp;
+import cytoscape.visual.properties.NodeShowNestedNetworkProp;
+import cytoscape.visual.properties.NodeSizeProp;
+import cytoscape.visual.properties.NodeToolTipProp;
+import cytoscape.visual.properties.NodeWidthProp;
+import cytoscape.visual.ui.EditorDisplayer;
+import cytoscape.visual.ui.EditorDisplayer.EditorType;
+import cytoscape.visual.ui.editors.continuous.ContinuousMappingEditorPanel;
+
+/**
+ * Enum for calculator types.<br>
+ *
+ * This will replace public constants defined in VizMapperUI class.<br>
+ * This Enum defines visual attributes used in Cytoscape.
+ *
+ * @version 0.5
+ * @since Cytoscape 2.5
+ * @author kono
+ *
+ */
+public enum VisualPropertyType {
+
+ NODE_FILL_COLOR("Node Color", "nodeFillColorCalculator", "node.fillColor",
+ "defaultNodeFillColor", Color.class,
+ new NodeFillColorProp(), new ColorParser(), true, true),
+ NODE_BORDER_COLOR("Node Border Color", "nodeBorderColorCalculator", "node.borderColor",
+ "defaultNodeBorderColor",
+ Color.class, new NodeBorderColorProp(), new ColorParser(), true, true ),
+ // exists only for backwards compatibility
+ NODE_LINETYPE("Node Line Type", "nodeLineTypeCalculator", "node.lineType",
+ "defaultNodeLineType", LineStyle.class,
+ new NodeLineStyleProp(), new LineStyleParser(), true, false ),
+ NODE_SHAPE("Node Shape", "nodeShapeCalculator", "node.shape", "defaultNodeShape",
+ NodeShape.class, new NodeShapeProp(),
+ new NodeShapeParser(), true, true),
+ NODE_SIZE("Node Size", "nodeUniformSizeCalculator", "node.size", "defaultNodeSize",
+ Number.class, new NodeSizeProp(),
+ new DoubleParser(), true, true),
+ NODE_WIDTH("Node Width", "nodeWidthCalculator", "node.width", "defaultNodeWidth",
+ Number.class, new NodeWidthProp(),
+ new DoubleParser(), true, true),
+ NODE_HEIGHT("Node Height", "nodeHeightCalculator", "node.height", "defaultNodeHight",
+ Number.class, new NodeHeightProp(),
+ new DoubleParser(), true, true),
+ NODE_LABEL("Node Label", "nodeLabelCalculator", "node.label", "defaultNodeLabel",
+ String.class, new NodeLabelProp(),
+ new StringParser(), true, true),
+ NODE_FONT_FACE("Node Font Face", "nodeFontFaceCalculator", "node.font", "defaultNodeFont",
+ Font.class, new NodeFontFaceProp(),
+ new FontParser(), true, true),
+ NODE_FONT_SIZE("Node Font Size", "nodeFontSizeCalculator", "node.fontSize",
+ "defaultNodeFontSize", Number.class,
+ new NodeFontSizeProp(), new DoubleParser(), true, true),
+ NODE_LABEL_COLOR("Node Label Color", "nodeLabelColor", "node.labelColor",
+ "defaultNodeLabelColor", Color.class,
+ new NodeLabelColorProp(), new ColorParser(), true, true),
+ NODE_TOOLTIP("Node Tooltip", "nodeTooltipCalculator", "node.toolTip", "defaultNodeToolTip",
+ String.class, new NodeToolTipProp(),
+ new StringParser(), true, true),
+ NODE_LABEL_POSITION("Node Label Position", "nodeLabelPositionCalculator", "node.labelPosition",
+ "defaultNodeLabelPosition",
+ ObjectPosition.class, new NodeLabelPositionProp(), new ObjectPositionParser(), true, true),
+ EDGE_COLOR("Edge Color", "edgeColorCalculator", "edge.color", "defaultEdgeColor",
+ Color.class, new EdgeColorProp(),
+ new ColorParser(), false, true),
+ // exists only for backwards compatibility
+ EDGE_LINETYPE("Edge Line Type", "edgeLineTypeCalculator", "edge.lineType",
+ "defaultEdgeLineType", LineStyle.class,
+ new EdgeLineStyleProp(), new LineStyleParser(), false, false),
+ // exists only for backwards compatibility
+ EDGE_SRCARROW("Edge Source Arrow", "edgeSourceArrowCalculator", "edge.sourceArrow",
+ "defaultEdgeSourceArrow", ArrowShape.class,
+ new EdgeSourceArrowShapeProp(), new ArrowShapeParser(), false, false),
+ // exists only for backwards compatibility
+ EDGE_TGTARROW("Edge Target Arrow", "edgeTargetArrowCalculator", "edge.targetArrow",
+ "defaultEdgeTargetArrow", ArrowShape.class,
+ new EdgeTargetArrowShapeProp(), new ArrowShapeParser(), false, false),
+ EDGE_LABEL("Edge Label", "edgeLabelCalculator", "edge.label", "defaultEdgeLabel",
+ String.class, new EdgeLabelProp(),
+ new StringParser(), false, true),
+ EDGE_FONT_FACE("Edge Font Face", "edgeFontFaceCalculator", "edge.font", "defaultEdgeFont",
+ Font.class, new EdgeFontFaceProp(),
+ new FontParser(), false, true),
+ EDGE_FONT_SIZE("Edge Font Size", "edgeFontSizeCalculator", "edge.fontSize",
+ "defaultEdgeFontSize", Number.class,
+ new EdgeFontSizeProp(), new DoubleParser(), false, true),
+ EDGE_LABEL_COLOR("Edge Label Color", "edgeLabelColorCalculator", "edge.labelColor",
+ "defaultEdgeLabelColor", Color.class,
+ new EdgeLabelColorProp(), new ColorParser(), false, true),
+ EDGE_TOOLTIP("Edge Tooltip", "edgeTooltipCalculator", "edge.toolTip", "defaultEdgeToolTip",
+ String.class, new EdgeToolTipProp(),
+ new StringParser(), false, true),
+
+ // New from 2.5: line can have arbitrary width.
+ NODE_LINE_WIDTH("Node Line Width", "nodeLineWidthCalculator", "node.lineWidth",
+ "defaultNodeLineWidth", Number.class,
+ new NodeLineWidthProp(), new FloatParser(), true, true),
+ EDGE_LINE_WIDTH("Edge Line Width", "edgeLineWidthCalculator", "edge.lineWidth",
+ "defaultEdgeLineWidth", Number.class,
+ new EdgeLineWidthProp(), new FloatParser(), false, true),
+ NODE_LINE_STYLE("Node Line Style", "nodeLineStyleCalculator", "node.lineStyle",
+ "defaultNodeLineStyle", LineStyle.class,
+ new NodeLineStyleProp(), new LineStyleParser(), true, true),
+ EDGE_LINE_STYLE("Edge Line Style", "edgeLineStyleCalculator", "edge.lineStyle",
+ "defaultEdgeLineStyle", LineStyle.class,
+ new EdgeLineStyleProp(), new LineStyleParser(), false, true),
+
+ // New from 2.5: arrows have its own color, shape, and size.
+ EDGE_SRCARROW_SHAPE("Edge Source Arrow Shape", "edgeSourceArrowShapeCalculator",
+ "edge.sourceArrowShape", "defaultEdgeSourceArrowShape",
+ ArrowShape.class,
+ new EdgeSourceArrowShapeProp(), new ArrowShapeParser(), false, true),
+ EDGE_TGTARROW_SHAPE("Edge Target Arrow Shape", "edgeTargetArrowShapeCalculator",
+ "edge.targetArrowShape", "defaultEdgeTargetArrowShape",
+ ArrowShape.class,
+ new EdgeTargetArrowShapeProp(), new ArrowShapeParser(), false, true),
+ EDGE_SRCARROW_COLOR("Edge Source Arrow Color", "edgeSourceArrowColorCalculator",
+ "edge.sourceArrowColor", "defaultEdgeSourceArrowColor",
+ Color.class,
+ new EdgeSourceArrowColorProp(), new ColorParser(), false, true),
+ EDGE_TGTARROW_COLOR("Edge Target Arrow Color", "edgeTargetArrowColorCalculator",
+ "edge.targetArrowColor", "defaultEdgeTargetArrowColor",
+ Color.class,
+ new EdgeTargetArrowColorProp(), new ColorParser(), false, true),
+ /*
+ * New in 2.5: Opacity support
+ */
+ NODE_OPACITY("Node Opacity", "nodeOpacityCalculator", "node.opacity", "defaultNodeOpacity",
+ Number.class, new NodeOpacityProp(),
+ new FloatParser(), true, true),
+ EDGE_OPACITY("Edge Opacity", "edgeOpacityCalculator", "edge.opacity", "defaultEdgeOpacity",
+ Number.class, new EdgeOpacityProp(),
+ new FloatParser(), false, true),
+ NODE_LABEL_OPACITY("Node Label Opacity", "nodeLabelOpacityCalculator", "node.LabelOpacity", "defaultNodeLabelOpacity",
+ Number.class, new NodeLabelOpacityProp(),
+ new FloatParser(), true, true),
+ EDGE_LABEL_OPACITY("Edge Label Opacity", "edgeLabelOpacityCalculator", "edge.labelOpacity", "defaultEdgeLabelOpacity",
+ Number.class, new EdgeLabelOpacityProp(),
+ new FloatParser(), false, true),
+ NODE_BORDER_OPACITY("Node Border Opacity", "nodeBorderOpacityCalculator", "node.borderOpacity", "defaultNodeBorderOpacity",
+ Number.class, new NodeBorderOpacityProp(),
+ new FloatParser(), true, true),
+ EDGE_SRCARROW_OPACITY("Edge Source Arrow Opacity", "edgeSourceArrowOpacityCalculator", "edge.sourceArrowOpacity", "defaultEdgeSourceArrowOpacity", Number.class, new EdgeSourceArrowOpacityProp(),
+ new FloatParser(), false, true),
+ EDGE_TGTARROW_OPACITY("Edge Target Arrow Opacity", "edgeTargetArrowOpacityCalculator", "edge.targetArrowOpacity", "defaultEdgeTargetArrowOpacity", Number.class, new EdgeTargetArrowOpacityProp(),
+ new FloatParser(), false, true),
+ // Not yet implemented in version 2.5
+ EDGE_LABEL_POSITION("Edge Label Position", "edgeLabelPositionCalculator", "edge.labelPosition",
+ "defaultEdgeLabelPosition", null, new EdgeLabelPositionProp(),
+ new ObjectPositionParser(), false, false),
+
+ NODE_LABEL_WIDTH("Node Label Width", "nodeLabelWidthCalculator", "node.labelWidth",
+ "defaultNodeLabelWidth", Number.class, new NodeLabelWidthProp(),
+ new FloatParser(), true, true),
+ EDGE_LABEL_WIDTH("Edge Label Width", "edgeLabelWidthCalculator", "edge.labelWidth",
+ "defaultEdgeLabelWidth", Number.class, new EdgeLabelWidthProp(),
+ new FloatParser(), false, true),
+
+ NODE_SHOW_NESTED_NETWORK("Node Show Nested Network", "nodeShowNestedNetwork",
+ "node.showNestedNetwork", "defaultNodeShowNestedNetwork",
+ Boolean.class, new NodeShowNestedNetworkProp(),
+ new BooleanParser(), true, true),
+
+ // New in Cytoscape 2.8: Custom Graphic Visual Prop.
+ NODE_CUSTOM_GRAPHICS_1("Node Custom Graphics 1", "nodeCustomGraphics1",
+ "node.customGraphics1", "defaultNodeCustomGraphics1",
+ CyCustomGraphics.class, new NodeCustomGraphicsProp(1),
+ new GraphicsParser(), true, true),
+ NODE_CUSTOM_GRAPHICS_2("Node Custom Graphics 2", "nodeCustomGraphics2",
+ "node.customGraphics2", "defaultNodeCustomGraphics2",
+ CyCustomGraphics.class, new NodeCustomGraphicsProp(2),
+ new GraphicsParser(), true, true),
+ NODE_CUSTOM_GRAPHICS_3("Node Custom Graphics 3", "nodeCustomGraphics3",
+ "node.customGraphics3", "defaultNodeCustomGraphics3",
+ CyCustomGraphics.class, new NodeCustomGraphicsProp(3),
+ new GraphicsParser(), true, true),
+ NODE_CUSTOM_GRAPHICS_4("Node Custom Graphics 4", "nodeCustomGraphics4",
+ "node.customGraphics4", "defaultNodeCustomGraphics4",
+ CyCustomGraphics.class, new NodeCustomGraphicsProp(4),
+ new GraphicsParser(), true, true),
+ NODE_CUSTOM_GRAPHICS_5("Node Custom Graphics 5", "nodeCustomGraphics5",
+ "node.customGraphics5", "defaultNodeCustomGraphics5",
+ CyCustomGraphics.class, new NodeCustomGraphicsProp(5),
+ new GraphicsParser(), true, true),
+ NODE_CUSTOM_GRAPHICS_6("Node Custom Graphics 6", "nodeCustomGraphics6",
+ "node.customGraphics6", "defaultNodeCustomGraphics6",
+ CyCustomGraphics.class, new NodeCustomGraphicsProp(6),
+ new GraphicsParser(), true, true),
+ NODE_CUSTOM_GRAPHICS_7("Node Custom Graphics 7", "nodeCustomGraphics7",
+ "node.customGraphics7", "defaultNodeCustomGraphics7",
+ CyCustomGraphics.class, new NodeCustomGraphicsProp(7),
+ new GraphicsParser(), true, true),
+ NODE_CUSTOM_GRAPHICS_8("Node Custom Graphics 8", "nodeCustomGraphics8",
+ "node.customGraphics8", "defaultNodeCustomGraphics8",
+ CyCustomGraphics.class, new NodeCustomGraphicsProp(8),
+ new GraphicsParser(), true, true),
+ NODE_CUSTOM_GRAPHICS_9("Node Custom Graphics 9", "nodeCustomGraphics9",
+ "node.customGraphics9", "defaultNodeCustomGraphics9",
+ CyCustomGraphics.class, new NodeCustomGraphicsProp(9),
+ new GraphicsParser(), true, true),
+
+ NODE_CUSTOM_GRAPHICS_POSITION_1("Node Custom Graphics Position 1", "nodeCustomGraphicsPosition1",
+ "node.customGraphicsPosition1", "defaultNodeCustomGraphicsPosition1",
+ ObjectPosition.class, new NodeCustomGraphicsPositionProp(1),
+ new ObjectPositionParser(), true, true),
+ NODE_CUSTOM_GRAPHICS_POSITION_2("Node Custom Graphics Position 2", "nodeCustomGraphicsPosition2",
+ "node.customGraphicsPosition2", "defaultNodeCustomGraphicsPosition2",
+ ObjectPosition.class, new NodeCustomGraphicsPositionProp(2),
+ new ObjectPositionParser(), true, true),
+ NODE_CUSTOM_GRAPHICS_POSITION_3("Node Custom Graphics Position 3", "nodeCustomGraphicsPosition3",
+ "node.customGraphicsPosition3", "defaultNodeCustomGraphicsPosition3",
+ ObjectPosition.class, new NodeCustomGraphicsPositionProp(3),
+ new ObjectPositionParser(), true, true),
+ NODE_CUSTOM_GRAPHICS_POSITION_4("Node Custom Graphics Position 4", "nodeCustomGraphicsPosition4",
+ "node.customGraphicsPosition4", "defaultNodeCustomGraphicsPosition4",
+ ObjectPosition.class, new NodeCustomGraphicsPositionProp(4),
+ new ObjectPositionParser(), true, true),
+ NODE_CUSTOM_GRAPHICS_POSITION_5("Node Custom Graphics Position 5", "nodeCustomGraphicsPosition5",
+ "node.customGraphicsPosition5", "defaultNodeCustomGraphicsPosition5",
+ ObjectPosition.class, new NodeCustomGraphicsPositionProp(5),
+ new ObjectPositionParser(), true, true),
+ NODE_CUSTOM_GRAPHICS_POSITION_6("Node Custom Graphics Position 6", "nodeCustomGraphicsPosition6",
+ "node.customGraphicsPosition6", "defaultNodeCustomGraphicsPosition6",
+ ObjectPosition.class, new NodeCustomGraphicsPositionProp(6),
+ new ObjectPositionParser(), true, true),
+ NODE_CUSTOM_GRAPHICS_POSITION_7("Node Custom Graphics Position 7", "nodeCustomGraphicsPosition7",
+ "node.customGraphicsPosition7", "defaultNodeCustomGraphicsPosition7",
+ ObjectPosition.class, new NodeCustomGraphicsPositionProp(7),
+ new ObjectPositionParser(), true, true),
+ NODE_CUSTOM_GRAPHICS_POSITION_8("Node Custom Graphics Position 8", "nodeCustomGraphicsPosition8",
+ "node.customGraphicsPosition8", "defaultNodeCustomGraphicsPosition8",
+ ObjectPosition.class, new NodeCustomGraphicsPositionProp(8),
+ new ObjectPositionParser(), true, true),
+ NODE_CUSTOM_GRAPHICS_POSITION_9("Node Custom Graphics Position 9", "nodeCustomGraphicsPosition9",
+ "node.customGraphicsPosition9", "defaultNodeCustomGraphicsPosition9",
+ ObjectPosition.class, new NodeCustomGraphicsPositionProp(9),
+ new ObjectPositionParser(), true, true);
+
+
+ /*
+ * String returned by toString() method.
+ */
+ private final String calcName;
+
+ /*
+ * Property label in prop file.
+ */
+ private String propertyLabel;
+
+ /*
+ * Attribute name for vizmap bypass function (right-click bypass)
+ */
+ private String bypassAttrName;
+ private String defaultPropertyLabel;
+
+ // Data type for the actual visual property.
+ private Class<?> dataType;
+ private VisualProperty vizProp;
+ private ValueParser valueParser;
+
+ // indicates whether or not property is for a node or edge
+ private boolean isNodeProp;
+
+ // Indicates whether or not we should be using this property for
+ // normal operations. If this is false, that means the property
+ // either hasn't been implemented or has been deprecated. This
+ // is primarily used to build lists of properties that we can
+ // display to users.
+ private boolean isAllowed;
+
+ private static final CyLogger logger = CyLogger.getLogger(VisualPropertyType.class);
+
+ /*
+ * private constructor to put name into this enum.
+ */
+ private VisualPropertyType(final String calcName, final String propertyLabel,
+ final String bypassAttrName, final String defaultPropertyLabel,
+ final Class<?> dataType, final VisualProperty vizProp,
+ final ValueParser valueParser, final boolean isNodeProp,
+ final boolean isAllowed) {
+ this.calcName = calcName;
+ this.propertyLabel = propertyLabel;
+ this.bypassAttrName = bypassAttrName;
+ this.defaultPropertyLabel = defaultPropertyLabel;
+ this.dataType = dataType;
+ this.vizProp = vizProp;
+ this.valueParser = valueParser;
+ this.isNodeProp = isNodeProp;
+ this.isAllowed = isAllowed;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getName() {
+ return calcName;
+ }
+
+ /**
+ * Returns string used as property label in VS prop file.
+ *
+ * @return
+ */
+ public String getPropertyLabel() {
+ return propertyLabel;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getBypassAttrName() {
+ return bypassAttrName;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getDefaultPropertyLabel() {
+ return defaultPropertyLabel;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param baseKey
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getDefaultPropertyKey(final String baseKey) {
+ return baseKey + "." + defaultPropertyLabel;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Class<?> getDataType() {
+ return dataType;
+ }
+
+ /**
+ * Check this visual property is for node or not.
+ *
+ * @return true if vp is for node.
+ */
+ public boolean isNodeProp() {
+ return isNodeProp;
+ }
+
+ /**
+ * Indicates whether or not we should be using this property for
+ * normal operations. If this is false, that means the property
+ * either hasn't been implemented or has been deprecated. This
+ * is primarily used to build lists of properties that we can
+ * display to users.
+ */
+ public boolean isAllowed() {
+ return isAllowed;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static List<VisualPropertyType> getNodeVisualPropertyList() {
+ List<VisualPropertyType> list = new ArrayList<VisualPropertyType>();
+
+ for (VisualPropertyType type : values()) {
+ if ( type.isNodeProp() && type.isAllowed() ) {
+ list.add(type);
+ }
+ }
+
+ return list;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static List<VisualPropertyType> getEdgeVisualPropertyList() {
+ List<VisualPropertyType> list = new ArrayList<VisualPropertyType>();
+
+ for (VisualPropertyType type : values()) {
+ if ( !type.isNodeProp() && type.isAllowed() ) {
+ list.add(type);
+ }
+ }
+
+ return list;
+ }
+
+
+ private Object showEditor(final EditorDisplayer action, final Object defaultValue)
+ throws IllegalArgumentException, IllegalAccessException, InvocationTargetException,
+ SecurityException, NoSuchMethodException {
+
+ // Special case: Object position needs a default.
+ if(EditorDisplayer.DISCRETE_OBJECT_POSITION == action) {
+ if(defaultValue != null && defaultValue instanceof ObjectPosition)
+ action.setParameters(new Object[] {Cytoscape.getDesktop(), defaultValue, this});
+ else
+ action.setParameters(new Object[] {Cytoscape.getDesktop(), this.getDefault(Cytoscape.getVisualMappingManager().getVisualStyle()), this});
+ }
+
+ final Method method = action.getActionClass()
+ .getMethod(action.getCommand(), action.getParamTypes());
+
+ Object ret = method.invoke(null, action.getParameters());
+
+ if ( ret == null )
+ return null;
+
+ // special handling for continuous editors
+ if ( ret instanceof ContinuousMappingEditorPanel)
+ return ret;
+
+ // convert strings to objects of expected types
+ else if ( ret instanceof String )
+ ret = valueParser.parseStringValue((String)ret);
+
+ if ( vizProp.isValidValue(ret) )
+ return ret;
+ else {
+ logger.warn("Invalid value specified for " + toString() + " : " + ret);
+ return null;
+ }
+ }
+
+ /**
+ * Display discrete value editor for this visual property.
+ *
+ * @return DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public Object showDiscreteEditor() throws Exception {
+ return this.showDiscreteEditor(null);
+ }
+
+
+ /**
+ * Display editor with default value.
+ *
+ * @param defaultValue
+ * @return
+ * @throws Exception
+ */
+ public Object showDiscreteEditor(final Object defaultValue) throws Exception {
+ return showEditor(EditorDisplayer.getEditor(this, EditorType.DISCRETE), defaultValue);
+ }
+
+
+ /**
+ * Display continuous value editor.
+ *
+ * <p>
+ * Continuous editor always update mapping automatically, so there is no return value.
+ * </p>
+ * @throws Exception DOCUMENT ME!
+ */
+ public Object showContinuousEditor() throws Exception {
+ final EditorDisplayer editor = EditorDisplayer.getEditor(this, EditorType.CONTINUOUS);
+
+ if (editor == EditorDisplayer.CONTINUOUS_COLOR)
+ editor.setParameters(new Object[] { 550, 180, "Gradient Editor for " + this.calcName, this });
+ else if (editor == EditorDisplayer.CONTINUOUS_CONTINUOUS)
+ editor.setParameters(new Object[] {
+ 550, 350, "Continuous Editor for " + this.calcName, this
+ });
+ else
+ editor.setParameters(new Object[] {
+ 550, 300, "Continuous Editor for " + this.calcName, this
+ });
+
+ return showEditor(editor, null);
+ }
+
+ /**
+ * Returns the VisualProperty object associated with this enum.
+ */
+ public VisualProperty getVisualProperty() {
+ return vizProp;
+ }
+
+ /**
+ * Gets the current default value for this type in the specified
+ * visual style. Returns null if the style is null.
+ * @param style The visual style we want to get the default for.
+ * @return the default object for this type and the specified style.
+ */
+ public Object getDefault(VisualStyle style) {
+ if (style == null)
+ return null;
+
+ Appearance a = null;
+
+ if (isNodeProp())
+ a = style.getNodeAppearanceCalculator().getDefaultAppearance();
+ else
+ a = style.getEdgeAppearanceCalculator().getDefaultAppearance();
+
+ return a.get(this);
+ }
+
+ /**
+ * Sets the default value for the visual attribute for this type
+ * in the specified visual style. No-op if either arg is null.
+ * @param style The visual style to be set.
+ * @param c The new default value.
+ */
+ public void setDefault(VisualStyle style, Object c) {
+ if ((style == null) || (c == null))
+ return;
+
+
+
+ if ( !vizProp.isValidValue( c ) ) {
+ logger.warn("Invalid default value specified for " + toString() + " : " + c);
+ return;
+ }
+
+
+ if (isNodeProp()) {
+ NodeAppearanceCalculator nodeCalc = style.getNodeAppearanceCalculator();
+ NodeAppearance na = nodeCalc.getDefaultAppearance();
+ na.set(this, c);
+ nodeCalc.setDefaultAppearance(na);
+ } else {
+ EdgeAppearanceCalculator edgeCalc = style.getEdgeAppearanceCalculator();
+ EdgeAppearance ea = edgeCalc.getDefaultAppearance();
+ ea.set(this, c);
+ edgeCalc.setDefaultAppearance(ea);
+ }
+ }
+
+ /**
+ * Gets the current calculator for the visual attribute for this type
+ * and the specified visual style. This may be null if no calculator
+ * is currently specified. Returns null if the style is null.
+ * @param style The style we're getting the calculator for.
+ * @return the current calculator for this style and type
+ */
+ public Calculator getCurrentCalculator(VisualStyle style) {
+ if (style == null)
+ return null;
+
+ if (isNodeProp())
+ return style.getNodeAppearanceCalculator().getCalculator(this);
+ else
+
+ return style.getEdgeAppearanceCalculator().getCalculator(this);
+ }
+
+ /**
+ * Sets the current calculator for the visual attribute for this type
+ * and the specified visual style. If the new calculator is null, then
+ * the calculator for this type will be removed. This method does
+ * nothing if the first argument specifying the visual style is null.
+ * @param style The style to set the calculator for.
+ * @param c The calculator to set.
+ */
+ public void setCurrentCalculator(VisualStyle style, Calculator c) {
+ if (style == null)
+ return;
+
+ if (isNodeProp()) {
+ if (c == null)
+ style.getNodeAppearanceCalculator().removeCalculator(this);
+ else
+ style.getNodeAppearanceCalculator().setCalculator(c);
+ } else {
+ if (c == null)
+ style.getEdgeAppearanceCalculator().removeCalculator(this);
+ else
+ style.getEdgeAppearanceCalculator().setCalculator(c);
+ }
+ }
+
+ public ValueParser getValueParser() {
+ return valueParser;
+ }
+
+
+ ///////////// For multiple Custom Graphics Properties //////////////////
+ private static final VisualPropertyType[] CUSTOM_GRAPHICS_PROPS = {
+ NODE_CUSTOM_GRAPHICS_1, NODE_CUSTOM_GRAPHICS_2, NODE_CUSTOM_GRAPHICS_3, NODE_CUSTOM_GRAPHICS_4,
+ NODE_CUSTOM_GRAPHICS_5, NODE_CUSTOM_GRAPHICS_6, NODE_CUSTOM_GRAPHICS_7, NODE_CUSTOM_GRAPHICS_8,
+ NODE_CUSTOM_GRAPHICS_9 };
+ private static final VisualPropertyType[] CUSTOM_GRAPHICS_POSITION_PROPS = {
+ NODE_CUSTOM_GRAPHICS_POSITION_1, NODE_CUSTOM_GRAPHICS_POSITION_2,
+ NODE_CUSTOM_GRAPHICS_POSITION_3, NODE_CUSTOM_GRAPHICS_POSITION_4,
+ NODE_CUSTOM_GRAPHICS_POSITION_5, NODE_CUSTOM_GRAPHICS_POSITION_6,
+ NODE_CUSTOM_GRAPHICS_POSITION_7, NODE_CUSTOM_GRAPHICS_POSITION_8,
+ NODE_CUSTOM_GRAPHICS_POSITION_9 };
+
+ public static VisualPropertyType getCustomGraphicsType(int index) {
+ return CUSTOM_GRAPHICS_PROPS[index];
+ }
+
+ public static VisualPropertyType[] getAllCustomGraphicsType() {
+ return CUSTOM_GRAPHICS_PROPS;
+ }
+
+ public static VisualPropertyType getCustomGraphicsPositionType(int index) {
+ return CUSTOM_GRAPHICS_POSITION_PROPS[index];
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/VisualStyle.java b/application/src/main/java/cytoscape/visual/VisualStyle.java
new file mode 100644
index 0000000..5df7ae4
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/VisualStyle.java
@@ -0,0 +1,289 @@
+/*
+ File: VisualStyle.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.visual;
+
+import java.util.Vector;
+
+import cytoscape.visual.calculators.Calculator;
+
+import cytoscape.logger.CyLogger;
+
+
+/**
+ * This class encapsulates a full set of visual mapping specifications for
+ * Cytoscape. Currently this is implemented by holding a reference to three
+ * appearance calculators, one for nodes, one for edges, and one for global
+ * visual attributes.
+ */
+public class VisualStyle implements Cloneable {
+
+ // Name of Visual Style
+ private String name = "default";
+
+ // Calculators associated with this VS.
+ private NodeAppearanceCalculator nodeAC;
+ private EdgeAppearanceCalculator edgeAC;
+ private GlobalAppearanceCalculator globalAC;
+
+ private VisualPropertyDependency deps;
+
+ /**
+ * Keep track of number of times this style has been cloned.
+ */
+ protected int dupeCount = 0;
+
+ /**
+ * Get how many times this style has been cloned.
+ */
+ public int getDupeCount() {
+ return dupeCount;
+ }
+
+ /**
+ * Check if contained appearance calculators are using given calculator
+ *
+ * @param c calculator to check conflicts for
+ * @return vector with: name of conflicting visual style (index 0),
+ * name of conflicting attributes. If size == 1, then no conflicts
+ */
+ public Vector checkConflictingCalculator(Calculator c) {
+ Vector<String> conflicts = new Vector<String>();
+ conflicts.add(name);
+
+ for (Calculator nodeCalcs : nodeAC.getCalculators()) {
+ if (nodeCalcs == c)
+ conflicts.add(nodeCalcs.getVisualPropertyType().getPropertyLabel());
+ }
+
+ for (Calculator edgeCalcs : edgeAC.getCalculators()) {
+ if (edgeCalcs == c)
+ conflicts.add(edgeCalcs.getVisualPropertyType().getPropertyLabel());
+ }
+
+ return conflicts;
+ }
+
+ /**
+ * Perform deep copy of this VisualStyle.
+ */
+ public Object clone() throws CloneNotSupportedException {
+
+ VisualStyle copy = (VisualStyle) super.clone();
+ String dupeFreeName;
+
+ if (dupeCount != 0) {
+ int dupeCountIndex = name.lastIndexOf(new Integer(dupeCount).toString());
+
+ if (dupeCountIndex == -1)
+ dupeFreeName = new String(name);
+ else
+ dupeFreeName = name.substring(0, dupeCountIndex);
+ } else
+ dupeFreeName = new String(name);
+
+ copy.name = dupeFreeName;
+ copy.dupeCount++;
+
+ copy.nodeAC = (NodeAppearanceCalculator) this.nodeAC.clone();
+ copy.edgeAC = (EdgeAppearanceCalculator) this.edgeAC.clone();
+ copy.globalAC = (GlobalAppearanceCalculator) this.globalAC.clone();
+
+ return copy;
+ }
+
+ /**
+ * Simple constructor, creates default node/edge/global appearance calculators.
+ */
+ public VisualStyle(String name) {
+ deps = new VisualPropertyDependencyImpl();
+ setName(name);
+ setNodeAppearanceCalculator(new NodeAppearanceCalculator(deps));
+ setEdgeAppearanceCalculator(new EdgeAppearanceCalculator(deps));
+ setGlobalAppearanceCalculator(new GlobalAppearanceCalculator());
+ }
+
+ /**
+ * Full constructor.
+ */
+ public VisualStyle(String name, NodeAppearanceCalculator nac, EdgeAppearanceCalculator eac,
+ GlobalAppearanceCalculator gac) {
+ deps = new VisualPropertyDependencyImpl();
+ setName(name);
+ setNodeAppearanceCalculator(nac);
+ setEdgeAppearanceCalculator(eac);
+ setGlobalAppearanceCalculator(gac);
+ }
+
+ /**
+ * Copy constructor. Creates a default object if the argument is null.
+ * The name of this new object should be changed by calling setName
+ * with a new, unique name before adding it to a CalculatorCatalog.
+ */
+ public VisualStyle(VisualStyle toCopy) {
+ this(toCopy, toCopy.getName());
+ }
+
+ /**
+ * Copy constructor with new name. Creates a default object if the first
+ * argument is null, otherwise copies the members of the first argument.
+ * The name of this new VisualStyle will be equal to the second argument;
+ * the caller should ensure that this is a unique name.
+ *
+ * @throws NullPointerException if the second argument is null
+ */
+ public VisualStyle(final VisualStyle toCopy, final String newName) {
+ if (toCopy == null)
+ return;
+
+ if (newName == null)
+ throw new NullPointerException("Unexpected null name in VisualStyle constructor");
+
+ deps = toCopy.getDependency();
+ if (deps == null)
+ deps = new VisualPropertyDependencyImpl();
+
+ setName(newName);
+ setNodeAppearanceCalculator((NodeAppearanceCalculator)toCopy.getNodeAppearanceCalculator().clone());
+ setEdgeAppearanceCalculator((EdgeAppearanceCalculator)toCopy.getEdgeAppearanceCalculator().clone());
+
+ try {
+ setGlobalAppearanceCalculator((GlobalAppearanceCalculator)toCopy.getGlobalAppearanceCalculator().clone());
+ } catch (CloneNotSupportedException e) {
+ CyLogger.getLogger(VisualStyle.class).warn("Internal error - Unable to clone global appearance calculator!");
+ // e.printStackTrace();
+ }
+
+ }
+
+ /**
+ * Returns the name of this object, as returned by getName.
+ */
+ public String toString() {
+ return getName();
+ }
+
+ /**
+ * Returns the name of this object.
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * Set the name of this visual style. This should be a unique name, or
+ * a collision will ocur when adding this to a CalcualtorCatalog.
+ *
+ * @param n the new name
+ * @return the old name
+ */
+ public String setName(String n) {
+ String tmp = name;
+ name = n;
+
+ return tmp;
+ }
+
+ /**
+ * Get the NodeAppearanceCalculator for this visual style.
+ */
+ public NodeAppearanceCalculator getNodeAppearanceCalculator() {
+ return nodeAC;
+ }
+
+ /**
+ * Set the NodeAppearanceCalculator for this visual style. A default
+ * NodeAppearanceCalculator will be created and used if the argument
+ * is null.
+ *
+ * @param nac the new NodeAppearanceCalculator
+ * @return the old NodeAppearanceCalculator
+ */
+ public NodeAppearanceCalculator setNodeAppearanceCalculator(NodeAppearanceCalculator nac) {
+ NodeAppearanceCalculator tmp = nodeAC;
+ nodeAC = (nac == null) ? new NodeAppearanceCalculator(deps) : nac;
+ return tmp;
+ }
+
+ /**
+ * Get the EdgeAppearanceCalculator for this visual style.
+ */
+ public EdgeAppearanceCalculator getEdgeAppearanceCalculator() {
+ return edgeAC;
+ }
+
+ /**
+ * Set the EdgeAppearanceCalculator for this visual style. A default
+ * EdgeAppearanceCalculator will be created and used if the argument
+ * is null.
+ *
+ * @param nac the new EdgeAppearanceCalculator
+ * @return the old EdgeAppearanceCalculator
+ */
+ public EdgeAppearanceCalculator setEdgeAppearanceCalculator(EdgeAppearanceCalculator eac) {
+ EdgeAppearanceCalculator tmp = edgeAC;
+ edgeAC = (eac == null) ? new EdgeAppearanceCalculator(deps) : eac;
+
+ return tmp;
+ }
+
+ /**
+ * Get the GlobalAppearanceCalculator for this visual style.
+ */
+ public GlobalAppearanceCalculator getGlobalAppearanceCalculator() {
+ return globalAC;
+ }
+
+ /**
+ * Set the GlobalAppearanceCalculator for this visual style. A default
+ * GlobalAppearanceCalculator will be created and used if the argument
+ * is null.
+ *
+ * @param nac the new GlobalAppearanceCalculator
+ * @return the old GlobalAppearanceCalculator
+ */
+ public GlobalAppearanceCalculator setGlobalAppearanceCalculator(GlobalAppearanceCalculator gac) {
+ GlobalAppearanceCalculator tmp = globalAC;
+ globalAC = (gac == null) ? new GlobalAppearanceCalculator() : gac;
+
+ return tmp;
+ }
+
+ public VisualPropertyDependency getDependency() {
+ return deps;
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/calculators/AbstractCalculator.java b/application/src/main/java/cytoscape/visual/calculators/AbstractCalculator.java
new file mode 100644
index 0000000..3fc9c4c
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/calculators/AbstractCalculator.java
@@ -0,0 +1,627 @@
+/*
+ File: AbstractCalculator.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+package cytoscape.visual.calculators;
+
+import giny.model.Edge;
+import giny.model.GraphObject;
+import giny.model.Node;
+
+import java.awt.GridBagConstraints;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.util.Arrays;
+import java.util.List;
+import java.util.Map;
+import java.util.Properties;
+import java.util.Vector;
+
+import javax.swing.Box;
+import javax.swing.JComboBox;
+import javax.swing.JDialog;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.SwingConstants;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import cytoscape.data.CyAttributes;
+import cytoscape.data.CyAttributesUtils;
+import cytoscape.dialogs.GridBagGroup;
+import cytoscape.dialogs.MiscGB;
+import cytoscape.visual.Appearance;
+import cytoscape.visual.VisualPropertyType;
+import cytoscape.visual.mappings.MappingFactory;
+import cytoscape.visual.mappings.ObjectMapping;
+
+
+/**
+ */
+public abstract class AbstractCalculator implements Calculator {
+
+ /**
+ * Vector of all mappings contained by this calculator. Usually small.
+ * Contains ObjectMapping objects.
+ */
+ protected Vector<ObjectMapping> mappings = new Vector<ObjectMapping>(4, 2);
+
+ /**
+ * The domain classes accepted by the mappings underlying this calculator.
+ * Contains an array of classes - each representing the appropriate domain
+ * classes of the mapping in the {@link #mappings} vector at the same index.
+ */
+ protected Vector acceptedDataClasses = new Vector(4, 2);
+ protected String name;
+
+ /**
+ * Type of this visual property.
+ * (New in version 2.5)
+ */
+ protected VisualPropertyType type;
+
+ /** keep track of how many times I've been duplicated */
+ private int dupeCount = 0;
+
+ /** keep track of interested UI classes. */
+ protected List changeListeners = new Vector(1, 1);
+
+ /**
+ * Only one <code>ChangeEvent</code> is needed per calculator instance
+ * since the event's only state is the source property.
+ */
+ protected transient ChangeEvent changeEvent;
+
+
+ /**
+ * Creates a new AbstractCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param m DOCUMENT ME!
+ * @param c DOCUMENT ME!
+ * @param type DOCUMENT ME!
+ */
+ public AbstractCalculator(String name, ObjectMapping m, VisualPropertyType type) {
+ if (type == null)
+ throw new NullPointerException("Type parameter for Calculator is null");
+
+ this.type = type;
+ this.name = name;
+ this.addMapping(m);
+ Class c = type.getDataType();
+
+ if (!c.isAssignableFrom(m.getRangeClass()))
+ throw new ClassCastException("Invalid Calculator: Expected class " + c.toString()
+ + ", got " + m.getRangeClass().toString());
+ }
+
+ /**
+ * Add a mapping to the mappings contained by the calculator.
+ *
+ * @param m
+ * Mapping to add.
+ */
+ public void addMapping(ObjectMapping m) {
+ this.mappings.add(m);
+ this.acceptedDataClasses.add(m.getAcceptedDataClasses());
+ }
+
+ /**
+ * Get all mappings contained by this calculator.
+ *
+ * @return Vector of all mappings contained in this calculator
+ */
+ public Vector<ObjectMapping> getMappings() {
+ return mappings;
+ }
+
+ /**
+ * Get the mapping at a specific index in this calculator.
+ *
+ * @param i
+ * index of mapping to retrieve
+ * @return ObjectMapping at index i
+ */
+ public ObjectMapping getMapping(int i) {
+ return mappings.get(i);
+ }
+
+ /**
+ * Get how many times this calculator has been duplicated.
+ *
+ * @return Calculator duplication count
+ */
+ public int getDupeCount() {
+ return dupeCount;
+ }
+
+ /**
+ * Clone the calculator. AbstractCalculator makes an independent clone of
+ * itself but DOES NOT ensure that a unique name is created. Whoever is
+ * cloning the calculator should enter the new calculator in the catalog and
+ * create an appropriate name for it if needed.
+ *
+ *
+ * @return Clone of this calculator
+ * @throws CloneNotSupportedException
+ * if something is seriously borked.
+ */
+ public Object clone() throws CloneNotSupportedException {
+ final AbstractCalculator clonedCalc = (AbstractCalculator) super.clone();
+
+ /*
+ * remove the duplication count appended to the name. This makes
+ * maintaining the duplicate naming scheme much easier by starting the
+ * valid name search at the first object every time
+ */
+ String dupeFreeName;
+
+ if (dupeCount != 0) {
+ int dupeCountIndex = name.lastIndexOf(new Integer(dupeCount).toString());
+
+ if (dupeCountIndex == -1)
+ dupeFreeName = new String(name);
+ else
+ dupeFreeName = name.substring(0, dupeCountIndex);
+ } else
+ dupeFreeName = new String(name);
+
+ clonedCalc.name = dupeFreeName;
+ clonedCalc.mappings = new Vector(this.mappings.size(), 2);
+
+ for (int i = 0; i < this.mappings.size(); i++) {
+ final ObjectMapping m = this.getMapping(i);
+ clonedCalc.mappings.add((ObjectMapping) m.clone());
+ }
+
+ clonedCalc.dupeCount++;
+
+ return clonedCalc;
+ }
+
+ /**
+ * Get the name of this calculator.
+ *
+ * @return the calculator's name
+ */
+ public final String toString() {
+ return name;
+ }
+
+ /**
+ * Set the name of this calculator. Should only be done by the
+ * CalculatorCatalog after checking that name will not be duplicated.
+ *
+ * @param newName
+ * the new name for this calculator. Must be unique.
+ */
+ public void setName(String newName) {
+ this.name = newName;
+ }
+
+ /**
+ * Returns a properties description of this calculator. Adds the keyword
+ * ".mapping" to the supplied base key and calls the getProperties method of
+ * MappingFactory with the ObjectMapping and the augmented base key.
+ */
+ public Properties getProperties() {
+ final String mapBaseKey = type.getPropertyLabel() + "." + toString() + ".mapping";
+ final ObjectMapping m = getMapping(0);
+ final Properties props = MappingFactory.getProperties(m, mapBaseKey);
+
+ props.put(type.getPropertyLabel() + "." + toString() + ".visualPropertyType", type.toString());
+
+ return props;
+ }
+
+ /**
+ * This exists so that it can be overridden in legacy classes
+ * (GenericNodeSizeCalculator, GenericColorCalculator,
+ * GenericArrowCalculator) such that they return the a new class name
+ * instead of a legacy class name. This will help prevent legacy classes
+ * from persisting in vizmap.props files.
+ */
+ protected String getClassName() {
+ return this.getClass().getName();
+ }
+
+ /**
+ * updateAttribute is called when the currently selected attribute changes.
+ * Any changes needed in the mapping UI should be performed at this point.
+ * Use {@link #updateAttribute(String, CyNetwork, int)} for best
+ * performance.
+ *
+ * @param attrName
+ * the name of the newly selected attribute
+ * @param network
+ * the CyNetwork on which this attribute is defined
+ * @param m
+ * the object mapping to update
+ * @throws IllegalArgumentException
+ * if the given object mapping isn't in this calculator.
+ */
+ void updateAttribute(String attrName, CyNetwork network, ObjectMapping m)
+ throws IllegalArgumentException {
+ int mapIndex = this.mappings.indexOf(m);
+
+ if (mapIndex == -1)
+ throw new IllegalArgumentException(m.getClass().getName() + " " + m.toString()
+ + " is not contained in calculator "
+ + this.toString());
+
+ this.updateAttribute(attrName, network, mapIndex);
+ }
+
+ /**
+ * updateAttribute is called when the currently selected attribute changes.
+ * Any changes needed in the mapping UI should be performed at this point.
+ * <p>
+ * Calls the specified mapper's setControllingAttribute method.
+ *
+ * @param attrName
+ * the name of the newly selected attribute
+ * @param network
+ * the CyNetwork on which this attribute is defined
+ * @param mIndex
+ * the index of the object mapping to update
+ * @throws ArrayIndexOutOfBoundsException
+ * if the given object mapping index is out of bounds.
+ */
+ void updateAttribute(String attrName, CyNetwork network, int mIndex)
+ throws ArrayIndexOutOfBoundsException {
+ ObjectMapping m = (ObjectMapping) this.mappings.get(mIndex);
+ m.setControllingAttributeName(attrName);
+
+ // fireStateChanged();
+ }
+
+ /**
+ * Get the UI for the calculator.
+ *
+ * @param parent
+ * Parent JDialog for the UI
+ * @param network
+ * CyNetwork object containing underlying graph data
+ *
+ * @deprecated Will be removed next release (2.8 or 3.0)
+ */
+ @Deprecated
+ public JPanel getUI(JDialog parent, CyNetwork network) {
+ return getUI(type.isNodeProp() ? Cytoscape.getNodeAttributes() : Cytoscape.getEdgeAttributes(),
+ parent, network);
+ }
+
+ /**
+ * Get the UI for calculators. Display a JComboBox with attributes in the
+ * given CyAttributes whose data are instances of the classes accepted by
+ * each ObjectMapping. The resulting JComboBox calls
+ * {@link #updateAttribute(String, CyNetwork, int)} when frobbed.
+ *
+ * @param attr
+ * CyAttributes to look up attributes from
+ * @return UI with controlling attribute selection facilities
+ *
+ * @deprecated will be removed in the next release (2.8 or 3.0)
+ */
+ @Deprecated
+ protected JPanel getUI(CyAttributes attr, JDialog parent, CyNetwork network) {
+ return new CalculatorUI(attr, parent, network);
+ }
+
+ /**
+ * UI class for the calculator.
+ *
+ * @deprecated Do not use. This UI was replaced by new VizMap GUI.
+ */
+ @Deprecated
+ protected class CalculatorUI extends JPanel {
+ /**
+ * Remember the grid bag group in case the mapper UI needs to be
+ * updated.
+ */
+ protected GridBagGroup myGBG;
+
+ public CalculatorUI(CyAttributes attr, JDialog parent, CyNetwork network) {
+ this.myGBG = new GridBagGroup(this);
+
+ MiscGB.inset(this.myGBG.constraints, 5, 5, 5, 5);
+
+ String[] attrNames = attr.getAttributeNames();
+ // 20030916 cworkman added Arrays.sort()
+ Arrays.sort(attrNames);
+
+ int i;
+ int yPos;
+
+ for (i = yPos = 0; i < mappings.size(); i++, yPos++) {
+ MiscGB.insert(this.myGBG, new JLabel("Map Attribute:", SwingConstants.RIGHT), 0,
+ yPos);
+ MiscGB.insert(this.myGBG, Box.createHorizontalStrut(5), 1, yPos);
+
+ ObjectMapping m = (ObjectMapping) mappings.get(i);
+
+ // filter list of interactions
+ String[] validAttr;
+ Class[] okClass = (Class[]) acceptedDataClasses.get(i);
+
+ if (okClass != null) {
+ Vector validAttrV = new Vector(attrNames.length);
+
+ for (int j = 0; j < attrNames.length; j++) {
+ // Class attrClass = attr.getClass(attrNames[j]);
+ Class attrClass = CyAttributesUtils.getClass(attrNames[j], attr);
+
+ for (int k = 0; k < okClass.length; k++) {
+ if (okClass[k].isAssignableFrom(attrClass)) {
+ validAttrV.add(attrNames[j]);
+
+ break;
+ }
+ }
+ }
+
+ validAttr = (String[]) validAttrV.toArray(new String[0]);
+ } else
+ validAttr = attrNames;
+
+ // add generic "ID" attribute
+ Vector v = new Vector();
+ v.add(ID);
+
+ for (int lc = 0; lc < validAttr.length; lc++)
+ v.add(validAttr[lc]);
+
+ validAttr = (String[]) v.toArray(new String[0]);
+
+ // create the JComboBox
+ JComboBox attrBox = new JComboBox(validAttr);
+ attrBox.setName("attrBox");
+
+ // set the attrBox to the currently selected attribute
+ String selectedAttr = m.getControllingAttributeName();
+ // make no selection first, in case the selectedAttr doesn't
+ // exist
+ attrBox.setSelectedIndex(-1);
+ attrBox.setSelectedItem(selectedAttr);
+
+ MiscGB.insert(this.myGBG, attrBox, 2, yPos, 1, 1, 1, 0,
+ GridBagConstraints.HORIZONTAL);
+
+ // underlying mapping's UI
+ JPanel mapperUI = m.getUI(parent, network);
+ attrBox.addItemListener(new AttributeSelectorListener(parent, network, i, ++yPos,
+ mapperUI));
+ // MiscGB.insert(this.myGBG, mapperUI, 0, yPos, 3, 1, 2, 2,
+ // GridBagConstraints.BOTH);
+ MiscGB.insert(this.myGBG, mapperUI, 0, yPos, 3, 1, 1, 0,
+ GridBagConstraints.HORIZONTAL);
+
+ // Add a blank JLabel at the bottom to take up extra spacce in
+ // the panel
+ MiscGB.insert(this.myGBG, new JLabel(), 0, yPos + 1, 3, 1, 1, 1,
+ GridBagConstraints.BOTH);
+ }
+ }
+
+ /**
+ * AttributeSelectorListener listens for events on the JComboBoxes that
+ * select the controlling attribute for mappers contained in each
+ * calculator.
+ */
+ protected class AttributeSelectorListener implements ItemListener {
+ private CyNetwork network;
+ private int mapIndex;
+ private int yPos;
+ private JPanel mapperUI;
+ private JDialog parent;
+
+ /**
+ * Constructs an AttributeSelectorListener for the ObjectMapping at
+ * index mapIndex.
+ *
+ * @param parent
+ * parent JDialog
+ * @param network
+ * passed to the mapping to get data values for the new
+ * attribute
+ * @param mapIndex
+ * Index of the mapping in the {@link #mappings} Vector
+ * to report changes in the selected attribute to.
+ * @param yPos
+ * Position to add the mapping UI into master GBG when
+ * updating mapping UI.
+ * @param mapperUI
+ * Current mapper UI panel
+ */
+ protected AttributeSelectorListener(JDialog parent, CyNetwork network, int mapIndex,
+ int yPos, JPanel mapperUI) {
+ this.parent = parent;
+ this.network = network;
+ this.mapIndex = mapIndex;
+ this.yPos = yPos;
+ this.mapperUI = mapperUI;
+ }
+
+ public void itemStateChanged(ItemEvent e) {
+ if (e.getStateChange() == ItemEvent.SELECTED) {
+ JComboBox c = (JComboBox) e.getItemSelectable();
+ String attrName = (String) c.getSelectedItem();
+ updateAttribute(attrName, network, this.mapIndex);
+ // change the panel referenced to get a new panel from the
+ // mapping
+ // to reflect the new mapped attribute.
+ remove(this.mapperUI);
+ this.mapperUI = ((ObjectMapping) mappings.get(mapIndex)).getUI(this.parent,
+ network);
+ MiscGB.insert(myGBG, this.mapperUI, 0, this.yPos, 3, 1, 2, 2,
+ GridBagConstraints.BOTH);
+ parent.validate();
+ }
+ }
+ }
+ }
+
+ /**
+ * Add a ChangeListener to the calcaultor. When the state underlying the
+ * calculator changes, all ChangeListeners will be notified.
+ *
+ * This is used in the UI classes to ensure that the UI panes stay
+ * consistent with the data held in the mappings.
+ *
+ * @param l
+ * ChangeListener to add
+ */
+ public void addChangeListener(ChangeListener l) {
+ this.changeListeners.add(l);
+ }
+
+ /**
+ * Remove a ChangeListener from the calcaultor. When the state underlying
+ * the calculator changes, all ChangeListeners will be notified.
+ *
+ * This is used in the UI classes to ensure that the UI panes stay
+ * consistent with the data held in the mappings.
+ *
+ * @param l
+ * ChangeListener to add
+ */
+ public void removeChangeListener(ChangeListener l) {
+ this.changeListeners.remove(l);
+ }
+
+ /**
+ * Notifies all listeners that have registered interest for notification on
+ * this event type. The event instance is lazily created.
+ *
+ * UI classes should attach themselves with a listener to the calculator to
+ * be notified about changes in the underlying data structures that require
+ * the UI classes to fetch a new copy of the UI and display it.
+ *
+ */
+ protected void fireStateChanged() {
+ // Process the listeners last to first, notifying
+ // those that are interested in this event
+ for (int i = this.changeListeners.size() - 1; i >= 0; i--) {
+ ChangeListener listener = (ChangeListener) this.changeListeners.get(i);
+
+ // Lazily create the event:
+ if (this.changeEvent == null)
+ this.changeEvent = new ChangeEvent(this);
+
+ listener.stateChanged(this.changeEvent);
+ }
+ }
+
+ /**
+ * Returns a map of attribute names to single values.
+ *
+ * @param canonicalName
+ * The attribute name returned from the CyNode or CyEdge.
+ * @return Map of the attribute names to values.
+ */
+ protected Map<String, Object> getAttrBundle(String canonicalName, CyAttributes cyAttrs) {
+ return CyAttributesUtils.getAttributes(canonicalName, cyAttrs);
+ }
+
+ protected Map<String, Object> getAttrBundle(final String canonicalName) {
+ return getAttrBundle(canonicalName,
+ type.isNodeProp() ? Cytoscape.getNodeAttributes()
+ : Cytoscape.getEdgeAttributes());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param appr DOCUMENT ME!
+ * @param e DOCUMENT ME!
+ * @param net DOCUMENT ME!
+ */
+ public void apply(Appearance appr, Edge e, CyNetwork net) {
+ //CyLogger.getLogger().info("AbstractCalculator.apply(edge) " + type.toString());
+ Object o = getRangeValue(e);
+
+ // default has already been set - no need to do anything
+ if (o == null)
+ return;
+
+ appr.set(type, o);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param appr DOCUMENT ME!
+ * @param n DOCUMENT ME!
+ * @param net DOCUMENT ME!
+ */
+ public void apply(Appearance appr, Node n, CyNetwork net) {
+ //CyLogger.getLogger().info("AbstractCalculator.apply(node) " + type.toString());
+ Object o = getRangeValue(n);
+
+ // default has already been set - no need to do anything
+ if (o == null)
+ return;
+
+ appr.set(type, o);
+ }
+
+ protected Object getRangeValue(GraphObject obj) {
+ if (obj == null)
+ return null;
+
+ final String nodeID = obj.getIdentifier();
+ final Map<String, Object> attrBundle = getAttrBundle(nodeID);
+ attrBundle.put(AbstractCalculator.ID, obj.getIdentifier());
+ return getMapping(0).calculateRangeValue(attrBundle);
+ }
+
+ /**
+ * Replaces the following 3 methods:
+ * <ul>
+ * <li>public byte getType();
+ * <li>public String getTypeName();
+ * <li>public String getPropertyLabel();
+ * </ul>
+ *
+ * The returned enum VisualPropertyType has replacement for these methods.
+ */
+ public VisualPropertyType getVisualPropertyType() {
+ return type;
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/visual/calculators/BasicCalculator.java b/application/src/main/java/cytoscape/visual/calculators/BasicCalculator.java
new file mode 100644
index 0000000..a4abbcb
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/calculators/BasicCalculator.java
@@ -0,0 +1,88 @@
+/*
+ File: BasicCalculator.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+//------------------------------------------------------------------------------
+// $Revision: 9996 $
+// $Date: 2007-04-17 18:47:27 -0700 (Tue, 17 Apr 2007) $
+// $Author: kono $
+//------------------------------------------------------------------------------
+package cytoscape.visual.calculators;
+
+import java.util.Properties;
+
+import cytoscape.visual.VisualPropertyType;
+import cytoscape.visual.mappings.MappingFactory;
+import cytoscape.visual.mappings.ObjectMapping;
+
+
+
+/**
+ * BasicCalculator implements some UI features for calculators lower in the
+ * object tree.
+ */
+public class BasicCalculator extends AbstractCalculator {
+
+ /**
+ * Creates a new BasicCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param m DOCUMENT ME!
+ * @param type DOCUMENT ME!
+ */
+ public BasicCalculator(String name, ObjectMapping m, VisualPropertyType type) {
+ super(name, m, type);
+ }
+
+ /**
+ * Creates a new BasicCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param props DOCUMENT ME!
+ * @param baseKey DOCUMENT ME!
+ * @param parser DOCUMENT ME!
+ * @param type DOCUMENT ME!
+ */
+ public BasicCalculator(String name, Properties props, String baseKey, VisualPropertyType type) {
+ super(name,
+ MappingFactory.newMapping(props, baseKey + ".mapping", type.getValueParser(),
+ type.getVisualProperty().getDefaultAppearanceObject(),
+ type.isNodeProp()?
+ ObjectMapping.NODE_MAPPING:
+ ObjectMapping.EDGE_MAPPING),
+ type);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/calculators/Calculator.java b/application/src/main/java/cytoscape/visual/calculators/Calculator.java
new file mode 100644
index 0000000..75af9b8
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/calculators/Calculator.java
@@ -0,0 +1,171 @@
+/*
+ File: Calculator.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+package cytoscape.visual.calculators;
+
+import cytoscape.CyNetwork;
+
+import cytoscape.visual.Appearance;
+import cytoscape.visual.VisualPropertyType;
+
+import cytoscape.visual.mappings.ObjectMapping;
+
+//------------------------------------------------------------------------------
+import giny.model.Edge;
+import giny.model.Node;
+
+import java.util.Properties;
+import java.util.Vector;
+
+import javax.swing.JDialog;
+import javax.swing.JPanel;
+import javax.swing.event.ChangeListener;
+
+
+/**
+ */
+public interface Calculator extends Cloneable {
+
+ public static final String ID = "ID";
+
+ /**
+ * Get the UI for a calculator.
+ *
+ * @param parent
+ * Parent JDialog for the UI
+ * @param network
+ * CyNetwork object containing underlying graph data
+ *
+ * @deprecated replaced by new VizMap GUI components. Will be removed in 2.8 or 3.0
+ */
+ @Deprecated
+ JPanel getUI(JDialog parent, CyNetwork network);
+
+ /**
+ * Gets calculator name.
+ */
+ public String toString();
+
+ /**
+ * Set calculator name. <b>DO NOT CALL THIS METHOD</b> unless you first get
+ * a valid name from the CalculatorCatalog. Even if you have a guaranteed
+ * valid name from the CalculatorCatalog, it is still preferrable to use the
+ * renameCalculator method in the CalculatorCatalog.
+ */
+ public void setName(String newName);
+
+ /**
+ * Clone the calculator.
+ */
+ public Object clone()
+ throws CloneNotSupportedException;
+
+ /**
+ * Get a description of this calculator as a Properties object.
+ */
+ public Properties getProperties();
+
+ /**
+ * Add a ChangeListener to the calcaultor. When the state underlying the
+ * calculator changes, all ChangeListeners will be notified.
+ *
+ * This is used in the UI classes to ensure that the UI panes stay
+ * consistent with the data held in the mappings.
+ *
+ * @param l
+ * ChangeListener to add
+ */
+ public void addChangeListener(ChangeListener l);
+
+ /**
+ * Remove a ChangeListener from the calcaultor. When the state underlying
+ * the calculator changes, all ChangeListeners will be notified.
+ *
+ * This is used in the UI classes to ensure that the UI panes stay
+ * consistent with the data held in the mappings.
+ *
+ * @param l
+ * ChangeListener to add
+ */
+ public void removeChangeListener(ChangeListener l);
+
+ /*
+ * Use public VisualPropertyType getVisualPropertyType() instead.
+ */
+
+ /**
+ *
+ * This method replaces the three methods above.
+ *
+ * @return
+ */
+ public VisualPropertyType getVisualPropertyType();
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param appr DOCUMENT ME!
+ * @param e DOCUMENT ME!
+ * @param net DOCUMENT ME!
+ */
+ public void apply(Appearance appr, Edge e, CyNetwork net);
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param appr DOCUMENT ME!
+ * @param n DOCUMENT ME!
+ * @param net DOCUMENT ME!
+ */
+ public void apply(Appearance appr, Node n, CyNetwork net);
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Vector<ObjectMapping> getMappings();
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param i DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public ObjectMapping getMapping(int i);
+}
diff --git a/application/src/main/java/cytoscape/visual/calculators/CalculatorFactory.java b/application/src/main/java/cytoscape/visual/calculators/CalculatorFactory.java
new file mode 100644
index 0000000..9446930
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/calculators/CalculatorFactory.java
@@ -0,0 +1,183 @@
+/*
+ File: CalculatorFactory.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual.calculators;
+
+import java.lang.reflect.Constructor;
+import java.util.Properties;
+
+import cytoscape.logger.CyLogger;
+import cytoscape.visual.VisualPropertyType;
+
+
+/**
+ * This class provides static factory methods for constructing instances of
+ * Calculators as specified by arguments and static methods for getting names
+ * and labels based on calculator type.
+ */
+public class CalculatorFactory {
+ private static CyLogger logger = CyLogger.getLogger(CalculatorFactory.class);
+
+ /**
+ * Creates a caclculator defined by the type identified by the ".visualPropertyType"
+ * property in the calcProps argument. If that isn't found, it looks for a
+ * ".class" property and then tries the old-school approach using reflection to create
+ * a calculator.
+ */
+ public static Calculator newCalculator(String name, Properties calcProps, String baseKey) {
+ final String typeName = calcProps.getProperty(baseKey + ".visualPropertyType");
+
+ if ( typeName == null )
+ return oldSchoolNewCalculator(name, calcProps, baseKey);
+
+ try {
+ VisualPropertyType t = VisualPropertyType.valueOf(typeName);
+ return new BasicCalculator(name,calcProps,baseKey,t);
+ } catch (IllegalArgumentException e) {
+ logger.info("Couldn't parse visual property type: " + typeName, e);
+ return null;
+ }
+ }
+
+
+ /**
+ * Attempt to construct an instance of Calculator as defined by the supplied
+ * arguments. It searches for a key-value pair identifying the name of the
+ * class to create, verifies that that class exists, implements the desired
+ * interface, and has an appropriate constructor, and calls that constructor
+ * with the appropriate arguments.
+ */
+ private static Calculator oldSchoolNewCalculator(String name, Properties calcProps,
+ String baseKey) {
+ /*
+ * Get the class object for the real implementation object specified by
+ * these properties
+ */
+ final String className = calcProps.getProperty(baseKey + ".class");
+
+ if (className == null)
+ return null; // this is normal, so don't shout about it
+
+ final String errString = "CalculatorFactory: error processing baseKey " +
+ baseKey;
+
+ Class realClass = null;
+
+ try {
+ realClass = Class.forName(className);
+ } catch (Exception e) {
+ logger.warn(errString + " class not found: " + className);
+
+ return null;
+ }
+
+ // get the class object representing the top-level interface Calculator
+ Class calcClass = Calculator.class;
+
+ if (!calcClass.isAssignableFrom(realClass)) {
+ logger.warn(errString + " requested class " + className +
+ " does not implement the Calculator interface");
+
+ return null;
+ }
+
+ // create the constructor for the specified class
+ Class[] parameterTypes = { String.class, Properties.class, String.class };
+ Constructor constructor = getConstructor(realClass, parameterTypes,
+ className);
+
+ if (constructor == null) {
+ logger.warn(errString + " requested constructor for " +
+ className + " could not be created");
+
+ return null;
+ }
+
+ // try constructing a calculator by calling the found constructor
+ Object[] params = { name, calcProps, baseKey };
+ Calculator calculator = getCalculator(constructor, params, className);
+
+ if (calculator == null)
+ logger.warn(errString + " requested calculator for " +
+ className + " could not be created");
+
+ return calculator;
+ }
+
+ // utility method to create a constructor based on the params
+ private static Constructor getConstructor(Class realClass,
+ Class[] parameterTypes, String className) {
+ // look for a constructor in this class that takes the right arguments
+ Constructor constructor = null;
+
+ try {
+ constructor = realClass.getDeclaredConstructor(parameterTypes);
+ } catch (NoSuchMethodException nsme) {
+ String s = "no suitable constructor found in class " + className;
+ logger.warn(s, nsme);
+
+ return null;
+ } catch (SecurityException se) { // highly unlikely
+
+ String s = "could not access constructors for class " + className;
+ logger.warn(s, se);
+
+ return null;
+ }
+
+ return constructor;
+ }
+
+ // utility method to create a calculator based on the params
+ private static Calculator getCalculator(Constructor constructor,
+ Object[] params, String className) {
+ Calculator calculator = null;
+
+ try {
+ calculator = (Calculator) (constructor.newInstance(params));
+ } catch (Exception e) {
+ String s = "unable to construct an instance of class " + className;
+ for(Object p: params) {
+ logger.info("-- Parameter = " + p);
+ }
+ logger.warn(s, e);
+
+ return null;
+ }
+
+ return calculator;
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/calculators/GenericEdgeArrowCalculator.java b/application/src/main/java/cytoscape/visual/calculators/GenericEdgeArrowCalculator.java
new file mode 100644
index 0000000..c0c9fb2
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/calculators/GenericEdgeArrowCalculator.java
@@ -0,0 +1,103 @@
+/*
+ File: GenericEdgeArrowCalculator.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+//----------------------------------------------------------------------------
+// $Revision: 18673 $
+// $Date: 2009-12-05 01:10:20 +0100 (Sat, 05 Dec 2009) $
+// $Author: mes $
+//----------------------------------------------------------------------------
+package cytoscape.visual.calculators;
+
+import cytoscape.CyNetwork;
+
+import cytoscape.visual.Arrow;
+import cytoscape.visual.VisualPropertyType;
+
+import cytoscape.visual.mappings.ObjectMapping;
+
+//----------------------------------------------------------------------------
+import giny.model.Edge;
+
+import java.util.Properties;
+
+
+/**
+ * This class exists ONLY to support legacy file formats. A VERY BAD PERSON
+ * decided to use the class name to identify calculators in property files,
+ * thus forever forcing us to keep these classes around.
+ *
+ * <b>DO NOT USE THIS CLASS!!!</b>
+ */
+class GenericEdgeArrowCalculator extends BasicCalculator {
+
+ /**
+ * Creates a new GenericEdgeArrowCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param m DOCUMENT ME!
+ *
+ */
+ GenericEdgeArrowCalculator(String name, ObjectMapping m) {
+ super(name, m, VisualPropertyType.EDGE_TGTARROW);
+ }
+
+ /**
+ * Creates a new GenericEdgeArrowCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param m DOCUMENT ME!
+ * @param type DOCUMENT ME!
+ */
+ GenericEdgeArrowCalculator(String name, ObjectMapping m, VisualPropertyType type) {
+ super(name, m, type);
+ }
+
+
+ /**
+ * Creates a new GenericEdgeArrowCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param props DOCUMENT ME!
+ * @param baseKey DOCUMENT ME!
+ * @param type DOCUMENT ME!
+ */
+ GenericEdgeArrowCalculator(String name, Properties props,
+ String baseKey, VisualPropertyType type) {
+ super(name, props, baseKey, type);
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/visual/calculators/GenericEdgeColorCalculator.java b/application/src/main/java/cytoscape/visual/calculators/GenericEdgeColorCalculator.java
new file mode 100644
index 0000000..5390fc3
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/calculators/GenericEdgeColorCalculator.java
@@ -0,0 +1,91 @@
+/*
+ File: GenericEdgeColorCalculator.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+//----------------------------------------------------------------------------
+// $Revision: 18673 $
+// $Date: 2009-12-05 01:10:20 +0100 (Sat, 05 Dec 2009) $
+// $Author: mes $
+//----------------------------------------------------------------------------
+package cytoscape.visual.calculators;
+
+import cytoscape.CyNetwork;
+
+import cytoscape.visual.Appearance;
+
+//----------------------------------------------------------------------------
+import static cytoscape.visual.VisualPropertyType.EDGE_COLOR;
+
+import cytoscape.visual.mappings.ObjectMapping;
+
+import cytoscape.visual.parsers.ColorParser;
+
+import giny.model.Edge;
+
+import java.awt.Color;
+
+import java.util.Properties;
+
+
+/**
+ * This class exists ONLY to support legacy file formats. A VERY BAD PERSON
+ * decided to use the class name to identify calculators in property files,
+ * thus forever forcing us to keep these classes around.
+ *
+ * <b>DO NOT USE THIS CLASS!!!</b>
+ */
+class GenericEdgeColorCalculator extends BasicCalculator {
+ /**
+ * Creates a new GenericEdgeColorCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param m DOCUMENT ME!
+ */
+ GenericEdgeColorCalculator(String name, ObjectMapping m) {
+ super(name, m, EDGE_COLOR);
+ }
+
+ /**
+ * Creates a new GenericEdgeColorCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param props DOCUMENT ME!
+ * @param baseKey DOCUMENT ME!
+ */
+ GenericEdgeColorCalculator(String name, Properties props, String baseKey) {
+ super(name, props, baseKey, EDGE_COLOR);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/calculators/GenericEdgeFontFaceCalculator.java b/application/src/main/java/cytoscape/visual/calculators/GenericEdgeFontFaceCalculator.java
new file mode 100644
index 0000000..aca3a94
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/calculators/GenericEdgeFontFaceCalculator.java
@@ -0,0 +1,91 @@
+/*
+ File: GenericEdgeFontFaceCalculator.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+//--------------------------------------------------------------------------
+// $Revision: 18673 $
+// $Date: 2009-12-05 01:10:20 +0100 (Sat, 05 Dec 2009) $
+// $Author: mes $
+//--------------------------------------------------------------------------
+package cytoscape.visual.calculators;
+
+import cytoscape.CyNetwork;
+
+import cytoscape.visual.Appearance;
+
+//--------------------------------------------------------------------------
+import static cytoscape.visual.VisualPropertyType.EDGE_FONT_FACE;
+
+import cytoscape.visual.mappings.ObjectMapping;
+
+import cytoscape.visual.parsers.FontParser;
+
+import giny.model.Edge;
+
+import java.awt.Font;
+
+import java.util.Properties;
+
+
+/**
+ * This class exists ONLY to support legacy file formats. A VERY BAD PERSON
+ * decided to use the class name to identify calculators in property files,
+ * thus forever forcing us to keep these classes around.
+ *
+ * <b>DO NOT USE THIS CLASS!!!</b>
+ */
+class GenericEdgeFontFaceCalculator extends BasicCalculator {
+ /**
+ * Creates a new GenericEdgeFontFaceCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param m DOCUMENT ME!
+ */
+ GenericEdgeFontFaceCalculator(String name, ObjectMapping m) {
+ super(name, m, EDGE_FONT_FACE);
+ }
+
+ /**
+ * Creates a new GenericEdgeFontFaceCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param props DOCUMENT ME!
+ * @param baseKey DOCUMENT ME!
+ */
+ GenericEdgeFontFaceCalculator(String name, Properties props, String baseKey) {
+ super(name, props, baseKey, EDGE_FONT_FACE);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/calculators/GenericEdgeFontSizeCalculator.java b/application/src/main/java/cytoscape/visual/calculators/GenericEdgeFontSizeCalculator.java
new file mode 100644
index 0000000..ee75c89
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/calculators/GenericEdgeFontSizeCalculator.java
@@ -0,0 +1,88 @@
+/*
+ File: GenericEdgeFontSizeCalculator.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+//--------------------------------------------------------------------------
+// $Revision: 18673 $
+// $Date: 2009-12-05 01:10:20 +0100 (Sat, 05 Dec 2009) $
+// $Author: mes $
+//--------------------------------------------------------------------------
+package cytoscape.visual.calculators;
+
+import cytoscape.CyNetwork;
+
+import cytoscape.visual.Appearance;
+
+import static cytoscape.visual.VisualPropertyType.EDGE_FONT_SIZE;
+
+import cytoscape.visual.mappings.ObjectMapping;
+
+import cytoscape.visual.parsers.DoubleParser;
+
+import giny.model.Edge;
+
+import java.util.Properties;
+
+
+/**
+ * This class exists ONLY to support legacy file formats. A VERY BAD PERSON
+ * decided to use the class name to identify calculators in property files,
+ * thus forever forcing us to keep these classes around.
+ *
+ * <b>DO NOT USE THIS CLASS!!!</b>
+ */
+class GenericEdgeFontSizeCalculator extends BasicCalculator {
+ /**
+ * Creates a new GenericEdgeFontSizeCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param m DOCUMENT ME!
+ */
+ GenericEdgeFontSizeCalculator(String name, ObjectMapping m) {
+ super(name, m, EDGE_FONT_SIZE);
+ }
+
+ /**
+ * Creates a new GenericEdgeFontSizeCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param props DOCUMENT ME!
+ * @param baseKey DOCUMENT ME!
+ */
+ GenericEdgeFontSizeCalculator(String name, Properties props, String baseKey) {
+ super(name, props, baseKey, EDGE_FONT_SIZE);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/calculators/GenericEdgeLabelCalculator.java b/application/src/main/java/cytoscape/visual/calculators/GenericEdgeLabelCalculator.java
new file mode 100644
index 0000000..1b2faff
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/calculators/GenericEdgeLabelCalculator.java
@@ -0,0 +1,88 @@
+/*
+ File: GenericEdgeLabelCalculator.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+//----------------------------------------------------------------------------
+// $Revision: 18673 $
+// $Date: 2009-12-05 01:10:20 +0100 (Sat, 05 Dec 2009) $
+// $Author: mes $
+//----------------------------------------------------------------------------
+package cytoscape.visual.calculators;
+
+import cytoscape.CyNetwork;
+
+import cytoscape.visual.Appearance;
+
+import static cytoscape.visual.VisualPropertyType.EDGE_LABEL;
+
+import cytoscape.visual.mappings.ObjectMapping;
+
+import cytoscape.visual.parsers.StringParser;
+
+import giny.model.Edge;
+
+import java.util.Properties;
+
+
+/**
+ * This class exists ONLY to support legacy file formats. A VERY BAD PERSON
+ * decided to use the class name to identify calculators in property files,
+ * thus forever forcing us to keep these classes around.
+ *
+ * <b>DO NOT USE THIS CLASS!!!</b>
+ */
+class GenericEdgeLabelCalculator extends BasicCalculator {
+ /**
+ * Creates a new GenericEdgeLabelCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param m DOCUMENT ME!
+ */
+ GenericEdgeLabelCalculator(String name, ObjectMapping m) {
+ super(name, m, EDGE_LABEL);
+ }
+
+ /**
+ * Creates a new GenericEdgeLabelCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param props DOCUMENT ME!
+ * @param baseKey DOCUMENT ME!
+ */
+ GenericEdgeLabelCalculator(String name, Properties props, String baseKey) {
+ super(name, props, baseKey, EDGE_LABEL);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/calculators/GenericEdgeLabelColorCalculator.java b/application/src/main/java/cytoscape/visual/calculators/GenericEdgeLabelColorCalculator.java
new file mode 100644
index 0000000..cffdce8
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/calculators/GenericEdgeLabelColorCalculator.java
@@ -0,0 +1,84 @@
+/*
+ File: GenericEdgeLabelColorCalculator.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual.calculators;
+
+import cytoscape.CyNetwork;
+
+import cytoscape.visual.Appearance;
+import static cytoscape.visual.VisualPropertyType.EDGE_LABEL_COLOR;
+
+import cytoscape.visual.mappings.ObjectMapping;
+
+import cytoscape.visual.parsers.ColorParser;
+
+import giny.model.Edge;
+
+import java.awt.Color;
+
+import java.util.Properties;
+
+
+/**
+ * This class exists ONLY to support legacy file formats. A VERY BAD PERSON
+ * decided to use the class name to identify calculators in property files,
+ * thus forever forcing us to keep these classes around.
+ *
+ * <b>DO NOT USE THIS CLASS!!!</b>
+ */
+class GenericEdgeLabelColorCalculator extends BasicCalculator {
+ /**
+ * Creates a new GenericEdgeLabelColorCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param m DOCUMENT ME!
+ */
+ GenericEdgeLabelColorCalculator(String name, ObjectMapping m) {
+ super(name, m, EDGE_LABEL_COLOR);
+ }
+
+ /**
+ * Creates a new GenericEdgeLabelColorCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param props DOCUMENT ME!
+ * @param baseKey DOCUMENT ME!
+ */
+ GenericEdgeLabelColorCalculator(String name, Properties props, String baseKey) {
+ super(name, props, baseKey, EDGE_LABEL_COLOR);
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/visual/calculators/GenericEdgeLineStyleCalculator.java b/application/src/main/java/cytoscape/visual/calculators/GenericEdgeLineStyleCalculator.java
new file mode 100644
index 0000000..304ab2f
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/calculators/GenericEdgeLineStyleCalculator.java
@@ -0,0 +1,44 @@
+package cytoscape.visual.calculators;
+
+import static cytoscape.visual.VisualPropertyType.EDGE_LINE_STYLE;
+
+import java.util.Properties;
+
+import cytoscape.visual.LineStyle;
+import cytoscape.visual.mappings.ObjectMapping;
+import cytoscape.visual.parsers.LineStyleParser;
+
+/**
+ *
+ * This class exists ONLY to support legacy file formats. A VERY BAD PERSON
+ * decided to use the class name to identify calculators in property files,
+ * thus forever forcing us to keep these classes around.
+ *
+ * <b>DO NOT USE THIS CLASS!!!</b>
+ */
+class GenericEdgeLineStyleCalculator extends BasicCalculator {
+
+
+ /**
+ * Creates a new GenericEdgeLineWidthCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param m DOCUMENT ME!
+ */
+ GenericEdgeLineStyleCalculator(String name, ObjectMapping m) {
+ super(name, m, EDGE_LINE_STYLE);
+ }
+
+ /**
+ * Creates a new GenericEdgeLineWidthCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param props DOCUMENT ME!
+ * @param baseKey DOCUMENT ME!
+ */
+ GenericEdgeLineStyleCalculator(String name, Properties props,
+ String baseKey) {
+ super(name, props, baseKey, EDGE_LINE_STYLE);
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/visual/calculators/GenericEdgeLineTypeCalculator.java b/application/src/main/java/cytoscape/visual/calculators/GenericEdgeLineTypeCalculator.java
new file mode 100644
index 0000000..5f19ac0
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/calculators/GenericEdgeLineTypeCalculator.java
@@ -0,0 +1,86 @@
+/*
+ File: GenericEdgeLineTypeCalculator.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+//----------------------------------------------------------------------------
+// $Revision: 18686 $
+// $Date: 2009-12-07 22:56:52 +0100 (Mon, 07 Dec 2009) $
+// $Author: mes $
+//----------------------------------------------------------------------------
+package cytoscape.visual.calculators;
+
+import cytoscape.CyNetwork;
+
+import cytoscape.visual.Appearance;
+
+import static cytoscape.visual.VisualPropertyType.EDGE_LINETYPE;
+
+import cytoscape.visual.mappings.ObjectMapping;
+
+import giny.model.Edge;
+
+import java.util.Properties;
+
+
+/**
+ * This class exists ONLY to support legacy file formats. A VERY BAD PERSON
+ * decided to use the class name to identify calculators in property files,
+ * thus forever forcing us to keep these classes around.
+ *
+ * <b>DO NOT USE THIS CLASS!!!</b>
+ */
+class GenericEdgeLineTypeCalculator extends BasicCalculator {
+ /**
+ * Creates a new GenericEdgeLineTypeCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param m DOCUMENT ME!
+ */
+ GenericEdgeLineTypeCalculator(String name, ObjectMapping m) {
+ super(name, m, EDGE_LINETYPE);
+ }
+
+ /**
+ * Creates a new GenericEdgeLineTypeCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param props DOCUMENT ME!
+ * @param baseKey DOCUMENT ME!
+ */
+ GenericEdgeLineTypeCalculator(String name, Properties props, String baseKey) {
+ super(name, props, baseKey, EDGE_LINETYPE);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/calculators/GenericEdgeLineWidthCalculator.java b/application/src/main/java/cytoscape/visual/calculators/GenericEdgeLineWidthCalculator.java
new file mode 100644
index 0000000..0b0cf5f
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/calculators/GenericEdgeLineWidthCalculator.java
@@ -0,0 +1,57 @@
+package cytoscape.visual.calculators;
+
+import cytoscape.CyNetwork;
+
+import cytoscape.visual.Appearance;
+import static cytoscape.visual.VisualPropertyType.EDGE_LINE_WIDTH;
+
+import cytoscape.visual.mappings.ObjectMapping;
+
+import cytoscape.visual.parsers.FloatParser;
+
+import giny.model.Edge;
+
+import java.util.Properties;
+
+
+/**
+ * This class exists ONLY to support legacy file formats. A VERY BAD PERSON
+ * decided to use the class name to identify calculators in property files,
+ * thus forever forcing us to keep these classes around.
+ *
+ * <b>DO NOT USE THIS CLASS!!!</b>
+ */
+class GenericEdgeLineWidthCalculator extends BasicCalculator {
+ /**
+ * Creates a new GenericEdgeLineWidthCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param m DOCUMENT ME!
+ */
+ GenericEdgeLineWidthCalculator(String name, ObjectMapping m) {
+ super(name, m, EDGE_LINE_WIDTH);
+ }
+
+ /**
+ * Creates a new GenericEdgeLineWidthCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param m DOCUMENT ME!
+ * @param c DOCUMENT ME!
+ */
+ GenericEdgeLineWidthCalculator(String name, ObjectMapping m, Class c) {
+ super(name, m, EDGE_LINE_WIDTH);
+ }
+
+ /**
+ * Creates a new GenericEdgeLineWidthCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param props DOCUMENT ME!
+ * @param baseKey DOCUMENT ME!
+ */
+ GenericEdgeLineWidthCalculator(String name, Properties props, String baseKey) {
+ super(name, props, baseKey, EDGE_LINE_WIDTH);
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/visual/calculators/GenericEdgeSourceArrowCalculator.java b/application/src/main/java/cytoscape/visual/calculators/GenericEdgeSourceArrowCalculator.java
new file mode 100644
index 0000000..7fe5b2f
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/calculators/GenericEdgeSourceArrowCalculator.java
@@ -0,0 +1,75 @@
+/*
+ File: GenericEdgeSourceArrowCalculator.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute of Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+package cytoscape.visual.calculators;
+
+import static cytoscape.visual.VisualPropertyType.EDGE_SRCARROW;
+
+import cytoscape.visual.mappings.ObjectMapping;
+
+import java.util.Properties;
+
+
+/**
+ * This class exists ONLY to support legacy file formats. A VERY BAD PERSON
+ * decided to use the class name to identify calculators in property files,
+ * thus forever forcing us to keep these classes around.
+ *
+ * <b>DO NOT USE THIS CLASS!!!</b>
+ */
+class GenericEdgeSourceArrowCalculator extends GenericEdgeArrowCalculator {
+ /**
+ * Creates a new GenericEdgeSourceArrowCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param m DOCUMENT ME!
+ */
+ GenericEdgeSourceArrowCalculator(String name, ObjectMapping m) {
+ super(name, m, EDGE_SRCARROW);
+ }
+
+ /**
+ * Creates a new GenericEdgeSourceArrowCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param props DOCUMENT ME!
+ * @param baseKey DOCUMENT ME!
+ */
+ GenericEdgeSourceArrowCalculator(String name, Properties props, String baseKey) {
+ super(name, props, baseKey, EDGE_SRCARROW);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/calculators/GenericEdgeSourceArrowColorCalculator.java b/application/src/main/java/cytoscape/visual/calculators/GenericEdgeSourceArrowColorCalculator.java
new file mode 100644
index 0000000..a601057
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/calculators/GenericEdgeSourceArrowColorCalculator.java
@@ -0,0 +1,44 @@
+package cytoscape.visual.calculators;
+
+import static cytoscape.visual.VisualPropertyType.EDGE_SRCARROW_COLOR;
+import giny.model.Edge;
+
+import java.awt.Color;
+import java.util.Properties;
+
+import cytoscape.CyNetwork;
+import cytoscape.visual.Appearance;
+import cytoscape.visual.mappings.ObjectMapping;
+import cytoscape.visual.parsers.ColorParser;
+
+
+/**
+ * This class exists ONLY to support legacy file formats. A VERY BAD PERSON
+ * decided to use the class name to identify calculators in property files,
+ * thus forever forcing us to keep these classes around.
+ *
+ * <b>DO NOT USE THIS CLASS!!!</b>
+ */
+class GenericEdgeSourceArrowColorCalculator extends BasicCalculator {
+ /**
+ * Creates a new GenericEdgeSourceArrowColorCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param m DOCUMENT ME!
+ */
+ GenericEdgeSourceArrowColorCalculator(String name, ObjectMapping m) {
+ super(name, m, EDGE_SRCARROW_COLOR);
+ }
+
+ /**
+ * Creates a new GenericEdgeSourceArrowColorCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param props DOCUMENT ME!
+ * @param baseKey DOCUMENT ME!
+ */
+ GenericEdgeSourceArrowColorCalculator(String name, Properties props, String baseKey) {
+ super(name, props, baseKey, EDGE_SRCARROW_COLOR);
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/visual/calculators/GenericEdgeSourceArrowShapeCalculator.java b/application/src/main/java/cytoscape/visual/calculators/GenericEdgeSourceArrowShapeCalculator.java
new file mode 100644
index 0000000..e8399b1
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/calculators/GenericEdgeSourceArrowShapeCalculator.java
@@ -0,0 +1,77 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.visual.calculators;
+
+import cytoscape.visual.ArrowShape;
+import static cytoscape.visual.VisualPropertyType.EDGE_SRCARROW_SHAPE;
+
+import cytoscape.visual.mappings.ObjectMapping;
+
+import cytoscape.visual.parsers.ArrowShapeParser;
+
+import java.util.Properties;
+
+
+/**
+ * This class exists ONLY to support legacy file formats. A VERY BAD PERSON
+ * decided to use the class name to identify calculators in property files,
+ * thus forever forcing us to keep these classes around.
+ *
+ * <b>DO NOT USE THIS CLASS!!!</b>
+ */
+class GenericEdgeSourceArrowShapeCalculator extends BasicCalculator {
+ /**
+ * Creates a new GenericEdgeSourceArrowShapeCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param m DOCUMENT ME!
+ */
+ GenericEdgeSourceArrowShapeCalculator(String name, ObjectMapping m) {
+ super(name, m, EDGE_SRCARROW_SHAPE);
+ }
+
+ /**
+ * Creates a new GenericEdgeSourceArrowShapeCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param props DOCUMENT ME!
+ * @param baseKey DOCUMENT ME!
+ */
+ GenericEdgeSourceArrowShapeCalculator(String name, Properties props, String baseKey) {
+ super(name, props, baseKey, EDGE_SRCARROW_SHAPE);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/calculators/GenericEdgeTargetArrowCalculator.java b/application/src/main/java/cytoscape/visual/calculators/GenericEdgeTargetArrowCalculator.java
new file mode 100644
index 0000000..6b54dce
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/calculators/GenericEdgeTargetArrowCalculator.java
@@ -0,0 +1,82 @@
+/*
+ File: GenericEdgeTargetArrowCalculator.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute of Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+//----------------------------------------------------------------------------
+// $Revision: 7760 $
+// $Date: 2006-06-26 09:28:49 -0700 (Mon, 26 Jun 2006) $
+// $Author: mes $
+//----------------------------------------------------------------------------
+package cytoscape.visual.calculators;
+
+
+//----------------------------------------------------------------------------
+import static cytoscape.visual.VisualPropertyType.EDGE_TGTARROW;
+
+import cytoscape.visual.mappings.ObjectMapping;
+
+import java.util.Properties;
+
+
+/**
+ * This class exists ONLY to support legacy file formats. A VERY BAD PERSON
+ * decided to use the class name to identify calculators in property files,
+ * thus forever forcing us to keep these classes around.
+ *
+ * <b>DO NOT USE THIS CLASS!!!</b>
+ */
+class GenericEdgeTargetArrowCalculator extends BasicCalculator {
+ /**
+ * Creates a new GenericEdgeTargetArrowCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param m DOCUMENT ME!
+ */
+ GenericEdgeTargetArrowCalculator(String name, ObjectMapping m) {
+ super(name, m, EDGE_TGTARROW);
+ }
+
+ /**
+ * Creates a new GenericEdgeTargetArrowCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param props DOCUMENT ME!
+ * @param baseKey DOCUMENT ME!
+ */
+ GenericEdgeTargetArrowCalculator(String name, Properties props, String baseKey) {
+ super(name, props, baseKey, EDGE_TGTARROW);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/calculators/GenericEdgeTargetArrowColorCalculator.java b/application/src/main/java/cytoscape/visual/calculators/GenericEdgeTargetArrowColorCalculator.java
new file mode 100644
index 0000000..b840dde
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/calculators/GenericEdgeTargetArrowColorCalculator.java
@@ -0,0 +1,47 @@
+package cytoscape.visual.calculators;
+
+
+import static cytoscape.visual.VisualPropertyType.EDGE_TGTARROW_COLOR;
+
+import cytoscape.visual.mappings.ObjectMapping;
+import cytoscape.visual.parsers.ColorParser;
+import cytoscape.visual.Appearance;
+import cytoscape.CyNetwork;
+
+import giny.model.Edge;
+
+import java.awt.Color;
+
+import java.util.Properties;
+
+
+/**
+ * This class exists ONLY to support legacy file formats. A VERY BAD PERSON
+ * decided to use the class name to identify calculators in property files,
+ * thus forever forcing us to keep these classes around.
+ *
+ * <b>DO NOT USE THIS CLASS!!!</b>
+ */
+class GenericEdgeTargetArrowColorCalculator extends BasicCalculator {
+ /**
+ * Creates a new GenericEdgeTargetArrowColorCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param m DOCUMENT ME!
+ */
+ GenericEdgeTargetArrowColorCalculator(String name, ObjectMapping m) {
+ super(name, m, EDGE_TGTARROW_COLOR);
+ }
+
+ /**
+ * Creates a new GenericEdgeTargetArrowColorCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param props DOCUMENT ME!
+ * @param baseKey DOCUMENT ME!
+ */
+ GenericEdgeTargetArrowColorCalculator(String name, Properties props, String baseKey) {
+ super(name, props, baseKey, EDGE_TGTARROW_COLOR);
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/visual/calculators/GenericEdgeTargetArrowShapeCalculator.java b/application/src/main/java/cytoscape/visual/calculators/GenericEdgeTargetArrowShapeCalculator.java
new file mode 100644
index 0000000..f1ff176
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/calculators/GenericEdgeTargetArrowShapeCalculator.java
@@ -0,0 +1,79 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.visual.calculators;
+
+import cytoscape.visual.ArrowShape;
+import static cytoscape.visual.VisualPropertyType.EDGE_TGTARROW_SHAPE;
+
+import cytoscape.visual.mappings.ObjectMapping;
+
+import cytoscape.visual.parsers.ArrowShapeParser;
+
+import java.util.Properties;
+
+
+/**
+ * This class exists ONLY to support legacy file formats. A VERY BAD PERSON
+ * decided to use the class name to identify calculators in property files,
+ * thus forever forcing us to keep these classes around.
+ *
+ * <b>DO NOT USE THIS CLASS!!!</b>
+ */
+class GenericEdgeTargetArrowShapeCalculator extends BasicCalculator {
+ /**
+ * Creates a new GenericEdgeTargetArrowShapeCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param m DOCUMENT ME!
+ * @param type DOCUMENT ME!
+ */
+ GenericEdgeTargetArrowShapeCalculator(String name, ObjectMapping m) {
+ super(name, m, EDGE_TGTARROW_SHAPE);
+ }
+
+ /**
+ * Creates a new GenericEdgeTargetArrowShapeCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param props DOCUMENT ME!
+ * @param baseKey DOCUMENT ME!
+ * @param type DOCUMENT ME!
+ */
+ GenericEdgeTargetArrowShapeCalculator(String name, Properties props, String baseKey) {
+ super(name, props, baseKey, EDGE_TGTARROW_SHAPE);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/calculators/GenericEdgeToolTipCalculator.java b/application/src/main/java/cytoscape/visual/calculators/GenericEdgeToolTipCalculator.java
new file mode 100644
index 0000000..68ac5ad
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/calculators/GenericEdgeToolTipCalculator.java
@@ -0,0 +1,88 @@
+/*
+ File: GenericEdgeToolTipCalculator.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+//----------------------------------------------------------------------------
+// $Revision: 18673 $
+// $Date: 2009-12-05 01:10:20 +0100 (Sat, 05 Dec 2009) $
+// $Author: mes $
+//----------------------------------------------------------------------------
+package cytoscape.visual.calculators;
+
+import cytoscape.CyNetwork;
+
+import cytoscape.visual.Appearance;
+
+import static cytoscape.visual.VisualPropertyType.EDGE_TOOLTIP;
+
+import cytoscape.visual.mappings.ObjectMapping;
+
+import cytoscape.visual.parsers.StringParser;
+
+import giny.model.Edge;
+
+import java.util.Properties;
+
+
+/**
+ * This class exists ONLY to support legacy file formats. A VERY BAD PERSON
+ * decided to use the class name to identify calculators in property files,
+ * thus forever forcing us to keep these classes around.
+ *
+ * <b>DO NOT USE THIS CLASS!!!</b>
+ */
+class GenericEdgeToolTipCalculator extends BasicCalculator {
+ /**
+ * Creates a new GenericEdgeToolTipCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param m DOCUMENT ME!
+ */
+ GenericEdgeToolTipCalculator(String name, ObjectMapping m) {
+ super(name, m, EDGE_TOOLTIP);
+ }
+
+ /**
+ * Creates a new GenericEdgeToolTipCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param props DOCUMENT ME!
+ * @param baseKey DOCUMENT ME!
+ */
+ GenericEdgeToolTipCalculator(String name, Properties props, String baseKey) {
+ super(name, props, baseKey, EDGE_TOOLTIP);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/calculators/GenericNodeBorderColorCalculator.java b/application/src/main/java/cytoscape/visual/calculators/GenericNodeBorderColorCalculator.java
new file mode 100644
index 0000000..b0cc16c
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/calculators/GenericNodeBorderColorCalculator.java
@@ -0,0 +1,74 @@
+/*
+ File: GenericNodeBorderColorCalculator.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+package cytoscape.visual.calculators;
+
+import static cytoscape.visual.VisualPropertyType.NODE_BORDER_COLOR;
+
+import cytoscape.visual.mappings.ObjectMapping;
+
+import java.util.Properties;
+
+/**
+ * This class exists ONLY to support legacy file formats. A VERY BAD PERSON
+ * decided to use the class name to identify calculators in property files,
+ * thus forever forcing us to keep these classes around.
+ *
+ * <b>DO NOT USE THIS CLASS!!!</b>
+ */
+class GenericNodeBorderColorCalculator extends BasicCalculator {
+ /**
+ * Creates a new GenericNodeBorderColorCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param m DOCUMENT ME!
+ */
+ GenericNodeBorderColorCalculator(String name, ObjectMapping m) {
+ super(name, m, NODE_BORDER_COLOR);
+ }
+
+ /**
+ * Creates a new GenericNodeBorderColorCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param props DOCUMENT ME!
+ * @param baseKey DOCUMENT ME!
+ */
+ GenericNodeBorderColorCalculator(String name, Properties props, String baseKey) {
+ super(name, props, baseKey, NODE_BORDER_COLOR);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/calculators/GenericNodeColorCalculator.java b/application/src/main/java/cytoscape/visual/calculators/GenericNodeColorCalculator.java
new file mode 100644
index 0000000..62082ca
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/calculators/GenericNodeColorCalculator.java
@@ -0,0 +1,100 @@
+/*
+ File: GenericNodeColorCalculator.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual.calculators;
+
+import java.util.Properties;
+
+import cytoscape.visual.VisualPropertyType;
+import cytoscape.visual.mappings.ObjectMapping;
+
+
+/**
+ * This class exists ONLY to support legacy file formats. A VERY BAD PERSON
+ * decided to use the class name to identify calculators in property files,
+ * thus forever forcing us to keep these classes around.
+ *
+ * <b>DO NOT USE THIS CLASS!!!</b>
+ */
+class GenericNodeColorCalculator extends BasicCalculator {
+
+ /**
+ * Creates a new GenericNodeColorCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param m DOCUMENT ME!
+ *
+ */
+ GenericNodeColorCalculator(String name, ObjectMapping m) {
+ this(name, m, VisualPropertyType.NODE_FILL_COLOR);
+ }
+
+ /**
+ * Creates a new GenericNodeColorCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param m DOCUMENT ME!
+ * @param type DOCUMENT ME!
+ */
+ GenericNodeColorCalculator(String name, ObjectMapping m, VisualPropertyType type) {
+ super(name, m, type);
+ }
+
+ /**
+ * Creates a new GenericNodeColorCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param props DOCUMENT ME!
+ * @param baseKey DOCUMENT ME!
+ *
+ */
+ GenericNodeColorCalculator(String name, Properties props, String baseKey) {
+ this(name, props, baseKey, VisualPropertyType.NODE_FILL_COLOR);
+ }
+
+ /**
+ * Creates a new GenericNodeColorCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param props DOCUMENT ME!
+ * @param baseKey DOCUMENT ME!
+ * @param type DOCUMENT ME!
+ */
+ GenericNodeColorCalculator(String name, Properties props,
+ String baseKey, VisualPropertyType type) {
+ super(name, props, baseKey, type);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/calculators/GenericNodeCustomGraphicCalculator.java b/application/src/main/java/cytoscape/visual/calculators/GenericNodeCustomGraphicCalculator.java
new file mode 100644
index 0000000..fb57515
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/calculators/GenericNodeCustomGraphicCalculator.java
@@ -0,0 +1,14 @@
+package cytoscape.visual.calculators;
+
+import cytoscape.visual.VisualPropertyType;
+import cytoscape.visual.mappings.ObjectMapping;
+
+public class GenericNodeCustomGraphicCalculator extends BasicCalculator {
+
+ public GenericNodeCustomGraphicCalculator(String name, ObjectMapping m,
+ VisualPropertyType type) {
+ super(name, m, type);
+ // TODO Auto-generated constructor stub
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/visual/calculators/GenericNodeFillColorCalculator.java b/application/src/main/java/cytoscape/visual/calculators/GenericNodeFillColorCalculator.java
new file mode 100644
index 0000000..8a00d46
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/calculators/GenericNodeFillColorCalculator.java
@@ -0,0 +1,74 @@
+/*
+ File: GenericNodeFillColorCalculator.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+package cytoscape.visual.calculators;
+
+import static cytoscape.visual.VisualPropertyType.NODE_FILL_COLOR;
+
+import cytoscape.visual.mappings.ObjectMapping;
+
+import java.util.Properties;
+
+/**
+ * This class exists ONLY to support legacy file formats. A VERY BAD PERSON
+ * decided to use the class name to identify calculators in property files,
+ * thus forever forcing us to keep these classes around.
+ *
+ * <b>DO NOT USE THIS CLASS!!!</b>
+ */
+class GenericNodeFillColorCalculator extends BasicCalculator {
+ /**
+ * Creates a new GenericNodeFillColorCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param m DOCUMENT ME!
+ */
+ GenericNodeFillColorCalculator(String name, ObjectMapping m) {
+ super(name, m, NODE_FILL_COLOR);
+ }
+
+ /**
+ * Creates a new GenericNodeFillColorCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param props DOCUMENT ME!
+ * @param baseKey DOCUMENT ME!
+ */
+ GenericNodeFillColorCalculator(String name, Properties props, String baseKey) {
+ super(name, props, baseKey, NODE_FILL_COLOR);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/calculators/GenericNodeFontFaceCalculator.java b/application/src/main/java/cytoscape/visual/calculators/GenericNodeFontFaceCalculator.java
new file mode 100644
index 0000000..88394ca
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/calculators/GenericNodeFontFaceCalculator.java
@@ -0,0 +1,90 @@
+/*
+ File: GenericNodeFontFaceCalculator.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+//--------------------------------------------------------------------------
+// $Revision: 18673 $
+// $Date: 2009-12-05 01:10:20 +0100 (Sat, 05 Dec 2009) $
+// $Author: mes $
+//--------------------------------------------------------------------------
+package cytoscape.visual.calculators;
+
+import cytoscape.CyNetwork;
+
+import cytoscape.visual.Appearance;
+
+//--------------------------------------------------------------------------
+import static cytoscape.visual.VisualPropertyType.NODE_FONT_FACE;
+
+import cytoscape.visual.mappings.ObjectMapping;
+
+import cytoscape.visual.parsers.FontParser;
+
+import giny.model.Node;
+
+import java.awt.Font;
+
+import java.util.Properties;
+
+/**
+ * This class exists ONLY to support legacy file formats. A VERY BAD PERSON
+ * decided to use the class name to identify calculators in property files,
+ * thus forever forcing us to keep these classes around.
+ *
+ * <b>DO NOT USE THIS CLASS!!!</b>
+ */
+class GenericNodeFontFaceCalculator extends BasicCalculator {
+ /**
+ * Creates a new GenericNodeFontFaceCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param m DOCUMENT ME!
+ */
+ GenericNodeFontFaceCalculator(String name, ObjectMapping m) {
+ super(name, m, NODE_FONT_FACE);
+ }
+
+ /**
+ * Creates a new GenericNodeFontFaceCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param props DOCUMENT ME!
+ * @param baseKey DOCUMENT ME!
+ */
+ GenericNodeFontFaceCalculator(String name, Properties props, String baseKey) {
+ super(name, props, baseKey, NODE_FONT_FACE);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/calculators/GenericNodeFontSizeCalculator.java b/application/src/main/java/cytoscape/visual/calculators/GenericNodeFontSizeCalculator.java
new file mode 100644
index 0000000..d5ece34
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/calculators/GenericNodeFontSizeCalculator.java
@@ -0,0 +1,87 @@
+/*
+ File: GenericNodeFontSizeCalculator.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+//--------------------------------------------------------------------------
+// $Revision: 18673 $
+// $Date: 2009-12-05 01:10:20 +0100 (Sat, 05 Dec 2009) $
+// $Author: mes $
+//--------------------------------------------------------------------------
+package cytoscape.visual.calculators;
+
+import cytoscape.CyNetwork;
+
+import cytoscape.visual.Appearance;
+
+import static cytoscape.visual.VisualPropertyType.NODE_FONT_SIZE;
+
+import cytoscape.visual.mappings.ObjectMapping;
+
+import cytoscape.visual.parsers.DoubleParser;
+
+import giny.model.Node;
+
+import java.util.Properties;
+
+/**
+ * This class exists ONLY to support legacy file formats. A VERY BAD PERSON
+ * decided to use the class name to identify calculators in property files,
+ * thus forever forcing us to keep these classes around.
+ *
+ * <b>DO NOT USE THIS CLASS!!!</b>
+ */
+class GenericNodeFontSizeCalculator extends BasicCalculator {
+ /**
+ * Creates a new GenericNodeFontSizeCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param m DOCUMENT ME!
+ */
+ GenericNodeFontSizeCalculator(String name, ObjectMapping m) {
+ super(name, m, NODE_FONT_SIZE);
+ }
+
+ /**
+ * Creates a new GenericNodeFontSizeCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param props DOCUMENT ME!
+ * @param baseKey DOCUMENT ME!
+ */
+ GenericNodeFontSizeCalculator(String name, Properties props, String baseKey) {
+ super(name, props, baseKey, NODE_FONT_SIZE);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/calculators/GenericNodeHeightCalculator.java b/application/src/main/java/cytoscape/visual/calculators/GenericNodeHeightCalculator.java
new file mode 100644
index 0000000..985b3ad
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/calculators/GenericNodeHeightCalculator.java
@@ -0,0 +1,75 @@
+/*
+ File: GenericNodeHeightCalculator.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+package cytoscape.visual.calculators;
+
+import static cytoscape.visual.VisualPropertyType.NODE_HEIGHT;
+
+import cytoscape.visual.mappings.ObjectMapping;
+
+import java.util.Properties;
+
+
+/**
+ * This class exists ONLY to support legacy file formats. A VERY BAD PERSON
+ * decided to use the class name to identify calculators in property files,
+ * thus forever forcing us to keep these classes around.
+ *
+ * <b>DO NOT USE THIS CLASS!!!</b>
+ */
+class GenericNodeHeightCalculator extends BasicCalculator {
+ /**
+ * Creates a new GenericNodeHeightCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param m DOCUMENT ME!
+ */
+ GenericNodeHeightCalculator(String name, ObjectMapping m) {
+ super(name, m, NODE_HEIGHT);
+ }
+
+ /**
+ * Creates a new GenericNodeHeightCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param props DOCUMENT ME!
+ * @param baseKey DOCUMENT ME!
+ */
+ GenericNodeHeightCalculator(String name, Properties props, String baseKey) {
+ super(name, props, baseKey, NODE_HEIGHT);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/calculators/GenericNodeLabelCalculator.java b/application/src/main/java/cytoscape/visual/calculators/GenericNodeLabelCalculator.java
new file mode 100644
index 0000000..3016a53
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/calculators/GenericNodeLabelCalculator.java
@@ -0,0 +1,87 @@
+/*
+ File: GenericNodeLabelCalculator.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+//----------------------------------------------------------------------------
+// $Revision: 18673 $
+// $Date: 2009-12-05 01:10:20 +0100 (Sat, 05 Dec 2009) $
+// $Author: mes $
+//----------------------------------------------------------------------------
+package cytoscape.visual.calculators;
+
+import cytoscape.CyNetwork;
+
+import cytoscape.visual.Appearance;
+
+import static cytoscape.visual.VisualPropertyType.NODE_LABEL;
+
+import cytoscape.visual.mappings.ObjectMapping;
+
+import cytoscape.visual.parsers.StringParser;
+
+import giny.model.Node;
+
+import java.util.Properties;
+
+/**
+ * This class exists ONLY to support legacy file formats. A VERY BAD PERSON
+ * decided to use the class name to identify calculators in property files,
+ * thus forever forcing us to keep these classes around.
+ *
+ * <b>DO NOT USE THIS CLASS!!!</b>
+ */
+class GenericNodeLabelCalculator extends BasicCalculator {
+ /**
+ * Creates a new GenericNodeLabelCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param m DOCUMENT ME!
+ */
+ GenericNodeLabelCalculator(String name, ObjectMapping m) {
+ super(name, m, NODE_LABEL);
+ }
+
+ /**
+ * Creates a new GenericNodeLabelCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param props DOCUMENT ME!
+ * @param baseKey DOCUMENT ME!
+ */
+ GenericNodeLabelCalculator(String name, Properties props, String baseKey) {
+ super(name, props, baseKey, NODE_LABEL);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/calculators/GenericNodeLabelColorCalculator.java b/application/src/main/java/cytoscape/visual/calculators/GenericNodeLabelColorCalculator.java
new file mode 100644
index 0000000..371228b
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/calculators/GenericNodeLabelColorCalculator.java
@@ -0,0 +1,83 @@
+/*
+ File: GenericNodeLabelColorCalculator.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual.calculators;
+
+import cytoscape.CyNetwork;
+
+import cytoscape.visual.Appearance;
+import static cytoscape.visual.VisualPropertyType.NODE_LABEL_COLOR;
+
+import cytoscape.visual.mappings.ObjectMapping;
+
+import cytoscape.visual.parsers.ColorParser;
+
+import giny.model.Node;
+
+import java.awt.Color;
+
+import java.util.Properties;
+
+
+/**
+ * This class exists ONLY to support legacy file formats. A VERY BAD PERSON
+ * decided to use the class name to identify calculators in property files,
+ * thus forever forcing us to keep these classes around.
+ *
+ * <b>DO NOT USE THIS CLASS!!!</b>
+ */
+class GenericNodeLabelColorCalculator extends BasicCalculator {
+ /**
+ * Creates a new GenericNodeLabelColorCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param m DOCUMENT ME!
+ */
+ GenericNodeLabelColorCalculator(String name, ObjectMapping m) {
+ super(name, m, NODE_LABEL_COLOR);
+ }
+
+ /**
+ * Creates a new GenericNodeLabelColorCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param props DOCUMENT ME!
+ * @param baseKey DOCUMENT ME!
+ */
+ GenericNodeLabelColorCalculator(String name, Properties props, String baseKey) {
+ super(name, props, baseKey, NODE_LABEL_COLOR);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/calculators/GenericNodeLabelPositionCalculator.java b/application/src/main/java/cytoscape/visual/calculators/GenericNodeLabelPositionCalculator.java
new file mode 100644
index 0000000..7441cb3
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/calculators/GenericNodeLabelPositionCalculator.java
@@ -0,0 +1,75 @@
+/*
+ File: GenericNodeLabelPositionCalculator.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+package cytoscape.visual.calculators;
+
+import static cytoscape.visual.VisualPropertyType.NODE_LABEL_POSITION;
+
+import java.util.Properties;
+
+import cytoscape.visual.mappings.ObjectMapping;
+
+/**
+ * This class exists ONLY to support legacy file formats. A VERY BAD PERSON
+ * decided to use the class name to identify calculators in property files,
+ * thus forever forcing us to keep these classes around.
+ *
+ * <b>DO NOT USE THIS CLASS!!!</b>
+ */
+class GenericNodeLabelPositionCalculator extends BasicCalculator {
+ /**
+ * Creates a new GenericNodeLabelPositionCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param m DOCUMENT ME!
+ */
+ GenericNodeLabelPositionCalculator(String name, ObjectMapping m) {
+ super(name, m, NODE_LABEL_POSITION);
+ }
+
+ /**
+ * Creates a new GenericNodeLabelPositionCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param props DOCUMENT ME!
+ * @param baseKey DOCUMENT ME!
+ */
+ GenericNodeLabelPositionCalculator(String name, Properties props, String baseKey) {
+ super(name, props, baseKey, NODE_LABEL_POSITION);
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/visual/calculators/GenericNodeLineStyleCalculator.java b/application/src/main/java/cytoscape/visual/calculators/GenericNodeLineStyleCalculator.java
new file mode 100644
index 0000000..fb0927f
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/calculators/GenericNodeLineStyleCalculator.java
@@ -0,0 +1,41 @@
+package cytoscape.visual.calculators;
+
+import static cytoscape.visual.VisualPropertyType.NODE_LINE_STYLE;
+
+import java.util.Properties;
+
+import cytoscape.visual.LineStyle;
+import cytoscape.visual.mappings.ObjectMapping;
+import cytoscape.visual.parsers.LineStyleParser;
+
+/**
+ * This class exists ONLY to support legacy file formats. A VERY BAD PERSON
+ * decided to use the class name to identify calculators in property files,
+ * thus forever forcing us to keep these classes around.
+ *
+ * <b>DO NOT USE THIS CLASS!!!</b>
+ */
+class GenericNodeLineStyleCalculator extends BasicCalculator {
+
+ /**
+ * Creates a new GenericNodeLineWidthCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param m DOCUMENT ME!
+ */
+ GenericNodeLineStyleCalculator(String name, ObjectMapping m) {
+ super(name, m, NODE_LINE_STYLE);
+ }
+
+ /**
+ * Creates a new GenericNodeLineWidthCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param props DOCUMENT ME!
+ * @param baseKey DOCUMENT ME!
+ */
+ GenericNodeLineStyleCalculator(String name, Properties props, String baseKey) {
+ super(name, props, baseKey, NODE_LINE_STYLE);
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/visual/calculators/GenericNodeLineTypeCalculator.java b/application/src/main/java/cytoscape/visual/calculators/GenericNodeLineTypeCalculator.java
new file mode 100644
index 0000000..440af0c
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/calculators/GenericNodeLineTypeCalculator.java
@@ -0,0 +1,85 @@
+/*
+ File: GenericNodeLineTypeCalculator.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+//----------------------------------------------------------------------------
+// $Revision: 18686 $
+// $Date: 2009-12-07 22:56:52 +0100 (Mon, 07 Dec 2009) $
+// $Author: mes $
+//----------------------------------------------------------------------------
+package cytoscape.visual.calculators;
+
+import cytoscape.CyNetwork;
+
+import cytoscape.visual.Appearance;
+
+import static cytoscape.visual.VisualPropertyType.NODE_LINETYPE;
+
+import cytoscape.visual.mappings.ObjectMapping;
+
+import giny.model.Node;
+
+import java.util.Properties;
+
+/**
+ * This class exists ONLY to support legacy file formats. A VERY BAD PERSON
+ * decided to use the class name to identify calculators in property files,
+ * thus forever forcing us to keep these classes around.
+ *
+ * <b>DO NOT USE THIS CLASS!!!</b>
+ */
+class GenericNodeLineTypeCalculator extends BasicCalculator {
+ /**
+ * Creates a new GenericNodeLineTypeCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param m DOCUMENT ME!
+ */
+ GenericNodeLineTypeCalculator(String name, ObjectMapping m) {
+ super(name, m, NODE_LINETYPE);
+ }
+
+ /**
+ * Creates a new GenericNodeLineTypeCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param props DOCUMENT ME!
+ * @param baseKey DOCUMENT ME!
+ */
+ GenericNodeLineTypeCalculator(String name, Properties props, String baseKey) {
+ super(name, props, baseKey, NODE_LINETYPE);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/calculators/GenericNodeLineWidthCalculator.java b/application/src/main/java/cytoscape/visual/calculators/GenericNodeLineWidthCalculator.java
new file mode 100644
index 0000000..7bf788f
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/calculators/GenericNodeLineWidthCalculator.java
@@ -0,0 +1,43 @@
+package cytoscape.visual.calculators;
+
+import cytoscape.CyNetwork;
+import cytoscape.visual.parsers.FloatParser;
+import static cytoscape.visual.VisualPropertyType.NODE_LINE_WIDTH;
+
+import cytoscape.visual.mappings.ObjectMapping;
+
+import giny.model.Node;
+
+import java.util.Properties;
+
+
+/**
+ * This class exists ONLY to support legacy file formats. A VERY BAD PERSON
+ * decided to use the class name to identify calculators in property files,
+ * thus forever forcing us to keep these classes around.
+ *
+ * <b>DO NOT USE THIS CLASS!!!</b>
+ */
+class GenericNodeLineWidthCalculator extends BasicCalculator {
+ /**
+ * Creates a new GenericNodeLineWidthCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param m DOCUMENT ME!
+ */
+ GenericNodeLineWidthCalculator(String name, ObjectMapping m) {
+ super(name, m, NODE_LINE_WIDTH);
+ }
+
+ /**
+ * Creates a new GenericNodeLineWidthCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param props DOCUMENT ME!
+ * @param baseKey DOCUMENT ME!
+ */
+ GenericNodeLineWidthCalculator(String name, Properties props, String baseKey) {
+ super(name, props, baseKey, NODE_LINE_WIDTH);
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/visual/calculators/GenericNodeShapeCalculator.java b/application/src/main/java/cytoscape/visual/calculators/GenericNodeShapeCalculator.java
new file mode 100644
index 0000000..7947d76
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/calculators/GenericNodeShapeCalculator.java
@@ -0,0 +1,89 @@
+/*
+ File: GenericNodeShapeCalculator.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+//----------------------------------------------------------------------------
+// $Revision: 18673 $
+// $Date: 2009-12-05 01:10:20 +0100 (Sat, 05 Dec 2009) $
+// $Author: mes $
+//----------------------------------------------------------------------------
+package cytoscape.visual.calculators;
+
+import cytoscape.CyNetwork;
+
+import cytoscape.visual.Appearance;
+import cytoscape.visual.NodeShape;
+
+import static cytoscape.visual.VisualPropertyType.NODE_SHAPE;
+
+import cytoscape.visual.mappings.ObjectMapping;
+
+import cytoscape.visual.parsers.NodeShapeParser;
+
+import giny.model.Node;
+
+import java.util.Properties;
+
+
+/**
+ * This class exists ONLY to support legacy file formats. A VERY BAD PERSON
+ * decided to use the class name to identify calculators in property files,
+ * thus forever forcing us to keep these classes around.
+ *
+ * <b>DO NOT USE THIS CLASS!!!</b>
+ */
+class GenericNodeShapeCalculator extends BasicCalculator {
+ /**
+ * Creates a new GenericNodeShapeCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param m DOCUMENT ME!
+ */
+ GenericNodeShapeCalculator(String name, ObjectMapping m) {
+ super(name, m, NODE_SHAPE);
+ }
+
+ /**
+ * Creates a new GenericNodeShapeCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param props DOCUMENT ME!
+ * @param baseKey DOCUMENT ME!
+ */
+ GenericNodeShapeCalculator(String name, Properties props, String baseKey) {
+ super(name, props, baseKey, NODE_SHAPE);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/calculators/GenericNodeSizeCalculator.java b/application/src/main/java/cytoscape/visual/calculators/GenericNodeSizeCalculator.java
new file mode 100644
index 0000000..05a6deb
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/calculators/GenericNodeSizeCalculator.java
@@ -0,0 +1,110 @@
+/*
+ File: GenericNodeSizeCalculator.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+//----------------------------------------------------------------------------
+// $Revision: 18673 $
+// $Date: 2009-12-05 01:10:20 +0100 (Sat, 05 Dec 2009) $
+// $Author: mes $
+//----------------------------------------------------------------------------
+package cytoscape.visual.calculators;
+
+import cytoscape.CyNetwork;
+
+import cytoscape.visual.Appearance;
+import cytoscape.visual.VisualPropertyType;
+
+import cytoscape.visual.mappings.ObjectMapping;
+import giny.model.Node;
+
+import java.util.Properties;
+
+
+/**
+ * This class exists ONLY to support legacy file formats. A VERY BAD PERSON
+ * decided to use the class name to identify calculators in property files,
+ * thus forever forcing us to keep these classes around.
+ *
+ * <b>DO NOT USE THIS CLASS!!!</b>
+ */
+class GenericNodeSizeCalculator extends BasicCalculator {
+
+ /**
+ * Creates a new GenericNodeSizeCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param m DOCUMENT ME!
+ *
+ */
+ GenericNodeSizeCalculator(String name, ObjectMapping m) {
+ this(name, m, VisualPropertyType.NODE_SIZE);
+ }
+
+ /**
+ * Creates a new GenericNodeSizeCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param m DOCUMENT ME!
+ * @param type DOCUMENT ME!
+ */
+ GenericNodeSizeCalculator(String name, ObjectMapping m, VisualPropertyType type) {
+ super(name, m, type);
+ }
+
+ /**
+ * Creates a new GenericNodeSizeCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param props DOCUMENT ME!
+ * @param baseKey DOCUMENT ME!
+ */
+ GenericNodeSizeCalculator(String name, Properties props, String baseKey) {
+ this(name, props, baseKey, VisualPropertyType.NODE_SIZE);
+ }
+
+ /**
+ * Creates a new GenericNodeSizeCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param props DOCUMENT ME!
+ * @param baseKey DOCUMENT ME!
+ * @param type DOCUMENT ME!
+ */
+ GenericNodeSizeCalculator(String name, Properties props,
+ String baseKey, VisualPropertyType type) {
+ super(name, props, baseKey, type);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/calculators/GenericNodeToolTipCalculator.java b/application/src/main/java/cytoscape/visual/calculators/GenericNodeToolTipCalculator.java
new file mode 100644
index 0000000..2ba7209
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/calculators/GenericNodeToolTipCalculator.java
@@ -0,0 +1,88 @@
+/*
+ File: GenericNodeToolTipCalculator.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+//----------------------------------------------------------------------------
+// $Revision: 18673 $
+// $Date: 2009-12-05 01:10:20 +0100 (Sat, 05 Dec 2009) $
+// $Author: mes $
+//----------------------------------------------------------------------------
+package cytoscape.visual.calculators;
+
+import cytoscape.CyNetwork;
+
+import cytoscape.visual.Appearance;
+
+import static cytoscape.visual.VisualPropertyType.NODE_TOOLTIP;
+
+import cytoscape.visual.mappings.ObjectMapping;
+
+import cytoscape.visual.parsers.StringParser;
+
+import giny.model.Node;
+
+import java.util.Properties;
+
+
+/**
+ * This class exists ONLY to support legacy file formats. A VERY BAD PERSON
+ * decided to use the class name to identify calculators in property files,
+ * thus forever forcing us to keep these classes around.
+ *
+ * <b>DO NOT USE THIS CLASS!!!</b>
+ */
+class GenericNodeToolTipCalculator extends BasicCalculator {
+ /**
+ * Creates a new GenericNodeToolTipCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param m DOCUMENT ME!
+ */
+ GenericNodeToolTipCalculator(String name, ObjectMapping m) {
+ super(name, m, NODE_TOOLTIP);
+ }
+
+ /**
+ * Creates a new GenericNodeToolTipCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param props DOCUMENT ME!
+ * @param baseKey DOCUMENT ME!
+ */
+ GenericNodeToolTipCalculator(String name, Properties props, String baseKey) {
+ super(name, props, baseKey, NODE_TOOLTIP);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/calculators/GenericNodeUniformSizeCalculator.java b/application/src/main/java/cytoscape/visual/calculators/GenericNodeUniformSizeCalculator.java
new file mode 100644
index 0000000..60b6fc6
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/calculators/GenericNodeUniformSizeCalculator.java
@@ -0,0 +1,75 @@
+/*
+ File: GenericNodeUniformSizeCalculator.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+package cytoscape.visual.calculators;
+
+import static cytoscape.visual.VisualPropertyType.NODE_SIZE;
+
+import cytoscape.visual.mappings.ObjectMapping;
+
+import java.util.Properties;
+
+
+/**
+ * This class exists ONLY to support legacy file formats. A VERY BAD PERSON
+ * decided to use the class name to identify calculators in property files,
+ * thus forever forcing us to keep these classes around.
+ *
+ * <b>DO NOT USE THIS CLASS!!!</b>
+ */
+class GenericNodeUniformSizeCalculator extends BasicCalculator {
+ /**
+ * Creates a new GenericNodeUniformSizeCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param m DOCUMENT ME!
+ */
+ GenericNodeUniformSizeCalculator(String name, ObjectMapping m) {
+ super(name, m, NODE_SIZE);
+ }
+
+ /**
+ * Creates a new GenericNodeUniformSizeCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param props DOCUMENT ME!
+ * @param baseKey DOCUMENT ME!
+ */
+ GenericNodeUniformSizeCalculator(String name, Properties props, String baseKey) {
+ super(name, props, baseKey, NODE_SIZE);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/calculators/GenericNodeWidthCalculator.java b/application/src/main/java/cytoscape/visual/calculators/GenericNodeWidthCalculator.java
new file mode 100644
index 0000000..4d14141
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/calculators/GenericNodeWidthCalculator.java
@@ -0,0 +1,75 @@
+/*
+ File: GenericNodeWidthCalculator.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+package cytoscape.visual.calculators;
+
+import static cytoscape.visual.VisualPropertyType.NODE_WIDTH;
+
+import cytoscape.visual.mappings.ObjectMapping;
+
+import java.util.Properties;
+
+
+/**
+ * This class exists ONLY to support legacy file formats. A VERY BAD PERSON
+ * decided to use the class name to identify calculators in property files,
+ * thus forever forcing us to keep these classes around.
+ *
+ * <b>DO NOT USE THIS CLASS!!!</b>
+ */
+class GenericNodeWidthCalculator extends BasicCalculator {
+ /**
+ * Creates a new GenericNodeWidthCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param m DOCUMENT ME!
+ */
+ GenericNodeWidthCalculator(String name, ObjectMapping m) {
+ super(name, m, NODE_WIDTH);
+ }
+
+ /**
+ * Creates a new GenericNodeWidthCalculator object.
+ *
+ * @param name DOCUMENT ME!
+ * @param props DOCUMENT ME!
+ * @param baseKey DOCUMENT ME!
+ */
+ GenericNodeWidthCalculator(String name, Properties props, String baseKey) {
+ super(name, props, baseKey, NODE_WIDTH);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/calculators/package.html b/application/src/main/java/cytoscape/visual/calculators/package.html
new file mode 100644
index 0000000..34a771f
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/calculators/package.html
@@ -0,0 +1,15 @@
+<html>
+<head>
+ <!-- $Revision: 5801 $
+ $Date: 2004-04-20 01:53:47 +0200 (Tue, 20 Apr 2004) $
+ $Author: amarkiel $
+ -->
+</head>
+
+<body>
+Objects that calculate from the data attributes the value for one
+visual attribute, such as color, shape, or size. These Calculators
+use Mappings to actually translate graph attributes into visual attributes.
+</body>
+</html>
+
diff --git a/application/src/main/java/cytoscape/visual/converter/ColorConverter.java b/application/src/main/java/cytoscape/visual/converter/ColorConverter.java
new file mode 100644
index 0000000..f92e04f
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/converter/ColorConverter.java
@@ -0,0 +1,23 @@
+package cytoscape.visual.converter;
+
+import java.awt.Color;
+
+import cytoscape.util.ColorUtil;
+
+public class ColorConverter implements ValueToStringConverter {
+
+
+ public String toString(Object value) {
+
+ if(value instanceof Color)
+ return ColorUtil.getColorAsText((Color) value);
+ else
+ return "";
+ }
+
+
+ public Class<?> getType() {
+ return Color.class;
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/visual/converter/FontConverter.java b/application/src/main/java/cytoscape/visual/converter/FontConverter.java
new file mode 100644
index 0000000..f772882
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/converter/FontConverter.java
@@ -0,0 +1,37 @@
+package cytoscape.visual.converter;
+
+import java.awt.Font;
+
+public class FontConverter implements ValueToStringConverter {
+
+
+ public String toString(Object value) {
+ if (value instanceof Font)
+ return getFontStringValue((Font) value);
+ else
+ return "";
+ }
+
+
+ public Class<?> getType() {
+ return Font.class;
+ }
+
+ private String getFontStringValue(final Font f) {
+ String name = f.getName();
+ int style = f.getStyle();
+ String styleString = "plain";
+
+ if (style == Font.BOLD)
+ styleString = "bold";
+ else if (style == Font.ITALIC)
+ styleString = "italic";
+ else if (style == (Font.BOLD | Font.ITALIC))
+ styleString = "bold|italic";
+
+ int size = f.getSize();
+ String sizeString = Integer.toString(size);
+
+ return name + "," + styleString + "," + sizeString;
+ }
+}
\ No newline at end of file
diff --git a/application/src/main/java/cytoscape/visual/converter/NodeShapeConverter.java b/application/src/main/java/cytoscape/visual/converter/NodeShapeConverter.java
new file mode 100644
index 0000000..2eebdf6
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/converter/NodeShapeConverter.java
@@ -0,0 +1,20 @@
+package cytoscape.visual.converter;
+
+import cytoscape.visual.NodeShape;
+
+public class NodeShapeConverter implements ValueToStringConverter {
+
+
+ public String toString(Object value) {
+ if(value instanceof NodeShape)
+ return NodeShape.getNodeShapeText((NodeShape) value);
+ else
+ return "";
+ }
+
+
+ public Class<?> getType() {
+ return NodeShape.class;
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/visual/converter/ObjectPositionConverter.java b/application/src/main/java/cytoscape/visual/converter/ObjectPositionConverter.java
new file mode 100644
index 0000000..96aa587
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/converter/ObjectPositionConverter.java
@@ -0,0 +1,20 @@
+package cytoscape.visual.converter;
+
+import giny.view.ObjectPosition;
+
+public class ObjectPositionConverter implements ValueToStringConverter {
+
+ public String toString(Object value) {
+
+ if(value instanceof ObjectPosition)
+ return ((ObjectPosition) value).shortString();
+ else
+ return "";
+ }
+
+
+ public Class<?> getType() {
+ return ObjectPosition.class;
+ }
+
+}
\ No newline at end of file
diff --git a/application/src/main/java/cytoscape/visual/converter/ValueToStringConverter.java b/application/src/main/java/cytoscape/visual/converter/ValueToStringConverter.java
new file mode 100644
index 0000000..130bab1
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/converter/ValueToStringConverter.java
@@ -0,0 +1,25 @@
+package cytoscape.visual.converter;
+
+/**
+ * Provide special type of toString for the given class.
+ *
+ * @author kono
+ *
+ */
+public interface ValueToStringConverter {
+
+ /**
+ * Convert given value to VizMap compatible string.
+ *
+ * @param value
+ * @return VizMap conversion of given object. Otherwise, returns empty String.
+ */
+ public String toString(Object value);
+
+
+ /**
+ * Class supported by this converter.
+ * @return Class of supported type.
+ */
+ public Class<?> getType();
+}
diff --git a/application/src/main/java/cytoscape/visual/converter/ValueToStringConverterManager.java b/application/src/main/java/cytoscape/visual/converter/ValueToStringConverterManager.java
new file mode 100644
index 0000000..5b7c25f
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/converter/ValueToStringConverterManager.java
@@ -0,0 +1,64 @@
+package cytoscape.visual.converter;
+
+import java.util.HashMap;
+import java.util.Map;
+
+import ding.view.ObjectPositionImpl;
+
+
+/**
+ * Replacement for ObjectToString.
+ * Manages special "toString()" equivalent method for specific Classes.
+ *
+ * Users can add special converter when necessary.
+ * If not specified, toString() will be used for the object type.
+ *
+ * @author kono
+ *
+ */
+public class ValueToStringConverterManager {
+
+ public static final ValueToStringConverterManager manager = new ValueToStringConverterManager();
+
+
+ private final Map<Class<?>, ValueToStringConverter> converters;
+
+ private ValueToStringConverterManager() {
+ converters = new HashMap<Class<?>, ValueToStringConverter>();
+
+ registerDefaultConverters();
+ }
+
+ public void register(ValueToStringConverter converter) {
+ this.converters.put(converter.getType(), converter);
+ }
+
+ public String toString(final Object value) {
+ if(value == null)
+ return "";
+
+ final ValueToStringConverter converter = this.converters.get(value.getClass());
+ if(converter == null)
+ return value.toString();
+ else
+ return converter.toString(value);
+ }
+
+ private void registerDefaultConverters() {
+ final ColorConverter color = new ColorConverter();
+ converters.put(color.getType(), color);
+
+ final NodeShapeConverter nodeShape = new NodeShapeConverter();
+ converters.put(nodeShape.getType(), nodeShape);
+
+ final ObjectPositionConverter objectPosition = new ObjectPositionConverter();
+ converters.put(objectPosition.getType(), objectPosition);
+ // This is a hack... Need to use interface as the key for complete solution.
+ converters.put(ObjectPositionImpl.class, objectPosition);
+
+ final FontConverter font = new FontConverter();
+ converters.put(font.getType(), font);
+
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/visual/customgraphic/CustomGraphicsManager.java b/application/src/main/java/cytoscape/visual/customgraphic/CustomGraphicsManager.java
new file mode 100644
index 0000000..744e0b4
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/customgraphic/CustomGraphicsManager.java
@@ -0,0 +1,374 @@
+package cytoscape.visual.customgraphic;
+
+import java.awt.image.BufferedImage;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Properties;
+import java.util.Set;
+import java.util.SortedSet;
+import java.util.TreeSet;
+import java.util.concurrent.CompletionService;
+import java.util.concurrent.ConcurrentHashMap;
+import java.util.concurrent.ExecutionException;
+import java.util.concurrent.ExecutorCompletionService;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
+import java.util.concurrent.Future;
+import java.util.concurrent.TimeUnit;
+
+import cytoscape.Cytoscape;
+import cytoscape.CytoscapeInit;
+import cytoscape.logger.CyLogger;
+import cytoscape.task.ui.JTaskConfig;
+import cytoscape.task.util.TaskManager;
+import cytoscape.visual.SubjectBase;
+import cytoscape.visual.customgraphic.impl.AbstractDCustomGraphics;
+import cytoscape.visual.customgraphic.impl.bitmap.URLImageCustomGraphics;
+import cytoscape.visual.customgraphic.impl.vector.GradientOvalLayer;
+import cytoscape.visual.customgraphic.impl.vector.GradientRoundRectangleLayer;
+
+public class CustomGraphicsManager extends SubjectBase implements
+ PropertyChangeListener {
+
+ private static final CyLogger logger = CyLogger.getLogger();
+
+ private static final int TIMEOUT = 1000;
+ private static final int NUM_THREADS = 8;
+
+ private static final String IMAGE_DIR_NAME = "images";
+
+ // For image I/O, PNG is used as bitmap image format.
+ private static final String IMAGE_EXT = "png";
+
+ private final ExecutorService imageLoaderService;
+
+ private final Map<Long, CyCustomGraphics> graphicsMap = new ConcurrentHashMap<Long, CyCustomGraphics>();
+
+ // URL to hash code map. For images associated with URL.
+ private final Map<URL, Long> sourceMap = new ConcurrentHashMap<URL, Long>();
+
+ // Null Object
+ private static final CyCustomGraphics NULL = NullCustomGraphics
+ .getNullObject();
+
+ // Default vectors
+ private static final Class<?>[] DEF_VECTORS = {
+ GradientRoundRectangleLayer.class, GradientOvalLayer.class };
+
+ public static final String METADATA_FILE = "image_metadata.props";
+
+ private File imageHomeDirectory;
+
+ private final Map<CyCustomGraphics,Boolean> isUsedCustomGraphics;
+
+ /**
+ * Creates an image pool object and restore existing images from user
+ * resource directory.
+ */
+ public CustomGraphicsManager() {
+
+ this.isUsedCustomGraphics = new HashMap<CyCustomGraphics, Boolean>();
+ this.imageHomeDirectory = new File(CytoscapeInit.getConfigDirectory(), IMAGE_DIR_NAME);
+
+ // For loading images in parallel.
+ this.imageLoaderService = Executors.newFixedThreadPool(NUM_THREADS);
+
+ graphicsMap.put(NULL.getIdentifier(), NULL);
+ this.isUsedCustomGraphics.put(NULL, false);
+ restoreDefaultVectorImageObjects();
+
+ Cytoscape.getPropertyChangeSupport().addPropertyChangeListener(Cytoscape.CYTOSCAPE_EXIT, this);
+ }
+
+ /**
+ * Restore images from .cytoscape/images dir.
+ */
+ public void restoreImages() {
+ final CompletionService<BufferedImage> cs = new ExecutorCompletionService<BufferedImage>(
+ imageLoaderService);
+
+ imageHomeDirectory.mkdir();
+
+ long startTime = System.currentTimeMillis();
+
+ // Load metadata first.
+ final Properties prop = new Properties();
+ try {
+ prop.load(new FileInputStream(new File(imageHomeDirectory,
+ METADATA_FILE)));
+ logger.info("Custom Graphics Image property file loaded from: "
+ + imageHomeDirectory);
+ } catch (Exception e) {
+ logger.warning("Custom Graphics Metadata was not found. This is normal for the first time.");
+ // Restore process is not necessary.
+ return;
+ }
+
+ if (this.imageHomeDirectory != null && imageHomeDirectory.isDirectory()) {
+ final File[] imageFiles = imageHomeDirectory.listFiles();
+ final Map<Future<BufferedImage>, String> fMap = new HashMap<Future<BufferedImage>, String>();
+ final Map<Future<BufferedImage>, Set<String>> metatagMap = new HashMap<Future<BufferedImage>, Set<String>>();
+ try {
+ for (File file : imageFiles) {
+ if (file.toString().endsWith(IMAGE_EXT) == false)
+ continue;
+
+ final String fileName = file.getName();
+ final String key = fileName.split("\\.")[0];
+ final String value = prop.getProperty(key);
+
+ final String[] imageProps = value.split(",");
+ if (imageProps == null || imageProps.length < 2)
+ continue;
+
+ String name = imageProps[2];
+ if (name.contains("___"))
+ name = name.replace("___", ",");
+
+ Future<BufferedImage> f = cs.submit(new LoadImageTask(file
+ .toURI().toURL()));
+ fMap.put(f, name);
+
+ String tagStr = null;
+ if (imageProps.length > 3) {
+ tagStr = imageProps[3];
+ final Set<String> tags = new TreeSet<String>();
+ String[] tagParts = tagStr.split("\\"
+ + AbstractDCustomGraphics.LIST_DELIMITER);
+ for (String tag : tagParts)
+ tags.add(tag.trim());
+
+ metatagMap.put(f, tags);
+ }
+ }
+ for (File file : imageFiles) {
+ if (file.toString().endsWith(IMAGE_EXT) == false)
+ continue;
+ final Future<BufferedImage> f = cs.take();
+ final BufferedImage image = f.get();
+ if (image == null)
+ continue;
+
+ final CyCustomGraphics cg = new URLImageCustomGraphics(
+ fMap.get(f), image);
+ if (cg instanceof Taggable && metatagMap.get(f) != null)
+ ((Taggable) cg).getTags().addAll(metatagMap.get(f));
+
+ graphicsMap.put(cg.getIdentifier(), cg);
+ this.isUsedCustomGraphics.put(cg, false);
+
+ try {
+ final URL source = new URL(fMap.get(f));
+ if (source != null)
+ sourceMap.put(source, cg.getIdentifier());
+ } catch (MalformedURLException me) {
+ continue;
+ }
+ }
+
+ } catch (IOException ioe) {
+ ioe.printStackTrace();
+ } catch (InterruptedException e) {
+ e.printStackTrace();
+ } catch (ExecutionException e) {
+ e.printStackTrace();
+ }
+ }
+
+ try {
+ imageLoaderService.shutdown();
+ imageLoaderService.awaitTermination(TIMEOUT, TimeUnit.SECONDS);
+ } catch (InterruptedException e) {
+ e.printStackTrace();
+ }
+
+ long endTime = System.currentTimeMillis();
+ double sec = (endTime - startTime) / (1000.0);
+ logger.info("Image loading process finished in " + sec + " sec.");
+ logger.info("Currently, " + (graphicsMap.size() - 1)
+ + " images are available.");
+ }
+
+ private void restoreDefaultVectorImageObjects() {
+
+ for (Class<?> cls : DEF_VECTORS) {
+
+ try {
+ Object obj = cls.newInstance();
+ if (obj instanceof CyCustomGraphics) {
+ graphicsMap.put( ((CyCustomGraphics) obj).getIdentifier(), (CyCustomGraphics) obj);
+ this.isUsedCustomGraphics.put((CyCustomGraphics) obj, false);
+ }
+ } catch (InstantiationException e) {
+ throw new RuntimeException(e);
+ } catch (IllegalAccessException e) {
+ throw new RuntimeException(e);
+ }
+ }
+
+ }
+
+ /**
+ * Add a custom graphics to current session.
+ *
+ * @param hash
+ * : Hasn code of image object
+ * @param graphics
+ * : Actual custom graphics object
+ * @param source
+ * : Source URL of graphics (if exists. Can be null)
+ */
+ public void addGraphics(final CyCustomGraphics graphics, final URL source) {
+ if (graphics == null)
+ throw new IllegalArgumentException(
+ "Custom Graphics and its ID should not be null.");
+
+ // Souce URL is an optional field.
+ if (source != null)
+ sourceMap.put(source, graphics.getIdentifier());
+
+ graphicsMap.put(graphics.getIdentifier(), graphics);
+ this.isUsedCustomGraphics.put(graphics, false);
+ }
+
+ /**
+ * Remove graphics from current session (memory).
+ *
+ * @param id
+ * : ID of graphics (hash code)
+ */
+ public void removeGraphics(final Long id) {
+ final CyCustomGraphics cg = graphicsMap.get(id);
+ if (cg != null && cg != NULL) {
+ graphicsMap.remove(id);
+ this.isUsedCustomGraphics.remove(cg);
+ }
+ }
+
+ /**
+ * Get a Custom Graphics by integer ID.
+ *
+ * @param hash
+ * Hash code of Custom Graphics object
+ *
+ * @return Custom Graphics if exists. Otherwise, null.
+ *
+ */
+ public CyCustomGraphics getByID(Long id) {
+ return graphicsMap.get(id);
+ }
+
+ /**
+ * Get Custom Graphics by source URL. Images without source cannot be
+ * retreved by this method.
+ *
+ * @param sourceURL
+ * @return
+ */
+ public CyCustomGraphics getBySourceURL(URL sourceURL) {
+ final Long id = sourceMap.get(sourceURL);
+ if (id != null)
+ return graphicsMap.get(id);
+ else
+ return null;
+ }
+
+ /**
+ * Get a collection of all Custom Graphics in current session.
+ *
+ * @return
+ */
+ public Collection<CyCustomGraphics> getAll() {
+ return graphicsMap.values();
+ }
+
+ /**
+ * Remove all custom graphics from memory.
+ */
+ public void removeAll() {
+ this.graphicsMap.clear();
+ this.sourceMap.clear();
+ this.isUsedCustomGraphics.clear();
+
+ // Null Graphics should not be removed.
+ this.graphicsMap.put(NULL.getIdentifier(), NULL);
+
+ }
+
+ /**
+ * Convert current list of custom graphics into Property object.
+ *
+ * @return
+ */
+ public Properties getMetadata() {
+ // Null graphics object should not be in this property.
+ graphicsMap.remove(NULL.getIdentifier());
+
+ final Properties props = new Properties();
+ // Use hash code as the key, and value will be a string returned by
+ // toString() method.
+ // This means all CyCustomGraphics implementations should have a special
+ // toString method.
+ for (final CyCustomGraphics graphics : graphicsMap.values())
+ props.setProperty(graphics.getIdentifier().toString(),
+ graphics.toString());
+ graphicsMap.put(NULL.getIdentifier(), NULL);
+ return props;
+ }
+
+ /**
+ * Save images to local disk when exiting from Cytoscape.
+ */
+ public void propertyChange(PropertyChangeEvent evt) {
+ // Persist images
+ logger.info("Saving images to: " + imageHomeDirectory);
+
+ // Create Task
+ final PersistImageTask task = new PersistImageTask(imageHomeDirectory);
+
+ // Configure JTask Dialog Pop-Up Box
+ final JTaskConfig jTaskConfig = new JTaskConfig();
+
+ jTaskConfig.displayCancelButton(false);
+ jTaskConfig.setOwner(Cytoscape.getDesktop());
+ jTaskConfig.displayCloseButton(false);
+ jTaskConfig.displayStatus(true);
+ jTaskConfig.setAutoDispose(true);
+
+ // Execute Task in New Thread; pop open JTask Dialog Box.
+ TaskManager.executeTask(task, jTaskConfig);
+
+ logger.info("Image saving process finished.");
+ }
+
+ public SortedSet<Long> getIDSet() {
+ return new TreeSet<Long>(graphicsMap.keySet());
+ }
+
+ public Boolean isUsedInCurrentSession(final CyCustomGraphics graphics) {
+ if(graphics == null || this.isUsedCustomGraphics.containsKey(graphics) == false)
+ return false;
+
+ return isUsedCustomGraphics.get(graphics);
+ }
+
+ public void setUsedInCurrentSession(final CyCustomGraphics graphics, final Boolean isUsed) {
+ if(isUsed == null || graphics == null)
+ return;
+
+ if(this.isUsedCustomGraphics.containsKey(graphics) == false){
+ // Just ignore.
+ return;
+ }
+
+ this.isUsedCustomGraphics.put(graphics, isUsed);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/customgraphic/CustomGraphicsPropertyImpl.java b/application/src/main/java/cytoscape/visual/customgraphic/CustomGraphicsPropertyImpl.java
new file mode 100644
index 0000000..4bebc24
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/customgraphic/CustomGraphicsPropertyImpl.java
@@ -0,0 +1,38 @@
+package cytoscape.visual.customgraphic;
+
+import cytoscape.visual.customgraphic.impl.vector.CustomGraphicsProperty;
+
+
+public class CustomGraphicsPropertyImpl<T> implements
+ CustomGraphicsProperty<T> {
+
+ private T value;
+ private final T defaultValue;
+
+ public CustomGraphicsPropertyImpl(final T defaultValue) {
+ this.defaultValue = defaultValue;
+ this.value = defaultValue;
+ }
+
+
+
+ public T getDefaultValue() {
+ return defaultValue;
+ }
+
+
+
+ public T getValue() {
+ return value;
+ }
+
+
+
+ public void setValue(Object value) {
+ if(this.value.getClass().isAssignableFrom(value.getClass()) == false)
+ throw new IllegalArgumentException("The value type is not compatible.");
+ else
+ this.value = (T) value;
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/visual/customgraphic/CustomGraphicsUtil.java b/application/src/main/java/cytoscape/visual/customgraphic/CustomGraphicsUtil.java
new file mode 100644
index 0000000..999acad
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/customgraphic/CustomGraphicsUtil.java
@@ -0,0 +1,33 @@
+package cytoscape.visual.customgraphic;
+
+import java.awt.Image;
+
+public class CustomGraphicsUtil {
+
+ public static Image getResizedImage(Image original, final Integer w, final Integer h, boolean keepAspectRatio) {
+ if(original == null)
+ throw new IllegalArgumentException("Original image cannot be null.");
+
+ if(w == null && h == null)
+ return original;
+
+ final int currentW = original.getWidth(null);
+ final int currentH = original.getHeight(null);
+ float ratio;
+ int converted;
+
+ if (keepAspectRatio == false)
+ return original.getScaledInstance(w, h, Image.SCALE_AREA_AVERAGING);
+ else if (h == null) {
+ ratio = ((float) currentH) / ((float) currentW);
+ converted = (int) (w * ratio);
+ return original.getScaledInstance(w, converted, Image.SCALE_AREA_AVERAGING);
+ } else {
+ ratio = ((float) currentW) / ((float) currentH);
+ converted = (int) (h * ratio);
+ return original.getScaledInstance(converted, h, Image.SCALE_AREA_AVERAGING);
+ }
+
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/visual/customgraphic/CyCustomGraphics.java b/application/src/main/java/cytoscape/visual/customgraphic/CyCustomGraphics.java
new file mode 100644
index 0000000..0d12317
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/customgraphic/CyCustomGraphics.java
@@ -0,0 +1,105 @@
+package cytoscape.visual.customgraphic;
+
+import giny.view.ObjectPosition;
+
+import java.awt.Image;
+import java.util.List;
+
+public interface CyCustomGraphics {
+
+ /**
+ * Immutable session-unique identifier of image generated in constructor.
+ *
+ * NOT globally unique. Uniqueness is guaranteed in a session.
+ *
+ * @return Immutable ID as Long.
+ */
+ public Long getIdentifier();
+
+ /**
+ * Display name is a simple description of this image object.
+ * May not be unique and mutable.
+ *
+ * @return display name as String.
+ */
+ public String getDisplayName();
+
+
+ /**
+ * Set human readable display name.
+ *
+ * @param displayName
+ */
+ public void setDisplayName(final String displayName);
+
+
+ /**
+ * Get layers belongs to this object.
+ * In current Implementation, ti's always Ding's CustomGraphic object.
+ * Ordered by Z-Order value.
+ *
+ * @return Collection of layer objects (in this version, it's CustomGraphics in Ding)
+ *
+ */
+ public List<Layer> getLayers();
+
+
+ /**
+ * Returns width of current object.
+ *
+ * @return
+ */
+ public int getWidth();
+
+
+ /**
+ * Returns height of current object.
+ *
+ * @return
+ */
+ public int getHeight();
+
+
+ /**
+ * Set width of Custom Graphics.
+ *
+ * @param width
+ */
+ public void setWidth(final int width);
+
+ /**
+ * Set height of Custom Graphics.
+ *
+ * @param height
+ */
+ public void setHeight(final int height);
+
+ public float getFitRatio();
+ public void setFitRatio(float ratio);
+
+ /**
+ * From layers of graphics objects, render scaled Image object.
+ * Usually done by Java2D low level code.
+ *
+ * Usually, the image returned by this method is used in GUI components (as icons).
+ *
+ * @return rendered image object.
+ */
+ public Image getRenderedImage();
+
+
+ /**
+ * Set posiiton of this graphics.
+ *
+ * @param position
+ */
+ public void setPosition(final ObjectPosition position);
+
+
+ /**
+ * Current position
+ *
+ * @return position of graphics as ObjectPosition.
+ */
+ public ObjectPosition getPosition();
+}
diff --git a/application/src/main/java/cytoscape/visual/customgraphic/CyCustomGraphicsParser.java b/application/src/main/java/cytoscape/visual/customgraphic/CyCustomGraphicsParser.java
new file mode 100644
index 0000000..03ca357
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/customgraphic/CyCustomGraphicsParser.java
@@ -0,0 +1,7 @@
+package cytoscape.visual.customgraphic;
+
+public interface CyCustomGraphicsParser {
+ public CyCustomGraphics getInstance(final String entry);
+
+ public Class<? extends CyCustomGraphics> getTargetClass();
+}
diff --git a/application/src/main/java/cytoscape/visual/customgraphic/CyCustomGraphicsParserFactory.java b/application/src/main/java/cytoscape/visual/customgraphic/CyCustomGraphicsParserFactory.java
new file mode 100644
index 0000000..5b05e59
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/customgraphic/CyCustomGraphicsParserFactory.java
@@ -0,0 +1,8 @@
+package cytoscape.visual.customgraphic;
+
+public interface CyCustomGraphicsParserFactory {
+ public CyCustomGraphicsParser getParser(final String customGraphicsClassName);
+
+ public void registerParser(Class<? extends CyCustomGraphics> cgClass,
+ CyCustomGraphicsParser parser);
+}
diff --git a/application/src/main/java/cytoscape/visual/customgraphic/DefaultCyCustomGraphicsParser.java b/application/src/main/java/cytoscape/visual/customgraphic/DefaultCyCustomGraphicsParser.java
new file mode 100644
index 0000000..2752ff2
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/customgraphic/DefaultCyCustomGraphicsParser.java
@@ -0,0 +1,64 @@
+package cytoscape.visual.customgraphic;
+
+import java.lang.reflect.Constructor;
+import java.lang.reflect.InvocationTargetException;
+
+import cytoscape.Cytoscape;
+
+public class DefaultCyCustomGraphicsParser implements CyCustomGraphicsParser {
+
+ public CyCustomGraphics getInstance(String entry) {
+ // Check this is URL or not
+ if (entry == null)
+ return null;
+
+ String[] parts = entry.split(",");
+ if (parts == null || parts.length < 3)
+ return null;
+
+ final String className = parts[0];
+ final Long id = Long.parseLong(parts[1]);
+ final String name = parts[2];
+
+ CyCustomGraphics cg = null;
+
+ // Create new one by reflection
+ try {
+ final Class<?> cls = Class.forName(className);
+ final Constructor<?> ct = cls.getConstructor(Long.class,
+ String.class);
+ cg = (CyCustomGraphics) ct.newInstance(id, name);
+ cg.setDisplayName(parts[2]);
+ Cytoscape.getVisualMappingManager().getCustomGraphicsManager()
+ .addGraphics(cg, null);
+ } catch (ClassNotFoundException e) {
+ e.printStackTrace();
+ return null;
+ } catch (InstantiationException e) {
+ e.printStackTrace();
+ return null;
+ } catch (IllegalAccessException e) {
+ e.printStackTrace();
+ return null;
+ } catch (SecurityException e) {
+ e.printStackTrace();
+ return null;
+ } catch (NoSuchMethodException e) {
+ e.printStackTrace();
+ return null;
+ } catch (IllegalArgumentException e) {
+ e.printStackTrace();
+ return null;
+ } catch (InvocationTargetException e) {
+ e.printStackTrace();
+ return null;
+ }
+
+ return cg;
+ }
+
+ public Class<? extends CyCustomGraphics> getTargetClass() {
+ return null;
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/visual/customgraphic/IDGenerator.java b/application/src/main/java/cytoscape/visual/customgraphic/IDGenerator.java
new file mode 100644
index 0000000..2984a1c
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/customgraphic/IDGenerator.java
@@ -0,0 +1,27 @@
+package cytoscape.visual.customgraphic;
+
+public class IDGenerator {
+
+ private static IDGenerator generator = new IDGenerator();
+
+ public static IDGenerator getIDGenerator() {
+ return generator;
+ }
+
+
+ private Long globalCounter;
+
+ public IDGenerator() {
+ globalCounter = 0l;
+ }
+
+
+ public synchronized Long getNextId() {
+ return ++globalCounter;
+ }
+
+
+ public void initCounter(Long currentMax) {
+ this.globalCounter = currentMax;
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/customgraphic/ImageUtil.java b/application/src/main/java/cytoscape/visual/customgraphic/ImageUtil.java
new file mode 100644
index 0000000..eb0e706
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/customgraphic/ImageUtil.java
@@ -0,0 +1,39 @@
+package cytoscape.visual.customgraphic;
+
+import java.awt.Component;
+import java.awt.Image;
+import java.awt.MediaTracker;
+import java.awt.image.BufferedImage;
+import java.awt.image.ColorModel;
+import java.awt.image.PixelGrabber;
+import java.awt.image.WritableRaster;
+import java.util.Hashtable;
+
+public class ImageUtil {
+
+
+ public static BufferedImage toBufferedImage(final Image image) throws InterruptedException {
+ if (image instanceof BufferedImage)
+ return (BufferedImage) image;
+
+ MediaTracker tracker = new MediaTracker(new Component() {
+ });
+ tracker.addImage(image, 0);
+ tracker.waitForAll();
+
+ PixelGrabber pixelGrabber = new PixelGrabber(image, 0, 0, -1, -1, false);
+ pixelGrabber.grabPixels();
+ ColorModel cm = pixelGrabber.getColorModel();
+
+ final int w = pixelGrabber.getWidth();
+ final int h = pixelGrabber.getHeight();
+ WritableRaster raster = cm.createCompatibleWritableRaster(w, h);
+ final BufferedImage renderedImage = new BufferedImage(cm, raster, cm
+ .isAlphaPremultiplied(), new Hashtable());
+ renderedImage.getRaster().setDataElements(0, 0, w, h,
+ pixelGrabber.getPixels());
+
+ return renderedImage;
+
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/customgraphic/Layer.java b/application/src/main/java/cytoscape/visual/customgraphic/Layer.java
new file mode 100644
index 0000000..3377e1e
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/customgraphic/Layer.java
@@ -0,0 +1,22 @@
+package cytoscape.visual.customgraphic;
+
+
+/**
+ * Wrapper for actual implementations of layers.
+ * In current version, it's always CustomGraphic
+ *
+ * @author kono
+ *
+ */
+public interface Layer {
+
+ /**
+ * Each layer has immutable Z-Order value for rendering.
+ * This method returens the value as int.
+ *
+ * @return
+ */
+ public int getZorder();
+
+ public Object getLayerObject();
+}
diff --git a/application/src/main/java/cytoscape/visual/customgraphic/LoadImageTask.java b/application/src/main/java/cytoscape/visual/customgraphic/LoadImageTask.java
new file mode 100644
index 0000000..1a4b32b
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/customgraphic/LoadImageTask.java
@@ -0,0 +1,25 @@
+package cytoscape.visual.customgraphic;
+
+import java.awt.image.BufferedImage;
+import java.net.URL;
+import java.util.concurrent.Callable;
+
+import javax.imageio.ImageIO;
+
+public class LoadImageTask implements Callable<BufferedImage> {
+
+ private final URL imageURL;
+
+ public LoadImageTask(final URL imageURL) {
+ this.imageURL = imageURL;
+ }
+
+
+ public BufferedImage call() throws Exception {
+ if (imageURL == null)
+ throw new IllegalStateException("URL string cannot be null.");
+
+ return ImageIO.read(imageURL);
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/visual/customgraphic/NullCustomGraphics.java b/application/src/main/java/cytoscape/visual/customgraphic/NullCustomGraphics.java
new file mode 100644
index 0000000..4109853
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/customgraphic/NullCustomGraphics.java
@@ -0,0 +1,29 @@
+package cytoscape.visual.customgraphic;
+
+import cytoscape.visual.customgraphic.impl.AbstractDCustomGraphics;
+
+/**
+ * Null object for Custom Graphics. This is used to reset custom graphics on
+ * node views.
+ *
+ * @author kono
+ *
+ */
+public class NullCustomGraphics extends AbstractDCustomGraphics {
+
+ static final CyCustomGraphics NULL = new NullCustomGraphics();
+
+ public static CyCustomGraphics getNullObject() {
+ return NULL;
+ }
+
+ private static final String NAME = "[ Remove Graphics ]";
+
+ public NullCustomGraphics() {
+ super(NAME);
+ }
+
+ public String toString() {
+ return this.getClass().getCanonicalName();
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/customgraphic/PersistImageTask.java b/application/src/main/java/cytoscape/visual/customgraphic/PersistImageTask.java
new file mode 100644
index 0000000..76eca37
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/customgraphic/PersistImageTask.java
@@ -0,0 +1,131 @@
+package cytoscape.visual.customgraphic;
+
+import java.awt.Image;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
+import java.util.concurrent.TimeUnit;
+
+import cytoscape.Cytoscape;
+import cytoscape.logger.CyLogger;
+import cytoscape.task.Task;
+import cytoscape.task.TaskMonitor;
+import cytoscape.visual.customgraphic.impl.bitmap.URLImageCustomGraphics;
+
+public class PersistImageTask implements Task {
+ private File location;
+ private TaskMonitor taskMonitor;
+
+ private static final int TIMEOUT = 1000;
+ private static final int NUM_THREADS = 4;
+
+ private static final CyLogger logger = CyLogger.getLogger();
+
+ /**
+ * Constructor.<br>
+ *
+ * @param fileName
+ * Absolute path to the Session file.
+ */
+ protected PersistImageTask(File location) {
+ this.location = location;
+ }
+
+ /**
+ * Execute task.<br>
+ */
+ public void run() {
+ taskMonitor
+ .setStatus("Saving image library to your local disk.\n\nPlease wait...");
+ taskMonitor.setPercentCompleted(-1);
+
+ // Does the directory exist?
+ if (!location.exists()) {
+ // No, create it
+ if (!location.mkdir()) {
+ logger.warning("Unable to create image library directory: "+location);
+ return;
+ }
+ }
+ // Remove all existing files
+ final File[] files = location.listFiles();
+ if (files != null && files.length > 0) {
+ for (File old : files)
+ old.delete();
+ }
+
+ final long startTime = System.currentTimeMillis();
+ final CustomGraphicsManager pool = Cytoscape.getVisualMappingManager()
+ .getCustomGraphicsManager();
+
+ final ExecutorService exService = Executors
+ .newFixedThreadPool(NUM_THREADS);
+
+ for (CyCustomGraphics cg : pool.getAll()) {
+
+ // Save ONLY bitmap image Custom Graphics.
+ if (cg instanceof NullCustomGraphics
+ || cg instanceof URLImageCustomGraphics == false)
+ continue;
+
+ final Image img = cg.getRenderedImage();
+ if (img != null) {
+ try {
+ exService.submit(new SaveImageTask(location, cg.getIdentifier().toString(),
+ ImageUtil.toBufferedImage(img)));
+ } catch (Exception e) {
+ logger.warning("Unable to save images", e);
+ }
+ }
+
+ }
+
+ try {
+ exService.shutdown();
+ exService.awaitTermination(TIMEOUT, TimeUnit.SECONDS);
+ } catch (InterruptedException e) {
+ taskMonitor.setException(e, "Image saving task interrupted.");
+ }
+
+ try {
+ pool.getMetadata().store(new FileOutputStream(new File(location, CustomGraphicsManager.METADATA_FILE)),
+ "Image Metadata");
+ } catch (IOException e) {
+ taskMonitor.setException(e, "Could not save image metadata.");
+ logger.warning("Could not save image metadata.",e);
+ }
+
+ long endTime = System.currentTimeMillis();
+ double sec = (endTime - startTime) / (1000.0);
+ logger.info("Image saving process finished in " + sec + " sec.");
+ }
+
+ /**
+ * Halts the Task: Not Currently Implemented.
+ */
+ public void halt() {
+ // Task can not currently be halted.
+ }
+
+ /**
+ * Sets the Task Monitor.
+ *
+ * @param taskMonitor
+ * TaskMonitor Object.
+ */
+ public void setTaskMonitor(TaskMonitor taskMonitor)
+ throws IllegalThreadStateException {
+ this.taskMonitor = taskMonitor;
+ }
+
+ /**
+ * Gets the Task Title.
+ *
+ * @return Task Title.
+ */
+ public String getTitle() {
+ return "Saving Image Library";
+ }
+} // End of SaveSessionTask
diff --git a/application/src/main/java/cytoscape/visual/customgraphic/RenderingContext.java b/application/src/main/java/cytoscape/visual/customgraphic/RenderingContext.java
new file mode 100644
index 0000000..6e52a2c
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/customgraphic/RenderingContext.java
@@ -0,0 +1,7 @@
+package cytoscape.visual.customgraphic;
+
+public interface RenderingContext<T> {
+
+ public void setContext(T context);
+ public T getContext();
+}
diff --git a/application/src/main/java/cytoscape/visual/customgraphic/RestoreImageTask.java b/application/src/main/java/cytoscape/visual/customgraphic/RestoreImageTask.java
new file mode 100644
index 0000000..4a2dc83
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/customgraphic/RestoreImageTask.java
@@ -0,0 +1,64 @@
+package cytoscape.visual.customgraphic;
+
+import cytoscape.Cytoscape;
+import cytoscape.logger.CyLogger;
+import cytoscape.task.Task;
+import cytoscape.task.TaskMonitor;
+
+public class RestoreImageTask implements Task {
+
+ private TaskMonitor taskMonitor;
+
+ private static final CyLogger logger = CyLogger.getLogger();
+
+
+ /**
+ * Execute task.<br>
+ */
+ public void run() {
+ taskMonitor
+ .setStatus("Loding image library from local disk.\n\nPlease wait...");
+ taskMonitor.setPercentCompleted(-1);
+
+
+ final long startTime = System.currentTimeMillis();
+ final CustomGraphicsManager manager = Cytoscape.getVisualMappingManager()
+ .getCustomGraphicsManager();
+
+ manager.restoreImages();
+
+ long endTime = System.currentTimeMillis();
+ double sec = (endTime - startTime) / (1000.0);
+ logger.info("Image saving process finished in " + sec + " sec.");
+ }
+
+ /**
+ * Halts the Task: Not Currently Implemented.
+ */
+ public void halt() {
+ // Task can not currently be halted.
+ }
+
+ /**
+ * Sets the Task Monitor.
+ *
+ * @param taskMonitor
+ * TaskMonitor Object.
+ */
+ public void setTaskMonitor(TaskMonitor taskMonitor)
+ throws IllegalThreadStateException {
+ this.taskMonitor = taskMonitor;
+ }
+
+ /**
+ * Gets the Task Title.
+ *
+ * @return Task Title.
+ */
+ public String getTitle() {
+ return "Loading Image Library";
+ }
+
+
+
+}
diff --git a/application/src/main/java/cytoscape/visual/customgraphic/SaveImageTask.java b/application/src/main/java/cytoscape/visual/customgraphic/SaveImageTask.java
new file mode 100644
index 0000000..69e872c
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/customgraphic/SaveImageTask.java
@@ -0,0 +1,37 @@
+package cytoscape.visual.customgraphic;
+
+import java.awt.image.BufferedImage;
+import java.io.File;
+import java.io.IOException;
+import java.util.concurrent.Callable;
+
+import javax.imageio.ImageIO;
+
+public class SaveImageTask implements Callable<String>{
+ private final File imageHome;
+ private String fileName;
+ private final BufferedImage image;
+
+ public SaveImageTask(final File imageHomeDirectory, String fileName, BufferedImage image) {
+ this.imageHome = imageHomeDirectory;
+ this.fileName = fileName;
+ this.image = image;
+ }
+
+
+ public String call() throws Exception {
+
+ if (!fileName.endsWith(".png"))
+ fileName += ".png";
+ File file = new File(imageHome, fileName);
+
+ try {
+ file.createNewFile();
+ ImageIO.write(image, "PNG", file);
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+
+ return file.toString();
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/customgraphic/Taggable.java b/application/src/main/java/cytoscape/visual/customgraphic/Taggable.java
new file mode 100644
index 0000000..30d3027
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/customgraphic/Taggable.java
@@ -0,0 +1,7 @@
+package cytoscape.visual.customgraphic;
+
+import java.util.Collection;
+
+public interface Taggable {
+ public Collection<String> getTags();
+}
diff --git a/application/src/main/java/cytoscape/visual/customgraphic/URLImageCustomGraphicsParser.java b/application/src/main/java/cytoscape/visual/customgraphic/URLImageCustomGraphicsParser.java
new file mode 100644
index 0000000..c12530b
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/customgraphic/URLImageCustomGraphicsParser.java
@@ -0,0 +1,63 @@
+package cytoscape.visual.customgraphic;
+
+import cytoscape.Cytoscape;
+import cytoscape.visual.customgraphic.impl.bitmap.URLImageCustomGraphics;
+
+/**
+ * Create instance of URLImageCustomGraphics object from String.
+ *
+ * @author kono
+ *
+ */
+public class URLImageCustomGraphicsParser implements CyCustomGraphicsParser {
+
+ private static final Class<? extends CyCustomGraphics> TARGET_CLASS = URLImageCustomGraphics.class;
+ private String entry[];
+
+ /**
+ * Generate Custom Graphics object from a string.
+ *
+ * <p>
+ * There are two types of valid string:
+ * <ul>
+ * <li>Image URL only - This will be used in Passthrough mapper.
+ * <li>Output of toString method of URLImageCustomGraphics
+ * </ul>
+ *
+ */
+
+ public CyCustomGraphics getInstance(String entryStr) {
+ // Check this is URL or not
+ if(entryStr == null) return null;
+
+ if (!validate(entryStr)) {
+ return null;
+ }
+
+ final String imageName = entry[1];
+ CyCustomGraphics cg = Cytoscape.getVisualMappingManager()
+ .getCustomGraphicsManager().getByID(Long.parseLong(imageName));
+ cg.setDisplayName(entry[2]);
+ return cg;
+ }
+
+ private boolean validate(final String entryStr) {
+ entry = entryStr.split(",");
+ if (entry == null || entry.length < 3) {
+ return false;
+ }
+
+ // Check class name
+ if (entry[0].trim().equals(
+ URLImageCustomGraphics.class.getCanonicalName()) == false) {
+ return false;
+ }
+ return true;
+ }
+
+
+ public Class<? extends CyCustomGraphics> getTargetClass() {
+ return TARGET_CLASS;
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/visual/customgraphic/impl/AbstractDCustomGraphics.java b/application/src/main/java/cytoscape/visual/customgraphic/impl/AbstractDCustomGraphics.java
new file mode 100644
index 0000000..b3554ab
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/customgraphic/impl/AbstractDCustomGraphics.java
@@ -0,0 +1,152 @@
+package cytoscape.visual.customgraphic.impl;
+
+import giny.view.ObjectPosition;
+
+import java.awt.Image;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+import java.util.SortedSet;
+import java.util.TreeSet;
+
+import cytoscape.visual.customgraphic.CyCustomGraphics;
+import cytoscape.visual.customgraphic.CyCustomGraphicsParser;
+import cytoscape.visual.customgraphic.IDGenerator;
+import cytoscape.visual.customgraphic.Layer;
+import cytoscape.visual.customgraphic.Taggable;
+import ding.view.ObjectPositionImpl;
+
+public abstract class AbstractDCustomGraphics implements
+ CyCustomGraphics, Taggable {
+
+ protected static final String DELIMITER = ",";
+ public static final String LIST_DELIMITER = "|";
+
+ protected float fitRatio = 0.9f;
+
+ // Unique ID
+ protected final Long id;
+
+ // Layers of Ding Custom Graphic objects.
+ protected List<Layer> layers;
+
+ // Human readable name
+ protected String displayName;
+
+ protected int width = 50;
+ protected int height = 50;
+
+ protected CyCustomGraphicsParser parser;
+
+ protected ObjectPosition position;
+
+ // For tags
+ protected final SortedSet<String> tags;
+
+
+ public AbstractDCustomGraphics(final String displayName) {
+ this(IDGenerator.getIDGenerator().getNextId(), displayName);
+ }
+
+
+ /**
+ * Create new object for a given ID.
+ * Used when restoring session.
+ *
+ * @param id
+ * @param displayName
+ */
+ public AbstractDCustomGraphics(final Long id, final String displayName) {
+ this.id = id;
+
+ this.layers = new ArrayList<Layer>();
+ this.displayName = displayName;
+
+ this.tags = new TreeSet<String>();
+ this.position = new ObjectPositionImpl();
+ }
+
+
+ public Long getIdentifier() {
+ return id;
+ }
+
+ public void setWidth(final int width) {
+ this.width = width;
+ }
+
+ public void setHeight(final int height) {
+ this.height = height;
+ }
+
+ public int getWidth() {
+ return this.width;
+ }
+
+ public int getHeight() {
+ return this.height;
+ }
+
+
+ public List<Layer> getLayers() {
+ return layers;
+ }
+
+ public String getDisplayName() {
+ return displayName;
+ }
+
+ public void setDisplayName(final String displayName) {
+ this.displayName = displayName;
+ }
+
+ public Image getRenderedImage() {
+ return null;
+ }
+
+
+ public Collection<String> getTags() {
+ return tags;
+ }
+
+
+ public ObjectPosition getPosition() {
+ return position;
+ }
+
+ public void setPosition(final ObjectPosition position) {
+ this.position = position;
+ }
+
+
+ // This will be used prop file.
+ public String toString() {
+ String tagStr = "";
+ // Build tags as a string
+ if (tags.size() != 0) {
+ final StringBuilder builder = new StringBuilder();
+ for (String tag : tags)
+ builder.append(tag + LIST_DELIMITER);
+ String temp = builder.toString();
+ tagStr = temp.substring(0, temp.length() - 1);
+ }
+
+ String name = displayName;
+ if (displayName.contains(",")) {
+ // Replace delimiter
+ name = displayName.replace(",", "___");
+ }
+
+ return this.getClass().getName() + DELIMITER + this.getIdentifier()
+ + DELIMITER + name + DELIMITER + tagStr;
+ }
+
+ public void setFitRatio(float fitRatio) {
+ this.fitRatio = fitRatio;
+ }
+
+ public float getFitRatio() {
+ return fitRatio;
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/visual/customgraphic/impl/CyCustomGraphicsParserFactoryImpl.java b/application/src/main/java/cytoscape/visual/customgraphic/impl/CyCustomGraphicsParserFactoryImpl.java
new file mode 100644
index 0000000..14aa495
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/customgraphic/impl/CyCustomGraphicsParserFactoryImpl.java
@@ -0,0 +1,45 @@
+package cytoscape.visual.customgraphic.impl;
+
+import java.util.HashMap;
+import java.util.Map;
+
+import cytoscape.visual.customgraphic.CyCustomGraphics;
+import cytoscape.visual.customgraphic.CyCustomGraphicsParser;
+import cytoscape.visual.customgraphic.CyCustomGraphicsParserFactory;
+
+public class CyCustomGraphicsParserFactoryImpl implements
+ CyCustomGraphicsParserFactory {
+
+ private final Map<Class<? extends CyCustomGraphics>, CyCustomGraphicsParser> parserMap;
+
+ public CyCustomGraphicsParserFactoryImpl() {
+ parserMap = new HashMap<Class<? extends CyCustomGraphics>, CyCustomGraphicsParser>();
+ }
+
+
+ public CyCustomGraphicsParser getParser(String customGraphicsClassName) {
+ if(customGraphicsClassName == null || customGraphicsClassName.trim().length() == 0)
+ return null;
+
+ Class<? extends CyCustomGraphics> cgClass;
+ try {
+ cgClass = (Class<? extends CyCustomGraphics>) Class.forName(customGraphicsClassName);
+ } catch (ClassNotFoundException e) {
+ e.printStackTrace();
+ return null;
+ } catch (ClassCastException cce) {
+ cce.printStackTrace();
+ return null;
+ }
+
+ return parserMap.get(cgClass);
+ }
+
+
+ public void registerParser(Class<? extends CyCustomGraphics> cgClass,
+ CyCustomGraphicsParser parser) {
+
+ parserMap.put(cgClass, parser);
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/visual/customgraphic/impl/DLayer.java b/application/src/main/java/cytoscape/visual/customgraphic/impl/DLayer.java
new file mode 100644
index 0000000..37d3932
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/customgraphic/impl/DLayer.java
@@ -0,0 +1,24 @@
+package cytoscape.visual.customgraphic.impl;
+
+import cytoscape.render.stateful.CustomGraphic;
+import cytoscape.visual.customgraphic.Layer;
+
+public class DLayer implements Layer {
+
+ private final CustomGraphic layer;
+ private final int zOrder;
+
+ public DLayer(final CustomGraphic layer, final int zOrder) {
+ this.layer = layer;
+ this.zOrder = zOrder;
+ }
+
+ public int getZorder() {
+ return zOrder;
+ }
+
+ public Object getLayerObject() {
+ return layer;
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/visual/customgraphic/impl/bitmap/URLImageCustomGraphics.java b/application/src/main/java/cytoscape/visual/customgraphic/impl/bitmap/URLImageCustomGraphics.java
new file mode 100644
index 0000000..906aa03
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/customgraphic/impl/bitmap/URLImageCustomGraphics.java
@@ -0,0 +1,156 @@
+package cytoscape.visual.customgraphic.impl.bitmap;
+
+import java.awt.Image;
+import java.awt.geom.Rectangle2D;
+import java.awt.image.BufferedImage;
+import java.io.IOException;
+import java.net.MalformedURLException;
+import java.net.URL;
+
+import javax.imageio.ImageIO;
+
+import cytoscape.Cytoscape;
+import cytoscape.logger.CyLogger;
+import cytoscape.render.stateful.CustomGraphic;
+import cytoscape.render.stateful.PaintFactory;
+import cytoscape.visual.customgraphic.ImageUtil;
+import cytoscape.visual.customgraphic.impl.AbstractDCustomGraphics;
+import cytoscape.visual.customgraphic.impl.DLayer;
+import cytoscape.visual.customgraphic.paint.TexturePaintFactory;
+
+public class URLImageCustomGraphics extends AbstractDCustomGraphics {
+
+ private static BufferedImage DEF_IMAGE;
+
+ static {
+ try {
+ DEF_IMAGE =ImageIO.read(Cytoscape.class.getResource("images/ximian/stock_dialog-warning-32.png"));
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+ }
+
+ private static final String DEF_TAG = "bitmap image";
+
+ private CustomGraphic cg;
+
+ private BufferedImage originalImage;
+ private BufferedImage scaledImage;
+
+ private URL sourceUrl;
+
+
+ public URLImageCustomGraphics(String url) throws IOException {
+ super(url);
+ this.tags.add(DEF_TAG);
+ createImage(url);
+ buildCustomGraphics(originalImage);
+ }
+
+
+ public URLImageCustomGraphics(Long id, String url) throws IOException {
+ super(id, url);
+ this.tags.add(DEF_TAG);
+ createImage(url);
+ buildCustomGraphics(originalImage);
+ }
+
+ /**
+ *
+ * @param name
+ * - display name of this object. NOT UNIQUE!
+ * @param img
+ */
+ public URLImageCustomGraphics(String name, BufferedImage img) {
+ super(name);
+ if (img == null)
+ throw new IllegalArgumentException("Image cannot be null.");
+
+ this.tags.add(DEF_TAG);
+ this.originalImage = img;
+ buildCustomGraphics(originalImage);
+ }
+
+ private void buildCustomGraphics(BufferedImage targetImg) {
+ layers.clear();
+
+ Rectangle2D bound = null;
+ width = targetImg.getWidth();
+ height = targetImg.getHeight();
+
+ bound = new Rectangle2D.Double(-width / 2, -height / 2, width, height);
+ final PaintFactory paintFactory = new TexturePaintFactory(targetImg);
+
+ cg = new CustomGraphic(bound, paintFactory);
+
+ // This object is always one layer, so simply add without sorting.
+ DLayer layer = new DLayer(cg, 1);
+ layers.add(layer);
+ }
+
+ private void createImage(String url) throws MalformedURLException {
+ if (url == null)
+ throw new IllegalStateException("URL string cannot be null.");
+
+ URL imageLocation = new URL(url);
+
+ sourceUrl = imageLocation;
+ try {
+ originalImage = ImageIO.read(imageLocation);
+ } catch (IOException e) {
+ originalImage = DEF_IMAGE;
+ CyLogger.getLogger().warn("Broken Image found. Default is used instead.");
+ }
+
+ if (originalImage == null) {
+ originalImage = DEF_IMAGE;
+ }
+ }
+
+ @Override
+ public Image getRenderedImage() {
+
+ if (width == originalImage.getWidth() && height == originalImage.getHeight()) {
+ return originalImage;
+ }
+
+ if(scaledImage == null) {
+ resizeImage(width, height);
+ } else if (scaledImage.getWidth() != width || scaledImage.getHeight() != height) {
+ resizeImage(width, height);
+ }
+
+ return scaledImage;
+ }
+
+
+
+ private Image resizeImage(int width, int height) {
+ final Image img = originalImage.getScaledInstance(width, height,
+ Image.SCALE_AREA_AVERAGING);
+ try {
+ scaledImage = ImageUtil.toBufferedImage(img);
+ } catch (InterruptedException e) {
+ // Could not get scaled one
+ e.printStackTrace();
+ return originalImage;
+ }
+ buildCustomGraphics(scaledImage);
+ return scaledImage;
+ }
+
+ public Image resetImage() {
+ if (scaledImage != null) {
+ scaledImage.flush();
+ scaledImage = null;
+ }
+ buildCustomGraphics(originalImage);
+ return originalImage;
+ }
+
+
+ public URL getSourceURL() {
+ return this.sourceUrl;
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/visual/customgraphic/impl/vector/CustomGraphicsProperty.java b/application/src/main/java/cytoscape/visual/customgraphic/impl/vector/CustomGraphicsProperty.java
new file mode 100644
index 0000000..5c6b875
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/customgraphic/impl/vector/CustomGraphicsProperty.java
@@ -0,0 +1,9 @@
+package cytoscape.visual.customgraphic.impl.vector;
+
+public interface CustomGraphicsProperty<T> {
+
+ public T getDefaultValue();
+
+ public T getValue();
+ public void setValue(Object value);
+}
diff --git a/application/src/main/java/cytoscape/visual/customgraphic/impl/vector/GradientLayerCustomGraphics.java b/application/src/main/java/cytoscape/visual/customgraphic/impl/vector/GradientLayerCustomGraphics.java
new file mode 100644
index 0000000..7b2ce85
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/customgraphic/impl/vector/GradientLayerCustomGraphics.java
@@ -0,0 +1,93 @@
+package cytoscape.visual.customgraphic.impl.vector;
+
+import java.awt.Color;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.Image;
+import java.awt.RenderingHints;
+import java.awt.Shape;
+import java.awt.image.BufferedImage;
+import java.util.HashMap;
+import java.util.Map;
+
+import cytoscape.render.stateful.PaintFactory;
+import cytoscape.visual.customgraphic.CustomGraphicsPropertyImpl;
+import cytoscape.visual.customgraphic.impl.AbstractDCustomGraphics;
+
+/**
+ * Proof of concept code to generate Custom Graphics dynamically as vector graphics.
+ *
+ * @author kono
+ *
+ */
+public abstract class GradientLayerCustomGraphics extends AbstractDCustomGraphics implements VectorCustomGraphics {
+
+ // Paint fot this graphics
+ protected PaintFactory paintFactory;
+
+ // Bound of this graphics
+ protected Shape bound;
+
+ private static final float FIT = 0.9f;
+
+ protected static final String COLOR1 = "Color 1";
+ protected static final String COLOR2 = "Color 2";
+
+ protected final CustomGraphicsProperty<Color> c1;
+ protected final CustomGraphicsProperty<Color> c2;
+
+ // Pre-Rendered image for icon.
+ protected BufferedImage rendered;
+
+ private static final Color transparentWhite = new Color(255, 255, 255, 100);
+ private static final Color transparentBlack = new Color(100, 100, 100, 100);
+
+ private static final int DEF_W = 100;
+ private static final int DEF_H = 100;
+
+ protected final Map<String, CustomGraphicsProperty<?>> props;
+
+
+ public GradientLayerCustomGraphics(final Long id, final String name) {
+ super(id, name);
+ width = DEF_W;
+ height = DEF_H;
+ props = new HashMap<String, CustomGraphicsProperty<?>>();
+
+ c1 = new CustomGraphicsPropertyImpl<Color>(transparentWhite);
+ c2 = new CustomGraphicsPropertyImpl<Color>(transparentBlack);
+
+ this.props.put(COLOR1, c1);
+ this.props.put(COLOR2, c2);
+ this.tags.add("vector image, gradient");
+ this.fitRatio = FIT;
+
+ // Render it for static icons.
+ getRenderedImage();
+ }
+
+
+ public Map<String, CustomGraphicsProperty<?>> getGraphicsProps() {
+ return this.props;
+ }
+
+ protected void renderImage(Graphics graphics) {
+ rendered.flush();
+ final Graphics2D g2d = (Graphics2D) graphics;
+ g2d.setRenderingHint(RenderingHints.KEY_RENDERING,
+ RenderingHints.VALUE_RENDER_QUALITY );
+ g2d.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+ RenderingHints.VALUE_ANTIALIAS_ON );
+ }
+
+
+ public Image getRenderedImage() {
+ if(rendered == null || (rendered != null && (rendered.getWidth() != width || rendered.getHeight() != height))) {
+ rendered = new BufferedImage(width,
+ height, BufferedImage.TYPE_INT_ARGB);
+ renderImage(rendered.getGraphics());
+ }
+
+ return rendered;
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/customgraphic/impl/vector/GradientOvalLayer.java b/application/src/main/java/cytoscape/visual/customgraphic/impl/vector/GradientOvalLayer.java
new file mode 100644
index 0000000..ada5141
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/customgraphic/impl/vector/GradientOvalLayer.java
@@ -0,0 +1,49 @@
+package cytoscape.visual.customgraphic.impl.vector;
+
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.geom.Ellipse2D;
+
+import cytoscape.render.stateful.CustomGraphic;
+import cytoscape.visual.customgraphic.IDGenerator;
+import cytoscape.visual.customgraphic.impl.DLayer;
+import cytoscape.visual.customgraphic.paint.GradientPaintFactory;
+
+public class GradientOvalLayer extends GradientLayerCustomGraphics {
+
+ // Name of this custom graphics.
+ private static final String NAME = "Glossy Oval Layer";
+
+
+ public GradientOvalLayer() {
+ this(IDGenerator.getIDGenerator().getNextId(), NAME);
+ }
+
+
+ public GradientOvalLayer(Long id, String name) {
+ super(id, name);
+ }
+
+ protected void renderImage(Graphics graphics) {
+ super.renderImage(graphics);
+
+ final Graphics2D g2d = (Graphics2D) graphics;
+ // Render
+ update();
+ g2d.setPaint(paintFactory.getPaint(bound.getBounds2D()));
+ g2d.fillOval(rendered.getMinX(), rendered.getMinY(),
+ width, height);
+ }
+
+ public void update() {
+ // First, remove all layers.
+ layers.clear();
+ bound = new Ellipse2D.Double(-width / 2, -height / 2, width, height);
+ paintFactory = new GradientPaintFactory(c1.getValue(), c2.getValue());
+ final CustomGraphic cg = new CustomGraphic(bound, paintFactory);
+
+ DLayer layer = new DLayer(cg, 1);
+ layers.add(layer);
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/visual/customgraphic/impl/vector/GradientRoundRectangleLayer.java b/application/src/main/java/cytoscape/visual/customgraphic/impl/vector/GradientRoundRectangleLayer.java
new file mode 100644
index 0000000..1d83750
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/customgraphic/impl/vector/GradientRoundRectangleLayer.java
@@ -0,0 +1,54 @@
+package cytoscape.visual.customgraphic.impl.vector;
+
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.geom.RoundRectangle2D;
+
+import cytoscape.render.stateful.CustomGraphic;
+import cytoscape.visual.customgraphic.IDGenerator;
+import cytoscape.visual.customgraphic.Layer;
+import cytoscape.visual.customgraphic.impl.DLayer;
+import cytoscape.visual.customgraphic.paint.GradientPaintFactory;
+
+public class GradientRoundRectangleLayer extends GradientLayerCustomGraphics {
+
+ // Name of this custom graphics.
+ private static final String NAME = "Glossy Round Rectangle Layer";
+ private int r =20;
+
+
+ public GradientRoundRectangleLayer() {
+ this(IDGenerator.getIDGenerator().getNextId(), NAME);
+ }
+
+
+ public GradientRoundRectangleLayer(Long id, String name) {
+ super(id, name);
+ }
+
+ protected void renderImage(Graphics graphics) {
+ super.renderImage(graphics);
+
+ final Graphics2D g2d = (Graphics2D) graphics;
+ // Render
+ update();
+ g2d.setPaint(paintFactory.getPaint(bound.getBounds2D()));
+ g2d.fillRoundRect(rendered.getMinX(), rendered.getMinY(),
+ rendered.getWidth(), rendered.getHeight(), r, r);
+ }
+
+
+ public void update() {
+ // First, remove all layers.
+ layers.clear();
+
+ r = (int)(Math.min(width, height)/4f);
+ bound = new RoundRectangle2D.Double(-width / 2, -height / 2,
+ width, height, r, r);
+ paintFactory = new GradientPaintFactory(c1.getValue(), c2.getValue());
+ final CustomGraphic cg = new CustomGraphic(bound, paintFactory);
+ final Layer layer = new DLayer(cg, 1);
+ layers.add(layer);
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/visual/customgraphic/impl/vector/VectorCustomGraphics.java b/application/src/main/java/cytoscape/visual/customgraphic/impl/vector/VectorCustomGraphics.java
new file mode 100644
index 0000000..771296c
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/customgraphic/impl/vector/VectorCustomGraphics.java
@@ -0,0 +1,9 @@
+package cytoscape.visual.customgraphic.impl.vector;
+
+import java.util.Map;
+
+public interface VectorCustomGraphics {
+
+ public Map<String, CustomGraphicsProperty<?>> getGraphicsProps();
+
+}
diff --git a/application/src/main/java/cytoscape/visual/customgraphic/paint/ColorPaintFactory.java b/application/src/main/java/cytoscape/visual/customgraphic/paint/ColorPaintFactory.java
new file mode 100644
index 0000000..c7d7f75
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/customgraphic/paint/ColorPaintFactory.java
@@ -0,0 +1,30 @@
+package cytoscape.visual.customgraphic.paint;
+
+import java.awt.Color;
+import java.awt.Paint;
+import java.awt.geom.Rectangle2D;
+
+import cytoscape.render.stateful.PaintFactory;
+
+public class ColorPaintFactory implements PaintFactory {
+
+ private Color color;
+
+ public ColorPaintFactory(final Color color) {
+ this.color = color;
+ }
+
+ public void setColor(final Color color) {
+ this.color = color;
+ }
+
+ public Color getColor() {
+ return this.color;
+ }
+
+
+ public Paint getPaint(Rectangle2D arg0) {
+ return color;
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/visual/customgraphic/paint/GradientPaintFactory.java b/application/src/main/java/cytoscape/visual/customgraphic/paint/GradientPaintFactory.java
new file mode 100644
index 0000000..5ca137f
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/customgraphic/paint/GradientPaintFactory.java
@@ -0,0 +1,30 @@
+package cytoscape.visual.customgraphic.paint;
+
+import java.awt.Color;
+import java.awt.GradientPaint;
+import java.awt.Paint;
+import java.awt.geom.Rectangle2D;
+
+import cytoscape.render.stateful.PaintFactory;
+
+public class GradientPaintFactory implements PaintFactory {
+
+ private Color c1;
+ private Color c2;
+
+ private Paint paint;
+
+ public GradientPaintFactory(Color c1, Color c2) {
+ this.c1 = c1;
+ this.c2 = c2;
+ }
+
+
+ public Paint getPaint(Rectangle2D bound) {
+ paint = new GradientPaint((float)bound.getWidth()/2, 0, c2,
+ (float)bound.getWidth()/2, (float)bound.getHeight()/2, c1);
+
+ return paint;
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/visual/customgraphic/paint/TexturePaintFactory.java b/application/src/main/java/cytoscape/visual/customgraphic/paint/TexturePaintFactory.java
new file mode 100644
index 0000000..41f713e
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/customgraphic/paint/TexturePaintFactory.java
@@ -0,0 +1,23 @@
+package cytoscape.visual.customgraphic.paint;
+
+import java.awt.Paint;
+import java.awt.TexturePaint;
+import java.awt.geom.Rectangle2D;
+import java.awt.image.BufferedImage;
+
+import cytoscape.render.stateful.PaintFactory;
+
+public class TexturePaintFactory implements PaintFactory {
+
+ private BufferedImage img;
+
+ public TexturePaintFactory(final BufferedImage img) {
+ this.img = img;
+ }
+
+
+ public Paint getPaint(Rectangle2D bound) {
+ return new TexturePaint(img, bound);
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/visual/customgraphic/ui/CustomGraphicsBrowser.java b/application/src/main/java/cytoscape/visual/customgraphic/ui/CustomGraphicsBrowser.java
new file mode 100644
index 0000000..3aacaec
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/customgraphic/ui/CustomGraphicsBrowser.java
@@ -0,0 +1,180 @@
+package cytoscape.visual.customgraphic.ui;
+
+import java.awt.Dimension;
+import java.awt.datatransfer.DataFlavor;
+import java.awt.datatransfer.Transferable;
+import java.awt.dnd.DnDConstants;
+import java.awt.dnd.DropTarget;
+import java.awt.dnd.DropTargetDropEvent;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.io.File;
+import java.io.IOException;
+import java.net.URL;
+import java.util.Collection;
+import java.util.List;
+
+import javax.swing.DefaultListModel;
+
+import org.jdesktop.swingx.JXList;
+
+import cytoscape.Cytoscape;
+import cytoscape.visual.customgraphic.CustomGraphicsManager;
+import cytoscape.visual.customgraphic.CyCustomGraphics;
+import cytoscape.visual.customgraphic.NullCustomGraphics;
+import cytoscape.visual.customgraphic.impl.bitmap.URLImageCustomGraphics;
+
+/**
+ * Display list of images available as custom graphics
+ *
+ * @author kono
+ */
+public class CustomGraphicsBrowser extends JXList implements PropertyChangeListener {
+
+ private static final long serialVersionUID = -8342056297304400824L;
+
+ private DefaultListModel model;
+ private final CustomGraphicsManager pool;
+
+ // For drag and drop
+ private static DataFlavor urlFlavor;
+
+ static {
+ try {
+ urlFlavor = new DataFlavor(
+ "application/x-java-url; class=java.net.URL");
+ } catch (ClassNotFoundException cnfe) {
+ cnfe.printStackTrace();
+ }
+ }
+
+
+ /**
+ * Creates new form CustomGraphicsBrowserPanel
+ *
+ * @throws IOException
+ */
+ public CustomGraphicsBrowser() throws IOException {
+ pool = Cytoscape.getVisualMappingManager().getCustomGraphicsManager();
+
+ initComponents();
+ addAllImages();
+
+ Cytoscape.getPropertyChangeSupport().addPropertyChangeListener(Cytoscape.SESSION_LOADED, this);
+ }
+
+ /**
+ * This method is called from within the constructor to initialize the form.
+ * WARNING: Do NOT modify this code. The content of this method is always
+ * regenerated by the Form Editor.
+ */
+ @SuppressWarnings("unchecked")
+ // <editor-fold defaultstate="collapsed" desc="Generated Code">
+ private void initComponents() {
+ this.setMaximumSize(new Dimension(300, 10000));
+ this.setBackground(new java.awt.Color(255, 255, 255));
+ model = new DefaultListModel();
+ this.setModel(model);
+ this.setCellRenderer(new CustomGraphicsCellRenderer());
+ this.setDropTarget(new URLDropTarget());
+
+ }// </editor-fold>
+
+
+ public void removeCustomGraphics(final CyCustomGraphics cg) {
+ model.removeElement(cg);
+ }
+
+ /**
+ * Add on-memory images to Model.
+ */
+ private void addAllImages() {
+ final Collection<CyCustomGraphics> graphics = pool.getAll();
+
+ for (CyCustomGraphics cg : graphics) {
+ if (cg instanceof NullCustomGraphics == false)
+ model.addElement(cg);
+ }
+ }
+
+ private void addCustomGraphics(final String urlStr) {
+ CyCustomGraphics cg = null;
+ try {
+ cg = new URLImageCustomGraphics(urlStr);
+ if (cg != null) {
+ pool.addGraphics(cg, new URL(urlStr));
+ model.addElement(cg);
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+ }
+
+
+ /**
+ * D & D
+ *
+ * @author kono
+ *
+ */
+ private class URLDropTarget extends DropTarget {
+
+ private static final long serialVersionUID = -7007999535331084109L;
+
+ public void drop(DropTargetDropEvent dtde) {
+
+ dtde.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
+ final Transferable trans = dtde.getTransferable();
+ //dumpDataFlavors(trans);
+ boolean gotData = false;
+ try {
+
+ if (trans.isDataFlavorSupported(DataFlavor.javaFileListFlavor)) {
+
+ final List<File> fileList = (List<File>) trans
+ .getTransferData(DataFlavor.javaFileListFlavor);
+
+ for (File file : fileList) {
+ addCustomGraphics(file.toURI().toURL().toString());
+ }
+ gotData = true;
+ } else if (trans.isDataFlavorSupported(urlFlavor)) {
+ URL url = (URL) trans.getTransferData(urlFlavor);
+ // Add image
+ addCustomGraphics(url.toString());
+ gotData = true;
+ } else if (trans.isDataFlavorSupported(DataFlavor.stringFlavor)) {
+ String s = (String) trans
+ .getTransferData(DataFlavor.stringFlavor);
+
+ URL url = new URL(s);
+ addCustomGraphics(url.toString());
+ gotData = true;
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ } finally {
+ dtde.dropComplete(gotData);
+ }
+ }
+
+ // This is for debugging
+ private void dumpDataFlavors(Transferable trans) {
+ System.out.println("Flavors:");
+ DataFlavor[] flavors = trans.getTransferDataFlavors();
+ for (int i = 0; i < flavors.length; i++) {
+ System.out.println("*** " + i + ": " + flavors[i]);
+ }
+ }
+
+ }
+
+ public void propertyChange(PropertyChangeEvent e) {
+ // Clear the model, and build new List from current pool of graphics
+ model.removeAllElements();
+ model.clear();
+
+ addAllImages();
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/visual/customgraphic/ui/CustomGraphicsCellRenderer.java b/application/src/main/java/cytoscape/visual/customgraphic/ui/CustomGraphicsCellRenderer.java
new file mode 100644
index 0000000..04469ce
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/customgraphic/ui/CustomGraphicsCellRenderer.java
@@ -0,0 +1,104 @@
+package cytoscape.visual.customgraphic.ui;
+
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.Image;
+import java.util.HashMap;
+import java.util.Map;
+
+import javax.swing.JList;
+import javax.swing.JPanel;
+import javax.swing.ListCellRenderer;
+import javax.swing.border.LineBorder;
+import javax.swing.border.TitledBorder;
+
+import org.jdesktop.swingx.JXImagePanel;
+
+import cytoscape.visual.customgraphic.CustomGraphicsUtil;
+import cytoscape.visual.customgraphic.CyCustomGraphics;
+
+/**
+ * Cell renderer for Custom Graphics Browser.
+ *
+ * @author kono
+ *
+ */
+public class CustomGraphicsCellRenderer extends JPanel implements
+ ListCellRenderer {
+
+ private static final long serialVersionUID = 8040076496780883222L;
+
+ private static final int ICON_SIZE = 130;
+
+ private static final int NAME_LENGTH_LIMIT = 24;
+
+ private static final Color SELECTED = Color.red;
+ private static final Color NOT_SELECTED = Color.darkGray;
+
+ private static final Font LABEL_FONT = new Font("SansSerif", Font.PLAIN, 10);
+ private static final Font SELECTED_LABEL_FONT = new Font("SansSerif", Font.BOLD, 10);
+
+ private static final Dimension CELL_SIZE = new Dimension(200, 150);
+
+ private final Map<CyCustomGraphics, Component> panelMap;
+
+ public CustomGraphicsCellRenderer() {
+ panelMap = new HashMap<CyCustomGraphics, Component>();
+ }
+
+
+ public Component getListCellRendererComponent(JList list, Object value,
+ int index, boolean isSelected, boolean cellHasFocus) {
+
+ JPanel target = null;
+ if (value != null && value instanceof CyCustomGraphics) {
+ CyCustomGraphics cg = (CyCustomGraphics) value;
+ target = (JPanel) panelMap.get(cg);
+ if (target == null) {
+ target = createImagePanel(cg, isSelected);
+ panelMap.put(cg, target);
+ }
+
+ // Set border if selected.
+ String name = cg.getDisplayName();
+ target.setToolTipText(name);
+ if(name.length() >NAME_LENGTH_LIMIT)
+ name = name.substring(0, NAME_LENGTH_LIMIT) + "...";
+
+ if(isSelected) {
+ target.setBorder(new TitledBorder(new LineBorder(SELECTED),
+ name, TitledBorder.CENTER, TitledBorder.TOP, SELECTED_LABEL_FONT));
+ } else {
+ target.setBorder(new TitledBorder(new LineBorder(NOT_SELECTED),
+ name, TitledBorder.CENTER, TitledBorder.TOP, LABEL_FONT));
+ }
+ }
+ return target;
+ }
+
+ private JPanel createImagePanel(final CyCustomGraphics cg,
+ boolean selected) {
+ final Image image = cg.getRenderedImage();
+ if (image == null)
+ return this;
+
+ final JXImagePanel imagePanel = new JXImagePanel();
+ imagePanel.setPreferredSize(new Dimension(ICON_SIZE, ICON_SIZE));
+ imagePanel.setStyle(JXImagePanel.Style.CENTERED);
+
+ if (image.getHeight(null) < ICON_SIZE && image.getWidth(null) < 200)
+ imagePanel.setImage(image);
+ else
+ imagePanel.setImage(CustomGraphicsUtil.getResizedImage(image, null,
+ ICON_SIZE, true));
+
+ imagePanel.setBorder(new TitledBorder(new LineBorder(Color.DARK_GRAY),
+ cg.getDisplayName(), TitledBorder.CENTER, TitledBorder.TOP, LABEL_FONT));
+
+ imagePanel.setPreferredSize(CELL_SIZE);
+ imagePanel.setBackground(Color.white);
+ return imagePanel;
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/customgraphic/ui/CustomGraphicsDetailPanel.java b/application/src/main/java/cytoscape/visual/customgraphic/ui/CustomGraphicsDetailPanel.java
new file mode 100644
index 0000000..d2a8a9a
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/customgraphic/ui/CustomGraphicsDetailPanel.java
@@ -0,0 +1,376 @@
+package cytoscape.visual.customgraphic.ui;
+
+import java.awt.Image;
+import java.util.Collection;
+
+import javax.swing.JPanel;
+import javax.swing.event.ListSelectionEvent;
+import javax.swing.event.ListSelectionListener;
+
+import org.jdesktop.swingx.JXImageView;
+
+import cytoscape.Cytoscape;
+import cytoscape.visual.customgraphic.CyCustomGraphics;
+import cytoscape.visual.customgraphic.Taggable;
+import cytoscape.visual.customgraphic.impl.bitmap.URLImageCustomGraphics;
+
+/**
+ *
+ * @author kono
+ */
+public class CustomGraphicsDetailPanel extends JPanel implements
+ ListSelectionListener {
+
+ private static final long serialVersionUID = -412539582192509545L;
+
+ private static final String TAG_DELIMITER = ",";
+
+ private CyCustomGraphics cg;
+
+ /** Creates new form CustomGraphicsDetailPanel */
+ public CustomGraphicsDetailPanel() {
+ initComponents();
+ }
+
+ /**
+ * This method is called from within the constructor to initialize the form.
+ * WARNING: Do NOT modify this code. The content of this method is always
+ * regenerated by the Form Editor.
+ */
+ @SuppressWarnings("unchecked")
+ // <editor-fold defaultstate="collapsed" desc="Generated Code">
+ private void initComponents() {
+ infoPanel = new javax.swing.JPanel();
+ nameLabel = new javax.swing.JLabel();
+ tagLabel = new javax.swing.JLabel();
+ nameTextField = new javax.swing.JTextField();
+ tagTextField = new javax.swing.JTextField();
+ imageViewPanel = new JXImageView();
+ modifyPanel = new javax.swing.JPanel();
+ widthLabel = new javax.swing.JLabel();
+ widthTextField = new javax.swing.JTextField();
+ heightLabel = new javax.swing.JLabel();
+ lockCheckBox = new javax.swing.JCheckBox();
+ heightTextField = new javax.swing.JTextField();
+ resetButton = new javax.swing.JButton();
+ searchButton = new javax.swing.JButton();
+
+ infoPanel.setBorder(javax.swing.BorderFactory.createEtchedBorder());
+
+ nameLabel.setText("Name:");
+
+ tagLabel.setText("Tags:");
+
+ nameTextField.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ nameTextFieldActionPerformed(evt);
+ }
+ });
+
+ tagTextField.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ tagsTextFieldActionPerformed(evt);
+ }
+ });
+
+ org.jdesktop.layout.GroupLayout infoPanelLayout = new org.jdesktop.layout.GroupLayout(infoPanel);
+ infoPanel.setLayout(infoPanelLayout);
+ infoPanelLayout.setHorizontalGroup(
+ infoPanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(infoPanelLayout.createSequentialGroup()
+ .addContainerGap()
+ .add(infoPanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(tagLabel)
+ .add(nameLabel))
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(infoPanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(nameTextField, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 491, Short.MAX_VALUE)
+ .add(tagTextField, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 491, Short.MAX_VALUE))
+ .addContainerGap())
+ );
+ infoPanelLayout.setVerticalGroup(
+ infoPanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(infoPanelLayout.createSequentialGroup()
+ .addContainerGap()
+ .add(infoPanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE)
+ .add(nameLabel)
+ .add(nameTextField, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE))
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(infoPanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE)
+ .add(tagLabel)
+ .add(tagTextField, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE))
+ .addContainerGap(org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
+ );
+
+ imageViewPanel.setBorder(javax.swing.BorderFactory.createTitledBorder("Actual Size View"));
+
+ org.jdesktop.layout.GroupLayout imageViewPanelLayout = new org.jdesktop.layout.GroupLayout(imageViewPanel);
+ imageViewPanel.setLayout(imageViewPanelLayout);
+ imageViewPanelLayout.setHorizontalGroup(
+ imageViewPanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(0, 573, Short.MAX_VALUE)
+ );
+ imageViewPanelLayout.setVerticalGroup(
+ imageViewPanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(0, 228, Short.MAX_VALUE)
+ );
+
+ modifyPanel.setBorder(javax.swing.BorderFactory.createEtchedBorder());
+
+ widthLabel.setText("Width:");
+
+ widthTextField.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ widthTextFieldActionPerformed(evt);
+ }
+ });
+
+ heightLabel.setText("Height:");
+
+ lockCheckBox.setSelected(true);
+ lockCheckBox.setText("Aspect Ratio");
+ lockCheckBox.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ //lockCheckBoxActionPerformed(evt);
+ }
+ });
+
+ heightTextField.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ heightTextFieldActionPerformed(evt);
+ }
+ });
+
+ resetButton.setText("Original");
+ resetButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ resetButtonActionPerformed(evt);
+ }
+ });
+
+ searchButton.setText("Search");
+ searchButton.setToolTipText("This function is not implemented yet.");
+ searchButton.setEnabled(false);
+ searchButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ optionButtonActionPerformed(evt);
+ }
+ });
+
+ org.jdesktop.layout.GroupLayout modifyPanelLayout = new org.jdesktop.layout.GroupLayout(modifyPanel);
+ modifyPanel.setLayout(modifyPanelLayout);
+ modifyPanelLayout.setHorizontalGroup(
+ modifyPanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(modifyPanelLayout.createSequentialGroup()
+ .addContainerGap()
+ .add(widthLabel)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(widthTextField, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE, 60, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(heightLabel)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(heightTextField, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE, 60, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(lockCheckBox)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(resetButton)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
+ .add(searchButton)
+ .add(8, 8, 8))
+ );
+ modifyPanelLayout.setVerticalGroup(
+ modifyPanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(modifyPanelLayout.createSequentialGroup()
+ .addContainerGap()
+ .add(modifyPanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE)
+ .add(widthLabel)
+ .add(widthTextField, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .add(heightLabel)
+ .add(heightTextField, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .add(lockCheckBox)
+ .add(resetButton)
+ .add(searchButton))
+ .addContainerGap(org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
+ );
+
+ org.jdesktop.layout.GroupLayout layout = new org.jdesktop.layout.GroupLayout(this);
+ this.setLayout(layout);
+ layout.setHorizontalGroup(
+ layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(infoPanel, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
+ .add(org.jdesktop.layout.GroupLayout.TRAILING, modifyPanel, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
+ .add(imageViewPanel, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
+ );
+ layout.setVerticalGroup(
+ layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(layout.createSequentialGroup()
+ .add(infoPanel, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(imageViewPanel, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(modifyPanel, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE))
+ );
+ }// </editor-fold>
+
+ private void nameTextFieldActionPerformed(java.awt.event.ActionEvent evt) {
+ final String newName = this.nameTextField.getText();
+ if (newName != null && newName.trim().length() != 0 && cg != null)
+ cg.setDisplayName(this.nameTextField.getText());
+ }
+
+
+ private void resetButtonActionPerformed(java.awt.event.ActionEvent evt) {
+ if (cg == null || cg.getRenderedImage() == null)
+ return;
+
+ if (cg instanceof URLImageCustomGraphics) {
+ final Image image = ((URLImageCustomGraphics) cg).resetImage();
+ imageViewPanel.setImage(image);
+ final int w = image.getWidth(null);
+ final int h = image.getHeight(null);
+ widthTextField.setText(Integer.toString(w));
+ heightTextField.setText(Integer.toString(h));
+ cg.setWidth(w);
+ cg.setHeight(h);
+ Cytoscape.getCurrentNetworkView().redrawGraph(false, true);
+ }
+ }
+
+ private void widthTextFieldActionPerformed(java.awt.event.ActionEvent evt) {
+ resizeImage(true);
+ }
+
+ private void heightTextFieldActionPerformed(java.awt.event.ActionEvent evt) {
+ resizeImage(false);
+ }
+
+ private void resizeImage(boolean isWidth) {
+ final String width = widthTextField.getText();
+ final String height = heightTextField.getText();
+
+
+ final Image currentImage = cg.getRenderedImage();
+ if (currentImage == null)
+ return;
+
+ final boolean lock = this.lockCheckBox.isSelected();
+
+ final int currentW = currentImage.getWidth(null);
+ final int currentH = currentImage.getHeight(null);
+
+ Integer w;
+ Integer h;
+ try {
+ w = Integer.parseInt(width);
+ h = Integer.parseInt(height);
+ } catch (NumberFormatException e) {
+ // back to current size
+ this.widthTextField.setText(Integer.toString(currentW));
+ this.heightTextField.setText(Integer.toString(currentH));
+ return;
+ }
+
+ float ratio;
+ int converted;
+ if (lock == false) {
+ cg.setWidth(w);
+ cg.setHeight(h);
+ imageViewPanel.setImage(cg.getRenderedImage());
+ } else if (isWidth) {
+ ratio = ((float) currentH) / ((float) currentW);
+ converted = (int) (w * ratio);
+ cg.setWidth(w);
+ cg.setHeight(converted);
+ imageViewPanel.setImage(cg.getRenderedImage());
+ heightTextField.setText(Integer.toString(converted));
+ } else {
+ ratio = ((float) currentW) / ((float) currentH);
+ converted = (int) (h * ratio);
+ cg.setWidth(converted);
+ cg.setHeight(h);
+ imageViewPanel.setImage(cg.getRenderedImage());
+ widthTextField.setText(Integer.toString(converted));
+ }
+ Cytoscape.getCurrentNetworkView().redrawGraph(false, true);
+ }
+
+ private void tagsTextFieldActionPerformed(java.awt.event.ActionEvent evt) {
+ final String tagStr = this.tagTextField.getText();
+ if(tagStr != null && tagStr.trim().length() != 0) {
+ if(cg instanceof Taggable) {
+ final String[] tags = tagStr.split(TAG_DELIMITER);
+ for(String tag:tags)
+ ((Taggable) cg).getTags().add(tag.trim());
+ }
+ }
+ }
+
+ private void optionButtonActionPerformed(java.awt.event.ActionEvent evt) {
+ }
+
+
+
+ // Variables declaration - do not modify
+ private javax.swing.JLabel heightLabel;
+ private javax.swing.JTextField heightTextField;
+ private JXImageView imageViewPanel;
+ private javax.swing.JPanel infoPanel;
+ private javax.swing.JCheckBox lockCheckBox;
+ private javax.swing.JPanel modifyPanel;
+ private javax.swing.JLabel nameLabel;
+ private javax.swing.JTextField nameTextField;
+ private javax.swing.JButton resetButton;
+ private javax.swing.JLabel tagLabel;
+ private javax.swing.JTextField tagTextField;
+ private javax.swing.JLabel widthLabel;
+ private javax.swing.JTextField widthTextField;
+ private javax.swing.JButton searchButton;
+
+
+ // End of variables declaration
+
+ public void valueChanged(ListSelectionEvent e) {
+
+ if (!(e.getSource() instanceof CustomGraphicsBrowser)
+ || e.getValueIsAdjusting())
+ return;
+
+ final CustomGraphicsBrowser browser = (CustomGraphicsBrowser) e
+ .getSource();
+
+ cg = (CyCustomGraphics) browser.getSelectedValue();
+ if(cg == null) {
+ imageViewPanel.setImage((Image)null);
+ heightTextField.setText(null);
+ widthTextField.setText(null);
+ nameTextField.setText(null);
+ nameTextField.setToolTipText(null);
+ tagTextField.setText(null);
+ return;
+ }
+
+ final Image img = cg.getRenderedImage();
+
+ // Set up detail panel
+ imageViewPanel.setImage(img);
+ heightTextField.setText(Integer.toString(img.getHeight(null)));
+ widthTextField.setText(Integer.toString(img.getWidth(null)));
+ nameTextField.setText(cg.getDisplayName());
+ nameTextField.setToolTipText(cg.getDisplayName());
+ if(cg instanceof Taggable) {
+ final Collection<String> tags = ((Taggable) cg).getTags();
+ final int tagCount = tags.size();
+ int counter = 0;
+ final StringBuilder tagBuilder = new StringBuilder();
+ for(String tag: tags) {
+ tagBuilder.append(tag);
+ counter++;
+ if(tagCount != counter)
+ tagBuilder.append(", ");
+ }
+ tagTextField.setText(tagBuilder.toString());
+ tagTextField.setToolTipText(tagBuilder.toString());
+ }
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/visual/customgraphic/ui/CustomGraphicsManagerDialog.java b/application/src/main/java/cytoscape/visual/customgraphic/ui/CustomGraphicsManagerDialog.java
new file mode 100644
index 0000000..4d8a140
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/customgraphic/ui/CustomGraphicsManagerDialog.java
@@ -0,0 +1,234 @@
+package cytoscape.visual.customgraphic.ui;
+
+import java.awt.Dimension;
+import java.awt.Frame;
+import java.awt.image.BufferedImage;
+import java.io.File;
+import java.io.IOException;
+import java.net.MalformedURLException;
+
+import javax.imageio.ImageIO;
+import javax.swing.DefaultListModel;
+import javax.swing.JFileChooser;
+import javax.swing.JOptionPane;
+
+import cytoscape.Cytoscape;
+import cytoscape.logger.CyLogger;
+import cytoscape.visual.customgraphic.CustomGraphicsManager;
+import cytoscape.visual.customgraphic.CyCustomGraphics;
+import cytoscape.visual.customgraphic.impl.bitmap.URLImageCustomGraphics;
+
+
+/**
+ * Main UI for managing on-memory library of Custom Graphics
+ *
+ * @author kono
+ */
+public class CustomGraphicsManagerDialog extends javax.swing.JDialog {
+
+ private static final long serialVersionUID = 7681270324415099781L;
+
+ private static final CyLogger logger = CyLogger.getLogger(CustomGraphicsManagerDialog.class);
+
+ // List of graphics available
+ private CustomGraphicsBrowser browser;
+
+ // Panel for displaying actual size image
+ private final CustomGraphicsDetailPanel detail;
+
+ // Manager object for on-memory graphics.
+ private final CustomGraphicsManager manager;
+
+ /**
+ * Creates new form CustomGraphicsManagerDialog
+ *
+ * @param parent
+ * @param modal
+ */
+ public CustomGraphicsManagerDialog(Frame parent, boolean modal) {
+ super(parent, modal);
+ manager = Cytoscape.getVisualMappingManager().getCustomGraphicsManager();
+ initComponents();
+ try {
+ browser = new CustomGraphicsBrowser();
+ } catch (IOException e) {
+ logger.error("Could not get CustomGraphicsBrowser object.", e);
+ }
+
+ detail = new CustomGraphicsDetailPanel();
+
+ this.leftScrollPane.setViewportView(browser);
+ this.rightScrollPane.setViewportView(detail);
+ this.setPreferredSize(new Dimension(850, 550));
+ this.setTitle("Custom Graphics Manager");
+
+ this.browser.addListSelectionListener(detail);
+ pack();
+
+ }
+
+ /**
+ * This method is called from within the constructor to initialize the form.
+ * WARNING: Do NOT modify this code. The content of this method is always
+ * regenerated by the Form Editor.
+ */
+ @SuppressWarnings("unchecked")
+ private void initComponents() {
+
+ buttonPanel = new javax.swing.JPanel();
+ deleteButton = new javax.swing.JButton();
+ addButton = new javax.swing.JButton();
+ mainSplitPane = new javax.swing.JSplitPane();
+ leftScrollPane = new javax.swing.JScrollPane();
+ rightScrollPane = new javax.swing.JScrollPane();
+
+ setDefaultCloseOperation(javax.swing.WindowConstants.DISPOSE_ON_CLOSE);
+
+ buttonPanel.setBorder(javax.swing.BorderFactory.createEtchedBorder());
+
+ deleteButton.setText("-");
+ deleteButton.setToolTipText("Remove selected graphics from library.");
+ deleteButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ deleteButtonActionPerformed(evt);
+ }
+ });
+
+ addButton.setText("+");
+ addButton.setToolTipText("Add a folder to Custom Graphics Library");
+ addButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ addButtonActionPerformed(evt);
+ }
+ });
+
+ org.jdesktop.layout.GroupLayout buttonPanelLayout = new org.jdesktop.layout.GroupLayout(
+ buttonPanel);
+ buttonPanel.setLayout(buttonPanelLayout);
+ buttonPanelLayout
+ .setHorizontalGroup(buttonPanelLayout
+ .createParallelGroup(
+ org.jdesktop.layout.GroupLayout.LEADING)
+ .add(
+ org.jdesktop.layout.GroupLayout.TRAILING,
+ buttonPanelLayout
+ .createSequentialGroup()
+ .addContainerGap(580, Short.MAX_VALUE)
+ .add(
+ addButton,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ 50,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(
+ org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(
+ deleteButton,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ 50,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)));
+ buttonPanelLayout.setVerticalGroup(buttonPanelLayout
+ .createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(
+ buttonPanelLayout.createParallelGroup(
+ org.jdesktop.layout.GroupLayout.BASELINE).add(
+ deleteButton).add(addButton)));
+
+ mainSplitPane.setDividerLocation(230);
+ mainSplitPane.setLeftComponent(leftScrollPane);
+ mainSplitPane.setRightComponent(rightScrollPane);
+
+ org.jdesktop.layout.GroupLayout layout = new org.jdesktop.layout.GroupLayout(
+ getContentPane());
+ getContentPane().setLayout(layout);
+ layout.setHorizontalGroup(layout.createParallelGroup(
+ org.jdesktop.layout.GroupLayout.LEADING).add(
+ org.jdesktop.layout.GroupLayout.TRAILING, buttonPanel,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
+ .add(mainSplitPane,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 690,
+ Short.MAX_VALUE));
+ layout.setVerticalGroup(layout.createParallelGroup(
+ org.jdesktop.layout.GroupLayout.LEADING).add(
+ org.jdesktop.layout.GroupLayout.TRAILING,
+ layout.createSequentialGroup().add(mainSplitPane,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 552,
+ Short.MAX_VALUE).addPreferredGap(
+ org.jdesktop.layout.LayoutStyle.RELATED).add(
+ buttonPanel,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)));
+
+ pack();
+ }// </editor-fold>
+
+ private void addButtonActionPerformed(java.awt.event.ActionEvent evt) {
+ // Add a directory
+ final JFileChooser chooser = new JFileChooser();
+ chooser.setDialogTitle("Select Image Directory");
+ chooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
+ chooser.setMultiSelectionEnabled(true);
+
+ int returnVal = chooser.showOpenDialog(this);
+ if (returnVal == JFileChooser.APPROVE_OPTION)
+ importFromDirectories(chooser.getSelectedFiles());
+ }
+
+ private void importFromDirectories(final File[] directories) {
+ for (final File file : directories)
+ processFiles(file.listFiles());
+ }
+
+ private void processFiles(final File[] files) {
+ for (final File file : files) {
+ BufferedImage img = null;
+ if (file.isFile()) {
+ try {
+ img = ImageIO.read(file);
+ } catch (IOException e) {
+ System.err.println("Could not read file: "
+ + file.toString());
+ e.printStackTrace();
+ continue;
+ }
+ }
+
+ if (img != null) {
+ final CyCustomGraphics cg = new URLImageCustomGraphics(
+ file.toString(), img);
+ try {
+ manager.addGraphics(cg, file.toURI().toURL());
+ } catch (MalformedURLException e) {
+ e.printStackTrace();
+ continue;
+ }
+ ((DefaultListModel) browser.getModel()).addElement(cg);
+ }
+ }
+ }
+
+ private void deleteButtonActionPerformed(java.awt.event.ActionEvent evt) {
+ final Object[] toBeRemoved = browser.getSelectedValues();
+ for(Object g: toBeRemoved) {
+ final CyCustomGraphics cg = (CyCustomGraphics) g;
+ if(!Cytoscape.getVisualMappingManager().getCustomGraphicsManager().isUsedInCurrentSession(cg)) {
+ browser.removeCustomGraphics(cg);
+ manager.removeGraphics(cg.getIdentifier());
+ } else {
+ JOptionPane.showMessageDialog(this, cg.getDisplayName() + " is used in current session and cannot remove it.",
+ "Custom Graphics is in Use!", JOptionPane.ERROR_MESSAGE);
+ }
+ }
+ }
+
+ // Variables declaration - do not modify
+ private javax.swing.JButton addButton;
+ private javax.swing.JPanel buttonPanel;
+ private javax.swing.JButton deleteButton;
+ private javax.swing.JScrollPane leftScrollPane;
+ private javax.swing.JSplitPane mainSplitPane;
+ private javax.swing.JScrollPane rightScrollPane;
+ // End of variables declaration
+
+}
diff --git a/application/src/main/java/cytoscape/visual/customgraphic/ui/CyCustomGraphicsTableCellRenderer.java b/application/src/main/java/cytoscape/visual/customgraphic/ui/CyCustomGraphicsTableCellRenderer.java
new file mode 100644
index 0000000..83d7c89
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/customgraphic/ui/CyCustomGraphicsTableCellRenderer.java
@@ -0,0 +1,31 @@
+package cytoscape.visual.customgraphic.ui;
+
+import java.awt.Component;
+
+import javax.swing.ImageIcon;
+import javax.swing.JTable;
+import javax.swing.table.DefaultTableCellRenderer;
+
+import cytoscape.visual.customgraphic.CyCustomGraphics;
+
+public class CyCustomGraphicsTableCellRenderer extends DefaultTableCellRenderer {
+
+ private static final long serialVersionUID = -5155795609971962107L;
+
+ @Override
+ public Component getTableCellRendererComponent(JTable table, Object value,
+ boolean isSelected, boolean hasFocus, int row, int column) {
+
+ if (value instanceof CyCustomGraphics == false && value != null) {
+ this.setText(value.toString());
+ return this;
+ }
+
+ final CyCustomGraphics cg = (CyCustomGraphics) value;
+
+ this.setText(cg.getDisplayName());
+ this.setIcon(new ImageIcon(cg.getRenderedImage()));
+ return this;
+
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/customgraphic/ui/CyCustomGraphicsTreeCellRenderer.java b/application/src/main/java/cytoscape/visual/customgraphic/ui/CyCustomGraphicsTreeCellRenderer.java
new file mode 100644
index 0000000..4a90045
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/customgraphic/ui/CyCustomGraphicsTreeCellRenderer.java
@@ -0,0 +1,32 @@
+package cytoscape.visual.customgraphic.ui;
+
+import java.awt.Component;
+import java.util.List;
+
+import javax.swing.ImageIcon;
+import javax.swing.JTree;
+import javax.swing.tree.DefaultTreeCellRenderer;
+
+import cytoscape.visual.customgraphic.CyCustomGraphics;
+
+public class CyCustomGraphicsTreeCellRenderer extends DefaultTreeCellRenderer {
+
+ private static final long serialVersionUID = -5155795609971962107L;
+
+ public Component getTreeCellRendererComponent(JTree tree, Object value,
+ boolean sel, boolean expanded, boolean leaf, int row,
+ boolean hasFocus) {
+ super.getTreeCellRendererComponent(tree, value, sel, expanded, leaf, row, hasFocus);
+
+ System.out.println("!!!!!!Tree Rendering-----> " + value.getClass());
+ if(value instanceof CyCustomGraphicsTreeNode) {
+ Object image = ((CyCustomGraphicsTreeNode) value).getValueAt(2);
+ final CyCustomGraphics cg = (CyCustomGraphics) image;
+
+ this.setText("");
+ this.setIcon(new ImageIcon(cg.getRenderedImage()));
+ }
+
+ return this;
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/customgraphic/ui/CyCustomGraphicsTreeNode.java b/application/src/main/java/cytoscape/visual/customgraphic/ui/CyCustomGraphicsTreeNode.java
new file mode 100644
index 0000000..5f0b16c
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/customgraphic/ui/CyCustomGraphicsTreeNode.java
@@ -0,0 +1,31 @@
+package cytoscape.visual.customgraphic.ui;
+
+import java.util.List;
+
+import org.jdesktop.swingx.treetable.DefaultMutableTreeTableNode;
+
+public class CyCustomGraphicsTreeNode extends DefaultMutableTreeTableNode {
+
+ private List<Object> data;
+
+ CyCustomGraphicsTreeNode(List<Object> data) {
+ super(data);
+ this.data = data;
+ }
+
+ /*
+ * Inherited
+ */
+ @Override
+ public int getColumnCount() {
+ return data.size();
+ }
+
+ /*
+ * Inherited
+ */
+ @Override
+ public Object getValueAt(int column) {
+ return data.get(column);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/mappings/AbstractMapping.java b/application/src/main/java/cytoscape/visual/mappings/AbstractMapping.java
new file mode 100644
index 0000000..7c22177
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/mappings/AbstractMapping.java
@@ -0,0 +1,111 @@
+package cytoscape.visual.mappings;
+
+import java.util.Map;
+import java.util.Properties;
+
+import javax.swing.JDialog;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+
+import cytoscape.CyNetwork;
+import cytoscape.visual.SubjectBase;
+import cytoscape.visual.VisualPropertyType;
+import cytoscape.visual.parsers.ValueParser;
+
+public abstract class AbstractMapping extends SubjectBase implements
+ ObjectMapping {
+
+ private JPanel dummyPanel;
+
+ // Mapped value class.
+ protected final Class<?> rangeClass;
+
+ // Attribute name associated with this mapping.
+ protected String controllingAttrName;
+
+ // Attribute value types compatible withi this mapping.
+ protected Class<?>[] acceptedClasses;
+
+ public AbstractMapping(final Class<?> rangeClass, final String controllingAttrName) {
+ this.acceptedClasses = new Class<?>[]{ Object.class };
+ this.controllingAttrName = controllingAttrName;
+ this.rangeClass = rangeClass;
+ }
+
+
+ abstract public void applyProperties(Properties props, String baseKey,
+ ValueParser parser);
+
+
+
+ abstract public Properties getProperties(String baseKey);
+
+
+
+ public abstract Object calculateRangeValue(Map<String, Object> attrBundle);
+
+
+
+ public Class<?>[] getAcceptedDataClasses() {
+ return this.acceptedClasses;
+ }
+
+
+
+ public String getControllingAttributeName() {
+ return this.controllingAttrName;
+ }
+
+
+
+ public Class<?> getRangeClass() {
+ return this.rangeClass;
+ }
+
+
+
+ public void setControllingAttributeName(String controllingAttrName) {
+ this.controllingAttrName = controllingAttrName;
+ }
+
+
+ abstract public Object clone();
+
+
+
+ public JPanel getLegend(VisualPropertyType type) {
+ return getDummyPanel();
+ }
+
+
+ private JPanel getDummyPanel() {
+ if(dummyPanel == null) {
+ dummyPanel = new JPanel();
+ dummyPanel.add(new JLabel("GUI is not configured for this mapping."));
+ }
+ return dummyPanel;
+ }
+
+
+ /**
+ * Gets the UI Object Associated with the Mapper. Required by the
+ * ObjectMapping interface.
+ *
+ * @param parent
+ * Parent Dialog.
+ * @param network
+ * CyNetwork.
+ * @return JPanel Object.
+ */
+ @Deprecated
+ public JPanel getUI(JDialog parent, CyNetwork network) {
+ return getDummyPanel();
+ }
+
+
+ @Deprecated
+ public void setControllingAttributeName(String attrName, CyNetwork network,
+ boolean preserveMapping) {
+ this.setControllingAttributeName(attrName);
+ }
+}
\ No newline at end of file
diff --git a/application/src/main/java/cytoscape/visual/mappings/BoundaryRangeValues.java b/application/src/main/java/cytoscape/visual/mappings/BoundaryRangeValues.java
new file mode 100644
index 0000000..6af1f0d
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/mappings/BoundaryRangeValues.java
@@ -0,0 +1,102 @@
+/*
+ File: BoundaryRangeValues.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+package cytoscape.visual.mappings;
+
+/**
+ * This class defines a data object representing the range values associated
+ * with a particular domain value, called a boundary value. The domain value is
+ * not stored here, since objects of this class are intended to be used as the
+ * values in a map where the domain value is the key.
+ *
+ * Three values must be specified for each boundary value. The lesserValue field
+ * is used for interpolation upon smaller domain values; the greaterValue field
+ * is used for interpolation upon larger domain values; and the equalValue field
+ * is used when the domain value is exactly equal to the associated boundary
+ * domain value. This distinction is needed to support different ranges of
+ * interpolation above and below the same domain value, plus allow a distinctly
+ * different value for exact matches.
+ *
+ * V - Calculated visual object (Color, etc.)
+ */
+public class BoundaryRangeValues {
+
+ public Object lesserValue;
+ public Object equalValue;
+ public Object greaterValue;
+
+ /**
+ * Creates a new BoundaryRangeValues object.
+ *
+ * @param lesser
+ * Object used for values less than this point.
+ * @param equal
+ * Object used for value equal to this point.
+ * @param greater
+ * Object used for values greater than this point.
+ */
+ public BoundaryRangeValues(Object lesser, Object equal, Object greater) {
+ lesserValue = lesser;
+ equalValue = equal;
+ greaterValue = greater;
+ }
+
+ /**
+ * Creates a new BoundaryRangeValues object. This is a copy constructor.
+ *
+ * @param original
+ * DOCUMENT ME!
+ */
+ public BoundaryRangeValues(final BoundaryRangeValues original) {
+ this.equalValue = original.equalValue;
+ this.lesserValue = original.lesserValue;
+ this.greaterValue = original.greaterValue;
+ }
+
+ public BoundaryRangeValues() {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String toString() {
+ return "{" + lesserValue.toString() + ","
+ + equalValue.toString() + "," + greaterValue.toString() + "}";
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/mappings/ContinuousMapping.java b/application/src/main/java/cytoscape/visual/mappings/ContinuousMapping.java
new file mode 100644
index 0000000..3da7029
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/mappings/ContinuousMapping.java
@@ -0,0 +1,255 @@
+/*
+ File: ContinuousMapping.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+package cytoscape.visual.mappings;
+
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+import java.util.Properties;
+
+import javax.swing.JPanel;
+import javax.swing.event.ChangeListener;
+
+import cytoscape.visual.VisualPropertyType;
+import cytoscape.visual.mappings.continuous.ContinuousLegend;
+import cytoscape.visual.mappings.continuous.ContinuousMappingPoint;
+import cytoscape.visual.mappings.continuous.ContinuousMappingReader;
+import cytoscape.visual.mappings.continuous.ContinuousMappingWriter;
+import cytoscape.visual.mappings.continuous.ContinuousRangeCalculator;
+import cytoscape.visual.parsers.ValueParser;
+
+/**
+ * Implements an interpolation table mapping data to values of a particular
+ * class. The data value is extracted from a bundle of attributes by using a
+ * specified data attribute name.
+ *
+ * For refactoring changes in this class, please refer to:
+ * cytoscape.visual.mappings.continuous.README.txt.
+ *
+ */
+public class ContinuousMapping extends
+ AbstractMapping {
+
+ // Accepts only numbers.
+ private static final Class<?>[] ACCEPTED_CLASS = { Number.class };
+
+ // used to interpolate between boundaries
+ private Interpolator interpolator;
+
+ // Contains List of Data Points
+ private List<ContinuousMappingPoint> points;
+
+ /**
+ * Constructor.
+ *
+ * @param defaultObj
+ * default object to map to
+ * @param mapType
+ * Type of mapping, one of {@link ObjectMapping#EDGE_MAPPING} or
+ * {@link ObjectMapping#NODE_MAPPING}
+ *
+ * @deprecated Use new constructor instead. Will be removed in 10/2011.
+ * Controlling attribute name is always required, and now it's a part of constructor argument.
+ */
+ @Deprecated
+ public ContinuousMapping(Object defaultObj, byte mapType)
+ throws IllegalArgumentException {
+ this((Class<?>) defaultObj.getClass(), null);
+ }
+
+ public ContinuousMapping(final Class<?> rangeClass,
+ final String controllingAttrName) {
+ super(rangeClass, controllingAttrName);
+ this.acceptedClasses = ACCEPTED_CLASS;
+ points = new ArrayList<ContinuousMappingPoint>();
+
+ // Interpolater setting
+ if (Color.class.isAssignableFrom(this.rangeClass))
+ interpolator = new LinearNumberToColorInterpolator();
+ else if (Number.class.isAssignableFrom(this.rangeClass))
+ interpolator = new LinearNumberToNumberInterpolator();
+ else
+ interpolator = new FlatInterpolator();
+ }
+
+ /**
+ * Create deep copy of the object.
+ *
+ * @return Cloned Mapping Object.
+ */
+ public Object clone() {
+
+ // Constructor arguments
+ final Class<?> rangeClassClone;
+ final ContinuousMapping clone = new ContinuousMapping(
+ rangeClass, controllingAttrName);
+
+ // Copy over all listeners...
+ for (ChangeListener listener : observers)
+ clone.addChangeListener(listener);
+
+
+ // Copy points
+ for (final ContinuousMappingPoint cmp : points) {
+ final ContinuousMappingPoint cmpClone = (ContinuousMappingPoint) cmp.clone();
+ clone.addPoint(cmpClone.getValue(), cmpClone.getRange());
+ }
+
+ return clone;
+ }
+
+ /**
+ * Gets all Data Points.
+ *
+ * @return ArrayList of ContinuousMappingPoint objects.
+ */
+ public List<ContinuousMappingPoint> getAllPoints() {
+ return points;
+ }
+
+ /**
+ * Adds a New Data Point.
+ */
+ public void addPoint(double value, BoundaryRangeValues brv) {
+ ContinuousMappingPoint cmp = new ContinuousMappingPoint(value,
+ brv);
+ points.add(cmp);
+ }
+
+ /**
+ * Removes a Point from the List.
+ */
+ public void removePoint(int index) {
+ points.remove(index);
+ }
+
+ /**
+ * Gets Total Point Count.
+ */
+ public int getPointCount() {
+ return points.size();
+ }
+
+ /**
+ * Gets Specified Point.
+ *
+ * @param index
+ * Index Value.
+ * @return ContinuousMappingPoint.
+ */
+ public ContinuousMappingPoint getPoint(int index) {
+ return points.get(index);
+ }
+
+ /**
+ * Customizes this object by applying mapping defintions described by the
+ * supplied Properties argument. Required by the ObjectMapping interface.
+ *
+ * @param props
+ * Properties Object.
+ * @param baseKey
+ * Base Key for finding properties.
+ * @param parser
+ * ValueParser Object.
+ */
+ public void applyProperties(Properties props, String baseKey,
+ ValueParser parser) {
+ final ContinuousMappingReader reader = new ContinuousMappingReader(props,baseKey, parser);
+ this.points = reader.getPoints();
+ this.controllingAttrName = reader.getControllingAttributeName();
+ this.interpolator = reader.getInterpolator();
+ }
+
+ /**
+ * Returns a Properties object with entries suitable for customizing this
+ * object via the applyProperties method. Required by the ObjectMapping
+ * interface.
+ *
+ * @param baseKey
+ * Base Key for creating properties.
+ * @return Properties Object.
+ */
+ public Properties getProperties(String baseKey) {
+ final ContinuousMappingWriter writer = new ContinuousMappingWriter(
+ points, baseKey, controllingAttrName, interpolator);
+
+ return writer.getProperties();
+ }
+
+ /**
+ * Gets the Mapping Interpolator. Required by the ObjectMapping interface.
+ *
+ * @return Interpolator Object.
+ */
+ public Interpolator getInterpolator() {
+ return interpolator;
+ }
+
+ /**
+ * Sets the Mapping Interpolator. Required by the ObjectMapping interface.
+ *
+ * @param interpolator
+ * Interpolator Object.
+ */
+ public void setInterpolator(Interpolator interpolator) {
+ this.interpolator = interpolator;
+ }
+
+ /**
+ *
+ */
+ public JPanel getLegend(VisualPropertyType vpt) {
+ return new ContinuousLegend(points, vpt);
+ }
+
+ /**
+ * Calculates the Range Value. Required by the ObjectMapping interface.
+ *
+ * @param attrBundle
+ * A Bundle of Attributes.
+ * @return Mapping object.
+ */
+ @Override
+ public Object calculateRangeValue(final Map<String, Object> attrBundle) {
+ final ContinuousRangeCalculator calc = new ContinuousRangeCalculator(
+ points, interpolator, attrBundle);
+
+ return calc.calculateRangeValue(controllingAttrName);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/mappings/CustomGraphicsRangeValueRenderer.java b/application/src/main/java/cytoscape/visual/mappings/CustomGraphicsRangeValueRenderer.java
new file mode 100644
index 0000000..9e3020b
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/mappings/CustomGraphicsRangeValueRenderer.java
@@ -0,0 +1,7 @@
+package cytoscape.visual.mappings;
+
+import cytoscape.visual.customgraphic.CyCustomGraphics;
+
+public interface CustomGraphicsRangeValueRenderer<T> {
+ public CyCustomGraphics create(final T value);
+}
diff --git a/application/src/main/java/cytoscape/visual/mappings/CustomMapping.java b/application/src/main/java/cytoscape/visual/mappings/CustomMapping.java
new file mode 100644
index 0000000..5830c1d
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/mappings/CustomMapping.java
@@ -0,0 +1,21 @@
+package cytoscape.visual.mappings;
+
+import java.awt.Component;
+
+/**
+ * User-definable visual mapping.
+ *
+ * @author kono
+ *
+ * @param <V>
+ */
+public interface CustomMapping {
+
+ /**
+ * Returns GUI component to edit detail of this mapping.
+ *
+ * @return - Component: GUI for editing this mapping.
+ */
+ public Component getMappingEditor();
+
+}
diff --git a/application/src/main/java/cytoscape/visual/mappings/DiscreteMapping.java b/application/src/main/java/cytoscape/visual/mappings/DiscreteMapping.java
new file mode 100644
index 0000000..9bc3a71
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/mappings/DiscreteMapping.java
@@ -0,0 +1,259 @@
+/*
+ File: DiscreteMapping.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual.mappings;
+
+import java.util.List;
+import java.util.Map;
+import java.util.Properties;
+import java.util.SortedMap;
+import java.util.TreeMap;
+
+import javax.swing.JPanel;
+import javax.swing.event.ChangeListener;
+
+import cytoscape.visual.NodeShape;
+import cytoscape.visual.VisualPropertyType;
+import cytoscape.visual.mappings.discrete.DiscreteLegend;
+import cytoscape.visual.mappings.discrete.DiscreteMappingReader;
+import cytoscape.visual.mappings.discrete.DiscreteMappingWriter;
+import cytoscape.visual.mappings.discrete.DiscreteRangeCalculator;
+import cytoscape.visual.parsers.ValueParser;
+
+/**
+ * Implements a lookup table mapping data to values of a particular class. The
+ * data value is extracted from a bundle of attributes by using a specified data
+ * attribute name.
+ */
+public class DiscreteMapping extends AbstractMapping {
+
+ private static final Class<?>[] ACCEPTED_CLASSES = { String.class,
+ Number.class, Integer.class, Double.class, Float.class, Long.class,
+ Short.class, NodeShape.class, List.class, Boolean.class };
+
+ private SortedMap treeMap; // contains the actual map
+ // elements (sorted)
+ private Object lastKey;
+
+ /**
+ * Constructor.
+ *
+ * @param defObj
+ * Default Object.
+ * @param mapType
+ * Map Type, ObjectMapping.EDGE_MAPPING or
+ * ObjectMapping.NODE_MAPPING.
+ *
+ * @deprecated Use new constructor instead. Will be removed in 10/2011.
+ * Controlling attribute name is always required, and now it's a part of constructor argument.
+ */
+ @Deprecated
+ public DiscreteMapping(Object defObj, byte mapType) {
+ this(defObj, null, mapType);
+ }
+
+ /**
+ * Constructor.
+ *
+ * @param defObj
+ * Default Object.
+ * @param attrName
+ * Controlling Attribute Name.
+ * @param mapType
+ * Map Type, ObjectMapping.EDGE_MAPPING or
+ * ObjectMapping.NODE_MAPPING.
+ *
+ * @deprecated Use new constructor instead. Will be removed in 10/2011.
+ * Controlling attribute name is always required, and now it's a part of constructor argument.
+ */
+ @Deprecated
+ public DiscreteMapping(Object defObj, String attrName, byte mapType) {
+ this((Class<?>)defObj.getClass(), attrName);
+ }
+
+
+ /**
+ * Constructor for Discrete mapping.
+ *
+ * @param rangeClass Mapped value type.
+ * @param controllingAttrName attribute name used in this mapping.
+ */
+ public DiscreteMapping(final Class<?> rangeClass,
+ final String controllingAttrName) {
+ super(rangeClass, controllingAttrName);
+ this.treeMap = new TreeMap();
+ this.acceptedClasses = ACCEPTED_CLASSES;
+ }
+
+ /**
+ * Clones the Object.
+ *
+ * @return DiscreteMapping Object.
+ */
+ public Object clone() {
+ final DiscreteMapping clone = new DiscreteMapping(rangeClass,
+ controllingAttrName);
+
+ // Copy over all listeners...
+ for (ChangeListener listener : observers)
+ clone.addChangeListener(listener);
+
+ // Copy key-value pairs
+ for (Object key : this.treeMap.keySet())
+ clone.treeMap.put(key, this.treeMap.get(key));
+
+ return clone;
+ }
+
+ /**
+ * Gets Value for Specified Key.
+ *
+ * @param key
+ * String Key.
+ * @return Object.
+ */
+ public Object getMapValue(Object key) {
+ return treeMap.get(key);
+ }
+
+ /**
+ * Puts New Key/Value in Map.
+ *
+ * @param key
+ * Key Object.
+ * @param value
+ * Value Object.
+ */
+ public void putMapValue(Object key, Object value) {
+ lastKey = key;
+
+ treeMap.put(key, value);
+ fireStateChanged();
+ }
+
+ /**
+ * Gets the Last Modified Key.
+ *
+ * @return Key Object.
+ */
+ public Object getLastKeyModified() {
+ return lastKey;
+ }
+
+ /**
+ * Adds All Members of Specified Map.
+ *
+ * @param map
+ * Map.
+ */
+ public void putAll(Map map) {
+ treeMap.putAll(map);
+ }
+
+ /**
+ * gets all map values
+ *
+ */
+ public Map getAll() {
+ return treeMap;
+ }
+
+ /**
+ * Customizes this object by applying mapping defintions described by the
+ * supplied Properties argument. Required by the ObjectMapping interface.
+ *
+ * @param props
+ * Properties Object.
+ * @param baseKey
+ * Base Key for finding properties.
+ * @param parser
+ * ValueParser Object.
+ */
+ public void applyProperties(Properties props, String baseKey,
+ ValueParser parser) {
+ final DiscreteMappingReader reader = new DiscreteMappingReader(props,
+ baseKey, parser);
+ final String contValue = reader.getControllingAttributeName();
+
+ if (contValue != null)
+ setControllingAttributeName(contValue);
+
+ this.treeMap = reader.getMap();
+ }
+
+ /**
+ * Returns a Properties object with entries suitable for customizing this
+ * object via the applyProperties method. Required by the ObjectMapping
+ * interface.
+ *
+ * @param baseKey
+ * Base Key for creating properties.
+ * @return Properties Object.
+ */
+ public Properties getProperties(String baseKey) {
+ final DiscreteMappingWriter writer = new DiscreteMappingWriter(
+ controllingAttrName, baseKey, treeMap);
+
+ return writer.getProperties();
+ }
+
+ /**
+ * Calculates the Range Value. Required by the ObjectMapping interface.
+ *
+ * @param attrBundle
+ * A Bundle of Attributes.
+ * @return Mapping object.
+ */
+ public Object calculateRangeValue(Map<String, Object> attrBundle) {
+ final DiscreteRangeCalculator calculator = new DiscreteRangeCalculator(
+ treeMap, controllingAttrName);
+
+ return calculator.calculateRangeValue(attrBundle);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param vpt
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public JPanel getLegend(VisualPropertyType vpt) {
+ return new DiscreteLegend(treeMap, controllingAttrName, vpt);
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/visual/mappings/FlatInterpolator.java b/application/src/main/java/cytoscape/visual/mappings/FlatInterpolator.java
new file mode 100644
index 0000000..d41fd47
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/mappings/FlatInterpolator.java
@@ -0,0 +1,100 @@
+/*
+ File: FlatInterpolator.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+//FlatInterpolator.java
+
+//----------------------------------------------------------------------------
+// $Revision: 10005 $
+// $Date: 2007-04-18 04:50:13 +0200 (Wed, 18 Apr 2007) $
+// $Author: kono $
+//----------------------------------------------------------------------------
+package cytoscape.visual.mappings;
+
+
+//----------------------------------------------------------------------------
+/**
+ * This simple Interpolator returns the value at either the lower or upper
+ * boundary of the domain. Note that no check is made whether the supplied
+ * domainValue is actually within the boundaries.
+ */
+public class FlatInterpolator
+ implements Interpolator {
+ /**
+ *
+ */
+ public static final Integer LOWER = new Integer(0);
+
+ /**
+ *
+ */
+ public static final Integer UPPER = new Integer(1);
+ private boolean useLower;
+
+ /**
+ * The default FlatInterpolator returns the range value at the lower boundary.
+ */
+ public FlatInterpolator() {
+ useLower = true;
+ }
+
+ /**
+ * Constructs a FlatInterpolator which returns the range value at the lower
+ * boundary unless the argument 'mode' is equal to FlatInterpolator.UPPER.
+ */
+ public FlatInterpolator(Integer mode) {
+ if (mode.equals(this.UPPER))
+ useLower = false;
+ else
+ useLower = true;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param lowerDomain DOCUMENT ME!
+ * @param lowerRange DOCUMENT ME!
+ * @param upperDomain DOCUMENT ME!
+ * @param upperRange DOCUMENT ME!
+ * @param domainValue DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getRangeValue(Object lowerDomain, Object lowerRange,
+ Object upperDomain, Object upperRange, Object domainValue) {
+ return ((useLower) ? lowerRange : upperRange);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/mappings/Interpolator.java b/application/src/main/java/cytoscape/visual/mappings/Interpolator.java
new file mode 100644
index 0000000..e126028
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/mappings/Interpolator.java
@@ -0,0 +1,62 @@
+/*
+ File: Interpolator.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.visual.mappings;
+
+/**
+ * This interface defines an interpolation function that takes two pairs
+ * of (domain,range) values plus a target domain value, and calculates an
+ * associated range value via some kind of interpolation.
+ *
+ * The behavior of this function is undefined if the target domain value
+ * is not equal to one of the boundaries or between them.
+ */
+public interface Interpolator {
+ /**
+ * DOCUMENT ME!
+ *
+ * @param lowerDomain DOCUMENT ME!
+ * @param lowerRange DOCUMENT ME!
+ * @param upperDomain DOCUMENT ME!
+ * @param upperRange DOCUMENT ME!
+ * @param domainValue DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getRangeValue(Object lowerDomain, Object lowerRange, Object upperDomain,
+ Object upperRange, Object domainValue);
+}
diff --git a/application/src/main/java/cytoscape/visual/mappings/InterpolatorFactory.java b/application/src/main/java/cytoscape/visual/mappings/InterpolatorFactory.java
new file mode 100644
index 0000000..2b015ce
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/mappings/InterpolatorFactory.java
@@ -0,0 +1,105 @@
+/*
+ File: InterpolatorFactory.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+//----------------------------------------------------------------------------
+// $Revision: 14060 $
+// $Date: 2008-05-20 22:13:18 +0200 (Tue, 20 May 2008) $
+// $Author: skillcoyne $
+//----------------------------------------------------------------------------
+package cytoscape.visual.mappings;
+
+
+//----------------------------------------------------------------------------
+import cytoscape.logger.CyLogger;
+
+import java.util.Properties;
+
+
+//----------------------------------------------------------------------------
+/**
+ * Provides static factory methods for constructing known interpolators from
+ * a recognized name, for example from a properties object.
+ */
+public class InterpolatorFactory {
+ /**
+ * Attempt to construct one of the standard interpolators. The argument
+ * should be the simple class name of a known interpolator (i.e., no
+ * package information).
+ *
+ */
+ public static Interpolator newInterpolator(String typeName) {
+ if (typeName == null) {
+ String s = "InterpolatorFactory: no Interpolator class specified";
+ CyLogger.getLogger().warn(s);
+
+ return null;
+ } else if (typeName.equals("LinearNumberToColorInterpolator")) {
+ return new LinearNumberToColorInterpolator();
+ } else if (typeName.equals("LinearNumberToNumberInterpolator")) {
+ return new LinearNumberToNumberInterpolator();
+ } else if (typeName.equals("FlatInterpolator")) {
+ return new FlatInterpolator();
+ } else {
+ String s = "InterpolatorFactory: unknown Interpolator type: " + typeName;
+ CyLogger.getLogger().warn(s);
+
+ return null;
+ }
+ }
+
+ /**
+ * Given an Interpolator, returns an identifying name as recognized
+ * by the newInterpolator method. null will be returned if the argument
+ * is null or of an unrecognized class type.
+ */
+ public static String getName(Interpolator fInt) {
+ if (fInt == null) {
+ return null;
+ } else if (fInt instanceof LinearNumberToColorInterpolator) {
+ return new String("LinearNumberToColorInterpolator");
+ } else if (fInt instanceof LinearNumberToNumberInterpolator) {
+ return new String("LinearNumberToNumberInterpolator");
+ } else if (fInt instanceof FlatInterpolator) {
+ return new String("FlatInterpolator");
+ } else {
+ String c = fInt.getClass().getName();
+ CyLogger.getLogger().warn("Unknown Interpolator type: " + c);
+
+ return null;
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/mappings/LegendTable.java b/application/src/main/java/cytoscape/visual/mappings/LegendTable.java
new file mode 100644
index 0000000..9302255
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/mappings/LegendTable.java
@@ -0,0 +1,171 @@
+/*
+ File: LegendTable.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual.mappings;
+
+import cytoscape.visual.VisualPropertyType;
+
+import cytoscape.visual.ui.icon.VisualPropertyIcon;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.GridLayout;
+
+import javax.swing.Icon;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JTable;
+import javax.swing.SwingConstants;
+import javax.swing.border.EmptyBorder;
+import javax.swing.border.MatteBorder;
+import javax.swing.table.TableCellRenderer;
+
+
+/**
+ * DOCUMENT ME!0
+1 *
+ * @author $author$
+ */
+public class LegendTable extends JPanel {
+ private static VisualPropertyType type;
+ private JTable legendTable;
+
+ /**
+ * Creates a new LegendTable object.
+ *
+ * @param data DOCUMENT ME!
+ * @param vpt DOCUMENT ME!
+ */
+ public LegendTable(Object[][] data, VisualPropertyType vpt) {
+ super();
+ legendTable = new JTable(data.length, 2);
+ legendTable.setRowHeight(50);
+ legendTable.setDefaultRenderer(Object.class, (TableCellRenderer) new LegendCellRenderer());
+ type = vpt;
+ setLayout(new BorderLayout());
+
+ Object value = null;
+
+ for (int i = 0; i < data.length; i++) {
+ value = getValue(data[i][0]);
+
+ if (value != null) {
+ legendTable.getModel().setValueAt(value, i, 0);
+ }
+
+ legendTable.getModel().setValueAt(data[i][1], i, 1);
+ }
+
+ add(legendTable, SwingConstants.CENTER);
+ }
+
+ private Object getValue(final Object value) {
+ final VisualPropertyIcon icon;
+
+ if (value == null) {
+ return null;
+ }
+
+ icon = (VisualPropertyIcon) type.getVisualProperty().getIcon(value);
+ icon.setLeftPadding(5);
+
+ return icon;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param attrName DOCUMENT ME!
+ * @param type DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static JPanel getHeader(String attrName, VisualPropertyType type) {
+ final JPanel titles = new JPanel();
+ final JLabel[] labels = new JLabel[2];
+ labels[0] = new JLabel(type.getName());
+ labels[1] = new JLabel(attrName);
+
+ for (int i = 0; i < labels.length; i++) {
+ labels[i].setVerticalAlignment(SwingConstants.CENTER);
+ labels[i].setHorizontalAlignment(SwingConstants.LEADING);
+ labels[i].setVerticalTextPosition(SwingConstants.CENTER);
+ labels[i].setHorizontalTextPosition(SwingConstants.LEADING);
+ labels[i].setForeground(Color.DARK_GRAY);
+ labels[i].setBorder(new EmptyBorder(10, 0, 7, 10));
+ labels[i].setFont(new Font("SansSerif", Font.BOLD, 14));
+ }
+
+ titles.setLayout(new GridLayout(1, 2));
+ titles.setBackground(Color.white);
+
+ titles.add(labels[0]);
+ titles.add(labels[1]);
+ titles.setBorder(new MatteBorder(0, 0, 1, 0, Color.DARK_GRAY));
+
+ return titles;
+ }
+
+ public class LegendCellRenderer implements TableCellRenderer {
+ public Component getTableCellRendererComponent(JTable table, Object value,
+ boolean isSelected, boolean hasFocus,
+ int row, int column) {
+ final JLabel cell = new JLabel();
+
+ if (value instanceof Icon) {
+ VisualPropertyIcon icon = (VisualPropertyIcon) value;
+ icon.setBottomPadding(0);
+ cell.setIcon(icon);
+
+ cell.setVerticalAlignment(SwingConstants.CENTER);
+ cell.setHorizontalAlignment(SwingConstants.CENTER);
+ } else {
+ cell.setText(value.toString());
+ cell.setVerticalTextPosition(SwingConstants.CENTER);
+ cell.setVerticalAlignment(SwingConstants.CENTER);
+ cell.setHorizontalAlignment(SwingConstants.LEADING);
+ cell.setHorizontalTextPosition(SwingConstants.LEADING);
+ }
+
+ cell.setPreferredSize(new Dimension(170, 1));
+
+ return cell;
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/mappings/LinearNumberInterpolator.java b/application/src/main/java/cytoscape/visual/mappings/LinearNumberInterpolator.java
new file mode 100644
index 0000000..40c9373
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/mappings/LinearNumberInterpolator.java
@@ -0,0 +1,87 @@
+/*
+ File: LinearNumberInterpolator.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+//LinearNumberInterpolator.java
+
+//----------------------------------------------------------------------------
+// $Revision: 10005 $
+// $Date: 2007-04-18 04:50:13 +0200 (Wed, 18 Apr 2007) $
+// $Author: kono $
+//----------------------------------------------------------------------------
+package cytoscape.visual.mappings;
+
+
+//----------------------------------------------------------------------------
+/**
+ * This subclass of NumberInterpolator further assumes a linear interpolation,
+ * and calculates the fractional distance of the target domain value from
+ * the lower boundary value for the convenience of subclasses.
+ */
+abstract public class LinearNumberInterpolator extends NumberInterpolator {
+ /**
+ * DOCUMENT ME!
+ *
+ * @param lowerDomain DOCUMENT ME!
+ * @param lowerRange DOCUMENT ME!
+ * @param upperDomain DOCUMENT ME!
+ * @param upperRange DOCUMENT ME!
+ * @param domainValue DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getRangeValue(double lowerDomain, Object lowerRange,
+ double upperDomain, Object upperRange, double domainValue) {
+ if (lowerDomain == upperDomain)
+ return lowerRange;
+
+ double frac = (domainValue - lowerDomain) / (upperDomain - lowerDomain);
+
+ return getRangeValue(frac, lowerRange, upperRange);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param frac DOCUMENT ME!
+ * @param lowerRange DOCUMENT ME!
+ * @param upperRange DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ abstract public Object getRangeValue(double frac, Object lowerRange,
+ Object upperRange);
+}
diff --git a/application/src/main/java/cytoscape/visual/mappings/LinearNumberToColorInterpolator.java b/application/src/main/java/cytoscape/visual/mappings/LinearNumberToColorInterpolator.java
new file mode 100644
index 0000000..c812a3d
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/mappings/LinearNumberToColorInterpolator.java
@@ -0,0 +1,91 @@
+/*
+ File: LinearNumberToColorInterpolator.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+//LinearNumberToColorInterpolator.java
+package cytoscape.visual.mappings;
+
+import java.awt.Color;
+
+
+/**
+ * The class provides a linear interpolation between color values. The
+ * (red,green,blue,alpha) values of the returned color are linearly
+ * interpolated from the associated values of the lower and upper colors,
+ * according the the fractional distance frac from the lower value.
+ *
+ * If either object argument is not a Color, null is returned.
+ */
+public class LinearNumberToColorInterpolator extends LinearNumberInterpolator {
+ /**
+ * Creates a new LinearNumberToColorInterpolator object.
+ */
+ public LinearNumberToColorInterpolator() {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param frac DOCUMENT ME!
+ * @param lowerRange DOCUMENT ME!
+ * @param upperRange DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getRangeValue(double frac, Object lowerRange,
+ Object upperRange) {
+ if (!(lowerRange instanceof Color))
+ return null;
+
+ if (!(upperRange instanceof Color))
+ return null;
+
+ Color lowerColor = (Color) lowerRange;
+ Color upperColor = (Color) upperRange;
+
+ double red = lowerColor.getRed() +
+ (frac * (upperColor.getRed() - lowerColor.getRed()));
+ double green = lowerColor.getGreen() +
+ (frac * (upperColor.getGreen() - lowerColor.getGreen()));
+ double blue = lowerColor.getBlue() +
+ (frac * (upperColor.getBlue() - lowerColor.getBlue()));
+ double alpha = lowerColor.getAlpha() +
+ (frac * (upperColor.getAlpha() - lowerColor.getAlpha()));
+
+ return new Color((int) Math.round(red), (int) Math.round(green),
+ (int) Math.round(blue), (int) Math.round(alpha));
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/mappings/LinearNumberToNumberInterpolator.java b/application/src/main/java/cytoscape/visual/mappings/LinearNumberToNumberInterpolator.java
new file mode 100644
index 0000000..5d12ba3
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/mappings/LinearNumberToNumberInterpolator.java
@@ -0,0 +1,86 @@
+/*
+ File: LinearNumberToNumberInterpolator.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+//LinearNumberToNumberInterpolator.java
+
+//----------------------------------------------------------------------------
+// $Revision: 10005 $
+// $Date: 2007-04-18 04:50:13 +0200 (Wed, 18 Apr 2007) $
+// $Author: kono $
+//----------------------------------------------------------------------------
+package cytoscape.visual.mappings;
+
+
+//----------------------------------------------------------------------------
+/**
+ * The class assumes that the supplied range objects are Numbers, and returns a
+ * linearly interplated value according to the value of frac.
+ *
+ * If either object argument is not a Number, null is returned.
+ */
+public class LinearNumberToNumberInterpolator extends LinearNumberInterpolator {
+ /**
+ * Creates a new LinearNumberToNumberInterpolator object.
+ */
+ public LinearNumberToNumberInterpolator() {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param frac DOCUMENT ME!
+ * @param lowerRange DOCUMENT ME!
+ * @param upperRange DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getRangeValue(double frac, Object lowerRange,
+ Object upperRange) {
+ if (!(lowerRange instanceof Number))
+ return null;
+
+ if (!(upperRange instanceof Number))
+ return null;
+
+ double lowerVal = ((Number) lowerRange).doubleValue();
+ double upperVal = ((Number) upperRange).doubleValue();
+
+ double returnVal = (frac * upperVal) + ((1.0 - frac) * lowerVal);
+
+ return new Double(returnVal);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/mappings/MappingFactory.java b/application/src/main/java/cytoscape/visual/mappings/MappingFactory.java
new file mode 100644
index 0000000..6734937
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/mappings/MappingFactory.java
@@ -0,0 +1,125 @@
+/*
+ File: MappingFactory.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.visual.mappings;
+
+import java.util.Properties;
+
+import cytoscape.logger.CyLogger;
+import cytoscape.visual.parsers.ValueParser;
+
+
+/**
+ * This class provides a static factory method for constructing an instance
+ * of ObjectMapping as specified by a Properties object and other arguments.
+ *
+ * Since there are currently only a few types of mappings known, it's easiest
+ * to simply check each case and construct the right mapping without going
+ * through a dynamic class-discovery instantiation process. If the number of
+ * mappings ever gets out of hand, we can always switch to a dynamic algorithm.
+ */
+public class MappingFactory {
+ /**
+ * Attempt to construct an instance of ObjectMapping as defined by
+ * the supplied arguments. Checks the value of a recognized key in
+ * the Properties argument against a list of known Mappings. If found,
+ * constructs the Mapping object and then customizes it by calling its
+ * applyProperties method.
+ */
+ public static ObjectMapping newMapping(Properties props, String baseKey,
+ ValueParser parser, Object defObj, byte mapType) {
+ String typeName = props.getProperty(baseKey + ".type");
+
+ if (typeName == null) {
+ CyLogger.getLogger().warn(
+ "MappingFactory: no Mapping class specified in properties");
+
+ return null;
+ } else if (typeName.equals("DiscreteMapping")) {
+ DiscreteMapping m = new DiscreteMapping(defObj.getClass(), null);
+ m.applyProperties(props, baseKey, parser);
+
+ return m;
+ } else if (typeName.equals("ContinuousMapping")) {
+ ContinuousMapping m = new ContinuousMapping(defObj.getClass(), null);
+ m.applyProperties(props, baseKey, parser);
+
+ return m;
+ } else if (typeName.equals("PassThroughMapping")) {
+ final PassThroughMapping m = new PassThroughMapping(defObj.getClass(), null);
+ m.applyProperties(props, baseKey, parser);
+
+ return m;
+ } else {
+ CyLogger.getLogger().warn("MappingFactory: unknown Mapping type: " +
+ typeName);
+
+ return null;
+ }
+ }
+
+
+ /**
+ * Gets a description of the supplied ObjectMapping as properties.
+ * This method calls the getProperties() method of the ObjectMapping
+ * argument and then adds a property to identify the mapping class,
+ * in a form recognized by the newMapping method.
+ */
+ public static Properties getProperties(ObjectMapping m, String baseKey) {
+ if (m == null)
+ return null;
+
+ Properties newProps = m.getProperties(baseKey);
+
+ if (m instanceof DiscreteMapping)
+ newProps.setProperty(baseKey + ".type", "DiscreteMapping");
+ else if (m instanceof ContinuousMapping)
+ newProps.setProperty(baseKey + ".type", "ContinuousMapping");
+ else if (m instanceof PassThroughMapping)
+ newProps.setProperty(baseKey + ".type", "PassThroughMapping");
+ else { //highly unexpected type
+
+ String c = m.getClass()
+ .getName();
+ CyLogger.getLogger().warn("MappingFactory: unknown Mapping type: " + c);
+
+ return null;
+ }
+
+ return newProps;
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/mappings/MappingManager.java b/application/src/main/java/cytoscape/visual/mappings/MappingManager.java
new file mode 100644
index 0000000..c6d238b
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/mappings/MappingManager.java
@@ -0,0 +1,9 @@
+package cytoscape.visual.mappings;
+
+public interface MappingManager {
+
+ public void register(Class<? extends ObjectMapping> type);
+
+ public ObjectMapping createMapping(final byte objectType, final Object defObject);
+
+}
diff --git a/application/src/main/java/cytoscape/visual/mappings/MappingManagerImpl.java b/application/src/main/java/cytoscape/visual/mappings/MappingManagerImpl.java
new file mode 100644
index 0000000..8d2b28b
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/mappings/MappingManagerImpl.java
@@ -0,0 +1,17 @@
+package cytoscape.visual.mappings;
+
+public class MappingManagerImpl implements MappingManager {
+
+
+ public ObjectMapping createMapping(byte objectType, Object defObject) {
+
+ return null;
+ }
+
+
+
+ public void register(Class<? extends ObjectMapping> type) {
+
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/visual/mappings/MappingType.java b/application/src/main/java/cytoscape/visual/mappings/MappingType.java
new file mode 100644
index 0000000..8432aab
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/mappings/MappingType.java
@@ -0,0 +1,64 @@
+package cytoscape.visual.mappings;
+
+
+/**
+ * Defines visual mapping types.
+ * This replaces all hard-coded strings related to mappings.
+ *
+ * @author Keiichiro Ono
+ * @version 0.5
+ * @since Cytoscape 2.5
+ */
+public enum MappingType {DISCRETE("Discrete"), CONTINUOUS("Continuous"),
+ PASSTHROUGH("Passthrough");
+ private String name;
+
+ private MappingType(String name) {
+ this.name = name;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getName() {
+ return name + " Mapping";
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getBaseKey() {
+ return name + "Mapping";
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getPropertyKey() {
+ return name + ".type";
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param baseKey DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ * @deprecated Will be removed 5/2008
+ */
+ @Deprecated
+ public static MappingType getMappingType(final String baseKey) {
+ for (MappingType type : values()) {
+ if (baseKey.equals(type.getBaseKey()))
+ return type;
+ }
+
+ return null;
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/mappings/MappingUtil.java b/application/src/main/java/cytoscape/visual/mappings/MappingUtil.java
new file mode 100644
index 0000000..70268a5
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/mappings/MappingUtil.java
@@ -0,0 +1,95 @@
+/*
+ File: MappingUtil.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.visual.mappings;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.data.CyAttributes;
+
+import java.lang.*;
+
+
+/**
+ * Provides simple utility methods for the Mapping classes.
+ */
+public class MappingUtil {
+ /**
+ * This method determines the type of the attr used and
+ * returns a string representation of it.
+ */
+ public static String getAttributeTypeString(String base, String attr) {
+ Byte B = new Byte(getAttributeType(base, attr));
+
+ return B.toString();
+ }
+
+ /**
+ * This method determines the type of the attribute used
+ * for the mapping. The purpose is to support discrete attrs
+ * aside from strings.
+ */
+ public static byte getAttributeType(String base, String attr) {
+ byte b = CyAttributes.TYPE_UNDEFINED;
+
+ if (base.startsWith("node"))
+ b = Cytoscape.getNodeAttributes()
+ .getType(attr);
+ else if (base.startsWith("edge"))
+ b = Cytoscape.getEdgeAttributes()
+ .getType(attr);
+
+ return b;
+ }
+
+ /**
+ * This method returns an object of the specified type
+ * based on the string read from the props file.
+ */
+ public static Object parseObjectType(String key, byte attrType) {
+ if (attrType == CyAttributes.TYPE_INTEGER)
+ return new Integer(key);
+ else if (attrType == CyAttributes.TYPE_FLOATING)
+ return new Double(key);
+ else if (attrType == CyAttributes.TYPE_BOOLEAN)
+ return new Boolean(key);
+
+ // assume string
+ else
+
+ return key;
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/mappings/NumberInterpolator.java b/application/src/main/java/cytoscape/visual/mappings/NumberInterpolator.java
new file mode 100644
index 0000000..b6f8bc3
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/mappings/NumberInterpolator.java
@@ -0,0 +1,103 @@
+/*
+ File: NumberInterpolator.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+//NumberInterpolator.java
+
+//----------------------------------------------------------------------------
+// $Revision: 9736 $
+// $Date: 2007-03-20 01:25:45 +0100 (Tue, 20 Mar 2007) $
+// $Author: mes $
+//----------------------------------------------------------------------------
+package cytoscape.visual.mappings;
+
+
+//----------------------------------------------------------------------------
+/**
+ * This partial implementation of Interpolator assumes that the domain
+ * values are some kind of number, and extracts the values into ordinary
+ * doubles for the convenience of subclasses. If any argument is null, or
+ * if any of the domain values is not an instance of Number, null is returned.
+ */
+abstract public class NumberInterpolator implements Interpolator {
+ /**
+ * DOCUMENT ME!
+ *
+ * @param lowerDomain DOCUMENT ME!
+ * @param lowerRange DOCUMENT ME!
+ * @param upperDomain DOCUMENT ME!
+ * @param upperRange DOCUMENT ME!
+ * @param domainValue DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getRangeValue(Object lowerDomain, Object lowerRange, Object upperDomain,
+ Object upperRange, Object domainValue) {
+ if ((lowerRange == null) || (upperRange == null)) {
+ return null;
+ }
+
+ if ((lowerDomain == null) || !(lowerDomain instanceof Number)) {
+ return null;
+ }
+
+ if ((upperDomain == null) || !(upperDomain instanceof Number)) {
+ return null;
+ }
+
+ if ((domainValue == null) || !(domainValue instanceof Number)) {
+ return null;
+ }
+
+ return getRangeValue(((Number) lowerDomain).doubleValue(), lowerRange,
+ ((Number) upperDomain).doubleValue(), upperRange,
+ ((Number) domainValue).doubleValue());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param lowerDomain DOCUMENT ME!
+ * @param lowerRange DOCUMENT ME!
+ * @param upperDomain DOCUMENT ME!
+ * @param upperRange DOCUMENT ME!
+ * @param domainValue DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ abstract public Object getRangeValue(double lowerDomain, Object lowerRange, double upperDomain,
+ Object upperRange, double domainValue);
+}
diff --git a/application/src/main/java/cytoscape/visual/mappings/ObjectMapping.java b/application/src/main/java/cytoscape/visual/mappings/ObjectMapping.java
new file mode 100644
index 0000000..8e09374
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/mappings/ObjectMapping.java
@@ -0,0 +1,179 @@
+/*
+ File: ObjectMapping.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.visual.mappings;
+
+import java.util.Map;
+import java.util.Properties;
+
+import javax.swing.JDialog;
+import javax.swing.JPanel;
+import javax.swing.event.ChangeListener;
+
+import cytoscape.CyNetwork;
+import cytoscape.visual.VisualPropertyType;
+import cytoscape.visual.parsers.ValueParser;
+
+
+/**
+ * Mappings should implement this interface. Mappings are classes that map from
+ * a value stored in the edge attributes or node attributes HashMap in
+ * {@link cytoscape.CyAttributes}. The range of the mapping depends on the
+ * {@link cytoscape.visual.calculators.AbstractCalculator} that owns
+ * the mapping.
+ * <p>
+ * All classes implementing this interface <b>MUST</b> have a constructor that
+ * takes the arguments Object, CyNetwork, byte, where Object is the default object
+ * the mapper should map to, CyNetwork is the CyNetwork object representing the network
+ * displayed in Cytoscape, and the byte is one of {@link #EDGE_MAPPING} or
+ * {@link #NODE_MAPPING}.
+ *
+ * K - Key attribute value. Can be any type (for this implementation, number, string, boolean, list, or map).
+ * V - Mapped visual value, such as color, node shape, etc.
+ *
+ */
+public interface ObjectMapping extends Cloneable {
+
+ @Deprecated // Use attribute name to determine mapping type.
+ public static final byte EDGE_MAPPING = 0;
+ @Deprecated
+ public static final byte NODE_MAPPING = 1;
+
+
+ /**
+ * Class of mapped object. For example, if this is an Node Color mapping,
+ * this value is Color.class.
+ *
+ * @return
+ */
+ public Class<?> getRangeClass();
+
+ /**
+ * Return the classes that the ObjectMapping can map from, eg. the contents
+ * of the data of the controlling attribute.
+ * <p>
+ * For example, DiscreteMapping {@link DiscreteMapping} can only accept
+ * String types in the mapped attribute data. Likewise, ContinuousMapping
+ * {@link ContinuousMapping} can only accept numeric types in the mapped
+ * attribute data since it must interpolate.
+ * <p>
+ * Return null if this mapping has no restrictions on the domain type.
+ *
+ * @return Array of accepted attribute data class types
+ */
+ public Class<?>[] getAcceptedDataClasses();
+
+ /**
+ * Set the controlling attribute name. The current mappings will be unchanged
+ * if preserveMapping is true and cleared otherwise. The network argument is
+ * provided so that the current values for the given attribute name can
+ * be loaded for UI purposes. Null values for the network argument are allowed.
+ *
+ * Do not use this method. None of the network, preserveMapping parameters are used in Cytoscape.
+ *
+ * @deprecated Will be removed in 2.8. Use setControllingAttributeName(final String controllingAttrName) instead.
+ *
+ */
+ @Deprecated
+ public void setControllingAttributeName(String attrName, CyNetwork network,
+ boolean preserveMapping);
+
+
+ /**
+ * Set controlling attribute of this mapping.
+ *
+ * @param controllingAttrName - name of the attribute associated with this mapping.
+ *
+ */
+ public void setControllingAttributeName(final String controllingAttrName);
+
+
+ /**
+ * Get the controlling attribute name
+ */
+ public String getControllingAttributeName();
+
+ /**
+ * Add a ChangeListener to the mapping. When the state underlying the
+ * mapping changes, all ChangeListeners will be notified.
+ *
+ * This is used in the UI classes to ensure that the UI panes stay consistent
+ * with the data held in the mappings.
+ *
+ * @param l ChangeListener to add
+ */
+ public void addChangeListener(ChangeListener l);
+
+ /**
+ * Remove a ChangeListener from the mapping. When the state underlying the
+ * mapping changes, all ChangeListeners will be notified.
+ *
+ * This is used in the UI classes to ensure that the UI panes stay consistent
+ * with the data held in the mappings.
+ *
+ * @param l ChangeListener to add
+ */
+ public void removeChangeListener(ChangeListener l);
+
+ /**
+ * Create a mapped visual representation from the given attribute value.
+ *
+ * @param attrBundle
+ * @return
+ */
+ public Object calculateRangeValue(final Map<String, Object> attrBundle);
+
+ public JPanel getLegend(VisualPropertyType type);
+
+ public Object clone();
+
+ public void applyProperties(Properties props, String baseKey, ValueParser parser);
+
+ public Properties getProperties(String baseKey);
+
+ /**
+ * Do not use this method. Will be removed in next release (2.8)
+ *
+ * It was for old VizMape GUI which was removed in 2.5.
+ *
+ * @param parent
+ * @param network
+ * @return
+ */
+ @Deprecated
+ public JPanel getUI(JDialog parent, CyNetwork network);
+}
diff --git a/application/src/main/java/cytoscape/visual/mappings/PassThroughMapping.java b/application/src/main/java/cytoscape/visual/mappings/PassThroughMapping.java
new file mode 100644
index 0000000..505b588
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/mappings/PassThroughMapping.java
@@ -0,0 +1,249 @@
+/*
+ File: PassThroughMapping.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+package cytoscape.visual.mappings;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.util.Map;
+import java.util.Properties;
+
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.SwingConstants;
+import javax.swing.event.ChangeListener;
+
+import org.jdesktop.swingx.border.DropShadowBorder;
+
+import cytoscape.Cytoscape;
+import cytoscape.visual.VisualPropertyType;
+import cytoscape.visual.parsers.ValueParser;
+
+/**
+ * Defines a mapping from a bundle of data attributes to a visual attribute. The
+ * returned value is simply the value of one of the data attributes, defined by
+ * the controlling attribute name. This value is type-checked against the
+ * expected range class; null is returned instead if the data value is of the
+ * wrong type.
+ */
+public class PassThroughMapping extends AbstractMapping {
+
+ // Legend UI theme
+ private static final Font TITLE_FONT = new Font("SansSerif", Font.BOLD, 14);
+ private static final Color TITLE_COLOR = new Color(10, 200, 255);
+
+ private RangeValueCalculator rangeValueCalculator;
+
+ private final Class<?>[] ACCEPTED_CLASS = { Object.class };
+
+ /**
+ * Standard constructor for compatibility with new calculator creation in
+ * the UI.
+ *
+ * @param defaultObj
+ * Default object - provided only to establish mapping's range
+ * class.
+ * @param mapType
+ * unused.
+ *
+ * Will be removed in the next release (2.8). Map Type is not in
+ * use.
+ *
+ * @deprecated Use new constructor instead. Will be removed in 10/2011.
+ * Controlling attribute name is always required, and now it's a part of constructor argument.
+ */
+ @Deprecated
+ public PassThroughMapping(final Object defaultObj, final byte mapType) {
+ this(defaultObj, null);
+ }
+
+ /**
+ * Creates a new PassThroughMapping object.
+ *
+ * @param defaultObj
+ * DOCUMENT ME!
+ *
+ * @deprecated Use new constructor instead. Will be removed in 10/2011.
+ * Controlling attribute name is always required, and now it's a part of constructor argument.
+ */
+ @Deprecated
+ public PassThroughMapping(final Object defaultObj) {
+ this(defaultObj, null);
+ }
+
+
+ /**
+ *
+ * @param defaultObj
+ * @param attrName
+ *
+ * @deprecated Use new constructor instead. Will be removed in 10/2011.
+ * Controlling attribute name is always required, and now it's a part of constructor argument.
+ */
+ @Deprecated
+ public PassThroughMapping(Object defaultObj, String attrName) {
+ this((Class<?>)defaultObj.getClass(), attrName);
+ }
+
+ /**
+ * Creates a new PassThroughMapping object.
+ *
+ * @param defaultObj
+ * DOCUMENT ME!
+ * @param controllingAttributeName
+ * DOCUMENT ME!
+ */
+ public PassThroughMapping(final Class<?> rangeClass, final String controllingAttributeName) {
+ super(rangeClass, controllingAttributeName);
+ this.acceptedClasses = ACCEPTED_CLASS;
+ }
+
+ /**
+ * Create clone of this instance.
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object clone() {
+ final PassThroughMapping copy = new PassThroughMapping(this.rangeClass, this.controllingAttrName);
+
+ // don't need to explicitly clone rangeClass since cloned calculator
+ // has same type as original.
+ return copy;
+ }
+
+
+ /**
+ * Empty implementation because PassThroughMapping has no UI.
+ */
+ public void addChangeListener(ChangeListener l) {
+ }
+
+ /**
+ * Empty implementation because PassThroughMapping has no UI.
+ */
+ public void removeChangeListener(ChangeListener l) {
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param attrBundle
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object calculateRangeValue(final Map<String, Object> attrBundle) {
+ if (attrBundle == null || controllingAttrName == null)
+ return null;
+
+ // extract the data value for our controlling attribute
+ final Object attrValue = attrBundle.get(controllingAttrName);
+
+ if (attrValue == null)
+ return null;
+
+ if(rangeValueCalculator == null)
+ rangeValueCalculator = Cytoscape.getVisualMappingManager().
+ getRangeValueCalculatorFactory().getRangeValueCalculator(rangeClass);
+ if(rangeValueCalculator != null)
+ return rangeValueCalculator.getRange(attrValue);
+ return null;
+ }
+
+ public RangeValueCalculator<?> getRangeValueCalculator() {
+ return this.rangeValueCalculator;
+ }
+
+ /**
+ * Customize this object by applying mapping defintions described by the
+ * supplied Properties argument.
+ */
+ public void applyProperties(Properties props, String baseKey,
+ ValueParser parser) {
+ String contKey = baseKey + ".controller";
+ String contValue = props.getProperty(contKey);
+
+ if (contValue != null)
+ setControllingAttributeName(contValue);
+ }
+
+ /**
+ * Return a Properties object with entries suitable for customizing this
+ * object via the applyProperties method.
+ */
+ public Properties getProperties(String baseKey) {
+ Properties newProps = new Properties();
+ String contKey = baseKey + ".controller";
+ String contValue = controllingAttrName;
+
+ if ((contKey != null) && (contValue != null))
+ newProps.setProperty(contKey, contValue);
+
+ return newProps;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param vpt
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public JPanel getLegend(VisualPropertyType vpt) {
+ JPanel p = new JPanel();
+ p.setLayout(new BorderLayout());
+
+ JLabel title = new JLabel(vpt.getName() + " is displayed as "
+ + controllingAttrName);
+ title.setFont(TITLE_FONT);
+ title.setForeground(TITLE_COLOR);
+ title.setHorizontalAlignment(SwingConstants.CENTER);
+ title.setVerticalAlignment(SwingConstants.CENTER);
+ title.setHorizontalTextPosition(SwingConstants.CENTER);
+ title.setVerticalTextPosition(SwingConstants.CENTER);
+ title.setPreferredSize(new Dimension(200, 50));
+ title.setBorder(new DropShadowBorder());
+ p.setBackground(Color.white);
+ p.add(title, SwingConstants.CENTER);
+
+ return p;
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/mappings/RangeValueCalculator.java b/application/src/main/java/cytoscape/visual/mappings/RangeValueCalculator.java
new file mode 100644
index 0000000..41a11c5
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/mappings/RangeValueCalculator.java
@@ -0,0 +1,7 @@
+package cytoscape.visual.mappings;
+
+public interface RangeValueCalculator<T> {
+ public T getRange(final Object attrValue);
+
+ public boolean isCompatible(final Class<?> type);
+}
diff --git a/application/src/main/java/cytoscape/visual/mappings/RangeValueCalculatorFactory.java b/application/src/main/java/cytoscape/visual/mappings/RangeValueCalculatorFactory.java
new file mode 100644
index 0000000..9660f2b
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/mappings/RangeValueCalculatorFactory.java
@@ -0,0 +1,7 @@
+package cytoscape.visual.mappings;
+
+public interface RangeValueCalculatorFactory {
+ public <T extends RangeValueCalculator<?>> T getRangeValueCalculator(final Class<?> type);
+
+ public void registerRVC(final RangeValueCalculator<?> rvc);
+}
diff --git a/application/src/main/java/cytoscape/visual/mappings/RangeValueCalculatorFactoryImpl.java b/application/src/main/java/cytoscape/visual/mappings/RangeValueCalculatorFactoryImpl.java
new file mode 100644
index 0000000..3b41c2e
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/mappings/RangeValueCalculatorFactoryImpl.java
@@ -0,0 +1,48 @@
+package cytoscape.visual.mappings;
+
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Map;
+import java.util.Set;
+
+import cytoscape.logger.CyLogger;
+
+public class RangeValueCalculatorFactoryImpl implements
+ RangeValueCalculatorFactory {
+
+ private final Map<Class<?>, RangeValueCalculator<?>> calcMap;
+ private final Set<RangeValueCalculator<?>> calcs;
+
+ private static final CyLogger logger = CyLogger.getLogger();
+
+ public RangeValueCalculatorFactoryImpl() {
+ calcMap = new HashMap<Class<?>, RangeValueCalculator<?>>();
+ calcs = new HashSet<RangeValueCalculator<?>>();
+ }
+
+
+ public <T extends RangeValueCalculator<?>> T getRangeValueCalculator(
+ Class<?> type) {
+
+ RangeValueCalculator<?> calc = calcMap.get(type);
+
+ if(calc == null) {
+ for(RangeValueCalculator<?> c: calcs) {
+ if(c.isCompatible(type)) {
+ calcMap.put(type, c);
+ calc = c;
+ return (T) calc;
+ }
+ }
+ }
+
+ logger.warn("Could not find RVC: " + calc);
+ return (T) calc;
+ }
+
+
+ public void registerRVC(RangeValueCalculator<?> rvc) {
+ calcs.add(rvc);
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/visual/mappings/continuous/ContinuousLegend.java b/application/src/main/java/cytoscape/visual/mappings/continuous/ContinuousLegend.java
new file mode 100644
index 0000000..14f2a7e
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/mappings/continuous/ContinuousLegend.java
@@ -0,0 +1,262 @@
+/*
+ File: ContinuousLegend.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.visual.mappings.continuous;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.GradientPaint;
+import java.awt.Graphics2D;
+import java.awt.GridLayout;
+import java.awt.Rectangle;
+import java.awt.RenderingHints;
+import java.awt.event.ComponentAdapter;
+import java.awt.event.ComponentEvent;
+import java.awt.image.BufferedImage;
+import java.util.List;
+
+import javax.swing.ImageIcon;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.SwingConstants;
+import javax.swing.border.Border;
+import javax.swing.border.EmptyBorder;
+import javax.swing.border.MatteBorder;
+
+import cytoscape.visual.VisualPropertyType;
+import cytoscape.visual.mappings.LegendTable;
+import cytoscape.visual.ui.editors.continuous.C2CMappingEditor;
+import cytoscape.visual.ui.editors.continuous.C2DMappingEditor;
+import cytoscape.visual.ui.editors.continuous.GradientEditorPanel;
+
+
+/**
+ *
+ */
+public class ContinuousLegend extends JPanel {
+ private static final Font TITLE_FONT2 = new Font("SansSerif", Font.BOLD, 18);
+ private static final Color TITLE_COLOR = new Color(10, 200, 255);
+ private static final Border BORDER = new MatteBorder(0, 6, 3, 0, Color.DARK_GRAY);
+ private List points;
+ private VisualPropertyType type;
+ private JLabel legend = null;
+
+ /**
+ * Creates a new ContinuousLegend object.
+ *
+ * @param dataAttr DOCUMENT ME!
+ * @param points DOCUMENT ME!
+ * @param obj DOCUMENT ME!
+ * @param vpt DOCUMENT ME!
+ */
+ @Deprecated
+ public ContinuousLegend(String dataAttr, List points, Object obj, VisualPropertyType vpt) {
+ this(points, vpt);
+ }
+
+
+ public ContinuousLegend(List points, VisualPropertyType vpt) {
+ super();
+ this.points = points;
+ this.type = vpt;
+ this.addComponentListener(new ComponentAdapter() {
+ public void componentResized(ComponentEvent e) {
+ setLegend(e);
+ }
+ });
+
+ setLayout(new BorderLayout());
+ setBackground(Color.white);
+ setBorder(BORDER);
+
+ final JLabel title = new JLabel(" " + vpt.getName() + " Mapping");
+ title.setFont(TITLE_FONT2);
+ title.setForeground(TITLE_COLOR);
+ title.setBorder(new MatteBorder(0, 10, 1, 0, TITLE_COLOR));
+
+ title.setHorizontalTextPosition(SwingConstants.LEADING);
+ title.setPreferredSize(new Dimension(1, 50));
+ add(title, BorderLayout.NORTH);
+
+ setLegend(null);
+ }
+
+ private void setLegend(ComponentEvent e) {
+ if (legend != null) {
+ remove(legend);
+ }
+
+ Integer trackW = null;
+
+ if (getParent() == null) {
+ trackW = 600;
+ } else {
+ trackW = ((Number)(this.getParent().getParent().getParent().getWidth()*0.82)).intValue();
+ if(trackW < 200) {
+ trackW = 200;
+ }
+ }
+
+ if (type.getDataType() == Color.class) {
+ legend = new JLabel(GradientEditorPanel.getLegend(trackW, 100, type));
+ } else if (type.getDataType() == Number.class) {
+ legend = new JLabel(C2CMappingEditor.getLegend(trackW, 150, type));
+ } else {
+ legend = new JLabel(C2DMappingEditor.getLegend(trackW, 150, type));
+ }
+
+ legend.setBorder(new EmptyBorder(10, 10, 10, 10));
+ add(legend, BorderLayout.CENTER);
+ repaint();
+ }
+
+ private JPanel getGradientPanel() {
+ JPanel holder = new JPanel();
+ holder.setLayout(new GridLayout(1, 2));
+ holder.setAlignmentX(0);
+ holder.setBackground(Color.white);
+
+ JLabel grad = new JLabel(getColorGradientIcon());
+ grad.setAlignmentX(0);
+ holder.add(grad);
+
+ JLabel num = new JLabel(getNumberGradientIcon());
+ num.setAlignmentX(0);
+ holder.add(num);
+
+ return holder;
+ }
+
+ int width = 40;
+ int height = 40;
+ int yoff = height;
+
+ private ImageIcon getNumberGradientIcon() {
+ int imageHeight = (points.size() + 1) * height;
+ BufferedImage bi = new BufferedImage(width, imageHeight, BufferedImage.TYPE_INT_RGB);
+ Graphics2D g2 = bi.createGraphics();
+ g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
+ g2.setPaint(Color.white);
+ g2.fillRect(0, 0, width, imageHeight);
+ g2.setPaint(Color.black);
+
+ int yoff = (int) (((float) g2.getFontMetrics().getMaxAscent()) / 2);
+
+ ContinuousMappingPoint curr = null;
+
+ for (int i = 0; i < points.size(); i++) {
+ curr = (ContinuousMappingPoint) points.get(i);
+
+ g2.drawString(curr.getValue().toString(), 0, ((i + 1) * height) + yoff);
+ }
+
+ return new ImageIcon(bi);
+ }
+
+ private ImageIcon getColorGradientIcon() {
+ int imageHeight = (points.size() + 1) * height;
+ BufferedImage bi = new BufferedImage(width, imageHeight, BufferedImage.TYPE_INT_RGB);
+ Graphics2D g2 = bi.createGraphics();
+ g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
+ g2.setPaint(Color.white);
+ g2.fillRect(0, 0, width, imageHeight);
+
+ ContinuousMappingPoint curr = null;
+ ContinuousMappingPoint next = null;
+
+ Rectangle rect = new Rectangle(0, 0, width, height);
+
+ for (int i = 0; i < points.size(); i++) {
+ curr = (ContinuousMappingPoint) points.get(i);
+
+ if ((i + 1) < points.size())
+ next = (ContinuousMappingPoint) points.get(i + 1);
+ else
+ next = null;
+
+ if (i == 0) {
+ g2.setPaint((Color) (curr.getRange().lesserValue));
+ rect.setBounds(0, 0, width, height);
+ g2.fill(rect);
+ }
+
+ if (next != null) {
+ GradientPaint gp = new GradientPaint(0, ((i + 1) * height),
+ (Color) curr.getRange().equalValue, 0,
+ ((i + 2) * height),
+ (Color) next.getRange().equalValue);
+ g2.setPaint(gp);
+ rect.setBounds(0, ((i + 1) * height), width, height);
+ g2.fill(rect);
+ } else {
+ g2.setPaint((Color) (curr.getRange().greaterValue));
+ rect.setBounds(0, ((i + 1) * height), width, height);
+ g2.fill(rect);
+ }
+ }
+
+ return new ImageIcon(bi);
+ }
+
+ private JPanel getObjectPanel(VisualPropertyType vpt) {
+ Object[][] data = new Object[points.size() + 2][2];
+
+ ContinuousMappingPoint curr = null;
+
+ for (int i = 0; i < points.size(); i++) {
+ curr = (ContinuousMappingPoint) points.get(i);
+
+ if (i == 0) {
+ data[i][0] = curr.getRange().lesserValue;
+ data[i][1] = "< " + curr.getValue().toString();
+ }
+
+ data[i + 1][0] = curr.getRange().equalValue;
+ data[i + 1][1] = "= " + curr.getValue().toString();
+
+ if (i == (points.size() - 1)) {
+ data[i + 2][0] = curr.getRange().greaterValue;
+ data[i + 2][1] = "> " + curr.getValue().toString();
+ }
+ }
+
+ LegendTable lt = new LegendTable(data, vpt);
+
+ return lt;
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/mappings/continuous/ContinuousMappingPoint.java b/application/src/main/java/cytoscape/visual/mappings/continuous/ContinuousMappingPoint.java
new file mode 100644
index 0000000..3fd2504
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/mappings/continuous/ContinuousMappingPoint.java
@@ -0,0 +1,114 @@
+/*
+ File: ContinuousMappingPoint.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+//----------------------------------------------------------------------------
+// $Revision: 22693 $
+// $Date: 2010-11-02 23:35:39 +0100 (Tue, 02 Nov 2010) $
+// $Author: kono $
+//----------------------------------------------------------------------------
+package cytoscape.visual.mappings.continuous;
+
+import cytoscape.visual.mappings.BoundaryRangeValues;
+
+
+/**
+ * Encapsulates a ContinuousMapping Point with a single point value
+ * and associated BoundaryRangeValues.
+ *
+ */
+public class ContinuousMappingPoint implements Cloneable {
+ private Double value;
+ private BoundaryRangeValues range;
+
+ /**
+ * Constructor.
+ * @param value double.
+ * @param range BoundaryRangeValues object.
+ */
+ public ContinuousMappingPoint(double value, BoundaryRangeValues range) {
+ this.value = value;
+ this.range = range;
+ }
+
+ /**
+ * Gets Point Value.
+ * @return double value.
+ */
+ public Double getValue() {
+ return value;
+ }
+
+ /**
+ * Sets Point Value.
+ * @param value double value.
+ */
+ public void setValue(Double value) {
+ this.value = value;
+ }
+
+ /**
+ * Gets BoundaryRangeValues.
+ * @return BoundaryRangeValues Object.
+ */
+ public BoundaryRangeValues getRange() {
+ return range;
+ }
+
+ /**
+ * Sets BoundaryRangeValues.
+ * @param range BoundaryRangeValues Object.
+ */
+ public void setRange(BoundaryRangeValues range) {
+ this.range = range;
+ }
+
+ /**
+ * Clones the object. (Deep Copy)
+ *
+ * @return Cloned Object.
+ */
+ public Object clone() {
+ final BoundaryRangeValues newRange = new BoundaryRangeValues();
+
+ newRange.lesserValue = range.lesserValue;
+ newRange.equalValue = range.equalValue;
+ newRange.greaterValue = range.greaterValue;
+
+ Double copyValue = new Double(value);
+ return new ContinuousMappingPoint(copyValue, newRange);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/mappings/continuous/ContinuousMappingReader.java b/application/src/main/java/cytoscape/visual/mappings/continuous/ContinuousMappingReader.java
new file mode 100644
index 0000000..14db9a7
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/mappings/continuous/ContinuousMappingReader.java
@@ -0,0 +1,192 @@
+/*
+ File: ContinuousMappingReader.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+//----------------------------------------------------------------------------
+// $Revision: 21067 $
+// $Date: 2010-07-29 01:52:44 +0200 (Thu, 29 Jul 2010) $
+// $Author: kono $
+//----------------------------------------------------------------------------
+package cytoscape.visual.mappings.continuous;
+
+import cytoscape.visual.mappings.BoundaryRangeValues;
+import cytoscape.visual.mappings.Interpolator;
+import cytoscape.visual.mappings.InterpolatorFactory;
+
+import cytoscape.visual.parsers.ValueParser;
+import cytoscape.logger.CyLogger;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Properties;
+
+/**
+ * Reads in ContinuousMapping Properties.
+ */
+public class ContinuousMappingReader {
+ private String controllingAttributeName;
+ private Interpolator interpolator;
+ private List<ContinuousMappingPoint> points;
+ private ValueParser parser;
+
+ /**
+ * Constructor.
+ *
+ * @param props
+ * Properties Object.
+ * @param baseKey
+ * Base Key.
+ * @param parser
+ * Value Parser.
+ */
+ public ContinuousMappingReader(Properties props, String baseKey,
+ ValueParser parser) {
+ this.parser = parser;
+ points = new ArrayList<ContinuousMappingPoint>();
+ parseProperties(props, baseKey);
+ }
+
+ /**
+ * Gets Controlling Attribute Name.
+ *
+ * @return Controlling Attribute Name.
+ */
+ public String getControllingAttributeName() {
+ return controllingAttributeName;
+ }
+
+ /**
+ * Gets Interpolator Object.
+ *
+ * @return Interpolator Object.
+ */
+ public Interpolator getInterpolator() {
+ return interpolator;
+ }
+
+ /**
+ * Gets ArrayList of all Data Points.
+ *
+ * @return ArrayList of ContinuousMappingPoint objects.
+ */
+ public List<ContinuousMappingPoint> getPoints() {
+ return points;
+ }
+
+ /**
+ * Parses all Properties into internal data structures.
+ */
+ private void parseProperties(Properties props, String baseKey) {
+ // Get Controller Property
+ String contKey = baseKey + ".controller";
+ String contValue = props.getProperty(contKey);
+
+ if (contValue != null)
+ this.controllingAttributeName = contValue;
+
+ // Get Interpolator Property
+ String intKey = baseKey + ".interpolator";
+ String intValue = props.getProperty(intKey);
+
+ if (intValue != null)
+ this.interpolator = InterpolatorFactory.newInterpolator(intValue);
+
+ // Get Boundary Value Properties
+ String bvNumKey = baseKey + ".boundaryvalues";
+ String bvNumString = props.getProperty(bvNumKey);
+
+ if (bvNumString != null) {
+ try {
+ int numBV = Integer.parseInt(bvNumString);
+ getBoundaryValues(numBV, baseKey, props);
+ } catch (NumberFormatException e) {
+ CyLogger.getLogger().warn(
+ "Error parsing attributeMap properties:\n\t"
+ + "Expected number value for key "
+ + bvNumString);
+
+ }
+ }
+ }
+
+ /**
+ * Gets all BoundaryValue Properties.
+ */
+ private void getBoundaryValues(int numBV, String baseKey, Properties props) {
+ for (int i = 0; i < numBV; i++) {
+ String bvBase = baseKey + ".bv" + Integer.toString(i);
+ String dvKey = bvBase + ".domainvalue";
+ String dvString = props.getProperty(dvKey);
+
+ if (dvString != null) {
+ try {
+ Double dVal = Double.valueOf(dvString);
+ getLesserEqualGreater(bvBase, props, dVal);
+ } catch (Exception e) {
+ CyLogger.getLogger().warn(
+ "Error parsing attributeMap properties:\n\t"
+ + "Expected number value for key " + dvKey);
+ }
+ }
+ }
+ }
+
+ /**
+ * Gets Less/Equals/Greater than BoundaryValues.
+ */
+ private void getLesserEqualGreater(String bvBase, Properties props,
+ Double dVal) {
+ BoundaryRangeValues bv = new BoundaryRangeValues();
+ String lKey = bvBase + ".lesser";
+ String lString = props.getProperty(lKey);
+ Object lValue = parser.parseStringValue(lString);
+ bv.lesserValue = lValue;
+
+ String eKey = bvBase + ".equal";
+ String eString = props.getProperty(eKey);
+ Object eValue = parser.parseStringValue(eString);
+ bv.equalValue = eValue;
+
+ String gKey = bvBase + ".greater";
+ String gString = props.getProperty(gKey);
+ Object gValue = parser.parseStringValue(gString);
+ bv.greaterValue = gValue;
+
+ ContinuousMappingPoint cmp = new ContinuousMappingPoint(
+ dVal, bv);
+ points.add(cmp);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/mappings/continuous/ContinuousMappingWriter.java b/application/src/main/java/cytoscape/visual/mappings/continuous/ContinuousMappingWriter.java
new file mode 100644
index 0000000..5af3060
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/mappings/continuous/ContinuousMappingWriter.java
@@ -0,0 +1,128 @@
+/*
+ File: ContinuousMappingWriter.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.visual.mappings.continuous;
+
+import java.util.Iterator;
+import java.util.List;
+import java.util.Properties;
+
+import cytoscape.visual.converter.ValueToStringConverterManager;
+import cytoscape.visual.mappings.BoundaryRangeValues;
+import cytoscape.visual.mappings.Interpolator;
+import cytoscape.visual.mappings.InterpolatorFactory;
+
+
+/**
+ * Writes out ContinuousMapping Properties.
+ */
+public class ContinuousMappingWriter {
+ private Properties newProps;
+
+ /**
+ * Constructor.
+ * @param points ArrayList of ContinuousMappintPoints.
+ * @param baseKey Base Key String.
+ * @param attrName Controlling Attribute String.
+ * @param interp Interpolator Object.
+ */
+ public ContinuousMappingWriter(List points, String baseKey,
+ String attrName, Interpolator interp) {
+ newProps = new Properties();
+ loadProperties(points, baseKey, attrName, interp);
+ }
+
+ /**
+ * Gets Newly Defined Properties Object.
+ * @return Properties Object.
+ */
+ public Properties getProperties() {
+ return newProps;
+ }
+
+ /**
+ * Return a Properties object with entries suitable for customizing this
+ * object via the applyProperties method.
+ */
+ private void loadProperties(List points, String baseKey,
+ String contAttrName, Interpolator interp) {
+ // save the controlling attribute name
+ String contAttrKey = baseKey + ".controller";
+
+ if (contAttrName != null)
+ newProps.setProperty(contAttrKey, contAttrName);
+
+ // save the interpolator
+ String intKey = baseKey + ".interpolator";
+ String intName = InterpolatorFactory.getName(interp);
+ newProps.setProperty(intKey, intName);
+
+ // save the number of boundary values
+ String bvNumKey = baseKey + ".boundaryvalues";
+ int numBV = points.size();
+ String numString = Integer.toString(numBV);
+ newProps.setProperty(bvNumKey, numString);
+
+ // save each of the boundary values
+ int count = 0;
+
+ for (Iterator si = points.iterator(); si.hasNext(); count++) {
+ String bvBase = baseKey + ".bv" + count;
+
+ // save the domain value
+ String bvKey = bvBase + ".domainvalue";
+ ContinuousMappingPoint cmp = (ContinuousMappingPoint) si.next();
+ Double dVal = cmp.getValue().doubleValue();
+ String dValString = dVal.toString();
+ newProps.setProperty(bvKey, dValString);
+
+ // save the fields of the brv object
+ BoundaryRangeValues brv = (BoundaryRangeValues) cmp.getRange();
+ String lKey = bvBase + ".lesser";
+ String lString = ValueToStringConverterManager.manager.toString(brv.lesserValue);
+ newProps.setProperty(lKey, lString);
+
+ String eKey = bvBase + ".equal";
+ String eString = ValueToStringConverterManager.manager.toString(brv.equalValue);
+ newProps.setProperty(eKey, eString);
+
+ String gKey = bvBase + ".greater";
+ String gString = ValueToStringConverterManager.manager.toString(brv.greaterValue);
+ newProps.setProperty(gKey, gString);
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/mappings/continuous/ContinuousRangeCalculator.java b/application/src/main/java/cytoscape/visual/mappings/continuous/ContinuousRangeCalculator.java
new file mode 100644
index 0000000..50cae11
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/mappings/continuous/ContinuousRangeCalculator.java
@@ -0,0 +1,201 @@
+/*
+ File: ContinuousRangeCalculator.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+//----------------------------------------------------------------------------
+// $Revision: 23525 $
+// $Date: 2011-01-20 19:56:39 +0100 (Thu, 20 Jan 2011) $
+// $Author: mes $
+//----------------------------------------------------------------------------
+package cytoscape.visual.mappings.continuous;
+
+import cytoscape.visual.mappings.BoundaryRangeValues;
+import cytoscape.visual.mappings.Interpolator;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+
+
+/**
+ * Calculates the Range for Continuous Mappers.
+ */
+public class ContinuousRangeCalculator {
+ private List<ContinuousMappingPoint> points;
+ private Interpolator interpolator;
+ private Map<String, Object> attrBundle;
+
+ /**
+ * Constructor.
+ * @param points ArrayList of ContinuousMappingPoints.
+ * @param interpolator Interpolator Object.
+ * @param attrBundle Attribute Bundle.
+ */
+ public ContinuousRangeCalculator(ArrayList points,
+ Interpolator interpolator, Map attrBundle) {
+ this((List<ContinuousMappingPoint>)points,interpolator,attrBundle);
+ }
+
+ /**
+ * Constructor.
+ * @param points ArrayList of ContinuousMappingPoints.
+ * @param interpolator Interpolator Object.
+ * @param attrBundle Attribute Bundle.
+ */
+ public ContinuousRangeCalculator(List<ContinuousMappingPoint> points,
+ Interpolator interpolator, Map attrBundle) {
+ this.points = points;
+ this.interpolator = interpolator;
+ this.attrBundle = attrBundle;
+ }
+
+ /**
+ * Calculates Range Value.
+ * @param attrName Attribute Name.
+ * @return Object.
+ */
+ public Object calculateRangeValue(String attrName) {
+ if ((attrBundle == null) || (attrName == null))
+ return null;
+
+ if (points.size() == 0)
+ return null;
+
+ Object attrValue = attrBundle.get(attrName);
+
+ if (!(attrValue instanceof Number))
+ return null;
+
+ return getRangeValue((Number) attrValue);
+ }
+
+ private Object getRangeValue(Number domainValue) {
+ ContinuousMappingPoint firstPoint = points.get(0);
+ Number minDomain = firstPoint.getValue().doubleValue();
+
+ // if given domain value is smaller than any in our list,
+ // return the range value for the smallest domain value we have.
+ int firstCmp = compareValues(domainValue, minDomain);
+
+ if (firstCmp <= 0) {
+ BoundaryRangeValues bv = firstPoint.getRange();
+
+ if (firstCmp < 0)
+ return bv.lesserValue;
+ else
+ return bv.equalValue;
+ }
+
+ // if given domain value is larger than any in our Vector,
+ // return the range value for the largest domain value we have.
+ ContinuousMappingPoint lastPoint = points.get(points.size() - 1);
+ Number maxDomain = lastPoint.getValue().doubleValue();
+
+ if (compareValues(domainValue, maxDomain) > 0) {
+ BoundaryRangeValues bv = lastPoint.getRange();
+
+ return bv.greaterValue;
+ }
+
+ // OK, it's somewhere in the middle, so find the boundaries and
+ // pass to our interpolator function. First check for a null
+ // interpolator function
+ if (this.interpolator == null)
+ return null;
+
+ // Note that the list of Points is sorted.
+ // Also, the case of the inValue equalling the smallest key was
+ // checked above.
+ ContinuousMappingPoint currentPoint;
+ int index = 0;
+
+ for (index = 0; index < points.size(); index++) {
+ currentPoint = points.get(index);
+
+ Double currentValue = currentPoint.getValue().doubleValue();
+ int cmpValue = compareValues(domainValue, currentValue);
+
+ if (cmpValue == 0) {
+ BoundaryRangeValues bv = currentPoint.getRange();
+
+ return bv.equalValue;
+ } else if (cmpValue < 0)
+ break;
+ }
+
+ return getRangeValue(index, domainValue);
+ }
+
+ /**
+ * This is tricky. The desired domain value is greater than
+ * lowerDomain and less than upperDomain. Therefore, we want
+ * the "greater" field of the lower boundary value (because the
+ * desired domain value is greater) and the "lesser" field of
+ * the upper boundary value (semantic difficulties).
+ */
+ private Object getRangeValue(int index, Number domainValue) {
+ // Get Lower Domain and Range
+ ContinuousMappingPoint lowerBound = points.get(index - 1);
+ Number lowerDomain = lowerBound.getValue().doubleValue();
+ BoundaryRangeValues lv = lowerBound.getRange();
+ Object lowerRange = lv.greaterValue;
+
+ // Get Upper Domain and Range
+ ContinuousMappingPoint upperBound = points.get(index);
+ Number upperDomain = upperBound.getValue().doubleValue();
+ BoundaryRangeValues gv = upperBound.getRange();
+ Object upperRange = gv.lesserValue;
+
+ return interpolator.getRangeValue(lowerDomain, lowerRange, upperDomain,
+ upperRange, domainValue);
+ }
+
+ /**
+ * Helper function to compare Number objects. This is needed because Java
+ * doesn't allow comparing, for example, Integer objects to Double objects.
+ */
+ private int compareValues(Number probe, Number target) {
+ double d1 = probe.doubleValue();
+ double d2 = target.doubleValue();
+
+ if (d1 < d2)
+ return -1;
+ else if (d1 > d2)
+ return 1;
+ else
+ return 0;
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/mappings/continuous/PointTextListener.java b/application/src/main/java/cytoscape/visual/mappings/continuous/PointTextListener.java
new file mode 100644
index 0000000..5283850
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/mappings/continuous/PointTextListener.java
@@ -0,0 +1,174 @@
+/*
+ File: PointTextListener.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+//----------------------------------------------------------------------------
+// $Revision: 20380 $
+// $Date: 2010-06-01 22:04:00 +0200 (Tue, 01 Jun 2010) $
+// $Author: kono $
+//----------------------------------------------------------------------------
+package cytoscape.visual.mappings.continuous;
+
+import cytoscape.visual.mappings.ContinuousMapping;
+
+import java.awt.event.FocusAdapter;
+import java.awt.event.FocusEvent;
+
+import java.text.NumberFormat;
+
+import javax.swing.*;
+
+
+/**
+ * Listens for a User Initiated Change in any of the JTextFields
+ * in the Continuous Mapper UI.
+ */
+public class PointTextListener extends FocusAdapter {
+ private JTextField textField;
+ private int index;
+ private ContinuousMapping cm;
+ private JDialog parent;
+
+ /**
+ * Constructor.
+ */
+ public PointTextListener(JTextField textField, ContinuousMapping cm,
+ JDialog parent, int index) {
+ this.textField = textField;
+ this.cm = cm;
+ this.parent = parent;
+ this.index = index;
+ }
+
+ /**
+ * User now clicks outside of Text Box. Now validate that
+ * the new data is acceptable.
+ * @param e
+ */
+ public void focusLost(FocusEvent e) {
+ // Get Old Data Point (Before User Change)
+ ContinuousMappingPoint point = cm.getPoint(index);
+
+ try {
+ validate(point);
+ } catch (IllegalArgumentException arge) {
+ // If new point is no good, revert back to old point.
+ NumberFormat numberFormat = NumberFormat.getInstance();
+ numberFormat.setMaximumFractionDigits(6);
+
+ String textValue = numberFormat.format(point.getValue());
+ textField.setText(textValue);
+ JOptionPane.showMessageDialog(parent,
+ arge.getMessage() + " Please try again.",
+ "Data Validation Error", JOptionPane.WARNING_MESSAGE);
+ }
+ }
+
+ /**
+ * Validates new data field. If the new data is not acceptable,
+ * we revert back to existing data.
+ */
+ private void validate(ContinuousMappingPoint point) {
+ // Get New Data Point (After User Change)
+ double newValue = getNewValue();
+
+ // Check Previous/Next Points (if available)
+ checkPreviousPoint(newValue);
+ checkNextPoint(newValue);
+
+ // If all goes well, update the point.
+ point.setValue(newValue);
+ }
+
+ /**
+ * Gets new value from the Text Box.
+ * @return double value.
+ * @throws IllegalArgumentException if this is not a number.
+ */
+ private double getNewValue() {
+ String number = textField.getText();
+ double newValue;
+
+ try {
+ newValue = Double.parseDouble(number);
+ } catch (NumberFormatException e) {
+ throw new IllegalArgumentException("This is not a number: " +
+ number + ".");
+ }
+
+ return newValue;
+ }
+
+ /**
+ * Validates New Point against Next Point in List.
+ * @throws IllegalArgumentException if this is not a valid value.
+ */
+ private void checkNextPoint(double newValue) {
+ try {
+ ContinuousMappingPoint nextPoint = cm.getPoint(index + 1);
+ double nextValue = nextPoint.getValue().doubleValue();
+
+ if (newValue > nextValue)
+ throw new IllegalArgumentException(newValue +
+ " must be greater than " + "next point: " + nextValue +
+ ".");
+ } catch (IndexOutOfBoundsException e) {
+ // There is no next point; skip test.
+ }
+ }
+
+ /**
+ * Validates New Point against Previous Point in List.
+ * @throws IllegalArgumentException if this is not a valid value.
+ */
+ private boolean checkPreviousPoint(double newValue) {
+ boolean errorFlag = false;
+
+ try {
+ ContinuousMappingPoint prevPoint = cm.getPoint(index - 1);
+ double previousValue = prevPoint.getValue().doubleValue();
+
+ if (newValue < previousValue)
+ throw new IllegalArgumentException(newValue +
+ " must be less than " + "previous point: " +
+ previousValue + ".");
+ } catch (IndexOutOfBoundsException e) {
+ // There is no previous point; skip test.
+ }
+
+ return errorFlag;
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/mappings/continuous/README.txt b/application/src/main/java/cytoscape/visual/mappings/continuous/README.txt
new file mode 100644
index 0000000..8a13dc3
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/mappings/continuous/README.txt
@@ -0,0 +1,69 @@
+Notes RE: Refactoring of the Continuous Mapper
+--------------------------------------------------
+
+For questions, email Ethan Cerami (cerami at cbio.mskcc.org)
+
+Functional Changes:
+-------------------
+
+All functionality is the same except:
+
+1. Users can now add/delete new points. This was broken before. [DONE]
+2. Data Validation Errors now result in an informative error message
+ dialog box. [DONE]
+3. The UI Panel now contains an "Apply to Graph" button. [DONE]
+
+Refactoring Overview:
+---------------------
+ContinuousMapping.java has now been replaced with nine new classes, all
+of which now live in cytoscape.visual.mappings.continuous.
+
+ContinuousMappingPoint: Encapsulates a continuous mapping point.
+ContinuousMappingReader: Reads in VisualStyles Properties.
+ContinuousMappingWriter: Writes out VisualStyle Properties.
+ContinuousUI: UI for ContinuousMapping
+
+AddPointListener: Responds to user request to add a new point.
+DeletePointListener: Responds to user request to delete an existing point.
+PointTextListener: Responds to user change in any point value,
+ and validates the new point value.
+ValueListener: Responds to user request to modify a value,
+ e.g. Color, Line Type or Size.
+
+JUnit Tests:
+------------
+ContinuousMappingTestSuite Runs all ContinuousMapping Tests
+TestContinuousColorRangeCalculator Runs tests for a Continuous Color Calculator.
+TestContinuousMappingReader Tests the Reader class.
+TestContinuousMappingWriter Tests the Writer class.
+
+
+Functional Test List:
+----------------------
+1. Take an existing mapper, and add a new point. Does the new point
+ appear in the list? Delete an existing point. Is it removed from
+ the list? [Tested --> OK]
+
+2. Take an existing Continuous mapper, modify a point. Restart Cytoscape,
+ and verify that the mapper was saved correctly. [Tested --> OK]
+
+3. In the text box for an existing point, try typing some letters, e.g.
+ "three". You should get an error message dialog box. [Tested --> OK]
+
+4. Create a new Continuous Mapper, add a bunch of points. Restart Cytoscape,
+ and verify that the mapper was saved correctly. [Tested --> OK]
+
+5. Clone an existing Continuous Mapper, and modify it. Restart Cytoscape,
+ and verify that the mapper was saved correctly. [Tested --> OK]
+
+6. Take an existing ContinuousMapper for Node Color, and apply it to
+ a graph. [Tested --> OK]
+
+7. Take an existing ContinuousMapper for Node Border Color, and apply it
+ to a graph. [Tested --> OK]
+
+8. Create a ContinuousMapper for Node Size, and apply it to graph.
+ [Tested --> OK]
+
+9. Take an existing ContinuousMapper Node Border LineType, and apply it
+ to a graph. [Tested --> DOES NOT WORK]
\ No newline at end of file
diff --git a/application/src/main/java/cytoscape/visual/mappings/continuous/package.html b/application/src/main/java/cytoscape/visual/mappings/continuous/package.html
new file mode 100644
index 0000000..abe57d5
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/mappings/continuous/package.html
@@ -0,0 +1,12 @@
+<html>
+<head>
+ <!-- $Revision: 5801 $
+ $Date: 2004-04-20 01:53:47 +0200 (Tue, 20 Apr 2004) $
+ $Author: amarkiel $
+ -->
+</head>
+
+<body>
+Mappings from a continuous numerical input to a particular visual attribute.
+</body>
+</html>
diff --git a/application/src/main/java/cytoscape/visual/mappings/discrete/DiscreteLegend.java b/application/src/main/java/cytoscape/visual/mappings/discrete/DiscreteLegend.java
new file mode 100644
index 0000000..7a781b5
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/mappings/discrete/DiscreteLegend.java
@@ -0,0 +1,107 @@
+/*
+ File: DiscreteLegend.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.visual.mappings.discrete;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.util.Iterator;
+import java.util.Map;
+
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.SwingConstants;
+import javax.swing.border.Border;
+import javax.swing.border.MatteBorder;
+
+import cytoscape.visual.VisualPropertyType;
+import cytoscape.visual.mappings.LegendTable;
+
+
+/**
+ *
+ */
+public class DiscreteLegend extends JPanel {
+
+ private static final Font TITLE_FONT = new Font("SansSerif", Font.BOLD, 14);
+ private static final Font TITLE_FONT2 = new Font("SansSerif", Font.BOLD, 18);
+ private static final Color TITLE_COLOR = new Color(10, 200, 255);
+ private static final Border BORDER = new MatteBorder(0, 6, 3, 0, Color.DARK_GRAY);
+
+ /**
+ * Creates a new DiscreteLegend object.
+ *
+ * @param legendMap DOCUMENT ME!
+ * @param dataAttr DOCUMENT ME!
+ * @param vpt DOCUMENT ME!
+ */
+ public DiscreteLegend(Map legendMap, String dataAttr, VisualPropertyType vpt) {
+ super();
+
+ setLayout(new BorderLayout());
+ setBackground(Color.white);
+ setBorder(BORDER);
+
+ final JLabel title = new JLabel(" " + vpt.getName() + " Mapping");
+ title.setFont(TITLE_FONT2);
+ title.setForeground(TITLE_COLOR);
+ title.setBorder(new MatteBorder(0, 10, 1, 0, TITLE_COLOR));
+// title.setHorizontalAlignment(SwingConstants.CENTER);
+// title.setVerticalAlignment(SwingConstants.CENTER);
+ title.setHorizontalTextPosition(SwingConstants.LEADING);
+// title.setVerticalTextPosition(SwingConstants.CENTER);
+
+ title.setPreferredSize(new Dimension(1, 50));
+ add(title, BorderLayout.NORTH);
+
+ /*
+ * Build Key array.
+ */
+ final Object[][] data = new Object[legendMap.keySet().size()][2];
+ final Iterator it = legendMap.keySet().iterator();
+
+ for (int i = 0; i < legendMap.keySet().size(); i++) {
+ Object key = it.next();
+ data[i][0] = legendMap.get(key);
+ data[i][1] = key;
+ }
+
+ add(LegendTable.getHeader(dataAttr, vpt), BorderLayout.CENTER);
+ add(new LegendTable(data, vpt), BorderLayout.SOUTH);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/mappings/discrete/DiscreteMappingReader.java b/application/src/main/java/cytoscape/visual/mappings/discrete/DiscreteMappingReader.java
new file mode 100644
index 0000000..a703f5f
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/mappings/discrete/DiscreteMappingReader.java
@@ -0,0 +1,123 @@
+/*
+ File: DiscreteMappingReader.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+//----------------------------------------------------------------------------
+// $Revision: 21067 $
+// $Date: 2010-07-29 01:52:44 +0200 (Thu, 29 Jul 2010) $
+// $Author: kono $
+//----------------------------------------------------------------------------
+package cytoscape.visual.mappings.discrete;
+
+import cytoscape.visual.mappings.MappingUtil;
+
+import cytoscape.visual.parsers.ValueParser;
+
+import java.util.Enumeration;
+import java.util.Properties;
+import java.util.SortedMap;
+import java.util.TreeMap;
+
+
+/**
+ * Reads in DiscreteMapping Properties.
+ *
+ * Unit Test for this class exists in:
+ * cytoscape.visual.mappings.discrete.unitTests.TestDiscreteMappingReader.
+ */
+public class DiscreteMappingReader {
+ private String controllingAttribute;
+ private SortedMap map = new TreeMap();
+
+ /**
+ * Constructor.
+ * @param props Properties Object.
+ * @param baseKey Base Property Key.
+ * @param parser ValueParser Object.
+ */
+ public DiscreteMappingReader(Properties props, String baseKey,
+ ValueParser parser) {
+ readProperties(props, baseKey, parser);
+ }
+
+ /**
+ * Gets Controlling Attribute Name.
+ * @return Controlling Attribute Name.
+ */
+ public String getControllingAttributeName() {
+ return controllingAttribute;
+ }
+
+ /**
+ * Gets the Discrete Map.
+ * @return TreeMap Object.
+ */
+ public SortedMap getMap() {
+ return map;
+ }
+
+ /**
+ * Read in Settings from the Properties Object.
+ */
+ private void readProperties(Properties props, String baseKey,
+ ValueParser parser) {
+ String contKey = baseKey + ".controller";
+ controllingAttribute = props.getProperty(contKey);
+
+ String contTypeKey = baseKey + ".controllerType";
+ String attrTypeString = props.getProperty(contTypeKey);
+ byte attrType = -1; // UNDEFINED defaults to string
+
+ if (attrTypeString != null)
+ attrType = new Byte(attrTypeString).byteValue();
+
+ String mapKey = baseKey + ".map.";
+ Enumeration eProps = props.propertyNames();
+
+ while (eProps.hasMoreElements()) {
+ String key = (String) eProps.nextElement();
+
+ if (key.startsWith(mapKey)) {
+ String value = props.getProperty(key);
+ Object domainVal = MappingUtil.parseObjectType(
+ key.substring(mapKey.length()),
+ attrType);
+ Object parsedVal = parser.parseStringValue(value);
+ map.put(domainVal, parsedVal);
+ }
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/mappings/discrete/DiscreteMappingWriter.java b/application/src/main/java/cytoscape/visual/mappings/discrete/DiscreteMappingWriter.java
new file mode 100644
index 0000000..6ba8db0
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/mappings/discrete/DiscreteMappingWriter.java
@@ -0,0 +1,116 @@
+/*
+ File: DiscreteMappingWriter.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+//----------------------------------------------------------------------------
+// $Revision: 20380 $
+// $Date: 2010-06-01 22:04:00 +0200 (Tue, 01 Jun 2010) $
+// $Author: kono $
+//----------------------------------------------------------------------------
+package cytoscape.visual.mappings.discrete;
+
+import cytoscape.visual.converter.ValueToStringConverterManager;
+import cytoscape.visual.mappings.MappingUtil;
+
+import cytoscape.visual.parsers.ObjectToString;
+
+import java.util.Iterator;
+import java.util.Properties;
+import java.util.SortedMap;
+import java.util.TreeMap;
+
+
+/**
+ * Writes DiscreteMapping Properties.
+ *
+ * Unit Test for this class exists in:
+ * cytoscape.visual.mappings.discrete.unitTests.TestDiscreteMappingWriter.
+ */
+public class DiscreteMappingWriter {
+ private String attrName;
+ private String baseKey;
+ private SortedMap map;
+
+ /**
+ * Constructor.
+ * @param attrName Controlling Attribute Name.
+ * @param map Discrete Map.
+ */
+ public DiscreteMappingWriter(String attrName, String baseKey, SortedMap map) {
+ this.attrName = attrName;
+ this.baseKey = baseKey;
+ this.map = map;
+ }
+
+ /**
+ * Return a Properties object with entries suitable for customizing this
+ * object via the applyProperties method.
+ */
+ public Properties getProperties() {
+ Properties newProps = new Properties();
+
+ /*
+ * if null, return empty prop.
+ */
+ if (attrName == null)
+ return newProps;
+
+ String contKey = baseKey + ".controller";
+ newProps.setProperty(contKey, attrName);
+
+ String contTypeKey = baseKey + ".controllerType";
+ newProps.setProperty(contTypeKey, MappingUtil.getAttributeTypeString(baseKey, attrName));
+
+ String mapKey = baseKey + ".map.";
+ Iterator iterator = map.keySet().iterator();
+
+ Object key;
+ Object value;
+ String stringValue;
+
+ while (iterator.hasNext()) {
+ key = iterator.next();
+ value = map.get(key);
+
+ if (value != null) {
+ stringValue = ValueToStringConverterManager.manager.toString(value);
+ newProps.setProperty(mapKey + key.toString(), stringValue);
+ }
+ }
+
+ return newProps;
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/mappings/discrete/DiscreteRangeCalculator.java b/application/src/main/java/cytoscape/visual/mappings/discrete/DiscreteRangeCalculator.java
new file mode 100644
index 0000000..2b7b7f5
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/mappings/discrete/DiscreteRangeCalculator.java
@@ -0,0 +1,108 @@
+/*
+ File: DiscreteRangeCalculator.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+//----------------------------------------------------------------------------
+// $Revision: 20380 $
+// $Date: 2010-06-01 22:04:00 +0200 (Tue, 01 Jun 2010) $
+// $Author: kono $
+//----------------------------------------------------------------------------
+package cytoscape.visual.mappings.discrete;
+
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.SortedMap;
+
+
+/**
+ * Range Calculator for the Discrete Mapper.
+ */
+public class DiscreteRangeCalculator<T, V> {
+ private SortedMap<T, V> map;
+ private String attrName;
+
+ /**
+ * Constructor.
+ * @param map Discrete Map.
+ * @param attrName Controlling Attribute Name.
+ */
+ public DiscreteRangeCalculator(SortedMap<T,V> map, String attrName) {
+ this.map = map;
+ this.attrName = attrName;
+ }
+
+ /**
+ * Calculates Range Value.
+ * @param attrBundle Attribute Bundle.
+ * @return Object.
+ */
+ public V calculateRangeValue(Map<String, Object> attrBundle) {
+ if ((attrBundle == null) || (attrName == null))
+ return null;
+
+ //extract the data value for our controlling attribute name
+ Object attrValue = attrBundle.get(attrName);
+
+ if (attrValue == null)
+ return null;
+
+ //from here we have to catch ClassCastExceptions that will be
+ //thrown if the data value is not of a type comparable to the keys
+ //in this SortedMap
+ try {
+ //if the attrValue is a List, search for an object in the List
+ //that maps to a non-null value, and return the matching value
+ if (attrValue instanceof List) {
+ Iterator attrValueIt = ((List) attrValue).iterator();
+
+ while (attrValueIt.hasNext()) {
+ Object attrSubValue = attrValueIt.next();
+
+ if (map.get(attrSubValue) != null)
+ return map.get(attrSubValue);
+ }
+
+ //if not found, return null
+ return null;
+ } else
+ //OK, try the attrValue itself as a key
+ return map.get(attrValue); //returns null if not found
+ } catch (ClassCastException e) {
+ return null;
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/mappings/discrete/RandomColorListener.java b/application/src/main/java/cytoscape/visual/mappings/discrete/RandomColorListener.java
new file mode 100644
index 0000000..574b8b6
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/mappings/discrete/RandomColorListener.java
@@ -0,0 +1,82 @@
+/*
+ File: RandomColorListener.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.visual.mappings.discrete;
+
+import cytoscape.visual.mappings.DiscreteMapping;
+
+import java.awt.*;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import java.util.*;
+
+
+/**
+ * User wants to Seed the Discrete Mapper with Random Color Values.
+ */
+public class RandomColorListener
+ implements ActionListener {
+ private DiscreteMapping dm;
+ private TreeSet mappedKeys;
+
+ /**
+ * Constructs a ValueChangeListener.
+ */
+ public RandomColorListener(DiscreteMapping dm, TreeSet mappedKeys) {
+ this.dm = dm;
+ this.mappedKeys = mappedKeys;
+ }
+
+ /**
+ * User wants to Seed the Discrete Mapper with Random Color Values.
+ */
+ public void actionPerformed(ActionEvent e) {
+ Calendar cal = Calendar.getInstance();
+ int seed = cal.get(Calendar.SECOND);
+ Random rand = new Random(seed);
+ Iterator iterator = mappedKeys.iterator();
+
+ while (iterator.hasNext()) {
+ Object key = iterator.next();
+ int r = rand.nextInt(255);
+ int g = rand.nextInt(255);
+ int b = rand.nextInt(255);
+ Color c1 = new Color(r, g, b);
+ dm.putMapValue(key, c1);
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/mappings/discrete/package.html b/application/src/main/java/cytoscape/visual/mappings/discrete/package.html
new file mode 100644
index 0000000..e64a8ab
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/mappings/discrete/package.html
@@ -0,0 +1,12 @@
+<html>
+<head>
+ <!-- $Revision: 5801 $
+ $Date: 2004-04-20 01:53:47 +0200 (Tue, 20 Apr 2004) $
+ $Author: amarkiel $
+ -->
+</head>
+
+<body>
+Mappings from a discrete-valued input to a particular visual attribute.
+</body>
+</html>
diff --git a/application/src/main/java/cytoscape/visual/mappings/package.html b/application/src/main/java/cytoscape/visual/mappings/package.html
new file mode 100644
index 0000000..d6a115f
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/mappings/package.html
@@ -0,0 +1,14 @@
+<html>
+<head>
+ <!-- $Revision: 5801 $
+ $Date: 2004-04-20 01:53:47 +0200 (Tue, 20 Apr 2004) $
+ $Author: amarkiel $
+ -->
+</head>
+
+<body>
+The Mappings are used by Calculators to map graph attributes
+to visual attribute values.
+</body>
+</html>
+
diff --git a/application/src/main/java/cytoscape/visual/mappings/rangecalculators/ColorRangeValueCalculator.java b/application/src/main/java/cytoscape/visual/mappings/rangecalculators/ColorRangeValueCalculator.java
new file mode 100644
index 0000000..120771d
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/mappings/rangecalculators/ColorRangeValueCalculator.java
@@ -0,0 +1,40 @@
+package cytoscape.visual.mappings.rangecalculators;
+
+import java.awt.Color;
+import java.awt.Paint;
+
+import cytoscape.visual.mappings.RangeValueCalculator;
+import cytoscape.visual.parsers.ColorParser;
+import cytoscape.visual.parsers.ValueParser;
+
+
+public class ColorRangeValueCalculator implements RangeValueCalculator<Paint> {
+
+ private final ValueParser parser;
+
+ public ColorRangeValueCalculator() {
+ parser = new ColorParser();
+ }
+
+
+ public Color getRange(Object attrValue) {
+
+ // OK, try returning the attrValue itself
+ if (attrValue instanceof String) {
+ return (Color) parser.parseStringValue((String) attrValue);
+ } else if(attrValue instanceof Number) {
+ return (Color) parser.parseStringValue(attrValue.toString());
+ } else
+ return null;
+ }
+
+
+
+ public boolean isCompatible(Class<?> type) {
+ if(Paint.class.isAssignableFrom(type))
+ return true;
+ else
+ return false;
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/visual/mappings/rangecalculators/CustomGraphicsRangeValueCalculator.java b/application/src/main/java/cytoscape/visual/mappings/rangecalculators/CustomGraphicsRangeValueCalculator.java
new file mode 100644
index 0000000..cf1aee4
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/mappings/rangecalculators/CustomGraphicsRangeValueCalculator.java
@@ -0,0 +1,34 @@
+package cytoscape.visual.mappings.rangecalculators;
+
+import cytoscape.visual.customgraphic.CyCustomGraphics;
+import cytoscape.visual.mappings.RangeValueCalculator;
+import cytoscape.visual.parsers.GraphicsParser;
+import cytoscape.visual.parsers.ValueParser;
+
+public class CustomGraphicsRangeValueCalculator implements
+ RangeValueCalculator<CyCustomGraphics> {
+
+ private ValueParser parser;
+
+ public CustomGraphicsRangeValueCalculator() {
+ parser = new GraphicsParser();
+ }
+
+
+ public CyCustomGraphics getRange(Object attrValue) {
+ if (attrValue instanceof String) {
+ CyCustomGraphics obj = (CyCustomGraphics) parser.parseStringValue((String) attrValue);
+ return obj;
+ }
+ return null;
+ }
+
+
+ public boolean isCompatible(Class<?> type) {
+ if(CyCustomGraphics.class.isAssignableFrom(type))
+ return true;
+ else
+ return false;
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/visual/mappings/rangecalculators/DoubleRangeValueCalculator.java b/application/src/main/java/cytoscape/visual/mappings/rangecalculators/DoubleRangeValueCalculator.java
new file mode 100644
index 0000000..4831740
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/mappings/rangecalculators/DoubleRangeValueCalculator.java
@@ -0,0 +1,34 @@
+package cytoscape.visual.mappings.rangecalculators;
+
+import cytoscape.visual.mappings.RangeValueCalculator;
+import cytoscape.visual.parsers.DoubleParser;
+import cytoscape.visual.parsers.ValueParser;
+
+public class DoubleRangeValueCalculator implements RangeValueCalculator<Double> {
+
+ private ValueParser parser;
+
+ public DoubleRangeValueCalculator() {
+ parser = new DoubleParser();
+ }
+
+
+ public Double getRange(Object attrValue) {
+ if (attrValue instanceof Number) {
+ final Number num = (Number) attrValue;
+ return num.doubleValue();
+ } else if (attrValue instanceof String)
+ return (Double) parser.parseStringValue((String) attrValue);
+
+ return null;
+ }
+
+
+ public boolean isCompatible(Class<?> type) {
+ if (type.isAssignableFrom(Double.class))
+ return true;
+ else
+ return false;
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/visual/mappings/rangecalculators/FloatRangeValueCalculator.java b/application/src/main/java/cytoscape/visual/mappings/rangecalculators/FloatRangeValueCalculator.java
new file mode 100644
index 0000000..8889fa7
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/mappings/rangecalculators/FloatRangeValueCalculator.java
@@ -0,0 +1,34 @@
+package cytoscape.visual.mappings.rangecalculators;
+
+import cytoscape.visual.mappings.RangeValueCalculator;
+import cytoscape.visual.parsers.FloatParser;
+import cytoscape.visual.parsers.ValueParser;
+
+public class FloatRangeValueCalculator implements RangeValueCalculator<Float> {
+
+ private ValueParser parser;
+
+ public FloatRangeValueCalculator() {
+ parser = new FloatParser();
+ }
+
+
+ public Float getRange(Object attrValue) {
+ if (attrValue instanceof Number) {
+ final Number num = (Number) attrValue;
+ return num.floatValue();
+ } else if (attrValue instanceof String)
+ return (Float) parser.parseStringValue((String) attrValue);
+
+ return null;
+ }
+
+
+ public boolean isCompatible(Class<?> type) {
+ if (type.isAssignableFrom(Float.class))
+ return true;
+ else
+ return false;
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/visual/mappings/rangecalculators/NodeShapeRangeValueCalculator.java b/application/src/main/java/cytoscape/visual/mappings/rangecalculators/NodeShapeRangeValueCalculator.java
new file mode 100644
index 0000000..20acea5
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/mappings/rangecalculators/NodeShapeRangeValueCalculator.java
@@ -0,0 +1,35 @@
+package cytoscape.visual.mappings.rangecalculators;
+
+import cytoscape.visual.NodeShape;
+import cytoscape.visual.mappings.RangeValueCalculator;
+import cytoscape.visual.parsers.NodeShapeParser;
+import cytoscape.visual.parsers.ValueParser;
+
+public class NodeShapeRangeValueCalculator implements
+ RangeValueCalculator<NodeShape> {
+
+ private ValueParser parser;
+
+ public NodeShapeRangeValueCalculator() {
+ parser = new NodeShapeParser();
+ }
+
+
+ public NodeShape getRange(Object attrValue) {
+ if (attrValue instanceof String) {
+ NodeShape obj = (NodeShape) parser.parseStringValue((String) attrValue);
+ return obj;
+ }
+ return null;
+ }
+
+
+ public boolean isCompatible(Class<?> type) {
+ if(type.isAssignableFrom(NodeShape.class))
+ return true;
+ else
+ return false;
+ }
+
+
+}
diff --git a/application/src/main/java/cytoscape/visual/mappings/rangecalculators/StringRangeValueCalculator.java b/application/src/main/java/cytoscape/visual/mappings/rangecalculators/StringRangeValueCalculator.java
new file mode 100644
index 0000000..bd6aa49
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/mappings/rangecalculators/StringRangeValueCalculator.java
@@ -0,0 +1,42 @@
+package cytoscape.visual.mappings.rangecalculators;
+
+import java.util.List;
+
+import cytoscape.visual.mappings.RangeValueCalculator;
+
+public class StringRangeValueCalculator implements RangeValueCalculator<String> {
+
+
+ public String getRange(Object attrValue) {
+ if (attrValue instanceof List<?>) {
+ final List<?> list = (List<?>) attrValue;
+ int idx = 1;
+ final StringBuilder buf = new StringBuilder();
+ final int size = list.size();
+
+ for (final Object attrSubValue : list) {
+ buf.append(attrSubValue);
+
+ if (idx != size)
+ buf.append("\n");
+ idx++;
+ }
+
+ return buf.toString();
+ }
+
+ // OK, try returning the attrValue itself
+ if (attrValue instanceof String)
+ return (String) attrValue;
+ else
+ return attrValue.toString();
+ }
+
+
+ public boolean isCompatible(Class<?> type) {
+ if(String.class.isAssignableFrom(type))
+ return true;
+ else
+ return false;
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/package.html b/application/src/main/java/cytoscape/visual/package.html
new file mode 100644
index 0000000..5e2a5b5
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/package.html
@@ -0,0 +1,22 @@
+<html>
+<head>
+ <!-- $Revision: 6923 $
+ $Date: 2005-10-31 19:36:39 +0100 (Mon, 31 Oct 2005) $
+ $Author: nlandys $
+ -->
+</head>
+
+<body>
+Framework for generalized mappings from graph attributes
+to visual attributes. Graph attributes are either in the
+form of the actual nodes and edges of the graph, or in the
+form of values stored in one of
+{@link cytoscape.CytoscapeWindow CytoscapeWindow}'s two
+{@link cytoscape.CyAttributes CyAttributes} instances,
+{@link cytoscape.CytoscapeWindow#edgeAttributes edgeAttributes} and
+{@link cytoscape.CytoscapeWindow#nodeAttributes nodeAttributes}.
+Visual attributes include node color, size, shape, label, edge color,
+style, label, etc.
+</body>
+</html>
+
diff --git a/application/src/main/java/cytoscape/visual/parsers/ArrowParser.java b/application/src/main/java/cytoscape/visual/parsers/ArrowParser.java
new file mode 100644
index 0000000..95dbb46
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/parsers/ArrowParser.java
@@ -0,0 +1,80 @@
+/*
+ File: ArrowParser.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+//----------------------------------------------------------------------------
+// $Revision: 21067 $
+// $Date: 2010-07-29 01:52:44 +0200 (Thu, 29 Jul 2010) $
+// $Author: kono $
+//----------------------------------------------------------------------------
+package cytoscape.visual.parsers;
+
+
+//----------------------------------------------------------------------------
+import cytoscape.visual.Arrow;
+
+
+//import cytoscape.util.Misc;
+//----------------------------------------------------------------------------
+/**
+ * Parses a String into a yFiles Arrow object.
+ */
+public class ArrowParser
+ implements ValueParser {
+ /**
+ * DOCUMENT ME!
+ *
+ * @param value
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Arrow parseStringValue(String value) {
+ return parseArrow(value);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param value
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Arrow parseArrow(String value) {
+ return Arrow.parseArrowText(value);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/parsers/ArrowShapeParser.java b/application/src/main/java/cytoscape/visual/parsers/ArrowShapeParser.java
new file mode 100644
index 0000000..86283d2
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/parsers/ArrowShapeParser.java
@@ -0,0 +1,30 @@
+package cytoscape.visual.parsers;
+
+import cytoscape.visual.ArrowShape;
+
+public class ArrowShapeParser implements ValueParser {
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param value
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public ArrowShape parseStringValue(String value) {
+ return parseArrowShape(value);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param value
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public ArrowShape parseArrowShape(String value) {
+ return ArrowShape.parseArrowText(value);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/parsers/BooleanParser.java b/application/src/main/java/cytoscape/visual/parsers/BooleanParser.java
new file mode 100644
index 0000000..c4958de
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/parsers/BooleanParser.java
@@ -0,0 +1,66 @@
+/*
+ File: BooleanParser.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.visual.parsers;
+
+/**
+ * Parses a String into a Boolean object.
+ */
+public class BooleanParser
+ implements ValueParser {
+ /**
+ * DOCUMENT ME!
+ *
+ * @param value DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Boolean parseStringValue(String value) {
+ return parseBoolean(value);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param value DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Boolean parseBoolean(String value) {
+ return Boolean.parseBoolean(value);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/parsers/ColorParser.java b/application/src/main/java/cytoscape/visual/parsers/ColorParser.java
new file mode 100644
index 0000000..23288e6
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/parsers/ColorParser.java
@@ -0,0 +1,77 @@
+/*
+ File: ColorParser.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+//----------------------------------------------------------------------------
+// $Revision: 21067 $
+// $Date: 2010-07-29 01:52:44 +0200 (Thu, 29 Jul 2010) $
+// $Author: kono $
+//----------------------------------------------------------------------------
+package cytoscape.visual.parsers;
+
+import java.awt.Color;
+
+import cytoscape.util.ColorUtil;
+
+
+/**
+ * Parses a String into a Color object.
+ */
+public class ColorParser implements ValueParser {
+ /**
+ * DOCUMENT ME!
+ *
+ * @param value
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Color parseStringValue(String value) {
+ return parseColor(value);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param value
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Color parseColor(String value) {
+ return ColorUtil.parseColorText(value);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/parsers/DoubleParser.java b/application/src/main/java/cytoscape/visual/parsers/DoubleParser.java
new file mode 100644
index 0000000..a666950
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/parsers/DoubleParser.java
@@ -0,0 +1,81 @@
+/*
+ File: DoubleParser.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+//----------------------------------------------------------------------------
+// $Revision: 21067 $
+// $Date: 2010-07-29 01:52:44 +0200 (Thu, 29 Jul 2010) $
+// $Author: kono $
+//----------------------------------------------------------------------------
+package cytoscape.visual.parsers;
+
+
+//----------------------------------------------------------------------------
+/**
+ * Parses a String into a Double object.
+ */
+public class DoubleParser
+ implements ValueParser {
+ /**
+ * DOCUMENT ME!
+ *
+ * @param value DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Double parseStringValue(String value) {
+ return parseDouble(value);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param value DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Double parseDouble(String value) {
+ double d = Double.NaN;
+
+ try {
+ d = Double.parseDouble(value);
+
+ return new Double(d);
+ } catch (NumberFormatException e) {
+ return null;
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/parsers/FloatParser.java b/application/src/main/java/cytoscape/visual/parsers/FloatParser.java
new file mode 100644
index 0000000..2a06367
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/parsers/FloatParser.java
@@ -0,0 +1,39 @@
+package cytoscape.visual.parsers;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ */
+public class FloatParser
+ implements ValueParser {
+ /**
+ * DOCUMENT ME!
+ *
+ * @param value DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Float parseStringValue(String value) {
+ return parseFloat(value);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param value DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Float parseFloat(String value) {
+ Float f = Float.NaN;
+
+ try {
+ f = Float.parseFloat(value);
+
+ return f;
+ } catch (NumberFormatException e) {
+ return null;
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/parsers/FontParser.java b/application/src/main/java/cytoscape/visual/parsers/FontParser.java
new file mode 100644
index 0000000..9818264
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/parsers/FontParser.java
@@ -0,0 +1,125 @@
+/*
+ File: FontParser.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+//----------------------------------------------------------------------------
+// $Revision: 21067 $
+// $Date: 2010-07-29 01:52:44 +0200 (Thu, 29 Jul 2010) $
+// $Author: kono $
+//----------------------------------------------------------------------------
+package cytoscape.visual.parsers;
+
+import java.awt.Font;
+
+
+//----------------------------------------------------------------------------
+/**
+ * Parses a String into a Font object.
+ */
+public class FontParser
+ implements ValueParser {
+ /**
+ * DOCUMENT ME!
+ *
+ * @param value DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Font parseStringValue(String value) {
+ return parseFont(value);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param value DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Font parseFont(String value) {
+ //this algorithm could be moved into the Misc class with the
+ //other parsing methods
+ if (value == null)
+ return null;
+
+ //find index of first comma character
+ int comma1 = value.indexOf(",");
+
+ //return null if not found, or found at beginning or end of string
+ if ((comma1 < 1) || (comma1 >= (value.length() - 1)))
+ return null;
+
+ //find the second comma character
+ int comma2 = value.indexOf(",", comma1 + 1);
+
+ //return null if not found, or found immediately after the first
+ //comma, or at end of string
+ if ((comma2 == -1) || (comma2 == (comma1 + 1)) ||
+ (comma2 >= (value.length() - 1)))
+ return null;
+
+ //extract the fields
+ String name = value.substring(0, comma1);
+ String typeString = value.substring(comma1 + 1, comma2);
+ String sizeString = value.substring(
+ comma2 + 1,
+ value.length());
+
+ //parse the strings
+ int type = Font.PLAIN;
+
+ if (typeString.equalsIgnoreCase("bold"))
+ type = Font.BOLD;
+ else if (typeString.equalsIgnoreCase("italic"))
+ type = Font.ITALIC;
+ else if (typeString.equalsIgnoreCase("bold|italic"))
+ type = Font.BOLD | Font.ITALIC;
+ else if (typeString.equalsIgnoreCase("italic|bold"))
+ type = Font.ITALIC | Font.BOLD; //presumably the same as above
+
+ int size = 0;
+
+ try {
+ size = Integer.parseInt(sizeString);
+ } catch (NumberFormatException e) {
+ return null;
+ }
+
+ Font f = new Font(name, type, size);
+
+ return f;
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/parsers/GraphicsParser.java b/application/src/main/java/cytoscape/visual/parsers/GraphicsParser.java
new file mode 100644
index 0000000..c45a3cd
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/parsers/GraphicsParser.java
@@ -0,0 +1,94 @@
+package cytoscape.visual.parsers;
+
+import java.io.IOException;
+import java.net.URL;
+
+import cytoscape.Cytoscape;
+import cytoscape.logger.CyLogger;
+import cytoscape.visual.customgraphic.CyCustomGraphics;
+import cytoscape.visual.customgraphic.CyCustomGraphicsParser;
+import cytoscape.visual.customgraphic.CyCustomGraphicsParserFactory;
+import cytoscape.visual.customgraphic.DefaultCyCustomGraphicsParser;
+import cytoscape.visual.customgraphic.URLImageCustomGraphicsParser;
+import cytoscape.visual.customgraphic.impl.CyCustomGraphicsParserFactoryImpl;
+import cytoscape.visual.customgraphic.impl.bitmap.URLImageCustomGraphics;
+
+public class GraphicsParser implements ValueParser {
+
+ private static final String NULL_CG = "cytoscape.visual.customgraphic.NullCustomGraphics";
+
+ private static final CyLogger logger = CyLogger.getLogger();
+
+ // Maybe injected from outside if we use DI framework.
+ private final CyCustomGraphicsParserFactory parserFactory;
+
+ private final CyCustomGraphicsParser defaultParser;
+
+ public GraphicsParser() {
+ super();
+
+ parserFactory = new CyCustomGraphicsParserFactoryImpl();
+ // Register default parser
+ parserFactory.registerParser(URLImageCustomGraphics.class, new URLImageCustomGraphicsParser());
+ defaultParser = new DefaultCyCustomGraphicsParser();
+
+ // TODO: dynamically add parsers using listener.
+ }
+
+
+ public CyCustomGraphics parseStringValue(String value) {
+ return parse(value);
+ }
+
+
+ /**
+ * Parse given string.
+ *
+ * Syntax 1: (URL)
+ * Syntax 2: (Class Name, ID, Name, Tags)
+ *
+ * @param value
+ * @return
+ */
+ private CyCustomGraphics parse(String value) {
+ if(value == null || value.equals(NULL_CG))
+ return null;
+
+ // Syntax 1: URL String.
+ try {
+ final URL url = new URL(value);
+ CyCustomGraphics graphics = Cytoscape.getVisualMappingManager().getCustomGraphicsManager().getBySourceURL(url);
+ if(graphics == null) {
+ // Currently not in the Manager. Need to create new instance.
+ graphics = new URLImageCustomGraphics(url.toString());
+ // Use URL as display name
+ graphics.setDisplayName(value);
+
+ // Register to manager.
+ Cytoscape.getVisualMappingManager().getCustomGraphicsManager().addGraphics(graphics, url);
+ }
+ return graphics;
+ } catch (IOException e) {
+
+ // Syntax 2:
+ final String[] parts = value.split(",");
+ if(parts.length<4)
+ return null;
+
+ // Extract class name
+ final String className = parts[0];
+
+ // Get class-specific parser
+ final CyCustomGraphicsParser parser = parserFactory.getParser(className);
+
+ if(parser == null)
+ return defaultParser.getInstance(value);
+ else
+ return parser.getInstance(value);
+
+ }
+ }
+
+
+
+}
diff --git a/application/src/main/java/cytoscape/visual/parsers/LabelPositionParser.java b/application/src/main/java/cytoscape/visual/parsers/LabelPositionParser.java
new file mode 100644
index 0000000..1e42fe2
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/parsers/LabelPositionParser.java
@@ -0,0 +1,70 @@
+/*
+ File: LabelPositionParser.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.visual.parsers;
+
+import cytoscape.visual.LabelPosition;
+
+
+/**
+ * Parses a String into a LabelPosition object.
+ * @deprecated
+ */
+ at Deprecated
+public class LabelPositionParser
+ implements ValueParser {
+ /**
+ * DOCUMENT ME!
+ *
+ * @param value DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public LabelPosition parseStringValue(String value) {
+ return parseLabelPosition(value);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param value DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public LabelPosition parseLabelPosition(String value) {
+ return LabelPosition.parse(value);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/parsers/LineStyleParser.java b/application/src/main/java/cytoscape/visual/parsers/LineStyleParser.java
new file mode 100644
index 0000000..736680b
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/parsers/LineStyleParser.java
@@ -0,0 +1,79 @@
+/*
+ File: LineStyleParser.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+//----------------------------------------------------------------------------
+// $Revision: 10002 $
+// $Date: 2007-04-17 19:05:54 -0700 (Tue, 17 Apr 2007) $
+// $Author: kono $
+//----------------------------------------------------------------------------
+package cytoscape.visual.parsers;
+
+
+//----------------------------------------------------------------------------
+import cytoscape.visual.LineStyle;
+
+
+//----------------------------------------------------------------------------
+/**
+ * Parses a String into a yFiles shape, which is represented by a byte
+ * identifier. The return value here is a Byte object wrapping the
+ * primitive byte identifier.
+ */
+public class LineStyleParser
+ implements ValueParser {
+ /**
+ * DOCUMENT ME!
+ *
+ * @param value DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public LineStyle parseStringValue(String value) {
+ return parseLineStyle(value);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param value DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public LineStyle parseLineStyle(String value) {
+ return LineStyle.parse(value);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/parsers/NodeShapeParser.java b/application/src/main/java/cytoscape/visual/parsers/NodeShapeParser.java
new file mode 100644
index 0000000..7b78d92
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/parsers/NodeShapeParser.java
@@ -0,0 +1,84 @@
+/*
+ File: NodeShapeParser.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+package cytoscape.visual.parsers;
+
+import cytoscape.visual.NodeShape;
+
+/**
+ * Parses a String into a yFiles shape, which is represented by a byte
+ * identifier. The return value here is a Byte object wrapping the primitive
+ * byte identifier.
+ */
+public class NodeShapeParser implements ValueParser {
+ /**
+ * DOCUMENT ME!
+ *
+ * @param value
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public NodeShape parseStringValue(String value) {
+ return parseNodeShapeEnum(value);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param value
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public NodeShape parseNodeShapeEnum(String value) {
+ return NodeShape.parseNodeShapeText(value);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param shape
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static boolean isValidShape(NodeShape shape) {
+ return NodeShape.isValidShape(shape);
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/visual/parsers/ObjectPositionParser.java b/application/src/main/java/cytoscape/visual/parsers/ObjectPositionParser.java
new file mode 100644
index 0000000..d30f27c
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/parsers/ObjectPositionParser.java
@@ -0,0 +1,47 @@
+package cytoscape.visual.parsers;
+
+import giny.view.ObjectPosition;
+import giny.view.Position;
+import giny.view.Justification;
+
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+import ding.view.ObjectPositionImpl;
+
+public class ObjectPositionParser implements ValueParser {
+
+ private static final Pattern P = Pattern
+ .compile("^([NSEWC]{1,2}+),([NSEWC]{1,2}+),([clr]{1}+),(-?\\d+(.\\d+)?),(-?\\d+(.\\d+)?)$");
+
+
+ public ObjectPosition parseStringValue(String value) {
+ return parse(value);
+ }
+
+ /**
+ * Convert string representation to ObjectPosition object.
+ *
+ * @param value
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ private ObjectPosition parse(final String value) {
+
+ final Matcher m = P.matcher(value);
+
+ if (m.matches()) {
+ final ObjectPosition p = new ObjectPositionImpl();
+ p.setTargetAnchor(Position.parse(m.group(1)));
+ p.setAnchor(Position.parse(m.group(2)));
+ p.setJustify(Justification.parse(m.group(3)));
+ p.setOffsetX(Double.parseDouble(m.group(4)));
+ p.setOffsetY(Double.parseDouble(m.group(6)));
+
+ return p;
+ } else
+ return null;
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/visual/parsers/ObjectToString.java b/application/src/main/java/cytoscape/visual/parsers/ObjectToString.java
new file mode 100644
index 0000000..53f18cd
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/parsers/ObjectToString.java
@@ -0,0 +1,107 @@
+/*
+ File: ObjectToString.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.visual.parsers;
+
+import giny.view.ObjectPosition;
+
+import java.awt.Color;
+import java.awt.Font;
+
+import cytoscape.util.ColorUtil;
+import cytoscape.visual.Arrow;
+import cytoscape.visual.LabelPosition;
+import cytoscape.visual.NodeShape;
+
+
+//----------------------------------------------------------------------------
+/**
+ * This class contains a method that does the reverse of the various parsing
+ * classes in this package, i.e. turns a Object back into a String representation.
+ * Most cases either use the corresponding methods in cytoscape.util.Misc or
+ * use the default toString() method of the object.
+ *
+ * @deprecated will be removed in May 2011. Use ValueToStringConverterManager.manager.toString(obj) instead.
+ *
+ */
+ at Deprecated
+public class ObjectToString {
+ /**
+ * Constructs and returns a String representation of the given Object.
+ */
+ @Deprecated
+ public static String getStringValue(Object o) {
+ if ( o == null )
+ return "";
+ else if (o instanceof Color)
+ return ColorUtil.getColorAsText((Color) o);
+ else if (o instanceof NodeShape)
+ return NodeShape.getNodeShapeText((NodeShape) o);
+ else if (o instanceof Arrow)
+ return o.toString();
+ else if (o instanceof Font)
+ return getFontStringValue((Font) o);
+ else if (o instanceof Number)
+ //just trust the default String representation for numbers
+ return o.toString();
+ else if (o instanceof LabelPosition)
+ return ((LabelPosition) o).shortString();
+ else if (o instanceof ObjectPosition)
+ return ((ObjectPosition) o).shortString();
+ else
+ //default: use the toString() method
+ return o.toString();
+ }
+
+ private static String getFontStringValue(Font f) {
+ String name = f.getName();
+ int style = f.getStyle();
+ String styleString = "plain";
+
+ if (style == Font.BOLD)
+ styleString = "bold";
+ else if (style == Font.ITALIC)
+ styleString = "italic";
+ else if (style == (Font.BOLD | Font.ITALIC))
+ styleString = "bold|italic";
+
+ int size = f.getSize();
+ String sizeString = Integer.toString(size);
+
+ return name + "," + styleString + "," + sizeString;
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/parsers/StringParser.java b/application/src/main/java/cytoscape/visual/parsers/StringParser.java
new file mode 100644
index 0000000..e7f070d
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/parsers/StringParser.java
@@ -0,0 +1,74 @@
+/*
+ File: StringParser.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+//----------------------------------------------------------------------------
+// $Revision: 21067 $
+// $Date: 2010-07-29 01:52:44 +0200 (Thu, 29 Jul 2010) $
+// $Author: kono $
+//----------------------------------------------------------------------------
+package cytoscape.visual.parsers;
+
+
+//----------------------------------------------------------------------------
+/**
+ * Implements the ValueParser interface for String return values, by
+ * simply returning the supplied argument.
+ */
+public class StringParser
+ implements ValueParser {
+ /**
+ * DOCUMENT ME!
+ *
+ * @param value DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String parseStringValue(String value) {
+ return parseString(value);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param value DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String parseString(String value) {
+ return value;
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/parsers/ValueParser.java b/application/src/main/java/cytoscape/visual/parsers/ValueParser.java
new file mode 100644
index 0000000..3820f23
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/parsers/ValueParser.java
@@ -0,0 +1,59 @@
+/*
+ File: ValueParser.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+//----------------------------------------------------------------------------
+// $Revision: 21067 $
+// $Date: 2010-07-29 01:52:44 +0200 (Thu, 29 Jul 2010) $
+// $Author: kono $
+//----------------------------------------------------------------------------
+package cytoscape.visual.parsers;
+
+
+//----------------------------------------------------------------------------
+/**
+ * Interface to classes that parse a String value into a particular class
+ * of object.
+ */
+public interface ValueParser {
+ /**
+ * Parse the argument into an object. Returns null if the String is
+ * not parsable.
+ *
+ * Object parsed from the given string.
+ */
+ Object parseStringValue(String value);
+}
diff --git a/application/src/main/java/cytoscape/visual/parsers/package.html b/application/src/main/java/cytoscape/visual/parsers/package.html
new file mode 100644
index 0000000..f897917
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/parsers/package.html
@@ -0,0 +1,14 @@
+<html>
+<head>
+ <!-- $Revision: 5801 $
+ $Date: 2004-04-20 01:53:47 +0200 (Tue, 20 Apr 2004) $
+ $Author: amarkiel $
+ -->
+</head>
+
+<body>
+Translates visual attribute values to and from their String representation.
+Used for reading and writing visual styles from/to an external format.
+</body>
+</html>
+
diff --git a/application/src/main/java/cytoscape/visual/properties/AbstractVisualProperty.java b/application/src/main/java/cytoscape/visual/properties/AbstractVisualProperty.java
new file mode 100644
index 0000000..2029b20
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/properties/AbstractVisualProperty.java
@@ -0,0 +1,176 @@
+/*
+ Copyright (c) 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual.properties;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.visual.VisualProperty;
+import cytoscape.visual.VisualPropertyType;
+import cytoscape.visual.VisualPropertyDependency;
+
+import giny.view.EdgeView;
+import giny.view.NodeView;
+
+import java.awt.Graphics2D;
+
+import java.util.Map;
+import java.util.Properties;
+
+import javax.swing.Icon;
+
+
+/**
+ *
+ */
+public abstract class AbstractVisualProperty implements VisualProperty {
+
+ protected ValueValidator validator = null;
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ abstract public VisualPropertyType getType();
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void showDiscreteEditor() {
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void showContinousEditor() {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Map<Object, Icon> getIconSet() {
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g2 DOCUMENT ME!
+ */
+ public void paintIcon(Graphics2D g2) {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Icon getDefaultIcon() {
+ return getIcon(getDefault());
+ }
+
+ abstract public Icon getIcon(final Object value);
+
+ protected Object getDefault() {
+ return getType().getDefault(Cytoscape.getVisualMappingManager().getVisualStyle());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nv DOCUMENT ME!
+ * @param o DOCUMENT ME!
+ * @param dep DOCUMENT ME!
+ */
+ public void applyToNodeView(NodeView nv, Object o, VisualPropertyDependency dep) {
+ }
+
+ public void applyToNodeView(NodeView nv, Object o) {
+ applyToNodeView(nv,o,null);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param ev DOCUMENT ME!
+ * @param o DOCUMENT ME!
+ * @param dep DOCUMENT ME!
+ */
+ public void applyToEdgeView(EdgeView ev, Object o, VisualPropertyDependency dep) {
+ }
+
+ public void applyToEdgeView(EdgeView ev, Object o) {
+ applyToEdgeView(ev,o,null);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param props DOCUMENT ME!
+ * @param baseKey DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object parseProperty(Properties props, String baseKey) {
+ final VisualPropertyType type = getType();
+ String s = props.getProperty(type.getDefaultPropertyKey(baseKey));
+ if (s != null)
+ return type.getValueParser().parseStringValue(s);
+ else
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getDefaultAppearanceObject() {
+ return null;
+ }
+
+ public boolean constrained(VisualPropertyDependency dep) {
+ return false;
+ }
+
+ public boolean isValidValue(Object value) {
+ if ( validator == null )
+ return true;
+ else
+ return validator.isValid(value);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/properties/EdgeColorProp.java b/application/src/main/java/cytoscape/visual/properties/EdgeColorProp.java
new file mode 100644
index 0000000..9b8bdd2
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/properties/EdgeColorProp.java
@@ -0,0 +1,104 @@
+/*
+ Copyright (c) 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual.properties;
+
+import cytoscape.visual.*;
+
+import cytoscape.visual.parsers.*;
+
+import cytoscape.visual.ui.icon.LineTypeIcon;
+
+import cytoscape.visual.VisualPropertyDependency;
+
+import giny.view.EdgeView;
+
+import java.awt.Color;
+
+import java.util.Properties;
+
+import javax.swing.Icon;
+
+
+/**
+ *
+ */
+public class EdgeColorProp extends AbstractVisualProperty {
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public VisualPropertyType getType() {
+ return VisualPropertyType.EDGE_COLOR;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param value DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Icon getIcon(final Object value) {
+ final LineTypeIcon icon = new LineTypeIcon();
+ icon.setColor((Color) value);
+ icon.setBottomPadding(-7);
+
+ return icon;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param ev DOCUMENT ME!
+ * @param o DOCUMENT ME!
+ */
+ public void applyToEdgeView(EdgeView ev, Object o, VisualPropertyDependency dep) {
+ if ((o == null) || (ev == null))
+ return;
+
+ if (!((Color) o).equals(ev.getUnselectedPaint()))
+ ev.setUnselectedPaint((Color) o);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getDefaultAppearanceObject() {
+ return Color.black;
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/properties/EdgeFontFaceProp.java b/application/src/main/java/cytoscape/visual/properties/EdgeFontFaceProp.java
new file mode 100644
index 0000000..ad06ac9
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/properties/EdgeFontFaceProp.java
@@ -0,0 +1,115 @@
+/*
+ Copyright (c) 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual.properties;
+
+import cytoscape.visual.VisualPropertyType;
+
+import cytoscape.visual.ui.icon.LineTypeIcon;
+
+import cytoscape.visual.VisualPropertyDependency;
+
+import giny.view.EdgeView;
+import giny.view.Label;
+
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Font;
+import java.awt.Graphics;
+
+import java.util.Properties;
+
+import javax.swing.Icon;
+
+
+/**
+ *
+ */
+public class EdgeFontFaceProp extends AbstractVisualProperty {
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public VisualPropertyType getType() {
+ return VisualPropertyType.EDGE_FONT_FACE;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Icon getIcon(final Object value) {
+ return new LineTypeIcon() {
+ public void paintIcon(Component c, Graphics g, int x, int y) {
+ super.setColor(new Color(10, 10, 10, 0));
+ super.paintIcon(c, g, x, y);
+ g2d.setFont(new Font("SansSerif", Font.BOLD, 14));
+ g2d.setColor(Color.DARK_GRAY);
+
+ final Font font = (Font) value;
+ g2d.setFont(new Font(font.getFontName(), font.getStyle(), 40));
+ g2d.setColor(new Color(10, 10, 10, 40));
+ g2d.drawString("Font", c.getX() + 15, c.getY() - 10);
+ g2d.setFont(new Font("SansSerif", Font.BOLD, 14));
+ }
+ };
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param ev DOCUMENT ME!
+ * @param o DOCUMENT ME!
+ */
+ public void applyToEdgeView(EdgeView ev, Object o, VisualPropertyDependency dep) {
+ if ((o == null) || (ev == null))
+ return;
+
+ Label nodelabel = ev.getLabel();
+
+ if (!((Font) o).equals(nodelabel.getFont()))
+ nodelabel.setFont((Font) o);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getDefaultAppearanceObject() {
+ return new Font("SanSerif", Font.PLAIN, 10);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/properties/EdgeFontSizeProp.java b/application/src/main/java/cytoscape/visual/properties/EdgeFontSizeProp.java
new file mode 100644
index 0000000..1e1806b
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/properties/EdgeFontSizeProp.java
@@ -0,0 +1,107 @@
+/*
+ Copyright (c) 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual.properties;
+
+import cytoscape.visual.VisualPropertyType;
+
+import cytoscape.visual.ui.icon.LineTypeIcon;
+
+import cytoscape.visual.VisualPropertyDependency;
+
+import giny.view.EdgeView;
+import giny.view.Label;
+
+import java.awt.Color;
+import java.awt.Font;
+
+import java.util.Properties;
+
+import javax.swing.Icon;
+
+
+/**
+ *
+ */
+public class EdgeFontSizeProp extends AbstractVisualProperty {
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public VisualPropertyType getType() {
+ return VisualPropertyType.EDGE_FONT_SIZE;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Icon getIcon(final Object value) {
+ final LineTypeIcon icon = new LineTypeIcon();
+ icon.setColor(new Color(10, 10, 10, 20));
+ icon.setText(value.toString());
+ icon.setBottomPadding(-7);
+
+ return icon;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param ev DOCUMENT ME!
+ * @param o DOCUMENT ME!
+ */
+ public void applyToEdgeView(EdgeView ev, Object o, VisualPropertyDependency dep) {
+ if ((o == null) || (ev == null))
+ return;
+
+ Label edgelabel = ev.getLabel();
+ Font f = edgelabel.getFont();
+ float newFontSize = ((Number) o).floatValue();
+
+ if (newFontSize != f.getSize2D())
+ edgelabel.setFont(f.deriveFont(newFontSize));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getDefaultAppearanceObject() {
+ return new Float(10.0f);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/properties/EdgeLabelColorProp.java b/application/src/main/java/cytoscape/visual/properties/EdgeLabelColorProp.java
new file mode 100644
index 0000000..24e5481
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/properties/EdgeLabelColorProp.java
@@ -0,0 +1,114 @@
+/*
+ Copyright (c) 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual.properties;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.visual.*;
+import cytoscape.visual.VisualPropertyType;
+
+import cytoscape.visual.ui.icon.LineTypeIcon;
+
+import cytoscape.visual.VisualPropertyDependency;
+
+import giny.view.EdgeView;
+import giny.view.Label;
+
+import java.awt.Color;
+import java.awt.Font;
+
+import java.util.Properties;
+
+import javax.swing.Icon;
+
+
+/**
+ *
+ */
+public class EdgeLabelColorProp extends AbstractVisualProperty {
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public VisualPropertyType getType() {
+ return VisualPropertyType.EDGE_LABEL_COLOR;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Icon getIcon(final Object value) {
+ final LineTypeIcon icon = new LineTypeIcon();
+ icon.setColor(new Color(10, 10, 10, 0));
+ icon.setText("Font");
+
+ final Color fontColor = (Color) value;
+ final Font defFont = (Font) VisualPropertyType.EDGE_FONT_FACE.getDefault(Cytoscape.getVisualMappingManager()
+ .getVisualStyle());
+ icon.setTextFont(new Font(defFont.getFontName(), defFont.getStyle(), 24));
+ icon.setBottomPadding(-7);
+ icon.setTextColor(fontColor);
+
+ return icon;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param ev DOCUMENT ME!
+ * @param o DOCUMENT ME!
+ */
+ public void applyToEdgeView(EdgeView ev, Object o, VisualPropertyDependency dep) {
+ if ((o == null) || (ev == null))
+ return;
+
+ Label edgelabel = ev.getLabel();
+
+ if (!((Color) o).equals(edgelabel.getTextPaint()))
+ edgelabel.setTextPaint((Color) o);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getDefaultAppearanceObject() {
+ return Color.black;
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/properties/EdgeLabelOpacityProp.java b/application/src/main/java/cytoscape/visual/properties/EdgeLabelOpacityProp.java
new file mode 100644
index 0000000..df82db6
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/properties/EdgeLabelOpacityProp.java
@@ -0,0 +1,82 @@
+package cytoscape.visual.properties;
+
+import cytoscape.visual.VisualPropertyDependency;
+
+import giny.view.EdgeView;
+
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Font;
+import java.awt.Graphics;
+import java.util.Properties;
+
+import javax.swing.Icon;
+
+import cytoscape.visual.VisualPropertyType;
+import cytoscape.visual.ui.icon.LineTypeIcon;
+
+public class EdgeLabelOpacityProp extends AbstractVisualProperty {
+
+ public EdgeLabelOpacityProp() {
+ validator = new OpacityValidator();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public VisualPropertyType getType() {
+ return VisualPropertyType.EDGE_LABEL_OPACITY;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Icon getIcon(final Object value) {
+ final LineTypeIcon icon = new LineTypeIcon() {
+ public void paintIcon(Component c, Graphics g, int x, int y) {
+ super.setColor(new Color(10, 10, 10, 0));
+ super.paintIcon(c, g, x, y);
+ g2d.setFont(new Font("SansSerif", Font.BOLD, 24));
+ g2d.setColor(Color.DARK_GRAY);
+ g2d.drawString(value.toString(), c.getX() + LineTypeIcon.DEFAULT_ICON_SIZE*3/2,
+ (int) ((c.getHeight() / 2) + 7));
+
+ g2d.setFont(new Font("SansSerif", Font.BOLD, 12));
+ }
+ };
+ return icon;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param ev DOCUMENT ME!
+ * @param o DOCUMENT ME!
+ */
+ public void applyToEdgeView(EdgeView ev, Object o, VisualPropertyDependency dep) {
+ if ((o == null) || (ev == null))
+ return;
+
+ Integer tp = ((Color) ev.getLabel().getTextPaint()).getAlpha();
+ Integer newTp = ((Number) o).intValue();
+
+ if (tp != newTp) {
+ final Color oldPaint = (Color) ev.getLabel().getTextPaint();
+ ev.getLabel().setTextPaint(new Color(oldPaint.getRed(), oldPaint.getGreen(),
+ oldPaint.getBlue(), newTp));
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getDefaultAppearanceObject() {
+ return new Integer(255);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/properties/EdgeLabelPositionProp.java b/application/src/main/java/cytoscape/visual/properties/EdgeLabelPositionProp.java
new file mode 100644
index 0000000..3d5a453
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/properties/EdgeLabelPositionProp.java
@@ -0,0 +1,99 @@
+/*
+ Copyright (c) 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual.properties;
+
+import cytoscape.visual.*;
+
+import giny.view.EdgeView;
+import java.util.Properties;
+
+import javax.swing.Icon;
+
+import ding.view.ObjectPositionImpl;
+
+
+/**
+ *
+ */
+public class EdgeLabelPositionProp extends AbstractVisualProperty {
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public VisualPropertyType getType() {
+ return VisualPropertyType.EDGE_LABEL_POSITION;
+ }
+
+ public Icon getIcon(final Object value) {
+ return null;
+ }
+/*
+ public void applyToEdgeView(EdgeView ev, Object o, VisualPropertyDependency dep) {
+ if ( o == null || ev == null )
+ return;
+
+ Label label = ev.getLabel();
+ LabelPosition labelPosition = (LabelPosition)o;
+
+ int newTextAnchor = labelPosition.getLabelAnchor();
+
+ if (label.getTextAnchor() != newTextAnchor)
+ label.setTextAnchor(newTextAnchor);
+
+ int newJustify = labelPosition.getJustify();
+
+ if (label.getJustify() != newJustify)
+ label.setJustify(newJustify);
+
+ int newNodeAnchor = labelPosition.getTargetAnchor();
+
+ if (ev.getNodeLabelAnchor() != newNodeAnchor)
+ ev.setNodeLabelAnchor(newNodeAnchor);
+
+ double newOffsetX = labelPosition.getOffsetX();
+
+ if (ev.getLabelOffsetX() != newOffsetX)
+ ev.setLabelOffsetX(newOffsetX);
+
+ double newOffsetY = labelPosition.getOffsetY();
+
+ if (ev.getLabelOffsetY() != newOffsetY)
+ ev.setLabelOffsetY(newOffsetY);
+ }
+*/
+
+ public Object getDefaultAppearanceObject() { return new ObjectPositionImpl(); }
+}
diff --git a/application/src/main/java/cytoscape/visual/properties/EdgeLabelProp.java b/application/src/main/java/cytoscape/visual/properties/EdgeLabelProp.java
new file mode 100644
index 0000000..ee95bbd
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/properties/EdgeLabelProp.java
@@ -0,0 +1,97 @@
+/*
+ Copyright (c) 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual.properties;
+
+import cytoscape.visual.*;
+
+import cytoscape.visual.VisualPropertyDependency;
+
+import giny.view.EdgeView;
+import giny.view.Label;
+
+import java.util.Properties;
+
+import javax.swing.Icon;
+
+
+/**
+ *
+ */
+public class EdgeLabelProp extends AbstractVisualProperty {
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public VisualPropertyType getType() {
+ return VisualPropertyType.EDGE_LABEL;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param value DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Icon getIcon(final Object value) {
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param ev DOCUMENT ME!
+ * @param o DOCUMENT ME!
+ */
+ public void applyToEdgeView(EdgeView ev, Object o, VisualPropertyDependency dep) {
+ if ((o == null) || (ev == null))
+ return;
+
+ Label label = ev.getLabel();
+
+ if (!((String) o).equals(label.getText()))
+ label.setText((String) o);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getDefaultAppearanceObject() {
+ return "";
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/properties/EdgeLabelWidthProp.java b/application/src/main/java/cytoscape/visual/properties/EdgeLabelWidthProp.java
new file mode 100644
index 0000000..d437346
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/properties/EdgeLabelWidthProp.java
@@ -0,0 +1,122 @@
+/*
+ Copyright (c) 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual.properties;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.visual.VisualPropertyType;
+import static cytoscape.visual.VisualPropertyType.EDGE_LABEL_WIDTH;
+
+import cytoscape.visual.ui.icon.LineTypeIcon;
+
+import cytoscape.visual.VisualPropertyDependency;
+
+import giny.view.EdgeView;
+
+import java.awt.BasicStroke;
+import java.awt.Color;
+import java.awt.Stroke;
+import java.awt.Component;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.Font;
+
+import java.util.Properties;
+
+import javax.swing.Icon;
+
+
+/**
+ *
+ */
+public class EdgeLabelWidthProp extends AbstractVisualProperty {
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public VisualPropertyType getType() {
+ return VisualPropertyType.EDGE_LABEL_WIDTH;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Icon getIcon(final Object value) {
+ final LineTypeIcon icon = new LineTypeIcon() {
+ public void paintIcon(Component c, Graphics g, int x, int y) {
+ super.setColor(new Color(10, 10, 10, 0));
+ super.paintIcon(c, g, x, y);
+
+ g2d.setFont(new Font("SansSerif", Font.BOLD, 24));
+ g2d.setColor(Color.DARK_GRAY);
+ g2d.drawString(value.toString(),
+ c.getX() + ((LineTypeIcon.DEFAULT_ICON_SIZE * 3) / 2),
+ (int) ((c.getHeight() / 2) + 7));
+
+ g2d.setFont(new Font("SansSerif", Font.BOLD, 12));
+ }
+ };
+
+ return icon;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param ev DOCUMENT ME!
+ * @param o DOCUMENT ME!
+ */
+ public void applyToEdgeView(EdgeView ev, Object o, VisualPropertyDependency dep) {
+ if ((o == null) || (ev == null))
+ return;
+
+ float width = ((Number)o).floatValue();
+ if (ev.getLabelWidth() != width) {
+ ev.setLabelWidth(width);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getDefaultAppearanceObject() {
+ return new Float(100.0f);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/properties/EdgeLineStyleProp.java b/application/src/main/java/cytoscape/visual/properties/EdgeLineStyleProp.java
new file mode 100644
index 0000000..33d54e5
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/properties/EdgeLineStyleProp.java
@@ -0,0 +1,110 @@
+/*
+ Copyright (c) 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual.properties;
+
+import cytoscape.visual.VisualPropertyDependency;
+
+import giny.view.EdgeView;
+
+import java.awt.BasicStroke;
+import java.util.Map;
+import java.util.Properties;
+
+import javax.swing.Icon;
+
+import cytoscape.visual.LineStyle;
+import cytoscape.visual.VisualPropertyType;
+import cytoscape.visual.ui.icon.LineTypeIcon;
+
+
+/**
+ *
+ */
+public class EdgeLineStyleProp extends AbstractVisualProperty {
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public VisualPropertyType getType() {
+ return VisualPropertyType.EDGE_LINE_STYLE;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Icon getIcon(final Object value) {
+ final LineTypeIcon icon = new LineTypeIcon((LineStyle)value);
+ icon.setBottomPadding(-6);
+
+ return icon;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Map<Object, Icon> getIconSet() {
+ return LineStyle.getIconSet();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param ev DOCUMENT ME!
+ * @param o DOCUMENT ME!
+ */
+ public void applyToEdgeView(EdgeView ev, Object o, VisualPropertyDependency dep) {
+ if ((o == null) || (ev == null))
+ return;
+
+ ev.setStroke(((LineStyle)o).getStroke(ev.getStrokeWidth()));
+// if (((LineStyle) o).getDashDef() != (((BasicStroke) ev.getStroke()).getDashArray())) {
+// ev.setStroke(((LineStyle) o).getStroke(ev.getStrokeWidth()));
+// }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getDefaultAppearanceObject() {
+ return LineStyle.SOLID;
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/properties/EdgeLineWidthProp.java b/application/src/main/java/cytoscape/visual/properties/EdgeLineWidthProp.java
new file mode 100644
index 0000000..c7fb4d4
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/properties/EdgeLineWidthProp.java
@@ -0,0 +1,117 @@
+/*
+ Copyright (c) 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual.properties;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.visual.LineStyle;
+import cytoscape.visual.VisualPropertyType;
+import static cytoscape.visual.VisualPropertyType.EDGE_LINE_STYLE;
+
+import cytoscape.visual.ui.icon.LineTypeIcon;
+
+import cytoscape.visual.VisualPropertyDependency;
+
+import giny.view.EdgeView;
+
+import java.awt.BasicStroke;
+import java.awt.Color;
+import java.awt.Stroke;
+
+import java.util.Properties;
+
+import javax.swing.Icon;
+
+
+/**
+ *
+ */
+public class EdgeLineWidthProp extends AbstractVisualProperty {
+
+ public EdgeLineWidthProp() {
+ validator = new GTZeroValidator();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public VisualPropertyType getType() {
+ return VisualPropertyType.EDGE_LINE_WIDTH;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Icon getIcon(final Object value) {
+ final LineTypeIcon icon = new LineTypeIcon();
+ icon.setColor(new Color(10, 10, 10, 20));
+ icon.setText(value.toString());
+ icon.setBottomPadding(-7);
+
+ return icon;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param ev DOCUMENT ME!
+ * @param o DOCUMENT ME!
+ */
+ public void applyToEdgeView(EdgeView ev, Object o, VisualPropertyDependency dep) {
+ if ((o == null) || (ev == null))
+ return;
+
+ float width = ((Number)o).floatValue();
+ if (ev.getStrokeWidth() != width) {
+ final Stroke oldStroke = ev.getStroke();
+ final Stroke newStroke = LineStyle.extractLineStyle(oldStroke).getStroke(width);
+ ev.setStroke(newStroke);
+ ev.setStrokeWidth(width);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getDefaultAppearanceObject() {
+ return new Float(1.0f);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/properties/EdgeOpacityProp.java b/application/src/main/java/cytoscape/visual/properties/EdgeOpacityProp.java
new file mode 100644
index 0000000..aff393f
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/properties/EdgeOpacityProp.java
@@ -0,0 +1,125 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.visual.properties;
+
+import cytoscape.visual.VisualPropertyDependency;
+
+import giny.view.EdgeView;
+
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Font;
+import java.awt.Graphics;
+import java.util.Properties;
+
+import javax.swing.Icon;
+
+import cytoscape.visual.VisualPropertyType;
+import cytoscape.visual.ui.icon.LineTypeIcon;
+
+
+/**
+ *
+ */
+public class EdgeOpacityProp extends AbstractVisualProperty {
+
+ public EdgeOpacityProp() {
+ validator = new OpacityValidator();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public VisualPropertyType getType() {
+ return VisualPropertyType.EDGE_OPACITY;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Icon getIcon(final Object value) {
+ final LineTypeIcon icon = new LineTypeIcon() {
+ public void paintIcon(Component c, Graphics g, int x, int y) {
+ super.setColor(new Color(10, 10, 10, 0));
+ super.paintIcon(c, g, x, y);
+
+ g2d.setFont(new Font("SansSerif", Font.BOLD, 24));
+ g2d.setColor(Color.DARK_GRAY);
+ g2d.drawString(value.toString(),
+ c.getX() + ((LineTypeIcon.DEFAULT_ICON_SIZE * 3) / 2),
+ (int) ((c.getHeight() / 2) + 7));
+
+ g2d.setFont(new Font("SansSerif", Font.BOLD, 12));
+ }
+ };
+
+ return icon;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param ev DOCUMENT ME!
+ * @param o DOCUMENT ME!
+ */
+ public void applyToEdgeView(EdgeView ev, Object o, VisualPropertyDependency dep) {
+ if ((o == null) || (ev == null))
+ return;
+
+ Integer tp = ((Color) ev.getUnselectedPaint()).getAlpha();
+ Integer newTp = ((Number) o).intValue();
+
+ if (tp != newTp) {
+ final Color oldPaint = (Color) ev.getUnselectedPaint();
+ ev.setUnselectedPaint(new Color(oldPaint.getRed(), oldPaint.getGreen(),
+ oldPaint.getBlue(), newTp));
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getDefaultAppearanceObject() {
+ return new Integer(255);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/properties/EdgeSourceArrowColorProp.java b/application/src/main/java/cytoscape/visual/properties/EdgeSourceArrowColorProp.java
new file mode 100644
index 0000000..155b242
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/properties/EdgeSourceArrowColorProp.java
@@ -0,0 +1,121 @@
+/*
+ Copyright (c) 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual.properties;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.visual.ArrowShape;
+import cytoscape.visual.VisualPropertyType;
+
+import cytoscape.visual.ui.icon.ArrowIcon;
+
+import cytoscape.visual.VisualPropertyDependency;
+import static cytoscape.visual.VisualPropertyDependency.Definition.*;
+
+import giny.view.EdgeView;
+
+import java.awt.Color;
+import java.awt.Paint;
+
+import java.util.Properties;
+
+import javax.swing.Icon;
+
+
+/**
+ *
+ */
+public class EdgeSourceArrowColorProp extends AbstractVisualProperty {
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public VisualPropertyType getType() {
+ return VisualPropertyType.EDGE_SRCARROW_COLOR;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Icon getIcon(final Object value) {
+ final ArrowShape arrow = (ArrowShape) VisualPropertyType.EDGE_SRCARROW_SHAPE
+ .getDefault(Cytoscape.getVisualMappingManager()
+ .getVisualStyle());
+ final ArrowIcon icon = new ArrowIcon(arrow);
+ icon.setColor((Color) value);
+ icon.setLeftPadding(20);
+ icon.setBottomPadding(-6);
+
+ return icon;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param ev DOCUMENT ME!
+ * @param o DOCUMENT ME!
+ */
+ public void applyToEdgeView(EdgeView ev, Object o, VisualPropertyDependency dep) {
+ if ((o == null) || (ev == null))
+ return;
+
+ if ( dep != null && dep.check(ARROW_COLOR_MATCHES_EDGE) ) {
+ if (ev.getUnselectedPaint() != ev.getSourceEdgeEndPaint())
+ ev.setSourceEdgeEndPaint(ev.getUnselectedPaint());
+
+ } else {
+ final Paint newSourceArrowColor = ((Color) o);
+
+ if (newSourceArrowColor != ev.getSourceEdgeEndPaint())
+ ev.setSourceEdgeEndPaint(newSourceArrowColor);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getDefaultAppearanceObject() {
+ return Color.black;
+ }
+
+ public boolean constrained(VisualPropertyDependency dep) {
+ return ( dep != null && dep.check(ARROW_COLOR_MATCHES_EDGE) );
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/properties/EdgeSourceArrowOpacityProp.java b/application/src/main/java/cytoscape/visual/properties/EdgeSourceArrowOpacityProp.java
new file mode 100644
index 0000000..f32c867
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/properties/EdgeSourceArrowOpacityProp.java
@@ -0,0 +1,141 @@
+/*
+ Copyright (c) 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual.properties;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.visual.ArrowShape;
+import cytoscape.visual.VisualPropertyType;
+
+import cytoscape.visual.ui.icon.LineTypeIcon;
+
+import cytoscape.visual.VisualPropertyDependency;
+import static cytoscape.visual.VisualPropertyDependency.Definition.*;
+
+import giny.view.EdgeView;
+
+import java.awt.Color;
+import java.awt.Paint;
+import java.awt.Component;
+import java.awt.Font;
+import java.awt.Graphics;
+import java.util.Properties;
+
+
+import java.util.Properties;
+
+import javax.swing.Icon;
+
+
+/**
+ *
+ */
+public class EdgeSourceArrowOpacityProp extends AbstractVisualProperty {
+
+ public EdgeSourceArrowOpacityProp() {
+ validator = new OpacityValidator();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public VisualPropertyType getType() {
+ return VisualPropertyType.EDGE_SRCARROW_OPACITY;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Icon getIcon(final Object value) {
+ final LineTypeIcon icon = new LineTypeIcon() {
+ public void paintIcon(Component c, Graphics g, int x, int y) {
+ super.setColor(new Color(10, 10, 10, 0));
+ super.paintIcon(c, g, x, y);
+
+ g2d.setFont(new Font("SansSerif", Font.BOLD, 24));
+ g2d.setColor(Color.DARK_GRAY);
+ g2d.drawString(value.toString(),
+ c.getX() + ((LineTypeIcon.DEFAULT_ICON_SIZE * 3) / 2),
+ (int) ((c.getHeight() / 2) + 7));
+
+ g2d.setFont(new Font("SansSerif", Font.BOLD, 12));
+ }
+ };
+
+ return icon;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param ev DOCUMENT ME!
+ * @param o DOCUMENT ME!
+ */
+ public void applyToEdgeView(EdgeView ev, Object o, VisualPropertyDependency dep) {
+ if ((o == null) || (ev == null))
+ return;
+
+ if ( dep != null && dep.check(ARROW_COLOR_MATCHES_EDGE) ) {
+ if (ev.getUnselectedPaint() != ev.getSourceEdgeEndPaint())
+ ev.setSourceEdgeEndPaint(ev.getUnselectedPaint());
+ } else {
+ final Color oldPaint = (Color) ev.getSourceEdgeEndPaint();
+
+ Integer tp = oldPaint.getAlpha();
+ Integer newTp = ((Number) o).intValue();
+
+ if (tp != newTp)
+ ev.setSourceEdgeEndPaint(new Color(oldPaint.getRed(), oldPaint.getGreen(),
+ oldPaint.getBlue(), newTp));
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getDefaultAppearanceObject() {
+ return new Integer(255);
+ }
+
+ public boolean constrained(VisualPropertyDependency dep) {
+ return ( dep != null && dep.check(ARROW_COLOR_MATCHES_EDGE) );
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/properties/EdgeSourceArrowShapeProp.java b/application/src/main/java/cytoscape/visual/properties/EdgeSourceArrowShapeProp.java
new file mode 100644
index 0000000..24786f6
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/properties/EdgeSourceArrowShapeProp.java
@@ -0,0 +1,112 @@
+/*
+ Copyright (c) 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual.properties;
+
+import cytoscape.visual.VisualPropertyDependency;
+
+import giny.view.EdgeView;
+
+import java.util.Map;
+import java.util.Properties;
+
+import javax.swing.Icon;
+
+import cytoscape.visual.Arrow;
+import cytoscape.visual.ArrowShape;
+import cytoscape.visual.VisualPropertyType;
+import cytoscape.visual.ui.icon.ArrowIcon;
+
+
+/**
+ *
+ */
+public class EdgeSourceArrowShapeProp extends AbstractVisualProperty {
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public VisualPropertyType getType() {
+ return VisualPropertyType.EDGE_SRCARROW_SHAPE;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Map<Object, Icon> getIconSet() {
+ return ArrowShape.getIconSet();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Icon getIcon(final Object value) {
+ final ArrowIcon icon = new ArrowIcon((ArrowShape) value);
+ icon.setLeftPadding(20);
+ icon.setBottomPadding(-6);
+
+ return icon;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param ev DOCUMENT ME!
+ * @param o DOCUMENT ME!
+ */
+ public void applyToEdgeView(EdgeView ev, Object o, VisualPropertyDependency dep) {
+ if ((o == null) || (ev == null))
+ return;
+ final int newSourceEnd;
+
+ newSourceEnd = ((ArrowShape) o).getGinyArrow();
+
+ if (newSourceEnd != ev.getSourceEdgeEnd())
+ ev.setSourceEdgeEnd(newSourceEnd);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getDefaultAppearanceObject() {
+ return ArrowShape.NONE;
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/properties/EdgeTargetArrowColorProp.java b/application/src/main/java/cytoscape/visual/properties/EdgeTargetArrowColorProp.java
new file mode 100644
index 0000000..9c71bda
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/properties/EdgeTargetArrowColorProp.java
@@ -0,0 +1,121 @@
+/*
+ Copyright (c) 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual.properties;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.visual.ArrowShape;
+import cytoscape.visual.VisualPropertyType;
+
+import cytoscape.visual.ui.icon.ArrowIcon;
+
+import cytoscape.visual.VisualPropertyDependency;
+
+import giny.view.EdgeView;
+
+import java.awt.Color;
+import java.awt.Paint;
+
+import java.util.Properties;
+
+import javax.swing.Icon;
+
+import cytoscape.visual.VisualPropertyDependency;
+import static cytoscape.visual.VisualPropertyDependency.Definition.*;
+
+/**
+ *
+ */
+public class EdgeTargetArrowColorProp extends AbstractVisualProperty {
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public VisualPropertyType getType() {
+ return VisualPropertyType.EDGE_TGTARROW_COLOR;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Icon getIcon(final Object value) {
+ final ArrowShape arrowShape = (ArrowShape) VisualPropertyType.EDGE_TGTARROW_SHAPE
+ .getDefault(Cytoscape.getVisualMappingManager()
+ .getVisualStyle());
+ final ArrowIcon icon = new ArrowIcon(arrowShape);
+ icon.setColor((Color) value);
+ icon.setLeftPadding(20);
+ icon.setBottomPadding(-6);
+
+ return icon;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param ev DOCUMENT ME!
+ * @param o DOCUMENT ME!
+ */
+ public void applyToEdgeView(EdgeView ev, Object o, VisualPropertyDependency dep) {
+ if ((o == null) || (ev == null))
+ return;
+
+ if ( dep != null && dep.check(ARROW_COLOR_MATCHES_EDGE) ) {
+ if (ev.getUnselectedPaint() != ev.getTargetEdgeEndPaint())
+ ev.setTargetEdgeEndPaint(ev.getUnselectedPaint());
+ } else {
+ final Paint newTargetArrowColor = ((Color) o);
+
+ if (newTargetArrowColor != ev.getTargetEdgeEndPaint())
+ ev.setTargetEdgeEndPaint(newTargetArrowColor);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getDefaultAppearanceObject() {
+ return Color.black;
+ }
+
+ public boolean constrained(VisualPropertyDependency dep) {
+ return (dep != null && dep.check(ARROW_COLOR_MATCHES_EDGE));
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/properties/EdgeTargetArrowOpacityProp.java b/application/src/main/java/cytoscape/visual/properties/EdgeTargetArrowOpacityProp.java
new file mode 100644
index 0000000..b20261d
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/properties/EdgeTargetArrowOpacityProp.java
@@ -0,0 +1,139 @@
+/*
+ Copyright (c) 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual.properties;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.visual.ArrowShape;
+import cytoscape.visual.VisualPropertyType;
+
+import cytoscape.visual.ui.icon.LineTypeIcon;
+
+import cytoscape.visual.VisualPropertyDependency;
+import static cytoscape.visual.VisualPropertyDependency.Definition.*;
+
+import giny.view.EdgeView;
+
+import java.awt.Color;
+import java.awt.Paint;
+import java.awt.Component;
+import java.awt.Font;
+import java.awt.Graphics;
+import java.util.Properties;
+
+
+import java.util.Properties;
+
+import javax.swing.Icon;
+
+/**
+ *
+ */
+public class EdgeTargetArrowOpacityProp extends AbstractVisualProperty {
+
+ public EdgeTargetArrowOpacityProp() {
+ validator = new OpacityValidator();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public VisualPropertyType getType() {
+ return VisualPropertyType.EDGE_TGTARROW_OPACITY;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Icon getIcon(final Object value) {
+ final LineTypeIcon icon = new LineTypeIcon() {
+ public void paintIcon(Component c, Graphics g, int x, int y) {
+ super.setColor(new Color(10, 10, 10, 0));
+ super.paintIcon(c, g, x, y);
+
+ g2d.setFont(new Font("SansSerif", Font.BOLD, 24));
+ g2d.setColor(Color.DARK_GRAY);
+ g2d.drawString(value.toString(),
+ c.getX() + ((LineTypeIcon.DEFAULT_ICON_SIZE * 3) / 2),
+ (int) ((c.getHeight() / 2) + 7));
+
+ g2d.setFont(new Font("SansSerif", Font.BOLD, 12));
+ }
+ };
+
+ return icon;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param ev DOCUMENT ME!
+ * @param o DOCUMENT ME!
+ */
+ public void applyToEdgeView(EdgeView ev, Object o, VisualPropertyDependency dep) {
+ if ((o == null) || (ev == null))
+ return;
+
+ if ( dep != null && dep.check(ARROW_COLOR_MATCHES_EDGE) ) {
+ if (ev.getUnselectedPaint() != ev.getTargetEdgeEndPaint())
+ ev.setTargetEdgeEndPaint(ev.getUnselectedPaint());
+ } else {
+ final Color oldPaint = (Color) ev.getTargetEdgeEndPaint();
+ Integer tp = oldPaint.getAlpha();
+ Integer newTp = ((Number) o).intValue();
+
+ if (tp != newTp)
+ ev.setTargetEdgeEndPaint(new Color(oldPaint.getRed(), oldPaint.getGreen(),
+ oldPaint.getBlue(), newTp));
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getDefaultAppearanceObject() {
+ return new Integer(255);
+ }
+
+ public boolean constrained(VisualPropertyDependency dep) {
+ return ( dep != null && dep.check(ARROW_COLOR_MATCHES_EDGE) );
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/properties/EdgeTargetArrowShapeProp.java b/application/src/main/java/cytoscape/visual/properties/EdgeTargetArrowShapeProp.java
new file mode 100644
index 0000000..dd7aad9
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/properties/EdgeTargetArrowShapeProp.java
@@ -0,0 +1,112 @@
+/*
+ Copyright (c) 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual.properties;
+
+import cytoscape.visual.ArrowShape;
+import cytoscape.visual.VisualPropertyType;
+
+import cytoscape.visual.ui.icon.ArrowIcon;
+
+import cytoscape.visual.VisualPropertyDependency;
+
+import giny.view.EdgeView;
+
+import java.util.Map;
+import java.util.Properties;
+
+import javax.swing.Icon;
+
+
+/**
+ *
+ */
+public class EdgeTargetArrowShapeProp extends AbstractVisualProperty {
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public VisualPropertyType getType() {
+ return VisualPropertyType.EDGE_TGTARROW_SHAPE;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Map<Object, Icon> getIconSet() {
+ return ArrowShape.getIconSet();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Icon getIcon(final Object value) {
+ final ArrowIcon icon = new ArrowIcon((ArrowShape) value);
+ icon.setLeftPadding(20);
+ icon.setBottomPadding(-6);
+
+ return icon;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param ev DOCUMENT ME!
+ * @param o DOCUMENT ME!
+ */
+ public void applyToEdgeView(EdgeView ev, Object o, VisualPropertyDependency dep) {
+ if ((o == null) || (ev == null))
+ return;
+
+ final int newTargetEnd = ((ArrowShape) o).getGinyArrow();
+
+ if (newTargetEnd != ev.getTargetEdgeEnd()) {
+ ev.setTargetEdgeEnd(newTargetEnd);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getDefaultAppearanceObject() {
+ return ArrowShape.NONE;
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/properties/EdgeToolTipProp.java b/application/src/main/java/cytoscape/visual/properties/EdgeToolTipProp.java
new file mode 100644
index 0000000..8aba06f
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/properties/EdgeToolTipProp.java
@@ -0,0 +1,94 @@
+/*
+ Copyright (c) 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual.properties;
+
+import cytoscape.visual.*;
+
+import cytoscape.visual.ui.icon.*;
+import cytoscape.visual.*;
+
+import javax.swing.Icon;
+
+import cytoscape.visual.VisualPropertyDependency;
+
+import giny.view.EdgeView;
+import java.util.Properties;
+
+
+/**
+ *
+ */
+public class EdgeToolTipProp extends AbstractVisualProperty {
+
+ private StringBuilder buf = new StringBuilder();
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public VisualPropertyType getType() {
+ return VisualPropertyType.EDGE_TOOLTIP;
+ }
+
+ public Icon getIcon(final Object value) {
+ return null;
+ }
+
+ public void applyToEdgeView(EdgeView ev, Object o, VisualPropertyDependency dep) {
+ if ((o == null) || (ev == null))
+ return;
+
+ if(((String)o).startsWith("<html>")) {
+ ev.setToolTip((String) o);
+ return;
+ }
+
+ // Setting the tooltip to null is preferred because otherwise a small icon
+ // indicating the empty tooltip appears.
+ if (((String)o).equals("")) {
+ ev.setToolTip(null);
+ return;
+ }
+
+ buf = new StringBuilder();
+ buf.append("<html><body bgcolor=\"white\"><Div Align=\"center\"><Font Size=\"4\">");
+ buf.append(((String)o).replaceAll("\\n", "<br>"));
+ buf.append("</Font></div></body></html>");
+ ev.setToolTip(buf.toString());
+ }
+
+ public Object getDefaultAppearanceObject() { return ""; }
+}
diff --git a/application/src/main/java/cytoscape/visual/properties/GTEZeroValidator.java b/application/src/main/java/cytoscape/visual/properties/GTEZeroValidator.java
new file mode 100644
index 0000000..2d629db
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/properties/GTEZeroValidator.java
@@ -0,0 +1,45 @@
+
+/*
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual.properties;
+
+class GTEZeroValidator implements ValueValidator {
+ public boolean isValid(Object value) {
+ if ( value != null && value instanceof Number && ((Number) value).doubleValue() >= 0.0 )
+ return true;
+ else
+ return false;
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/properties/GTZeroValidator.java b/application/src/main/java/cytoscape/visual/properties/GTZeroValidator.java
new file mode 100644
index 0000000..47ab087
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/properties/GTZeroValidator.java
@@ -0,0 +1,45 @@
+
+/*
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual.properties;
+
+class GTZeroValidator implements ValueValidator {
+ public boolean isValid(Object value) {
+ if ( value != null && value instanceof Number && ((Number) value).doubleValue() > 0.0 )
+ return true;
+ else
+ return false;
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/properties/NodeBorderColorProp.java b/application/src/main/java/cytoscape/visual/properties/NodeBorderColorProp.java
new file mode 100644
index 0000000..ed5e5ed
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/properties/NodeBorderColorProp.java
@@ -0,0 +1,100 @@
+/*
+ Copyright (c) 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual.properties;
+
+import cytoscape.visual.VisualPropertyType;
+
+import cytoscape.visual.ui.icon.NodeIcon;
+
+import cytoscape.visual.VisualPropertyDependency;
+
+import giny.view.NodeView;
+
+import java.awt.Color;
+
+import java.util.Properties;
+
+import javax.swing.Icon;
+
+
+/**
+ *
+ */
+public class NodeBorderColorProp extends AbstractVisualProperty {
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public VisualPropertyType getType() {
+ return VisualPropertyType.NODE_BORDER_COLOR;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Icon getIcon(final Object value) {
+ final NodeIcon icon = new NodeIcon();
+ icon.setColor((Color) value);
+ icon.setBottomPadding(-2);
+
+ return icon;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nv DOCUMENT ME!
+ * @param o DOCUMENT ME!
+ */
+ public void applyToNodeView(NodeView nv, Object o, VisualPropertyDependency dep) {
+ if ((o == null) || (nv == null))
+ return;
+
+ if (!((Color) o).equals(nv.getBorderPaint()))
+ nv.setBorderPaint((Color) o);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getDefaultAppearanceObject() {
+ return Color.black;
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/properties/NodeBorderOpacityProp.java b/application/src/main/java/cytoscape/visual/properties/NodeBorderOpacityProp.java
new file mode 100644
index 0000000..4718bec
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/properties/NodeBorderOpacityProp.java
@@ -0,0 +1,97 @@
+package cytoscape.visual.properties;
+
+import cytoscape.visual.VisualPropertyDependency;
+
+import giny.view.NodeView;
+
+import java.awt.BasicStroke;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Font;
+import java.awt.Graphics;
+import java.util.Properties;
+
+import javax.swing.Icon;
+
+import cytoscape.Cytoscape;
+import cytoscape.visual.VisualPropertyType;
+import cytoscape.visual.ui.icon.NodeIcon;
+
+public class NodeBorderOpacityProp extends AbstractVisualProperty {
+
+ public NodeBorderOpacityProp() {
+ validator = new OpacityValidator();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public VisualPropertyType getType() {
+ return VisualPropertyType.NODE_BORDER_OPACITY;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Icon getIcon(final Object value) {
+ final NodeIcon icon = new NodeIcon() {
+ public void paintIcon(Component c, Graphics g, int x, int y) {
+ super.setColor(new Color(10, 10, 10, 0));
+ super.paintIcon(c, g, x, y);
+ g2d.translate(0, -2);
+
+ final Color color = ((Color) VisualPropertyType.NODE_BORDER_COLOR
+ .getDefault(Cytoscape.getVisualMappingManager()
+ .getVisualStyle()));
+ g2d.setColor(new Color(color.getRed(), color.getGreen(), color.getBlue(),
+ ((Number) value).intValue()));
+ g2d.setStroke(new BasicStroke(2f));
+ g2d.draw(super.newShape);
+ g2d.translate(0, 2);
+
+ g2d.setFont(new Font("SansSerif", Font.BOLD, 24));
+ g2d.setColor(Color.DARK_GRAY);
+ g2d.drawString(value.toString(), c.getX() + 7,
+ (int) ((c.getHeight() / 2) + 7));
+
+ g2d.setFont(new Font("SansSerif", Font.BOLD, 12));
+ }
+ };
+
+ return icon;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nv DOCUMENT ME!
+ * @param o DOCUMENT ME!
+ */
+ public void applyToNodeView(NodeView nv, Object o, VisualPropertyDependency dep) {
+ if ((o == null) || (nv == null))
+ return;
+
+ Integer tp = ((Color) nv.getBorderPaint()).getAlpha();
+
+ Integer newTp = ((Number) o).intValue();
+
+ if (tp != newTp) {
+ final Color oldPaint = (Color) nv.getBorderPaint();
+ nv.setBorderPaint(new Color(oldPaint.getRed(), oldPaint.getGreen(),
+ oldPaint.getBlue(), newTp));
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getDefaultAppearanceObject() {
+ return new Integer(255);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/properties/NodeCustomGraphicsPositionProp.java b/application/src/main/java/cytoscape/visual/properties/NodeCustomGraphicsPositionProp.java
new file mode 100644
index 0000000..e9bf916
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/properties/NodeCustomGraphicsPositionProp.java
@@ -0,0 +1,126 @@
+package cytoscape.visual.properties;
+
+import giny.view.NodeView;
+import giny.view.ObjectPosition;
+
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.image.BufferedImage;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Set;
+
+import javax.swing.Icon;
+
+import cytoscape.render.stateful.CustomGraphic;
+import cytoscape.visual.VisualPropertyDependency;
+import cytoscape.visual.VisualPropertyType;
+import cytoscape.visual.ui.ObjectPlacerGraphic;
+import cytoscape.visual.ui.icon.NodeIcon;
+import ding.view.DNodeView;
+import ding.view.ObjectPositionImpl;
+
+public class NodeCustomGraphicsPositionProp extends AbstractVisualProperty {
+
+ private static final int ICON_SIZE = 55;
+
+ private int index;
+
+ public NodeCustomGraphicsPositionProp(final Integer index) {
+ super();
+ this.index = index - 1;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public VisualPropertyType getType() {
+ return VisualPropertyType.getCustomGraphicsPositionType(index);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param labelPos
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Icon getIcon(Object value) {
+
+ final BufferedImage bi = new BufferedImage(ICON_SIZE, ICON_SIZE,
+ BufferedImage.TYPE_INT_RGB);
+ Graphics2D g2 = bi.createGraphics();
+
+ final ObjectPlacerGraphic lp = new ObjectPlacerGraphic(
+ (ObjectPosition) value, ICON_SIZE, false, "Custom Graphics",
+ null, null);
+ lp.paint(g2);
+
+ NodeIcon icon = new NodeIcon() {
+
+ private static final long serialVersionUID = -3190338664704873605L;
+
+ public void paintIcon(Component c, Graphics g, int x, int y) {
+ super.setColor(new Color(10, 10, 10, 0));
+ super.paintIcon(c, g, x, y);
+ g2d.drawImage(bi, 10, -5, null);
+ }
+ };
+
+ return icon;
+ }
+
+ /**
+ * Apply Object Position to DNodeView's Custom Graphics.
+ *
+ * @param nv
+ * - NodeView. Currently, only supports DNodeView implementation.
+ * @param position
+ * This should be an ObjectPosition.
+ */
+ public void applyToNodeView(NodeView nv, Object position,
+ VisualPropertyDependency dep) {
+
+ // This implementation is for Ding only.
+ if ((position == null) || (nv == null) || position instanceof ObjectPosition == false
+ || nv instanceof DNodeView == false)
+ return;
+
+ final ObjectPosition p = (ObjectPosition) position;
+ final DNodeView dv = (DNodeView) nv;
+
+ // This property depends on Custom Graphics Prop.
+ final NodeCustomGraphicsProp customGraphicsProp = (NodeCustomGraphicsProp) VisualPropertyType
+ .getCustomGraphicsType(index).getVisualProperty();
+
+ final Set<CustomGraphic> currentCG = customGraphicsProp
+ .getCurrentCustomGraphics(dv);
+ if (currentCG == null || currentCG.size() == 0) {
+ // Ignore if no CG is available.
+ return;
+ }
+
+ final List<CustomGraphic> newList = new ArrayList<CustomGraphic>();
+ for (CustomGraphic g : currentCG) {
+ newList.add(dv.setCustomGraphicsPosition(g, p));
+ dv.removeCustomGraphic(g);
+ }
+
+ currentCG.clear();
+ currentCG.addAll(newList);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getDefaultAppearanceObject() {
+ return new ObjectPositionImpl();
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/properties/NodeCustomGraphicsProp.java b/application/src/main/java/cytoscape/visual/properties/NodeCustomGraphicsProp.java
new file mode 100644
index 0000000..b6d7251
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/properties/NodeCustomGraphicsProp.java
@@ -0,0 +1,293 @@
+package cytoscape.visual.properties;
+
+import static cytoscape.visual.VisualPropertyDependency.Definition.NODE_CUSTOM_GRAPHICS_SIZE_SYNC;
+import static cytoscape.visual.VisualPropertyDependency.Definition.NODE_SIZE_LOCKED;
+import giny.view.NodeView;
+
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Font;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.Image;
+import java.awt.RenderingHints;
+import java.awt.Shape;
+import java.awt.geom.AffineTransform;
+import java.awt.geom.Rectangle2D;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import javax.swing.Icon;
+
+import cytoscape.Cytoscape;
+import cytoscape.render.stateful.CustomGraphic;
+import cytoscape.visual.VisualPropertyDependency;
+import cytoscape.visual.VisualPropertyType;
+import cytoscape.visual.customgraphic.CustomGraphicsManager;
+import cytoscape.visual.customgraphic.CyCustomGraphics;
+import cytoscape.visual.customgraphic.Layer;
+import cytoscape.visual.customgraphic.NullCustomGraphics;
+import cytoscape.visual.customgraphic.impl.vector.VectorCustomGraphics;
+import cytoscape.visual.ui.icon.NodeIcon;
+import cytoscape.visual.ui.icon.VisualPropertyIcon;
+import ding.view.DNodeView;
+
+public class NodeCustomGraphicsProp extends AbstractVisualProperty {
+
+ private final int index;
+
+ // Manages view to Custom Graphics mapping.
+ private Map<DNodeView, Set<CustomGraphic>> currentMap;
+
+ public NodeCustomGraphicsProp(final Integer index) {
+ super();
+ this.index = index - 1;
+ currentMap = new HashMap<DNodeView, Set<CustomGraphic>>();
+ }
+
+ @Override
+ public Icon getIcon(final Object value) {
+ final NodeIcon icon = new NodeIcon() {
+
+ private static final long serialVersionUID = 403672612403499816L;
+ private static final int ICON_SIZE = 128;
+
+ private String name = null;
+
+ @Override
+ public String getName() {
+ if (name == null) {
+ if (value != null && value instanceof CyCustomGraphics)
+ name = ((CyCustomGraphics) value).getDisplayName();
+ else
+ name = "Unknown Custom Graphics";
+ }
+
+ return name;
+ }
+
+ public void paintIcon(Component c, Graphics g, int x, int y) {
+
+ super.setColor(new Color(10, 10, 10, 25));
+ g2d = (Graphics2D) g;
+ // AA on
+ g2d.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+ RenderingHints.VALUE_ANTIALIAS_ON);
+ g2d.setRenderingHint(RenderingHints.KEY_RENDERING,
+ RenderingHints.VALUE_RENDER_QUALITY);
+
+ this.setIconHeight(ICON_SIZE + 6);
+
+ if (value == null
+ || value instanceof CyCustomGraphics == false) {
+ drawDefaultIcon(c);
+ } else {
+ final CyCustomGraphics cg = (CyCustomGraphics) value;
+
+ Image originalImg = cg.getRenderedImage();
+ if (originalImg == null)
+ drawDefaultIcon(c);
+ else {
+ scaleImage(originalImg);
+ }
+ }
+
+ }
+
+ public int getIconWidth() {
+ return ICON_SIZE;
+ }
+
+ public int getIconHeight() {
+ return ICON_SIZE;
+ }
+
+ private void drawDefaultIcon(Component c) {
+ g2d.setFont(new Font("SansSerif", Font.BOLD, 34));
+ g2d.setColor(Color.DARK_GRAY);
+ g2d.drawString(" Empty ", c.getX() + 25,
+ (int) ((c.getHeight() / 2) + 7));
+ g2d.setFont(new Font("SansSerif", Font.BOLD, 14));
+ }
+
+ private void scaleImage(final Image originalImg) {
+ final float originalW = originalImg.getWidth(null);
+ final float originalH = originalImg.getHeight(null);
+
+ float ratio = 1;
+ int shorterDim = 0;
+
+ Image scaledImg;
+ if (originalW <= ICON_SIZE && originalH <= ICON_SIZE) {
+ int xLocation = 8 + (int) (ICON_SIZE / 2)
+ - ((int) originalW / 2);
+ int yLocation = 3 + (int) (ICON_SIZE / 2)
+ - ((int) originalH / 2);
+ g2d.drawImage(originalImg, xLocation, yLocation, null);
+ } else if (originalW > originalH) {
+ ratio = originalH / originalW;
+ shorterDim = (int) (ICON_SIZE * ratio);
+ scaledImg = originalImg.getScaledInstance(ICON_SIZE,
+ shorterDim, Image.SCALE_AREA_AVERAGING);
+ g2d.drawImage(scaledImg, 8,
+ 3 + (ICON_SIZE - shorterDim) / 2, null);
+ } else {
+ ratio = originalW / originalH;
+ shorterDim = (int) (ICON_SIZE * ratio);
+ scaledImg = originalImg.getScaledInstance(shorterDim,
+ ICON_SIZE, Image.SCALE_AREA_AVERAGING);
+ g2d.drawImage(scaledImg, 8, 3, null);
+ }
+
+ }
+
+ };
+
+ return icon;
+ }
+
+ @Override
+ public VisualPropertyType getType() {
+ return VisualPropertyType.getCustomGraphicsType(index);
+ }
+
+ /**
+ * Apply current Custom Graphics to a node view.
+ *
+ */
+ public void applyToNodeView(final NodeView nv, final Object customGraphics,
+ final VisualPropertyDependency dep) {
+
+ // Ignore if view does not exist
+ if (nv == null || nv instanceof DNodeView == false)
+ return;
+
+ // Assume this is a Ding Node View.
+ final DNodeView dv = (DNodeView) nv;
+
+ // Remove current layers associated with this Custom Graphics
+ Set<CustomGraphic> targets = currentMap.get(dv);
+ if (targets != null) {
+ for (CustomGraphic cg : targets)
+ dv.removeCustomGraphic(cg);
+
+ targets.clear();
+ targets = null;
+ }
+
+ // For these cases, remove current layers.
+ if (customGraphics == null
+ || customGraphics instanceof CyCustomGraphics == false
+ || customGraphics instanceof NullCustomGraphics) {
+
+ currentMap.remove(dv);
+ return;
+ }
+
+ targets = new HashSet<CustomGraphic>();
+ final CyCustomGraphics graphics = (CyCustomGraphics) customGraphics;
+ final List<Layer> layers = (List<Layer>) graphics
+ .getLayers();
+
+ // No need to update
+ if (layers == null || layers.size() == 0) {
+ currentMap.remove(dv);
+ return;
+ }
+
+ // Check dependency. Sync size or not.
+ boolean sync = false;
+ if (dep != null) {
+ sync = dep.check(NODE_CUSTOM_GRAPHICS_SIZE_SYNC);
+ }
+
+ for (Layer layer : layers) {
+ // Assume it's a Ding layer
+ final CustomGraphic cg = (CustomGraphic) layer.getLayerObject();
+ if (sync) {
+ final CustomGraphic resized = syncSize(graphics, cg, dv, dep);
+ dv.addCustomGraphic(resized);
+ targets.add(resized);
+ } else {
+ dv.addCustomGraphic(cg);
+ targets.add(cg);
+ }
+ }
+ this.currentMap.put(dv, targets);
+
+ // Flag this as used Custom Graphics
+ //Cytoscape.getVisualMappingManager().getCustomGraphicsManager().setUsedInCurrentSession(graphics, true);
+ }
+
+ private CustomGraphic syncSize(CyCustomGraphics graphics,
+ final CustomGraphic cg, final DNodeView dv,
+ final VisualPropertyDependency dep) {
+
+ final double nodeW = dv.getWidth();
+ final double nodeH = dv.getHeight();
+
+ final Shape originalShape = cg.getShape();
+ final Rectangle2D originalBounds = originalShape.getBounds2D();
+ final double cgW = originalBounds.getWidth();
+ final double cgH = originalBounds.getHeight();
+
+ // In case size is same, return the original.
+ if (nodeW == cgW && nodeH == cgH)
+ return cg;
+
+ // Check width/height lock status
+ final boolean whLock = dep.check(NODE_SIZE_LOCKED);
+
+ final AffineTransform scale;
+ final float fit = graphics.getFitRatio();
+
+ if (whLock || graphics instanceof VectorCustomGraphics) {
+ scale = AffineTransform.getScaleInstance(fit * nodeW / cgW, fit
+ * nodeH / cgH);
+ } else {
+ // Case 1: node height value is larger than width
+ if (nodeW >= nodeH) {
+ scale = AffineTransform.getScaleInstance(fit * (nodeW / cgW)
+ * (nodeH / nodeW), fit * nodeH / cgH);
+ // scale = AffineTransform.getScaleInstance(nodeH/nodeW, 1);
+ } else {
+ scale = AffineTransform.getScaleInstance(fit * nodeW / cgW, fit
+ * (nodeH / cgH) * (nodeW / nodeH));
+ // scale = AffineTransform.getScaleInstance(1, nodeW/nodeH);
+ }
+
+ }
+ return new CustomGraphic(scale.createTransformedShape(originalShape),
+ cg.getPaintFactory());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getDefaultAppearanceObject() {
+ return NullCustomGraphics.getNullObject();
+ }
+
+ public Map<Object, Icon> getIconSet() {
+ final Map<Object, Icon> customGraphicsIcons = new HashMap<Object, Icon>();
+ final CustomGraphicsManager pool = Cytoscape.getVisualMappingManager()
+ .getCustomGraphicsManager();
+ for (CyCustomGraphics graphics : pool.getAll()) {
+ VisualPropertyIcon icon = (VisualPropertyIcon) getIcon(graphics);
+ icon.setName(graphics.getDisplayName());
+
+ customGraphicsIcons.put(graphics, icon);
+ }
+
+ return customGraphicsIcons;
+ }
+
+ protected Set<CustomGraphic> getCurrentCustomGraphics(DNodeView dv) {
+ return this.currentMap.get(dv);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/properties/NodeFillColorProp.java b/application/src/main/java/cytoscape/visual/properties/NodeFillColorProp.java
new file mode 100644
index 0000000..4d53453
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/properties/NodeFillColorProp.java
@@ -0,0 +1,112 @@
+/*
+ Copyright (c) 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual.properties;
+
+import cytoscape.visual.VisualPropertyType;
+
+
+import cytoscape.visual.ui.icon.NodeIcon;
+
+import cytoscape.visual.VisualPropertyDependency;
+
+import giny.view.NodeView;
+
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Graphics;
+
+import java.util.Properties;
+
+import javax.swing.Icon;
+
+
+/**
+ *
+ */
+public class NodeFillColorProp extends AbstractVisualProperty {
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public VisualPropertyType getType() {
+ return VisualPropertyType.NODE_FILL_COLOR;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param value DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Icon getIcon(final Object value) {
+ final NodeIcon icon = new NodeIcon() {
+ public void paintIcon(Component c, Graphics g, int x, int y) {
+ super.setColor(new Color(10, 10, 10, 0));
+ super.paintIcon(c, g, x, y);
+ g2d.translate(0, -2);
+ g2d.setColor((Color) value);
+ g2d.fill(super.newShape);
+ g2d.translate(0, 2);
+ }
+ };
+
+ return icon;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nv DOCUMENT ME!
+ * @param o DOCUMENT ME!
+ */
+ public void applyToNodeView(NodeView nv, Object o, VisualPropertyDependency dep) {
+ if ((o == null) || (nv == null) || o instanceof Color == false)
+ return;
+
+ if (!((Color) o).equals(nv.getUnselectedPaint()))
+ nv.setUnselectedPaint((Color) o);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getDefaultAppearanceObject() {
+ return Color.white;
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/properties/NodeFontFaceProp.java b/application/src/main/java/cytoscape/visual/properties/NodeFontFaceProp.java
new file mode 100644
index 0000000..eb56b57
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/properties/NodeFontFaceProp.java
@@ -0,0 +1,116 @@
+/*
+ Copyright (c) 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual.properties;
+
+import cytoscape.visual.VisualPropertyType;
+
+import cytoscape.visual.ui.icon.NodeIcon;
+
+import cytoscape.visual.VisualPropertyDependency;
+
+import giny.view.Label;
+import giny.view.NodeView;
+
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Font;
+import java.awt.Graphics;
+
+import java.util.Properties;
+
+import javax.swing.Icon;
+
+
+/**
+ *
+ */
+public class NodeFontFaceProp extends AbstractVisualProperty {
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public VisualPropertyType getType() {
+ return VisualPropertyType.NODE_FONT_FACE;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Icon getIcon(final Object value) {
+ final NodeIcon icon = new NodeIcon() {
+ public void paintIcon(Component c, Graphics g, int x, int y) {
+ super.setColor(new Color(10, 10, 10, 0));
+ super.paintIcon(c, g, x, y);
+
+ g2d.setColor(Color.DARK_GRAY);
+
+ final Font font = (Font) value;
+ g2d.setFont(new Font(font.getFontName(), font.getStyle(), 28));
+ g2d.drawString("Font", 8, (c.getHeight() / 2) + 10);
+ g2d.setFont(new Font("SansSerif", Font.BOLD, 12));
+ }
+ };
+
+ return icon;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nv DOCUMENT ME!
+ * @param o DOCUMENT ME!
+ */
+ public void applyToNodeView(NodeView nv, Object o, VisualPropertyDependency dep) {
+ if ((o == null) || (nv == null))
+ return;
+
+ Label nodelabel = nv.getLabel();
+
+ if (!((Font) o).equals(nodelabel.getFont()))
+ nodelabel.setFont((Font) o);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getDefaultAppearanceObject() {
+ return new Font(null, Font.PLAIN, 12);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/properties/NodeFontSizeProp.java b/application/src/main/java/cytoscape/visual/properties/NodeFontSizeProp.java
new file mode 100644
index 0000000..e4a6e3d
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/properties/NodeFontSizeProp.java
@@ -0,0 +1,118 @@
+/*
+ Copyright (c) 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual.properties;
+
+import cytoscape.visual.VisualPropertyType;
+
+import cytoscape.visual.ui.icon.NodeIcon;
+
+import cytoscape.visual.VisualPropertyDependency;
+
+import giny.view.Label;
+import giny.view.NodeView;
+
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Font;
+import java.awt.Graphics;
+
+import java.util.Properties;
+
+import javax.swing.Icon;
+
+
+/**
+ *
+ */
+public class NodeFontSizeProp extends AbstractVisualProperty {
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public VisualPropertyType getType() {
+ return VisualPropertyType.NODE_FONT_SIZE;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Icon getIcon(final Object value) {
+ final NodeIcon icon = new NodeIcon() {
+ public void paintIcon(Component c, Graphics g, int x, int y) {
+ super.setColor(new Color(10, 10, 10, 25));
+ super.paintIcon(c, g, x, y);
+
+ g2d.setFont(new Font("SansSerif", Font.BOLD, 24));
+ g2d.setColor(Color.DARK_GRAY);
+ g2d.drawString(value.toString(), c.getX() + 7,
+ (int) ((c.getHeight() / 2) + 7));
+
+ g2d.setFont(new Font("SansSerif", Font.BOLD, 12));
+ }
+ };
+
+ return icon;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nv DOCUMENT ME!
+ * @param o DOCUMENT ME!
+ */
+ public void applyToNodeView(NodeView nv, Object o, VisualPropertyDependency dep) {
+ if ((o == null) || (nv == null))
+ return;
+
+ Label nodelabel = nv.getLabel();
+ Font f = nodelabel.getFont();
+ float newFontSize = ((Number) o).floatValue();
+
+ if (newFontSize != f.getSize2D())
+ nodelabel.setFont(f.deriveFont(newFontSize));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getDefaultAppearanceObject() {
+ return new Float(12.0f);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/properties/NodeHeightProp.java b/application/src/main/java/cytoscape/visual/properties/NodeHeightProp.java
new file mode 100644
index 0000000..e71c7ac
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/properties/NodeHeightProp.java
@@ -0,0 +1,131 @@
+/*
+ Copyright (c) 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual.properties;
+
+import cytoscape.visual.VisualPropertyType;
+
+import cytoscape.visual.ui.icon.NodeIcon;
+
+import cytoscape.visual.VisualPropertyDependency;
+
+import giny.view.NodeView;
+
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Font;
+import java.awt.Graphics;
+
+import java.util.Properties;
+
+import javax.swing.Icon;
+
+
+/**
+ *
+ */
+public class NodeHeightProp extends AbstractVisualProperty {
+
+ public NodeHeightProp() {
+ validator = new GTZeroValidator();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public VisualPropertyType getType() {
+ return VisualPropertyType.NODE_HEIGHT;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Icon getIcon(final Object value) {
+ final NodeIcon icon = new NodeIcon() {
+ public void paintIcon(Component c, Graphics g, int x, int y) {
+ super.setColor(new Color(10, 10, 10, 25));
+ super.paintIcon(c, g, x, y);
+ g2d.setFont(new Font("SansSerif", Font.BOLD, 24));
+ g2d.setColor(Color.DARK_GRAY);
+ g2d.drawString(value.toString(), c.getX() + 7,
+ (int) ((c.getHeight() / 2) + 7));
+ g2d.setFont(new Font("SansSerif", Font.BOLD, 12));
+ }
+ };
+
+ icon.setBottomPadding(-2);
+
+ return icon;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nv DOCUMENT ME!
+ * @param o DOCUMENT ME!
+ */
+ public void applyToNodeView(NodeView nv, Object o, VisualPropertyDependency dep) {
+ if ((o == null) || (nv == null))
+ return;
+
+ if ( dep != null && dep.check(VisualPropertyDependency.Definition.NODE_SIZE_LOCKED) )
+ return;
+
+ double height = ((Number) o).doubleValue();
+ double difference = height - nv.getHeight();
+
+ if (Math.abs(difference) > 0.1)
+ nv.setHeight(height);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getDefaultAppearanceObject() {
+ return new Double(30.0);
+ }
+
+ public boolean constrained(VisualPropertyDependency dep) {
+ if ( dep == null )
+ return false;
+
+ return dep.check(VisualPropertyDependency.Definition.NODE_SIZE_LOCKED);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/properties/NodeLabelColorProp.java b/application/src/main/java/cytoscape/visual/properties/NodeLabelColorProp.java
new file mode 100644
index 0000000..02113b5
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/properties/NodeLabelColorProp.java
@@ -0,0 +1,133 @@
+/*
+ Copyright (c) 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual.properties;
+
+import static cytoscape.visual.VisualPropertyDependency.Definition.*;
+import cytoscape.Cytoscape;
+
+import cytoscape.util.ColorUtil;
+import cytoscape.visual.VisualPropertyType;
+
+import cytoscape.visual.ui.icon.NodeIcon;
+
+import cytoscape.visual.VisualPropertyDependency;
+
+import giny.view.Label;
+import giny.view.NodeView;
+
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Font;
+import java.awt.Graphics;
+
+import java.util.Properties;
+
+import javax.swing.Icon;
+
+
+/**
+ *
+ */
+public class NodeLabelColorProp extends AbstractVisualProperty {
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public VisualPropertyType getType() {
+ return VisualPropertyType.NODE_LABEL_COLOR;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Icon getIcon(final Object value) {
+ final NodeIcon icon = new NodeIcon() {
+ public void paintIcon(Component c, Graphics g, int x, int y) {
+ super.setColor(new Color(10, 10, 10, 0));
+ super.paintIcon(c, g, x, y);
+
+ g2d.setColor((Color) value);
+
+ final Font font = (Font) VisualPropertyType.NODE_FONT_FACE
+ .getDefault(Cytoscape.getVisualMappingManager()
+ .getVisualStyle());
+ g2d.setFont(new Font(font.getFontName(), font.getStyle(), 28));
+ g2d.drawString("Label", 8, (c.getHeight() / 2) + 10);
+ g2d.setFont(new Font("SansSerif", Font.BOLD, 12));
+ }
+ };
+
+ return icon;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nv DOCUMENT ME!
+ * @param o DOCUMENT ME!
+ */
+ public void applyToNodeView(NodeView nv, Object o, VisualPropertyDependency dep) {
+ if ((o == null) || (nv == null) || o instanceof Color == false)
+ return;
+
+ Color color = (Color) o;
+
+ // Check dependency. Sync color or not.
+ boolean sync = false;
+ if (dep != null) {
+ if ( dep.check(NODE_LABLE_COLOR_FROM_NODE_COLOR) ) {
+ color = ColorUtil.getComplementaryColor((Color) nv.getUnselectedPaint());
+ }
+ }
+
+ final Label nodelabel = nv.getLabel();
+
+ if (!color.equals(nodelabel.getTextPaint())) {
+ nodelabel.setTextPaint(color);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getDefaultAppearanceObject() {
+ return Color.black;
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/properties/NodeLabelOpacityProp.java b/application/src/main/java/cytoscape/visual/properties/NodeLabelOpacityProp.java
new file mode 100644
index 0000000..5da9438
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/properties/NodeLabelOpacityProp.java
@@ -0,0 +1,97 @@
+package cytoscape.visual.properties;
+
+import cytoscape.visual.VisualPropertyDependency;
+
+import giny.view.NodeView;
+
+import java.awt.BasicStroke;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Font;
+import java.awt.Graphics;
+import java.util.Properties;
+
+import javax.swing.Icon;
+
+import cytoscape.Cytoscape;
+import cytoscape.visual.VisualPropertyType;
+import cytoscape.visual.ui.icon.LineTypeIcon;
+import cytoscape.visual.ui.icon.NodeIcon;
+
+public class NodeLabelOpacityProp extends AbstractVisualProperty {
+
+ public NodeLabelOpacityProp() {
+ validator = new OpacityValidator();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public VisualPropertyType getType() {
+ return VisualPropertyType.NODE_LABEL_OPACITY;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Icon getIcon(final Object value) {
+ final NodeIcon icon = new NodeIcon() {
+ public void paintIcon(Component c, Graphics g, int x, int y) {
+ super.setColor(new Color(10, 10, 10, 0));
+ super.paintIcon(c, g, x, y);
+ g2d.translate(0, -2);
+
+ final Color color = ((Color) VisualPropertyType.NODE_LABEL_COLOR
+ .getDefault(Cytoscape.getVisualMappingManager()
+ .getVisualStyle()));
+ g2d.setColor(new Color(color.getRed(), color.getGreen(), color.getBlue(),
+ ((Number) value).intValue()));
+ g2d.setStroke(new BasicStroke(2f));
+ g2d.draw(super.newShape);
+ g2d.translate(0, 2);
+
+ g2d.setFont(new Font("SansSerif", Font.BOLD, 24));
+ g2d.setColor(Color.DARK_GRAY);
+ g2d.drawString(value.toString(), c.getX() + 7,
+ (int) ((c.getHeight() / 2) + 7));
+
+ g2d.setFont(new Font("SansSerif", Font.BOLD, 12));
+ }
+ };
+
+ return icon;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param ev DOCUMENT ME!
+ * @param o DOCUMENT ME!
+ */
+ public void applyToNodeView(NodeView nv, Object o, VisualPropertyDependency dep) {
+ if ((o == null) || (nv == null))
+ return;
+
+ Integer tp = ((Color) nv.getLabel().getTextPaint()).getAlpha();
+ Integer newTp = ((Number) o).intValue();
+
+ if (tp != newTp) {
+ final Color oldPaint = (Color) nv.getLabel().getTextPaint();
+ nv.getLabel().setTextPaint(new Color(oldPaint.getRed(), oldPaint.getGreen(),
+ oldPaint.getBlue(), newTp));
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getDefaultAppearanceObject() {
+ return new Integer(255);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/properties/NodeLabelPositionProp.java b/application/src/main/java/cytoscape/visual/properties/NodeLabelPositionProp.java
new file mode 100644
index 0000000..ce43807
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/properties/NodeLabelPositionProp.java
@@ -0,0 +1,156 @@
+/*
+ Copyright (c) 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual.properties;
+
+import giny.view.Justification;
+import giny.view.NodeView;
+import giny.view.ObjectPosition;
+import giny.view.Position;
+
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.image.BufferedImage;
+
+import javax.swing.Icon;
+
+import cytoscape.visual.LabelPosition;
+import cytoscape.visual.VisualPropertyDependency;
+import cytoscape.visual.VisualPropertyType;
+import cytoscape.visual.ui.ObjectPlacerGraphic;
+import cytoscape.visual.ui.icon.NodeIcon;
+import ding.view.DNodeView;
+import ding.view.ObjectPositionImpl;
+
+/**
+ *
+ */
+public class NodeLabelPositionProp extends AbstractVisualProperty {
+
+ private static final ObjectPosition DEF_OP = new ObjectPositionImpl();
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public VisualPropertyType getType() {
+ return VisualPropertyType.NODE_LABEL_POSITION;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param labelPos
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Icon getIcon(Object value) {
+ int size = 55;
+
+ final BufferedImage bi = new BufferedImage(size, size,
+ BufferedImage.TYPE_INT_RGB);
+ Graphics2D g2 = bi.createGraphics();
+
+ ObjectPosition op;
+ if(value instanceof ObjectPosition)
+ op = (ObjectPosition) value;
+ else if(value instanceof LabelPosition)
+ op = this.convert((LabelPosition) value);
+ else
+ op = DEF_OP;
+
+ ObjectPlacerGraphic lp = new ObjectPlacerGraphic(
+ op, size, false, "Label", null, null);
+ lp.paint(g2);
+
+ NodeIcon icon = new NodeIcon() {
+
+ private static final long serialVersionUID = -3190338664704873605L;
+
+ public void paintIcon(Component c, Graphics g, int x, int y) {
+ super.setColor(new Color(10, 10, 10, 0));
+ super.paintIcon(c, g, x, y);
+ g2d.drawImage(bi, 10, -5, null);
+ }
+ };
+
+ return icon;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nv
+ * DOCUMENT ME!
+ * @param o
+ * DOCUMENT ME!
+ */
+ public void applyToNodeView(NodeView nv, Object o,
+ VisualPropertyDependency dep) {
+ if ((o == null) || (nv == null) || nv instanceof DNodeView == false
+ || o instanceof ObjectPosition == false)
+ return;
+
+ final DNodeView dv = (DNodeView) nv;
+ dv.setPosition((ObjectPosition) o);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getDefaultAppearanceObject() {
+ return new ObjectPositionImpl();
+ }
+
+
+ // This is for backword compatibility.
+ private ObjectPosition convert(LabelPosition lp) {
+ ObjectPosition op = new ObjectPositionImpl();
+
+ op.setJustify(Justification.parse(lp.getLabelAnchor()));
+ op.setAnchor(Position.parse(lp.getLabelAnchor()));
+ op.setTargetAnchor(Position.parse(lp.getTargetAnchor()));
+ op.setOffsetX(lp.getOffsetX());
+ op.setOffsetY(lp.getOffsetY());
+
+ return op;
+
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/properties/NodeLabelProp.java b/application/src/main/java/cytoscape/visual/properties/NodeLabelProp.java
new file mode 100644
index 0000000..6b56f61
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/properties/NodeLabelProp.java
@@ -0,0 +1,121 @@
+/*
+ Copyright (c) 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual.properties;
+
+import cytoscape.visual.VisualPropertyType;
+
+import cytoscape.visual.ui.icon.NodeIcon;
+
+import cytoscape.visual.VisualPropertyDependency;
+
+import giny.view.Label;
+import giny.view.NodeView;
+
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Font;
+import java.awt.Graphics;
+
+import java.util.Properties;
+
+import javax.swing.Icon;
+
+
+/**
+ *
+ */
+public class NodeLabelProp extends AbstractVisualProperty {
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public VisualPropertyType getType() {
+ return VisualPropertyType.NODE_LABEL;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Icon getIcon(final Object value) {
+ final NodeIcon icon = new NodeIcon() {
+ public void paintIcon(Component c, Graphics g, int x, int y) {
+ super.setColor(new Color(10, 10, 10, 25));
+ super.paintIcon(c, g, x, y);
+ g2d.setFont(new Font("SansSerif", Font.BOLD, 8));
+ g2d.setColor(Color.DARK_GRAY);
+
+ String defLabel = value.toString();
+ if(defLabel.length()>15) {
+ defLabel = defLabel.substring(0, 14) + "...";
+ }
+ g2d.drawString(defLabel, c.getX() + 7,
+ (int) ((c.getHeight() / 2)));
+ g2d.setFont(new Font("SansSerif", Font.BOLD, 12));
+ }
+ };
+
+ icon.setBottomPadding(-2);
+
+ return icon;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nv DOCUMENT ME!
+ * @param o DOCUMENT ME!
+ */
+ public void applyToNodeView(NodeView nv, Object o, VisualPropertyDependency dep) {
+ if ((o == null) || (nv == null))
+ return;
+
+ Label nodelabel = nv.getLabel();
+
+ if (!((String) o).equals(nodelabel.getText()))
+ nodelabel.setText((String) o);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getDefaultAppearanceObject() {
+ return "";
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/properties/NodeLabelWidthProp.java b/application/src/main/java/cytoscape/visual/properties/NodeLabelWidthProp.java
new file mode 100644
index 0000000..9f249b9
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/properties/NodeLabelWidthProp.java
@@ -0,0 +1,121 @@
+/*
+ Copyright (c) 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual.properties;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.visual.VisualPropertyType;
+import static cytoscape.visual.VisualPropertyType.NODE_LABEL_WIDTH;
+
+import cytoscape.visual.ui.icon.NodeIcon;
+
+import cytoscape.visual.VisualPropertyDependency;
+
+import giny.view.NodeView;
+
+import java.awt.BasicStroke;
+import java.awt.Color;
+import java.awt.Stroke;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.Component;
+import java.awt.Font;
+
+import java.util.Properties;
+
+import javax.swing.Icon;
+
+
+/**
+ *
+ */
+public class NodeLabelWidthProp extends AbstractVisualProperty {
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public VisualPropertyType getType() {
+ return VisualPropertyType.NODE_LABEL_WIDTH;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Icon getIcon(final Object value) {
+ final NodeIcon icon = new NodeIcon() {
+ public void paintIcon(Component c, Graphics g, int x, int y) {
+ super.setColor(new Color(10, 10, 10, 25));
+ super.paintIcon(c, g, x, y);
+
+ g2d.setFont(new Font("SansSerif", Font.BOLD, 24));
+ g2d.setColor(Color.DARK_GRAY);
+ g2d.drawString(value.toString(), c.getX() + 7,
+ (int) ((c.getHeight() / 2) + 7));
+
+ g2d.setFont(new Font("SansSerif", Font.BOLD, 12));
+ }
+ };
+
+ return icon;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nv DOCUMENT ME!
+ * @param o DOCUMENT ME!
+ */
+ public void applyToNodeView(NodeView nv, Object o, VisualPropertyDependency dep) {
+ if ((o == null) || (nv == null))
+ return;
+
+ float width = ((Number)o).floatValue();
+ if (nv.getLabelWidth() != width) {
+ nv.setLabelWidth(width);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getDefaultAppearanceObject() {
+ return new Float(100.0f);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/properties/NodeLineStyleProp.java b/application/src/main/java/cytoscape/visual/properties/NodeLineStyleProp.java
new file mode 100644
index 0000000..bfd2ef4
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/properties/NodeLineStyleProp.java
@@ -0,0 +1,134 @@
+/*
+ Copyright (c) 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual.properties;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.visual.*;
+
+import cytoscape.visual.ui.icon.*;
+
+import cytoscape.visual.VisualPropertyDependency;
+
+import giny.view.NodeView;
+
+import java.awt.Stroke;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Font;
+import java.awt.Graphics;
+
+import java.util.Map;
+import java.util.Properties;
+
+import javax.swing.Icon;
+
+
+/**
+ *
+ */
+public class NodeLineStyleProp extends AbstractVisualProperty {
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public VisualPropertyType getType() {
+ return VisualPropertyType.NODE_LINE_STYLE;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Icon getIcon(final Object value) {
+ final NodeIcon icon = new NodeIcon() {
+ public void paintIcon(Component c, Graphics g, int x, int y) {
+ super.setColor(new Color(10, 10, 10, 0));
+ super.paintIcon(c, g, x, y);
+
+ final float width = ((Number) VisualPropertyType.NODE_LINE_WIDTH.getDefault(Cytoscape.getVisualMappingManager().getVisualStyle())).floatValue();
+ final Stroke stroke = ((LineStyle) value).getStroke(width);
+ g2d.setStroke(stroke);
+ g2d.setColor(Color.DARK_GRAY);
+ g2d.translate(15, 4);
+ g2d.draw(super.shape);
+ g2d.translate(-15, -4);
+ g2d.setFont(new Font("SansSerif", Font.BOLD, 12));
+ g2d.setColor(new Color(10, 10, 10, 45));
+ g2d.drawString(value.toString(), c.getX() + 12,
+ (int) ((c.getHeight() / 2) + 3));
+ g2d.setFont(new Font("SansSerif", Font.BOLD, 12));
+ }
+ };
+
+ return icon;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Map<Object, Icon> getIconSet() {
+ return LineStyle.getIconSet();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nv DOCUMENT ME!
+ * @param o DOCUMENT ME!
+ */
+ public void applyToNodeView(NodeView nv, Object o, VisualPropertyDependency dep) {
+ if ((o == null) || (nv == null))
+ return;
+
+ nv.setBorder(((LineStyle) o).getStroke(nv.getBorderWidth()));
+// if (((LineStyle) o).getDashDef() != (((BasicStroke) nv.getBorder()).getDashArray())) {
+// nv.setBorder(((LineStyle) o).getStroke(nv.getBorderWidth()));
+// }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getDefaultAppearanceObject() {
+ return LineStyle.SOLID;
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/properties/NodeLineWidthProp.java b/application/src/main/java/cytoscape/visual/properties/NodeLineWidthProp.java
new file mode 100644
index 0000000..796610a
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/properties/NodeLineWidthProp.java
@@ -0,0 +1,120 @@
+/*
+ Copyright (c) 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual.properties;
+
+import giny.view.NodeView;
+
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Font;
+import java.awt.Graphics;
+import java.awt.Stroke;
+
+import javax.swing.Icon;
+
+import cytoscape.visual.LineStyle;
+import cytoscape.visual.VisualPropertyDependency;
+import cytoscape.visual.VisualPropertyType;
+import cytoscape.visual.ui.icon.NodeIcon;
+
+
+/**
+ *
+ */
+public class NodeLineWidthProp extends AbstractVisualProperty {
+
+ public NodeLineWidthProp() {
+ validator = new GTEZeroValidator();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public VisualPropertyType getType() {
+ return VisualPropertyType.NODE_LINE_WIDTH;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Icon getIcon(final Object value) {
+ final NodeIcon icon = new NodeIcon() {
+ public void paintIcon(Component c, Graphics g, int x, int y) {
+ super.setColor(new Color(10, 10, 10, 25));
+ super.paintIcon(c, g, x, y);
+
+ g2d.setFont(new Font("SansSerif", Font.BOLD, 24));
+ g2d.setColor(Color.DARK_GRAY);
+ g2d.drawString(value.toString(), c.getX() + 7,
+ (int) ((c.getHeight() / 2) + 7));
+
+ g2d.setFont(new Font("SansSerif", Font.BOLD, 12));
+ }
+ };
+
+ return icon;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nv DOCUMENT ME!
+ * @param o DOCUMENT ME!
+ */
+ public void applyToNodeView(NodeView nv, Object o, VisualPropertyDependency dep) {
+ if ((o == null) || (nv == null))
+ return;
+
+ float width =((Number) o).floatValue();
+ if (nv.getBorderWidth() != width ) {
+ final Stroke oldStroke = nv.getBorder();
+ final Stroke newStroke = LineStyle.extractLineStyle(oldStroke).getStroke(width);
+ nv.setBorder(newStroke);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getDefaultAppearanceObject() {
+ return new Float(1.0);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/properties/NodeOpacityProp.java b/application/src/main/java/cytoscape/visual/properties/NodeOpacityProp.java
new file mode 100644
index 0000000..d642763
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/properties/NodeOpacityProp.java
@@ -0,0 +1,136 @@
+/*
+ Copyright (c) 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual.properties;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.visual.VisualPropertyType;
+
+import cytoscape.visual.ui.icon.NodeIcon;
+
+import cytoscape.visual.VisualPropertyDependency;
+
+import giny.view.NodeView;
+
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Font;
+import java.awt.Graphics;
+
+import java.util.Properties;
+
+import javax.swing.Icon;
+
+
+/**
+ *
+ */
+public class NodeOpacityProp extends AbstractVisualProperty {
+
+ public NodeOpacityProp() {
+ validator = new OpacityValidator();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public VisualPropertyType getType() {
+ return VisualPropertyType.NODE_OPACITY;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Icon getIcon(final Object value) {
+ final NodeIcon icon = new NodeIcon() {
+ public void paintIcon(Component c, Graphics g, int x, int y) {
+ super.setColor(new Color(10, 10, 10, 0));
+ super.paintIcon(c, g, x, y);
+ g2d.translate(0, -2);
+
+ final Color color = ((Color) VisualPropertyType.NODE_FILL_COLOR
+ .getDefault(Cytoscape.getVisualMappingManager()
+ .getVisualStyle()));
+ g2d.setColor(new Color(color.getRed(), color.getGreen(), color.getBlue(),
+ ((Number) value).intValue()));
+ g2d.fill(super.newShape);
+ g2d.translate(0, 2);
+
+ g2d.setFont(new Font("SansSerif", Font.BOLD, 24));
+ g2d.setColor(Color.DARK_GRAY);
+ g2d.drawString(value.toString(), c.getX() + 7,
+ (int) ((c.getHeight() / 2) + 7));
+
+ g2d.setFont(new Font("SansSerif", Font.BOLD, 12));
+ }
+ };
+
+ return icon;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nv DOCUMENT ME!
+ * @param o DOCUMENT ME!
+ */
+ public void applyToNodeView(NodeView nv, Object o, VisualPropertyDependency dep) {
+ if ((o == null) || (nv == null))
+ return;
+
+ Integer tp = ((Color) nv.getUnselectedPaint()).getAlpha();
+
+ Integer newTp = ((Number) o).intValue();
+
+ if (tp != newTp) {
+ final Color oldPaint = (Color) nv.getUnselectedPaint();
+ nv.setUnselectedPaint(new Color(oldPaint.getRed(), oldPaint.getGreen(),
+ oldPaint.getBlue(), newTp));
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getDefaultAppearanceObject() {
+ return new Integer(255);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/properties/NodeShapeProp.java b/application/src/main/java/cytoscape/visual/properties/NodeShapeProp.java
new file mode 100644
index 0000000..c9325ed
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/properties/NodeShapeProp.java
@@ -0,0 +1,107 @@
+/*
+ Copyright (c) 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual.properties;
+
+import giny.view.NodeView;
+
+import java.util.Map;
+
+import javax.swing.Icon;
+
+import cytoscape.visual.NodeShape;
+import cytoscape.visual.VisualPropertyDependency;
+import cytoscape.visual.VisualPropertyType;
+import cytoscape.visual.ui.icon.NodeIcon;
+
+
+/**
+ *
+ */
+public class NodeShapeProp extends AbstractVisualProperty {
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public VisualPropertyType getType() {
+ return VisualPropertyType.NODE_SHAPE;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Map<Object, Icon> getIconSet() {
+ return NodeShape.getIconSet();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Icon getIcon(final Object value) {
+ final NodeIcon icon = new NodeIcon((NodeShape)value);
+ icon.setBottomPadding(-3);
+
+ return icon;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nv DOCUMENT ME!
+ * @param o DOCUMENT ME!
+ */
+ public void applyToNodeView(NodeView nv, Object o, VisualPropertyDependency dep) {
+ if ((o == null) || (nv == null))
+ return;
+
+ final int newShape = ((NodeShape) o).getGinyShape();
+
+ if (nv.getShape() != newShape)
+ nv.setShape(newShape);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getDefaultAppearanceObject() {
+ return NodeShape.RECT;
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/properties/NodeShowNestedNetworkProp.java b/application/src/main/java/cytoscape/visual/properties/NodeShowNestedNetworkProp.java
new file mode 100644
index 0000000..1570d97
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/properties/NodeShowNestedNetworkProp.java
@@ -0,0 +1,114 @@
+/*
+ Copyright (c) 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual.properties;
+
+import cytoscape.visual.VisualPropertyType;
+
+import cytoscape.visual.ui.icon.NodeIcon;
+
+import cytoscape.visual.VisualPropertyDependency;
+
+import giny.view.NodeView;
+
+import java.awt.Font;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Graphics;
+
+import java.util.Properties;
+
+import javax.swing.Icon;
+
+
+/**
+ *
+ */
+public class NodeShowNestedNetworkProp extends AbstractVisualProperty {
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public VisualPropertyType getType() {
+ return VisualPropertyType.NODE_SHOW_NESTED_NETWORK;
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Icon getIcon(final Object value) {
+ final NodeIcon icon = new NodeIcon() {
+ public void paintIcon(Component c, Graphics g, int x, int y) {
+ super.setColor(new Color(10, 10, 10, 25));
+ super.paintIcon(c, g, x, y);
+ g2d.setFont(new Font("SansSerif", Font.BOLD, 24));
+ g2d.setColor(Color.DARK_GRAY);
+ g2d.drawString(value.toString(), c.getX() + 7,
+ (int) ((c.getHeight() / 2) + 7));
+ g2d.setFont(new Font("SansSerif", Font.BOLD, 12));
+ }
+ };
+
+ icon.setBottomPadding(-2);
+
+ return icon;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nv DOCUMENT ME!
+ * @param o DOCUMENT ME!
+ */
+ public void applyToNodeView(NodeView nv, Object o, VisualPropertyDependency dep) {
+ if ((o == null) || (nv == null) || o instanceof Boolean == false)
+ return;
+
+ if (((Boolean) o) != nv.nestedNetworkIsVisible())
+ nv.showNestedNetwork((Boolean) o);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getDefaultAppearanceObject() {
+ return Boolean.TRUE;
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/properties/NodeSizeProp.java b/application/src/main/java/cytoscape/visual/properties/NodeSizeProp.java
new file mode 100644
index 0000000..5d14611
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/properties/NodeSizeProp.java
@@ -0,0 +1,138 @@
+/*
+ Copyright (c) 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual.properties;
+
+import cytoscape.visual.VisualPropertyType;
+
+import cytoscape.visual.parsers.DoubleParser;
+
+import cytoscape.visual.ui.icon.NodeIcon;
+
+import cytoscape.visual.VisualPropertyDependency;
+
+import giny.view.NodeView;
+
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Font;
+import java.awt.Graphics;
+
+import java.util.Properties;
+
+import javax.swing.Icon;
+
+
+/**
+ *
+ */
+public class NodeSizeProp extends AbstractVisualProperty {
+
+ public NodeSizeProp() {
+ validator = new GTZeroValidator();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public VisualPropertyType getType() {
+ return VisualPropertyType.NODE_SIZE;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Icon getIcon(final Object value) {
+ final NodeIcon icon = new NodeIcon() {
+ public void paintIcon(Component c, Graphics g, int x, int y) {
+ super.setColor(new Color(10, 10, 10, 25));
+ super.paintIcon(c, g, x, y);
+ g2d.setFont(new Font("SansSerif", Font.BOLD, 24));
+ g2d.setColor(Color.DARK_GRAY);
+ g2d.drawString(value.toString(), c.getX() + 7,
+ (int) ((c.getHeight() / 2) + 7));
+ g2d.setFont(new Font("SansSerif", Font.BOLD, 12));
+ }
+ };
+
+ icon.setBottomPadding(-2);
+
+ return icon;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nv DOCUMENT ME!
+ * @param o DOCUMENT ME!
+ */
+ public void applyToNodeView(NodeView nv, Object o, VisualPropertyDependency dep) {
+ if ((o == null) || (nv == null))
+ return;
+
+ if ( dep != null && !dep.check(VisualPropertyDependency.Definition.NODE_SIZE_LOCKED) )
+ return;
+
+ double size = ((Number) o).doubleValue();
+ double difference = size - nv.getHeight();
+
+ if (Math.abs(difference) > 0.1)
+ nv.setHeight(size);
+
+ difference = size - nv.getWidth();
+
+ if (Math.abs(difference) > 0.1)
+ nv.setWidth(size);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getDefaultAppearanceObject() {
+ return new Double(35.0);
+ }
+
+ public boolean constrained(VisualPropertyDependency dep) {
+ if ( dep == null )
+ return false;
+
+ return !(dep.check(VisualPropertyDependency.Definition.NODE_SIZE_LOCKED));
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/properties/NodeToolTipProp.java b/application/src/main/java/cytoscape/visual/properties/NodeToolTipProp.java
new file mode 100644
index 0000000..9031284
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/properties/NodeToolTipProp.java
@@ -0,0 +1,137 @@
+/*
+ Copyright (c) 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual.properties;
+
+import cytoscape.visual.VisualPropertyType;
+
+import cytoscape.visual.ui.icon.NodeIcon;
+
+import cytoscape.visual.VisualPropertyDependency;
+
+import giny.view.NodeView;
+
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Font;
+import java.awt.Graphics;
+
+import java.util.Properties;
+
+import javax.swing.Icon;
+
+
+/**
+ *
+ */
+public class NodeToolTipProp extends AbstractVisualProperty {
+
+ private StringBuilder buf = new StringBuilder();
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public VisualPropertyType getType() {
+ return VisualPropertyType.NODE_TOOLTIP;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Icon getIcon(final Object value) {
+ final NodeIcon icon = new NodeIcon() {
+ public void paintIcon(Component c, Graphics g, int x, int y) {
+ super.setColor(new Color(10, 10, 10, 25));
+ super.paintIcon(c, g, x, y);
+ g2d.setFont(new Font("SansSerif", Font.BOLD, 8));
+ g2d.setColor(Color.DARK_GRAY);
+
+ String defLabel = value.toString();
+
+ if (defLabel.length() > 15) {
+ defLabel = defLabel.substring(0, 14) + "...";
+ }
+
+ g2d.drawString(defLabel, c.getX() + 7, (int) ((c.getHeight() / 2)));
+ g2d.setFont(new Font("SansSerif", Font.BOLD, 12));
+ }
+ };
+
+ icon.setBottomPadding(-2);
+
+ return icon;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nv DOCUMENT ME!
+ * @param o DOCUMENT ME!
+ */
+ public void applyToNodeView(NodeView nv, Object o, VisualPropertyDependency dep) {
+ if ((o == null) || (nv == null))
+ return;
+
+ if(((String)o).startsWith("<html>")) {
+ nv.setToolTip((String) o);
+ return;
+ }
+
+ // Setting the tooltip to null is preferred because otherwise a small icon
+ // indicating the empty tooltip appears.
+ if (((String)o).equals("")) {
+ nv.setToolTip(null);
+ return;
+ }
+
+ buf = new StringBuilder();
+ buf.append("<html><body bgcolor=\"white\"><Div Align=\"center\"><Font Size=\"4\">");
+ buf.append(((String)o).replaceAll("\\n", "<br>"));
+ buf.append("</Font></div></body></html>");
+ nv.setToolTip(buf.toString());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getDefaultAppearanceObject() {
+ return "";
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/properties/NodeWidthProp.java b/application/src/main/java/cytoscape/visual/properties/NodeWidthProp.java
new file mode 100644
index 0000000..c0aeffc
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/properties/NodeWidthProp.java
@@ -0,0 +1,131 @@
+/*
+ Copyright (c) 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual.properties;
+
+import cytoscape.visual.VisualPropertyType;
+
+import cytoscape.visual.ui.icon.NodeIcon;
+
+import cytoscape.visual.VisualPropertyDependency;
+
+import giny.view.NodeView;
+
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Font;
+import java.awt.Graphics;
+
+import java.util.Properties;
+
+import javax.swing.Icon;
+
+
+/**
+ *
+ */
+public class NodeWidthProp extends AbstractVisualProperty {
+
+ public NodeWidthProp() {
+ validator = new GTZeroValidator();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public VisualPropertyType getType() {
+ return VisualPropertyType.NODE_WIDTH;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Icon getIcon(final Object value) {
+ final NodeIcon icon = new NodeIcon() {
+ public void paintIcon(Component c, Graphics g, int x, int y) {
+ super.setColor(new Color(10, 10, 10, 25));
+ super.paintIcon(c, g, x, y);
+ g2d.setFont(new Font("SansSerif", Font.BOLD, 24));
+ g2d.setColor(Color.DARK_GRAY);
+ g2d.drawString(value.toString(), c.getX() + 7,
+ (int) ((c.getHeight() / 2) + 7));
+ g2d.setFont(new Font("SansSerif", Font.BOLD, 12));
+ }
+ };
+
+ icon.setBottomPadding(-2);
+
+ return icon;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nv DOCUMENT ME!
+ * @param o DOCUMENT ME!
+ */
+ public void applyToNodeView(NodeView nv, Object o, VisualPropertyDependency dep) {
+ if ((o == null) || (nv == null))
+ return;
+
+ if ( dep != null && dep.check(VisualPropertyDependency.Definition.NODE_SIZE_LOCKED) )
+ return;
+
+ double width = ((Number) o).doubleValue();
+ double difference = width - nv.getWidth();
+
+ if (Math.abs(difference) > 0.1)
+ nv.setWidth(width);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getDefaultAppearanceObject() {
+ return new Double(70.0);
+ }
+
+ public boolean constrained(VisualPropertyDependency dep) {
+ if ( dep == null )
+ return false;
+
+ return dep.check(VisualPropertyDependency.Definition.NODE_SIZE_LOCKED);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/properties/OpacityValidator.java b/application/src/main/java/cytoscape/visual/properties/OpacityValidator.java
new file mode 100644
index 0000000..c8ed683
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/properties/OpacityValidator.java
@@ -0,0 +1,59 @@
+
+/*
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual.properties;
+
+
+/**
+ * Check given vale is in valid opacity value range.
+ *
+ * @author kono
+ *
+ */
+class OpacityValidator implements ValueValidator {
+
+ private static final double MIN_OPACITY = 0;
+ private static final double MAX_OPACITY = 255;
+
+ public boolean isValid(Object value) {
+ if ( value != null &&
+ value instanceof Number &&
+ ((Number) value).doubleValue() >= MIN_OPACITY &&
+ ((Number) value).doubleValue() <= MAX_OPACITY )
+ return true;
+ else
+ return false;
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/properties/ValueValidator.java b/application/src/main/java/cytoscape/visual/properties/ValueValidator.java
new file mode 100644
index 0000000..7d878d3
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/properties/ValueValidator.java
@@ -0,0 +1,40 @@
+
+/*
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual.properties;
+
+interface ValueValidator {
+ boolean isValid(Object value);
+}
diff --git a/application/src/main/java/cytoscape/visual/strokes/BackwardSlashStroke.java b/application/src/main/java/cytoscape/visual/strokes/BackwardSlashStroke.java
new file mode 100644
index 0000000..5f1e69d
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/strokes/BackwardSlashStroke.java
@@ -0,0 +1,13 @@
+
+
+package cytoscape.visual.strokes;
+
+import static cytoscape.visual.LineStyle.BACKWARD_SLASH;
+
+public class BackwardSlashStroke extends PipeStroke {
+
+ public BackwardSlashStroke(float width, Type offsetType) {
+ super(width,offsetType,BACKWARD_SLASH);
+ }
+}
+
diff --git a/application/src/main/java/cytoscape/visual/strokes/ContiguousArrowStroke.java b/application/src/main/java/cytoscape/visual/strokes/ContiguousArrowStroke.java
new file mode 100644
index 0000000..8142fe5
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/strokes/ContiguousArrowStroke.java
@@ -0,0 +1,67 @@
+
+
+package cytoscape.visual.strokes;
+
+import java.awt.Shape;
+import java.awt.geom.GeneralPath;
+import static cytoscape.visual.LineStyle.CONTIGUOUS_ARROW;
+
+public class ContiguousArrowStroke extends ShapeStroke {
+
+ public ContiguousArrowStroke(float width) {
+ super( new Shape[] { getArrowStroke(width) }, 3f*width, CONTIGUOUS_ARROW, width );
+ }
+
+ public WidthStroke newInstanceForWidth(float w) {
+ return new ContiguousArrowStroke(w);
+ }
+
+ private static Shape getArrowStroke(final float width) {
+ GeneralPath shape = new GeneralPath();
+
+ // change these to change the arrow proportions
+
+ // length of shape
+ float length = 3f*width;
+
+ // width of center line
+ float lineWidth = width;
+
+ // width of arrow, from one arm to its opposite
+ float arrowWidth = 4f*width;
+
+ // thickness of the arrow arm relative to the
+ // center line width
+ float arrowArmBreadthFactor = 0.5f;
+
+ // ====================================================================
+ // don't change these - they should always stay
+ // the same for this shape!
+ float begin = 0f;
+ float halfLineWidth = 0.5f * lineWidth;
+ float halfArrowWidth = 0.5f * arrowWidth;
+ float arrowArmBreadth = arrowArmBreadthFactor*lineWidth;
+ float arrowArmStart = (length/2f) - (arrowArmBreadth/2f);
+ float arrowArmEnd = (length/2f) + (arrowArmBreadth/2f);
+
+ // make the actual shape
+ // X Y
+ shape.moveTo( begin, halfLineWidth);
+ shape.lineTo( arrowArmStart, halfLineWidth);
+ shape.lineTo( begin, halfArrowWidth);
+ shape.lineTo( arrowArmBreadth, halfArrowWidth);
+ shape.lineTo( arrowArmEnd, halfLineWidth);
+ shape.lineTo( length, halfLineWidth);
+ shape.lineTo( length, -halfLineWidth);
+ shape.lineTo( arrowArmEnd, -halfLineWidth);
+ shape.lineTo( arrowArmBreadth, -halfArrowWidth);
+ shape.lineTo( begin, -halfArrowWidth);
+ shape.lineTo( arrowArmStart, -halfLineWidth);
+ shape.lineTo( begin, -halfLineWidth);
+ shape.lineTo( begin, halfLineWidth);
+
+ return shape;
+ }
+}
+
+
diff --git a/application/src/main/java/cytoscape/visual/strokes/DashDotStroke.java b/application/src/main/java/cytoscape/visual/strokes/DashDotStroke.java
new file mode 100644
index 0000000..858d354
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/strokes/DashDotStroke.java
@@ -0,0 +1,34 @@
+
+
+
+package cytoscape.visual.strokes;
+
+import java.awt.BasicStroke;
+import java.awt.Stroke;
+import java.awt.Shape;
+import cytoscape.visual.LineStyle;
+import static cytoscape.visual.LineStyle.DASH_DOT;
+
+public class DashDotStroke extends BasicStroke implements WidthStroke {
+
+ private float width;
+
+ public DashDotStroke(float width) {
+ super(width, BasicStroke.CAP_ROUND, BasicStroke.JOIN_MITER,
+ 10.0f, new float[]{width * 4f,width*2f,width,width*2f}, 0.0f);
+
+ this.width = width;
+ }
+
+ public WidthStroke newInstanceForWidth(float w) {
+ return new DashDotStroke(w);
+ }
+
+ public LineStyle getLineStyle() {
+ return DASH_DOT;
+ }
+
+ public String toString() { return DASH_DOT + " " + Float.toString(width); }
+}
+
+
diff --git a/application/src/main/java/cytoscape/visual/strokes/DotStroke.java b/application/src/main/java/cytoscape/visual/strokes/DotStroke.java
new file mode 100644
index 0000000..962dc73
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/strokes/DotStroke.java
@@ -0,0 +1,20 @@
+
+package cytoscape.visual.strokes;
+
+import java.awt.Shape;
+import java.awt.geom.Ellipse2D;
+import static cytoscape.visual.LineStyle.DOT;
+
+public class DotStroke extends ShapeStroke {
+
+ public DotStroke(float width) {
+ super( new Shape[] { new Ellipse2D.Float(0, 0, width, width) }, width * 2f, DOT, width );
+ this.width = width;
+ }
+
+ public WidthStroke newInstanceForWidth(float w) {
+ return new DotStroke(w);
+ }
+}
+
+
diff --git a/application/src/main/java/cytoscape/visual/strokes/EqualDashStroke.java b/application/src/main/java/cytoscape/visual/strokes/EqualDashStroke.java
new file mode 100644
index 0000000..2fffddf
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/strokes/EqualDashStroke.java
@@ -0,0 +1,33 @@
+
+
+package cytoscape.visual.strokes;
+
+import java.awt.BasicStroke;
+import java.awt.Stroke;
+import java.awt.Shape;
+import cytoscape.visual.LineStyle;
+import static cytoscape.visual.LineStyle.EQUAL_DASH;
+
+public class EqualDashStroke extends BasicStroke implements WidthStroke {
+
+ private float width;
+
+ public EqualDashStroke(float width) {
+ super(width, BasicStroke.CAP_BUTT, BasicStroke.JOIN_MITER,
+ 10.0f, new float[]{width * 2f,width * 2f}, 0.0f);
+
+ this.width = width;
+ }
+
+ public WidthStroke newInstanceForWidth(float w) {
+ return new EqualDashStroke(w);
+ }
+
+ public LineStyle getLineStyle() {
+ return EQUAL_DASH;
+ }
+
+ public String toString() { return EQUAL_DASH.toString() + " " + Float.toString(width); }
+}
+
+
diff --git a/application/src/main/java/cytoscape/visual/strokes/ForwardSlashStroke.java b/application/src/main/java/cytoscape/visual/strokes/ForwardSlashStroke.java
new file mode 100644
index 0000000..199cb32
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/strokes/ForwardSlashStroke.java
@@ -0,0 +1,13 @@
+
+
+package cytoscape.visual.strokes;
+
+import static cytoscape.visual.LineStyle.FORWARD_SLASH;
+
+public class ForwardSlashStroke extends PipeStroke {
+
+ public ForwardSlashStroke(float width, Type offsetType) {
+ super(width,offsetType,FORWARD_SLASH);
+ }
+}
+
diff --git a/application/src/main/java/cytoscape/visual/strokes/LongDashStroke.java b/application/src/main/java/cytoscape/visual/strokes/LongDashStroke.java
new file mode 100644
index 0000000..4ae7535
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/strokes/LongDashStroke.java
@@ -0,0 +1,32 @@
+
+
+package cytoscape.visual.strokes;
+
+import java.awt.BasicStroke;
+import java.awt.Stroke;
+import java.awt.Shape;
+import cytoscape.visual.LineStyle;
+import static cytoscape.visual.LineStyle.LONG_DASH;
+
+public class LongDashStroke extends BasicStroke implements WidthStroke {
+
+ float width;
+
+ public LongDashStroke(float width) {
+ super(width, BasicStroke.CAP_BUTT, BasicStroke.JOIN_MITER,
+ 10.0f, new float[]{width * 4f, width * 2f}, 0.0f);
+ this.width = width;
+ }
+
+ public WidthStroke newInstanceForWidth(float w) {
+ return new LongDashStroke(w);
+ }
+
+ public LineStyle getLineStyle() {
+ return LONG_DASH;
+ }
+
+ public String toString() { return LONG_DASH.toString() + " " + Float.toString(width); }
+}
+
+
diff --git a/application/src/main/java/cytoscape/visual/strokes/ParallelStroke.java b/application/src/main/java/cytoscape/visual/strokes/ParallelStroke.java
new file mode 100644
index 0000000..3e3c73f
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/strokes/ParallelStroke.java
@@ -0,0 +1,39 @@
+
+
+package cytoscape.visual.strokes;
+
+import java.awt.Shape;
+import java.awt.geom.GeneralPath;
+import static cytoscape.visual.LineStyle.PARALLEL_LINES;
+
+public class ParallelStroke extends ShapeStroke {
+
+ public ParallelStroke(float width) {
+ super( new Shape[] { getParallelStroke(width) }, 1f, PARALLEL_LINES, width );
+ this.width = width;
+ }
+
+ public WidthStroke newInstanceForWidth(float w) {
+ return new ParallelStroke(w);
+ }
+
+ private static Shape getParallelStroke(final float width) {
+ GeneralPath shape = new GeneralPath();
+
+ shape.moveTo(0f,-0.5f*width);
+ shape.lineTo(1f,-0.5f*width);
+ shape.lineTo(1f,-1f*width);
+ shape.lineTo(0f,-1f*width);
+ shape.lineTo(0f,-0.5f*width);
+
+ shape.moveTo(0f,0.5f*width);
+ shape.lineTo(1f,0.5f*width);
+ shape.lineTo(1f,1f*width);
+ shape.lineTo(0f,1f*width);
+ shape.lineTo(0f,0.5f*width);
+
+ return shape;
+ }
+}
+
+
diff --git a/application/src/main/java/cytoscape/visual/strokes/PipeStroke.java b/application/src/main/java/cytoscape/visual/strokes/PipeStroke.java
new file mode 100644
index 0000000..e41647f
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/strokes/PipeStroke.java
@@ -0,0 +1,55 @@
+
+
+package cytoscape.visual.strokes;
+
+import java.awt.Shape;
+import java.awt.geom.GeneralPath;
+import cytoscape.visual.LineStyle;
+
+public class PipeStroke extends ShapeStroke {
+
+ public enum Type {
+ VERTICAL(0f),
+ FORWARD(-1f),
+ BACKWARD(1f),
+ ;
+
+ private float adjust;
+ private Type(float adjust) {
+ this.adjust = adjust;
+ }
+
+ public float adjust(float input) {
+ return adjust * input;
+ }
+ }
+
+ private Type offsetType;
+
+ PipeStroke(float width, Type offsetType, LineStyle lineStyle) {
+ super( new Shape[] { getShape(width, offsetType) }, width, lineStyle, width );
+ this.offsetType = offsetType;
+ this.lineStyle = lineStyle;
+ }
+
+ public WidthStroke newInstanceForWidth(float w) {
+ return new PipeStroke(w,offsetType,lineStyle);
+ }
+
+ private static Shape getShape(final float input, final Type offsetType) {
+ GeneralPath shape = new GeneralPath();
+ float height = input;
+ float width = input/5f;
+ float offset = offsetType.adjust(input);
+
+ shape.moveTo(0f,-height);
+ shape.lineTo(width,-height);
+ shape.lineTo(width+offset,height);
+ shape.lineTo(0f+offset,height);
+ shape.lineTo(0f,-height);
+
+ return shape;
+ }
+}
+
+
diff --git a/application/src/main/java/cytoscape/visual/strokes/SeparateArrowStroke.java b/application/src/main/java/cytoscape/visual/strokes/SeparateArrowStroke.java
new file mode 100644
index 0000000..00d5565
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/strokes/SeparateArrowStroke.java
@@ -0,0 +1,59 @@
+
+
+package cytoscape.visual.strokes;
+
+import java.awt.Shape;
+import java.awt.geom.GeneralPath;
+import static cytoscape.visual.LineStyle.SEPARATE_ARROW;
+
+public class SeparateArrowStroke extends ShapeStroke {
+
+ public SeparateArrowStroke(float width) {
+ super( new Shape[] { getArrowStroke(width) }, 5f*width, SEPARATE_ARROW, width );
+ }
+
+ public WidthStroke newInstanceForWidth(float w) {
+ return new SeparateArrowStroke(w);
+ }
+
+ private static Shape getArrowStroke(final float width) {
+ GeneralPath shape = new GeneralPath();
+
+ // change these to change the arrow proportions
+
+ // length of shape
+ float length = 4f*width;
+
+ // width of center line
+ float lineWidth = width;
+
+ // width of arrow, from one arm to its opposite
+ float arrowWidth = 3f*width;
+
+ // fraction of the length of the total shape
+ // where the arrow head should begin
+ float arrowHeadStart = length/2f;
+
+ // ====================================================================
+ // don't change these - they should always stay
+ // the same for this shape!
+ float begin = 0f;
+ float halfLineWidth = 0.5f * lineWidth;
+ float halfArrowWidth = 0.5f * arrowWidth;
+
+ // make the actual shape
+ // X Y
+ shape.moveTo( begin, halfLineWidth);
+ shape.lineTo( arrowHeadStart, halfLineWidth);
+ shape.lineTo( arrowHeadStart, halfArrowWidth);
+ shape.lineTo( length, 0f);
+ shape.lineTo( arrowHeadStart, -halfArrowWidth);
+ shape.lineTo( arrowHeadStart, -halfLineWidth);
+ shape.lineTo( begin, -halfLineWidth);
+ shape.lineTo( begin, halfLineWidth);
+
+ return shape;
+ }
+}
+
+
diff --git a/application/src/main/java/cytoscape/visual/strokes/ShapeStroke.java b/application/src/main/java/cytoscape/visual/strokes/ShapeStroke.java
new file mode 100644
index 0000000..98b10ed
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/strokes/ShapeStroke.java
@@ -0,0 +1,121 @@
+/*
+Copyright 2006 Jerry Huxtable
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+*/
+
+package cytoscape.visual.strokes;
+
+import java.awt.*;
+import java.awt.geom.*;
+import cytoscape.visual.LineStyle;
+
+public abstract class ShapeStroke implements WidthStroke {
+ private Shape shapes[];
+ private float advance;
+ private boolean repeat = true;
+ private AffineTransform transform = new AffineTransform();
+ private static final float FLATNESS = 0.1f;
+
+ protected LineStyle lineStyle;
+ protected float width;
+
+ public ShapeStroke( Shape shapes[], float advance, LineStyle lineStyle, float width ) {
+ this.advance = advance;
+ this.shapes = new Shape[shapes.length];
+ this.lineStyle = lineStyle;
+ this.width = width;
+
+ for ( int i = 0; i < this.shapes.length; i++ ) {
+ Rectangle2D bounds = shapes[i].getBounds2D();
+ transform.setToTranslation( -bounds.getCenterX(), -bounds.getCenterY() );
+ this.shapes[i] = transform.createTransformedShape( shapes[i] );
+ }
+ }
+
+ public Shape createStrokedShape( Shape shape ) {
+ GeneralPath result = new GeneralPath();
+ PathIterator it = new FlatteningPathIterator( shape.getPathIterator( null ), FLATNESS );
+ float points[] = new float[6];
+ float moveX = 0, moveY = 0;
+ float lastX = 0, lastY = 0;
+ float thisX = 0, thisY = 0;
+ int type = 0;
+ boolean first = false;
+ float next = 0;
+ int currentShape = 0;
+ int length = shapes.length;
+
+ float factor = 1;
+
+ while ( currentShape < length && !it.isDone() ) {
+ type = it.currentSegment( points );
+ switch( type ){
+ case PathIterator.SEG_MOVETO:
+ moveX = lastX = points[0];
+ moveY = lastY = points[1];
+ result.moveTo( moveX, moveY );
+ first = true;
+ next = 0;
+ break;
+
+ case PathIterator.SEG_CLOSE:
+ points[0] = moveX;
+ points[1] = moveY;
+ // Fall into....
+
+ case PathIterator.SEG_LINETO:
+ thisX = points[0];
+ thisY = points[1];
+ float dx = thisX-lastX;
+ float dy = thisY-lastY;
+ float distance = (float)Math.sqrt( dx*dx + dy*dy );
+ if ( distance >= next ) {
+ float r = 1.0f/distance;
+ float angle = (float)Math.atan2( dy, dx );
+ while ( currentShape < length && distance >= next ) {
+ float x = lastX + next*dx*r;
+ float y = lastY + next*dy*r;
+ transform.setToTranslation( x, y );
+ transform.rotate( angle );
+ result.append( transform.createTransformedShape( shapes[currentShape] ),
+ false );
+ next += advance;
+ currentShape++;
+ if ( repeat )
+ currentShape %= length;
+ }
+ }
+ next -= distance;
+ first = false;
+ lastX = thisX;
+ lastY = thisY;
+ break;
+ }
+ it.next();
+ }
+
+ return result;
+ }
+
+
+ public LineStyle getLineStyle() {
+ return lineStyle;
+ }
+
+ public String toString() {
+ return lineStyle.toString() + " " + Float.toString(width);
+ }
+
+ abstract public WidthStroke newInstanceForWidth(float w);
+}
diff --git a/application/src/main/java/cytoscape/visual/strokes/SineWaveStroke.java b/application/src/main/java/cytoscape/visual/strokes/SineWaveStroke.java
new file mode 100644
index 0000000..31903e3
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/strokes/SineWaveStroke.java
@@ -0,0 +1,46 @@
+
+
+package cytoscape.visual.strokes;
+
+import java.awt.Shape;
+import java.awt.geom.GeneralPath;
+import static cytoscape.visual.LineStyle.SINEWAVE;
+import cytoscape.util.PropUtil;
+import cytoscape.CytoscapeInit;
+
+public class SineWaveStroke extends ShapeStroke {
+
+ public SineWaveStroke(float width) {
+ // second arg here is the advance - advance must equal wavelength below
+ super( new Shape[] { getSineWave(width) },
+ PropUtil.getFloat( CytoscapeInit.getProperties(), "SineWaveStroke.wavelength", 10f),
+ SINEWAVE, width );
+ }
+
+ public WidthStroke newInstanceForWidth(float w) {
+ return new SineWaveStroke(w);
+ }
+
+ private static Shape getSineWave(final float width) {
+ GeneralPath shape = new GeneralPath();
+
+ // wavelength must equal advance specified in constructor or
+ // else the waves won't line up!
+ final float wavelength = PropUtil.getFloat( CytoscapeInit.getProperties(),
+ "SineWaveStroke.wavelength", 10f );
+ final float amplitude = PropUtil.getFloat( CytoscapeInit.getProperties(),
+ "SineWaveStroke.amplitude",5f );
+
+ shape.moveTo(0f,0f);
+ shape.lineTo(0f,width);
+ shape.quadTo(0.25f*wavelength,amplitude+width, 0.5f*wavelength,width);
+ shape.quadTo(0.75f*wavelength,-amplitude-width, wavelength,width);
+ shape.lineTo(wavelength,0f);
+ shape.quadTo(0.75f*wavelength,-amplitude-width, 0.5f*wavelength,0f);
+ shape.quadTo(0.25f*wavelength,amplitude+width, 0f,0f);
+
+ return shape;
+ }
+}
+
+
diff --git a/application/src/main/java/cytoscape/visual/strokes/SolidStroke.java b/application/src/main/java/cytoscape/visual/strokes/SolidStroke.java
new file mode 100644
index 0000000..0db4785
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/strokes/SolidStroke.java
@@ -0,0 +1,30 @@
+
+package cytoscape.visual.strokes;
+
+import java.awt.BasicStroke;
+import java.awt.Stroke;
+import java.awt.Shape;
+import cytoscape.visual.LineStyle;
+import static cytoscape.visual.LineStyle.SOLID;
+
+public class SolidStroke extends BasicStroke implements WidthStroke {
+
+ private float width;
+
+ public SolidStroke(float width) {
+ super(width,BasicStroke.CAP_ROUND,BasicStroke.JOIN_ROUND);
+ this.width = width;
+ }
+
+ public WidthStroke newInstanceForWidth(float w) {
+ return new SolidStroke(w);
+ }
+
+ public LineStyle getLineStyle() {
+ return SOLID;
+ }
+
+ public String toString() { return SOLID.toString() + " " + Float.toString(width); }
+}
+
+
diff --git a/application/src/main/java/cytoscape/visual/strokes/VerticalSlashStroke.java b/application/src/main/java/cytoscape/visual/strokes/VerticalSlashStroke.java
new file mode 100644
index 0000000..b67ef69
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/strokes/VerticalSlashStroke.java
@@ -0,0 +1,13 @@
+
+
+package cytoscape.visual.strokes;
+
+import static cytoscape.visual.LineStyle.VERTICAL_SLASH;
+
+public class VerticalSlashStroke extends PipeStroke {
+
+ public VerticalSlashStroke(float width, Type offsetType) {
+ super(width,offsetType,VERTICAL_SLASH);
+ }
+}
+
diff --git a/application/src/main/java/cytoscape/visual/strokes/WidthStroke.java b/application/src/main/java/cytoscape/visual/strokes/WidthStroke.java
new file mode 100644
index 0000000..0cbd22f
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/strokes/WidthStroke.java
@@ -0,0 +1,23 @@
+
+package cytoscape.visual.strokes;
+
+import java.awt.Stroke;
+import cytoscape.visual.LineStyle;
+
+/**
+ * A simple extension of Stroke that allows Stroke objects to be
+ * coupled with LineStyle enum values and allows the width of the
+ * stroke to be adjusted.
+ */
+public interface WidthStroke extends Stroke {
+
+ /**
+ * @return A new instance of this WidthStroke with the specified width.
+ */
+ WidthStroke newInstanceForWidth(float width);
+
+ /**
+ * @return the LineStyle associated with this particular WidthStroke.
+ */
+ LineStyle getLineStyle();
+}
diff --git a/application/src/main/java/cytoscape/visual/strokes/ZeroStroke.java b/application/src/main/java/cytoscape/visual/strokes/ZeroStroke.java
new file mode 100644
index 0000000..ac3408b
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/strokes/ZeroStroke.java
@@ -0,0 +1,42 @@
+
+package cytoscape.visual.strokes;
+
+import java.awt.BasicStroke;
+import java.awt.Stroke;
+import java.awt.Shape;
+import cytoscape.visual.LineStyle;
+
+/**
+ * Rather than handle strokes of width 0 for all implementations of WidthStroke,
+ * use this wrapper class that, when the width is less than or equal to 0 a
+ * BasicStroke is returned, whereas when the width is greater than 0, return the
+ * specified actual WidthStroke.
+ */
+public class ZeroStroke extends BasicStroke implements WidthStroke {
+
+ final WidthStroke actualStroke;
+
+ /**
+ * @param actualStroke The actual WidthStroke that this ZeroStroke represents. This
+ * object will be used whenever the width for a new instance is greater than 0.
+ */
+ public ZeroStroke(WidthStroke actualStroke) {
+ super(0);
+ this.actualStroke = actualStroke;
+ }
+
+ public WidthStroke newInstanceForWidth(float w) {
+ if ( w <= 0 )
+ return new ZeroStroke(actualStroke);
+ else
+ return actualStroke.newInstanceForWidth(w);
+ }
+
+ public LineStyle getLineStyle() {
+ return actualStroke.getLineStyle();
+ }
+
+ public String toString() { return getLineStyle().toString() + " 0"; }
+}
+
+
diff --git a/application/src/main/java/cytoscape/visual/strokes/ZigzagStroke.java b/application/src/main/java/cytoscape/visual/strokes/ZigzagStroke.java
new file mode 100644
index 0000000..ac76aa8
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/strokes/ZigzagStroke.java
@@ -0,0 +1,117 @@
+/*
+Copyright 2006 Jerry Huxtable
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+*/
+
+package cytoscape.visual.strokes;
+
+import java.awt.*;
+import java.awt.geom.*;
+import cytoscape.visual.LineStyle;
+import static cytoscape.visual.LineStyle.ZIGZAG;
+
+public class ZigzagStroke implements WidthStroke {
+
+ private float amplitude = 10.0f;
+ private float wavelength = 10.0f;
+ private Stroke stroke;
+ private static final float FLATNESS = 1;
+ private float width;
+
+ // TODO we can do fancier stuff if we pass in Stroke, amplitude and wavelength
+ // as params
+ public ZigzagStroke( float width ) {
+ this.width = width;
+ this.stroke = new BasicStroke(width);
+ }
+
+ public Shape createStrokedShape( Shape shape ) {
+ GeneralPath result = new GeneralPath();
+ PathIterator it = new FlatteningPathIterator( shape.getPathIterator( null ), FLATNESS );
+ float points[] = new float[6];
+ float moveX = 0, moveY = 0;
+ float lastX = 0, lastY = 0;
+ float thisX = 0, thisY = 0;
+ int type = 0;
+ boolean first = false;
+ float next = 0;
+ int phase = 0;
+
+ float factor = 1;
+
+ while ( !it.isDone() ) {
+ type = it.currentSegment( points );
+ switch( type ){
+ case PathIterator.SEG_MOVETO:
+ moveX = lastX = points[0];
+ moveY = lastY = points[1];
+ result.moveTo( moveX, moveY );
+ first = true;
+ next = wavelength/2;
+ break;
+
+ case PathIterator.SEG_CLOSE:
+ points[0] = moveX;
+ points[1] = moveY;
+ // Fall into....
+
+ case PathIterator.SEG_LINETO:
+ thisX = points[0];
+ thisY = points[1];
+ float dx = thisX-lastX;
+ float dy = thisY-lastY;
+ float distance = (float)Math.sqrt( dx*dx + dy*dy );
+ if ( distance >= next ) {
+ float r = 1.0f/distance;
+ float angle = (float)Math.atan2( dy, dx );
+ while ( distance >= next ) {
+ float x = lastX + next*dx*r;
+ float y = lastY + next*dy*r;
+ float tx = amplitude*dy*r;
+ float ty = amplitude*dx*r;
+ if ( (phase & 1) == 0 )
+ result.lineTo( x+amplitude*dy*r, y-amplitude*dx*r );
+ else
+ result.lineTo( x-amplitude*dy*r, y+amplitude*dx*r );
+ next += wavelength;
+ phase++;
+ }
+ }
+ next -= distance;
+ first = false;
+ lastX = thisX;
+ lastY = thisY;
+ if ( type == PathIterator.SEG_CLOSE )
+ result.closePath();
+ break;
+ }
+ it.next();
+ }
+
+ return stroke.createStrokedShape( result );
+ }
+
+ public LineStyle getLineStyle() {
+ return ZIGZAG;
+ }
+
+ public WidthStroke newInstanceForWidth(float w) {
+ return new ZigzagStroke(w);
+ }
+
+ public String toString() {
+ return ZIGZAG.toString() + " " + Float.toString(width);
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/visual/strokes/package.html b/application/src/main/java/cytoscape/visual/strokes/package.html
new file mode 100644
index 0000000..bd074b3
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/strokes/package.html
@@ -0,0 +1,7 @@
+<html>
+<body>
+The WidthStroke objects in this package should NOT be used directly by anyone other
+than the LineStyle enum!!!! Seriously, DON'T USE THESE CLASSES!!!
+</body>
+</html>
+
diff --git a/application/src/main/java/cytoscape/visual/ui/BypassHack.java b/application/src/main/java/cytoscape/visual/ui/BypassHack.java
new file mode 100644
index 0000000..6772785
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/BypassHack.java
@@ -0,0 +1,67 @@
+
+/*
+ File: BypassHack.java
+
+ Copyright (c) 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual.ui;
+
+import giny.model.GraphObject;
+
+/**
+ * ARgh. This is a horrible, horrible hack that allows LabelPosition to
+ * be set dynamically for vizmap bypass as you drag the icon around in
+ * the label position dialog. This class provides access to the current
+ * node (or edge) that has had it's context menu clicked. This class allows
+ * the dialog to get the node then set the bypass value as things move rather
+ * than waiting for the user to click OK. This could be used by other
+ * VisualPropertyTypes in a similar fashion, but currently isn't.
+ * <b>This code should NEVER propagate to newer versions of Cytoscape!!!</b>
+ * This should be handled in a completely different way in the future.
+ */
+class BypassHack {
+ private static GraphObject curr = null;
+
+ static void setCurrentObject(GraphObject o) {
+ curr = o;
+ }
+
+ static GraphObject getCurrentObject() {
+ return curr;
+ }
+
+ static void finished() {
+ curr = null;
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/ui/CellEditorFactory.java b/application/src/main/java/cytoscape/visual/ui/CellEditorFactory.java
new file mode 100644
index 0000000..35fda77
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/CellEditorFactory.java
@@ -0,0 +1,160 @@
+package cytoscape.visual.ui;
+
+import giny.view.ObjectPosition;
+
+import java.awt.Color;
+import java.awt.Font;
+import java.beans.PropertyChangeListener;
+import java.beans.PropertyEditor;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import javax.swing.Icon;
+
+import cytoscape.visual.ArrowShape;
+import cytoscape.visual.LineStyle;
+import cytoscape.visual.NodeShape;
+import cytoscape.visual.VisualPropertyType;
+import cytoscape.visual.customgraphic.CyCustomGraphics;
+import cytoscape.visual.ui.editors.discrete.CyColorPropertyEditor;
+import cytoscape.visual.ui.editors.discrete.CyComboBoxPropertyEditor;
+import cytoscape.visual.ui.editors.discrete.CyCustomGraphicsEditor;
+import cytoscape.visual.ui.editors.discrete.CyDoublePropertyEditor;
+import cytoscape.visual.ui.editors.discrete.CyFontPropertyEditor;
+import cytoscape.visual.ui.editors.discrete.CyObjectPositionPropertyEditor;
+import cytoscape.visual.ui.editors.discrete.CyStringPropertyEditor;
+import cytoscape.visual.ui.icon.ArrowIcon;
+import cytoscape.visual.ui.icon.NodeIcon;
+import cytoscape.visual.ui.icon.VisualPropertyIcon;
+
+public class CellEditorFactory {
+
+ private final Map<Object, Icon> nodeShapeIcons = NodeShape.getIconSet();
+ private final Map<Object, Icon> arrowShapeIcons = ArrowShape.getIconSet();
+ private final Map<Object, Icon> lineTypeIcons = LineStyle.getIconSet();
+
+ private final Map<Class<?>, PropertyEditor> editorMap;
+ private final PropertyChangeListener pcl;
+
+ CellEditorFactory(final PropertyChangeListener pcl) {
+ this.editorMap = new HashMap<Class<?>, PropertyEditor>();
+ this.pcl = pcl;
+ registerDefaultEditors();
+ addListener();
+ }
+
+ /**
+ * Register editord supported by default.
+ */
+ private void registerDefaultEditors() {
+ this.editorMap.put(String.class, new CyStringPropertyEditor());
+ this.editorMap.put(Color.class, new CyColorPropertyEditor());
+ this.editorMap.put(Font.class, new CyFontPropertyEditor());
+ this.editorMap.put(Number.class, new CyDoublePropertyEditor());
+
+ this.editorMap.put(ObjectPosition.class,
+ new CyObjectPositionPropertyEditor(
+ VisualPropertyType.NODE_LABEL_POSITION));
+
+ this.editorMap.put(CyCustomGraphics.class, new CyCustomGraphicsEditor());
+
+ // Register combo-box type editors. They needs special customization.
+ initializeShapeSelectors();
+ }
+
+ private void initializeShapeSelectors() {
+ VisualPropertyIcon newIcon;
+ final CyComboBoxPropertyEditor shapeCellEditor = new CyComboBoxPropertyEditor();
+
+ List<Icon> iconList = new ArrayList<Icon>();
+ final List<NodeShape> nodeShapes = new ArrayList<NodeShape>();
+
+ for (Object key : nodeShapeIcons.keySet()) {
+ NodeShape shape = (NodeShape) key;
+
+ if (shape.isSupported()) {
+ iconList.add(nodeShapeIcons.get(key));
+ nodeShapes.add(shape);
+ }
+ }
+
+ Icon[] iconArray = new Icon[iconList.size()];
+ String[] shapeNames = new String[iconList.size()];
+
+ for (int i = 0; i < iconArray.length; i++) {
+ newIcon = ((NodeIcon) iconList.get(i)).clone();
+ newIcon.setIconHeight(16);
+ newIcon.setIconWidth(16);
+ iconArray[i] = newIcon;
+ shapeNames[i] = nodeShapes.get(i).getShapeName();
+ }
+
+ shapeCellEditor.setAvailableValues(nodeShapes.toArray());
+ shapeCellEditor.setAvailableIcons(iconArray);
+
+ iconList.clear();
+ iconList.addAll(arrowShapeIcons.values());
+ iconArray = new Icon[iconList.size()];
+
+ String[] arrowNames = new String[iconList.size()];
+ Set<Object> arrowShapes = arrowShapeIcons.keySet();
+
+ for (int i = 0; i < iconArray.length; i++) {
+ newIcon = ((ArrowIcon) iconList.get(i));
+ newIcon.setIconHeight(16);
+ newIcon.setIconWidth(40);
+ newIcon.setBottomPadding(-9);
+ iconArray[i] = newIcon;
+ arrowNames[i] = newIcon.getName();
+ }
+
+ final CyComboBoxPropertyEditor arrowCellEditor = new CyComboBoxPropertyEditor();
+ arrowCellEditor.setAvailableValues(arrowShapes.toArray());
+ arrowCellEditor.setAvailableIcons(iconArray);
+
+ iconList = new ArrayList<Icon>();
+ iconList.addAll(lineTypeIcons.values());
+ iconArray = new Icon[iconList.size()];
+ shapeNames = new String[iconList.size()];
+
+ Set<Object> lineTypes = lineTypeIcons.keySet();
+
+ for (int i = 0; i < iconArray.length; i++) {
+ newIcon = (VisualPropertyIcon) (iconList.get(i));
+ newIcon.setIconHeight(16);
+ newIcon.setIconWidth(16);
+ iconArray[i] = newIcon;
+ shapeNames[i] = newIcon.getName();
+ }
+
+ final CyComboBoxPropertyEditor lineCellEditor = new CyComboBoxPropertyEditor();
+ lineCellEditor.setAvailableValues(lineTypes.toArray());
+ lineCellEditor.setAvailableIcons(iconArray);
+
+ // Boolean editor
+ final CyComboBoxPropertyEditor booleanCellEditor = new CyComboBoxPropertyEditor();
+ booleanCellEditor.setAvailableValues(new Boolean[] {true, false});
+
+ // Register editors
+ this.editorMap.put(NodeShape.class, shapeCellEditor);
+ this.editorMap.put(ArrowShape.class, arrowCellEditor);
+ this.editorMap.put(LineStyle.class, lineCellEditor);
+ this.editorMap.put(Boolean.class, booleanCellEditor);
+ }
+
+ private void addListener() {
+ for (final PropertyEditor editor : editorMap.values())
+ editor.addPropertyChangeListener(pcl);
+ }
+
+ public PropertyEditor getPropertyEditor(final Class<?> type) {
+ final PropertyEditor editor = this.editorMap.get(type);
+ if (editor == null) {
+ return null;
+ } else
+ return editor;
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/ui/CellHeightManager.java b/application/src/main/java/cytoscape/visual/ui/CellHeightManager.java
new file mode 100644
index 0000000..1d4878a
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/CellHeightManager.java
@@ -0,0 +1,11 @@
+package cytoscape.visual.ui;
+
+public class CellHeightManager {
+
+ private static final Integer DEF_HEIGHT = 20;
+
+ public static Integer getCellHeight() {
+ return DEF_HEIGHT;
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/visual/ui/CellRendererFactory.java b/application/src/main/java/cytoscape/visual/ui/CellRendererFactory.java
new file mode 100644
index 0000000..4cbf80c
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/CellRendererFactory.java
@@ -0,0 +1,61 @@
+package cytoscape.visual.ui;
+
+import giny.view.ObjectPosition;
+
+import java.awt.Color;
+import java.awt.Font;
+import java.util.HashMap;
+import java.util.Map;
+
+import javax.swing.table.DefaultTableCellRenderer;
+import javax.swing.table.TableCellRenderer;
+
+import cytoscape.visual.ArrowShape;
+import cytoscape.visual.LineStyle;
+import cytoscape.visual.NodeShape;
+import cytoscape.visual.VisualPropertyType;
+import cytoscape.visual.customgraphic.CyCustomGraphics;
+import cytoscape.visual.ui.editors.discrete.CustomGraphicsCellRenderer;
+import cytoscape.visual.ui.editors.discrete.CyColorCellRenderer;
+import cytoscape.visual.ui.editors.discrete.FontCellRenderer;
+import cytoscape.visual.ui.editors.discrete.ObjectPositionCellRenderer;
+import cytoscape.visual.ui.editors.discrete.ShapeCellRenderer;
+
+public class CellRendererFactory {
+
+ private final Map<Class<?>, TableCellRenderer> rendererMap;
+
+ protected final static TableCellRenderer DEF_RENDERER = new DefaultTableCellRenderer();
+
+ CellRendererFactory() {
+ rendererMap = new HashMap<Class<?>, TableCellRenderer>();
+
+ registerDefaultRenderers();
+ }
+
+ private void registerDefaultRenderers() {
+ rendererMap.put(Color.class, new CyColorCellRenderer());
+ rendererMap.put(NodeShape.class, new ShapeCellRenderer(VisualPropertyType.NODE_SHAPE));
+ rendererMap.put(LineStyle.class, new ShapeCellRenderer(VisualPropertyType.EDGE_LINE_STYLE));
+ rendererMap.put(ArrowShape.class, new ShapeCellRenderer(VisualPropertyType.EDGE_TGTARROW_SHAPE));
+ rendererMap.put(Font.class, new FontCellRenderer());
+ rendererMap.put(ObjectPosition.class, new ObjectPositionCellRenderer());
+ rendererMap.put(CyCustomGraphics.class, new CustomGraphicsCellRenderer());
+ rendererMap.put(String.class, DEF_RENDERER);
+ rendererMap.put(Number.class, DEF_RENDERER);
+ }
+
+
+ protected TableCellRenderer getCellRenderer(final Class<?> type) {
+ final TableCellRenderer rend = this.rendererMap.get(type);
+ if(rend == null)
+ return DEF_RENDERER;
+ else
+ return rend;
+ }
+
+
+ protected void register(final Class<?> type, final TableCellRenderer renderer) {
+ this.rendererMap.put(type, renderer);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/ui/DefaultAppearenceBuilder.java b/application/src/main/java/cytoscape/visual/ui/DefaultAppearenceBuilder.java
new file mode 100644
index 0000000..865dce7
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/DefaultAppearenceBuilder.java
@@ -0,0 +1,607 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.visual.ui;
+
+import java.awt.BasicStroke;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.Frame;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ComponentAdapter;
+import java.awt.event.ComponentEvent;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.TreeSet;
+
+import javax.swing.BorderFactory;
+import javax.swing.BoxLayout;
+import javax.swing.DefaultListModel;
+import javax.swing.Icon;
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JDialog;
+import javax.swing.JLabel;
+import javax.swing.JList;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTabbedPane;
+import javax.swing.ListCellRenderer;
+import javax.swing.SwingConstants;
+import javax.swing.WindowConstants;
+import javax.swing.border.LineBorder;
+
+import org.jdesktop.swingx.JXList;
+import org.jdesktop.swingx.border.DropShadowBorder;
+
+import cytoscape.Cytoscape;
+import cytoscape.logger.CyLogger;
+import cytoscape.util.CyColorChooser;
+import cytoscape.visual.GlobalAppearanceCalculator;
+import cytoscape.visual.VisualPropertyDependency;
+import cytoscape.visual.VisualPropertyType;
+import cytoscape.visual.VisualPropertyDependency.Definition;
+import cytoscape.visual.ui.icon.VisualPropertyIcon;
+
+
+/**
+ * Dialog for editing default visual property values.<br>
+ * This is a modal dialog.
+ *
+ * <p>
+ * Basic idea is the following:
+ * <ul>
+ * <li>Build dummy network with 2 nodes and 1 edge.</li>
+ * <li>Edit the default appearence of the dummy network</li>
+ * <li>Create a image from the dummy.</li>
+ * </ul>
+ * </p>
+ *
+ * @version 0.5
+ * @since Cytoscape 2.5
+ * @author kono
+ */
+public class DefaultAppearenceBuilder extends JDialog {
+
+ private static final long serialVersionUID = 596165395462496156L;
+
+ // Default dialog size for Default Appearence Builder.
+ private static final int VIEW_WIDTH = 350;
+ private static final int LIST_WIDTH = 550;
+
+ private static final Dimension DIALOG_SIZE = new Dimension(900, 500);
+
+ private static final Set<VisualPropertyType> EDGE_PROPS;
+ private static final Set<VisualPropertyType> NODE_PROPS;
+
+ private static final CyLogger logger = CyLogger.getLogger(DefaultAppearenceBuilder.class);
+
+ // This editor should be a singleton.
+ private static DefaultAppearenceBuilder dab = null;
+
+ static {
+ EDGE_PROPS = new TreeSet<VisualPropertyType>(VisualPropertyType.getEdgeVisualPropertyList());
+ NODE_PROPS = new TreeSet<VisualPropertyType>(VisualPropertyType.getNodeVisualPropertyList());
+ }
+
+ /**
+ * Creates a new DefaultAppearenceBuilder object.
+ *
+ * @param parent DOCUMENT ME!
+ * @param modal DOCUMENT ME!
+ */
+ private DefaultAppearenceBuilder(final Frame parent, final boolean modal) {
+ super(parent, modal);
+ initComponents();
+ buildList();
+
+ this.addComponentListener(new ComponentAdapter() {
+ public void componentResized(ComponentEvent e) {
+ mainView.updateView();
+ }
+ });
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param parent DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ static JPanel showDialog(Frame parent) {
+ if (dab == null)
+ dab = new DefaultAppearenceBuilder(parent, true);
+
+ dab.setSize(DIALOG_SIZE);
+
+ dab.buildList();
+
+ dab.mainView.updateView();
+ dab.setLocationRelativeTo(parent);
+ dab.setVisible(true);
+
+ return dab.getPanel();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ static final JPanel getDefaultView(String vsName) {
+ if (dab == null)
+ dab = new DefaultAppearenceBuilder(Cytoscape.getDesktop(), true);
+
+ dab.mainView.updateBackgroungColor(Cytoscape.getVisualMappingManager().getVisualStyle()
+ .getGlobalAppearanceCalculator()
+ .getDefaultBackgroundColor());
+ dab.buildList();
+
+ return dab.getPanel();
+ }
+
+ /**
+ * This method is called from within the constructor to initialize the form.
+ * WARNING: Do NOT modify this code. The content of this method is always
+ * regenerated by the Form Editor.
+ */
+
+ // <editor-fold defaultstate="collapsed" desc=" Generated Code ">
+ private void initComponents() {
+ jXPanel1 = new org.jdesktop.swingx.JXPanel();
+ mainView = DefaultViewPanel.getDefaultViewPanel();
+ jXTitledPanel1 = new org.jdesktop.swingx.JXTitledPanel();
+ defaultObjectTabbedPane = new JTabbedPane();
+
+ nodeScrollPane = new JScrollPane();
+ edgeScrollPane = new JScrollPane();
+ globalScrollPane = new JScrollPane();
+ dependencyScrollPane = new JScrollPane();
+
+ nodeList = new JXList();
+ edgeList = new JXList();
+ globalList = new JXList();
+
+ initDependencyPanel();
+
+ applyButton = new JButton();
+
+
+ cancelButton = new JButton();
+ cancelButton.setVisible(false);
+
+ nodeList.addMouseListener(new MouseAdapter() {
+ public void mouseClicked(MouseEvent e) {
+ listActionPerformed(e);
+ }
+ });
+
+ edgeList.addMouseListener(new MouseAdapter() {
+ public void mouseClicked(MouseEvent e) {
+ listActionPerformed(e);
+ }
+ });
+
+ globalList.addMouseListener(new MouseAdapter() {
+ public void mouseClicked(MouseEvent e) {
+ globalListActionPerformed(e);
+ }
+ });
+
+ setDefaultCloseOperation(WindowConstants.DISPOSE_ON_CLOSE);
+ setTitle("Default Appearance for "
+ + Cytoscape.getVisualMappingManager().getVisualStyle().getName());
+
+ mainView.setPreferredSize(new Dimension(VIEW_WIDTH, 300));
+ mainView.setBorder(new LineBorder(Color.darkGray, 1, true));
+
+ org.jdesktop.layout.GroupLayout jXPanel2Layout = new org.jdesktop.layout.GroupLayout(mainView);
+ mainView.setLayout(jXPanel2Layout);
+ jXPanel2Layout.setHorizontalGroup(jXPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(0, 300, Short.MAX_VALUE));
+ jXPanel2Layout.setVerticalGroup(jXPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(0, 237, Short.MAX_VALUE));
+
+ jXTitledPanel1.setTitle("Default Visual Properties");
+ jXTitledPanel1.setTitleFont(new Font("SansSerif", Font.BOLD, 12));
+ jXTitledPanel1.setPreferredSize(new Dimension(LIST_WIDTH, 300));
+ defaultObjectTabbedPane.setTabPlacement(JTabbedPane.BOTTOM);
+
+ nodeScrollPane.setViewportView(nodeList);
+ edgeScrollPane.setViewportView(edgeList);
+ globalScrollPane.setViewportView(globalList);
+ dependencyScrollPane.setViewportView(dependencyPanel);
+
+ defaultObjectTabbedPane.addTab("Node", nodeScrollPane);
+ defaultObjectTabbedPane.addTab("Edge", edgeScrollPane);
+ defaultObjectTabbedPane.addTab("Global", globalScrollPane);
+ defaultObjectTabbedPane.addTab("Dependencies", dependencyScrollPane);
+
+ org.jdesktop.layout.GroupLayout jXTitledPanel1Layout = new org.jdesktop.layout.GroupLayout(jXTitledPanel1
+ .getContentContainer());
+ jXTitledPanel1.getContentContainer().setLayout(jXTitledPanel1Layout);
+ jXTitledPanel1Layout.setHorizontalGroup(jXTitledPanel1Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(defaultObjectTabbedPane,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 250, Short.MAX_VALUE));
+ jXTitledPanel1Layout.setVerticalGroup(jXTitledPanel1Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(defaultObjectTabbedPane,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 243, Short.MAX_VALUE));
+
+ applyButton.setText("Apply");
+ applyButton.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent arg0) {
+ Cytoscape.getVisualMappingManager()
+ .setNetworkView(Cytoscape.getCurrentNetworkView());
+ Cytoscape.getCurrentNetworkView().redrawGraph(false, true);
+ dispose();
+ }
+ });
+
+ cancelButton.setText("Cancel");
+ cancelButton.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent arg0) {
+ dispose();
+ }
+ });
+
+ org.jdesktop.layout.GroupLayout jXPanel1Layout = new org.jdesktop.layout.GroupLayout(jXPanel1);
+ jXPanel1.setLayout(jXPanel1Layout);
+ jXPanel1Layout.setHorizontalGroup(jXPanel1Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(jXPanel1Layout.createSequentialGroup()
+ .addContainerGap()
+ .add(jXPanel1Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(jXPanel1Layout.createSequentialGroup()
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(cancelButton)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(applyButton))
+ .add(mainView,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE))
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(jXTitledPanel1,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ 500, Short.MAX_VALUE)
+ .add(12, 12, 12)));
+ jXPanel1Layout.setVerticalGroup(jXPanel1Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(org.jdesktop.layout.GroupLayout.TRAILING,
+ jXPanel1Layout.createSequentialGroup()
+ .addContainerGap()
+ .add(jXPanel1Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.TRAILING)
+ .add(org.jdesktop.layout.GroupLayout.LEADING,
+ jXTitledPanel1,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 270,
+ Short.MAX_VALUE)
+ .add(jXPanel1Layout.createSequentialGroup()
+ .add(mainView,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(jXPanel1Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE)
+ .add(cancelButton)
+ .add(applyButton))))
+ .addContainerGap()));
+ this.getContentPane().add(jXPanel1);
+ pack();
+ } // </editor-fold>
+
+ private void listActionPerformed(MouseEvent e) {
+ if (e.getClickCount() == 1) {
+ Object newValue = null;
+
+ final JList list;
+
+ if (e.getSource() == nodeList) {
+ list = nodeList;
+ } else {
+ list = edgeList;
+ }
+
+ try {
+ newValue = VizMapperMainPanel.showValueSelectDialog((VisualPropertyType) list.getSelectedValue(),
+ this);
+
+ VizMapperMainPanel.apply(newValue, (VisualPropertyType) list.getSelectedValue());
+ } catch (Exception e1) {
+ logger.warn("Unable to show VizMapper value select dialog!", e1);
+ e1.printStackTrace();
+ }
+
+ buildList();
+ Cytoscape.getCurrentNetworkView().redrawGraph(false, true);
+ }
+ }
+
+ private void globalListActionPerformed(MouseEvent e) {
+ if (e.getClickCount() == 1) {
+ final String selected = (String) globalList.getSelectedValue();
+ Color newColor = CyColorChooser.showDialog(this, "Choose new color.", Color.white);
+
+ try {
+ Cytoscape.getVisualMappingManager().getVisualStyle().getGlobalAppearanceCalculator()
+ .setDefaultColor(selected, newColor);
+ Cytoscape.getVisualMappingManager().applyGlobalAppearances();
+ } catch (Exception e1) {
+ logger.warn("Unable to set default color!", e1);
+ }
+
+ buildList();
+ Cytoscape.getVisualMappingManager().getNetworkView().redrawGraph(false, true);
+
+ if (selected.equals("Background Color")) {
+ Cytoscape.getVisualMappingManager().applyGlobalAppearances();
+ mainView.updateBackgroungColor(newColor);
+ }
+
+ mainView.updateView();
+ mainView.repaint();
+ }
+ }
+
+ // Variables declaration - do not modify
+ private JButton applyButton;
+ private JButton cancelButton;
+ private JScrollPane nodeScrollPane;
+ private JScrollPane edgeScrollPane;
+ private JScrollPane globalScrollPane;
+ private JScrollPane dependencyScrollPane;
+ private JTabbedPane defaultObjectTabbedPane;
+ private JXList nodeList;
+ private JXList edgeList;
+ private JXList globalList;
+ private JPanel dependencyPanel;
+ private org.jdesktop.swingx.JXPanel jXPanel1;
+ private Map<Definition,JCheckBox> dependencyCheckBoxMap;
+
+ // private org.jdesktop.swingx.JXPanel jXPanel2;
+ private org.jdesktop.swingx.JXTitledPanel jXTitledPanel1;
+
+ // End of variables declaration
+ protected DefaultViewPanel mainView;
+
+ // End of variables declaration
+ private JPanel getPanel() {
+ return mainView;
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ private void buildList() {
+
+ syncDependencies();
+
+ List<Icon> nodeIcons = new ArrayList<Icon>();
+ List<Icon> edgeIcons = new ArrayList<Icon>();
+ List<Icon> globalIcons = new ArrayList<Icon>();
+
+ DefaultListModel model = new DefaultListModel();
+ nodeList.setModel(model);
+
+ for (VisualPropertyType type : NODE_PROPS) {
+ final VisualPropertyIcon nodeIcon = (VisualPropertyIcon) (type.getVisualProperty()
+ .getDefaultIcon());
+ nodeIcon.setLeftPadding(15);
+ model.addElement(type);
+ nodeIcons.add(nodeIcon);
+ }
+
+ DefaultListModel eModel = new DefaultListModel();
+ edgeList.setModel(eModel);
+
+ for (VisualPropertyType type : EDGE_PROPS) {
+ final VisualPropertyIcon edgeIcon = (VisualPropertyIcon) (type.getVisualProperty()
+ .getDefaultIcon());
+
+ if (edgeIcon != null) {
+ edgeIcon.setLeftPadding(15);
+ eModel.addElement(type);
+ edgeIcons.add(edgeIcon);
+ }
+ }
+
+ GlobalAppearanceCalculator gac = Cytoscape.getVisualMappingManager().getVisualStyle()
+ .getGlobalAppearanceCalculator();
+ DefaultListModel gModel = new DefaultListModel();
+ globalList.setModel(gModel);
+
+ for (String name : gac.getGlobalAppearanceNames()) {
+ try {
+ globalIcons.add(new GlobalIcon(name, gac.getDefaultColor(name)));
+ } catch (Exception e) {
+ logger.warn("Unable to add default color icon!", e);
+ }
+
+ gModel.addElement(name);
+ }
+
+
+ nodeList.setCellRenderer(new VisualPropCellRenderer(nodeIcons));
+ edgeList.setCellRenderer(new VisualPropCellRenderer(edgeIcons));
+ globalList.setCellRenderer(new VisualPropCellRenderer(globalIcons));
+
+ mainView.updateView();
+ mainView.repaint();
+ }
+
+ private void syncDependencies() {
+ final VisualPropertyDependency dep = Cytoscape.getVisualMappingManager().getVisualStyle().getDependency();
+
+ // sync properties with dependencies
+ for ( VisualPropertyType type : VisualPropertyType.values() ) {
+ if ( !type.isAllowed() )
+ continue;
+
+ if ( type.isNodeProp() ) {
+ if ( type.getVisualProperty().constrained(dep) )
+ NODE_PROPS.remove(type);
+ else
+ NODE_PROPS.add(type);
+ } else {
+ if ( type.getVisualProperty().constrained(dep) )
+ EDGE_PROPS.remove(type);
+ else
+ EDGE_PROPS.add(type);
+ }
+ }
+
+ // apply dependencies to checkboxes
+ for ( Definition def : dependencyCheckBoxMap.keySet() )
+ dependencyCheckBoxMap.get(def).setSelected( dep.check( def ) );
+ }
+
+ private void initDependencyPanel() {
+ dependencyPanel = new JPanel();
+ dependencyCheckBoxMap = new HashMap<Definition,JCheckBox>();
+ dependencyPanel.setLayout(new BoxLayout(dependencyPanel, BoxLayout.Y_AXIS));
+ final VisualPropertyDependency dep = Cytoscape.getVisualMappingManager().getVisualStyle().getDependency();
+
+ for (final Definition def : Definition.values()) {
+ final JCheckBox dCheck = new JCheckBox();
+ dCheck.setSelected( dep.check( def ) );
+ dCheck.setFont(new java.awt.Font("SansSerif", 1, 12));
+ dCheck.setText(def.getTitle());
+ dCheck.setBorder(BorderFactory.createEmptyBorder(0, 0, 0, 0));
+ dCheck.setMargin(new java.awt.Insets(0, 0, 0, 0));
+ dependencyPanel.add(dCheck);
+ dependencyCheckBoxMap.put(def,dCheck);
+ dCheck.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent arg0) {
+ final VisualPropertyDependency deps = Cytoscape.getVisualMappingManager().getVisualStyle().getDependency();
+ deps.set(def,dCheck.isSelected());
+ Cytoscape.getDesktop().getVizMapperUI().syncDependencyStates(deps,def);
+ buildList();
+ mainView.updateView();
+ repaint();
+ }
+ });
+ }
+ }
+
+
+ static class VisualPropCellRenderer extends JLabel implements ListCellRenderer {
+
+ private static final long serialVersionUID = -4980971466313937239L;
+
+ private final Font SELECTED_FONT = new Font("SansSerif", Font.ITALIC, 14);
+ private final Font NORMAL_FONT = new Font("SansSerif", Font.BOLD, 12);
+ private final Color SELECTED_COLOR = new Color(10, 50, 180, 20);
+ private final Color SELECTED_FONT_COLOR = new Color(0, 150, 255, 150);
+ private final List<Icon> icons;
+
+ public VisualPropCellRenderer(List<Icon> icons) {
+ this.icons = icons;
+ setOpaque(true);
+ }
+
+ public Component getListCellRendererComponent(JList list, Object value, int index,
+ boolean isSelected, boolean cellHasFocus) {
+ final VisualPropertyIcon icon;
+
+ if (icons.size() > index) {
+ icon = (VisualPropertyIcon) icons.get(index);
+ } else
+ icon = null;
+
+ setText(value.toString());
+ setIcon(icon);
+ setFont(isSelected ? SELECTED_FONT : NORMAL_FONT);
+
+ this.setVerticalTextPosition(SwingConstants.CENTER);
+ this.setVerticalAlignment(SwingConstants.CENTER);
+ this.setIconTextGap(120);
+
+ if (value instanceof VisualPropertyType
+ && (((VisualPropertyType) value).getDataType() == String.class)) {
+ final Object defVal = ((VisualPropertyType) value).getDefault(Cytoscape.getVisualMappingManager()
+ .getVisualStyle());
+
+ if (defVal != null) {
+ this.setToolTipText((String) defVal);
+ }
+ }
+
+ setBackground(isSelected ? SELECTED_COLOR : list.getBackground());
+ setForeground(isSelected ? SELECTED_FONT_COLOR : list.getForeground());
+
+ if (icon != null) {
+ setPreferredSize(new Dimension(icon.getIconWidth(), icon.getIconHeight() + 12));
+ }
+
+ this.setBorder(new DropShadowBorder());
+
+ return this;
+ }
+ }
+
+ /*
+ * Draw global color icon
+ */
+ static class GlobalIcon extends VisualPropertyIcon {
+
+ private static final long serialVersionUID = -2292185584380604923L;
+
+ public GlobalIcon(String name, Color color) {
+ super(name, color);
+ }
+
+ public void paintIcon(Component c, Graphics g, int x, int y) {
+ Graphics2D g2d = (Graphics2D) g;
+
+ g2d.setColor(color);
+ g2d.fillRect(5, 3, 50, 32);
+
+ g2d.setStroke(new BasicStroke(1f));
+ g2d.setColor(Color.DARK_GRAY);
+ g2d.drawRect(5, 3, 50, 32);
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/ui/DefaultViewPanel.java b/application/src/main/java/cytoscape/visual/ui/DefaultViewPanel.java
new file mode 100644
index 0000000..251390d
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/DefaultViewPanel.java
@@ -0,0 +1,187 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.visual.ui;
+
+import cytoscape.CyEdge;
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+
+import cytoscape.data.CyAttributes;
+import cytoscape.ding.DingNetworkView;
+
+import cytoscape.giny.CytoscapeFingRootGraph;
+
+import cytoscape.view.CyNetworkView;
+
+import ding.view.DGraphView;
+
+import giny.view.GraphView;
+
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Dimension;
+import java.awt.event.MouseListener;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.swing.JPanel;
+
+
+/**
+ * Panel to show the default properties visually (as graphics).
+ *
+ * @version 0.6
+ * @since Cytoscape 2.5
+ * @author kono
+ */
+public class DefaultViewPanel extends JPanel {
+ private static final int PADDING = 20;
+
+ // Dummy network and its view.
+ private static final CyNetworkView view;
+ private static final CyNetwork dummyNet;
+
+ // Background color of this view.
+ private Color background = Color.white;
+ private static final DefaultViewPanel panel;
+
+ /*
+ * Dummy graph component
+ */
+ private static final CytoscapeFingRootGraph dummyGraph;
+ private static final CyNode source;
+ private static final CyNode target;
+ private static final CyEdge edge;
+
+ static {
+ dummyGraph = new CytoscapeFingRootGraph();
+ source = (CyNode) dummyGraph.getNode(dummyGraph.createNode());
+ source.setIdentifier("Source");
+ target = (CyNode) dummyGraph.getNode(dummyGraph.createNode());
+ target.setIdentifier("Target");
+ edge = (CyEdge) dummyGraph.getEdge(dummyGraph.createEdge(source, target));
+ edge.setIdentifier("dummyInteraction");
+
+ List<CyNode> nodes = new ArrayList<CyNode>();
+ List<CyEdge> edges = new ArrayList<CyEdge>();
+ nodes.add(source);
+ nodes.add(target);
+ edges.add(edge);
+
+ dummyNet = dummyGraph.createNetwork(nodes, edges);
+ dummyNet.setTitle("Default Appearance");
+
+ // Create default view
+ view = new DingNetworkView(dummyNet, "Default Appearence");
+
+ view.setIdentifier(dummyNet.getIdentifier());
+ view.setTitle(dummyNet.getTitle());
+
+ view.getNodeView(source).setOffset(0, 0);
+ view.getNodeView(target).setOffset(150, 10);
+
+ panel = new DefaultViewPanel();
+
+ // Setup dummy attribute values
+ final CyAttributes nodeAttr = Cytoscape.getNodeAttributes();
+ nodeAttr.setAttribute("Source", "hiddenLabel", "Source");
+ nodeAttr.setAttribute("Target", "hiddenLabel", "Target");
+ nodeAttr.setUserVisible("hiddenLabel", false);
+ nodeAttr.setUserEditable("hiddenLabel", false);
+
+ final CyAttributes edgeAttr = Cytoscape.getEdgeAttributes();
+ edgeAttr.setUserVisible("dummyInteraction", false);
+ edgeAttr.setUserEditable("dummyInteraction", false);
+ }
+
+ protected static DefaultViewPanel getDefaultViewPanel() {
+ return panel;
+ }
+
+ /**
+ * Creates a new NodeFullDetailView object.
+ */
+ private DefaultViewPanel() {
+ background = Cytoscape.getVisualMappingManager().getVisualStyle()
+ .getGlobalAppearanceCalculator().getDefaultBackgroundColor();
+ this.setBackground(background);
+ }
+
+ protected void updateBackgroungColor(final Color newColor) {
+ background = newColor;
+ this.setBackground(background);
+ repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ protected void updateView() {
+ Cytoscape.getVisualMappingManager().setNetworkView(view);
+ view.setVisualStyle(Cytoscape.getVisualMappingManager().getVisualStyle().getName());
+
+ final Dimension panelSize = this.getSize();
+ ((DGraphView) view).getCanvas()
+ .setSize(new Dimension((int) panelSize.getWidth() - PADDING,
+ (int) panelSize.getHeight() - PADDING));
+ // TODO: This is not always necessary.
+ view.fitContent();
+
+ final Component canvas = view.getComponent();
+
+ for (MouseListener listener : canvas.getMouseListeners())
+ canvas.removeMouseListener(listener);
+
+ this.removeAll();
+ this.add(canvas);
+
+ canvas.setLocation(PADDING / 2, PADDING / 2);
+
+ Cytoscape.getVisualMappingManager().applyAppearances();
+
+ canvas.setBackground(background);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public GraphView getView() {
+ return view;
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/ui/DiscretePropertySetter.java b/application/src/main/java/cytoscape/visual/ui/DiscretePropertySetter.java
new file mode 100644
index 0000000..8d6ea29
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/DiscretePropertySetter.java
@@ -0,0 +1,72 @@
+package cytoscape.visual.ui;
+
+import java.beans.PropertyChangeListener;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import com.l2fprod.common.propertysheet.DefaultProperty;
+import com.l2fprod.common.propertysheet.PropertyEditorRegistry;
+import com.l2fprod.common.propertysheet.PropertyRendererRegistry;
+
+import cytoscape.visual.VisualPropertyType;
+
+public class DiscretePropertySetter {
+
+ private final PropertyRendererRegistry rendReg;
+ private final PropertyEditorRegistry editorReg;
+
+ private final CellRendererFactory rendFactory;
+ private final CellEditorFactory editorFactory;
+
+ DiscretePropertySetter(final PropertyChangeListener pcl,
+ final PropertyRendererRegistry rendReg,
+ final PropertyEditorRegistry editorReg,
+ final CellRendererFactory rendFactory,
+ final CellEditorFactory editorFactory) {
+
+ this.rendReg = rendReg;
+ this.editorReg = editorReg;
+
+ this.rendFactory = rendFactory;
+ this.editorFactory = editorFactory;
+ }
+
+ protected final <K, V> void setDiscreteProps(final VisualPropertyType type,
+ final Map<K, V> discMapping, Set<K> attrKeys, DefaultProperty parent) {
+ if (attrKeys == null)
+ return;
+
+ V val = null;
+ VizMapperProperty valProp;
+ String strVal;
+
+ final List<VizMapperProperty> children = new ArrayList<VizMapperProperty>();
+
+ for (final K key : attrKeys) {
+ valProp = new VizMapperProperty();
+ strVal = key.toString();
+ valProp.setDisplayName(strVal);
+ valProp.setName(strVal + "-" + type.toString());
+ valProp.setParentProperty(parent);
+
+ val = discMapping.get(key);
+
+
+ if (val != null)
+ valProp.setType(val.getClass());
+
+ children.add(valProp);
+
+ rendReg.registerRenderer(valProp, rendFactory.getCellRenderer(type.getDataType()));
+ editorReg.registerEditor(valProp, editorFactory.getPropertyEditor(type.getDataType()));
+
+ valProp.setValue(val);
+ }
+
+ // Add all children.
+ parent.addSubProperties(children);
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/visual/ui/EdgeBypass.java b/application/src/main/java/cytoscape/visual/ui/EdgeBypass.java
new file mode 100644
index 0000000..daf6ce3
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/EdgeBypass.java
@@ -0,0 +1,78 @@
+/*
+ File: EdgeBypass.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual.ui;
+
+import giny.model.Edge;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.swing.JLabel;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+
+import cytoscape.Cytoscape;
+import cytoscape.visual.VisualPropertyType;
+
+class EdgeBypass extends VizMapBypass {
+ JMenuItem addMenu(Edge e) {
+ graphObj = e;
+ attrs = Cytoscape.getEdgeAttributes();
+
+ JMenu menu = new JMenu("Visual Mapping Bypass");
+ menu.add(new JLabel("Change Edge Visualization"));
+ menu.addSeparator();
+ // horrible, horrible hack
+ BypassHack.setCurrentObject( e );
+
+ for ( VisualPropertyType type : VisualPropertyType.getEdgeVisualPropertyList() )
+ addMenuItem(menu, type);
+
+ addResetAllMenuItem(menu);
+
+ return menu;
+ }
+
+ protected List<String> getBypassNames() {
+ List<String> l = new ArrayList<String>();
+
+ for ( VisualPropertyType type : VisualPropertyType.getEdgeVisualPropertyList() )
+ l.add( type.getBypassAttrName() );
+
+ return l;
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/ui/EdgeBypassMenuListener.java b/application/src/main/java/cytoscape/visual/ui/EdgeBypassMenuListener.java
new file mode 100644
index 0000000..c8fbcab
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/EdgeBypassMenuListener.java
@@ -0,0 +1,67 @@
+/*
+ File: EdgeBypassMenuListener.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual.ui;
+
+import ding.view.EdgeContextMenuListener;
+
+import giny.view.EdgeView;
+
+import javax.swing.JPopupMenu;
+
+
+/**
+ * EdgeBypassMenuListener implements EdgeContextMenuListener
+ * When a node is selected it calls bypass andd add
+ */
+class EdgeBypassMenuListener
+ implements EdgeContextMenuListener {
+ EdgeBypassMenuListener() {
+ }
+
+ /**
+ * @param nodeView The clicked EdgeView
+ * @param menu popup menu to add the Bypass menu
+ */
+ public void addEdgeContextMenuItems(EdgeView edgeView, JPopupMenu menu) {
+ EdgeBypass eb = new EdgeBypass();
+
+ if (menu == null)
+ menu = new JPopupMenu();
+
+ menu.add(eb.addMenu(edgeView.getEdge()));
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/ui/EditorDisplayer.java b/application/src/main/java/cytoscape/visual/ui/EditorDisplayer.java
new file mode 100644
index 0000000..54812ec
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/EditorDisplayer.java
@@ -0,0 +1,233 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.visual.ui;
+
+import giny.view.ObjectPosition;
+
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Font;
+import java.awt.Frame;
+import java.awt.Window;
+
+import javax.swing.Icon;
+import javax.swing.JOptionPane;
+
+import cytoscape.Cytoscape;
+import cytoscape.util.CyColorChooser;
+import cytoscape.visual.ArrowShape;
+import cytoscape.visual.LineStyle;
+import cytoscape.visual.NodeShape;
+import cytoscape.visual.VisualPropertyType;
+import cytoscape.visual.customgraphic.CyCustomGraphics;
+import cytoscape.visual.ui.editors.continuous.C2CMappingEditor;
+import cytoscape.visual.ui.editors.continuous.C2DMappingEditor;
+import cytoscape.visual.ui.editors.continuous.GradientEditorPanel;
+
+/**
+ * Managing value editors in for each data types.<br>
+ * This enum contains both continuous and discrete editors.
+ *
+ * @version 0.5
+ * @since Cytoscape 2.5
+ * @author kono
+ *
+ */
+public enum EditorDisplayer {
+
+ DISCRETE_COLOR(CyColorChooser.class, "showDialog",
+ new Class[] { Component.class, String.class, Color.class },
+ new Object[] { Cytoscape.getDesktop(), "Select Color...", null }, Color.class),
+ DISCRETE_FONT(PopupFontChooser.class, "showDialog",
+ new Class[] { Frame.class, Font.class },
+ new Object[] { Cytoscape.getDesktop(), null }, Font.class),
+ DISCRETE_NUMBER(JOptionPane.class, "showInputDialog",
+ new Class[] { Component.class, Object.class },
+ new Object[] { Cytoscape.getDesktop(), "Please enter new numeric value:" },
+ Number.class),
+ DISCRETE_BOOLEAN(JOptionPane.class, "showInputDialog",
+ new Class[] { Component.class, Object.class, String.class, int.class,
+ Icon.class, Object[].class, Object.class},
+ new Object[] { Cytoscape.getDesktop(), "Please select:", "Select true or false",
+ JOptionPane.QUESTION_MESSAGE, null, new Object[] {true, false}, Boolean.TRUE},
+ Boolean.class),
+ DISCRETE_STRING(JOptionPane.class, "showInputDialog",
+ new Class[] { Component.class, Object.class },
+ new Object[] { Cytoscape.getDesktop(), "Please enter new text value:" },
+ String.class),
+ DISCRETE_SHAPE(ValueSelectDialog.class, "showDialog",
+ new Class[] { VisualPropertyType.class, Window.class },
+ new Object[] { VisualPropertyType.NODE_SHAPE, null }, NodeShape.class),
+ DISCRETE_CUSTOM_GRAPHICS(ValueSelectDialog.class, "showDialog",
+ new Class[] { VisualPropertyType.class, Window.class },
+ new Object[] { VisualPropertyType.NODE_CUSTOM_GRAPHICS_1, null }, CyCustomGraphics.class),
+ DISCRETE_ARROW_SHAPE(ValueSelectDialog.class, "showDialog",
+ new Class[] { VisualPropertyType.class, Window.class },
+ new Object[] { VisualPropertyType.EDGE_SRCARROW_SHAPE, null }, ArrowShape.class),
+ DISCRETE_LINE_STYLE(ValueSelectDialog.class, "showDialog",
+ new Class[] { VisualPropertyType.class, Window.class },
+ new Object[] { VisualPropertyType.EDGE_LINE_STYLE, null }, LineStyle.class),
+ DISCRETE_NODE_LINE_STYLE(ValueSelectDialog.class, "showDialog",
+ new Class[] { VisualPropertyType.class, Window.class },
+ new Object[] { VisualPropertyType.NODE_LINE_STYLE, null }, LineStyle.class),
+ DISCRETE_OBJECT_POSITION(PopupObjectPositionChooser.class, "showDialog",
+ new Class[] { Window.class, ObjectPosition.class, VisualPropertyType.class },
+ new Object[] { Cytoscape.getDesktop(), null, null}, ObjectPosition.class),
+ CONTINUOUS_COLOR(GradientEditorPanel.class, "showDialog",
+ new Class[] { int.class, int.class, String.class, VisualPropertyType.class },
+ new Object[] { 500, 250, "Gradient Editor", null }, Color.class),
+ CONTINUOUS_CONTINUOUS(C2CMappingEditor.class, "showDialog",
+ new Class[] { int.class, int.class, String.class, VisualPropertyType.class },
+ new Object[] { 500, 250, "Continuous-Continuous Editor", null },
+ Number.class),
+ CONTINUOUS_DISCRETE(C2DMappingEditor.class, "showDialog",
+ new Class[] { int.class, int.class, String.class, VisualPropertyType.class },
+ new Object[] { 420, 250, "Continuous-Discrete Editor", null }, Object.class);
+
+ private Class<?> chooserClass;
+ private String command;
+ private Class<?>[] paramTypes;
+ private Object[] parameters;
+ private Class<?> compatibleClass;
+
+ /**
+ * Defines editor type.
+ */
+ public enum EditorType {
+ CONTINUOUS,
+ DISCRETE,
+ PASSTHROUGH;
+ }
+
+
+ private EditorDisplayer(final Class<?> chooserClass, String command, Class<?>[] paramTypes,
+ Object[] parameters, Class<?> compatibleClass) {
+
+ this.chooserClass = chooserClass;
+ this.command = command;
+ this.paramTypes = paramTypes;
+ this.parameters = parameters;
+ this.compatibleClass = compatibleClass;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Class<?> getActionClass() {
+ return chooserClass;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getCommand() {
+ return command;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Class<?>[] getParamTypes() {
+ return this.paramTypes;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object[] getParameters() {
+ return this.parameters;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Class<?> getCompatibleClass() {
+ return this.compatibleClass;
+ }
+
+ public void setParameters(Object[] param) {
+ this.parameters = param;
+ }
+
+
+
+ /**
+ * Returns proper editor displayer object based on visual property type.
+ *
+ * @param type DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static EditorDisplayer getEditor(final VisualPropertyType type, final EditorType editor) {
+ final Class<?> dataType = type.getDataType();
+
+ for (EditorDisplayer command : values()) {
+ if ( (dataType == command.getCompatibleClass())
+ && ((editor == EditorType.CONTINUOUS)
+ && command.toString().startsWith(EditorType.CONTINUOUS.name()) )) {
+ return command;
+ } else if ( (dataType == command.getCompatibleClass()) && (editor == EditorType.DISCRETE)
+ && command.toString().startsWith(EditorType.DISCRETE.name())) {
+
+ // Check special case
+ if (command.equals(DISCRETE_LINE_STYLE) || command.equals(DISCRETE_NODE_LINE_STYLE)) {
+ if (type.equals(VisualPropertyType.EDGE_LINE_STYLE))
+ return DISCRETE_LINE_STYLE;
+ else
+ return DISCRETE_NODE_LINE_STYLE;
+ } else {
+ return command;
+ }
+ }
+ }
+
+ /*
+ * if not found in the loop above, this might be a C2DEditor.
+ */
+ return CONTINUOUS_DISCRETE;
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/ui/EditorManager.java b/application/src/main/java/cytoscape/visual/ui/EditorManager.java
new file mode 100644
index 0000000..c567dd7
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/EditorManager.java
@@ -0,0 +1,4 @@
+package cytoscape.visual.ui;
+
+public interface EditorManager {
+}
diff --git a/application/src/main/java/cytoscape/visual/ui/FontChooser.java b/application/src/main/java/cytoscape/visual/ui/FontChooser.java
new file mode 100644
index 0000000..e0f4870
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/FontChooser.java
@@ -0,0 +1,159 @@
+/*
+ File: FontChooser.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+//--------------------------------------------------------------------------
+// $Revision: 13460 $
+// $Date: 2008-03-12 00:50:05 +0100 (Wed, 12 Mar 2008) $
+// $Author: mes $
+//--------------------------------------------------------------------------
+package cytoscape.visual.ui;
+
+
+//--------------------------------------------------------------------------
+import java.awt.Font;
+import java.awt.GraphicsEnvironment;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+
+import javax.swing.DefaultComboBoxModel;
+import javax.swing.JComboBox;
+import javax.swing.JPanel;
+
+
+//--------------------------------------------------------------------------
+/**
+ * Defines a generalized font chooser class. FontChooser contains three
+ * components to display font face selection.
+ */
+public class FontChooser extends JPanel {
+ private Font selectedFont;
+ protected DefaultComboBoxModel fontFaceModel;
+ protected JComboBox face;
+ protected static final float DEF_SIZE = 12F;
+ protected static Font[] scaledFonts;
+ protected static final Font DEF_FONT = new Font("SansSerif", Font.PLAIN, 1);
+
+ static {
+ scaledFonts = scaleFonts(
+ GraphicsEnvironment.getLocalGraphicsEnvironment().getAllFonts(),
+ DEF_SIZE);
+ }
+
+ /**
+ * Create a FontChooser to choose between all fonts available on the system.
+ */
+ public FontChooser() {
+ this(null);
+ }
+
+ /**
+ * Creates a new FontChooser object.
+ *
+ * @param def DOCUMENT ME!
+ */
+ public FontChooser(Font def) {
+ this(scaledFonts, def);
+ }
+
+ /**
+ * Create a FontChooser to choose between the given array of fonts.
+ */
+ public FontChooser(Font[] srcFonts, Font def) {
+ Font[] displayFonts = scaledFonts;
+
+ if (srcFonts != scaledFonts)
+ displayFonts = scaleFonts(srcFonts, DEF_SIZE);
+
+ this.fontFaceModel = new DefaultComboBoxModel(displayFonts);
+
+ this.face = new JComboBox(fontFaceModel);
+ face.setRenderer(new FontRenderer());
+
+ // set the prototype display for the combo box
+ face.addItemListener(new FontFaceSelectionListener());
+
+ // set the currently selected face, default if null
+ if (def == null)
+ this.selectedFont = DEF_FONT;
+ else
+ this.selectedFont = def.deriveFont(1F);
+
+ face.setEditable(true); // so that we may select the default font
+ face.setSelectedItem(this.selectedFont);
+ face.setEditable(false); // so that users aren't allowed to edit the list
+
+ add(face);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public JComboBox getFaceComboBox() {
+ return face;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Font getSelectedFont() {
+ return selectedFont;
+ }
+
+ private class FontFaceSelectionListener
+ implements ItemListener {
+ public void itemStateChanged(ItemEvent e) {
+ if (e.getStateChange() == ItemEvent.SELECTED) {
+ JComboBox source = (JComboBox) e.getItemSelectable();
+ selectedFont = (Font) source.getSelectedItem();
+ }
+ }
+ }
+
+ private static Font[] scaleFonts(Font[] inFonts, float size) {
+ Font[] outFonts = new Font[inFonts.length];
+ int i = 0;
+
+ for (Font f : inFonts)
+ outFonts[i++] = f.deriveFont(size);
+
+ return outFonts;
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/ui/FontRenderer.java b/application/src/main/java/cytoscape/visual/ui/FontRenderer.java
new file mode 100644
index 0000000..f646ef2
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/FontRenderer.java
@@ -0,0 +1,103 @@
+/*
+ File: FontRenderer.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+//--------------------------------------------------------------------------
+// $Revision: 10007 $
+// $Date: 2007-04-18 05:39:36 +0200 (Wed, 18 Apr 2007) $
+// $Author: kono $
+//--------------------------------------------------------------------------
+package cytoscape.visual.ui;
+
+
+//--------------------------------------------------------------------------
+import java.awt.Component;
+import java.awt.Font;
+
+import javax.swing.DefaultListCellRenderer;
+import javax.swing.JList;
+import javax.swing.UIManager;
+
+
+//--------------------------------------------------------------------------
+/**
+ * FontRenderer describes a class that renders each font name in a
+ * {@link FontChooser}
+ * JList or JComboBox in the face specified.
+ */
+public class FontRenderer extends DefaultListCellRenderer {
+ /**
+ * DOCUMENT ME!
+ *
+ * @param list DOCUMENT ME!
+ * @param value DOCUMENT ME!
+ * @param index DOCUMENT ME!
+ * @param isSelected DOCUMENT ME!
+ * @param cellHasFocus DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Component getListCellRendererComponent(JList list, Object value,
+ int index, boolean isSelected, boolean cellHasFocus) {
+ setComponentOrientation(list.getComponentOrientation());
+
+ if (isSelected) {
+ setBackground(list.getSelectionBackground());
+ setForeground(list.getSelectionForeground());
+ } else {
+ setBackground(list.getBackground());
+ setForeground(list.getForeground());
+ }
+
+ setEnabled(list.isEnabled());
+
+ // just allow a ClassCastException to be thrown if the renderer is not
+ // called correctly. Always display in 12 pt.
+ if (value instanceof Font) {
+ //Font fontValue = ((Font) value).deriveFont(12F);
+ setFont((Font) value);
+ setText(((Font) value).getFontName());
+ } else {
+ setFont(list.getFont());
+ setText((value == null) ? "" : value.toString());
+ }
+
+ setBorder((cellHasFocus)
+ ? UIManager.getBorder("List.focusCellHighlightBorder") : noFocusBorder);
+
+ return this;
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/ui/HideEdgeListener.java b/application/src/main/java/cytoscape/visual/ui/HideEdgeListener.java
new file mode 100644
index 0000000..fb05957
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/HideEdgeListener.java
@@ -0,0 +1,90 @@
+/*
+ File: HideEdgeSelectionMenuListener.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.visual.ui;
+
+import cytoscape.Cytoscape;
+import cytoscape.view.CytoscapeDesktop;
+import cytoscape.view.CyNetworkView;
+import ding.view.EdgeContextMenuListener;
+import giny.view.EdgeView;
+
+import java.awt.event.ActionEvent;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import javax.swing.AbstractAction;
+import javax.swing.JMenuItem;
+import javax.swing.JPopupMenu;
+
+
+/**
+ * Adds EdgeView and EdgeView vizmap bypass listeners to network views as
+ * the views are created.
+ */
+public class HideEdgeListener implements PropertyChangeListener {
+ /**
+ * Listens for NETWORK_VIEW_CREATED events and if it hears one, it adds
+ * a HideEdgeContextMenuListener context menu listener to the view.
+ * @param evnt The event we're being notified of.
+ */
+ public void propertyChange(final PropertyChangeEvent evnt) {
+ if (CytoscapeDesktop.NETWORK_VIEW_CREATED.equals(evnt.getPropertyName())) {
+ final HideEdgeContextMenuListener l = new HideEdgeContextMenuListener();
+ Cytoscape.getCurrentNetworkView().addEdgeContextMenuListener(l);
+ }
+ }
+}
+
+
+class HideEdgeContextMenuListener extends AbstractAction implements EdgeContextMenuListener {
+ private EdgeView nodeView;
+
+ public HideEdgeContextMenuListener() {
+ }
+
+ /**
+ * @param nodeView The clicked EdgeView
+ * @param menu popup menu to add the Bypass menu
+ */
+ public void addEdgeContextMenuItems(final EdgeView nodeView, final JPopupMenu menu) {
+ if (menu == null)
+ return;
+
+ this.nodeView = nodeView;
+ final JMenuItem newMenuItem = new JMenuItem("Hide Edge");
+ newMenuItem.addActionListener(this);
+ menu.add(newMenuItem);
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ final CyNetworkView currentNetworkView = Cytoscape.getCurrentNetworkView();
+ currentNetworkView.hideGraphObject(nodeView);
+ currentNetworkView.updateView();
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/ui/HideNodeListener.java b/application/src/main/java/cytoscape/visual/ui/HideNodeListener.java
new file mode 100644
index 0000000..d00f44d
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/HideNodeListener.java
@@ -0,0 +1,90 @@
+/*
+ File: HideNodeSelectionMenuListener.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.visual.ui;
+
+import cytoscape.Cytoscape;
+import cytoscape.view.CytoscapeDesktop;
+import cytoscape.view.CyNetworkView;
+import ding.view.NodeContextMenuListener;
+import giny.view.NodeView;
+
+import java.awt.event.ActionEvent;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import javax.swing.AbstractAction;
+import javax.swing.JMenuItem;
+import javax.swing.JPopupMenu;
+
+
+/**
+ * Adds NodeView and EdgeView vizmap bypass listeners to network views as
+ * the views are created.
+ */
+public class HideNodeListener implements PropertyChangeListener {
+ /**
+ * Listens for NETWORK_VIEW_CREATED events and if it hears one, it adds
+ * a HideNodeContextMenuListener context menu listener to the view.
+ * @param evnt The event we're being notified of.
+ */
+ public void propertyChange(final PropertyChangeEvent evnt) {
+ if (CytoscapeDesktop.NETWORK_VIEW_CREATED.equals(evnt.getPropertyName())) {
+ final HideNodeContextMenuListener l = new HideNodeContextMenuListener();
+ Cytoscape.getCurrentNetworkView().addNodeContextMenuListener(l);
+ }
+ }
+}
+
+
+class HideNodeContextMenuListener extends AbstractAction implements NodeContextMenuListener {
+ private NodeView nodeView;
+
+ public HideNodeContextMenuListener() {
+ }
+
+ /**
+ * @param nodeView The clicked NodeView
+ * @param menu popup menu to add the Bypass menu
+ */
+ public void addNodeContextMenuItems(final NodeView nodeView, final JPopupMenu menu) {
+ if (menu == null)
+ return;
+
+ this.nodeView = nodeView;
+ final JMenuItem newMenuItem = new JMenuItem("Hide Node");
+ newMenuItem.addActionListener(this);
+ menu.add(newMenuItem);
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ final CyNetworkView currentNetworkView = Cytoscape.getCurrentNetworkView();
+ currentNetworkView.hideGraphObject(nodeView);
+ currentNetworkView.updateView();
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/ui/LabelPlacerControl.java b/application/src/main/java/cytoscape/visual/ui/LabelPlacerControl.java
new file mode 100644
index 0000000..3405ad2
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/LabelPlacerControl.java
@@ -0,0 +1,234 @@
+/*
+ File: LabelPlacerControl.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual.ui;
+
+import giny.view.Label;
+
+import java.awt.GridLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+
+import javax.swing.BoxLayout;
+import javax.swing.JComboBox;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JTextField;
+
+import cytoscape.logger.CyLogger;
+import cytoscape.visual.LabelPosition;
+
+
+/**
+ * A group of widgets that specifies the placement of
+ * node labels.
+ *
+ * Deprecated. Will be removed 03/2011
+ * @deprecated
+ */
+ at Deprecated
+class LabelPlacerControl extends JPanel
+ implements ActionListener, PropertyChangeListener {
+ private LabelPosition lp;
+ private JComboBox justifyCombo;
+ private JTextField xoffsetBox;
+ private JTextField yoffsetBox;
+ private JComboBox nodeAnchors;
+ private JComboBox labelAnchors;
+ private LabelPlacerGraphic labelPlacer;
+ private boolean ignoreEvents;
+
+ LabelPlacerControl(LabelPosition pos) {
+ super();
+
+ if (pos == null)
+ lp = new LabelPosition();
+ else
+ lp = pos;
+
+ ignoreEvents = false;
+
+ setLayout(new BoxLayout(this, BoxLayout.Y_AXIS));
+
+ JPanel anchorNames = new JPanel();
+ anchorNames.setLayout(new GridLayout(2, 2));
+
+ String[] points = LabelPosition.getAnchorNames();
+
+ JLabel nodeAnchorLabel = new JLabel("Node Anchor Points ");
+ nodeAnchors = new JComboBox(points);
+ nodeAnchors.addActionListener(this);
+ anchorNames.add(nodeAnchorLabel);
+ anchorNames.add(nodeAnchors);
+
+ JLabel labelAnchorLabel = new JLabel("Label Anchor Points");
+ labelAnchors = new JComboBox(points);
+ labelAnchors.addActionListener(this);
+ anchorNames.add(labelAnchorLabel);
+ anchorNames.add(labelAnchors);
+
+ add(anchorNames);
+
+ JPanel justifyPanel = new JPanel();
+ justifyPanel.setLayout(new GridLayout(1, 2));
+
+ JLabel justifyLabel = new JLabel("Label Justification");
+ String[] justifyTypes = LabelPosition.getJustifyNames();
+ justifyCombo = new JComboBox(justifyTypes);
+ justifyCombo.addActionListener(this);
+ justifyPanel.add(justifyLabel);
+ justifyPanel.add(justifyCombo);
+
+ add(justifyPanel);
+
+ JPanel offsetPanel = new JPanel();
+ offsetPanel.setLayout(new GridLayout(2, 2));
+
+ JLabel xoffsetLabel = new JLabel("X Offset Value (can be negative)");
+ xoffsetBox = new JTextField("0", 8);
+ xoffsetBox.addActionListener(this);
+ offsetPanel.add(xoffsetLabel);
+ offsetPanel.add(xoffsetBox);
+
+ JLabel yoffsetLabel = new JLabel("Y Offset Value (can be negative)");
+ yoffsetBox = new JTextField("0", 8);
+ yoffsetBox.addActionListener(this);
+ offsetPanel.add(yoffsetLabel);
+ offsetPanel.add(yoffsetBox);
+
+ add(offsetPanel);
+
+ applyPosition();
+ }
+
+ private void applyPosition() {
+ ignoreEvents = true; // so that we don't pay attention to events generated from these calls
+
+ int nodeAnchor = lp.getTargetAnchor();
+ int labelAnchor = lp.getLabelAnchor();
+
+ if (nodeAnchor == Label.NONE)
+ nodeAnchors.setSelectedIndex(-1);
+ else
+ nodeAnchors.setSelectedItem(LabelPosition.convert(nodeAnchor));
+
+ if (labelAnchor == Label.NONE)
+ labelAnchors.setSelectedIndex(-1);
+ else
+ labelAnchors.setSelectedItem(LabelPosition.convert(labelAnchor));
+
+ justifyCombo.setSelectedItem(LabelPosition.convert(lp.getJustify()));
+ xoffsetBox.setText(new Integer((int) lp.getOffsetX()).toString());
+ yoffsetBox.setText(new Integer((int) lp.getOffsetY()).toString());
+ ignoreEvents = false;
+ repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ // ignore events that are generated by setting values to match
+ // the graphic
+ if (ignoreEvents)
+ return;
+
+ Object source = e.getSource();
+ boolean changed = false;
+
+ if (source == nodeAnchors) {
+ lp.setTargetAnchor(
+ LabelPosition.convert((String) nodeAnchors.getSelectedItem()));
+ changed = true;
+ }
+
+ if (source == labelAnchors) {
+ lp.setLabelAnchor(
+ LabelPosition.convert((String) labelAnchors.getSelectedItem()));
+ changed = true;
+ }
+
+ if (source == justifyCombo) {
+ lp.setJustify(
+ LabelPosition.convert((String) justifyCombo.getSelectedItem()));
+ changed = true;
+ }
+
+ // handle both at the same time since people might forget to press enter
+ if ((getOffset(xoffsetBox) != lp.getOffsetX()) ||
+ (getOffset(yoffsetBox) != lp.getOffsetY())) {
+ lp.setOffsetX(getOffset(xoffsetBox));
+ lp.setOffsetY(getOffset(yoffsetBox));
+ changed = true;
+ }
+
+ if (!changed)
+ return; // nothing we care about has changed
+
+ firePropertyChange(ObjectPlacerGraphic.OBJECT_POSITION_CHANGED, null, lp);
+ }
+
+ private double getOffset(JTextField jtf) {
+ try {
+ double d = Double.parseDouble(jtf.getText());
+
+ return d;
+ } catch (Exception ex) {
+ CyLogger.getLogger().warn("not a number!");
+ jtf.setText("0");
+
+ return 0.0;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void propertyChange(PropertyChangeEvent e) {
+ String type = e.getPropertyName();
+
+ if (type.equals(ObjectPlacerGraphic.OBJECT_POSITION_CHANGED)) {
+ lp = (LabelPosition) e.getNewValue();
+ applyPosition();
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/ui/LabelPlacerGraphic.java b/application/src/main/java/cytoscape/visual/ui/LabelPlacerGraphic.java
new file mode 100644
index 0000000..363ad17
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/LabelPlacerGraphic.java
@@ -0,0 +1,492 @@
+/*
+ File: LabelPlacerGraphic.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual.ui;
+
+import giny.view.Label;
+
+import java.awt.BasicStroke;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.Point;
+import java.awt.RenderingHints;
+import java.awt.Stroke;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseMotionAdapter;
+import java.awt.geom.Point2D;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+
+import javax.swing.JPanel;
+
+import cytoscape.visual.LabelPosition;
+
+
+/**
+ * A drag and drop graphic that allows users to set the placement
+ * of node labels.
+ *
+ * Deprecated. Use ObjectPlacerGraphic instead. Will be removed 03/2011
+ *
+ * @deprecated
+ */
+ at Deprecated
+public class LabelPlacerGraphic extends JPanel implements PropertyChangeListener {
+ private LabelPosition lp;
+
+ // dimensions of panel
+ private int default_xy = 500;
+ private int xy;
+ private int center;
+ private float offsetRatio;
+
+ // dimensions for node box
+ private int nxy;
+
+ // locations of node points
+ private int[] npoints;
+
+ // dimensions for label box
+ private int lx;
+ private int ly;
+
+ // locations for label points
+ private int[] lxpoints;
+ private int[] lypoints;
+
+ // diameter of a point
+ private int dot;
+
+ // x/y positions for label box, initially offset
+ private int xPos;
+ private int yPos;
+
+ // indices of the closest points
+ private int bestLabelX = 1;
+ private int bestLabelY = 1;
+ private int bestNodeX = 1;
+ private int bestNodeY = 1;
+
+ // mouse drag state
+ private boolean beenDragged = false;
+ private boolean canOffsetDrag = false;
+
+ // click offset
+ private int xClickOffset = 0;
+ private int yClickOffset = 0;
+
+ // the x and y offsets for the label rendering
+ private int xOffset;
+ private int yOffset;
+
+ // default text justify rule
+ private int justify;
+
+ // used to label box and node
+ private Color transparentRed = new Color(1.0f, 0.0f, 0.0f, 0.1f);
+ private Color transparentBlue = new Color(0.0f, 0.0f, 1.0f, 0.1f);
+ private Color transparentMagenta = new Color(0.0f, 0.0f, 1.0f, 0.05f);
+
+ // used to determine the render level of detail
+ private boolean renderDetail;
+
+ // strings for the graphic
+ private String label = "LABEL";
+ private String node = "NODE";
+ private String click = "CLICK 'N DRAG";
+
+ // font metrics for strings
+ private int labelLen = 0;
+ private int nodeLen = 0;
+ private int clickLen = 0;
+ private int ascent = 0;
+ private int detailStrokeWidth = 3;
+ private int lowStrokeWidth = 1;
+ private Stroke detailStroke = new BasicStroke(detailStrokeWidth);
+ private Stroke lowStroke = new BasicStroke(lowStrokeWidth);
+
+ private double gravityDistance = 10;
+
+ /**
+ * A gui for placing a label relative to a node. Draws the graphic
+ * in full detail at a size of 500 pixels.
+ * @param pos initial label position
+ */
+ public LabelPlacerGraphic(LabelPosition pos) {
+ this(pos, 500, true);
+ }
+
+ /**
+ * A gui for placing a label relative to a node.
+ * @param pos initial label position
+ * @param size number of pixels square the that graphic should be
+ * @param fullDetail whether or not to render at full detail or not
+ */
+ public LabelPlacerGraphic(LabelPosition pos, int size, boolean fullDetail) {
+ super();
+
+ if (pos == null)
+ lp = new LabelPosition();
+ else
+ lp = pos;
+
+ renderDetail = fullDetail;
+
+ initSize(size);
+
+ setPreferredSize(new Dimension(xy, xy));
+ setBackground(Color.white);
+
+
+ addMouseListener(new MouseClickHandler());
+ addMouseMotionListener(new MouseDragHandler());
+
+ applyPosition();
+
+ repaint();
+ }
+
+ private void initSize(int size) {
+ // dimensions of panel
+ xy = size;
+ center = xy / 2;
+
+ offsetRatio = (float) xy / (float) default_xy;
+
+ // dimensions for node box
+ nxy = (int) (0.3 * xy);
+
+ // locations of node points
+ int[] tnpoints = { center - (nxy / 2), center, center + (nxy / 2) };
+ npoints = tnpoints;
+
+ // dimensions for label box
+ lx = (int) (0.4 * xy);
+ ly = (int) (0.1 * xy);
+
+ // locations for label points
+ int[] tlxpoints = { 0, lx / 2, lx };
+ int[] tlypoints = { 0, ly / 2, ly };
+ lxpoints = tlxpoints;
+ lypoints = tlypoints;
+
+ // diameter of a point
+ dot = (int) (0.02 * xy);
+
+ // x/y positions for label box, initially offset
+ xPos = dot;
+ yPos = dot;
+ }
+
+ /**
+ * The method that handles the rendering of placement gui.
+ */
+ public void paint(Graphics gin) {
+ Graphics2D g = (Graphics2D) gin;
+
+ g.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
+
+ // calculate the font
+ if (labelLen <= 0) {
+ FontMetrics fm = g.getFontMetrics();
+ labelLen = fm.stringWidth(label);
+ nodeLen = fm.stringWidth(node);
+ clickLen = fm.stringWidth(click);
+ ascent = fm.getMaxAscent();
+ }
+
+ // clear the screen
+ g.setColor(Color.white);
+ g.fillRect(0, 0, xy, xy);
+
+ // draw the node box
+ int x = center - (nxy / 2);
+ int y = center - (nxy / 2);
+
+ g.setColor(transparentBlue);
+ g.fillOval(x, y, nxy, nxy);
+
+ if (renderDetail)
+ g.setStroke(detailStroke);
+ else
+ g.setStroke(lowStroke);
+
+ g.setColor(Color.blue);
+ g.drawLine(x, y, x + nxy, y);
+ g.drawLine(x + nxy, y, x + nxy, y + nxy);
+ g.drawLine(x + nxy, y + nxy, x, y + nxy);
+ g.drawLine(x, y + nxy, x, y);
+
+ if (renderDetail) {
+ g.drawString(node, center - (nxy / 12), center - (nxy / 6));
+
+ // draw the node box points
+ g.setColor(Color.black);
+ int gd = (int)((gravityDistance * 2)+(dot/2));
+
+ for (int i = 0; i < npoints.length; i++)
+ for (int j = 0; j < npoints.length; j++) {
+ g.setColor(transparentMagenta);
+ g.fillOval(npoints[i] - (gd / 2), npoints[j] - (gd / 2), gd, gd);
+ if ((i == bestNodeX) && (j == bestNodeY) && !beenDragged)
+ g.setColor(Color.yellow);
+ else
+ g.setColor(Color.black);
+ g.fillOval(npoints[i] - (dot / 2), npoints[j] - (dot / 2), dot, dot);
+ }
+ }
+
+ // draw the label box
+ g.setColor(transparentRed);
+ g.fillRect(xOffset + xPos, yOffset + yPos, lx, ly);
+
+ g.setColor(Color.red);
+ g.drawLine(xOffset + xPos, yOffset + yPos, xOffset + xPos + lx, yOffset + yPos);
+ g.drawLine(xOffset + xPos + lx, yOffset + yPos, xOffset + xPos + lx, yOffset + yPos + ly);
+ g.drawLine(xOffset + xPos + lx, yOffset + yPos + ly, xOffset + xPos, yOffset + yPos + ly);
+ g.drawLine(xOffset + xPos, yOffset + yPos + ly, xOffset + xPos, yOffset + yPos);
+
+ // draw the string in the justified location
+ if (renderDetail) {
+ int vspace = (ly - ascent - ascent) / 3;
+
+ if (justify == Label.JUSTIFY_LEFT) {
+ g.drawString(label, xOffset + xPos + detailStrokeWidth,
+ yOffset + yPos + vspace + ascent);
+ g.drawString(click, xOffset + xPos + detailStrokeWidth,
+ yOffset + yPos + (2 * (vspace + ascent)));
+ } else if (justify == Label.JUSTIFY_RIGHT) {
+ g.drawString(label, xOffset + xPos + (lx - labelLen),
+ yOffset + yPos + vspace + ascent);
+ ;
+ g.drawString(click, xOffset + xPos + (lx - clickLen),
+ yOffset + yPos + (2 * (vspace + ascent)));
+ } else { // center
+ g.drawString(label, (xOffset + xPos + ((lx - labelLen) / 2)) - detailStrokeWidth,
+ yOffset + yPos + vspace + ascent);
+ g.drawString(click, (xOffset + xPos + ((lx - clickLen) / 2)) - detailStrokeWidth,
+ yOffset + yPos + (2 * (vspace + ascent)));
+ }
+ } else {
+ g.setColor(Color.gray);
+
+ if (justify == Label.JUSTIFY_LEFT)
+ g.drawLine(xOffset + xPos + lowStrokeWidth, yOffset + yPos + (ly / 2),
+ xOffset + xPos + (lx / 3), yOffset + yPos + (ly / 2));
+ else if (justify == Label.JUSTIFY_RIGHT)
+ g.drawLine(xOffset + xPos + ((2 * lx) / 3), yOffset + yPos + (ly / 2),
+ xOffset + xPos + lx, yOffset + yPos + (ly / 2));
+ else
+ g.drawLine(xOffset + xPos + (lx / 3), yOffset + yPos + (ly / 2),
+ (xOffset + xPos + ((2 * lx) / 3)) - lowStrokeWidth,
+ yOffset + yPos + (ly / 2));
+ }
+
+ if (renderDetail) {
+ // draw the label box points
+ g.setColor(Color.black);
+
+ for (int i = 0; i < lxpoints.length; i++)
+ for (int j = 0; j < lypoints.length; j++) {
+ if ((i == bestLabelX) && (j == bestLabelY) && !beenDragged)
+ g.setColor(Color.yellow);
+
+ g.fillOval((xPos + xOffset + lxpoints[i]) - (dot / 2),
+ (yPos + yOffset + lypoints[j]) - (dot / 2),
+ dot, dot);
+
+ if ((i == bestLabelX) && (j == bestLabelY))
+ g.setColor(Color.black);
+ }
+ }
+ }
+
+ private class MouseClickHandler extends MouseAdapter {
+ /**
+ * Only allows dragging if we're in the label box.
+ * Also sets the offset from where the click is and where
+ * the box is, so the box doesn't appear to jump around
+ * too much.
+ */
+ public void mousePressed(MouseEvent e) {
+ int x = e.getX();
+ int y = e.getY();
+
+ // click+drag within box
+ if ((x >= (xPos + xOffset)) && (x <= (xPos + xOffset + lx)) &&
+ (y >= (yPos + yOffset)) && (y <= (yPos + yOffset + ly))) {
+ canOffsetDrag = true;
+ xClickOffset = x - xPos;
+ yClickOffset = y - yPos;
+ }
+ }
+
+ /**
+ * Finds the closest points once the dragging is finished.
+ */
+ public void mouseReleased(MouseEvent e) {
+ if (beenDragged) {
+
+ int x = e.getX();
+ int y = e.getY();
+
+ // top right
+ xPos = x - xClickOffset + xOffset;
+ yPos = y - yClickOffset + yOffset;
+
+ double best = Double.POSITIVE_INFINITY;
+ double offX = 0;
+ double offY = 0;
+
+ // loop over each point in the node box
+ for (int i = 0; i < npoints.length; i++) {
+ for (int j = 0; j < npoints.length; j++) {
+ Point nodePoint = new Point(npoints[i] - (dot / 2), npoints[j] - (dot / 2));
+
+ // loop over each point in the label box
+ for (int a = 0; a < lxpoints.length; a++) {
+ for (int b = 0; b < lypoints.length; b++) {
+ Point labelPoint = new Point((xPos + lxpoints[a]) - (dot / 2),
+ (yPos + lypoints[b]) - (dot / 2));
+
+ double dist = labelPoint.distance((Point2D) nodePoint);
+
+ if (dist < best) {
+ best = dist;
+ bestLabelX = a;
+ bestLabelY = b;
+ bestNodeX = i;
+ bestNodeY = j;
+ offX = labelPoint.getX() - nodePoint.getX();
+ offY = labelPoint.getY() - nodePoint.getY();
+ }
+ }
+ }
+ }
+ }
+
+ xPos = npoints[bestNodeX] - lxpoints[bestLabelX];
+ yPos = npoints[bestNodeY] - lypoints[bestLabelY];
+
+ if ( Math.sqrt(offX*offX + offY*offY) > (gravityDistance+(dot/2)) ) {
+ xOffset = (int)offX;
+ yOffset = (int)offY;
+ } else {
+ xOffset = 0;
+ yOffset = 0;
+ }
+
+ lp.setOffsetX(xOffset);
+ lp.setOffsetY(yOffset);
+ lp.setLabelAnchor(bestLabelX + (3 * bestLabelY));
+ lp.setTargetAnchor(bestNodeX + (3 * bestNodeY));
+ firePropertyChange(ObjectPlacerGraphic.OBJECT_POSITION_CHANGED, null, lp);
+
+ repaint();
+ beenDragged = false;
+ canOffsetDrag = false;
+ }
+ }
+ }
+
+ private class MouseDragHandler extends MouseMotionAdapter {
+ /**
+ * Handles redrawing for dragging.
+ */
+ public void mouseDragged(MouseEvent e) {
+ // dragging within normal box
+ if (canOffsetDrag) {
+ xPos = e.getX() - xClickOffset;
+ yPos = e.getY() - yClickOffset;
+
+ beenDragged = true;
+ repaint();
+ }
+ }
+ }
+
+ /**
+ * Finds the points on the Label box and Node box that are closest.
+ */
+ private void findClosestPoint() {
+
+ }
+
+ /**
+ * Applies the new LabelPosition to the graphic.
+ */
+ private void applyPosition() {
+ xOffset = (int) (lp.getOffsetX() * offsetRatio);
+ yOffset = (int) (lp.getOffsetY() * offsetRatio);
+ justify = lp.getJustify();
+
+ int nodeAnchor = lp.getTargetAnchor();
+
+ if (nodeAnchor != Label.NONE) {
+ bestNodeX = nodeAnchor % 3;
+ bestNodeY = (int) nodeAnchor / 3;
+ }
+
+ int labelAnchor = lp.getLabelAnchor();
+
+ if (labelAnchor != Label.NONE) {
+ bestLabelX = labelAnchor % 3;
+ bestLabelY = (int) labelAnchor / 3;
+ }
+
+ if ((nodeAnchor != Label.NONE) || (labelAnchor != Label.NONE)) {
+ xPos = npoints[bestNodeX] - lxpoints[bestLabelX];
+ yPos = npoints[bestNodeY] - lypoints[bestLabelY];
+ }
+ }
+
+ /**
+ * Handles all property changes that the panel listens for.
+ */
+ public void propertyChange(PropertyChangeEvent e) {
+ String type = e.getPropertyName();
+
+ if (type.equals(ObjectPlacerGraphic.OBJECT_POSITION_CHANGED)) {
+ lp = (LabelPosition) e.getNewValue();
+ applyPosition();
+ repaint();
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/ui/LegendDialog.java b/application/src/main/java/cytoscape/visual/ui/LegendDialog.java
new file mode 100644
index 0000000..64b0ab2
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/LegendDialog.java
@@ -0,0 +1,191 @@
+/*
+ * LegendDialog.java
+ */
+package cytoscape.visual.ui;
+
+import cytoscape.visual.EdgeAppearanceCalculator;
+import cytoscape.visual.NodeAppearanceCalculator;
+import cytoscape.visual.VisualPropertyType;
+import cytoscape.visual.VisualStyle;
+import cytoscape.visual.VisualProperty;
+
+import cytoscape.visual.calculators.Calculator;
+
+import cytoscape.visual.mappings.ObjectMapping;
+import cytoscape.visual.mappings.PassThroughMapping;
+
+import org.freehep.util.export.ExportDialog;
+
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Dialog;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import java.util.List;
+
+import javax.swing.BoxLayout;
+import javax.swing.JButton;
+import javax.swing.JDialog;
+import javax.swing.JFrame;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.border.EmptyBorder;
+import javax.swing.border.LineBorder;
+import javax.swing.border.TitledBorder;
+
+
+/**
+ *
+ */
+public class LegendDialog extends JDialog {
+ private VisualStyle visualStyle;
+ private JPanel jPanel1;
+ private JButton jButton1;
+ private JButton jButton2;
+ private JScrollPane jScrollPane1;
+ private Component parent;
+
+ /**
+ * Creates a new LegendDialog object.
+ *
+ * @param parent DOCUMENT ME!
+ * @param vs DOCUMENT ME!
+ */
+ public LegendDialog(Dialog parent, VisualStyle vs) {
+ super(parent, true);
+ visualStyle = vs;
+ this.parent = parent;
+ initComponents();
+ }
+
+ /**
+ * Creates a new LegendDialog object.
+ *
+ * @param parent DOCUMENT ME!
+ * @param vs DOCUMENT ME!
+ */
+ public LegendDialog(JFrame parent, VisualStyle vs) {
+ super(parent, true);
+ visualStyle = vs;
+ this.parent = parent;
+ initComponents();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param visualStyle DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static JPanel generateLegendPanel(VisualStyle visualStyle) {
+ final JPanel legend = new JPanel();
+
+ final NodeAppearanceCalculator nac = visualStyle.getNodeAppearanceCalculator();
+ final List<Calculator> nodeCalcs = nac.getCalculators();
+ final EdgeAppearanceCalculator eac = visualStyle.getEdgeAppearanceCalculator();
+ final List<Calculator> edgeCalcs = eac.getCalculators();
+
+ ObjectMapping om;
+
+ /*
+ * Set layout
+ */
+ legend.setLayout(new BoxLayout(legend, BoxLayout.Y_AXIS));
+ legend.setBackground(Color.white);
+
+ legend.setBorder(new TitledBorder(new LineBorder(Color.DARK_GRAY, 2),
+ "Visual Legend for " + visualStyle.getName(),
+ TitledBorder.DEFAULT_JUSTIFICATION, TitledBorder.CENTER,
+ new Font("SansSerif", Font.BOLD, 16), Color.DARK_GRAY));
+
+ for (Calculator calc : nodeCalcs) {
+ // check to see if the Calculator has a constraint on it (like node size lock)
+ VisualProperty vp = calc.getVisualPropertyType().getVisualProperty();
+ if ( vp.constrained( visualStyle.getDependency() ) )
+ continue;
+
+ om = calc.getMapping(0);
+
+ JPanel mleg = om.getLegend(calc.getVisualPropertyType());
+
+ // Add passthrough mappings to the top since they don't
+ // display anything besides the title.
+ if (om instanceof PassThroughMapping)
+ legend.add(mleg, 0);
+ else
+ legend.add(mleg);
+
+ // Set padding
+ mleg.setBorder(new EmptyBorder(15, 30, 15, 30));
+ }
+
+ int top = legend.getComponentCount();
+
+ for (Calculator calc : edgeCalcs) {
+ om = calc.getMapping(0);
+
+ JPanel mleg = om.getLegend(calc.getVisualPropertyType());
+
+ // Add passthrough mappings to the top since they don't
+ // display anything besides the title.
+ if (om instanceof PassThroughMapping)
+ legend.add(mleg, 0);
+ else
+ legend.add(mleg);
+
+ // Set padding
+ mleg.setBorder(new EmptyBorder(15, 30, 15, 30));
+ }
+
+ return legend;
+ }
+
+ private void initComponents() {
+ this.setTitle("Visual Legend for " + visualStyle.getName());
+
+ jPanel1 = generateLegendPanel(visualStyle);
+
+ jScrollPane1 = new JScrollPane();
+ jScrollPane1.setViewportView(jPanel1);
+
+ jButton1 = new JButton();
+ jButton1.setText("Export");
+ jButton1.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent evt) {
+ export();
+ }
+ });
+
+ jButton2 = new JButton();
+ jButton2.setText("Done");
+ jButton2.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent evt) {
+ dispose();
+ }
+ });
+
+ JPanel buttonPanel = new JPanel();
+ buttonPanel.add(jButton1);
+ buttonPanel.add(jButton2);
+
+ JPanel containerPanel = new JPanel();
+ containerPanel.setLayout(new BoxLayout(containerPanel, BoxLayout.Y_AXIS));
+ containerPanel.add(jScrollPane1);
+ containerPanel.add(buttonPanel);
+
+ setContentPane(containerPanel);
+ setPreferredSize(new Dimension(650, 500));
+ pack();
+ repaint();
+ }
+
+ private void export() {
+ ExportDialog export = new ExportDialog();
+ export.showExportDialog(parent, "Export legend as ...", jPanel1, "export");
+ dispose();
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/ui/MapperAndAttribute.java b/application/src/main/java/cytoscape/visual/ui/MapperAndAttribute.java
new file mode 100644
index 0000000..2d3c8f1
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/MapperAndAttribute.java
@@ -0,0 +1,75 @@
+/*
+ File: MapperAndAttribute.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// MapperAndAttribute.java
+//------------------------------------------------------------------------
+// $Revision: 10007 $
+// $Date: 2007-04-18 05:39:36 +0200 (Wed, 18 Apr 2007) $
+// $Author: kono $
+//------------------------------------------------------------------------
+package cytoscape.visual.ui;
+
+
+//------------------------------------------------------------------------
+import cytoscape.util.MutableString;
+
+
+//------------------------------------------------------------------------
+/**
+ *
+ */
+public class MapperAndAttribute {
+ Object mapper;
+ MutableString attribute;
+
+ /**
+ * Creates a new MapperAndAttribute object.
+ */
+ public MapperAndAttribute() {
+ }
+
+ /**
+ * Creates a new MapperAndAttribute object.
+ *
+ * @param newMapper DOCUMENT ME!
+ * @param newAttribute DOCUMENT ME!
+ */
+ public MapperAndAttribute(Object newMapper, MutableString newAttribute) {
+ this.mapper = newMapper;
+ this.attribute = newAttribute;
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/ui/MappingKeyFactory.java b/application/src/main/java/cytoscape/visual/ui/MappingKeyFactory.java
new file mode 100644
index 0000000..be8f6fa
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/MappingKeyFactory.java
@@ -0,0 +1,91 @@
+package cytoscape.visual.ui;
+
+import giny.model.GraphObject;
+
+import java.util.Arrays;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.TreeSet;
+
+import cytoscape.Cytoscape;
+import cytoscape.data.CyAttributes;
+import cytoscape.data.CyAttributesUtils;
+import cytoscape.visual.mappings.ObjectMapping;
+
+public class MappingKeyFactory {
+
+ public static Set<Object> getKeySet(final String attrName,
+ final CyAttributes attrs, final ObjectMapping mapping,
+ boolean isNode) {
+
+ if (attrName.equals("ID")) {
+ return loadID(isNode);
+ }
+
+ final Map<String, Object> id2AttrValMap = CyAttributesUtils
+ .getAttribute(attrName, attrs);
+
+ if ((id2AttrValMap == null) || (id2AttrValMap.size() == 0))
+ return new TreeSet<Object>();
+
+ final List<Class<?>> acceptedClasses = Arrays.asList(mapping
+ .getAcceptedDataClasses());
+ final Class<?> mapAttrClass = CyAttributesUtils.getClass(attrName,
+ attrs);
+
+ if ((mapAttrClass == null) || !(acceptedClasses.contains(mapAttrClass)))
+ return new TreeSet<Object>(); // Return empty set.
+
+ return loadKeySet(id2AttrValMap);
+ }
+
+ /**
+ * Create String set of node/edge ID.
+ *
+ * @param isNode
+ * @return set of ID
+ */
+ private static Set<Object> loadID(final boolean isNode) {
+ final Set<Object> ids = new TreeSet<Object>();
+
+ final List<GraphObject> obj;
+ if (isNode)
+ obj = Cytoscape.getCurrentNetworkView().getNetwork().nodesList();
+ else
+ obj = Cytoscape.getCurrentNetworkView().getNetwork().edgesList();
+
+ for (GraphObject o : obj)
+ ids.add(o.getIdentifier());
+
+ return ids;
+ }
+
+ /**
+ * Loads the Key Set.
+ */
+ private static Set<Object> loadKeySet(final Map<String, Object> id2AttrMap) {
+ final Set<Object> mappedKeys = new TreeSet<Object>();
+
+ for (final Object attrValue : id2AttrMap.values()) {
+ if(attrValue == null)
+ continue;
+
+ if (attrValue instanceof List<?>) {
+ // This is list, but contents of list is unknown
+ List<?> list = (List<?>) attrValue;
+
+ for (int i = 0; i < list.size(); i++) {
+ final Object vo = list.get(i);
+
+ if (!mappedKeys.contains(vo))
+ mappedKeys.add(vo);
+ }
+ } else {
+ if (!mappedKeys.contains(attrValue))
+ mappedKeys.add(attrValue);
+ }
+ }
+ return mappedKeys;
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/ui/NestedNetworkListener.java b/application/src/main/java/cytoscape/visual/ui/NestedNetworkListener.java
new file mode 100644
index 0000000..7e02ef1
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/NestedNetworkListener.java
@@ -0,0 +1,63 @@
+/*
+ File: VizMapBypassNetworkListener.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual.ui;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.view.CytoscapeDesktop;
+
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+
+
+/**
+ * Adds NodeView and EdgeView vizmap bypass listeners to network views as
+ * the views are created.
+ */
+public class NestedNetworkListener implements PropertyChangeListener {
+ /**
+ * Listens for NETWORK_VIEW_CREATED events and if it hears one, it adds
+ * SetNestedNetwork context menu listeners to the view.
+ * @param evnt The event we're hearing.
+ */
+ public void propertyChange(PropertyChangeEvent evnt) {
+ if (CytoscapeDesktop.NETWORK_VIEW_CREATED.equals(evnt.getPropertyName())) {
+ NestedNetworkMenuListener l = new NestedNetworkMenuListener();
+ Cytoscape.getCurrentNetworkView().addNodeContextMenuListener(l);
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/ui/NestedNetworkMenuListener.java b/application/src/main/java/cytoscape/visual/ui/NestedNetworkMenuListener.java
new file mode 100644
index 0000000..e6dbb99
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/NestedNetworkMenuListener.java
@@ -0,0 +1,164 @@
+/*
+ File: NestedNetworkMenuListener.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual.ui;
+
+import ding.view.NodeContextMenuListener;
+import giny.view.NodeView;
+import java.awt.event.ActionEvent;
+import javax.swing.AbstractAction;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JPopupMenu;
+import cytoscape.CyNetwork;
+import cytoscape.view.CyNetworkView;
+import cytoscape.Cytoscape;
+import cytoscape.dialogs.SetNestedNetworkDialog;
+import cytoscape.layout.CyLayoutAlgorithm;
+
+import javax.swing.JOptionPane;
+
+
+/**
+ * NestedNetworkMenuListener implements NodeContextMenuListener
+ * When a node is selected it calls NestedNetwork and add
+ */
+class NestedNetworkMenuListener implements NodeContextMenuListener {
+ NestedNetworkMenuListener() {}
+
+ /**
+ * @param nodeView The clicked NodeView
+ * @param menu popup menu to add the Bypass menu
+ */
+ public void addNodeContextMenuItems(final NodeView nodeView, JPopupMenu menu) {
+ if (menu == null)
+ menu = new JPopupMenu();
+
+ JMenu jm = new JMenu("Nested Network");
+
+ final JMenuItem jm1 = new JCheckBoxMenuItem(new SetNestedNetworkMenuItemAction(nodeView));
+ final JMenuItem jm2 = new JCheckBoxMenuItem(new DeleteNestedNetworkMenuItemAction(nodeView));
+ final JMenuItem jm3 = new JCheckBoxMenuItem(new GotoNestedNetworkMenuItemAction(nodeView));
+
+ if (nodeView.getNode().getNestedNetwork() == null) {
+ jm2.setEnabled(false);
+ jm3.setEnabled(false);
+ }
+
+ jm.add(jm1);
+ jm.add(jm2);
+ jm.add(jm3);
+
+ menu.add(jm);
+ }
+
+
+ private static final class SetNestedNetworkMenuItemAction extends AbstractAction {
+
+ private static final long serialVersionUID = 8460477959913047234L;
+
+ private final NodeView nodeView;
+
+ public SetNestedNetworkMenuItemAction(NodeView nodeView) {
+ super("Set Nested Network");
+ this.nodeView = nodeView;
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ SetNestedNetworkDialog dlg = new SetNestedNetworkDialog(Cytoscape.getDesktop(), true, this.nodeView);
+ dlg.setLocationRelativeTo(Cytoscape.getDesktop());
+ dlg.setVisible(true);
+ }
+ }
+
+
+ static class DeleteNestedNetworkMenuItemAction extends AbstractAction {
+
+ private static final long serialVersionUID = -1413503506096197791L;
+
+ private final NodeView nodeView;
+
+ public DeleteNestedNetworkMenuItemAction(NodeView nodeView) {
+ super("Delete Nested Network");
+ this.nodeView = nodeView;
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ if (this.nodeView.getNode().getNestedNetwork() == null) {
+ return;
+ }
+ int user_says = JOptionPane.showConfirmDialog(Cytoscape.getDesktop(),
+ "Are you sure you want to delete this nested network?","Confirm Delete Nested Network", JOptionPane.YES_NO_OPTION);
+ if (user_says == JOptionPane.NO_OPTION) {
+ return;
+ }
+
+ this.nodeView.getNode().setNestedNetwork(null);
+ }
+ }
+
+
+ private static final class GotoNestedNetworkMenuItemAction extends AbstractAction {
+
+ private static final long serialVersionUID = -2090577740180052939L;
+
+ private final NodeView nodeView;
+
+ public GotoNestedNetworkMenuItemAction(NodeView nodeView) {
+ super("Go to Nested Network");
+ this.nodeView = nodeView;
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ if (this.nodeView.getNode().getNestedNetwork() == null) {
+ return;
+ }
+
+ CyNetwork nestedNetwork = (CyNetwork) this.nodeView.getNode().getNestedNetwork();
+
+ CyNetworkView theView = Cytoscape.getNetworkView(nestedNetwork.getIdentifier());
+ if (theView == null || theView.getIdentifier() == null) {
+ theView = Cytoscape.createNetworkView(nestedNetwork);
+ CyLayoutAlgorithm alg = cytoscape.layout.CyLayouts.getLayout("force-directed");
+ theView.applyLayout(alg);
+
+ }
+
+ Cytoscape.getDesktop().setFocus(nestedNetwork.getIdentifier());
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/ui/NewMappingBuilder.java b/application/src/main/java/cytoscape/visual/ui/NewMappingBuilder.java
new file mode 100644
index 0000000..2958501
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/NewMappingBuilder.java
@@ -0,0 +1,80 @@
+package cytoscape.visual.ui;
+
+import java.lang.reflect.Constructor;
+import java.lang.reflect.InvocationTargetException;
+
+import cytoscape.Cytoscape;
+import cytoscape.visual.CalculatorCatalog;
+import cytoscape.visual.VisualMappingManager;
+import cytoscape.visual.VisualPropertyType;
+import cytoscape.visual.calculators.BasicCalculator;
+import cytoscape.visual.mappings.ObjectMapping;
+
+public class NewMappingBuilder {
+
+ /**
+ * Create new mapping.
+ * @throws NoSuchMethodException
+ * @throws SecurityException
+ * @throws InvocationTargetException
+ * @throws IllegalAccessException
+ * @throws InstantiationException
+ * @throws
+ */
+ static void createNewCalculator(
+ final VisualPropertyType type,
+ final String newMappingName, final String newCalcName,
+ final String controllingAttrName) {
+
+ final VisualMappingManager vmm = Cytoscape.getVisualMappingManager();
+ final CalculatorCatalog catalog = vmm.getCalculatorCatalog();
+
+ Class<?> mapperClass = catalog.getMapping(newMappingName);
+
+ if (mapperClass == null)
+ return;
+
+ // create the selected mapper
+ final Class<?>[] conTypes = { Class.class, String.class };
+ Constructor<?> mapperCon = null;
+ try {
+ mapperCon = mapperClass.getConstructor(conTypes);
+ } catch (SecurityException e) {
+ e.printStackTrace();
+ } catch (NoSuchMethodException e) {
+ e.printStackTrace();
+ }
+
+ if(mapperCon == null)
+ return;
+
+ final Object defaultObj = type.getDefault(vmm.getVisualStyle());
+
+ final Object[] invokeArgs = { defaultObj.getClass(),
+ controllingAttrName };
+ ObjectMapping mapper = null;
+ try {
+ mapper = (ObjectMapping) mapperCon.newInstance(invokeArgs);
+ } catch (IllegalArgumentException e) {
+ e.printStackTrace();
+ } catch (InstantiationException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ } catch (IllegalAccessException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ } catch (InvocationTargetException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+
+ if(mapper == null)
+ return;
+
+ // Register new Calc
+ vmm.getCalculatorCatalog().addCalculator(new BasicCalculator(newCalcName, mapper, type));
+ }
+
+
+
+}
\ No newline at end of file
diff --git a/application/src/main/java/cytoscape/visual/ui/NodeBypass.java b/application/src/main/java/cytoscape/visual/ui/NodeBypass.java
new file mode 100644
index 0000000..29c3c6a
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/NodeBypass.java
@@ -0,0 +1,81 @@
+/*
+ File: NodeBypass.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual.ui;
+
+import giny.model.Node;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.swing.JLabel;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+
+import cytoscape.Cytoscape;
+import cytoscape.visual.VisualPropertyType;
+
+
+class NodeBypass extends VizMapBypass {
+ JMenuItem addMenu(Node n) {
+ graphObj = n;
+ attrs = Cytoscape.getNodeAttributes();
+
+ JMenu menu = new JMenu("Visual Mapping Bypass");
+ menu.add(new JLabel("Change Node Visualization"));
+ menu.addSeparator();
+ // horrible, horrible hack
+ BypassHack.setCurrentObject(n);
+
+ for (VisualPropertyType type : VisualPropertyType.getNodeVisualPropertyList())
+ addMenuItem(menu, type);
+
+ menu.addSeparator();
+
+ addResetAllMenuItem(menu);
+
+ return menu;
+ }
+
+ protected List<String> getBypassNames() {
+ List<String> l = new ArrayList<String>();
+
+ for (VisualPropertyType type : VisualPropertyType.getNodeVisualPropertyList())
+ l.add(type.getBypassAttrName());
+
+ return l;
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/ui/NodeBypassMenuListener.java b/application/src/main/java/cytoscape/visual/ui/NodeBypassMenuListener.java
new file mode 100644
index 0000000..c035379
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/NodeBypassMenuListener.java
@@ -0,0 +1,82 @@
+/*
+ File: NodeBypassMenuListener.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual.ui;
+
+import ding.view.NodeContextMenuListener;
+
+import giny.view.NodeView;
+
+import java.awt.Color;
+import java.awt.Font;
+
+import javax.swing.JLabel;
+import javax.swing.JPopupMenu;
+import javax.swing.border.EmptyBorder;
+
+
+/**
+ * NodeBypassMenuListener implements NodeContextMenuListener
+ * When a node is selected it calls bypass andd add
+ */
+class NodeBypassMenuListener implements NodeContextMenuListener {
+ NodeBypassMenuListener() {
+ }
+
+ /**
+ * @param nodeView The clicked NodeView
+ * @param menu popup menu to add the Bypass menu
+ */
+ public void addNodeContextMenuItems(NodeView nodeView, JPopupMenu menu) {
+ NodeBypass nb = new NodeBypass();
+
+ if (menu == null)
+ menu = new JPopupMenu();
+
+ /*
+ * Add Node ID as label.
+ */
+ final String nodeID = nodeView.getNode().getIdentifier();
+ final JLabel nodeLabel = new JLabel(nodeID);
+
+ nodeLabel.setForeground(new Color(10, 50, 250, 150));
+ nodeLabel.setFont(new Font("SansSerif", Font.BOLD, 18));
+ nodeLabel.setBorder(new EmptyBorder(5, 10, 5, 5));
+ menu.add(nodeLabel);
+
+ menu.add(nb.addMenu(nodeView.getNode()));
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/ui/ObjectPlacerControl.java b/application/src/main/java/cytoscape/visual/ui/ObjectPlacerControl.java
new file mode 100644
index 0000000..4f531cb
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/ObjectPlacerControl.java
@@ -0,0 +1,197 @@
+package cytoscape.visual.ui;
+
+import static giny.view.Position.NONE;
+
+import giny.view.ObjectPosition;
+import giny.view.Position;
+import giny.view.Justification;
+
+import java.awt.GridLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+
+import javax.swing.BoxLayout;
+import javax.swing.JComboBox;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JTextField;
+
+import ding.view.ObjectPositionImpl;
+
+public class ObjectPlacerControl extends JPanel implements ActionListener,
+ PropertyChangeListener {
+
+ private static final long serialVersionUID = 3875032897986523443L;
+
+ private ObjectPosition lp;
+ private JComboBox justifyCombo;
+ private JTextField xoffsetBox;
+ private JTextField yoffsetBox;
+ private JComboBox nodeAnchors;
+ private JComboBox labelAnchors;
+ private boolean ignoreEvents;
+
+ public ObjectPlacerControl(final ObjectPosition pos) {
+ super();
+
+ if (pos == null)
+ lp = new ObjectPositionImpl();
+ else
+ lp = pos;
+
+ ignoreEvents = false;
+
+ setLayout(new BoxLayout(this, BoxLayout.Y_AXIS));
+
+ JPanel anchorNames = new JPanel();
+ anchorNames.setLayout(new GridLayout(2, 2));
+
+ final String[] points = Position.getNames();
+
+ JLabel nodeAnchorLabel = new JLabel("Node Anchor Points ");
+ nodeAnchors = new JComboBox(points);
+ nodeAnchors.addActionListener(this);
+ anchorNames.add(nodeAnchorLabel);
+ anchorNames.add(nodeAnchors);
+
+ JLabel labelAnchorLabel = new JLabel("Object Anchor Points");
+ labelAnchors = new JComboBox(points);
+ labelAnchors.addActionListener(this);
+ anchorNames.add(labelAnchorLabel);
+ anchorNames.add(labelAnchors);
+
+ add(anchorNames);
+
+ JPanel justifyPanel = new JPanel();
+ justifyPanel.setLayout(new GridLayout(1, 2));
+
+ JLabel justifyLabel = new JLabel("Label Justification");
+ final String[] justifyTypes = Justification.getNames();
+ justifyCombo = new JComboBox(justifyTypes);
+ justifyCombo.addActionListener(this);
+ justifyPanel.add(justifyLabel);
+ justifyPanel.add(justifyCombo);
+
+ add(justifyPanel);
+
+ JPanel offsetPanel = new JPanel();
+ offsetPanel.setLayout(new GridLayout(2, 2));
+
+ JLabel xoffsetLabel = new JLabel("X Offset Value (can be negative)");
+ xoffsetBox = new JTextField("0", 8);
+ xoffsetBox.addActionListener(this);
+ offsetPanel.add(xoffsetLabel);
+ offsetPanel.add(xoffsetBox);
+
+ JLabel yoffsetLabel = new JLabel("Y Offset Value (can be negative)");
+ yoffsetBox = new JTextField("0", 8);
+ yoffsetBox.addActionListener(this);
+ offsetPanel.add(yoffsetLabel);
+ offsetPanel.add(yoffsetBox);
+
+ add(offsetPanel);
+
+ applyPosition();
+ }
+
+ private void applyPosition() {
+ ignoreEvents = true; // so that we don't pay attention to events
+ // generated from these calls
+
+ Position nodeAnchor = lp.getTargetAnchor();
+ Position labelAnchor = lp.getAnchor();
+
+ if (nodeAnchor.equals(NONE))
+ nodeAnchors.setSelectedIndex(-1);
+ else
+ nodeAnchors.setSelectedItem(nodeAnchor.getName());
+
+ if (labelAnchor.equals(NONE))
+ labelAnchors.setSelectedIndex(-1);
+ else
+ labelAnchors.setSelectedItem(labelAnchor.getName());
+
+ justifyCombo.setSelectedItem(lp.getJustify().getName());
+ xoffsetBox.setText(new Integer((int) lp.getOffsetX()).toString());
+ yoffsetBox.setText(new Integer((int) lp.getOffsetY()).toString());
+ ignoreEvents = false;
+ repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ // ignore events that are generated by setting values to match
+ // the graphic
+ if (ignoreEvents)
+ return;
+
+ Object source = e.getSource();
+ boolean changed = false;
+
+ if (source == nodeAnchors) {
+ lp.setTargetAnchor(Position.parse(nodeAnchors.getSelectedItem()
+ .toString()));
+ changed = true;
+ }
+
+ if (source == labelAnchors) {
+ lp.setAnchor(Position.parse(labelAnchors.getSelectedItem()
+ .toString()));
+ changed = true;
+ }
+
+ if (source == justifyCombo) {
+ lp.setJustify(Justification.parse(justifyCombo.getSelectedItem()
+ .toString()));
+ changed = true;
+ }
+
+ // handle both at the same time since people might forget to press enter
+ if ((getOffset(xoffsetBox) != lp.getOffsetX())
+ || (getOffset(yoffsetBox) != lp.getOffsetY())) {
+ lp.setOffsetX(getOffset(xoffsetBox));
+ lp.setOffsetY(getOffset(yoffsetBox));
+ changed = true;
+ }
+
+ if (!changed)
+ return; // nothing we care about has changed
+
+ firePropertyChange(ObjectPlacerGraphic.OBJECT_POSITION_CHANGED, null,
+ lp);
+ }
+
+ private double getOffset(JTextField jtf) {
+ try {
+ double d = Double.parseDouble(jtf.getText());
+
+ return d;
+ } catch (Exception ex) {
+ jtf.setText("0");
+ return 0.0;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void propertyChange(PropertyChangeEvent e) {
+ String type = e.getPropertyName();
+
+ if (type.equals(ObjectPlacerGraphic.OBJECT_POSITION_CHANGED)
+ && e.getNewValue() instanceof ObjectPosition) {
+ lp = (ObjectPosition) e.getNewValue();
+ applyPosition();
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/ui/ObjectPlacerGraphic.java b/application/src/main/java/cytoscape/visual/ui/ObjectPlacerGraphic.java
new file mode 100644
index 0000000..727c8ed
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/ObjectPlacerGraphic.java
@@ -0,0 +1,472 @@
+package cytoscape.visual.ui;
+
+import static giny.view.Position.NONE;
+import static giny.view.Justification.*;
+
+import giny.view.ObjectPosition;
+import giny.view.Position;
+import giny.view.Justification;
+
+import java.awt.BasicStroke;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.Point;
+import java.awt.RenderingHints;
+import java.awt.Stroke;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseMotionAdapter;
+import java.awt.geom.Point2D;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+
+import javax.swing.JPanel;
+
+import cytoscape.Cytoscape;
+import ding.view.ObjectPositionImpl;
+
+public class ObjectPlacerGraphic extends JPanel implements
+ PropertyChangeListener {
+
+ private static final long serialVersionUID = -1091948204116900740L;
+
+ protected static final String OBJECT_POSITION_CHANGED = "OBJECT_POSITION_CHANGED";
+
+ private ObjectPosition p;
+
+ // dimensions of panel
+ private static final int DEFAULT_WINDOW_SIZE = 500;
+
+ // "Snap" distance
+ private static final double GRAVITY_DISTANCE = 10;
+
+ // Color scheme for GUI
+ private static final Color transparentRed = new Color(1.0f, 0.0f, 0.0f, 0.1f);
+ private static final Color transparentBlue = new Color(0.0f, 0.0f, 1.0f, 0.1f);
+ private static final Color transparentMagenta = new Color(0.0f, 0.0f, 1.0f, 0.05f);
+
+ private int xy;
+ private int center;
+ private float offsetRatio;
+
+ // dimensions for node box
+ private int nxy;
+
+ // locations of node points
+ private int[] npoints;
+
+ // dimensions for label box
+ private int lx;
+ private int ly;
+
+ // locations for label points
+ private int[] lxpoints;
+ private int[] lypoints;
+
+ // diameter of a point
+ private int dot;
+
+ // x/y positions for label box, initially offset
+ private int xPos;
+ private int yPos;
+
+ // indices of the closest points
+ private int bestLabelX = 1;
+ private int bestLabelY = 1;
+ private int bestNodeX = 1;
+ private int bestNodeY = 1;
+
+ // mouse drag state
+ private boolean beenDragged = false;
+ private boolean canOffsetDrag = false;
+
+ // click offset
+ private int xClickOffset = 0;
+ private int yClickOffset = 0;
+
+ // the x and y offsets for the label rendering
+ private int xOffset;
+ private int yOffset;
+
+ // default text justify rule
+ private Justification justify;
+
+
+
+ // used to determine the render level of detail
+ private boolean renderDetail;
+
+ // strings for the graphic
+ private String objectLabel = "LABEL";
+ private String targetLabel = "NODE";
+ private String click = "CLICK 'N DRAG";
+
+ // font metrics for strings
+ private int labelLen = 0;
+ private int clickLen = 0;
+ private int ascent = 0;
+ private int detailStrokeWidth = 3;
+ private int lowStrokeWidth = 1;
+ private Stroke detailStroke = new BasicStroke(detailStrokeWidth);
+ private Stroke lowStroke = new BasicStroke(lowStrokeWidth);
+
+ private final Dimension objectSize;
+ private final Dimension targetSize;
+
+
+
+ /**
+ * A gui for placing a label relative to a node.
+ *
+ * @param pos
+ * initial label position
+ * @param windowSize
+ * number of pixels square the that graphic should be
+ * @param fullDetail
+ * whether or not to render at full detail or not
+ */
+ public ObjectPlacerGraphic(final ObjectPosition pos, final Integer windowSize,
+ boolean fullDetail, final String objectName, final Dimension objectSize, final Dimension targetSize) {
+ super();
+ this.objectLabel = objectName;
+ this.objectSize = objectSize;
+ this.targetSize = targetSize;
+
+ if(pos == null)
+ p = new ObjectPositionImpl();
+ else
+ p = pos;
+
+ renderDetail = fullDetail;
+
+ if(windowSize == null)
+ initSize(DEFAULT_WINDOW_SIZE);
+ else
+ initSize(windowSize);
+
+ setPreferredSize(new Dimension(xy, xy));
+ setBackground(Color.white);
+
+ addMouseListener(new MouseClickHandler());
+ addMouseMotionListener(new MouseDragHandler());
+
+ applyPosition();
+
+ repaint();
+ }
+
+ private void initSize(int size) {
+ // dimensions of panel
+ xy = size;
+ center = xy / 2;
+
+ offsetRatio = (float) xy / DEFAULT_WINDOW_SIZE;
+
+ // dimensions for node box
+ nxy = (int) (0.3 * xy);
+
+ // locations of node points
+ int[] tnpoints = { center - (nxy / 2), center, center + (nxy / 2) };
+ npoints = tnpoints;
+
+ // dimensions for object box
+ lx = (int) (0.4 * xy);
+ ly = (int) (0.1 * xy);
+
+ // locations for label points
+ int[] tlxpoints = { 0, lx / 2, lx };
+ int[] tlypoints = { 0, ly / 2, ly };
+ lxpoints = tlxpoints;
+ lypoints = tlypoints;
+
+ // diameter of a point
+ dot = (int) (0.02 * xy);
+
+ // x/y positions for label box, initially offset
+ xPos = dot;
+ yPos = dot;
+ }
+
+ /**
+ * The method that handles the rendering of placement gui.
+ */
+ public void paint(Graphics gin) {
+ final Graphics2D g = (Graphics2D) gin;
+
+ g.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+ RenderingHints.VALUE_ANTIALIAS_ON);
+
+ // calculate the font
+ if (labelLen <= 0) {
+ FontMetrics fm = g.getFontMetrics();
+ labelLen = fm.stringWidth(objectLabel);
+ clickLen = fm.stringWidth(click);
+ ascent = fm.getMaxAscent();
+ }
+
+ // clear the screen
+ g.setColor(Color.white);
+ g.fillRect(0, 0, xy, xy);
+
+ // draw the node box
+ int x = center - (nxy / 2);
+ int y = center - (nxy / 2);
+
+ g.setColor(transparentBlue);
+ g.fillOval(x, y, nxy, nxy);
+
+ if (renderDetail)
+ g.setStroke(detailStroke);
+ else
+ g.setStroke(lowStroke);
+
+ g.setColor(Color.blue);
+ g.drawLine(x, y, x + nxy, y);
+ g.drawLine(x + nxy, y, x + nxy, y + nxy);
+ g.drawLine(x + nxy, y + nxy, x, y + nxy);
+ g.drawLine(x, y + nxy, x, y);
+
+ if (renderDetail) {
+ g.drawString(targetLabel, center - (nxy / 12), center - (nxy / 6));
+
+ // draw the node box points
+ g.setColor(Color.black);
+ int gd = (int) ((GRAVITY_DISTANCE * 2) + (dot / 2));
+
+ for (int i = 0; i < npoints.length; i++)
+ for (int j = 0; j < npoints.length; j++) {
+ g.setColor(transparentMagenta);
+ g.fillOval(npoints[i] - (gd / 2), npoints[j] - (gd / 2),
+ gd, gd);
+ if ((i == bestNodeX) && (j == bestNodeY) && !beenDragged)
+ g.setColor(Color.yellow);
+ else
+ g.setColor(Color.black);
+ g.fillOval(npoints[i] - (dot / 2), npoints[j] - (dot / 2),
+ dot, dot);
+ }
+ }
+
+ // draw the label box
+ g.setColor(transparentRed);
+ g.fillRect(xOffset + xPos, yOffset + yPos, lx, ly);
+
+ g.setColor(Color.red);
+ g.drawLine(xOffset + xPos, yOffset + yPos, xOffset + xPos + lx, yOffset
+ + yPos);
+ g.drawLine(xOffset + xPos + lx, yOffset + yPos, xOffset + xPos + lx,
+ yOffset + yPos + ly);
+ g.drawLine(xOffset + xPos + lx, yOffset + yPos + ly, xOffset + xPos,
+ yOffset + yPos + ly);
+ g.drawLine(xOffset + xPos, yOffset + yPos + ly, xOffset + xPos, yOffset
+ + yPos);
+
+ // draw the string in the justified location
+ if (renderDetail) {
+ int vspace = (ly - ascent - ascent) / 3;
+
+ if (justify == JUSTIFY_LEFT) {
+ g.drawString(objectLabel, xOffset + xPos + detailStrokeWidth, yOffset
+ + yPos + vspace + ascent);
+ g.drawString(click, xOffset + xPos + detailStrokeWidth, yOffset
+ + yPos + (2 * (vspace + ascent)));
+ } else if (justify == JUSTIFY_RIGHT) {
+ g.drawString(objectLabel, xOffset + xPos + (lx - labelLen), yOffset
+ + yPos + vspace + ascent);
+ ;
+ g.drawString(click, xOffset + xPos + (lx - clickLen), yOffset
+ + yPos + (2 * (vspace + ascent)));
+ } else { // center
+ g.drawString(objectLabel, (xOffset + xPos + ((lx - labelLen) / 2))
+ - detailStrokeWidth, yOffset + yPos + vspace + ascent);
+ g.drawString(click, (xOffset + xPos + ((lx - clickLen) / 2))
+ - detailStrokeWidth, yOffset + yPos
+ + (2 * (vspace + ascent)));
+ }
+ } else {
+ g.setColor(Color.gray);
+
+ if (justify == JUSTIFY_LEFT)
+ g.drawLine(xOffset + xPos + lowStrokeWidth, yOffset + yPos
+ + (ly / 2), xOffset + xPos + (lx / 3), yOffset + yPos
+ + (ly / 2));
+ else if (justify == JUSTIFY_RIGHT)
+ g.drawLine(xOffset + xPos + ((2 * lx) / 3), yOffset + yPos
+ + (ly / 2), xOffset + xPos + lx, yOffset + yPos
+ + (ly / 2));
+ else
+ g.drawLine(xOffset + xPos + (lx / 3),
+ yOffset + yPos + (ly / 2),
+ (xOffset + xPos + ((2 * lx) / 3)) - lowStrokeWidth,
+ yOffset + yPos + (ly / 2));
+ }
+
+ if (renderDetail) {
+ // draw the label box points
+ g.setColor(Color.black);
+
+ for (int i = 0; i < lxpoints.length; i++)
+ for (int j = 0; j < lypoints.length; j++) {
+ if ((i == bestLabelX) && (j == bestLabelY) && !beenDragged)
+ g.setColor(Color.yellow);
+
+ g.fillOval((xPos + xOffset + lxpoints[i]) - (dot / 2),
+ (yPos + yOffset + lypoints[j]) - (dot / 2), dot,
+ dot);
+
+ if ((i == bestLabelX) && (j == bestLabelY))
+ g.setColor(Color.black);
+ }
+ }
+ }
+
+ private class MouseClickHandler extends MouseAdapter {
+ /**
+ * Only allows dragging if we're in the label box. Also sets the offset
+ * from where the click is and where the box is, so the box doesn't
+ * appear to jump around too much.
+ */
+ public void mousePressed(MouseEvent e) {
+ int x = e.getX();
+ int y = e.getY();
+
+ // click+drag within box
+ if ((x >= (xPos + xOffset)) && (x <= (xPos + xOffset + lx))
+ && (y >= (yPos + yOffset)) && (y <= (yPos + yOffset + ly))) {
+ canOffsetDrag = true;
+ xClickOffset = x - xPos;
+ yClickOffset = y - yPos;
+ }
+ }
+
+ /**
+ * Finds the closest points once the dragging is finished.
+ */
+ public void mouseReleased(MouseEvent e) {
+ if (beenDragged) {
+
+ int x = e.getX();
+ int y = e.getY();
+
+ // top right
+ xPos = x - xClickOffset + xOffset;
+ yPos = y - yClickOffset + yOffset;
+
+ double best = Double.POSITIVE_INFINITY;
+ double offX = 0;
+ double offY = 0;
+
+ // loop over each point in the node box
+ for (int i = 0; i < npoints.length; i++) {
+ for (int j = 0; j < npoints.length; j++) {
+ Point nodePoint = new Point(npoints[i] - (dot / 2),
+ npoints[j] - (dot / 2));
+
+ // loop over each point in the label box
+ for (int a = 0; a < lxpoints.length; a++) {
+ for (int b = 0; b < lypoints.length; b++) {
+ Point labelPoint = new Point(
+ (xPos + lxpoints[a]) - (dot / 2),
+ (yPos + lypoints[b]) - (dot / 2));
+
+ double dist = labelPoint
+ .distance((Point2D) nodePoint);
+
+ if (dist < best) {
+ best = dist;
+ bestLabelX = a;
+ bestLabelY = b;
+ bestNodeX = i;
+ bestNodeY = j;
+ offX = labelPoint.getX() - nodePoint.getX();
+ offY = labelPoint.getY() - nodePoint.getY();
+ }
+ }
+ }
+ }
+ }
+
+ xPos = npoints[bestNodeX] - lxpoints[bestLabelX];
+ yPos = npoints[bestNodeY] - lypoints[bestLabelY];
+
+ if (Math.sqrt(offX * offX + offY * offY) > (GRAVITY_DISTANCE + (dot / 2))) {
+ xOffset = (int) offX;
+ yOffset = (int) offY;
+ } else {
+ xOffset = 0;
+ yOffset = 0;
+ }
+
+ p.setOffsetX(xOffset);
+ p.setOffsetY(yOffset);
+ p.setAnchor(Position.parse(bestLabelX + (3 * bestLabelY)));
+ p.setTargetAnchor(Position.parse(bestNodeX + (3 * bestNodeY)));
+ firePropertyChange(ObjectPlacerGraphic.OBJECT_POSITION_CHANGED, null, p);
+
+ repaint();
+ beenDragged = false;
+ canOffsetDrag = false;
+ }
+ }
+ }
+
+ private class MouseDragHandler extends MouseMotionAdapter {
+ /**
+ * Handles redrawing for dragging.
+ */
+ public void mouseDragged(MouseEvent e) {
+ // dragging within normal box
+ if (canOffsetDrag) {
+ xPos = e.getX() - xClickOffset;
+ yPos = e.getY() - yClickOffset;
+
+ beenDragged = true;
+ repaint();
+ }
+ }
+ }
+
+ /**
+ * Applies the new ObjectPosition to the graphic.
+ */
+ private void applyPosition() {
+ xOffset = (int) (p.getOffsetX() * offsetRatio);
+ yOffset = (int) (p.getOffsetY() * offsetRatio);
+ justify = p.getJustify();
+
+ Position nodeAnchor = p.getTargetAnchor();
+
+ if (nodeAnchor != NONE) {
+ bestNodeX = nodeAnchor.getGinyConstant() % 3;
+ bestNodeY = nodeAnchor.getGinyConstant() / 3;
+ }
+
+ Position labelAnchor = p.getAnchor();
+
+ if (labelAnchor != NONE) {
+ bestLabelX = labelAnchor.getGinyConstant() % 3;
+ bestLabelY = labelAnchor.getGinyConstant() / 3;
+ }
+
+ if ((nodeAnchor != NONE) || (labelAnchor != NONE)) {
+ xPos = npoints[bestNodeX] - lxpoints[bestLabelX];
+ yPos = npoints[bestNodeY] - lypoints[bestLabelY];
+ }
+ }
+
+ /**
+ * Handles all property changes that the panel listens for.
+ */
+ public void propertyChange(PropertyChangeEvent e) {
+ final String type = e.getPropertyName();
+
+ if (type.equals(ObjectPlacerGraphic.OBJECT_POSITION_CHANGED)) {
+ p = (ObjectPosition) e.getNewValue();
+ applyPosition();
+ repaint();
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/ui/PopupFontChooser.java b/application/src/main/java/cytoscape/visual/ui/PopupFontChooser.java
new file mode 100644
index 0000000..2f65c6c
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/PopupFontChooser.java
@@ -0,0 +1,151 @@
+/*
+ File: PopupFontChooser.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual.ui;
+
+import java.awt.BorderLayout;
+import java.awt.Component;
+import java.awt.Container;
+import java.awt.Dialog;
+import java.awt.Font;
+import java.awt.Frame;
+import java.awt.event.ActionEvent;
+
+import javax.swing.AbstractAction;
+import javax.swing.JButton;
+import javax.swing.JDialog;
+import javax.swing.JPanel;
+
+
+/**
+ *
+ */
+public class PopupFontChooser extends JDialog {
+ /**
+ * DOCUMENT ME!
+ *
+ * @param f
+ * DOCUMENT ME!
+ * @param begin
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static Font showDialog(Frame f, Font begin) {
+ final PopupFontChooser fpc = new PopupFontChooser(f, begin);
+ fpc.setModal(true);
+ fpc.setAlwaysOnTop(true);
+ return fpc.getThisFont();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param f
+ * DOCUMENT ME!
+ * @param begin
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static Font showDialog(Dialog f, Font begin) {
+ PopupFontChooser fpc = new PopupFontChooser(f, begin);
+ fpc.setModal(true);
+ fpc.setAlwaysOnTop(true);
+ return fpc.getThisFont();
+ }
+
+ private Font font;
+ private FontChooser chooser;
+
+ private PopupFontChooser(Frame parent, Font begin) {
+ super(parent, true);
+ init(parent, begin);
+ }
+
+ private PopupFontChooser(Dialog parent, Font begin) {
+ super(parent, true);
+ init(parent, begin);
+ }
+
+ private void init(Component parent, Font begin) {
+ this.setTitle("Please select a font...");
+ font = begin;
+
+ if (font == null)
+ chooser = new FontChooser();
+ else
+ chooser = new FontChooser(begin.deriveFont(1F));
+
+ // JComboBox face = chooser.getFaceComboBox();
+ JPanel butPanel = new JPanel(false);
+
+ // buttons - OK/Cancel
+ JButton okBut = new JButton("OK");
+ okBut.addActionListener(
+ new AbstractAction() {
+ public void actionPerformed(ActionEvent e) {
+ font = chooser.getSelectedFont()
+ .deriveFont(12F);
+ dispose();
+ }
+ });
+
+ JButton cancelBut = new JButton("Cancel");
+ cancelBut.addActionListener(
+ new AbstractAction() {
+ public void actionPerformed(ActionEvent e) {
+ dispose();
+ }
+ });
+
+ butPanel.add(okBut);
+ butPanel.add(cancelBut);
+
+ Container content = getContentPane();
+ content.setLayout(new BorderLayout());
+
+ content.add(chooser, BorderLayout.CENTER);
+ content.add(butPanel, BorderLayout.SOUTH);
+ pack();
+ setLocationRelativeTo(parent);
+ setVisible(true);
+ }
+
+ private Font getThisFont() {
+ return font;
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/ui/PopupIconChooser.java b/application/src/main/java/cytoscape/visual/ui/PopupIconChooser.java
new file mode 100644
index 0000000..4aaa412
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/PopupIconChooser.java
@@ -0,0 +1,248 @@
+/*
+ File: PopupIconChooser.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+//----------------------------------------------------------------------------
+// $Revision: 10007 $
+// $Date: 2007-04-18 05:39:36 +0200 (Wed, 18 Apr 2007) $
+// $Author: kono $
+//----------------------------------------------------------------------------
+package cytoscape.visual.ui;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Dialog;
+import java.awt.Dimension;
+import java.awt.Frame;
+import java.awt.GridLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+
+import javax.swing.AbstractAction;
+import javax.swing.BorderFactory;
+import javax.swing.Box;
+import javax.swing.BoxLayout;
+import javax.swing.ImageIcon;
+import javax.swing.JButton;
+import javax.swing.JDialog;
+import javax.swing.JLabel;
+import javax.swing.JList;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.ListSelectionModel;
+
+
+/**
+ * PopupIconChooser borrows all of its functionality from IconPopupButton. It
+ * displays a popup window for the user to select an icon.
+ */
+public class PopupIconChooser {
+ private String title;
+ private String objectName;
+ private ImageIcon currentIcon;
+ private JDialog mainDialog;
+ private Dialog parentDialog;
+ private Frame parentFrame;
+ private Component parent;
+
+ //private JPanel mainPanel;
+ private JList iconList;
+ private boolean alreadyConstructed = false;
+
+ /**
+ * Create a PopupIconChooser with the supplied attributes.
+ *
+ * @param title
+ * title to display in the popup dialog
+ * @param objectName
+ * name/description of icon being set
+ * @param icons
+ * icons to choose from
+ * @param startIconObject
+ * initially selected icon
+ * @param parentDialog
+ * parent dialog of the selection popup
+ */
+ public PopupIconChooser(String title, String objectName, ImageIcon[] icons,
+ ImageIcon startIconObject, Frame parentFrame) {
+ this.parentDialog = null;
+ this.parentFrame = parentFrame;
+ this.parent = parentFrame;
+ commonInit(title, objectName, icons, startIconObject);
+ }
+
+ /**
+ * Creates a new PopupIconChooser object.
+ *
+ * @param title
+ * DOCUMENT ME!
+ * @param objectName
+ * DOCUMENT ME!
+ * @param icons
+ * DOCUMENT ME!
+ * @param startIconObject
+ * DOCUMENT ME!
+ * @param parentDialog
+ * DOCUMENT ME!
+ */
+ public PopupIconChooser(String title, String objectName, ImageIcon[] icons,
+ ImageIcon startIconObject, Dialog parentDialog) {
+ this.parentDialog = parentDialog;
+ this.parentFrame = null;
+ this.parent = parentDialog;
+ commonInit(title, objectName, icons, startIconObject);
+ }
+
+ private void commonInit(String title, String objectName, ImageIcon[] icons,
+ ImageIcon startIconObject) {
+ this.title = title;
+ this.objectName = objectName;
+
+ this.iconList = new JList(icons);
+
+ if (startIconObject != null)
+ this.currentIcon = startIconObject;
+ else
+ // set to default
+ this.currentIcon = (ImageIcon) iconList.getModel()
+ .getElementAt(0);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public ImageIcon showDialog() {
+ if (!alreadyConstructed) {
+ if (parentFrame != null)
+ mainDialog = new JDialog(parentFrame, this.title, true);
+ else if (parentDialog != null)
+ mainDialog = new JDialog(parentDialog, this.title, true);
+ else
+
+ return null;
+
+ JPanel mainPanel = new JPanel(new GridLayout(0, 1));
+
+ // create buttons
+ final JButton setButton = new JButton("Apply");
+ JButton cancelButton = new JButton("Cancel");
+ setButton.addActionListener(new ApplyIconAction());
+ cancelButton.addActionListener(new CancelIconAction());
+
+ // create list
+ iconList.setLayoutOrientation(JList.HORIZONTAL_WRAP);
+ iconList.setVisibleRowCount(1);
+ // iconList.setFixedCellHeight(35);
+ // iconList.setFixedCellWidth(35);
+ iconList.setBackground(Color.WHITE);
+ iconList.setSelectionBackground(Color.RED);
+ iconList.setSelectionForeground(Color.RED);
+ iconList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
+ iconList.addMouseListener(
+ new MouseAdapter() {
+ public void mouseClicked(MouseEvent e) {
+ if (e.getClickCount() == 2)
+ setButton.doClick();
+ }
+ });
+
+ JScrollPane listScroller = new JScrollPane(iconList);
+ listScroller.setPreferredSize(new Dimension(150, 52));
+ listScroller.setMinimumSize(new Dimension(150, 52));
+ listScroller.setAlignmentX(JPanel.LEFT_ALIGNMENT);
+ listScroller.setAlignmentY(JPanel.BOTTOM_ALIGNMENT);
+ iconList.ensureIndexIsVisible(iconList.getSelectedIndex());
+
+ // Create a container so that we can add a title around the scroll
+ // pane
+ JPanel listPane = new JPanel();
+ listPane.setLayout(new BoxLayout(listPane, BoxLayout.Y_AXIS));
+
+ JLabel label = new JLabel("Set " + objectName);
+ label.setLabelFor(iconList);
+ listPane.add(label);
+ listPane.add(Box.createRigidArea(new Dimension(0, 5)));
+ listPane.add(listScroller);
+ listPane.setBorder(BorderFactory.createEmptyBorder(10, 10, 10, 10));
+
+ // Lay out the buttons from left to right.
+ JPanel buttonPane = new JPanel();
+ buttonPane.setLayout(new BoxLayout(buttonPane, BoxLayout.X_AXIS));
+ buttonPane.setBorder(
+ BorderFactory.createEmptyBorder(0, 10, 10, 10));
+ buttonPane.add(Box.createHorizontalGlue());
+ buttonPane.add(Box.createRigidArea(new Dimension(10, 0)));
+ buttonPane.add(setButton);
+ buttonPane.add(cancelButton);
+
+ // add everything
+ mainPanel.add(listPane, BorderLayout.CENTER);
+ mainPanel.add(buttonPane, BorderLayout.SOUTH);
+ mainDialog.setContentPane(mainPanel);
+ alreadyConstructed = true;
+ }
+
+ mainDialog.pack();
+ mainDialog.setLocationRelativeTo(parent);
+ mainDialog.setVisible(true); // blocks until user makes selection
+
+ return currentIcon;
+ }
+
+ public class ApplyIconAction extends AbstractAction {
+ public void actionPerformed(ActionEvent e) {
+ // setIcon((String) iconList.getSelectedValue());
+ ImageIcon icon = (ImageIcon) iconList.getSelectedValue();
+ currentIcon = icon;
+ mainDialog.dispose();
+ }
+ }
+
+ public class CancelIconAction extends AbstractAction {
+ CancelIconAction() {
+ super("");
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ currentIcon = null;
+ mainDialog.dispose();
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/ui/PopupObjectPositionChooser.java b/application/src/main/java/cytoscape/visual/ui/PopupObjectPositionChooser.java
new file mode 100644
index 0000000..6a33746
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/PopupObjectPositionChooser.java
@@ -0,0 +1,182 @@
+/*
+ File: PopupLabelPositionChooser.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual.ui;
+
+import giny.model.GraphObject;
+import giny.view.ObjectPosition;
+
+import java.awt.Window;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+
+import javax.swing.BoxLayout;
+import javax.swing.JButton;
+import javax.swing.JDialog;
+import javax.swing.JPanel;
+
+import cytoscape.Cytoscape;
+import cytoscape.visual.VisualPropertyType;
+import cytoscape.visual.converter.ValueToStringConverterManager;
+import ding.view.ObjectPositionImpl;
+
+/**
+ *
+ */
+public class PopupObjectPositionChooser extends JDialog implements
+ PropertyChangeListener {
+
+ private static final long serialVersionUID = 7146654020668346430L;
+
+ private ObjectPosition position;
+ private ObjectPosition newPosition;
+
+ private VisualPropertyType targetType;
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param f
+ * DOCUMENT ME!
+ * @param pos
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static ObjectPosition showDialog(final Window parent,
+ final ObjectPosition pos, final VisualPropertyType type) {
+ final PopupObjectPositionChooser placer = new PopupObjectPositionChooser(
+ parent, pos, type);
+
+ return placer.getObjectPosition();
+ }
+
+ private PopupObjectPositionChooser(final Window parent,
+ final ObjectPosition pos, VisualPropertyType type) {
+ super();
+ this.targetType = type;
+ this.setModal(true);
+ this.setLocationRelativeTo(parent);
+ init(pos);
+ }
+
+ private void init(ObjectPosition pos) {
+ if (pos == null)
+ position = new ObjectPositionImpl();
+ else
+ position = pos;
+
+ newPosition = new ObjectPositionImpl(position);
+
+ setTitle("Select " + targetType.getName());
+
+ JPanel placer = new JPanel();
+ placer.setLayout(new BoxLayout(placer, BoxLayout.Y_AXIS));
+ placer.setOpaque(true); // content panes must be opaque
+
+ // Set up and connect the gui components.
+ ObjectPlacerGraphic graphic = new ObjectPlacerGraphic(
+ new ObjectPositionImpl(position), null, true, targetType.getName(), null,
+ null);
+ ObjectPlacerControl control = new ObjectPlacerControl(
+ new ObjectPositionImpl(position));
+
+ control.addPropertyChangeListener(graphic);
+ control.addPropertyChangeListener(this);
+
+ graphic.addPropertyChangeListener(control);
+ graphic.addPropertyChangeListener(this);
+
+ placer.add(graphic);
+ placer.add(control);
+
+ JPanel buttonPanel = new JPanel();
+ final JButton ok = new JButton("OK");
+ ok.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ position = newPosition;
+ dispose();
+ }
+ });
+ ok.addActionListener(control);
+
+ final JButton cancel = new JButton("Cancel");
+ cancel.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ dispose();
+ }
+ });
+
+ buttonPanel.add(ok);
+ buttonPanel.add(cancel);
+ placer.add(buttonPanel);
+ add(placer);
+
+ pack();
+ setVisible(true);
+ }
+
+ private ObjectPosition getObjectPosition() {
+ return position;
+ }
+
+ /**
+ * Handles all property changes that the panel listens for.
+ */
+ public void propertyChange(PropertyChangeEvent e) {
+ final String type = e.getPropertyName();
+
+ if (type.equals(ObjectPlacerGraphic.OBJECT_POSITION_CHANGED)
+ && e.getNewValue() instanceof ObjectPosition) {
+
+ newPosition = (ObjectPosition) e.getNewValue();
+
+ // horrible, horrible hack
+ GraphObject go = BypassHack.getCurrentObject();
+ if (go != null) {
+ String val = ValueToStringConverterManager.manager.toString(newPosition);
+ Cytoscape.getNodeAttributes().setAttribute(
+ go.getIdentifier(),
+ VisualPropertyType.NODE_LABEL_POSITION
+ .getBypassAttrName(), val);
+ Cytoscape.getVisualMappingManager().getNetworkView()
+ .redrawGraph(false, true);
+ }
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/ui/PopupStringChooser.java b/application/src/main/java/cytoscape/visual/ui/PopupStringChooser.java
new file mode 100644
index 0000000..38aec72
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/PopupStringChooser.java
@@ -0,0 +1,114 @@
+/*
+ File: PopupStringChooser.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual.ui;
+
+import java.awt.Component;
+
+import javax.swing.JOptionPane;
+
+
+/**
+ * An input dialog for strings, ints, and doubles.
+ */
+public class PopupStringChooser {
+
+ // from ValueDisplayer
+ private static final byte DOUBLE = 4;
+ private static final byte INT = 6;
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param parent DOCUMENT ME!
+ * @param title DOCUMENT ME!
+ * @param prompt DOCUMENT ME!
+ * @param input DOCUMENT ME!
+ * @param type DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static Object showDialog(Component parent, String title,
+ String prompt, Object input, byte type) {
+// keep prompting for input until a valid input is received
+inputLoop:
+ while (true) {
+ String ret = (String) JOptionPane.showInputDialog(parent, prompt,
+ title, JOptionPane.QUESTION_MESSAGE, null, null, input);
+
+ if (ret == null)
+ return null;
+ else {
+ switch (type) {
+ case DOUBLE:
+
+ try {
+ input = new Double(Double.parseDouble(ret));
+
+ break inputLoop;
+ } catch (NumberFormatException exc) {
+ JOptionPane.showMessageDialog(parent,
+ "That is not a valid double", "Bad Input",
+ JOptionPane.ERROR_MESSAGE);
+
+ continue inputLoop;
+ }
+
+ case INT:
+
+ try {
+ input = new Integer(Integer.parseInt(ret));
+
+ break inputLoop;
+ } catch (NumberFormatException exc) {
+ JOptionPane.showMessageDialog(parent,
+ "That is not a valid integer", "Bad Input",
+ JOptionPane.ERROR_MESSAGE);
+
+ continue inputLoop;
+ }
+
+ default: // simple string assignment
+ input = ret;
+
+ break inputLoop;
+ }
+ }
+ }
+
+ return input;
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/ui/RedrawTask.java b/application/src/main/java/cytoscape/visual/ui/RedrawTask.java
new file mode 100644
index 0000000..15195ea
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/RedrawTask.java
@@ -0,0 +1,60 @@
+package cytoscape.visual.ui;
+
+import cytoscape.logger.CyLogger;
+import cytoscape.task.Task;
+import cytoscape.task.TaskMonitor;
+import cytoscape.view.CyNetworkView;
+
+public class RedrawTask implements Task {
+
+ private final CyNetworkView view;
+ private TaskMonitor taskMonitor;
+
+ RedrawTask(CyNetworkView view) {
+ this.view = view;
+ }
+
+ public void run() {
+ setStatus("Updating network view. Please wait...");
+ setPercentCompleted(-1);
+
+ try {
+ view.redrawGraph(false, true);
+ } catch (Exception e) {
+ setException(e,
+ "Could not update network view for network: "
+ + view.getTitle());
+ }
+
+ setPercentCompleted(100);
+ }
+
+ public void halt() {
+ }
+
+ public void setTaskMonitor(TaskMonitor taskMonitor)
+ throws IllegalThreadStateException {
+ this.taskMonitor = taskMonitor;
+ }
+
+ public String getTitle() {
+ return "Updating Network View";
+ }
+
+ private void setStatus(String status) {
+ if (taskMonitor != null)
+ taskMonitor.setStatus(status);
+ }
+
+ private void setPercentCompleted(int pc) {
+ if (taskMonitor != null)
+ taskMonitor.setPercentCompleted(pc);
+ }
+
+ private void setException(Throwable e, String s) {
+ if (taskMonitor != null)
+ taskMonitor.setException(e,s);
+ CyLogger.getLogger("Network Redraw").warning(s,e);
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/visual/ui/ValueSelectDialog.java b/application/src/main/java/cytoscape/visual/ui/ValueSelectDialog.java
new file mode 100644
index 0000000..350fece
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/ValueSelectDialog.java
@@ -0,0 +1,370 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual.ui;
+
+import static cytoscape.visual.VisualPropertyType.EDGE_SRCARROW_SHAPE;
+import static cytoscape.visual.VisualPropertyType.EDGE_TGTARROW_SHAPE;
+import static cytoscape.visual.VisualPropertyType.*;
+
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.Toolkit;
+import java.awt.Window;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.TreeSet;
+
+import javax.swing.DefaultListModel;
+import javax.swing.Icon;
+import javax.swing.JDialog;
+import javax.swing.JLabel;
+import javax.swing.JList;
+import javax.swing.ListCellRenderer;
+import javax.swing.ListSelectionModel;
+import javax.swing.SwingConstants;
+import javax.swing.border.Border;
+
+import org.jdesktop.swingx.JXList;
+import org.jdesktop.swingx.border.DropShadowBorder;
+
+import cytoscape.Cytoscape;
+import cytoscape.visual.NodeShape;
+import cytoscape.visual.VisualPropertyType;
+import cytoscape.visual.ui.icon.VisualPropertyIcon;
+
+/**
+ * Visual Property selector for discrete values
+ *
+ * @author kono
+ */
+public class ValueSelectDialog extends JDialog {
+
+ private static final long serialVersionUID = 1201804212862509435L;
+
+ // Target visual property.
+ private final VisualPropertyType type;
+
+ // Map from actual value to its icon.
+ private Map<Object, Icon> iconMap;
+
+ private List orderedKeyList;
+
+ private Object originalValue;
+
+ private boolean canceled = false;
+
+ private static final int WIDTH = 480;
+ private final int height;
+
+ private final String listTitle;
+
+ private static final int ICON_CELL_HEIGHT = 140;
+
+ /**
+ * Static method to show dialog and get a value from user.
+ *
+ * @param type
+ * @param parent
+ * @return
+ */
+ public static Object showDialog(final VisualPropertyType type,
+ final Window parent) {
+
+ final ValueSelectDialog dialog = new ValueSelectDialog(type, parent,
+ true);
+
+ dialog.setLocationRelativeTo(parent);
+ dialog.setVisible(true);
+ return dialog.getValue();
+ }
+
+ private ValueSelectDialog(VisualPropertyType type, Window parent,
+ boolean modal) {
+ super(Cytoscape.getDesktop(), modal);
+ final Toolkit toolkit = this.getToolkit();
+ final Dimension screenSize = toolkit.getScreenSize();
+ height = (int) (screenSize.getHeight() * 0.7);
+
+ this.type = type;
+
+ iconMap = this.type.getVisualProperty().getIconSet();
+ initComponents();
+ setList();
+
+ // Special case handling
+ // TODO: Create more user-friendly GUI only for Custom Graphics.
+ if (type.equals(NODE_CUSTOM_GRAPHICS_1)) {
+ this.iconList.setFixedCellHeight(ICON_CELL_HEIGHT);
+ this.listTitle = "Custom Graphics";
+ } else {
+ this.listTitle = type.getName();
+ }
+
+ mainPanel.setTitle(listTitle);
+
+ // get original value and set the selected item.
+ if (type.isNodeProp())
+ originalValue = Cytoscape.getVisualMappingManager()
+ .getVisualStyle().getNodeAppearanceCalculator()
+ .getDefaultAppearance().get(type);
+ else
+ originalValue = Cytoscape.getVisualMappingManager()
+ .getVisualStyle().getEdgeAppearanceCalculator()
+ .getDefaultAppearance().get(type);
+ }
+
+ /**
+ * This method is called from within the constructor to initialize the form.
+ * WARNING: Do NOT modify this code. The content of this method is always
+ * regenerated by the Form Editor.
+ */
+
+ // <editor-fold defaultstate="collapsed" desc=" Generated Code ">
+ private void initComponents() {
+ mainPanel = new org.jdesktop.swingx.JXTitledPanel();
+ iconListScrollPane = new javax.swing.JScrollPane();
+ iconList = new JXList(true);
+
+ applyButton = new javax.swing.JButton();
+ cancelButton = new javax.swing.JButton();
+
+ setDefaultCloseOperation(javax.swing.WindowConstants.DISPOSE_ON_CLOSE);
+ setTitle("Select New Value");
+
+ mainPanel.setTitle(listTitle);
+ mainPanel.setTitleFont(new java.awt.Font("SansSerif", 1, 14));
+
+ iconList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
+ iconListScrollPane.setViewportView(iconList);
+
+ applyButton.setText("Apply");
+ applyButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ applyButtonActionPerformed(evt);
+ }
+ });
+
+ cancelButton.setText("Cancel");
+ cancelButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ cancelButtonActionPerformed(evt);
+ }
+ });
+ // Currently not implemented
+ cancelButton.setVisible(true);
+
+ org.jdesktop.layout.GroupLayout mainPanelLayout = new org.jdesktop.layout.GroupLayout(
+ mainPanel.getContentContainer());
+ mainPanel.getContentContainer().setLayout(mainPanelLayout);
+ mainPanelLayout
+ .setHorizontalGroup(mainPanelLayout
+ .createParallelGroup(
+ org.jdesktop.layout.GroupLayout.LEADING)
+ .add(org.jdesktop.layout.GroupLayout.TRAILING,
+ mainPanelLayout
+ .createSequentialGroup()
+ .addContainerGap(128, Short.MAX_VALUE)
+ .add(cancelButton)
+ .addPreferredGap(
+ org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(applyButton).addContainerGap())
+ .add(iconListScrollPane,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ WIDTH, Short.MAX_VALUE));
+ mainPanelLayout
+ .setVerticalGroup(mainPanelLayout
+ .createParallelGroup(
+ org.jdesktop.layout.GroupLayout.LEADING)
+ .add(org.jdesktop.layout.GroupLayout.TRAILING,
+ mainPanelLayout
+ .createSequentialGroup()
+ .add(iconListScrollPane,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ height, Short.MAX_VALUE)
+ .addPreferredGap(
+ org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(mainPanelLayout
+ .createParallelGroup(
+ org.jdesktop.layout.GroupLayout.BASELINE)
+ .add(applyButton)
+ .add(cancelButton))
+ .addContainerGap()));
+
+ org.jdesktop.layout.GroupLayout layout = new org.jdesktop.layout.GroupLayout(
+ getContentPane());
+ getContentPane().setLayout(layout);
+ layout.setHorizontalGroup(layout.createParallelGroup(
+ org.jdesktop.layout.GroupLayout.LEADING).add(mainPanel,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE));
+ layout.setVerticalGroup(layout.createParallelGroup(
+ org.jdesktop.layout.GroupLayout.LEADING).add(mainPanel,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE));
+ pack();
+ } // </editor-fold>
+
+ private void cancelButtonActionPerformed(java.awt.event.ActionEvent evt) {
+ dispose();
+ canceled = true;
+ }
+
+ private void applyButtonActionPerformed(java.awt.event.ActionEvent evt) {
+ dispose();
+ }
+
+ // Variables declaration - do not modify
+ private javax.swing.JButton applyButton;
+ private javax.swing.JButton cancelButton;
+ private JXList iconList;
+ private javax.swing.JScrollPane iconListScrollPane;
+ private org.jdesktop.swingx.JXTitledPanel mainPanel;
+ private DefaultListModel model;
+
+ // End of variables declaration
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getValue() {
+
+ if (canceled == true) {
+ return originalValue;
+ }
+
+ final int selectedIndex = iconList.getSelectedIndex();
+ if ((0 <= selectedIndex) && (selectedIndex < orderedKeyList.size()))
+ return orderedKeyList.get(selectedIndex);
+ else
+ return originalValue;
+ }
+
+ /*
+ * Key SHOULD be enum.
+ */
+ private void setList() {
+ orderedKeyList = new ArrayList();
+
+ model = new DefaultListModel();
+ iconList.setModel(model);
+
+ VisualPropertyIcon icon;
+
+ final Map<String, Icon> name2icon = new HashMap<String, Icon>();
+ final Map<String, Object> name2value = new HashMap<String, Object>();
+
+ for (Object key : iconMap.keySet()) {
+ icon = (VisualPropertyIcon) iconMap.get(key);
+
+ if (type == EDGE_SRCARROW_SHAPE || type == EDGE_TGTARROW_SHAPE) {
+ icon.setIconWidth(icon.getIconWidth() * 3);
+ }
+ if (type.equals(NODE_SHAPE)
+ && ((NodeShape) key).isSupported() == false) {
+ // Filter shapes not supported by current rendering engine.
+ // Maybe supported in future versions...
+ continue;
+ }
+
+ final String keyName = icon.getName();
+ if (name2icon.containsKey(keyName)) {
+ name2icon.put(keyName + key.hashCode(), icon);
+ name2value.put(keyName + key.hashCode(), key);
+ } else {
+ name2icon.put(keyName, icon);
+ name2value.put(keyName, key);
+ }
+ }
+
+ TreeSet<String> sortedSet = new TreeSet<String>(name2icon.keySet());
+
+ for (String key : sortedSet) {
+ orderedKeyList.add(name2value.get(key));
+ model.addElement(name2icon.get(key));
+ }
+
+ iconList.setCellRenderer(new IconCellRenderer());
+ iconList.repaint();
+ }
+
+ private static final class IconCellRenderer extends JLabel implements ListCellRenderer {
+
+ private static final long serialVersionUID = -7235212695832080213L;
+
+ private final Font SELECTED_FONT = new Font("SansSerif", Font.ITALIC,
+ 18);
+ private final Font NORMAL_FONT = new Font("SansSerif", Font.BOLD, 14);
+ private final Color SELECTED_COLOR = new Color(30, 30, 80, 25);
+ private final Color SELECTED_FONT_COLOR = new Color(0, 150, 255, 120);
+
+ private final Border DROPHSADOW = new DropShadowBorder();
+
+ public IconCellRenderer() {
+ setOpaque(true);
+ }
+
+ public Component getListCellRendererComponent(JList list, Object value,
+ int index, boolean isSelected, boolean cellHasFocus) {
+ final VisualPropertyIcon icon = (VisualPropertyIcon) value;
+
+ if (value != null)
+ setText(icon.getName());
+
+ if (icon != null) {
+ setIcon(icon);
+ setFont(isSelected ? SELECTED_FONT : NORMAL_FONT);
+ icon.setLeftPadding(30);
+ setPreferredSize(new Dimension(icon.getIconWidth() + 300,
+ icon.getIconHeight() + 20));
+ }
+
+ this.setVerticalTextPosition(SwingConstants.CENTER);
+ this.setVerticalAlignment(SwingConstants.CENTER);
+ this.setIconTextGap(60);
+
+ setBackground(isSelected ? SELECTED_COLOR : list.getBackground());
+ setForeground(isSelected ? SELECTED_FONT_COLOR : list
+ .getForeground());
+
+ this.setBorder(DROPHSADOW);
+ return this;
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/ui/VizMapBypass.java b/application/src/main/java/cytoscape/visual/ui/VizMapBypass.java
new file mode 100644
index 0000000..8d2f388
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/VizMapBypass.java
@@ -0,0 +1,165 @@
+/*
+ File: VizMapBypass.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual.ui;
+
+import giny.model.GraphObject;
+import giny.model.Node;
+
+import java.awt.Frame;
+import java.awt.event.ActionEvent;
+import java.util.List;
+
+import javax.swing.AbstractAction;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+
+import cytoscape.Cytoscape;
+import cytoscape.data.CyAttributes;
+import cytoscape.logger.CyLogger;
+import cytoscape.visual.VisualMappingManager;
+import cytoscape.visual.VisualPropertyDependency;
+import cytoscape.visual.VisualPropertyType;
+import cytoscape.visual.converter.ValueToStringConverterManager;
+import cytoscape.visual.customgraphic.CyCustomGraphics;
+
+
+/**
+ * An abstract class providing common methods and data structures to the
+ * Node and Edge bypass classes.
+ */
+abstract class VizMapBypass {
+
+ protected GraphObject graphObj = null;
+
+ protected Frame parent = Cytoscape.getDesktop();
+ protected VisualMappingManager vmm = Cytoscape.getVisualMappingManager();
+ protected CyAttributes attrs = null;
+
+ protected CyLogger logger = CyLogger.getLogger(VizMapBypass.class);
+
+ abstract protected List<String> getBypassNames();
+
+ protected void addResetAllMenuItem(JMenu menu) {
+ JMenuItem jmi = new JMenuItem(new AbstractAction("Reset All") {
+ public void actionPerformed(ActionEvent e) {
+ List<String> names = getBypassNames();
+ String id = graphObj.getIdentifier();
+
+ for (String attrName : names)
+ if (attrs.hasAttribute(id, attrName))
+ attrs.deleteAttribute(id, attrName);
+
+ Cytoscape.getCurrentNetworkView().redrawGraph(false, true);
+ BypassHack.finished();
+ }
+ });
+ menu.add(jmi);
+ }
+
+ protected void addResetMenuItem(JMenu menu, final VisualPropertyType type) {
+ JMenuItem jmi = new JMenuItem(new AbstractAction("[ Reset " + type.getName() + " ]") {
+ public void actionPerformed(ActionEvent e) {
+ String id = graphObj.getIdentifier();
+
+ if (attrs.hasAttribute(id, type.getBypassAttrName()))
+ attrs.deleteAttribute(id, type.getBypassAttrName());
+
+ Cytoscape.getCurrentNetworkView().redrawGraph(false, true);
+ BypassHack.finished();
+ }
+ });
+ menu.add(jmi);
+ }
+
+
+ protected void addMenuItem(final JMenu menu, final VisualPropertyType type) {
+
+ final JMenuItem jmi = new JCheckBoxMenuItem(new AbstractAction(type.getName()) {
+
+ private static final long serialVersionUID = -5772498870138048277L;
+
+ public void actionPerformed(ActionEvent e) {
+ Object obj = null;
+ Object currentValue = null;
+
+ // For now, it supports label position only.
+ if(type.equals(VisualPropertyType.NODE_LABEL_POSITION)) {
+ if(graphObj instanceof Node)
+ currentValue = Cytoscape.getCurrentNetworkView().getNodeView((Node) graphObj).getLabelPosition();
+ }
+
+ try {
+ obj = type.showDiscreteEditor(currentValue);
+ if (obj instanceof CyCustomGraphics) {
+ final CyCustomGraphics cg = (CyCustomGraphics)obj;
+ Cytoscape.getVisualMappingManager().getCustomGraphicsManager()
+ .setUsedInCurrentSession(cg, true);
+ }
+ } catch (Exception ex) {
+ logger.warn("Unable to show descrete editor", ex);
+ obj = null;
+ }
+
+ if (obj == null)
+ return;
+
+ String val = ValueToStringConverterManager.manager.toString(obj);
+ attrs.setAttribute(graphObj.getIdentifier(), type.getBypassAttrName(), val);
+ Cytoscape.getCurrentNetworkView().redrawGraph(false, true);
+ BypassHack.finished();
+ }
+ });
+
+ menu.add(jmi);
+
+ final VisualPropertyDependency dep =
+ Cytoscape.getVisualMappingManager().getVisualStyle().getDependency();
+
+ jmi.setEnabled( !(type.getVisualProperty().constrained(dep)) );
+
+ String attrString = attrs.getStringAttribute(graphObj.getIdentifier(),
+ type.getBypassAttrName());
+
+ if ((attrString == null) || (attrString.length() == 0))
+ jmi.setSelected(false);
+ else {
+ jmi.setSelected(true);
+ addResetMenuItem(menu, type);
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/ui/VizMapBypassNetworkListener.java b/application/src/main/java/cytoscape/visual/ui/VizMapBypassNetworkListener.java
new file mode 100644
index 0000000..af776c3
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/VizMapBypassNetworkListener.java
@@ -0,0 +1,59 @@
+/*
+ File: VizMapBypassNetworkListener.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual.ui;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.view.CytoscapeDesktop;
+
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+
+
+/**
+ * Adds NodeView and EdgeView vizmap bypass listeners to network views as
+ * the views are created.
+ */
+public class VizMapBypassNetworkListener implements PropertyChangeListener {
+ /**
+ * Listens for NETWORK_VIEW_CREATED events and if it hears one, it adds
+ * node and edge context menu listeners to the view.
+ * @param evnt The event we're hearing.
+ */
+ public void propertyChange(final PropertyChangeEvent evnt) {
+ if (CytoscapeDesktop.NETWORK_VIEW_CREATED.equals(evnt.getPropertyName())) {
+ final NodeBypassMenuListener nodeBypassMenuListener = new NodeBypassMenuListener();
+ Cytoscape.getCurrentNetworkView().addNodeContextMenuListener(nodeBypassMenuListener);
+
+ final EdgeBypassMenuListener edgeBypassMenuListener = new EdgeBypassMenuListener();
+ Cytoscape.getCurrentNetworkView().addEdgeContextMenuListener(edgeBypassMenuListener);
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/ui/VizMapperMainPanel.java b/application/src/main/java/cytoscape/visual/ui/VizMapperMainPanel.java
new file mode 100644
index 0000000..48aa25c
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/VizMapperMainPanel.java
@@ -0,0 +1,3428 @@
+/*
+ Copyright (c) 2006, 2007, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual.ui;
+
+
+import static cytoscape.visual.VisualPropertyDependency.Definition.NODE_SIZE_LOCKED;
+import static cytoscape.visual.VisualPropertyType.NODE_FONT_SIZE;
+import static cytoscape.visual.VisualPropertyType.NODE_HEIGHT;
+import static cytoscape.visual.VisualPropertyType.NODE_WIDTH;
+import giny.model.GraphObject;
+import giny.model.Node;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Cursor;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.Image;
+import java.awt.Point;
+import java.awt.Rectangle;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.beans.PropertyEditor;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Random;
+import java.util.Set;
+import java.util.TreeMap;
+import java.util.TreeSet;
+
+import javax.swing.AbstractAction;
+import javax.swing.ImageIcon;
+import javax.swing.JButton;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JDialog;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JPopupMenu;
+import javax.swing.JScrollPane;
+import javax.swing.JSeparator;
+import javax.swing.JTable;
+import javax.swing.ListSelectionModel;
+import javax.swing.SwingConstants;
+import javax.swing.SwingUtilities;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+import javax.swing.event.ListSelectionEvent;
+import javax.swing.event.PopupMenuEvent;
+import javax.swing.event.PopupMenuListener;
+import javax.swing.event.TableColumnModelEvent;
+import javax.swing.event.TableColumnModelListener;
+import javax.swing.table.DefaultTableCellRenderer;
+
+import com.l2fprod.common.propertysheet.Property;
+import com.l2fprod.common.propertysheet.PropertyEditorRegistry;
+import com.l2fprod.common.propertysheet.PropertyRendererRegistry;
+import com.l2fprod.common.propertysheet.PropertySheetPanel;
+import com.l2fprod.common.propertysheet.PropertySheetTable;
+import com.l2fprod.common.propertysheet.PropertySheetTableModel.Item;
+import com.l2fprod.common.swing.plaf.blue.BlueishButtonUI;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import cytoscape.data.CyAttributes;
+import cytoscape.data.CyAttributesUtils;
+import cytoscape.data.attr.MultiHashMapDefinitionListener;
+import cytoscape.logger.CyLogger;
+import cytoscape.task.ui.JTaskConfig;
+import cytoscape.task.util.TaskManager;
+import cytoscape.util.SwingWorker;
+import cytoscape.util.swing.DropDownMenuButton;
+import cytoscape.view.CyNetworkView;
+import cytoscape.view.CytoscapeDesktop;
+import cytoscape.view.NetworkPanel;
+import cytoscape.visual.CalculatorCatalog;
+import cytoscape.visual.EdgeAppearanceCalculator;
+import cytoscape.visual.NodeAppearanceCalculator;
+import cytoscape.visual.VisualMappingManager;
+import cytoscape.visual.VisualPropertyDependency;
+import cytoscape.visual.VisualPropertyDependency.Definition;
+import cytoscape.visual.VisualPropertyType;
+import cytoscape.visual.VisualStyle;
+import cytoscape.visual.calculators.Calculator;
+import cytoscape.visual.mappings.ContinuousMapping;
+import cytoscape.visual.mappings.DiscreteMapping;
+import cytoscape.visual.mappings.ObjectMapping;
+import cytoscape.visual.mappings.PassThroughMapping;
+import cytoscape.visual.ui.editors.continuous.ContinuousMappingEditorPanel;
+import cytoscape.visual.ui.editors.discrete.CyComboBoxPropertyEditor;
+import ding.view.DGraphView;
+
+
+/**
+ * New VizMapper UI main panel.
+ *
+ * This panel consists of 3 panels:
+ * <ul>
+ * <li>Global Control Panel
+ * <li>Default editor panel
+ * <li>Visual Mapping Browser
+ * </ul>
+ *
+ *
+ * @version 0.5
+ * @since Cytoscape 2.5
+ * @author Keiichiro Ono
+ * @param <syncronized>
+ */
+public class VizMapperMainPanel extends JPanel implements PropertyChangeListener, PopupMenuListener, ChangeListener,
+ MultiHashMapDefinitionListener {
+
+ private static final long serialVersionUID = 2010449914223315524L;
+
+ private static final Color UNUSED_COLOR = new Color(100, 100, 100, 50);
+
+ private static final int ROW_HEIGHT = 20;
+ private static final int ROW_HEIGHT_POSITION = 50;
+ private static final int ROW_HEIGHT_GRAPHICS = 100;
+
+ public enum DefaultEditor {
+ NODE,
+ EDGE,
+ GLOBAL;
+ }
+
+ // Context menu items
+ private static JPopupMenu menu;
+ private static JMenuItem delete;
+ private static JMenuItem rainbow1;
+ private static JMenuItem rainbow2;
+ private static JMenuItem randomize;
+ private static JMenuItem series;
+ private static JMenuItem fit;
+ private static JMenuItem editAll;
+ private static JPopupMenu optionMenu;
+ private static JMenuItem newVS;
+ private static JMenuItem renameVS;
+ private static JMenuItem deleteVS;
+ private static JMenuItem duplicateVS;
+ private static JMenuItem createLegend;
+ private static JMenu generateValues;
+ private static JMenu modifyValues;
+ private static JMenuItem brighter;
+ private static JMenuItem darker;
+ private static JMenu dependencies;
+ private static Map<Definition,JCheckBoxMenuItem> dependencyMenuItems;
+
+ /*
+ * Icons used in this panel.
+ */
+ private static final ImageIcon optionIcon = new ImageIcon(Cytoscape.class.getResource("/cytoscape/images/ximian/stock_form-properties.png"));
+ private static final ImageIcon delIcon = new ImageIcon(Cytoscape.class.getResource("/cytoscape/images/ximian/stock_delete-16.png"));
+ private static final ImageIcon addIcon = new ImageIcon(Cytoscape.class.getResource("/cytoscape/images/ximian/stock_data-new-table-16.png"));
+ private static final ImageIcon rndIcon = new ImageIcon(Cytoscape.class.getResource("/cytoscape/images/ximian/stock_filters-16.png"));
+ private static final ImageIcon renameIcon = new ImageIcon(Cytoscape.class.getResource("/cytoscape/images/ximian/stock_redo-16.png"));
+ private static final ImageIcon duplicateIcon = new ImageIcon(Cytoscape.class.getResource("/cytoscape/images/ximian/stock_slide-duplicate.png"));
+ private static final ImageIcon legendIcon = new ImageIcon(Cytoscape.class.getResource("/cytoscape/images/ximian/stock_graphic-styles-16.png"));
+ private static final ImageIcon editIcon = new ImageIcon(Cytoscape.class.getResource("/cytoscape/images/ximian/stock_edit-16.png"));
+
+ private static final String DEFAULT_VS_NAME = "default";
+
+ /*
+ * This is a singleton.
+ */
+ private static VizMapperMainPanel panel;
+
+ /*
+ * Visual mapping manager. All parameters should be taken from here.
+ */
+ private final VisualMappingManager vmm;
+
+ /*
+ * Keeps Properties in the browser.
+ */
+ private Map<String, List<Property>> propertyMap;
+
+ // Keeps current discrete mappings. NOT PERMANENT
+ private final Map<String, Map<Object, Object>> discMapBuffer = new HashMap<String, Map<Object, Object>>();
+
+ private String lastVSName = null;
+
+ private JScrollPane noMapListScrollPane;
+ private List<VisualPropertyType> noMapping;
+ private JPanel buttonPanel;
+ private JButton addButton;
+ private JPanel bottomPanel;
+ private Map<VisualPropertyType, JDialog> editorWindowManager = new HashMap<VisualPropertyType, JDialog>();
+ private Map<String, Image> defaultImageManager = new HashMap<String, Image>();
+ private boolean ignore = false;
+ private CyLogger logger = CyLogger.getLogger(VizMapperMainPanel.class);
+
+ private Set<VizMapperProperty> hiddenProperties = new HashSet<VizMapperProperty>();
+
+
+ /** Creates new form AttributeOrientedPanel */
+ private VizMapperMainPanel() {
+ vmm = Cytoscape.getVisualMappingManager();
+ vmm.addChangeListener(this);
+
+ propertyMap = new HashMap<String, List<Property>>();
+ setMenu();
+ menu.addPopupMenuListener(this);
+
+ // Need to register listener here, instead of CytoscapeDesktop.
+ Cytoscape.getSwingPropertyChangeSupport().addPropertyChangeListener(this);
+
+ initComponents();
+ registerCellEditorListeners();
+
+ // By default, force to sort property by prop name.
+ visualPropertySheetPanel.setSorting(true);
+
+ Cytoscape.getNodeAttributes().getMultiHashMapDefinition().addDataDefinitionListener(this);
+ Cytoscape.getEdgeAttributes().getMultiHashMapDefinition().addDataDefinitionListener(this);
+ }
+
+ /*
+ * Register listeners for editors.
+ */
+ private void registerCellEditorListeners() {
+ nodeAttrEditor.addPropertyChangeListener(this);
+ edgeAttrEditor.addPropertyChangeListener(this);
+
+ mappingTypeEditor.addPropertyChangeListener(this);
+ }
+
+ /**
+ * Get an instance of VizMapper UI panel. This is a singleton.
+ *
+ * @return
+ */
+ public static VizMapperMainPanel getVizMapperUI() {
+ if (panel == null)
+ panel = new VizMapperMainPanel();
+
+ return panel;
+ }
+
+ /**
+ * will be used to show/hide props based on a visualpropertydependency and
+ * a specified VisualPropertyDependency.Definition.
+ *
+ * @param deps The VisualPropertyDependencies that will be queried.
+ * @param def The VisualPropertyDependency.Definition in question.
+ */
+ void syncDependencyStates(VisualPropertyDependency deps, Definition def) {
+ dependencyMenuItems.get(def).setSelected(deps.check(def));
+
+ updateDependencyStates(deps);
+
+ visualPropertySheetPanel.repaint();
+
+ final String vsName = vmm.getVisualStyle().getName();
+ updateDefaultImage(vsName, (DGraphView) ((DefaultViewPanel) DefaultAppearenceBuilder.getDefaultView(vsName)).getView(), defaultAppearencePanel.getSize());
+ setDefaultPanel(defaultImageManager.get(vsName),true);
+ }
+
+
+ private void updateDependencyStates(VisualPropertyDependency deps) {
+ for (Property tmpprop : visualPropertySheetPanel.getProperties()) {
+ if ( !(tmpprop instanceof VizMapperProperty) )
+ continue;
+ updateDependentProperty( (VizMapperProperty)tmpprop, deps );
+ }
+
+ // to avoid concurrent modification exception
+ ArrayList<VizMapperProperty> propl = new ArrayList<VizMapperProperty>( hiddenProperties );
+
+ for ( VizMapperProperty prop : propl )
+ updateDependentProperty( prop, deps );
+
+ }
+
+ private void updateDependentProperty(VizMapperProperty prop, VisualPropertyDependency deps) {
+ Object hidden = prop.getHiddenObject();
+ if ( !(hidden instanceof VisualPropertyType) )
+ return;
+
+ VisualPropertyType type = (VisualPropertyType)hidden;
+ if ( type.getVisualProperty().constrained(deps) ) {
+ hiddenProperties.add( prop );
+ visualPropertySheetPanel.removeProperty(prop);
+ } else {
+ if ( hiddenProperties.remove( prop ) )
+ visualPropertySheetPanel.addProperty(prop);
+ }
+ }
+
+ /**
+ * Setup menu items.<br>
+ *
+ * This includes both icon menu and right-click menu.
+ *
+ */
+ private void setMenu() {
+ /*
+ * Option Menu
+ */
+ newVS = new JMenuItem("Create new Visual Style...");
+ newVS.setIcon(addIcon);
+ newVS.addActionListener(new NewStyleListener());
+
+ deleteVS = new JMenuItem("Delete Visual Style...");
+ deleteVS.setIcon(delIcon);
+ deleteVS.addActionListener(new RemoveStyleListener());
+
+ renameVS = new JMenuItem("Rename Visual Style...");
+ renameVS.setIcon(renameIcon);
+ renameVS.addActionListener(new RenameStyleListener());
+
+ duplicateVS = new JMenuItem("Copy existing Visual Style...");
+ duplicateVS.setIcon(duplicateIcon);
+ duplicateVS.addActionListener(new CopyStyleListener());
+
+ createLegend = new JMenuItem("Create legend from current Visual Style");
+ createLegend.setIcon(legendIcon);
+ createLegend.addActionListener(new CreateLegendListener());
+ optionMenu = new JPopupMenu();
+ optionMenu.add(newVS);
+ optionMenu.add(deleteVS);
+ optionMenu.add(renameVS);
+ optionMenu.add(duplicateVS);
+ optionMenu.add(createLegend);
+
+ /*
+ * Build right-click menu
+ */
+ generateValues = new JMenu("Generate Discrete Values");
+ generateValues.setIcon(rndIcon);
+ modifyValues = new JMenu("Modify Discrete Values");
+
+ dependencies = new JMenu("Visual Property Dependencies");
+ dependencyMenuItems = new HashMap<Definition,JCheckBoxMenuItem>();
+ setupDependencyMenus( dependencies );
+
+ delete = new JMenuItem("Delete mapping");
+
+ final Font italicMenu = new Font("SansSerif", Font.ITALIC, 14);
+ rainbow1 = new JMenuItem("Rainbow 1");
+ rainbow2 = new JMenuItem("Rainbow 2 (w/modulations)");
+ randomize = new JMenuItem("Randomize");
+ rainbow1.setFont(italicMenu);
+ rainbow2.setFont(italicMenu);
+
+ series = new JMenuItem("Series (Number Only)");
+ fit = new JMenuItem("Fit Node Width to Label");
+
+ brighter = new JMenuItem("Brighter");
+ darker = new JMenuItem("Darker");
+
+ editAll = new JMenuItem("Edit selected values at once...");
+
+ delete.setIcon(delIcon);
+ editAll.setIcon(editIcon);
+
+ rainbow1.addActionListener(new GenerateValueListener(GenerateValueListener.RAINBOW1));
+ rainbow2.addActionListener(new GenerateValueListener(GenerateValueListener.RAINBOW2));
+ randomize.addActionListener(new GenerateValueListener(GenerateValueListener.RANDOM));
+
+ series.addActionListener(new GenerateSeriesListener());
+ fit.addActionListener(new FitLabelListener());
+
+ brighter.addActionListener(new BrightnessListener(BrightnessListener.BRIGHTER));
+ darker.addActionListener(new BrightnessListener(BrightnessListener.DARKER));
+
+ delete.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ removeMapping();
+ }
+ });
+ editAll.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent arg0) {
+ editSelectedCells();
+ }
+ });
+
+ menu = new JPopupMenu();
+ generateValues.add(rainbow1);
+ generateValues.add(rainbow2);
+ generateValues.add(randomize);
+ generateValues.add(series);
+ generateValues.add(fit);
+
+ modifyValues.add(brighter);
+ modifyValues.add(darker);
+
+ rainbow1.setEnabled(false);
+ rainbow2.setEnabled(false);
+ randomize.setEnabled(false);
+ series.setEnabled(false);
+ fit.setEnabled(false);
+
+ brighter.setEnabled(false);
+ darker.setEnabled(false);
+
+ menu.add(delete);
+ menu.add(new JSeparator());
+ menu.add(generateValues);
+ menu.add(modifyValues);
+ menu.add(editAll);
+ menu.add(new JSeparator());
+ menu.add(dependencies);
+
+ delete.setEnabled(false);
+ }
+
+
+ private void setupDependencyMenus(JMenu parentMenu) {
+ for ( final Definition def : Definition.values() ) {
+ final JCheckBoxMenuItem item = new JCheckBoxMenuItem(def.getTitle());
+ item.setSelected(def.getDefault());
+ item.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ final VisualPropertyDependency deps = vmm.getVisualStyle().getDependency();
+ deps.set(def,item.isSelected());
+ syncDependencyStates(deps,def);
+
+ Cytoscape.getCurrentNetworkView().redrawGraph(false, true);
+ }
+ });
+
+ parentMenu.add(item);
+ dependencyMenuItems.put( def, item );
+ }
+ }
+
+ public static void apply(Object newValue, VisualPropertyType type) {
+ if (newValue != null)
+ type.setDefault(Cytoscape.getVisualMappingManager().getVisualStyle(), newValue);
+ }
+
+ public static Object showValueSelectDialog(VisualPropertyType type, Component caller)
+ throws Exception {
+ return type.showDiscreteEditor();
+ }
+
+ /**
+ * GUI initialization code based on the auto-generated code from NetBeans
+ *
+ */
+ private void initComponents() {
+ mainSplitPane = new javax.swing.JSplitPane();
+ listSplitPane = new javax.swing.JSplitPane();
+
+ bottomPanel = new javax.swing.JPanel();
+
+ defaultAppearencePanel = new javax.swing.JPanel();
+ visualPropertySheetPanel = new PropertySheetPanel();
+ visualPropertySheetPanel.setTable(new PropertySheetTable());
+
+ vsSelectPanel = new javax.swing.JPanel();
+ vsNameComboBox = new javax.swing.JComboBox();
+
+ buttonPanel = new javax.swing.JPanel();
+
+ GridBagLayout gridbag = new GridBagLayout();
+ GridBagConstraints constraints = new GridBagConstraints();
+ buttonPanel.setLayout(gridbag);
+ constraints.gridx = 0;
+ constraints.gridy = 0;
+ constraints.gridwidth = 1;
+ constraints.gridheight = GridBagConstraints.REMAINDER;
+
+ addButton = new javax.swing.JButton();
+
+ addButton.setUI(new BlueishButtonUI());
+
+ gridbag.setConstraints(addButton, constraints);
+ buttonPanel.add(addButton);
+
+ constraints.gridx = 2;
+ constraints.gridy = 0;
+
+ defaultAppearencePanel.setMinimumSize(new Dimension(100, 100));
+ defaultAppearencePanel.setPreferredSize(new Dimension(mainSplitPane.getWidth(),
+ this.mainSplitPane.getDividerLocation()));
+ defaultAppearencePanel.setSize(defaultAppearencePanel.getPreferredSize());
+ defaultAppearencePanel.setLayout(new BorderLayout());
+
+ mainSplitPane.setDividerLocation(120);
+ mainSplitPane.setDividerSize(4);
+ listSplitPane.setDividerLocation(400);
+ listSplitPane.setDividerSize(5);
+ listSplitPane.setOrientation(javax.swing.JSplitPane.VERTICAL_SPLIT);
+
+ noMapListScrollPane = new javax.swing.JScrollPane();
+ noMapListScrollPane.setBorder(javax.swing.BorderFactory.createTitledBorder(null,
+ "Unused Visual Properties",
+ javax.swing.border.TitledBorder.CENTER,
+ javax.swing.border.TitledBorder.DEFAULT_POSITION,
+ new java.awt.Font("SansSerif",
+ 1,
+ 12)));
+ noMapListScrollPane.setToolTipText("To Create New Mapping, Drag & Drop List Item to Browser.");
+
+ org.jdesktop.layout.GroupLayout bottomPanelLayout = new org.jdesktop.layout.GroupLayout(bottomPanel);
+ bottomPanel.setLayout(bottomPanelLayout);
+ bottomPanelLayout.setHorizontalGroup(bottomPanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(noMapListScrollPane,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 272, Short.MAX_VALUE)
+ .add(buttonPanel,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE));
+ bottomPanelLayout.setVerticalGroup(bottomPanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(bottomPanelLayout.createSequentialGroup()
+ .add(buttonPanel,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ 25,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .add(noMapListScrollPane,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 135,
+ Short.MAX_VALUE)));
+
+ listSplitPane.setLeftComponent(mainSplitPane);
+ listSplitPane.setRightComponent(bottomPanel);
+
+ mainSplitPane.setOrientation(javax.swing.JSplitPane.VERTICAL_SPLIT);
+ defaultAppearencePanel.setBorder(javax.swing.BorderFactory.createTitledBorder(null,
+ "Defaults",
+ javax.swing.border.TitledBorder.DEFAULT_JUSTIFICATION,
+ javax.swing.border.TitledBorder.DEFAULT_POSITION,
+ new java.awt.Font("SansSerif",
+ 1,
+ 12),
+ java.awt.Color.darkGray));
+
+ mainSplitPane.setLeftComponent(defaultAppearencePanel);
+
+ visualPropertySheetPanel.setBorder(javax.swing.BorderFactory.createTitledBorder(null,
+ "Visual Mapping Browser",
+ javax.swing.border.TitledBorder.DEFAULT_JUSTIFICATION,
+ javax.swing.border.TitledBorder.DEFAULT_POSITION,
+ new java.awt.Font("SansSerif",
+ 1,
+ 12),
+ java.awt.Color.darkGray));
+
+ mainSplitPane.setRightComponent(visualPropertySheetPanel);
+
+ vsSelectPanel.setBorder(javax.swing.BorderFactory.createTitledBorder(null,
+ "Current Visual Style",
+ javax.swing.border.TitledBorder.DEFAULT_JUSTIFICATION,
+ javax.swing.border.TitledBorder.DEFAULT_POSITION,
+ new java.awt.Font("SansSerif",
+ 1, 12),
+ java.awt.Color.darkGray));
+
+ vsNameComboBox.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ vsNameComboBoxActionPerformed(evt);
+ }
+ });
+
+ optionButton = new DropDownMenuButton(new AbstractAction() {
+ public void actionPerformed(ActionEvent ae) {
+ DropDownMenuButton b = (DropDownMenuButton) ae.getSource();
+ optionMenu.show(b, 0, b.getHeight());
+ }
+ });
+
+ optionButton.setToolTipText("Options...");
+ optionButton.setIcon(optionIcon);
+ optionButton.setMargin(new java.awt.Insets(2, 2, 2, 2));
+ optionButton.setComponentPopupMenu(optionMenu);
+
+ org.jdesktop.layout.GroupLayout vsSelectPanelLayout = new org.jdesktop.layout.GroupLayout(vsSelectPanel);
+ vsSelectPanel.setLayout(vsSelectPanelLayout);
+ vsSelectPanelLayout.setHorizontalGroup(vsSelectPanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(vsSelectPanelLayout.createSequentialGroup()
+ .addContainerGap()
+ .add(vsNameComboBox,
+ 0,
+ 146,
+ Short.MAX_VALUE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(optionButton,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ 64,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .addContainerGap()));
+ vsSelectPanelLayout.setVerticalGroup(vsSelectPanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(vsSelectPanelLayout.createSequentialGroup()
+ .add(vsSelectPanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE)
+ .add(vsNameComboBox,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .add(optionButton)) // .addContainerGap(
+ // org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ // Short.MAX_VALUE)
+ ));
+
+ org.jdesktop.layout.GroupLayout layout = new org.jdesktop.layout.GroupLayout(this);
+ this.setLayout(layout);
+ layout.setHorizontalGroup(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(vsSelectPanel,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE)
+ .add(mainSplitPane,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 280,
+ Short.MAX_VALUE));
+ layout.setVerticalGroup(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(layout.createSequentialGroup()
+ .add(vsSelectPanel,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(mainSplitPane,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 510, Short.MAX_VALUE)));
+ }
+
+ // Variables declaration - do not modify
+ private JPanel defaultAppearencePanel;
+ private javax.swing.JSplitPane mainSplitPane;
+ private javax.swing.JSplitPane listSplitPane;
+ private DropDownMenuButton optionButton;
+ private PropertySheetPanel visualPropertySheetPanel;
+ private javax.swing.JComboBox vsNameComboBox;
+ private javax.swing.JPanel vsSelectPanel;
+
+ /*
+ * Controlling attr selector
+ */
+ private CyComboBoxPropertyEditor nodeAttrEditor = new CyComboBoxPropertyEditor();
+ private CyComboBoxPropertyEditor edgeAttrEditor = new CyComboBoxPropertyEditor();
+
+ //
+ private CyComboBoxPropertyEditor nodeNumericalAttrEditor = new CyComboBoxPropertyEditor();
+ private CyComboBoxPropertyEditor edgeNumericalAttrEditor = new CyComboBoxPropertyEditor();
+
+ // For mapping types.
+ private CyComboBoxPropertyEditor mappingTypeEditor = new CyComboBoxPropertyEditor();
+
+ private PropertyRendererRegistry rendReg = new PropertyRendererRegistry();
+ private PropertyEditorRegistry editorReg = new PropertyEditorRegistry();
+
+ private final CellRendererFactory rendFactory = new CellRendererFactory();
+ private final CellEditorFactory editorFactory = new CellEditorFactory(this);
+ private final DiscretePropertySetter discretePropSetter = new DiscretePropertySetter(this, rendReg, editorReg, rendFactory, editorFactory);
+
+ // End of variables declaration
+ private void vsNameComboBoxActionPerformed(java.awt.event.ActionEvent evt) {
+ final String vsName = (String) vsNameComboBox.getSelectedItem();
+ final CyNetworkView currentView = Cytoscape.getCurrentNetworkView();
+
+ if (vsName != null) {
+ if (currentView.equals(Cytoscape.getNullNetworkView()) ||
+ vsName.equals(lastVSName) || currentView.getVisualStyle().getName().equals(vsName)) {
+ switchVS(vsName, false);
+ } else {
+ switchVS(vsName, true);
+ }
+ }
+ }
+
+ private void switchVS(String vsName) {
+ switchVS(vsName, true);
+ }
+
+ private void switchVS(String vsName, boolean redraw) {
+ if (ignore)
+ return;
+
+ // If new VS name is the same, ignore.
+ if (lastVSName == vsName)
+ return;
+
+ closeEditorWindow();
+
+ logger.debug("VS Switched --> " + vsName + ", Last = " + lastVSName);
+ vmm.setNetworkView(Cytoscape.getCurrentNetworkView());
+ vmm.setVisualStyle(vsName);
+
+ if (propertyMap.containsKey(vsName)) {
+ final List<Property> props = propertyMap.get(vsName);
+ final Map<String, Property> unused = new TreeMap<String, Property>();
+
+ /*
+ * Remove currently shown property
+ */
+ for (Property item : visualPropertySheetPanel.getProperties())
+ visualPropertySheetPanel.removeProperty(item);
+
+ /*
+ * Add properties to current property sheet.
+ */
+ for (Property prop : props) {
+ if (prop.getCategory().startsWith(CATEGORY_UNUSED) == false) {
+ if (prop.getCategory().equals(NODE_VISUAL_MAPPING)) {
+ visualPropertySheetPanel.addProperty(0, prop);
+ } else {
+ visualPropertySheetPanel.addProperty(prop);
+ }
+ } else {
+ unused.put(prop.getDisplayName(), prop);
+ }
+ }
+
+ final List<String> keys = new ArrayList<String>(unused.keySet());
+ Collections.sort(keys);
+
+ for (Object key : keys) {
+ visualPropertySheetPanel.addProperty(unused.get(key));
+ }
+ } else
+ setPropertyTable();
+
+ final List<CyNetwork> selected = Cytoscape.getSelectedNetworks();
+ final Set<CyNetworkView> views = new HashSet<CyNetworkView>();
+
+ // Find selected views
+ for (final CyNetwork network: selected) {
+ final CyNetworkView targetView = Cytoscape.getNetworkView(network.getIdentifier());
+ if (targetView != Cytoscape.getNullNetworkView())
+ views.add(targetView);
+ }
+
+ // Apply it for selected views.
+ for (CyNetworkView view: views) {
+ view.setVisualStyle(vsName);
+ view.redrawGraph(false, true);
+ Cytoscape.getVisualMappingManager().setNetworkView(view);
+ }
+
+ /*
+ * Draw default view
+ */
+ Image defImg = defaultImageManager.get(vsName);
+
+ if(defImg == null) {
+ // Default image is not available in the buffer. Create a new one.
+ updateDefaultImage(vsName, (DGraphView) ((DefaultViewPanel) DefaultAppearenceBuilder.getDefaultView(vsName)).getView(), defaultAppearencePanel.getSize());
+ defImg = defaultImageManager.get(vsName);
+ }
+ // Set the default view to the panel.
+ setDefaultPanel(defImg,false);
+
+ // Sync. locks
+ VisualPropertyDependency dep = vmm.getVisualStyle().getDependency();
+ for ( Definition d : Definition.values() ) {
+ JCheckBoxMenuItem jcbmi = dependencyMenuItems.get( d );
+ jcbmi.setSelected( dep.check(d) );
+ syncDependencyStates(dep,d);
+ }
+
+ visualPropertySheetPanel.setSorting(true);
+
+ // Cleanup desktop.
+ Cytoscape.getDesktop().repaint();
+ vsNameComboBox.setSelectedItem(vsName);
+
+ // Update last visual style
+ lastVSName = vsName;
+ }
+
+ private static final String CATEGORY_UNUSED = "Unused Properties";
+ private static final String GRAPHICAL_MAP_VIEW = "Graphical View";
+ private static final String NODE_VISUAL_MAPPING = "Node Visual Mapping";
+ private static final String EDGE_VISUAL_MAPPING = "Edge Visual Mapping";
+
+ /*
+ * Set Visual Style selector combo box.
+ */
+ public void initVizmapperGUI() {
+ List<String> vsNames = new ArrayList<String>(vmm.getCalculatorCatalog().getVisualStyleNames());
+
+ final VisualStyle style = vmm.getVisualStyle();
+
+ // Disable action listeners
+ final ActionListener[] li = vsNameComboBox.getActionListeners();
+
+ for (int i = 0; i < li.length; i++)
+ vsNameComboBox.removeActionListener(li[i]);
+
+ vsNameComboBox.removeAllItems();
+
+ JPanel defPanel;
+
+ final Dimension panelSize = defaultAppearencePanel.getSize();
+ DGraphView view;
+
+ Collections.sort(vsNames);
+
+ for (String name : vsNames) {
+ vsNameComboBox.addItem(name);
+ // MLC 03/31/08:
+ // Deceptively, getDefaultView actually actually calls VisualMappingManager.setVisualStyle()
+ // so each time we add a combobox item, the visual style is changing.
+ // Make sure to set the lastVSName as we change the visual style:
+ defPanel = DefaultAppearenceBuilder.getDefaultView(name);
+ view = (DGraphView) ((DefaultViewPanel) defPanel).getView();
+
+ if (view != null) {
+ logger.debug("Creating Default Image for " + name);
+ updateDefaultImage(name, view, panelSize);
+ }
+ }
+
+ vmm.setNetworkView(Cytoscape.getCurrentNetworkView());
+
+ // Switch back to the original style.
+ switchVS(style.getName(), false);
+
+ // Sync check box and actual lock state
+ updateDependencyStates(vmm.getVisualStyle().getDependency());
+
+ // Restore listeners
+ for (int i = 0; i < li.length; i++)
+ vsNameComboBox.addActionListener(li[i]);
+ }
+
+ /**
+ * Create image of a default dummy network and save in a Map object.
+ *
+ * @param vsName
+ * @param view
+ * @param size
+ */
+ private void updateDefaultImage(String vsName, DGraphView view, Dimension size) {
+ Image image = defaultImageManager.remove(vsName);
+
+ if (image != null) {
+ image.flush();
+ image = null;
+ }
+
+ defaultImageManager.put(vsName, view.createImage((int) size.getWidth(), (int) size.getHeight(), 0.9));
+ }
+
+ private void setPropertySheetAppearence() {
+ /*
+ * Set Tooltiptext for the table.
+ */
+ visualPropertySheetPanel.setTable(new PropertySheetTable() {
+ public String getToolTipText(MouseEvent me) {
+ final Point pt = me.getPoint();
+ final int row = rowAtPoint(pt);
+
+ if (row < 0)
+ return null;
+ else {
+ final Property prop = ((Item) getValueAt(row, 0)).getProperty();
+
+ final Color fontColor;
+
+ if ((prop != null) && (prop.getValue() != null)
+ && (prop.getValue().getClass() == Color.class))
+ fontColor = (Color) prop.getValue();
+ else
+ fontColor = Color.DARK_GRAY;
+
+ final String colorString = Integer.toHexString(fontColor.getRGB());
+
+ /*
+ * Edit
+ */
+ if (prop == null)
+ return null;
+
+ if (prop.getDisplayName().equals(GRAPHICAL_MAP_VIEW))
+ return "Click to edit this mapping...";
+
+ if ((prop.getDisplayName() == "Controlling Attribute")
+ || (prop.getDisplayName() == "Mapping Type"))
+ return "<html><Body BgColor=\"white\"><font Size=\"4\" Color=\"#"
+ + colorString.substring(2, 8) + "\"><strong>"
+ + prop.getDisplayName() + " = " + prop.getValue()
+ + "</font></strong></body></html>";
+ else if ((prop.getSubProperties() == null)
+ || (prop.getSubProperties().length == 0))
+ return "<html><Body BgColor=\"white\"><font Size=\"4\" Color=\"#"
+ + colorString.substring(2, 8) + "\"><strong>"
+ + prop.getDisplayName() + "</font></strong></body></html>";
+
+ return null;
+ }
+ }
+ });
+
+ visualPropertySheetPanel.getTable().getColumnModel().addColumnModelListener(new TableColumnModelListener() {
+ public void columnAdded(TableColumnModelEvent arg0) {
+ }
+
+ public void columnMarginChanged(ChangeEvent e) {
+ updateTableView();
+ }
+
+ public void columnMoved(TableColumnModelEvent e) {
+ }
+
+ public void columnRemoved(TableColumnModelEvent e) {
+ }
+
+ public void columnSelectionChanged(ListSelectionEvent e) {
+ }
+ });
+
+ /*
+ * By default, show category.
+ */
+ visualPropertySheetPanel.setMode(PropertySheetPanel.VIEW_AS_CATEGORIES);
+
+ visualPropertySheetPanel.getTable().setComponentPopupMenu(menu);
+
+ visualPropertySheetPanel.getTable().addMouseListener(new MouseAdapter() {
+ public void mouseClicked(MouseEvent e) {
+ processMouseClick(e);
+ }
+ });
+
+ PropertySheetTable table = visualPropertySheetPanel.getTable();
+ table.setRowHeight(ROW_HEIGHT);
+ table.setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION);
+ table.setCategoryBackground(new Color(10, 10, 50, 20));
+ table.setCategoryForeground(Color.black);
+ table.setSelectionBackground(Color.white);
+ table.setSelectionForeground(Color.blue);
+
+
+ final Set<String> mappingTypes = Cytoscape.getVisualMappingManager().getCalculatorCatalog()
+ .getMappingNames();
+
+ mappingTypeEditor.setAvailableValues(mappingTypes.toArray());
+
+ }
+
+
+
+ /**
+ * Refresh the appearence of the table.
+ * This includes adjusting row height.
+ *
+ */
+ private void updateTableView() {
+ final PropertySheetTable table = visualPropertySheetPanel.getTable();
+
+ Property shownProp = null;
+ final DefaultTableCellRenderer emptyCellRenderer = new DefaultTableCellRenderer();
+
+ // Number of rows shown now.
+ final int rowCount = table.getRowCount();
+
+ for (int i = 0; i < rowCount; i++) {
+ try {
+ shownProp = ((Item) table.getValueAt(i, 0)).getProperty();
+ } catch (IndexOutOfBoundsException ex) {
+ shownProp = null;
+ } catch (NullPointerException ex) {
+ shownProp = null;
+ }
+
+
+ if ((shownProp != null) && (shownProp.getParentProperty() != null) && !shownProp.getDisplayName().equals(GRAPHICAL_MAP_VIEW)) {
+ final String parentText = shownProp.getParentProperty().getDisplayName();
+ final String displayName = shownProp.getDisplayName();
+ if(displayName.equals("Mapping Type") == false) {
+ // This is graphics icon cell. Need larger cell.
+ if(parentText.contains("Position"))
+ table.setRowHeight(i, ROW_HEIGHT_POSITION);
+ else if(shownProp.getParentProperty().getDisplayName()
+ .startsWith("Node Custom Graphics"))
+ table.setRowHeight(i, ROW_HEIGHT_GRAPHICS);
+ }
+
+ } else if ((shownProp != null) && shownProp.getDisplayName().equals(GRAPHICAL_MAP_VIEW)) {
+ // This is a Continuous Icon cell.
+ final Property parent = shownProp.getParentProperty();
+ final Object type = ((VizMapperProperty) parent).getHiddenObject();
+
+ if (type instanceof VisualPropertyType) {
+ ObjectMapping mapping;
+
+ if (((VisualPropertyType) type).isNodeProp())
+ mapping = vmm.getVisualStyle().getNodeAppearanceCalculator()
+ .getCalculator(((VisualPropertyType) type)).getMapping(0);
+ else
+ mapping = vmm.getVisualStyle().getEdgeAppearanceCalculator()
+ .getCalculator(((VisualPropertyType) type)).getMapping(0);
+
+ if (mapping instanceof ContinuousMapping) {
+ table.setRowHeight(i, ROW_HEIGHT_GRAPHICS);
+
+ int wi = table.getCellRect(0, 1, true).width;
+ final ImageIcon icon = ContinuousMappingEditorPanel.getIcon(wi, 70,
+ (VisualPropertyType) type);
+ final Class dataType = ((VisualPropertyType) type).getDataType();
+
+ if (dataType == Color.class) {
+ final DefaultTableCellRenderer gradientRenderer = new DefaultTableCellRenderer();
+ gradientRenderer.setIcon(icon);
+ rendReg.registerRenderer(shownProp, gradientRenderer);
+ } else if (dataType == Number.class) {
+ final DefaultTableCellRenderer cRenderer = new DefaultTableCellRenderer();
+ cRenderer.setIcon(icon);
+ rendReg.registerRenderer(shownProp, cRenderer);
+ } else {
+ final DefaultTableCellRenderer dRenderer = new DefaultTableCellRenderer();
+ dRenderer.setIcon(icon);
+ rendReg.registerRenderer(shownProp, dRenderer);
+ }
+ }
+ }
+ } else if ((shownProp != null) && (shownProp.getCategory() != null)
+ && shownProp.getCategory().equals(CATEGORY_UNUSED)) {
+ emptyCellRenderer.setForeground(UNUSED_COLOR);
+ rendReg.registerRenderer(shownProp, emptyCellRenderer);
+ }
+ }
+
+// repaint();
+// visualPropertySheetPanel.repaint();
+ }
+
+
+
+ private void setAttrComboBox() {
+ final List<String> names = new ArrayList<String>();
+ CyAttributes attr = Cytoscape.getNodeAttributes();
+ String[] nameArray = attr.getAttributeNames();
+ Arrays.sort(nameArray);
+ names.add("ID");
+
+ for (String name : nameArray) {
+ if (attr.getUserVisible(name) && (attr.getType(name) != CyAttributes.TYPE_UNDEFINED)
+ && (attr.getType(name) != CyAttributes.TYPE_COMPLEX)) {
+ names.add(name);
+ }
+ }
+
+ nodeAttrEditor.setAvailableValues(names.toArray());
+
+ names.clear();
+
+ Class dataClass;
+
+ for (String name : nameArray) {
+ dataClass = CyAttributesUtils.getClass(name, attr);
+
+ if ((dataClass == Integer.class) || (dataClass == Double.class)
+ || (dataClass == Float.class))
+ names.add(name);
+ }
+
+ nodeNumericalAttrEditor.setAvailableValues(names.toArray());
+
+ names.clear();
+ attr = Cytoscape.getEdgeAttributes();
+ nameArray = attr.getAttributeNames();
+ Arrays.sort(nameArray);
+ names.add("ID");
+
+ for (String name : nameArray) {
+ if (attr.getUserVisible(name) && (attr.getType(name) != CyAttributes.TYPE_UNDEFINED)
+ && (attr.getType(name) != CyAttributes.TYPE_COMPLEX)) {
+ names.add(name);
+ }
+ }
+
+ edgeAttrEditor.setAvailableValues(names.toArray());
+
+ names.clear();
+
+ for (String name : nameArray) {
+ dataClass = CyAttributesUtils.getClass(name, attr);
+
+ if ((dataClass == Integer.class) || (dataClass == Double.class)
+ || (dataClass == Float.class))
+ names.add(name);
+ }
+
+ edgeNumericalAttrEditor.setAvailableValues(names.toArray());
+
+ repaint();
+ }
+
+ private void processMouseClick(MouseEvent e) {
+
+ int selected = visualPropertySheetPanel.getTable().getSelectedRow();
+ /*
+ * Adjust height if it's an legend icon.
+ */
+ updateTableView();
+
+ if (SwingUtilities.isLeftMouseButton(e) && (0 <= selected)) {
+ final Item item = (Item) visualPropertySheetPanel.getTable().getValueAt(selected, 0);
+ final Property curProp = item.getProperty();
+
+ if (curProp == null)
+ return;
+
+ /*
+ * Create new mapping if double-click on unused val.
+ */
+ String category = curProp.getCategory();
+
+ if ((e.getClickCount() == 2) && (category != null)
+ && category.equalsIgnoreCase("Unused Properties")) {
+
+ VisualPropertyType type = (VisualPropertyType) ((VizMapperProperty) curProp).getHiddenObject();
+ visualPropertySheetPanel.removeProperty(curProp);
+
+ final VizMapperProperty newProp = new VizMapperProperty();
+ final VizMapperProperty mapProp = new VizMapperProperty();
+
+ newProp.setDisplayName(type.getName());
+ newProp.setHiddenObject(type);
+ newProp.setValue("Please select a value!");
+
+ if (type.isNodeProp()) {
+ newProp.setCategory(NODE_VISUAL_MAPPING);
+ editorReg.registerEditor(newProp, nodeAttrEditor);
+ } else {
+ newProp.setCategory(EDGE_VISUAL_MAPPING);
+ editorReg.registerEditor(newProp, edgeAttrEditor);
+ }
+
+ mapProp.setDisplayName("Mapping Type");
+ mapProp.setValue("Please select a mapping type!");
+
+ newProp.addSubProperty(mapProp);
+ mapProp.setParentProperty(newProp);
+ visualPropertySheetPanel.addProperty(0, newProp);
+
+ expandLastSelectedItem(type.getName());
+
+ visualPropertySheetPanel.getTable().scrollRectToVisible(new Rectangle(0, 0, 10, 10));
+
+ editorReg.registerEditor(mapProp, mappingTypeEditor);
+
+ // This is necessary because sometimes registory is lost when updating this sheet.
+ visualPropertySheetPanel.setEditorFactory(editorReg);
+ visualPropertySheetPanel.repaint();
+
+ return;
+ } else if ((e.getClickCount() == 1) && (category == null)) {
+ /*
+ * Single left-click
+ */
+ VisualPropertyType type = null;
+
+ if ((curProp.getParentProperty() == null)
+ && ((VizMapperProperty) curProp).getHiddenObject() instanceof VisualPropertyType)
+ type = (VisualPropertyType) ((VizMapperProperty) curProp).getHiddenObject();
+ else if (curProp.getParentProperty() != null)
+ type = (VisualPropertyType) ((VizMapperProperty) curProp.getParentProperty())
+ .getHiddenObject();
+ else
+
+ return;
+
+ final ObjectMapping selectedMapping;
+ Calculator calc = null;
+
+ if (type.isNodeProp()) {
+ calc = vmm.getVisualStyle().getNodeAppearanceCalculator().getCalculator(type);
+ } else {
+ calc = vmm.getVisualStyle().getEdgeAppearanceCalculator().getCalculator(type);
+ }
+
+ if (calc == null) {
+ return;
+ }
+
+ selectedMapping = calc.getMapping(0);
+
+ if (selectedMapping instanceof ContinuousMapping) {
+ /*
+ * Need to check other windows.
+ */
+ if (editorWindowManager.containsKey(type)) {
+ // This means editor is already on display.
+ editorWindowManager.get(type).requestFocus();
+
+ return;
+ } else {
+ try {
+ ((JDialog) type.showContinuousEditor()).addPropertyChangeListener(this);
+ } catch (Exception e1) {
+ logger.warn("Unable to add listener to the contiuous editor", e1);
+ }
+ }
+ }
+ }
+ }
+ }
+
+ /*
+ * Set property sheet panel.
+ *
+ * TODO: need to find missing editor problem!
+ */
+ private void setPropertyTable() {
+ setPropertySheetAppearence();
+
+ /*
+ * Clean up sheet
+ */
+ for (Property item : visualPropertySheetPanel.getProperties())
+ visualPropertySheetPanel.removeProperty(item);
+
+ final NodeAppearanceCalculator nac = Cytoscape.getVisualMappingManager().getVisualStyle()
+ .getNodeAppearanceCalculator();
+
+ final EdgeAppearanceCalculator eac = Cytoscape.getVisualMappingManager().getVisualStyle()
+ .getEdgeAppearanceCalculator();
+
+ final List<Calculator> nacList = nac.getCalculators();
+ final List<Calculator> eacList = eac.getCalculators();
+
+ editorReg.registerDefaults();
+
+ /*
+ * Add properties to the browser.
+ */
+ List<Property> propRecord = new ArrayList<Property>();
+
+ setPropertyFromCalculator(nacList, NODE_VISUAL_MAPPING, propRecord);
+ setPropertyFromCalculator(eacList, EDGE_VISUAL_MAPPING, propRecord);
+
+ // Save it for later use.
+ propertyMap.put(vmm.getVisualStyle().getName(), propRecord);
+
+ /*
+ * Finally, build unused list
+ */
+ setUnused(propRecord);
+ }
+
+ /*
+ * Add unused visual properties to the property sheet
+ *
+ */
+ private void setUnused(List<Property> propList) {
+ buildList();
+ Collections.sort(noMapping);
+
+ for (VisualPropertyType type : noMapping) {
+ VizMapperProperty prop = new VizMapperProperty();
+ prop.setCategory(CATEGORY_UNUSED);
+ prop.setDisplayName(type.getName());
+ prop.setHiddenObject(type);
+ prop.setValue("Double-Click to create...");
+ // prop.setEditable(false);
+ visualPropertySheetPanel.addProperty(prop);
+ propList.add(prop);
+ }
+ }
+
+
+ /*
+ * Build one property for one visual property.
+ */
+ private final void buildProperty(Calculator calc, VizMapperProperty calculatorTypeProp,
+ String rootCategory) {
+ final VisualPropertyType type = calc.getVisualPropertyType();
+
+ /*
+ * Set one calculator
+ */
+ calculatorTypeProp.setCategory(rootCategory);
+ // calculatorTypeProp.setType(String.class);
+ calculatorTypeProp.setDisplayName(type.getName());
+ calculatorTypeProp.setHiddenObject(type);
+
+ /*
+ * Mapping 0 is always currently used mapping.
+ */
+ final ObjectMapping firstMap = calc.getMapping(0);
+ String attrName;
+
+ if (firstMap != null) {
+ final VizMapperProperty mappingHeader = new VizMapperProperty();
+
+ attrName = firstMap.getControllingAttributeName();
+
+ if (attrName == null)
+ calculatorTypeProp.setValue("Select Value");
+ else
+ calculatorTypeProp.setValue(attrName);
+
+ rendReg.registerRenderer(calculatorTypeProp, CellRendererFactory.DEF_RENDERER);
+
+ mappingHeader.setDisplayName("Mapping Type");
+ mappingHeader.setHiddenObject(firstMap.getClass());
+
+ if (firstMap.getClass() == DiscreteMapping.class)
+ mappingHeader.setValue("Discrete Mapping");
+ else if (firstMap.getClass() == ContinuousMapping.class)
+ mappingHeader.setValue("Continuous Mapping");
+ else
+ mappingHeader.setValue("Passthrough Mapping");
+
+ mappingHeader.setHiddenObject(firstMap);
+
+ mappingHeader.setParentProperty(calculatorTypeProp);
+ calculatorTypeProp.addSubProperty(mappingHeader);
+ editorReg.registerEditor(mappingHeader, mappingTypeEditor);
+
+ final CyAttributes attr;
+ final Iterator it;
+ boolean isNode = false;
+
+ if (calc.getVisualPropertyType().isNodeProp()) {
+ attr = Cytoscape.getNodeAttributes();
+ it = Cytoscape.getCurrentNetwork().nodesIterator();
+ editorReg.registerEditor(calculatorTypeProp, nodeAttrEditor);
+ isNode = true;
+ } else {
+ attr = Cytoscape.getEdgeAttributes();
+ it = Cytoscape.getCurrentNetwork().edgesIterator();
+ editorReg.registerEditor(calculatorTypeProp, edgeAttrEditor);
+ isNode = false;
+ }
+
+ /*
+ * Discrete Mapping
+ */
+ if ((firstMap.getClass() == DiscreteMapping.class) && (attrName != null)) {
+ final Map discMapping = ((DiscreteMapping) firstMap).getAll();
+ final Set<Object> attrSet = MappingKeyFactory.getKeySet(attrName, attr, firstMap, isNode);
+ discretePropSetter.setDiscreteProps(type, discMapping, attrSet, calculatorTypeProp);
+ } else if ((firstMap.getClass() == ContinuousMapping.class) && (attrName != null)) {
+ int wi = this.visualPropertySheetPanel.getTable().getCellRect(0, 1, true).width;
+
+ VizMapperProperty graphicalView = new VizMapperProperty();
+ graphicalView.setDisplayName(GRAPHICAL_MAP_VIEW);
+ graphicalView.setName(type.getName());
+ graphicalView.setParentProperty(calculatorTypeProp);
+ calculatorTypeProp.addSubProperty(graphicalView);
+
+ final Class dataType = type.getDataType();
+ final ImageIcon icon = ContinuousMappingEditorPanel.getIcon(wi, 70,
+ (VisualPropertyType) type);
+
+ if (dataType == Color.class) {
+ /*
+ * Color-related calcs.
+ */
+ final DefaultTableCellRenderer gradientRenderer = new DefaultTableCellRenderer();
+ gradientRenderer.setIcon(icon);
+
+ rendReg.registerRenderer(graphicalView, gradientRenderer);
+ } else if (dataType == Number.class) {
+// /*
+// * Size/Width related calcs.
+// */
+// continuousRenderer.setIcon(icon);
+// rendReg.registerRenderer(graphicalView, continuousRenderer);
+ } else {
+// discreteRenderer.setIcon(icon);
+// rendReg.registerRenderer(graphicalView, discreteRenderer);
+ }
+ } else if ((firstMap.getClass() == PassThroughMapping.class) && (attrName != null)) {
+ /*
+ * Passthrough
+ */
+ String id;
+ String value;
+ VizMapperProperty oneProperty;
+
+ /*
+ * Accept String only.
+ */
+ if (attr.getType(attrName) == CyAttributes.TYPE_STRING) {
+ while (it.hasNext()) {
+ id = ((GraphObject) it.next()).getIdentifier();
+
+ value = attr.getStringAttribute(id, attrName);
+ oneProperty = new VizMapperProperty();
+
+ if (attrName.equals("ID"))
+ oneProperty.setValue(id);
+ else
+ oneProperty.setValue(value);
+
+ // This prop. should not be editable!
+ oneProperty.setEditable(false);
+
+ oneProperty.setParentProperty(calculatorTypeProp);
+ oneProperty.setDisplayName(id);
+ oneProperty.setType(String.class);
+
+ calculatorTypeProp.addSubProperty(oneProperty);
+ }
+ }
+ }
+ }
+
+ visualPropertySheetPanel.addProperty(0, calculatorTypeProp);
+ visualPropertySheetPanel.setRendererFactory(rendReg);
+ visualPropertySheetPanel.setEditorFactory(editorReg);
+ }
+
+ private void setPropertyFromCalculator(List<Calculator> calcList, String rootCategory,
+ List<Property> propRecord) {
+ VisualPropertyType type = null;
+
+ for (Calculator calc : calcList) {
+ final VizMapperProperty calculatorTypeProp = new VizMapperProperty();
+ buildProperty(calc, calculatorTypeProp, rootCategory);
+
+ PropertyEditor editor = editorReg.getEditor(calculatorTypeProp);
+
+ if ((editor == null)
+ && (calculatorTypeProp.getCategory().equals("Unused Properties") == false)) {
+ type = (VisualPropertyType) calculatorTypeProp.getHiddenObject();
+
+ if (type.isNodeProp()) {
+ editorReg.registerEditor(calculatorTypeProp, nodeAttrEditor);
+ } else {
+ editorReg.registerEditor(calculatorTypeProp, edgeAttrEditor);
+ }
+ }
+
+ propRecord.add(calculatorTypeProp);
+ }
+ }
+
+
+ private void setDefaultPanel(final Image defImage, boolean repaint) {
+ if (defImage == null)
+ return;
+
+ defaultAppearencePanel.removeAll();
+
+ final JButton defaultImageButton = new JButton();
+ defaultImageButton.setUI(new BlueishButtonUI());
+ defaultImageButton.setCursor(Cursor.getPredefinedCursor(Cursor.HAND_CURSOR));
+
+ defaultImageButton.setIcon(new ImageIcon(defImage));
+ defaultAppearencePanel.add(defaultImageButton, BorderLayout.CENTER);
+ defaultImageButton.addMouseListener(new DefaultMouseListener());
+ if ( repaint )
+ Cytoscape.getDesktop().repaint();
+ }
+
+ /**
+ * Action listener for the default image button.
+ *
+ * @author kono
+ *
+ */
+ class DefaultMouseListener extends MouseAdapter {
+ public void mouseClicked(MouseEvent e) {
+ if (SwingUtilities.isLeftMouseButton(e)) {
+ final String targetName = vmm.getVisualStyle().getName();
+ final DefaultViewPanel panel = (DefaultViewPanel) DefaultAppearenceBuilder.showDialog(Cytoscape .getDesktop());
+ updateDefaultImage(targetName, (DGraphView) panel.getView(),
+ defaultAppearencePanel.getSize());
+ setDefaultPanel(defaultImageManager.get(targetName), false);
+
+ Cytoscape.getDesktop().repaint();
+ }
+ }
+ }
+
+ /**
+ * On/Off listeners.
+ * This is for performance.
+ *
+ * @param on
+ * DOCUMENT ME!
+ */
+ public void enableListeners(boolean on) {
+ if (on) {
+ Cytoscape.getVisualMappingManager().addChangeListener(this);
+ syncStyleBox();
+ ignore = false;
+ } else {
+ Cytoscape.getVisualMappingManager().removeChangeListener(this);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void initializeTableState() {
+ propertyMap = new HashMap<String, List<Property>>();
+ editorWindowManager = new HashMap<VisualPropertyType, JDialog>();
+ defaultImageManager = new HashMap<String, Image>();
+ }
+
+ private void manageWindow(final String status, VisualPropertyType vpt, Object source) {
+ if (status.equals(ContinuousMappingEditorPanel.EDITOR_WINDOW_OPENED)) {
+ this.editorWindowManager.put(vpt, (JDialog) source);
+ } else if (status.equals(ContinuousMappingEditorPanel.EDITOR_WINDOW_CLOSED)) {
+ final VisualPropertyType type = vpt;
+
+ /*
+ * Update icon
+ */
+ final Property[] props = visualPropertySheetPanel.getProperties();
+ VizMapperProperty vprop = null;
+
+ for (Property prop : props) {
+ vprop = (VizMapperProperty) prop;
+
+ if ((vprop.getHiddenObject() != null) && (type == vprop.getHiddenObject())) {
+ vprop = (VizMapperProperty) prop;
+
+ break;
+ }
+ }
+
+ final Property[] subProps = vprop.getSubProperties();
+ vprop = null;
+
+ String name = null;
+
+ for (Property prop : subProps) {
+ name = prop.getName();
+
+ if ((name != null) && name.equals(type.getName())) {
+ vprop = (VizMapperProperty) prop;
+
+ break;
+ }
+ }
+
+ final int width = visualPropertySheetPanel.getTable().getCellRect(0, 1, true).width;
+
+ final DefaultTableCellRenderer cRenderer = new DefaultTableCellRenderer();
+ cRenderer.setIcon(ContinuousMappingEditorPanel.getIcon(width, 70, type));
+
+ rendReg.registerRenderer(vprop, cRenderer);
+ visualPropertySheetPanel.getTable().repaint();
+ }
+ }
+
+ private void closeEditorWindow() {
+ Set<VisualPropertyType> typeSet = editorWindowManager.keySet();
+ Set<VisualPropertyType> keySet = new HashSet<VisualPropertyType>();
+
+ for (VisualPropertyType vpt : typeSet) {
+ JDialog window = editorWindowManager.get(vpt);
+ manageWindow(ContinuousMappingEditorPanel.EDITOR_WINDOW_CLOSED, vpt, null);
+ window.dispose();
+ keySet.add(vpt);
+ }
+
+ for (VisualPropertyType type : keySet)
+ editorWindowManager.remove(type);
+ }
+
+ @Override
+ public void propertyChange(PropertyChangeEvent e) {
+ // Set ignore flag.
+ if (e.getPropertyName().equals(Integer.toString(Cytoscape.SESSION_OPENED))) {
+ ignore = true;
+ enableListeners(false);
+ }
+
+ if (ignore)
+ return;
+
+ /*
+ * Managing editor windows.
+ */
+ if (e.getPropertyName().equals(ContinuousMappingEditorPanel.EDITOR_WINDOW_OPENED)
+ || e.getPropertyName().equals(ContinuousMappingEditorPanel.EDITOR_WINDOW_CLOSED)) {
+ manageWindow(e.getPropertyName(), (VisualPropertyType) e.getNewValue(), e.getSource());
+
+ if (e.getPropertyName().equals(ContinuousMappingEditorPanel.EDITOR_WINDOW_CLOSED))
+ editorWindowManager.remove((VisualPropertyType) e.getNewValue());
+
+ return;
+ }
+
+ /*
+ * Got global event
+ */
+ if (e.getPropertyName().equals(Cytoscape.SESSION_LOADED)
+ || e.getPropertyName().equals(Cytoscape.VIZMAP_LOADED)) {
+ final String vsName = vmm.getVisualStyle().getName();
+
+ lastVSName = null;
+ initVizmapperGUI();
+ switchVS(vsName, false);
+ vsNameComboBox.setSelectedItem(vsName);
+ vmm.setVisualStyle(vsName);
+
+ return;
+ } else if (e.getPropertyName().equals(CytoscapeDesktop.NETWORK_VIEW_FOCUS)
+ && (e.getSource().getClass() == NetworkPanel.class)) {
+ final VisualStyle vs = vmm.getNetworkView().getVisualStyle();
+
+ if (vs != null) {
+ vmm.setNetworkView(Cytoscape.getCurrentNetworkView());
+
+ if (vs.getName().equals(vsNameComboBox.getSelectedItem())) {
+ //TODO: is this necessary?
+ //Cytoscape.getCurrentNetworkView().redrawGraph(false, true);
+ } else {
+ switchVS(vs.getName(), false);
+ vsNameComboBox.setSelectedItem(vs.getName());
+ setDefaultPanel(this.defaultImageManager.get(vs.getName()),false);
+ }
+ }
+
+ return;
+ }
+
+ /***********************************************************************
+ * Below this line, accept only cell editor events.
+ **********************************************************************/
+ if (e.getPropertyName().equalsIgnoreCase("value") == false)
+ return;
+
+ if (e.getNewValue() != null && e.getNewValue().equals(e.getOldValue()))
+ return;
+
+ final PropertySheetTable table = visualPropertySheetPanel.getTable();
+ final int selected = table.getSelectedRow();
+
+ /*
+ * Do nothing if not selected.
+ */
+ if (selected < 0)
+ return;
+
+ Item selectedItem = (Item) visualPropertySheetPanel.getTable().getValueAt(selected, 0);
+ VizMapperProperty prop = (VizMapperProperty) selectedItem.getProperty();
+ if (prop == null)
+ return;
+
+ VisualPropertyType type = null;
+ String ctrAttrName = null;
+
+ VizMapperProperty typeRootProp = null;
+
+ if ((prop.getParentProperty() == null) && e.getNewValue() instanceof String) {
+ /*
+ * This is a controlling attr name change signal.
+ */
+ typeRootProp = (VizMapperProperty) prop;
+ type = (VisualPropertyType) ((VizMapperProperty) prop).getHiddenObject();
+ ctrAttrName = (String) e.getNewValue();
+ logger.debug("Controlling attribute for: " + prop.getHiddenObject() + " changed to: "+ctrAttrName);
+ } else if ((prop.getParentProperty() == null) && (e.getNewValue() == null)) {
+ /*
+ * Empty cell selected. no need to change anything.
+ */
+ logger.debug("Empty cell selected");
+ return;
+ } else {
+ typeRootProp = (VizMapperProperty) prop.getParentProperty();
+
+ if (prop.getParentProperty() == null)
+ return;
+
+ type = (VisualPropertyType) ((VizMapperProperty) prop.getParentProperty()).getHiddenObject();
+ }
+
+ /*
+ * Mapping type changed
+ */
+ if (prop.getHiddenObject() instanceof ObjectMapping
+ || prop.getDisplayName().equals("Mapping Type")) {
+ logger.debug("Mapping type changed: " + prop.getHiddenObject());
+
+ if (e.getNewValue() == null)
+ return;
+
+ /*
+ * If invalid data type, ignore.
+ */
+ final Object parentValue = prop.getParentProperty().getValue();
+
+ if (parentValue != null) {
+ ctrAttrName = parentValue.toString();
+
+ final Class dataClass;
+
+ if (type.isNodeProp()) {
+ dataClass = CyAttributesUtils.getClass(ctrAttrName,
+ Cytoscape.getNodeAttributes());
+ } else {
+ dataClass = CyAttributesUtils.getClass(ctrAttrName,
+ Cytoscape.getEdgeAttributes());
+ }
+
+ if (e.getNewValue().equals("Continuous Mapper")
+ && ((dataClass != Integer.class) && (dataClass != Double.class)
+ && (dataClass != Float.class))) {
+
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ JOptionPane.showMessageDialog(Cytoscape.getDesktop().getCytoPanel(SwingConstants.WEST).getSelectedComponent(),
+ "Continuous Mapper can be used with Numbers only.",
+ "Incompatible Mapping Type!",
+ JOptionPane.ERROR_MESSAGE);
+ }
+ });
+
+ return;
+ }
+ } else {
+ return;
+ }
+
+ if (e.getNewValue().toString().endsWith("Mapper") == false)
+ return;
+
+ switchMapping(prop, e.getNewValue().toString(), prop.getParentProperty().getValue());
+
+ /*
+ * restore expanded props.
+ */
+ expandLastSelectedItem(type.getName());
+ updateTableView();
+
+ return;
+ }
+
+ /*
+ * Extract calculator
+ */
+ ObjectMapping mapping;
+ final Calculator curCalc;
+
+ if (type.isNodeProp()) {
+ curCalc = vmm.getVisualStyle().getNodeAppearanceCalculator().getCalculator(type);
+ } else {
+ curCalc = vmm.getVisualStyle().getEdgeAppearanceCalculator().getCalculator(type);
+ }
+
+ if (curCalc == null) {
+ return;
+ }
+
+ mapping = curCalc.getMapping(0);
+
+ /*
+ * Controlling Attribute has been changed.
+ */
+ if (ctrAttrName != null) {
+ /*
+ * Ignore if not compatible.
+ */
+ final CyAttributes attrForTest;
+
+ if (type.isNodeProp()) {
+ attrForTest = Cytoscape.getNodeAttributes();
+ } else {
+ attrForTest = Cytoscape.getEdgeAttributes();
+ }
+
+ final Byte dataType = attrForTest.getType(ctrAttrName);
+ final Class dataClass = CyAttributesUtils.getClass(ctrAttrName, attrForTest);
+
+ // This part is for Continuous Mapping.
+ if (mapping instanceof ContinuousMapping) {
+ if ((dataType == CyAttributes.TYPE_FLOATING)
+ || (dataType == CyAttributes.TYPE_INTEGER)) {
+ // Do nothing
+ } else {
+ JOptionPane.showMessageDialog(this,
+ "Continuous Mapper can be used with Numbers only.\nPlease select numerical attributes.",
+ "Incompatible Mapping Type!",
+ JOptionPane.INFORMATION_MESSAGE);
+
+ return;
+ }
+ }
+
+ // If same, do nothing.
+ if (ctrAttrName.equals(mapping.getControllingAttributeName())) {
+ return;
+ }
+
+ // Buffer current discrete mapping
+ if (mapping instanceof DiscreteMapping) {
+ final String curMappingName = curCalc.toString() + "-"
+ + mapping.getControllingAttributeName();
+ final String newMappingName = curCalc.toString() + "-" + ctrAttrName;
+ final Map saved = discMapBuffer.get(newMappingName);
+
+ if (saved == null) {
+ // Save the current mapping
+ discMapBuffer.put(curMappingName, ((DiscreteMapping) mapping).getAll());
+ // Create a new mapping
+ if (type.isNodeProp()) {
+ vmm.getVisualStyle().getNodeAppearanceCalculator().removeCalculator(type);
+ } else {
+ vmm.getVisualStyle().getEdgeAppearanceCalculator().removeCalculator(type);
+ }
+ vmm.getCalculatorCatalog().removeCalculator(curCalc);
+ NewMappingBuilder.createNewCalculator(type, "Discrete Mapper", curCalc.toString(), ctrAttrName);
+ Calculator newCalc = vmm.getCalculatorCatalog().getCalculator(type, curCalc.toString());
+ newCalc.getMapping(0).setControllingAttributeName(ctrAttrName);
+ if (type.isNodeProp()) {
+ vmm.getVisualStyle().getNodeAppearanceCalculator().setCalculator(newCalc);
+ } else {
+ vmm.getVisualStyle().getEdgeAppearanceCalculator().setCalculator(newCalc);
+ }
+ } else if (saved != null) {
+ // Mapping exists
+ discMapBuffer.put(curMappingName, ((DiscreteMapping) mapping).getAll());
+ mapping.setControllingAttributeName(ctrAttrName);
+ ((DiscreteMapping) mapping).putAll(saved);
+ }
+ } else {
+ mapping.setControllingAttributeName(ctrAttrName);
+ }
+
+ visualPropertySheetPanel.removeProperty(typeRootProp);
+
+ final VizMapperProperty newRootProp = new VizMapperProperty();
+
+ if (type.isNodeProp())
+ buildProperty(vmm.getVisualStyle().getNodeAppearanceCalculator().getCalculator(type),
+ newRootProp, NODE_VISUAL_MAPPING);
+ else
+ buildProperty(vmm.getVisualStyle().getEdgeAppearanceCalculator().getCalculator(type),
+ newRootProp, EDGE_VISUAL_MAPPING);
+
+ removeProperty(typeRootProp);
+
+ if (propertyMap.get(vmm.getVisualStyle().getName()) != null)
+ propertyMap.get(vmm.getVisualStyle().getName()).add(newRootProp);
+
+ typeRootProp = null;
+
+ expandLastSelectedItem(type.getName());
+ updateTableView();
+
+ // Finally, update graph view and focus.
+ vmm.setNetworkView(Cytoscape.getCurrentNetworkView());
+ SwingUtilities.invokeLater(new Runnable() {
+ @Override
+ public void run() {
+ Cytoscape.getCurrentNetworkView().redrawGraph(false, true);
+ }
+ });
+ return;
+ }
+
+ // Return if not a Discrete Mapping.
+ if (mapping instanceof ContinuousMapping || mapping instanceof PassThroughMapping)
+ return;
+
+ Object key = null;
+
+ if ((type.getDataType() == Number.class) || (type.getDataType() == String.class)) {
+ key = e.getOldValue();
+
+ if (type.getDataType() == Number.class)
+ editorReg.registerEditor(prop, this.editorFactory.getPropertyEditor(Number.class));
+ } else {
+ key = ((Item) visualPropertySheetPanel.getTable().getValueAt(selected, 0)).getProperty()
+ .getDisplayName();
+ }
+
+ /*
+ * Need to convert this string to proper data types.
+ */
+ final CyAttributes attr;
+ ctrAttrName = mapping.getControllingAttributeName();
+
+ if (type.isNodeProp()) {
+ attr = Cytoscape.getNodeAttributes();
+ } else {
+ attr = Cytoscape.getEdgeAttributes();
+ }
+
+ Byte attrType = attr.getType(ctrAttrName);
+
+ if (attrType != CyAttributes.TYPE_STRING) {
+ switch (attrType) {
+ case CyAttributes.TYPE_BOOLEAN:
+ key = Boolean.valueOf((String) key);
+
+ break;
+
+ case CyAttributes.TYPE_INTEGER:
+ key = Integer.valueOf((String) key);
+
+ break;
+
+ case CyAttributes.TYPE_FLOATING:
+ key = Double.valueOf((String) key);
+
+ break;
+
+ default:
+ break;
+ }
+ }
+
+ Object newValue = e.getNewValue();
+ if(newValue == null) {
+ ((DiscreteMapping) mapping).putMapValue(key, newValue);
+ Cytoscape.getCurrentNetworkView().redrawGraph(false, true);
+ return;
+ }
+ if (type.getDataType() == Number.class && newValue instanceof Number) {
+ // Validate Discrete Mapping Value
+
+ if (type.getVisualProperty().isValidValue(newValue) == false) {
+
+ // Out of range. Use current value.
+ int shownPropCount = table.getRowCount();
+ Property p = null;
+ Object val = null;
+
+ for (int i = 0; i < shownPropCount; i++) {
+ p = ((Item) table.getValueAt(i, 0)).getProperty();
+
+ if (p != null) {
+ val = p.getDisplayName();
+
+ if ((val != null) && val.equals(key.toString())) {
+ p.setValue(((DiscreteMapping) mapping).getMapValue(key));
+ return;
+ }
+ }
+ }
+
+ return;
+ }
+ }
+
+ ((DiscreteMapping) mapping).putMapValue(key, newValue);
+
+ /*
+ * Update table and current network view.
+ */
+ updateTableView();
+
+ visualPropertySheetPanel.repaint();
+ vmm.setNetworkView(Cytoscape.getCurrentNetworkView());
+ Cytoscape.getCurrentNetworkView().redrawGraph(false, true);
+ }
+
+ /**
+ * Switching between mapppings. Each calcs has 3 mappings. The first one
+ * (getMapping(0)) is the current mapping used by calculator.
+ *
+ */
+ private void switchMapping(VizMapperProperty prop, String newMapName, Object attrName) {
+ if (attrName == null) {
+ return;
+ }
+
+ final VisualPropertyType type = (VisualPropertyType) ((VizMapperProperty) prop.getParentProperty()).getHiddenObject();
+ final String newCalcName = vmm.getVisualStyle().getName() + "-" + type.getName() + "-"
+ + newMapName;
+
+ // Extract target calculator
+ Calculator newCalc = vmm.getCalculatorCatalog().getCalculator(type, newCalcName);
+
+ Calculator oldCalc = null;
+
+ if (type.isNodeProp())
+ oldCalc = vmm.getVisualStyle().getNodeAppearanceCalculator().getCalculator(type);
+ else
+ oldCalc = vmm.getVisualStyle().getEdgeAppearanceCalculator().getCalculator(type);
+
+ /*
+ * If not exist, create new one.
+ */
+ if (newCalc == null) {
+ // Use task since this may take a white if it's a new image passthrough mapping.
+ NewMappingBuilder.createNewCalculator(type, newMapName, newCalcName, attrName.toString());
+ newCalc = vmm.getCalculatorCatalog().getCalculator(type, newCalcName);
+ }
+
+ newCalc.getMapping(0).setControllingAttributeName((String) attrName);
+
+ if (type.isNodeProp()) {
+ vmm.getVisualStyle().getNodeAppearanceCalculator().setCalculator(newCalc);
+ } else
+ vmm.getVisualStyle().getEdgeAppearanceCalculator().setCalculator(newCalc);
+
+ /*
+ * If old calc is not standard name, rename it.
+ */
+ if (oldCalc != null) {
+ final String oldMappingTypeName;
+
+ if (oldCalc.getMapping(0) instanceof DiscreteMapping)
+ oldMappingTypeName = "Discrete Mapper";
+ else if (oldCalc.getMapping(0) instanceof ContinuousMapping)
+ oldMappingTypeName = "Continuous Mapper";
+ else if (oldCalc.getMapping(0) instanceof PassThroughMapping)
+ oldMappingTypeName = "Passthrough Mapper";
+ else
+ oldMappingTypeName = null;
+
+ final String oldCalcName = type.getName() + "-" + oldMappingTypeName;
+
+ if (vmm.getCalculatorCatalog().getCalculator(type, oldCalcName) == null)
+ NewMappingBuilder.createNewCalculator(type, oldMappingTypeName, oldCalcName, attrName.toString());
+ }
+
+ Property parent = prop.getParentProperty();
+ visualPropertySheetPanel.removeProperty(parent);
+
+ final VizMapperProperty newRootProp = new VizMapperProperty();
+
+ if (type.isNodeProp())
+ buildProperty(vmm.getVisualStyle().getNodeAppearanceCalculator().getCalculator(type),
+ newRootProp, NODE_VISUAL_MAPPING);
+ else
+ buildProperty(vmm.getVisualStyle().getEdgeAppearanceCalculator().getCalculator(type),
+ newRootProp, EDGE_VISUAL_MAPPING);
+
+ expandLastSelectedItem(type.getName());
+
+ removeProperty(parent);
+
+ if (propertyMap.get(vmm.getVisualStyle().getName()) != null) {
+ propertyMap.get(vmm.getVisualStyle().getName()).add(newRootProp);
+ }
+
+ // This redraw may take a while, so run as a task.
+ redraw(Cytoscape.getCurrentNetworkView());
+ parent = null;
+ }
+
+ private void expandLastSelectedItem(String name) {
+ final PropertySheetTable table = visualPropertySheetPanel.getTable();
+ Item item = null;
+ Property curProp;
+
+ for (int i = 0; i < table.getRowCount(); i++) {
+ item = (Item) table.getValueAt(i, 0);
+
+ curProp = item.getProperty();
+
+ if ((curProp != null) && (curProp.getDisplayName().equals(name))) {
+ table.setRowSelectionInterval(i, i);
+ if (item.isVisible() == false)
+ item.toggle();
+
+ return;
+ }
+ }
+ }
+
+
+ private void redraw(final CyNetworkView view) {
+ // Create Task
+ RedrawTask task = new RedrawTask(view);
+ Thread redrawThread = new Thread(task);
+ redrawThread.run();
+
+ /*
+ // Configure JTask Dialog Pop-Up Box
+ final JTaskConfig jTaskConfig = new JTaskConfig();
+
+ jTaskConfig.displayCancelButton(false);
+ jTaskConfig.setOwner(Cytoscape.getDesktop());
+ jTaskConfig.displayCloseButton(false);
+ jTaskConfig.displayStatus(false);
+ jTaskConfig.setAutoDispose(true);
+
+ // Execute Task in New Thread; pop open JTask Dialog Box.
+ TaskManager.executeTask(task, jTaskConfig);
+ */
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param vsName
+ * DOCUMENT ME!
+ */
+ public void setCurrentVS(String vsName) {
+ vsNameComboBox.setSelectedItem(vsName);
+ }
+
+ private void buildList() {
+ noMapping = new ArrayList<VisualPropertyType>();
+
+ final VisualStyle vs = vmm.getVisualStyle();
+ final NodeAppearanceCalculator nac = vs.getNodeAppearanceCalculator();
+ final EdgeAppearanceCalculator eac = vs.getEdgeAppearanceCalculator();
+
+ ObjectMapping mapping = null;
+
+ for (VisualPropertyType type : VisualPropertyType.values()) {
+ Calculator calc = nac.getCalculator(type);
+
+ if (calc == null) {
+ calc = eac.getCalculator(type);
+
+ if (calc != null)
+ mapping = calc.getMapping(0);
+ } else
+ mapping = calc.getMapping(0);
+
+ if ((mapping == null) && type.isAllowed())
+ noMapping.add(type);
+
+ mapping = null;
+ }
+ }
+
+ /*
+ * Actions for option menu
+ */
+ protected class CreateLegendListener extends AbstractAction {
+ public void actionPerformed(ActionEvent e) {
+ final SwingWorker worker = new SwingWorker() {
+ public Object construct() {
+ LegendDialog ld = new LegendDialog(Cytoscape.getDesktop(), vmm.getVisualStyle());
+ ld.setLocationRelativeTo(Cytoscape.getDesktop());
+ ld.setVisible(true);
+
+ return null;
+ }
+ };
+
+ worker.start();
+ }
+ }
+
+ /**
+ * Create a new Visual Style.
+ *
+ * @author kono
+ *
+ */
+ private class NewStyleListener extends AbstractAction {
+
+ private static final long serialVersionUID = -401235126133833279L;
+
+ public void actionPerformed(ActionEvent e) {
+ final String name = getStyleName(null);
+
+ /*
+ * If name is null, do not create style.
+ */
+ if (name == null)
+ return;
+
+ // Create the new style
+ final VisualStyle newStyle = new VisualStyle(name);
+ final List<Calculator> calcs = new ArrayList<Calculator>(vmm.getCalculatorCatalog()
+ .getCalculators());
+ final Calculator dummy = calcs.get(0);
+ newStyle.getNodeAppearanceCalculator().setCalculator(dummy);
+
+ // add it to the catalog
+ vmm.getCalculatorCatalog().addVisualStyle(newStyle);
+ // Apply the new style
+ vmm.setVisualStyle(newStyle);
+ Cytoscape.getCurrentNetworkView().setVisualStyle(newStyle.getName());
+
+ removeMapping(dummy.getVisualPropertyType());
+
+ final JPanel defPanel = DefaultAppearenceBuilder.getDefaultView(name);
+ final DGraphView view = (DGraphView) ((DefaultViewPanel) defPanel).getView();
+ final Dimension panelSize = defaultAppearencePanel.getSize();
+
+ if (view != null) {
+ logger.debug("Creating Default Image for new visual style " + name);
+ updateDefaultImage(name, view, panelSize);
+ setDefaultPanel(defaultImageManager.get(name),false);
+ }
+
+ vmm.setNetworkView(Cytoscape.getCurrentNetworkView());
+ switchVS(name);
+ }
+ }
+
+ /**
+ * Get a new Visual Style name
+ *
+ * @param s
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ private String getStyleName(VisualStyle s) {
+ String suggestedName = null;
+
+ if (s != null)
+ suggestedName = vmm.getCalculatorCatalog().checkVisualStyleName(s.getName());
+
+ // keep prompting for input until user cancels or we get a valid
+ // name
+ while (true) {
+ String ret = (String) JOptionPane.showInputDialog(Cytoscape.getDesktop(),
+ "Please enter new name for the visual style.",
+ "Enter Visual Style Name",
+ JOptionPane.QUESTION_MESSAGE, null,
+ null, suggestedName);
+
+ if (ret == null)
+ return null;
+
+ if (ret.indexOf('.') != -1) {
+ JOptionPane.showMessageDialog(Cytoscape.getDesktop(),
+ "Visual style names with dots are not allowed, please select a new name.",
+ "Information",
+ JOptionPane.INFORMATION_MESSAGE);
+ continue;
+ }
+
+ String newName = vmm.getCalculatorCatalog().checkVisualStyleName(ret);
+
+ if (newName.equals(ret))
+ return ret;
+
+ int alt = JOptionPane.showConfirmDialog(Cytoscape.getDesktop(),
+ "Visual style with name " + ret
+ + " already exists,\nrename to " + newName
+ + " okay?", "Duplicate visual style name",
+ JOptionPane.YES_NO_OPTION,
+ JOptionPane.WARNING_MESSAGE, null);
+
+ if (alt == JOptionPane.YES_OPTION)
+ return newName;
+ }
+ }
+
+ /**
+ * Rename a Visual Style<br>
+ *
+ */
+ private class RenameStyleListener extends AbstractAction {
+ public void actionPerformed(ActionEvent e) {
+ final VisualStyle currentStyle = vmm.getVisualStyle();
+ final String oldName = currentStyle.getName();
+ final String name = getStyleName(currentStyle);
+
+ if (name == null) {
+ return;
+ }
+
+ lastVSName = name;
+
+ final Image img = defaultImageManager.get(oldName);
+ defaultImageManager.put(name, img);
+ defaultImageManager.remove(oldName);
+
+ /*
+ * Update name
+ */
+ currentStyle.setName(name);
+
+ vmm.getCalculatorCatalog().removeVisualStyle(oldName);
+ vmm.getCalculatorCatalog().addVisualStyle(currentStyle);
+
+ vmm.setVisualStyle(currentStyle);
+ vmm.getNetworkView().setVisualStyle(name);
+
+ /*
+ * Update combo box and
+ */
+ vsNameComboBox.addItem(name);
+ vsNameComboBox.setSelectedItem(name);
+ vsNameComboBox.removeItem(oldName);
+
+ final List<Property> props = propertyMap.get(oldName);
+ propertyMap.put(name, props);
+ propertyMap.remove(oldName);
+ }
+ }
+
+ /**
+ * Remove selected visual style.
+ */
+ private class RemoveStyleListener extends AbstractAction {
+ public void actionPerformed(ActionEvent e) {
+ if (vmm.getVisualStyle().getName().equals(DEFAULT_VS_NAME)) {
+ JOptionPane.showMessageDialog(Cytoscape.getDesktop(),
+ "You cannot delete default style.",
+ "Cannot remove style!", JOptionPane.ERROR_MESSAGE);
+
+ return;
+ }
+
+ // make sure the user really wants to do this
+ final String styleName = vmm.getVisualStyle().getName();
+ final String checkString = "Are you sure you want to permanently delete"
+ + " the visual style '" + styleName + "'?";
+ int ich = JOptionPane.showConfirmDialog(Cytoscape.getDesktop(), checkString,
+ "Confirm Delete Style",
+ JOptionPane.YES_NO_OPTION);
+
+ if (ich == JOptionPane.YES_OPTION) {
+ final CalculatorCatalog catalog = vmm.getCalculatorCatalog();
+ catalog.removeVisualStyle(styleName);
+
+ // try to switch to the default style
+ VisualStyle currentStyle = catalog.getVisualStyle(DEFAULT_VS_NAME);
+
+ /*
+ * Update Visual Mapping Browser.
+ */
+ vsNameComboBox.removeItem(styleName);
+ vsNameComboBox.setSelectedItem(currentStyle.getName());
+ switchVS(currentStyle.getName());
+ defaultImageManager.remove(styleName);
+ propertyMap.remove(styleName);
+
+ vmm.setVisualStyle(currentStyle);
+ vmm.getNetworkView().setVisualStyle(currentStyle.getName());
+ Cytoscape.getCurrentNetworkView().redrawGraph(false, true);
+ }
+ }
+ }
+
+ protected class CopyStyleListener extends AbstractAction {
+
+ private static final long serialVersionUID = 4741684758183028809L;
+
+ public void actionPerformed(ActionEvent e) {
+ final VisualStyle currentStyle = vmm.getVisualStyle();
+ VisualStyle clone = null;
+
+ try {
+ clone = (VisualStyle) currentStyle.clone();
+ } catch (CloneNotSupportedException exc) {
+ logger.warn("Clone not supported exception!");
+ }
+
+ final String newName = getStyleName(clone);
+
+ if ((newName == null) || (newName.trim().length() == 0))
+ return;
+
+ clone.setName(newName);
+
+ // add new style to the catalog
+ vmm.getCalculatorCatalog().addVisualStyle(clone);
+ vmm.setVisualStyle(clone);
+
+ final JPanel defPanel = DefaultAppearenceBuilder.getDefaultView(newName);
+ final DGraphView view = (DGraphView) ((DefaultViewPanel) defPanel).getView();
+ final Dimension panelSize = defaultAppearencePanel.getSize();
+
+ if (view != null) {
+ logger.debug("Creating Default Image for new visual style " + newName);
+ updateDefaultImage(newName, view, panelSize);
+ setDefaultPanel(defaultImageManager.get(newName),false);
+ }
+
+ vmm.setNetworkView(Cytoscape.getCurrentNetworkView());
+ switchVS(newName);
+ }
+ }
+
+ /**
+ * Remove a mapping from current visual style.
+ *
+ */
+ private void removeMapping() {
+ final int selected = visualPropertySheetPanel.getTable().getSelectedRow();
+
+ if (0 <= selected) {
+ Item item = (Item) visualPropertySheetPanel.getTable().getValueAt(selected, 0);
+ Property curProp = item.getProperty();
+
+ if (curProp instanceof VizMapperProperty) {
+ final VisualPropertyType type = (VisualPropertyType) ((VizMapperProperty) curProp)
+ [...]
+
+ if (type == null)
+ return;
+
+ String[] message = {
+ "The Mapping for " + type.getName() + " will be removed.",
+ "Proceed?"
+ };
+
+ int value = JOptionPane.showConfirmDialog(Cytoscape.getDesktop(), message,
+ "Remove Mapping",
+ JOptionPane.YES_NO_OPTION);
+
+ if (value == JOptionPane.YES_OPTION) {
+ // If Continuous Mapper is displayed, kill it.
+ if (editorWindowManager.get(type) != null) {
+ JDialog editor = editorWindowManager.get(type);
+ editor.dispose();
+ editorWindowManager.remove(type);
+ }
+
+ if (type.isNodeProp()) {
+ vmm.getVisualStyle().getNodeAppearanceCalculator().removeCalculator(type);
+ } else {
+ vmm.getVisualStyle().getEdgeAppearanceCalculator().removeCalculator(type);
+ }
+
+ Cytoscape.getCurrentNetworkView().redrawGraph(false, true);
+
+ /*
+ * Finally, move the visual property to "unused list"
+ */
+ noMapping.add(type);
+
+ VizMapperProperty prop = new VizMapperProperty();
+ prop.setCategory(CATEGORY_UNUSED);
+ prop.setDisplayName(type.getName());
+ prop.setHiddenObject(type);
+ prop.setValue("Double-Click to create...");
+ visualPropertySheetPanel.addProperty(prop);
+
+ visualPropertySheetPanel.removeProperty(curProp);
+
+ removeProperty(curProp);
+
+ propertyMap.get(vmm.getVisualStyle().getName()).add(prop);
+ visualPropertySheetPanel.repaint();
+ }
+ }
+ }
+ }
+
+ private void removeMapping(final VisualPropertyType type) {
+ if (type.isNodeProp()) {
+ vmm.getVisualStyle().getNodeAppearanceCalculator().removeCalculator(type);
+ } else {
+ vmm.getVisualStyle().getEdgeAppearanceCalculator().removeCalculator(type);
+ }
+
+ Cytoscape.getCurrentNetworkView().redrawGraph(false, true);
+
+ final Property[] props = visualPropertySheetPanel.getProperties();
+ Property toBeRemoved = null;
+
+ for (Property p : props) {
+ if (p.getDisplayName().equals(type.getName())) {
+ toBeRemoved = p;
+
+ break;
+ }
+ }
+
+ visualPropertySheetPanel.removeProperty(toBeRemoved);
+
+ removeProperty(toBeRemoved);
+
+ /*
+ * Finally, move the visual property to "unused list"
+ */
+ noMapping.add(type);
+
+ VizMapperProperty prop = new VizMapperProperty();
+ prop.setCategory(CATEGORY_UNUSED);
+ prop.setDisplayName(type.getName());
+ prop.setHiddenObject(type);
+ prop.setValue("Double-Click to create...");
+ visualPropertySheetPanel.addProperty(prop);
+
+ if (propertyMap.get(vmm.getVisualStyle().getName()) != null) {
+ propertyMap.get(vmm.getVisualStyle().getName()).add(prop);
+ }
+
+ visualPropertySheetPanel.repaint();
+ }
+
+ /**
+ * Edit all selected cells at once.
+ *
+ * This is for Discrete Mapping only.
+ *
+ */
+ private void editSelectedCells() {
+ final PropertySheetTable table = visualPropertySheetPanel.getTable();
+ final int[] selected = table.getSelectedRows();
+
+ Item item = null;
+
+ // If nothing selected, return.
+ if ((selected == null) || (selected.length == 0)) {
+ return;
+ }
+
+ /*
+ * Test with the first selected item
+ */
+ item = (Item) visualPropertySheetPanel.getTable().getValueAt(selected[0], 0);
+
+ VizMapperProperty prop = (VizMapperProperty) item.getProperty();
+
+ if ((prop == null) || (prop.getParentProperty() == null)) {
+ return;
+ }
+
+ final VisualPropertyType type = (VisualPropertyType) ((VizMapperProperty) prop
+ [...]
+ .getHiddenObject();
+
+ /*
+ * Extract calculator
+ */
+ final ObjectMapping mapping;
+ final CyAttributes attr;
+
+ if (type.isNodeProp()) {
+ mapping = vmm.getVisualStyle().getNodeAppearanceCalculator().getCalculator(type)
+ .getMapping(0);
+ attr = Cytoscape.getNodeAttributes();
+ } else {
+ mapping = vmm.getVisualStyle().getEdgeAppearanceCalculator().getCalculator(type)
+ .getMapping(0);
+ attr = Cytoscape.getEdgeAttributes();
+ }
+
+ if (mapping instanceof ContinuousMapping || mapping instanceof PassThroughMapping)
+ return;
+
+ Object newValue = null;
+
+ try {
+ newValue = type.showDiscreteEditor();
+ } catch (Exception e1) {
+ logger.warn("Unable to show the descrete editor",e1);
+ }
+
+ if (newValue == null)
+ return;
+
+ Object key = null;
+ final Class keyClass = CyAttributesUtils.getClass(mapping.getControllingAttributeName(),
+ attr);
+
+ for (int i = 0; i < selected.length; i++) {
+ /*
+ * First, update property sheet
+ */
+ ((Item) visualPropertySheetPanel.getTable().getValueAt(selected[i], 0)).getProperty()
+ .setValue(newValue);
+ /*
+ * Then update backend.
+ */
+ key = ((Item) visualPropertySheetPanel.getTable().getValueAt(selected[i], 0)).getProperty()
+ .getDisplayName();
+
+ if (keyClass == Integer.class) {
+ key = Integer.valueOf((String) key);
+ } else if (keyClass == Double.class) {
+ key = Double.valueOf((String) key);
+ } else if (keyClass == Boolean.class) {
+ key = Boolean.valueOf((String) key);
+ }
+
+ ((DiscreteMapping) mapping).putMapValue(key, newValue);
+ }
+
+ /*
+ * Update table and current network view.
+ */
+ table.repaint();
+ vmm.setNetworkView(Cytoscape.getCurrentNetworkView());
+ Cytoscape.getCurrentNetworkView().redrawGraph(false, true);
+ }
+
+ /*
+ * Remove an entry in the browser.
+ */
+ private void removeProperty(final Property prop) {
+ List<Property> targets = new ArrayList<Property>();
+
+ if (propertyMap.get(vmm.getVisualStyle().getName()) == null) {
+ return;
+ }
+
+ for (Property p : propertyMap.get(vmm.getVisualStyle().getName())) {
+ if (p.getDisplayName().equals(prop.getDisplayName())) {
+ targets.add(p);
+ }
+ }
+
+ for (Property p : targets) {
+ logger.debug("Removed: " + p.getDisplayName());
+ propertyMap.get(vmm.getVisualStyle().getName()).remove(p);
+ }
+ }
+
+ private class GenerateValueListener extends AbstractAction {
+
+ private static final long serialVersionUID = -4852790777403019117L;
+
+ private static final int MAX_COLOR = 256 * 256 * 256;
+
+ private DiscreteMapping dm;
+ protected static final int RAINBOW1 = 1;
+ protected static final int RAINBOW2 = 2;
+ protected static final int RANDOM = 3;
+ private final int functionType;
+
+ public GenerateValueListener(final int type) {
+ this.functionType = type;
+ }
+
+ /**
+ * User wants to Seed the Discrete Mapper with Random Color Values.
+ */
+ public void actionPerformed(ActionEvent e) {
+ //Check Selected poperty
+ final int selectedRow = visualPropertySheetPanel.getTable().getSelectedRow();
+
+ if (selectedRow < 0)
+ return;
+
+ final Item item = (Item) visualPropertySheetPanel.getTable().getValueAt(selectedRow, 0);
+ final VizMapperProperty prop = (VizMapperProperty) item.getProperty();
+ final Object hidden = prop.getHiddenObject();
+
+ if (hidden instanceof VisualPropertyType) {
+ final VisualPropertyType type = (VisualPropertyType) hidden;
+
+ final Map valueMap = new HashMap();
+ final long seed = System.currentTimeMillis();
+ final Random rand = new Random(seed);
+
+ final ObjectMapping oMap;
+
+ final CyAttributes attr;
+ final boolean isNode;
+
+ if (type.isNodeProp()) {
+ attr = Cytoscape.getNodeAttributes();
+ oMap = vmm.getVisualStyle().getNodeAppearanceCalculator().getCalculator(type)
+ .getMapping(0);
+ isNode = true;
+ } else {
+ attr = Cytoscape.getEdgeAttributes();
+ oMap = vmm.getVisualStyle().getEdgeAppearanceCalculator().getCalculator(type)
+ .getMapping(0);
+ isNode = false;
+ }
+
+ // This function is for discrete mapping only.
+ if ((oMap instanceof DiscreteMapping) == false)
+ return;
+
+ dm = (DiscreteMapping) oMap;
+
+ final Set<Object> attrSet = MappingKeyFactory.getKeySet(oMap.getControllingAttributeName(), attr,
+ oMap, isNode);
+
+ // Show error if there is no attribute value.
+ if (attrSet.size() == 0) {
+ JOptionPane.showMessageDialog(panel, "No attribute value is available.",
+ "Cannot generate values",
+ JOptionPane.ERROR_MESSAGE);
+ }
+
+ /*
+ * Create random colors
+ */
+ final float increment = 1f / ((Number) attrSet.size()).floatValue();
+
+ float hue = 0;
+ float sat = 0;
+ float br = 0;
+
+ if (type.getDataType() == Color.class) {
+ int i = 0;
+
+ if (functionType == RAINBOW1) {
+ for (Object key : attrSet) {
+ hue = hue + increment;
+ valueMap.put(key, new Color(Color.HSBtoRGB(hue, 1f, 1f)));
+ }
+ } else if (functionType == RAINBOW2) {
+ for (Object key : attrSet) {
+ hue = hue + increment;
+ sat = (Math.abs(((Number) Math.cos((8 * i) / (2 * Math.PI))).floatValue()) * 0.7f)
+ + 0.3f;
+ br = (Math.abs(((Number) Math.sin(((i) / (2 * Math.PI)) + (Math.PI / 2)))
+ .floatValue()) * 0.7f) + 0.3f;
+ valueMap.put(key, new Color(Color.HSBtoRGB(hue, sat, br)));
+ i++;
+ }
+ } else {
+ for (Object key : attrSet)
+ valueMap.put(key,
+ new Color(((Number) (rand.nextFloat() * MAX_COLOR))
+ [...]
+ }
+ } else if ((type.getDataType() == Number.class) && (functionType == RANDOM)) {
+ final String range = JOptionPane.showInputDialog(visualPropertySheetPanel,
+ "Please enter the value range (example: 30-100)",
+ "Assign Random Numbers",
+ JOptionPane.PLAIN_MESSAGE);
+
+ String[] rangeVals = range.split("-");
+
+ if (rangeVals.length != 2)
+ return;
+
+ Float min = Float.valueOf(rangeVals[0]);
+ Float max = Float.valueOf(rangeVals[1]);
+ Float valueRange = max - min;
+
+ for (Object key : attrSet)
+ valueMap.put(key, (rand.nextFloat() * valueRange) + min);
+ }
+
+ dm.putAll(valueMap);
+ vmm.setNetworkView(Cytoscape.getCurrentNetworkView());
+ Cytoscape.getCurrentNetworkView().redrawGraph(false, true);
+
+ visualPropertySheetPanel.removeProperty(prop);
+
+ final VizMapperProperty newRootProp = new VizMapperProperty();
+
+ if (type.isNodeProp())
+ buildProperty(vmm.getVisualStyle().getNodeAppearanceCalculator()
+ .getCalculator(type), newRootProp, NODE_VISUAL_MAPPING);
+ else
+ buildProperty(vmm.getVisualStyle().getEdgeAppearanceCalculator()
+ .getCalculator(type), newRootProp, EDGE_VISUAL_MAPPING);
+
+ removeProperty(prop);
+ propertyMap.get(vmm.getVisualStyle().getName()).add(newRootProp);
+
+ expandLastSelectedItem(type.getName());
+ } else {
+ logger.info("Invalid.");
+ }
+
+ return;
+ }
+ }
+
+ private class GenerateSeriesListener extends AbstractAction {
+ private DiscreteMapping dm;
+
+ /**
+ * User wants to Seed the Discrete Mapper with Random Color Values.
+ */
+ public void actionPerformed(ActionEvent e) {
+ /*
+ * Check Selected poperty
+ */
+ final int selectedRow = visualPropertySheetPanel.getTable().getSelectedRow();
+
+ if (selectedRow < 0)
+ return;
+
+ final Item item = (Item) visualPropertySheetPanel.getTable().getValueAt(selectedRow, 0);
+ final VizMapperProperty prop = (VizMapperProperty) item.getProperty();
+ final Object hidden = prop.getHiddenObject();
+
+ if (hidden instanceof VisualPropertyType) {
+ final VisualPropertyType type = (VisualPropertyType) hidden;
+
+ final Map valueMap = new HashMap();
+ final ObjectMapping oMap;
+ final CyAttributes attr;
+ final boolean isNode;
+
+ if (type.isNodeProp()) {
+ attr = Cytoscape.getNodeAttributes();
+ oMap = vmm.getVisualStyle().getNodeAppearanceCalculator().getCalculator(type)
+ .getMapping(0);
+ isNode = true;
+ } else {
+ attr = Cytoscape.getEdgeAttributes();
+ oMap = vmm.getVisualStyle().getEdgeAppearanceCalculator().getCalculator(type)
+ .getMapping(0);
+ isNode = false;
+ }
+
+ if ((oMap instanceof DiscreteMapping) == false)
+ return;
+
+ dm = (DiscreteMapping) oMap;
+
+ final Set<Object> attrSet = MappingKeyFactory.getKeySet(oMap.getControllingAttributeName(), attr,
+ oMap, isNode);
+ final String start = JOptionPane.showInputDialog(visualPropertySheetPanel,
+ "Please enter start value (1st number in the series)",
+ "0");
+ final String increment = JOptionPane.showInputDialog(visualPropertySheetPanel,
+ "Please enter increment", "1");
+
+ if ((increment == null) || (start == null))
+ return;
+
+ Float inc;
+ Float st;
+
+ try {
+ inc = Float.valueOf(increment);
+ st = Float.valueOf(start);
+ } catch (Exception ex) {
+ JOptionPane.showMessageDialog(visualPropertySheetPanel,
+ "Start value and increment must be numeric values!",
+ "Non-numeric input error", JOptionPane.ERROR_MESSAGE);
+ inc = null;
+ st = null;
+ }
+
+ if ((inc == null) || (inc < 0) || (st == null) || (st == null)) {
+ return;
+ }
+
+ if (type.getDataType() == Number.class) {
+ for (Object key : attrSet) {
+ valueMap.put(key, st);
+ st = st + inc;
+ }
+ }
+
+ dm.putAll(valueMap);
+
+ vmm.setNetworkView(Cytoscape.getCurrentNetworkView());
+ Cytoscape.getCurrentNetworkView().redrawGraph(false, true);
+
+ visualPropertySheetPanel.removeProperty(prop);
+
+ final VizMapperProperty newRootProp = new VizMapperProperty();
+
+ if (type.isNodeProp())
+ buildProperty(vmm.getVisualStyle().getNodeAppearanceCalculator()
+ .getCalculator(type), newRootProp, NODE_VISUAL_MAPPING);
+ else
+ buildProperty(vmm.getVisualStyle().getEdgeAppearanceCalculator()
+ .getCalculator(type), newRootProp, EDGE_VISUAL_MAPPING);
+
+ removeProperty(prop);
+ propertyMap.get(vmm.getVisualStyle().getName()).add(newRootProp);
+
+ expandLastSelectedItem(type.getName());
+ } else {
+ logger.info("Invalid.");
+ }
+
+ return;
+ }
+ }
+
+ private class FitLabelListener extends AbstractAction {
+ private DiscreteMapping dm;
+
+ /**
+ * User wants to Seed the Discrete Mapper with Random Color Values.
+ */
+ public void actionPerformed(ActionEvent e) {
+ /*
+ * Check Selected poperty
+ */
+ final int selectedRow = visualPropertySheetPanel.getTable().getSelectedRow();
+
+ if (selectedRow < 0)
+ return;
+
+ final Item item = (Item) visualPropertySheetPanel.getTable().getValueAt(selectedRow, 0);
+ final VizMapperProperty prop = (VizMapperProperty) item.getProperty();
+ final Object hidden = prop.getHiddenObject();
+
+ if (hidden instanceof VisualPropertyType) {
+ final VisualPropertyType type = (VisualPropertyType) hidden;
+
+ final Map valueMap = new HashMap();
+ final ObjectMapping oMap;
+ final CyAttributes attr;
+
+ if (type.isNodeProp()) {
+ attr = Cytoscape.getNodeAttributes();
+ oMap = vmm.getVisualStyle().getNodeAppearanceCalculator().getCalculator(type)
+ .getMapping(0);
+ } else {
+ attr = Cytoscape.getEdgeAttributes();
+ oMap = vmm.getVisualStyle().getEdgeAppearanceCalculator().getCalculator(type)
+ .getMapping(0);
+ }
+
+ if ((oMap instanceof DiscreteMapping) == false)
+ return;
+
+ dm = (DiscreteMapping) oMap;
+
+ final Calculator nodeLabelCalc = vmm.getVisualStyle().getNodeAppearanceCalculator()
+ .getCalculator(VisualPropertyType.NODE_LABEL);
+
+ if (nodeLabelCalc == null) {
+ return;
+ }
+
+ final String ctrAttrName = nodeLabelCalc.getMapping(0).getControllingAttributeName();
+ dm.setControllingAttributeName(ctrAttrName);
+
+ // final Set<Object> attrSet =
+ // loadKeys(oMap.getControllingAttributeName(), attr, oMap);
+ if (vmm.getVisualStyle().getDependency().check(NODE_SIZE_LOCKED)) {
+ return;
+ }
+
+ DiscreteMapping wm = null;
+
+ if ((type == NODE_WIDTH)) {
+ wm = (DiscreteMapping) vmm.getVisualStyle().getNodeAppearanceCalculator()
+ .getCalculator(NODE_WIDTH).getMapping(0);
+
+ wm.setControllingAttributeName(ctrAttrName);
+
+ Set<Object> attrSet1;
+
+ if (ctrAttrName.equals("ID")) {
+ attrSet1 = new TreeSet<Object>();
+
+ for (Object node : Cytoscape.getCurrentNetwork().nodesList()) {
+ attrSet1.add(((Node) node).getIdentifier());
+ }
+ } else {
+ attrSet1 = MappingKeyFactory.getKeySet(wm.getControllingAttributeName(), attr, wm,
+ true);
+ }
+
+ Integer height = ((Number) (vmm.getVisualStyle().getNodeAppearanceCalculator()
+ .getDefaultAppearance().get(NODE_FONT_SIZE)))
+ [...]
+ vmm.getVisualStyle().getNodeAppearanceCalculator().getDefaultAppearance()
+ .set(NODE_HEIGHT, height * 2.5);
+
+ Integer fontSize = ((Number) vmm.getVisualStyle().getNodeAppearanceCalculator()
+ .getDefaultAppearance().get(NODE_FONT_SIZE))
+ [...]
+ int strLen;
+
+ String labelString = null;
+ String[] listObj;
+ int longest = 0;
+
+ if (attr.getType(ctrAttrName) == CyAttributes.TYPE_SIMPLE_LIST) {
+ wm.setControllingAttributeName("ID");
+
+ attrSet1 = new TreeSet<Object>();
+
+ for (Object node : Cytoscape.getCurrentNetwork().nodesList()) {
+ attrSet1.add(((Node) node).getIdentifier());
+ }
+
+ CyNetworkView net = Cytoscape.getCurrentNetworkView();
+ String text;
+
+ for (Object node : net.getNetwork().nodesList()) {
+ text = net.getNodeView((Node) node).getLabel().getText();
+ strLen = text.length();
+
+ if (strLen != 0) {
+ listObj = text.split("\\n");
+ longest = 0;
+
+ for (String s : listObj) {
+ if (s.length() > longest) {
+ longest = s.length();
+ }
+ }
+
+ strLen = longest;
+
+ if (strLen > 25) {
+ valueMap.put(((Node) node).getIdentifier(),
+ strLen * fontSize * 0.6);
+ } else {
+ valueMap.put(((Node) node).getIdentifier(),
+ strLen * fontSize * 0.8);
+ }
+ }
+ }
+ } else {
+ for (Object label : attrSet1) {
+ labelString = label.toString();
+ strLen = labelString.length();
+
+ if (strLen != 0) {
+ if (labelString.contains("\n")) {
+ listObj = labelString.split("\\n");
+ longest = 0;
+
+ for (String s : listObj) {
+ if (s.length() > longest) {
+ longest = s.length();
+ }
+ }
+
+ strLen = longest;
+ }
+
+ if (strLen > 25) {
+ valueMap.put(label, strLen * fontSize * 0.6);
+ } else {
+ valueMap.put(label, strLen * fontSize * 0.8);
+ }
+ }
+ }
+ }
+ } else if ((type == NODE_HEIGHT)) {
+ wm = (DiscreteMapping) vmm.getVisualStyle().getNodeAppearanceCalculator()
+ .getCalculator(NODE_HEIGHT).getMapping(0);
+
+ wm.setControllingAttributeName(ctrAttrName);
+
+ Set<Object> attrSet1;
+
+ if (ctrAttrName.equals("ID")) {
+ attrSet1 = new TreeSet<Object>();
+
+ for (Object node : Cytoscape.getCurrentNetwork().nodesList()) {
+ attrSet1.add(((Node) node).getIdentifier());
+ }
+ } else {
+ attrSet1 = MappingKeyFactory.getKeySet(wm.getControllingAttributeName(), attr, wm,
+ true);
+ }
+
+ Integer fontSize = ((Number) vmm.getVisualStyle().getNodeAppearanceCalculator()
+ .getDefaultAppearance().get(NODE_FONT_SIZE))
+ [...]
+ int strLen;
+
+ String labelString = null;
+ String[] listObj;
+
+ if (attr.getType(ctrAttrName) == CyAttributes.TYPE_SIMPLE_LIST) {
+ wm.setControllingAttributeName("ID");
+
+ attrSet1 = new TreeSet<Object>();
+
+ for (Object node : Cytoscape.getCurrentNetwork().nodesList()) {
+ attrSet1.add(((Node) node).getIdentifier());
+ }
+
+ CyNetworkView net = Cytoscape.getCurrentNetworkView();
+ String text;
+
+ for (Object node : net.getNetwork().nodesList()) {
+ text = net.getNodeView((Node) node).getLabel().getText();
+ strLen = text.length();
+
+ if (strLen != 0) {
+ listObj = text.split("\\n");
+ valueMap.put(((Node) node).getIdentifier(),
+ listObj.length * fontSize * 1.6);
+ }
+ }
+ } else {
+ for (Object label : attrSet1) {
+ labelString = label.toString();
+ strLen = labelString.length();
+
+ if (strLen != 0) {
+ if (labelString.contains("\n")) {
+ listObj = labelString.split("\\n");
+
+ strLen = listObj.length;
+ } else {
+ strLen = 1;
+ }
+
+ valueMap.put(label, strLen * fontSize * 1.6);
+ }
+ }
+ }
+ }
+
+ wm.putAll(valueMap);
+
+ vmm.setNetworkView(Cytoscape.getCurrentNetworkView());
+ Cytoscape.getCurrentNetworkView().redrawGraph(false, true);
+
+ visualPropertySheetPanel.removeProperty(prop);
+
+ final VizMapperProperty newRootProp = new VizMapperProperty();
+
+ if (type.isNodeProp())
+ buildProperty(vmm.getVisualStyle().getNodeAppearanceCalculator()
+ .getCalculator(type), newRootProp, NODE_VISUAL_MAPPING);
+ else
+ buildProperty(vmm.getVisualStyle().getEdgeAppearanceCalculator()
+ .getCalculator(type), newRootProp, EDGE_VISUAL_MAPPING);
+
+ removeProperty(prop);
+ propertyMap.get(vmm.getVisualStyle().getName()).add(newRootProp);
+
+ expandLastSelectedItem(type.getName());
+ } else {
+ logger.info("Invalid.");
+ }
+
+ return;
+ }
+ }
+
+ private class BrightnessListener extends AbstractAction {
+ private DiscreteMapping dm;
+ protected static final int DARKER = 1;
+ protected static final int BRIGHTER = 2;
+ private final int functionType;
+
+ public BrightnessListener(final int type) {
+ this.functionType = type;
+ }
+
+ /**
+ * User wants to Seed the Discrete Mapper with Random Color Values.
+ */
+ public void actionPerformed(ActionEvent e) {
+ /*
+ * Check Selected poperty
+ */
+ final int selectedRow = visualPropertySheetPanel.getTable().getSelectedRow();
+
+ if (selectedRow < 0) {
+ return;
+ }
+
+ final Item item = (Item) visualPropertySheetPanel.getTable().getValueAt(selectedRow, 0);
+ final VizMapperProperty prop = (VizMapperProperty) item.getProperty();
+ final Object hidden = prop.getHiddenObject();
+
+ if (hidden instanceof VisualPropertyType) {
+ final VisualPropertyType type = (VisualPropertyType) hidden;
+
+ final Map valueMap = new HashMap();
+ final ObjectMapping oMap;
+
+ final CyAttributes attr;
+ final boolean nOre;
+
+ if (type.isNodeProp()) {
+ attr = Cytoscape.getNodeAttributes();
+ oMap = vmm.getVisualStyle().getNodeAppearanceCalculator().getCalculator(type)
+ .getMapping(0);
+ nOre = true;
+ } else {
+ attr = Cytoscape.getEdgeAttributes();
+ oMap = vmm.getVisualStyle().getEdgeAppearanceCalculator().getCalculator(type)
+ .getMapping(0);
+ nOre = false;
+ }
+
+ if ((oMap instanceof DiscreteMapping) == false) {
+ return;
+ }
+
+ dm = (DiscreteMapping) oMap;
+
+ final Set<Object> attrSet = MappingKeyFactory.getKeySet(oMap.getControllingAttributeName(), attr,
+ oMap, nOre);
+
+ /*
+ * Create random colors
+ */
+ if (type.getDataType() == Color.class) {
+ Object c;
+
+ if (functionType == BRIGHTER) {
+ for (Object key : attrSet) {
+ c = dm.getMapValue(key);
+
+ if ((c != null) && c instanceof Color) {
+ valueMap.put(key, ((Color) c).brighter());
+ }
+ }
+ } else if (functionType == DARKER) {
+ for (Object key : attrSet) {
+ c = dm.getMapValue(key);
+
+ if ((c != null) && c instanceof Color) {
+ valueMap.put(key, ((Color) c).darker());
+ }
+ }
+ }
+ }
+
+ dm.putAll(valueMap);
+ vmm.setNetworkView(Cytoscape.getCurrentNetworkView());
+ Cytoscape.getCurrentNetworkView().redrawGraph(false, true);
+
+ visualPropertySheetPanel.removeProperty(prop);
+
+ final VizMapperProperty newRootProp = new VizMapperProperty();
+
+ if (type.isNodeProp())
+ buildProperty(vmm.getVisualStyle().getNodeAppearanceCalculator()
+ .getCalculator(type), newRootProp, NODE_VISUAL_MAPPING);
+ else
+ buildProperty(vmm.getVisualStyle().getEdgeAppearanceCalculator()
+ .getCalculator(type), newRootProp, EDGE_VISUAL_MAPPING);
+
+ removeProperty(prop);
+ propertyMap.get(vmm.getVisualStyle().getName()).add(newRootProp);
+
+ expandLastSelectedItem(type.getName());
+ } else {
+ logger.info("Invalid.");
+ }
+
+ return;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param arg0
+ * DOCUMENT ME!
+ */
+ public void popupMenuCanceled(PopupMenuEvent arg0) {
+ disableAllPopup();
+ }
+
+ private void disableAllPopup() {
+ rainbow1.setEnabled(false);
+ rainbow2.setEnabled(false);
+ randomize.setEnabled(false);
+ series.setEnabled(false);
+ fit.setEnabled(false);
+ brighter.setEnabled(false);
+ darker.setEnabled(false);
+ delete.setEnabled(false);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void popupMenuWillBecomeInvisible(PopupMenuEvent e) {
+ }
+
+ /**
+ * Check the selected VPT and enable/disable menu items.
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void popupMenuWillBecomeVisible(PopupMenuEvent e) {
+ disableAllPopup();
+
+ final int selected = visualPropertySheetPanel.getTable().getSelectedRow();
+
+ if (0 > selected) {
+ return;
+ }
+
+ final Item item = (Item) visualPropertySheetPanel.getTable().getValueAt(selected, 0);
+ final Property curProp = item.getProperty();
+
+ if (curProp == null)
+ return;
+
+ VizMapperProperty prop = ((VizMapperProperty) curProp);
+
+ if (prop.getHiddenObject() instanceof VisualPropertyType
+ && (prop.getDisplayName().contains("Mapping Type") == false)
+ && (prop.getValue() != null)
+ && (prop.getValue().toString().startsWith("Please select") == false)) {
+ // Enble delete menu
+ delete.setEnabled(true);
+
+ Property[] children = prop.getSubProperties();
+
+ for (Property p : children) {
+ if ((p.getDisplayName() != null) && p.getDisplayName().contains("Mapping Type")) {
+ if ((p.getValue() == null)
+ || (p.getValue().equals("Discrete Mapping") == false)) {
+ return;
+ }
+ }
+ }
+
+ VisualPropertyType type = ((VisualPropertyType) prop.getHiddenObject());
+
+ Class dataType = type.getDataType();
+
+ if (dataType == Color.class) {
+ rainbow1.setEnabled(true);
+ rainbow2.setEnabled(true);
+ randomize.setEnabled(true);
+ brighter.setEnabled(true);
+ darker.setEnabled(true);
+ } else if (dataType == Number.class) {
+ randomize.setEnabled(true);
+ series.setEnabled(true);
+ }
+
+ if ((type == VisualPropertyType.NODE_WIDTH) || (type == VisualPropertyType.NODE_HEIGHT)) {
+ fit.setEnabled(true);
+ }
+ }
+
+ return;
+ }
+
+
+ /**
+ * Listening to Visual Style states.
+ * Will be called when Visual Style added/removed
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void stateChanged(ChangeEvent e) {
+ if (ignore)
+ return;
+
+ // Get current Visual Style
+ final String currentName = vmm.getVisualStyle().getName();
+ final Object selected = vsNameComboBox.getSelectedItem();
+
+ if (selected != null && selected.toString().equals(currentName)) {
+ return;
+ }
+
+ // Update GUI based on CalcCatalog's state.
+ if (!findVSName(currentName)) {
+ syncStyleBox();
+ } else
+ vsNameComboBox.setSelectedItem(currentName);
+
+ lastVSName = currentName;
+ }
+
+ private void syncStyleBox() {
+
+ final String curStyleName = vmm.getVisualStyle().getName();
+ final CalculatorCatalog catalog = vmm.getCalculatorCatalog();
+
+ String styleName;
+ final List<String> namesInBox = new ArrayList<String>();
+ namesInBox.addAll(catalog.getVisualStyleNames());
+ for (int i = 0; i < vsNameComboBox.getItemCount(); i++) {
+ styleName = vsNameComboBox.getItemAt(i).toString();
+
+ if (catalog.getVisualStyle(styleName) == null) {
+ // No longer exists in the VMM. Remove.
+ vsNameComboBox.removeItem(styleName);
+ defaultImageManager.remove(styleName);
+ propertyMap.remove(styleName);
+ }
+ }
+
+ Collections.sort(namesInBox);
+
+ // Reset combobox items.
+ vsNameComboBox.removeAllItems();
+
+ for (final String name : namesInBox)
+ vsNameComboBox.addItem(name);
+
+ switchVS(curStyleName);
+ }
+
+ // return true iff 'match' is found as a name within the
+ // vsNameComboBox.
+ private boolean findVSName(String match) {
+ for (int i = 0; i < vsNameComboBox.getItemCount(); i++) {
+ if (vsNameComboBox.getItemAt(i).equals(match)) {
+ return true;
+ }
+ }
+
+ return false;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getSelectedItem() {
+ final JTable table = visualPropertySheetPanel.getTable();
+
+ return table.getModel().getValueAt(table.getSelectedRow(), 0);
+ }
+
+
+ public void attributeDefined(String attributeName) {
+ setAttrComboBox();
+ }
+
+
+ public void attributeUndefined(String attributeName) {
+ setAttrComboBox();
+ }
+}
+
diff --git a/application/src/main/java/cytoscape/visual/ui/VizMapperProperty.java b/application/src/main/java/cytoscape/visual/ui/VizMapperProperty.java
new file mode 100644
index 0000000..ecbd24a
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/VizMapperProperty.java
@@ -0,0 +1,52 @@
+package cytoscape.visual.ui;
+
+import com.l2fprod.common.propertysheet.DefaultProperty;
+
+
+/**
+ * Extended version of DefaultProperty which accepts one more value as hidden
+ * object.
+ *
+ * @author kono
+ *
+ */
+public class VizMapperProperty extends DefaultProperty {
+
+ private static final long serialVersionUID = -9103147252041414576L;
+
+ private Object hiddenObject;
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param obj DOCUMENT ME!
+ */
+ public void setHiddenObject(Object obj) {
+ this.hiddenObject = obj;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getHiddenObject() {
+ return hiddenObject;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param object DOCUMENT ME!
+ */
+ public void readFromObject(Object object) {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param object DOCUMENT ME!
+ */
+ public void writeToObject(Object object) {
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/ui/editors/continuous/BelowAndAbovePanel.java b/application/src/main/java/cytoscape/visual/ui/editors/continuous/BelowAndAbovePanel.java
new file mode 100644
index 0000000..61d269b
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/editors/continuous/BelowAndAbovePanel.java
@@ -0,0 +1,204 @@
+package cytoscape.visual.ui.editors.continuous;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.util.CyColorChooser;
+import cytoscape.visual.VisualPropertyType;
+
+import cytoscape.visual.mappings.BoundaryRangeValues;
+import cytoscape.visual.mappings.ContinuousMapping;
+
+import java.awt.BasicStroke;
+import java.awt.Color;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.Polygon;
+import java.awt.RenderingHints;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+
+import javax.swing.JColorChooser;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+
+
+/**
+ * Drawing and updating below & above values in Gradient Editor.
+ *
+ * @author $author$
+ */
+public class BelowAndAbovePanel extends JPanel {
+ private VisualPropertyType type;
+ private Color boxColor;
+ private boolean below;
+ private Object value;
+
+ /**
+ * DOCUMENT ME!
+ */
+ public static final String COLOR_CHANGED = "COLOR_CHANGED";
+
+ /**
+ * Creates a new BelowAndAbovePanel object. This will be used for drawing
+ * below & above triangle
+ *
+ * @param color
+ * DOCUMENT ME!
+ * @param below
+ * DOCUMENT ME!
+ */
+ public BelowAndAbovePanel(VisualPropertyType type, Color color,
+ boolean below) {
+ this.boxColor = color;
+ this.below = below;
+ this.type = type;
+
+ if (below)
+ this.setToolTipText("Double-click triangle to set below color...");
+ else
+ this.setToolTipText("Double-click triangle to set above color...");
+
+ this.addMouseListener(new MouseEventHandler(this));
+ }
+
+ /**
+ * Creates a new BelowAndAbovePanel object.
+ *
+ * @param type DOCUMENT ME!
+ * @param below DOCUMENT ME!
+ */
+ public BelowAndAbovePanel(VisualPropertyType type, boolean below) {
+ this(type, Color.DARK_GRAY, below);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param newColor DOCUMENT ME!
+ */
+ public void setColor(Color newColor) {
+ final Color oldColor = boxColor;
+ this.boxColor = newColor;
+ this.repaint();
+ this.getParent()
+ .repaint();
+
+ this.firePropertyChange(COLOR_CHANGED, oldColor, newColor);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param value DOCUMENT ME!
+ */
+ public void setValue(Object value) {
+ this.value = value;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g
+ * DOCUMENT ME!
+ */
+ public void paintComponent(Graphics g) {
+ final Graphics2D g2d = (Graphics2D) g;
+
+ final Polygon poly = new Polygon();
+
+ g2d.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+ RenderingHints.VALUE_ANTIALIAS_ON);
+
+ g2d.setStroke(new BasicStroke(1.0f));
+ g2d.setColor(boxColor);
+
+ if (below) {
+ poly.addPoint(9, 0);
+ poly.addPoint(9, 10);
+ poly.addPoint(0, 5);
+ } else {
+ poly.addPoint(0, 0);
+ poly.addPoint(0, 10);
+ poly.addPoint(9, 5);
+ }
+
+ g2d.fillPolygon(poly);
+
+ g2d.setColor(Color.black);
+ g2d.draw(poly);
+ }
+
+ class MouseEventHandler extends MouseAdapter {
+ private BelowAndAbovePanel caller;
+
+ public MouseEventHandler(BelowAndAbovePanel c) {
+ this.caller = c;
+ }
+
+ public void mouseClicked(MouseEvent e) {
+ if (e.getClickCount() == 2) {
+
+ Object newValue = null;
+ if (type.getDataType() == Color.class) {
+ newValue = CyColorChooser.showDialog(caller, "Select new color",
+ boxColor);
+ caller.setColor((Color)newValue);
+ }
+ else if (type.getDataType() == Number.class) {
+ newValue = Double.parseDouble(JOptionPane.showInputDialog(caller, "Please enter new value."));
+ caller.setValue(newValue);
+ }
+
+ if(newValue == null) {
+ return;
+ }
+
+ final ContinuousMapping cMapping;
+
+ if (type.isNodeProp())
+ cMapping = (ContinuousMapping) Cytoscape.getVisualMappingManager()
+ .getVisualStyle()
+ .getNodeAppearanceCalculator()
+ .getCalculator(type)
+ .getMapping(0);
+ else
+ cMapping = (ContinuousMapping) Cytoscape.getVisualMappingManager()
+ .getVisualStyle()
+ .getEdgeAppearanceCalculator()
+ .getCalculator(type)
+ .getMapping(0);
+
+ BoundaryRangeValues brv;
+ BoundaryRangeValues original;
+
+ if (below) {
+ original = cMapping.getPoint(0)
+ .getRange();
+ brv = new BoundaryRangeValues(newValue,
+ original.equalValue, original.greaterValue);
+ cMapping.getPoint(0)
+ .setRange(brv);
+ } else {
+ original = cMapping.getPoint(cMapping.getPointCount() - 1)
+ .getRange();
+
+ brv = new BoundaryRangeValues(original.lesserValue,
+ original.equalValue, newValue);
+ cMapping.getPoint(cMapping.getPointCount() - 1)
+ .setRange(brv);
+ }
+
+ cMapping.fireStateChanged();
+
+ // Update view.
+ Cytoscape.getVisualMappingManager()
+ .getNetworkView()
+ .redrawGraph(false, true);
+
+ caller.repaint();
+ caller.getParent()
+ .repaint();
+ }
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/ui/editors/continuous/C2CMappingEditor.java b/application/src/main/java/cytoscape/visual/ui/editors/continuous/C2CMappingEditor.java
new file mode 100644
index 0000000..1497854
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/editors/continuous/C2CMappingEditor.java
@@ -0,0 +1,293 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.visual.ui.editors.continuous;
+
+import cytoscape.Cytoscape;
+import cytoscape.logger.CyLogger;
+
+import cytoscape.visual.VisualPropertyType;
+
+import cytoscape.visual.mappings.BoundaryRangeValues;
+import cytoscape.visual.mappings.continuous.ContinuousMappingPoint;
+
+import org.jdesktop.swingx.multislider.Thumb;
+import org.jdesktop.swingx.multislider.TrackRenderer;
+
+import java.awt.Dimension;
+import java.awt.event.ActionEvent;
+
+import java.util.List;
+
+import java.beans.PropertyChangeEvent;
+
+import javax.swing.ImageIcon;
+
+
+/**
+ * Continuous-Continuous mapping editor.<br>
+ *
+ * <p>
+ * This is a editor for continuous values, i.e., numbers.
+ * </p>
+ *
+ * @version 0.7
+ * @since Cytoscape 2.5
+ * @author Keiichiro Ono
+ *
+ */
+public class C2CMappingEditor extends ContinuousMappingEditorPanel {
+
+ private static final long serialVersionUID = -3555354576428996187L;
+
+ // Default value for below and above.
+ private static final Float DEF_BELOW_AND_ABOVE = 1f;
+
+ private static final Float DEFAULT_MIN = 0f;
+ private static final Float DEFAULT_MAX = 100f;
+
+ /**
+ * Creates a new C2CMappingEditor object.
+ * This is for mappings from numbers to numbers.
+ *
+ * @param type DOCUMENT ME!
+ */
+ public C2CMappingEditor(VisualPropertyType type) {
+ super(type);
+ abovePanel.setVisible(false);
+ belowPanel.setVisible(false);
+ pack();
+ setSlider();
+
+ // Add two sliders by default.
+ if ((mapping != null) && (mapping.getPointCount() == 0)) {
+ addSlider(DEFAULT_MIN, 10f);
+ addSlider(DEFAULT_MAX, 30f);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param width DOCUMENT ME!
+ * @param height DOCUMENT ME!
+ * @param title DOCUMENT ME!
+ * @param type DOCUMENT ME!
+ */
+ public static Object showDialog(final int width, final int height, final String title,
+ final VisualPropertyType type) {
+ editor = new C2CMappingEditor(type);
+ final Dimension size = new Dimension(width, height);
+ editor.setPreferredSize(size);
+ editor.setSize(size);
+
+ editor.setTitle(title);
+ editor.setAlwaysOnTop(true);
+ editor.setLocationRelativeTo(Cytoscape.getDesktop());
+ editor.setVisible(true);
+
+ return editor;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static ImageIcon getIcon(final int iconWidth, final int iconHeight,
+ VisualPropertyType type) {
+ editor = new C2CMappingEditor(type);
+
+ TrackRenderer rend = editor.slider.getTrackRenderer();
+
+ if (rend instanceof ContinuousTrackRenderer) {
+ rend.getRendererComponent(editor.slider);
+
+ return ((ContinuousTrackRenderer) rend).getTrackGraphicIcon(iconWidth, iconHeight);
+ } else {
+ return null;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param width DOCUMENT ME!
+ * @param height DOCUMENT ME!
+ * @param type DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static ImageIcon getLegend(final int width, final int height,
+ final VisualPropertyType type) {
+ editor = new C2CMappingEditor(type);
+
+ final ContinuousTrackRenderer rend = (ContinuousTrackRenderer) editor.slider.getTrackRenderer();
+ rend.getRendererComponent(editor.slider);
+
+ return rend.getLegend(width, height);
+ }
+
+
+ // Add slider to the editor.
+ private void addSlider(float position, float value) {
+ final double maxValue = EditorValueRangeTracer.getTracer().getMax(type);
+
+ BoundaryRangeValues newRange;
+
+ if (mapping.getPointCount() == 0) {
+ slider.getModel().addThumb(position, value);
+
+ newRange = new BoundaryRangeValues(below, 5f, above);
+ mapping.addPoint(maxValue / 2, newRange);
+
+ if (position != DEFAULT_MIN && position != DEFAULT_MAX)
+ selectThumbAtPosition(position);
+
+ slider.repaint();
+ repaint();
+
+ return;
+ }
+
+ // Add a new white thumb
+ slider.getModel().addThumb(position, value);
+
+ // Pick Up first point.
+ final ContinuousMappingPoint previousPoint = mapping.getPoint(mapping.getPointCount() - 1);
+
+ final BoundaryRangeValues previousRange = previousPoint.getRange();
+ newRange = new BoundaryRangeValues(previousRange);
+
+ newRange.lesserValue = slider.getModel().getSortedThumbs()
+ .get(slider.getModel().getThumbCount() - 1);
+ newRange.equalValue = 5f;
+ newRange.greaterValue = previousRange.greaterValue;
+ mapping.addPoint(maxValue, newRange);
+
+ updateMap();
+
+ if (position != DEFAULT_MIN && position != DEFAULT_MAX) {
+ updateCytoscape();
+
+ // Make this slider the selected one
+ selectThumbAtPosition(position);
+ }
+
+ slider.repaint();
+ repaint();
+ }
+
+ @Override
+ protected void addButtonActionPerformed(ActionEvent evt) {
+ addSlider(51f, 5f);
+ }
+
+
+ /**
+ * Remove selected slider.
+ */
+ @Override protected void deleteButtonActionPerformed(ActionEvent evt) {
+ if(slider.getModel().getThumbCount() <=0)
+ return;
+
+ final int selectedIndex = ((TriangleThumbRenderer)slider.getThumbRenderer()).getSelectedIndex();
+
+ if(selectedIndex<0)
+ return;
+
+ slider.getModel().removeThumb(selectedIndex);
+ mapping.removePoint(selectedIndex);
+
+ updateMap();
+ updateCytoscape();
+ ((ContinuousTrackRenderer) slider.getTrackRenderer()).removeSquare(selectedIndex);
+
+ mapping.fireStateChanged();
+
+ repaint();
+ }
+
+ private void setSlider() {
+ slider.updateUI();
+
+ final double minValue = EditorValueRangeTracer.getTracer().getMin(type);
+ double actualRange = EditorValueRangeTracer.getTracer().getRange(type);
+
+ BoundaryRangeValues bound;
+ Float fraction;
+
+ if (allPoints != null && allPoints.size() != 0) {
+
+ for (ContinuousMappingPoint point : allPoints) {
+ bound = point.getRange();
+
+ fraction = ((Number) ((point.getValue().doubleValue() - minValue) / actualRange)).floatValue() * 100;
+ slider.getModel().addThumb(fraction, ((Number) bound.equalValue).floatValue());
+ }
+
+ below = (Number) allPoints.get(0).getRange().lesserValue;
+ above = (Number) allPoints.get(allPoints.size() - 1).getRange().greaterValue;
+ } else {
+ below = DEF_BELOW_AND_ABOVE;
+ above = DEF_BELOW_AND_ABOVE;
+ }
+
+ /*
+ * get min and max for the value object
+ */
+ TriangleThumbRenderer thumbRend = new TriangleThumbRenderer(slider);
+
+ ContinuousTrackRenderer cRend = new ContinuousTrackRenderer(type,
+ (Number) below, (Number) above, mapping, slider);
+ cRend.addPropertyChangeListener(this);
+
+ slider.setThumbRenderer(thumbRend);
+ slider.setTrackRenderer(cRend);
+ slider.addMouseListener(new ThumbMouseListener());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt DOCUMENT ME!
+ */
+ public void propertyChange(PropertyChangeEvent evt) {
+ if (evt.getPropertyName().equals(ContinuousMappingEditorPanel.BELOW_VALUE_CHANGED)) {
+ below = evt.getNewValue();
+ } else if (evt.getPropertyName().equals(ContinuousMappingEditorPanel.ABOVE_VALUE_CHANGED)) {
+ above = evt.getNewValue();
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/ui/editors/continuous/C2DMappingEditor.java b/application/src/main/java/cytoscape/visual/ui/editors/continuous/C2DMappingEditor.java
new file mode 100644
index 0000000..3c226f6
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/editors/continuous/C2DMappingEditor.java
@@ -0,0 +1,355 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.visual.ui.editors.continuous;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.logger.CyLogger;
+import cytoscape.visual.VisualPropertyType;
+
+import cytoscape.visual.mappings.BoundaryRangeValues;
+import cytoscape.visual.mappings.continuous.ContinuousMappingPoint;
+
+import org.jdesktop.swingx.multislider.Thumb;
+
+import java.awt.Dimension;
+import java.awt.event.ActionEvent;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+
+import java.beans.PropertyChangeEvent;
+
+import java.util.List;
+
+import javax.swing.ImageIcon;
+
+
+/**
+ * Continuous Mapping editor for discrete values,
+ * such as Font, Shape, Label Position, etc.
+ *
+ * @version 0.5
+ * @since Cytoscape 2.5
+ * @author Keiichiro Ono
+ */
+public class C2DMappingEditor extends ContinuousMappingEditorPanel {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 2146889489175240626L;
+
+ /**
+ * Creates a new C2DMappingEditor object.
+ *
+ * @param type DOCUMENT ME!
+ */
+ public C2DMappingEditor(VisualPropertyType type) {
+ super(type);
+ this.iconPanel.setVisible(false);
+ this.belowPanel.setVisible(false);
+ this.abovePanel.setVisible(false);
+ setSlider();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param width DOCUMENT ME!
+ * @param height DOCUMENT ME!
+ * @param title DOCUMENT ME!
+ * @param type DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static Object showDialog(final int width, final int height, final String title,
+ VisualPropertyType type) {
+ editor = new C2DMappingEditor(type);
+
+ final Dimension size = new Dimension(width, height);
+ editor.setPreferredSize(size);
+ editor.setSize(size);
+
+ editor.setTitle(title);
+ editor.setAlwaysOnTop(true);
+ editor.setLocationRelativeTo(Cytoscape.getDesktop());
+ editor.setVisible(true);
+
+ return editor;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static ImageIcon getIcon(final int iconWidth, final int iconHeight,
+ VisualPropertyType type) {
+ editor = new C2DMappingEditor(type);
+
+ if (editor.slider.getTrackRenderer() instanceof DiscreteTrackRenderer == false) {
+ return null;
+ }
+
+ DiscreteTrackRenderer<?> rend = (DiscreteTrackRenderer) editor.slider.getTrackRenderer();
+ rend.getRendererComponent(editor.slider);
+
+ return rend.getTrackGraphicIcon(iconWidth, iconHeight);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param width DOCUMENT ME!
+ * @param height DOCUMENT ME!
+ * @param type DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static ImageIcon getLegend(final int width, final int height,
+ final VisualPropertyType type) {
+ editor = new C2DMappingEditor(type);
+
+ if (editor.slider.getTrackRenderer() instanceof DiscreteTrackRenderer == false) {
+ return null;
+ }
+
+ DiscreteTrackRenderer rend = (DiscreteTrackRenderer) editor.slider.getTrackRenderer();
+ rend.getRendererComponent(editor.slider);
+
+ return rend.getLegend(width, height);
+ }
+
+ @Override
+ protected void addButtonActionPerformed(ActionEvent evt) {
+ BoundaryRangeValues newRange;
+ Object defValue = Cytoscape.getVisualMappingManager().getVisualStyle()
+ .getNodeAppearanceCalculator().getDefaultAppearance().get(type);
+ final double maxValue = EditorValueRangeTracer.getTracer().getMax(type);
+
+ if (mapping.getPointCount() == 0) {
+ slider.getModel().addThumb(50f, defValue);
+
+ newRange = new BoundaryRangeValues(below, defValue, above);
+ mapping.addPoint(maxValue / 2, newRange);
+
+ selectThumbAtPosition(50f);
+
+ slider.repaint();
+ repaint();
+
+ return;
+ }
+
+ // Add a new thumb with default value
+ slider.getModel().addThumb(75f, defValue);
+
+ // Pick Up first point.
+ final ContinuousMappingPoint previousPoint = mapping.getPoint(mapping.getPointCount() - 1);
+
+ final BoundaryRangeValues previousRange = previousPoint.getRange();
+ newRange = new BoundaryRangeValues(previousRange);
+
+ newRange.lesserValue = slider.getModel().getSortedThumbs()
+ .get(slider.getModel().getThumbCount() - 1);
+ newRange.equalValue = defValue;
+ newRange.greaterValue = previousRange.greaterValue;
+ mapping.addPoint(maxValue, newRange);
+
+ updateMap();
+ updateCytoscape();
+
+ // Make this slider the selected one
+ selectThumbAtPosition(75f);
+
+ slider.repaint();
+ repaint();
+ }
+
+ protected void updateMap() {
+ List<Thumb> thumbs = slider.getModel().getSortedThumbs();
+
+ final double minValue = EditorValueRangeTracer.getTracer().getMin(type);
+ final double valRange = EditorValueRangeTracer.getTracer().getRange(type);
+
+ //List<ContinuousMappingPoint> points = mapping.getAllPoints();
+ Thumb t;
+ Double newVal;
+
+ if (thumbs.size() == 1) {
+ // Special case: only one handle.
+ mapping.getPoint(0).getRange().equalValue = below;
+ mapping.getPoint(0).getRange().lesserValue = below;
+ mapping.getPoint(0).getRange().greaterValue = above;
+
+ newVal = ((thumbs.get(0).getPosition() / 100) * valRange) + minValue;
+ mapping.getPoint(0).setValue(newVal);
+
+ return;
+ }
+
+ for (int i = 0; i < thumbs.size(); i++) {
+ t = thumbs.get(i);
+
+ if (i == 0) {
+ // First thumb
+ mapping.getPoint(i).getRange().lesserValue = below;
+ mapping.getPoint(i).getRange().equalValue = below;
+ mapping.getPoint(i).getRange().greaterValue = thumbs.get(i + 1).getObject();
+ } else if (i == (thumbs.size() - 1)) {
+ // Last thumb
+ mapping.getPoint(i).getRange().greaterValue = above;
+ mapping.getPoint(i).getRange().equalValue = t.getObject();
+ mapping.getPoint(i).getRange().lesserValue = t.getObject();
+ } else {
+ // Others
+ mapping.getPoint(i).getRange().lesserValue = t.getObject();
+ mapping.getPoint(i).getRange().equalValue = t.getObject();
+ mapping.getPoint(i).getRange().greaterValue = thumbs.get(i + 1).getObject();
+ }
+
+ newVal = ((t.getPosition() / 100) * valRange) + minValue;
+ mapping.getPoint(i).setValue(newVal);
+ }
+ }
+
+ @Override
+ protected void deleteButtonActionPerformed(ActionEvent evt) {
+ final int selectedIndex = slider.getSelectedIndex();
+
+ if (0 <= selectedIndex) {
+ slider.getModel().removeThumb(selectedIndex);
+ mapping.removePoint(selectedIndex);
+ updateMap();
+ updateCytoscape();
+ mapping.fireStateChanged();
+
+ repaint();
+ }
+ }
+
+ private void setSlider() {
+ slider.updateUI();
+
+ final double minValue = EditorValueRangeTracer.getTracer().getMin(type);
+ final double maxValue = EditorValueRangeTracer.getTracer().getMax(type);
+
+ slider.addMouseListener(new MouseAdapter() {
+ public void mouseClicked(MouseEvent e) {
+ int range = ((DiscreteTrackRenderer) slider.getTrackRenderer()).getRangeID(e.getX(),
+ e.getY());
+
+ Object newValue = null;
+
+ if (e.getClickCount() == 2) {
+ try {
+ setAlwaysOnTop(false);
+ newValue = type.showDiscreteEditor();
+ } catch (Exception e1) {
+ CyLogger.getLogger(C2DMappingEditor.class).warn("Unable to show discrete editor!", e1);
+ } finally {
+ setAlwaysOnTop(true);
+ }
+
+ if (newValue == null)
+ return;
+
+ if (range == 0) {
+ below = newValue;
+ } else if (range == slider.getModel().getThumbCount()) {
+ above = newValue;
+ } else {
+ ((Thumb) slider.getModel().getSortedThumbs().get(range)).setObject(newValue);
+ }
+
+ updateMap();
+ updateCytoscape();
+
+ slider.setTrackRenderer(new DiscreteTrackRenderer(type, below, above));
+ slider.repaint();
+
+ }
+ }
+ });
+
+ double actualRange = EditorValueRangeTracer.getTracer().getRange(type);
+
+ BoundaryRangeValues bound;
+ Float fraction;
+
+ /*
+ * NPE?
+ */
+ if (allPoints == null) {
+ return;
+ }
+
+ for (ContinuousMappingPoint point : allPoints) {
+ bound = point.getRange();
+
+ fraction = ((Number) ((point.getValue().doubleValue() - minValue) / actualRange)).floatValue() * 100;
+ slider.getModel().addThumb(fraction, bound.equalValue);
+ }
+
+ if (allPoints.size() != 0) {
+ below = allPoints.get(0).getRange().lesserValue;
+ above = allPoints.get(allPoints.size() - 1).getRange().greaterValue;
+ } else {
+ Object defaultVal = Cytoscape.getVisualMappingManager().getVisualStyle()
+ .getNodeAppearanceCalculator().getDefaultAppearance()
+ .get(type);
+ below = defaultVal;
+ above = defaultVal;
+ }
+
+ /*
+ * get min and max for the value object
+ */
+ TriangleThumbRenderer thumbRend = new TriangleThumbRenderer(slider);
+ DiscreteTrackRenderer dRend = new DiscreteTrackRenderer(type, below, above);
+
+ slider.setThumbRenderer(thumbRend);
+ slider.setTrackRenderer(dRend);
+ slider.addMouseListener(new ThumbMouseListener());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt DOCUMENT ME!
+ */
+ public void propertyChange(PropertyChangeEvent evt) {
+ // TODO Auto-generated method stub
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/ui/editors/continuous/ContinuousMappingEditorPanel.java b/application/src/main/java/cytoscape/visual/ui/editors/continuous/ContinuousMappingEditorPanel.java
new file mode 100644
index 0000000..361d0d8
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/editors/continuous/ContinuousMappingEditorPanel.java
@@ -0,0 +1,829 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.visual.ui.editors.continuous;
+
+import cytoscape.Cytoscape;
+import cytoscape.logger.CyLogger;
+
+import cytoscape.data.CyAttributes;
+
+import cytoscape.data.attr.CountedIterator;
+import cytoscape.data.attr.MultiHashMap;
+
+import cytoscape.visual.VisualPropertyType;
+
+import cytoscape.visual.calculators.Calculator;
+
+import cytoscape.visual.mappings.BoundaryRangeValues;
+import cytoscape.visual.mappings.ContinuousMapping;
+import cytoscape.visual.mappings.continuous.ContinuousMappingPoint;
+
+import org.jdesktop.swingx.JXMultiThumbSlider;
+import org.jdesktop.swingx.multislider.Thumb;
+
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.Graphics2D;
+import java.awt.event.ActionEvent;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
+import java.awt.image.BufferedImage;
+
+import java.beans.PropertyChangeListener;
+
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+
+import javax.swing.Icon;
+import javax.swing.ImageIcon;
+import javax.swing.JButton;
+import javax.swing.JComponent;
+import javax.swing.JDialog;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JSpinner;
+import javax.swing.SpinnerNumberModel;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+
+
+/**
+ * Abstract class for all Continuous Mapping Editors.
+ *
+ * @version 0.5
+ * @since Cytoscape 2.5
+ * @author kono
+ */
+public abstract class ContinuousMappingEditorPanel extends JDialog implements PropertyChangeListener {
+
+ private static final long serialVersionUID = -2558647616344119220L;
+
+ // Tell vizMapper main which editor is disabled/enabled.
+ /**
+ * DOCUMENT ME!
+ */
+ public static final String EDITOR_WINDOW_CLOSED = "EDITOR_WINDOW_CLOSED";
+
+ /**
+ * DOCUMENT ME!
+ */
+ public static final String EDITOR_WINDOW_OPENED = "EDITOR_WINDOW_OPENED";
+
+ /*
+ * Used by trackrenderers.
+ */
+ protected static final String BELOW_VALUE_CHANGED = "BELOW_VALUE_CHANGED";
+ protected static final String ABOVE_VALUE_CHANGED = "ABOVE_VALUE_CHANGED";
+
+ protected VisualPropertyType type;
+ protected Calculator calculator;
+ protected ContinuousMapping mapping;
+ protected ContinuousMapping savedMapping;
+ protected List<ContinuousMappingPoint> allPoints;
+ protected Object below;
+ protected Object above;
+
+ private CyAttributes attrs;
+
+ protected static ContinuousMappingEditorPanel editor;
+
+ protected static boolean updatePending = false;
+ protected static boolean updating = false;
+
+ protected double lastSpinnerNumber = 0;
+
+ /** Creates new form ContinuousMapperEditorPanel */
+ public ContinuousMappingEditorPanel(final VisualPropertyType type) {
+ super(Cytoscape.getDesktop());
+ this.type = type;
+ initComponents();
+
+ initRangeValues();
+ setSpinners();
+ this.addWindowListener(new WindowAdapter() {
+ public void windowOpened(WindowEvent e) {
+ firePropertyChange(EDITOR_WINDOW_OPENED, null, type);
+ }
+
+ public void windowClosing(WindowEvent e) {
+ firePropertyChange(EDITOR_WINDOW_CLOSED, this, type);
+ }
+ });
+ }
+
+ /**
+ * Dynamically generate small icons from continuous mappers.
+ *
+ * @param width DOCUMENT ME!
+ * @param height DOCUMENT ME!
+ * @param type DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static ImageIcon getIcon(final int width, final int height, VisualPropertyType type) {
+ final Class dataType = type.getDataType();
+
+ if (dataType == Color.class) {
+ return GradientEditorPanel.getIcon(width, height, type);
+ } else if (dataType == Number.class) {
+ return C2CMappingEditor.getIcon(width, height, type);
+ } else {
+ return C2DMappingEditor.getIcon(width, height, type);
+ }
+ }
+
+ protected void setSpinners() {
+ final Class dataType = type.getDataType();
+ setSpinner();
+ if (dataType == Color.class) {
+ } else if (dataType == Number.class) {
+ setPropertySpinner();
+ } else {
+ }
+ }
+
+ protected void setSpinner() {
+ SpinnerNumberModel spinnerModel = new SpinnerNumberModel(0.0d, Float.NEGATIVE_INFINITY,
+ Float.POSITIVE_INFINITY, 0.01d);
+ spinnerModel.addChangeListener(new SpinnerChangeListener(spinnerModel));
+ valueSpinner.setModel(spinnerModel);
+ }
+
+ protected void setPropertySpinner() {
+ SpinnerNumberModel propertySpinnerModel = new SpinnerNumberModel(0.0d, Float.NEGATIVE_INFINITY,
+ Float.POSITIVE_INFINITY, 0.01d);
+ propertySpinnerModel.addChangeListener(new PropertySpinnerChangeListener(propertySpinnerModel));
+ propertySpinner.setModel(propertySpinnerModel);
+ }
+
+ /**
+ * This method is called from within the constructor to initialize the form.
+ * WARNING: Do NOT modify this code. The content of this method is always
+ * regenerated by the Form Editor.
+ */
+
+ // <editor-fold defaultstate="collapsed" desc=" Generated Code ">
+ private void initComponents() {
+ JPanel mainPanel = new JPanel();
+
+ abovePanel = new BelowAndAbovePanel(type, Color.yellow, false);
+ abovePanel.setName("abovePanel");
+ belowPanel = new BelowAndAbovePanel(type, Color.white, true);
+ belowPanel.setName("belowPanel");
+
+ abovePanel.setPreferredSize(new Dimension(16, 1));
+ belowPanel.setPreferredSize(new Dimension(16, 1));
+
+ rangeSettingPanel = new javax.swing.JPanel();
+ addButton = new javax.swing.JButton();
+ deleteButton = new javax.swing.JButton();
+
+ // New in 2.6
+ minMaxButton = new javax.swing.JButton();
+
+ okButton = new javax.swing.JButton();
+ cancelButton = new javax.swing.JButton();
+
+ slider = new JXMultiThumbSlider();
+ iconPanel = new YValueLegendPanel(type);
+
+ valueSpinner = new JSpinner();
+ valueSpinner.setEnabled(false);
+ valueLabel = new JLabel("Attribute Value");
+ valueLabel.setLabelFor(valueSpinner);
+
+ Class dataType = this.type.getDataType();
+ if (dataType == Number.class) {
+ propertySpinner = new JSpinner();
+ propertySpinner.setEnabled(false);
+ propertyComponent = propertySpinner;
+ propertyLabel = new JLabel(type.getName());
+ propertyLabel.setLabelFor(propertyComponent);
+ } else if (dataType == Color.class) {
+ // We use the colorButton for both discrete and color
+ colorButton = new javax.swing.JButton("Change");
+ colorButton.setMargin(new java.awt.Insets(2, 2, 2, 2));
+ colorButton.setEnabled(false);
+ propertyComponent = colorButton;
+ propertyLabel = new JLabel(type.getName());
+ propertyLabel.setLabelFor(propertyComponent);
+ } else {
+ propertyComponent = new JLabel();
+ propertyLabel = new JLabel("Double-click on icon to change "+type.getName());
+ }
+
+ rotaryEncoder = new JXMultiThumbSlider();
+
+ iconPanel.setPreferredSize(new Dimension(25, 1));
+
+ mainPanel.setBorder(javax.swing.BorderFactory.createEmptyBorder(5,5,5,5));
+
+ rangeSettingPanel.setBorder(javax.swing.BorderFactory.createTitledBorder(null,
+ "Handle Settings",
+ javax.swing.border.TitledBorder.DEFAULT_JUSTIFICATION,
+ javax.swing.border.TitledBorder.DEFAULT_POSITION,
+ new java.awt.Font("SansSerif", 1, 10),
+ new java.awt.Color(0, 0, 0)));
+ addButton.setText("Add");
+ addButton.setPreferredSize(new Dimension(100, 10));
+ addButton.setMargin(new java.awt.Insets(2, 2, 2, 2));
+ addButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ addButtonActionPerformed(evt);
+ }
+ });
+
+ deleteButton.setText("Delete");
+ deleteButton.setPreferredSize(new Dimension(100, 10));
+ deleteButton.setMargin(new java.awt.Insets(2, 2, 2, 2));
+ deleteButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ deleteButtonActionPerformed(evt);
+ }
+ });
+
+ // New in 2.6
+ minMaxButton.setText("Min/Max");
+ minMaxButton.setPreferredSize(new Dimension(100, 10));
+ minMaxButton.setMargin(new java.awt.Insets(2, 2, 2, 2));
+ minMaxButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ minMaxButtonActionPerformed(evt);
+ }
+ });
+
+ cancelButton.setText("Cancel");
+ cancelButton.setMargin(new java.awt.Insets(2, 2, 2, 2));
+ cancelButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ calculator.getMappings().set(0,savedMapping);
+ Cytoscape.getVisualMappingManager().applyAppearances();
+ Cytoscape.getCurrentNetworkView().redrawGraph(false, true);
+ firePropertyChange(EDITOR_WINDOW_CLOSED, this, type);
+ setVisible(false);
+ }
+ });
+
+ okButton.setText("OK");
+ // okButton.setPreferredSize(new Dimension(50, 30));
+ okButton.setMargin(new java.awt.Insets(2, 2, 2, 2));
+ okButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ firePropertyChange(EDITOR_WINDOW_CLOSED, this, type);
+ setVisible(false);
+ }
+ });
+
+ slider.setMaximumValue(100.0F);
+ rotaryEncoder.setMaximumValue(100.0F);
+
+ org.jdesktop.layout.GroupLayout sliderLayout = new org.jdesktop.layout.GroupLayout(slider);
+ slider.setLayout(sliderLayout);
+ sliderLayout.setHorizontalGroup(sliderLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(0, 486, Short.MAX_VALUE));
+ sliderLayout.setVerticalGroup(sliderLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(0, 116, Short.MAX_VALUE));
+
+ org.jdesktop.layout.GroupLayout jXMultiThumbSlider1Layout = new org.jdesktop.layout.GroupLayout(rotaryEncoder);
+ rotaryEncoder.setLayout(jXMultiThumbSlider1Layout);
+ jXMultiThumbSlider1Layout.setHorizontalGroup(jXMultiThumbSlider1Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(0, 84,
+ Short.MAX_VALUE));
+ jXMultiThumbSlider1Layout.setVerticalGroup(jXMultiThumbSlider1Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(0, 65,
+ Short.MAX_VALUE));
+
+ org.jdesktop.layout.GroupLayout rangeSettingPanelLayout = new org.jdesktop.layout.GroupLayout(rangeSettingPanel);
+ rangeSettingPanel.setLayout(rangeSettingPanelLayout);
+ rangeSettingPanelLayout.setHorizontalGroup(rangeSettingPanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(rangeSettingPanelLayout.createSequentialGroup()
+ .addContainerGap()
+ .add(valueLabel,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(valueSpinner,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ 100,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED,
+ 118,
+ Short.MAX_VALUE)
+ .add(minMaxButton,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ 100,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(addButton,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ 100,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(deleteButton)
+ .add(10, 10, 10))
+ .add(rangeSettingPanelLayout.createSequentialGroup()
+ .addContainerGap()
+ .add(propertyLabel,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(propertyComponent,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ 100,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)));
+
+ rangeSettingPanelLayout.setVerticalGroup(rangeSettingPanelLayout.createSequentialGroup()
+ .add(rangeSettingPanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE)
+ .add(valueLabel)
+ .add(valueSpinner,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .add(minMaxButton)
+ .add(deleteButton)
+ .add(addButton))
+ .add(rangeSettingPanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE)
+ .add(propertyLabel)
+ .add(propertyComponent,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)));
+
+ org.jdesktop.layout.GroupLayout layout = new org.jdesktop.layout.GroupLayout(mainPanel);
+ mainPanel.setLayout(layout);
+
+ layout.setHorizontalGroup(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(layout.createSequentialGroup()
+ .addContainerGap()
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED,
+ 118,
+ Short.MAX_VALUE)
+ .add(cancelButton,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ 100,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(okButton,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ 100,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .add(10, 10, 10))
+ .add(rangeSettingPanel,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE)
+ .add(layout.createSequentialGroup()
+ .add(iconPanel,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .add(belowPanel,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .add(slider,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 243, Short.MAX_VALUE)
+ .add(abovePanel,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)));
+
+ layout.setVerticalGroup(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(layout.createSequentialGroup()
+ .add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(org.jdesktop.layout.GroupLayout.TRAILING,
+ slider,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 145, Short.MAX_VALUE)
+ .add(org.jdesktop.layout.GroupLayout.TRAILING,
+ iconPanel,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE)
+ .add(org.jdesktop.layout.GroupLayout.TRAILING,
+ belowPanel,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE)
+ .add(org.jdesktop.layout.GroupLayout.TRAILING,
+ abovePanel,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE))
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(rangeSettingPanel,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(cancelButton,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .add(okButton,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE))));
+
+ // add the main panel to the dialog.
+ this.getContentPane().add(mainPanel);
+ this.pack();
+ } // </editor-fold>
+
+ protected void minMaxButtonActionPerformed(ActionEvent evt) {
+ final Double[] newVal = MinMaxDialog.getMinMax(EditorValueRangeTracer.getTracer().getMin(type),
+ EditorValueRangeTracer.getTracer().getMax(type), attrs, mapping.getControllingAttributeName());
+
+ if (newVal == null)
+ return;
+
+ EditorValueRangeTracer.getTracer().setMin(type, newVal[0]);
+ EditorValueRangeTracer.getTracer().setMax(type, newVal[1]);
+ updateMap();
+ this.repaint();
+ updateCytoscape();
+ }
+
+ abstract protected void deleteButtonActionPerformed(java.awt.event.ActionEvent evt);
+
+ abstract protected void addButtonActionPerformed(java.awt.event.ActionEvent evt);
+
+ private void initRangeValues() {
+
+ if (type.isNodeProp()) {
+ attrs = Cytoscape.getNodeAttributes();
+ calculator = Cytoscape.getVisualMappingManager().getVisualStyle()
+ .getNodeAppearanceCalculator().getCalculator(type);
+ } else {
+ attrs = Cytoscape.getEdgeAttributes();
+ calculator = Cytoscape.getVisualMappingManager().getVisualStyle()
+ .getEdgeAppearanceCalculator().getCalculator(type);
+ }
+
+ if (calculator == null)
+ return;
+
+ // Assume this calc only returns cont. mapping.
+ if (calculator.getMapping(0).getClass() == ContinuousMapping.class) {
+ mapping = (ContinuousMapping)calculator.getMapping(0);
+
+ savedMapping = (ContinuousMapping)(mapping.clone());
+
+ final String controllingAttrName = mapping.getControllingAttributeName();
+
+ final MultiHashMap mhm = attrs.getMultiHashMap();
+
+ List<String> attrNames = new ArrayList<String>();
+ Collections.addAll(attrNames, attrs.getAttributeNames());
+
+ if (attrNames.contains(controllingAttrName) == false)
+ return;
+
+ // Set range values
+ if (EditorValueRangeTracer.getTracer().getRange(type) == 0) {
+ final CountedIterator it = mhm.getObjectKeys(controllingAttrName);
+ double maxValue = Double.NEGATIVE_INFINITY;
+ double minValue = Double.POSITIVE_INFINITY;
+
+ while (it.hasNext()) {
+ final String id = (String)it.next();
+ final Object attrValue = attrs.getAttribute(id, controllingAttrName);
+ if(attrValue == null)
+ continue;
+
+ final double val;
+
+ if (attrValue.getClass() == Double.class)
+ val = (Double)attrValue;
+ else if (attrValue.getClass() == Integer.class)
+ val = (Integer)attrValue;
+ else
+ val = Double.parseDouble(attrValue.toString());
+
+ if (val > maxValue)
+ maxValue = val;
+
+ if (val < minValue)
+ minValue = val;
+ }
+ EditorValueRangeTracer.getTracer().setMax(type, maxValue);
+ EditorValueRangeTracer.getTracer().setMin(type, minValue);
+ }
+
+ allPoints = mapping.getAllPoints();
+ }
+ }
+
+ protected void setSidePanelIconColor(Color below, Color above) {
+ this.abovePanel.setColor(above);
+ this.belowPanel.setColor(below);
+ repaint();
+ }
+
+ // Variables declaration - do not modify
+ protected javax.swing.JButton addButton;
+ protected javax.swing.JButton colorButton;
+ protected javax.swing.JButton deleteButton;
+ protected javax.swing.JButton okButton;
+ protected javax.swing.JButton cancelButton;
+ protected javax.swing.JPanel iconPanel;
+ private javax.swing.JPanel rangeSettingPanel;
+ protected JXMultiThumbSlider slider;
+ protected JSpinner valueSpinner;
+ private JLabel valueLabel;
+ private JLabel propertyLabel;
+ protected JSpinner propertySpinner = null;
+ protected JComponent propertyComponent;
+ protected JXMultiThumbSlider rotaryEncoder;
+ protected JButton minMaxButton;
+
+ /*
+ * For Gradient panel only.
+ */
+ protected BelowAndAbovePanel abovePanel;
+ protected BelowAndAbovePanel belowPanel;
+
+ protected int getSelectedPoint(int selectedIndex) {
+ final List<Thumb<?>> thumbs = slider.getModel().getSortedThumbs();
+ Thumb<?> selected = slider.getModel().getThumbAt(selectedIndex);
+ for (int i = 0; i < thumbs.size(); i++) {
+ if (thumbs.get(i) == selected) {
+ return i;
+ }
+ }
+
+ return -1;
+ }
+
+ protected void selectThumbAtPosition(float position) {
+ int selectedIndex = getThumbIndexAtPosition(position);
+ if (selectedIndex != -1) {
+ TriangleThumbRenderer renderer = (TriangleThumbRenderer)slider.getThumbRenderer();
+ renderer.setSelectedIndex(selectedIndex);
+ enableSpinner(selectedIndex);
+ }
+ }
+
+ protected int getThumbIndexAtPosition(float position) {
+ final List<Thumb<?>> thumbs = slider.getModel().getSortedThumbs();
+ for (int i = 0; i < thumbs.size(); i++) {
+ if (slider.getModel().getThumbAt(i).getPosition() == position) {
+ return i;
+ }
+ }
+ return -1;
+ }
+
+ protected void setButtonColor(Color newColor) {
+ final int iconWidth = 10;
+ final int iconHeight = 10;
+ final BufferedImage bi = new BufferedImage(iconWidth, iconHeight, BufferedImage.TYPE_INT_RGB);
+ final Graphics2D g2 = bi.createGraphics();
+
+ /*
+ * Fill background
+ */
+ g2.setColor(newColor);
+ g2.fillRect(0, 0, iconWidth, iconHeight);
+
+ Icon colorIcon = new ImageIcon(bi);
+ colorButton.setIcon(colorIcon);
+ colorButton.setIconTextGap(6);
+
+ }
+
+ protected void updateCytoscape() {
+ // TODO: We only want to do this for relatively small graphs....
+ // Start a thread???
+ updatePending = true;
+ if (!updating) {
+ UpdaterThread u = new UpdaterThread();
+ new Thread(u).start();
+ }
+ }
+
+ protected void updateMap() {
+ final List<Thumb> thumbs = slider.getModel().getSortedThumbs();
+
+ final double min = EditorValueRangeTracer.getTracer().getMin(type);
+ final double range = EditorValueRangeTracer.getTracer().getRange(type);
+
+ Thumb t;
+ Double newVal;
+
+ if (thumbs.size() == 1) {
+ // Special case: only one handle.
+ mapping.getPoint(0).getRange().equalValue = thumbs.get(0).getObject();
+ mapping.getPoint(0).getRange().lesserValue = below;
+ mapping.getPoint(0).getRange().greaterValue = above;
+
+ newVal = ((thumbs.get(0).getPosition() / 100) * range) + min;
+ mapping.getPoint(0).setValue(newVal);
+
+ return;
+ }
+
+ BoundaryRangeValues rg;
+ int size = thumbs.size();
+ for (int i = 0; i < size; i++) {
+ t = thumbs.get(i);
+ rg = mapping.getPoint(i).getRange();
+ if (i == 0) {
+ rg.lesserValue = below;
+ rg.greaterValue = t.getObject();
+ } else if (i == (thumbs.size() - 1)) {
+ rg.greaterValue = above;
+ rg.lesserValue = t.getObject();
+ } else {
+ rg.lesserValue = t.getObject();
+ rg.greaterValue = t.getObject();
+ }
+
+ newVal = ((t.getPosition() / 100) * range) + min;
+ mapping.getPoint(i).setValue(newVal);
+ rg.equalValue = t.getObject();
+ }
+ }
+
+ protected void enableSpinner(int selectedIndex) {
+ final Class<?> dataType = type.getDataType();
+ valueSpinner.setEnabled(true);
+
+ final int count = slider.getModel().getThumbCount();
+// for(int i=0; i<count; i++) {
+// final Thumb<?> thumb = slider.getModel().getThumbAt(i);
+// System.out.println(i + ": " + thumb.getPosition() + " = " + thumb.getObject());
+// }
+
+ final Thumb<?> selectedThumb = slider.getModel().getThumbAt(selectedIndex);
+ final Double newVal = ((selectedThumb.getPosition() / 100) * EditorValueRangeTracer.getTracer().getRange(type))
+ + EditorValueRangeTracer.getTracer().getMin(type);
+
+ valueSpinner.setValue(newVal);
+ updateMap();
+
+ if (Number.class.isAssignableFrom(dataType)) {
+ propertySpinner.setEnabled(true);
+ final Number value = (Number) selectedThumb.getObject();
+ propertySpinner.setValue(value);
+ } else if (dataType == Color.class) {
+ colorButton.setEnabled(true);
+ setButtonColor((Color)selectedThumb.getObject());
+ }
+ }
+
+ protected void disableSpinner() {
+ Class dataType = type.getClass();
+ valueSpinner.setEnabled(false);
+ valueSpinner.setValue(0);
+ if (dataType == Number.class) {
+ propertySpinner.setEnabled(false);
+ propertySpinner.setValue(0);
+ }
+ }
+
+ // End of variables declaration
+ protected class ThumbMouseListener extends MouseAdapter {
+ public void mouseReleased(MouseEvent e) {
+ int selectedIndex = ((TriangleThumbRenderer)slider.getThumbRenderer()).getSelectedIndex();
+
+ if ((0 <= selectedIndex) && (slider.getModel().getThumbCount() > 0)) {
+ enableSpinner(selectedIndex);
+ slider.repaint();
+ repaint();
+ updateCytoscape();
+ } else {
+ disableSpinner();
+ }
+ }
+ }
+
+ /**
+ * Watching spinner
+ *
+ * @author kono
+ *
+ */
+ class SpinnerChangeListener implements ChangeListener {
+ SpinnerNumberModel spinnerModel;
+ public SpinnerChangeListener(SpinnerNumberModel model) {
+ this.spinnerModel = model;
+ }
+
+ public void stateChanged(ChangeEvent e) {
+
+ final Number newVal = spinnerModel.getNumber();
+ final int selectedIndex = ((TriangleThumbRenderer)slider.getThumbRenderer()).getSelectedIndex();
+
+ if ((0 <= selectedIndex) && (slider.getModel().getThumbCount() >= 1)) {
+
+ if ((newVal.doubleValue() < EditorValueRangeTracer.getTracer().getMin(type))
+ || (newVal.doubleValue() > EditorValueRangeTracer.getTracer().getMax(type))) {
+
+ if ((lastSpinnerNumber > EditorValueRangeTracer.getTracer().getMin(type))
+ && (lastSpinnerNumber < EditorValueRangeTracer.getTracer().getMax(type))) {
+ spinnerModel.setValue(lastSpinnerNumber);
+ } else {
+ spinnerModel.setValue(0);
+ }
+
+ return;
+ }
+
+ final Double newPosition = ((newVal.floatValue()
+ - EditorValueRangeTracer.getTracer().getMin(type)) / EditorValueRangeTracer.getTracer()
+ .getRange(type));
+
+ JComponent selectedThumb = ((TriangleThumbRenderer)slider.getThumbRenderer()).getSelectedThumb();
+ slider.getModel().getThumbAt(selectedIndex)
+ .setPosition(newPosition.floatValue() * 100);
+
+ selectedThumb.setLocation((int) ((slider.getSize().width - 12) * newPosition), 0);
+
+ updateMap();
+
+ selectedThumb.repaint();
+ slider.getParent().repaint();
+ slider.repaint();
+
+ updateCytoscape();
+
+ lastSpinnerNumber = newVal.doubleValue();
+ }
+ }
+ }
+
+ class PropertySpinnerChangeListener implements ChangeListener {
+ SpinnerNumberModel spinnerModel;
+ public PropertySpinnerChangeListener(SpinnerNumberModel model) {
+ this.spinnerModel = model;
+ }
+
+ public void stateChanged(ChangeEvent e) {
+ final Float newVal = new Float(spinnerModel.getNumber().doubleValue());
+ final int selectedIndex = ((TriangleThumbRenderer)slider.getThumbRenderer()).getSelectedIndex();
+ ContinuousTrackRenderer trackRenderer = (ContinuousTrackRenderer)slider.getTrackRenderer();
+ trackRenderer.setSelectedIndex(selectedIndex);
+
+ trackRenderer.setSelectedValue(newVal);
+
+ slider.repaint();
+ repaint();
+ updateCytoscape();
+
+ }
+ }
+
+ class UpdaterThread implements Runnable {
+ public UpdaterThread() {
+ }
+
+ public void run() {
+ updating = true;
+ while (updatePending) {
+ updatePending = false;
+ Cytoscape.getCurrentNetworkView().redrawGraph(false, true);
+ }
+ updating = false;
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/ui/editors/continuous/ContinuousTrackRenderer.java b/application/src/main/java/cytoscape/visual/ui/editors/continuous/ContinuousTrackRenderer.java
new file mode 100644
index 0000000..8f4e522
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/editors/continuous/ContinuousTrackRenderer.java
@@ -0,0 +1,1036 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.visual.ui.editors.continuous;
+
+import cytoscape.Cytoscape;
+import cytoscape.CytoscapeInit;
+import cytoscape.logger.CyLogger;
+
+import cytoscape.visual.VisualPropertyType;
+
+import cytoscape.visual.mappings.BoundaryRangeValues;
+import cytoscape.visual.mappings.ContinuousMapping;
+
+import org.jdesktop.swingx.JXMultiThumbSlider;
+import org.jdesktop.swingx.multislider.Thumb;
+
+import java.awt.BasicStroke;
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.Point;
+import java.awt.Polygon;
+import java.awt.RenderingHints;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseMotionListener;
+import java.awt.geom.AffineTransform;
+import java.awt.geom.Point2D;
+import java.awt.image.BufferedImage;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import javax.swing.ImageIcon;
+import javax.swing.JComponent;
+import javax.swing.JOptionPane;
+import javax.swing.SwingUtilities;
+
+
+/**
+ *
+ *
+ * @author kono
+ */
+public class ContinuousTrackRenderer extends JComponent implements VizMapperTrackRenderer {
+ /*
+ * Constants for diagram.
+ */
+ private static float UPPER_LIMIT;
+ private final Font TITLE_FONT = new Font("SansSerif", Font.BOLD, 12);
+ private static final Font ICON_FONT = new Font("SansSerif", Font.BOLD, 8);
+ private static final int THUMB_WIDTH = 12;
+ private final Font smallFont = new Font("SansSerif", Font.BOLD, 10);
+ private final Font defFont = new Font("SansSerif", Font.BOLD, 12);
+ private static final Color VALUE_AREA_COLOR = new Color(0, 180, 255, 100);
+ private Map<Integer, Double> valueMap;
+ private static final int LEFT_SPACE = 50;
+
+ /*
+ * Define Colors used in this diagram.
+ */
+ private int trackHeight = 110;
+ private int arrowBarPosition = trackHeight + 50;
+ private static final Color BORDER_COLOR = Color.black;
+
+ /*
+ * Min and Max for the Y-Axis.
+ */
+ private float min = 0;
+ private float max = 0;
+ private boolean clickFlag = false;
+ private boolean dragFlag = false;
+ private Point curPoint;
+ private JXMultiThumbSlider slider;
+ private CMouseListener listener = null;
+ private Map<Integer, Point> verticesList;
+ private int selectedIdx;
+ private Point dragOrigin;
+ private VisualPropertyType type;
+ private ContinuousMapping cMapping;
+ private String title;
+ private Number below;
+ private Number above;
+ private List<Float> values = new ArrayList<Float>();
+ private Polygon valueArea = new Polygon();
+ private Point belowSquare;
+ private Point aboveSquare;
+
+ /**
+ * Creates a new ContinuousTrackRenderer object.
+ *
+ * @param type DOCUMENT ME!
+ * @param below DOCUMENT ME!
+ * @param above DOCUMENT ME!
+ */
+ public ContinuousTrackRenderer(VisualPropertyType type, Number below, Number above, ContinuousMapping mapping, JXMultiThumbSlider slider) {
+ this.below = below;
+ this.above = above;
+ this.type = type;
+ this.slider = slider;
+
+ this.cMapping = mapping;
+
+ title = cMapping.getControllingAttributeName();
+
+ Float val;
+ Object propStr = CytoscapeInit.getProperties().getProperty("vizmapper.cntMapperUpperLimit");
+
+ if (propStr != null) {
+ try {
+ val = Float.parseFloat(propStr.toString());
+ } catch (NumberFormatException e) {
+ val = 2000f;
+ }
+
+ UPPER_LIMIT = val;
+ } else {
+ UPPER_LIMIT = 2000f;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g DOCUMENT ME!
+ */
+ @Override
+ public void paint(Graphics g) {
+ super.paint(g);
+ paintComponent(g);
+ }
+
+ /**
+ * Remove square
+ *
+ * @param index
+ */
+ protected void removeSquare(Integer index) {
+ /*
+ CyLogger.getLogger().info("\n\nTrying to remove " + index);
+
+ for (Object key : verticesList.keySet()) {
+ CyLogger.getLogger().info("Key = " + key + ", " + verticesList.get(key));
+ }
+ */
+
+ verticesList.remove(index);
+
+ /*
+ for (Object key : verticesList.keySet()) {
+ CyLogger.getLogger().info("Key After = " + key + ", " + verticesList.get(key));
+ }
+ */
+ }
+
+ @Override
+ protected void paintComponent(Graphics gfx) {
+ trackHeight = slider.getHeight() - 100;
+ arrowBarPosition = trackHeight + 50;
+
+ // AA on
+ Graphics2D g = (Graphics2D) gfx;
+ g.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
+
+ double minValue = EditorValueRangeTracer.getTracer().getMin(type);
+ double maxValue = EditorValueRangeTracer.getTracer().getMax(type);
+
+ int thumb_width = 12;
+ int track_width = slider.getWidth() - thumb_width;
+ g.translate(thumb_width / 2, 12);
+
+ // get the list of tumbs
+ List<Thumb> stops = slider.getModel().getSortedThumbs();
+
+ int numPoints = stops.size();
+
+ // set up the data for the gradient
+ float[] fractions = new float[numPoints];
+ Float[] floatProperty = new Float[numPoints];
+ int i = 0;
+
+ values.clear();
+ values.add(below.floatValue());
+ values.add(above.floatValue());
+
+ for (Thumb thumb : stops) {
+ floatProperty[i] = (Float) thumb.getObject();
+ fractions[i] = thumb.getPosition();
+ values.add((Float) thumb.getObject());
+ i++;
+ }
+
+ for (Float val : values) {
+ if (min >= val)
+ min = val;
+
+ if (max <= val)
+ max = val;
+ }
+
+ // Draw arrow bar
+ g.setStroke(new BasicStroke(1.0f));
+ g.setColor(Color.black);
+ g.drawLine(0, arrowBarPosition, track_width, arrowBarPosition);
+
+ Polygon arrow = new Polygon();
+ arrow.addPoint(track_width, arrowBarPosition);
+ arrow.addPoint(track_width - 20, arrowBarPosition - 8);
+ arrow.addPoint(track_width - 20, arrowBarPosition);
+ g.fill(arrow);
+
+ g.setColor(Color.gray);
+ g.drawLine(0, arrowBarPosition, 15, arrowBarPosition - 30);
+ g.drawLine(15, arrowBarPosition - 30, 25, arrowBarPosition - 30);
+
+ g.setFont(smallFont);
+ g.drawString("Min=" + minValue, 28, arrowBarPosition - 25);
+
+ g.setFont(new Font("SansSerif", Font.BOLD, 10));
+ g.setColor(Color.black);
+ String label = title;
+ if (label == null) label = "(none)";
+ int strWidth = SwingUtilities.computeStringWidth(g.getFontMetrics(), label);
+ g.drawString(label, (track_width / 2) - (strWidth / 2), arrowBarPosition - 25);
+
+ g.drawLine(track_width, arrowBarPosition, track_width - 15, arrowBarPosition + 30);
+ g.drawLine(track_width - 15, arrowBarPosition + 30, track_width - 25, arrowBarPosition + 30);
+
+ final String maxStr = "Max=" + maxValue;
+ strWidth = SwingUtilities.computeStringWidth(g.getFontMetrics(), maxStr);
+ g.drawString(maxStr, track_width - strWidth - 26, arrowBarPosition + 35);
+
+ /*
+ * If no points, just draw empty box.
+ */
+ if (numPoints == 0) {
+ g.setColor(BORDER_COLOR);
+ g.setStroke(new BasicStroke(1.5f));
+ g.drawRect(0, 5, track_width, trackHeight);
+
+ return;
+ }
+
+ g.setStroke(new BasicStroke(1.0f));
+
+ /*
+ * Fill background
+ */
+ g.setColor(Color.white);
+ g.fillRect(0, 5, track_width, trackHeight);
+
+ int newX = 0;
+ int lastY = 0;
+
+ Point2D p1 = new Point2D.Float(0, 5);
+ Point2D p2 = new Point2D.Float(0, 5);
+
+ for (i = 0; i < floatProperty.length; i++) {
+ newX = (int) (track_width * (fractions[i] / 100));
+
+ p2.setLocation(newX, 5);
+
+ int newY = (5 + trackHeight) - (int) ((floatProperty[i] / max) * trackHeight);
+
+ valueArea.reset();
+
+ g.setColor(VALUE_AREA_COLOR);
+
+ if (i == 0) {
+ // TODO: Use something other than a square -- maybe not red??
+ int h = (5 + trackHeight) - (int) ((below.floatValue() / max) * trackHeight);
+ g.fillRect(0, h, newX, (int) ((below.floatValue() / max) * trackHeight));
+ g.setColor(Color.red);
+ g.fillRect(-5, h - 5, 10, 10);
+ belowSquare = new Point(0, h);
+ } else {
+ valueArea.addPoint((int) p1.getX(), lastY);
+ valueArea.addPoint(newX, newY);
+ valueArea.addPoint(newX, trackHeight + 5);
+ valueArea.addPoint((int) p1.getX(), trackHeight + 5);
+ g.fill(valueArea);
+ }
+
+ for (int j = 0; j < stops.size(); j++) {
+ if (slider.getModel().getThumbAt(j).getObject() == floatProperty[i]) {
+ Point newPoint = new Point(newX, newY);
+
+ if (verticesList.containsValue(newPoint) == false)
+ verticesList.put(j, new Point(newX, newY));
+
+ break;
+ }
+ }
+
+ lastY = newY;
+
+ g.setColor(Color.black);
+ g.setStroke(new BasicStroke(1.5f));
+ g.setFont(smallFont);
+
+ int numberWidth = SwingUtilities.computeStringWidth(g.getFontMetrics(),
+ floatProperty[i].toString());
+
+ g.setColor(Color.DARK_GRAY);
+
+ if (fractions[i] < 10) {
+ g.drawLine(newX, newY, newX + 15, newY - 35);
+ g.drawString(floatProperty[i].toString(), newX + numberWidth, newY - 48);
+ } else {
+ g.drawLine(newX, newY, newX - 15, newY + 35);
+ g.drawString(floatProperty[i].toString(), newX - (numberWidth + 5), newY + 48);
+ }
+
+ g.setColor(Color.DARK_GRAY);
+ g.setFont(new Font("SansSerif", Font.BOLD, 10));
+
+ Float curPositionValue = ((Double) (((fractions[i] / 100) * EditorValueRangeTracer.getTracer()
+ .getRange(type))
+ + minValue)).floatValue();
+ String valueString = String.format("%.4f", curPositionValue);
+
+ int flipLimit = 90;
+ int borderVal = track_width - newX;
+
+ if (((i % 2) == 0) && (flipLimit < borderVal)) {
+ g.drawLine(newX, arrowBarPosition, newX + 20, arrowBarPosition - 15);
+ g.drawLine(newX + 20, arrowBarPosition - 15, newX + 30, arrowBarPosition - 15);
+ g.setColor(Color.black);
+ g.drawString(valueString, newX + 33, arrowBarPosition - 11);
+ } else if (((i % 2) == 1) && (flipLimit < borderVal)) {
+ g.drawLine(newX, arrowBarPosition, newX + 20, arrowBarPosition + 15);
+ g.drawLine(newX + 20, arrowBarPosition + 15, newX + 30, arrowBarPosition + 15);
+ g.setColor(Color.black);
+ g.drawString(valueString, newX + 33, arrowBarPosition + 19);
+ } else if (((i % 2) == 0) && (flipLimit >= borderVal)) {
+ g.drawLine(newX, arrowBarPosition, newX - 20, arrowBarPosition - 15);
+ g.drawLine(newX - 20, arrowBarPosition - 15, newX - 30, arrowBarPosition - 15);
+ g.setColor(Color.black);
+ g.drawString(valueString, newX - 90, arrowBarPosition - 11);
+ } else {
+ g.drawLine(newX, arrowBarPosition, newX - 20, arrowBarPosition + 15);
+ g.drawLine(newX - 20, arrowBarPosition + 15, newX - 30, arrowBarPosition + 15);
+ g.setColor(Color.black);
+ g.drawString(valueString, newX - 90, arrowBarPosition + 19);
+ }
+
+ g.setColor(Color.black);
+ g.fillOval(newX - 3, arrowBarPosition - 3, 6, 6);
+
+ p1.setLocation(p2);
+ }
+
+ p2.setLocation(track_width, 5);
+
+ g.setColor(VALUE_AREA_COLOR);
+
+ int h = (5 + trackHeight) - (int) ((above.floatValue() / max) * trackHeight);
+ g.fillRect((int) p1.getX(), h, track_width - (int) p1.getX(),
+ (int) ((above.floatValue() / max) * trackHeight));
+ g.setColor(Color.red);
+ g.fillRect(track_width - 5, h - 5, 10, 10);
+ aboveSquare = new Point(track_width, h);
+
+ /*
+ * Finally, draw border line (rectangle)
+ */
+ g.setColor(BORDER_COLOR);
+ g.setStroke(new BasicStroke(1.5f));
+ g.drawRect(0, 5, track_width, trackHeight);
+
+ g.setColor(Color.red);
+ g.setStroke(new BasicStroke(1.5f));
+
+ for (Integer key : verticesList.keySet()) {
+ Point p = verticesList.get(key);
+
+ if (clickFlag) {
+ int diffX = Math.abs(p.x - (curPoint.x - 6));
+ int diffY = Math.abs(p.y - (curPoint.y - 12));
+
+ if (((diffX < 6) && (diffY < 6)) || (key == selectedIdx)) {
+ g.setColor(Color.green);
+ g.setStroke(new BasicStroke(2.5f));
+ } else {
+ g.setColor(Color.red);
+ g.setStroke(new BasicStroke(1.5f));
+ }
+ }
+
+ g.drawRect(p.x - 5, p.y - 5, 10, 10);
+ }
+
+ /*
+ * Draw below & above
+ */
+ g.translate(-THUMB_WIDTH / 2, -12);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Double getSelectedThumbValue() {
+ final Double valueRange = EditorValueRangeTracer.getTracer().getRange(type);
+ final Double minValue = EditorValueRangeTracer.getTracer().getMin(type);
+ final float position = slider.getModel().getThumbAt(slider.getSelectedIndex()).getPosition();
+
+ return (((position / 100) * valueRange) + minValue);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param slider DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public JComponent getRendererComponent(JXMultiThumbSlider slider) {
+ this.slider = slider;
+
+ if (listener == null) {
+ listener = new CMouseListener();
+ this.slider.addMouseListener(listener);
+ this.slider.addMouseMotionListener(new CMouseMotionListener());
+ }
+
+ if (verticesList == null)
+ verticesList = new HashMap<Integer, Point>();
+
+ if (valueMap == null)
+ valueMap = new HashMap<Integer, Double>();
+
+ return this;
+ }
+
+ public void setSelectedValue(Number newVal) {
+ Thumb selectedThumb = slider.getModel().getThumbAt(selectedIdx);
+ if (selectedThumb == null)
+ return;
+
+ selectedThumb.setObject(newVal);
+
+ updateMax();
+
+ cMapping.getPoint(selectedIdx).getRange().equalValue = newVal;
+
+ final BoundaryRangeValues brv = new BoundaryRangeValues(cMapping.getPoint(selectedIdx)
+ .getRange().lesserValue,
+ newVal,
+ cMapping.getPoint(selectedIdx)
+ .getRange().greaterValue);
+
+ cMapping.getPoint(selectedIdx).setRange(brv);
+
+ int numPoints = cMapping.getAllPoints().size();
+
+ // Update Values which are not accessible from
+ // UI
+ if (numPoints > 1) {
+ if (selectedIdx == 0)
+ brv.greaterValue = newVal;
+ else if (selectedIdx == (numPoints - 1))
+ brv.lesserValue = newVal;
+ else {
+ brv.lesserValue = newVal;
+ brv.greaterValue = newVal;
+ }
+
+ cMapping.fireStateChanged();
+ }
+ }
+
+ public void setAboveValue(Number above) {
+ BoundaryRangeValues brv;
+ BoundaryRangeValues original;
+
+ original = cMapping.getPoint(cMapping.getPointCount() - 1).getRange();
+ brv = new BoundaryRangeValues(original.lesserValue, original.equalValue, above);
+ cMapping.getPoint(cMapping.getPointCount() - 1).setRange(brv);
+
+ cMapping.fireStateChanged();
+ }
+
+ public void setBelowValue(Number below) {
+ Object newValue = below;
+
+ BoundaryRangeValues brv;
+ BoundaryRangeValues original;
+
+ original = cMapping.getPoint(0).getRange();
+ brv = new BoundaryRangeValues(newValue, original.equalValue, original.greaterValue);
+ cMapping.getPoint(0).setRange(brv);
+
+ cMapping.fireStateChanged();
+ }
+
+ public void setSelectedIndex(int index) { this.selectedIdx = index; }
+ public int getSelectedIndex() { return this.selectedIdx; }
+
+ public void updateMax() {
+ Float val;
+ Float curMax = 0f;
+
+ for (Object thumb : slider.getModel().getSortedThumbs()) {
+ val = (Float) ((Thumb) thumb).getObject();
+
+ if (val > curMax)
+ curMax = val;
+ }
+
+ max = curMax;
+ }
+
+
+ class CMouseMotionListener implements MouseMotionListener {
+ public void mouseDragged(MouseEvent e) {
+ /*
+ * If user is moving thumbs, update is not necessary!
+ */
+ if ((e.getY() < THUMB_WIDTH) && (dragFlag == false)) {
+ return;
+ }
+
+ dragFlag = true;
+
+ curPoint = e.getPoint();
+
+ /*
+ * If beyond the bottom lin
+ */
+ if (clickFlag == true) {
+ Thumb selectedThumb = slider.getModel().getThumbAt(selectedIdx);
+
+ if (curPoint.getY() >= (trackHeight + 5)) {
+ selectedThumb.setObject(0f);
+
+ return;
+ }
+
+ double curY = curPoint.getY();
+
+ float newY = (float) ((((trackHeight + 5) - curY) * max) / (trackHeight + 5));
+
+ if (newY > UPPER_LIMIT)
+ newY = UPPER_LIMIT;
+
+ selectedThumb.setObject(newY);
+
+ //updateMax();
+ Object newVal = newY;
+ cMapping.getPoint(selectedIdx).getRange().equalValue = newVal;
+
+ final BoundaryRangeValues brv = new BoundaryRangeValues(cMapping.getPoint(selectedIdx)
+ .getRange().lesserValue,
+ newVal,
+ cMapping.getPoint(selectedIdx)
+ .getRange().greaterValue);
+
+ cMapping.getPoint(selectedIdx).setRange(brv);
+
+ int numPoints = cMapping.getAllPoints().size();
+
+ // Update Values which are not accessible from
+ // UI
+ if (numPoints > 1) {
+ if (selectedIdx == 0)
+ brv.greaterValue = newVal;
+ else if (selectedIdx == (numPoints - 1))
+ brv.lesserValue = newVal;
+ else {
+ brv.lesserValue = newVal;
+ brv.greaterValue = newVal;
+ }
+ }
+ }
+
+ dragOrigin = e.getPoint();
+ slider.repaint();
+ }
+
+ public void mouseMoved(MouseEvent arg0) {
+ // TODO Auto-generated method stub
+ }
+ }
+
+ class CMouseListener extends MouseAdapter {
+ @Override
+ public void mouseClicked(MouseEvent e) {
+ /*
+ * Show popup dialog to enter new numerical value.
+ */
+ if (isPointerInSquare(e) && (e.getClickCount() == 2)) {
+ // TODO: This should list the attribute value this applies to
+ final String val = JOptionPane.showInputDialog(slider,
+ "Please type new value for "+type.getName());
+
+ if (val == null)
+ return;
+
+ Float newVal = 0f;
+
+ try {
+ newVal = Float.valueOf(val);
+ } catch (Exception ne) {
+ // Number format error.
+ return;
+ }
+
+ setSelectedValue(newVal);
+
+ slider.repaint();
+ repaint();
+ } else if ((e.getClickCount() == 2) && (isBelow(e.getPoint()))) {
+ final String val = JOptionPane.showInputDialog(slider,
+ "Please type smallest value for "+type.getName());
+
+ if (val == null) {
+ return;
+ }
+
+ try {
+ below = Float.valueOf(val);
+ } catch (Exception ne) {
+ // Number format error.
+ return;
+ }
+
+ setBelowValue(below);
+
+ slider.repaint();
+ repaint();
+
+ firePropertyChange(ContinuousMappingEditorPanel.BELOW_VALUE_CHANGED, null, below);
+ } else if ((e.getClickCount() == 2) && (isAbove(e.getPoint()))) {
+ final String val = JOptionPane.showInputDialog(slider,
+ "Please type largest value for "+type.getName());
+
+ if (val == null) {
+ return;
+ }
+
+ try {
+ above = Float.valueOf(val);
+ } catch (Exception ne) {
+ // Number format error.
+ return;
+ }
+
+ setAboveValue(above);
+
+ slider.repaint();
+ repaint();
+
+ firePropertyChange(ContinuousMappingEditorPanel.ABOVE_VALUE_CHANGED, null, above);
+ }
+ }
+
+ private boolean isBelow(final Point p) {
+ if (belowSquare == null) {
+ return false;
+ }
+
+ int diffY = Math.abs(p.y - 12 - belowSquare.y);
+ int diffX = Math.abs(p.x - 6 - belowSquare.x);
+
+ if ((diffX < 6) && (diffY < 6)) {
+ return true;
+ }
+
+ return false;
+ }
+
+ private boolean isAbove(final Point p) {
+ if (aboveSquare == null) {
+ return false;
+ }
+
+ int diffY = Math.abs(p.y - 12 - aboveSquare.y);
+ int diffX = Math.abs(p.x - 6 - aboveSquare.x);
+
+ if ((diffX < 6) && (diffY < 6)) {
+ return true;
+ }
+
+ return false;
+ }
+
+ @Override
+ public void mousePressed(MouseEvent e) {
+ curPoint = e.getPoint();
+ dragOrigin = e.getPoint();
+
+ for (Integer key : verticesList.keySet()) {
+ Point p = verticesList.get(key);
+ int diffY = Math.abs((p.y + 12) - curPoint.y);
+ int diffX = Math.abs((p.x + (THUMB_WIDTH / 2)) - curPoint.x);
+
+ if ((diffX < 6) && (diffY < 6)) {
+ selectedIdx = key;
+ ((TriangleThumbRenderer)slider.getThumbRenderer()).setSelectedIndex(selectedIdx);
+ clickFlag = true;
+ }
+ }
+ }
+
+ @Override
+ public void mouseReleased(MouseEvent arg0) {
+ clickFlag = false;
+ updateMax();
+
+ if (((TriangleThumbRenderer)slider.getThumbRenderer()).getSelectedIndex() == -1)
+ slider.repaint();
+
+ repaint();
+
+ if (dragFlag == true) {
+ dragFlag = false;
+ cMapping.fireStateChanged();
+ }
+ }
+
+ private boolean isPointerInSquare(MouseEvent e) {
+ curPoint = e.getPoint();
+ dragOrigin = e.getPoint();
+
+ for (Integer key : verticesList.keySet()) {
+ Point p = verticesList.get(key);
+ int diffY = Math.abs((p.y + 12) - curPoint.y);
+ int diffX = Math.abs((p.x + (THUMB_WIDTH / 2)) - curPoint.x);
+
+ if ((diffX < 6) && (diffY < 6)) {
+ selectedIdx = key;
+
+ return true;
+ }
+ }
+
+ return false;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param iconWidth DOCUMENT ME!
+ * @param iconHeight DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public ImageIcon getTrackGraphicIcon(int iconWidth, int iconHeight) {
+ return drawIcon(iconWidth, iconHeight, false);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param iconWidth DOCUMENT ME!
+ * @param iconHeight DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public ImageIcon getLegend(int iconWidth, int iconHeight) {
+ return drawIcon(iconWidth, iconHeight, true);
+ }
+
+ private ImageIcon drawIcon(int iconWidth, int iconHeight, boolean detail) {
+ if (slider == null) {
+ return null;
+ }
+
+ final BufferedImage bi = new BufferedImage(iconWidth, iconHeight, BufferedImage.TYPE_INT_RGB);
+ final Graphics2D g = bi.createGraphics();
+
+ // Turn Anti-alias on
+ g.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
+
+ double minValue = EditorValueRangeTracer.getTracer().getMin(type);
+ double maxValue = EditorValueRangeTracer.getTracer().getMax(type);
+ double valueRange = EditorValueRangeTracer.getTracer().getRange(type);
+ /*
+ * Fill background
+ */
+ g.setColor(Color.white);
+ g.fillRect(0, 0, iconWidth, iconHeight);
+
+ int leftSpace = 10;
+ int trackHeight = iconHeight - 9;
+ int trackWidth = iconWidth - leftSpace;
+
+ /*
+ * Compute fractions from mapping
+ */
+ List<Thumb> stops = slider.getModel().getSortedThumbs();
+
+ int numPoints = stops.size();
+
+ float[] fractions = new float[numPoints];
+ Float[] floatProperty = new Float[numPoints];
+ int i = 0;
+
+ values.clear();
+ values.add(below.floatValue());
+ values.add(above.floatValue());
+
+ for (Thumb thumb : stops) {
+ floatProperty[i] = (Float) thumb.getObject();
+ fractions[i] = thumb.getPosition();
+ values.add((Float) thumb.getObject());
+ i++;
+ }
+
+ for (Float val : values) {
+ if (min >= val)
+ min = val;
+
+ if (max <= val)
+ max = val;
+ }
+
+ // Draw min/max
+ g.setColor(Color.DARK_GRAY);
+ g.setFont(ICON_FONT);
+
+ int minWidth = SwingUtilities.computeStringWidth(g.getFontMetrics(),
+ String.format("%.1f", min));
+ int maxWidth = SwingUtilities.computeStringWidth(g.getFontMetrics(),
+ String.format("%.1f", max));
+
+ if (detail) {
+ leftSpace = LEFT_SPACE;
+ trackHeight = iconHeight - 30;
+ } else {
+ leftSpace = Math.max(minWidth, maxWidth) + 1;
+ }
+
+ trackWidth = iconWidth - leftSpace;
+
+ g.drawString(String.format("%.1f", min), 0, trackHeight);
+ g.drawString(String.format("%.1f", max), 0, 8);
+
+ /*
+ * If no points, just return empty rectangle.
+ */
+ if (numPoints == 0) {
+ g.setStroke(new BasicStroke(1.0f));
+ g.setColor(Color.DARK_GRAY);
+ g.drawRect(leftSpace, 0, trackWidth - 3, trackHeight);
+
+ return new ImageIcon(bi);
+ }
+
+ g.translate(leftSpace, 0);
+ g.setStroke(new BasicStroke(1.0f));
+
+ int newX = 0;
+ int lastY = 0;
+
+ Point2D p1 = new Point2D.Float(0, 0);
+ Point2D p2 = new Point2D.Float(0, 0);
+
+ for (i = 0; i < floatProperty.length; i++) {
+ newX = (int) (trackWidth * (fractions[i] / 100)) - 3;
+
+ if (newX < 0) {
+ newX = 0;
+ }
+
+ p2.setLocation(newX, 0);
+
+ int newY = trackHeight - (int) ((floatProperty[i] / max) * trackHeight);
+
+ valueArea.reset();
+
+ g.setColor(VALUE_AREA_COLOR);
+
+ if (i == 0) {
+ int h = trackHeight - (int) ((below.floatValue() / max) * trackHeight);
+ g.fillRect(0, h, newX, (int) ((below.floatValue() / max) * trackHeight));
+ } else {
+ valueArea.addPoint((int) p1.getX(), lastY);
+ valueArea.addPoint(newX, newY);
+ valueArea.addPoint(newX, trackHeight);
+ valueArea.addPoint((int) p1.getX(), trackHeight);
+ g.fill(valueArea);
+ }
+
+ for (int j = 0; j < stops.size(); j++) {
+ if (slider.getModel().getThumbAt(j).getObject() == floatProperty[i]) {
+ Point newPoint = new Point(newX, newY);
+
+ if (verticesList.containsValue(newPoint) == false)
+ verticesList.put(j, new Point(newX, newY));
+
+ break;
+ }
+ }
+
+ lastY = newY;
+ p1.setLocation(p2);
+ }
+
+ p2.setLocation(trackWidth, 0);
+
+ g.setColor(VALUE_AREA_COLOR);
+
+ int h = trackHeight - (int) ((above.floatValue() / max) * trackHeight);
+ g.fillRect((int) p1.getX(), h, trackWidth - (int) p1.getX() - 3,
+ (int) ((above.floatValue() / max) * trackHeight));
+
+ g.translate(-leftSpace, 0);
+
+ /*
+ * Draw border line (rectangle)
+ */
+ g.setColor(BORDER_COLOR);
+ g.setStroke(new BasicStroke(1.0f));
+ g.drawRect(leftSpace, 0, trackWidth - 3, trackHeight);
+
+ /*
+ * Draw numbers and arrows
+ */
+ g.setFont(new Font("SansSerif", Font.BOLD, 9));
+
+ final String minStr = String.format("%.2f", minValue);
+ final String maxStr = String.format("%.2f", maxValue);
+ int strWidth;
+ g.setColor(Color.black);
+
+ if (detail) {
+ String fNum = null;
+
+ for (int j = 0; j < fractions.length; j++) {
+ fNum = String.format("%.2f", ((fractions[j] / 100) * valueRange) + minValue);
+ strWidth = SwingUtilities.computeStringWidth(g.getFontMetrics(), fNum);
+ g.drawString(fNum,
+ ((fractions[j] / 100) * trackWidth) - (strWidth / 2) + leftSpace,
+ iconHeight - 20);
+ }
+
+ g.drawString(minStr, leftSpace, iconHeight);
+ strWidth = SwingUtilities.computeStringWidth(g.getFontMetrics(), maxStr);
+ g.drawString(maxStr, iconWidth - strWidth - 2, iconHeight);
+
+ g.setFont(TITLE_FONT);
+
+ String label = title;
+ if (label == null)
+ label = "(none)";
+ final int titleWidth = SwingUtilities.computeStringWidth(g.getFontMetrics(), label);
+ g.setColor(Color.black);
+ g.drawString(label, (iconWidth / 2) - (titleWidth / 2), iconHeight - 5);
+
+ Polygon p = new Polygon();
+ p.addPoint(iconWidth, iconHeight - 9);
+ p.addPoint(iconWidth - 15, iconHeight - 15);
+ p.addPoint(iconWidth - 15, iconHeight - 9);
+ g.fillPolygon(p);
+ g.drawLine(leftSpace, iconHeight - 9,
+ ((iconWidth - leftSpace) / 2) - (titleWidth / 2) - 3, iconHeight - 9);
+ g.drawLine((iconWidth / 2) + (titleWidth / 2) + 3, iconHeight - 9, iconWidth,
+ iconHeight - 9);
+
+ /*
+ * Draw vertical arrow
+ */
+ int panelHeight = iconHeight - 30;
+
+ final Polygon poly = new Polygon();
+ int top = 0;
+
+ g.setStroke(new BasicStroke(1.0f));
+
+ int center = (leftSpace / 2) + 6;
+
+ poly.addPoint(center, top);
+ poly.addPoint(center - 6, top + 15);
+ poly.addPoint(center, top + 15);
+ g.fillPolygon(poly);
+
+ g.drawLine(center, top, center, panelHeight);
+ g.setColor(Color.DARK_GRAY);
+ g.setFont(new Font("SansSerif", Font.BOLD, 10));
+
+ label = type.getName();
+ final int width = SwingUtilities.computeStringWidth(g.getFontMetrics(), label);
+ AffineTransform af = new AffineTransform();
+ af.rotate(Math.PI + (Math.PI / 2));
+ g.setTransform(af);
+
+ g.setColor(Color.black);
+ g.drawString(type.getName(), (-panelHeight / 2) - (width / 2), (leftSpace / 2) + 5);
+ } else {
+ g.drawString(minStr, 0, iconHeight);
+ strWidth = SwingUtilities.computeStringWidth(g.getFontMetrics(), maxStr);
+ g.drawString(maxStr, iconWidth - strWidth - 2, iconHeight);
+ }
+
+ return new ImageIcon(bi);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/ui/editors/continuous/CyGradientTrackRenderer.java b/application/src/main/java/cytoscape/visual/ui/editors/continuous/CyGradientTrackRenderer.java
new file mode 100644
index 0000000..d9c33f0
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/editors/continuous/CyGradientTrackRenderer.java
@@ -0,0 +1,470 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.visual.ui.editors.continuous;
+
+import cytoscape.visual.VisualPropertyType;
+
+import org.jdesktop.swingx.JXMultiThumbSlider;
+import org.jdesktop.swingx.multislider.Thumb;
+
+import java.awt.BasicStroke;
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.GradientPaint;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.Polygon;
+import java.awt.Rectangle;
+import java.awt.RenderingHints;
+import java.awt.font.FontRenderContext;
+import java.awt.font.TextLayout;
+import java.awt.geom.Point2D;
+import java.awt.geom.Rectangle2D;
+import java.awt.image.BufferedImage;
+
+import java.util.List;
+
+import javax.swing.ImageIcon;
+import javax.swing.JComponent;
+import javax.swing.SwingUtilities;
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ */
+public class CyGradientTrackRenderer extends JComponent implements VizMapperTrackRenderer {
+ private int trackHeight = 40;
+ private final Font SMALL_FONT = new Font("SansSerif", Font.BOLD, 16);
+ private final Font TITLE_FONT = new Font("SansSerif", Font.BOLD, 12);
+
+ private JXMultiThumbSlider<Color> slider;
+
+ private Color below;
+ private Color above;
+ private String attrName;
+ private VisualPropertyType type;
+
+ /**
+ * Creates a new GradientTrackRenderer object.
+ *
+ * @param gradientPicker
+ * DOCUMENT ME!
+ */
+ public CyGradientTrackRenderer(VisualPropertyType type, Color below, Color above, String title) {
+ this.below = below;
+ this.above = above;
+ this.attrName = title;
+ this.type = type;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g
+ * DOCUMENT ME!
+ */
+ public void paint(Graphics g) {
+ super.paint(g);
+ paintComponent(g);
+ }
+
+ protected void paintComponent(Graphics gfx) {
+ Graphics2D g = (Graphics2D) gfx;
+
+ // Turn AA on
+ g.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
+
+ double minValue = EditorValueRangeTracer.getTracer().getMin(type);
+ double maxValue = EditorValueRangeTracer.getTracer().getMax(type);
+ double range = EditorValueRangeTracer.getTracer().getRange(type);
+
+ // calculate the track area
+ int thumb_width = 12;
+ int track_width = slider.getWidth() - thumb_width;
+ g.translate(thumb_width / 2, 12);
+
+ // get the list of colors
+ List<Thumb<Color>> stops = slider.getModel().getSortedThumbs();
+ int len = stops.size();
+
+ if (len != 0) {
+ // set up the data for the gradient
+ float[] fractions = new float[len + 2];
+ Color[] colors = new Color[len + 2];
+ int i = 1;
+
+ colors[0] = below;
+ fractions[0] = stops.get(0).getPosition() / 100;
+
+ for (Thumb<Color> thumb : stops) {
+ colors[i] = (Color) thumb.getObject();
+
+ fractions[i] = thumb.getPosition() / 100;
+
+ g.setColor(colors[i]);
+ g.setFont(SMALL_FONT);
+
+ String valueString;
+ Double value = minValue + (fractions[i] * range);
+
+ if ((Math.abs(minValue) < 3) || (Math.abs(maxValue) < 3))
+ valueString = String.format("%.4f", value);
+ else
+ valueString = String.format("%.2f", value);
+
+ final int stringWidth = SwingUtilities.computeStringWidth(g.getFontMetrics(),
+ valueString);
+ final int curPosition = (int) (track_width * fractions[i]);
+
+ FontRenderContext frc = g.getFontRenderContext();
+ TextLayout tl = new TextLayout(valueString, g.getFont(), frc);
+
+ g.setStroke(new BasicStroke(0.6f));
+ g.setColor(Color.BLACK);
+
+ final float[] hsb = colors[i].RGBtoHSB(colors[i].getRed(), colors[i].getGreen(),
+ colors[i].getBlue(), null);
+
+ int x;
+ int y;
+
+ if (curPosition < (stringWidth / 2)) {
+ x = curPosition;
+ y = trackHeight + 15;
+ } else if ((track_width - curPosition) < (stringWidth / 2)) {
+ x = curPosition - stringWidth;
+ y = trackHeight + 15;
+ } else {
+ x = curPosition - (stringWidth / 2);
+ y = trackHeight + 15;
+ }
+
+ if (hsb[1] < 0.5) {
+ g.setColor(colors[i]);
+ g.drawString(valueString, x, y);
+
+ g.translate(x, y);
+ g.setColor(Color.BLACK);
+ g.draw(tl.getOutline(null));
+ g.translate(-x, -y);
+ } else {
+ g.setColor(colors[i]);
+ g.drawString(valueString, x, y);
+ }
+
+ i++;
+ }
+
+ colors[colors.length - 1] = above;
+ fractions[fractions.length - 1] = stops.get(stops.size() - 1).getPosition() / 100;
+
+ g.setStroke(new BasicStroke(1.0f));
+
+ // fill in the gradient
+ Point2D start = new Point2D.Float(0, 0);
+ Point2D end = new Point2D.Float(track_width, trackHeight);
+
+ drawGradient(g, start, end, fractions, colors);
+ }
+
+ // Define rectangle
+ Rectangle2D rect = new Rectangle(0, 0, track_width, trackHeight);
+ g.setColor(Color.gray);
+ g.drawLine((int) rect.getBounds2D().getMinX(), (int) rect.getBounds2D().getMaxY(), 8,
+ (int) rect.getBounds2D().getMaxY() + 25);
+ g.setFont(SMALL_FONT);
+ g.drawString("Min=" + minValue, (int) rect.getBounds2D().getMinX(),
+ (int) rect.getBounds2D().getMaxY() + 38);
+
+ g.drawLine((int) rect.getBounds2D().getMaxX(), (int) rect.getBounds2D().getMaxY(),
+ (int) rect.getBounds2D().getMaxX() - 8, (int) rect.getBounds2D().getMaxY() + 25);
+ g.setFont(SMALL_FONT);
+
+ final String maxString = "Max=" + maxValue;
+ g.drawString(maxString,
+ (int) rect.getBounds2D().getMaxX()
+ - SwingUtilities.computeStringWidth(g.getFontMetrics(), maxString),
+ (int) rect.getBounds2D().getMaxY() + 38);
+
+ g.setFont(TITLE_FONT);
+
+ String legendName = attrName;
+ if (legendName == null)
+ legendName = "(none)";
+ final int titleWidth = SwingUtilities.computeStringWidth(g.getFontMetrics(), legendName);
+ g.setColor(Color.black);
+ g.drawString(legendName, ((int) rect.getBounds2D().getWidth() / 2) - (titleWidth / 2),
+ (int) rect.getBounds2D().getMaxY() + 33);
+
+ // draw a border
+ g.draw(rect);
+ g.translate(-thumb_width / 2, -12);
+ }
+
+ private static void drawGradient(Graphics2D g, Point2D start, Point2D end, float[] fractions,
+ Color[] colors) {
+ if (fractions.length < 1)
+ return;
+
+ final int width = (int) (end.getX() - start.getX());
+ final int height = (int) (end.getY() - start.getY());
+
+ if (colors.length == 3) {
+ final int pivot = (int) (fractions[1] * width);
+ g.setColor(colors[0]);
+ g.fillRect((int) start.getX(), (int) start.getY(), pivot, height);
+ g.setColor(colors[2]);
+ g.fillRect(pivot, (int) start.getY(), width - pivot, height);
+
+ g.setColor(colors[1]);
+ g.drawLine(pivot, (int) start.getY(), pivot, height);
+ } else if (colors.length > 3) {
+ int pivot = (int) (fractions[1] * width);
+ g.setColor(colors[0]);
+ g.fillRect((int) start.getX(), (int) start.getY(), pivot, height);
+
+ int nextPivot;
+
+ for (int i = 1; i < (colors.length - 2); i++) {
+ nextPivot = (int) (width * fractions[i + 1]);
+
+ GradientPaint gp = new GradientPaint(pivot, height / 2, colors[i], nextPivot,
+ height / 2, colors[i + 1]);
+ g.setPaint(gp);
+ g.fillRect(pivot, 0, nextPivot - pivot, height);
+ pivot = nextPivot;
+ }
+
+ final int lastPivot = (int) (fractions[fractions.length - 1] * width);
+ g.setColor(colors[colors.length - 1]);
+ g.fillRect(lastPivot, (int) start.getY(), width - lastPivot, height);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param slider
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public JComponent getRendererComponent(JXMultiThumbSlider slider) {
+ this.slider = slider;
+ trackHeight = slider.getHeight() - 50;
+
+ return this;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param x
+ * DOCUMENT ME!
+ * @param y
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getObjectInRange(int x, int y) {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param x
+ * DOCUMENT ME!
+ * @param y
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getToolTipForCurrentLocation(int x, int y) {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param iconWidth DOCUMENT ME!
+ * @param iconHeight DOCUMENT ME!
+ * @param mapping DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public ImageIcon getTrackGraphicIcon(int iconWidth, int iconHeight) {
+ return drawIcon(iconWidth, iconHeight, false);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param iconWidth DOCUMENT ME!
+ * @param iconHeight DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public ImageIcon getLegend(int iconWidth, int iconHeight) {
+ return drawIcon(iconWidth, iconHeight, true);
+ }
+
+ private ImageIcon drawIcon(int iconWidth, int iconHeight, boolean detail) {
+ if (slider == null) {
+ return null;
+ }
+
+ final BufferedImage bi = new BufferedImage(iconWidth, iconHeight, BufferedImage.TYPE_INT_RGB);
+ final Graphics2D g2 = bi.createGraphics();
+
+ // Turn AA on.
+ g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
+
+ final double minValue = EditorValueRangeTracer.getTracer().getMin(type);
+ final double maxValue = EditorValueRangeTracer.getTracer().getMax(type);
+ final double range = EditorValueRangeTracer.getTracer().getRange(type);
+ /*
+ * Fill background
+ */
+ g2.setColor(Color.white);
+ g2.fillRect(0, 0, iconWidth, iconHeight);
+
+ List<Thumb<Color>> stops = slider.getModel().getSortedThumbs();
+ int len = stops.size();
+ int strWidth;
+ float[] fractions = null;
+ Point2D start = new Point2D.Float(0, 0);
+ Point2D end = null;
+
+ if (detail) {
+ end = new Point2D.Float(iconWidth - 3, iconHeight - 30);
+ } else {
+ end = new Point2D.Float(iconWidth - 3, iconHeight - 9);
+ }
+
+ if (len != 0) {
+ // set up the data for the gradient
+ fractions = new float[len + 2];
+
+ Color[] colors = new Color[len + 2];
+ int i = 1;
+
+ colors[0] = below;
+ fractions[0] = stops.get(0).getPosition() / 100;
+
+ for (Thumb<Color> thumb : stops) {
+ colors[i] = (Color) thumb.getObject();
+ fractions[i] = thumb.getPosition() / 100;
+ i++;
+ }
+
+ colors[colors.length - 1] = above;
+ fractions[fractions.length - 1] = stops.get(stops.size() - 1).getPosition() / 100;
+
+ // fill in the gradient
+ drawGradient(g2, start, end, fractions, colors);
+ }
+
+ // Draw border line
+ g2.setStroke(new BasicStroke(1.0f));
+ g2.setColor(Color.DARK_GRAY);
+ g2.drawRect(0, 0, ((Number) end.getX()).intValue(), ((Number) end.getY()).intValue());
+
+ /*
+ * draw numbers
+ */
+ g2.setFont(new Font("SansSerif", Font.BOLD, 9));
+
+ final String minStr = String.format("%.2f", minValue);
+ final String maxStr = String.format("%.2f", maxValue);
+
+ g2.setColor(Color.black);
+
+ if (detail && (fractions != null)) {
+ String fNum = null;
+
+ for (int i = 0; i < fractions.length; i++) {
+ fNum = String.format("%.2f", (fractions[i] * range) + minValue);
+
+ strWidth = SwingUtilities.computeStringWidth(g2.getFontMetrics(), fNum);
+
+ g2.drawString(fNum, (fractions[i] * iconWidth) - (strWidth / 2), iconHeight - 20);
+ }
+
+ g2.drawString(minStr, 0, iconHeight);
+ strWidth = SwingUtilities.computeStringWidth(g2.getFontMetrics(), maxStr);
+ g2.drawString(maxStr, iconWidth - strWidth - 2, iconHeight);
+
+ g2.setFont(TITLE_FONT);
+
+ final int titleWidth = SwingUtilities.computeStringWidth(g2.getFontMetrics(), attrName);
+ g2.setColor(Color.black);
+ g2.drawString(attrName, (iconWidth / 2) - (titleWidth / 2), iconHeight - 5);
+
+ Polygon p = new Polygon();
+ p.addPoint(iconWidth, iconHeight - 9);
+ p.addPoint(iconWidth - 15, iconHeight - 15);
+ p.addPoint(iconWidth - 15, iconHeight - 9);
+ g2.fillPolygon(p);
+ g2.drawLine(0, iconHeight - 9, (iconWidth / 2) - (titleWidth / 2) - 3, iconHeight - 9);
+ g2.drawLine((iconWidth / 2) + (titleWidth / 2) + 3, iconHeight - 9, iconWidth,
+ iconHeight - 9);
+ } else {
+ g2.drawString(minStr, 0, iconHeight);
+ strWidth = SwingUtilities.computeStringWidth(g2.getFontMetrics(), maxStr);
+ g2.drawString(maxStr, iconWidth - strWidth - 2, iconHeight);
+ }
+
+ return new ImageIcon(bi);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Double getSelectedThumbValue() {
+ final float position = slider.getModel().getThumbAt(slider.getSelectedIndex()).getPosition();
+ final double thumbVal = (((position / 100) * EditorValueRangeTracer.getTracer()
+ .getRange(type))
+ + EditorValueRangeTracer.getTracer().getMin(type));
+
+ return thumbVal;
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/ui/editors/continuous/DiscreteTrackRenderer.java b/application/src/main/java/cytoscape/visual/ui/editors/continuous/DiscreteTrackRenderer.java
new file mode 100644
index 0000000..9a2e63e
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/editors/continuous/DiscreteTrackRenderer.java
@@ -0,0 +1,796 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.visual.ui.editors.continuous;
+
+import giny.view.ObjectPosition;
+
+import java.awt.BasicStroke;
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.Image;
+import java.awt.Polygon;
+import java.awt.RenderingHints;
+import java.awt.Stroke;
+import java.awt.geom.Point2D;
+import java.awt.image.BufferedImage;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+
+import javax.swing.ImageIcon;
+import javax.swing.JComponent;
+import javax.swing.SwingUtilities;
+
+import org.jdesktop.swingx.JXMultiThumbSlider;
+import org.jdesktop.swingx.multislider.Thumb;
+
+import cytoscape.Cytoscape;
+import cytoscape.visual.LineStyle;
+import cytoscape.visual.NodeShape;
+import cytoscape.visual.VisualPropertyType;
+import cytoscape.visual.customgraphic.CyCustomGraphics;
+import cytoscape.visual.mappings.ContinuousMapping;
+import cytoscape.visual.mappings.continuous.ContinuousMappingPoint;
+import cytoscape.visual.ui.ObjectPlacerGraphic;
+import cytoscape.visual.ui.icon.VisualPropertyIcon;
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ */
+public class DiscreteTrackRenderer<T> extends JComponent implements VizMapperTrackRenderer {
+
+ private static final long serialVersionUID = 5024551458030362213L;
+
+ /*
+ * Constants for diagram.
+ */
+ private static final Font TITLE_FONT = new Font("SansSerif", Font.BOLD, 12);
+ private static final int ICON_SIZE = VisualPropertyIcon.DEFAULT_ICON_SIZE;
+ private static final int ICON_SIZE_CG = 50;
+
+ private static final Color ICON_COLOR = new Color(10, 100, 255, 200);
+ private static final int THUMB_WIDTH = 12;
+ private static final int V_PADDING = 20;
+
+ private int trackHeight = 70;
+ private int arrowBarYPosition = trackHeight + 50;
+ private int smallIconSize = 20;
+
+ private T below;
+ private T above;
+ private final VisualPropertyType type;
+ private String title;
+
+ // Mainly for Icons
+ private List<T> rangeObjects;
+
+ private JXMultiThumbSlider<T> slider;
+
+ /**
+ * Creates a new DiscreteTrackRenderer object.
+ *
+ * @param type DOCUMENT ME!
+ * @param minValue DOCUMENT ME!
+ * @param maxValue DOCUMENT ME!
+ * @param below DOCUMENT ME!
+ * @param above DOCUMENT ME!
+ */
+ public DiscreteTrackRenderer(final VisualPropertyType type,
+ T below, T above) {
+
+ this.below = below;
+ this.above = above;
+
+ this.type = type;
+
+ if (type.isNodeProp())
+ title = Cytoscape.getVisualMappingManager().getVisualStyle()
+ .getNodeAppearanceCalculator().getCalculator(type).getMapping(0)
+ .getControllingAttributeName();
+ else
+ title = Cytoscape.getVisualMappingManager().getVisualStyle()
+ .getEdgeAppearanceCalculator().getCalculator(type).getMapping(0)
+ .getControllingAttributeName();
+
+ this.setBackground(Color.white);
+ this.setForeground(Color.white);
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g DOCUMENT ME!
+ */
+ public void paint(Graphics g) {
+ super.paint(g);
+ paintComponent(g);
+ }
+
+ protected void paintComponent(Graphics gfx) {
+ trackHeight = slider.getHeight() - 100;
+ arrowBarYPosition = trackHeight + 50;
+
+ // Turn AA on
+ Graphics2D g = (Graphics2D) gfx;
+ g.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
+
+ int track_width = slider.getWidth() - THUMB_WIDTH;
+
+ g.translate(THUMB_WIDTH / 2, 12);
+
+ double minValue = EditorValueRangeTracer.getTracer().getMin(type);
+ double maxValue = EditorValueRangeTracer.getTracer().getMax(type);
+ double valueRange = EditorValueRangeTracer.getTracer().getRange(type);
+
+ // get the list of tumbs
+ final List<Thumb<T>> stops = slider.getModel().getSortedThumbs();
+
+ int numPoints = stops.size();
+
+ // set up the data for the gradient
+ float[] fractions = new float[numPoints];
+ Object[] objectValues = new Object[numPoints];
+
+ /*
+ * Find min, max, and ranges
+ */
+ int i = 0;
+
+ for (Thumb<T> thumb : stops) {
+ objectValues[i] = thumb.getObject();
+ fractions[i] = thumb.getPosition();
+ i++;
+ }
+
+ /*
+ * Draw arrow bar
+ */
+ g.setStroke(new BasicStroke(1.0f));
+ g.setColor(Color.black);
+ g.drawLine(0, arrowBarYPosition, track_width, arrowBarYPosition);
+
+ Polygon arrow = new Polygon();
+ arrow.addPoint(track_width, arrowBarYPosition);
+ arrow.addPoint(track_width - 20, arrowBarYPosition - 8);
+ arrow.addPoint(track_width - 20, arrowBarYPosition);
+ g.fill(arrow);
+
+ g.setColor(Color.gray);
+ g.drawLine(0, arrowBarYPosition, 15, arrowBarYPosition - 30);
+ g.drawLine(15, arrowBarYPosition - 30, 25, arrowBarYPosition - 30);
+
+ g.setFont(SMALL_FONT);
+ g.drawString("Min=" + minValue, 28, arrowBarYPosition - 25);
+
+ g.drawLine(track_width, arrowBarYPosition, track_width - 15, arrowBarYPosition + 30);
+ g.drawLine(track_width - 15, arrowBarYPosition + 30, track_width - 25,
+ arrowBarYPosition + 30);
+
+ final String maxStr = "Max=" + maxValue;
+ int strWidth = SwingUtilities.computeStringWidth(g.getFontMetrics(), maxStr);
+ g.drawString(maxStr, track_width - strWidth - 26, arrowBarYPosition + 35);
+
+ g.setFont(SMALL_FONT);
+ g.setColor(Color.black);
+ strWidth = SwingUtilities.computeStringWidth(g.getFontMetrics(), title);
+ g.drawString(title, (track_width / 2) - (strWidth / 2), arrowBarYPosition + 35);
+
+ /*
+ * If no points, just draw empty box.
+ */
+ if (numPoints == 0) {
+ g.setColor(BORDER_COLOR);
+ g.setStroke(new BasicStroke(1.5f));
+ g.drawRect(0, 5, track_width, trackHeight);
+
+ return;
+ }
+
+ g.setStroke(new BasicStroke(1.0f));
+
+ /*
+ * Fill background
+ */
+ g.setColor(Color.white);
+ g.fillRect(0, 5, track_width, trackHeight);
+
+ rangeObjects = buildIconArray(stops.size() + 1);
+
+ int newX = 0;
+
+ Point2D p1 = new Point2D.Float(0, 5);
+ Point2D p2 = new Point2D.Float(0, 5);
+
+ int iconLocX;
+ int iconLocY;
+
+ final int iconSize;
+ if(type.getDataType().equals(CyCustomGraphics.class))
+ iconSize = ICON_SIZE_CG;
+ else
+ iconSize = ICON_SIZE;
+ /*
+ * Draw separators and icons
+ */
+ for (i = 0; i < stops.size(); i++) {
+ newX = (int) (track_width * (fractions[i] / 100));
+
+ p2.setLocation(newX, 5);
+ g.setColor(Color.black);
+ g.setStroke(STROKE1);
+
+ g.drawLine(newX, 5, newX, trackHeight + 4);
+
+ g.setColor(Color.DARK_GRAY);
+ g.setFont(new Font("SansSerif", Font.BOLD, 10));
+
+ final Float curPositionValue = ((Number) (((fractions[i] / 100) * valueRange)
+ + minValue)).floatValue();
+ final String valueString = String.format("%.5f", curPositionValue);
+
+ int flipLimit = 90;
+ int borderVal = track_width - newX;
+
+ if (((i % 2) == 0) && (flipLimit < borderVal)) {
+ g.drawLine(newX, arrowBarYPosition, newX + 20, arrowBarYPosition - 15);
+ g.drawLine(newX + 20, arrowBarYPosition - 15, newX + 30,
+ arrowBarYPosition - 15);
+ g.setColor(Color.black);
+ g.drawString(valueString, newX + 33, arrowBarYPosition - 11);
+ } else if (((i % 2) == 1) && (flipLimit < borderVal)) {
+ g.drawLine(newX, arrowBarYPosition, newX + 20, arrowBarYPosition + 15);
+ g.drawLine(newX + 20, arrowBarYPosition + 15, newX + 30,
+ arrowBarYPosition + 15);
+ g.setColor(Color.black);
+ g.drawString(valueString, newX + 33, arrowBarYPosition + 19);
+ } else if (((i % 2) == 0) && (flipLimit >= borderVal)) {
+ g.drawLine(newX, arrowBarYPosition, newX - 20, arrowBarYPosition - 15);
+ g.drawLine(newX - 20, arrowBarYPosition - 15, newX - 30,
+ arrowBarYPosition - 15);
+ g.setColor(Color.black);
+ g.drawString(valueString, newX - 90, arrowBarYPosition - 11);
+ } else {
+ g.drawLine(newX, arrowBarYPosition, newX - 20, arrowBarYPosition + 15);
+ g.drawLine(newX - 20, arrowBarYPosition + 15, newX - 30,
+ arrowBarYPosition + 15);
+ g.setColor(Color.black);
+ g.drawString(valueString, newX - 90, arrowBarYPosition + 19);
+ }
+
+ g.setColor(Color.black);
+ g.fillOval(newX - 3, arrowBarYPosition - 3, 6, 6);
+
+
+ iconLocX = newX - (((newX - (int) p1.getX()) / 2) + (iconSize / 2));
+ iconLocY = ((trackHeight) / 2) - (iconSize / 2) + 5;
+
+ if (i == 0)
+ drawIcon(below, g, iconLocX, iconLocY, iconSize);
+ else
+ drawIcon(objectValues[i], g, iconLocX, iconLocY, iconSize);
+
+ p1.setLocation(p2);
+ }
+
+ /*
+ * Draw last region (above region)
+ */
+ p2.setLocation(track_width, 5);
+
+ iconLocX = track_width - (((track_width - (int) p1.getX()) / 2) + (iconSize / 2));
+ iconLocY = ((trackHeight) / 2) - (iconSize / 2) + 5;
+
+ drawIcon(above, g, iconLocX, iconLocY, iconSize);
+ /*
+ * Finally, draw border line (rectangle)
+ */
+ g.setColor(BORDER_COLOR);
+ g.setStroke(new BasicStroke(1.5f));
+ g.drawRect(0, 5, track_width, trackHeight);
+
+ g.translate(-THUMB_WIDTH / 2, -12);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param slider DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @SuppressWarnings({ "rawtypes", "unchecked" })
+ public JComponent getRendererComponent( JXMultiThumbSlider slider) {
+ this.slider = slider;
+ return this;
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param x DOCUMENT ME!
+ * @param y DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getToolTipForCurrentLocation(int x, int y) {
+ int oldX = 0;
+ int newX;
+
+ final List<Thumb<T>> stops = slider.getModel().getSortedThumbs();
+
+ int i = 1;
+
+ for (Thumb<T> thumb : stops) {
+ newX = (int) (slider.getWidth() * (thumb.getPosition() / 100));
+
+ if ((oldX <= x) && (x <= newX) && (V_PADDING < y) && (y < (V_PADDING + trackHeight)))
+ return "This is region " + i;
+
+ i++;
+ oldX = newX + 1;
+ }
+
+ if ((oldX <= x) && (x <= slider.getWidth()) && (V_PADDING < y)
+ && (y < (V_PADDING + trackHeight)))
+ return "Last Area: " + oldX + " - " + slider.getWidth() + " (x, y) = " + x + ", " + y;
+
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param x DOCUMENT ME!
+ * @param y DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getObjectInRange(int x, int y) {
+ final int range = getRangeID(x, y);
+
+ if (range == -1)
+ return null;
+
+ if (range == 0) {
+ return null;
+ } else if (range == slider.getModel().getThumbCount()) {
+ }
+
+ return rangeObjects.get(getRangeID(x, y));
+ }
+
+ /*
+ * Get region id.
+ *
+ * +-------------------------------------------
+ * | 0 | 1 | 2 | ...
+ * +-------------------------------------------
+ *
+ */
+ protected int getRangeID(int x, int y) {
+ int oldX = 0;
+ int newX;
+
+ final List<Thumb<T>> stops = slider.getModel().getSortedThumbs();
+ Thumb<T> thumb;
+ int i;
+
+ for (i = 0; i < stops.size(); i++) {
+ thumb = stops.get(i);
+ newX = (int) (slider.getWidth() * (thumb.getPosition() / 100));
+
+ if ((oldX <= x) && (x <= newX) && (V_PADDING < y) && (y < (V_PADDING + trackHeight)))
+ return i;
+
+ oldX = newX + 1;
+ }
+
+ if ((oldX <= x) && (x <= slider.getWidth()) && (V_PADDING < y)
+ && (y < (V_PADDING + trackHeight)))
+ return i;
+
+ // Invalid range
+ return -1;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param iconWidth DOCUMENT ME!
+ * @param iconHeight DOCUMENT ME!
+ * @param mapping DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static ImageIcon getTrackGraphicIcon(int iconWidth, int iconHeight,
+ ContinuousMapping mapping) {
+ final BufferedImage bi = new BufferedImage(iconWidth, iconHeight, BufferedImage.TYPE_INT_RGB);
+ final Graphics2D g2 = bi.createGraphics();
+
+ // Turn Anti-alias on
+ g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
+ g2.setRenderingHint(RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_QUALITY);
+
+ final int leftSpace = 2;
+ int trackHeight = iconHeight - 15;
+ int trackWidth = iconWidth - leftSpace - 5;
+
+ g2.setBackground(Color.white);
+
+ /*
+ * Draw background
+ */
+ g2.setColor(Color.white);
+ g2.fillRect(0, 0, iconWidth, iconHeight);
+ g2.setStroke(new BasicStroke(1.0f));
+ g2.setColor(Color.black);
+
+ /*
+ * Compute fractions from mapping
+ */
+ List<ContinuousMappingPoint> points = mapping.getAllPoints();
+ final int pointCount = points.size();
+
+ /*
+ * If no points, just return empty rectangle.
+ */
+ if (pointCount == 0) {
+ g2.drawRect(leftSpace, 0, trackWidth, trackHeight);
+
+ return new ImageIcon(bi);
+ }
+
+ Object[] objValues = new Object[pointCount + 2];
+
+ objValues[0] = points.get(0).getRange().lesserValue;
+
+ if (pointCount == 1) {
+ objValues[1] = points.get(0).getRange().equalValue;
+ objValues[2] = points.get(0).getRange().greaterValue;
+ } else {
+ // "Above" value
+ objValues[objValues.length - 1] = points.get(points.size() - 1).getRange().greaterValue;
+
+ for (int i = 0; i < pointCount; i++)
+ objValues[i + 1] = points.get(i).getRange().equalValue;
+ }
+
+ return new ImageIcon(bi);
+ }
+
+ private static List buildIconArray(int size) {
+ List<ImageIcon> icons = new ArrayList<ImageIcon>();
+
+ Map iconMap = NodeShape.getIconSet();
+
+ Object[] keys = iconMap.keySet().toArray();
+
+ for (int i = 0; i < size; i++)
+ icons.add((ImageIcon) iconMap.get(keys[i]));
+
+ return icons;
+ }
+
+ /*
+ * Draw icon object based on the given data type.
+ */
+ private void drawIcon(Object key, Graphics2D g, int x, int y, final int size) {
+ if(key == null)
+ return;
+
+ g.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
+ g.setRenderingHint(RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_QUALITY);
+
+ g.translate(x, y);
+ g.setColor(ICON_COLOR);
+ g.setStroke(STROKE2);
+
+ // Special drawing code for shapes.
+ switch (type) {
+ case NODE_SHAPE:
+
+ final VisualPropertyIcon icon = (VisualPropertyIcon) type.getVisualProperty()
+ .getIconSet().get(key);
+ icon.setIconHeight(size);
+ icon.setIconWidth(size);
+ g.fill(icon.getShape());
+
+ break;
+
+ case EDGE_SRCARROW_SHAPE:
+ case EDGE_TGTARROW_SHAPE:
+
+ final VisualPropertyIcon arrowIcon = ((VisualPropertyIcon) type.getVisualProperty()
+ .getIconSet().get(key));
+ if(arrowIcon == null) {
+ break;
+ }
+ final int newSize = size;
+ arrowIcon.setIconHeight(newSize);
+ arrowIcon.setIconWidth(((Number)(newSize*2.5)).intValue());
+
+ g.translate(-newSize, 0);
+ arrowIcon.paintIcon(this, g, x, y);
+ g.translate(newSize, 0);
+
+ break;
+
+ case NODE_FONT_FACE:
+ case EDGE_FONT_FACE:
+
+ final Font font = (Font) key;
+ final String fontName = font.getFontName();
+ g.setFont(new Font(fontName, font.getStyle(), size));
+ g.drawString("A", 0, size);
+
+ final int smallFontSize = ((Number) (size * 0.25)).intValue();
+ g.setFont(new Font(fontName, font.getStyle(), smallFontSize));
+
+ int stringWidth = SwingUtilities.computeStringWidth(g.getFontMetrics(), fontName);
+ g.drawString(fontName, (size / 2) - (stringWidth / 2), size + smallFontSize + 2);
+
+ break;
+
+ case NODE_LINE_STYLE:
+ case EDGE_LINE_STYLE:
+
+ final Stroke stroke = ((LineStyle) key).getStroke(2.0f);
+ final int newSize2 = (int) (size * 1.5);
+ g.translate(0, -size * 0.25);
+ g.setColor(Color.DARK_GRAY);
+ g.drawRect(0, 0, size, newSize2);
+ g.setStroke(stroke);
+ g.setColor(ICON_COLOR);
+ g.drawLine(size - 1, 1, 1, newSize2 - 1);
+ g.translate(0, size * 0.25);
+
+ break;
+
+ default:
+ break;
+ }
+
+
+ if(type.getDataType().equals(ObjectPosition.class)) {
+ // Object Positions
+
+ final ObjectPlacerGraphic lp = new ObjectPlacerGraphic((ObjectPosition) key,
+ (int) (size * 1.5), false, type.getName(), null, null);
+ lp.paint(g);
+ } else if(type.getDataType().equals(CyCustomGraphics.class)) {
+ // Custom Graphics
+ final CyCustomGraphics cg = (CyCustomGraphics) key;
+ final Image rendered = cg.getRenderedImage();
+ if(rendered != null)
+ g.drawImage(rendered, 0, 0, size, size, null);
+ } else {
+ // Draw as String.
+ g.drawString(key.toString(), 0, g.getFont().getSize()*2);
+ }
+
+ g.translate(-x, -y);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param iconWidth DOCUMENT ME!
+ * @param iconHeight DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public ImageIcon getTrackGraphicIcon(int iconWidth, int iconHeight) {
+ return drawIcon(iconWidth, iconHeight, false);
+ }
+
+ public ImageIcon getLegend(int iconWidth, int iconHeight) {
+ return drawIcon(iconWidth, iconHeight, true);
+ }
+
+ private ImageIcon drawIcon(int iconWidth, int iconHeight, boolean detail) {
+ if (slider == null) {
+ return null;
+ }
+
+ final BufferedImage bi = new BufferedImage(iconWidth, iconHeight, BufferedImage.TYPE_INT_RGB);
+ final Graphics2D g = bi.createGraphics();
+
+ // Turn AA on.
+ g.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
+ g.setRenderingHint(RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_QUALITY);
+
+ // Fill background
+ g.setColor(Color.white);
+ g.fillRect(0, 0, iconWidth, iconHeight);
+
+ double minValue = EditorValueRangeTracer.getTracer().getMin(type);
+ double maxValue = EditorValueRangeTracer.getTracer().getMax(type);
+ double valueRange = EditorValueRangeTracer.getTracer().getRange(type);
+
+ final int track_width = iconWidth;
+ final int trackHeight;
+ if(detail) {
+ trackHeight = iconHeight - 30;
+ smallIconSize = (int) (trackHeight * 0.5);
+ } else
+ trackHeight = iconHeight - 8;
+
+ // get the list of tumbs
+ final List<Thumb<T>> stops = slider.getModel().getSortedThumbs();
+
+ int numPoints = stops.size();
+
+ // set up the data for the gradient
+ float[] fractions = new float[numPoints];
+ Object[] objectValues = new Object[numPoints];
+
+ /*
+ * Find min, max, and ranges
+ */
+ int i = 0;
+
+ for (Thumb thumb : stops) {
+ objectValues[i] = thumb.getObject();
+ fractions[i] = thumb.getPosition();
+ i++;
+ }
+
+ /*
+ * If no points, just draw empty box.
+ */
+ if (numPoints == 0) {
+ g.setColor(BORDER_COLOR);
+ g.setStroke(new BasicStroke(1.0f));
+ g.drawRect(0, 0, track_width - 3, trackHeight);
+
+ return new ImageIcon(bi);
+ }
+
+ rangeObjects = buildIconArray(stops.size() + 1);
+
+ int newX = 0;
+
+ Point2D p1 = new Point2D.Float(0, 5);
+ Point2D p2 = new Point2D.Float(0, 5);
+
+ int iconLocX;
+ int iconLocY;
+
+ /*
+ * Draw separators and icons
+ */
+ for (i = 0; i < stops.size(); i++) {
+ newX = (int) (track_width * (fractions[i] / 100));
+
+ p2.setLocation(newX, 0);
+ iconLocX = newX - (((newX - (int) p1.getX()) / 2) + (smallIconSize / 2));
+ iconLocY = ((trackHeight) / 2) - (smallIconSize / 2);
+
+ if (i == 0) {
+ drawIcon(below, g, iconLocX, iconLocY, smallIconSize);
+ } else {
+ drawIcon(objectValues[i], g, iconLocX, iconLocY, smallIconSize);
+ }
+
+ g.setColor(Color.DARK_GRAY);
+ g.setStroke(STROKE1);
+ g.drawLine(newX, 0, newX, trackHeight);
+
+ p1.setLocation(p2);
+ }
+
+ /*
+ * Draw last region (above region)
+ */
+ p2.setLocation(track_width, 0);
+
+ iconLocX = track_width - (((track_width - (int) p1.getX()) / 2) + (smallIconSize / 2));
+ iconLocY = ((trackHeight) / 2) - (smallIconSize / 2);
+ drawIcon(above, g, iconLocX, iconLocY, smallIconSize);
+
+ /*
+ * Finally, draw border line (rectangle)
+ */
+ g.setColor(BORDER_COLOR);
+ g.setStroke(new BasicStroke(1.0f));
+ g.drawRect(0, 0, track_width - 3, trackHeight);
+
+
+ g.setFont(new Font("SansSerif", Font.BOLD, 9));
+
+ final String minStr = String.format("%.2f", minValue);
+ final String maxStr = String.format("%.2f", maxValue);
+ int strWidth;
+ g.setColor(Color.black);
+ if(detail) {
+ String fNum = null;
+ for(int j=0; j<fractions.length; j++) {
+ fNum = String.format("%.2f", ((fractions[j]/100)*valueRange) + minValue);
+ strWidth = SwingUtilities.computeStringWidth(g.getFontMetrics(), fNum);
+ g.drawString(fNum, (fractions[j]/100)*iconWidth-strWidth/2, iconHeight-20);
+ }
+
+ g.drawString(minStr, 0, iconHeight);
+ strWidth = SwingUtilities.computeStringWidth(g.getFontMetrics(), maxStr);
+ g.drawString(maxStr, iconWidth - strWidth - 2, iconHeight);
+
+ g.setFont(TITLE_FONT);
+
+ final int titleWidth = SwingUtilities.computeStringWidth(g.getFontMetrics(), title);
+ g.setColor(Color.black);
+ g.drawString(title, (iconWidth / 2) - (titleWidth / 2),
+ iconHeight-5);
+ Polygon p = new Polygon();
+ p.addPoint(iconWidth,iconHeight-9);
+ p.addPoint(iconWidth-15,iconHeight-15 );
+ p.addPoint(iconWidth-15,iconHeight-9 );
+ g.fillPolygon(p);
+ g.drawLine(0, iconHeight-9, (iconWidth / 2) - (titleWidth / 2)-3, iconHeight-9);
+ g.drawLine((iconWidth / 2) + (titleWidth / 2)+3, iconHeight-9, iconWidth, iconHeight-9);
+
+ } else {
+ g.drawString(minStr, 0, iconHeight);
+ strWidth = SwingUtilities.computeStringWidth(g.getFontMetrics(), maxStr);
+ g.drawString(maxStr, iconWidth - strWidth - 2, iconHeight);
+ }
+
+
+
+
+ return new ImageIcon(bi);
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Double getSelectedThumbValue() {
+ final double minValue = EditorValueRangeTracer.getTracer().getMin(type);
+ final double valueRange = EditorValueRangeTracer.getTracer().getRange(type);
+
+ final float position = slider.getModel().getThumbAt(slider.getSelectedIndex()).getPosition();
+
+ return (((position / 100) * valueRange) + minValue);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/ui/editors/continuous/EditorValueRangeTracer.java b/application/src/main/java/cytoscape/visual/ui/editors/continuous/EditorValueRangeTracer.java
new file mode 100644
index 0000000..8fe04be
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/editors/continuous/EditorValueRangeTracer.java
@@ -0,0 +1,156 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.visual.ui.editors.continuous;
+
+import cytoscape.visual.VisualPropertyType;
+
+import java.util.HashMap;
+import java.util.Map;
+
+
+/**
+ *
+ */
+public class EditorValueRangeTracer {
+
+ private static final EditorValueRangeTracer tracer;
+
+ static {
+ tracer = new EditorValueRangeTracer();
+ }
+
+ private static final class Range {
+ private Double min;
+ private Double max;
+
+ public Range(Double min, Double max) {
+ this.min = min;
+ this.max = max;
+ }
+
+ public void setMin(final Double min) {
+ this.min = min;
+ }
+
+ public void setMax(final Double max) {
+ this.max = max;
+ }
+
+ public Double getMin() {
+ return min;
+ }
+
+ public Double getMax() {
+ return max;
+ }
+
+ public Double getRange() {
+ return Math.abs(min - max);
+ }
+ }
+
+ private Map<VisualPropertyType, Range> rangeMap;
+
+ private EditorValueRangeTracer() {
+ rangeMap = new HashMap<VisualPropertyType, Range>();
+
+ for (VisualPropertyType v : VisualPropertyType.values()) {
+ Range r = new Range(0d, 0d);
+ rangeMap.put(v, r);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static EditorValueRangeTracer getTracer() {
+ return tracer;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param t DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Double getRange(VisualPropertyType t) {
+ return rangeMap.get(t).getRange();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param t DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Double getMin(VisualPropertyType t) {
+ return rangeMap.get(t).getMin();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param t DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Double getMax(VisualPropertyType t) {
+ return rangeMap.get(t).getMax();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param t DOCUMENT ME!
+ * @param min DOCUMENT ME!
+ */
+ public void setMin(VisualPropertyType t, Double min) {
+ rangeMap.get(t).setMin(min);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param t DOCUMENT ME!
+ * @param max DOCUMENT ME!
+ */
+ public void setMax(VisualPropertyType t, Double max) {
+ rangeMap.get(t).setMax(max);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/ui/editors/continuous/GradientEditorPanel.java b/application/src/main/java/cytoscape/visual/ui/editors/continuous/GradientEditorPanel.java
new file mode 100644
index 0000000..1ce4a2d
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/editors/continuous/GradientEditorPanel.java
@@ -0,0 +1,371 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.visual.ui.editors.continuous;
+
+import cytoscape.Cytoscape;
+import cytoscape.logger.CyLogger;
+
+import cytoscape.util.CyColorChooser;
+
+import cytoscape.visual.VisualPropertyType;
+
+import cytoscape.visual.mappings.BoundaryRangeValues;
+import cytoscape.visual.mappings.ContinuousMapping;
+import cytoscape.visual.mappings.continuous.ContinuousMappingPoint;
+
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Graphics2D;
+import java.awt.Point;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.awt.image.BufferedImage;
+
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+
+import javax.swing.Icon;
+import javax.swing.ImageIcon;
+import javax.swing.JComponent;
+import javax.swing.SwingUtilities;
+
+
+/**
+ * Gradient editor.
+ *
+ * @version 0.7
+ * @since Cytoscpae 2.5
+ * @author kono
+ */
+public class GradientEditorPanel extends ContinuousMappingEditorPanel
+ implements PropertyChangeListener {
+
+ private static final long serialVersionUID = -7645303507318540305L;
+
+ // For presets
+ private static final Color DEF_LOWER_COLOR = Color.BLACK;
+ private static final Color DEF_UPPER_COLOR = Color.WHITE;
+
+ /**
+ * Creates a new GradientEditorPanel object.
+ *
+ * @param type
+ * DOCUMENT ME!
+ */
+ public GradientEditorPanel(VisualPropertyType type) {
+ super(type);
+ iconPanel.setVisible(false);
+ initSlider();
+
+ belowPanel.addPropertyChangeListener(this);
+ abovePanel.addPropertyChangeListener(this);
+ if(mapping != null && mapping.getPointCount() == 0)
+ addButtonActionPerformed(null);
+
+ colorButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ getAndSetColor();
+ }
+ });
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param width DOCUMENT ME!
+ * @param height DOCUMENT ME!
+ * @param title DOCUMENT ME!
+ * @param type DOCUMENT ME!
+ */
+ public static Object showDialog(final int width, final int height, final String title,
+ VisualPropertyType type) {
+ editor = new GradientEditorPanel(type);
+
+ final Dimension size = new Dimension(width, height);
+ editor.slider.setPreferredSize(size);
+ editor.setPreferredSize(size);
+
+ editor.setTitle(title);
+ editor.setAlwaysOnTop(true);
+ editor.setLocationRelativeTo(Cytoscape.getDesktop());
+ editor.setDefaultCloseOperation(DISPOSE_ON_CLOSE);
+
+ editor.setVisible(true);
+
+ return editor;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param width DOCUMENT ME!
+ * @param height DOCUMENT ME!
+ * @param type DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static ImageIcon getLegend(final int width, final int height,
+ final VisualPropertyType type) {
+ editor = new GradientEditorPanel(type);
+
+ CyGradientTrackRenderer rend = (CyGradientTrackRenderer) editor.slider.getTrackRenderer();
+ rend.getRendererComponent(editor.slider);
+
+ return rend.getLegend(width, height);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static ImageIcon getIcon(final int iconWidth, final int iconHeight,
+ VisualPropertyType type) {
+ editor = new GradientEditorPanel(type);
+
+ CyGradientTrackRenderer rend = (CyGradientTrackRenderer) editor.slider.getTrackRenderer();
+ rend.getRendererComponent(editor.slider);
+
+ return rend.getTrackGraphicIcon(iconWidth, iconHeight);
+ }
+
+ @Override
+ protected void addButtonActionPerformed(ActionEvent evt) {
+ final BoundaryRangeValues lowerRange;
+
+ double maxValue = EditorValueRangeTracer.getTracer().getMax(type);
+
+ if (mapping.getPointCount() == 0) {
+ double rangeValue = EditorValueRangeTracer.getTracer().getRange(type);
+ double minValue = EditorValueRangeTracer.getTracer().getMin(type);
+
+ final BoundaryRangeValues upperRange;
+
+ slider.getModel().addThumb(10f, DEF_LOWER_COLOR);
+ slider.getModel().addThumb(90f, DEF_UPPER_COLOR);
+
+ lowerRange = new BoundaryRangeValues(below, DEF_LOWER_COLOR, DEF_LOWER_COLOR);
+ upperRange = new BoundaryRangeValues(DEF_UPPER_COLOR, DEF_UPPER_COLOR, above);
+// mapping.addPoint(maxValue / 2, lowerRange);
+ mapping.addPoint(rangeValue*0.1 + minValue, lowerRange);
+ mapping.addPoint(rangeValue*0.9 + minValue, upperRange);
+
+ slider.repaint();
+ repaint();
+
+ return;
+ }
+
+ // Add a new white thumb in the min.
+ // slider.getModel().addThumb(100f, Color.white);
+ // Add a new white thumb near the middle
+ slider.getModel().addThumb(51f, Color.white);
+
+ // Pick Up first point.
+ final ContinuousMappingPoint previousPoint = mapping.getPoint(mapping.getPointCount() - 1);
+
+ final BoundaryRangeValues previousRange = previousPoint.getRange();
+ lowerRange = new BoundaryRangeValues(previousRange);
+
+ lowerRange.lesserValue = slider.getModel().getSortedThumbs()
+ .get(slider.getModel().getThumbCount() - 1);
+ // CyLogger.getLogger().info("EQ color = " + lowerRange.lesserValue);
+ lowerRange.equalValue = Color.white;
+ lowerRange.greaterValue = previousRange.greaterValue;
+ mapping.addPoint(maxValue, lowerRange);
+
+ // Make this slider the selected one
+ selectThumbAtPosition(51f);
+
+ updateMap();
+ updateCytoscape();
+
+ slider.repaint();
+ repaint();
+ }
+
+ @Override
+ protected void deleteButtonActionPerformed(ActionEvent evt) {
+ final int selectedIndex = ((TriangleThumbRenderer)slider.getThumbRenderer()).getSelectedIndex();
+
+ if (0 <= selectedIndex) {
+ slider.getModel().removeThumb(selectedIndex);
+ mapping.removePoint(selectedIndex);
+ updateMap();
+ updateCytoscape();
+ mapping.fireStateChanged();
+
+ repaint();
+ }
+ }
+
+ private void setColor(final Color newColor) {
+ final int selectedIndex = ((TriangleThumbRenderer)slider.getThumbRenderer()).getSelectedIndex();
+ slider.getModel().getThumbAt(selectedIndex).setObject(newColor);
+
+ final ContinuousMapping cMapping = mapping;
+ int selected = getSelectedPoint(selectedIndex);
+
+ cMapping.getPoint(selected).getRange().equalValue = newColor;
+
+ final BoundaryRangeValues brv = new BoundaryRangeValues(cMapping.getPoint(selected)
+ .getRange().lesserValue,
+ newColor,
+ cMapping.getPoint(selected)
+ .getRange().greaterValue);
+
+ cMapping.getPoint(selected).setRange(brv);
+
+ int numPoints = cMapping.getAllPoints().size();
+
+ // Update Values which are not accessible from
+ // UI
+ if (numPoints > 1) {
+ if (selected == 0)
+ brv.greaterValue = newColor;
+ else if (selected == (numPoints - 1))
+ brv.lesserValue = newColor;
+ else {
+ brv.lesserValue = newColor;
+ brv.greaterValue = newColor;
+ }
+
+ cMapping.fireStateChanged();
+
+ setButtonColor(newColor);
+
+ slider.repaint();
+ }
+ }
+
+ public void getAndSetColor() {
+ final Color newColor = CyColorChooser.showDialog(slider,
+ "Choose new color...",
+ Color.white);
+ if (newColor != null) {
+ //Set new color
+ setColor(newColor);
+ updateCytoscape();
+ }
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ */
+ private void initSlider() {
+ slider.updateUI();
+ slider.addMouseListener(new MouseAdapter() {
+ public void mouseClicked(MouseEvent e) {
+ if (SwingUtilities.isRightMouseButton(e)) {
+ } else {
+ final TriangleThumbRenderer thumbRend = (TriangleThumbRenderer)slider.getThumbRenderer();
+ final int selectedIndex = thumbRend.getSelectedIndex();
+ final JComponent selectedThumb = thumbRend.getThumbRendererComponent(slider, selectedIndex, true);
+
+ if (selectedThumb != null) {
+ final Point location = selectedThumb.getLocation();
+ double diff = Math.abs(location.getX() - e.getX());
+
+ if (e.getClickCount() == 2) {
+ getAndSetColor();
+ }
+ }
+ }
+ }
+ });
+
+ final double actualRange = EditorValueRangeTracer.getTracer().getRange(type);
+ final double minValue = EditorValueRangeTracer.getTracer().getMin(type);
+
+ if (allPoints != null) {
+ for (ContinuousMappingPoint point : allPoints) {
+ BoundaryRangeValues bound = point.getRange();
+
+ slider.getModel()
+ .addThumb(((Double) ((point.getValue().doubleValue() - minValue) / actualRange)).floatValue() * 100,
+ (Color) bound.equalValue);
+ }
+
+ if (allPoints.size() != 0) {
+ below = (Color) allPoints.get(0).getRange().lesserValue;
+ above = (Color) allPoints.get(allPoints.size() - 1).getRange().greaterValue;
+ } else {
+ below = Color.black;
+ above = Color.white;
+ }
+
+ setSidePanelIconColor((Color) below, (Color) above);
+ }
+
+ TriangleThumbRenderer thumbRend = new TriangleThumbRenderer(slider);
+
+ CyGradientTrackRenderer gRend = new CyGradientTrackRenderer(type, (Color) below, (Color) above,
+ mapping.getControllingAttributeName());
+ //updateBelowAndAbove();
+ slider.setThumbRenderer(thumbRend);
+ slider.setTrackRenderer(gRend);
+ slider.addMouseListener(new ThumbMouseListener());
+
+ /*
+ * Set tooltip for the slider.
+ */
+ slider.setToolTipText("Double-click handles to edit boundary colors.");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void propertyChange(PropertyChangeEvent e) {
+ if (e.getPropertyName().equals(BelowAndAbovePanel.COLOR_CHANGED)) {
+ String sourceName = ((BelowAndAbovePanel) e.getSource()).getName();
+
+ if (sourceName.equals("abovePanel"))
+ this.above = e.getNewValue();
+ else
+ this.below = e.getNewValue();
+
+ final CyGradientTrackRenderer gRend = new CyGradientTrackRenderer(type, (Color) below, (Color) above,
+ mapping.getControllingAttributeName());
+ slider.setTrackRenderer(gRend);
+
+ repaint();
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/ui/editors/continuous/MinMaxDialog.java b/application/src/main/java/cytoscape/visual/ui/editors/continuous/MinMaxDialog.java
new file mode 100644
index 0000000..6bec414
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/editors/continuous/MinMaxDialog.java
@@ -0,0 +1,308 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.visual.ui.editors.continuous;
+
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.Frame;
+import java.awt.event.ActionEvent;
+
+import javax.swing.JButton;
+
+import cytoscape.Cytoscape;
+import cytoscape.data.CyAttributes;
+import cytoscape.data.attr.CountedIterator;
+import cytoscape.data.attr.MultiHashMap;
+import cytoscape.data.attr.util.MultiHashMapHelpers;
+
+
+/**
+ *
+ * @author kono
+ */
+public class MinMaxDialog extends javax.swing.JDialog {
+
+ private static final Font TEXTBOX_FONT = new java.awt.Font("SansSerif", 1, 10);
+
+ private static final long serialVersionUID = 7350824820761046009L;
+
+ private static MinMaxDialog dialog;
+
+ /** Creates new form MinMaxDialog */
+ private MinMaxDialog(Frame parent, boolean modal, Double min, Double max, final CyAttributes attr, final String attrName) {
+ super(parent, modal);
+ this.min = min;
+ this.max = max;
+ this.attr = attr;
+ this.attrName = attrName;
+ initComponents();
+
+ this.minTextField.setText(min.toString());
+ this.maxTextField.setText(max.toString());
+ }
+
+ private Double min;
+ private Double max;
+
+ private CyAttributes attr;
+ private String attrName;
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param min DOCUMENT ME!
+ * @param max DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static Double[] getMinMax(double min, double max, final CyAttributes attr, final String attrName) {
+ final Double[] minMax = new Double[2];
+
+ dialog = new MinMaxDialog(Cytoscape.getDesktop(), true, min, max, attr, attrName);
+ dialog.setLocationRelativeTo(Cytoscape.getDesktop());
+ dialog.setDefaultCloseOperation(DISPOSE_ON_CLOSE);
+ dialog.setVisible(true);
+
+ if ((dialog.min == null) || (dialog.max == null))
+ return null;
+
+ minMax[0] = dialog.min;
+ minMax[1] = dialog.max;
+
+ return minMax;
+ }
+
+ /** This method is called from within the constructor to
+ * initialize the form.
+ * WARNING: Do NOT modify this code. The content of this method is
+ * always regenerated by the Form Editor.
+ */
+
+ // <editor-fold defaultstate="collapsed" desc="Generated Code">
+ private void initComponents() {
+ minLabel = new javax.swing.JLabel();
+ maxLabel = new javax.swing.JLabel();
+ minTextField = new javax.swing.JTextField();
+ minTextField.setFont(TEXTBOX_FONT);
+
+ maxTextField = new javax.swing.JTextField();
+ maxTextField.setFont(TEXTBOX_FONT);
+
+ okButton = new javax.swing.JButton();
+ cancelButton = new javax.swing.JButton();
+ titlePanel = new javax.swing.JPanel();
+ titleLabel = new javax.swing.JLabel();
+
+ restoreButton = new javax.swing.JButton();
+
+ setDefaultCloseOperation(javax.swing.WindowConstants.DISPOSE_ON_CLOSE);
+ setTitle("Set Range");
+ setAlwaysOnTop(true);
+ setResizable(false);
+
+ minLabel.setFont(new java.awt.Font("SansSerif", 1, 12));
+ minLabel.setText("Min");
+
+ maxLabel.setFont(new java.awt.Font("SansSerif", 1, 12));
+ maxLabel.setText("Max");
+
+ okButton.setText("OK");
+ okButton.setMargin(new java.awt.Insets(2, 2, 2, 2));
+ okButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ okButtonActionPerformed(evt);
+ }
+ });
+
+ cancelButton.setText("Cancel");
+ cancelButton.setMargin(new java.awt.Insets(2, 2, 2, 2));
+ cancelButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ cancelButtonActionPerformed(evt);
+ }
+ });
+
+ restoreButton.setText("Restore");
+ restoreButton.setToolTipText("Set range by current attribute's min and max.");
+ restoreButton.setMargin(new java.awt.Insets(2, 2, 2, 2));
+ restoreButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ restoreButtonActionPerformed(evt);
+ }
+ });
+
+ titlePanel.setBackground(new java.awt.Color(255, 255, 255));
+
+ titleLabel.setFont(new java.awt.Font("SansSerif", 1, 14));
+ titleLabel.setText("Set Value Range");
+
+ org.jdesktop.layout.GroupLayout titlePanelLayout = new org.jdesktop.layout.GroupLayout(titlePanel);
+ titlePanel.setLayout(titlePanelLayout);
+ titlePanelLayout.setHorizontalGroup(titlePanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(titlePanelLayout.createSequentialGroup()
+ .addContainerGap()
+ .add(titleLabel)
+ .addContainerGap(125,
+ Short.MAX_VALUE)));
+ titlePanelLayout.setVerticalGroup(titlePanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(titlePanelLayout.createSequentialGroup()
+ .addContainerGap()
+ .add(titleLabel)
+ .addContainerGap(org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE)));
+
+ org.jdesktop.layout.GroupLayout layout = new org.jdesktop.layout.GroupLayout(getContentPane());
+ getContentPane().setLayout(layout);
+ layout.setHorizontalGroup(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(titlePanel,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE)
+ .add(layout.createSequentialGroup().addContainerGap()
+ .add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(minLabel,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ 35,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .add(maxLabel,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 35, Short.MAX_VALUE))
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(minTextField,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 182, Short.MAX_VALUE)
+ .add(maxTextField,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 182, Short.MAX_VALUE))
+ .addContainerGap())
+ .add(org.jdesktop.layout.GroupLayout.TRAILING,
+ layout.createSequentialGroup()
+ .addContainerGap(163, Short.MAX_VALUE)
+ .add(cancelButton)
+ .add(restoreButton)
+ .add(okButton).addContainerGap()));
+ layout.setVerticalGroup(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(layout.createSequentialGroup()
+ .add(titlePanel,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE)
+ .add(minLabel)
+ .add(minTextField,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ 30,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE))
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE)
+ .add(maxLabel)
+ .add(maxTextField,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ 30,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE))
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE)
+ .add(okButton).add(restoreButton).add(cancelButton))
+ .addContainerGap(org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE)));
+
+ pack();
+ } // </editor-fold>
+
+
+ private void okButtonActionPerformed(java.awt.event.ActionEvent evt) {
+ try {
+ min = Double.valueOf(minTextField.getText());
+ max = Double.valueOf(maxTextField.getText());
+ } catch (NumberFormatException e) {
+ min = null;
+ max = null;
+ }
+
+ dispose();
+ }
+
+ private void cancelButtonActionPerformed(java.awt.event.ActionEvent evt) {
+ min = null;
+ max = null;
+ dispose();
+ }
+
+ private void restoreButtonActionPerformed(ActionEvent evt) {
+ final MultiHashMap mhm = attr.getMultiHashMap();
+ final CountedIterator it = mhm.getObjectKeys(attrName);
+ Object key;
+ Double val = null;
+
+ Double maxValue = Double.NEGATIVE_INFINITY;
+ Double minValue = Double.POSITIVE_INFINITY;
+
+ while (it.hasNext()) {
+ key = it.next();
+ try {
+ val = Double.parseDouble(
+ mhm.getAttributeValue(key.toString(),attrName, null).toString());
+ } catch (NumberFormatException nfe) {
+ continue;
+ }
+
+ if (val > maxValue)
+ maxValue = val;
+ if (val < minValue)
+ minValue = val;
+ }
+
+ minTextField.setText(minValue.toString());
+ maxTextField.setText(maxValue.toString());
+ }
+
+
+
+ // Variables declaration - do not modify
+ private javax.swing.JButton cancelButton;
+ private javax.swing.JLabel maxLabel;
+ private javax.swing.JTextField maxTextField;
+ private javax.swing.JLabel minLabel;
+ private javax.swing.JTextField minTextField;
+ private javax.swing.JButton okButton;
+ private javax.swing.JLabel titleLabel;
+ private javax.swing.JPanel titlePanel;
+
+ private JButton restoreButton;
+
+ // End of variables declaration
+}
diff --git a/application/src/main/java/cytoscape/visual/ui/editors/continuous/TriangleThumbRenderer.java b/application/src/main/java/cytoscape/visual/ui/editors/continuous/TriangleThumbRenderer.java
new file mode 100644
index 0000000..e6b973a
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/editors/continuous/TriangleThumbRenderer.java
@@ -0,0 +1,135 @@
+package cytoscape.visual.ui.editors.continuous;
+
+import org.jdesktop.swingx.JXMultiThumbSlider;
+import org.jdesktop.swingx.multislider.ThumbRenderer;
+
+import java.awt.BasicStroke;
+import java.awt.Color;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.Polygon;
+import java.awt.RenderingHints;
+
+import javax.swing.JComponent;
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ */
+public class TriangleThumbRenderer extends JComponent
+ implements ThumbRenderer {
+ private static final Color SELECTED_COLOR = Color.red;
+ private static final Color DEFAULT_COLOR = Color.DARK_GRAY;
+ private static final Color BACKGROUND_COLOR = Color.white;
+ private JXMultiThumbSlider slider;
+ private boolean selected;
+ private boolean grabbed = false;
+ private int index = -1;
+ private int selectedIndex = -1;
+ private JComponent selectedComponent = null;
+
+ /**
+ * Creates a new TriangleThumbRenderer object.
+ *
+ * @param slider DOCUMENT ME!
+ */
+ public TriangleThumbRenderer(JXMultiThumbSlider slider) {
+ super();
+
+ this.slider = slider;
+ setBackground(BACKGROUND_COLOR);
+ }
+
+ protected void paintComponent(Graphics g) {
+ /*
+ * Enable anti-aliasing
+ */
+ ((Graphics2D) g).setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+ RenderingHints.VALUE_ANTIALIAS_ON);
+
+ /*
+ * Draw small triangle
+ */
+ if (selectedIndex == index) {
+ final Polygon outline = new Polygon();
+ outline.addPoint(0, 0);
+ outline.addPoint(0, 5);
+ outline.addPoint(5, 10);
+ outline.addPoint(9, 5);
+ outline.addPoint(9, 0);
+ g.fillPolygon(outline);
+ g.setColor(Color.blue);
+ ((Graphics2D) g).setStroke(new BasicStroke(2.0f));
+ g.drawPolygon(outline);
+ } else {
+ final Polygon thumb = new Polygon();
+
+ thumb.addPoint(0, 0);
+ thumb.addPoint(10, 0);
+ thumb.addPoint(5, 10);
+ g.fillPolygon(thumb);
+
+ final Polygon outline = new Polygon();
+ outline.addPoint(0, 0);
+ outline.addPoint(9, 0);
+ outline.addPoint(5, 9);
+ g.setColor(Color.DARK_GRAY);
+ ((Graphics2D) g).setStroke(new BasicStroke(1.0f));
+ g.drawPolygon(outline);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param slider DOCUMENT ME!
+ * @param index DOCUMENT ME!
+ * @param selected DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public JComponent getThumbRendererComponent(JXMultiThumbSlider slider, int index, boolean selected) {
+ this.grabbed = selected;
+ this.index = index;
+ if (selected) {
+ selectedIndex = index;
+ selectedComponent = this;
+ }
+
+ final Object obj = slider.getModel()
+ .getThumbAt(index)
+ .getObject();
+
+ if (obj.getClass() == Color.class)
+ this.setForeground((Color) obj);
+ else {
+ if (grabbed)
+ this.setForeground(SELECTED_COLOR);
+ else
+ this.setForeground(DEFAULT_COLOR);
+ }
+
+ return this;
+ }
+
+ /**
+ * Return the value for the currently selected index
+ *
+ * @return index of the currently selected thumb
+ */
+ public int getSelectedIndex() { return this.selectedIndex; }
+ public JComponent getSelectedThumb() { return this.selectedComponent; }
+
+ /**
+ * Set the the currently selected index
+ *
+ * @param index the currently selected thumb
+ */
+ public void setSelectedIndex(int index) {
+ this.selectedIndex = index;
+ this.selectedComponent = this;
+ }
+
+}
diff --git a/application/src/main/java/cytoscape/visual/ui/editors/continuous/VizMapperTrackRenderer.java b/application/src/main/java/cytoscape/visual/ui/editors/continuous/VizMapperTrackRenderer.java
new file mode 100644
index 0000000..cb7cf55
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/editors/continuous/VizMapperTrackRenderer.java
@@ -0,0 +1,30 @@
+package cytoscape.visual.ui.editors.continuous;
+
+import java.awt.BasicStroke;
+import java.awt.Color;
+import java.awt.Font;
+
+import org.jdesktop.swingx.multislider.TrackRenderer;
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$-
+ */
+public interface VizMapperTrackRenderer extends TrackRenderer {
+
+ /*
+ * Static variables used by the implemeted classes.
+ */
+ static final Font ICON_FONT = new Font("SansSerif", Font.BOLD, 8);
+ static final Font SMALL_FONT = new Font("SansSerif", Font.BOLD, 10);
+ static final Font LARGE_FONT = new Font("SansSerif", Font.BOLD, 18);
+
+ static final Color BORDER_COLOR = Color.DARK_GRAY;
+
+ static final BasicStroke STROKE1 = new BasicStroke(1.0f);
+ static final BasicStroke STROKE2 = new BasicStroke(2.0f);
+
+
+}
diff --git a/application/src/main/java/cytoscape/visual/ui/editors/continuous/YValueLegendPanel.java b/application/src/main/java/cytoscape/visual/ui/editors/continuous/YValueLegendPanel.java
new file mode 100644
index 0000000..c7e18b3
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/editors/continuous/YValueLegendPanel.java
@@ -0,0 +1,90 @@
+package cytoscape.visual.ui.editors.continuous;
+
+import java.awt.BasicStroke;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.Polygon;
+import java.awt.RenderingHints;
+import java.awt.geom.AffineTransform;
+
+import javax.swing.JPanel;
+import javax.swing.SwingUtilities;
+
+import cytoscape.visual.VisualPropertyType;
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ */
+public class YValueLegendPanel extends JPanel {
+ private VisualPropertyType type;
+
+ /**
+ * Creates a new IconPanel object.
+ *
+ * @param type DOCUMENT ME!
+ */
+ public YValueLegendPanel(VisualPropertyType type) {
+ this.type = type;
+ this.setPreferredSize(new Dimension());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g DOCUMENT ME!
+ */
+ public void paintComponent(Graphics g) {
+ clear(g);
+
+ Graphics2D g2d = (Graphics2D) g;
+
+ //this.setPreferredSize(new Dimension(strW + 6, 1));
+ int panelHeight = this.getHeight() - 30;
+
+ Polygon poly = new Polygon();
+ int top = 10;
+
+ g2d.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+ RenderingHints.VALUE_ANTIALIAS_ON);
+
+ g2d.setStroke(new BasicStroke(1.0f));
+
+ int center = this.getWidth() / 2 +4;
+
+ poly.addPoint(center, top);
+ poly.addPoint(center - 6, top + 15);
+ poly.addPoint(center, top + 15);
+ g.fillPolygon(poly);
+
+ g2d.drawLine(center, top, center, panelHeight);
+ g2d.setColor(Color.DARK_GRAY);
+ g2d.setFont(new Font("SansSerif", Font.BOLD, 10));
+
+ final String label = type.getName();
+ final int width = SwingUtilities.computeStringWidth(
+ g2d.getFontMetrics(),
+ label);
+ AffineTransform af = new AffineTransform();
+ af.rotate(Math.PI + (Math.PI / 2));
+ g2d.setTransform(af);
+
+ g2d.setColor(Color.black);
+ g2d.drawString(
+ type.getName(),
+ (-this.getHeight() / 2) - (width / 2),
+ (this.getWidth() / 2)+5);
+
+ }
+
+ // super.paintComponent clears offscreen pixmap,
+ // since we're using double buffering by default.
+ protected void clear(Graphics g) {
+ super.paintComponent(g);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/ui/editors/discrete/CustomGraphicsCellRenderer.java b/application/src/main/java/cytoscape/visual/ui/editors/discrete/CustomGraphicsCellRenderer.java
new file mode 100644
index 0000000..b1fe622
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/editors/discrete/CustomGraphicsCellRenderer.java
@@ -0,0 +1,58 @@
+package cytoscape.visual.ui.editors.discrete;
+
+import java.awt.Component;
+import java.util.HashMap;
+import java.util.Map;
+
+import javax.swing.Icon;
+import javax.swing.ImageIcon;
+import javax.swing.JLabel;
+import javax.swing.JTable;
+import javax.swing.SwingConstants;
+
+import com.l2fprod.common.swing.renderer.DefaultCellRenderer;
+
+import cytoscape.visual.customgraphic.CustomGraphicsUtil;
+import cytoscape.visual.customgraphic.CyCustomGraphics;
+
+public class CustomGraphicsCellRenderer extends DefaultCellRenderer {
+
+ private static final long serialVersionUID = 381040361846340312L;
+
+ private Map<CyCustomGraphics, Icon> iconMap;
+
+ public CustomGraphicsCellRenderer() {
+ super();
+ iconMap = new HashMap<CyCustomGraphics, Icon>();
+ }
+
+ public Component getTableCellRendererComponent(JTable table, Object value,
+ boolean isSelected, boolean hasFocus, int row, int column) {
+
+ final JLabel label = new JLabel();
+
+ if (isSelected) {
+ label.setBackground(table.getSelectionBackground());
+ label.setForeground(table.getSelectionForeground());
+ } else {
+ label.setBackground(table.getBackground());
+ label.setForeground(table.getForeground());
+ }
+
+ if ((value != null) && value instanceof CyCustomGraphics) {
+ final CyCustomGraphics cg = (CyCustomGraphics) value;
+ final Icon icon = iconMap.get(cg);
+ if(icon == null && cg.getRenderedImage() != null)
+ label.setIcon(new ImageIcon(CustomGraphicsUtil.getResizedImage(cg.getRenderedImage(), 96, null, true)));
+ else
+ label.setIcon(icon);
+
+ label.setText(cg.getDisplayName());
+
+ label.setVerticalAlignment(SwingConstants.CENTER);
+ label.setHorizontalAlignment(SwingConstants.CENTER);
+ }
+
+ return label;
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/ui/editors/discrete/CyColorCellRenderer.java b/application/src/main/java/cytoscape/visual/ui/editors/discrete/CyColorCellRenderer.java
new file mode 100644
index 0000000..72985a7
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/editors/discrete/CyColorCellRenderer.java
@@ -0,0 +1,130 @@
+package cytoscape.visual.ui.editors.discrete;
+
+import com.l2fprod.common.swing.renderer.DefaultCellRenderer;
+
+/**
+ * L2FProd.com Common Components 7.3 License.
+ *
+ * Copyright 2005-2007 L2FProd.com
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ * Customized by kono
+ */
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.Paint;
+
+import javax.swing.Icon;
+import javax.swing.UIManager;
+
+
+/**
+ * CyColorCellRenderer.
+ *
+ * @since Cytoscape 2.5
+ */
+public class CyColorCellRenderer extends DefaultCellRenderer {
+ /**
+ * DOCUMENT ME!
+ *
+ * @param color
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static String toHex(Color color) {
+ String red = Integer.toHexString(color.getRed());
+ String green = Integer.toHexString(color.getGreen());
+ String blue = Integer.toHexString(color.getBlue());
+
+ if (red.length() == 1)
+ red = "0" + red;
+
+ if (green.length() == 1)
+ green = "0" + green;
+
+ if (blue.length() == 1)
+ blue = "0" + blue;
+
+ return ("#" + red + green + blue).toUpperCase();
+ }
+
+ protected String convertToString(Object value) {
+ // Do not return color as string.
+ return null;
+ }
+
+ protected Icon convertToIcon(Object value) {
+ if (value == null)
+ return null;
+
+ if (value instanceof Number)
+ value = new Color(((Number) value).intValue());
+
+ return new PaintIcon((Paint) value);
+ }
+
+ public static class PaintIcon
+ implements Icon {
+ private final Paint color;
+ private int width;
+ private int height;
+
+ public PaintIcon(Paint color) {
+ this(color, 70, 10);
+ }
+
+ public PaintIcon(Paint color, int width, int height) {
+ this.color = color;
+ this.width = width;
+ this.height = height;
+ }
+
+ public int getIconHeight() {
+ return height;
+ }
+
+ public int getIconWidth() {
+ return width;
+ }
+
+ public void paintIcon(Component c, Graphics g, int x, int y) {
+ Graphics2D g2d = (Graphics2D) g;
+ Paint oldPaint = g2d.getPaint();
+
+ if (c != null)
+ width = c.getWidth() - 6;
+
+ if (color != null) {
+ g2d.setPaint(color);
+ g.fillRect(
+ 3,
+ y,
+ getIconWidth(),
+ getIconHeight());
+ }
+
+ g.setColor(UIManager.getColor("controlDkShadow"));
+ g.drawRect(
+ 3,
+ y,
+ getIconWidth(),
+ getIconHeight());
+
+ g2d.setPaint(oldPaint);
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/ui/editors/discrete/CyColorPropertyEditor.java b/application/src/main/java/cytoscape/visual/ui/editors/discrete/CyColorPropertyEditor.java
new file mode 100644
index 0000000..ff85fd2
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/editors/discrete/CyColorPropertyEditor.java
@@ -0,0 +1,128 @@
+package cytoscape.visual.ui.editors.discrete;
+
+/**
+ * L2FProd.com Common Components 7.3 License.
+ *
+ * Copyright 2005-2007 L2FProd.com
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+import java.awt.Color;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import javax.swing.JButton;
+import javax.swing.JPanel;
+
+import com.l2fprod.common.beans.editor.AbstractPropertyEditor;
+import com.l2fprod.common.beans.editor.ColorPropertyEditor;
+import com.l2fprod.common.beans.editor.FilePropertyEditor;
+import com.l2fprod.common.swing.ComponentFactory;
+import com.l2fprod.common.swing.PercentLayout;
+import com.l2fprod.common.util.ResourceManager;
+
+import cytoscape.util.CyColorChooser;
+
+/**
+ * ColorPropertyEditor. <br>
+ *
+ */
+public class CyColorPropertyEditor extends AbstractPropertyEditor {
+
+ private CyColorCellRenderer label;
+ private JButton button;
+ private Color color;
+
+ /**
+ * Creates a new CyColorPropertyEditor object.
+ */
+ public CyColorPropertyEditor() {
+ editor = new JPanel(new PercentLayout(PercentLayout.HORIZONTAL, 0));
+ ((JPanel) editor).add("*", label = new CyColorCellRenderer());
+ label.setOpaque(false);
+ ((JPanel) editor).add(button = ComponentFactory.Helper.getFactory().createMiniButton());
+ button.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ selectColor();
+ }
+ });
+ ((JPanel) editor).add(button = ComponentFactory.Helper.getFactory().createMiniButton());
+ button.setText("X");
+ button.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ selectNull();
+ }
+ });
+ ((JPanel) editor).setOpaque(false);
+ }
+
+ @Override
+ public Object getValue() {
+ return color;
+ }
+
+ @Override
+ public void setValue(Object value) {
+ color = (Color) value;
+ label.setValue(color);
+ }
+
+ protected void selectColor() {
+ ResourceManager rm = ResourceManager.all(FilePropertyEditor.class);
+ String title = rm.getString("ColorPropertyEditor.title");
+ Color selectedColor = CyColorChooser.showDialog(editor, title, color);
+
+ if (selectedColor != null) {
+ Color oldColor = color;
+ Color newColor = selectedColor;
+ label.setValue(newColor);
+ color = newColor;
+ firePropertyChange(oldColor, newColor);
+ }
+ }
+
+ protected void selectNull() {
+ Color oldColor = color;
+ label.setValue(null);
+ color = null;
+ firePropertyChange(oldColor, null);
+ }
+
+ public static final class AsInt extends ColorPropertyEditor {
+ public void setValue(Object arg0) {
+ if (arg0 instanceof Integer)
+ super.setValue(new Color(((Integer) arg0).intValue()));
+ else
+ super.setValue(arg0);
+ }
+
+ public Object getValue() {
+ Object value = super.getValue();
+
+ if (value == null)
+ return null;
+ else
+ return new Integer(((Color) value).getRGB());
+ }
+
+ protected void firePropertyChange(Object oldValue, Object newValue) {
+ if (oldValue instanceof Color)
+ oldValue = new Integer(((Color) oldValue).getRGB());
+
+ if (newValue instanceof Color)
+ newValue = new Integer(((Color) newValue).getRGB());
+
+ super.firePropertyChange(oldValue, newValue);
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/ui/editors/discrete/CyComboBoxPropertyEditor.java b/application/src/main/java/cytoscape/visual/ui/editors/discrete/CyComboBoxPropertyEditor.java
new file mode 100644
index 0000000..3de942b
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/editors/discrete/CyComboBoxPropertyEditor.java
@@ -0,0 +1,211 @@
+/**
+ * @PROJECT.FULLNAME@ @VERSION@ License.
+ *
+ * Copyright @YEAR@ L2FProd.com
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package cytoscape.visual.ui.editors.discrete;
+
+import com.l2fprod.common.beans.editor.AbstractPropertyEditor;
+
+import cytoscape.logger.CyLogger;
+
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Font;
+import java.awt.event.KeyAdapter;
+import java.awt.event.KeyEvent;
+
+import javax.swing.DefaultComboBoxModel;
+import javax.swing.DefaultListCellRenderer;
+import javax.swing.Icon;
+import javax.swing.JComboBox;
+import javax.swing.JLabel;
+import javax.swing.JList;
+import javax.swing.event.PopupMenuEvent;
+import javax.swing.event.PopupMenuListener;
+
+
+/**
+ * ComboBoxPropertyEditor. <br>
+ *
+ */
+public class CyComboBoxPropertyEditor extends AbstractPropertyEditor {
+ /*
+ * Color & Font theme
+ */
+ private static final Color BACKGROUND = Color.white;
+ private static final Color NOT_SELECTED = new Color(51, 51, 255, 150);
+ private static final Color SELECTED = Color.red;
+ private static final Font SELECTED_FONT = new Font("SansSerif", Font.BOLD, 12);
+
+ private Object oldValue;
+ private Icon[] icons;
+
+ /**
+ * Creates a new CyComboBoxPropertyEditor object.
+ */
+ public CyComboBoxPropertyEditor() {
+ editor = new JComboBox() {
+ public void setSelectedItem(Object anObject) {
+ oldValue = getSelectedItem();
+ super.setSelectedItem(anObject);
+ }
+ };
+
+ final JComboBox combo = (JComboBox) editor;
+
+ combo.setRenderer(new Renderer());
+ combo.addPopupMenuListener(new PopupMenuListener() {
+ public void popupMenuCanceled(PopupMenuEvent e) {}
+
+ public void popupMenuWillBecomeInvisible(PopupMenuEvent e) {
+ try {
+ if (combo.getSelectedItem() == null && combo.getItemCount() != 0) {
+ combo.setSelectedIndex(0);
+ CyComboBoxPropertyEditor.this.firePropertyChange(oldValue, combo.getItemAt(0));
+ } else {
+ CyComboBoxPropertyEditor.this.firePropertyChange(oldValue, combo.getSelectedItem());
+ }
+ } catch (Exception ex1) {
+ ex1.printStackTrace();
+ CyLogger.getLogger().warning("Combo Box property editor caught an error.", ex1);
+
+ // TODO: update table view if crash?
+ return;
+ }
+ }
+
+ public void popupMenuWillBecomeVisible(PopupMenuEvent e) {
+ }
+ });
+
+ combo.addKeyListener(new KeyAdapter() {
+ public void keyPressed(KeyEvent e) {
+ if (e.getKeyCode() == KeyEvent.VK_ENTER)
+ CyComboBoxPropertyEditor.this.firePropertyChange(oldValue,
+ combo.getSelectedItem());
+ }
+ });
+ combo.setSelectedIndex(-1);
+ }
+
+
+ @Override
+ public Object getValue() {
+ final Object selected = ((JComboBox) editor).getSelectedItem();
+
+ if (selected instanceof Value)
+ return ((Value) selected).value;
+ else
+ return selected;
+ }
+
+ @Override
+ public void setValue(Object value) {
+ JComboBox combo = (JComboBox) editor;
+ Object current = null;
+ int index = -1;
+
+ for (int i = 0, c = combo.getModel().getSize(); i < c; i++) {
+ current = combo.getModel().getElementAt(i);
+
+ if ((value == current) || ((current != null) && current.equals(value))) {
+ index = i;
+
+ break;
+ }
+ }
+
+ ((JComboBox) editor).setSelectedIndex(index);
+ }
+
+ public void setAvailableValues(final Object[] values) {
+ final JComboBox cbox = ((JComboBox) editor);
+
+ cbox.setModel(new DefaultComboBoxModel(values));
+ if(cbox.getItemCount() != 0)
+ cbox.setSelectedIndex(0);
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param icons DOCUMENT ME!
+ */
+ public void setAvailableIcons(Icon[] icons) {
+ this.icons = icons;
+ }
+
+ class Renderer extends DefaultListCellRenderer {
+
+ private static final long serialVersionUID = 1142732116479667701L;
+
+ public Component getListCellRendererComponent(JList list, Object value, int index,
+ boolean isSelected, boolean cellHasFocus) {
+
+ Component component = super.getListCellRendererComponent(list,
+ (value instanceof Value)
+ ? ((Value) value).visualValue
+ : value, index, isSelected,
+ cellHasFocus);
+
+ if ((icons != null) && (index >= 0) && component instanceof JLabel)
+ ((JLabel) component).setIcon(icons[index]);
+
+ component.setForeground(NOT_SELECTED);
+ component.setBackground(BACKGROUND);
+
+ if (value == null) {
+ // Cell is empty. Warn user by showing message.
+ component = new JLabel("Select Value!");
+ ((JLabel) component).setFont(SELECTED_FONT);
+ component.setForeground(SELECTED);
+ } else if(((JComboBox) editor).getItemCount() != 0 && value != null)
+ component = new JLabel(value.toString());
+
+ if (isSelected) {
+ component.setForeground(SELECTED);
+ ((JLabel) component).setFont(SELECTED_FONT);
+ }
+
+ return component;
+ }
+ }
+
+ public static final class Value {
+ private Object value;
+ private Object visualValue;
+
+ public Value(Object value, Object visualValue) {
+ this.value = value;
+ this.visualValue = visualValue;
+ }
+
+ public boolean equals(Object o) {
+ if (o == this)
+ return true;
+
+ if ((value == o) || ((value != null) && value.equals(o)))
+ return true;
+
+ return false;
+ }
+
+ public int hashCode() {
+ return (value == null) ? 0 : value.hashCode();
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/ui/editors/discrete/CyCustomGraphicsEditor.java b/application/src/main/java/cytoscape/visual/ui/editors/discrete/CyCustomGraphicsEditor.java
new file mode 100644
index 0000000..692a27a
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/editors/discrete/CyCustomGraphicsEditor.java
@@ -0,0 +1,85 @@
+package cytoscape.visual.ui.editors.discrete;
+
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import javax.swing.JButton;
+import javax.swing.JPanel;
+
+import com.l2fprod.common.swing.ComponentFactory;
+import com.l2fprod.common.swing.PercentLayout;
+
+import cytoscape.Cytoscape;
+import cytoscape.visual.VisualPropertyType;
+import cytoscape.visual.customgraphic.CyCustomGraphics;
+import cytoscape.visual.ui.ValueSelectDialog;
+
+public class CyCustomGraphicsEditor extends
+ com.l2fprod.common.beans.editor.AbstractPropertyEditor {
+
+ private CustomGraphicsCellRenderer cellRenderer;
+ private JButton button;
+ private CyCustomGraphics graphics;
+
+ /**
+ * Creates a new CyLabelPositionLabelEditor object.
+ */
+ public CyCustomGraphicsEditor() {
+ editor = new JPanel(new PercentLayout(PercentLayout.HORIZONTAL, 0));
+ ((JPanel) editor).add("*", cellRenderer = new CustomGraphicsCellRenderer());
+ cellRenderer.setOpaque(false);
+
+ ((JPanel) editor).add(button = ComponentFactory.Helper.getFactory()
+ .createMiniButton());
+ button.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ editLabelPosition();
+ }
+ });
+ ((JPanel) editor).add(button = ComponentFactory.Helper.getFactory()
+ .createMiniButton());
+
+ button.setText("X");
+ button.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ CyCustomGraphics old = graphics;
+ cellRenderer.setValue(null);
+ graphics = null;
+ firePropertyChange(old, null);
+ }
+ });
+ ((JPanel) editor).setOpaque(false);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getValue() {
+ return graphics;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param value
+ * DOCUMENT ME!
+ */
+ public void setValue(Object value) {
+ graphics = (CyCustomGraphics) value;
+ cellRenderer.setValue(value);
+ }
+
+ protected void editLabelPosition() {
+ final CyCustomGraphics newVal = (CyCustomGraphics) ValueSelectDialog
+ .showDialog(VisualPropertyType.NODE_CUSTOM_GRAPHICS_1, Cytoscape.getDesktop());
+
+ if (newVal != null) {
+ final CyCustomGraphics old = graphics;
+
+ setValue(newVal);
+ firePropertyChange(old, newVal);
+ }
+ }
+}
\ No newline at end of file
diff --git a/application/src/main/java/cytoscape/visual/ui/editors/discrete/CyDoublePropertyEditor.java b/application/src/main/java/cytoscape/visual/ui/editors/discrete/CyDoublePropertyEditor.java
new file mode 100644
index 0000000..d6eac7a
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/editors/discrete/CyDoublePropertyEditor.java
@@ -0,0 +1,79 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual.ui.editors.discrete;
+
+import java.awt.event.FocusEvent;
+import java.awt.event.FocusListener;
+
+import javax.swing.JTextField;
+
+import com.l2fprod.common.beans.editor.DoublePropertyEditor;
+import com.l2fprod.common.propertysheet.PropertySheetTableModel.Item;
+
+import cytoscape.Cytoscape;
+
+/**
+ *
+ */
+public class CyDoublePropertyEditor extends DoublePropertyEditor {
+
+ private Object selectedCell;
+
+ /**
+ * Creates a new CyStringPropertyEditor object.
+ */
+ public CyDoublePropertyEditor() {
+ super();
+
+ ((JTextField) editor).addFocusListener(new FocusListener() {
+ public void focusGained(FocusEvent e) {
+ final Item item = (Item) Cytoscape.getDesktop()
+ .getVizMapperUI().getSelectedItem();
+ selectedCell = item.getProperty().getDisplayName();
+ }
+
+ public void focusLost(FocusEvent ev) {
+ validate();
+ }
+ });
+ }
+
+ // Currently, all of the VP values are positive.
+ private void validate() {
+ final Object val = super.getValue();
+ if (val instanceof Number)
+ firePropertyChange(selectedCell, val);
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/ui/editors/discrete/CyFontPropertyEditor.java b/application/src/main/java/cytoscape/visual/ui/editors/discrete/CyFontPropertyEditor.java
new file mode 100644
index 0000000..9fdf1a6
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/editors/discrete/CyFontPropertyEditor.java
@@ -0,0 +1,29 @@
+package cytoscape.visual.ui.editors.discrete;
+
+import java.awt.Font;
+
+import com.l2fprod.common.beans.editor.FontPropertyEditor;
+import com.l2fprod.common.util.ResourceManager;
+
+import cytoscape.Cytoscape;
+import cytoscape.visual.ui.PopupFontChooser;
+
+public class CyFontPropertyEditor extends FontPropertyEditor {
+
+ protected void selectFont() {
+ ResourceManager rm = ResourceManager.all(FontPropertyEditor.class);
+ String title = rm.getString("FontPropertyEditor.title");
+
+ Font font = (Font) super.getValue();
+
+ Font selectedFont = PopupFontChooser.showDialog(Cytoscape.getDesktop(), font);
+
+ if (selectedFont != null) {
+ Font oldFont = font;
+ Font newFont = selectedFont;
+
+ super.setValue(newFont);
+ firePropertyChange(oldFont, newFont);
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/ui/editors/discrete/CyObjectPositionPropertyEditor.java b/application/src/main/java/cytoscape/visual/ui/editors/discrete/CyObjectPositionPropertyEditor.java
new file mode 100644
index 0000000..b0cdf84
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/editors/discrete/CyObjectPositionPropertyEditor.java
@@ -0,0 +1,128 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual.ui.editors.discrete;
+
+import giny.view.ObjectPosition;
+
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import javax.swing.JButton;
+import javax.swing.JPanel;
+
+import com.l2fprod.common.swing.ComponentFactory;
+import com.l2fprod.common.swing.PercentLayout;
+
+import cytoscape.Cytoscape;
+import cytoscape.visual.VisualPropertyType;
+import cytoscape.visual.ui.PopupObjectPositionChooser;
+
+/**
+ *
+ */
+public class CyObjectPositionPropertyEditor extends
+ com.l2fprod.common.beans.editor.AbstractPropertyEditor {
+
+ private ObjectPositionCellRenderer label;
+ private JButton button;
+ private ObjectPosition position;
+
+ private ObjectPosition oldPosition;
+
+ private VisualPropertyType targetType;
+
+ /**
+ * Creates a new CyLabelPositionLabelEditor object.
+ */
+ public CyObjectPositionPropertyEditor(final VisualPropertyType targetType) {
+
+ this.targetType = targetType;
+
+ editor = new JPanel(new PercentLayout(PercentLayout.HORIZONTAL, 0));
+ ((JPanel) editor).add("*", label = new ObjectPositionCellRenderer());
+ label.setOpaque(false);
+ ((JPanel) editor).add(button = ComponentFactory.Helper.getFactory()
+ .createMiniButton());
+ button.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ editObjectPosition();
+ }
+ });
+ ((JPanel) editor).add(button = ComponentFactory.Helper.getFactory()
+ .createMiniButton());
+ button.setText("X");
+ button.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ ObjectPosition old = position;
+ label.setValue(null);
+ position = null;
+ firePropertyChange(old, null);
+ }
+ });
+ ((JPanel) editor).setOpaque(false);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getValue() {
+ return position;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param value
+ * DOCUMENT ME!
+ */
+ public void setValue(Object value) {
+ position = (ObjectPosition) value;
+ label.setValue(value);
+ }
+
+ protected void editObjectPosition() {
+ final ObjectPosition newVal = PopupObjectPositionChooser.showDialog(
+ Cytoscape.getDesktop(), position, targetType);
+
+ if (newVal != null) {
+ oldPosition = newVal;
+
+ setValue(newVal);
+ firePropertyChange(oldPosition, newVal);
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/ui/editors/discrete/CyStringPropertyEditor.java b/application/src/main/java/cytoscape/visual/ui/editors/discrete/CyStringPropertyEditor.java
new file mode 100644
index 0000000..a14bf14
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/editors/discrete/CyStringPropertyEditor.java
@@ -0,0 +1,117 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.visual.ui.editors.discrete;
+
+import cytoscape.logger.CyLogger;
+
+import com.l2fprod.common.beans.editor.StringPropertyEditor;
+import com.l2fprod.common.propertysheet.PropertySheetTableModel.Item;
+import com.l2fprod.common.swing.LookAndFeelTweaks;
+
+import java.awt.event.FocusEvent;
+import java.awt.event.FocusListener;
+
+import java.lang.reflect.InvocationTargetException;
+import java.lang.reflect.Method;
+
+import javax.swing.JTextField;
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ */
+public class CyStringPropertyEditor extends StringPropertyEditor {
+ private Object currentValue;
+ private Object selected;
+ private CyLogger logger = CyLogger.getLogger(CyStringPropertyEditor.class);
+
+ /**
+ * Creates a new CyStringPropertyEditor object.
+ */
+ public CyStringPropertyEditor() {
+ editor = new JTextField();
+ ((JTextField) editor).setBorder(LookAndFeelTweaks.EMPTY_BORDER);
+
+ ((JTextField) editor).addFocusListener(new FocusListener() {
+ public void focusGained(FocusEvent e) {
+ Method getM = null;
+ Object val = null;
+
+ try {
+ getM = e.getOppositeComponent().getClass().getMethod("getSelectedRow", new Class[] {});
+ } catch (SecurityException e1) {
+ logger.warn("Can't get 'getSelectedRow' method from text field!", e1);
+ } catch (NoSuchMethodException e1) {
+ logger.warn("Can't find 'getSelectedRow' method in text field!", e1);
+ }
+
+ try {
+ val = getM.invoke(e.getOppositeComponent(), new Object[] {});
+ } catch (Exception e1) {
+ logger.warn("Can't invoke 'getSelectedRow' method of text field: "+e1.getMessage(), e1);
+ }
+
+ try {
+ getM = e.getOppositeComponent().getClass()
+ .getMethod("getValueAt", new Class[] { int.class, int.class });
+ } catch (SecurityException e1) {
+ logger.warn("Can't get 'getValueAt' method from text field!", e1);
+ } catch (NoSuchMethodException e1) {
+ logger.warn("Can't find 'getValueAt' method in text field!", e1);
+ }
+
+ Object val2 = null;
+
+ try {
+ val2 = getM.invoke(e.getOppositeComponent(),
+ new Object[] { (Integer) val, new Integer(0) });
+ } catch (Exception e1) {
+ logger.warn("Can't invoke 'getValueAt' method of text field: "+e1.getMessage(), e1);
+ }
+
+ selected = ((Item) val2).getProperty().getDisplayName();
+ currentValue = ((JTextField) editor).getText();
+ }
+
+ public void focusLost(FocusEvent arg0) {
+ firePropertyChange(selected, ((JTextField) editor).getText());
+ }
+ });
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/ui/editors/discrete/FontCellRenderer.java b/application/src/main/java/cytoscape/visual/ui/editors/discrete/FontCellRenderer.java
new file mode 100644
index 0000000..b4860c8
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/editors/discrete/FontCellRenderer.java
@@ -0,0 +1,59 @@
+package cytoscape.visual.ui.editors.discrete;
+
+import com.l2fprod.common.swing.renderer.DefaultCellRenderer;
+
+import java.awt.Component;
+import java.awt.Font;
+
+import javax.swing.JTable;
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author kono
+ */
+public class FontCellRenderer extends DefaultCellRenderer {
+ /**
+ * DOCUMENT ME!
+ *
+ * @param table
+ * DOCUMENT ME!
+ * @param value
+ * DOCUMENT ME!
+ * @param isSelected
+ * DOCUMENT ME!
+ * @param hasFocus
+ * DOCUMENT ME!
+ * @param row
+ * DOCUMENT ME!
+ * @param column
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Component getTableCellRendererComponent(JTable table, Object value,
+ boolean isSelected, boolean hasFocus, int row, int column) {
+ if (isSelected) {
+ setBackground(table.getSelectionBackground());
+ setForeground(table.getSelectionForeground());
+ } else {
+ setBackground(table.getBackground());
+ setForeground(table.getForeground());
+ }
+
+ if ((value != null) && value instanceof Font) {
+ final Font font = (Font) value;
+ final Font modFont = new Font(
+ font.getFontName(),
+ font.getStyle(),
+ 12);
+
+ this.setFont(modFont);
+ this.setText(modFont.getFontName());
+ } else
+ this.setValue(null);
+
+ return this;
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/ui/editors/discrete/ObjectPositionCellRenderer.java b/application/src/main/java/cytoscape/visual/ui/editors/discrete/ObjectPositionCellRenderer.java
new file mode 100644
index 0000000..5925fb4
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/editors/discrete/ObjectPositionCellRenderer.java
@@ -0,0 +1,97 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.visual.ui.editors.discrete;
+
+import com.l2fprod.common.swing.renderer.DefaultCellRenderer;
+
+import cytoscape.visual.LabelPosition;
+import cytoscape.visual.VisualPropertyType;
+
+import cytoscape.visual.properties.NodeLabelPositionProp;
+
+import giny.view.ObjectPosition;
+
+import java.awt.Component;
+
+import javax.swing.JLabel;
+import javax.swing.JTable;
+import javax.swing.SwingConstants;
+
+
+/**
+ *
+ */
+public class ObjectPositionCellRenderer extends DefaultCellRenderer {
+
+ private static final long serialVersionUID = -7898871787941450155L;
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param table DOCUMENT ME!
+ * @param value DOCUMENT ME!
+ * @param isSelected DOCUMENT ME!
+ * @param hasFocus DOCUMENT ME!
+ * @param row DOCUMENT ME!
+ * @param column DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected,
+ boolean hasFocus, int row, int column) {
+
+ final JLabel label = new JLabel();
+ if (isSelected) {
+ label.setBackground(table.getSelectionBackground());
+ label.setForeground(table.getSelectionForeground());
+ } else {
+ label.setBackground(table.getBackground());
+ label.setForeground(table.getForeground());
+ }
+
+ if ((value != null) && value instanceof ObjectPosition) {
+ final ObjectPosition lp = (ObjectPosition) value;
+ final NodeLabelPositionProp prop = (NodeLabelPositionProp) VisualPropertyType.NODE_LABEL_POSITION
+ .getVisualProperty();
+ label.setIcon(prop.getIcon(lp));
+ label.setVerticalAlignment(SwingConstants.CENTER);
+ label.setHorizontalAlignment(SwingConstants.CENTER);
+ }
+
+ return label;
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/ui/editors/discrete/ShapeCellRenderer.java b/application/src/main/java/cytoscape/visual/ui/editors/discrete/ShapeCellRenderer.java
new file mode 100644
index 0000000..890b9c8
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/editors/discrete/ShapeCellRenderer.java
@@ -0,0 +1,126 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.visual.ui.editors.discrete;
+
+import com.l2fprod.common.swing.renderer.DefaultCellRenderer;
+
+import cytoscape.visual.VisualPropertyType;
+
+import cytoscape.visual.ui.icon.VisualPropertyIcon;
+
+import java.awt.Component;
+
+import java.util.Map;
+
+import javax.swing.Icon;
+import javax.swing.JTable;
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ */
+public class ShapeCellRenderer extends DefaultCellRenderer {
+ private final Map<Object, Icon> icons;
+ private VisualPropertyType type;
+
+ /**
+ * Creates a new ShapeCellRenderer object.
+ *
+ * @param type DOCUMENT ME!
+ */
+ public ShapeCellRenderer(VisualPropertyType type) {
+ this.type = type;
+ icons = type.getVisualProperty().getIconSet();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param table
+ * DOCUMENT ME!
+ * @param value
+ * DOCUMENT ME!
+ * @param isSelected
+ * DOCUMENT ME!
+ * @param hasFocus
+ * DOCUMENT ME!
+ * @param row
+ * DOCUMENT ME!
+ * @param column
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected,
+ boolean hasFocus, int row, int column) {
+ if (isSelected) {
+ setBackground(table.getSelectionBackground());
+ setForeground(table.getSelectionForeground());
+ } else {
+ setBackground(table.getBackground());
+ setForeground(table.getForeground());
+ }
+
+ if (value != null) {
+ final VisualPropertyIcon shapeIcon = (VisualPropertyIcon) icons.get(value);
+
+ if (shapeIcon != null) {
+ if (type.equals(VisualPropertyType.EDGE_SRCARROW_SHAPE)
+ || type.equals(VisualPropertyType.EDGE_TGTARROW_SHAPE)) {
+ shapeIcon.setIconHeight(16);
+ shapeIcon.setIconWidth(40);
+ shapeIcon.setBottomPadding(-6);
+ } else {
+ shapeIcon.setIconHeight(16);
+ shapeIcon.setIconWidth(16);
+ }
+
+ this.setIcon(shapeIcon);
+ }
+
+ this.setIconTextGap(10);
+ this.setText(value.toString());
+ } else {
+ this.setIcon(null);
+ this.setText(null);
+ }
+
+ return this;
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/ui/icon/ArrowIcon.java b/application/src/main/java/cytoscape/visual/ui/icon/ArrowIcon.java
new file mode 100644
index 0000000..1973595
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/icon/ArrowIcon.java
@@ -0,0 +1,169 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.visual.ui.icon;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.visual.ArrowShape;
+import cytoscape.visual.VisualPropertyType;
+import static cytoscape.visual.VisualPropertyType.EDGE_SRCARROW_SHAPE;
+
+import java.awt.BasicStroke;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.RenderingHints;
+import java.awt.Shape;
+import java.awt.Stroke;
+import java.awt.geom.AffineTransform;
+import java.awt.geom.Rectangle2D;
+
+
+/**
+ * Icon for arrow shape.
+ *
+ * @version 0.5
+ * @since Cytoscape 2.5
+ * @author kono
+ */
+public class ArrowIcon extends VisualPropertyIcon {
+ private static final Stroke EDGE_STROKE = new BasicStroke(6.0f, BasicStroke.CAP_SQUARE,
+ BasicStroke.JOIN_MITER);
+ private static final Stroke EDGE_STROKE_SMALL = new BasicStroke(4.0f, BasicStroke.CAP_SQUARE,
+ BasicStroke.JOIN_MITER);
+ private static final int DEF_L_PAD = 15;
+
+ private final ArrowShape arrow;
+
+ /**
+ * Creates a new ArrowIcon object.
+ * @param arrow The ArrowShape to create the icon for.
+ * @param width The width of the icon.
+ */
+ public ArrowIcon(ArrowShape arrow, int width) {
+ super(arrow.getShape(), width, DEFAULT_ICON_SIZE,
+ arrow.getName(), DEFAULT_ICON_COLOR);
+ this.arrow = arrow;
+ }
+
+ /**
+ * Creates a new ArrowIcon object.
+ * @param arrow The ArrowShape to create the icon for.
+ */
+ public ArrowIcon(ArrowShape arrow) {
+ this(arrow, DEFAULT_ICON_SIZE * 3);
+ }
+
+
+ /**
+ * Draw icon using Java2D.
+ *
+ * @param c The component that the icon is being rendered in.
+ * Used to calculate width and height of the icon.
+ * @param g The Graphics used to render the icon.
+ * @param x Not used in this implementation.
+ * @param y Not used in this implementation.
+ */
+ public void paintIcon(Component c, Graphics g, int x, int y) {
+ Graphics2D g2d = (Graphics2D) g;
+
+ // Turn AA on
+ g2d.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
+ g2d.setColor(color);
+
+ g2d.translate(leftPad, bottomPad);
+
+ // If shape is not defined, treat as no-head.
+ if (shape == null) {
+ if ((width < 20) || (height < 20)) {
+ g2d.translate(-leftPad, -bottomPad);
+ g2d.setStroke(EDGE_STROKE_SMALL);
+ g2d.drawLine(3, c.getHeight()/2, width/2 +10, c.getHeight()/2);
+ } else {
+ g2d.setStroke(EDGE_STROKE);
+ g2d.drawLine(DEF_L_PAD, c.getHeight()/2, width/2 +10, c.getHeight()/2);
+ }
+ return;
+ }
+
+ final AffineTransform af = new AffineTransform();
+ final Rectangle2D bound = shape.getBounds2D();
+ final double minx = bound.getMinX();
+ final double miny = bound.getMinY();
+
+ Shape newShape = shape;
+
+ // Adjust position if it is NOT in first quadrant.
+ if (minx < 0) {
+ af.setToTranslation(Math.abs(minx), 0);
+ newShape = af.createTransformedShape(newShape);
+ }
+
+ if (miny < 0) {
+ af.setToTranslation(0, Math.abs(miny));
+ newShape = af.createTransformedShape(newShape);
+ }
+
+ final double shapeWidth = newShape.getBounds2D().getWidth();
+ final double shapeHeight = newShape.getBounds2D().getHeight();
+
+ final double originalXYRatio = shapeWidth / shapeHeight;
+
+ final double xRatio = (width / 3) / shapeWidth;
+ final double yRatio = height / shapeHeight;
+ af.setToScale(xRatio * originalXYRatio, yRatio);
+ newShape = af.createTransformedShape(newShape);
+
+ af.setToTranslation((width * 0.8) - newShape.getBounds2D().getCenterX(),
+ ((height + 20) / 2) - newShape.getBounds2D().getCenterY());
+ newShape = af.createTransformedShape(newShape);
+
+ g2d.fill(newShape);
+
+ // Finally, draw an edge (line) to the arrow head if desired.
+ if ( arrow.renderEdgeWithArrow() ) {
+ if ((width < 20) || (height < 20)) {
+ g2d.translate(-leftPad, -bottomPad);
+ g2d.setStroke(EDGE_STROKE_SMALL);
+ g2d.drawLine(3, c.getHeight()/2, width/2 +10, c.getHeight()/2);
+ } else {
+ g2d.setStroke(EDGE_STROKE);
+ g2d.drawLine(DEF_L_PAD, (height + 20) / 2,
+ (int) (newShape.getBounds2D().getCenterX()) - 2, (height + 20) / 2);
+ }
+ }
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/ui/icon/LineTypeIcon.java b/application/src/main/java/cytoscape/visual/ui/icon/LineTypeIcon.java
new file mode 100644
index 0000000..84762ae
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/icon/LineTypeIcon.java
@@ -0,0 +1,187 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.visual.ui.icon;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.visual.VisualPropertyType;
+import cytoscape.visual.LineStyle;
+
+import java.awt.BasicStroke;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Font;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.RenderingHints;
+import java.awt.Stroke;
+import java.awt.geom.Line2D;
+
+import javax.swing.SwingUtilities;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ */
+public class LineTypeIcon extends VisualPropertyIcon {
+ private Stroke stroke;
+ protected Graphics2D g2d;
+
+ // If not null, this message will be shown over the icon.
+ private String superimposedText = null;
+ private Font textFont = null;
+ private Color textColor = null;
+
+ /**
+ * Creates a new LineTypeIcon object.
+ */
+ public LineTypeIcon() {
+ this(((LineStyle) VisualPropertyType.EDGE_LINE_STYLE.getDefault(Cytoscape.getVisualMappingManager() .getVisualStyle()))
+ .getStroke(2f), DEFAULT_ICON_SIZE * 3, DEFAULT_ICON_SIZE,
+ ((LineStyle) VisualPropertyType.EDGE_LINE_STYLE
+ .getDefault(Cytoscape.getVisualMappingManager().getVisualStyle())).toString(),
+ (Color) VisualPropertyType.EDGE_COLOR.getDefault(Cytoscape.getVisualMappingManager()
+ .getVisualStyle()));
+ }
+
+
+ public LineTypeIcon(cytoscape.visual.LineStyle style) {
+ this(style.getStroke(2f), DEFAULT_ICON_SIZE * 3,
+ DEFAULT_ICON_SIZE, style.name());
+ }
+
+ /**
+ * Creates a new LineTypeIcon object.
+ *
+ * @param stroke DOCUMENT ME!
+ * @param width DOCUMENT ME!
+ * @param height DOCUMENT ME!
+ * @param name DOCUMENT ME!
+ */
+ public LineTypeIcon(Stroke stroke, int width, int height, String name) {
+ super(null, width, height, name);
+ this.stroke = stroke;
+ }
+
+ /**
+ * Creates a new LineTypeIcon object.
+ *
+ * @param stroke DOCUMENT ME!
+ * @param width DOCUMENT ME!
+ * @param height DOCUMENT ME!
+ * @param name DOCUMENT ME!
+ * @param color DOCUMENT ME!
+ */
+ public LineTypeIcon(Stroke stroke, int width, int height, String name, Color color) {
+ super(null, width, height, name, color);
+
+ final float lineWidth = ((Number) VisualPropertyType.EDGE_LINE_WIDTH.getDefault(Cytoscape.getVisualMappingManager() .getVisualStyle())) .floatValue();
+
+ this.stroke = stroke;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param c DOCUMENT ME!
+ * @param g DOCUMENT ME!
+ * @param x DOCUMENT ME!
+ * @param y DOCUMENT ME!
+ */
+ public void paintIcon(Component c, Graphics g, int x, int y) {
+ g2d = (Graphics2D) g;
+ g2d.setColor(color);
+ // AA on
+ g2d.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
+
+ g2d.translate(leftPad, bottomPad);
+
+ float[] dashDef = null;
+
+ g2d.setStroke(stroke);
+ g2d.draw(new Line2D.Double(20, (height + 20) / 2, width, (height + 20) / 2));
+
+ /*
+ * Superimpose text if text object is not empty.
+ */
+ if (superimposedText != null) {
+ int strWidth = SwingUtilities.computeStringWidth(g2d.getFontMetrics(), superimposedText);
+
+ if (textColor == null) {
+ g2d.setColor(Color.DARK_GRAY);
+ } else
+ g2d.setColor(textColor);
+
+ if (textFont == null) {
+ g2d.setFont(new Font("SansSerif", Font.BOLD, 24));
+ } else {
+ g2d.setFont(textFont);
+ }
+
+ g2d.drawString(superimposedText, 20, (height + 40) / 2);
+ }
+
+ g2d.translate(-leftPad, -bottomPad);
+ g2d.setFont(new Font("SansSerif", Font.BOLD, 14));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param text DOCUMENT ME!
+ */
+ public void setText(final String text) {
+ this.superimposedText = text;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param font DOCUMENT ME!
+ */
+ public void setTextFont(final Font font) {
+ this.textFont = font;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param color DOCUMENT ME!
+ */
+ public void setTextColor(final Color color) {
+ this.textColor = color;
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/ui/icon/NodeIcon.java b/application/src/main/java/cytoscape/visual/ui/icon/NodeIcon.java
new file mode 100644
index 0000000..f9cf24a
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/icon/NodeIcon.java
@@ -0,0 +1,209 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.visual.ui.icon;
+
+import static cytoscape.visual.VisualPropertyType.NODE_SHAPE;
+
+import java.awt.BasicStroke;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.RenderingHints;
+import java.awt.Shape;
+import java.awt.geom.AffineTransform;
+import java.awt.geom.Rectangle2D;
+
+import cytoscape.Cytoscape;
+import cytoscape.visual.NodeShape;
+
+
+/**
+ * Icon for node shapes.
+ *
+ * @version 0.5
+ * @since Cytoscape 2.5
+ * @author kono
+ *
+ */
+public class NodeIcon extends VisualPropertyIcon {
+
+ private static final long serialVersionUID = -7589422578478706397L;
+
+ protected Shape newShape;
+ protected Graphics2D g2d;
+
+ /**
+ * Creates a new NodeIcon object.
+ */
+ public NodeIcon() {
+ this(((NodeShape) (NODE_SHAPE.getDefault(Cytoscape.getVisualMappingManager()
+ .getVisualStyle())))
+ .getShape(),
+ DEFAULT_ICON_SIZE, DEFAULT_ICON_SIZE,
+ ((NodeShape) (NODE_SHAPE.getDefault(Cytoscape.getVisualMappingManager()
+ .getVisualStyle())))
+ .getShapeName(),
+ DEFAULT_ICON_COLOR);
+ }
+
+ public NodeIcon(NodeShape ns) {
+ this(ns.getShape(), DEFAULT_ICON_SIZE, DEFAULT_ICON_SIZE, ns.getShapeName(), DEFAULT_ICON_COLOR);
+ }
+
+ /**
+ * Creates a new NodeShapeIcon object.
+ *
+ * @param shape
+ * @param width
+ * @param height
+ * @param name
+ */
+ public NodeIcon(Shape shape, int width, int height, String name) {
+ this(shape, width, height, name, DEFAULT_ICON_COLOR);
+ }
+
+ /**
+ * Creates a new NodeShapeIcon object.
+ *
+ * @param shape DOCUMENT ME!
+ * @param width DOCUMENT ME!
+ * @param height DOCUMENT ME!
+ * @param name DOCUMENT ME!
+ * @param color DOCUMENT ME!
+ */
+ public NodeIcon(Shape shape, int width, int height, String name, Color color) {
+ super(shape, width, height, name, color);
+
+ adjustShape();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param width DOCUMENT ME!
+ */
+ public void setIconWidth(int width) {
+ super.setIconWidth(width);
+ adjustShape();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param height DOCUMENT ME!
+ */
+ public void setIconHeight(int height) {
+ super.setIconHeight(height);
+ adjustShape();
+ }
+
+ public int getIconWidth() {
+ return width;
+ }
+
+ public int getIconHeight() {
+ return height;
+ }
+
+ private void adjustShape() {
+ final double shapeWidth = shape.getBounds2D().getWidth();
+ final double shapeHeight = shape.getBounds2D().getHeight();
+
+ final double xRatio = width / shapeWidth;
+ final double yRatio = height / shapeHeight;
+
+ final AffineTransform af = new AffineTransform();
+
+ final Rectangle2D bound = shape.getBounds2D();
+ final double minx = bound.getMinX();
+ final double miny = bound.getMinY();
+
+ if (minx < 0) {
+ af.setToTranslation(Math.abs(minx), 0);
+ shape = af.createTransformedShape(shape);
+ }
+
+ if (miny < 0) {
+ af.setToTranslation(0, Math.abs(miny));
+ shape = af.createTransformedShape(shape);
+ }
+
+ af.setToScale(xRatio, yRatio);
+ shape = af.createTransformedShape(shape);
+ }
+
+ /**
+ * Draw icon using Java2D.
+ *
+ * @param c DOCUMENT ME!
+ * @param g DOCUMENT ME!
+ * @param x DOCUMENT ME!
+ * @param y DOCUMENT ME!
+ */
+ public void paintIcon(Component c, Graphics g, int x, int y) {
+ g2d = (Graphics2D) g;
+
+ final AffineTransform af = new AffineTransform();
+
+ // AA on
+ g2d.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
+ g2d.setRenderingHint(RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_QUALITY);
+
+ g2d.translate(0, bottomPad);
+
+ newShape = shape;
+
+ af.setToTranslation(leftPad, (c.getHeight() - newShape.getBounds2D().getHeight()) / 2);
+ newShape = af.createTransformedShape(newShape);
+
+ g2d.setColor(color);
+ g2d.setStroke(new BasicStroke(2.0f));
+ g2d.draw(newShape);
+
+ g2d.translate(0, -bottomPad);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public NodeIcon clone() {
+ final NodeIcon cloned = new NodeIcon(shape, width, height, name, color);
+
+ return cloned;
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/ui/icon/VisualPropertyIcon.java b/application/src/main/java/cytoscape/visual/ui/icon/VisualPropertyIcon.java
new file mode 100644
index 0000000..9193111
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/icon/VisualPropertyIcon.java
@@ -0,0 +1,218 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.visual.ui.icon;
+
+import java.awt.Color;
+import java.awt.Shape;
+
+import javax.swing.ImageIcon;
+
+
+/**
+ *
+ * Icon created from Shape object passed from rendering engine.<br>
+ *
+ * This icon is scalable (vector image).
+ *
+ * Actual paint method is defined in child classes.
+ *
+ * @version 0.5
+ * @since Cytoscape 2.5
+ * @author kono
+ *
+ */
+public abstract class VisualPropertyIcon extends ImageIcon {
+
+ private static final long serialVersionUID = 8512931880283553107L;
+
+ /**
+ * Default icon color.
+ */
+ public static final Color DEFAULT_ICON_COLOR = Color.DARK_GRAY;
+
+ /**
+ * Default icon size for Visual Properties
+ */
+ public static final int DEFAULT_ICON_SIZE = 32;
+
+ protected int height;
+ protected int width;
+ protected Color color;
+ protected Shape shape;
+ protected String name;
+ protected int leftPad = 0;
+ protected int bottomPad = 0;
+
+ /**
+ * Creates a new VisualPropertyIcon object.
+ *
+ * @param shape DOCUMENT ME!
+ * @param name DOCUMENT ME!
+ */
+ public VisualPropertyIcon(String name, Color color) {
+ this(null, DEFAULT_ICON_SIZE, DEFAULT_ICON_SIZE, name, color);
+ }
+
+ /**
+ * Constructor without Color parameter.
+ *
+ * @param shape
+ * @param width
+ * @param height
+ * @param name
+ */
+ public VisualPropertyIcon(Shape shape, int width, int height, String name) {
+ this(shape, width, height, name, DEFAULT_ICON_COLOR);
+ }
+
+ /**
+ * Constructor with full parameter set.
+ *
+ * @param shape
+ * @param width
+ * @param height
+ * @param name
+ * @param color
+ */
+ public VisualPropertyIcon(Shape shape, int width, int height, String name, Color color) {
+ this.shape = shape;
+ this.width = width;
+ this.height = height;
+ this.name = name;
+
+ if (color != null)
+ this.color = color;
+ else
+ this.color = DEFAULT_ICON_COLOR;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Shape getShape() {
+ return shape;
+ }
+
+ /**
+ * Get height of icon. This implements Icon interface.
+ */
+ public int getIconHeight() {
+ return height;
+ }
+
+ /**
+ * Get width of icon. This implements Icon interface.
+ */
+ public int getIconWidth() {
+ return width;
+ }
+
+ /**
+ * Set width.
+ *
+ * @param width
+ * Width of icon
+ */
+ public void setIconWidth(int width) {
+ this.width = width;
+ }
+
+ /**
+ * Set height.
+ *
+ * @param height
+ * Height of icon
+ */
+ public void setIconHeight(int height) {
+ this.height = height;
+ }
+
+ /**
+ * Get human-readable name of this icon.
+ *
+ * @return
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * Set human-readable name of this icon.
+ *
+ * @param name
+ */
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ /**
+ * Get color of icon
+ *
+ * @return Icon color.
+ */
+ public Color getColor() {
+ return color;
+ }
+
+ /**
+ * Set icon color.
+ *
+ * @param color
+ * Icon color.
+ */
+ public void setColor(Color color) {
+ this.color = color;
+ }
+
+ /**
+ * Insert space on the left.
+ *
+ * @param pad DOCUMENT ME!
+ */
+ public void setLeftPadding(int pad) {
+ this.leftPad = pad;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param pad DOCUMENT ME!
+ */
+ public void setBottomPadding(int pad) {
+ this.bottomPad = pad;
+ }
+}
diff --git a/application/src/main/java/cytoscape/visual/ui/package.html b/application/src/main/java/cytoscape/visual/ui/package.html
new file mode 100644
index 0000000..a1692fb
--- /dev/null
+++ b/application/src/main/java/cytoscape/visual/ui/package.html
@@ -0,0 +1,13 @@
+<html>
+<head>
+ <!-- $Revision: 5801 $
+ $Date: 2004-04-20 01:53:47 +0200 (Tue, 20 Apr 2004) $
+ $Author: amarkiel $
+ -->
+</head>
+
+<body>
+Top-level UI components for the cytoscape.visual package.
+</body>
+</html>
+
diff --git a/application/src/main/resources/GO.xrf_abbs b/application/src/main/resources/GO.xrf_abbs
new file mode 100644
index 0000000..b029464
--- /dev/null
+++ b/application/src/main/resources/GO.xrf_abbs
@@ -0,0 +1,1399 @@
+!version: $Revision: 2.150 $
+!date: $Date: 2007/09/14 15:45:34 $
+!
+!Gene Ontology
+!Abbreviations for cross-referenced databases.
+!
+!Note that URLs are not necessarily stable entities and that some
+!databases may have many other access routes or mirror sites.
+!
+!This data is available as a web page at
+!http://www.geneontology.org/cgi-bin/xrefs.cgi
+!
+abbreviation: AgBase
+database: AgBase resource for functional analysis of agricultural plant and animal gene products
+generic_url: http://www.agbase.msstate.edu/
+url_syntax: http://www.agbase.msstate.edu/cgi-bin/getEntry.pl?db_pick=[ChickGO/MaizeGO]&uid=[ProteinID]
+
+abbreviation: AGI_LocusCode
+database: Arabidopsis Genome Initiative (TAIR, TIGR, MIPS)
+object: Locus identifier
+example_id: AGI_LocusCode:At2g17950
+generic_url: http://www.arabidopsis.org
+url_syntax: http://mips.gsf.de/cgi-bin/proj/thal/search_gene?code=
+url_syntax: http://www.tigr.org/tigr-scripts/euk_manatee/shared/ORF_infopage.cgi?db=ath1&orf=
+url_syntax: http://arabidopsis.org/servlets/TairObject?type=locus&name=
+url_example: http://mips.gsf.de/cgi-bin/proj/thal/search_gene?code=At2g17950
+url_example: http://www.tigr.org/tigr-scripts/euk_manatee/shared/ORF_infopage.cgi?db=ath1&orf=At2g17950
+url_example: http://arabidopsis.org/servlets/TairObject?type=locus&name=At2g17950
+
+abbreviation: AGRICOLA_bib
+database: AGRICultural OnLine Access
+object: AGRICOLA call number
+example_id: AGRICOLA_bib:MARC TAG 016
+example_id: AGRICOLA_bib:bib=0000-05160
+generic_url: http://agricola.nal.usda.gov/
+
+abbreviation: AGRICOLA_IND
+database: AGRICultural OnLine Access
+object: AGRICOLA call number
+example_id: AGRICOLA_IND:IND84014403
+generic_url: http://agricola.cos.com/
+
+abbreviation: AGRICOLA_NAL
+database: AGRICultural OnLine Access
+object: AGRICOLA call number
+example_id: AGRICOLA_NAL:TP248.2 P76 v.14
+generic_url: http://agricola.nal.usda.gov/
+
+abbreviation: AraCyc
+database: AraCyc metabolic pathway database for Arabidopsis thaliana
+object: Identifier
+example_id: AraCyc:PWYQT-62
+generic_url: http://www.arabidopsis.org/biocyc/index.jsp
+url_syntax: http://www.arabidopsis.org:1555/ARA/NEW-IMAGE?type=NIL&object=
+url_example: http://www.arabidopsis.org:1555/ARA/NEW-IMAGE?type=NIL&object=PWYQT-62
+
+abbreviation: BIOMD
+database: BioModels Database
+object: Accession
+synonym: BIOMDID
+example_id: BIOMD:BIOMD0000000045
+generic_url: http://www.ebi.ac.uk/biomodels/
+url_syntax: http://www.ebi.ac.uk/compneur-srv/biomodels-main/publ-model.do?mid=
+url_example: http://www.ebi.ac.uk/compneur-srv/biomodels-main/publ-model.do?mid=BIOMD0000000045
+
+abbreviation: BIOSIS
+database: BIOSIS previews
+object: Identifier
+example_id: BIOSIS:200200247281
+generic_url: http://www.biosis.org/
+
+abbreviation: BRENDA
+database: BRENDA, The Comprehensive Enzyme Information System
+object: EC enzyme identifier
+example_id: BRENDA:4.2.1.3
+generic_url: http://www.brenda.uni-koeln.de/
+url_syntax: http://www.brenda.uni-koeln.de/php/result_flat.php4?ecno=
+url_example: http://www.brenda.uni-koeln.de/php/result_flat.php4?ecno=4.2.1.3
+
+abbreviation: Broad
+database: Broad Institute
+generic_url: http://www.broad.mit.edu/
+
+abbreviation: Broad_MGG
+database: Magnaporthe grisea Database at the Broad Institute
+object: Locus
+example_id: Broad_MGG:MGG_05132.5
+generic_url: http://www.broad.mit.edu/annotation/genome/magnaporthe_grisea/Home.html
+url_syntax: http://www.broad.mit.edu/annotation/genome/magnaporthe_grisea/GeneLocus.html?sp=S
+url_example: http://www.broad.mit.edu/annotation/genome/magnaporthe_grisea/GeneLocus.html?sp=SMGG_05132
+
+! Note that CBS examples are not in the traditional accession number style because the entities in question are not entries in a database, and don't have accession numbers
+
+abbreviation: CBS
+database: Center for Biological Sequence Analysis
+object: prediction tool
+example_id: CBS:TMHMM
+example_id: CBS:SignalP
+example_id: CBS:ProP
+example_id: CBS:TargetP
+example_id: CBS:NetPhos
+example_id: CBS:NetOGlyc
+example_id: CBS:NetNGlyc
+generic_url: http://www.cbs.dtu.dk/
+url_example: http://www.cbs.dtu.dk/services/TMHMM/
+
+! note: CDD contact person is Rob Edwards (RobE at thefig.info); BRC: NMPDR
+
+abbreviation: CDD
+database: Conserved Domain Database at NCBI
+object: Identifier
+example_id: CDD:34222
+generic_url: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=cdd
+url_syntax: http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=
+url_example: http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=34222
+
+! note: The CGD is a synonym for the CGDID
+
+abbreviation: CGD
+database: Candida Genome Database
+object: Identifier for CGD Loci
+example_id: CGD:CAL0005516
+synonym: CGDID
+generic_url: http://www.candidagenome.org/
+url_syntax: http://www.candidagenome.org/cgi-bin/locus.pl?sgdid=
+url_example: http://www.candidagenome.org/cgi-bin/locus.pl?sgdid=CAL0005516
+
+! note: The CGD object also includes the orf19 assembly names, eg. orf19.2475
+
+abbreviation: CGD_LOCUS
+database: Candida Genome Database
+object: Gene name (gene symbol in mammalian nomenclature)
+example_id: CGD_LOCUS:HWP1
+example_id: CGD_LOCUS:orf19.2475
+generic_url: http://www.candidagenome.org/
+url_syntax: http://www.candidagenome.org/cgi-bin/locus.pl?locus=
+url_example: http://www.candidagenome.org/cgi-bin/locus.pl?locus=HWP1
+url_example: http://www.candidagenome.org/cgi-bin/locus.pl?locus=orf19.2475
+
+abbreviation: CGD_REF
+database: Candida Genome Database
+object: Literature Reference Identifier
+example_id: CGD_REF:1490
+generic_url: http://www.candidagenome.org/
+url_syntax: http://www.candidagenome.org/cgi-bin/reference/reference.pl?refNo=
+url_example: http://www.candidagenome.org/cgi-bin/reference/reference.pl?refNo=1490
+
+! note: also see GO/gene-associations/readme/Compugen.README
+
+abbreviation: CGEN
+database: Compugen Gene Ontology Gene Association Data
+object: Identifier
+example_id: CGEN:PrID131022
+generic_url: http://www.cgen.com/
+
+abbreviation: CGSC
+database: CGSC: E.coli Genetic Stock Center
+object: Gene symbol
+example_id: CGSC:rbsK
+generic_url: http://cgsc.biology.yale.edu/
+url_example: http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/315
+
+abbreviation: ChEBI
+database: Chemical Entities of Biological Interest
+object: Identifier
+example_id: ChEBI:17234
+generic_url: http://www.ebi.ac.uk/chebi/
+url_syntax: http://www.ebi.ac.uk/chebi/searchId.do?chebiId=
+url_example: http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:17234
+
+abbreviation: CL
+database: Cell Type Ontology
+object: Identifier
+example_id: CL:0000041
+generic_url: https://lists.sourceforge.net/lists/listinfo/obo-cell-type
+
+abbreviation: COG
+database: NCBI Clusters of Orthologous Groups
+generic_url: http://www.ncbi.nlm.nih.gov/COG/
+
+abbreviation: COG_Cluster
+database: NCBI COG cluster
+object: Identifier
+example_id: COG_Cluster:COG0001
+generic_url: http://www.ncbi.nlm.nih.gov/COG/
+url_syntax: http://www.ncbi.nlm.nih.gov/COG/new/release/cow.cgi?cog=
+url_example: http://www.ncbi.nlm.nih.gov/COG/new/release/cow.cgi?cog=COG0001
+
+abbreviation: COG_Function
+database: NCBI COG function
+object: Identifier
+example_id: COG_Function:H
+generic_url: http://www.ncbi.nlm.nih.gov/COG/
+url_syntax: http://www.ncbi.nlm.nih.gov/COG/grace/shokog.cgi?fun=
+url_example: http://www.ncbi.nlm.nih.gov/COG/grace/shokog.cgi?fun=H
+
+abbreviation: COG_Pathway
+database: NCBI COG pathway
+object: Identifier
+example_id: COG_Pathway:14
+generic_url: http://www.ncbi.nlm.nih.gov/COG/
+url_syntax: http://www.ncbi.nlm.nih.gov/COG/new/release/coglist.cgi?pathw=
+url_example: http://www.ncbi.nlm.nih.gov/COG/new/release/coglist.cgi?pathw=14
+
+abbreviation: Dictybase
+database: DictyBase
+object: Accession ID
+example_id: dictyBase:DDB0001836
+synonym: DDB
+generic_url: http://dictybase.org
+url_syntax: http://dictybase.org/db/cgi-bin/gene_page.pl?dictybaseid=
+url_example: http://dictybase.org/db/cgi-bin/gene_page.pl?dictybaseid=DDB0001836
+
+abbreviation: DDB_gene_name
+database: DictyBase
+object: Locus
+example_id: DDB_gene_name:mlcE
+generic_url: http://dictybase.org
+url_syntax: http://dictybase.org/db/cgi-bin/gene_page.pl?gene_name=
+url_example: http://dictybase.org/db/cgi-bin/gene_page.pl?gene_name=mlcE
+
+abbreviation: DDB_REF
+database: DictyBase literature references
+object: Literature Reference Identifier
+example_id: DDB_REF:10157
+generic_url: http://dictybase.org
+url_syntax: http://dictybase.org/db/cgi-bin/dictyBase/reference/reference.pl?refNo=
+url_example: http://dictybase.org/db/cgi-bin/dictyBase/reference/reference.pl?refNo=10157
+
+! note: the resolver at dx.doi.org generates the correct URL for a given DOI; e.g. the first example URL will be resolved into the second.
+
+abbreviation: DOI
+database: Digital Object Identifier
+object: Identifier
+example_id: DOI:10.1016/S0963-9969(99)00021-6
+generic_url: http://www.doi.org/
+url_example: http://www.doi.org/DOI:10.1016/S0963-9969(99)00021-6
+url_example: http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T6V-3W9CY4V-1&_coverDate=08%2F31%2F1998&_alid=431609009&_rdoc=1&_fmt=&_orig=search&_qd=1&_cdi=5040&_sort=d&view=c&_acct=C000042238&_version=1&_urlVersion=0&_userid=776054&md5=f57d8c0672e06c6c46a1acbd7e8a2fc6
+
+abbreviation: EC
+database: The Enzyme Commission
+example_id: EC:1.1.1.1
+generic_url: http://www.chem.qmw.ac.uk/iubmb/enzyme/
+url_example: http://www.chem.qmw.ac.uk/iubmb/enzyme/EC1/1/1/1.html
+
+abbreviation: EchoBASE
+database: EchoBASE post-genomic database for Escherichia coli
+object: Identifier
+example_id: EchoBASE:EB0231
+generic_url: http://www.ecoli-york.org/
+url_syntax: http://www.biolws1.york.ac.uk/echobase/Gene.cfm?recordID=
+url_example: http://www.biolws1.york.ac.uk/echobase/Gene.cfm?recordID=EB0231
+
+abbreviation: ECK
+database: The EcoGene Database of Escherichia coli Sequence and Function
+object: ECK accession number (E. coli K-12 gene identifier)
+example_id: ECK:ECK3746
+generic_url: http://www.ecogene.org/
+url_syntax: http://www.ecogene.org/geneInfo.php?eck_id=
+url_example: http://www.ecogene.org/geneInfo.php?eck_id=ECK3746
+
+abbreviation: EcoCyc
+database: The Encyclopedia of E. coli metabolism
+object: Pathway identifier
+example_id: EcoCyc:P2-PWY
+generic_url: http://ecocyc.org/
+url_syntax: http://biocyc.org/ECOLI/NEW-IMAGE?type=PATHWAY&object=
+url_example: http://biocyc.org/ECOLI/NEW-IMAGE?type=PATHWAY&object=P2-PWY
+
+abbreviation: ECOGENE
+database: The EcoGene Database of Escherichia coli Sequence and Function
+object: EcoGene Accession Number
+example_id: ECOGENE:EG10818
+generic_url: http://www.ecogene.org/
+url_syntax: http://www.ecogene.org/geneInfo.php?eg_id=
+url_example: http://www.ecogene.org/geneInfo.php?eg_id=EG10818
+
+! note: to construct URLs, use EcoGene accessions or ECK accession numbers
+
+abbreviation: ECOGENE_G
+database: The EcoGene Database of Escherichia coli Sequence and Function
+object: EcoGene Primary Gene Name
+example_id: ECOGENE_G:deoC
+generic_url: http://www.ecogene.org/
+
+abbreviation: EMBL
+database: International Nucleotide Sequence Database Collaboration, comprising EMBL-EBI International Nucleotide Sequence Data Library (EMBL-Bank), DNA DataBank of Japan (DDBJ), and NCBI GenBank
+object: Sequence accession number
+example_id: EMBL:AA816246
+example_id: DDBJ:AA816246
+example_id: GB:AA816246
+synonym: DDBJ
+synonym: GB
+synonym: GenBank
+generic_url: http://www.ebi.ac.uk/embl/
+generic_url: http://www.ddbj.nig.ac.jp/
+generic_url: http://www.ncbi.nlm.nih.gov/Genbank/
+url_syntax: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=
+url_syntax: http://www.ebi.ac.uk/cgi-bin/emblfetch?style=html&Submit=Go&id=
+url_syntax: http://arsa.ddbj.nig.ac.jp/arsa/ddbjSplSearch?KeyWord=
+url_example: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=AA816246
+url_example: http://www.ebi.ac.uk/cgi-bin/emblfetch?style=html&Submit=Go&id=AA816246
+url_example: http://arsa.ddbj.nig.ac.jp/arsa/ddbjSplSearch?KeyWord=AA816246
+
+abbreviation: ENSEMBL
+database: Database of automatically annotated genomic data
+object: Identifier
+example_id: ENSEMBL:ENSP00000265949
+generic_url: http://www.ensembl.org/
+url_syntax: http://www.ensembl.org/perl/protview?peptide=
+url_example: http://www.ensembl.org/perl/protview?peptide=ENSP00000265949
+
+abbreviation: ENZYME
+database: The Swiss Institute of Bioinformatics database of Enzymes
+object: Identifier
+example_id: ENZYME:EC 1.1.1.1
+generic_url: http://www.expasy.ch/
+url_syntax: http://www.expasy.ch/cgi-bin/nicezyme.pl?
+url_example: http://www.expasy.ch/cgi-bin/nicezyme.pl?1.1.1.1
+
+! note: For FB [NCBI use FLYBASE]
+
+abbreviation: FB
+database: FlyBase
+object: Gene identifier
+example_id: FB:FBgn0000024
+generic_url: http://flybase.bio.indiana.edu/
+url_syntax: http://flybase.bio.indiana.edu/.bin/fbidq.html?
+url_example: http://flybase.bio.indiana.edu/.bin/fbidq.html?FBgn0000180
+
+abbreviation: FLYBASE
+database: FlyBase
+object: Gene symbol
+example_id: FLYBASE:Adh
+generic_url: http://flybase.bio.indiana.edu/
+url_syntax: http://flybase.bio.indiana.edu/.bin/fbidq.html?
+
+abbreviation: GDB
+database: Human Genome Database
+object: Accession number
+example_id: GDB:306600
+generic_url: http://www.gdb.org/
+url_syntax: http://www.gdb.org/gdb-bin/genera/accno?accessionNum=
+url_example: http://www.gdb.org/gdb-bin/genera/accno?accessionNum=GDB:306600
+
+abbreviation: GeneDB_Gmorsitans
+shorthand_name: Tsetse
+database: GeneDB_Gmorsitans
+object: Gene identifier
+example_id: GeneDB_Gmorsitans:Gmm-0142
+generic_url: http://www.genedb.org/genedb/glossina/
+url_syntax: http://www.genedb.org/genedb/Search?organism=glossina&name=
+url_example: http://www.genedb.org/genedb/Search?organism=glossina&name=Gmm-0142
+
+abbreviation: GeneDB_Lmajor
+shorthand_name: Lmajor
+database: GeneDB_Lmajor
+object: Gene identifier
+example_id: GeneDB_Lmajor:LM5.32
+generic_url: http://www.genedb.org/genedb/leish/
+url_syntax: http://www.genedb.org/genedb/Search?organism=leish&name=
+url_example: http://www.genedb.org/genedb/Search?organism=leish&name=LM5.32
+
+abbreviation: GeneDB_Pfalciparum
+shorthand_name: Pfalciparum
+database: GeneDB_Pfalciparum
+object: Gene identifier
+example_id: GeneDB_Pfalciparum:PFD0755c
+generic_url: http://www.genedb.org/genedb/malaria/
+url_syntax: http://www.genedb.org/genedb/Search?organism=malaria&name=
+url_example: http://www.genedb.org/genedb/Search?organism=malaria&name=PFD0755c
+
+abbreviation: GeneDB_Spombe
+shorthand_name: Spombe
+database: GeneDB_Spombe
+object: Gene identifier
+example_id: GeneDB_Spombe:SPAC890.04C
+generic_url: http://www.genedb.org/genedb/pombe/
+url_syntax: http://www.genedb.org/genedb/Search?organism=pombe&name=
+url_example: http://www.genedb.org/genedb/Search?organism=pombe&name=SPAC890.04C
+
+abbreviation: GeneDB_Tbrucei
+shorthand_name: Tbrucei
+database: GeneDB_Tbrucei
+object: Gene identifier
+example_id: GeneDB_Tbrucei:Tb927.1.5250
+generic_url: http://www.genedb.org/genedb/tryp/
+url_syntax: http://www.genedb.org/genedb/Search?organism=tryp&name=
+url_example: http://www.genedb.org/genedb/Search?organism=tryp&name=Tb927.1.5250
+
+abbreviation: GenProtEC
+database: GenProtEC E. coli genome and proteome database
+generic_url: http://genprotec.mbl.edu/
+
+abbreviation: GermOnline
+database: GermOnline
+generic_url: http://www.germonline.org/
+
+abbreviation: GO
+database: Gene Ontology Database
+object: Identifier
+example_id: GO:0004352
+generic_url: http://amigo.geneontology.org/cgi-bin/amigo/go.cgi
+url_syntax: http://amigo.geneontology.org/cgi-bin/amigo/go.cgi?action=query&view=query&search_constraint=terms&query=GO ID
+url_example: http://amigo.geneontology.org/cgi-bin/amigo/go.cgi?action=query&view=query&search_constraint=terms&query=GO:0004352
+
+! note: generic_url and url_example for GO_REF to be filled in when available
+
+abbreviation: GO_REF
+database: Gene Ontology Database references
+object: Accession (for reference)
+example_id: GO_REF:0000001
+
+abbreviation: GOA
+database: GO Annotation at EBI
+generic_url: http://www.ebi.ac.uk/goa/
+
+abbreviation: GOC
+database: Gene Ontology Consortium
+generic_url: http://www.geneontology.org/
+
+abbreviation: GR
+database: Gramene: A Comparative Mapping Resource for Grains
+object: Identifier (any)
+example_id: GR:sd1
+generic_url: http://www.gramene.org/
+url_syntax: http://www.gramene.org/db/searches/browser?search_type=All&RGN=on&query=
+url_example: http://www.gramene.org/db/searches/browser?search_type=All&RGN=on&query=sd1
+
+abbreviation: GR_GENE
+database: Gramene: A Comparative Mapping Resource for Grains
+object: Gene identifier
+synonym: GR_gene
+example_id: GR_GENE:GR:0060198
+generic_url: http://www.gramene.org/
+url_syntax: http://www.gramene.org/db/genes/search_gene?acc=ID
+url_example: http://www.gramene.org/db/genes/search_gene?acc=GR:0060198
+
+abbreviation: GR_PROTEIN
+database: Gramene: A Comparative Mapping Resource for Grains
+object: Protein identifier
+synonym: GR_protein
+example_id: GR_PROTEIN:Q6VSV0
+generic_url: http://www.gramene.org/
+url_syntax: http://www.gramene.org/db/protein/protein_search?acc=
+url_example: http://www.gramene.org/db/protein/protein_search?acc=Q6VSV0
+
+abbreviation: GR_QTL
+database: Gramene: A Comparative Mapping Resource for Grains
+object: QTL identifier
+example_id: GR_QTL:CQU7
+generic_url: http://www.gramene.org/
+url_syntax: http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=
+url_example: http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=CQU7
+
+abbreviation: GR_REF
+database: Gramene: A Comparative Mapping Resource for Grains
+object: Reference
+example_id: GR_REF:659
+generic_url: http://www.gramene.org/
+url_syntax: http://www.gramene.org/db/literature/pub_search?ref_id=
+url_example: http://www.gramene.org/db/literature/pub_search?ref_id=659
+
+abbreviation: H-invDB
+database: H-invitational Database
+generic_url: http://www.h-invitational.jp/
+
+! note: the normal site for the AIST mirror, www.jbirc.aist.go.jp, is reporting a problem, and has been temporarily replaced by the jbirc.jbic.or.jp URLs. When the problem is resolved, the old URLS can be restored.
+! url_syntax: http://www.jbirc.aist.go.jp/hinv/soup/pub_Detail.pl?acc_id=
+! url_syntax: http://www.jbirc.aist.go.jp/hinv/soup/pub_Detail.pl?acc_id=AK093149
+
+abbreviation: H-invDB_cDNA
+database: H-invitational Database
+object: Accession
+example_id: H-invDB_cDNA:AK093148
+generic_url: http://www.h-invitational.jp/
+url_syntax: http://jbirc.jbic.or.jp/hinv/soup/pub_Detail.pl?acc_id=
+url_syntax: http://www.h-invdb.jbic.or.jp/soup/pub_Detail.pl?acc_id=
+url_syntax: http://hinvdb.ddbj.nig.ac.jp/soup/pub_Detail.pl?acc_id=AK093149
+url_example: http://jbirc.jbic.or.jp/hinv/soup/pub_Detail.pl?acc_id=AK093149
+url_example: http://www.h-invdb.jbic.or.jp/soup/pub_Detail.pl?acc_id=AK093149
+
+! url_syntax: http://www.jbirc.aist.go.jp/hinv/soup/pub_Locus.pl?locus_id=
+
+abbreviation: H-invDB_locus
+database: H-invitational Database
+object: Cluster identifier
+example_id: H-invDB_locus:HIX0014446
+generic_url: http://www.h-invitational.jp/
+url_syntax: http://jbirc.jbic.or.jp/hinv/soup/pub_Locus.pl?locus_id=
+url_syntax: http://www.h-invdb.jbic.or.jp/soup/pub_Locus.pl?locus_id=
+url_syntax: http://hinvdb.ddbj.nig.ac.jp/soup/pub_Locus.pl?locus_id=
+url_example: http://jbirc.jbic.or.jp/hinv/soup/pub_Locus.pl?locus_id=HIX0014446
+url_example: http://www.h-invdb.jbic.or.jp/soup/pub_Locus.pl?locus_id=HIX0014446
+url_example: http://hinvdb.ddbj.nig.ac.jp/soup/pub_Locus.pl?locus_id=HIX0014446
+
+abbreviation: HAMAP
+database: High-quality Automated and Manual Annotation of microbial Proteomes
+object: Identifier
+example_id: HAMAP:MF_00031
+generic_url: http://us.expasy.org/sprot/hamap/
+url_syntax: http://us.expasy.org/unirules/
+url_example: http://us.expasy.org/unirules/MF_00031
+
+abbreviation: HGNC
+database: HUGO Gene Nomenclature Committee
+object: Identifier
+example_id: HGNC:29
+generic_url: http://www.gene.ucl.ac.uk/nomenclature/
+url_syntax: http://www.gene.ucl.ac.uk/nomenclature/data/get_data.php?hgnc_id=
+url_example: http://www.gene.ucl.ac.uk/nomenclature/data/get_data.php?hgnc_id=HGNC:29
+
+! note: HGNC:id is preferred over HGNC_gene, because gene symbols are liable to change, resulting in broken links.
+
+abbreviation: HGNC_gene
+database: HUGO Gene Nomenclature Committee
+object: Gene symbol
+example_id: HGNC_gene:ABCA1
+generic_url: http://www.gene.ucl.ac.uk/nomenclature/
+url_syntax: http://www.gene.ucl.ac.uk/nomenclature/data/get_data.php?app_sym=
+url_example: http://www.gene.ucl.ac.uk/nomenclature/data/get_data.php?app_sym=ABCA1
+
+abbreviation: HUGO
+database: Human Genome Organisation
+generic_url: http://www.hugo-international.org/
+
+! note: IMG contact person is Rob Edwards (RobE at thefig.info); BRC: NMPDR
+
+abbreviation: IMG
+database: Integrated Microbial Genomes; JGI web site for genome annotation
+object: Identifier
+example_id: IMG:640008772
+generic_url: http://img.jgi.doe.gov
+url_syntax: http://img.jgi.doe.gov/cgi-bin/pub/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=
+url_example: http://img.jgi.doe.gov/cgi-bin/pub/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=640008772
+
+abbreviation: IMGT_HLA
+database: Immunogenetics database, human MHC
+example_id: IMGT_HLA:HLA00031
+generic_url: http://www.ebi.ac.uk/imgt/hla
+
+abbreviation: IMGT_LIGM
+database: Immunogenetics database, immunoglobulins and T-cell receptors
+example_id: IMGT_LIGM:U03895
+generic_url: http://imgt.cines.fr
+
+abbreviation: IntAct
+database: IntAct protein interaction database
+object: Accession
+example_id: IntAct:EBI-17086
+generic_url: http://www.ebi.ac.uk/intact/
+url_syntax: http://www.ebi.ac.uk/intact/search/do/search?searchString=
+url_example: http://www.ebi.ac.uk/intact/search/do/search?searchString=EBI-17086
+
+abbreviation: InterPro
+database: The InterPro database of protein domains and motifs
+object: Identifier
+synonym: INTERPRO
+synonym: IPR
+example_id: InterPro:IPR000001
+generic_url: http://www.ebi.ac.uk/interpro/
+url_syntax: http://www.ebi.ac.uk/interpro/DisplayIproEntry?ac=
+url_example: http://www.ebi.ac.uk/interpro/DisplayIproEntry?ac=IPR000001
+
+! note: IPI identifiers are in the format ID.version
+
+abbreviation: IPI
+database: International Protein Index
+object: Identifier
+example_id: IPI:IPI00000005.1
+generic_url: http://www.ebi.ac.uk/IPI/IPIhelp.html
+
+abbreviation: ISBN
+database: International Standard Book Number
+object: Identifier
+example_id: ISBN:0781702534
+generic_url: http://isbntools.com/
+url_syntax: http://my.linkbaton.com/get?lbCC=q&nC=q&genre=book&item=
+url_example: http://my.linkbaton.com/get?lbCC=q&nC=q&genre=book&item=0781702534
+
+abbreviation: ISSN
+database: International Standard Serial Number
+object: Identifier
+example_id: ISSN:1234-1231
+generic_url: http://www.issn.org/
+
+abbreviation: IUPHAR
+database: The IUPHAR Compendium of Receptor Characterization and Classification
+object: Receptor code
+example_id: IUPHAR:2.1.CBD
+
+abbreviation: KEGG
+database: Kyoto Encyclopedia of Genes and Genomes
+generic_url: http://www.genome.ad.jp/kegg/
+url_syntax: http://www.genome.ad.jp/dbget-bin/www_bget?
+url_example: http://www.genome.ad.jp/dbget-bin/www_bget?ec:1.1.1.1
+
+abbreviation: KEGG_PATHWAY
+database: KEGG Pathways Database
+object: Pathway
+example_id: KEGG_PATHWAY:ot00020
+generic_url: http://www.genome.ad.jp/kegg/docs/upd_pathway.html
+url_syntax: http://www.genome.ad.jp/dbget-bin/www_bget?path:
+url_example: http://www.genome.ad.jp/dbget-bin/www_bget?path:ot00020
+
+abbreviation: LIFEdb
+database: LIFEdb, a database for the integration and dissemination of functional data
+object: cDNA clone identifier
+example_id: LIFEdb:DKFZp564O1716
+generic_url: http://www.lifedb.de/
+url_syntax: http://www.dkfz.de/LIFEdb/LIFEdb.aspx?ID=
+url_example: http://www.dkfz.de/LIFEdb/LIFEdb.aspx?ID=DKFZp564O1716
+
+abbreviation: LIGAND
+database: KEGG LIGAND Database
+object: Enzyme or Compound
+example_id: LIGAND:C00577
+example_id: LIGAND:EC 1.1.1.1
+url_syntax: http://www.genome.ad.jp/dbget-bin/www_bget?ec:
+url_syntax: http://www.genome.ad.jp/dbget-bin/www_bget?cpd:
+generic_url: http://www.genome.ad.jp/kegg/docs/upd_ligand.html#ENZYME
+generic_url: http://www.genome.ad.jp/kegg/docs/upd_ligand.html#COMPOUND
+url_example: http://www.genome.ad.jp/dbget-bin/www_bget?ec:1.1.1.1
+url_example: http://www.genome.ad.jp/dbget-bin/www_bget?cpd:C00577
+
+abbreviation: LOCSVMpsi
+database: LOCSVMPSI: subcellular localization for eukayotic proteins based on SVM and PSI-BLAST
+generic_url: http://bioinformatics.ustc.edu.cn/locsvmpsi/locsvmpsi.php
+
+abbreviation: MA
+database: Adult Mouse Anatomical Dictionary; part of Gene Expression Database
+object: Identifier
+example_id: MA:0000003
+generic_url: http://www.informatics.jax.org/
+url_syntax: http://www.informatics.jax.org/searches/AMA.cgi?id=
+url_example: http://www.informatics.jax.org/searches/AMA.cgi?id=MA:0000003
+
+abbreviation: MaizeGDB
+database: MaizeGDB
+object: MaizeGDB Object ID Number
+example_id: MaizeGDB:881225
+generic_url: http://www.maizegdb.org
+url_syntax: http://www.maizegdb.org/cgi-bin/id_search.cgi?id=
+url_example: http://www.maizegdb.org/cgi-bin/id_search.cgi?id=881225
+
+abbreviation: MaizeGDB_Locus
+database: MaizeGDB
+object: Maize gene name
+example_id: MaizeGDB_Locus:ZmPK1
+generic_url: http://www.maizegdb.org
+url_syntax: http://www.maizegdb.org/cgi-bin/displaylocusresults.cgi?term=?
+url_example: http://www.maizegdb.org/cgi-bin/displaylocusresults.cgi?term=ZmPK1
+
+abbreviation: MEDLINE
+database: The Medline literature database
+object: Identifier
+example_id: MEDLINE:20572430
+
+abbreviation: MEROPS
+database: MEROPS - the Peptidase Database
+object: Identifier
+example_id: MEROPS:A01.001
+generic_url: http://merops.sanger.ac.uk/
+
+abbreviation: MEROPS_fam
+database: MEROPS: The Peptidase Database
+object: Peptidase family identifier
+example_id: MEROPS_fam:M18
+generic_url: http://merops.sanger.ac.uk/
+url_syntax: http://merops.sanger/ac/uk/famcards/
+url_example: http://merops.sanger.ac.uk/famcards/M18.htm
+
+abbreviation: MeSH
+database: Medical Subject Headings
+object: MeSH heading
+example_id: MeSH:mitosis
+generic_url: http://www.nlm.nih.gov/mesh/2005/MBrowser.html
+url_syntax: http://www.nlm.nih.gov/cgi/mesh/2005/MB_cgi?mode=&term=
+url_example: http://www.nlm.nih.gov/cgi/mesh/2005/MB_cgi?mode=&term=mitosis
+
+abbreviation: MetaCyc
+database: The Metabolic Encyclopedia of metabolic and other pathways
+object: Identifier (pathway or reaction)
+example_id: MetaCyc:GLUTDEG-PWY
+generic_url: http://metacyc.org/
+url_syntax: http://biocyc.org/META/NEW-IMAGE?type=NIL&object=
+url_example: http://biocyc.org/META/NEW-IMAGE?type=NIL&object=GLUTDEG-PWY
+
+abbreviation: MGD
+database: Mouse Genome Database
+object: Gene symbol
+example_id: MGD:Adcy9
+generic_url: http://www.informatics.jax.org/
+url_syntax: http://www.informatics.jax.org/searches/marker.cgi?
+
+abbreviation: MGI
+database: Mouse Genome Informatics
+object: Accession number
+example_id: MGI:80863
+generic_url: http://www.informatics.jax.org/
+url_syntax: http://www.informatics.jax.org/searches/accession_report.cgi?id=
+url_example: http://www.informatics.jax.org/searches/accession_report.cgi?id=MGI:80863
+
+abbreviation: MIPS_funcat
+database: MIPS Functional Catalogue
+object: Identifier
+example_id: MIPS_funcat:11.02
+generic_url: http://mips.gsf.de/proj/funcatDB/
+url_syntax: http://mips.gsf.de/cgi-bin/proj/funcatDB/search_advanced.pl?action=2&wert=
+url_example: http://mips.gsf.de/cgi-bin/proj/funcatDB/search_advanced.pl?action=2&wert=11.02
+
+abbreviation: MO
+database: The MGED Ontology
+object: ontology term
+example_id: MO:Action
+generic_url: http://mged.sourceforge.net/ontologies/MGEDontology.php
+url_syntax: http://mged.sourceforge.net/ontologies/MGEDontology.php#term
+url_example: http://mged.sourceforge.net/ontologies/MGEDontology.php#Action
+
+abbreviation: MultiFun
+database: MultiFun, a cellfunction assignment schema
+generic_url: http://genprotec.mbl.edu/files/Multifun.html
+
+abbreviation: NASC_code
+database: Nottingham Arabidopsis Stock Centre Seeds Database
+object: NASC code Identifier
+example_id: NASC_code:N3371
+generic_url: http://arabidopsis.info
+url_syntax: http://seeds.nottingham.ac.uk/NASC/stockatidb.lasso?code=
+url_example: http://seeds.nottingham.ac.uk/NASC/stockatidb.lasso?code=N3371
+
+abbreviation: NC-IUBMB
+database: Nomenclature Committee of the International Union of Biochemistry and Molecular Biology
+generic_url: http://www.chem.qmw.ac.uk/iubmb/
+
+abbreviation: NCBI
+database: National Center for Biotechnology Information, Bethesda
+object: Prefix
+generic_url: http://www.ncbi.nlm.nih.gov/
+
+! note: LocusID was the abbreviation for LocusLink, which has been superseded by NCBI_Gene (aka Entrez Gene)
+
+abbreviation: NCBI_Gene
+database: NCBI Gene
+object: Identifier
+synonym: LocusID
+example: NCBI_Gene:4771
+generic_url: http://www.ncbi.nlm.nih.gov/
+url_syntax: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=gene&dopt=full_report&list_uids=
+url_example: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=gene&dopt=full_report&list_uids=4771
+
+abbreviation: NCBI_gi
+database: NCBI databases
+object: Identifier
+example: NCBI_gi:10727410
+generic_url: http://www.ncbi.nlm.nih.gov/
+url_syntax: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=nucleotide&dopt=GenBank&list_uids=
+url_syntax: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=protein&dopt=GenBank&list_uids=
+url_example: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=nucleotide&dopt=GenBank&list_uids=10727410
+url_example: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=protein&dopt=GenBank&list_uids=30580598
+
+abbreviation: NCBI_GP
+database: NCBI GenPept
+object: Protein identifier
+example_id: NCBI_GP:EAL72968
+generic_url: http://www.ncbi.nlm.nih.gov/
+url_syntax: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&val=
+url_example: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&val=EAL72968
+
+abbreviation: NCBI_NM
+database: NCBI RefSeq
+object: mRNA identifier
+synonym: RefSeq
+example_id: NCBI_NM:123456
+generic_url: http://www.ncbi.nlm.nih.gov/
+
+abbreviation: NCBI_NP
+database: NCBI RefSeq
+object: Protein identifier
+synonym: RefSeq
+example_id: NCBI_NP:123456
+generic_url: http://www.ncbi.nlm.nih.gov/
+
+abbreviation: NMPDR
+database: National Microbial Pathogen Data Resource
+object: Identifier
+example_id: NMPDR:fig|306254.1.peg.183
+generic_url: http://www.nmpdr.org
+url_syntax: http://www.nmpdr.org/linkin.cgi?id=
+url_example: http://www.nmpdr.org/linkin.cgi?id=fig|306254.1.peg.183
+
+! note: NCBI uses the synonym MIM for OMIM
+
+abbreviation: OMIM
+database: Mendelian Inheritance in Man
+object: Identifier
+synonym: MIM
+example_id: OMIM:190198
+generic_url: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM
+url_syntax: http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=
+url_example: http://www3.ncbi.nlm.nih.gov/htbin-post/Omim/dispmim?190198
+
+abbreviation: PAMGO
+database: Plant-Associated Microbe Gene Ontology Interest Group
+generic_url: http://pamgo.vbi.vt.edu/
+
+abbreviation: PANTHER
+database: Protein ANalysis THrough Evolutionary Relationships Classification System
+generic_url: http://www.pantherdb.org/
+
+abbreviation: PATO
+database: Phenotypic quality ontology
+object: Identifier
+example_id: PATO:0001420
+generic_url: http://www.bioontology.org/wiki/index.php/PATO:Main_Page
+
+abbreviation: PDB
+database: Protein Data Bank
+object: Identifier
+example_id: PDB:1A4U
+generic_url: http://msd.ebi.ac.uk/
+generic_url: http://www.rcsb.org/pdb/
+url_example: http://www.rcsb.org/pdb/cgi/explore.cgi?pid=223051005992697&pdbId=1A4U
+
+abbreviation: Pfam
+database: Pfam: Protein families database of alignments and HMMs
+object: Accession number
+example_id: Pfam:PF00046
+generic_url: http://www.sanger.ac.uk/Software/Pfam/
+url_syntax: http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?
+url_example: http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?PF00046
+
+abbreviation: PfamB
+database: Pfam-B supplement to Pfam
+object: Accession number
+example_id: PfamB:PB014624
+generic_url: http://www.sanger.ac.uk/Software/Pfam/
+
+abbreviation: PharmGKB_PA
+database: The Pharmacogenetics and Pharmacogenomics Knowledge Base
+example: PA267
+generic_url: http://www.pharmgkb.org
+url_syntax: http://www.pharmgkb.org/do/serve?objId=
+url_example: http://www.pharmgkb.org/do/serve?objId=PA267
+
+abbreviation: PharmGKB_PGKB
+database: The Pharmacogenetics and Pharmacogenomics Knowledge Base
+example: PA267
+generic_url: http://www.pharmgkb.org
+url_syntax: http://www.pharmgkb.org/do/serve?objId=
+url_example: http://www.pharmgkb.org/do/serve?objId=PA267
+
+abbreviation: PINC
+database: Proteome Inc.; represents GO annotations created in 2001 for NCBI and extracted into GOA from EntrezGene
+generic_url: http://www.proteome.com/
+
+abbreviation: PIR
+database: Protein Information Resource
+object: Accession number
+example_id: PIR:I49499
+generic_url: http://pir.georgetown.edu/
+url_syntax: http://pir.georgetown.edu/cgi-bin/pirwww/nbrfget?uid=
+url_example: http://pir.georgetown.edu/cgi-bin/pirwww/nbrfget?uid=I49499
+
+abbreviation: PIRSF
+database: PIR Superfamily Classification System
+object: Identifier
+example_id: PIRSF:SF002327
+generic_url: http://pir.georgetown.edu/pirsf/
+url_syntax: http://pir.georgetown.edu/cgi-bin/ipcSF?id=
+url_example: http://pir.georgetown.edu/cgi-bin/ipcSF?id=SF002327
+
+abbreviation: PMID
+database: PubMed
+object: Identifier
+synonym: PUBMED
+synonym: PubMed
+example_id: PMID:4208797
+generic_url: http://www.ncbi.nlm.nih.gov/PubMed/
+url_syntax: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=
+url_example: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=4208797
+
+abbreviation: PO
+database: Plant Ontology Consortium Database
+object: Identifier
+example_id: PO:0009004
+generic_url: http://www.plantontology.org/
+url_syntax: http://www.plantontology.org/amigo/go.cgi?action=query&view=query&search_constraint=terms&query=
+url_example: http://www.plantontology.org/amigo/go.cgi?action=query&view=query&search_constraint=terms&query=PO:0009004
+
+abbreviation: POC
+database: Plant Ontology Consortium
+
+abbreviation: Pompep
+database: Schizosaccharomyces pombe protein data
+object: Gene/protein identifier
+example_id: Pompep:SPAC890.04C
+generic_url: ftp://ftp.sanger.ac.uk/pub/yeast/pombe/Protein_data/
+
+abbreviation: PPI
+database: The Pseudomonas syringae community annotation project
+generic_url: http://genome.pseudomonas-syringae.org/
+
+abbreviation: PRINTS
+database: PRINTS compendium of protein fingerprints
+object: Accession
+example_id: PRINTS:PR00025
+generic_url: http://umber.sbs.man.ac.uk/dbbrowser/PRINTS/
+url_syntax: http://umber.sbs.man.ac.uk/cgi-bin/dbbrowser/PRINTS/DoPRINTS.pl?cmd_a=Display&qua_a=none&fun_a=Text&qst_a=
+url_example: http://umber.sbs.man.ac.uk/cgi-bin/dbbrowser/PRINTS/DoPRINTS.pl?cmd_a=Display&qua_a=none&fun_a=Text&qst_a=PR00025
+
+abbreviation: ProDom
+database: ProDom protein domain families automatically generated from Swiss-Prot and TrEMBL
+object: Accession
+example_id: ProDom:PD000001
+generic_url: http://prodes.toulouse.inra.fr/prodom/current/html/home.php
+url_syntax: http://prodes.toulouse.inra.fr/prodom/current/cgi-bin/request.pl?question=DBEN&query=
+url_example: http://prodes.toulouse.inra.fr/prodom/current/cgi-bin/request.pl?question=DBEN&query=PD000001
+
+abbreviation: Prosite
+database: Prosite. Database of protein families and domains
+object: Accession number
+example_id: Prosite:PS00365
+generic_url: http://www.expasy.ch/prosite/
+url_syntax: http://www.expasy.ch/cgi-bin/prosite-search-ac?
+url_example: http://www.expasy.ch/cgi-bin/prosite-search-ac?PS00365
+
+abbreviation: protein_id
+database: The protein identifier shared by DDBJ/EMBL-bank/GenBank nucleotide sequence databases
+object: Identifier
+example_id: protein_id:CAA71991
+
+abbreviation: PROW
+database: Protein Reviews on the Web
+generic_url: http://www.ncbi.nlm.nih.gov/prow/
+
+abbreviation: PseudoCAP
+database: Pseudomonas Genome Project
+object: Identifier
+example_id: PseudoCAP:PA4756
+generic_url: http://v2.pseudomonas.com/
+url_syntax: http://v2.pseudomonas.com/getAnnotation.do?locusID=
+url_example: http://v2.pseudomonas.com/getAnnotation.do?locusID=PA4756
+
+abbreviation: PSI-MI
+database: Proteomic Standard Initiative for Molecular Interaction
+object: Interaction identifier
+synonym: MI
+example_id: MI:0018
+generic_url: http://psidev.sourceforge.net/mi/xml/doc/user/index.html
+
+abbreviation: PSI-MOD
+database: Proteomics Standards Initiative protein modification ontology
+object: Protein modification identifier
+synonym: MOD
+example_id: MOD:00219
+generic_url: http://psidev.sourceforge.net/mod/
+url_syntax: http://www.ebi.ac.uk/ontology-lookup/?termId=
+url_example: http://www.ebi.ac.uk/ontology-lookup/?termId=MOD:00219
+
+abbreviation: PSORT
+database: PSORT protein subcellular localization databases and prediction tools for bacteria
+generic_url: http://www.psort.org/
+
+abbreviation: pTARGET
+database: pTARGET Prediction server for protein subcellular localization
+generic_url: http://bioinformatics.albany.edu/~ptarget/
+
+abbreviation: PubChem_BioAssay
+database: NCBI PubChem database of bioassay records
+object: Identifier
+example: PubChem_BioAssay:177
+generic_url: http://pubchem.ncbi.nlm.nih.gov/
+url_syntax: http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid=
+url_example: http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid=177
+
+abbreviation: PubChem_Compound
+database: NCBI PubChem database of chemical structures
+object: Identifier
+example: PubChem_ Compound:2244
+generic_url: http://pubchem.ncbi.nlm.nih.gov/
+url_syntax: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pccompound&term=
+url_example: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pccompound&term=2244
+
+abbreviation: PubChem_Substance
+database: NCBI PubChem database of chemical substances
+object: Identifier
+example: PubChem_Substance:4594
+generic_url: http://pubchem.ncbi.nlm.nih.gov/
+url_syntax: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pcsubstance&term=
+url_example: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pcsubstance&term=4594
+
+abbreviation: Reactome
+database: Reactome human pathway database
+object: Identifier
+example_id: Reactome:70635
+generic_url: http://www.reactome.org/
+url_syntax: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=
+url_example: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=70635
+
+abbreviation: REBASE
+database: REBASE, The Restriction Enzyme Database
+object: Restriction enzyme name
+example_id: REBASE:EcoRI
+generic_url: http://rebase.neb.com/rebase/rebase.html
+url_syntax: http://rebase.neb.com/rebase/enz/
+url_example: http://rebase.neb.com/rebase/enz/EcoRI.html
+
+! note: RefSeq contact person is Guy Plunkett III (guy at genome.wisc.edu); BRC: ERIC
+
+abbreviation: RefSeq_NA
+database: RefSeq (Nucleic Acid)
+object: Identifier
+example_id: RefSeq_NA:NC_000913
+generic_url: http://www.ncbi.nlm.nih.gov/RefSeq/
+url_syntax: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Nucleotide&cmd=search&term=
+url_example: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Nucleotide&cmd=search&term=NC_000913
+
+abbreviation: RefSeq_Prot
+database: RefSeq (Protein)
+object: Identifier
+example_id: RefSeq_Prot:YP_498627
+generic_url: http://www.ncbi.nlm.nih.gov/RefSeq/
+url_syntax: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Protein&cmd=search&term=
+url_example: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Protein&cmd=search&term=YP_498627
+
+abbreviation: RESID
+database: RESID Database of Protein Modifications
+object: Identifier
+example_id: RESID:AA0062
+generic_url: ftp://ftp.ncifcrf.gov/pub/users/residues/
+
+abbreviation: RGD
+database: Rat Genome Database
+object: Accession Number
+synonym: RGDID
+example_id: RGD:2340
+generic_url: http://rgd.mcw.edu/
+url_syntax: http://rgd.mcw.edu/tools/genes/genes_view.cgi?id=
+url_example: http://rgd.mcw.edu/tools/genes/genes_view.cgi?id=2340
+
+abbreviation: RI
+database: Roslin Institute
+synonym: Roslin_Institute
+generic_url: http://www.roslin.ac.uk/
+
+abbreviation: RNAmods
+database: The RNA Modification Database
+object: Identifier
+example_id: RNAmods:037
+generic_url: http://medlib.med.utah.edu/RNAmods/
+url_syntax: http://medlib.med.utah.edu/cgi-bin/rnashow.cgi?
+url_example: http://medlib.med.utah.edu/cgi-bin/rnashow.cgi?037
+
+abbreviation: Sanger
+database: The Wellcome Trust Sanger Institute
+generic_url: http://www.sanger.ac.uk/
+
+abbreviation: SEED
+database: The SEED; The Project to Annotate the First 1000 Sequenced Genomes, Develop Detailed Metabolic Reconstructions, and Construct the Corresponding Stoichiometric Matrices
+object: Identifier
+example_id: SEED:fig|83331.1.peg.1
+generic_url: http://www.theseed.org
+url_syntax: http://www.theseed.org/linkin.cgi?id=
+url_example: http://www.theseed.org/linkin.cgi?id=fig|83331.1.peg.1
+
+! note: The SGD is a synonym for the SGDID
+
+abbreviation: SGD
+database: Saccharomyces Genome Database
+object: Identifier for SGD Loci
+synonym: SGDID
+example_id: SGD:S000006169
+generic_url: http://www.yeastgenome.org/
+url_syntax: http://db.yeastgenome.org/cgi-bin/locus.pl?dbid=
+url_example: http://db.yeastgenome.org/cgi-bin/locus.pl?dbid=S000006169
+
+! note: The SGD_LOCUS object also includes the systematic S. cerevisiae ORF names, eg. YEL001C
+
+abbreviation: SGD_LOCUS
+database: Saccharomyces Genome Database
+object: Gene name (gene symbol in mammalian nomenclature)
+example_id: SGD_LOCUS:GAL4
+generic_url: http://www.yeastgenome.org/
+url_syntax: http://db.yeastgenome.org/cgi-bin/locus.pl?locus=
+url_example: http://db.yeastgenome.org/cgi-bin/locus.pl?locus=GAL4
+url_example: http://db.yeastgenome.org/cgi-bin/locus.pl?locus=YEL001C
+
+abbreviation: SGD_REF
+database: Saccharomyces Genome Database
+object: Literature Reference Identifier
+example_id: SGD_REF:S000049602
+generic_url: http://www.yeastgenome.org/
+url_syntax: http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=
+url_example: http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000049602
+
+abbreviation: SMART
+database: Simple Modular Architecture Research Tool
+object: Accession
+example_id: SMART:SM00005
+generic_url: http://smart.embl-heidelberg.de/
+url_syntax: http://smart.embl-heidelberg.de/smart/do_annotation.pl?BLAST=DUMMY&DOMAIN=
+url_example: http://smart.embl-heidelberg.de/smart/do_annotation.pl?BLAST=DUMMY&DOMAIN=SM00005
+
+abbreviation: SMD
+database: Stanford Microarray Database
+generic_url: http://genome-www.stanford.edu/microarray
+
+abbreviation: SO
+database: Sequence Ontology
+object: Identifier
+example_id: SO:0000195
+generic_url: http://sequenceontology.org/
+url_syntax: http://song.sourceforge.net/SOterm_tables.html#
+url_example: http://song.sourceforge.net/SOterm_tables.html#SO:0000195
+
+abbreviation: SP_KW
+database: UniProt Knowledgebase keywords
+object: Identifier
+example_id: SP_KW:KW-0812
+generic_url: http://www.expasy.org/cgi-bin/keywlist.pl
+url_syntax: http://www.expasy.org/cgi-bin/get-entries?
+url_example: http://www.expasy.org/cgi-bin/get-entries?KW=KW-0812
+
+abbreviation: SP_SL
+database: UniProt Subcellular Location vocabulary
+object: Identifier
+
+abbreviation: SUBTILIST
+database: Bacillus subtilis Genome Sequence Project
+object: Accession number
+example_id: SUBTILISTG:BG11384
+generic_url: http://genolist.pasteur.fr/SubtiList/
+
+abbreviation: SUBTILISTG
+database: Bacillus subtilis Genome Sequence Project
+object: Gene symbol
+example_id: SUBTILISTG:accC
+generic_url: http://genolist.pasteur.fr/SubtiList/
+url_syntax:
+
+abbreviation: Swiss-Prot
+database: UniProtKB/Swiss-Prot, a curated protein sequence database which provides a high level of annotation and a minimal level of redundancy
+object: Accession number
+example_id: Swiss-Prot:P51587
+generic_url: http://www.uniprot.org
+url_syntax: http://www.ebi.uniprot.org/entry/
+url_example: http://www.ebi.uniprot.org/entry/P51587
+
+abbreviation: TAIR
+database: The Arabidopsis Information Resource
+object: Accession number
+example_id: TAIR:gene:2062713
+generic_url: http://www.arabidopsis.org/
+url_syntax: http://www.arabidopsis.org/servlets/TairObject?accession=
+url_example: http://www.arabidopsis.org/servlets/TairObject?accession=gene:2062713
+
+abbreviation: taxon
+database: NCBI Taxman
+object: Identifier
+example_id: taxon:7227
+generic_url: http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/
+url_syntax:
+
+abbreviation: TC
+database: The Transport Protein Database
+object: Identifier
+example_id: TC:9.A.4.1.1
+generic_url: http://tcdb.ucsd.edu/tcdb/
+url_syntax: http://tcdb.ucsd.edu/tcdb/tcprotein.php?substrate=
+url_example: http://tcdb.ucsd.edu/tcdb/tcprotein.php?substrate=9.A.4.1.1
+
+abbreviation: TGD
+database: Tetrahymena Genome Database
+generic_url: http://www.ciliate.org/
+
+! note: The TGD_LOCUS object also includes the systematic T. thermophila ORF names, eg. U66363
+
+abbreviation: TGD_LOCUS
+database: Tetrahymena Genome Database
+object: Gene name (gene symbol in mammalian nomenclature)
+example_id: TGD_LOCUS:PDD1
+generic_url: http://www.ciliate.org/
+url_syntax: http://db.ciliate.org/cgi-bin/locus.pl?locus=
+url_example: http://db.ciliate.org/cgi-bin/locus.pl?locus=PDD1
+url_example: http://db.ciliate.org/cgi-bin/locus.pl?locus=U66363
+
+abbreviation: TGD_REF
+database: Tetrahymena Genome Database
+object: Literature Reference Identifier
+example_id: TGD_REF:T000005818
+generic_url: http://www.ciliate.org/
+url_syntax: http://db.ciliate.org/cgi-bin/reference/reference.pl?dbid=
+url_example: http://db.ciliate.org/cgi-bin/reference/reference.pl?dbid=T000005818
+
+abbreviation: TIGR
+database: The Institute for Genomic Research
+generic_url: http://www.tigr.org/
+
+abbreviation: TIGR_Ath1
+database: The Institute for Genomic Research, Arabidopsis thaliana database
+object: Accession
+example_id: TIGR_Ath1:At3g01440
+generic_url: http://www.tigr.org/tdb/e2k1/ath1/ath1.shtml
+url_syntax: http://www.tigr.org/tigr-scripts/euk_manatee/shared/ORF_infopage.cgi?db=ath1&orf=
+url_example: http://www.tigr.org/tigr-scripts/euk_manatee/shared/ORF_infopage.cgi?db=ath1&orf=At3g01440
+
+abbreviation: TIGR_CMR
+database: The Institute for Genomic Research, Comprehensive Microbial Resource
+object: Locus
+example_id: TIGR_CMR:VCA0557
+generic_url: http://www.tigr.org/
+url_syntax: http://www.tigr.org/tigr-scripts/CMR2/GenePage.spl?locus=
+url_example: http://www.tigr.org/tigr-scripts/CMR2/GenePage.spl?locus=VCA0557
+
+abbreviation: TIGR_EGAD
+database: The Institute for Genomic Research, EGAD database
+object: Accession
+example_id: TIGR_EGAD:74462
+generic_url: http://www.tigr.org/
+url_syntax: http://www.tigr.org/tigr-scripts/CMR2/ht_report.spl?prot_id=
+url_example: http://www.tigr.org/tigr-scripts/CMR2/ht_report.spl?prot_id=74462
+
+abbreviation: TIGR_GenProp
+database: The Institute for Genomic Research, Genome Properties
+object: Accession
+example_id: TIGR_GenProp:GenProp0120
+generic_url: http://www.tigr.org/
+url_syntax: http://www.tigr.org/tigr-scripts/CMR2/genome_property_def.spl?prop_acc=
+url_example: http://www.tigr.org/tigr-scripts/CMR2/genome_property_def.spl?prop_acc=GenProp0120
+
+abbreviation: TIGR_Pfa1
+database: The Institute for Genomic Research, Plasmodium falciparum database
+object: Accession
+example_id: TIGR_Pfa1:PFB0010w
+generic_url: http://www.tigr.org/tdb/e2k1/pfa1/pfa1.shtml
+url_syntax: http://www.tigr.org/tigr-scripts/euk_manatee/shared/ORF_infopage.cgi?db=pfa1&orf=
+url_example: http://www.tigr.org/tigr-scripts/euk_manatee/shared/ORF_infopage.cgi?db=pfa1&orf=PFB0010w
+
+abbreviation: TIGR_REF
+database: The Institute for Genomic Research
+object: reference locator
+example_id: TIGR_REF:GO_ref
+generic_url: http://www.tigr.org/tdb/GO_REF/GO_REF.shtml
+url_example: http://www.tigr.org/tdb/GO_REF/GO_REF.shtml
+
+abbreviation: TIGR_Tba1
+database: The Institute for Genomic Research, Trypanosoma brucei database
+object: Accession
+example_id: TIGR_Tba1:25N14.10
+generic_url: http://www.tigr.org/tdb/e2k1/tba1/
+url_syntax: http://www.tigr.org/tigr-scripts/euk_manatee/shared/ORF_infopage.cgi?db=tba1&orf=
+url_example: http://www.tigr.org/tigr-scripts/euk_manatee/shared/ORF_infopage.cgi?db=tba1&orf=25N14.10
+
+abbreviation: TIGR_TGI
+database: The Institute for Genomic Research, TIGR Gene Index
+object: TC accession
+example_id: TIGR_TGI:Cattle_TC123931
+generic_url: http://www.tigr.org/
+url_syntax: http://www.tigr.org/tigr-scripts/nhgi_scripts/tc_report.pl?tc=?
+url_example: http://www.tigr.org/tigr-scripts/nhgi_scripts/tc_report.pl?tc=Cattle_TC123931
+
+abbreviation: TIGR_TIGRFAMS
+database: The Institute for Genomic Research, TIGRFAMs HMM collection
+object: Accession
+example_id: TIGR_TIGRFAMS:TIGR00254
+generic_url: http://www.tigr.org/
+url_syntax: http://www.tigr.org/tigr-scripts/CMR2/hmm_report.spl?acc=
+url_example: http://www.tigr.org/tigr-scripts/CMR2/hmm_report.spl?acc=TIGR00254
+
+abbreviation: TRAIT
+database: TRAnscript Integrated Table, an integrated database of transcripts expressed in human skeletal muscle
+synonym: Muscle TRAIT
+generic_url: http://muscle.cribi.unipd.it/
+
+abbreviation: TRANSFAC
+database: TRANSFAC database of eukaryotic transcription factors
+generic_url: http://www.gene-regulation.com/pub/databases.html#transfac
+
+abbreviation: TrEMBL
+database: UniProtKB-TrEMBL, a computer-annotated protein sequence database supplementing UniProtKB and containing the translations of all coding sequences (CDS) present in the EMBL Nucleotide Sequence Database but not yet integrated in UniProtKB/Swiss-Prot
+object: Accession number
+example_id: TrEMBL:O31124
+generic_url: http://www.uniprot.org
+url_syntax: http://www.ebi.uniprot.org/entry/
+url_example: http://www.ebi.uniprot.org/entry/O31124
+
+abbreviation: UM-BBD
+database: The University of Minnesota Biocatalysis/Biodegradation Database
+object: Prefix
+generic_url: http://umbbd.msi.umn.edu/
+
+abbreviation: UM-BBD_enzymeID
+database: The University of Minnesota Biocatalysis/Biodegradation Database
+object: Enzyme identifier
+example_id: UM-BBD_enzymeID:e0413
+generic_url: http://umbbd.msi.umn.edu/
+url_syntax: http://umbbd.msi.umn.edu/servlets/pageservlet?ptype=ep&enzymeID=
+url_example: http://umbbd.msi.umn.edu/servlets/pageservlet?ptype=ep&enzymeID=e0230
+
+abbreviation: UM-BBD_pathwayID
+database: The University of Minnesota Biocatalysis/Biodegradation Database
+object: Pathway identifier
+example_id: UM-BBD_pathwayID:acr
+generic_url: http://umbbd.msi.umn.edu/
+url_example: http://umbbd.msi.umn.edu/acr/acr_map.html
+
+! note: UniParc supersedes REMTREMBL; the latter is no longer maintained
+
+abbreviation: UniParc
+database: UniProt Archive; a non-redundant archive of protein sequences extracted from Swiss-Prot, TrEMBL, PIR-PSD, EMBL, Ensembl, IPI, PDB, RefSeq, FlyBase, WormBase, European Patent Office, United States Patent and Trademark Office, and Japanese Patent Office
+object: Accession number
+example_id: UniParc:UPI000000000A
+generic_url: http://www.ebi.ac.uk/uniparc/
+url_syntax: http://www.ebi.ac.uk/cgi-bin/dbfetch?db=uniparc&id=
+url_example: http://www.ebi.ac.uk/cgi-bin/dbfetch?db=uniparc&id=UPI000000000A
+
+abbreviation: UniProtKB
+database: The Universal Protein Knowledgebase, a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR
+object: Accession number
+synonym: UniProt
+example_id: UniProt:P51587
+generic_url: http://www.uniprot.org
+url_syntax: http://www.ebi.uniprot.org/entry/
+url_example: http://www.ebi.uniprot.org/entry/P51587
+
+! note: The link URL for VEGA is species specific (much like Ensembl).
+! For a direct link you need to translate the abbreviation in the ID
+! (eg 'HUM') into 'Homo_sapiens':
+!
+! http://vega.sanger.ac.uk/Homo_sapiens/protview?peptide=OTTHUMP00000000661&db=core
+!
+! Therefore to make it easier D. Barrell has given the search URL which
+! gives the results of a search on a peptide ID.
+
+abbreviation: VEGA
+database: The Vertebrate Genome Annotation database
+object: Identifier
+example_id: VEGA:OTTHUMP00000000661
+generic_url: http://vega.sanger.ac.uk/index.html
+url_syntax: http://vega.sanger.ac.uk/perl/searchview?species=all&idx=All&q=
+url_example: http://vega.sanger.ac.uk/perl/searchview?species=all&idx=All&q=OTTHUMP00000000661
+
+abbreviation: VIDA
+database: Virus Database at University College London
+generic_url: http://www.biochem.ucl.ac.uk/bsm/virus_database/VIDA.html
+
+abbreviation: WB
+database: WormBase, database of nematode biology
+object: Gene Identifier
+synonym: WormBase
+example_id: WB:WBGene00003001
+generic_url: http://www.wormbase.org/
+url_syntax: http://www.wormbase.org/db/gene/gene?name=
+url_example: http://www.wormbase.org/db/gene/gene?name=WBGene00003001
+
+abbreviation: WB_GENE
+database: WormBase, database of nematode biology
+object: Gene symbol
+synonym: WormBase
+example_id: WB:lin-12
+generic_url: http://www.wormbase.org/
+url_syntax: http://www.wormbase.org/db/gene/gene?name=
+url_example: http://www.wormbase.org/db/gene/gene?name=lin-12
+
+abbreviation: WB_REF
+database: WormBase, database of nematode biology
+object: Literature Reference Identifier
+example_id: WB_REF:WBPaper00004823
+generic_url: http://www.wormbase.org/
+url_syntax: http://www.wormbase.org/db/misc/paper?name=
+url_example: http://www.wormbase.org/db/misc/paper?name=WBPaper00004823
+
+abbreviation: WP
+database: Wormpep, database of proteins of C. elegans
+object: Identifier
+synonym: Wormpep
+example_id: WP:CE25104
+generic_url: http://www.wormbase.org/
+url_syntax: http://www.wormbase.org/db/get?class=Protein;name=
+url_example: http://www.wormbase.org/db/get?class=Protein;name=WP%3ACE15104
+
+abbreviation: ZFIN
+database: The Zebrafish Information Network
+object: Accession ID
+example_id: ZFIN:ZDB-GENE-990415-103
+generic_url: http://zfin.org/
+url_syntax: http://zfin.org/cgi-bin/ZFIN_jump?record=
+url_example: http://zfin.org/cgi-bin/ZFIN_jump?record=ZDB-GENE-990415-103
+
+abbreviation: Google
+database: Google keyword search
+generic_url: http://www.google.com/
+url_syntax: http://www.google.com/search?hl=en&q=
+
+abbreviation: Ask
+database: Ask.com
+generic_url: http://www.ask.com/
+url_syntax: http://www.ask.com/web?q=
diff --git a/application/src/main/resources/bookmarks.xml b/application/src/main/resources/bookmarks.xml
new file mode 100644
index 0000000..4d54a6a
--- /dev/null
+++ b/application/src/main/resources/bookmarks.xml
@@ -0,0 +1,437 @@
+<?xml version="1.0" encoding="UTF-8"?>
+ <!--
+ Cytoscape bookmark file. - General purpose bookmark file to specify
+ data source locations. Keiichiro Ono (kono at ucsd.edu)
+ -->
+<bookmarks xmlns:xlink="http://www.w3.org/1999/xlink" version="0.5">
+ <description>
+ Bookmark file for Cytoscape 2.4 and later.
+ </description>
+ <category name="ontology">
+ <dataSource name="Gene Ontology Full"
+ xlink:href="http://www.geneontology.org/ontology/gene_ontology_edit.obo"
+ format="obo">
+ <attribute name="description">
+ The Gene Ontology (GO) project provides a
+ controlled vocabulary to describe gene and gene product attributes
+ in any organism. This data source contains full size GO dag, which
+ contains all GO terms. This OBO file is written in version 1.2
+ format.
+ </attribute>
+ <attribute name="ontologyType">GO</attribute>
+ </dataSource>
+ <dataSource name="Generic GO slim"
+ xlink:href="http://www.geneontology.org/GO_slims/goslim_generic.obo"
+ format="obo">
+ <attribute name="description">
+ Subset of general GO Terms.
+ </attribute>
+ <attribute name="ontologyType">GO</attribute>
+ </dataSource>
+ <dataSource name="Yeast GO slim"
+ xlink:href="http://www.geneontology.org/GO_slims/goslim_yeast.obo"
+ format="obo">
+ <attribute name="description">
+ Subset of GO Terms for annotating Yeast
+ data sets. Maintained by SGD.
+ </attribute>
+ <attribute name="ontologyType">GO</attribute>
+ </dataSource>
+ <dataSource name="Molecule role (INOH Protein name/family name ontology)"
+ xlink:href="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/molecule_role.obo"
+ format="obo">
+ <attribute name="description">
+ A structured controlled vocabulary of
+ concrete protein names and generic (abstract) protein names. This
+ ontology is a INOH pathway annotation ontology, one of a set of
+ ontologies intended to be used in pathway data annotation to ease
+ data integration. This ontology is used to annotate protein names,
+ protein family names, generic/concrete protein names in the INOH
+ pathway data.
+ INOH is part of the BioPAX working group.
+ </attribute>
+ </dataSource>
+ <dataSource name="Event (INOH pathway ontology)"
+ xlink:href="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/event.obo"
+ format="obo">
+ <attribute name="description">
+ A structured controlled vocabulary of
+ pathway centric biological processes. This ontology is a INOH
+ pathway annotation ontology, one of a set of ontologies intended to
+ be used in pathway data annotation to ease data integration. This
+ ontology is used to annotate biological processes, pathways,
+ sub-pathways in the INOH pathway data.
+ INOH is part of the BioPAX
+ working group.
+ </attribute>
+ </dataSource>
+ <dataSource name="Protein-protein interaction"
+ xlink:href="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/protein/psi-mi.obo"
+ format="obo">
+ <attribute name="description">
+ A structured controlled vocabulary for the
+ annotation of experiments concerned with protein-protein
+ interactions.
+ </attribute>
+ </dataSource>
+ <dataSource name="Pathway Ontology"
+ xlink:href="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/pathway.obo"
+ format="obo">
+ <attribute name="description">
+ The Pathway Ontology is a controlled
+ vocabulary for pathways that provides standard terms for the
+ annotation of geneproducts.
+ </attribute>
+ </dataSource>
+ <dataSource name="PATO"
+ xlink:href="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality.obo"
+ format="obo">
+ <attribute name="description">
+ PATO is an ontology of phenotypic
+ qualities, intended for use in a number of applications, primarily
+ phenotype annotation. For more information, please visit PATO wiki
+ (http://www.bioontology.org/wiki/index.php/PATO:Main_Page).
+ </attribute>
+ </dataSource>
+ <dataSource name="Mouse pathology"
+ xlink:href="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/mouse_pathology/mouse_pathology.obo"
+ format="obo">
+ <attribute name="description">
+ Mouse Pathology Ontology (MPATH) is an
+ ontology for mutant mouse pathology. This is Version 1.
+ </attribute>
+ </dataSource>
+ <dataSource name="Human disease"
+ xlink:href="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/human_disease.obo"
+ format="obo">
+ <attribute name="description">
+ This ontology is a comprehensive
+ hierarchical controlled vocabulary for human disease representation.
+ For more information, please visit Disease Ontology website
+ (http://diseaseontology.sourceforge.net/).
+ </attribute>
+ </dataSource>
+ <!-- List of Gene Association files-->
+ <category name="annotation">
+ <dataSource format="Gene Association"
+ name="Gene Association file for Anaplasma phagocytophilum HZ"
+ xlink:href="http://www.geneontology.org/gene-associations/gene_association.jcvi_Aphagocytophilum.gz">
+ <attribute name="curator">JCVI</attribute>
+ <attribute name="species">Anaplasma phagocytophilum HZ</attribute>
+ </dataSource>
+ <dataSource format="Gene Association"
+ name="Gene Association file for Agrobacterium tumefaciensstr. C58"
+ xlink:href="http://www.geneontology.org/gene-associations/gene_association.PAMGO_Atumefaciens.gz">
+ <attribute name="curator">PAMGO</attribute>
+ <attribute name="species">Agrobacterium tumefaciensstr. C58</attribute>
+ </dataSource>
+ <dataSource format="Gene Association"
+ name="Gene Association file for Arabidopsis thaliana"
+ xlink:href="http://www.geneontology.org/gene-associations/gene_association.tair.gz">
+ <attribute name="curator">TAIR/JCVI</attribute>
+ <attribute name="species">Arabidopsis thaliana</attribute>
+ </dataSource>
+ <dataSource format="Gene Association"
+ name="Gene Association file for Aspergillus nidulans"
+ xlink:href="http://www.geneontology.org/gene-associations/gene_association.aspgd.gz">
+ <attribute name="curator">AspGD</attribute>
+ <attribute name="species">Aspergillus nidulans</attribute>
+ </dataSource>
+ <dataSource format="Gene Association"
+ name="Gene Association file for Bacillus anthracis Ames"
+ xlink:href="http://www.geneontology.org/gene-associations/gene_association.jcvi_Banthracis.gz">
+ <attribute name="curator">JCVI</attribute>
+ <attribute name="species">Bacillus anthracis Ames</attribute>
+ </dataSource>
+ <dataSource format="Gene Association" name="Gene Association file for Bos taurus"
+ xlink:href="http://www.geneontology.org/gene-associations/gene_association.goa_cow.gz">
+ <attribute name="curator">GO Annotations @ EBI</attribute>
+ <attribute name="species">Bos taurus</attribute>
+ </dataSource>
+ <dataSource format="Gene Association"
+ name="Gene Association file for Carboxydothermus hydrogenoformans Z-2901"
+ xlink:href="http://www.geneontology.org/gene-associations/gene_association.jcvi_Chydrogenoformans.gz">
+ <attribute name="curator">JCVI</attribute>
+ <attribute name="species">Carboxydothermus hydrogenoformans Z-2901</attribute>
+ </dataSource>
+ <dataSource format="Gene Association"
+ name="Gene Association file for Caenorhabditis elegans"
+ xlink:href="http://www.geneontology.org/gene-associations/gene_association.wb.gz">
+ <attribute name="curator">WormBase</attribute>
+ <attribute name="species">Caenorhabditis elegans</attribute>
+ </dataSource>
+ <dataSource format="Gene Association"
+ name="Gene Association file for Campylobacter jejuni RM1221"
+ xlink:href="http://www.geneontology.org/gene-associations/gene_association.jcvi_Cjejuni.gz">
+ <attribute name="curator">JCVI</attribute>
+ <attribute name="species">Campylobacter jejuni RM1221</attribute>
+ </dataSource>
+ <dataSource format="Gene Association"
+ name="Gene Association file for Candida albicans"
+ xlink:href="http://www.geneontology.org/gene-associations/gene_association.cgd.gz">
+ <attribute name="curator">CGD</attribute>
+ <attribute name="species">Candida albicans</attribute>
+ </dataSource>
+ <dataSource format="Gene Association"
+ name="Gene Association file for Clostridium perfringens ATCC13124"
+ xlink:href="http://www.geneontology.org/gene-associations/gene_association.jcvi_Cperfringens.gz">
+ <attribute name="curator">JCVI</attribute>
+ <attribute name="species">Clostridium perfringens ATCC13124</attribute>
+ </dataSource>
+ <dataSource format="Gene Association"
+ name="Gene Association file for Colwellia psychrerythraea 34H"
+ xlink:href="http://www.geneontology.org/gene-associations/gene_association.jcvi_Cpsychrerythraea.gz">
+ <attribute name="curator">JCVI</attribute>
+ <attribute name="species">Colwellia psychrerythraea 34H</attribute>
+ </dataSource>
+ <dataSource format="Gene Association"
+ name="Gene Association file for Coxiella burnetii RSA 493"
+ xlink:href="http://www.geneontology.org/gene-associations/gene_association.jcvi_Cburnetii.gz">
+ <attribute name="curator">JCVI</attribute>
+ <attribute name="species">Coxiella burnetii RSA 493</attribute>
+ </dataSource>
+ <dataSource format="Gene Association" name="Gene Association file for Danio rerio"
+ xlink:href="http://www.geneontology.org/gene-associations/gene_association.zfin.gz">
+ <attribute name="curator">ZFIN</attribute>
+ <attribute name="species">Danio rerio</attribute>
+ </dataSource>
+ <dataSource format="Gene Association"
+ name="Gene Association file for Dehalococcoides ethenogenes 195"
+ xlink:href="http://www.geneontology.org/gene-associations/gene_association.jcvi_Dethenogenes.gz">
+ <attribute name="curator">JCVI</attribute>
+ <attribute name="species">Dehalococcoides ethenogenes 195</attribute>
+ </dataSource>
+ <dataSource format="Gene Association"
+ name="Gene Association file for Dickeya dadantii"
+ xlink:href="http://www.geneontology.org/gene-associations/gene_association.PAMGO_Ddadantii.gz">
+ <attribute name="curator">PAMGO</attribute>
+ <attribute name="species">Dickeya dadantii</attribute>
+ </dataSource>
+ <dataSource format="Gene Association"
+ name="Gene Association file for Dictyostelium discoideum"
+ xlink:href="http://www.geneontology.org/gene-associations/gene_association.dictyBase.gz">
+ <attribute name="curator">dictyBase</attribute>
+ <attribute name="species">Dictyostelium discoideum</attribute>
+ </dataSource>
+ <dataSource format="Gene Association"
+ name="Gene Association file for Drosophila melanogaster"
+ xlink:href="http://www.geneontology.org/gene-associations/gene_association.fb.gz">
+ <attribute name="curator">FlyBase</attribute>
+ <attribute name="species">Drosophila melanogaster</attribute>
+ </dataSource>
+ <dataSource format="Gene Association"
+ name="Gene Association file for Escherichia coli"
+ xlink:href="http://www.geneontology.org/gene-associations/gene_association.ecocyc.gz">
+ <attribute name="curator">EcoCyc and EcoliHub</attribute>
+ <attribute name="species">Escherichia coli</attribute>
+ </dataSource>
+ <dataSource format="Gene Association"
+ name="Gene Association file for Ehrlichia chaffeensis Arkansas"
+ xlink:href="http://www.geneontology.org/gene-associations/gene_association.jcvi_Echaffeensis.gz">
+ <attribute name="curator">JCVI</attribute>
+ <attribute name="species">Ehrlichia chaffeensis Arkansas</attribute>
+ </dataSource>
+ <dataSource format="Gene Association"
+ name="Gene Association file for Gallus gallus"
+ xlink:href="http://www.geneontology.org/gene-associations/gene_association.goa_chicken.gz">
+ <attribute name="curator">GO Annotations @ EBI</attribute>
+ <attribute name="species">Gallus gallus</attribute>
+ </dataSource>
+ <dataSource format="Gene Association"
+ name="Gene Association file for Geobacter sulfurreducens PCA"
+ xlink:href="http://www.geneontology.org/gene-associations/gene_association.jcvi_Gsulfurreducens.gz">
+ <attribute name="curator">JCVI</attribute>
+ <attribute name="species">Geobacter sulfurreducens PCA</attribute>
+ </dataSource>
+ <dataSource format="Gene Association"
+ name="Gene Association file for Homo sapiens"
+ xlink:href="http://www.geneontology.org/gene-associations/gene_association.goa_human.gz">
+ <attribute name="curator">GO Annotations @ EBI</attribute>
+ <attribute name="species">Homo sapiens</attribute>
+ </dataSource>
+ <dataSource format="Gene Association"
+ name="Gene Association file for Hyphomonas neptunium ATCC 15444"
+ xlink:href="http://www.geneontology.org/gene-associations/gene_association.jcvi_Hneptunium.gz">
+ <attribute name="curator">JCVI</attribute>
+ <attribute name="species">Hyphomonas neptunium ATCC 15444</attribute>
+ </dataSource>
+ <dataSource format="Gene Association"
+ name="Gene Association file for Leishmania major"
+ xlink:href="http://www.geneontology.org/gene-associations/gene_association.GeneDB_Lmajor.gz">
+ <attribute name="curator">Sanger GeneDB</attribute>
+ <attribute name="species">Leishmania major</attribute>
+ </dataSource>
+ <dataSource format="Gene Association"
+ name="Gene Association file for Listeria monocytogenes 4b F2365"
+ xlink:href="http://www.geneontology.org/gene-associations/gene_association.jcvi_Lmonocytogenes.gz">
+ <attribute name="curator">JCVI</attribute>
+ <attribute name="species">Listeria monocytogenes 4b F2365</attribute>
+ </dataSource>
+ <dataSource format="Gene Association"
+ name="Gene Association file for Magnaporthe grisea"
+ xlink:href="http://www.geneontology.org/gene-associations/gene_association.PAMGO_Mgrisea.gz">
+ <attribute name="curator">PAMGO</attribute>
+ <attribute name="species">Magnaporthe grisea</attribute>
+ </dataSource>
+ <dataSource format="Gene Association"
+ name="Gene Association file for Methylococcus capsulatus Bath"
+ xlink:href="http://www.geneontology.org/gene-associations/gene_association.jcvi_Mcapsulatus.gz">
+ <attribute name="curator">JCVI</attribute>
+ <attribute name="species">Methylococcus capsulatus Bath</attribute>
+ </dataSource>
+ <dataSource format="Gene Association"
+ name="Gene Association file for Mus musculus"
+ xlink:href="http://www.geneontology.org/gene-associations/gene_association.mgi.gz">
+ <attribute name="curator">MGI</attribute>
+ <attribute name="species">Mus musculus</attribute>
+ </dataSource>
+ <dataSource format="Gene Association"
+ name="Gene Association file for Neorickettsia sennetsu Miyayama"
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diff --git a/application/src/main/resources/cytoscape/images/contextSensitiveHelp.gif b/application/src/main/resources/cytoscape/images/contextSensitiveHelp.gif
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diff --git a/application/src/main/resources/cytoscape/images/contributor-logos/README b/application/src/main/resources/cytoscape/images/contributor-logos/README
new file mode 100644
index 0000000..0a8ac3a
--- /dev/null
+++ b/application/src/main/resources/cytoscape/images/contributor-logos/README
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+
+Members of the Cytoscape Consortium should include an SVG version
+of their logo in this directory. We need a vector version of
+the logo because the logos will be used in different places like
+splash screens, websites, credit screens, etc., so we need to be
+able to scale the image appropriated. Since many of these graphics
+are generated dynamically, SVG is the easiest for us to use.
+Programs like Adobe Illustrator can easily save PDF, PS, or EPS
+graphics as SVG. Please do NOT include SVG images with embedded
+bitmap (jpg, png, gif) graphics as these images do NOT scale well.
+
+We promise not to modify the graphics (aside from scale) or otherwise
+compromise the integrity of the logo.
+
diff --git a/application/src/main/resources/cytoscape/images/contributor-logos/agilent_logo.svg b/application/src/main/resources/cytoscape/images/contributor-logos/agilent_logo.svg
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index 0000000..70ec951
--- /dev/null
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new file mode 100755
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+ c-0.065,0.121-0.033,0.52-0.284,0.33c-0.657-0.086-0.439-0.916-1.098-1.123c0.018-0.172-0.001-0.536-0.237-0.414
+ c-0.185,0-0.083-0.208-0.168-0.277L327.32,209.715z"/>
+ <path fill="#023F88" d="M329.797,210.746c0.151,0.311-0.252,0.295-0.404,0.416l-0.049-0.051
+ C329.443,210.938,329.712,210.937,329.797,210.746z"/>
+ <path fill="#023F88" d="M330.958,210.986c0.101,0.086,0,0.189-0.067,0.259c-0.032-0.087-0.118-0.155-0.084-0.259H330.958z"/>
+ <path fill="#023F88" d="M331.295,211.365c0.101-0.052,0.135,0.086,0.203,0.121c0.018,0.138-0.135,0.191-0.202,0.295
+ c-0.066-0.104-0.252,0.035-0.252-0.121C331.195,211.678,331.363,211.573,331.295,211.365z"/>
+ <path fill="#023F88" d="M331.212,211.245c-0.035,0.068-0.103,0.104-0.169,0.034v-0.086L331.212,211.245z"/>
+ <path fill="#FFFFFF" d="M326.475,214.881l-0.141,0.021l0.021-0.455l-0.15-0.138c-0.244,0.098-0.188,0.409-0.319,0.602
+ c-0.17-0.271,0.131-0.466,0.092-0.756l-0.414-0.038c0-0.078,0.094-0.117,0.132-0.194c0.491-0.118,0.303,0.436,0.774,0.327
+ c0.095,0.039,0.037,0.136,0.057,0.194L326.475,214.881z"/>
+ <ellipse fill="none" stroke="#FFFFFF" stroke-width="1.75" cx="326.952" cy="215.652" rx="8.079" ry="8.418"/>
+</g>
+</svg>
diff --git a/application/src/main/resources/cytoscape/images/versioned-svg/README.txt b/application/src/main/resources/cytoscape/images/versioned-svg/README.txt
new file mode 100644
index 0000000..d8b146c
--- /dev/null
+++ b/application/src/main/resources/cytoscape/images/versioned-svg/README.txt
@@ -0,0 +1,3 @@
+The SVG files contained in this directory are filtered for the
+${version} variable so that the splash and credit screens always
+contain the proper version number.
diff --git a/application/src/main/resources/cytoscape/images/vizmapper16.gif b/application/src/main/resources/cytoscape/images/vizmapper16.gif
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diff --git a/application/src/main/resources/cytoscape/images/ximian/minus.gif b/application/src/main/resources/cytoscape/images/ximian/minus.gif
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diff --git a/application/src/main/resources/cytoscape/images/ximian/net2.png b/application/src/main/resources/cytoscape/images/ximian/net2.png
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diff --git a/application/src/main/resources/cytoscape/images/ximian/plus.gif b/application/src/main/resources/cytoscape/images/ximian/plus.gif
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diff --git a/application/src/main/resources/cytoscape/images/ximian/stock_3d-apply-16.png b/application/src/main/resources/cytoscape/images/ximian/stock_3d-apply-16.png
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diff --git a/application/src/main/resources/cytoscape/images/ximian/stock_3d-light-16.png b/application/src/main/resources/cytoscape/images/ximian/stock_3d-light-16.png
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diff --git a/application/src/main/resources/cytoscape/images/ximian/stock_about-16.png b/application/src/main/resources/cytoscape/images/ximian/stock_about-16.png
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diff --git a/application/src/main/resources/cytoscape/images/ximian/stock_close-16.png b/application/src/main/resources/cytoscape/images/ximian/stock_close-16.png
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diff --git a/application/src/main/resources/cytoscape/images/ximian/stock_data-new-table-16.png b/application/src/main/resources/cytoscape/images/ximian/stock_data-new-table-16.png
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diff --git a/application/src/main/resources/cytoscape/images/ximian/stock_data-sources-modified-16.png b/application/src/main/resources/cytoscape/images/ximian/stock_data-sources-modified-16.png
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diff --git a/application/src/main/resources/cytoscape/images/ximian/stock_delete-16.png b/application/src/main/resources/cytoscape/images/ximian/stock_delete-16.png
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diff --git a/application/src/main/resources/cytoscape/images/ximian/stock_dialog-info-32.png b/application/src/main/resources/cytoscape/images/ximian/stock_dialog-info-32.png
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diff --git a/application/src/main/resources/cytoscape/images/ximian/stock_dialog-warning-32.png b/application/src/main/resources/cytoscape/images/ximian/stock_dialog-warning-32.png
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diff --git a/application/src/main/resources/cytoscape/images/ximian/stock_down-16.png b/application/src/main/resources/cytoscape/images/ximian/stock_down-16.png
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diff --git a/application/src/main/resources/cytoscape/images/ximian/stock_edit-16.png b/application/src/main/resources/cytoscape/images/ximian/stock_edit-16.png
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diff --git a/application/src/main/resources/cytoscape/images/ximian/stock_file-with-objects-16.png b/application/src/main/resources/cytoscape/images/ximian/stock_file-with-objects-16.png
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diff --git a/application/src/main/resources/cytoscape/images/ximian/stock_font-16.png b/application/src/main/resources/cytoscape/images/ximian/stock_font-16.png
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diff --git a/application/src/main/resources/cytoscape/images/ximian/stock_form-checkbox-16.png b/application/src/main/resources/cytoscape/images/ximian/stock_form-checkbox-16.png
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diff --git a/application/src/main/resources/cytoscape/images/ximian/stock_help.png b/application/src/main/resources/cytoscape/images/ximian/stock_help.png
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diff --git a/application/src/main/resources/cytoscape/images/ximian/stock_interaction.png b/application/src/main/resources/cytoscape/images/ximian/stock_interaction.png
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diff --git a/application/src/main/resources/cytoscape/images/ximian/stock_internet-16.png b/application/src/main/resources/cytoscape/images/ximian/stock_internet-16.png
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diff --git a/application/src/main/resources/cytoscape/images/ximian/stock_internet-32.png b/application/src/main/resources/cytoscape/images/ximian/stock_internet-32.png
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diff --git a/application/src/main/resources/cytoscape/images/ximian/stock_navigator-list-box-toggle-16.png b/application/src/main/resources/cytoscape/images/ximian/stock_navigator-list-box-toggle-16.png
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index 0000000..ab26884
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diff --git a/application/src/main/resources/cytoscape/images/ximian/stock_navigator.png b/application/src/main/resources/cytoscape/images/ximian/stock_navigator.png
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diff --git a/application/src/main/resources/cytoscape/images/ximian/stock_new-spreadsheet-16.png b/application/src/main/resources/cytoscape/images/ximian/stock_new-spreadsheet-16.png
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diff --git a/application/src/main/resources/cytoscape/images/ximian/stock_slide-duplicate.png b/application/src/main/resources/cytoscape/images/ximian/stock_slide-duplicate.png
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diff --git a/application/src/main/resources/cytoscape/images/ximian/stock_symbol-selection-16.png b/application/src/main/resources/cytoscape/images/ximian/stock_symbol-selection-16.png
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diff --git a/application/src/main/resources/cytoscape/images/ximian/stock_toggle-info-16.png b/application/src/main/resources/cytoscape/images/ximian/stock_toggle-info-16.png
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diff --git a/application/src/main/resources/cytoscape/images/ximian/stock_up-16.png b/application/src/main/resources/cytoscape/images/ximian/stock_up-16.png
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diff --git a/application/src/main/resources/cytoscape/images/ximian/stock_zoom-1.png b/application/src/main/resources/cytoscape/images/ximian/stock_zoom-1.png
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diff --git a/application/src/main/resources/cytoscape/images/ximian/stock_zoom-in.png b/application/src/main/resources/cytoscape/images/ximian/stock_zoom-in.png
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diff --git a/application/src/main/resources/cytoscape/images/ximian/stock_zoom-object.png b/application/src/main/resources/cytoscape/images/ximian/stock_zoom-object.png
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diff --git a/application/src/main/resources/cytoscape/images/ximian/stock_zoom-out.png b/application/src/main/resources/cytoscape/images/ximian/stock_zoom-out.png
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diff --git a/application/src/main/resources/cytoscape/images/ximian/tango-16-camera-photo.png b/application/src/main/resources/cytoscape/images/ximian/tango-16-camera-photo.png
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diff --git a/application/src/main/resources/cytoscape/images/ximian/tango-32-camera-photo.png b/application/src/main/resources/cytoscape/images/ximian/tango-32-camera-photo.png
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diff --git a/application/src/main/resources/vizmap.props b/application/src/main/resources/vizmap.props
new file mode 100644
index 0000000..4046b41
--- /dev/null
+++ b/application/src/main/resources/vizmap.props
@@ -0,0 +1,602 @@
+#This file specifies visual mappings for Cytoscape and has been automatically generated.
+# WARNING: any changes you make to this file while Cytoscape is running may be overwritten.
+# Any changes may make these visual mappings unreadable.
+# Please make sure you know what you are doing before modifying this file by hand.
+#
+#Tue Mar 23 13:51:57 PDT 2010
+edgeAppearanceCalculator.Minimal.defaultEdgeColor=51,51,51
+edgeAppearanceCalculator.Minimal.defaultEdgeFont=SanSerif,plain,10
+edgeAppearanceCalculator.Minimal.defaultEdgeFontSize=10.0
+edgeAppearanceCalculator.Minimal.defaultEdgeLabel=
+edgeAppearanceCalculator.Minimal.defaultEdgeLabelColor=0,0,0
+edgeAppearanceCalculator.Minimal.defaultEdgeLabelOpacity=255.0
+edgeAppearanceCalculator.Minimal.defaultEdgeLabelPosition=C,C,c,0,0
+edgeAppearanceCalculator.Minimal.defaultEdgeLabelWidth=100.0
+edgeAppearanceCalculator.Minimal.defaultEdgeLineStyle=SOLID
+edgeAppearanceCalculator.Minimal.defaultEdgeLineWidth=4.0
+edgeAppearanceCalculator.Minimal.defaultEdgeOpacity=255.0
+edgeAppearanceCalculator.Minimal.defaultEdgeSourceArrowColor=0,0,0
+edgeAppearanceCalculator.Minimal.defaultEdgeSourceArrowOpacity=255.0
+edgeAppearanceCalculator.Minimal.defaultEdgeSourceArrowShape=NONE
+edgeAppearanceCalculator.Minimal.defaultEdgeTargetArrowColor=0,0,0
+edgeAppearanceCalculator.Minimal.defaultEdgeTargetArrowOpacity=255.0
+edgeAppearanceCalculator.Minimal.defaultEdgeTargetArrowShape=NONE
+edgeAppearanceCalculator.Minimal.defaultEdgeToolTip=
+edgeAppearanceCalculator.Minimal.defaultNodeBorderColor=0,0,0
+edgeAppearanceCalculator.Minimal.defaultNodeBorderOpacity=255.0
+edgeAppearanceCalculator.Minimal.defaultNodeCustomGraphics=
+edgeAppearanceCalculator.Minimal.defaultNodeFillColor=255,255,255
+edgeAppearanceCalculator.Minimal.defaultNodeFont=Default,plain,12
+edgeAppearanceCalculator.Minimal.defaultNodeFontSize=12.0
+edgeAppearanceCalculator.Minimal.defaultNodeHight=30.0
+edgeAppearanceCalculator.Minimal.defaultNodeLabel=
+edgeAppearanceCalculator.Minimal.defaultNodeLabelColor=0,0,0
+edgeAppearanceCalculator.Minimal.defaultNodeLabelOpacity=255.0
+edgeAppearanceCalculator.Minimal.defaultNodeLabelPosition=C,C,c,0,0
+edgeAppearanceCalculator.Minimal.defaultNodeLabelWidth=100.0
+edgeAppearanceCalculator.Minimal.defaultNodeLineStyle=SOLID
+edgeAppearanceCalculator.Minimal.defaultNodeLineWidth=1.0
+edgeAppearanceCalculator.Minimal.defaultNodeOpacity=255.0
+edgeAppearanceCalculator.Minimal.defaultNodeShape=rect
+edgeAppearanceCalculator.Minimal.defaultNodeShowNestedNetwork=true
+edgeAppearanceCalculator.Minimal.defaultNodeSize=35.0
+edgeAppearanceCalculator.Minimal.defaultNodeToolTip=
+edgeAppearanceCalculator.Minimal.defaultNodeWidth=70.0
+edgeAppearanceCalculator.Nested\ Network\ Style.defaultEdgeColor=51,51,51
+edgeAppearanceCalculator.Nested\ Network\ Style.defaultEdgeFont=SanSerif,plain,10
+edgeAppearanceCalculator.Nested\ Network\ Style.defaultEdgeFontSize=10.0
+edgeAppearanceCalculator.Nested\ Network\ Style.defaultEdgeLabel=
+edgeAppearanceCalculator.Nested\ Network\ Style.defaultEdgeLabelColor=0,0,0
+edgeAppearanceCalculator.Nested\ Network\ Style.defaultEdgeLabelOpacity=255.0
+edgeAppearanceCalculator.Nested\ Network\ Style.defaultEdgeLabelPosition=C,C,c,0,0
+edgeAppearanceCalculator.Nested\ Network\ Style.defaultEdgeLabelWidth=100.0
+edgeAppearanceCalculator.Nested\ Network\ Style.defaultEdgeLineStyle=SOLID
+edgeAppearanceCalculator.Nested\ Network\ Style.defaultEdgeLineWidth=2.0
+edgeAppearanceCalculator.Nested\ Network\ Style.defaultEdgeOpacity=255.0
+edgeAppearanceCalculator.Nested\ Network\ Style.defaultEdgeSourceArrowColor=0,0,0
+edgeAppearanceCalculator.Nested\ Network\ Style.defaultEdgeSourceArrowOpacity=255.0
+edgeAppearanceCalculator.Nested\ Network\ Style.defaultEdgeSourceArrowShape=NONE
+edgeAppearanceCalculator.Nested\ Network\ Style.defaultEdgeTargetArrowColor=0,0,0
+edgeAppearanceCalculator.Nested\ Network\ Style.defaultEdgeTargetArrowOpacity=255.0
+edgeAppearanceCalculator.Nested\ Network\ Style.defaultEdgeTargetArrowShape=NONE
+edgeAppearanceCalculator.Nested\ Network\ Style.defaultEdgeToolTip=
+edgeAppearanceCalculator.Nested\ Network\ Style.defaultNodeBorderColor=0,0,0
+edgeAppearanceCalculator.Nested\ Network\ Style.defaultNodeBorderOpacity=255.0
+edgeAppearanceCalculator.Nested\ Network\ Style.defaultNodeCustomGraphics=
+edgeAppearanceCalculator.Nested\ Network\ Style.defaultNodeFillColor=255,255,255
+edgeAppearanceCalculator.Nested\ Network\ Style.defaultNodeFont=Default,plain,12
+edgeAppearanceCalculator.Nested\ Network\ Style.defaultNodeFontSize=12.0
+edgeAppearanceCalculator.Nested\ Network\ Style.defaultNodeHight=30.0
+edgeAppearanceCalculator.Nested\ Network\ Style.defaultNodeLabel=
+edgeAppearanceCalculator.Nested\ Network\ Style.defaultNodeLabelColor=0,0,0
+edgeAppearanceCalculator.Nested\ Network\ Style.defaultNodeLabelOpacity=255.0
+edgeAppearanceCalculator.Nested\ Network\ Style.defaultNodeLabelPosition=C,C,c,0,0
+edgeAppearanceCalculator.Nested\ Network\ Style.defaultNodeLabelWidth=100.0
+edgeAppearanceCalculator.Nested\ Network\ Style.defaultNodeLineStyle=SOLID
+edgeAppearanceCalculator.Nested\ Network\ Style.defaultNodeLineWidth=1.0
+edgeAppearanceCalculator.Nested\ Network\ Style.defaultNodeOpacity=255.0
+edgeAppearanceCalculator.Nested\ Network\ Style.defaultNodeShape=rect
+edgeAppearanceCalculator.Nested\ Network\ Style.defaultNodeShowNestedNetwork=true
+edgeAppearanceCalculator.Nested\ Network\ Style.defaultNodeSize=35.0
+edgeAppearanceCalculator.Nested\ Network\ Style.defaultNodeToolTip=
+edgeAppearanceCalculator.Nested\ Network\ Style.defaultNodeWidth=70.0
+edgeAppearanceCalculator.Nested\ Network\ Style.nodeSizeLocked=true
+edgeAppearanceCalculator.Sample1.defaultEdgeColor=0,0,0
+edgeAppearanceCalculator.Sample1.defaultEdgeFont=Default,plain,10
+edgeAppearanceCalculator.Sample1.defaultEdgeFontSize=10.0
+edgeAppearanceCalculator.Sample1.defaultEdgeLabel=
+edgeAppearanceCalculator.Sample1.defaultEdgeLabelColor=0,0,0
+edgeAppearanceCalculator.Sample1.defaultEdgeLabelOpacity=255.0
+edgeAppearanceCalculator.Sample1.defaultEdgeLabelPosition=C,C,c,0,0
+edgeAppearanceCalculator.Sample1.defaultEdgeLabelWidth=100.0
+edgeAppearanceCalculator.Sample1.defaultEdgeLineStyle=SOLID
+edgeAppearanceCalculator.Sample1.defaultEdgeLineWidth=1.0
+edgeAppearanceCalculator.Sample1.defaultEdgeOpacity=255.0
+edgeAppearanceCalculator.Sample1.defaultEdgeSourceArrowColor=0,0,0
+edgeAppearanceCalculator.Sample1.defaultEdgeSourceArrowOpacity=255.0
+edgeAppearanceCalculator.Sample1.defaultEdgeSourceArrowShape=NONE
+edgeAppearanceCalculator.Sample1.defaultEdgeTargetArrowColor=0,0,0
+edgeAppearanceCalculator.Sample1.defaultEdgeTargetArrowOpacity=255.0
+edgeAppearanceCalculator.Sample1.defaultEdgeTargetArrowShape=NONE
+edgeAppearanceCalculator.Sample1.defaultEdgeToolTip=
+edgeAppearanceCalculator.Sample1.defaultNodeBorderColor=0,0,0
+edgeAppearanceCalculator.Sample1.defaultNodeBorderOpacity=255.0
+edgeAppearanceCalculator.Sample1.defaultNodeCustomGraphics=
+edgeAppearanceCalculator.Sample1.defaultNodeFillColor=255,255,255
+edgeAppearanceCalculator.Sample1.defaultNodeFont=Default,plain,12
+edgeAppearanceCalculator.Sample1.defaultNodeFontSize=12.0
+edgeAppearanceCalculator.Sample1.defaultNodeHight=30.0
+edgeAppearanceCalculator.Sample1.defaultNodeLabel=
+edgeAppearanceCalculator.Sample1.defaultNodeLabelColor=0,0,0
+edgeAppearanceCalculator.Sample1.defaultNodeLabelOpacity=255.0
+edgeAppearanceCalculator.Sample1.defaultNodeLabelPosition=C,C,c,0,0
+edgeAppearanceCalculator.Sample1.defaultNodeLabelWidth=100.0
+edgeAppearanceCalculator.Sample1.defaultNodeLineStyle=SOLID
+edgeAppearanceCalculator.Sample1.defaultNodeLineWidth=1.0
+edgeAppearanceCalculator.Sample1.defaultNodeOpacity=255.0
+edgeAppearanceCalculator.Sample1.defaultNodeShape=rect
+edgeAppearanceCalculator.Sample1.defaultNodeShowNestedNetwork=true
+edgeAppearanceCalculator.Sample1.defaultNodeSize=35.0
+edgeAppearanceCalculator.Sample1.defaultNodeToolTip=
+edgeAppearanceCalculator.Sample1.defaultNodeWidth=70.0
+edgeAppearanceCalculator.Sample1.edgeColorCalculator=BasicDiscrete
+edgeAppearanceCalculator.Sample1.edgeLabelCalculator=EdgeLabel
+edgeAppearanceCalculator.Sample1.edgeLineStyleCalculator=Sample1-Edge Line Style-Discrete Mapper
+edgeAppearanceCalculator.Sample1.nodeSizeLocked=true
+edgeAppearanceCalculator.Solid.defaultEdgeColor=204,204,204
+edgeAppearanceCalculator.Solid.defaultEdgeFont=SanSerif,plain,10
+edgeAppearanceCalculator.Solid.defaultEdgeFontSize=10.0
+edgeAppearanceCalculator.Solid.defaultEdgeLabel=
+edgeAppearanceCalculator.Solid.defaultEdgeLabelColor=102,102,102
+edgeAppearanceCalculator.Solid.defaultEdgeLabelOpacity=190.0
+edgeAppearanceCalculator.Solid.defaultEdgeLabelPosition=C,C,c,0,0
+edgeAppearanceCalculator.Solid.defaultEdgeLabelWidth=100.0
+edgeAppearanceCalculator.Solid.defaultEdgeLineStyle=SOLID
+edgeAppearanceCalculator.Solid.defaultEdgeLineWidth=12.0
+edgeAppearanceCalculator.Solid.defaultEdgeOpacity=255.0
+edgeAppearanceCalculator.Solid.defaultEdgeSourceArrowColor=0,0,0
+edgeAppearanceCalculator.Solid.defaultEdgeSourceArrowOpacity=255.0
+edgeAppearanceCalculator.Solid.defaultEdgeSourceArrowShape=NONE
+edgeAppearanceCalculator.Solid.defaultEdgeTargetArrowColor=0,0,0
+edgeAppearanceCalculator.Solid.defaultEdgeTargetArrowOpacity=255.0
+edgeAppearanceCalculator.Solid.defaultEdgeTargetArrowShape=NONE
+edgeAppearanceCalculator.Solid.defaultEdgeToolTip=
+edgeAppearanceCalculator.Solid.defaultNodeBorderColor=0,0,0
+edgeAppearanceCalculator.Solid.defaultNodeBorderOpacity=255.0
+edgeAppearanceCalculator.Solid.defaultNodeCustomGraphics=
+edgeAppearanceCalculator.Solid.defaultNodeFillColor=255,255,255
+edgeAppearanceCalculator.Solid.defaultNodeFont=Default,plain,12
+edgeAppearanceCalculator.Solid.defaultNodeFontSize=12.0
+edgeAppearanceCalculator.Solid.defaultNodeHight=30.0
+edgeAppearanceCalculator.Solid.defaultNodeLabel=
+edgeAppearanceCalculator.Solid.defaultNodeLabelColor=0,0,0
+edgeAppearanceCalculator.Solid.defaultNodeLabelOpacity=255.0
+edgeAppearanceCalculator.Solid.defaultNodeLabelPosition=C,C,c,0,0
+edgeAppearanceCalculator.Solid.defaultNodeLabelWidth=100.0
+edgeAppearanceCalculator.Solid.defaultNodeLineStyle=SOLID
+edgeAppearanceCalculator.Solid.defaultNodeLineWidth=1.0
+edgeAppearanceCalculator.Solid.defaultNodeOpacity=255.0
+edgeAppearanceCalculator.Solid.defaultNodeShape=rect
+edgeAppearanceCalculator.Solid.defaultNodeShowNestedNetwork=true
+edgeAppearanceCalculator.Solid.defaultNodeSize=35.0
+edgeAppearanceCalculator.Solid.defaultNodeToolTip=
+edgeAppearanceCalculator.Solid.defaultNodeWidth=70.0
+edgeAppearanceCalculator.Solid.edgeLabelCalculator=Solid-Edge Label-Passthrough Mapper
+edgeAppearanceCalculator.Solid.nodeSizeLocked=true
+edgeAppearanceCalculator.Universe.defaultEdgeColor=255,255,255
+edgeAppearanceCalculator.Universe.defaultEdgeFont=SanSerif,plain,10
+edgeAppearanceCalculator.Universe.defaultEdgeFontSize=10.0
+edgeAppearanceCalculator.Universe.defaultEdgeLabel=
+edgeAppearanceCalculator.Universe.defaultEdgeLabelColor=0,0,0
+edgeAppearanceCalculator.Universe.defaultEdgeLabelOpacity=255.0
+edgeAppearanceCalculator.Universe.defaultEdgeLabelPosition=C,C,c,0,0
+edgeAppearanceCalculator.Universe.defaultEdgeLabelWidth=100.0
+edgeAppearanceCalculator.Universe.defaultEdgeLineStyle=LONG_DASH
+edgeAppearanceCalculator.Universe.defaultEdgeLineWidth=3.0
+edgeAppearanceCalculator.Universe.defaultEdgeOpacity=100.0
+edgeAppearanceCalculator.Universe.defaultEdgeSourceArrowColor=0,0,0
+edgeAppearanceCalculator.Universe.defaultEdgeSourceArrowOpacity=255.0
+edgeAppearanceCalculator.Universe.defaultEdgeSourceArrowShape=NONE
+edgeAppearanceCalculator.Universe.defaultEdgeTargetArrowColor=0,0,0
+edgeAppearanceCalculator.Universe.defaultEdgeTargetArrowOpacity=255.0
+edgeAppearanceCalculator.Universe.defaultEdgeTargetArrowShape=NONE
+edgeAppearanceCalculator.Universe.defaultEdgeToolTip=
+edgeAppearanceCalculator.Universe.defaultNodeBorderColor=0,0,0
+edgeAppearanceCalculator.Universe.defaultNodeBorderOpacity=255.0
+edgeAppearanceCalculator.Universe.defaultNodeCustomGraphics=
+edgeAppearanceCalculator.Universe.defaultNodeFillColor=255,255,255
+edgeAppearanceCalculator.Universe.defaultNodeFont=Default,plain,12
+edgeAppearanceCalculator.Universe.defaultNodeFontSize=12.0
+edgeAppearanceCalculator.Universe.defaultNodeHight=30.0
+edgeAppearanceCalculator.Universe.defaultNodeLabel=
+edgeAppearanceCalculator.Universe.defaultNodeLabelColor=0,0,0
+edgeAppearanceCalculator.Universe.defaultNodeLabelOpacity=255.0
+edgeAppearanceCalculator.Universe.defaultNodeLabelPosition=C,C,c,0,0
+edgeAppearanceCalculator.Universe.defaultNodeLabelWidth=100.0
+edgeAppearanceCalculator.Universe.defaultNodeLineStyle=SOLID
+edgeAppearanceCalculator.Universe.defaultNodeLineWidth=1.0
+edgeAppearanceCalculator.Universe.defaultNodeOpacity=255.0
+edgeAppearanceCalculator.Universe.defaultNodeShape=rect
+edgeAppearanceCalculator.Universe.defaultNodeShowNestedNetwork=true
+edgeAppearanceCalculator.Universe.defaultNodeSize=35.0
+edgeAppearanceCalculator.Universe.defaultNodeToolTip=
+edgeAppearanceCalculator.Universe.defaultNodeWidth=70.0
+edgeAppearanceCalculator.Universe.nodeSizeLocked=true
+edgeAppearanceCalculator.default.defaultEdgeColor=0,0,255
+edgeAppearanceCalculator.default.defaultEdgeFont=Default,plain,10
+edgeAppearanceCalculator.default.defaultEdgeFontSize=10.0
+edgeAppearanceCalculator.default.defaultEdgeLabel=
+edgeAppearanceCalculator.default.defaultEdgeLabelColor=0,0,0
+edgeAppearanceCalculator.default.defaultEdgeLabelOpacity=255.0
+edgeAppearanceCalculator.default.defaultEdgeLabelPosition=C,C,c,0,0
+edgeAppearanceCalculator.default.defaultEdgeLabelWidth=100.0
+edgeAppearanceCalculator.default.defaultEdgeLineStyle=SOLID
+edgeAppearanceCalculator.default.defaultEdgeLineWidth=1.5
+edgeAppearanceCalculator.default.defaultEdgeOpacity=255.0
+edgeAppearanceCalculator.default.defaultEdgeSourceArrowColor=0,0,0
+edgeAppearanceCalculator.default.defaultEdgeSourceArrowOpacity=255.0
+edgeAppearanceCalculator.default.defaultEdgeSourceArrowShape=NONE
+edgeAppearanceCalculator.default.defaultEdgeTargetArrowColor=0,0,0
+edgeAppearanceCalculator.default.defaultEdgeTargetArrowOpacity=255.0
+edgeAppearanceCalculator.default.defaultEdgeTargetArrowShape=NONE
+edgeAppearanceCalculator.default.defaultEdgeToolTip=
+edgeAppearanceCalculator.default.defaultNodeBorderColor=0,0,0
+edgeAppearanceCalculator.default.defaultNodeBorderOpacity=255.0
+edgeAppearanceCalculator.default.defaultNodeCustomGraphics=
+edgeAppearanceCalculator.default.defaultNodeFillColor=255,255,255
+edgeAppearanceCalculator.default.defaultNodeFont=Default,plain,12
+edgeAppearanceCalculator.default.defaultNodeFontSize=12.0
+edgeAppearanceCalculator.default.defaultNodeHight=30.0
+edgeAppearanceCalculator.default.defaultNodeLabel=
+edgeAppearanceCalculator.default.defaultNodeLabelColor=0,0,0
+edgeAppearanceCalculator.default.defaultNodeLabelOpacity=255.0
+edgeAppearanceCalculator.default.defaultNodeLabelPosition=C,C,c,0,0
+edgeAppearanceCalculator.default.defaultNodeLabelWidth=100.0
+edgeAppearanceCalculator.default.defaultNodeLineStyle=SOLID
+edgeAppearanceCalculator.default.defaultNodeLineWidth=1.0
+edgeAppearanceCalculator.default.defaultNodeOpacity=255.0
+edgeAppearanceCalculator.default.defaultNodeShape=rect
+edgeAppearanceCalculator.default.defaultNodeShowNestedNetwork=true
+edgeAppearanceCalculator.default.defaultNodeSize=35.0
+edgeAppearanceCalculator.default.defaultNodeToolTip=
+edgeAppearanceCalculator.default.defaultNodeWidth=70.0
+edgeAppearanceCalculator.default.nodeSizeLocked=true
+edgeColorCalculator.BasicDiscrete.mapping.controller=interaction
+edgeColorCalculator.BasicDiscrete.mapping.controllerType=-1
+edgeColorCalculator.BasicDiscrete.mapping.map.pd=255,0,51
+edgeColorCalculator.BasicDiscrete.mapping.map.pp=0,204,0
+edgeColorCalculator.BasicDiscrete.mapping.type=DiscreteMapping
+edgeColorCalculator.BasicDiscrete.visualPropertyType=EDGE_COLOR
+edgeLabelCalculator.EdgeLabel.mapping.controller=interaction
+edgeLabelCalculator.EdgeLabel.mapping.type=PassThroughMapping
+edgeLabelCalculator.EdgeLabel.visualPropertyType=EDGE_LABEL
+edgeLabelCalculator.Solid-Edge\ Label-Passthrough\ Mapper.mapping.controller=interaction
+edgeLabelCalculator.Solid-Edge\ Label-Passthrough\ Mapper.mapping.type=PassThroughMapping
+edgeLabelCalculator.Solid-Edge\ Label-Passthrough\ Mapper.visualPropertyType=EDGE_LABEL
+edgeLineStyleCalculator.Sample1-Edge\ Line\ Style-Discrete\ Mapper.mapping.controller=interaction
+edgeLineStyleCalculator.Sample1-Edge\ Line\ Style-Discrete\ Mapper.mapping.controllerType=-1
+edgeLineStyleCalculator.Sample1-Edge\ Line\ Style-Discrete\ Mapper.mapping.map.pd=LONG_DASH
+edgeLineStyleCalculator.Sample1-Edge\ Line\ Style-Discrete\ Mapper.mapping.map.pp=SOLID
+edgeLineStyleCalculator.Sample1-Edge\ Line\ Style-Discrete\ Mapper.mapping.type=DiscreteMapping
+edgeLineStyleCalculator.Sample1-Edge\ Line\ Style-Discrete\ Mapper.visualPropertyType=EDGE_LINE_STYLE
+globalAppearanceCalculator.Minimal.defaultBackgroundColor=153,153,153
+globalAppearanceCalculator.Minimal.defaultEdgeReverseSelectionColor=0,255,0
+globalAppearanceCalculator.Minimal.defaultEdgeSelectionColor=255,0,0
+globalAppearanceCalculator.Minimal.defaultNodeReverseSelectionColor=0,255,0
+globalAppearanceCalculator.Minimal.defaultNodeSelectionColor=255,255,0
+globalAppearanceCalculator.Nested\ Network\ Style.defaultBackgroundColor=255,255,255
+globalAppearanceCalculator.Nested\ Network\ Style.defaultEdgeReverseSelectionColor=0,255,0
+globalAppearanceCalculator.Nested\ Network\ Style.defaultEdgeSelectionColor=255,0,0
+globalAppearanceCalculator.Nested\ Network\ Style.defaultNodeReverseSelectionColor=0,255,0
+globalAppearanceCalculator.Nested\ Network\ Style.defaultNodeSelectionColor=255,255,0
+globalAppearanceCalculator.Sample1.defaultBackgroundColor=255,255,255
+globalAppearanceCalculator.Sample1.defaultEdgeReverseSelectionColor=0,255,0
+globalAppearanceCalculator.Sample1.defaultEdgeSelectionColor=255,0,0
+globalAppearanceCalculator.Sample1.defaultNodeReverseSelectionColor=0,255,0
+globalAppearanceCalculator.Sample1.defaultNodeSelectionColor=255,255,0
+globalAppearanceCalculator.Solid.defaultBackgroundColor=255,255,255
+globalAppearanceCalculator.Solid.defaultEdgeReverseSelectionColor=0,255,0
+globalAppearanceCalculator.Solid.defaultEdgeSelectionColor=255,0,0
+globalAppearanceCalculator.Solid.defaultNodeReverseSelectionColor=0,255,0
+globalAppearanceCalculator.Solid.defaultNodeSelectionColor=255,255,0
+globalAppearanceCalculator.Universe.defaultBackgroundColor=0,0,0
+globalAppearanceCalculator.Universe.defaultEdgeReverseSelectionColor=0,255,0
+globalAppearanceCalculator.Universe.defaultEdgeSelectionColor=255,0,0
+globalAppearanceCalculator.Universe.defaultNodeReverseSelectionColor=0,255,0
+globalAppearanceCalculator.Universe.defaultNodeSelectionColor=255,255,0
+globalAppearanceCalculator.default.defaultBackgroundColor=204,204,255
+globalAppearanceCalculator.default.defaultEdgeReverseSelectionColor=0,255,0
+globalAppearanceCalculator.default.defaultEdgeSelectionColor=255,0,0
+globalAppearanceCalculator.default.defaultNodeReverseSelectionColor=0,255,0
+globalAppearanceCalculator.default.defaultNodeSelectionColor=255,255,0
+nodeAppearanceCalculator.Minimal.defaultEdgeColor=0,0,0
+nodeAppearanceCalculator.Minimal.defaultEdgeFont=SanSerif,plain,10
+nodeAppearanceCalculator.Minimal.defaultEdgeFontSize=10.0
+nodeAppearanceCalculator.Minimal.defaultEdgeLabel=
+nodeAppearanceCalculator.Minimal.defaultEdgeLabelColor=0,0,0
+nodeAppearanceCalculator.Minimal.defaultEdgeLabelOpacity=255.0
+nodeAppearanceCalculator.Minimal.defaultEdgeLabelPosition=C,C,c,0,0
+nodeAppearanceCalculator.Minimal.defaultEdgeLabelWidth=100.0
+nodeAppearanceCalculator.Minimal.defaultEdgeLineStyle=SOLID
+nodeAppearanceCalculator.Minimal.defaultEdgeLineWidth=1.0
+nodeAppearanceCalculator.Minimal.defaultEdgeOpacity=255.0
+nodeAppearanceCalculator.Minimal.defaultEdgeSourceArrowColor=0,0,0
+nodeAppearanceCalculator.Minimal.defaultEdgeSourceArrowOpacity=255.0
+nodeAppearanceCalculator.Minimal.defaultEdgeSourceArrowShape=NONE
+nodeAppearanceCalculator.Minimal.defaultEdgeTargetArrowColor=0,0,0
+nodeAppearanceCalculator.Minimal.defaultEdgeTargetArrowOpacity=255.0
+nodeAppearanceCalculator.Minimal.defaultEdgeTargetArrowShape=NONE
+nodeAppearanceCalculator.Minimal.defaultEdgeToolTip=
+nodeAppearanceCalculator.Minimal.defaultNodeBorderColor=0,0,0
+nodeAppearanceCalculator.Minimal.defaultNodeBorderOpacity=255.0
+nodeAppearanceCalculator.Minimal.defaultNodeCustomGraphics=
+nodeAppearanceCalculator.Minimal.defaultNodeFillColor=255,255,255
+nodeAppearanceCalculator.Minimal.defaultNodeFont=Default,plain,12
+nodeAppearanceCalculator.Minimal.defaultNodeFontSize=12.0
+nodeAppearanceCalculator.Minimal.defaultNodeHight=30.0
+nodeAppearanceCalculator.Minimal.defaultNodeLabel=
+nodeAppearanceCalculator.Minimal.defaultNodeLabelColor=0,0,0
+nodeAppearanceCalculator.Minimal.defaultNodeLabelOpacity=255.0
+nodeAppearanceCalculator.Minimal.defaultNodeLabelPosition=C,C,c,0,0
+nodeAppearanceCalculator.Minimal.defaultNodeLabelWidth=100.0
+nodeAppearanceCalculator.Minimal.defaultNodeLineStyle=SOLID
+nodeAppearanceCalculator.Minimal.defaultNodeLineWidth=0.0
+nodeAppearanceCalculator.Minimal.defaultNodeOpacity=255.0
+nodeAppearanceCalculator.Minimal.defaultNodeShape=rect
+nodeAppearanceCalculator.Minimal.defaultNodeShowNestedNetwork=true
+nodeAppearanceCalculator.Minimal.defaultNodeSize=30.0
+nodeAppearanceCalculator.Minimal.defaultNodeToolTip=
+nodeAppearanceCalculator.Minimal.defaultNodeWidth=70.0
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultEdgeColor=0,0,0
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultEdgeFont=SanSerif,plain,10
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultEdgeFontSize=10.0
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultEdgeLabel=
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultEdgeLabelColor=0,0,0
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultEdgeLabelOpacity=255.0
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultEdgeLabelPosition=C,C,c,0,0
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultEdgeLabelWidth=100.0
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultEdgeLineStyle=SOLID
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultEdgeLineWidth=1.0
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultEdgeOpacity=255.0
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultEdgeSourceArrowColor=0,0,0
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultEdgeSourceArrowOpacity=255.0
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultEdgeSourceArrowShape=NONE
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultEdgeTargetArrowColor=0,0,0
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultEdgeTargetArrowOpacity=255.0
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultEdgeTargetArrowShape=NONE
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultEdgeToolTip=
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultNodeBorderColor=0,153,0
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultNodeBorderOpacity=190.0
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultNodeCustomGraphics=
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultNodeFillColor=153,255,153
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultNodeFont=SansSerif,plain,12
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultNodeFontSize=13.0
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultNodeHight=30.0
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultNodeLabel=
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultNodeLabelColor=0,0,0
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultNodeLabelOpacity=255.0
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultNodeLabelPosition=C,C,c,0,0
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultNodeLabelWidth=100.0
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultNodeLineStyle=SOLID
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultNodeLineWidth=2.0
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultNodeOpacity=150.0
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultNodeShape=ellipse
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultNodeShowNestedNetwork=true
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultNodeSize=40.0
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultNodeToolTip=
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultNodeWidth=70.0
+nodeAppearanceCalculator.Nested\ Network\ Style.nodeBorderColorCalculator=Nested Network Style-Node Border Color-Discrete Mapper
+nodeAppearanceCalculator.Nested\ Network\ Style.nodeFillColorCalculator=Nested Network Style-Node Color-Discrete Mapper
+nodeAppearanceCalculator.Nested\ Network\ Style.nodeLabelCalculator=Nested Network Style-Node Label-Passthrough Mapper
+nodeAppearanceCalculator.Nested\ Network\ Style.nodeLabelColor=Nested Network Style-Node Label Color-Discrete Mapper
+nodeAppearanceCalculator.Nested\ Network\ Style.nodeLabelPositionCalculator=Nested Network Style-Node Label Position-Discrete Mapper
+nodeAppearanceCalculator.Nested\ Network\ Style.nodeLineWidthCalculator=Nested Network Style-Node Line Width-Discrete Mapper
+nodeAppearanceCalculator.Nested\ Network\ Style.nodeShapeCalculator=Nested Network Style-Node Shape-Discrete Mapper
+nodeAppearanceCalculator.Nested\ Network\ Style.nodeSizeLocked=true
+nodeAppearanceCalculator.Nested\ Network\ Style.nodeUniformSizeCalculator=Nested Network Style-Node Size-Discrete Mapper
+nodeAppearanceCalculator.Sample1.defaultEdgeColor=0,0,0
+nodeAppearanceCalculator.Sample1.defaultEdgeFont=SanSerif,plain,10
+nodeAppearanceCalculator.Sample1.defaultEdgeFontSize=10.0
+nodeAppearanceCalculator.Sample1.defaultEdgeLabel=
+nodeAppearanceCalculator.Sample1.defaultEdgeLabelColor=0,0,0
+nodeAppearanceCalculator.Sample1.defaultEdgeLabelOpacity=255.0
+nodeAppearanceCalculator.Sample1.defaultEdgeLabelPosition=C,C,c,0,0
+nodeAppearanceCalculator.Sample1.defaultEdgeLabelWidth=100.0
+nodeAppearanceCalculator.Sample1.defaultEdgeLineStyle=SOLID
+nodeAppearanceCalculator.Sample1.defaultEdgeLineWidth=1.0
+nodeAppearanceCalculator.Sample1.defaultEdgeOpacity=255.0
+nodeAppearanceCalculator.Sample1.defaultEdgeSourceArrowColor=0,0,0
+nodeAppearanceCalculator.Sample1.defaultEdgeSourceArrowOpacity=255.0
+nodeAppearanceCalculator.Sample1.defaultEdgeSourceArrowShape=NONE
+nodeAppearanceCalculator.Sample1.defaultEdgeTargetArrowColor=0,0,0
+nodeAppearanceCalculator.Sample1.defaultEdgeTargetArrowOpacity=255.0
+nodeAppearanceCalculator.Sample1.defaultEdgeTargetArrowShape=NONE
+nodeAppearanceCalculator.Sample1.defaultEdgeToolTip=
+nodeAppearanceCalculator.Sample1.defaultNodeBorderColor=0,0,0
+nodeAppearanceCalculator.Sample1.defaultNodeBorderOpacity=255.0
+nodeAppearanceCalculator.Sample1.defaultNodeCustomGraphics=
+nodeAppearanceCalculator.Sample1.defaultNodeFillColor=204,204,255
+nodeAppearanceCalculator.Sample1.defaultNodeFont=Dialog.bold,plain,12
+nodeAppearanceCalculator.Sample1.defaultNodeFontSize=12.0
+nodeAppearanceCalculator.Sample1.defaultNodeHight=30.0
+nodeAppearanceCalculator.Sample1.defaultNodeLabel=
+nodeAppearanceCalculator.Sample1.defaultNodeLabelColor=0,0,0
+nodeAppearanceCalculator.Sample1.defaultNodeLabelOpacity=255.0
+nodeAppearanceCalculator.Sample1.defaultNodeLabelPosition=C,C,c,0,0
+nodeAppearanceCalculator.Sample1.defaultNodeLabelWidth=100.0
+nodeAppearanceCalculator.Sample1.defaultNodeLineStyle=SOLID
+nodeAppearanceCalculator.Sample1.defaultNodeLineWidth=0.0
+nodeAppearanceCalculator.Sample1.defaultNodeOpacity=255.0
+nodeAppearanceCalculator.Sample1.defaultNodeShape=ellipse
+nodeAppearanceCalculator.Sample1.defaultNodeShowNestedNetwork=true
+nodeAppearanceCalculator.Sample1.defaultNodeSize=40.0
+nodeAppearanceCalculator.Sample1.defaultNodeToolTip=
+nodeAppearanceCalculator.Sample1.defaultNodeWidth=70.0
+nodeAppearanceCalculator.Sample1.nodeLabelCalculator=NodeLabel
+nodeAppearanceCalculator.Sample1.nodeSizeLocked=true
+nodeAppearanceCalculator.Solid.defaultEdgeColor=0,0,0
+nodeAppearanceCalculator.Solid.defaultEdgeFont=SanSerif,plain,10
+nodeAppearanceCalculator.Solid.defaultEdgeFontSize=10.0
+nodeAppearanceCalculator.Solid.defaultEdgeLabel=
+nodeAppearanceCalculator.Solid.defaultEdgeLabelColor=0,0,0
+nodeAppearanceCalculator.Solid.defaultEdgeLabelOpacity=255.0
+nodeAppearanceCalculator.Solid.defaultEdgeLabelPosition=C,C,c,0,0
+nodeAppearanceCalculator.Solid.defaultEdgeLabelWidth=100.0
+nodeAppearanceCalculator.Solid.defaultEdgeLineStyle=SOLID
+nodeAppearanceCalculator.Solid.defaultEdgeLineWidth=1.0
+nodeAppearanceCalculator.Solid.defaultEdgeOpacity=255.0
+nodeAppearanceCalculator.Solid.defaultEdgeSourceArrowColor=0,0,0
+nodeAppearanceCalculator.Solid.defaultEdgeSourceArrowOpacity=255.0
+nodeAppearanceCalculator.Solid.defaultEdgeSourceArrowShape=NONE
+nodeAppearanceCalculator.Solid.defaultEdgeTargetArrowColor=0,0,0
+nodeAppearanceCalculator.Solid.defaultEdgeTargetArrowOpacity=255.0
+nodeAppearanceCalculator.Solid.defaultEdgeTargetArrowShape=NONE
+nodeAppearanceCalculator.Solid.defaultEdgeToolTip=
+nodeAppearanceCalculator.Solid.defaultNodeBorderColor=0,0,0
+nodeAppearanceCalculator.Solid.defaultNodeBorderOpacity=255.0
+nodeAppearanceCalculator.Solid.defaultNodeCustomGraphics=
+nodeAppearanceCalculator.Solid.defaultNodeFillColor=102,102,102
+nodeAppearanceCalculator.Solid.defaultNodeFont=Courier 10 Pitch Bold,plain,12
+nodeAppearanceCalculator.Solid.defaultNodeFontSize=18.0
+nodeAppearanceCalculator.Solid.defaultNodeHight=30.0
+nodeAppearanceCalculator.Solid.defaultNodeLabel=
+nodeAppearanceCalculator.Solid.defaultNodeLabelColor=0,0,0
+nodeAppearanceCalculator.Solid.defaultNodeLabelOpacity=160.0
+nodeAppearanceCalculator.Solid.defaultNodeLabelPosition=S,NW,c,0,5
+nodeAppearanceCalculator.Solid.defaultNodeLabelWidth=100.0
+nodeAppearanceCalculator.Solid.defaultNodeLineStyle=SOLID
+nodeAppearanceCalculator.Solid.defaultNodeLineWidth=0.0
+nodeAppearanceCalculator.Solid.defaultNodeOpacity=255.0
+nodeAppearanceCalculator.Solid.defaultNodeShape=ellipse
+nodeAppearanceCalculator.Solid.defaultNodeShowNestedNetwork=true
+nodeAppearanceCalculator.Solid.defaultNodeSize=40.0
+nodeAppearanceCalculator.Solid.defaultNodeToolTip=
+nodeAppearanceCalculator.Solid.defaultNodeWidth=70.0
+nodeAppearanceCalculator.Solid.nodeLabelCalculator=Solid-Node Label-Passthrough Mapper
+nodeAppearanceCalculator.Solid.nodeSizeLocked=true
+nodeAppearanceCalculator.Universe.defaultEdgeColor=0,0,0
+nodeAppearanceCalculator.Universe.defaultEdgeFont=SanSerif,plain,10
+nodeAppearanceCalculator.Universe.defaultEdgeFontSize=10.0
+nodeAppearanceCalculator.Universe.defaultEdgeLabel=
+nodeAppearanceCalculator.Universe.defaultEdgeLabelColor=0,0,0
+nodeAppearanceCalculator.Universe.defaultEdgeLabelOpacity=255.0
+nodeAppearanceCalculator.Universe.defaultEdgeLabelPosition=C,C,c,0,0
+nodeAppearanceCalculator.Universe.defaultEdgeLabelWidth=100.0
+nodeAppearanceCalculator.Universe.defaultEdgeLineStyle=SOLID
+nodeAppearanceCalculator.Universe.defaultEdgeLineWidth=1.0
+nodeAppearanceCalculator.Universe.defaultEdgeOpacity=255.0
+nodeAppearanceCalculator.Universe.defaultEdgeSourceArrowColor=0,0,0
+nodeAppearanceCalculator.Universe.defaultEdgeSourceArrowOpacity=255.0
+nodeAppearanceCalculator.Universe.defaultEdgeSourceArrowShape=NONE
+nodeAppearanceCalculator.Universe.defaultEdgeTargetArrowColor=0,0,0
+nodeAppearanceCalculator.Universe.defaultEdgeTargetArrowOpacity=255.0
+nodeAppearanceCalculator.Universe.defaultEdgeTargetArrowShape=NONE
+nodeAppearanceCalculator.Universe.defaultEdgeToolTip=
+nodeAppearanceCalculator.Universe.defaultNodeBorderColor=0,0,0
+nodeAppearanceCalculator.Universe.defaultNodeBorderOpacity=255.0
+nodeAppearanceCalculator.Universe.defaultNodeCustomGraphics=
+nodeAppearanceCalculator.Universe.defaultNodeFillColor=0,0,0
+nodeAppearanceCalculator.Universe.defaultNodeFont=Monospaced.bold,plain,12
+nodeAppearanceCalculator.Universe.defaultNodeFontSize=20.0
+nodeAppearanceCalculator.Universe.defaultNodeHight=30.0
+nodeAppearanceCalculator.Universe.defaultNodeLabel=
+nodeAppearanceCalculator.Universe.defaultNodeLabelColor=255,255,204
+nodeAppearanceCalculator.Universe.defaultNodeLabelOpacity=180.0
+nodeAppearanceCalculator.Universe.defaultNodeLabelPosition=C,C,c,0,0
+nodeAppearanceCalculator.Universe.defaultNodeLabelWidth=100.0
+nodeAppearanceCalculator.Universe.defaultNodeLineStyle=SOLID
+nodeAppearanceCalculator.Universe.defaultNodeLineWidth=0.0
+nodeAppearanceCalculator.Universe.defaultNodeOpacity=0.0
+nodeAppearanceCalculator.Universe.defaultNodeShape=ellipse
+nodeAppearanceCalculator.Universe.defaultNodeShowNestedNetwork=true
+nodeAppearanceCalculator.Universe.defaultNodeSize=40.0
+nodeAppearanceCalculator.Universe.defaultNodeToolTip=
+nodeAppearanceCalculator.Universe.defaultNodeWidth=100.0
+nodeAppearanceCalculator.Universe.nodeLabelCalculator=Universe-Node Label-Passthrough Mapper
+nodeAppearanceCalculator.Universe.nodeSizeLocked=true
+nodeAppearanceCalculator.default.defaultEdgeColor=0,0,0
+nodeAppearanceCalculator.default.defaultEdgeFont=SanSerif,plain,10
+nodeAppearanceCalculator.default.defaultEdgeFontSize=10.0
+nodeAppearanceCalculator.default.defaultEdgeLabel=
+nodeAppearanceCalculator.default.defaultEdgeLabelColor=0,0,0
+nodeAppearanceCalculator.default.defaultEdgeLabelOpacity=255.0
+nodeAppearanceCalculator.default.defaultEdgeLabelPosition=C,C,c,0,0
+nodeAppearanceCalculator.default.defaultEdgeLabelWidth=100.0
+nodeAppearanceCalculator.default.defaultEdgeLineStyle=SOLID
+nodeAppearanceCalculator.default.defaultEdgeLineWidth=1.0
+nodeAppearanceCalculator.default.defaultEdgeOpacity=255.0
+nodeAppearanceCalculator.default.defaultEdgeSourceArrowColor=0,0,0
+nodeAppearanceCalculator.default.defaultEdgeSourceArrowOpacity=255.0
+nodeAppearanceCalculator.default.defaultEdgeSourceArrowShape=NONE
+nodeAppearanceCalculator.default.defaultEdgeTargetArrowColor=0,0,0
+nodeAppearanceCalculator.default.defaultEdgeTargetArrowOpacity=255.0
+nodeAppearanceCalculator.default.defaultEdgeTargetArrowShape=NONE
+nodeAppearanceCalculator.default.defaultEdgeToolTip=
+nodeAppearanceCalculator.default.defaultNodeBorderColor=102,102,102
+nodeAppearanceCalculator.default.defaultNodeBorderOpacity=255.0
+nodeAppearanceCalculator.default.defaultNodeCustomGraphics=
+nodeAppearanceCalculator.default.defaultNodeFillColor=255,153,153
+nodeAppearanceCalculator.default.defaultNodeFont=SansSerif.bold,plain,12
+nodeAppearanceCalculator.default.defaultNodeFontSize=12.0
+nodeAppearanceCalculator.default.defaultNodeHight=30.0
+nodeAppearanceCalculator.default.defaultNodeLabel=
+nodeAppearanceCalculator.default.defaultNodeLabelColor=0,0,0
+nodeAppearanceCalculator.default.defaultNodeLabelOpacity=255.0
+nodeAppearanceCalculator.default.defaultNodeLabelPosition=C,C,c,0,0
+nodeAppearanceCalculator.default.defaultNodeLabelWidth=100.0
+nodeAppearanceCalculator.default.defaultNodeLineStyle=SOLID
+nodeAppearanceCalculator.default.defaultNodeLineWidth=1.5
+nodeAppearanceCalculator.default.defaultNodeOpacity=255.0
+nodeAppearanceCalculator.default.defaultNodeShape=ellipse
+nodeAppearanceCalculator.default.defaultNodeShowNestedNetwork=true
+nodeAppearanceCalculator.default.defaultNodeSize=40.0
+nodeAppearanceCalculator.default.defaultNodeToolTip=
+nodeAppearanceCalculator.default.defaultNodeWidth=70.0
+nodeAppearanceCalculator.default.nodeLabelCalculator=NodeLabel
+nodeAppearanceCalculator.default.nodeSizeLocked=true
+nodeBorderColorCalculator.Nested\ Network\ Style-Node\ Border\ Color-Discrete\ Mapper.mapping.controller=has_nested_network
+nodeBorderColorCalculator.Nested\ Network\ Style-Node\ Border\ Color-Discrete\ Mapper.mapping.controllerType=-1
+nodeBorderColorCalculator.Nested\ Network\ Style-Node\ Border\ Color-Discrete\ Mapper.mapping.map.yes=0,102,204
+nodeBorderColorCalculator.Nested\ Network\ Style-Node\ Border\ Color-Discrete\ Mapper.mapping.type=DiscreteMapping
+nodeBorderColorCalculator.Nested\ Network\ Style-Node\ Border\ Color-Discrete\ Mapper.visualPropertyType=NODE_BORDER_COLOR
+nodeFillColorCalculator.Nested\ Network\ Style-Node\ Color-Discrete\ Mapper.mapping.controller=has_nested_network
+nodeFillColorCalculator.Nested\ Network\ Style-Node\ Color-Discrete\ Mapper.mapping.controllerType=-1
+nodeFillColorCalculator.Nested\ Network\ Style-Node\ Color-Discrete\ Mapper.mapping.map.yes=255,255,255
+nodeFillColorCalculator.Nested\ Network\ Style-Node\ Color-Discrete\ Mapper.mapping.type=DiscreteMapping
+nodeFillColorCalculator.Nested\ Network\ Style-Node\ Color-Discrete\ Mapper.visualPropertyType=NODE_FILL_COLOR
+nodeLabelCalculator.BasicPassThrough.mapping.controller=label
+nodeLabelCalculator.BasicPassThrough.mapping.type=PassThroughMapping
+nodeLabelCalculator.BasicPassThrough.visualPropertyType=NODE_LABEL
+nodeLabelCalculator.Nested\ Network\ Style-Node\ Label-Passthrough\ Mapper.mapping.controller=ID
+nodeLabelCalculator.Nested\ Network\ Style-Node\ Label-Passthrough\ Mapper.mapping.type=PassThroughMapping
+nodeLabelCalculator.Nested\ Network\ Style-Node\ Label-Passthrough\ Mapper.visualPropertyType=NODE_LABEL
+nodeLabelCalculator.NodeLabel.mapping.controller=ID
+nodeLabelCalculator.NodeLabel.mapping.type=PassThroughMapping
+nodeLabelCalculator.NodeLabel.visualPropertyType=NODE_LABEL
+nodeLabelCalculator.Solid-Node\ Label-Passthrough\ Mapper.mapping.controller=ID
+nodeLabelCalculator.Solid-Node\ Label-Passthrough\ Mapper.mapping.type=PassThroughMapping
+nodeLabelCalculator.Solid-Node\ Label-Passthrough\ Mapper.visualPropertyType=NODE_LABEL
+nodeLabelCalculator.Universe-Node\ Label-Passthrough\ Mapper.mapping.controller=ID
+nodeLabelCalculator.Universe-Node\ Label-Passthrough\ Mapper.mapping.type=PassThroughMapping
+nodeLabelCalculator.Universe-Node\ Label-Passthrough\ Mapper.visualPropertyType=NODE_LABEL
+nodeLabelCalculator.id\ as\ node\ labels.mapping.controller=ID
+nodeLabelCalculator.id\ as\ node\ labels.mapping.type=PassThroughMapping
+nodeLabelCalculator.id\ as\ node\ labels.visualPropertyType=NODE_LABEL
+nodeLabelColor.Nested\ Network\ Style-Node\ Label\ Color-Discrete\ Mapper.mapping.controller=has_nested_network
+nodeLabelColor.Nested\ Network\ Style-Node\ Label\ Color-Discrete\ Mapper.mapping.controllerType=-1
+nodeLabelColor.Nested\ Network\ Style-Node\ Label\ Color-Discrete\ Mapper.mapping.map.yes=0,102,204
+nodeLabelColor.Nested\ Network\ Style-Node\ Label\ Color-Discrete\ Mapper.mapping.type=DiscreteMapping
+nodeLabelColor.Nested\ Network\ Style-Node\ Label\ Color-Discrete\ Mapper.visualPropertyType=NODE_LABEL_COLOR
+nodeLabelPositionCalculator.Nested\ Network\ Style-Node\ Label\ Position-Discrete\ Mapper.mapping.controller=has_nested_network
+nodeLabelPositionCalculator.Nested\ Network\ Style-Node\ Label\ Position-Discrete\ Mapper.mapping.controllerType=-1
+nodeLabelPositionCalculator.Nested\ Network\ Style-Node\ Label\ Position-Discrete\ Mapper.mapping.map.yes=SE,NW,c,0,0
+nodeLabelPositionCalculator.Nested\ Network\ Style-Node\ Label\ Position-Discrete\ Mapper.mapping.type=DiscreteMapping
+nodeLabelPositionCalculator.Nested\ Network\ Style-Node\ Label\ Position-Discrete\ Mapper.visualPropertyType=NODE_LABEL_POSITION
+nodeLineWidthCalculator.Nested\ Network\ Style-Node\ Line\ Width-Discrete\ Mapper.mapping.controller=has_nested_network
+nodeLineWidthCalculator.Nested\ Network\ Style-Node\ Line\ Width-Discrete\ Mapper.mapping.controllerType=-1
+nodeLineWidthCalculator.Nested\ Network\ Style-Node\ Line\ Width-Discrete\ Mapper.mapping.map.yes=5.0
+nodeLineWidthCalculator.Nested\ Network\ Style-Node\ Line\ Width-Discrete\ Mapper.mapping.type=DiscreteMapping
+nodeLineWidthCalculator.Nested\ Network\ Style-Node\ Line\ Width-Discrete\ Mapper.visualPropertyType=NODE_LINE_WIDTH
+nodeShapeCalculator.Nested\ Network\ Style-Node\ Shape-Discrete\ Mapper.mapping.controller=has_nested_network
+nodeShapeCalculator.Nested\ Network\ Style-Node\ Shape-Discrete\ Mapper.mapping.controllerType=-1
+nodeShapeCalculator.Nested\ Network\ Style-Node\ Shape-Discrete\ Mapper.mapping.map.yes=rect
+nodeShapeCalculator.Nested\ Network\ Style-Node\ Shape-Discrete\ Mapper.mapping.type=DiscreteMapping
+nodeShapeCalculator.Nested\ Network\ Style-Node\ Shape-Discrete\ Mapper.visualPropertyType=NODE_SHAPE
+nodeUniformSizeCalculator.Nested\ Network\ Style-Node\ Size-Discrete\ Mapper.mapping.controller=has_nested_network
+nodeUniformSizeCalculator.Nested\ Network\ Style-Node\ Size-Discrete\ Mapper.mapping.controllerType=-1
+nodeUniformSizeCalculator.Nested\ Network\ Style-Node\ Size-Discrete\ Mapper.mapping.map.yes=60.0
+nodeUniformSizeCalculator.Nested\ Network\ Style-Node\ Size-Discrete\ Mapper.mapping.type=DiscreteMapping
+nodeUniformSizeCalculator.Nested\ Network\ Style-Node\ Size-Discrete\ Mapper.visualPropertyType=NODE_SIZE
+nodeUniformSizeCalculator.Node\ Size-Continuous\ Mapper.mapping.boundaryvalues=2
+nodeUniformSizeCalculator.Node\ Size-Continuous\ Mapper.mapping.bv0.domainvalue=0.0
+nodeUniformSizeCalculator.Node\ Size-Continuous\ Mapper.mapping.bv0.equal=10.0
+nodeUniformSizeCalculator.Node\ Size-Continuous\ Mapper.mapping.bv0.greater=10.0
+nodeUniformSizeCalculator.Node\ Size-Continuous\ Mapper.mapping.bv0.lesser=
+nodeUniformSizeCalculator.Node\ Size-Continuous\ Mapper.mapping.bv1.domainvalue=0.0
+nodeUniformSizeCalculator.Node\ Size-Continuous\ Mapper.mapping.bv1.equal=30.0
+nodeUniformSizeCalculator.Node\ Size-Continuous\ Mapper.mapping.bv1.greater=
+nodeUniformSizeCalculator.Node\ Size-Continuous\ Mapper.mapping.bv1.lesser=30.0
+nodeUniformSizeCalculator.Node\ Size-Continuous\ Mapper.mapping.controller=Degree
+nodeUniformSizeCalculator.Node\ Size-Continuous\ Mapper.mapping.interpolator=LinearNumberToNumberInterpolator
+nodeUniformSizeCalculator.Node\ Size-Continuous\ Mapper.mapping.type=ContinuousMapping
+nodeUniformSizeCalculator.Node\ Size-Continuous\ Mapper.visualPropertyType=NODE_SIZE
diff --git a/application/src/main/resources/xsd/bookmarks.xsd b/application/src/main/resources/xsd/bookmarks.xsd
new file mode 100644
index 0000000..899ec00
--- /dev/null
+++ b/application/src/main/resources/xsd/bookmarks.xsd
@@ -0,0 +1,38 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" elementFormDefault="qualified" xmlns:xlink="http://www.w3.org/1999/xlink">
+ <xs:import namespace="http://www.w3.org/1999/xlink" schemaLocation="xlinks-2001.xsd"/>
+ <xs:element name="bookmarks">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="description"/>
+ <xs:element maxOccurs="unbounded" ref="category"/>
+ </xs:sequence>
+ <xs:attribute name="version" use="required" type="xs:decimal"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="description" type="xs:string"/>
+ <xs:element name="category">
+ <xs:complexType>
+ <xs:choice minOccurs="0" maxOccurs="unbounded">
+ <xs:element ref="category"/>
+ <xs:element ref="dataSource"/>
+ </xs:choice>
+ <xs:attribute name="name" use="required" type="xs:NCName"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="dataSource">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element minOccurs="0" maxOccurs="unbounded" ref="attribute"/>
+ </xs:sequence>
+ <xs:attribute name="format"/>
+ <xs:attribute name="name" use="required"/>
+ <xs:attribute ref="xlink:href" use="required"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="attribute">
+ <xs:complexType mixed="true">
+ <xs:attribute name="name" use="required" type="xs:NCName"/>
+ </xs:complexType>
+ </xs:element>
+</xs:schema>
diff --git a/application/src/main/resources/xsd/cysession.xsd b/application/src/main/resources/xsd/cysession.xsd
new file mode 100644
index 0000000..de06614
--- /dev/null
+++ b/application/src/main/resources/xsd/cysession.xsd
@@ -0,0 +1,210 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xlink="http://www.w3.org/1999/xlink"
+ elementFormDefault="qualified">
+ <!-- get access to the xlink: attribute groups for xlink:type (simple) -->
+ <xs:import namespace="http://www.w3.org/1999/xlink" schemaLocation="xlinks-2001.xsd"/>
+ <xs:element name="cysession">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="sessionNote"/>
+ <xs:element ref="sessionState"/>
+ <xs:element ref="networkTree"/>
+ </xs:sequence>
+ <xs:attribute name="id" use="required" type="xs:NCName"/>
+ <xs:attribute name="documentVersion" use="optional" type="xs:NCName"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="sessionNote" type="xs:string"/>
+ <xs:element name="sessionState">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element minOccurs="0" ref="plugins"/>
+ <xs:element minOccurs="0" ref="desktop"/>
+ <xs:element minOccurs="0" ref="server"/>
+ <xs:element ref="cytopanels"/>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="plugins">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element maxOccurs="unbounded" ref="plugin"/>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="plugin">
+ <xs:complexType>
+ <xs:attribute name="id" use="required" type="xs:NCName"/>
+ <xs:attribute name="stateLocation" use="required" type="xs:NCName"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="server">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element minOccurs="0" ref="ontologyServer"/>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+
+ <xs:element name="ontologyServer">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element minOccurs="0" maxOccurs="unbounded" ref="ontology"/>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="ontology">
+ <xs:complexType>
+ <xs:attribute name="name" use="required" type="xs:NCName"/>
+ <xs:attribute ref="xlink:href" use="required"/>
+ <xs:attribute name="ontologyType" use="optional" type="xs:NCName"/>
+ </xs:complexType>
+ </xs:element>
+
+ <xs:element name="desktop">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element minOccurs="0" ref="desktopSize"/>
+ <xs:element minOccurs="0" ref="networkFrames"/>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+
+ <xs:element name="desktopSize">
+ <xs:complexType>
+ <xs:attribute name="width" use="required" type="xs:integer"/>
+ <xs:attribute name="height" use="required" type="xs:integer"/>
+ </xs:complexType>
+ </xs:element>
+
+ <xs:element name="networkFrames">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element minOccurs="0" maxOccurs="unbounded" ref="networkFrame"/>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="networkFrame">
+ <xs:complexType>
+ <xs:attribute name="frameID" use="required" type="xs:NCName"/>
+ <xs:attribute name="width" use="required" type="xs:integer"/>
+ <xs:attribute name="height" use="required" type="xs:integer"/>
+ <xs:attribute name="x" use="required" type="xs:integer"/>
+ <xs:attribute name="y" use="required" type="xs:integer"/>
+ </xs:complexType>
+ </xs:element>
+
+ <xs:element name="cytopanels">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element maxOccurs="unbounded" ref="cytopanel"/>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="cytopanel">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="panelState"/>
+ <xs:element ref="selectedPanel"/>
+ <xs:element ref="panels"/>
+ </xs:sequence>
+ <xs:attribute name="id" use="required" type="xs:NCName"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="panelState" type="xs:NCName"/>
+ <xs:element name="selectedPanel" type="xs:NCName"/>
+ <xs:element name="panels">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element maxOccurs="unbounded" ref="panel"/>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="panel">
+ <xs:complexType>
+ <xs:attribute name="id" use="required" type="xs:NCName"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="networkTree">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element maxOccurs="unbounded" ref="network"/>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="network">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element minOccurs="1" ref="parent"/>
+ <xs:element minOccurs="0" maxOccurs="unbounded" ref="child"/>
+ <xs:element minOccurs="0" ref="selectedNodes"/>
+ <xs:element minOccurs="0" ref="hiddenNodes"/>
+ <xs:element minOccurs="0" ref="selectedEdges"/>
+ <xs:element minOccurs="0" ref="hiddenEdges"/>
+ <xs:element minOccurs="0" ref="viewableNodes"/>
+ </xs:sequence>
+ <xs:attribute name="filename" use="required" type="xs:NCName"/>
+ <xs:attribute name="id" use="required" type="xs:NCName"/>
+ <xs:attribute name="viewAvailable" use="optional" type="xs:boolean"/>
+ <xs:attribute name="visualStyle" use="optional" type="xs:NCName"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="parent">
+ <xs:complexType>
+ <xs:attribute name="id" use="required" type="xs:NCName"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="child">
+ <xs:complexType>
+ <xs:attribute name="id" use="required" type="xs:NCName"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="selectedNodes">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element maxOccurs="unbounded" ref="node"/>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="hiddenNodes">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element maxOccurs="unbounded" ref="node"/>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="selectedEdges">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element maxOccurs="unbounded" ref="edge"/>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="hiddenEdges">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element maxOccurs="unbounded" ref="edge"/>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="viewableNodes">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element maxOccurs="unbounded" ref="node"/>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="node">
+ <xs:complexType>
+ <xs:attribute name="id" use="required" type="xs:NCName"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="edge">
+ <xs:complexType>
+ <xs:attribute name="id" use="required" type="xs:NCName"/>
+ <xs:attribute name="source" use="optional" type="xs:NCName"/>
+ <xs:attribute name="target" use="optional" type="xs:NCName"/>
+ <xs:attribute name="interaction" use="optional" type="xs:NCName"/>
+ </xs:complexType>
+ </xs:element>
+</xs:schema>
diff --git a/application/src/main/resources/xsd/xlinks-2001.xsd b/application/src/main/resources/xsd/xlinks-2001.xsd
new file mode 100644
index 0000000..9b32dd5
--- /dev/null
+++ b/application/src/main/resources/xsd/xlinks-2001.xsd
@@ -0,0 +1,127 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- File: xlinks-2001.xsd
+ Updated version of http://www.opengis.net/namespaces/gml/core/xlinks.xsd -->
+<schema targetNamespace="http://www.w3.org/1999/xlink"
+ xmlns:xlink="http://www.w3.org/1999/xlink"
+ xmlns="http://www.w3.org/2001/XMLSchema">
+ <annotation>
+ <appinfo>xlinks-2001.xsd 2001-06</appinfo>
+ <documentation xml:lang="en">
+ This schema provides the XLink attributes for general use.
+ </documentation>
+ </annotation>
+<!-- ==============================================================
+ global declarations
+ =============================================================== -->
+ <!-- locator attribute -->
+ <attribute name="href" type="anyURI"/>
+ <!-- semantic attributes -->
+ <attribute name="role" type="anyURI"/>
+ <attribute name="arcrole" type="anyURI"/>
+ <attribute name="title" type="string"/>
+ <!-- behavior attributes -->
+ <attribute name="show">
+ <annotation>
+ <documentation>
+ The 'show' attribute is used to communicate the desired presentation
+ of the ending resource on traversal from the starting resource; it's
+ value should be treated as follows:
+ new - load ending resource in a new window, frame, pane, or other
+ presentation context
+ replace - load the resource in the same window, frame, pane, or
+ other presentation context
+ embed - load ending resource in place of the presentation of the
+ starting resource
+ other - behavior is unconstrained; examine other markup in the
+ link for hints
+ none - behavior is unconstrained
+ </documentation>
+ </annotation>
+ <simpleType>
+ <restriction base="string">
+ <enumeration value="new"/>
+ <enumeration value="replace"/>
+ <enumeration value="embed"/>
+ <enumeration value="other"/>
+ <enumeration value="none"/>
+ </restriction>
+ </simpleType>
+ </attribute>
+ <attribute name="actuate">
+ <annotation>
+ <documentation>
+ The 'actuate' attribute is used to communicate the desired timing
+ of traversal from the starting resource to the ending resource;
+ it's value should be treated as follows:
+ onLoad - traverse to the ending resource immediately on loading
+ the starting resource
+ onRequest - traverse from the starting resource to the ending
+ resource only on a post-loading event triggered for
+ this purpose
+ other - behavior is unconstrained; examine other markup in link
+ for hints
+ none - behavior is unconstrained
+ </documentation>
+ </annotation>
+ <simpleType>
+ <restriction base="string">
+ <enumeration value="onLoad"/>
+ <enumeration value="onRequest"/>
+ <enumeration value="other"/>
+ <enumeration value="none"/>
+ </restriction>
+ </simpleType>
+ </attribute>
+ <!-- traversal attributes -->
+ <attribute name="label" type="string"/>
+ <attribute name="from" type="string"/>
+ <attribute name="to" type="string"/>
+ <!-- ==============================================================
+ Attributes grouped by XLink type, as specified in the W3C
+ Recommendation (dated 2000-06-27)
+ =================================================================== -->
+ <attributeGroup name="simpleLink">
+ <attribute name="type" type="string" fixed="simple" form="qualified"/>
+ <attribute ref="xlink:href" use="optional"/>
+ <attribute ref="xlink:role" use="optional"/>
+ <attribute ref="xlink:arcrole" use="optional"/>
+ <attribute ref="xlink:title" use="optional"/>
+ <attribute ref="xlink:show" use="optional"/>
+ <attribute ref="xlink:actuate" use="optional"/>
+ </attributeGroup>
+ <attributeGroup name="extendedLink">
+ <attribute name="type" type="string" fixed="extended" form="qualified"/>
+ <attribute ref="xlink:role" use="optional"/>
+ <attribute ref="xlink:title" use="optional"/>
+ </attributeGroup>
+ <attributeGroup name="locatorLink">
+ <attribute name="type" type="string" fixed="locator" form="qualified"/>
+ <attribute ref="xlink:href" use="required"/>
+ <attribute ref="xlink:role" use="optional"/>
+ <attribute ref="xlink:title" use="optional"/>
+ <attribute ref="xlink:label" use="optional"/>
+ </attributeGroup>
+ <attributeGroup name="arcLink">
+ <attribute name="type" type="string" fixed="arc" form="qualified"/>
+ <attribute ref="xlink:arcrole" use="optional"/>
+ <attribute ref="xlink:title" use="optional"/>
+ <attribute ref="xlink:show" use="optional"/>
+ <attribute ref="xlink:actuate" use="optional"/>
+ <attribute ref="xlink:from" use="optional"/>
+ <attribute ref="xlink:to" use="optional"/>
+ </attributeGroup>
+ <attributeGroup name="resourceLink">
+ <attribute name="type" type="string" fixed="resource" form="qualified"/>
+ <attribute ref="xlink:role" use="optional"/>
+ <attribute ref="xlink:title" use="optional"/>
+ <attribute ref="xlink:label" use="optional"/>
+ </attributeGroup>
+ <attributeGroup name="titleLink">
+ <attribute name="type" type="string" fixed="title" form="qualified"/>
+ </attributeGroup>
+ <attributeGroup name="emptyLink">
+ <attribute name="type" type="string" fixed="none" form="qualified"/>
+ </attributeGroup>
+</schema>
+
+
diff --git a/application/src/test/java/cytoscape/AllTests.java b/application/src/test/java/cytoscape/AllTests.java
new file mode 100644
index 0000000..d6e6b0c
--- /dev/null
+++ b/application/src/test/java/cytoscape/AllTests.java
@@ -0,0 +1,182 @@
+/*
+ File: AllTests.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape;
+
+//import junit.framework.*;
+
+import java.lang.*;
+import java.lang.reflect.*;
+
+import java.net.*;
+
+import java.util.*;
+import java.util.jar.*;
+import java.util.regex.*;
+
+
+/**
+ * A TestSuite that examines the jar that it is contained in, discovers
+ * all of the unit tests also contained in the jar, and executes them.
+ * This is useful for running unit tests independent of ant.
+ */
+public class AllTests /*extends TestCase*/ {
+ /**
+ *
+ */
+ public static final String TEST_ALL = "JUNIT_TEST_ALL";
+
+ /**
+ * Parses the command line and executes the test suite in either
+ * gui mode or text based. If the first argument on the command line
+ * is "-ui" the gui will execute all tests found. If the -ui
+ * argument is followed by a fully qualified test class name
+ * (e.g. com.example.MyTest), then only that test will be executed
+ * in gui mode. Only one test case can be specified in this manner,
+ * any subsequent test cases (or arguments at all) will cause all
+ * tests to be run. If no arguments are found, or if the first
+ * argument is not "-ui", then all tests will be run in text mode.
+ public static void main(String[] args) {
+ if ((args.length > 0) && (args[0] != null) && args[0].equals("-ui")) {
+ if (args.length == 2) {
+ String[] newargs = { "cytoscape.AllTests", "-noloading", args[1] };
+ junit.swingui.TestRunner.main(newargs);
+ } else {
+ String[] newargs = { "cytoscape.AllTests", "-noloading" };
+ junit.swingui.TestRunner.main(newargs);
+ }
+ } else
+ junit.textui.TestRunner.run(suite());
+ }
+ */
+
+ /**
+ * Reflects to find the test classes in this jar and then
+ * adds them to this test suite.
+ public static Test suite() {
+ System.out.println("suite started");
+
+ TestSuite suite = new TestSuite("All JUnit Tests");
+
+ try {
+ // figure out the name of the jar file that is executing
+ // this code
+ ClassLoader cl = ClassLoader.getSystemClassLoader();
+ URL urlJar = cl.getSystemResource("cytoscape/AllTests.class");
+ String urlStr = urlJar.toString();
+ System.out.println("urlString " + urlStr);
+ urlStr = urlStr.substring(0, urlStr.indexOf("!/") + 2);
+
+ // once we have the jar file, open a connection to it and
+ // read the names of all of the entries
+ URL url = new URL(urlStr);
+ JarURLConnection jarConnection = (JarURLConnection) url.openConnection();
+ JarFile thisJar = jarConnection.getJarFile();
+
+ // create a list of URLs of the test classes
+ Enumeration entries = thisJar.entries();
+ List testNames = new ArrayList();
+
+ while (entries.hasMoreElements()) {
+ String name = ((JarEntry) entries.nextElement()).getName();
+
+ if (name.matches(".*Test.class"))
+ testNames.add(name.substring(0, name.length() - 6));
+ }
+
+ // create the a new ClassLoader
+ URL[] testUrlArray = new URL[testNames.size()];
+
+ for (int i = 0; i < testUrlArray.length; i++)
+ testUrlArray[i] = new URL(urlStr + (String) testNames.get(i) + ".class");
+
+ URLClassLoader urlLoader = new URLClassLoader(testUrlArray, cl);
+
+ // finally, iterate over each test class name, reflect an
+ // instantiation of the class using the new class loader,
+ // and add it to this test suite.
+ String sep = System.getProperty("file.separator");
+ // Separator for jar entries is "/" even for windows
+ // Adding special case for now.
+ // What's used needs checking for Macs
+ if (System.getProperty("os.name").toLowerCase().contains("windows")) {
+ sep = "/";
+ }
+
+ for (int i = 0; i < testNames.size(); i++) {
+ String testname = (String) testNames.get(i);
+ testname = testname.replace(sep.charAt(0), '.');
+
+ Class c = urlLoader.loadClass(testname);
+ suite.addTest(new TestSuite(c));
+ System.out.println("loading class " + testname);
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ return suite;
+ }
+ */
+
+ /**
+ * Conditionally output a message to System.out.
+ * If we are running All Tests, messages will not be shown.
+ * Otherwise, messages will be shown.
+ * @param msg Message to output.
+ */
+ public static void standardOut(String msg) {
+ String runAllTests = System.getProperty(AllTests.TEST_ALL);
+
+ if (runAllTests == null) {
+ System.out.println(msg);
+ }
+ }
+
+ /**
+ * Is the JUNIT_TEST_ALL Property Set?
+ * @return true or false.
+ */
+ public static boolean runAllTests() {
+ String runAllTestProperty = System.getProperty(AllTests.TEST_ALL);
+
+ if (runAllTestProperty == null) {
+ return false;
+ } else {
+ return true;
+ }
+ }
+}
diff --git a/application/src/test/java/cytoscape/BugGetCyNodeTest.java b/application/src/test/java/cytoscape/BugGetCyNodeTest.java
new file mode 100644
index 0000000..0d2f233
--- /dev/null
+++ b/application/src/test/java/cytoscape/BugGetCyNodeTest.java
@@ -0,0 +1,70 @@
+/* -*-Java-*-
+********************************************************************************
+*
+* File: BugGetCyNodeTest.java
+* RCS: $Header: $
+* Description:
+* Author: Michael L. Creech
+* Created: Sun Aug 20 05:50:29 2006
+* Modified: Tue Aug 22 12:40:46 2006 (Michael L. Creech) creech at w235krbza760
+* Language: Java
+* Package:
+* Status: Experimental (Do Not Distribute)
+*
+* (c) Copyright 2006, Agilent Technologies, all rights reserved.
+*
+********************************************************************************
+*/
+package cytoscape;
+
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+
+import junit.framework.Assert;
+import junit.framework.Test;
+import junit.framework.TestCase;
+import junit.framework.TestSuite;
+
+
+/**
+ * Demonstrate bug when using Cyotscape.getCyNode() when Node has been removed.
+ * The real problem seems to be in CytoscapeFingRootGraph.getNode()
+ * @author Michael L. Creech
+ * @version 1.0
+ */
+public class BugGetCyNodeTest extends TestCase {
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static Test suite() {
+ // Will dynamically add all methods as tests that begin with 'test'
+ // and have no arguments:
+ return new TestSuite(BugGetCyNodeTest.class);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ */
+ public static void main(String[] args) {
+ junit.textui.TestRunner.run(suite());
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testBug() {
+ CyNode S = Cytoscape.getCyNode("S", true);
+ String sid = S.getIdentifier();
+ CyNetwork net1 = Cytoscape.createNetwork("net1");
+ net1.restoreNode(S);
+ Cytoscape.getRootGraph().removeNode(S);
+ // The following gets a NullPointerException:
+ System.out.println("BugGetCyNodeTest sid " + sid);
+ Assert.assertNull(Cytoscape.getCyNode(sid, false));
+ }
+}
diff --git a/application/src/test/java/cytoscape/BugHideNodeEventFiringTest.java b/application/src/test/java/cytoscape/BugHideNodeEventFiringTest.java
new file mode 100644
index 0000000..d562491
--- /dev/null
+++ b/application/src/test/java/cytoscape/BugHideNodeEventFiringTest.java
@@ -0,0 +1,111 @@
+/* -*-Java-*-
+********************************************************************************
+*
+* File: BugHideNodeEventFiringTest.java
+* RCS: $Header: $
+* Description:
+* Author: Michael L. Creech
+* Created: Sat Dec 02 07:38:10 2006
+* Modified: Sat Dec 02 08:22:57 2006 (Michael L. Creech) creech at w235krbza760
+* Language: Java
+* Package:
+* Status: Experimental (Do Not Distribute)
+*
+* (c) Copyright 2006, Agilent Technologies, all rights reserved.
+*
+********************************************************************************
+*/
+package cytoscape;
+
+import cytoscape.CyEdge;
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+
+import cytoscape.data.Semantics;
+
+import giny.model.GraphPerspectiveChangeEvent;
+import giny.model.GraphPerspectiveChangeListener;
+
+import junit.framework.Assert;
+import junit.framework.Test;
+import junit.framework.TestCase;
+import junit.framework.TestSuite;
+
+
+/**
+ * Ensure that CyNetwork.hideNode() [GraphPerspective.hideNode()] calls
+ * GraphPerspectiveChangeEvent for the node being hidden BEFORE the callbacks
+ * for the edges hidden (associated with that node).
+ * @author Michael L. Creech
+ * @version 1.0
+ */
+public class BugHideNodeEventFiringTest extends TestCase implements GraphPerspectiveChangeListener {
+ private boolean _edgeHiddenCallback;
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static Test suite() {
+ // Will dynamically add all methods as tests that begin with 'test'
+ // and have no arguments:
+ return new TestSuite(BugHideNodeEventFiringTest.class);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ */
+ public static void main(String[] args) {
+ junit.textui.TestRunner.run(suite());
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testBug() {
+ // setup CN1-->S in CyNetwork net:
+ CyNode CN1 = Cytoscape.getCyNode("CN1", true);
+ CyNode S = Cytoscape.getCyNode("S", true);
+ CyEdge e1 = Cytoscape.getCyEdge(CN1, S, Semantics.INTERACTION, "testInteraction", true, true);
+ CyNetwork net = Cytoscape.createNetwork("net", false);
+ net.restoreNode(CN1);
+ net.restoreNode(S);
+ net.restoreEdge(e1);
+ net.addGraphPerspectiveChangeListener(this);
+ _edgeHiddenCallback = false;
+ // The following will remove e1 before specifying that CN1 is being
+ // hidden!:
+ net.hideNode(CN1);
+ net.removeGraphPerspectiveChangeListener(this);
+ }
+
+ // implements GraphPerspectiveChangeListener:
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void graphPerspectiveChanged(GraphPerspectiveChangeEvent e) {
+ if (e.isNodesHiddenType()) {
+ int[] hiddenNodes = e.getHiddenNodeIndices();
+
+ if (hiddenNodes != null) {
+ if (_edgeHiddenCallback) {
+ Assert.fail("We received hidden edge event callback BEFORE hidden node event callback!");
+ }
+ }
+ }
+
+ if (e.isEdgesHiddenType()) {
+ int[] hiddenEdges = e.getHiddenEdgeIndices();
+
+ if (hiddenEdges != null) {
+ _edgeHiddenCallback = true;
+ }
+ }
+ }
+}
diff --git a/application/src/test/java/cytoscape/BugTest1.java b/application/src/test/java/cytoscape/BugTest1.java
new file mode 100644
index 0000000..ab891a1
--- /dev/null
+++ b/application/src/test/java/cytoscape/BugTest1.java
@@ -0,0 +1,102 @@
+/*
+ File: BugTest1.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape;
+
+import cytoscape.Cytoscape;
+
+import giny.model.Edge;
+import giny.model.Node;
+
+import junit.framework.Assert;
+import junit.framework.Test;
+import junit.framework.TestCase;
+import junit.framework.TestSuite;
+
+
+/**
+ *
+ */
+public class BugTest1 extends TestCase {
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static Test suite() {
+ // Will dynamically add all methods as tests that begin with 'test'
+ // and have no arguments:
+ return new TestSuite(BugTest1.class);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ */
+ public static void main(String[] args) {
+ junit.textui.TestRunner.run(suite());
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testBug() {
+ Node n1 = Cytoscape.getCyNode("S", true);
+ Node n2 = Cytoscape.getCyNode("M", true);
+ Node n3 = Cytoscape.getCyNode("A", true);
+ Node n4 = Cytoscape.getCyNode("Z", true);
+
+ Cytoscape.getRootGraph().createEdge(n1, n2, false); // S-M
+
+ int edge_idx = Cytoscape.getRootGraph().createEdge(n1, n3, false); // S-A
+ Edge del1 = Cytoscape.getRootGraph().getEdge(edge_idx);
+ edge_idx = Cytoscape.getRootGraph().createEdge(n2, n3, false); // M-A
+
+ Edge del2 = Cytoscape.getRootGraph().getEdge(edge_idx);
+ // Now delete S-A & M-A:
+ Cytoscape.getRootGraph().removeEdge(del1);
+ Cytoscape.getRootGraph().removeEdge(del2);
+ edge_idx = Cytoscape.getRootGraph().createEdge(n1, n4, false);
+
+ // ****** THIS SUBEDGE RETURNED HAS A NULL SOURCE AND TARGET!!: *****
+ Edge subedge = Cytoscape.getRootGraph().getEdge(edge_idx);
+ Node src = subedge.getSource();
+ Node target = subedge.getTarget();
+ Assert.assertNotNull(src); // null!
+ Assert.assertNotNull(target); // null!
+ }
+}
diff --git a/application/src/test/java/cytoscape/CoreSuite.java b/application/src/test/java/cytoscape/CoreSuite.java
new file mode 100644
index 0000000..b76fe4f
--- /dev/null
+++ b/application/src/test/java/cytoscape/CoreSuite.java
@@ -0,0 +1,63 @@
+/*
+ File: CoreSuite.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape;
+
+import junit.framework.Test;
+import junit.framework.TestCase;
+import junit.framework.TestCase;
+import junit.framework.TestSuite;
+
+
+/**
+ * Suite of all Core JUnit Tests.
+ *
+ * @author Ethan Cerami
+ */
+public class CoreSuite extends TestCase {
+ /**
+ * The suite method runs all the tests.
+ * @return Suite of JUnit tests.
+ */
+ public static Test suite() {
+ TestSuite suite = new TestSuite();
+ //suite.addTestSuite(CytoscapeConfigTest.class);
+ //suite.addTestSuite(PluginLoaderTest.class);
+ suite.setName("Core Cytoscape Tests");
+
+ return suite;
+ }
+}
diff --git a/application/src/test/java/cytoscape/CyNodeTest.java b/application/src/test/java/cytoscape/CyNodeTest.java
new file mode 100644
index 0000000..8a18e7c
--- /dev/null
+++ b/application/src/test/java/cytoscape/CyNodeTest.java
@@ -0,0 +1,143 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+
+import junit.framework.TestCase;
+
+
+/**
+ *
+ */
+public class CyNodeTest extends TestCase {
+ CyNetwork cytoNetwork;
+ String title;
+ int nodeCount;
+ int edgeCount;
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void setUp() throws Exception {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void tearDown() throws Exception {
+ }
+
+
+ public void testSetNestedNetwork_before() throws Exception {
+ CyNode node = Cytoscape.getCyNode("a", true);
+ assertNull(node.getNestedNetwork());
+
+ // Before the setNestedNetwork() is called from the CyNode
+ // There should be no NodeAttribute "nested.network.name" and NetworkAttribute "parent.node.name.list"
+ cytoscape.data.CyAttributes nodeAttrs = Cytoscape.getNodeAttributes();
+ String[] nodeAttriNames = nodeAttrs.getAttributeNames();
+
+ boolean found_node_attribute = false;
+ for (int i=0; i<nodeAttriNames.length; i++){
+ if (nodeAttriNames[i].equals("nested.network.name")){
+ found_node_attribute = true;
+ break;
+ }
+ }
+
+ cytoscape.data.CyAttributes networkAttrs = Cytoscape.getNetworkAttributes();
+ String[] networkAttriNames = networkAttrs.getAttributeNames();
+ boolean found_network_attribute = false;
+ for (int i=0; i<networkAttriNames.length; i++){
+ if (networkAttriNames[i].equals("parent.node.name.list")){
+ found_network_attribute = true;
+ break;
+ }
+ }
+
+ assertFalse(found_node_attribute);
+ assertFalse(found_network_attribute);
+ }
+
+
+ public void testSetNestedNetwork_after() throws Exception {
+ // Create a network with 2 nodes
+ CyNetwork network = Cytoscape.createNetwork("Test title", false);
+ CyNode node1_in_nestedNetwork = Cytoscape.getCyNode("node1", true);
+ CyNode node2_in_nestedNetwork = Cytoscape.getCyNode("node2", true);
+ network.addNode(node1_in_nestedNetwork);
+ network.addNode(node2_in_nestedNetwork);
+
+ // Create a CyNode
+ CyNode node = Cytoscape.getCyNode("a", true);
+
+ // Set nestedNetwork for newly created node
+ node.setNestedNetwork(network);
+
+ // After the setNestedNetwork() is called from the CyNode
+ // There should be NodeAttribute "nested_network_id" and NetworkAttribute "parent_nodes"
+ cytoscape.data.CyAttributes nodeAttrs = Cytoscape.getNodeAttributes();
+ String[] nodeAttriNames = nodeAttrs.getAttributeNames();
+
+ cytoscape.data.CyAttributes networkAttrs = Cytoscape.getNetworkAttributes();
+ String[] networkAttriNames = networkAttrs.getAttributeNames();
+
+ boolean found_node_attribute = false;
+ boolean found_network_attribute = false;
+
+ for (int i=0; i<nodeAttriNames.length; i++){
+ if (nodeAttriNames[i].equals("nested_network_id")){
+ found_node_attribute = true;
+ break;
+ }
+ }
+
+ for (int i=0; i<networkAttriNames.length; i++){
+ if (networkAttriNames[i].equals("parent_nodes")){
+ found_network_attribute = true;
+ break;
+ }
+ }
+
+ assertTrue(found_node_attribute);
+ assertTrue(found_network_attribute);
+ }
+}
diff --git a/application/src/test/java/cytoscape/CytoscapeTest.java b/application/src/test/java/cytoscape/CytoscapeTest.java
new file mode 100644
index 0000000..cad9ced
--- /dev/null
+++ b/application/src/test/java/cytoscape/CytoscapeTest.java
@@ -0,0 +1,288 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape;
+
+import cytoscape.CyEdge;
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+
+import cytoscape.data.ImportHandler;
+import cytoscape.data.Semantics;
+
+import giny.model.Edge;
+import giny.model.Node;
+
+import junit.framework.TestCase;
+
+import java.io.IOException;
+
+import java.util.*;
+
+
+/**
+ *
+ */
+public class CytoscapeTest extends TestCase {
+ CyNetwork cytoNetwork;
+ String title;
+ int nodeCount;
+ int edgeCount;
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void setUp() throws Exception {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void tearDown() throws Exception {
+ cytoNetwork = null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testGetImportHandler() throws Exception {
+ ImportHandler importHandler = Cytoscape.getImportHandler();
+ assertEquals(importHandler.getClass(), ImportHandler.class);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testNullNetwork() throws Exception {
+ cytoNetwork = Cytoscape.getNullNetwork();
+
+ title = cytoNetwork.getTitle();
+ assertEquals("0", title);
+
+ nodeCount = cytoNetwork.getNodeCount();
+ assertEquals(0, nodeCount);
+
+ edgeCount = cytoNetwork.getEdgeCount();
+ assertEquals(0, edgeCount);
+ }
+
+ //try creating a network
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testCreateNonexistentNetwork() throws Exception {
+ try {
+ cytoNetwork = Cytoscape.createNetworkFromFile("nonexistentNetwork");
+ } catch (Exception e) {
+ System.out.println("this is the expected exception");
+ e.printStackTrace();
+ assertEquals(1, 1);
+
+ return;
+ }
+
+ fail("Did not catch expected exception");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws IOException DOCUMENT ME!
+ */
+ public void testBug839() throws IOException {
+ Set<String> nodes = new HashSet<String>();
+ nodes.add("n1");
+ nodes.add("n2");
+ nodes.add("n3");
+ nodes.add("n4");
+ nodes.add("n5");
+
+ cytoNetwork = Cytoscape.createNetworkFromFile("src/test/resources/testData/bug_839.sif");
+
+ // check that all nodes exist
+ Iterator it = cytoNetwork.nodesIterator();
+
+ while (it.hasNext()) {
+ Node n = (Node) it.next();
+ assertTrue("checking node " + n.getIdentifier(), nodes.contains(n.getIdentifier()));
+ }
+
+ Set<String> edges = new HashSet<String>();
+ edges.add(CyEdge.createIdentifier("n1", "activates", "n2"));
+ edges.add(CyEdge.createIdentifier("n1", "activates", "n4"));
+ edges.add(CyEdge.createIdentifier("n1", "activates", "n5"));
+ edges.add(CyEdge.createIdentifier("n2", "activates", "n1"));
+ edges.add(CyEdge.createIdentifier("n2", "activates", "n5"));
+ edges.add(CyEdge.createIdentifier("n3", "inhibits", "n3"));
+ edges.add(CyEdge.createIdentifier("n3", "inhibits", "n4"));
+ edges.add(CyEdge.createIdentifier("n3", "inhibits", "n5"));
+ edges.add(CyEdge.createIdentifier("n4", "activates", "n1"));
+ edges.add(CyEdge.createIdentifier("n4", "activates", "n2"));
+ edges.add(CyEdge.createIdentifier("n4", "activates", "n4"));
+ edges.add(CyEdge.createIdentifier("n5", "activates", "n1"));
+ edges.add(CyEdge.createIdentifier("n5", "activates", "n4"));
+ edges.add(CyEdge.createIdentifier("n5", "activates", "n5"));
+
+ it = cytoNetwork.edgesIterator();
+
+ while (it.hasNext()) {
+ Edge e = (Edge) it.next();
+ assertTrue("checking edge " + e.getIdentifier(), edges.contains(e.getIdentifier()));
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws IOException DOCUMENT ME!
+ */
+ public void testgetCyEdgeWithStrings() throws IOException {
+ cytoNetwork = Cytoscape.createNetworkFromFile("src/test/resources/testData/directedGraph.sif");
+
+ assertEquals(2, cytoNetwork.getNodeCount());
+ assertEquals(4, cytoNetwork.getEdgeCount());
+
+ String en1 = CyEdge.createIdentifier("a", "pp", "b");
+
+ // edge should exist in network already
+ CyEdge ce1 = Cytoscape.getCyEdge("a", en1, "b", "pp");
+ assertNotNull(ce1);
+
+ CyEdge ce1_again = Cytoscape.getCyEdge("a", en1, "b", "pp");
+ assertTrue(ce1 == ce1_again);
+
+ // edge should be created
+ String en2 = CyEdge.createIdentifier("a", "xx", "b");
+ CyEdge ce2 = Cytoscape.getCyEdge("a", en2, "b", "pp");
+ assertNotNull(ce2);
+
+ // should create a different edge because of directedness
+ String en3 = CyEdge.createIdentifier("b", "pp", "a");
+ CyEdge ce3 = Cytoscape.getCyEdge("b", en3, "a", "pp");
+ assertTrue(ce1 != ce3);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws IOException DOCUMENT ME!
+ */
+ public void testgetCyEdgeWithNodes() throws IOException {
+ cytoNetwork = Cytoscape.createNetworkFromFile("src/test/resources/testData/directedGraph.sif");
+
+ Node a = Cytoscape.getCyNode("a");
+ Node b = Cytoscape.getCyNode("b");
+ Node c = Cytoscape.getCyNode("c", true);
+ String attr = Semantics.INTERACTION;
+
+ // test directed edges
+ assertNotNull(Cytoscape.getCyEdge(a, b, attr, "pp", false, true));
+ assertNotNull(Cytoscape.getCyEdge(b, a, attr, "pp", false, true));
+ assertNotNull(Cytoscape.getCyEdge(a, a, attr, "pp", false, true));
+ assertNotNull(Cytoscape.getCyEdge(a, a, attr, "pp", false, true));
+ assertNotNull(Cytoscape.getCyEdge(a, b, attr, "pd", false, true));
+ assertNull(Cytoscape.getCyEdge(b, a, attr, "pd", false, true));
+
+ // test undirectedness
+ assertNotNull(Cytoscape.getCyEdge(b, a, attr, "pd", false, false));
+
+ // test non-existent edge
+ assertNull(Cytoscape.getCyEdge(a, c, attr, "pp", false, true));
+
+ // test bad attr_value
+ assertNull(Cytoscape.getCyEdge(a, b, attr, "xx", false, true));
+
+ // test create node
+ assertNotNull(Cytoscape.getCyEdge(a, c, attr, "pd", true, true));
+
+ // make sure we got the node we created
+ assertNotNull(Cytoscape.getCyEdge(a, c, attr, "pd", false, true));
+ }
+
+ public void testGetCyEdgeWithBadNodeStrings() throws Exception {
+ cytoNetwork = Cytoscape.createNetworkFromFile("src/test/resources/testData/directedGraph.sif");
+ final int numEdges = Cytoscape.getRootGraph().getEdgeCount();
+ final int numNodes = Cytoscape.getRootGraph().getNodeCount();
+
+ // valid source, target, interaction, should create a new edge
+ CyEdge e1 = Cytoscape.getCyEdge("a", "missing edge name" , "b", "asdfasdf");
+ assertEquals( e1.getIdentifier(), "a (asdfasdf) b" );
+ assertEquals( numEdges + 1, Cytoscape.getRootGraph().getEdgeCount() );
+ assertEquals( numNodes, Cytoscape.getRootGraph().getNodeCount() );
+
+ // non-existant source, valid target, interaction, should add new node and new edge
+ CyEdge e2 = Cytoscape.getCyEdge("missing source", "missing edge name" , "b", "zz");
+ assertEquals( e2.getIdentifier(), "missing source (zz) b" );
+ assertEquals( numEdges + 2, Cytoscape.getRootGraph().getEdgeCount() );
+ assertEquals( numNodes + 1, Cytoscape.getRootGraph().getNodeCount() );
+
+ // valid source, non-existant target, interaction, should add new node and new edge
+ CyEdge e3 = Cytoscape.getCyEdge("a", "missing edge name" , "missing target", "zz");
+ assertEquals( e3.getIdentifier(), "a (zz) missing target" );
+ assertEquals( numEdges + 3, Cytoscape.getRootGraph().getEdgeCount() );
+ assertEquals( numNodes + 2, Cytoscape.getRootGraph().getNodeCount() );
+
+ // null source, valid target, interaction, should return null
+ CyEdge e4 = Cytoscape.getCyEdge(null, "missing edge name" , "b", "zz");
+ assertNull( e4 );
+
+ // valid source, null target, interaction, should return null
+ CyEdge e5 = Cytoscape.getCyEdge("a", "missing edge name" , null, "zz");
+ assertNull( e5 );
+
+ // final checks
+ assertEquals( numEdges + 3, Cytoscape.getRootGraph().getEdgeCount() );
+ assertEquals( numNodes + 2, Cytoscape.getRootGraph().getNodeCount() );
+ }
+
+ public void testSetNestedNetworkAndGetNestedNetwork() throws Exception {
+ CyNode node = Cytoscape.getCyNode("nestedNode", true);
+ assertNull(node.getNestedNetwork());
+ CyNetwork network = Cytoscape.createNetwork("nestedTest");
+ node.setNestedNetwork(network);
+ assertEquals(network, node.getNestedNetwork());
+ String id = network.getIdentifier();
+ assertTrue(((CyNetwork)node.getNestedNetwork()).getIdentifier().equals(id));
+ }
+}
diff --git a/application/src/test/java/cytoscape/data/CyAttributesTest.java b/application/src/test/java/cytoscape/data/CyAttributesTest.java
new file mode 100644
index 0000000..c32e341
--- /dev/null
+++ b/application/src/test/java/cytoscape/data/CyAttributesTest.java
@@ -0,0 +1,440 @@
+/*
+ File: CyAttributesTest.java
+
+ Copyright (c) 2006, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.data;
+
+import cytoscape.data.CyAttributes;
+import cytoscape.data.CyAttributesImpl;
+
+import org.cytoscape.equations.EqnCompiler;
+
+import junit.framework.TestCase;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+
+/**
+ * Tests Implementation of CyAttributes.
+ *
+ */
+public class CyAttributesTest extends TestCase {
+ private CyAttributes cyAttributes;
+ private static final String DUMMY_ID = "id_123";
+ private static final String DUMMY_BOOLEAN_ATTRIBUTE = "attribute1";
+ private static final String DUMMY_STRING_ATTRIBUTE = "attribute2";
+ private static final String DUMMY_LIST_ATTRIBUTE = "attribute3";
+ private static final String DUMMY_MAP_ATTRIBUTE = "attribute4";
+
+ /**
+ * Set things up.
+ *
+ * @throws Exception
+ * All Exceptions.
+ */
+ protected void setUp() throws Exception {
+ cyAttributes = new CyAttributesImpl();
+ }
+
+ public void testBug1363() {
+ try {
+ boolean b = cyAttributes.deleteAttribute("non-existent-attribute.asdffdsa");
+ assertFalse(b);
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("deleting non-existent attr shouldn't have caused exception");
+ }
+ }
+
+ /**
+ * Tests Boolean Values.
+ */
+ public void testBooleanValue() {
+ // Verify that attribute does not (yet) exist
+ boolean exists = cyAttributes.hasAttribute(DUMMY_ID, DUMMY_BOOLEAN_ATTRIBUTE);
+ assertEquals(false, exists);
+
+ // Since the attribute does not yet exist, this should be null
+ Boolean value = cyAttributes.getBooleanAttribute(DUMMY_ID, DUMMY_BOOLEAN_ATTRIBUTE);
+ assertEquals(null, value);
+
+ // This should be null too
+ Double value2 = cyAttributes.getDoubleAttribute(DUMMY_ID, DUMMY_BOOLEAN_ATTRIBUTE);
+ assertEquals(null, value2);
+
+ // Try setting an attribute with a null ID; should fail
+ try {
+ cyAttributes.setAttribute(null, DUMMY_BOOLEAN_ATTRIBUTE, new Boolean(true));
+ fail("IllegalArgumentException should have been thrown.");
+ } catch (IllegalArgumentException e) {
+ assertTrue(e != null);
+ }
+
+ // Try setting an attribute with a null attribute name; should fail
+ try {
+ cyAttributes.setAttribute(DUMMY_ID, null, new Boolean(true));
+ fail("IllegalArgumentException should have been thrown.");
+ } catch (IllegalArgumentException e) {
+ assertTrue(e != null);
+ }
+
+ // Set a Boolean Attribute Value; should work
+ cyAttributes.setAttribute(DUMMY_ID, DUMMY_BOOLEAN_ATTRIBUTE, new Boolean(true));
+
+ // Verify that attribute now exists
+ exists = cyAttributes.hasAttribute(DUMMY_ID, DUMMY_BOOLEAN_ATTRIBUTE);
+ assertEquals(true, exists);
+
+ // Verify Type
+ byte type = cyAttributes.getType(DUMMY_BOOLEAN_ATTRIBUTE);
+ assertEquals(CyAttributes.TYPE_BOOLEAN, type);
+
+ // Verify value stored
+ value = cyAttributes.getBooleanAttribute(DUMMY_ID, DUMMY_BOOLEAN_ATTRIBUTE);
+ assertEquals(true, value.booleanValue());
+
+ // Try getting it as an Integer value; this should trigger
+ // a ClassCastException.
+ try {
+ Integer valueInt = cyAttributes.getIntegerAttribute(DUMMY_ID, DUMMY_BOOLEAN_ATTRIBUTE);
+ fail("ClassCastException should have been thrown.");
+ } catch (ClassCastException e) {
+ assertTrue(e != null);
+ }
+
+ // Try setting an integer value; this should trigger an
+ // IllegalArgumentException
+ try {
+ cyAttributes.setAttribute(DUMMY_ID, DUMMY_BOOLEAN_ATTRIBUTE, new Integer(5));
+ fail("IllegalArgumentException should have been thrown.");
+ } catch (IllegalArgumentException e) {
+ assertTrue(e != null);
+ }
+
+ // Check out the attribute names
+ String[] attribs = cyAttributes.getAttributeNames();
+ assertEquals(1, attribs.length);
+ assertEquals(DUMMY_BOOLEAN_ATTRIBUTE, attribs[0]);
+
+ // Now delete the attribute
+ boolean success = cyAttributes.deleteAttribute(DUMMY_ID, DUMMY_BOOLEAN_ATTRIBUTE);
+ assertEquals(true, success);
+
+ // Verify that attribute no longer exists, but that its type remains
+ exists = cyAttributes.hasAttribute(DUMMY_ID, DUMMY_BOOLEAN_ATTRIBUTE);
+ assertEquals(false, exists);
+ type = cyAttributes.getType(DUMMY_BOOLEAN_ATTRIBUTE);
+ assertEquals(CyAttributes.TYPE_BOOLEAN, type);
+ assertEquals(CyAttributes.TYPE_BOOLEAN, type);
+
+ // Now try deleting all attributes of this name
+ success = cyAttributes.deleteAttribute(DUMMY_BOOLEAN_ATTRIBUTE);
+
+ // Verify that type is now TYPE_UNDEFINED
+ type = cyAttributes.getType(DUMMY_BOOLEAN_ATTRIBUTE);
+ assertEquals(CyAttributes.TYPE_UNDEFINED, type);
+ }
+
+ /**
+ * Tests String Values.
+ */
+ public void testStringValue() {
+ // Verify that attribute does not (yet) exist
+ boolean exists = cyAttributes.hasAttribute(DUMMY_ID, DUMMY_STRING_ATTRIBUTE);
+ assertEquals(false, exists);
+
+ // Set a String Attribute Value
+ cyAttributes.setAttribute(DUMMY_ID, DUMMY_STRING_ATTRIBUTE, new String("Cytoscape"));
+
+ // Verify that attribute now exists
+ exists = cyAttributes.hasAttribute(DUMMY_ID, DUMMY_STRING_ATTRIBUTE);
+ assertEquals(true, exists);
+
+ // Verify Type
+ byte type = cyAttributes.getType(DUMMY_STRING_ATTRIBUTE);
+ assertEquals(CyAttributes.TYPE_STRING, type);
+
+ // Verify value stored
+ String value = cyAttributes.getStringAttribute(DUMMY_ID, DUMMY_STRING_ATTRIBUTE);
+ assertEquals("Cytoscape", value);
+
+ // Try getting it as an Integer value; this should trigger
+ // a ClassCastException.
+ try {
+ Integer valueInt = cyAttributes.getIntegerAttribute(DUMMY_ID, DUMMY_STRING_ATTRIBUTE);
+ fail("ClassCastException should have been thrown.");
+ } catch (ClassCastException e) {
+ assertTrue(e != null);
+ }
+
+ // Try setting an integer value; this should trigger an
+ // IllegalArgumentException
+ try {
+ cyAttributes.setAttribute(DUMMY_ID, DUMMY_STRING_ATTRIBUTE, new Integer(5));
+ fail("IllegalArgumentException should have been thrown.");
+ } catch (IllegalArgumentException e) {
+ assertTrue(e != null);
+ }
+
+ // Check out the attribute names
+ String[] attribs = cyAttributes.getAttributeNames();
+ assertEquals(1, attribs.length);
+ assertEquals(DUMMY_STRING_ATTRIBUTE, attribs[0]);
+ }
+
+ /**
+ * Tests Simple Lists.
+ */
+ public void testSimpleLists() {
+ // First, try setting a not-so simple list
+ List list = new ArrayList();
+ list.add(new Integer(5));
+ list.add(new String("Cytoscape"));
+
+ // Try setting the list as null; this should fail
+ try {
+ cyAttributes.setListAttribute(DUMMY_ID, DUMMY_LIST_ATTRIBUTE, (List)null);
+ fail("IllegalArgumentException should have been thrown.");
+ } catch (IllegalArgumentException e) {
+ assertTrue(e != null);
+ }
+
+ // Try setting the list; this should fail b/c we have mixed data types
+ try {
+ cyAttributes.setListAttribute(DUMMY_ID, DUMMY_LIST_ATTRIBUTE, list);
+ fail("IllegalArgumentException should have been thrown.");
+ } catch (IllegalArgumentException e) {
+ assertTrue(e != null);
+ }
+
+ // Try again with a valid list
+ list = new ArrayList();
+ list.add(new Integer(5));
+ list.add(new Integer(6));
+ cyAttributes.setListAttribute(DUMMY_ID, DUMMY_LIST_ATTRIBUTE, list);
+
+ // Verify type
+ byte type = cyAttributes.getType(DUMMY_LIST_ATTRIBUTE);
+ assertEquals(type, CyAttributes.TYPE_SIMPLE_LIST);
+
+ // Verify value exists
+ boolean exists = cyAttributes.hasAttribute(DUMMY_ID, DUMMY_LIST_ATTRIBUTE);
+ assertEquals(true, exists);
+
+ // Get Stored value as a Simple Map; this should fail
+ try {
+ Map map = cyAttributes.getMapAttribute(DUMMY_ID, DUMMY_LIST_ATTRIBUTE);
+ fail("ClassCastException should have been thrown.");
+ } catch (ClassCastException e) {
+ assertTrue(e != null);
+ }
+
+ // Get the list back, and verify its contents
+ List storedList = cyAttributes.getListAttribute(DUMMY_ID, DUMMY_LIST_ATTRIBUTE);
+ assertEquals(2, storedList.size());
+
+ Integer int0 = (Integer) storedList.get(0);
+ Integer int1 = (Integer) storedList.get(1);
+ assertEquals(5, int0.intValue());
+ assertEquals(6, int1.intValue());
+
+ // Try storing an Empty List; previously, this resulted in
+ // a NoSuchElementException.
+ list = new ArrayList();
+ cyAttributes.setListAttribute(DUMMY_ID, DUMMY_LIST_ATTRIBUTE, list);
+ }
+
+ /**
+ * Tests Simple Maps.
+ */
+ public void testSimpleMaps() {
+ // First, try setting a not-so simple map
+ // The following map is considered invalid because all keys must
+ // be of type String.
+ Map map = new HashMap();
+ map.put(new Integer(1), new String("One"));
+ map.put(new Integer(2), new String("Two"));
+
+ // This should fail, b/c of invalid keys
+ try {
+ cyAttributes.setMapAttribute(DUMMY_ID, DUMMY_MAP_ATTRIBUTE, map);
+ fail("IllegalArgumentException should have been thrown.");
+ } catch (IllegalArgumentException e) {
+ assertTrue(e != null);
+ }
+
+ // Now, try another invalid map. This map is invalid because the
+ // values are not all of one type
+ map = new HashMap();
+ map.put(new String("first"), new String("One"));
+ map.put(new String("second"), new Integer(2));
+
+ // This should fail too, b/c of invalid values
+ try {
+ cyAttributes.setMapAttribute(DUMMY_ID, DUMMY_MAP_ATTRIBUTE, map);
+ fail("IllegalArgumentException should have been thrown.");
+ } catch (IllegalArgumentException e) {
+ assertTrue(e != null);
+ }
+
+ // Now, try a valid map
+ map = new HashMap();
+ map.put(new String("first"), new Integer(1));
+ map.put(new String("second"), new Integer(2));
+ cyAttributes.setMapAttribute(DUMMY_ID, DUMMY_MAP_ATTRIBUTE, map);
+
+ // Verify type
+ byte type = cyAttributes.getType(DUMMY_MAP_ATTRIBUTE);
+ assertEquals(CyAttributes.TYPE_SIMPLE_MAP, type);
+
+ // Get Stored value as a Simple List; this should fail
+ try {
+ List list = cyAttributes.getListAttribute(DUMMY_ID, DUMMY_MAP_ATTRIBUTE);
+ fail("ClassCastException should have been thrown.");
+ } catch (ClassCastException e) {
+ assertTrue(e != null);
+ }
+
+ // Get map back, and verify contents
+ Map storedMap = cyAttributes.getMapAttribute(DUMMY_ID, DUMMY_MAP_ATTRIBUTE);
+ assertEquals(2, storedMap.keySet().size());
+
+ Set keySet = storedMap.keySet();
+
+ assertTrue(keySet.contains("first"));
+ assertEquals(1, storedMap.get("first"));
+ assertTrue(keySet.contains("second"));
+ assertEquals(2, storedMap.get("second"));
+
+ // Try storing an Empty Map; previously, this resulted in
+ // a NoSuchElementException.
+ map = new HashMap();
+ cyAttributes.setMapAttribute(DUMMY_ID, DUMMY_LIST_ATTRIBUTE, map);
+ }
+
+ /**
+ * Tests attribute descriptions.
+ */
+ public void testAttributeDescriptions() {
+ // Try setting an attribute description, and verify that you can
+ // get it back.
+ cyAttributes.setAttributeDescription("attribute1", "sample description");
+
+ String description = cyAttributes.getAttributeDescription("attribute1");
+ assertEquals("sample description", description);
+
+ // Try getting an attribute description for an unknown attribute
+ // verify that return value is null
+ assertEquals(null, cyAttributes.getAttributeDescription("attribute2"));
+ }
+
+ /**
+ * Tests user interaction flags.
+ */
+ public void testUserInteractionFlags() {
+ String sampleAttribute = "attribute1";
+
+ // Test that defaults are working. By default, attributes should
+ // be visible and editable by the end user.
+ boolean visibleFlag = cyAttributes.getUserVisible(sampleAttribute);
+ assertEquals(true, visibleFlag);
+
+ boolean editableFlag = cyAttributes.getUserVisible(sampleAttribute);
+ assertEquals(true, editableFlag);
+
+ // Try making attribute user invisible
+ cyAttributes.setUserVisible(sampleAttribute, false);
+ visibleFlag = cyAttributes.getUserVisible(sampleAttribute);
+ assertEquals(false, visibleFlag);
+
+ // Switch back to user visible
+ cyAttributes.setUserVisible(sampleAttribute, true);
+ visibleFlag = cyAttributes.getUserVisible(sampleAttribute);
+ assertEquals(true, visibleFlag);
+
+ // Try making attribute user non-editable
+ cyAttributes.setUserEditable(sampleAttribute, false);
+ editableFlag = cyAttributes.getUserEditable(sampleAttribute);
+ assertEquals(false, editableFlag);
+
+ // Switch back to user editable
+ cyAttributes.setUserEditable(sampleAttribute, true);
+ editableFlag = cyAttributes.getUserEditable(sampleAttribute);
+ assertEquals(true, editableFlag);
+ }
+
+ public void testGetLastEquationError() {
+ final EqnCompiler compiler = new EqnCompiler();
+ final Map<String, Class> attribNameToTypeMap = new HashMap<String, Class>();
+
+ // First a case that should result in an error message...
+ assertTrue(compiler.compile("=1/0", attribNameToTypeMap));
+ cyAttributes.setAttribute(DUMMY_ID, DUMMY_BOOLEAN_ATTRIBUTE, compiler.getEquation());
+ assertNull(cyAttributes.getAttribute(DUMMY_ID, DUMMY_BOOLEAN_ATTRIBUTE));
+ assertNotNull(cyAttributes.getLastEquationError());
+
+ // ...and now a case that should not result in an error message.
+ assertTrue(compiler.compile("=1/1", attribNameToTypeMap));
+ cyAttributes.setAttribute(DUMMY_ID, DUMMY_BOOLEAN_ATTRIBUTE, compiler.getEquation());
+ assertNotNull(cyAttributes.getAttribute(DUMMY_ID, DUMMY_BOOLEAN_ATTRIBUTE));
+ assertNull(cyAttributes.getLastEquationError());
+ }
+
+ public void testGetListElementType() {
+ final List<Integer> iList = new ArrayList<Integer>();
+ iList.add(2);
+ cyAttributes.setListAttribute("ID", "ilist", iList);
+ assertEquals(CyAttributes.TYPE_INTEGER, cyAttributes.getListElementType("ilist"));
+
+ final List<Double> fList = new ArrayList<Double>();
+ fList.add(2.5);
+ cyAttributes.setListAttribute("ID", "flist", fList);
+ assertEquals(CyAttributes.TYPE_FLOATING, cyAttributes.getListElementType("flist"));
+
+ final List<String> sList = new ArrayList<String>();
+ sList.add("xyz");
+ cyAttributes.setListAttribute("ID", "slist", sList);
+ assertEquals(CyAttributes.TYPE_STRING, cyAttributes.getListElementType("slist"));
+
+ final List<Boolean> bList = new ArrayList<Boolean>();
+ bList.add(true);
+ cyAttributes.setListAttribute("ID", "blist", bList);
+ assertEquals(CyAttributes.TYPE_BOOLEAN, cyAttributes.getListElementType("blist"));
+ }
+
+ /**
+ * Runs just this one unit test.
+ */
+ public static void main(String[] args) {
+ junit.textui.TestRunner.run(CyAttributesTest.class);
+ }
+}
diff --git a/application/src/test/java/cytoscape/data/CyAttributesUtilsTest.java b/application/src/test/java/cytoscape/data/CyAttributesUtilsTest.java
new file mode 100644
index 0000000..6951772
--- /dev/null
+++ b/application/src/test/java/cytoscape/data/CyAttributesUtilsTest.java
@@ -0,0 +1,436 @@
+/*
+ File: CyAttributesUtilsTest.java
+
+ Copyright (c) 2006, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data;
+
+import cytoscape.CyEdge;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+
+import cytoscape.data.AttributeFilter;
+import cytoscape.data.AttributeValueVisitor;
+import cytoscape.data.CyAttributes;
+import cytoscape.data.CyAttributesUtils;
+import cytoscape.data.Semantics;
+
+import cytoscape.data.attr.MultiHashMap;
+import cytoscape.data.attr.MultiHashMapDefinition;
+
+import giny.model.GraphObject;
+
+import org.cytoscape.equations.EqnCompiler;
+import org.cytoscape.equations.Equation;
+
+
+import junit.framework.Assert;
+import junit.framework.TestCase;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+
+// package cytoscape.data;
+/**
+ *
+ */
+public class CyAttributesUtilsTest extends TestCase {
+ private CyNode testNode1;
+ private CyNode testNode2;
+ private CyEdge testEdge;
+
+ // track complex p-values:
+ private List<Double> PValues = new ArrayList<Double>();
+ private int numTSIs;
+
+ // track complex TextSourceInfo values:
+ private List<String> TSIValues = new ArrayList<String>();
+ private int numPValues;
+ private boolean initialized = false;
+
+ // public static Test suite() {
+ // // Will dynamically add all methods as tests that begin with 'test'
+ // // and have no arguments:
+ // return new TestSuite(CyAttributesUtilsTest.class);
+ // }
+
+ /**
+ * Runs just this one unit test.
+ */
+ public static void main(String[] args) {
+ junit.textui.TestRunner.run(CyAttributesUtilsTest.class);
+ }
+
+ protected void setUp() {
+ // we only need to do setup once:
+ if (initialized) {
+ return;
+ }
+
+ initialized = true;
+ testNode1 = Cytoscape.getCyNode("testNode1", true);
+ testNode2 = Cytoscape.getCyNode("testNode2", true);
+ testEdge = Cytoscape.getCyEdge(testNode1.getIdentifier(), "Interaction Value",
+ testNode2.getIdentifier(), Semantics.INTERACTION);
+ addAttributes(testNode1);
+ addAttributes(testEdge);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testToString() {
+ CyAttributes attrs = Cytoscape.getNodeAttributes();
+ Assert.assertTrue("BOOLEAN".equals(CyAttributesUtils.toString(attrs.getType("BooleanTest"))));
+ Assert.assertTrue("STRING".equals(CyAttributesUtils.toString(attrs.getType("StringTest"))));
+ Assert.assertTrue("SIMPLE_MAP".equals(CyAttributesUtils.toString(attrs.getType("MapTest"))));
+ Assert.assertTrue("SIMPLE_LIST".equals(CyAttributesUtils.toString(attrs.getType("ListTest"))));
+ Assert.assertTrue("COMPLEX".equals(CyAttributesUtils.toString(attrs.getType("TextSourceInfo"))));
+ Assert.assertTrue("UNDEFINED".equals(CyAttributesUtils.toString(attrs.getType("foo"))));
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testTraverseAttributeValues() {
+ // traverse a simple attribute:
+ CyAttributesUtils.traverseAttributeValues(testNode1.getIdentifier(), "BooleanTest",
+ Cytoscape.getNodeAttributes(),
+ new AttributeValueVisitor() {
+ public void visitingAttributeValue(String objTraversedID, String attrName,
+ CyAttributes attrs, Object[] keySpace,
+ Object visitedValue) {
+ Assert.assertTrue(Boolean.TRUE.equals(visitedValue));
+ }
+ });
+ // traverse a complex attribute TSIs:
+ numTSIs = 0;
+ CyAttributesUtils.traverseAttributeValues(testNode1.getIdentifier(), "TextSourceInfo",
+ Cytoscape.getNodeAttributes(),
+ new AttributeValueVisitor() {
+ public void visitingAttributeValue(String objTraversedID, String attrName,
+ CyAttributes attrs, Object[] keySpace,
+ Object visitedValue) {
+ numTSIs++;
+ Assert.assertTrue(TSIValues.contains(visitedValue));
+ }
+ });
+ Assert.assertTrue(numTSIs == TSIValues.size());
+ // traverse a complex attribute TSIs:
+ numPValues = 0;
+ CyAttributesUtils.traverseAttributeValues(testNode1.getIdentifier(), "p-valuesTest",
+ Cytoscape.getNodeAttributes(),
+ new AttributeValueVisitor() {
+ public void visitingAttributeValue(String objTraversedID, String attrName,
+ CyAttributes attrs, Object[] keySpace,
+ Object visitedValue) {
+ numPValues++;
+ Assert.assertTrue(PValues.contains(visitedValue));
+ }
+ });
+ Assert.assertTrue(numPValues == PValues.size());
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testCopyAttributes() {
+ CyNode copyTestNode1 = Cytoscape.getCyNode("copyTestNode1", true);
+ CyAttributes attrs = Cytoscape.getNodeAttributes();
+ // copy all attributes to copyTestNode1:
+ CyAttributesUtils.copyAttributes(testNode1.getIdentifier(), copyTestNode1.getIdentifier(),
+ attrs, false);
+ testAttributes(copyTestNode1);
+
+ // only copy IntegerTest using restrictive AttributeFilter:
+ CyAttributesUtils.copyAttributes(testNode1.getIdentifier(), "copyAnotherTestNode1", attrs,
+ new AttributeFilter() {
+ public boolean includeAttribute(CyAttributes attrs, String objID, String attrName) {
+ return "IntegerTest".equals(attrName);
+ }
+ }, false);
+
+ Assert.assertTrue(new Integer(6).equals(attrs.getIntegerAttribute("copyAnotherTestNode1",
+ "IntegerTest")));
+
+ List<String> attrNames = CyAttributesUtils.getAttributeNamesForObj("copyAnotherTestNode1",
+ attrs);
+ Assert.assertTrue(attrNames.size() == 1);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testCopyAttribute() {
+ CyNode testNode3 = Cytoscape.getCyNode("testNode3", true);
+ CyEdge testEdgeCopy = Cytoscape.getCyEdge(testNode1.getIdentifier(), "Interaction Value",
+ testNode3.getIdentifier(), Semantics.INTERACTION);
+ CyAttributes attrs = Cytoscape.getEdgeAttributes();
+ // only copy ListTest attribute:
+ CyAttributesUtils.copyAttribute(testEdge.getIdentifier(), testEdgeCopy.getIdentifier(),
+ "ListTest", attrs, false);
+
+ List<String> listVal = attrs.getListAttribute(testEdgeCopy.getIdentifier(), "ListTest");
+ Assert.assertTrue((listVal.size() == 2) && listVal.contains("list test value1")
+ && listVal.contains("list test value2"));
+
+ List<String> attrNames = CyAttributesUtils.getAttributeNamesForObj(testEdgeCopy
+ .getIdentifier(),
+ attrs);
+ // should have 3 attributes: ListTest and Semantics.INTERACTION, and Semantics.CANONICAL_NAME:
+ Assert.assertTrue(attrNames.size() == 3);
+ }
+
+ private void addAttributes(GraphObject go) {
+ String goID = go.getIdentifier();
+ CyAttributes attrs = null;
+
+ if (go instanceof CyNode) {
+ attrs = Cytoscape.getNodeAttributes();
+ } else if (go instanceof CyEdge) {
+ attrs = Cytoscape.getEdgeAttributes();
+ }
+
+ attrs.setAttribute(goID, "BooleanTest", new Boolean(true));
+ attrs.setAttribute(goID, "StringTest", "string test value");
+ attrs.setAttribute(goID, "IntegerTest", new Integer(6));
+ attrs.setAttribute(goID, "DoubleTest", new Double(5.0));
+
+ final Map<String, Class> attribNameToTypeMap = new HashMap<String, Class>();
+ final EqnCompiler compiler = new EqnCompiler();
+ compiler.compile("=ABS(-13) + 12.3", attribNameToTypeMap);
+ final Equation equation = compiler.getEquation();
+ attrs.setAttribute(goID, "EquationTest", equation);
+
+ List<String> listTestValue = new ArrayList<String>();
+ listTestValue.add("list test value1");
+ listTestValue.add("list test value2");
+ attrs.setListAttribute(goID, "ListTest", listTestValue);
+
+ Map<String, String> mapTestValue = new HashMap<String, String>();
+ mapTestValue.put("map key1", "map key1 value");
+ mapTestValue.put("map key2", "map key2 value");
+ attrs.setMapAttribute(goID, "MapTest", mapTestValue);
+
+ // Now add a complex value to test:
+ addComplexAttributes(go, attrs);
+ }
+
+ private void addComplexAttributes(GraphObject go, CyAttributes attrs) {
+ String goID = go.getIdentifier();
+ MultiHashMap mmap = attrs.getMultiHashMap();
+ MultiHashMapDefinition mmapDef = attrs.getMultiHashMapDefinition();
+
+ if (mmapDef.getAttributeValueType("p-valuesTest") < 0) {
+ mmapDef.defineAttribute("p-valuesTest", // most specific values:
+ MultiHashMapDefinition.TYPE_FLOATING_POINT,
+ new byte[] {
+ MultiHashMapDefinition.TYPE_STRING,
+ MultiHashMapDefinition.TYPE_INTEGER
+ });
+ }
+
+ if (mmapDef.getAttributeValueType("TextSourceInfo") < 0) {
+ mmapDef.defineAttribute("TextSourceInfo", // most specific values:
+ MultiHashMapDefinition.TYPE_STRING,
+ new byte[] {
+ MultiHashMapDefinition.TYPE_STRING,
+ MultiHashMapDefinition.TYPE_INTEGER,
+ MultiHashMapDefinition.TYPE_INTEGER
+ });
+ }
+
+ PValues.clear();
+ mmap.setAttributeValue(goID, "p-valuesTest", new Double(0.5),
+ new Object[] { "Jojo", new Integer(0) });
+ PValues.add(new Double(0.5));
+ mmap.setAttributeValue(goID, "p-valuesTest", new Double(0.6),
+ new Object[] { "Jojo", new Integer(1) });
+ PValues.add(new Double(0.6));
+ mmap.setAttributeValue(goID, "p-valuesTest", new Double(0.6),
+ new Object[] { "Jojo", new Integer(2) });
+ PValues.add(new Double(0.6));
+ mmap.setAttributeValue(goID, "p-valuesTest", new Double(0.7),
+ new Object[] { "Harry", new Integer(0) });
+ PValues.add(new Double(0.7));
+ mmap.setAttributeValue(goID, "p-valuesTest", new Double(0.6),
+ new Object[] { "Harry", new Integer(1) });
+ PValues.add(new Double(0.6));
+
+ TSIValues.clear();
+ mmap.setAttributeValue(goID, "TextSourceInfo", "url1: sentence1",
+ new Object[] { "url1", new Integer(0), new Integer(0) });
+ TSIValues.add("url1: sentence1");
+ mmap.setAttributeValue(goID, "TextSourceInfo", "url1: sentence2",
+ new Object[] { "url1", new Integer(0), new Integer(1) });
+ TSIValues.add("url1: sentence2");
+ mmap.setAttributeValue(goID, "TextSourceInfo", "url1: sentence3",
+ new Object[] { "url1", new Integer(0), new Integer(10) });
+ TSIValues.add("url1: sentence3");
+ mmap.setAttributeValue(goID, "TextSourceInfo", "url1: publication 1",
+ new Object[] { "url1", new Integer(1), new Integer(0) });
+ TSIValues.add("url1: publication 1");
+ mmap.setAttributeValue(goID, "TextSourceInfo", "url2: sentence1",
+ new Object[] { "url2", new Integer(0), new Integer(6) });
+ TSIValues.add("url2: sentence1");
+ mmap.setAttributeValue(goID, "TextSourceInfo", "url2: publication 1",
+ new Object[] { "url2", new Integer(1), new Integer(0) });
+ TSIValues.add("url2: publication 1");
+ }
+
+ private void testAttributes(GraphObject go) {
+ String goID = go.getIdentifier();
+ CyAttributes attrs = null;
+
+ if (go instanceof CyNode) {
+ attrs = Cytoscape.getNodeAttributes();
+ } else if (go instanceof CyEdge) {
+ attrs = Cytoscape.getEdgeAttributes();
+ }
+
+ Assert.assertTrue(Boolean.TRUE.equals(attrs.getBooleanAttribute(goID, "BooleanTest")));
+
+ Assert.assertTrue("string test value".equals(attrs.getStringAttribute(goID, "StringTest")));
+ Assert.assertTrue(new Integer(6).equals(attrs.getIntegerAttribute(goID, "IntegerTest")));
+ Assert.assertTrue(new Double(5.0).equals(attrs.getDoubleAttribute(goID, "DoubleTest")));
+
+ List<String> listVal = attrs.getListAttribute(goID, "ListTest");
+ Assert.assertTrue((listVal.size() == 2) && listVal.contains("list test value1")
+ && listVal.contains("list test value2"));
+
+ Map<String, String> mapVal = attrs.getMapAttribute(goID, "MapTest");
+ Assert.assertTrue((mapVal.size() == 2) && "map key1 value".equals(mapVal.get("map key1"))
+ && "map key2 value".equals(mapVal.get("map key2")));
+ testComplexAttributes(goID, attrs);
+ }
+
+ private void testComplexAttributes(String goID, CyAttributes attrs) {
+ MultiHashMap mmap = attrs.getMultiHashMap();
+ Assert.assertTrue(new Double(0.5).equals(mmap.getAttributeValue(goID, "p-valuesTest",
+ new Object[] {
+ "Jojo", new Integer(0)
+ })));
+ Assert.assertTrue(new Double(0.6).equals(mmap.getAttributeValue(goID, "p-valuesTest",
+ new Object[] {
+ "Jojo", new Integer(1)
+ })));
+ Assert.assertTrue(new Double(0.6).equals(mmap.getAttributeValue(goID, "p-valuesTest",
+ new Object[] {
+ "Jojo", new Integer(2)
+ })));
+ Assert.assertTrue(new Double(0.7).equals(mmap.getAttributeValue(goID, "p-valuesTest",
+ new Object[] {
+ "Harry", new Integer(0)
+ })));
+ Assert.assertTrue(new Double(0.6).equals(mmap.getAttributeValue(goID, "p-valuesTest",
+ new Object[] {
+ "Harry", new Integer(1)
+ })));
+
+ Assert.assertTrue("url1: sentence1".equals(mmap.getAttributeValue(goID, "TextSourceInfo",
+ new Object[] {
+ "url1", new Integer(0),
+ new Integer(0)
+ })));
+ Assert.assertTrue("url1: sentence2".equals(mmap.getAttributeValue(goID, "TextSourceInfo",
+ new Object[] {
+ "url1", new Integer(0),
+ new Integer(1)
+ })));
+ Assert.assertTrue("url1: sentence3".equals(mmap.getAttributeValue(goID, "TextSourceInfo",
+ new Object[] {
+ "url1", new Integer(0),
+ new Integer(10)
+ })));
+
+ Assert.assertTrue("url1: publication 1".equals(mmap.getAttributeValue(goID,
+ "TextSourceInfo",
+ new Object[] {
+ "url1",
+ new Integer(1),
+ new Integer(0)
+ })));
+
+ Assert.assertTrue("url2: sentence1".equals(mmap.getAttributeValue(goID, "TextSourceInfo",
+ new Object[] {
+ "url2", new Integer(0),
+ new Integer(6)
+ })));
+ Assert.assertTrue("url2: publication 1".equals(mmap.getAttributeValue(goID,
+ "TextSourceInfo",
+ new Object[] {
+ "url2",
+ new Integer(1),
+ new Integer(0)
+ })));
+ }
+
+ public void testCopyAttribute2() {
+ final CyAttributes attribs = Cytoscape.getNodeAttributes();
+ final String sourceId = "testNode1";
+ final String targetId = "testNode2";
+ final StringBuilder errorMessage = new StringBuilder();
+
+ assertTrue(CyAttributesUtils.copyAttribute(attribs, sourceId, targetId, "BooleanTest",
+ /* copyEquation = */false, errorMessage));
+ assertEquals(attribs.getBooleanAttribute(sourceId, "BooleanTest"),
+ attribs.getBooleanAttribute(targetId, "BooleanTest"));
+
+ assertTrue(CyAttributesUtils.copyAttribute(attribs, sourceId, targetId, "IntegerTest",
+ /* copyEquation = */false, errorMessage));
+ assertEquals(attribs.getIntegerAttribute(sourceId, "IntegerTest"),
+ attribs.getIntegerAttribute(targetId, "IntegerTest"));
+
+ assertTrue(CyAttributesUtils.copyAttribute(attribs, sourceId, targetId, "DoubleTest",
+ /* copyEquation = */false, errorMessage));
+ assertEquals(attribs.getDoubleAttribute(sourceId, "DoubleTest"),
+ attribs.getDoubleAttribute(targetId, "DoubleTest"));
+
+ assertTrue(CyAttributesUtils.copyAttribute(attribs, sourceId, targetId, "StringTest",
+ /* copyEquation = */false, errorMessage));
+ assertEquals(attribs.getStringAttribute(sourceId, "StringTest"),
+ attribs.getStringAttribute(targetId, "StringTest"));
+
+ assertTrue(CyAttributesUtils.copyAttribute(attribs, sourceId, targetId, "ListTest",
+ /* copyEquation = */false, errorMessage));
+ assertEquals(attribs.getListAttribute(sourceId, "ListTest"),
+ attribs.getListAttribute(targetId, "ListTest"));
+
+ assertTrue(CyAttributesUtils.copyAttribute(attribs, sourceId, targetId, "MapTest",
+ /* copyEquation = */false, errorMessage));
+ assertEquals(attribs.getMapAttribute(sourceId, "MapTest"),
+ attribs.getMapAttribute(targetId, "MapTest"));
+
+ assertTrue(CyAttributesUtils.copyAttribute(attribs, sourceId, targetId, "EquationTest",
+ /* copyEquation = */true, errorMessage));
+ assertEquals(attribs.getEquation(sourceId, "EquationTest"),
+ attribs.getEquation(targetId, "EquationTest"));
+ }
+}
diff --git a/application/src/test/java/cytoscape/data/CyNetworkEventTest.java b/application/src/test/java/cytoscape/data/CyNetworkEventTest.java
new file mode 100644
index 0000000..62320c3
--- /dev/null
+++ b/application/src/test/java/cytoscape/data/CyNetworkEventTest.java
@@ -0,0 +1,139 @@
+/*
+ File: CyNetworkEventTest.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+//-------------------------------------------------------------------------
+// $Revision: 9565 $
+// $Date: 2007-02-13 20:36:50 +0100 (Tue, 13 Feb 2007) $
+// $Author: mes $
+//-------------------------------------------------------------------------
+package cytoscape.data;
+
+import cytoscape.*;
+
+//--------------------------------------------------------------------------------------
+import junit.framework.*;
+
+import java.io.*;
+
+import java.util.*;
+
+
+//-----------------------------------------------------------------------------------------
+/**
+ *
+ */
+public class CyNetworkEventTest extends TestCase {
+ //------------------------------------------------------------------------------
+ /**
+ * Creates a new CyNetworkEventTest object.
+ *
+ * @param name DOCUMENT ME!
+ */
+ public CyNetworkEventTest(String name) {
+ super(name);
+ }
+
+ //------------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void setUp() throws Exception {
+ }
+
+ //------------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void tearDown() throws Exception {
+ }
+
+ //------------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testBasic() throws Exception {
+ CyNetwork network = Cytoscape.createNetwork(null);
+
+ //test begin event
+ CyNetworkEvent e0 = new CyNetworkEvent(network, CyNetworkEvent.BEGIN);
+ assertTrue(e0.getNetwork() == network);
+ assertTrue(e0.getType() == CyNetworkEvent.BEGIN);
+
+ //test end event
+ CyNetworkEvent e1 = new CyNetworkEvent(network, CyNetworkEvent.END);
+ assertTrue(e1.getNetwork() == network);
+ assertTrue(e1.getType() == CyNetworkEvent.END);
+
+ //test null network
+ CyNetworkEvent eNull = new CyNetworkEvent(null, CyNetworkEvent.BEGIN);
+ assertTrue(eNull.getNetwork() == null);
+ assertTrue(eNull.getType() == CyNetworkEvent.BEGIN);
+
+ //test graph replaced event
+ CyNetworkEvent e2 = new CyNetworkEvent(network, CyNetworkEvent.GRAPH_REPLACED);
+ assertTrue(e2.getNetwork() == network);
+ assertTrue(e2.getType() == CyNetworkEvent.GRAPH_REPLACED);
+
+ //test unknown event
+ CyNetworkEvent e3 = new CyNetworkEvent(network, CyNetworkEvent.UNKNOWN);
+ assertTrue(e3.getNetwork() == network);
+ assertTrue(e3.getType() == CyNetworkEvent.UNKNOWN);
+
+ //test invalid type
+ CyNetworkEvent eBad = new CyNetworkEvent(network, -7);
+ assertTrue(eBad.getNetwork() == network);
+ assertTrue(eBad.getType() == CyNetworkEvent.UNKNOWN);
+ }
+
+ //-------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ */
+ public static void main(String[] args) {
+ junit.textui.TestRunner.run(new TestSuite(CyNetworkEventTest.class));
+ }
+
+ //-------------------------------------------------------------------------
+}
diff --git a/application/src/test/java/cytoscape/data/CyNetworkTest.java b/application/src/test/java/cytoscape/data/CyNetworkTest.java
new file mode 100644
index 0000000..2f67994
--- /dev/null
+++ b/application/src/test/java/cytoscape/data/CyNetworkTest.java
@@ -0,0 +1,369 @@
+/**
+ *
+ */
+package cytoscape.data;
+
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+
+import cytoscape.*;
+import cytoscape.data.Semantics;
+import junit.framework.TestCase;
+
+public class CyNetworkTest extends TestCase {
+ private String title = "My Network";
+ private CyNetwork network;
+ private int defaultNodeSetSize = 10;
+
+ /* (non-Javadoc)
+ * @see junit.framework.TestCase#setUp()
+ */
+ protected void setUp() throws Exception {
+ super.setUp();
+
+ java.util.Collection<CyNode> nodes = this.getNodes(defaultNodeSetSize);
+ java.util.Collection<CyEdge> edges = this.getEdges(nodes);
+ network = Cytoscape.createNetwork(nodes, edges, title);
+ }
+
+ /* (non-Javadoc)
+ * @see junit.framework.TestCase#tearDown()
+ */
+ protected void tearDown() throws Exception {
+ super.tearDown();
+ Cytoscape.destroyNetwork(network);
+ }
+
+ public void testCreateNetwork() {
+ //CyNetwork net = new CyNetwork(new CytoscapeFingRootGraph(), );
+ assertNotNull(network);
+ assertEquals(network.getNodeCount(), defaultNodeSetSize);
+ assertEquals(network.getEdgeCount(), defaultNodeSetSize-1);
+ System.err.println("Should be creating the network the way it's done in Fing!");
+ }
+
+ /**
+ * Test method for {@link cytoscape.giny.CyNetwork#getTitle()}.
+ */
+ public void testGetTitle() {
+ assertEquals(network.getTitle(), title);
+ }
+
+ /**
+ * Test method for {@link cytoscape.giny.CyNetwork#setTitle(java.lang.String)}.
+ */
+ public void testSetTitle() {
+ network.setTitle("foobar");
+ assertEquals(network.getTitle(), "foobar");
+ }
+
+ /**
+ * Test method for {@link cytoscape.giny.CyNetwork#getIdentifier()}.
+ */
+ public void testGetIdentifier() {
+ assertNotNull(network.getIdentifier());
+ }
+
+ /**
+ * Test method for {@link cytoscape.giny.CyNetwork#setIdentifier(java.lang.String)}.
+ */
+ public void testSetIdentifier() {
+ String id = "12345";
+ network.setIdentifier(id);
+ assertEquals(network.getIdentifier(), id);
+ }
+
+ /**
+ * Test method for {@link cytoscape.giny.CyNetwork#appendNetwork(cytoscape.CyNetwork)}.
+ */
+ public void testAppendNetwork() {
+ java.util.Collection<CyNode> nodes = new java.util.ArrayList<CyNode>();
+ nodes.add( Cytoscape.getCyNode("foobar", true) );
+ nodes.add( Cytoscape.getCyNode("blat", true) );
+ nodes.add( Cytoscape.getCyNode("some name", true) );
+ java.util.Collection<CyEdge> edges = this.getEdges(nodes);
+
+ CyNetwork appNet = Cytoscape.createNetwork(nodes, edges, "My network");
+ assertNotNull(appNet);
+ assertNotSame(appNet, network);
+
+ network.appendNetwork(appNet);
+
+ assertEquals(network.getNodeCount(), this.defaultNodeSetSize+3);
+ assertEquals(network.getEdgeCount(), this.defaultNodeSetSize+1);
+ }
+
+ /**
+ * Test method for {@link cytoscape.giny.CyNetwork#selectAllNodes()}.
+ */
+ public void testSelectAllNodes() {
+ network.selectAllNodes();
+ assertNotNull(network.getSelectedNodes());
+ assertEquals(network.getSelectedNodes().size(), network.getNodeCount());
+ }
+
+ /**
+ * Test method for {@link cytoscape.giny.CyNetwork#selectAllEdges()}.
+ */
+ public void testSelectAllEdges() {
+ network.selectAllEdges();
+ assertNotNull(network.getSelectedEdges());
+ assertEquals(network.getSelectedEdges().size(), network.getEdgeCount());
+ }
+
+ /**
+ * Test method for {@link cytoscape.giny.CyNetwork#unselectAllNodes()}.
+ */
+ public void testUnselectAllNodes() {
+ network.selectAllNodes();
+ assertNotNull(network.getSelectedNodes());
+ assertEquals(network.getSelectedNodes().size(), network.getNodeCount());
+
+ network.unselectAllNodes();
+ assertEquals(network.getSelectedNodes().size(), 0);
+
+ }
+
+ /**
+ * Test method for {@link cytoscape.giny.CyNetwork#unselectAllEdges()}.
+ */
+ public void testUnselectAllEdges() {
+ network.selectAllEdges();
+ assertNotNull(network.getSelectedEdges());
+ assertEquals(network.getSelectedEdges().size(), network.getEdgeCount());
+
+ network.unselectAllEdges();
+ assertEquals(network.getSelectedEdges().size(), 0);
+ }
+
+ /**
+ * Test method for {@link cytoscape.giny.CyNetwork#setSelectedNodeState(java.util.Collection, boolean)}.
+ */
+ public void testSetSelectedNodeStateCollectionBoolean() {
+ network.setSelectedNodeState(this.getNodes(3), true);
+ assertEquals(network.getSelectedNodes().size(), 3);
+ }
+
+ /**
+ * Test method for {@link cytoscape.giny.CyNetwork#setSelectedNodeState(giny.model.Node, boolean)}.
+ */
+ public void testSetSelectedNodeStateNodeBoolean() {
+ network.setSelectedNodeState(Cytoscape.getCyNode("1"), true);
+ assertEquals(network.getSelectedNodes().size(), 1);
+ }
+
+ /**
+ * Test method for {@link cytoscape.giny.CyNetwork#setSelectedEdgeState(java.util.Collection, boolean)}.
+ */
+ public void testSetSelectedEdgeStateCollectionBoolean() {
+ network.unselectAllNodes();
+ network.unselectAllEdges();
+
+ network.setSelectedNodeState(this.getNodes(3), true);
+ java.util.Set<CyNode> selectedNodes = network.getSelectedNodes();
+
+ for (CyNode node: selectedNodes) {
+ assertTrue(network.containsNode(node));
+ }
+
+ java.util.Collection<CyEdge> edges = this.getEdges(selectedNodes);
+ assertEquals(2, edges.size());
+
+ // XXX Why does this fix the getSelected edges test???
+// for (CyEdge edge: edges) {
+// assertTrue(network.containsEdge(edge));
+// }
+//
+ network.setSelectedEdgeState(edges, true);
+ // TODO WTF?
+// assertEquals(edges.size(), network.getSelectedEdges().size());
+ }
+
+ /**
+ * Test method for {@link cytoscape.giny.CyNetwork#setSelectedEdgeState(giny.model.Edge, boolean)}.
+ */
+ public void testSetSelectedEdgeStateEdgeBoolean() {
+ network.setSelectedNodeState(this.getNodes(2), true);
+ java.util.Set<CyNode> selectedNodes = network.getSelectedNodes();
+
+ assertEquals(this.getEdges(selectedNodes).size(), 1);
+ java.util.Iterator<CyEdge> edgeI = this.getEdges(selectedNodes).iterator();
+ while (edgeI.hasNext()) {
+ CyEdge edge = edgeI.next();
+ network.setSelectedEdgeState(edge, true);
+ }
+ assertEquals(network.getSelectedEdges().size(), 1);
+ }
+
+ /**
+ * Test method for {@link cytoscape.giny.CyNetwork#isSelected(giny.model.Node)}.
+ */
+ public void testIsSelectedNode() {
+ CyNode node = Cytoscape.getCyNode("1");
+ network.setSelectedNodeState(node, true);
+ assertTrue(network.isSelected(node));
+ }
+
+ /**
+ * Test method for {@link cytoscape.giny.CyNetwork#isSelected(giny.model.Edge)}.
+ */
+ public void testIsSelectedEdge() {
+ CyNode node_1 = Cytoscape.getCyNode("1");
+ CyNode node_2 = Cytoscape.getCyNode("2");
+
+ CyEdge edge = Cytoscape.getCyEdge(node_1, node_2, Semantics.INTERACTION, "test", false);
+ assertNotNull(edge);
+
+ network.setSelectedEdgeState(edge, true);
+ assertTrue(network.isSelected(edge));
+
+ }
+
+ /**
+ * Test method for {@link cytoscape.giny.CyNetwork#getSelectedNodes()}.
+ */
+ public void testGetSelectedNodes() {
+ network.selectAllNodes();
+ assertNotNull(network.getSelectedNodes());
+ assertEquals(network.getSelectedNodes().size(), this.defaultNodeSetSize);
+ }
+
+ /**
+ * Test method for {@link cytoscape.giny.CyNetwork#getSelectedEdges()}.
+ */
+ public void testGetSelectedEdges() {
+ network.selectAllEdges();
+ assertNotNull(network.getSelectedEdges());
+ assertEquals(network.getSelectedEdges().size(), this.defaultNodeSetSize-1);
+ }
+
+
+
+ /**
+ * Test method for {@link cytoscape.giny.CyNetwork#addCyNetworkListener(cytoscape.CyNetworkListener)}
+ * and {@link cytoscape.giny.CyNetwork#getCyNetworkListeners()}
+ * and and {@link cytoscape.giny.CyNetwork#removeCyNetworkListener(cytoscape.CyNetworkListener}
+ */
+ public void testCyNetworkListener() {
+ CyNetworkListener listener = new CyNetworkAdapter() {
+ public void onCyNetworkEvent(CyNetworkEvent event) {
+ }
+ };
+ network.addCyNetworkListener(listener);
+ assertEquals(network.getCyNetworkListeners().size(), 1);
+ assertTrue(network.removeCyNetworkListener(listener));
+ }
+
+ /**
+ /**
+ * Test method for {@link cytoscape.giny.CyNetwork#addNode(int)}.
+ */
+ public void testAddNodeInt() {
+ CyNode newNode = Cytoscape.getCyNode("123", true);
+ assertNotNull(network.addNode(newNode.getRootGraphIndex()));
+ assertTrue(network.containsNode(newNode));
+ }
+
+ /**
+ * Test method for {@link cytoscape.giny.CyNetwork#addNode(giny.model.Node)}.
+ */
+ public void testAddNodeNode() {
+ CyNode newNode = Cytoscape.getCyNode("321", true);
+ assertNotNull(network.addNode(newNode));
+ assertTrue(network.containsNode(newNode));
+ }
+
+ /**
+ * Test method for {@link cytoscape.giny.CyNetwork#removeNode(int, boolean)}.
+ */
+ public void testRemoveNode() {
+ CyNode node = Cytoscape.getCyNode("1");
+ assertNotNull(node);
+ assertTrue(network.removeNode(node.getRootGraphIndex(), true));
+ }
+
+
+ /**
+ * Test method for {@link cytoscape.giny.CyNetwork#addEdge(int)}.
+ */
+ public void testAddEdgeInt() {
+ CyEdge edge = Cytoscape.getCyEdge( Cytoscape.getCyNode("1"), Cytoscape.getCyNode("4"), Semantics.INTERACTION, "test", true);
+ assertNotNull(edge);
+ assertNotNull(network.addEdge(edge.getRootGraphIndex()));
+ }
+
+ /**
+ * Test method for {@link cytoscape.giny.CyNetwork#addEdge(giny.model.Edge)}.
+ */
+ public void testAddEdgeEdge() {
+ CyEdge edge = Cytoscape.getCyEdge( Cytoscape.getCyNode("1"), Cytoscape.getCyNode("4"), Semantics.INTERACTION, "test", true);
+ assertNotNull(edge);
+ assertNotNull(network.addEdge(edge));
+ }
+
+ /**
+ * Test method for {@link cytoscape.giny.CyNetwork#removeEdge(int, boolean)}.
+ */
+ public void testRemoveEdge() {
+ CyEdge edge = Cytoscape.getCyEdge( Cytoscape.getCyNode("1"), Cytoscape.getCyNode("2"), Semantics.INTERACTION, "test", true);
+ assertNotNull(edge);
+ assertTrue(network.removeEdge(edge.getRootGraphIndex(), true));
+ }
+
+
+ public void testSetTitleEvent() {
+ String InitialTitle = "My Network";
+ String NewTitle = "Foobar";
+ CyNetwork network = Cytoscape.createNetwork(InitialTitle);
+ TitleListener tl = new TitleListener();
+ Cytoscape.getPropertyChangeSupport().addPropertyChangeListener(tl);
+ network.setTitle(NewTitle);
+ PropertyChangeEvent event = tl.getEvent();
+ assertEquals(event.getPropertyName(), Cytoscape.NETWORK_TITLE_MODIFIED);
+ assertEquals( ((CyNetworkTitleChange)event.getOldValue()).getNetworkIdentifier(),
+ ((CyNetworkTitleChange)event.getNewValue()).getNetworkIdentifier());
+ assertEquals( ((CyNetworkTitleChange)event.getOldValue()).getNetworkTitle(), InitialTitle);
+ assertEquals( ((CyNetworkTitleChange)event.getNewValue()).getNetworkTitle(), NewTitle);
+
+ }
+
+ /* ----------------------------------------------------------------- */
+ // use only for testSetTitleEvent()
+ private class TitleListener implements PropertyChangeListener {
+ private PropertyChangeEvent pcEvent;
+
+ public void propertyChange(PropertyChangeEvent event) {
+ pcEvent = event;
+ }
+
+ public PropertyChangeEvent getEvent() {
+ return pcEvent;
+ }
+ }
+
+
+ private java.util.Collection<CyNode> getNodes(int size) {
+ java.util.List<CyNode> Nodes = new java.util.ArrayList<CyNode>();
+ for (int i=0; i<size; i++) {
+ Nodes.add(Cytoscape.getCyNode(Integer.toString(i), true));
+ }
+ return Nodes;
+ }
+
+ private java.util.Collection<CyEdge> getEdges(java.util.Collection<CyNode> Nodes) {
+ java.util.List<CyEdge> Edges = new java.util.ArrayList<CyEdge>();
+
+ java.util.Iterator<CyNode> nodeI = Nodes.iterator();
+ CyNode LastNode = null;
+ while (nodeI.hasNext()) {
+ CyNode Node = nodeI.next();
+ if (LastNode != null)
+ Edges.add(Cytoscape.getCyEdge(LastNode, Node, Semantics.INTERACTION, "test", true));
+
+ LastNode = Node;
+ }
+ return Edges;
+ }
+
+
+}
diff --git a/application/src/test/java/cytoscape/data/ExpressionDataTest.java b/application/src/test/java/cytoscape/data/ExpressionDataTest.java
new file mode 100644
index 0000000..600238b
--- /dev/null
+++ b/application/src/test/java/cytoscape/data/ExpressionDataTest.java
@@ -0,0 +1,175 @@
+/*
+ File: ExpressionDataTest.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// ExpressionDataTest.java
+
+//------------------------------------------------------------------------------
+// $Revision: 21132 $
+// $Date: 2010-08-03 18:49:02 +0200 (Tue, 03 Aug 2010) $
+// $Author: mes $
+//--------------------------------------------------------------------------------------
+package cytoscape.data;
+
+import cytoscape.AllTests;
+import cytoscape.Cytoscape;
+
+import cytoscape.data.ExpressionData;
+import cytoscape.data.mRNAMeasurement;
+
+import junit.framework.TestCase;
+import junit.framework.TestSuite;
+
+import java.io.File;
+
+import java.util.Vector;
+
+
+/**
+ * Tests the ExpressionData Object.
+ *
+ */
+public class ExpressionDataTest extends TestCase {
+ /**
+ * Test Data Directory.
+ */
+ private static String testDataDir = "src/test/resources/testData";
+
+ /**
+ * Test File Names.
+ */
+ private static String testDataFilename_1st = "/gal1.22x5.mRNA";
+ private static String testDataFilename_2nd = "/gal1.22x5.mRNA_wo_descript";
+
+ /**
+ * Tests Loading of Sample Data.
+ * @throws Exception All Errors.
+ */
+ public void testExpressionDataLoading() throws Exception {
+ expressionDataLoading(testDataFilename_1st);
+ expressionDataLoading(testDataFilename_2nd);
+ }
+
+ private void expressionDataLoading(String pTestDataFilename) throws Exception {
+ // Load the specified Expression Data File
+ ExpressionData data = new ExpressionData(testDataDir + pTestDataFilename);
+ Vector measurements = data.getAllMeasurements();
+ assertTrue(data.getNumberOfGenes() == measurements.size());
+ assertTrue(data.getNumberOfGenes() > 0);
+
+ // Validate the first row of data
+ String geneName = data.getGeneNames()[0];
+ assertTrue(data.getGeneNames().length == data.getNumberOfGenes());
+
+ // Validate the Gene Name
+ assertEquals("YHR051W", geneName);
+
+ // Validate the Gene Descriptor.
+ String geneDescriptor = data.getGeneDescriptors()[0];
+ if (!pTestDataFilename.contains("_wo_descript")) {
+ assertEquals("COX6", geneDescriptor);
+ }
+ else {
+ assertEquals("", geneDescriptor);
+ }
+
+ // Validate the 0th Experimental Condition
+ String conditionName = data.getConditionNames()[0];
+ assertEquals("gal1RG.sig", conditionName);
+ assertTrue(data.getConditionNames().length == data.getNumberOfConditions());
+
+ // Validate data for the 0th Experimental Condition
+ Vector geneInfo = (Vector) measurements.get(0);
+ mRNAMeasurement measurement = (mRNAMeasurement) geneInfo.get(0);
+ assertEquals(-0.034, measurement.getRatio(), 0.001);
+ assertEquals(1.177, measurement.getSignificance(), 0.001);
+
+ // Validate the extreme values
+ double[][] extremes = data.getExtremeValues();
+ assertEquals(-0.71, extremes[0][0], 0.01);
+ assertEquals(0.432, extremes[0][1], 0.01);
+ assertEquals(-0.717, extremes[1][0], 0.01);
+ assertEquals(27.075, extremes[1][1], 0.01);
+ }
+
+ /**
+ * Tests Loading of Sample Data.
+ * @throws Exception All Errors.
+ */
+ public void testGetMeasurement() throws Exception {
+ getMeasurement(testDataFilename_1st);
+ getMeasurement(testDataFilename_2nd);
+ }
+
+ private void getMeasurement(String pTestDataFilename) throws Exception {
+ ExpressionData data = new ExpressionData(testDataDir + pTestDataFilename);
+
+ // Validate data for all rows.
+ for (int i = 0; i < data.getGeneNames().length; i++) {
+ String gene = data.getGeneNames()[i];
+ String condition = data.getConditionNames()[0];
+
+ mRNAMeasurement measurement = data.getMeasurement(gene, condition);
+ double ratio = measurement.getRatio();
+ double sig = measurement.getSignificance();
+
+ assertTrue(ratio > -100.0);
+ assertTrue(ratio < 1000.0);
+
+ assertTrue(sig >= -1);
+ assertTrue(sig < 10000.0);
+ }
+ }
+
+ /**
+ * Main method, used for testing from the command line.
+ * @param args Command Line Arguments.
+ */
+ public static void main(String[] args) {
+ if (args.length == 1)
+ testDataDir = args[0];
+
+ File tester = new File(testDataDir);
+
+ if (!(tester.canRead() && tester.isDirectory())) {
+ System.err.println("error! ExpressionDataTest cannot read relative directory '"
+ + testDataDir + "'");
+ Cytoscape.exit(1);
+ }
+
+ junit.textui.TestRunner.run(new TestSuite(ExpressionDataTest.class));
+ }
+}
diff --git a/application/src/test/java/cytoscape/data/ImportHandlerTest.java b/application/src/test/java/cytoscape/data/ImportHandlerTest.java
new file mode 100644
index 0000000..f9f91ab
--- /dev/null
+++ b/application/src/test/java/cytoscape/data/ImportHandlerTest.java
@@ -0,0 +1,374 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data;
+
+import cytoscape.AllTests;
+
+import cytoscape.Cytoscape;
+import cytoscape.data.ImportHandler;
+
+import cytoscape.data.readers.GraphReader;
+import cytoscape.data.readers.InteractionsReader;
+
+import cytoscape.util.CyFileFilter;
+import cytoscape.util.SIFFileFilter;
+
+import junit.framework.TestCase;
+
+import java.io.*;
+import java.io.File;
+
+import java.lang.String;
+
+import java.net.URL;
+
+import java.util.*;
+
+import giny.model.RootGraph;
+
+
+/**
+ * Tests Implementation of ImportHandler.
+ *
+ * TODO: Add to DataSuite
+ */
+public class ImportHandlerTest extends TestCase {
+ private File DUMMY_SIF_FILE;
+ private File DUMMY_XGMML_FILE;
+ private File DUMMY_GML_FILE;
+ private File DUMMY_XML_FILE;
+ private File DUMMY_DOC_FILE;
+ private File TEST_XGMML_FILE;
+ private GraphReader graphReader;
+ private InteractionsReader DUMMY_GRAPH_READER;
+ private Collection dummyCollection;
+ private List DUMMY_LIST;
+ private CyFileFilter DUMMY_DOC_FILTER;
+ private CyFileFilter DUMMY_SIF_FILTER;
+ private CyFileFilter DUMMY_XML_FILTER;
+ private CyFileFilter DUMMY_XLS_FILTER;
+ private static String DUMMY_GRAPH_NATURE = "NETWORK";
+ private static String DUMMY_NATURE = "xxxx";
+ private ImportHandler importHandler;
+ private static String testDataDir;
+
+ private static final String FILE_LOCATION = "src/test/resources/testData";
+
+ /**
+ * Set things up.
+ * @throws Exception All Exceptions.
+ */
+ public void setUp() throws Exception {
+ importHandler = new ImportHandler();
+ DUMMY_DOC_FILTER = new CyFileFilter("doc", "Documents", "dummy");
+ DUMMY_XLS_FILTER = new CyFileFilter("xls", "Excel", "dummy");
+ DUMMY_SIF_FILTER = new CyFileFilter("sif", "Another Sif Filter", DUMMY_GRAPH_NATURE);
+ DUMMY_XML_FILTER = new CyFileFilter("xml", "Another Xml Filter", DUMMY_GRAPH_NATURE);
+ DUMMY_SIF_FILE = File.createTempFile("inputSifTest", ".sif");
+ DUMMY_XGMML_FILE = File.createTempFile("inputXgmmlTest", ".xgmml");
+ DUMMY_GML_FILE = File.createTempFile("inputGmlTest", ".gml");
+ DUMMY_XML_FILE = File.createTempFile("inputXmlTest", ".xml");
+ DUMMY_DOC_FILE = File.createTempFile("inputDocTest", ".doc");
+ TEST_XGMML_FILE = new File(FILE_LOCATION+"/galFiltered2.xgmml");
+ DUMMY_GRAPH_READER = new InteractionsReader(DUMMY_SIF_FILE.toString());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void tearDown() throws Exception {
+ importHandler = null;
+ DUMMY_DOC_FILTER = null;
+ DUMMY_XLS_FILTER = null;
+ DUMMY_SIF_FILTER = null;
+ DUMMY_XML_FILTER = null;
+ DUMMY_SIF_FILE.delete();
+ DUMMY_XGMML_FILE.delete();
+ DUMMY_GML_FILE.delete();
+ DUMMY_XML_FILE.delete();
+ DUMMY_DOC_FILE.delete();
+ graphReader = null;
+ }
+
+ /**
+ * Tests ImportHandler Default Constructor.
+ */
+ public void testConstructor() {
+ // should contain four (SIF, XGMML, NNF, and GML) filters + the ALL File filter
+ DUMMY_LIST = importHandler.getAllFilters();
+ assertTrue(DUMMY_LIST != null);
+
+ // test getSize
+ int value = DUMMY_LIST.size();
+ assertEquals(5, value);
+ }
+
+ /**
+ * Tests the initial set up ImportHandler with no extra filters registered.
+ */
+ public void testGetAlls() {
+ // Try getting descriptions for all files of type: GRAPH_NATURE.
+ dummyCollection = importHandler.getAllTypes(ImportHandler.GRAPH_NATURE);
+ assertTrue(dummyCollection != null);
+ // By default, there are four supported graph file types (SIF, XGMML, NNF, and GML)
+ assertEquals(4, dummyCollection.size());
+
+ // Validate one filter description
+ boolean xgmmlFlag = false;
+ Iterator iterator = dummyCollection.iterator();
+
+ while (iterator.hasNext()) {
+ String description = (String) iterator.next();
+
+ if (description.equals("XGMML files")) {
+ xgmmlFlag = true;
+ }
+ }
+
+ assertTrue(xgmmlFlag);
+
+ // Try getting a list of all registered file extensions.
+ dummyCollection = importHandler.getAllExtensions();
+ assertTrue(dummyCollection != null);
+ assertEquals(5, dummyCollection.size());
+
+ // Validate one file extension.
+ boolean sifFlag = false;
+ iterator = dummyCollection.iterator();
+
+ while (iterator.hasNext()) {
+ String fileExtension = (String) iterator.next();
+
+ if (fileExtension.equals("sif")) {
+ sifFlag = true;
+ }
+ }
+
+ assertTrue(sifFlag);
+
+ // Try getting a list of all filter descriptions (w/ file extensions).
+ dummyCollection = importHandler.getAllDescriptions();
+ assertTrue(dummyCollection != null);
+ assertEquals(4, dummyCollection.size());
+
+ // Validate one filter description
+ boolean gmlFlag = false;
+ iterator = dummyCollection.iterator();
+
+ while (iterator.hasNext()) {
+ String description = (String) iterator.next();
+
+ if (description.equals("GML files (*.gml)")) {
+ gmlFlag = true;
+ }
+ }
+
+ assertTrue(gmlFlag);
+
+ // Try getting descriptions w/ out extensions for filters of type: XXX,
+ // when no filters of type XXX exist.
+ dummyCollection = importHandler.getAllTypes(DUMMY_NATURE);
+ assertTrue(dummyCollection != null);
+
+ // Should be equal to 0, since no such filters exist.
+ assertEquals(0, dummyCollection.size());
+
+ // Try getting filters of type: XXX, when no filters of type XXX exist.
+ DUMMY_LIST = importHandler.getAllFilters(DUMMY_NATURE);
+ assertTrue(dummyCollection != null);
+
+ // Should be equal to 0, since no such filters exist.
+ assertEquals(0, dummyCollection.size());
+
+ // Try getting all filters
+ dummyCollection = importHandler.getAllFilters();
+ assertTrue(dummyCollection != null);
+ assertEquals(5, dummyCollection.size());
+
+ // Validate one filter
+ sifFlag = false;
+ iterator = dummyCollection.iterator();
+
+ while (iterator.hasNext()) {
+ Object o = iterator.next();
+
+ if (o instanceof SIFFileFilter) {
+ sifFlag = true;
+ }
+ }
+
+ assertTrue(sifFlag);
+
+ // Try getting only filters of a good nature
+ DUMMY_LIST = importHandler.getAllFilters(DUMMY_GRAPH_NATURE);
+ assertTrue(dummyCollection != null);
+ assertEquals(5, dummyCollection.size());
+
+ // Validate one filter
+ sifFlag = false;
+ iterator = dummyCollection.iterator();
+
+ while (iterator.hasNext()) {
+ Object o = iterator.next();
+
+ if (o instanceof SIFFileFilter) {
+ sifFlag = true;
+ }
+ }
+
+ assertTrue(sifFlag);
+ }
+
+ /**
+ * Tests the registering of new filters.
+ */
+ public void testAddFilter() {
+ importHandler.resetImportHandler();
+
+ // try adding a duplicate filter; this should fail
+ boolean success = importHandler.addFilter(DUMMY_SIF_FILTER);
+ assertEquals(false, success);
+
+ // try adding a new filter; this should succeed
+ success = importHandler.addFilter(DUMMY_DOC_FILTER);
+ assertEquals(true, success);
+
+ // Should now have 6 filters.
+ DUMMY_LIST = importHandler.getAllFilters();
+ assertEquals(6, DUMMY_LIST.size());
+ }
+
+ /**
+ * Tests the registering of multiple filters.
+ */
+ public void testAddFilters() {
+ CyFileFilter[] cff1 = { DUMMY_SIF_FILTER, DUMMY_XML_FILTER };
+ CyFileFilter[] cff2 = { DUMMY_DOC_FILTER, DUMMY_XLS_FILTER };
+
+ // reset, should have 5 filters (graph readers + all)
+ importHandler.resetImportHandler();
+ DUMMY_LIST = importHandler.getAllFilters();
+ assertEquals(5, DUMMY_LIST.size());
+
+ // try adding two duplicate filters; this should fail
+ boolean success = importHandler.addFilter(cff1);
+ assertEquals(false, success);
+
+ // should still have 5 filters
+ DUMMY_LIST = importHandler.getAllFilters();
+ assertEquals(5, DUMMY_LIST.size());
+
+ // try adding a new filter
+ success = importHandler.addFilter(cff2);
+ assertEquals(true, success);
+
+ // should now have seven filers
+ DUMMY_LIST = importHandler.getAllFilters();
+ assertEquals(7, DUMMY_LIST.size());
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testGetFileAttributes() {
+ //check description
+ String value = importHandler.getFileType(DUMMY_SIF_FILE.toString());
+ assertEquals("SIF files", value);
+
+ //check extension
+ Collection extensions = importHandler.getAllExtensions();
+ boolean exists = extensions.contains("sif");
+ assertEquals(true, exists);
+
+ //check reader
+ //An arbitrary string call (locationless) should return null
+ graphReader = importHandler.getReader(DUMMY_GRAPH_NATURE);
+ assertEquals(null, graphReader);
+
+ //a real file should return a real reader
+ //test to make sure it's not null
+ //error ouput showed that this does get an interactions reader
+ graphReader = importHandler.getReader(DUMMY_SIF_FILE.toString());
+ exists = (graphReader == null);
+ assertFalse(exists);
+ }
+
+ /**
+ * Test to make sure getReader does the right thing with URL's
+ */
+ public void testGetReaderURL() throws Exception {
+ URL url = TEST_XGMML_FILE.toURI().toURL();
+ System.out.println(url);
+ graphReader = importHandler.getReader(url);
+ assertTrue(graphReader != null);
+ RootGraph network = Cytoscape.getRootGraph();
+ network.removeNodes(network.nodesList());
+ graphReader.read();
+ System.out.println("GetReaderURL: Node count = " + network.getNodeCount());
+ System.out.println("GetReaderURL: Edge count = " + network.getEdgeCount());
+
+ assertTrue("GetReaderURL: Node count, expect 331, got " + network.getNodeCount(),
+ network.getNodeCount() == 331);
+ assertTrue("GetReaderURL: Edge count, expect 362, got " + network.getEdgeCount(),
+ network.getEdgeCount() == 362);
+
+ }
+
+ //not sure if I should test a private method
+ //technically by testing all the public methods all the
+ //private ones are indirectly tested
+ /* public void testConcatAllExtensions()
+ {
+ DUMMY_LIST = importHandler.getAllFilters();
+ String[] Str1 = importHandler.concatAllExtensions();
+ DUMMY_LIST = importHandler.getAllFilters(DUMMY_GRAPH_FILTER);
+ String[] Str2 = importHandler.concatAllExtensions();
+ assertEquals (Str1, Str2);
+
+ //check that it added an "All filters" filter to the list
+ int value = List.size();
+ assertEquals(4, value);
+
+ }*/
+
+ /**
+ * Runs just this one unit test.
+ */
+ public static void main(String[] args) {
+ junit.textui.TestRunner.run(ImportHandlerTest.class);
+ }
+}
diff --git a/application/src/test/java/cytoscape/data/InteractionTest.java b/application/src/test/java/cytoscape/data/InteractionTest.java
new file mode 100644
index 0000000..825cf12
--- /dev/null
+++ b/application/src/test/java/cytoscape/data/InteractionTest.java
@@ -0,0 +1,155 @@
+/*
+ File: InteractionTest.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// InteractionTest.java
+package cytoscape.data;
+
+import cytoscape.AllTests;
+
+import cytoscape.data.Interaction;
+
+import junit.framework.*;
+
+import java.io.*;
+
+import java.rmi.*;
+
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.Vector;
+
+
+/**
+ *
+ */
+public class InteractionTest extends TestCase {
+ /**
+ * Creates a new InteractionTest object.
+ *
+ * @param name DOCUMENT ME!
+ */
+ public InteractionTest(String name) {
+ super(name);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void setUp() throws Exception {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void tearDown() throws Exception {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void test3ArgCtor() throws Exception {
+ AllTests.standardOut("test3ArgCtor");
+
+ String source = "YNL312W";
+ String type = "pd";
+ String target = "YPL111W";
+
+ Interaction inter0 = new Interaction(source, target, type);
+ assertTrue(inter0.getSource().equals(source));
+ assertTrue(inter0.getType().equals(type));
+ assertTrue(inter0.numberOfTargets() == 1);
+ assertTrue(inter0.getTargets()[0].equals(target));
+ } // test3ArgCtor
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void test1ArgCtor() throws Exception {
+ AllTests.standardOut("test1ArgCtor");
+
+ String rawText0 = "YNL312W pp YPL111W";
+ Interaction inter0 = new Interaction(rawText0);
+ assertTrue(inter0.getSource().equals("YNL312W"));
+ assertTrue(inter0.getType().equals("pp"));
+ assertTrue(inter0.numberOfTargets() == 1);
+ assertTrue(inter0.getTargets()[0].equals("YPL111W"));
+
+ String rawText1 = "YPL075W pd YDR050C YGR254W YHR174W";
+ Interaction inter1 = new Interaction(rawText1);
+ assertTrue(inter1.getSource().equals("YPL075W"));
+ assertTrue(inter1.getType().equals("pd"));
+ assertTrue(inter1.numberOfTargets() == 3);
+ assertTrue(inter1.getTargets()[0].equals("YDR050C"));
+ assertTrue(inter1.getTargets()[1].equals("YGR254W"));
+ assertTrue(inter1.getTargets()[2].equals("YHR174W"));
+ } // test1ArgCtor
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void test1ArgCtorOnDegenerateFrom()
+ throws Exception // a degenerate form has -only- a source node: no interaction type
+ // and no target node
+ {
+ AllTests.standardOut("test1ArgCtorOnDegenerateForm");
+
+ String rawText0 = "YNL312W";
+ Interaction inter0 = new Interaction(rawText0);
+ assertTrue(inter0.getSource().equals("YNL312W"));
+ assertTrue(inter0.getType() == null);
+ assertTrue(inter0.numberOfTargets() == 0);
+ } // test1ArgCtorOnDegenerateForm
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ */
+ public static void main(String[] args) {
+ junit.textui.TestRunner.run(new TestSuite(InteractionTest.class));
+ }
+} // InteractionTest
diff --git a/application/src/test/java/cytoscape/data/NetworkDataTest.java b/application/src/test/java/cytoscape/data/NetworkDataTest.java
new file mode 100755
index 0000000..5850cb6
--- /dev/null
+++ b/application/src/test/java/cytoscape/data/NetworkDataTest.java
@@ -0,0 +1,227 @@
+/*
+ File: NetworkDataTest.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data;
+
+import cytoscape.AllTests;
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+
+import cytoscape.data.NetworkData;
+
+import giny.model.*;
+
+import junit.framework.*;
+
+
+/**
+ *
+ */
+public class NetworkDataTest extends TestCase {
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void setUp() throws Exception {
+ // no set up required
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void tearDown() throws Exception {
+ // TODO: clear all data structires in case other test reference.
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testAddNodeAttribute() throws Exception {
+ String testObjectAttribute0 = "testObjectAttribute0";
+ int id = NetworkData.addNodeAttribute(testObjectAttribute0);
+ assertTrue(id > 0);
+
+ int type = NetworkData.getNodeAttributeType(testObjectAttribute0);
+ assertTrue(type == NetworkData.OBJECT_TYPE);
+ assertTrue(type > 0);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testSetNodeAttributeValue() throws Exception {
+ Object otest1 = new String("object1");
+ Object otest2 = new String("object2");
+ String stest1 = new String("string1");
+ String stest2 = new String("string2");
+ double dtest1 = 1;
+ double dtest2 = 2;
+ Double dtest3 = new Double(3);
+ String dtest4 = new String("4");
+ String dtest5 = new String("five");
+
+ String testObjectAttribute1 = "testObjectAttribute1";
+ String testObjectAttribute2 = "testObjectAttribute2";
+ String testDoubleAttribute1 = "testDoubleAttribute1";
+ String testDoubleAttribute2 = "testDoubleAttribute2";
+ String testDoubleAttribute3 = "testDoubleAttribute3";
+ String testDoubleAttribute4 = "testDoubleAttribute4";
+ String testDoubleAttribute5 = "testDoubleAttribute5";
+ String testStringAttribute1 = "testStringAttribute1";
+ String testStringAttribute2 = "testStringAttribute2";
+
+ Node node = Cytoscape.getCyNode("node1", true);
+
+ // object
+ int r1 = NetworkData.setNodeAttributeValue(node, testObjectAttribute1, otest1,
+ NetworkData.OBJECT_TYPE);
+ System.out.println(r1);
+ assertTrue(r1 > 0);
+
+ int r2 = NetworkData.setNodeAttributeObjectValue(node, testObjectAttribute2, otest2);
+ System.out.println(r2);
+ assertTrue(r2 > 0);
+
+ // string
+ int r3 = NetworkData.setNodeAttributeValue(node, testStringAttribute1, stest1,
+ NetworkData.STRING_TYPE);
+ System.out.println(r3);
+ assertTrue(r3 > 0);
+
+ int r4 = NetworkData.setNodeAttributeStringValue(node, testStringAttribute2, stest2);
+ System.out.println(r4);
+ assertTrue(r4 > 0);
+
+ // double
+ int r5 = NetworkData.setNodeAttributeValue(node, testDoubleAttribute1, new Double(dtest1),
+ NetworkData.DOUBLE_TYPE);
+ System.out.println(r5);
+ assertTrue(r5 > 0);
+
+ int r6 = NetworkData.setNodeAttributeDoubleValue(node, testDoubleAttribute2, dtest2);
+ System.out.println(r6);
+ assertTrue(r6 > 0);
+
+ int r7 = NetworkData.setNodeAttributeValue(node, testDoubleAttribute3, dtest3,
+ NetworkData.DOUBLE_TYPE);
+ System.out.println(r7);
+ assertTrue(r7 > 0);
+
+ int r8 = NetworkData.setNodeAttributeValue(node, testDoubleAttribute4, dtest4,
+ NetworkData.DOUBLE_TYPE);
+ System.out.println(r8);
+ assertTrue(r8 > 0);
+
+ int r9 = NetworkData.setNodeAttributeValue(node, testDoubleAttribute5, dtest5,
+ NetworkData.DOUBLE_TYPE);
+ System.out.println(r9);
+ assertTrue(r9 < 0);
+
+ // test the att types.
+ // object
+ assertTrue(NetworkData.getNodeAttributeType(testObjectAttribute1) == NetworkData.OBJECT_TYPE);
+ assertTrue(NetworkData.getNodeAttributeType(testObjectAttribute2) == NetworkData.OBJECT_TYPE);
+ // string
+ assertTrue(NetworkData.getNodeAttributeType(testStringAttribute2) == NetworkData.STRING_TYPE);
+ assertTrue(NetworkData.getNodeAttributeType(testStringAttribute1) == NetworkData.STRING_TYPE);
+ // double
+ assertTrue(NetworkData.getNodeAttributeType(testDoubleAttribute5) == NetworkData.DOUBLE_TYPE);
+ assertTrue(NetworkData.getNodeAttributeType(testDoubleAttribute4) == NetworkData.DOUBLE_TYPE);
+ assertTrue(NetworkData.getNodeAttributeType(testDoubleAttribute3) == NetworkData.DOUBLE_TYPE);
+ assertTrue(NetworkData.getNodeAttributeType(testDoubleAttribute2) == NetworkData.DOUBLE_TYPE);
+ assertTrue(NetworkData.getNodeAttributeType(testDoubleAttribute1) == NetworkData.DOUBLE_TYPE);
+
+ // now test the get methods
+ // object
+ Object o1 = NetworkData.getNodeAttributeValue(node, testObjectAttribute1);
+ System.out.println(otest1 + " :o1: " + o1);
+
+ // assertTrue( o1.equals( otest1 ) );
+ Object o2 = NetworkData.getNodeAttributeObjectValue(node, testObjectAttribute2);
+ System.out.println(otest2 + " :o2: " + o2);
+
+ //assertTrue( o2.equals( otest2 ) );
+ // string
+ Object s1 = NetworkData.getNodeAttributeValue(node, testStringAttribute1);
+ System.out.println(stest1 + " :s1: " + s1);
+
+ //assertTrue( s1 instanceof String );
+ //assertTrue( s1.equals( stest1 ) );
+ String s2 = NetworkData.getNodeAttributeStringValue(node, testStringAttribute2);
+ System.out.println(stest2 + " :s2: " + s2);
+
+ //assertTrue( s2.equals( stest2 ) );
+ // double
+ Object d1 = NetworkData.getNodeAttributeValue(node, testDoubleAttribute1);
+ System.out.println(dtest1 + " :d1: " + d1);
+
+ //assertTrue( d1 instanceof Double );
+ //assertTrue( ( ( Double )d1).doubleValue() == dtest1 );
+ double d2 = NetworkData.getNodeAttributeDoubleValue(node, testDoubleAttribute2);
+ System.out.println(dtest2 + " :d2: " + d2);
+
+ //assertTrue( d2 == dtest2 );
+ double d3 = NetworkData.getNodeAttributeDoubleValue(node, testDoubleAttribute3);
+ System.out.println(dtest3 + " :d3: " + d3);
+
+ //assertTrue( d3 == dtest3.doubleValue() );
+ double d4 = NetworkData.getNodeAttributeDoubleValue(node, testDoubleAttribute4);
+ System.out.println(dtest4 + " :d4: " + d4);
+
+ //assertTrue( d4 == 4 );
+ Object d5 = NetworkData.getNodeAttributeValue(node, testDoubleAttribute5);
+ System.err.println("Double test5: " + d5);
+
+ double d6 = NetworkData.getNodeAttributeDoubleValue(node, "blah");
+ System.err.println("Double test6: " + d6);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ */
+ public static void main(String[] args) {
+ junit.textui.TestRunner.run(new TestSuite(NetworkDataTest.class));
+ }
+}
diff --git a/application/src/test/java/cytoscape/data/SelectEventTest.java b/application/src/test/java/cytoscape/data/SelectEventTest.java
new file mode 100644
index 0000000..da9470e
--- /dev/null
+++ b/application/src/test/java/cytoscape/data/SelectEventTest.java
@@ -0,0 +1,169 @@
+/*
+ File: FlagEventTest.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data;
+
+import cytoscape.AllTests;
+import cytoscape.Cytoscape;
+
+import cytoscape.data.SelectEvent;
+import cytoscape.data.SelectFilter;
+
+import giny.model.*;
+
+import junit.framework.*;
+
+import java.io.*;
+
+import java.util.*;
+
+
+/**
+ *
+ */
+public class SelectEventTest extends TestCase {
+ /**
+ * Creates a new SelectEventTest object.
+ *
+ * @param name DOCUMENT ME!
+ */
+ public SelectEventTest(String name) {
+ super(name);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void setUp() throws Exception {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void tearDown() throws Exception {
+ }
+
+ /**
+ * This method makes sure that all of the static contants defined in the class
+ * have different values.
+ */
+ public void testConstants() throws Exception {
+ assertTrue(SelectEvent.SINGLE_NODE != SelectEvent.SINGLE_EDGE);
+ assertTrue(SelectEvent.SINGLE_NODE != SelectEvent.NODE_SET);
+ assertTrue(SelectEvent.SINGLE_NODE != SelectEvent.EDGE_SET);
+ assertTrue(SelectEvent.SINGLE_EDGE != SelectEvent.NODE_SET);
+ assertTrue(SelectEvent.SINGLE_EDGE != SelectEvent.EDGE_SET);
+ assertTrue(SelectEvent.NODE_SET != SelectEvent.EDGE_SET);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testCtor() throws Exception {
+ RootGraph rootGraph = Cytoscape.getRootGraph();
+ Node node1 = rootGraph.getNode(rootGraph.createNode());
+ Node node2 = rootGraph.getNode(rootGraph.createNode());
+ Edge edge1 = rootGraph.getEdge(rootGraph.createEdge(node1, node2));
+ Edge edge2 = rootGraph.getEdge(rootGraph.createEdge(node2, node1));
+ Node[] nodeArray = { node1, node2 };
+ Edge[] edgeArray = { edge1, edge2 };
+ GraphPerspective gp = rootGraph.createGraphPerspective(nodeArray, edgeArray);
+ SelectFilter source = new SelectFilter(gp);
+ Set nodeSet = new HashSet();
+ nodeSet.add(node1);
+ nodeSet.add(node2);
+
+ Set edgeSet = new HashSet();
+ edgeSet.add(edge1);
+ edgeSet.add(edge2);
+
+ SelectEvent singleNodeOn = new SelectEvent(source, node1, true);
+ checkEvent(singleNodeOn, source, node1, SelectEvent.SINGLE_NODE, true);
+
+ SelectEvent singleNodeOff = new SelectEvent(source, node2, false);
+ checkEvent(singleNodeOff, source, node2, SelectEvent.SINGLE_NODE, false);
+
+ SelectEvent singleEdgeOn = new SelectEvent(source, edge1, true);
+ checkEvent(singleEdgeOn, source, edge1, SelectEvent.SINGLE_EDGE, true);
+
+ SelectEvent singleEdgeOff = new SelectEvent(source, edge2, false);
+ checkEvent(singleEdgeOff, source, edge2, SelectEvent.SINGLE_EDGE, false);
+
+ SelectEvent nodeSetOn = new SelectEvent(source, nodeSet, true);
+ checkEvent(nodeSetOn, source, nodeSet, SelectEvent.NODE_SET, true);
+
+ SelectEvent nodeSetOff = new SelectEvent(source, nodeSet, false);
+ checkEvent(nodeSetOff, source, nodeSet, SelectEvent.NODE_SET, false);
+
+ SelectEvent edgeSetOn = new SelectEvent(source, edgeSet, true);
+ checkEvent(edgeSetOn, source, edgeSet, SelectEvent.EDGE_SET, true);
+
+ SelectEvent edgeSetOff = new SelectEvent(source, edgeSet, false);
+ checkEvent(edgeSetOff, source, edgeSet, SelectEvent.EDGE_SET, false);
+ } // testCtor
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param event DOCUMENT ME!
+ * @param source DOCUMENT ME!
+ * @param target DOCUMENT ME!
+ * @param targetType DOCUMENT ME!
+ * @param selectOn DOCUMENT ME!
+ */
+ public void checkEvent(SelectEvent event, SelectFilter source, Object target, int targetType,
+ boolean selectOn) {
+ assertTrue(event.getSource() == source);
+ assertTrue(event.getTarget() == target);
+ assertTrue(event.getTargetType() == targetType);
+ assertTrue(event.getEventType() == selectOn);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ */
+ public static void main(String[] args) {
+ junit.textui.TestRunner.run(new TestSuite(SelectEventTest.class));
+ }
+}
diff --git a/application/src/test/java/cytoscape/data/SelectFilterTest.java b/application/src/test/java/cytoscape/data/SelectFilterTest.java
new file mode 100644
index 0000000..57b9639
--- /dev/null
+++ b/application/src/test/java/cytoscape/data/SelectFilterTest.java
@@ -0,0 +1,473 @@
+/*
+ File: SelectFilterTest.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data;
+
+import cytoscape.AllTests;
+import cytoscape.Cytoscape;
+
+import cytoscape.data.SelectEvent;
+import cytoscape.data.SelectEventListener;
+import cytoscape.data.SelectFilter;
+
+import giny.model.*;
+
+import junit.framework.*;
+
+import java.io.*;
+
+import java.util.*;
+
+
+/**
+ *
+ */
+public class SelectFilterTest extends TestCase {
+ SelectFilter filter;
+ Node node1;
+ Node node2;
+ Node otherNode;
+ Edge edge1;
+ Edge edge2;
+ Edge otherEdge;
+ GraphPerspective gp;
+ TestListener listener;
+ SelectEvent savedEvent;
+
+ /**
+ * Creates a new SelectFilterTest object.
+ *
+ * @param name DOCUMENT ME!
+ */
+ public SelectFilterTest(String name) {
+ super(name);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void setUp() throws Exception {
+ RootGraph rootGraph = Cytoscape.getRootGraph();
+ node1 = rootGraph.getNode(rootGraph.createNode());
+ node2 = rootGraph.getNode(rootGraph.createNode());
+ edge1 = rootGraph.getEdge(rootGraph.createEdge(node1, node2));
+ edge2 = rootGraph.getEdge(rootGraph.createEdge(node2, node1));
+
+ Node[] nodeArray = { node1, node2 };
+ Edge[] edgeArray = { edge1, edge2 };
+ gp = rootGraph.createGraphPerspective(nodeArray, edgeArray);
+ //some objects not in this GraphPerspective
+ otherNode = rootGraph.getNode(rootGraph.createNode());
+ otherEdge = rootGraph.getEdge(rootGraph.createEdge(node1, otherNode));
+ filter = new SelectFilter(gp);
+ listener = new TestListener();
+ filter.addSelectEventListener(listener);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void tearDown() throws Exception {
+ }
+
+ /**
+ * Checks that the current state of the filter matches the state described
+ * by the arguments.
+ */
+ public void checkState(boolean n1, boolean n2, boolean e1, boolean e2) {
+ assertTrue(filter.isSelected(node1) == n1);
+ assertTrue(filter.isSelected(node2) == n2);
+ assertTrue(filter.isSelected(edge1) == e1);
+ assertTrue(filter.isSelected(edge2) == e2);
+ assertTrue(filter.passesFilter(node1) == n1);
+ assertTrue(filter.passesFilter(node2) == n2);
+ assertTrue(filter.passesFilter(edge1) == e1);
+ assertTrue(filter.passesFilter(edge2) == e2);
+
+ if (n1) {
+ assertTrue(filter.getSelectedNodes().contains(node1));
+ }
+
+ if (n2) {
+ assertTrue(filter.getSelectedNodes().contains(node2));
+ }
+
+ if (e1) {
+ assertTrue(filter.getSelectedEdges().contains(edge1));
+ }
+
+ if (e2) {
+ assertTrue(filter.getSelectedEdges().contains(edge2));
+ }
+
+ int nodeCount = 0;
+
+ if (n1) {
+ nodeCount++;
+ }
+
+ if (n2) {
+ nodeCount++;
+ }
+
+ assertTrue(filter.getSelectedNodes().size() == nodeCount);
+
+ int edgeCount = 0;
+
+ if (e1) {
+ edgeCount++;
+ }
+
+ if (e2) {
+ edgeCount++;
+ }
+
+ assertTrue(filter.getSelectedEdges().size() == edgeCount);
+ }
+
+ /**
+ * Checks that the most recently fired event matches the supplied arguments.
+ */
+ public void checkEvent(Object target, int targetType, boolean flagOn) {
+ SelectEvent event = listener.getEvent();
+ assertTrue(event.getSource() == filter);
+ assertTrue(event.getTarget() == target);
+ assertTrue(event.getTargetType() == targetType);
+ assertTrue(event.getEventType() == flagOn);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testSingleFlags() throws Exception {
+ checkState(false, false, false, false);
+
+ filter.setSelected(node1, true);
+ checkState(true, false, false, false);
+ checkEvent(node1, SelectEvent.SINGLE_NODE, true);
+
+ filter.setSelected(edge1, true);
+ checkState(true, false, true, false);
+ checkEvent(edge1, SelectEvent.SINGLE_EDGE, true);
+
+ filter.setSelected(node2, true);
+ checkState(true, true, true, false);
+ checkEvent(node2, SelectEvent.SINGLE_NODE, true);
+
+ filter.setSelected(edge2, true);
+ checkState(true, true, true, true);
+ checkEvent(edge2, SelectEvent.SINGLE_EDGE, true);
+
+ filter.setSelected(edge1, false);
+ checkState(true, true, false, true);
+ checkEvent(edge1, SelectEvent.SINGLE_EDGE, false);
+
+ filter.setSelected(node1, false);
+ checkState(false, true, false, true);
+ checkEvent(node1, SelectEvent.SINGLE_NODE, false);
+
+ savedEvent = listener.getEvent();
+ filter.setSelected(edge2, true); //should do nothing
+ checkState(false, true, false, true);
+ assertTrue(listener.getEvent() == savedEvent); //no event should have been fired
+ filter.setSelected(node2, true); //should do nothing
+ checkState(false, true, false, true);
+ assertTrue(listener.getEvent() == savedEvent); //no event should have been fired
+
+ filter.setSelected(edge2, false);
+ checkState(false, true, false, false);
+ checkEvent(edge2, SelectEvent.SINGLE_EDGE, false);
+
+ filter.setSelected(node2, false);
+ checkState(false, false, false, false);
+ checkEvent(node2, SelectEvent.SINGLE_NODE, false);
+
+ savedEvent = listener.getEvent();
+ filter.setSelected(node1, false); //should do nothing
+ checkState(false, false, false, false);
+ assertTrue(listener.getEvent() == savedEvent); //no event should have been fired
+ filter.setSelected(edge1, false); //should do nothing
+ checkState(false, false, false, false);
+ assertTrue(listener.getEvent() == savedEvent); //no event should have been fired
+
+ //test objects not in this perspective
+ /* these tests embargoed due to a bug in GraphPerspective.containsNode
+ filter.setSelected(otherNode, true); //should do nothing
+ checkState(false, false, false, false);
+ assertTrue( listener.getEvent() == savedEvent ); //no event should have been fired
+ filter.setSelected(otherNode, false); //should do nothing
+ checkState(false, false, false, false);
+ assertTrue( listener.getEvent() == savedEvent ); //no event should have been fired
+ filter.setSelected(otherEdge, true); //should do nothing
+ checkState(false, false, false, false);
+ assertTrue( listener.getEvent() == savedEvent ); //no event should have been fired
+ filter.setSelected(otherEdge, false); //should do nothing
+ checkState(false, false, false, false);
+ assertTrue( listener.getEvent() == savedEvent ); //no event should have been fired
+ */
+ } // testCtor
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testGroupFlags() {
+ Set testSet = null; //return value from filter methods
+ checkState(false, false, false, false);
+
+ Set nodeSet1 = new HashSet();
+ nodeSet1.add(node1);
+ testSet = filter.setSelectedNodes(nodeSet1, true);
+ checkState(true, false, false, false);
+ checkEvent(testSet, SelectEvent.NODE_SET, true);
+ assertTrue(testSet.size() == 1);
+ assertTrue(testSet.contains(node1));
+
+ Set edgeSet1 = new HashSet();
+ edgeSet1.add(edge2);
+ testSet = filter.setSelectedEdges(edgeSet1, true);
+ checkState(true, false, false, true);
+ checkEvent(testSet, SelectEvent.EDGE_SET, true);
+ assertTrue(testSet.size() == 1);
+ assertTrue(testSet.contains(edge2));
+
+ Set nodeSet2 = new HashSet();
+ nodeSet2.add(node1);
+ nodeSet2.add(node2);
+ testSet = filter.setSelectedNodes(nodeSet2, true);
+ checkState(true, true, false, true);
+ checkEvent(testSet, SelectEvent.NODE_SET, true);
+ assertTrue(testSet.size() == 1);
+ assertTrue(testSet.contains(node2));
+
+ Set edgeSet2 = new HashSet();
+ edgeSet2.add(edge1);
+ edgeSet2.add(edge2);
+ testSet = filter.setSelectedEdges(edgeSet2, true);
+ checkState(true, true, true, true);
+ checkEvent(testSet, SelectEvent.EDGE_SET, true);
+ assertTrue(testSet.size() == 1);
+ assertTrue(testSet.contains(edge1));
+
+ testSet = filter.setSelectedNodes(nodeSet1, false);
+ checkState(false, true, true, true);
+ checkEvent(testSet, SelectEvent.NODE_SET, false);
+ assertTrue(testSet.size() == 1);
+ assertTrue(testSet.contains(node1));
+
+ testSet = filter.setSelectedEdges(edgeSet1, false);
+ checkState(false, true, true, false);
+ checkEvent(testSet, SelectEvent.EDGE_SET, false);
+ assertTrue(testSet.size() == 1);
+ assertTrue(testSet.contains(edge2));
+
+ testSet = filter.setSelectedNodes(nodeSet2, false);
+ checkState(false, false, true, false);
+ checkEvent(testSet, SelectEvent.NODE_SET, false);
+ assertTrue(testSet.size() == 1);
+ assertTrue(testSet.contains(node2));
+
+ testSet = filter.setSelectedEdges(edgeSet2, false);
+ checkState(false, false, false, false);
+ checkEvent(testSet, SelectEvent.EDGE_SET, false);
+ assertTrue(testSet.size() == 1);
+ assertTrue(testSet.contains(edge1));
+
+ testSet = filter.setSelectedNodes(nodeSet2, true);
+ checkState(true, true, false, false);
+ checkEvent(testSet, SelectEvent.NODE_SET, true);
+ assertTrue(testSet.size() == 2);
+ assertTrue(testSet.contains(node1));
+ assertTrue(testSet.contains(node2));
+
+ testSet = filter.setSelectedNodes(nodeSet2, false);
+ checkState(false, false, false, false);
+ checkEvent(testSet, SelectEvent.NODE_SET, false);
+ assertTrue(testSet.size() == 2);
+ assertTrue(testSet.contains(node1));
+ assertTrue(testSet.contains(node2));
+
+ testSet = filter.setSelectedEdges(edgeSet2, true);
+ checkState(false, false, true, true);
+ checkEvent(testSet, SelectEvent.EDGE_SET, true);
+ assertTrue(testSet.size() == 2);
+ assertTrue(testSet.contains(edge1));
+ assertTrue(testSet.contains(edge2));
+
+ testSet = filter.setSelectedEdges(edgeSet2, false);
+ checkState(false, false, false, false);
+ checkEvent(testSet, SelectEvent.EDGE_SET, false);
+ assertTrue(testSet.size() == 2);
+ assertTrue(testSet.contains(edge1));
+ assertTrue(testSet.contains(edge2));
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testFlagAll() {
+ checkState(false, false, false, false);
+
+ filter.selectAllNodes();
+ checkState(true, true, false, false);
+ checkSelectAllEvent(2, SelectEvent.NODE_SET, true);
+ filter.unselectAllNodes();
+ checkState(false, false, false, false);
+ checkSelectAllEvent(2, SelectEvent.NODE_SET, false);
+ filter.selectAllEdges();
+ checkState(false, false, true, true);
+ checkSelectAllEvent(2, SelectEvent.EDGE_SET, true);
+ filter.unselectAllEdges();
+ checkState(false, false, false, false);
+ checkSelectAllEvent(2, SelectEvent.EDGE_SET, false);
+
+ filter.setSelected(node1, true);
+ checkState(true, false, false, false);
+ filter.selectAllNodes();
+ checkState(true, true, false, false);
+ checkSelectAllEvent(1, SelectEvent.NODE_SET, true);
+ filter.setSelected(node1, false);
+ checkState(false, true, false, false);
+ filter.unselectAllNodes();
+ checkState(false, false, false, false);
+ checkSelectAllEvent(1, SelectEvent.NODE_SET, false);
+
+ filter.setSelected(edge1, true);
+ checkState(false, false, true, false);
+ filter.selectAllEdges();
+ checkState(false, false, true, true);
+ checkSelectAllEvent(1, SelectEvent.EDGE_SET, true);
+ filter.setSelected(edge1, false);
+ checkState(false, false, false, true);
+ filter.unselectAllEdges();
+ checkState(false, false, false, false);
+ checkSelectAllEvent(1, SelectEvent.EDGE_SET, false);
+ }
+
+ /**
+ * The event fired in response to a flagAll or unflagAll method call contains
+ * a Set that we don't have a reference to. This method tests the contents of
+ * that Set in addition to the other event parameters.
+ */
+ public void checkSelectAllEvent(int setSize, int targetType, boolean flagOn) {
+
+ // SelectEvent event = listener.getEvent();
+ // assertTrue( event.getSource() == filter );
+ // assertTrue( event.getTarget() instanceof Set );
+ // Set targetSet = (Set)event.getTarget();
+ // assertTrue( targetSet.size() == setSize );
+ // assertTrue( event.getTargetType() == targetType );
+ // assertTrue( event.getEventType() == flagOn );
+ }
+
+ /**
+ * Test the add and remove listener methods, as well as responding to object
+ * removal in the underlying GraphPerspective.
+ */
+ public void testListeners() {
+ checkState(false, false, false, false);
+ filter.setSelected(node1, true);
+ checkEvent(node1, SelectEvent.SINGLE_NODE, true);
+ savedEvent = listener.getEvent();
+ filter.removeSelectEventListener(listener);
+ filter.setSelected(node1, false);
+ //this should be the same event since the listener is detached
+ assertTrue(listener.getEvent() == savedEvent);
+ checkEvent(node1, SelectEvent.SINGLE_NODE, true);
+ filter.setSelected(edge1, true);
+ assertTrue(listener.getEvent() == savedEvent);
+ checkEvent(node1, SelectEvent.SINGLE_NODE, true);
+ filter.addSelectEventListener(listener);
+ filter.setSelected(edge1, false);
+ assertTrue(listener.getEvent() != savedEvent);
+ checkEvent(edge1, SelectEvent.SINGLE_EDGE, false);
+
+ checkState(false, false, false, false);
+ filter.selectAllNodes();
+ filter.selectAllEdges();
+ checkState(true, true, true, true);
+ gp.hideEdge(edge1);
+ checkState(true, true, false, true);
+ checkSelectAllEvent(1, SelectEvent.EDGE_SET, false);
+ savedEvent = listener.getEvent();
+ gp.restoreEdge(edge1); //shouldn't change flagged state or fire an event
+ checkState(true, true, false, true);
+ assertTrue(listener.getEvent() == savedEvent);
+ filter.unselectAllNodes();
+ filter.unselectAllEdges();
+
+ checkState(false, false, false, false);
+ filter.selectAllNodes();
+ filter.selectAllEdges();
+ checkState(true, true, true, true);
+ gp.hideNode(node1); //implicitly hides both edges
+ checkState(false, true, false, false);
+ //two events get fired, we only catch the second one for the edges
+ checkSelectAllEvent(2, SelectEvent.EDGE_SET, false);
+ savedEvent = listener.getEvent();
+ gp.restoreNode(node1); //shouldn't change flagged state or fire an event
+ checkState(false, true, false, false);
+ assertTrue(listener.getEvent() == savedEvent);
+ filter.unselectAllNodes();
+ filter.unselectAllEdges();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ */
+ public static void main(String[] args) {
+ junit.textui.TestRunner.run(new TestSuite(SelectFilterTest.class));
+ }
+
+ private class TestListener implements SelectEventListener {
+ private SelectEvent event;
+
+ public void onSelectEvent(SelectEvent newEvent) {
+ event = newEvent;
+ }
+
+ public SelectEvent getEvent() {
+ return event;
+ }
+ }
+}
diff --git a/application/src/test/java/cytoscape/data/annotation/AnnotationAndOntologyFullTest.java b/application/src/test/java/cytoscape/data/annotation/AnnotationAndOntologyFullTest.java
new file mode 100755
index 0000000..cea476b
--- /dev/null
+++ b/application/src/test/java/cytoscape/data/annotation/AnnotationAndOntologyFullTest.java
@@ -0,0 +1,149 @@
+/*
+ File: AnnotationAndOntologyFullTest.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// AnnotationAndOntologyFullTest.java
+package cytoscape.data.annotation;
+
+import cytoscape.AllTests;
+
+import cytoscape.data.annotation.*;
+import cytoscape.data.annotation.readers.*;
+
+import junit.framework.*;
+
+import java.io.*;
+
+
+/**
+ * test the Annotation class
+ */
+public class AnnotationAndOntologyFullTest extends TestCase {
+ /**
+ * Creates a new AnnotationAndOntologyFullTest object.
+ *
+ * @param name DOCUMENT ME!
+ */
+ public AnnotationAndOntologyFullTest(String name) {
+ super(name);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void setUp() throws Exception {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void tearDown() throws Exception {
+ }
+
+ /**
+ * an ad hoc test which pinpointed a bug in the following term in my xml version
+ * of kegg pathway ontology. i had reversed the 'id' and 'isa' values.
+ *
+ * <ontologyTerm>
+ * <name> Unknown Metabolism of Other Amino Acids Subtype </name>
+ * <id> 80106 </id>
+ * <isa> 80006 </isa>
+ * </ontologyTerm>
+ *
+ * 80006 is 'Metabolism of Other Amino Acids'
+ * this reversal caused halo's VNG0606G to be described as
+ *
+ * VNG0606G: 90001 80005 272
+ * VNG0606G: 80006 450
+ * VNG0606G: 90001 80002 920
+ *
+ * rather than
+ *
+ * VNG0606G: 90001 80005 272
+ * VNG0606G: 90001 80006 450
+ * VNG0606G: 90001 80002 920
+ *
+ * with my xml bug, the 1st level categorization of annotation #2 is 80006, not 90001
+ *
+ */
+ public void testHaloKegg() throws Exception {
+ AllTests.standardOut("testHaloKegg");
+
+ String filename = "src/test/resources/testData/haloMetabolicPathway.xml";
+
+ //if (AllTests.runAllTests()) {
+ // filename = "src/cytoscape/data/kegg/haloMetabolicPathway.xml";
+ // } else {
+ // filename = "../../kegg/haloMetabolicPathway.xml";
+ // }
+ AnnotationXmlReader reader = new AnnotationXmlReader(new File(filename));
+ Annotation keggHalo = reader.getAnnotation();
+ AllTests.standardOut(keggHalo.toString());
+
+ String orf = "VNG0606G";
+ int[] terms = keggHalo.getClassifications(orf);
+
+ Ontology ontology = keggHalo.getOntology();
+ assertTrue(terms.length == 3);
+
+ for (int i = 0; i < terms.length; i++) {
+ int[][] paths = ontology.getAllHierarchyPaths(terms[i]);
+ AllTests.standardOut(orf + ": " + terms[i] + " paths: " + paths.length + ": ");
+
+ for (int p = 0; p < paths.length; p++) {
+ assertTrue(paths[p].length == 3);
+
+ for (int q = 0; q < paths[p].length; q++)
+ AllTests.standardOut(paths[p][q] + " ");
+ } // for p
+
+ AllTests.standardOut("\n");
+ } // for i
+ } // testHaloKegg
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ */
+ public static void main(String[] args) {
+ junit.textui.TestRunner.run(new TestSuite(AnnotationAndOntologyFullTest.class));
+ }
+} // AnnotationAndOntologyFullTest
diff --git a/application/src/test/java/cytoscape/data/annotation/AnnotationDescriptionTest.java b/application/src/test/java/cytoscape/data/annotation/AnnotationDescriptionTest.java
new file mode 100755
index 0000000..7b68c11
--- /dev/null
+++ b/application/src/test/java/cytoscape/data/annotation/AnnotationDescriptionTest.java
@@ -0,0 +1,129 @@
+/*
+ File: AnnotationDescriptionTest.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// AnnotationDescriptionTest
+package cytoscape.data.annotation;
+
+import cytoscape.AllTests;
+
+import cytoscape.data.annotation.*;
+
+import junit.framework.*;
+
+import java.io.*;
+
+
+/**
+ * test the AnnotationDescription class, especially with regard to
+ * the 'equals' and 'hashCode' member functions
+ */
+public class AnnotationDescriptionTest extends TestCase {
+ /**
+ * Creates a new AnnotationDescriptionTest object.
+ *
+ * @param name DOCUMENT ME!
+ */
+ public AnnotationDescriptionTest(String name) {
+ super(name);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void setUp() throws Exception {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void tearDown() throws Exception {
+ }
+
+ /**
+ * make sure that the ctor properly initializes all relevant data structures
+ * as seen through the standard getter methods
+ */
+ public void testCtor() throws Exception {
+ AllTests.standardOut("testCtor");
+
+ String species = "Halobacterium sp.";
+ String curator = "KEGG";
+ String type = "Metabolic Pathway";
+
+ AnnotationDescription desc = new AnnotationDescription(species, curator, type);
+
+ assertTrue(desc.getSpecies().equals(species));
+ assertTrue(desc.getCurator().equals(curator));
+ assertTrue(desc.getType().equals(type));
+ } // testCtor
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testEquals() throws Exception {
+ AllTests.standardOut("testEquals");
+
+ String species = "Halobacterium sp.";
+ String curator = "KEGG";
+ String type = "Metabolic Pathway";
+
+ AnnotationDescription desc0 = new AnnotationDescription(species, curator, type);
+
+ AnnotationDescription desc1 = new AnnotationDescription(species, curator, type);
+
+ AnnotationDescription desc2 = new AnnotationDescription("home sapiens", curator, type);
+
+ assertTrue(desc0.equals(desc1));
+ assertTrue(!desc0.equals(desc2));
+ assertTrue(!desc0.equals(new Integer(99)));
+ } // testEquals
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ */
+ public static void main(String[] args) {
+ junit.textui.TestRunner.run(new TestSuite(AnnotationDescriptionTest.class));
+ }
+} // AnnotationDescriptionTest
diff --git a/application/src/test/java/cytoscape/data/annotation/AnnotationTest.java b/application/src/test/java/cytoscape/data/annotation/AnnotationTest.java
new file mode 100755
index 0000000..0b67261
--- /dev/null
+++ b/application/src/test/java/cytoscape/data/annotation/AnnotationTest.java
@@ -0,0 +1,195 @@
+/*
+ File: AnnotationTest.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// AnnotationTest.java
+
+// todo (pshannon, 19 jan 2003): test the new ctor (with receives no Ontology)
+// both with and without an separately assigned ontology
+package cytoscape.data.annotation;
+
+import cytoscape.AllTests;
+
+import cytoscape.data.annotation.*;
+
+import junit.framework.*;
+
+import java.io.*;
+
+
+/**
+ * test the Annotation class
+ */
+public class AnnotationTest extends TestCase {
+ /**
+ * Creates a new AnnotationTest object.
+ *
+ * @param name DOCUMENT ME!
+ */
+ public AnnotationTest(String name) {
+ super(name);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void setUp() throws Exception {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void tearDown() throws Exception {
+ }
+
+ /**
+ * make sure that the ctor properly initializes all relevant data structures
+ * as seen through the standard getter methods
+ */
+ public void testCtor() throws Exception {
+ AllTests.standardOut("testCtor");
+
+ Ontology ontology = Utils.createMinimalKeggMetabolicPathwayOntology();
+ String species = "Saccharomyces cerevisiae";
+ String type = "pathways";
+ Annotation annotation = new Annotation(species, type, ontology);
+
+ assertTrue(annotation.size() == 0);
+ assertTrue(annotation.count() == 0);
+ assertTrue(annotation.getCurator().equals(ontology.getCurator()));
+ assertTrue(annotation.getType().equals(type));
+ assertTrue(annotation.getOntologyType().equals(ontology.getType()));
+ assertTrue(annotation.getSpecies().equals(species));
+ } // testCtor
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testAdd() throws Exception {
+ AllTests.standardOut("testAdd");
+
+ Ontology ontology = Utils.createMinimalKeggMetabolicPathwayOntology();
+ Annotation annotation = new Annotation("Halobacterium Sp.", "pathways", ontology);
+
+ assertTrue(annotation.size() == 0);
+ annotation.add("VNG0006G", 251);
+ annotation.add("VNG0006G", 530);
+ annotation.add("VNG0008G", 520);
+ annotation.add("VNG0008G", 522);
+ annotation.add("VNG0009G", 520);
+ annotation.add("VNG0009G", 522);
+ annotation.add("VNG0046G", 40);
+ annotation.add("VNG0046G", 500);
+ annotation.add("VNG0046G", 520);
+
+ assertTrue(annotation.size() == 9);
+ assertTrue(annotation.count() == 4);
+ } // testAdd
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testGet() throws Exception {
+ AllTests.standardOut("testGet");
+
+ Ontology ontology = Utils.createMinimalKeggMetabolicPathwayOntology();
+ Annotation annotation = new Annotation("Halobacterium Sp.", "pathways", ontology);
+
+ annotation.add("VNG0006G", 251);
+ annotation.add("VNG0006G", 530);
+ annotation.add("VNG0008G", 520);
+ annotation.add("VNG0008G", 522);
+ annotation.add("VNG0009G", 520);
+ annotation.add("VNG0046G", 40);
+ annotation.add("VNG0046G", 500);
+ annotation.add("VNG0046G", 520);
+
+ String[] names = annotation.getNames();
+ assertTrue(names.length == 4);
+
+ int[] classifications = annotation.getClassifications("VNG0006G");
+ assertTrue(classifications.length == 2);
+ assertTrue(classifications[0] == 251);
+ assertTrue(classifications[1] == 530);
+
+ classifications = annotation.getClassifications("VNG0008G");
+ assertTrue(classifications.length == 2);
+ assertTrue(classifications[0] == 520);
+ assertTrue(classifications[1] == 522);
+
+ classifications = annotation.getClassifications("VNG0009G");
+ assertTrue(classifications.length == 1);
+ assertTrue(classifications[0] == 520);
+
+ classifications = annotation.getClassifications("VNG0046G");
+ assertTrue(classifications.length == 3);
+ assertTrue(classifications[0] == 40);
+ assertTrue(classifications[1] == 500);
+ assertTrue(classifications[2] == 520);
+ } // testGet
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testMaxDepth() throws Exception {
+ AllTests.standardOut("testMaxDepth");
+
+ Ontology ontology = Utils.createMinimalKeggMetabolicPathwayOntology();
+ Annotation annotation = new Annotation("Halobacterium Sp.", "pathways", ontology);
+
+ annotation.add("VNG0009G", 520);
+ assertTrue(annotation.maxDepth() == 3);
+ } // testMaxDepth
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ */
+ public static void main(String[] args) {
+ junit.textui.TestRunner.run(new TestSuite(AnnotationTest.class));
+ }
+} // AnnotationTest
diff --git a/application/src/test/java/cytoscape/data/annotation/OntologyTermTest.java b/application/src/test/java/cytoscape/data/annotation/OntologyTermTest.java
new file mode 100755
index 0000000..fbf4438
--- /dev/null
+++ b/application/src/test/java/cytoscape/data/annotation/OntologyTermTest.java
@@ -0,0 +1,154 @@
+/*
+ File: OntologyTermTest.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// OntologyTermTest.java
+package cytoscape.data.annotation;
+
+import cytoscape.AllTests;
+
+import cytoscape.data.annotation.*;
+
+import junit.framework.*;
+
+import java.io.*;
+
+
+/**
+ * test the OntologyTerm class
+ */
+public class OntologyTermTest extends TestCase {
+ /**
+ * Creates a new OntologyTermTest object.
+ *
+ * @param name DOCUMENT ME!
+ */
+ public OntologyTermTest(String name) {
+ super(name);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void setUp() throws Exception {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void tearDown() throws Exception {
+ }
+
+ /**
+ * make sure that the ctor properly initializes all relevant data structures
+ * as seen through the standard getter methods
+ */
+ public void testCtor() throws Exception {
+ AllTests.standardOut("testCtor");
+
+ String name = "Carbohydrate Metabolism";
+ int id = 80001;
+ OntologyTerm term = new OntologyTerm(name, id);
+
+ assertTrue(term.getName().equals(name));
+ assertTrue(term.getId() == id);
+
+ assertTrue(term.numberOfParents() == 0);
+ assertTrue(term.numberOfContainers() == 0);
+ assertTrue(term.numberOfParentsAndContainers() == 0);
+
+ assertTrue(term.getParents().length == 0);
+ assertTrue(term.getContainers().length == 0);
+ assertTrue(term.getParentsAndContainers().length == 0);
+ } // testCtor
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testAddParentsAndContainers() throws Exception {
+ AllTests.standardOut("testAddParentsAndContainers");
+
+ String name = "Carbohydrate Metabolism";
+ int id = 80001;
+ OntologyTerm term = new OntologyTerm(name, id);
+
+ int[] parents = { 123, 456 };
+
+ for (int i = 0; i < parents.length; i++)
+ term.addParent(parents[i]);
+
+ int[] containers = { 1, 2, 3, 4 };
+
+ for (int i = 0; i < containers.length; i++)
+ term.addContainer(containers[i]);
+
+ assertTrue(term.getName().equals(name));
+ assertTrue(term.getId() == id);
+
+ assertTrue(term.numberOfParents() == 2);
+ assertTrue(term.numberOfContainers() == 4);
+ assertTrue(term.numberOfParentsAndContainers() == 6);
+
+ assertTrue(term.getParents().length == 2);
+ assertTrue(term.getContainers().length == 4);
+ assertTrue(term.getParentsAndContainers().length == 6);
+
+ int[] retrievedParents = term.getParents();
+ assertTrue(retrievedParents[0] == parents[0]);
+ assertTrue(retrievedParents[1] == parents[1]);
+
+ int[] retrievedContainers = term.getContainers();
+ assertTrue(retrievedContainers[0] == containers[0]);
+ assertTrue(retrievedContainers[1] == containers[1]);
+ assertTrue(retrievedContainers[2] == containers[2]);
+ assertTrue(retrievedContainers[3] == containers[3]);
+ } // testAddParentsAndContainers
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ */
+ public static void main(String[] args) {
+ junit.textui.TestRunner.run(new TestSuite(OntologyTermTest.class));
+ }
+} // OntologyTermTest
diff --git a/application/src/test/java/cytoscape/data/annotation/OntologyTest.java b/application/src/test/java/cytoscape/data/annotation/OntologyTest.java
new file mode 100755
index 0000000..ea54d58
--- /dev/null
+++ b/application/src/test/java/cytoscape/data/annotation/OntologyTest.java
@@ -0,0 +1,256 @@
+/*
+ File: OntologyTest.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// OntologyTest.java
+package cytoscape.data.annotation;
+
+import cytoscape.AllTests;
+
+import cytoscape.data.annotation.*;
+
+import junit.framework.*;
+
+import java.io.*;
+
+import java.util.*;
+
+
+/**
+ * test the Ontology class
+ */
+public class OntologyTest extends TestCase {
+ /**
+ * Creates a new OntologyTest object.
+ *
+ * @param name DOCUMENT ME!
+ */
+ public OntologyTest(String name) {
+ super(name);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void setUp() throws Exception {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void tearDown() throws Exception {
+ }
+
+ /**
+ * make sure that the ctor properly initializes all relevant data structures
+ * as seen through the standard getter methods
+ */
+ public void testCtor() throws Exception {
+ AllTests.standardOut("testCtor");
+
+ String expectedCurator = "KEGG";
+ String expectedOntologyType = "Metabolic Pathways";
+
+ Ontology ontology = Utils.createMinimalKeggMetabolicPathwayOntology();
+
+ assertTrue(ontology.getCurator().equals(expectedCurator));
+ assertTrue(ontology.getType().equals(expectedOntologyType));
+
+ OntologyDescription description = ontology.getDescription();
+ assertTrue(description.getCurator().equals(expectedCurator));
+ assertTrue(description.getType().equals(expectedOntologyType));
+ } // testCtor
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testAdd() throws Exception {
+ AllTests.standardOut("testAdd");
+
+ String curator = "KEGG";
+ String ontologyType = "Metabolic Pathways";
+ Ontology ontology = new Ontology(curator, ontologyType);
+
+ OntologyTerm metabolism = new OntologyTerm("Metabolism", 90001);
+ OntologyTerm carbohydrateMetabolism = new OntologyTerm("Carbohydrate Metabolism", 80001);
+ carbohydrateMetabolism.addParent(metabolism.getId());
+
+ ontology.add(metabolism);
+ ontology.add(carbohydrateMetabolism);
+
+ assertTrue(ontology.size() == 2);
+ assertTrue(ontology.containsTerm(metabolism.getId()));
+ assertTrue(ontology.containsTerm(carbohydrateMetabolism.getId()));
+
+ OntologyTerm retrievedTerm0 = ontology.getTerm(metabolism.getId());
+ OntologyTerm retrievedTerm1 = ontology.getTerm(carbohydrateMetabolism.getId());
+
+ assertTrue(retrievedTerm0.getName().equals("Metabolism"));
+ assertTrue(retrievedTerm1.getName().equals("Carbohydrate Metabolism"));
+
+ assertTrue(ontology.getTerms().size() == 2);
+ } // testAdd
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testGetHierarchyInts() throws Exception {
+ AllTests.standardOut("testGetHierarchyInts");
+
+ Ontology ontology = Utils.createMinimalKeggMetabolicPathwayOntology();
+
+ // a node with a single parent
+ int[][] h = ontology.getAllHierarchyPaths(80001);
+ assertTrue(h.length == 1);
+ assertTrue(h[0].length == 2);
+ assertTrue(h[0][0] == 90001);
+ assertTrue(h[0][1] == 80001);
+
+ // a node with one parent, one grandparent
+ h = ontology.getAllHierarchyPaths(40);
+ assertTrue(h.length == 1);
+ assertTrue(h[0].length == 3);
+ assertTrue(h[0][0] == 90001);
+ assertTrue(h[0][1] == 80001);
+ assertTrue(h[0][2] == 40);
+
+ // a node with two parents, each with a parent and grandparent
+ h = ontology.getAllHierarchyPaths(666);
+
+ assertTrue(h.length == 2);
+ assertTrue(h[0].length == 4);
+ assertTrue(h[0][0] == 90001);
+ assertTrue(h[0][1] == 80007);
+ assertTrue(h[0][2] == 500);
+ assertTrue(h[0][3] == 666);
+
+ assertTrue(h[1].length == 4);
+ assertTrue(h[1][0] == 90001);
+ assertTrue(h[1][1] == 80007);
+ assertTrue(h[1][2] == 530);
+ assertTrue(h[1][3] == 666);
+ } // testGetHierarchyInts
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testGetHierarchyNames() throws Exception {
+ AllTests.standardOut("testGetHierarchyNames");
+
+ Ontology ontology = Utils.createMinimalKeggMetabolicPathwayOntology();
+
+ // a node with a single parent
+ String[][] h = ontology.getAllHierarchyPathsAsNames(80001);
+
+ printHierarchy(h);
+
+ assertTrue(h.length == 1);
+ assertTrue(h[0].length == 2);
+ assertTrue(h[0][0].equals("Metabolism"));
+ assertTrue(h[0][1].equals("Carbohydrate Metabolism"));
+
+ // a node with one parent, one grandparent
+ h = ontology.getAllHierarchyPathsAsNames(40);
+ assertTrue(h.length == 1);
+ assertTrue(h[0].length == 3);
+ assertTrue(h[0][0].equals("Metabolism"));
+ assertTrue(h[0][1].equals("Carbohydrate Metabolism"));
+ assertTrue(h[0][2].equals("Nucleotide Metabolism"));
+
+ // a node with two parents, each with a parent and grandparent
+ h = ontology.getAllHierarchyPathsAsNames(666);
+ printHierarchy(h);
+
+ assertTrue(h.length == 2);
+
+ assertTrue(h[0].length == 4);
+ assertTrue(h[0][0].equals("Metabolism"));
+ assertTrue(h[0][1].equals("Glutamate metabolism"));
+ assertTrue(h[0][2].equals("Biosynthesis of Secondary Metabolites"));
+ assertTrue(h[0][3].equals("Two Parents"));
+
+ assertTrue(h[1].length == 4);
+ assertTrue(h[1][0].equals("Metabolism"));
+ assertTrue(h[1][1].equals("Glutamate metabolism"));
+ assertTrue(h[1][2].equals("Starch and sucrose metabolism"));
+ assertTrue(h[1][3].equals("Two Parents"));
+ } // testGetHierarchy
+
+ private void printHierarchy(int[][] hierarchy) {
+ for (int i = 0; i < hierarchy.length; i++) {
+ int[] path = hierarchy[i];
+
+ for (int j = 0; j < path.length; j++)
+ AllTests.standardOut(path[j] + " ");
+
+ AllTests.standardOut("\n");
+ } // for i
+ } // printHierarchy
+
+ private void printHierarchy(String[][] hierarchy) {
+ for (int i = 0; i < hierarchy.length; i++) {
+ String[] path = hierarchy[i];
+
+ for (int j = 0; j < path.length; j++) {
+ AllTests.standardOut(path[j]);
+
+ if (j < (path.length - 1))
+ AllTests.standardOut(", ");
+ }
+
+ AllTests.standardOut("\n");
+ } // for i
+ } // printHierarchy
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ */
+ public static void main(String[] args) {
+ junit.textui.TestRunner.run(new TestSuite(OntologyTest.class));
+ }
+} // OntologyTest
diff --git a/application/src/test/java/cytoscape/data/annotation/Utils.java b/application/src/test/java/cytoscape/data/annotation/Utils.java
new file mode 100755
index 0000000..884be6f
--- /dev/null
+++ b/application/src/test/java/cytoscape/data/annotation/Utils.java
@@ -0,0 +1,133 @@
+/*
+ File: Utils.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// Utils
+package cytoscape.data.annotation;
+
+import cytoscape.data.annotation.*;
+
+
+class Utils {
+ /**
+ * creates a 12 term ontology, for use with the Annotation and Ontology tests.
+ *
+ * for background; annotations -- which are basically, a list of name/number pairs,
+ * -require- an ontology. and an antology is a controlled vocabulary of terms,
+ * usually in a hierarchy, that allows us to map the annotation's number to a
+ * node in the hierarchy and (implicitly) to the entire branch of the hierarchy of
+ * which that node is the leaf.
+ *
+ * this ontology looks like this:
+ *
+ * [90001]
+ * [80001] [80005] [80007] [80004] [80010]
+ * [40] [251] [500,530] [520] [522]
+ * [666]
+ *
+ */
+ static Ontology createMinimalKeggMetabolicPathwayOntology() {
+ Ontology ontology = new Ontology("KEGG", "Metabolic Pathways");
+
+ String[] names = {
+ "Metabolism", "Carbohydrate Metabolism", "Amino Acid Metabolism",
+ "Glutamate metabolism", "Metabolism of Complex Carbohydrates",
+ "Aminosugars metabolism", "Nucleotide Metabolism",
+ "Nucleotide sugars metabolism", "Biosynthesis of Secondary Metabolites",
+ "Erythromycin biosynthesis", "Pentose and glucuronate interconversions",
+ "Starch and sucrose metabolism", "Two Parents",
+ };
+
+ int[] ids = { 90001, 80001, 80005, 80007, 80004, 80010, 40, 251, 500, 520, 522, 530, 666 };
+ int[][] parents = {
+ { },
+ { 90001 },
+ { 90001 },
+ { 90001 },
+ { 90001 },
+ { 90001 },
+ { 80001 },
+ { 80005 },
+ { 80007 },
+ { 80004 },
+ { 80010 },
+ { 80007 },
+ { 500, 530 }
+ };
+
+ OntologyTerm[] terms = new OntologyTerm[names.length];
+
+ for (int i = 0; i < names.length; i++) {
+ terms[i] = new OntologyTerm(names[i], ids[i]);
+
+ for (int p = 0; p < parents[i].length; p++)
+ terms[i].addParent(parents[i][p]);
+
+ ontology.add(terms[i]);
+ } // for i
+
+ /************************
+ carbohydrateMetabolism.addParent (metabolism.getId ());
+ aminoAcidMetabolism.addParent (metabolism.getId ());
+ glutamateMetabolism.addParent (aminoAcidMetabolism.getId ());
+ metabolismOfComplexCarbohydrates.addParent (metabolism.getId ());
+ aminosugarsMetabolism.addParent (metabolismOfComplexCarbohydrates.getId ());
+ nucleotideMetabolism.addParent (metabolism.getId ());
+ nucleotideSugarsMetabolism.addParent (nucleotideMetabolism.getId ());
+ biosynthesisOfSecondaryMetabolites.addParent (metabolism.getId ());
+ erythromycinBiosynthesis.addParent (biosynthesisOfSecondaryMetabolites.getId ());
+ pentoseAndGlucuronateInterconversions.addParent (carbohydrateMetabolism.getId ());
+ starchAndSucroseMetabolism.addParent (metabolismOfComplexCarbohydrates.getId ());
+ twoParents.addParent (530);
+ twoParents.addParent (500);
+
+ ontology.add (metabolism);
+ ontology.add (carbohydrateMetabolism);
+ ontology.add (aminoAcidMetabolism);
+ ontology.add (glutamateMetabolism);
+ ontology.add (metabolismOfComplexCarbohydrates);
+ ontology.add (aminosugarsMetabolism);
+ ontology.add (nucleotideMetabolism);
+ ontology.add (nucleotideSugarsMetabolism);
+ ontology.add (biosynthesisOfSecondaryMetabolites);
+ ontology.add (erythromycinBiosynthesis);
+ ontology.add (pentoseAndGlucuronateInterconversions);
+ ontology.add (starchAndSucroseMetabolism);
+ ontology.add (twoParents);
+ *****************/
+ return ontology;
+ } // createMinimalKeggMetabolicPathwayOntology
+} // class Utils
diff --git a/application/src/test/java/cytoscape/data/attr/util/MultiHashMapTest.java b/application/src/test/java/cytoscape/data/attr/util/MultiHashMapTest.java
new file mode 100644
index 0000000..aaaf51c
--- /dev/null
+++ b/application/src/test/java/cytoscape/data/attr/util/MultiHashMapTest.java
@@ -0,0 +1,149 @@
+/*
+ File: TestMultiHashMap.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data.attr.util;
+
+import cytoscape.data.attr.CountedIterator;
+import cytoscape.data.attr.MultiHashMap;
+import cytoscape.data.attr.MultiHashMapDefinition;
+import cytoscape.data.attr.util.MultiHashMapFactory;
+import cytoscape.data.attr.util.MultiHashMapHelpers;
+
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+
+import junit.framework.Assert;
+import junit.framework.Test;
+import junit.framework.TestCase;
+import junit.framework.TestSuite;
+
+public final class MultiHashMapTest extends TestCase {
+
+
+ public static Test suite() {
+ return new TestSuite(MultiHashMapTest.class);
+ }
+
+ MultiHashMapDefinition def;
+ MultiHashMap data;
+ RuntimeException exc;
+
+ public void setUp() {
+
+ Object mm = MultiHashMapFactory.instantiateDataModel();
+ def = (MultiHashMapDefinition) mm;
+ data = (MultiHashMap) mm;
+
+ def.defineAttribute("p-values", MultiHashMapDefinition.TYPE_FLOATING_POINT,
+ new byte[] {
+ MultiHashMapDefinition.TYPE_STRING,
+ MultiHashMapDefinition.TYPE_INTEGER
+ });
+ data.setAttributeValue("node1", "p-values", new Double(0.5),
+ new Object[] { "Ideker", new Integer(0) });
+ data.setAttributeValue("node1", "p-values", new Double(0.6),
+ new Object[] { "Ideker", new Integer(1) });
+ data.setAttributeValue("node1", "p-values", new Double(0.6),
+ new Object[] { "Ideker", new Integer(2) });
+ data.setAttributeValue("node1", "p-values", new Double(0.7),
+ new Object[] { "Salk", new Integer(0) });
+ data.setAttributeValue("node1", "p-values", new Double(0.6),
+ new Object[] { "Salk", new Integer(1) });
+ data.setAttributeValue("node2", "p-values", new Double(0.4),
+ new Object[] { "Salk", new Integer(0) });
+ data.setAttributeValue("node2", "p-values", new Double(0.2),
+ new Object[] { "Weirdo", new Integer(0) });
+ data.setAttributeValue("node3", "p-values", new Double(0.1),
+ new Object[] { "Foofoo", new Integer(11) });
+ data.setAttributeValue("node4", "p-values", new Double(0.9),
+ new Object[] { "BarBar", new Integer(9) });
+
+ exc = null;
+ }
+
+ public void testSetAttrValue1() {
+
+ try {
+ data.setAttributeValue("node4", "p-values", new Double(0.4),
+ new Object[] { "BarBar", new Long(1) });
+ } catch (ClassCastException e) {
+ exc = e;
+ }
+
+ assertNotNull(exc);
+ }
+
+ public void testSetAttrValue2() {
+
+ try {
+ data.setAttributeValue("node5", "p-values", new Double(0.4),
+ new Object[] { "BarBar", new Long(1) });
+ } catch (ClassCastException e) {
+ exc = e;
+ }
+
+ assertNotNull(exc);
+ }
+
+ public void testDefineAttr() {
+
+ def.defineAttribute("color", MultiHashMapDefinition.TYPE_STRING, null);
+ data.setAttributeValue("node1", "color", "red", null);
+ data.setAttributeValue("node8", "color", "yellow", null);
+
+ try {
+ data.removeAttributeValue("node1", "p-values", new Object[] { "Salk", new Long(1) });
+ } catch (ClassCastException e) {
+ exc = e;
+ }
+
+ assertNotNull(exc);
+
+ }
+
+ public void testRemoveAttr() {
+ Object o = data.removeAttributeValue("node4", "p-values", new Object[] { "BarBar", new Integer(9) });
+ assertEquals(new Double(0.9), (Double)o);
+
+ def.defineAttribute("color", MultiHashMapDefinition.TYPE_STRING, null);
+ data.setAttributeValue("node4", "color", "cyan", null);
+
+ o = data.removeAttributeValue("node4", "color", null);
+ assertEquals("cyan",(String)o);
+
+ }
+}
diff --git a/application/src/test/java/cytoscape/data/mRNAMeasurementTest.java b/application/src/test/java/cytoscape/data/mRNAMeasurementTest.java
new file mode 100644
index 0000000..c92fcd2
--- /dev/null
+++ b/application/src/test/java/cytoscape/data/mRNAMeasurementTest.java
@@ -0,0 +1,100 @@
+/*
+ File: mRNAMeasurementTest.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// mRNAMeasurementTest.java
+package cytoscape.data;
+
+import cytoscape.AllTests;
+
+import cytoscape.data.mRNAMeasurement;
+
+import junit.framework.*;
+
+import java.io.*;
+
+
+/**
+ *
+ */
+public class mRNAMeasurementTest extends TestCase {
+ /**
+ * Creates a new mRNAMeasurementTest object.
+ *
+ * @param name DOCUMENT ME!
+ */
+ public mRNAMeasurementTest(String name) {
+ super(name);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void setUp() throws Exception {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void tearDown() throws Exception {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testCtor() throws Exception {
+ AllTests.standardOut("testCtor");
+
+ mRNAMeasurement measurement = new mRNAMeasurement("-0.315", "10.495");
+ assertTrue(measurement.getRatio() == -0.315);
+ assertTrue(measurement.getSignificance() == 10.495);
+ } // testCtor
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ */
+ public static void main(String[] args) {
+ junit.textui.TestRunner.run(new TestSuite(mRNAMeasurementTest.class));
+ }
+} // mRNAMeasurementTest
diff --git a/application/src/test/java/cytoscape/data/networkProject.pro b/application/src/test/java/cytoscape/data/networkProject.pro
new file mode 100644
index 0000000..1fdc269
--- /dev/null
+++ b/application/src/test/java/cytoscape/data/networkProject.pro
@@ -0,0 +1,6 @@
+gml=../../testData/galFiltered.gml
+noa=../../testData/galFiltered.nodeAttrs1
+noa=../../testData/galFiltered.nodeAttrs2
+eda=../../testData/galFiltered.edgeAttrs1
+eda=../../testData/galFiltered.edgeAttrs2
+expr=../../testData/gal.274x20.mrna
diff --git a/application/src/test/java/cytoscape/data/ontology/OntologyTest.java b/application/src/test/java/cytoscape/data/ontology/OntologyTest.java
new file mode 100644
index 0000000..7863ab8
--- /dev/null
+++ b/application/src/test/java/cytoscape/data/ontology/OntologyTest.java
@@ -0,0 +1,274 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data.ontology;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.data.ontology.Ontology;
+import cytoscape.data.ontology.OntologyTerm;
+
+import junit.framework.TestCase;
+
+import org.biojava.ontology.AlreadyExistsException;
+import org.biojava.ontology.Term;
+import org.biojava.ontology.Triple;
+
+import org.biojava.utils.ChangeVetoException;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Set;
+
+
+/**
+ *
+ */
+public class OntologyTest extends TestCase {
+ private Ontology onto;
+ private OntologyTerm newTerm1;
+ private OntologyTerm newTerm2;
+
+ protected void setUp() throws Exception {
+ super.setUp();
+ onto = new Ontology("Sample Ontology", "GO", "Fake ontology", null);
+
+ Cytoscape.buildOntologyServer();
+ Cytoscape.getOntologyServer().addOntology(onto);
+
+ newTerm1 = new OntologyTerm("GO Term1", "Sample Ontology", "This is a fake description 1.");
+ onto.add(newTerm1);
+
+ newTerm2 = new OntologyTerm("GO Term2", "Sample Ontology", "This is a fake description 2.");
+ onto.add(newTerm2);
+ }
+
+ protected void tearDown() throws Exception {
+ super.tearDown();
+ onto = null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testGetName() {
+ assertNotNull(onto.getName());
+ assertEquals("Sample Ontology", onto.getName());
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testGetCurator() {
+ assertNotNull(onto.getCurator());
+ assertEquals("GO", onto.getCurator());
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testAdd() {
+ OntologyTerm newTerm3 = new OntologyTerm("GO Term3", "Sample Ontology",
+ "This is a fake description 3.");
+ onto.add(newTerm3);
+
+ OntologyTerm newTerm4 = new OntologyTerm("GO Term4", "Sample Ontology",
+ "This is a fake description 4.");
+ onto.add(newTerm4);
+ assertEquals(4, onto.size());
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testSize() {
+ assertEquals(2, onto.size());
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testGetTerms() {
+ Set<Term> terms = onto.getTerms();
+ List<String> termNames = new ArrayList<String>();
+
+ assertNotNull(terms);
+ assertEquals(2, terms.size());
+
+ for (Term term : terms) {
+ System.out.println("Term in Set = " + term.getName());
+ termNames.add(term.getName());
+ }
+
+ assertTrue(termNames.contains("GO Term2"));
+ assertTrue(termNames.contains("GO Term1"));
+ assertFalse(terms.contains(new OntologyTerm("foo", "Sample Ontology", null)));
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testContainsTerm() {
+ assertTrue(onto.containsTerm("GO Term1"));
+ assertTrue(onto.containsTerm("GO Term2"));
+ assertFalse(onto.containsTerm("foo"));
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testGetTerm() {
+ final Term target = onto.getTerm("GO Term1");
+ assertNotNull(target);
+ assertEquals(newTerm1.getName(), target.getName());
+ assertEquals(newTerm1.getDescription(), target.getDescription());
+ assertEquals(newTerm1.getOntology().getName(), target.getOntology().getName());
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testToString() {
+ String message = onto.toString();
+ System.out.println("# Ontology toString() method = " + message);
+ assertEquals("Ontology Name: Sample Ontology, Curator: GO, Description: Fake ontology",
+ message);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testContainsTriple() {
+ //fail("Not yet implemented");
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testCreateTermStringString() {
+ try {
+ Term testTerm = onto.createTerm("TestTerm1", "Test Term description1.");
+
+ assertNotNull(testTerm);
+ assertEquals("TestTerm1", testTerm.getName());
+ assertEquals("Test Term description1.", testTerm.getDescription());
+ assertEquals(onto.getName(), testTerm.getOntology().getName());
+ } catch (AlreadyExistsException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ } catch (IllegalArgumentException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ } catch (ChangeVetoException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testCreateTermStringStringObjectArray() {
+ //fail("Not yet implemented");
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testCreateTriple() {
+ Term object = null;
+ Term subject = null;
+ Term predicate = null;
+
+ try {
+ object = onto.createTerm("object", "Fro triple test");
+ subject = onto.createTerm("subject", "test subject.");
+ predicate = new OntologyTerm("pred", onto.getName(), "pred test");
+ } catch (AlreadyExistsException e1) {
+ // TODO Auto-generated catch block
+ e1.printStackTrace();
+ } catch (IllegalArgumentException e1) {
+ // TODO Auto-generated catch block
+ e1.printStackTrace();
+ } catch (ChangeVetoException e1) {
+ // TODO Auto-generated catch block
+ e1.printStackTrace();
+ }
+
+ try {
+ Triple triple = onto.createTriple(subject, object, predicate, "Sample Triple",
+ "Test triple creation.");
+
+ assertNotNull(triple);
+ assertEquals("Sample Triple", triple.getName());
+ assertEquals("Test triple creation.", triple.getDescription());
+ } catch (AlreadyExistsException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ } catch (ChangeVetoException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testDeleteTerm() {
+ Term toBeDeleted = onto.getTerm("GO Term1");
+
+ try {
+ onto.deleteTerm(toBeDeleted);
+ assertEquals(1, onto.size());
+ } catch (ChangeVetoException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testGetDescription() {
+ String desc = onto.getDescription();
+ assertEquals("Fake ontology", desc);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testGetTriples() {
+ //fail("Not yet implemented");
+ }
+}
diff --git a/application/src/test/java/cytoscape/data/ontology/readers/DBCrossReferenceReaderTest.java b/application/src/test/java/cytoscape/data/ontology/readers/DBCrossReferenceReaderTest.java
new file mode 100644
index 0000000..c49512c
--- /dev/null
+++ b/application/src/test/java/cytoscape/data/ontology/readers/DBCrossReferenceReaderTest.java
@@ -0,0 +1,175 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data.ontology.readers;
+
+import cytoscape.data.ontology.DBReference;
+import cytoscape.data.ontology.readers.DBCrossReferenceReader;
+import cytoscape.util.URLUtil;
+
+import junit.framework.TestCase;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+
+import java.net.MalformedURLException;
+import java.net.SocketTimeoutException;
+import java.net.URL;
+import java.net.URLConnection;
+
+import java.util.Map;
+
+
+/**
+ * This class actually tests the following:
+ *
+ * DBReference DBCrossReferences DBCrossReferenceReader
+ *
+ * @author kono
+ *
+ */
+public class DBCrossReferenceReaderTest extends TestCase {
+ DBCrossReferenceReader rd;
+
+ protected void setUp() throws Exception {
+ super.setUp();
+
+ rd = new DBCrossReferenceReader();
+ }
+
+ protected void tearDown() throws Exception {
+ super.tearDown();
+
+ rd = null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testGetXrefMap() {
+ try {
+ rd.readResourceFile();
+ } catch (IOException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+
+ Map<String, DBReference> sampleMap = rd.getXrefMap();
+
+ assertTrue(sampleMap.size() > 0);
+ assertTrue(sampleMap.containsKey("KEGG_PATHWAY"));
+ assertTrue(sampleMap.containsKey("AgBase"));
+ assertTrue(sampleMap.containsKey("ZFIN"));
+
+ DBReference ref = sampleMap.get("SGD");
+ assertEquals("Saccharomyces Genome Database", ref.getFullName());
+
+ try {
+ URL url = ref.getGenericURL();
+ assertEquals("http://www.yeastgenome.org/", url.toString());
+ } catch (MalformedURLException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+
+ assertEquals("Identifier for SGD Loci", ref.getObject());
+
+ /*
+ * The following lines of codes requirs network connection.
+ */
+
+ // try {
+ // String result = connectToURL(ref.getQueryURL("S000006169"));
+ // assertNotNull(result);
+ //
+ // /*
+ // * Check this is a correct web page or not.
+ // */
+ // assertTrue(result.contains("YPL248C"));
+ // assertTrue(result.contains("GAL4"));
+ // assertTrue(result.contains("DNA-binding transcription"));
+ //
+ // } catch (SocketTimeoutException e) {
+ // System.out
+ // .print("======= Connection to SGD timeout. Check connection or try again later ======");
+ // } catch (MalformedURLException e) {
+ // // TODO Auto-generated catch block
+ // e.printStackTrace();
+ // } catch (IOException e) {
+ // // TODO Auto-generated catch block
+ //
+ // }
+ }
+
+ private String connectToURL(URL url) throws IOException {
+ // URLConnection uc = url.openConnection();
+ // ignore cached pages and handle proxy settings:
+ URLConnection uc = URLUtil.getURLConnection(url);
+
+ /*
+ * Set timeout.
+ */
+ uc.setReadTimeout(5000);
+
+ StringBuffer sb = new StringBuffer();
+ InputStream is = null;
+
+ try {
+ is = uc.getInputStream();
+
+ BufferedReader reader = null;
+
+ try {
+ String s;
+
+ reader = new BufferedReader(new InputStreamReader(is));
+ while ((s = reader.readLine()) != null) {
+ sb.append(s);
+ }
+ }
+ finally {
+ reader.close();
+ }
+ }
+ finally {
+ if (is != null) {
+ is.close();
+ }
+ }
+
+ return sb.toString();
+ }
+}
diff --git a/application/src/test/java/cytoscape/data/ontology/readers/OBOFlatFileReaderTest.java b/application/src/test/java/cytoscape/data/ontology/readers/OBOFlatFileReaderTest.java
new file mode 100644
index 0000000..d2f5b7a
--- /dev/null
+++ b/application/src/test/java/cytoscape/data/ontology/readers/OBOFlatFileReaderTest.java
@@ -0,0 +1,151 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data.ontology.readers;
+
+import cytoscape.CyNetwork;
+
+import cytoscape.data.CyAttributes;
+
+import cytoscape.data.ontology.readers.OBOFlatFileReader;
+import cytoscape.data.ontology.readers.OBOTags;
+import cytoscape.util.URLUtil;
+
+import junit.framework.TestCase;
+
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+
+import java.net.URL;
+
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+
+/**
+ *
+ */
+public class OBOFlatFileReaderTest extends TestCase {
+ private static final String REMOTE_OBO = "http://www.geneontology.org/ontology/gene_ontology.obo";
+ private static final String LOCAL_OBO = "src/test/resources/testData/annotation/goslim_generic.obo";
+ private static final int DAG_SIZE = 10738;
+ private InputStream is;
+
+ protected void setUp() throws Exception {
+ super.setUp();
+
+ File sampleOBO = new File(LOCAL_OBO);
+
+ URL oboUrl = sampleOBO.toURL();
+ // is = oboUrl.openStream();
+ // Use URLUtil to get the InputStream since we might be using a proxy server
+ // and because pages may be cached:
+ is = URLUtil.getBasicInputStream(oboUrl);
+ }
+
+ protected void tearDown() throws Exception {
+ super.tearDown();
+
+ try {
+ if (is != null) {
+ is.close();
+ }
+ } catch (IOException ioe) {
+ } finally {
+ is = null;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testReadOBO() {
+ long start = System.currentTimeMillis();
+ OBOFlatFileReader obor = new OBOFlatFileReader(is, null);
+
+ try {
+ obor.readOntology();
+ assertNotNull(obor.getHeader());
+
+ Map header = obor.getHeader();
+ Set<String> keys = obor.getHeader().keySet();
+
+ for (String key : keys) {
+ System.out.println("Key = " + key + ", Value = " + header.get(key));
+ }
+
+ assertTrue(keys.contains("format-version"));
+ assertTrue(keys.contains("date"));
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+
+ System.out.println("## OBO Loading time = " + (System.currentTimeMillis() - start)
+ + " msec.");
+
+ start = System.currentTimeMillis();
+
+ CyAttributes goTermAttr = obor.getTermsAttributes();
+ String[] names = goTermAttr.getAttributeNames();
+
+ for (int i = 0; i < names.length; i++) {
+ System.out.println("Name = " + names[i]);
+ }
+
+ String curString = goTermAttr.getStringAttribute("GO:0000004", "ontology.name");
+ System.out.println("GO:0000004 = " + curString);
+ assertEquals(curString, "biological process unknown");
+
+ curString = goTermAttr.getStringAttribute("GO:0016049", "ontology.name");
+ System.out.println("GO:0016049 = " + curString);
+ assertEquals(curString, "cell growth");
+
+ Map synoMap = goTermAttr.getMapAttribute("GO:0016049",
+ "ontology." + OBOTags.SYNONYM.toString());
+ assertNotNull(synoMap);
+ assertEquals(4, synoMap.size());
+
+ for (Object val : synoMap.keySet()) {
+ System.out.print("GO:0016049 Synonyms = " + val.toString());
+ System.out.println(" ( " + synoMap.get(val) + " )");
+ }
+
+ CyNetwork dag = obor.getDag();
+ assertNotNull(dag);
+
+ System.out.println("## OBO Test time = " + (System.currentTimeMillis() - start) + " msec.");
+ }
+}
diff --git a/application/src/test/java/cytoscape/data/readers/BookmarkReaderTest.java b/application/src/test/java/cytoscape/data/readers/BookmarkReaderTest.java
new file mode 100644
index 0000000..03bfa06
--- /dev/null
+++ b/application/src/test/java/cytoscape/data/readers/BookmarkReaderTest.java
@@ -0,0 +1,98 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data.readers;
+
+import cytoscape.bookmarks.Bookmarks;
+import cytoscape.bookmarks.Category;
+
+import cytoscape.data.readers.BookmarkReader;
+
+import junit.framework.TestCase;
+
+import java.io.IOException;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.xml.bind.JAXBException;
+
+
+/**
+ * Unit test fopr the bookmark reader.
+ *
+ * @author kono
+ *
+ */
+public class BookmarkReaderTest extends TestCase {
+ private BookmarkReader reader;
+
+ protected void setUp() throws Exception {
+ super.setUp();
+ reader = new BookmarkReader();
+ }
+
+ protected void tearDown() throws Exception {
+ super.tearDown();
+ reader = null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testReadBookmarks() {
+ try {
+ reader.readBookmarks();
+
+ Bookmarks bkm = reader.getBookmarks();
+ List cat = bkm.getCategory();
+ List<String> nameList = new ArrayList<String>();
+
+ for (Object item : cat) {
+ if (item.getClass() == Category.class) {
+ nameList.add(((Category) item).getName());
+ }
+ }
+
+ assertTrue(nameList.contains("ontology"));
+ assertTrue(nameList.contains("network"));
+ } catch (JAXBException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ } catch (IOException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ }
+}
diff --git a/application/src/test/java/cytoscape/data/readers/CyAttributesReaderTest.java b/application/src/test/java/cytoscape/data/readers/CyAttributesReaderTest.java
new file mode 100644
index 0000000..89feb4c
--- /dev/null
+++ b/application/src/test/java/cytoscape/data/readers/CyAttributesReaderTest.java
@@ -0,0 +1,270 @@
+/*
+ File: CyAttributesReaderTest.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data.readers;
+
+import cytoscape.data.CyAttributes;
+import cytoscape.data.CyAttributesImpl;
+
+import cytoscape.data.readers.CyAttributesReader;
+
+import junit.framework.TestCase;
+
+import java.io.File;
+import java.io.FileReader;
+import java.io.IOException;
+
+import java.util.List;
+
+
+/**
+ * Tests the CyAttributesReader Class.
+ */
+public class CyAttributesReaderTest extends TestCase {
+ /**
+ * Testing Reading, Take 1.
+ * @throws IOException IO Errors.
+ */
+ public void testRead1() throws IOException {
+ String attributeName = "TestNodeAttribute1";
+ CyAttributes cyAttributes = new CyAttributesImpl();
+ File file = new File("src/test/resources/testData/galFiltered.nodeAttrs1");
+ FileReader reader = null;
+
+ try {
+ reader = new FileReader(file);
+ CyAttributesReader.loadAttributes(cyAttributes, reader);
+ }
+ finally {
+ if (reader != null) {
+ reader.close();
+ }
+ }
+
+ byte type = cyAttributes.getType(attributeName);
+ assertEquals(CyAttributes.TYPE_INTEGER, type);
+
+ // Test a value
+ Integer value = cyAttributes.getIntegerAttribute("YKR026C", attributeName);
+ assertEquals(1, value.intValue());
+
+ // Test a Second value
+ value = cyAttributes.getIntegerAttribute("YMR043W", attributeName);
+ assertEquals(2, value.intValue());
+
+ // Test the last value in the file
+ value = cyAttributes.getIntegerAttribute("YBR043C", attributeName);
+ assertEquals(3, value.intValue());
+
+ // Test a non-existent value
+ value = cyAttributes.getIntegerAttribute("Nerius", attributeName);
+ assertTrue(value == null);
+ }
+
+ /**
+ * Testing Reading, Take 2.
+ * @throws IOException IO Errors.
+ */
+ public void testRead2() throws IOException {
+ CyAttributes cyAttributes = new CyAttributesImpl();
+ File file = new File("src/test/resources/testData/galFiltered.edgeAttrs2");
+ FileReader reader = null;
+
+ try {
+ reader = new FileReader(file);
+ CyAttributesReader.loadAttributes(cyAttributes, reader);
+ }
+ finally {
+ if (reader != null) {
+ reader.close();
+ }
+ }
+
+ byte type = cyAttributes.getType("TestEdgeAttribute2");
+ assertEquals(CyAttributes.TYPE_INTEGER, type);
+
+ // Test a value
+ Integer value = cyAttributes.getIntegerAttribute("YKR026C (pp) YGL122C",
+ "TestEdgeAttribute2");
+ assertEquals(2, value.intValue());
+
+ // Test a Second value
+ value = cyAttributes.getIntegerAttribute("YDR382W (pp) YFL029C", "TestEdgeAttribute2");
+ assertEquals(3, value.intValue());
+
+ // Test the last value in the file
+ value = cyAttributes.getIntegerAttribute("YBL026W (pp) YOR127C", "TestEdgeAttribute2");
+ assertEquals(3, value.intValue());
+
+ // Test a non-existent value
+ value = cyAttributes.getIntegerAttribute("Nerius", "TestEdgeAttribute2");
+ assertTrue(value == null);
+ }
+
+ /**
+ * Testing Read, Take 3
+ * @throws IOException IO Errors.
+ */
+ public void testRead3() throws IOException {
+ CyAttributes cyAttributes = new CyAttributesImpl();
+
+ // This file contains an explicit class declaration, like so:
+ // Score (class=Java.lang.Double)
+ // All the integer values should therefore be stored as Doubles.
+ File file = new File("src/test/resources/testData/explicitDouble.attribute");
+ FileReader reader = null;
+
+ try {
+ reader = new FileReader(file);
+ CyAttributesReader.loadAttributes(cyAttributes, reader);
+ }
+ finally {
+ if (reader != null) {
+ reader.close();
+ }
+ }
+
+ byte type = cyAttributes.getType("Score");
+ assertEquals(CyAttributes.TYPE_FLOATING, type);
+
+ // Test a value
+ Double value = cyAttributes.getDoubleAttribute("a", "Score");
+ assertEquals(1.0, value.doubleValue(), 0.01);
+
+ // Test the last value in the file
+ value = cyAttributes.getDoubleAttribute("c", "Score");
+ assertEquals(3.7, value.doubleValue(), 0.01);
+ }
+
+ private void checkReadSimpleLists(String fileToRead, char sep) throws IOException
+ {
+ String attributeName = "GO_molecular_function_level_4";
+ CyAttributes cyAttributes = new CyAttributesImpl();
+ File file = new File(fileToRead);
+ FileReader reader = null;
+
+ try {
+ reader = new FileReader(file);
+ CyAttributesReader.loadAttributes(cyAttributes, reader);
+ }
+ finally {
+ if (reader != null) {
+ reader.close();
+ }
+ }
+
+ byte type = cyAttributes.getType(attributeName);
+ assertEquals(CyAttributes.TYPE_SIMPLE_LIST, type);
+
+ // Test the First List
+ List list = cyAttributes.getListAttribute("AP1G1", attributeName);
+ assertEquals(3, list.size());
+
+ String value = (String) list.get(0);
+ assertEquals("intracellular", value);
+ value = (String) list.get(1);
+ assertEquals("clathrin" + sep + "adaptor", value);
+ value = (String) list.get(2);
+ assertEquals("intracellular" + sep + "transporter", value);
+
+ // Test the Last List
+ list = cyAttributes.getListAttribute("CDH3", attributeName);
+ assertEquals(1, list.size());
+ value = (String) list.get(0);
+ assertEquals("cell" + sep + "adhesion" + sep + "molecule", value);
+ }
+
+ /**
+ * Testing Reading of Simple Lists.
+ * @throws IOException IO Errors.
+ */
+ public void testReadSimpleLists1() throws IOException {
+ System.clearProperty(CyAttributesReader.DECODE_PROPERTY);
+ checkReadSimpleLists("src/test/resources/testData/implicitStringArray.attribute", ' ');
+ }
+
+ /**
+ * Testing Reading of Simple Lists.
+ * @throws IOException IO Errors.
+ */
+ public void testReadSimpleLists2() throws IOException {
+ System.clearProperty(CyAttributesReader.DECODE_PROPERTY);
+ checkReadSimpleLists("src/test/resources/testData/implicitStringArrayEnc.attribute", ' ');
+ }
+
+ /**
+ * Testing Reading of Simple Lists.
+ * @throws IOException IO Errors.
+ */
+ public void testReadSimpleLists3() throws IOException {
+ System.setProperty(CyAttributesReader.DECODE_PROPERTY, "false");
+ checkReadSimpleLists("src/test/resources/testData/implicitStringArray.attribute", ' ');
+ }
+
+ /**
+ * Testing Reading of Simple Lists.
+ * @throws IOException IO Errors.
+ */
+ public void testReadSimpleLists4() throws IOException {
+ System.setProperty(CyAttributesReader.DECODE_PROPERTY, "false");
+ checkReadSimpleLists("src/test/resources/testData/implicitStringArrayEnc.attribute", '+');
+ }
+
+ /**
+ * Testing Reading of Simple Lists.
+ * @throws IOException IO Errors.
+ */
+ public void testReadSimpleLists5() throws IOException {
+ System.setProperty(CyAttributesReader.DECODE_PROPERTY, "true");
+ checkReadSimpleLists("src/test/resources/testData/implicitStringArray.attribute", ' ');
+ }
+
+ /**
+ * Testing Reading of Simple Lists.
+ * @throws IOException IO Errors.
+ */
+ public void testReadSimpleLists6() throws IOException {
+ System.setProperty(CyAttributesReader.DECODE_PROPERTY, "true");
+ checkReadSimpleLists("src/test/resources/testData/implicitStringArrayEnc.attribute", ' ');
+ }
+
+ /**
+ * Runs just this one unit test.
+ */
+ public static void main(String[] args) {
+ junit.textui.TestRunner.run(CyAttributesReaderTest.class);
+ }
+}
diff --git a/application/src/test/java/cytoscape/data/readers/CytoscapeSessionReaderTest.java b/application/src/test/java/cytoscape/data/readers/CytoscapeSessionReaderTest.java
new file mode 100644
index 0000000..160dc83
--- /dev/null
+++ b/application/src/test/java/cytoscape/data/readers/CytoscapeSessionReaderTest.java
@@ -0,0 +1,184 @@
+/*
+ File: XGMMLWriterTest.java
+
+ Copyright (c) 2009, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.data.readers;
+
+import giny.model.Node;
+
+import java.lang.reflect.Method;
+import java.util.Set;
+
+import junit.framework.TestCase;
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+import cytoscape.data.CyAttributes;
+
+/**
+ * Tests the CytoscapeSessionReader class.
+ *
+ * @author noel.ruddock
+ */
+public class CytoscapeSessionReaderTest extends TestCase {
+
+
+ private void invokeReader(String file) throws Exception {
+ CytoscapeSessionReader sr;
+ Cytoscape.buildOntologyServer();
+ sr = new CytoscapeSessionReader(file, null);
+
+ // Run session reader without Desktop using reflection
+ Class<?> cls = sr.getClass();
+ Method method = cls.getDeclaredMethod("unzipSessionFromURL", boolean.class);
+ method.setAccessible(true);
+ Object ret = method.invoke(sr, false);
+ }
+
+
+ public void testNestedNetworkReconstruction1() throws Exception {
+ Cytoscape.createNewSession();
+
+ invokeReader("src/test/resources/testData/NNFData/t3.cys");
+
+ //Check all networks are available.
+ final Set<CyNetwork> networks = Cytoscape.getNetworkSet();
+
+ CyNetwork targetNet = null;
+ for (CyNetwork net:networks) {
+ System.out.println("Network: "+net.getTitle());
+ if (net.getTitle().equals("Module_Overview")) {
+ targetNet = net;
+ }
+ }
+
+ assertNotNull(targetNet);
+ assertEquals(4, targetNet.getNodeCount());
+ assertEquals(5, targetNet.getEdgeCount());
+
+ CyNode m1 = Cytoscape.getCyNode("M1");
+ assertNotNull(m1);
+ CyNode m1InOverview = (CyNode) targetNet.getNode(m1.getRootGraphIndex());
+ assertNotNull(m1InOverview);
+ assertTrue(m1InOverview.getIdentifier().equals("M1"));
+ assertNotNull(m1InOverview.getNestedNetwork());
+ assertTrue(m1InOverview.getNestedNetwork() instanceof CyNetwork);
+ assertTrue(((CyNetwork)m1InOverview.getNestedNetwork()).getTitle().equals("M1"));
+ }
+
+ public void testNestedNetworkReconstruction2() throws Exception {
+ Cytoscape.createNewSession();
+
+ invokeReader("src/test/resources/testData/NNFData/t4.cys");
+
+ //Check all networks are available.
+ final Set<CyNetwork> networks = Cytoscape.getNetworkSet();
+
+ CyNetwork targetNet = null;
+ for (CyNetwork net:networks) {
+ if (net.getTitle().equals("Top_Level_Network")) {
+ targetNet = net;
+ }
+ }
+
+ assertNotNull(targetNet);
+ assertEquals(7, targetNet.getNodeCount());
+ assertEquals(5, targetNet.getEdgeCount());
+
+ CyNode m3 = Cytoscape.getCyNode("M3");
+ assertNotNull(m3);
+ Node m3InOverview = targetNet.getNode(m3.getRootGraphIndex());
+ assertNotNull(m3InOverview);
+ CyNetwork nestedNetwork = (CyNetwork) m3InOverview.getNestedNetwork();
+ assertNotNull(nestedNetwork);
+ assertTrue(nestedNetwork.getTitle().equals("M3"));
+ assertEquals(4, nestedNetwork.getNodeCount());
+ assertEquals(3, nestedNetwork.getEdgeCount());
+ CyNode m2 = (CyNode) nestedNetwork.getNode(Cytoscape.getCyNode("M2").getRootGraphIndex());
+ assertNotNull(m2);
+ assertNotNull(m2.getNestedNetwork());
+ assertNotNull(m2.getNestedNetwork().getNode(Cytoscape.getCyNode("D").getRootGraphIndex()));
+
+ // Check attributes
+ CyAttributes nodeAttr = Cytoscape.getNodeAttributes();
+ assertTrue(nodeAttr.getStringAttribute("M1", CyNode.NESTED_NETWORK_ID_ATTR).equals("M1"));
+ assertTrue(nodeAttr.getStringAttribute("M2", CyNode.NESTED_NETWORK_ID_ATTR).equals("M2"));
+ assertTrue(nodeAttr.getStringAttribute("M3", CyNode.NESTED_NETWORK_ID_ATTR).equals("M3"));
+ assertNull(nodeAttr.getStringAttribute("M4", CyNode.NESTED_NETWORK_ID_ATTR));
+ assertNull(nodeAttr.getStringAttribute("A", CyNode.NESTED_NETWORK_ID_ATTR));
+ assertNull(nodeAttr.getStringAttribute("B", CyNode.NESTED_NETWORK_ID_ATTR));
+ assertNull(nodeAttr.getStringAttribute("C", CyNode.NESTED_NETWORK_ID_ATTR));
+ assertNull(nodeAttr.getStringAttribute("D", CyNode.NESTED_NETWORK_ID_ATTR));
+
+ }
+
+ // These tests work and pass, but are commented out because they disturb
+ // one of the PluginManager tests when run using "ant test"
+ // All tests function undisturbed when run using "ant test-slow"
+ // public void testBug0001929a() throws Exception {
+ // CytoscapeSessionReader sr;
+ //
+ // Cytoscape.buildOntologyServer();
+ // sr = new CytoscapeSessionReader("testData/Bug1929TestA.cys", null);
+ // sr.read();
+ // }
+ //
+ // public void testBug0001929b() throws Exception {
+ // CytoscapeSessionReader sr;
+ //
+ // //new CytoscapeInit().init(null);
+ // Cytoscape.buildOntologyServer();
+ // sr = new CytoscapeSessionReader("testData/Bug1929TestB.cys", null);
+ // sr.read();
+ // }
+ //
+ // public void testBug0001929c() throws Exception {
+ // CytoscapeSessionReader sr;
+ //
+ // //new CytoscapeInit().init(null);
+ // Cytoscape.buildOntologyServer();
+ // sr = new CytoscapeSessionReader("testData/Bug1929TestC.cys", null);
+ // sr.read();
+ // }
+ //
+ // public void testBug0001929d() throws Exception {
+ // CytoscapeSessionReader sr;
+ //
+ // //new CytoscapeInit().init(null);
+ // Cytoscape.buildOntologyServer();
+ // sr = new CytoscapeSessionReader("testData/Bug1929TestD.cys", null);
+ // sr.read();
+ // }
+}
diff --git a/application/src/test/java/cytoscape/data/readers/FileImporterTest.java b/application/src/test/java/cytoscape/data/readers/FileImporterTest.java
new file mode 100644
index 0000000..02562ad
--- /dev/null
+++ b/application/src/test/java/cytoscape/data/readers/FileImporterTest.java
@@ -0,0 +1,150 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data.readers;
+
+import cytoscape.AllTests;
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+
+import cytoscape.data.readers.GraphReader;
+
+import cytoscape.dialogs.*;
+
+import cytoscape.view.NetworkPanel;
+
+//--------------------------------------------------------------------------------------
+import cytoscape.view.NetworkViewManager;
+
+import junit.framework.TestCase;
+import junit.framework.TestSuite;
+
+
+//-----------------------------------------------------------------------------------------
+/**
+ *
+ */
+public class FileImporterTest extends TestCase {
+ String location;
+ String title;
+ int nodeCount;
+ int edgeCount;
+ CyNetwork network;
+
+ // VisualStyleBuilderDialog vsd;
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void setUp() throws Exception {
+ }
+
+ // ------------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void tearDown() throws Exception {
+ }
+
+ // ------------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testGMLImport() throws Exception {
+ location = "src/test/resources/testData/gal.gml";
+ network = Cytoscape.createNetworkFromFile(location);
+
+ title = network.getTitle();
+ assertEquals("gal", title);
+
+ nodeCount = network.getNodeCount();
+ assertEquals("number of nodes", 11, nodeCount);
+
+ edgeCount = network.getEdgeCount();
+ assertEquals("number of edges", 10, edgeCount);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testXGMMLImport() throws Exception {
+ location = "src/test/resources/testData/galFiltered2.xgmml";
+ network = Cytoscape.createNetworkFromFile(location, false);
+
+ title = network.getTitle();
+ assertEquals("GAL Filtered (Yeast)", title);
+
+ nodeCount = network.getNodeCount();
+ assertEquals("num nodes", 331, nodeCount);
+
+ edgeCount = network.getEdgeCount();
+ assertEquals("num edges", 362, edgeCount);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testSIFImport() throws Exception {
+ location = "src/test/resources/testData/galFiltered.sif";
+ network = Cytoscape.createNetworkFromFile(location, false);
+
+ title = network.getTitle();
+ assertEquals("galFiltered", title);
+
+ nodeCount = network.getNodeCount();
+ assertEquals("num nodes", 331, nodeCount);
+
+ edgeCount = network.getEdgeCount();
+ assertEquals("num edge", 362, edgeCount);
+ }
+
+ //test sessions importer ?
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ */
+ public static void main(String[] args) {
+ junit.textui.TestRunner.run(FileImporterTest.class);
+ }
+}
diff --git a/application/src/test/java/cytoscape/data/readers/GMLReaderTest.java b/application/src/test/java/cytoscape/data/readers/GMLReaderTest.java
new file mode 100644
index 0000000..38e2477
--- /dev/null
+++ b/application/src/test/java/cytoscape/data/readers/GMLReaderTest.java
@@ -0,0 +1,189 @@
+/*
+ File: GMLReaderTest.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+// GMLReaderTest.java
+
+//------------------------------------------------------------------------------
+// $Revision: 21129 $
+// $Date: 2010-08-03 03:13:49 +0200 (Tue, 03 Aug 2010) $
+// $Author: mes $
+//--------------------------------------------------------------------------------------
+package cytoscape.data.readers;
+
+import cytoscape.AllTests;
+import cytoscape.Cytoscape;
+
+import cytoscape.data.readers.GMLReader;
+
+//--------------------------------------------------------------------------------------
+import giny.model.RootGraph;
+
+import junit.framework.TestCase;
+import junit.framework.TestSuite;
+
+
+//-----------------------------------------------------------------------------------------
+/**
+ *
+ */
+public class GMLReaderTest extends TestCase {
+ private static String testDataDir;
+
+ // ------------------------------------------------------------------------------
+ /**
+ * Creates a new GMLReaderTest object.
+ *
+ * @param name DOCUMENT ME!
+ */
+ public GMLReaderTest(String name) {
+ super(name);
+
+ if (AllTests.runAllTests()) {
+ testDataDir = "src/test/resources/testData";
+ }
+ }
+
+ // ------------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void setUp() throws Exception {
+ }
+
+ // ------------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void tearDown() throws Exception {
+ }
+
+ // ------------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testSmallGraphRead() throws Exception {
+ AllTests.standardOut("testSmallGraphRead");
+
+ GMLReader reader = new GMLReader("src/test/resources/testData/gal.gml");
+ reader.read();
+
+ int[] nodeArray = reader.getNodeIndicesArray();
+ int[] edgeArray = reader.getEdgeIndicesArray();
+
+ assertEquals("node count", 11, nodeArray.length);
+ assertEquals("edge count", 10, edgeArray.length);
+ } // testSmallGraphRead
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testMediumGraphRead() throws Exception {
+ AllTests.standardOut("testMediumGraphRead");
+
+ GMLReader reader = new GMLReader("src/test/resources/testData/noLabels.gml");
+ reader.read();
+
+ int[] nodeArray = reader.getNodeIndicesArray();
+ int[] edgeArray = reader.getEdgeIndicesArray();
+
+ assertEquals("node count", 332, nodeArray.length);
+ assertEquals("edge count", 362, edgeArray.length);
+ } // testMediumGraphRead
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testIllFormattedGML() throws Exception {
+ AllTests.standardOut("testIllFormattedGML");
+
+ // this file comes from http://darwin.uvigo.es/software/tcs.html
+ // their style of gml has caused problems in the past,
+ // particularly newlines within quoted words
+ GMLReader reader = new GMLReader("src/test/resources/testData/broken_t.gml");
+ reader.read();
+
+ int[] nodeArray = reader.getNodeIndicesArray();
+ int[] edgeArray = reader.getEdgeIndicesArray();
+
+ assertEquals("node count", 30, nodeArray.length);
+ assertEquals("edge count", 19, edgeArray.length);
+ }
+
+ /**
+ * This gml file was causing an exception to be thrown
+ * because the outline_width attribute was a Double and
+ * not a String.
+ */
+ public void testBug1565() throws Exception {
+ GMLReader reader = new GMLReader("src/test/resources/testData/bug1565.gml");
+ reader.read();
+
+ int[] nodeArray = reader.getNodeIndicesArray();
+ int[] edgeArray = reader.getEdgeIndicesArray();
+
+ assertEquals("node count", 71, nodeArray.length);
+ assertEquals("edge count", 95, edgeArray.length);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ */
+ public static void main(String[] args) {
+ if (args.length != 1) {
+ System.out.println("Error! must supply path to test data directory on command line");
+ Cytoscape.exit(0);
+ }
+
+ testDataDir = args[0];
+
+ junit.textui.TestRunner.run(new TestSuite(GMLReaderTest.class));
+ }
+
+ // ------------------------------------------------------------------------------
+} // GMLReaderTest
diff --git a/application/src/test/java/cytoscape/data/readers/InteractionsReaderTest.java b/application/src/test/java/cytoscape/data/readers/InteractionsReaderTest.java
new file mode 100755
index 0000000..1d1c4ba
--- /dev/null
+++ b/application/src/test/java/cytoscape/data/readers/InteractionsReaderTest.java
@@ -0,0 +1,279 @@
+/*
+ File: InteractionsReaderTest.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// InteractionsReaderTest.java
+package cytoscape.data.readers;
+
+import cytoscape.AllTests;
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+
+import cytoscape.data.Interaction;
+
+import cytoscape.data.readers.InteractionsReader;
+
+import cytoscape.data.servers.BioDataServer;
+
+import giny.model.RootGraph;
+
+import junit.framework.*;
+
+import java.io.*;
+
+import java.util.Enumeration;
+import java.util.HashMap;
+import java.util.Vector;
+
+
+/**
+ *
+ */
+public class InteractionsReaderTest extends TestCase {
+ private BioDataServer nullServer = null;
+ private String species = "unknown";
+
+ /**
+ * Creates a new InteractionsReaderTest object.
+ *
+ * @param name DOCUMENT ME!
+ */
+ public InteractionsReaderTest(String name) {
+ super(name);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void setUp() throws Exception {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void tearDown() throws Exception {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testReadFromTypicalFile()
+ throws Exception // 'typical' means that all lines have the form "node1 pd node2 [node3 node4 ...]
+ {
+ AllTests.standardOut("testFromTypicalFile");
+
+ InteractionsReader reader = this.getReader("sample.sif");
+ reader.read();
+ assertTrue(reader.getCount() == 25);
+
+ Interaction[] interactions = reader.getAllInteractions();
+ assertTrue(interactions[0].getSource().equals("YNL312W"));
+ assertTrue(interactions[0].getType().equals("pd"));
+ assertTrue(interactions[0].numberOfTargets() == 1);
+ assertTrue(interactions[0].getTargets()[0].equals("YPL111W"));
+
+ assertTrue(interactions[11].numberOfTargets() == 3);
+ } // testReadFromTypicalFile
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testReadFileWithNoInteractions()
+ throws Exception // all lines have the degenerate form
+ // "node1"
+ // that is, with no interaction type and no target
+ {
+ AllTests.standardOut("testReadFileWithNoInteractions");
+
+ InteractionsReader reader = this.getReader("degenerate.sif");
+ reader.read();
+ assertTrue(reader.getCount() == 9);
+
+ Interaction[] interactions = reader.getAllInteractions();
+
+ for (int i = 0; i < interactions.length; i++) {
+ assertTrue(interactions[i].getSource().startsWith("Y"));
+ assertTrue(interactions[i].getType() == null);
+ assertTrue(interactions[i].numberOfTargets() == 0);
+ }
+ } // testReadFileWithNoInteractions
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testGetGraph() throws Exception {
+ AllTests.standardOut("testGetGraph");
+
+ InteractionsReader reader = this.getReader("sample.sif");
+ reader.read();
+ assertTrue(reader.getCount() == 25);
+
+ int[] nodes = reader.getNodeIndicesArray();
+ int[] edges = reader.getEdgeIndicesArray();
+
+ assertTrue("node count: expect 31, got " + nodes.length, nodes.length == 31);
+ assertTrue("edge count: expect 27, got " + edges.length, edges.length == 27);
+ } // testGetGraph
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testGetGraphAndEdgeAttributes()
+ throws Exception // when an interactions file is read, and a graph created, an
+ // GraphObjAttrib*tes hash is created, and all of the edge types are added
+ // to it. make sure that works: make sure the reader returns an
+ // GraphObjAttrib*tes object; that it has the right size; that the keys
+ // look like "node1::node2", and that the values are simple strings
+ {
+ AllTests.standardOut("testGetGraphAndEdgeAttributes");
+
+ InteractionsReader reader = this.getReader("sample.sif");
+ reader.read();
+ assertTrue(reader.getCount() == 25);
+
+ int[] nodes = reader.getNodeIndicesArray();
+ int[] edges = reader.getEdgeIndicesArray();
+
+ assertTrue("node count: expect 31, got " + nodes.length, nodes.length == 31);
+ assertTrue("edge count: expect 27, got " + edges.length, edges.length == 27);
+
+ // assertTrue ("attribute count", Cytoscape.getEdgeNetworkData().size () == 2);
+
+ // HashMap interactions = Cytoscape.getEdgeNetworkData().getAttribute ("interaction");
+ // assertTrue ("non-null interactions", interactions != null);
+
+ // String [] edgeNames = Cytoscape.getEdgeNetworkData().getObjectNames ("interaction");
+ // assertTrue ("edgeNames count", edgeNames.length == 27);
+
+ // for (int i=0; i < edgeNames.length; i++) {
+ // assertTrue ("looking for ' (pd) '", edgeNames[i].indexOf (" (pd) ") > 0);
+ // String interactionType = (String) Cytoscape.getEdgeNetworkData().getValue ("interaction", edgeNames [i]);
+ // assertTrue (interactionType.equals ("pd"));
+ // }
+ } // testGetGraphAndEdgeAttributes
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testReadMultiWordProteinsFile() throws Exception {
+ AllTests.standardOut("testReadMultiWordProteinsFile");
+
+ String filename = "multiWordProteins.sif";
+ InteractionsReader reader = this.getReader(filename);
+ reader.read();
+ assertTrue(reader.getCount() == 29);
+
+ Interaction[] interactions = reader.getAllInteractions();
+
+ // interaction 16:
+ // 26S ubiquitin dependent proteasome
+ // interactsWith
+ // I-kappa-B-alpha
+ assertTrue(interactions[16].getSource().equals("26S ubiquitin dependent proteasome"));
+ assertTrue(interactions[16].getType().equals("interactsWith"));
+ assertTrue(interactions[16].numberOfTargets() == 1);
+ assertTrue(interactions[16].getTargets()[0].equals("I-kappa-B-alpha"));
+
+ assertTrue(interactions[28].getSource().equals("TRAF6"));
+ assertTrue(interactions[28].getType().equals("interactsWith"));
+ assertTrue(interactions[28].numberOfTargets() == 3);
+ assertTrue(interactions[28].getTargets()[0].equals("RIP2"));
+ assertTrue(interactions[28].getTargets()[1].equals("ABCDE oopah"));
+ assertTrue(interactions[28].getTargets()[2].equals("HJKOL coltrane"));
+ } // testReadMultiWordProteinsFile
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testReadMultiWordProteinsFileWithErrantSpaces() throws Exception {
+ AllTests.standardOut("testReadMultiWordProteinsFileWithErrantSpaces");
+
+ String filename = "multiWordProteinsFileTrailingSpaces.sif";
+ InteractionsReader reader = this.getReader(filename);
+ reader.read();
+ assertTrue(reader.getCount() == 29);
+
+ Interaction[] interactions = reader.getAllInteractions();
+
+ // interaction 16:
+ // 26S ubiquitin dependent proteasome
+ // interactsWith
+ // I-kappa-B-alpha
+ assertTrue(interactions[16].getSource().equals("26S ubiquitin dependent proteasome"));
+ assertTrue(interactions[16].getType().equals("interactsWith"));
+ assertTrue(interactions[16].numberOfTargets() == 1);
+ assertTrue(interactions[16].getTargets()[0].equals("I-kappa-B-alpha"));
+
+ assertTrue(interactions[28].getSource().equals("TRAF6"));
+ assertTrue(interactions[28].getType().equals("interactsWith"));
+ assertTrue(interactions[28].numberOfTargets() == 3);
+ assertTrue(interactions[28].getTargets()[0].equals("RIP2"));
+ assertTrue(interactions[28].getTargets()[1].equals("ABCDE oopah"));
+ assertTrue(interactions[28].getTargets()[2].equals("HJKOL coltrane"));
+ } // testReadMultiWordProteinsFileWithErrantSpaces
+
+ private InteractionsReader getReader(String file) {
+
+ InteractionsReader reader = new InteractionsReader( "src/test/resources/testData/" + file);
+
+ return reader;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ */
+ public static void main(String[] args) {
+ junit.textui.TestRunner.run(new TestSuite(InteractionsReaderTest.class));
+ }
+} // InteractionsReaderTest
diff --git a/application/src/test/java/cytoscape/data/readers/MetadataParserTest.java b/application/src/test/java/cytoscape/data/readers/MetadataParserTest.java
new file mode 100644
index 0000000..c88ef97
--- /dev/null
+++ b/application/src/test/java/cytoscape/data/readers/MetadataParserTest.java
@@ -0,0 +1,99 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data.readers;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+
+import cytoscape.data.readers.MetadataEntries;
+import cytoscape.data.readers.MetadataParser;
+
+import junit.framework.TestCase;
+
+import java.net.URISyntaxException;
+
+import java.util.Map;
+
+
+/**
+ * Test cases for MetadataParser.<br>
+ *
+ * @author kono
+ *
+ */
+public class MetadataParserTest extends TestCase {
+ MetadataParser mdp;
+ CyNetwork network;
+
+ protected void setUp() throws Exception {
+ super.setUp();
+ network = Cytoscape.getCurrentNetwork();
+ mdp = new MetadataParser(network);
+ }
+
+ protected void tearDown() throws Exception {
+ super.tearDown();
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testMakeNewMetadataMap() {
+ Map newMap = mdp.makeNewMetadataMap();
+ assertNotNull(newMap);
+ assertEquals(MetadataEntries.values().length, newMap.size());
+ assertEquals("http://www.cytoscape.org/", newMap.get(MetadataEntries.SOURCE.toString()));
+ assertEquals("N/A", newMap.get(MetadataEntries.IDENTIFIER.toString()));
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testSetMetadata() {
+ System.out.println("### Metadata Parser is testing with network: " + network.getTitle()
+ + " ###");
+
+ mdp.setMetadata(MetadataEntries.SOURCE, "Gene Ontology");
+ mdp.setMetadata(MetadataEntries.DESCRIPTION, "DAG created form OBO file.");
+
+ Map metadata = Cytoscape.getNetworkAttributes()
+ .getMapAttribute(network.getIdentifier(),
+ mdp.DEFAULT_NETWORK_METADATA_LABEL);
+ assertNotNull(metadata);
+ assertEquals("Gene Ontology", metadata.get(MetadataEntries.SOURCE.toString()));
+ assertEquals("DAG created form OBO file.",
+ metadata.get(MetadataEntries.DESCRIPTION.toString()));
+ }
+}
diff --git a/application/src/test/java/cytoscape/data/readers/NNFReaderTest.java b/application/src/test/java/cytoscape/data/readers/NNFReaderTest.java
new file mode 100644
index 0000000..e2d9ab0
--- /dev/null
+++ b/application/src/test/java/cytoscape/data/readers/NNFReaderTest.java
@@ -0,0 +1,195 @@
+package cytoscape.data.readers;
+
+import giny.model.GraphPerspective;
+import giny.model.Node;
+
+import java.io.IOException;
+import java.util.Set;
+
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+import cytoscape.util.TestUtil;
+
+import junit.framework.TestCase;
+
+
+/**
+ * Test code for Nested Network Format file reader.
+ *
+ * @author kono, ruschein
+ * @since Cytoscape 2.7.0
+ */
+public class NNFReaderTest extends TestCase {
+
+ // All test data files are in this directory.
+ private static final String FILE_LOCATION = "src/test/resources/testData/NNFData/";
+
+
+ public void setUp() throws Exception {
+ /* Intentionally empty! */
+ }
+
+
+ public void tearDown() throws Exception {
+ /* Intentionally empty! */
+ }
+
+
+ public void testGood1() throws Exception {
+ TestUtil.destroyNetworksEdgesAndNodes();
+
+ final NNFReader reader = new NNFReader(FILE_LOCATION + "good1.nnf");
+ reader.read();
+
+ assertNotNull(reader.getNetworks().get(0));
+ assertEquals("root", reader.getNetworks().get(0).getTitle());
+ }
+
+
+ public void testGood2() throws Exception {
+ TestUtil.destroyNetworksEdgesAndNodes();
+
+ final NNFReader reader = new NNFReader(FILE_LOCATION + "good2.nnf");
+ reader.read();
+
+ assertNotNull(reader.getNetworks().get(0));
+ assertEquals("root", reader.getNetworks().get(0).getTitle());
+ }
+
+
+ public void testGood3() throws Exception {
+ TestUtil.destroyNetworksEdgesAndNodes();
+
+ final NNFReader reader = new NNFReader(FILE_LOCATION + "good3.nnf");
+ reader.read();
+
+ assertNotNull(reader.getNetworks().get(0));
+ assertEquals("Module_Overview", reader.getNetworks().get(0).getTitle());
+
+ // Check number of graph objects
+ final Set<CyNetwork> networks = Cytoscape.getNetworkSet();
+ CyNetwork targetNetwork = null;
+ for (CyNetwork net:networks) {
+ if (net.getTitle().equals("Module_Overview")) {
+ targetNetwork = net;
+ }
+ }
+
+ assertNotNull(targetNetwork);
+ assertEquals("Module_Overview", targetNetwork.getTitle());
+ assertEquals(4, targetNetwork.getNodeCount());
+ assertEquals(5, targetNetwork.getEdgeCount());
+ }
+
+
+ public void testGood4() throws Exception {
+ TestUtil.destroyNetworksEdgesAndNodes();
+
+ final NNFReader reader = new NNFReader(FILE_LOCATION + "good4.nnf");
+ reader.read();
+
+ assertNotNull(reader.getNetworks().get(0));
+ assertEquals("Top_Level_Network", reader.getNetworks().get(0).getTitle());
+
+ final Set<CyNetwork> networks = Cytoscape.getNetworkSet();
+ CyNetwork targetNetwork = null;
+ for (CyNetwork net : networks) {
+ if (net.getTitle().equals("M3")) {
+ targetNetwork = net;
+ }
+ }
+
+ assertNotNull(targetNetwork);
+ assertEquals("M3", targetNetwork.getTitle());
+ assertEquals(4, targetNetwork.getNodeCount());
+ assertEquals(3, targetNetwork.getEdgeCount());
+ CyNode node = Cytoscape.getCyNode("M2");
+ assertNotNull(node);
+ Node m2 = targetNetwork.getNode(node.getRootGraphIndex());
+ assertNotNull(m2);
+ GraphPerspective nestedNetwork = m2.getNestedNetwork();
+ assertNotNull(nestedNetwork);
+ assertTrue(((CyNetwork)nestedNetwork).getTitle().equals("M2"));
+ assertEquals(1, nestedNetwork.getNodeCount());
+ assertEquals(0, nestedNetwork.getEdgeCount());
+ }
+
+
+ public void testGood5() throws Exception {
+ TestUtil.destroyNetworksEdgesAndNodes();
+
+ final NNFReader reader = new NNFReader(FILE_LOCATION + "good5.nnf");
+ reader.read();
+
+ assertNotNull(reader.getNetworks().get(0));
+ assertEquals("TopLevelNetwork", reader.getNetworks().get(0).getTitle());
+ }
+
+
+ public void testGood6() throws Exception {
+ TestUtil.destroyNetworksEdgesAndNodes();
+
+ final NNFReader reader = new NNFReader(FILE_LOCATION + "good6.nnf");
+ reader.read();
+
+ assertNotNull(reader.getNetworks().get(0));
+ assertNotNull(reader.getNetworks().get(1));
+ }
+
+
+ public void testBad1() throws Exception {
+ TestUtil.destroyNetworksEdgesAndNodes();
+
+ final NNFReader reader = new NNFReader(FILE_LOCATION + "bad1.nnf");
+ try {
+ reader.read();
+ } catch (IOException e) {
+ e.printStackTrace();
+ assertNotNull(reader.getNetworks().get(0));
+ return;
+ }
+
+ //If not caught by the above, something is wrong!
+ fail();
+ }
+
+
+ public void testBad2() throws Exception {
+ TestUtil.destroyNetworksEdgesAndNodes();
+
+ final NNFReader reader = new NNFReader(FILE_LOCATION + "bad2.nnf");
+ try {
+ reader.read();
+ } catch (IOException e) {
+ e.printStackTrace();
+ assertNotNull(reader.getNetworks().get(0));
+ return;
+ }
+
+ //If not caught by the above, something is wrong!
+ fail();
+ }
+
+ public void testMultipleFiles() throws Exception {
+ TestUtil.destroyNetworksEdgesAndNodes();
+
+ final NNFReader reader1 = new NNFReader(FILE_LOCATION + "good3.nnf");
+ reader1.read();
+
+ final NNFReader reader2 = new NNFReader(FILE_LOCATION + "good4.nnf");
+ reader2.read();
+ final Set<CyNetwork> networks = Cytoscape.getNetworkSet();
+ CyNetwork targetNetwork = null;
+ for (CyNetwork net : networks) {
+ if (net.getTitle().equals("M3")) {
+ targetNetwork = net;
+ }
+ }
+
+ assertNotNull(targetNetwork);
+ assertEquals("M3", targetNetwork.getTitle());
+ assertEquals(6, targetNetwork.getNodeCount());
+ assertEquals(4, targetNetwork.getEdgeCount());
+ }
+}
diff --git a/application/src/test/java/cytoscape/data/readers/TextFileReaderTest.java b/application/src/test/java/cytoscape/data/readers/TextFileReaderTest.java
new file mode 100644
index 0000000..355c0d1
--- /dev/null
+++ b/application/src/test/java/cytoscape/data/readers/TextFileReaderTest.java
@@ -0,0 +1,112 @@
+/*
+ File: TextFileReaderTest.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// TextFileReaderTest.java
+package cytoscape.data.readers;
+
+import cytoscape.AllTests;
+
+import cytoscape.data.readers.TextFileReader;
+
+import junit.framework.*;
+
+import java.io.*;
+
+import java.util.*;
+
+
+/**
+ *
+ */
+public class TextFileReaderTest extends TestCase {
+ /**
+ * Creates a new TextFileReaderTest object.
+ *
+ * @param name DOCUMENT ME!
+ */
+ public TextFileReaderTest(String name) {
+ super(name);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void setUp() throws Exception {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void tearDown() throws Exception {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testSimple() throws Exception {
+ AllTests.standardOut("testCtor");
+
+ TextFileReader reader = new TextFileReader("src/test/resources/testData/randomTextFile.txt");
+
+ /* if (AllTests.runAllTests()) {
+ reader = new TextFileReader
+ ("src/cytoscape/data/readers/unitTests/TextFileReaderTest.java");
+
+ } else {
+ reader = new TextFileReader ("TextFileReaderTest.java");
+ }*/
+ int count = reader.read();
+ String text = reader.getText();
+ String signature = "nonsense";
+ assertTrue(text.indexOf(signature) > 0);
+ } // testSimple
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ */
+ public static void main(String[] args) {
+ junit.textui.TestRunner.run(new TestSuite(TextFileReaderTest.class));
+ }
+} // TextFileReaderTest
diff --git a/application/src/test/java/cytoscape/data/readers/TextJarReaderTest.java b/application/src/test/java/cytoscape/data/readers/TextJarReaderTest.java
new file mode 100644
index 0000000..7f1545e
--- /dev/null
+++ b/application/src/test/java/cytoscape/data/readers/TextJarReaderTest.java
@@ -0,0 +1,140 @@
+/*
+ File: TextJarReaderTest.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// TextJarReaderTest.java
+package cytoscape.data.readers;
+
+import cytoscape.AllTests;
+
+import cytoscape.data.readers.TextJarReader;
+
+import junit.framework.*;
+
+import java.io.IOException;
+
+import java.net.URL;
+
+
+/**
+ *
+ */
+public class TextJarReaderTest extends TestCase {
+ /**
+ * Creates a new TextJarReaderTest object.
+ *
+ * @param name DOCUMENT ME!
+ */
+ public TextJarReaderTest(String name) {
+ super(name);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testOldSchool() throws Exception {
+ TextJarReader reader = new TextJarReader("jar://vizmap.props");
+ int count = reader.read();
+ String text = reader.getText();
+ assertTrue(text.length() > 0);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testNewSchool() throws Exception {
+ // rather than hardcoding the url, do it this way because
+ // we won't know where the jar file actually lives
+ // While this may not appear like it's testing anything, it
+ // is. This only makes sure the url is constructed
+ // properly.
+ URL url = getClass().getResource("/vizmap.props");
+ System.out.println("url: " + url.toString());
+
+ if (url.toString().startsWith("file")) {
+ try {
+ TextJarReader reader = new TextJarReader(url.toString());
+ } catch (IOException e) {
+ System.out.println("We expect the following error since "
+ + "TextJarReader only supports jar urls.");
+ e.printStackTrace();
+ assertTrue(1 == 1);
+
+ return;
+ }
+
+ fail("didn't catch expected exception");
+ } else {
+ TextJarReader reader = new TextJarReader(url.toString());
+ int count = reader.read();
+ String text = reader.getText();
+ System.out.println(text);
+ assertTrue(text.length() > 0);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testBadURL() throws Exception {
+ URL url = new URL("http://google.com");
+
+ try {
+ TextJarReader reader = new TextJarReader(url.toString());
+ } catch (IOException ioe) {
+ assertTrue(1 == 1);
+
+ return;
+ }
+
+ fail("didn't catch an expected exception for url: " + url.toString());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ */
+ public static void main(String[] args) {
+ junit.textui.TestRunner.run(new TestSuite(TextJarReaderTest.class));
+ }
+} // TextJarReaderTest
diff --git a/application/src/test/java/cytoscape/data/readers/XGMMLReaderTest.java b/application/src/test/java/cytoscape/data/readers/XGMMLReaderTest.java
new file mode 100644
index 0000000..4a048ac
--- /dev/null
+++ b/application/src/test/java/cytoscape/data/readers/XGMMLReaderTest.java
@@ -0,0 +1,163 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data.readers;
+
+import cytoscape.AllTests;
+import cytoscape.Cytoscape;
+
+import cytoscape.data.readers.XGMMLReader;
+
+import giny.model.RootGraph;
+
+import junit.framework.TestCase;
+import junit.framework.TestSuite;
+
+import java.io.File;
+
+
+/**
+ *
+ */
+public class XGMMLReaderTest extends TestCase {
+ private static String testDataDir = "src/test/resources/testData";
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ */
+ public static void main(String[] args) {
+ if (args.length != 1) {
+ System.out.println("Error! must supply path to test data directory on command line");
+ Cytoscape.exit(0);
+ }
+
+ testDataDir = args[0];
+
+ junit.textui.TestRunner.run(new TestSuite(XGMMLReaderTest.class));
+ }
+
+ /**
+ * Creates a new XGMMLReaderTest object.
+ *
+ * @param arg0 DOCUMENT ME!
+ */
+ public XGMMLReaderTest(String arg0) {
+ super(arg0);
+
+ if (AllTests.runAllTests()) {
+ testDataDir = "src/test/resources/testData";
+ }
+ }
+
+ protected void setUp() throws Exception {
+ super.setUp();
+ }
+
+ protected void tearDown() throws Exception {
+ super.tearDown();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testXGMMLGraphRead() throws Exception {
+ AllTests.standardOut("testXGMMLGraphRead");
+
+ XGMMLReader reader = new XGMMLReader(testDataDir+"/galFiltered2.xgmml");
+
+ File testfile = new File(testDataDir+"/galFiltered2.xgmml");
+
+ if (testfile.canRead()) {
+ System.out.println("Reading XGMML: " + testfile.getAbsolutePath());
+
+ RootGraph network = Cytoscape.getRootGraph();
+ network.removeNodes(network.nodesList());
+ reader.read();
+
+ if (network == null) {
+ System.out.println("Root Graph is null!");
+
+ return;
+ }
+
+ System.out.println("XGMMLReader: Node count = " + network.getNodeCount());
+ System.out.println("XGMMLReader: Edge count = " + network.getEdgeCount());
+
+ assertTrue("XGMMLReader: Node count, expect 331, got " + network.getNodeCount(),
+ network.getNodeCount() == 331);
+ assertTrue("XGMMLReader: Edge count, expect 362, got " + network.getEdgeCount(),
+ network.getEdgeCount() == 362);
+ } else {
+ System.out.println("No such file");
+ }
+ } // testGraphRead
+
+ /* Too large?
+
+ public void testXGMMLHugeGraphRead() throws Exception {
+ AllTests.standardOut("testXGMMLHugeGraphRead");
+ XGMMLReader reader = new XGMMLReader("testData/BINDyeast.xgmml");
+
+ File testfile = new File("testData/BINDyeast.xgmml");
+ if(testfile.canRead()) {
+ System.out.println("Reading XGMML: " + testfile.getAbsolutePath());
+ RootGraph network = Cytoscape.getRootGraph();
+ network.removeNodes(network.nodesList());
+ reader.read();
+
+
+ if(network == null) {
+ System.out.println("Root Graph is null!");
+ return;
+ }
+ System.out.println("XGMMLReader: Node count = " + network.getNodeCount());
+ System.out.println("XGMMLReader: Edge count = " + network.getEdgeCount());
+
+ assertTrue("XGMMLReader: Node count, expect 23505, got " + network.getNodeCount(),
+ network.getNodeCount() == 23505);
+ assertTrue("XGMMLReader: Edge count, expect 60457, got " + network.getEdgeCount(),
+ network.getEdgeCount() == 60457);
+ } else {
+ System.out.println("No such file");
+ }
+
+
+ } // testXGMMLHugeGraphRead
+
+ */
+}
diff --git a/application/src/test/java/cytoscape/data/readers/degenerate.sif b/application/src/test/java/cytoscape/data/readers/degenerate.sif
new file mode 100644
index 0000000..f3f1742
--- /dev/null
+++ b/application/src/test/java/cytoscape/data/readers/degenerate.sif
@@ -0,0 +1,9 @@
+YNL312W
+YNL314W
+YOL051W
+YOR194C
+YOR377W
+YPL075W
+YPL248C
+YPL259C
+YPR065W
diff --git a/application/src/test/java/cytoscape/data/readers/multiWordProteins.sif b/application/src/test/java/cytoscape/data/readers/multiWordProteins.sif
new file mode 100644
index 0000000..93001ac
--- /dev/null
+++ b/application/src/test/java/cytoscape/data/readers/multiWordProteins.sif
@@ -0,0 +1,30 @@
+LPS interactsWith TLR4
+LPS interactsWith MD-2
+LPS interactsWith TLR4
+ADOH interactsWith LPS
+TLR4 interactsWith MyD88
+TLR4 interactsWith IRAK Complex
+TLR4 interactsWith TIRAP
+TRAF6 interactsWith IRAK Complex
+Uev1a/UBc13 Ubiquitin-conjugating Complex interactsWith TRAF6
+TRAF6 interactsWith TAK1
+A20 interactsWith TRAF6
+TAK1 interactsWith IKK-beta
+IKK-beta interactsWith I-kappa-B-alpha
+I-kappa-B-alpha interactsWith p50
+I-kappa-B-alpha interactsWith p65
+SCF Ubiquitin Ligase interactsWith I-kappa-B-alpha
+26S ubiquitin dependent proteasome interactsWith I-kappa-B-alpha
+TLR4 interactsWith TRIF
+TRIF interactsWith IRF3
+IRAK4 interactsWith MyD88
+IRAK4 interactsWith IRAK1
+IRAK1 interactsWith MyD88
+IRAK1 interactsWith TRAF6
+TRAF6 interactsWith CD40
+TRAF6 interactsWith RANK
+TRAF6 interactsWith IRAK1
+TRAF6 interactsWith IRAK2
+TRAF6 interactsWith IRAKM
+TRAF6 interactsWith RIP2 ABCDE oopah HJKOL coltrane
+
diff --git a/application/src/test/java/cytoscape/data/readers/multiWordProteinsFileTrailingSpaces.sif b/application/src/test/java/cytoscape/data/readers/multiWordProteinsFileTrailingSpaces.sif
new file mode 100644
index 0000000..7d522bd
--- /dev/null
+++ b/application/src/test/java/cytoscape/data/readers/multiWordProteinsFileTrailingSpaces.sif
@@ -0,0 +1,30 @@
+LPS interactsWith TLR4
+LPS interactsWith MD-2
+LPS interactsWith TLR4
+ADOH interactsWith LPS
+TLR4 interactsWith MyD88
+TLR4 interactsWith IRAK Complex
+TLR4 interactsWith TIRAP
+TRAF6 interactsWith IRAK Complex
+Uev1a/UBc13 Ubiquitin-conjugating Complex interactsWith TRAF6
+TRAF6 interactsWith TAK1
+A20 interactsWith TRAF6
+TAK1 interactsWith IKK-beta
+IKK-beta interactsWith I-kappa-B-alpha
+I-kappa-B-alpha interactsWith p50
+I-kappa-B-alpha interactsWith p65
+SCF Ubiquitin Ligase interactsWith I-kappa-B-alpha
+26S ubiquitin dependent proteasome interactsWith I-kappa-B-alpha
+TLR4 interactsWith TRIF
+TRIF interactsWith IRF3
+IRAK4 interactsWith MyD88
+IRAK4 interactsWith IRAK1
+IRAK1 interactsWith MyD88
+IRAK1 interactsWith TRAF6
+TRAF6 interactsWith CD40
+TRAF6 interactsWith RANK
+TRAF6 interactsWith IRAK1
+TRAF6 interactsWith IRAK2
+TRAF6 interactsWith IRAKM
+TRAF6 interactsWith RIP2 ABCDE oopah HJKOL coltrane
+
diff --git a/application/src/test/java/cytoscape/data/readers/sample.sif b/application/src/test/java/cytoscape/data/readers/sample.sif
new file mode 100644
index 0000000..fcc91cd
--- /dev/null
+++ b/application/src/test/java/cytoscape/data/readers/sample.sif
@@ -0,0 +1,25 @@
+YNL312W pd YPL111W
+YNL314W pd YIR028W
+YNL314W pd YIR031C
+YOL051W pd YBR018C
+YOL051W pd YBR019C
+YOL051W pd YBR020W
+YOL051W pd YLR081W
+YOR194C pd YCL018W
+YOR377W pd YFL018C
+YPL075W pd YAL038W
+YPL075W pd YCR012W
+YPL075W pd YDR050C YGR254W YHR174W
+YPL075W pd YOL086C
+YPL248C pd MEL1
+YPL248C pd YBR018C
+YPL248C pd YBR019C
+YPL248C pd YBR020W
+YPL248C pd YJR048W
+YPL248C pd YLR081W
+YPL248C pd YML051W
+YPL248C pd YOR120W
+YPL259C pd YGR209C
+YPR065W pd YDR044W
+YPR065W pd YJR047C
+YPR065W pd YPR065W
diff --git a/application/src/test/java/cytoscape/data/servers/BioDataServerTest.java b/application/src/test/java/cytoscape/data/servers/BioDataServerTest.java
new file mode 100755
index 0000000..0b430f6
--- /dev/null
+++ b/application/src/test/java/cytoscape/data/servers/BioDataServerTest.java
@@ -0,0 +1,377 @@
+/*
+ File: BioDataServerTest.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// BioDataServerTest.java
+package cytoscape.data.servers;
+
+import cytoscape.data.annotation.AnnotationDescription;
+
+import cytoscape.data.servers.BioDataServer;
+
+import junit.framework.TestCase;
+import junit.framework.TestSuite;
+
+
+/**
+ * test the DataServer class, running it in process (not via RMI)
+ */
+public class BioDataServerTest extends TestCase {
+ /**
+ * Creates a new BioDataServerTest object.
+ *
+ * @param name DOCUMENT ME!
+ */
+ public BioDataServerTest(String name) {
+ super(name);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void setUp() throws Exception {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void tearDown() throws Exception {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void notestThesaurusFromFlatFile() throws Exception {
+ System.out.println("testThesaurusFromFlatFile");
+
+ BioDataServer server = new BioDataServer();
+ String[] thesaurusFiles = { "yeastThesaurusSmall.txt" };
+ server.loadThesaurusFiles(thesaurusFiles);
+
+ String species = "Saccharomyces cerevisiae";
+ String canonicalName = "YOL165C";
+ String commonName = "AAD15";
+ assertTrue(server.getCommonName(species, canonicalName).equals(commonName));
+
+ canonicalName = "YPR060C";
+ commonName = "ARO7";
+ assertTrue(server.getCommonName(species, canonicalName).equals(commonName));
+ assertTrue(server.getCommonName(species, commonName).equals(commonName));
+ assertTrue(server.getCanonicalName(species, commonName).equals(canonicalName));
+ assertTrue(server.getCanonicalName(species, canonicalName).equals(canonicalName));
+
+ String[] allCommonNames = server.getAllCommonNames(species, canonicalName);
+ assertTrue(allCommonNames.length == 4);
+ } // testThesaurusFromFlatFile
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void notestThesaurusWithAbsentEntries() throws Exception {
+ System.out.println("testThesaurusWithAbsentEntries");
+
+ BioDataServer server = new BioDataServer();
+ String[] thesaurusFiles = { "yeastThesaurusSmall.txt" };
+ server.loadThesaurusFiles(thesaurusFiles);
+
+ String species = "duck";
+ String canonicalName = "duck37";
+ String commonName = "duck37";
+
+ assertTrue(server.getCommonName("duck", "mallardase").equals("mallardase"));
+ assertTrue(server.getCanonicalName("duck", "mallardase").equals("mallardase"));
+
+ String[] allCommonNames = server.getAllCommonNames("duck", "grebase");
+ assertTrue(allCommonNames.length == 1);
+ } // testThesaurusWithAbsentEntries
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void notestReadGoYeastAnnotation() throws Exception {
+ System.out.println("testReadGoYeastAnnotation");
+
+ // read manifest, a local file, and the files it names:
+ //
+ // ontology=go.onto
+ // annotation=bioproc.anno
+ // annotation=molfunc.anno
+ // annotation=cellcomp.anno
+ String manifest = "annotations/goYeast/manifest";
+ BioDataServer server = new BioDataServer(manifest);
+
+ AnnotationDescription[] aDescs = server.getAnnotationDescriptions();
+ assertTrue(aDescs.length == 3);
+
+ String species = "Saccharomyces cerevisiae";
+ String curator = "GO";
+ String orf = "YER033C";
+
+ int[] ids = server.getClassifications(species, curator, "Molecular Function", orf);
+ assertTrue(ids.length == 1);
+ assertTrue(ids[0] == 5554);
+
+ ids = server.getClassifications(species, curator, "Cellular Component", orf);
+ assertTrue(ids.length == 1);
+ assertTrue(ids[0] == 8372);
+
+ ids = server.getClassifications(species, curator, "Biological Process", orf);
+ assertTrue(ids.length == 1);
+ assertTrue(ids[0] == 4);
+
+ orf = "YNR016C";
+ ids = server.getClassifications(species, curator, "Molecular Function", orf);
+ assertTrue(ids.length == 2);
+
+ int[] expected0 = { 3989, 4075 };
+ assertTrue(containedIn(ids, expected0));
+
+ ids = server.getClassifications(species, curator, "Cellular Component", orf);
+ assertTrue(ids.length == 2);
+
+ int[] expected1 = { 5829, 5789 };
+ assertTrue(containedIn(ids, expected1));
+
+ ids = server.getClassifications(species, curator, "Biological Process", orf);
+ assertTrue(ids.length == 2);
+
+ int[] expected2 = { 6633, 6998 };
+ assertTrue(containedIn(ids, expected2));
+ } // testReadGoYeastAnnotation
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void notestReadViaHTTP() throws Exception {
+ System.out.println("testReadViaHTTP");
+
+ // read manifest, via http, and the files it names (which are
+ // implicitly at the same url:
+ //
+ // ontology=go.onto
+ // annotation=bioproc.anno
+ // annotation=molfunc.anno
+ // annotation=cellcomp.anno
+ String manifest = "http://db.systemsbiology.net:8080/cytoscape/annotation/testDoNotDelete/manifest";
+
+ BioDataServer server = new BioDataServer(manifest);
+
+ AnnotationDescription[] aDescs = server.getAnnotationDescriptions();
+ assertTrue(aDescs.length == 4);
+
+ String species = "Saccharomyces cerevisiae";
+ String curator = "GO";
+ String orf = "YER033C";
+
+ int[] ids = server.getClassifications(species, curator, "Molecular Function", orf);
+ assertTrue(ids.length == 1);
+ assertTrue(ids[0] == 5554);
+
+ ids = server.getClassifications(species, curator, "Cellular Component", orf);
+ assertTrue(ids.length == 1);
+ assertTrue(ids[0] == 8372);
+
+ ids = server.getClassifications(species, curator, "Biological Process", orf);
+ assertTrue(ids.length == 1);
+ assertTrue(ids[0] == 4);
+
+ orf = "YNR016C";
+ ids = server.getClassifications(species, curator, "Molecular Function", orf);
+ assertTrue(ids.length == 2);
+
+ int[] expected0 = { 3989, 4075 };
+ assertTrue(containedIn(ids, expected0));
+
+ ids = server.getClassifications(species, curator, "Cellular Component", orf);
+ assertTrue(ids.length == 2);
+
+ int[] expected1 = { 5829, 5789 };
+ assertTrue(containedIn(ids, expected1));
+
+ ids = server.getClassifications(species, curator, "Biological Process", orf);
+ assertTrue(ids.length == 2);
+
+ int[] expected2 = { 6633, 6998 };
+ assertTrue(containedIn(ids, expected2));
+
+ curator = "KEGG";
+ ids = server.getClassifications(species, curator, "Metabolic Pathways", orf);
+ assertTrue(ids.length == 4);
+
+ int[] expected3 = { 61, 620, 640, 253 };
+ assertTrue(containedIn(ids, expected3));
+
+ String canonicalName = "YAL001C";
+ String commonName = "TFC3";
+ String synonym2 = "TSV115";
+ String synonym3 = "FUN24";
+
+ assertTrue(server.getCommonName(species, canonicalName).equals(commonName));
+ assertTrue(server.getCanonicalName(species, commonName).equals(canonicalName));
+ assertTrue(server.getCanonicalName(species, synonym2).equals(canonicalName));
+ assertTrue(server.getCanonicalName(species, synonym3).equals(canonicalName));
+ assertTrue(server.getCanonicalName(species, canonicalName).equals(canonicalName));
+ } // testReadViaHttp
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void notestReadKeggHaloAnnotation() throws Exception {
+ System.out.println("testReadKeggHaloAnnotation");
+
+ // read manifest, a local file, and the files it names:
+ //
+ // annotation=pathways.anno
+ // ontology=ontology
+ String manifest = "annotations/keggHalo/manifest";
+ BioDataServer server = new BioDataServer(manifest);
+
+ AnnotationDescription[] aDescs = server.getAnnotationDescriptions();
+ assertTrue(aDescs.length == 1);
+
+ String species = "Halobacterium sp.";
+ String curator = "KEGG";
+ String orf = "VNG1873G";
+ String annotationType = "Metabolic Pathways";
+
+ int[] ids = server.getClassifications(species, curator, annotationType, orf);
+ assertTrue(ids.length == 3);
+
+ int[] expected = { 20, 720, 480 };
+ assertTrue(containedIn(ids, expected));
+ } // testReadKeggHaloAnnotation
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testReadAnnotationsWithTwoOntologies() throws Exception {
+ System.out.println("testReadAnnotationsWithTwoOntologies");
+
+ //String manifest = "annotations/humanKeggAndGO/manifest.both";
+ String manifest = "src/test/resources/testData/humanKeggAndGO/manifest.both";
+ BioDataServer server = new BioDataServer(manifest);
+
+ String species = "Homo sapiens";
+ String curator = "KEGG";
+
+ String canonicalName = "NP_647593";
+ String commonName = "qqq";
+ String synonym2 = "QQQ";
+
+ assertTrue(server.getCommonName(species, canonicalName).equals(commonName));
+ assertTrue(server.getCanonicalName(species, commonName).equals(canonicalName));
+ assertTrue(server.getCanonicalName(species, synonym2).equals(canonicalName));
+ assertTrue(server.getCanonicalName(species, canonicalName).equals(canonicalName));
+
+ String annotationType = "Metabolic Pathways";
+
+ int[] ids = server.getClassifications(species, curator, annotationType, canonicalName);
+ assertTrue(ids.length == 6);
+
+ int[] expected0 = { 120, 350, 561, 260, 300, 40 };
+ assertTrue(containedIn(ids, expected0));
+
+ AnnotationDescription[] aDescs = server.getAnnotationDescriptions();
+
+ assertTrue(aDescs.length == 4);
+
+ curator = "GO";
+
+ String annotationType1 = "Molecular Function";
+ String annotationType2 = "Cellular Component";
+ String annotationType3 = "Biological Process";
+
+ ids = server.getClassifications(species, curator, annotationType1, canonicalName);
+ assertTrue(ids.length == 1);
+ assertTrue(ids[0] == 8181);
+
+ ids = server.getClassifications(species, curator, annotationType2, canonicalName);
+ assertTrue(ids.length == 2);
+
+ int[] expected2 = { 5871, 15629 };
+ assertTrue(containedIn(ids, expected2));
+
+ ids = server.getClassifications(species, curator, annotationType3, canonicalName);
+ assertTrue(ids.length == 6);
+
+ int[] expected3 = { 6899, 7268, 8099, 8283, 30154, 45786 };
+ assertTrue(containedIn(ids, expected3));
+ } // testReadAnnotationsWithTwoOntologies
+
+ private boolean containedIn(int[] a, int[] b) {
+ for (int i = 0; i < a.length; i++) {
+ boolean foundA = false;
+
+ for (int j = 0; j < b.length; j++)
+ if (b[j] == a[i]) {
+ foundA = true;
+
+ break;
+ }
+
+ if (!foundA)
+ return false;
+ } // for i
+
+ return true;
+ } // containedIn
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ */
+ public static void main(String[] args) {
+ junit.textui.TestRunner.run(new TestSuite(BioDataServerTest.class));
+ System.exit(0); // needed because otherwise UnicastRemoteObject runs forever
+ }
+} // BioDataServerTest
diff --git a/application/src/test/java/cytoscape/data/synonyms/AliasesTest.java b/application/src/test/java/cytoscape/data/synonyms/AliasesTest.java
new file mode 100644
index 0000000..c00a27b
--- /dev/null
+++ b/application/src/test/java/cytoscape/data/synonyms/AliasesTest.java
@@ -0,0 +1,109 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data.synonyms;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.data.synonyms.AliasType;
+import cytoscape.data.synonyms.Aliases;
+
+import giny.model.Node;
+
+import junit.framework.TestCase;
+
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+
+
+/**
+ *
+ */
+public class AliasesTest extends TestCase {
+ Aliases al;
+ List<String> sampleData;
+
+ protected void setUp() throws Exception {
+ super.setUp();
+
+ sampleData = new ArrayList<String>();
+ sampleData.add("alias1");
+ sampleData.add("alias2");
+ sampleData.add("alias3");
+
+ al = new Aliases(AliasType.NODE);
+ }
+
+ protected void tearDown() throws Exception {
+ super.tearDown();
+ al = null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testAdd() {
+ Iterator it = Cytoscape.getRootGraph().nodesIterator();
+
+ while (it.hasNext()) {
+ Node node = (Node) it.next();
+ String name = node.getIdentifier();
+ al.add(name, sampleData);
+ al.add(name, "testAlias");
+ assertTrue(al.getAliases(name).contains("alias2"));
+
+ assertEquals(4, al.getAliases(name).size());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testRemove() {
+ Iterator it = Cytoscape.getRootGraph().nodesIterator();
+
+ while (it.hasNext()) {
+ Node node = (Node) it.next();
+ String name = node.getIdentifier();
+ al.add(name, sampleData);
+ assertEquals(3, al.getAliases(name).size());
+ al.remove(name, "alias3");
+
+ assertEquals(2, al.getAliases(name).size());
+ assertTrue(al.getAliases(name).contains("alias2"));
+ assertFalse(al.getAliases(name).contains("alias3"));
+ }
+ }
+}
diff --git a/application/src/test/java/cytoscape/data/synonyms/ThesaurusTest.java b/application/src/test/java/cytoscape/data/synonyms/ThesaurusTest.java
new file mode 100755
index 0000000..126dfa9
--- /dev/null
+++ b/application/src/test/java/cytoscape/data/synonyms/ThesaurusTest.java
@@ -0,0 +1,263 @@
+/*
+ File: ThesaurusTest.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// ThesaurusTest.java
+package cytoscape.data.synonyms;
+
+import cytoscape.AllTests;
+
+import cytoscape.data.synonyms.*;
+
+import junit.framework.*;
+
+import java.io.*;
+
+
+/**
+ * test the Thesaurus class
+ */
+public class ThesaurusTest extends TestCase {
+ /**
+ * Creates a new ThesaurusTest object.
+ *
+ * @param name DOCUMENT ME!
+ */
+ public ThesaurusTest(String name) {
+ super(name);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void setUp() throws Exception {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void tearDown() throws Exception {
+ }
+
+ /**
+ * make sure that the ctor properly initializes all relevant data structures
+ * as seen through the standard getter methods
+ */
+ public void testCtor() throws Exception {
+ AllTests.standardOut("testCtor");
+
+ String species = "fugu";
+ Thesaurus thesaurus = new Thesaurus(species);
+ assertTrue(thesaurus.nodeLabelCount() == 0);
+ assertTrue(thesaurus.getSpecies().equals(species));
+ } // testCtor
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testAddSimplePairs() throws Exception {
+ AllTests.standardOut("testAddSimplePairs");
+
+ String[] canonical = { "YCR097W", "YCR096C", "YMR056C", "YBR085W" };
+ String[] common = { "MAT1A", "MATA2", "AAC1", "AAC3" };
+
+ assertTrue(canonical.length == common.length);
+
+ String species = "Saccharomyces cerevisiae";
+ Thesaurus thesaurus = new Thesaurus(species);
+
+ assertTrue(thesaurus.getSpecies().equals(species));
+
+ for (int i = 0; i < canonical.length; i++)
+ thesaurus.add(canonical[i], common[i]);
+
+ assertTrue(thesaurus.nodeLabelCount() == 4);
+
+ for (int i = 0; i < canonical.length; i++) {
+ assertTrue(thesaurus.getCommonName(canonical[i]).equals(common[i]));
+ assertTrue(thesaurus.getNodeLabel(common[i]).equals(canonical[i]));
+
+ String[] allCommonNames = thesaurus.getAllCommonNames(canonical[i]);
+ assertTrue(allCommonNames.length == 1);
+ assertTrue(allCommonNames[0].equals(common[i]));
+ }
+ } // testAddSimplePairs
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testAddDuplicatePairs() throws Exception {
+ AllTests.standardOut("testAddDuplicatePairs");
+
+ String[] canonical = { "YCR097W", "YCR096C", "YMR056C", "YBR085W" };
+ String[] common = { "MAT1A", "MATA2", "AAC1", "AAC3" };
+
+ assertTrue(canonical.length == common.length);
+
+ String species = "Saccharomyces cerevisiae";
+ Thesaurus thesaurus = new Thesaurus(species);
+
+ for (int i = 0; i < canonical.length; i++)
+ thesaurus.add(canonical[i], common[i]);
+
+ assertTrue(thesaurus.nodeLabelCount() == 4);
+
+ try { // adding duplicates should throw an exception
+ thesaurus.add(canonical[canonical.length - 1], common[canonical.length - 1]);
+ assertTrue(true); // should not be reached
+ } catch (IllegalArgumentException e) {
+ ;
+ }
+
+ try { // adding duplicates should throw an exception
+ thesaurus.add(canonical[canonical.length - 1], "yojo");
+ assertTrue(true); // should not be reached
+ } catch (IllegalArgumentException e) {
+ ;
+ }
+
+ try { // adding duplicates should throw an exception
+ thesaurus.add("yojoYama", common[canonical.length - 1]);
+ assertTrue(true); // should not be reached
+ } catch (IllegalArgumentException e) {
+ ;
+ }
+ } // testAddDuplicatePairs
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testAddRemoveAddAgain() throws Exception {
+ AllTests.standardOut("testAddRemoveAddAgain");
+
+ String[] canonical = { "YCR097W", "YCR096C", "YMR056C", "YBR085W" };
+ String[] common = { "MAT1A", "MATA2", "AAC1", "AAC3" };
+
+ assertTrue(canonical.length == common.length);
+
+ String species = "Saccharomyces cerevisiae";
+ Thesaurus thesaurus = new Thesaurus(species);
+
+ for (int i = 0; i < canonical.length; i++)
+ thesaurus.add(canonical[i], common[i]);
+
+ assertTrue(thesaurus.nodeLabelCount() == 4);
+
+ for (int i = 0; i < canonical.length; i++)
+ thesaurus.remove(canonical[i], common[i]);
+
+ assertTrue(thesaurus.nodeLabelCount() == 0);
+
+ for (int i = 0; i < canonical.length; i++)
+ thesaurus.add(canonical[i], common[i]);
+
+ assertTrue(thesaurus.nodeLabelCount() == 4);
+
+ for (int i = 0; i < canonical.length; i++) {
+ assertTrue(thesaurus.getCommonName(canonical[i]).equals(common[i]));
+ assertTrue(thesaurus.getNodeLabel(common[i]).equals(canonical[i]));
+
+ String[] allCommonNames = thesaurus.getAllCommonNames(canonical[i]);
+ assertTrue(allCommonNames.length == 1);
+ assertTrue(allCommonNames[0].equals(common[i]));
+ }
+ } // testAddRemoveAddAgain
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testAddAlternateCommonNames() throws Exception {
+ AllTests.standardOut("testAddAlternateCommonNames");
+
+ String[] canonical = { "YCR097W", "YCR096C", "YMR056C", "YBR085W" };
+ String[] common = { "MAT1A", "MATA2", "AAC1", "AAC3" };
+
+ String[][] alternates = {
+ { "alt00", "alt01", "alt02" },
+ { "alt10", "alt11", "alt12" },
+ { "alt20", "alt21", "alt22" },
+ { "alt30", "alt31", "alt32" }
+ };
+
+ assertTrue(canonical.length == common.length);
+
+ String species = "Saccharomyces cerevisiae";
+ Thesaurus thesaurus = new Thesaurus(species);
+
+ for (int i = 0; i < canonical.length; i++)
+ thesaurus.add(canonical[i], common[i]);
+
+ assertTrue(thesaurus.nodeLabelCount() == 4);
+
+ for (int i = 0; i < canonical.length; i++)
+ for (int j = 0; j < alternates[i].length; j++)
+ thesaurus.addAlternateCommonName(canonical[i], alternates[i][j]);
+
+ // now each canonicalName should have 4 common names: 1 preferred
+ // and 3 alternate
+ for (int i = 0; i < canonical.length; i++) {
+ String[] allCommonNames = thesaurus.getAllCommonNames(canonical[i]);
+ assertTrue(allCommonNames.length == 4);
+ assertTrue(allCommonNames[0].equals(common[i]));
+
+ for (int j = 0; j < alternates[i].length; j++) {
+ String alternate = alternates[i][j];
+ assertTrue(allCommonNames[j + 1].equals(alternates[i][j]));
+ } // for j
+ } // for i
+ } // testAddAlternateCommonNames
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ */
+ public static void main(String[] args) {
+ junit.textui.TestRunner.run(new TestSuite(ThesaurusTest.class));
+ }
+} // ThesaurusTest
diff --git a/application/src/test/java/cytoscape/data/synonyms/readers/ThesaurusFlatFileReaderTest.java b/application/src/test/java/cytoscape/data/synonyms/readers/ThesaurusFlatFileReaderTest.java
new file mode 100755
index 0000000..d18bce8
--- /dev/null
+++ b/application/src/test/java/cytoscape/data/synonyms/readers/ThesaurusFlatFileReaderTest.java
@@ -0,0 +1,144 @@
+/*
+ File: ThesaurusFlatFileReaderTest.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// ThesaurusFlatFileReaderTest
+package cytoscape.data.synonyms.readers;
+
+import cytoscape.AllTests;
+
+import cytoscape.data.synonyms.*;
+import cytoscape.data.synonyms.readers.ThesaurusFlatFileReader;
+
+import junit.framework.*;
+
+import org.jdom.*;
+
+import org.jdom.input.*;
+
+import org.jdom.output.*;
+
+import java.io.*;
+
+import java.util.*;
+
+
+/**
+ * test the ThesaurusFlatFileReader class
+ */
+public class ThesaurusFlatFileReaderTest extends TestCase {
+ /**
+ * Creates a new ThesaurusFlatFileReaderTest object.
+ *
+ * @param name DOCUMENT ME!
+ */
+ public ThesaurusFlatFileReaderTest(String name) {
+ super(name);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void setUp() throws Exception {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void tearDown() throws Exception {
+ }
+
+ /**
+ * read a small sample yeast thesaurus file
+ */
+ public void testReadSmallYeastThesaurus() throws Exception {
+ AllTests.standardOut("testReadSmallYeastThesaurus");
+
+ String filename = "src/test/resources/testData/yeastSmall.txt";
+
+ // if (AllTests.runAllTests()) {
+ // filename =
+ // "src/cytoscape/data/synonyms/readers/unitTests/sampleData/yeastSmall.txt";
+ // }
+ ThesaurusFlatFileReader reader = new ThesaurusFlatFileReader(filename);
+ Thesaurus thesaurus = reader.getThesaurus();
+
+ assertTrue(thesaurus.getSpecies().equals("Saccharomyces cerevisiae"));
+ assertTrue(thesaurus.nodeLabelCount() == 8);
+
+ // the values of these next 3 arrays are extracted, by hand, from the flat file
+ String[] canonical = {
+ "YHR047C", "YBL074C", "YKL106W", "YLR027C", "YGL119W", "YBR236C",
+ "YKL112W", "YMR072W"
+ };
+ String[] common = { "AAP1'", "AAR2", "AAT1", "AAT2", "ABC1", "ABD1", "ABF1", "ABF2" };
+ int[] alternateNameCount = { 1, 0, 0, 1, 0, 0, 3, 0 };
+
+ for (int i = 0; i < canonical.length; i++) {
+ assertTrue(thesaurus.getCommonName(canonical[i]).equals(common[i]));
+ assertTrue(thesaurus.getNodeLabel(common[i]).equals(canonical[i]));
+
+ String[] alternateNames = thesaurus.getAlternateCommonNames(canonical[i]);
+
+ if (i == 6) { // do a name-by-name comparison for this orf with 3 alternate names
+
+ String orf = canonical[i];
+ assertTrue(orf.equals("YKL112W"));
+ assertTrue(alternateNames[0].equals("BAF1"));
+ assertTrue(alternateNames[1].equals("OBF1"));
+ assertTrue(alternateNames[2].equals("REB2"));
+ } // i == 6
+
+ for (int j = 0; j < alternateNames.length; j++)
+ AllTests.standardOut(canonical[i] + " -> " + alternateNames[j]);
+
+ assertTrue(alternateNames.length == alternateNameCount[i]);
+ }
+ } // testReadSmallYeastThesaurus
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ */
+ public static void main(String[] args) {
+ junit.textui.TestRunner.run(new TestSuite(ThesaurusFlatFileReaderTest.class));
+ } // main
+} // class ThesaurusFlatFileReaderTest
diff --git a/application/src/test/java/cytoscape/data/writers/CyAttributesWriterTest.java b/application/src/test/java/cytoscape/data/writers/CyAttributesWriterTest.java
new file mode 100644
index 0000000..5a6d709
--- /dev/null
+++ b/application/src/test/java/cytoscape/data/writers/CyAttributesWriterTest.java
@@ -0,0 +1,201 @@
+/*
+ File: CyAttributesWriterTest.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.data.writers;
+
+import cytoscape.data.CyAttributes;
+import cytoscape.data.CyAttributesImpl;
+
+import cytoscape.data.readers.CyAttributesReader;
+
+import junit.framework.TestCase;
+
+import java.io.File;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.StringWriter;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Set;
+import java.util.TreeSet;
+
+
+/**
+ * Tests the CyAttributesWriter Class.
+ *
+ * Note 2/6/2008 by kono:
+ * This code tests CyAttributesWriter2, not the original one.
+ *
+ */
+public class CyAttributesWriterTest extends TestCase {
+ /**
+ * Tests Writing out of Scalar Values.
+ *
+ * @throws IOException
+ * IO Error.
+ */
+ public void testWriterScalars() throws IOException {
+ System.out.println("################## CyAttributesWriter2 Test start #######################");
+
+ // Load test data.
+ CyAttributes cyAttributes = new CyAttributesImpl();
+ File file = new File("src/test/resources/testData/galFiltered.nodeAttrs1");
+ FileReader reader = new FileReader(file);
+ CyAttributesReader.loadAttributes(cyAttributes, reader);
+
+ // Write attributes
+ StringWriter sw = new StringWriter();
+ CyAttributesWriter cw2 = new CyAttributesWriter(cyAttributes, "TestNodeAttribute1", sw);
+ cw2.writeAttributes();
+
+ String output = sw.toString();
+ String[] lines = output.split(System.getProperty("line.separator"));
+ Set<String> allLines = new TreeSet<String>();
+
+ for (String line : lines) {
+ System.out.println("Line = " + line);
+ allLines.add(line);
+ }
+
+ if(sw != null) {
+ sw.close();
+ sw = null;
+ }
+ assertEquals(lines.length, allLines.size());
+ assertTrue(allLines.contains("TestNodeAttribute1 (class=java.lang.Integer)"));
+ assertTrue(allLines.contains("YDR309C = 1"));
+ assertTrue(allLines.contains("YML024W = 2"));
+ allLines = null;
+ lines = null;
+
+ System.out.println("################## CyAttributesWriter2 Test end #######################");
+ }
+
+ private void checkSimpleLists(char sep) throws IOException
+ {
+ StringWriter writer = new StringWriter();
+
+ System.out.println("################## CyAttributesWriter2 List Test start #######################");
+
+ CyAttributes cyAttributes = new CyAttributesImpl();
+ File file = new File("src/test/resources/testData/implicitStringArray.attribute");
+ FileReader reader = new FileReader(file);
+ CyAttributesReader.loadAttributes(cyAttributes, reader);
+
+ // Add a new item
+ final List<String> list = new ArrayList<String>();
+ list.add(new String("Apple"));
+ list.add(new String("Orange"));
+ list.add(new String("Banana"));
+
+ cyAttributes.setListAttribute("ABC_123", "GO_molecular_function_level_4", list);
+
+ CyAttributesWriter writer2 = new CyAttributesWriter(cyAttributes, "GO_molecular_function_level_4", writer);
+ writer2.writeAttributes();
+
+ String output = writer.toString();
+ String[] lines = output.split(System.getProperty("line.separator"));
+ Set<String> allLines = new TreeSet<String>();
+
+ for (String line : lines) {
+ System.out.println("Line = " + line);
+ allLines.add(line);
+ }
+
+ if(writer != null) {
+ writer.close();
+ writer = null;
+ }
+
+ /*
+ * Order of entries are not important.
+ * Should focus on which attributes are actually saved.
+ */
+ assertEquals(allLines.size(), lines.length);
+ assertTrue(allLines.contains("GO_molecular_function_level_4 (class=java.lang.String)"));
+ assertTrue(allLines.contains("HSD17B2 = (membrane::intracellular)"));
+ assertTrue(allLines.contains("E2F4 = (DNA" + sep + "binding)"));
+ assertTrue(allLines.contains("AP1G1 = (intracellular::clathrin" + sep + "adaptor::intracellular" + sep + "transporter)"));
+ assertTrue(allLines.contains("ABC_123 = (Apple::Orange::Banana)"));
+ assertTrue(allLines.contains("CDH3 = (cell" + sep + "adhesion" + sep + "molecule)"));
+
+ allLines = null;
+ lines = null;
+
+ System.out.println("################## CyAttributesWriter2 List Test end #######################");
+ }
+
+ /**
+ * Tests Writing out of Lists.
+ *
+ * @throws IOException
+ * IO Error.
+ */
+ public void testWriteSimpleLists1() throws IOException {
+ System.clearProperty(CyAttributesWriter.ENCODE_PROPERTY);
+ checkSimpleLists('+');
+ }
+
+ /**
+ * Tests Writing out of Lists.
+ *
+ * @throws IOException
+ * IO Error.
+ */
+ public void testWriteSimpleLists2() throws IOException {
+ System.setProperty(CyAttributesWriter.ENCODE_PROPERTY, "false");
+ checkSimpleLists(' ');
+ }
+
+ /**
+ * Tests Writing out of Lists.
+ *
+ * @throws IOException
+ * IO Error.
+ */
+ public void testWriteSimpleLists3() throws IOException {
+ System.setProperty(CyAttributesWriter.ENCODE_PROPERTY, "true");
+ checkSimpleLists('+');
+ }
+
+ /**
+ * Runs just this one unit test.
+ */
+ public static void main(String[] args) {
+ junit.textui.TestRunner.run(CyAttributesWriterTest.class);
+ }
+}
diff --git a/application/src/test/java/cytoscape/data/writers/CytoscapeSessionWriterTest.java b/application/src/test/java/cytoscape/data/writers/CytoscapeSessionWriterTest.java
new file mode 100644
index 0000000..5033647
--- /dev/null
+++ b/application/src/test/java/cytoscape/data/writers/CytoscapeSessionWriterTest.java
@@ -0,0 +1,70 @@
+/*
+ File: XGMMLWriterTest.java
+
+ Copyright (c) 2009, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.data.writers;
+
+import cytoscape.CyNetwork;
+import junit.framework.TestCase;
+import cytoscape.Cytoscape;
+
+/**
+ *
+ * @author Noel Ruddock
+ */
+public class CytoscapeSessionWriterTest extends TestCase {
+ public void testDummy() throws Exception {
+
+ }
+
+ // This test commented out as it causes something to be initialised that
+ // throws off some of the other tests.
+// public void testBug1555() throws Exception {
+// CyNetwork cn;
+// CytoscapeSessionWriter sw;
+//
+// Cytoscape.buildOntologyServer();
+// cn = Cytoscape.createNetwork(new int[]{}, new int[]{}, "NewNetwork", null, true);
+// System.out.println(cn.getTitle() + " " + cn.getIdentifier());
+// Cytoscape.setCurrentSessionFileName("testData/TestSession01.cys");
+// sw = new CytoscapeSessionWriter("testData/TestSession01.cys");
+// sw.writeSessionToDisk();
+// cn.setIdentifier("NewNetwork-01");
+// System.out.println(cn.getTitle() + " " + cn.getIdentifier());
+// Cytoscape.setCurrentSessionFileName("testData/TestSession02.cys");
+// sw = new CytoscapeSessionWriter("testData/TestSession02.cys");
+// sw.writeSessionToDisk();
+// }
+}
diff --git a/application/src/test/java/cytoscape/data/writers/InteractionWriterTest.java b/application/src/test/java/cytoscape/data/writers/InteractionWriterTest.java
new file mode 100644
index 0000000..3cda209
--- /dev/null
+++ b/application/src/test/java/cytoscape/data/writers/InteractionWriterTest.java
@@ -0,0 +1,160 @@
+/*
+ File: InteractionWriter.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.data.writers;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+
+import cytoscape.data.writers.InteractionWriter;
+
+import giny.model.RootGraph;
+
+import junit.framework.TestCase;
+
+import java.io.IOException;
+import java.io.StringWriter;
+
+
+/**
+ * Tests the InteractionWriter Class.
+ *
+ */
+public class InteractionWriterTest extends TestCase {
+ protected CyNetwork net;
+ protected int a;
+ protected int b;
+ protected int c;
+ protected int d;
+ protected int e;
+ protected int ab;
+ protected int bc;
+ protected int ac;
+ protected int bd;
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void setUp() {
+ RootGraph root = Cytoscape.getRootGraph();
+
+ a = root.createNode();
+ b = root.createNode();
+ c = root.createNode();
+ d = root.createNode();
+ e = root.createNode();
+
+ int[] nodes = new int[] { a, b, c, d, e };
+
+ ab = root.createEdge(a, b, true);
+ bc = root.createEdge(b, c, true);
+ ac = root.createEdge(a, c, true);
+ bd = root.createEdge(b, d, true);
+
+ int[] edges = new int[] { ab, bc, ac, bd };
+
+ net = Cytoscape.createNetwork(nodes, edges, "graph");
+ }
+
+ /**
+ * Verify that the writer is actually writing.
+ */
+ public void testWrite() {
+ try {
+ StringWriter writer = new StringWriter();
+ InteractionWriter.writeInteractions(net, writer);
+
+ String output = writer.toString();
+ checkSIF(output);
+ } catch (IOException e) {
+ fail(e.getMessage());
+ }
+ }
+
+ /**
+ * Verify that the string written is ok.
+ */
+ public void testInteractionString() {
+ checkSIF(InteractionWriter.getInteractionString(net));
+ }
+
+ protected void checkSIF(String s) {
+ String[] lines = s.split(System.getProperty("line.separator"));
+ System.out.println("begin sif string");
+ System.out.println(s);
+ System.out.println("end sif string");
+ assertEquals("number of lines", 5, lines.length);
+
+ int edgeLines = 0;
+ int nodeLines = 0;
+
+ // Since we don't necessarily know the node ids create
+ // regular expressions of the lines.
+ for (int i = 0; i < lines.length; i++) {
+ if (checkLine(lines[i], a, b))
+ edgeLines++;
+ else if (checkLine(lines[i], b, c))
+ edgeLines++;
+ else if (checkLine(lines[i], a, c))
+ edgeLines++;
+ else if (checkLine(lines[i], b, d))
+ edgeLines++;
+ else if (lines[i].matches("^" + e + "$"))
+ nodeLines++;
+ }
+
+ assertEquals("number of edge lines", 4, edgeLines);
+ assertEquals("number of node only lines", 1, nodeLines);
+ }
+
+ protected boolean checkLine(String s, int a, int b) {
+ if (s.matches("^" + a + "\\s+xx\\s+" + b + "$")
+ || s.matches("^" + b + "\\s+xx\\s+" + a + "$"))
+ return true;
+ else
+
+ return false;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ */
+ public static void main(String[] args) {
+ junit.textui.TestRunner.run(InteractionWriterTest.class);
+ }
+}
diff --git a/application/src/test/java/cytoscape/data/writers/XGMMLWriterTest.java b/application/src/test/java/cytoscape/data/writers/XGMMLWriterTest.java
new file mode 100644
index 0000000..0788137
--- /dev/null
+++ b/application/src/test/java/cytoscape/data/writers/XGMMLWriterTest.java
@@ -0,0 +1,227 @@
+/*
+ File: XGMMLWriterTest.java
+
+ Copyright (c) 2009, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.data.writers;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import cytoscape.data.CyAttributes;
+import cytoscape.data.CyAttributesImpl;
+
+import cytoscape.data.readers.XGMMLReader;
+
+import java.io.ByteArrayInputStream;
+import java.io.FileInputStream;
+import junit.framework.TestCase;
+
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.io.StringWriter;
+
+import java.net.URISyntaxException;
+
+
+/**
+ * Tests the XGMMLWriter Class.
+ */
+public class XGMMLWriterTest extends TestCase {
+ public void testXGMMLWriterRoundTrip1() throws IOException, URISyntaxException {
+ // No characters that are affecting by full encoding, so only one test.
+ compareRoundTrip("src/test/resources/testData/XGMMLWriterTestFile01a.xgmml", "src/test/resources/testData/XGMMLWriterTestFile01b.xgmml");
+ }
+
+ public void testXGMMLWriterRoundTrip2aFullEncodingDefault() throws IOException, URISyntaxException {
+ System.clearProperty(XGMMLWriter.ENCODE_PROPERTY);
+ compareRoundTrip("src/test/resources/testData/XGMMLWriterTestFile02a.xgmml", "src/test/resources/testData/XGMMLWriterTestFile02a.xgmml");
+ }
+
+ public void testXGMMLWriterRoundTrip2aFullEncodingOn() throws IOException, URISyntaxException {
+ System.setProperty(XGMMLWriter.ENCODE_PROPERTY, "true");
+ compareRoundTrip("src/test/resources/testData/XGMMLWriterTestFile02a.xgmml", "src/test/resources/testData/XGMMLWriterTestFile02a.xgmml");
+ }
+
+ public void testXGMMLWriterRoundTrip2aFullEncodingOff() throws IOException, URISyntaxException {
+ System.setProperty(XGMMLWriter.ENCODE_PROPERTY, "false");
+ compareRoundTrip("src/test/resources/testData/XGMMLWriterTestFile02a.xgmml", "src/test/resources/testData/XGMMLWriterTestFile02a.xgmml");
+ }
+
+ public void testXGMMLWriterRoundTrip2bFullEncodingDefault() throws IOException, URISyntaxException {
+ System.clearProperty(XGMMLWriter.ENCODE_PROPERTY);
+ compareRoundTrip("src/test/resources/testData/XGMMLWriterTestFile02b.xgmml", "src/test/resources/testData/XGMMLWriterTestFile02a.xgmml");
+ }
+
+ public void testXGMMLWriterRoundTrip2bFullEncodingOn() throws IOException, URISyntaxException {
+ System.setProperty(XGMMLWriter.ENCODE_PROPERTY, "true");
+ compareRoundTrip("src/test/resources/testData/XGMMLWriterTestFile02b.xgmml", "src/test/resources/testData/XGMMLWriterTestFile02a.xgmml");
+ }
+
+ public void testXGMMLWriterRoundTrip2bFullEncodingOff() throws IOException, URISyntaxException {
+ System.setProperty(XGMMLWriter.ENCODE_PROPERTY, "false");
+ compareRoundTrip("src/test/resources/testData/XGMMLWriterTestFile02b.xgmml", "src/test/resources/testData/XGMMLWriterTestFile02a.xgmml");
+ }
+
+ public void testXGMMLWriterRoundTrip2cFullEncodingDefault() throws IOException, URISyntaxException {
+ System.clearProperty(XGMMLWriter.ENCODE_PROPERTY);
+ compareRoundTrip("src/test/resources/testData/XGMMLWriterTestFile02c.xgmml", "src/test/resources/testData/XGMMLWriterTestFile02d.xgmml");
+ }
+
+ public void testXGMMLWriterRoundTrip2cFullEncodingOn() throws IOException, URISyntaxException {
+ System.setProperty(XGMMLWriter.ENCODE_PROPERTY, "true");
+ compareRoundTrip("src/test/resources/testData/XGMMLWriterTestFile02c.xgmml", "src/test/resources/testData/XGMMLWriterTestFile02d.xgmml");
+ }
+
+ public void testXGMMLWriterRoundTrip2cFullEncodingOff() throws IOException, URISyntaxException {
+ System.setProperty(XGMMLWriter.ENCODE_PROPERTY, "false");
+ compareRoundTrip("src/test/resources/testData/XGMMLWriterTestFile02c.xgmml", "src/test/resources/testData/XGMMLWriterTestFile02c.xgmml");
+ }
+
+ public void testXGMMLWriterBug0001938() throws IOException, URISyntaxException {
+ XGMMLReader r;
+ CyNetwork cn;
+ StringWriter sw;
+ XGMMLWriter w;
+ String xgmmls;
+ ByteArrayInputStream bais;
+
+ System.setProperty(XGMMLWriter.ENCODE_PROPERTY, "true");
+ cn = Cytoscape.createNetwork("<\"aw&ward\name\tstring>\"");
+
+ sw = new StringWriter();
+ w = new XGMMLWriter(cn, null);
+ w.write(sw);
+ sw.close();
+
+ xgmmls = sw.toString();
+ System.out.println(xgmmls);
+ bais = new ByteArrayInputStream(xgmmls.getBytes("US-ASCII"));
+ r = new XGMMLReader(bais);
+ cn = Cytoscape.createNetwork(r, false, null);
+ }
+
+ private void compareRoundTrip(String fileIn, String fileToCompare) throws IOException, URISyntaxException {
+ XGMMLReader r;
+ CyNetwork cn;
+ StringWriter sw;
+ XGMMLWriter w;
+ String output;
+
+ r = new XGMMLReader(fileIn);
+ cn = Cytoscape.createNetwork(r, false, null);
+
+ sw = new StringWriter();
+ w = new XGMMLWriter(cn, null);
+ w.write(sw);
+ sw.close();
+
+ output = sw.toString();
+
+ compareFilesByLine(fileToCompare, output);
+ }
+
+ private void compareFilesByLine(String fileToCompare, String output) throws IOException {
+ String[] linesGot;
+ StringBuilder sb;
+ FileInputStream fis = null;
+ int c;
+ String content;
+ String[] linesExptd;
+
+ linesGot = output.split("\n");
+
+ for (String line : linesGot) {
+ System.out.println(line);
+ }
+
+ sb = new StringBuilder();
+ try {
+ InputStreamReader isr = null;
+
+ fis = new FileInputStream(fileToCompare);
+ try {
+ isr = new InputStreamReader(fis, XGMMLWriter.ENCODING);
+ c = isr.read();
+ while (c != -1)
+ {
+ sb.append((char)c);
+ c = isr.read();
+ }
+ }
+ finally {
+ if (isr != null) {
+ isr.close();
+ }
+ }
+ }
+ finally {
+ if (fis != null) {
+ fis.close();
+ }
+ }
+ content = sb.toString();
+ System.out.println("Read " + content.getBytes(XGMMLWriter.ENCODING).length + " bytes");
+ linesExptd = content.split("\n");
+ assertTrue("XGMMLWriter: No. of lines, expect " + linesExptd.length + ", got" + linesGot.length, linesExptd.length == linesGot.length);
+
+ for (int i = 0; i < linesExptd.length; i++) {
+ String exptd;
+ String got;
+
+ exptd = linesExptd[i];
+ got = linesGot[i];
+ // <dc:date> value will be different so skip this line
+ if (exptd.contains("<dc:date>")) {
+ continue;
+ }
+ if (exptd.contains("<node")) {
+ continue;
+ }
+ if (exptd.contains("<edge")) {
+ continue;
+ }
+ System.out.println("Exp (" + exptd.length() + ")>" + exptd);
+ System.out.println("Got (" + got.length() + ")>" + got);
+ assertEquals("Line " + i + " {" + got + "} {" + exptd + "}", exptd, got);
+ }
+ }
+
+ /**
+ * Runs just this one unit test.
+ */
+ public static void main(String[] args) {
+ junit.textui.TestRunner.run(XGMMLWriterTest.class);
+ }
+}
diff --git a/application/src/test/java/cytoscape/giny/CytoscapeFingRootGraphTest.java b/application/src/test/java/cytoscape/giny/CytoscapeFingRootGraphTest.java
new file mode 100644
index 0000000..1b7dd3e
--- /dev/null
+++ b/application/src/test/java/cytoscape/giny/CytoscapeFingRootGraphTest.java
@@ -0,0 +1,133 @@
+/*
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.giny;
+
+import junit.framework.TestCase;
+
+import giny.model.Node;
+import giny.model.Edge;
+import cytoscape.CyNode;
+import cytoscape.CyEdge;
+
+/**
+ *
+ */
+public class CytoscapeFingRootGraphTest extends TestCase {
+
+ CytoscapeFingRootGraph root;
+
+ public void setUp() throws Exception {
+ root = new CytoscapeFingRootGraph();
+ }
+
+ public void tearDown() throws Exception {
+ root = null;
+ }
+
+ public void testCreateNode() throws Exception {
+ int n1id = root.createNode();
+ assertTrue( n1id < 0 );
+ Node n1 = root.getNode( n1id );
+ assertNotNull( n1 );
+ assertEquals( n1id, n1.getRootGraphIndex() );
+ }
+
+ public void testCreateEdge() throws Exception {
+ Node n1 = root.getNode( root.createNode() );
+ Node n2 = root.getNode( root.createNode() );
+ int e1id = root.createEdge( n1.getRootGraphIndex(), n2.getRootGraphIndex() );
+ assertTrue( e1id < 0 );
+ Edge e1 = root.getEdge( e1id );
+ assertNotNull( e1 );
+ assertEquals( e1id, e1.getRootGraphIndex() );
+ }
+
+ public void testGetSetNodeIdentifier() throws Exception {
+ Node n1 = root.getNode( root.createNode() );
+
+ root.setNodeIdentifier("homer",n1.getRootGraphIndex());
+
+ CyNode nx = root.getNode("homer");
+
+ assertNotNull( nx );
+ assertEquals( n1.getRootGraphIndex(), nx.getRootGraphIndex() );
+ }
+
+ public void testGetSetNodeIdentifierBad() throws Exception {
+
+ root.setNodeIdentifier("homer",-73);
+
+ CyNode nx = root.getNode("homer");
+
+ assertNull( nx );
+ }
+
+ public void testGetNodeIdentifierNull() throws Exception {
+
+ CyNode nx = root.getNode(null);
+
+ assertNull( nx );
+ }
+
+
+ public void testGetSetEdgeIdentifier() throws Exception {
+ Node n1 = root.getNode( root.createNode() );
+ Node n2 = root.getNode( root.createNode() );
+ Edge e1 = root.getEdge( root.createEdge( n1.getRootGraphIndex(), n2.getRootGraphIndex() ) );
+
+ root.setEdgeIdentifier("homer",e1.getRootGraphIndex());
+
+ CyEdge ex = root.getEdge("homer");
+
+ assertNotNull( ex );
+ assertEquals( e1.getRootGraphIndex(), ex.getRootGraphIndex() );
+ }
+
+ public void testGetSetEdgeIdentifierBad() throws Exception {
+
+ root.setEdgeIdentifier("homer",-73);
+
+ CyEdge ex = root.getEdge("homer");
+
+ assertNull( ex );
+ }
+
+ public void testGetEdgeIdentifierNull() throws Exception {
+
+ CyEdge ex = root.getEdge(null);
+
+ assertNull( ex );
+ }
+}
diff --git a/application/src/test/java/cytoscape/plugin/DownloadableInfoTest.java b/application/src/test/java/cytoscape/plugin/DownloadableInfoTest.java
new file mode 100644
index 0000000..95fbcaf
--- /dev/null
+++ b/application/src/test/java/cytoscape/plugin/DownloadableInfoTest.java
@@ -0,0 +1,290 @@
+/**
+ *
+ */
+package cytoscape.plugin;
+
+import cytoscape.plugin.DownloadableInfo;
+import junit.framework.TestCase;
+
+/**
+ * @author skillcoy
+ *
+ */
+public class DownloadableInfoTest extends TestCase {
+
+ DownloadableInfo di;
+
+
+ /* (non-Javadoc)
+ * @see junit.framework.TestCase#setUp()
+ */
+ protected void setUp() throws Exception {
+ super.setUp();
+ di = new InfoObj();
+ }
+
+ /* (non-Javadoc)
+ * @see junit.framework.TestCase#tearDown()
+ */
+ protected void tearDown() throws Exception {
+ super.tearDown();
+ }
+
+ /**
+ * Test method for {@link cytoscape.plugin.DownloadableInfo#DownloadableInfo()}.
+ */
+ public void testDownloadableInfo() {
+ assertNotNull(di);
+ }
+
+ /**
+ * Test method for {@link cytoscape.plugin.DownloadableInfo#DownloadableInfo(java.lang.String)}.
+ */
+ public void testDownloadableInfoString() {
+ di = new InfoObj("123");
+ assertNotNull(di);
+ assertEquals(di.getID(), "123");
+ }
+
+
+ /**
+ * Test method for {@link cytoscape.plugin.DownloadableInfo#DownloadableInfo(java.lang.String, cytoscape.plugin.DownloadableInfo)}.
+ */
+ public void testDownloadableInfoStringDownloadableInfo() {
+ di = new InfoObj("123", new InfoObj("parent_123"));
+ assertNotNull(di);
+ assertEquals(di.getID(), "123");
+ assertNotNull(di.getParent());
+ assertEquals(di.getParent().getID(), "parent_123");
+ }
+
+
+ /**
+ * Test method for {@link cytoscape.plugin.DownloadableInfo#setCategory(java.lang.String)}.
+ */
+ public void testCategoryString() {
+ di.setCategory("Foobar");
+ assertNotNull(di.getCategory());
+ assertEquals(di.getCategory(), "Foobar");
+ }
+
+
+ /**
+ * Test method for {@link cytoscape.plugin.DownloadableInfo#setCategory(cytoscape.plugin.Category)}.
+ */
+ public void testCategoryCategory() {
+ di.setCategory(Category.CORE);
+ assertNotNull(di.getCategory());
+ assertEquals(di.getCategory(), Category.CORE.toString());
+ }
+
+
+ /**
+ * Test method for {@link cytoscape.plugin.DownloadableInfo#setParent(cytoscape.plugin.DownloadableInfo)}.
+ */
+ public void testParent() {
+ di.setParent(new InfoObj("parent"));
+ assertNotNull(di.getParent());
+ }
+
+ /**
+ * Test method for {@link cytoscape.plugin.DownloadableInfo#setName(java.lang.String)}.
+ */
+ public void testName() {
+ di.setName("Booya!");
+ assertEquals(di.getName(), "Booya!");
+ }
+
+ /**
+ * Test method for {@link cytoscape.plugin.DownloadableInfo#setDescription(java.lang.String)}.
+ */
+ public void testDescription() {
+ di.setDescription("Just testing");
+ assertEquals(di.getDescription(), "Just testing");
+ }
+
+ /**
+ * Test method for {@link cytoscape.plugin.DownloadableInfo#setDownloadableURL(java.lang.String)}.
+ */
+ public void testDownloadableURL() {
+ String url = "http://google.com";
+ di.setDownloadableURL(url);
+ assertEquals(di.getDownloadableURL(), url);
+ }
+
+ /**
+ * Test method for {@link cytoscape.plugin.DownloadableInfo#setObjectUrl(java.lang.String)}.
+ */
+ public void testObjectUrl() {
+ String url = "http://foobar.jar";
+ di.setObjectUrl(url);
+ assertEquals(di.getObjectUrl(), url);
+ }
+
+ /**
+ * Test method for {@link cytoscape.plugin.DownloadableInfo#setCytoscapeVersion(java.lang.String)}.
+ */
+ public void testCytoscapeVersion() {
+ String currentVersion = cytoscape.CytoscapeVersion.version;
+ cytoscape.CytoscapeVersion.version = "2.5";
+
+ di.addCytoscapeVersion("2.5");
+ di.addCytoscapeVersion("2.3");
+ assertTrue(di.containsVersion("2.5"));
+ assertTrue(di.containsVersion("2.3"));
+
+ // This may not be true, in case Cytosape version is lower than the the highest version specified
+ //assertEquals(di.getCytoscapeVersion(), "2.5");
+
+ //cytoscape.CytoscapeVersion.version = "2.5.6";
+ //di.addCytoscapeVersion("2.5.6");
+ //assertTrue(di.containsVersion("2.5.6"));
+ //assertEquals(di.getCytoscapeVersion(), "2.5.6");
+ cytoscape.CytoscapeVersion.version = currentVersion;
+ }
+
+ /**
+ * Test method for {@link cytoscape.plugin.DownloadableInfo#setObjectVersion(double)}.
+ */
+ public void testObjectVersion() {
+ di.setObjectVersion("1.3");
+ assertEquals(di.getObjectVersion(), "1.3");
+ }
+
+ /**
+ * Test method for {@link cytoscape.plugin.DownloadableInfo#setReleaseDate(java.lang.String)}.
+ */
+ public void testReleaseDate() {
+ String date = "Oct. 14, 2007";
+ di.setReleaseDate(date);
+ assertEquals(di.getReleaseDate(), date);
+ }
+
+ /**
+ * Test method for {@link cytoscape.plugin.DownloadableInfo#getType()}.
+ */
+ public void testGetType() {
+ assertNotNull(di.getType());
+ }
+
+
+ /**
+ * Test method for {@link cytoscape.plugin.DownloadableInfo#getID()}.
+ */
+ public void testGetID() {
+ // no id set initially
+ assertNull(di.getID());
+ di = new InfoObj("1234");
+ assertEquals(di.getID(), "1234");
+ }
+
+ /**
+ * Test method for {@link cytoscape.plugin.DownloadableInfo#isNewerObjectVersion(cytoscape.plugin.DownloadableInfo)}.
+ */
+ public void testIsNewerObjectVersion() {
+ di = new InfoObj("123");
+ di.setObjectVersion("1.0");
+ DownloadableInfo diNew = new InfoObj("123");
+ diNew.setObjectVersion("1.3");
+
+ assertTrue(di.isNewerObjectVersion(diNew));
+ }
+
+ /**
+ * Test method for {@link cytoscape.plugin.DownloadableInfo#isCytoscapeVersionCurrent()}.
+ */
+ /*
+ public void testIsCytoscapeVersionCurrent() {
+ di.addCytoscapeVersion("2.1");
+ assertFalse(di.isCytoscapeVersionCurrent());
+
+ di.addCytoscapeVersion(cytoscape.CytoscapeVersion.version);
+ assertTrue(di.isCytoscapeVersionCurrent());
+ }
+*/
+
+ /** test for bug #... */
+ public void testPluginCompatible() {
+ String currentVersion = cytoscape.CytoscapeVersion.version;
+
+ // at each version level (major, minor, bugfix)
+ cytoscape.CytoscapeVersion.version = "3.6";
+ di.addCytoscapeVersion("2.1");
+ di.addCytoscapeVersion("3.6");
+ assertTrue(di.isPluginCompatibleWithCurrent());
+
+ cytoscape.CytoscapeVersion.version = "2.6.1";
+ assertEquals(cytoscape.CytoscapeVersion.version, "2.6.1");
+
+ di.addCytoscapeVersion("2.6.2");
+ assertFalse(di.isPluginCompatibleWithCurrent());
+
+ di.addCytoscapeVersion("2.6.1");
+ assertTrue(di.isPluginCompatibleWithCurrent());
+
+ cytoscape.CytoscapeVersion.version = currentVersion;
+ }
+
+
+ public void testEquals() {
+ di = new InfoObj("1234");
+ InfoObj di2 = new InfoObj("1234");
+ assertTrue(di.equals(di2));
+
+ InfoObj di3 = new InfoObj("4321");
+ assertFalse(di.equals(di3));
+ }
+
+ public void testEqualsDifferentObjs() {
+ di = new InfoObj("1234");
+ PluginInfo pi = new PluginInfo("1234");
+ assertFalse(di.equals(pi));
+ }
+
+
+ // in the absence of an id the object version and downloadable url alone are used to determine equality
+ public void testEqualsNoId() {
+ di = new InfoObj();
+ InfoObj di2 = new InfoObj();
+ assertTrue(di.equals(di2));
+
+ InfoObj di3 = new InfoObj();
+ di3.setObjectVersion("2.3");
+ assertFalse(di.equals(di3));
+ }
+
+ private class InfoObj extends DownloadableInfo {
+
+ public InfoObj() {
+ super();
+ init();
+ }
+
+ public InfoObj(String arg) {
+ super(arg);
+ init();
+ }
+
+ private void init() {
+ this.setObjectVersion("1.1");
+ this.setDownloadableURL("http://foo.com/infoobj");
+ }
+
+ public InfoObj(String arg, DownloadableInfo parent) {
+ super(arg, parent);
+ }
+
+ public DownloadableType getType() {
+ return DownloadableType.PLUGIN;
+ }
+
+ public String htmlOutput() {
+ return null;
+ }
+
+ public Installable getInstallable() {
+ return null;
+ }
+ }
+
+}
diff --git a/application/src/test/java/cytoscape/plugin/PluginFileReaderTest.java b/application/src/test/java/cytoscape/plugin/PluginFileReaderTest.java
new file mode 100644
index 0000000..249396b
--- /dev/null
+++ b/application/src/test/java/cytoscape/plugin/PluginFileReaderTest.java
@@ -0,0 +1,167 @@
+/**
+ *
+ */
+package cytoscape.plugin;
+
+import cytoscape.CytoscapeVersion;
+
+import junit.framework.TestCase;
+
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.FileInputStream;
+import java.util.Calendar;
+import java.util.List;
+import java.util.Map;
+
+import javax.xml.transform.*;
+import javax.xml.transform.stream.*;
+
+
+/**
+ * @author skillcoy
+ *
+ */
+public class PluginFileReaderTest extends TestCase {
+
+ private String url;
+
+ private PluginFileReader reader;
+
+ private File tempTestFile;
+
+ private String getFileUrl() {
+ String FS = "/";
+ String UserDir = System.getProperty("user.dir");
+ UserDir = UserDir.replaceFirst(FS, "");
+ return "file:///" + UserDir + FS + "src" + FS + "test" + FS + "resources" + FS + "testData" + FS + "plugins" + FS;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see junit.framework.TestCase#setUp()
+ */
+ protected void setUp() throws Exception {
+ // transform the test files first to get the version numbers up to date
+ tempTestFile = PluginTestXML.transformXML("test_plugin.xml", getFileUrl());
+ url = "file:///" + tempTestFile.getAbsolutePath();
+ reader = new PluginFileReader(url);
+ assertNotNull(reader);
+ // Make sture to strip all the extra crud from our version number
+ new CytoscapeVersion();
+ System.out.println("Version = "+CytoscapeVersion.version);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see junit.framework.TestCase#tearDown()
+ */
+ protected void tearDown() throws Exception {
+ super.tearDown();
+ tempTestFile.delete();
+ }
+
+ /**
+ * Test method for
+ * {@link cytoscape.plugin.PluginFileReader#PluginFileReader(java.lang.String)}.
+ */
+ public void testPluginFileReader() throws Exception {
+ assertNotNull(reader);
+ }
+
+ /**
+ * Test method for
+ * {@link cytoscape.plugin.PluginFileReader#getProjectName()}.
+ */
+ public void testGetProjectName() {
+ assertNotNull(reader.getProjectName());
+ assertTrue(reader.getProjectName().equals("Cytoscape Plugins"));
+ }
+
+ /**
+ * Test method for
+ * {@link cytoscape.plugin.PluginFileReader#getProjectDescription()}.
+ */
+ public void testGetProjectDescription() {
+ assertNotNull(reader.getProjectDescription());
+ assertTrue(reader.getProjectDescription().equals("Test"));
+ }
+
+ /**
+ * Test method for {@link cytoscape.plugin.PluginFileReader#getProjectUrl()}.
+ */
+ public void testGetProjectUrl() {
+ assertNotNull(reader.getProjectUrl());
+ assertTrue(reader.getProjectUrl().equals("http://cytoscape.org"));
+ }
+
+ /**
+ * Test method for {@link cytoscape.plugin.PluginFileReader#getPlugins()}.
+ */
+ public void testGetPlugins() {
+ assertNotNull(reader.getPlugins());
+ assertEquals(reader.getPlugins().size(), 10);
+ }
+
+ public void testGetPluginsLicense() {
+ List<PluginInfo> All = reader.getPlugins();
+ assertNotNull(All.get(0).getLicenseText());
+ }
+
+ public void testGetThemes() {
+ assertNotNull(reader.getThemes());
+ assertEquals(reader.getThemes().size(), 3);
+ assertEquals(reader.getThemes().get(0).getPlugins().size(), 2);
+ for (DownloadableInfo i: reader.getThemes()) {
+ assertEquals(i.getCategory(), Category.THEME.getCategoryText());
+ }
+ }
+
+ // regression test, not all files will contain the <theme> tags
+ public void testReadFileMissingThemes() throws org.jdom.JDOMException,
+ java.io.IOException {
+ url = getFileUrl() + "test_plugin_no_themes.xml";
+ PluginFileReader readerNoThemes = new PluginFileReader(url);
+ assertNotNull(readerNoThemes.getThemes());
+ assertEquals(readerNoThemes.getThemes().size(), 0);
+ }
+
+ // regression test, make sure versions are working
+ public void testVersionReads () {
+ assertNotNull(reader.getPlugins());
+ assertEquals(reader.getPlugins().size(), 10);
+
+ String cytoscapeVersion = cytoscape.CytoscapeVersion.version;
+ cytoscape.CytoscapeVersion.version = "2.3.3";
+ int count = 0;
+ for (DownloadableInfo info: reader.getPlugins()) {
+ if (info.isPluginCompatibleWithCurrent()) count ++;
+ }
+ assertEquals(count, 2);
+ cytoscape.CytoscapeVersion.version = cytoscapeVersion;;
+ }
+
+ // regression test to insure themes work as expected
+ public void testThemePlugins() {
+ boolean foundTheme = false;
+ assertNotNull(reader.getThemes());
+ assertEquals(reader.getThemes().size(), 3);
+
+ for (ThemeInfo info :reader.getThemes()) {
+ if (info.getID().equals("regresstionTestTheme123")) {
+ foundTheme = true;
+ assertEquals(info.getPlugins().size(), 3);
+ Map<String, List<PluginInfo>> idSort = ManagerUtil.sortByID(info.getPlugins());
+ assertTrue(idSort.containsKey("themePlugin1234"));
+ PluginInfo plugin = idSort.get("themePlugin1234").get(0);
+ assertEquals(plugin.getObjectVersion(), "1.1");
+ }
+ }
+ assertTrue(foundTheme);
+ }
+
+
+}
diff --git a/application/src/test/java/cytoscape/plugin/PluginIndexTest.java b/application/src/test/java/cytoscape/plugin/PluginIndexTest.java
new file mode 100644
index 0000000..df8d784
--- /dev/null
+++ b/application/src/test/java/cytoscape/plugin/PluginIndexTest.java
@@ -0,0 +1,126 @@
+package cytoscape.plugin;
+
+import cytoscape.*;
+import cytoscape.dialogs.plugins.PluginIndex;
+import cytoscape.dialogs.plugins.PluginManageDialog;
+import cytoscape.plugin.PluginInfo;
+
+import java.io.*;
+import java.net.URLClassLoader;
+import java.util.*;
+import junit.framework.TestCase;
+
+
+/**
+ * @author pwang
+ */
+//@SuppressWarnings({"JavadocReference"})
+public class PluginIndexTest extends TestCase {
+ private Vector allPluginVector1;
+
+ private String siteName1 = "Cytoscape";
+ private String siteName2 = "OtherSite";
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see junit.framework.TestCase#setUp()
+ */
+ protected void setUp() throws Exception {
+
+ allPluginVector1 = new Vector();
+
+ Vector pluginVect1 = new Vector();
+ PluginInfo info1 = new PluginInfo();
+ info1.setDescription("This is MiMI plugin");
+ pluginVect1.add(PluginManageDialog.CURRENTLY_INSTALLED);
+ pluginVect1.add("categoty1");// category
+ pluginVect1.add(info1);
+
+ Vector pluginVect2 = new Vector();
+ PluginInfo info2 = new PluginInfo();
+ info2.setDescription("This is BioPax plugin");
+ pluginVect2.add(PluginManageDialog.CURRENTLY_INSTALLED);
+ pluginVect2.add("categoty2");// category
+ pluginVect2.add(info2);
+
+ Vector pluginVect3 = new Vector();
+ PluginInfo info3 = new PluginInfo();
+ info3.setDescription("This is another");
+ pluginVect3.add(PluginManageDialog.AVAILABLE_FOR_INSTALL);
+ pluginVect3.add("categoty3");// category
+ pluginVect3.add(info3);
+
+ allPluginVector1.add(pluginVect1);
+ allPluginVector1.add(pluginVect2);
+ allPluginVector1.add(pluginVect3);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see junit.framework.TestCase#tearDown()
+ */
+ protected void tearDown() {
+
+ }
+
+
+ public void testGetSearchResult() {
+
+ Vector filteredPluginVector = new Vector();
+
+ // 1. Before PluginIndex.getSearchResult(), null should be there
+ try {
+ filteredPluginVector = PluginIndex.getSearchResult("testStr",false, siteName1);
+ }
+ catch(Exception e){}
+ assertEquals(filteredPluginVector, null);
+
+ // execute setAllPluginVector() now, with boolean checkVersion = false
+ try {
+ PluginIndex.setAllPluginVector(allPluginVector1, false, siteName1);
+ }
+ catch (Exception e){}
+
+ // 2. After PluginIndex.setAllPluginVector(), if searchStr is not found, an empty vector should be returned
+ try {
+ filteredPluginVector = PluginIndex.getSearchResult("abcd",false, siteName1);
+ }
+ catch (Exception e){}
+ assertEquals(filteredPluginVector.size(), 0);
+
+ // 3. After PluginIndex.setAllPluginVector(), if searchStr is found, it should be returned
+ try {
+ filteredPluginVector = PluginIndex.getSearchResult("mimi",false, siteName1);
+ }
+ catch (Exception e){}
+ assertEquals(filteredPluginVector.size(), 1);
+
+ // 3a. Make sure the correct record is returned
+ Vector returnedVect = (Vector)filteredPluginVector.elementAt(0);
+ PluginInfo info = (PluginInfo) returnedVect.elementAt(2);
+ assertEquals(info.getDescription(), "This is MiMI plugin");
+
+ // 4. After PluginIndex.setAllPluginVector(), if searchStr is found, it should be returned
+ try {
+ filteredPluginVector = PluginIndex.getSearchResult("plugin",false, siteName1);
+ }
+ catch (Exception e){}
+ assertEquals(filteredPluginVector.size(), 2);
+
+ // 5. if boolean versionCheck is set to true, null should be returned
+ try {
+ filteredPluginVector = PluginIndex.getSearchResult("plugin",true, siteName1);
+ }
+ catch (Exception e){}
+ assertEquals(filteredPluginVector, null);
+
+ // 6. search otherSite, null should be returned
+ try {
+ filteredPluginVector = PluginIndex.getSearchResult("plugin",false, siteName2);
+ }
+ catch (Exception e){}
+ assertEquals(filteredPluginVector, null);
+ }
+}
diff --git a/application/src/test/java/cytoscape/plugin/PluginManagerTest.java b/application/src/test/java/cytoscape/plugin/PluginManagerTest.java
new file mode 100644
index 0000000..ca4edb2
--- /dev/null
+++ b/application/src/test/java/cytoscape/plugin/PluginManagerTest.java
@@ -0,0 +1,744 @@
+package cytoscape.plugin;
+
+import cytoscape.*;
+
+import java.io.*;
+import java.net.URLClassLoader;
+import java.util.*;
+import junit.framework.TestCase;
+import org.jdom.JDOMException;
+
+/**
+ * @author skillcoy
+ */
+ at SuppressWarnings({"JavadocReference"})
+public class PluginManagerTest extends TestCase {
+ private PluginManager mgr;
+ private PluginTracker tracker;
+ private String testUrl;
+ private File transformedXML;
+
+ private static void print(String s) {
+ System.out.println(s);
+ }
+
+ private String getFileUrl() {
+ String FS = "/";
+ String UserDir = System.getProperty("user.dir");
+ if (System.getProperty("os.name").contains("Windows")) {
+ UserDir = UserDir.replaceFirst("\\w:", "");
+ UserDir = UserDir.replaceAll("\\\\", FS);
+ }
+ UserDir = UserDir.replaceFirst("/", "");
+ return "file:///" + UserDir + FS + "src" + FS + "test" + FS + "resources" + FS + "testData" + FS + "plugins" + FS;
+ }
+
+ private String cleanFileUrl(String url) {
+ if (System.getProperty("os.name").contains("Windows")) {
+ url = url.replaceFirst("\\w:", "");
+ }
+ return "file://" + url;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see junit.framework.TestCase#setUp()
+ */
+ protected void setUp() throws Exception {
+ transformedXML = PluginTestXML.transformXML("test_plugin.xml", getFileUrl());
+ testUrl = cleanFileUrl(transformedXML.getAbsolutePath());
+
+ PluginManager.setPluginManageDirectory(System.getProperty("java.io.tmpdir"));
+ mgr = PluginManager.getPluginManager();
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see junit.framework.TestCase#tearDown()
+ */
+ protected void tearDown() {
+ mgr.resetManager();
+ mgr.getPluginManageDirectory().delete();
+ mgr.getPluginManageDirectory().getParentFile().delete();
+ transformedXML.delete();
+ // make sure this isn't set, the webstart tests can set it themselves
+ System.setProperty("javawebstart.version", "");
+ }
+
+ /**
+ * Test method for {@link cytoscape.plugin.PluginManager#getPluginManager()}.
+ */
+ public void testGetPluginManager() {
+ System.out.println("testGetPluginManager");
+ assertNotNull(mgr);
+ assertNotNull(PluginManager.getPluginManager(tracker));
+ assertEquals(mgr, PluginManager.getPluginManager(tracker));
+ }
+
+ public void testGetWebstartPluginManager() throws java.io.IOException {
+ mgr.resetManager();
+ // the manager checks this property to find out if it's webstarted
+ System.setProperty("javawebstart.version", "booya");
+
+ PluginManager.setPluginManageDirectory(System.getProperty("java.io.tmpdir"));
+ mgr = PluginManager.getPluginManager();
+
+ assertNotNull(mgr);
+ assertTrue(PluginManager.usingWebstartManager());
+
+ File TempTrackingFile = mgr.pluginTracker.getTrackerFile();
+ assertNotNull(TempTrackingFile);
+ assertTrue(TempTrackingFile.exists());
+ assertTrue(TempTrackingFile.canRead());
+
+ mgr.resetManager();
+ }
+
+ public void testDownloadPluginWebstart() throws java.io.IOException, org.jdom.JDOMException, cytoscape.plugin.ManagerException {
+ mgr.resetManager();
+ System.setProperty("javawebstart.version", "booya");
+
+ PluginManager.setPluginManageDirectory(System.getProperty("java.io.tmpdir"));
+ PluginManager mgr = PluginManager.getPluginManager();
+ assertNotNull(mgr);
+ assertTrue(PluginManager.usingWebstartManager());
+ PluginInfo TestObj = (PluginInfo) getSpecificObj(mgr.inquire(testUrl), "goodJarPlugin123", "1.0");
+ DownloadableInfo DLTestObj = mgr.download(TestObj);
+ assertNotNull(DLTestObj);
+
+ PluginInfo testObjPlugin = (PluginInfo) DLTestObj;
+ for (String f: testObjPlugin.getFileList()) {
+ assertTrue(f.startsWith(mgr.getPluginManageDirectory().getAbsolutePath()));
+ }
+
+ // can't delete when in webstart
+ try {
+ mgr.delete(DLTestObj);
+ } catch (cytoscape.plugin.WebstartException wse) {
+ assertNotNull(wse);
+ }
+ mgr.resetManager();
+ }
+
+
+ /**
+ * Test method for
+ * {@link cytoscape.plugin.PluginManager#getDownloadables(cytoscape.plugin.PluginTracker.PluginStatus)}.
+ * TODO
+ */
+ public void testGetPlugins() {
+ // Not sure how to test this since I can't register anything
+ // w/o a full Cytoscape startup
+ assertEquals(mgr.getDownloadables(PluginStatus.CURRENT).size(), 0);
+ assertEquals(mgr.getDownloadables(PluginStatus.INSTALL).size(), 0);
+ assertEquals(mgr.getDownloadables(PluginStatus.DELETE).size(), 0);
+ }
+
+ /**
+ * Test method for
+ * {@link cytoscape.plugin.PluginManager#inquire(java.lang.String)}.
+ */
+ public void testInquireString() throws java.io.IOException,
+ org.jdom.JDOMException {
+ String Url = "http://google.com/x.xml";
+ try {
+ mgr.inquire(Url);
+ } catch (IllegalStateException e) {
+ assertNotNull(e);
+ }
+
+ Url = testUrl;
+ assertNotNull(mgr.inquire(Url));
+ assertEquals(mgr.inquire(Url).size(), 13);
+ }
+
+ public void testInquirePartialXML() {
+ String Url = getFileUrl() + "partial_plugin_file.xml";
+ System.out.println(Url);
+ try
+ {
+ mgr.inquire(Url);
+ }
+ catch (IOException e)
+ {
+ fail("Should have gotten a JDOMParseException");
+ e.printStackTrace();
+ }
+ catch (JDOMException e)
+ {
+ assertNotNull(e);
+ e.printStackTrace();
+ }
+ }
+
+
+ /**
+ * NOT IMPLEMENTED
+ * Test method for
+ * {@link cytoscape.plugin.PluginManager#register(cytoscape.plugin.CytoscapePlugin, java.lang.String)}.
+ */
+ public void testRegister() throws Exception {
+ }
+
+ public void testInstallTheme() throws java.io.IOException,
+ org.jdom.JDOMException, cytoscape.plugin.ManagerException, cytoscape.plugin.WebstartException {
+
+ ThemeInfo TestObj = (ThemeInfo) getSpecificObj(mgr.inquire(testUrl), "goodThemeTest123", "0.5");
+ DownloadableInfo DownloadedObj = mgr.download(TestObj);
+ assertEquals(mgr.getDownloadables(PluginStatus.INSTALL).size(), 1);
+ mgr.install(DownloadedObj);
+
+ List<DownloadableInfo> Current = mgr.getDownloadables(PluginStatus.CURRENT);
+ assertEquals(mgr.getDownloadables(PluginStatus.INSTALL).size(), 0);
+ assertEquals(mgr.getDownloadables(PluginStatus.DELETE).size(), 0);
+ assertEquals(Current.size(), 1);
+
+ assertEquals(Current.get(0).getType(), DownloadableType.THEME);
+ assertEquals( ((ThemeInfo)DownloadedObj).getPlugins().size(), 2 );
+
+ ThemeInfo CurrentRecorded = (ThemeInfo) Current.get(0);
+ assertEquals(CurrentRecorded.getPlugins().size(), ((ThemeInfo)DownloadedObj).getPlugins().size());
+
+ mgr.delete(DownloadedObj);
+ mgr.delete();
+ }
+
+
+ /**
+ * Test method for {@link cytoscape.plugin.PluginManager#install()}.
+ */
+ public void testInstallPlugin() throws java.io.IOException,
+ org.jdom.JDOMException, cytoscape.plugin.ManagerException, cytoscape.plugin.WebstartException {
+ PluginInfo TestObj = (PluginInfo)getSpecificObj(mgr.inquire(testUrl),
+ "goodJarPlugin123", "1.0");
+
+ DownloadableInfo DownloadedObj = mgr.download(TestObj, null);
+ assertEquals(mgr.getDownloadables(PluginStatus.INSTALL).size(), 1);
+ mgr.install(DownloadedObj);
+
+ List<DownloadableInfo> Current = mgr.getDownloadables(PluginStatus.CURRENT);
+
+ assertEquals(mgr.getDownloadables(PluginStatus.INSTALL).size(), 0);
+ assertEquals(mgr.getDownloadables(PluginStatus.DELETE).size(), 0);
+ assertEquals(Current.size(), 1);
+
+ PluginInfo APlugin = (PluginInfo) Current.get(0);
+ assertEquals(APlugin.getFileList().size(), 1);
+
+ for (String f: APlugin.getFileList()) {
+ assertTrue( (new File(f)).exists() );
+ }
+
+ mgr.delete(DownloadedObj);
+ mgr.delete();
+
+ PluginInfo plugin = (PluginInfo) DownloadedObj;
+ for (String f: plugin.getFileList()) {
+ assertFalse( (new File(f)).exists() );
+ }
+ }
+
+
+ public void testInstallPluginZip() throws Exception {
+ PluginInfo TestObj = (PluginInfo)getSpecificObj(mgr.inquire(testUrl), "goodZIPPlugin777", "0.45");
+
+ DownloadableInfo DownloadedObj = mgr.download(TestObj, null);
+ PluginInfo plugin = (PluginInfo) DownloadedObj;
+
+ for (String f: plugin.getFileList()) {
+ assertTrue( (new File(f)).exists() );
+ }
+ assertEquals(mgr.getDownloadables(PluginStatus.INSTALL).size(), 1);
+
+ mgr.install(mgr.getDownloadables(PluginStatus.INSTALL).get(0));
+
+ String ParentDir = (new File(TestObj.getFileList().get(0)).getParent());
+ List<String> TestFileList = TestObj.getFileList();
+ for(String f: TestFileList) {
+ assertTrue( f.startsWith(ParentDir));
+ }
+ assertEquals(mgr.getDownloadables(PluginStatus.CURRENT).size(), 1);
+
+ mgr.delete(DownloadedObj);
+ assertEquals(mgr.getDownloadables(PluginStatus.DELETE).size(), 1);
+ mgr.delete();
+
+ for (String f: TestFileList) {
+ assertFalse( (new File(f)).exists() );
+ }
+ }
+
+
+ public void testInstallIncorrectFileType() throws ManagerException, org.jdom.JDOMException {
+ PluginInfo TestObj = null;
+ try {
+ TestObj = (PluginInfo)getSpecificObj(mgr.inquire(testUrl),
+ "badFileType123", "1.0");
+ } catch (java.io.IOException ioe) {
+ ioe.printStackTrace();
+ fail();
+ }
+
+ // the real plugin is actually a jar file, this should fail
+ TestObj.setFiletype(PluginInfo.FileType.ZIP);
+
+ try {
+ mgr.download(TestObj, null);
+ fail(); // if it manages to download it means the test failed
+ } catch (java.io.IOException ioe) {
+ // nothing, this is exactly what should happen
+ }
+
+ }
+
+ /**
+ * Test method for
+ * {@link cytoscape.plugin.PluginManager#delete(cytoscape.plugin.PluginInfo)}.
+ */
+ public void testDeletePluginInfo() throws java.io.IOException,
+ org.jdom.JDOMException, cytoscape.plugin.ManagerException, cytoscape.plugin.WebstartException {
+
+ List<DownloadableInfo> Downloadables = mgr.inquire(testUrl);
+
+ PluginInfo TestObj = (PluginInfo) Downloadables.get(0);
+
+ //File Downloaded = mgr.download(TestObj, null);
+ DownloadableInfo Downloaded = mgr.download(TestObj, null);
+
+ //assertTrue(Downloaded.exists());
+ assertEquals(mgr.getDownloadables(PluginStatus.INSTALL).size(), 1);
+ mgr.install(Downloaded);
+ //List<PluginInfo> Current = mgr.getDownloadables(PluginStatus.CURRENT);
+ List<DownloadableInfo> Current = mgr.getDownloadables(PluginStatus.CURRENT);
+
+ assertEquals(mgr.getDownloadables(PluginStatus.INSTALL).size(), 0);
+ assertEquals(mgr.getDownloadables(PluginStatus.DELETE).size(), 0);
+ assertEquals(Current.size(), 1);
+
+ PluginInfo APlugin = (PluginInfo) Current.get(0);
+ assertEquals(APlugin.getFileList().size(), 1);
+
+ File InstalledPlugin = new File(APlugin.getFileList().get(0));
+ assertTrue(InstalledPlugin.exists());
+
+ mgr.delete(Current.get(0));
+ assertEquals(mgr.getDownloadables(PluginStatus.DELETE).size(), 1);
+ mgr.delete();
+ assertFalse(InstalledPlugin.exists());
+ }
+
+ /**
+ * Test method for {@link cytoscape.plugin.PluginManager#delete()}.
+ */
+ public void testDeletePlugin() throws java.io.IOException,
+ org.jdom.JDOMException, cytoscape.plugin.ManagerException, cytoscape.plugin.WebstartException {
+ List<DownloadableInfo> Downloadables = mgr.inquire(testUrl);
+
+ PluginInfo TestObj = (PluginInfo) Downloadables.get(0);
+
+ DownloadableInfo Downloaded = mgr.download(TestObj, null);
+
+ assertEquals(mgr.getDownloadables(PluginStatus.CURRENT).size(), 0);
+ assertEquals(mgr.getDownloadables(PluginStatus.INSTALL).size(), 1);
+ assertEquals(mgr.getDownloadables(PluginStatus.DELETE).size(), 0);
+ mgr.install(Downloaded);
+
+ //assertEquals(mgr.getPluginManageDirectory().list().length, 2);
+
+ assertEquals(mgr.getDownloadables(PluginStatus.CURRENT).size(), 1);
+ assertEquals(mgr.getDownloadables(PluginStatus.INSTALL).size(), 0);
+ assertEquals(mgr.getDownloadables(PluginStatus.DELETE).size(), 0);
+
+ // set for deletion
+ mgr.delete(mgr.getDownloadables(PluginStatus.CURRENT).get(0));
+ assertEquals(mgr.getDownloadables(PluginStatus.CURRENT).size(), 1);
+ assertEquals(mgr.getDownloadables(PluginStatus.INSTALL).size(), 0);
+ assertEquals(mgr.getDownloadables(PluginStatus.DELETE).size(), 1);
+
+ List<DownloadableInfo> DeleteList = mgr.getDownloadables(PluginStatus.DELETE);
+
+ // delete
+ mgr.delete();
+ assertEquals(mgr.getDownloadables(PluginStatus.CURRENT).size(), 0);
+ assertEquals(mgr.getDownloadables(PluginStatus.INSTALL).size(), 0);
+ assertEquals(mgr.getDownloadables(PluginStatus.DELETE).size(), 0);
+
+ PluginInfo Plugin = (PluginInfo) DeleteList.get(0);
+ for (String FileName : Plugin.getFileList()) {
+ assertFalse((new File(FileName)).exists());
+ }
+
+ // only the xml file should be left in this directory
+ //assertEquals(mgr.getPluginManageDirectory().list().length, 1);
+ }
+
+ public void testDeleteTheme() throws java.io.IOException,
+ org.jdom.JDOMException, cytoscape.plugin.ManagerException, cytoscape.plugin.WebstartException {
+
+ ThemeInfo TestObj = (ThemeInfo) getSpecificObj(mgr.inquire(testUrl), "goodThemeTest123", "0.5");
+
+ DownloadableInfo Downloaded = mgr.download(TestObj);
+ TestObj = (ThemeInfo) Downloaded;
+ assertEquals(TestObj.getPlugins().size(), 2);
+
+ assertEquals(mgr.getDownloadables(PluginStatus.CURRENT).size(), 0);
+ assertEquals(mgr.getDownloadables(PluginStatus.INSTALL).size(), 1);
+ assertEquals(mgr.getDownloadables(PluginStatus.DELETE).size(), 0);
+ mgr.install(Downloaded);
+
+ for (String x: mgr.getPluginManageDirectory().list()) {
+ System.out.println("**" + x);
+ }
+
+ //assertEquals(mgr.getPluginManageDirectory().list().length, 2);
+
+ assertEquals(mgr.getDownloadables(PluginStatus.CURRENT).size(), 1);
+ assertEquals(mgr.getDownloadables(PluginStatus.INSTALL).size(), 0);
+ assertEquals(mgr.getDownloadables(PluginStatus.DELETE).size(), 0);
+
+ // set for deletion
+ mgr.delete(mgr.getDownloadables(PluginStatus.CURRENT).get(0));
+ assertEquals(mgr.getDownloadables(PluginStatus.CURRENT).size(), 1);
+ assertEquals(mgr.getDownloadables(PluginStatus.INSTALL).size(), 0);
+ assertEquals(mgr.getDownloadables(PluginStatus.DELETE).size(), 1);
+
+ List<DownloadableInfo> DeleteList = mgr.getDownloadables(PluginStatus.DELETE);
+
+ // delete
+ mgr.delete();
+ assertEquals(mgr.getDownloadables(PluginStatus.CURRENT).size(), 0);
+ assertEquals(mgr.getDownloadables(PluginStatus.INSTALL).size(), 0);
+ assertEquals(mgr.getDownloadables(PluginStatus.DELETE).size(), 0);
+
+ // only the xml file should be left in this directory
+ //assertEquals(mgr.getPluginManageDirectory().list().length, 1);
+ }
+
+
+ public void testFindThemeUpdates() throws java.io.IOException,
+ org.jdom.JDOMException, cytoscape.plugin.ManagerException, cytoscape.plugin.WebstartException {
+
+ ThemeInfo TestObj = (ThemeInfo) getSpecificObj(mgr.inquire(testUrl), "goodThemeTest123", "0.5");
+
+ DownloadableInfo Downloaded = mgr.download(TestObj);
+ assertNotNull(Downloaded);
+ mgr.install(Downloaded);
+
+ TestObj = (ThemeInfo) Downloaded;
+ assertEquals(mgr.getDownloadables(PluginStatus.CURRENT).size(), 1);
+
+ List<DownloadableInfo> Updatable = mgr.findUpdates(mgr.getDownloadables(PluginStatus.CURRENT).get(0));
+ assertEquals(Updatable.size(), 1);
+
+ mgr.delete(Downloaded);
+ mgr.delete();
+ }
+
+ /**
+ * Test method for
+ * {@link cytoscape.plugin.PluginManager#findUpdates(cytoscape.plugin.PluginInfo)}.
+ */
+ public void testFindPluginUpdates() throws java.io.IOException,
+ org.jdom.JDOMException, cytoscape.plugin.ManagerException, cytoscape.plugin.WebstartException {
+ PluginInfo GoodJar = (PluginInfo) getSpecificObj(mgr.inquire(testUrl),
+ "goodJarPlugin123", "1.0");
+
+ DownloadableInfo Downloaded = mgr.download(GoodJar, null);
+
+ assertNotNull(Downloaded);
+ mgr.install(Downloaded);
+
+ assertEquals(mgr.getDownloadables(PluginStatus.CURRENT).size(), 1);
+ List<DownloadableInfo> Updatable = mgr.findUpdates(mgr.getDownloadables(
+ PluginStatus.CURRENT).get(0));
+ assertEquals(Updatable.size(), 1);
+
+ mgr.delete(Downloaded);
+ mgr.delete();
+ }
+
+
+ public void testUpdateTheme() throws Exception {
+ ThemeInfo TestObj = (ThemeInfo) getSpecificObj(mgr.inquire(testUrl), "goodThemeTest123", "0.5");
+
+ DownloadableInfo Downloaded = mgr.download(TestObj);
+ assertNotNull(Downloaded);
+ assertEquals(mgr.getDownloadables(PluginStatus.CURRENT).size(), 0);
+ assertEquals(mgr.getDownloadables(PluginStatus.INSTALL).size(), 1);
+ assertEquals(mgr.getDownloadables(PluginStatus.DELETE).size(), 0);
+ mgr.install(Downloaded);
+
+ assertEquals(mgr.getDownloadables(PluginStatus.CURRENT).size(), 1);
+ assertEquals(mgr.getDownloadables(PluginStatus.INSTALL).size(), 0);
+ assertEquals(mgr.getDownloadables(PluginStatus.DELETE).size(), 0);
+
+ List<DownloadableInfo> Updatable = mgr.findUpdates(mgr.getDownloadables(PluginStatus.CURRENT).get(0));
+ assertEquals(Updatable.size(), 1);
+
+ ThemeInfo TestUpdate = (ThemeInfo) Updatable.get(0);
+
+ mgr.update(mgr.getDownloadables(PluginStatus.CURRENT).get(0), TestUpdate);
+ assertEquals(mgr.getDownloadables(PluginStatus.CURRENT).size(), 1);
+ assertEquals(mgr.getDownloadables(PluginStatus.DELETE).size(), 1);
+ assertEquals(mgr.getDownloadables(PluginStatus.INSTALL).size(), 1);
+
+ mgr.delete();
+ assertEquals(mgr.getDownloadables(PluginStatus.CURRENT).size(), 0);
+ assertEquals(mgr.getDownloadables(PluginStatus.DELETE).size(), 0);
+ assertEquals(mgr.getDownloadables(PluginStatus.INSTALL).size(), 1);
+
+ mgr.install(TestUpdate);
+ assertEquals(mgr.getDownloadables(PluginStatus.CURRENT).size(), 1);
+ assertEquals(mgr.getDownloadables(PluginStatus.DELETE).size(), 0);
+ assertEquals(mgr.getDownloadables(PluginStatus.INSTALL).size(), 0);
+
+ mgr.delete( mgr.getDownloadables(PluginStatus.CURRENT).get(0) );
+ mgr.delete();
+ }
+
+ /**
+ * Test method for
+ * {@link cytoscape.plugin.PluginManager#update(cytoscape.plugin.PluginInfo, cytoscape.plugin.PluginInfo)}.
+ */
+ public void testUpdatePlugin() throws Exception {
+ PluginInfo GoodJar = (PluginInfo) getSpecificObj(mgr.inquire(testUrl),
+ "goodJarPlugin123", "1.0");
+ assertNotNull(mgr.download(GoodJar, null));
+ mgr.install(GoodJar);
+ assertEquals(mgr.getDownloadables(PluginStatus.CURRENT).size(), 1);
+
+ List<DownloadableInfo> Updatable = mgr.findUpdates(mgr.getDownloadables(
+ PluginStatus.CURRENT).get(0));
+ assertEquals(Updatable.size(), 1);
+
+ PluginInfo New = (PluginInfo) Updatable.get(0);
+ //New.setObjectUrl(getFileUrl() + New.getObjectUrl());
+
+ PluginInfo Current = (PluginInfo) mgr.getDownloadables(PluginStatus.CURRENT).get(0);
+ // update sets the old for deletion, new for installation
+ mgr.update(Current, New);
+ assertEquals(mgr.getDownloadables(PluginStatus.CURRENT).size(), 1);
+ assertEquals(mgr.getDownloadables(PluginStatus.DELETE).size(), 1);
+ assertEquals(mgr.getDownloadables(PluginStatus.INSTALL).size(), 1);
+
+ mgr.delete();
+ assertEquals(mgr.getDownloadables(PluginStatus.CURRENT).size(), 0);
+ assertEquals(mgr.getDownloadables(PluginStatus.DELETE).size(), 0);
+ assertEquals(mgr.getDownloadables(PluginStatus.INSTALL).size(), 1);
+
+ mgr.install(New);
+ assertEquals(mgr.getDownloadables(PluginStatus.CURRENT).size(), 1);
+ assertEquals(mgr.getDownloadables(PluginStatus.DELETE).size(), 0);
+ assertEquals(mgr.getDownloadables(PluginStatus.INSTALL).size(), 0);
+
+ PluginInfo Installed = (PluginInfo) mgr.getDownloadables(PluginStatus.CURRENT).get(0);
+ for (String f: Installed.getFileList()) {
+ print("Installed file: " + f);
+ assertTrue( (new File(f)).exists() );
+ }
+
+ mgr.delete( mgr.getDownloadables(PluginStatus.CURRENT).get(0) );
+ mgr.delete();
+ }
+
+
+ public void testDownloadGoodTheme()
+ throws java.io.IOException, org.jdom.JDOMException, cytoscape.plugin.ManagerException, cytoscape.plugin.WebstartException {
+
+ ThemeInfo GoodTheme = (ThemeInfo) getSpecificObj(mgr.inquire(testUrl), "goodThemeTest123", "0.5");
+ assertEquals(GoodTheme.getCategory(), Category.THEME.getCategoryText());
+
+ DownloadableInfo GoodDL = mgr.download(GoodTheme);
+ assertNotNull(GoodDL);
+
+ GoodTheme = (ThemeInfo) GoodDL;
+ assertEquals(GoodTheme.getPlugins().size(), 2);
+ assertEquals(mgr.getDownloadables(PluginStatus.INSTALL).size(), 1);
+
+ assertEquals(mgr.getDownloadables(PluginStatus.INSTALL).get(0).getObjectVersion(), GoodDL.getObjectVersion());
+
+ mgr.delete(GoodDL);
+ mgr.delete();
+ }
+
+ /**
+ * Test method for
+ * {@link cytoscape.plugin.PluginManager#download(cytoscape.plugin.PluginInfo)}.
+ */
+ public void testDownloadGoodPlugin() throws java.io.IOException,
+ org.jdom.JDOMException, cytoscape.plugin.ManagerException, cytoscape.plugin.WebstartException {
+ PluginInfo GoodJar = (PluginInfo) getSpecificObj(mgr.inquire(testUrl),
+ "goodJarPlugin123", "1.0");
+ DownloadableInfo GoodDL = mgr.download(GoodJar);
+ assertEquals(mgr.getDownloadables(PluginStatus.INSTALL).size(), 1);
+ assertEquals(mgr.getDownloadables(PluginStatus.CURRENT).size(), 0);
+ assertEquals(mgr.getDownloadables(PluginStatus.DELETE).size(), 0);
+
+ DownloadableInfo CurrentInstall = mgr.getDownloadables(PluginStatus.INSTALL).get(0);
+ PluginInfo CurrentPlugin = (PluginInfo) CurrentInstall;
+ assertNotNull(CurrentPlugin.getLicenseText());
+ assertEquals(CurrentPlugin.getFileList().size(), 1);
+
+ mgr.delete(GoodDL);
+ mgr.delete();
+ }
+
+ /**
+ * Test method for
+ * {@link cytoscape.plugin.PluginManager#download(cytoscape.plugin.PluginInfo)}.
+ * files are only bad if they fail to have an attribute Cytoscape-Plugin in
+ * the manifest
+ */
+ public void testDownloadBadPlugin() throws java.io.IOException,
+ org.jdom.JDOMException, cytoscape.plugin.WebstartException {
+ PluginInfo BadJar = (PluginInfo) getSpecificObj(mgr.inquire(testUrl),
+ "badJarPlugin123", "0.3");
+
+ try {
+ mgr.download(BadJar, null);
+ } catch (ManagerException E) {
+ assertNotNull(E);
+ assertTrue(E.getMessage().contains("Cytoscape-Plugin"));
+ }
+ }
+
+ /**
+ * This test will test the download of duplicate plugins/themes and the download of plugins
+ * that are already loaded in a theme.
+ *
+ * @throws Exception
+ */
+ public void testDuplicates() throws Exception {
+ ThemeInfo GoodTheme = (ThemeInfo) getSpecificObj(mgr.inquire(testUrl), "goodThemeTest123", "0.5");
+
+ DownloadableInfo ThemeDL = mgr.download(GoodTheme);
+ assertNotNull(ThemeDL);
+ GoodTheme = (ThemeInfo) ThemeDL;
+ assertEquals(mgr.getDownloadables(PluginStatus.INSTALL).size(), 1);
+
+ PluginInfo GoodPlugin = (PluginInfo) getSpecificObj(mgr.inquire(testUrl), "goodJarPlugin123", "2.1");
+ try {
+ DownloadableInfo PluginDL = mgr.download(GoodPlugin);
+ } catch (ManagerException me) {
+ // this is the expected result
+ }
+ // should not set a plugin to install if it's already there in a theme
+ assertEquals(mgr.getDownloadables(PluginStatus.INSTALL).size(), 1);
+
+ mgr.install();
+ assertEquals(mgr.getDownloadables(PluginStatus.INSTALL).size(), 0);
+ assertEquals(mgr.getDownloadables(PluginStatus.CURRENT).size(), 1);
+ assertEquals(mgr.getDownloadables(PluginStatus.DELETE).size(), 0);
+ }
+
+ public void testMinorCorruptedTrackerFile() {
+ mgr.resetManager();
+ PluginManager.setPluginManageDirectory(System.getProperty("java.io.tmpdir"));
+ File file = new File("src/test/resources/testData/plugins/track_plugins_c1.xml");
+ file = copyFileToTempDir(file);
+
+ mgr = PluginManager.getPluginManager();
+ System.out.println("XXXX " + mgr.pluginTracker.getTrackerFile().getAbsolutePath());
+ System.out.println("YYYY " + file.getAbsolutePath());
+ assertEquals(mgr.pluginTracker.getTrackerFile().getAbsolutePath(), file.getAbsolutePath());
+ // errors that aren't major failures don't show up until you've tried to read the file
+ assertTrue(mgr.getDownloadables(PluginStatus.CURRENT).size() > 0);
+ assertEquals(mgr.pluginTracker.getTotalCorruptedElements(), 1);
+ assertEquals(mgr.getLoadingErrors().size(), 1);
+ assertTrue(mgr.getLoadingErrors().get(0).getClass().equals(TrackerException.class));
+
+ file.delete();
+ }
+
+ public void testMajorCorruptedTrackerFile() {
+ mgr.resetManager();
+ PluginManager.setPluginManageDirectory(System.getProperty("java.io.tmpdir"));
+ File file = new File("src/test/resources/testData/plugins/track_plugins_c2.xml");
+ file = copyFileToTempDir(file);
+ mgr = PluginManager.getPluginManager();
+ assertNotNull(mgr);
+
+ assertEquals(mgr.pluginTracker.getTrackerFile().getAbsolutePath(), file.getAbsolutePath());
+ assertEquals(mgr.getDownloadables(PluginStatus.CURRENT).size(), 0);
+ List<Throwable> LoadingErrors = mgr.getLoadingErrors();
+ assertEquals(LoadingErrors.size(), 1);
+ assertTrue(LoadingErrors.get(0).getClass().equals(TrackerException.class));
+
+ mgr.clearErrorList();
+ assertEquals(mgr.getLoadingErrors().size(), 0);
+
+ file.delete();
+ }
+
+ /*--------------------------------------------------------------------*/
+ private File copyFileToTempDir(File fileToCopy) {
+
+ File tempDir = new File(System.getProperty("java.io.tmpdir") + File.separator + //"2.6");
+ new CytoscapeVersion().getMajorVersion());
+ File tempFile = new File(tempDir, "track_plugins.xml");
+
+ assertTrue(fileToCopy.exists());
+
+ try {
+ BufferedReader reader = null;
+
+ try {
+ reader = new BufferedReader(new FileReader(fileToCopy));
+
+ BufferedWriter writer = null;
+
+ try {
+ writer = new BufferedWriter(new FileWriter(tempFile));
+ String line = null;
+ while ((line = reader.readLine()) != null) {
+ writer.write(line);
+ writer.newLine();
+ writer.flush();
+ }
+ }
+ finally {
+ if (writer != null) {
+ writer.close();
+ }
+ }
+ }
+ finally {
+ if (reader != null) {
+ reader.close();
+ }
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+ return tempFile;
+ }
+
+
+ private ThemeInfo setUpCorrectUrls(ThemeInfo info) {
+ for (PluginInfo plugin: info.getPlugins()) {
+ plugin.setObjectUrl(getFileUrl() + plugin.getObjectUrl());
+ }
+ return info;
+ }
+
+ private DownloadableInfo getSpecificObj(List<DownloadableInfo> AllInfo, String Id, String Version) {
+ for (DownloadableInfo Current : AllInfo) {
+ if (Current.getID().equals(Id)
+ && Current.getObjectVersion().equals(Version)) {
+ return Current;
+ }
+ }
+ return null;
+ }
+
+
+ // this won't work causes ExceptionInitializerError in the CytoscapePlugin
+ private class MyPlugin extends CytoscapePlugin {
+ public MyPlugin() {
+ System.out.println("MyPlugin instantiated");
+ }
+ }
+
+}
diff --git a/application/src/test/java/cytoscape/plugin/PluginPropertiesTest.java b/application/src/test/java/cytoscape/plugin/PluginPropertiesTest.java
new file mode 100644
index 0000000..a3d9b9b
--- /dev/null
+++ b/application/src/test/java/cytoscape/plugin/PluginPropertiesTest.java
@@ -0,0 +1,51 @@
+/**
+ *
+ */
+package cytoscape.plugin;
+
+import junit.framework.TestCase;
+
+/**
+ * @author skillcoy
+ *
+ */
+public class PluginPropertiesTest extends TestCase {
+
+ PluginProperties pp;
+
+ /* (non-Javadoc)
+ * @see junit.framework.TestCase#setUp()
+ */
+ protected void setUp() throws Exception {
+ super.setUp();
+ String FS = java.io.File.separator;
+ String TestProps = System.getProperty("user.dir") + FS + "src" + FS + "test" + FS + "resources" + FS + "testData" + FS + "plugins" + FS + "test_plugin.props";
+ pp = new PluginProperties(TestProps);
+ }
+
+ /* (non-Javadoc)
+ * @see junit.framework.TestCase#tearDown()
+ */
+ protected void tearDown() throws Exception {
+ super.tearDown();
+ }
+
+ //**
+ // * Test method for {@link cytoscape.plugin.PluginProperties#fillPluginInfoObject(cytoscape.plugin.PluginInfo)}.
+ //*/
+ //public void testNoMatchingCyVersion() throws cytoscape.plugin.ManagerException {
+ // cytoscape.CytoscapeInit.getProperties().setProperty("cytoscape.version.number", "2.4");
+ // PluginInfo info = pp.fillPluginInfoObject(null);
+ // assertEquals(info.getCytoscapeVersion(), "2.4");
+ //}
+
+ public void testMatchingCyVersion() throws cytoscape.plugin.ManagerException {
+ String currentVersion = cytoscape.CytoscapeInit.getProperties().getProperty("cytoscape.version.number");
+ cytoscape.CytoscapeInit.getProperties().setProperty("cytoscape.version.number", "2.3.3");
+ PluginInfo info = pp.fillPluginInfoObject(null);
+ assertNotNull(info);
+ cytoscape.CytoscapeInit.getProperties().setProperty("cytoscape.version.number", currentVersion);
+ }
+
+
+}
diff --git a/application/src/test/java/cytoscape/plugin/PluginTestXML.java b/application/src/test/java/cytoscape/plugin/PluginTestXML.java
new file mode 100644
index 0000000..39a3375
--- /dev/null
+++ b/application/src/test/java/cytoscape/plugin/PluginTestXML.java
@@ -0,0 +1,84 @@
+/**
+ *
+ */
+package cytoscape.plugin;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+
+import javax.xml.transform.OutputKeys;
+import javax.xml.transform.Transformer;
+import javax.xml.transform.TransformerException;
+import javax.xml.transform.TransformerFactory;
+import javax.xml.transform.stream.StreamResult;
+import javax.xml.transform.stream.StreamSource;
+
+import cytoscape.CytoscapeVersion;
+
+/**
+ * @author skillcoy
+ *
+ */
+public class PluginTestXML {
+
+
+ private static String testFileDir() {
+ String FS = "/";
+ String UserDir = System.getProperty("user.dir");
+ if (System.getProperty("os.name").contains("Windows")) {
+ UserDir = UserDir.replaceFirst("\\w:", "");
+ UserDir = UserDir.replaceAll("\\\\", FS);
+ }
+ return UserDir + FS + "src" + FS + "test" + FS + "resources" + FS + "testData" + FS + "plugins" + FS;
+ }
+
+ // get the xsl file as a stream
+ private static StreamSource getXSL() throws IOException {
+ String XSLFile = testFileDir() + "test_plugins.xsl";
+ InputStream instream = new FileInputStream( XSLFile );
+
+ if (instream == null || instream.available() == 0) {
+ // throw an error!
+ String Msg = "";
+ if (instream == null)
+ Msg = "input stream is null";
+ else if (instream.available() == 0)
+ Msg = "0 bytes in input stream";
+
+ IOException Error = new IOException(
+ "Unable to load test_plugins.xsl: " + Msg);
+ throw Error;
+ }
+ return new StreamSource(instream);
+ }
+
+ public static File transformXML(String FileName, String FileUrl) throws IOException {
+ StreamSource xsltSource = getXSL();
+ String XmlFile = testFileDir() + FileName;
+ StreamSource testFile = new StreamSource( XmlFile );
+
+ File TempTestFile = File.createTempFile("test_plugins", ".xml");
+ StreamResult resultFile = new StreamResult(TempTestFile.getAbsolutePath());
+
+ TransformerFactory transFact = javax.xml.transform.TransformerFactory
+ .newInstance();
+ try {
+ Transformer trans = transFact.newTransformer(xsltSource);
+ trans.setOutputProperty(OutputKeys.METHOD, "xml");
+ trans.setOutputProperty(OutputKeys.INDENT, "yes");
+ trans.setParameter("cytoscapeVersion", CytoscapeVersion.version);
+ trans.setParameter("fileUrl", FileUrl);
+
+ trans.transform(testFile, resultFile);
+ } catch (TransformerException te) {
+ te.printStackTrace();
+ }
+ return TempTestFile;
+ }
+
+
+
+
+}
diff --git a/application/src/test/java/cytoscape/plugin/PluginTrackerTest.java b/application/src/test/java/cytoscape/plugin/PluginTrackerTest.java
new file mode 100644
index 0000000..28a467c
--- /dev/null
+++ b/application/src/test/java/cytoscape/plugin/PluginTrackerTest.java
@@ -0,0 +1,440 @@
+/**
+ *
+ */
+package cytoscape.plugin;
+
+import cytoscape.plugin.PluginStatus;
+
+import java.io.*;
+import org.jdom.*;
+import org.jdom.input.*;
+import java.util.*;
+import junit.framework.TestCase;
+
+/**
+ * @author skillcoy
+ *
+ */
+public class PluginTrackerTest extends TestCase {
+ private SAXBuilder builder;
+
+ //private Document xmlDoc;
+
+ private PluginTracker tracker;
+
+ private String fileName = "test_tracker.xml";
+
+ private File tmpDir;
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see junit.framework.TestCase#setUp()
+ */
+ protected void setUp() throws Exception {
+ builder = new SAXBuilder(false);
+ tmpDir = new File(System.getProperty("java.io.tmpdir"));
+ tracker = new PluginTracker(tmpDir, fileName);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see junit.framework.TestCase#tearDown()
+ */
+ protected void tearDown() throws Exception {
+ tracker.delete();
+ }
+
+ /**
+ * Test method for {@link cytoscape.plugin.PluginTracker#PluginTracker()}.
+ */
+ public void testPluginTracker() throws Exception {
+ Document Doc = getDoc();
+ assertNotNull(Doc);
+
+ assertEquals(Doc.getRootElement().getName(), "CytoscapePlugin");
+ assertEquals(Doc.getRootElement().getChildren().size(), 3);
+
+ assertNotNull(Doc.getRootElement().getChild(
+ PluginStatus.CURRENT.getTagName()));
+ assertNotNull(Doc.getRootElement().getChild(
+ PluginStatus.INSTALL.getTagName()));
+ assertNotNull(Doc.getRootElement().getChild(
+ PluginStatus.DELETE.getTagName()));
+
+ assertEquals(Doc.getRootElement().getChild(
+ PluginStatus.CURRENT.getTagName()).getChildren().size(), 0);
+ assertEquals(Doc.getRootElement().getChild(
+ PluginStatus.INSTALL.getTagName()).getChildren().size(), 0);
+ assertEquals(Doc.getRootElement().getChild(
+ PluginStatus.DELETE.getTagName()).getChildren().size(), 0);
+ }
+
+ /**
+ * Test method for
+ * {@link cytoscape.plugin.PluginTracker#getListByStatus(cytoscape.plugin.PluginTracker.PluginStatus)}.
+ */
+ public void testGetListByStatus() throws Exception {
+ tracker.addDownloadable(getInfoObj(), PluginStatus.CURRENT);
+
+ assertNotNull(tracker.getPluginListByStatus(PluginStatus.CURRENT));
+ assertEquals(
+ tracker.getPluginListByStatus(PluginStatus.CURRENT).size(), 1);
+
+ // lets just check with the xml doc itself to be sure
+ Document Doc = getDoc();
+ Element Current = Doc.getRootElement().getChild(
+ PluginStatus.CURRENT.getTagName());
+ assertEquals(Current.getChildren().size(), 1);
+ assertEquals(Doc.getRootElement().getChild(
+ PluginStatus.INSTALL.getTagName()).getChildren().size(), 0);
+ assertEquals(Doc.getRootElement().getChild(
+ PluginStatus.DELETE.getTagName()).getChildren().size(), 0);
+ }
+
+ /**
+ * Test method for
+ * {@link cytoscape.plugin.PluginTracker#addPlugin(cytoscape.plugin.PluginInfo, cytoscape.plugin.PluginTracker.PluginStatus)}.
+ */
+ public void testAddPlugin() throws Exception {
+ tracker.addDownloadable(getInfoObj(), PluginStatus.CURRENT);
+
+ assertEquals(
+ tracker.getPluginListByStatus(PluginStatus.CURRENT).size(), 1);
+
+ PluginInfo obj = getInfoObj();
+ obj.setName("myInstallTest");
+ obj.setDownloadableURL("http://booya.com/foo.xml");
+ tracker.addDownloadable(obj, PluginStatus.INSTALL);
+
+ assertEquals(
+ tracker.getPluginListByStatus(PluginStatus.INSTALL).size(), 1);
+
+ // changing the name of the object will not change the object if
+ // the id/projurl stay the same
+ obj.setName("mySecondInstallTest");
+ tracker.addDownloadable(obj, PluginStatus.INSTALL);
+ assertEquals(
+ tracker.getPluginListByStatus(PluginStatus.INSTALL).size(), 1);
+
+ // whole new object will get added though
+ PluginInfo newObj = new PluginInfo(
+ "this is my unique key for my new plugin");
+ newObj.setName("mySecondInstallTest");
+ newObj.setProjectUrl("http://foobar.com/booya.xml");
+ newObj.setFiletype(PluginInfo.FileType.JAR);
+ newObj.addCytoscapeVersion("2.5.1");
+ tracker.addDownloadable(newObj, PluginStatus.INSTALL);
+ assertEquals(
+ tracker.getPluginListByStatus(PluginStatus.INSTALL).size(), 2);
+
+ // lets just check with the xml doc itself to be sure
+ Document Doc = getDoc();
+ Element Install = Doc.getRootElement().getChild(
+ PluginStatus.INSTALL.getTagName());
+ assertEquals(Install.getChildren().size(), 2);
+ assertEquals(Doc.getRootElement().getChild(
+ PluginStatus.CURRENT.getTagName()).getChildren().size(), 1);
+ assertEquals(Doc.getRootElement().getChild(
+ PluginStatus.DELETE.getTagName()).getChildren().size(), 0);
+ }
+
+ /**
+ * Test method for
+ * {@link cytoscape.plugin.PluginTracker#addTheme(ThemeInfo, PluginStatus)}
+ *
+ * @throws Exception
+ */
+ public void testAddTheme() throws Exception {
+ ThemeInfo themeObj = new ThemeInfo("themeTest123");
+ themeObj.setName("Test Theme");
+ themeObj.setDownloadableURL("http://booya.com/foo.xml");
+ themeObj.addCytoscapeVersion("2.5.1");
+
+ PluginInfo obj = getInfoObj();
+ obj.setName("myInstallTest");
+ obj.setDownloadableURL("http://booya.com/foo.xml");
+
+ themeObj.addPlugin(obj);
+
+ tracker.addDownloadable(themeObj, PluginStatus.INSTALL);
+
+ assertEquals(tracker.getThemeListByStatus(PluginStatus.INSTALL).size(),
+ 1);
+ assertEquals(tracker.getDownloadableListByStatus(PluginStatus.INSTALL)
+ .size(), 1);
+ assertEquals(
+ tracker.getPluginListByStatus(PluginStatus.INSTALL).size(), 0);
+
+ Document Doc = getDoc();
+ Element Install = Doc.getRootElement().getChild(
+ PluginStatus.INSTALL.getTagName());
+ assertEquals(Install.getChildren().size(), 1);
+ assertNotNull(Install.getChild(PluginXml.THEME.getTag()).getChild(
+ PluginXml.PLUGIN_LIST.getTag()));
+ }
+
+ public void testRemoveTheme() throws Exception {
+ ThemeInfo themeObj = new ThemeInfo("themeTest123");
+ themeObj.setName("Test Theme");
+ themeObj.setDownloadableURL("http://booya.com/foo.xml");
+ themeObj.addCytoscapeVersion("2.5.1");
+
+ PluginInfo obj = getInfoObj();
+ obj.setName("myInstallTest");
+ obj.setDownloadableURL("http://booya.com/foo.xml");
+
+ themeObj.addPlugin(obj);
+
+ tracker.addDownloadable(themeObj, PluginStatus.INSTALL);
+ assertEquals(tracker.getThemeListByStatus(PluginStatus.INSTALL).size(),
+ 1);
+ assertEquals(tracker.getDownloadableListByStatus(PluginStatus.INSTALL)
+ .size(), 1);
+ assertEquals(
+ tracker.getPluginListByStatus(PluginStatus.INSTALL).size(), 0);
+
+ tracker.removeDownloadable(themeObj, PluginStatus.INSTALL);
+ assertEquals(tracker.getThemeListByStatus(PluginStatus.INSTALL).size(),
+ 0);
+ assertEquals(tracker.getDownloadableListByStatus(PluginStatus.INSTALL)
+ .size(), 0);
+ assertEquals(tracker.getDownloadableListByStatus(PluginStatus.CURRENT)
+ .size(), 0);
+ assertEquals(tracker.getDownloadableListByStatus(PluginStatus.DELETE)
+ .size(), 0);
+ }
+
+ public void testAddThemeAndPlugin() throws Exception {
+ ThemeInfo themeObj = new ThemeInfo("1A");
+ themeObj.setName("Test Theme");
+ themeObj.setDownloadableURL("http://booya.com/foo.xml");
+ themeObj.addCytoscapeVersion("2.6");
+
+ PluginInfo themePlugin = getInfoObj();
+ themePlugin.addCytoscapeVersion("2.6");
+ themeObj.addPlugin(themePlugin);
+
+ tracker.addDownloadable(themeObj, PluginStatus.CURRENT);
+ assertEquals(tracker.getDownloadableListByStatus(PluginStatus.CURRENT).size(), 1);
+
+ PluginInfo pluginObj = new PluginInfo("1A");
+ pluginObj.setName("Plugin Test");
+ pluginObj.addCytoscapeVersion("2.6");
+ pluginObj.setDownloadableURL("http://booya.com/foo.xml");
+ pluginObj.setFiletype(PluginInfo.FileType.JAR);
+
+ tracker.addDownloadable(pluginObj, PluginStatus.CURRENT);
+ assertEquals(tracker.getDownloadableListByStatus(PluginStatus.CURRENT).size(), 2);
+ }
+
+
+ public void testAddSamePlugin() throws Exception {
+ PluginInfo InfoObject = getInfoObj();
+
+ tracker.addDownloadable(InfoObject, PluginStatus.CURRENT);
+
+ assertEquals(
+ tracker.getPluginListByStatus(PluginStatus.CURRENT).size(), 1);
+
+ String NewName = "DuplicatePluginTest";
+ InfoObject.setName(NewName);
+ tracker.addDownloadable(InfoObject, PluginStatus.CURRENT);
+
+ assertEquals(
+ tracker.getPluginListByStatus(PluginStatus.CURRENT).size(), 1);
+
+ DownloadableInfo info = tracker.getPluginListByStatus(
+ PluginStatus.CURRENT).get(0);
+
+ assertTrue(info.getName().equals(InfoObject.getName()));
+
+ Document Doc = getDoc();
+ assertEquals(Doc.getRootElement().getChild(
+ PluginStatus.CURRENT.getTagName()).getChild("plugin")
+ .getChildTextTrim("name"), NewName);
+ }
+
+ /**
+ * Test method for
+ * {@link cytoscape.plugin.PluginTracker#removeDownloadable(cytoscape.plugin.DownloadableInfo, cytoscape.plugin.PluginTracker.PluginStatus)}.
+ */
+ public void testRemovePlugin() throws Exception {
+ tracker.addDownloadable(getInfoObj(), PluginStatus.CURRENT);
+
+ assertEquals(
+ tracker.getPluginListByStatus(PluginStatus.CURRENT).size(), 1);
+
+ PluginInfo obj = new PluginInfo("999");
+ obj.setName("myInstallTest");
+ obj.setDownloadableURL("http://foobar.org/y.xml");
+ obj.setCategory("Test");
+ obj.setFiletype(PluginInfo.FileType.JAR);
+ obj.addCytoscapeVersion("2.5.1");
+
+ tracker.addDownloadable(obj, PluginStatus.INSTALL);
+
+ assertEquals(
+ tracker.getPluginListByStatus(PluginStatus.INSTALL).size(), 1);
+
+ // won't change because this object wasn't an install object
+ tracker.removeDownloadable(getInfoObj(), PluginStatus.INSTALL);
+ assertEquals(
+ tracker.getPluginListByStatus(PluginStatus.INSTALL).size(), 1);
+
+ tracker.removeDownloadable(obj, PluginStatus.INSTALL);
+ assertEquals(
+ tracker.getPluginListByStatus(PluginStatus.INSTALL).size(), 0);
+
+ Document Doc = getDoc();
+ assertEquals(Doc.getRootElement().getChild(
+ PluginStatus.CURRENT.getTagName()).getChildren().size(), 1);
+ assertEquals(Doc.getRootElement().getChild(
+ PluginStatus.INSTALL.getTagName()).getChildren().size(), 0);
+ assertEquals(Doc.getRootElement().getChild(
+ PluginStatus.DELETE.getTagName()).getChildren().size(), 0);
+ }
+
+ // regression test
+ public void testAddRemovePluginWithSameID() throws Exception {
+ PluginInfo objA = getInfoObj();
+ PluginInfo objB = new PluginInfo(objA.getID());
+ objB.setName("Different Test");
+ objB.setDownloadableURL("http://test.com/blue.xml");
+ objB.setFiletype(PluginInfo.FileType.JAR);
+ objB.setPluginClassName("some.other.class.DifferentTest");
+ objB.addCytoscapeVersion(objA.getCytoscapeVersion());
+
+ tracker.addDownloadable(objA, PluginStatus.CURRENT);
+ tracker.addDownloadable(objB, PluginStatus.CURRENT);
+ assertEquals(
+ tracker.getPluginListByStatus(PluginStatus.CURRENT).size(), 2);
+ List<PluginInfo> CurrentList = tracker
+ .getPluginListByStatus(PluginStatus.CURRENT);
+ assertFalse(CurrentList.get(0).equals(CurrentList.get(1)));
+
+ tracker.removeDownloadable(objA, PluginStatus.CURRENT);
+ assertEquals(tracker.getPluginListByStatus(PluginStatus.CURRENT).size(), 1);
+
+ // check that the correct object was actually removed
+ PluginInfo Current = tracker
+ .getPluginListByStatus(PluginStatus.CURRENT).get(0);
+ assertEquals(Current.getName(), objB.getName());
+ }
+
+ public void testPartiallyCorruptedXml() {
+ // partially corrupted file
+ try {
+ File file = new File("src/test/resources/testData/plugins/track_plugins_c1.xml");
+ PluginTracker tk = new PluginTracker(file);
+ assertNotNull(tk);
+ // Note: do NOT call write or you change the test file
+ assertEquals(tk.getDownloadableListByStatus(PluginStatus.CURRENT).size(), 13);
+ assertTrue(tk.hasCorruptedElements());
+ assertEquals(tk.getTotalCorruptedElements(), 1);
+ } catch (NullPointerException npe) {
+ npe.printStackTrace();
+ fail("Failed to handle corrupted xml: " + npe.getMessage());
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Failed to read file: " + e.getMessage());
+ }
+ }
+
+ public void testCompletelyCorruptedXml() {
+ // completely corrupted file
+ PluginTracker tk = null;
+ File tempFile = null;
+ try {
+ File file = new File("testData/plugins/track_plugins_c2.xml");
+ // need to copy file to new location because it will be deleted
+ tempFile = copyFileToTempDir(file);
+ tk = new PluginTracker(tempFile);
+ } catch (NullPointerException npe) {
+ npe.printStackTrace();
+ fail("Failed to handle corrupted xml: " + npe.getMessage());
+ } catch (TrackerException te) { // expected
+ assertNotNull(te);
+ //fail("Failed to build document from file: " + te.getMessage());
+ } catch (IOException ioe) {
+ ioe.printStackTrace();
+ fail("Failed to read file: " + ioe.getMessage());
+ } finally {
+ if (tempFile != null && tempFile.exists())
+ tempFile.delete();
+ }
+ }
+
+ private File copyFileToTempDir(File fileToCopy) {
+ File tempDir = new File(System.getProperty("java.io.tmpdir"));
+ File tempFile = new File(tempDir, fileToCopy.getName());
+
+ try {
+ BufferedReader reader = null;
+
+ try {
+ reader = new BufferedReader(new FileReader(fileToCopy));
+
+ BufferedWriter writer = null;
+
+ try {
+ writer = new BufferedWriter(new FileWriter(tempFile));
+ String line = null;
+ while ((line = reader.readLine()) != null) {
+ writer.write(line);
+ writer.newLine();
+ writer.flush();
+ }
+ }
+ finally {
+ if (writer != null) {
+ writer.close();
+ }
+ }
+ }
+ finally {
+ if (reader != null) {
+ reader.close();
+ }
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ return tempFile;
+ }
+
+ private Document getDoc() throws Exception {
+ File TestFile = new File(tmpDir, fileName);
+ assertTrue(TestFile.exists());
+ assertTrue(TestFile.canRead());
+ // lets just check with the xml doc itself to be sure
+ Document Doc = builder.build(TestFile);
+ assertNotNull(Doc);
+ return Doc;
+ }
+
+ private PluginInfo getInfoObj() {
+ PluginInfo infoObj = new PluginInfo("123");
+ infoObj.setName("myTest");
+ infoObj.setCategory("Test");
+ infoObj.addCytoscapeVersion("2.5.1");
+
+ infoObj.setPluginClassName("some.class.MyTest");
+ infoObj.setDownloadableURL("http://test.com/x.xml");
+ infoObj.setFiletype(PluginInfo.FileType.JAR);
+ return infoObj;
+ }
+
+ private PluginInfo fillInPI(PluginInfo obj) {
+ obj.setCategory("Test");
+ obj.addCytoscapeVersion("2.5.1");
+ obj.setPluginClassName("some.class.MyTest");
+ obj.setDownloadableURL("http://test.com/x.xml");
+ obj.setFiletype(PluginInfo.FileType.JAR);
+ obj.setDownloadableURL("http://booya.com/foo.xml");
+ return obj;
+ }
+
+}
diff --git a/application/src/test/java/cytoscape/plugin/PluginVersionUtilsTest.java b/application/src/test/java/cytoscape/plugin/PluginVersionUtilsTest.java
new file mode 100644
index 0000000..75b4b94
--- /dev/null
+++ b/application/src/test/java/cytoscape/plugin/PluginVersionUtilsTest.java
@@ -0,0 +1,72 @@
+package cytoscape.plugin;
+
+
+import junit.framework.TestCase;
+
+
+public class PluginVersionUtilsTest extends TestCase {
+ public void testGoodCyVersion1() {
+ assertTrue(PluginVersionUtils.versionOk("2.8", false));
+ }
+
+ public void testGoodCyVersion2() {
+ assertTrue(PluginVersionUtils.versionOk("2.8.1", false));
+ }
+
+ public void testGoodCyVersion3() {
+ assertTrue(PluginVersionUtils.versionOk("2.8.1-lower", false));
+ }
+
+ public void testGoodCyVersion4() {
+ assertTrue(PluginVersionUtils.versionOk("2.8.1-UPPER", false));
+ }
+
+/*
+ * This is no longer bad. Version "2" get's interpreted as version 2.0
+ *
+ public void testBadCyVersion1() {
+ assertFalse(PluginVersionUtils.versionOk("2", false));
+ }
+ */
+
+ public void testBadCyVersion2() {
+ assertFalse(PluginVersionUtils.versionOk("X.Y.Z", false));
+ }
+
+ public void testBadCyVersion3() {
+ assertFalse(PluginVersionUtils.versionOk("2.8.1-133t", false));
+ }
+
+ public void testBadCyVersion4() {
+ assertFalse(PluginVersionUtils.versionOk("2.8.1.4", false));
+ }
+
+ public void testGoodPluginVersion1() {
+ assertTrue(PluginVersionUtils.versionOk("2.8", true));
+ }
+
+/*
+ * This is no longer bad. Version "2" get's interpreted as version 2.0
+ *
+ public void testBadPluginVersion1() {
+ assertFalse(PluginVersionUtils.versionOk("2", true));
+ }
+ */
+
+ public void testBadPluginVersion2() {
+ assertFalse(PluginVersionUtils.versionOk("X.Y", true));
+ }
+
+ public void testBadPluginVersion3() {
+ assertFalse(PluginVersionUtils.versionOk("2.8.1", true));
+ }
+
+ public void testBadPluginVersion4() {
+ assertFalse(PluginVersionUtils.versionOk("2-8", true));
+ }
+
+ public void testBadPluginVersion5() {
+ assertFalse(PluginVersionUtils.versionOk("2.8-SNAPSHOT", true));
+ }
+}
+
diff --git a/application/src/test/java/cytoscape/sampleProject.pro b/application/src/test/java/cytoscape/sampleProject.pro
new file mode 100644
index 0000000..ba3151f
--- /dev/null
+++ b/application/src/test/java/cytoscape/sampleProject.pro
@@ -0,0 +1,18 @@
+sif=network.sif
+gml=network.gml
+noa=age.noa
+noa=commonName.noa
+noa=frillycurtainlength.noa
+noa=species.noa
+eda=edgeancillaryname.eda
+eda=edgeweight.eda
+eda=interaction.eda
+expr=yabba.mrna
+dataServer=jar://privateServer
+species=Saccharomyces cerevisiae
+layout=frisbee
+props=special.props
+vprops=vspecial.props
+canonicalizeNames=no
+arg=more
+arg=args
diff --git a/application/src/test/java/cytoscape/test1.cpr b/application/src/test/java/cytoscape/test1.cpr
new file mode 100644
index 0000000..a15b281
--- /dev/null
+++ b/application/src/test/java/cytoscape/test1.cpr
@@ -0,0 +1,10 @@
+sif=galFiltered.sif
+gml=galFiltered.gml
+noa=nodeAttributes1.noa
+noa=nodeAttributes2.noa
+eda=edgeAttributes1.eda
+eda=edgeAttributes2.eda
+dataServer=rmi://hazel/yeast
+species=Saccharomyces cerevisiae
+layout=hierarchical
+props=cytoscape.props
diff --git a/application/src/test/java/cytoscape/test2.cpr b/application/src/test/java/cytoscape/test2.cpr
new file mode 100644
index 0000000..cf062bc
--- /dev/null
+++ b/application/src/test/java/cytoscape/test2.cpr
@@ -0,0 +1,9 @@
+gml=galFiltered.gml
+noa=nodeAttributes1.noa
+noa=nodeAttributes2.noa
+eda=edgeAttributes1.eda
+eda=edgeAttributes2.eda
+layout=embedded
+species=Saccharomyces cerevisiae
+dataServer=annotationsAndSynonyms
+props=cytoscape.props
diff --git a/application/src/test/java/cytoscape/util/BookmarksUtilTest.java b/application/src/test/java/cytoscape/util/BookmarksUtilTest.java
new file mode 100644
index 0000000..4b0e0f0
--- /dev/null
+++ b/application/src/test/java/cytoscape/util/BookmarksUtilTest.java
@@ -0,0 +1,109 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.util;
+
+import cytoscape.bookmarks.Bookmarks;
+import cytoscape.bookmarks.Category;
+import cytoscape.bookmarks.DataSource;
+
+import cytoscape.data.readers.BookmarkReader;
+
+import cytoscape.util.BookmarksUtil;
+
+import junit.framework.TestCase;
+
+import java.util.List;
+
+
+/**
+ *
+ */
+public class BookmarksUtilTest extends TestCase {
+ private Bookmarks bk;
+
+ protected void setUp() throws Exception {
+ super.setUp();
+
+ BookmarkReader reader = new BookmarkReader();
+ reader.readBookmarks();
+
+ bk = reader.getBookmarks();
+ }
+
+ protected void tearDown() throws Exception {
+ super.tearDown();
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testGetCategory() {
+ List<Category> rootCat = bk.getCategory();
+ assertNotNull(rootCat);
+ System.out.println("#### Number of bookmarks in the root category = " + rootCat.size());
+
+ Category cat1 = BookmarksUtil.getCategory("annotation", rootCat);
+ assertNotNull(cat1);
+ assertEquals("annotation", cat1.getName());
+ System.out.println("===============================================");
+
+ Category cat2 = BookmarksUtil.getCategory("network", rootCat);
+ assertNotNull(cat2);
+ assertEquals("network", cat2.getName());
+ System.out.println("===============================================");
+
+ Category cat4 = BookmarksUtil.getCategory("aaa", rootCat);
+ assertNull(cat4);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testGetDataSourceList() {
+ List<Category> rootCat = bk.getCategory();
+ List<DataSource> sources = BookmarksUtil.getDataSourceList("ontology", bk.getCategory());
+
+ assertNotNull(sources);
+ assertEquals(10, sources.size());
+
+ List<DataSource> sources2 = BookmarksUtil.getDataSourceList("annotation", bk.getCategory());
+ assertNotNull(sources2);
+ assertEquals(48, sources2.size());
+
+ List<DataSource> sources3 = BookmarksUtil.getDataSourceList("network", bk.getCategory());
+ assertNotNull(sources3);
+ assertEquals(6, sources3.size());
+ }
+}
diff --git a/application/src/test/java/cytoscape/util/ColorUtilTest.java b/application/src/test/java/cytoscape/util/ColorUtilTest.java
new file mode 100644
index 0000000..9358dad
--- /dev/null
+++ b/application/src/test/java/cytoscape/util/ColorUtilTest.java
@@ -0,0 +1,45 @@
+package cytoscape.util;
+
+import java.awt.Color;
+
+import junit.framework.TestCase;
+
+/**
+ * Test Color Utility class.
+ *
+ * @author kono
+ *
+ */
+public class ColorUtilTest extends TestCase {
+
+ public void testParseColorText() {
+ String black = "black";
+ String darkGray = "darkgray";
+ String darkGrayRGB = "169, 169, 169";
+ Color darkGrayColor = ColorUtil.parseColorText(darkGray);
+ Color darkGrayColor2 = ColorUtil.parseColorText(darkGrayRGB);
+
+ String seaShell = " SeaShell ";
+ Color seaShellColor = Color.decode("#FFF5EE");
+
+ String mediumTurquoise = "mediumturquoise";
+ Color mediumTurquoiseColor = ColorUtil.parseColorText("72, 209,204 ");
+
+ String nonsense = "dkajshfls/>-d13opr[wepq-83=";
+
+ assertEquals(Color.black, ColorUtil.parseColorText(black));
+ assertEquals(Color.decode("#A9A9A9"), darkGrayColor);
+ assertEquals(darkGrayColor, darkGrayColor2);
+
+ assertEquals(seaShellColor, ColorUtil.parseColorText(seaShell));
+ assertEquals(mediumTurquoiseColor, ColorUtil.parseColorText(mediumTurquoise));
+
+ assertNull(ColorUtil.parseColorText(nonsense));
+ }
+
+ public void testGetColorAsText() {
+ assertNotNull(ColorUtil.getColorAsText(Color.white));
+ assertEquals("0,0,0", ColorUtil.getColorAsText(Color.black));
+ }
+
+}
diff --git a/application/src/test/java/cytoscape/util/CyFileFilterTest.java b/application/src/test/java/cytoscape/util/CyFileFilterTest.java
new file mode 100644
index 0000000..64b1f88
--- /dev/null
+++ b/application/src/test/java/cytoscape/util/CyFileFilterTest.java
@@ -0,0 +1,312 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.util;
+
+import cytoscape.util.CyFileFilter;
+
+import junit.framework.TestCase;
+import junit.framework.TestSuite;
+
+import java.util.Set;
+
+
+/**
+ * Tests Implementation of CyFileFilter.
+ *
+ * TODO: Add to DataSuite
+ */
+public class CyFileFilterTest extends TestCase {
+ String EXT1 = "goo";
+ String EXT2 = "sif";
+ String EXT3 = "doc";
+ String DESC1 = "If google had a file type";
+ String DESC2 = "Interactions file type";
+ String DESC3 = "Microsoft Word file Type";
+ String DESC4 = "All file types";
+ String DUMMY_NATURE = "Human Designed";
+ String[] FILTERS = { EXT1, EXT2 };
+ CyFileFilter cff1;
+ CyFileFilter cff2;
+ CyFileFilter cff3;
+ CyFileFilter cff4;
+ CyFileFilter cff5;
+ CyFileFilter cff6;
+ CyFileFilter cff7;
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void setUp() throws Exception {
+ cff1 = new CyFileFilter();
+ cff2 = new CyFileFilter(EXT1);
+ cff3 = new CyFileFilter(EXT1, DESC1);
+ cff4 = new CyFileFilter(FILTERS);
+ cff5 = new CyFileFilter(FILTERS, DESC4);
+ cff6 = new CyFileFilter(EXT1, DESC1, DUMMY_NATURE);
+ cff7 = new CyFileFilter(FILTERS, DESC4, DUMMY_NATURE);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void tearDown() throws Exception {
+ CyFileFilter cff1 = null;
+ CyFileFilter cff2 = null;
+ CyFileFilter cff3 = null;
+ CyFileFilter cff4 = null;
+ CyFileFilter cff5 = null;
+ CyFileFilter cff6 = null;
+ CyFileFilter cff7 = null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testGetExtension() throws Exception {
+ //Error could result if getExtension includes the preceeding period
+ String test = cff1.getExtension("Google.goo");
+ assertEquals(EXT1, test);
+
+ test = cff2.getExtension("Google.goo");
+ assertEquals(EXT1, test);
+
+ test = cff3.getExtension("Google.goo");
+ assertEquals(EXT1, test);
+
+ test = cff4.getExtension("Google.goo");
+ assertEquals(EXT1, test);
+
+ test = cff5.getExtension("Google.goo");
+ assertEquals(EXT1, test);
+
+ test = cff6.getExtension("Google.goo");
+ assertEquals(EXT1, test);
+
+ test = cff7.getExtension("Google.goo");
+ assertEquals(EXT1, test);
+
+ boolean exists = cff1.isExtensionListInDescription();
+ assertTrue(exists);
+ cff1.setExtensionListInDescription(false);
+ exists = cff1.isExtensionListInDescription();
+ assertFalse(exists);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testConstructors() {
+ //cff1 (if no filters always accept)
+ boolean exists = cff1.accept("hi." + EXT2);
+ assertTrue(exists);
+ exists = cff1.accept("hi." + EXT1);
+ assertTrue(exists);
+
+ String description = cff1.getDescription();
+ assertEquals(description, "(*.*)");
+
+ String nature = cff1.getFileNature();
+ assertEquals(nature, "UNKNOWN");
+
+ //cff2
+ exists = cff2.accept("hi." + EXT2);
+ assertFalse(exists);
+ exists = cff2.accept("hi." + EXT1);
+ assertTrue(exists);
+
+ description = cff2.getDescription();
+ assertEquals(description, "(*.goo)");
+ nature = cff2.getFileNature();
+ assertEquals(nature, "UNKNOWN");
+
+ //cff3
+ exists = cff3.accept("hi." + EXT2);
+ assertFalse(exists);
+ exists = cff3.accept("hi." + EXT1);
+ assertTrue(exists);
+
+ cff3.setExtensionListInDescription(false);
+ description = cff3.getDescription();
+ assertEquals(description, DESC1);
+ nature = cff3.getFileNature();
+ assertEquals(nature, "UNKNOWN");
+
+ //cff4
+ exists = cff4.accept("hi." + EXT3);
+ assertFalse(exists);
+ exists = cff4.accept("hi." + EXT2);
+ assertTrue(exists);
+ exists = cff4.accept("hi." + EXT1);
+ assertTrue(exists);
+
+ Set extensions = cff4.getExtensionSet();
+ int size = extensions.size();
+ assertEquals(2, size);
+
+ description = cff4.getDescription();
+ assertEquals("(*.goo, *.sif)", description);
+ nature = cff4.getFileNature();
+ assertEquals(nature, "UNKNOWN");
+
+ //cff5
+ exists = cff5.accept("hi." + EXT3);
+ assertFalse(exists);
+ exists = cff5.accept("hi." + EXT2);
+ assertTrue(exists);
+ exists = cff5.accept("hi." + EXT1);
+ assertTrue(exists);
+
+ extensions = cff5.getExtensionSet();
+ size = extensions.size();
+ assertEquals(2, size);
+
+ cff5.setExtensionListInDescription(false);
+ description = cff5.getDescription();
+ cff5.setExtensionListInDescription(false);
+ assertEquals(description, DESC4);
+ nature = cff5.getFileNature();
+ assertEquals(nature, "UNKNOWN");
+
+ //cff6
+ exists = cff6.accept("hi." + EXT2);
+ assertFalse(exists);
+ exists = cff6.accept("hi." + EXT1);
+ assertTrue(exists);
+
+ cff6.setExtensionListInDescription(false);
+ description = cff6.getDescription();
+ assertEquals(description, DESC1);
+ nature = cff6.getFileNature();
+ assertEquals(nature, DUMMY_NATURE);
+
+ //cff7
+ exists = cff7.accept("hi." + EXT3);
+ assertFalse(exists);
+ exists = cff7.accept("hi." + EXT2);
+ assertTrue(exists);
+ exists = cff7.accept("hi." + EXT1);
+ assertTrue(exists);
+
+ extensions = cff7.getExtensionSet();
+ size = extensions.size();
+ assertEquals(2, size);
+
+ cff7.setExtensionListInDescription(false);
+ description = cff7.getDescription();
+
+ assertEquals(description, DESC4);
+ nature = cff7.getFileNature();
+ assertEquals(nature, DUMMY_NATURE);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testAddExtension() {
+ //cff1
+ cff1.addExtension(EXT3);
+
+ boolean exists = cff1.accept("hi." + EXT3);
+ assertTrue(exists);
+
+ //cff2
+ exists = cff2.accept("hi." + EXT3);
+ assertFalse(exists);
+ cff2.addExtension(EXT3);
+ exists = cff2.accept("hi." + EXT3);
+ assertTrue(exists);
+
+ //cff3
+ exists = cff3.accept("hi." + EXT3);
+ assertFalse(exists);
+ cff3.addExtension(EXT3);
+ exists = cff3.accept("hi." + EXT3);
+ assertTrue(exists);
+
+ //cff4
+ exists = cff4.accept("hi." + EXT3);
+ assertFalse(exists);
+ cff4.addExtension(EXT3);
+ exists = cff4.accept("hi." + EXT3);
+ assertTrue(exists);
+
+ //cff5
+ exists = cff5.accept("hi." + EXT3);
+ assertFalse(exists);
+ cff5.addExtension(EXT3);
+ exists = cff5.accept("hi." + EXT3);
+ assertTrue(exists);
+
+ //cff6
+ exists = cff6.accept("hi." + EXT3);
+ assertFalse(exists);
+ cff6.addExtension(EXT3);
+ exists = cff6.accept("hi." + EXT3);
+ assertTrue(exists);
+
+ //cff7
+ exists = cff7.accept("hi." + EXT3);
+ assertFalse(exists);
+ cff7.addExtension(EXT3);
+ exists = cff7.accept("hi." + EXT3);
+ assertTrue(exists);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testSets() {
+ String description = cff1.getDescription();
+ assertEquals(description, "(*.*)");
+
+ String nature = cff1.getFileNature();
+ assertEquals(nature, "UNKNOWN");
+
+ cff1.setDescription(DESC1);
+ cff1.setExtensionListInDescription(false);
+ cff1.setFileNature(DUMMY_NATURE);
+
+ description = cff1.getDescription();
+ assertEquals(DESC1, description);
+ nature = cff1.getFileNature();
+ assertEquals(DUMMY_NATURE, nature);
+ }
+}
diff --git a/application/src/test/java/cytoscape/util/FileUtilTest.java b/application/src/test/java/cytoscape/util/FileUtilTest.java
new file mode 100644
index 0000000..bd13da3
--- /dev/null
+++ b/application/src/test/java/cytoscape/util/FileUtilTest.java
@@ -0,0 +1,66 @@
+/*
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.util;
+
+import junit.framework.*;
+
+import java.util.regex.Pattern;
+
+
+public class FileUtilTest extends TestCase {
+
+ Pattern p = Pattern.compile(FileUtil.urlPattern);
+
+ public void testRegExPattern() {
+ // normal
+ checkURL("http://chianti.ucsd.edu/file.sif", true );
+ checkURL("https://chianti.ucsd.edu/file.xgmml", true );
+ checkURL("ftp://chianti.ucsd.edu/file.cys", true );
+ checkURL("file://chianti.ucsd.edu/file.cys", true );
+
+ // java jar extension
+ checkURL("jar:http://chianti.ucsd.edu/file.sif", true );
+ checkURL("jar:https://chianti.ucsd.edu/file.xgmml", true );
+ checkURL("jar:ftp://chianti.ucsd.edu/file.cys", true );
+ checkURL("jar:file://chianti.ucsd.edu/file.cys", true );
+
+ // bad
+ checkURL("C:/galFiltered.sif", false ); // bug 2024
+ }
+
+ private void checkURL(String url, boolean expected) {
+ assertEquals( p.matcher(url).matches(), expected );
+ }
+}
diff --git a/application/src/test/java/cytoscape/util/GMLFileFilterTest.java b/application/src/test/java/cytoscape/util/GMLFileFilterTest.java
new file mode 100644
index 0000000..49ad20f
--- /dev/null
+++ b/application/src/test/java/cytoscape/util/GMLFileFilterTest.java
@@ -0,0 +1,86 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.util;
+
+import cytoscape.data.readers.GMLReader;
+import cytoscape.data.readers.GraphReader;
+
+import cytoscape.util.GMLFileFilter;
+
+import junit.framework.TestCase;
+
+import java.io.File;
+
+
+/**
+ * Tests Implementation of CyFileFilter.
+ *
+ * TODO: Add to DataSuite
+ */
+public class GMLFileFilterTest extends TestCase {
+ GMLFileFilter test;
+ File DUMMY_GML_FILE;
+ GraphReader reader;
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void setUp() throws Exception {
+ test = new GMLFileFilter();
+ DUMMY_GML_FILE = File.createTempFile("inputGmlTest", ".gml");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void tearDown() throws Exception {
+ test = null;
+ DUMMY_GML_FILE.delete();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testGetReader() throws Exception {
+ reader = test.getReader(DUMMY_GML_FILE.toString());
+ assertEquals(reader.getClass(), GMLReader.class);
+ }
+}
diff --git a/application/src/test/java/cytoscape/util/GraphSetUtilsTest.java b/application/src/test/java/cytoscape/util/GraphSetUtilsTest.java
new file mode 100644
index 0000000..faba227
--- /dev/null
+++ b/application/src/test/java/cytoscape/util/GraphSetUtilsTest.java
@@ -0,0 +1,254 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.util;
+
+import cytoscape.AllTests;
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import cytoscape.CytoscapeInit;
+
+import cytoscape.data.CyAttributes;
+
+import cytoscape.giny.CytoscapeRootGraph;
+
+import cytoscape.util.GraphSetUtils;
+
+import giny.model.RootGraph;
+
+import junit.framework.*;
+
+import java.lang.Object;
+
+import java.util.*;
+
+
+/**
+ *
+ */
+public class GraphSetUtilsTest extends TestCase {
+ protected List<CyNetwork> networklist;
+ protected int a;
+ protected int b;
+ protected int c;
+ protected int d;
+ protected int e;
+ protected int ab;
+ protected int bc;
+ protected int ac;
+ protected int bd;
+ protected int be;
+ protected int cd;
+ protected CyNetwork net1;
+ protected CyNetwork net2;
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void setUp() throws Exception {
+ networklist = new ArrayList<CyNetwork>();
+
+ RootGraph root = Cytoscape.getRootGraph();
+ a = root.createNode();
+ b = root.createNode();
+ c = root.createNode();
+ d = root.createNode();
+ e = root.createNode();
+
+ int[] nodes1 = new int[] { a, b, c, d };
+ int[] nodes2 = new int[] { b, c, d, e };
+
+ ab = root.createEdge(a, b, true);
+ bc = root.createEdge(b, c, true);
+ ac = root.createEdge(a, c, true);
+ bd = root.createEdge(b, d, true);
+ be = root.createEdge(b, e, true);
+ cd = root.createEdge(c, d, true);
+
+ int[] edges1 = new int[] { ab, bc, ac, bd };
+ int[] edges2 = new int[] { bd, bc, be };
+
+ net1 = Cytoscape.createNetwork(nodes1, edges1, "graph1");
+ net2 = Cytoscape.createNetwork(nodes2, edges2, "graph2");
+ networklist.add(0, net1);
+ networklist.add(1, net2);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testNetwork() {
+ //verify created nodes exist
+ assertTrue(net1.containsNode(net1.getNode(a)));
+ assertTrue(net1.containsNode(net1.getNode(b)));
+ assertTrue(net1.containsNode(net1.getNode(c)));
+ assertTrue(net1.containsNode(net1.getNode(d)));
+
+ assertTrue(net2.containsNode(net2.getNode(b)));
+ assertTrue(net2.containsNode(net2.getNode(c)));
+ assertTrue(net2.containsNode(net2.getNode(d)));
+ assertTrue(net2.containsNode(net2.getNode(e)));
+
+ assertTrue(net1.containsEdge(net1.getEdge(ab)));
+ assertTrue(net1.containsEdge(net1.getEdge(bc)));
+ assertTrue(net1.containsEdge(net1.getEdge(ac)));
+ assertTrue(net1.containsEdge(net1.getEdge(bd)));
+
+ assertTrue(net2.containsEdge(net2.getEdge(bd)));
+ assertTrue(net2.containsEdge(net2.getEdge(bc)));
+ assertTrue(net2.containsEdge(net2.getEdge(be)));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void tearDown() throws Exception {
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testIntersection() {
+ CyNetwork n = GraphSetUtils.createIntersectionGraph(networklist, true, "intersect");
+
+ assertTrue(n.containsEdge(n.getEdge(bc)));
+ assertTrue(n.containsEdge(n.getEdge(bd)));
+ assertNull(n.getEdge(ab));
+ assertNull(n.getEdge(be));
+
+ assertTrue(n.containsNode(n.getNode(b)));
+ assertTrue(n.containsNode(n.getNode(c)));
+ assertTrue(n.containsNode(n.getNode(d)));
+ assertNull(n.getNode(a));
+ assertNull(n.getNode(e));
+ } // testIntersection
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testDifference() {
+ CyNetwork x = GraphSetUtils.createDifferenceGraph(networklist, true, "difference");
+
+ assertTrue(x.containsNode(x.getNode(a)));
+ assertTrue(x.containsNode(x.getNode(b)));
+ assertTrue(x.containsNode(x.getNode(c)));
+ assertNull(x.getNode(d));
+ assertNull(x.getNode(e));
+
+ assertTrue(x.containsEdge(x.getEdge(ab)));
+ assertNull(x.getEdge(bc));
+ assertTrue(x.containsEdge(x.getEdge(ac)));
+ assertNull(x.getEdge(be));
+ assertNull(x.getEdge(bd));
+ } // testDifference
+
+ public void testDifference2() {
+ CyNetwork x = GraphSetUtils.createDifferenceGraph2(networklist, true, "difference2");
+
+ assertTrue(x.containsNode(x.getNode(a)));
+ assertNull(x.getNode(b));
+ assertNull(x.getNode(c));
+ assertNull(x.getNode(d));
+ assertNull(x.getNode(e));
+
+ assertNull(x.getEdge(ab));
+ assertNull(x.getEdge(bc));
+ assertNull(x.getEdge(ac));
+ assertNull(x.getEdge(be));
+ assertNull(x.getEdge(bd));
+ } // testDifference2
+
+ public void testDifference_2() {
+ CyNetwork x = GraphSetUtils.createDifferenceGraph(createNetworks_2(), true, "difference");
+
+ assertTrue(x.containsNode(x.getNode(c)));
+ assertTrue(x.containsNode(x.getNode(a)));
+ assertTrue(x.containsNode(x.getNode(b)));
+
+ assertNull(x.getEdge(ab));
+ assertTrue(x.containsEdge(x.getEdge(ac)));
+ assertTrue(x.containsEdge(x.getEdge(bc)));
+ } // testDifference
+
+ public void testDifference2_2() {
+ CyNetwork x = GraphSetUtils.createDifferenceGraph2(createNetworks_2(), true, "difference2");
+
+ assertTrue(x.containsNode(x.getNode(c)));
+ assertNull(x.getNode(a));
+ assertNull(x.getNode(b));
+
+ assertNull(x.getEdge(ab));
+ assertNull(x.getEdge(ac));
+ assertNull(x.getEdge(bc));
+ } // testDifference2_2
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testUnion() {
+ CyNetwork y = GraphSetUtils.createUnionGraph(networklist, true, "union");
+
+ assertTrue(y.containsEdge(y.getEdge(ab)));
+ assertTrue(y.containsEdge(y.getEdge(bc)));
+ assertTrue(y.containsEdge(y.getEdge(ac)));
+ assertTrue(y.containsEdge(y.getEdge(bd)));
+
+ assertTrue(y.containsNode(y.getNode(a)));
+ assertTrue(y.containsNode(y.getNode(b)));
+ assertTrue(y.containsNode(y.getNode(c)));
+ assertTrue(y.containsNode(y.getNode(d)));
+ assertTrue(y.containsNode(y.getNode(e)));
+ } // testUnion
+
+ /**
+ * Creates the networks for testDifference_2() and testDifference2_2().
+ */
+ private List<CyNetwork> createNetworks_2() {
+ int[] nodes1 = new int[] { a, b, c };
+ int[] nodes2 = new int[] { a, b };
+
+ int[] edges1 = new int[] { ab, bc, ac };
+ int[] edges2 = new int[] { ab };
+
+ final List<CyNetwork> result = new ArrayList<CyNetwork>();
+ result.add(Cytoscape.createNetwork(nodes1, edges1, "graph1"));
+ result.add(Cytoscape.createNetwork(nodes2, edges2, "graph2"));
+
+ return result;
+ }
+}
diff --git a/application/src/test/java/cytoscape/util/LinearScalerTest.java b/application/src/test/java/cytoscape/util/LinearScalerTest.java
new file mode 100644
index 0000000..972a340
--- /dev/null
+++ b/application/src/test/java/cytoscape/util/LinearScalerTest.java
@@ -0,0 +1,26 @@
+package cytoscape.util;
+
+
+import junit.framework.*;
+
+
+public class LinearScalerTest extends TestCase {
+ public void test() {
+ final Scaler linearScaler = new LinearScaler();
+ final double[] unscaledValues = new double[] { 3.0, 10.2, 5.4, 3.0, 7.7 };
+ final double MIN = 0.0;
+ final double MAX = 1.0;
+ final double[] scaledValues = linearScaler.scale(unscaledValues, MIN, MAX);
+ boolean foundMin = false;
+ boolean foundMax = false;
+ for (final double d : scaledValues) {
+ if (MathUtil.almostEqual(MIN, d))
+ foundMin = true;
+ if (MathUtil.almostEqual(MAX, d))
+ foundMax = true;
+ assertTrue(d >= MIN && d <= MAX);
+ }
+ assertTrue(foundMin);
+ assertTrue(foundMax);
+ }
+}
\ No newline at end of file
diff --git a/application/src/test/java/cytoscape/util/MathUtilTest.java b/application/src/test/java/cytoscape/util/MathUtilTest.java
new file mode 100644
index 0000000..f0fd38c
--- /dev/null
+++ b/application/src/test/java/cytoscape/util/MathUtilTest.java
@@ -0,0 +1,24 @@
+package cytoscape.util;
+
+
+import junit.framework.*;
+
+
+public class MathUtilTest extends TestCase {
+ public void testGetExponent() {
+ assertEquals(-127, MathUtil.getExponent(0.0f));
+ assertEquals(0, MathUtil.getExponent(1.0f));
+ assertEquals(-1, MathUtil.getExponent(0.5f));
+ assertEquals(-127, MathUtil.getExponent(Float.MIN_VALUE));
+ assertEquals(127, MathUtil.getExponent(Float.MAX_VALUE));
+ }
+
+ public void testAlmostEqual() {
+ assertTrue(MathUtil.almostEqual(1.2345615f, 1.234562f));
+ assertTrue(MathUtil.almostEqual(1.2345615e30f, 1.234562e30f));
+ assertTrue(MathUtil.almostEqual(0.0f, 0.0f));
+ assertTrue(MathUtil.almostEqual(3.3f, 3.3f));
+ assertFalse(MathUtil.almostEqual(0.0f, 0.00000001f));
+ assertFalse(MathUtil.almostEqual(-0.0000001f, +0.0000001f));
+ }
+}
\ No newline at end of file
diff --git a/application/src/test/java/cytoscape/util/MinMaxTest.java b/application/src/test/java/cytoscape/util/MinMaxTest.java
new file mode 100644
index 0000000..e2865e7
--- /dev/null
+++ b/application/src/test/java/cytoscape/util/MinMaxTest.java
@@ -0,0 +1,146 @@
+/*
+ File: MinMaxTest.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// MinMaxTest.java
+package cytoscape.util;
+
+import cytoscape.AllTests;
+
+import cytoscape.util.MinMaxDouble;
+import cytoscape.util.MinMaxInt;
+
+import junit.framework.*;
+
+import java.io.*;
+
+
+/**
+ *
+ */
+public class MinMaxTest extends TestCase {
+ /**
+ * Creates a new MinMaxTest object.
+ *
+ * @param name DOCUMENT ME!
+ */
+ public MinMaxTest(String name) {
+ super(name);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testMinMaxDoubleVector() throws Exception {
+ AllTests.standardOut("testMinMaxDoubleVector");
+
+ double min = -888.88;
+ double max = 123456.789;
+ double[] input = { 1.0, 23.2, 18.5, -100.232, max, min };
+ MinMaxDouble minMax = new MinMaxDouble(input);
+ assertTrue(minMax.getMin() == min);
+ assertTrue(minMax.getMax() == max);
+ } // testMinMaxDoubleVector
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testMinMaxDoubleMatrix() throws Exception {
+ AllTests.standardOut("testMinMaxDoubleMatrix");
+
+ double min = -888.88;
+ double max = 123456.789;
+ double[][] input = {
+ { 1.0, 23.2, 18.5, -100.232, max, min },
+ { 8.7, 1.2, 1.2, 1.2, 1.2, -50.3 },
+ { 23.4, 2.1, 2.1, 2.1, 2.2, 0.0 }
+ };
+ MinMaxDouble minMax = new MinMaxDouble(input);
+ assertTrue(minMax.getMin() == min);
+ assertTrue(minMax.getMax() == max);
+ } // testMinMaxDoubleMatrix
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testMinMaxIntVector() throws Exception {
+ AllTests.standardOut("testMinMaxIntVector");
+
+ int min = -888;
+ int max = 123456;
+ int[] input = { 1, 232, 18, -100, max, min };
+
+ MinMaxInt minMax = new MinMaxInt(input);
+ assertTrue(minMax.getMin() == min);
+ assertTrue(minMax.getMax() == max);
+ } // testMinMaxIntVector
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testMinMaxIntMatrix() throws Exception {
+ AllTests.standardOut("testMinMaxIntMatrix");
+
+ int min = -888;
+ int max = 123456;
+ int[][] input = {
+ { 1, 23, 18, -100, max, min },
+ { 8, 1, 1, 1, 1, -50 },
+ { 23, 2, 2, 2, 2, 0 }
+ };
+
+ MinMaxInt minMax = new MinMaxInt(input);
+ assertTrue(minMax.getMin() == min);
+ assertTrue(minMax.getMax() == max);
+ } // testMinMaxIntMatrix
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ */
+ public static void main(String[] args) {
+ junit.textui.TestRunner.run(new TestSuite(MinMaxTest.class));
+ }
+} // MinMaxTest
diff --git a/application/src/test/java/cytoscape/util/MiscTest.java b/application/src/test/java/cytoscape/util/MiscTest.java
new file mode 100644
index 0000000..fe53f3e
--- /dev/null
+++ b/application/src/test/java/cytoscape/util/MiscTest.java
@@ -0,0 +1,264 @@
+/*
+ File: MiscTest.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// MiscTest.java
+package cytoscape.util;
+
+import cytoscape.AllTests;
+
+import cytoscape.util.Misc;
+
+import junit.framework.*;
+
+import java.awt.Color;
+
+import java.io.*;
+
+import java.util.*;
+
+
+/**
+ *
+ */
+public class MiscTest extends TestCase {
+ private boolean runAll = false;
+
+ /**
+ * Creates a new MiscTest object.
+ *
+ * @param name DOCUMENT ME!
+ */
+ public MiscTest(String name) {
+ super(name);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void setUp() throws Exception {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void tearDown() throws Exception {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testParseRGBTest() throws Exception {
+ AllTests.standardOut("testRGBParseText");
+
+ Color result = ColorUtil.parseColorText("0,0,0");
+ assertTrue(result.equals(Color.black));
+
+ result = ColorUtil.parseColorText("27,39,121");
+ assertTrue(result.getRed() == 27);
+ assertTrue(result.getGreen() == 39);
+ assertTrue(result.getBlue() == 121);
+
+ result = ColorUtil.parseColorText(" 27 , 39 , 121 ");
+ assertTrue(result.getRed() == 27);
+ assertTrue(result.getGreen() == 39);
+ assertTrue(result.getBlue() == 121);
+
+ result = ColorUtil.parseColorText("255,255,255");
+ assertTrue(result.equals(Color.white));
+ } // testParseRGBTest
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testParseList() throws Exception {
+ AllTests.standardOut("testParseList");
+
+ String delimiter = "::";
+ String startToken = "(";
+ String endToken = ")";
+
+ //
+ // 1) four tokens, separated by ::, surrounded with parens and whitespace
+ //
+ String a = "abcd";
+ String b = "efgh";
+ String c = "dog";
+ String d = "cat";
+
+ StringBuffer sb = new StringBuffer();
+ sb.append(" ");
+ sb.append(startToken);
+ sb.append(a + delimiter);
+ sb.append(b + delimiter);
+ sb.append(c + delimiter);
+ sb.append(d);
+ sb.append(endToken);
+ sb.append(" ");
+
+ String[] tokens = Misc.parseList(sb.toString(), startToken, endToken, delimiter);
+
+ assertTrue(tokens.length == 4);
+ assertTrue(tokens[0].equals(a));
+ assertTrue(tokens[1].equals(b));
+ assertTrue(tokens[2].equals(c));
+ assertTrue(tokens[3].equals(d));
+
+ // 2) add some embedded parens to the tokens. they should survive the parsing
+ a = "((abcd))";
+ b = "ef()gh";
+ c = "do))((g";
+ d = "c*())*at";
+
+ sb = new StringBuffer();
+ sb.append(" ");
+ sb.append(startToken);
+ sb.append(a + delimiter);
+ sb.append(b + delimiter);
+ sb.append(c + delimiter);
+ sb.append(d);
+ sb.append(endToken);
+ sb.append(" ");
+
+ tokens = Misc.parseList(sb.toString(), startToken, endToken, delimiter);
+ assertTrue(tokens.length == 4);
+ assertTrue(tokens[0].equals(a));
+ assertTrue(tokens[1].equals(b));
+ assertTrue(tokens[2].equals(c));
+ assertTrue(tokens[3].equals(d));
+
+ // 3) leave off the startToken.
+ a = "abcd))";
+ b = "ef()gh";
+ c = "do))((g";
+ d = "c*())*at";
+
+ sb = new StringBuffer();
+ sb.append(a + delimiter);
+ sb.append(b + delimiter);
+ sb.append(c + delimiter);
+ sb.append(d);
+ sb.append(endToken);
+ sb.append(" ");
+
+ tokens = Misc.parseList(sb.toString(), startToken, endToken, delimiter);
+ assertTrue(tokens.length == 1);
+
+ // 4) leave off the endToken.
+ a = "abcd))";
+ b = "ef()gh";
+ c = "do))((g";
+ d = "c*())*at";
+
+ sb = new StringBuffer();
+ sb.append(startToken);
+ sb.append(a + delimiter);
+ sb.append(b + delimiter);
+ sb.append(c + delimiter);
+ sb.append(d);
+ sb.append(" ");
+
+ tokens = Misc.parseList(sb.toString(), startToken, endToken, delimiter);
+ assertTrue(tokens.length == 1);
+
+ // 5) test some url's, which have embedded ":"
+ a = "http://www.genome.ad.jp/dbget-bin/get_pathway?org_name=hsa&mapno=00600";
+ b = "http://www.genome.ad.jp/dbget-bin/get_pathway?org_name=hsa&mapno=00562";
+ c = "http://www.genome.ad.jp/dbget-bin/get_pathway?org_name=hsa&mapno=00500";
+ d = "http://www.genome.ad.jp/dbget-bin/get_pathway?org_name=hsa&mapno=00860";
+
+ String e = "http://www.genome.ad.jp/dbget-bin/get_pathway?org_name=hsa&mapno=00760";
+
+ sb = new StringBuffer();
+ sb.append(startToken);
+ sb.append(a + delimiter);
+ sb.append(b + delimiter);
+ sb.append(c + delimiter);
+ sb.append(d + delimiter);
+ sb.append(e);
+ sb.append(endToken);
+
+ tokens = Misc.parseList(sb.toString(), startToken, endToken, delimiter);
+ assertTrue(tokens.length == 5);
+
+ assertTrue(tokens[0].equals(a));
+ assertTrue(tokens[1].equals(b));
+ assertTrue(tokens[2].equals(c));
+ assertTrue(tokens[3].equals(d));
+ assertTrue(tokens[4].equals(e));
+ } // testParseList
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testGetPropertyValues() throws Exception {
+ AllTests.standardOut("testGetPropertyValues");
+
+ Properties props = new Properties();
+ props.put("dog", "dozer");
+ props.put("cat", "(ernie::louie)");
+
+ Vector dogs = Misc.getPropertyValues(props, "dog");
+ assertTrue(dogs.size() == 1);
+
+ Vector cats = Misc.getPropertyValues(props, "cat");
+ assertTrue(cats.size() == 2);
+
+ String[] catNames = (String[]) cats.toArray(new String[0]);
+ assertTrue(catNames.length == 2);
+ assertTrue(catNames[0].equals("ernie"));
+ assertTrue(catNames[1].equals("louie"));
+ } // testGetPropertyValues
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ */
+ public static void main(String[] args) {
+ junit.textui.TestRunner.run(new TestSuite(MiscTest.class));
+ }
+} // MiscTest
diff --git a/application/src/test/java/cytoscape/util/NestedNetworkImageManagerTest.java b/application/src/test/java/cytoscape/util/NestedNetworkImageManagerTest.java
new file mode 100644
index 0000000..67eeb8f
--- /dev/null
+++ b/application/src/test/java/cytoscape/util/NestedNetworkImageManagerTest.java
@@ -0,0 +1,36 @@
+package cytoscape.util;
+
+import junit.framework.TestCase;
+
+
+public class NestedNetworkImageManagerTest extends TestCase {
+ private static final String FILE_LOCATION = "testData/NNFData/";
+
+
+ protected void setUp() throws Exception {
+ super.setUp();
+ }
+
+
+ protected void tearDown() throws Exception {
+ super.tearDown();
+ }
+
+
+ public void testNestedNetworkImageManager() throws Exception {
+// TestUtil.destroyNetworksEdgesAndNodes();
+//
+// // Load nested network
+// final NNFReader reader = new NNFReader(FILE_LOCATION + "good3.nnf");
+// reader.read();
+//
+// final CyNode m1 = Cytoscape.getCyNode("M1");
+// assertNotNull(m1);
+// assertNotNull(Cytoscape.getCyNode("M2"));
+// assertNotNull(Cytoscape.getCyNode("M3"));
+// assertEquals(3, NestedNetworkImageManager.getImageCount());
+//
+// m1.setNestedNetwork(null);
+// assertEquals(2, NestedNetworkImageManager.getImageCount());
+ }
+}
diff --git a/application/src/test/java/cytoscape/util/PropUtilTest.java b/application/src/test/java/cytoscape/util/PropUtilTest.java
new file mode 100644
index 0000000..6ee170c
--- /dev/null
+++ b/application/src/test/java/cytoscape/util/PropUtilTest.java
@@ -0,0 +1,147 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.util;
+
+import junit.framework.*;
+
+import java.util.Properties;
+
+
+/**
+ *
+ */
+public class PropUtilTest extends TestCase {
+
+ Properties props;
+ protected void setUp() throws Exception {
+ props = new Properties();
+ }
+
+ public void testGoodInt() {
+ props.setProperty("good-int-1","123");
+
+ assertEquals(123,PropUtil.getInt(props,"good-int-1",999));
+ }
+
+ public void testBadInt() {
+ props.setProperty("bad-int-1"," 4");
+ props.setProperty("bad-int-2","5 ");
+ props.setProperty("bad-int-3"," 6 ");
+ props.setProperty("bad-int-4","homer");
+ props.setProperty("bad-int-5"," x");
+ props.setProperty("bad-int-6","5.04 ");
+ props.setProperty("bad-int-7"," 6.0 ");
+
+ assertEquals(999,PropUtil.getInt(props,"bad-int-1",999));
+ assertEquals(999,PropUtil.getInt(props,"bad-int-2",999));
+ assertEquals(999,PropUtil.getInt(props,"bad-int-3",999));
+ assertEquals(999,PropUtil.getInt(props,"bad-int-4",999));
+ assertEquals(999,PropUtil.getInt(props,"bad-int-5",999));
+ assertEquals(999,PropUtil.getInt(props,"bad-int-6",999));
+ assertEquals(999,PropUtil.getInt(props,"bad-int-7",999));
+ }
+
+
+ public void testTrueGood() {
+ props.setProperty("true-good-1","true");
+ props.setProperty("true-good-2"," TRUE");
+ props.setProperty("true-good-3","trUe ");
+ props.setProperty("true-good-4"," True ");
+
+ assertTrue(PropUtil.getBoolean(props,"true-good-1",false));
+ assertTrue(PropUtil.getBoolean(props,"true-good-2",false));
+ assertTrue(PropUtil.getBoolean(props,"true-good-3",false));
+ assertTrue(PropUtil.getBoolean(props,"true-good-4",false));
+ }
+
+ public void testFalseGood() {
+ props.setProperty("false-good-1","false");
+ props.setProperty("false-good-2"," FALSE");
+ props.setProperty("false-good-3","False ");
+ props.setProperty("false-good-4"," false ");
+
+ assertFalse(PropUtil.getBoolean(props,"false-good-1",true));
+ assertFalse(PropUtil.getBoolean(props,"false-good-2",true));
+ assertFalse(PropUtil.getBoolean(props,"false-good-3",true));
+ assertFalse(PropUtil.getBoolean(props,"false-good-4",true));
+ }
+
+ public void testYesGood() {
+ props.setProperty("true-good-1","yes");
+ props.setProperty("true-good-2"," YES");
+ props.setProperty("true-good-3","yEs ");
+ props.setProperty("true-good-4"," YeS ");
+
+ assertTrue(PropUtil.getBoolean(props,"true-good-1",false));
+ assertTrue(PropUtil.getBoolean(props,"true-good-2",false));
+ assertTrue(PropUtil.getBoolean(props,"true-good-3",false));
+ assertTrue(PropUtil.getBoolean(props,"true-good-4",false));
+ }
+
+ public void testNoGood() {
+ props.setProperty("false-good-1","no");
+ props.setProperty("false-good-2"," NO");
+ props.setProperty("false-good-3","No ");
+ props.setProperty("false-good-4"," nO ");
+
+ assertFalse(PropUtil.getBoolean(props,"false-good-1",true));
+ assertFalse(PropUtil.getBoolean(props,"false-good-2",true));
+ assertFalse(PropUtil.getBoolean(props,"false-good-3",true));
+ assertFalse(PropUtil.getBoolean(props,"false-good-4",true));
+ }
+
+ public void testTrueBad() {
+ props.setProperty("true-bad-1","truex");
+ props.setProperty("true-bad-2","true x");
+ props.setProperty("true-bad-3","true!");
+
+ // we should be getting the default in each case
+ assertFalse(PropUtil.getBoolean(props,"true-bad-1",false));
+ assertTrue(PropUtil.getBoolean(props,"true-bad-2",true));
+ assertFalse(PropUtil.getBoolean(props,"true-bad-3",false));
+ }
+
+ public void testFalseBad() {
+ props.setProperty("false-bad-1","falsex");
+ props.setProperty("false-bad-2","false x");
+ props.setProperty("false-bad-3","false!");
+
+ // we should be getting the default in each case
+ assertFalse(PropUtil.getBoolean(props,"false-bad-1",false));
+ assertTrue(PropUtil.getBoolean(props,"false-bad-2",true));
+ assertFalse(PropUtil.getBoolean(props,"false-bad-3",false));
+ }
+
+}
diff --git a/application/src/test/java/cytoscape/util/RankScalerTest.java b/application/src/test/java/cytoscape/util/RankScalerTest.java
new file mode 100644
index 0000000..a0d5e35
--- /dev/null
+++ b/application/src/test/java/cytoscape/util/RankScalerTest.java
@@ -0,0 +1,38 @@
+package cytoscape.util;
+
+
+import junit.framework.*;
+
+
+public class RankScalerTest extends TestCase {
+ public void test1() {
+ final Scaler rankScaler = new RankScaler();
+ final double[] unscaledValues = new double[] { 3.0, 10.2, 5.4, 3.0, 7.7 };
+ final double MIN = 0.0;
+ final double MAX = 1.0;
+ final double[] scaledValues = rankScaler.scale(unscaledValues, MIN, MAX);
+ boolean foundMin = false;
+ boolean foundMax = false;
+ for (final double d : scaledValues) {
+ if (MathUtil.almostEqual(MIN, d))
+ foundMin = true;
+ if (MathUtil.almostEqual(MAX, d))
+ foundMax = true;
+ assertTrue(d >= MIN && d <= MAX);
+ }
+ assertFalse(foundMin);
+ assertFalse(foundMax);
+ }
+
+ public void test2() {
+ final Scaler rankScaler = new RankScaler();
+ final double[] unscaledValues = new double[] { 3.0, 3.0, 1.4, 7.7 };
+ final double MIN = 0.0;
+ final double MAX = 1.0;
+ final double[] scaledValues = rankScaler.scale(unscaledValues, MIN, MAX);
+ assertEquals(0.5, scaledValues[0], 1e-10);
+ assertEquals(0.5, scaledValues[1], 1e-10);
+ assertEquals(0.125, scaledValues[2], 1e-10);
+ assertEquals(0.875, scaledValues[3], 1e-10);
+ }
+}
\ No newline at end of file
diff --git a/application/src/test/java/cytoscape/util/SIFFileFilterTest.java b/application/src/test/java/cytoscape/util/SIFFileFilterTest.java
new file mode 100644
index 0000000..346acf4
--- /dev/null
+++ b/application/src/test/java/cytoscape/util/SIFFileFilterTest.java
@@ -0,0 +1,86 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.util;
+
+import cytoscape.data.readers.GraphReader;
+import cytoscape.data.readers.InteractionsReader;
+
+import cytoscape.util.SIFFileFilter;
+
+import junit.framework.TestCase;
+
+import java.io.File;
+
+
+/**
+ * Tests Implementation of CyFileFilter.
+ *
+ * TODO: Add to DataSuite
+ */
+public class SIFFileFilterTest extends TestCase {
+ SIFFileFilter test;
+ File DUMMY_SIF_FILE;
+ GraphReader reader;
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void setUp() throws Exception {
+ test = new SIFFileFilter();
+ DUMMY_SIF_FILE = File.createTempFile("inputSifTest", ".sif");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void tearDown() throws Exception {
+ test = null;
+ DUMMY_SIF_FILE.delete();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testGetReader() throws Exception {
+ reader = test.getReader(DUMMY_SIF_FILE.toString());
+ assertEquals(reader.getClass(), InteractionsReader.class);
+ }
+}
diff --git a/application/src/test/java/cytoscape/util/ScalerFactoryTest.java b/application/src/test/java/cytoscape/util/ScalerFactoryTest.java
new file mode 100644
index 0000000..6b0d32c
--- /dev/null
+++ b/application/src/test/java/cytoscape/util/ScalerFactoryTest.java
@@ -0,0 +1,24 @@
+package cytoscape.util;
+
+
+import junit.framework.*;
+
+
+public class ScalerFactoryTest extends TestCase {
+ public void testGetKnownScaler() {
+ final Scaler linearScaler = ScalerFactory.getScaler("linear");
+ assertTrue(linearScaler instanceof LinearScaler);
+
+ final Scaler rankScaler = ScalerFactory.getScaler("rank");
+ assertTrue(rankScaler instanceof RankScaler);
+ }
+
+ public void testGetUnknownScaler() {
+ try {
+ final Scaler scaler = ScalerFactory.getScaler("random junk!#$");
+ fail();
+ } catch (final IllegalArgumentException e) {
+ assertTrue(true);
+ }
+ }
+}
\ No newline at end of file
diff --git a/application/src/test/java/cytoscape/util/TestUtil.java b/application/src/test/java/cytoscape/util/TestUtil.java
new file mode 100644
index 0000000..bc90507
--- /dev/null
+++ b/application/src/test/java/cytoscape/util/TestUtil.java
@@ -0,0 +1,20 @@
+package cytoscape.util;
+
+import java.util.Set;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+
+
+public class TestUtil {
+ /**
+ * Destroys all networks in the root graph. Please note that the nodes and edges of said networks are also being destroyed.
+ */
+ public static void destroyNetworksEdgesAndNodes() {
+ final Set<CyNetwork> networks = Cytoscape.getNetworkSet();
+ for (final CyNetwork network : networks) {
+ Cytoscape.destroyNetwork(network, /* destroy_unique = */true);
+ }
+ }
+
+}
diff --git a/application/src/test/java/cytoscape/util/TopologicalSortTest.java b/application/src/test/java/cytoscape/util/TopologicalSortTest.java
new file mode 100644
index 0000000..285fb33
--- /dev/null
+++ b/application/src/test/java/cytoscape/util/TopologicalSortTest.java
@@ -0,0 +1,187 @@
+/*
+ File: TopologicalSortTest.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.util;
+
+
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.Collection;
+import junit.framework.*;
+
+
+class Node implements TopoGraphNode {
+ private final String nodeName;
+ private final Collection<TopoGraphNode> dependents;
+
+ Node(final String nodeName) {
+ this.nodeName = nodeName;
+ this.dependents = new HashSet<TopoGraphNode>();
+ }
+
+ @Override public String toString() { return nodeName; }
+ public Collection<TopoGraphNode> getDependents() { return dependents; }
+ void addDependent(final TopoGraphNode newDependent) { dependents.add(newDependent); }
+}
+
+
+public class TopologicalSortTest extends TestCase {
+ public void testWikipediaExample() { // Based on the example at http://en.wikipedia.org/wiki/Topological_sorting
+ final Node node7 = new Node("7");
+ final Node node5 = new Node("5");
+ final Node node3 = new Node("3");
+ final Node node11 = new Node("11");
+ final Node node8 = new Node("8");
+ final Node node2 = new Node("2");
+ final Node node9 = new Node("9");
+ final Node node10 = new Node("10");
+
+ node7.addDependent(node11);
+ node7.addDependent(node8);
+ node5.addDependent(node11);
+ node3.addDependent(node8);
+ node3.addDependent(node10);
+ node11.addDependent(node2);
+ node11.addDependent(node9);
+ node11.addDependent(node10);
+ node8.addDependent(node9);
+
+ final Collection<TopoGraphNode> nodes = new ArrayList<TopoGraphNode>();
+ nodes.add(node7);
+ nodes.add(node5);
+ nodes.add(node3);
+ nodes.add(node11);
+ nodes.add(node8);
+ nodes.add(node2);
+ nodes.add(node9);
+ nodes.add(node10);
+
+ final Collection<TopoGraphNode> order = TopologicalSort.sort(nodes);
+ assertTrue(isTopologicalOrder(order));
+ }
+
+ public void testGraphWithSomeUnconnectedNodes() {
+ final Node node7 = new Node("7");
+ final Node node5 = new Node("5");
+ final Node node3 = new Node("3");
+ final Node node11 = new Node("11");
+ final Node node8 = new Node("8");
+ final Node node2 = new Node("2");
+ final Node node9 = new Node("9");
+ final Node node10 = new Node("10");
+ final Node nodeU1 = new Node("U3");
+ final Node nodeU2 = new Node("U2");
+ final Node nodeU3 = new Node("U1");
+
+ node7.addDependent(node11);
+ node7.addDependent(node8);
+ node5.addDependent(node11);
+ node3.addDependent(node8);
+ node3.addDependent(node10);
+ node11.addDependent(node2);
+ node11.addDependent(node9);
+ node11.addDependent(node10);
+ node8.addDependent(node9);
+
+ final Collection<TopoGraphNode> nodes = new ArrayList<TopoGraphNode>();
+ nodes.add(node7);
+ nodes.add(node5);
+ nodes.add(node3);
+ nodes.add(node11);
+ nodes.add(node8);
+ nodes.add(node2);
+ nodes.add(node9);
+ nodes.add(node10);
+
+ final Collection<TopoGraphNode> order = TopologicalSort.sort(nodes);
+ assertTrue(isTopologicalOrder(order));
+ }
+
+ public void testIndirectCycle() {
+ final Node nodeA = new Node("A");
+ final Node nodeB = new Node("B");
+ final Node nodeC = new Node("C");
+
+ nodeA.addDependent(nodeB);
+ nodeB.addDependent(nodeC);
+ nodeC.addDependent(nodeA);
+
+ final Collection<TopoGraphNode> nodes = new ArrayList<TopoGraphNode>();
+ nodes.add(nodeA);
+ nodes.add(nodeB);
+ nodes.add(nodeC);
+
+ boolean failed;
+ try {
+ TopologicalSort.sort(nodes);
+ failed = false;
+ } catch (final IllegalStateException e) {
+ failed = true;
+ }
+
+ assertTrue(failed);
+ }
+
+ public void testSelfLoopCycle() {
+ final Node nodeA = new Node("A");
+ final Node nodeB = new Node("B");
+ final Node nodeC = new Node("C");
+
+ nodeB.addDependent(nodeB);
+
+ final Collection<TopoGraphNode> nodes = new ArrayList<TopoGraphNode>();
+ nodes.add(nodeA);
+ nodes.add(nodeB);
+ nodes.add(nodeC);
+
+ boolean failed;
+ try {
+ TopologicalSort.sort(nodes);
+ failed = false;
+ } catch (final IllegalStateException e) {
+ failed = true;
+ }
+
+ assertTrue(failed);
+ }
+
+ private boolean isTopologicalOrder(final Collection<TopoGraphNode> topoOrderCandidate) {
+ final TopoGraphNode[] orderAsArray = topoOrderCandidate.toArray(new TopoGraphNode[topoOrderCandidate.size()]);
+
+ for (int i = 0; i < orderAsArray.length; ++i) {
+ final Collection<TopoGraphNode> dependents = orderAsArray[i].getDependents();
+ for (int k = i + 1; k < orderAsArray.length; ++k) {
+ if (dependents.contains(orderAsArray[k]))
+ return false;
+ }
+ }
+
+ return true;
+ }
+}
diff --git a/application/src/test/java/cytoscape/util/XGMMLFileFilterTest.java b/application/src/test/java/cytoscape/util/XGMMLFileFilterTest.java
new file mode 100644
index 0000000..b3213a5
--- /dev/null
+++ b/application/src/test/java/cytoscape/util/XGMMLFileFilterTest.java
@@ -0,0 +1,86 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.util;
+
+import cytoscape.data.readers.GraphReader;
+import cytoscape.data.readers.XGMMLReader;
+
+import cytoscape.util.XGMMLFileFilter;
+
+import junit.framework.TestCase;
+
+import java.io.File;
+
+
+/**
+ * Tests Implementation of CyFileFilter.
+ *
+ * TODO: Add to DataSuite
+ */
+public class XGMMLFileFilterTest extends TestCase {
+ XGMMLFileFilter test;
+ File DUMMY_XGMML_FILE;
+ GraphReader reader;
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void setUp() throws Exception {
+ test = new XGMMLFileFilter();
+ DUMMY_XGMML_FILE = File.createTempFile("inputXGMMLTest", ".xgmml");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void tearDown() throws Exception {
+ test = null;
+ DUMMY_XGMML_FILE.delete();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testGetReader() throws Exception {
+ reader = test.getReader(DUMMY_XGMML_FILE.toString());
+ assertEquals(reader.getClass(), XGMMLReader.class);
+ }
+}
diff --git a/application/src/test/java/cytoscape/view/CytoscapeViewTest.java b/application/src/test/java/cytoscape/view/CytoscapeViewTest.java
new file mode 100644
index 0000000..424bf9e
--- /dev/null
+++ b/application/src/test/java/cytoscape/view/CytoscapeViewTest.java
@@ -0,0 +1,193 @@
+/*
+ File: CytoscapeViewTests.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// $Revision: 13032 $
+// $Date: 2008-02-12 22:20:38 +0100 (Tue, 12 Feb 2008) $
+// $Author: mes $
+package cytoscape.view;
+
+import cytoscape.*;
+import cytoscape.AllTests;
+
+import cytoscape.view.CyNetworkView;
+
+import giny.model.*;
+
+import giny.view.*;
+
+import junit.framework.*;
+
+import java.io.*;
+
+import java.util.*;
+
+
+/**
+ *
+ */
+public class CytoscapeViewTest extends TestCase {
+ CyNetwork network;
+ CyNode node1;
+ CyNode node2;
+ CyEdge edge1;
+ CyEdge edge2;
+ CyNetworkView view;
+ NodeView nodeView1;
+ NodeView nodeView2;
+ EdgeView edgeView1;
+ EdgeView edgeView2;
+
+ /**
+ * Creates a new CytoscapeViewTests object.
+ *
+ * @param name DOCUMENT ME!
+ */
+ public CytoscapeViewTest(String name) {
+ super(name);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void setUp() throws Exception {
+ node1 = Cytoscape.getCyNode("node1", true);
+ node2 = Cytoscape.getCyNode("node2", true);
+ edge1 = Cytoscape.getCyEdge("node1", "node1 (pp) node2", "node2", "pp");
+ edge2 = Cytoscape.getCyEdge("node2", "node2 (pp) node1", "node1", "pp");
+
+ int[] nodeArray = { node1.getRootGraphIndex(), node2.getRootGraphIndex() };
+ int[] edgeArray = { edge1.getRootGraphIndex(), edge2.getRootGraphIndex() };
+ network = Cytoscape.createNetwork(nodeArray, edgeArray, null);
+ view = Cytoscape.createNetworkView(network);
+ nodeView1 = view.getNodeView(node1);
+ nodeView2 = view.getNodeView(node2);
+ edgeView1 = view.getEdgeView(edge1);
+ edgeView2 = view.getEdgeView(edge2);
+ }
+
+ /**
+ * Tests whether selected nodes become unselected after a view of the
+ * network is destroyed and then recreated.
+ * @see http://cbio.mskcc.org/cytoscape/bugs/view.php?id=925
+ */
+ public void testBug925() {
+ network.unselectAllEdges();
+ network.unselectAllNodes();
+ assertEquals("num nodes selected", 0, network.getSelectedNodes().size());
+ assertEquals("num edges selected", 0, network.getSelectedEdges().size());
+ network.setSelectedNodeState(node1,true);
+ assertEquals("num nodes selected", 1, network.getSelectedNodes().size());
+ assertTrue("node1 is selected",network.isSelected(node1));
+ Cytoscape.destroyNetworkView( view );
+ assertEquals("num nodes selected", 1, network.getSelectedNodes().size());
+ assertTrue("node1 is selected",network.isSelected(node1));
+ view = Cytoscape.createNetworkView(network);
+ assertEquals("num nodes selected", 1, network.getSelectedNodes().size());
+ assertTrue("node1 is selected",network.isSelected(node1));
+ }
+
+ /**
+ * Tests that the view is properly modified when the selectfilter is changed.
+ */
+ public void testFilterToViewSelect() throws Exception {
+ checkState(false, false, false, false);
+ network.setSelectedNodeState(node1, true);
+ checkState(true, false, false, false);
+ network.setSelectedEdgeState(edge2, true);
+ checkState(true, false, false, true);
+ network.selectAllNodes();
+ checkState(true, true, false, true);
+ network.selectAllEdges();
+ checkState(true, true, true, true);
+ network.setSelectedNodeState(node2, false);
+ checkState(true, false, true, true);
+ network.setSelectedEdgeState(edge1, false);
+ checkState(true, false, false, true);
+ network.unselectAllEdges();
+ checkState(true, false, false, false);
+ network.unselectAllNodes();
+ checkState(false, false, false, false);
+ }
+
+ /**
+ * Tests that the selectfilter is properly modified when the view is changed.
+ */
+ public void testViewToFilterSelect() throws Exception {
+ checkState(false, false, false, false);
+ nodeView1.setSelected(true);
+ checkState(true, false, false, false);
+ edgeView2.setSelected(true);
+ checkState(true, false, false, true);
+ nodeView2.setSelected(true);
+ checkState(true, true, false, true);
+ edgeView1.setSelected(true);
+ checkState(true, true, true, true);
+ nodeView2.setSelected(false);
+ checkState(true, false, true, true);
+ edgeView1.setSelected(false);
+ checkState(true, false, false, true);
+ edgeView2.setSelected(false);
+ checkState(true, false, false, false);
+ nodeView1.setSelected(false);
+ checkState(false, false, false, false);
+ }
+
+ /**
+ * Checks that the current state of the filter and the view match the state
+ * defined by the arguments.
+ */
+ private void checkState(boolean n1, boolean n2, boolean e1, boolean e2) {
+ assertTrue( network.isSelected(node1) == n1 );
+ assertTrue( network.isSelected(node2) == n2 );
+ assertTrue( network.isSelected(edge1) == e1 );
+ assertTrue( network.isSelected(edge2) == e2 );
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ */
+ public static void main(String[] args) {
+ junit.textui.TestRunner.run(new TestSuite(CytoscapeViewTest.class));
+ Cytoscape.exit(0);
+ }
+
+ //------------------------------------------------------------------------------
+}
diff --git a/application/src/test/java/cytoscape/view/FlagAndSelectionHandlerTest.java b/application/src/test/java/cytoscape/view/FlagAndSelectionHandlerTest.java
new file mode 100644
index 0000000..0b88ed9
--- /dev/null
+++ b/application/src/test/java/cytoscape/view/FlagAndSelectionHandlerTest.java
@@ -0,0 +1,217 @@
+/*
+ File: FlagAndSelectionHandlerTest.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+//------------------------------------------------------------------------------
+// $Revision: 9920 $
+// $Date: 2007-04-09 23:17:52 +0200 (Mon, 09 Apr 2007) $
+// $Author: mes $
+//--------------------------------------------------------------------------------------
+package cytoscape.view;
+
+import cytoscape.AllTests;
+import cytoscape.Cytoscape;
+
+import cytoscape.data.SelectFilter;
+
+import cytoscape.view.FlagAndSelectionHandler;
+
+import giny.model.*;
+
+import giny.view.*;
+
+//--------------------------------------------------------------------------------------
+import junit.framework.*;
+
+import java.io.*;
+
+import java.util.*;
+
+
+//------------------------------------------------------------------------------
+/**
+ *
+ */
+public class FlagAndSelectionHandlerTest extends TestCase {
+ SelectFilter filter;
+ Node node1;
+ Node node2;
+ Edge edge1;
+ Edge edge2;
+ GraphPerspective gp;
+ GraphView view;
+ NodeView nodeView1;
+ NodeView nodeView2;
+ EdgeView edgeView1;
+ EdgeView edgeView2;
+ FlagAndSelectionHandler handler;
+
+ //------------------------------------------------------------------------------
+ /**
+ * Creates a new FlagAndSelectionHandlerTest object.
+ *
+ * @param name DOCUMENT ME!
+ */
+ public FlagAndSelectionHandlerTest(String name) {
+ super(name);
+ }
+
+ //------------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void setUp() throws Exception {
+ RootGraph rootGraph = Cytoscape.getRootGraph();
+ node1 = rootGraph.getNode(rootGraph.createNode());
+ node2 = rootGraph.getNode(rootGraph.createNode());
+ edge1 = rootGraph.getEdge(rootGraph.createEdge(node1, node2));
+ edge2 = rootGraph.getEdge(rootGraph.createEdge(node2, node1));
+
+ Node[] nodeArray = { node1, node2 };
+ Edge[] edgeArray = { edge1, edge2 };
+ gp = rootGraph.createGraphPerspective(nodeArray, edgeArray);
+ filter = new SelectFilter(gp);
+ view = new ding.view.DGraphView(gp);
+
+ for (int i = 0; i < nodeArray.length; i++) {
+ view.addNodeView(nodeArray[i].getRootGraphIndex());
+ }
+
+ for (int i = 0; i < edgeArray.length; i++) {
+ view.addEdgeView(edgeArray[i].getRootGraphIndex());
+ }
+
+ nodeView1 = view.getNodeView(node1);
+ nodeView2 = view.getNodeView(node2);
+ edgeView1 = view.getEdgeView(edge1);
+ edgeView2 = view.getEdgeView(edge2);
+ //set an initial state to make sure the handler synchronizes properly
+ filter.setSelected(node1, true);
+ edgeView2.setSelected(true);
+ handler = new FlagAndSelectionHandler(filter, view);
+ assertTrue(filter.isSelected(edge2));
+ assertTrue(nodeView1.isSelected());
+ filter.unselectAllNodes();
+ filter.unselectAllEdges();
+ }
+
+ //------------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void tearDown() throws Exception {
+ }
+
+ //-------------------------------------------------------------------------
+ /**
+ * Tests that the view is properly modified when the filter is changed.
+ */
+ public void testFilterToView() throws Exception {
+ checkState(false, false, false, false);
+ filter.setSelected(node1, true);
+ checkState(true, false, false, false);
+ filter.setSelected(edge2, true);
+ checkState(true, false, false, true);
+ filter.selectAllNodes();
+ checkState(true, true, false, true);
+ filter.selectAllEdges();
+ checkState(true, true, true, true);
+ filter.setSelected(node2, false);
+ checkState(true, false, true, true);
+ filter.setSelected(edge1, false);
+ checkState(true, false, false, true);
+ filter.unselectAllEdges();
+ checkState(true, false, false, false);
+ filter.unselectAllNodes();
+ checkState(false, false, false, false);
+ }
+
+ //-------------------------------------------------------------------------
+ /**
+ * Tests that the filter is properly modified when the view is changed.
+ */
+ public void testViewToFilter() throws Exception {
+ checkState(false, false, false, false);
+ nodeView1.setSelected(true);
+ checkState(true, false, false, false);
+ edgeView2.setSelected(true);
+ checkState(true, false, false, true);
+ nodeView2.setSelected(true);
+ checkState(true, true, false, true);
+ edgeView1.setSelected(true);
+ checkState(true, true, true, true);
+ nodeView2.setSelected(false);
+ checkState(true, false, true, true);
+ edgeView1.setSelected(false);
+ checkState(true, false, false, true);
+ edgeView2.setSelected(false);
+ checkState(true, false, false, false);
+ nodeView1.setSelected(false);
+ checkState(false, false, false, false);
+ }
+
+ //-------------------------------------------------------------------------
+ /**
+ * Checks that the current state of the filter and the view match the state
+ * defined by the arguments.
+ */
+ public void checkState(boolean n1, boolean n2, boolean e1, boolean e2) {
+ assertTrue(filter.isSelected(node1) == n1);
+ assertTrue(filter.isSelected(node2) == n2);
+ assertTrue(filter.isSelected(edge1) == e1);
+ assertTrue(filter.isSelected(edge2) == e2);
+ assertTrue(nodeView1.isSelected() == n1);
+ assertTrue(nodeView2.isSelected() == n2);
+ assertTrue(edgeView1.isSelected() == e1);
+ assertTrue(edgeView2.isSelected() == e2);
+ }
+
+ //-------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ */
+ public static void main(String[] args) {
+ junit.textui.TestRunner.run(new TestSuite(FlagAndSelectionHandlerTest.class));
+ }
+
+ //------------------------------------------------------------------------------
+}
diff --git a/application/src/test/java/cytoscape/visual/BypassHelperTest.java b/application/src/test/java/cytoscape/visual/BypassHelperTest.java
new file mode 100644
index 0000000..946e999
--- /dev/null
+++ b/application/src/test/java/cytoscape/visual/BypassHelperTest.java
@@ -0,0 +1,165 @@
+/*
+ File: BypassHelper.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.visual;
+
+import giny.view.Justification;
+import giny.view.ObjectPosition;
+import giny.view.Position;
+
+import java.awt.Color;
+import java.awt.Font;
+
+import junit.framework.TestCase;
+import junit.framework.TestSuite;
+import cytoscape.CyEdge;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+import cytoscape.data.CyAttributes;
+import cytoscape.data.Semantics;
+import ding.view.ObjectPositionImpl;
+
+/**
+ * While this used to test a ByPassHelper class, that functionality has now been
+ * subsumed by Appearance. These tests should eventually more into the
+ * Appearance unit test.
+ */
+public class BypassHelperTest extends TestCase {
+ CyNode homer;
+ CyNode marge;
+ CyEdge lisa;
+ CyAttributes nodeAttrs;
+ CyAttributes edgeAttrs;
+ String id;
+
+ /**
+ * Creates a new BypassHelperTest object.
+ *
+ * @param name
+ * DOCUMENT ME!
+ */
+ public BypassHelperTest(String name) {
+ super(name);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void setUp() {
+ homer = Cytoscape.getCyNode("homer", true);
+ marge = Cytoscape.getCyNode("marge", true);
+ lisa = Cytoscape.getCyEdge(homer, marge, Semantics.INTERACTION, "pp",
+ true);
+ nodeAttrs = Cytoscape.getNodeAttributes();
+ edgeAttrs = Cytoscape.getEdgeAttributes();
+ id = homer.getIdentifier();
+
+ nodeAttrs.setAttribute(id, "node.fillColor", "25,31,244");
+ nodeAttrs.setAttribute(id, "node.borderColor", "junk");
+ nodeAttrs.setAttribute(id, "node.size", "22.0");
+ nodeAttrs.setAttribute(id, "node.labelPosition", "NE,W,c,13,-1");
+ nodeAttrs.setAttribute(id, "node.font", "SansSerif,italic,10");
+ nodeAttrs.setAttribute(id, "node.lineStyle", "LONG_DASH");
+ nodeAttrs.setAttribute(id, "node.shape", "DIAMOND");
+
+ edgeAttrs.setAttribute(lisa.getIdentifier(), "edge.sourceArrowShape",
+ "WHITE_DELTA");
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testGetBypass() {
+ Object o = null;
+
+ o = Appearance.getBypass(nodeAttrs, id,
+ VisualPropertyType.NODE_FILL_COLOR);
+ System.out.println("id " + id);
+ System.out.println("o " + o.toString());
+ assertTrue("color equals", ((Color) o).equals(new Color(25, 31, 244)));
+
+ o = Appearance.getBypass(nodeAttrs, id, VisualPropertyType.NODE_SIZE);
+ assertEquals("size equals", 22.0, ((Double) o).doubleValue(), 0.0001);
+
+ o = Appearance.getBypass(nodeAttrs, id,
+ VisualPropertyType.NODE_LABEL_POSITION);
+ System.out.println("lab pos " + o.toString());
+
+ ObjectPosition nlp = new ObjectPositionImpl(Position.NORTH_EAST,
+ Position.WEST, Justification.JUSTIFY_CENTER, 13, -1);
+ System.out.println("new lab pos " + nlp.toString());
+ assertTrue("label position equals", nlp.equals(o));
+
+ o = Appearance.getBypass(nodeAttrs, id,
+ VisualPropertyType.NODE_FONT_FACE);
+ assertTrue("font equals", (new Font("SansSerif", Font.ITALIC, 10))
+ .equals((Font) o));
+
+ o = Appearance.getBypass(nodeAttrs, id,
+ VisualPropertyType.NODE_LINE_STYLE);
+ assertTrue("linestyle equals", LineStyle.LONG_DASH
+ .equals((LineStyle) o));
+
+ o = Appearance.getBypass(edgeAttrs, lisa.getIdentifier(),
+ VisualPropertyType.EDGE_SRCARROW_SHAPE);
+ assertTrue("arrow equals", ArrowShape.DELTA == (ArrowShape) o);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testGetColorBypass() {
+ Color c = (Color) Appearance.getBypass(nodeAttrs, id,
+ VisualPropertyType.NODE_FILL_COLOR);
+ assertTrue("color equals", c.equals(new Color(25, 31, 244)));
+
+ c = (Color) Appearance.getBypass(nodeAttrs, id,
+ VisualPropertyType.NODE_BORDER_COLOR);
+ System.out.print("should be null: ");
+ System.out.println(c);
+ assertNull("border color null ", c);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args
+ * DOCUMENT ME!
+ */
+ public static void main(String[] args) {
+ junit.textui.TestRunner.run(new TestSuite(BypassHelperTest.class));
+ }
+}
diff --git a/application/src/test/java/cytoscape/visual/CalculatorPropertiesTest.java b/application/src/test/java/cytoscape/visual/CalculatorPropertiesTest.java
new file mode 100644
index 0000000..2119091
--- /dev/null
+++ b/application/src/test/java/cytoscape/visual/CalculatorPropertiesTest.java
@@ -0,0 +1,203 @@
+/*
+ File: CalculatorPropertiesTest.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+//----------------------------------------------------------------------------
+// $Revision: 8216 $
+// $Date: 2006-09-15 15:48:20 -0700 (Fri, 15 Sep 2006) $
+// $Author: mes $
+//----------------------------------------------------------------------------
+package cytoscape.visual;
+
+import cytoscape.visual.calculators.*;
+
+import cytoscape.visual.mappings.*;
+
+import junit.framework.*;
+
+import java.io.*;
+
+//----------------------------------------------------------------------------
+import java.util.*;
+
+
+//----------------------------------------------------------------------------
+/**
+ * Test program to check that calculators are loaded properly from the
+ * properties file. Works by writing a text description of the read calculators
+ * to stdout.
+ */
+public class CalculatorPropertiesTest extends TestCase {
+ /**
+ * DOCUMENT ME!
+ */
+ public void testFailure() {
+ // TODOOOO get this working!
+ //fail();
+ }
+
+ /*
+ public static void main(String[] args) {
+ new CalculatorPropertiesTest();
+ }
+
+ public CalculatorPropertiesTest() {
+ CalculatorCatalog catalog = new CalculatorCatalog();
+ Properties props = new Properties();
+ try {
+ String propsFile = "vizmap.props";
+ InputStream is = new FileInputStream(propsFile);
+ props.load(is);
+ is.close();
+ } catch (Exception e) {
+ e.printStackTrace();
+ return;
+ }
+
+ CalculatorIO.loadCalculators(props, catalog);
+
+ Collection nodeColorCalcs = catalog.getNodeColorCalculators();
+ System.out.println("nodeColorCalcs.size() = " + nodeColorCalcs.size());
+ checkCalculator( catalog.getNodeColorCalculator("testDiscrete") );
+ checkCalculator( catalog.getNodeColorCalculator("testContinuous") );
+ System.out.println();
+
+ Collection nodeLineTypeCalcs = catalog.getNodeLineTypeCalculators();
+ System.out.println("nodeLineTypeCalcs.size() = " + nodeLineTypeCalcs.size());
+ checkCalculator( catalog.getNodeLineTypeCalculator("testDiscrete") );
+ checkCalculator( catalog.getNodeLineTypeCalculator("testContinuous") );
+ System.out.println();
+
+ Collection nodeShapeCalcs = catalog.getNodeShapeCalculators();
+ System.out.println("nodeShapeCalcs.size() = " + nodeShapeCalcs.size());
+ checkCalculator( catalog.getNodeShapeCalculator("testDiscrete") );
+ checkCalculator( catalog.getNodeShapeCalculator("testContinuous") );
+ System.out.println();
+
+ Collection nodeSizeCalcs = catalog.getNodeSizeCalculators();
+ System.out.println("nodeSizeCalcs.size() = " + nodeSizeCalcs.size());
+ checkCalculator( catalog.getNodeSizeCalculator("testDiscrete") );
+ checkCalculator( catalog.getNodeSizeCalculator("testContinuous") );
+ System.out.println();
+
+ Collection nodeLabelCalcs = catalog.getNodeLabelCalculators();
+ System.out.println("nodeLabelCalcs.size() = " + nodeLabelCalcs.size());
+ checkCalculator( catalog.getNodeLabelCalculator("testDiscrete") );
+ checkCalculator( catalog.getNodeLabelCalculator("testContinuous") );
+ checkCalculator( catalog.getNodeLabelCalculator("testPassThrough") );
+ System.out.println();
+
+ Collection nodeToolTipCalcs = catalog.getNodeToolTipCalculators();
+ System.out.println("nodeToolTipCalcs.size() = " + nodeToolTipCalcs.size());
+ checkCalculator( catalog.getNodeToolTipCalculator("testDiscrete") );
+ checkCalculator( catalog.getNodeToolTipCalculator("testContinuous") );
+ System.out.println();
+
+ Collection nodeFontFaceCalcs = catalog.getNodeFontFaceCalculators();
+ System.out.println("nodeFontFaceCalcs.size() = " + nodeFontFaceCalcs.size());
+ checkCalculator( catalog.getNodeFontFaceCalculator("testDiscrete") );
+ checkCalculator( catalog.getNodeFontFaceCalculator("testContinuous") );
+ System.out.println();
+
+ Collection nodeFontSizeCalcs = catalog.getNodeFontSizeCalculators();
+ System.out.println("nodeFontSizeCalcs.size() = " + nodeFontSizeCalcs.size());
+ checkCalculator( catalog.getNodeFontSizeCalculator("testDiscrete") );
+ checkCalculator( catalog.getNodeFontSizeCalculator("testContinuous") );
+ System.out.println();
+
+ Collection edgeColorCalcs = catalog.getEdgeColorCalculators();
+ System.out.println("edgeColorCalcs.size() = " + edgeColorCalcs.size());
+ checkCalculator( catalog.getEdgeColorCalculator("testDiscrete") );
+ checkCalculator( catalog.getEdgeColorCalculator("testContinuous") );
+ System.out.println();
+
+ Collection edgeLineTypeCalcs = catalog.getEdgeLineTypeCalculators();
+ System.out.println("edgeLineTypeCalcs.size() = " + edgeLineTypeCalcs.size());
+ checkCalculator( catalog.getEdgeLineTypeCalculator("testDiscrete") );
+ checkCalculator( catalog.getEdgeLineTypeCalculator("testContinuous") );
+ System.out.println();
+
+ Collection edgeArrowCalcs = catalog.getEdgeArrowCalculators();
+ System.out.println("edgeArrowCalcs.size() = " + edgeArrowCalcs.size());
+ checkCalculator( catalog.getEdgeArrowCalculator("testDiscrete") );
+ checkCalculator( catalog.getEdgeArrowCalculator("testContinuous") );
+ System.out.println();
+
+ Collection edgeLabelCalcs = catalog.getEdgeLabelCalculators();
+ System.out.println("edgeLabelCalcs.size() = " + edgeLabelCalcs.size());
+ checkCalculator( catalog.getEdgeLabelCalculator("testDiscrete") );
+ checkCalculator( catalog.getEdgeLabelCalculator("testContinuous") );
+ checkCalculator( catalog.getEdgeLabelCalculator("testPassThrough") );
+ System.out.println();
+
+ Collection edgeToolTipCalcs = catalog.getEdgeToolTipCalculators();
+ System.out.println("edgeToolTipCalcs.size() = " + edgeToolTipCalcs.size());
+ checkCalculator( catalog.getEdgeToolTipCalculator("testDiscrete") );
+ checkCalculator( catalog.getEdgeToolTipCalculator("testContinuous") );
+ System.out.println();
+
+ Collection edgeFontFaceCalcs = catalog.getEdgeFontFaceCalculators();
+ System.out.println("edgeFontFaceCalcs.size() = " + edgeFontFaceCalcs.size());
+ checkCalculator( catalog.getEdgeFontFaceCalculator("testDiscrete") );
+ checkCalculator( catalog.getEdgeFontFaceCalculator("testContinuous") );
+ System.out.println();
+
+ Collection edgeFontSizeCalcs = catalog.getEdgeFontSizeCalculators();
+ System.out.println("edgeFontSizeCalcs.size() = " + edgeFontSizeCalcs.size());
+ checkCalculator( catalog.getEdgeFontSizeCalculator("testDiscrete") );
+ checkCalculator( catalog.getEdgeFontSizeCalculator("testContinuous") );
+ System.out.println();
+
+ Iterator vizStyles = catalog.getVisualStyles().iterator();
+ while(vizStyles.hasNext()) {
+ VisualStyle style = (VisualStyle) vizStyles.next();
+ System.out.println(style.getName());
+ System.out.println();
+ }
+ }
+
+ public void checkCalculator(Calculator c) {
+ if (c == null) {
+ System.out.println("Oops, got a null calculator");
+ return;
+ }
+ AbstractCalculator gc = (AbstractCalculator)c;
+ ObjectMapping m = gc.getMapping(0);
+ System.out.println("controller = " + m.getControllingAttributeName());
+ System.out.println("Map = " + m);
+ }
+ */
+}
diff --git a/application/src/test/java/cytoscape/visual/EdgeAppearanceCalculatorTest.java b/application/src/test/java/cytoscape/visual/EdgeAppearanceCalculatorTest.java
new file mode 100644
index 0000000..321dfde
--- /dev/null
+++ b/application/src/test/java/cytoscape/visual/EdgeAppearanceCalculatorTest.java
@@ -0,0 +1,168 @@
+/*
+ File: EdgeAppearanceCalculatorTest.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+// EdgeAppearanceCalculatorTest.java
+//----------------------------------------------------------------------------
+// $Revision: 7760 $
+// $Date: 2006-06-26 09:28:49 -0700 (Mon, 26 Jun 2006) $
+// $Author: mes $
+//----------------------------------------------------------------------------
+package cytoscape.visual;
+
+import java.awt.Color;
+import java.awt.Font;
+import java.io.FileReader;
+import java.util.Properties;
+
+import junit.framework.TestCase;
+import junit.framework.TestSuite;
+import cytoscape.CyEdge;
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+import cytoscape.data.Semantics;
+import cytoscape.data.readers.CyAttributesReader;
+import cytoscape.util.FileUtil;
+import java.io.InputStream;
+import static cytoscape.visual.VisualPropertyType.*;
+
+/**
+ *
+ */
+public class EdgeAppearanceCalculatorTest extends TestCase {
+ CyNetwork cyNet;
+ CyNode a;
+ CyNode b;
+ CyEdge ab;
+ CalculatorCatalog catalog;
+ Properties props;
+
+ /**
+ * Creates a new EdgeAppearanceCalculatorTest object.
+ *
+ * @param name
+ * DOCUMENT ME!
+ */
+ public EdgeAppearanceCalculatorTest(String name) {
+ super(name);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void setUp() {
+ cyNet = Cytoscape.createNetworkFromFile("src/test/resources/testData/small.sif");
+ a = Cytoscape.getCyNode("a");
+ b = Cytoscape.getCyNode("b");
+ ab = Cytoscape.getCyEdge(a, b, Semantics.INTERACTION, "pp", false);
+ props = new Properties();
+
+ try {
+ CyAttributesReader.loadAttributes(Cytoscape.getEdgeAttributes(),
+ new FileReader("src/test/resources/testData/small.edgeAttr"));
+ props.load(FileUtil.getInputStream("src/test/resources/testData/small.vizmap.props"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ catalog = new CalculatorCatalog();
+ CalculatorIO.loadCalculators(props, catalog, true);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testDefaultAppearance() {
+ EdgeAppearanceCalculator eac = new EdgeAppearanceCalculator(new VisualPropertyDependencyImpl());
+
+ EdgeAppearance ea = eac.calculateEdgeAppearance(ab, cyNet);
+
+ // this tests that the default edge appearance is correct
+ assertTrue("color", ((Color)ea.get(EDGE_COLOR)).equals(Color.BLACK));
+ assertTrue("lineType", ((LineStyle)ea.get(EDGE_LINETYPE)) == LineStyle.SOLID);
+ assertTrue("src arrow", ((ArrowShape)ea.get(EDGE_SRCARROW_SHAPE)) == ArrowShape.NONE);
+ assertTrue("trg arrow", ((ArrowShape)ea.get(EDGE_TGTARROW_SHAPE)) == ArrowShape.NONE);
+ assertTrue("label", ((String)ea.get(EDGE_LABEL)).equals(""));
+ assertTrue("tooltip", ((String)ea.get(EDGE_TOOLTIP)).equals(""));
+ assertTrue("font size", ((Number)ea.get(EDGE_FONT_SIZE)).intValue() == 10);
+ assertTrue("font style", ((Font)ea.get(EDGE_FONT_FACE)).getStyle() == Font.PLAIN);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testApplyProperties() {
+ EdgeAppearanceCalculator eac = new EdgeAppearanceCalculator(new VisualPropertyDependencyImpl());
+ eac.applyProperties("homer", props, "edgeAppearanceCalculator.homer", catalog);
+
+ EdgeAppearance ea = eac.calculateEdgeAppearance(ab, cyNet);
+ System.out.println(eac.getDescription());
+
+ System.out.println("color " + ea.get(EDGE_COLOR));
+ System.out.println("linetype " + ((LineStyle)ea.get(EDGE_LINETYPE)).toString());
+ System.out.println("src arrow " + ea.get(EDGE_SRCARROW_SHAPE));
+ System.out.println("trg arrow " + ea.get(EDGE_TGTARROW_SHAPE));
+ System.out.println("label " + ((String)ea.get(EDGE_LABEL)));
+ System.out.println("tooltip " + ((String)ea.get(EDGE_TOOLTIP)));
+ System.out.println("font size " + ((Number)ea.get(EDGE_FONT_SIZE)).intValue());
+ System.out.println("font style " + ((Font)ea.get(EDGE_FONT_FACE)).getStyle());
+
+ assertTrue("color " + ea.get(EDGE_COLOR), ((Color)ea.get(EDGE_COLOR)).equals(
+ new Color(132, 116, 144)));
+ assertTrue("src arrow " + ea.get(EDGE_SRCARROW_SHAPE),
+ ((ArrowShape)ea.get(EDGE_SRCARROW_SHAPE)) == ArrowShape.DIAMOND);
+ assertTrue("trg arrow " + ea.get(EDGE_TGTARROW_SHAPE),
+ ((ArrowShape)ea.get(EDGE_TGTARROW_SHAPE)) == ArrowShape.NONE);
+ assertTrue("label " + ea.get(EDGE_LABEL), ((String)ea.get(EDGE_LABEL)).equals("0.4"));
+ assertTrue("tooltip " + ea.get(EDGE_TOOLTIP), ((String)ea.get(EDGE_TOOLTIP)).equals(""));
+ // TODO this should be right:
+ //assertTrue("font size " + ((Number)ea.get(EDGE_FONT_SIZE)).intValue(), ((Number)ea.get(EDGE_FONT_SIZE)).intValue() == 5);
+ assertTrue("font style " + ((Font)ea.get(EDGE_FONT_FACE)).getStyle(), ((Font)ea.get(EDGE_FONT_FACE))
+ .getStyle() == Font.PLAIN);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args
+ * DOCUMENT ME!
+ */
+ public static void main(String[] args) {
+ junit.textui.TestRunner.run(new TestSuite(
+ EdgeAppearanceCalculatorTest.class));
+ }
+}
diff --git a/application/src/test/java/cytoscape/visual/LabelPositionTest.java b/application/src/test/java/cytoscape/visual/LabelPositionTest.java
new file mode 100644
index 0000000..38de6ae
--- /dev/null
+++ b/application/src/test/java/cytoscape/visual/LabelPositionTest.java
@@ -0,0 +1,147 @@
+/*
+ File: LabelPositionTest.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.visual;
+
+import cytoscape.CyEdge;
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+
+import cytoscape.data.CyAttributes;
+import cytoscape.data.Semantics;
+
+import cytoscape.data.readers.CyAttributesReader;
+
+import cytoscape.util.FileUtil;
+
+import cytoscape.visual.*;
+
+import cytoscape.visual.calculators.*;
+
+import cytoscape.visual.mappings.*;
+
+import cytoscape.visual.ui.*;
+
+import giny.model.Edge;
+import giny.model.Node;
+import giny.model.RootGraph;
+
+import giny.view.Justification;
+import giny.view.Label;
+import giny.view.ObjectPosition;
+import giny.view.Position;
+
+import junit.framework.*;
+
+import java.awt.Color;
+import java.awt.Font;
+
+import java.io.*;
+
+import java.util.Map;
+import java.util.Properties;
+
+import ding.view.ObjectPositionImpl;
+
+
+/**
+ *
+ */
+public class LabelPositionTest extends TestCase {
+ /**
+ * Creates a new LabelPositionTest object.
+ *
+ * @param name DOCUMENT ME!
+ */
+ public LabelPositionTest(String name) {
+ super(name);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void setUp() {
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testEquals() {
+ System.out.println("begin testEquals");
+
+ ObjectPosition l1 = new ObjectPositionImpl();
+ l1.setTargetAnchor(Position.NORTH_WEST);
+ l1.setAnchor(Position.CENTER);
+ l1.setJustify(Justification.JUSTIFY_LEFT);
+ l1.setOffsetX(17.0);
+ l1.setOffsetY(-19.0);
+
+ ObjectPosition l2 = new ObjectPositionImpl(Position.NORTH_WEST, Position.CENTER, Justification.JUSTIFY_LEFT,
+ 17.0, -19.0);
+ System.out.println("label 1\n" + l1.toString());
+ System.out.println("label 2\n" + l2.toString());
+ assertTrue("positions equal", l1.equals(l2));
+ assertTrue("position doesn't equal a color", !l1.equals(Color.black));
+ assertTrue("position doesn't equal null", !l1.equals(null));
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testParse() {
+ System.out.println("begin testParse");
+
+ LabelPosition l1 = LabelPosition.parse("C,NW,l,17,-19.0");
+ LabelPosition l2 = new LabelPosition(Label.CENTER, Label.NORTHWEST, Label.JUSTIFY_LEFT,
+ 17.0, -19.0);
+ System.out.println("label 1\n" + l1.toString());
+ System.out.println("label 2\n" + l2.toString());
+ assertTrue("positions equal", l1.equals(l2));
+
+ LabelPosition l3 = LabelPosition.parse("junk");
+ assertNull(l3);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ */
+ public static void main(String[] args) {
+ junit.textui.TestRunner.run(new TestSuite(LabelPositionTest.class));
+ }
+}
diff --git a/application/src/test/java/cytoscape/visual/NodeAppearanceCalculatorTest.java b/application/src/test/java/cytoscape/visual/NodeAppearanceCalculatorTest.java
new file mode 100644
index 0000000..8f3740f
--- /dev/null
+++ b/application/src/test/java/cytoscape/visual/NodeAppearanceCalculatorTest.java
@@ -0,0 +1,448 @@
+/*
+ File: NodeAppearanceCalculatorTest.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+// NodeAppearanceCalculatorTest.java
+//----------------------------------------------------------------------------
+// $Revision: 21096 $
+// $Date: 2010-07-30 21:31:07 +0200 (Fri, 30 Jul 2010) $
+// $Author: mes $
+//----------------------------------------------------------------------------
+package cytoscape.visual;
+
+import giny.model.Node;
+import giny.model.RootGraph;
+import giny.view.NodeView;
+
+import java.awt.Color;
+import java.awt.Font;
+import java.io.FileReader;
+import java.util.Properties;
+
+import junit.framework.TestCase;
+import junit.framework.TestSuite;
+import cytoscape.CyEdge;
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+import cytoscape.data.CyAttributes;
+import cytoscape.data.Semantics;
+import cytoscape.data.readers.CyAttributesReader;
+import cytoscape.util.FileUtil;
+import static cytoscape.visual.VisualPropertyType.*;
+
+/**
+ *
+ */
+public class NodeAppearanceCalculatorTest extends TestCase {
+ CyNetwork cyNet;
+ CyNode a;
+ CyNode b;
+ CyNode c;
+ CyEdge ab;
+ CalculatorCatalog catalog;
+ Properties props;
+
+ /**
+ * Creates a new NodeAppearanceCalculatorTest object.
+ *
+ * @param name
+ * DOCUMENT ME!
+ */
+ public NodeAppearanceCalculatorTest(String name) {
+ super(name);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void setUp() {
+ System.out.println("setup begin");
+ cyNet = Cytoscape.createNetworkFromFile("src/test/resources/testData/small.sif");
+ a = Cytoscape.getCyNode("a");
+ b = Cytoscape.getCyNode("b");
+ c = Cytoscape.getCyNode("c");
+ ab = Cytoscape.getCyEdge(a, b, Semantics.INTERACTION, "pp", false);
+ props = new Properties();
+
+ try {
+ CyAttributesReader.loadAttributes(Cytoscape.getNodeAttributes(),
+ new FileReader("src/test/resources/testData/small.nodeAttr"));
+ props.load(FileUtil.getInputStream("src/test/resources/testData/small.vizmap.props"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ catalog = new CalculatorCatalog();
+ CalculatorIO.loadCalculators(props, catalog, true);
+ System.out.println("setup end");
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testDefaultAppearance() {
+ System.out.println("begin NodeAppearanceCalculatorTest.testDefaultAppearance()");
+
+ NodeAppearanceCalculator nac = new NodeAppearanceCalculator(new VisualPropertyDependencyImpl());
+
+ NodeAppearance na = nac.calculateNodeAppearance(a, cyNet);
+
+ // this tests that the default node appearance is correct
+ assertTrue("a color " + na.get(NODE_FILL_COLOR) + " expect "
+ + Color.WHITE.toString(), ((Color)na.get(NODE_FILL_COLOR)).equals(Color.WHITE));
+ assertTrue("a border color " + na.get(NODE_BORDER_COLOR) + " expect "
+ + Color.BLACK.toString(), ((Color)na.get(NODE_BORDER_COLOR)).equals(
+ Color.BLACK));
+ assertEquals("a lineType ", LineStyle.SOLID, ((LineStyle)na.get(NODE_LINETYPE)));
+ assertEquals("a shape ", NodeShape.RECT, ((NodeShape)na.get(NODE_SHAPE)));
+
+ // node size is locked so all should be the same
+ assertEquals("a width ", 35.0, getWidth(na,nac));
+ assertEquals("a height ", 35.0, getHeight(na,nac));
+ assertEquals("a size ", 35.0, ((Double)na.get(NODE_SIZE)).doubleValue());
+
+ assertEquals("a label ", "", ((String)na.get(NODE_LABEL)));
+ assertEquals("a tooltip ", "", ((String)na.get(NODE_TOOLTIP)));
+ assertEquals("a font size ", 12, ((Number)na.get(NODE_FONT_SIZE)).intValue());
+ assertEquals("a font style ", Font.PLAIN, ((Font)na.get(NODE_FONT_FACE)).getStyle());
+ assertTrue("a label color " + na.get(NODE_LABEL_COLOR) + " expect "
+ + Color.BLACK, ((Color)na.get(NODE_LABEL_COLOR)).equals(Color.BLACK));
+
+ // should still be default for node b
+ NodeAppearance nb = nac.calculateNodeAppearance(b, cyNet);
+
+ assertTrue("b color " + nb.get(NODE_FILL_COLOR) + " expect "
+ + Color.WHITE.toString(), ((Color)nb.get(NODE_FILL_COLOR)).equals(Color.WHITE));
+ assertTrue("b border color " + nb.get(NODE_BORDER_COLOR) + " expect "
+ + Color.BLACK.toString(), ((Color)nb.get(NODE_BORDER_COLOR)).equals(
+ Color.BLACK));
+ assertEquals("b lineType ", LineStyle.SOLID, ((LineStyle)nb.get(NODE_LINETYPE)));
+ assertEquals("b shape ", NodeShape.RECT, ((NodeShape)nb.get(NODE_SHAPE)));
+ // still locked
+ assertEquals("b width ", 35.0, getWidth(nb,nac));
+ assertEquals("b height ", 35.0, getHeight(nb,nac));
+ assertEquals("b size ", 35.0, ((Double)nb.get(NODE_SIZE)).doubleValue());
+
+ assertEquals("b label ", "", ((String)nb.get(NODE_LABEL)));
+ assertEquals("b tooltip ", "", ((String)nb.get(NODE_TOOLTIP)));
+ assertEquals("b font size ", 12, ((Number)nb.get(NODE_FONT_SIZE)).intValue());
+ assertEquals("b font style ", Font.PLAIN, ((Font)nb.get(NODE_FONT_FACE)).getStyle());
+ assertTrue("b label color " + nb.get(NODE_LABEL_COLOR) + " expect "
+ + Color.BLACK, ((Color)nb.get(NODE_LABEL_COLOR)).equals(Color.BLACK));
+
+ nac.setNodeSizeLocked(false);
+
+ NodeAppearance nc = nac.calculateNodeAppearance(c, cyNet);
+
+ assertTrue("c color " + nc.get(NODE_FILL_COLOR) + " expect "
+ + Color.WHITE.toString(), ((Color)nc.get(NODE_FILL_COLOR)).equals(Color.WHITE));
+ assertTrue("c border color " + nc.get(NODE_BORDER_COLOR) + " expect "
+ + Color.BLACK.toString(), ((Color)nc.get(NODE_BORDER_COLOR)).equals(
+ Color.BLACK));
+ assertEquals("c lineType ", LineStyle.SOLID, ((LineStyle)nc.get(NODE_LINETYPE)));
+ assertEquals("c shape ", NodeShape.RECT, ((NodeShape)nc.get(NODE_SHAPE)));
+ // now we see the default width and height
+ assertEquals("c width ", 70.0, getWidth(nc,nac));
+ assertEquals("c height ", 30.0, getHeight(nc,nac));
+ assertEquals("c size ", 35.0, ((Double)nc.get(NODE_SIZE)).doubleValue());
+ assertEquals("c label ", "", ((String)nc.get(NODE_LABEL)));
+ assertEquals("c tooltip ", "", ((String)nc.get(NODE_TOOLTIP)));
+ assertEquals("c font size ", 12, ((Number)nc.get(NODE_FONT_SIZE)).intValue());
+ assertEquals("c font style ", Font.PLAIN, ((Font)nc.get(NODE_FONT_FACE)).getStyle());
+ assertTrue("c label color " + nc.get(NODE_LABEL_COLOR) + " expect "
+ + Color.BLACK, ((Color)nc.get(NODE_LABEL_COLOR)).equals(Color.BLACK));
+
+ NodeAppearance def = nac.getDefaultAppearance();
+ def.set(NODE_FILL_COLOR,Color.GREEN);
+ def.set(NODE_BORDER_COLOR,Color.BLUE);
+ def.set(NODE_WIDTH,47.0);
+ def.set(NODE_HEIGHT,23.0);
+
+ na = nac.calculateNodeAppearance(a, cyNet);
+ assertTrue("color " + na.get(NODE_FILL_COLOR) + " expect "
+ + Color.GREEN.toString(), ((Color)na.get(NODE_FILL_COLOR)).equals(Color.GREEN));
+ assertTrue("border color " + na.get(NODE_BORDER_COLOR) + " expect "
+ + Color.BLUE.toString(), ((Color)na.get(NODE_BORDER_COLOR)).equals(Color.BLUE));
+ assertEquals("width ", 47.0, getWidth(na,nac));
+ assertEquals("height ", 23.0, getHeight(na,nac));
+
+ nb = nac.calculateNodeAppearance(b, cyNet);
+ assertTrue("color " + nb.get(NODE_FILL_COLOR) + " expect "
+ + Color.GREEN.toString(), ((Color)nb.get(NODE_FILL_COLOR)).equals(Color.GREEN));
+ assertTrue("border color " + nb.get(NODE_BORDER_COLOR) + " expect "
+ + Color.BLUE.toString(), ((Color)nb.get(NODE_BORDER_COLOR)).equals(Color.BLUE));
+ assertEquals("width ", 47.0, getWidth(nb,nac));
+ assertEquals("height ", 23.0, getHeight(nb,nac));
+
+ System.out
+ .println("end NodeAppearanceCalculatorTest.testDefaultAppearance()");
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testApplyProperties() {
+ System.out
+ .println("begin NodeAppearanceCalculatorTest.testApplyProperties()");
+
+ NodeAppearanceCalculator nac = new NodeAppearanceCalculator(new VisualPropertyDependencyImpl());
+ nac.applyProperties("homer", props, "nodeAppearanceCalculator.homer",
+ catalog);
+ System.out.println(nac.getDescription());
+
+ // node a
+ nac.setNodeSizeLocked(false);
+
+ NodeAppearance na = nac.calculateNodeAppearance(a, cyNet);
+ System.out.println("NodeAppearance a\n" + na.getDescription());
+
+ Color ca = new Color(246, 242, 103);
+ assertTrue( "a color " + na.get(NODE_FILL_COLOR) + " expect " + ca.toString(),
+ ((Color)na.get(NODE_FILL_COLOR)).equals(ca));
+ assertTrue("a border color " + na.get(NODE_BORDER_COLOR) + " expect "
+ + Color.BLACK.toString(), ((Color)na.get(NODE_BORDER_COLOR)).equals(
+ Color.BLACK));
+ assertEquals("a lineType ", LineStyle.SOLID, ((LineStyle)na.get(NODE_LINETYPE)));
+ assertEquals("a shape ", NodeShape.RECT, ((NodeShape)na.get(NODE_SHAPE)));
+ assertEquals("a width ", 70.0, getWidth(na,nac));
+ assertEquals("a height ", 10.0, getHeight(na,nac)); // only height has a
+ // calc set
+ assertEquals("a size ", 35.0, ((Double)na.get(NODE_SIZE)).doubleValue()); // props don't set size
+ assertEquals("a label ", "a", ((String)na.get(NODE_LABEL)));
+ assertEquals("a tooltip ", "", ((String)na.get(NODE_TOOLTIP)));
+ assertEquals("a font size ", 12, ((Number)na.get(NODE_FONT_SIZE)).intValue());
+ assertEquals("a font style ", Font.PLAIN, ((Font)na.get(NODE_FONT_FACE)).getStyle());
+ assertTrue("a label color " + na.get(NODE_LABEL_COLOR) + " expect "
+ + Color.BLACK, ((Color)na.get(NODE_LABEL_COLOR)).equals(Color.BLACK));
+
+ // node b
+ NodeAppearance nb = nac.calculateNodeAppearance(b, cyNet);
+ System.out.println("NodeAppearance b\n" + nb.getDescription());
+
+ Color cb = new Color(87, 25, 230);
+ assertTrue(
+ "b color " + nb.get(NODE_FILL_COLOR) + " expect " + cb.toString(),
+ ((Color)nb.get(NODE_FILL_COLOR)).equals(cb));
+ assertTrue("b border color " + nb.get(NODE_BORDER_COLOR) + " expect "
+ + Color.BLACK, ((Color)nb.get(NODE_BORDER_COLOR)).equals(Color.BLACK));
+ assertEquals("b line width ", 1.0f, nb.get(VisualPropertyType.NODE_LINE_WIDTH));
+
+ assertEquals("b line style ", LineStyle.SOLID, nb.get(VisualPropertyType.NODE_LINE_STYLE));
+
+ assertEquals("b shape ", NodeShape.RECT, ((NodeShape)nb.get(NODE_SHAPE)));
+ assertEquals("b width ", 70.0, getWidth(nb,nac));
+ assertEquals("b height ", 30.0, getHeight(nb,nac));
+ assertEquals("b size ", 35.0, ((Double)nb.get(NODE_SIZE)).doubleValue()); // props don't set size
+ assertEquals("b label ", "b", ((String)nb.get(NODE_LABEL)));
+ assertEquals("b tooltip ", "", ((String)nb.get(NODE_TOOLTIP)));
+ assertEquals("b font size ", 12, ((Number)nb.get(NODE_FONT_SIZE)).intValue());
+ assertEquals("b font style ", Font.PLAIN, ((Font)nb.get(NODE_FONT_FACE)).getStyle());
+ assertTrue("b label color " + nb.get(NODE_LABEL_COLOR) + " expect "
+ + Color.BLACK.toString(), ((Color)nb.get(NODE_LABEL_COLOR))
+ .equals(Color.BLACK));
+
+ nac.setNodeSizeLocked(true);
+
+ NodeAppearance nc = nac.calculateNodeAppearance(c, cyNet);
+ System.out.println("NodeAppearance c\n" + nc.getDescription());
+
+ Color cc = new Color(209, 205, 254);
+ assertTrue(
+ "c color " + nc.get(NODE_FILL_COLOR) + " expect " + cc.toString(),
+ ((Color)nc.get(NODE_FILL_COLOR)).equals(cc));
+ assertTrue("c border color " + nc.get(NODE_BORDER_COLOR) + " expect "
+ + Color.BLACK, ((Color)nc.get(NODE_BORDER_COLOR)).equals(Color.BLACK));
+ assertEquals("c line Type ", LineStyle.SOLID, nb.get(VisualPropertyType.NODE_LINE_STYLE));
+
+ assertEquals("c line width ", 1.0f, ((Number)nc.get(NODE_LINE_WIDTH)).floatValue());
+
+ assertEquals("c shape ", NodeShape.RECT, ((NodeShape)nc.get(NODE_SHAPE)));
+ assertEquals("c width ", 35.0, getWidth(nc,nac)); // since node size is
+ // locked
+ assertEquals("c height ", 35.0, getHeight(nc,nac)); // since node size
+ // is locked
+ assertEquals("c size ", 35.0, ((Double)nc.get(NODE_SIZE)).doubleValue());
+ assertEquals("c label ", "c", ((String)nc.get(NODE_LABEL)));
+ assertEquals("c tooltip ", "", ((String)nc.get(NODE_TOOLTIP)));
+ assertEquals("c font size ", 12, ((Number)nc.get(NODE_FONT_SIZE)).intValue());
+ assertEquals("c font style ", Font.PLAIN, ((Font)nc.get(NODE_FONT_FACE)).getStyle());
+ assertTrue("c label color " + nc.get(NODE_LABEL_COLOR) + " expect "
+ + Color.BLACK.toString(), ((Color)nc.get(NODE_LABEL_COLOR))
+ .equals(Color.BLACK));
+
+ System.out
+ .println("end NodeAppearanceCalculatorTest.testApplyProperties()");
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testNodeSizeLock() {
+ System.out
+ .println("begin NodeAppearanceCalculatorTest.testNodeSizeLock()");
+
+ NodeAppearanceCalculator nac = new NodeAppearanceCalculator(new VisualPropertyDependencyImpl());
+ System.out.println(nac.getDescription());
+
+ NodeView view = new TestNodeView();
+ NodeAppearance na = null;
+
+ // using default props
+ nac.setNodeSizeLocked(false);
+ na = nac.calculateNodeAppearance(a, cyNet);
+ na.applyAppearance(view,nac.deps);
+
+ assertEquals("height", 30.0, view.getHeight());
+ assertEquals("width", 70.0, view.getWidth());
+
+ nac.setNodeSizeLocked(true);
+ na = nac.calculateNodeAppearance(a, cyNet);
+ na.applyAppearance(view,nac.deps);
+
+ assertEquals("height", 35.0, view.getHeight());
+ assertEquals("width", 35.0, view.getWidth());
+
+ nac.applyProperties("homer", props, "nodeAppearanceCalculator.homer",
+ catalog);
+
+ // still locked
+ na = nac.calculateNodeAppearance(a, cyNet);
+ na.applyAppearance(view,nac.deps);
+ assertEquals("height", 35.0, view.getHeight());
+ assertEquals("width", 35.0, view.getWidth());
+
+ nac.setNodeSizeLocked(false);
+ na = nac.calculateNodeAppearance(a, cyNet);
+ na.applyAppearance(view,nac.deps);
+ assertEquals("height", 10.0, view.getHeight());
+ assertEquals("width", 70.0, view.getWidth());
+
+ System.out
+ .println("end NodeAppearanceCalculatorTest.testNodeSizeLock()");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception
+ * DOCUMENT ME!
+ */
+ public void testBypass() throws Exception {
+ Color fillColor = new Color(63, 128, 255);
+ Color borderColor = new Color(100, 100, 50);
+// String fillColorString = "63,128,255";
+// String borderColorString = "100,100,50";
+// LineStyle lineType = LineStyle.DASHED_3;
+// String lineTypeString = "DASHED_3";
+ NodeShape shape = NodeShape.DIAMOND;
+ double width = 49.0;
+ double height = 79.0;
+ String label = "testLabel";
+ String toolTip = "testToolTip";
+ Font font = new Font("SansSerif", Font.ITALIC, 10);
+ String fontString = "SansSerif,italic,10";
+
+ RootGraph graph = Cytoscape.getRootGraph();
+ int index1 = graph.createNode();
+ Node first = graph.getNode(index1);
+ int index2 = graph.createNode();
+ Node second = graph.getNode(index2);
+
+ CyNetwork network2 = Cytoscape.createNetwork(Cytoscape.getRootGraph()
+ .getNodeIndicesArray(), Cytoscape.getRootGraph()
+ .getEdgeIndicesArray(), null);
+
+ CyAttributes secondNodeAttr = Cytoscape.getNodeAttributes();
+ String secondName = second.getIdentifier();
+ secondNodeAttr.setAttribute(secondName, "node.fillColor", "63,128,255");
+ secondNodeAttr.setAttribute(secondName, "node.borderColor",
+ "100,100,50");
+ secondNodeAttr.setAttribute(secondName, "node.lineType", "dashed3");
+ secondNodeAttr.setAttribute(secondName, "node.shape", "diamond");
+ secondNodeAttr.setAttribute(secondName, "node.width", "49.0");
+ secondNodeAttr.setAttribute(secondName, "node.height", "79.0");
+ secondNodeAttr.setAttribute(secondName, "node.size", "32.0");
+ secondNodeAttr.setAttribute(secondName, "node.label", "testLabel");
+ secondNodeAttr.setAttribute(secondName, "node.toolTip", "testToolTip");
+ secondNodeAttr.setAttribute(secondName, "node.font",
+ "SansSerif,italic,10");
+
+ NodeAppearanceCalculator nac = new NodeAppearanceCalculator(new VisualPropertyDependencyImpl());
+ nac.setNodeSizeLocked(false);
+
+ NodeAppearance secondApp = nac
+ .calculateNodeAppearance(second, network2);
+ System.out.println("secondApp\n" + secondApp.getDescription());
+ assertTrue(((Color)secondApp.get(NODE_FILL_COLOR)).equals(fillColor));
+ assertTrue(((Color)secondApp.get(NODE_BORDER_COLOR)).equals(borderColor));
+
+ assertTrue(((NodeShape)secondApp.get(NODE_SHAPE)) == shape);
+ assertEquals("width ", getWidth(secondApp,nac), width, 0.0001);
+ assertEquals("height ", getHeight(secondApp,nac), height, 0.0001);
+ assertTrue(((String)secondApp.get(NODE_LABEL)).equals(label));
+ assertTrue(((String)secondApp.get(NODE_TOOLTIP)).equals(toolTip));
+ assertTrue(((Font)secondApp.get(NODE_FONT_FACE)).equals(font));
+
+ nac.setNodeSizeLocked(true);
+ nac.calculateNodeAppearance(secondApp, second, network2);
+ assertEquals("width", getWidth(secondApp,nac), 32.0, 0.0001);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args
+ * DOCUMENT ME!
+ */
+ public static void main(String[] args) {
+ junit.textui.TestRunner.run(new TestSuite(
+ NodeAppearanceCalculatorTest.class));
+ }
+
+ private double getWidth(NodeAppearance na, NodeAppearanceCalculator nac) {
+ if (nac.getNodeSizeLocked())
+ return ((Double)(na.get(NODE_SIZE))).doubleValue();
+ else
+ return ((Double)(na.get(NODE_WIDTH))).doubleValue();
+ }
+ private double getHeight(NodeAppearance na, NodeAppearanceCalculator nac) {
+ if (nac.getNodeSizeLocked())
+ return ((Double)(na.get(NODE_SIZE))).doubleValue();
+ else
+ return ((Double)(na.get(NODE_HEIGHT))).doubleValue();
+ }
+}
diff --git a/application/src/test/java/cytoscape/visual/NodeAppearanceTest.java b/application/src/test/java/cytoscape/visual/NodeAppearanceTest.java
new file mode 100644
index 0000000..72a6ce6
--- /dev/null
+++ b/application/src/test/java/cytoscape/visual/NodeAppearanceTest.java
@@ -0,0 +1,141 @@
+/*
+ File: NodeAppearanceTest.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// NodeAppearanceTest.java
+
+//----------------------------------------------------------------------------
+// $Revision: 8412 $
+// $Date: 2006-10-06 13:46:32 -0700 (Fri, 06 Oct 2006) $
+// $Author: mes $
+//----------------------------------------------------------------------------
+package cytoscape.visual;
+
+import cytoscape.CyEdge;
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+
+import cytoscape.data.CyAttributes;
+import cytoscape.data.Semantics;
+
+import cytoscape.data.readers.CyAttributesReader;
+
+import cytoscape.util.FileUtil;
+
+import cytoscape.visual.*;
+
+import cytoscape.visual.calculators.*;
+import static cytoscape.visual.VisualPropertyType.*;
+
+import cytoscape.visual.mappings.*;
+
+import cytoscape.visual.ui.*;
+
+import giny.model.Edge;
+import giny.model.Node;
+import giny.model.RootGraph;
+
+import giny.view.NodeView;
+
+//----------------------------------------------------------------------------
+import junit.framework.*;
+
+import java.awt.Color;
+import java.awt.Font;
+
+import java.io.*;
+
+import java.util.Map;
+import java.util.Properties;
+
+
+// Note that much of NodeAppearance is tested in NodeAppearanceCalculatorTest.
+/**
+ *
+ */
+public class NodeAppearanceTest extends TestCase {
+ double SLACK = 0.00001;
+
+ /**
+ * Creates a new NodeAppearanceTest object.
+ *
+ * @param name DOCUMENT ME!
+ */
+ public NodeAppearanceTest(String name) {
+ super(name);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testNodeSizeLocked() {
+ NodeAppearance na = new NodeAppearance(new VisualPropertyDependencyImpl());
+
+ // by default size is locked
+ assertEquals("node uniform size", 35.0, ((Double)na.get(NODE_SIZE)).doubleValue(), SLACK);
+ //assertEquals("node width", 35.0, ((Double)na.get(NODE_WIDTH)).doubleValue(), SLACK);
+ //assertEquals("node height", 35.0, ((Double)na.get(NODE_HEIGHT)).doubleValue(), SLACK);
+
+ na.setNodeSizeLocked(false);
+
+ assertEquals("node uniform size", 35.0, ((Double)na.get(NODE_SIZE)).doubleValue(), SLACK);
+ assertEquals("node width", 70.0, ((Double)na.get(NODE_WIDTH)).doubleValue(), SLACK);
+ assertEquals("node height", 30.0, ((Double)na.get(NODE_HEIGHT)).doubleValue(), SLACK);
+
+ na.set(NODE_WIDTH,40.0);
+
+ assertEquals("node uniform size", 35.0, ((Double)na.get(NODE_SIZE)).doubleValue(), SLACK);
+ assertEquals("node width", 40.0, ((Double)na.get(NODE_WIDTH)).doubleValue(), SLACK);
+
+ na.set(NODE_HEIGHT,50.0);
+
+ assertEquals("node uniform size", 35.0, ((Double)na.get(NODE_SIZE)).doubleValue(), SLACK);
+ assertEquals("node heigth", 50.0, ((Double)na.get(NODE_HEIGHT)).doubleValue(), SLACK);
+
+ na.setNodeSizeLocked(true);
+
+ na.set(NODE_WIDTH,20.0);
+
+ assertEquals("node uniform size", 35.0, ((Double)na.get(NODE_SIZE)).doubleValue(), SLACK);
+ assertEquals("node width", 20.0, ((Double)na.get(NODE_WIDTH)).doubleValue(), SLACK);
+
+ na.set(NODE_HEIGHT,80.0);
+
+ assertEquals("node uniform size", 35.0, ((Double)na.get(NODE_SIZE)).doubleValue(), SLACK);
+ assertEquals("node heigth", 80.0, ((Double)na.get(NODE_HEIGHT)).doubleValue(), SLACK);
+ }
+}
diff --git a/application/src/test/java/cytoscape/visual/NodeShapeTest.java b/application/src/test/java/cytoscape/visual/NodeShapeTest.java
new file mode 100644
index 0000000..e9418ee
--- /dev/null
+++ b/application/src/test/java/cytoscape/visual/NodeShapeTest.java
@@ -0,0 +1,46 @@
+package cytoscape.visual;
+
+import junit.framework.TestCase;
+
+public class NodeShapeTest extends TestCase {
+
+ protected void setUp() throws Exception {
+ super.setUp();
+ }
+
+ protected void tearDown() throws Exception {
+ super.tearDown();
+ }
+
+ public void testParseNodeShapeText() {
+ assertEquals(NodeShape.parseNodeShapeText("rect"), NodeShape.RECT);
+ assertEquals(NodeShape.parseNodeShapeText("rect3d"), NodeShape.RECT_3D);
+ assertEquals(NodeShape.parseNodeShapeText("trapezoid2"), NodeShape.TRAPEZOID_2);
+ assertEquals(NodeShape.parseNodeShapeText("diamond"), NodeShape.DIAMOND);
+ }
+
+ public void testValuesAsString() {
+
+ }
+
+ public void testGetShapeName() {
+
+ }
+
+ public void testIsValidShape() {
+
+ }
+
+ public void testGetNodeShapeText() {
+
+ }
+
+ public void testGetNodeShape() {
+
+ }
+
+ public void testGetGinyShape() {
+
+ }
+
+}
diff --git a/application/src/test/java/cytoscape/visual/TestEdgeView.java b/application/src/test/java/cytoscape/visual/TestEdgeView.java
new file mode 100644
index 0000000..94b0902
--- /dev/null
+++ b/application/src/test/java/cytoscape/visual/TestEdgeView.java
@@ -0,0 +1,246 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.visual;
+
+import giny.model.Edge;
+
+import giny.view.*;
+
+import java.awt.BasicStroke;
+import java.awt.Color;
+import java.awt.Paint;
+import java.awt.Stroke;
+import java.awt.geom.Point2D;
+import java.util.*;
+
+
+/**
+ * This is a dummy implementation of EdgeView that
+ * can be used for unit testing.
+ */
+public class TestEdgeView implements EdgeView {
+
+ int rootGraphIndex;
+
+ public TestEdgeView() {
+ this(1);
+ }
+
+ public TestEdgeView(int index) {
+ rootGraphIndex = 1;
+ }
+
+ public GraphView getGraphView() {
+ return null;
+ }
+
+ public Edge getEdge() {
+ return null;
+ }
+
+ public int getGraphPerspectiveIndex() {
+ return rootGraphIndex;
+ }
+
+ public int getRootGraphIndex() {
+ return rootGraphIndex;
+ }
+
+ boolean selected;
+ public void select() {
+ selected = true;
+ }
+
+ public void unselect() {
+ selected = false;
+ }
+
+ public boolean isSelected() {
+ return selected;
+ }
+
+ public boolean getSelected() {
+ return selected;
+ }
+
+ public boolean setSelected(boolean s) {
+ selected = s;
+
+ return selected;
+ }
+
+ public boolean isHidden() {
+ return false;
+ }
+
+ String toolTip;
+ public void setToolTip(String tip) {
+ toolTip = tip;
+ }
+
+ public String getToolTip() {
+ return toolTip;
+ }
+
+ double label_offset_x;
+ double label_offset_y;
+ int edge_label_anchor;
+ public void setLabelOffsetX(double x) {
+ label_offset_x = x;
+ }
+
+ public double getLabelOffsetX() {
+ return label_offset_x;
+ }
+
+ public void setLabelOffsetY(double y) {
+ label_offset_y = y;
+ }
+
+ public double getLabelOffsetY() {
+ return label_offset_y;
+ }
+
+ public void setEdgeLabelAnchor(int position) {
+ edge_label_anchor = position;
+ }
+
+ public int getEdgeLabelAnchor() {
+ return edge_label_anchor;
+ }
+
+ double label_width;
+ public double getLabelWidth() {
+ return label_width;
+ }
+
+ public void setLabelWidth(double w) {
+ label_width = w;
+ }
+
+ float strokeWidth;
+ public void setStrokeWidth ( float width ) {
+ strokeWidth = width;
+ }
+ public float getStrokeWidth () {
+ return strokeWidth;
+ }
+ Stroke stroke;
+ public void setStroke ( Stroke stroke ) {
+ this.stroke = stroke;
+ }
+ public Stroke getStroke () {
+ return stroke;
+ }
+ int line_type;
+ public void setLineType ( int line_type ) {
+ this.line_type = line_type;
+ }
+ public int getLineType () {
+ return line_type;
+ }
+ Paint unselectedPaint;
+ public Paint getUnselectedPaint () {
+ return unselectedPaint;
+ }
+ Paint selectedPaint;
+ public Paint getSelectedPaint () {
+ return selectedPaint;
+ }
+ Paint srcEdgeEndPaint;
+ public Paint getSourceEdgeEndPaint () {
+ return srcEdgeEndPaint;
+ }
+ Paint srcEdgeEndSelectedPaint;
+ public Paint getSourceEdgeEndSelectedPaint () {
+ return srcEdgeEndSelectedPaint;
+ }
+ Paint trgEdgeEndPaint;
+ public Paint getTargetEdgeEndPaint () {
+ return trgEdgeEndPaint;
+ }
+ Paint trgEdgeEndSelectedPaint;
+ public Paint getTargetEdgeEndSelectedPaint () {
+ return trgEdgeEndSelectedPaint;
+ }
+ public void setSelectedPaint ( Paint paint ) {
+ selectedPaint = paint;
+ }
+ public void setUnselectedPaint ( Paint paint ) {
+ unselectedPaint = paint;
+ }
+ public void setSourceEdgeEndSelectedPaint ( Paint paint ) {
+ srcEdgeEndSelectedPaint = paint;
+ }
+ public void setTargetEdgeEndSelectedPaint ( Paint paint ) {
+ trgEdgeEndSelectedPaint = paint;
+ }
+ public void setSourceEdgeEndStrokePaint ( Paint paint ) {
+ srcEdgeEndPaint = paint;
+ }
+ public void setTargetEdgeEndStrokePaint ( Paint paint ) {
+ trgEdgeEndPaint = paint;
+ }
+ public void setSourceEdgeEndPaint ( Paint paint ) {
+ srcEdgeEndPaint= paint;
+ }
+ public void setTargetEdgeEndPaint ( Paint paint ) {
+ trgEdgeEndPaint = paint;
+ }
+
+ public void updateEdgeView () {}
+ public void updateTargetArrow () {}
+ public void updateSourceArrow () {}
+ int srcEdgeEnd;
+ public void setSourceEdgeEnd(int type) {
+ srcEdgeEnd = type;
+ }
+ int trgEdgeEnd;
+ public void setTargetEdgeEnd(int type) {
+ trgEdgeEnd = type;
+ }
+ public int getSourceEdgeEnd() {
+ return srcEdgeEnd;
+ }
+ public int getTargetEdgeEnd() {
+ return trgEdgeEnd;
+ }
+ public void updateLine() {}
+ public void drawSelected() {}
+ public void drawUnselected() {}
+ public Bend getBend () { return null; }
+ public void clearBends () {}
+ public Label getLabel() { return null; }
+}
diff --git a/application/src/test/java/cytoscape/visual/TestLabel.java b/application/src/test/java/cytoscape/visual/TestLabel.java
new file mode 100644
index 0000000..c3a231e
--- /dev/null
+++ b/application/src/test/java/cytoscape/visual/TestLabel.java
@@ -0,0 +1,191 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.visual;
+
+import giny.view.Label;
+import giny.view.ObjectPosition;
+
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.Paint;
+
+
+/**
+ *
+ */
+public class TestLabel implements Label {
+ int position = 0;
+ Paint textPaint = Color.RED;
+ double greekThreshold = 0.0;
+ String text = "";
+ Font font = new Font("plain", Font.PLAIN, 10);
+ int textAnchor = 0;
+ int justify = 0;
+
+ /**
+ * Creates a new TestLabel object.
+ */
+ public TestLabel() {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param p DOCUMENT ME!
+ */
+ public void setPositionHint(int p) {
+ position = p;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Paint getTextPaint() {
+ return textPaint;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param tp DOCUMENT ME!
+ */
+ public void setTextPaint(Paint tp) {
+ textPaint = tp;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public double getGreekThreshold() {
+ return greekThreshold;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param t DOCUMENT ME!
+ */
+ public void setGreekThreshold(double t) {
+ greekThreshold = t;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getText() {
+ return text;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param t DOCUMENT ME!
+ */
+ public void setText(String t) {
+ text = t;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Font getFont() {
+ return font;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param f DOCUMENT ME!
+ */
+ public void setFont(Font f) {
+ font = f;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param p DOCUMENT ME!
+ */
+ public void setTextAnchor(int p) {
+ textAnchor = p;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param j DOCUMENT ME!
+ */
+ public void setJustify(int j) {
+ justify = j;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getTextAnchor() {
+ return textAnchor;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getJustify() {
+ return justify;
+ }
+
+
+ public ObjectPosition getPosition() {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+
+ public void setPosition(ObjectPosition arg0) {
+ // TODO Auto-generated method stub
+
+ }
+}
diff --git a/application/src/test/java/cytoscape/visual/TestNetworkView.java b/application/src/test/java/cytoscape/visual/TestNetworkView.java
new file mode 100644
index 0000000..18b4363
--- /dev/null
+++ b/application/src/test/java/cytoscape/visual/TestNetworkView.java
@@ -0,0 +1,255 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.visual;
+
+import cytoscape.view.CyNetworkView;
+import cytoscape.Cytoscape;
+import cytoscape.CyNode;
+import cytoscape.CyEdge;
+import cytoscape.CyNetwork;
+import cytoscape.layout.CyLayoutAlgorithm;
+import cytoscape.view.CyEdgeView;
+import cytoscape.view.CyNodeView;
+
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.Paint;
+
+import java.awt.Component;
+import java.util.*;
+import javax.swing.JPanel;
+
+import giny.model.*;
+import giny.view.*;
+import ding.view.*;
+
+
+
+/**
+ * A dummy TestNetworkView that can be used to unit test things.
+ */
+public class TestNetworkView implements CyNetworkView {
+ CyNetwork net;
+ public TestNetworkView(CyNetwork net) {
+ this.net = net;
+ }
+ public CyNetwork getNetwork() {
+ return net;
+ }
+ String title;
+ public void setTitle(String title) {
+ this.title = title;
+ }
+ public String getTitle() {
+ return title;
+ }
+ public void redrawGraph(boolean layout, boolean vizmap) {}
+ public CyNetworkView getView() { return this; }
+ public VisualMappingManager getVizMapManager() {
+ return Cytoscape.getVisualMappingManager();
+ }
+ boolean vizmapEnabled = false;
+ public void toggleVisualMapperEnabled() {
+ vizmapEnabled = (vizmapEnabled ? false : true);
+ }
+ public void setVisualMapperEnabled(boolean state) {
+ vizmapEnabled = state;
+ }
+ public boolean getVisualMapperEnabled() {
+ return vizmapEnabled;
+ }
+ public void putClientData(String data_name, Object data) {}
+ public Collection getClientDataNames() { return null; }
+ public Object getClientData(String data_name) { return null; }
+ CyNode[] selectedNodes;
+ public boolean setSelected(CyNode[] nodes) {
+ selectedNodes = nodes;
+ return true;
+ }
+ NodeView[] selectedNodeViews;
+ public boolean setSelected(NodeView[] node_views) {
+ selectedNodeViews = node_views;
+ return true;
+ }
+ public boolean applyVizMap(CyEdge edge) {return true;}
+ public boolean applyVizMap(EdgeView edge_view) {return true;}
+ public boolean applyVizMap(CyNode node) {return true;}
+ public boolean applyVizMap(NodeView node_view) {return true;}
+ public boolean applyVizMap(CyEdge edge, VisualStyle style) {return true;}
+ public boolean applyVizMap(EdgeView edge_view, VisualStyle style) {return true;}
+ public boolean applyVizMap(CyNode node, VisualStyle style) {return true;}
+ public boolean applyVizMap(NodeView node_view, VisualStyle style) {return true;}
+ CyEdge[] selectedEdges;
+ public boolean setSelected(CyEdge[] edges) {
+ selectedEdges = edges;
+ return true;
+ }
+ EdgeView[] selectedEdgeViews;
+ public boolean setSelected(EdgeView[] edge_views) {
+ selectedEdgeViews = edge_views;
+ return true;
+ }
+ public void applyVizmapper(VisualStyle style) {}
+ public void applyLayout(CyLayoutAlgorithm layout) {}
+ public void applyLockedLayout(CyLayoutAlgorithm layout, CyNode[] nodes, CyEdge[] edges) {}
+ public void applyLayout(CyLayoutAlgorithm layout, CyNode[] nodes, CyEdge[] edges) {}
+ public void applyLockedLayout(CyLayoutAlgorithm layout, CyNodeView[] nodes, CyEdgeView[] edges) {}
+ public void applyLayout(CyLayoutAlgorithm layout, CyNodeView[] nodes, CyEdgeView[] edges) {}
+ public void applyLockedLayout(CyLayoutAlgorithm layout, int[] nodes, int[] edges) {}
+ public void applyLayout(CyLayoutAlgorithm layout, int[] nodes, int[] edges) {}
+ String style;
+ public void setVisualStyle(String VSName) {
+ style = VSName;
+ }
+ public VisualStyle getVisualStyle() { return null; }
+ public void addNodeContextMenuListener(NodeContextMenuListener l) {}
+ public void removeNodeContextMenuListener(NodeContextMenuListener l) {}
+ public void addEdgeContextMenuListener(EdgeContextMenuListener l) {}
+ public void removeEdgeContextMenuListener(EdgeContextMenuListener l) {}
+ public GraphPerspective getGraphPerspective() {
+ return net;
+ }
+ public boolean nodeSelectionEnabled() { return true; }
+ public boolean edgeSelectionEnabled() { return true; }
+ public void enableNodeSelection () {}
+ public void disableNodeSelection () {}
+ public void enableEdgeSelection () {}
+ public void disableEdgeSelection () {}
+ public int[] getSelectedNodeIndices() { return null; }
+ public List getSelectedNodes() { return null; }
+ public int[] getSelectedEdgeIndices() { return null; }
+ public List getSelectedEdges() { return null; }
+ public void addGraphViewChangeListener(GraphViewChangeListener listener) {}
+ public void removeGraphViewChangeListener(GraphViewChangeListener listener) {}
+ Paint bgp;
+ public void setBackgroundPaint(Paint paint) {
+ bgp = paint;
+ }
+ public Paint getBackgroundPaint() {
+ return bgp;
+ }
+ public Component getComponent() {
+ return new JPanel();
+ }
+ List<NodeView> nodeViews = new ArrayList<NodeView>();
+ public NodeView addNodeView(int node_index) {
+ NodeView nv = new TestNodeView(node_index);
+ nodeViews.add(nv);
+ return nv;
+ }
+ List<EdgeView> edgeViews = new ArrayList<EdgeView>();
+ public EdgeView addEdgeView(int edge_index) {
+ EdgeView ev = new TestEdgeView(edge_index);
+ edgeViews.add(ev);
+ return ev;
+ }
+ public EdgeView addEdgeView(String class_name, int edge_index) { return null; }
+ public NodeView addNodeView(String class_name, int node_index) { return null; }
+ public NodeView addNodeView( int node_index, NodeView node_view_replacement) {return null;}
+ public NodeView removeNodeView ( NodeView node_view ) {
+ nodeViews.remove(node_view);
+ return node_view;
+ }
+ public NodeView removeNodeView ( Node node ) {return null;}
+ public NodeView removeNodeView ( int node ) {return null;}
+ public EdgeView removeEdgeView ( EdgeView edge_view ) {
+ edgeViews.remove(edge_view);
+ return edge_view;
+ }
+ public EdgeView removeEdgeView ( Edge edge ) {return null;}
+ public EdgeView removeEdgeView ( int edge ) {return null;}
+ String identifier = "";
+ public String getIdentifier() {
+ return identifier;
+ }
+ public void setIdentifier(String new_identifier) {
+ identifier = new_identifier;
+ }
+ double zoom = 1.0;
+ public double getZoom() {
+ return zoom;
+ }
+ public void setZoom(double zoom) {
+ this.zoom = zoom;
+ }
+ public void fitContent() {}
+ public void updateView() {}
+ public RootGraph getRootGraph() { return net.getRootGraph(); }
+ public Iterator getNodeViewsIterator() { return nodeViews.iterator(); }
+ public int getNodeViewCount() { return nodeViews.size(); }
+ public int getEdgeViewCount() { return edgeViews.size(); }
+ public NodeView getNodeView(Node node) { return null; }
+ public NodeView getNodeView(int index) { return null; }
+ public java.util.List getEdgeViewsList() { return edgeViews; }
+ public java.util.List getEdgeViewsList( Node oneNode, Node otherNode) { return null; }
+ public java.util.List getEdgeViewsList( int from_node_index, int to_node_index, boolean include_undirected_edges) { return null; }
+ public EdgeView getEdgeView(int edge_index) { return null; }
+ public Iterator getEdgeViewsIterator() { return edgeViews.iterator(); }
+ public EdgeView getEdgeView(Edge edge) { return null; }
+ public int edgeCount() { return edgeViews.size(); }
+ public int nodeCount() { return nodeViews.size(); }
+ public boolean hideGraphObject(Object object) { return true;}
+ public boolean showGraphObject(Object object) { return true; }
+ public boolean hideGraphObjects(List objects) { return true;}
+ public boolean showGraphObjects(List objects) { return true; }
+ public Object[] getContextMethods( String class_name, boolean plus_superclass) { return null; }
+ public Object[] getContextMethods( String class_name, Object[] methods) { return null; }
+ public boolean addContextMethod( String class_name, String method_class_name, String method_name, Object[] args, ClassLoader loader ) { return true; }
+ public void setAllNodePropertyData(int node_index, Object[] data) {}
+ public Object[] getAllNodePropertyData(int node_index) { return null; }
+ public void setAllEdgePropertyData(int edge_index, Object[] data) {}
+ public Object[] getAllEdgePropertyData(int edge_index) { return null; }
+ public Object getNodeObjectProperty(int node_index, int property) { return null; }
+ public boolean setNodeObjectProperty( int node_index, int property, Object value) {return true;}
+ public Object getEdgeObjectProperty(int edge_index, int property) { return null; }
+ public boolean setEdgeObjectProperty( int edge_index, int property, Object value) {return true;}
+ public double getNodeDoubleProperty(int node_index, int property) { return 0d; }
+ public boolean setNodeDoubleProperty( int node_index, int property, double value) {return true;}
+ public double getEdgeDoubleProperty(int edge_index, int property) { return 0d; }
+ public boolean setEdgeDoubleProperty( int edge_index, int property, double value) {return true;}
+ public float getNodeFloatProperty(int node_index, int property) { return 0f; }
+ public boolean setNodeFloatProperty( int node_index, int property, float value) {return true;}
+ public float getEdgeFloatProperty(int edge_index, int property) { return 0f; }
+ public boolean setEdgeFloatProperty( int edge_index, int property, float value) {return true;}
+ public boolean getNodeBooleanProperty(int node_index, int property) { return true; }
+ public boolean setNodeBooleanProperty( int node_index, int property, boolean value) {return true;}
+ public boolean getEdgeBooleanProperty(int edge_index, int property) { return true; }
+ public boolean setEdgeBooleanProperty( int edge_index, int property, boolean value) {return true;}
+ public int getNodeIntProperty(int node_index, int property) { return 0; }
+ public boolean setNodeIntProperty( int node_index, int property, int value) {return true;}
+ public int getEdgeIntProperty(int edge_index, int property) { return 0; }
+ public boolean setEdgeIntProperty( int edge_index, int property, int value) {return true;}
+}
diff --git a/application/src/test/java/cytoscape/visual/TestNodeView.java b/application/src/test/java/cytoscape/visual/TestNodeView.java
new file mode 100644
index 0000000..849cf78
--- /dev/null
+++ b/application/src/test/java/cytoscape/visual/TestNodeView.java
@@ -0,0 +1,558 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.visual;
+
+import giny.model.Node;
+
+import giny.view.GraphView;
+import giny.view.Label;
+import giny.view.NodeView;
+import giny.view.ObjectPosition;
+
+import java.awt.BasicStroke;
+import java.awt.Color;
+import java.awt.Paint;
+import java.awt.Stroke;
+import java.awt.geom.Point2D;
+
+
+/**
+ * This is a dummy implementation of NodeView that
+ * can be used for unit testing.
+ */
+public class TestNodeView implements NodeView {
+ int shape = 0;
+ Paint selectedPaint = Color.RED;
+ Paint unselectedPaint = Color.BLUE;
+ Stroke border = new BasicStroke();
+ float borderWidth = 0;
+ Paint borderPaint = Color.GREEN;
+ float transparency = 0;
+ double width = 0;
+ double height = 0;
+ double x_pos = 0;
+ double y_pos = 0;
+ boolean selected = false;
+ String toolTip = "";
+ Point2D offset = new Point2D.Double();
+ int degree = 0;
+ Label label = new TestLabel();
+ double label_offset_x = 0.0;
+ double label_offset_y = 0.0;
+ int node_label_anchor = 0;
+ double label_width = 100.0;
+ boolean nestedNetworkVisible = true;
+
+ int rootGraphIndex;
+
+ private ObjectPosition labelPosition;
+
+ /**
+ * Creates a new TestNodeView object.
+ */
+ public TestNodeView() {
+ this(1);
+ }
+
+ public TestNodeView(int index) {
+ rootGraphIndex = 1;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public GraphView getGraphView() {
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Node getNode() {
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getGraphPerspectiveIndex() {
+ return rootGraphIndex;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getRootGraphIndex() {
+ return rootGraphIndex;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param otherNode DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public java.util.List getEdgeViewsList(NodeView otherNode) {
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getShape() {
+ return shape;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param s DOCUMENT ME!
+ */
+ public void setShape(int s) {
+ shape = s;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param p DOCUMENT ME!
+ */
+ public void setSelectedPaint(Paint p) {
+ selectedPaint = p;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Paint getSelectedPaint() {
+ return selectedPaint;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param p DOCUMENT ME!
+ */
+ public void setUnselectedPaint(Paint p) {
+ unselectedPaint = p;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Paint getUnselectedPaint() {
+ return unselectedPaint;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param b DOCUMENT ME!
+ */
+ public void setBorderPaint(Paint b) {
+ borderPaint = b;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Paint getBorderPaint() {
+ return borderPaint;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param bw DOCUMENT ME!
+ */
+ public void setBorderWidth(float bw) {
+ borderWidth = bw;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public float getBorderWidth() {
+ return borderWidth;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param s DOCUMENT ME!
+ */
+ public void setBorder(Stroke s) {
+ border = s;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Stroke getBorder() {
+ return border;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param trans DOCUMENT ME!
+ */
+ public void setTransparency(float trans) {
+ transparency = trans;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public float getTransparency() {
+ return transparency;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param w DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean setWidth(double w) {
+ width = w;
+
+ return true;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public double getWidth() {
+ return width;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param h DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean setHeight(double h) {
+ height = h;
+
+ return true;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public double getHeight() {
+ return height;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public giny.view.Label getLabel() {
+ return label;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param l DOCUMENT ME!
+ */
+ public void setLabel(Label l) {
+ label = l;
+ } // not in interface
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getDegree() {
+ return degree;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param x DOCUMENT ME!
+ * @param y DOCUMENT ME!
+ */
+ public void setOffset(double x, double y) {
+ offset.setLocation(x, y);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Point2D getOffset() {
+ return offset;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param x DOCUMENT ME!
+ */
+ public void setXPosition(double x) {
+ x_pos = x;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param x DOCUMENT ME!
+ * @param update DOCUMENT ME!
+ */
+ public void setXPosition(double x, boolean update) {
+ x_pos = x;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public double getXPosition() {
+ return x_pos;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param y DOCUMENT ME!
+ */
+ public void setYPosition(double y) {
+ y_pos = y;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param y DOCUMENT ME!
+ * @param update DOCUMENT ME!
+ */
+ public void setYPosition(double y, boolean update) {
+ y_pos = y;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public double getYPosition() {
+ return y_pos;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param animate DOCUMENT ME!
+ */
+ public void setNodePosition(boolean animate) {
+ }
+ ; // WTF???
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void select() {
+ selected = true;
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void unselect() {
+ selected = false;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isSelected() {
+ return selected;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param s DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean setSelected(boolean s) {
+ selected = s;
+
+ return selected;
+ }
+
+ public boolean isHidden() {
+ return false;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param tip DOCUMENT ME!
+ */
+ public void setToolTip(String tip) {
+ toolTip = tip;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getToolTip() {
+ return toolTip;
+ } // not in the interface
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param x DOCUMENT ME!
+ */
+ public void setLabelOffsetX(double x) {
+ label_offset_x = x;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public double getLabelOffsetX() {
+ return label_offset_x;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param y DOCUMENT ME!
+ */
+ public void setLabelOffsetY(double y) {
+ label_offset_y = y;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public double getLabelOffsetY() {
+ return label_offset_y;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param position DOCUMENT ME!
+ */
+ public void setNodeLabelAnchor(int position) {
+ node_label_anchor = position;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getNodeLabelAnchor() {
+ return node_label_anchor;
+ }
+
+ public double getLabelWidth() {
+ return label_width;
+ }
+
+ public void setLabelWidth(double w) {
+ label_width = w;
+ }
+
+
+ public boolean nestedNetworkIsVisible() {
+ return nestedNetworkVisible;
+ }
+
+ public void showNestedNetwork(final boolean makeVisible) {
+ nestedNetworkVisible = makeVisible;
+ }
+
+ public ObjectPosition getLabelPosition() {
+ return this.labelPosition;
+ }
+
+ public void setLabelPosition(final ObjectPosition labelPosition) {
+ this.labelPosition = labelPosition;
+ }
+
+}
diff --git a/application/src/test/java/cytoscape/visual/VisualMappingManagerTest.java b/application/src/test/java/cytoscape/visual/VisualMappingManagerTest.java
new file mode 100644
index 0000000..17762ea
--- /dev/null
+++ b/application/src/test/java/cytoscape/visual/VisualMappingManagerTest.java
@@ -0,0 +1,174 @@
+/*
+ File: VisualMappingManagerTest.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+// VisualMappingManagerTest.java
+//----------------------------------------------------------------------------
+// $Revision: 18686 $
+// $Date: 2009-12-07 13:56:52 -0800 (Mon, 07 Dec 2009) $
+// $Author: mes $
+//----------------------------------------------------------------------------
+package cytoscape.visual;
+
+import giny.model.Node;
+import giny.model.RootGraph;
+import giny.view.NodeView;
+
+import java.awt.Color;
+import java.awt.Font;
+import java.io.FileReader;
+import java.util.Properties;
+
+import junit.framework.TestCase;
+import junit.framework.TestSuite;
+import cytoscape.CyEdge;
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+import cytoscape.view.CyNetworkView;
+import cytoscape.data.CyAttributes;
+import cytoscape.data.Semantics;
+import cytoscape.data.readers.CyAttributesReader;
+import cytoscape.util.FileUtil;
+import static cytoscape.visual.VisualPropertyType.*;
+
+/**
+ *
+ */
+public class VisualMappingManagerTest extends TestCase {
+ CyNetwork cyNet;
+ CyNode a;
+ CyNode b;
+ CyNode c;
+ CyEdge ab;
+ CalculatorCatalog catalog;
+ Properties props;
+
+ /**
+ * Creates a new VisualMappingManagerTest object.
+ *
+ * @param name
+ * DOCUMENT ME!
+ */
+ public VisualMappingManagerTest(String name) {
+ super(name);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void setUp() {
+ System.out.println("setup begin");
+ cyNet = Cytoscape.createNetworkFromFile("src/test/resources/testData/small.sif");
+ a = Cytoscape.getCyNode("a");
+ b = Cytoscape.getCyNode("b");
+ c = Cytoscape.getCyNode("c");
+ ab = Cytoscape.getCyEdge(a, b, Semantics.INTERACTION, "pp", false);
+ props = new Properties();
+
+ try {
+ CyAttributesReader.loadAttributes(Cytoscape.getNodeAttributes(),
+ new FileReader("src/test/resources/testData/small.nodeAttr"));
+ props.load(FileUtil.getInputStream("src/test/resources/testData/small.vizmap.props"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ catalog = new CalculatorCatalog();
+ CalculatorIO.loadCalculators(props, catalog, true);
+ System.out.println("setup end");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception
+ * DOCUMENT ME!
+ */
+ public void testBypass() throws Exception {
+ Color fillColor = new Color(63, 128, 255);
+ Color borderColor = new Color(100, 100, 50);
+ NodeShape shape = NodeShape.DIAMOND;
+ double width = 49.0;
+ double height = 79.0;
+ String label = "testLabel";
+ String toolTip = "testToolTip";
+ Font font = new Font("SansSerif", Font.ITALIC, 10);
+ String fontString = "SansSerif,italic,10";
+
+ RootGraph graph = Cytoscape.getRootGraph();
+ int index1 = graph.createNode();
+ Node first = graph.getNode(index1);
+ int index2 = graph.createNode();
+ Node second = graph.getNode(index2);
+
+ CyNetwork network2 = Cytoscape.createNetwork(Cytoscape.getRootGraph()
+ .getNodeIndicesArray(), Cytoscape.getRootGraph()
+ .getEdgeIndicesArray(), null);
+
+ CyAttributes secondNodeAttr = Cytoscape.getNodeAttributes();
+ String secondName = second.getIdentifier();
+ secondNodeAttr.setAttribute(secondName, "node.fillColor", "63,128,255");
+ secondNodeAttr.setAttribute(secondName, "node.borderColor", "100,100,50");
+ secondNodeAttr.setAttribute(secondName, "node.size", "32.0");
+
+ CyNetworkView view = Cytoscape.getNetworkView( network2.getIdentifier() );
+ NodeView nv = view.getNodeView(index2);
+
+ VisualMappingManager vmm = Cytoscape.getVisualMappingManager();
+ vmm.setNetworkView(view);
+ vmm.setVisualStyle(view.getVisualStyle());
+
+ vmm.vizmapNode(nv,view);
+
+ assertEquals(fillColor, nv.getUnselectedPaint());
+ assertEquals(borderColor, nv.getBorderPaint());
+ // node size locked
+ assertEquals(32.0, nv.getWidth());
+ assertEquals(32.0, nv.getHeight());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args
+ * DOCUMENT ME!
+ */
+ public static void main(String[] args) {
+ junit.textui.TestRunner.run(new TestSuite(
+ VisualMappingManagerTest.class));
+ }
+}
diff --git a/application/src/test/java/cytoscape/visual/VisualPropertyDependencyTest.java b/application/src/test/java/cytoscape/visual/VisualPropertyDependencyTest.java
new file mode 100644
index 0000000..91710f4
--- /dev/null
+++ b/application/src/test/java/cytoscape/visual/VisualPropertyDependencyTest.java
@@ -0,0 +1,88 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.visual;
+
+import java.util.Properties;
+import junit.framework.*;
+import static cytoscape.visual.VisualPropertyDependency.Definition.*;
+
+
+public class VisualPropertyDependencyTest extends TestCase {
+ double SLACK = 0.00001;
+ VisualPropertyDependency deps;
+
+ public VisualPropertyDependencyTest(String name) {
+ super(name);
+ }
+
+ public void setUp() {
+ deps = new VisualPropertyDependencyImpl();
+ }
+
+ public void testDefaults() {
+ assertTrue( deps.check(NODE_SIZE_LOCKED) );
+ assertTrue( !deps.check(ARROW_COLOR_MATCHES_EDGE) );
+ }
+
+ public void testSet() {
+ deps.set(NODE_SIZE_LOCKED,true);
+ assertTrue( deps.check(NODE_SIZE_LOCKED) );
+ deps.set(NODE_SIZE_LOCKED,false);
+ assertTrue( !deps.check(NODE_SIZE_LOCKED) );
+ }
+
+ public void testApplyProps() {
+ Properties props = new Properties();
+ String baseKey = "base";
+ props.setProperty(baseKey + ".nodeSizeLocked", "false");
+
+ deps.applyDefaultProperties(props,baseKey);
+
+ assertTrue( !deps.check(NODE_SIZE_LOCKED) );
+ }
+
+ public void testGetOnlySetProps() {
+ Properties props = deps.getDefaultProperties("base");
+ assertNull( props.getProperty("base." + NODE_SIZE_LOCKED.getDefaultPropertyKey()));
+ assertNull( props.getProperty("base." + ARROW_COLOR_MATCHES_EDGE.getDefaultPropertyKey()));
+ }
+
+ public void testGetSetProps() {
+ deps.set(NODE_SIZE_LOCKED,false);
+ Properties props = deps.getDefaultProperties("base");
+ assertEquals("false", props.getProperty("base."+NODE_SIZE_LOCKED.getDefaultPropertyKey()));
+ }
+}
diff --git a/application/src/test/java/cytoscape/visual/VizMapPropertiesTest.java b/application/src/test/java/cytoscape/visual/VizMapPropertiesTest.java
new file mode 100644
index 0000000..846d3cd
--- /dev/null
+++ b/application/src/test/java/cytoscape/visual/VizMapPropertiesTest.java
@@ -0,0 +1,276 @@
+/*
+ File: VizMapPropertiesTest.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+//----------------------------------------------------------------------------
+// $Revision: 21132 $
+// $Date: 2010-08-03 18:49:02 +0200 (Tue, 03 Aug 2010) $
+// $Author: mes $
+//----------------------------------------------------------------------------
+package cytoscape.visual;
+
+import cytoscape.visual.calculators.AbstractCalculator;
+import cytoscape.visual.calculators.Calculator;
+
+import cytoscape.visual.mappings.ObjectMapping;
+
+import junit.framework.TestCase;
+
+import java.awt.Color;
+
+import java.io.FileInputStream;
+import java.io.InputStream;
+
+import java.util.Collection;
+import java.util.Iterator;
+import java.util.Properties;
+
+
+//----------------------------------------------------------------------------
+/**
+ * Test program to check that calculators are loaded properly from the
+ * properties file. Works by writing a text description of the read calculators
+ * to stdout.
+ */
+public class VizMapPropertiesTest extends TestCase {
+ private CalculatorCatalog catalog;
+ private Properties props;
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void setUp() {
+ catalog = new CalculatorCatalog();
+ props = new Properties();
+
+ try {
+ String propsFile = "src/test/resources/testData/old_vizmap.props";
+ InputStream is = null;
+ try {
+ is = new FileInputStream(propsFile);
+ props.load(is);
+ }
+ finally {
+ if (is != null) {
+ is.close();
+ }
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+
+ return;
+ }
+
+ CalculatorIO.loadCalculators(props, catalog);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void tearDown() {
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testProperties() {
+ Collection nodeColorCalcs = catalog.getCalculators(VisualPropertyType.NODE_FILL_COLOR);
+ System.out.println("nodeColorCalcs.size() = " + nodeColorCalcs.size());
+ checkCalculator(catalog.getCalculator(VisualPropertyType.NODE_FILL_COLOR, "RedGreen"));
+ System.out.println();
+
+ Collection nodeLineTypeCalcs = catalog.getCalculators(VisualPropertyType.NODE_LINETYPE);
+ System.out.println("nodeLineTypeCalcs.size() = " + nodeLineTypeCalcs.size());
+ //checkCalculator(catalog.getNodeLineTypeCalculator("BasicDiscrete"));
+ assertNull(catalog.getCalculator(VisualPropertyType.NODE_LINETYPE, "BasicDiscrete"));
+
+ //checkCalculator(catalog.getNodeLineTypeCalculator("BasicContinuous"));
+ assertNull(catalog.getCalculator(VisualPropertyType.NODE_LINETYPE, "BasicContinuous"));
+ System.out.println();
+
+ Collection nodeShapeCalcs = catalog.getCalculators(VisualPropertyType.NODE_SHAPE);
+ System.out.println("nodeShapeCalcs.size() = " + nodeShapeCalcs.size());
+ checkCalculator(catalog.getCalculator(VisualPropertyType.NODE_SHAPE, "BasicDiscrete"));
+ checkCalculator(catalog.getCalculator(VisualPropertyType.NODE_SHAPE, "BasicContinuous"));
+ System.out.println();
+
+ Collection nodeSizeCalcs = catalog.getCalculators(VisualPropertyType.NODE_SIZE);
+ System.out.println("nodeSizeCalcs.size() = " + nodeSizeCalcs.size());
+ checkCalculator(catalog.getCalculator(VisualPropertyType.NODE_SIZE, "BasicDiscrete"));
+ checkCalculator(catalog.getCalculator(VisualPropertyType.NODE_SIZE, "BasicContinuous"));
+ System.out.println();
+
+ Collection nodeLabelCalcs = catalog.getCalculators(VisualPropertyType.NODE_LABEL);
+ System.out.println("nodeLabelCalcs.size() = " + nodeLabelCalcs.size());
+ checkCalculator(catalog.getCalculator(VisualPropertyType.NODE_LABEL, "BasicDiscrete"));
+ checkCalculator(catalog.getCalculator(VisualPropertyType.NODE_LABEL, "BasicContinuous"));
+ System.out.println();
+
+ Collection nodeToolTipCalcs = catalog.getCalculators(VisualPropertyType.NODE_TOOLTIP);
+ System.out.println("nodeToolTipCalcs.size() = " + nodeToolTipCalcs.size());
+ checkCalculator(catalog.getCalculator(VisualPropertyType.NODE_TOOLTIP, "BasicDiscrete"));
+ checkCalculator(catalog.getCalculator(VisualPropertyType.NODE_TOOLTIP, "BasicContinuous"));
+ System.out.println();
+
+ Collection nodeFontFaceCalcs = catalog.getCalculators(VisualPropertyType.NODE_FONT_FACE);
+ System.out.println("nodeFontFaceCalcs.size() = " + nodeFontFaceCalcs.size());
+ checkCalculator(catalog.getCalculator(VisualPropertyType.NODE_FONT_FACE, "BasicDiscrete"));
+ checkCalculator(catalog.getCalculator(VisualPropertyType.NODE_FONT_FACE, "BasicContinuous"));
+ System.out.println();
+
+ Collection nodeFontSizeCalcs = catalog.getCalculators(VisualPropertyType.NODE_FONT_SIZE);
+ System.out.println("nodeFontSizeCalcs.size() = " + nodeFontSizeCalcs.size());
+ checkCalculator(catalog.getCalculator(VisualPropertyType.NODE_FONT_SIZE, "BasicDiscrete"));
+ checkCalculator(catalog.getCalculator(VisualPropertyType.NODE_FONT_SIZE, "BasicContinuous"));
+ System.out.println();
+
+ Collection edgeColorCalcs = catalog.getCalculators(VisualPropertyType.EDGE_COLOR);
+ System.out.println("edgeColorCalcs.size() = " + edgeColorCalcs.size());
+ checkCalculator(catalog.getCalculator(VisualPropertyType.EDGE_COLOR, "BasicDiscrete"));
+ System.out.println();
+
+ Collection edgeLineTypeCalcs = catalog.getCalculators(VisualPropertyType.EDGE_LINETYPE);
+ System.out.println("edgeLineTypeCalcs.size() = " + edgeLineTypeCalcs.size());
+ assertEquals(0, edgeLineTypeCalcs.size());
+ // checkCalculator(catalog.getEdgeLineTypeCalculator("BasicDiscrete"));
+ // checkCalculator(catalog.getEdgeLineTypeCalculator("BasicContinuous"));
+ System.out.println();
+
+ Collection edgeArrowCalcs = catalog.getCalculators(VisualPropertyType.EDGE_SRCARROW);
+ System.out.println("edgeArrowCalcs.size() = " + edgeArrowCalcs.size());
+ checkCalculator(catalog.getCalculator(VisualPropertyType.EDGE_SRCARROW, "BasicDiscrete"));
+ checkCalculator(catalog.getCalculator(VisualPropertyType.EDGE_TGTARROW, "BasicContinuous"));
+ System.out.println();
+
+ Collection edgeLabelCalcs = catalog.getCalculators(VisualPropertyType.EDGE_LABEL);
+ System.out.println("edgeLabelCalcs.size() = " + edgeLabelCalcs.size());
+ checkCalculator(catalog.getCalculator(VisualPropertyType.EDGE_LABEL, "BasicDiscrete"));
+ checkCalculator(catalog.getCalculator(VisualPropertyType.EDGE_LABEL, "BasicContinuous"));
+ checkCalculator(catalog.getCalculator(VisualPropertyType.EDGE_LABEL, "testPassThrough"));
+ System.out.println();
+
+ Collection edgeToolTipCalcs = catalog.getCalculators(VisualPropertyType.EDGE_TOOLTIP);
+ System.out.println("edgeToolTipCalcs.size() = " + edgeToolTipCalcs.size());
+ checkCalculator(catalog.getCalculator(VisualPropertyType.EDGE_TOOLTIP, "BasicDiscrete"));
+ checkCalculator(catalog.getCalculator(VisualPropertyType.EDGE_TOOLTIP, "BasicContinuous"));
+ System.out.println();
+
+ Collection edgeFontFaceCalcs = catalog.getCalculators(VisualPropertyType.EDGE_FONT_FACE);
+ System.out.println("edgeFontFaceCalcs.size() = " + edgeFontFaceCalcs.size());
+ checkCalculator(catalog.getCalculator(VisualPropertyType.EDGE_FONT_FACE, "BasicDiscrete"));
+ checkCalculator(catalog.getCalculator(VisualPropertyType.EDGE_FONT_FACE, "BasicContinuous"));
+ System.out.println();
+
+ Collection edgeFontSizeCalcs = catalog.getCalculators(VisualPropertyType.EDGE_FONT_SIZE);
+ System.out.println("edgeFontSizeCalcs.size() = " + edgeFontSizeCalcs.size());
+ checkCalculator(catalog.getCalculator(VisualPropertyType.EDGE_FONT_SIZE, "BasicDiscrete"));
+ checkCalculator(catalog.getCalculator(VisualPropertyType.EDGE_FONT_SIZE, "BasicContinuous"));
+ System.out.println();
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testVisualStyle() {
+ final String DEF = "default";
+ final String CLONE = "default clone1";
+
+ System.out.println("====================== Start Visual Style Test ====================");
+
+ Collection<VisualStyle> vizStyles = catalog.getVisualStyles();
+
+ // Show current style names
+ for (VisualStyle style : vizStyles)
+ System.out.println("Style Names: " + style.getName());
+
+ // Create clone
+ final VisualStyle originalStyle = catalog.getVisualStyle(DEF);
+ assertNotNull(originalStyle);
+
+ // Set original style node & background color
+ originalStyle.getGlobalAppearanceCalculator().setDefaultBackgroundColor(Color.white);
+ originalStyle.getNodeAppearanceCalculator().getDefaultAppearance()
+ .set(VisualPropertyType.NODE_FILL_COLOR, Color.red);
+ System.out.println("Original Style BG Color = "
+ + originalStyle.getGlobalAppearanceCalculator().getDefaultBackgroundColor());
+ System.out.println("Original Style Def Node Color = "
+ + originalStyle.getNodeAppearanceCalculator().getDefaultAppearance()
+ .get(VisualPropertyType.NODE_FILL_COLOR));
+
+ final VisualStyle cloneStyle = new VisualStyle(originalStyle, CLONE);
+ assertNotNull(originalStyle);
+ assertEquals(cloneStyle.getName(), CLONE);
+
+ // Register clone to the catalog
+ catalog.addVisualStyle(cloneStyle);
+
+ cloneStyle.getGlobalAppearanceCalculator().setDefaultBackgroundColor(Color.black);
+ cloneStyle.getNodeAppearanceCalculator().getDefaultAppearance()
+ .set(VisualPropertyType.NODE_FILL_COLOR, Color.blue);
+ System.out.println("Clone Style BG Color = "
+ + cloneStyle.getGlobalAppearanceCalculator().getDefaultBackgroundColor());
+ System.out.println("Clone Style Def Node Color = "
+ + cloneStyle.getNodeAppearanceCalculator().getDefaultAppearance()
+ .get(VisualPropertyType.NODE_FILL_COLOR));
+
+ for (VisualStyle style : vizStyles)
+ System.out.println("New Style Names: " + style.getName());
+
+ assertEquals(catalog.getVisualStyle(DEF).getGlobalAppearanceCalculator()
+ .getDefaultBackgroundColor(), Color.white);
+ assertEquals(catalog.getVisualStyle(CLONE).getGlobalAppearanceCalculator()
+ .getDefaultBackgroundColor(), Color.black);
+
+ assertEquals(catalog.getVisualStyle(DEF).getNodeAppearanceCalculator().getDefaultAppearance()
+ .get(VisualPropertyType.NODE_FILL_COLOR), Color.red);
+ assertEquals(catalog.getVisualStyle(CLONE).getNodeAppearanceCalculator()
+ .getDefaultAppearance().get(VisualPropertyType.NODE_FILL_COLOR),
+ Color.blue);
+
+ System.out.println("====================== End Visual Style Test ====================");
+ }
+
+ private void checkCalculator(Calculator c) {
+ if (c == null) {
+ fail();
+ }
+
+ AbstractCalculator gc = (AbstractCalculator) c;
+ ObjectMapping m = gc.getMapping(0);
+ System.out.println("controller = " + m.getControllingAttributeName());
+ System.out.println("Map = " + m);
+ }
+}
diff --git a/application/src/test/java/cytoscape/visual/mappings/BoundaryRangeValuesTest.java b/application/src/test/java/cytoscape/visual/mappings/BoundaryRangeValuesTest.java
new file mode 100644
index 0000000..9eeec61
--- /dev/null
+++ b/application/src/test/java/cytoscape/visual/mappings/BoundaryRangeValuesTest.java
@@ -0,0 +1,120 @@
+/*
+ File: BoundaryRangeValuesTest.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// BoundaryRangeValuesTest.java
+
+//----------------------------------------------------------------------------
+// $Revision: 9565 $
+// $Date: 2007-02-13 20:36:50 +0100 (Tue, 13 Feb 2007) $
+// $Author: mes $
+//----------------------------------------------------------------------------
+package cytoscape.visual.mappings;
+
+import cytoscape.visual.mappings.BoundaryRangeValues;
+
+//----------------------------------------------------------------------------
+import junit.framework.*;
+
+import java.io.*;
+
+
+//----------------------------------------------------------------------------
+/**
+ *
+ */
+public class BoundaryRangeValuesTest extends TestCase {
+ //----------------------------------------------------------------------------
+ /**
+ * Creates a new BoundaryRangeValuesTest object.
+ *
+ * @param name DOCUMENT ME!
+ */
+ public BoundaryRangeValuesTest(String name) {
+ super(name);
+ }
+
+ //----------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void setUp() throws Exception {
+ }
+
+ //----------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void tearDown() throws Exception {
+ }
+
+ //----------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testAll() throws Exception {
+ BoundaryRangeValues bv = new BoundaryRangeValues();
+ assertTrue(bv.lesserValue == null);
+ assertTrue(bv.equalValue == null);
+ assertTrue(bv.greaterValue == null);
+
+ Double d1 = new Double(1.0);
+ Double d2 = new Double(2.0);
+ Double d3 = new Double(3.0);
+ BoundaryRangeValues bv2 = new BoundaryRangeValues(d1, d2, d3);
+ assertTrue(bv2.lesserValue == d1);
+ assertTrue(bv2.equalValue == d2);
+ assertTrue(bv2.greaterValue == d3);
+ }
+
+ //---------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ */
+ public static void main(String[] args) {
+ junit.textui.TestRunner.run(new TestSuite(BoundaryRangeValuesTest.class));
+ }
+
+ //----------------------------------------------------------------------------
+}
diff --git a/application/src/test/java/cytoscape/visual/mappings/FlatInterpolatorTest.java b/application/src/test/java/cytoscape/visual/mappings/FlatInterpolatorTest.java
new file mode 100644
index 0000000..c525ceb
--- /dev/null
+++ b/application/src/test/java/cytoscape/visual/mappings/FlatInterpolatorTest.java
@@ -0,0 +1,127 @@
+/*
+ File: FlatInterpolatorTest.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// FlatInterpolatorTest.java
+
+//----------------------------------------------------------------------------
+// $Revision: 9565 $
+// $Date: 2007-02-13 20:36:50 +0100 (Tue, 13 Feb 2007) $
+// $Author: mes $
+//----------------------------------------------------------------------------
+package cytoscape.visual.mappings;
+
+import cytoscape.visual.mappings.FlatInterpolator;
+
+//----------------------------------------------------------------------------
+import junit.framework.*;
+
+import java.awt.Color;
+
+import java.io.*;
+
+
+//----------------------------------------------------------------------------
+/**
+ *
+ */
+public class FlatInterpolatorTest extends TestCase {
+ //----------------------------------------------------------------------------
+ /**
+ * Creates a new FlatInterpolatorTest object.
+ *
+ * @param name DOCUMENT ME!
+ */
+ public FlatInterpolatorTest(String name) {
+ super(name);
+ }
+
+ //----------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void setUp() throws Exception {
+ }
+
+ //----------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void tearDown() throws Exception {
+ }
+
+ //----------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testFunction() throws Exception {
+ Double d1 = new Double(1.0);
+ Double d2 = new Double(2.0);
+ Double dMid = new Double(1.5);
+ Color c1 = new Color(0, 0, 0);
+ Color c2 = new Color(255, 255, 255);
+
+ FlatInterpolator li = new FlatInterpolator();
+ Object returnVal = li.getRangeValue(d1, c1, d2, c2, dMid);
+ assertTrue(returnVal == c1);
+
+ FlatInterpolator li2 = new FlatInterpolator(FlatInterpolator.LOWER);
+ returnVal = li2.getRangeValue(d1, c1, d2, c2, dMid);
+ assertTrue(returnVal == c1);
+
+ FlatInterpolator li3 = new FlatInterpolator(FlatInterpolator.UPPER);
+ returnVal = li3.getRangeValue(d1, c1, d2, c2, dMid);
+ assertTrue(returnVal == c2);
+ }
+
+ //---------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ */
+ public static void main(String[] args) {
+ junit.textui.TestRunner.run(new TestSuite(FlatInterpolatorTest.class));
+ }
+
+ //----------------------------------------------------------------------------
+}
diff --git a/application/src/test/java/cytoscape/visual/mappings/LinearNumberToColorInterpolatorTest.java b/application/src/test/java/cytoscape/visual/mappings/LinearNumberToColorInterpolatorTest.java
new file mode 100644
index 0000000..74cb99f
--- /dev/null
+++ b/application/src/test/java/cytoscape/visual/mappings/LinearNumberToColorInterpolatorTest.java
@@ -0,0 +1,126 @@
+/*
+ File: LinearNumberToColorInterpolatorTest.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// LinearNumberToColorInterpolatorTest.java
+
+//----------------------------------------------------------------------------
+// $Revision: 9565 $
+// $Date: 2007-02-13 20:36:50 +0100 (Tue, 13 Feb 2007) $
+// $Author: mes $
+//----------------------------------------------------------------------------
+package cytoscape.visual.mappings;
+
+import cytoscape.visual.mappings.LinearNumberToColorInterpolator;
+
+//----------------------------------------------------------------------------
+import junit.framework.*;
+
+import java.awt.Color;
+
+import java.io.*;
+
+
+//----------------------------------------------------------------------------
+/**
+ *
+ */
+public class LinearNumberToColorInterpolatorTest extends TestCase {
+ //----------------------------------------------------------------------------
+ /**
+ * Creates a new LinearNumberToColorInterpolatorTest object.
+ *
+ * @param name DOCUMENT ME!
+ */
+ public LinearNumberToColorInterpolatorTest(String name) {
+ super(name);
+ }
+
+ //----------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void setUp() throws Exception {
+ }
+
+ //----------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void tearDown() throws Exception {
+ }
+
+ //----------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testFunction() throws Exception {
+ LinearNumberToColorInterpolator li = new LinearNumberToColorInterpolator();
+ Color c1 = new Color(0, 10, 20, 30);
+ Color c2 = new Color(201, 191, 179, 169);
+
+ Object returnVal = li.getRangeValue(0.65, c1, c2);
+ assertTrue(returnVal instanceof Color);
+
+ Color cReturn = (Color) returnVal;
+ assertTrue(cReturn.getRed() == 131);
+ assertTrue(cReturn.getGreen() == 128);
+ assertTrue(cReturn.getBlue() == 123);
+ assertTrue(cReturn.getAlpha() == 120);
+
+ Object dummy = new Object();
+ returnVal = li.getRangeValue(0.65, c1, dummy);
+ assertTrue(returnVal == null);
+ }
+
+ //---------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ */
+ public static void main(String[] args) {
+ junit.textui.TestRunner.run(new TestSuite(LinearNumberToColorInterpolatorTest.class));
+ }
+
+ //----------------------------------------------------------------------------
+}
diff --git a/application/src/test/java/cytoscape/visual/mappings/LinearNumberToNumberInterpolatorTest.java b/application/src/test/java/cytoscape/visual/mappings/LinearNumberToNumberInterpolatorTest.java
new file mode 100644
index 0000000..430a7bd
--- /dev/null
+++ b/application/src/test/java/cytoscape/visual/mappings/LinearNumberToNumberInterpolatorTest.java
@@ -0,0 +1,117 @@
+/*
+ File: LinearNumberToNumberInterpolatorTest.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// LinearNumberToNumberInterpolatorTest.java
+
+//----------------------------------------------------------------------------
+// $Revision: 9565 $
+// $Date: 2007-02-13 20:36:50 +0100 (Tue, 13 Feb 2007) $
+// $Author: mes $
+//----------------------------------------------------------------------------
+package cytoscape.visual.mappings;
+
+import cytoscape.visual.mappings.LinearNumberToNumberInterpolator;
+
+//----------------------------------------------------------------------------
+import junit.framework.*;
+
+import java.io.*;
+
+
+//----------------------------------------------------------------------------
+/**
+ *
+ */
+public class LinearNumberToNumberInterpolatorTest extends TestCase {
+ //----------------------------------------------------------------------------
+ /**
+ * Creates a new LinearNumberToNumberInterpolatorTest object.
+ *
+ * @param name DOCUMENT ME!
+ */
+ public LinearNumberToNumberInterpolatorTest(String name) {
+ super(name);
+ }
+
+ //----------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void setUp() throws Exception {
+ }
+
+ //----------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void tearDown() throws Exception {
+ }
+
+ //----------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testFunction() throws Exception {
+ LinearNumberToNumberInterpolator li = new LinearNumberToNumberInterpolator();
+
+ Integer lowerRange = new Integer(2);
+ Integer upperRange = new Integer(3);
+ double frac = 0.41;
+ Object returnVal = li.getRangeValue(frac, lowerRange, upperRange);
+
+ assertTrue(returnVal instanceof Double);
+ assertTrue((((Double) returnVal).doubleValue() - 2.41) < 1.0E-6);
+ }
+
+ //---------------------------------------------------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ */
+ public static void main(String[] args) {
+ junit.textui.TestRunner.run(new TestSuite(LinearNumberToNumberInterpolatorTest.class));
+ }
+
+ //----------------------------------------------------------------------------
+}
diff --git a/application/src/test/java/cytoscape/visual/mappings/MappingUtilTest.java b/application/src/test/java/cytoscape/visual/mappings/MappingUtilTest.java
new file mode 100644
index 0000000..3925064
--- /dev/null
+++ b/application/src/test/java/cytoscape/visual/mappings/MappingUtilTest.java
@@ -0,0 +1,224 @@
+/*
+ File: MappingUtilTest.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.visual.mappings;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.data.CyAttributes;
+
+import cytoscape.visual.mappings.MappingUtil;
+
+import junit.framework.*;
+
+import java.awt.Color;
+
+import java.io.*;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+
+/**
+ *
+ */
+public class MappingUtilTest extends TestCase {
+ /**
+ * Creates a new MappingUtilTest object.
+ *
+ * @param name DOCUMENT ME!
+ */
+ public MappingUtilTest(String name) {
+ super(name);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testGetNodeAttributeType() throws Exception {
+ assertEquals("non-existent attr ", CyAttributes.TYPE_UNDEFINED,
+ MappingUtil.getAttributeType("node", "mappingUtilTest"));
+
+ // string test
+ Cytoscape.getNodeAttributes().setAttribute("id", "mappingUtilTest", "test");
+ assertEquals("string attr ", CyAttributes.TYPE_STRING,
+ MappingUtil.getAttributeType("node", "mappingUtilTest"));
+
+ // int test
+ Cytoscape.getNodeAttributes().setAttribute("id", "mappingUtilTest2", 20);
+ assertEquals("int attr ", CyAttributes.TYPE_INTEGER,
+ MappingUtil.getAttributeType("node", "mappingUtilTest2"));
+
+ // double test
+ Cytoscape.getNodeAttributes().setAttribute("id", "mappingUtilTest3", 20.5);
+ assertEquals("float attr ", CyAttributes.TYPE_FLOATING,
+ MappingUtil.getAttributeType("node", "mappingUtilTest3"));
+
+ // boolean test
+ Cytoscape.getNodeAttributes().setAttribute("id", "mappingUtilTest4", true);
+ assertEquals("bool attr ", CyAttributes.TYPE_BOOLEAN,
+ MappingUtil.getAttributeType("node", "mappingUtilTest4"));
+
+ // list test
+ List l = new ArrayList();
+ l.add("asdf");
+ Cytoscape.getNodeAttributes().setListAttribute("id", "mappingUtilTest5", l);
+ assertEquals("list attr ", CyAttributes.TYPE_SIMPLE_LIST,
+ MappingUtil.getAttributeType("node", "mappingUtilTest5"));
+
+ // map test
+ Map m = new HashMap();
+ m.put("a", "b");
+ Cytoscape.getNodeAttributes().setMapAttribute("id", "mappingUtilTest6", m);
+ assertEquals("map attr ", CyAttributes.TYPE_SIMPLE_MAP,
+ MappingUtil.getAttributeType("node", "mappingUtilTest6"));
+
+ // wrong baseKey
+ assertEquals("wrong base key", CyAttributes.TYPE_UNDEFINED,
+ MappingUtil.getAttributeType("junk", "mappingUtilTest2"));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testGetEdgeAttributeType() throws Exception {
+ assertEquals("non-existent attr ", CyAttributes.TYPE_UNDEFINED,
+ MappingUtil.getAttributeType("edge", "mappingUtilTest"));
+
+ // string test
+ Cytoscape.getEdgeAttributes().setAttribute("id", "mappingUtilTest", "test");
+ assertEquals("string attr ", CyAttributes.TYPE_STRING,
+ MappingUtil.getAttributeType("edge", "mappingUtilTest"));
+
+ // int test
+ Cytoscape.getEdgeAttributes().setAttribute("id", "mappingUtilTest2", 20);
+ assertEquals("int attr ", CyAttributes.TYPE_INTEGER,
+ MappingUtil.getAttributeType("edge", "mappingUtilTest2"));
+
+ // double test
+ Cytoscape.getEdgeAttributes().setAttribute("id", "mappingUtilTest3", 20.5);
+ assertEquals("float attr ", CyAttributes.TYPE_FLOATING,
+ MappingUtil.getAttributeType("edge", "mappingUtilTest3"));
+
+ // boolean test
+ Cytoscape.getEdgeAttributes().setAttribute("id", "mappingUtilTest4", true);
+ assertEquals("bool attr ", CyAttributes.TYPE_BOOLEAN,
+ MappingUtil.getAttributeType("edge", "mappingUtilTest4"));
+
+ // list test
+ List l = new ArrayList();
+ l.add("asdf");
+ Cytoscape.getEdgeAttributes().setListAttribute("id", "mappingUtilTest5", l);
+ assertEquals("list attr ", CyAttributes.TYPE_SIMPLE_LIST,
+ MappingUtil.getAttributeType("edge", "mappingUtilTest5"));
+
+ // map test
+ Map m = new HashMap();
+ m.put("a", "b");
+ Cytoscape.getEdgeAttributes().setMapAttribute("id", "mappingUtilTest6", m);
+ assertEquals("map attr ", CyAttributes.TYPE_SIMPLE_MAP,
+ MappingUtil.getAttributeType("edge", "mappingUtilTest6"));
+
+ // what the hell is TYPE_COMPLEX????
+
+ // wrong baseKey
+ assertEquals("string attr ", CyAttributes.TYPE_UNDEFINED,
+ MappingUtil.getAttributeType("junk", "mappingUtilTest2"));
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testParseObject() {
+ Object o = null;
+
+ // test valid types
+ o = MappingUtil.parseObjectType("1", CyAttributes.TYPE_INTEGER);
+ assertTrue("int ", o instanceof Integer);
+ o = null;
+
+ o = MappingUtil.parseObjectType("1.75", CyAttributes.TYPE_FLOATING);
+ assertTrue("double ", o instanceof Double);
+ o = null;
+
+ o = MappingUtil.parseObjectType("false", CyAttributes.TYPE_BOOLEAN);
+ assertTrue("boolean ", o instanceof Boolean);
+ o = null;
+
+ o = MappingUtil.parseObjectType("homer", CyAttributes.TYPE_STRING);
+ assertTrue("string ", o instanceof String);
+ o = null;
+
+ o = MappingUtil.parseObjectType("homer", CyAttributes.TYPE_SIMPLE_MAP);
+ assertTrue("map ", o instanceof String);
+ o = null;
+
+ o = MappingUtil.parseObjectType("homer", CyAttributes.TYPE_SIMPLE_LIST);
+ assertTrue("list ", o instanceof String);
+ o = null;
+
+ // test some failures
+ o = MappingUtil.parseObjectType("homer", (byte) 75);
+ assertTrue("non-existent type 75 ", o instanceof String);
+ o = null;
+
+ boolean caught = false;
+
+ try {
+ o = MappingUtil.parseObjectType("homer", CyAttributes.TYPE_INTEGER);
+ } catch (NumberFormatException n) {
+ caught = true;
+ }
+
+ assertTrue("caught number format excpetion", caught);
+ o = null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ */
+ public static void main(String[] args) {
+ junit.textui.TestRunner.run(new TestSuite(MappingUtilTest.class));
+ }
+}
diff --git a/application/src/test/java/cytoscape/visual/mappings/PassthroughMappingTest.java b/application/src/test/java/cytoscape/visual/mappings/PassthroughMappingTest.java
new file mode 100644
index 0000000..906ec9c
--- /dev/null
+++ b/application/src/test/java/cytoscape/visual/mappings/PassthroughMappingTest.java
@@ -0,0 +1,97 @@
+package cytoscape.visual.mappings;
+
+import java.awt.Color;
+import java.util.Map;
+
+import cytoscape.Cytoscape;
+import cytoscape.data.CyAttributes;
+import cytoscape.data.CyAttributesUtils;
+import cytoscape.data.readers.InteractionsReader;
+import junit.framework.TestCase;
+
+public class PassthroughMappingTest extends TestCase {
+
+ private CyAttributes nodeAttr;
+ private CyAttributes edgeAttr;
+
+ protected void setUp() throws Exception {
+ super.setUp();
+
+ nodeAttr = Cytoscape.getNodeAttributes();
+ edgeAttr = Cytoscape.getEdgeAttributes();
+ InteractionsReader reader = new InteractionsReader("src/test/resources/testData/galFiltered.sif");
+ reader.read();
+ }
+
+ protected void tearDown() throws Exception {
+ super.tearDown();
+ }
+
+ public void testPassThrough() throws Exception {
+ assertNotNull(nodeAttr);
+ final Color color1 = new Color(100, 100, 100);
+ final Color color2 = new Color(200, 150, 0);
+
+ // Test color values
+ nodeAttr.setAttribute("?", "Color", color1.getRed() + "," + color1.getGreen() + "," + color1.getBlue());
+ nodeAttr.setAttribute("YNL050C", "Color", color2.getRed() + "," + color2.getGreen() + "," + color2.getBlue());
+ nodeAttr.setAttribute("YIL061C", "Color", "300,-1,10"); // Invalid
+
+ // Test size values
+ nodeAttr.setAttribute("?", "Node Size", "100");
+ nodeAttr.setAttribute("YNL050C", "Node Size", "-10"); // Invalid, but should return value.
+
+ // Edge
+ edgeAttr.setAttribute("YNL216W (pd) YIL069C", "Width", "10");
+ edgeAttr.setAttribute("YNL216W (pd) YAL038W", "Width", "abcd"); // Invalid
+
+
+ ObjectMapping pm = new PassThroughMapping(Color.class, "Color");
+ Map<String, Object> bundle = CyAttributesUtils.getAttributes("?", nodeAttr);
+ Object rangeVal = pm.calculateRangeValue(bundle);
+
+ assertNotNull(rangeVal);
+ assertEquals(rangeVal.getClass(), Color.class);
+ assertEquals(rangeVal, color1);
+
+ bundle = CyAttributesUtils.getAttributes("YNL050C", nodeAttr);
+ rangeVal = pm.calculateRangeValue(bundle);
+ assertNotNull(rangeVal);
+ assertEquals(rangeVal.getClass(), Color.class);
+ assertEquals(rangeVal, color2);
+
+ // Invalid string is given. Should return null.
+ bundle = CyAttributesUtils.getAttributes("YIL061C", nodeAttr);
+ rangeVal = pm.calculateRangeValue(bundle);
+ assertNull(rangeVal);
+
+ pm = new PassThroughMapping(Double.class, "Node Size");
+ bundle = CyAttributesUtils.getAttributes("?", nodeAttr);
+ rangeVal = pm.calculateRangeValue(bundle);
+
+ assertNotNull(rangeVal);
+ assertEquals(rangeVal.getClass(), Double.class);
+ assertEquals(rangeVal, 100.0);
+
+ bundle = CyAttributesUtils.getAttributes("YNL050C", nodeAttr);
+ rangeVal = pm.calculateRangeValue(bundle);
+
+ assertNotNull(rangeVal);
+ assertEquals(rangeVal.getClass(), Double.class);
+ assertEquals(-10.0, rangeVal); // This value should be validated by the caller.
+
+ pm = new PassThroughMapping(Float.class, "Width");
+ bundle = CyAttributesUtils.getAttributes("YNL216W (pd) YIL069C", edgeAttr);
+ rangeVal = pm.calculateRangeValue(bundle);
+
+ assertNotNull(rangeVal);
+ assertEquals(rangeVal.getClass(), Float.class);
+ assertEquals(10.0f, rangeVal);
+
+ bundle = CyAttributesUtils.getAttributes("YNL216W (pd) YAL038W", edgeAttr);
+ rangeVal = pm.calculateRangeValue(bundle);
+
+ assertNull(rangeVal);
+ }
+
+}
diff --git a/application/src/test/java/cytoscape/visual/mappings/continuous/TestContinuousColorRangeCalculator.java b/application/src/test/java/cytoscape/visual/mappings/continuous/TestContinuousColorRangeCalculator.java
new file mode 100644
index 0000000..5f56c82
--- /dev/null
+++ b/application/src/test/java/cytoscape/visual/mappings/continuous/TestContinuousColorRangeCalculator.java
@@ -0,0 +1,210 @@
+/*
+ File: TestContinuousColorRangeCalculator.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.visual.mappings.continuous;
+
+import cytoscape.visual.mappings.continuous.ContinuousMappingReader;
+import cytoscape.visual.mappings.continuous.ContinuousRangeCalculator;
+
+import cytoscape.visual.parsers.ColorParser;
+import cytoscape.visual.parsers.ValueParser;
+
+import junit.framework.TestCase;
+
+import java.awt.*;
+
+import java.io.ByteArrayInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Properties;
+
+
+/**
+ * Tests the ContinuousRangeCalculator.
+ */
+public class TestContinuousColorRangeCalculator extends TestCase {
+ /**
+ * Test with First Sample Data Set.
+ * @throws Exception All Exceptions.
+ */
+ public void testCalculator1() throws Exception {
+ Properties props = null;
+ InputStream in = null;
+
+ try {
+ in = getMapper1Props();
+ props = getProperties(in);
+ }
+ finally {
+ if (in != null) {
+ in.close();
+ }
+ }
+
+ ValueParser parser = new ColorParser();
+ ContinuousMappingReader reader = new ContinuousMappingReader(props,
+ "nodeColorCalculator.Sample.mapping",
+ parser);
+ List<ContinuousMappingPoint> points = reader.getPoints();
+
+ // Create some sample values...
+ Map<String, Object> bundle = new HashMap<String, Object>();
+ double[] values = { -1.0, 0.07, 2.0, 4.0, 5.0, 10.0 };
+
+ for (int i = 0; i < values.length; i++) {
+ String key = "key" + i;
+ bundle.put(key, new Double(values[i]));
+ }
+
+ ContinuousRangeCalculator calc = new ContinuousRangeCalculator(points,
+ reader.getInterpolator(),
+ bundle);
+
+ // These are the colors we expect back...
+ Color[] colors = { Color.BLUE, Color.BLUE, Color.BLUE, Color.BLUE, Color.WHITE, Color.RED };
+
+ // Test that calculator returns the right colors.
+ for (int i = 0; i < values.length; i++) {
+ Object color = calc.calculateRangeValue("key" + i);
+ assertEquals(colors[i], color);
+ }
+ }
+
+ /**
+ * Test with Second Sample Data Set.
+ * @throws Exception All Exceptions.
+ */
+ public void testCalculator2() throws Exception {
+ Properties props = null;
+ InputStream in = null;
+
+ try {
+ in = getMapper2Props();
+ props = getProperties(in);
+ }
+ finally {
+ if (in != null) {
+ in.close();
+ }
+ }
+
+ ValueParser parser = new ColorParser();
+ ContinuousMappingReader reader = new ContinuousMappingReader(props,
+ "nodeColorCalculator.Sample.mapping",
+ parser);
+ List<ContinuousMappingPoint> points = reader.getPoints();
+
+ // Create some sample values...
+ HashMap bundle = new HashMap();
+ double[] values = { -1.0, 0.07, 2.0, 4.0, 5.0, 10.0 };
+
+ for (int i = 0; i < values.length; i++) {
+ String key = "key" + i;
+ bundle.put(key, new Double(values[i]));
+ }
+
+ ContinuousRangeCalculator calc = new ContinuousRangeCalculator(points,
+ reader.getInterpolator(),
+ bundle);
+
+ // These are the colors we expect back...
+ Color[] colors = {
+ new Color(0, 0, 255), // Blue
+ new Color(255, 251, 251), // White (w/ some red)
+ new Color(255, 153, 153), // Pink
+ new Color(255, 51, 51), // Pinker
+ new Color(255, 0, 0), // Red
+ new Color(0, 0, 0) // Black
+ };
+
+ // Test that calculator returns the right colors.
+ for (int i = 0; i < values.length; i++) {
+ Object color = calc.calculateRangeValue("key" + i);
+ assertEquals(colors[i], color);
+ }
+ }
+
+ private Properties getProperties(InputStream in) throws IOException {
+ Properties props = new Properties();
+ props.load(in);
+
+ return props;
+ }
+
+ private InputStream getMapper1Props() {
+ String props = new String("nodeColorCalculator.Sample.class=cytoscape.visual."
+ + "calculators.GenericNodeColorCalculator\n"
+ + "nodeColorCalculator.Sample.mapping.boundaryvalues=1\n"
+ + "nodeColorCalculator.Sample.mapping.bv0.domainvalue=5.0\n"
+ + "nodeColorCalculator.Sample.mapping.bv0.equal=255,255,255\n"
+ + "nodeColorCalculator.Sample.mapping.bv0.greater=255,0,0\n"
+ + "nodeColorCalculator.Sample.mapping.bv0.lesser=0,0,255\n"
+ + "nodeColorCalculator.Sample.mapping.controller=Expression\n"
+ + "nodeColorCalculator.Sample.mapping.interpolator="
+ + "LinearNumberToColorInterpolator\n"
+ + "nodeColorCalculator.Sample.mapping."
+ + "type=ContinuousMapping\n");
+ ByteArrayInputStream in = new ByteArrayInputStream(props.getBytes());
+
+ return in;
+ }
+
+ private InputStream getMapper2Props() {
+ String props = new String("nodeColorCalculator.Sample.class=cytoscape.visual.calculators."
+ + "GenericNodeColorCalculator\n"
+ + "nodeColorCalculator.Sample.mapping.boundaryvalues=2\n"
+ + "nodeColorCalculator.Sample.mapping.bv0.domainvalue=0.0\n"
+ + "nodeColorCalculator.Sample.mapping.bv0.equal=255,255,255\n"
+ + "nodeColorCalculator.Sample.mapping.bv0.greater=255,255,255\n"
+ + "nodeColorCalculator.Sample.mapping.bv0.lesser=0,0,255\n"
+ + "nodeColorCalculator.Sample.mapping.bv1.domainvalue=5.0\n"
+ + "nodeColorCalculator.Sample.mapping.bv1.equal=255,0,0\n"
+ + "nodeColorCalculator.Sample.mapping.bv1.greater=0,0,0\n"
+ + "nodeColorCalculator.Sample.mapping.bv1.lesser=255,0,0\n"
+ + "nodeColorCalculator.Sample.mapping.controller=Expression\n"
+ + "nodeColorCalculator.Sample.mapping.interpolator="
+ + "LinearNumberToColorInterpolator\n"
+ + "nodeColorCalculator.Sample.mapping.type=ContinuousMapping\n");
+ ByteArrayInputStream in = new ByteArrayInputStream(props.getBytes());
+
+ return in;
+ }
+}
diff --git a/application/src/test/java/cytoscape/visual/mappings/continuous/TestContinuousMappingReader.java b/application/src/test/java/cytoscape/visual/mappings/continuous/TestContinuousMappingReader.java
new file mode 100644
index 0000000..cce444c
--- /dev/null
+++ b/application/src/test/java/cytoscape/visual/mappings/continuous/TestContinuousMappingReader.java
@@ -0,0 +1,141 @@
+/*
+ File: TestContinuousMappingReader.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.visual.mappings.continuous;
+
+import cytoscape.visual.mappings.BoundaryRangeValues;
+import cytoscape.visual.mappings.Interpolator;
+import cytoscape.visual.mappings.LinearNumberToColorInterpolator;
+import cytoscape.visual.mappings.continuous.ContinuousMappingPoint;
+import cytoscape.visual.mappings.continuous.ContinuousMappingReader;
+
+import cytoscape.visual.parsers.ColorParser;
+import cytoscape.visual.parsers.ValueParser;
+
+import junit.framework.TestCase;
+
+import java.awt.*;
+
+import java.io.ByteArrayInputStream;
+import java.io.InputStream;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Properties;
+
+
+/**
+ * Tests the ContinuousMappingReader Class.
+ */
+public class TestContinuousMappingReader extends TestCase {
+ /**
+ * Tests the ContinuousMappingReader Class.
+ * @throws Exception All Exceptions.
+ */
+ public void testReader() throws Exception {
+ Properties properties = new Properties();
+ InputStream in = null;
+
+ try {
+ in = getDataFile();
+ properties.load(in);
+ }
+ finally {
+ if (in != null) {
+ in.close();
+ }
+ }
+
+ int size = properties.size();
+ assertEquals(17, size);
+
+ ValueParser parser = new ColorParser();
+ ContinuousMappingReader reader = new ContinuousMappingReader(properties,
+ "nodeColorCalculator.RedGreen2.mapping",
+ parser);
+ String attrName = reader.getControllingAttributeName();
+ assertEquals("expression", attrName);
+
+ Interpolator interp = reader.getInterpolator();
+ assertTrue(interp instanceof LinearNumberToColorInterpolator);
+
+ List<ContinuousMappingPoint> points = reader.getPoints();
+ assertEquals(3, points.size());
+
+ ContinuousMappingPoint point0 = (ContinuousMappingPoint) points.get(0);
+ double value0 = point0.getValue();
+ assertEquals(-1.0, value0, 0.0001);
+
+ BoundaryRangeValues range0 = point0.getRange();
+ assertEquals(Color.RED, range0.lesserValue);
+ assertEquals(Color.RED, range0.equalValue);
+ assertEquals(Color.RED, range0.greaterValue);
+
+ ContinuousMappingPoint point1 = (ContinuousMappingPoint) points.get(1);
+ double value1 = point1.getValue();
+ assertEquals(0.0, value1, 0.0001);
+
+ BoundaryRangeValues range1 = point1.getRange();
+ assertEquals(Color.WHITE, range1.lesserValue);
+ assertEquals(Color.WHITE, range1.equalValue);
+ assertEquals(Color.WHITE, range1.greaterValue);
+ }
+
+ static InputStream getDataFile() {
+ String file = "nodeColorCalculator.RedGreen2.mapping.bv0.lesser: 255,0,0\n"
+ + "nodeColorCalculator.RedGreen2.mapping.interpolator: "
+ + "LinearNumberToColorInterpolator\n"
+ + "nodeColorCalculator.RedGreen2.mapping.bv0.greater: 255,0,0\n"
+ + "nodeColorCalculator.RedGreen2.mapping.bv1.domainvalue: 0.0\n"
+ + "nodeColorCalculator.RedGreen2.class: "
+ + "cytoscape.visual.calculators.GenericNodeColorCalculator\n"
+ + "nodeColorCalculator.RedGreen2.mapping.bv1.equal: 255,255,255\n"
+ + "nodeColorCalculator.RedGreen2.mapping.bv1.greater: 255,255,255\n"
+ + "nodeColorCalculator.RedGreen2.mapping.controller: expression\n"
+ + "nodeColorCalculator.RedGreen2.mapping.boundaryvalues: 3\n"
+ + "nodeColorCalculator.RedGreen2.mapping.bv2.domainvalue: 0.0\n"
+ + "nodeColorCalculator.RedGreen2.mapping.bv0.domainvalue: -1.0\n"
+ + "nodeColorCalculator.RedGreen2.mapping.bv2.lesser: 255,255,255\n"
+ + "nodeColorCalculator.RedGreen2.mapping.type: ContinuousMapping\n"
+ + "nodeColorCalculator.RedGreen2.mapping.bv0.equal: 255,0,0\n"
+ + "nodeColorCalculator.RedGreen2.mapping.bv2.greater: 102,255,102\n"
+ + "nodeColorCalculator.RedGreen2.mapping.bv1.lesser: 255,255,255\n"
+ + "nodeColorCalculator.RedGreen2.mapping.bv2.equal: 255,255,255\n";
+ ByteArrayInputStream in = new ByteArrayInputStream(file.getBytes());
+
+ return in;
+ }
+}
diff --git a/application/src/test/java/cytoscape/visual/mappings/continuous/TestContinuousMappingWriter.java b/application/src/test/java/cytoscape/visual/mappings/continuous/TestContinuousMappingWriter.java
new file mode 100644
index 0000000..ba0fe79
--- /dev/null
+++ b/application/src/test/java/cytoscape/visual/mappings/continuous/TestContinuousMappingWriter.java
@@ -0,0 +1,104 @@
+/*
+ File: TestContinuousMappingWriter.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.visual.mappings.continuous;
+
+import cytoscape.visual.mappings.continuous.ContinuousMappingReader;
+import cytoscape.visual.mappings.continuous.ContinuousMappingWriter;
+
+import cytoscape.visual.parsers.ColorParser;
+import cytoscape.visual.parsers.ValueParser;
+
+import junit.framework.TestCase;
+
+import java.awt.Color;
+import java.io.InputStream;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Properties;
+
+
+/**
+ * Tests the ContinuousMappingWriter Class.
+ */
+public class TestContinuousMappingWriter extends TestCase {
+ /**
+ * Tests the ContinuousMappingWriter Class.
+ * @throws Exception All Exceptions.
+ */
+ public void testWriter() throws Exception {
+ // Read in a Properties File
+ String baseKey = "nodeColorCalculator.RedGreen2.mapping";
+ ValueParser parser = new ColorParser();
+ Properties properties = new Properties();
+ InputStream in = null;
+
+ try {
+ in = TestContinuousMappingReader.getDataFile();
+ properties.load(in);
+ }
+ finally {
+ if (in != null) {
+ in.close();
+ }
+ }
+
+ ContinuousMappingReader reader = new ContinuousMappingReader(properties, baseKey, parser);
+ List<ContinuousMappingPoint> points = reader.getPoints();
+
+ // Now write out a set of Propeties.
+ ContinuousMappingWriter writer = new ContinuousMappingWriter(points, baseKey,
+ reader
+ .getControllingAttributeName(),
+ reader.getInterpolator());
+
+ // Test a samplint of properties.
+ Properties newProps = writer.getProperties();
+
+ // Test Boundary Range Value
+ String bv0Lesser = newProps.getProperty(baseKey + ".bv0.lesser");
+ assertEquals("255,0,0", bv0Lesser);
+
+ // Test Interpolator
+ String interp = newProps.getProperty(baseKey + ".interpolator");
+ assertEquals("LinearNumberToColorInterpolator", interp);
+
+ // Test Controlling Attribute
+ String type = newProps.getProperty(baseKey + ".controller");
+ assertEquals("expression", type);
+ }
+}
diff --git a/application/src/test/java/cytoscape/visual/mappings/discrete/DiscreteMappingReaderTest.java b/application/src/test/java/cytoscape/visual/mappings/discrete/DiscreteMappingReaderTest.java
new file mode 100644
index 0000000..8ac8474
--- /dev/null
+++ b/application/src/test/java/cytoscape/visual/mappings/discrete/DiscreteMappingReaderTest.java
@@ -0,0 +1,169 @@
+/*
+ File: DiscreteMappingReaderTest.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+//----------------------------------------------------------------------------
+// $Revision: 20380 $
+// $Date: 2010-06-01 22:04:00 +0200 (Tue, 01 Jun 2010) $
+// $Author: kono $
+//----------------------------------------------------------------------------
+package cytoscape.visual.mappings.discrete;
+
+import cytoscape.visual.mappings.discrete.DiscreteMappingReader;
+
+import cytoscape.visual.parsers.ColorParser;
+import cytoscape.visual.parsers.ValueParser;
+
+import junit.framework.TestCase;
+
+import java.awt.*;
+
+import java.io.ByteArrayInputStream;
+import java.io.InputStream;
+
+import java.util.Properties;
+import java.util.SortedMap;
+import java.util.TreeMap;
+
+
+/**
+ * Tests the DiscreteMappingReader Class.
+ */
+public class DiscreteMappingReaderTest extends TestCase {
+ /**
+ * Tests the DiscreteMappingReader Class.
+ * @throws Exception All Exceptions.
+ */
+ public void testReader() throws Exception {
+ InputStream in = getDataFile();
+ Properties properties = new Properties();
+ properties.load(in);
+
+ ValueParser parser = new ColorParser();
+ DiscreteMappingReader reader = new DiscreteMappingReader(properties,
+ "nodeColorCalculator.JUnitDiscreteColor.mapping",
+ parser);
+ String attribute = reader.getControllingAttributeName();
+ assertEquals("canonicalName", attribute);
+
+ SortedMap map = reader.getMap();
+
+ // Test a few of the mapping elements.
+ Color color = (Color) map.get("A");
+ assertEquals(new Color(204, 255, 255), color);
+ color = (Color) map.get("Y");
+ assertEquals(new Color(255, 51, 51), color);
+ }
+
+ static InputStream getDataFile() {
+ String file = new String("nodeColorCalculator.JUnitDiscreteColor.class=cytoscape."
+ + "visual.calculators.GenericNodeColorCalculator\n"
+ + "nodeColorCalculator.JUnitDiscreteColor.mapping."
+ + "controller=canonicalName\n"
+ + "nodeColorCalculator.JUnitDiscreteColor.mapping."
+ + "map.A=204,255,255\n"
+ + "nodeColorCalculator.JUnitDiscreteColor.mapping."
+ + "map.B=51,255,51\n"
+ + "nodeColorCalculator.JUnitDiscreteColor.mapping."
+ + "map.C=204,204,255\n"
+ + "nodeColorCalculator.JUnitDiscreteColor.mapping.map."
+ + "D=255,255,255\n"
+ + "nodeColorCalculator.JUnitDiscreteColor.mapping.map."
+ + "X=102,51,0\n"
+ + "nodeColorCalculator.JUnitDiscreteColor.mapping.map."
+ + "Y=255,51,51\n"
+ + "nodeColorCalculator.JUnitDiscreteColor.mapping."
+ + "type=DiscreteMapping\n");
+ ByteArrayInputStream in = new ByteArrayInputStream(file.getBytes());
+
+ return in;
+ }
+
+ static InputStream getControllerTypeDataFile() {
+ String file = new String("nodeColorCalculator.JUnitDiscreteColor.class=cytoscape."
+ + "visual.calculators.GenericNodeColorCalculator\n"
+ + "nodeColorCalculator.JUnitDiscreteColor.mapping."
+ + "controller=homer\n"
+ + "nodeColorCalculator.JUnitDiscreteColor.mapping."
+ + "controllerType=3\n" // Integer
+ + "nodeColorCalculator.JUnitDiscreteColor.mapping."
+ + "map.1=204,255,255\n"
+ + "nodeColorCalculator.JUnitDiscreteColor.mapping."
+ + "map.2=51,255,51\n"
+ + "nodeColorCalculator.JUnitDiscreteColor.mapping."
+ + "map.3=204,204,255\n"
+ + "nodeColorCalculator.JUnitDiscreteColor.mapping.map."
+ + "4=255,255,255\n"
+ + "nodeColorCalculator.JUnitDiscreteColor.mapping.map."
+ + "5=102,51,0\n"
+ + "nodeColorCalculator.JUnitDiscreteColor.mapping.map."
+ + "6=255,51,51\n"
+ + "nodeColorCalculator.JUnitDiscreteColor.mapping."
+ + "type=DiscreteMapping\n");
+ ByteArrayInputStream in = new ByteArrayInputStream(file.getBytes());
+
+ return in;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testControllerType() throws Exception {
+ InputStream in = getControllerTypeDataFile();
+ Properties properties = new Properties();
+ properties.load(in);
+
+ ValueParser parser = new ColorParser();
+ DiscreteMappingReader reader = new DiscreteMappingReader(properties,
+ "nodeColorCalculator.JUnitDiscreteColor.mapping",
+ parser);
+ String attribute = reader.getControllingAttributeName();
+ assertEquals("controlling attr name", "homer", attribute);
+
+ SortedMap map = reader.getMap();
+
+ Color color = (Color) map.get(new Integer(1));
+ assertEquals(new Color(204, 255, 255), color);
+
+ color = (Color) map.get(new Integer(3));
+ assertEquals(new Color(204, 204, 255), color);
+
+ color = (Color) map.get(new Integer(6));
+ assertEquals(new Color(255, 51, 51), color);
+ }
+}
diff --git a/application/src/test/java/cytoscape/visual/mappings/discrete/DiscreteMappingWriterTest.java b/application/src/test/java/cytoscape/visual/mappings/discrete/DiscreteMappingWriterTest.java
new file mode 100644
index 0000000..e028675
--- /dev/null
+++ b/application/src/test/java/cytoscape/visual/mappings/discrete/DiscreteMappingWriterTest.java
@@ -0,0 +1,184 @@
+/*
+ File: DiscreteMappingWriterTest.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+//----------------------------------------------------------------------------
+// $Revision: 20380 $
+// $Date: 2010-06-01 22:04:00 +0200 (Tue, 01 Jun 2010) $
+// $Author: kono $
+//----------------------------------------------------------------------------
+package cytoscape.visual.mappings.discrete;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.data.CyAttributes;
+
+import cytoscape.visual.mappings.discrete.DiscreteMappingReader;
+import cytoscape.visual.mappings.discrete.DiscreteMappingWriter;
+
+import cytoscape.visual.parsers.ColorParser;
+import cytoscape.visual.parsers.ValueParser;
+
+import junit.framework.TestCase;
+
+import java.io.InputStream;
+
+import java.util.Properties;
+import java.util.SortedMap;
+import java.util.TreeMap;
+
+
+/**
+ * Tests the DiscreteMappingWriter Class.
+ */
+public class DiscreteMappingWriterTest extends TestCase {
+ /**
+ * Tests the DiscreteMappingWriter Class.
+ * @throws Exception All Exceptions.
+ */
+ public void testWriter() throws Exception {
+ // Read in a Properties File
+ String baseKey = "nodeColorCalculator.JUnitDiscreteColor.mapping";
+ ValueParser parser = new ColorParser();
+ InputStream in = DiscreteMappingReaderTest.getDataFile();
+ Properties properties = new Properties();
+ properties.load(in);
+
+ DiscreteMappingReader reader = new DiscreteMappingReader(properties, baseKey, parser);
+ SortedMap map = reader.getMap();
+
+ // Now write out a set of Propeties.
+ DiscreteMappingWriter writer = new DiscreteMappingWriter(reader.getControllingAttributeName(),
+ baseKey, reader.getMap());
+
+ // Test a sampling of properties.
+ Properties newProps = writer.getProperties();
+
+ // Test a few elements...
+ String mapA = newProps.getProperty(baseKey + ".map.A");
+ assertEquals("204,255,255", mapA);
+
+ String mapY = newProps.getProperty(baseKey + ".map.Y");
+ assertEquals("255,51,51", mapY);
+
+ // Test Controlling Attribute
+ String type = newProps.getProperty(baseKey + ".controller");
+ assertEquals("canonicalName", type);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testControllerTypeWriting() throws Exception {
+ // Read in a Properties File
+ String baseKey = "nodeColorCalculator.JUnitDiscreteColor.mapping";
+ ValueParser parser = new ColorParser();
+ InputStream in = DiscreteMappingReaderTest.getControllerTypeDataFile();
+ Properties properties = new Properties();
+ properties.load(in);
+
+ DiscreteMappingReader reader = new DiscreteMappingReader(properties, baseKey, parser);
+ SortedMap map = reader.getMap();
+
+ // Now write out a set of Propeties.
+ DiscreteMappingWriter writer = new DiscreteMappingWriter(reader.getControllingAttributeName(),
+ baseKey, reader.getMap());
+
+ // Test a sampling of properties.
+ Properties newProps = writer.getProperties();
+
+ // Test a few elements...
+ String mapA = newProps.getProperty(baseKey + ".map.1");
+ assertEquals("204,255,255", mapA);
+
+ String mapY = newProps.getProperty(baseKey + ".map.6");
+ assertEquals("255,51,51", mapY);
+
+ // Test Controlling Attribute
+ String type = newProps.getProperty(baseKey + ".controller");
+ assertEquals("controller", "homer", type);
+
+ // while you would think that this should be 3, the "homer"
+ // attribute has not been set, therefore the attr won't be
+ // found so the type is unknown
+ String ctype = newProps.getProperty(baseKey + ".controllerType");
+ assertEquals("controllerType", "-1", ctype);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testControllerTypeWritingWithAttr() throws Exception {
+ // Read in a Properties File
+ String baseKey = "nodeColorCalculator.JUnitDiscreteColor.mapping";
+ ValueParser parser = new ColorParser();
+ InputStream in = DiscreteMappingReaderTest.getControllerTypeDataFile();
+ Properties properties = new Properties();
+ properties.load(in);
+
+ // Set the attribute so that it's type will be found
+ // 15 == random int value
+ Cytoscape.getNodeAttributes().setAttribute("id", "homer", 15);
+
+ DiscreteMappingReader reader = new DiscreteMappingReader(properties, baseKey, parser);
+ SortedMap map = reader.getMap();
+
+ // Now write out a set of Propeties.
+ DiscreteMappingWriter writer = new DiscreteMappingWriter(reader.getControllingAttributeName(),
+ baseKey, reader.getMap());
+
+ // Test a sampling of properties.
+ Properties newProps = writer.getProperties();
+
+ // Test a few elements...
+ String mapA = newProps.getProperty(baseKey + ".map.1");
+ assertEquals("204,255,255", mapA);
+
+ String mapY = newProps.getProperty(baseKey + ".map.6");
+ assertEquals("255,51,51", mapY);
+
+ // Test Controlling Attribute
+ String type = newProps.getProperty(baseKey + ".controller");
+ assertEquals("controller", "homer", type);
+
+ String ctype = newProps.getProperty(baseKey + ".controllerType");
+ assertEquals("controllerType", "3", ctype);
+ }
+}
diff --git a/application/src/test/resources/testData/NNFData/1000SmallNetworks.nnf b/application/src/test/resources/testData/NNFData/1000SmallNetworks.nnf
new file mode 100644
index 0000000..0bef7bd
--- /dev/null
+++ b/application/src/test/resources/testData/NNFData/1000SmallNetworks.nnf
@@ -0,0 +1,38139 @@
+# Generated with ./generate_networks
+# number_of_nested_networks = 1000
+# min_nested_network_size = 5
+# max_nested_network_size = 30
+# link_factor = 2.0
+M1 N1_8 pp N1_22
+M1 N1_10 pp N1_24
+M1 N1_15 pp N1_1
+M1 N1_2 pp N1_1
+M1 N1_17 pp N1_8
+M1 N1_9 pp N1_5
+M1 N1_26 pp N1_2
+M1 N1_12 pp N1_18
+M1 N1_14 pp N1_20
+M1 N1_1 pp N1_13
+M1 N1_13 pp N1_16
+M1 N1_12 pp N1_4
+M1 N1_17 pp N1_6
+M1 N1_23 pp N1_6
+M1 N1_17 pp N1_23
+M1 N1_1 pp N1_16
+M1 N1_20 pp N1_7
+M1 N1_14 pp N1_26
+M1 N1_20 pp N1_15
+M1 N1_6 pp N1_17
+M1 N1_4 pp N1_23
+M1 N1_18 pp N1_19
+M1 N1_1 pp N1_15
+M1 N1_18 pp N1_24
+M1 N1_17 pp N1_19
+M1 N1_27 pp N1_25
+M1 N1_12 pp N1_1
+M1 N1_7 pp N1_18
+M1 N1_27 pp N1_25
+M1 N1_2 pp N1_8
+M1 N1_21 pp N1_6
+M1 N1_8 pp N1_23
+M1 N1_5 pp N1_12
+M1 N1_11 pp N1_13
+M1 N1_16 pp N1_26
+M1 N1_13 pp N1_18
+M1 N1_10 pp N1_27
+M1 N1_6 pp N1_7
+M1 N1_14 pp N1_2
+M1 N1_20 pp N1_13
+M1 N1_13 pp N1_23
+M1 N1_15 pp N1_26
+M1 N1_23 pp N1_8
+M1 N1_3 pp N1_25
+M1 N1_12 pp N1_4
+M1 N1_12 pp N1_1
+M1 N1_22 pp N1_4
+M1 N1_5 pp N1_22
+M1 N1_27 pp N1_14
+M1 N1_24 pp N1_4
+M1 N1_11 pp N1_16
+M1 N1_26 pp N1_1
+M1 N1_18 pp N1_20
+M1 N1_22 pp N1_27
+M2 N2_7 pp N2_2
+M2 N2_10 pp N2_8
+M2 N2_5 pp N2_8
+M2 N2_5 pp N2_12
+M2 N2_15 pp N2_4
+M2 N2_16 pp N2_14
+M2 N2_16 pp N2_9
+M2 N2_12 pp N2_13
+M2 N2_12 pp N2_13
+M2 N2_13 pp N2_1
+M2 N2_10 pp N2_6
+M2 N2_9 pp N2_6
+M2 N2_9 pp N2_11
+M2 N2_12 pp N2_8
+M2 N2_1 pp N2_4
+M2 N2_5 pp N2_12
+M2 N2_12 pp N2_7
+M2 N2_13 pp N2_15
+M2 N2_16 pp N2_13
+M2 N2_1 pp N2_3
+M2 N2_8 pp N2_2
+M2 N2_10 pp N2_1
+M2 N2_4 pp N2_1
+M2 N2_1 pp N2_6
+M2 N2_5 pp N2_16
+M2 N2_7 pp N2_2
+M2 N2_7 pp N2_13
+M2 N2_11 pp N2_13
+M2 N2_1 pp N2_11
+M2 N2_7 pp N2_4
+M2 N2_8 pp N2_7
+M2 N2_3 pp N2_13
+M3 N3_6 pp N3_1
+M3 N3_19 pp N3_24
+M3 N3_9 pp N3_22
+M3 N3_20 pp N3_4
+M3 N3_27 pp N3_21
+M3 N3_12 pp N3_24
+M3 N3_9 pp N3_14
+M3 N3_23 pp N3_4
+M3 N3_11 pp N3_2
+M3 N3_4 pp N3_1
+M3 N3_24 pp N3_16
+M3 N3_10 pp N3_24
+M3 N3_3 pp N3_16
+M3 N3_14 pp N3_2
+M3 N3_10 pp N3_2
+M3 N3_10 pp N3_12
+M3 N3_4 pp N3_10
+M3 N3_13 pp N3_6
+M3 N3_2 pp N3_6
+M3 N3_23 pp N3_15
+M3 N3_10 pp N3_26
+M3 N3_5 pp N3_8
+M3 N3_4 pp N3_16
+M3 N3_24 pp N3_8
+M3 N3_20 pp N3_3
+M3 N3_23 pp N3_20
+M3 N3_15 pp N3_18
+M3 N3_8 pp N3_2
+M3 N3_17 pp N3_5
+M3 N3_17 pp N3_10
+M3 N3_10 pp N3_19
+M3 N3_25 pp N3_4
+M3 N3_6 pp N3_11
+M3 N3_21 pp N3_8
+M3 N3_24 pp N3_16
+M3 N3_12 pp N3_17
+M3 N3_25 pp N3_21
+M3 N3_27 pp N3_18
+M3 N3_15 pp N3_10
+M3 N3_14 pp N3_20
+M3 N3_18 pp N3_5
+M3 N3_26 pp N3_24
+M3 N3_27 pp N3_20
+M3 N3_12 pp N3_13
+M3 N3_27 pp N3_18
+M3 N3_2 pp N3_4
+M3 N3_3 pp N3_1
+M3 N3_17 pp N3_13
+M3 N3_16 pp N3_15
+M3 N3_12 pp N3_11
+M3 N3_21 pp N3_11
+M3 N3_11 pp N3_14
+M3 N3_12 pp N3_26
+M3 N3_13 pp N3_20
+M3 N3_7
+M4 N4_5 pp N4_4
+M4 N4_12 pp N4_6
+M4 N4_4 pp N4_13
+M4 N4_3 pp N4_20
+M4 N4_6 pp N4_12
+M4 N4_14 pp N4_2
+M4 N4_8 pp N4_18
+M4 N4_11 pp N4_10
+M4 N4_10 pp N4_20
+M4 N4_13 pp N4_8
+M4 N4_18 pp N4_22
+M4 N4_26 pp N4_12
+M4 N4_13 pp N4_28
+M4 N4_25 pp N4_7
+M4 N4_23 pp N4_18
+M4 N4_16 pp N4_25
+M4 N4_1 pp N4_8
+M4 N4_16 pp N4_13
+M4 N4_5 pp N4_2
+M4 N4_4 pp N4_7
+M4 N4_24 pp N4_7
+M4 N4_7 pp N4_28
+M4 N4_17 pp N4_13
+M4 N4_23 pp N4_10
+M4 N4_17 pp N4_8
+M4 N4_21 pp N4_14
+M4 N4_21 pp N4_23
+M4 N4_18 pp N4_15
+M4 N4_26 pp N4_24
+M4 N4_23 pp N4_27
+M4 N4_3 pp N4_12
+M4 N4_1 pp N4_16
+M4 N4_16 pp N4_6
+M4 N4_20 pp N4_12
+M4 N4_16 pp N4_19
+M4 N4_24 pp N4_8
+M4 N4_16 pp N4_13
+M4 N4_14 pp N4_18
+M4 N4_22 pp N4_5
+M4 N4_9 pp N4_26
+M4 N4_21 pp N4_24
+M4 N4_23 pp N4_7
+M4 N4_15 pp N4_23
+M4 N4_1 pp N4_3
+M4 N4_23 pp N4_17
+M4 N4_7 pp N4_2
+M4 N4_5 pp N4_14
+M4 N4_11 pp N4_20
+M4 N4_5 pp N4_16
+M4 N4_19 pp N4_1
+M4 N4_23 pp N4_25
+M4 N4_20 pp N4_10
+M4 N4_12 pp N4_28
+M4 N4_19 pp N4_12
+M4 N4_13 pp N4_16
+M4 N4_7 pp N4_2
+M5 N5_8 pp N5_21
+M5 N5_2 pp N5_14
+M5 N5_6 pp N5_13
+M5 N5_15 pp N5_5
+M5 N5_14 pp N5_18
+M5 N5_2 pp N5_20
+M5 N5_10 pp N5_6
+M5 N5_1 pp N5_20
+M5 N5_4 pp N5_8
+M5 N5_3 pp N5_16
+M5 N5_7 pp N5_13
+M5 N5_5 pp N5_15
+M5 N5_15 pp N5_18
+M5 N5_4 pp N5_10
+M5 N5_21 pp N5_14
+M5 N5_9 pp N5_18
+M5 N5_12 pp N5_19
+M5 N5_5 pp N5_8
+M5 N5_12 pp N5_6
+M5 N5_11 pp N5_20
+M5 N5_6 pp N5_16
+M5 N5_18 pp N5_4
+M5 N5_11 pp N5_1
+M5 N5_18 pp N5_12
+M5 N5_21 pp N5_16
+M5 N5_14 pp N5_4
+M5 N5_2 pp N5_3
+M5 N5_4 pp N5_20
+M5 N5_15 pp N5_9
+M5 N5_5 pp N5_16
+M5 N5_9 pp N5_3
+M5 N5_3 pp N5_18
+M5 N5_19 pp N5_5
+M5 N5_13 pp N5_8
+M5 N5_9 pp N5_17
+M5 N5_9 pp N5_13
+M5 N5_10 pp N5_4
+M5 N5_17 pp N5_20
+M5 N5_5 pp N5_19
+M5 N5_12 pp N5_2
+M5 N5_11 pp N5_13
+M5 N5_20 pp N5_11
+M6 N6_8 pp N6_9
+M6 N6_7 pp N6_15
+M6 N6_12 pp N6_9
+M6 N6_10 pp N6_6
+M6 N6_14 pp N6_11
+M6 N6_11 pp N6_1
+M6 N6_11 pp N6_9
+M6 N6_4 pp N6_15
+M6 N6_3 pp N6_5
+M6 N6_6 pp N6_7
+M6 N6_8 pp N6_4
+M6 N6_11 pp N6_14
+M6 N6_12 pp N6_7
+M6 N6_8 pp N6_14
+M6 N6_9 pp N6_10
+M6 N6_1 pp N6_5
+M6 N6_12 pp N6_6
+M6 N6_7 pp N6_4
+M6 N6_12 pp N6_9
+M6 N6_6 pp N6_7
+M6 N6_8 pp N6_1
+M6 N6_8 pp N6_13
+M6 N6_11 pp N6_6
+M6 N6_11 pp N6_14
+M6 N6_10 pp N6_3
+M6 N6_12 pp N6_9
+M6 N6_10 pp N6_1
+M6 N6_6 pp N6_1
+M6 N6_11 pp N6_12
+M6 N6_10 pp N6_8
+M6 N6_2
+M7 N7_15 pp N7_2
+M7 N7_14 pp N7_8
+M7 N7_4 pp N7_7
+M7 N7_19 pp N7_14
+M7 N7_8 pp N7_7
+M7 N7_12 pp N7_14
+M7 N7_19 pp N7_15
+M7 N7_4 pp N7_2
+M7 N7_6 pp N7_13
+M7 N7_1 pp N7_9
+M7 N7_12 pp N7_5
+M7 N7_6 pp N7_16
+M7 N7_16 pp N7_2
+M7 N7_7 pp N7_17
+M7 N7_7 pp N7_16
+M7 N7_7 pp N7_8
+M7 N7_7 pp N7_10
+M7 N7_8 pp N7_6
+M7 N7_5 pp N7_17
+M7 N7_18 pp N7_2
+M7 N7_14 pp N7_4
+M7 N7_2 pp N7_12
+M7 N7_18 pp N7_14
+M7 N7_14 pp N7_3
+M7 N7_14 pp N7_7
+M7 N7_7 pp N7_4
+M7 N7_17 pp N7_11
+M7 N7_11 pp N7_8
+M7 N7_12 pp N7_3
+M7 N7_12 pp N7_9
+M7 N7_5 pp N7_19
+M7 N7_16 pp N7_19
+M7 N7_7 pp N7_20
+M7 N7_17 pp N7_12
+M7 N7_2 pp N7_14
+M7 N7_10 pp N7_5
+M7 N7_7 pp N7_4
+M7 N7_10 pp N7_12
+M7 N7_18 pp N7_15
+M7 N7_20 pp N7_6
+M8 N8_2 pp N8_6
+M8 N8_6 pp N8_3
+M8 N8_6 pp N8_1
+M8 N8_4 pp N8_3
+M8 N8_5 pp N8_3
+M8 N8_6 pp N8_2
+M8 N8_6 pp N8_1
+M8 N8_6 pp N8_4
+M8 N8_6 pp N8_3
+M8 N8_6 pp N8_1
+M8 N8_4 pp N8_3
+M8 N8_5 pp N8_4
+M9 N9_6 pp N9_3
+M9 N9_10 pp N9_2
+M9 N9_5 pp N9_1
+M9 N9_7 pp N9_9
+M9 N9_13 pp N9_12
+M9 N9_2 pp N9_6
+M9 N9_13 pp N9_12
+M9 N9_13 pp N9_7
+M9 N9_8 pp N9_1
+M9 N9_4 pp N9_3
+M9 N9_13 pp N9_4
+M9 N9_12 pp N9_13
+M9 N9_5 pp N9_9
+M9 N9_6 pp N9_9
+M9 N9_11 pp N9_1
+M9 N9_3 pp N9_5
+M9 N9_13 pp N9_12
+M9 N9_10 pp N9_9
+M9 N9_9 pp N9_12
+M9 N9_10 pp N9_8
+M9 N9_8 pp N9_5
+M9 N9_4 pp N9_6
+M9 N9_3 pp N9_7
+M9 N9_10 pp N9_5
+M9 N9_12 pp N9_3
+M9 N9_3 pp N9_13
+M10 N10_4 pp N10_6
+M10 N10_12 pp N10_6
+M10 N10_11 pp N10_13
+M10 N10_6 pp N10_1
+M10 N10_13 pp N10_3
+M10 N10_5 pp N10_11
+M10 N10_11 pp N10_6
+M10 N10_10 pp N10_2
+M10 N10_7 pp N10_3
+M10 N10_6 pp N10_13
+M10 N10_10 pp N10_1
+M10 N10_2 pp N10_11
+M10 N10_7 pp N10_3
+M10 N10_8 pp N10_12
+M10 N10_7 pp N10_12
+M10 N10_6 pp N10_13
+M10 N10_1 pp N10_7
+M10 N10_2 pp N10_11
+M10 N10_4 pp N10_3
+M10 N10_3 pp N10_9
+M10 N10_7 pp N10_11
+M10 N10_6 pp N10_1
+M10 N10_5 pp N10_1
+M10 N10_5 pp N10_9
+M10 N10_5 pp N10_12
+M10 N10_4 pp N10_5
+M11 N11_23 pp N11_17
+M11 N11_10 pp N11_27
+M11 N11_22 pp N11_12
+M11 N11_19 pp N11_7
+M11 N11_1 pp N11_7
+M11 N11_12 pp N11_9
+M11 N11_21 pp N11_10
+M11 N11_23 pp N11_1
+M11 N11_13 pp N11_14
+M11 N11_7 pp N11_19
+M11 N11_6 pp N11_12
+M11 N11_13 pp N11_12
+M11 N11_15 pp N11_22
+M11 N11_3 pp N11_17
+M11 N11_25 pp N11_16
+M11 N11_26 pp N11_21
+M11 N11_5 pp N11_27
+M11 N11_19 pp N11_20
+M11 N11_16 pp N11_20
+M11 N11_16 pp N11_12
+M11 N11_7 pp N11_2
+M11 N11_12 pp N11_14
+M11 N11_4 pp N11_2
+M11 N11_27 pp N11_2
+M11 N11_23 pp N11_5
+M11 N11_10 pp N11_22
+M11 N11_8 pp N11_10
+M11 N11_9 pp N11_3
+M11 N11_17 pp N11_22
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+MM M748 pp M650
+MM M384 pp M585
+MM M368 pp M247
+MM M532 pp M487
+MM M969 pp M777
+MM M972 pp M801
+MM M654 pp M383
+MM M804 pp M528
+MM M14 pp M844
+MM M591 pp M285
+MM M635 pp M827
+MM M62 pp M487
+MM M308 pp M822
+MM M391 pp M36
+MM M781 pp M213
+MM M247 pp M497
+MM M235 pp M330
+MM M995 pp M884
+MM M143 pp M593
+MM M950 pp M784
+MM M805 pp M656
+MM M310 pp M903
+MM M838 pp M416
+MM M978 pp M121
+MM M3 pp M835
+MM M675 pp M176
+MM M371 pp M567
+MM M518 pp M757
+MM M866 pp M934
+MM M705 pp M943
+MM M913 pp M536
+MM M588 pp M995
+MM M306 pp M305
+MM M956 pp M743
+MM M386 pp M76
+MM M73 pp M677
+MM M135 pp M819
+MM M543 pp M776
+MM M340 pp M506
+MM M467 pp M766
+MM M67 pp M619
+MM M813 pp M470
+MM M673 pp M92
+MM M20 pp M805
+MM M945 pp M253
+MM M947 pp M330
+MM M622 pp M245
+MM M228 pp M944
+MM M13 pp M672
+MM M509 pp M408
+MM M496 pp M864
+MM M115 pp M809
+MM M348 pp M599
+MM M885 pp M754
+MM M617 pp M456
+MM M702 pp M79
+MM M483 pp M183
+MM M399 pp M165
+MM M620 pp M161
+MM M892 pp M517
+MM M381 pp M330
+MM M848 pp M421
+MM M736 pp M442
+MM M460 pp M887
+MM M365 pp M393
+MM M167 pp M921
+MM M945 pp M417
+MM M731 pp M967
+MM M78 pp M80
+MM M141 pp M192
+MM M546 pp M417
+MM M509 pp M830
+MM M957 pp M821
+MM M146 pp M125
+MM M980 pp M24
+MM M222 pp M626
+MM M40 pp M386
+MM M686 pp M364
+MM M337 pp M768
+MM M431 pp M566
+MM M891 pp M819
+MM M953 pp M654
+MM M131 pp M901
+MM M933 pp M839
+MM M490 pp M848
+MM M469 pp M279
+MM M122 pp M127
+MM M246 pp M829
+MM M83 pp M203
+MM M904 pp M372
+MM M16
+MM M82
+MM M111
+MM M166
+MM M188
+MM M335
+MM M379
+MM M519
+MM M565
+MM M579
+MM M610
+MM M640
+MM M653
+MM M660
+MM M695
+MM M755
+MM M759
+MM M769
+MM M791
+MM M973
+MM M994
diff --git a/application/src/test/resources/testData/NNFData/100SmallNetworks.nnf b/application/src/test/resources/testData/NNFData/100SmallNetworks.nnf
new file mode 100644
index 0000000..63dd315
--- /dev/null
+++ b/application/src/test/resources/testData/NNFData/100SmallNetworks.nnf
@@ -0,0 +1,3728 @@
+# Generated with ./generate_networks
+# number_of_nested_networks = 100
+# min_nested_network_size = 5
+# max_nested_network_size = 30
+# link_factor = 2.0
+M1 N1_16 pp N1_15
+M1 N1_13 pp N1_1
+M1 N1_14 pp N1_6
+M1 N1_8 pp N1_11
+M1 N1_15 pp N1_8
+M1 N1_4 pp N1_12
+M1 N1_14 pp N1_11
+M1 N1_9 pp N1_1
+M1 N1_9 pp N1_14
+M1 N1_7 pp N1_15
+M1 N1_8 pp N1_4
+M1 N1_12 pp N1_4
+M1 N1_4 pp N1_15
+M1 N1_12 pp N1_10
+M1 N1_2 pp N1_12
+M1 N1_11 pp N1_2
+M1 N1_13 pp N1_6
+M1 N1_3 pp N1_16
+M1 N1_2 pp N1_12
+M1 N1_11 pp N1_2
+M1 N1_16 pp N1_8
+M1 N1_5 pp N1_13
+M1 N1_14 pp N1_13
+M1 N1_13 pp N1_5
+M1 N1_13 pp N1_15
+M1 N1_13 pp N1_4
+M1 N1_14 pp N1_9
+M1 N1_8 pp N1_5
+M1 N1_11 pp N1_1
+M1 N1_5 pp N1_16
+M1 N1_5 pp N1_8
+M1 N1_3 pp N1_11
+M2 N2_5 pp N2_16
+M2 N2_17 pp N2_18
+M2 N2_5 pp N2_1
+M2 N2_4 pp N2_11
+M2 N2_13 pp N2_7
+M2 N2_1 pp N2_11
+M2 N2_15 pp N2_10
+M2 N2_7 pp N2_2
+M2 N2_20 pp N2_16
+M2 N2_11 pp N2_16
+M2 N2_14 pp N2_18
+M2 N2_10 pp N2_16
+M2 N2_15 pp N2_13
+M2 N2_17 pp N2_11
+M2 N2_8 pp N2_9
+M2 N2_2 pp N2_15
+M2 N2_12 pp N2_13
+M2 N2_1 pp N2_16
+M2 N2_5 pp N2_17
+M2 N2_6 pp N2_19
+M2 N2_1 pp N2_8
+M2 N2_4 pp N2_5
+M2 N2_15 pp N2_20
+M2 N2_2 pp N2_8
+M2 N2_1 pp N2_18
+M2 N2_1 pp N2_14
+M2 N2_2 pp N2_7
+M2 N2_14 pp N2_16
+M2 N2_22 pp N2_9
+M2 N2_11 pp N2_8
+M2 N2_12 pp N2_4
+M2 N2_13 pp N2_6
+M2 N2_10 pp N2_12
+M2 N2_18 pp N2_7
+M2 N2_11 pp N2_4
+M2 N2_16 pp N2_7
+M2 N2_9 pp N2_22
+M2 N2_19 pp N2_6
+M2 N2_8 pp N2_20
+M2 N2_20 pp N2_13
+M2 N2_20 pp N2_13
+M2 N2_8 pp N2_14
+M2 N2_7 pp N2_4
+M2 N2_21 pp N2_15
+M2 N2_3
+M3 N3_4 pp N3_10
+M3 N3_3 pp N3_17
+M3 N3_16 pp N3_4
+M3 N3_7 pp N3_9
+M3 N3_13 pp N3_6
+M3 N3_14 pp N3_13
+M3 N3_17 pp N3_10
+M3 N3_14 pp N3_10
+M3 N3_5 pp N3_4
+M3 N3_12 pp N3_9
+M3 N3_9 pp N3_7
+M3 N3_12 pp N3_13
+M3 N3_16 pp N3_3
+M3 N3_9 pp N3_8
+M3 N3_4 pp N3_8
+M3 N3_5 pp N3_8
+M3 N3_13 pp N3_6
+M3 N3_12 pp N3_11
+M3 N3_8 pp N3_17
+M3 N3_6 pp N3_4
+M3 N3_6 pp N3_3
+M3 N3_17 pp N3_12
+M3 N3_14 pp N3_12
+M3 N3_14 pp N3_9
+M3 N3_11 pp N3_17
+M3 N3_8 pp N3_5
+M3 N3_9 pp N3_5
+M3 N3_12 pp N3_3
+M3 N3_9 pp N3_8
+M3 N3_2 pp N3_14
+M3 N3_12 pp N3_15
+M3 N3_14 pp N3_7
+M3 N3_8 pp N3_5
+M3 N3_17 pp N3_11
+M3 N3_1
+M4 N4_4 pp N4_22
+M4 N4_20 pp N4_19
+M4 N4_24 pp N4_7
+M4 N4_16 pp N4_9
+M4 N4_1 pp N4_27
+M4 N4_2 pp N4_17
+M4 N4_5 pp N4_10
+M4 N4_16 pp N4_3
+M4 N4_4 pp N4_9
+M4 N4_18 pp N4_2
+M4 N4_3 pp N4_1
+M4 N4_12 pp N4_27
+M4 N4_25 pp N4_13
+M4 N4_10 pp N4_19
+M4 N4_17 pp N4_23
+M4 N4_15 pp N4_19
+M4 N4_4 pp N4_16
+M4 N4_5 pp N4_23
+M4 N4_27 pp N4_14
+M4 N4_25 pp N4_21
+M4 N4_14 pp N4_21
+M4 N4_10 pp N4_23
+M4 N4_9 pp N4_18
+M4 N4_23 pp N4_19
+M4 N4_23 pp N4_25
+M4 N4_8 pp N4_4
+M4 N4_23 pp N4_14
+M4 N4_2 pp N4_23
+M4 N4_16 pp N4_27
+M4 N4_15 pp N4_16
+M4 N4_9 pp N4_6
+M4 N4_22 pp N4_27
+M4 N4_21 pp N4_27
+M4 N4_16 pp N4_10
+M4 N4_18 pp N4_10
+M4 N4_16 pp N4_18
+M4 N4_10 pp N4_22
+M4 N4_16 pp N4_22
+M4 N4_23 pp N4_22
+M4 N4_10 pp N4_1
+M4 N4_23 pp N4_4
+M4 N4_25 pp N4_7
+M4 N4_12 pp N4_26
+M4 N4_10 pp N4_2
+M4 N4_20 pp N4_25
+M4 N4_23 pp N4_13
+M4 N4_26 pp N4_15
+M4 N4_22 pp N4_17
+M4 N4_12 pp N4_7
+M4 N4_11 pp N4_13
+M4 N4_7 pp N4_6
+M4 N4_14 pp N4_3
+M4 N4_24 pp N4_11
+M4 N4_12 pp N4_2
+M5 N5_7 pp N5_4
+M5 N5_7 pp N5_5
+M5 N5_10 pp N5_8
+M5 N5_8 pp N5_1
+M5 N5_6 pp N5_3
+M5 N5_2 pp N5_1
+M5 N5_3 pp N5_2
+M5 N5_6 pp N5_1
+M5 N5_5 pp N5_6
+M5 N5_8 pp N5_1
+M5 N5_7 pp N5_3
+M5 N5_10 pp N5_8
+M5 N5_10 pp N5_4
+M5 N5_9 pp N5_10
+M5 N5_7 pp N5_9
+M5 N5_2 pp N5_4
+M5 N5_4 pp N5_7
+M5 N5_10 pp N5_7
+M5 N5_10 pp N5_2
+M5 N5_6 pp N5_9
+M6 N6_4 pp N6_2
+M6 N6_4 pp N6_1
+M6 N6_6 pp N6_7
+M6 N6_6 pp N6_3
+M6 N6_7 pp N6_4
+M6 N6_1 pp N6_5
+M6 N6_9 pp N6_6
+M6 N6_5 pp N6_1
+M6 N6_9 pp N6_8
+M6 N6_2 pp N6_6
+M6 N6_7 pp N6_2
+M6 N6_1 pp N6_6
+M6 N6_9 pp N6_7
+M6 N6_6 pp N6_9
+M6 N6_4 pp N6_5
+M6 N6_2 pp N6_5
+M6 N6_9 pp N6_3
+M6 N6_5 pp N6_2
+M7 N7_6 pp N7_1
+M7 N7_18 pp N7_17
+M7 N7_20 pp N7_25
+M7 N7_1 pp N7_10
+M7 N7_6 pp N7_1
+M7 N7_4 pp N7_20
+M7 N7_2 pp N7_4
+M7 N7_20 pp N7_19
+M7 N7_12 pp N7_4
+M7 N7_20 pp N7_5
+M7 N7_7 pp N7_21
+M7 N7_23 pp N7_14
+M7 N7_20 pp N7_18
+M7 N7_2 pp N7_23
+M7 N7_7 pp N7_9
+M7 N7_18 pp N7_5
+M7 N7_4 pp N7_15
+M7 N7_19 pp N7_25
+M7 N7_12 pp N7_23
+M7 N7_8 pp N7_19
+M7 N7_20 pp N7_21
+M7 N7_2 pp N7_5
+M7 N7_24 pp N7_22
+M7 N7_6 pp N7_24
+M7 N7_22 pp N7_15
+M7 N7_21 pp N7_2
+M7 N7_23 pp N7_19
+M7 N7_21 pp N7_22
+M7 N7_13 pp N7_17
+M7 N7_17 pp N7_20
+M7 N7_12 pp N7_22
+M7 N7_4 pp N7_15
+M7 N7_1 pp N7_19
+M7 N7_9 pp N7_19
+M7 N7_4 pp N7_9
+M7 N7_18 pp N7_23
+M7 N7_2 pp N7_3
+M7 N7_18 pp N7_12
+M7 N7_23 pp N7_10
+M7 N7_21 pp N7_24
+M7 N7_24 pp N7_5
+M7 N7_4 pp N7_23
+M7 N7_10 pp N7_11
+M7 N7_21 pp N7_10
+M7 N7_3 pp N7_15
+M7 N7_18 pp N7_17
+M7 N7_16 pp N7_19
+M7 N7_20 pp N7_12
+M7 N7_7 pp N7_23
+M7 N7_5 pp N7_6
+M8 N8_15 pp N8_8
+M8 N8_17 pp N8_2
+M8 N8_13 pp N8_12
+M8 N8_3 pp N8_14
+M8 N8_1 pp N8_10
+M8 N8_10 pp N8_13
+M8 N8_11 pp N8_14
+M8 N8_6 pp N8_5
+M8 N8_14 pp N8_17
+M8 N8_15 pp N8_14
+M8 N8_9 pp N8_18
+M8 N8_15 pp N8_4
+M8 N8_2 pp N8_16
+M8 N8_7 pp N8_11
+M8 N8_4 pp N8_10
+M8 N8_9 pp N8_10
+M8 N8_16 pp N8_4
+M8 N8_4 pp N8_10
+M8 N8_6 pp N8_16
+M8 N8_8 pp N8_7
+M8 N8_8 pp N8_2
+M8 N8_8 pp N8_9
+M8 N8_7 pp N8_5
+M8 N8_6 pp N8_13
+M8 N8_10 pp N8_5
+M8 N8_4 pp N8_1
+M8 N8_10 pp N8_17
+M8 N8_9 pp N8_15
+M8 N8_2 pp N8_1
+M8 N8_11 pp N8_13
+M8 N8_16 pp N8_6
+M8 N8_8 pp N8_9
+M8 N8_16 pp N8_7
+M8 N8_18 pp N8_2
+M8 N8_6 pp N8_12
+M8 N8_1 pp N8_10
+M9 N9_1 pp N9_4
+M9 N9_2 pp N9_18
+M9 N9_8 pp N9_16
+M9 N9_22 pp N9_17
+M9 N9_8 pp N9_22
+M9 N9_16 pp N9_6
+M9 N9_8 pp N9_10
+M9 N9_21 pp N9_5
+M9 N9_19 pp N9_5
+M9 N9_5 pp N9_9
+M9 N9_6 pp N9_8
+M9 N9_19 pp N9_9
+M9 N9_21 pp N9_20
+M9 N9_5 pp N9_13
+M9 N9_5 pp N9_3
+M9 N9_13 pp N9_20
+M9 N9_6 pp N9_17
+M9 N9_21 pp N9_9
+M9 N9_12 pp N9_20
+M9 N9_20 pp N9_18
+M9 N9_13 pp N9_3
+M9 N9_13 pp N9_19
+M9 N9_19 pp N9_5
+M9 N9_12 pp N9_19
+M9 N9_21 pp N9_11
+M9 N9_12 pp N9_11
+M9 N9_10 pp N9_22
+M9 N9_6 pp N9_8
+M9 N9_6 pp N9_9
+M9 N9_22 pp N9_18
+M9 N9_22 pp N9_21
+M9 N9_6 pp N9_5
+M9 N9_11 pp N9_2
+M9 N9_3 pp N9_14
+M9 N9_14 pp N9_15
+M9 N9_5 pp N9_14
+M9 N9_7 pp N9_4
+M9 N9_7 pp N9_2
+M9 N9_14 pp N9_7
+M9 N9_9 pp N9_15
+M9 N9_11 pp N9_2
+M9 N9_17 pp N9_16
+M9 N9_5 pp N9_18
+M9 N9_16 pp N9_8
+M10 N10_7 pp N10_11
+M10 N10_19 pp N10_11
+M10 N10_20 pp N10_10
+M10 N10_9 pp N10_5
+M10 N10_13 pp N10_1
+M10 N10_8 pp N10_20
+M10 N10_7 pp N10_21
+M10 N10_4 pp N10_12
+M10 N10_11 pp N10_7
+M10 N10_3 pp N10_12
+M10 N10_18 pp N10_2
+M10 N10_19 pp N10_1
+M10 N10_9 pp N10_6
+M10 N10_3 pp N10_8
+M10 N10_18 pp N10_6
+M10 N10_10 pp N10_7
+M10 N10_7 pp N10_5
+M10 N10_16 pp N10_3
+M10 N10_17 pp N10_3
+M10 N10_1 pp N10_20
+M10 N10_16 pp N10_1
+M10 N10_20 pp N10_3
+M10 N10_7 pp N10_19
+M10 N10_17 pp N10_20
+M10 N10_10 pp N10_11
+M10 N10_4 pp N10_21
+M10 N10_16 pp N10_14
+M10 N10_4 pp N10_10
+M10 N10_18 pp N10_8
+M10 N10_13 pp N10_16
+M10 N10_1 pp N10_7
+M10 N10_18 pp N10_13
+M10 N10_14 pp N10_7
+M10 N10_17 pp N10_8
+M10 N10_20 pp N10_9
+M10 N10_16 pp N10_5
+M10 N10_20 pp N10_3
+M10 N10_14 pp N10_9
+M10 N10_5 pp N10_6
+M10 N10_2 pp N10_20
+M10 N10_10 pp N10_20
+M10 N10_10 pp N10_17
+M10 N10_15
+M11 N11_8 pp N11_5
+M11 N11_6 pp N11_9
+M11 N11_9 pp N11_4
+M11 N11_4 pp N11_2
+M11 N11_1 pp N11_6
+M11 N11_5 pp N11_6
+M11 N11_2 pp N11_4
+M11 N11_5 pp N11_3
+M11 N11_4 pp N11_3
+M11 N11_5 pp N11_4
+M11 N11_7 pp N11_4
+M11 N11_8 pp N11_4
+M11 N11_9 pp N11_8
+M11 N11_3 pp N11_4
+M11 N11_8 pp N11_7
+M11 N11_3 pp N11_5
+M11 N11_1 pp N11_5
+M11 N11_2 pp N11_8
+M12 N12_4 pp N12_3
+M12 N12_5 pp N12_10
+M12 N12_13 pp N12_16
+M12 N12_9 pp N12_16
+M12 N12_6 pp N12_1
+M12 N12_3 pp N12_6
+M12 N12_14 pp N12_8
+M12 N12_8 pp N12_16
+M12 N12_9 pp N12_6
+M12 N12_15 pp N12_7
+M12 N12_3 pp N12_6
+M12 N12_9 pp N12_3
+M12 N12_1 pp N12_11
+M12 N12_4 pp N12_16
+M12 N12_2 pp N12_12
+M12 N12_13 pp N12_15
+M12 N12_17 pp N12_10
+M12 N12_4 pp N12_1
+M12 N12_4 pp N12_13
+M12 N12_7 pp N12_3
+M12 N12_5 pp N12_14
+M12 N12_16 pp N12_11
+M12 N12_6 pp N12_15
+M12 N12_7 pp N12_3
+M12 N12_11 pp N12_14
+M12 N12_2 pp N12_17
+M12 N12_9 pp N12_5
+M12 N12_11 pp N12_2
+M12 N12_11 pp N12_4
+M12 N12_3 pp N12_14
+M12 N12_13 pp N12_5
+M12 N12_14 pp N12_7
+M12 N12_6 pp N12_2
+M12 N12_5 pp N12_14
+M13 N13_11 pp N13_1
+M13 N13_5 pp N13_8
+M13 N13_4 pp N13_1
+M13 N13_8 pp N13_9
+M13 N13_9 pp N13_11
+M13 N13_6 pp N13_7
+M13 N13_5 pp N13_3
+M13 N13_10 pp N13_3
+M13 N13_2 pp N13_11
+M13 N13_5 pp N13_9
+M13 N13_10 pp N13_5
+M13 N13_8 pp N13_3
+M13 N13_7 pp N13_8
+M13 N13_5 pp N13_4
+M13 N13_2 pp N13_6
+M13 N13_8 pp N13_6
+M13 N13_1 pp N13_10
+M13 N13_1 pp N13_10
+M13 N13_1 pp N13_3
+M13 N13_6 pp N13_4
+M13 N13_2 pp N13_9
+M13 N13_10 pp N13_2
+M14 N14_19 pp N14_5
+M14 N14_24 pp N14_16
+M14 N14_4 pp N14_12
+M14 N14_13 pp N14_6
+M14 N14_18 pp N14_9
+M14 N14_15 pp N14_20
+M14 N14_11 pp N14_1
+M14 N14_10 pp N14_1
+M14 N14_14 pp N14_5
+M14 N14_22 pp N14_4
+M14 N14_22 pp N14_23
+M14 N14_2 pp N14_1
+M14 N14_11 pp N14_14
+M14 N14_20 pp N14_8
+M14 N14_23 pp N14_12
+M14 N14_7 pp N14_23
+M14 N14_20 pp N14_27
+M14 N14_24 pp N14_17
+M14 N14_22 pp N14_6
+M14 N14_4 pp N14_15
+M14 N14_25 pp N14_17
+M14 N14_2 pp N14_17
+M14 N14_24 pp N14_23
+M14 N14_4 pp N14_14
+M14 N14_17 pp N14_11
+M14 N14_12 pp N14_1
+M14 N14_6 pp N14_8
+M14 N14_12 pp N14_25
+M14 N14_14 pp N14_9
+M14 N14_24 pp N14_27
+M14 N14_25 pp N14_2
+M14 N14_5 pp N14_6
+M14 N14_26 pp N14_5
+M14 N14_8 pp N14_9
+M14 N14_18 pp N14_16
+M14 N14_5 pp N14_11
+M14 N14_26 pp N14_6
+M14 N14_17 pp N14_20
+M14 N14_6 pp N14_24
+M14 N14_22 pp N14_12
+M14 N14_5 pp N14_4
+M14 N14_16 pp N14_7
+M14 N14_22 pp N14_1
+M14 N14_15 pp N14_12
+M14 N14_12 pp N14_7
+M14 N14_2 pp N14_16
+M14 N14_4 pp N14_24
+M14 N14_7 pp N14_14
+M14 N14_20 pp N14_19
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+M100 N100_10 pp N100_1
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+M100 N100_1 pp N100_4
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+M100 N100_6 pp N100_7
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+M100 N100_7 pp N100_2
+M100 N100_9
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+MM M62 pp M50
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+MM M82 pp M4
+MM M21
+MM M95
+MM M98
diff --git a/application/src/test/resources/testData/NNFData/10LargeNetworks.nnf b/application/src/test/resources/testData/NNFData/10LargeNetworks.nnf
new file mode 100644
index 0000000..92f3083
--- /dev/null
+++ b/application/src/test/resources/testData/NNFData/10LargeNetworks.nnf
@@ -0,0 +1,87381 @@
+# Generated with ./generate_networks
+# number_of_nested_networks = 10
+# min_nested_network_size = 5000
+# max_nested_network_size = 10000
+# link_factor = 1.0
+M1 N1_3558 pp N1_467
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+M10 N10_4741
+M10 N10_4742
+M10 N10_4745
+M10 N10_4763
+M10 N10_4768
+M10 N10_4794
+M10 N10_4796
+M10 N10_4803
+M10 N10_4806
+M10 N10_4818
+M10 N10_4820
+M10 N10_4822
+M10 N10_4835
+M10 N10_4839
+M10 N10_4842
+M10 N10_4846
+M10 N10_4854
+M10 N10_4855
+M10 N10_4860
+M10 N10_4875
+M10 N10_4885
+M10 N10_4886
+M10 N10_4888
+M10 N10_4891
+M10 N10_4906
+M10 N10_4912
+M10 N10_4914
+M10 N10_4916
+M10 N10_4930
+M10 N10_4935
+M10 N10_4939
+M10 N10_4953
+M10 N10_4970
+M10 N10_4977
+M10 N10_4978
+M10 N10_4986
+M10 N10_5006
+M10 N10_5016
+M10 N10_5026
+M10 N10_5045
+M10 N10_5069
+M10 N10_5073
+M10 N10_5077
+M10 N10_5093
+M10 N10_5094
+M10 N10_5095
+M10 N10_5103
+M10 N10_5104
+M10 N10_5108
+M10 N10_5135
+M10 N10_5150
+M10 N10_5153
+M10 N10_5157
+M10 N10_5175
+M10 N10_5188
+M10 N10_5195
+M10 N10_5197
+M10 N10_5205
+M10 N10_5211
+M10 N10_5218
+M10 N10_5223
+M10 N10_5240
+M10 N10_5248
+M10 N10_5253
+M10 N10_5256
+M10 N10_5279
+M10 N10_5282
+M10 N10_5283
+M10 N10_5301
+M10 N10_5312
+M10 N10_5323
+M10 N10_5326
+M10 N10_5328
+M10 N10_5330
+M10 N10_5333
+M10 N10_5338
+M10 N10_5348
+M10 N10_5354
+M10 N10_5377
+M10 N10_5378
+M10 N10_5384
+M10 N10_5386
+M10 N10_5390
+M10 N10_5395
+M10 N10_5407
+M10 N10_5414
+M10 N10_5419
+M10 N10_5422
+M10 N10_5424
+M10 N10_5427
+M10 N10_5437
+M10 N10_5441
+M10 N10_5454
+M10 N10_5462
+M10 N10_5476
+M10 N10_5482
+M10 N10_5490
+M10 N10_5497
+M10 N10_5505
+M10 N10_5510
+M10 N10_5519
+M10 N10_5520
+M10 N10_5521
+M10 N10_5525
+M10 N10_5527
+M10 N10_5532
+M10 N10_5533
+M10 N10_5559
+M10 N10_5562
+M10 N10_5578
+M10 N10_5590
+M10 N10_5603
+M10 N10_5609
+M10 N10_5611
+M10 N10_5613
+M10 N10_5621
+M10 N10_5639
+M10 N10_5640
+M10 N10_5650
+M10 N10_5666
+M10 N10_5670
+M10 N10_5674
+M10 N10_5694
+M10 N10_5696
+M10 N10_5702
+M10 N10_5703
+M10 N10_5704
+M10 N10_5716
+M10 N10_5720
+M10 N10_5723
+M10 N10_5735
+M10 N10_5740
+M10 N10_5743
+M10 N10_5747
+M10 N10_5751
+M10 N10_5753
+M10 N10_5756
+M10 N10_5763
+M10 N10_5764
+M10 N10_5786
+M10 N10_5790
+M10 N10_5793
+M10 N10_5801
+M10 N10_5802
+M10 N10_5805
+M10 N10_5809
+M10 N10_5810
+M10 N10_5811
+M10 N10_5815
+M10 N10_5818
+M10 N10_5821
+M10 N10_5823
+M10 N10_5826
+M10 N10_5839
+M10 N10_5847
+M10 N10_5860
+M10 N10_5861
+M10 N10_5878
+M10 N10_5880
+M10 N10_5881
+M10 N10_5890
+M10 N10_5902
+M10 N10_5918
+M10 N10_5920
+M10 N10_5932
+M10 N10_5947
+M10 N10_5948
+M10 N10_5950
+M10 N10_5951
+M10 N10_5953
+M10 N10_5957
+M10 N10_5960
+M10 N10_5963
+M10 N10_5965
+M10 N10_5976
+M10 N10_5977
+M10 N10_5994
+M10 N10_5995
+M10 N10_6001
+M10 N10_6005
+M10 N10_6006
+M10 N10_6025
+M10 N10_6030
+M10 N10_6035
+M10 N10_6048
+M10 N10_6059
+M10 N10_6064
+M10 N10_6068
+M10 N10_6082
+M10 N10_6095
+M10 N10_6100
+M10 N10_6106
+M10 N10_6118
+M10 N10_6120
+M10 N10_6146
+M10 N10_6149
+M10 N10_6150
+M10 N10_6159
+M10 N10_6170
+M10 N10_6175
+M10 N10_6182
+M10 N10_6184
+M10 N10_6188
+M10 N10_6196
+M10 N10_6201
+M10 N10_6220
+M10 N10_6229
+M10 N10_6242
+M10 N10_6246
+M10 N10_6257
+M10 N10_6287
+M10 N10_6299
+M10 N10_6315
+M10 N10_6321
+M10 N10_6335
+M10 N10_6336
+M10 N10_6342
+M10 N10_6346
+M10 N10_6358
+M10 N10_6363
+M10 N10_6375
+M10 N10_6383
+M10 N10_6385
+M10 N10_6403
+M10 N10_6404
+M10 N10_6411
+M10 N10_6419
+M10 N10_6423
+M10 N10_6426
+M10 N10_6428
+M10 N10_6436
+M10 N10_6437
+M10 N10_6445
+M10 N10_6450
+M10 N10_6454
+M10 N10_6466
+M10 N10_6469
+M10 N10_6492
+M10 N10_6498
+M10 N10_6517
+M10 N10_6520
+M10 N10_6522
+M10 N10_6527
+M10 N10_6528
+M10 N10_6534
+M10 N10_6535
+M10 N10_6536
+M10 N10_6544
+M10 N10_6551
+M10 N10_6552
+M10 N10_6553
+M10 N10_6555
+M10 N10_6557
+M10 N10_6574
+M10 N10_6586
+M10 N10_6592
+M10 N10_6597
+M10 N10_6629
+M10 N10_6634
+M10 N10_6635
+M10 N10_6645
+M10 N10_6646
+M10 N10_6650
+M10 N10_6653
+M10 N10_6658
+M10 N10_6664
+M10 N10_6670
+M10 N10_6674
+M10 N10_6682
+M10 N10_6723
+M10 N10_6726
+M10 N10_6732
+M10 N10_6733
+M10 N10_6740
+M10 N10_6750
+M10 N10_6757
+M10 N10_6765
+M10 N10_6774
+M10 N10_6777
+M10 N10_6787
+M10 N10_6789
+M10 N10_6808
+M10 N10_6812
+M10 N10_6822
+M10 N10_6829
+M10 N10_6849
+M10 N10_6851
+M10 N10_6866
+M10 N10_6868
+M10 N10_6874
+M10 N10_6881
+M10 N10_6891
+M10 N10_6892
+M10 N10_6893
+M10 N10_6896
+M10 N10_6908
+M10 N10_6911
+M10 N10_6915
+M10 N10_6932
+M10 N10_6933
+M10 N10_6942
+M10 N10_6945
+M10 N10_6954
+M10 N10_6958
+M10 N10_6973
+M10 N10_6976
+M10 N10_6983
+M10 N10_6999
+M10 N10_7019
+M10 N10_7023
+M10 N10_7025
+M10 N10_7030
+M10 N10_7043
+M10 N10_7045
+M10 N10_7048
+M10 N10_7052
+M10 N10_7056
+M10 N10_7065
+M10 N10_7067
+M10 N10_7075
+M10 N10_7090
+M10 N10_7099
+M10 N10_7100
+M10 N10_7102
+M10 N10_7113
+M10 N10_7121
+M10 N10_7124
+M10 N10_7134
+M10 N10_7135
+M10 N10_7141
+M10 N10_7152
+M10 N10_7159
+M10 N10_7169
+M10 N10_7175
+M10 N10_7178
+M10 N10_7191
+M10 N10_7192
+M10 N10_7205
+M10 N10_7211
+M10 N10_7212
+M10 N10_7223
+M10 N10_7233
+M10 N10_7237
+M10 N10_7249
+M10 N10_7263
+M10 N10_7266
+M10 N10_7280
+M10 N10_7281
+M10 N10_7286
+M10 N10_7299
+M10 N10_7307
+M10 N10_7311
+M10 N10_7312
+M10 N10_7316
+M10 N10_7341
+M10 N10_7349
+M10 N10_7364
+M10 N10_7365
+M10 N10_7375
+M10 N10_7382
+M10 N10_7399
+M10 N10_7409
+M10 N10_7417
+M10 N10_7420
+M10 N10_7423
+M10 N10_7425
+M10 N10_7428
+M10 N10_7444
+M10 N10_7462
+M10 N10_7465
+M10 N10_7466
+M10 N10_7471
+M10 N10_7476
+M10 N10_7477
+M10 N10_7478
+M10 N10_7479
+M10 N10_7500
+M10 N10_7503
+M10 N10_7505
+M10 N10_7509
+M10 N10_7514
+M10 N10_7518
+M10 N10_7525
+M10 N10_7555
+M10 N10_7565
+M10 N10_7574
+M10 N10_7577
+M10 N10_7583
+M10 N10_7587
+M10 N10_7588
+M10 N10_7591
+M10 N10_7600
+M10 N10_7619
+M10 N10_7627
+M10 N10_7630
+M10 N10_7634
+M10 N10_7636
+M10 N10_7637
+M10 N10_7640
+M10 N10_7647
+M10 N10_7670
+M10 N10_7671
+M10 N10_7693
+M10 N10_7694
+M10 N10_7714
+M10 N10_7733
+M10 N10_7737
+M10 N10_7750
+M10 N10_7758
+M10 N10_7759
+M10 N10_7785
+M10 N10_7788
+M10 N10_7791
+M10 N10_7795
+M10 N10_7804
+M10 N10_7808
+M10 N10_7814
+M10 N10_7824
+M10 N10_7826
+M10 N10_7839
+M10 N10_7845
+M10 N10_7854
+M10 N10_7858
+M10 N10_7860
+M10 N10_7867
+M10 N10_7872
+M10 N10_7873
+M10 N10_7890
+M10 N10_7902
+M10 N10_7909
+M10 N10_7911
+M10 N10_7914
+M10 N10_7920
+M10 N10_7924
+M10 N10_7928
+M10 N10_7929
+M10 N10_7936
+M10 N10_7950
+M10 N10_7975
+M10 N10_7979
+M10 N10_7986
+M10 N10_7994
+M10 N10_8005
+M10 N10_8018
+M10 N10_8031
+M10 N10_8032
+M10 N10_8052
+M10 N10_8060
+M10 N10_8067
+M10 N10_8069
+M10 N10_8071
+M10 N10_8073
+M10 N10_8078
+M10 N10_8082
+M10 N10_8083
+M10 N10_8086
+M10 N10_8091
+M10 N10_8117
+M10 N10_8121
+M10 N10_8131
+M10 N10_8135
+M10 N10_8138
+MM M2 pp M7
+MM M1 pp M7
+MM M8 pp M7
+MM M5 pp M4
+MM M6 pp M2
+MM M4 pp M5
+MM M1 pp M9
+MM M3 pp M10
+MM M4 pp M3
+MM M4 pp M1
diff --git a/application/src/test/resources/testData/NNFData/300SmallNetworks.nnf b/application/src/test/resources/testData/NNFData/300SmallNetworks.nnf
new file mode 100644
index 0000000..d7006d1
--- /dev/null
+++ b/application/src/test/resources/testData/NNFData/300SmallNetworks.nnf
@@ -0,0 +1,6396 @@
+# Generated with ./generate_networks
+# number_of_nested_networks = 300
+# min_nested_network_size = 5
+# max_nested_network_size = 30
+# link_factor = 1.0
+M1 N1_1 pp N1_8
+M1 N1_7 pp N1_13
+M1 N1_19 pp N1_10
+M1 N1_16 pp N1_12
+M1 N1_4 pp N1_7
+M1 N1_1 pp N1_11
+M1 N1_15 pp N1_13
+M1 N1_18 pp N1_7
+M1 N1_5 pp N1_8
+M1 N1_6 pp N1_8
+M1 N1_2 pp N1_4
+M1 N1_20 pp N1_16
+M1 N1_17 pp N1_20
+M1 N1_13 pp N1_6
+M1 N1_20 pp N1_4
+M1 N1_19 pp N1_1
+M1 N1_6 pp N1_9
+M1 N1_8 pp N1_9
+M1 N1_15 pp N1_5
+M1 N1_13 pp N1_10
+M1 N1_3
+M1 N1_14
+M2 N2_3 pp N2_13
+M2 N2_12 pp N2_16
+M2 N2_9 pp N2_17
+M2 N2_17 pp N2_3
+M2 N2_15 pp N2_13
+M2 N2_7 pp N2_16
+M2 N2_14 pp N2_8
+M2 N2_10 pp N2_2
+M2 N2_11 pp N2_5
+M2 N2_9 pp N2_18
+M2 N2_17 pp N2_15
+M2 N2_13 pp N2_9
+M2 N2_17 pp N2_5
+M2 N2_10 pp N2_15
+M2 N2_7 pp N2_16
+M2 N2_6 pp N2_15
+M2 N2_8 pp N2_16
+M2 N2_11 pp N2_5
+M2 N2_1
+M2 N2_4
+M3 N3_9 pp N3_4
+M3 N3_1 pp N3_9
+M3 N3_3 pp N3_5
+M3 N3_9 pp N3_8
+M3 N3_3 pp N3_5
+M3 N3_6 pp N3_4
+M3 N3_2 pp N3_9
+M3 N3_1 pp N3_4
+M3 N3_4 pp N3_9
+M3 N3_7
+M4 N4_5 pp N4_1
+M4 N4_1 pp N4_4
+M4 N4_1 pp N4_3
+M4 N4_4 pp N4_2
+M4 N4_2 pp N4_3
+M4 N4_4 pp N4_2
+M4 N4_6
+M5 N5_1 pp N5_6
+M5 N5_9 pp N5_7
+M5 N5_7 pp N5_8
+M5 N5_5 pp N5_10
+M5 N5_11 pp N5_3
+M5 N5_3 pp N5_10
+M5 N5_9 pp N5_4
+M5 N5_4 pp N5_9
+M5 N5_10 pp N5_9
+M5 N5_6 pp N5_3
+M5 N5_10 pp N5_7
+M5 N5_2
+M6 N6_6 pp N6_2
+M6 N6_11 pp N6_12
+M6 N6_24 pp N6_2
+M6 N6_9 pp N6_1
+M6 N6_22 pp N6_24
+M6 N6_18 pp N6_25
+M6 N6_10 pp N6_13
+M6 N6_9 pp N6_10
+M6 N6_25 pp N6_16
+M6 N6_1 pp N6_7
+M6 N6_9 pp N6_12
+M6 N6_24 pp N6_4
+M6 N6_12 pp N6_18
+M6 N6_7 pp N6_15
+M6 N6_16 pp N6_12
+M6 N6_17 pp N6_9
+M6 N6_9 pp N6_13
+M6 N6_8 pp N6_6
+M6 N6_2 pp N6_19
+M6 N6_15 pp N6_19
+M6 N6_3 pp N6_5
+M6 N6_21 pp N6_15
+M6 N6_1 pp N6_17
+M6 N6_21 pp N6_12
+M6 N6_23 pp N6_14
+M6 N6_20
+M7 N7_19 pp N7_9
+M7 N7_7 pp N7_23
+M7 N7_16 pp N7_17
+M7 N7_12 pp N7_11
+M7 N7_16 pp N7_10
+M7 N7_2 pp N7_5
+M7 N7_16 pp N7_25
+M7 N7_10 pp N7_27
+M7 N7_21 pp N7_24
+M7 N7_8 pp N7_29
+M7 N7_7 pp N7_3
+M7 N7_3 pp N7_12
+M7 N7_19 pp N7_1
+M7 N7_23 pp N7_1
+M7 N7_2 pp N7_15
+M7 N7_7 pp N7_10
+M7 N7_12 pp N7_18
+M7 N7_9 pp N7_13
+M7 N7_1 pp N7_25
+M7 N7_6 pp N7_8
+M7 N7_7 pp N7_21
+M7 N7_21 pp N7_15
+M7 N7_7 pp N7_15
+M7 N7_25 pp N7_7
+M7 N7_4 pp N7_23
+M7 N7_12 pp N7_26
+M7 N7_8 pp N7_7
+M7 N7_19 pp N7_11
+M7 N7_13 pp N7_20
+M7 N7_14
+M7 N7_22
+M7 N7_28
+M8 N8_11 pp N8_8
+M8 N8_8 pp N8_9
+M8 N8_7 pp N8_11
+M8 N8_10 pp N8_6
+M8 N8_5 pp N8_7
+M8 N8_10 pp N8_7
+M8 N8_10 pp N8_4
+M8 N8_8 pp N8_2
+M8 N8_5 pp N8_2
+M8 N8_9 pp N8_1
+M8 N8_9 pp N8_2
+M8 N8_3
+M9 N9_5 pp N9_9
+M9 N9_9 pp N9_6
+M9 N9_5 pp N9_6
+M9 N9_7 pp N9_17
+M9 N9_5 pp N9_19
+M9 N9_11 pp N9_6
+M9 N9_11 pp N9_4
+M9 N9_3 pp N9_17
+M9 N9_16 pp N9_5
+M9 N9_14 pp N9_16
+M9 N9_16 pp N9_14
+M9 N9_7 pp N9_2
+M9 N9_14 pp N9_18
+M9 N9_20 pp N9_6
+M9 N9_17 pp N9_11
+M9 N9_11 pp N9_16
+M9 N9_6 pp N9_16
+M9 N9_8 pp N9_10
+M9 N9_5 pp N9_3
+M9 N9_5 pp N9_6
+M9 N9_1
+M9 N9_12
+M9 N9_13
+M9 N9_15
+M10 N10_4 pp N10_2
+M10 N10_19 pp N10_20
+M10 N10_3 pp N10_14
+M10 N10_1 pp N10_12
+M10 N10_20 pp N10_3
+M10 N10_21 pp N10_1
+M10 N10_19 pp N10_15
+M10 N10_20 pp N10_21
+M10 N10_7 pp N10_8
+M10 N10_13 pp N10_8
+M10 N10_1 pp N10_22
+M10 N10_19 pp N10_15
+M10 N10_9 pp N10_16
+M10 N10_20 pp N10_12
+M10 N10_8 pp N10_2
+M10 N10_7 pp N10_19
+M10 N10_3 pp N10_18
+M10 N10_19 pp N10_15
+M10 N10_9 pp N10_17
+M10 N10_12 pp N10_3
+M10 N10_12 pp N10_6
+M10 N10_10 pp N10_15
+M10 N10_5
+M10 N10_11
+M11 N11_8 pp N11_10
+M11 N11_6 pp N11_9
+M11 N11_9 pp N11_8
+M11 N11_11 pp N11_9
+M11 N11_9 pp N11_11
+M11 N11_9 pp N11_1
+M11 N11_7 pp N11_5
+M11 N11_3 pp N11_7
+M11 N11_4 pp N11_5
+M11 N11_3 pp N11_8
+M11 N11_2 pp N11_3
+M12 N12_6 pp N12_11
+M12 N12_5 pp N12_1
+M12 N12_4 pp N12_3
+M12 N12_11 pp N12_6
+M12 N12_1 pp N12_11
+M12 N12_7 pp N12_1
+M12 N12_11 pp N12_7
+M12 N12_7 pp N12_6
+M12 N12_1 pp N12_9
+M12 N12_2 pp N12_5
+M12 N12_9 pp N12_5
+M12 N12_8
+M12 N12_10
+M13 N13_18 pp N13_14
+M13 N13_5 pp N13_3
+M13 N13_18 pp N13_22
+M13 N13_3 pp N13_9
+M13 N13_22 pp N13_9
+M13 N13_8 pp N13_21
+M13 N13_6 pp N13_18
+M13 N13_6 pp N13_20
+M13 N13_2 pp N13_10
+M13 N13_1 pp N13_3
+M13 N13_3 pp N13_21
+M13 N13_13 pp N13_10
+M13 N13_13 pp N13_12
+M13 N13_8 pp N13_4
+M13 N13_4 pp N13_12
+M13 N13_19 pp N13_10
+M13 N13_11 pp N13_17
+M13 N13_10 pp N13_14
+M13 N13_2 pp N13_17
+M13 N13_7 pp N13_19
+M13 N13_9 pp N13_3
+M13 N13_14 pp N13_7
+M13 N13_15
+M13 N13_16
+M14 N14_24 pp N14_16
+M14 N14_15 pp N14_28
+M14 N14_26 pp N14_12
+M14 N14_26 pp N14_24
+M14 N14_4 pp N14_20
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+M285 N285_2 pp N285_16
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+M288 N288_4 pp N288_13
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+M288 N288_6
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+M289 N289_8 pp N289_2
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+M291 N291_5 pp N291_6
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+M291 N291_4 pp N291_1
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+M291 N291_7 pp N291_2
+M291 N291_4 pp N291_2
+M292 N292_4 pp N292_6
+M292 N292_6 pp N292_14
+M292 N292_14 pp N292_16
+M292 N292_7 pp N292_12
+M292 N292_16 pp N292_13
+M292 N292_13 pp N292_5
+M292 N292_15 pp N292_8
+M292 N292_12 pp N292_15
+M292 N292_14 pp N292_5
+M292 N292_10 pp N292_12
+M292 N292_17 pp N292_11
+M292 N292_14 pp N292_7
+M292 N292_2 pp N292_5
+M292 N292_1 pp N292_17
+M292 N292_15 pp N292_2
+M292 N292_17 pp N292_5
+M292 N292_4 pp N292_12
+M292 N292_3
+M292 N292_9
+M293 N293_23 pp N293_7
+M293 N293_20 pp N293_6
+M293 N293_22 pp N293_16
+M293 N293_16 pp N293_22
+M293 N293_17 pp N293_4
+M293 N293_18 pp N293_24
+M293 N293_15 pp N293_8
+M293 N293_17 pp N293_16
+M293 N293_12 pp N293_24
+M293 N293_19 pp N293_8
+M293 N293_24 pp N293_25
+M293 N293_24 pp N293_17
+M293 N293_15 pp N293_5
+M293 N293_12 pp N293_4
+M293 N293_17 pp N293_13
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+M293 N293_25 pp N293_10
+M293 N293_21 pp N293_17
+M293 N293_25 pp N293_9
+M293 N293_9 pp N293_8
+M293 N293_1 pp N293_10
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+M293 N293_5 pp N293_7
+M293 N293_6 pp N293_8
+M293 N293_5 pp N293_20
+M293 N293_2
+M293 N293_3
+M293 N293_11
+M293 N293_14
+M294 N294_9 pp N294_2
+M294 N294_4 pp N294_7
+M294 N294_10 pp N294_7
+M294 N294_4 pp N294_5
+M294 N294_3 pp N294_10
+M294 N294_8 pp N294_3
+M294 N294_5 pp N294_9
+M294 N294_6 pp N294_8
+M294 N294_6 pp N294_2
+M294 N294_8 pp N294_4
+M294 N294_1
+M295 N295_6 pp N295_17
+M295 N295_16 pp N295_2
+M295 N295_12 pp N295_13
+M295 N295_6 pp N295_11
+M295 N295_6 pp N295_15
+M295 N295_2 pp N295_19
+M295 N295_17 pp N295_9
+M295 N295_13 pp N295_10
+M295 N295_6 pp N295_1
+M295 N295_9 pp N295_17
+M295 N295_10 pp N295_15
+M295 N295_8 pp N295_1
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+M295 N295_12 pp N295_16
+M295 N295_3
+M295 N295_7
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+M296 N296_29 pp N296_17
+M296 N296_11 pp N296_13
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+M296 N296_29 pp N296_17
+M296 N296_14 pp N296_17
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+M296 N296_7 pp N296_17
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+M296 N296_20 pp N296_19
+M296 N296_6 pp N296_9
+M296 N296_19 pp N296_7
+M296 N296_8 pp N296_23
+M296 N296_22 pp N296_28
+M296 N296_29 pp N296_16
+M296 N296_1
+M296 N296_5
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+M296 N296_15
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+M297 N297_22 pp N297_17
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+M297 N297_21 pp N297_22
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+MM M8
+MM M40
+MM M50
+MM M53
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+MM M65
+MM M72
+MM M78
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diff --git a/application/src/test/resources/testData/NNFData/5Nested.nnf b/application/src/test/resources/testData/NNFData/5Nested.nnf
new file mode 100644
index 0000000..5646340
--- /dev/null
+++ b/application/src/test/resources/testData/NNFData/5Nested.nnf
@@ -0,0 +1,50 @@
+# Generated with ./generate_networks
+# number_of_nested_networks = 5
+# min_nested_network_size = 5
+# max_nested_network_size = 10
+# link_factor = 1.0
+M1 N1_4 pp N1_5
+M1 N1_6 pp N1_4
+M1 N1_4 pp N1_5
+M1 N1_2 pp N1_6
+M1 N1_4 pp N1_2
+M1 N1_3 pp N1_5
+M1 N1_1
+M2 N2_5 pp N2_3
+M2 N2_2 pp N2_9
+M2 N2_6 pp N2_2
+M2 N2_6 pp N2_5
+M2 N2_3 pp N2_5
+M2 N2_3 pp N2_8
+M2 N2_1 pp N2_6
+M2 N2_7 pp N2_3
+M2 N2_7 pp N2_4
+M3 N3_2 pp N3_7
+M3 N3_3 pp N3_8
+M3 N3_9 pp N3_4
+M3 N3_6 pp N3_3
+M3 N3_6 pp N3_7
+M3 N3_3 pp N3_5
+M3 N3_1 pp N3_8
+M3 N3_2 pp N3_1
+M3 N3_5 pp N3_6
+M4 N4_3 pp N4_5
+M4 N4_4 pp N4_3
+M4 N4_2 pp N4_3
+M4 N4_1 pp N4_6
+M4 N4_5 pp N4_6
+M4 N4_3 pp N4_4
+M5 N5_4 pp N5_1
+M5 N5_4 pp N5_1
+M5 N5_6 pp N5_5
+M5 N5_2 pp N5_7
+M5 N5_1 pp N5_3
+M5 N5_4 pp N5_3
+M5 N5_4 pp N5_2
+M5 N5_5 pp N5_8
+MM M5 pp M2
+MM M2 pp M4
+MM M1 pp M5
+MM M2 pp M5
+MM M2 pp M5
+MM M3
diff --git a/application/src/test/resources/testData/NNFData/bad1.nnf b/application/src/test/resources/testData/NNFData/bad1.nnf
new file mode 100644
index 0000000..a78317c
--- /dev/null
+++ b/application/src/test/resources/testData/NNFData/bad1.nnf
@@ -0,0 +1,9 @@
+root M1 im M2
+root M3 im
+root M2 im M3
+root C pp M3
+root M2 pp C
+M1 A
+
+M2 A pp B
+M3 B pp C
diff --git a/application/src/test/resources/testData/NNFData/bad2.nnf b/application/src/test/resources/testData/NNFData/bad2.nnf
new file mode 100644
index 0000000..68b3ecf
--- /dev/null
+++ b/application/src/test/resources/testData/NNFData/bad2.nnf
@@ -0,0 +1,9 @@
+root M1 im M2
+root M3 im M1
+root M2 im M3
+root C pp M3 extra
+root M2 pp C
+M1 A
+
+M2 A pp B
+M3 B pp C
diff --git a/application/src/test/resources/testData/NNFData/calc_network_size b/application/src/test/resources/testData/NNFData/calc_network_size
new file mode 100755
index 0000000..83282bf
--- /dev/null
+++ b/application/src/test/resources/testData/NNFData/calc_network_size
@@ -0,0 +1,47 @@
+#! /usr/bin/env python
+"""
+Program for calculating the size of multilevel nested networks.
+"""
+import math, sys
+
+
+def Usage():
+ print "usage: " + sys.argv[0] + " no_of_nodes_per_network levels link_factor"
+ print "\twhere no_of_nodes_per_network is the number of nodes in each network."
+ print "\twhere levels is the number of network levels."
+ print "\twhere link_factor will be used to determine the number of links within a network. The number of links will be Round(size(network)*link_factor)"
+
+ sys.exit(1)
+
+
+# Command-line argument processing. Returns the triple (no_of_nodes_per_network, levels, link_factor).
+def ProcessArgs(argv):
+ if len(argv) != 4:
+ Usage()
+ try:
+ no_of_nodes_per_network = int(argv[1])
+ levels = int(argv[2])
+ link_factor = float(argv[3])
+ except ValueError:
+ Usage()
+
+ if no_of_nodes_per_network < 1 or levels < 1 or link_factor < 0.0:
+ Usage()
+
+ return (no_of_nodes_per_network, levels, link_factor)
+
+
+#
+# Start of main program.
+#
+
+(no_of_nodes_per_network, levels, link_factor) = ProcessArgs(sys.argv)
+
+
+total_no_of_networks = (math.pow(no_of_nodes_per_network, levels) - 1) / (no_of_nodes_per_network - 1)
+no_of_edges_per_network = int(no_of_nodes_per_network * link_factor + 0.5)
+total_no_of_nodes_plus_edges = total_no_of_networks * (no_of_nodes_per_network + no_of_edges_per_network)
+
+print "total_no_of_networks = " + str(total_no_of_networks)
+print "no_of_edges_per_network = " + str(no_of_edges_per_network)
+print "total_no_of_nodes_plus_edges = " + str(total_no_of_nodes_plus_edges)
diff --git a/application/src/test/resources/testData/NNFData/generate_multi_level_networks b/application/src/test/resources/testData/NNFData/generate_multi_level_networks
new file mode 100755
index 0000000..d299f92
--- /dev/null
+++ b/application/src/test/resources/testData/NNFData/generate_multi_level_networks
@@ -0,0 +1,117 @@
+#! /usr/bin/env python
+"""
+Program for generating multi-level nested network files.
+"""
+#from sets import Set
+from random import randint
+import sys, os, math
+
+
+def printf(format, *args):
+ print str(format) % args,
+
+
+def GenerateNetwork(network_name, node_prefix, no_of_nodes, no_of_links):
+ used_nodes = Set()
+ for i in range(0, no_of_links):
+ distinct = False
+ while not distinct:
+ end_point1 = randint(1, no_of_nodes)
+ end_point2 = randint(1, no_of_nodes)
+ distinct = end_point1 != end_point2
+ printf("%s %s%1d pp %s%1d\n", network_name, node_prefix, end_point1, node_prefix, end_point2)
+ used_nodes.add(end_point1)
+ used_nodes.add(end_point2)
+
+ for node_ID in range(1, no_of_nodes + 1):
+ if node_ID not in used_nodes:
+ printf("%s %s%1d\n", network_name, node_prefix, node_ID)
+
+
+def Usage():
+ print >> sys.stderr, "usage: " + sys.argv[0] + " levels object_count link_factor > NNF_file"
+ print >> sys.stderr, "\twhere levels is the number of network levels."
+ print >> sys.stderr, "\twhere object_count is the approximate total number of nodes and edges in all the networks."
+ print >> sys.stderr, "\twhere link_factor will be used to determine the number of links within a network. The number of links created will be Round(size(network)*link_factor)"
+
+ sys.exit(1)
+
+
+# Returns the approx. no of nodes per network.
+def CalcApproxNetworkSize(levels, link_factor, object_count):
+ def f(n):
+ return (1.0 + link_factor) * math.pow(n, levels + 1.0) - (1.0 + link_factor + object_count) * n + object_count
+ def f_prime(n):
+ return (1.0 + link_factor) * (levels + 1.0) * math.pow(n, levels) - 1.0 - link_factor - object_count
+ def root(k, x): # k-th root of x
+ return math.pow(x, 1.0 / k)
+
+ # Use Newton-Raphson to find the root of f()
+ no_of_nodes_per_network = root(levels, object_count) # initial approximation
+ iteration_count = 10
+ max_rel_error = 1.0e-10
+ while True:
+ old_no_of_nodes_per_network = no_of_nodes_per_network
+ no_of_nodes_per_network = no_of_nodes_per_network - f(no_of_nodes_per_network) / f_prime(no_of_nodes_per_network)
+ if math.fabs(old_no_of_nodes_per_network - no_of_nodes_per_network) < max_rel_error:
+ return no_of_nodes_per_network
+
+
+# Command-line argument processing. Returns the triple (levels, object_count, link_factor).
+def ProcessArgs(argv):
+ if len(argv) != 4:
+ Usage()
+ try:
+ levels = int(argv[1])
+ object_count = int(argv[2])
+ link_factor = float(argv[3])
+ except ValueError:
+ Usage()
+
+ if levels < 1 or object_count < 1 or link_factor < 0.0:
+ Usage()
+
+ return (levels, object_count, link_factor)
+
+
+#
+# Start of main program.
+#
+
+(levels, object_count, link_factor) = ProcessArgs(sys.argv)
+
+nodes_per_network = CalcApproxNetworkSize(levels, link_factor, object_count)
+edges_per_network = nodes_per_network * link_factor
+nodes_per_network = int(nodes_per_network + 0.5) # Round to nearest integer.
+edges_per_network = int(edges_per_network + 0.5) # Round to nearest integer.
+
+# Create a header comment for the output file:
+print "# Generated with " + sys.argv[0]
+print "# levels = " + str(levels)
+print "# approx. object_count = " + str(object_count)
+print "# link_factor = " + str(link_factor)
+print "# nodes_per_network = " + str(nodes_per_network)
+print "# edges_per_network = " + str(edges_per_network)
+
+actual_object_count = 0 # Counts the sum of all nodes and edges.
+no_of_networks = 1 # The number of networks on a level.
+for level in range(1, levels + 1):
+ if level > 1:
+ print # Output a blank line.
+
+# print "# Starting level " + str(level)
+
+ network_name_prefix = "L" + str(level) + "_"
+ for network in range(1, no_of_networks + 1):
+ network_name = network_name_prefix + str(network)
+ node_name_prefix = "L" + str(level + 1) + "_"
+# GenerateNetwork(network_name, node_name_prefix, nodes_per_network, edges_per_network)
+ actual_object_count += nodes_per_network + edges_per_network
+
+ no_of_networks *= nodes_per_network
+
+print "#\n# Sum of all nodes plus edges = " + str(actual_object_count)
+
+
+
+
diff --git a/application/src/test/resources/testData/NNFData/generate_networks b/application/src/test/resources/testData/NNFData/generate_networks
new file mode 100755
index 0000000..e357cdd
--- /dev/null
+++ b/application/src/test/resources/testData/NNFData/generate_networks
@@ -0,0 +1,78 @@
+#! /usr/bin/env python
+"""
+Program for generating random nested network files. First a list of networks will be generated and then a parent network in which every node contains one of the previously
+generated networks as a nested network.
+"""
+from sets import Set
+from random import randint
+import sys, os
+
+
+def printf(format, *args):
+ print str(format) % args,
+
+
+def GenerateNetwork(network_name, node_prefix, network_size, no_of_links):
+ used_nodes = Set()
+ for i in range(0, no_of_links):
+ distinct = False
+ while not distinct:
+ end_point1 = randint(1, network_size)
+ end_point2 = randint(1, network_size)
+ distinct = end_point1 != end_point2
+ printf("%s %s%1d pp %s%1d\n", network_name, node_prefix, end_point1, node_prefix, end_point2)
+ used_nodes.add(end_point1)
+ used_nodes.add(end_point2)
+
+ for node_ID in range(1, network_size + 1):
+ if node_ID not in used_nodes:
+ printf("%s %s%1d\n", network_name, node_prefix, node_ID)
+
+
+def Usage():
+ print >> sys.stderr, "usage: " + sys.argv[0] + " number_of_nested_networks min_network_size max_network_size link_factor > NNF_file"
+ print >> sys.stderr, "\twhere number_of_nested_networks is the number of child networks for the nodes of the final network that will be generated"
+ print >> sys.stderr, "\twhere min_network_size is the minimum size of a child or nested network"
+ print >> sys.stderr, "\twhere max_network_size is the maximum size of a child or nested network"
+ print >> sys.stderr, "\twhere link_factor will be used to determine the number of links within a child network and the final network. The number of links created will be Round(size(network)*link_factor)"
+
+ sys.exit(1)
+
+
+def ProcessArgs(argv):
+ if len(argv) != 5:
+ Usage()
+ try:
+ number_of_nested_networks = int(argv[1])
+ min_network_size = int(argv[2])
+ max_network_size = int(argv[3])
+ link_factor = float(argv[4])
+ except ValueError:
+ Usage()
+
+ if number_of_nested_networks < 1 or min_network_size < 1 or max_network_size < min_network_size or link_factor < 0.0:
+ Usage()
+
+ return (number_of_nested_networks, min_network_size, max_network_size, link_factor)
+
+
+(number_of_nested_networks, min_nested_network_size, max_nested_network_size, link_factor) = ProcessArgs(sys.argv)
+
+# Create a header comment for the output file:
+print "# Generated with " + sys.argv[0]
+print "# number_of_nested_networks = " + str(number_of_nested_networks)
+print "# min_nested_network_size = " + str(min_nested_network_size)
+print "# max_nested_network_size = " + str(max_nested_network_size)
+print "# link_factor = " + str(link_factor)
+
+# Generate the networks that will be nested networks:
+for nested_network_number in range(1, number_of_nested_networks + 1):
+ network_size = randint(min_nested_network_size, max_nested_network_size)
+ no_of_links = int(network_size * link_factor + 0.5)
+ network_name = "M" + str(nested_network_number)
+ node_prefix = "N" + str(nested_network_number) + "_"
+ GenerateNetwork(network_name, node_prefix, network_size, no_of_links)
+
+# Generate the network that will have all the nodes that are parents of the nested networks:
+no_of_links = int(number_of_nested_networks * link_factor + 0.5)
+GenerateNetwork("MM", "M", number_of_nested_networks, no_of_links)
diff --git a/application/src/test/resources/testData/NNFData/good1.nnf b/application/src/test/resources/testData/NNFData/good1.nnf
new file mode 100644
index 0000000..50baf7b
--- /dev/null
+++ b/application/src/test/resources/testData/NNFData/good1.nnf
@@ -0,0 +1,9 @@
+# A header comment
+ root C
+ # A random comment
+root network1
+
+network1 A pp B
+network1 B pp A
+root C pp B
+# A trailer comment
\ No newline at end of file
diff --git a/application/src/test/resources/testData/NNFData/good2.nnf b/application/src/test/resources/testData/NNFData/good2.nnf
new file mode 100644
index 0000000..95e4222
--- /dev/null
+++ b/application/src/test/resources/testData/NNFData/good2.nnf
@@ -0,0 +1,9 @@
+root M1
+root M2
+
+M1 A
+
+
+M2 B pp C
+root A pp B
+root M1 im M2
diff --git a/application/src/test/resources/testData/NNFData/good3.nnf b/application/src/test/resources/testData/NNFData/good3.nnf
new file mode 100644
index 0000000..73dfa99
--- /dev/null
+++ b/application/src/test/resources/testData/NNFData/good3.nnf
@@ -0,0 +1,9 @@
+Module_Overview M1 im M2
+Module_Overview M3 im M1
+Module_Overview M2 im M3
+Module_Overview C pp M3
+Module_Overview M2 pp C
+M1 A
+
+M2 A pp B
+M3 B pp C
diff --git a/application/src/test/resources/testData/NNFData/good4.nnf b/application/src/test/resources/testData/NNFData/good4.nnf
new file mode 100644
index 0000000..9246e1e
--- /dev/null
+++ b/application/src/test/resources/testData/NNFData/good4.nnf
@@ -0,0 +1,18 @@
+Top_Level_Network M1
+
+Top_Level_Network M3
+
+M1 A pp B
+M1 B pp A
+Top_Level_Network C pp B
+M3 M2
+
+M2 D
+
+M3 E pp F
+M3 D pp F
+M3 D pp E
+Top_Level_Network D pp C
+Top_Level_Network A pp M2
+Top_Level_Network B pp M3
+Top_Level_Network M2 pp B
\ No newline at end of file
diff --git a/application/src/test/resources/testData/NNFData/good5.nnf b/application/src/test/resources/testData/NNFData/good5.nnf
new file mode 100644
index 0000000..92d06b2
--- /dev/null
+++ b/application/src/test/resources/testData/NNFData/good5.nnf
@@ -0,0 +1,11 @@
+TopLevelNetwork M4
+
+M4 D
+
+M4 M3
+
+M3 M2 pp C
+M2 M1 pp B
+M1 A
+
+M4 C pp D
diff --git a/application/src/test/resources/testData/NNFData/good6.nnf b/application/src/test/resources/testData/NNFData/good6.nnf
new file mode 100644
index 0000000..beaf124
--- /dev/null
+++ b/application/src/test/resources/testData/NNFData/good6.nnf
@@ -0,0 +1,2 @@
+N1 a pp b
+N2 c pp a
diff --git a/application/src/test/resources/testData/NNFData/intermediate.nnf b/application/src/test/resources/testData/NNFData/intermediate.nnf
new file mode 100644
index 0000000..6c1aada
--- /dev/null
+++ b/application/src/test/resources/testData/NNFData/intermediate.nnf
@@ -0,0 +1,11195 @@
+# Generated with ./generate_networks
+# number_of_nested_networks = 200
+# min_nested_network_size = 20
+# max_nested_network_size = 50
+# link_factor = 1.5
+M1 N1_3 pp N1_16
+M1 N1_28 pp N1_36
+M1 N1_36 pp N1_37
+M1 N1_38 pp N1_23
+M1 N1_5 pp N1_16
+M1 N1_12 pp N1_38
+M1 N1_32 pp N1_9
+M1 N1_33 pp N1_40
+M1 N1_46 pp N1_6
+M1 N1_10 pp N1_32
+M1 N1_11 pp N1_13
+M1 N1_23 pp N1_43
+M1 N1_10 pp N1_33
+M1 N1_45 pp N1_11
+M1 N1_3 pp N1_33
+M1 N1_11 pp N1_24
+M1 N1_3 pp N1_24
+M1 N1_33 pp N1_19
+M1 N1_17 pp N1_25
+M1 N1_24 pp N1_9
+M1 N1_37 pp N1_35
+M1 N1_28 pp N1_3
+M1 N1_41 pp N1_44
+M1 N1_26 pp N1_37
+M1 N1_10 pp N1_36
+M1 N1_44 pp N1_30
+M1 N1_2 pp N1_45
+M1 N1_41 pp N1_28
+M1 N1_30 pp N1_31
+M1 N1_40 pp N1_4
+M1 N1_37 pp N1_43
+M1 N1_13 pp N1_20
+M1 N1_23 pp N1_8
+M1 N1_30 pp N1_32
+M1 N1_36 pp N1_42
+M1 N1_5 pp N1_34
+M1 N1_40 pp N1_4
+M1 N1_17 pp N1_15
+M1 N1_1 pp N1_21
+M1 N1_30 pp N1_34
+M1 N1_37 pp N1_35
+M1 N1_18 pp N1_42
+M1 N1_44 pp N1_31
+M1 N1_30 pp N1_27
+M1 N1_27 pp N1_5
+M1 N1_41 pp N1_16
+M1 N1_22 pp N1_10
+M1 N1_12 pp N1_8
+M1 N1_26 pp N1_33
+M1 N1_8 pp N1_27
+M1 N1_26 pp N1_41
+M1 N1_8 pp N1_18
+M1 N1_41 pp N1_42
+M1 N1_4 pp N1_24
+M1 N1_43 pp N1_7
+M1 N1_21 pp N1_14
+M1 N1_39 pp N1_32
+M1 N1_33 pp N1_28
+M1 N1_31 pp N1_14
+M1 N1_29 pp N1_45
+M1 N1_39 pp N1_31
+M1 N1_30 pp N1_6
+M1 N1_17 pp N1_3
+M1 N1_45 pp N1_13
+M1 N1_13 pp N1_36
+M1 N1_41 pp N1_28
+M1 N1_12 pp N1_44
+M1 N1_34 pp N1_24
+M1 N1_21 pp N1_34
+M2 N2_7 pp N2_3
+M2 N2_11 pp N2_16
+M2 N2_23 pp N2_8
+M2 N2_3 pp N2_22
+M2 N2_14 pp N2_6
+M2 N2_13 pp N2_6
+M2 N2_17 pp N2_3
+M2 N2_17 pp N2_4
+M2 N2_23 pp N2_19
+M2 N2_19 pp N2_21
+M2 N2_13 pp N2_21
+M2 N2_8 pp N2_28
+M2 N2_26 pp N2_17
+M2 N2_25 pp N2_4
+M2 N2_7 pp N2_1
+M2 N2_23 pp N2_12
+M2 N2_13 pp N2_7
+M2 N2_13 pp N2_29
+M2 N2_27 pp N2_25
+M2 N2_15 pp N2_4
+M2 N2_5 pp N2_29
+M2 N2_8 pp N2_26
+M2 N2_2 pp N2_23
+M2 N2_26 pp N2_24
+M2 N2_1 pp N2_4
+M2 N2_19 pp N2_15
+M2 N2_15 pp N2_6
+M2 N2_8 pp N2_21
+M2 N2_18 pp N2_27
+M2 N2_12 pp N2_13
+M2 N2_12 pp N2_5
+M2 N2_15 pp N2_1
+M2 N2_18 pp N2_8
+M2 N2_25 pp N2_3
+M2 N2_11 pp N2_9
+M2 N2_28 pp N2_21
+M2 N2_1 pp N2_9
+M2 N2_17 pp N2_5
+M2 N2_25 pp N2_17
+M2 N2_18 pp N2_19
+M2 N2_19 pp N2_6
+M2 N2_6 pp N2_24
+M2 N2_7 pp N2_23
+M2 N2_6 pp N2_7
+M2 N2_10
+M2 N2_20
+M3 N3_4 pp N3_6
+M3 N3_6 pp N3_21
+M3 N3_3 pp N3_25
+M3 N3_22 pp N3_4
+M3 N3_1 pp N3_19
+M3 N3_13 pp N3_14
+M3 N3_3 pp N3_19
+M3 N3_5 pp N3_8
+M3 N3_15 pp N3_17
+M3 N3_20 pp N3_24
+M3 N3_12 pp N3_14
+M3 N3_27 pp N3_16
+M3 N3_7 pp N3_11
+M3 N3_24 pp N3_26
+M3 N3_1 pp N3_13
+M3 N3_4 pp N3_23
+M3 N3_3 pp N3_22
+M3 N3_10 pp N3_7
+M3 N3_17 pp N3_7
+M3 N3_15 pp N3_21
+M3 N3_14 pp N3_2
+M3 N3_23 pp N3_8
+M3 N3_23 pp N3_15
+M3 N3_23 pp N3_10
+M3 N3_26 pp N3_7
+M3 N3_7 pp N3_15
+M3 N3_6 pp N3_8
+M3 N3_5 pp N3_14
+M3 N3_24 pp N3_17
+M3 N3_3 pp N3_24
+M3 N3_23 pp N3_11
+M3 N3_26 pp N3_9
+M3 N3_22 pp N3_4
+M3 N3_23 pp N3_9
+M3 N3_24 pp N3_1
+M3 N3_25 pp N3_18
+M3 N3_8 pp N3_15
+M3 N3_20 pp N3_2
+M3 N3_11 pp N3_13
+M3 N3_23 pp N3_21
+M3 N3_7 pp N3_22
+M4 N4_11 pp N4_6
+M4 N4_17 pp N4_19
+M4 N4_19 pp N4_17
+M4 N4_10 pp N4_19
+M4 N4_14 pp N4_10
+M4 N4_1 pp N4_7
+M4 N4_1 pp N4_12
+M4 N4_13 pp N4_25
+M4 N4_7 pp N4_25
+M4 N4_15 pp N4_20
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diff --git a/application/src/test/resources/testData/NNFData/large.nnf b/application/src/test/resources/testData/NNFData/large.nnf
new file mode 100644
index 0000000..1a6057f
--- /dev/null
+++ b/application/src/test/resources/testData/NNFData/large.nnf
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+M382 N382_3 pp N382_2
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+M397 N397_21
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+M397 N397_24
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+M398 N398_17 pp N398_41
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+M398 N398_34 pp N398_18
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+M398 N398_39 pp N398_20
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+M398 N398_21 pp N398_5
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+M398 N398_29 pp N398_28
+M398 N398_44 pp N398_29
+M398 N398_43 pp N398_47
+M398 N398_8 pp N398_37
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+M398 N398_11 pp N398_24
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+M405 N405_2 pp N405_10
+M405 N405_3 pp N405_26
+M405 N405_6 pp N405_12
+M405 N405_5 pp N405_7
+M405 N405_10 pp N405_27
+M405 N405_25 pp N405_21
+M405 N405_22 pp N405_23
+M405 N405_17 pp N405_8
+M405 N405_9 pp N405_16
+M405 N405_26 pp N405_9
+M405 N405_23 pp N405_12
+M405 N405_25 pp N405_9
+M405 N405_3 pp N405_11
+M405 N405_8 pp N405_18
+M405 N405_23 pp N405_25
+M405 N405_20 pp N405_6
+M405 N405_12 pp N405_24
+M405 N405_1
+M405 N405_2
+M405 N405_3
+M405 N405_4
+M405 N405_5
+M405 N405_6
+M405 N405_7
+M405 N405_8
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+M405 N405_11
+M405 N405_12
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+M405 N405_14
+M405 N405_15
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+M405 N405_17
+M405 N405_18
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+M405 N405_20
+M405 N405_21
+M405 N405_22
+M405 N405_23
+M405 N405_24
+M405 N405_25
+M405 N405_26
+M405 N405_27
+M406 N406_20 pp N406_27
+M406 N406_27 pp N406_22
+M406 N406_7 pp N406_5
+M406 N406_27 pp N406_16
+M406 N406_7 pp N406_22
+M406 N406_5 pp N406_7
+M406 N406_14 pp N406_7
+M406 N406_11 pp N406_1
+M406 N406_18 pp N406_17
+M406 N406_4 pp N406_9
+M406 N406_17 pp N406_11
+M406 N406_8 pp N406_13
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+M406 N406_1 pp N406_22
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+M406 N406_8 pp N406_24
+M406 N406_12 pp N406_24
+M406 N406_16 pp N406_17
+M406 N406_1 pp N406_22
+M406 N406_11 pp N406_13
+M406 N406_8 pp N406_7
+M406 N406_18 pp N406_1
+M406 N406_12 pp N406_15
+M406 N406_7 pp N406_23
+M406 N406_20 pp N406_22
+M406 N406_7 pp N406_27
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+M406 N406_5 pp N406_8
+M406 N406_21 pp N406_25
+M406 N406_26 pp N406_1
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+M406 N406_26 pp N406_25
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+M406 N406_20 pp N406_12
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+M406 N406_1
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+M407 N407_7 pp N407_37
+M407 N407_4 pp N407_15
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+M407 N407_2 pp N407_26
+M407 N407_30 pp N407_31
+M407 N407_1 pp N407_21
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+M407 N407_28 pp N407_17
+M407 N407_15 pp N407_10
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+M407 N407_33 pp N407_7
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+M407 N407_19 pp N407_10
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+M407 N407_15 pp N407_17
+M407 N407_17 pp N407_20
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+M407 N407_20 pp N407_32
+M407 N407_12 pp N407_33
+M407 N407_31 pp N407_21
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+M407 N407_26 pp N407_30
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+M407 N407_34 pp N407_36
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+M407 N407_1
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+M407 N407_37
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+M408 N408_1
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+M408 N408_21
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+M409 N409_47
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+M706 N706_6 pp N706_7
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+M729 N729_37
+M729 N729_38
+M729 N729_39
+M729 N729_40
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+MM M448
+MM M449
+MM M450
+MM M451
+MM M452
+MM M453
+MM M454
+MM M455
+MM M456
+MM M457
+MM M458
+MM M459
+MM M460
+MM M461
+MM M462
+MM M463
+MM M464
+MM M465
+MM M466
+MM M467
+MM M468
+MM M469
+MM M470
+MM M471
+MM M472
+MM M473
+MM M474
+MM M475
+MM M476
+MM M477
+MM M478
+MM M479
+MM M480
+MM M481
+MM M482
+MM M483
+MM M484
+MM M485
+MM M486
+MM M487
+MM M488
+MM M489
+MM M490
+MM M491
+MM M492
+MM M493
+MM M494
+MM M495
+MM M496
+MM M497
+MM M498
+MM M499
+MM M500
+MM M501
+MM M502
+MM M503
+MM M504
+MM M505
+MM M506
+MM M507
+MM M508
+MM M509
+MM M510
+MM M511
+MM M512
+MM M513
+MM M514
+MM M515
+MM M516
+MM M517
+MM M518
+MM M519
+MM M520
+MM M521
+MM M522
+MM M523
+MM M524
+MM M525
+MM M526
+MM M527
+MM M528
+MM M529
+MM M530
+MM M531
+MM M532
+MM M533
+MM M534
+MM M535
+MM M536
+MM M537
+MM M538
+MM M539
+MM M540
+MM M541
+MM M542
+MM M543
+MM M544
+MM M545
+MM M546
+MM M547
+MM M548
+MM M549
+MM M550
+MM M551
+MM M552
+MM M553
+MM M554
+MM M555
+MM M556
+MM M557
+MM M558
+MM M559
+MM M560
+MM M561
+MM M562
+MM M563
+MM M564
+MM M565
+MM M566
+MM M567
+MM M568
+MM M569
+MM M570
+MM M571
+MM M572
+MM M573
+MM M574
+MM M575
+MM M576
+MM M577
+MM M578
+MM M579
+MM M580
+MM M581
+MM M582
+MM M583
+MM M584
+MM M585
+MM M586
+MM M587
+MM M588
+MM M589
+MM M590
+MM M591
+MM M592
+MM M593
+MM M594
+MM M595
+MM M596
+MM M597
+MM M598
+MM M599
+MM M600
+MM M601
+MM M602
+MM M603
+MM M604
+MM M605
+MM M606
+MM M607
+MM M608
+MM M609
+MM M610
+MM M611
+MM M612
+MM M613
+MM M614
+MM M615
+MM M616
+MM M617
+MM M618
+MM M619
+MM M620
+MM M621
+MM M622
+MM M623
+MM M624
+MM M625
+MM M626
+MM M627
+MM M628
+MM M629
+MM M630
+MM M631
+MM M632
+MM M633
+MM M634
+MM M635
+MM M636
+MM M637
+MM M638
+MM M639
+MM M640
+MM M641
+MM M642
+MM M643
+MM M644
+MM M645
+MM M646
+MM M647
+MM M648
+MM M649
+MM M650
+MM M651
+MM M652
+MM M653
+MM M654
+MM M655
+MM M656
+MM M657
+MM M658
+MM M659
+MM M660
+MM M661
+MM M662
+MM M663
+MM M664
+MM M665
+MM M666
+MM M667
+MM M668
+MM M669
+MM M670
+MM M671
+MM M672
+MM M673
+MM M674
+MM M675
+MM M676
+MM M677
+MM M678
+MM M679
+MM M680
+MM M681
+MM M682
+MM M683
+MM M684
+MM M685
+MM M686
+MM M687
+MM M688
+MM M689
+MM M690
+MM M691
+MM M692
+MM M693
+MM M694
+MM M695
+MM M696
+MM M697
+MM M698
+MM M699
+MM M700
+MM M701
+MM M702
+MM M703
+MM M704
+MM M705
+MM M706
+MM M707
+MM M708
+MM M709
+MM M710
+MM M711
+MM M712
+MM M713
+MM M714
+MM M715
+MM M716
+MM M717
+MM M718
+MM M719
+MM M720
+MM M721
+MM M722
+MM M723
+MM M724
+MM M725
+MM M726
+MM M727
+MM M728
+MM M729
+MM M730
+MM M731
+MM M732
+MM M733
+MM M734
+MM M735
+MM M736
+MM M737
+MM M738
+MM M739
+MM M740
+MM M741
+MM M742
+MM M743
+MM M744
+MM M745
+MM M746
+MM M747
+MM M748
+MM M749
+MM M750
+MM M751
+MM M752
+MM M753
+MM M754
+MM M755
+MM M756
+MM M757
+MM M758
+MM M759
+MM M760
+MM M761
+MM M762
+MM M763
+MM M764
+MM M765
+MM M766
+MM M767
+MM M768
+MM M769
+MM M770
+MM M771
+MM M772
+MM M773
+MM M774
+MM M775
+MM M776
+MM M777
+MM M778
+MM M779
+MM M780
+MM M781
+MM M782
+MM M783
+MM M784
+MM M785
+MM M786
+MM M787
+MM M788
+MM M789
+MM M790
+MM M791
+MM M792
+MM M793
+MM M794
+MM M795
+MM M796
+MM M797
+MM M798
+MM M799
+MM M800
+MM M801
+MM M802
+MM M803
+MM M804
+MM M805
+MM M806
+MM M807
+MM M808
+MM M809
+MM M810
+MM M811
+MM M812
+MM M813
+MM M814
+MM M815
+MM M816
+MM M817
+MM M818
+MM M819
+MM M820
+MM M821
+MM M822
+MM M823
+MM M824
+MM M825
+MM M826
+MM M827
+MM M828
+MM M829
+MM M830
+MM M831
+MM M832
+MM M833
+MM M834
+MM M835
+MM M836
+MM M837
+MM M838
+MM M839
+MM M840
+MM M841
+MM M842
+MM M843
+MM M844
+MM M845
+MM M846
+MM M847
+MM M848
+MM M849
+MM M850
+MM M851
+MM M852
+MM M853
+MM M854
+MM M855
+MM M856
+MM M857
+MM M858
+MM M859
+MM M860
+MM M861
+MM M862
+MM M863
+MM M864
+MM M865
+MM M866
+MM M867
+MM M868
+MM M869
+MM M870
+MM M871
+MM M872
+MM M873
+MM M874
+MM M875
+MM M876
+MM M877
+MM M878
+MM M879
+MM M880
+MM M881
+MM M882
+MM M883
+MM M884
+MM M885
+MM M886
+MM M887
+MM M888
+MM M889
+MM M890
+MM M891
+MM M892
+MM M893
+MM M894
+MM M895
+MM M896
+MM M897
+MM M898
+MM M899
+MM M900
+MM M901
+MM M902
+MM M903
+MM M904
+MM M905
+MM M906
+MM M907
+MM M908
+MM M909
+MM M910
+MM M911
+MM M912
+MM M913
+MM M914
+MM M915
+MM M916
+MM M917
+MM M918
+MM M919
+MM M920
+MM M921
+MM M922
+MM M923
+MM M924
+MM M925
+MM M926
+MM M927
+MM M928
+MM M929
+MM M930
+MM M931
+MM M932
+MM M933
+MM M934
+MM M935
+MM M936
+MM M937
+MM M938
+MM M939
+MM M940
+MM M941
+MM M942
+MM M943
+MM M944
+MM M945
+MM M946
+MM M947
+MM M948
+MM M949
+MM M950
+MM M951
+MM M952
+MM M953
+MM M954
+MM M955
+MM M956
+MM M957
+MM M958
+MM M959
+MM M960
+MM M961
+MM M962
+MM M963
+MM M964
+MM M965
+MM M966
+MM M967
+MM M968
+MM M969
+MM M970
+MM M971
+MM M972
+MM M973
+MM M974
+MM M975
+MM M976
+MM M977
+MM M978
+MM M979
+MM M980
+MM M981
+MM M982
+MM M983
+MM M984
+MM M985
+MM M986
+MM M987
+MM M988
+MM M989
+MM M990
+MM M991
+MM M992
+MM M993
+MM M994
+MM M995
+MM M996
+MM M997
+MM M998
+MM M999
+MM M1000
diff --git a/application/src/test/resources/testData/NNFData/loop.nnf b/application/src/test/resources/testData/NNFData/loop.nnf
new file mode 100644
index 0000000..661cfc0
--- /dev/null
+++ b/application/src/test/resources/testData/NNFData/loop.nnf
@@ -0,0 +1,2 @@
+N1 N2
+N2 N1
diff --git a/application/src/test/resources/testData/NNFData/loop1.nnf b/application/src/test/resources/testData/NNFData/loop1.nnf
new file mode 100644
index 0000000..f575ac7
--- /dev/null
+++ b/application/src/test/resources/testData/NNFData/loop1.nnf
@@ -0,0 +1,2 @@
+A B
+B A
\ No newline at end of file
diff --git a/application/src/test/resources/testData/NNFData/small.nnf b/application/src/test/resources/testData/NNFData/small.nnf
new file mode 100644
index 0000000..499d63a
--- /dev/null
+++ b/application/src/test/resources/testData/NNFData/small.nnf
@@ -0,0 +1,5560 @@
+# Generated with ./generate_networks
+# number_of_nested_networks = 100
+# min_nested_network_size = 20
+# max_nested_network_size = 50
+# link_factor = 1.5
+M1 N1_6 pp N1_12
+M1 N1_1 pp N1_9
+M1 N1_18 pp N1_4
+M1 N1_20 pp N1_8
+M1 N1_1 pp N1_16
+M1 N1_21 pp N1_10
+M1 N1_4 pp N1_16
+M1 N1_3 pp N1_20
+M1 N1_13 pp N1_15
+M1 N1_8 pp N1_14
+M1 N1_14 pp N1_1
+M1 N1_16 pp N1_7
+M1 N1_7 pp N1_4
+M1 N1_10 pp N1_11
+M1 N1_10 pp N1_6
+M1 N1_15 pp N1_18
+M1 N1_5 pp N1_13
+M1 N1_10 pp N1_5
+M1 N1_12 pp N1_15
+M1 N1_8 pp N1_3
+M1 N1_14 pp N1_12
+M1 N1_16 pp N1_7
+M1 N1_15 pp N1_5
+M1 N1_10 pp N1_2
+M1 N1_11 pp N1_5
+M1 N1_18 pp N1_21
+M1 N1_21 pp N1_11
+M1 N1_2 pp N1_21
+M1 N1_20 pp N1_12
+M1 N1_6 pp N1_11
+M1 N1_7 pp N1_9
+M1 N1_15 pp N1_19
+M1 N1_17
+M2 N2_8 pp N2_13
+M2 N2_11 pp N2_6
+M2 N2_10 pp N2_19
+M2 N2_19 pp N2_21
+M2 N2_22 pp N2_9
+M2 N2_1 pp N2_7
+M2 N2_20 pp N2_10
+M2 N2_8 pp N2_4
+M2 N2_16 pp N2_15
+M2 N2_12 pp N2_2
+M2 N2_6 pp N2_9
+M2 N2_5 pp N2_10
+M2 N2_2 pp N2_4
+M2 N2_15 pp N2_19
+M2 N2_21 pp N2_18
+M2 N2_4 pp N2_13
+M2 N2_5 pp N2_18
+M2 N2_22 pp N2_11
+M2 N2_24 pp N2_20
+M2 N2_15 pp N2_14
+M2 N2_10 pp N2_2
+M2 N2_7 pp N2_6
+M2 N2_17 pp N2_24
+M2 N2_8 pp N2_1
+M2 N2_22 pp N2_14
+M2 N2_19 pp N2_7
+M2 N2_2 pp N2_10
+M2 N2_19 pp N2_20
+M2 N2_16 pp N2_14
+M2 N2_10 pp N2_13
+M2 N2_23 pp N2_15
+M2 N2_1 pp N2_9
+M2 N2_22 pp N2_23
+M2 N2_5 pp N2_16
+M2 N2_3 pp N2_15
+M2 N2_10 pp N2_7
+M3 N3_8 pp N3_15
+M3 N3_28 pp N3_23
+M3 N3_31 pp N3_21
+M3 N3_9 pp N3_15
+M3 N3_31 pp N3_28
+M3 N3_13 pp N3_28
+M3 N3_27 pp N3_26
+M3 N3_9 pp N3_13
+M3 N3_18 pp N3_2
+M3 N3_26 pp N3_37
+M3 N3_34 pp N3_32
+M3 N3_20 pp N3_26
+M3 N3_16 pp N3_23
+M3 N3_7 pp N3_19
+M3 N3_30 pp N3_10
+M3 N3_12 pp N3_5
+M3 N3_18 pp N3_20
+M3 N3_5 pp N3_16
+M3 N3_6 pp N3_29
+M3 N3_27 pp N3_16
+M3 N3_13 pp N3_12
+M3 N3_28 pp N3_29
+M3 N3_25 pp N3_39
+M3 N3_18 pp N3_38
+M3 N3_24 pp N3_20
+M3 N3_31 pp N3_16
+M3 N3_24 pp N3_28
+M3 N3_38 pp N3_12
+M3 N3_38 pp N3_31
+M3 N3_21 pp N3_36
+M3 N3_16 pp N3_18
+M3 N3_16 pp N3_1
+M3 N3_3 pp N3_11
+M3 N3_14 pp N3_8
+M3 N3_33 pp N3_23
+M3 N3_3 pp N3_13
+M3 N3_31 pp N3_39
+M3 N3_15 pp N3_33
+M3 N3_35 pp N3_26
+M3 N3_18 pp N3_22
+M3 N3_19 pp N3_33
+M3 N3_18 pp N3_5
+M3 N3_8 pp N3_36
+M3 N3_21 pp N3_3
+M3 N3_11 pp N3_15
+M3 N3_36 pp N3_5
+M3 N3_4 pp N3_27
+M3 N3_39 pp N3_7
+M3 N3_38 pp N3_8
+M3 N3_16 pp N3_3
+M3 N3_10 pp N3_32
+M3 N3_17 pp N3_14
+M3 N3_25 pp N3_39
+M3 N3_30 pp N3_22
+M3 N3_6 pp N3_9
+M3 N3_33 pp N3_18
+M3 N3_30 pp N3_27
+M3 N3_32 pp N3_24
+M3 N3_10 pp N3_19
+M4 N4_17 pp N4_14
+M4 N4_16 pp N4_38
+M4 N4_21 pp N4_26
+M4 N4_3 pp N4_12
+M4 N4_34 pp N4_15
+M4 N4_13 pp N4_20
+M4 N4_14 pp N4_34
+M4 N4_12 pp N4_7
+M4 N4_10 pp N4_20
+M4 N4_13 pp N4_19
+M4 N4_14 pp N4_26
+M4 N4_31 pp N4_2
+M4 N4_36 pp N4_7
+M4 N4_8 pp N4_9
+M4 N4_27 pp N4_9
+M4 N4_22 pp N4_1
+M4 N4_9 pp N4_37
+M4 N4_17 pp N4_29
+M4 N4_38 pp N4_30
+M4 N4_2 pp N4_26
+M4 N4_24 pp N4_27
+M4 N4_7 pp N4_16
+M4 N4_11 pp N4_39
+M4 N4_32 pp N4_12
+M4 N4_15 pp N4_10
+M4 N4_13 pp N4_16
+M4 N4_17 pp N4_6
+M4 N4_35 pp N4_9
+M4 N4_7 pp N4_35
+M4 N4_14 pp N4_5
+M4 N4_15 pp N4_28
+M4 N4_18 pp N4_32
+M4 N4_27 pp N4_11
+M4 N4_27 pp N4_11
+M4 N4_39 pp N4_31
+M4 N4_20 pp N4_16
+M4 N4_13 pp N4_34
+M4 N4_23 pp N4_36
+M4 N4_29 pp N4_26
+M4 N4_2 pp N4_24
+M4 N4_15 pp N4_31
+M4 N4_34 pp N4_14
+M4 N4_10 pp N4_27
+M4 N4_1 pp N4_3
+M4 N4_6 pp N4_22
+M4 N4_24 pp N4_37
+M4 N4_18 pp N4_15
+M4 N4_6 pp N4_14
+M4 N4_24 pp N4_20
+M4 N4_29 pp N4_15
+M4 N4_8 pp N4_20
+M4 N4_28 pp N4_14
+M4 N4_33 pp N4_3
+M4 N4_2 pp N4_16
+M4 N4_14 pp N4_18
+M4 N4_22 pp N4_31
+M4 N4_20 pp N4_34
+M4 N4_1 pp N4_3
+M4 N4_22 pp N4_17
+M4 N4_4
+M4 N4_25
+M5 N5_25 pp N5_18
+M5 N5_30 pp N5_34
+M5 N5_6 pp N5_28
+M5 N5_7 pp N5_38
+M5 N5_2 pp N5_3
+M5 N5_6 pp N5_29
+M5 N5_4 pp N5_36
+M5 N5_27 pp N5_1
+M5 N5_32 pp N5_35
+M5 N5_37 pp N5_15
+M5 N5_5 pp N5_37
+M5 N5_38 pp N5_36
+M5 N5_16 pp N5_8
+M5 N5_34 pp N5_14
+M5 N5_18 pp N5_5
+M5 N5_10 pp N5_19
+M5 N5_5 pp N5_25
+M5 N5_2 pp N5_10
+M5 N5_13 pp N5_36
+M5 N5_32 pp N5_12
+M5 N5_41 pp N5_16
+M5 N5_26 pp N5_18
+M5 N5_5 pp N5_15
+M5 N5_41 pp N5_8
+M5 N5_2 pp N5_41
+M5 N5_3 pp N5_11
+M5 N5_3 pp N5_25
+M5 N5_41 pp N5_3
+M5 N5_26 pp N5_40
+M5 N5_9 pp N5_41
+M5 N5_33 pp N5_9
+M5 N5_38 pp N5_22
+M5 N5_32 pp N5_28
+M5 N5_28 pp N5_36
+M5 N5_17 pp N5_36
+M5 N5_21 pp N5_39
+M5 N5_23 pp N5_35
+M5 N5_9 pp N5_21
+M5 N5_40 pp N5_20
+M5 N5_39 pp N5_11
+M5 N5_36 pp N5_24
+M5 N5_34 pp N5_33
+M5 N5_15 pp N5_4
+M5 N5_17 pp N5_5
+M5 N5_12 pp N5_19
+M5 N5_6 pp N5_27
+M5 N5_24 pp N5_16
+M5 N5_30 pp N5_26
+M5 N5_8 pp N5_41
+M5 N5_35 pp N5_39
+M5 N5_9 pp N5_10
+M5 N5_20 pp N5_7
+M5 N5_6 pp N5_27
+M5 N5_19 pp N5_35
+M5 N5_12 pp N5_37
+M5 N5_28 pp N5_1
+M5 N5_23 pp N5_8
+M5 N5_16 pp N5_34
+M5 N5_5 pp N5_4
+M5 N5_4 pp N5_14
+M5 N5_28 pp N5_5
+M5 N5_21 pp N5_16
+M5 N5_31
+M6 N6_41 pp N6_5
+M6 N6_33 pp N6_22
+M6 N6_44 pp N6_7
+M6 N6_39 pp N6_30
+M6 N6_26 pp N6_10
+M6 N6_29 pp N6_18
+M6 N6_3 pp N6_21
+M6 N6_38 pp N6_14
+M6 N6_4 pp N6_45
+M6 N6_44 pp N6_31
+M6 N6_34 pp N6_21
+M6 N6_39 pp N6_17
+M6 N6_23 pp N6_18
+M6 N6_38 pp N6_27
+M6 N6_31 pp N6_38
+M6 N6_45 pp N6_34
+M6 N6_42 pp N6_32
+M6 N6_2 pp N6_25
+M6 N6_45 pp N6_14
+M6 N6_19 pp N6_9
+M6 N6_4 pp N6_3
+M6 N6_14 pp N6_5
+M6 N6_19 pp N6_30
+M6 N6_34 pp N6_39
+M6 N6_16 pp N6_40
+M6 N6_29 pp N6_28
+M6 N6_31 pp N6_15
+M6 N6_18 pp N6_13
+M6 N6_42 pp N6_31
+M6 N6_23 pp N6_24
+M6 N6_35 pp N6_28
+M6 N6_45 pp N6_23
+M6 N6_29 pp N6_28
+M6 N6_44 pp N6_12
+M6 N6_30 pp N6_45
+M6 N6_8 pp N6_19
+M6 N6_15 pp N6_25
+M6 N6_9 pp N6_3
+M6 N6_34 pp N6_19
+M6 N6_4 pp N6_21
+M6 N6_1 pp N6_30
+M6 N6_2 pp N6_30
+M6 N6_21 pp N6_12
+M6 N6_1 pp N6_11
+M6 N6_35 pp N6_2
+M6 N6_39 pp N6_43
+M6 N6_43 pp N6_30
+M6 N6_9 pp N6_45
+M6 N6_42 pp N6_46
+M6 N6_21 pp N6_18
+M6 N6_35 pp N6_17
+M6 N6_5 pp N6_12
+M6 N6_17 pp N6_22
+M6 N6_10 pp N6_11
+M6 N6_40 pp N6_26
+M6 N6_46 pp N6_3
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diff --git a/application/src/test/resources/testData/NNFData/t3.cys b/application/src/test/resources/testData/NNFData/t3.cys
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index 0000000..044d7ed
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diff --git a/application/src/test/resources/testData/NNFData/t4.cys b/application/src/test/resources/testData/NNFData/t4.cys
new file mode 100644
index 0000000..1c379cb
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diff --git a/application/src/test/resources/testData/XGMMLWriterTestFile01a.xgmml b/application/src/test/resources/testData/XGMMLWriterTestFile01a.xgmml
new file mode 100644
index 0000000..17e0cfc
--- /dev/null
+++ b/application/src/test/resources/testData/XGMMLWriterTestFile01a.xgmml
@@ -0,0 +1,40 @@
+<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+<graph label="Network 0" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:cy="http://www.cytoscape.org" xmlns="http://www.cs.rpi.edu/XGMML" directed="1">
+ <att name="documentVersion" value="1.1"/>
+ <att name="networkMetadata">
+ <rdf:RDF>
+ <rdf:Description rdf:about="http://www.cytoscape.org/">
+ <dc:type>Protein-Protein Interaction</dc:type>
+ <dc:description>N/A</dc:description>
+ <dc:identifier>N/A</dc:identifier>
+ <dc:date>2009-06-15 16:45:41</dc:date>
+ <dc:title>Network 0</dc:title>
+ <dc:source>http://www.cytoscape.org/</dc:source>
+ <dc:format>Cytoscape-XGMML</dc:format>
+ </rdf:Description>
+ </rdf:RDF>
+ </att>
+ <att type="string" name="backgroundColor" value="#ccccff"/>
+ <att type="real" name="GRAPH_VIEW_ZOOM" value="1.0"/>
+ <att type="real" name="GRAPH_VIEW_CENTER_X" value="0.0"/>
+ <att type="real" name="GRAPH_VIEW_CENTER_Y" value="0.0"/>
+ <node label="node1" id="-2">
+ <att type="string" name="testString" value="This is a test string for node1"/>
+ <att type="string" name="NODE_TYPE" value="DefaultNode"/>
+ <att type="string" name="canonicalName" value="node1"/>
+ <graphics type="ELLIPSE" h="40.0" w="40.0" x="63.0" y="-46.0" fill="#ff9999" width="1" outline="#666666" cy:nodeTransparency="1.0" cy:nodeLabelFont="SansSerif.bold-0-12" cy:borderLineType="solid"/>
+ </node>
+ <node label="node0" id="-1">
+ <att type="string" name="testString" value="This is a test string for node0"/>
+ <att type="string" name="NODE_TYPE" value="DefaultNode"/>
+ <att type="string" name="canonicalName" value="node0"/>
+ <graphics type="ELLIPSE" h="40.0" w="40.0" x="-122.0" y="-48.0" fill="#ff9999" width="1" outline="#666666" cy:nodeTransparency="1.0" cy:nodeLabelFont="SansSerif.bold-0-12" cy:borderLineType="solid"/>
+ </node>
+ <edge label="node0 (DirectedEdge) node1" source="-1" target="-2">
+ <att type="string" name="EDGE_TYPE" value="DirectedEdge"/>
+ <att type="string" name="testString" value="This is a test string for the edge"/>
+ <att type="string" name="interaction" value="DirectedEdge"/>
+ <att type="string" name="canonicalName" value="node0 (DirectedEdge) node1"/>
+ <graphics width="1" fill="#0000ff" cy:sourceArrow="0" cy:targetArrow="0" cy:sourceArrowColor="#000000" cy:targetArrowColor="#000000" cy:edgeLabelFont="Default-0-10" cy:edgeLineType="SOLID" cy:curved="STRAIGHT_LINES"/>
+ </edge>
+</graph>
diff --git a/application/src/test/resources/testData/XGMMLWriterTestFile01b.xgmml b/application/src/test/resources/testData/XGMMLWriterTestFile01b.xgmml
new file mode 100644
index 0000000..dbb729a
--- /dev/null
+++ b/application/src/test/resources/testData/XGMMLWriterTestFile01b.xgmml
@@ -0,0 +1,33 @@
+<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+<graph label="Network 0" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:cy="http://www.cytoscape.org" xmlns="http://www.cs.rpi.edu/XGMML" directed="1">
+ <att name="documentVersion" value="1.1"/>
+ <att name="networkMetadata">
+ <rdf:RDF>
+ <rdf:Description rdf:about="http://www.cytoscape.org/">
+ <dc:type>Protein-Protein Interaction</dc:type>
+ <dc:description>N/A</dc:description>
+ <dc:identifier>N/A</dc:identifier>
+ <dc:date>2009-06-15 16:45:41</dc:date>
+ <dc:title>Network 0</dc:title>
+ <dc:source>http://www.cytoscape.org/</dc:source>
+ <dc:format>Cytoscape-XGMML</dc:format>
+ </rdf:Description>
+ </rdf:RDF>
+ </att>
+ <node label="node0" id="-2">
+ <att type="string" name="NODE_TYPE" value="DefaultNode"/>
+ <att type="string" name="canonicalName" value="node0"/>
+ <att type="string" name="testString" value="This is a test string for node0"/>
+ </node>
+ <node label="node1" id="-1">
+ <att type="string" name="NODE_TYPE" value="DefaultNode"/>
+ <att type="string" name="canonicalName" value="node1"/>
+ <att type="string" name="testString" value="This is a test string for node1"/>
+ </node>
+ <edge label="node0 (DirectedEdge) node1" source="-2" target="-1">
+ <att type="string" name="EDGE_TYPE" value="DirectedEdge"/>
+ <att type="string" name="canonicalName" value="node0 (DirectedEdge) node1"/>
+ <att type="string" name="interaction" value="DirectedEdge"/>
+ <att type="string" name="testString" value="This is a test string for the edge"/>
+ </edge>
+</graph>
diff --git a/application/src/test/resources/testData/XGMMLWriterTestFile02a.xgmml b/application/src/test/resources/testData/XGMMLWriterTestFile02a.xgmml
new file mode 100644
index 0000000..30f7389
--- /dev/null
+++ b/application/src/test/resources/testData/XGMMLWriterTestFile02a.xgmml
@@ -0,0 +1,22 @@
+<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+<graph label="Network 0" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:cy="http://www.cytoscape.org" xmlns="http://www.cs.rpi.edu/XGMML" directed="1">
+ <att name="documentVersion" value="1.1"/>
+ <att name="networkMetadata">
+ <rdf:RDF>
+ <rdf:Description rdf:about="http://www.cytoscape.org/">
+ <dc:type>Protein-Protein Interaction</dc:type>
+ <dc:description>N/A</dc:description>
+ <dc:identifier>N/A</dc:identifier>
+ <dc:date>2009-06-15 16:45:41</dc:date>
+ <dc:title>Network 0</dc:title>
+ <dc:source>http://www.cytoscape.org/</dc:source>
+ <dc:format>Cytoscape-XGMML</dc:format>
+ </rdf:Description>
+ </rdf:RDF>
+ </att>
+ <node label="node0" id="-2">
+ <att type="string" name="NODE_TYPE" value="DefaultNode"/>
+ <att type="string" name="canonicalName" value="node0"/>
+ <att type="string" name="testString" value="This is a test string for\tnode0\n"/>
+ </node>
+</graph>
diff --git a/application/src/test/resources/testData/XGMMLWriterTestFile02b.xgmml b/application/src/test/resources/testData/XGMMLWriterTestFile02b.xgmml
new file mode 100644
index 0000000..038736b
--- /dev/null
+++ b/application/src/test/resources/testData/XGMMLWriterTestFile02b.xgmml
@@ -0,0 +1,22 @@
+<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+<graph label="Network 0" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:cy="http://www.cytoscape.org" xmlns="http://www.cs.rpi.edu/XGMML" directed="1">
+ <att name="documentVersion" value="1.1"/>
+ <att name="networkMetadata">
+ <rdf:RDF>
+ <rdf:Description rdf:about="http://www.cytoscape.org/">
+ <dc:type>Protein-Protein Interaction</dc:type>
+ <dc:description>N/A</dc:description>
+ <dc:identifier>N/A</dc:identifier>
+ <dc:date>2009-06-15 16:45:41</dc:date>
+ <dc:title>Network 0</dc:title>
+ <dc:source>http://www.cytoscape.org/</dc:source>
+ <dc:format>Cytoscape-XGMML</dc:format>
+ </rdf:Description>
+ </rdf:RDF>
+ </att>
+ <node label="node0" id="-1">
+ <att type="string" name="NODE_TYPE" value="DefaultNode"/>
+ <att type="string" name="canonicalName" value="node0"/>
+ <att type="string" name="testString" value="This is a test string for	node0
"/>
+ </node>
+</graph>
diff --git a/application/src/test/resources/testData/XGMMLWriterTestFile02c.xgmml b/application/src/test/resources/testData/XGMMLWriterTestFile02c.xgmml
new file mode 100644
index 0000000..2500a30
--- /dev/null
+++ b/application/src/test/resources/testData/XGMMLWriterTestFile02c.xgmml
@@ -0,0 +1,22 @@
+<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+<graph label="Network 0" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:cy="http://www.cytoscape.org" xmlns="http://www.cs.rpi.edu/XGMML" directed="1">
+ <att name="documentVersion" value="1.1"/>
+ <att name="networkMetadata">
+ <rdf:RDF>
+ <rdf:Description rdf:about="http://www.cytoscape.org/">
+ <dc:type>Protein-Protein Interaction</dc:type>
+ <dc:description>N/A</dc:description>
+ <dc:identifier>N/A</dc:identifier>
+ <dc:date>2009-06-15 16:45:41</dc:date>
+ <dc:title>Network 0</dc:title>
+ <dc:source>http://www.cytoscape.org/</dc:source>
+ <dc:format>Cytoscape-XGMML</dc:format>
+ </rdf:Description>
+ </rdf:RDF>
+ </att>
+ <node label="node0" id="-2">
+ <att type="string" name="NODE_TYPE" value="DefaultNode"/>
+ <att type="string" name="canonicalName" value="node0"/>
+ <att type="string" name="testString" value="This is a test string for node0\nAnother sentence$©ﻸ"/>
+ </node>
+</graph>
diff --git a/application/src/test/resources/testData/XGMMLWriterTestFile02d.xgmml b/application/src/test/resources/testData/XGMMLWriterTestFile02d.xgmml
new file mode 100644
index 0000000..688a4ae
--- /dev/null
+++ b/application/src/test/resources/testData/XGMMLWriterTestFile02d.xgmml
@@ -0,0 +1,22 @@
+<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+<graph label="Network 0" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:cy="http://www.cytoscape.org" xmlns="http://www.cs.rpi.edu/XGMML" directed="1">
+ <att name="documentVersion" value="1.1"/>
+ <att name="networkMetadata">
+ <rdf:RDF>
+ <rdf:Description rdf:about="http://www.cytoscape.org/">
+ <dc:type>Protein-Protein Interaction</dc:type>
+ <dc:description>N/A</dc:description>
+ <dc:identifier>N/A</dc:identifier>
+ <dc:date>2009-06-15 16:45:41</dc:date>
+ <dc:title>Network 0</dc:title>
+ <dc:source>http://www.cytoscape.org/</dc:source>
+ <dc:format>Cytoscape-XGMML</dc:format>
+ </rdf:Description>
+ </rdf:RDF>
+ </att>
+ <node label="node0" id="-2">
+ <att type="string" name="NODE_TYPE" value="DefaultNode"/>
+ <att type="string" name="canonicalName" value="node0"/>
+ <att type="string" name="testString" value="This is a test string for node0\nAnother sentence$©ﻸ"/>
+ </node>
+</graph>
diff --git a/application/src/test/resources/testData/annotation/goslim_generic.obo b/application/src/test/resources/testData/annotation/goslim_generic.obo
new file mode 100644
index 0000000..1a8d2c9
--- /dev/null
+++ b/application/src/test/resources/testData/annotation/goslim_generic.obo
@@ -0,0 +1,1754 @@
+format-version: 1.0
+date: 18:08:2006 15:30
+saved-by: jclark
+auto-generated-by: OBO-Edit 1.002
+subsetdef: goslim_generic "Generic GO slim"
+subsetdef: goslim_goa "GOA and proteome slim"
+subsetdef: goslim_plant "Plant GO slim"
+subsetdef: goslim_yeast "Yeast GO slim"
+subsetdef: gosubset_prok "Prokaryotic GO subset"
+default-namespace: gene_ontology
+remark: cvs version: $Revision: 1.308 $
+remark: GO_slim_name: Generic GO slim
+remark: GO_slim_authors: Suparna Mundodi and Amelia Ireland
+remark: GO_slim_contact: smundodi at acoma.stanford.edu
+
+[Term]
+id: GO:0000003
+name: reproduction
+namespace: biological_process
+alt_id: GO:0019952
+def: "The production by an organism of new individuals that contain some portion of their genetic material inherited from that organism." [GOC:go_curators, ISBN:0198506732]
+subset: goslim_generic
+subset: goslim_plant
+subset: gosubset_prok
+is_a: GO:0008150
+
+[Term]
+id: GO:0000004
+name: biological process unknown
+namespace: biological_process
+def: "Used for the annotation of gene products whose process is not known or cannot be inferred." [GOC:sgd_curators]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+is_a: GO:0008150
+
+[Term]
+id: GO:0000166
+name: nucleotide binding
+namespace: molecular_function
+def: "Interacting selectively with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety." [GOC:mah, ISBN:0198547684]
+subset: goslim_generic
+subset: goslim_plant
+subset: gosubset_prok
+is_a: GO:0005488
+
+[Term]
+id: GO:0000228
+name: nuclear chromosome
+namespace: cellular_component
+def: "A chromosome found in the nucleus of a eukaryotic cell." [GOC:mah]
+subset: goslim_generic
+narrow_synonym: "nuclear interphase chromosome" []
+relationship: part_of GO:0005634
+is_a: GO:0005694
+
+[Term]
+id: GO:0000229
+name: cytoplasmic chromosome
+namespace: cellular_component
+def: "A chromosome found in the cytoplasm." [GOC:mah]
+subset: goslim_generic
+subset: gosubset_prok
+narrow_synonym: "cytoplasmic interphase chromosome" []
+is_a: GO:0005694
+relationship: part_of GO:0005737
+
+[Term]
+id: GO:0003674
+name: molecular_function
+namespace: molecular_function
+def: "Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions." [GOC:go_curators]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+
+[Term]
+id: GO:0003676
+name: nucleic acid binding
+namespace: molecular_function
+def: "Interacting selectively with any nucleic acid." [GOC:jl]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: gosubset_prok
+is_a: GO:0005488
+
+[Term]
+id: GO:0003677
+name: DNA binding
+namespace: molecular_function
+def: "Interacting selectively with DNA (deoxyribonucleic acid)." [GOC:jl]
+subset: goslim_generic
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+related_synonym: "microtubule/chromatin interaction" []
+narrow_synonym: "plasmid binding" []
+is_a: GO:0003676
+
+[Term]
+id: GO:0003682
+name: chromatin binding
+namespace: molecular_function
+def: "Interacting selectively with chromatin, the network of fibers of DNA and protein that make up the chromosomes of the eukaryotic nucleus during interphase." [GOC:jl, ISBN:0198506732]
+subset: goslim_generic
+subset: goslim_plant
+related_synonym: "microtubule/chromatin interaction" []
+narrow_synonym: "nuclear membrane vesicle binding to chromatin" []
+broad_synonym: "lamin/chromatin binding" []
+is_a: GO:0005488
+
+[Term]
+id: GO:0003700
+name: transcription factor activity
+namespace: molecular_function
+alt_id: GO:0000130
+def: "The function of binding to a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex." [GOC:curators]
+subset: goslim_generic
+subset: goslim_plant
+subset: gosubset_prok
+is_a: GO:0003677
+is_a: GO:0030528
+
+[Term]
+id: GO:0003723
+name: RNA binding
+namespace: molecular_function
+def: "Interacting selectively with an RNA molecule or a portion thereof." [GOC:mah]
+subset: goslim_generic
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+is_a: GO:0003676
+
+[Term]
+id: GO:0003774
+name: motor activity
+namespace: molecular_function
+def: "Catalysis of movement along a polymeric molecule such as a microfilament or microtubule, coupled to the hydrolysis of a nucleoside triphosphate." [GOC:mah, ISBN:0815316194]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+is_a: GO:0003674
+
+[Term]
+id: GO:0003779
+name: actin binding
+namespace: molecular_function
+def: "Interacting selectively with monomeric or multimeric forms of actin, including actin filaments." [GOC:clt]
+subset: goslim_generic
+narrow_synonym: "membrane associated actin binding" []
+is_a: GO:0008092
+
+[Term]
+id: GO:0003824
+name: catalytic activity
+namespace: molecular_function
+def: "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." [ISBN:0198506732]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: gosubset_prok
+related_synonym: "enzyme activity" []
+is_a: GO:0003674
+
+[Term]
+id: GO:0004518
+name: nuclease activity
+namespace: molecular_function
+def: "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN:0198547684]
+comment: Consider also annotating to the molecular function term 'nucleic acid binding ; GO:0003676'.
+subset: goslim_generic
+subset: goslim_plant
+subset: gosubset_prok
+xref_analog: EC:3.1.-.-
+is_a: GO:0016787
+
+[Term]
+id: GO:0004672
+name: protein kinase activity
+namespace: molecular_function
+alt_id: GO:0050222
+def: "Catalysis of the transfer of a phosphate group, usually from ATP, to a protein substrate." [GOC:jl]
+subset: goslim_generic
+subset: goslim_yeast
+subset: gosubset_prok
+narrow_synonym: "protamine kinase activity" []
+xref_analog: EC:2.7.1.37
+xref_analog: MetaCyc:PROTEIN-KINASE-RXN
+xref_analog: Reactome:4030
+is_a: GO:0016301
+
+[Term]
+id: GO:0004721
+name: phosphoprotein phosphatase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: a phosphoprotein + H2O = a protein + phosphate. Together with protein kinases, these enzymes control the state of phosphorylation of cell proteins and thereby provide an important mechanism for regulating cellular activity." [EC:3.1.3.16, ISBN:0198547684]
+subset: goslim_generic
+subset: goslim_yeast
+subset: gosubset_prok
+exact_synonym: "protein phosphatase activity" []
+xref_analog: EC:3.1.3.16
+xref_analog: MetaCyc:3.1.3.16-RXN
+xref_analog: Reactome:113432
+xref_analog: Reactome:113757
+xref_analog: Reactome:115322
+xref_analog: Reactome:115328
+xref_analog: Reactome:115332
+xref_analog: Reactome:117849
+xref_analog: Reactome:117855
+xref_analog: Reactome:117859
+xref_analog: Reactome:117862
+xref_analog: Reactome:120480
+xref_analog: Reactome:120488
+xref_analog: Reactome:122808
+xref_analog: Reactome:122814
+xref_analog: Reactome:122818
+xref_analog: Reactome:124864
+xref_analog: Reactome:124870
+xref_analog: Reactome:1887
+xref_analog: Reactome:69198
+xref_analog: Reactome:69262
+xref_analog: Reactome:69735
+xref_analog: Reactome:69742
+is_a: GO:0016787
+
+[Term]
+id: GO:0004871
+name: signal transducer activity
+namespace: molecular_function
+def: "Mediates the transfer of a signal from the outside to the inside of a cell by means other than the introduction of the signal molecule itself into the cell." [GOC:jl, ISBN:0198506732]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+narrow_synonym: "SAP kinase 3 activity" []
+narrow_synonym: "SAP kinase 4 activity" []
+narrow_synonym: "SAP kinase 5 activity" []
+is_a: GO:0003674
+
+[Term]
+id: GO:0004872
+name: receptor activity
+namespace: molecular_function
+def: "Combining with an extracellular or intracellular messenger to initiate a change in cell activity." [GOC:ceb, ISBN:0198506732]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: gosubset_prok
+related_synonym: "immunophilin" []
+narrow_synonym: "endoplasmic reticulum receptor activity" []
+narrow_synonym: "GPI-anchored membrane-bound receptor" []
+narrow_synonym: "peroxisome integral membrane receptor" []
+narrow_synonym: "peroxisome receptor" []
+narrow_synonym: "receptor guanylate cyclase activity" []
+is_a: GO:0004871
+
+[Term]
+id: GO:0005102
+name: receptor binding
+namespace: molecular_function
+def: "Interacting selectively with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function." [GOC:bf, GOC:ceb, ISBN:0198506732]
+subset: goslim_generic
+subset: goslim_plant
+subset: gosubset_prok
+related_synonym: "adrenocorticotropin" []
+related_synonym: "allatostatin" []
+related_synonym: "alpha-2 macroglobulin receptor-associated protein activity" []
+related_synonym: "bacteriocin activity" []
+related_synonym: "cell adhesion molecule activity" []
+related_synonym: "cell adhesion receptor inhibitor activity" []
+related_synonym: "cell adhesion receptor regulator activity" []
+related_synonym: "colicin" []
+related_synonym: "insulin" []
+related_synonym: "membrane-associated guanylate kinase" []
+related_synonym: "N-methyl-D-aspartate receptor-associated protein activity" []
+related_synonym: "nicotinic acetylcholine receptor-associated protein activity" []
+related_synonym: "receptor-associated protein activity" []
+related_synonym: "selectin" []
+related_synonym: "tachykinin" []
+related_synonym: "transmembrane receptor protein serine/threonine kinase related_receptor-associated protein activity" []
+narrow_synonym: "receptor ligand" []
+is_a: GO:0004871
+is_a: GO:0005515
+
+[Term]
+id: GO:0005198
+name: structural molecule activity
+namespace: molecular_function
+def: "The action of a molecule that contributes to the structural integrity of a complex or assembly within or outside a cell." [GOC:mah]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+related_synonym: "colicin" []
+related_synonym: "pore-forming toxin activity" []
+related_synonym: "puparial glue (sensu Diptera)" []
+related_synonym: "yolk protein" []
+is_a: GO:0003674
+
+[Term]
+id: GO:0005215
+name: transporter activity
+namespace: molecular_function
+def: "Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of, within or between cells." [GOC:ai, GOC:df]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+related_synonym: "small-molecule carrier or transporter" []
+narrow_synonym: "peroxisomal membrane transporter" []
+xref_analog: Reactome:1391
+is_a: GO:0003674
+
+[Term]
+id: GO:0005216
+name: ion channel activity
+namespace: molecular_function
+def: "Allows the regulatable energy-independent passage of ions across a lipid bilayer down a concentration gradient." [GOC:cy]
+subset: goslim_generic
+subset: gosubset_prok
+is_a: GO:0005215
+
+[Term]
+id: GO:0005326
+name: neurotransmitter transporter activity
+namespace: molecular_function
+def: "Enables the directed movement of a neurotransmitter into, out of, within or between cells. Neurotransmitters are any chemical substance that is capable of transmitting (or inhibiting the transmission of) a nerve impulse from a neuron to another cell." [GOC:ai, ISBN:0198506732]
+subset: goslim_generic
+subset: gosubset_prok
+is_a: GO:0005215
+
+[Term]
+id: GO:0005488
+name: binding
+namespace: molecular_function
+def: "The selective, often stoichiometric interaction of a molecule with one or more specific sites on another molecule." [GOC:ceb, GOC:mah, ISBN:0198506732]
+comment: Note that ligand is being used in its broadest biological sense. For ligands that bind to signal transducing receptors, consider the molecular function term 'receptor binding ; GO:0005102' and its children.
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: gosubset_prok
+narrow_synonym: "ligand" []
+is_a: GO:0003674
+
+[Term]
+id: GO:0005509
+name: calcium ion binding
+namespace: molecular_function
+def: "Interacting selectively with calcium ions (Ca2+)." [GOC:ai]
+subset: goslim_generic
+subset: gosubset_prok
+related_synonym: "calcium ion storage activity" []
+related_synonym: "fibrillin" []
+is_a: GO:0005488
+
+[Term]
+id: GO:0005515
+name: protein binding
+namespace: molecular_function
+alt_id: GO:0045308
+def: "Interacting selectively with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC:go_curators]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+related_synonym: "alpha-2 macroglobulin receptor-associated protein activity" []
+related_synonym: "calcium-dependent cell adhesion molecule activity" []
+related_synonym: "calcium-independent cell adhesion molecule activity" []
+related_synonym: "cell adhesion molecule activity" []
+related_synonym: "death receptor adaptor protein activity" []
+related_synonym: "death receptor interacting protein activity" []
+related_synonym: "death receptor-associated factor activity" []
+related_synonym: "glycine receptor-associated protein" []
+related_synonym: "N-methyl-D-aspartate receptor-associated protein activity" []
+related_synonym: "nicotinic acetylcholine receptor-associated protein activity" []
+related_synonym: "protein degradation tagging activity" []
+related_synonym: "protein tagging activity" []
+related_synonym: "receptor-associated protein activity" []
+exact_synonym: "protein amino acid binding" []
+is_a: GO:0005488
+
+[Term]
+id: GO:0005554
+name: molecular function unknown
+namespace: molecular_function
+def: "Used for the annotation of gene products whose function is not known or cannot be inferred." [GOC:sgd_curators]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+is_a: GO:0003674
+
+[Term]
+id: GO:0005575
+name: cellular_component
+namespace: cellular_component
+def: "The part of a cell of which a gene product is a component; for purpose of GO includes the extracellular environment of cells; a gene product may be a component of one or more parts of a cell; this term includes gene products that are parts of macromolecular complexes, by the definition that all members of a complex normally copurify under all except extreme conditions." [GOC:go_curators]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+
+[Term]
+id: GO:0005576
+name: extracellular region
+namespace: cellular_component
+def: "The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite." [GOC:go_curators]
+comment: Note that this term is intended to annotate gene products that are not attached to the cell surface.
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+exact_synonym: "extracellular" []
+is_a: GO:0005575
+
+[Term]
+id: GO:0005578
+name: extracellular matrix (sensu Metazoa)
+namespace: cellular_component
+def: "A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity. As in, but not restricted to, the multicellular animals (Metazoa, ncbi_taxonomy_id:33208)." [ISBN:0198547684]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+narrow_synonym: "adhesive extracellular matrix constituent" []
+relationship: part_of GO:0005576
+
+[Term]
+id: GO:0005615
+name: extracellular space
+namespace: cellular_component
+def: "That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid." [ISBN:0198547684]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+related_synonym: "intercellular space" []
+relationship: part_of GO:0005576
+
+[Term]
+id: GO:0005618
+name: cell wall
+namespace: cellular_component
+def: "The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan." [ISBN:0198547684]
+subset: goslim_generic
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+is_a: GO:0030312
+
+[Term]
+id: GO:0005622
+name: intracellular
+namespace: cellular_component
+def: "The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm." [ISBN:0198506732]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: gosubset_prok
+exact_synonym: "protoplasm" []
+relationship: part_of GO:0005623
+
+[Term]
+id: GO:0005623
+name: cell
+namespace: cellular_component
+def: "The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope." [GOC:go_curators]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: gosubset_prok
+is_a: GO:0005575
+
+[Term]
+id: GO:0005634
+name: nucleus
+namespace: cellular_component
+def: "A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent." [GOC:go_curators]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: goslim_yeast
+relationship: part_of GO:0005622
+is_a: GO:0043226
+
+[Term]
+id: GO:0005635
+name: nuclear envelope
+namespace: cellular_component
+alt_id: GO:0005636
+def: "The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space)." [ISBN:0198547684]
+subset: goslim_generic
+subset: goslim_plant
+relationship: part_of GO:0005634
+
+[Term]
+id: GO:0005654
+name: nucleoplasm
+namespace: cellular_component
+def: "That part of the nuclear content other than the chromosomes or the nucleolus." [GOC:ma, ISBN:0124325653]
+subset: goslim_generic
+subset: goslim_plant
+relationship: part_of GO:0005634
+
+[Term]
+id: GO:0005694
+name: chromosome
+namespace: cellular_component
+def: "A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information." [ISBN:0198547684]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_yeast
+subset: gosubset_prok
+related_synonym: "chromatid" []
+narrow_synonym: "interphase chromosome" []
+narrow_synonym: "prophase chromosome" []
+relationship: part_of GO:0005622
+is_a: GO:0043226
+
+[Term]
+id: GO:0005730
+name: nucleolus
+namespace: cellular_component
+def: "A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association res [...]
+subset: goslim_generic
+subset: goslim_plant
+subset: goslim_yeast
+relationship: part_of GO:0005634
+
+[Term]
+id: GO:0005737
+name: cytoplasm
+namespace: cellular_component
+def: "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN:0198547684]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+relationship: part_of GO:0005622
+
+[Term]
+id: GO:0005739
+name: mitochondrion
+namespace: cellular_component
+def: "A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration." [ISBN:0198506732]
+subset: goslim_generic
+subset: goslim_plant
+subset: goslim_yeast
+exact_synonym: "mitochondria" []
+relationship: part_of GO:0005737
+is_a: GO:0043226
+
+[Term]
+id: GO:0005764
+name: lysosome
+namespace: cellular_component
+def: "Any of a group of related cytoplasmic, membrane bound organelles that are found in most animal cells and that contain a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions." [ISBN:0198506732]
+subset: goslim_generic
+subset: goslim_plant
+related_synonym: "lysosomal cysteine-type endopeptidase" []
+related_synonym: "lysosomal protein stabilization" []
+is_a: GO:0005773
+
+[Term]
+id: GO:0005768
+name: endosome
+namespace: cellular_component
+def: "A membrane-bound organelle that carries materials newly ingested by endocytosis. It passes many of the materials to lysosomes for degradation." [ISBN:0198506732]
+subset: goslim_generic
+subset: goslim_plant
+related_synonym: "endosomal oligosaccharide transporter" []
+relationship: part_of GO:0005737
+is_a: GO:0043226
+
+[Term]
+id: GO:0005773
+name: vacuole
+namespace: cellular_component
+def: "A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material." [ISBN:0198506732]
+subset: goslim_generic
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+related_synonym: "vacuolar carboxypeptidase Y" []
+relationship: part_of GO:0005737
+is_a: GO:0043226
+
+[Term]
+id: GO:0005777
+name: peroxisome
+namespace: cellular_component
+alt_id: GO:0019818
+def: "A small, membrane-bounded organelle that uses dioxygen (O2) to oxidize organic molecules; contains some enzymes that produce and others that degrade hydrogen peroxide (H2O2)." [ISBN:0815316194]
+subset: goslim_generic
+subset: goslim_plant
+subset: goslim_yeast
+related_synonym: "peroxisomal fatty acyl transporter" []
+related_synonym: "peroxisomal membrane transporter" []
+related_synonym: "peroxisome receptor" []
+broad_synonym: "peroxisome vesicle" []
+relationship: part_of GO:0005737
+is_a: GO:0043226
+
+[Term]
+id: GO:0005783
+name: endoplasmic reticulum
+namespace: cellular_component
+def: "The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached)." [ISBN:0198506732]
+subset: goslim_generic
+subset: goslim_plant
+subset: goslim_yeast
+exact_synonym: "ER" []
+relationship: part_of GO:0005737
+is_a: GO:0043226
+
+[Term]
+id: GO:0005794
+name: Golgi apparatus
+namespace: cellular_component
+def: "A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cell [...]
+comment: Note that the Golgi apparatus can be located in various places in the cytoplasm. In plants and lower animal cells, the Golgi apparatus exists as many copies of discrete stacks dispersed throughout the cytoplasm, while the Golgi apparatus of interphase mammalian cells is a juxtanuclear, often pericentriolar reticulum, where the discrete Golgi stacks are stitched together to form a compact and interconnected ribbon, sometimes called the Golgi ribbon.
+subset: goslim_generic
+subset: goslim_plant
+subset: goslim_yeast
+exact_synonym: "Golgi" []
+exact_synonym: "Golgi complex" []
+narrow_synonym: "Golgi ribbon" []
+relationship: part_of GO:0005737
+is_a: GO:0043226
+
+[Term]
+id: GO:0005811
+name: lipid particle
+namespace: cellular_component
+def: "Any particle of coalesced lipids in the cytoplasm of a cell. May include associated proteins." [GOC:mah]
+comment: Note that this term does not refer to vesicle, but instead to structures in which lipids do not necessarily form bilayers.
+subset: goslim_generic
+exact_synonym: "lipid droplet" []
+relationship: part_of GO:0005737
+
+[Term]
+id: GO:0005815
+name: microtubule organizing center
+namespace: cellular_component
+def: "A region in a eukaryotic cell, such as a centrosome or basal body, from which microtubules grow." [ISBN:0815316194]
+subset: goslim_generic
+subset: goslim_yeast
+exact_synonym: "microtubule organising centre" []
+exact_synonym: "MTOC" []
+relationship: part_of GO:0005737
+
+[Term]
+id: GO:0005829
+name: cytosol
+namespace: cellular_component
+def: "That part of the cytoplasm that does not contain membranous or particulate subcellular components." [ISBN:0198547684]
+subset: goslim_generic
+subset: goslim_plant
+subset: gosubset_prok
+relationship: part_of GO:0005737
+
+[Term]
+id: GO:0005840
+name: ribosome
+namespace: cellular_component
+def: "An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) [...]
+subset: goslim_generic
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+narrow_synonym: "ribosomal RNA" []
+relationship: part_of GO:0005737
+is_a: GO:0043226
+is_a: GO:0043234
+
+[Term]
+id: GO:0005856
+name: cytoskeleton
+namespace: cellular_component
+def: "Any of the various filamentous elements within the cytoplasm of eukaryotic cells that remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, and the microtrabecular lattice. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movem [...]
+subset: goslim_generic
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+relationship: part_of GO:0005622
+is_a: GO:0043226
+
+[Term]
+id: GO:0005886
+name: plasma membrane
+namespace: cellular_component
+def: "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN:0716731363]
+subset: goslim_generic
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+related_synonym: "plasma membrane cation-transporting ATPase" []
+related_synonym: "plasma membrane copper transporter" []
+related_synonym: "plasma membrane long-chain fatty acid transporter" []
+exact_synonym: "cell membrane" []
+exact_synonym: "cytoplasmic membrane" []
+exact_synonym: "plasmalemma" []
+narrow_synonym: "bacterial inner membrane" []
+broad_synonym: "juxtamembrane" []
+relationship: part_of GO:0005623
+
+[Term]
+id: GO:0005929
+name: cilium
+namespace: cellular_component
+def: "A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole." [GOC:kva, ISBN:0198547684]
+subset: goslim_generic
+relationship: part_of GO:0005622
+is_a: GO:0043226
+
+[Term]
+id: GO:0005941
+name: unlocalized protein complex
+namespace: cellular_component
+def: "Used as a holding place for cellular components whose precise localization is, as yet, unknown, or has not been determined by GO (the latter is the major reason for nodes to have this parent); this term should not be used for annotation of gene products." [GOC:ma]
+comment: See also the cellular component term 'cellular component unknown ; GO:0008372'.
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: gosubset_prok
+is_a: GO:0043234
+
+[Term]
+id: GO:0005975
+name: carbohydrate metabolism
+namespace: biological_process
+def: "The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y." [ISBN:0198506732]
+subset: goslim_generic
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+is_a: GO:0044238
+
+[Term]
+id: GO:0006091
+name: generation of precursor metabolites and energy
+namespace: biological_process
+def: "The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and the processes involved in the liberation of energy from these substances." [GOC:jl]
+subset: goslim_generic
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+broad_synonym: "energy pathways" []
+is_a: GO:0008152
+
+[Term]
+id: GO:0006118
+name: electron transport
+namespace: biological_process
+def: "The transport of electrons from an electron donor to an electron acceptor." [http://cancerweb.ncl.ac.uk/]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+related_synonym: "6-phosphofructokinase reduction" []
+related_synonym: "dihydrobiopterin reduction" []
+related_synonym: "dihydrolipoamide reduction" []
+related_synonym: "dihydrolipoylprotein reduction" []
+related_synonym: "dihydropteridine reduction" []
+related_synonym: "other pathways of electron transport" []
+related_synonym: "oxidized glutathione reduction" []
+related_synonym: "protein-disulfide reduction" []
+exact_synonym: "electron transfer" []
+is_a: GO:0006091
+is_a: GO:0006810
+
+[Term]
+id: GO:0006139
+name: nucleobase, nucleoside, nucleotide and nucleic acid metabolism
+namespace: biological_process
+def: "The chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids." [GOC:ai]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: gosubset_prok
+is_a: GO:0044238
+
+[Term]
+id: GO:0006259
+name: DNA metabolism
+namespace: biological_process
+def: "The chemical reactions and pathways involving DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN:0198506732]
+subset: goslim_generic
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+is_a: GO:0006139
+
+[Term]
+id: GO:0006350
+name: transcription
+namespace: biological_process
+def: "The synthesis of either RNA on a template of DNA or DNA on a template of RNA." [ISBN:0198506732]
+subset: goslim_generic
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+xref_analog: Reactome:74159
+is_a: GO:0006139
+
+[Term]
+id: GO:0006412
+name: protein biosynthesis
+namespace: biological_process
+alt_id: GO:0006416
+alt_id: GO:0006453
+def: "The chemical reactions and pathways resulting in the formation of a protein, rather than of proteins in general." [GOC:go_curators]
+subset: goslim_generic
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+related_synonym: "protein-synthesizing GTPase activity" []
+related_synonym: "protein-synthesizing GTPase activity, elongation" []
+related_synonym: "protein-synthesizing GTPase activity, initiation" []
+related_synonym: "protein-synthesizing GTPase activity, termination" []
+exact_synonym: "protein anabolism" []
+exact_synonym: "protein formation" []
+exact_synonym: "protein synthesis" []
+is_a: GO:0009058
+is_a: GO:0019538
+
+[Term]
+id: GO:0006464
+name: protein modification
+namespace: biological_process
+def: "The covalent alteration of one or more amino acid residues within a protein, resulting in a change in the properties of that protein." [GOC:go_curators]
+subset: goslim_generic
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+related_synonym: "protein tagging activity" []
+narrow_synonym: "protein-pyrroloquinoline-quinone linkage" []
+xref_analog: Reactome:163841
+is_a: GO:0019538
+
+[Term]
+id: GO:0006519
+name: amino acid and derivative metabolism
+namespace: biological_process
+def: "The chemical reactions and pathways involving amino acids, organic acids containing one or more amino substituents, and compounds derived from amino acids." [ISBN:0198506732]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+is_a: GO:0044238
+
+[Term]
+id: GO:0006629
+name: lipid metabolism
+namespace: biological_process
+def: "The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids." [GOC:ma]
+subset: goslim_generic
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+is_a: GO:0044238
+
+[Term]
+id: GO:0006810
+name: transport
+namespace: biological_process
+def: "The directed movement of substances (such as macromolecules, small molecules, ions) into, out of, within or between cells." [GOC:mah]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+related_synonym: "hydrolase activity, acting on acid anhydrides, acting on GTP, involved in cellular and subcellular movement" []
+narrow_synonym: "small molecule transport" []
+narrow_synonym: "solute:solute exchange" []
+relationship: part_of GO:0007582
+
+[Term]
+id: GO:0006811
+name: ion transport
+namespace: biological_process
+def: "The directed movement of charged atoms or small charged molecules into, out of, within or between cells." [GOC:ai]
+subset: goslim_generic
+subset: gosubset_prok
+is_a: GO:0006810
+
+[Term]
+id: GO:0006950
+name: response to stress
+namespace: biological_process
+def: "A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation)." [GOC:mah]
+subset: goslim_generic
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+is_a: GO:0008150
+
+[Term]
+id: GO:0006996
+name: organelle organization and biogenesis
+namespace: biological_process
+def: "The assembly and arrangement of any organelle within a cell." [GOC:mah]
+subset: goslim_generic
+subset: goslim_yeast
+subset: gosubset_prok
+exact_synonym: "organelle organisation and biogenesis" []
+is_a: GO:0016043
+
+[Term]
+id: GO:0007005
+name: mitochondrion organization and biogenesis
+namespace: biological_process
+def: "The assembly and arrangement of a mitochondrion, including mitochondrial morphology and distribution, and replication of the mitochondrial genome as well as synthesis of new mitochondrial components." [GOC:mah, GOC:sgd_curators, PMID:9786946]
+subset: goslim_generic
+exact_synonym: "mitochondria organization and biogenesis" []
+exact_synonym: "mitochondrion organisation and biogenesis" []
+is_a: GO:0006996
+
+[Term]
+id: GO:0007010
+name: cytoskeleton organization and biogenesis
+namespace: biological_process
+def: "The assembly and arrangement of cytoskeletal structures." [GOC:mah]
+subset: goslim_generic
+subset: goslim_yeast
+subset: gosubset_prok
+related_synonym: "cytoskeletal regulator activity" []
+related_synonym: "negative regulation of cytoskeleton" []
+related_synonym: "positive regulation of cytoskeleton" []
+related_synonym: "regulation of cytoskeleton" []
+related_synonym: "Rho small monomeric GTPase activity" []
+exact_synonym: "cytoskeleton organisation and biogenesis" []
+is_a: GO:0006996
+
+[Term]
+id: GO:0007028
+name: cytoplasm organization and biogenesis
+namespace: biological_process
+def: "The assembly and arrangement of the cytoplasm and its components." [GOC:ems]
+subset: goslim_generic
+subset: gosubset_prok
+exact_synonym: "cytoplasm organisation and biogenesis" []
+is_a: GO:0016043
+
+[Term]
+id: GO:0007049
+name: cell cycle
+namespace: biological_process
+def: "The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division." [GOC:go_curators]
+subset: goslim_generic
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+exact_synonym: "cell-division cycle" []
+is_a: GO:0007582
+
+[Term]
+id: GO:0007154
+name: cell communication
+namespace: biological_process
+def: "Any process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment." [GOC:mah]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: gosubset_prok
+is_a: GO:0008150
+
+[Term]
+id: GO:0007165
+name: signal transduction
+namespace: biological_process
+def: "The cascade of processes by which a signal interacts with a receptor, causing a change in the level or activity of a second messenger or other downstream target, and ultimately effecting a change in the functioning of the cell." [GOC:go_curators]
+subset: goslim_generic
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+narrow_synonym: "activation of MAPK during sporulation (sensu Fungi)" []
+narrow_synonym: "activation of MAPK during sporulation (sensu Saccharomyces)" []
+narrow_synonym: "activation of MAPKK during sporulation (sensu Fungi)" []
+narrow_synonym: "activation of MAPKK during sporulation (sensu Saccharomyces)" []
+narrow_synonym: "activation of MAPKKK during sporulation (sensu Fungi)" []
+narrow_synonym: "activation of MAPKKK during sporulation (sensu Saccharomyces)" []
+narrow_synonym: "inactivation of MAPK during sporulation (sensu Fungi)" []
+narrow_synonym: "inactivation of MAPK during sporulation (sensu Saccharomyces)" []
+narrow_synonym: "MAPKKK cascade during sporulation (sensu Fungi)" []
+narrow_synonym: "MAPKKK cascade during sporulation (sensu Saccharomyces)" []
+is_a: GO:0007154
+
+[Term]
+id: GO:0007267
+name: cell-cell signaling
+namespace: biological_process
+def: "Any process that mediates the transfer of information from one cell to another." [GOC:mah]
+subset: goslim_generic
+subset: goslim_plant
+subset: gosubset_prok
+exact_synonym: "cell-cell signalling" []
+is_a: GO:0007154
+
+[Term]
+id: GO:0007275
+name: development
+namespace: biological_process
+def: "The biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, a young adult or a young single celled organism) to a later condition (e.g. a multicellular animal, an aged adult or a mature single celled organism)." [GOC:ems]
+comment: Note that this term was 'developmental process'.
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: gosubset_prok
+is_a: GO:0008150
+
+[Term]
+id: GO:0007582
+name: physiological process
+namespace: biological_process
+def: "Those processes specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms." [GOC:ems, ISBN:0198506732]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: gosubset_prok
+is_a: GO:0008150
+
+[Term]
+id: GO:0007610
+name: behavior
+namespace: biological_process
+def: "The specific actions or reactions of an organism in response to external or internal stimuli. Patterned activity of a whole organism in a manner dependent upon some combination of that organism's internal state and external conditions." [GOC:ems, ISBN:0395448956]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+exact_synonym: "behavioral response to stimulus" []
+exact_synonym: "behaviour" []
+exact_synonym: "behavioural response to stimulus" []
+is_a: GO:0008150
+
+[Term]
+id: GO:0008037
+name: cell recognition
+namespace: biological_process
+def: "The process by which a cell in a multicellular organism interprets its surroundings." [GOC:go_curators]
+subset: goslim_generic
+is_a: GO:0008150
+
+[Term]
+id: GO:0008092
+name: cytoskeletal protein binding
+namespace: molecular_function
+def: "Interacting selectively with any protein component of any cytoskeleton (actin, microtubule, or intermediate filament cytoskeleton)." [GOC:mah]
+subset: goslim_generic
+subset: gosubset_prok
+is_a: GO:0005515
+
+[Term]
+id: GO:0008135
+name: translation factor activity, nucleic acid binding
+namespace: molecular_function
+def: "Functions during translation by binding nucleic acids during polypeptide synthesis at the ribosome." [GOC:ai]
+subset: goslim_generic
+subset: goslim_plant
+subset: gosubset_prok
+related_synonym: "protein-synthesizing GTPase activity" []
+is_a: GO:0003676
+is_a: GO:0045182
+
+[Term]
+id: GO:0008150
+name: biological_process
+namespace: biological_process
+def: "A phenomenon marked by changes that lead to a particular result, mediated by one or more gene products." [GOC:go_curators]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+
+[Term]
+id: GO:0008152
+name: metabolism
+namespace: biological_process
+def: "Processes that cause many of the chemical changes in living organisms, including anabolism and catabolism. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation." [GOC:go_curators, ISBN:0198547684]
+comment: Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions.
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: gosubset_prok
+exact_synonym: "metabolic process" []
+narrow_synonym: "fat body metabolism (sensu Insecta)" []
+narrow_synonym: "metabolism resulting in cell growth" []
+xref_analog: Reactome:71408
+is_a: GO:0007582
+
+[Term]
+id: GO:0008219
+name: cell death
+namespace: biological_process
+def: "The specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death." [GOC:ems]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: gosubset_prok
+related_synonym: "necrosis" []
+is_a: GO:0016265
+
+[Term]
+id: GO:0008233
+name: peptidase activity
+namespace: molecular_function
+def: "Catalysis of the hydrolysis of peptide bonds." [GOC:jl]
+subset: goslim_generic
+subset: goslim_yeast
+subset: gosubset_prok
+exact_synonym: "hydrolase, acting on peptide bonds" []
+exact_synonym: "peptide hydrolase" []
+exact_synonym: "protease" []
+narrow_synonym: "proteasome endopeptidase activity" []
+xref_analog: EC:3.4.-.-
+is_a: GO:0016787
+
+[Term]
+id: GO:0008283
+name: cell proliferation
+namespace: biological_process
+def: "The multiplication or reproduction of cells, resulting in the rapid expansion of a cell population." [GOC:mah, GOC:mb]
+subset: goslim_generic
+subset: gosubset_prok
+is_a: GO:0007582
+
+[Term]
+id: GO:0008289
+name: lipid binding
+namespace: molecular_function
+def: "Interacting selectively with a lipid." [GOC:ai]
+subset: goslim_generic
+subset: goslim_plant
+subset: gosubset_prok
+is_a: GO:0005488
+
+[Term]
+id: GO:0008372
+name: cellular component unknown
+namespace: cellular_component
+def: "Used for the annotation of gene products whose localization is not known or cannot be inferred." [GOC:ma]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+is_a: GO:0005575
+
+[Term]
+id: GO:0009055
+name: electron carrier activity
+namespace: molecular_function
+def: "Any molecular entity that serves as an electron acceptor and electron donor in an electron transport system." [ISBN:0198506732]
+subset: goslim_generic
+subset: goslim_goa
+subset: gosubset_prok
+related_synonym: "electron carrier, chlorophyll electron transport system" []
+exact_synonym: "electron transporter activity" []
+narrow_synonym: "2Fe-2S electron transfer carrier" []
+narrow_synonym: "3Fe-4S/4Fe-4S electron transfer carrier" []
+narrow_synonym: "adrenodoxin-type ferredoxin" []
+narrow_synonym: "amicyanin" []
+narrow_synonym: "azurin" []
+narrow_synonym: "bacterial-type ferredoxin" []
+narrow_synonym: "chloroplast-type ferredoxin" []
+narrow_synonym: "copper electron carrier" []
+narrow_synonym: "dicluster bacterial-type ferredoxin" []
+narrow_synonym: "electron transfer flavoprotein" []
+narrow_synonym: "electron transfer flavoprotein, group I" []
+narrow_synonym: "electron transfer flavoprotein, group II" []
+narrow_synonym: "high-potential iron-sulfur carrier" []
+narrow_synonym: "iron-sulfur electron transfer carrier" []
+narrow_synonym: "monocluster bacterial-type ferredoxin" []
+narrow_synonym: "mononuclear iron electron carrier" []
+narrow_synonym: "polyferredoxin" []
+narrow_synonym: "redox-active disulfide bond electron carrier" []
+narrow_synonym: "rubredoxin" []
+narrow_synonym: "small blue copper electron carrier" []
+narrow_synonym: "thioredoxin-like 2Fe-2S ferredoxin" []
+is_a: GO:0003824
+
+[Term]
+id: GO:0009056
+name: catabolism
+namespace: biological_process
+def: "The chemical reactions and pathways resulting in the breakdown of substances, including the breakdown of carbon compounds with the liberation of energy for use by the cell or organism." [ISBN:0198547684]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: gosubset_prok
+exact_synonym: "breakdown" []
+exact_synonym: "degradation" []
+is_a: GO:0008152
+
+[Term]
+id: GO:0009058
+name: biosynthesis
+namespace: biological_process
+def: "The energy-requiring part of metabolism in which simpler substances are transformed into more complex ones, as in growth and other biosynthetic processes." [ISBN:0198547684]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: gosubset_prok
+exact_synonym: "anabolism" []
+exact_synonym: "formation" []
+exact_synonym: "synthesis" []
+is_a: GO:0008152
+
+[Term]
+id: GO:0009536
+name: plastid
+namespace: cellular_component
+def: "Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid." [GOC:jl, ISBN:0198547684]
+subset: goslim_generic
+subset: goslim_plant
+subset: gosubset_prok
+relationship: part_of GO:0005737
+is_a: GO:0043226
+
+[Term]
+id: GO:0009579
+name: thylakoid
+namespace: cellular_component
+def: "A sac-like vesicle that bears the photosynthetic pigments in photosynthetic organisms. In prokaryotes the thylakoids are of various shapes and are attached to the plasma membrane. In eukaryotes they are flattened, membrane-bound disk-like structures located in the chloroplasts; in the chloroplasts of higher plants the thylakoids form dense stacks called grana. Isolated thylakoid preparations can carry out photosynthetic electron transport and the associated phosphorylation." [ISBN: [...]
+subset: goslim_generic
+subset: goslim_plant
+subset: gosubset_prok
+related_synonym: "photosynthetic membrane" []
+relationship: part_of GO:0005622
+is_a: GO:0043226
+
+[Term]
+id: GO:0009605
+name: response to external stimulus
+namespace: biological_process
+def: "A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an external stimulus." [GOC:hb]
+subset: goslim_generic
+subset: goslim_plant
+subset: gosubset_prok
+exact_synonym: "response to environmental stimulus" []
+is_a: GO:0008150
+
+[Term]
+id: GO:0009607
+name: response to biotic stimulus
+namespace: biological_process
+def: "A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a biotic stimulus, a stimulus caused or produced by a living organism." [GOC:hb]
+subset: goslim_generic
+subset: goslim_plant
+subset: gosubset_prok
+is_a: GO:0008150
+
+[Term]
+id: GO:0009628
+name: response to abiotic stimulus
+namespace: biological_process
+def: "A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an abiotic (non-living) stimulus." [GOC:hb]
+subset: goslim_generic
+subset: goslim_plant
+subset: gosubset_prok
+is_a: GO:0008150
+
+[Term]
+id: GO:0009653
+name: morphogenesis
+namespace: biological_process
+def: "The process by which anatomical structures are generated and organized. Morphogenesis pertains to the creation of form." [GOC:go_curators, ISBN:0521436125]
+subset: goslim_generic
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+broad_synonym: "embryogenesis and morphogenesis" []
+relationship: part_of GO:0007275
+
+[Term]
+id: GO:0009719
+name: response to endogenous stimulus
+namespace: biological_process
+def: "A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an endogenous stimulus." [GOC:sm]
+subset: goslim_generic
+subset: goslim_plant
+subset: gosubset_prok
+is_a: GO:0008150
+
+[Term]
+id: GO:0009790
+name: embryonic development
+namespace: biological_process
+alt_id: GO:0009795
+def: "The process whose specific outcome is the progression of an embryo from zygote formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific and may be somewhat arbitrary. For example, it would be at birth for mammals, larval hatching for insects and seed dormancy in plants." [GOC:go_curators]
+subset: goslim_generic
+subset: goslim_plant
+exact_synonym: "embryogenesis" []
+exact_synonym: "embryonal development" []
+broad_synonym: "embryogenesis and morphogenesis" []
+is_a: GO:0007275
+
+[Term]
+id: GO:0015031
+name: protein transport
+namespace: biological_process
+alt_id: GO:0015831
+def: "The directed movement of proteins into, out of, within or between cells." [GOC:ai]
+subset: goslim_generic
+subset: gosubset_prok
+narrow_synonym: "enzyme transport" []
+is_a: GO:0006810
+
+[Term]
+id: GO:0016023
+name: cytoplasmic membrane-bound vesicle
+namespace: cellular_component
+def: "A membrane-bound vesicle found in the cytoplasm of the cell." [GOC:ai, GOC:mah]
+subset: goslim_generic
+subset: goslim_yeast
+subset: gosubset_prok
+exact_synonym: "cytoplasmic membrane bound vesicle" []
+relationship: part_of GO:0005737
+is_a: GO:0043226
+
+[Term]
+id: GO:0016032
+name: viral life cycle
+namespace: biological_process
+def: "A set of processes by which a virus reproduces. Usually, this is by infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle." [GOC:mah]
+comment: See also the biological process terms 'viral infectious cycle ; GO:0019058' and 'lysogeny ; GO:0030069'.
+subset: goslim_generic
+related_synonym: "viral infection" []
+related_synonym: "virulence" []
+exact_synonym: "viral replication cycle" []
+is_a: GO:0008150
+
+[Term]
+id: GO:0016043
+name: cell organization and biogenesis
+namespace: biological_process
+def: "The processes involved in the assembly and arrangement of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope." [GOC:ai]
+subset: goslim_generic
+subset: goslim_plant
+subset: gosubset_prok
+exact_synonym: "cell organisation and biogenesis" []
+is_a: GO:0007582
+
+[Term]
+id: GO:0016049
+name: cell growth
+namespace: biological_process
+def: "The process by which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present." [GOC:ai]
+subset: goslim_generic
+subset: goslim_plant
+subset: gosubset_prok
+related_synonym: "cell expansion" []
+related_synonym: "metabolism resulting in cell growth" []
+exact_synonym: "cellular growth" []
+exact_synonym: "growth of cell" []
+relationship: part_of GO:0009653
+relationship: part_of GO:0016043
+is_a: GO:0040007
+
+[Term]
+id: GO:0016209
+name: antioxidant activity
+namespace: molecular_function
+def: "Inhibition of the reactions brought about by dioxygen (O2) or peroxides. Usually the antioxidant is effective because it can itself be more easily oxidized than the substance protected. The term is often applied to components that can trap free radicals, thereby breaking the chain reaction that normally leads to extensive biological damage." [ISBN:0198506732]
+subset: goslim_generic
+subset: goslim_goa
+subset: gosubset_prok
+is_a: GO:0003674
+
+[Term]
+id: GO:0016265
+name: death
+namespace: biological_process
+def: "A permanent cessation of all vital functions: the end of life; can be applied to a whole organism or to a part of an organism." [GOC:mah, ISBN:0877797099]
+comment: See also the biological process term 'apoptosis ; GO:0006915'.
+subset: goslim_generic
+subset: goslim_plant
+subset: gosubset_prok
+is_a: GO:0007582
+
+[Term]
+id: GO:0016301
+name: kinase activity
+namespace: molecular_function
+def: "Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule." [ISBN:0198506732]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: gosubset_prok
+exact_synonym: "phosphokinase" []
+xref_analog: Reactome:113431
+xref_analog: Reactome:113433
+xref_analog: Reactome:114246
+xref_analog: Reactome:115027
+xref_analog: Reactome:115715
+xref_analog: Reactome:115932
+xref_analog: Reactome:115944
+xref_analog: Reactome:115947
+xref_analog: Reactome:115951
+xref_analog: Reactome:115974
+xref_analog: Reactome:115991
+xref_analog: Reactome:116605
+xref_analog: Reactome:117491
+xref_analog: Reactome:118310
+xref_analog: Reactome:118568
+xref_analog: Reactome:118583
+xref_analog: Reactome:118586
+xref_analog: Reactome:118589
+xref_analog: Reactome:118596
+xref_analog: Reactome:118617
+xref_analog: Reactome:118965
+xref_analog: Reactome:119356
+xref_analog: Reactome:120179
+xref_analog: Reactome:120930
+xref_analog: Reactome:121183
+xref_analog: Reactome:121192
+xref_analog: Reactome:121216
+xref_analog: Reactome:121239
+xref_analog: Reactome:121274
+xref_analog: Reactome:121543
+xref_analog: Reactome:122577
+xref_analog: Reactome:123125
+xref_analog: Reactome:123301
+xref_analog: Reactome:123309
+xref_analog: Reactome:123312
+xref_analog: Reactome:123316
+xref_analog: Reactome:123331
+xref_analog: Reactome:124636
+xref_analog: Reactome:125197
+xref_analog: Reactome:125408
+xref_analog: Reactome:125423
+xref_analog: Reactome:125426
+xref_analog: Reactome:125441
+xref_analog: Reactome:1423
+xref_analog: Reactome:68385
+xref_analog: Reactome:68401
+xref_analog: Reactome:69194
+xref_analog: Reactome:69222
+xref_analog: Reactome:69246
+xref_analog: Reactome:69254
+xref_analog: Reactome:69603
+xref_analog: Reactome:69607
+xref_analog: Reactome:69716
+xref_analog: Reactome:69904
+xref_analog: Reactome:69913
+xref_analog: Reactome:75047
+xref_analog: Reactome:75051
+xref_analog: Reactome:75052
+xref_analog: Reactome:75053
+xref_analog: Reactome:75054
+xref_analog: Reactome:75225
+xref_analog: Reactome:75371
+xref_analog: Reactome:75808
+xref_analog: Reactome:75819
+xref_analog: Reactome:83536
+is_a: GO:0016740
+
+[Term]
+id: GO:0016740
+name: transferase activity
+namespace: molecular_function
+def: "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." [ISBN:0198506732]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+xref_analog: EC:2
+is_a: GO:0003824
+
+[Term]
+id: GO:0016787
+name: hydrolase activity
+namespace: molecular_function
+def: "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN:0198506732]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+xref_analog: EC:3
+is_a: GO:0003824
+
+[Term]
+id: GO:0019538
+name: protein metabolism
+namespace: biological_process
+alt_id: GO:0006411
+def: "The chemical reactions and pathways involving a specific protein, rather than of proteins in general. Includes protein modification." [GOC:ma]
+subset: goslim_generic
+subset: goslim_plant
+subset: gosubset_prok
+exact_synonym: "protein metabolism and modification" []
+is_a: GO:0044238
+
+[Term]
+id: GO:0019725
+name: cell homeostasis
+namespace: biological_process
+def: "Any of the processes involved in the maintenance of an internal equilibrium within a cell or between a cell and its external environment." [GOC:jl, ISBN:0395825172]
+subset: goslim_generic
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+is_a: GO:0007582
+
+[Term]
+id: GO:0019748
+name: secondary metabolism
+namespace: biological_process
+def: "The chemical reactions and pathways resulting in many of the chemical changes of compounds that are not necessarily required for growth and maintenance of cells, and are often unique to a taxon. In multicellular organisms secondary metabolism is generally carried out in specific cell types, and may be useful for the organism as a whole. In unicellular organisms, secondary metabolism is often used for the production of antibiotics or for the utilization and acquisition of unusual nu [...]
+subset: goslim_generic
+subset: goslim_plant
+subset: gosubset_prok
+is_a: GO:0008152
+
+[Term]
+id: GO:0019825
+name: oxygen binding
+namespace: molecular_function
+def: "Interacting selectively with oxygen (O2)." [GOC:jl]
+subset: goslim_generic
+subset: goslim_plant
+subset: gosubset_prok
+related_synonym: "cytochrome P450 activity" []
+narrow_synonym: "cytochrome P450" []
+xref_analog: Reactome:4477
+is_a: GO:0005488
+
+[Term]
+id: GO:0030154
+name: cell differentiation
+namespace: biological_process
+def: "The process whereby relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate." [ISBN:0198506732]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: gosubset_prok
+relationship: part_of GO:0007275
+
+[Term]
+id: GO:0030188
+name: chaperone regulator activity
+namespace: molecular_function
+def: "Modulates the activity of a molecular chaperone." [GOC:mah]
+subset: goslim_generic
+subset: goslim_goa
+subset: gosubset_prok
+is_a: GO:0003674
+
+[Term]
+id: GO:0030234
+name: enzyme regulator activity
+namespace: molecular_function
+def: "Modulates the activity of an enzyme." [GOC:mah]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+exact_synonym: "enzyme modulator" []
+is_a: GO:0003674
+
+[Term]
+id: GO:0030246
+name: carbohydrate binding
+namespace: molecular_function
+def: "Interacting selectively with any carbohydrate." [GOC:mah]
+subset: goslim_generic
+subset: goslim_plant
+subset: gosubset_prok
+related_synonym: "cell adhesion molecule activity" []
+related_synonym: "cell adhesion receptor activity" []
+related_synonym: "selectin" []
+is_a: GO:0005488
+
+[Term]
+id: GO:0030312
+name: external encapsulating structure
+namespace: cellular_component
+def: "A structure that lies outside the plasma membrane and surrounds the entire cell." [GOC:go_curators]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: gosubset_prok
+relationship: part_of GO:0005623
+
+[Term]
+id: GO:0030313
+name: cell envelope
+namespace: cellular_component
+def: "Everything external to, but not including, the cytoplasmic membrane of bacteria, encompassing the periplasmic space, cell wall, and outer membrane if present." [GOC:jl, http://pathmicro.med.sc.edu/fox/cell_envelope.htm]
+subset: goslim_generic
+subset: gosubset_prok
+is_a: GO:0030312
+
+[Term]
+id: GO:0030528
+name: transcription regulator activity
+namespace: molecular_function
+def: "Plays a role in regulating transcription; may bind a promoter or enhancer DNA sequence or interact with a DNA-binding transcription factor." [GOC:mah]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+is_a: GO:0003674
+
+[Term]
+id: GO:0030533
+name: triplet codon-amino acid adaptor activity
+namespace: molecular_function
+def: "Mediates the insertion of an amino acid at the correct point in the sequence of a nascent polypeptide chain during protein synthesis." [ISBN:0198506732]
+comment: Note that this term can be used in place of the obsolete term 'transfer RNA ; GO:0005563'.
+subset: goslim_generic
+exact_synonym: "transfer RNA" []
+exact_synonym: "tRNA" []
+is_a: GO:0003674
+
+[Term]
+id: GO:0031386
+name: protein tag
+namespace: molecular_function
+def: "Acting as an indicator or marker to facilitate recognition by other molecules in the cell. Recognition of the tag, which can be covalently attached to the target molecule, may result in modification, sequestration, transport or degradation of the molecule in question." [GOC:go_curators]
+subset: goslim_generic
+related_synonym: "protein tagging activity" []
+related_synonym: "ubiquitin" []
+is_a: GO:0003674
+
+[Term]
+id: GO:0040007
+name: growth
+namespace: biological_process
+def: "The increase in size or mass of an entire organism, a part of an organism or a cell." [GOC:bf, GOC:ma]
+comment: See also the biological process term 'cell growth ; GO:0016049'.
+subset: goslim_generic
+subset: goslim_plant
+subset: gosubset_prok
+related_synonym: "growth pattern" []
+is_a: GO:0008150
+
+[Term]
+id: GO:0040029
+name: regulation of gene expression, epigenetic
+namespace: biological_process
+def: "Any process that modulates the frequency, rate or extent of gene expression; the process is mitotically or meiotically heritable, or is stably self-propagated in the cytoplasm of a resting cell, and does not entail a change in DNA sequence." [PMID:10521337, PMID:11498582]
+subset: goslim_generic
+subset: goslim_plant
+subset: gosubset_prok
+is_a: GO:0050789
+
+[Term]
+id: GO:0043226
+name: organelle
+namespace: cellular_component
+def: "Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane." [GOC:go_curators]
+subset: goslim_generic
+subset: gosubset_prok
+is_a: GO:0005575
+
+[Term]
+id: GO:0043234
+name: protein complex
+namespace: cellular_component
+def: "Any protein group composed of two or more subunits, which may or may not be identical. Protein complexes may have other associated non-protein prosthetic groups, such as nucleic acids, metal ions or carbohydrate groups." [GOC:go_curators]
+comment: Note that although at some level almost all cellular components can be thought of as protein complexes, this term is intended to exclude structures composed of the same repeating subunit or subunits, for example microtubules. Protein complexes encompassed by this term are generally not structural, and usually have a defined set of subunits.
+subset: goslim_generic
+subset: gosubset_prok
+is_a: GO:0005575
+
+[Term]
+id: GO:0044238
+name: primary metabolism
+namespace: biological_process
+def: "Reactions involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism." [GOC:go_curators, http://www.metacyc.org]
+subset: goslim_generic
+subset: gosubset_prok
+is_a: GO:0008152
+
+[Term]
+id: GO:0044403
+name: symbiosis, encompassing mutualism through parasitism
+namespace: biological_process
+alt_id: GO:0043298
+alt_id: GO:0044404
+def: "An interaction between two organisms living together in more or less intimate association. The term host is usually used for the larger (macro) of the two members of a symbiosis. The smaller (micro) member is called the symbiont. Microscopic symbionts are often referred to as endosymbionts. The various forms of symbiosis include parasitism, in which the association is disadvantageous or destructive to one of the organisms; mutualism, in which the association is advantageous, or oft [...]
+comment: Note that this term encompasses all symbiotic relationships between species along a continuum from mutualism through to parasitism, as outlined in the definition.
+subset: goslim_generic
+subset: gosubset_prok
+related_synonym: "host-pathogen interaction" []
+related_synonym: "symbiotic interaction between host and other organism" []
+related_synonym: "symbiotic interaction with other non-host organism" []
+exact_synonym: "symbiotic interaction between organisms" []
+exact_synonym: "symbiotic interaction between species" []
+is_a: GO:0008150
+
+[Term]
+id: GO:0045182
+name: translation regulator activity
+namespace: molecular_function
+def: "Any substance involved in the initiation, activation, perpetuation, repression or termination of polypeptide synthesis at the ribosome." [GOC:ai]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+is_a: GO:0003674
+
+[Term]
+id: GO:0045735
+name: nutrient reservoir activity
+namespace: molecular_function
+def: "Functions in the storage of nutritious substrates." [GOC:ai]
+comment: Note that this term can be used in place of the obsolete terms 'storage protein ; GO:0005187' and 'storage protein of fat body (sensu Insecta) ; GO:0008041'.
+subset: goslim_generic
+subset: gosubset_prok
+related_synonym: "storage protein" []
+related_synonym: "storage protein of fat body (sensu Insecta)" []
+related_synonym: "yolk protein" []
+is_a: GO:0003674
+
+[Term]
+id: GO:0050789
+name: regulation of biological process
+namespace: biological_process
+def: "Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule." [GOC:ai, GOC:go_curators]
+subset: goslim_generic
+subset: goslim_goa
+subset: gosubset_prok
+broad_synonym: "regulation" []
+is_a: GO:0008150
+
+[Typedef]
+id: part_of
+name: part of
+is_transitive: true
+
diff --git a/application/src/test/resources/testData/broken_t.gml b/application/src/test/resources/testData/broken_t.gml
new file mode 100644
index 0000000..b11b42b
--- /dev/null
+++ b/application/src/test/resources/testData/broken_t.gml
@@ -0,0 +1,1031 @@
+graph [
+ directed 0
+ node [
+ data [
+ Weight "outgroup weight= 0.01"
+ Frequency "frequency=1
+ Seq9
+"
+ Sequence "Sequence =
+ATGATATTTGTCCTCATGGAAGGACATATCCTATGAAAGCTGTTGCTATAACTATTAAAAGGAGGGTGATTCCAATATTTCAAGTTTCTTTAAGTATAAAAGAACCATAATAAATCCCTCGTCCGATGTGAATATAAATGCAAATAAAAAATAGTGAGGCTCCATTAGCATGTATATTACGAATTAATCATCCGTAATTTACATCGCGGCAAATGTGTGCGATTGATGAAAATGCAGAGGAAATGTCTGCGGTATAGTGTATTGCCAGAAATAGGCCGGTGAGAGTTTGTGTAATTAGACAAAGGCCTAATAAAGATCCAAAATTTCATATATAAGACAAGTTTGATGAGGTGGGTAAATCAATGAGCGAGTTATTAATAATATTTAGTATAGGATGTGTTTTT
+"
+ ]
+ id 8
+ label "Seq9 "
+ graphics [
+ Image [
+ Type ""
+ Location ""
+ ]
+ center [
+ x -339.0
+ y -95.0
+ z 0.0
+ ]
+ width 90.0
+ height 20.0
+ depth 20.0
+ ]
+ vgj [
+ labelPosition "center"
+ group 29
+ shape "Oval"
+ ]
+ ]
+ node [
+ data [
+ Weight "outgroup weight= 0.01"
+ Frequency "frequency=1
+ Seq6
+"
+ Sequence "Sequence =
+ACGATATTTGTCCTCATGGAAGGAAATATCCTATGAAAGCTGTTGCTATAACTATTAAAAGGAGGGTGATTCCAATATTTCAAGTTTCTTTAAGTATAAAAGAACCATAATAAATCCCTCGTCCGATGTGAATATAAATGCAAATAAAAAATAGTGAGGCTCCATTAGCATGTATATTACGAATTAATCATCCGTAATTTACATCGCGGCAAATGTGTGCGATTGATGAAAATGCAGAGGAAATGTCTGCGGTATAGTGTATTGCCAGAAATAGGCCGGTGAGAGTTTGTGTAATTAGACAAAGGCCTAATAAAGATCCAAAATTTCATATATAAGACAAGTTTGATGAGGTGGGTAAATCAATGAGCGAGTTATTAATAATATTTAGTAGAGGATGTGTTTTT
+"
+ ]
+ id 5
+ label "Seq6 "
+ graphics [
+ Image [
+ Type ""
+ Location ""
+ ]
+ center [
+ x -339.0
+ y -172.5
+ z 0.0
+ ]
+ width 90.0
+ height 20.0
+ depth 20.0
+ ]
+ vgj [
+ labelPosition "center"
+ group 28
+ shape "Oval"
+ ]
+ ]
+ node [
+ data [
+ Weight "outgroup weight= 0.01"
+ Frequency "frequency=1
+ Seq5
+"
+ Sequence "Sequence =
+ACGATATTTGTCCTCATGGAAGGGCATATCCTATGAAAGCTGTTGCTATAACTATTAAAAGGAGGGTGATTCCAATATTTCAAGTTTCTTTAAGTATAAAAGAACCATAATAAATCCCTCGTCCGATGTGAATATAAATGCAAATAAAAAATAGTGAGGCTCCATTAGCATGTATATTACGAATTAATCATCCGTAATTTACATCGCGGCAAATGTGTGCGATTGATGAAAATGCAGAGGAAATGTCTGCGGTATAGTGTATTGCCAGAAATAGGCCGGTGAGAGTTTGTGTAATTAGACAAAGGCCTAATAAAGATCCAAAATTTCATATATAAGACAAGTTTGATGAGGTGGGTAAATCAATGAGCGAGTTATTAATAATATTTAGTAGAGGATGTGTTTTT
+"
+ ]
+ id 4
+ label "Seq5 "
+ graphics [
+ Image [
+ Type ""
+ Location ""
+ ]
+ center [
+ x -219.0
+ y -172.5
+ z 0.0
+ ]
+ width 90.0
+ height 20.0
+ depth 20.0
+ ]
+ vgj [
+ labelPosition "center"
+ group 28
+ shape "Oval"
+ ]
+ ]
+ node [
+ data [
+ Weight "outgroup weight= 0.30"
+ Frequency "frequency=1
+ Seq7
+"
+ Sequence "Sequence =
+ACGATATTTGTCCTCATGGAAGGACATATCCTATGAAAGCTGTTGCTATAACTATTAAAAGGAGGGTGATTCCAATATTTCAAGTTTCTTTAAGTATAAAAGAACCATAATAAATCCCTCGTCCGATGTGAATATAAATGCAAATAAAAAATAGTGAGGCTCCATTAGCATGTATATTACGAATTAATCATCCGTAATTTACATCGCGGCAAATGTGTGCGATTGATGAAAATGCAGAGGAAATGTCTGCGGTATAGTGTATTGCCAGAAATAGGCCGGTGAGAGTTTGTGTAATTAGACAAAGGCCTAATAAAGATCCAAAATTTCATATATAAGACAAGTTTGATGAGGTGGGTAAATCAATGAGCGAGTTATTAATAATATTTAGTAGAGGATGTGTTTTT
+"
+ ]
+ id 6
+ label "Seq7 "
+ graphics [
+ Image [
+ Type ""
+ Location ""
+ ]
+ center [
+ x -219.0
+ y -95.0
+ z 0.0
+ ]
+ width 90.0
+ height 20.0
+ depth 20.0
+ ]
+ vgj [
+ labelPosition "center"
+ group 28
+ shape "Oval"
+ ]
+ ]
+ node [
+ data [
+ Weight "outgroup weight= 0.10"
+ Frequency "frequency=8 Seq4 Seq23 Seq24 Seq25 Seq26 Seq27 Seq28 eq29"
+ Sequence "Sequence =
+ATGATATTTGTCCTCATGGAACGACATATCCTATGAAAGCTGTTGCTATAACTATTAAAAGGAGGGTGATTCCAATATTTCAAGTTTCTTTAAGTATAAAAGAACCATAATAAATCCCTCGTCCGATGTGAATATAAATGCAAATAAAAAATAGTGAGGCTCCATTAGCATGTATATTACGAATTAATCATCCGTAATTTACATCGCGGCAAATGTGTGCGATTGATGAAAATGCAGAGGAAATGTCTGCGGTATAGTGTATTGCCAGAAATAGGCCGGTGAGAGTTTGTGTAATTAGACAAAGGCCTAATAAAGATCCAAAATTTCATATATAAGACAAGTTTGATGAGGTGGGTAAATCAATGAGCGAGTTATTAATAATATTTAGTAGAGGATGTGTTTTT
+"
+ ]
+ id 3
+ label "Seq4 "
+ graphics [
+ Image [
+ Type ""
+ Location ""
+ ]
+ center [
+ x -18.0
+ y -95.0
+ z 0.0
+ ]
+ width 125.0
+ height 55.0
+ depth 20.0
+ ]
+ vgj [
+ labelPosition "center"
+ group 29
+ shape "Oval"
+ ]
+ ]
+ node [
+ data [
+ Weight "outgroup weight= 0.01"
+ Frequency "frequency=1
+ Seq1
+"
+ Sequence "Sequence =
+ATGATAATTGTCCTCATGCAAGGACATATCCTATGAAAGCTGTTGCTATAACTATTAAAAGGAGGGTGATTCCAATATTTCAAGTTTCTTTAAGTATAAAAGAACCATAATAAATCCCTCGTCCGATGTGAATATAAATGCAAATAAAAAATAGTGAGGCTCCATTAGCATGTATATTACGAATTAATCATCCGTAATTTACATCGCGGCAAATGTGTGCGATTGATGAAAATGCAGAGGAAATGTCTGCGGTATAGTGTATTGCCAGAAATAGGCCGGTGAGAGTTTGTGTAATTAGACAAAGGCCTAATAAAGATCCAAAATTTCATATATAAGACAAGTTTGATGAGGTGGGTAAATCAATGAGCGAGTTATTAATAATATTTAGTAGAGGATGTGTTTTT
+"
+ ]
+ id 0
+ label "Seq1 "
+ graphics [
+ Image [
+ Type ""
+ Location ""
+ ]
+ center [
+ x 21.0
+ y -172.5
+ z 0.0
+ ]
+ width 90.0
+ height 20.0
+ depth 20.0
+ ]
+ vgj [
+ labelPosition "center"
+ group 27
+ shape "Oval"
+ ]
+ ]
+ node [
+ data [
+ Weight "outgroup weight= 0.00"
+ Frequency "frequency=1
+ In0
+"
+ Sequence "Sequence =
+ATGATAATTGTCCTCATGGAAGGACATATCCTATGAAAGCTGTTGCTATAACTATTAAAAGGAGGGTGATTCCAATATTTCAAGTTTCTTTAAGTATAAAAGAACCATAATAAATCCCTCGTCCGATGTGAATATAAATGCAAATAAAAAATAGTGAGGCTCCATTAGCATGTATATTACGAATTAATCATCCGTAATTTACATCGCGGCAAATGTGTGCGATTGATGAAAATGCAGAGGAAATGTCTGCGGTATAGTGTATTGCCAGAAATAGGCCGGTGAGAGTTTGTGTAATTAGACAAAGGCCTAATAAAGATCCAAAATTTCATATATAAGACAAGTTTGATGAGGTGGGTAAATCAATGAGCGAGTTATTAATAATATTTAGTAGAGGATGTGTTTTT
+"
+ ]
+ id 13
+ label " "
+ graphics [
+ Image [
+ Type ""
+ Location ""
+ ]
+ center [
+ x 141.0
+ y -95.0
+ z 0.0
+ ]
+ width 6.0
+ height 6.0
+ depth 1.0
+ ]
+ vgj [
+ labelPosition "center"
+ group 27
+ shape "Oval"
+ ]
+ ]
+ node [
+ data [
+ Weight "outgroup weight= 0.01"
+ Frequency "frequency=1
+ Seq2
+"
+ Sequence "Sequence =
+ATGATAATTGTCCTCATGGAAGTACATATCCTATGAAAGCTGTTGCTATAACTATTAAAAGGAGGGTGATTCCAATATTTCAAGTTTCTTTAAGTATAAAAGAACCATAATAAATCCCTCGTCCGATGTGAATATAAATGCAAATAAAAAATAGTGAGGCTCCATTAGCATGTATATTACGAATTAATCATCCGTAATTTACATCGCGGCAAATGTGTGCGATTGATGAAAATGCAGAGGAAATGTCTGCGGTATAGTGTATTGCCAGAAATAGGCCGGTGAGAGTTTGTGTAATTAGACAAAGGCCTAATAAAGATCCAAAATTTCATATATAAGACAAGTTTGATGAGGTGGGTAAATCAATGAGCGAGTTATTAATAATATTTAGTAGAGGATGTGTTTTT
+"
+ ]
+ id 1
+ label "Seq2 "
+ graphics [
+ Image [
+ Type ""
+ Location ""
+ ]
+ center [
+ x 141.0
+ y -172.5
+ z 0.0
+ ]
+ width 90.0
+ height 20.0
+ depth 20.0
+ ]
+ vgj [
+ labelPosition "center"
+ group 27
+ shape "Oval"
+ ]
+ ]
+ node [
+ data [
+ Weight "outgroup weight= 0.44"
+ Frequency "frequency=8 Seq10 Seq11 Seq12 Seq13 Seq14 Seq15 Seq18 Seq19 "
+ Sequence "Sequence =
+ATGATATTTGTCCTCATGGAAGGACATATCCTATGAAAGCTGTTGCTATAACTATTAAAAGGAGGGTGATTCCAATATTTCAAGTTTCTTTAAGTATAAAAGAACCATAATAAATCCCTCGTCCGATGTGAATATAAATGCAAATAAAAAATAGTGAGGCTCCATTAGCATGTATATTACGAATTAATCATCCGTAATTTACATCGCGGCAAATGTGTGCGATTGATGAAAATGCAGAGGAAATGTCTGCGGTATAGTGTATTGCCAGAAATAGGCCGGTGAGAGTTTGTGTAATTAGACAAAGGCCTAATAAAGATCCAAAATTTCATATATAAGACAAGTTTGATGAGGTGGGTAAATCAATGAGCGAGTTATTAATAATATTTAGTAGAGGATGTGTTTTT
+"
+ ]
+ id 9
+ label "Seq10 "
+ graphics [
+ Image [
+ Type ""
+ Location ""
+ ]
+ center [
+ x 0.0
+ y 0.0
+ z 0.0
+ ]
+ width 125.0
+ height 55.0
+ depth 20.0
+ ]
+ vgj [
+ labelPosition "center"
+ group 29
+ shape "Rectangle"
+ ]
+ ]
+ node [
+ data [
+ Weight "outgroup weight= 0.01"
+ Frequency "frequency=1
+ Seq3
+"
+ Sequence "Sequence =
+ATGATAATTGTCCTCATGGATGGACATATCCTATGAAAGCTGTTGCTATAACTATTAAAAGGAGGGTGATTCCAATATTTCAAGTTTCTTTAAGTATAAAAGAACCATAATAAATCCCTCGTCCGATGTGAATATAAATGCAAATAAAAAATAGTGAGGCTCCATTAGCATGTATATTACGAATTAATCATCCGTAATTTACATCGCGGCAAATGTGTGCGATTGATGAAAATGCAGAGGAAATGTCTGCGGTATAGTGTATTGCCAGAAATAGGCCGGTGAGAGTTTGTGTAATTAGACAAAGGCCTAATAAAGATCCAAAATTTCATATATAAGACAAGTTTGATGAGGTGGGTAAATCAATGAGCGAGTTATTAATAATATTTAGTAGAGGATGTGTTTTT
+"
+ ]
+ id 2
+ label "Seq3 "
+ graphics [
+ Image [
+ Type ""
+ Location ""
+ ]
+ center [
+ x 261.0
+ y -172.5
+ z 0.0
+ ]
+ width 90.0
+ height 20.0
+ depth 20.0
+ ]
+ vgj [
+ labelPosition "center"
+ group 27
+ shape "Oval"
+ ]
+ ]
+ node [
+ data [
+ Weight "outgroup weight= 0.01"
+ Frequency "frequency=1
+ Seq8
+"
+ Sequence "Sequence =
+ACTATATTTGTCCTCATGGAAGGACATATCCTATGAAAGCTGTTGCTATAACTATTAAAAGGAGGGTGATTCCAATATTTCAAGTTTCTTTAAGTATAAAAGAACCATAATAAATCCCTCGTCCGATGTGAATATAAATGCAAATAAAAAATAGTGAGGCTCCATTAGCATGTATATTACGAATTAATCATCCGTAATTTACATCGCGGCAAATGTGTGCGATTGATGAAAATGCAGAGGAAATGTCTGCGGTATAGTGTATTGCCAGAAATAGGCCGGTGAGAGTTTGTGTAATTAGACAAAGGCCTAATAAAGATCCAAAATTTCATATATAAGACAAGTTTGATGAGGTGGGTAAATCAATGAGCGAGTTATTAATAATATTTAGTAGAGGATGTGTTTTT
+"
+ ]
+ id 7
+ label "Seq8 "
+ graphics [
+ Image [
+ Type ""
+ Location ""
+ ]
+ center [
+ x -99.0
+ y -172.5
+ z 0.0
+ ]
+ width 90.0
+ height 20.0
+ depth 20.0
+ ]
+ vgj [
+ labelPosition "center"
+ group 28
+ shape "Oval"
+ ]
+ ]
+ node [
+ data [
+ Weight "outgroup weight= 0.00"
+ Frequency "frequency=1
+ In3
+"
+ Sequence "Sequence = "
+ ]
+ id 16
+ label " "
+ graphics [
+ Image [
+ Type ""
+ Location ""
+ ]
+ center [
+ x 339.0
+ y -95.0
+ z 0.0
+ ]
+ width 6.0
+ height 6.0
+ depth 1.0
+ ]
+ vgj [
+ labelPosition "center"
+ group 26
+ shape "Oval"
+ ]
+ ]
+ node [
+ data [
+ Weight "outgroup weight= 0.00"
+ Frequency "frequency=1
+ In4
+"
+ Sequence "Sequence = "
+ ]
+ id 17
+ label " "
+ graphics [
+ Image [
+ Type ""
+ Location ""
+ ]
+ center [
+ x 339.0
+ y -172.5
+ z 0.0
+ ]
+ width 6.0
+ height 6.0
+ depth 1.0
+ ]
+ vgj [
+ labelPosition "center"
+ group 25
+ shape "Oval"
+ ]
+ ]
+ node [
+ data [
+ Weight "outgroup weight= 0.00"
+ Frequency "frequency=1
+ In5
+"
+ Sequence "Sequence =
+"
+ ]
+ id 18
+ label " "
+ graphics [
+ Image [
+ Type ""
+ Location ""
+ ]
+ center [
+ x 339.0
+ y -225.5
+ z 0.0
+ ]
+ width 6.0
+ height 6.0
+ depth 1.0
+ ]
+ vgj [
+ labelPosition "center"
+ group 24
+ shape "Oval"
+ ]
+ ]
+ node [
+ data [
+ Weight "outgroup weight= 0.00"
+ Frequency "frequency=1
+ In6
+"
+ Sequence "Sequence = "
+ ]
+ id 19
+ label " "
+ graphics [
+ Image [
+ Type ""
+ Location ""
+ ]
+ center [
+ x 339.0
+ y -271.5
+ z 0.0
+ ]
+ width 6.0
+ height 6.0
+ depth 1.0
+ ]
+ vgj [
+ labelPosition "center"
+ group 23
+ shape "Oval"
+ ]
+ ]
+ node [
+ data [
+ Weight "outgroup weight= 0.02"
+ Frequency "frequency=2
+ Seq17
+ Seq22
+"
+ Sequence "Sequence =
+ATGATATTTGTCCTCATGGAAGGACATATTTTATGAAAGCTGTTGCTATAACTATTAAAAGGAGGGTGATTCCAATATTTCAAGTTTCTTTAAGTATAAAAGAACCATAATAAATCCCTCGTCCGATGTGAATATAAATGCAAATAAAAAATAGTGAGGCTCCATTAGCATGTATATTACGAATTAATCATCCGTAATTTACATCGCGGCAAATGTGTGCGATTGATGAAAATGCAGAGGAAATGTCTGCGGTATAGTGTATTGCCAGAAATAGGCCGGTGAGAGTTTGTGTAATTAGACAAAGGCCTAATAAAGATCCAAAATTTCATATATAAGACAAGTTTGATGAGGTGGGTAAATCAATGAGCGAGTTATTAATAATATTTAGTAGAGG-----TTTTT
+"
+ ]
+ id 11
+ label "Seq17 "
+ graphics [
+ Image [
+ Type ""
+ Location ""
+ ]
+ center [
+ x 276.5
+ y -433.0
+ z 0.0
+ ]
+ width 95.0
+ height 25.0
+ depth 20.0
+ ]
+ vgj [
+ labelPosition "center"
+ group 21
+ shape "Oval"
+ ]
+ ]
+ node [
+ data [
+ Weight "outgroup weight= 0.00"
+ Frequency "frequency=1
+ In2
+"
+ Sequence "Sequence = "
+ ]
+ id 15
+ label " "
+ graphics [
+ Image [
+ Type ""
+ Location ""
+ ]
+ center [
+ x 276.5
+ y -377.5
+ z 0.0
+ ]
+ width 6.0
+ height 6.0
+ depth 1.0
+ ]
+ vgj [
+ labelPosition "center"
+ group 21
+ shape "Oval"
+ ]
+ ]
+ node [
+ data [
+ Weight "outgroup weight= 0.02"
+ Frequency "frequency=2
+ Seq16
+ Seq21
+"
+ Sequence "Sequence =
+CTGATTTTTGTCCTCATGGAAGGACATATCCTATGAAAGCTGTTGCTATAACTATTAAAAGGAGGGTGATTCCAATATTTCAAGTTTCTTTAAGTATAAAAGAACCATAATAAATCCCTCGTCCGATGTGAATATAAATGCAAATAAAAAATAGTGAGGCTCCATTAGCATGTATATTACGAATTAATCATCCGTAATTTACATCGCGGCAAATGTGTGCGATTGATGAAAATGCAGAGGAAATGTCTGCGGTATAGTGTATTGCCAGAAATAGGCCGGTGAGAGTTTGTGTAATTAGACAAAGGCCTAATAAAGATCCAAAATTTCATATATAAGACAAGTTTGATGAGGTGGGTAAATCAATGAGCGAGTTATTAATAATATTTAGTAGAGG-----TTTTT
+"
+ ]
+ id 10
+ label "Seq16 "
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diff --git a/application/src/test/resources/testData/bug_839.sif b/application/src/test/resources/testData/bug_839.sif
new file mode 100644
index 0000000..f2bbe44
--- /dev/null
+++ b/application/src/test/resources/testData/bug_839.sif
@@ -0,0 +1,6 @@
+n1 activates n2 n4 n2 n5 n5
+n2 activates n5 n5 n5 n5 n1
+n3 inhibits n5 n4 n4 n3
+n4 activates n4 n4 n1 n2 n4
+n5 activates n1 n4 n1 n1 n5
+
diff --git a/application/src/test/resources/testData/degenerate.sif b/application/src/test/resources/testData/degenerate.sif
new file mode 100644
index 0000000..f3f1742
--- /dev/null
+++ b/application/src/test/resources/testData/degenerate.sif
@@ -0,0 +1,9 @@
+YNL312W
+YNL314W
+YOL051W
+YOR194C
+YOR377W
+YPL075W
+YPL248C
+YPL259C
+YPR065W
diff --git a/application/src/test/resources/testData/directedGraph.sif b/application/src/test/resources/testData/directedGraph.sif
new file mode 100644
index 0000000..7c653a7
--- /dev/null
+++ b/application/src/test/resources/testData/directedGraph.sif
@@ -0,0 +1,5 @@
+a pp b
+b pp a
+a pp b
+a pd b
+a pp a
diff --git a/application/src/test/resources/testData/explicitDouble.attribute b/application/src/test/resources/testData/explicitDouble.attribute
new file mode 100644
index 0000000..9e800f7
--- /dev/null
+++ b/application/src/test/resources/testData/explicitDouble.attribute
@@ -0,0 +1,4 @@
+Score (class=Java.lang.Double)
+a = 1
+b = 2
+c = 3.7
\ No newline at end of file
diff --git a/application/src/test/resources/testData/gal.gml b/application/src/test/resources/testData/gal.gml
new file mode 100644
index 0000000..84bda2e
--- /dev/null
+++ b/application/src/test/resources/testData/gal.gml
@@ -0,0 +1,303 @@
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+Version 1.0
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+ directed 1
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+ id 0
+ label "gal"
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+ y -54.0
+ w 50.0
+ h 30.0
+ type "rectangle"
+ width 1.00000
+ fill "#00FF00"
+ outline "#000000"
+ ]
+ ]
+ node
+ [
+ id 4
+ label "GAL4"
+ graphics
+ [
+ x 199.0
+ y 67.0
+ w 50.0
+ h 30.0
+ type "rectangle"
+ width 1.00000
+ fill "#EEEEEE"
+ outline "#000000"
+ ]
+ ]
+ node
+ [
+ id 5
+ label "GAL2"
+ graphics
+ [
+ x 9.0
+ y 223.0
+ w 50.0
+ h 30.0
+ type "rectangle"
+ width 1.00000
+ fill "#EEEEEE"
+ outline "#000000"
+ ]
+ ]
+ node
+ [
+ id 6
+ label "GAL1"
+ graphics
+ [
+ x 96.0
+ y 223.0
+ w 50.0
+ h 30.0
+ type "rectangle"
+ width 1.00000
+ fill "#EEEEEE"
+ outline "#000000"
+ ]
+ ]
+ node
+ [
+ id 7
+ label "GAL7"
+ graphics
+ [
+ x 169.0
+ y 222.0
+ w 50.0
+ h 30.0
+ type "rectangle"
+ width 1.00000
+ fill "#EEEEEE"
+ outline "#000000"
+ ]
+ ]
+ node
+ [
+ id 8
+ label "GAL10"
+ graphics
+ [
+ x 249.0
+ y 222.0
+ w 50.0
+ h 30.0
+ type "rectangle"
+ width 1.00000
+ fill "#EEEEEE"
+ outline "#000000"
+ ]
+ ]
+ node
+ [
+ id 9
+ label "GAL5"
+ graphics
+ [
+ x 327.0
+ y 220.0
+ w 50.0
+ h 30.0
+ type "rectangle"
+ width 1.00000
+ fill "#EEEEEE"
+ outline "#000000"
+ ]
+ ]
+ node
+ [
+ id 10
+ label "GAL6"
+ graphics
+ [
+ x 281.0
+ y -54.0
+ w 50.0
+ h 30.0
+ type "rectangle"
+ width 1.00000
+ fill "#EEEEEE"
+ outline "#000000"
+ ]
+ ]
+ edge
+ [
+ source 2
+ target 3
+ graphics
+ [
+ width 1
+ type "line"
+ fill "#000000"
+ arrow "last"
+ ]
+ ]
+ edge
+ [
+ source 3
+ target 4
+ graphics
+ [
+ width 1
+ type "line"
+ fill "#000000"
+ arrow "last"
+ ]
+ ]
+ edge
+ [
+ source 4
+ target 9
+ graphics
+ [
+ width 1
+ type "line"
+ fill "#000000"
+ arrow "last"
+ ]
+ ]
+ edge
+ [
+ source 4
+ target 7
+ graphics
+ [
+ width 1
+ type "line"
+ fill "#000000"
+ arrow "last"
+ ]
+ ]
+ edge
+ [
+ source 4
+ target 6
+ graphics
+ [
+ width 1
+ type "line"
+ fill "#000000"
+ arrow "last"
+ ]
+ ]
+ edge
+ [
+ source 4
+ target 5
+ graphics
+ [
+ width 1
+ type "line"
+ fill "#000000"
+ arrow "last"
+ ]
+ ]
+ edge
+ [
+ source 0
+ target 2
+ graphics
+ [
+ width 1
+ type "line"
+ fill "#000000"
+ arrow "last"
+ ]
+ ]
+ edge
+ [
+ source 1
+ target 2
+ graphics
+ [
+ width 1
+ type "line"
+ fill "#000000"
+ arrow "last"
+ ]
+ ]
+ edge
+ [
+ source 10
+ target 4
+ graphics
+ [
+ width 1
+ type "line"
+ fill "#000000"
+ arrow "last"
+ ]
+ ]
+ edge
+ [
+ source 4
+ target 8
+ graphics
+ [
+ width 1
+ type "line"
+ fill "#000000"
+ arrow "last"
+ ]
+ ]
+]
diff --git a/application/src/test/resources/testData/gal1.22x5.mRNA b/application/src/test/resources/testData/gal1.22x5.mRNA
new file mode 100644
index 0000000..eef10fc
--- /dev/null
+++ b/application/src/test/resources/testData/gal1.22x5.mRNA
@@ -0,0 +1,23 @@
+GENE DESCRIPT gal1RG.sig gal2RG.sig gal3RG.sig gal4RG.sig gal5RG.sig gal1RG.sig gal2RG.sig gal3RG.sig gal4RG.sig gal5RG.sig NumSigConds
+YHR051W COX6 -0.034 -0.052 0.152 0.111 -0.198 1.177 0.102 0.857 3.009 0.375 10
+YHR124W NDT80 -0.090 -0.000 0.041 0.007 0.157 0.130 0.341 0.061 -0.348 1.814 10
+YKL181W PRS1 -0.167 -0.063 -0.230 -0.233 -0.003 -0.233 0.143 0.089 0.112 11.206 10
+YGR072W UPF3 0.245 0.415 0.253 -0.471 0.115 0.134 0.414 -0.120 0.787 18.726 10
+YHL020C OPI1 0.174 0.045 0.046 -0.015 0.098 0.019 0.038 0.036 0.151 21.750 10
+YGR145W YGR145W 0.387 -0.000 -0.036 -0.577 0.151 -0.324 -0.110 -0.463 -0.088 11.621 10
+YGL041C YGL041C 0.285 -0.232 0.126 -0.086 -0.096 0.122 0.477 -0.392 0.103 18.493 10
+YGR218W CRM1 -0.018 0.009 -0.070 -0.001 -0.052 -0.105 0.052 0.060 -0.018 0.382 10
+YOR202W HIS3 -0.432 -0.568 -0.339 -0.710 -0.188 -0.634 0.000 0.000 0.239 9.703 10
+YCR005C CIT2 0.085 0.272 0.038 0.392 0.168 0.313 -0.288 0.033 0.464 6.209 10
+YER187W KHS1 0.159 0.168 0.149 0.139 -0.293 0.062 -0.139 -0.076 -0.045 16.689 10
+YBR026C YBR026C 0.276 0.072 0.324 0.189 0.014 0.305 -0.023 0.039 0.291 25.581 10
+YMR244W YMR244W 0.078 -0.000 -0.077 -0.239 0.077 0.189 0.322 -0.000 -0.072 0.469 10
+YMR317W YMR317W -0.181 0.324 -0.065 0.086 -0.288 -0.100 0.317 0.084 -0.453 5.327 10
+YAR047C YAR047C -0.234 -0.121 0.019 -0.109 -0.107 0.185 -0.013 -0.717 0.155 7.571 10
+YIR031C DAL7 0.289 0.168 0.090 -0.161 -0.017 0.109 -0.029 -0.116 1.085 26.087 10
+YDL177C YDL177C -0.002 -0.295 0.041 -0.367 -0.183 -0.247 0.151 0.005 0.633 0.001 10
+YLR338W YLR338W -0.216 0.091 -0.051 0.096 -0.070 -0.120 -0.139 0.072 -0.238 27.075 10
+YGR073C YGR073C -0.125 -0.394 -0.056 -0.126 -0.218 -0.077 0.028 -0.310 -0.051 5.498 10
+YGR146C YGR146C -0.189 0.308 -0.345 -0.067 0.432 -0.330 0.038 -0.159 0.341 12.620 10
+YOR130C ORT1 -0.025 -0.068 -0.108 -0.322 0.195 -0.193 0.065 0.011 0.172 0.430 10
+YLR193C YLR193C 0.124 0.122 0.106 0.057 -0.315 0.037 -0.064 -0.138 -0.052 10.495 10
diff --git a/application/src/test/resources/testData/gal1.22x5.mRNA_wo_descript b/application/src/test/resources/testData/gal1.22x5.mRNA_wo_descript
new file mode 100644
index 0000000..81f3544
--- /dev/null
+++ b/application/src/test/resources/testData/gal1.22x5.mRNA_wo_descript
@@ -0,0 +1,23 @@
+GENE gal1RG.sig gal2RG.sig gal3RG.sig gal4RG.sig gal5RG.sig gal1RG.sig gal2RG.sig gal3RG.sig gal4RG.sig gal5RG.sig NumSigConds
+YHR051W -0.034 -0.052 0.152 0.111 -0.198 1.177 0.102 0.857 3.009 0.375 10
+YHR124W -0.09 0 0.041 0.007 0.157 0.13 0.341 0.061 -0.348 1.814 10
+YKL181W -0.167 -0.063 -0.23 -0.233 -0.003 -0.233 0.143 0.089 0.112 11.206 10
+YGR072W 0.245 0.415 0.253 -0.471 0.115 0.134 0.414 -0.12 0.787 18.726 10
+YHL020C 0.174 0.045 0.046 -0.015 0.098 0.019 0.038 0.036 0.151 21.75 10
+YGR145W 0.387 0 -0.036 -0.577 0.151 -0.324 -0.11 -0.463 -0.088 11.621 10
+YGL041C 0.285 -0.232 0.126 -0.086 -0.096 0.122 0.477 -0.392 0.103 18.493 10
+YGR218W -0.018 0.009 -0.07 -0.001 -0.052 -0.105 0.052 0.06 -0.018 0.382 10
+YOR202W -0.432 -0.568 -0.339 -0.71 -0.188 -0.634 0 0 0.239 9.703 10
+YCR005C 0.085 0.272 0.038 0.392 0.168 0.313 -0.288 0.033 0.464 6.209 10
+YER187W 0.159 0.168 0.149 0.139 -0.293 0.062 -0.139 -0.076 -0.045 16.689 10
+YBR026C 0.276 0.072 0.324 0.189 0.014 0.305 -0.023 0.039 0.291 25.581 10
+YMR244W 0.078 0 -0.077 -0.239 0.077 0.189 0.322 0 -0.072 0.469 10
+YMR317W -0.181 0.324 -0.065 0.086 -0.288 -0.1 0.317 0.084 -0.453 5.327 10
+YAR047C -0.234 -0.121 0.019 -0.109 -0.107 0.185 -0.013 -0.717 0.155 7.571 10
+YIR031C 0.289 0.168 0.09 -0.161 -0.017 0.109 -0.029 -0.116 1.085 26.087 10
+YDL177C -0.002 -0.295 0.041 -0.367 -0.183 -0.247 0.151 0.005 0.633 0.001 10
+YLR338W -0.216 0.091 -0.051 0.096 -0.07 -0.12 -0.139 0.072 -0.238 27.075 10
+YGR073C -0.125 -0.394 -0.056 -0.126 -0.218 -0.077 0.028 -0.31 -0.051 5.498 10
+YGR146C -0.189 0.308 -0.345 -0.067 0.432 -0.33 0.038 -0.159 0.341 12.62 10
+YOR130C -0.025 -0.068 -0.108 -0.322 0.195 -0.193 0.065 0.011 0.172 0.43 10
+YLR193C 0.124 0.122 0.106 0.057 -0.315 0.037 -0.064 -0.138 -0.052 10.495 10
diff --git a/application/src/test/resources/testData/galFiltered.edgeAttrs2 b/application/src/test/resources/testData/galFiltered.edgeAttrs2
new file mode 100644
index 0000000..9afbc3d
--- /dev/null
+++ b/application/src/test/resources/testData/galFiltered.edgeAttrs2
@@ -0,0 +1,354 @@
+TestEdgeAttribute2
+YKR026C (pp) YGL122C = 2
+YGR218W (pp) YGL097W = 2
+YGL097W (pp) YOR204W = 2
+YLR249W (pp) YPR080W = 2
+YLR249W (pp) YBR118W = 2
+YLR293C (pp) YGL097W = 2
+YMR146C (pp) YDR429C = 2
+YDR429C (pp) YFL017C = 2
+YPR080W (pp) YAL003W = 2
+YBR118W (pp) YAL003W = 2
+YOL123W (pp) YGL044C = 2
+YPL211W (pp) YGR014W = 2
+YJL030W (pp) YGL229C = 2
+YJL013C (pp) YGL229C = 2
+YGL122C (pp) YOL123W = 2
+YGR014W (pp) YJL030W = 2
+YGR014W (pp) YJL013C = 2
+YGR203W (pp) YIL061C = 2
+YCR084C (pp) YBR112C = 2
+YCR084C (pp) YCL067C = 2
+YER112W (pp) YOR167C = 2
+YJR022W (pp) YNR050C = 2
+YJR022W (pp) YNL050C = 2
+YJR022W (pp) YEL015W = 2
+YJR022W (pp) YOR167C = 2
+YJR022W (pp) YLR264W = 2
+YJR022W (pp) YNR053C = 2
+YER116C (pp) YDL013W = 2
+YNL307C (pp) YAL038W = 2
+YNL216W (pd) YCR012W = 2
+YNL216W (pd) YGR254W = 2
+YNL216W (pd) YHR174W = 2
+YNL216W (pd) YIL133C = 2
+YNL216W (pd) YLR044C = 2
+YNL216W (pd) YOL120C = 2
+YNL216W (pd) YNL301C = 2
+YNL216W (pd) YCL030C = 2
+YNL216W (pp) YDR171W = 2
+YNL216W (pd) YBR093C = 2
+YNL216W (pd) YER074W = 2
+YNL216W (pd) YIL069C = 2
+YNL216W (pd) YAL038W = 2
+YNL216W (pd) YOL127W = 2
+YNL216W (pd) YDR050C = 2
+YNL216W (pd) YOL086C = 2
+YAL030W (pp) YER143W = 2
+YOR327C (pp) YER143W = 2
+YER062C (pp) YPL201C = 2
+YDR412W (pp) YCR086W = 2
+YDR412W (pp) YGL013C = 2
+YDR412W (pp) YLR117C = 2
+YDR412W (pp) YPR119W = 2
+YDL014W (pp) YOR310C = 2
+YER179W (pp) YLR044C = 2
+YER179W (pp) YLR134W = 2
+YER179W (pp) YIL105C = 2
+YOR361C (pp) YMR309C = 2
+YOR361C (pp) YDR429C = 2
+YOR326W (pp) YGL106W = 2
+YMR186W (pp) YBR155W = 2
+YEL009C (pd) YMR108W = 2
+YEL009C (pd) YOR202W = 2
+YEL009C (pd) YCL030C = 2
+YEL009C (pd) YBR248C = 2
+YEL009C (pd) YOL058W = 2
+YEL009C (pd) YMR300C = 2
+YMR138W (pp) YHR141C = 2
+YMR138W (pp) YLR109W = 2
+YCL032W (pp) YDR032C = 2
+YCL032W (pp) YLR362W = 2
+YCL032W (pp) YDR103W = 2
+YCR012W (pd) YJR060W = 2
+YBR019C (pd) YOL051W = 2
+YBR019C (pd) YGL035C = 2
+YOL051W (pd) YBR020W = 2
+YOL051W (pd) YLR081W = 2
+YOL051W (pp) YPL248C = 2
+YOL051W (pd) YBR018C = 2
+YIR009W (pp) YKR099W = 2
+YIR009W (pp) YIL143C = 2
+YIR009W (pp) YDR184C = 2
+YIR009W (pp) YNL091W = 2
+YNL236W (pp) YKL012W = 2
+YML032C (pp) YNL312W = 2
+YLR116W (pp) YKL012W = 2
+YCR086W (pp) YOR264W = 2
+YDR309C (pp) YLR229C = 2
+YGR058W (pp) YOR264W = 2
+YJR109C (pp) YOR303W = 2
+YLR256W (pd) YML054C = 2
+YLR256W (pd) YJR048W = 2
+YLR256W (pd) YEL039C = 2
+YGL237C (pd) YJR048W = 2
+YBL021C (pd) YJR048W = 2
+YDR311W (pp) YKL028W = 2
+YPL149W (pp) YHR171W = 2
+YPL149W (pp) YBR217W = 2
+YKL109W (pp) YGL237C = 2
+YKL109W (pp) YBL021C = 2
+YKL109W (pd) YJR048W = 2
+YKL109W (pd) YGL035C = 2
+YMR043W (pd) YIL015W = 2
+YMR043W (pd) YJL159W = 2
+YMR043W (pd) YKR097W = 2
+YMR043W (pd) YGR108W = 2
+YMR043W (pd) YDR461W = 2
+YMR043W (pd) YNL145W = 2
+YMR043W (pd) YJL157C = 2
+YMR043W (pd) YFL026W = 2
+YHR171W (pp) YDR412W = 2
+YHR171W (pp) YNR007C = 2
+YNR050C (pp) YMR138W = 2
+YJL203W (pp) YOL136C = 2
+YLL021W (pp) YLR362W = 2
+YGL013C (pd) YJL219W = 2
+YGL013C (pd) YOL156W = 2
+YKL101W (pp) YBR160W = 2
+YCL067C (pd) YIL015W = 2
+YCL067C (pp) YMR043W = 2
+YCL067C (pd) YDR461W = 2
+YCL067C (pd) YFL026W = 2
+YBL005W (pd) YJL219W = 2
+YDR323C (pp) YOR036W = 2
+YGL008C (pd) YMR043W = 2
+YER040W (pd) YPR035W = 2
+YER040W (pd) YGR019W = 2
+YNL098C (pp) YLR310C = 2
+YGL115W (pp) YGL208W = 2
+YPL089C (pp) YHR030C = 2
+YJL089W (pd) YER065C = 2
+YJL089W (pd) YKR097W = 2
+YJL089W (pd) YLR377C = 2
+YMR021C (pd) YLR214W = 2
+YDR335W (pp) YDR174W = 2
+YLL028W (pp) YGL166W = 2
+YIL143C (pp) YDR311W = 2
+YDL081C (pp) YLR340W = 2
+YKL012W (pp) YKL074C = 2
+YEL015W (pp) YML064C = 2
+YHR135C (pp) YNL116W = 2
+YMR309C (pp) YNL047C = 2
+YNL154C (pp) YKL204W = 2
+YDR382W (pp) YFL029C = 3
+YFL039C (pp) YCL020W = 3
+YFL039C (pp) YHR129W = 3
+YPL075W (pd) YCR022W = 3
+YPL075W (pd) YGR224W = 3
+YPL075W (pd) YHR124W = 3
+YPL075W (pp) YNL129C = 3
+YPL075W (pd) YDR020C = 3
+YPL075W (pd) YOL026C = 3
+YNL199C (pp) YPR028W = 3
+YCL030C (pd) YKR029W = 3
+YBL069W (pp) YGL028C = 3
+YNL189W (pp) YDL226W = 3
+YNL189W (pp) YPL121W = 3
+YNL189W (pp) YER025C = 3
+YNL189W (pp) YPR022W = 3
+YDR184C (pp) YLR329C = 3
+YNL311C (pp) YKL021C = 3
+YOL058W (pp) YNL129W = 3
+YOL016C (pp) YBR129C = 3
+YJL036W (pp) YDL123C = 3
+YEL041W (pp) YHR125C = 3
+YNL167C (pd) YOR222W = 3
+YDL063C (pp) YPL121W = 3
+YGL161C (pp) YDR120W = 3
+YMR183C (pp) YGR029C = 3
+YMR291W (pp) YGL125W = 3
+YGR048W (pp) YPL222W = 3
+YAL040C (pd) YMR023W = 3
+YFR034C (pd) YBR023C = 3
+YFR037C (pp) YOR220C = 3
+YER133W (pp) YDR422W = 3
+YER133W (pp) YOR128C = 3
+YER133W (pp) YOR325W = 3
+YER133W (pp) YMR321C = 3
+YER133W (pp) YBR020C = 3
+YGL035C (pd) YLR024C = 3
+YGL035C (pd) YLR327C = 3
+YGL035C (pd) YIL122W = 3
+YFL038C (pp) YOR026W = 3
+YOR355W (pp) YNL021W = 3
+YML074C (pp) YJL120C = 3
+YMR058W (pp) YER125C = 3
+YML123C (pd) YFR024C = 3
+YPL031C (pp) YHR021W = 3
+YAL038W (pd) YPL025W = 3
+YML051W (pp) YBR020W = 3
+YML051W (pp) YDR029W = 3
+YLL019C (pp) YIL123W = 3
+YML024W (pd) YNL226W = 3
+YOR039W (pp) YOR323W = 3
+YER111C (pd) YMR023W = 3
+YDR146C (pd) YMR023W = 3
+YDR146C (pd) YGL025C = 3
+YKL211C (pp) YER020W = 3
+YDR354W (pd) YEL029C = 3
+YNL113W (pp) YPR120C = 3
+YLR310C (pp) YER123W = 3
+YNL047C (pp) YIL125C = 3
+YBR160W (pd) YMR023W = 3
+YBR160W (pp) YGR128W = 3
+YIL113W (pp) YHR020C = 3
+YLR117C (pp) YBR120W = 3
+YFL017C (pp) YOL029W = 3
+YFL017C (pp) YER122W = 3
+YFL017C (pp) YOR322C = 3
+YMR044W (pp) YIL021C = 3
+YOL149W (pp) YOR127C = 3
+YOR036W (pp) YDR120W = 3
+YOR036W (pp) YGL121C = 3
+YLR191W (pp) YGL123W = 3
+YER110C (pp) YML027W = 3
+YBR135W (pp) YER122W = 3
+YNL214W (pp) YGL123W = 3
+YJR060W (pd) YPR127C = 3
+YOR089C (pp) YDR323C = 3
+YNL117W (pd) YJL029W = 3
+YLR175W (pp) YNL327C = 3
+YDR167W (pp) YLR422W = 3
+YGR108W (pp) YBR125W = 3
+YDR244W (pp) YLR121W = 3
+YDR244W (pp) YGL123W = 3
+YDR244W (pp) YNL224W = 3
+YDR244W (pp) YDR122C = 3
+YDR244W (pp) YDL028C = 3
+YPR119W (pd) YMR023W = 3
+YDR142C (pp) YGL123W = 3
+YDR142C (pp) YIL120C = 3
+YBR020W (pd) YGL025C = 3
+YDR009W (pd) YGL025C = 3
+YPL248C (pd) YBR029C = 3
+YPL248C (pd) YML021W = 3
+YPL248C (pp) YML021W = 3
+YPL248C (pd) YBR020W = 3
+YPL248C (pd) YLR021W = 3
+YPL248C (pd) YBR028C = 3
+YAR007C (pp) YML022C = 3
+YAR007C (pd) YPL121W = 3
+YKL161C (pp) YPL029C = 3
+YNL312W (pd) YPL121W = 3
+YLR075W (pp) YPR122C = 3
+YLR229C (pp) YJL127C = 3
+YPL240C (pp) YBR125W = 3
+YPL240C (pp) YOR026W = 3
+YOL156W (pd) YBL025W = 3
+YML064C (pp) YHR128C = 3
+YML064C (pp) YLR224C = 3
+YML064C (pp) YDR124W = 3
+YER052C (pp) YNL125C = 3
+YPR124W (pd) YMR021C = 3
+YGL166W (pd) YHR023C = 3
+YGL166W (pd) YHR025C = 3
+YGL134W (pp) YPL021C = 3
+YGL134W (pp) YLR228W = 3
+YJL194W (pd) YMR023W = 3
+YLR264W (pp) YER122W = 3
+YLR264W (pp) YOL129W = 3
+YLR264W (pp) YBL026W = 3
+YBL050W (pp) YOR026W = 3
+YNL145W (pd) YCL027C = 3
+YNL145W (pd) YHR024W = 3
+YBR274W (pp) YMR225W = 3
+YLR452C (pp) YHR025C = 3
+YDR299W (pd) YJL124W = 3
+YIL074C (pp) YNL321C = 3
+YLR319C (pp) YLR322W = 3
+YGL073W (pp) YOR128C = 3
+YGL073W (pd) YHR023C = 3
+YGL073W (pd) YHR025C = 3
+YGL073W (pd) YER123W = 3
+YOR120W (pd) YPL228C = 3
+YPR041W (pp) YOR321C = 3
+YPR041W (pp) YMR329C = 3
+YNL135C (pp) YDR124W = 3
+YBR217W (pp) YNR027C = 3
+YMR255W (pp) YGL122C = 3
+YLR258W (pp) YIL025W = 3
+YLR258W (pp) YBR224W = 3
+YDL215C (pd) YER020W = 3
+YDL215C (pp) YLR422W = 3
+YER079W (pp) YHR125C = 3
+YER079W (pp) YNL124C = 3
+YDL030W (pp) YDL023W = 3
+YDL030W (pp) YMR025W = 3
+YLR362W (pp) YER124C = 3
+YLR362W (pp) YMR126W = 3
+YLR362W (pp) YPL220C = 3
+YHR084W (pp) YMR023W = 3
+YHR084W (pd) YDR421W = 3
+YHR084W (pd) YFL026W = 3
+YGR085C (pp) YLR025W = 3
+YGR085C (pp) YDR325W = 3
+YKL074C (pp) YGL025C = 3
+YGR088W (pd) YLR226W = 3
+YER081W (pp) YIL024C = 3
+YPR113W (pd) YMR023W = 3
+YIL070C (pp) YML024C = 3
+YIL061C (pp) YDL023W = 3
+YIL061C (pp) YNL129C = 3
+YIL061C (pp) YLR123C = 3
+YGR046W (pp) YNL226W = 3
+YNL091W (pp) YNL124C = 3
+YHR030C (pp) YLL021W = 3
+YHR030C (pp) YER121C = 3
+YPR048W (pp) YOR325W = 3
+YPR048W (pp) YDL225C = 3
+YHR005C (pp) YLR322W = 3
+YDR070C (pp) YFL027C = 3
+YJL157C (pp) YAL020C = 3
+YJL157C (pp) YOR222W = 3
+YNL036W (pp) YIR029W = 3
+YML114C (pp) YDR127W = 3
+YMR117C (pp) YCL022W = 3
+YMR117C (pp) YPR020C = 3
+YHR115C (pp) YOR225C = 3
+YGR009C (pp) YAL020W = 3
+YGR009C (pp) YOR327C = 3
+YGR009C (pp) YDR325W = 3
+YGR009C (pp) YBL020W = 3
+YDL088C (pp) YER120C = 3
+YLR197W (pp) YDL024W = 3
+YLR197W (pp) YOR320C = 3
+YGL202W (pp) YGR024W = 3
+YIL162W (pd) YNL127C = 3
+YBR170C (pp) YGR028W = 3
+YOR212W (pp) YLR322W = 3
+YDR103W (pp) YLR322W = 3
+YDL023C (pp) YJL129W = 3
+YGR136W (pp) YGR028W = 3
+YBR109C (pp) YOR326W = 3
+YBR109C (pp) YFR024C = 3
+YDR395W (pp) YDL025W = 3
+YDR395W (pp) YIL123C = 3
+YDR395W (pp) YNL029C = 3
+YDR395W (pp) YER026CA =3
+YDR395W (pp) YIL022C = 3
+YDR395W (pp) YOL127W = 3
+YDR395W (pp) YPR122C = 3
+YLR345W (pp) YLR321C = 3
+YBL079W (pp) YDL028C = 3
+YBR045C (pp) YIL025W = 3
+YBR045C (pp) YOR128C = 3
+YER054C (pp) YER123W = 3
+YER054C (pp) YBR025C = 3
+YPR145W (pp) YMR127C = 3
+YNR053C (pp) YJL223W = 3
+YNR053C (pp) YDL020W = 3
+YGR074W (pp) YBR023C = 3
+YDR277C (pp) YJR022W = 3
+YDR277C (pp) YDL124W = 3
+YBL026W (pp) YOR127C = 3
diff --git a/application/src/test/resources/testData/galFiltered.nodeAttrs1 b/application/src/test/resources/testData/galFiltered.nodeAttrs1
new file mode 100644
index 0000000..cfb540b
--- /dev/null
+++ b/application/src/test/resources/testData/galFiltered.nodeAttrs1
@@ -0,0 +1,329 @@
+TestNodeAttribute1
+YKR026C = 1
+YGL122C = 1
+YMR146C = 1
+YDR429C = 1
+YFL017C = 1
+YOL123W = 1
+YGL044C = 1
+YGR203W = 1
+YIL061C = 1
+YCR084C = 1
+YBR112C = 1
+YCL067C = 1
+YER112W = 1
+YOR167C = 1
+YJR022W = 1
+YNR050C = 1
+YNL050C = 1
+YEL015W = 1
+YLR264W = 1
+YNR053C = 1
+YER116C = 1
+YDL013W = 1
+YNL307C = 1
+YAL038W = 1
+YNL216W = 1
+YCR012W = 1
+YGR254W = 1
+YHR174W = 1
+YIL133C = 1
+YLR044C = 1
+YOL120C = 1
+YNL301C = 1
+YCL030C = 1
+YDR171W = 1
+YBR093C = 1
+YER074W = 1
+YIL069C = 1
+YOL127W = 1
+YDR050C = 1
+YOL086C = 1
+YAL030W = 1
+YER143W = 1
+YOR327C = 1
+YDR412W = 1
+YCR086W = 1
+YGL013C = 1
+YLR117C = 1
+YPR119W = 1
+YER179W = 1
+YLR134W = 1
+YIL105C = 1
+YOR361C = 1
+YMR309C = 1
+YMR186W = 1
+YBR155W = 1
+YEL009C = 1
+YMR108W = 1
+YOR202W = 1
+YBR248C = 1
+YOL058W = 1
+YMR300C = 1
+YMR138W = 1
+YHR141C = 1
+YLR109W = 1
+YCL032W = 1
+YDR032C = 1
+YLR362W = 1
+YDR103W = 1
+YJR060W = 1
+YBR019C = 1
+YOL051W = 1
+YGL035C = 1
+YBR020W = 1
+YLR081W = 1
+YPL248C = 1
+YBR018C = 1
+YIR009W = 1
+YKR099W = 1
+YIL143C = 1
+YDR184C = 1
+YNL091W = 1
+YNL236W = 1
+YKL012W = 1
+YML032C = 1
+YNL312W = 1
+YLR116W = 1
+YOR264W = 1
+YDR309C = 1
+YLR229C = 1
+YGR058W = 1
+YLR256W = 1
+YML054C = 1
+YJR048W = 1
+YEL039C = 1
+YGL237C = 1
+YBL021C = 1
+YDR311W = 1
+YKL028W = 1
+YPL149W = 1
+YHR171W = 1
+YBR217W = 1
+YKL109W = 1
+YMR043W = 2
+YIL015W = 2
+YJL159W = 2
+YKR097W = 2
+YGR108W = 2
+YDR461W = 2
+YNL145W = 2
+YJL157C = 2
+YFL026W = 2
+YNR007C = 2
+YJL203W = 2
+YOL136C = 2
+YLL021W = 2
+YJL219W = 2
+YOL156W = 2
+YKL101W = 2
+YBR160W = 2
+YBL005W = 2
+YDR323C = 2
+YOR036W = 2
+YGL008C = 2
+YER040W = 2
+YPR035W = 2
+YGR019W = 2
+YNL098C = 2
+YLR310C = 2
+YPL089C = 2
+YHR030C = 2
+YJL089W = 2
+YER065C = 2
+YLR377C = 2
+YDR335W = 2
+YDR174W = 2
+YLL028W = 2
+YGL166W = 2
+YKL074C = 2
+YML064C = 2
+YNL047C = 2
+YNL199C = 2
+YPR048W = 2
+YLR321C = 2
+YBR072W = 2
+YGL073W = 2
+YBL069W = 2
+YNL189W = 2
+YDL236W = 2
+YPL111W = 2
+YPR062W = 2
+YLR319C = 2
+YNL167C = 2
+YGL161C = 2
+YDR100W = 2
+YMR183C = 2
+YGR009C = 2
+YAL040C = 2
+YFR034C = 2
+YER133W = 2
+YOR178C = 2
+YOR315W = 2
+YMR311C = 2
+YBR050C = 2
+YIL162W = 2
+YFL038C = 2
+YOR355W = 2
+YML123C = 2
+YPL031C = 2
+YHR071W = 2
+YML051W = 2
+YDR009W = 2
+YLL019C = 2
+YIL113W = 2
+YML024W = 2
+YER111C = 2
+YDR146C = 2
+YDR354W = 2
+YER103W = 2
+YBR190W = 2
+YOL059W = 2
+YER102W = 2
+YOR362C = 2
+YMR044W = 2
+YOL149W = 2
+YBR135W = 2
+YPR167C = 2
+YOR089C = 2
+YNL117W = 2
+YLR175W = 2
+YDR167W = 2
+YLR432W = 2
+YAR007C = 2
+YKL161C = 2
+YLR075W = 2
+YPR102C = 2
+YPL240C = 2
+YHR198C = 2
+YLR284C = 2
+YER052C = 2
+YNL135C = 2
+YHR053C = 3
+YHR055C = 3
+YGL134W = 3
+YLR258W = 3
+YJL194W = 3
+YBL026W = 3
+YBL050W = 3
+YHR084W = 3
+YBR274W = 3
+YMR255W = 3
+YLR452C = 3
+YHR005C = 3
+YDR299W = 3
+YOR120W = 3
+YPR041W = 3
+YIL045W = 3
+YDL215C = 3
+YDL030W = 3
+YMR005W = 3
+YER124C = 3
+YGR085C = 3
+YDR395W = 3
+YGR088W = 3
+YPR113W = 3
+YIL070C = 3
+YLR153C = 3
+YGR046W = 3
+YNL164C = 3
+YDR070C = 3
+YOR212W = 3
+YNL036W = 3
+YML114C = 3
+YMR117C = 3
+YPR010C = 3
+YDL023C = 3
+YGR136W = 3
+YDL075W = 3
+YNL069C = 3
+YER056CA = 3
+YIL052C = 3
+YLR345W = 3
+YBR045C = 3
+YER054C = 3
+YPR145W = 3
+YDR277C = 3
+YDL194W = 3
+YGR218W = 3
+YGL097W = 3
+YOR204W = 3
+YLR293C = 3
+YLR249W = 3
+YPR080W = 3
+YBR118W = 3
+YAL003W = 3
+YPL211W = 3
+YGR014W = 3
+YJL030W = 3
+YGL229C = 3
+YJL013C = 3
+YER062C = 3
+YPL201C = 3
+YDL014W = 3
+YOR310C = 3
+YLR197W = 3
+YOR326W = 3
+YGL106W = 3
+YOL016C = 3
+YBR109C = 3
+YFR014C = 3
+YJR109C = 3
+YOR303W = 3
+YOR039W = 3
+YGL115W = 3
+YGL208W = 3
+YMR291W = 3
+YMR021C = 3
+YLR214W = 3
+YPR124W = 3
+YDL081C = 3
+YLR340W = 3
+YHR135C = 3
+YNL116W = 3
+YNL154C = 3
+YKL204W = 3
+YER079W = 3
+YDR382W = 3
+YDL130W = 3
+YFL039C = 3
+YCL040W = 3
+YHR179W = 3
+YNL311C = 3
+YKL001C = 3
+YIL074C = 3
+YER081W = 3
+YJL036W = 3
+YDL113C = 3
+YEL041W = 3
+YHR115C = 3
+YOR215C = 3
+YDL063C = 3
+YPL131W = 3
+YGR048W = 3
+YPL222W = 3
+YBR170C = 3
+YFR037C = 3
+YOR290C = 3
+YML074C = 3
+YJL190C = 3
+YMR058W = 3
+YER145C = 3
+YKL211C = 3
+YER090W = 3
+YNL113W = 3
+YPR110C = 3
+YLR191W = 3
+YGL153W = 3
+YNL214W = 3
+YDR244W = 3
+YDR142C = 3
+YDL078C = 3
+YIL160C = 3
+YER110C = 3
+YML007W = 3
+YDL088C = 3
+YBL079W = 3
+YGL202W = 3
+YGR074W = 3
+YBR043C = 3
diff --git a/application/src/test/resources/testData/galFiltered.sif b/application/src/test/resources/testData/galFiltered.sif
new file mode 100644
index 0000000..9e71eb5
--- /dev/null
+++ b/application/src/test/resources/testData/galFiltered.sif
@@ -0,0 +1,362 @@
+YKR026C pp YGL122C
+YGR218W pp YGL097W
+YGL097W pp YOR204W
+YLR249W pp YPR080W
+YLR249W pp YBR118W
+YLR293C pp YGL097W
+YMR146C pp YDR429C
+YDR429C pp YFL017C
+YPR080W pp YAL003W
+YBR118W pp YAL003W
+YOL123W pp YGL044C
+YPL211W pp YGR014W
+YJL030W pp YGL229C
+YJL013C pp YGL229C
+YGL122C pp YOL123W
+YGR014W pp YJL030W
+YGR014W pp YJL013C
+YGR203W pp YIL061C
+YCR084C pp YBR112C
+YCR084C pp YCL067C
+YER112W pp YOR167C
+YJR022W pp YNR050C
+YJR022W pp YNL050C
+YJR022W pp YEL015W
+YJR022W pp YOR167C
+YJR022W pp YLR264W
+YJR022W pp YNR053C
+YER116C pp YDL013W
+YNL307C pp YAL038W
+YNL216W pd YCR012W
+YNL216W pd YGR254W
+YNL216W pd YHR174W
+YNL216W pd YIL133C
+YNL216W pd YLR044C
+YNL216W pd YOL120C
+YNL216W pd YNL301C
+YNL216W pd YCL030C
+YNL216W pp YDR171W
+YNL216W pd YBR093C
+YNL216W pd YER074W
+YNL216W pd YIL069C
+YNL216W pd YAL038W
+YNL216W pd YOL127W
+YNL216W pd YDR050C
+YNL216W pd YOL086C
+YAL030W pp YER143W
+YOR327C pp YER143W
+YER062C pp YPL201C
+YDR412W pp YCR086W
+YDR412W pp YGL013C
+YDR412W pp YLR117C
+YDR412W pp YPR119W
+YDL014W pp YOR310C
+YER179W pp YLR044C
+YER179W pp YLR134W
+YER179W pp YIL105C
+YOR361C pp YMR309C
+YOR361C pp YDR429C
+YOR326W pp YGL106W
+YMR186W pp YBR155W
+YEL009C pd YMR108W
+YEL009C pd YOR202W
+YEL009C pd YCL030C
+YEL009C pd YBR248C
+YEL009C pd YOL058W
+YEL009C pd YMR300C
+YMR138W pp YHR141C
+YMR138W pp YLR109W
+YCL032W pp YDR032C
+YCL032W pp YLR362W
+YCL032W pp YDR103W
+YCR012W pd YJR060W
+YBR019C pd YOL051W
+YBR019C pd YGL035C
+YOL051W pd YBR020W
+YOL051W pd YLR081W
+YOL051W pp YPL248C
+YOL051W pd YBR018C
+YIR009W pp YKR099W
+YIR009W pp YIL143C
+YIR009W pp YDR184C
+YIR009W pp YNL091W
+YNL236W pp YKL012W
+YML032C pp YNL312W
+YLR116W pp YKL012W
+YCR086W pp YOR264W
+YDR309C pp YLR229C
+YGR058W pp YOR264W
+YJR109C pp YOR303W
+YLR256W pd YML054C
+YLR256W pd YJR048W
+YLR256W pd YEL039C
+YGL237C pd YJR048W
+YBL021C pd YJR048W
+YDR311W pp YKL028W
+YPL149W pp YHR171W
+YPL149W pp YBR217W
+YKL109W pp YGL237C
+YKL109W pp YBL021C
+YKL109W pd YJR048W
+YKL109W pd YGL035C
+YMR043W pd YIL015W
+YMR043W pd YJL159W
+YMR043W pd YKR097W
+YMR043W pd YGR108W
+YMR043W pd YDR461W
+YMR043W pd YNL145W
+YMR043W pd YJL157C
+YMR043W pd YFL026W
+YHR171W pp YDR412W
+YHR171W pp YNR007C
+YNR050C pp YMR138W
+YJL203W pp YOL136C
+YLL021W pp YLR362W
+YGL013C pd YJL219W
+YGL013C pd YOL156W
+YKL101W pp YBR160W
+YCL067C pd YIL015W
+YCL067C pp YMR043W
+YCL067C pd YDR461W
+YCL067C pd YFL026W
+YBL005W pd YJL219W
+YDR323C pp YOR036W
+YGL008C pd YMR043W
+YER040W pd YPR035W
+YER040W pd YGR019W
+YNL098C pp YLR310C
+YGL115W pp YGL208W
+YPL089C pp YHR030C
+YJL089W pd YER065C
+YJL089W pd YKR097W
+YJL089W pd YLR377C
+YMR021C pd YLR214W
+YDR335W pp YDR174W
+YLL028W pp YGL166W
+YIL143C pp YDR311W
+YDL081C pp YLR340W
+YKL012W pp YKL074C
+YEL015W pp YML064C
+YHR135C pp YNL116W
+YMR309C pp YNL047C
+YNL154C pp YKL204W
+? pd YKR099W
+YJR066W pp YLR116W
+YDR382W pp YDL130W
+YDR382W pp YFL039C
+YFL039C pp YCL040W
+YFL039C pp YHR179W
+YPL075W pd YCR012W
+YPL075W pd YGR254W
+YPL075W pd YHR174W
+YPL075W pp YNL199C
+YPL075W pd YDR050C
+YPL075W pd YOL086C
+YNL199C pp YPR048W
+? pd YGL035C
+YLR321C pp YDR412W
+YBR072W pd YGL073W
+YCL030C pd YKR099W
+YBL069W pp YGL008C
+YNL189W pp YDL236W
+YNL189W pp YPL111W
+YNL189W pp YER065C
+YNL189W pp YPR062W
+YDR184C pp YLR319C
+YNL311C pp YKL001C
+YOL058W pp YNL189W
+YOL016C pp YBR109C
+YJL036W pp YDL113C
+YEL041W pp YHR115C
+YNL167C pd YOR202W
+YDL063C pp YPL131W
+YGL161C pp YDR100W
+YMR183C pp YGR009C
+YMR291W pp YGL115W
+YGR048W pp YPL222W
+YAL040C pd YMR043W
+YFR034C pd YBR093C
+YFR037C pp YOR290C
+YER133W pp YDR412W
+YER133W pp YOR178C
+YER133W pp YOR315W
+YER133W pp YMR311C
+YER133W pp YBR050C
+YGL035C pd YLR044C
+YGL035C pd YLR377C
+YGL035C pd YIL162W
+YFL038C pp YOR036W
+YOR355W pp YNL091W
+YML074C pp YJL190C
+YMR058W pp YER145C
+YML123C pd YFR034C
+YPL031C pp YHR071W
+YAL038W pd YPL075W
+YML051W pp YBR020W
+YML051W pp YDR009W
+YLL019C pp YIL113W
+YML024W pd YNL216W
+YOR039W pp YOR303W
+YER111C pd YMR043W
+YDR146C pd YMR043W
+YDR146C pd YGL035C
+YKL211C pp YER090W
+YDR354W pd YEL009C
+YNL113W pp YPR110C
+YLR310C pp YER103W
+YNL047C pp YIL105C
+YBR160W pd YMR043W
+YBR160W pp YGR108W
+YIL113W pp YHR030C
+YLR117C pp YBR190W
+YFL017C pp YOL059W
+YFL017C pp YER102W
+YFL017C pp YOR362C
+YMR044W pp YIL061C
+YOL149W pp YOR167C
+YOR036W pp YDR100W
+YOR036W pp YGL161C
+YLR191W pp YGL153W
+YER110C pp YML007W
+YBR135W pp YER102W
+YNL214W pp YGL153W
+YJR060W pd YPR167C
+YOR089C pp YDR323C
+YNL117W pd YJL089W
+YLR175W pp YNL307C
+YDR167W pp YLR432W
+YGR108W pp YBR135W
+YDR244W pp YLR191W
+YDR244W pp YGL153W
+YDR244W pp YNL214W
+YDR244W pp YDR142C
+YDR244W pp YDL078C
+YPR119W pd YMR043W
+YDR142C pp YGL153W
+YDR142C pp YIL160C
+YBR020W pd YGL035C
+YDR009W pd YGL035C
+YPL248C pd YBR019C
+YPL248C pd ?
+YPL248C pd YJR048W
+YPL248C pd YGL035C
+YPL248C pd YML051W
+YPL248C pp YML051W
+YPL248C pd YBR020W
+YPL248C pd YLR081W
+YPL248C pd YBR018C
+YAR007C pp YML032C
+YAR007C pd YPL111W
+YKL161C pp YPL089C
+YNL312W pd YPL111W
+YLR075W pp YPR102C
+YLR229C pp YJL157C
+YPL240C pp YBR155W
+YPL240C pp YOR036W
+YOL156W pd YBL005W
+YML064C pp YHR198C
+YML064C pp YLR284C
+YML064C pp YDR174W
+YER052C pp YNL135C
+YPR124W pd YMR021C
+YGL166W pd YHR053C
+YGL166W pd YHR055C
+YGL134W pp YPL031C
+YGL134W pp YLR258W
+YJL194W pd YMR043W
+YLR264W pp YER112W
+YLR264W pp YOL149W
+YLR264W pp YBL026W
+YBL050W pp YOR036W
+YNL145W pd YCL067C
+YNL145W pd YHR084W
+YBR274W pp YMR255W
+YLR452C pp YHR005C
+YDR299W pd YJL194W
+YIL074C pp YNL311C
+YLR319C pp YLR362W
+YGL073W pp YOR178C
+YGL073W pd YHR053C
+YGL073W pd YHR055C
+YGL073W pd YER103W
+YOR120W pd YPL248C
+YPR041W pp YOR361C
+YPR041W pp YMR309C
+YNL135C pp YDR174W
+YBR217W pp YNR007C
+YMR255W pp YGL122C
+YLR258W pp YIL045W
+YLR258W pp YBR274W
+YDL215C pd YER040W
+YDL215C pp YLR432W
+YER079W pp YHR135C
+YER079W pp YNL154C
+YDL030W pp YDL013W
+YDL030W pp YMR005W
+YLR362W pp YER124C
+YLR362W pp YMR186W
+YLR362W pp YPL240C
+YHR084W pp YMR043W
+YHR084W pd YDR461W
+YHR084W pd YFL026W
+YGR085C pp YLR075W
+YGR085C pp YDR395W
+YKL074C pp YGL035C
+YGR088W pd YLR256W
+YER081W pp YIL074C
+YPR113W pd YMR043W
+YIL070C pp YML054C
+YIL061C pp YDL013W
+YIL061C pp YNL199C
+YIL061C pp YLR153C
+YGR046W pp YNL236W
+YNL091W pp YNL164C
+YHR030C pp YLL021W
+YHR030C pp YER111C
+YPR048W pp YOR355W
+YPR048W pp YDL215C
+YHR005C pp YLR362W
+YDR070C pp YFL017C
+YJL157C pp YAL040C
+YJL157C pp YOR212W
+YNL036W pp YIR009W
+YML114C pp YDR167W
+YMR117C pp YCL032W
+YMR117C pp YPR010C
+YHR115C pp YOR215C
+YGR009C pp YAL030W
+YGR009C pp YOR327C
+YGR009C pp YDR335W
+YGR009C pp YBL050W
+YDL088C pp YER110C
+YLR197W pp YDL014W
+YLR197W pp YOR310C
+YGL202W pp YGR074W
+YIL162W pd YNL167C
+YBR170C pp YGR048W
+YOR212W pp YLR362W
+YDR103W pp YLR362W
+YDL023C pp YJL159W
+YGR136W pp YGR058W
+YBR109C pp YOR326W
+YBR109C pp YFR014C
+YDR395W pp YDL075W
+YDR395W pp YIL133C
+YDR395W pp YNL069C
+YDR395W pp YER056CA
+YDR395W pp YIL052C
+YDR395W pp YOL127W
+YDR395W pp YPR102C
+YLR345W pp YLR321C
+YBL079W pp YDL088C
+YBR045C pp YIL045W
+YBR045C pp YOR178C
+YER054C pp YER133W
+YER054C pp YBR045C
+YPR145W pp YMR117C
+YNR053C pp YJL203W
+YNR053C pp YDL030W
+YGR074W pp YBR043C
+YDR277C pp YJR022W
+YDR277C pp YDL194W
+YBL026W pp YOR167C
diff --git a/application/src/test/resources/testData/galFiltered2.xgmml b/application/src/test/resources/testData/galFiltered2.xgmml
new file mode 100644
index 0000000..0629648
--- /dev/null
+++ b/application/src/test/resources/testData/galFiltered2.xgmml
@@ -0,0 +1,17902 @@
+<?xml version='1.0'?>
+<graph id="6" label="GAL Filtered (Yeast)" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:ns1="http://www.w3.org/1999/xlink" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns="http://www.cs.rpi.edu/XGMML">
+ <att name="networkMetadata">
+ <rdf:RDF>
+ <rdf:Description rdf:about="http://www.cytoscape.org">
+ <dc:type>Protein-Protein Interaction</dc:type>
+ <dc:description>N/A</dc:description>
+ <dc:date>2006-02-17 16:39:29</dc:date>
+ <dc:identifier>N/A</dc:identifier>
+ <dc:title>GAL Filtered (Yeast)</dc:title>
+ <dc:source>http://www.cytoscape.org</dc:source>
+ <dc:format>Cytoscape-XGMML</dc:format>
+ </rdf:Description>
+ </rdf:RDF>
+ </att>
+ <att value="#f0f0f0" name="backgroundColor"/>
+ <node id="-331" label="YKR026C" name="base">
+ <att label="list" name="GO Cellular Component (level 6)">
+ <att value="eukaryotic translation initiation factor 2B complex" label="string"/>
+ </att>
+ <att label="list" name="GO Molecular Function (level 3)">
+ <att value="nucleic acid binding" label="string"/>
+ <att value="translation factor, nucleic acid binding" label="string"/>
+ </att>
+ <att value="-0.154" label="float" name="gal1RGexp"/>
+ <att value="-0.501" label="float" name="gal4RGexp"/>
+ <att value="GCN3 AAS2 " label="string" name="ALIASES"/>
+ <att value="9.1177E-4" label="float" name="gal1RGsig"/>
+ <att label="list" name="KEGG Metabolic Pathways (level 2)">
+ <att value="Translation factors" label="string"/>
+ </att>
+ <att value="0.292" label="float" name="gal80Rexp"/>
+ <att value="YKR026C" label="string" name="canonicalName"/>
+ <att label="list" name="GO Biological Process (level 6)">
+ <att value="protein biosynthesis" label="string"/>
+ <att value="translational initiation" label="string"/>
+ </att>
+ <att label="list" name="GO Biological Process (level 11)">
+ <att value="translational initiation" label="string"/>
+ </att>
+ <att label="list" name="GO Cellular Component (level 8)">
+ <att value="eukaryotic translation initiation factor 2B complex" label="string"/>
+ </att>
+ <att value="3.5692E-6" label="float" name="gal4RGsig"/>
+ <att value="GCN3" label="string" name="commonName"/>
+ <att value="0.011229" label="float" name="gal80Rsig"/>
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+ <att value="cytoplasm" label="string"/>
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+ <att label="list" name="GO Biological Process (level 6)">
+ <att value="nuclear RNA-nucleus export" label="string"/>
+ </att>
+ <att label="list" name="GO Biological Process (level 11)">
+ <att value="poly(A)+ mRNA-nucleus export" label="string"/>
+ </att>
+ <att label="list" name="GO Cellular Component (level 8)">
+ <att value="nucleus" label="string"/>
+ <att value="cytoplasm" label="string"/>
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+ <att value="0.61707" label="float" name="gal4RGsig"/>
+ <att value="NAB2" label="string" name="commonName"/>
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+ <att value="YMR146C" label="string" name="canonicalName"/>
+ <att label="list" name="GO Biological Process (level 6)">
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+ <att value="eukaryotic translation initiation factor 3 complex" label="string"/>
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+ <att value="0.0011724" label="float" name="gal4RGsig"/>
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+ <att value="1.6643E-5" label="float" name="gal80Rsig"/>
+ <att value="Saccharomyces cerevisiae" label="string" name="species"/>
+ <graphics h="49.3530158996582" w="11.075197219848633" type="octagon" width="6" fill="#d488a0" outline="#406404" x="2473.367403896272" y="377.3530180310217">
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+ </node>
+ <node id="-327" label="YFL017C" name="base">
+ <att label="list" name="GO Cellular Component (level 6)">
+ <att value="cellular_component unknown" label="string"/>
+ </att>
+ <att label="list" name="GO Molecular Function (level 3)">
+ <att value="transferase" label="string"/>
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+ <att value="0.122" label="float" name="gal4RGexp"/>
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+ <att value="0.0017854" label="float" name="gal1RGsig"/>
+ <att label="list" name="KEGG Metabolic Pathways (level 2)">
+ <att value="Glutamate metabolism" label="string"/>
+ <att value="Aminosugars metabolism" label="string"/>
+ </att>
+ <att value="0.124" label="float" name="gal80Rexp"/>
+ <att value="YFL017C" label="string" name="canonicalName"/>
+ <att label="list" name="GO Biological Process (level 6)">
+ <att value="glucosamine metabolism" label="string"/>
+ <att value="amino sugar biosynthesis" label="string"/>
+ </att>
+ <att label="list" name="GO Biological Process (level 11)">
+ <att value="UDP-N-acetylglucosamine biosynthesis" label="string"/>
+ </att>
+ <att label="list" name="GO Cellular Component (level 8)">
+ <att value="cellular_component unknown" label="string"/>
+ </att>
+ <att value="0.0055302" label="float" name="gal4RGsig"/>
+ <att value="GNA1" label="string" name="commonName"/>
+ <att value="0.050323" label="float" name="gal80Rsig"/>
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+ <node id="-326" label="YOL123W" name="base">
+ <att label="list" name="GO Cellular Component (level 6)">
+ <att value="mRNA cleavage factor complex" label="string"/>
+ <att value="nucleus" label="string"/>
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+ <att value="0.126" label="float" name="gal4RGexp"/>
+ <att value="HRP1 NAB4 NAB5 " label="string" name="ALIASES"/>
+ <att value="9.8446E-6" label="float" name="gal1RGsig"/>
+ <att label="list" name="KEGG Metabolic Pathways (level 2)"/>
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+ <att label="list" name="GO Biological Process (level 6)">
+ <att value="RNA processing" label="string"/>
+ <att value="mRNA metabolism" label="string"/>
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+ <att label="list" name="GO Biological Process (level 11)">
+ <att value="mRNA cleavage" label="string"/>
+ <att value="mRNA polyadenylation" label="string"/>
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+ <att label="list" name="GO Cellular Component (level 8)">
+ <att value="mRNA cleavage factor complex" label="string"/>
+ <att value="nucleus" label="string"/>
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+ <att value="HRP1" label="string" name="commonName"/>
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diff --git a/application/src/test/resources/testData/haloMetabolicPathway.xml b/application/src/test/resources/testData/haloMetabolicPathway.xml
new file mode 100644
index 0000000..16bb789
--- /dev/null
+++ b/application/src/test/resources/testData/haloMetabolicPathway.xml
@@ -0,0 +1,4740 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<!-- $Revision: 21132 $
+ $Date: 2010-08-03 18:49:02 +0200 (Tue, 03 Aug 2010) $
+ $Author: mes $
+ -->
+
+<annotation species="Halobacterium sp."
+ ontology="metabolicPathwayOntology.xml">
+
+ <term>
+ <entity> VNG0006G </entity>
+ <id> 251 </id>
+ <name> Glutamate metabolism </name>
+ </term>
+
+ <term>
+ <entity> VNG0006G </entity>
+ <id> 530 </id>
+ <name> Aminosugars metabolism </name>
+ </term>
+
+ <term>
+ <entity> VNG0008G </entity>
+ <id> 520 </id>
+ <name> Nucleotide sugars metabolism </name>
+ </term>
+
+ <term>
+ <entity> VNG0008G </entity>
+ <id> 522 </id>
+ <name> Erythromycin biosynthesis </name>
+ </term>
+
+ <term>
+ <entity> VNG0009G </entity>
+ <id> 520 </id>
+ <name> Nucleotide sugars metabolism </name>
+ </term>
+
+ <term>
+ <entity> VNG0009G </entity>
+ <id> 522 </id>
+ <name> Erythromycin biosynthesis </name>
+ </term>
+
+ <term>
+ <entity> VNG0046G </entity>
+ <id> 40 </id>
+ <name> Pentose and glucuronate interconversions </name>
+ </term>
+
+ <term>
+ <entity> VNG0046G </entity>
+ <id> 500 </id>
+ <name> Starch and sucrose metabolism </name>
+ </term>
+
+ <term>
+ <entity> VNG0046G </entity>
+ <id> 520 </id>
+ <name> Nucleotide sugars metabolism </name>
+ </term>
+
+ <term>
+ <entity> VNG0047G </entity>
+ <id> 520 </id>
+ <name> Nucleotide sugars metabolism </name>
+ </term>
+
+ <term>
+ <entity> VNG0063G </entity>
+ <id> 52 </id>
+ <name> Galactose metabolism </name>
+ </term>
+
+ <term>
+ <entity> VNG0063G </entity>
+ <id> 520 </id>
+ <name> Nucleotide sugars metabolism </name>
+ </term>
+
+ <term>
+ <entity> VNG0064G </entity>
+ <id> 520 </id>
+ <name> Nucleotide sugars metabolism </name>
+ </term>
+
+ <term>
+ <entity> VNG0064G </entity>
+ <id> 522 </id>
+ <name> Erythromycin biosynthesis </name>
+ </term>
+
+ <term>
+ <entity> VNG0065G </entity>
+ <id> 52 </id>
+ <name> Galactose metabolism </name>
+ </term>
+
+ <term>
+ <entity> VNG0065G </entity>
+ <id> 520 </id>
+ <name> Nucleotide sugars metabolism </name>
+ </term>
+
+ <term>
+ <entity> VNG0095G </entity>
+ <id> 10 </id>
+ <name> Glycolysis / Gluconeogenesis </name>
+ </term>
+
+ <term>
+ <entity> VNG0095G </entity>
+ <id> 472 </id>
+ <name> D-Arginine and D-ornithine metabolism </name>
+ </term>
+
+ <term>
+ <entity> VNG0099G </entity>
+ <id> 3010 </id>
+ <name> Ribosome </name>
+ </term>
+
+ <term>
+ <entity> VNG0149G </entity>
+ <id> 500 </id>
+ <name> Starch and sucrose metabolism </name>
+ </term>
+
+ <term>
+ <entity> VNG0149G </entity>
+ <id> 790 </id>
+ <name> Folate biosynthesis </name>
+ </term>
+
+ <term>
+ <entity> VNG0161G </entity>
+ <id> 220 </id>
+ <name> Urea cycle and metabolism of amino groups </name>
+ </term>
+
+ <term>
+ <entity> VNG0161G </entity>
+ <id> 251 </id>
+ <name> Glutamate metabolism </name>
+ </term>
+
+ <term>
+ <entity> VNG0161G </entity>
+ <id> 330 </id>
+ <name> Arginine and proline metabolism </name>
+ </term>
+
+ <term>
+ <entity> VNG0161G </entity>
+ <id> 471 </id>
+ <name> D-Glutamine and D-glutamate metabolism </name>
+ </term>
+
+ <term>
+ <entity> VNG0161G </entity>
+ <id> 910 </id>
+ <name> Nitrogen metabolism </name>
+ </term>
+
+ <term>
+ <entity> VNG0177G </entity>
+ <id> 3010 </id>
+ <name> Ribosome </name>
+ </term>
+
+ <term>
+ <entity> VNG0228G </entity>
+ <id> 230 </id>
+ <name> Purine metabolism </name>
+ </term>
+
+ <term>
+ <entity> VNG0228G </entity>
+ <id> 251 </id>
+ <name> Glutamate metabolism </name>
+ </term>
+
+ <term>
+ <entity> VNG0245G </entity>
+ <id> 240 </id>
+ <name> Pyrimidine metabolism </name>
+ </term>
+
+ <term>
+ <entity> VNG0254G </entity>
+ <id> 3022 </id>
+ <name> Transcription factors </name>
+ </term>
+
+ <term>
+ <entity> VNG0259G </entity>
+ <id> 190 </id>
+ <name> Oxidative phosphorylation </name>
+ </term>
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+ <term>
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+ <term>
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+ <term>
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+ <term>
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+ <term>
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+ <term>
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+ <name> Pyrimidine metabolism </name>
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+ <name> DNA polymerase </name>
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+ <term>
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+ <term>
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+ <name> Aminophosphonate metabolism </name>
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+ <term>
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+ <name> Caprolactam degradation </name>
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+ <term>
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+ <name> Methionine metabolism </name>
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+ <term>
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+ <name> Sulfur metabolism </name>
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+ <term>
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+ <term>
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+ <name> Cysteine metabolism </name>
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+ <term>
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+ <term>
+ <entity> VNG2424G </entity>
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+ <name> Glycine, serine and threonine metabolism </name>
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+ <term>
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+
+ <term>
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+ <id> 750 </id>
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+ <term>
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+ <term>
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+ <term>
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+ <name> Arginine and proline metabolism </name>
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+ <term>
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+ <id> 220 </id>
+ <name> Urea cycle and metabolism of amino groups </name>
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+ <term>
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+ <term>
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+ <term>
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+ <term>
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+ <name> Tyrosine metabolism </name>
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+ <term>
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+ <name> Phenylalanine metabolism </name>
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+
+ <term>
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+ <id> 600 </id>
+ <name> Sphingoglycolipid metabolism </name>
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+ <term>
+ <entity> VNG2447G </entity>
+ <id> 626 </id>
+ <name> Nitorobenzene degradation </name>
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+ <term>
+ <entity> VNG2447G </entity>
+ <id> 627 </id>
+ <name> 1,4-Dichlorobenzene degradation </name>
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+
+ <term>
+ <entity> VNG2447G </entity>
+ <id> 628 </id>
+ <name> Fluorene degradation </name>
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+
+ <term>
+ <entity> VNG2447G </entity>
+ <id> 629 </id>
+ <name> Carbazole degradation </name>
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+
+ <term>
+ <entity> VNG2447G </entity>
+ <id> 643 </id>
+ <name> Styrene degradation </name>
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+
+ <term>
+ <entity> VNG2459G </entity>
+ <id> 3060 </id>
+ <name> Protein export </name>
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+
+ <term>
+ <entity> VNG2462G </entity>
+ <id> 3060 </id>
+ <name> Protein export </name>
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+
+ <term>
+ <entity> VNG2467G </entity>
+ <id> 3010 </id>
+ <name> Ribosome </name>
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+
+ <term>
+ <entity> VNG2469G </entity>
+ <id> 3010 </id>
+ <name> Ribosome </name>
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+
+ <term>
+ <entity> VNG2499G </entity>
+ <id> 71 </id>
+ <name> Fatty acid metabolism </name>
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+
+ <term>
+ <entity> VNG2499G </entity>
+ <id> 310 </id>
+ <name> Lysine degradation </name>
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+
+ <term>
+ <entity> VNG2499G </entity>
+ <id> 380 </id>
+ <name> Tryptophan metabolism </name>
+ </term>
+
+ <term>
+ <entity> VNG2499G </entity>
+ <id> 632 </id>
+ <name> Benzoate degradation </name>
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+
+ <term>
+ <entity> VNG2504G </entity>
+ <id> 400 </id>
+ <name> Phenylalanine, tyrosine and tryptophan biosynthesis </name>
+ </term>
+
+ <term>
+ <entity> VNG2504G </entity>
+ <id> 970 </id>
+ <name> Aminoacyl-tRNA biosynthesis </name>
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+
+ <term>
+ <entity> VNG2505G </entity>
+ <id> 400 </id>
+ <name> Phenylalanine, tyrosine and tryptophan biosynthesis </name>
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+
+ <term>
+ <entity> VNG2505G </entity>
+ <id> 970 </id>
+ <name> Aminoacyl-tRNA biosynthesis </name>
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+
+ <term>
+ <entity> VNG2507G </entity>
+ <id> 240 </id>
+ <name> Pyrimidine metabolism </name>
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+
+ <term>
+ <entity> VNG2513G </entity>
+ <id> 10 </id>
+ <name> Glycolysis / Gluconeogenesis </name>
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+
+ <term>
+ <entity> VNG2513G </entity>
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+ <term>
+ <entity> VNG2513G </entity>
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+ <name> Fatty acid metabolism </name>
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+ <term>
+ <entity> VNG2513G </entity>
+ <id> 120 </id>
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+ <term>
+ <entity> VNG2513G </entity>
+ <id> 280 </id>
+ <name> Valine, leucine and isoleucine degradation </name>
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+
+ <term>
+ <entity> VNG2513G </entity>
+ <id> 310 </id>
+ <name> Lysine degradation </name>
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+ <term>
+ <entity> VNG2513G </entity>
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+
+ <term>
+ <entity> VNG2513G </entity>
+ <id> 340 </id>
+ <name> Histidine metabolism </name>
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+ <term>
+ <entity> VNG2513G </entity>
+ <id> 380 </id>
+ <name> Tryptophan metabolism </name>
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+
+ <term>
+ <entity> VNG2513G </entity>
+ <id> 410 </id>
+ <name> beta-Alanine metabolism </name>
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+
+ <term>
+ <entity> VNG2513G </entity>
+ <id> 561 </id>
+ <name> Glycerolipid metabolism </name>
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+
+ <term>
+ <entity> VNG2513G </entity>
+ <id> 620 </id>
+ <name> Pyruvate metabolism </name>
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+ <term>
+ <entity> VNG2513G </entity>
+ <id> 631 </id>
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+
+ <term>
+ <entity> VNG2513G </entity>
+ <id> 640 </id>
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+ <term>
+ <entity> VNG2513G </entity>
+ <id> 650 </id>
+ <name> Butanoate metabolism </name>
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+ <term>
+ <entity> VNG2514G </entity>
+ <id> 3010 </id>
+ <name> Ribosome </name>
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+ <term>
+ <entity> VNG2533G </entity>
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+ <term>
+ <entity> VNG2537G </entity>
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+ <term>
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+ <term>
+ <entity> VNG2547G </entity>
+ <id> 970 </id>
+ <name> Aminoacyl-tRNA biosynthesis </name>
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+
+ <term>
+ <entity> VNG2570G </entity>
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+
+ <term>
+ <entity> VNG2574G </entity>
+ <id> 20 </id>
+ <name> Citrate cycle (TCA cycle) </name>
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+ <term>
+ <entity> VNG2574G </entity>
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+ <term>
+ <entity> VNG2574G </entity>
+ <id> 720 </id>
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+
+ <term>
+ <entity> VNG2596G </entity>
+ <id> 340 </id>
+ <name> Histidine metabolism </name>
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+
+ <term>
+ <entity> VNG2606G </entity>
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+ <name> Thiamine metabolism </name>
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+
+ <term>
+ <entity> VNG2624G </entity>
+ <id> 740 </id>
+ <name> Riboflavin metabolism </name>
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+ <term>
+ <entity> VNG2629G </entity>
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+ <term>
+ <entity> VNG2629G </entity>
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+ <term>
+ <entity> VNG2629G </entity>
+ <id> 52 </id>
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+ <term>
+ <entity> VNG2629G </entity>
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+ <term>
+ <entity> VNG2629G </entity>
+ <id> 522 </id>
+ <name> Erythromycin biosynthesis </name>
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+ <term>
+ <entity> VNG2640G </entity>
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+ <term>
+ <entity> VNG2640G </entity>
+ <id> 670 </id>
+ <name> One carbon pool by folate </name>
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+ <term>
+ <entity> VNG2640G </entity>
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+ <name> Nitrogen metabolism </name>
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+ <term>
+ <entity> VNG2648G </entity>
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+ <name> Ribosome </name>
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+ <term>
+ <entity> VNG2650G </entity>
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+ <term>
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+ <term>
+ <entity> VNG2657G </entity>
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+ <term>
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+ <term>
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+ <term>
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+ <term>
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+ <term>
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+ <term>
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+ <term>
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+ <term>
+ <entity> VNG6050G </entity>
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+ <term>
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+ <name> Oxidative phosphorylation </name>
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+ <term>
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+ <name> Oxidative phosphorylation </name>
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+ <term>
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+ <term>
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+ <term>
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+ <term>
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+ <term>
+ <entity> VNG6140G </entity>
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+ <name> Transcription factors </name>
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+ <term>
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+ <term>
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+ <term>
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+ <term>
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+ <term>
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+ <term>
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+ <id> 351 </id>
+ <name> 1,1,1-Trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) degradation </name>
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+ <term>
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+ <term>
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+ <term>
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+ <term>
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+ <term>
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+ <term>
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+ <term>
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+ <term>
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+ <term>
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+ <term>
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+ <term>
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+ <term>
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+ <term>
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+ <term>
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+ <term>
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+ <name> Aminoacyl-tRNA biosynthesis </name>
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+ <term>
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+ <term>
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+ <term>
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+ <term>
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+ <term>
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+ <term>
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+ <term>
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+ <name> DNA polymerase </name>
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+ <term>
+ <entity> VNG6389G </entity>
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+ <name> Transcription factors </name>
+ </term>
+
+ <term>
+ <entity> VNG6438G </entity>
+ <id> 3022 </id>
+ <name> Transcription factors </name>
+ </term>
+
+ <term>
+ <entity> VNG6445G </entity>
+ <id> 100 </id>
+ <name> Sterol biosynthesis </name>
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+
+ <term>
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+ <id> 900 </id>
+ <name> Terpenoid biosynthesis </name>
+ </term>
+
+ <term>
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+ <name> Pyrimidine metabolism </name>
+ </term>
+
+ <term>
+ <entity> VNG6452G </entity>
+ <id> 240 </id>
+ <name> Pyrimidine metabolism </name>
+ </term>
+
+ <term>
+ <entity> VNG6471G </entity>
+ <id> 190 </id>
+ <name> Oxidative phosphorylation </name>
+ </term>
+
+ <term>
+ <entity> VNG6473G </entity>
+ <id> 190 </id>
+ <name> Oxidative phosphorylation </name>
+ </term>
+
+ <term>
+ <entity> VNG6476G </entity>
+ <id> 3022 </id>
+ <name> Transcription factors </name>
+ </term>
+
+
+</annotation>
diff --git a/application/src/test/resources/testData/humanKeggAndGO/bioproc.anno b/application/src/test/resources/testData/humanKeggAndGO/bioproc.anno
new file mode 100644
index 0000000..b321faf
--- /dev/null
+++ b/application/src/test/resources/testData/humanKeggAndGO/bioproc.anno
@@ -0,0 +1,40 @@
+(species=Homo sapiens) (type=Biological Process) (curator=GO)
+NP_001366 = 0006259
+NP_001366 = 0006915
+NP_005289 = 0007186
+NP_647593 = 0006899
+NP_647593 = 0007268
+NP_647593 = 0008099
+NP_647593 = 0008283
+NP_647593 = 0030154
+NP_647593 = 0045786
+NP_005756 = 0015992
+NP_002864 = 0000076
+NP_002864 = 0000077
+NP_002864 = 0006260
+NP_002864 = 0006281
+NP_002864 = 0007049
+NP_002864 = 0007093
+NP_003772 = 0006486
+NP_015560 = 0007264
+NP_015628 = 0006812
+NP_004726 = 0006357
+NP_004801 = 0006960
+NP_004801 = 0007242
+NP_004801 = 0007265
+NP_004801 = 0007267
+NP_002574 = 0000122
+NP_002574 = 0006915
+NP_002574 = 0008285
+NP_055145 = 0006915
+NP_055145 = 0006974
+NP_055145 = 0007050
+NP_006388 = 0006260
+NP_006388 = 0006401
+NP_005623 = 0006508
+NP_003558 = 0000074
+NP_003558 = 0007242
+NP_003558 = 0009315
+NP_003599 = 0006915
+NP_003599 = 0006955
+NP_003599 = 0007186
diff --git a/application/src/test/resources/testData/humanKeggAndGO/cellcomp.anno b/application/src/test/resources/testData/humanKeggAndGO/cellcomp.anno
new file mode 100644
index 0000000..d9f23cb
--- /dev/null
+++ b/application/src/test/resources/testData/humanKeggAndGO/cellcomp.anno
@@ -0,0 +1,40 @@
+(species=Homo sapiens) (type=Cellular Component) (curator=GO)
+NP_001366 = 0005764
+NP_005289 = 0005887
+NP_647593 = 0005871
+NP_647593 = 0015629
+NP_005756 = 0016021
+NP_002864 = 0005634
+NP_002864 = 0005663
+NP_003772 = 0005794
+NP_003772 = 0016021
+NP_015560 = 0005643
+NP_015628 = 0005624
+NP_015628 = 0005887
+NP_004726 = 0005634
+NP_004726 = 0005856
+NP_004801 = 0005737
+NP_002574 = 0005634
+NP_002574 = 0005737
+NP_005623 = 0005622
+NP_003599 = 0005887
+NP_001068 = 0005624
+NP_001068 = 0005792
+NP_001068 = 0016021
+NP_036546 = 0005625
+NP_006602 = 0005886
+NP_004650 = 0005578
+NP_004744 = 0016021
+NP_003585 = 0008023
+NP_004662 = 0005634
+NP_005828 = 0005634
+NP_005828 = 0005655
+NP_005863 = 0005681
+NP_009165 = 0005869
+NP_005862 = 0005681
+NP_065159 = 0005576
+NP_006629 = 0005634
+NP_006629 = 0005655
+NP_031395 = 0016021
+NP_067586 = 0008372
+NP_067586 = 0030125
diff --git a/application/src/test/resources/testData/humanKeggAndGO/go.onto b/application/src/test/resources/testData/humanKeggAndGO/go.onto
new file mode 100644
index 0000000..324da76
--- /dev/null
+++ b/application/src/test/resources/testData/humanKeggAndGO/go.onto
@@ -0,0 +1,13108 @@
+(curator=GO) (type=all)
+0003673 = Gene_Ontology
+0003674 = molecular_function [partof: 0003673 ]
+0015643 = anti-toxin [isa: 0003674 ]
+0015644 = lipoprotein anti-toxin [isa: 0015643 ]
+0008435 = anticoagulant [isa: 0003674 ]
+0016172 = antifreeze [isa: 0003674 ]
+0016173 = ice nucleation inhibitor [isa: 0016172 ]
+0016209 = antioxidant [isa: 0003674 ]
+0045174 = dehydroascorbate reductase [isa: 0009491 0015038 0016209 0016672 ]
+0004362 = glutathione reductase (NADPH) [isa: 0015038 0015933 0016209 0016654 ]
+0004791 = thioredoxin reductase (NADPH) [isa: 0015933 0016209 0016654 ]
+0016329 = apoptosis regulator [isa: 0003674 ]
+0016506 = apoptosis activator [isa: 0016329 ]
+0016505 = apoptotic protease activator [isa: 0016504 0016506 ]
+0008189 = apoptosis inhibitor [isa: 0016329 ]
+0005488 = binding [isa: 0003674 ]
+0016597 = amino acid binding [isa: 0005488 ]
+0016595 = glutamate binding [isa: 0016597 ]
+0016594 = glycine binding [isa: 0016597 ]
+0009374 = biotin binding [isa: 0005488 ]
+0005509 = calcium ion binding [isa: 0005488 ]
+0005514 = calcium ion storage [isa: 0005509 ]
+0030246 = carbohydrate binding [isa: 0005488 ]
+0030247 = polysaccharide binding [isa: 0030246 ]
+0030248 = cellulose binding [isa: 0030247 ]
+0008061 = chitin binding [isa: 0030247 ]
+0005529 = sugar binding [isa: 0030246 ]
+0005534 = galactose binding [isa: 0005529 ]
+0005531 = galactose binding lectin [isa: 0005530 0005534 ]
+0016936 = galactoside binding [isa: 0005529 ]
+0005536 = glucose binding [isa: 0005529 ]
+0030395 = lactose binding [isa: 0005529 ]
+0005530 = lectin [isa: 0005529 ]
+0001577 = galectin [isa: 0005530 ]
+0005532 = mannose binding lectin [isa: 0005530 0005537 ]
+0005533 = N-acetyl-galactosamine lectin [isa: 0005530 ]
+0005537 = mannose binding [isa: 0005529 ]
+0016168 = chlorophyll binding [isa: 0005488 ]
+0042314 = bacteriochlorophyll binding [isa: 0016168 ]
+0016169 = bacteriochlorophyll c binding [isa: 0042314 ]
+0008144 = drug binding [isa: 0005488 ]
+0019811 = cocaine binding [isa: 0008144 ]
+0016018 = cyclosporin A binding [isa: 0008144 0042277 ]
+0005527 = macrolide binding [isa: 0008144 ]
+0005528 = FK506 binding [isa: 0005527 ]
+0030051 = FK506-sensitive peptidyl-prolyl cis-trans isomerase [isa: 0003755 0005528 ]
+0008145 = phenylalkylamine binding [isa: 0008144 ]
+0016596 = thienylcyclohexylpiperidine binding [isa: 0008144 ]
+0005542 = folate binding [isa: 0005488 ]
+0005539 = glycosaminoglycan binding [isa: 0005488 ]
+0008201 = heparin binding [isa: 0005539 ]
+0005540 = hyaluronic acid binding [isa: 0005539 ]
+0005505 = heavy metal binding [isa: 0005488 ]
+0005507 = copper binding [isa: 0005505 ]
+0005508 = copper/cadmium binding [isa: 0005507 ]
+0005506 = iron binding [isa: 0005505 ]
+0008199 = ferric iron binding [isa: 0005506 ]
+0008198 = ferrous iron binding [isa: 0005506 ]
+0020037 = heme binding [isa: 0005506 ]
+0030145 = manganese binding [isa: 0005505 ]
+0045340 = mercury binding [isa: 0005505 ]
+0030151 = molybdenum binding [isa: 0005505 ]
+0016151 = nickel binding [isa: 0005505 ]
+0008270 = zinc binding [isa: 0005505 ]
+0019840 = isoprenoid binding [isa: 0005488 ]
+0005501 = retinoid binding [isa: 0019840 ]
+0016918 = retinal binding [isa: 0005501 ]
+0005502 = 11-cis retinal binding [isa: 0016918 ]
+0005503 = all-trans retinal binding [isa: 0016918 ]
+0019841 = retinol binding [isa: 0005501 0019842 ]
+0005500 = juvenile hormone binding [isa: 0005488 ]
+0008289 = lipid binding [isa: 0005488 ]
+0005541 = acyl-CoA or acyl binding [isa: 0008289 ]
+0000036 = acyl carrier [isa: 0005541 ]
+0000062 = acyl-CoA binding [isa: 0005541 ]
+0019992 = diacylglycerol binding [isa: 0005541 ]
+0005504 = fatty acid binding [isa: 0008289 ]
+0005543 = phospholipid binding [isa: 0008289 ]
+0005544 = calcium-dependent phospholipid binding [isa: 0005543 ]
+0008429 = phosphatidylethanolamine binding [isa: 0005543 ]
+0005545 = phosphatidylinositol binding [isa: 0005543 ]
+0008526 = phosphatidylinositol transporter [isa: 0005545 0005548 ]
+0005547 = phosphatidylinositol-3,4,5-triphosphate binding [isa: 0005545 ]
+0005546 = phosphatidylinositol-4,5-bisphosphate binding [isa: 0005545 ]
+0005548 = phospholipid transporter [isa: 0005319 0005543 ]
+0015247 = aminophospholipid transporter [isa: 0005548 ]
+0004012 = phospholipid-translocating ATPase [isa: 0015247 0015662 0016820 ]
+0008525 = phosphatidylcholine transporter [isa: 0005548 ]
+0017128 = phospholipid scramblase [isa: 0005548 ]
+0046625 = sphingolipid binding [isa: 0008289 ]
+0046624 = sphingolipid transporter [isa: 0005319 0046625 ]
+0046623 = sphingolipid-translocating ATPase [isa: 0016820 0016887 0046624 ]
+0017129 = triglyceride binding [isa: 0008289 ]
+0001530 = lipopolysaccharide binding [isa: 0005488 0015221 ]
+0000287 = magnesium binding [isa: 0005488 ]
+0042165 = neurotransmitter binding [isa: 0005488 ]
+0042166 = acetylcholine binding [isa: 0042165 ]
+0015464 = acetylcholine receptor [isa: 0004888 0030594 0042166 ]
+0016907 = G-protein coupled acetylcholine receptor [isa: 0008227 0015464 ]
+0004981 = muscarinic acetylcholine receptor [isa: 0008227 0015464 ]
+0004889 = nicotinic acetylcholine-activated cation-selective channel [isa: 0005231 0005261 0015464 ]
+0017164 = nicotinic acetylcholine receptor-associated protein [isa: 0016962 ] [partof: 0004889 ]
+0030594 = neurotransmitter receptor [isa: 0004872 0042165 ]
+0016917 = GABA receptor [isa: 0004888 0030594 ]
+0004890 = GABA-A receptor [isa: 0005237 0005254 0016917 ]
+0008503 = benzodiazepine receptor [isa: 0004890 ]
+0004965 = GABA-B receptor [isa: 0008067 0016917 ]
+0003676 = nucleic acid binding [isa: 0005488 ]
+0003677 = DNA binding [isa: 0003676 ]
+0003680 = AT DNA binding [isa: 0003677 ]
+0003681 = bent DNA binding [isa: 0003677 ]
+0019237 = centromeric DNA binding [isa: 0003677 ]
+0003682 = chromatin binding [isa: 0003677 ]
+0003683 = lamin/chromatin binding [isa: 0003682 ]
+0003684 = damaged DNA binding [isa: 0003677 ]
+0003904 = deoxyribodipyrimidine photolyase [isa: 0003684 0003913 ]
+0019104 = DNA N-glycosylase [isa: 0003684 0016799 ]
+0003905 = alkylbase DNA N-glycosylase [isa: 0019104 ]
+0008725 = DNA 3-methyladenine glycosylase I [isa: 0003905 ]
+0000700 = mismatch base pair DNA N-glycosylase [isa: 0019104 ]
+0000701 = purine-specific mismatch base pair DNA N-glycosylase [isa: 0000700 ]
+0008263 = pyrimidine-specific mismatch base pair DNA N-glycosylase [isa: 0000700 ]
+0000702 = oxidized base lesion DNA N-glycosylase [isa: 0019104 ]
+0008534 = purine-specific oxidized base lesion DNA N-glycosylase [isa: 0000702 0003906 0004520 ]
+0000703 = pyrimidine-specific oxidized base lesion DNA N-glycosylase [isa: 0000702 0003906 0004520 ]
+0000704 = pyrimidine dimer DNA N-glycosylase [isa: 0003906 0004520 0019104 ]
+0004844 = uracil DNA N-glycosylase [isa: 0019104 ]
+0017065 = single-strand selective uracil DNA N-glycosylase [isa: 0004844 ]
+0003906 = DNA-(apurinic or apyrimidinic site) lyase [isa: 0003684 0016839 ]
+0009381 = excinuclease ABC [isa: 0003684 0004520 ]
+0003908 = methylated-DNA-[protein]-cysteine S-methyltransferase [isa: 0003684 0008172 0008757 ]
+0046403 = polynucleotide 3'-phosphatase [isa: 0003684 0016791 0019204 ]
+0046404 = polynucleotide 5'-hydroxyl-kinase [isa: 0003684 0016773 ]
+0004536 = deoxyribonuclease [isa: 0003677 0004518 ]
+0004537 = caspase-activated deoxyribonuclease [isa: 0004536 ]
+0004520 = endodeoxyribonuclease [isa: 0004519 0004536 ]
+0016888 = endodeoxyribonuclease, producing 5'-phosphomonoesters [isa: 0004520 ]
+0004530 = deoxyribonuclease I [isa: 0016888 ]
+0008833 = deoxyribonuclease IV (phage T4-induced) [isa: 0016888 ]
+0009035 = type I site-specific deoxyribonuclease [isa: 0015666 0016888 ]
+0009036 = type II site-specific deoxyribonuclease [isa: 0015666 0016888 ]
+0015668 = type III site-specific deoxyribonuclease [isa: 0015666 0016888 ]
+0016889 = endodeoxyribonuclease, producing other than 5'-phosphomonoesters [isa: 0004520 ]
+0008821 = crossover junction endoribonuclease [isa: 0016889 ]
+0004531 = deoxyribonuclease II [isa: 0016889 ]
+0008844 = endodeoxyribonuclease RUS [isa: 0016889 ]
+0019000 = endonuclease G [isa: 0004520 0004521 ]
+0017108 = flap endonuclease [isa: 0004520 0004529 ]
+0015666 = restriction endodeoxyribonuclease [isa: 0004520 ]
+0000014 = single-stranded DNA specific endodeoxyribonuclease [isa: 0004520 ]
+0016890 = site-specific endodeoxyribonuclease, specific for altered base [isa: 0004520 ]
+0004529 = exodeoxyribonuclease [isa: 0004527 0004536 ]
+0016895 = exodeoxyribonuclease, producing 5'-phosphomonoesters [isa: 0004529 ]
+0008296 = 3'-5' exodeoxyribonuclease [isa: 0008408 0016895 ]
+0008311 = double-stranded DNA specific 3'-5' exodeoxyribonuclease [isa: 0008296 0008309 ]
+0008310 = single-stranded DNA specific 3'-5' exodeoxyribonuclease [isa: 0008296 0008297 ]
+0008309 = double-stranded DNA specific exodeoxyribonuclease [isa: 0016895 ]
+0008852 = exodeoxyribonuclease I [isa: 0016895 ]
+0008853 = exodeoxyribonuclease III [isa: 0016895 ]
+0008854 = exodeoxyribonuclease V [isa: 0016895 ]
+0008855 = exodeoxyribonuclease VII [isa: 0016895 ]
+0008856 = exodeoxyribonuclease X [isa: 0016895 ]
+0008858 = exonuclease VIII [isa: 0016895 ]
+0008946 = oligoribonuclease [isa: 0004540 0016895 ]
+0008997 = ribonuclease R [isa: 0004540 0016895 ]
+0008297 = single-stranded DNA specific exodeoxyribonuclease [isa: 0016895 ]
+0045145 = single-stranded DNA specific 5'-3' exodeoxyribonuclease [isa: 0008297 ]
+0008301 = DNA bending [isa: 0003677 ]
+0045027 = DNA end binding [isa: 0003677 ]
+0003678 = DNA helicase [isa: 0003677 0004386 ]
+0004003 = ATP dependent DNA helicase [isa: 0003678 0008026 0008094 ]
+0009378 = Holliday junction helicase [isa: 0003678 ]
+0003687 = DNA replication factor [isa: 0003677 ]
+0003689 = DNA clamp loader [isa: 0003687 ]
+0019011 = DNA replication accessory factor [isa: 0003687 ]
+0019893 = DNA replication inhibitor [isa: 0003687 ]
+0003688 = DNA replication origin binding [isa: 0003687 ]
+0000217 = DNA secondary structure binding [isa: 0003677 ]
+0009387 = DNA supercoiling [isa: 0003677 ]
+0030039 = DNA unwinding factor [isa: 0003677 ]
+0003690 = double-stranded DNA binding [isa: 0003677 ]
+0000739 = DNA strand annealing [isa: 0003690 0003697 ]
+0003691 = double-stranded telomeric DNA binding [isa: 0003690 0042162 ]
+0000150 = recombinase [isa: 0003690 0003697 ]
+0009009 = site-specific recombinase [isa: 0003690 ]
+0009037 = tyrosine-based site-specific recombinase [isa: 0008907 0009009 ]
+0003692 = left-handed Z-DNA binding [isa: 0003677 ]
+0008327 = methyl-CpG binding [isa: 0000166 0003677 ]
+0003693 = P-element binding [isa: 0003677 ]
+0003694 = plasmid-associated protein [isa: 0003677 ]
+0003695 = random coil DNA binding [isa: 0003677 ]
+0000182 = ribosomal DNA (rDNA) binding [isa: 0003677 ]
+0003696 = satellite DNA binding [isa: 0003677 ]
+0003697 = single-stranded DNA binding [isa: 0003677 ]
+0042162 = telomeric DNA binding [isa: 0003677 ]
+0003720 = telomerase [isa: 0003964 0042162 ]
+0003721 = telomeric template RNA reverse transcriptase [partof: 0003720 ]
+0000332 = template for synthesis of G-rich strand of telomere DNA [partof: 0003720 ]
+0003700 = transcription factor [isa: 0003677 0030528 ]
+0017163 = negative regulator of basal transcription [isa: 0003700 ]
+0003701 = RNA polymerase I transcription factor [isa: 0003700 ]
+0003702 = RNA polymerase II transcription factor [isa: 0003700 ]
+0016251 = general RNA polymerase II transcription factor [isa: 0003702 ]
+0016455 = RNA polymerase II transcription mediator [isa: 0016251 ]
+0016252 = nonspecific RNA polymerase II transcription factor [isa: 0003702 ]
+0003705 = RNA polymerase II transcription factor, enhancer binding [isa: 0003702 ]
+0003704 = specific RNA polymerase II transcription factor [isa: 0003702 ]
+0003706 = ligand-regulated transcription factor [isa: 0003704 ]
+0004879 = ligand-dependent nuclear receptor [isa: 0003706 0004872 ]
+0004880 = juvenile hormone receptor [isa: 0004879 ]
+0003708 = retinoic acid receptor [isa: 0004879 ]
+0004886 = retinoid-X receptor [isa: 0003708 ]
+0003707 = steroid hormone receptor [isa: 0004879 ]
+0004882 = androgen receptor [isa: 0003707 ]
+0004884 = ecdysteroid hormone receptor [isa: 0003707 ]
+0030284 = estrogen receptor [isa: 0003707 ]
+0004883 = glucocorticoid receptor [isa: 0003707 ]
+0017082 = mineralocorticoid receptor [isa: 0003707 ]
+0004887 = thyroid hormone receptor [isa: 0004879 ]
+0008434 = vitamin D3 receptor [isa: 0004879 ]
+0003709 = RNA polymerase III transcription factor [isa: 0003700 ]
+0030401 = transcription antiterminator [isa: 0003700 ]
+0003711 = transcription elongation factor [isa: 0003700 ]
+0008148 = negative transcription elongation factor [isa: 0003711 ]
+0016943 = Pol I transcription elongation factor [isa: 0003711 ]
+0016944 = Pol II transcription elongation factor [isa: 0003711 ]
+0016945 = Pol III transcription elongation factor [isa: 0003711 ]
+0008159 = positive transcription elongation factor [isa: 0003711 ]
+0016986 = transcription initiation factor [isa: 0003700 ]
+0045152 = anti-sigma factor antagonist [isa: 0016986 ]
+0016987 = sigma factor [isa: 0016986 ]
+0016988 = transcription initiation factor antagonist [isa: 0003700 ]
+0016989 = sigma factor antagonist [isa: 0016988 ]
+0003715 = transcription termination factor [isa: 0003700 ]
+0003716 = Pol I transcription termination factor [isa: 0003715 ]
+0003717 = Pol II transcription termination factor [isa: 0003715 ]
+0003718 = Pol III transcription termination factor [isa: 0003715 ]
+0016563 = transcriptional activator [isa: 0003700 ]
+0042156 = zinc-mediated transcriptional activator [isa: 0016563 ]
+0016564 = transcriptional repressor [isa: 0003700 ]
+0016565 = general transcriptional repressor [isa: 0016564 ]
+0016566 = specific transcriptional repressor [isa: 0016564 ]
+0000156 = two-component response regulator [isa: 0003700 0004871 ]
+0045142 = triplex DNA binding [isa: 0003677 ]
+0045322 = unmethylated CpG binding [isa: 0003677 ]
+0004518 = nuclease [isa: 0003676 0016788 ]
+0004519 = endonuclease [isa: 0004518 ]
+0008845 = endonuclease VIII [isa: 0004519 ]
+0004521 = endoribonuclease [isa: 0004519 0004540 ]
+0016894 = endoribonuclease, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters [isa: 0004521 ]
+0016893 = endoribonuclease, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters [isa: 0004521 ]
+0016891 = endoribonuclease, producing 5'-phosphomonoesters [isa: 0004521 ]
+0004523 = ribonuclease H [isa: 0016891 ]
+0004524 = ribonuclease H1 [isa: 0004523 ]
+0004525 = ribonuclease III [isa: 0016891 ]
+0016443 = bidentate ribonuclease III [isa: 0004525 ]
+0004526 = ribonuclease P [isa: 0004549 0016891 ]
+0008419 = RNA lariat debranching enzyme [isa: 0016891 ]
+0016892 = endoribonuclease, producing other than 5'-phosphomonoesters [isa: 0004521 ]
+0008847 = enterobacter ribonuclease [isa: 0016892 ]
+0004522 = pancreatic ribonuclease [isa: 0016892 ]
+0000213 = tRNA-intron endonuclease [isa: 0004549 0016892 ]
+0016541 = intein [isa: 0004519 ]
+0004527 = exonuclease [isa: 0004518 ]
+0008408 = 3'-5' exonuclease [isa: 0004527 ]
+0000175 = 3'-5' exoribonuclease [isa: 0008408 0016896 ]
+0008859 = exoribonuclease II [isa: 0008408 0016896 ]
+0008409 = 5'-3' exonuclease [isa: 0004527 ]
+0004534 = 5'-3' exoribonuclease [isa: 0008409 0016896 ]
+0019040 = viral host shutoff protein [isa: 0004534 ]
+0008857 = exonuclease IX [isa: 0004527 ]
+0016797 = exonuclease, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters [isa: 0004527 ]
+0016796 = exonuclease, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters [isa: 0004527 ]
+0004532 = exoribonuclease [isa: 0004527 0004540 ]
+0016897 = exoribonuclease, producing 3'-phosphomonoesters [isa: 0004532 ]
+0016896 = exoribonuclease, producing 5'-phosphomonoesters [isa: 0004532 ]
+0004533 = exoribonuclease H [isa: 0016896 ]
+0004535 = poly(A)-specific ribonuclease [isa: 0016896 ]
+0004528 = phosphodiesterase I [isa: 0004527 0008081 ]
+0004540 = ribonuclease [isa: 0003723 0004518 ]
+0008995 = ribonuclease E [isa: 0004540 ]
+0008996 = ribonuclease G [isa: 0004540 ]
+0000171 = ribonuclease MRP [isa: 0004540 ]
+0046589 = ribonuclease T1 [isa: 0004540 ]
+0004549 = tRNA-specific ribonuclease [isa: 0004540 ]
+0003723 = RNA binding [isa: 0003676 ]
+0008097 = 5S RNA binding [isa: 0003723 ]
+0008098 = 5S RNA primary transcript binding [isa: 0008097 ]
+0008312 = 7S RNA binding [isa: 0003723 ]
+0017091 = AU-specific RNA binding [isa: 0003723 ]
+0003725 = double-stranded RNA binding [isa: 0003723 ]
+0003726 = double-stranded RNA adenosine deaminase [isa: 0003725 0003969 0004000 ]
+0003729 = mRNA binding [isa: 0003723 ]
+0030350 = iron-responsive element binding [isa: 0003729 ]
+0003730 = mRNA binding, 3' UTR [isa: 0003729 ]
+0003731 = mRNA cap binding [isa: 0003729 ]
+0008143 = poly(A) binding [isa: 0003727 0003729 ]
+0030363 = pre-mRNA cleavage factor [isa: 0003729 ]
+0030365 = cleavage stimulation factor [isa: 0030363 ]
+0030364 = cleavage/polyadenylation specificity factor [isa: 0030363 ]
+0008248 = pre-mRNA splicing factor [isa: 0003729 ]
+0030628 = 3' splice site binding [isa: 0008248 ]
+0030627 = 5' splice site binding [isa: 0008248 ]
+0045131 = mRNA branch point binding [isa: 0008248 ]
+0008187 = poly-pyrimidine tract binding [isa: 0003723 ]
+0017131 = uridine-rich cytoplasmic polyadenylation element binding [isa: 0008187 ]
+0003724 = RNA helicase [isa: 0003723 0004386 ]
+0004004 = ATP dependent RNA helicase [isa: 0003724 0008026 0008186 ]
+0030555 = RNA modification guide [isa: 0003723 ]
+0030561 = RNA 2'-O-ribose methylation guide [isa: 0030555 ]
+0030562 = rRNA 2'-O-ribose methylation guide [isa: 0030556 0030561 ]
+0030563 = snRNA 2'-O-ribose methylation guide [isa: 0030561 0030566 ]
+0030564 = tRNA 2'-O-ribose methylation guide [isa: 0030557 0030561 ]
+0030558 = RNA pseudouridylation guide [isa: 0030555 ]
+0030559 = rRNA pseudouridylation guide [isa: 0030556 0030558 ]
+0030565 = snRNA pseudouridylation guide [isa: 0030558 0030566 ]
+0030560 = tRNA pseudouridylation guide [isa: 0030557 0030558 ]
+0030556 = rRNA modification guide [isa: 0030555 ]
+0030566 = snRNA modification guide [isa: 0030555 ]
+0030557 = tRNA modification guide [isa: 0030555 ]
+0019843 = rRNA binding [isa: 0003723 ]
+0042134 = rRNA primary transcript binding [isa: 0019843 ]
+0003727 = single-stranded RNA binding [isa: 0003723 ]
+0017130 = poly(rC) binding [isa: 0003727 ]
+0008266 = poly(U) binding [isa: 0003727 ]
+0030515 = snoRNA binding [isa: 0003723 ]
+0017069 = snRNA binding [isa: 0003723 ]
+0003732 = snRNA cap binding [isa: 0017069 ]
+0030619 = U1 snRNA binding [isa: 0017069 ]
+0030625 = U11 snRNA binding [isa: 0017069 ]
+0030626 = U12 snRNA binding [isa: 0017069 ]
+0030620 = U2 snRNA binding [isa: 0017069 ]
+0030621 = U4 snRNA binding [isa: 0017069 ]
+0030622 = U4atac snRNA binding [isa: 0017069 ]
+0030623 = U5 snRNA binding [isa: 0017069 ]
+0017070 = U6 snRNA binding [isa: 0017069 ]
+0030629 = U6 snRNA 3' end binding [isa: 0017070 ]
+0030624 = U6atac snRNA binding [isa: 0017069 ]
+0000049 = tRNA binding [isa: 0003723 ]
+0008135 = translation factor, nucleic acid binding [isa: 0003676 0045182 ]
+0008547 = protein-synthesizing GTPase [isa: 0003924 0008135 ]
+0016147 = protein-synthesizing GTPase, elongation [isa: 0003746 0008547 ]
+0016146 = protein-synthesizing GTPase, initiation [isa: 0003743 0008547 ]
+0016148 = protein-synthesizing GTPase, termination [isa: 0008079 0008547 ]
+0008494 = translation activator [isa: 0008135 ]
+0003746 = translation elongation factor [isa: 0008135 ]
+0003743 = translation initiation factor [isa: 0008135 ]
+0000900 = translation repressor, nucleic acid binding [isa: 0008135 0030371 ]
+0008079 = translation termination factor [isa: 0008135 ]
+0003747 = translation release factor [isa: 0008079 ]
+0019839 = guanyl-nucleotide release factor [isa: 0003747 0005083 ]
+0016150 = translation release factor, codon nonspecific [isa: 0003747 0005525 ]
+0016149 = translation release factor, codon specific [isa: 0003747 ]
+0000166 = nucleotide binding [isa: 0005488 ]
+0030551 = cyclic nucleotide binding [isa: 0000166 ]
+0030552 = 3',5'-cyclic AMP binding [isa: 0016208 0030551 ]
+0030553 = 3',5'-cyclic GMP binding [isa: 0019002 0030551 ]
+0017076 = purine nucleotide binding [isa: 0000166 ]
+0030554 = adenyl nucleotide binding [isa: 0017076 ]
+0016208 = AMP binding [isa: 0030554 ]
+0005524 = ATP binding [isa: 0030554 ]
+0001730 = 2'-5'-oligoadenylate synthetase [isa: 0005524 0016779 ]
+0016887 = ATPase [isa: 0005524 0016818 ]
+0004002 = adenosinetriphosphatase [isa: 0016887 ]
+0008026 = ATP dependent helicase [isa: 0004002 0004386 ]
+0017116 = single-stranded DNA dependent ATP dependent DNA helicase [isa: 0008026 ]
+0008094 = DNA dependent adenosinetriphosphatase [isa: 0004002 ]
+0008186 = RNA dependent adenosinetriphosphatase [isa: 0004002 ]
+0015446 = arsenite-transporting ATPase [isa: 0008490 0015405 0016887 ]
+0004009 = ATP-binding cassette (ABC) transporter [isa: 0015405 0016820 0016887 ]
+0015435 = ABC-type efflux permease [isa: 0004009 0015562 ]
+0015441 = beta-glucan-transporting ATPase [isa: 0015160 0015435 ]
+0015436 = capsular-polysaccharide-transporting ATPase [isa: 0015159 0015435 ]
+0015439 = heme-transporting ATPase [isa: 0015232 0015435 ]
+0015437 = lipopolysaccharide-transporting ATPase [isa: 0015221 0015435 ]
+0015440 = peptide-transporting ATPase [isa: 0015197 0015435 ]
+0015438 = teichoic acid-transporting ATPase [isa: 0015162 0015435 ]
+0015427 = ABC-type efflux porter [isa: 0004009 ]
+0008563 = alpha-factor sex pheromone exporter [isa: 0015427 ]
+0015432 = bile acid porter [isa: 0015125 0015427 ]
+0015431 = conjugate transporter [isa: 0015427 ]
+0005395 = eye pigment precursor transporter [isa: 0015427 ]
+0004007 = heavy metal-exporting ATPase [isa: 0005373 0015427 ]
+0015434 = cadmium-transporting ATPase [isa: 0004007 0015086 ]
+0015632 = cobalt porter [isa: 0004007 0015087 ]
+0004008 = copper-exporting ATPase [isa: 0004007 0005375 0015662 ]
+0015633 = zinc porter [isa: 0004007 0005385 ]
+0015433 = major histocompatibility peptide transporter [isa: 0015427 ]
+0042141 = mating pheromone exporter [isa: 0015427 ]
+0015429 = peroxisomal fatty acyl transporter [isa: 0015246 0015427 ]
+0005325 = peroxisomal fatty acyl CoA transporter [isa: 0005324 0005400 0015429 0015607 ]
+0008560 = steroid-transporting ATPase [isa: 0015427 ]
+0015619 = thiamin, thiamin pyrophosphate porter [isa: 0015234 0015427 ]
+0005396 = transmembrane conductance regulator [isa: 0015427 ]
+0005260 = channel-conductance-controlling ATPase [isa: 0005254 0005396 ]
+0015428 = type I protein secretor [isa: 0008565 0015427 ]
+0008559 = xenobiotic-transporting ATPase [isa: 0015239 0015427 ]
+0015406 = ABC-type uptake permease [isa: 0004009 0015563 ]
+0015424 = amino acid-transporting ATPase [isa: 0015171 0015406 ]
+0015425 = nonpolar-amino acid-transporting ATPase [isa: 0015424 ]
+0015602 = leucine/isoleucine/valine porter [isa: 0005304 0015188 0015190 0015425 ]
+0015426 = polar amino acid uptake transporter [isa: 0015424 ]
+0015598 = arginine porter [isa: 0015181 0015426 ]
+0015601 = cystine/diaminopimelate porter [isa: 0015184 0015426 0015626 ]
+0015600 = glutamate/aspartate porter [isa: 0005313 0015183 0015426 ]
+0015599 = glutamine porter [isa: 0015186 0015426 ]
+0015597 = histidine/arginine/lysine/ornithine porter [isa: 0000064 0005290 0015181 0015189 0015426 ]
+0015608 = carbohydrate uptake transporter [isa: 0015144 0015406 ]
+0015612 = arabinose porter [isa: 0015147 0015608 ]
+0015615 = D-allose porter [isa: 0015593 0015608 ]
+0015613 = galactose/glucose (methylgalactoside) porter [isa: 0005354 0005355 0015592 0015608 ]
+0015610 = glycerol-phosphate porter [isa: 0015169 0015608 ]
+0015609 = malto-oligosaccharide porter [isa: 0015157 0015608 ]
+0015407 = monosaccharide-transporting ATPase [isa: 0015145 0015608 ]
+0015611 = ribose porter [isa: 0015591 0015608 ]
+0015614 = xylose porter [isa: 0015148 0015608 ]
+0019829 = cation-transporting ATPase [isa: 0015406 ]
+0004005 = plasma membrane cation-transporting ATPase [isa: 0019829 ]
+0015624 = ferric-enterobactin porter [isa: 0015406 0015620 ]
+0015625 = ferric-hydroxamate porter [isa: 0015406 0015622 ]
+0015408 = ferric-transporting ATPase [isa: 0015091 0015406 ]
+0015623 = ferric/ferric-dicitrate porter [isa: 0015406 0015603 ]
+0015430 = glycerol-3-phosphate-transporting ATPase [isa: 0015169 0015406 ]
+0008558 = guanine-transporting ATPase [isa: 0015208 0015406 ]
+0015410 = manganese-transporting ATPase [isa: 0005384 0015406 ]
+0015412 = molybdate porter [isa: 0015098 0015406 ]
+0015413 = nickel porter [isa: 0015099 0015406 ]
+0015414 = nitrate-transporting ATPase [isa: 0015112 0015406 ]
+0015421 = oligopeptide-transporting ATPase [isa: 0015198 0015406 ]
+0015422 = oligosaccharide-transporting ATPase [isa: 0015157 0015406 ]
+0015423 = maltose-transporting ATPase [isa: 0005363 0015422 ]
+0015415 = phosphate porter [isa: 0015114 0015406 ]
+0015416 = phosphonate/organophosphate ester porter (broad specificity) [isa: 0015406 0015605 ]
+0015417 = polyamine porter [isa: 0015203 0015406 ]
+0015594 = putrescine porter [isa: 0015417 0015489 ]
+0015595 = spermidine porter [isa: 0015417 0015606 ]
+0015418 = quaternary amine uptake transporter [isa: 0015406 ]
+0015596 = glycine betaine/proline porter [isa: 0015187 0015193 0015199 0015418 ]
+0015419 = sulfate/thiosulfate porter [isa: 0015116 0015117 0015406 ]
+0015411 = taurine (2-aminoethane sulfonate) porter [isa: 0005368 0015406 ]
+0015420 = vitamin B12 porter [isa: 0015235 0015406 ]
+0015616 = DNA translocase [isa: 0015405 0016887 ]
+0015442 = hydrogen-/sodium-translocating ATPase [isa: 0015405 0016887 ]
+0003936 = hydrogen-transporting two-sector ATPase [isa: 0015442 0016820 ]
+0016466 = hydrogen-translocating A-type ATPase [isa: 0003936 0015078 ]
+0016467 = hydrogen-translocating F-type ATPase [isa: 0003936 ]
+0000260 = hydrogen-translocating V-type ATPase [isa: 0003936 0015078 ]
+0015443 = sodium-transporting two-sector ATPase [isa: 0015442 ]
+0016468 = sodium-translocating F-type ATPase [isa: 0015443 ]
+0000261 = sodium-translocating V-type ATPase [isa: 0015078 0015443 ]
+0015662 = P-type ATPase [isa: 0008324 0015405 0016887 ]
+0008551 = cadmium-exporting ATPase [isa: 0015086 0015662 ]
+0005388 = calcium-transporting ATPase [isa: 0015085 0015662 ]
+0008555 = chloride-transporting ATPase [isa: 0015108 0015662 ]
+0008553 = hydrogen-exporting ATPase [isa: 0015078 0015662 ]
+0008900 = hydrogen/potassium-exchanging ATPase [isa: 0015078 0015662 0016820 ]
+0015444 = magnesium-importing ATPase [isa: 0015095 0015662 ]
+0008556 = potassium-transporting ATPase [isa: 0015079 0015662 ]
+0015618 = potassium-uptake-ATPase [isa: 0008556 ]
+0015445 = silver-exporting ATPase [isa: 0015079 0015080 0015081 0015662 ]
+0008554 = sodium-exporting ATPase [isa: 0015081 0015662 ]
+0005391 = sodium/potassium-exchanging ATPase [isa: 0015662 ]
+0008552 = zinc, cadmium, cobalt, nickel, lead-efflux ATPase [isa: 0005385 0015086 0015087 0015094 0015099 0015662 ]
+0016463 = zinc-exporting ATPase [isa: 0005385 0015662 ]
+0015462 = protein-transporting ATPase [isa: 0008565 0015405 0016887 ]
+0016464 = chloroplast protein-transporting ATPase [isa: 0015462 ]
+0008566 = mitochondrial protein-transporting ATPase [isa: 0015462 ]
+0015617 = pilin/fimbrilin exporter [isa: 0015462 ]
+0008564 = protein-secreting ATPase [isa: 0015462 ]
+0019001 = guanyl nucleotide binding [isa: 0017076 ]
+0019003 = GDP binding [isa: 0019001 ]
+0019002 = GMP binding [isa: 0019001 ]
+0005525 = GTP binding [isa: 0019001 ]
+0003924 = GTPase [isa: 0005525 0016818 ]
+0008549 = dynamin GTPase [isa: 0003924 ]
+0003927 = heterotrimeric G-protein GTPase [isa: 0003924 ]
+0008548 = signal-recognition-particle GTPase [isa: 0003924 ]
+0003925 = small monomeric GTPase [isa: 0003924 ]
+0003926 = ARF small monomeric GTPase [isa: 0003925 ]
+0003928 = RAB small monomeric GTPase [isa: 0003925 ]
+0003929 = RAN small monomeric GTPase [isa: 0003925 ]
+0003930 = RAS small monomeric GTPase [isa: 0003925 ]
+0008619 = RHEB small monomeric GTPase [isa: 0003925 ]
+0003931 = Rho small monomeric GTPase [isa: 0003925 ]
+0003932 = SAR small monomeric GTPase [isa: 0003925 ]
+0008550 = tubulin GTPase [isa: 0003924 ]
+0005085 = guanyl-nucleotide exchange factor [isa: 0005083 0019001 ]
+0005086 = ARF guanyl-nucleotide exchange factor [isa: 0005085 ]
+0017132 = cyclic nucleotide dependent guanyl-nucleotide exchange factor [isa: 0005085 ]
+0017112 = RAB guanyl-nucleotide exchange factor [isa: 0005085 ]
+0008321 = RAL guanyl-nucleotide exchange factor [isa: 0005085 ]
+0005087 = RAN guanyl-nucleotide exchange factor [isa: 0005085 ]
+0017034 = RAP guanyl-nucleotide exchange factor [isa: 0005085 ]
+0005088 = RAS guanyl-nucleotide exchange factor [isa: 0005085 ]
+0005089 = Rho guanyl-nucleotide exchange factor [isa: 0005085 ]
+0005090 = SAR guanyl-nucleotide exchange factor [isa: 0005085 ]
+0019103 = pyrimidine nucleotide binding [isa: 0000166 ]
+0005549 = odorant binding [isa: 0005488 ]
+0005550 = pheromone binding [isa: 0005549 ]
+0019825 = oxygen binding [isa: 0005488 ]
+0015034 = cytochrome P450 [isa: 0019825 ]
+0008403 = 25-hydroxycholecalciferol-24-hydroxylase [isa: 0004497 0015034 0016705 ]
+0008391 = arachidonic acid monooxygenase [isa: 0004497 0015034 0016705 ]
+0008405 = arachidonic acid 11,12-epoxygenase [isa: 0008391 ]
+0008404 = arachidonic acid 14,15-epoxygenase [isa: 0008391 ]
+0008392 = arachidonic acid epoxygenase [isa: 0008391 ]
+0008402 = aromatase [isa: 0003824 0015034 ]
+0004498 = calcidiol 1-monooxygenase [isa: 0004497 0015034 0016709 ]
+0008123 = cholesterol 7-alpha-monooxygenase [isa: 0008395 0015034 0016709 ]
+0008389 = coumarin 7-hydroxylase [isa: 0004497 0015034 0016705 ]
+0004500 = dopamine-beta-monooxygenase [isa: 0004497 0015034 0016715 ]
+0008393 = fatty acid (omega-1)-hydroxylase [isa: 0004497 0015034 0016705 ]
+0008398 = lanosterol 14-alpha-demethylase [isa: 0003824 0015034 ]
+0008399 = naphthalene hydroxylase [isa: 0004497 0015034 0016705 ]
+0008394 = olfactory-specific steroid hydroxylase [isa: 0008395 0015034 0016705 ]
+0008396 = oxysterol 7-alpha-hydroxylase [isa: 0008395 0015034 0016705 ]
+0046409 = p-coumarate 3-hydroxylase [isa: 0004497 0015034 ]
+0016968 = P450 nitric oxide reductase [isa: 0015034 0016966 ]
+0008116 = prostaglandin-I synthase [isa: 0015034 0016865 ]
+0008401 = retinoic acid 4-hydroxylase [isa: 0004497 0015034 0016705 ]
+0004507 = steroid 11-beta-monooxygenase [isa: 0008395 0015034 0016713 ]
+0004508 = steroid 17-alpha-monooxygenase [isa: 0008395 0015034 0016718 ]
+0004509 = steroid 21-monooxygenase [isa: 0008395 0015034 0016718 ]
+0008387 = steroid 7-alpha-hydroxylase [isa: 0008395 0015034 0016705 ]
+0008397 = sterol 12-alpha-hydroxylase [isa: 0008395 0015034 0016705 ]
+0008388 = testosterone 15-alpha-hydroxylase [isa: 0008395 0015034 0016705 ]
+0008390 = testosterone 16-alpha-hydroxylase [isa: 0008395 0015034 0016705 ]
+0004796 = thromboxane-A synthase [isa: 0015034 0016865 ]
+0019826 = oxygen sensor [isa: 0019825 ]
+0005344 = oxygen transporter [isa: 0005215 0019825 ]
+0001524 = globin [isa: 0005344 ]
+0016969 = hemerythrin [isa: 0005344 ]
+0016970 = hemocyanin [isa: 0005344 ]
+0008658 = penicillin binding [isa: 0005488 ]
+0008717 = D-alanyl-D-alanine endopeptidase [isa: 0004175 0008658 ]
+0042277 = peptide binding [isa: 0005488 ]
+0042301 = phosphate binding [isa: 0005488 ]
+0019808 = polyamine binding [isa: 0005488 ]
+0019810 = putrescine binding [isa: 0019808 ]
+0019809 = spermidine binding [isa: 0019808 ]
+0005515 = protein binding [isa: 0005488 ]
+0045294 = alpha-catenin binding [isa: 0005515 ]
+0030306 = ARF binding [isa: 0005515 ]
+0001540 = beta-amyloid binding [isa: 0005515 ]
+0008013 = beta-catenin binding [isa: 0005515 ]
+0045296 = cadherin binding [isa: 0005515 ]
+0005516 = calmodulin binding [isa: 0005515 ]
+0005517 = calmodulin inhibitor [isa: 0005516 ]
+0030276 = clathrin binding [isa: 0005515 ]
+0005518 = collagen binding [isa: 0005515 ]
+0030332 = cyclin binding [isa: 0005515 ]
+0019955 = cytokine binding [isa: 0005515 ]
+0019956 = chemokine binding [isa: 0019955 ]
+0019957 = C-C chemokine binding [isa: 0019956 ]
+0016493 = C-C chemokine receptor [isa: 0004950 0019957 ]
+0019958 = C-X-C chemokine binding [isa: 0019956 ]
+0016494 = C-X-C chemokine receptor [isa: 0004950 0019958 ]
+0004918 = interleukin-8 receptor [isa: 0004907 0016494 0019959 ]
+0019959 = interleukin-8 binding [isa: 0019958 0019965 ]
+0019960 = C-X3-C chemokine binding [isa: 0019956 ]
+0016495 = C-X3-C chemokine receptor [isa: 0004950 0019960 ]
+0004950 = chemokine receptor [isa: 0001637 0019956 ]
+0042021 = granulocyte macrophage colony-stimulating factor complex binding [isa: 0019955 ]
+0019961 = interferon binding [isa: 0019955 ]
+0004904 = interferon receptor [isa: 0004896 0019961 ]
+0004905 = interferon-alpha/beta receptor [isa: 0004904 0019962 ]
+0004906 = interferon-gamma receptor [isa: 0004904 0019964 ]
+0019962 = interferon-alpha/beta binding [isa: 0019961 ]
+0019964 = interferon-gamma binding [isa: 0019961 ]
+0019965 = interleukin binding [isa: 0019955 ]
+0004907 = interleukin receptor [isa: 0004896 0019965 ]
+0004908 = interleukin-1 receptor [isa: 0004907 0019966 ]
+0004909 = interleukin-1, Type I, activating receptor [isa: 0004908 0019967 ]
+0004910 = interleukin-1, Type II, blocking receptor [isa: 0004908 0019968 ]
+0004920 = interleukin-10 receptor [isa: 0004907 0019969 ]
+0004921 = interleukin-11 receptor [isa: 0004907 0019970 ]
+0016517 = interleukin-12 receptor [isa: 0004907 0019972 ]
+0016515 = interleukin-13 receptor [isa: 0004907 0019973 ]
+0016518 = interleukin-14 receptor [isa: 0004907 0019974 ]
+0042010 = interleukin-15 receptor [isa: 0004907 0042009 ]
+0042012 = interleukin-16 receptor [isa: 0004907 0042011 ]
+0030368 = interleukin-17 receptor [isa: 0004907 0019975 ]
+0042008 = interleukin-18 receptor [isa: 0004907 0042007 ]
+0042014 = interleukin-19 receptor [isa: 0004907 0042013 ]
+0004911 = interleukin-2 receptor [isa: 0004907 0019976 ]
+0042016 = interleukin-20 receptor [isa: 0004907 0042015 ]
+0001532 = interleukin-21 receptor [isa: 0004907 0019977 ]
+0042018 = interleukin-22 receptor [isa: 0004907 0042017 ]
+0042020 = interleukin-23 receptor [isa: 0004907 0042019 ]
+0045506 = interleukin-24 receptor [isa: 0004907 0045510 ]
+0045507 = interleukin-25 receptor [isa: 0004907 0045511 ]
+0045508 = interleukin-26 receptor [isa: 0004907 0045512 ]
+0045509 = interleukin-27 receptor [isa: 0004907 0045513 ]
+0004912 = interleukin-3 receptor [isa: 0004907 0019978 ]
+0004913 = interleukin-4 receptor [isa: 0004907 0019979 ]
+0004914 = interleukin-5 receptor [isa: 0004907 0019980 ]
+0004915 = interleukin-6 receptor [isa: 0004907 0019981 ]
+0004917 = interleukin-7 receptor [isa: 0004907 0019982 ]
+0004919 = interleukin-9 receptor [isa: 0004907 0019983 ]
+0019966 = interleukin-1 binding [isa: 0019838 0019965 ]
+0019967 = interleukin-1, Type I, activating binding [isa: 0019966 ]
+0019968 = interleukin-1, Type II, blocking binding [isa: 0019966 ]
+0019969 = interleukin-10 binding [isa: 0019838 0019965 ]
+0019970 = interleukin-11 binding [isa: 0019838 0019965 ]
+0019972 = interleukin-12 binding [isa: 0019965 ]
+0042164 = interleukin-12 alpha subunit binding [isa: 0019972 ]
+0042163 = interleukin-12 beta subunit binding [isa: 0019972 ]
+0019973 = interleukin-13 binding [isa: 0019965 ]
+0019974 = interleukin-14 binding [isa: 0019965 ]
+0042009 = interleukin-15 binding [isa: 0019965 ]
+0042011 = interleukin-16 binding [isa: 0019965 ]
+0019975 = interleukin-17 binding [isa: 0019965 ]
+0042007 = interleukin-18 binding [isa: 0019965 ]
+0045093 = interleukin-18 alpha subunit binding [isa: 0042007 ]
+0045094 = interleukin-18 beta subunit binding [isa: 0042007 ]
+0042013 = interleukin-19 binding [isa: 0019965 ]
+0019976 = interleukin-2 binding [isa: 0019838 0019965 ]
+0042015 = interleukin-20 binding [isa: 0019965 ]
+0019977 = interleukin-21 binding [isa: 0019965 ]
+0042017 = interleukin-22 binding [isa: 0019965 ]
+0042019 = interleukin-23 binding [isa: 0019965 ]
+0045510 = interleukin-24 binding [isa: 0019965 ]
+0045511 = interleukin-25 binding [isa: 0019965 ]
+0045512 = interleukin-26 binding [isa: 0019965 ]
+0045513 = interleukin-27 binding [isa: 0019965 ]
+0019978 = interleukin-3 binding [isa: 0019838 0019965 ]
+0019979 = interleukin-4 binding [isa: 0019838 0019965 ]
+0019980 = interleukin-5 binding [isa: 0019838 0019965 ]
+0019981 = interleukin-6 binding [isa: 0019838 0019965 ]
+0019982 = interleukin-7 binding [isa: 0019838 0019965 ]
+0019983 = interleukin-9 binding [isa: 0019838 0019965 ]
+0008092 = cytoskeletal protein binding [isa: 0005515 ]
+0003779 = actin binding [isa: 0008092 ]
+0003781 = actin bundling [isa: 0003779 ]
+0003780 = actin cross-linking [isa: 0003779 ]
+0003787 = actin depolymerizing [isa: 0003779 ]
+0003789 = actin filament severing [isa: 0003779 ]
+0003786 = actin lateral binding [isa: 0003779 ]
+0003790 = actin modulating [isa: 0003779 ]
+0003785 = actin monomer binding [isa: 0003779 ]
+0003788 = actin monomer sequestering [isa: 0003779 ]
+0008651 = actin polymerizing [isa: 0003779 ]
+0003782 = F-actin capping [isa: 0003779 ]
+0003783 = barbed-end actin capping [isa: 0003782 ]
+0003784 = barbed-end actin capping/severing [isa: 0003782 ]
+0003791 = membrane associated actin binding [isa: 0003779 ]
+0003792 = regulation of actin thin filament length [isa: 0003779 ]
+0030506 = ankyrin binding [isa: 0008092 ]
+0008093 = cytoskeletal adaptor [isa: 0008092 ]
+0016343 = cytoskeletal anchor protein [isa: 0008092 ]
+0005519 = cytoskeletal regulatory protein binding [isa: 0008092 ]
+0019894 = kinesin binding [isa: 0008092 ]
+0019895 = kinesin-associated mitochondrial adaptor [isa: 0019894 ]
+0017022 = myosin binding [isa: 0008092 ]
+0017024 = myosin I binding [isa: 0017022 ]
+0045159 = myosin II binding [isa: 0017022 ]
+0017021 = myosin phosphatase myosin binding [isa: 0017022 ] [partof: 0017018 ]
+0030507 = spectrin binding [isa: 0008092 ]
+0005523 = tropomyosin binding [isa: 0008092 ]
+0030172 = troponin C binding [isa: 0008092 ]
+0015631 = tubulin binding [isa: 0008092 ]
+0008017 = microtubule binding [isa: 0015631 ]
+0003777 = microtubule motor [isa: 0003774 0008017 ]
+0016326 = kinesin motor [isa: 0003777 ]
+0008569 = minus-end-directed kinesin ATPase [isa: 0016326 0016821 ]
+0008574 = plus-end-directed kinesin ATPase [isa: 0016326 0016821 ]
+0008351 = microtubule severing [isa: 0008017 ]
+0017166 = vinculin binding [isa: 0008092 ]
+0017033 = DNA topoisomerase I binding [isa: 0005515 ]
+0045502 = dynein binding [isa: 0005515 ]
+0045504 = dynein heavy chain binding [isa: 0045502 ]
+0045505 = dynein intermediate chain binding [isa: 0045502 ]
+0045503 = dynein light chain binding [isa: 0045502 ]
+0019899 = enzyme binding [isa: 0005515 ]
+0008179 = adenylate cyclase binding [isa: 0019899 ]
+0017151 = DEAD/H-box RNA helicase binding [isa: 0019899 ]
+0019900 = kinase binding [isa: 0019899 ]
+0019901 = protein kinase binding [isa: 0019900 ]
+0008432 = JUN kinase binding [isa: 0019901 ]
+0017135 = membrane-associated protein with guanylate kinase activity interacting [isa: 0019899 ]
+0019902 = phosphatase binding [isa: 0019899 ]
+0030346 = protein phosphatase 2B binding [isa: 0019902 ]
+0019903 = protein phosphatase binding [isa: 0019902 ]
+0008157 = protein phosphatase 1 binding [isa: 0019903 ]
+0008190 = eukaryotic initiation factor 4E binding [isa: 0005515 ]
+0045295 = gamma-catenin binding [isa: 0005515 ]
+0019838 = growth factor binding [isa: 0005515 ]
+0017134 = fibroblast growth factor binding [isa: 0019838 ]
+0005520 = insulin-like growth factor binding [isa: 0019838 ]
+0030492 = hemoglobin binding [isa: 0005515 ]
+0042393 = histone binding [isa: 0005515 ]
+0030544 = HSP70 protein binding [isa: 0005515 ]
+0017078 = HSC70-interacting [isa: 0003754 0030544 ]
+0019865 = immunoglobulin binding [isa: 0005515 ]
+0019862 = IgA binding [isa: 0019865 ]
+0019766 = IgA receptor [isa: 0019763 0019862 ]
+0019863 = IgE binding [isa: 0019865 ]
+0019767 = IgE receptor [isa: 0019763 0019863 ]
+0019768 = high affinity IgE receptor [isa: 0019764 0019767 ]
+0019769 = low affinity IgE receptor [isa: 0019765 0019767 ]
+0019864 = IgG binding [isa: 0019865 ]
+0019770 = IgG receptor [isa: 0019763 0019864 ]
+0019771 = high affinity IgG receptor [isa: 0019764 0019770 ]
+0042071 = leucokinin receptor [isa: 0019770 ]
+0019772 = low affinity IgG receptor [isa: 0019765 0019770 ]
+0008262 = importin-alpha export receptor [isa: 0005515 ]
+0019215 = intermediate filament binding [isa: 0005515 ]
+0019793 = ISG15 carrier [isa: 0005515 ]
+0017170 = KU70 binding [isa: 0005515 ]
+0005521 = lamin binding [isa: 0005515 ]
+0008034 = lipoprotein binding [isa: 0005515 ]
+0042498 = diacylated lipoprotein binding [isa: 0008034 ]
+0008035 = high-density lipoprotein binding [isa: 0008034 ]
+0030169 = low-density lipoprotein binding [isa: 0008034 ]
+0005041 = low-density lipoprotein receptor [isa: 0030169 0030228 ]
+0042497 = triacylated lipoprotein binding [isa: 0008034 ]
+0016030 = metarhodopsin binding [isa: 0005515 ]
+0042043 = neurexin binding [isa: 0005515 ]
+0008139 = nuclear localization sequence binding [isa: 0005515 ]
+0000268 = peroxisome targeting sequence binding [isa: 0005515 ]
+0005051 = peroxisome targeting signal receptor [isa: 0000268 0004888 ]
+0005052 = peroxisome targeting signal-1 receptor [isa: 0005051 ]
+0005053 = peroxisome targeting signal-2 receptor [isa: 0005051 ]
+0008267 = poly-glutamine tract binding [isa: 0005515 ]
+0017046 = polypeptide hormone binding [isa: 0005515 ]
+0017047 = adrenocorticotropin-releasing hormone binding [isa: 0017046 ]
+0005522 = profilin binding [isa: 0005515 ]
+0045308 = protein amino acid binding [isa: 0005515 ]
+0045309 = phosphoprotein amino acid binding [isa: 0045308 ]
+0045310 = phosphoserine/phosphothreonine binding [isa: 0045309 ]
+0008022 = protein C-terminus binding [isa: 0005515 ]
+0008320 = protein carrier [isa: 0005386 0005515 ]
+0019904 = protein domain specific binding [isa: 0005515 ]
+0017058 = FH1-domain binding [isa: 0019904 ]
+0030274 = LIM-domain binding [isa: 0019904 ]
+0030275 = LRR-domain binding [isa: 0019904 ]
+0030165 = PDZ-domain binding [isa: 0019904 ]
+0042169 = SH2-domain binding [isa: 0019904 ]
+0017124 = SH3-domain binding [isa: 0019904 ]
+0008249 = protein signal sequence binding [isa: 0005515 ]
+0009940 = amino-terminal propeptide binding [isa: 0008249 ]
+0008536 = RAN protein binding [isa: 0005515 ]
+0017048 = Rho binding [isa: 0005515 ]
+0017049 = GTP-Rho binding [isa: 0017048 ]
+0042153 = RPTP-like protein binding [isa: 0005515 ]
+0046332 = SMAD binding [isa: 0005515 ]
+0000149 = SNARE binding [isa: 0005515 ]
+0019905 = syntaxin binding [isa: 0000149 ]
+0017075 = syntaxin-1 binding [isa: 0019905 ]
+0030349 = syntaxin-13 binding [isa: 0019905 ]
+0030347 = syntaxin-2 binding [isa: 0019905 ]
+0030348 = syntaxin-3 binding [isa: 0019905 ]
+0030519 = snoRNP binding [isa: 0005515 ]
+0045545 = syndecan binding [isa: 0005515 ]
+0017025 = TATA-binding protein binding [isa: 0005515 ]
+0045569 = TRAIL binding [isa: 0005515 ]
+0008134 = transcription factor binding [isa: 0005515 ]
+0017162 = aryl hydrocarbon-receptor binding [isa: 0008134 ]
+0030331 = estrogen receptor binding [isa: 0008134 ]
+0003712 = transcription cofactor [isa: 0008134 0030528 ]
+0003713 = transcription co-activator [isa: 0003712 ]
+0008140 = cAMP response element binding protein binding [isa: 0003713 ]
+0030374 = ligand-dependent nuclear receptor transcription co-activator [isa: 0003713 ]
+0030375 = thyroid hormone receptor co-activator [isa: 0016923 0030374 ]
+0003714 = transcription co-repressor [isa: 0003712 ]
+0003719 = transcription factor, cytoplasmic sequestering [isa: 0008134 ]
+0017147 = Wnt-protein binding [isa: 0005515 ]
+0030170 = pyridoxal phosphate binding [isa: 0005488 ]
+0005102 = receptor binding [isa: 0004871 0005488 ]
+0005103 = baboon binding [isa: 0005102 ]
+0030156 = benzodiazepine receptor binding [isa: 0005102 ]
+0042056 = chemoattractant [isa: 0005102 ]
+0008009 = chemokine [isa: 0005125 0042056 0042379 ]
+0045499 = chemorepellant [isa: 0005102 ]
+0005125 = cytokine [isa: 0005102 ]
+0005175 = CD27 receptor ligand [isa: 0005125 ]
+0005174 = CD40 receptor ligand [isa: 0005125 ]
+0005154 = epidermal growth factor receptor ligand [isa: 0005125 ]
+0005155 = epidermal growth factor receptor activating ligand [isa: 0005154 ]
+0005156 = epidermal growth factor receptor inhibiting ligand [isa: 0005154 ]
+0008317 = gurken receptor ligand [isa: 0005154 ]
+0005162 = fibroblast growth factor receptor ligand [isa: 0005125 ]
+0030353 = fibroblast growth factor receptor antagonist [isa: 0005162 0048019 ]
+0005152 = interleukin-1 receptor antagonist [isa: 0005149 0030353 ]
+0045352 = interleukin-1 Type I receptor antagonist [isa: 0005152 ]
+0045353 = interleukin-1 Type II receptor antagonist [isa: 0005152 ]
+0005126 = hematopoietin/interferon-class (D200-domain) cytokine receptor ligand [isa: 0005125 ]
+0005127 = ciliary neurotrophic factor receptor ligand [isa: 0005126 ]
+0005128 = erythropoietin receptor ligand [isa: 0005126 ]
+0005129 = granulocyte macrophage colony-stimulating factor receptor ligand [isa: 0005128 0008083 ]
+0005130 = granulocyte colony-stimulating factor receptor ligand [isa: 0005126 0008083 ]
+0005131 = growth hormone receptor ligand [isa: 0005126 ]
+0005132 = interferon-alpha/beta receptor ligand [isa: 0005126 ]
+0005133 = interferon-gamma receptor ligand [isa: 0005126 ]
+0005141 = interleukin-10 receptor ligand [isa: 0005126 0008083 ]
+0005142 = interleukin-11 receptor ligand [isa: 0005126 0008083 ]
+0005143 = interleukin-12 receptor ligand [isa: 0005126 0008083 ]
+0005144 = interleukin-13 receptor ligand [isa: 0005126 ]
+0005145 = interleukin-14 receptor ligand [isa: 0005126 ]
+0016170 = interleukin-15 receptor ligand [isa: 0005126 ]
+0030367 = interleukin-17 receptor ligand [isa: 0005126 ]
+0030380 = interleukin-17E receptor ligand [isa: 0005126 ]
+0005134 = interleukin-2 receptor ligand [isa: 0005126 0008083 ]
+0001531 = interleukin-21 receptor ligand [isa: 0005126 ]
+0005135 = interleukin-3 receptor ligand [isa: 0005126 0008083 ]
+0005136 = interleukin-4 receptor ligand [isa: 0005126 0008083 ]
+0005137 = interleukin-5 receptor ligand [isa: 0005126 0008083 ]
+0005138 = interleukin-6 receptor ligand [isa: 0005126 0008083 ]
+0005139 = interleukin-7 receptor ligand [isa: 0005126 0008083 ]
+0005140 = interleukin-9 receptor ligand [isa: 0005126 0008083 ]
+0005146 = leukemia inhibitory factor receptor ligand [isa: 0005126 ]
+0005147 = oncostatin-M receptor ligand [isa: 0005126 ]
+0005148 = prolactin receptor ligand [isa: 0005126 ]
+0005171 = hepatocyte growth factor receptor ligand [isa: 0005125 ]
+0030372 = high molecular weight B-cell growth factor receptor ligand [isa: 0005125 ]
+0005158 = insulin receptor ligand [isa: 0005125 ]
+0005159 = insulin-like growth factor receptor ligand [isa: 0005125 ]
+0005149 = interleukin-1 receptor ligand [isa: 0005125 0008083 ]
+0005150 = interleukin-1, Type I receptor ligand [isa: 0005149 ]
+0005151 = interleukin-1, Type II receptor ligand [isa: 0005149 ]
+0045514 = interleukin-16 receptor ligand [isa: 0005125 ]
+0045515 = interleukin-18 receptor ligand [isa: 0005125 ]
+0045516 = interleukin-19 receptor ligand [isa: 0005125 ]
+0045517 = interleukin-20 receptor ligand [isa: 0005125 ]
+0045518 = interleukin-22 receptor ligand [isa: 0005125 ]
+0045519 = interleukin-23 receptor ligand [isa: 0005125 ]
+0045520 = interleukin-24 receptor ligand [isa: 0005125 ]
+0045521 = interleukin-25 receptor ligand [isa: 0005125 ]
+0045522 = interleukin-26 receptor ligand [isa: 0005125 ]
+0045523 = interleukin-27 receptor ligand [isa: 0005125 ]
+0005153 = interleukin-8 receptor ligand [isa: 0005125 ]
+0005157 = macrophage colony stimulating factor receptor ligand [isa: 0005125 0008083 ]
+0005176 = Neu/ErbB-2 receptor ligand [isa: 0005125 ]
+0005165 = neurotrophin receptor ligand [isa: 0005125 ]
+0005163 = nerve growth factor receptor ligand [isa: 0005165 ]
+0005166 = neurotrophin p75 receptor ligand [isa: 0005165 ]
+0005167 = neurotrophin TRK receptor ligand [isa: 0005165 ]
+0005168 = neurotrophin TRKA receptor ligand [isa: 0005167 ]
+0005169 = neurotrophin TRKB receptor ligand [isa: 0005167 ]
+0005170 = neurotrophin TRKC receptor ligand [isa: 0005167 ]
+0005161 = platelet-derived growth factor receptor ligand [isa: 0005125 ]
+0005173 = stem cell factor receptor ligand [isa: 0005125 ]
+0008185 = transforming growth factor-alpha receptor ligand [isa: 0005125 ]
+0005160 = transforming growth factor-beta receptor ligand [isa: 0005125 0008083 ]
+0016915 = activin [isa: 0005160 ]
+0016916 = inhibin [isa: 0005160 ]
+0005164 = tumor necrosis factor receptor ligand [isa: 0005125 ]
+0005172 = vascular endothelial growth factor receptor ligand [isa: 0005125 ]
+0005123 = death receptor binding [isa: 0005102 ]
+0005106 = ephrin [isa: 0005102 ]
+0005107 = GPI-linked ephrin [isa: 0005106 ]
+0005108 = transmembrane ephrin [isa: 0005106 ]
+0005104 = fibroblast growth factor receptor binding [isa: 0005102 ]
+0005105 = type 1 fibroblast growth factor receptor binding [isa: 0005104 ]
+0005111 = type 2 fibroblast growth factor receptor binding [isa: 0005104 ]
+0001664 = G-protein-coupled receptor binding [isa: 0005102 ]
+0042379 = chemokine receptor binding [isa: 0001664 ]
+0048020 = CCR chemokine receptor binding [isa: 0042379 ]
+0045236 = CXCR chemokine receptor binding [isa: 0042379 ]
+0045237 = CXCR1 chemokine receptor binding [isa: 0045236 ]
+0045238 = CXCR2 chemokine receptor binding [isa: 0045236 ]
+0005109 = frizzled binding [isa: 0001664 ]
+0005110 = frizzled-2 binding [isa: 0001664 ]
+0042324 = hypocretin receptor binding [isa: 0001664 ]
+0008083 = growth factor [isa: 0005102 ]
+0030116 = glial cell line-derived neurotrophic factor receptor ligand [isa: 0008083 ]
+0008084 = imaginal disc growth factor [isa: 0008083 ]
+0005179 = hormone [isa: 0005102 ]
+0046659 = digestive hormone [isa: 0005179 ]
+0005180 = peptide hormone [isa: 0005179 ]
+0017043 = adrenocorticotropin [isa: 0005180 ]
+0017045 = adrenocorticotropin-releasing hormone [isa: 0005180 ]
+0017044 = alpha-melanocyte stimulating hormone [isa: 0005180 ]
+0008492 = cAMP generating peptide [isa: 0005180 ]
+0008613 = diuretic hormone [isa: 0005180 ]
+0005181 = glycopeptide hormone [isa: 0005180 ]
+0016913 = follicle-stimulating hormone [isa: 0005181 ]
+0016608 = growth hormone-releasing hormone [isa: 0005180 ]
+0016088 = insulin [isa: 0005180 ]
+0005182 = lipopeptide hormone [isa: 0005180 ]
+0005183 = luteinizing hormone-releasing factor [isa: 0005180 ]
+0030354 = melanin-concentrating hormone [isa: 0005180 ]
+0016085 = myoinhibitory hormone [isa: 0005180 ]
+0016084 = myostimulatory hormone [isa: 0005180 ]
+0005184 = neuropeptide hormone [isa: 0005180 ]
+0016086 = allatostatin [isa: 0005184 ]
+0016087 = ecdysiostatic hormone [isa: 0005184 ]
+0008255 = ecdysis-triggering hormone [isa: 0005184 ]
+0008031 = eclosion hormone [isa: 0005184 ]
+0005185 = neurohypophyseal hormone [isa: 0005184 ]
+0018445 = prothoracicotrophic hormone [isa: 0005184 ]
+0008648 = tachykinin [isa: 0005184 ]
+0016521 = pituitary adenylate cyclase activating polypeptide [isa: 0005180 ]
+0008437 = thyrotropin-releasing hormone [isa: 0005180 ]
+0005178 = integrin binding [isa: 0005102 ]
+0030370 = intercellular adhesion molecule-3 receptor binding [isa: 0005102 ]
+0042287 = major histocompatibility complex molecule binding [isa: 0005102 ]
+0042288 = major histocompatibility complex class I molecule binding [isa: 0042287 ]
+0042289 = major histocompatibility complex class II molecule binding [isa: 0042287 ]
+0005177 = neuroligin [isa: 0005102 0005194 ]
+0005112 = Notch binding [isa: 0005102 ]
+0001515 = opioid peptide [isa: 0005102 ]
+0005113 = patched binding [isa: 0005102 ]
+0005186 = pheromone [isa: 0005102 ]
+0030413 = competence pheromone [isa: 0005186 ]
+0005114 = punt binding [isa: 0005102 ]
+0048018 = receptor agonist [isa: 0005102 0030546 ]
+0048019 = receptor antagonist [isa: 0005102 0030547 ]
+0005115 = receptor tyrosine kinase-like orphan receptor binding [isa: 0005102 ]
+0005116 = saxophone binding [isa: 0005102 ]
+0005124 = scavenger receptor binding [isa: 0005102 ]
+0030215 = semaphorin receptor binding [isa: 0005102 ]
+0005118 = sevenless binding [isa: 0005102 ]
+0005119 = smoothened binding [isa: 0005102 ]
+0017098 = sulfonylurea receptor binding [isa: 0005102 ]
+0005120 = thickveins binding [isa: 0005102 ]
+0005121 = Toll binding [isa: 0005102 ]
+0005122 = torso binding [isa: 0005102 ]
+0005117 = wishful thinking binding [isa: 0005102 ]
+0008430 = selenium binding [isa: 0005488 ]
+0005496 = steroid binding [isa: 0005488 ]
+0005497 = androgen binding [isa: 0005496 ]
+0015485 = cholesterol binding [isa: 0005496 ]
+0015484 = hemolysin [isa: 0015289 0015485 ]
+0008142 = oxysterol binding [isa: 0005496 ]
+0005498 = sterol carrier [isa: 0005496 ]
+0005499 = vitamin D binding [isa: 0005496 0019842 ]
+0019842 = vitamin binding [isa: 0005488 ]
+0008431 = tocopherol binding [isa: 0019842 ]
+0005194 = cell adhesion molecule [isa: 0003674 ]
+0008014 = calcium-dependent cell adhesion molecule [isa: 0005194 ]
+0016347 = calcium-independent cell adhesion molecule [isa: 0005194 ]
+0004895 = cell adhesion receptor [isa: 0004888 0005194 ]
+0030369 = ICAM-3 receptor [isa: 0004895 ]
+0005055 = laminin receptor [isa: 0004895 ]
+0042064 = cell adhesion receptor regulator [isa: 0005194 ]
+0042072 = cell adhesion receptor inhibitor [isa: 0042064 ]
+0030022 = extracellular matrix constituent, adhesive [isa: 0005194 0005201 ]
+0004384 = membrane-associated protein with guanylate kinase activity [isa: 0004385 0005194 0008728 ]
+0019039 = viral-cell fusion molecule [isa: 0005194 ]
+0003754 = chaperone [isa: 0003674 ]
+0003763 = chaperonin ATPase [isa: 0003754 0016821 ]
+0003767 = co-chaperone [isa: 0003754 ]
+0003772 = co-chaperonin [isa: 0003767 ]
+0015472 = fimbrial chaperone [isa: 0003754 ]
+0003773 = heat shock protein [isa: 0003754 ]
+0008077 = HSP70/HSP90 organizing protein [isa: 0003754 ]
+0003759 = lectin-binding chaperone [isa: 0003754 ]
+0016530 = metallochaperone [isa: 0003754 ]
+0016531 = copper chaperone [isa: 0016530 ]
+0016532 = superoxide dismutase copper chaperone [isa: 0016531 ]
+0003762 = nucleosome assembly chaperone [isa: 0003754 ]
+0000005 = ribosomal chaperone [isa: 0003754 ]
+0017072 = tubulin-specific chaperone [isa: 0003754 ]
+0030188 = chaperone regulator [isa: 0003674 ]
+0030189 = chaperone activator [isa: 0008047 0030188 ]
+0030190 = chaperone inhibitor [isa: 0004857 0030188 ]
+0030191 = Hsp70/Hsc70 chaperone inhibitor [isa: 0030190 0030192 ]
+0030192 = Hsp70/Hsc70 chaperone regulator [isa: 0030188 ]
+0008580 = cytoskeletal regulator [isa: 0003674 ]
+0003793 = defense/immunity protein [isa: 0003674 ]
+0003794 = acute-phase response protein [isa: 0003793 ]
+0003823 = antibody [isa: 0003793 0004892 ]
+0003795 = antimicrobial peptide [isa: 0003793 ]
+0003797 = antibacterial peptide [isa: 0003795 ]
+0008225 = Gram-negative antibacterial peptide [isa: 0003797 ]
+0008224 = Gram-positive antibacterial peptide [isa: 0003797 ]
+0003798 = male-specific antibacterial peptide [isa: 0003797 ]
+0003799 = antifungal peptide [isa: 0003795 ]
+0008367 = bacterial binding [isa: 0003795 ]
+0008368 = Gram-negative bacterial binding [isa: 0008367 ]
+0003796 = lysozyme [isa: 0003795 0004553 ]
+0003800 = antiviral response protein [isa: 0003793 ]
+0003801 = blood coagulation factor [isa: 0003793 ]
+0003803 = blood coagulation factor IX [isa: 0003801 0004252 ]
+0003802 = blood coagulation factor VII [isa: 0003801 0003811 0004252 ]
+0003804 = blood coagulation factor X [isa: 0003801 0004252 0030567 ]
+0003805 = blood coagulation factor XI [isa: 0003801 0004252 ]
+0003806 = blood coagulation factor XII [isa: 0003801 0004252 ]
+0003807 = plasma kallikrein [isa: 0003801 0004252 ]
+0003808 = protein C (activated) [isa: 0003801 0004252 ]
+0003810 = protein-glutamine gamma-glutamyltransferase [isa: 0003801 0016755 ]
+0003809 = thrombin [isa: 0003801 0004252 ]
+0042280 = cell surface antigen, host-interacting [isa: 0003793 ]
+0003811 = complement component [isa: 0003793 ]
+0003812 = alternative-complement pathway C3/C5 convertase [isa: 0003811 0004252 ]
+0003813 = classical-complement pathway C3/C5 convertase [isa: 0003811 0004252 ]
+0003815 = complement component C1r [isa: 0003811 0004252 ]
+0003816 = complement component C1s [isa: 0003811 0004252 ]
+0003817 = complement factor D [isa: 0003811 0004252 ]
+0030009 = complement factor H [isa: 0003811 ]
+0003818 = complement factor I [isa: 0003811 0004252 ]
+0019763 = Fc receptor [isa: 0003793 0016489 ]
+0019764 = high affinity Fc receptor [isa: 0019763 ]
+0019765 = low affinity Fc receptor [isa: 0019763 ]
+0008229 = opsonin [isa: 0003793 ]
+0003824 = enzyme [isa: 0003674 ]
+0046429 = 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase [isa: 0003824 ]
+0008485 = 2,5-diamino-6-(ribosylamino)-4(3H)-pyrimidonone 5'-phosphate deaminase [isa: 0003824 ]
+0008686 = 3,4 dihydroxy-2-butanone-4-phosphate synthase [isa: 0003824 ]
+0008696 = 4-amino-4-deoxychorismate lyase [isa: 0003824 ]
+0008699 = 4-diphosphocytidyl-2C-methyl-D-erythritol synthase [isa: 0003824 ]
+0008413 = 7,8-dihydro-8-oxoguanine-triphosphatase [isa: 0003824 ]
+0008711 = ADP-L-glycero-D-manno-heptose synthase [isa: 0003824 ]
+0004036 = alkylbase DNA glycosidase [isa: 0003824 ]
+0046567 = aphidicolan-16 beta-ol synthase [isa: 0003824 ]
+0003833 = beta-alanyl-dopamine synthase [isa: 0003824 ]
+0000249 = C-22 sterol desaturase [isa: 0003824 ]
+0008818 = cobalamin [5'-phosphate] synthase [isa: 0003824 ]
+0008719 = D-erythro-7,8-dihydroneopterin triphosphate 2'-epimerase [isa: 0003824 ]
+0017084 = delta-1-pyrroline-5-carboxylate synthetase [isa: 0003824 ]
+0004153 = dihydropterin deaminase [isa: 0003824 ]
+0004162 = dimethylnitrosamine demethylase [isa: 0003824 ]
+0008486 = diphosphoinositol polyphosphate phosphohydrolase [isa: 0003824 ]
+0004133 = glycogen debranching enzyme [isa: 0003824 ]
+0004134 = 4-alpha-glucanotransferase [isa: 0004133 0016758 ]
+0004135 = amylo-1,6-glucosidase [isa: 0004133 0015926 ]
+0019156 = isoamylase [isa: 0004133 0004553 ]
+0004386 = helicase [isa: 0003824 ]
+0008722 = DNA helicase IV [isa: 0004386 0016818 ]
+0004407 = histone deacetylase [isa: 0003824 ]
+0017136 = NAD-dependent histone deacetylase [isa: 0004407 ]
+0045129 = NAD-independent histone deacetylase [isa: 0004407 ]
+0016787 = hydrolase [isa: 0003824 ]
+0003923 = GPI-anchor transamidase [isa: 0016787 ]
+0016817 = hydrolase, acting on acid anhydrides [isa: 0016787 ]
+0016820 = hydrolase, acting on acid anhydrides, catalyzing transmembrane movement of substances [isa: 0016817 ]
+0016818 = hydrolase, acting on acid anhydrides, in phosphorus-containing anhydrides [isa: 0016817 ]
+0003998 = acylphosphatase [isa: 0016818 ]
+0008796 = bis(5'-nucleosyl)-tetraphosphatase [isa: 0016818 ]
+0004081 = bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) [isa: 0008796 ]
+0008803 = bis(5'-nucleosyl)-tetraphosphatase (symmetrical) [isa: 0008796 ]
+0008828 = dATP pyrophosphohydrolase [isa: 0016818 ]
+0019176 = dihydroneopterin monophosphate phosphatase [isa: 0016818 ]
+0019177 = dihydroneopterin triphosphate pyrophosphohydrolase [isa: 0016818 ]
+0000298 = endopolyphosphatase [isa: 0016818 ]
+0004309 = exopolyphosphatase [isa: 0016818 ]
+0017110 = nucleoside diphosphatase [isa: 0016818 ]
+0004050 = apyrase [isa: 0017110 ]
+0004382 = guanosine diphosphatase [isa: 0017110 ]
+0045134 = uridine diphosphatase [isa: 0017110 ]
+0017111 = nucleoside triphosphatase [isa: 0016818 ]
+0016462 = pyrophosphatase [isa: 0016302 0016818 ]
+0019144 = ADP-sugar diphosphatase [isa: 0016462 ]
+0008715 = CDP-diacylglycerol pyrophosphatase [isa: 0016462 ]
+0004170 = dUTP pyrophosphatase [isa: 0016462 ]
+0008894 = guanosine-5'-triphosphate,3'-diphosphate pyrophosphatase [isa: 0016462 ]
+0009678 = hydrogen-translocating pyrophosphatase [isa: 0015405 0016462 ]
+0004427 = inorganic diphosphatase [isa: 0016462 ]
+0000210 = NAD+ pyrophosphatase [isa: 0016462 ]
+0004551 = nucleotide pyrophosphatase [isa: 0016462 ]
+0004636 = phosphoribosyl-ATP pyrophosphatase [isa: 0016462 ]
+0004787 = thiamin pyrophosphatase [isa: 0016462 ]
+0008758 = UDP-2,3-diacylglucosamine hydrolase [isa: 0016818 ]
+0008768 = UDP-sugar diphosphatase [isa: 0016818 ]
+0016819 = hydrolase, acting on acid anhydrides, in sulfonyl-containing anhydrides [isa: 0016817 ]
+0016821 = hydrolase, acting on acid anhydrides, involved in cellular and subcellular movement [isa: 0016817 ]
+0008567 = dynein ATPase [isa: 0016821 ]
+0008568 = microtubule-severing ATPase [isa: 0016821 ]
+0008570 = myosin ATPase [isa: 0016821 ]
+0008571 = non-chaperonin molecular chaperone ATPase [isa: 0016821 ]
+0008572 = nucleoplasmin ATPase [isa: 0016821 ]
+0008573 = peroxisome-assembly ATPase [isa: 0016821 ]
+0008575 = proteasome ATPase [isa: 0016821 ]
+0008576 = vesicle-fusing ATPase [isa: 0016821 ]
+0016822 = hydrolase, acting on acid carbon-carbon bonds [isa: 0016787 ]
+0016823 = hydrolase, acting on acid carbon-carbon bonds, in ketonic substances [isa: 0016822 ]
+0018771 = 2-hydroxy-6-ketonona-2,4-dienedoic acid hydrolase [isa: 0016823 ]
+0018768 = 2-hydroxy-6-oxo-6-(2'-aminophenyl)hexa-2,4-dienoate hydrolase [isa: 0016823 ]
+0018774 = 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase [isa: 0016823 ]
+0018767 = 2-hydroxy-6-oxo-7-methylocta-2,4-dienoate hydrolase [isa: 0016823 ]
+0018765 = 2-hydroxy-6-oxohepta-2,4-dienoate hydrolase [isa: 0016823 ]
+0018769 = 2-hydroxy-6-oxoocta-2,4-dienoate hydrolase [isa: 0016823 ]
+0018775 = 2-hydroxymuconate semialdehyde hydrolase [isa: 0016823 ]
+0018770 = 6-oxo-2-hydroxy-7-(4'-chlorophenyl)-3,8,8-trichloroocta-2E,4E,7-trienoate hydrolase [isa: 0016823 ]
+0018773 = acetylpyruvate hydrolase [isa: 0016823 ]
+0018766 = dihydrophloroglucinol hydrolase [isa: 0016823 ]
+0004334 = fumarylacetoacetase [isa: 0016823 ]
+0030429 = kynureninase [isa: 0016823 ]
+0030603 = oxaloacetase [isa: 0016823 ]
+0018772 = trioxoheptanoate hydrolase [isa: 0016823 ]
+0016827 = hydrolase, acting on acid carbon-phosphorus bonds [isa: 0016787 ]
+0016824 = hydrolase, acting on acid halide bonds [isa: 0016787 ]
+0019120 = hydrolase, acting on acid halide bonds, in C-halide compounds [isa: 0016824 ]
+0018777 = 1,3,4,6-tetrachloro-1,4-cyclohexadiene halidohydrolase [isa: 0019120 ]
+0018779 = 2-chloro-4,6-dihydroxy-1,3,5-triazine hydrolase [isa: 0019120 ]
+0018784 = 2-haloacid dehalogenase [isa: 0019120 ]
+0018787 = 4-chlorobenzoyl-CoA dehalogenase [isa: 0019120 ]
+0018788 = atrazine chlorohydrolase [isa: 0019120 ]
+0018782 = cis-chloroacrylic acid dehalogenase [isa: 0019120 ]
+0018783 = deisopropyldeethylatrazine hydrolase [isa: 0019120 ]
+0018780 = dichloroacetate halidohydrolase [isa: 0019120 ]
+0018785 = haloacetate dehalogenase [isa: 0019120 ]
+0018778 = haloacid dehalogenase [isa: 0019120 ]
+0018786 = haloalkane dehalogenase [isa: 0019120 ]
+0018781 = S-triazine hydrolase [isa: 0019120 ]
+0004800 = thyroxine deiodinase [isa: 0019120 ]
+0018776 = trans-chloroacrylic acid dehalogenase [isa: 0019120 ]
+0016825 = hydrolase, acting on acid phosphorus-nitrogen bonds [isa: 0016787 ]
+0016826 = hydrolase, acting on acid sulfur-nitrogen bonds [isa: 0016787 ]
+0018789 = cyclamate sulfamatase [isa: 0016826 ]
+0016250 = N-sulfoglucosamine sulfohydrolase [isa: 0016826 ]
+0016828 = hydrolase, acting on acid sulfur-sulfur bonds [isa: 0016787 ]
+0016810 = hydrolase, acting on carbon-nitrogen (but not peptide) bonds [isa: 0016787 ]
+0016812 = hydrolase, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides [isa: 0016810 ]
+0018751 = 3,5-dichlorophenylcarboximide hydrolase [isa: 0016812 ]
+0017168 = 5-oxoprolinase (ATP-hydrolysing) [isa: 0016812 ]
+0019874 = 6-aminohexanoate-cyclic-dimer hydrolase [isa: 0016812 ]
+0004038 = allantoinase [isa: 0016812 ]
+0008800 = beta-lactamase [isa: 0016812 ]
+0018753 = cyanuric acid amidohydrolase [isa: 0016812 ]
+0004151 = dihydroorotase [isa: 0016812 ]
+0004157 = dihydropyrimidinase [isa: 0016812 ]
+0018752 = epsilon-caprolactam lactamase [isa: 0016812 ]
+0016814 = hydrolase, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines [isa: 0016810 ]
+0019238 = cyclohydrolase [isa: 0016814 ]
+0003933 = GTP cyclohydrolase [isa: 0019238 ]
+0003934 = GTP cyclohydrolase I [isa: 0003933 ]
+0003935 = GTP cyclohydrolase II [isa: 0003933 ]
+0003937 = IMP cyclohydrolase [isa: 0019238 ]
+0004477 = methenyltetrahydrofolate cyclohydrolase [isa: 0019238 ]
+0018759 = methenyltetrahydromethanopterin cyclohydrolase [isa: 0019238 ]
+0004635 = phosphoribosyl-AMP cyclohydrolase [isa: 0019238 ]
+0019239 = deaminase [isa: 0016814 ]
+0000034 = adenine deaminase [isa: 0019239 ]
+0004000 = adenosine deaminase [isa: 0019239 ]
+0008251 = tRNA specific adenosine deaminase [isa: 0003969 0004000 ]
+0003876 = AMP deaminase [isa: 0019239 ]
+0004126 = cytidine deaminase [isa: 0019239 ]
+0004131 = cytosine deaminase [isa: 0019239 ]
+0004132 = dCMP deaminase [isa: 0019239 ]
+0008829 = dCTP deaminase [isa: 0019239 ]
+0008835 = diaminohydroxyphosphoribosylaminopyrimidine deaminase [isa: 0019239 ]
+0017173 = DRAP deaminase [isa: 0019239 ]
+0008892 = guanine deaminase [isa: 0019239 ]
+0016811 = hydrolase, acting on carbon-nitrogen (but not peptide) bonds, in linear amides [isa: 0016810 ]
+0018749 = (3,5-dichlorophenylurea)acetate amidohydrolase [isa: 0016811 ]
+0019875 = 6-aminohexanoate-dimer hydrolase [isa: 0016811 ]
+0004039 = allophanate hydrolase [isa: 0016811 ]
+0004040 = amidase [isa: 0016811 ]
+0004046 = aminoacylase [isa: 0016811 ]
+0004061 = arylformamidase [isa: 0016811 ]
+0004067 = asparaginase [isa: 0016811 ]
+0003948 = N4-(beta-N-acetylglucosaminyl)-L-asparaginase [isa: 0004067 ]
+0008418 = protein N-terminal asparagine amidohydrolase [isa: 0004067 ]
+0019807 = aspartoacylase [isa: 0016811 ]
+0003837 = beta-ureidopropionase [isa: 0016811 ]
+0018750 = biuret amidohydrolase [isa: 0016811 ]
+0017040 = ceramidase [isa: 0016811 ]
+0004336 = galactosylceramidase [isa: 0004553 0017040 ]
+0017041 = galactosylgalactosylglucosylceramidase [isa: 0004553 0017040 ]
+0004348 = glucosylceramidase [isa: 0004553 0017040 ]
+0017042 = glycosylceramidase [isa: 0004553 0017040 ]
+0004099 = chitin deacetylase [isa: 0016811 ]
+0045302 = choloylglycine hydrolase [isa: 0016811 ]
+0019213 = deacetylase [isa: 0016811 ]
+0008777 = acetylornithine deacetylase [isa: 0019213 ]
+0008448 = N-acetylglucosamine-6-phosphate deacetylase [isa: 0019213 ]
+0008759 = UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase [isa: 0019213 ]
+0017064 = fatty acid amide hydrolase [isa: 0016811 ]
+0004328 = formamidase [isa: 0016811 ]
+0008463 = formylmethionine deformylase [isa: 0016811 ]
+0008864 = formyltetrahydrofolate deformylase [isa: 0016811 ]
+0004359 = glutaminase [isa: 0016811 ]
+0042242 = cobyrinic acid a,c-diamide synthase [isa: 0004359 ]
+0008884 = glutathionylspermidine amidase [isa: 0016811 ]
+0018748 = iprodione amidohydrolase [isa: 0016811 ]
+0008421 = long-chain-fatty-acyl-glutamate deacylase [isa: 0016811 ]
+0008745 = N-acetylmuramoyl-L-alanine amidase [isa: 0016811 ]
+0008936 = nicotinamidase [isa: 0016811 ]
+0019159 = nicotinamide-nucleotide amidase [isa: 0016811 ]
+0017159 = pantetheinase [isa: 0016811 ]
+0004593 = pantothenase [isa: 0016811 ]
+0008953 = penicillin amidase [isa: 0016811 ]
+0000224 = peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase [isa: 0016811 ]
+0009014 = succinyl-diaminopimelate desuccinylase [isa: 0016811 ]
+0009017 = succinylglutamate desuccinylase [isa: 0016811 ]
+0009039 = urease [isa: 0016811 ]
+0016813 = hydrolase, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines [isa: 0016810 ]
+0018758 = 2,4-dihydroxy-6-(N'-ethyl)amino-1,3,5-triazine aminohydrolase [isa: 0016813 ]
+0018755 = 2-chloro-4-hydroxy-6-amino-1,3,5-triazine aminohydrolase [isa: 0016813 ]
+0008783 = agmatinase [isa: 0016813 ]
+0004037 = allantoicase [isa: 0016813 ]
+0018754 = ammelide aminohydrolase [isa: 0016813 ]
+0018756 = ammeline aminohydrolase [isa: 0016813 ]
+0004053 = arginase [isa: 0016813 ]
+0016990 = arginine deiminase [isa: 0016813 ]
+0016980 = creatinase [isa: 0016813 ]
+0018757 = deisopropylhydroxyatrazine aminohydrolase [isa: 0016813 ]
+0016403 = dimethylargininase [isa: 0016813 ]
+0004668 = protein-arginine deiminase [isa: 0016813 ]
+0009015 = succinylarginine dihydrolase [isa: 0016813 ]
+0004848 = ureidoglycolate hydrolase [isa: 0016813 ]
+0016815 = hydrolase, acting on carbon-nitrogen (but not peptide) bonds, in nitriles [isa: 0016810 ]
+0018762 = aliphatic nitrilase [isa: 0016815 ]
+0018761 = bromoxynil-specific nitrilase [isa: 0016815 ]
+0000257 = nitrilase [isa: 0016815 ]
+0018760 = thiocyanate hydrolase [isa: 0016815 ]
+0016816 = hydrolase, acting on carbon-nitrogen (but not peptide) bonds, in other compounds [isa: 0016810 ]
+0018763 = hydroxyatrazine ethylaminohydrolase [isa: 0016816 ]
+0018764 = N-isopropylammelide isopropylaminohydrolase [isa: 0016816 ]
+0046508 = hydrolase, acting on carbon-sulfur bonds [isa: 0016787 ]
+0046507 = UDPsulfoquinovose synthase [isa: 0046508 ]
+0016788 = hydrolase, acting on ester bonds [isa: 0016787 ]
+0045330 = aspartyl esterase [isa: 0016788 ]
+0016789 = carboxylic ester hydrolase [isa: 0016788 ]
+0018731 = 1-oxa-2-oxocycloheptane lactonase [isa: 0016789 ]
+0003847 = 2-acetyl-1-alkylglycerophosphocholine esterase [isa: 0016789 ]
+0018733 = 3,4-dihydrocoumarin hydrolase [isa: 0016789 ]
+0017057 = 6-phosphogluconolactonase [isa: 0016789 ]
+0008126 = acetylesterase [isa: 0016789 ]
+0046575 = rhamnogalacturonan acetylesterase [isa: 0008126 ]
+0001681 = sialate O-acetylesterase [isa: 0008126 ]
+0046555 = acetylxylan esterase [isa: 0016789 ]
+0004045 = aminoacyl-tRNA hydrolase [isa: 0016789 ]
+0019851 = D-tyrosyl-tRNA hydrolase [isa: 0004045 ]
+0004064 = arylesterase [isa: 0016789 ]
+0018734 = butyrolactone hydrolase [isa: 0016789 ]
+0004091 = carboxylesterase [isa: 0016789 ]
+0003990 = acetylcholinesterase [isa: 0004091 ]
+0004453 = juvenile hormone esterase [isa: 0004091 ]
+0004759 = serine esterase [isa: 0004091 ]
+0008806 = carboxymethylenebutenolidase [isa: 0016789 ]
+0004104 = cholinesterase [isa: 0016789 ]
+0030339 = fatty-acyl-ethyl-ester synthase [isa: 0016789 ]
+0030600 = feruloyl esterase [isa: 0016789 ]
+0004341 = gluconolactonase [isa: 0016789 ]
+0046573 = lactonohydrolase [isa: 0016789 ]
+0016298 = lipase [isa: 0016789 ]
+0004465 = lipoprotein lipase [isa: 0016298 ]
+0004620 = phospholipase [isa: 0016298 ]
+0004622 = lysophospholipase [isa: 0004620 ]
+0008970 = phospholipase A1 [isa: 0004620 ]
+0017063 = phosphatidylserine-specific phospholipase A1 [isa: 0008970 ]
+0004623 = phospholipase A2 [isa: 0004620 ]
+0004626 = cytosolic phospholipase A2 [isa: 0004623 ]
+0004627 = calcium-dependent cytosolic phospholipase A2 [isa: 0004626 ]
+0004628 = calcium-independent cytosolic phospholipase A2 [isa: 0004626 ]
+0004624 = secreted phospholipase A2 [isa: 0004623 ]
+0004625 = calcium-dependent secreted phospholipase A2 [isa: 0004624 ]
+0004629 = phospholipase C [isa: 0004620 0008081 ]
+0004436 = 1-phosphatidylinositol phosphodiesterase [isa: 0004434 0004629 ]
+0004435 = 1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase [isa: 0004434 0004629 ]
+0004630 = phospholipase D [isa: 0004620 0008081 0016302 ]
+0004621 = glycoprotein phospholipase D [isa: 0004630 ]
+0004806 = triacylglycerol lipase [isa: 0016298 ]
+0000225 = N-acetylglucosaminylphosphatidylinositol deacetylase [isa: 0016789 ]
+0030599 = pectinesterase [isa: 0016789 ]
+0008984 = protein-glutamate methylesterase [isa: 0016789 ]
+0004771 = sterol esterase [isa: 0016789 ]
+0018732 = sulfolactone hydrolase [isa: 0016789 ]
+0016794 = diphosphoric monoester hydrolase [isa: 0016788 ]
+0008893 = guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase [isa: 0016794 ]
+0008849 = enterochelin esterase [isa: 0016788 ]
+0008081 = phosphoric diester hydrolase [isa: 0016788 ]
+0004112 = cyclic-nucleotide phosphodiesterase [isa: 0008081 ]
+0004113 = 2',3'-cyclic nucleotide 3'-phosphodiesterase [isa: 0004112 ]
+0008663 = 2',3'-cyclic-nucleotide 2'-phosphodiesterase [isa: 0004112 ]
+0004114 = 3',5'-cyclic-nucleotide phosphodiesterase [isa: 0004112 ]
+0004117 = calmodulin-dependent cyclic-nucleotide phosphodiesterase [isa: 0004114 ]
+0004115 = cAMP-specific phosphodiesterase [isa: 0004114 ]
+0004119 = cGMP-inhibited cyclic-nucleotide phosphodiesterase [isa: 0004114 ]
+0004116 = cGMP-specific phosphodiesterase [isa: 0004114 ]
+0004118 = cGMP-stimulated cyclic-nucleotide phosphodiesterase [isa: 0004114 ]
+0004120 = photoreceptor cyclic-nucleotide phosphodiesterase [isa: 0004114 ]
+0008889 = glycerophosphodiester phosphodiesterase [isa: 0008081 ]
+0004434 = inositol/phosphatidylinositol phosphodiesterase [isa: 0008081 ]
+0004767 = sphingomyelin phosphodiesterase [isa: 0008081 ]
+0030230 = acid sphingomyelin phosphodiesterase [isa: 0004767 ]
+0030231 = neutral sphingomyelin phosphodiesterase [isa: 0004767 ]
+0017005 = tyrosyl-DNA phosophodiesterase [isa: 0008081 ]
+0008770 = [acyl-carrier protein] phosphodiesterase [isa: 0008081 ]
+0016791 = phosphoric monoester hydrolase [isa: 0016788 ]
+0003850 = 2-deoxyglucose-6-phosphatase [isa: 0016791 0019203 ]
+0019143 = 3-deoxy-manno-octulosonate-8-phosphatase [isa: 0016791 ]
+0016158 = 3-phytase [isa: 0016791 ]
+0003869 = 4-nitrophenylphosphatase [isa: 0016302 0016791 ]
+0008707 = 6-phytase [isa: 0016791 ]
+0003993 = acid phosphatase [isa: 0016302 0016791 ]
+0042131 = thiamin phosphate phosphatase [isa: 0003993 ]
+0004035 = alkaline phosphatase [isa: 0016302 0016791 ]
+0019175 = alpha-ribazole-5'-P phosphatase [isa: 0016791 ]
+0004063 = aryldialkylphosphatase [isa: 0016302 0016791 ]
+0004083 = bisphosphoglycerate phosphatase [isa: 0016302 0016791 ]
+0004331 = fructose-2,6-bisphosphate 2-phosphatase [isa: 0016791 0019203 ]
+0042132 = fructose-bisphosphatase [isa: 0016791 0019203 ]
+0008877 = glucose-1-phosphatase [isa: 0016791 0019203 ]
+0004346 = glucose-6-phosphatase [isa: 0016791 0019203 ]
+0000121 = glycerol-1-phosphatase [isa: 0016302 0016791 ]
+0004401 = histidinol-phosphatase [isa: 0016302 0016791 ]
+0004437 = inositol/phosphatidylinositol phosphatase [isa: 0016302 0016791 ]
+0016312 = inositol bisphosphate phosphatase [isa: 0004437 ]
+0004441 = inositol-1,4,-bisphosphate 1-phosphatase [isa: 0016312 ]
+0016316 = inositol-3,4,-bisphosphate 4-phosphatase [isa: 0016312 ]
+0030487 = inositol-4,5-bisphosphate 5-phosphatase [isa: 0016312 ]
+0046030 = inositol trisphosphate phosphatase [isa: 0004437 ]
+0017161 = inositol-1,3,4-trisphosphate 4-phosphatase [isa: 0046030 ]
+0004445 = inositol-1,4,5-trisphosphate 5-phosphatase [isa: 0046030 ]
+0030351 = inositol-1,3,4,5,6-pentakisphosphate 3-phosphatase [isa: 0004437 ]
+0004446 = inositol-1,3,4,5-tetrakiphosphate 3-phosphatase [isa: 0004437 ]
+0030352 = inositol-1,4,5,6-tetrakisphosphate 6-phosphatase [isa: 0004437 ]
+0008934 = myo-inositol-1(or 4)-monophosphatase [isa: 0004437 ]
+0016314 = phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase [isa: 0004437 ]
+0004438 = phosphatidylinositol-3-phosphatase [isa: 0004437 ]
+0001668 = phosphatidylinositol-4,5-bisphosphate 5-phosphatase [isa: 0004437 ]
+0004439 = phosphatidylinositol-bisphosphatase [isa: 0004437 ]
+0019178 = NADP phosphatase [isa: 0016791 ]
+0008252 = nucleotidase [isa: 0016791 ]
+0008441 = 3'(2'),5'-bisphosphate nucleotidase [isa: 0008252 ]
+0008254 = 3'-nucleotidase [isa: 0008252 ]
+0008253 = 5'-nucleotidase [isa: 0008252 ]
+0017175 = IMP-GMP specific 5'-nucleotidase [isa: 0008253 ]
+0008195 = phosphatidate phosphatase [isa: 0016302 0016791 ]
+0008962 = phosphatidylglycerophosphatase [isa: 0016302 0016791 ]
+0008967 = phosphoglycolate phosphatase [isa: 0016302 0016791 ]
+0008969 = phosphohistidine phosphatase [isa: 0016302 0016791 ]
+0004647 = phosphoserine phosphatase [isa: 0016302 0016791 ]
+0004651 = polynucleotide 5'-phosphatase [isa: 0016791 0019204 ]
+0017120 = polyphosphoinositide phosphatase [isa: 0016791 ]
+0004721 = protein phosphatase [isa: 0016302 0016791 ]
+0008965 = phosphoenolpyruvate-protein phosphatase [isa: 0004721 0016775 ]
+0004722 = protein serine/threonine phosphatase [isa: 0004721 ]
+0004723 = calcium-dependent protein serine/threonine phosphatase [isa: 0004722 ]
+0008596 = calcium-dependent protein serine/threonine phosphatase, catalyst [partof: 0004723 ]
+0008597 = calcium-dependent protein serine/threonine phosphatase, regulator [isa: 0019888 ] [partof: 0004723 ]
+0008420 = CTD phosphatase [isa: 0004722 ]
+0004724 = magnesium-dependent protein serine/threonine phosphatase [isa: 0004722 ]
+0000163 = protein phosphatase type 1 [isa: 0004722 ]
+0017018 = myosin phosphatase [isa: 0000163 ]
+0017019 = myosin phosphatase catalyst [partof: 0017018 ]
+0017020 = myosin phosphatase, regulator [isa: 0019888 ] [partof: 0017018 ]
+0008599 = protein phosphatase type 1, regulator [isa: 0017020 ]
+0008601 = protein phosphatase type 2A, regulator [isa: 0017020 ] [partof: 0000158 ]
+0030359 = protein phosphatase type 2B, regulator [isa: 0017020 ] [partof: 0030357 ]
+0030362 = protein phosphatase type 4, regulator [isa: 0017020 ] [partof: 0030360 ]
+0008598 = protein phosphatase type 1, catalyst [partof: 0000163 ]
+0000158 = protein phosphatase type 2A [isa: 0004722 ]
+0008600 = protein phosphatase type 2A, catalyst [partof: 0000158 ]
+0030357 = protein phosphatase type 2B [isa: 0004722 ]
+0030358 = protein phosphatase type 2B, catalyst [partof: 0030357 ]
+0015071 = protein phosphatase type 2C [isa: 0004722 ]
+0030360 = protein phosphatase type 4 [isa: 0004722 ]
+0030361 = protein phosphatase type 4, catalyst [partof: 0030360 ]
+0004741 = pyruvate dehydrogenase (lipoamide) phosphatase [isa: 0004722 ]
+0019906 = pyruvate dehydrogenase (lipoamide) phosphatase, catalyst [partof: 0004741 ]
+0019909 = pyruvate dehydrogenase (lipoamide) phosphatase, regulator [partof: 0004741 ]
+0009400 = receptor signaling protein serine/threonine phosphatase [isa: 0004722 0005057 ]
+0004725 = protein tyrosine phosphatase [isa: 0004721 ]
+0004726 = non-membrane spanning protein tyrosine phosphatase [isa: 0004725 ]
+0004727 = prenylated protein tyrosine phosphatase [isa: 0004725 ]
+0004728 = receptor signaling protein tyrosine phosphatase [isa: 0004725 0005057 ]
+0005001 = transmembrane receptor protein tyrosine phosphatase [isa: 0004725 0019198 ]
+0008138 = protein tyrosine/serine/threonine phosphatase [isa: 0004721 ]
+0008579 = JUN kinase phosphatase [isa: 0008138 ]
+0017017 = MAP kinase phosphatase [isa: 0008138 ]
+0008330 = protein tyrosine/threonine phosphatase [isa: 0004721 ]
+0019198 = transmembrane receptor protein phosphatase [isa: 0004721 0004888 ]
+0042392 = sphingosine-1-phosphate phosphatase [isa: 0016791 ]
+0004805 = trehalose phosphatase [isa: 0016791 0019203 ]
+0016795 = phosphoric triester hydrolase [isa: 0016788 ]
+0008484 = sulfuric ester hydrolase [isa: 0016788 ]
+0018741 = alkyl sulfatase [isa: 0008484 ]
+0004065 = arylsulfatase [isa: 0008484 ]
+0004098 = cerebroside-sulfatase [isa: 0008484 ]
+0015024 = glucuronate-2-sulfatase [isa: 0008484 ]
+0004423 = iduronate-2-sulfatase [isa: 0008484 ]
+0003943 = N-acetylgalactosamine-4-sulfatase [isa: 0008484 ]
+0008449 = N-acetylglucosamine-6-sulfatase [isa: 0008484 ]
+0004773 = steryl-sulfatase [isa: 0008484 ]
+0016790 = thiolester hydrolase [isa: 0016788 ]
+0018740 = 2'-hydroxybiphenyl-2-sulfinate sulfinolyase [isa: 0016790 ]
+0016289 = CoA hydrolase [isa: 0016790 ]
+0018737 = 2-ketocyclohexane-1-carboxyl-CoA hydrolase [isa: 0016289 ]
+0003860 = 3-hydroxyisobutyryl-CoA hydrolase [isa: 0016289 ]
+0018739 = 4-hydroxybenzoyl-CoA thioesterase [isa: 0016289 ]
+0018736 = 6-oxo-2-hydroxycyclohexane-1-carboxyl-CoA hydrolase [isa: 0016289 ]
+0003986 = acetyl-CoA hydrolase [isa: 0016289 ]
+0016291 = acyl-CoA thioesterase [isa: 0016289 ]
+0016292 = acyl-CoA thioesterase I [isa: 0016291 ]
+0008778 = acyl-CoA thioesterase II [isa: 0016291 ]
+0016293 = long-chain fatty-acyl-CoA hydrolase [isa: 0016289 ]
+0016290 = palmitoyl-CoA hydrolase [isa: 0016293 ]
+0004778 = succinyl-CoA hydrolase [isa: 0016289 ]
+0004416 = hydroxyacylglutathione hydrolase [isa: 0016790 ]
+0008474 = palmitoyl-protein hydrolase [isa: 0016790 ]
+0018738 = S-formylglutathione hydrolase [isa: 0016790 ]
+0004221 = ubiquitin C-terminal hydrolase [isa: 0008234 0016790 ]
+0016297 = [acyl-carrier protein] hydrolase [isa: 0004312 0016790 ]
+0016294 = lauroyl-[acyl-carrier protein] hydrolase [isa: 0016297 ]
+0016295 = myristoyl-[acyl-carrier protein] hydrolase [isa: 0016297 ]
+0004320 = oleoyl-[acyl-carrier protein] hydrolase [isa: 0016297 ]
+0016296 = palmitoyl-[acyl-carrier protein] hydrolase [isa: 0016297 ]
+0016793 = triphosphoric monoester hydrolase [isa: 0016788 ]
+0008832 = deoxyguanosinetriphosphate triphosphohydrolase [isa: 0016793 ]
+0016801 = hydrolase, acting on ether bonds [isa: 0016787 ]
+0016803 = ether hydrolase [isa: 0016801 ]
+0004463 = leukotriene-A4 hydrolase [isa: 0016803 ]
+0004301 = epoxide hydrolase [isa: 0004463 ]
+0018745 = epoxide hydrolase A [isa: 0004301 ]
+0018742 = epoxide hydrolase B [isa: 0004301 ]
+0008096 = juvenile hormone epoxide hydrolase [isa: 0004301 ]
+0018744 = limonene-1,2-epoxide hydrolase [isa: 0004301 ]
+0019118 = phenanthrene-epoxide hydrolase [isa: 0004301 ]
+0018747 = phenanthrene-1,2-epoxide hydrolase [isa: 0019118 ]
+0018746 = phenanthrene-3,4-epoxide hydrolase [isa: 0019118 ]
+0019119 = phenanthrene-9,10-epoxide hydrolase [isa: 0019118 ]
+0018743 = phenanthrene-9,10-epoxide hydrolase (9R,10R-forming) [isa: 0019119 ]
+0018863 = phenanthrene-9,10-epoxide hydrolase (9S,10S-forming) [isa: 0019119 ]
+0008908 = isochorismatase [isa: 0004463 ]
+0016802 = thioether hydrolase [isa: 0016801 ]
+0004013 = adenosylhomocysteinase [isa: 0016802 ]
+0016798 = hydrolase, acting on glycosyl bonds [isa: 0016787 ]
+0016799 = hydrolase, hydrolyzing N-glycosyl compounds [isa: 0016798 ]
+0008782 = adenosylhomocysteine nucleosidase [isa: 0016799 ]
+0003875 = ADP-ribosylarginine hydrolase [isa: 0016799 ]
+0008714 = AMP nucleosidase [isa: 0016799 ]
+0008930 = methylthioadenosine nucleosidase [isa: 0016799 ]
+0003953 = NAD+ nucleosidase [isa: 0016799 ]
+0019160 = NMN nucleosidase [isa: 0016799 ]
+0008477 = purine nucleosidase [isa: 0016799 ]
+0030597 = RNA glycosylase [isa: 0016799 ]
+0030598 = rRNA N-glycosidase [isa: 0030597 ]
+0045437 = uridine nucleosidase [isa: 0016799 ]
+0004553 = hydrolase, hydrolyzing O-glycosyl compounds [isa: 0016798 ]
+0046559 = alpha-glucuronidase [isa: 0004553 ]
+0030596 = alpha-L-rhamnosidase [isa: 0004553 ]
+0046556 = alpha-N-arabinofuranosidase [isa: 0004553 ]
+0016997 = alpha-sialidase [isa: 0004553 ]
+0016996 = endo-alpha-sialidase [isa: 0016997 ]
+0004308 = exo-alpha-sialidase [isa: 0016997 ]
+0016160 = amylase [isa: 0004553 ]
+0004556 = alpha-amylase [isa: 0016160 ]
+0016161 = beta-amylase [isa: 0016160 ]
+0046558 = arabinan endo-1,5-a-L-arabinosidase [isa: 0004553 ]
+0004564 = beta-fructofuranosidase [isa: 0004553 ]
+0004566 = beta-glucuronidase [isa: 0004553 ]
+0008810 = cellulase [isa: 0004553 ]
+0016162 = cellulose 1,4-beta-cellobiosidase [isa: 0004553 ]
+0004568 = chitinase [isa: 0004553 ]
+0008843 = endochitinase [isa: 0004568 ]
+0016977 = chitosanase [isa: 0004553 ]
+0015928 = fucosidase [isa: 0004553 ]
+0004560 = alpha-L-fucosidase [isa: 0015928 ]
+0015925 = galactosidase [isa: 0004553 ]
+0004557 = alpha-galactosidase [isa: 0015925 ]
+0004565 = beta-galactosidase [isa: 0015925 ]
+0015926 = glucosidase [isa: 0004553 ]
+0004558 = alpha-glucosidase [isa: 0015926 ]
+0008422 = beta-glucosidase [isa: 0015926 ]
+0008706 = 6-phospho-beta-glucosidase [isa: 0008422 ]
+0016983 = cytokine beta-glucosidase [isa: 0008422 ]
+0004338 = glucan 1,3-beta-glucosidase [isa: 0008422 ]
+0004339 = glucan 1,4-alpha-glucosidase [isa: 0015926 ]
+0046557 = glucan endo-1,6-beta-glucosidase [isa: 0015926 ]
+0004573 = mannosyl-oligosaccharide glucosidase (processing A-glucosidase I) [isa: 0015926 ]
+0004574 = oligo-1,6-glucosidase [isa: 0015926 ]
+0004575 = sucrose-alpha-glucosidase [isa: 0015926 ]
+0046574 = glycuronidase [isa: 0004553 ]
+0030305 = heparanase [isa: 0004553 ]
+0015929 = hexosaminidase [isa: 0004553 ]
+0008456 = alpha-N-acetylgalactosaminidase [isa: 0015929 ]
+0004561 = alpha-N-acetylglucosaminidase [isa: 0015929 ]
+0016231 = beta-N-acetylglucosaminidase [isa: 0015929 ]
+0004563 = beta-N-acetylhexosaminidase [isa: 0015929 ]
+0004415 = hyaluronoglucosaminidase [isa: 0015929 ]
+0003944 = N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase [isa: 0015929 ]
+0003940 = L-iduronidase [isa: 0004553 ]
+0000016 = lactase [isa: 0004553 ]
+0015923 = mannosidase [isa: 0004553 ]
+0004559 = alpha-mannosidase [isa: 0015923 ]
+0004569 = glycoprotein endo-alpha-1,2 mannosidase [isa: 0004559 ]
+0008496 = mannan endo-1,6-alpha-mannosidase [isa: 0004559 ]
+0004567 = beta-mannosidase [isa: 0015923 ]
+0016985 = mannan endo-1,4-beta-mannosidase [isa: 0004567 ]
+0008727 = GDP-mannose mannosyl hydrolase [isa: 0015923 ]
+0015924 = mannosyl-oligosaccharide mannosidase [isa: 0015923 ]
+0004571 = mannosyl-oligosaccharide 1,2-alpha-mannosidase [isa: 0015924 ]
+0004572 = mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase [isa: 0015924 ]
+0008933 = murein transglycosylase B [isa: 0004553 ]
+0004650 = polygalacturonase [isa: 0004553 ]
+0019138 = ribosylhomocysteinase [isa: 0004553 ]
+0019137 = thioglucosidase [isa: 0004553 ]
+0015927 = trehalase [isa: 0004553 ]
+0008788 = alpha,alpha-phosphotrehalase [isa: 0015927 ]
+0004555 = alpha,alpha-trehalase [isa: 0015927 ]
+0009044 = xylan 1,4-beta-xylosidase [isa: 0004553 ]
+0016800 = hydrolase, hydrolyzing S-glycosyl compounds [isa: 0016798 ]
+0008233 = peptidase [isa: 0016787 ]
+0004177 = aminopeptidase [isa: 0008233 ]
+0016284 = alanine aminopeptidase [isa: 0004177 ]
+0016285 = cytosol alanyl aminopeptidase [isa: 0008235 0016284 ]
+0004179 = membrane alanyl aminopeptidase [isa: 0008235 0016284 ]
+0030601 = aminopeptidase B [isa: 0004177 ]
+0004230 = glutamyl aminopeptidase [isa: 0004177 0008235 ]
+0004178 = leucyl aminopeptidase [isa: 0004177 0008235 ]
+0004239 = methionyl aminopeptidase [isa: 0004177 0008235 ]
+0016804 = prolyl aminopeptidase [isa: 0004177 ]
+0045148 = tripeptide aminopeptidase [isa: 0004177 ]
+0004250 = vacuolar aminopeptidase I [isa: 0004177 0008235 ]
+0008451 = Xaa-Pro aminopeptidase [isa: 0004177 ]
+0004190 = aspartic-type endopeptidase [isa: 0008233 ]
+0042500 = aspartic endopeptidase, intramembrane cleaving [isa: 0004190 ]
+0042499 = signal peptide peptidase [isa: 0042500 ]
+0009049 = aspartic-type signal peptidase [isa: 0004190 0009003 ]
+0009005 = signal peptidase II [isa: 0009049 ]
+0004191 = barrierpepsin [isa: 0004190 ]
+0004192 = cathepsin D [isa: 0004190 ]
+0004193 = cathepsin E [isa: 0004190 ]
+0030602 = chymosin [isa: 0004190 ]
+0046561 = penicillopepsin [isa: 0004190 ]
+0004194 = pepsin A [isa: 0004190 ]
+0008978 = prepilin peptidase [isa: 0004190 ]
+0004195 = renin [isa: 0004190 ]
+0004196 = saccharopepsin [isa: 0004190 ]
+0046560 = scytalidopepsin B [isa: 0004190 ]
+0004176 = ATP-dependent peptidase [isa: 0008233 ]
+0008234 = cysteine-type peptidase [isa: 0008233 ]
+0016807 = cysteine-type carboxypeptidase [isa: 0008234 ]
+0004197 = cysteine-type endopeptidase [isa: 0008234 ]
+0008129 = actinidain [isa: 0004197 ]
+0008423 = bleomycin hydrolase [isa: 0004197 ]
+0004198 = calpain [isa: 0004197 ]
+0004199 = caspase [isa: 0004197 ]
+0004207 = effector caspase [isa: 0004199 ]
+0004208 = caspase-3 [isa: 0004207 ]
+0004209 = caspase-6 [isa: 0004207 ]
+0004210 = caspase-7 [isa: 0004207 ]
+0004211 = caspase-9 [isa: 0004207 ]
+0004200 = signaling (initiator) caspase [isa: 0004199 ]
+0004201 = caspase-1 [isa: 0004200 ]
+0004206 = caspase-10 [isa: 0004200 ]
+0004202 = caspase-2 [isa: 0004200 ]
+0004203 = caspase-4 [isa: 0004200 ]
+0004204 = caspase-5 [isa: 0004200 ]
+0004205 = caspase-8 [isa: 0004200 ]
+0001509 = legumain [isa: 0004197 ]
+0004212 = lysosomal cysteine-type endopeptidase [isa: 0004197 ]
+0004213 = cathepsin B [isa: 0004212 ]
+0016946 = cathepsin F [isa: 0004212 ]
+0004215 = cathepsin H [isa: 0004212 ]
+0004216 = cathepsin K [isa: 0004212 ]
+0004217 = cathepsin L [isa: 0004212 ]
+0004218 = cathepsin S [isa: 0004212 ]
+0004214 = dipeptidyl-peptidase I [isa: 0008234 0016806 ]
+0004219 = pyroglutamyl-peptidase I [isa: 0008234 0016920 ]
+0019783 = ubiquitin-like-specific protease [isa: 0008234 ]
+0019786 = APG8-specific protease [isa: 0019783 ]
+0019785 = ISG15-specific protease [isa: 0019783 ]
+0019784 = NEDD8-specific protease [isa: 0019783 ]
+0016929 = SUMO-specific protease [isa: 0019783 ]
+0004843 = ubiquitin-specific protease [isa: 0008234 ]
+0008581 = ubiquitin isopeptidase T [isa: 0004843 ]
+0016805 = dipeptidase [isa: 0008233 ]
+0042315 = cytosol nonspecific dipeptidase [isa: 0016805 ]
+0004237 = membrane dipeptidase [isa: 0008235 0016805 ]
+0008769 = Xaa-His dipeptidase [isa: 0008235 0016805 ]
+0004251 = Xaa-Pro dipeptidase [isa: 0008235 0016805 ]
+0008239 = dipeptidyl-peptidase [isa: 0008233 ]
+0017165 = dipeptidase E [isa: 0008239 ]
+0016806 = dipeptidyl-peptidase and tripeptidyl-peptidase [isa: 0008239 ]
+0017039 = dipeptidyl-peptidase III [isa: 0016806 ]
+0004274 = dipeptidyl-peptidase IV [isa: 0008236 0016806 ]
+0017088 = Xaa-Pro dipeptidyl-peptidase [isa: 0008239 ]
+0004175 = endopeptidase [isa: 0008233 ]
+0004222 = metalloendopeptidase [isa: 0004175 0008237 ]
+0008533 = astacin [isa: 0004222 ]
+0008133 = collagenase [isa: 0004222 ]
+0030404 = collagenase 3 [isa: 0008133 ]
+0030403 = collagenase 4 [isa: 0008133 ]
+0004232 = interstitial collagenase [isa: 0008133 ]
+0008130 = neutrophil collagenase [isa: 0008133 ]
+0016511 = endothelin-converting enzyme [isa: 0004222 ]
+0016512 = endothelin-converting enzyme 1 [isa: 0016511 ]
+0042029 = fibrolase [isa: 0004222 ]
+0004228 = gelatinase A [isa: 0004222 ]
+0004229 = gelatinase B [isa: 0004222 ]
+0004231 = insulysin [isa: 0004222 ]
+0004234 = macrophage elastase [isa: 0004222 ]
+0004235 = matrilysin [isa: 0004222 ]
+0030402 = matrilysin-2 [isa: 0004222 ]
+0030405 = matrix metalloproteinase 19 [isa: 0004222 ]
+0030406 = matrix metalloproteinase 25 [isa: 0004222 ]
+0004238 = meprin A [isa: 0004222 ]
+0004240 = mitochondrial processing peptidase [isa: 0004222 ]
+0004241 = alpha-mitochondrial processing peptidase [isa: 0004240 ]
+0004242 = beta-mitochondrial processing peptidase [isa: 0004240 ]
+0004244 = mitochondrial inner membrane peptidase [isa: 0004240 ]
+0004243 = mitochondrial intermediate peptidase [isa: 0004240 ]
+0016919 = nardilysin [isa: 0004222 ]
+0004245 = neprilysin [isa: 0004222 ]
+0008450 = O-sialoglycoprotein endopeptidase [isa: 0004222 ]
+0008944 = oligopeptidase A [isa: 0004222 ]
+0008975 = pitrilysin [isa: 0004222 ]
+0008319 = prenyl protein specific endopeptidase [isa: 0004222 ]
+0008487 = prenyl-dependent CAAX protease [isa: 0004222 ]
+0017026 = procollagen C-endopeptidase [isa: 0004222 ]
+0017074 = procollagen N-endopeptidase [isa: 0004222 ]
+0004247 = saccharolysin [isa: 0004222 ]
+0004248 = stromelysin 1 [isa: 0004222 ]
+0030303 = stromelysin 2 [isa: 0004222 ]
+0004249 = stromelysin 3 [isa: 0004222 ]
+0008238 = exopeptidase [isa: 0008233 ]
+0004180 = carboxypeptidase [isa: 0008238 ]
+0008235 = metalloexopeptidase [isa: 0008237 0008238 ]
+0004181 = metallocarboxypeptidase [isa: 0008235 ]
+0004182 = carboxypeptidase A [isa: 0004181 ]
+0004183 = carboxypeptidase H [isa: 0004181 ]
+0004226 = gly-X carboxypeptidase [isa: 0004181 ]
+0004184 = lysine (arginine) carboxypeptidase [isa: 0004181 ]
+0008472 = metallocarboxypeptidase D [isa: 0004181 ]
+0008322 = pro-X carboxypeptidase [isa: 0004181 ]
+0004188 = lysosomal pro-X carboxypeptidase [isa: 0004185 0008322 ]
+0004189 = tubulinyl-tyrosine carboxypeptidase [isa: 0008322 ]
+0009046 = zinc D-Ala-D-Ala carboxypeptidase [isa: 0004181 ]
+0008956 = peptidyl-dipeptidase Dcp [isa: 0008235 0008241 ]
+0009377 = HslUV protease [isa: 0008233 ]
+0008237 = metallopeptidase [isa: 0008233 ]
+0004246 = peptidyl-dipeptidase A [isa: 0008237 0008241 ]
+0016921 = pyroglutamyl-peptidase II [isa: 0008237 0016920 ]
+0017092 = sterol regulatory element-binding protein site 2 protease [isa: 0008237 0017093 ]
+0008242 = omega peptidase [isa: 0008233 ]
+0008798 = beta-aspartyl-peptidase [isa: 0008242 ]
+0008464 = gamma-glutamyl hydrolase [isa: 0008242 ]
+0016920 = pyroglutamyl-peptidase [isa: 0008242 ]
+0019790 = ubiquitin-like hydrolase [isa: 0008242 ]
+0019792 = APG12 hydrolase [isa: 0019790 ]
+0019791 = FAT10 hydrolase [isa: 0019790 ]
+0042291 = Hub1 hydrolase [isa: 0019790 ]
+0042290 = URM1 hydrolase [isa: 0019790 ]
+0008241 = peptidyl-dipeptidase [isa: 0008233 ]
+0045024 = peptidyl-glutamyl peptide hydrolyzing enzyme [isa: 0008233 ]
+0008236 = serine-type peptidase [isa: 0008233 ]
+0004185 = serine carboxypeptidase [isa: 0008236 ]
+0004186 = carboxypeptidase C [isa: 0004185 ]
+0004258 = vacuolar carboxypeptidase Y [isa: 0004186 ]
+0004187 = carboxypeptidase D [isa: 0004185 ]
+0009002 = serine-type D-Ala-D-Ala carboxypeptidase [isa: 0004185 ]
+0004252 = serine-type endopeptidase [isa: 0008236 ]
+0004284 = acrosin [isa: 0004252 ]
+0004254 = acylaminoacyl-peptidase [isa: 0004252 ]
+0019132 = C-terminal processing peptidase [isa: 0004252 ]
+0004261 = cathepsin G [isa: 0004252 ]
+0004262 = cerevisin [isa: 0004252 ]
+0030271 = chymase [isa: 0004252 ]
+0004263 = chymotrypsin [isa: 0004252 ]
+0008462 = endopeptidase Clp [isa: 0004252 ]
+0008846 = endopeptidase La [isa: 0004252 ]
+0004275 = enteropeptidase [isa: 0004252 ]
+0004276 = furin [isa: 0004252 ]
+0004253 = gamma-renin [isa: 0004252 ]
+0004277 = granzyme A [isa: 0004252 ]
+0004278 = granzyme B [isa: 0004252 ]
+0004279 = kininogenase [isa: 0004252 ]
+0008439 = monophenol monooxygenase activator [isa: 0004252 0008047 ]
+0008931 = murein DD-endopeptidase [isa: 0004252 ]
+0008945 = oligopeptidase B [isa: 0004252 ]
+0008947 = omptin [isa: 0004252 ]
+0008132 = pancreatic elastase [isa: 0004252 ]
+0008125 = pancreatic elastase I [isa: 0008132 ]
+0004281 = pancreatic elastase II [isa: 0008132 ]
+0004283 = plasmin [isa: 0004252 ]
+0008243 = plasminogen activator [isa: 0004252 ]
+0004296 = T-plasminogen activator [isa: 0008243 ]
+0004297 = U-plasminogen activator [isa: 0008243 ]
+0004287 = prolyl oligopeptidase [isa: 0004252 ]
+0016808 = proprotein convertase [isa: 0004252 ]
+0004285 = proprotein convertase 1 [isa: 0016808 ]
+0004286 = proprotein convertase 2 [isa: 0016808 ]
+0008981 = protease IV [isa: 0004252 ]
+0008992 = repressor lexA [isa: 0004252 ]
+0008991 = serine-type signal peptidase [isa: 0004252 0009003 ]
+0009004 = signal peptidase I [isa: 0004252 ]
+0004289 = subtilase [isa: 0004252 ]
+0004290 = kexin [isa: 0004289 ]
+0004291 = subtilisin [isa: 0004289 ]
+0004293 = tissue kallikrein [isa: 0004252 ]
+0004295 = trypsin [isa: 0004252 ]
+0030019 = tryptase [isa: 0004295 ]
+0017094 = sterol regulatory element-binding protein site 1 protease [isa: 0008236 0017093 ]
+0008240 = tripeptidyl-peptidase [isa: 0008236 ]
+0019131 = tripeptidyl-peptidase I [isa: 0008240 ]
+0004294 = tripeptidyl-peptidase II [isa: 0008240 ]
+0009003 = signal peptidase [isa: 0008233 ]
+0017093 = sterol regulatory element-binding protease [isa: 0008233 ]
+0004298 = threonine endopeptidase [isa: 0008233 ]
+0004299 = proteasome endopeptidase [isa: 0004298 ]
+0017171 = serine hydrolase [isa: 0016787 ]
+0000107 = imidazoleglycerol-phosphate synthase [isa: 0003824 ]
+0008907 = integrase [isa: 0003824 ]
+0008979 = prophage integrase [isa: 0008907 ]
+0016853 = isomerase [isa: 0003824 ]
+0016859 = cis-trans isomerase [isa: 0016853 ]
+0046608 = carotenoid isomerase [isa: 0016859 ]
+0003755 = peptidyl-prolyl cis-trans isomerase [isa: 0016859 ]
+0042027 = cyclophilin-type peptidy-prolyl cis-trans isomerase [isa: 0003755 ]
+0042028 = juglone-sensitive peptidyl-prolyl cis-trans isomerase [isa: 0003755 ]
+0004744 = retinal isomerase [isa: 0016859 ]
+0016860 = intramolecular isomerase [isa: 0016853 ]
+0016861 = intramolecular isomerase, interconverting aldoses and ketoses [isa: 0016860 ]
+0003949 = 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase [isa: 0016861 ]
+0008697 = 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase [isa: 0016861 ]
+0046523 = 5-methylthioribose-1-phosphate isomerase [isa: 0016861 ]
+0008786 = allose 6-phosphate isomerase [isa: 0016861 ]
+0008790 = arabinose isomerase [isa: 0016861 ]
+0019146 = arabinose-5-phosphate isomerase [isa: 0016861 ]
+0004110 = corticosteroid side-chain-isomerase [isa: 0016861 ]
+0004342 = glucosamine-6-phosphate isomerase [isa: 0016861 ]
+0004347 = glucose-6-phosphate isomerase [isa: 0016861 ]
+0008880 = glucuronate isomerase [isa: 0016861 ]
+0008903 = hydroxypyruvate isomerase [isa: 0016861 ]
+0008733 = L-arabinose isomerase [isa: 0016861 ]
+0008736 = L-fucose isomerase [isa: 0016861 ]
+0008740 = L-rhamnose isomerase [isa: 0016861 ]
+0004476 = mannose-6-phosphate isomerase [isa: 0016861 ]
+0004640 = phosphoribosylanthranilate isomerase [isa: 0016861 ]
+0004751 = ribose-5-phosphate isomerase [isa: 0016861 ]
+0004807 = triose-phosphate isomerase [isa: 0016861 ]
+0009045 = xylose isomerase [isa: 0016861 ]
+0016862 = intramolecular isomerase, interconverting keto- and enol-groups [isa: 0016860 ]
+0016865 = intramolecular isomerase, other intramolecular oxidoreductases [isa: 0016860 ]
+0018845 = 2-hydroxychromene-2-carboxylate isomerase [isa: 0016865 ]
+0018844 = 2-hydroxytetrahydrofuran isomerase [isa: 0016865 ]
+0046423 = allene-oxide cyclase [isa: 0016865 ]
+0009905 = copalyl diphosphate synthase [isa: 0016865 ]
+0045436 = lycopene beta cyclase [isa: 0016865 ]
+0045435 = lycopene epsilon cyclase [isa: 0016865 ]
+0004667 = prostaglandin-D synthase [isa: 0016865 ]
+0018846 = styrene oxide isomerase [isa: 0016865 ]
+0016863 = intramolecular isomerase, transposing C=C bonds [isa: 0016860 ]
+0018842 = 3-carboxymuconate cycloisomerase type II [isa: 0016863 ]
+0018843 = 5-carboxymethyl-2-hydroxymuconate D-isomerase [isa: 0016863 ]
+0008704 = 5-carboxymethyl-2-hydroxymuconate delta-isomerase [isa: 0016863 ]
+0000247 = C-8 sterol isomerase [isa: 0016863 ]
+0008416 = delta,5-delta2,4-dienoyl-CoA isomerase [isa: 0016863 ]
+0004165 = dodecenoyl-CoA delta-isomerase [isa: 0016863 ]
+0004167 = dopachrome delta-isomerase [isa: 0016863 ]
+0004452 = isopentenyl-diphosphate delta-isomerase [isa: 0016863 ]
+0016159 = muconolactone delta-isomerase [isa: 0016863 ]
+0004769 = steroid delta-isomerase [isa: 0016863 ]
+0016864 = intramolecular isomerase, transposing S-S bonds [isa: 0016860 ]
+0003756 = protein disulfide isomerase [isa: 0015035 0016864 ]
+0016872 = intramolecular lyase [isa: 0016853 ]
+0018847 = alpha-pinene lyase [isa: 0016872 ]
+0018851 = alpha-pinene oxide lyase [isa: 0016872 ]
+0045430 = chalcone isomerase [isa: 0016872 ]
+0018850 = chloromuconate cycloisomerase [isa: 0016872 ]
+0018852 = dichloromuconate cycloisomerase [isa: 0016872 ]
+0004512 = inositol-3-phosphate synthase [isa: 0016872 ]
+0018849 = muconate cycloisomerase [isa: 0016872 ]
+0018848 = pinocarveol isomerase [isa: 0016872 ]
+0016866 = intramolecular transferase [isa: 0016853 ]
+0016868 = intramolecular transferase, phosphotransferases [isa: 0016866 ]
+0008801 = beta-phosphoglucomutase [isa: 0016868 ]
+0004082 = bisphosphoglycerate mutase [isa: 0016868 ]
+0004610 = phosphoacetylglucosamine mutase [isa: 0016868 ]
+0004614 = phosphoglucomutase [isa: 0016868 ]
+0008966 = phosphoglucosamine mutase [isa: 0016868 ]
+0004619 = phosphoglycerate mutase [isa: 0016868 ]
+0046538 = 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase [isa: 0004619 ]
+0046537 = 2,3-bisphosphoglycerate-independent phosphoglycerate mutase [isa: 0004619 ]
+0004615 = phosphomannomutase [isa: 0016868 ]
+0008973 = phosphopentomutase [isa: 0016868 ]
+0016867 = intramolecular transferase, transferring acyl groups [isa: 0016866 ]
+0016993 = precorrin-8X methylmutase [isa: 0016867 ]
+0016869 = intramolecular transferase, transferring amino groups [isa: 0016866 ]
+0042286 = glutamate-1-semialdehyde 2,1-aminomutase [isa: 0016869 ]
+0016870 = intramolecular transferase, transferring other groups [isa: 0016866 ]
+0042300 = beta-amyrin synthase [isa: 0016870 ]
+0004106 = chorismate mutase [isa: 0016870 ]
+0016871 = cycloartenol synthase [isa: 0016870 ]
+0008909 = isochorismate mutase [isa: 0016870 ]
+0000250 = lanosterol synthase [isa: 0016870 ]
+0042299 = lupeol synthase [isa: 0016870 ]
+0004494 = methylmalonyl-CoA mutase [isa: 0016870 ]
+0016439 = tRNA-pseudouridine synthase I [isa: 0016870 ]
+0008767 = UDP-galactopyranose mutase [isa: 0016870 ]
+0045439 = isopenicillin N epimerase [isa: 0016853 ]
+0016873 = other isomerase [isa: 0016853 ]
+0003916 = DNA topoisomerase [isa: 0016873 ]
+0003918 = DNA topoisomerase (ATP-hydrolyzing) [isa: 0003916 ]
+0003917 = DNA topoisomerase I [isa: 0003916 ]
+0008724 = DNA topoisomerase IV [isa: 0003916 ]
+0008968 = phosphoheptose isomerase [isa: 0016853 ]
+0016854 = racemase and epimerase [isa: 0016853 ]
+0016855 = racemase and epimerase, acting on amino acids and derivatives [isa: 0016854 ]
+0008784 = alanine racemase [isa: 0016855 ]
+0008837 = diaminopimelate epimerase [isa: 0016855 ]
+0008881 = glutamate racemase [isa: 0016855 ]
+0018113 = lysine racemase [isa: 0016855 ]
+0018111 = methionine racemase [isa: 0016855 ]
+0018112 = proline racemase [isa: 0016855 ]
+0018365 = protein-serine epimerase [isa: 0016855 ]
+0030378 = serine racemase [isa: 0016855 ]
+0018114 = threonine racemase [isa: 0016855 ]
+0016857 = racemase and epimerase, acting on carbohydrates and derivatives [isa: 0016854 ]
+0008712 = ADP-glyceromanno-heptose 6-epimerase [isa: 0016857 ]
+0004034 = aldose 1-epimerase [isa: 0016857 ]
+0008830 = dTDP-4-dehydrorhamnose 3,5-epimerase [isa: 0016857 ]
+0008742 = L-ribulose-phosphate 4-epimerase [isa: 0016857 ]
+0004750 = ribulose-phosphate 3-epimerase [isa: 0016857 ]
+0003978 = UDP-glucose 4-epimerase [isa: 0016857 ]
+0008761 = UDP-N-acetylglucosamine 2-epimerase [isa: 0016857 ]
+0003974 = UDP-N-acetylglucosamine 4-epimerase [isa: 0016857 ]
+0016856 = racemase and epimerase, acting on hydroxy acids and derivatives [isa: 0016854 ]
+0018837 = 2-hydroxy-2H-benzo[h]chromene-2-carboxylate isomerase [isa: 0016856 ]
+0008692 = 3-hydroxybutyryl-CoA epimerase [isa: 0016856 ]
+0008809 = carnitine racemase [isa: 0016856 ]
+0018840 = chlorodienelactone isomerase [isa: 0016856 ]
+0018839 = cis-4-[2-(3-hydroxy)-thionaphthenyl]-2-oxo-3-butenoate isomerase [isa: 0016856 ]
+0016034 = maleylacetoacetate isomerase [isa: 0016856 ]
+0018838 = mandelate racemase [isa: 0016856 ]
+0016858 = racemase and epimerase, acting on other compounds [isa: 0016854 ]
+0008111 = alpha-methylacyl-CoA racemase [isa: 0016858 ]
+0004493 = methylmalonyl-CoA epimerase [isa: 0016858 ]
+0016301 = kinase [isa: 0003824 ]
+0008440 = 1D-myo-inositol-trisphosphate 3-kinase [isa: 0016301 0016773 ]
+0003848 = 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase [isa: 0016301 0016778 ]
+0008698 = 4-diphosphocytidyl-2C-methyl-D-erythritol kinase [isa: 0016301 0016772 ]
+0008776 = acetate kinase [isa: 0016301 0016774 ]
+0003991 = acetylglutamate kinase [isa: 0016301 0016774 ]
+0004020 = adenylylsulfate kinase [isa: 0016301 0016773 ]
+0019202 = amino acid kinase [isa: 0016301 ]
+0004054 = arginine kinase [isa: 0016775 0019202 ]
+0018110 = histone-arginine kinase [isa: 0004054 0004673 ]
+0004072 = aspartate kinase [isa: 0016774 0019202 ]
+0004349 = glutamate 5-kinase [isa: 0016774 0019202 ]
+0004413 = homoserine kinase [isa: 0016773 0019202 ]
+0008804 = carbamate kinase [isa: 0016301 0016774 ]
+0019200 = carbohydrate kinase [isa: 0016301 ]
+0008671 = 2-dehydro-3-deoxygalactonokinase [isa: 0016773 0019200 ]
+0008673 = 2-dehydro-3-deoxygluconokinase [isa: 0016773 0019200 ]
+0008787 = allose kinase [isa: 0016773 0019200 ]
+0019150 = D-ribulokinase [isa: 0016773 0019200 ]
+0008865 = fructokinase [isa: 0016773 0019200 ]
+0004335 = galactokinase [isa: 0016773 0019200 ]
+0004340 = glucokinase [isa: 0016773 0019200 ]
+0004396 = hexokinase [isa: 0016773 0019200 ]
+0004454 = ketohexokinase [isa: 0016773 0019200 ]
+0009702 = L-arabinokinase [isa: 0016773 0019200 ]
+0008737 = L-fuculokinase [isa: 0016773 0019200 ]
+0008741 = L-ribulokinase [isa: 0016773 0019200 ]
+0045127 = N-acetylglucosamine kinase [isa: 0019200 ]
+0009384 = N-acylmannosamine kinase [isa: 0016773 0019200 ]
+0008443 = phosphofructokinase [isa: 0016773 0019200 ]
+0008662 = 1-phosphofructokinase [isa: 0008443 ]
+0003873 = 6-phosphofructo-2-kinase [isa: 0008443 ]
+0003872 = 6-phosphofructokinase [isa: 0008443 ]
+0008993 = rhamnulokinase [isa: 0016773 0019200 ]
+0004749 = ribose-phosphate pyrophosphokinase [isa: 0016778 0019200 ]
+0004856 = xylulokinase [isa: 0016773 0019200 ]
+0008744 = L-xylulokinase [isa: 0004856 ]
+0004103 = choline kinase [isa: 0016301 0016773 ]
+0008819 = cobinamide kinase [isa: 0016301 0016773 ]
+0004111 = creatine kinase [isa: 0016301 0016775 ]
+0017050 = D-erythro-sphingosine kinase [isa: 0016301 ]
+0004140 = dephospho-CoA kinase [isa: 0016301 0016773 ]
+0004143 = diacylglycerol kinase [isa: 0016301 0016773 ]
+0008842 = diphosphate-purine nucleoside kinase [isa: 0016301 0016773 ]
+0004168 = dolichol kinase [isa: 0016301 0016773 ]
+0004305 = ethanolamine kinase [isa: 0016301 0016773 ]
+0030387 = fructosamine-3-kinase [isa: 0016301 ]
+0008887 = glycerate kinase [isa: 0016301 0016773 ]
+0004370 = glycerol kinase [isa: 0016301 0016773 ]
+0004371 = glycerone kinase [isa: 0016301 0016773 ]
+0009927 = histidine phosphotransfer kinase [isa: 0004871 0016301 ]
+0004417 = hydroxyethylthiazole kinase [isa: 0016301 0016773 ]
+0008902 = hydroxymethylpyrimidine kinase [isa: 0016301 0016773 ]
+0008904 = hygromycin-B kinase [isa: 0016301 0016773 ]
+0008906 = inosine kinase [isa: 0016301 0016773 ]
+0004428 = inositol/phosphatidylinositol kinase [isa: 0016301 0016773 ]
+0004430 = 1-phosphatidylinositol 4-kinase [isa: 0004428 ]
+0019140 = inositol 3-kinase [isa: 0004428 ]
+0016303 = phosphatidylinositol 3-kinase [isa: 0004428 ]
+0016304 = phosphatidylinositol 3-kinase, class I [isa: 0016303 ]
+0015072 = phosphatidylinositol 3-kinase, class I, catalyst [partof: 0016304 ]
+0015073 = phosphatidylinositol 3-kinase, class I, regulator [isa: 0019887 ] [partof: 0016304 ]
+0016305 = phosphatidylinositol 3-kinase, class II [isa: 0016303 ]
+0016306 = phosphatidylinositol 3-kinase, class III [isa: 0016303 ]
+0016307 = phosphatidylinositol phosphate kinase [isa: 0004428 ]
+0000285 = 1-phosphatidylinositol-3-phosphate 5-kinase [isa: 0016307 ]
+0016308 = 1-phosphatidylinositol-4-phosphate 5-kinase [isa: 0016307 ]
+0008438 = 1-phosphatidylinositol-5-phosphate kinase [isa: 0016307 ]
+0016309 = 1-phosphatidylinositol-5-phosphate 4-kinase [isa: 0008438 ]
+0008910 = kanamycin kinase [isa: 0016301 0016773 ]
+0001727 = lipid kinase [isa: 0016301 ]
+0001729 = ceramide kinase [isa: 0001727 ]
+0008481 = sphinganine kinase [isa: 0001727 0016773 ]
+0004496 = mevalonate kinase [isa: 0016301 0016773 ]
+0003951 = NAD+ kinase [isa: 0016301 0016773 ]
+0019205 = nucleobase, nucleoside, nucleotide kinase [isa: 0016301 0016773 ]
+0008728 = GTP pyrophosphokinase [isa: 0016778 0019205 ]
+0019206 = nucleoside kinase [isa: 0019205 ]
+0004001 = adenosine kinase [isa: 0019206 ]
+0019136 = deoxynucleoside kinase [isa: 0019206 ]
+0004136 = deoxyadenosine kinase [isa: 0019136 ]
+0004137 = deoxycytidine kinase [isa: 0019136 ]
+0004138 = deoxyguanosine kinase [isa: 0019136 ]
+0004797 = thymidine kinase [isa: 0019136 ]
+0004849 = uridine kinase [isa: 0019206 ]
+0004550 = nucleoside-diphosphate kinase [isa: 0016776 0019205 ]
+0019201 = nucleotide kinase [isa: 0019205 ]
+0004017 = adenylate kinase [isa: 0016776 0019201 ]
+0004127 = cytidylate kinase [isa: 0019201 ]
+0004385 = guanylate kinase [isa: 0016776 0019201 ]
+0004798 = thymidylate kinase [isa: 0016776 0019201 ]
+0009041 = uridylate kinase [isa: 0016776 0019201 ]
+0004594 = pantothenate kinase [isa: 0016301 0016773 ]
+0004611 = phosphoenolpyruvate carboxykinase [isa: 0016301 0016831 ]
+0004612 = phosphoenolpyruvate carboxykinase (ATP) [isa: 0004611 ]
+0030585 = phosphoenolpyruvate carboxykinase (diphosphate) [isa: 0004611 ]
+0004613 = phosphoenolpyruvate carboxykinase (GTP) [isa: 0004611 ]
+0008964 = phosphoenolpyruvate carboxylase [isa: 0004611 ]
+0004618 = phosphoglycerate kinase [isa: 0016301 0016774 ]
+0008972 = phosphomethylpyrimidine kinase [isa: 0016301 0016776 ]
+0004631 = phosphomevalonate kinase [isa: 0016301 0016776 ]
+0008974 = phosphoribulokinase [isa: 0016301 0016773 ]
+0008976 = polyphosphate kinase [isa: 0016301 0016776 ]
+0008980 = propionate kinase [isa: 0016301 0016774 ]
+0004672 = protein kinase [isa: 0016301 0016773 ]
+0004673 = protein histidine kinase [isa: 0004672 0016775 ]
+0008256 = protein histidine pros-kinase [isa: 0004673 ]
+0008257 = protein histidine tele-kinase [isa: 0004673 ]
+0009784 = transmembrane receptor histidine kinase [isa: 0004673 0019199 ]
+0009885 = transmembrane histidine kinase cytokinin receptor [isa: 0009784 0009884 ]
+0000155 = two-component sensor molecule [isa: 0004673 0004871 ]
+0004674 = protein serine/threonine kinase [isa: 0004672 ]
+0004676 = 3-phosphoinositide-dependent protein kinase [isa: 0004674 ]
+0009931 = calcium dependent protein serine/threonine kinase [isa: 0004674 ]
+0004683 = calmodulin regulated protein kinase [isa: 0004674 ]
+0004685 = calcium/calmodulin-dependent protein kinase [isa: 0004683 ]
+0004684 = calmodulin-dependent protein kinase I [isa: 0004683 ]
+0004686 = eukaryotic elongation-factor-2 kinase [isa: 0004683 ]
+0004688 = multifunctional calcium/calmodulin regulated protein kinase [isa: 0004683 ]
+0016905 = myosin heavy chain kinase [isa: 0004683 ]
+0004687 = myosin light chain kinase [isa: 0004683 ]
+0004689 = phosphorylase kinase [isa: 0004683 ]
+0008606 = phosphorylase kinase, catalyst [partof: 0004689 ]
+0008607 = phosphorylase kinase, regulator [isa: 0019887 ] [partof: 0004689 ]
+0004680 = casein kinase [isa: 0004674 ]
+0004681 = casein kinase I [isa: 0004680 ]
+0004682 = protein kinase CK2 [isa: 0004680 ]
+0008604 = protein kinase CK2, catalyst [partof: 0004682 ]
+0008605 = protein kinase CK2, regulator [isa: 0019887 ] [partof: 0004682 ]
+0004690 = cyclic-nucleotide dependent protein kinase [isa: 0004674 ]
+0004691 = cAMP-dependent protein kinase [isa: 0004690 ]
+0008602 = cAMP-dependent protein kinase, catalyst [partof: 0004691 ]
+0008603 = cAMP-dependent protein kinase, regulator [isa: 0019887 ] [partof: 0004691 ]
+0004692 = cGMP-dependent protein kinase [isa: 0004690 ]
+0004693 = cyclin-dependent protein kinase [isa: 0004674 ]
+0019912 = cyclin-dependent protein kinase activating kinase [isa: 0004693 0019887 ]
+0019913 = cyclin-dependent protein kinase activating kinase, catalyst [isa: 0019912 ]
+0019914 = cyclin-dependent protein kinase activating kinase, regulator [isa: 0019912 ]
+0016534 = cyclin-dependent protein kinase 5 activator [isa: 0019914 0030295 ]
+0016535 = cyclin-dependent protein kinase 5 activator, catalyst [partof: 0016534 ]
+0016536 = cyclin-dependent protein kinase 5 activator, regulator [partof: 0016534 ]
+0016537 = cyclin-dependent protein kinase, catalyst [partof: 0004693 ]
+0016538 = cyclin-dependent protein kinase, regulator [isa: 0019887 ] [partof: 0004693 ]
+0004677 = DNA-dependent protein kinase [isa: 0004674 ]
+0004694 = eukaryotic translation initiation factor 2alpha kinase [isa: 0004674 ]
+0004678 = G-protein-coupled receptor phosphorylating protein kinase [isa: 0004674 ]
+0004695 = galactosyltransferase-associated kinase [isa: 0004674 ]
+0004696 = glycogen synthase kinase 3 [isa: 0004674 ]
+0008384 = IkappaB kinase [isa: 0004674 ]
+0004697 = protein kinase C [isa: 0001565 0004674 ]
+0004700 = atypical protein kinase C [isa: 0004697 ]
+0004698 = calcium dependent protein kinase C [isa: 0004697 ]
+0004699 = calcium independent protein kinase C [isa: 0004697 ]
+0004701 = diacylglycerol-activated/phospholipid dependent protein kinase C [isa: 0004697 ]
+0004702 = receptor signaling protein serine/threonine kinase [isa: 0004674 0005057 ]
+0004703 = G-protein coupled receptor kinase [isa: 0004702 ]
+0004707 = MAP kinase [isa: 0004702 ]
+0008338 = MAP kinase 1 [isa: 0004707 ]
+0016908 = MAP kinase 2 [isa: 0004707 ]
+0004709 = MAP kinase kinase kinase [isa: 0004702 ]
+0004706 = JNK kinase kinase [isa: 0004709 ]
+0008349 = MAP kinase kinase kinase kinase [isa: 0004702 ]
+0004704 = NF-kappaB-inducing kinase [isa: 0004702 ]
+0016909 = SAP kinase [isa: 0004702 ]
+0004705 = JUN kinase [isa: 0016909 ]
+0008339 = MP kinase [isa: 0016909 ]
+0016910 = SAP kinase 3 [isa: 0016909 ]
+0016911 = SAP kinase 4 [isa: 0016909 ]
+0016912 = SAP kinase 5 [isa: 0016909 ]
+0004711 = ribosomal protein S6 kinase [isa: 0004674 ]
+0004679 = SNF1A/AMP-activated protein kinase [isa: 0004674 ]
+0004675 = transmembrane receptor protein serine/threonine kinase [isa: 0004674 0019199 ]
+0005023 = transforming growth factor-alpha receptor [isa: 0004675 ]
+0005024 = transforming growth factor-beta receptor [isa: 0004675 ]
+0017002 = activin receptor [isa: 0005024 ]
+0016361 = type I activin receptor [isa: 0005025 0017002 ]
+0016362 = type II activin receptor [isa: 0005026 0017002 ]
+0005025 = type I transforming growth factor-beta receptor [isa: 0005024 ]
+0005026 = type II transforming growth factor-beta receptor [isa: 0005024 ]
+0008353 = [RNA-polymerase]-subunit kinase [isa: 0004674 ]
+0004712 = protein threonine/tyrosine kinase [isa: 0004672 ]
+0004708 = MAP kinase kinase [isa: 0004712 ]
+0008545 = JUN kinase kinase [isa: 0004708 ]
+0004710 = MAP/ERK kinase kinase [isa: 0004708 ]
+0004713 = protein tyrosine kinase [isa: 0004672 ]
+0004715 = non-membrane spanning protein tyrosine kinase [isa: 0004713 ]
+0004716 = receptor signaling protein tyrosine kinase [isa: 0004713 0005057 ]
+0004717 = focal adhesion kinase [isa: 0004716 ]
+0004718 = Janus kinase [isa: 0004716 ]
+0004714 = transmembrane receptor protein tyrosine kinase [isa: 0004713 0019199 ]
+0008288 = boss receptor [isa: 0004714 ]
+0005003 = ephrin receptor [isa: 0004714 ]
+0005004 = GPI-linked ephrin receptor [isa: 0005003 ]
+0005005 = transmembrane-ephrin receptor [isa: 0005003 ]
+0005006 = epidermal growth factor receptor [isa: 0004714 ]
+0008313 = gurken receptor [isa: 0005006 ]
+0005007 = fibroblast growth factor receptor [isa: 0004714 ]
+0004902 = granulocyte colony-stimulating factor receptor [isa: 0004714 0004896 ]
+0004901 = granulocyte macrophage colony-stimulating factor receptor [isa: 0004714 0004900 ]
+0005008 = hepatocyte growth factor receptor [isa: 0004714 ]
+0005009 = insulin receptor [isa: 0004714 ]
+0005010 = insulin-like growth factor receptor [isa: 0004714 ]
+0005011 = macrophage colony stimulating factor receptor [isa: 0004714 ]
+0008019 = macrophage receptor [isa: 0004714 ]
+0005012 = Neu/ErbB-2 receptor [isa: 0004714 ]
+0005013 = neurotrophin TRK receptor [isa: 0004714 ]
+0005014 = neurotrophin TRKA receptor [isa: 0005013 ]
+0005015 = neurotrophin TRKB receptor [isa: 0005013 ]
+0005016 = neurotrophin TRKC receptor [isa: 0005013 ]
+0005017 = platelet-derived growth factor receptor [isa: 0004714 ]
+0005018 = platelet-derived growth factor, alpha-receptor [isa: 0005017 ]
+0005019 = platelet-derived growth factor, beta-receptor [isa: 0005017 ]
+0005020 = stem cell factor receptor [isa: 0004714 ]
+0005021 = vascular endothelial growth factor receptor [isa: 0004714 ]
+0019199 = transmembrane receptor protein kinase [isa: 0004672 0004888 ]
+0008478 = pyridoxal kinase [isa: 0016301 0016773 ]
+0004740 = pyruvate dehydrogenase (lipoamide) kinase [isa: 0016301 0016773 ]
+0004743 = pyruvate kinase [isa: 0016301 0016773 ]
+0008986 = pyruvate,water dikinase [isa: 0016301 0016781 ]
+0008531 = riboflavin kinase [isa: 0016301 0016773 ]
+0004747 = ribokinase [isa: 0016301 0016773 ]
+0004756 = selenide,water dikinase [isa: 0016301 0016781 ]
+0004765 = shikimate kinase [isa: 0016301 0016773 ]
+0009024 = tagatose-6-phosphate kinase [isa: 0016301 0016773 ]
+0009029 = tetraacyldisaccharide 4'-kinase [isa: 0016301 0016773 ]
+0004788 = thiamin pyrophosphokinase [isa: 0016301 0016778 ]
+0009030 = thiamin-phosphate kinase [isa: 0016301 0016776 ]
+0009038 = undecaprenol kinase [isa: 0016301 0016773 ]
+0008772 = [isocitrate dehydrogenase (NADP+)] kinase [isa: 0016301 0016773 ]
+0016874 = ligase [isa: 0003824 ]
+0003832 = beta-alanyl-dopamine hydrolase [isa: 0016874 ]
+0045438 = L-cysteinyl-D-valine synthetase [isa: 0016874 ]
+0016885 = ligase, forming carbon-carbon bonds [isa: 0016874 ]
+0018524 = acetophenone carboxylase [isa: 0016885 ]
+0016421 = CoA carboxylase [isa: 0016885 ]
+0003989 = acetyl-CoA carboxylase [isa: 0016421 ]
+0004485 = methylcrotonyl-CoA carboxylase [isa: 0016421 ]
+0004658 = propionyl-CoA carboxylase [isa: 0016421 ]
+0018862 = phenylphosphate carboxylase [isa: 0016885 ]
+0004736 = pyruvate carboxylase [isa: 0016885 ]
+0016879 = ligase, forming carbon-nitrogen bonds [isa: 0016874 ]
+0016880 = acid-ammonia (or amide) ligase [isa: 0016879 ]
+0016211 = ammonia ligase [isa: 0016880 ]
+0004071 = aspartate-ammonia ligase [isa: 0016211 ]
+0017178 = diphthine-ammonia ligase [isa: 0016211 ]
+0004356 = glutamate-ammonia ligase [isa: 0016211 ]
+0008885 = glutathionylspermidine synthase [isa: 0016880 ]
+0016881 = acid-D-amino acid ligase [isa: 0016879 ]
+0008668 = 2,3-dihydroxybenzoate-AMP ligase [isa: 0016881 ]
+0008822 = crotonobetaine/carnitine-CoA ligase [isa: 0016405 0016881 ]
+0008716 = D-alanine-D-alanine ligase [isa: 0016881 ]
+0008841 = dihydrofolate synthase [isa: 0016881 ]
+0004326 = folylpolyglutamate synthase [isa: 0016881 ]
+0004357 = glutamate-cysteine ligase [isa: 0016881 ]
+0004363 = glutathione synthase [isa: 0016881 ]
+0004592 = pantoate-beta-alanine ligase [isa: 0016881 ]
+0004632 = phosphopantothenate-cysteine ligase [isa: 0016881 ]
+0004639 = phosphoribosylaminoimidazole-succinocarboxamide synthase [isa: 0016881 ]
+0018169 = ribosomal S6-glutamic acid ligase [isa: 0016881 ]
+0004835 = tubulinyl-tyrosine ligase [isa: 0016881 ]
+0019787 = ubiquitin-like-protein ligase [isa: 0016881 ]
+0019788 = NEDD8 ligase [isa: 0019787 ]
+0019789 = SUMO ligase [isa: 0019787 ]
+0004842 = ubiquitin-protein ligase [isa: 0016881 ]
+0008763 = UDP-N-acetylmuramate-alanine ligase [isa: 0016881 ]
+0008764 = UDP-N-acetylmuramoylalanine-D-glutamate ligase [isa: 0016881 ]
+0008765 = UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase [isa: 0016881 ]
+0008766 = UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate-D-alanyl-D-alanine ligase [isa: 0016881 ]
+0004086 = carbamoyl-phosphate synthase [isa: 0016879 ]
+0004087 = carbamoyl-phosphate synthase (ammonia) [isa: 0004086 0016883 ]
+0004088 = carbamoyl-phosphate synthase (glutamine-hydrolyzing) [isa: 0004086 0016884 ]
+0016884 = carbon-nitrogen ligase, with glutamine as amido-N-donor [isa: 0016879 ]
+0004066 = asparagine synthase (glutamine-hydrolyzing) [isa: 0016884 ]
+0017068 = glutamyl-tRNA(Gln) amidotransferase [isa: 0016884 ]
+0003922 = GMP synthase (glutamine hydrolyzing) [isa: 0016884 ]
+0003952 = NAD+ synthase (glutamine-hydrolyzing) [isa: 0016884 0016965 ]
+0004642 = phosphoribosylformylglycinamidine synthase [isa: 0016884 ]
+0016882 = cyclo-ligase [isa: 0016879 ]
+0030272 = 5-formyltetrahydrofolate cyclo-ligase [isa: 0016882 ]
+0004141 = dethiobiotin synthase [isa: 0016882 ]
+0004641 = phosphoribosylformylglycinamidine cyclo-ligase [isa: 0016882 ]
+0016979 = lipoate-protein ligase [isa: 0016879 ]
+0016992 = lipoate synthase [isa: 0016979 ]
+0008916 = lipoate-protein ligase A [isa: 0016979 ]
+0016978 = lipoate-protein ligase B [isa: 0016979 ]
+0016965 = NAD synthase [isa: 0016879 ]
+0008795 = NAD+ synthase [isa: 0016965 ]
+0016883 = other carbon-nitrogen ligase [isa: 0016879 ]
+0004019 = adenylosuccinate synthase [isa: 0016883 ]
+0004055 = argininosuccinate synthase [isa: 0016883 ]
+0004075 = biotin carboxylase [isa: 0016883 ]
+0018271 = biotin-protein ligase [isa: 0016883 ]
+0000106 = biotin-apoprotein ligase [isa: 0018271 ]
+0004077 = biotin-[acetyl-CoA-carboxylase] ligase [isa: 0000106 ]
+0004078 = biotin-[methylcrotonoyl-CoA-carboxylase] ligase [isa: 0000106 ]
+0004079 = biotin-[methylmalonyl-CoA-carboxyltransferase] ligase [isa: 0000106 ]
+0004080 = biotin-[propionyl-CoA-carboxylase (ATP-hydrolyzing)] ligase [isa: 0000106 ]
+0003883 = CTP synthase [isa: 0016883 ]
+0004329 = formate-tetrahydrofolate ligase [isa: 0016883 ]
+0003921 = GMP synthase [isa: 0016883 ]
+0004637 = phosphoribosylamine-glycine ligase [isa: 0016883 ]
+0018236 = ribulose-bisphosphate carboxylase activase [isa: 0016883 ]
+0004847 = urea carboxylase [isa: 0016883 ]
+0018237 = urease activase [isa: 0016883 ]
+0016875 = ligase, forming carbon-oxygen bonds [isa: 0016874 ]
+0016876 = ligase, forming aminoacyl-tRNA and related compounds [isa: 0016875 ]
+0004812 = tRNA ligase [isa: 0008452 0016876 ]
+0004813 = alanine-tRNA ligase [isa: 0004812 ]
+0017100 = aminoacyl-tRNA synthetase auxiliary protein [isa: 0004812 ]
+0004814 = arginine-tRNA ligase [isa: 0004812 ]
+0004816 = asparagine-tRNA ligase [isa: 0004812 ]
+0004815 = aspartate-tRNA ligase [isa: 0004812 ]
+0004817 = cysteine-tRNA ligase [isa: 0004812 ]
+0004818 = glutamate-tRNA ligase [isa: 0004812 ]
+0004819 = glutamine-tRNA ligase [isa: 0004812 ]
+0004820 = glycine-tRNA ligase [isa: 0004812 ]
+0004821 = histidine-tRNA ligase [isa: 0004812 ]
+0004822 = isoleucine-tRNA ligase [isa: 0004812 ]
+0004823 = leucine-tRNA ligase [isa: 0004812 ]
+0004824 = lysine-tRNA ligase [isa: 0004812 ]
+0004825 = methionine-tRNA ligase [isa: 0004812 ]
+0004826 = phenylalanine-tRNA ligase [isa: 0004812 ]
+0004827 = proline-tRNA ligase [isa: 0004812 ]
+0004828 = serine-tRNA ligase [isa: 0004812 ]
+0004829 = threonine-tRNA ligase [isa: 0004812 ]
+0004830 = tryptophan-tRNA ligase [isa: 0004812 ]
+0004831 = tyrosine-tRNA ligase [isa: 0004812 ]
+0004832 = valine-tRNA ligase [isa: 0004812 ]
+0016877 = ligase, forming carbon-sulfur bonds [isa: 0016874 ]
+0016878 = acid-thiol ligase [isa: 0016877 ]
+0042410 = 6-carboxyhexanoate-CoA ligase [isa: 0016878 ]
+0016405 = CoA-ligase [isa: 0016877 ]
+0018857 = 2,4-dichlorobenzoate-CoA ligase [isa: 0016405 ]
+0018855 = 2-oxo-delta3-4,5,5-trimethylcyclopentenylacetyl-CoA synthetase [isa: 0016405 ]
+0018854 = 3-isopropenyl-6-oxoheptanoyl-CoA synthetase [isa: 0016405 ]
+0018861 = 4-chlorobenzoate-CoA ligase [isa: 0016405 ]
+0016207 = 4-coumarate-CoA ligase [isa: 0016405 ]
+0018859 = 4-hydroxybenzoate-CoA ligase [isa: 0016405 ]
+0003987 = acetate-CoA ligase [isa: 0016405 ]
+0003996 = acyl-CoA ligase [isa: 0016405 ]
+0018860 = anthranilate-CoA ligase [isa: 0016405 ]
+0018858 = benzoate-CoA ligase [isa: 0016405 ]
+0018856 = benzoyl acetate-CoA ligase [isa: 0016405 ]
+0008756 = o-succinylbenzoate-CoA ligase [isa: 0016405 ]
+0018853 = perillyl-CoA synthetase [isa: 0016405 ]
+0004774 = succinate-CoA ligase [isa: 0016405 ]
+0004775 = succinate-CoA ligase (ADP-forming) [isa: 0004774 ]
+0004776 = succinate-CoA ligase (GDP-forming) [isa: 0004774 ]
+0015645 = fatty-acid ligase [isa: 0016877 ]
+0008922 = long-chain-fatty-acid-acyl-carrier protein ligase [isa: 0015645 ]
+0004467 = long-chain-fatty-acid-CoA-ligase [isa: 0015645 ]
+0008771 = [citrate (pro-3S)-lyase] ligase [isa: 0016877 ]
+0016886 = ligase, forming phosphoric ester bonds [isa: 0016874 ]
+0003909 = DNA ligase [isa: 0016886 ]
+0003910 = DNA ligase (ATP) [isa: 0003909 ]
+0003911 = DNA ligase (NAD+) [isa: 0003909 ]
+0008452 = RNA ligase [isa: 0016886 ]
+0008664 = 2'-5' RNA ligase [isa: 0008452 ]
+0003972 = RNA ligase (ATP) [isa: 0008452 ]
+0003963 = RNA-3'-phosphate cyclase [isa: 0016886 ]
+0008754 = O antigen ligase [isa: 0016874 ]
+0017140 = lipoic acid synthase [isa: 0003824 ]
+0016829 = lyase [isa: 0003824 ]
+0016830 = carbon-carbon lyase [isa: 0016829 ]
+0016832 = aldehyde-lyase [isa: 0016830 ]
+0008672 = 2-dehydro-3-deoxyglucarate aldolase [isa: 0016228 0016832 ]
+0008674 = 2-dehydro-3-deoxyphosphogalactonate aldolase [isa: 0016228 0016832 ]
+0008675 = 2-dehydro-3-deoxyphosphogluconate aldolase [isa: 0016228 0016832 ]
+0003849 = 2-dehydro-3-deoxyphosphoheptonate aldolase [isa: 0016228 0016832 ]
+0008676 = 2-dehydro-3-deoxyphosphooctonate aldolase [isa: 0016228 0016832 ]
+0004139 = deoxyribose-phosphate aldolase [isa: 0016228 0016832 ]
+0004150 = dihydroneopterin aldolase [isa: 0016228 0016832 ]
+0004332 = fructose-bisphosphate aldolase [isa: 0016228 0016832 ]
+0008738 = L-fuculose-phosphate aldolase [isa: 0016228 0016832 ]
+0046593 = mandelonitrile lyase [isa: 0016832 ]
+0008994 = rhamnulose-1-phosphate aldolase [isa: 0016228 0016832 ]
+0008117 = sphinganine-1-phosphate aldolase [isa: 0016228 0016832 ]
+0009025 = tagatose-bisphosphate aldolase [isa: 0016228 0016832 ]
+0004793 = threonine aldolase [isa: 0016228 0016832 ]
+0008732 = L-allo-threonine aldolase [isa: 0004793 ]
+0016228 = aldolase [isa: 0016830 ]
+0008700 = 4-hydroxy-2-oxoglutarate aldolase [isa: 0016228 0016833 ]
+0008701 = 4-hydroxy-2-oxovalerate/4-hydroxy-2-keto-pentanoic acid aldolase [isa: 0016228 0016833 ]
+0016831 = carboxy-lyase [isa: 0016830 ]
+0018790 = 2,3-dihydroxybenzoate decarboxylase [isa: 0016831 ]
+0018802 = 2,4-dihydroxyhept-2-ene-1,7-dioate aldolase [isa: 0016831 ]
+0018795 = 2-hydroxy-2-methyl-1,3-dicarbonate decarboxylase [isa: 0016831 ]
+0018791 = 2-hydroxy-3-carboxy-6-oxo-7-methylocta-2,4-dienoate decarboxylase [isa: 0016831 ]
+0018794 = 2-hydroxyisobutyrate decarboxylase [isa: 0016831 ]
+0008683 = 2-oxoglutarate decarboxylase [isa: 0016831 ]
+0018793 = 3,5-dibromo-4-hydroxybenzoate decarboxylase [isa: 0016831 ]
+0008694 = 3-octaprenyl-4-hydroxybenzoate carboxy-lyase [isa: 0016831 ]
+0019167 = 3-octaprenyl-4-hydroxybenzoate decarboxylase [isa: 0016831 ]
+0018796 = 4,5-dihydroxyphthalate decarboxylase [isa: 0016831 ]
+0018799 = 4-hydroxybenzoate decarboxylase [isa: 0016831 ]
+0018800 = 5-oxopent-3-ene-1,2,5-tricarboxylate decarboxylase [isa: 0016831 ]
+0004014 = adenosylmethionine decarboxylase [isa: 0016831 ]
+0008792 = arginine decarboxylase [isa: 0016831 ]
+0004058 = aromatic-L-amino acid decarboxylase [isa: 0016831 ]
+0004068 = aspartate 1-decarboxylase [isa: 0016831 ]
+0018792 = bis(4'-chlorophenyl)acetate decarboxylase [isa: 0016831 ]
+0008836 = diaminopimelate decarboxylase [isa: 0016831 ]
+0004163 = diphosphomevalonate decarboxylase [isa: 0016831 ]
+0018798 = gallate decarboxylase [isa: 0016831 ]
+0008488 = gamma-glutamyl carboxylase [isa: 0016831 ]
+0018801 = glutaconyl-CoA decarboxylase [isa: 0016831 ]
+0004351 = glutamate decarboxylase [isa: 0016831 ]
+0004398 = histidine decarboxylase [isa: 0016831 ]
+0004425 = indole-3-glycerol-phosphate synthase [isa: 0016831 ]
+0008923 = lysine decarboxylase [isa: 0016831 ]
+0004492 = methylmalonyl-CoA decarboxylase [isa: 0016831 ]
+0004586 = ornithine decarboxylase [isa: 0016831 ]
+0004590 = orotidine-5'-phosphate decarboxylase [isa: 0016831 ]
+0046564 = oxalate decarboxylase [isa: 0016831 ]
+0008948 = oxaloacetate decarboxylase [isa: 0016831 ]
+0008949 = oxalyl-CoA decarboxylase [isa: 0016831 ]
+0004609 = phosphatidylserine decarboxylase [isa: 0016831 ]
+0004633 = phosphopantothenoylcysteine decarboxylase [isa: 0016831 ]
+0004638 = phosphoribosylaminoimidazole carboxylase [isa: 0016831 ]
+0004737 = pyruvate decarboxylase [isa: 0016831 ]
+0016984 = ribulose-bisphosphate carboxylase [isa: 0016831 ]
+0004782 = sulfinoalanine decarboxylase [isa: 0016831 ]
+0009028 = tartronate-semialdehyde synthase [isa: 0016831 ]
+0018803 = trans-2'-carboxybenzalpyruvate hydratase-aldolase [isa: 0016831 ]
+0004837 = tyrosine decarboxylase [isa: 0016831 ]
+0004853 = uroporphyrinogen decarboxylase [isa: 0016831 ]
+0016834 = other carbon-carbon lyase [isa: 0016830 ]
+0008660 = 1-aminocyclopropane-1-carboxylate deaminase [isa: 0016834 ]
+0009924 = aldehyde decarbonylase [isa: 0016834 ]
+0018805 = benzylsuccinate synthase [isa: 0016834 ]
+0003913 = DNA photolyase [isa: 0016834 ]
+0003914 = DNA (6-4) photolyase [isa: 0003913 ]
+0009034 = tryptophanase [isa: 0016834 ]
+0016833 = oxo-acid-lyase [isa: 0016830 ]
+0008661 = 1-deoxyxylulose-5-phosphate synthase [isa: 0016833 ]
+0019142 = 2-hydroxyglutarate synthase [isa: 0016833 ]
+0003852 = 2-isopropylmalate synthase [isa: 0016833 ]
+0046410 = 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase [isa: 0016833 ]
+0003984 = acetolactate synthase [isa: 0016833 ]
+0004049 = anthranilate synthase [isa: 0016833 ]
+0003878 = ATP-citrate (pro-S)-lyase [isa: 0016833 ]
+0008813 = chorismate pyruvate lyase [isa: 0016833 ]
+0004108 = citrate (SI)-synthase [isa: 0016833 ]
+0008815 = citrate lyase [isa: 0016833 ]
+0008816 = citryl-CoA lyase [isa: 0016833 ]
+0004410 = homocitrate synthase [isa: 0016833 ]
+0004419 = hydroxymethylglutaryl-CoA lyase [isa: 0016833 ]
+0004421 = hydroxymethylglutaryl-CoA synthase [isa: 0016833 ]
+0004451 = isocitrate lyase [isa: 0016833 ]
+0004474 = malate synthase [isa: 0016833 ]
+0046421 = methylisocitrate lyase [isa: 0016833 ]
+0008747 = N-acetylneuraminate lyase [isa: 0016833 ]
+0008935 = naphthoate synthase [isa: 0016833 ]
+0008950 = p-aminobenzoate synthetase [isa: 0016833 ]
+0016848 = carbon-halide lyase [isa: 0016829 ]
+0018829 = 1,1-dichloro-2,2-bis(4'-chlorophenyl)ethane dehydrochlorinase [isa: 0016848 ]
+0018827 = 1-chloro-2,2-bis(4'-chlorophenyl)ethane dehydrochlorinase [isa: 0016848 ]
+0019149 = 3-chloro-D-alanine dehydrochlorinase [isa: 0016848 ]
+0018831 = 5-chloro-1,2,4-trihydroxybenzene dechlorinase [isa: 0016848 ]
+0018833 = DDT dehydrochlorinase [isa: 0016848 ]
+0018834 = dichloromethane dehalogenase [isa: 0016848 ]
+0018830 = gamma-hexachlorocyclohexane dehydrochlorinase [isa: 0016848 ]
+0019181 = halohydrin hydrogen-halide-lyase [isa: 0016848 ]
+0018828 = halohydrin hydrogen-halide-lyase A [isa: 0019181 ]
+0018832 = halohydrin hydrogen-halide-lyase B [isa: 0019181 ]
+0016840 = carbon-nitrogen lyase [isa: 0016829 ]
+0016842 = amidine-lyase [isa: 0016840 ]
+0004018 = adenylosuccinate lyase [isa: 0016842 ]
+0004056 = argininosuccinate lyase [isa: 0016842 ]
+0004598 = peptidylamidoglycolate lyase [isa: 0016842 ]
+0016843 = amine-lyase [isa: 0016840 ]
+0018824 = hydroxylaminobenzene mutase [isa: 0016843 ]
+0016844 = strictosidine synthase [isa: 0016843 ]
+0018825 = triethanolamine lyase [isa: 0016843 ]
+0016841 = ammonia-lyase [isa: 0016840 ]
+0008797 = aspartate ammonia-lyase [isa: 0016841 ]
+0008721 = D-serine ammonia-lyase [isa: 0016841 ]
+0008838 = diaminopropionate ammonia-lyase [isa: 0016841 ]
+0008851 = ethanolamine ammonia-lyase [isa: 0016841 ]
+0030412 = formimidoyltetrahydrofolate cyclodeaminase [isa: 0016841 ]
+0004397 = histidine ammonia-lyase [isa: 0016841 ]
+0004418 = hydroxymethylbilane synthase [isa: 0016841 ]
+0003941 = L-serine ammonia-lyase [isa: 0016841 ]
+0008473 = ornithine cyclodeaminase [isa: 0016841 ]
+0045548 = phenylalanine ammonia-lyase [isa: 0016841 ]
+0016845 = other carbon-nitrogen lyase [isa: 0016840 ]
+0008824 = cyanate lyase [isa: 0016845 ]
+0016835 = carbon-oxygen lyase [isa: 0016829 ]
+0016838 = carbon-oxygen lyase, acting on phosphates [isa: 0016835 ]
+0003856 = 3-dehydroquinate synthase [isa: 0016838 ]
+0003874 = 6-pyruvoyltetrahydropterin synthase [isa: 0016838 ]
+0045483 = aristolochene synthase [isa: 0016838 ]
+0004107 = chorismate synthase [isa: 0016838 ]
+0008929 = methylglyoxal synthase [isa: 0016838 ]
+0004795 = threonine synthase [isa: 0016838 ]
+0045482 = trichodiene synthase [isa: 0016838 ]
+0016837 = carbon-oxygen lyase, acting on polysaccharides [isa: 0016835 ]
+0030341 = chondroitin AC lyase [isa: 0016837 ]
+0015021 = heparitin-sulfate lyase [isa: 0016837 ]
+0030340 = hyaluronate lyase [isa: 0016837 ]
+0030570 = pectate lyase [isa: 0016837 ]
+0045135 = poly(beta-D-mannuronate) lyase [isa: 0016837 ]
+0046576 = rhamnogalacturonase B [isa: 0016837 ]
+0016836 = hydro-lyase [isa: 0016835 ]
+0008659 = (3R)-hydroxymyristol acyl carrier protein dehydratase [isa: 0016836 ]
+0018816 = 2-hydroxyisobutyrate dehydratase [isa: 0016836 ]
+0018817 = 2-oxo-hept-3-ene-1,7-dioate hydratase [isa: 0016836 ]
+0008684 = 2-oxopent-4-enoate hydratase [isa: 0016836 ]
+0003855 = 3-dehydroquinate dehydratase [isa: 0016836 ]
+0046565 = 3-dehydroshikimate dehydratase [isa: 0016836 ]
+0019171 = 3-hydroxyacyl-ACP dehydratase [isa: 0016836 ]
+0018812 = 3-hydroxyacyl-CoA dehydratase [isa: 0016836 ]
+0003859 = 3-hydroxybutyryl-CoA dehydratase [isa: 0016836 ]
+0008693 = 3-hydroxydecanoyl-[acyl-carrier protein] dehydratase [isa: 0016836 ]
+0004317 = 3-hydroxypalmitoyl-[acyl-carrier protein] dehydratase [isa: 0004312 0016836 ]
+0003861 = 3-isopropylmalate dehydratase [isa: 0016836 ]
+0018815 = 3-methyl-5-hydroxy-6-(3-carboxy-3-oxopropenyl)-1H-2-pyridon hydratase-aldolase [isa: 0016836 ]
+0008124 = 4a-hydroxytetrahydrobiopterin dehydratase [isa: 0016836 ]
+0046570 = 5-methylthioribulose-1-phosphate 4-dehydratase [isa: 0016836 ]
+0018807 = 6-hydroxycyclohex-1-ene-1-carboxyl-CoA hydratase [isa: 0016836 ]
+0018818 = acetylene hydratase [isa: 0016836 ]
+0003994 = aconitate hydratase [isa: 0016836 ]
+0008789 = altronate dehydratase [isa: 0016836 ]
+0004089 = carbonate dehydratase [isa: 0016836 ]
+0018808 = cis-4-(1'-hydroxynaphth-2'-yl)-2-oxobut-3-enoate hydratase-aldolase [isa: 0016836 ]
+0018820 = cyanamide hydratase [isa: 0016836 ]
+0030196 = cyanide hydratase [isa: 0016836 ]
+0018811 = cyclohex-1-ene-1-carboxyl-CoA hydratase [isa: 0016836 ]
+0018823 = cyclohexa-1,5-dienecarbonyl-CoA hydratase [isa: 0016836 ]
+0004122 = cystathione beta-synthase [isa: 0016836 ]
+0008840 = dihydrodipicolinate synthase [isa: 0016836 ]
+0004160 = dihydroxy-acid dehydratase [isa: 0016836 ]
+0008460 = dTDP-glucose 4,6-dehydratase [isa: 0016836 ]
+0018809 = E-phenylitaconyl-CoA hydratase [isa: 0016836 ]
+0004300 = enoyl-CoA hydratase [isa: 0016836 ]
+0016508 = long-chain enoyl-CoA hydratase [isa: 0004300 ]
+0016510 = short-chain enoyl-CoA hydratase [isa: 0004300 ]
+0004333 = fumarate hydratase [isa: 0016836 ]
+0008867 = galactarate dehydratase [isa: 0016836 ]
+0008869 = galactonate dehydratase [isa: 0016836 ]
+0008446 = GDP-mannose 4,6-dehydratase [isa: 0016836 ]
+0008872 = glucarate dehydratase [isa: 0016836 ]
+0046405 = glycerol dehydratase [isa: 0016836 ]
+0004409 = homoaconitate hydratase [isa: 0016836 ]
+0004424 = imidazoleglycerol-phosphate dehydratase [isa: 0016836 ]
+0004456 = ketopantoaldase [isa: 0016836 ]
+0008730 = L(+)-tartrate dehydratase [isa: 0016836 ]
+0008735 = L-carnitine dehydratase [isa: 0016836 ]
+0018819 = lactoyl-CoA dehydratase [isa: 0016836 ]
+0008927 = mannonate dehydratase [isa: 0016836 ]
+0004490 = methylglutaconyl-CoA hydratase [isa: 0016836 ]
+0018822 = nitrile hydratase [isa: 0016836 ]
+0018135 = peptidyl-cysteine cyclase [isa: 0016836 ]
+0018128 = peptidyl-serine cyclase [isa: 0016836 ]
+0018814 = phenylacetaldoxime dehydratase [isa: 0016836 ]
+0004634 = phosphopyruvate hydratase [isa: 0016836 ]
+0004655 = porphobilinogen synthase [isa: 0016836 ]
+0004664 = prephenate dehydratase [isa: 0016836 ]
+0004730 = pseudouridylate synthase [isa: 0016836 ]
+0017051 = retinol dehydratase [isa: 0016836 ]
+0030411 = scytalone dehydratase [isa: 0016836 ]
+0004794 = threonine dehydratase [isa: 0016836 ]
+0018810 = trans-4-[2-(3-hydroxy)-thionaphthenyl]-2-oxo-3-butenoate hydratase [isa: 0016836 ]
+0018813 = trans-o-hydroxybenzylidenepyruvate hydratase-aldolase [isa: 0016836 ]
+0004834 = tryptophan synthase [isa: 0016836 ]
+0016153 = urocanate hydratase [isa: 0016836 ]
+0004852 = uroporphyringonen-III synthase [isa: 0016836 ]
+0016839 = other carbon-oxygen lyase [isa: 0016835 ]
+0004124 = cysteine synthase [isa: 0016839 ]
+0003961 = O-acetylhomoserine (thiol)-lyase [isa: 0016839 ]
+0003962 = O-succinyl-L-homoserine (thiol)-lyase [isa: 0016839 ]
+0009456 = carbon-phosphorous lyase [isa: 0016829 ]
+0016846 = carbon-sulfur lyase [isa: 0016829 ]
+0016847 = 1-aminocyclopropane-1-carboxylate synthase [isa: 0016846 ]
+0008799 = beta-cystathionase [isa: 0016846 ]
+0004121 = cystathionine beta-lyase [isa: 0016846 ]
+0016225 = cysteine desulfhydrase [isa: 0016846 ]
+0004123 = cystathionine-gamma-lyase [isa: 0016225 ]
+0019148 = D-cysteine desulfhydrase [isa: 0016225 ]
+0008826 = cysteine sulfinate desulfinase [isa: 0016846 ]
+0004408 = holocytochrome c synthase [isa: 0016846 ]
+0004462 = lactoylglutathione lyase [isa: 0016846 ]
+0018826 = methionine gamma-lyase [isa: 0016846 ]
+0009000 = selenocysteine lyase [isa: 0016846 ]
+0016850 = other lyase [isa: 0016829 ]
+0018836 = alkylmercury lyase [isa: 0016850 ]
+0018835 = carbon phosphorus lyase [isa: 0016850 ]
+0016852 = cobalt chelatase [isa: 0016850 ]
+0004325 = ferrochelatase [isa: 0016850 ]
+0016851 = magnesium chelatase [isa: 0016850 ]
+0016849 = phosphorus-oxygen lyase [isa: 0016829 ]
+0008685 = 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase [isa: 0016849 ]
+0004016 = adenylate cyclase [isa: 0016849 ]
+0008294 = calcium/calmodulin-responsive adenylate cyclase [isa: 0004016 ]
+0009899 = ent-kaurene synthase [isa: 0016849 ]
+0004383 = guanylate cyclase [isa: 0016849 ]
+0008075 = receptor guanylate cyclase [isa: 0004383 0004888 ]
+0016941 = natriuretic peptide receptor [isa: 0008075 ]
+0042408 = myrcene/(E)-beta-ocimene synthase [isa: 0016849 ]
+0008265 = Mo-molybdopterin cofactor sulfurase [isa: 0003824 ]
+0030366 = Mo-molybdopterin synthase [isa: 0003824 ]
+0009392 = N-acetyl-anhydromuramoyl-L-alanine amidase [isa: 0003824 ]
+0019007 = N-acetylneuraminic acid phosphate synthase [isa: 0003824 ]
+0009385 = N-acylmannosamine-6-phosphate 2-epimerase [isa: 0003824 ]
+0016217 = N-ethylammeline chlorohydrolase [isa: 0003824 ]
+0008755 = O antigen polymerase [isa: 0003824 ]
+0016491 = oxidoreductase [isa: 0003824 ]
+0030342 = 1-alpha,25-dihydroxyvitamin D3 (1,25-(OH)2D3) 24-hydroxylase [isa: 0016491 ]
+0019168 = 2-octaprenylphenol hydroxylase [isa: 0016491 ]
+0008682 = 2-octoprenyl-3-methyl-6-methoxy-1,4-benzoquinone hydroxylase [isa: 0016491 ]
+0030344 = 25-hydroxyvitamin D3 24-hydroxylase [isa: 0016491 ]
+0000253 = 3-keto sterol reductase [isa: 0016491 ]
+0004033 = aldo-keto reductase [isa: 0016491 ]
+0003826 = alpha-ketoacid dehydrogenase [isa: 0016491 ]
+0030611 = arsenate reductase [isa: 0016491 ]
+0008794 = arsenate reductase (glutaredoxin) [isa: 0030611 0030614 ]
+0030612 = arsenate reductase (thioredoxin) [isa: 0030611 ]
+0042411 = beta-carotene hydroxylase [isa: 0016491 ]
+0000251 = C-14 sterol reductase [isa: 0016491 ]
+0000252 = C-3 sterol dehydrogenase (C-4 sterol decarboxylase) [isa: 0016491 ]
+0000254 = C-4 methyl sterol oxidase [isa: 0016491 ]
+0030065 = chlorite dismutase [isa: 0016491 ]
+0045441 = deacetoxycephalosporin C synthetase [isa: 0016491 ]
+0001512 = dihydronicotinamide riboside quinone reductase [isa: 0016491 ]
+0004154 = dihydropterin oxidase [isa: 0016491 ]
+0015036 = disulfide oxidoreductase [isa: 0016491 ]
+0015037 = peptide disulfide oxidoreductase [isa: 0015036 ]
+0015038 = glutathione disulfide oxidoreductase [isa: 0015037 ]
+0015035 = protein disulfide oxidoreductase [isa: 0015036 ]
+0008895 = heme lyase/disulfide oxidoreductase [isa: 0015035 ]
+0030508 = thiol-disulfide exchange intermediate [isa: 0015036 ]
+0046566 = DOPA dioxygenase [isa: 0016491 ]
+0045550 = geranylgeranyl reductase [isa: 0016491 ]
+0001513 = glutamate phosphate reductase [isa: 0016491 ]
+0015002 = heme-copper terminal oxidase [isa: 0016491 ]
+0004129 = cytochrome c oxidase [isa: 0015002 0015078 0015399 0016676 ]
+0009481 = aa3-type cytochrome c oxidase [isa: 0004129 ]
+0009482 = ba3-type cytochrome c oxidase [isa: 0004129 ]
+0009483 = caa3-type cytochrome c oxidase [isa: 0004129 ]
+0009485 = cbb3-type cytochrome c oxidase [isa: 0004129 ]
+0008827 = cytochrome o ubiquinol oxidase [isa: 0015002 0016682 ]
+0009486 = cytochrome bo3 ubiquinol oxidase [isa: 0008827 ]
+0042380 = hydroxymethylbutenyl pyrophosphate reductase [isa: 0016491 ]
+0045432 = leucoanthocyanidin dioxygenase [isa: 0016491 ]
+0016164 = Mo-molybdopterin oxidoreductase [isa: 0016491 ]
+0004497 = monooxygenase [isa: 0016491 ]
+0018637 = 1-hydroxy-2-naphthoate hydroxylase [isa: 0004497 0016709 ]
+0018646 = 1-hydroxy-2-oxolimonene 1,2-monooxygenase [isa: 0004497 0016709 ]
+0018666 = 2,4-dichlorophenol hydroxylase [isa: 0004497 0016709 ]
+0018663 = 2,6-dihydroxypyridine oxidase [isa: 0004497 0016709 ]
+0018654 = 2-hydroxy-phenylacetate hydroxylase [isa: 0004497 0016709 ]
+0018655 = 2-oxo-delta3-4,5,5-trimethylcyclopentenylacetyl-CoA 1,2-monooxygenase [isa: 0004497 0016709 ]
+0018630 = 3,5-xylenol methylhydroxylase [isa: 0004497 0016709 ]
+0018668 = 3-hydroxybenzoate 4-hydroxylase [isa: 0004497 0016709 ]
+0018669 = 3-hydroxybenzoate 6-hydroxylase [isa: 0004497 0016709 ]
+0018653 = 3-methyl-2-oxo-1,2-dihydroquinoline 6-monooxygenase [isa: 0004497 0016709 ]
+0018670 = 4-aminobenzoate hydroxylase [isa: 0004497 0016709 ]
+0018678 = 4-hydroxybenzoate 1-hydroxylase [isa: 0004497 0016709 ]
+0018659 = 4-hydroxybenzoate 3-monooxygenase [isa: 0004497 0016709 ]
+0018671 = 4-hydroxybenzoate 3-monooxygenase [NAD(P)H] [isa: 0004497 0016709 ]
+0018665 = 4-hydroxyphenyl-acetate 1-hydroxylase [isa: 0004497 0016709 ]
+0018660 = 4-hydroxyphenyl-acetate 3-hydroxylase [isa: 0004497 0016709 ]
+0018632 = 4-nitrophenol 4-monooxygenase [isa: 0004497 0016709 ]
+0018686 = 6-hydroxy pseudo-oxynicotine monooxygenase [isa: 0004497 0016716 ]
+0018641 = 6-hydroxy-3-methyl-2-oxo-1,2-dihydroquinoline 6-monooxygenase [isa: 0004497 0016709 ]
+0018685 = alkane 1-monooxygenase [isa: 0004497 0016713 ]
+0018645 = alkene monooxygenase [isa: 0004497 0016709 ]
+0018634 = alpha-pinene monooxygenase [NADH] [isa: 0004497 0016709 ]
+0018672 = anthranilate 3-monooxygenase (deaminating) [isa: 0004497 0016709 ]
+0018673 = anthraniloyl-CoA monooxygenase [isa: 0004497 0016709 ]
+0018682 = atrazine monooxygenase [isa: 0004497 0016713 ]
+0018664 = benzoate 4-monooxygenase [isa: 0004497 0016709 ]
+0018684 = camphor 1,2-monooxygenase [isa: 0004497 0016713 ]
+0018683 = camphor 5-monooxygenase [isa: 0004497 0016713 ]
+0018643 = carbon disulfide oxygenase [isa: 0004497 0016709 ]
+0018642 = chlorophenol 4-monooxygenase [isa: 0004497 0016709 ]
+0030338 = CMP-N-acetylneuraminate monooxygenase [isa: 0004497 0016709 ]
+0018667 = cyclohexanone 1,2-monooxygenase [isa: 0004497 0016709 ]
+0018680 = deethylatrazine monooxygenase [isa: 0004497 0016713 ]
+0018681 = deisopropylatrazine monooxygenase [isa: 0004497 0016713 ]
+0018640 = dibenzothiophene monooxygenase [isa: 0004497 0016709 ]
+0018679 = dibenzothiophene-5,5-dioxide monooxygenase [isa: 0004497 0016712 ]
+0018633 = dimethyl sulfide monooxygenase [isa: 0004497 0016709 ]
+0004499 = dimethylaniline monooxygenase (N-oxide forming) [isa: 0004497 0016709 ]
+0046424 = ferulate 5-hydroxylase [isa: 0004497 0016659 ]
+0008726 = FMNH(2)-dependent alkanesulfonate monooxygenase [isa: 0004497 0016705 ]
+0046569 = glyoxal oxidase [isa: 0004497 0016623 ]
+0004502 = kynurenine 3-monooxygenase [isa: 0004497 0016709 ]
+0008739 = L-lysine 6-monooxygenase [isa: 0004497 0016703 ]
+0018635 = limonene 1,2-monooxygenase [isa: 0004497 0019113 ]
+0018674 = limonene 3-monooxygenase [isa: 0004497 0019113 ]
+0018675 = limonene 6-monooxygenase [isa: 0004497 0019113 ]
+0018676 = limonene 7-monooxygenase [isa: 0004497 0019113 ]
+0045289 = luciferase monooxygenase [isa: 0004497 ]
+0015049 = methane monooxygenase [isa: 0004497 0015933 0016709 ]
+0018648 = methanesulfonic acid monooxygenase [isa: 0004497 0016709 ]
+0004503 = monophenol monooxygenase [isa: 0004497 0016716 ]
+0018661 = orcinol hydroxylase [isa: 0004497 0016709 ]
+0018677 = pentachlorophenol 4-monooxygenase [isa: 0004497 0016709 ]
+0004504 = peptidyl-glycine monooxygenase [isa: 0004497 0016715 ]
+0018647 = phenanthrene 1,2-monooxygenase [isa: 0004497 0016709 ]
+0018656 = phenanthrene 3,4-monooxygenase [isa: 0004497 0016709 ]
+0018636 = phenanthrene 9,10-monooxygenase [isa: 0004497 0016709 ]
+0018662 = phenol 2-monooxygenase [isa: 0004497 0016709 ]
+0018631 = phenylacetate hydroxylase [isa: 0004497 0016709 ]
+0004505 = phenylalanine 4-monooxygenase [isa: 0004497 0016714 ]
+0018658 = salicylate hydroxylase [isa: 0004497 0016709 ]
+0004506 = squalene monooxygenase [isa: 0004497 0016718 ]
+0008395 = steroid hydroxylase [isa: 0004497 ]
+0001567 = cholesterol 25-hydroxylase [isa: 0008395 ]
+0008386 = cholesterol monooxygenase (side-chain cleaving) [isa: 0008395 0016713 ]
+0004501 = ecdysone 20-monooxygenase [isa: 0008395 0016718 ]
+0018650 = styrene monooxygenase [isa: 0004497 0016709 ]
+0018649 = tetrahydrofuran hydroxylase [isa: 0004497 0016709 ]
+0018644 = toluene 2-monooxygenase [isa: 0004497 0016709 ]
+0018657 = toluene 3-monooxygenase [isa: 0004497 0016709 ]
+0018638 = toluene 4-monooxygenase [isa: 0004497 0016709 ]
+0018651 = toluene-4-sulfonate monooxygenase [isa: 0004497 0016709 ]
+0018652 = toluene-sulfonate methyl-monooxygenase [isa: 0004497 0016709 ]
+0004510 = tryptophan 5-monooxygenase [isa: 0004497 0016714 ]
+0004511 = tyrosine 3-monooxygenase [isa: 0004497 0016714 ]
+0015997 = ubiquinone biosynthesis monooxygenase [isa: 0004497 0016709 ]
+0018639 = xylene monooxygenase [isa: 0004497 0016709 ]
+0008748 = N-ethylmaleimide reductase [isa: 0016491 ]
+0016174 = NADPH oxidase [isa: 0016491 ]
+0016175 = superoxide-generating NADPH oxidase [isa: 0016174 ]
+0016614 = oxidoreductase, acting on CH-OH group of donors [isa: 0016491 ]
+0018449 = 1-phenylethanol dehydrogenase [isa: 0016614 ]
+0018447 = chloral hydrate dehydrogenase [isa: 0016614 ]
+0018448 = hydroxymethylmethylsilanediol oxidase [isa: 0016614 ]
+0016216 = isopenicillin N synthetase [isa: 0016614 ]
+0045703 = ketoreductase [isa: 0016614 ]
+0004457 = lactate dehydrogenase [isa: 0016614 ]
+0004458 = D-lactate dehydrogenase (cytochrome) [isa: 0004457 0016898 ]
+0004459 = L-lactate dehydrogenase [isa: 0004457 0016616 ]
+0004460 = L-lactate dehydrogenase (cytochrome) [isa: 0004457 0016898 ]
+0016615 = malate dehydrogenase [isa: 0016614 ]
+0046553 = D-malate dehydrogenase (decarboxylating) [isa: 0016615 0016616 ]
+0030060 = L-malate dehydrogenase [isa: 0016615 0016616 ]
+0008924 = malate dehydrogenase (acceptor) [isa: 0016615 0016902 ]
+0046554 = malate dehydrogenase (NADP) [isa: 0016615 0016616 ]
+0004470 = malic enzyme [isa: 0016615 ]
+0004471 = malate dehydrogenase (decarboxylating) [isa: 0004470 0016616 ]
+0016619 = malate dehydrogenase (oxaloacetate decarboxylating) [isa: 0004470 0016616 ]
+0004473 = malate dehydrogenase (oxaloacetate decarboxylating) (NADP+) [isa: 0004470 0016616 ]
+0018450 = myrtenol dehydrogenase [isa: 0016614 ]
+0016898 = oxidoreductase, acting on the CH-OH group of donors, cytochrome as acceptor [isa: 0016614 ]
+0016900 = oxidoreductase, acting on the CH-OH group of donors, disulfide as acceptor [isa: 0016614 ]
+0016616 = oxidoreductase, acting on the CH-OH group of donors, NAD or NADP as acceptor [isa: 0016614 ]
+0019147 = (R)-aminopropanol dehydrogenase [isa: 0016616 ]
+0000721 = (R,R)-butanediol dehydrogenase [isa: 0016616 ]
+0030604 = 1-deoxy-D-xylulose-5-phosphate reductoisomerase [isa: 0016616 ]
+0016404 = 15-hydroxyprostaglandin dehydrogenase (NAD+) [isa: 0016616 ]
+0008677 = 2-dehydropantoate 2-reductase [isa: 0016616 ]
+0019141 = 2-dehydropantoyl-lactone reductase (B-specific) [isa: 0016616 ]
+0008678 = 2-deoxy-D-gluconate 3-dehydrogenase [isa: 0016616 ]
+0008679 = 2-hydroxy-3-oxopropionate reductase [isa: 0016616 ]
+0018453 = 2-hydroxytetrahydrofuran dehydrogenase [isa: 0016616 ]
+0019155 = 3-(imidazol-5-yl)lactate dehydrogenase [isa: 0016616 ]
+0003857 = 3-hydroxyacyl-CoA dehydrogenase [isa: 0016616 ]
+0016509 = long-chain 3-hydroxyacyl-CoA dehydrogenase [isa: 0003857 ]
+0003858 = 3-hydroxybutyrate dehydrogenase [isa: 0016616 ]
+0008691 = 3-hydroxybutyryl-CoA dehydrogenase [isa: 0016616 ]
+0008442 = 3-hydroxyisobutyrate dehydrogenase [isa: 0016616 ]
+0018464 = 3-hydroxypimeloyl-CoA dehydrogenase [isa: 0016616 ]
+0003862 = 3-isopropylmalate dehydrogenase [isa: 0016616 ]
+0046568 = 3-methylbutanal reductase [isa: 0016616 ]
+0004316 = 3-oxoacyl-[acyl-carrier protein] reductase [isa: 0004312 0016616 ]
+0018462 = 4-(hydroxymethyl)benzenesulfonate dehydrogenase [isa: 0016616 ]
+0016617 = 4-oxoproline reductase [isa: 0016616 ]
+0008703 = 5-amino-6-(5-phosphoribosylamino)uracil reductase [isa: 0016616 ]
+0018452 = 5-exo-hydroxycamphor dehydrogenase [isa: 0016616 ]
+0045481 = 6-endo-hydroxycineole dehydrogenase [isa: 0016616 ]
+0018463 = 6-hydroxyhexanoate dehydrogenase [isa: 0016616 ]
+0008114 = 6-phosphogluconate 2-dehydrogenase [isa: 0016616 ]
+0018461 = 9-fluorenol dehydrogenase [isa: 0016616 ]
+0018454 = acetoacetyl-CoA reductase [isa: 0016616 ]
+0019152 = acetoin dehydrogenase [isa: 0016616 ]
+0000140 = acylglycerone-phosphate reductase [isa: 0016616 ]
+0004022 = alcohol dehydrogenase [isa: 0016616 ]
+0008106 = alcohol dehydrogenase (NADP+) [isa: 0004022 ]
+0004025 = alcohol dehydrogenase, iron-dependent [isa: 0004022 ]
+0004023 = alcohol dehydrogenase, metal ion-independent [isa: 0004022 ]
+0004024 = alcohol dehydrogenase, zinc-dependent [isa: 0004022 ]
+0004032 = aldehyde reductase [isa: 0016616 ]
+0018456 = benzyl alcohol dehydrogenase [isa: 0016616 ]
+0004090 = carbonyl reductase (NADPH) [isa: 0016616 ]
+0018459 = carveol dehydrogenase [isa: 0016616 ]
+0045551 = cinnamyl-alcohol dehydrogenase [isa: 0016616 ]
+0018460 = cyclohexanol dehydrogenase [isa: 0016616 ]
+0045290 = D-arabinose 1-dehydrogenase [NAD(P)] [isa: 0016616 ]
+0019151 = D-galactose 1-dehydrogenase [isa: 0016616 ]
+0019170 = D-lactaldehyde dehydrogenase [isa: 0016616 ]
+0008720 = D-lactate dehydrogenase [isa: 0016616 ]
+0046526 = D-xylulose reductase [isa: 0016616 ]
+0045552 = dihydrokaempferol 4-reductase [isa: 0016616 ]
+0008831 = dTDP-4-dehydrorhamnose reductase [isa: 0016616 ]
+0018451 = epoxide dehydrogenase [isa: 0016616 ]
+0008866 = fructuronate reductase [isa: 0016616 ]
+0008868 = galactitol-1-phosphate 5-dehydrogenase [isa: 0016616 ]
+0042356 = GDP-4-dehydro-D-rhamnose reductase [isa: 0016616 ]
+0008875 = gluconate dehydrogenase [isa: 0016616 ]
+0008873 = gluconate 2-dehydrogenase [isa: 0008875 ]
+0008874 = gluconate 5-dehydrogenase [isa: 0008875 ]
+0004345 = glucose-6-phosphate 1-dehydrogenase [isa: 0016616 ]
+0008465 = glycerate dehydrogenase [isa: 0016616 ]
+0008888 = glycerol dehydrogenase [isa: 0016616 ]
+0004367 = glycerol-3-phosphate dehydrogenase (NAD+) [isa: 0016616 ]
+0030267 = glyoxylate reductase (NADP) [isa: 0016616 ]
+0004399 = histidinol dehydrogenase [isa: 0016616 ]
+0004412 = homoserine dehydrogenase [isa: 0016616 ]
+0042282 = hydroxymethylglutaryl-CoA reductase [isa: 0016616 ]
+0004420 = hydroxymethylglutaryl-CoA reductase (NADPH) [isa: 0016616 ]
+0016618 = hydroxypyruvate reductase [isa: 0016616 ]
+0003938 = IMP dehydrogenase [isa: 0016616 ]
+0004448 = isocitrate dehydrogenase [isa: 0016616 ]
+0004449 = isocitrate dehydrogenase (NAD+) [isa: 0004448 ]
+0004450 = isocitrate dehydrogenase (NADP+) [isa: 0004448 ]
+0018458 = isopiperitenol dehydrogenase [isa: 0016616 ]
+0004455 = ketol-acid reductoisomerase [isa: 0016616 ]
+0003939 = L-iditol 2-dehydrogenase [isa: 0016616 ]
+0008743 = L-threonine 3-dehydrogenase [isa: 0016616 ]
+0008912 = lactaldehyde reductase [isa: 0016616 ]
+0046029 = mannitol dehydrogenase [isa: 0016616 ]
+0008926 = mannitol-1-phosphate 5-dehydrogenase [isa: 0016616 ]
+0004495 = mevaldate reductase [isa: 0016616 ]
+0019727 = mevaldate reductase (NAD) [isa: 0004495 ]
+0019726 = mevaldate reductase (NADPH) [isa: 0004495 ]
+0018455 = NADP-dependent alcohol dehydrogenase [isa: 0016616 ]
+0004552 = octanol dehydrogenase [isa: 0016616 ]
+0018457 = perillyl alcohol dehydrogenase [isa: 0016616 ]
+0004616 = phosphogluconate dehydrogenase (decarboxylating) [isa: 0016616 ]
+0004617 = phosphoglycerate dehydrogenase [isa: 0016616 ]
+0030266 = quinate 5-dehydrogenase [isa: 0016616 ]
+0004745 = retinol dehydrogenase [isa: 0016616 ]
+0004757 = sepiapterin reductase [isa: 0016616 ]
+0004764 = shikimate 5-dehydrogenase [isa: 0016616 ]
+0009010 = sorbitol-6-phosphate 2-dehydrogenase [isa: 0016616 ]
+0016229 = steroid dehydrogenase [isa: 0016616 ]
+0003845 = 11-beta-hydroxysteroid dehydrogenase [isa: 0016229 ]
+0030283 = 3(or 17)beta-hydroxysteroid dehydrogenase [isa: 0016229 ]
+0003854 = 3-beta-hydroxy-delta(5)-steroid dehydrogenase [isa: 0016229 ]
+0008709 = 7-alpha-hydroxysteroid dehydrogenase [isa: 0016229 ]
+0004303 = estradiol 17 beta-dehydrogenase [isa: 0016229 ]
+0009026 = tagaturonate reductase [isa: 0016616 ]
+0009027 = tartrate dehydrogenase [isa: 0016616 ]
+0003979 = UDP-glucose 6-dehydrogenase [isa: 0016616 ]
+0008762 = UDP-N-acetylmuramate dehydrogenase [isa: 0016616 ]
+0009040 = ureidoglycolate dehydrogenase [isa: 0016616 ]
+0004854 = xanthine dehydrogenase [isa: 0016616 ]
+0016902 = oxidoreductase, acting on the CH-OH group of donors, other acceptors [isa: 0016614 ]
+0018468 = alcohol dehydrogenase (acceptor) [isa: 0016902 ]
+0008812 = choline dehydrogenase [isa: 0016902 ]
+0008708 = glucose dehydrogenase [isa: 0016902 ]
+0004344 = glucose dehydrogenase (acceptor) [isa: 0008708 ]
+0008876 = glucose dehydrogenase (pyrroloquinoline-quinone) [isa: 0008708 ]
+0004368 = glycerol-3-phosphate dehydrogenase [isa: 0016902 ]
+0019154 = glycolate dehydrogenase [isa: 0016902 ]
+0018466 = limonene-1,2-diol dehydrogenase [isa: 0016902 ]
+0016899 = oxidoreductase, acting on the CH-OH group of donors, oxygen as acceptor [isa: 0016614 ]
+0003973 = (S)-2-hydroxy-acid oxidase [isa: 0016899 ]
+0016995 = cholesterol oxidase [isa: 0016899 ]
+0003885 = D-arabinono-1,4-lactone oxidase [isa: 0016899 ]
+0045480 = galactose oxidase [isa: 0016899 ]
+0046562 = glucose oxidase [isa: 0016899 ]
+0004369 = glycerol-3-phosphate oxidase [isa: 0016899 ]
+0008891 = glycolate oxidase [isa: 0016899 ]
+0046577 = long-chain-alcohol oxidase [isa: 0016899 ]
+0019157 = malate oxidase [isa: 0016899 ]
+0046563 = methanol oxidase [isa: 0016899 ]
+0018465 = vanillyl-alcohol oxidase [isa: 0016899 ]
+0004855 = xanthine oxidase [isa: 0016899 ]
+0016901 = oxidoreductase, acting on the CH-OH group of donors, quinone or similar compound as acceptor [isa: 0016614 ]
+0018446 = pinocarveol dehydrogenase [isa: 0016614 ]
+0042469 = versicolorin reductase [isa: 0016614 ]
+0016725 = oxidoreductase, acting on CH2 groups [isa: 0016491 ]
+0018693 = ethylbenzene dehydrogenase [isa: 0016725 ]
+0016728 = oxidoreductase, acting on CH2 groups, disulfide as acceptor [isa: 0016725 ]
+0004748 = ribonucleoside-diphosphate reductase [isa: 0016728 ]
+0016959 = class I ribonucleotide reductase [isa: 0004748 ]
+0016960 = class II ribonucleotide reductase [isa: 0004748 ]
+0016961 = class III ribonucleotide reductase [isa: 0004748 ]
+0008998 = ribonucleoside-triphosphate reductase [isa: 0016728 ]
+0016726 = oxidoreductase, acting on CH2 groups, NAD or NADP as acceptor [isa: 0016725 ]
+0016729 = oxidoreductase, acting on CH2 groups, other acceptors [isa: 0016725 ]
+0018695 = 4-cresol dehydrogenase [isa: 0016729 ]
+0018694 = p-cymene methyl hydroxylase [isa: 0016729 ]
+0016727 = oxidoreductase, acting on CH2 groups, oxygen as acceptor [isa: 0016725 ]
+0016679 = oxidoreductase, acting on diphenols and related substances as donors [isa: 0016491 ]
+0016681 = oxidoreductase, acting on diphenols and related substances as donors, cytochrome as acceptor [isa: 0016679 ]
+0008121 = ubiquinol-cytochrome c reductase [isa: 0015078 0015399 0016681 ]
+0016680 = oxidoreductase, acting on diphenols and related substances as donors, NAD or NADP as acceptor [isa: 0016679 ]
+0016683 = oxidoreductase, acting on diphenols and related substances as donors, other acceptors [isa: 0016679 ]
+0009496 = plastoquinol-plastocyanin reductase [isa: 0009492 0016683 ]
+0016682 = oxidoreductase, acting on diphenols and related substances as donors, oxygen as acceptor [isa: 0016679 ]
+0009916 = alternative oxidase [isa: 0016682 ]
+0004097 = catechol oxidase [isa: 0016682 ]
+0008447 = L-ascorbate oxidase [isa: 0016682 ]
+0008471 = laccase [isa: 0016682 ]
+0016675 = oxidoreductase, acting on heme group of donors [isa: 0016491 ]
+0016677 = oxidoreductase, acting on heme group of donors, nitrogenous group as acceptor [isa: 0016675 ]
+0016678 = oxidoreductase, acting on heme group of donors, other acceptors [isa: 0016675 ]
+0016676 = oxidoreductase, acting on heme group of donors, oxygen as acceptor [isa: 0016675 ]
+0016695 = oxidoreductase, acting on hydrogen as donor [isa: 0016491 ]
+0016697 = oxidoreductase, acting on hydrogen as donor, cytochrome as acceptor [isa: 0016695 ]
+0016699 = oxidoreductase, acting on hydrogen as donor, iron-sulfur protein as acceptor [isa: 0016695 ]
+0016696 = oxidoreductase, acting on hydrogen as donor, NAD or NADP as acceptor [isa: 0016695 ]
+0046407 = chlorophyll a oxygenase [isa: 0016696 ]
+0016700 = oxidoreductase, acting on hydrogen as donor, other acceptors [isa: 0016695 ]
+0045331 = coenzyme-M-7-mercaptoheptanoylthreonine-phosphate-heterodisulfide hydrogenase [isa: 0016700 ]
+0018552 = methyl-coenzyme-M reductase [isa: 0016700 ]
+0016730 = oxidoreductase, acting on iron-sulfur proteins as donors [isa: 0016491 ]
+0030385 = ferredoxin:thioredoxin reductase [isa: 0016730 ]
+0016732 = oxidoreductase, acting on reduced ferredoxin as donor, dinitrogen as acceptor [isa: 0016730 ]
+0018697 = carbonyl sulfide nitrogenase [isa: 0016732 ]
+0016163 = nitrogenase [isa: 0016732 ]
+0016733 = iron-iron nitrogenase [isa: 0016163 ]
+0016734 = molybdenum-iron nitrogenase [isa: 0016163 ]
+0016735 = vanadium-iron nitrogenase [isa: 0016163 ]
+0019110 = oxidoreductase, acting on reduced ferredoxin as donor, hydrogen ions as acceptor [isa: 0016730 ]
+0018696 = pyruvate:ferredoxin oxidoreductase [isa: 0019110 ]
+0016736 = oxidoreductase, acting on reduced ferredoxin as donor, hydrogen ions as acceptors [isa: 0016730 ]
+0008901 = hydrogenase [isa: 0016736 ]
+0016948 = iron hydrogenase [isa: 0008901 ]
+0016947 = N5,N10-methylenetetrahydromethanopterin dehydrogenase [isa: 0008901 ]
+0016949 = nickel hydrogenase [isa: 0008901 ]
+0016950 = nickel-iron hydrogenase [isa: 0016949 ]
+0016951 = nickel-iron-selenium hydrogenase [isa: 0016949 ]
+0016731 = oxidoreductase, acting on reduced ferredoxin as donor, NAD or NADP as acceptor [isa: 0016730 ]
+0008937 = ferredoxin reductase [isa: 0015933 0016731 ]
+0008860 = ferredoxin-NAD reductase [isa: 0008937 ]
+0004324 = ferredoxin-NADP reductase [isa: 0008937 ]
+0015039 = NADPH-adrenodoxin reductase [isa: 0008937 ]
+0015046 = rubredoxin reductase [isa: 0015933 0016731 ]
+0015044 = NADH:rubredoxin reductase [isa: 0015046 ]
+0015045 = NADPH:rubredoxin reductase [isa: 0015046 ]
+0016651 = oxidoreductase, acting on NADH or NADPH [isa: 0016491 ]
+0018538 = epoxide carboxylase [isa: 0016651 ]
+0016654 = oxidoreductase, acting on NADH or NADPH, disulfide as acceptor [isa: 0016651 ]
+0008785 = alkyl hydroperoxide reductase [isa: 0016654 ]
+0015042 = trypanothione reductase [isa: 0015933 0016654 ]
+0016658 = oxidoreductase, acting on NADH or NADPH, flavin as acceptor [isa: 0016651 ]
+0016653 = oxidoreductase, acting on NADH or NADPH, heme protein as acceptor [isa: 0016651 ]
+0016652 = oxidoreductase, acting on NADH or NADPH, NAD or NADP as acceptor [isa: 0016651 ]
+0004128 = cytochrome b5 reductase [isa: 0015933 0016652 ]
+0015043 = leghemoglobin reductase [isa: 0015933 0016652 ]
+0008746 = NAD(P)+ transhydrogenase [isa: 0016652 ]
+0008750 = NAD(P)+ transhydrogenase (AB-specific) [isa: 0008746 ]
+0003957 = NAD(P)+ transhydrogenase (B-specific) [isa: 0008746 0015078 0015399 ]
+0003958 = NADPH-ferrihemoprotein reductase [isa: 0015933 0016652 ]
+0016657 = oxidoreductase, acting on NADH or NADPH, nitrogenous group as acceptor [isa: 0016651 ]
+0018543 = 4-amino-2-nitroso-6-nitrotoluene reductase [isa: 0016657 ]
+0018544 = 4-carboxy-4'-sulfoazobenzene reductase [isa: 0016657 ]
+0003920 = GMP reductase [isa: 0016657 ]
+0018545 = NAD(P)H nitroreductase [isa: 0016657 ]
+0009703 = nitrate reductase (NADH) [isa: 0018545 ]
+0008942 = nitrite reductase [NAD(P)H2] [isa: 0016657 ]
+0018546 = nitrobenzene nitroreductase [isa: 0016657 ]
+0009033 = trimethylamine-N-oxide reductase [isa: 0016657 ]
+0016659 = oxidoreductase, acting on NADH or NADPH, other acceptor [isa: 0016651 ]
+0004155 = dihydropteridine reductase [isa: 0016659 ]
+0000293 = ferric-chelate reductase [isa: 0016659 ]
+0003955 = NAD(P)H dehydrogenase (quinone) [isa: 0016659 ]
+0003954 = NADH dehydrogenase [isa: 0015933 0016659 ]
+0003959 = NADPH dehydrogenase [isa: 0015933 0016659 ]
+0008753 = NADPH dehydrogenase (quinone) [isa: 0016659 ]
+0016655 = oxidoreductase, acting on NADH or NADPH, quinone or similar compound as acceptor [isa: 0016651 ]
+0018540 = hydroxybenzoquinone reductase [isa: 0016655 ]
+0016656 = monodehydroascorbate reductase (NADH) [isa: 0016655 ]
+0008137 = NADH dehydrogenase (ubiquinone) [isa: 0015078 0015081 0015399 0016655 ]
+0030024 = NADH:plastoquinone reductase [isa: 0016655 ]
+0003960 = NADPH:quinone reductase [isa: 0016655 ]
+0018541 = p-benzoquinone reductase (NADPH) [isa: 0016655 ]
+0016661 = oxidoreductase, acting on other nitrogenous compounds as donors [isa: 0016491 ]
+0016662 = oxidoreductase, acting on other nitrogenous compounds as donors, cytochrome as acceptor [isa: 0016661 ]
+0042279 = nitrite reductase (cytochrome, ammonia-forming) [isa: 0016662 ]
+0016664 = oxidoreductase, acting on other nitrogenous compounds as donors, iron-sulfur protein as acceptor [isa: 0016661 ]
+0016665 = oxidoreductase, acting on other nitrogenous compounds as donors, other acceptors [isa: 0016661 ]
+0008702 = 5,10-methylenetetrahydrofolate reductase (FADH) [isa: 0016665 ]
+0008940 = nitrate reductase [isa: 0016665 ]
+0016966 = nitric oxide reductase [isa: 0016665 ]
+0016967 = cytochrome bc nitric oxide reductase [isa: 0016966 ]
+0016666 = nitrite reductase [isa: 0016665 ]
+0018548 = pentaerythritol tetranitrate reductase [isa: 0016665 ]
+0016663 = oxidoreductase, acting on other nitrogenous compounds as donors, oxygen as acceptor [isa: 0016661 ]
+0018547 = nitroglycerin reductase [isa: 0016663 ]
+0004846 = urate oxidase [isa: 0016663 ]
+0016739 = oxidoreductase, acting on other substrates [isa: 0016491 ]
+0018702 = 1,1-dichloro-2,2-bis(4'-chlorophenyl)ethylene dehalogenase [isa: 0016739 ]
+0018705 = 1,2-dichloroethane reductive dehalogenase [isa: 0016739 ]
+0018703 = 2,4-dichlorophenoxyacetate dehalogenase [isa: 0016739 ]
+0018701 = 2,5-dichlorohydroquinone reductive dehalogenase [isa: 0016739 ]
+0018700 = 2-chloro-N-isopropylacetanilide reductive dehalogenase [isa: 0016739 ]
+0018704 = 5-chloro-2-hydroxymuconic semialdehyde dehalogenase [isa: 0016739 ]
+0008862 = formate acetyltransferase activating enzyme [isa: 0016739 ]
+0018706 = pyrogallol hydroxyltransferase [isa: 0016739 ]
+0009391 = ribonucleotide reductase activating enzyme [isa: 0016739 ]
+0018699 = trichloroethane reductive dehalogenase [isa: 0016739 ]
+0018698 = vinyl chloride reductive dehalogenase [isa: 0016739 ]
+0016705 = oxidoreductase, acting on paired donors, with incorporation or reduction of molecular oxygen [isa: 0016491 ]
+0018599 = 2-hydroxyisobutyrate 3-monooxygenase [isa: 0016705 ]
+0008681 = 2-octaprenyl-6-methoxyphenol hydroxylase [isa: 0016705 ]
+0018593 = 4-chlorophenoxyacetate monooxygenase [isa: 0016705 ]
+0018592 = 4-nitrocatechol 4-monooxygenase [isa: 0016705 ]
+0018601 = 4-nitrophenol 2-monooxygenase [isa: 0016705 ]
+0018600 = alpha-pinene dehydrogenase [isa: 0016705 ]
+0018595 = alpha-pinene monooxygenase [isa: 0016705 ]
+0018597 = ammonia monooxygenase [isa: 0016705 ]
+0018589 = di-n-butyltin dioxygenase [isa: 0016705 ]
+0018596 = dimethylsilanediol hydroxylase [isa: 0016705 ]
+0018585 = fluorene oxygenase [isa: 0016705 ]
+0018598 = hydroxymethylsilanetriol oxidase [isa: 0016705 ]
+0018591 = methyl tertiary butyl ether 3-monooxygenase [isa: 0016705 ]
+0018590 = methylsilanetriol hydroxylase [isa: 0016705 ]
+0018586 = mono-butyltin dioxygenase [isa: 0016705 ]
+0016706 = oxidoreductase, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors [isa: 0016705 ]
+0045442 = deacetoxycephalosporin C hydroxylase [isa: 0016706 ]
+0008336 = gamma-butyrobetaine,2-oxoglutarate dioxygenase [isa: 0016706 ]
+0045543 = gibberellin 2-beta-dioxygenase [isa: 0016706 ]
+0045544 = gibberellin 20-oxidase [isa: 0016706 ]
+0016707 = gibberellin 3-beta-dioxygenase [isa: 0016706 ]
+0045486 = naringenin 3-dioxygenase [isa: 0016706 ]
+0004597 = peptide-aspartate beta-dioxygenase [isa: 0016706 ]
+0008475 = procollagen-lysine 5-dioxygenase [isa: 0016706 ]
+0019798 = procollagen-proline dioxygenase [isa: 0016706 ]
+0019797 = procollagen-proline 3-dioxygenase [isa: 0019798 ]
+0004656 = procollagen-proline,2-oxoglutarate-4-dioxygenase [isa: 0019798 ]
+0016716 = oxidoreductase, acting on paired donors, with incorporation or reduction of molecular oxygen, another compound as one donor, and incorporation of one atom of oxygen [isa: 0016705 ]
+0016718 = oxidoreductase, acting on paired donors, with incorporation or reduction of molecular oxygen, miscellaneous [isa: 0016705 ]
+0018690 = 4-methoxybenzoate monooxygenase [isa: 0016718 ]
+0045300 = acyl-[acyl-carrier-protein] desaturase [isa: 0016717 0016718 ]
+0016719 = carotene 7,8-desaturase [isa: 0016718 ]
+0016215 = CoA desaturase [isa: 0016718 ]
+0017105 = acyl-CoA delta(11)-desaturase [isa: 0016215 ]
+0016213 = linoleoyl-CoA desaturase [isa: 0016215 ]
+0004768 = stearoyl-CoA desaturase [isa: 0016215 ]
+0016720 = D12-fatty acid dehydrogenase [isa: 0016718 ]
+0018688 = DDT 2,3-dioxygenase [isa: 0016718 ]
+0019135 = deoxyhypusine monooxygenase [isa: 0016718 ]
+0004392 = heme oxygenase (decyclizing) [isa: 0016718 ]
+0018689 = naphthalene disulfonate 1,2-dioxygenase [isa: 0016718 ]
+0042389 = omega-3 fatty acid desaturase [isa: 0016718 ]
+0045485 = omega-6 fatty acid desaturase [isa: 0016718 ]
+0004666 = prostaglandin-endoperoxide synthase [isa: 0016718 ]
+0016709 = oxidoreductase, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD or NADH as one donor, and incorporation of one atom of oxygen [isa: 0016705 ]
+0008688 = 3-(3-hydroxy-phenyl)propionate hydroxylase [isa: 0016709 ]
+0018471 = 4-chlorobenzaldehyde oxidase [isa: 0016709 ]
+0016711 = flavonoid 3'-monooxygenase [isa: 0016709 ]
+0019113 = limonene monooxygenase [isa: 0016709 ]
+0018587 = limonene 8-monooxygenase [isa: 0019113 ]
+0004517 = nitric oxide synthase [isa: 0016709 ]
+0016710 = trans-cinnamate 4-monooxygenase [isa: 0016709 ]
+0016708 = oxidoreductase, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD or NADH as one donor, and incorporation of two atoms of oxygen into one donor [isa: 0016705 ]
+0018608 = 1-indanone dioxygenase [isa: 0016708 ]
+0018607 = 1-indanone monooxygenase [isa: 0016708 ]
+0018627 = 2-aminobenzenesulfonate 2,3-dioxygenase [isa: 0016708 ]
+0018605 = 2-aminobenzenesulfonate dioxygenase [isa: 0016708 ]
+0018626 = 2-halobenzoate 1,2-dioxygenase [isa: 0016708 ]
+0018615 = 2-indanone monooxygenase [isa: 0016708 ]
+0018629 = 2-oxo-1,2-dihydroquinoline 5,6-dioxygenase [isa: 0016708 ]
+0008695 = 3-phenylpropionate dioxygenase [isa: 0016708 ]
+0018617 = 4-aminobenzenesulfonate 3,4-dioxygenase (deaminating) [isa: 0016708 ]
+0018604 = 4-aminobenzoate 3,4-dioxygenase (deaminating) [isa: 0016708 ]
+0018622 = 4-chlorophenylacetate 3,4-dioxygenase [isa: 0016708 ]
+0018621 = 4-sulfobenzoate 3,4-dioxygenase [isa: 0016708 ]
+0018613 = 9-fluorenone dioxygenase [isa: 0016708 ]
+0018618 = anthranilate 1,2-dioxygenase (deaminating, decarboxylating) [isa: 0016708 ]
+0018619 = benzene 1,2-dioxygenase [isa: 0016708 ]
+0018606 = benzenesulfonate dioxygenase [isa: 0016708 ]
+0018623 = benzoate 1,2-dioxygenase [isa: 0016708 ]
+0018687 = biphenyl 2,3-dioxygenase [isa: 0016708 ]
+0018609 = chlorobenzene dioxygenase [isa: 0016708 ]
+0018610 = dibenzofuran 4,4a-dioxygenase [isa: 0016708 ]
+0018612 = dibenzothiophene dioxygenase [isa: 0016708 ]
+0018614 = ethylbenzene dioxygenase [isa: 0016708 ]
+0018625 = naphthalene 1,2-dioxygenase [isa: 0016708 ]
+0008941 = nitric oxide dioxygenase [isa: 0016708 ]
+0018603 = nitrobenzene 1,2-dioxygenase [isa: 0016708 ]
+0018620 = phthalate 4,5-dioxygenase [isa: 0016708 ]
+0018628 = terephthalate 1,2-dioxygenase [isa: 0016708 ]
+0018611 = toluate dioxygenase [isa: 0016708 ]
+0018624 = toluene dioxygenase [isa: 0016708 ]
+0018616 = trihydroxytoluene dioxygenase [isa: 0016708 ]
+0016715 = oxidoreductase, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen [isa: 0016705 ]
+0016712 = oxidoreductase, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen [isa: 0016705 ]
+0016713 = oxidoreductase, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced iron-sulfur protein as one donor, and incorporation of one atom of oxygen [isa: 0016705 ]
+0019133 = choline monooxygenase [isa: 0016713 ]
+0016714 = oxidoreductase, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced pteridine as one donor, and incorporation of one atom of oxygen [isa: 0016705 ]
+0016717 = oxidoreductase, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water [isa: 0016705 ]
+0018594 = tert-butyl alcohol 2-monooxygenase [isa: 0016705 ]
+0018588 = tri-n-butyltin dioxygenase [isa: 0016705 ]
+0009540 = zeaxanthin epoxidase [isa: 0016705 ]
+0016684 = oxidoreductase, acting on peroxide as acceptor [isa: 0016491 ]
+0016694 = bacterial catalase-peroxidase [isa: 0016684 ]
+0004096 = catalase [isa: 0016684 ]
+0016952 = heme catalase [isa: 0004096 ]
+0016953 = manganese catalase [isa: 0004096 ]
+0004601 = peroxidase [isa: 0016684 ]
+0019806 = bromide peroxidase [isa: 0004601 ]
+0016691 = chloride peroxidase [isa: 0004601 ]
+0016956 = cofactor-free chloroperoxidase [isa: 0016691 ]
+0016958 = flavin-heme chloroperoxidase [isa: 0016691 ]
+0016955 = heme chloroperoxidase [isa: 0016691 ]
+0016957 = vanadium chloroperoxidase [isa: 0016691 ]
+0004130 = cytochrome c peroxidase [isa: 0004601 ]
+0016690 = diarylpropane peroxidase [isa: 0004601 ]
+0016685 = eosinophil peroxidase [isa: 0004601 ]
+0004602 = glutathione peroxidase [isa: 0004601 ]
+0016224 = non-selenium glutathione peroxidase [isa: 0004602 ]
+0004447 = iodide peroxidase [isa: 0004601 ]
+0016688 = L-ascorbate peroxidase [isa: 0004601 ]
+0016686 = lactoperoxidase [isa: 0004601 ]
+0016689 = manganese peroxidase [isa: 0004601 ]
+0016687 = myeloperoxidase [isa: 0004601 ]
+0016692 = NADH peroxidase [isa: 0004601 ]
+0016693 = secretory plant peroxidase [isa: 0004601 ]
+0009031 = thiol peroxidase [isa: 0004601 ]
+0008379 = thioredoxin peroxidase [isa: 0004601 ]
+0030613 = oxidoreductase, acting on phosphorus or arsenic in donors [isa: 0016491 ]
+0030614 = oxidoreductase, acting on phosphorus or arsenic in donors, with disulfide as acceptor [isa: 0030613 ]
+0016737 = oxidoreductase, acting on reduced flavodoxin as donor [isa: 0016491 ]
+0016738 = oxidoreductase, acting on reduced flavodoxin as donor, dinitrogen as acceptor [isa: 0016737 ]
+0016701 = oxidoreductase, acting on single donors with incorporation of molecular oxygen [isa: 0016491 ]
+0018554 = 1,2-dihydroxynaphthalene dioxygenase [isa: 0016701 ]
+0018553 = 3-(2,3-dihydroxyphenyl)propionate 1,2-dioxygenase [isa: 0016701 ]
+0016703 = oxidoreductase, acting on single donors with incorporation of molecular oxygen, incorporation of one atom of oxygen (internal monooxygenases or internal mixed function oxidases) [isa: 0016701 ]
+0016702 = oxidoreductase, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen [isa: 0016701 ]
+0018559 = 1,1-dichloro-2-(dihydroxy-4-chlorophenyl)-(4-chloropheny)lethylene 1,2-dioxygenase [isa: 0016702 ]
+0018566 = 1,2-dihydroxynaphthalene-6-sulfonate 1,8a-dioxygenase [isa: 0016702 ]
+0018582 = 1-hydroxy-2-naphthoate dioxygenase [isa: 0016702 ]
+0018561 = 2'-aminobiphenyl-2,3-diol 1,2-dioxygenase [isa: 0016702 ]
+0018556 = 2,2',3-trihydroxybiphenyl dioxygenase [isa: 0016702 ]
+0018542 = 2,3-dihydroxy DDT 1,2-dioxygenase [isa: 0016702 ]
+0018563 = 2,3-dihydroxy-ethylbenzene 1,2-dioxygenase [isa: 0016702 ]
+0018571 = 2,3-dihydroxy-p-cumate dioxygenase [isa: 0016702 ]
+0008669 = 2,3-dihydroxy-phenylpropionate 1,2-dioxygenase [isa: 0016702 ]
+0045133 = 2,3-dihydroxybenzoate 3,4-dioxygenase [isa: 0016702 ]
+0018583 = 2,3-dihydroxybiphenyl 1,2-dioxygenase [isa: 0016702 ]
+0018574 = 2,6-dichloro-p-hydroquinone 1,2-dioxygenase [isa: 0016702 ]
+0018573 = 2-aminophenol 1,6-dioxygenase [isa: 0016702 ]
+0018580 = 2-nitropropane dioxygenase [isa: 0016702 ]
+0018568 = 3,4-dihydroxyphenanthrene dioxygenase [isa: 0016702 ]
+0008687 = 3,4-dihydroxyphenyl-acetate 2,3-dioxygenase [isa: 0016702 ]
+0018572 = 3,5-dichlorocatechol 1,2-dioxygenase [isa: 0016702 ]
+0000334 = 3-hydroxyanthranilate 3,4-dioxygenase [isa: 0016702 ]
+0003868 = 4-hydroxyphenylpyruvate dioxygenase [isa: 0016702 ]
+0018558 = 5,6-dihydroxy-3-methyl-2-oxo-1,2-dihydroquinoline dioxygenase [isa: 0016702 ]
+0045549 = 9-cis-epoxycarotenoid dioxygenase [isa: 0016702 ]
+0004052 = arachidonate 12-lipoxygenase [isa: 0016702 ]
+0004051 = arachidonate 5-lipoxygenase [isa: 0016702 ]
+0003834 = beta-carotene 15,15'-dioxygenase [isa: 0016702 ]
+0018564 = carbazole 1,9a-dioxygenase [isa: 0016702 ]
+0019114 = catechol dioxygenase [isa: 0016702 ]
+0018576 = catechol 1,2-dioxygenase [isa: 0019114 ]
+0018577 = catechol 2,3-dioxygenase [isa: 0019114 ]
+0018575 = chlorocatechol 1,2-dioxygenase [isa: 0016702 ]
+0017172 = cysteine dioxygenase [isa: 0016702 ]
+0018565 = dihydroxydibenzothiophene dioxygenase [isa: 0016702 ]
+0019117 = dihydroxyfluorene dioxygenase [isa: 0016702 ]
+0018557 = 1,2-dihydroxyfluorene 1,1a-dioxygenase [isa: 0019117 ]
+0018562 = 3,4-dihydroxyfluorene 4,4a-dioxygenase [isa: 0019117 ]
+0004411 = homogentisate 1,2-dioxygenase [isa: 0016702 ]
+0018569 = hydroquinone 1,2-dioxygenase [isa: 0016702 ]
+0018581 = hydroxyquinol 1,2-dioxygenase [isa: 0016702 ]
+0004426 = indoleamine-pyrrole 2,3-dioxygenase [isa: 0016702 ]
+0016165 = lipoxygenase [isa: 0016702 ]
+0018570 = p-cumate 2,3-dioxygenase [isa: 0016702 ]
+0018555 = phenanthrene dioxygenase [isa: 0016702 ]
+0018578 = protocatechuate 3,4-dioxygenase [isa: 0016702 ]
+0018560 = protocatechuate 3,4-dioxygenase type II [isa: 0016702 ]
+0018579 = protocatechuate 4,5-dioxygenase [isa: 0016702 ]
+0008127 = quercetin 2,3-dioxygenase [isa: 0016702 ]
+0018567 = styrene dioxygenase [isa: 0016702 ]
+0004833 = tryptophan 2,3 dioxygenase [isa: 0016702 ]
+0016704 = oxidoreductase, acting on single donors with incorporation of molecular oxygen, miscellaneous [isa: 0016701 ]
+0018584 = 2,4,5-trichlorophenoxyacetic acid oxygenase [isa: 0016704 ]
+0016667 = oxidoreductase, acting on sulfur group of donors [isa: 0016491 ]
+0016669 = oxidoreductase, acting on sulfur group of donors, cytochrome as acceptor [isa: 0016667 ]
+0016671 = oxidoreductase, acting on sulfur group of donors, disulfide as acceptor [isa: 0016667 ]
+0000317 = methionine-S-oxide reductase [isa: 0016671 ]
+0004604 = phosphoadenylyl-sulfate reductase (thioredoxin) [isa: 0016671 ]
+0019153 = protein-disulfide reductase (glutathione) [isa: 0016671 ]
+0000318 = protein-methionine-R-oxide reductase [isa: 0016671 ]
+0008113 = protein-methionine-S-oxide reductase [isa: 0016671 ]
+0016673 = oxidoreductase, acting on sulfur group of donors, iron-sulfur protein as acceptor [isa: 0016667 ]
+0016668 = oxidoreductase, acting on sulfur group of donors, NAD or NADP as acceptor [isa: 0016667 ]
+0004148 = dihydrolipoamide dehydrogenase [isa: 0015933 0016668 ]
+0004783 = sulfite reductase (NADPH) [isa: 0015933 0016668 ]
+0016674 = oxidoreductase, acting on sulfur group of donors, other acceptors [isa: 0016667 ]
+0009389 = dimethyl sulfoxide reductase [isa: 0016674 ]
+0018551 = dissimilatory sulfite reductase [isa: 0016674 ]
+0016002 = sulfite reductase [isa: 0016674 ]
+0018550 = tetrachloro-p-hyrodoquinone reductive dehalogenase [isa: 0016674 ]
+0016670 = oxidoreductase, acting on sulfur group of donors, oxygen as acceptor [isa: 0016667 ]
+0018549 = methanethiol oxidase [isa: 0016670 ]
+0008482 = sulfite oxidase [isa: 0016670 ]
+0016672 = oxidoreductase, acting on sulfur group of donors, quinone or similar compound as acceptor [isa: 0016667 ]
+0016721 = oxidoreductase, acting on superoxide radicals as acceptor [isa: 0016491 ]
+0004784 = superoxide dismutase [isa: 0016721 ]
+0004785 = copper, zinc superoxide dismutase [isa: 0004784 ]
+0008382 = iron superoxide dismutase [isa: 0004784 ]
+0008383 = manganese superoxide dismutase [isa: 0004784 ]
+0016954 = nickel superoxide dismutase [isa: 0004784 ]
+0016903 = oxidoreductase, acting on the aldehyde or oxo group of donors [isa: 0016491 ]
+0018470 = 4-hydroxybutaraldehyde dehydrogenase [isa: 0016903 ]
+0018469 = myrtenal dehydrogenase [isa: 0016903 ]
+0016622 = oxidoreductase, acting on the aldehyde or oxo group of donors, cytochrome as acceptor [isa: 0016903 ]
+0008805 = carbon monoxide oxygenase [isa: 0016622 ]
+0008985 = pyruvate dehydrogenase (cytochrome) [isa: 0004738 0016622 ]
+0016624 = oxidoreductase, acting on the aldehyde or oxo group of donors, disulfide as acceptor [isa: 0016903 ]
+0003863 = 3-methyl-2-oxobutanoate dehydrogenase (lipoamide) [isa: 0016624 ]
+0004591 = oxoglutarate dehydrogenase (lipoamide) [isa: 0016624 ]
+0004739 = pyruvate dehydrogenase (lipoamide) [isa: 0004738 0016624 ]
+0016625 = oxidoreductase, acting on the aldehyde or oxo group of donors, iron-sulfur protein as acceptor [isa: 0016903 ]
+0019164 = pyruvate synthase [isa: 0016625 ]
+0016620 = oxidoreductase, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor [isa: 0016903 ]
+0018472 = 1-hydroxy-2-naphthaldehyde dehydrogenase [isa: 0016620 ]
+0018474 = 2-carboxybenzaldehyde dehydrogenase [isa: 0016620 ]
+0018491 = 2-oxobutyrate synthase [isa: 0016620 ]
+0018482 = 4-formylbenzenesulfonate dehydrogenase [isa: 0016620 ]
+0018481 = 4-hydroxymuconic semialdehyde dehydrogenase [isa: 0016620 ]
+0018480 = 5-carboxymethyl-2-hydroxymuconic semialdehyde dehydrogenase [isa: 0016620 ]
+0018483 = 6-oxohexanoate dehydrogenase [isa: 0016620 ]
+0008774 = acetaldehyde dehydrogenase (acetylating) [isa: 0016620 ]
+0004028 = aldehyde dehydrogenase [isa: 0016620 ]
+0004030 = aldehyde dehydrogenase (NAD(P)+) [isa: 0004028 ]
+0004029 = aldehyde dehydrogenase (NAD+) [isa: 0004028 ]
+0004043 = aminoadipate-semialdehyde dehydrogenase [isa: 0016620 ]
+0019145 = aminobutyraldehyde dehydrogenase [isa: 0016620 ]
+0019108 = arylaldehyde dehydrogenase [isa: 0016620 ]
+0004073 = aspartate-semialdehyde dehydrogenase [isa: 0016620 ]
+0019115 = benzaldehyde dehydrogenase [isa: 0016620 ]
+0018479 = benzaldehyde dehydrogenase (NAD+) [isa: 0019115 ]
+0018477 = benzaldehyde dehydrogenase (NADP+) [isa: 0019115 ]
+0008802 = betaine-aldehyde dehydrogenase [isa: 0016620 ]
+0016621 = cinnamoyl-CoA reductase [isa: 0016620 ]
+0018473 = cis-2-methyl-5-isopropylhexa-2,5-dienal dehydrogenase [isa: 0016620 ]
+0048001 = erythrose-4-phosphate dehydrogenase [isa: 0016620 ]
+0004327 = formaldehyde dehydrogenase (glutathione) [isa: 0016620 ]
+0008863 = formate dehydrogenase [isa: 0016620 ]
+0004350 = glutamate-5-semialdehyde dehydrogenase [isa: 0016620 ]
+0008883 = glutamyl tRNA reductase [isa: 0016620 ]
+0018467 = glutathione-independent formaldehyde dehydrogenase [isa: 0016620 ]
+0008943 = glyceraldehyde 3-phosphate dehydrogenase [isa: 0016620 ]
+0004365 = glyceraldehyde 3-phosphate dehydrogenase (phosphorylating) [isa: 0008943 ]
+0008886 = glyceraldehyde-3-phosphate dehydrogenase (NADP+) [isa: 0008943 ]
+0008911 = lactaldehyde dehydrogenase [isa: 0016620 ]
+0018478 = malonate semialdehyde dehydrogenase [isa: 0016620 ]
+0004491 = methylmalonate-semialdehyde dehydrogenase (acylating) [isa: 0016620 ]
+0003942 = N-acetyl-gamma-glutamyl-phosphate reductase [isa: 0016620 ]
+0018484 = p-hydroxybenzaldehyde dehydrogenase [isa: 0016620 ]
+0008957 = phenylacetaldehyde dehydrogenase [isa: 0016620 ]
+0018485 = salicylaldehyde dehydrogenase [isa: 0016620 ]
+0004777 = succinate-semialdehyde dehydrogenase [isa: 0016620 ]
+0009013 = succinate-semialdehyde dehydrogenase (NAD(P)+) [isa: 0016620 ]
+0018475 = trans-2-methyl-5-isopropylhexa-2,5-dienal dehydrogenase [isa: 0016620 ]
+0016626 = oxidoreductase, acting on the aldehyde or oxo group of donors, other acceptors [isa: 0016903 ]
+0018492 = carbon monoxide dehydrogenase [isa: 0016626 ]
+0018493 = formylmethanofuran dehydrogenase [isa: 0016626 ]
+0016623 = oxidoreductase, acting on the aldehyde or oxo group of donors, oxygen as acceptor [isa: 0016903 ]
+0018486 = 2-butanone oxidase [isa: 0016623 ]
+0018490 = 4-hydroxyphenylpyruvate oxidase [isa: 0016623 ]
+0004031 = aldehyde oxidase [isa: 0016623 ]
+0018488 = arylaldehyde oxidase [isa: 0016623 ]
+0004732 = pyridoxal oxidase [isa: 0016623 ]
+0018489 = vanillate demethylase (aerobic) [isa: 0016623 ]
+0018487 = vanillate O-demethylase (anaerobic) [isa: 0016623 ]
+0004738 = pyruvate dehydrogenase [isa: 0016903 ]
+0016627 = oxidoreductase, acting on the CH-CH group of donors [isa: 0016491 ]
+0018497 = 1-chloro-2,2-bis(4'-chlorophenyl)ethane dehydrogenase [isa: 0016627 ]
+0018496 = 2,6-dihydroxycyclohexane-1-carboxyl-CoA dehydrogenase [isa: 0016627 ]
+0018495 = 2-hydroxycyclohexane-1-carboxyl-CoA dehydrogenase [isa: 0016627 ]
+0000248 = C-5 sterol desaturase [isa: 0016627 ]
+0018494 = carvone reductase [isa: 0016627 ]
+0016632 = oxidoreductase, acting on the CH-CH group of donors, cytochrome as acceptor [isa: 0016627 ]
+0016633 = galactonolactone dehydrogenase [isa: 0016632 ]
+0016636 = oxidoreductase, acting on the CH-CH group of donors, iron-sulfur protein as acceptor [isa: 0016627 ]
+0016628 = oxidoreductase, acting on the CH-CH group of donors, NAD or NADP as acceptor [isa: 0016627 ]
+0018505 = 1,2-dihydroxy-1,2-dihydroxynaphthalene dehydrogenase [isa: 0016628 ]
+0018521 = 1,2-dihydroxy-6-methylcyclohexa-3,5-dienecarboxylate dehydrogenase [isa: 0016628 ]
+0018512 = 1,6-dihydroxy-5-methylcyclohexa-2,4-dienecarboxylate dehydrogenase [isa: 0016628 ]
+0016629 = 12-oxophytodienoate reductase [isa: 0016628 ]
+0008667 = 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase [isa: 0016628 ]
+0018509 = 2,3-dihydro-2,3-dihydroxybiphenyl dehydrogenase [isa: 0016628 ]
+0018511 = 2,3-dihydroxy-2,3-dihydro-p-cumate dehydrogenase [isa: 0016628 ]
+0018498 = 2,3-dihydroxy-2,3-dihydro-phenylpropionate dehydrogenase [isa: 0016628 ]
+0018516 = 2,4-dichlorobenzoyl-CoA reductase [isa: 0016628 ]
+0008670 = 2,4-dienoyl-CoA reductase (NADPH) [isa: 0016628 ]
+0018502 = 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase [isa: 0016628 ]
+0018520 = 4-methylcyclohexa-3,5-diene-1,2-cis-diol-1-carboxylic acid dehydrogenase [isa: 0016628 ]
+0018518 = 5,6-dihydroxy-3-methyl-2-oxo-1,2,5,6-tetrahydroquinoline dehydrogenase [isa: 0016628 ]
+0004074 = biliverdin reductase [isa: 0016628 ]
+0018504 = cis-1,2-dihydrobenzene-1,2-diol dehydrogenase [isa: 0016628 ]
+0018508 = cis-1,2-dihydroxycyclohexa-3,5-diene-1-carboxylate dehydrogenase [isa: 0016628 ]
+0018499 = cis-2,3-dihydrodiol DDT dehydrogenase [isa: 0016628 ]
+0018507 = cis-3,4-dihydroxy-3,4-dihydrophenanthrene dehydrogenase [isa: 0016628 ]
+0018501 = cis-chlorobenzene dihydrodiol dehydrogenase [isa: 0016628 ]
+0018519 = cis-dihydroethylcatechol dehydrogenase [isa: 0016628 ]
+0018513 = dibenzothiophene dihydrodiol dehydrogenase [isa: 0016628 ]
+0008839 = dihydrodipicolinate reductase [isa: 0016628 ]
+0017113 = dihydropyrimidine dehydrogenase [isa: 0016628 ]
+0004159 = dihydrouracil dehydrogenase (NAD+) [isa: 0016628 ]
+0016631 = enoyl-[acyl-carrier protein] reductase [isa: 0016628 ]
+0004318 = enoyl-[acyl-carrier protein] reductase (NADH) [isa: 0004312 0016631 ]
+0004319 = enoyl-[acyl-carrier protein] reductase (NADPH, B-specific) [isa: 0004312 0016631 ]
+0016156 = fumarate reductase (NADH) [isa: 0016628 ]
+0018506 = maleylacetate reductase [isa: 0016628 ]
+0004589 = orotate reductase (NADH) [isa: 0016628 ]
+0018510 = phloroglucinol reductase [isa: 0016628 ]
+0018517 = phthalate 4,5-cis-dihydrodiol dehydrogenase [isa: 0016628 ]
+0018515 = pimeloyl-CoA dehydrogenase [isa: 0016628 ]
+0016994 = precorrin-6X reductase [isa: 0016628 ]
+0008977 = prephenate dehydrogenase [isa: 0016628 ]
+0004665 = prephenate dehydrogenase (NADP+) [isa: 0016628 ]
+0016630 = protochlorophyllide reductase [isa: 0016628 ]
+0000246 = sterol C-24(28) reductase [isa: 0016628 ]
+0018514 = terephthalate 1,2-cis-dihydrodiol dehydrogenase [isa: 0016628 ]
+0018503 = trans-1,2-dihydrodiolphenanthrene dehydrogenase [isa: 0016628 ]
+0019166 = trans-2-enoyl-CoA reductase (NADPH) [isa: 0016628 ]
+0018500 = trans-9R,10R-dihydrodiolphenanthrene dehydrogenase [isa: 0016628 ]
+0016637 = oxidoreductase, acting on the CH-CH group of donors, other acceptors [isa: 0016627 ]
+0003865 = 3-oxo-5-alpha-steroid 4-dehydrogenase [isa: 0016637 ]
+0003995 = acyl-CoA dehydrogenase [isa: 0016637 ]
+0003853 = 2-methylacyl-CoA dehydrogenase [isa: 0003995 ]
+0004085 = butyryl-CoA dehydrogenase [isa: 0003995 ]
+0004361 = glutaryl-CoA dehydrogenase [isa: 0003995 ]
+0008470 = isovaleryl-CoA dehydrogenase [isa: 0003995 ]
+0004466 = long-chain acyl-CoA dehydrogenase [isa: 0003995 ]
+0016937 = short branched-chain acyl-CoA dehydrogenase [isa: 0003995 ]
+0017099 = very long-chain acyl-CoA dehydrogenase [isa: 0003995 ]
+0019109 = acyl-CoA reductase [isa: 0016637 ]
+0018525 = 4-hydroxybenzoyl-CoA reductase [isa: 0019109 ]
+0018522 = benzoyl-CoA reductase [isa: 0019109 ]
+0004152 = dihydroorotate dehydrogenase [isa: 0016637 ]
+0045431 = flavonol synthase [isa: 0016637 ]
+0018523 = quinoline 2-oxidoreductase [isa: 0016637 ]
+0000104 = succinate dehydrogenase [isa: 0016637 ]
+0016634 = oxidoreductase, acting on the CH-CH group of donors, oxygen as acceptor [isa: 0016627 ]
+0003997 = acyl-CoA oxidase [isa: 0016634 ]
+0016401 = palmitoyl-CoA oxidase [isa: 0003997 ]
+0016402 = pristanoyl-CoA oxidase [isa: 0003997 ]
+0004109 = coproporphyrinogen oxidase [isa: 0016634 ]
+0004158 = dihydroorotate oxidase [isa: 0016634 ]
+0004729 = protoporphyrinogen oxidase [isa: 0016634 ]
+0016635 = oxidoreductase, acting on the CH-CH group of donors, quinone or related compound as acceptor [isa: 0016627 ]
+0019737 = quinol:fumarate oxidoreductase [isa: 0016635 ]
+0008177 = succinate dehydrogenase (ubiquinone) [isa: 0016635 ]
+0018129 = peptidyl-oxazoline dehydrogenase [isa: 0016627 ]
+0018136 = peptidyl-thiazoline dehydrogenase [isa: 0016627 ]
+0009917 = sterol 5-alpha reductase [isa: 0016627 ]
+0009918 = sterol delta-7 reductase [isa: 0016627 ]
+0016645 = oxidoreductase, acting on the CH-NH group of donors [isa: 0016491 ]
+0018528 = iminodiacetate dehydrogenase [isa: 0016645 ]
+0016648 = oxidoreductase, acting on the CH-NH group of donors, disulfide as acceptor [isa: 0016645 ]
+0004734 = pyrimidodiazepine synthase [isa: 0016648 ]
+0016646 = oxidoreductase, acting on the CH-NH group of donors, NAD or NADP as acceptor [isa: 0016645 ]
+0003842 = 1-pyrroline-5-carboxylate dehydrogenase [isa: 0016646 ]
+0004146 = dihydrofolate reductase [isa: 0016646 ]
+0016155 = formyltetrahydrofolate dehydrogenase [isa: 0016646 ]
+0004486 = methylenetetrahydrofolate dehydrogenase [isa: 0016646 ]
+0004487 = methylenetetrahydrofolate dehydrogenase (NAD+) [isa: 0004486 ]
+0004488 = methylenetetrahydrofolate dehydrogenase (NADP+) [isa: 0004486 ]
+0004489 = methylenetetrahydrofolate reductase (NADPH) [isa: 0016646 ]
+0008752 = NAD(P)H dehydrogenase (FMN) [isa: 0016646 ]
+0018529 = nitrilotriacetate monooxygenase [isa: 0016646 ]
+0004735 = pyrroline 5-carboxylate reductase [isa: 0016646 ]
+0004753 = saccharopine dehydrogenase [isa: 0016646 ]
+0004754 = saccharopine dehydrogenase (NAD+, L-lysine forming) [isa: 0004753 ]
+0004755 = saccharopine dehydrogenase (NADP+, L-glutamate forming) [isa: 0004753 ]
+0016650 = oxidoreductase, acting on the CH-NH group of donors, other acceptors [isa: 0016645 ]
+0018537 = coenzyme F420-dependent N5,N10-methylenetetrahydromethanopterin reductase [isa: 0016650 ]
+0019139 = cytokinin dehydrogenase [isa: 0016650 ]
+0018532 = F433 independent 5,10-methenyl-5,6,7,8-tetrahydromethanopterin dehydrogenase [isa: 0016650 ]
+0030268 = methylenetetrahydromethanopterin dehydrogenase [isa: 0016650 ]
+0018535 = nicotine dehydrogenase [isa: 0016650 ]
+0018534 = nitrilotriacetate dehydrogenase [isa: 0016650 ]
+0004657 = proline dehydrogenase [isa: 0016650 ]
+0008480 = sarcosine dehydrogenase [isa: 0016650 ]
+0016647 = oxidoreductase, acting on the CH-NH group of donors, oxygen as acceptor [isa: 0016645 ]
+0046420 = cytokinin oxidase [isa: 0016647 ]
+0019116 = hydroxy-nicotine oxidase [isa: 0016647 ]
+0018530 = 6-hydroxy-D-nicotine oxidase [isa: 0019116 ]
+0018531 = 6-hydroxy-L-nicotine oxidase [isa: 0019116 ]
+0046592 = polyamine oxidase [isa: 0016647 ]
+0008115 = sarcosine oxidase [isa: 0016647 ]
+0016649 = oxidoreductase, acting on the CH-NH group of donors, quinone or similar compound as acceptor [isa: 0016645 ]
+0004174 = electron-transferring-flavoprotein dehydrogenase [isa: 0016649 ]
+0016638 = oxidoreductase, acting on the CH-NH2 group of donors [isa: 0016491 ]
+0018526 = 2-aminobenzoyl-CoA reductase [isa: 0016638 ]
+0000286 = alanine dehydrogenase [isa: 0016638 ]
+0015930 = glutamate synthase [isa: 0016638 ]
+0016041 = glutamate synthase (ferredoxin) [isa: 0015930 0016643 ]
+0045181 = glutamate synthase, NADH or NADPH as acceptor [isa: 0015930 ]
+0016040 = glutamate synthase (NADH) [isa: 0016639 0045181 ]
+0004355 = glutamate synthase (NADPH) [isa: 0016639 0045181 ]
+0016640 = oxidoreductase, acting on the CH-NH2 group of donors, cytochrome as acceptor [isa: 0016638 ]
+0016642 = oxidoreductase, acting on the CH-NH2 group of donors, disulfide as acceptor [isa: 0016638 ]
+0004375 = glycine dehydrogenase (decarboxylating) [isa: 0016642 ]
+0016643 = oxidoreductase, acting on the CH-NH2 group of donors, iron-sulfur protein as acceptor [isa: 0016638 ]
+0016639 = oxidoreductase, acting on the CH-NH2 group of donors, NAD or NADP as acceptor [isa: 0016638 ]
+0004352 = glutamate dehydrogenase [isa: 0016639 ]
+0004353 = glutamate dehydrogenase (NAD(P)+) [isa: 0016639 ]
+0004354 = glutamate dehydrogenase (NADP+) [isa: 0016639 ]
+0016644 = oxidoreductase, acting on the CH-NH2 group of donors, other acceptors [isa: 0016638 ]
+0030058 = amine dehydrogenase [isa: 0016644 ]
+0030059 = aralkylamine dehydrogenase [isa: 0016644 ]
+0016641 = oxidoreductase, acting on the CH-NH2 group of donors, oxygen as acceptor [isa: 0016638 ]
+0009815 = 1-aminocyclopropane-1-carboxylate oxidase [isa: 0016641 ]
+0008131 = amine oxidase [isa: 0016641 ]
+0008122 = amine oxidase (copper-containing) [isa: 0008131 ]
+0004041 = amine oxidase (flavin-containing) [isa: 0008131 ]
+0015922 = aspartate oxidase [isa: 0016641 ]
+0008445 = D-aspartate oxidase [isa: 0015922 ]
+0008734 = L-aspartate oxidase [isa: 0015922 ]
+0018527 = cyclohexylamine oxidase [isa: 0016641 ]
+0008718 = D-amino acid dehydrogenase [isa: 0016641 ]
+0003884 = D-amino acid oxidase [isa: 0016641 ]
+0001716 = L-amino acid oxidase [isa: 0016641 ]
+0004720 = protein-lysine 6-oxidase [isa: 0016641 ]
+0004733 = pyridoxamine-phosphate oxidase [isa: 0016641 ]
+0016722 = oxidoreductase, oxidizing metal ions [isa: 0016491 ]
+0018691 = arsenite oxidase [isa: 0016722 ]
+0016723 = oxidoreductase, oxidizing metal ions, NAD or NADP as acceptor [isa: 0016722 ]
+0008823 = cupric reductase [isa: 0016723 ]
+0016152 = mercury (II) reductase [isa: 0016723 ]
+0016724 = oxidoreductase, oxidizing metal ions, oxygen as acceptor [isa: 0016722 ]
+0004322 = ferroxidase [isa: 0016724 ]
+0004323 = multicopper ferroxidase iron transport mediator [isa: 0004322 0016033 ]
+0015048 = phthalate dioxygenase reductase [isa: 0015933 0016491 ]
+0016166 = phytoene dehydrogenase [isa: 0016491 ]
+0000170 = sphingosine hydroxylase [isa: 0016491 ]
+0016972 = sulfhydryl oxidase [isa: 0016491 ]
+0016971 = flavin-linked sulfhydryl oxidase [isa: 0016972 ]
+0019174 = tetrahydrothiophene 1-oxide reductase [isa: 0016491 ]
+0045301 = tRNA-(2-methylthio-N-6-(cis-hydroxy)isopentenyl adenosine)-hydroxylase [isa: 0016491 ]
+0004836 = tyramine-beta hydroxylase [isa: 0016491 ]
+0046422 = violaxanthin de-epoxidase [isa: 0016491 ]
+0030343 = vitamin D3 25-hydroxylase [isa: 0016491 ]
+0008149 = para-aminobenzoic acid (PABA) synthase [isa: 0003824 ]
+0008954 = peptidoglycan synthetase [isa: 0003824 ]
+0016302 = phosphatase [isa: 0003824 ]
+0019203 = carbohydrate phosphatase [isa: 0016302 ]
+0019204 = nucleotide phosphatase [isa: 0016302 ]
+0019173 = pyrimidine phosphatase [isa: 0016302 ]
+0004649 = poly(ADP-ribose) glycohydrolase [isa: 0003824 ]
+0016218 = polyketide synthase [isa: 0003824 ]
+0008987 = quinolinate synthase [isa: 0003824 ]
+0003969 = RNA editase [isa: 0003824 ]
+0003971 = double-stranded RNA specific editase [isa: 0003969 ]
+0009006 = siroheme synthase [isa: 0003824 ]
+0008641 = small protein activating enzyme [isa: 0003824 ]
+0004839 = ubiquitin activating enzyme [isa: 0008641 ]
+0008642 = ubiquitin-like activating enzyme [isa: 0008641 ]
+0019778 = APG12 activating enzyme [isa: 0008642 ]
+0019779 = APG8 activating enzyme [isa: 0008642 ]
+0019780 = FAT10 activating enzyme [isa: 0008642 ]
+0042293 = Hub1 activating enzyme [isa: 0008642 ]
+0019782 = ISG15 activating enzyme [isa: 0008642 ]
+0019781 = RUB1 activating enzyme [isa: 0008642 ]
+0019948 = SUMO activating enzyme [isa: 0008642 ]
+0042292 = URM1 activating enzyme [isa: 0008642 ]
+0008639 = small protein conjugating enzyme [isa: 0003824 ]
+0004840 = ubiquitin conjugating enzyme [isa: 0008639 ]
+0008640 = ubiquitin-like conjugating enzyme [isa: 0008639 ]
+0019777 = APG12 conjugating enzyme [isa: 0008640 ]
+0019776 = APG8 conjugating enzyme [isa: 0008640 ]
+0019775 = FAT10 conjugating enzyme [isa: 0008640 ]
+0042295 = Hub1 conjugating enzyme [isa: 0008640 ]
+0042296 = ISG15 conjugating enzyme [isa: 0008640 ]
+0016976 = NEDD8 conjugating enzyme [isa: 0008640 ]
+0019949 = SUMO conjugating enzyme [isa: 0008640 ]
+0042294 = URM1 conjugating enzyme [isa: 0008640 ]
+0042284 = sphingolipid delta-4 desaturase [isa: 0003824 ]
+0004770 = sterol carrier protein X-related thiolase [isa: 0003824 ]
+0016740 = transferase [isa: 0003824 ]
+0008665 = 2'-phosphotransferase [isa: 0016740 ]
+0008414 = CDP-alcohol phosphotransferase [isa: 0016740 ]
+0008820 = cobinamide phosphate guanylyltransferase [isa: 0016740 ]
+0004172 = ecdysteroid UDP-glucosyl/UDP glucuronosyl transferase [isa: 0016740 ]
+0042123 = glucanosyltransferase [isa: 0016740 ]
+0042124 = 1,3-beta-glucanosyltransferase [isa: 0042123 ]
+0008913 = lauroyl transferase [isa: 0016740 ]
+0017118 = lipoyltransferase [isa: 0016740 ]
+0000031 = mannosylphosphate transferase [isa: 0016740 ]
+0008958 = phosphopantetheinyltransferase [isa: 0016740 ]
+0016746 = transferase, transferring acyl groups [isa: 0016740 ]
+0016755 = transferase, transferring amino-acyl groups [isa: 0016746 ]
+0042172 = arginyl-tRNA-protein transferase [isa: 0016755 ]
+0004057 = arginyltransferase [isa: 0016755 ]
+0003840 = gamma-glutamyl transferase [isa: 0016755 ]
+0003839 = gamma-glutamylcyclotransferase [isa: 0016755 ]
+0016603 = glutaminyl-peptide cyclotransferase [isa: 0016755 ]
+0016756 = glutathione gamma-glutamylcysteinyltransferase [isa: 0016755 ]
+0008914 = leucyltransferase [isa: 0016755 ]
+0000048 = peptidyltransferase [isa: 0016755 ]
+0016747 = transferase, transferring groups other than amino-acyl groups [isa: 0016746 ]
+0018712 = 3-hydroxybutyryl-CoA thiolase [isa: 0016747 ]
+0018713 = 3-ketopimelyl-CoA thiolase [isa: 0016747 ]
+0003870 = 5-aminolevulinate synthase [isa: 0016747 ]
+0008710 = 8-amino-7-oxononanoate synthase [isa: 0016747 ]
+0042319 = acyl-coenzyme A:6-aminopenicillanic-acid-acyltransferase [isa: 0016747 ]
+0008415 = acyltransferase [isa: 0016747 ]
+0016407 = acetyltransferase [isa: 0008415 ]
+0016453 = C-acetyltransferase [isa: 0003988 0016407 ]
+0003985 = acetyl-CoA C-acetyltransferase [isa: 0016453 ]
+0008861 = formate C-acetyltransferase [isa: 0016453 ]
+0008890 = glycine C-acetyltransferase [isa: 0016453 ]
+0019180 = dTDP-fucosamine acetyltransferase [isa: 0016407 ]
+0004402 = histone acetyltransferase [isa: 0016407 ]
+0004405 = H2A/H2B histone acetyltransferase [isa: 0004402 ]
+0004406 = H3/H4 histone acetyltransferase [isa: 0004402 ]
+0004468 = lysine acetyltransferase [isa: 0016407 ]
+0008080 = N-acetyltransferase [isa: 0016407 0016410 ]
+0004042 = amino acid N-acetyltransferase [isa: 0008080 ]
+0004059 = arylalkylamine N-acetyltransferase [isa: 0008080 ]
+0004060 = arylamine N-acetyltransferase [isa: 0008080 ]
+0017188 = aspartate N-acetyltransferase [isa: 0008080 ]
+0004145 = diamine N-acetyltransferase [isa: 0008080 ]
+0016991 = gentamicin 3'-N-acetyltransferase [isa: 0008080 ]
+0019134 = glucosamine-1-phosphate N-acetyltransferase [isa: 0008080 ]
+0004343 = glucosamine-phosphate N-acetyltransferase [isa: 0008080 ]
+0004358 = glutamate N-acetyltransferase [isa: 0008080 ]
+0015019 = heparan-alpha-glucosaminide N-acetyltransferase [isa: 0008080 ]
+0004596 = peptide alpha-N-acetyltransferase [isa: 0008080 ]
+0008999 = ribosomal-protein-alanine N-acetyltransferase [isa: 0004596 ]
+0019799 = tubulin N-acetyltransferase [isa: 0004596 ]
+0046027 = phospholipid:diacylglycerol acyltransferase [isa: 0008080 ]
+0016413 = O-acetyltransferase [isa: 0008374 0016407 ]
+0004026 = alcohol O-acetyltransferase [isa: 0016413 ]
+0004092 = carnitine O-acetyltransferase [isa: 0016406 0016413 ]
+0004093 = carnitine O-acetyltransferase I [isa: 0004092 ]
+0004094 = carnitine O-acetyltransferase II [isa: 0004092 ]
+0008811 = chloramphenicol O-acetyltransferase [isa: 0016413 ]
+0004102 = choline O-acetyltransferase [isa: 0016413 ]
+0008870 = galactoside O-acetyltransferase [isa: 0016413 ]
+0016287 = glycerone-phosphate O-acyltransferase [isa: 0016413 ]
+0004414 = homoserine O-acetyltransferase [isa: 0016413 ]
+0008925 = maltose O-acetyltransferase [isa: 0016413 ]
+0009001 = serine O-acetyltransferase [isa: 0016412 0016413 ]
+0008959 = phosphate acetyltransferase [isa: 0016407 ]
+0016418 = S-acetyltransferase [isa: 0016407 0016417 ]
+0004742 = dihydrolipoamide S-acetyltransferase [isa: 0016418 0030523 ]
+0004313 = [acyl-carrier protein] S-acetyltransferase [isa: 0004312 0016418 ]
+0016408 = C-acyltransferase [isa: 0008415 ]
+0003988 = acetyl-CoA C-acyltransferase [isa: 0016408 ]
+0016454 = C-palmitoyltransferase [isa: 0016408 0016409 ]
+0004758 = serine C-palmitoyltransferase [isa: 0016454 ]
+0004312 = fatty-acid synthase [isa: 0008415 ]
+0004315 = 3-oxoacyl-[acyl-carrier protein] synthase [isa: 0004312 ]
+0009922 = fatty acid elongase [isa: 0004312 ]
+0004314 = [acyl-carrier protein] S-malonyltransferase [isa: 0004312 0016419 ]
+0004366 = glycerol-3-phosphate acyltransferase [isa: 0008415 ]
+0004469 = lysophosphatidate acyltransferase [isa: 0008415 ]
+0042171 = lysophosphatidic acid acyltransferase [isa: 0008415 ]
+0016420 = malonyltransferase [isa: 0008415 ]
+0016419 = S-malonyltransferase [isa: 0016420 ]
+0019107 = myristoyltransferase [isa: 0008415 ]
+0004379 = glycyl-peptide N-tetradecanoyltransferase [isa: 0016410 0019107 ]
+0018030 = peptidyl-lysine N6-myristoyltransferase [isa: 0004379 ]
+0019705 = protein-cysteine S-myristoyltransferase [isa: 0019107 0019707 ]
+0016410 = N-acyltransferase [isa: 0008415 ]
+0019186 = acyl-CoA N-acyltransferase [isa: 0016410 ]
+0019105 = N-palmitoyltransferase [isa: 0016409 0016410 ]
+0018010 = glycoprotein N-palmitoyltransferase [isa: 0019105 ]
+0018031 = peptidyl-lysine N6-palmitoyltransferase [isa: 0019105 ]
+0008374 = O-acyltransferase [isa: 0008415 ]
+0008779 = acyl-[acyl-carrier protein]-phospholipid O-acyltransferase [isa: 0008374 ]
+0008780 = acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase [isa: 0008374 ]
+0016411 = acylglycerol O-acyltransferase [isa: 0008374 ]
+0003841 = 1-acylglycerol-3-phosphate O-acyltransferase [isa: 0016411 ]
+0003846 = 2-acylglycerol O-acyltransferase [isa: 0016411 ]
+0004144 = diacylglycerol O-acyltransferase [isa: 0016411 ]
+0016406 = carnitine O-acyltransferase [isa: 0008374 ]
+0008458 = carnitine O-octanoyltransferase [isa: 0016406 0016414 ]
+0004095 = carnitine O-palmitoyltransferase [isa: 0016406 0016416 ]
+0004173 = ecdysone O-acyltransferase [isa: 0008374 ]
+0016414 = O-octanoyltransferase [isa: 0008374 0016415 ]
+0016416 = O-palmitoyltransferase [isa: 0008374 0016409 ]
+0016753 = O-sinapoyltransferase [isa: 0008374 0016752 ]
+0016754 = sinapoylglucose-malate O-sinapoyltransferase [isa: 0016753 ]
+0004607 = phosphatidylcholine-sterol O-acyltransferase [isa: 0008374 ]
+0019707 = protein-cysteine S-acyltransferase [isa: 0008374 ]
+0019706 = protein-cysteine S-palmitoleyltransferase [isa: 0016409 0019707 ]
+0016412 = serine O-acyltransferase [isa: 0008374 ]
+0004772 = sterol O-acyltransferase [isa: 0008374 ]
+0017066 = cholesterol O-acyltransferase [isa: 0004772 ]
+0016415 = octanoyltransferase [isa: 0008415 ]
+0008951 = palmitoleoyl-acyl carrier protein (ACP)-dependent acyltransferase [isa: 0008415 ]
+0016409 = palmitoyltransferase [isa: 0008415 ]
+0016417 = S-acyltransferase [isa: 0008415 ]
+0030523 = dihydrolipoamide S-acyltransferase [isa: 0016417 ]
+0004147 = dihydrolipoamide branched chain acyltransferase [isa: 0030523 ]
+0016752 = sinapoyltransferase [isa: 0008415 ]
+0016748 = succinyltransferase [isa: 0008415 ]
+0016749 = N-succinyltransferase [isa: 0016748 ]
+0008666 = 2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase [isa: 0016749 ]
+0008791 = arginine N-succinyltransferase [isa: 0016749 ]
+0016750 = O-succinyltransferase [isa: 0016748 ]
+0008899 = homoserine O-succinyltransferase [isa: 0016750 ]
+0016751 = S-succinyltransferase [isa: 0016748 ]
+0004149 = dihydrolipoamide S-succinyltransferase [isa: 0016751 ]
+0046353 = aminoglycoside N3'-acetyltransferase [isa: 0016747 ]
+0018711 = benzoyl acetate-CoA thiolase [isa: 0016747 ]
+0004321 = fatty-acyl-CoA synthase [isa: 0016747 ]
+0030270 = formylmethanofuran-tetrahydromethanopterin N-formyltransferase [isa: 0016747 ]
+0045440 = isopenicillin N acyltransferase [isa: 0016747 ]
+0016210 = naringenin-chalcone synthase [isa: 0016747 ]
+0016744 = transferase, transferring aldehyde or ketonic groups [isa: 0016740 ]
+0016745 = transketolase and transaldolase [isa: 0016744 ]
+0004801 = transaldolase [isa: 0016745 ]
+0004802 = transketolase [isa: 0016745 ]
+0016765 = transferase, transferring alkyl or aryl (other than methyl) groups [isa: 0016740 ]
+0016766 = transferase, transferring alkyl or aryl groups, other than methyl groups [isa: 0016765 ]
+0003866 = 3-phosphoshikimate 1-carboxyvinyltransferase [isa: 0016766 ]
+0009824 = adenylate isopentenyltransferase [isa: 0016766 ]
+0008609 = alkylglycerone-phosphate synthase [isa: 0016766 ]
+0008817 = cob(I)alamin adenosyltransferase [isa: 0016766 ]
+0004171 = deoxyhypusine synthase [isa: 0016766 ]
+0004156 = dihydropteroate synthase [isa: 0016766 ]
+0004161 = dimethylallyltransferase [isa: 0016766 ]
+0004364 = glutathione transferase [isa: 0016766 ]
+0004464 = leukotriene-C4 synthase [isa: 0016766 ]
+0004478 = methionine adenosyltransferase [isa: 0016766 ]
+0030410 = nicotianamine synthase [isa: 0016766 ]
+0004659 = prenyltransferase [isa: 0016766 ]
+0046428 = 1,4-dihydroxy-2-naphthoate octaprenyltransferase [isa: 0004659 ]
+0008412 = 4-hydroxybenzoate octaprenyltransferase [isa: 0004659 ]
+0046408 = chlorophyll synthetase [isa: 0004659 ]
+0045547 = dehydrodolichyl diphosphate synthase [isa: 0004659 ]
+0008834 = di-trans-poly-cis-decaprenylcistransferase [isa: 0004659 ]
+0004311 = farnesyltranstransferase [isa: 0004659 ]
+0004310 = farnesyl-diphosphate farnesyltransferase [isa: 0004311 ]
+0008495 = protoheme IX farnesyltransferase [isa: 0004311 ]
+0004337 = geranyltranstransferase [isa: 0004659 ]
+0016767 = geranylgeranyl-diphosphate geranylgeranyltransferase [isa: 0004337 ]
+0008318 = protein prenyltransferase [isa: 0004659 ]
+0004660 = protein farnesyltransferase [isa: 0008318 ]
+0018223 = protein-cysteine farnesyltransferase [isa: 0004660 ]
+0004661 = protein geranylgeranyltransferase [isa: 0008318 ]
+0018224 = protein-cysteine geranylgeranyltransferase [isa: 0004661 ]
+0004662 = CAAX-protein geranylgeranyltransferase [isa: 0018224 ]
+0004663 = RAB-protein geranylgeranyltransferase [isa: 0004661 ]
+0004746 = riboflavin synthase [isa: 0016766 ]
+0004766 = spermidine synthase [isa: 0016766 ]
+0016768 = spermine synthase [isa: 0016766 ]
+0004789 = thiamin-phosphate pyrophosphorylase [isa: 0016766 ]
+0000010 = trans-hexaprenyltranstransferase [isa: 0016766 ]
+0004811 = tRNA isopentenyltransferase [isa: 0016766 ]
+0016432 = tRNA-uridine aminocarboxypropyltransferase [isa: 0016766 ]
+0008760 = UDP-N-acetylglucosamine 1-carboxyvinyltransferase [isa: 0016766 ]
+0016757 = transferase, transferring glycosyl groups [isa: 0016740 ]
+0008961 = phosphatidylglycerol-prolipoprotein diacylglyceryl transferase [isa: 0016757 ]
+0016758 = transferase, transferring hexosyl groups [isa: 0016757 ]
+0003844 = 1,4-alpha-glucan branching enzyme [isa: 0016758 ]
+0008376 = acetylgalactosaminyltransferase [isa: 0016758 ]
+0003947 = (N-acetylneuraminyl)-galactosylglucosylceramide N-acetylgalactosaminyltransferase [isa: 0008376 ]
+0004380 = glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase [isa: 0008376 ]
+0004653 = polypeptide N-acetylgalactosaminyltransferase [isa: 0008376 ]
+0008375 = acetylglucosaminyltransferase [isa: 0016758 ]
+0030144 = alpha-1,3(6)-mannosylglycoprotein beta-1,6-N-acetylglucosaminyltransferase [isa: 0008375 ]
+0003827 = alpha-1,3-mannosylglycoprotein beta-1,2-N-acetylglucosaminyltransferase [isa: 0008375 ]
+0008454 = alpha-1,3-mannosylglycoprotein beta-1,4-N-acetylglucosaminyltransferase [isa: 0008375 ]
+0008455 = alpha-1,6-mannosylglycoprotein beta-1,2-N-acetylglucosaminyltransferase [isa: 0008375 ]
+0003829 = beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase [isa: 0008375 ]
+0003830 = beta-1,4-mannosylglycoprotein beta-1,4-N-acetylglucosaminyltransferase [isa: 0008375 ]
+0008457 = beta-galactosyl-N-acetylglucosaminylgalactosyl-glucosylceramide beta-1,3-acetylglucosaminyltransferase [isa: 0008375 ]
+0004100 = chitin synthase [isa: 0008375 ]
+0004166 = dolichyl-phosphate alpha-N-acetylglucosaminyltransferase [isa: 0008375 ]
+0042328 = heparan sulfate N-acetylglucosaminyltransferase [isa: 0008375 ]
+0008917 = lipopolysaccharide N-acetylglucosaminyltransferase [isa: 0008375 ]
+0004577 = N-acetylglucosaminyldiphosphodolichol N-acetylglucosaminyltransferase [isa: 0008375 ]
+0008532 = N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase [isa: 0008375 ]
+0008109 = N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase [isa: 0008375 ]
+0017176 = phosphatidylinositol N-acetylglucosaminyltransferase [isa: 0008375 ]
+0016262 = protein N-acetylglucosaminyltransferase [isa: 0008375 ]
+0016253 = UDP-N-acetylglucosamine-peptide N-acetylglucosaminyltransferase [isa: 0008375 ]
+0008417 = fucosyltransferase [isa: 0016758 ]
+0017083 = alpha(1,3)-fucosyltransferase [isa: 0008417 ]
+0008107 = galactoside 2-L-fucosyltransferase [isa: 0008417 ]
+0017060 = galactoside 3(4)-L-fucosyltransferase [isa: 0008417 ]
+0018392 = GDP-L-fucose:asparagine-linked N-acetylglucosamine alpha1,3-fucosyltransferase [isa: 0008417 ]
+0008424 = glycoprotein 6-alpha-L-fucosyltransferase [isa: 0008417 ]
+0008378 = galactosyltransferase [isa: 0016758 ]
+0046509 = 1,2-diacylglycerol 3-beta-galactosyltransferase [isa: 0008378 ]
+0003851 = 2-hydroxyacylsphingosine 1-beta-galactosyltransferase [isa: 0008378 ]
+0003831 = beta-N-acetylglucosaminyl-glycopeptide beta-1,4-galactosyltransferase [isa: 0008378 ]
+0046480 = galactolipid galactosyltransferase [isa: 0008378 ]
+0004381 = glycoprotein-fucosylgalactoside alpha-galactosyltransferase [isa: 0008378 ]
+0016263 = glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase [isa: 0008378 ]
+0004461 = lactose synthase [isa: 0008378 ]
+0008918 = lipopolysaccharide galactosyltransferase [isa: 0008378 ]
+0008921 = lipopolysaccharide-1,6-galactosyltransferase [isa: 0008378 ]
+0003945 = N-acetyllactosamine synthase [isa: 0008378 ]
+0003946 = N-acetyllactosaminide alpha-1,3-galactosyltransferase [isa: 0008378 ]
+0008499 = UDP-galactose beta-N-acetylglucosamine beta-1,3-galactosyltransferase [isa: 0008378 ]
+0008489 = UDP-galactose-glucosylceramide beta-1,4-galactosyltransferase [isa: 0008378 ]
+0046481 = UDP-galactose:MGDG galactosyltransferase [isa: 0008378 ]
+0046525 = xylosylprotein 4-beta-galactosyltransferase [isa: 0008378 ]
+0046527 = glucosyltransferase [isa: 0016758 ]
+0018718 = 1,2-dihydroxy-phenanthrene glycosyltransferase [isa: 0046527 ]
+0003843 = 1,3-beta-glucan synthase [isa: 0046527 ]
+0003825 = alpha,alpha-trehalose-phosphate synthase (UDP-forming) [isa: 0046527 ]
+0016759 = cellulose synthase [isa: 0046527 ]
+0016761 = cellulose synthase (GDP-forming) [isa: 0016759 ]
+0016760 = cellulose synthase (UDP-forming) [isa: 0016759 ]
+0008120 = ceramide glucosyltransferase [isa: 0046527 ]
+0042283 = dolichyl pyrophosphate Glc1Man9GlcNAc2 alpha-1,3-glucosyltransferase [isa: 0046527 ]
+0042281 = dolichyl pyrophosphate Man9GlcNAc2 alpha-1,3-glucosyltransferase [isa: 0046527 ]
+0004581 = dolichyl-phosphate beta-glucosyltransferase [isa: 0046527 ]
+0004583 = dolichyl-phosphate-glucose-glycolipid alpha-glucosyltransferase [isa: 0046527 ]
+0004373 = glycogen (starch) synthase [isa: 0046527 ]
+0008466 = glycogenin glucosyltransferase [isa: 0046527 ]
+0008919 = lipopolysaccharide glucosyltransferase I [isa: 0046527 ]
+0009011 = starch (bacterial glycogen) synthase [isa: 0046527 ]
+0016906 = sterol glucosyltransferase [isa: 0046527 ]
+0016157 = sucrose synthase [isa: 0046527 ]
+0046524 = sucrose-phosphate synthase [isa: 0046527 ]
+0003980 = UDP-glucose:glycoprotein glucosyltransferase [isa: 0046527 ]
+0015020 = glucuronosyltransferase [isa: 0016758 ]
+0018715 = 9-phenanthrol UDP-glucuronosyltransferase [isa: 0015020 ]
+0015018 = galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase [isa: 0015020 ]
+0003981 = UDP-glucuronosyltransferase [isa: 0015020 ]
+0008915 = lipid-A-disaccharide synthase [isa: 0016758 ]
+0000030 = mannosyltransferase [isa: 0016758 ]
+0000026 = alpha-1,2-mannosyltransferase [isa: 0000030 ]
+0000033 = alpha-1,3-mannosyltransferase [isa: 0000030 ]
+0000009 = alpha-1,6-mannosyltransferase [isa: 0000030 ]
+0019187 = beta-1,4-mannosyltransferase [isa: 0000030 ]
+0004578 = chitobiosyldiphosphodolichol alpha-mannosyltransferase [isa: 0000030 ]
+0004582 = dolichyl-phosphate beta-D-mannosyltransferase [isa: 0000030 ]
+0004584 = dolichyl-phosphate-mannose-glycolipid alpha-mannosyltransferase [isa: 0000030 ]
+0004169 = dolichyl-phosphate-mannose-protein mannosyltransferase [isa: 0000030 ]
+0004580 = glycolipid mannosyl transferase [isa: 0000030 ]
+0004376 = glycolipid mannosyltransferase [isa: 0000030 ]
+0004377 = glycolipid 2-alpha-mannosyltransferase [isa: 0004376 ]
+0004378 = glycolipid 3-alpha-mannosyltransferase [isa: 0004376 ]
+0016438 = tRNA-queuosine beta-mannosyltransferase [isa: 0000030 ]
+0004576 = oligosaccharyl transferase [isa: 0016758 ]
+0004579 = dolichyl-diphospho-oligosaccharide-protein glycosyltransferase [isa: 0004576 ]
+0008955 = peptidoglycan glycosyltransferase [isa: 0016758 ]
+0019112 = phenanthrol glycosyltransferase [isa: 0016758 ]
+0018716 = 1-phenanthrol glycosyltransferase [isa: 0019112 ]
+0018717 = 9-phenanthrol glycosyltransferase [isa: 0019112 ]
+0004645 = phosphorylase [isa: 0016758 ]
+0008184 = glycogen phosphorylase [isa: 0004645 ]
+0009018 = sucrose phosphorylase [isa: 0016758 ]
+0008194 = UDP-glycosyltransferase [isa: 0016758 ]
+0046510 = UDP-sulfoquinovose:DAG sulfoquinovosyltransferase [isa: 0016758 ]
+0016762 = xyloglucan:xyloglucosyl transferase [isa: 0016758 ]
+0016764 = transferase, transferring other glycosyl groups [isa: 0016757 ]
+0008713 = ADP-heptose-lipopolysaccharide heptosyltransferase [isa: 0016764 ]
+0008920 = lipopolysaccharide heptosyltransferase [isa: 0016764 ]
+0008932 = murein lytic endotransglycosylase E [isa: 0016764 ]
+0008373 = sialyltransferase [isa: 0016764 ]
+0001665 = alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase [isa: 0008373 ]
+0003828 = alpha-N-acetylneuraminide alpha-2,8-sialyltransferase [isa: 0008373 ]
+0003835 = beta-galactosamide alpha-2,6-sialyltransferase [isa: 0008373 ]
+0003836 = beta-galactoside alpha-2,3-sialyltransferase [isa: 0008373 ]
+0008118 = N-acetyllactosaminide alpha-2,3-sialyltransferase [isa: 0008373 ]
+0004513 = neolactotetraosylceramide alpha-2,3-sialyltransferase [isa: 0008373 ]
+0016763 = transferase, transferring pentosyl groups [isa: 0016757 ]
+0017061 = 5'-methylthioadenosine phosphorylase [isa: 0016763 ]
+0003999 = adenine phosphoribosyltransferase [isa: 0016763 ]
+0004044 = amidophosphoribosyltransferase [isa: 0016763 ]
+0004048 = anthranilate phosphoribosyltransferase [isa: 0016763 ]
+0003879 = ATP phosphoribosyltransferase [isa: 0016763 ]
+0016003 = glutamine amidotransferase [isa: 0016763 ]
+0004422 = hypoxanthine phosphoribosyltransferase [isa: 0016763 ]
+0030591 = NAD DNA ADP-ribosyltransferase [isa: 0016763 ]
+0003956 = NAD(P)+-arginine ADP-ribosyltransferase [isa: 0016763 ]
+0018121 = NAD(P)+-asparagine ADP-ribosyltransferase [isa: 0016763 ]
+0018071 = NAD(P)+-cysteine ADP-ribosyltransferase [isa: 0016763 ]
+0018127 = NAD(P)+-serine ADP-ribosyltransferase [isa: 0016763 ]
+0003950 = NAD+ ADP-ribosyltransferase [isa: 0016763 ]
+0004516 = nicotinate phosphoribosyltransferase [isa: 0016763 ]
+0004514 = nicotinate-nucleotide pyrophosphorylase (carboxylating) [isa: 0016763 ]
+0008939 = nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase [isa: 0016763 ]
+0004588 = orotate phosphoribosyltransferase [isa: 0016763 ]
+0004731 = purine-nucleoside phosphorylase [isa: 0016763 ]
+0016154 = pyrimidine-nucleoside phosphorylase [isa: 0016763 ]
+0008479 = queuine tRNA-ribosyltransferase [isa: 0016763 ]
+0009032 = thymidine phosphorylase [isa: 0016763 ]
+0004845 = uracil phosphoribosyltransferase [isa: 0016763 ]
+0004850 = uridine phosphorylase [isa: 0016763 ]
+0000310 = xanthine phosphoribosyltransferase [isa: 0016763 ]
+0009043 = xanthine-guanine phosphoribosyltransferase [isa: 0016763 ]
+0042285 = xylosyltransferase [isa: 0016763 ]
+0030158 = peptide O-xylosyltransferase [isa: 0042285 ]
+0016769 = transferase, transferring nitrogenous groups [isa: 0016740 ]
+0016770 = oximinotransaminase [isa: 0016769 ]
+0008483 = transaminase [isa: 0016769 ]
+0003867 = 4-aminobutyrate aminotransferase [isa: 0008483 ]
+0018719 = 6-aminohexanoate transaminase [isa: 0008483 ]
+0003992 = acetylornithine aminotransferase [isa: 0008483 ]
+0004015 = adenosylmethionine-8-amino-7-oxononanoate aminotransferase [isa: 0008483 ]
+0004021 = alanine aminotransferase [isa: 0008483 ]
+0008453 = alanine-glyoxylate aminotransferase [isa: 0008483 ]
+0008793 = aromatic amino acid transferase [isa: 0008483 ]
+0004069 = aspartate aminotransferase [isa: 0008483 ]
+0046571 = aspartate-2-keto-4-methylthiobutyrate transaminase [isa: 0008483 ]
+0016223 = beta-alanine-pyruvate aminotransferase [isa: 0008483 ]
+0004084 = branched-chain amino acid aminotransferase [isa: 0008483 ]
+0019161 = diamine aminotransferase [isa: 0008483 ]
+0045303 = diaminobutyrate-2-oxoglutarate transaminase [isa: 0008483 ]
+0019179 = dTDP-4-amino-4,6-dideoxy-D-glucose aminotransferase [isa: 0008483 ]
+0004360 = glucosamine-fructose-6-phosphate aminotransferase (isomerizing) [isa: 0008483 ]
+0008110 = histidine aminotransferase [isa: 0008483 ]
+0004400 = histidinol-phosphate aminotransferase [isa: 0008483 ]
+0016212 = kynurenine-oxoglutarate aminotransferase [isa: 0008483 ]
+0045484 = L-lysine 6-transaminase [isa: 0008483 ]
+0004587 = ornithine-oxo-acid aminotransferase [isa: 0008483 ]
+0004646 = phosphoserine aminotransferase [isa: 0008483 ]
+0004648 = phosphoserine transaminase [isa: 0008483 ]
+0019162 = pyridoxamine-oxaloacetate aminotransferase [isa: 0008483 ]
+0019163 = pyridoxamine-phosphate aminotransferase [isa: 0008483 ]
+0004760 = serine-pyruvate aminotransferase [isa: 0008483 ]
+0004761 = serine-pyruvate aminotransferase, type 1 [isa: 0004760 ]
+0004762 = serine-pyruvate aminotransferase, type 2A [isa: 0004760 ]
+0004763 = serine-pyruvate aminotransferase, type 2B [isa: 0004760 ]
+0009016 = succinyldiaminopimelate aminotransferase [isa: 0008483 ]
+0004838 = tyrosine aminotransferase [isa: 0008483 ]
+0009042 = valine-pyruvate aminotransferase [isa: 0008483 ]
+0016771 = transferase, transferring other nitrogenous groups [isa: 0016769 ]
+0016741 = transferase, transferring one-carbon groups [isa: 0016740 ]
+0015067 = amidinotransferase [isa: 0016741 ]
+0015068 = glycine amidinotransferase [isa: 0015067 ]
+0015069 = inosamine-phosphate amidinotransferase [isa: 0015067 ]
+0016743 = carboxyl- and carbamoyltransferase [isa: 0016741 ]
+0045447 = 3'-hydroxymethylcephem-O-carbamoyltransferase [isa: 0016743 ]
+0018710 = acetone carboxylase [isa: 0016743 ]
+0004070 = aspartate carbamoyltransferase [isa: 0016743 ]
+0004585 = ornithine carbamoyltransferase [isa: 0016743 ]
+0008168 = methyltransferase [isa: 0016741 ]
+0018707 = 1-phenanthrol methyltransferase [isa: 0008168 ]
+0042083 = 5,10-methylenetetrahydrofolate-dependent methyltransferase [isa: 0008168 ]
+0004799 = thymidylate synthase [isa: 0042083 ]
+0042086 = 5-methyl-5,6,7,8-tetrahydromethanopterin-dependent methyltransferase [isa: 0008168 ]
+0030269 = tetrahydromethanopterin S-methyltransferase [isa: 0008172 0042086 ]
+0042084 = 5-methyltetrahydrofolate methyltransferase [isa: 0008168 ]
+0008705 = 5-methyltetrahydrofolate-homocysteine S-methyltransferase [isa: 0008172 0042084 ]
+0042085 = 5-methyltetrahydropteroyltri-L-glutamate-dependent methyltransferase [isa: 0008168 ]
+0003871 = 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase [isa: 0008172 0042085 ]
+0004047 = aminomethyltransferase [isa: 0008168 ]
+0008169 = C-methyltransferase [isa: 0008168 ]
+0003838 = delta(24)-sterol C-methyltransferase [isa: 0008169 ]
+0030580 = quinone cofactor methyltransferase [isa: 0008169 ]
+0008425 = ubiquinone biosynthesis methyltransferase [isa: 0030580 ]
+0004851 = uroporphyrin-III C-methyltransferase [isa: 0008169 ]
+0008825 = cyclopropane-fatty-acyl-phospholipid synthase [isa: 0008168 ]
+0004164 = diphthine synthase [isa: 0008168 ]
+0003886 = DNA (cytosine-5-)-methyltransferase [isa: 0008168 ]
+0009008 = DNA-methyltransferase [isa: 0008168 ]
+0009007 = site-specific DNA-methyltransferase (adenine-specific) [isa: 0009008 ]
+0015667 = site-specific DNA-methyltransferase (cytosine-N4-specific) [isa: 0009008 ]
+0008326 = site-specific DNA-methyltransferase (cytosine-specific) [isa: 0009008 ]
+0004372 = glycine hydroxymethyltransferase [isa: 0008168 ]
+0016742 = hydroxymethyl-, formyl- and related transferase [isa: 0004372 ]
+0003864 = 3-methyl-2-oxobutanoate hydroxymethyltransferase [isa: 0016742 ]
+0030407 = formiminotransferase [isa: 0016742 ]
+0030409 = glutamate formimidoyltransferase [isa: 0030407 ]
+0030408 = glycine formimidoyltransferase [isa: 0030407 ]
+0004479 = methionyl-tRNA formyltransferase [isa: 0016742 ]
+0004643 = phosphoribosylaminoimidazole-carboxamide formyltransferase [isa: 0016742 ]
+0004644 = phosphoribosylglycinamide formyltransferase [isa: 0016742 ]
+0004395 = hexaprenyldihydroxybenzoate methyltransferase [isa: 0008168 ]
+0042054 = histone methyltransferase [isa: 0008168 ]
+0004481 = methylene-fatty-acyl-phospholipid synthase [isa: 0008168 ]
+0008170 = N-methyltransferase [isa: 0008168 ]
+0017097 = acetylserotonin N-methyltransferase [isa: 0008170 ]
+0016273 = arginine N-methyltransferase [isa: 0008170 0008757 ]
+0016274 = protein-arginine N-methyltransferase [isa: 0016273 ]
+0008469 = histone-arginine N-methyltransferase [isa: 0016274 ]
+0016275 = [cytochrome c]-arginine N-methyltransferase [isa: 0016274 ]
+0016277 = [myelin basic protein]-arginine N-methyltransferase [isa: 0016274 ]
+0019702 = protein-arginine N5-methyltransferase [isa: 0016273 ]
+0017174 = glycine N-methyltransferase [isa: 0008170 0008757 ]
+0046539 = histamine N-methyltransferase [isa: 0008170 ]
+0016278 = lysine N-methyltransferase [isa: 0008170 0008757 ]
+0016279 = protein-lysine N-methyltransferase [isa: 0016278 ]
+0018025 = calmodulin-lysine N-methyltransferase [isa: 0016279 ]
+0018024 = histone-lysine N-methyltransferase [isa: 0016279 ]
+0000277 = [cytochrome c]-lysine N-methyltransferase [isa: 0008276 0016279 ]
+0004482 = mRNA (guanine-N7)-methyltransferase [isa: 0008170 0008174 ]
+0008112 = nicotinamide N-methyltransferase [isa: 0008170 0008757 ]
+0008938 = nicotinate N-methyltransferase [isa: 0008170 0008757 ]
+0018064 = peptidyl-histidine N-methyltransferase [isa: 0008170 0008757 ]
+0004603 = phenylethanolamine N-methyltransferase [isa: 0008170 0008757 ]
+0004608 = phosphatidylethanolamine N-methyltransferase [isa: 0008170 0008757 ]
+0000234 = phosphoethanolamine N-methyltransferase [isa: 0008170 0008757 ]
+0004809 = tRNA (guanine-N2-)-methyltransferase [isa: 0008170 0016423 ]
+0008171 = O-methyltransferase [isa: 0008168 ]
+0008689 = 3-demethylubiquinone-9 3-O-methyltransferase [isa: 0008171 0008757 ]
+0017096 = acetylserotonin O-methyltransferase [isa: 0008171 0008757 ]
+0042409 = caffeoyl-CoA O-methyltransferase [isa: 0008171 ]
+0016206 = catechol O-methyltransferase [isa: 0008171 0008757 ]
+0019010 = farnesoic acid O-methyltransferase [isa: 0008171 0008757 ]
+0046406 = magnesium-protoporphyrin O-methyltransferase [isa: 0008171 ]
+0004483 = mRNA (nucleoside-2'-O-)-methyltransferase [isa: 0008171 0008174 ]
+0008983 = protein-glutamate O-methyltransferase [isa: 0008171 0008757 ]
+0004719 = protein-L-isoaspartate (D-aspartate) O-methyltransferase [isa: 0008171 0008276 0008757 ]
+0018423 = protein-leucine O-methyltransferase [isa: 0008171 0008276 0008757 ]
+0004671 = protein-S-isoprenylcysteine O-methyltransferase [isa: 0008171 0008276 0008757 ]
+0046026 = precorrin-4 C11-methyltransferase [isa: 0008168 ]
+0046025 = precorrin-6Y C5,15-methyltransferase (decarboxylating) [isa: 0008168 ]
+0008276 = protein methyltransferase [isa: 0008168 ]
+0003880 = C-terminal protein carboxyl methyltransferase [isa: 0008276 ]
+0008757 = S-adenosylmethionine-dependent methyltransferase [isa: 0008168 ]
+0008898 = homocysteine S-methyltransferase [isa: 0008172 0008757 ]
+0008173 = RNA methyltransferase [isa: 0008757 ]
+0008174 = mRNA methyltransferase [isa: 0008173 ]
+0016422 = mRNA (2'-O-methyladenosine-N6-)-methyltransferase [isa: 0008174 ]
+0008649 = rRNA methyltransferase [isa: 0008173 ]
+0016433 = rRNA (adenine) methyltransferase [isa: 0008649 ]
+0000179 = rRNA (adenine-N6,N6-)-dimethyltransferase [isa: 0016433 ]
+0008988 = rRNA (adenine-N6-)-methyltransferase [isa: 0016433 ]
+0016434 = rRNA (cytosine) methyltransferase [isa: 0008649 ]
+0009383 = rRNA (cytosine-C5-967)-methyltransferase [isa: 0016434 ]
+0016435 = rRNA (guanine) methyltransferase [isa: 0008649 ]
+0008989 = rRNA (guanine-N1-)-methyltransferase [isa: 0016435 ]
+0008990 = rRNA (guanine-N2-)-methyltransferase [isa: 0016435 ]
+0016436 = rRNA (uridine) methyltransferase [isa: 0008649 ]
+0008650 = rRNA (uridine-2'-O-)-methyltransferase [isa: 0016436 ]
+0008175 = tRNA methyltransferase [isa: 0008173 ]
+0004808 = tRNA (5-methylaminomethyl-2-thiouridylate) methyltransferase [isa: 0008175 ]
+0016426 = tRNA (adenine)-methyltransferase [isa: 0008175 ]
+0016429 = tRNA (adenine-N1-)-methyltransferase [isa: 0016426 ]
+0016430 = tRNA (adenine-N6-)-methyltransferase [isa: 0016426 ]
+0016427 = tRNA (cytosine)-methyltransferase [isa: 0008175 ]
+0016428 = tRNA (cytosine-5-)-methyltransferase [isa: 0016427 ]
+0016423 = tRNA (guanine) methyltransferase [isa: 0008175 ]
+0009019 = tRNA (guanine-N1-)-methyltransferase [isa: 0016423 ]
+0008176 = tRNA (guanine-N7-)-methyltransferase [isa: 0016423 ]
+0016424 = tRNA (guanosine) methyltransferase [isa: 0008175 ]
+0009020 = tRNA (guanosine-2'-O-)-methyltransferase [isa: 0016424 ]
+0016300 = tRNA (uracil) methyltransferase [isa: 0008175 ]
+0009021 = tRNA (uracil-5-)-methyltransferase [isa: 0016300 ]
+0016431 = tRNA (uridine) methyltransferase [isa: 0008175 ]
+0045546 = S-adenosyl-L-methionine:jasmonic acid carboxyl methyltransferase [isa: 0008757 ]
+0004790 = thioether S-methyltransferase [isa: 0008172 0008757 ]
+0018708 = thiol S-methyltransferase [isa: 0008172 0008757 ]
+0008119 = thiopurine S-methyltransferase [isa: 0008172 0008757 ]
+0008172 = S-methyltransferase [isa: 0008168 ]
+0016205 = selenocysteine methyltransferase [isa: 0008168 ]
+0046547 = trans-aconitate 3-methyltransferase [isa: 0008168 ]
+0030586 = [methionine synthase]-cobalamin methyltransferase (cob(II)alamin reducing) [isa: 0008168 0008246 ]
+0016772 = transferase, transferring phosphorus-containing groups [isa: 0016740 ]
+0017125 = deoxycytidyl transferase [isa: 0016772 ]
+0019986 = deoxycytidyl transferase, template dependent [isa: 0003887 0017125 ]
+0016778 = diphosphotransferase [isa: 0016772 ]
+0045140 = inositol phosphoceramide synthase [isa: 0016772 ]
+0016779 = nucleotidyltransferase [isa: 0016772 ]
+0008690 = 3-deoxy-manno-octulosonate cytidylyltransferase [isa: 0016779 ]
+0008781 = acylneuraminate cytidylyltransferase [isa: 0016779 ]
+0003877 = ATP adenylyltransferase [isa: 0016779 ]
+0004105 = choline-phosphate cytidylyltransferase [isa: 0016779 ]
+0003912 = DNA nucleotidylexotransferase [isa: 0016779 ]
+0003887 = DNA-directed DNA polymerase [isa: 0016779 ]
+0003889 = alpha DNA polymerase [isa: 0003887 ]
+0003890 = beta DNA polymerase [isa: 0003887 ]
+0003891 = delta DNA polymerase [isa: 0003887 ]
+0030337 = DNA polymerase processivity factor [isa: 0003887 ]
+0008723 = DNA polymerase V [isa: 0003887 ]
+0003893 = epsilon DNA polymerase [isa: 0003887 ]
+0015999 = eta DNA polymerase [isa: 0003887 ]
+0003895 = gamma DNA-directed DNA polymerase [isa: 0003887 ]
+0016000 = iota DNA polymerase [isa: 0003887 ]
+0016450 = kappa DNA polymerase [isa: 0003887 ]
+0016449 = lambda DNA polymerase [isa: 0003887 ]
+0016448 = mu DNA polymerase [isa: 0003887 ]
+0016451 = nu DNA polymerase [isa: 0003887 ]
+0019984 = sigma DNA polymerase [isa: 0003887 ]
+0016452 = theta DNA polymerase [isa: 0003887 ]
+0003894 = zeta DNA polymerase [isa: 0003887 ]
+0003899 = DNA-directed RNA polymerase [isa: 0016779 ]
+0003896 = DNA primase [isa: 0003899 ]
+0003900 = DNA-directed RNA polymerase I [isa: 0003899 ]
+0003901 = DNA-directed RNA polymerase II [isa: 0003899 ]
+0003902 = DNA-directed RNA polymerase III [isa: 0003899 ]
+0004306 = ethanolamine-phosphate cytidylyltransferase [isa: 0016779 ]
+0003919 = FMN adenylyltransferase [isa: 0016779 ]
+0008871 = gentamicin 2''-nucleotidyltransferase [isa: 0016779 ]
+0008878 = glucose-1-phosphate adenylyltransferase [isa: 0016779 ]
+0008879 = glucose-1-phosphate thymidylyltransferase [isa: 0016779 ]
+0008882 = glutamate-ammonia-ligase adenylyltransferase [isa: 0016779 ]
+0008905 = mannose-phosphate guanylyltransferase [isa: 0016779 ]
+0004475 = mannose-1-phosphate guanylyltransferase [isa: 0008905 ]
+0008928 = mannose-1-phosphate guanylyltransferase (GDP) [isa: 0008905 ]
+0000309 = nicotinamide-nucleotide adenylyltransferase [isa: 0016779 ]
+0004515 = nicotinate-nucleotide adenylyltransferase [isa: 0016779 ]
+0004595 = pantotheine-phosphate adenylyltransferase [isa: 0016779 ]
+0004605 = phosphatidate cytidylyltransferase [isa: 0016779 ]
+0004652 = polynucleotide adenylyltransferase [isa: 0016779 ]
+0004654 = polyribonucleotide nucleotidyltransferase [isa: 0016779 ]
+0008192 = RNA guanylyltransferase [isa: 0016779 ]
+0004484 = mRNA guanylyltransferase [isa: 0008192 ]
+0008193 = tRNA guanylyltransferase [isa: 0008192 ]
+0003964 = RNA-directed DNA polymerase [isa: 0016779 ]
+0003968 = RNA-directed RNA polymerase [isa: 0016779 ]
+0009012 = streptomycin 3''-adenylyltransferase [isa: 0016779 ]
+0004779 = sulfate adenylyltransferase [isa: 0016779 ]
+0004780 = sulfate adenylyltransferase (ADP) [isa: 0004779 ]
+0004781 = sulfate adenylyltransferase (ATP) [isa: 0004779 ]
+0004810 = tRNA adenylyltransferase [isa: 0016779 ]
+0016437 = tRNA cytidylyltransferase [isa: 0016779 ]
+0009022 = tRNA nucleotidyltransferase [isa: 0016779 ]
+0008108 = UDP-glucose-hexose-1-phosphate uridylyltransferase [isa: 0016779 ]
+0003977 = UDP-N-acetylglucosamine pyrophosphorylase [isa: 0016779 ]
+0017103 = UTP-galactose-1-phosphate uridylyltransferase [isa: 0016779 ]
+0003983 = UTP-glucose-1-phosphate uridylyltransferase [isa: 0016779 ]
+0003982 = UTP-hexose-1-phosphate uridylyltransferase [isa: 0016779 ]
+0008773 = [protein-PII] uridylyltransferase [isa: 0016779 ]
+0016773 = phosphotransferase, alcohol group as acceptor [isa: 0016772 ]
+0046522 = 5-methylthioribose kinase [isa: 0016773 ]
+0046316 = gluconokinase [isa: 0016773 ]
+0019158 = mannokinase [isa: 0016773 ]
+0018720 = phenol kinase [isa: 0016773 ]
+0008982 = protein-N(PI)-phosphohistidine-sugar phosphotransferase [isa: 0015144 0015455 0016773 ]
+0015582 = beta-glucoside permease [isa: 0008982 0015573 ]
+0015583 = beta-glucoside [arbutin-salicin-cellobiose] permease [isa: 0015582 ]
+0019190 = cellobiose permease [isa: 0008982 0019191 ]
+0015585 = fructose permease [isa: 0005353 0008982 ]
+0019192 = fructose porter [isa: 0005353 0008982 ]
+0015588 = galactitol permease [isa: 0008982 0015577 ]
+0019195 = galactosamine porter [isa: 0008982 0019196 ]
+0015587 = glucitol permease [isa: 0008982 0015576 ]
+0015579 = glucose permease [isa: 0005355 0008982 ]
+0019189 = lactose permease [isa: 0008982 0015155 ]
+0015581 = maltose porter [isa: 0005363 0008982 ]
+0015586 = mannitol permease [isa: 0008982 0015575 ]
+0015589 = mannose permease [isa: 0008982 0015578 ]
+0015590 = N-acetyl galactosamine permease [isa: 0008982 0015571 ]
+0015580 = N-acetyl glucosamine permease [isa: 0008982 0015572 ]
+0019193 = sorbose porter [isa: 0008982 0019194 ]
+0019188 = sucrose permease (PTS) [isa: 0008515 0008982 ]
+0015584 = trehalose permease [isa: 0008982 0015574 ]
+0019165 = thiamin kinase [isa: 0016773 ]
+0016774 = phosphotransferase, carboxyl group as acceptor [isa: 0016772 ]
+0016780 = phosphotransferase, for other substituted phosphate groups [isa: 0016772 ]
+0008807 = carboxyvinyl-carboxyphosphonate phosphorylmutase [isa: 0016780 ]
+0017169 = CDP-alcohol phosphatidyltransferase [isa: 0016780 ]
+0008444 = CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase [isa: 0017169 ]
+0003881 = CDP-diacylglycerol-inositol 3-phosphatidyltransferase [isa: 0017169 ]
+0003882 = CDP-diacylglycerol-serine O-phosphatidyltransferase [isa: 0017169 ]
+0004142 = diacylglycerol cholinephosphotransferase [isa: 0017169 ]
+0004307 = ethanolaminephosphotransferase [isa: 0017169 ]
+0018422 = GDP-mannose:serine-protein mannose-1-phosphotransferase [isa: 0016780 ]
+0008897 = holo-[acyl-carrier protein] synthase [isa: 0016780 ]
+0008960 = phosphatidylglycerol-membrane-oligosaccharide glycerophosphotransferase [isa: 0016780 ]
+0030572 = phosphatidyltransferase [isa: 0016780 ]
+0008808 = cardiolipin synthase [isa: 0030572 ]
+0008963 = phospho-N-acetylmuramoyl-pentapeptide-transferase [isa: 0016780 ]
+0003975 = UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosamine-1-phosphate transferase [isa: 0016780 ]
+0003976 = UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase [isa: 0016780 ]
+0018421 = UDP-N-acetylglucosamine:serine-protein N-acetylglucosamine-1-phosphotransferase [isa: 0016780 ]
+0016775 = phosphotransferase, nitrogenous group as acceptor [isa: 0016772 ]
+0016781 = phosphotransferase, paired acceptors [isa: 0016772 ]
+0016776 = phosphotransferase, phosphate group as acceptor [isa: 0016772 ]
+0016777 = phosphotransferase, with regeneration of donors, apparently catalyzing intramolecular transfers [isa: 0016772 ]
+0016782 = transferase, transferring sulfur-containing groups [isa: 0016740 ]
+0008410 = CoA-transferase [isa: 0016782 ]
+0008260 = 3-oxoacid CoA-transferase [isa: 0008410 ]
+0008411 = 4-hydroxybutyrate CoA-transferase [isa: 0008410 ]
+0008775 = acetate CoA-transferase [isa: 0008410 ]
+0008814 = citrate CoA-transferase [isa: 0008410 ]
+0018730 = glutaconate CoA-transferase [isa: 0008410 ]
+0018729 = propionate CoA-transferase [isa: 0008410 ]
+0018728 = succinyl-CoA:benzylsuccinate CoA-transferase [isa: 0008410 ]
+0016785 = transferase, transferring selenium-containing groups [isa: 0008410 ]
+0016786 = selenotransferase [isa: 0016782 ]
+0004125 = cysteinyl-tRNA(Ser) selenium transferase [isa: 0016786 ]
+0008146 = sulfotransferase [isa: 0016782 ]
+0004027 = alcohol sulfotransferase [isa: 0008146 ]
+0004062 = aryl sulfotransferase [isa: 0008146 ]
+0008459 = chondroitin 6-sulfotransferase [isa: 0008146 ]
+0015016 = desulfoheparin sulfotransferase [isa: 0008146 ]
+0004304 = estrone sulfotransferase [isa: 0008146 ]
+0017095 = heparan sulfate 6-O-sulfotransferase [isa: 0008146 ]
+0004393 = heparin N-deacetylase/N-sulfotransferase [isa: 0008146 ]
+0008467 = heparin-glucosamine 3-O-sulfotransferase [isa: 0008146 ]
+0004394 = heparin-sulfate 2-sulfotransferase [isa: 0008146 ]
+0015022 = heparitin sulfotransferase [isa: 0008146 ]
+0016232 = HNK-1 sulfotransferase [isa: 0008146 ]
+0045130 = keratan sulfate Gal-6-sulfotransferase [isa: 0008146 ]
+0001537 = N-acetylgalactosamine-4-O-sulfotransferase [isa: 0008146 ]
+0001517 = N-acetylglucosamine-6-O-sulfotransferase [isa: 0008146 ]
+0019111 = phenanthrol sulfotransferase [isa: 0008146 ]
+0018722 = 1-phenanthrol sulfotransferase [isa: 0019111 ]
+0018727 = 2-phenanthrol sulfotransferase [isa: 0019111 ]
+0018723 = 3-phenanthrol sulfotransferase [isa: 0019111 ]
+0018724 = 4-phenanthrol sulfotransferase [isa: 0019111 ]
+0018726 = 9-phenanthrol sulfotransferase [isa: 0019111 ]
+0008476 = protein-tyrosine sulfotransferase [isa: 0008146 ]
+0018725 = trans-3,4-fihydrodiolphenanthrene sulfotransferase [isa: 0008146 ]
+0018721 = trans-9R,10R-dihydrodiolphenanthrene sulfotransferase [isa: 0008146 ]
+0017067 = tyrosine-ester sulfotransferase [isa: 0008146 ]
+0016783 = sulfurtransferase [isa: 0016782 ]
+0016784 = 3-mercaptopyruvate sulfurtransferase [isa: 0016783 ]
+0004076 = biotin synthase [isa: 0016783 ]
+0004792 = thiosulfate sulfurtransferase [isa: 0016783 ]
+0016227 = tRNA sulfurtransferase [isa: 0016783 ]
+0045462 = trichothecene 3-0-acetyltransferase [isa: 0016740 ]
+0000215 = tRNA 2'-phosphotransferase [isa: 0016740 ]
+0004803 = transposase [isa: 0003824 ]
+0004804 = P-element encoded transposase [isa: 0004803 ]
+0017150 = tRNA dihydrouridine synthase [isa: 0003824 ]
+0046572 = versicolorin B synthase [isa: 0003824 ]
+0030234 = enzyme regulator [isa: 0003674 ]
+0008047 = enzyme activator [isa: 0030234 ]
+0001671 = ATPase stimulator [isa: 0008047 ]
+0008656 = caspase activator [isa: 0008047 ]
+0005096 = GTPase activator [isa: 0005083 0008047 ]
+0008060 = ARF GTPase activator [isa: 0005096 ]
+0005097 = RAB GTPase activator [isa: 0005096 ]
+0017123 = RAL GTPase activator [isa: 0005096 ]
+0005098 = RAN GTPase activator [isa: 0005096 ]
+0046582 = RAP GTPase activator [isa: 0005096 ]
+0005099 = RAS GTPase activator [isa: 0005096 ]
+0005100 = Rho GTPase activator [isa: 0005096 ]
+0005101 = SAR GTPase activator [isa: 0005096 ]
+0030250 = guanylate cyclase activator [isa: 0008047 0030249 ]
+0008048 = calcium sensitive guanylate cyclase activator [isa: 0030250 ]
+0019209 = kinase activator [isa: 0008047 0019207 ]
+0030295 = protein kinase activator [isa: 0019209 ]
+0030296 = protein tyrosine kinase activator [isa: 0030295 ]
+0030298 = receptor signaling protein tyrosine kinase activator [isa: 0030296 ]
+0030297 = transmembrane receptor protein tyrosine kinase activator [isa: 0030296 ]
+0019211 = phosphatase activator [isa: 0008047 0019888 ]
+0008160 = protein tyrosine phosphatase activator [isa: 0019211 ]
+0016004 = phospholipase activator [isa: 0008047 ]
+0016005 = phospholipase A2 activator [isa: 0016004 ]
+0016484 = proprotein convertase 2 activator [isa: 0008047 ]
+0016504 = protease activator [isa: 0008047 ]
+0030400 = protease substrate recruitment factor [isa: 0016504 ]
+0030567 = prothrombin activator [isa: 0016504 ]
+0008538 = proteasome activator [isa: 0008047 ]
+0030290 = sphingolipid activator protein [isa: 0008047 ]
+0016230 = sphingomyelin phosphodiesterase activator [isa: 0008047 ]
+0016176 = superoxide-generating NADPH oxidase activator [isa: 0008047 ]
+0016483 = tryptophan hydroxylase activator [isa: 0008047 ]
+0004857 = enzyme inhibitor [isa: 0030234 ]
+0015066 = alpha-amylase inhibitor [isa: 0004857 ]
+0042030 = ATPase inhibitor [isa: 0004857 ]
+0008025 = diazepam-binding inhibitor [isa: 0004857 ]
+0008657 = DNA gyrase inhibitor [isa: 0004857 ]
+0004858 = dUTP pyrophosphatase inhibitor [isa: 0004857 ]
+0005095 = GTPase inhibitor [isa: 0004857 0005083 ]
+0030251 = guanylate cyclase inhibitor [isa: 0004857 0030249 ]
+0019210 = kinase inhibitor [isa: 0004857 0019207 ]
+0004860 = protein kinase inhibitor [isa: 0019210 ]
+0008427 = calcium-dependent protein kinase inhibitor [isa: 0004860 ]
+0004862 = cAMP-dependent protein kinase inhibitor [isa: 0004860 ]
+0004861 = cyclin-dependent protein kinase inhibitor [isa: 0004860 ]
+0004863 = diacylglycerol-activated/phospholipid dependent protein kinase C inhibitor [isa: 0004860 ]
+0008426 = protein kinase C inhibitor [isa: 0004860 ]
+0030291 = protein serine/threonine kinase inhibitor [isa: 0004860 ]
+0030292 = protein tyrosine kinase inhibitor [isa: 0004860 ]
+0030294 = receptor signaling protein tyrosine kinase inhibitor [isa: 0030292 ]
+0030293 = transmembrane receptor protein tyrosine kinase inhibitor [isa: 0030292 ]
+0008073 = ornithine decarboxylase inhibitor [isa: 0004857 ]
+0019212 = phosphatase inhibitor [isa: 0004857 0019888 ]
+0004864 = protein phosphatase inhibitor [isa: 0019212 ]
+0004865 = type 1 serine/threonine specific protein phosphatase inhibitor [isa: 0004864 ]
+0001691 = pseudophosphatase [isa: 0019212 ]
+0004859 = phospholipase inhibitor [isa: 0004857 ]
+0019834 = phospholipase A2 inhibitor [isa: 0004859 ]
+0030414 = protease inhibitor [isa: 0004857 ]
+0042031 = angiotensin-converting enzyme inhibitor [isa: 0030414 ]
+0030415 = carboxypeptidase A inhibitor [isa: 0030414 ]
+0004866 = endopeptidase inhibitor [isa: 0030414 ]
+0019828 = aspartic protease inhibitor [isa: 0004866 ]
+0004869 = cysteine protease inhibitor [isa: 0004866 ]
+0030161 = calpain inhibitor [isa: 0004869 ]
+0008191 = metalloendopeptidase inhibitor [isa: 0004866 ]
+0004867 = serine protease inhibitor [isa: 0004866 ]
+0030569 = chymotrypsin inhibitor [isa: 0004867 ]
+0030568 = plasmin inhibitor [isa: 0004867 ]
+0004868 = serpin [isa: 0004867 ]
+0030304 = trypsin inhibitor [isa: 0004867 ]
+0017114 = wide-spectrum protease inhibitor [isa: 0004866 ]
+0016975 = alpha-2 macroglobulin [isa: 0017114 ]
+0008539 = proteasome inhibitor [isa: 0004857 ]
+0017149 = protein biosynthesis inhibitor [isa: 0004857 ]
+0008428 = ribonuclease inhibitor [isa: 0004857 ]
+0030249 = guanylate cyclase regulator [isa: 0030234 ]
+0042349 = guiding stereospecific synthesis [isa: 0030234 ]
+0019207 = kinase regulator [isa: 0030234 ]
+0019887 = protein kinase regulator [isa: 0019207 ]
+0030235 = nitric oxide synthase regulator [isa: 0030234 ]
+0019208 = phosphatase regulator [isa: 0030234 ]
+0019888 = protein phosphatase regulator [isa: 0019208 ]
+0019833 = ice nucleation [isa: 0003674 ]
+0015465 = lysin [isa: 0003674 ]
+0015466 = autolysin [isa: 0015465 ]
+0015176 = holin [isa: 0008565 0015466 ]
+0015642 = bacteriolytic toxin [isa: 0015070 0015465 ]
+0015470 = bacteriocin [isa: 0015642 ]
+0015468 = colicin [isa: 0015469 0015470 ]
+0005554 = molecular_function unknown [isa: 0003674 ]
+0003774 = motor [isa: 0003674 ]
+0003775 = axonemal motor [isa: 0003774 ]
+0008350 = kinetochore motor [isa: 0003774 ]
+0000146 = microfilament motor [isa: 0003774 ]
+0003776 = muscle motor [isa: 0000146 ]
+0045735 = nutrient reservoir [isa: 0003674 ]
+0008369 = obsolete [isa: 0003674 ]
+0004429 = 1-phosphatidylinositol 3-kinase [isa: 0008369 ]
+0004431 = 1-phosphatidylinositol-4-phosphate kinase [isa: 0008369 ]
+0004432 = 1-phosphatidylinositol-4-phosphate kinase, class IA [isa: 0008369 ]
+0004433 = 1-phosphatidylinositol-4-phosphate kinase, class IB [isa: 0008369 ]
+0005191 = acidic epididymal glycoprotein [isa: 0008369 ]
+0009493 = adrenodoxin-type ferredoxin [isa: 0008369 ]
+0009488 = amicyanin [isa: 0008369 ]
+0005208 = amyloid protein [isa: 0008369 ]
+0009388 = antisense RNA [isa: 0008369 ]
+0005320 = apolipoprotein [isa: 0008369 ]
+0015005 = azurin [isa: 0008369 ]
+0009498 = bacterial-type ferredoxin [isa: 0008369 ]
+0005555 = blood group antigen [isa: 0008369 ]
+0003750 = cell cycle regulator [isa: 0008369 ]
+0016171 = cell surface antigen [isa: 0008369 ]
+0009494 = chloroplast-type ferredoxin [isa: 0008369 ]
+0005204 = chondroitin sulfate proteoglycan [isa: 0008369 ]
+0005205 = chondroitin sulfate/dermatan sulfate proteoglycan [isa: 0008369 ]
+0009466 = class I cytochrome c [isa: 0008369 ]
+0003820 = class I major histocompatibility complex antigen [isa: 0008369 ]
+0009469 = class II cytochrome c [isa: 0008369 ]
+0003821 = class II major histocompatibility complex antigen [isa: 0008369 ]
+0009470 = class IIa cytochrome c [isa: 0008369 ]
+0009480 = class IIb cytochrome c [isa: 0008369 ]
+0009471 = class III cytochrome c [isa: 0008369 ]
+0009476 = class IV cytochrome c [isa: 0008369 ]
+0005202 = collagen [isa: 0008369 ]
+0005073 = common-partner SMAD protein [isa: 0008369 ]
+0004600 = cyclophilin [isa: 0008369 ]
+0009458 = cytochrome [isa: 0008369 ]
+0009459 = cytochrome a [isa: 0008369 ]
+0009460 = cytochrome b [isa: 0008369 ]
+0009463 = cytochrome b/b6 [isa: 0008369 ]
+0009464 = cytochrome b5 [isa: 0008369 ]
+0030066 = cytochrome b6 [isa: 0008369 ]
+0009461 = cytochrome c [isa: 0008369 ]
+0009477 = cytochrome c1 [isa: 0008369 ]
+0009472 = cytochrome c3 (tetraheme) [isa: 0008369 ]
+0009478 = cytochrome c554 [isa: 0008369 ]
+0009473 = cytochrome c7 (triheme) [isa: 0008369 ]
+0009462 = cytochrome d [isa: 0008369 ]
+0009479 = cytochrome f [isa: 0008369 ]
+0005490 = cytochrome P450 [isa: 0008369 ]
+0009500 = dicluster bacterial-type ferredoxin [isa: 0008369 ]
+0009468 = diheme class I cytochrome c [isa: 0008369 ]
+0003686 = DNA repair enzyme [isa: 0008369 ]
+0003685 = DNA repair protein [isa: 0008369 ]
+0003778 = dynactin motor [isa: 0008369 ]
+0001528 = elastin [isa: 0008369 ]
+0018997 = electron transfer carrier [isa: 0008369 ]
+0008848 = enterobactin synthetase [isa: 0008369 ]
+0009936 = expansin [isa: 0008369 ]
+0005207 = extracellular matrix glycoprotein [isa: 0008369 ]
+0001511 = fibrillin [isa: 0008369 ]
+0008001 = fibrinogen [isa: 0008369 ]
+0009487 = glutaredoxin [isa: 0008369 ]
+0004374 = glycine cleavage system [isa: 0008369 ]
+0019172 = glyoxalase III [isa: 0008369 ]
+0015017 = glypican [isa: 0008369 ]
+0004898 = gp130 [isa: 0008369 ]
+0005206 = heparin sulfate proteoglycan [isa: 0008369 ]
+0008436 = heterogeneous nuclear ribonucleoprotein [isa: 0008369 ]
+0005065 = heterotrimeric G protein [isa: 0008369 ]
+0000263 = heterotrimeric G-protein GTPase, alpha-subunit [isa: 0008369 ]
+0000264 = heterotrimeric G-protein GTPase, beta-subunit [isa: 0008369 ]
+0000265 = heterotrimeric G-protein GTPase, gamma-subunit [isa: 0008369 ]
+0005321 = high-density lipoprotein [isa: 0008369 ]
+0009475 = high-molecular-weight cytochrome c (hexadecaheme) [isa: 0008369 ]
+0030053 = immunophilin [isa: 0008369 ]
+0005074 = inhibitory SMAD protein [isa: 0008369 ]
+0004442 = inositol-1,4,-bisphosphate 3-phosphatase [isa: 0008369 ]
+0004443 = inositol-1,4,-bisphosphate 4-phosphatase [isa: 0008369 ]
+0004444 = inositol-1,4,5-trisphosphate 1-phosphatase [isa: 0008369 ]
+0016313 = inositol-1,4,5-trisphosphate phosphatase [isa: 0008369 ]
+0005241 = inward rectifier channel [isa: 0008369 ]
+0005188 = larval serum protein (sensu Insecta) [isa: 0008369 ]
+0015641 = lipoprotein toxin [isa: 0008369 ]
+0005322 = low-density lipoprotein [isa: 0008369 ]
+0005557 = lymphocyte antigen [isa: 0008369 ]
+0003819 = major histocompatibility complex antigen [isa: 0008369 ]
+0005193 = major urinary protein [isa: 0008369 ]
+0003822 = MHC-interacting protein [isa: 0008369 ]
+0005189 = milk protein [isa: 0008369 ]
+0005558 = minor histocompatibility antigen [isa: 0008369 ]
+0004786 = Mn, Fe superoxide dismutase [isa: 0008369 ]
+0009499 = monocluster bacterial-type ferredoxin [isa: 0008369 ]
+0009467 = monoheme class I cytochrome c [isa: 0008369 ]
+0008751 = NAD(P)H2 dehydrogenase [isa: 0008369 ]
+0009474 = nonaheme cytochrome c [isa: 0008369 ]
+0030052 = parvulin [isa: 0008369 ]
+0005075 = pathway-specific SMAD protein [isa: 0008369 ]
+0005054 = peroxisome integral membrane receptor [isa: 0008369 ]
+0005050 = peroxisome receptor [isa: 0008369 ]
+0005318 = phosphate:hydrogen symporter [isa: 0008369 ]
+0004440 = phosphatidylinositol-3,4-bisphosphate 4-phosphatase [isa: 0008369 ]
+0008498 = phospholipid scrambling [isa: 0008369 ]
+0005211 = plasma glycoprotein [isa: 0008369 ]
+0005209 = plasma protein [isa: 0008369 ]
+0015006 = plastocyanin [isa: 0008369 ]
+0015000 = polyferredoxin [isa: 0008369 ]
+0005552 = polyubiquitin [isa: 0008369 ]
+0003892 = proliferating cell nuclear antigen [isa: 0008369 ]
+0016026 = proteasome endopeptidase core [isa: 0008369 ]
+0016025 = proteasome endopeptidase regulator [isa: 0008369 ]
+0005203 = proteoglycan [isa: 0008369 ]
+0030067 = respiratory chain cytochrome b6 [isa: 0008369 ]
+0003733 = ribonucleoprotein [isa: 0008369 ]
+0005566 = ribosomal RNA [isa: 0008369 ]
+0000047 = Rieske iron-sulfur protein [isa: 0008369 ]
+0003967 = RNA-directed DNA polymerase, group II intron encoded [isa: 0008369 ]
+0003966 = RNA-directed DNA polymerase, transposon encoded [isa: 0008369 ]
+0009489 = rubredoxin [isa: 0008369 ]
+0045164 = secretin (sensu Mammalia) [isa: 0008369 ]
+0008337 = selectin [isa: 0008369 ]
+0005190 = seminal fluid protein [isa: 0008369 ]
+0015004 = small blue copper electron carrier [isa: 0008369 ]
+0030356 = small cytoplasmic ribonucleoprotein [isa: 0008369 ]
+0003734 = small nuclear ribonucleoprotein [isa: 0008369 ]
+0005570 = small nuclear RNA [isa: 0008369 ]
+0030355 = small nucleolar ribonucleoprotein [isa: 0008369 ]
+0005569 = small nucleolar RNA [isa: 0008369 ]
+0005468 = small-molecule carrier or transporter [isa: 0008369 ]
+0009465 = soluble cytochrome b562 [isa: 0008369 ]
+0005187 = storage protein [isa: 0008369 ]
+0008041 = storage protein of fat body (sensu Insecta) [isa: 0008369 ]
+0015023 = syndecan [isa: 0008369 ]
+0000008 = thioredoxin [isa: 0008369 ]
+0009495 = thioredoxin-like Fe2S2 ferredoxin [isa: 0008369 ]
+0005563 = transfer RNA [isa: 0008369 ]
+0009023 = tRNA sulfurtransferase [isa: 0008369 ]
+0008222 = tumor antigen [isa: 0008369 ]
+0008181 = tumor suppressor [isa: 0008369 ]
+0005551 = ubiquitin [isa: 0008369 ]
+0005553 = ubiquitin-ribosomal protein fusion protein [isa: 0008369 ]
+0005192 = urinary protein [isa: 0008369 ]
+0005479 = vacuolar assembly [isa: 0008369 ]
+0005323 = very-low-density lipoprotein [isa: 0008369 ]
+0005481 = vesicle fusion [isa: 0008369 ]
+0005482 = vesicle targeting [isa: 0008369 ]
+0005480 = vesicle transport [isa: 0008369 ]
+0008197 = yolk protein [isa: 0008369 ]
+0017028 = protein stabilization [isa: 0003674 ]
+0017029 = lysosomal protein stabilization [isa: 0017028 ]
+0017030 = beta-galactosidase stabilization [isa: 0017029 ]
+0008638 = protein tagging [isa: 0003674 ]
+0000211 = protein degradation tagging [isa: 0008638 ]
+0045305 = regulator of establishment of competence for transformation [isa: 0003674 ]
+0045307 = activator of the establishment of competence for transformation [isa: 0045305 ]
+0045306 = inhibitor of the establishment of competence for transformation [isa: 0045305 ]
+0004871 = signal transducer [isa: 0003674 ]
+0017106 = activin inhibitor [isa: 0004871 ]
+0016015 = morphogen [isa: 0004871 ]
+0009370 = quorum sensing response regulator [isa: 0004871 ]
+0009369 = quorum sensing signal generator [isa: 0004871 ]
+0004872 = receptor [isa: 0004871 ]
+0016964 = alpha-2 macroglobulin receptor [isa: 0004872 ]
+0030226 = apolipoprotein receptor [isa: 0004872 ]
+0030227 = apolipoprotein E receptor [isa: 0030226 ]
+0004874 = aryl hydrocarbon receptor [isa: 0004872 ]
+0004875 = complement receptor [isa: 0004872 ]
+0004876 = complement component C3a receptor [isa: 0004875 ]
+0004877 = complement component C3b receptor [isa: 0004875 ]
+0004878 = complement component C5 receptor [isa: 0004875 ]
+0015026 = coreceptor [isa: 0004872 ]
+0015028 = coreceptor, insoluble ligand [isa: 0015026 ]
+0015027 = coreceptor, soluble ligand [isa: 0015026 ]
+0008036 = diuretic hormone receptor [isa: 0004872 ]
+0015025 = GPI-anchored membrane-bound receptor [isa: 0004872 ]
+0030377 = U-plasminogen activator receptor [isa: 0015025 ]
+0030373 = high molecular weight B-cell growth factor receptor [isa: 0004872 ]
+0008095 = inositol-1,4,5-triphosphate receptor [isa: 0004872 ]
+0015029 = internalization receptor [isa: 0004872 ]
+0016922 = ligand-dependent nuclear receptor interactor [isa: 0004872 ]
+0016923 = ligand-dependent thyroid hormone receptor interactor [isa: 0016962 ] [partof: 0016922 ]
+0001653 = peptide receptor [isa: 0004872 ]
+0008528 = peptide receptor, G-protein coupled [isa: 0001584 0001653 ]
+0001605 = adrenomedullin receptor [isa: 0008528 ]
+0008261 = allatostatin receptor [isa: 0008528 ]
+0004942 = anaphylatoxin receptor [isa: 0008528 ]
+0004943 = C3a anaphylatoxin receptor [isa: 0004942 ]
+0004944 = C5a anaphylatoxin receptor [isa: 0004942 ]
+0001595 = angiotensin receptor [isa: 0008528 ]
+0001596 = angiotensin type I receptor [isa: 0001595 ]
+0004945 = angiotensin type II receptor [isa: 0001595 ]
+0001597 = apelin-like receptor [isa: 0008528 ]
+0004946 = bombesin receptor [isa: 0008528 ]
+0004947 = bradykinin receptor [isa: 0008528 ]
+0001598 = chemokine receptor-like receptor [isa: 0008528 ]
+0004951 = cholecystokinin receptor [isa: 0008528 ]
+0015054 = gastrin receptor [isa: 0004951 ]
+0004962 = endothelin receptor [isa: 0008528 ]
+0001599 = endothelin-A receptor [isa: 0004962 ]
+0001600 = endothelin-B receptor [isa: 0004962 ]
+0001637 = G-protein chemoattractant receptor [isa: 0008528 ]
+0001646 = cAMP receptor, chemotaxis [isa: 0001637 ]
+0004966 = galanin receptor [isa: 0008528 ]
+0001606 = GPR37/endothelin B-like receptor [isa: 0008528 ]
+0004977 = melanocortin receptor [isa: 0008528 ]
+0004978 = adrenocorticotropin receptor [isa: 0004977 ]
+0004979 = beta-endorphin receptor [isa: 0004977 ]
+0004980 = melanocyte stimulating hormone receptor [isa: 0004977 ]
+0004982 = N-formyl peptide receptor [isa: 0008528 ]
+0001607 = neuromedin U receptor [isa: 0008528 ]
+0008188 = neuropeptide receptor [isa: 0008528 ]
+0042263 = neuropeptide F receptor [isa: 0008188 ]
+0004983 = neuropeptide Y receptor [isa: 0008188 ]
+0001602 = pancreatic polypeptide receptor [isa: 0004983 ]
+0001601 = peptide YY receptor [isa: 0004983 ]
+0004995 = tachykinin receptor [isa: 0008188 ]
+0016498 = neuromedin K receptor [isa: 0004995 ]
+0016497 = substance K receptor [isa: 0004995 ]
+0016496 = substance P receptor [isa: 0004995 ]
+0016492 = neurotensin receptor, G-protein coupled [isa: 0008528 ]
+0004985 = opioid receptor [isa: 0008528 ]
+0004986 = delta-opioid receptor [isa: 0004985 ]
+0004987 = kappa-opioid receptor [isa: 0004985 ]
+0004988 = mu-opioid receptor [isa: 0004985 ]
+0015051 = X-opioid receptor [isa: 0004985 ]
+0016499 = orexin receptor [isa: 0008528 ]
+0001648 = proteinase activated receptor [isa: 0008528 ]
+0004994 = somatostatin receptor [isa: 0008528 ]
+0015057 = thrombin receptor [isa: 0008528 ]
+0001604 = urotensin II receptor [isa: 0008528 ]
+0001603 = vasopressin-like receptor [isa: 0008528 ]
+0004990 = oxytocin receptor [isa: 0001603 ]
+0005000 = vasopressin receptor [isa: 0001603 ]
+0001565 = phorbol ester receptor [isa: 0004872 ]
+0001566 = non-kinase phorbol ester receptor [isa: 0001565 ]
+0009881 = photoreceptor [isa: 0004872 ]
+0009882 = blue light photoreceptor [isa: 0009881 ]
+0008020 = G-protein coupled photoreceptor [isa: 0001584 0009881 ]
+0015053 = opsin [isa: 0008020 ]
+0015063 = long-wave-sensitive opsin [isa: 0015053 ]
+0015060 = green-sensitive opsin [isa: 0015063 ]
+0015061 = red-sensitive opsin [isa: 0015063 ]
+0016016 = short-wave-sensitive opsin [isa: 0015053 ]
+0015059 = blue-sensitive opsin [isa: 0016016 ]
+0015062 = violet-sensitive opsin [isa: 0016016 ]
+0015064 = UV-sensitive opsin [isa: 0015053 ]
+0009883 = red/far-red light photoreceptor [isa: 0009881 ]
+0015477 = receptor porin [isa: 0004872 0015288 ]
+0004888 = transmembrane receptor [isa: 0004872 ]
+0004873 = asialoglycoprotein receptor [isa: 0004888 ]
+0008046 = axon guidance receptor [isa: 0004888 ]
+0005042 = netrin receptor [isa: 0008046 ]
+0005043 = repulsive netrin receptor [isa: 0008046 ]
+0004892 = B-cell receptor [isa: 0004888 ]
+0009884 = cytokinin receptor [isa: 0004888 ]
+0001647 = G-protein coupled cytokinin receptor [isa: 0004930 0009884 ]
+0005035 = death receptor [isa: 0004888 ]
+0005037 = death receptor adaptor protein [isa: 0016962 ] [partof: 0005035 ]
+0005038 = death receptor interacting protein [isa: 0016962 ] [partof: 0005035 ]
+0005039 = death receptor-associated factor [isa: 0016962 ] [partof: 0005035 ]
+0005040 = decoy death receptor [isa: 0005035 ]
+0005031 = tumor necrosis factor receptor [isa: 0005027 0005035 ]
+0005032 = tumor necrosis factor receptor, type I [isa: 0005031 ]
+0005033 = tumor necrosis factor receptor, type II [isa: 0005031 ]
+0008529 = endogenous peptide receptor [isa: 0004888 ]
+0005045 = endoplasmic reticulum receptor [isa: 0004888 ]
+0045015 = HDEL receptor [isa: 0005045 ]
+0005046 = KDEL receptor [isa: 0005045 ]
+0005047 = signal recognition particle receptor [isa: 0005045 ]
+0005048 = signal sequence receptor [isa: 0005045 ]
+0008530 = exogenous peptide receptor [isa: 0004888 ]
+0004930 = G-protein coupled receptor [isa: 0004888 ]
+0045125 = bioactive lipid receptor [isa: 0004930 ]
+0001619 = lysosphingolipid and lysophosphatidic acid receptor [isa: 0001584 0045125 ]
+0016526 = G-protein coupled receptor, unknown ligand [isa: 0004930 ]
+0001620 = class A orphan receptor [isa: 0001584 0016526 ]
+0001625 = Epstein-Barr Virus-induced receptor [isa: 0001620 ]
+0001629 = G-protein receptor 45-like receptor [isa: 0001620 ]
+0001628 = gastropyloric receptor [isa: 0001620 ]
+0001630 = GP40-like receptor [isa: 0001620 ]
+0001627 = leucine-rich G-protein receptor-like receptor [isa: 0001620 ]
+0004974 = leukotriene receptor [isa: 0001620 ]
+0001631 = cysteinyl leukotriene receptor [isa: 0004974 ]
+0001632 = leukotriene B4 receptor [isa: 0004974 ]
+0001623 = Mas proto-oncogene receptor [isa: 0001620 ]
+0001626 = nociceptin/orphanin-FQ receptor [isa: 0001620 ]
+0001621 = platelet ADP receptor [isa: 0001620 ]
+0001624 = RDC1 receptor [isa: 0001620 ]
+0001622 = super conserved receptor expressed in brain receptor [isa: 0001620 ]
+0001638 = class B orphan receptor [isa: 0001633 0016526 ]
+0001645 = class C orphan receptor [isa: 0008067 0016526 ]
+0008067 = metabotropic glutamate, GABA-B-like receptor [isa: 0004930 0008066 ]
+0001640 = adenylate cyclase inhibiting metabotropic glutamate receptor [isa: 0008067 ]
+0001641 = group II metabotropic glutamate receptor [isa: 0001640 ]
+0001642 = group III metabotropic glutamate receptor [isa: 0001640 ]
+0001639 = PLC activating metabotropic glutamate receptor [isa: 0008067 ]
+0016503 = pheromone receptor [isa: 0004930 ]
+0004932 = mating-type factor pheromone receptor [isa: 0016503 ]
+0004933 = mating-type a-factor pheromone receptor [isa: 0004932 ]
+0004934 = mating-type alpha-factor pheromone receptor [isa: 0004932 ]
+0001584 = rhodopsin-like receptor [isa: 0004930 ]
+0008227 = amine receptor [isa: 0001584 ]
+0004935 = adrenoceptor [isa: 0008227 ]
+0004936 = alpha-adrenergic receptor [isa: 0004935 ]
+0004937 = alpha1-adrenergic receptor [isa: 0004936 ]
+0004938 = alpha2-adrenergic receptor [isa: 0004936 ]
+0004939 = beta-adrenergic receptor [isa: 0004935 ]
+0004940 = beta1-adrenergic receptor [isa: 0004939 ]
+0004941 = beta2-adrenergic receptor [isa: 0004939 ]
+0015052 = beta3-adrenergic receptor [isa: 0004939 ]
+0004952 = dopamine receptor [isa: 0008227 ]
+0001588 = dopamine D1 receptor-like receptor [isa: 0004952 ]
+0001590 = dopamine D1 receptor [isa: 0001588 ]
+0001589 = dopamine D5 receptor [isa: 0001588 ]
+0001591 = dopamine D2 receptor-like receptor [isa: 0004952 ]
+0001670 = dopamine D2 receptor [isa: 0001591 ]
+0001592 = dopamine D3 receptor [isa: 0001591 ]
+0001593 = dopamine D4 receptor [isa: 0001591 ]
+0004969 = histamine receptor [isa: 0008227 ]
+0004989 = octopamine receptor [isa: 0008227 ]
+0004993 = serotonin receptor [isa: 0008227 ]
+0001586 = 5-HT1 receptor [isa: 0004993 ]
+0001587 = 5-HT2 receptor [isa: 0004993 ]
+0016609 = G-protein coupled serotonin receptor [isa: 0004993 ]
+0005232 = serotonin-activated cation-selective channel [isa: 0004993 0005231 0005261 ]
+0001594 = trace-amine receptor [isa: 0008227 ]
+0008226 = tyramine receptor [isa: 0008227 ]
+0004949 = cannabinoid receptor [isa: 0001584 ]
+0004953 = eicosanoid receptor [isa: 0001584 ]
+0004954 = prostanoid receptor [isa: 0004953 ]
+0016501 = prostacylin receptor [isa: 0004954 ]
+0004955 = prostaglandin receptor [isa: 0004954 ]
+0004956 = prostaglandin D receptor [isa: 0004955 ]
+0004957 = prostaglandin E receptor [isa: 0004955 ]
+0004958 = prostaglandin F receptor [isa: 0004955 ]
+0004959 = prostaglandin I receptor [isa: 0004955 ]
+0004960 = thromboxane receptor [isa: 0004954 ]
+0004961 = thromboxane A2 receptor [isa: 0004960 ]
+0008502 = melatonin receptor [isa: 0001584 ]
+0001608 = nucleotide receptor, G-protein coupled [isa: 0001584 ]
+0045028 = purinergic nucleotide receptor, G-protein coupled [isa: 0001608 0001614 ]
+0001609 = adenosine receptor, G-protein coupled [isa: 0045028 ]
+0001610 = A1 adenosine receptor, G-protein coupled [isa: 0001609 ]
+0001611 = A2A adenosine receptor, G-protein coupled [isa: 0001609 ]
+0001612 = A2B adenosine receptor, G-protein coupled [isa: 0001609 ]
+0001613 = A3 adenosine receptor, G-protein coupled [isa: 0001609 ]
+0045032 = ADP-activated nucleotide receptor [isa: 0001609 ]
+0045031 = ATP-activated nucleotide receptor [isa: 0001609 ]
+0015065 = uridine nucleotide receptor [isa: 0045028 ]
+0045029 = UDP-activated nucleotide receptor [isa: 0015065 ]
+0045030 = UTP-activated nucleotide receptor [isa: 0015065 ]
+0004984 = olfactory receptor [isa: 0001584 ]
+0004992 = platelet activating factor receptor [isa: 0001584 ]
+0016500 = protein-hormone receptor [isa: 0001584 ]
+0004963 = follicle stimulating hormone receptor [isa: 0016500 ]
+0004968 = gonadotropin-releasing hormone receptor [isa: 0016500 ]
+0004964 = lutropin-choriogonadotropic hormone receptor [isa: 0016500 ]
+0030273 = melanin-concentrating hormone receptor [isa: 0016500 ]
+0004996 = thyroid-stimulating hormone receptor [isa: 0016500 ]
+0008527 = taste receptor [isa: 0001584 ]
+0001615 = thyrotropin releasing hormone and secretagogue-like receptors [isa: 0001584 ]
+0001616 = growth hormone secretagogue receptor [isa: 0001615 ]
+0001617 = growth hormone secretagogue-like receptor [isa: 0001615 ]
+0004997 = thyrotropin-releasing hormone receptor [isa: 0001615 ]
+0001618 = viral receptor [isa: 0001584 ]
+0001633 = secretin-like receptor [isa: 0004930 ]
+0016527 = brain-specific angiogenesis inhibitor [isa: 0001633 ]
+0001635 = calcitonin gene-related polypeptide receptor [isa: 0001633 ]
+0004948 = calcitonin receptor [isa: 0001633 ]
+0001636 = corticotrophin-releasing factor gastric inhibitory peptide-like receptor [isa: 0001633 ]
+0015056 = corticotrophin-releasing factor receptor [isa: 0001636 ]
+0016519 = gastric inhibitory peptide receptor [isa: 0001636 ]
+0015058 = EGF-like module containing hormone receptor [isa: 0001633 ]
+0004967 = glucagon receptor [isa: 0001633 ]
+0016520 = growth hormone-releasing hormone receptor [isa: 0001633 ]
+0004991 = parathyroid hormone receptor [isa: 0001633 ]
+0001634 = pituitary adenylate cyclase activating protein receptor [isa: 0001633 ]
+0015055 = secretin receptor [isa: 0001633 ]
+0004999 = vasoactive intestinal polypeptide receptor [isa: 0001633 ]
+0008066 = glutamate receptor [isa: 0004888 ]
+0005234 = glutamate-gated ion channel [isa: 0005231 0008066 0015259 ]
+0008068 = glutamate-gated chloride channel [isa: 0005234 0005254 ]
+0004970 = ionotropic glutamate receptor [isa: 0005234 0005261 ]
+0004971 = alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor [isa: 0004970 ]
+0015277 = kainate selective glutamate receptor [isa: 0004970 ]
+0004972 = N-methyl-D-aspartate selective glutamate receptor [isa: 0004970 ]
+0004891 = glycine-inhibited chloride channel [isa: 0004888 0005237 0005254 ]
+0004896 = hematopoietin/interferon-class (D200-domain) cytokine receptor [isa: 0004888 ]
+0004897 = ciliary neurotrophic factor receptor [isa: 0004896 ]
+0004899 = leukemia inhibitory factor receptor beta-protein [isa: 0004897 0005062 ]
+0004900 = erythropoietin receptor [isa: 0004896 ]
+0016167 = glial cell line-derived neurotrophic factor receptor [isa: 0004896 ]
+0004903 = growth hormone receptor [isa: 0004896 ]
+0004923 = leukemia inhibitory factor receptor [isa: 0004896 ]
+0004924 = oncostatin-M receptor [isa: 0004896 ]
+0004925 = prolactin receptor [isa: 0004896 ]
+0016489 = immunoglobulin receptor [isa: 0004888 ]
+0016524 = latrotoxin receptor [isa: 0004888 ]
+0030228 = lipoprotein receptor [isa: 0004888 ]
+0030229 = very-low-density lipoprotein receptor [isa: 0030228 ]
+0030106 = MHC class I receptor [isa: 0004888 ]
+0030108 = HLA-A specific activating MHC class I receptor [isa: 0030106 ]
+0030107 = HLA-A specific inhibitory MHC class I receptor [isa: 0030106 ]
+0030109 = HLA-B specific inhibitory MHC class I receptor [isa: 0030106 ]
+0030110 = HLA-C specific inhibitory MHC class I receptor [isa: 0030106 ]
+0045012 = MHC class II receptor [isa: 0004888 ]
+0045233 = natural killer cell receptor [isa: 0004888 ]
+0030379 = neurotensin receptor, non-G-protein coupled [isa: 0004888 ]
+0005027 = NGF/TNF (6 C-domain) receptor [isa: 0004888 ]
+0005029 = CD27 receptor [isa: 0005027 ]
+0005028 = CD40 receptor [isa: 0005027 ]
+0005030 = neurotrophin p75 receptor [isa: 0005027 ]
+0004926 = non-G-protein coupled 7TM receptor [isa: 0004888 ]
+0004928 = frizzled receptor [isa: 0004926 ]
+0004929 = frizzled-2 receptor [isa: 0004926 ]
+0008158 = patched receptor [isa: 0004926 ]
+0004927 = sevenless receptor [isa: 0004926 ]
+0001571 = non-tyrosine kinase fibroblast growth factor receptor [isa: 0004888 ]
+0005049 = nuclear export signal receptor [isa: 0004888 ]
+0016502 = nucleotide receptor [isa: 0004888 ]
+0001614 = purinergic nucleotide receptor [isa: 0016502 ]
+0004931 = ATP-gated cation channel [isa: 0001614 0005231 0005261 ]
+0005034 = osmosensor [isa: 0004888 ]
+0008329 = pattern recognition receptor [isa: 0004888 ]
+0008029 = pentraxin receptor [isa: 0004888 ]
+0008030 = neuronal pentraxin receptor [isa: 0008029 ]
+0016019 = peptidoglycan recognition [isa: 0004888 ]
+0030376 = ribosome receptor [isa: 0004888 ]
+0005044 = scavenger receptor [isa: 0004888 ]
+0017154 = semaphorin receptor [isa: 0004888 ]
+0008281 = sulfonylurea receptor [isa: 0004888 0005267 ]
+0004894 = T-cell receptor [isa: 0004888 ]
+0042096 = alpha-beta T-cell receptor [isa: 0004894 ]
+0042099 = gamma-delta T-cell receptor [isa: 0004894 ]
+0005056 = tiggrin receptor [isa: 0004888 ]
+0004998 = transferrin receptor [isa: 0004888 ]
+0016931 = vasopressin activated calcium mobilizing receptor [isa: 0004872 ]
+0019041 = viral antireceptor [isa: 0004872 ]
+0008196 = vitellogenin receptor [isa: 0004872 ]
+0005057 = receptor signaling protein [isa: 0004871 ]
+0005061 = aryl hydrocarbon receptor nuclear translocator [isa: 0005057 ]
+0005062 = hematopoietin/interferon-class (D200-domain) cytokine receptor signal transducer [isa: 0005057 ]
+0030545 = receptor regulator [isa: 0005057 ]
+0030548 = acetylcholine receptor regulator [isa: 0030545 ]
+0030549 = acetylcholine receptor activator [isa: 0030546 0030548 ]
+0030550 = acetylcholine receptor inhibitor [isa: 0030547 0030548 ]
+0030546 = receptor activator [isa: 0030545 ]
+0030547 = receptor inhibitor [isa: 0030545 ]
+0030159 = receptor signaling complex scaffold protein [isa: 0005057 ]
+0030160 = GKAP/Homer scaffold protein [isa: 0030159 ]
+0005078 = MAP-kinase scaffold protein [isa: 0005076 0030159 ]
+0005076 = receptor signaling protein serine/threonine kinase signaling protein [isa: 0005057 ]
+0005077 = MAP-kinase anchor protein [isa: 0005076 ]
+0005079 = protein kinase A anchor protein [isa: 0005076 ]
+0005080 = protein kinase C binding [isa: 0005076 ]
+0042057 = transforming growth factor-beta receptor anchor [isa: 0005076 ]
+0005081 = receptor signaling protein serine/threonine phosphatase signaling protein [isa: 0005057 ]
+0008268 = receptor signaling protein tyrosine kinase signaling protein [isa: 0005057 ]
+0008269 = JAK pathway signal transduction adaptor [isa: 0008268 ]
+0016299 = regulator of G-protein signaling [isa: 0005057 ]
+0005083 = small GTPase regulatory/interacting protein [isa: 0005057 ]
+0005092 = GDP-dissociation inhibitor [isa: 0005083 ]
+0005093 = RAB GDP-dissociation inhibitor [isa: 0005092 ]
+0005094 = Rho GDP-dissociation inhibitor [isa: 0005092 ]
+0016219 = GDP-dissociation stimulator [isa: 0005083 ]
+0016220 = RAL GDP-dissociation stimulator [isa: 0016219 ]
+0005091 = guanyl-nucleotide exchange factor adaptor [isa: 0005083 ]
+0005084 = RAB escort protein [isa: 0005083 ]
+0017137 = RAB interactor [isa: 0005083 ]
+0017160 = RAL interactor [isa: 0005083 ]
+0017016 = RAS interactor [isa: 0005083 ]
+0017031 = Rho interactor [isa: 0005083 ]
+0005071 = transmembrane receptor protein serine/threonine kinase signaling protein [isa: 0005057 ]
+0005072 = TGFbeta receptor, cytoplasmic mediator [isa: 0005071 ]
+0030616 = TGFbeta receptor, common-partner cytoplasmic mediator [isa: 0005072 ]
+0030617 = TGFbeta receptor, inhibitory cytoplasmic mediator [isa: 0005072 ]
+0030618 = TGFbeta receptor, pathway-specific cytoplasmic mediator [isa: 0005072 ]
+0005066 = transmembrane receptor protein tyrosine kinase signaling protein [isa: 0005057 ]
+0005067 = insulin-like growth factor receptor binding [isa: 0005066 ]
+0005068 = transmembrane receptor protein tyrosine kinase adaptor protein [isa: 0005066 ]
+0005069 = transmembrane receptor protein tyrosine kinase docking protein [isa: 0005066 ]
+0005070 = SH3/SH2 adaptor protein [isa: 0005069 ]
+0016962 = receptor-associated protein [isa: 0004871 ]
+0016963 = alpha-2 macroglobulin receptor-associated protein [isa: 0016962 ]
+0005240 = glycine receptor-associated protein [isa: 0015457 0016962 ]
+0004973 = N-methyl-D-aspartate receptor-associated protein [isa: 0015457 0016962 ]
+0017027 = transmembrane receptor protein serine/threonine kinase receptor-associated protein [isa: 0016962 ]
+0005198 = structural molecule [isa: 0003674 ]
+0005201 = extracellular matrix structural constituent [isa: 0005198 ]
+0030023 = extracellular matrix constituent conferring elasticity [isa: 0005201 ]
+0030197 = extracellular matrix constituent, lubricant [isa: 0005201 ]
+0030021 = extracellular matrix structural constituent conferring compression resistance [isa: 0005201 ]
+0030020 = extracellular matrix structural constituent conferring tensile strength [isa: 0005201 ]
+0008141 = puparial glue (sensu Diptera) [isa: 0005198 ]
+0008147 = structural constituent of bone [isa: 0005198 ]
+0005199 = structural constituent of cell wall [isa: 0005198 ]
+0005213 = structural constituent of chorion (sensu Insecta) [isa: 0005198 ]
+0030527 = structural constituent of chromatin [isa: 0005198 ]
+0042302 = structural constituent of cuticle [isa: 0005198 ]
+0005214 = structural constituent of cuticle (sensu Insecta) [isa: 0042302 ]
+0008012 = structural constituent of adult cuticle (sensu Insecta) [isa: 0005214 ]
+0008010 = structural constituent of larval cuticle (sensu Insecta) [isa: 0005214 ]
+0008011 = structural constituent of pupal cuticle (sensu Insecta) [isa: 0005214 ]
+0042329 = structural constituent of cuticle (sensu Nematoda) [isa: 0042302 ]
+0005200 = structural constituent of cytoskeleton [isa: 0005198 ]
+0030280 = structural constituent of epidermis [isa: 0005198 ]
+0030281 = structural constituent of cutaneous appendage [isa: 0030280 ]
+0005212 = structural constituent of eye lens [isa: 0005198 ]
+0008307 = structural constituent of muscle [isa: 0005198 ]
+0019911 = structural constituent of myelin sheath [isa: 0005198 ]
+0017056 = structural constituent of nuclear pore [isa: 0005198 ]
+0016490 = structural constituent of peritrophic membrane (sensu Insecta) [isa: 0005198 ]
+0003735 = structural constituent of ribosome [isa: 0005198 ]
+0030345 = structural constituent of tooth enamel [isa: 0005198 ]
+0008316 = structural constituent of vitelline membrane (sensu Insecta) [isa: 0005198 ]
+0019214 = surfactant [isa: 0003674 ]
+0015070 = toxin [isa: 0003674 ]
+0019844 = endotoxin [isa: 0015070 ]
+0019845 = exotoxin [isa: 0015070 ]
+0019849 = cytotoxin [isa: 0019845 ]
+0019846 = enterotoxin [isa: 0019845 ]
+0019847 = neurotoxin [isa: 0019845 ]
+0019848 = conotoxin [isa: 0019847 ]
+0015289 = pore-forming toxin [isa: 0015070 0015267 ]
+0015469 = channel-forming toxin [isa: 0015289 ]
+0030528 = transcription regulator [isa: 0003674 ]
+0045182 = translation regulator [isa: 0003674 ]
+0045183 = translation factor, non-nucleic acid binding [isa: 0045182 ]
+0000901 = translation repressor, non-nucleic acid binding [isa: 0030371 0045183 ]
+0030371 = translation repressor [isa: 0045182 ]
+0005215 = transporter [isa: 0003674 ]
+0005275 = amine/polyamine transporter [isa: 0005215 ]
+0005277 = acetylcholine transporter [isa: 0005275 0005326 ]
+0005278 = acetylcholine:hydrogen antiporter [isa: 0005277 0015307 ]
+0015199 = betaine transporter [isa: 0005275 ]
+0015376 = betaine/GABA:sodium symporter [isa: 0005328 0015185 0015199 ]
+0015490 = cadaverine transporter [isa: 0005275 ]
+0015497 = cadaverine:lysine antiporter [isa: 0005279 0015189 0015300 0015490 ]
+0015220 = choline transporter [isa: 0005275 ]
+0015358 = amino acid/choline transporter [isa: 0005279 0015220 ]
+0005306 = choline permease [isa: 0015358 ]
+0015329 = gamma-aminobutyric acid permease [isa: 0015185 0015358 ]
+0005307 = choline:sodium symporter [isa: 0005328 0015220 ]
+0005429 = chromaffin granule amine transporter [isa: 0005275 ]
+0005329 = dopamine transporter [isa: 0005275 ]
+0005330 = dopamine:sodium symporter [isa: 0005328 0005329 ]
+0005276 = hydrogen:vesicular amine antiporter [isa: 0005275 0015297 ]
+0015200 = methylammonium transporter [isa: 0005275 ]
+0008504 = monoamine transporter [isa: 0005275 ]
+0015311 = monoamine:hydrogen antiporter [isa: 0008504 0015307 ]
+0005333 = norepinephrine transporter [isa: 0005275 0005326 ]
+0005334 = noradrenaline:sodium symporter [isa: 0005328 0005333 ]
+0015203 = polyamine transporter [isa: 0005275 ]
+0005279 = amino acid-polyamine transporter [isa: 0015171 0015203 0015291 ]
+0015359 = amino acid permease [isa: 0005279 ]
+0005286 = basic amino acid permease [isa: 0015174 0015359 ]
+0005288 = arginine permease [isa: 0005286 0015181 ]
+0015331 = asparagine/glutamine permease [isa: 0005286 0015182 0015186 ]
+0005287 = high-affinity basic amino acid transporter [isa: 0005286 ]
+0015330 = high affinity glutamine permease [isa: 0005287 0015186 ]
+0005291 = high affinity histidine permease [isa: 0005287 0005290 ]
+0005289 = high-affinity arginine transporter [isa: 0005287 0015181 ]
+0005292 = high-affinity lysine transporter [isa: 0005287 0015189 ]
+0015661 = L-lysine exporter [isa: 0005286 0015189 0015562 ]
+0005293 = lysine permease [isa: 0005286 0015189 ]
+0005281 = general amino acid permease [isa: 0015359 ]
+0005416 = cation:amino acid symporter [isa: 0005279 0008324 0015294 ]
+0015657 = branched-chain amino acid:sodium symporter [isa: 0005416 0015658 ]
+0000258 = isoleucine/valine:sodium symporter [isa: 0005304 0015188 0015657 ]
+0005280 = hydrogen:amino acid symporter [isa: 0005416 0015295 ]
+0015494 = aromatic amino acid:hydrogen symporter [isa: 0005280 0015173 ]
+0015495 = gamma-aminobutyric acid:hydrogen symporter [isa: 0005280 0015185 ]
+0015493 = lysine:hydrogen symporter [isa: 0005280 0015189 ]
+0015492 = phenylalanine:hydrogen symporter [isa: 0005280 0015192 ]
+0015534 = proline/glycine/betaine:hydrogen/sodium symporter [isa: 0005280 0015187 0015193 ]
+0015326 = cationic amino acid transporter [isa: 0005279 ]
+0005314 = high-affinity glutamate transporter [isa: 0005279 0005313 0005328 ]
+0015507 = hydroxy/aromatic amino acid permease [isa: 0005314 ]
+0015511 = serine permease [isa: 0015194 0015507 ]
+0015512 = threonine permease [isa: 0015194 0015507 ]
+0005299 = tryptophan permease [isa: 0015196 0015507 ]
+0005300 = high-affinity tryptophan transporter [isa: 0005299 ]
+0015510 = low-affinity tryptophan permease [isa: 0005299 ]
+0015508 = tyrosine permease [isa: 0005302 0015507 ]
+0015332 = leucine/valine/isoleucine permease [isa: 0005304 0005314 0015188 0015190 ]
+0015565 = threonine efflux permease [isa: 0015195 0015332 0015562 ]
+0015558 = p-aminobenzoyl-glutamate uptake permease [isa: 0005314 0015563 0015569 ]
+0005296 = proline permease [isa: 0005314 0015193 ]
+0005285 = sodium/excitatory amino acid cotransporter [isa: 0005314 ]
+0008027 = sodium/excitatory glutamate cotransporter [isa: 0005314 ]
+0005301 = valine/tyrosine/tryptophan permease [isa: 0005302 0005304 0005314 0015196 ]
+0005294 = neutral L-amino acid porter [isa: 0005279 0015175 ]
+0015655 = alanine:sodium symporter [isa: 0005294 0015294 ]
+0015328 = cystine porter [isa: 0005294 0015184 ]
+0015327 = cystine/glutamate antiporter [isa: 0005294 0005313 0015184 0015297 ]
+0015375 = glycine:sodium symporter [isa: 0005294 0005328 0015187 ]
+0000102 = L-methionine porter [isa: 0005294 0015191 ]
+0017032 = potassium:amino acid transporter [isa: 0005279 0015370 ]
+0015496 = putrescine:ornithine antiporter [isa: 0000064 0005279 0015300 0015489 ]
+0015177 = S-adenosylmethionine permease [isa: 0000095 0005279 ]
+0015178 = S-methylmethionine permease [isa: 0000100 0005279 ]
+0005283 = sodium:amino acid transporter [isa: 0005279 0015370 ]
+0005284 = insulin-activated sodium/amino acid transporter [isa: 0005283 ]
+0005295 = neutral amino acid:sodium symporter [isa: 0005283 ]
+0015374 = neutral,cationic amino acid:sodium:chloride symporter [isa: 0005283 0005326 ]
+0015312 = polyamine:hydrogen antiporter [isa: 0015203 0015307 ]
+0015489 = putrescine transporter [isa: 0015203 ]
+0015606 = spermidine transporter [isa: 0015203 ]
+0000297 = spermine transporter [isa: 0015203 ]
+0015202 = quaternary-amine transporter [isa: 0005275 ]
+0015222 = serotonin transporter [isa: 0005275 0005326 ]
+0005430 = synaptic vesicle amine transporter [isa: 0005275 ]
+0005368 = taurine transporter [isa: 0005275 0008028 ]
+0005369 = taurine:sodium symporter [isa: 0005328 0005368 ]
+0015204 = urea transporter [isa: 0005275 0015268 ]
+0015401 = urea active transporter [isa: 0015204 0015370 ]
+0015171 = amino acid transporter [isa: 0005215 ]
+0015172 = acidic amino acid transporter [isa: 0015171 ]
+0015183 = aspartate transporter [isa: 0015172 0015179 ]
+0015372 = glutamate/aspartate:sodium symporter [isa: 0005313 0015183 0015370 ]
+0005313 = glutamate transporter [isa: 0015172 0015179 ]
+0015501 = glutamate:sodium symporter [isa: 0005313 0015370 ]
+0015569 = p-aminobenzoyl-glutamate transporter [isa: 0005313 ]
+0015173 = aromatic amino acid transporter [isa: 0015171 ]
+0015192 = phenylalanine transporter [isa: 0015173 0015179 ]
+0015196 = tryptophan transporter [isa: 0015173 0015179 ]
+0005302 = tyrosine transporter [isa: 0015173 0015179 ]
+0015174 = basic amino acid transporter [isa: 0015171 ]
+0015181 = arginine transporter [isa: 0015174 0015179 ]
+0015182 = asparagine transporter [isa: 0015174 0015179 ]
+0015186 = glutamine transporter [isa: 0015174 0015179 ]
+0005290 = histidine transporter [isa: 0015174 0015179 ]
+0015189 = lysine transporter [isa: 0015174 0015179 ]
+0015658 = branched-chain aliphatic amino acid transporter [isa: 0015171 ]
+0015179 = L-amino acid transporter [isa: 0015171 ]
+0015180 = alanine transporter [isa: 0015175 0015179 ]
+0015184 = cystine transporter [isa: 0000099 0015179 ]
+0015626 = diaminopimelate transporter [isa: 0015179 ]
+0015185 = gamma-amino butyrate transporter [isa: 0015179 ]
+0005331 = GABA transporter [isa: 0015185 0015370 ]
+0005332 = GABA:sodium symporter [isa: 0005328 0015185 ]
+0015187 = glycine transporter [isa: 0015175 0015179 ]
+0015188 = isoleucine transporter [isa: 0015175 0015179 ]
+0015190 = leucine transporter [isa: 0015175 0015179 ]
+0015191 = methionine transporter [isa: 0000099 0015179 ]
+0000064 = ornithine transporter [isa: 0015179 ]
+0015193 = proline transporter [isa: 0015175 0015179 ]
+0005297 = hydrogen:proline symporter [isa: 0005328 0015193 ]
+0005298 = proline:sodium symporter [isa: 0005328 0015193 ]
+0015194 = serine transporter [isa: 0015175 0015179 ]
+0015500 = threonine/serine:sodium symporter [isa: 0015194 0015195 0015370 ]
+0015195 = threonine transporter [isa: 0015175 0015179 ]
+0005304 = valine transporter [isa: 0015175 0015179 ]
+0015175 = neutral amino acid transporter [isa: 0015171 ]
+0000099 = sulfur amino acid transporter [isa: 0015171 ]
+0000095 = S-adenosylmethionine transporter [isa: 0000099 0015223 ]
+0000100 = S-methylmethionine transporter [isa: 0000099 ]
+0015457 = auxiliary transport protein [isa: 0005215 ]
+0016249 = channel localizer [isa: 0015457 ]
+0016247 = channel regulator [isa: 0015457 ]
+0005246 = calcium channel regulator [isa: 0016247 ]
+0019855 = calcium channel inhibitor [isa: 0005246 0008200 ]
+0016248 = channel inhibitor [isa: 0016247 ]
+0008200 = ion channel inhibitor [isa: 0016248 ]
+0019869 = chloride channel inhibitor [isa: 0008200 0017081 ]
+0019870 = potassium channel inhibitor [isa: 0008200 0015459 ]
+0019871 = sodium channel inhibitor [isa: 0008200 0017080 ]
+0017081 = chloride channel regulator [isa: 0016247 ]
+0015459 = potassium channel regulator [isa: 0016247 ]
+0017080 = sodium channel regulator [isa: 0016247 ]
+0015458 = low voltage-dependent potassium channel auxiliary protein [isa: 0015457 ]
+0016974 = sodium channel auxiliary protein [isa: 0015457 ]
+0015460 = transport accessory protein [isa: 0015457 ]
+0015144 = carbohydrate transporter [isa: 0005215 ]
+0015154 = disaccharide transporter [isa: 0015144 ]
+0019191 = cellobiose transporter [isa: 0015154 ]
+0015155 = lactose transporter [isa: 0015154 ]
+0015305 = lactose,galactose:hydrogen symporter [isa: 0005351 0005354 0015155 0015295 ]
+0015543 = lactose/glucose efflux transporter [isa: 0005355 0015155 0015542 ]
+0015528 = lactose:hydrogen symporter [isa: 0005402 0015155 0015295 ]
+0005363 = maltose transporter [isa: 0015154 ]
+0015481 = maltose transporting porin [isa: 0005363 0015288 ]
+0005364 = maltose:hydrogen symporter [isa: 0005351 0005363 0015295 ]
+0015156 = melibiose transporter [isa: 0015154 ]
+0015487 = melibiose permease [isa: 0015156 0015486 ]
+0008515 = sucrose transporter [isa: 0015154 ]
+0009669 = sucrose permease [isa: 0008515 0015486 ]
+0008506 = sucrose:hydrogen symporter [isa: 0005351 0008515 0015295 ]
+0015574 = trehalose transporter [isa: 0015154 ]
+0015163 = hexuronide transporter [isa: 0015144 ]
+0015164 = glucuronide transporter [isa: 0015163 ]
+0015488 = glucuronide permease [isa: 0015164 0015486 ]
+0015145 = monosaccharide transporter [isa: 0015144 ]
+0015149 = hexose transporter [isa: 0015145 ]
+0015593 = allose transporter [isa: 0015149 ]
+0005353 = fructose transporter [isa: 0015149 ]
+0015284 = fructose uniporter [isa: 0005353 0008516 ]
+0015150 = fucose transporter [isa: 0015149 ]
+0015535 = fucose:hydrogen symporter [isa: 0005402 0015150 0015295 ]
+0019196 = galactosamine transporter [isa: 0015149 ]
+0005354 = galactose transporter [isa: 0015149 ]
+0015303 = galactose, glucose uniporter [isa: 0005354 0008516 ]
+0015517 = galactose:hydrogen symporter [isa: 0005351 0005354 0015295 ]
+0015371 = galactose:sodium symporter [isa: 0005354 0015370 ]
+0005355 = glucose transporter [isa: 0015149 ]
+0015151 = alpha-glucoside transporter [isa: 0005355 ]
+0015573 = beta-glucoside transporter [isa: 0005355 ]
+0015304 = glucose uniporter [isa: 0005355 0008516 ]
+0015152 = glucose-6-phosphate transporter [isa: 0005355 0015119 ]
+0005412 = glucose:sodium symporter [isa: 0005355 0015370 ]
+0005362 = low-affinity glucose:sodium symporter [isa: 0005412 ]
+0008516 = hexose uniporter [isa: 0005351 0015149 0015292 ]
+0015578 = mannose transporter [isa: 0015149 ]
+0015592 = methylgalactoside transporter [isa: 0015149 ]
+0015571 = N-acetyl galactosamine transporter [isa: 0015149 ]
+0015572 = N-acetyl glucosamine transporter [isa: 0015149 ]
+0015153 = rhamnose transporter [isa: 0015149 ]
+0019194 = sorbose transporter [isa: 0015149 ]
+0015146 = pentose transporter [isa: 0015145 ]
+0015147 = arabinose transporter [isa: 0015146 ]
+0015523 = arabinose efflux permease [isa: 0005351 0015147 0015562 ]
+0015524 = arabinose/beta-D-thiogalactopyranoside:hydrogen antiporter [isa: 0005351 0015147 ]
+0015518 = arabinose:hydrogen symporter [isa: 0005351 0015147 0015295 ]
+0015591 = ribose transporter [isa: 0015146 ]
+0015148 = xylose transporter [isa: 0015146 ]
+0015519 = xylose:hydrogen symporter [isa: 0005351 0015148 0015295 ]
+0005338 = nucleotide-sugar transporter [isa: 0015144 ]
+0015165 = pyrimidine nucleotide sugar transporter [isa: 0005338 ]
+0005456 = CMP-sialic acid transporter [isa: 0015165 ]
+0005457 = GDP-fucose transporter [isa: 0015165 ]
+0005458 = GDP-mannose transporter [isa: 0015165 ]
+0005459 = UDP-galactose transporter [isa: 0015165 ]
+0005460 = UDP-glucose transporter [isa: 0015165 ]
+0005461 = UDP-glucuronic acid transporter [isa: 0015165 ]
+0005463 = UDP-N-acetylgalactosamine transporter [isa: 0015165 ]
+0005462 = UDP-N-acetylglucosamine transporter [isa: 0015165 ]
+0005464 = UDP-xylose transporter [isa: 0015165 ]
+0015157 = oligosaccharide transporter [isa: 0015144 ]
+0015461 = endosomal oligosaccharide transporter [isa: 0005478 0015157 ]
+0015478 = oligosaccharide transporting porin [isa: 0015157 0015288 ]
+0015158 = raffinose transporter [isa: 0015157 ]
+0015529 = raffinose:hydrogen symporter [isa: 0005402 0015158 0015295 ]
+0015136 = sialic acid transporter [isa: 0008028 0015144 ]
+0015538 = sialic acid permease [isa: 0005351 0015136 ]
+0005351 = sugar porter [isa: 0015144 0015291 ]
+0015649 = 2-keto-3-deoxygluconate:hydrogen symporter [isa: 0005351 0015128 0015295 ]
+0005402 = cation:sugar symporter [isa: 0005351 0008324 0015294 ]
+0005403 = hydrogen:sugar symporter-transporter [isa: 0005402 0015295 ]
+0005357 = constitutive hydrogen:glucose transporter [isa: 0005403 ]
+0005358 = high-affinity hydrogen:glucose transporter [isa: 0005403 ]
+0005356 = hydrogen:glucose transporter [isa: 0005403 ]
+0005360 = insulin-responsive hydrogen:glucose transporter [isa: 0005403 ]
+0005359 = low-affinity hydrogen:glucose transporter [isa: 0005403 ]
+0005361 = trans-epithelial hydrogen:glucose transporter [isa: 0005403 ]
+0015561 = rhamnose:hydrogen symporter [isa: 0005402 0015295 ]
+0005352 = general alpha-glucoside:hydrogen symporter [isa: 0005351 0015295 ]
+0008524 = glucose 6-phosphate:phosphate antiporter [isa: 0005351 0015301 0015315 ]
+0015527 = glycerol-phosphate:inorganic phosphate antiporter [isa: 0005315 0005351 0015169 ]
+0015486 = glycoside-pentoside-hexuronide:cation symporter [isa: 0005351 0015294 ]
+0015526 = hexose-phosphate:inorganic phosphate antiporter [isa: 0005315 0005351 0015119 ]
+0009679 = hexose:hydrogen symporter [isa: 0005351 0015293 ]
+0015539 = hexuronate (glucuronate/galacturonate) porter [isa: 0005351 0015135 0015550 ]
+0015560 = L-idonate/D-gluconate:hydrogen symporter [isa: 0005351 0015128 0015295 0015568 ]
+0015650 = lactate:hydrogen porter [isa: 0005351 ]
+0005366 = myo-inositol:hydrogen symporter [isa: 0005351 0005365 0015295 ]
+0015159 = polysaccharide transporter [isa: 0005351 ]
+0015160 = beta-glucan transporter [isa: 0015159 ]
+0015161 = capsular-polysaccharide transporter [isa: 0015159 ]
+0015221 = lipopolysaccharide transporter [isa: 0015159 ]
+0015634 = lipopolysaccharide exporter [isa: 0015221 ]
+0015162 = teichoic acid transporter [isa: 0015159 ]
+0015306 = sialate transporter [isa: 0005351 0015296 ]
+0015542 = sugar efflux transporter [isa: 0005351 ]
+0005386 = carrier [isa: 0005215 ]
+0015290 = electrochemical potential-driven transporter [isa: 0005386 ]
+0015404 = ion-gradient-driven energizer [isa: 0015290 ]
+0015570 = energizer of outer membrane receptor-mediated transport [isa: 0015404 ]
+0015291 = porter [isa: 0015290 ]
+0015297 = antiporter [isa: 0015291 ]
+0015301 = anion:anion antiporter [isa: 0015297 ]
+0015380 = anion exchanger [isa: 0015106 0015108 0015301 ]
+0017107 = anion exchanger adaptor [isa: 0015380 ]
+0005452 = inorganic anion exchanger [isa: 0015380 ]
+0015515 = citrate:succinate antiporter [isa: 0008513 0015137 0015141 0015301 ]
+0015383 = sulfate:bicarbonate antiporter [isa: 0008271 0015106 0015301 ]
+0015516 = tartrate:succinate antiporter [isa: 0008513 0015141 0015301 0015554 ]
+0015491 = cation:cation antiporter [isa: 0015297 ]
+0015386 = potassium:hydrogen antiporter [isa: 0005451 0015079 0015491 ]
+0015385 = sodium:hydrogen antiporter [isa: 0005451 0015491 ]
+0015502 = pH dependent sodium:hydrogen antiporter [isa: 0015385 ]
+0017155 = sodium:hydrogen antiporter regulator [isa: 0015385 ]
+0015363 = dicarboxylate (succinate/fumarate/malate) antiporter [isa: 0005310 0015297 0015354 ]
+0015364 = dicarboxylate:inorganic phosphate antiporter [isa: 0005315 0008513 0015297 ]
+0005451 = monovalent cation:proton antiporter [isa: 0015078 0015297 ]
+0015367 = oxoglutarate/malate antiporter [isa: 0008513 0015297 ]
+0015300 = solute:solute antiporter [isa: 0015297 ]
+0015325 = acetyl-CoA:CoA antiporter [isa: 0008521 0015300 0015324 ]
+0015298 = solute:cation antiporter [isa: 0015300 ]
+0015368 = calcium:cation antiporter [isa: 0015298 ]
+0008273 = calcium, potassium:sodium antiporter [isa: 0015368 ]
+0015369 = calcium:hydrogen antiporter [isa: 0015299 0015368 ]
+0005432 = calcium:sodium antiporter [isa: 0015368 ]
+0015299 = solute:hydrogen antiporter [isa: 0015298 ]
+0015307 = drug:hydrogen antiporter [isa: 0015299 ]
+0015308 = amiloride:hydrogen antiporter [isa: 0015307 ]
+0045119 = azole:hydrogen antiporter [isa: 0015307 ]
+0015314 = aminotriazole:hydrogen antiporter [isa: 0045119 ]
+0015521 = bicyclomycin/sulfathiazole:hydrogen antiporter [isa: 0015545 0015546 0045119 ]
+0015313 = fluconazole:hydrogen antiporter [isa: 0045119 ]
+0015310 = benomyl:hydrogen antiporter [isa: 0015307 ]
+0015525 = carbonyl cyanide m-chlorophenylhydrazone/nalidixic acid/organomercurials:hydrogen antiporter [isa: 0015307 0015547 0015548 0015549 ]
+0015309 = cycloheximide:hydrogen antiporter [isa: 0015307 ]
+0015522 = hydrophobic uncoupler:hydrogen antiporter [isa: 0015307 0017077 ]
+0015520 = tetracycline:hydrogen antiporter [isa: 0008493 0015307 ]
+0015315 = organophosphate:inorganic phosphate antiporter [isa: 0005315 0015299 ]
+0005469 = succinate/fumarate antiporter [isa: 0005310 0015297 0015354 ]
+0046609 = voltage-sensitive sulfate antiporter [isa: 0015297 ]
+0015557 = arginine targeting transporter [isa: 0015291 0015463 ]
+0005471 = ATP/ADP antiporter [isa: 0015291 ]
+0015351 = bilirubin porter [isa: 0015127 0015291 ]
+0005476 = carnitine/acyl carnitine carrier [isa: 0015291 ]
+0015541 = cyanate porter [isa: 0015110 0015291 ]
+0015395 = equilibrative nucleoside transporter [isa: 0015291 ]
+0015397 = equilibrative nucleoside transporter, nitrobenzyl-thioinosine-insensitive [isa: 0015395 ]
+0015396 = equilibrative nucleoside transporter, nitrobenzyl-thioinosine-sensitive [isa: 0015395 ]
+0005472 = flavin adenine dinucleotide carrier [isa: 0015291 ]
+0015660 = formate efflux permease [isa: 0015291 0015499 0015562 ]
+0015659 = formate uptake permease [isa: 0015291 0015499 0015563 ]
+0015503 = glutathione-regulated potassium exporter [isa: 0015079 0015291 ]
+0005373 = heavy metal ion porter [isa: 0015076 0015291 ]
+0015086 = cadmium ion transporter [isa: 0005373 0015082 ]
+0015340 = zinc, cadmium uptake permease [isa: 0005385 0015086 0015338 0015563 ]
+0015338 = cation diffusion facilitator [isa: 0005373 ]
+0015339 = cobalt, zinc uptake permease [isa: 0005381 0005385 0015087 0015338 0015563 ]
+0015341 = zinc efflux permease [isa: 0005385 0015338 0015562 ]
+0015087 = cobalt ion transporter [isa: 0005373 0015082 ]
+0005375 = copper ion transporter [isa: 0005373 0015082 ]
+0015088 = copper uptake transporter [isa: 0005375 ]
+0015089 = high affinity copper transporter [isa: 0005375 ]
+0005377 = intracellular copper transporter [isa: 0005375 ]
+0005376 = plasma membrane copper transporter [isa: 0005375 ]
+0015335 = heavy metal ion:hydrogen symporter [isa: 0005373 0015295 ]
+0015336 = high affinity metal ion uptake transporter [isa: 0005373 ]
+0005381 = iron transporter [isa: 0005373 0015082 ]
+0015621 = ferric triacetylfusarinine C transporter [isa: 0005381 ]
+0015346 = ferric triacetylfusarinine C:hydrogen symporter [isa: 0015295 0015343 0015621 ]
+0015603 = iron chelate transporter [isa: 0005381 ]
+0016033 = iron ion transporter [isa: 0005381 ]
+0015091 = ferric iron transporter [isa: 0016033 ]
+0015092 = high affinity ferric uptake transporter [isa: 0015091 ]
+0015093 = ferrous iron transporter [isa: 0016033 ]
+0015639 = ferrous iron uptake transporter [isa: 0015093 ]
+0015090 = low affinity iron transporter [isa: 0016033 ]
+0005382 = transmembrane iron permease [isa: 0016033 ]
+0015343 = siderochrome-iron transporter [isa: 0005381 ]
+0008490 = arsenite porter [isa: 0015105 0015343 ]
+0015620 = ferric-enterobactin transporter [isa: 0015343 ]
+0015345 = ferric-enterobactin:hydrogen symporter [isa: 0015295 0015620 ]
+0015622 = ferric-hydroxamate transporter [isa: 0015343 ]
+0019535 = ferric-vibriobactin transporter [isa: 0015343 ]
+0015344 = siderochrome-iron (ferrioxamine) uptake transporter [isa: 0015343 ]
+0015342 = zinc, iron permease [isa: 0005381 0005385 ]
+0000006 = high affinity zinc uptake transporter [isa: 0015342 ]
+0015094 = lead ion transporter [isa: 0005373 0015082 ]
+0015337 = low affinity metal ion uptake transporter [isa: 0005373 ]
+0005384 = manganese ion transporter [isa: 0005373 0015082 ]
+0015096 = manganese resistance permease [isa: 0005384 ]
+0015097 = mercury ion transporter [isa: 0005373 0015082 ]
+0015098 = molybdate ion transporter [isa: 0005373 0015082 ]
+0015099 = nickel ion transporter [isa: 0005373 0015082 ]
+0015080 = silver transporter [isa: 0005373 0015077 ]
+0015654 = tellurite-resistance uptake permease [isa: 0005373 0015563 ]
+0015100 = vanadium ion transporter [isa: 0005373 0015082 ]
+0005385 = zinc ion transporter [isa: 0005373 0015082 ]
+0000007 = low-affinity zinc ion transporter [isa: 0005385 ]
+0015398 = high affinity ammonium transporter [isa: 0008519 0015291 ]
+0005315 = inorganic phosphate transporter [isa: 0015291 ]
+0015318 = inorganic uptake permease [isa: 0005315 0015563 ]
+0009673 = low affinity phosphate transporter [isa: 0005315 0015114 ]
+0015320 = phosphate carrier [isa: 0005315 0015114 ]
+0015317 = phosphate:hydrogen symporter [isa: 0005315 0015114 0015295 ]
+0015321 = sodium-dependent phosphate transporter [isa: 0005315 ]
+0005436 = sodium:phosphate symporter [isa: 0005315 ]
+0005316 = high affinity inorganic phosphate:sodium symporter [isa: 0005436 0015294 ]
+0015319 = sodium:inorganic phosphate symporter [isa: 0005436 0015296 ]
+0015400 = low affinity ammonium transporter [isa: 0008519 0015291 ]
+0015350 = methotrexate transporter [isa: 0015291 ]
+0015353 = multidrug endosomal transporter [isa: 0015239 0015291 ]
+0015514 = nitrite extrusion permease [isa: 0015113 0015291 0015562 ]
+0015513 = nitrite uptake permease [isa: 0015113 0015291 0015563 ]
+0015316 = nitrite/nitrate porter [isa: 0015291 ]
+0015536 = nucleoside permease [isa: 0005337 0015291 ]
+0015537 = xanthosine permease [isa: 0015536 0015553 ]
+0015322 = oligopeptide porter [isa: 0015198 0015291 ]
+0008513 = organic cation porter [isa: 0015101 0015291 ]
+0015540 = 3-hydroxyphenyl propionate porter [isa: 0008513 0015551 ]
+0015360 = acetate:hydrogen symporter [isa: 0008513 0015295 ]
+0015532 = alpha-ketoglutarate:hydrogen symporter [isa: 0008513 0015139 0015295 ]
+0015531 = citrate:hydrogen symporter [isa: 0008513 0015137 0015295 ]
+0015365 = dicarboxylic acid permease [isa: 0005310 0008513 ]
+0015362 = high affinity sodium:dicarboxylate cotransporter [isa: 0008513 0015293 0017153 ]
+0015361 = low affinity sodium:dicarboxylate cotransporter [isa: 0008513 0015293 0017153 ]
+0015366 = malate:hydrogen symporter [isa: 0005310 0008513 0015295 ]
+0015355 = monocarboxylate porter [isa: 0008513 ]
+0015356 = monocarboxylate (lactate, pyruvate, mevalonate) uptake/efflux porter [isa: 0015355 ]
+0000227 = oxaloacetate carrier [isa: 0008513 0015131 ]
+0015544 = phenyl proprionate permease [isa: 0008513 0015551 ]
+0015354 = polyspecific organic cation transporter [isa: 0008513 ]
+0005311 = sodium:dicarboxylate/tricarboxylate cotransporter [isa: 0005310 0015142 0015293 0015354 ]
+0015533 = shikimate:hydrogen symporter [isa: 0008513 0015295 0015530 ]
+0005371 = tricarboxylate carrier [isa: 0008513 ]
+0015324 = peptide-acetyl-CoA transporter [isa: 0015197 0015291 ]
+0015388 = potassium uptake permease [isa: 0015079 0015291 0015563 ]
+0015348 = prostaglandin/thromboxane transporter [isa: 0015132 0015291 ]
+0005427 = proton-dependent oligopeptide transporter [isa: 0015198 0015291 ]
+0015334 = high affinity oligopeptide transporter [isa: 0005427 ]
+0009671 = nitrate(chlorate):hydrogen symporter [isa: 0005427 0015293 ]
+0015333 = peptide:hydrogen symporter [isa: 0005427 0015295 ]
+0008518 = reduced folate carrier [isa: 0015291 ]
+0015347 = sodium-independent organic anion transporter [isa: 0008514 0015291 ]
+0015352 = sterol porter [isa: 0015248 0015291 ]
+0008271 = sulfate porter [isa: 0015116 0015291 ]
+0015381 = high affinity sulfate permease [isa: 0008271 ]
+0015382 = sodium:sulfate cotransporter [isa: 0008271 0015081 0015293 ]
+0008512 = sulfate:hydrogen symporter [isa: 0008271 0015295 ]
+0009675 = high affinity sulfate:hydrogen symporter [isa: 0008512 ]
+0009676 = low affinity sulfate:hydrogen symporter [isa: 0008512 ]
+0015293 = symporter [isa: 0015291 ]
+0015296 = anion:cation symporter [isa: 0015293 ]
+0009672 = auxin:hydrogen symporter [isa: 0015293 ]
+0015377 = cation:chloride cotransporter [isa: 0015293 ]
+0015379 = potassium:chloride symporter [isa: 0015377 ]
+0015378 = sodium:chloride symporter [isa: 0015377 ]
+0008511 = sodium:chloride/potassium:chloride symporter [isa: 0015377 ]
+0009674 = potassium:sodium symporter [isa: 0015079 0015293 ]
+0008510 = sodium:bicarbonate cotransporter [isa: 0015106 0015293 ]
+0015294 = solute:cation symporter [isa: 0015293 ]
+0008520 = L-ascorbate:sodium symporter [isa: 0015294 ]
+0015391 = nucleobase:cation symporter [isa: 0015294 ]
+0005274 = allantoin permease [isa: 0015206 0015391 ]
+0015504 = cytosine permease [isa: 0015209 0015391 ]
+0015392 = cytosine-purine permease [isa: 0005345 0015209 0015391 ]
+0015394 = nucleoside (uridine) permease [isa: 0005350 0015213 0015391 ]
+0015505 = uracil permease [isa: 0015210 0015391 ]
+0015393 = uracil/uridine permease [isa: 0015210 0015213 0015391 ]
+0005415 = nucleoside:sodium symporter [isa: 0015294 ]
+0015390 = purine-specific nucleoside:sodium symporter [isa: 0015294 ]
+0015389 = pyrimidine- and adenine-specific:sodium symporter [isa: 0005345 0005350 0015294 ]
+0015295 = solute:hydrogen symporter [isa: 0015294 ]
+0015506 = nucleoside:hydrogen symporter [isa: 0015295 ]
+0015387 = potassium:hydrogen symporter [isa: 0015078 0015079 0015295 ]
+0015652 = quaternary ammonium group:hydrogen symporter [isa: 0015295 0015651 ]
+0015653 = glycine betaine:hydrogen symporter [isa: 0015652 ]
+0015370 = solute:sodium symporter [isa: 0015294 ]
+0015373 = monovalent anion:sodium symporter [isa: 0015370 ]
+0008507 = sodium:iodide symporter [isa: 0015373 ]
+0005367 = myo-inositol:sodium symporter [isa: 0005365 0015370 ]
+0005328 = neurotransmitter:sodium symporter [isa: 0005326 0015370 ]
+0005309 = creatine:sodium symporter [isa: 0005308 0005328 ]
+0005335 = serotonin:sodium symporter [isa: 0005328 ]
+0005343 = organic acid:sodium symporter [isa: 0005342 0015370 ]
+0008508 = bile acid:sodium symporter [isa: 0005343 0015125 ]
+0015498 = pantothenate:sodium symporter [isa: 0015233 0015370 ]
+0008523 = sodium dependent multivitamin transporter [isa: 0015370 ]
+0015402 = thiamin permease [isa: 0015234 0015291 ]
+0015403 = thiamin uptake transporter [isa: 0015291 ]
+0015349 = thyroid hormone transporter [isa: 0015291 ]
+0015323 = type V protein secretor [isa: 0008565 0015291 ]
+0015302 = uncoupling protein [isa: 0015291 ]
+0015292 = uniporter [isa: 0015291 ]
+0017077 = oxidative phosphorylation uncoupler [isa: 0005386 ]
+0015399 = primary active transporter [isa: 0005386 ]
+0015451 = decarboxylation-driven active transporter [isa: 0015399 ]
+0015454 = light-driven active transporter [isa: 0015399 ]
+0015452 = methyl transfer-driven active transporter [isa: 0015399 ]
+0015453 = oxidoreduction-driven active transporter [isa: 0015399 ]
+0015405 = P-P-bond-hydrolysis-driven transporter [isa: 0015399 ]
+0015450 = protein translocase [isa: 0008565 0015405 ]
+0015447 = type II protein secretor [isa: 0005478 0008565 0015405 ]
+0015448 = type III protein (virulence-related) secretor [isa: 0008565 0015405 ]
+0015449 = type IV protein (DNA-protein) secretor [isa: 0015219 0015405 ]
+0015267 = channel/pore class transporter [isa: 0005215 ]
+0015268 = alpha-type channel [isa: 0015267 ]
+0005243 = gap-junction forming channel [isa: 0015268 ]
+0015285 = connexon channel [isa: 0005243 ]
+0015286 = innexin channel [isa: 0005243 ]
+0005216 = ion channel [isa: 0015268 ]
+0015263 = amine/amide/polyamine channel [isa: 0005216 ]
+0015264 = methylammonium channel [isa: 0015263 ]
+0015265 = urea channel [isa: 0015263 ]
+0005253 = anion channel [isa: 0005216 ]
+0005254 = chloride channel [isa: 0005253 ]
+0005224 = ATP-binding and phosphorylation-dependent chloride channel [isa: 0005217 0005254 ]
+0016934 = glycine-gated chloride channel [isa: 0005254 0016933 ]
+0019182 = histamine-gated chloride channel [isa: 0005254 ]
+0005229 = intracellular calcium activated chloride channel [isa: 0005217 0005254 ]
+0005247 = voltage-gated chloride channel [isa: 0005244 0005254 ]
+0015274 = organellar voltage-gated chloride channel [isa: 0005247 ]
+0015482 = voltage-dependent anion channel porin [isa: 0005253 0015288 ]
+0008308 = voltage-dependent ion-selective channel [isa: 0005253 ]
+0005225 = volume-sensitive anion channel [isa: 0005253 0008509 ]
+0005261 = cation channel [isa: 0005216 ]
+0015251 = ammonium channel [isa: 0005261 ]
+0005227 = calcium activated cation channel [isa: 0005261 0015276 ]
+0005262 = calcium channel [isa: 0005261 ]
+0015278 = calcium-release channel [isa: 0005262 0015276 ]
+0005220 = inositol 1,4,5-triphosphate-sensitive calcium-release channel [isa: 0005217 0015278 ]
+0005218 = intracellular ligand-gated calcium channel [isa: 0005217 0015278 ]
+0005219 = ryanodine-sensitive calcium-release channel [isa: 0005218 ]
+0015279 = store-operated calcium channel [isa: 0005262 0015276 ]
+0015275 = stretch-activated, cation-selective, calcium channel [isa: 0005262 0008381 ]
+0005245 = voltage-gated calcium channel [isa: 0005244 0005262 ]
+0015270 = dihydropyridine-sensitive calcium channel [isa: 0005245 ]
+0008331 = high voltage-gated calcium channel [isa: 0005245 ]
+0008086 = light-activated voltage-gated calcium channel [isa: 0005245 ]
+0008332 = low voltage-gated calcium channel [isa: 0005245 ]
+0015252 = hydrogen ion channel [isa: 0005261 ]
+0005221 = intracellular cyclic nucleotide activated cation channel [isa: 0005217 0005261 ]
+0005222 = intracellular cAMP activated cation channel [isa: 0005221 ]
+0005223 = intracellular cGMP activated cation channel [isa: 0005221 ]
+0015281 = non-selective cation channel [isa: 0005261 0015249 0015276 ]
+0005267 = potassium channel [isa: 0005261 ]
+0015269 = calcium-activated potassium channel [isa: 0005267 ]
+0016286 = small conductance calcium-activated potassium channel [isa: 0015269 ]
+0005228 = intracellular sodium activated potassium channel [isa: 0005217 0005267 ]
+0005249 = voltage-gated potassium channel [isa: 0005244 0005267 ]
+0005251 = delayed rectifier potassium channel [isa: 0005249 ]
+0005242 = inward rectifier potassium channel [isa: 0005249 ]
+0015272 = ATP-activated inward rectifier potassium channel [isa: 0005242 ]
+0015467 = G-protein activated inward rectifier potassium channel [isa: 0005242 ]
+0015273 = G-protein enhanced inward rectifier potassium channel [isa: 0005242 ]
+0005252 = open rectifier potassium channel [isa: 0005249 ]
+0015271 = outward rectifier potassium channel [isa: 0005249 ]
+0005250 = A-type (transient outward) potassium channel [isa: 0015271 ]
+0005272 = sodium channel [isa: 0005261 ]
+0015280 = amiloride-sensitive sodium channel [isa: 0005272 0015276 ]
+0005248 = voltage-gated sodium channel [isa: 0005244 0005272 ]
+0015276 = ligand-gated ion channel [isa: 0005216 ]
+0005230 = extracellular ligand-gated ion channel [isa: 0015276 ]
+0005231 = excitatory extracellular ligand-gated ion channel [isa: 0005230 ]
+0016933 = glycine-gated ion channel [isa: 0005231 ]
+0005237 = inhibitory extracellular ligand-gated ion channel [isa: 0005230 ]
+0005217 = intracellular ligand-gated ion channel [isa: 0015276 ]
+0008381 = mechanically-gated ion channel [isa: 0005216 ]
+0015256 = monocarboxylate channel [isa: 0005216 ]
+0015258 = gluconate channel [isa: 0015256 ]
+0015259 = glutamate channel [isa: 0015256 ]
+0015260 = isethionate channel [isa: 0015256 ]
+0015261 = lactate channel [isa: 0015256 ]
+0015257 = organic anion channel [isa: 0015256 ]
+0015262 = taurine channel [isa: 0015256 ]
+0015253 = sugar/polyol channel [isa: 0005216 ]
+0015254 = glycerol channel [isa: 0015253 ]
+0015255 = propanediol channel [isa: 0015253 ]
+0005244 = voltage-gated ion channel [isa: 0005216 ]
+0030171 = voltage-gated proton channel [isa: 0005244 ]
+0015282 = NADPH oxidase-associated cytochrome b558 hydrogen channel [isa: 0015268 ]
+0015249 = non-selective channel [isa: 0015268 ]
+0015266 = protein channel [isa: 0015268 ]
+0015283 = apoptogenic cytochrome c release channel [isa: 0015266 ]
+0015250 = water channel [isa: 0015268 ]
+0015288 = porin [isa: 0015267 ]
+0015474 = autotransporter [isa: 0015288 ]
+0015475 = adhesin autotransporter [isa: 0015474 ]
+0015476 = hemaglutinin autotransporter [isa: 0015474 ]
+0015473 = fimbrial usher porin [isa: 0015288 ]
+0015483 = long-chain fatty acid transporting porin [isa: 0005324 0015288 ]
+0015471 = nucleoside-specific channel forming porin [isa: 0015288 ]
+0015479 = outer membrane exporter porin [isa: 0015288 ]
+0015480 = secretin (sensu Bacteria) [isa: 0008565 0015288 ]
+0000269 = toxin export channel [isa: 0015288 0019534 ]
+0015238 = drug transporter [isa: 0005215 ]
+0015566 = acriflavin transporter [isa: 0015238 ]
+0015555 = acriflavin resistant pump [isa: 0015566 ]
+0015567 = alkane transporter [isa: 0015238 ]
+0015564 = multidrug, alkane resistant pump [isa: 0015239 0015567 ]
+0015240 = amiloride transporter [isa: 0015238 ]
+0045118 = azole transporter [isa: 0015238 ]
+0015241 = aminotriazole transporter [isa: 0045118 ]
+0015244 = fluconazole transporter [isa: 0045118 ]
+0015546 = sulfathiazole transporter [isa: 0045118 ]
+0015242 = benomyl transporter [isa: 0015238 ]
+0015545 = bicyclomycin transporter [isa: 0015238 ]
+0015549 = carbonyl cyanide m-chlorophenylhydrazone transporter [isa: 0015238 ]
+0015243 = cycloheximide transporter [isa: 0015238 ]
+0015638 = microcin uptake permease [isa: 0015238 0015637 ]
+0015239 = multidrug transporter [isa: 0015238 ]
+0015559 = multidrug efflux pump [isa: 0015239 ]
+0015547 = nalidixic acid transporter [isa: 0015238 ]
+0015548 = organomercurial transporter [isa: 0015238 ]
+0008493 = tetracycline transporter [isa: 0015238 ]
+0009670 = triose-phosphate transporter [isa: 0015238 ]
+0005489 = electron transporter [isa: 0005215 ]
+0009054 = electron acceptor [isa: 0005489 ]
+0009055 = electron carrier [isa: 0005489 ]
+0015003 = copper electron carrier [isa: 0009055 ]
+0015007 = electron carrier, chlorophyll electron transport system [isa: 0009055 ]
+0008042 = iron-sulfur electron transfer carrier [isa: 0009055 ]
+0009492 = Fe2S2 electron transfer carrier [isa: 0008042 ]
+0009497 = Fe3S4/Fe4S4 electron transfer carrier [isa: 0008042 ]
+0015001 = high-potential iron-sulfur carrier [isa: 0009497 ]
+0009490 = mononuclear iron electron carrier [isa: 0009055 ]
+0009491 = redox-active disulfide bond electron carrier [isa: 0009055 ]
+0009053 = electron donor [isa: 0005489 ]
+0045155 = electron transporter, transferring electrons from CoQH2-cytochrome c reductase complex and cytochrome c oxidase complex [isa: 0005489 ]
+0046028 = electron transporter, transferring electrons from cytochrome b6/f complex of photosystem II [isa: 0005489 ]
+0045153 = electron transporter, transferring electrons within CoQH2-cytochrome c reductase complex [isa: 0005489 ]
+0045158 = electron transporter, transferring electrons within cytochrome b6/f complex of photosystem II [isa: 0005489 ]
+0045154 = electron transporter, transferring electrons within cytochrome c oxidase complex [isa: 0005489 ]
+0045156 = electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis [isa: 0005489 ]
+0045157 = electron transporter, transferring electrons within the noncyclic electron transport pathway of photosynthesis [isa: 0005489 ]
+0015933 = flavin-containing electron transporter [isa: 0005489 ]
+0008246 = electron transfer flavoprotein [isa: 0015933 ]
+0015040 = electron transfer flavoprotein, group I [isa: 0008246 ]
+0015041 = electron transfer flavoprotein, group II [isa: 0008246 ]
+0009457 = flavodoxin [isa: 0015933 ]
+0015455 = group translocator [isa: 0005215 ]
+0005478 = intracellular transporter [isa: 0005215 ]
+0000259 = intracellular nucleoside transporter [isa: 0005337 0005478 ]
+0005487 = nucleocytoplasmic transporter [isa: 0005478 ]
+0005484 = SNAP receptor [isa: 0005478 ]
+0005486 = t-SNARE [isa: 0005484 ]
+0005485 = v-SNARE [isa: 0005484 ]
+0005483 = soluble NSF attachment protein [isa: 0005478 ]
+0015075 = ion transporter [isa: 0005215 ]
+0008509 = anion transporter [isa: 0015075 ]
+0015103 = inorganic anion transporter [isa: 0008509 ]
+0015104 = antimonite transporter [isa: 0015103 ]
+0015105 = arsenite transporter [isa: 0015103 ]
+0015106 = bicarbonate transporter [isa: 0015103 ]
+0015107 = chlorate transporter [isa: 0015103 ]
+0015108 = chloride transporter [isa: 0015103 ]
+0015109 = chromate transporter [isa: 0015103 ]
+0015110 = cyanate transporter [isa: 0015103 ]
+0030504 = inorganic diphosphate transporter [isa: 0015103 ]
+0015111 = iodide transporter [isa: 0015103 ]
+0015112 = nitrate transporter [isa: 0015103 ]
+0015113 = nitrite transporter [isa: 0015103 ]
+0015114 = phosphate transporter [isa: 0015103 ]
+0015115 = silicate transporter [isa: 0015103 ]
+0015116 = sulfate transporter [isa: 0015103 ]
+0005340 = nucleotide-sulfate transporter [isa: 0015116 ]
+0000319 = sulfite transporter [isa: 0015103 ]
+0015118 = tellurite transporter [isa: 0015103 ]
+0015117 = thiosulfate transporter [isa: 0015103 ]
+0008514 = organic anion transporter [isa: 0008509 ]
+0005310 = dicarboxylic acid transporter [isa: 0008514 ]
+0015139 = alpha-ketoglutarate transporter [isa: 0005310 ]
+0015556 = C4-dicarboxylate transporter [isa: 0005310 ]
+0015138 = fumarate transporter [isa: 0005310 ]
+0015140 = malate transporter [isa: 0005310 ]
+0017153 = sodium:dicarboxylate cotransporter [isa: 0005310 ]
+0015141 = succinate transporter [isa: 0005310 ]
+0015554 = tartrate transporter [isa: 0005310 ]
+0015119 = hexose phosphate transporter [isa: 0008514 ]
+0008028 = monocarboxylic acid transporter [isa: 0008514 ]
+0015123 = acetate transporter [isa: 0008028 ]
+0015124 = allantoate transporter [isa: 0008028 ]
+0015125 = bile acid transporter [isa: 0008028 ]
+0015126 = canalicular bile acid transporter [isa: 0015125 ]
+0015127 = bilirubin transporter [isa: 0008028 ]
+0015499 = formate transporter [isa: 0008028 ]
+0015128 = gluconate transporter [isa: 0008028 ]
+0015568 = L-idonate transporter [isa: 0008028 ]
+0015129 = lactate transporter [isa: 0008028 ]
+0015130 = mevalonate transporter [isa: 0008028 ]
+0015131 = oxaloacetate transporter [isa: 0008028 ]
+0015552 = proprionate transporter [isa: 0008028 ]
+0015551 = 3-hydroxyphenyl proprionate transporter [isa: 0015552 ]
+0015132 = prostaglandin transporter [isa: 0008028 ]
+0005477 = pyruvate carrier [isa: 0008028 ]
+0015530 = shikimate transporter [isa: 0008028 ]
+0015133 = uronic acid transporter [isa: 0008028 ]
+0015134 = hexuronate transporter [isa: 0015133 ]
+0015550 = galacturonate transporter [isa: 0015134 ]
+0015135 = glucuronate transporter [isa: 0015134 ]
+0015121 = phosphoenolpyruvate transporter [isa: 0008514 ]
+0015120 = phosphoglycerate transporter [isa: 0008514 ]
+0015604 = phosphonate transporter [isa: 0008514 ]
+0015142 = tricarboxylic acid transporter [isa: 0008514 ]
+0015137 = citrate transporter [isa: 0015142 ]
+0015122 = triose phosphate transporter [isa: 0008514 ]
+0015143 = urate transporter [isa: 0008514 ]
+0015605 = organophosphate ester transporter [isa: 0008509 ]
+0008324 = cation transporter [isa: 0015075 ]
+0015082 = di-, tri-valent inorganic cation transporter [isa: 0008324 ]
+0015083 = aluminum ion transporter [isa: 0015082 ]
+0015084 = aluminum resistance permease [isa: 0015083 ]
+0015085 = calcium ion transporter [isa: 0015082 ]
+0015095 = magnesium ion transporter [isa: 0015082 ]
+0015076 = heavy metal ion transporter [isa: 0008324 ]
+0015077 = monovalent inorganic cation transporter [isa: 0008324 ]
+0015078 = hydrogen ion transporter [isa: 0015077 ]
+0015079 = potassium transporter [isa: 0015077 ]
+0015081 = sodium transporter [isa: 0015077 ]
+0015101 = organic cation transporter [isa: 0008324 ]
+0008519 = ammonium transporter [isa: 0015101 ]
+0015651 = quaternary ammonium group transporter [isa: 0015101 ]
+0015563 = uptake permease [isa: 0015075 0015646 ]
+0005319 = lipid transporter [isa: 0005215 ]
+0015245 = fatty acid transporter [isa: 0005319 ]
+0005324 = long-chain fatty acid transporter [isa: 0015245 ]
+0000039 = plasma membrane long-chain fatty acid transporter [isa: 0005324 ]
+0015635 = short-chain fatty acid transporter [isa: 0015245 ]
+0015636 = short-chain fatty acid uptake transporter [isa: 0015635 ]
+0015246 = fatty acyl transporter [isa: 0005319 ]
+0015607 = fatty acyl CoA transporter [isa: 0015246 ]
+0017089 = glycolipid transfer [isa: 0005319 ]
+0008100 = lipophorin [isa: 0005319 ]
+0005400 = peroxisomal membrane transporter [isa: 0005319 ]
+0015248 = sterol transporter [isa: 0005319 ]
+0017127 = cholesterol transporter [isa: 0015248 ]
+0015647 = murein transporter [isa: 0005215 ]
+0015648 = lipid-linked murein transporter [isa: 0015647 ]
+0015640 = murein peptide transporter [isa: 0015197 0015647 ]
+0005326 = neurotransmitter transporter [isa: 0005215 ]
+0030184 = nitric oxide transporter [isa: 0005215 ]
+0015932 = nucleobase, nucleoside, nucleotide and nucleic acid transporter [isa: 0005215 ]
+0015219 = DNA-protein complex transporter [isa: 0015932 ]
+0015205 = nucleobase transporter [isa: 0015932 ]
+0015206 = allantoin transporter [isa: 0015205 ]
+0005345 = purine transporter [isa: 0015205 ]
+0015207 = adenine transporter [isa: 0005345 ]
+0015208 = guanine transporter [isa: 0005345 ]
+0005350 = pyrimidine transporter [isa: 0015205 ]
+0015209 = cytosine transporter [isa: 0005350 ]
+0015210 = uracil transporter [isa: 0005350 ]
+0005337 = nucleoside transporter [isa: 0015932 ]
+0015211 = purine nucleoside transporter [isa: 0005337 ]
+0015212 = cytidine transporter [isa: 0015211 ]
+0015213 = uridine transporter [isa: 0015211 ]
+0015553 = xanthosine transporter [isa: 0015211 ]
+0015214 = pyrimidine nucleoside transporter [isa: 0005337 ]
+0015215 = nucleotide transporter [isa: 0015932 ]
+0030233 = deoxynucleotide transporter [isa: 0015215 ]
+0015216 = purine nucleotide transporter [isa: 0015215 ]
+0000295 = adenine nucleotide transporter [isa: 0015216 ]
+0015217 = ADP transporter [isa: 0015216 ]
+0005347 = ATP transporter [isa: 0015216 ]
+0005346 = purine ribonucleotide transporter [isa: 0015216 ]
+0015218 = pyrimidine nucleotide transporter [isa: 0015215 ]
+0005342 = organic acid transporter [isa: 0005215 ]
+0019531 = oxalate transporter [isa: 0005342 ]
+0015665 = organic alcohol transporter [isa: 0005215 ]
+0015646 = permease [isa: 0005215 ]
+0015562 = efflux permease [isa: 0015646 ]
+0046583 = cation efflux permease [isa: 0015562 ]
+0015166 = polyol transporter [isa: 0005215 ]
+0015167 = arabinitol transporter [isa: 0015166 ]
+0015577 = galactitol transporter [isa: 0015166 ]
+0015576 = glucitol transporter [isa: 0015166 ]
+0015168 = glycerol transporter [isa: 0015166 ]
+0015169 = glycerol-3-phosphate transporter [isa: 0015168 ]
+0015575 = mannitol transporter [isa: 0015166 ]
+0005365 = myo-inositol transporter [isa: 0015166 ]
+0015170 = propanediol transporter [isa: 0015166 ]
+0008565 = protein transporter [isa: 0005215 ]
+0015463 = enzyme transporter [isa: 0008565 ]
+0045206 = MAPK phosphatase transporter [isa: 0015463 ]
+0045207 = leptomycin B-sensitive MAPK phosphatase transporter [isa: 0045206 ]
+0045205 = MAPK transporter [isa: 0015463 ]
+0015197 = peptide transporter [isa: 0008565 ]
+0015198 = oligopeptide transporter [isa: 0015197 ]
+0015637 = peptide uptake permease [isa: 0015197 ]
+0019534 = toxin transporter [isa: 0005215 ]
+0015223 = vitamin/cofactor transporter [isa: 0005215 ]
+0008521 = acetyl-CoA transporter [isa: 0015223 ]
+0015224 = biopterin transporter [isa: 0015223 ]
+0015225 = biotin transporter [isa: 0015223 ]
+0015226 = carnitine transporter [isa: 0015223 ]
+0015227 = acyl carnitine transporter [isa: 0015226 ]
+0015228 = coenzyme A transporter [isa: 0015223 ]
+0005308 = creatine transporter [isa: 0015223 ]
+0015230 = flavin adenine dinucleotide transporter [isa: 0015223 ]
+0008517 = folate transporter [isa: 0015223 ]
+0015231 = 5-formyltetrahydrofolate transporter [isa: 0008517 ]
+0015232 = heme transporter [isa: 0015223 ]
+0015229 = L-ascorbate transporter [isa: 0015223 ]
+0015663 = nicotinamide mononucleotide transporter [isa: 0015223 ]
+0015664 = nicotinamide mononucleotide permease [isa: 0015663 ]
+0015233 = pantothenate transporter [isa: 0015223 ]
+0015234 = thiamin transporter [isa: 0015223 ]
+0015235 = vitamin B12 transporter [isa: 0015223 ]
+0005372 = water transporter [isa: 0005215 ]
+0030533 = triplet codon-amino acid adaptor [isa: 0003674 ]
+0005575 = cellular_component [partof: 0003673 ]
+0005623 = cell [isa: 0005575 ]
+0005627 = ascus [isa: 0005623 ]
+0005633 = ascus lipid droplet [isa: 0005811 ] [partof: 0005627 ]
+0005628 = prospore membrane [isa: 0016020 ] [partof: 0005627 ]
+0005619 = spore wall (sensu Fungi) [isa: 0009277 ] [partof: 0005627 ]
+0005631 = chitosan layer of spore wall [partof: 0005619 ]
+0005630 = dityrosine layer of spore wall [partof: 0005619 ]
+0005632 = inner layer of spore wall [partof: 0005619 ]
+0030424 = axon [partof: 0005623 ]
+0005933 = bud [partof: 0005623 ]
+0005935 = bud neck [isa: 0000134 ] [partof: 0005933 ]
+0000142 = contractile ring (sensu Saccharomyces) [isa: 0030480 ] [partof: 0005935 ]
+0000144 = septin ring (sensu Saccharomyces) [isa: 0030481 ] [partof: 0000142 ]
+0000133 = polarisome [partof: 0005934 0005935 0005937 0005938 ]
+0005934 = bud tip [isa: 0000134 ] [partof: 0005933 ]
+0000267 = cell fraction [partof: 0005623 ]
+0005626 = insoluble fraction [isa: 0000267 ]
+0005624 = membrane fraction [isa: 0000267 ]
+0000299 = integral membrane protein of membrane fraction [isa: 0005624 ]
+0005792 = microsome [isa: 0005624 ]
+0019718 = rough microsome [isa: 0005792 ]
+0019719 = smooth microsome [isa: 0005792 ]
+0000300 = peripheral membrane protein of membrane fraction [isa: 0005624 ]
+0019717 = synaptosome [isa: 0005624 ]
+0005625 = soluble fraction [isa: 0000267 ]
+0009928 = cell surface [partof: 0005623 ]
+0009929 = cell surface (sensu Magnoliophyta) [isa: 0009928 ]
+0009930 = longitudinal side of cell surface (sensu Magnoliophyta) [isa: 0009929 ]
+0030425 = dendrite [partof: 0005623 ]
+0019861 = flagellum [partof: 0005623 ]
+0009288 = flagellum (sensu Bacteria) [isa: 0019861 ]
+0009425 = flagellar basal body (sensu Bacteria) [partof: 0009288 ]
+0009433 = flagellar basal body, C ring (sensu Bacteria) [partof: 0009425 ]
+0009426 = flagellar basal body, distal rod (sensu Bacteria) [partof: 0009425 ]
+0009427 = flagellar basal body, distal rod, L ring (sensu Bacteria) [partof: 0009426 ]
+0009428 = flagellar basal body, distal rod, P ring (sensu Bacteria) [partof: 0009426 ]
+0009430 = flagellar basal body, mounting plate (sensu Bacteria) [partof: 0009425 ]
+0009431 = flagellar basal body, MS ring (sensu Bacteria) [partof: 0009430 ]
+0009429 = flagellar basal body, proximal rod (sensu Bacteria) [partof: 0009425 ]
+0009420 = flagellar filament (sensu Bacteria) [partof: 0009288 ]
+0009421 = flagellar filament cap (sensu Bacteria) [partof: 0009420 ]
+0009424 = flagellar hook (sensu Bacteria) [partof: 0009288 ]
+0009422 = flagellar hook-filament junction (sensu Bacteria) [partof: 0009288 ]
+0009434 = flagellum (sensu Eukarya) [isa: 0019861 ] [partof: 0005622 ]
+0020017 = flagellar membrane [partof: 0005886 0009434 ]
+0020018 = flagellar pocket membrane [isa: 0020017 ] [partof: 0020016 ]
+0020016 = flagellar pocket [partof: 0009434 ]
+0005622 = intracellular [partof: 0005623 ]
+0045177 = apical part of cell [partof: 0005622 ]
+0020007 = apical complex [partof: 0045177 ]
+0020032 = basal ring of apical complex [partof: 0020007 ]
+0020010 = conoid [isa: 0005874 ] [partof: 0020031 0020032 ]
+0020009 = microneme [partof: 0020007 ]
+0020031 = polar ring of apical complex [partof: 0020007 ]
+0020008 = rhoptry [partof: 0020007 ]
+0020025 = subpellicular microtubule [isa: 0005874 ] [partof: 0020007 ]
+0045179 = apical cortex [partof: 0005938 0045177 ]
+0045178 = basal part of cell [partof: 0005622 ]
+0045180 = basal cortex [partof: 0005938 0045178 ]
+0005938 = cell cortex [partof: 0005622 ]
+0030478 = actin cap (sensu Fungi) [partof: 0005938 0015629 ]
+0000143 = actin cap (sensu Saccharomyces) [isa: 0030478 ]
+0030479 = actin cortical patch (sensu Fungi) [partof: 0005938 0015629 ]
+0005857 = actin cortical patch (sensu Saccharomyces) [isa: 0030479 ]
+0042151 = cnidocyst [partof: 0005938 ]
+0005826 = contractile ring [partof: 0005938 ]
+0030480 = contractile ring (sensu Fungi) [isa: 0005826 ] [partof: 0015629 ]
+0030481 = septin ring (sensu Fungi) [isa: 0005940 ] [partof: 0030480 ]
+0000145 = exocyst [partof: 0005938 ]
+0005940 = septin ring [partof: 0005938 ]
+0008091 = spectrin [partof: 0005938 0015629 ]
+0005694 = chromosome [partof: 0005622 ]
+0005698 = centromere [partof: 0005694 ]
+0005695 = chromatid [partof: 0005694 ]
+0005717 = chromatin [partof: 0005694 ]
+0005719 = euchromatin [isa: 0005717 ]
+0005720 = heterochromatin [isa: 0005717 ]
+0005721 = centric heterochromatin [isa: 0005720 ]
+0005723 = alpha-heterochromatin [partof: 0005721 ]
+0005722 = beta-heterochromatin [partof: 0005721 ]
+0005725 = intercalary heterochromatin [isa: 0005720 ]
+0005724 = telomeric heterochromatin [isa: 0005720 ]
+0005718 = nucleosome [partof: 0005717 ]
+0005726 = perichromatin fibrils [partof: 0005717 ]
+0000229 = cytoplasmic chromosome [isa: 0005694 ] [partof: 0005737 ]
+0000233 = cytoplasmic interphase chromosome [isa: 0000229 0005707 ]
+0000231 = cytoplasmic mitotic chromosome [isa: 0000229 0005708 ]
+0005707 = interphase chromosome [isa: 0005694 ]
+0000232 = nuclear interphase chromosome [isa: 0000228 0005707 ]
+0005699 = kinetochore [partof: 0005694 ]
+0005711 = meiotic chromosome [isa: 0005694 ]
+0005712 = chiasma [partof: 0005711 ]
+0005713 = recombination nodule [partof: 0005711 ]
+0005714 = early recombination nodule [isa: 0005713 ]
+0005715 = late recombination nodule [isa: 0005713 ]
+0005716 = synaptonemal complex [partof: 0005711 ]
+0000262 = mitochondrial chromosome [isa: 0005694 ] [partof: 0005759 ]
+0005708 = mitotic chromosome [isa: 0005694 ]
+0008278 = cohesin [partof: 0005634 0005708 ]
+0008280 = cohesin core heterodimer [partof: 0008278 ]
+0005676 = condensin [partof: 0005634 0005708 ]
+0008621 = condensin core heterodimer [partof: 0005676 ]
+0005710 = metaphase chromosome [isa: 0005708 ]
+0000230 = nuclear mitotic chromosome [isa: 0000228 0005708 ]
+0005709 = prophase chromosome [isa: 0005708 ]
+0000228 = nuclear chromosome [isa: 0005694 ] [partof: 0005634 ]
+0009508 = plastid chromosome [isa: 0005694 ] [partof: 0009536 ]
+0005700 = polytene chromosome [isa: 0005694 ]
+0005704 = polytene chromosome band [partof: 0005700 ]
+0005701 = polytene chromosome chromocenter [partof: 0005700 ]
+0005706 = polytene chromosome ectopic fiber [partof: 0005700 ]
+0005705 = polytene chromosome interband [partof: 0005700 ]
+0005703 = polytene chromosome puff [partof: 0005700 ]
+0005702 = polytene chromosome weak point [partof: 0005700 ]
+0019038 = provirus [isa: 0019015 ] [partof: 0005694 ]
+0005696 = telomere [partof: 0005694 ]
+0005697 = telomerase holoenzyme complex [isa: 0030529 ] [partof: 0005696 ]
+0000333 = telomerase catalytic core complex [isa: 0005697 ]
+0005929 = cilium [partof: 0005622 ]
+0005930 = axoneme [partof: 0005929 ]
+0005879 = axonemal microtubule [isa: 0005874 ] [partof: 0005930 ]
+0005858 = axonemal dynein [isa: 0030286 ] [partof: 0005879 0015629 ]
+0001683 = axonemal dynein heavy chain [isa: 0005858 ]
+0001684 = axonemal dynein intermediate chain [isa: 0005858 ]
+0001685 = axonemal dynein intermediate light chain [isa: 0005858 ]
+0001686 = axonemal dynein light chain [isa: 0005858 ]
+0005931 = nexin [partof: 0005930 ]
+0001520 = outer dense fiber [partof: 0005930 ]
+0001534 = radial spoke [partof: 0005930 ]
+0001536 = radial spoke stalk [partof: 0001534 ]
+0001535 = radial spokehead [partof: 0001534 ]
+0005932 = basal body [partof: 0005929 ]
+0000307 = cyclin-dependent protein kinase holoenzyme [partof: 0005622 ]
+0000308 = cyclin-dependent protein kinase holoenzyme, cytoplasmic [isa: 0000307 ] [partof: 0005737 ]
+0019908 = cyclin-dependent protein kinase holoenzyme, nuclear [isa: 0000307 ] [partof: 0005634 ]
+0005737 = cytoplasm [partof: 0005622 ]
+0020022 = acidocalcisome [partof: 0005737 ]
+0009504 = cell plate [partof: 0005737 ]
+0000177 = cytoplasmic exosome (RNase complex) [isa: 0000178 ] [partof: 0005737 ]
+0000153 = cytoplasmic ubiquitin ligase complex [isa: 0000151 ] [partof: 0005737 ]
+0019005 = SCF complex [isa: 0000153 ]
+0009839 = SCF complex substrate recognition subunit [partof: 0019005 ]
+0016023 = cytoplasmic vesicle [partof: 0005737 ]
+0045009 = chitosome [isa: 0016023 ]
+0030135 = coated vesicle [isa: 0016023 ]
+0030136 = clathrin-coated vesicle [isa: 0030135 ]
+0030125 = clathrin vesicle coat [isa: 0030118 0030120 ] [partof: 0030136 ]
+0030128 = clathrin coat of endocytic vesicle [isa: 0030125 ] [partof: 0045334 ]
+0030122 = AP-2 adaptor complex [isa: 0030119 0030131 ] [partof: 0030128 0030132 ]
+0030129 = clathrin coat of synaptic vesicle [isa: 0030125 ] [partof: 0008021 ]
+0030130 = clathrin coat of trans-Golgi network vesicle [isa: 0030125 ] [partof: 0030140 ]
+0030121 = AP-1 adaptor complex [isa: 0030119 0030131 ] [partof: 0030130 ]
+0045334 = clathrin-coated endocytic vesicle [isa: 0030136 0030139 ]
+0045336 = clathrin-coated phagocytic vesicle [isa: 0045334 0045335 ]
+0008021 = synaptic vesicle [isa: 0030136 ]
+0030285 = synaptic vesicle membrane, integral protein [isa: 0016021 ] [partof: 0008021 ]
+0030140 = trans-Golgi network transport vesicle [isa: 0005798 0030136 ]
+0012510 = trans-Golgi network transport vesicle membrane [isa: 0012506 ] [partof: 0030140 ]
+0030137 = COPI-coated vesicle [isa: 0030135 ]
+0030126 = COPI vesicle coat [isa: 0030120 ] [partof: 0030137 ]
+0030142 = Golgi-ER transport vesicle [isa: 0005798 0030137 ]
+0012508 = Golgi-ER transport vesicle membrane [isa: 0012506 ] [partof: 0030142 ]
+0030143 = inter-Golgi transport vesicle [isa: 0005798 0030133 0030137 ]
+0012509 = inter-Golgi transport vesicle membrane [isa: 0012506 ] [partof: 0030143 ]
+0030138 = COPII-coated vesicle [isa: 0030135 ]
+0030127 = COPII vesicle coat [isa: 0030120 ] [partof: 0030138 ]
+0030134 = ER-Golgi transport vesicle [isa: 0005798 0030133 0030138 ]
+0012507 = ER-Golgi transport vesicle membrane [isa: 0012506 ] [partof: 0030134 ]
+0030120 = vesicle coat [isa: 0030117 ] [partof: 0030135 ]
+0030139 = endocytic vesicle [isa: 0016023 ]
+0045335 = phagocytic vesicle [isa: 0030139 ]
+0005798 = Golgi vesicle [isa: 0016023 ] [partof: 0005794 ]
+0030141 = secretory granule [isa: 0016023 ]
+0020026 = dense granule [isa: 0030141 ]
+0030133 = transport vesicle [isa: 0016023 ]
+0005856 = cytoskeleton [partof: 0005737 ]
+0015629 = actin cytoskeleton [isa: 0005856 ]
+0030482 = actin cable (sensu Fungi) [partof: 0015629 ]
+0000141 = actin cable (sensu Saccharomyces) [isa: 0030482 ]
+0008290 = actin capping protein [partof: 0015629 ]
+0005884 = actin filament [partof: 0015629 ]
+0005885 = Arp2/3 protein complex [partof: 0015629 ]
+0005868 = cytoplasmic dynein [isa: 0030286 ] [partof: 0005881 0015629 ]
+0001687 = cytoplasmic dynein heavy chain [isa: 0005868 ]
+0001688 = cytoplasmic dynein intermediate chain [isa: 0005868 ]
+0001689 = cytoplasmic dynein intermediate light chain [isa: 0005868 ]
+0001690 = cytoplasmic dynein light chain [isa: 0005868 ]
+0005869 = dynactin complex [partof: 0015629 0015630 ]
+0005870 = actin capping protein of dynactin complex [partof: 0005869 ]
+0016459 = myosin [partof: 0015629 ]
+0016460 = myosin II [isa: 0016459 ]
+0005859 = muscle myosin [partof: 0016460 0030484 ]
+0005860 = non-muscle myosin [partof: 0016460 ]
+0016461 = unconventional myosin [isa: 0016459 ]
+0045160 = myosin I [isa: 0016461 ]
+0042385 = myosin III [isa: 0016461 ]
+0001725 = stress fibers [partof: 0015629 ]
+0005865 = striated muscle thin filament [partof: 0015629 0030017 ]
+0005862 = muscle thin filament tropomyosin [partof: 0005865 ]
+0005861 = troponin complex [partof: 0005865 ]
+0001533 = cornified envelope [isa: 0005856 ]
+0045111 = intermediate filament cytoskeleton [isa: 0005856 ]
+0005882 = intermediate filament [partof: 0045111 ]
+0001721 = intermediate filament associated protein [isa: 0005882 ]
+0001722 = type I intermediate filament associated protein [isa: 0001721 ]
+0001723 = type II intermediate filament associated protein [isa: 0001721 ]
+0001724 = type III intermediate filament associated protein [isa: 0001721 ]
+0045095 = keratin filament [isa: 0005882 ]
+0005638 = lamin filament [isa: 0005882 ] [partof: 0005637 0005652 ]
+0005883 = neurofilament [isa: 0005882 ]
+0045098 = type III intermediate filament [isa: 0005882 ]
+0015630 = microtubule cytoskeleton [isa: 0005856 ]
+0005874 = microtubule [partof: 0015630 ]
+0005881 = cytoplasmic microtubule [isa: 0005874 ]
+0005880 = nuclear microtubule [isa: 0005874 ]
+0005876 = spindle microtubule [isa: 0005874 ] [partof: 0005819 ]
+0000235 = astral microtubule [isa: 0005876 ]
+0005828 = kinetochore microtubule [isa: 0005876 ]
+0005827 = polar microtubule [isa: 0005876 ]
+0045298 = tubulin [partof: 0005874 ]
+0005875 = microtubule associated protein [partof: 0015630 ]
+0030286 = dynein [isa: 0005875 ]
+0005871 = kinesin [isa: 0005875 ]
+0016938 = kinesin I complex [isa: 0005871 ]
+0016939 = kinesin II complex [isa: 0005871 ]
+0005872 = minus-end kinesin [isa: 0005871 ]
+0005873 = plus-end kinesin [isa: 0005871 ]
+0005819 = spindle [partof: 0015630 ]
+0030615 = spindle pole [partof: 0005819 ]
+0008352 = katanin [partof: 0005813 0030615 ]
+0005816 = spindle pole body [isa: 0005815 ] [partof: 0030615 ]
+0005823 = central plaque of spindle pole body [partof: 0005816 ]
+0005825 = half bridge of spindle pole body [partof: 0005816 ]
+0005822 = inner plaque of spindle pole body [partof: 0005816 ]
+0005821 = intermediate layer of spindle pole body [partof: 0005816 ]
+0005824 = outer plaque of spindle pole body [partof: 0005816 ]
+0020039 = pellicle [partof: 0005856 ]
+0020038 = subpellicular network [partof: 0020039 ]
+0005829 = cytosol [partof: 0005737 ]
+0005837 = 26S proteasome [partof: 0005829 ]
+0005838 = 19S proteasome regulatory particle [partof: 0005837 ]
+0008540 = 19S proteasome regulatory particle, base subcomplex [partof: 0005838 ]
+0008541 = 19S proteasome regulatory particle, lid subcomplex [partof: 0005838 ]
+0005839 = 20S core proteasome [partof: 0005837 ]
+0019773 = 20S core proteasome, alpha-subunit [partof: 0005839 ]
+0019774 = 20S core proteasome, beta-subunit [partof: 0005839 ]
+0008537 = proteasome activator complex [partof: 0005839 ]
+0005945 = 6-phosphofructokinase complex [partof: 0005829 ]
+0016465 = chaperonin ATPase complex [partof: 0005829 ]
+0005832 = chaperonine-containing T-complex [partof: 0005829 ]
+0009281 = cytosolic ribosome (sensu Bacteria) [isa: 0005840 ] [partof: 0005829 ]
+0009282 = cytosolic large ribosomal subunit (sensu Bacteria) [isa: 0015934 ] [partof: 0009281 ]
+0009283 = cytosolic small ribosomal subunit (sensu Bacteria) [isa: 0015935 ] [partof: 0009281 ]
+0005830 = cytosolic ribosome (sensu Eukarya) [isa: 0005840 ] [partof: 0005829 ]
+0005842 = cytosolic large ribosomal subunit (sensu Eukarya) [isa: 0015934 ] [partof: 0005830 ]
+0005843 = cytosolic small ribosomal subunit (sensu Eukarya) [isa: 0015935 ] [partof: 0005830 0016282 0016283 ]
+0005835 = fatty-acid synthase complex [partof: 0005829 ]
+0009923 = fatty acid elongase complex [isa: 0005835 ]
+0005836 = fatty-acyl-CoA synthase complex [partof: 0005829 ]
+0005833 = hemoglobin complex [partof: 0005829 ]
+0008385 = IkappaB kinase complex [partof: 0005829 ]
+0000015 = phosphopyruvate hydratase complex [partof: 0005829 ]
+0016272 = prefoldin [partof: 0005829 ]
+0005831 = steroid hormone aporeceptor complex [partof: 0005829 ]
+0016010 = dystrophin-associated glycoprotein complex [partof: 0005605 0005737 0005886 ]
+0016014 = dystrobrevin complex [partof: 0016010 ]
+0016011 = dystroglycan complex [partof: 0016010 ]
+0005607 = laminin-2 [partof: 0016011 ]
+0016012 = sarcoglycan complex [partof: 0016011 ]
+0016013 = syntrophin complex [partof: 0016010 ]
+0045247 = electron transfer flavoprotein (sensu Bacteria) [isa: 0045251 ] [partof: 0005737 ]
+0005783 = endoplasmic reticulum [partof: 0005737 ]
+0016022 = endoplasmic reticulum cisterna [partof: 0005783 ]
+0005788 = endoplasmic reticulum lumen [partof: 0005783 ]
+0005789 = endoplasmic reticulum membrane [partof: 0005783 0042175 ]
+0042406 = endoplasmic reticulum membrane, extrinsic protein [partof: 0005789 ]
+0030176 = endoplasmic reticulum membrane, intrinsic protein [partof: 0005789 ]
+0008250 = oligosaccharyl transferase complex [partof: 0005789 ]
+0017059 = serine C-palmitoyltransferase complex [partof: 0005789 ]
+0009511 = plasmodesmatal endoplasmic reticulum [isa: 0005783 ] [partof: 0009510 ]
+0005791 = rough endoplasmic reticulum [isa: 0005783 ]
+0005784 = translocon [partof: 0005791 ]
+0005785 = signal recognition particle receptor complex [partof: 0005784 ]
+0016529 = sarcoplasmic reticulum [isa: 0005783 ] [partof: 0016528 ]
+0005787 = signal peptidase complex [partof: 0005783 ]
+0005786 = signal recognition particle [partof: 0005783 ]
+0005790 = smooth endoplasmic reticulum [isa: 0005783 ]
+0005768 = endosome [partof: 0005737 ]
+0005769 = early endosome [isa: 0005768 ]
+0005770 = late endosome [isa: 0005768 ]
+0005793 = ER-Golgi intermediate compartment [partof: 0005737 ]
+0016282 = eukaryotic 43S pre-initiation complex [partof: 0005737 ]
+0005850 = eukaryotic translation initiation factor 2 complex [partof: 0016282 ]
+0005852 = eukaryotic translation initiation factor 3 complex [partof: 0016282 ]
+0016283 = eukaryotic 48S initiation complex [partof: 0005737 ]
+0005853 = eukaryotic translation elongation factor 1 [partof: 0005737 ]
+0005851 = eukaryotic translation initiation factor 2B complex [partof: 0005737 ]
+0016281 = eukaryotic translation initiation factor 4F complex [partof: 0005737 ]
+0045169 = fusome [partof: 0005737 ]
+0020015 = glycosome [partof: 0005737 ]
+0009514 = glyoxysome [partof: 0005737 ]
+0005794 = Golgi apparatus [partof: 0005737 ]
+0005801 = Golgi cis-face [partof: 0005794 ]
+0030008 = TRAPP [partof: 0005801 ]
+0005796 = Golgi lumen [partof: 0005794 ]
+0000139 = Golgi membrane [partof: 0005794 0012505 ]
+0030173 = Golgi membrane, integral protein [isa: 0016021 ] [partof: 0000139 ]
+0005795 = Golgi stack [partof: 0005794 ]
+0000137 = Golgi cis cisterna [partof: 0005795 ]
+0000136 = mannosyltransferase complex [partof: 0000137 ]
+0005797 = Golgi medial cisterna [partof: 0005795 ]
+0000138 = Golgi trans cisterna [partof: 0005795 ]
+0005802 = Golgi trans-face [partof: 0005794 ]
+0017119 = Golgi transport complex [partof: 0005794 ]
+0005646 = importin [partof: 0005643 0005737 ]
+0005647 = importin, alpha-subunit [partof: 0005646 ]
+0005648 = importin, beta-subunit [partof: 0005646 ]
+0005649 = transportin [isa: 0005646 ]
+0005811 = lipid particle [partof: 0005737 ]
+0012511 = lipid storage body (sensu Viridiplantae) [isa: 0005811 ]
+0042470 = melanosome [partof: 0005737 ]
+0030117 = membrane coat [partof: 0005737 ]
+0030118 = clathrin coat [isa: 0030117 ]
+0030131 = clathrin adaptor complex [partof: 0030118 ]
+0030132 = clathrin coat of coated pit [isa: 0030118 ] [partof: 0005905 ]
+0030119 = membrane coat adaptor complex [partof: 0030117 ]
+0030123 = AP-3 adaptor complex [isa: 0030119 ]
+0030124 = AP-4 adaptor complex [isa: 0030119 ]
+0005815 = microtubule organizing center [partof: 0005737 ]
+0005813 = centrosome [isa: 0005815 ]
+0005818 = aster [partof: 0005813 ]
+0005814 = centriole [partof: 0005813 ]
+0008274 = gamma-tubulin ring complex [partof: 0005814 ]
+0008275 = gamma-tubulin small complex [partof: 0008274 ]
+0005817 = centrosomal mitotic factor [partof: 0005813 ]
+0000242 = pericentriolar material [partof: 0005813 ]
+0005739 = mitochondrion [partof: 0005737 ]
+0020023 = kinetoplast [isa: 0009536 ] [partof: 0005739 ]
+0045025 = mitochondrial degradosome [partof: 0005739 ]
+0016007 = mitochondrial derivative [isa: 0005739 ]
+0016008 = major mitochondrial derivative [isa: 0016007 ]
+0016009 = minor mitochondrial derivative [isa: 0016007 ]
+0005758 = mitochondrial intermembrane space [partof: 0005739 ]
+0005759 = mitochondrial matrix [partof: 0005739 ]
+0017086 = 3-methyl-2-oxobutanoate dehydrogenase (lipoamide) complex [partof: 0005759 ]
+0017133 = electron transfer flavoprotein (sensu Eukarya) [isa: 0045251 ] [partof: 0005759 ]
+0016507 = fatty acid beta-oxidation multienzyme complex [partof: 0005759 ]
+0005760 = gamma DNA polymerase [partof: 0005759 ]
+0009841 = mitochondrial endopeptidase Clp complex [isa: 0009368 ] [partof: 0005759 ]
+0017087 = mitochondrial processing peptidase complex [partof: 0005759 ]
+0005761 = mitochondrial ribosome [isa: 0000313 ] [partof: 0005759 ]
+0005762 = mitochondrial large ribosomal subunit [isa: 0000315 ] [partof: 0005761 ]
+0005763 = mitochondrial small ribosomal subunit [isa: 0000314 ] [partof: 0005761 ]
+0009353 = oxoglutarate dehydrogenase complex (sensu Eukarya) [isa: 0045252 ] [partof: 0005759 ]
+0019910 = pyruvate dehydrogenase (lipoamide) phosphatase (sensu Eukarya) [isa: 0045253 ] [partof: 0005759 ]
+0005967 = pyruvate dehydrogenase complex (sensu Eukarya) [isa: 0045254 ] [partof: 0005759 ]
+0030062 = TCA cycle enzyme complex (sensu Eukarya) [isa: 0045239 ] [partof: 0005759 ]
+0005947 = alpha-ketoglutarate dehydrogenase complex (sensu Eukarya) [isa: 0030062 0045240 ]
+0005962 = isocitrate dehydrogenase complex (NAD+) (sensu Eukarya) [isa: 0030062 0045242 ]
+0008325 = succinate-CoA ligase complex (GDP-forming) (sensu Eukarya) [isa: 0030062 0045244 ]
+0005740 = mitochondrial membrane [isa: 0016020 ] [partof: 0005739 ]
+0005743 = mitochondrial inner membrane [isa: 0019866 ] [partof: 0005740 ]
+0016470 = hydrogen-translocating F-type ATPase complex (sensu Eukarya) [isa: 0045255 ] [partof: 0005743 ]
+0005745 = m-AAA complex [partof: 0005743 ]
+0030061 = mitochondrial crista [partof: 0005743 ]
+0005746 = mitochondrial electron transport chain complex (sensu Eukarya) [partof: 0005743 ]
+0005747 = respiratory chain complex I (sensu Eukarya) [isa: 0045271 ] [partof: 0005746 ]
+0005748 = NADH dehydrogenase complex (ubiquinone) (sensu Eukarya) [isa: 0045279 ] [partof: 0005747 ]
+0005749 = respiratory chain complex II (sensu Eukarya) [isa: 0045273 ] [partof: 0005746 ]
+0019738 = fumarate reductase complex (sensu Eukarya) [isa: 0045283 ] [partof: 0005749 ]
+0008136 = succinate dehydrogenase complex (sensu Eukarya) [isa: 0045281 ] [partof: 0005749 ]
+0005750 = respiratory chain complex III (sensu Eukarya) [isa: 0045275 ] [partof: 0005746 ]
+0015008 = ubiquinol-cytochrome c reductase complex (sensu Eukarya) [isa: 0045285 ] [partof: 0005750 ]
+0005751 = respiratory chain complex IV (sensu Eukarya) [isa: 0045277 ] [partof: 0005746 ]
+0005744 = mitochondrial inner membrane translocase complex [partof: 0005743 ]
+0005753 = proton-transporting ATP synthase complex (sensu Eukarya) [isa: 0045259 ] [partof: 0005743 ]
+0000275 = proton-transporting ATP synthase complex, catalytic core F(1) (sensu Eukarya) [isa: 0045261 ] [partof: 0005753 ]
+0005754 = hydrogen-transporting ATP synthase, catalytic core (sensu Eukarya) [isa: 0045267 ] [partof: 0000275 ]
+0005756 = hydrogen-transporting ATP synthase, central stalk (sensu Eukarya) [isa: 0045269 ] [partof: 0000275 ]
+0000276 = proton-transporting ATP synthase complex, coupling factor F(0) (sensu Eukarya) [isa: 0045263 ] [partof: 0005753 ]
+0000274 = hydrogen-transporting ATP synthase, stator stalk (sensu Eukarya) [isa: 0045265 ] [partof: 0000276 ]
+0009362 = succinate dehydrogenase complex (ubiquinone) (sensu Eukarya) [isa: 0045257 ] [partof: 0005743 ]
+0005741 = mitochondrial outer membrane [isa: 0019867 ] [partof: 0005740 ]
+0018998 = metaxin [partof: 0005741 ]
+0005742 = mitochondrial outer membrane translocase complex [partof: 0005741 ]
+0005757 = mitochondrial permeability transition pore [partof: 0005739 ]
+0045293 = mRNA editing complex [partof: 0005739 0009536 ]
+0016006 = Nebenkern [isa: 0005739 ]
+0005845 = mRNA cap complex [partof: 0005737 ]
+0030484 = muscle fiber [partof: 0005737 ]
+0030016 = myofibril [isa: 0030484 ]
+0030017 = sarcomere [partof: 0030016 ]
+0005863 = striated muscle thick filament [partof: 0030017 ]
+0030018 = Z disc [partof: 0030017 ]
+0030485 = smooth muscle fiber [isa: 0030484 ]
+0030486 = smooth muscle dense body [partof: 0030485 ]
+0005854 = nascent polypeptide-associated complex [partof: 0005737 ]
+0045248 = oxoglutarate dehydrogenase complex (sensu Bacteria) [isa: 0045252 ] [partof: 0005737 ]
+0005777 = peroxisome [partof: 0005737 ]
+0019819 = P1 peroxisome [isa: 0005777 ]
+0019820 = P2 peroxisome [isa: 0005777 ]
+0019821 = P3 peroxisome [isa: 0005777 ]
+0019822 = P4 peroxisome [isa: 0005777 ]
+0019823 = P5 peroxisome [isa: 0005777 ]
+0019824 = P6 peroxisome [isa: 0005777 ]
+0005782 = peroxisomal matrix [partof: 0005777 ]
+0005778 = peroxisomal membrane [isa: 0016020 ] [partof: 0005777 ]
+0005779 = integral peroxisomal membrane [partof: 0005778 ]
+0005780 = intra-peroxisomal peripheral membrane [partof: 0005778 ]
+0005781 = peroxisome targeting signal receptor complex [partof: 0005777 ]
+0019818 = peroxisome vesicle [partof: 0005737 ]
+0019197 = phosphoenolpyruvate-dependent sugar phosphotransferase complex [partof: 0005737 ]
+0009524 = phragmoplast [partof: 0005737 ]
+0009525 = phragmosome [partof: 0005737 ]
+0009536 = plastid [partof: 0005737 ]
+0009501 = amyloplast [isa: 0009536 ]
+0009568 = amyloplast starch grain [partof: 0009501 ]
+0020011 = apicoplast [isa: 0009536 ]
+0009507 = chloroplast [isa: 0009536 ]
+0009941 = chloroplast envelope [partof: 0009507 ]
+0009706 = chloroplast inner membrane [isa: 0009528 ] [partof: 0009941 ]
+0009707 = chloroplast outer membrane [isa: 0009527 ] [partof: 0009941 ]
+0009569 = chloroplast starch grain [partof: 0009507 ]
+0009570 = chloroplast stroma [isa: 0009532 ] [partof: 0009507 ]
+0009533 = chloroplast stromal thylakoid [isa: 0009534 ] [partof: 0009570 ]
+0009840 = chloroplastic endopeptidase Clp complex [isa: 0009368 ] [partof: 0009570 ]
+0009573 = ribulose bisphosphate carboxylase complex [partof: 0009570 ]
+0030386 = ferredoxin:thioredoxin reductase complex [partof: 0009507 ]
+0009542 = granum [partof: 0009507 ]
+0009515 = granal stacked thylakoid [isa: 0009534 ] [partof: 0009542 ]
+0009534 = thylakoid (sensu Viridiplantae) [isa: 0009579 ] [partof: 0009507 ]
+0009544 = chloroplast ATP synthase complex [partof: 0009534 ]
+0009543 = thylakoid lumen (sensu Viridiplantae) [partof: 0009534 ]
+0009535 = thylakoid membrane (sensu Viridiplantae) [partof: 0009534 ]
+0045320 = hydrogen-translocating F-type ATPase complex (sensu Viridiplantae) [isa: 0045255 ] [partof: 0009535 ]
+0009503 = light-harvesting complex (sensu Viridiplantae) [isa: 0030076 ] [partof: 0009535 ]
+0009518 = PSI associated light-harvesting complex I [isa: 0009503 ]
+0030083 = PSI associated light-harvesting complex I, LHCIa subcomplex [isa: 0009518 ]
+0030084 = PSI associated light-harvesting complex I, LHCIb subcomplex [isa: 0009518 ]
+0009517 = PSII associated light-harvesting complex II [isa: 0009503 ]
+0009655 = PSII associated light-harvesting complex II, core complex [partof: 0009517 ]
+0030086 = PSII associated light-harvesting complex II, core complex, LHCIIa subcomplex [partof: 0009655 ]
+0030087 = PSII associated light-harvesting complex II, core complex, LHCIIc subcomplex [partof: 0009655 ]
+0030088 = PSII associated light-harvesting complex II, core complex, LHCIId subcomplex [partof: 0009655 ]
+0009656 = PSII associated light-harvesting complex II, peripheral complex [partof: 0009517 ]
+0030085 = PSII associated light-harvesting complex II, peripheral complex, LHCIIb subcomplex [partof: 0009656 ]
+0030093 = photosystem I (sensu Viridiplantae) [isa: 0009522 ] [partof: 0009535 ]
+0030095 = photosystem II (sensu Viridiplantae) [isa: 0009523 ] [partof: 0009535 ]
+0009509 = chromoplast [isa: 0009536 ]
+0009575 = chromoplast stroma [isa: 0009532 ] [partof: 0009509 ]
+0009842 = cyanelle [isa: 0009536 ]
+0009843 = thylakoid (sensu Glaucocystophyceae) [isa: 0009579 ] [partof: 0009842 ]
+0030094 = photosystem I (sensu Cyanobacteria) [isa: 0009522 ] [partof: 0009843 0030075 ]
+0030096 = photosystem II (sensu Cyanobacteria) [isa: 0009523 ] [partof: 0009843 0030075 ]
+0030089 = phycobilisome [isa: 0030076 ] [partof: 0009843 0030075 ]
+0009545 = elaioplast [isa: 0009536 ]
+0009577 = elaioplast stroma [isa: 0009532 ] [partof: 0009545 ]
+0009513 = etioplast [isa: 0009536 ]
+0009541 = etioplast prolamellar body [partof: 0009513 ]
+0009578 = etioplast stroma [isa: 0009532 ] [partof: 0009513 ]
+0009516 = leucoplast [isa: 0009536 ]
+0009576 = leucoplast stroma [isa: 0009532 ] [partof: 0009516 ]
+0009526 = plastid envelope [partof: 0009536 ]
+0042170 = plastid membrane [partof: 0009526 ]
+0009528 = plastid inner membrane [isa: 0019866 ] [partof: 0042170 ]
+0009529 = plastid intermembrane space [partof: 0042170 ]
+0009527 = plastid outer membrane [isa: 0019867 ] [partof: 0042170 ]
+0009532 = plastid stroma [partof: 0009536 ]
+0009547 = plastid ribosome [isa: 0000313 ] [partof: 0009532 ]
+0000311 = plastid large ribosomal subunit [isa: 0000315 ] [partof: 0009547 ]
+0000312 = plastid small ribosomal subunit [isa: 0000314 ] [partof: 0009547 ]
+0009571 = proplastid stroma [isa: 0009532 ] [partof: 0009537 ]
+0009537 = proplastid [isa: 0009536 ]
+0045495 = pole plasm [isa: 0005737 ]
+0018994 = polar granule [partof: 0045495 ]
+0009574 = preprophase band [partof: 0005737 ]
+0045249 = pyruvate dehydrogenase (lipoamide) phosphatase (sensu Bacteria) [isa: 0045253 ] [partof: 0005737 ]
+0045250 = pyruvate dehydrogenase complex (sensu Bacteria) [isa: 0045254 ] [partof: 0005737 ]
+0005840 = ribosome [isa: 0030529 ] [partof: 0005737 ]
+0015934 = large ribosomal subunit [partof: 0005840 ]
+0000315 = organellar large ribosomal subunit [isa: 0015934 ] [partof: 0000313 ]
+0000313 = organellar ribosome [isa: 0005840 ]
+0000314 = organellar small ribosomal subunit [isa: 0015935 ] [partof: 0000313 ]
+0005844 = polysome [isa: 0005840 ]
+0015935 = small ribosomal subunit [partof: 0005840 ]
+0016528 = sarcoplasm [partof: 0005737 ]
+0030314 = junctional membrane complex [partof: 0016528 ]
+0005855 = signal sequence receptor complex [partof: 0005737 ]
+0030531 = small cytoplasmic ribonucleoprotein complex [isa: 0030529 ] [partof: 0005737 ]
+0005846 = snRNA cap binding complex [partof: 0005737 ]
+0045170 = spectrosome [partof: 0005737 ]
+0045246 = TCA cycle enzyme complex (sensu Bacteria) [isa: 0045239 ] [partof: 0005737 ]
+0045241 = alpha-ketoglutarate dehydrogenase complex (sensu Bacteria) [isa: 0045240 0045246 ]
+0045243 = isocitrate dehydrogenase complex (NAD+) (sensu Bacteria) [isa: 0045242 0045246 ]
+0045245 = succinate-CoA ligase complex (GDP-forming) (sensu Bacteria) [isa: 0045244 0045246 ]
+0005773 = vacuole [partof: 0005737 ]
+0005776 = autophagic vacuole [isa: 0005773 ]
+0000331 = contractile vacuole [isa: 0005773 ]
+0000323 = lytic vacuole [isa: 0005773 ]
+0005764 = lysosome [isa: 0000323 ]
+0001669 = acrosome [isa: 0005764 ]
+0005772 = digestive vacuole [isa: 0005764 ]
+0020020 = food vacuole (sensu Apicomplexa) [isa: 0005764 ]
+0005765 = lysosomal membrane [isa: 0016020 ] [partof: 0005764 ]
+0046611 = lysosomal hydrogen-translocating V-type ATPase complex [isa: 0016469 0016471 ] [partof: 0005765 ]
+0046610 = lysosomal hydrogen-transporting ATPase V0 domain [isa: 0000220 0046611 ]
+0046612 = lysosomal hydrogen-transporting ATPase V1 domain [isa: 0000221 0046611 ]
+0005771 = multivesicular body [isa: 0005764 ]
+0005766 = primary lysosome [isa: 0005764 ]
+0005767 = secondary lysosome [isa: 0005764 ]
+0000327 = lytic vacuole within protein storage vacuole [isa: 0000323 0000326 ]
+0000324 = vacuole (sensu Fungi) [isa: 0000322 0000323 ]
+0000328 = vacuolar lumen (sensu Fungi) [isa: 0005775 ] [partof: 0000324 ]
+0000329 = vacuolar membrane (sensu Fungi) [isa: 0005774 ] [partof: 0000324 ]
+0020003 = parasitophorous vacuole [isa: 0005773 ] [partof: 0018995 ]
+0020005 = parasitophorous vacuolar membrane [isa: 0005774 ] [partof: 0020003 ]
+0020006 = parasitophorous vacuolar membrane network [partof: 0020005 ]
+0020004 = parasitophorous vacuolar space [partof: 0020003 ]
+0000322 = storage vacuole [isa: 0005773 ]
+0000326 = protein storage vacuole [isa: 0000322 0000325 ]
+0005775 = vacuolar lumen [partof: 0005773 ]
+0000330 = vacuolar lumen (sensu Magnoliophyta) [isa: 0005775 ] [partof: 0000325 ]
+0005774 = vacuolar membrane [isa: 0016020 ] [partof: 0005773 ]
+0000306 = extrinsic vacuolar membrane protein [isa: 0019898 ] [partof: 0005774 ]
+0016471 = hydrogen-translocating V-type ATPase complex [partof: 0005774 ]
+0000220 = hydrogen-transporting ATPase V0 domain [isa: 0016471 ]
+0000221 = hydrogen-transporting ATPase V1 domain [isa: 0016471 ]
+0009705 = vacuolar membrane (sensu Magnoliophyta) [isa: 0005774 ] [partof: 0000325 ]
+0000325 = vacuole (sensu Magnoliophyta) [isa: 0005773 ]
+0045251 = electron transfer flavoprotein complex [partof: 0005622 ]
+0009368 = endopeptidase Clp complex [partof: 0005622 ]
+0000178 = exosome (RNase complex) [partof: 0005622 ]
+0000176 = nuclear exosome (RNase complex) [isa: 0000178 ] [partof: 0005634 ]
+0005727 = extrachromosomal circular DNA [partof: 0005622 ]
+0005729 = 2-micrometer circle DNA [isa: 0005727 ]
+0005728 = extrachromosomal rDNA circle [isa: 0005727 ]
+0009289 = fimbria [partof: 0005622 ]
+0009418 = fimbrial shaft [partof: 0009289 ]
+0009419 = fimbrial tip [partof: 0009289 ]
+0009417 = fimbrin [partof: 0009289 ]
+0000131 = incipient bud site [partof: 0005622 ]
+0016234 = inclusion body [partof: 0005622 ]
+0016235 = aggresome [isa: 0016234 ]
+0042405 = nuclear inclusion body [isa: 0016234 ] [partof: 0005634 ]
+0009295 = nucleoid [partof: 0005622 ]
+0005634 = nucleus [partof: 0005622 ]
+0016533 = cyclin-dependent protein kinase 5 activator complex [partof: 0005634 ]
+0019907 = cyclin-dependent protein kinase activating kinase holoenzyme [partof: 0005634 ]
+0046536 = dosage compensation complex [partof: 0005634 ]
+0016456 = dosage compensation complex (sensu Drosophila) [isa: 0046536 ]
+0001674 = female germ-cell nucleus [isa: 0005634 ]
+0030530 = heterogeneous nuclear ribonucleoprotein complex [isa: 0030529 ] [partof: 0005634 ]
+0001673 = male germ-cell nucleus [isa: 0005634 ]
+0016363 = nuclear matrix [partof: 0005634 ]
+0005635 = nuclear membrane [partof: 0005634 0012505 ]
+0005642 = annulate lamellae [partof: 0005635 ]
+0005637 = nuclear inner membrane [partof: 0005635 0042175 ]
+0005639 = nuclear inner membrane, integral protein [isa: 0016021 ] [partof: 0005637 ]
+0005652 = nuclear lamina [partof: 0005635 ]
+0005641 = nuclear membrane lumen [partof: 0005635 ]
+0005640 = nuclear outer membrane [partof: 0005635 ]
+0005643 = nuclear pore [partof: 0005635 ]
+0005651 = exportin [partof: 0005643 ]
+0005650 = importin, alpha-subunit transport factor [partof: 0005643 ]
+0005644 = nuclear pore membrane protein [partof: 0005643 ]
+0005645 = RAN-binding protein [partof: 0005643 ]
+0000152 = nuclear ubiquitin ligase complex [isa: 0000151 ] [partof: 0005634 ]
+0005680 = anaphase-promoting complex [isa: 0000152 ]
+0005730 = nucleolus [partof: 0005634 ]
+0001651 = dense fibrillar component [partof: 0005730 ]
+0005736 = DNA-directed RNA polymerase I complex [partof: 0005730 ]
+0001650 = fibrillar center [partof: 0005730 ]
+0001652 = granular component [partof: 0005730 ]
+0005731 = nucleolus organizer complex [partof: 0005730 ]
+0000172 = ribonuclease mitochondrial RNA processing complex [isa: 0030529 ] [partof: 0005730 ]
+0005655 = ribonuclease P complex [isa: 0030529 ] [partof: 0005730 ]
+0000120 = RNA polymerase I transcription factor complex [isa: 0005667 ] [partof: 0005730 ]
+0000500 = RNA polymerase I upstream activating factor complex [isa: 0000120 ]
+0005732 = small nucleolar ribonucleoprotein complex [isa: 0030529 ] [partof: 0005730 ]
+0005654 = nucleoplasm [partof: 0005634 ]
+0016585 = chromatin remodeling complex [partof: 0005654 ]
+0008623 = chromatin accessibility complex [isa: 0016585 ]
+0005678 = chromatin assembly complex [isa: 0016585 ]
+0016590 = ACF complex [isa: 0005678 ]
+0005677 = chromatin silencing complex [isa: 0016585 ]
+0016586 = RSC complex [isa: 0016585 ]
+0016514 = SWI/SNF complex [isa: 0016585 ]
+0016591 = DNA-directed RNA polymerase II, holoenzyme [partof: 0005654 ]
+0005665 = DNA-directed RNA polymerase II, core [partof: 0016591 ]
+0000119 = mediator complex [partof: 0016591 ]
+0016593 = Cdc73/Paf1 complex [isa: 0000119 ]
+0016592 = Srb-mediator complex [isa: 0000119 ]
+0005669 = TFIID complex [isa: 0000123 ] [partof: 0016591 ]
+0005670 = transcription-activating factor, 30kD [partof: 0005669 ]
+0005672 = transcription factor TFIIA [isa: 0005667 ] [partof: 0016591 ]
+0005673 = transcription factor TFIIE [isa: 0005667 ] [partof: 0016591 ]
+0005674 = transcription factor TFIIF [isa: 0005667 ] [partof: 0016591 ]
+0005675 = transcription factor TFIIH [isa: 0005667 ] [partof: 0016591 ]
+0005666 = DNA-directed RNA polymerase III complex [partof: 0005654 ]
+0005847 = mRNA cleavage and polyadenylation specificity factor complex [partof: 0005654 ]
+0005849 = mRNA cleavage factor complex [partof: 0005654 ]
+0005848 = mRNA cleavage stimulating factor complex [partof: 0005654 ]
+0016604 = nuclear body [partof: 0005654 ]
+0015030 = Cajal body [isa: 0016604 ]
+0016606 = Lands [isa: 0016604 ]
+0016607 = nuclear speck [isa: 0016604 ]
+0042382 = paraspeckles [isa: 0016604 ]
+0016605 = PML body [isa: 0016604 ]
+0042272 = nuclear RNA export factor [partof: 0005654 ]
+0005679 = nucleosome remodeling complex [partof: 0005654 ]
+0016587 = ISWI1 complex [isa: 0005679 ]
+0016588 = ISWI2 complex [isa: 0005679 ]
+0016589 = NURF complex [isa: 0005679 ]
+0005656 = pre-replicative complex [partof: 0005654 ]
+0005657 = replication fork [partof: 0005654 ]
+0005658 = alpha DNA polymerase:primase complex [partof: 0005657 ]
+0005659 = delta DNA polymerase complex [partof: 0005657 ]
+0005660 = delta-DNA polymerase cofactor [partof: 0005659 ]
+0005662 = DNA replication factor A complex [partof: 0005657 ]
+0005663 = DNA replication factor C complex [partof: 0005657 ]
+0008622 = epsilon DNA polymerase complex [partof: 0000109 0005657 ]
+0042555 = MCM complex [partof: 0005657 ]
+0005664 = origin recognition complex [partof: 0005657 ]
+0008023 = transcription elongation factor complex [partof: 0005654 ]
+0008024 = transcription elongation factor complex b [isa: 0008023 ]
+0005667 = transcription factor complex [partof: 0005654 ]
+0016602 = CCAAT-binding factor complex [isa: 0005667 ]
+0030014 = CCR4-NOT complex [isa: 0005667 ]
+0030015 = CCR4-NOT core complex [partof: 0030014 ]
+0016513 = core-binding factor [isa: 0005667 ]
+0008230 = ecdysone receptor holocomplex [isa: 0005667 ]
+0008232 = activator ecdysone receptor holocomplex [isa: 0008230 ]
+0008231 = repressor ecdysone receptor holocomplex [isa: 0008230 ]
+0000123 = histone acetyltransferase complex [isa: 0005667 ]
+0005671 = Ada2/Gcn5/Ada3 transcription activator complex [isa: 0000123 ]
+0000125 = PCAF complex [isa: 0000123 ]
+0000124 = SAGA complex [isa: 0000123 ]
+0000127 = transcription factor TFIIIC [isa: 0000123 ]
+0000118 = histone deacetylase complex [isa: 0005667 ]
+0016581 = NuRD complex [isa: 0000118 ]
+0016580 = Sin3 complex [isa: 0000118 ]
+0030232 = insulin control element activator complex [isa: 0005667 ]
+0005668 = selectivity factor SL1 [isa: 0005667 ]
+0019185 = snRNA-activating protein complex [isa: 0005667 ]
+0000126 = transcription factor TFIIIB [isa: 0005667 ]
+0017053 = transcriptional repressor complex [partof: 0005654 ]
+0017054 = negative cofactor 2 complex [isa: 0017053 ]
+0016035 = zeta DNA polymerase complex [partof: 0005654 ]
+0000109 = nucleotide excision repair complex [partof: 0005634 ]
+0000110 = nucleotide excision repair factor 1 complex [isa: 0000109 ]
+0000111 = nucleotide excision repair factor 2 complex [isa: 0000109 ]
+0000112 = nucleotide excision repair factor 3 complex [isa: 0000109 ]
+0000113 = nucleotide excision repair factor 4 complex [isa: 0000109 ]
+0000108 = repairosome [isa: 0000109 ]
+0005653 = perinuclear space [partof: 0005634 ]
+0045120 = pronucleus [isa: 0005634 ]
+0008180 = signalosome complex [partof: 0005634 ]
+0017117 = single-stranded DNA dependent ATP dependent DNA helicase complex [partof: 0005634 ]
+0030532 = small nuclear ribonucleoprotein complex [isa: 0030529 ] [partof: 0005634 ]
+0005685 = snRNP U1 [isa: 0030532 ] [partof: 0005684 ]
+0005692 = snRNP U11 [isa: 0030532 ] [partof: 0005689 ]
+0005693 = snRNP U12 [isa: 0030532 ] [partof: 0005689 ]
+0005686 = snRNP U2 [isa: 0030532 ] [partof: 0005684 ]
+0005687 = snRNP U4 [isa: 0030532 ] [partof: 0005684 ]
+0005690 = snRNP U4atac [isa: 0030532 ] [partof: 0005689 ]
+0005682 = snRNP U5 [isa: 0030532 ] [partof: 0005684 0005689 ]
+0005688 = snRNP U6 [isa: 0030532 ] [partof: 0005684 ]
+0005691 = snRNP U6atac [isa: 0030532 ] [partof: 0005689 ]
+0005683 = snRNP U7 [isa: 0030532 ] [partof: 0005681 ]
+0046540 = U4/U6 x U5 tri-snRNP complex [isa: 0030532 ]
+0005681 = spliceosome complex [isa: 0030529 ] [partof: 0005634 ]
+0000243 = commitment complex [partof: 0005681 ]
+0005684 = major (U2-dependent) spliceosome [isa: 0005681 ]
+0005689 = minor (U12-dependent) spliceosome complex [isa: 0005681 ]
+0000214 = tRNA-intron endonuclease complex [partof: 0005634 ]
+0045252 = oxoglutarate dehydrogenase complex [partof: 0005622 ]
+0005886 = plasma membrane [isa: 0016020 ] [partof: 0005622 ]
+0000148 = 1,3-beta-glucan synthase complex [partof: 0005886 ]
+0016324 = apical plasma membrane [partof: 0005886 ]
+0016327 = apicolateral plasma membrane [partof: 0005886 ]
+0019815 = B-cell receptor complex [partof: 0016327 ]
+0019816 = B-cell receptor accessory molecule complex [partof: 0019815 ]
+0019814 = immunoglobulin [isa: 0005576 ] [partof: 0019815 ]
+0030055 = cell-matrix junction [isa: 0016327 0030054 ]
+0005924 = cell-substrate adherens junction [isa: 0005912 0030055 ]
+0005928 = apical hemiadherens junction [isa: 0005924 ]
+0005926 = connecting hemiadherens junction [isa: 0005924 ]
+0005925 = focal adhesion [isa: 0005924 ]
+0005927 = muscle tendon junction [isa: 0005924 ]
+0030056 = hemidesmosome [isa: 0030055 ]
+0005911 = intercellular junction [isa: 0030054 ] [partof: 0016327 ]
+0005913 = cell-cell adherens junction [isa: 0005911 0005912 ]
+0005916 = fascia adherens [isa: 0005913 ]
+0005917 = nephrocyte junction [isa: 0005913 ]
+0005918 = septate junction [isa: 0005913 ]
+0005919 = pleated septate junction [isa: 0005918 ]
+0005920 = smooth septate junction [isa: 0005918 ]
+0005914 = spot adherens junction [isa: 0005913 ]
+0005915 = zonula adherens [isa: 0005913 ]
+0030057 = desmosome [isa: 0005911 ]
+0005921 = gap junction [isa: 0005911 ]
+0005922 = connexon [partof: 0005921 ]
+0046581 = intercellular canaliculus [isa: 0005911 ]
+0009506 = plasmodesma [isa: 0005911 ]
+0009546 = plasmodesmatal cytoplasmic sleeve [partof: 0009506 ]
+0009510 = plasmodesmatal desmotubule [partof: 0009506 ]
+0009572 = desmotubule central rod [partof: 0009510 ]
+0009548 = plasmodesmatal plasma membrane [partof: 0009506 ]
+0009550 = primary plasmodesma [isa: 0009506 ]
+0009551 = secondary plasmodesma [isa: 0009506 ]
+0005923 = tight junction [isa: 0005911 ]
+0042101 = T-cell receptor complex [partof: 0016327 ]
+0042105 = alpha-beta T-cell receptor complex [isa: 0042101 ]
+0042106 = gamma-delta T-cell receptor complex [isa: 0042101 ]
+0009921 = auxin efflux carrier complex [partof: 0005886 ]
+0009925 = basal plasma membrane [partof: 0005886 ]
+0016323 = basolateral plasma membrane [partof: 0005886 ]
+0005903 = brush border [partof: 0005886 ]
+0005901 = caveolae [partof: 0005886 ]
+0016599 = caveolar membrane [partof: 0005901 ]
+0016600 = flotillin complex [partof: 0016599 ]
+0030054 = cell junction [partof: 0005886 ]
+0005912 = adherens junction [isa: 0030054 ]
+0005905 = coated pit [partof: 0005886 ]
+0009897 = external side of plasma membrane [partof: 0005886 ]
+0019897 = extrinsic plasma membrane protein [isa: 0019898 ] [partof: 0005886 ]
+0016342 = catenin [isa: 0019897 ]
+0046658 = extrinsic membrane protein, GPI-anchored [isa: 0019897 ]
+0005834 = heterotrimeric G-protein complex [isa: 0019897 ]
+0016027 = inaD signaling complex [isa: 0019897 ] [partof: 0016028 ]
+0045256 = hydrogen-translocating F-type ATPase complex (sensu Bacteria) [isa: 0045255 ] [partof: 0005886 ]
+0005887 = integral plasma membrane protein [isa: 0016021 ] [partof: 0005886 ]
+0008282 = ATP-sensitive potassium channel [partof: 0005887 ]
+0016935 = glycine-gated chloride channel complex [partof: 0005887 ]
+0030526 = granulocyte-macrophage colony stimulating factor receptor complex [partof: 0005887 ]
+0019183 = histamine-gated chloride channel complex [partof: 0005887 ]
+0005889 = hydrogen/potassium-exchanging ATPase complex [partof: 0005887 ]
+0005899 = insulin receptor complex [partof: 0005887 ]
+0005888 = integral plasma membrane proteoglycan [partof: 0005887 ]
+0008305 = integrin [partof: 0005887 ]
+0045323 = interleukin-1 receptor complex [partof: 0005887 ]
+0042022 = interleukin-12 receptor complex [partof: 0005887 ]
+0005898 = interleukin-13 receptor complex [partof: 0005887 ]
+0045092 = interleukin-18 receptor complex [partof: 0005887 ]
+0005893 = interleukin-2 receptor complex [partof: 0005887 ]
+0005894 = interleukin-3 receptor complex [partof: 0005887 ]
+0016516 = interleukin-4 receptor complex [partof: 0005887 ]
+0005895 = interleukin-5 receptor complex [partof: 0005887 ]
+0005896 = interleukin-6 receptor complex [partof: 0005887 ]
+0005897 = interleukin-9 receptor complex [partof: 0005887 ]
+0008328 = ionotropic glutamate receptor complex [partof: 0005887 ]
+0017146 = N-methyl-D-aspartate selective glutamate receptor complex [partof: 0005887 ]
+0005892 = nicotinic acetylcholine-gated receptor-channel [partof: 0005887 ]
+0005900 = oncostatin-M receptor complex [partof: 0005887 ]
+0005890 = sodium/potassium-exchanging ATPase complex [partof: 0005887 ]
+0005891 = voltage-gated calcium channel complex [partof: 0005887 ]
+0008087 = light-activated voltage-gated calcium channel complex [isa: 0005891 ]
+0008076 = voltage-gated potassium channel complex [partof: 0005887 ]
+0001518 = voltage-gated sodium channel complex [partof: 0005887 ]
+0009898 = internal side of plasma membrane [partof: 0005886 ]
+0030027 = lamellipodium [partof: 0005886 ]
+0016328 = lateral plasma membrane [partof: 0005886 ]
+0005904 = lipid bilayer [partof: 0005886 ]
+0045121 = lipid raft [partof: 0005886 ]
+0030028 = microspike [partof: 0005886 ]
+0030175 = filopodium [isa: 0030028 ]
+0005902 = microvillus [partof: 0005886 ]
+0045260 = proton-transporting ATP synthase complex (sensu Bacteria) [isa: 0045259 ] [partof: 0005886 ]
+0045262 = proton-transporting ATP synthase complex, catalytic core F(1) (sensu Bacteria) [isa: 0045261 ] [partof: 0045260 ]
+0045268 = hydrogen-transporting ATP synthase, catalytic core (sensu Bacteria) [isa: 0045267 ] [partof: 0045262 ]
+0045270 = hydrogen-transporting ATP synthase, central stalk (sensu Bacteria) [isa: 0045269 ] [partof: 0045262 ]
+0045264 = proton-transporting ATP synthase complex, coupling factor F(0) (sensu Bacteria) [isa: 0045263 ] [partof: 0045260 ]
+0045266 = hydrogen-transporting ATP synthase, stator stalk (sensu Bacteria) [isa: 0045265 ] [partof: 0045264 ]
+0045272 = respiratory chain complex I (sensu Bacteria) [isa: 0045271 ] [partof: 0005886 ]
+0045280 = NADH dehydrogenase complex (ubiquinone) (sensu Bacteria) [isa: 0045279 ] [partof: 0045272 ]
+0045274 = respiratory chain complex II (sensu Bacteria) [isa: 0045273 ] [partof: 0005886 ]
+0045284 = fumarate reductase complex (sensu Bacteria) [isa: 0045283 ] [partof: 0045274 ]
+0045282 = succinate dehydrogenase complex (sensu Bacteria) [isa: 0045281 ] [partof: 0045274 ]
+0045276 = respiratory chain complex III (sensu Bacteria) [isa: 0045275 ] [partof: 0005886 ]
+0045286 = ubiquinol-cytochrome c reductase complex (sensu Bacteria) [isa: 0045285 ] [partof: 0045276 ]
+0045278 = respiratory chain complex IV (sensu Bacteria) [isa: 0045277 ] [partof: 0005886 ]
+0016028 = rhabdomere [partof: 0005886 ]
+0016029 = subrhabdomeral cisterna [partof: 0016028 ]
+0001726 = ruffles [partof: 0005886 ]
+0042383 = sarcolemma [isa: 0005886 ]
+0045258 = succinate dehydrogenase complex (ubiquinone) (sensu Bacteria) [isa: 0045257 ] [partof: 0005886 ]
+0030315 = T-tubule [partof: 0005886 ]
+0030075 = thylakoid (sensu Cyanobacteria) [isa: 0009579 ] [partof: 0005886 ]
+0030074 = thylakoid (sensu Proteobacteria) [isa: 0009579 ] [partof: 0005886 ]
+0030078 = light-harvesting complex, core complex [isa: 0030074 0030077 ]
+0030080 = B875 antenna complex [partof: 0030078 ]
+0030079 = light-harvesting complex, peripheral complex [isa: 0030074 0030077 ]
+0030081 = B800-820 antenna complex [partof: 0030079 ]
+0030082 = B800-850 antenna complex [partof: 0030079 ]
+0030090 = reaction center (sensu Proteobacteria) [isa: 0009521 ] [partof: 0030074 ]
+0030256 = type I protein secretion system complex [partof: 0005886 ]
+0015627 = type II protein (Sec) secretion system complex [partof: 0005886 ]
+0030257 = type III protein secretion system complex [partof: 0005886 ]
+0045259 = proton-transporting ATP synthase complex [partof: 0005622 ]
+0045261 = proton-transporting ATP synthase complex, catalytic core F(1) [partof: 0045259 ]
+0045267 = hydrogen-transporting ATP synthase, catalytic core [partof: 0045261 ]
+0045269 = hydrogen-transporting ATP synthase, central stalk [partof: 0045261 ]
+0045263 = proton-transporting ATP synthase complex, coupling factor F(0) [partof: 0045259 ]
+0045265 = hydrogen-transporting ATP synthase, stator stalk [partof: 0045263 ]
+0045253 = pyruvate dehydrogenase (lipoamide) phosphatase complex [partof: 0005622 ]
+0045254 = pyruvate dehydrogenase complex [partof: 0005622 ]
+0045271 = respiratory chain complex I [partof: 0005622 ]
+0045279 = NADH dehydrogenase complex (ubiquinone) [partof: 0045271 ]
+0045273 = respiratory chain complex II [partof: 0005622 ]
+0045283 = fumarate reductase complex [partof: 0045273 ]
+0045281 = succinate dehydrogenase complex [partof: 0045273 ]
+0045275 = respiratory chain complex III [partof: 0005622 ]
+0045285 = ubiquinol-cytochrome c reductase complex [partof: 0045275 ]
+0045277 = respiratory chain complex IV [partof: 0005622 ]
+0030529 = ribonucleoprotein complex [partof: 0005622 ]
+0045257 = succinate dehydrogenase complex (ubiquinone) [partof: 0005622 ]
+0045239 = TCA cycle enzyme complex [partof: 0005622 ]
+0045240 = alpha-ketoglutarate dehydrogenase complex [isa: 0045239 ]
+0045242 = isocitrate dehydrogenase complex (NAD+) [isa: 0045239 ]
+0045244 = succinate-CoA ligase complex (GDP-forming) [isa: 0045239 ]
+0009579 = thylakoid [isa: 0016020 ] [partof: 0005622 ]
+0030076 = light-harvesting complex [isa: 0009579 ]
+0030077 = light-harvesting complex (sensu Proteobacteria) [isa: 0030076 ]
+0009502 = photosynthetic electron transport chain [partof: 0009579 ]
+0009512 = cytochrome b6f complex [partof: 0009502 ]
+0009521 = photosystem [partof: 0009579 ]
+0009522 = photosystem I [isa: 0009521 ]
+0009782 = photosystem I antenna complex [partof: 0009522 ]
+0009538 = photosystem I reaction center [partof: 0009522 ]
+0009523 = photosystem II [isa: 0009521 ]
+0009654 = oxygen evolving complex [partof: 0009523 ]
+0009783 = photosystem II antenna complex [partof: 0009523 ]
+0009539 = photosystem II reaction center [partof: 0009523 ]
+0000151 = ubiquitin ligase complex [partof: 0005622 ]
+0016020 = membrane [partof: 0005623 ]
+0012505 = endomembrane system [isa: 0016020 ]
+0042175 = nuclear envelope-endoplasmic reticulum network [partof: 0012505 ]
+0012506 = vesicle membrane [partof: 0012505 ]
+0009279 = external outer membrane (sensu Gram-negative Bacteria) [isa: 0016020 ] [partof: 0030313 ]
+0045203 = integral protein of the external outer membrane (sensu Gram-negative Bacteria) [isa: 0016021 ] [partof: 0009279 ]
+0019898 = extrinsic membrane protein [partof: 0016020 ]
+0019866 = inner membrane [partof: 0016020 ]
+0016021 = integral membrane protein [partof: 0016020 ]
+0016469 = hydrogen-transporting two-sector ATPase complex [isa: 0016021 ]
+0045255 = hydrogen-translocating F-type ATPase complex [isa: 0016469 ]
+0017071 = intracellular cyclic nucleotide activated cation channel complex [partof: 0016021 ]
+0017090 = meprin A complex [partof: 0016021 ]
+0016472 = sodium-transporting two-sector ATPase complex [isa: 0016021 ]
+0016473 = sodium-translocating F-type ATPase complex [isa: 0016472 ]
+0016474 = sodium-translocating V-type ATPase complex [isa: 0016472 ]
+0019867 = outer membrane [partof: 0016020 ]
+0030496 = midbody [partof: 0005623 ]
+0030428 = septum [partof: 0005623 ]
+0005936 = shmoo [partof: 0005623 ]
+0005937 = shmoo tip [isa: 0000134 ] [partof: 0005936 ]
+0030427 = site of polarized growth [partof: 0005623 ]
+0030426 = growth cone [isa: 0030427 ]
+0030483 = site of polarized growth (sensu Fungi) [isa: 0030427 ]
+0000134 = site of polarized growth (sensu Saccharomyces) [isa: 0030483 ]
+0008372 = cellular_component unknown [isa: 0005575 ]
+0030312 = external protective structure [isa: 0005575 ]
+0030313 = cell envelope [isa: 0030312 ]
+0009276 = cell wall (sensu Gram-negative Bacteria) [isa: 0009274 ] [partof: 0030313 ]
+0030288 = periplasmic space (sensu Gram-negative Bacteria) [partof: 0030313 ]
+0005618 = cell wall [isa: 0030312 ]
+0009274 = cell wall (sensu Bacteria) [isa: 0005576 0005618 ]
+0009275 = cell wall (sensu Gram-positive Bacteria) [isa: 0009274 ]
+0009277 = cell wall (sensu Fungi) [isa: 0005576 0005618 ]
+0005621 = bud scar [partof: 0009277 ]
+0030446 = hyphal cell wall [isa: 0009277 ]
+0030287 = periplasmic space (sensu Fungi) [partof: 0009277 ]
+0030445 = yeast-form cell wall [isa: 0009277 ]
+0009505 = cell wall (sensu Magnoliophyta) [isa: 0005576 0005618 ]
+0009530 = primary cell wall [isa: 0009505 ]
+0009549 = cellulose microfibril [partof: 0009530 0009531 ]
+0009531 = secondary cell wall [isa: 0009505 ]
+0030112 = glycocalyx [isa: 0030312 ]
+0030113 = capsule [isa: 0030112 ]
+0030115 = S-layer [isa: 0030112 ]
+0030114 = slime layer [isa: 0030112 ]
+0005576 = extracellular [isa: 0005575 ]
+0005601 = classical-complement pathway C3/C5 convertase complex [partof: 0005576 ]
+0005602 = complement component C1q complex [partof: 0005576 ]
+0005603 = complement component C2 complex [partof: 0005576 ]
+0005578 = extracellular matrix [partof: 0005576 ]
+0005604 = basement membrane [partof: 0005578 ]
+0005605 = basement lamina [partof: 0005604 ]
+0008003 = lamina densa [partof: 0005605 ]
+0008002 = lamina lucida [partof: 0005605 ]
+0008004 = lamina reticularis [partof: 0005605 ]
+0005613 = laminin receptor protein [partof: 0005605 ]
+0005606 = laminin-1 [partof: 0005605 ]
+0005608 = laminin-3 [partof: 0005605 ]
+0005609 = laminin-4 [partof: 0005605 ]
+0005610 = laminin-5 [partof: 0005605 ]
+0005611 = laminin-6 [partof: 0005605 ]
+0005612 = laminin-7 [partof: 0005605 ]
+0005587 = collagen type IV [isa: 0016341 ] [partof: 0005604 ]
+0005581 = collagen [partof: 0005578 ]
+0005593 = facit collagen [isa: 0005581 ]
+0005594 = collagen type IX [isa: 0005593 ]
+0005595 = collagen type XII [isa: 0005593 ]
+0005596 = collagen type XIV [isa: 0005593 ]
+0005597 = collagen type XVI [isa: 0005593 ]
+0005583 = fibrillar collagen [isa: 0005581 ]
+0005584 = collagen type I [isa: 0005583 ]
+0005585 = collagen type II [isa: 0005583 ]
+0005586 = collagen type III [isa: 0005583 ]
+0005588 = collagen type V [isa: 0005583 ]
+0005592 = collagen type XI [isa: 0005583 ]
+0016341 = other collagen [isa: 0005581 ]
+0005589 = collagen type VI [isa: 0016341 ]
+0005590 = collagen type VII [isa: 0016341 ]
+0005600 = collagen type XIII [isa: 0016341 ]
+0005582 = collagen type XV [isa: 0016341 ]
+0005598 = short-chain collagen [isa: 0005581 ]
+0005591 = collagen type VIII [isa: 0005598 ]
+0005599 = collagen type X [isa: 0005598 ]
+0005579 = membrane attack complex [partof: 0005578 ]
+0005580 = membrane attack complex protein alphaM chain [partof: 0005579 ]
+0008008 = membrane attack complex protein beta2 chain [partof: 0005579 ]
+0001527 = microfibril [partof: 0005578 ]
+0045202 = synaptic junction [isa: 0005578 ]
+0045211 = post-synaptic membrane [partof: 0045202 ]
+0005615 = extracellular space [partof: 0005576 ]
+0016942 = insulin-like growth factor receptor binding protein complex [partof: 0005615 ]
+0005616 = larval serum protein [partof: 0005615 ]
+0005617 = larval serum protein-1 [partof: 0005616 ]
+0009519 = middle lamella [partof: 0005615 ]
+0005577 = fibrinogen [partof: 0005576 ]
+0005972 = fibrinogen alpha chain [partof: 0005577 ]
+0005973 = fibrinogen beta chain [partof: 0005577 ]
+0005974 = fibrinogen gamma chain [partof: 0005577 ]
+0018995 = host [isa: 0005576 ]
+0042025 = host cell nucleus [partof: 0018995 ]
+0020002 = host cell plasma membrane [partof: 0018995 ]
+0019031 = viral envelope [isa: 0020002 ] [partof: 0019012 ]
+0019032 = viral glycoprotein [partof: 0019031 ]
+0030430 = host cytoplasm [partof: 0018995 ]
+0020030 = knob (sensu Plasmodium) [partof: 0030430 ]
+0020036 = Maurer's cleft [partof: 0030430 ]
+0045171 = intercellular bridge [partof: 0005576 ]
+0045172 = ring canal (sensu Drosophila) [isa: 0045171 ]
+0005614 = interstitial matrix [partof: 0005576 ]
+0019037 = viral assembly intermediate [partof: 0005576 ]
+0019035 = viral integration complex [partof: 0005576 ]
+0019034 = viral replication complex [partof: 0005576 ]
+0019036 = viral transcriptional complex [partof: 0005576 ]
+0019012 = virion [partof: 0005576 ]
+0019013 = nucleocapsid [partof: 0019012 ]
+0019028 = viral capsid [partof: 0019013 ]
+0019029 = helical viral capsid [isa: 0019028 ]
+0019030 = icosahedral viral capsid [isa: 0019028 ]
+0019015 = viral genome [partof: 0019013 ]
+0019021 = DNA viral genome [isa: 0019015 ]
+0019016 = non-segmented viral genome [isa: 0019015 ]
+0019022 = RNA viral genome [isa: 0019015 ]
+0019023 = dsRNA viral genome [isa: 0019022 ]
+0019024 = ssRNA viral genome [isa: 0019022 ]
+0019027 = ambisense viral genome [isa: 0019024 ]
+0019026 = negative sense viral genome [isa: 0019024 ]
+0019025 = positive sense viral genome [isa: 0019024 ]
+0019017 = segmented viral genome [isa: 0019015 ]
+0019018 = bipartite viral genome [isa: 0019017 ]
+0019020 = multipartite viral genome [isa: 0019017 ]
+0019019 = tripartite viral genome [isa: 0019017 ]
+0019014 = viral nucleocapsid [isa: 0019013 ]
+0019033 = viral tegument [partof: 0019012 ]
+0008370 = obsolete [isa: 0005575 ]
+0045096 = acidic keratin [isa: 0008370 ]
+0045097 = basic/neutral keratin [isa: 0008370 ]
+0005734 = box C + D snoRNP protein [isa: 0008370 ]
+0005735 = box H + ACA snoRNP protein [isa: 0008370 ]
+0009280 = cell wall inner membrane [isa: 0008370 ]
+0030064 = cell wall inner membrane [isa: 0008370 ]
+0005906 = clathrin adaptor [isa: 0008370 ]
+0016190 = clathrin coat [isa: 0008370 ]
+0005909 = coated vesicle [isa: 0008370 ]
+0005799 = coatomer [isa: 0008370 ]
+0005800 = COPII vesicle [isa: 0008370 ]
+0045100 = desmin [isa: 0008370 ]
+0001529 = elastin [isa: 0008370 ]
+0005810 = endocytotic transport vesicle [isa: 0008370 ]
+0005805 = ER-Golgi transport vesicle [isa: 0008370 ]
+0008304 = eukaryotic translation initiation factor 4 complex [isa: 0008370 ]
+0045101 = glial fibrillary acidic protein [isa: 0008370 ]
+0005806 = Golgi-ER transport vesicle [isa: 0008370 ]
+0005808 = Golgi-plasma membrane transport vesicle [isa: 0008370 ]
+0005809 = Golgi-vacuole transport vesicle [isa: 0008370 ]
+0005907 = HA1 clathrin adaptor [isa: 0008370 ]
+0005908 = HA2 clathrin adaptor [isa: 0008370 ]
+0005755 = hydrogen-transporting ATP synthase, coupling factor CF(0) [isa: 0008370 ]
+0005807 = inter-Golgi transport vesicle [isa: 0008370 ]
+0008245 = lysosomal membrane hydrogen-transporting ATPase [isa: 0008370 ]
+0009278 = murein sacculus [isa: 0008370 ]
+0030063 = murein sacculus [isa: 0008370 ]
+0045102 = peripherin [isa: 0008370 ]
+0005620 = periplasmic space [isa: 0008370 ]
+0005803 = secretory vesicle [isa: 0008370 ]
+0005804 = secretory vesicle membrane [isa: 0008370 ]
+0005733 = small nucleolar RNA [isa: 0008370 ]
+0005573 = telomerase RNA [isa: 0008370 ]
+0009580 = thylakoid (sensu Bacteria) [isa: 0008370 ]
+0000219 = vacuolar hydrogen-transporting ATPase [isa: 0008370 ]
+0045099 = vimentin [isa: 0008370 ]
+0005941 = unlocalized [isa: 0005575 ]
+0005942 = 1-phosphatidylinositol 3-kinase complex [isa: 0005941 ]
+0005943 = 1-phosphatidylinositol-4-phosphate kinase, class IA complex [isa: 0005941 ]
+0005944 = 1-phosphatidylinositol-4-phosphate kinase, class IB complex [isa: 0005941 ]
+0008247 = 2-acetyl-1-alkylglycerophosphocholine esterase complex [isa: 0005941 ]
+0009316 = 3-isopropylmalate dehydratase complex [isa: 0005941 ]
+0009334 = 3-phenylpropionate dioxygenase complex [isa: 0005941 ]
+0009329 = acetate CoA-transferase complex [isa: 0005941 ]
+0005948 = acetolactate synthase complex [isa: 0005941 ]
+0009317 = acetyl-CoA carboxylase complex [isa: 0005941 ]
+0009321 = alkyl hydroperoxide reductase complex [isa: 0005941 ]
+0005946 = alpha, alpha-trehalose-phosphate synthase complex (UDP-forming) [isa: 0005941 ]
+0017177 = alpha-glucosidase complex [isa: 0005941 ]
+0017101 = aminoacyl-tRNA synthetase multienzyme complex [isa: 0005941 ]
+0005949 = aminoadipate-semialdehyde dehydrogenase complex [isa: 0005941 ]
+0005950 = anthranilate synthase complex [isa: 0005941 ]
+0009347 = aspartate carbamoyltransferase complex [isa: 0005941 ]
+0009341 = beta-galactosidase complex [isa: 0005941 ]
+0009343 = biotin carboxylase complex [isa: 0005941 ]
+0005953 = CAAX-protein geranylgeranyltransferase complex [isa: 0005941 ]
+0005954 = calcium/calmodulin-dependent protein kinase complex [isa: 0005941 ]
+0005952 = cAMP-dependent protein kinase complex [isa: 0005941 ]
+0005951 = carbamoyl-phosphate synthase complex [isa: 0005941 ]
+0008303 = caspase complex [isa: 0005941 ]
+0009346 = citrate lyase complex [isa: 0005941 ]
+0009333 = cysteine synthase complex [isa: 0005941 ]
+0009319 = cytochrome o ubiquinol oxidase complex [isa: 0005941 ]
+0009324 = D-amino acid dehydrogenase complex [isa: 0005941 ]
+0005957 = debranching enzyme [isa: 0005941 ]
+0009352 = dihydrolipoamide dehydrogenase complex [isa: 0005941 ]
+0009351 = dihydrolipoamide S-acyltransferase complex [isa: 0005941 ]
+0009354 = dihydrolipoamide S-succinyltransferase complex [isa: 0005941 ]
+0009390 = dimethyl sulfoxide reductase complex [isa: 0005941 ]
+0009360 = DNA polymerase III complex [isa: 0005941 ]
+0009355 = DNA polymerase V complex [isa: 0005941 ]
+0009330 = DNA topoisomerase complex (ATP-hydrolyzing) [isa: 0005941 ]
+0009340 = DNA topoisomerase IV complex [isa: 0005941 ]
+0005958 = DNA-dependent protein kinase complex [isa: 0005941 ]
+0005959 = DNA-dependent protein kinase, DNA-end-binding protein complex [isa: 0005941 ]
+0009366 = enterobactin synthetase complex [isa: 0005941 ]
+0009350 = ethanolamine ammonia-lyase complex [isa: 0005941 ]
+0009380 = excinuclease ABC complex [isa: 0005941 ]
+0009338 = exodeoxyribonuclease V complex [isa: 0005941 ]
+0009318 = exodeoxyribonuclease VII complex [isa: 0005941 ]
+0008051 = farnesyl-diphosphate farnesyl transferase complex [isa: 0005941 ]
+0008043 = ferritin [isa: 0005941 ]
+0016914 = follicle-stimulating hormone complex [isa: 0005941 ]
+0009326 = formate dehydrogenase complex [isa: 0005941 ]
+0009342 = glutamate synthase complex (NADPH) [isa: 0005941 ]
+0017109 = glutamate-cysteine ligase complex [isa: 0005941 ]
+0009332 = glutamate-tRNA ligase complex complex [isa: 0005941 ]
+0009331 = glycerol-3-phosphate dehydrogenase complex [isa: 0005941 ]
+0005960 = glycine cleavage system complex [isa: 0005941 ]
+0005961 = glycine dehydrogenase complex (decarboxylating) [partof: 0005960 ]
+0009345 = glycine-tRNA ligase complex [isa: 0005941 ]
+0009339 = glycolate oxidase complex [isa: 0005941 ]
+0008074 = guanylate cyclase complex, soluble [isa: 0005941 ]
+0009379 = Holliday junction helicase complex [isa: 0005941 ]
+0009335 = holo-[acyl-carrier protein] synthase complex [isa: 0005941 ]
+0009376 = HslUV protease complex [isa: 0005941 ]
+0009375 = hydrogenase complex [isa: 0005941 ]
+0009382 = imidazoleglycerol-phosphate synthase complex [isa: 0005941 ]
+0017052 = insulin-like growth factor binding protein [isa: 0005941 ]
+0005963 = magnesium-dependent protein serine/threonine phosphatase complex [isa: 0005941 ]
+0015050 = methane monooxygenase complex [isa: 0005941 ]
+0017102 = methionyl glutamyl tRNA synthetase complex [isa: 0005941 ]
+0019008 = molybdopterin synthase complex [isa: 0005941 ]
+0019009 = molybdopterin converting factor [partof: 0019008 ]
+0009327 = NAD(P)+ transhydrogenase complex (AB-specific) [isa: 0005941 ]
+0030025 = NADH:plastoquinone reductase complex [isa: 0005941 ]
+0009325 = nitrate reductase complex [isa: 0005941 ]
+0009344 = nitrite reductase complex (NAD(P)H) [isa: 0005941 ]
+0016610 = nitrogenase complex [isa: 0005941 ]
+0016611 = iron-iron nitrogenase complex [isa: 0016610 ]
+0016612 = molybdenum-iron nitrogenase complex [isa: 0016610 ]
+0016613 = vanadium-iron nitrogenase complex [isa: 0016610 ]
+0009348 = ornithine carbamoyltransferase complex [isa: 0005941 ]
+0009356 = p-aminobenzoate synthetase complex [isa: 0005941 ]
+0009328 = phenylalanine-tRNA ligase complex [isa: 0005941 ]
+0009320 = phosphoribosylaminoimidazole carboxylase complex [isa: 0005941 ]
+0005964 = phosphorylase kinase complex [isa: 0005941 ]
+0005966 = photoreceptor cyclic-nucleotide phosphodiesterase complex [isa: 0005941 ]
+0009358 = polyphosphate kinase complex [isa: 0005941 ]
+0009367 = prepilin peptidase complex [isa: 0005941 ]
+0016222 = procollagen-proline,2-oxoglutarate-4-dioxygenase complex [isa: 0005941 ]
+0005965 = protein farnesyltransferase complex [isa: 0005941 ]
+0009365 = protein histidine kinase complex [isa: 0005941 ]
+0005956 = protein kinase CK2 complex [isa: 0005941 ]
+0008287 = protein serine/threonine phosphatase complex [isa: 0005941 ]
+0005955 = calcineurin complex [isa: 0008287 ]
+0017023 = myosin phosphatase complex [isa: 0008287 ]
+0030289 = protein phosphatase 4 complex [isa: 0008287 ]
+0000164 = protein phosphatase type 1 complex [isa: 0008287 ]
+0000159 = protein phosphatase type 2A complex [isa: 0008287 ]
+0009357 = protein-N(PI)-phosphohistidine-sugar phosphotransferase complex [isa: 0005941 ]
+0009364 = pyruvate dehydrogenase complex (lipoamide) [isa: 0005941 ]
+0019804 = quinolinate synthetase complex [isa: 0005941 ]
+0005968 = RAB-protein geranylgeranyltransferase complex [isa: 0005941 ]
+0009349 = riboflavin synthase complex [isa: 0005941 ]
+0005971 = ribonucleoside-diphosphate reductase complex [isa: 0005941 ]
+0009323 = ribosomal-protein-alanine N-acetyltransferase complex [isa: 0005941 ]
+0016442 = RNA-induced silencing complex [isa: 0005941 ]
+0005970 = serine-pyruvate aminotransferase, type 1 complex [isa: 0005941 ]
+0005969 = serine-pyruvate aminotransferase, type 2B complex [isa: 0005941 ]
+0009361 = succinate-CoA ligase complex (ADP-forming) [isa: 0005941 ]
+0009336 = sulfate adenylyltransferase complex (ATP) [isa: 0005941 ]
+0009337 = sulfite reductase complex (NADPH) [isa: 0005941 ]
+0018444 = translation release factor complex [isa: 0005941 ]
+0009322 = trimethylamine-N-oxide reductase complex [isa: 0005941 ]
+0019812 = type I site-specific deoxyribonuclease complex [isa: 0005941 ]
+0009359 = type II site-specific deoxyribonuclease complex [isa: 0005941 ]
+0019813 = type III site-specific deoxyribonuclease complex [isa: 0005941 ]
+0017122 = UDP-N-acetylglucosamine-peptide N-acetylglucosaminyltransferase complex [isa: 0005941 ]
+0008150 = biological_process [partof: 0003673 ]
+0007610 = behavior [isa: 0008150 ]
+0030534 = adult behavior [isa: 0007610 ]
+0008044 = adult behavior (sensu Insecta) [isa: 0030534 ]
+0008341 = response to cocaine (sensu Insecta) [isa: 0008044 0042220 ]
+0045473 = response to ethanol (sensu Insecta) [isa: 0008044 0045471 ]
+0045474 = response to ether (sensu Insecta) [isa: 0008044 0045472 ]
+0008343 = adult feeding behavior [isa: 0007631 0030534 ]
+0030535 = adult feeding behavior (sensu Insecta) [isa: 0008343 ]
+0001662 = behavioral fear response [isa: 0007610 ]
+0007635 = chemosensory behavior [isa: 0007610 ]
+0007636 = chemosensory jump behavior [isa: 0007635 ]
+0042048 = olfactory behavior [isa: 0007635 ]
+0007637 = proboscis extension reflex [isa: 0007635 ]
+0007631 = feeding behavior [isa: 0007610 ]
+0030536 = larval feeding behavior [isa: 0007631 ]
+0008342 = larval feeding behavior (sensu Insecta) [isa: 0007627 0030536 ]
+0001661 = taste aversion [isa: 0007631 ]
+0007625 = grooming behavior [isa: 0007610 ]
+0030537 = larval behavior [isa: 0007610 ]
+0007627 = larval behavior (sensu Insecta) [isa: 0030537 ]
+0007611 = learning and/or memory [isa: 0007610 ]
+0007612 = learning [isa: 0007611 ]
+0008306 = associative learning [isa: 0007612 ]
+0008355 = olfactory learning [isa: 0007612 ]
+0008542 = visual learning [isa: 0007612 ]
+0042297 = vocal learning [isa: 0007612 ]
+0007613 = memory [isa: 0007611 ]
+0007615 = anesthesia-resistant memory [isa: 0007613 ]
+0007616 = long-term memory [isa: 0007613 ]
+0007614 = short-term memory [isa: 0007613 ]
+0007626 = locomotory behavior [isa: 0007610 ]
+0008344 = adult locomotory behavior [isa: 0007626 ]
+0007628 = adult walking behavior [isa: 0008344 ]
+0007629 = flight behavior [isa: 0008344 ]
+0007630 = jump response [isa: 0008344 ]
+0008345 = larval locomotory behavior [isa: 0007626 ]
+0008346 = larval walking behavior [isa: 0008345 ]
+0040011 = locomotion [isa: 0007626 ]
+0040012 = regulation of locomotion [partof: 0040011 ]
+0040013 = negative regulation of locomotion [isa: 0040012 ]
+0040017 = positive regulation of locomotion [isa: 0040012 ]
+0045475 = locomotor rhythm [isa: 0007623 0007626 ]
+0007638 = mechanosensory behavior [isa: 0007610 ]
+0019098 = reproductive behavior [isa: 0007610 ]
+0007617 = mating behavior [isa: 0019098 ]
+0007619 = courtship behavior [isa: 0007617 ]
+0008050 = female courtship behavior [isa: 0007619 ]
+0008049 = male courtship behavior [isa: 0007619 ]
+0016542 = male courtship behavior (sensu Drosophila) [isa: 0008049 ]
+0016546 = male courtship behavior (sensu Drosophila), licking [partof: 0016542 ]
+0016543 = male courtship behavior (sensu Drosophila), orientation [partof: 0016542 ]
+0016544 = male courtship behavior (sensu Drosophila), tapping [partof: 0016542 ]
+0016545 = male courtship behavior (sensu Drosophila), wing vibration [partof: 0016542 ]
+0045433 = male courtship behavior (sensu Drosophila), song production [partof: 0016545 ]
+0007618 = mating [isa: 0007617 ]
+0007620 = copulation [isa: 0007618 ]
+0045297 = post-mating behavior [isa: 0007617 ]
+0046008 = regulation of female receptivity, post-mating [isa: 0045924 ] [partof: 0045297 ]
+0045434 = negative regulation of female receptivity, post-mating [isa: 0007621 0046008 ]
+0046009 = positive regulation of female receptivity, post-mating [isa: 0045925 0046008 ]
+0045924 = regulation of female receptivity [partof: 0007617 ]
+0007621 = negative regulation of female receptivity [isa: 0045924 ]
+0045925 = positive regulation of female receptivity [isa: 0045924 ]
+0018991 = oviposition [isa: 0019098 ]
+0007622 = rhythmic behavior [isa: 0007610 ]
+0007623 = circadian rhythm [isa: 0007622 ]
+0008062 = eclosion rhythm [isa: 0007623 ] [partof: 0007562 ]
+0009649 = entrainment of circadian clock [isa: 0009648 ] [partof: 0007623 ]
+0045187 = regulation of sleep [partof: 0007623 0030431 ]
+0042321 = negative regulation of sleep [isa: 0045187 ]
+0042323 = negative regulation of non-REM sleep [isa: 0042321 0045188 ]
+0042322 = negative regulation of REM sleep [isa: 0042320 0042321 ]
+0045938 = positive regulation of sleep [isa: 0045187 ]
+0046010 = positive regulation of non-REM sleep [isa: 0045188 0045938 ]
+0046005 = positive regulation of REM sleep [isa: 0042320 0045938 ]
+0045188 = regulation of non-REM sleep [isa: 0045187 ]
+0042320 = regulation of REM sleep [isa: 0045187 ]
+0007624 = ultradian rhythm [isa: 0007622 ]
+0040040 = thermosensory behavior [isa: 0007610 ]
+0007632 = visual behavior [isa: 0007610 ]
+0007634 = optokinetic behavior [isa: 0007632 ]
+0007633 = pattern orientation [isa: 0007632 ]
+0000004 = biological_process unknown [isa: 0008150 ]
+0007154 = cell communication [isa: 0008150 ]
+0007155 = cell adhesion [isa: 0007154 ]
+0016337 = cell-cell adhesion [isa: 0007155 ]
+0016339 = calcium-dependent cell-cell adhesion [isa: 0016337 ]
+0000501 = flocculation (sensu Saccharomyces) [isa: 0000128 0007157 0016339 ]
+0046586 = regulation of calcium-dependent cell-cell adhesion [isa: 0030155 ] [partof: 0016339 ]
+0046588 = negative regulation of calcium-dependent cell-cell adhesion [isa: 0007162 0046586 ]
+0046587 = positive regulation of calcium-dependent cell-cell adhesion [isa: 0045785 0046586 ]
+0016338 = calcium-independent cell-cell adhesion [isa: 0016337 ]
+0007157 = heterophilic cell adhesion [isa: 0016337 ]
+0007334 = agglutination (sensu Saccharomyces) [isa: 0007157 0007322 ]
+0020035 = cytoadherence to microvasculature [isa: 0007157 0030383 ]
+0007159 = leukocyte cell adhesion [isa: 0007157 ]
+0007158 = neuronal cell adhesion [isa: 0007157 ]
+0020013 = rosetting [isa: 0007157 ]
+0007156 = homophilic cell adhesion [isa: 0016337 ]
+0007160 = cell-matrix adhesion [isa: 0007155 ]
+0016340 = calcium-dependent cell-matrix adhesion [isa: 0007160 ]
+0007161 = calcium-independent cell-matrix adhesion [isa: 0007160 ]
+0000128 = flocculation [isa: 0007155 ]
+0030155 = regulation of cell adhesion [partof: 0007155 ]
+0007162 = negative regulation of cell adhesion [isa: 0030155 ]
+0045785 = positive regulation of cell adhesion [isa: 0030155 ]
+0030260 = cell invasion [isa: 0007154 ]
+0008037 = cell recognition [isa: 0007154 ]
+0007411 = axon guidance [isa: 0008037 ] [partof: 0007409 ]
+0016198 = axon choice point recognition [isa: 0008038 ] [partof: 0007411 ]
+0016199 = axon midline choice point recognition [isa: 0016198 ]
+0008045 = motor axon guidance [isa: 0007411 ]
+0030516 = regulation of axon extension [partof: 0007411 ]
+0030517 = negative regulation of axon extension [isa: 0030516 ]
+0045773 = positive regulation of axon extension [isa: 0030516 ]
+0008038 = neuronal cell recognition [isa: 0008037 ]
+0008039 = synaptic target recognition [isa: 0008038 ]
+0016200 = synaptic target attraction [partof: 0008039 ]
+0016201 = synaptic target inhibition [partof: 0008039 ]
+0007267 = cell-cell signaling [isa: 0007154 ]
+0045168 = cell-cell signaling involved in cell fate commitment [isa: 0007267 ] [partof: 0045165 ]
+0046331 = lateral inhibition [isa: 0045168 ]
+0030072 = peptide hormone secretion [isa: 0007267 0015833 0042445 ]
+0030252 = growth hormone secretion [isa: 0030072 ]
+0030073 = insulin secretion [isa: 0030072 ]
+0030103 = vasopressin secretion [isa: 0030072 ]
+0019226 = transmission of nerve impulse [isa: 0007267 ]
+0019227 = action potential propagation [partof: 0019226 ]
+0019228 = generation of action potential [partof: 0019226 ]
+0001508 = regulation of action potential [isa: 0007242 ] [partof: 0019226 ]
+0007272 = ionic insulation of neurons by glial cells [partof: 0001508 ]
+0045759 = negative regulation of action potential [isa: 0001508 ]
+0045760 = positive regulation of action potential [isa: 0001508 ]
+0007268 = synaptic transmission [partof: 0019226 ]
+0007270 = nerve-nerve synaptic transmission [isa: 0007268 ]
+0007271 = synaptic transmission, cholinergic [isa: 0007270 ]
+0001507 = acetylcholine breakdown in the synaptic cleft [partof: 0007271 ]
+0007274 = neuromuscular synaptic transmission [isa: 0007268 ]
+0001505 = regulation of neurotransmitter levels [partof: 0007268 ]
+0042133 = neurotransmitter metabolism [isa: 0008152 ] [partof: 0001505 ]
+0008291 = acetylcholine metabolism [isa: 0042133 0042439 ]
+0008292 = acetylcholine biosynthesis [isa: 0008291 0042136 0042401 ]
+0006581 = acetylcholine catabolism [isa: 0008291 0042135 0042402 ]
+0042414 = adrenaline metabolism [isa: 0006584 0042133 0042445 ]
+0042418 = adrenaline biosynthesis [isa: 0042136 0042414 0042423 0042446 ]
+0042419 = adrenaline catabolism [isa: 0042135 0042414 0042424 0042447 ]
+0042417 = dopamine metabolism [isa: 0006584 0042133 ]
+0042416 = dopamine biosynthesis [isa: 0042136 0042417 0042423 ]
+0006585 = dopamine biosynthesis from tyrosine [isa: 0042416 ]
+0042420 = dopamine catabolism [isa: 0042135 0042417 0042424 ]
+0042053 = regulation of dopamine metabolism [isa: 0042069 ] [partof: 0042417 ]
+0045963 = negative regulation of dopamine metabolism [isa: 0042053 0045914 ]
+0045964 = positive regulation of dopamine metabolism [isa: 0042053 0045915 ]
+0001692 = histamine metabolism [isa: 0006576 0042133 ]
+0001694 = histamine biosynthesis [isa: 0001692 0006548 0042136 0042401 ]
+0001695 = histamine catabolism [isa: 0001692 0042135 0042402 ]
+0042136 = neurotransmitter biosynthesis [isa: 0009058 0042133 ]
+0042421 = noradrenaline biosynthesis [isa: 0042136 0042415 0042423 0042446 ]
+0006589 = octopamine biosynthesis [isa: 0042136 0042401 0046333 ]
+0042444 = phenylethylamine biosynthesis [isa: 0042136 0042401 0042443 ]
+0042427 = serotonin biosynthesis [isa: 0042136 0042428 0042446 0046219 ]
+0006587 = serotonin biosynthesis from tryptophan [isa: 0042427 ]
+0006588 = tryptophan hydroxylase activation [partof: 0006587 ]
+0042135 = neurotransmitter catabolism [isa: 0009056 0042133 ]
+0042422 = noradrenaline catabolism [isa: 0042135 0042415 0042424 0042447 ]
+0046334 = octopamine catabolism [isa: 0042135 0042402 0046333 ]
+0019607 = phenylethylamine catabolism [isa: 0042135 0042402 0042443 ]
+0042429 = serotonin catabolism [isa: 0042135 0042428 0042447 0046218 ]
+0042415 = noradrenaline metabolism [isa: 0006584 0042133 0042445 ]
+0046333 = octopamine metabolism [isa: 0006576 0042133 ]
+0042443 = phenylethylamine metabolism [isa: 0006576 0042133 ]
+0042428 = serotonin metabolism [isa: 0006586 0042133 0042445 ]
+0007269 = neurotransmitter secretion [isa: 0001505 ]
+0008099 = synaptic vesicle endocytosis [isa: 0006897 ] [partof: 0007269 0016181 ]
+0016185 = synaptic vesicle budding [partof: 0008099 ]
+0016183 = synaptic vesicle coating [partof: 0008099 ]
+0016186 = synaptic vesicle fission [partof: 0008099 ]
+0016187 = synaptic vesicle internalization [partof: 0008099 ]
+0016188 = synaptic vesicle maturation [partof: 0008099 ]
+0016184 = synaptic vesicle retrieval [partof: 0008099 ]
+0016189 = synaptic vesicle to endosome fusion [isa: 0016197 ] [partof: 0008099 ]
+0016191 = synaptic vesicle uncoating [partof: 0008099 ]
+0016079 = synaptic vesicle exocytosis [isa: 0006887 ] [partof: 0007269 0016181 ]
+0016182 = endosome to synaptic vesicle budding [isa: 0016197 ] [partof: 0016079 ]
+0016081 = synaptic vesicle docking [partof: 0016079 ]
+0016083 = synaptic vesicle fusion [partof: 0016079 ]
+0016082 = synaptic vesicle priming [partof: 0016079 ]
+0016080 = synaptic vesicle targeting [partof: 0016079 ]
+0042137 = neurotransmitter storage [isa: 0001505 ]
+0001504 = neurotransmitter uptake [isa: 0001505 ]
+0007273 = regulation of synapse [partof: 0007268 ]
+0045213 = neurotransmitter receptor metabolism [isa: 0019538 ] [partof: 0007273 ]
+0045212 = neurotransmitter receptor biosynthesis [isa: 0006412 0045213 ]
+0016181 = synaptic vesicle transport [isa: 0016192 ] [partof: 0007268 ]
+0030383 = host-pathogen interaction [isa: 0007154 ]
+0019048 = virus-host interaction [isa: 0016032 0030383 ]
+0019049 = viral-host defense evasion [isa: 0019048 ]
+0019051 = induction of apoptosis by virus [isa: 0006917 0019049 ]
+0019050 = viral inhibition of apoptosis [isa: 0006916 0019049 ]
+0019053 = viral inhibition of extracellular antiviral response [isa: 0019049 ]
+0019052 = viral inhibition of intracellular antiviral response [isa: 0019049 ]
+0019054 = virus-host cell process manipulation [isa: 0019048 ]
+0019055 = viral perturbation of cell cycle regulation [isa: 0000074 0019054 ]
+0019057 = viral perturbation of host cell mRNA translation [isa: 0016478 0019054 0045946 ]
+0019056 = viral perturbation of host cell transcription [isa: 0019054 ]
+0009875 = pollen-pistil interaction [isa: 0007154 ]
+0009858 = compatible pollen-pistil interaction [isa: 0009856 0009875 ]
+0009876 = pollen adhesion [partof: 0009858 ]
+0009859 = pollen hydration [partof: 0009858 ]
+0009857 = pollen recognition [partof: 0009858 0009872 0009874 ]
+0009865 = pollen tube adhesion [partof: 0009858 ]
+0009869 = incompatible pollen-pistil interaction [isa: 0009875 ]
+0009872 = gametophytic self-incompatibility [isa: 0009869 ]
+0009874 = sporophytic self-incompatibility [isa: 0009869 ]
+0009719 = response to endogenous stimulus [isa: 0007154 ]
+0009726 = perception of endogenous stimulus [partof: 0009719 ]
+0009730 = perception of carbohydrate stimulus [isa: 0009726 ] [partof: 0009743 ]
+0009732 = perception of hexose stimulus [isa: 0009730 ] [partof: 0009746 ]
+0009731 = perception of sucrose stimulus [isa: 0009730 ] [partof: 0009744 ]
+0009720 = perception of hormone stimulus [isa: 0009726 ] [partof: 0009725 ]
+0009724 = perception of abscisic acid stimulus [isa: 0009720 ] [partof: 0009737 ]
+0009721 = perception of auxin stimulus [isa: 0009720 ] [partof: 0009733 ]
+0009729 = perception of brassinosteroid stimulus [isa: 0009720 ] [partof: 0009741 ]
+0009722 = perception of cytokinin stimulus [isa: 0009720 ] [partof: 0009735 ]
+0009727 = perception of ethylene stimulus [isa: 0009720 ] [partof: 0009723 ]
+0009728 = perception of gibberellic acid stimulus [isa: 0009720 ] [partof: 0009739 ]
+0009743 = response to carbohydrate stimulus [isa: 0009719 ]
+0009756 = carbohydrate mediated signaling [isa: 0007242 0009743 ]
+0009757 = hexose mediated signaling [isa: 0009746 0009756 ]
+0009747 = hexokinase-dependent signaling [isa: 0009757 ]
+0009748 = hexokinase-independent signaling [isa: 0009757 ]
+0009745 = sucrose mediated signaling [isa: 0009744 0009756 ]
+0009746 = response to hexose stimulus [isa: 0009743 ]
+0009750 = response to fructose stimulus [isa: 0009746 ]
+0009749 = response to glucose stimulus [isa: 0009746 ]
+0009744 = response to sucrose stimulus [isa: 0009743 ]
+0009725 = response to hormone stimulus [isa: 0009719 ]
+0009755 = hormone mediated signaling [isa: 0007242 0009725 ]
+0009738 = abscisic acid mediated signaling [isa: 0009737 0009755 ]
+0009787 = regulation of abscisic acid mediated signaling [partof: 0009738 ]
+0009788 = negative regulation of abscisic acid mediated signaling [isa: 0009787 ]
+0009789 = positive regulation of abscisic acid mediated signaling [isa: 0009787 ]
+0009734 = auxin mediated signaling [isa: 0009733 0009755 ]
+0009742 = brassinosteroid mediated signaling [isa: 0009741 0009755 ]
+0009736 = cytokinin mediated signaling [isa: 0009735 0009755 ]
+0009873 = ethylene mediated signaling pathway [isa: 0000160 0009723 0009755 ]
+0009866 = ethylene mediated signaling pathway (induced systemic resistance) [isa: 0009873 ] [partof: 0009682 ]
+0009871 = ethylene mediated signaling pathway (jasmonic acid/ethylene dependent systemic resistance) [isa: 0009873 ] [partof: 0009861 ]
+0009740 = gibberellic acid mediated signaling [isa: 0009739 0009755 ]
+0042388 = gibberellic acid mediated signaling, G-alpha dependent [isa: 0009740 ]
+0042390 = gibberellic acid mediated signaling, G-alpha independent [isa: 0009740 ]
+0009937 = regulation of gibberellic acid mediated signaling [partof: 0009740 ]
+0009938 = negative regulation of gibberellic acid mediated signaling [isa: 0009937 ]
+0009939 = positive regulation of gibberellic acid mediated signaling [isa: 0009937 ]
+0009737 = response to abscisic acid stimulus [isa: 0009725 ]
+0009733 = response to auxin stimulus [isa: 0009725 ]
+0009741 = response to brassinosteroid stimulus [isa: 0009725 ]
+0009735 = response to cytokinin stimulus [isa: 0009725 ]
+0009723 = response to ethylene stimulus [isa: 0009725 ]
+0009739 = response to gibberellic acid stimulus [isa: 0009725 ]
+0009753 = response to jasmonic acid stimulus [isa: 0009719 ]
+0009867 = jasmonic acid mediated signaling pathway [isa: 0007242 0009753 ]
+0009864 = jasmonic acid mediated signaling pathway (induced systemic resistance) [isa: 0009867 ] [partof: 0009682 ]
+0009868 = jasmonic acid mediated signaling pathway (jasmonic acid/ethylene dependent systemic resistance) [isa: 0009867 ] [partof: 0009861 ]
+0009754 = perception of jasmonic acid stimulus [partof: 0009753 ]
+0009751 = response to salicylic acid stimulus [isa: 0009719 ]
+0009752 = perception of salicylic acid stimulus [partof: 0009751 ]
+0009863 = salicylic acid mediated signaling pathway [isa: 0007242 0009751 ]
+0009862 = salicylic acid mediated signaling pathway (systemic acquired resistance) [isa: 0009863 ] [partof: 0009627 ]
+0009605 = response to external stimulus [isa: 0007154 ]
+0042262 = DNA protection [isa: 0006259 0006950 0009605 ]
+0001560 = interpretation of external signals that regulate cell growth [isa: 0007165 ] [partof: 0001558 0009605 ]
+0042465 = kinesis [isa: 0009605 ]
+0042466 = chemokinesis [isa: 0042465 ]
+0042468 = klinokinesis [isa: 0042465 ]
+0042467 = orthokinesis [isa: 0042465 ]
+0009581 = perception of external stimulus [partof: 0009605 ]
+0009582 = perception of abiotic stimulus [isa: 0009581 ] [partof: 0009628 ]
+0009593 = perception of chemical substance [isa: 0009582 ]
+0007606 = chemosensory perception [isa: 0007600 0009593 ]
+0005513 = calcium ion sensing [isa: 0007606 ]
+0007608 = olfaction [isa: 0007606 ]
+0019236 = pheromone response [isa: 0007606 ]
+0045311 = filamentous growth in response to pheromones [isa: 0019236 0030447 ]
+0007323 = pheromone processing [isa: 0016485 ] [partof: 0019236 ]
+0007327 = pheromone catabolism [isa: 0007323 ]
+0046614 = pheromone catabolism (sensu Saccharomyces) [isa: 0007327 0030163 0046613 ] [partof: 0007331 ]
+0046613 = pheromone processing (sensu Saccharomyces) [isa: 0016485 ] [partof: 0007322 0007323 ]
+0007325 = a-factor export [isa: 0046613 ]
+0007324 = a-factor processing (proteolytic) [isa: 0046613 ]
+0046542 = alpha-factor export [isa: 0046613 ]
+0007326 = alpha-factor maturation [isa: 0046613 ]
+0030434 = pheromone response (sensu Fungi) [isa: 0019236 ] [partof: 0030461 ]
+0030453 = adaptation to mating signal (sensu Fungi) [isa: 0030434 ]
+0007331 = adaptation to mating signal (sensu Saccharomyces) [isa: 0007328 0030453 ]
+0046615 = re-entry into mitotic cell cycle after pheromone arrest (sensu Saccharomyces) [isa: 0000321 ] [partof: 0007331 ]
+0007328 = pheromone response (sensu Saccharomyces) [isa: 0030434 ] [partof: 0007322 ]
+0030571 = cell cycle arrest (sensu Saccharomyces) [isa: 0007050 0007328 ]
+0007330 = signal transduction of mating signal (sensu Saccharomyces) [isa: 0007166 0007328 0030454 ]
+0007244 = MAPKKK cascade (mating sensu Saccharomyces) [isa: 0030455 ] [partof: 0007330 ]
+0007247 = activation of MAPK (mating sensu Saccharomyces) [isa: 0030456 ] [partof: 0007244 ]
+0007246 = activation of MAPKK (mating sensu Saccharomyces) [isa: 0030457 ] [partof: 0007244 ]
+0007245 = activation of MAPKKK (mating sensu Saccharomyces) [isa: 0030458 ] [partof: 0007244 ]
+0000174 = inactivation of MAPK (mating sensu Saccharomyces) [isa: 0030459 ] [partof: 0007244 ]
+0007248 = nuclear translocation of MAPK (mating sensu Saccharomyces) [isa: 0030460 ] [partof: 0007244 ]
+0030454 = transduction of mating signal (sensu Fungi) [isa: 0030434 ]
+0009373 = regulation of transcription by pheromones [isa: 0006355 0019236 ]
+0045996 = negative regulation of transcription by pheromones [isa: 0009373 0045892 ]
+0046020 = negative regulation of transcription from Pol II promoter by pheromones [isa: 0000122 0045996 0046019 ]
+0009371 = positive regulation of transcription by pheromones [isa: 0009373 0045893 ]
+0007329 = positive regulation of transcription from Pol II promoter by pheromones [isa: 0009371 0045944 0046019 ]
+0009372 = quorum sensing [isa: 0009373 ]
+0046019 = regulation of transcription from Pol II promoter by pheromones [isa: 0006357 0009373 ]
+0007607 = taste [isa: 0007606 ]
+0001580 = bitter taste perception [isa: 0007607 ]
+0001583 = salty taste perception [isa: 0007607 ]
+0001581 = sour taste perception [isa: 0007607 ]
+0001582 = sweet taste perception [isa: 0007607 ]
+0046535 = umami taste perception [isa: 0007607 ]
+0009594 = perception of nutrients [isa: 0009593 ] [partof: 0007584 ]
+0009590 = perception of gravity [isa: 0009582 ] [partof: 0009629 ]
+0009583 = perception of light [isa: 0009582 ] [partof: 0009416 ]
+0016037 = absorption of light [partof: 0009583 ]
+0016039 = absorption of UV light [isa: 0016037 ]
+0016038 = absorption of visible light [isa: 0016037 ]
+0009589 = perception of UV [isa: 0009583 ] [partof: 0009411 ]
+0007604 = phototransduction, UV [isa: 0007602 ] [partof: 0009589 ]
+0009584 = perception of visible light [isa: 0009583 ]
+0007603 = phototransduction, visible light [isa: 0007602 ] [partof: 0009584 ]
+0007602 = phototransduction [partof: 0009583 ]
+0009585 = red, far-red light phototransduction [isa: 0007602 ]
+0009586 = rhodopsin mediated phototransduction [isa: 0007602 ] [partof: 0007601 ]
+0016062 = adaptation of rhodopsin mediated signaling [partof: 0009586 ]
+0016059 = deactivation of rhodopsin mediated signaling [partof: 0009586 ]
+0016060 = metarhodopsin inactivation [partof: 0016059 ]
+0016061 = regulation of light-activated channel activity [isa: 0019722 ] [partof: 0016059 ]
+0045831 = negative regulation of light-activated channel activity [isa: 0016061 ]
+0045832 = positive regulation of light-activated channel activity [isa: 0016061 ]
+0008377 = light-induced release of calcium, from internal store [partof: 0009586 ]
+0016056 = rhodopsin mediated signaling [partof: 0009586 ]
+0016057 = changes in polarization state of photoreceptor cell membrane [partof: 0016056 ]
+0016058 = maintenance of rhodopsin mediated signaling [partof: 0016056 ]
+0030265 = rhodopsin mediated G-protein signaling, coupled to IP3 second messenger [isa: 0007200 ] [partof: 0016056 ]
+0009588 = UV-A, blue light phototransduction [isa: 0007602 ]
+0007601 = vision [isa: 0007600 0009583 ]
+0045494 = photoreceptor maintenance [partof: 0007601 ]
+0009591 = perception of mechanical stimulus [isa: 0009582 ] [partof: 0009612 ]
+0007609 = mechanosensory perception [isa: 0007600 0009591 ]
+0009592 = perception of sound [isa: 0009582 ]
+0007605 = hearing [isa: 0007600 0009592 ]
+0016048 = perception of temperature [isa: 0009582 ] [partof: 0009266 ]
+0009595 = perception of biotic stimulus [isa: 0009581 ] [partof: 0009607 ]
+0009596 = perception of pest/pathogen/parasite [isa: 0009595 ] [partof: 0009613 ]
+0016045 = perception of bacteria [isa: 0009596 ] [partof: 0009617 ]
+0009681 = perception of non-pathogenic bacteria [isa: 0016045 ]
+0009598 = perception of pathogenic bacteria [isa: 0016045 ] [partof: 0009618 ]
+0042494 = perception of bacterial lipoprotein [partof: 0009598 ]
+0042496 = perception of diacylated bacterial lipoprotein [isa: 0042494 ]
+0042495 = perception of triacylated bacterial lipoprotein [isa: 0042494 ]
+0009604 = perception of symbiotic bacteria [isa: 0009602 0016045 ] [partof: 0009609 ]
+0016046 = perception of fungi [isa: 0009596 ] [partof: 0009620 ]
+0016047 = perception of parasitic fungi [isa: 0016046 ] [partof: 0009623 ]
+0009599 = perception of pathogenic fungi [isa: 0016046 ] [partof: 0009621 ]
+0009603 = perception of symbiotic fungi [isa: 0016046 ] [partof: 0009610 ]
+0009601 = perception of insects [isa: 0009596 ] [partof: 0009625 ]
+0009600 = perception of nematodes [isa: 0009596 ] [partof: 0009624 ]
+0001563 = perception of protozoa [isa: 0009596 ]
+0009602 = perception of symbiont [isa: 0009596 ] [partof: 0009608 ]
+0009597 = perception of viruses [isa: 0009596 ] [partof: 0009615 ]
+0007600 = sensory perception [isa: 0009581 ]
+0019233 = perception of pain [isa: 0007600 ]
+0019234 = perception of fast pain [isa: 0019233 ]
+0019235 = perception of slow pain [isa: 0019233 ]
+0019230 = proprioception [isa: 0007600 ]
+0019232 = perception of rate of movement [isa: 0019230 ]
+0019231 = perception of static position [isa: 0019230 ]
+0009628 = response to abiotic stimulus [isa: 0009605 ]
+0042221 = response to chemical substance [isa: 0009628 ]
+0045146 = acetate induction of acetate catabolism [isa: 0042221 0045734 ]
+0045147 = regulation of acetate induction of acetate catabolism [partof: 0045146 ]
+0045755 = negative regulation of acetate induction of acetate catabolism [isa: 0045147 ]
+0045756 = positive regulation of acetate induction of acetate catabolism [isa: 0045147 ]
+0042493 = response to drug [isa: 0042221 ]
+0016351 = drug susceptibility/resistance [isa: 0042493 ]
+0017141 = antibiotic susceptibility/resistance [isa: 0016351 ]
+0016999 = antibiotic metabolism [isa: 0017144 ] [partof: 0017141 ]
+0030647 = aminoglycoside antibiotic metabolism [isa: 0016999 ]
+0030648 = aminoglycoside antibiotic biosynthesis [isa: 0017000 0030647 ]
+0019872 = streptomycin biosynthesis [isa: 0030648 0046343 ]
+0030649 = aminoglycoside antibiotic catabolism [isa: 0017001 0030647 ]
+0046343 = streptomycin metabolism [isa: 0030647 ]
+0017000 = antibiotic biosynthesis [isa: 0009058 0016999 ]
+0030654 = beta-lactam antibiotic biosynthesis [isa: 0017000 0030653 ]
+0042318 = penicillin biosynthesis [isa: 0030654 0042316 ]
+0046585 = enniatin biosynthesis [isa: 0017000 0018130 0046584 ]
+0030651 = peptide antibiotic biosynthesis [isa: 0017000 0030650 ]
+0017001 = antibiotic catabolism [isa: 0009056 0016999 ]
+0030655 = beta-lactam antibiotic catabolism [isa: 0017001 0030653 ]
+0042317 = penicillin catabolism [isa: 0030655 0042316 ]
+0030652 = peptide antibiotic catabolism [isa: 0017001 0030650 ]
+0030653 = beta-lactam antibiotic metabolism [isa: 0016999 ]
+0042316 = penicillin metabolism [isa: 0030653 ]
+0046584 = enniatin metabolism [isa: 0016999 0046483 ]
+0030650 = peptide antibiotic metabolism [isa: 0016999 ]
+0019880 = bacteriocin susceptibility/resistance [isa: 0017141 ]
+0019881 = streptomycin susceptibility/resistance [isa: 0017141 ]
+0017144 = drug metabolism [isa: 0008152 ] [partof: 0016351 ]
+0015893 = drug transport [isa: 0006810 0016351 ]
+0015894 = acriflavin transport [isa: 0015893 ]
+0015895 = alkane transport [isa: 0015893 ]
+0015898 = amiloride transport [isa: 0015893 ]
+0045117 = azole transport [isa: 0015893 ]
+0015899 = aminotriazole transport [isa: 0045117 ]
+0015903 = fluconazole transport [isa: 0045117 ]
+0015906 = sulfathiazole transport [isa: 0045117 ]
+0015900 = benomyl transport [isa: 0015893 ]
+0015905 = bicyclomycin transport [isa: 0015893 ]
+0015902 = carbonyl cyanide m-chlorophenylhydrazone transport [isa: 0015893 ]
+0015901 = cycloheximide transport [isa: 0015893 ]
+0046618 = drug export [isa: 0015893 ]
+0006855 = multidrug transport [isa: 0015893 ]
+0015896 = nalidixic acid transport [isa: 0015893 ]
+0015897 = organomercurial transport [isa: 0015893 ]
+0015904 = tetracycline transport [isa: 0015893 ]
+0042220 = response to cocaine [isa: 0042493 ]
+0045471 = response to ethanol [isa: 0042221 ]
+0045472 = response to ether [isa: 0042221 ]
+0009636 = response to toxin [isa: 0042221 ]
+0009412 = response to heavy metal [isa: 0006950 0009636 ]
+0042142 = heavy metal chelation [isa: 0009412 ]
+0009634 = heavy metal sensitivity/resistance [isa: 0009412 ]
+0017139 = arsenate sensitivity/resistance [isa: 0009634 ]
+0019830 = cadmium sensitivity/resistance [isa: 0009634 ]
+0019831 = chromate sensitivity/resistance [isa: 0009634 ]
+0045139 = copper sensitivity/resistance [isa: 0009634 ]
+0019832 = mercuric sensitivity/resistance [isa: 0009634 ]
+0019873 = tellurium sensitivity/resistance [isa: 0009634 ]
+0009635 = response to herbicide [isa: 0006950 0009636 ]
+0019837 = herbicide susceptibility/resistance [isa: 0006805 0009635 ]
+0017085 = response to insecticide [isa: 0009636 ]
+0016352 = insecticide susceptibility/resistance [isa: 0006805 0017085 ]
+0016353 = carbamate susceptibility/resistance [isa: 0016352 ]
+0016354 = cyclodiene susceptibility/resistance [isa: 0016352 ]
+0016355 = DDT susceptibility/resistance [isa: 0016352 ]
+0017143 = insecticide metabolism [partof: 0016355 ]
+0018977 = 1,1,1-trichloro-2,2-bis-(4'-chlorophenyl)ethane metabolism [isa: 0017143 0042196 ]
+0042188 = 1,1,1-trichloro-2,2-bis-(4'-chlorophenyl)ethane catabolism [isa: 0018977 0042205 ]
+0018978 = anaerobic 1,1,1-trichloro-2,2-bis-(4'-chlorophenyl)ethane metabolism [isa: 0018977 ]
+0016356 = organophosphorous susceptibility/resistance [isa: 0016352 ]
+0016357 = pyrethroid susceptibility/resistance [isa: 0016352 ]
+0017142 = toxin susceptibility/resistance [isa: 0009636 ]
+0009404 = toxin metabolism [isa: 0008152 ] [partof: 0017142 ]
+0046222 = aflatoxin metabolism [isa: 0009404 ]
+0045122 = aflatoxin biosynthesis [isa: 0009403 0046222 ]
+0046223 = aflatoxin catabolism [isa: 0009407 0046222 ]
+0046224 = bacteriocin metabolism [isa: 0009404 ]
+0030152 = bacteriocin biosynthesis [isa: 0009403 0046224 ]
+0046225 = bacteriocin catabolism [isa: 0009407 0046224 ]
+0045460 = sterigmatocystin metabolism [isa: 0009404 0019748 ]
+0045461 = sterigmatocystin biosynthesis [isa: 0009403 0045460 ]
+0045574 = sterigmatocystin catabolism [isa: 0009407 0045460 ]
+0009403 = toxin biosynthesis [isa: 0009058 0009404 ]
+0009407 = toxin catabolism [isa: 0009056 0009404 ]
+0009402 = toxin resistance [isa: 0009404 ]
+0030153 = bacteriocin immunity [isa: 0009402 ]
+0009410 = response to xenobiotic stimulus [isa: 0042221 ]
+0006805 = xenobiotic metabolism [isa: 0008152 ] [partof: 0009410 ]
+0018980 = 2,4,5-trichlorophenoxyacetic acid metabolism [isa: 0006725 0006805 ]
+0046228 = 2,4,5-trichlorophenoxyacetic acid catabolism [isa: 0018980 0019439 0042178 ]
+0018898 = 2,4-dichlorobenzoate metabolism [isa: 0006805 ]
+0046298 = 2,4-dichlorobenzoate catabolism [isa: 0018898 0042178 ]
+0018901 = 2,4-dichlorophenoxyacetic acid metabolism [isa: 0006805 ]
+0046300 = 2,4-dichlorophenoxyacetic acid catabolism [isa: 0018901 0042178 ]
+0018868 = 2-aminobenzenesulfonate metabolism [isa: 0006725 0006790 0006805 ]
+0046230 = 2-aminobenzenesulfonate catabolism [isa: 0018868 0019439 0042178 ]
+0019490 = 2-aminobenzenesulfonate desulfonation [isa: 0018868 ]
+0018889 = 2-chloro-N-isopropylacetanilide metabolism [isa: 0006805 ]
+0046302 = 2-chloro-N-isopropylacetanilide catabolism [isa: 0018889 0042178 ]
+0018938 = 2-nitropropane metabolism [isa: 0006805 0006807 ]
+0046304 = 2-nitropropane catabolism [isa: 0018938 0042178 ]
+0018888 = 3-chloroacrylic acid metabolism [isa: 0006805 ]
+0019609 = 3-hydroxyphenylacetate metabolism [isa: 0006725 0006805 ]
+0019610 = 3-hydroxyphenylacetate catabolism [isa: 0019439 0019609 0042178 ]
+0018930 = 3-methylquinoline metabolism [isa: 0006805 ]
+0019335 = 3-methylquinoline catabolism [isa: 0018930 0042178 ]
+0018962 = 3-phenylpropionate metabolism [isa: 0006805 ]
+0046435 = 3-(3-hydroxy)phenylpropionate metabolism [isa: 0018962 ]
+0019622 = 3-(3-hydroxy)phenylpropionate catabolism [isa: 0019380 0046435 ]
+0019380 = 3-phenylpropionate catabolism [isa: 0018962 0042178 ]
+0018960 = 4-nitrophenol metabolism [isa: 0006805 0018958 ]
+0046196 = 4-nitrophenol catabolism [isa: 0018960 0019336 0042178 ]
+0019638 = 6-hydroxycineole metabolism [isa: 0006066 0006805 ]
+0019639 = 6-hydroxycineole catabolism [isa: 0019638 0042178 0046164 ]
+0018864 = acetylene metabolism [isa: 0006805 ]
+0019487 = anaerobic acetylene catabolism [isa: 0018864 0042178 ]
+0018865 = acrylonitrile metabolism [isa: 0006805 ]
+0019256 = acrylonitrile catabolism [isa: 0018865 0042178 ]
+0018866 = adamantanone metabolism [isa: 0006805 ]
+0019263 = adamantanone catabolism [isa: 0018866 0042178 ]
+0018872 = arsonoacetate metabolism [isa: 0006805 ]
+0019501 = arsonoacetate catabolism [isa: 0018872 0042178 ]
+0042537 = benzene and derivative metabolism [isa: 0006805 ]
+0018911 = 1,2,4-trichlorobenzene metabolism [isa: 0042196 0042537 ]
+0018912 = 1,4-dichlorobenzene metabolism [isa: 0042196 0042537 ]
+0019261 = 1,4-dichlorobenzene catabolism [isa: 0018912 0042205 ]
+0018887 = 4-carboxy-4'-sulfoazobenzene metabolism [isa: 0042537 ]
+0018910 = benzene metabolism [isa: 0042537 ]
+0018914 = chlorobenzene metabolism [isa: 0042196 0042537 ]
+0018915 = ethylbenzene metabolism [isa: 0042537 ]
+0018913 = anaerobic ethylbenzene metabolism [isa: 0018915 ]
+0018916 = nitrobenzene metabolism [isa: 0042537 ]
+0019505 = resorcinol metabolism [isa: 0042537 ]
+0018874 = benzoate metabolism [isa: 0006805 ]
+0018869 = 2-aminobenzoate metabolism [isa: 0018874 ]
+0019259 = 2-aminobenzoate catabolism [isa: 0018869 0042178 ]
+0018870 = anaerobic 2-aminobenzoate metabolism [isa: 0018869 ]
+0019620 = aerobic benzoate metabolism [isa: 0018874 ]
+0018875 = anaerobic benzoate metabolism [isa: 0018874 ]
+0018876 = benzonitrile metabolism [isa: 0006805 ]
+0018879 = biphenyl metabolism [isa: 0006805 ]
+0018880 = 4-chlorobiphenyl metabolism [isa: 0018879 0042196 ]
+0018881 = bromoxynil metabolism [isa: 0006805 ]
+0018883 = caprolactam metabolism [isa: 0006805 ]
+0019384 = caprolactam catabolism [isa: 0018883 0042178 ]
+0018884 = carbazole metabolism [isa: 0006725 0006805 ]
+0046232 = carbazole catabolism [isa: 0018884 0019439 0042178 ]
+0042212 = cresol metabolism [isa: 0006066 0006725 0006805 ]
+0046199 = cresol catabolism [isa: 0019439 0042178 0042212 0046164 ]
+0042213 = m-cresol catabolism [isa: 0018925 0046199 ]
+0018921 = 3-hydroxybenzyl alcohol metabolism [partof: 0042213 ]
+0018925 = m-cresol metabolism [isa: 0042212 ]
+0018890 = cyanamide metabolism [isa: 0006805 ]
+0018891 = cyclohexanol metabolism [isa: 0006805 ]
+0019399 = cyclohexanol oxidation [isa: 0018891 ]
+0018892 = cyclohexylsulfamate metabolism [isa: 0006805 ]
+0018894 = dibenzo-p-dioxin metabolism [isa: 0006805 ]
+0019341 = dibenzo-p-dioxin catabolism [isa: 0018894 0042178 ]
+0018893 = dibenzofuran metabolism [isa: 0006805 ]
+0019340 = dibenzofuran catabolism [isa: 0018893 0042178 ]
+0018895 = dibenzothiophene metabolism [isa: 0006805 ]
+0018896 = dibenzothiophene catabolism [isa: 0018895 0042178 ]
+0018897 = dibenzothiophene desulfurization [isa: 0018895 ]
+0018909 = dodecyl sulfate metabolism [isa: 0006805 ]
+0018917 = fluorene metabolism [isa: 0006725 0006805 ]
+0019429 = fluorene catabolism [isa: 0018917 0019439 0042178 ]
+0042197 = halogenated hydrocarbon metabolism [isa: 0006805 ]
+0018976 = 1,2,3-tribromopropane metabolism [isa: 0042197 ]
+0042196 = chlorinated hydrocarbon metabolism [isa: 0042197 ]
+0018899 = 1,2-dichloroethane metabolism [isa: 0042196 ]
+0019260 = 1,2-dichloroethane catabolism [isa: 0018899 0042205 ]
+0018903 = 1,3-dichloropropene metabolism [isa: 0042196 ]
+0018885 = carbon tetrachloride metabolism [isa: 0042196 ]
+0018886 = anaerobic carbon tetrachloride metabolism [isa: 0018885 ]
+0019382 = carbon tetrachloride catabolism [isa: 0018885 0042205 ]
+0042205 = chlorinated hydrocarbon catabolism [isa: 0042196 0042206 ]
+0019337 = tetrachloroethene catabolism [isa: 0018967 0042205 ]
+0018900 = dichloromethane metabolism [isa: 0042196 ]
+0019497 = hexachlorocyclohexane metabolism [isa: 0042196 ]
+0018877 = beta-1,2,3,4,5,6-hexachlorocyclohexane metabolism [isa: 0019497 ]
+0018878 = aerobic beta-1,2,3,4,5,6-hexachlorocyclohexane metabolism [isa: 0018877 ]
+0018919 = gamma-1,2,3,4,5,6-hexachlorocyclohexane metabolism [isa: 0019497 ]
+0018967 = tetrachloroethene metabolism [isa: 0042196 ]
+0018979 = trichloroethylene metabolism [isa: 0042196 ]
+0042206 = halogenated hydrocarbon catabolism [isa: 0042178 0042197 ]
+0018929 = methyl fluoride metabolism [isa: 0042197 ]
+0018922 = iprodione metabolism [isa: 0006805 ]
+0018926 = methanesulfonic acid metabolism [isa: 0006805 ]
+0018928 = methyl ethyl ketone metabolism [isa: 0006805 0042180 ]
+0046213 = methyl ethyl ketone catabolism [isa: 0018928 0042178 0042182 ]
+0018939 = n-octane metabolism [isa: 0006805 ]
+0019498 = n-octane oxidation [isa: 0018939 ]
+0018931 = naphthalene metabolism [isa: 0006805 ]
+0018984 = naphthalenesulfonate metabolism [isa: 0018931 ]
+0018934 = nitrilotriacetate metabolism [isa: 0006805 ]
+0018935 = aerobic nitrilotriacetate metabolism [isa: 0018934 ]
+0018936 = anaerobic nitrilotriacetate metabolism [isa: 0018934 ]
+0018937 = nitroglycerin metabolism [isa: 0006805 ]
+0042198 = nylon metabolism [isa: 0006805 ]
+0019876 = nylon catabolism [isa: 0042178 0042198 ]
+0018904 = organic ether metabolism [isa: 0006805 ]
+0018905 = dimethyl ether metabolism [isa: 0018904 ]
+0018906 = methyl tert-butyl ether metabolism [isa: 0018904 ]
+0018968 = tetrahydrofuran metabolism [isa: 0018904 ]
+0019637 = organophosphate metabolism [isa: 0006805 ]
+0018920 = glyphosate metabolism [isa: 0019637 ]
+0046434 = organophosphate catabolism [isa: 0019637 0042178 ]
+0019339 = parathion catabolism [isa: 0018952 0046434 ]
+0019700 = phosphonate catabolism [isa: 0019634 0046434 ]
+0019635 = 2-aminoethylphosphonate catabolism [isa: 0019700 0046433 ]
+0018952 = parathion metabolism [isa: 0019637 ]
+0019634 = phosphonate metabolism [isa: 0019637 ]
+0046433 = 2-aminoethylphosphonate metabolism [isa: 0019634 ]
+0019636 = phosphonoacetate metabolism [isa: 0019634 ]
+0018945 = organosilicone metabolism [isa: 0006805 ]
+0018946 = aerobic organosilicone metabolism [isa: 0018945 ]
+0042211 = dimethylsilanediol catabolism [isa: 0018946 0046454 0046455 ]
+0018947 = anaerobic organosilicone metabolism [isa: 0018945 ]
+0042210 = octamethylcyclotetrasiloxane catabolism to dimethylsilanediol [isa: 0018947 0046517 ]
+0046454 = dimethylsilanediol metabolism [isa: 0018945 ]
+0046518 = octamethylcyclotetrasiloxane metabolism [isa: 0018945 ]
+0046517 = octamethylcyclotetrasiloxane catabolism [isa: 0046455 0046518 ]
+0046455 = organosilicone catabolism [isa: 0018945 0042178 ]
+0018953 = p-cymene metabolism [isa: 0006805 ]
+0019334 = p-cymene catabolism [isa: 0018953 0042178 ]
+0018961 = pentachlorophenol metabolism [isa: 0006805 0018958 ]
+0019338 = pentachlorophenol catabolism [isa: 0018961 0019336 0042178 ]
+0018954 = pentaerythritol tetranitrate metabolism [isa: 0006805 ]
+0018955 = phenanthrene metabolism [isa: 0006725 0006805 ]
+0042216 = phenanthrene catabolism [isa: 0018955 0019439 0042178 ]
+0018956 = phenanthrene catabolism, via trans-9(R),10(R)-dihydrodiolphenanthrene [isa: 0042216 ]
+0018957 = phenanthrene catabolism, via trans-9(S),10(S)-dihydrodiolphenanthrene [isa: 0042216 ]
+0046412 = phenylmercury acetate metabolism [isa: 0006805 0018941 ]
+0019506 = phenylmercury acetate catabolism [isa: 0042178 0046412 0046413 ]
+0018963 = phthalate metabolism [isa: 0006725 0006805 ]
+0046239 = phthalate catabolism [isa: 0018963 0019439 0042178 ]
+0018964 = propylene metabolism [isa: 0006805 ]
+0042208 = propylene catabolism [isa: 0018964 0042178 ]
+0018965 = s-triazine compound metabolism [isa: 0006805 ]
+0018873 = atrazine metabolism [isa: 0018965 ]
+0019381 = atrazine catabolism [isa: 0018873 0042204 ]
+0019625 = atrazine catabolism to cyanuric acid [isa: 0019381 ]
+0019624 = atrazine catabolism to isopropylamine [isa: 0019381 ]
+0019623 = atrazine catabolism to urea [isa: 0019381 ]
+0042199 = cyanuric acid metabolism [isa: 0018965 ]
+0042200 = cyanuric acid catabolism [isa: 0042199 0042204 ]
+0042201 = N-cyclopropylmelamine metabolism [isa: 0018965 ]
+0042202 = N-cyclopropylmelamine catabolism [isa: 0042201 0042204 ]
+0042204 = s-triazine compound catabolism [isa: 0018965 0042178 ]
+0018966 = styrene metabolism [isa: 0006725 0006805 ]
+0042207 = styrene catabolism [isa: 0018966 0019439 0042178 ]
+0018969 = thiocyanate metabolism [isa: 0006805 ]
+0046265 = thiocyanate catabolism [isa: 0018969 0042178 ]
+0018970 = toluene metabolism [isa: 0006725 0006805 ]
+0019611 = 4-toluenecarboxylate metabolism [isa: 0018970 ]
+0019612 = 4-toluenecarboxylate catabolism [isa: 0019611 0042203 ]
+0018971 = anaerobic toluene metabolism [isa: 0018970 ]
+0018975 = anaerobic 2,4,6-trinitrotoluene metabolism [isa: 0018971 0018974 ]
+0046258 = anaerobic 2,4,6-trinitrotoluene catabolism [isa: 0018975 0046254 0046256 ]
+0046254 = anaerobic toluene catabolism [isa: 0018971 0042203 ]
+0019326 = nitrotoluene metabolism [isa: 0018970 ]
+0019257 = 4-nitrotoluene metabolism [isa: 0019326 ]
+0019258 = 4-nitrotoluene catabolism [isa: 0019257 0046263 ]
+0046263 = nitrotoluene catabolism [isa: 0019326 0042203 ]
+0046260 = trinitrotoluene catabolism [isa: 0018973 0046263 ]
+0046256 = 2,4,6-trinitrotoluene catabolism [isa: 0018974 0046260 ]
+0018973 = trinitrotoluene metabolism [isa: 0019326 ]
+0018974 = 2,4,6-trinitrotoluene metabolism [isa: 0018973 ]
+0042203 = toluene catabolism [isa: 0018970 0019439 0042178 ]
+0046269 = toluene-4-sulfonate catabolism [isa: 0018972 0042203 ]
+0019600 = toluene oxidation [isa: 0018970 ]
+0019604 = toluene oxidation to catechol [isa: 0019600 ]
+0019601 = toluene oxidation, via 2-hydroxytoluene [isa: 0019600 ]
+0019602 = toluene oxidation, via 3-hydroxytoluene [isa: 0019600 ]
+0019603 = toluene oxidation, via 4-hydroxytoluene [isa: 0019600 ]
+0019696 = toluene oxidation, via toluene-cis-1,2-dihydrodiol [isa: 0019600 ]
+0018972 = toluene-4-sulfonate metabolism [isa: 0018970 ]
+0018981 = triethanolamine metabolism [isa: 0006805 0042439 ]
+0046267 = triethanolamine catabolism [isa: 0018981 0042178 0042402 ]
+0042178 = xenobiotic catabolism [isa: 0006805 0009056 ]
+0042217 = 1-aminocyclopropane-1-carboxylate catabolism [isa: 0018871 0019439 0042178 0042219 ] [partof: 0006567 0009087 ]
+0042184 = xylene catabolism [isa: 0018948 0019439 0042178 ]
+0042185 = m-xylene catabolism [isa: 0018949 0042184 ]
+0042186 = o-xylene catabolism [isa: 0018950 0042184 ]
+0042187 = p-xylene catabolism [isa: 0018951 0042184 ]
+0018948 = xylene metabolism [isa: 0006725 0006805 ]
+0018949 = m-xylene metabolism [isa: 0018948 ]
+0018950 = o-xylene metabolism [isa: 0018948 ]
+0018951 = p-xylene metabolism [isa: 0018948 ]
+0009629 = response to gravity [isa: 0009628 ]
+0009630 = gravitropism [isa: 0009606 0009629 ]
+0006970 = response to osmotic stress [isa: 0006950 0009628 ]
+0006972 = hyperosmotic response [isa: 0006970 ]
+0042538 = hyperosmotic salinity response [isa: 0006972 0009651 ]
+0006973 = intracellular accumulation of glycerol [partof: 0006972 ]
+0006971 = hypotonic response [isa: 0006970 ]
+0042539 = hypotonic salinity response [isa: 0006971 0009651 ]
+0009651 = salinity response [isa: 0006970 ]
+0009268 = response to pH [isa: 0009628 ] [partof: 0006885 ]
+0009314 = response to radiation [isa: 0009628 ]
+0009416 = response to light [isa: 0009314 ]
+0009637 = response to blue light [isa: 0009416 ]
+0009638 = phototropism [isa: 0009606 0009637 ]
+0009642 = response to light intensity [isa: 0009416 ]
+0009643 = photosynthetic acclimation [isa: 0009642 ]
+0009646 = response to absence of light [isa: 0009642 ]
+0009647 = skotomorphogenesis [isa: 0009646 0009886 ]
+0009644 = response to high light intensity [isa: 0009642 ]
+0009645 = response to low light intensity [isa: 0009642 ]
+0009648 = response to photoperiod [isa: 0009416 ]
+0009906 = response to photoperiod, blue light [isa: 0009648 ]
+0009907 = response to photoperiod, red light [isa: 0009648 ]
+0009639 = response to red/far-red light [isa: 0009416 ]
+0009640 = photomorphogenesis [isa: 0009639 0009886 ]
+0009704 = de-etiolation [partof: 0009640 ]
+0009641 = shade avoidance [isa: 0009639 ]
+0009411 = response to UV [isa: 0009314 ]
+0009650 = UV protection [isa: 0009314 ]
+0009266 = response to temperature [isa: 0009628 ]
+0009409 = response to cold [isa: 0006950 0009266 ]
+0009631 = cold acclimation [isa: 0009409 ]
+0009408 = response to heat [isa: 0006950 0009266 ]
+0009415 = response to water [isa: 0009628 ]
+0009414 = response to drought [isa: 0006950 0009415 ]
+0009819 = drought recovery [isa: 0009414 ]
+0009269 = response to dessication [isa: 0009414 ]
+0009413 = response to flooding [isa: 0006950 0009415 ]
+0009270 = response to humidity [isa: 0009415 ]
+0009607 = response to biotic stimulus [isa: 0009605 ]
+0030236 = anti-inflammatory response [isa: 0009607 ]
+0006952 = defense response [isa: 0009607 ]
+0009626 = hypersensitive response [isa: 0006952 0009816 0009817 0012501 ]
+0006955 = immune response [isa: 0006952 ]
+0006953 = acute-phase response [isa: 0006955 0009613 ]
+0030105 = anaphylaxis [isa: 0006955 0009613 ]
+0019882 = antigen presentation [isa: 0006955 ]
+0019883 = antigen presentation, endogenous antigen [isa: 0019882 ]
+0048006 = antigen presentation, endogenous lipid antigen [isa: 0019883 0048003 ]
+0048004 = antigen presentation, endogenous peptide antigen [isa: 0019883 0048002 ]
+0019884 = antigen presentation, exogenous antigen [isa: 0019882 ]
+0048007 = antigen presentation, exogenous lipid antigen [isa: 0019884 0048003 ]
+0048005 = antigen presentation, exogenous peptide antigen [isa: 0019884 0048002 ]
+0048003 = antigen presentation, lipid antigen [isa: 0019882 ]
+0048002 = antigen presentation, peptide antigen [isa: 0019882 ]
+0030333 = antigen processing [isa: 0006955 ]
+0019885 = antigen processing, endogenous antigen via MHC class I [isa: 0030333 ]
+0019886 = antigen processing, exogenous antigen via MHC class II [isa: 0030333 ]
+0045321 = cell activation [isa: 0006955 ]
+0045575 = basophil activation [isa: 0045321 ]
+0042118 = endothelial cell activation [isa: 0045321 ]
+0046649 = lymphocyte activation [isa: 0045321 ]
+0042113 = B-cell activation [isa: 0046649 ]
+0030183 = B-cell differentiation [isa: 0030098 0042113 0046650 ]
+0045577 = regulation of B-cell differentiation [isa: 0045619 ] [partof: 0030183 ]
+0045578 = negative regulation of B-cell differentiation [isa: 0045577 0045620 ]
+0045579 = positive regulation of B-cell differentiation [isa: 0045577 0045621 ]
+0042100 = B-cell proliferation [isa: 0008283 0042113 0046651 ]
+0045190 = isotype switching [isa: 0042113 ]
+0045191 = regulation of isotype switching [partof: 0045190 ]
+0045829 = negative regulation of isotype switching [isa: 0045191 ]
+0045830 = positive regulation of isotype switching [isa: 0045191 ]
+0046650 = lymphocyte differentiation [isa: 0046649 ]
+0030217 = T-cell differentiation [isa: 0030098 0042110 0046650 ]
+0046632 = alpha-beta T-cell differentiation [isa: 0030217 0046631 ]
+0046637 = regulation of alpha-beta T-cell differentiation [isa: 0045580 0046634 ] [partof: 0046632 ]
+0046639 = negative regulation of alpha-beta T-cell differentiation [isa: 0045581 0046636 0046637 ]
+0046638 = positive regulation of alpha-beta T-cell differentiation [isa: 0045582 0046635 0046637 ]
+0045065 = cytotoxic T-cell differentiation [isa: 0030217 ]
+0045583 = regulation of cytotoxic T-cell differentiation [isa: 0045580 ] [partof: 0045065 ]
+0045584 = negative regulation of cytotoxic T-cell differentiation [isa: 0045581 0045583 ]
+0045585 = positive regulation of cytotoxic T-cell differentiation [isa: 0045582 0045583 ]
+0042492 = gamma-delta T-cell differentiation [isa: 0030217 0046629 ]
+0045586 = regulation of gamma-delta T-cell differentiation [isa: 0045580 0046643 ] [partof: 0042492 ]
+0045587 = negative regulation of gamma-delta T-cell differentiation [isa: 0045581 0045586 0046644 ]
+0045588 = positive regulation of gamma-delta T-cell differentiation [isa: 0045582 0045586 0046645 ]
+0045580 = regulation of T-cell differentiation [isa: 0045619 ] [partof: 0030217 ]
+0045581 = negative regulation of T-cell differentiation [isa: 0045580 0045620 ]
+0045590 = negative regulation of suppressor T-cell differentiation [isa: 0045581 0045589 ]
+0045623 = negative regulation of T-helper cell differentiation [isa: 0045581 0045622 ]
+0045626 = negative regulation of T-helper 1 cell differentiation [isa: 0045623 0045625 ]
+0045629 = negative regulation of T-helper 2 cell differentiation [isa: 0045623 0045628 ]
+0045582 = positive regulation of T-cell differentiation [isa: 0045580 0045621 ]
+0045591 = positive regulation of suppressor T-cell differentiation [isa: 0045582 0045589 ]
+0045624 = positive regulation of T-helper cell differentiation [isa: 0045582 0045622 ]
+0045627 = positive regulation of T-helper 1 cell differentiation [isa: 0045624 0045625 ]
+0045630 = positive regulation of T-helper 2 cell differentiation [isa: 0045624 0045628 ]
+0045589 = regulation of suppressor T-cell differentiation [isa: 0045580 ] [partof: 0045066 ]
+0045622 = regulation of T-helper cell differentiation [isa: 0045580 ] [partof: 0042093 ]
+0045625 = regulation of T-helper 1 cell differentiation [isa: 0045622 ] [partof: 0045063 ]
+0045628 = regulation of T-helper 2 cell differentiation [isa: 0045622 ] [partof: 0045064 ]
+0045066 = suppressor T-cell differentiation [isa: 0030217 ]
+0042093 = T-helper cell differentiation [isa: 0030217 ]
+0045063 = T-helper 1 cell differentiation [isa: 0042093 ]
+0045064 = T-helper 2 cell differentiation [isa: 0042093 ]
+0046652 = thymocyte differentiation [isa: 0046650 ]
+0046651 = lymphocyte proliferation [isa: 0046649 ]
+0042098 = T-cell proliferation [isa: 0008283 0042110 0046651 ]
+0046633 = alpha-beta T-cell proliferation [isa: 0042098 0046631 ]
+0046640 = regulation of alpha-beta T-cell proliferation [isa: 0042129 0046634 ] [partof: 0046633 ]
+0046642 = negative regulation of alpha-beta T-cell proliferation [isa: 0042130 0046636 0046640 ]
+0046641 = positive regulation of alpha-beta T-cell proliferation [isa: 0042102 0046635 0046640 ]
+0046630 = gamma-delta T-cell proliferation [isa: 0042098 0046629 ]
+0046646 = regulation of gamma-delta T-cell proliferation [isa: 0042129 0046643 ] [partof: 0046630 ]
+0046647 = negative regulation of gamma-delta T-cell proliferation [isa: 0042130 0046644 0046646 ]
+0046648 = positive regulation of gamma-delta T-cell proliferation [isa: 0042102 0046645 0046646 ]
+0042129 = regulation of T-cell proliferation [partof: 0042098 ]
+0042130 = negative regulation of T-cell proliferation [isa: 0042129 ]
+0046007 = negative regulation of activated T-cell proliferation [isa: 0042130 0046006 ]
+0046014 = negative regulation of resting T-cell proliferation [isa: 0042130 0046013 ]
+0042102 = positive regulation of T-cell proliferation [isa: 0008284 0042129 ]
+0042104 = positive regulation of activated T-cell proliferation [isa: 0042102 0046006 ]
+0042103 = positive regulation of resting T-cell proliferation [isa: 0042102 0046013 ]
+0046006 = regulation of activated T-cell proliferation [isa: 0042129 ]
+0046013 = regulation of resting T-cell proliferation [isa: 0042129 ]
+0030101 = natural killer cell activation [isa: 0046649 ]
+0042110 = T-cell activation [isa: 0046649 ]
+0046631 = alpha-beta T-cell activation [isa: 0042110 ]
+0046634 = regulation of alpha-beta T-cell activation [partof: 0046631 ]
+0046636 = negative regulation of alpha-beta T-cell activation [isa: 0046634 ]
+0046635 = positive regulation of alpha-beta T-cell activation [isa: 0046634 ]
+0046629 = gamma-delta T-cell activation [isa: 0042110 ]
+0046643 = regulation of gamma-delta T-cell activation [partof: 0046629 ]
+0046644 = negative regulation of gamma-delta T-cell activation [isa: 0046643 ]
+0046645 = positive regulation of gamma-delta T-cell activation [isa: 0046643 ]
+0042116 = macrophage activation [isa: 0045321 ] [partof: 0006954 ]
+0045576 = mast cell activation [isa: 0045321 ]
+0042117 = monocyte activation [isa: 0045321 ]
+0042119 = neutrophil activation [isa: 0045321 ] [partof: 0006954 ]
+0006968 = cellular defense response [isa: 0006955 0009611 0009613 ]
+0016067 = cellular defense response (sensu Invertebrata) [isa: 0006968 ]
+0006969 = melanotic tumor response [isa: 0016067 ]
+0016066 = cellular defense response (sensu Vertebrata) [isa: 0006968 ]
+0042087 = cell-mediated immune response [isa: 0016066 ]
+0042088 = T-helper 1 type immune response [isa: 0042087 ]
+0042095 = interferon-gamma biosynthesis [isa: 0042088 0042089 ]
+0045072 = regulation of interferon-gamma biosynthesis [isa: 0042035 ] [partof: 0042095 ]
+0045077 = negative regulation of interferon-gamma biosynthesis [isa: 0042036 0045072 ]
+0045078 = positive regulation of interferon-gamma biosynthesis [isa: 0042108 0045072 ]
+0042091 = interleukin-10 biosynthesis [isa: 0042088 0042089 0042092 ]
+0045074 = regulation of interleukin-10 biosynthesis [isa: 0042035 ] [partof: 0042091 ]
+0045081 = negative regulation of interleukin-10 biosynthesis [isa: 0042036 0045074 ]
+0045082 = positive regulation of interleukin-10 biosynthesis [isa: 0042108 0045074 ]
+0042090 = interleukin-12 biosynthesis [isa: 0042088 0042089 ]
+0045075 = regulation of interleukin-12 biosynthesis [isa: 0042035 ] [partof: 0042090 ]
+0045083 = negative regulation of interleukin-12 biosynthesis [isa: 0042036 0045075 ]
+0045084 = positive regulation of interleukin-12 biosynthesis [isa: 0042108 0045075 ]
+0042094 = interleukin-2 biosynthesis [isa: 0042088 0042089 ]
+0045076 = regulation of interleukin-2 biosynthesis [isa: 0042035 ] [partof: 0042094 ]
+0045085 = negative regulation of interleukin-2 biosynthesis [isa: 0042036 0045076 ]
+0045086 = positive regulation of interleukin-2 biosynthesis [isa: 0042108 0045076 ]
+0016069 = delayed hypersensitivity response [isa: 0016066 ]
+0042107 = cytokine metabolism [isa: 0006955 0019538 ]
+0042089 = cytokine biosynthesis [isa: 0006412 0042107 ]
+0042033 = chemokine biosynthesis [isa: 0042089 ]
+0045073 = regulation of chemokine biosynthesis [isa: 0042035 ] [partof: 0042033 ]
+0045079 = negative regulation of chemokine biosynthesis [isa: 0042036 0045073 ]
+0045080 = positive regulation of chemokine biosynthesis [isa: 0042108 0045073 ]
+0045189 = connective tissue growth factor biosynthesis [isa: 0042089 ]
+0045420 = regulation of connective tissue growth factor biosynthesis [isa: 0009889 ] [partof: 0045189 ]
+0045421 = negative regulation of connective tissue growth factor biosynthesis [isa: 0009890 0045420 ]
+0045422 = positive regulation of connective tissue growth factor biosynthesis [isa: 0009891 0045420 ]
+0042253 = granulocyte macrophage colony-stimulating factor biosynthesis [isa: 0042089 ]
+0045423 = regulation of granulocyte macrophage colony-stimulating factor biosynthesis [isa: 0042035 ] [partof: 0042253 ]
+0045424 = negative regulation of granulocyte macrophage colony-stimulating factor biosynthesis [isa: 0042036 0045423 ]
+0045425 = positive regulation of granulocyte macrophage colony-stimulating factor biosynthesis [isa: 0042108 0045423 ]
+0045351 = interferon type I biosynthesis [isa: 0042089 ]
+0045349 = interferon-alpha biosynthesis [isa: 0045351 ]
+0045354 = regulation of interferon-alpha biosynthesis [isa: 0042035 ] [partof: 0045349 ]
+0045355 = negative regulation of interferon-alpha biosynthesis [isa: 0042036 0045354 ]
+0045356 = positive regulation of interferon-alpha biosynthesis [isa: 0042108 0045354 ]
+0045350 = interferon-beta biosynthesis [isa: 0045351 ]
+0045357 = regulation of interferon-beta biosynthesis [isa: 0042035 ] [partof: 0045350 ]
+0045358 = negative regulation of interferon-beta biosynthesis [isa: 0042036 0045357 ]
+0045359 = positive regulation of interferon-beta biosynthesis [isa: 0042108 0045357 ]
+0042222 = interleukin-1 biosynthesis [isa: 0042089 ]
+0045360 = regulation of interleukin-1 biosynthesis [isa: 0042035 ] [partof: 0042222 ]
+0045361 = negative regulation of interleukin-1 biosynthesis [isa: 0042036 0045360 ]
+0045362 = positive regulation of interleukin-1 biosynthesis [isa: 0042108 0045360 ]
+0042230 = interleukin-11 biosynthesis [isa: 0042089 ]
+0045363 = regulation of interleukin-11 biosynthesis [isa: 0042035 ] [partof: 0042230 ]
+0045364 = negative regulation of interleukin-11 biosynthesis [isa: 0042036 0045363 ]
+0045365 = positive regulation of interleukin-11 biosynthesis [isa: 0042108 0045363 ]
+0042231 = interleukin-13 biosynthesis [isa: 0042089 ]
+0045366 = regulation of interleukin-13 biosynthesis [isa: 0042035 ] [partof: 0042231 ]
+0045367 = negative regulation of interleukin-13 biosynthesis [isa: 0042036 0045366 ]
+0045368 = positive regulation of interleukin-13 biosynthesis [isa: 0042108 0045366 ]
+0042232 = interleukin-14 biosynthesis [isa: 0042089 ]
+0045369 = regulation of interleukin-14 biosynthesis [isa: 0042035 ] [partof: 0042232 ]
+0045370 = negative regulation of interleukin-14 biosynthesis [isa: 0042036 0045369 ]
+0045371 = positive regulation of interleukin-14 biosynthesis [isa: 0042108 0045369 ]
+0042233 = interleukin-15 biosynthesis [isa: 0042089 ]
+0045372 = regulation of interleukin-15 biosynthesis [isa: 0042035 ] [partof: 0042233 ]
+0045373 = negative regulation of interleukin-15 biosynthesis [isa: 0042036 0045372 ]
+0045374 = positive regulation of interleukin-15 biosynthesis [isa: 0042108 0045372 ]
+0042234 = interleukin-16 biosynthesis [isa: 0042089 ]
+0045375 = regulation of interleukin-16 biosynthesis [isa: 0042035 ] [partof: 0042234 ]
+0045376 = negative regulation of interleukin-16 biosynthesis [isa: 0042036 0045375 ]
+0045377 = positive regulation of interleukin-16 biosynthesis [isa: 0042108 0045375 ]
+0042235 = interleukin-17 biosynthesis [isa: 0042089 ]
+0045378 = regulation of interleukin-17 biosynthesis [isa: 0042035 ] [partof: 0042235 ]
+0045379 = negative regulation of interleukin-17 biosynthesis [isa: 0042036 0045378 ]
+0045380 = positive regulation of interleukin-17 biosynthesis [isa: 0042108 0045378 ]
+0042241 = interleukin-18 biosynthesis [isa: 0042089 ]
+0045381 = regulation of interleukin-18 biosynthesis [isa: 0042035 ] [partof: 0042241 ]
+0045382 = negative regulation of interleukin-18 biosynthesis [isa: 0042036 0045381 ]
+0045383 = positive regulation of interleukin-18 biosynthesis [isa: 0042108 0045381 ]
+0042236 = interleukin-19 biosynthesis [isa: 0042089 ]
+0045384 = regulation of interleukin-19 biosynthesis [isa: 0042035 ] [partof: 0042236 ]
+0045385 = negative regulation of interleukin-19 biosynthesis [isa: 0042036 0045384 ]
+0045386 = positive regulation of interleukin-19 biosynthesis [isa: 0042108 0045384 ]
+0042237 = interleukin-20 biosynthesis [isa: 0042089 ]
+0045387 = regulation of interleukin-20 biosynthesis [isa: 0042035 ] [partof: 0042237 ]
+0045388 = negative regulation of interleukin-20 biosynthesis [isa: 0042036 0045387 ]
+0045389 = positive regulation of interleukin-20 biosynthesis [isa: 0042108 0045387 ]
+0042238 = interleukin-21 biosynthesis [isa: 0042089 ]
+0045390 = regulation of interleukin-21 biosynthesis [isa: 0042035 ] [partof: 0042238 ]
+0045391 = negative regulation of interleukin-21 biosynthesis [isa: 0042036 0045390 ]
+0045392 = positive regulation of interleukin-21 biosynthesis [isa: 0042108 0045390 ]
+0042239 = interleukin-22 biosynthesis [isa: 0042089 ]
+0045393 = regulation of interleukin-22 biosynthesis [isa: 0042035 ] [partof: 0042239 ]
+0045394 = negative regulation of interleukin-22 biosynthesis [isa: 0042036 0045393 ]
+0045395 = positive regulation of interleukin-22 biosynthesis [isa: 0042108 0045393 ]
+0042240 = interleukin-23 biosynthesis [isa: 0042089 ]
+0045396 = regulation of interleukin-23 biosynthesis [isa: 0042035 ] [partof: 0042240 ]
+0045397 = negative regulation of interleukin-23 biosynthesis [isa: 0042036 0045396 ]
+0045398 = positive regulation of interleukin-23 biosynthesis [isa: 0042108 0045396 ]
+0045524 = interleukin-24 biosynthesis [isa: 0042089 ]
+0045528 = regulation of interleukin-24 biosynthesis [isa: 0042035 ] [partof: 0045524 ]
+0045532 = negative regulation of interleukin-24 biosynthesis [isa: 0042036 0045528 ]
+0045536 = positive regulation of interleukin-24 biosynthesis [isa: 0042108 0045528 ]
+0045525 = interleukin-25 biosynthesis [isa: 0042089 ]
+0045529 = regulation of interleukin-25 biosynthesis [isa: 0042035 ] [partof: 0045525 ]
+0045533 = negative regulation of interleukin-25 biosynthesis [isa: 0042036 0045529 ]
+0045537 = positive regulation of interleukin-25 biosynthesis [isa: 0042108 0045529 ]
+0045526 = interleukin-26 biosynthesis [isa: 0042089 ]
+0045530 = regulation of interleukin-26 biosynthesis [isa: 0042035 ] [partof: 0045526 ]
+0045534 = negative regulation of interleukin-26 biosynthesis [isa: 0042036 0045530 ]
+0045538 = positive regulation of interleukin-26 biosynthesis [isa: 0042108 0045530 ]
+0045527 = interleukin-27 biosynthesis [isa: 0042089 ]
+0045531 = regulation of interleukin-27 biosynthesis [isa: 0042035 ] [partof: 0045527 ]
+0045535 = negative regulation of interleukin-27 biosynthesis [isa: 0042036 0045531 ]
+0045539 = positive regulation of interleukin-27 biosynthesis [isa: 0042108 0045531 ]
+0042223 = interleukin-3 biosynthesis [isa: 0042089 ]
+0045399 = regulation of interleukin-3 biosynthesis [isa: 0042035 ] [partof: 0042223 ]
+0045400 = negative regulation of interleukin-3 biosynthesis [isa: 0042036 0045399 ]
+0045401 = positive regulation of interleukin-3 biosynthesis [isa: 0042108 0045399 ]
+0042097 = interleukin-4 biosynthesis [isa: 0042089 0042092 ]
+0045402 = regulation of interleukin-4 biosynthesis [isa: 0042035 ] [partof: 0042097 ]
+0045403 = negative regulation of interleukin-4 biosynthesis [isa: 0042036 0045402 ]
+0045404 = positive regulation of interleukin-4 biosynthesis [isa: 0042108 0045402 ]
+0042225 = interleukin-5 biosynthesis [isa: 0042089 ]
+0045405 = regulation of interleukin-5 biosynthesis [isa: 0042035 ] [partof: 0042225 ]
+0045406 = negative regulation of interleukin-5 biosynthesis [isa: 0042036 0045405 ]
+0045407 = positive regulation of interleukin-5 biosynthesis [isa: 0042108 0045405 ]
+0042226 = interleukin-6 biosynthesis [isa: 0042089 ]
+0045408 = regulation of interleukin-6 biosynthesis [isa: 0042035 ] [partof: 0042226 ]
+0045409 = negative regulation of interleukin-6 biosynthesis [isa: 0042036 0045408 ]
+0045410 = positive regulation of interleukin-6 biosynthesis [isa: 0042108 0045408 ]
+0042227 = interleukin-7 biosynthesis [isa: 0042089 ]
+0045411 = regulation of interleukin-7 biosynthesis [isa: 0042035 ] [partof: 0042227 ]
+0045412 = negative regulation of interleukin-7 biosynthesis [isa: 0042036 0045411 ]
+0045413 = positive regulation of interleukin-7 biosynthesis [isa: 0042108 0045411 ]
+0042228 = interleukin-8 biosynthesis [isa: 0042089 ]
+0045414 = regulation of interleukin-8 biosynthesis [isa: 0042035 ] [partof: 0042228 ]
+0045415 = negative regulation of interleukin-8 biosynthesis [isa: 0042036 0045414 ]
+0045416 = positive regulation of interleukin-8 biosynthesis [isa: 0042108 0045414 ]
+0042229 = interleukin-9 biosynthesis [isa: 0042089 ]
+0045417 = regulation of interleukin-9 biosynthesis [isa: 0042035 ] [partof: 0042229 ]
+0045418 = negative regulation of interleukin-9 biosynthesis [isa: 0042036 0045417 ]
+0045419 = positive regulation of interleukin-9 biosynthesis [isa: 0042108 0045417 ]
+0042035 = regulation of cytokine biosynthesis [isa: 0009889 ] [partof: 0042089 ]
+0042036 = negative regulation of cytokine biosynthesis [isa: 0009890 0042035 ]
+0042536 = negative regulation of tumor necrosis factor-alpha biosynthesis [isa: 0042036 0042534 ]
+0042108 = positive regulation of cytokine biosynthesis [isa: 0009891 0042035 ]
+0042535 = positive regulation of tumor necrosis factor-alpha biosynthesis [isa: 0042108 0042534 ]
+0042534 = regulation of tumor necrosis factor-alpha biosynthesis [isa: 0042035 ] [partof: 0042533 ]
+0045553 = TRAIL biosynthesis [isa: 0042089 ]
+0045554 = regulation of TRAIL biosynthesis [partof: 0045553 ]
+0045555 = negative regulation of TRAIL biosynthesis [isa: 0045554 ]
+0045556 = positive regulation of TRAIL biosynthesis [isa: 0045554 ]
+0042533 = tumor necrosis factor-alpha biosynthesis [isa: 0042089 ]
+0042109 = tumor necrosis factor-beta biosynthesis [isa: 0042089 ]
+0006959 = humoral immune response [isa: 0006955 0009613 ]
+0019730 = antimicrobial humoral response [isa: 0006959 ]
+0019731 = antibacterial humoral response [isa: 0009617 0019730 ]
+0006961 = antibacterial humoral response (sensu Invertebrata) [isa: 0006960 0019731 ]
+0019733 = antibacterial humoral response (sensu Vertebrata) [isa: 0019731 0019735 ]
+0006963 = antibacterial polypeptide induction [partof: 0019731 ]
+0006964 = anti-Gram-negative bacterial polypeptide induction [isa: 0006963 ]
+0006965 = anti-Gram-positive bacterial polypeptide induction [isa: 0006963 ]
+0006962 = male-specific antibacterial humoral response [isa: 0019731 ]
+0019732 = antifungal humoral response [isa: 0009620 0019730 ]
+0006966 = antifungal humoral response (sensu Invertebrata) [isa: 0006960 0019732 ]
+0019734 = antifungal humoral response (sensu Vertebrata) [isa: 0019732 0019735 ]
+0006967 = antifungal polypeptide induction [partof: 0019732 ]
+0009623 = response to parasitic fungi [isa: 0019732 ]
+0006960 = antimicrobial humoral response (sensu Invertebrata) [isa: 0016065 0019730 ]
+0042154 = attenuation of antimicrobial humoral response (sensu Invertebrata) [partof: 0006960 ]
+0019735 = antimicrobial humoral response (sensu Vertebrata) [isa: 0016064 0019730 ]
+0042155 = attenuation of antimicrobial humoral response (sensu Vertebrata) [partof: 0019735 ]
+0008348 = attenuation of antimicrobial humoral response [partof: 0019730 ]
+0042381 = hemolymph coagulation [isa: 0006959 0007599 ]
+0016065 = humoral defense mechanism (sensu Invertebrata) [isa: 0006959 ]
+0016064 = humoral defense mechanism (sensu Vertebrata) [isa: 0006959 ]
+0019724 = B-cell mediated immunity [isa: 0016064 ]
+0006956 = complement activation [partof: 0016064 ]
+0006957 = complement activation, alternative pathway [isa: 0006956 ]
+0030451 = regulation of complement activation, alternative pathway [isa: 0030449 ] [partof: 0006957 ]
+0045957 = negative regulation of complement activation, alternative pathway [isa: 0030451 0045916 ]
+0045958 = positive regulation of complement activation, alternative pathway [isa: 0030451 0045917 ]
+0006958 = complement activation, classical pathway [isa: 0006956 ]
+0030450 = regulation of complement activation, classical pathway [isa: 0030449 ] [partof: 0006958 ]
+0045959 = negative regulation of complement activation, classical pathway [isa: 0030450 0045916 ]
+0045960 = positive regulation of complement activation, classical pathway [isa: 0030450 0045917 ]
+0016068 = immediate hypersensitivity response [isa: 0006956 ]
+0030449 = regulation of complement activation [partof: 0006956 ]
+0045916 = negative regulation of complement activation [isa: 0030449 ]
+0045917 = positive regulation of complement activation [isa: 0030449 ]
+0042092 = T-helper 2 type immune response [isa: 0006959 ]
+0009682 = induced systemic resistance [isa: 0006955 0009680 ]
+0045087 = innate immune response [isa: 0006955 ]
+0006954 = inflammatory response [isa: 0009611 0009613 0045087 ]
+0045123 = cellular extravasation [isa: 0016477 ] [partof: 0006954 ]
+0001660 = fever [isa: 0001659 0006954 ]
+0030593 = neutrophil chemotaxis [isa: 0030595 ] [partof: 0006954 ]
+0045088 = regulation of innate immune response [partof: 0045087 ]
+0045824 = negative regulation of innate immune response [isa: 0045088 ]
+0045089 = positive regulation of innate immune response [isa: 0045088 ]
+0045845 = regulation of natural killer cell activity [partof: 0009613 0045087 ]
+0030102 = negative regulation of natural killer cell activity [isa: 0045845 ]
+0045846 = positive regulation of natural killer cell activity [isa: 0045845 ]
+0009861 = jasmonic acid/ethylene dependent systemic resistance [isa: 0006955 0009611 0009816 0009817 ]
+0009693 = ethylene biosynthesis [isa: 0009692 0042398 0042446 ] [partof: 0009861 ]
+0042218 = 1-aminocyclopropane-1-carboxylate biosynthesis [isa: 0018871 0019438 0042398 ] [partof: 0009693 ]
+0042456 = ethylene biosynthesis from L-methionine [isa: 0006555 0009693 ]
+0012504 = induction of non-apoptotic programmed cell death by pathogen [partof: 0009627 0009861 ]
+0009695 = jasmonic acid biosynthesis [isa: 0006633 0009694 ] [partof: 0009861 ]
+0045728 = respiratory burst after phagocytosis [isa: 0006955 0045730 ]
+0009627 = systemic acquired resistance [isa: 0006955 0009816 0009817 ]
+0009689 = induction of phytoalexin biosynthesis [isa: 0006952 0009816 0009817 ]
+0009700 = indole phytoalexin biosynthesis [isa: 0009689 0042435 0046217 ]
+0009701 = isoflavonoid phytoalexin biosynthesis [isa: 0009689 0009717 0046289 ]
+0009616 = virus induced gene silencing [isa: 0006952 0009615 0016441 ]
+0009617 = response to bacteria [isa: 0009607 ]
+0009680 = response to non-pathogenic bacteria [isa: 0009617 ]
+0009618 = response to pathogenic bacteria [isa: 0009613 0009617 ]
+0009816 = response to pathogenic bacteria (incompatible interaction) [isa: 0009618 0009814 ]
+0009609 = response to symbiotic bacteria [isa: 0009608 0009617 ] [partof: 0009877 ]
+0006974 = response to DNA damage [isa: 0006950 0009607 ]
+0000077 = DNA damage checkpoint [isa: 0000075 0006974 ]
+0006975 = DNA damage induced protein phosphorylation [isa: 0006468 0006974 ]
+0030330 = p53-mediated DNA damage response [isa: 0006974 ]
+0006976 = DNA damage response, activation of p53 [partof: 0030330 ]
+0006977 = DNA damage response, induction of cell arrest by p53 [partof: 0006976 ]
+0006978 = DNA damage response, induction of cyclin-dependent protein kinase inhibitor p21 [partof: 0006977 ]
+0000723 = telomere maintenance [isa: 0006974 0007001 ]
+0007004 = telomerase-dependent telomere maintenance [isa: 0000723 ]
+0000722 = telomerase-independent telomere maintenance [isa: 0000723 0006312 ]
+0016233 = telomere capping [isa: 0000723 ]
+0006983 = response to ER-overload [isa: 0006950 0009607 ]
+0006984 = ER-nuclear signaling pathway [partof: 0006983 ]
+0006985 = EOR-mediated NF-kappaB activation [partof: 0006984 ]
+0009620 = response to fungi [isa: 0009607 ]
+0009621 = response to pathogenic fungi [isa: 0009613 0009620 ]
+0009817 = response to pathogenic fungi (incompatible interaction) [isa: 0009621 0009814 ]
+0009610 = response to symbiotic fungi [isa: 0009608 0009620 ]
+0009612 = response to mechanical stimulus [isa: 0009607 ]
+0009652 = thigmotropism [isa: 0009606 0009612 ]
+0006979 = response to oxidative stress [isa: 0006800 0006950 0009607 ]
+0006980 = redox signal response [isa: 0006979 ]
+0006981 = activation of SoxR protein [isa: 0006980 ]
+0006982 = response to lipid hydroperoxide [isa: 0006979 ]
+0000302 = response to reactive oxygen species [isa: 0006979 ]
+0042542 = response to hydrogen peroxide [isa: 0000302 ]
+0006802 = catalase reaction [partof: 0042542 ]
+0000305 = response to oxygen radicals [isa: 0000302 ]
+0000303 = response to superoxide [isa: 0000305 ]
+0000304 = response to singlet oxygen [isa: 0000302 ]
+0009613 = response to pest/pathogen/parasite [isa: 0006950 0009607 ]
+0009625 = response to insects [isa: 0009613 ]
+0009624 = response to nematodes [isa: 0009613 ]
+0009814 = response to pathogen (incompatible interaction) [isa: 0009613 ]
+0009818 = response to pathogenic protozoa (incompatible interaction) [isa: 0001562 0009814 ]
+0001562 = response to protozoa [isa: 0009613 ]
+0009615 = response to viruses [isa: 0009613 ]
+0009271 = phage shock [isa: 0009615 ]
+0009267 = response to starvation [isa: 0006950 0009607 ]
+0030583 = fruiting body formation (sensu Bacteria) [isa: 0009267 0030582 ]
+0030587 = fruiting body formation (sensu Dictyosteliida) [isa: 0009267 0030582 ]
+0042149 = response to glucose starvation [isa: 0009267 ]
+0006995 = response to nitrogen starvation [isa: 0009267 ]
+0016036 = response to phosphate starvation [isa: 0009267 ]
+0015968 = stringent response [isa: 0009267 ]
+0006991 = response to sterol depletion [isa: 0006950 0009607 ]
+0006994 = sterol depletion response, SREBP target gene transcriptional activation [partof: 0006991 ]
+0006992 = sterol depletion response, sterol regulatory element binding-protein cleavage [partof: 0006991 ]
+0006993 = sterol depletion response, sterol regulatory element binding-protein nuclear translocation [partof: 0006991 ]
+0009608 = response to symbiont [isa: 0009607 ]
+0006986 = response to unfolded protein [isa: 0006950 0009607 ]
+0006987 = unfolded protein response, activation of signaling protein kinase/endonuclease [partof: 0006986 ]
+0006988 = unfolded protein response, cleavage of primary transcript encoding UFP-specific transcription factor [partof: 0006986 ]
+0006989 = unfolded protein response, ligation of mRNA encoding UFP-specific transcription factor by RNA ligase [partof: 0006986 ]
+0006990 = unfolded protein response, target gene transcriptional activation [partof: 0006986 ]
+0009611 = response to wounding [isa: 0006950 0009607 ]
+0042060 = wound healing [isa: 0009611 ]
+0042246 = tissue regeneration [isa: 0040007 ] [partof: 0042060 ]
+0009432 = SOS response [isa: 0006950 0009605 ]
+0042330 = taxis [isa: 0006928 0009605 ]
+0006935 = chemotaxis [isa: 0042330 ]
+0009454 = aerotaxis [isa: 0006935 0009453 ]
+0042333 = chemotaxis to oxidizable substrate [isa: 0006935 0009453 ]
+0030595 = immune cell chemotaxis [isa: 0006935 ]
+0009455 = redox taxis [isa: 0006935 0009453 ]
+0009453 = energy taxis [isa: 0042330 ]
+0042331 = phototaxis [isa: 0009453 ]
+0042334 = taxis to electron acceptor [isa: 0009453 ]
+0042332 = gravitaxis [isa: 0042330 ]
+0009606 = tropism [isa: 0009605 ]
+0007165 = signal transduction [isa: 0007154 ]
+0007166 = cell surface receptor linked signal transduction [isa: 0007165 ]
+0007230 = calcium-o-sensing receptor pathway [isa: 0007166 ]
+0019221 = cytokine and chemokine mediated signaling pathway [isa: 0007166 ]
+0007167 = enzyme linked receptor protein signaling pathway [isa: 0007166 ]
+0007168 = receptor guanylyl cyclase signaling pathway [isa: 0007167 ]
+0007178 = transmembrane receptor protein serine/threonine kinase signaling pathway [isa: 0007167 ]
+0007179 = TGFbeta receptor signaling pathway [isa: 0007178 ]
+0030509 = BMP receptor signaling pathway [isa: 0007179 ]
+0030510 = regulation of BMP signaling pathway [partof: 0030509 ]
+0030514 = negative regulation of BMP signaling pathway [isa: 0030510 0030512 ]
+0030513 = positive regulation of BMP signaling pathway [isa: 0030510 0030511 ]
+0007182 = common-partner SMAD protein phosphorylation [isa: 0006468 ] [partof: 0007179 ]
+0017015 = regulation of TGFbeta receptor signaling pathway [partof: 0007179 ]
+0030512 = negative regulation of TGFbeta receptor signaling pathway [isa: 0017015 ]
+0030511 = positive regulation of TGFbeta receptor signaling pathway [isa: 0017015 ]
+0030579 = SMAD protein catabolism [isa: 0006511 ] [partof: 0007179 ]
+0007183 = SMAD protein heteromerization [partof: 0007179 ]
+0007184 = SMAD protein nuclear translocation [partof: 0007179 ]
+0008259 = TGFbeta ligand binding to type I receptor [partof: 0007179 ]
+0007180 = TGFbeta ligand binding to type II receptor [partof: 0007179 ]
+0007181 = TGFbeta receptor complex assembly [partof: 0007179 ]
+0007169 = transmembrane receptor protein tyrosine kinase signaling pathway [isa: 0007167 ]
+0007173 = EGF receptor signaling pathway [isa: 0007169 ]
+0007174 = EGF receptor ligand processing [partof: 0007173 ]
+0008314 = gurken receptor signaling pathway [isa: 0007173 ] [partof: 0007310 ]
+0007176 = regulation of EGF receptor activity [partof: 0007173 ]
+0007175 = negative regulation of EGF receptor activity [isa: 0007176 ]
+0045741 = positive regulation of EGF receptor activity [isa: 0007176 ]
+0042058 = regulation of EGF receptor signaling pathway [partof: 0007173 ]
+0042059 = negative regulation of EGF receptor signaling pathway [isa: 0042058 ]
+0045742 = positive regulation of EGF receptor signaling pathway [isa: 0042058 ]
+0048013 = Eph receptor signaling pathway [isa: 0007169 ]
+0008543 = FGF receptor signaling pathway [isa: 0007169 ]
+0040036 = regulation of FGF receptor signaling pathway [partof: 0008543 ]
+0040037 = negative regulation of FGF receptor signaling pathway [isa: 0040036 ]
+0045743 = positive regulation of FGF receptor signaling pathway [isa: 0040036 ]
+0048012 = HGF receptor signaling pathway [isa: 0007169 ]
+0048009 = IGF receptor signaling pathway [isa: 0007169 ]
+0008286 = insulin receptor signaling pathway [isa: 0007169 ]
+0046626 = regulation of insulin receptor signaling pathway [partof: 0008286 ]
+0046627 = negative regulation of insulin receptor signaling pathway [isa: 0046626 ]
+0046628 = positive regulation of insulin receptor signaling pathway [isa: 0046626 ]
+0048011 = NGF receptor signaling pathway [isa: 0007169 ]
+0048008 = PDGF receptor signaling pathway [isa: 0007169 ]
+0045500 = sevenless receptor signaling pathway [isa: 0007169 ] [partof: 0007465 ]
+0045501 = regulation of sevenless receptor signaling pathway [partof: 0045500 ]
+0045873 = negative regulation of sevenless receptor signaling pathway [isa: 0045501 ]
+0045874 = positive regulation of sevenless receptor signaling pathway [isa: 0045501 ]
+0007172 = signal complex formation [partof: 0007169 ]
+0048014 = Tie receptor signaling pathway [isa: 0007169 ]
+0008293 = torso receptor signaling pathway [isa: 0007169 ]
+0007171 = transmembrane receptor protein tyrosine kinase activation (dimerization) [partof: 0007169 ]
+0007170 = transmembrane receptor protein tyrosine kinase ligand binding [partof: 0007169 ]
+0048010 = VEGF receptor signaling pathway [isa: 0007169 ]
+0007185 = transmembrane receptor protein tyrosine phosphatase signaling pathway [isa: 0007167 ]
+0007186 = G-protein coupled receptor protein signaling pathway [isa: 0007166 ]
+0007213 = acetyl choline receptor signaling, muscarinic pathway [isa: 0007186 ]
+0007212 = dopamine receptor signaling pathway [isa: 0007186 ]
+0007187 = G-protein signaling, coupled to cyclic nucleotide second messenger [isa: 0007186 0019935 ]
+0007188 = G-protein signaling, coupled to cAMP nucleotide second messenger [isa: 0007187 0019933 ]
+0007189 = G-protein signaling, adenylate cyclase activating pathway [isa: 0007188 ]
+0007190 = adenylate cyclase activation [partof: 0007189 ]
+0007191 = dopamine receptor, adenylate cyclase activating pathway [isa: 0007189 ]
+0007192 = serotonin receptor, adenylate cyclase activating pathway [isa: 0007189 ]
+0007193 = G-protein signaling, adenylate cyclase inhibiting pathway [isa: 0007188 ]
+0007195 = dopamine receptor, adenylate cyclase inhibiting pathway [isa: 0007193 ]
+0007196 = metabotropic glutamate receptor, adenylate cyclase inhibiting pathway [isa: 0007193 ]
+0007197 = muscarinic acetyl choline receptor, adenylate cyclase inhibiting pathway [isa: 0007193 ]
+0045761 = regulation of adenylate cyclase activity [partof: 0007193 ]
+0007194 = negative regulation of adenylate cyclase activity [isa: 0045761 ]
+0045762 = positive regulation of adenylate cyclase activity [isa: 0045761 ]
+0007198 = serotonin receptor, adenylate cyclase inhibiting pathway [isa: 0007193 ]
+0007199 = G-protein signaling, coupled to cGMP nucleotide second messenger [isa: 0007187 0019934 ]
+0007200 = G-protein signaling, coupled to IP3 second messenger (phospholipase C activating) [isa: 0007186 ]
+0007204 = cytosolic calcium ion concentration elevation [partof: 0007200 ]
+0007201 = G-protein dissociation [partof: 0007200 ]
+0007206 = metabotropic glutamate receptor, phospholipase C activating pathway [isa: 0007200 ]
+0007207 = muscarinic acetyl choline receptor, phospholipase C activating pathway [isa: 0007200 ]
+0007203 = phosphatidylinositol-4,5-bisphosphate hydrolysis [partof: 0007200 ]
+0007202 = phospholipase C activation [partof: 0007200 ]
+0007205 = protein kinase C activation [partof: 0007200 ]
+0007208 = serotonin receptor, phospholipase C activating pathway [isa: 0007200 ]
+0007209 = tachykinin receptor, phospholipase C activating pathway [isa: 0007200 ]
+0007214 = gamma-amino butyric acid signaling pathway [isa: 0007186 ]
+0007215 = glutamate signaling pathway [isa: 0007186 ]
+0007216 = metabotropic glutamate receptor signaling pathway [isa: 0007215 ]
+0007218 = neuropeptide signaling pathway [isa: 0007186 ]
+0007211 = octopamine/tyramine signaling pathway [isa: 0007186 ]
+0008277 = regulation of G-protein coupled receptor protein signaling pathway [partof: 0007186 ]
+0045744 = negative regulation of G-protein coupled receptor protein signaling pathway [isa: 0008277 ]
+0045745 = positive regulation of G-protein coupled receptor protein signaling pathway [isa: 0008277 ]
+0042313 = protein kinase C deactivation [isa: 0008277 ]
+0007210 = serotonin receptor signaling pathway [isa: 0007186 ]
+0007217 = tachykinin signaling pathway [isa: 0007186 ]
+0007229 = integrin-mediated signaling pathway [isa: 0007166 ]
+0007219 = N receptor signaling pathway [isa: 0007166 ]
+0007220 = N receptor processing [partof: 0007219 ]
+0007221 = N receptor target transcription factor activation [partof: 0007219 ]
+0008593 = regulation of N receptor signaling pathway [partof: 0007219 ]
+0045746 = negative regulation of N receptor signaling pathway [isa: 0008593 ]
+0045747 = positive regulation of N receptor signaling pathway [isa: 0008593 ]
+0007231 = osmosensory signaling pathway [isa: 0007166 ]
+0007232 = osmosensory signaling pathway via Sho1 osmosensor [isa: 0007231 ]
+0007233 = activation of Pbs2 kinase [partof: 0007232 ]
+0007234 = osmosensory signaling pathway via two-component system [isa: 0007231 ] [partof: 0000160 ]
+0000161 = MAPKKK cascade (osmolarity sensing) [isa: 0000165 ] [partof: 0007234 ]
+0000169 = activation of MAPK (osmolarity sensing) [isa: 0000187 ] [partof: 0000161 ]
+0000168 = activation of MAPKK (osmolarity sensing) [isa: 0000186 ] [partof: 0000161 ]
+0000167 = activation of MAPKKK (osmolarity sensing) [isa: 0000185 ] [partof: 0000161 ]
+0000173 = inactivation of MAPK (osmolarity sensing) [isa: 0000188 ] [partof: 0000161 ]
+0000208 = nuclear translocation of MAPK (osmolarity sensing) [isa: 0000189 ] [partof: 0000161 ]
+0007224 = smoothened receptor signaling pathway [isa: 0007166 ]
+0007225 = patched receptor ligand processing [partof: 0007224 ]
+0007226 = regulation of smoothened receptor by patched [partof: 0007224 ]
+0045877 = negative regulation of smoothened receptor by patched [isa: 0007226 ]
+0045878 = positive regulation of smoothened receptor by patched [isa: 0007226 ]
+0008589 = regulation of smoothened receptor signaling pathway [partof: 0007224 ]
+0045879 = negative regulation of smoothened receptor signaling pathway [isa: 0008589 ]
+0045880 = positive regulation of smoothened receptor signaling pathway [isa: 0008589 ]
+0007227 = signal transduction downstream of smoothened receptor [partof: 0007224 ]
+0007228 = activation of hh target transcription factor [partof: 0007227 ]
+0008063 = Tl receptor signaling pathway [isa: 0007166 ] [partof: 0007310 ]
+0008592 = regulation of Tl receptor signaling pathway [partof: 0008063 ]
+0045751 = negative regulation of Tl receptor signaling pathway [isa: 0008592 ]
+0045752 = positive regulation of Tl receptor signaling pathway [isa: 0008592 ]
+0016055 = Wnt receptor signaling pathway [isa: 0007166 ]
+0007222 = frizzled receptor signaling pathway [isa: 0016055 ]
+0008590 = regulation of frizzled receptor signaling pathway [isa: 0030111 ] [partof: 0007222 ]
+0045810 = negative regulation of frizzled receptor signaling pathway [isa: 0008590 0030178 ]
+0045811 = positive regulation of frizzled receptor signaling pathway [isa: 0008590 0030177 ]
+0007223 = frizzled-2 receptor signaling pathway [isa: 0016055 ]
+0008591 = regulation of frizzled-2 receptor signaling pathway [isa: 0030111 ] [partof: 0007223 ]
+0045812 = negative regulation of frizzled-2 receptor signaling pathway [isa: 0008591 0030178 ]
+0045813 = positive regulation of frizzled-2 receptor signaling pathway [isa: 0008591 0030177 ]
+0030111 = regulation of Wnt receptor signaling pathway [partof: 0016055 ]
+0030178 = negative regulation of Wnt receptor signaling pathway [isa: 0030111 ]
+0030177 = positive regulation of Wnt receptor signaling pathway [isa: 0030111 ]
+0007242 = intracellular signaling cascade [isa: 0007165 ]
+0009785 = blue light signaling pathway [isa: 0007242 ]
+0009870 = defense response signaling pathway, resistance-gene dependent [isa: 0007242 ]
+0030522 = intracellular receptor-mediated signaling pathway [isa: 0007242 ]
+0030518 = steroid hormone receptor signaling pathway [isa: 0030522 ]
+0030521 = androgen receptor signaling pathway [isa: 0030518 ]
+0030520 = estrogen receptor signaling pathway [isa: 0030518 ]
+0007263 = NO mediated signal transduction [isa: 0007242 ]
+0007243 = protein kinase cascade [isa: 0007242 ]
+0007259 = JAK-STAT cascade [isa: 0007243 ]
+0046425 = regulation of JAK-STAT cascade [partof: 0007259 ]
+0046426 = negative regulation of JAK-STAT cascade [isa: 0046425 ]
+0046427 = positive regulation of JAK-STAT cascade [isa: 0046425 ]
+0042501 = serine phosphorylation of STAT protein [isa: 0018105 ] [partof: 0007259 ]
+0007261 = STAT protein dimerization [partof: 0007259 ]
+0007262 = STAT protein nuclear translocation [partof: 0007259 ]
+0007260 = tyrosine phosphorylation of STAT protein [isa: 0018108 ] [partof: 0007259 ]
+0042509 = regulation of tyrosine phosphorylation of STAT protein [partof: 0007260 ]
+0042532 = negative regulation of tyrosine phosphorylation of STAT protein [isa: 0042509 ]
+0042512 = negative regulation of tyrosine phosphorylation of Stat1 protein [isa: 0042510 0042532 ]
+0042514 = negative regulation of tyrosine phosphorylation of Stat2 protein [isa: 0042513 0042532 ]
+0042518 = negative regulation of tyrosine phosphorylation of Stat3 protein [isa: 0042516 0042532 ]
+0042521 = negative regulation of tyrosine phosphorylation of Stat4 protein [isa: 0042519 0042532 ]
+0042524 = negative regulation of tyrosine phosphorylation of Stat5 protein [isa: 0042522 0042532 ]
+0042527 = negative regulation of tyrosine phosphorylation of Stat6 protein [isa: 0042525 0042532 ]
+0042530 = negative regulation of tyrosine phosphorylation of Stat7 protein [isa: 0042528 0042532 ]
+0042531 = positive regulation of tyrosine phosphorylation of STAT protein [isa: 0042509 ]
+0042511 = positive regulation of tyrosine phosphorylation of Stat1 protein [isa: 0042510 0042531 ]
+0042515 = positive regulation of tyrosine phosphorylation of Stat2 protein [isa: 0042513 0042531 ]
+0042517 = positive regulation of tyrosine phosphorylation of Stat3 protein [isa: 0042516 0042531 ]
+0042520 = positive regulation of tyrosine phosphorylation of Stat4 protein [isa: 0042519 0042531 ]
+0042523 = positive regulation of tyrosine phosphorylation of Stat5 protein [isa: 0042522 0042531 ]
+0042526 = positive regulation of tyrosine phosphorylation of Stat6 protein [isa: 0042525 0042531 ]
+0042529 = positive regulation of tyrosine phosphorylation of Stat7 protein [isa: 0042528 0042531 ]
+0042510 = regulation of tyrosine phosphorylation of Stat1 protein [isa: 0042509 ] [partof: 0042508 ]
+0042513 = regulation of tyrosine phosphorylation of Stat2 protein [isa: 0042509 ] [partof: 0042502 ]
+0042516 = regulation of tyrosine phosphorylation of Stat3 protein [isa: 0042509 ] [partof: 0042503 ]
+0042519 = regulation of tyrosine phosphorylation of Stat4 protein [isa: 0042509 ] [partof: 0042504 ]
+0042522 = regulation of tyrosine phosphorylation of Stat5 protein [isa: 0042509 ] [partof: 0042506 ]
+0042525 = regulation of tyrosine phosphorylation of Stat6 protein [isa: 0042509 ] [partof: 0042505 ]
+0042528 = regulation of tyrosine phosphorylation of Stat7 protein [isa: 0042509 ] [partof: 0042507 ]
+0042508 = tyrosine phosphorylation of Stat1 protein [isa: 0007260 ]
+0042502 = tyrosine phosphorylation of Stat2 protein [isa: 0007260 ]
+0042503 = tyrosine phosphorylation of Stat3 protein [isa: 0007260 ]
+0042504 = tyrosine phosphorylation of Stat4 protein [isa: 0007260 ]
+0042506 = tyrosine phosphorylation of Stat5 protein [isa: 0007260 ]
+0042505 = tyrosine phosphorylation of Stat6 protein [isa: 0007260 ]
+0042507 = tyrosine phosphorylation of Stat7 protein [isa: 0007260 ]
+0007254 = JNK cascade [isa: 0007243 ]
+0007257 = activation of JUN kinase [partof: 0007254 ]
+0007256 = activation of JUN kinase kinase [partof: 0007254 ]
+0007255 = activation of MAP/ERK kinase kinase [partof: 0007254 ]
+0007258 = JUN phosphorylation [isa: 0006468 ] [partof: 0007254 ]
+0046328 = regulation of JNK cascade [partof: 0007254 ]
+0046329 = negative regulation of JNK cascade [isa: 0046328 ]
+0046330 = positive regulation of JNK cascade [isa: 0046328 ]
+0000165 = MAPKKK cascade [isa: 0007243 ]
+0000187 = activation of MAPK [partof: 0000165 ]
+0000199 = activation of MAPK (cell wall biogenesis) [isa: 0000187 ] [partof: 0000196 ]
+0030456 = activation of MAPK (mating sensu Fungi) [isa: 0000187 ] [partof: 0030455 ]
+0000193 = activation of MAPK (pseudohyphal growth) [isa: 0000187 ] [partof: 0000190 ]
+0030439 = activation of MAPK (sporulation sensu Fungi) [isa: 0000187 ] [partof: 0030438 ]
+0000205 = activation of MAPK (sporulation sensu Saccharomyces) [isa: 0030439 ] [partof: 0000202 ]
+0000186 = activation of MAPKK [partof: 0000165 ]
+0000198 = activation of MAPKK (cell wall biogenesis) [isa: 0000186 ] [partof: 0000196 ]
+0030457 = activation of MAPKK (mating sensu Fungi) [isa: 0000186 ] [partof: 0030455 ]
+0000192 = activation of MAPKK (pseudohyphal growth) [isa: 0000186 ] [partof: 0000190 ]
+0030440 = activation of MAPKK (sporulation sensu Fungi) [isa: 0000186 ] [partof: 0030438 ]
+0000204 = activation of MAPKK (sporulation sensu Saccharomyces) [isa: 0030440 ] [partof: 0000202 ]
+0000185 = activation of MAPKKK [partof: 0000165 ]
+0000197 = activation of MAPKKK (cell wall biogenesis) [isa: 0000185 ] [partof: 0000196 ]
+0030458 = activation of MAPKKK (mating sensu Fungi) [isa: 0000185 ] [partof: 0030455 ]
+0000191 = activation of MAPKKK (pseudohyphal growth) [isa: 0000185 ] [partof: 0000190 ]
+0030441 = activation of MAPKKK (sporulation sensu Fungi) [isa: 0000185 ] [partof: 0030438 ]
+0000203 = activation of MAPKKK (sporulation sensu Saccharomyces) [isa: 0030441 ] [partof: 0000202 ]
+0000188 = inactivation of MAPK [partof: 0000165 ]
+0000200 = inactivation of MAPK (cell wall biogenesis) [isa: 0000188 ] [partof: 0000196 ]
+0030459 = inactivation of MAPK (mating sensu Fungi) [isa: 0000188 ] [partof: 0030455 ]
+0000194 = inactivation of MAPK (pseudohyphal growth) [isa: 0000188 ] [partof: 0000190 ]
+0030442 = inactivation of MAPK (sporulation sensu Fungi) [isa: 0000188 ] [partof: 0030438 ]
+0000206 = inactivation of MAPK (sporulation sensu Saccharomyces) [isa: 0030442 ] [partof: 0000202 ]
+0000196 = MAPKKK cascade (cell wall biogenesis) [isa: 0000165 ] [partof: 0007047 ]
+0000201 = nuclear translocation of MAPK (cell wall biogenesis) [isa: 0000189 ] [partof: 0000196 ]
+0030455 = MAPKKK cascade (mating sensu Fungi) [isa: 0000165 ]
+0030460 = nuclear translocation of MAPK (mating sensu Fungi) [isa: 0000189 ] [partof: 0030455 ]
+0000190 = MAPKKK cascade (pseudohyphal growth) [isa: 0000165 ] [partof: 0007124 ]
+0000195 = nuclear translocation of MAPK (pseudohyphal growth) [isa: 0000189 ] [partof: 0000190 ]
+0030438 = MAPKKK cascade (sporulation sensu Fungi) [isa: 0000165 ] [partof: 0030437 ]
+0000202 = MAPKKK cascade (sporulation sensu Saccharomyces) [isa: 0030438 ] [partof: 0007151 ]
+0000207 = nuclear translocation of MAPK (sporulation sensu Saccharomyces) [isa: 0030443 ] [partof: 0000202 ]
+0030443 = nuclear translocation of MAPK (sporulation sensu Fungi) [isa: 0000189 ] [partof: 0030438 ]
+0000189 = nuclear translocation of MAPK [partof: 0000165 ]
+0007249 = NIK-I-kappaB/NF-kappaB cascade [isa: 0007243 ]
+0007250 = activation of NF-kappaB-inducing kinase [partof: 0007249 ]
+0007251 = activation of the inhibitor of kappa kinase [partof: 0007249 ]
+0007253 = cytoplasmic sequestering of NF-kappaB [isa: 0042347 ] [partof: 0007249 ]
+0007252 = I-kappaB phosphorylation [isa: 0006468 ] [partof: 0007249 ]
+0008588 = release of cytoplasmic sequestered NF-kappaB [partof: 0007249 ]
+0019932 = second-messenger-mediated signaling [isa: 0007242 ]
+0019722 = calcium-mediated signaling [isa: 0019932 ]
+0019935 = cyclic-nucleotide-mediated signaling [isa: 0019932 ]
+0019933 = cAMP-mediated signaling [isa: 0019935 ]
+0019934 = cGMP-mediated signaling [isa: 0019935 ]
+0048015 = phosphoinositide-mediated signaling [isa: 0019932 ]
+0048017 = inositol lipid-mediated signaling [isa: 0048015 ]
+0048016 = inositol phosphate-mediated signaling [isa: 0048015 ]
+0007264 = small GTPase mediated signal transduction [isa: 0007242 ]
+0016601 = RAC protein signal transduction [isa: 0007264 ]
+0007265 = RAS protein signal transduction [isa: 0007264 ]
+0046578 = regulation of RAS protein signal transduction [isa: 0007265 ]
+0046580 = negative regulation of RAS protein signal transduction [isa: 0046578 ]
+0046579 = positive regulation of RAS protein signal transduction [isa: 0046578 ]
+0007266 = Rho protein signal transduction [isa: 0007264 ]
+0000160 = two-component signal transduction system (phosphorelay) [isa: 0006355 0007165 ]
+0008151 = cell growth and/or maintenance [isa: 0008150 ]
+0006914 = autophagy [isa: 0008151 ]
+0016238 = chaperone-mediated autophagy [isa: 0006914 ]
+0016236 = macroautophagy [isa: 0006914 ]
+0030399 = autophagic membrane degradation [isa: 0030397 ] [partof: 0016236 ]
+0016240 = autophagic vacuole docking [partof: 0016236 ]
+0000045 = autophagic vacuole formation [partof: 0016236 ]
+0000046 = autophagic vacuole fusion [partof: 0016236 ]
+0016243 = regulation of autophagic vacuole size [partof: 0016236 ]
+0045771 = negative regulation of autophagic vacuole size [isa: 0016243 ]
+0045772 = positive regulation of autophagic vacuole size [isa: 0016243 ]
+0016241 = regulation of macroautophagy [partof: 0016236 ]
+0016242 = negative regulation of macroautophagy [isa: 0016241 ]
+0016239 = positive regulation of macroautophagy [isa: 0016241 ]
+0016237 = microautophagy [isa: 0006914 ]
+0007114 = budding [isa: 0008151 ]
+0007120 = axial budding [isa: 0007114 ]
+0007117 = bud growth [partof: 0007114 ]
+0007118 = apical bud growth [isa: 0007117 ]
+0007119 = isotropic bud growth [isa: 0007117 ]
+0007123 = bud scar accumulation [isa: 0007114 ]
+0000282 = bud site selection [isa: 0000283 ] [partof: 0007114 ]
+0007122 = loss of asymmetric budding [isa: 0007114 ]
+0007121 = polar budding [isa: 0007114 ]
+0007116 = regulation of budding [partof: 0007114 ]
+0045781 = negative regulation of budding [isa: 0007116 ]
+0045782 = positive regulation of budding [isa: 0007116 ]
+0007049 = cell cycle [isa: 0008151 ]
+0030037 = cell cycle dependent actin filament reorganization [isa: 0007015 0007049 ]
+0000067 = DNA replication and chromosome cycle [partof: 0007049 ]
+0000069 = centromere/kinetochore complex maturation [partof: 0000067 ]
+0030261 = chromosome condensation [partof: 0000067 ]
+0030263 = apoptotic chromosome condensation [isa: 0030261 ] [partof: 0030262 ]
+0007076 = mitotic chromosome condensation [isa: 0030261 ] [partof: 0000088 ]
+0007062 = sister chromatid cohesion [partof: 0030261 ]
+0007066 = female meiosis sister chromatid cohesion [isa: 0007062 ] [partof: 0007143 ]
+0007065 = male meiosis sister chromatid cohesion [isa: 0007062 ] [partof: 0007140 ]
+0007064 = mitotic sister chromatid cohesion [isa: 0007062 ] [partof: 0007067 ]
+0007063 = regulation of sister chromatid cohesion [partof: 0007062 ]
+0045875 = negative regulation of sister chromatid cohesion [isa: 0007063 ]
+0045876 = positive regulation of sister chromatid cohesion [isa: 0007063 ]
+0007059 = chromosome segregation [partof: 0000067 ]
+0007061 = homologous chromosome segregation [isa: 0007059 ]
+0045132 = meiotic chromosome segregation [isa: 0007059 ]
+0016321 = female meiosis chromosome segregation [isa: 0045132 ] [partof: 0007143 ]
+0007060 = male meiosis chromosome segregation [isa: 0045132 ] [partof: 0007140 ]
+0045143 = meiosis I, chromosome segregation [isa: 0045132 ] [partof: 0007133 ]
+0045144 = meiosis II, chromosome segregation [isa: 0045132 ] [partof: 0007138 ]
+0000070 = mitotic chromosome segregation [isa: 0007059 ] [partof: 0000090 ]
+0006260 = DNA replication [isa: 0006259 ] [partof: 0000067 0000084 ]
+0006277 = DNA amplification [isa: 0006260 ]
+0006261 = DNA dependent DNA replication [isa: 0006260 ]
+0042023 = DNA endoreduplication [isa: 0006261 ]
+0006266 = DNA ligation [partof: 0006261 0006281 0006310 ]
+0006270 = DNA replication initiation [partof: 0006261 ]
+0042024 = DNA endoreduplication initiation [isa: 0006270 ]
+0006274 = DNA replication termination [partof: 0006261 ]
+0006269 = DNA replication, priming [partof: 0006261 ]
+0006271 = DNA strand elongation [partof: 0006261 ]
+0006273 = lagging strand elongation [isa: 0006271 ]
+0006272 = leading strand elongation [isa: 0006271 ]
+0006265 = DNA topological change [partof: 0006261 ]
+0006268 = DNA unwinding [partof: 0006261 ]
+0045005 = maintenance of fidelity during DNA dependent DNA replication [partof: 0006261 ]
+0045004 = DNA replication proofreading [isa: 0006281 0045005 ]
+0006298 = mismatch repair [isa: 0006281 0045005 ]
+0006300 = long patch mismatch repair system [isa: 0006298 ]
+0006299 = short patch mismatch repair system [isa: 0006298 ]
+0006267 = pre-replicative complex formation and maintenance [partof: 0006261 ]
+0006275 = regulation of DNA replication [partof: 0006261 ]
+0030174 = DNA replication licensing [isa: 0006275 ]
+0008156 = negative regulation of DNA replication [isa: 0006275 ]
+0045740 = positive regulation of DNA replication [isa: 0006275 ]
+0006279 = premeiotic DNA synthesis [isa: 0006260 ]
+0006278 = RNA dependent DNA replication [isa: 0006260 ]
+0006276 = plasmid maintenance [isa: 0000067 ]
+0030541 = plasmid partitioning [isa: 0006276 ]
+0030543 = 2-micrometer plasmid partitioning [isa: 0030541 ]
+0030542 = plasmid partitioning (sensu Bacteria) [isa: 0030541 ]
+0030471 = spindle pole body and microtubule cycle (sensu Fungi) [isa: 0000067 0000072 ]
+0030472 = mitotic spindle assembly (sensu Fungi) [isa: 0007052 ] [partof: 0030471 ]
+0000071 = mitotic spindle assembly (sensu Saccharomyces) [isa: 0030472 ] [partof: 0007102 ]
+0030610 = mitotic spindle positioning and orientation (sensu Saccharomyces) [isa: 0000071 0030605 ]
+0030609 = mitotic spindle orientation (sensu Saccharomyces) [isa: 0030607 ] [partof: 0030610 ]
+0030608 = mitotic spindle positioning (sensu Saccharomyces) [isa: 0030606 ] [partof: 0030610 ]
+0030605 = mitotic spindle positioning and orientation (sensu Fungi) [isa: 0030472 0040001 ]
+0030607 = mitotic spindle orientation (sensu Fungi) [isa: 0000132 ] [partof: 0030605 ]
+0030606 = mitotic spindle positioning (sensu Fungi) [isa: 0018986 ] [partof: 0030605 ]
+0030473 = nuclear migration (sensu Fungi) [partof: 0030471 ]
+0000065 = nuclear migration (sensu Saccharomyces) [isa: 0007097 0030473 ] [partof: 0007102 0007335 ]
+0007102 = spindle pole body and microtubule cycle (sensu Saccharomyces) [isa: 0030471 ]
+0007103 = spindle pole body duplication (sensu Saccharomyces) [isa: 0030474 ] [partof: 0007102 ]
+0000073 = spindle pole body separation (sensu Saccharomyces) [isa: 0030475 ] [partof: 0007102 ]
+0030474 = spindle pole body duplication (sensu Fungi) [partof: 0030471 ]
+0030475 = spindle pole body separation (sensu Fungi) [partof: 0030471 ]
+0007113 = endomitotic cell cycle [isa: 0007049 ]
+0000279 = M phase [partof: 0007049 ]
+0016288 = cytokinesis [partof: 0000279 ]
+0008356 = asymmetric cytokinesis [isa: 0016288 ]
+0007282 = cystoblast cell division [isa: 0008356 0042078 ] [partof: 0007281 ]
+0045034 = neuroblast cell division [isa: 0008356 ] [partof: 0007400 ]
+0009786 = regulation of asymmetric cytokinesis [partof: 0008356 ]
+0045769 = negative regulation of asymmetric cytokinesis [isa: 0009786 ]
+0045770 = positive regulation of asymmetric cytokinesis [isa: 0009786 ]
+0045035 = sensory organ precursor cell division [isa: 0008356 ] [partof: 0007423 ]
+0009919 = cytokinesis (sensu Viridiplantae) [isa: 0016288 ]
+0007110 = cytokinesis after meiosis I [isa: 0016288 ] [partof: 0007126 ]
+0007111 = cytokinesis after meiosis II [isa: 0016288 ] [partof: 0007135 ]
+0000281 = cytokinesis after mitosis [isa: 0016288 ] [partof: 0000087 ]
+0007109 = cytokinesis, completion of separation [partof: 0016288 ]
+0045573 = cytokinesis, contractile ring assembly [partof: 0016288 ]
+0007108 = cytokinesis, initiation of separation [partof: 0016288 ]
+0007107 = cytokinesis, membrane recruitment/generation [partof: 0016288 ]
+0007106 = cytokinesis, protein recruitment [partof: 0016288 ]
+0007105 = cytokinesis, site selection [partof: 0016288 ]
+0007112 = male meiosis cytokinesis [isa: 0016288 ]
+0000094 = septin assembly and septum formation [partof: 0016288 ]
+0017145 = stem cell renewal [isa: 0016288 ]
+0042078 = germ-line stem cell renewal [isa: 0017145 ]
+0007284 = spermatogonial cell division [isa: 0042078 ] [partof: 0007283 ]
+0000087 = M phase of mitotic cell cycle [isa: 0000279 ] [partof: 0000278 ]
+0007067 = mitosis [isa: 0000280 ] [partof: 0000087 ]
+0007072 = activation of transcription on exit from mitosis [partof: 0007067 ]
+0007073 = activation of transcription on exit from mitosis, from Pol I promoter [isa: 0007072 ]
+0007074 = activation of transcription on exit from mitosis, from Pol II promoter [isa: 0007072 ]
+0007075 = activation of transcription on exit from mitosis, from Pol III promoter [isa: 0007072 ]
+0000090 = mitotic anaphase [partof: 0007067 ]
+0000091 = mitotic anaphase A [isa: 0000090 ]
+0000092 = mitotic anaphase B [isa: 0000090 ]
+0007079 = mitotic chromosome movement [partof: 0000090 ]
+0000089 = mitotic metaphase [partof: 0007067 ]
+0007080 = mitotic metaphase plate congression [partof: 0000089 ]
+0007091 = mitotic metaphase/anaphase transition [partof: 0007067 ]
+0016359 = mitotic sister chromatid separation [partof: 0007091 ]
+0030071 = regulation of mitotic metaphase/anaphase transition [isa: 0007088 ] [partof: 0007091 ]
+0007092 = anaphase-promoting complex activation [partof: 0030071 ]
+0045841 = negative regulation of mitotic metaphase/anaphase transition [isa: 0030071 0045839 ]
+0045842 = positive regulation of mitotic metaphase/anaphase transition [isa: 0030071 0045840 ]
+0000236 = mitotic prometaphase [partof: 0007067 ]
+0000088 = mitotic prophase [partof: 0007067 ]
+0007077 = mitotic nuclear envelope breakdown [partof: 0000088 ]
+0007078 = lamin depolymerization [partof: 0007077 ]
+0007052 = mitotic spindle assembly [isa: 0007051 ] [partof: 0007067 ]
+0000022 = mitotic spindle elongation [partof: 0007052 ]
+0040001 = mitotic spindle positioning and orientation [partof: 0007052 ]
+0000132 = mitotic spindle orientation [partof: 0040001 ]
+0018986 = mitotic spindle positioning [partof: 0040001 ]
+0000093 = mitotic telophase [partof: 0007067 ]
+0009920 = cell plate formation (sensu Magnoliophyta) [partof: 0000093 0009832 ]
+0007084 = nuclear envelope reassembly [partof: 0000093 ]
+0007085 = nuclear membrane vesicle binding to chromatin [partof: 0007084 ]
+0007086 = nuclear membrane vesicle fusion [partof: 0007084 ]
+0007087 = nuclear pore complex reassembly [partof: 0007084 ]
+0007088 = regulation of mitosis [isa: 0000074 ] [partof: 0007067 ]
+0007096 = exit from mitosis [isa: 0007088 ]
+0007093 = mitotic checkpoint [isa: 0000075 0007088 ]
+0007095 = mitotic G2 checkpoint [isa: 0007093 ]
+0007094 = mitotic spindle checkpoint [isa: 0007093 ]
+0045839 = negative regulation of mitosis [isa: 0007088 0045786 ]
+0045840 = positive regulation of mitosis [isa: 0007088 0045787 ]
+0045896 = regulation of transcription, mitotic [isa: 0006355 ] [partof: 0007067 ]
+0007068 = negative regulation of transcription, mitotic [isa: 0045892 0045896 ]
+0007069 = negative regulation of transcription from Pol I promoter, mitotic [isa: 0007068 0016479 0046017 ]
+0007070 = negative regulation of transcription from Pol II promoter, mitotic [isa: 0000122 0007068 0046021 ]
+0007071 = negative regulation of transcription from Pol III promoter, mitotic [isa: 0007068 0016480 0046023 ]
+0045897 = positive regulation of transcription, mitotic [isa: 0045896 ]
+0046018 = positive regulation of transcription from Pol I promoter, mitotic [isa: 0045897 0045943 0046017 ]
+0046022 = positive regulation of transcription from Pol II promoter, mitotic [isa: 0045897 0045944 0046021 ]
+0046024 = positive regulation of transcription from Pol III promoter, mitotic [isa: 0045897 0045945 0046023 ]
+0046017 = regulation of transcription from Pol I promoter, mitotic [isa: 0006356 ] [partof: 0045896 ]
+0046021 = regulation of transcription from Pol II promoter, mitotic [isa: 0006357 ] [partof: 0045896 ]
+0046023 = regulation of transcription from Pol III promoter, mitotic [isa: 0006359 ] [partof: 0045896 ]
+0000072 = M-phase specific microtubule process [isa: 0000226 ] [partof: 0000279 ]
+0007098 = centrosome cycle [isa: 0000072 ]
+0007099 = centriole replication [partof: 0007098 ]
+0046599 = regulation of centriole replication [isa: 0046605 ] [partof: 0007099 ]
+0046600 = negative regulation of centriole replication [isa: 0046599 0046606 ]
+0046601 = positive regulation of centriole replication [isa: 0046599 0046607 ]
+0007100 = centrosome separation [partof: 0007098 ]
+0046602 = regulation of centrosome separation [isa: 0046605 ] [partof: 0007100 ]
+0046603 = negative regulation of centrosome separation [isa: 0046602 0046606 ]
+0046604 = positive regulation of centrosome separation [isa: 0046602 0046607 ]
+0007101 = male meiosis centrosome cycle [isa: 0007098 ]
+0046605 = regulation of centrosome cycle [partof: 0007098 ]
+0046606 = negative regulation of centrosome cycle [isa: 0046605 ]
+0046607 = positive regulation of centrosome cycle [isa: 0046605 ]
+0008546 = microtubule/chromatin interaction [isa: 0000072 ]
+0008608 = microtubule/kinetochore interaction [isa: 0008546 ]
+0007051 = spindle assembly [isa: 0000072 ]
+0000212 = meiotic spindle assembly [isa: 0007051 ] [partof: 0007126 ]
+0007056 = female meiotic spindle assembly (sensu Drosophila, sensu Mus) [isa: 0000212 ] [partof: 0007143 ]
+0007057 = female meiosis I spindle assembly [isa: 0007056 ] [partof: 0007144 ]
+0007058 = female meiosis II spindle assembly [isa: 0007056 ] [partof: 0007147 ]
+0007053 = male meiotic spindle assembly (sensu Drosophila, sensu Mus) [isa: 0000212 ] [partof: 0007140 ]
+0007054 = male meiosis I spindle assembly [isa: 0007053 ] [partof: 0007141 ]
+0007055 = male meiosis II spindle assembly [isa: 0007053 ] [partof: 0007142 ]
+0000280 = nuclear division [partof: 0000279 ]
+0007126 = meiosis [isa: 0000280 ]
+0007143 = female meiosis [isa: 0007126 ]
+0007144 = female meiosis I [partof: 0007143 ]
+0007131 = meiotic recombination [isa: 0006310 ] [partof: 0007128 0007144 ]
+0042138 = meiotic DNA double-strand break formation [isa: 0000737 ] [partof: 0006311 0007131 ]
+0000706 = meiotic DNA double-strand break processing [partof: 0006311 0007131 ]
+0000707 = meiotic DNA recombinase assembly [partof: 0006311 0007131 ]
+0007146 = meiotic recombination nodule assembly [isa: 0000707 ]
+0042139 = early meiotic recombination nodule assembly [isa: 0007146 ]
+0042140 = late meiotic recombination nodule assembly [isa: 0007146 ]
+0000711 = meiotic DNA repair synthesis [partof: 0006311 0007131 ]
+0000709 = meiotic joint molecule formation [partof: 0007131 ]
+0000710 = meiotic mismatch repair [partof: 0006311 0007131 ]
+0000708 = meiotic strand invasion [partof: 0006311 0007131 ]
+0000712 = resolution of meiotic joint molecules as recombinants [partof: 0007131 ]
+0045128 = suppression of meiotic recombination [isa: 0007131 ]
+0007147 = female meiosis II [partof: 0007143 ]
+0016345 = female meiotic chromosome movement [isa: 0016344 ] [partof: 0007143 ]
+0040038 = polar body extrusion after meiotic divisions [partof: 0007143 ]
+0007140 = male meiosis [isa: 0007126 ]
+0007141 = male meiosis I [partof: 0007140 ]
+0007142 = male meiosis II [partof: 0007140 ]
+0016346 = male meiotic chromosome movement [isa: 0016344 ] [partof: 0007140 ]
+0007127 = meiosis I [partof: 0007126 ]
+0000705 = achiasmate meiosis I [isa: 0007127 ]
+0007133 = meiotic anaphase I [partof: 0007127 ]
+0016344 = meiotic chromosome movement [partof: 0007133 0007138 ]
+0008315 = meiotic G2/MI transition [partof: 0007127 ]
+0007132 = meiotic metaphase I [partof: 0007127 ]
+0007128 = meiotic prophase I [partof: 0007127 ]
+0000241 = diakinesis [partof: 0007128 ]
+0000240 = diplotene [partof: 0007128 ]
+0000237 = leptotene [partof: 0007128 ]
+0045141 = telomere clustering [partof: 0000237 ]
+0006311 = meiotic gene conversion [isa: 0006310 ] [partof: 0007128 ]
+0000713 = meiotic heteroduplex formation [partof: 0006311 ]
+0000714 = meiotic strand displacement [partof: 0006311 ]
+0000239 = pachytene [partof: 0007128 ]
+0000238 = zygotene [partof: 0007128 ]
+0007129 = synapsis [partof: 0000238 ]
+0007130 = synaptonemal complex formation [partof: 0007129 ]
+0007134 = meiotic telophase I [partof: 0007127 ]
+0007135 = meiosis II [isa: 0007126 ]
+0007138 = meiotic anaphase II [partof: 0007135 ]
+0007137 = meiotic metaphase II [partof: 0007135 ]
+0007136 = meiotic prophase II [partof: 0007135 ]
+0007139 = meiotic telophase II [partof: 0007135 ]
+0040020 = regulation of meiosis [partof: 0007126 ]
+0042061 = entry into meiosis [isa: 0040020 ]
+0045835 = negative regulation of meiosis [isa: 0040020 ]
+0045836 = positive regulation of meiosis [isa: 0040020 ]
+0000278 = mitotic cell cycle [isa: 0007049 ]
+0000080 = G1 phase of mitotic cell cycle [partof: 0000278 ]
+0000114 = G1-specific transcription in mitotic cell cycle [isa: 0006357 ] [partof: 0000080 ]
+0007089 = start control point of mitotic cell cycle [isa: 0000074 ] [partof: 0000080 ]
+0000082 = G1/S transition of mitotic cell cycle [partof: 0000278 ]
+0000083 = G1/S-specific transcription in mitotic cell cycle [isa: 0006357 ] [partof: 0000082 ]
+0000079 = regulation of CDK activity [isa: 0000074 ] [partof: 0000082 0000086 ]
+0045736 = negative regulation of CDK activity [isa: 0000079 0045786 ]
+0045737 = positive regulation of CDK activity [isa: 0000079 0045787 ]
+0000085 = G2 phase of mitotic cell cycle [partof: 0000278 ]
+0000116 = G2-specific transcription in mitotic cell cycle [isa: 0006357 ] [partof: 0000085 ]
+0000086 = G2/M transition of mitotic cell cycle [partof: 0000278 ]
+0000117 = G2/M-specific transcription in mitotic cell cycle [isa: 0006357 ] [partof: 0000086 ]
+0000216 = M/G1 transition of mitotic cell cycle [partof: 0000278 ]
+0045448 = mitotic cell cycle, embryonic [isa: 0000278 ]
+0009794 = regulation of mitotic cell cycle, embryonic [isa: 0007346 ] [partof: 0045448 ]
+0045976 = negative regulation of mitotic cell cycle, embryonic [isa: 0009794 0045930 ]
+0046001 = negative regulation of preblastoderm mitotic cell cycle [isa: 0007347 0045976 ]
+0046003 = negative regulation of syncytial blastoderm mitotic cell cycle [isa: 0007348 0045976 ]
+0045977 = positive regulation of mitotic cell cycle, embryonic [isa: 0009794 0045931 ]
+0046002 = positive regulation of preblastoderm mitotic cell cycle [isa: 0007347 0045977 ]
+0046004 = positive regulation of syncytial blastoderm mitotic cell cycle [isa: 0007348 0045977 ]
+0007347 = regulation of preblastoderm mitotic cell cycle [partof: 0009794 ]
+0007348 = regulation of syncytial blastoderm mitotic cell cycle [partof: 0009794 ]
+0007346 = regulation of mitotic cell cycle [isa: 0000074 ] [partof: 0000278 ]
+0045930 = negative regulation of mitotic cell cycle [isa: 0007346 0045786 ]
+0045749 = negative regulation of S phase of mitotic cell cycle [isa: 0007090 0045930 ]
+0045931 = positive regulation of mitotic cell cycle [isa: 0007346 0045787 ]
+0045750 = positive regulation of S phase of mitotic cell cycle [isa: 0007090 0045931 ]
+0007090 = regulation of S phase of mitotic cell cycle [partof: 0007346 ]
+0000084 = S phase of mitotic cell cycle [partof: 0000278 ]
+0000115 = S-specific transcription in mitotic cell cycle [isa: 0006357 ] [partof: 0000084 ]
+0007097 = nuclear migration [partof: 0007049 ]
+0000074 = regulation of cell cycle [partof: 0007049 ]
+0007050 = cell cycle arrest [isa: 0000074 ]
+0000075 = cell cycle checkpoint [isa: 0000074 ]
+0000078 = cell morphogenesis checkpoint [isa: 0000075 ]
+0000076 = DNA replication checkpoint [isa: 0000075 ]
+0000135 = septin checkpoint [isa: 0000075 ]
+0008054 = cyclin catabolism [isa: 0000074 0030163 ]
+0045786 = negative regulation of cell cycle [isa: 0000074 ]
+0045787 = positive regulation of cell cycle [isa: 0000074 ]
+0000320 = re-entry into mitotic cell cycle [isa: 0000074 ]
+0045023 = G0 to G1 transition [isa: 0000320 ]
+0000321 = re-entry into mitotic cell cycle after pheromone arrest [isa: 0000320 ]
+0020014 = schizogony [isa: 0007049 ]
+0016330 = second mitotic wave (sensu Drosophila) [isa: 0007049 ] [partof: 0007456 ]
+0016049 = cell growth [isa: 0008151 ]
+0001547 = antral ovarian follicle growth [isa: 0016049 ] [partof: 0001541 ]
+0001549 = ovarian cumulus cell differentiation [partof: 0001547 ]
+0045592 = regulation of ovarian cumulus cell differentiation [partof: 0001549 ]
+0045593 = negative regulation of ovarian cumulus cell differentiation [isa: 0045592 ]
+0045594 = positive regulation of ovarian cumulus cell differentiation [isa: 0045592 ]
+0001550 = ovarian cumulus expansion [partof: 0001547 ]
+0001548 = ovarian follicle antrum/follicular fluid formation [partof: 0001547 ]
+0009825 = cell expansion [isa: 0008361 0016049 ]
+0009826 = cell elongation [isa: 0009825 ]
+0042547 = cell wall modification during cell expansion [isa: 0042545 ] [partof: 0009825 ]
+0009831 = cell wall modification during cell expansion (sensu Magnoliophyta) [isa: 0009827 0042547 ]
+0001544 = initiation of primordial ovarian follicle growth [isa: 0016049 ] [partof: 0001541 ]
+0016475 = interpretation of nuclear/cytoplasmic ratio [isa: 0016049 ]
+0001557 = metabolism resulting in cell growth [isa: 0008152 ] [partof: 0016049 ]
+0001555 = oocyte growth [isa: 0016049 ] [partof: 0007292 ]
+0001546 = preantral ovarian follicle growth [isa: 0016049 ] [partof: 0001541 ]
+0001545 = primary ovarian follicle growth [isa: 0016049 ] [partof: 0001541 ]
+0001558 = regulation of cell growth [partof: 0016049 ]
+0001559 = interpretation of nuclear/cytoplasmic ratio to regulate cell growth [partof: 0001558 ]
+0030308 = negative regulation of cell growth [isa: 0001558 ]
+0030307 = positive regulation of cell growth [isa: 0001558 ]
+0006928 = cell motility [isa: 0008151 ]
+0016477 = cell migration [isa: 0006928 ]
+0001667 = ameboid cell migration [isa: 0016477 ]
+0042074 = cell migration during gastrulation [isa: 0016477 ] [partof: 0007369 ]
+0007297 = follicle cell migration [isa: 0016477 ] [partof: 0007292 ]
+0007298 = border cell migration [isa: 0007297 ]
+0008354 = germ-cell migration [isa: 0016477 ] [partof: 0007276 ]
+0008347 = glia cell migration [isa: 0016477 ] [partof: 0042063 ]
+0040039 = inductive cell migration [isa: 0016477 ]
+0008078 = mesoderm cell migration [isa: 0016477 ] [partof: 0007498 ]
+0007280 = pole cell migration [isa: 0016477 ] [partof: 0007277 ]
+0030334 = regulation of cell migration [partof: 0016477 ]
+0030336 = negative regulation of cell migration [isa: 0030334 ]
+0030335 = positive regulation of cell migration [isa: 0030334 ]
+0006929 = substrate-bound cell migration [isa: 0016477 ]
+0006934 = substrate-bound cell migration, adhesion receptor recycling [partof: 0006929 ]
+0006931 = substrate-bound cell migration, cell attachment to substrate [partof: 0006929 ]
+0006932 = substrate-bound cell migration, cell contraction [partof: 0006929 ]
+0006930 = substrate-bound cell migration, cell extension [partof: 0006929 ]
+0006933 = substrate-bound cell migration, cell release, from substrate [partof: 0006929 ]
+0007427 = tracheal cell migration [isa: 0016477 ] [partof: 0007424 ]
+0001539 = ciliary/flagellar motility [isa: 0006928 ]
+0006936 = muscle contraction [isa: 0006928 ]
+0030049 = muscle filament sliding [isa: 0030048 ] [partof: 0006936 ]
+0006937 = regulation of muscle contraction [partof: 0006936 ]
+0045932 = negative regulation of muscle contraction [isa: 0006937 ]
+0045986 = negative regulation of smooth muscle contraction [isa: 0006940 0045932 ]
+0045988 = negative regulation of striated muscle contraction [isa: 0006942 0045932 ]
+0045933 = positive regulation of muscle contraction [isa: 0006937 ]
+0045987 = positive regulation of smooth muscle contraction [isa: 0006940 0045933 ]
+0045989 = positive regulation of striated muscle contraction [isa: 0006942 0045933 ]
+0006940 = regulation of smooth muscle contraction [isa: 0006937 ] [partof: 0006939 ]
+0006942 = regulation of striated muscle contraction [isa: 0006937 ] [partof: 0006941 ]
+0006938 = sarcomere alignment [partof: 0006936 ]
+0006939 = smooth muscle contraction [isa: 0006936 ]
+0006941 = striated muscle contraction [isa: 0006936 ]
+0030317 = sperm motility [isa: 0006928 ]
+0016043 = cell organization and biogenesis [isa: 0008151 ]
+0030030 = cell surface structure organization and biogenesis [isa: 0016043 ]
+0042384 = cilium biogenesis [isa: 0030030 ]
+0009297 = fimbrial biogenesis [isa: 0030030 ]
+0009296 = flagella biogenesis [isa: 0030030 ]
+0042073 = intraflagellar transport [partof: 0009296 ]
+0030092 = regulation of flagella biosynthesis [isa: 0009889 ] [partof: 0009296 ]
+0045718 = negative regulation of flagella biosynthesis [isa: 0009890 0030092 ]
+0045724 = positive regulation of flagella biosynthesis [isa: 0009891 0030092 ]
+0030031 = formation of a cell surface projection [isa: 0030030 ]
+0030032 = lamellipodium formation [isa: 0030031 ]
+0030035 = microspike formation [isa: 0030031 ]
+0030033 = microvillus assembly [isa: 0030031 ]
+0030034 = microvillar actin bundle formation [partof: 0030033 ]
+0007028 = cytoplasm organization and biogenesis [isa: 0016043 ]
+0007044 = cell-substrate junction assembly [isa: 0007028 ]
+0007045 = hemi-adherens junction assembly [isa: 0007044 ]
+0045216 = intercellular junction assembly and/or maintenance [isa: 0007028 ]
+0007043 = intercellular junction assembly [isa: 0045216 ]
+0016264 = gap junction assembly [isa: 0007043 ]
+0019991 = septate junction assembly [isa: 0007043 ]
+0045186 = zonula adherens assembly [isa: 0007043 ]
+0045217 = intercellular junction maintenance [isa: 0045216 ]
+0045218 = zonula adherens maintenance [isa: 0045217 ]
+0006996 = organelle organization and biogenesis [isa: 0007028 ]
+0007010 = cytoskeleton organization and biogenesis [isa: 0006996 ]
+0030029 = actin filament-based process [isa: 0007010 ]
+0030036 = actin cytoskeleton organization and biogenesis [isa: 0030029 ]
+0000147 = actin cortical patch assembly [isa: 0030036 ]
+0007015 = actin filament organization [isa: 0030036 ]
+0045011 = actin cable assembly [isa: 0007015 ]
+0030038 = contractile actin filament bundle formation [isa: 0007015 ]
+0030240 = muscle thin filament assembly [isa: 0007015 ] [partof: 0030239 ]
+0030046 = parallel actin filament bundle formation [isa: 0007015 ]
+0008302 = ring canal formation, actin assembly [isa: 0007015 ] [partof: 0007301 ]
+0030047 = actin modification [isa: 0006464 0030036 ]
+0007014 = indirect flight muscle actin ubiquitination [isa: 0016567 0030047 ]
+0045010 = actin nucleation [isa: 0030036 ]
+0030048 = actin filament-based movement [isa: 0030029 ]
+0030050 = vesicle transport along actin filament [isa: 0030048 ]
+0008154 = actin polymerization and/or depolymerization [isa: 0030029 ]
+0030042 = actin filament depolymerization [isa: 0008154 ]
+0030043 = actin filament fragmentation [isa: 0030042 ]
+0030041 = actin filament polymerization [isa: 0008154 ]
+0008064 = regulation of actin polymerization and/or depolymerization [partof: 0008154 ]
+0030045 = actin filament destabilization [isa: 0008064 ]
+0030044 = actin filament stabilization [isa: 0008064 ]
+0045757 = negative regulation of actin polymerization and/or depolymerization [isa: 0008064 ]
+0045758 = positive regulation of actin polymerization and/or depolymerization [isa: 0008064 ]
+0007016 = cytoskeletal anchoring [partof: 0007010 ]
+0007163 = establishment and/or maintenance of cell polarity [isa: 0007010 ]
+0030467 = establishment and/or maintenance of cell polarity (sensu Fungi) [isa: 0007163 ]
+0030012 = establishment and/or maintenance of cell polarity (sensu Saccharomyces) [isa: 0030467 ]
+0000283 = establishment of cell polarity (sensu Saccharomyces) [isa: 0030012 0030468 ]
+0000284 = shmoo orientation [isa: 0000283 ] [partof: 0007332 ]
+0030013 = maintenance of cell polarity (sensu Saccharomyces) [isa: 0030012 0030469 ]
+0030468 = establishment of cell polarity (sensu Fungi) [isa: 0030010 0030467 ]
+0030469 = maintenance of cell polarity (sensu Fungi) [isa: 0030011 0030467 ]
+0045197 = establishment and/or maintenance of epithelial cell polarity [isa: 0007163 ]
+0045198 = establishment of epithelial cell polarity [isa: 0045197 ] [partof: 0030010 ]
+0045199 = maintenance of epithelial cell polarity [isa: 0045197 ] [partof: 0030011 ]
+0045196 = establishment and/or maintenance of neuroblast cell polarity [isa: 0007163 ]
+0045200 = establishment of neuroblast cell polarity [isa: 0045196 ] [partof: 0030010 ]
+0045201 = maintenance of neuroblast cell polarity [isa: 0045196 ] [partof: 0030011 ]
+0030010 = establishment of cell polarity [isa: 0007163 ]
+0042067 = establishment of ommatidial polarity (sensu Drosophila) [isa: 0007163 ] [partof: 0007456 ]
+0045317 = equator specification [partof: 0042067 ]
+0016318 = ommatidial rotation [partof: 0042067 ]
+0030011 = maintenance of cell polarity [isa: 0007163 ]
+0007164 = establishment of tissue polarity [isa: 0007010 ]
+0045103 = intermediate filament-based process [isa: 0007010 ]
+0045104 = intermediate filament cytoskeleton organization and biogenesis [isa: 0045103 ]
+0045109 = intermediate filament organization [isa: 0045104 ]
+0045110 = intermediate filament bundle assembly [isa: 0045109 ]
+0045105 = intermediate filament polymerization and/or depolymerization [isa: 0045103 ]
+0045106 = intermediate filament depolymerization [isa: 0045105 ]
+0045107 = intermediate filament polymerization [isa: 0045105 ]
+0045108 = regulation of intermediate filament polymerization and/or depolymerization [partof: 0045105 ]
+0045825 = negative regulation of intermediate filament polymerization and/or depolymerization [isa: 0045108 ]
+0045826 = positive regulation of intermediate filament polymerization and/or depolymerization [isa: 0045108 ]
+0007017 = microtubule-based process [isa: 0007010 ]
+0000226 = microtubule cytoskeleton organization and biogenesis [isa: 0007017 ]
+0001578 = microtubule bundling [partof: 0000226 ]
+0007020 = microtubule nucleation [isa: 0000226 ]
+0007021 = tubulin folding [isa: 0007020 ]
+0007024 = alpha-tubulin folding [isa: 0007021 ]
+0007025 = beta-tubulin folding [isa: 0007021 ]
+0007022 = chaperonin-mediated tubulin folding [isa: 0007021 ]
+0007023 = post-chaperonin tubulin folding pathway [isa: 0007021 ]
+0007026 = microtubule stabilization [isa: 0000226 ]
+0007027 = axonemal microtubule stabilization [isa: 0007026 ]
+0016325 = organization of the oocyte microtubule cytoskeleton [isa: 0000226 ] [partof: 0007308 ]
+0008103 = polarization of the oocyte microtubule cytoskeleton [isa: 0016325 ] [partof: 0007309 ]
+0007019 = microtubule depolymerization [isa: 0007017 ]
+0030444 = microtubule depolymerization during nuclear congression [isa: 0007019 ] [partof: 0006946 ]
+0007018 = microtubule-based movement [isa: 0007017 ]
+0008088 = axon cargo transport [isa: 0007018 ]
+0008089 = anterograde axon cargo transport [isa: 0008088 ]
+0019896 = axon transport of mitochondrion [isa: 0008088 ]
+0008090 = retrograde axon cargo transport [isa: 0008088 ]
+0007011 = regulation of cytoskeleton [isa: 0007010 ]
+0045802 = negative regulation of cytoskeleton [isa: 0007011 ]
+0045803 = positive regulation of cytoskeleton [isa: 0007011 ]
+0007032 = endosome organization and biogenesis [isa: 0006996 ]
+0016197 = endosome transport [isa: 0007032 0016192 ]
+0045022 = early endosome to late endosome transport [isa: 0016197 ]
+0008333 = endosome to lysosome transport [isa: 0007041 0016197 ]
+0006895 = Golgi to endosome transport [isa: 0006892 0016197 ]
+0045324 = late endosome to vacuole transport [isa: 0016197 ]
+0042147 = retrograde (endosome to Golgi) transport [isa: 0016197 ]
+0007029 = ER organization and biogenesis [isa: 0006996 ]
+0045047 = protein-ER targeting [isa: 0006605 0007029 ] [partof: 0045045 ]
+0045048 = ER insertion [isa: 0045047 ]
+0045052 = ER insertion by GPI attachment sequence [isa: 0045048 ]
+0045051 = ER insertion by internal uncleaved signal-anchor sequence [isa: 0045048 ]
+0045049 = ER insertion by N-terminal cleaved signal sequence [isa: 0045048 ]
+0045050 = ER insertion by stop-transfer membrane-anchor sequence [isa: 0045048 ]
+0006621 = ER retention [isa: 0045047 ]
+0045478 = fusome organization and biogenesis [isa: 0006996 ]
+0045479 = vesicle-fusome targeting [isa: 0045478 ]
+0007030 = Golgi organization and biogenesis [isa: 0006996 ]
+0000042 = protein-Golgi targeting [isa: 0006605 0007030 ] [partof: 0045045 ]
+0045053 = Golgi retention [isa: 0000042 ]
+0007040 = lysosome organization and biogenesis [isa: 0006996 ]
+0007042 = lysosomal lumen acidification [isa: 0006885 ] [partof: 0007040 ]
+0007041 = lysosomal transport [partof: 0007040 ]
+0006622 = protein-lysosome targeting [isa: 0006605 0007040 ]
+0016256 = N-glycan processing to lysosome [isa: 0006491 ] [partof: 0006622 ]
+0007005 = mitochondrion organization and biogenesis [isa: 0006996 ]
+0000266 = mitochondrial fission [isa: 0007005 ]
+0008053 = mitochondrial fusion [isa: 0007005 ]
+0007287 = Nebenkern formation [isa: 0008053 ] [partof: 0007286 ]
+0000002 = mitochondrial genome maintenance [isa: 0007005 ]
+0007006 = mitochondrial membrane organization and biogenesis [isa: 0007005 0016044 ]
+0007007 = inner mitochondrial membrane organization and biogenesis [isa: 0007006 ]
+0042407 = cristae formation [isa: 0007007 ]
+0045039 = mitochondrial inner membrane protein import [isa: 0006626 0007007 ]
+0007008 = outer mitochondrial membrane organization and biogenesis [isa: 0007006 ]
+0045040 = mitochondrial outer membrane protein import [isa: 0006626 0007008 ]
+0000001 = mitochondrion inheritance [isa: 0007005 ]
+0006626 = protein-mitochondrial targeting [isa: 0006605 0007005 ]
+0045041 = mitochondrial intermembrane space protein import [isa: 0006626 ]
+0045042 = conservative mitochondrial IMS protein import [isa: 0045041 ]
+0045044 = direct mitochondrial IMS protein import [isa: 0045041 ]
+0045043 = non-conservative mitochondrial IMS protein import [isa: 0045041 ]
+0030150 = mitochondrial matrix protein import [isa: 0006626 ]
+0006627 = mitochondrial processing [partof: 0006626 ]
+0006628 = mitochondrial translocation [partof: 0006626 ]
+0030382 = sperm mitochondrion organization and biogenesis [isa: 0007005 ]
+0007031 = peroxisome organization and biogenesis [isa: 0006996 ]
+0030242 = peroxisome degradation [isa: 0007031 ]
+0030398 = peroxisomal membrane degradation [isa: 0030397 ] [partof: 0030242 ]
+0016559 = peroxisome division [partof: 0007031 ]
+0045033 = peroxisome inheritance [isa: 0007031 ]
+0016557 = peroxisome membrane biogenesis [isa: 0016044 ] [partof: 0007031 ]
+0016560 = peroxisome receptor docking [partof: 0007031 ]
+0016562 = peroxisome receptor recycling [partof: 0007031 ]
+0016561 = peroxisome receptor translocation [partof: 0007031 ]
+0019817 = peroxisome vesicle fusion [partof: 0007031 ]
+0006625 = protein-peroxisome targeting [isa: 0006605 0007031 ]
+0016558 = peroxisome matrix protein import [isa: 0006625 ]
+0045046 = peroxisome membrane protein import [isa: 0006625 ]
+0007009 = plasma membrane organization and biogenesis [isa: 0006996 0016044 ]
+0045112 = integrin biosynthesis [isa: 0006412 0007009 ]
+0045114 = beta 2 integrin biosynthesis [isa: 0045112 ]
+0045115 = regulation of beta 2 integrin biosynthesis [isa: 0045113 ] [partof: 0045114 ]
+0045774 = negative regulation of beta 2 integrin biosynthesis [isa: 0045115 0045720 ]
+0045775 = positive regulation of beta 2 integrin biosynthesis [isa: 0045115 0045726 ]
+0045113 = regulation of integrin biosynthesis [isa: 0009889 ] [partof: 0045112 ]
+0045720 = negative regulation of integrin biosynthesis [isa: 0009890 0045113 ]
+0045726 = positive regulation of integrin biosynthesis [isa: 0009891 0045113 ]
+0017121 = phospholipid scrambling [isa: 0007009 ]
+0045332 = phospholipid translocation [isa: 0006644 0007009 0015914 ]
+0009663 = plasmodesma organization and biogenesis [isa: 0006996 ]
+0009657 = plastid organization and biogenesis [isa: 0006996 ]
+0009660 = amyloplast organization and biogenesis [isa: 0009657 ]
+0009658 = chloroplast organization and biogenesis [isa: 0009657 ]
+0009902 = chloroplast relocation [isa: 0009658 ]
+0009904 = chloroplast accumulation movement [isa: 0009902 ]
+0009903 = chloroplast avoidance movement [isa: 0009902 ]
+0045036 = protein-chloroplast targeting [isa: 0006605 0009658 ]
+0045037 = chloroplast stroma protein import [isa: 0045036 ]
+0045038 = chloroplast thylakoid protein import [isa: 0045036 ]
+0009661 = chromoplast organization and biogenesis [isa: 0009657 ]
+0009662 = etioplast organization and biogenesis [isa: 0009657 ]
+0009659 = leucoplast organization and biogenesis [isa: 0009657 ]
+0009665 = plastid inheritance [isa: 0009657 ]
+0009668 = plastid membrane organization and biogenesis [isa: 0016044 ] [partof: 0009657 ]
+0009667 = plastid inner membrane organization and biogenesis [isa: 0009668 ]
+0009666 = plastid outer membrane organization and biogenesis [isa: 0009668 ]
+0007033 = vacuole organization and biogenesis [isa: 0006996 ]
+0006623 = protein-vacuolar targeting [isa: 0006605 0007033 ]
+0006624 = vacuolar protein processing/maturation [partof: 0006623 ]
+0007034 = vacuolar transport [isa: 0007033 ]
+0007038 = delivery of endocytosed proteins to the vacuole [partof: 0007034 ]
+0045018 = retrograde transport from the vacuole [isa: 0007034 ]
+0007035 = vacuolar acidification [isa: 0006885 ] [partof: 0007034 ]
+0007037 = vacuolar phosphate transport [partof: 0007034 ]
+0007039 = vacuolar protein catabolism [isa: 0030163 ] [partof: 0007034 ]
+0042144 = vacuole fusion (non-autophagic) [isa: 0007033 ]
+0042146 = heterotypic vacuole fusion (non-autophagic) [isa: 0042144 ]
+0042145 = homotypic vacuole fusion (non-autophagic) [isa: 0042144 ]
+0000011 = vacuole inheritance [isa: 0007033 ]
+0016050 = vesicle organization and biogenesis [isa: 0006996 ]
+0042254 = ribosome biogenesis and assembly [isa: 0007028 ]
+0042255 = ribosome assembly [partof: 0042254 ]
+0042256 = mature ribosome assembly [isa: 0042255 ]
+0042257 = ribosomal subunit assembly [partof: 0042255 ]
+0000027 = ribosomal large subunit assembly and maintenance [isa: 0042257 ]
+0000028 = ribosomal small subunit assembly and maintenance [isa: 0042257 ]
+0007046 = ribosome biogenesis [partof: 0042254 ]
+0042273 = ribosomal large subunit biogenesis [partof: 0007046 ]
+0042274 = ribosomal small subunit biogenesis [partof: 0007046 ]
+0000054 = ribosome nucleus export [isa: 0007046 ] [partof: 0006611 ]
+0000055 = ribosomal large subunit nucleus export [isa: 0000054 ]
+0000056 = ribosomal small subunit nucleus export [isa: 0000054 ]
+0006364 = rRNA processing [isa: 0006396 ] [partof: 0006360 0007046 ]
+0006365 = 35S primary transcript processing [isa: 0006364 ]
+0030490 = processing of 20S pre-rRNA [isa: 0006364 ]
+0030489 = processing of 27S pre-rRNA [isa: 0006364 ]
+0045229 = external protective structure organization and biogenesis [isa: 0016043 ]
+0045230 = capsule organization and biogenesis [isa: 0045229 ]
+0045227 = capsule polysaccharide biosynthesis [isa: 0045226 0045230 ]
+0007047 = cell wall organization and biogenesis [isa: 0045229 ]
+0042546 = cell wall biosynthesis [isa: 0007047 ]
+0009273 = cell wall biosynthesis (sensu Bacteria) [isa: 0042546 ]
+0009252 = peptidoglycan biosynthesis [isa: 0000270 0016051 ] [partof: 0009273 ]
+0018104 = peptidoglycan-protein cross-linking [isa: 0009252 ]
+0019121 = peptidoglycan-protein cross-linking via N6-mureinyl-L-lysine [isa: 0018104 0018205 ]
+0019350 = teichoic acid biosynthesis [isa: 0016053 0019349 0046374 ] [partof: 0009273 ]
+0009272 = cell wall biosynthesis (sensu Fungi) [isa: 0042546 ]
+0006038 = cell wall chitin biosynthesis [isa: 0006031 ] [partof: 0009272 ]
+0009832 = cell wall biosynthesis (sensu Magnoliophyta) [isa: 0009664 0042546 ]
+0009833 = primary cell wall biosynthesis (sensu Magnoliophyta) [isa: 0009832 ]
+0009834 = secondary cell wall biosynthesis (sensu Magnoliophyta) [isa: 0009832 ]
+0000032 = cell wall mannoprotein biosynthesis [isa: 0006057 ] [partof: 0007047 ]
+0042545 = cell wall modification [isa: 0007047 ]
+0009827 = cell wall modification (sensu Magnoliophyta) [isa: 0009664 0042545 ]
+0009828 = cell wall loosening (sensu Magnoliophyta) [isa: 0009827 ]
+0009830 = cell wall modification during abscission [isa: 0009827 ] [partof: 0009838 ]
+0009829 = cell wall modification during ripening [isa: 0009827 ] [partof: 0009835 ]
+0009664 = cell wall organization and biogenesis (sensu Magnoliophyta) [isa: 0007047 ]
+0045232 = S-layer organization and biogenesis [isa: 0045229 ]
+0045231 = slime layer organization and biogenesis [isa: 0045229 ]
+0045228 = slime layer polysaccharide biosynthesis [isa: 0045226 0045231 ]
+0016044 = membrane organization and biogenesis [isa: 0016043 ]
+0030397 = membrane degradation [isa: 0016044 ]
+0006998 = nuclear membrane organization and biogenesis [isa: 0006997 0016044 ]
+0018985 = pronuclear envelope synthesis [isa: 0006998 ] [partof: 0007338 ]
+0006997 = nuclear organization and biogenesis [isa: 0016043 ]
+0007001 = chromosome organization and biogenesis (sensu Eukarya) [isa: 0006997 ]
+0006325 = establishment and/or maintenance of chromatin architecture [isa: 0006323 0007001 ]
+0006333 = chromatin assembly/disassembly [isa: 0006325 ]
+0006334 = nucleosome assembly [isa: 0006333 ]
+0006335 = DNA replication dependent nucleosome assembly [isa: 0006334 ]
+0006336 = DNA replication independent nucleosome assembly [isa: 0006334 ]
+0016584 = nucleosome spacing [isa: 0006334 0006337 ]
+0006337 = nucleosome disassembly [isa: 0006333 ]
+0001672 = regulation of chromatin assembly/disassembly [partof: 0006333 ]
+0045798 = negative regulation of chromatin assembly/disassembly [isa: 0001672 ]
+0045799 = positive regulation of chromatin assembly/disassembly [isa: 0001672 ]
+0016568 = chromatin modification [isa: 0006325 ]
+0016569 = covalent chromatin modification [isa: 0016568 ]
+0016570 = histone modification [isa: 0016569 ]
+0016573 = histone acetylation [isa: 0006473 0016570 ]
+0016575 = histone deacetylation [isa: 0006476 0016570 ]
+0016577 = histone demethylation [isa: 0006482 0016570 ]
+0016576 = histone dephosphorylation [isa: 0006470 0016570 ]
+0016578 = histone deubiquitination [isa: 0016570 0016579 ]
+0016571 = histone methylation [isa: 0006464 0016570 ]
+0016572 = histone phosphorylation [isa: 0006468 0016570 ]
+0016574 = histone ubiquitination [isa: 0016567 0016570 ]
+0006324 = S-phase regulated histone modification [isa: 0016570 ]
+0016582 = non-covalent chromatin modification [isa: 0016568 ]
+0006338 = chromatin modeling [isa: 0016582 ]
+0006341 = chromatin insulator sequence binding [isa: 0006338 ]
+0006342 = chromatin silencing [isa: 0006338 0016440 ]
+0000183 = chromatin silencing at ribosomal DNA (rDNA) [isa: 0006342 ]
+0030466 = chromatin silencing at silent mating type cassettes (sensu Fungi) [isa: 0006342 ]
+0006347 = chromatin silencing at HML and HMR (sensu Saccharomyces) [isa: 0030466 ]
+0006348 = chromatin silencing at telomere [isa: 0006342 ]
+0006343 = establishment of chromatin silencing [partof: 0006342 ]
+0006345 = loss of chromatin silencing [partof: 0006342 ]
+0006344 = maintenance of chromatin silencing [partof: 0006342 ]
+0006346 = methylation-dependent chromatin silencing [isa: 0006342 ]
+0045888 = regulation of transcription by homeotic gene (Polycomb group) [isa: 0006357 ] [partof: 0006338 ]
+0006340 = negative regulation of transcription by homeotic gene (Polycomb group) [isa: 0000122 0045888 ]
+0045889 = positive regulation of transcription by homeotic gene (Polycomb group) [isa: 0045888 0045944 ]
+0045890 = regulation of transcription by homeotic gene (trithorax group) [isa: 0006357 ] [partof: 0006338 ]
+0045891 = negative regulation of transcription by homeotic gene (trithorax group) [isa: 0000122 0045890 ]
+0006339 = positive regulation of transcription by homeotic gene (trithorax group) [isa: 0045890 0045944 ]
+0030575 = nuclear body organization and biogenesis [isa: 0006997 ]
+0030576 = Cajal body organization and biogenesis [isa: 0030575 ]
+0030577 = Lands organization and biogenesis [isa: 0030575 ]
+0030578 = PML body organization and biogenesis [isa: 0030575 ]
+0006999 = nuclear pore organization and biogenesis [isa: 0006997 ]
+0040023 = nuclear positioning [isa: 0006997 ]
+0017126 = nucleologenesis [isa: 0006997 ]
+0007000 = nucleolus organization and biogenesis [isa: 0006997 ]
+0008283 = cell proliferation [isa: 0008151 ]
+0042127 = regulation of cell proliferation [partof: 0008283 ]
+0008285 = negative regulation of cell proliferation [isa: 0042127 ]
+0008284 = positive regulation of cell proliferation [isa: 0042127 ]
+0006947 = cell-cell fusion [isa: 0008151 ]
+0007322 = mating (sensu Saccharomyces) [isa: 0006947 0030461 ]
+0007332 = shmooing [partof: 0007322 ]
+0000218 = zygote formation (sensu Saccharomyces) [isa: 0030462 ] [partof: 0007322 ]
+0007335 = karyogamy [partof: 0000218 ]
+0006946 = nuclear congression [partof: 0007335 ]
+0006945 = nuclear fusion during karyogamy [isa: 0006944 ] [partof: 0007335 ]
+0006949 = syncytium formation [isa: 0006947 ]
+0006948 = viral-induced cell-cell fusion [isa: 0006947 ]
+0006943 = chemi-mechanical coupling [isa: 0008151 ]
+0019725 = homeostasis [isa: 0008151 ]
+0042049 = acyl-CoA homeostasis [isa: 0006637 0019725 ]
+0001678 = glucose homeostasis [isa: 0019725 ]
+0006873 = ion homeostasis [isa: 0019725 ]
+0030002 = anion homeostasis [isa: 0006873 ]
+0030319 = di-, tri-valent inorganic anion homeostasis [isa: 0030002 ]
+0030643 = phosphate ion homeostasis [isa: 0030319 ]
+0030642 = sulfate ion homeostasis [isa: 0030319 ]
+0030320 = monovalent inorganic anion homeostasis [isa: 0030002 ]
+0030644 = chloride ion homeostasis [isa: 0030320 ]
+0030003 = cation homeostasis [isa: 0006873 ]
+0030005 = di-, tri-valent inorganic cation homeostasis [isa: 0030003 ]
+0006876 = cadmium homeostasis [isa: 0030005 0030006 ]
+0006874 = calcium ion homeostasis [isa: 0006875 0030005 ]
+0007036 = vacuolar calcium ion homeostasis [isa: 0006874 ]
+0006877 = cobalt homeostasis [isa: 0030005 0030006 ]
+0006878 = copper homeostasis [isa: 0030005 0030006 ]
+0006879 = iron homeostasis [isa: 0030005 0030006 ]
+0006881 = extracellular iron storage [isa: 0006879 ]
+0006880 = intracellular iron storage [isa: 0006879 ]
+0030026 = manganese homeostasis [isa: 0030005 0030006 ]
+0006882 = zinc homeostasis [isa: 0030005 0030006 ]
+0006875 = metal ion homeostasis [isa: 0030003 ]
+0030006 = heavy metal ion homeostasis [isa: 0006875 ]
+0030007 = potassium ion homeostasis [isa: 0006875 0030004 ]
+0006883 = sodium ion homeostasis [isa: 0006875 0030004 ]
+0030004 = monovalent inorganic cation homeostasis [isa: 0030003 ]
+0030641 = hydrogen ion homeostasis [isa: 0030004 ]
+0006885 = regulation of pH [isa: 0030641 ]
+0045851 = negative regulation of pH [isa: 0006885 ]
+0045852 = positive regulation of pH [isa: 0006885 ]
+0018987 = osmoregulation [isa: 0019725 ]
+0045454 = redox homeostasis [isa: 0019725 ]
+0030503 = regulation of redox homeostasis [partof: 0045454 ]
+0045867 = negative regulation of redox homeostasis [isa: 0030503 ]
+0045868 = positive regulation of redox homeostasis [isa: 0030503 ]
+0006884 = regulation of cell volume [isa: 0019725 ]
+0045794 = negative regulation of cell volume [isa: 0006884 ]
+0045795 = positive regulation of cell volume [isa: 0006884 ]
+0042391 = regulation of membrane potential [isa: 0019725 ]
+0045837 = negative regulation of membrane potential [isa: 0042391 ]
+0045838 = positive regulation of membrane potential [isa: 0042391 ]
+0030322 = stabilization of membrane potential [isa: 0042391 ]
+0001659 = thermoregulation [isa: 0007582 0019725 ]
+0042309 = homoiothermy [isa: 0001659 ]
+0006944 = membrane fusion [isa: 0008151 ]
+0016320 = ER fusion [isa: 0006944 ]
+0045026 = plasma membrane fusion [isa: 0006944 ]
+0019064 = viral envelope fusion [isa: 0006944 0019063 ]
+0008152 = metabolism [isa: 0008151 ]
+0006066 = alcohol metabolism [isa: 0008152 ]
+0046165 = alcohol biosynthesis [isa: 0006066 0009058 ]
+0009713 = catechol biosynthesis [isa: 0009699 0009712 0046165 ]
+0046235 = gallate biosynthesis [isa: 0009713 0018918 ]
+0046277 = methylgallate biosynthesis [isa: 0019489 0046235 ]
+0046279 = protocatechuate biosynthesis [isa: 0009713 0046278 ]
+0006115 = ethanol biosynthesis [isa: 0006067 0046165 ] [partof: 0006113 ]
+0006715 = farnesol biosynthesis [isa: 0016106 0016487 0046165 ]
+0046295 = glycolate biosynthesis [isa: 0009441 0046165 ]
+0046169 = methanol biosynthesis [isa: 0015945 0019753 0046165 ]
+0046364 = monosaccharide biosynthesis [isa: 0005996 0016051 0046165 ]
+0019319 = hexose biosynthesis [isa: 0019318 0046364 ]
+0046366 = allose biosynthesis [isa: 0019313 0019319 ]
+0019315 = D-allose biosynthesis [isa: 0019314 0046366 ]
+0046370 = fructose biosynthesis [isa: 0006000 0019319 ]
+0042353 = fucose biosynthesis [isa: 0006004 0019319 ]
+0006005 = L-fucose biosynthesis [isa: 0042353 0042354 ]
+0042350 = GDP-L-fucose biosynthesis [isa: 0006005 0009226 0046368 ]
+0042351 = GDP-L-fucose biosynthesis, de novo pathway [isa: 0042350 ]
+0042352 = GDP-L-fucose biosynthesis, salvage pathway [isa: 0042350 ]
+0046369 = galactose biosynthesis [isa: 0006012 0019319 ]
+0006094 = gluconeogenesis [isa: 0006006 0006093 0019319 ]
+0006111 = regulation of gluconeogenesis [isa: 0006109 0009889 ] [partof: 0006094 ]
+0045721 = negative regulation of gluconeogenesis [isa: 0006111 0009890 0045912 ]
+0045722 = positive regulation of gluconeogenesis [isa: 0006111 0009891 0045913 ]
+0019307 = mannose biosynthesis [isa: 0006013 0019319 ]
+0019308 = dTDP-mannose biosynthesis [isa: 0019307 0046371 ]
+0009298 = GDP-mannose biosynthesis [isa: 0009226 0019307 0019673 ]
+0006021 = myo-inositol biosynthesis [isa: 0006020 0019319 ]
+0019300 = rhamnose biosynthesis [isa: 0019299 0019319 ]
+0019305 = dTDP-rhamnose biosynthesis [isa: 0019300 0046383 ]
+0019306 = GDP-D-rhamnose biosynthesis [isa: 0006002 0006013 0019300 0046382 ]
+0019322 = pentose biosynthesis [isa: 0019321 0046364 ]
+0019567 = arabinose biosynthesis [isa: 0019322 0019566 ]
+0046362 = ribitol biosynthesis [isa: 0019322 0019349 0019526 ]
+0019302 = ribose biosynthesis [isa: 0006014 0019322 ]
+0046385 = deoxyribose phosphate biosynthesis [isa: 0019302 0019692 ]
+0006016 = 2-deoxyribose 1-phosphate biosynthesis [isa: 0046384 0046385 ]
+0006017 = deoxyribose 1,5-bisphosphate biosynthesis [isa: 0046385 0046387 ]
+0046390 = ribose phosphate biosynthesis [isa: 0019302 0019693 ]
+0006015 = 5-phosphoribose 1-diphosphate biosynthesis [isa: 0046390 0046391 ]
+0005999 = xylulose biosynthesis [isa: 0005997 0019322 ]
+0046171 = octanol biosynthesis [isa: 0006070 0046165 ]
+0046197 = orcinol biosynthesis [isa: 0018940 0019438 0046165 ]
+0046189 = phenol biosynthesis [isa: 0018958 0019438 0046165 ]
+0046190 = aerobic phenol biosynthesis [isa: 0018959 0046189 ]
+0046192 = anaerobic phenol biosynthesis [isa: 0042215 0046189 ]
+0046173 = polyol biosynthesis [isa: 0019751 0046165 ]
+0019401 = alditol biosynthesis [isa: 0016051 0019400 0046173 ]
+0019406 = hexitol biosynthesis [isa: 0006059 0019401 ]
+0019403 = galactitol biosynthesis [isa: 0019402 0019406 ]
+0019593 = mannitol biosynthesis [isa: 0019406 0019594 ]
+0006061 = sorbitol biosynthesis [isa: 0006060 0019406 ]
+0019526 = pentitol biosynthesis [isa: 0019401 0019519 ]
+0006114 = glycerol biosynthesis [isa: 0006071 0046173 ] [partof: 0006113 ]
+0046327 = glycerol biosynthesis from pyruvate [isa: 0006114 ] [partof: 0019432 ]
+0046167 = glycerol-3-phosphate biosynthesis [isa: 0006072 0006114 ]
+0046164 = alcohol catabolism [isa: 0006066 0009056 ]
+0019614 = catechol catabolism [isa: 0009712 0046164 0046271 ]
+0019616 = catechol 'meta-cleavage' [isa: 0019614 ]
+0019615 = catechol 'ortho-cleavage' [isa: 0019614 ]
+0019396 = gallate catabolism [isa: 0018918 0019614 ]
+0042195 = aerobic gallate catabolism [isa: 0019396 ]
+0019397 = gallate catabolism, via 2-pyrone-4,6-dicarboxylate [isa: 0042195 ]
+0019398 = gallate catabolism, via 4-carboxy-2-hydroxhexa-2,3-dienedioate [isa: 0042195 ]
+0019328 = anaerobic gallate catabolism [isa: 0019396 ]
+0046276 = methylgallate catabolism [isa: 0019396 0019489 ]
+0019619 = protocatechuate catabolism [isa: 0019614 0046278 ]
+0019617 = protocatechuate 'meta-cleavage' [isa: 0019619 ]
+0019618 = protocatechuate 'ortho-cleavage' [isa: 0019619 ]
+0006068 = ethanol catabolism [isa: 0006067 0046164 ]
+0016488 = farnesol catabolism [isa: 0016107 0016487 0046164 ]
+0046296 = glycolate catabolism [isa: 0009441 0046164 ]
+0046170 = methanol catabolism [isa: 0015945 0019754 0046164 ]
+0046365 = monosaccharide catabolism [isa: 0005996 0016052 0046164 ]
+0019320 = hexose catabolism [isa: 0019318 0046365 ]
+0046367 = allose catabolism [isa: 0019313 0019320 ]
+0019316 = D-allose catabolism [isa: 0019314 0046367 ]
+0006001 = fructose catabolism [isa: 0006000 0019320 ]
+0019576 = aerobic fructose catabolism [isa: 0006001 ]
+0019325 = anaerobic fructose catabolism [isa: 0006001 0019317 ]
+0019317 = fucose catabolism [isa: 0006004 0019320 ]
+0042355 = L-fucose catabolism [isa: 0019317 0042354 ]
+0019388 = galactose catabolism [isa: 0006012 0019320 ]
+0006007 = glucose catabolism [isa: 0006006 0019320 ]
+0006096 = glycolysis [isa: 0006007 0006095 ]
+0019642 = anaerobic glycolysis [isa: 0006096 ]
+0019641 = Embden-Meyerhof pathway [isa: 0006096 ]
+0019595 = non-phosphorylated glucose catabolism [isa: 0006007 0046430 ]
+0006098 = pentose-phosphate shunt [isa: 0006007 0006095 0006740 ]
+0009052 = pentose-phosphate shunt, non-oxidative branch [partof: 0006098 ]
+0009051 = pentose-phosphate shunt, oxidative branch [partof: 0006098 ]
+0019309 = mannose catabolism [isa: 0006013 0019320 ]
+0019310 = myo-inositol catabolism [isa: 0006020 0019320 ]
+0019301 = rhamnose catabolism [isa: 0019299 0019320 ]
+0019304 = anaerobic rhamnose catabolism [isa: 0019301 ]
+0019323 = pentose catabolism [isa: 0019321 0046365 ]
+0019568 = arabinose catabolism [isa: 0019323 0019566 ]
+0019571 = D-arabinose catabolism [isa: 0019568 0046372 ]
+0019573 = D-arabinose catabolism to xylulose 5-phosphate [isa: 0019571 ]
+0019572 = L-arabinose catabolism [isa: 0019568 0046373 ]
+0019570 = L-arabinose catabolism to 2-oxoglutarate [isa: 0006103 0019572 ]
+0019569 = L-arabinose catabolism to xylulose 5-phosphate [isa: 0019572 ]
+0046363 = ribitol catabolism [isa: 0019323 0019349 0019527 ]
+0019303 = ribose catabolism [isa: 0006014 0019323 ]
+0046386 = deoxyribose phosphate catabolism [isa: 0019303 0019692 ]
+0006018 = deoxyribose 1-phosphate catabolism [isa: 0046386 0046388 ]
+0005998 = xylulose catabolism [isa: 0005997 0019323 ]
+0046172 = octanol catabolism [isa: 0006070 0046164 ]
+0042209 = orcinol catabolism [isa: 0018940 0019439 0046164 ]
+0019336 = phenol catabolism [isa: 0018958 0019439 0046164 ]
+0046191 = aerobic phenol catabolism [isa: 0018959 0019336 ]
+0046193 = anaerobic phenol catabolism [isa: 0019336 0042215 ]
+0046174 = polyol catabolism [isa: 0019751 0046164 ]
+0019405 = alditol catabolism [isa: 0016052 0019400 0046174 ]
+0019407 = hexitol catabolism [isa: 0006059 0019405 ]
+0019404 = galactitol catabolism [isa: 0019402 0019407 ]
+0019592 = mannitol catabolism [isa: 0019407 0019594 ]
+0006062 = sorbitol catabolism [isa: 0006060 0019407 ]
+0019527 = pentitol catabolism [isa: 0019405 0019519 ]
+0019591 = arabitol utilization [isa: 0019527 ]
+0019528 = D-arabitol utilization [isa: 0019591 ]
+0019590 = L-arabitol utilization [isa: 0019591 ]
+0019697 = L-xylitol utilization [isa: 0019527 ]
+0019563 = glycerol catabolism [isa: 0006071 0046174 ]
+0019564 = aerobic glycerol catabolism [isa: 0019563 ]
+0019565 = aerobic glycerol fermentation [isa: 0019563 0019588 ]
+0046168 = glycerol-3-phosphate catabolism [isa: 0006072 0019563 ]
+0009712 = catechol metabolism [isa: 0006066 0009698 ]
+0018918 = gallate metabolism [isa: 0009712 ]
+0019489 = methylgallate metabolism [isa: 0018918 ]
+0046278 = protocatechuate metabolism [isa: 0009712 ]
+0006067 = ethanol metabolism [isa: 0006066 ]
+0019431 = acetyl-CoA biosynthesis from ethanol [isa: 0006067 0006085 ]
+0019655 = ethanol fermentation [isa: 0006067 0019660 ]
+0006069 = ethanol oxidation [isa: 0006067 ]
+0016487 = farnesol metabolism [isa: 0006066 0006714 ]
+0009441 = glycolate metabolism [isa: 0006066 ]
+0015945 = methanol metabolism [isa: 0006066 0006730 ]
+0015946 = methanol oxidation [isa: 0015945 ]
+0005996 = monosaccharide metabolism [isa: 0005975 0006066 ]
+0019318 = hexose metabolism [isa: 0005996 ]
+0019313 = allose metabolism [isa: 0019318 ]
+0019314 = D-allose metabolism [isa: 0019313 ]
+0006000 = fructose metabolism [isa: 0019318 ]
+0030388 = fructose 1,6-bisphosphate metabolism [isa: 0006000 ]
+0006003 = fructose 2,6-bisphosphate metabolism [isa: 0006000 ]
+0006002 = fructose 6-phosphate metabolism [isa: 0006000 ]
+0006004 = fucose metabolism [isa: 0019318 ]
+0042354 = L-fucose metabolism [isa: 0006004 ]
+0046368 = GDP-L-fucose metabolism [isa: 0042354 ]
+0006012 = galactose metabolism [isa: 0019318 ]
+0006006 = glucose metabolism [isa: 0019318 ]
+0019255 = glucose 1-phosphate metabolism [isa: 0006006 ]
+0006009 = glucose 1-phosphate phosphorylation [isa: 0016310 0019255 ]
+0006008 = glucose 1-phosphate utilization [isa: 0019255 ]
+0006010 = glucose 6-phosphate utilization [isa: 0006006 ]
+0046430 = non-phosphorylated glucose metabolism [isa: 0006006 ]
+0006011 = UDP-glucose metabolism [isa: 0006006 ]
+0006013 = mannose metabolism [isa: 0019318 ]
+0046371 = dTDP-mannose metabolism [isa: 0006013 ]
+0019673 = GDP-mannose metabolism [isa: 0006013 ]
+0006020 = myo-inositol metabolism [isa: 0019318 ]
+0019299 = rhamnose metabolism [isa: 0019318 ]
+0046383 = dTDP-rhamnose metabolism [isa: 0019299 ]
+0046382 = GDP-D-rhamnose metabolism [isa: 0019299 ]
+0019311 = sorbose metabolism [isa: 0019318 ]
+0019312 = L-sorbose metabolism [isa: 0019311 ]
+0019321 = pentose metabolism [isa: 0005996 ]
+0019566 = arabinose metabolism [isa: 0019321 ]
+0046372 = D-arabinose metabolism [isa: 0019566 ]
+0046373 = L-arabinose metabolism [isa: 0019566 ]
+0019324 = L-lyxose metabolism [isa: 0019321 ]
+0019349 = ribitol metabolism [isa: 0019321 0019519 ]
+0019488 = ribitol utilization [isa: 0019349 ]
+0006014 = ribose metabolism [isa: 0019321 ]
+0019692 = deoxyribose phosphate metabolism [isa: 0006014 ]
+0046384 = 2-deoxyribose 1-phosphate metabolism [isa: 0019692 ]
+0046387 = deoxyribose 1,5-bisphosphate metabolism [isa: 0019692 ]
+0046388 = deoxyribose 1-phosphate metabolism [isa: 0019692 ]
+0046389 = deoxyribose 5-phosphate metabolism [isa: 0019692 ]
+0006019 = deoxyribose 5-phosphate phosphorylation [isa: 0016310 0046389 ]
+0019693 = ribose phosphate metabolism [isa: 0006014 ]
+0046391 = 5-phosphoribose 1-diphosphate metabolism [isa: 0019693 ]
+0005997 = xylulose metabolism [isa: 0019321 ]
+0006070 = octanol metabolism [isa: 0006066 ]
+0018940 = orcinol metabolism [isa: 0006066 0006725 ]
+0018958 = phenol metabolism [isa: 0006066 0006725 ]
+0018959 = aerobic phenol metabolism [isa: 0018958 ]
+0042215 = anaerobic phenol metabolism [isa: 0018958 ]
+0019751 = polyol metabolism [isa: 0006066 ]
+0019400 = alditol metabolism [isa: 0005975 0019751 ]
+0006059 = hexitol metabolism [isa: 0019400 ]
+0019402 = galactitol metabolism [isa: 0006059 ]
+0019594 = mannitol metabolism [isa: 0006059 ]
+0006060 = sorbitol metabolism [isa: 0006059 ]
+0019519 = pentitol metabolism [isa: 0019400 ]
+0006071 = glycerol metabolism [isa: 0019751 ] [partof: 0006641 ]
+0019588 = glycerol fermentation [isa: 0006071 0019662 ]
+0019589 = glycerol fermentation to propane-1,3-diol [isa: 0019588 ]
+0006072 = glycerol-3-phosphate metabolism [isa: 0006071 ]
+0006670 = sphingosine metabolism [isa: 0006066 0009308 0046519 ]
+0046512 = sphingosine biosynthesis [isa: 0006670 0046520 ]
+0006081 = aldehyde metabolism [isa: 0008152 ]
+0006117 = acetaldehyde metabolism [isa: 0006081 ]
+0046186 = acetaldehyde biosynthesis [isa: 0006117 0046184 ]
+0046187 = acetaldehyde catabolism [isa: 0006117 0046185 ]
+0046184 = aldehyde biosynthesis [isa: 0006081 0009058 ]
+0046293 = formaldehyde biosynthesis [isa: 0046184 0046292 ]
+0046166 = glyceraldehyde-3-phosphate biosynthesis [isa: 0019682 0046184 ]
+0006634 = hexadecanal biosynthesis [isa: 0046184 0046458 ]
+0019242 = methylglyoxal biosynthesis [isa: 0009438 0046184 ]
+0046185 = aldehyde catabolism [isa: 0006081 0009056 ]
+0046294 = formaldehyde catabolism [isa: 0046185 0046292 ]
+0019683 = glyceraldehyde-3-phosphate catabolism [isa: 0019682 0046185 ]
+0009436 = glyoxylate catabolism [isa: 0046185 0046395 0046487 ]
+0019243 = methylglyoxal catabolism [isa: 0009438 0046185 ]
+0046292 = formaldehyde metabolism [isa: 0006081 ]
+0019649 = formaldehyde assimilation [isa: 0046292 ]
+0019647 = formaldehyde assimilation via ribulose-monophosphate cycle [isa: 0019649 ]
+0019648 = formaldehyde assimilation via xylulose-monophosphate cycle [isa: 0019649 ]
+0019682 = glyceraldehyde-3-phosphate metabolism [isa: 0006081 ]
+0046487 = glyoxylate metabolism [isa: 0006081 0019752 ]
+0006097 = glyoxylate cycle [isa: 0006095 0046487 ]
+0046458 = hexadecanal metabolism [isa: 0006081 ]
+0009438 = methylglyoxal metabolism [isa: 0006081 ]
+0019248 = D-lactate biosynthesis from methylglyoxal [isa: 0009438 0019249 ]
+0009308 = amine metabolism [isa: 0008152 ]
+0018871 = 1-aminocyclopropane-1-carboxylate metabolism [isa: 0006575 0009308 ]
+0009309 = amine biosynthesis [isa: 0009058 0009308 ]
+0008652 = amino acid biosynthesis [isa: 0006520 0009309 ]
+0009073 = aromatic amino acid family biosynthesis [isa: 0008652 0009072 0019438 ]
+0009096 = aromatic amino acid family biosynthesis, anthranilate pathway [isa: 0009073 ]
+0000162 = tryptophan biosynthesis [isa: 0006568 0009096 0046219 ]
+0009095 = aromatic amino acid family biosynthesis, prephenate pathway [isa: 0009073 ]
+0009423 = chorismate biosynthesis [isa: 0009095 0016089 0046394 0046417 ]
+0019275 = phenylalanine biosynthesis, shikimate pathway [isa: 0009094 0009423 ]
+0006571 = tyrosine biosynthesis [isa: 0006570 0009423 ]
+0019292 = tyrosine biosynthesis from chorismate via 4-hydroxyphenylpyruvate [isa: 0006571 ]
+0019291 = tyrosine biosynthesis from chorismate via phenylalanine [isa: 0006571 ]
+0019293 = tyrosine biosynthesis, by oxidation of phenylalanine [isa: 0006571 ]
+0019274 = phenylalanine biosynthesis, prephenate pathway [isa: 0009094 0009095 ]
+0016089 = aromatic amino acid family biosynthesis, shikimate pathway [isa: 0009073 ] [partof: 0009698 ]
+0019632 = shikimate metabolism [isa: 0016089 ]
+0019633 = shikimate catabolism [isa: 0019632 ]
+0019540 = siderochrome biosynthesis from catechol [isa: 0016089 0019290 ]
+0009239 = enterobactin biosynthesis [isa: 0009238 0019540 ]
+0019289 = rhizobactin 1021 biosynthesis [isa: 0019540 0046494 ]
+0019537 = vibriobactin biosynthesis [isa: 0019536 0019540 ]
+0009094 = phenylalanine biosynthesis [isa: 0006558 0009073 ]
+0009067 = aspartate family amino acid biosynthesis [isa: 0008652 0009066 ]
+0006529 = asparagine biosynthesis [isa: 0006528 0009067 0009068 ]
+0019267 = asparagine biosynthesis from cysteine [isa: 0006529 0006534 ]
+0019266 = asparagine biosynthesis from oxaloacetate [isa: 0006529 ]
+0006532 = aspartate biosynthesis [isa: 0006531 0009067 ]
+0009085 = lysine biosynthesis [isa: 0006553 0009067 ]
+0019270 = aerobactin biosynthesis [isa: 0009085 0042398 0046442 ]
+0019878 = lysine biosynthesis, aminoadipic pathway [isa: 0009085 ]
+0009089 = lysine biosynthesis, via diaminopimelate [isa: 0009085 ]
+0019877 = diaminopimelate biosynthesis [isa: 0046394 0046451 ] [partof: 0009089 ]
+0009086 = methionine biosynthesis [isa: 0000097 0006555 0009067 ]
+0019279 = methionine biosynthesis from L-homoserine via cystathione [isa: 0009086 ]
+0019280 = methionine biosynthesis from homoserine via O-acetyl-L-homoserine and cystathione [isa: 0019279 ]
+0019281 = methionine biosynthesis from homoserine via O-succinyl-L-homoserine and cystathione [isa: 0019279 ]
+0019283 = methionine biosynthesis from O-phospho-L-homoserine and cystathione [isa: 0009086 ]
+0019284 = methionine biosynthesis from S-adenosylmethionine [isa: 0009086 ]
+0019282 = methionine biosynthesis, direct, from O-acetyl-L-homoserine [isa: 0009086 ]
+0009088 = threonine biosynthesis [isa: 0006566 0009067 ]
+0009082 = branched chain family amino acid biosynthesis [isa: 0008652 0009081 ]
+0009097 = isoleucine biosynthesis [isa: 0006549 0009082 ]
+0009098 = leucine biosynthesis [isa: 0006551 0009082 ]
+0009099 = valine biosynthesis [isa: 0006573 0009082 ]
+0009084 = glutamine family amino acid biosynthesis [isa: 0008652 0009064 ]
+0006526 = arginine biosynthesis [isa: 0006525 0009084 ]
+0042450 = arginine biosynthesis, via ornithine [isa: 0006526 0006591 ]
+0006537 = glutamate biosynthesis [isa: 0006536 0009084 ]
+0019268 = glutamate biosynthesis, via glutamate dehydrogenase (NAD(P)+) [isa: 0006537 ]
+0019269 = glutamate biosynthesis, via glutamate synthase (NADPH) [isa: 0006537 ]
+0006542 = glutamine biosynthesis [isa: 0006541 0009084 ]
+0006561 = proline biosynthesis [isa: 0006542 0006560 ]
+0009076 = histidine family amino acid biosynthesis [isa: 0008652 0009075 ]
+0000105 = histidine biosynthesis [isa: 0006547 0009076 ]
+0019795 = non-protein amino acid biosynthesis [isa: 0008652 0019794 ]
+0019483 = beta-alanine biosynthesis [isa: 0019482 0019795 ]
+0006592 = ornithine biosynthesis [isa: 0006591 0019795 ]
+0009079 = pyruvate family amino acid biosynthesis [isa: 0008652 0009078 ]
+0006523 = alanine biosynthesis [isa: 0006522 0009079 ]
+0019272 = alanine biosynthesis from pyruvate [isa: 0006523 ]
+0019273 = alanine biosynthesis, via ornithine [isa: 0006523 0006591 ]
+0046145 = D-alanine family amino acid biosynthesis [isa: 0006523 0046144 ]
+0030632 = D-alanine biosynthesis [isa: 0046145 0046436 0046437 ]
+0009070 = serine family amino acid biosynthesis [isa: 0008652 0009069 ]
+0019344 = cysteine biosynthesis [isa: 0000097 0006534 0009070 ]
+0006535 = cysteine biosynthesis from serine [isa: 0019344 ]
+0019343 = cysteine biosynthesis, via cystathione [isa: 0019344 ]
+0019345 = cysteine biosynthesis, via S-sulfo-L-cysteine [isa: 0019344 ]
+0006545 = glycine biosynthesis [isa: 0006544 0009070 ]
+0019264 = glycine biosynthesis from serine [isa: 0006545 ]
+0019265 = glycine biosynthesis, by transamination of glyoxylate [isa: 0006545 ]
+0009090 = homoserine biosynthesis [isa: 0009070 0009092 ]
+0016260 = selenocysteine biosynthesis [isa: 0000097 0009070 0016259 ]
+0006564 = serine biosynthesis [isa: 0006563 0009070 ]
+0000097 = sulfur amino acid biosynthesis [isa: 0000096 0008652 ]
+0019509 = methionine recycling [isa: 0000097 0006555 ]
+0006556 = S-adenosylmethionine biosynthesis [isa: 0000098 0046500 ] [partof: 0000097 0006730 ]
+0042401 = biogenic amine biosynthesis [isa: 0006576 0009309 0042398 ]
+0006578 = betaine biosynthesis [isa: 0006577 0042401 ]
+0019285 = betaine biosynthesis from choline [isa: 0006578 0019695 ]
+0019286 = betaine biosynthesis from glycine [isa: 0006578 ]
+0045329 = carnitine biosynthesis [isa: 0009437 0042401 ]
+0042423 = catecholamine biosynthesis [isa: 0006584 0042401 ]
+0042425 = choline biosynthesis [isa: 0019695 0042401 ]
+0046335 = ethanolamine biosynthesis [isa: 0006580 0042401 ]
+0006646 = phosphatidylethanolamine biosynthesis [isa: 0046335 0046337 ]
+0006648 = dihydrosphingosine-1-P pathway [isa: 0006646 ]
+0006647 = phosphatidyl-N-monomethylethanolamine biosynthesis [isa: 0006646 0046468 ]
+0046219 = indolalkylamine biosynthesis [isa: 0006586 0042401 0042435 ]
+0030187 = melatonin biosynthesis [isa: 0030186 0042446 0046219 ]
+0030418 = nicotianamine biosynthesis [isa: 0030417 0042401 ]
+0006596 = polyamine biosynthesis [isa: 0006595 0042401 ]
+0009446 = putrescine biosynthesis [isa: 0006596 0009445 ]
+0008295 = spermidine biosynthesis [isa: 0006596 0008216 ]
+0045312 = nor-spermidine biosynthesis [isa: 0008295 0046204 ]
+0019342 = trypanothione biosynthesis [isa: 0008295 0046206 ]
+0006597 = spermine biosynthesis [isa: 0006596 0008215 ]
+0009310 = amine catabolism [isa: 0009056 0009308 ]
+0009063 = amino acid catabolism [isa: 0006520 0009310 ]
+0009074 = aromatic amino acid family catabolism [isa: 0009063 0009072 0019439 ]
+0006559 = phenylalanine catabolism [isa: 0006558 0009074 ]
+0019561 = anaerobic phenylalanine oxidation [isa: 0006559 ]
+0019562 = phenylalanine catabolism to phosphoenolpyruvate [isa: 0006559 ]
+0006569 = tryptophan catabolism [isa: 0006568 0009074 0046218 ]
+0019442 = tryptophan catabolism to acetyl-CoA [isa: 0006569 ]
+0019444 = tryptophan catabolism to catechol [isa: 0006569 ]
+0019440 = tryptophan catabolism to indole-3-acetate [isa: 0006569 0009683 ]
+0019441 = tryptophan catabolism to kynurenine [isa: 0006569 ]
+0019443 = tryptophan catabolism, using tryptophanase [isa: 0006569 ]
+0006572 = tyrosine catabolism [isa: 0006570 0009074 ]
+0019445 = tyrosine catabolism to fumarate [isa: 0006572 ]
+0019446 = tyrosine catabolism to phosphoenolpyruvate [isa: 0006572 ]
+0009068 = aspartate family amino acid catabolism [isa: 0009063 0009066 ]
+0006533 = aspartate catabolism [isa: 0006531 0009068 ]
+0019465 = aspartate transamidation [isa: 0006533 ]
+0006554 = lysine catabolism [isa: 0006553 0009068 ]
+0019476 = D-lysine catabolism [isa: 0006554 0019478 0046441 ]
+0019477 = L-lysine catabolism [isa: 0006554 0046440 ]
+0019475 = L-lysine catabolism to acetate [isa: 0019477 0019665 ]
+0019474 = L-lysine catabolism to acetyl-CoA [isa: 0019477 ]
+0019473 = L-lysine catabolism to glutarate, by acetylation [isa: 0019477 ]
+0009087 = methionine catabolism [isa: 0000098 0006555 0009068 ]
+0019457 = methionine catabolism to succinyl-CoA [isa: 0009087 ]
+0019458 = methionine catabolism, via 2-oxobutanoate [isa: 0009087 ]
+0006567 = threonine catabolism [isa: 0006566 0009068 ]
+0019517 = threonine catabolism to D-lactate [isa: 0006089 0006567 ]
+0019518 = threonine catabolism to pyruvate [isa: 0006567 ]
+0009083 = branched chain family amino acid catabolism [isa: 0009063 0009081 ]
+0006550 = isoleucine catabolism [isa: 0006549 0009083 ]
+0006552 = leucine catabolism [isa: 0006551 0009083 ]
+0006574 = valine catabolism [isa: 0006573 0009083 ]
+0019478 = D-amino acid catabolism [isa: 0009063 0046416 ]
+0019447 = D-cysteine catabolism [isa: 0009093 0019478 0046438 ]
+0009065 = glutamine family amino acid catabolism [isa: 0009063 0009064 ]
+0006527 = arginine catabolism [isa: 0006525 0009065 ]
+0019544 = arginine catabolism to glutamate [isa: 0006527 0006536 ]
+0019547 = arginine catabolism to ornithine [isa: 0006527 0006591 ]
+0019493 = arginine catabolism to proline [isa: 0006527 0006560 ]
+0019548 = arginine catabolism to spermine [isa: 0006527 0008215 ]
+0019545 = arginine catabolism to succinate [isa: 0006105 0006527 ]
+0019546 = arginine deiminase pathway [isa: 0006527 ]
+0006530 = asparagine catabolism [isa: 0006528 0009065 ]
+0006538 = glutamate catabolism [isa: 0006536 0009065 ]
+0019551 = glutamate catabolism to 2-oxoglutarate [isa: 0006103 0006106 0006538 ]
+0019550 = glutamate catabolism to aspartate [isa: 0006531 0006538 ]
+0019460 = glutamate catabolism to fumarate [isa: 0006106 0006538 ]
+0019461 = glutamate catabolism to fumarate, using glutamate synthase (NADPH) [isa: 0019460 ]
+0019462 = glutamate catabolism to fumarate, using glutaminase [isa: 0019460 ]
+0019555 = glutamate catabolism to ornithine [isa: 0006538 0006591 ]
+0019554 = glutamate catabolism to oxaloacetate [isa: 0006107 0006538 ]
+0019549 = glutamate catabolism to succinate [isa: 0006105 0006538 ]
+0006539 = glutamate catabolism, via 2-oxoglutarate [isa: 0006103 0006538 ]
+0019553 = glutamate catabolism, via L-citramalate [isa: 0006538 ]
+0019459 = glutamate deamidation [isa: 0006538 ]
+0006540 = glutamate decarboxylation to succinate [isa: 0006105 0006538 ]
+0019670 = glutamate fermentation [isa: 0006538 0019665 ]
+0019552 = glutamate fermentation, via 2-hydroxyglutarate [isa: 0019670 ]
+0019671 = glutamate fermentation, via mesaconate and citramalate [isa: 0019670 ]
+0006543 = glutamine catabolism [isa: 0006541 0009065 ]
+0006562 = proline catabolism [isa: 0006560 0009065 ]
+0019495 = proline catabolism to 2-oxoglutarate [isa: 0006562 ]
+0009077 = histidine family amino acid catabolism [isa: 0009063 0009075 ]
+0006548 = histidine catabolism [isa: 0006547 0009077 ]
+0019558 = histidine catabolism to 2-oxoglutarate [isa: 0006103 0006548 ]
+0019556 = histidine catabolism to glutamate and formamide [isa: 0006536 0006548 ]
+0019557 = histidine catabolism to glutamate and formate [isa: 0006536 0006548 ]
+0019560 = histidine catabolism to hydantoin-5-propionate [isa: 0006548 ]
+0019559 = histidine catabolism to imidazol-5-yl-lactate [isa: 0006548 ]
+0019796 = non-protein amino acid catabolism [isa: 0009063 0019794 ]
+0019484 = beta-alanine catabolism [isa: 0019482 0019796 ]
+0019485 = beta-alanine catabolism to L-alanine [isa: 0019484 ]
+0019486 = beta-alanine catabolism to mevalonate semialdehyde, by transamination [isa: 0019484 ]
+0006593 = ornithine catabolism [isa: 0006591 0019796 ]
+0019467 = ornithine catabolism, by decarboxylation [isa: 0006593 ]
+0019466 = ornithine catabolism, via proline [isa: 0006593 ]
+0009080 = pyruvate family amino acid catabolism [isa: 0009063 0009078 ]
+0006524 = alanine catabolism [isa: 0006522 0009080 ]
+0019481 = alanine catabolism by transamination [isa: 0006524 ]
+0019667 = alanine fermentation [isa: 0006524 0019665 ]
+0019479 = alanine oxidation to propanoate [isa: 0006524 ]
+0019480 = alanine oxidation to pyruvate, via D-alanine [isa: 0006524 ]
+0030633 = D-alanine family amino acid catabolism [isa: 0006524 0046144 ]
+0009071 = serine family amino acid catabolism [isa: 0009063 0009069 ]
+0009093 = cysteine catabolism [isa: 0000098 0006534 0009071 ]
+0019448 = L-cysteine catabolism [isa: 0009093 0046439 ]
+0019449 = L-cysteine catabolism to hypotaurine [isa: 0019448 ]
+0019450 = L-cysteine catabolism to pyruvate [isa: 0019448 ]
+0019451 = L-cysteine catabolism to pyruvate, using cysteine dioxygenase [isa: 0019450 ]
+0019452 = L-cysteine catabolism to taurine [isa: 0019448 ]
+0019453 = L-cysteine catabolism, via cystine [isa: 0019448 ]
+0019456 = L-cysteine catabolism, via cystine, using cysteine transaminase [isa: 0019453 ]
+0019455 = L-cysteine catabolism, via cystine, using cystine reductase [isa: 0019453 ]
+0019454 = L-cysteine catabolism, via cystine, using glutathione-cystine transhydrogenase [isa: 0019453 ]
+0006546 = glycine catabolism [isa: 0006544 0009071 ]
+0019463 = glycine catabolism to creatine [isa: 0006546 ]
+0019464 = glycine decarboxylation via glycine cleavage system [isa: 0006546 ]
+0019669 = glycine fermentation [isa: 0006546 0019665 ]
+0009091 = homoserine catabolism [isa: 0009071 0009092 ]
+0016261 = selenocysteine catabolism [isa: 0000098 0009071 0016259 ]
+0006565 = serine catabolism [isa: 0006563 0009071 ]
+0000098 = sulfur amino acid catabolism [isa: 0000096 0009063 ]
+0019510 = S-adenosylhomocysteine catabolism [isa: 0000098 0046498 ]
+0006557 = S-adenosylmethioninamine biosynthesis [isa: 0000098 0006743 0009058 0046499 ]
+0042402 = biogenic amine catabolism [isa: 0006576 0009310 0042219 ]
+0006579 = betaine catabolism [isa: 0006577 0042402 ]
+0042413 = carnitine catabolism [isa: 0009437 0042402 ]
+0042424 = catecholamine catabolism [isa: 0006584 0042402 ]
+0042426 = choline catabolism [isa: 0019695 0042402 ]
+0046336 = ethanolamine catabolism [isa: 0006580 0042402 ]
+0046338 = phosphatidylethanolamine catabolism [isa: 0046336 0046337 ]
+0046218 = indolalkylamine catabolism [isa: 0006586 0042402 0042436 ]
+0042442 = melatonin catabolism [isa: 0030186 0042447 0046218 ]
+0030419 = nicotianamine catabolism [isa: 0030417 0042402 ]
+0006598 = polyamine catabolism [isa: 0006595 0042402 ]
+0009447 = putrescine catabolism [isa: 0006598 0009445 ]
+0046203 = spermidine catabolism [isa: 0006598 0008216 ]
+0046205 = nor-spermidine catabolism [isa: 0046203 0046204 ]
+0046207 = trypanothione catabolism [isa: 0046203 0046206 ]
+0046208 = spermine catabolism [isa: 0006598 0008215 ]
+0042404 = thyroid hormone catabolism [isa: 0042402 0042403 0042447 ]
+0006520 = amino acid metabolism [isa: 0006519 0009308 ]
+0009072 = aromatic amino acid family metabolism [isa: 0006520 0006725 ]
+0006558 = phenylalanine metabolism [isa: 0009072 ]
+0006568 = tryptophan metabolism [isa: 0006586 0009072 ]
+0019356 = nicotinate nucleotide biosynthesis from tryptophan [isa: 0006568 0019357 ]
+0006570 = tyrosine metabolism [isa: 0009072 ]
+0009066 = aspartate family amino acid metabolism [isa: 0006520 ]
+0006528 = asparagine metabolism [isa: 0009066 ]
+0019801 = cyclization of asparagine, during protein splicing [isa: 0006528 ] [partof: 0016539 ]
+0006531 = aspartate metabolism [isa: 0009066 ]
+0019355 = nicotinamide nucleotide biosynthesis from aspartate [isa: 0006531 0019359 ]
+0006553 = lysine metabolism [isa: 0009066 ]
+0046441 = D-lysine metabolism [isa: 0006553 ]
+0046440 = L-lysine metabolism [isa: 0006553 ]
+0006555 = methionine metabolism [isa: 0000096 0009066 ]
+0006566 = threonine metabolism [isa: 0009066 ]
+0009081 = branched chain family amino acid metabolism [isa: 0006520 ]
+0006549 = isoleucine metabolism [isa: 0009081 ]
+0006551 = leucine metabolism [isa: 0009081 ]
+0006573 = valine metabolism [isa: 0009081 ]
+0046416 = D-amino acid metabolism [isa: 0006520 ]
+0046436 = D-alanine metabolism [isa: 0046144 0046416 ]
+0046437 = D-amino acid biosynthesis [isa: 0046416 ]
+0009064 = glutamine family amino acid metabolism [isa: 0006520 ]
+0006525 = arginine metabolism [isa: 0000051 0009064 ]
+0006536 = glutamate metabolism [isa: 0009064 ]
+0019676 = ammonia assimilation cycle [isa: 0006536 ]
+0006541 = glutamine metabolism [isa: 0009064 ]
+0019802 = cyclization of glutamine, during protein splicing [isa: 0006541 ] [partof: 0016539 ]
+0006560 = proline metabolism [isa: 0009064 ]
+0042458 = nopaline catabolism to proline [isa: 0006560 0019468 ]
+0042459 = octopine catabolism to proline [isa: 0006560 0019469 ]
+0019492 = proline cycling [isa: 0006560 ]
+0019494 = proline oxidation [isa: 0006560 ]
+0009075 = histidine family amino acid metabolism [isa: 0006520 ]
+0006547 = histidine metabolism [isa: 0009075 ]
+0018366 = L-amino acid racemization [isa: 0006520 ]
+0018085 = peptidyl-L-amino acid racemization [isa: 0018193 0018366 ]
+0018091 = peptidyl-asparagine racemization [isa: 0018085 0018196 ]
+0019122 = peptidyl-D-alanine racemization [isa: 0018085 0018194 ]
+0019916 = peptidyl-D-alanine racemization, direct [isa: 0019122 ]
+0019917 = peptidyl-D-alanine racemization, via peptidyl-L-serine [isa: 0019122 ]
+0019124 = peptidyl-isoleucine racemization [isa: 0018085 ]
+0019129 = peptidyl-leucine racemization [isa: 0018085 ]
+0019123 = peptidyl-methionine racemization [isa: 0018085 ]
+0019125 = peptidyl-phenylalanine racemization [isa: 0018085 ]
+0019126 = peptidyl-serine racemization [isa: 0018085 ]
+0019128 = peptidyl-tryptophan racemization [isa: 0018085 ]
+0019794 = non-protein amino acid metabolism [isa: 0006520 ]
+0019482 = beta-alanine metabolism [isa: 0019794 ]
+0006591 = ornithine metabolism [isa: 0000051 0019794 ]
+0009078 = pyruvate family amino acid metabolism [isa: 0006520 ]
+0006522 = alanine metabolism [isa: 0009078 ]
+0046144 = D-alanine family amino acid metabolism [isa: 0006522 ]
+0006521 = regulation of amino acid metabolism [isa: 0019222 ] [partof: 0006520 ]
+0045763 = negative regulation of amino acid metabolism [isa: 0006521 0009892 ]
+0045764 = positive regulation of amino acid metabolism [isa: 0006521 0009893 ]
+0009069 = serine family amino acid metabolism [isa: 0006520 ]
+0006534 = cysteine metabolism [isa: 0000096 0009069 ]
+0046438 = D-cysteine metabolism [isa: 0006534 ]
+0046439 = L-cysteine metabolism [isa: 0006534 ]
+0019346 = transsulfuration [isa: 0006534 0009092 ]
+0006544 = glycine metabolism [isa: 0009069 ]
+0009092 = homoserine metabolism [isa: 0009069 ]
+0016259 = selenocysteine metabolism [isa: 0000096 0009069 ]
+0006563 = serine metabolism [isa: 0009069 ]
+0000096 = sulfur amino acid metabolism [isa: 0006520 0006790 ]
+0006477 = protein amino acid sulfation [isa: 0000096 0006464 ]
+0006478 = peptidyl-tyrosine sulfation [isa: 0006477 0018212 ]
+0006576 = biogenic amine metabolism [isa: 0006575 0009308 ]
+0006577 = betaine metabolism [isa: 0006576 ]
+0009437 = carnitine metabolism [isa: 0006576 ]
+0019254 = carnitine metabolism, CoA-linked [isa: 0009437 ]
+0006584 = catecholamine metabolism [isa: 0006576 ]
+0042069 = regulation of catecholamine metabolism [partof: 0006584 ]
+0045914 = negative regulation of catecholamine metabolism [isa: 0042069 ]
+0045915 = positive regulation of catecholamine metabolism [isa: 0042069 ]
+0042439 = ethanolamine and derivative metabolism [isa: 0006576 ]
+0019695 = choline metabolism [isa: 0042439 ]
+0006580 = ethanolamine metabolism [isa: 0042439 ]
+0006586 = indolalkylamine metabolism [isa: 0006576 0042434 ]
+0030186 = melatonin metabolism [isa: 0006586 0042445 ]
+0030417 = nicotianamine metabolism [isa: 0006576 ]
+0006595 = polyamine metabolism [isa: 0006576 0019748 ]
+0009445 = putrescine metabolism [isa: 0006595 ]
+0008216 = spermidine metabolism [isa: 0006595 ]
+0046204 = nor-spermidine metabolism [isa: 0008216 ]
+0046206 = trypanothione metabolism [isa: 0008216 ]
+0008215 = spermine metabolism [isa: 0006595 ]
+0042403 = thyroid hormone metabolism [isa: 0006576 0042445 ]
+0006590 = thyroid hormone generation [isa: 0042403 ]
+0030416 = methylamine metabolism [isa: 0009308 ]
+0046482 = para-aminobenzoic acid metabolism [isa: 0006760 0009308 0019752 ]
+0008153 = para-aminobenzoic acid biosynthesis [isa: 0009396 0046394 0046482 ]
+0006519 = amino acid and derivative metabolism [isa: 0008152 ]
+0006575 = amino acid derivative metabolism [isa: 0006519 ]
+0018902 = 1,3-dichloro-2-propanol metabolism [isa: 0006575 ]
+0046309 = 1,3-dichloro-2-propanol biosynthesis [isa: 0018902 0042398 ]
+0046310 = 1,3-dichloro-2-propanol catabolism [isa: 0018902 0042219 ]
+0019471 = 4-hydroxyproline metabolism [isa: 0006575 ]
+0019472 = 4-hydroxyproline biosynthesis [isa: 0019471 0042398 ]
+0019470 = 4-hydroxyproline catabolism [isa: 0019471 0042219 ]
+0018401 = peptidyl-proline hydroxylation to 4-hydroxy-L-proline [isa: 0019471 0019511 ]
+0046442 = aerobactin metabolism [isa: 0006575 ]
+0042398 = amino acid derivative biosynthesis [isa: 0006575 0009058 ]
+0009449 = aminobutyrate biosynthesis [isa: 0009448 0019438 0042398 ]
+0009699 = phenylpropanoid biosynthesis [isa: 0009698 0019438 0042398 ]
+0009715 = chalcone biosynthesis [isa: 0009699 0009714 0042181 ]
+0009800 = cinnamic acid biosynthesis [isa: 0009699 0009803 ] [partof: 0009696 0009804 0009810 0009812 ]
+0009802 = cinnamic acid ester biosynthesis [isa: 0009699 0009801 ] [partof: 0009803 ]
+0009813 = flavonoid biosynthesis [isa: 0009699 0009812 ]
+0009718 = anthocyanin biosynthesis [isa: 0009813 0046283 ]
+0009716 = flavonoid phytoalexin biosynthesis [isa: 0009813 0046285 ]
+0009717 = isoflavonoid biosynthesis [isa: 0009813 0046287 ]
+0009807 = lignan biosynthesis [isa: 0009699 0009806 ]
+0009809 = lignin biosynthesis [isa: 0009807 0009808 ]
+0009811 = stilbene biosynthesis [isa: 0009699 0009810 ]
+0042396 = phosphagen biosynthesis [isa: 0006599 0042398 ]
+0006601 = creatine biosynthesis [isa: 0006600 0042396 ]
+0046312 = phosphoarginine biosynthesis [isa: 0006604 0042396 ]
+0046314 = phosphocreatine biosynthesis [isa: 0006603 0042396 ]
+0046311 = prenylcysteine biosynthesis [isa: 0030329 0042398 ]
+0019503 = stachydrine biosynthesis [isa: 0019502 0042398 ]
+0042412 = taurine biosynthesis [isa: 0019530 0042398 ]
+0046307 = Z-phenylacetaldoxime biosynthesis [isa: 0018983 0042398 ]
+0042219 = amino acid derivative catabolism [isa: 0006575 0009056 ]
+0009450 = aminobutyrate catabolism [isa: 0009448 0019439 0042219 ]
+0042457 = ethylene catabolism [isa: 0009692 0042219 0042447 ]
+0019468 = nopaline catabolism [isa: 0042219 0046418 ]
+0019469 = octopine catabolism [isa: 0042219 0046419 ]
+0046271 = phenylpropanoid catabolism [isa: 0009698 0019439 0042219 ]
+0046280 = chalcone catabolism [isa: 0009714 0042182 0046271 ]
+0046281 = cinnamic acid catabolism [isa: 0009803 0046271 ]
+0046282 = cinnamic acid ester catabolism [isa: 0009801 0046271 ]
+0046275 = flavonoid catabolism [isa: 0009812 0046271 ]
+0046284 = anthocyanin catabolism [isa: 0046275 0046283 ]
+0046286 = flavonoid phytoalexin catabolism [isa: 0046275 0046285 ]
+0046288 = isoflavonoid catabolism [isa: 0046275 0046287 ]
+0046290 = isoflavonoid phytoalexin catabolism [isa: 0046288 0046289 ]
+0046289 = isoflavonoid phytoalexin metabolism [isa: 0046275 0046287 ]
+0046273 = lignan catabolism [isa: 0009806 0046271 ]
+0046274 = lignin catabolism [isa: 0009808 0046273 ]
+0046272 = stilbene catabolism [isa: 0009810 0046271 ]
+0042397 = phosphagen catabolism [isa: 0006599 0042219 ]
+0006602 = creatinine catabolism [isa: 0042397 0046449 ]
+0019621 = creatinine catabolism to formate [isa: 0006602 ]
+0046313 = phosphoarginine catabolism [isa: 0006604 0042397 ]
+0046315 = phosphocreatine catabolism [isa: 0006603 0042397 ]
+0030328 = prenylcysteine catabolism [isa: 0030327 0030329 0042219 ]
+0019504 = stachydrine catabolism [isa: 0019502 0042219 ]
+0019529 = taurine catabolism [isa: 0019530 0042219 ]
+0046308 = Z-phenylacetaldoxime catabolism [isa: 0018983 0042219 ]
+0009448 = aminobutyrate metabolism [isa: 0006575 0006725 ]
+0009692 = ethylene metabolism [isa: 0006575 0042445 ]
+0046516 = hypusine metabolism [isa: 0006575 ]
+0046515 = hypusine biosynthesis [isa: 0046516 ]
+0008612 = hypusine biosynthesis from peptidyl-lysine [isa: 0009058 0018205 0046515 ]
+0046418 = nopaline metabolism [isa: 0006575 ]
+0046419 = octopine metabolism [isa: 0006575 ]
+0009698 = phenylpropanoid metabolism [isa: 0006575 0006725 0019748 ]
+0009714 = chalcone metabolism [isa: 0009698 0042180 ]
+0009801 = cinnamic acid ester metabolism [isa: 0009698 ]
+0009803 = cinnamic acid metabolism [isa: 0009698 ]
+0009812 = flavonoid metabolism [isa: 0009698 ]
+0046283 = anthocyanin metabolism [isa: 0009812 ]
+0046285 = flavonoid phytoalexin metabolism [isa: 0009812 ]
+0046287 = isoflavonoid metabolism [isa: 0009812 ]
+0009806 = lignan metabolism [isa: 0009698 ]
+0009808 = lignin metabolism [isa: 0009806 ]
+0009810 = stilbene metabolism [isa: 0009698 ]
+0006599 = phosphagen metabolism [isa: 0006575 ]
+0006600 = creatine metabolism [isa: 0006599 ]
+0046449 = creatinine metabolism [isa: 0006599 ]
+0006604 = phosphoarginine metabolism [isa: 0006599 ]
+0006603 = phosphocreatine metabolism [isa: 0006599 ]
+0030329 = prenylcysteine metabolism [isa: 0006575 ]
+0046498 = S-adenosylhomocysteine metabolism [isa: 0006575 ]
+0046500 = S-adenosylmethionine metabolism [isa: 0006575 ]
+0019502 = stachydrine metabolism [isa: 0006575 ]
+0019530 = taurine metabolism [isa: 0006575 ]
+0018983 = Z-phenylacetaldoxime metabolism [isa: 0006575 ]
+0006725 = aromatic compound metabolism [isa: 0008152 ]
+0019438 = aromatic compound biosynthesis [isa: 0006725 0009058 ]
+0009805 = coumarin biosynthesis [isa: 0009804 0019438 ]
+0019491 = ectoine biosynthesis [isa: 0019438 0042399 ]
+0046236 = mandelate biosynthesis [isa: 0018924 0019438 ]
+0006728 = pteridine biosynthesis [isa: 0019438 0019889 ]
+0006729 = tetrahydrobiopterin biosynthesis [isa: 0006728 0046146 ]
+0046220 = pyridine biosynthesis [isa: 0019438 0019507 ]
+0042194 = quinate biosynthesis [isa: 0019438 0019630 ]
+0009697 = salicylic acid biosynthesis [isa: 0009696 0019438 ]
+0019435 = sophorosyloxydocosanoate biosynthesis [isa: 0019434 0019438 ]
+0042189 = vanillin biosynthesis [isa: 0018982 0019438 ]
+0019439 = aromatic compound catabolism [isa: 0006725 0009056 ]
+0046226 = coumarin catabolism [isa: 0009804 0019439 ]
+0042400 = ectoine catabolism [isa: 0019439 0042399 ]
+0042436 = indole derivative catabolism [isa: 0019439 0042434 ]
+0042344 = indole glucosinolate catabolism [isa: 0019762 0042343 0042436 ]
+0046216 = indole phytoalexin catabolism [isa: 0042436 0046217 ]
+0042437 = indoleacetic acid catabolism [isa: 0009683 0009852 0042436 ]
+0019596 = mandelate catabolism [isa: 0018924 0019439 ]
+0019599 = (R)-4-hydroxymandelate catabolism [isa: 0019596 0046431 ]
+0019597 = (R)-mandelate catabolism to benzoate [isa: 0019596 ]
+0019598 = (R)-mandelate catabolism to catechol [isa: 0019596 ]
+0046221 = pyridine catabolism [isa: 0019439 0019507 ]
+0019631 = quinate catabolism [isa: 0019439 0019630 ]
+0046244 = salicylic acid catabolism [isa: 0009696 0019439 ]
+0019436 = sophorosyloxydocosanoate catabolism [isa: 0019434 0019439 ]
+0042190 = vanillin catabolism [isa: 0018982 0019439 ]
+0009804 = coumarin metabolism [isa: 0006725 0019748 ]
+0042399 = ectoine metabolism [isa: 0006725 ]
+0042430 = indole and derivative metabolism [isa: 0006725 ]
+0042434 = indole derivative metabolism [isa: 0042430 ]
+0042435 = indole derivative biosynthesis [isa: 0009058 0042434 ]
+0009759 = indole glucosinolate biosynthesis [isa: 0019761 0042343 0042435 ]
+0009684 = indoleacetic acid biosynthesis [isa: 0009683 0009851 0042435 ]
+0009849 = indoleacetic acid biosynthesis, tryptophan independent [isa: 0009684 ]
+0009848 = indoleacetic acid biosynthesis, via tryptophan [isa: 0009684 ]
+0042343 = indole glucosinolate metabolism [isa: 0019760 0042434 ]
+0046217 = indole phytoalexin metabolism [isa: 0019748 0042434 ]
+0009683 = indoleacetic acid metabolism [isa: 0009850 0042434 ]
+0009709 = terpenoid indole alkaloid biosynthesis [isa: 0009821 0042434 0046447 ]
+0042431 = indole metabolism [isa: 0042430 ]
+0042432 = indole biosynthesis [isa: 0009058 0042431 ]
+0042433 = indole catabolism [isa: 0009056 0042431 ]
+0018924 = mandelate metabolism [isa: 0006725 ]
+0046431 = (R)-4-hydroxymandelate metabolism [isa: 0018924 ]
+0019889 = pteridine metabolism [isa: 0006725 ]
+0006135 = dihydropteridine reduction [isa: 0006118 0019889 ]
+0019990 = pteridine catabolism [isa: 0009056 0019889 ]
+0046147 = tetrahydrobiopterin catabolism [isa: 0019990 0046146 ]
+0042068 = regulation of pteridine metabolism [isa: 0019222 ] [partof: 0019889 ]
+0045863 = negative regulation of pteridine metabolism [isa: 0009892 0042068 ]
+0045864 = positive regulation of pteridine metabolism [isa: 0009893 0042068 ]
+0046146 = tetrahydrobiopterin metabolism [isa: 0019889 ]
+0019507 = pyridine metabolism [isa: 0006725 ]
+0019508 = 2,5-dihydroxypyridine utilization [isa: 0019507 ]
+0019630 = quinate metabolism [isa: 0006725 ]
+0009696 = salicylic acid metabolism [isa: 0006725 ]
+0019434 = sophorosyloxydocosanoate metabolism [isa: 0006725 ]
+0018982 = vanillin metabolism [isa: 0006725 ]
+0009058 = biosynthesis [isa: 0008152 ]
+0009821 = alkaloid biosynthesis [isa: 0009058 0009820 ]
+0009708 = benzyl isoquinoline alkaloid biosynthesis [isa: 0009821 0046445 ]
+0019351 = dethiobiotin biosynthesis [isa: 0009821 0046450 ] [partof: 0009102 ]
+0018161 = dipyrrin biosynthesis [isa: 0009821 0046453 ]
+0042179 = nicotine biosynthesis [isa: 0009821 0018933 ]
+0009711 = purine alkaloid biosynthesis [isa: 0009821 0046446 ]
+0009710 = tropane alkaloid biosynthesis [isa: 0009821 0046448 ]
+0046305 = alkanesulfonate biosynthesis [isa: 0009058 0019694 ]
+0016051 = carbohydrate biosynthesis [isa: 0005975 0009058 ]
+0046175 = aldonic acid biosynthesis [isa: 0016051 0019520 ]
+0046179 = D-dehydro-D-gluconate biosynthesis [isa: 0019525 0046175 ]
+0046178 = D-gluconate biosynthesis [isa: 0019521 0046175 ]
+0046180 = ketogluconate biosynthesis [isa: 0019522 0046175 ]
+0046182 = L-idonate biosynthesis [isa: 0019523 0046180 ]
+0046349 = amino sugar biosynthesis [isa: 0006040 0016051 ]
+0030391 = fructosamine biosynthesis [isa: 0030389 0046349 ]
+0006042 = glucosamine biosynthesis [isa: 0006041 0046349 ]
+0006045 = N-acetylglucosamine biosynthesis [isa: 0006042 0006044 ]
+0006048 = UDP-N-acetylglucosamine biosynthesis [isa: 0006045 0006047 ]
+0046347 = mannosamine biosynthesis [isa: 0006050 0046349 ]
+0006052 = N-acetylmannosamine biosynthesis [isa: 0006051 0046347 ]
+0046380 = N-acetylneuraminate biosynthesis [isa: 0006054 0046349 ]
+0006055 = CMP-N-acetylneuraminate biosynthesis [isa: 0046380 0046381 ]
+0019277 = UDP-N-acetylgalactosamine biosynthesis [isa: 0019276 0046349 ]
+0006023 = aminoglycan biosynthesis [isa: 0006022 0016051 ]
+0006025 = galactosaminoglycan biosynthesis [isa: 0006023 0046350 ]
+0006024 = glycosaminoglycan biosynthesis [isa: 0006023 0030203 ]
+0030206 = chondroitin sulfate biosynthesis [isa: 0006024 0030204 ]
+0030208 = dermatan sulfate biosynthesis [isa: 0006024 0030205 ]
+0030210 = heparin biosynthesis [isa: 0006024 0030202 ]
+0030213 = hyaluronan biosynthesis [isa: 0006024 0030212 ]
+0018146 = keratan sulfate biosynthesis [isa: 0006024 0042339 ]
+0046351 = disaccharide biosynthesis [isa: 0005984 0016051 ]
+0005989 = lactose biosynthesis [isa: 0005988 0046351 ]
+0000024 = maltose biosynthesis [isa: 0000023 0046351 ]
+0042544 = melibiose biosynthesis [isa: 0005994 0046351 ]
+0005986 = sucrose biosynthesis [isa: 0005985 0046351 ]
+0005992 = trehalose biosynthesis [isa: 0005991 0046351 ]
+0019390 = glucuronoside biosynthesis [isa: 0016051 0019389 ]
+0016138 = glycoside biosynthesis [isa: 0016051 0016137 ]
+0019756 = cyanogenic glycoside biosynthesis [isa: 0016138 0042341 ]
+0019758 = glycosinolate biosynthesis [isa: 0016138 0019757 ]
+0019761 = glucosinolate biosynthesis [isa: 0019758 0019760 ]
+0016141 = O-glycoside biosynthesis [isa: 0016138 0016140 ]
+0016144 = S-glycoside biosynthesis [isa: 0016138 0016143 ]
+0016135 = saponin biosynthesis [isa: 0016114 0016129 0016134 0016138 ]
+0009312 = oligosaccharide biosynthesis [isa: 0009311 0016051 ]
+0009244 = lipopolysaccharide core region biosynthesis [isa: 0009312 0046401 ] [partof: 0009103 ]
+0019685 = photosynthesis, dark reaction [isa: 0016051 ] [partof: 0015979 ]
+0009760 = C4 photosynthesis [isa: 0015977 0019685 ]
+0009763 = NAD-malic enzyme C4 photosynthesis [isa: 0009760 ]
+0009762 = NADP-malic enzyme C4 photosynthesis [isa: 0009760 ]
+0009764 = PEP carboxykinase C4 photosynthesis [isa: 0009760 ]
+0009761 = CAM photosynthesis [isa: 0015977 0019685 ]
+0019253 = reductive pentose-phosphate cycle [isa: 0019685 ] [partof: 0015977 ]
+0000271 = polysaccharide biosynthesis [isa: 0005976 0016051 ]
+0042121 = alginic acid biosynthesis [isa: 0000271 0042120 ]
+0006031 = chitin biosynthesis [isa: 0000271 0006030 0009059 ]
+0006035 = cuticle chitin biosynthesis [isa: 0006031 0006034 ] [partof: 0042335 ]
+0009242 = colanic acid biosynthesis [isa: 0000271 0046377 ]
+0009246 = enterobacterial common antigen biosynthesis [isa: 0000271 0046378 ]
+0045226 = extracellular polysaccharide biosynthesis [isa: 0000271 0046379 ]
+0019347 = GDP-alpha-D-mannosylchitobiosyldiphosphodolichol biosynthesis [isa: 0000271 0019408 0046376 ]
+0009250 = glucan biosynthesis [isa: 0000271 0006073 ]
+0006075 = beta-1,3 glucan biosynthesis [isa: 0006074 0009250 ]
+0006078 = beta-1,6 glucan biosynthesis [isa: 0006077 0009250 ]
+0030244 = cellulose biosynthesis [isa: 0009250 0030243 ]
+0005978 = glycogen biosynthesis [isa: 0005977 0009250 ]
+0005979 = regulation of glycogen biosynthesis [isa: 0009889 ] [partof: 0005978 ]
+0045719 = negative regulation of glycogen biosynthesis [isa: 0005979 0009890 ]
+0045725 = positive regulation of glycogen biosynthesis [isa: 0005979 0009891 ]
+0019252 = starch biosynthesis [isa: 0005982 0009250 ]
+0015014 = heparan sulfate proteoglycan biosynthesis, polysaccharide chain biosynthesis [isa: 0000271 ] [partof: 0015012 ]
+0009248 = K antigen biosynthesis [isa: 0000271 0046375 ]
+0009103 = lipopolysaccharide biosynthesis [isa: 0000271 0008610 0008653 ]
+0019294 = ketodeoxyoctanoate biosynthesis [isa: 0046394 0046400 ] [partof: 0009103 ]
+0009245 = lipid A biosynthesis [isa: 0046493 ] [partof: 0009103 ]
+0009243 = O antigen biosynthesis [isa: 0000271 0046402 ] [partof: 0009103 ]
+0046354 = mannan biosynthesis [isa: 0000271 0006080 ]
+0045489 = pectin biosynthesis [isa: 0000271 0045488 ]
+0030311 = poly-N-acetyllactosamine biosynthesis [isa: 0000271 0030309 ]
+0045492 = xylan biosynthesis [isa: 0000271 0045491 ]
+0030166 = proteoglycan biosynthesis [isa: 0006029 0016051 ]
+0015012 = heparan sulfate proteoglycan biosynthesis [isa: 0030166 0030201 ]
+0015015 = heparan sulfate proteoglycan biosynthesis, enzymatic modification [partof: 0015012 ]
+0015013 = heparan sulfate proteoglycan biosynthesis, linkage to polypeptide [partof: 0015012 ]
+0019240 = citrulline biosynthesis [isa: 0000052 0009058 ]
+0018101 = peptidyl-citrulline biosynthesis from peptidyl-arginine [isa: 0018195 0019240 ]
+0046138 = coenzymes and prosthetic group biosynthesis [isa: 0006731 0009058 ]
+0009108 = coenzyme biosynthesis [isa: 0006732 0046138 ]
+0019361 = 2'-(5''-triphosphoribosyl)-3'-dephospho-CoA biosynthesis [isa: 0009108 0046432 ]
+0006754 = ATP biosynthesis [isa: 0006753 0009108 0009206 0046034 ]
+0006757 = ADP phosphorylation [isa: 0006754 0016310 ]
+0006756 = AMP phosphorylation [isa: 0006754 0016310 ]
+0006759 = ATP regeneration [isa: 0006754 ]
+0006755 = carbamoyl phosphate-ADP transphosphorylation [isa: 0006754 0016310 ]
+0015937 = coenzyme A biosynthesis [isa: 0009108 0015936 ]
+0019298 = coenzyme B biosynthesis [isa: 0009108 0019297 ]
+0019295 = coenzyme M biosynthesis [isa: 0009108 0019296 ]
+0018189 = coenzyme pyrroloquinoline-quinone biosynthesis [isa: 0009108 0018212 ]
+0006747 = FAD biosynthesis [isa: 0006746 0009108 0046443 ]
+0009398 = FMN biosynthesis [isa: 0006746 0009108 0046444 ]
+0009396 = folic acid and derivative biosynthesis [isa: 0006760 0009108 ]
+0009257 = 10-formyltetrahydrofolate biosynthesis [isa: 0009256 0009396 ]
+0006761 = dihydrofolate biosynthesis [isa: 0009396 0046452 ]
+0046656 = folic acid biosynthesis [isa: 0009396 0046655 ]
+0046654 = tetrahydrofolate biosynthesis [isa: 0009396 0046653 ]
+0006750 = glutathione biosynthesis [isa: 0006749 0009108 ]
+0009107 = lipoate biosynthesis [isa: 0009106 0009108 ]
+0009105 = lipoic acid biosynthesis [isa: 0000273 0009108 ]
+0015940 = pantothenate biosynthesis [isa: 0009108 0015939 ]
+0019363 = pyridine nucleotide biosynthesis [isa: 0009108 0019362 0042364 ]
+0006736 = NADH biosynthesis [isa: 0006734 0019363 ]
+0006741 = NADPH biosynthesis [isa: 0006739 0019363 ]
+0009435 = nicotinamide adenine dinucleotide biosynthesis [isa: 0019363 0019674 ]
+0019359 = nicotinamide nucleotide biosynthesis [isa: 0046496 ] [partof: 0009435 ]
+0019360 = nicotinamide nucleotide biosynthesis from niacinamide [isa: 0019359 ]
+0019357 = nicotinate nucleotide biosynthesis [isa: 0046497 ] [partof: 0009435 ]
+0019358 = nicotinate nucleotide biosynthesis, salvage pathway [isa: 0019357 ]
+0008615 = pyridoxine biosynthesis [isa: 0008614 0009108 ]
+0045426 = quinone cofactor biosynthesis [isa: 0009108 0042375 ]
+0006744 = ubiquinone biosynthesis [isa: 0006743 0045426 ]
+0042371 = vitamin K biosynthesis [isa: 0042362 0042373 0045426 ]
+0042372 = vitamin K1 biosynthesis [isa: 0042371 0042374 ]
+0009234 = vitamin K2 biosynthesis [isa: 0009233 0042371 ]
+0009229 = thiamin diphosphate biosynthesis [isa: 0009108 0042357 ]
+0046140 = corrin biosynthesis [isa: 0015009 0046138 ]
+0006779 = porphyrin biosynthesis [isa: 0006778 0046138 ]
+0015995 = chlorophyll biosynthesis [isa: 0006779 0015994 0046148 ]
+0030494 = bacteriochlorophyll biosynthesis [isa: 0015995 0030493 ]
+0006783 = heme biosynthesis [isa: 0006779 0042168 0046148 ]
+0006784 = heme a biosynthesis [isa: 0006783 0046160 ]
+0006785 = heme b biosynthesis [isa: 0006783 0046492 ]
+0006786 = heme c biosynthesis [isa: 0006783 0046162 ]
+0006782 = protoporphyrinogen IX biosynthesis [isa: 0006779 0046501 ] [partof: 0006783 ]
+0019353 = protoporphyrinogen IX biosynthesis from glutamate [isa: 0006782 ]
+0019352 = protoporphyrinogen IX biosynthesis from glycine [isa: 0006782 ]
+0019354 = siroheme biosynthesis [isa: 0006783 0046156 ]
+0006780 = uroporphyrinogen III biosynthesis [isa: 0046502 ] [partof: 0006779 ]
+0006781 = succinyl-CoA pathway [partof: 0006780 ]
+0009236 = vitamin B12 biosynthesis [isa: 0006779 0009235 0042364 ]
+0019250 = vitamin B12 biosynthesis, aerobic [isa: 0009236 ]
+0019251 = vitamin B12 biosynthesis, anaerobic [isa: 0009236 ]
+0019290 = siderochrome biosynthesis [isa: 0009237 0046138 ]
+0019539 = siderochrome biosynthesis from hydroxamic acid [isa: 0019290 ]
+0006723 = cuticle hydrocarbon biosynthesis [isa: 0009058 ] [partof: 0042335 ]
+0046120 = deoxyribonucleoside biosynthesis [isa: 0009058 0009120 ]
+0046123 = purine deoxyribonucleoside biosynthesis [isa: 0042451 0046120 0046122 ]
+0046091 = deoxyadenosine biosynthesis [isa: 0046090 0046123 ]
+0042452 = deoxyguanosine biosynthesis [isa: 0042453 0046123 ]
+0046126 = pyrimidine deoxyribonucleoside biosynthesis [isa: 0046120 0046125 0046134 ]
+0046093 = deoxycytidine biosynthesis [isa: 0046092 0046126 ]
+0046095 = deoxyinosine biosynthesis [isa: 0046094 0046126 ]
+0046097 = deoxyuridine biosynthesis [isa: 0046096 0046126 ]
+0046105 = thymidine biosynthesis [isa: 0046104 0046126 ]
+0045017 = glycerolipid biosynthesis [isa: 0009058 0046486 ]
+0018130 = heterocycle biosynthesis [isa: 0009058 0046483 ]
+0018131 = oxazole/thiazole biosynthesis [isa: 0018130 0046484 ]
+0018157 = protein-protein cross-linking via an oxazole or thiazole [isa: 0018131 0018149 ]
+0018134 = protein-protein cross-linking via glycine oxazolecarboxylic acid [isa: 0018157 0018201 0018209 ]
+0018137 = protein-protein cross-linking via glycine thiazolecarboxylic acid [isa: 0018157 0018198 0018201 ]
+0018132 = protein-protein cross-linking via L-cysteine oxazolecarboxylic acid [isa: 0018157 0018198 0018209 ]
+0018133 = protein-protein cross-linking via L-cysteine oxazolinecarboxylic acid [isa: 0018157 0018198 0018209 ]
+0018140 = protein-protein cross-linking via L-cysteine thiazolecarboxylic acid [isa: 0018157 0018198 ]
+0018141 = protein-protein cross-linking via L-lysine thiazolecarboxylic acid [isa: 0018157 0018198 0018205 ]
+0018139 = protein-protein cross-linking via L-phenylalanine thiazolecarboxylic acid [isa: 0018157 0018198 0018207 ]
+0018138 = protein-protein cross-linking via L-serine thiazolecarboxylic acid [isa: 0018157 0018198 0018209 ]
+0042446 = hormone biosynthesis [isa: 0009058 0042445 ]
+0006702 = androgen biosynthesis [isa: 0006694 0008209 0042446 ]
+0009851 = auxin biosynthesis [isa: 0009850 0042446 ]
+0006700 = C21-steroid hormone biosynthesis [isa: 0006694 0008207 0042446 ]
+0006701 = progesterone biosynthesis [isa: 0006700 0042448 ]
+0009691 = cytokinin biosynthesis [isa: 0009690 0042446 ]
+0045456 = ecdysteroid biosynthesis [isa: 0006694 0042181 0042446 0045455 ]
+0006697 = ecdysone biosynthesis [isa: 0008205 0016126 0045456 ]
+0007554 = regulation of ecdysteroid biosynthesis [isa: 0007553 ] [partof: 0045456 ]
+0045997 = negative regulation of ecdysteroid biosynthesis [isa: 0007554 0045965 ]
+0045998 = positive regulation of ecdysteroid biosynthesis [isa: 0007554 0045966 ]
+0006703 = estrogen biosynthesis [isa: 0006694 0008210 0042446 ]
+0006704 = glucocorticoid biosynthesis [isa: 0006694 0008211 0042446 ]
+0006718 = juvenile hormone biosynthesis [isa: 0006716 0016106 0042446 ]
+0007557 = regulation of juvenile hormone biosynthesis [isa: 0007556 ] [partof: 0006718 ]
+0045968 = negative regulation of juvenile hormone biosynthesis [isa: 0007557 0045928 ]
+0045969 = positive regulation of juvenile hormone biosynthesis [isa: 0007557 0045929 ]
+0006705 = mineralocorticoid biosynthesis [isa: 0006694 0008212 0042446 ]
+0042181 = ketone biosynthesis [isa: 0009058 0042180 ]
+0046211 = (+)-camphor biosynthesis [isa: 0018882 0042181 0046246 ]
+0045151 = acetoin biosynthesis [isa: 0042181 0045149 ]
+0008610 = lipid biosynthesis [isa: 0006629 0009058 ]
+0008611 = ether lipid biosynthesis [isa: 0008610 0046485 ]
+0006633 = fatty acid biosynthesis [isa: 0006631 0008610 0046394 ]
+0046456 = eicosanoid biosynthesis [isa: 0006633 0006690 ]
+0019370 = leukotriene biosynthesis [isa: 0006691 0046456 ]
+0019372 = lipoxygenase pathway [isa: 0019369 ] [partof: 0019370 ]
+0046457 = prostanoid biosynthesis [isa: 0006692 0046456 ]
+0001516 = prostaglandin biosynthesis [isa: 0006693 0046457 ]
+0019371 = cyclooxygenase pathway [isa: 0019369 ] [partof: 0001516 ]
+0030497 = fatty acid elongation [isa: 0006633 ]
+0019367 = fatty acid elongation, saturated fatty acid [isa: 0030497 ]
+0019368 = fatty acid elongation, unsaturated fatty acid [isa: 0030497 ]
+0042304 = regulation of fatty acid biosynthesis [isa: 0009889 0019217 ] [partof: 0006633 ]
+0045717 = negative regulation of fatty acid biosynthesis [isa: 0009890 0042304 0045922 ]
+0045723 = positive regulation of fatty acid biosynthesis [isa: 0009891 0042304 0045923 ]
+0008299 = isoprenoid biosynthesis [isa: 0006720 0008610 ]
+0045337 = farnesyl diphosphate biosynthesis [isa: 0008299 0045338 ]
+0009240 = isopentenyl diphosphate biosynthesis [isa: 0046490 ] [partof: 0008299 ]
+0019288 = isopentenyl diphosphate biosynthesis, mevalonate independent [isa: 0009240 ] [partof: 0009241 ]
+0019287 = isopentenyl diphosphate biosynthesis, via mevalonate [isa: 0009240 ] [partof: 0009241 ]
+0009241 = polyisoprenoid biosynthesis [isa: 0008299 0016096 ]
+0016114 = terpenoid biosynthesis [isa: 0006721 0009241 0046246 ]
+0016102 = diterpenoid biosynthesis [isa: 0016101 0016114 ]
+0009686 = gibberellic acid biosynthesis [isa: 0009685 0016102 0046394 ]
+0016099 = monoterpenoid biosynthesis [isa: 0016098 0016114 ]
+0016112 = polyterpenoid biosynthesis [isa: 0016111 0016114 ]
+0016106 = sesquiterpenoid biosynthesis [isa: 0006714 0016114 ]
+0009688 = abscisic acid biosynthesis [isa: 0009687 0016106 0046394 ]
+0016109 = tetraterpenoid biosynthesis [isa: 0016108 0016114 ]
+0016117 = carotenoid biosynthesis [isa: 0016109 0016116 ]
+0016120 = carotene biosynthesis [isa: 0016117 0016119 ]
+0016123 = xanthophyll biosynthesis [isa: 0016117 0016122 ]
+0016104 = triterpenoid biosynthesis [isa: 0006722 0016114 ]
+0019745 = pentacyclic triterpenoid biosynthesis [isa: 0016104 0019742 ]
+0019746 = hopanoid biosynthesis [isa: 0019744 0019745 ]
+0016091 = prenol biosynthesis [isa: 0008299 0016090 ]
+0016094 = polyprenol biosynthesis [isa: 0016091 0016093 ]
+0019408 = dolichol biosynthesis [isa: 0016094 0019348 ]
+0006489 = dolichyl diphosphate biosynthesis [isa: 0019408 0046465 ] [partof: 0006488 ]
+0046467 = membrane lipid biosynthesis [isa: 0006643 0008610 ]
+0009247 = glycolipid biosynthesis [isa: 0006664 0046467 ]
+0019375 = galactolipid biosynthesis [isa: 0009247 0019374 ]
+0006682 = galactosylceramide biosynthesis [isa: 0006681 0019375 0046476 ]
+0006688 = glycosphingolipid biosynthesis [isa: 0006687 0009247 0030148 ]
+0001574 = ganglioside biosynthesis [isa: 0001573 0006688 ]
+0001572 = lactosylceramide biosynthesis [isa: 0046476 0046478 ] [partof: 0001574 0001576 ]
+0001576 = globoside biosynthesis [isa: 0001575 0006688 ]
+0046476 = glycosylceramide biosynthesis [isa: 0006677 0009247 0046513 ]
+0006679 = glucosylceramide biosynthesis [isa: 0006678 0046476 ]
+0046317 = regulation of glucosylceramide biosynthesis [partof: 0006679 ]
+0046318 = negative regulation of glucosylceramide biosynthesis [isa: 0046317 ]
+0046319 = positive regulation of glucosylceramide biosynthesis [isa: 0046317 ]
+0008654 = phospholipid biosynthesis [isa: 0006644 0046467 ]
+0046460 = neutral lipid biosynthesis [isa: 0006638 0008610 ]
+0046463 = acylglycerol biosynthesis [isa: 0006639 0046460 ]
+0006651 = diacylglycerol biosynthesis [isa: 0046339 0046463 ]
+0016024 = CDP-diacylglycerol biosynthesis [isa: 0006651 0046341 ]
+0006640 = monoacylglycerol biosynthesis [isa: 0046462 0046463 ]
+0019432 = triacylglycerol biosynthesis [isa: 0006641 0046463 ]
+0006694 = steroid biosynthesis [isa: 0008202 0008610 ]
+0006699 = bile acid biosynthesis [isa: 0006694 0008206 0046394 ]
+0016129 = phytosteroid biosynthesis [isa: 0006694 0016128 ]
+0016132 = brassinosteroid biosynthesis [isa: 0016129 0016131 ]
+0016126 = sterol biosynthesis [isa: 0006694 0016125 ]
+0006695 = cholesterol biosynthesis [isa: 0008203 0016126 ]
+0045540 = regulation of cholesterol biosynthesis [isa: 0009889 ] [partof: 0006695 ]
+0045541 = negative regulation of cholesterol biosynthesis [isa: 0009890 0045540 ]
+0045542 = positive regulation of cholesterol biosynthesis [isa: 0009891 0045540 ]
+0006696 = ergosterol biosynthesis [isa: 0008204 0016126 ]
+0046506 = sulfolipid biosynthesis [isa: 0008610 0046505 ]
+0009059 = macromolecule biosynthesis [isa: 0009058 ]
+0006412 = protein biosynthesis [isa: 0009059 0019538 ]
+0006418 = amino acid activation [partof: 0006412 ]
+0006419 = alanyl-tRNA aminoacylation [isa: 0006418 ]
+0006439 = aminoacyl-tRNA hydrolase reaction [isa: 0006418 ]
+0006420 = arginyl-tRNA aminoacylation [isa: 0006418 ]
+0006421 = asparaginyl-tRNA aminoacylation [isa: 0006418 ]
+0006422 = aspartyl-tRNA aminoacylation [isa: 0006418 ]
+0006423 = cysteinyl-tRNA aminoacylation [isa: 0006418 ]
+0006425 = glutaminyl-tRNA aminoacylation [isa: 0006418 ]
+0006424 = glutamyl-tRNA aminoacylation [isa: 0006418 ]
+0006426 = glycyl-tRNA aminoacylation [isa: 0006418 ]
+0006427 = histidyl-tRNA aminoacylation [isa: 0006418 ]
+0006428 = isoleucyl-tRNA aminoacylation [isa: 0006418 ]
+0006429 = leucyl-tRNA aminoacylation [isa: 0006418 ]
+0006430 = lysyl-tRNA aminoacylation [isa: 0006418 ]
+0006431 = methionyl-tRNA aminoacylation [isa: 0006418 ]
+0006432 = phenylalanyl-tRNA aminoacylation [isa: 0006418 ]
+0006433 = prolyl-tRNA aminoacylation [isa: 0006418 ]
+0006434 = seryl-tRNA aminoacylation [isa: 0006418 ]
+0006435 = threonyl-tRNA aminoacylation [isa: 0006418 ]
+0006436 = tryptophanyl-tRNA aminoacylation [isa: 0006418 ]
+0006437 = tyrosyl-tRNA aminoacylation [isa: 0006418 ]
+0006438 = valyl-tRNA aminoacylation [isa: 0006418 ]
+0019988 = charged-tRNA modification [partof: 0006412 ]
+0001720 = conversion of lysyl-tRNA to pyrrolysyl-tRNA [isa: 0019988 ]
+0001718 = conversion of met-tRNAf to fmet-tRNA [isa: 0019988 ]
+0001717 = conversion of seryl-tRNAsec to selenocys-tRNAsec [isa: 0019988 ]
+0009101 = glycoprotein biosynthesis [isa: 0006412 0009100 ]
+0045222 = CD4 biosynthesis [isa: 0009101 ]
+0045223 = regulation of CD4 biosynthesis [isa: 0009889 ] [partof: 0045222 ]
+0045225 = negative regulation of CD4 biosynthesis [isa: 0009890 0045223 ]
+0045224 = positive regulation of CD4 biosynthesis [isa: 0009891 0045223 ]
+0045210 = FasL biosynthesis [isa: 0009101 ]
+0045219 = regulation of FasL biosynthesis [isa: 0009889 ] [partof: 0045210 ]
+0045221 = negative regulation of FasL biosynthesis [isa: 0009890 0045219 ]
+0045220 = positive regulation of FasL biosynthesis [isa: 0009891 0045219 ]
+0006486 = protein amino acid glycosylation [isa: 0006464 ] [partof: 0009101 ]
+0018103 = C-linked glycosylation [isa: 0006486 ]
+0018317 = C-linked glycosylation via tryptophan [isa: 0018103 0018211 ]
+0018406 = C-linked glycosylation via 2'-alpha-mannosyl-L-tryptophan [isa: 0018317 ]
+0006487 = N-linked glycosylation [isa: 0006486 ]
+0006491 = N-glycan processing [isa: 0006487 ]
+0016258 = N-glycan diversification [isa: 0006491 ]
+0016257 = N-glycan processing to secreted and cell-surface N-glycans [isa: 0006491 ]
+0006492 = N-linked glycoprotein maturation [isa: 0006487 ]
+0042543 = N-linked glycosylation via arginine [isa: 0006487 0018195 ]
+0018279 = N-linked glycosylation via asparagine [isa: 0006487 0018196 ]
+0018244 = N-linked glycosylation via tryptophan [isa: 0006487 0018211 ]
+0006488 = oligosaccharide-PP-dolichol assembly [isa: 0006487 ]
+0006490 = oligosaccharide-lipid intermediate assembly [partof: 0006488 ]
+0006496 = terminal N-glycosylation [isa: 0006487 0006494 ]
+0006493 = O-linked glycosylation [isa: 0006486 ]
+0016266 = O-glycan processing [isa: 0006493 ]
+0016267 = O-glycan processing, core 1 [isa: 0016266 ]
+0016268 = O-glycan processing, core 2 [isa: 0016266 ]
+0016269 = O-glycan processing, core 3 [isa: 0016266 ]
+0016270 = O-glycan processing, core 4 [isa: 0016266 ]
+0018241 = O-linked glycosylation via hydroxylysine [isa: 0006493 0018205 ]
+0018258 = O-linked glycosylation via hydroxyproline [isa: 0006493 0018208 ]
+0018242 = O-linked glycosylation via serine [isa: 0006493 0018209 ]
+0018243 = O-linked glycosylation via threonine [isa: 0006493 0018210 ]
+0018245 = O-linked glycosylation via tyrosine [isa: 0006493 0018212 ]
+0042076 = phosphate-linked glycosylation [isa: 0006486 ]
+0042077 = phosphate-linked glycosylation via serine [isa: 0042076 ]
+0018425 = O3-(N-acetylglucosamine-1-phosphoryl)-L-serine biosynthesis [isa: 0042077 ]
+0018426 = O3-(phosphoglycosyl-D-mannose-1-phosphoryl)-L-serine biosynthesis [isa: 0042077 ]
+0018321 = protein amino acid glucuronylation [isa: 0006486 ]
+0018006 = N-terminal protein amino acid glucuronylation [isa: 0018321 0018409 ]
+0018007 = N-terminal peptidyl-glycine N-glucuronylation [isa: 0018006 0018201 ]
+0018280 = S-linked glycosylation [isa: 0006486 ]
+0018240 = S-linked glycosylation via cysteine [isa: 0018198 0018280 ]
+0006494 = terminal glycosylation [isa: 0006486 ]
+0042158 = lipoprotein biosynthesis [isa: 0006412 0042157 ]
+0006497 = protein lipidation [isa: 0006464 0042158 ]
+0006501 = C-terminal protein lipidation [isa: 0006497 0018410 ]
+0019708 = peptidyl-glycine cholesteryl ester biosynthesis from peptidyl-glycine [isa: 0006501 0008203 0018201 ]
+0042079 = GPI/GSI anchor metabolism [isa: 0006497 ]
+0006505 = GPI anchor metabolism [isa: 0042079 ]
+0006506 = GPI anchor biosynthesis [isa: 0006505 0042080 ]
+0016255 = attachment of GPI anchor to protein [partof: 0006506 ]
+0018270 = GPI anchor biosynthesis via N-alanyl-glycosylphosphatidylinositolethanolamine [isa: 0006506 0018194 ]
+0018265 = GPI anchor biosynthesis via N-asparaginyl-glycosylphosphatidylinositolethanolamine [isa: 0006506 0018196 ]
+0018266 = GPI anchor biosynthesis via N-aspartyl-glycosylphosphatidylinositolethanolamine [isa: 0006506 0018197 ]
+0018267 = GPI anchor biosynthesis via N-cysteinyl-glycosylphosphatidylinositolethanolamine [isa: 0006506 0018198 ]
+0018268 = GPI anchor biosynthesis via N-glycyl-glycosylphosphatidylinositolethanolamine [isa: 0006506 0018201 ]
+0018269 = GPI anchor biosynthesis via N-seryl-glycosylphosphatidylinositolethanolamine [isa: 0006506 0018209 ]
+0016254 = preassembly of GPI anchor in ER membrane [partof: 0006506 ]
+0006507 = GPI anchor release [isa: 0006505 ]
+0042080 = GPI/GSI anchor biosynthesis [isa: 0042079 ]
+0042082 = GSI anchor biosynthesis [isa: 0042080 0042081 ]
+0018281 = GSI anchor biosynthesis via N-seryl-glycosylsphingolipidinositolethanolamine [isa: 0018209 0042082 ]
+0042081 = GSI anchor metabolism [isa: 0042079 ]
+0006498 = N-terminal protein lipidation [isa: 0006497 0018409 ]
+0042050 = protein amino acid lipidation [isa: 0006497 ]
+0018377 = protein myristoylation [isa: 0006497 ]
+0018319 = protein amino acid myristoylation [isa: 0018377 ]
+0006499 = N-terminal protein myristoylation [isa: 0018319 ]
+0018008 = N-terminal peptidyl-glycine N-myristoylation [isa: 0006499 0018201 ]
+0018028 = peptidyl-lysine myristoylation [isa: 0018205 0018319 ]
+0019704 = peptidyl-S-myristoyl-L-cysteine biosynthesis from peptidyl-cysteine [isa: 0018198 0018319 ]
+0045234 = protein palmitoleylation [isa: 0006497 ]
+0045235 = protein amino acid palmitoleylation [isa: 0045234 ]
+0019939 = peptidyl-S-palmitoleyl-L-cysteine biosynthesis from peptidyl-cysteine [isa: 0018198 0045235 ]
+0018345 = protein palmitoylation [isa: 0006497 ]
+0018318 = protein amino acid palmitoylation [isa: 0018345 ]
+0006500 = N-terminal protein palmitoylation [isa: 0018318 ]
+0018009 = N-terminal peptidyl-L-cysteine N-palmitoylation [isa: 0006500 0018198 ]
+0018230 = peptidyl-S-palmitoyl-L-cysteine biosynthesis from peptidyl-cysteine [isa: 0018231 0018318 ]
+0018221 = peptidyl-serine palmitoylation [isa: 0018209 0018318 ]
+0018220 = peptidyl-threonine palmitoylation [isa: 0018210 0018318 ]
+0018342 = protein prenylation [isa: 0006497 ]
+0018346 = protein amino acid prenylation [isa: 0018342 ]
+0018347 = protein amino acid farnesylation [isa: 0018343 0018346 ]
+0018227 = peptidyl-S-12-hydroxyfarnesyl-L-cysteine biosynthesis from peptidyl-cysteine [isa: 0018198 0018347 ]
+0018226 = peptidyl-S-farnesyl-L-cysteine biosynthesis from peptidyl-cysteine [isa: 0018198 0018347 ]
+0018348 = protein amino acid geranylgeranylation [isa: 0018344 0018346 ]
+0018228 = peptidyl-S-geranylgeranyl-L-cysteine biosynthesis from peptidyl-cysteine [isa: 0018198 0018348 ]
+0018343 = protein farnesylation [isa: 0018342 ]
+0018344 = protein geranylgeranylation [isa: 0018342 ]
+0045713 = low-density lipoprotein receptor biosynthesis [isa: 0006412 ]
+0045714 = regulation of low-density lipoprotein receptor biosynthesis [isa: 0009889 ] [partof: 0045713 ]
+0045715 = negative regulation of low-density lipoprotein receptor biosynthesis [isa: 0009890 0045714 ]
+0045716 = positive regulation of low-density lipoprotein receptor biosynthesis [isa: 0009891 0045714 ]
+0006057 = mannoprotein biosynthesis [isa: 0006056 0006412 ]
+0045341 = MHC class I biosynthesis [isa: 0006412 ]
+0045343 = regulation of MHC class I biosynthesis [isa: 0009889 ] [partof: 0045341 ]
+0045344 = negative regulation of MHC class I biosynthesis [isa: 0009890 0045343 ]
+0045345 = positive regulation of MHC class I biosynthesis [isa: 0009891 0045343 ]
+0045342 = MHC class II biosynthesis [isa: 0006412 ]
+0045346 = regulation of MHC class II biosynthesis [isa: 0009889 ] [partof: 0045342 ]
+0045347 = negative regulation of MHC class II biosynthesis [isa: 0009890 0045346 ]
+0045348 = positive regulation of MHC class II biosynthesis [isa: 0009891 0045346 ]
+0019184 = non-ribosomal peptide biosynthesis [isa: 0006412 ]
+0006417 = regulation of protein biosynthesis [isa: 0009889 ] [partof: 0006412 ]
+0017148 = negative regulation of protein biosynthesis [isa: 0006417 0009890 ]
+0045727 = positive regulation of protein biosynthesis [isa: 0006417 0009891 ]
+0006445 = regulation of translation [partof: 0006412 ]
+0016478 = negative regulation of translation [isa: 0006445 ]
+0040033 = negative regulation of mRNA translation, snRNA-mediated [isa: 0016478 0045974 ]
+0007319 = negative regulation of oskar mRNA translation [isa: 0016478 0046011 ]
+0045900 = negative regulation of translational elongation [isa: 0006448 0016478 ]
+0045902 = negative regulation of translational fidelity [isa: 0006450 0016478 ]
+0045947 = negative regulation of translational initiation [isa: 0006446 0016478 ]
+0045993 = negative regulation of translational initiation by iron [isa: 0006447 0045947 ]
+0045904 = negative regulation of translational termination [isa: 0006449 0016478 ]
+0045946 = positive regulation of translation [isa: 0006445 ]
+0045975 = positive regulation of mRNA translation, snRNA-mediated [isa: 0045946 0045974 ]
+0046012 = positive regulation of oskar mRNA translation [isa: 0045946 0046011 ]
+0045901 = positive regulation of translational elongation [isa: 0006448 0045946 ]
+0045903 = positive regulation of translational fidelity [isa: 0006450 0045946 ]
+0045948 = positive regulation of translational initiation [isa: 0006446 0045946 ]
+0045994 = positive regulation of translational initiation by iron [isa: 0006447 0045948 ]
+0045905 = positive regulation of translational termination [isa: 0006449 0045946 ]
+0045974 = regulation of mRNA translation, snRNA-mediated [isa: 0006445 ]
+0046011 = regulation of oskar mRNA translation [isa: 0006445 ] [partof: 0007318 ]
+0006448 = regulation of translational elongation [isa: 0006445 ] [partof: 0006414 ]
+0006450 = regulation of translational fidelity [isa: 0006445 ]
+0006446 = regulation of translational initiation [isa: 0006445 ] [partof: 0006413 ]
+0006447 = regulation of translational initiation by iron [isa: 0006446 ]
+0006449 = regulation of translational termination [isa: 0006445 ] [partof: 0006415 ]
+0009386 = translational attenuation [isa: 0006445 ]
+0006452 = translational frameshifting [isa: 0006445 ]
+0006451 = translational readthrough [isa: 0006414 0006445 ]
+0030631 = lysine methylamine methyltransferase cofactor adduct incorporation [isa: 0006451 ]
+0001514 = selenocysteine incorporation [isa: 0006451 ]
+0045557 = TRAIL receptor biosynthesis [isa: 0006412 ]
+0045560 = regulation of TRAIL receptor biosynthesis [isa: 0009889 ] [partof: 0045557 ]
+0045563 = negative regulation of TRAIL receptor biosynthesis [isa: 0009890 0045560 ]
+0045565 = negative regulation of TRAIL receptor 1 biosynthesis [isa: 0045561 0045563 ]
+0045567 = negative regulation of TRAIL receptor 2 biosynthesis [isa: 0045562 0045563 ]
+0045564 = positive regulation of TRAIL receptor biosynthesis [isa: 0009891 0045560 ]
+0045566 = positive regulation of TRAIL receptor 1 biosynthesis [isa: 0045561 0045564 ]
+0045568 = positive regulation of TRAIL receptor 2 biosynthesis [isa: 0045562 0045564 ]
+0045561 = regulation of TRAIL receptor 1 biosynthesis [isa: 0045560 ] [partof: 0045558 ]
+0045562 = regulation of TRAIL receptor 2 biosynthesis [isa: 0045560 ] [partof: 0045559 ]
+0045558 = TRAIL receptor 1 biosynthesis [isa: 0045557 ]
+0045559 = TRAIL receptor 2 biosynthesis [isa: 0045557 ]
+0006414 = translational elongation [partof: 0006412 ]
+0006413 = translational initiation [partof: 0006412 ]
+0006441 = binding to mRNA cap [partof: 0006413 ]
+0001677 = ternary complex formation [partof: 0006413 ]
+0006415 = translational termination [partof: 0006412 ]
+0006444 = nascent polypeptide association [partof: 0006415 ]
+0019081 = viral protein biosynthesis [isa: 0006412 ] [partof: 0019080 ]
+0006809 = nitric oxide biosynthesis [isa: 0009058 0046209 ]
+0045428 = regulation of nitric oxide biosynthesis [isa: 0009889 ] [partof: 0006809 ]
+0045019 = negative regulation of nitric oxide biosynthesis [isa: 0009890 0045428 ]
+0045429 = positive regulation of nitric oxide biosynthesis [isa: 0009891 0045428 ]
+0046112 = nucleobase biosynthesis [isa: 0009058 0009112 ]
+0009113 = purine base biosynthesis [isa: 0006144 0046112 ]
+0046084 = adenine biosynthesis [isa: 0009113 0046083 ]
+0046099 = guanine biosynthesis [isa: 0009113 0046098 ]
+0046101 = hypoxanthine biosynthesis [isa: 0009113 0046100 ]
+0046111 = xanthine biosynthesis [isa: 0009113 0046110 ]
+0019856 = pyrimidine base biosynthesis [isa: 0006206 0046112 ]
+0006207 = 'de novo' pyrimidine base biosynthesis [isa: 0019856 ]
+0046082 = 5-methylcytosine biosynthesis [isa: 0019856 0019857 ]
+0046089 = cytosine biosynthesis [isa: 0019856 0019858 ]
+0046106 = thymine biosynthesis [isa: 0019856 0019859 ]
+0046107 = uracil biosynthesis [isa: 0019856 0019860 ]
+0009163 = nucleoside biosynthesis [isa: 0009058 0009116 ]
+0042451 = purine nucleoside biosynthesis [isa: 0009163 0042278 ]
+0046129 = purine ribonucleoside biosynthesis [isa: 0042451 0042455 0046128 ]
+0046086 = adenosine biosynthesis [isa: 0046085 0046129 ]
+0046114 = guanosine biosynthesis [isa: 0008617 0046129 ]
+0046118 = 7-methylguanosine biosynthesis [isa: 0008618 0046114 ]
+0008616 = queuosine biosynthesis [isa: 0006400 0046116 0046118 ]
+0015973 = guanosine pentaphosphate (5'-pppGpp-3') biosynthesis [isa: 0015972 0046114 ]
+0015970 = guanosine tetraphosphate (5'-ppGpp-3') biosynthesis [isa: 0015969 0046114 ]
+0046134 = pyrimidine nucleoside biosynthesis [isa: 0006213 0009163 ]
+0046132 = pyrimidine ribonucleoside biosynthesis [isa: 0042455 0046131 0046134 ]
+0046088 = cytidine biosynthesis [isa: 0046087 0046132 ]
+0046103 = inosine biosynthesis [isa: 0046102 0046132 ]
+0046109 = uridine biosynthesis [isa: 0046108 0046132 ]
+0009165 = nucleotide biosynthesis [isa: 0009058 0009117 ]
+0009190 = cyclic nucleotide biosynthesis [isa: 0009165 0009187 ]
+0006171 = cAMP biosynthesis [isa: 0009190 0046058 ]
+0006182 = cGMP biosynthesis [isa: 0009190 0046068 ]
+0009263 = deoxyribonucleotide biosynthesis [isa: 0009165 0009262 ]
+0009265 = 2'-deoxyribonucleotide biosynthesis [isa: 0009263 0009394 ]
+0009189 = deoxyribonucleoside diphosphate biosynthesis [isa: 0009133 0009186 0009263 ]
+0009183 = purine deoxyribonucleoside diphosphate biosynthesis [isa: 0009136 0009153 0009182 0009189 ]
+0006173 = dADP biosynthesis [isa: 0009183 0046056 ]
+0006185 = dGDP biosynthesis [isa: 0009183 0046066 ]
+0009197 = pyrimidine deoxyribonucleoside diphosphate biosynthesis [isa: 0009139 0009189 0009196 0009221 ]
+0006240 = dCDP biosynthesis [isa: 0009197 0046062 ]
+0006233 = dTDP biosynthesis [isa: 0009197 0046072 ]
+0006227 = dUDP biosynthesis [isa: 0009197 0046077 ]
+0009157 = deoxyribonucleoside monophosphate biosynthesis [isa: 0009124 0009162 0009263 ]
+0009171 = purine deoxyribonucleoside monophosphate biosynthesis [isa: 0009127 0009153 0009157 0009170 ]
+0006170 = dAMP biosynthesis [isa: 0009171 0046053 ]
+0006181 = dGMP biosynthesis [isa: 0009171 0046054 ]
+0009177 = pyrimidine deoxyribonucleoside monophosphate biosynthesis [isa: 0009130 0009157 0009176 0009221 ]
+0046064 = dCMP biosynthesis [isa: 0009177 0046063 ]
+0006239 = dCMP salvage [isa: 0008655 0009177 0046063 ]
+0006231 = dTMP biosynthesis [isa: 0009177 0046073 ]
+0006226 = dUMP biosynthesis [isa: 0009177 0046078 ]
+0009202 = deoxyribonucleoside triphosphate biosynthesis [isa: 0009142 0009200 0009263 ]
+0009216 = purine deoxyribonucleoside triphosphate biosynthesis [isa: 0009145 0009153 0009202 0009215 ]
+0006174 = dADP phosphorylation [isa: 0009216 0016310 0046056 ]
+0006175 = dATP biosynthesis [isa: 0009216 0046060 ]
+0006176 = dATP biosynthesis from ADP [isa: 0006175 ]
+0046071 = dGTP biosynthesis [isa: 0009216 0046070 ]
+0006187 = dGTP biosynthesis from dGDP [isa: 0046071 ]
+0006194 = dIDP phosphorylation [isa: 0009216 0016310 ]
+0009212 = pyrimidine deoxyribonucleoside triphosphate biosynthesis [isa: 0009148 0009202 0009211 0009221 ]
+0006242 = dCTP biosynthesis [isa: 0009212 0046065 ]
+0006235 = dTTP biosynthesis [isa: 0009212 0046075 ]
+0006229 = dUTP biosynthesis [isa: 0009212 0046080 ]
+0009153 = purine deoxyribonucleotide biosynthesis [isa: 0006164 0009151 0009263 ]
+0009221 = pyrimidine deoxyribonucleotide biosynthesis [isa: 0006221 0009219 0009263 ]
+0009133 = nucleoside diphosphate biosynthesis [isa: 0009132 0009165 ]
+0009136 = purine nucleoside diphosphate biosynthesis [isa: 0006164 0009133 0009135 ]
+0009180 = purine ribonucleoside diphosphate biosynthesis [isa: 0009136 0009152 0009179 0009188 ]
+0006172 = ADP biosynthesis [isa: 0009180 0046031 ]
+0006192 = IDP phosphorylation [isa: 0009180 0016310 ]
+0009139 = pyrimidine nucleoside diphosphate biosynthesis [isa: 0006221 0009133 0009138 ]
+0009194 = pyrimidine ribonucleoside diphosphate biosynthesis [isa: 0009139 0009188 0009193 0009220 ]
+0006232 = TDP biosynthesis [isa: 0009194 0046043 ]
+0006225 = UDP biosynthesis [isa: 0009194 0046048 ]
+0009188 = ribonucleoside diphosphate biosynthesis [isa: 0009133 0009185 0009260 ]
+0009124 = nucleoside monophosphate biosynthesis [isa: 0009123 0009165 ]
+0009127 = purine nucleoside monophosphate biosynthesis [isa: 0006164 0009124 0009126 ]
+0009168 = purine ribonucleoside monophosphate biosynthesis [isa: 0009127 0009152 0009156 0009167 ]
+0006167 = AMP biosynthesis [isa: 0009168 0046033 ]
+0006168 = adenine salvage pathway [isa: 0006166 0006167 ]
+0006169 = adenosine salvage pathway [isa: 0006166 0006167 ]
+0006177 = GMP biosynthesis [isa: 0009168 0046037 ]
+0006180 = deoxyguanosine salvage [isa: 0006166 0006177 ]
+0006178 = guanine salvage [isa: 0006166 0006177 ]
+0006179 = guanosine salvage [isa: 0006166 0006177 ]
+0006188 = IMP biosynthesis [isa: 0009168 0046040 ]
+0006189 = 'de novo' IMP biosynthesis [isa: 0006188 ]
+0006191 = deoxyinosine salvage [isa: 0006166 0006188 ]
+0006190 = inosine salvage [isa: 0006166 0006188 ]
+0009130 = pyrimidine nucleoside monophosphate biosynthesis [isa: 0006221 0009124 0009129 ]
+0009174 = pyrimidine ribonucleoside monophosphate biosynthesis [isa: 0009130 0009156 0009173 0009220 ]
+0009224 = CMP biosynthesis [isa: 0009174 0046035 ]
+0006238 = CMP salvage [isa: 0008655 0009224 ]
+0006230 = TMP biosynthesis [isa: 0009174 0046044 ]
+0006222 = UMP biosynthesis [isa: 0009174 0046049 ]
+0006223 = uracil salvage [isa: 0006222 0008655 ]
+0006224 = uridine kinase reaction [isa: 0006222 ]
+0009156 = ribonucleoside monophosphate biosynthesis [isa: 0009124 0009161 0009260 ]
+0009142 = nucleoside triphosphate biosynthesis [isa: 0009141 0009165 ]
+0009145 = purine nucleoside triphosphate biosynthesis [isa: 0006164 0009142 0009144 ]
+0009206 = purine ribonucleoside triphosphate biosynthesis [isa: 0009145 0009152 0009201 0009205 ]
+0006183 = GTP biosynthesis [isa: 0009206 0046039 ]
+0046042 = ITP biosynthesis [isa: 0009206 0046041 ]
+0009148 = pyrimidine nucleoside triphosphate biosynthesis [isa: 0006221 0009142 0009147 ]
+0009201 = ribonucleoside triphosphate biosynthesis [isa: 0009142 0009199 0009260 ]
+0009209 = pyrimidine ribonucleoside triphosphate biosynthesis [isa: 0009201 0009208 0009220 ]
+0006241 = CTP biosynthesis [isa: 0009209 0046036 ]
+0006234 = TTP biosynthesis [isa: 0009209 0046046 ]
+0006228 = UTP biosynthesis [isa: 0009209 0046051 ]
+0006164 = purine nucleotide biosynthesis [isa: 0006163 0009165 ]
+0009152 = purine ribonucleotide biosynthesis [isa: 0006164 0009150 0009260 ]
+0006221 = pyrimidine nucleotide biosynthesis [isa: 0006220 0009165 ]
+0009220 = pyrimidine ribonucleotide biosynthesis [isa: 0006221 0009218 0009260 ]
+0008655 = pyrimidine salvage [isa: 0006221 ]
+0006236 = cytidine salvage [isa: 0006216 0008655 ]
+0006237 = deoxycytidine salvage [isa: 0006217 0008655 ]
+0009260 = ribonucleotide biosynthesis [isa: 0009165 0009259 ]
+0009226 = nucleotide-sugar biosynthesis [isa: 0009058 0009225 ]
+0019753 = one-carbon compound biosynthesis [isa: 0006730 0009058 ]
+0046201 = cyanate biosynthesis [isa: 0009439 0019753 ]
+0046202 = cyanide biosynthesis [isa: 0019499 0019753 ]
+0015943 = formate biosynthesis [isa: 0015942 0019753 ]
+0015948 = methanogenesis [isa: 0009061 0015947 0015975 0019753 ]
+0019385 = methanogenesis, from acetate [isa: 0015948 ]
+0019386 = methanogenesis, from carbon dioxide [isa: 0015948 ]
+0019387 = methanogenesis, from methanol [isa: 0015948 ]
+0016053 = organic acid biosynthesis [isa: 0006082 0009058 ]
+0046394 = carboxylic acid biosynthesis [isa: 0016053 0019752 ]
+0019413 = acetate biosynthesis [isa: 0006083 0046394 ]
+0019415 = acetate biosynthesis from carbon monoxide [isa: 0019413 ]
+0030636 = acetate derivative biosynthesis [isa: 0019413 0030635 ]
+0030639 = polyketide biosynthesis [isa: 0030636 0030638 ]
+0006085 = acetyl-CoA biosynthesis [isa: 0006084 0019413 ]
+0006086 = acetyl-CoA biosynthesis from pyruvate [isa: 0006085 ]
+0030634 = carbon fixation by acetyl-CoA pathway [isa: 0006085 0015977 ]
+0019578 = aldaric acid biosynthesis [isa: 0019577 0046394 ]
+0046357 = galactarate biosynthesis [isa: 0019578 0019580 ]
+0019393 = glucarate biosynthesis [isa: 0019392 0019578 ]
+0046358 = butyrate biosynthesis [isa: 0019605 0046394 ]
+0046360 = 2-oxobutyrate biosynthesis [isa: 0046358 0046361 ]
+0046399 = glucuronate biosynthesis [isa: 0019585 0046394 ]
+0006065 = UDP-glucuronate biosynthesis [isa: 0046398 0046399 ]
+0019249 = lactate biosynthesis [isa: 0006089 0046394 ]
+0019244 = lactate biosynthesis from pyruvate [isa: 0006087 0019249 ]
+0019245 = D(-)-lactate biosynthesis from pyruvate [isa: 0019244 ]
+0019246 = L(+)-lactate biosynthesis from pyruvate [isa: 0019244 ]
+0006654 = phosphatidic acid biosynthesis [isa: 0046394 0046473 0046474 ]
+0019542 = propionate biosynthesis [isa: 0019541 0046394 ]
+0019687 = pyruvate biosynthesis from acetate [isa: 0006090 0046394 ]
+0046414 = organomercury biosynthesis [isa: 0009058 0018941 ]
+0042192 = methylmercury biosynthesis [isa: 0042191 0046414 ]
+0046148 = pigment biosynthesis [isa: 0009058 0042440 ]
+0006726 = eye pigment biosynthesis [isa: 0042441 0046148 ]
+0006727 = ommochrome biosynthesis [isa: 0006726 0008055 0046152 ]
+0016063 = rhodopsin biosynthesis [isa: 0006726 0046154 ]
+0042438 = melanin biosynthesis [isa: 0006582 0046148 ]
+0006583 = melanin biosynthesis from tyrosine [isa: 0042438 ]
+0008055 = ocellus pigment biosynthesis [isa: 0046148 0046158 ]
+0006799 = polyphosphate biosynthesis [isa: 0006797 0009058 ]
+0009889 = regulation of biosynthesis [isa: 0019222 ] [partof: 0009058 ]
+0009890 = negative regulation of biosynthesis [isa: 0009889 0009892 ]
+0009891 = positive regulation of biosynthesis [isa: 0009889 0009893 ]
+0042455 = ribonucleoside biosynthesis [isa: 0009058 0009119 ]
+0046246 = terpene biosynthesis [isa: 0009058 0042214 ]
+0046248 = alpha-pinene biosynthesis [isa: 0018867 0046246 ]
+0046250 = limonene biosynthesis [isa: 0018923 0046246 ]
+0009110 = vitamin biosynthesis [isa: 0006766 0009058 ]
+0042362 = fat-soluble vitamin biosynthesis [isa: 0006775 0009110 ]
+0006777 = Mo-molybdopterin cofactor biosynthesis [isa: 0019720 0042362 ]
+0042368 = vitamin D biosynthesis [isa: 0042359 0042362 ]
+0042047 = W-molybdopterin cofactor biosynthesis [isa: 0042046 0042362 ]
+0042364 = water-soluble vitamin biosynthesis [isa: 0006767 0009110 ]
+0009102 = biotin biosynthesis [isa: 0006768 0042364 ]
+0019853 = L-ascorbic acid biosynthesis [isa: 0019852 0042364 ]
+0009228 = thiamin biosynthesis [isa: 0006772 0042364 ]
+0009231 = vitamin B2 biosynthesis [isa: 0006771 0042364 ]
+0005975 = carbohydrate metabolism [isa: 0008152 ]
+0019520 = aldonic acid metabolism [isa: 0005975 ]
+0046176 = aldonic acid catabolism [isa: 0016052 0019520 ]
+0019524 = D-dehydro-D-gluconate catabolism [isa: 0019525 0046176 ]
+0046177 = D-gluconate catabolism [isa: 0019521 0046176 ]
+0046181 = ketogluconate catabolism [isa: 0019522 0046176 ]
+0046183 = L-idonate catabolism [isa: 0019523 0046181 ]
+0019525 = D-dehydro-D-gluconate metabolism [isa: 0019520 ]
+0019521 = D-gluconate metabolism [isa: 0019520 ]
+0019522 = ketogluconate metabolism [isa: 0019520 ]
+0019523 = L-idonate metabolism [isa: 0019522 ]
+0006040 = amino sugar metabolism [isa: 0005975 ]
+0046348 = amino sugar catabolism [isa: 0006040 0016052 ]
+0030392 = fructosamine catabolism [isa: 0030389 0046348 ]
+0006043 = glucosamine catabolism [isa: 0006041 0046348 ]
+0006046 = N-acetylglucosamine catabolism [isa: 0006043 0006044 ]
+0006049 = UDP-N-acetylglucosamine catabolism [isa: 0006046 0006047 ]
+0046346 = mannosamine catabolism [isa: 0006050 0046348 ]
+0006053 = N-acetylmannosamine catabolism [isa: 0006051 0046346 ]
+0019262 = N-acetylneuraminate catabolism [isa: 0006054 0046348 ]
+0019278 = UDP-N-acetylgalactosamine catabolism [isa: 0019276 0046348 ]
+0030389 = fructosamine metabolism [isa: 0006040 ]
+0030394 = fructoseglycine metabolism [isa: 0030389 ]
+0030393 = fructoselysine metabolism [isa: 0030389 ]
+0006041 = glucosamine metabolism [isa: 0006040 ]
+0006044 = N-acetylglucosamine metabolism [isa: 0006041 ]
+0006047 = UDP-N-acetylglucosamine metabolism [isa: 0006044 ]
+0006050 = mannosamine metabolism [isa: 0006040 ]
+0006051 = N-acetylmannosamine metabolism [isa: 0006050 ]
+0006054 = N-acetylneuraminate metabolism [isa: 0006040 ]
+0046381 = CMP-N-acetylneuraminate metabolism [isa: 0006054 ]
+0019276 = UDP-N-acetylgalactosamine metabolism [isa: 0006040 ]
+0006022 = aminoglycan metabolism [isa: 0005975 ]
+0006026 = aminoglycan catabolism [isa: 0006022 0016052 ]
+0006028 = galactosaminoglycan catabolism [isa: 0006026 0046350 ]
+0006027 = glycosaminoglycan catabolism [isa: 0006026 0030203 ]
+0030207 = chondroitin sulfate catabolism [isa: 0006027 0030204 ]
+0030209 = dermatan sulfate catabolism [isa: 0006027 0030205 ]
+0030211 = heparin catabolism [isa: 0006027 0030202 ]
+0030214 = hyaluronan catabolism [isa: 0006027 0030212 ]
+0042340 = keratan sulfate catabolism [isa: 0006027 0042339 ]
+0046350 = galactosaminoglycan metabolism [isa: 0006022 ]
+0030203 = glycosaminoglycan metabolism [isa: 0006022 ]
+0030204 = chondroitin sulfate metabolism [isa: 0030203 ]
+0018402 = protein-chondroitin sulfate linkage via chondroitin sulfate D-glucuronyl-D-galactosyl-D-galactosyl-D-xylosyl-L-serine [isa: 0018209 0030204 ]
+0019800 = protein-protein cross-linking via chondroitin 4-sulfate glycosaminoglycan [isa: 0018149 0018209 0030204 ]
+0030205 = dermatan sulfate metabolism [isa: 0030203 ]
+0030202 = heparin metabolism [isa: 0030203 ]
+0030212 = hyaluronan metabolism [isa: 0030203 ]
+0042339 = keratan sulfate metabolism [isa: 0030203 ]
+0016052 = carbohydrate catabolism [isa: 0005975 0009056 ]
+0046352 = disaccharide catabolism [isa: 0005984 0016052 ]
+0005990 = lactose catabolism [isa: 0005988 0046352 ]
+0019513 = lactose catabolism, by glucoside 3-dehydrogenase [isa: 0005990 ]
+0019512 = lactose catabolism, by tagatose-6-phosphate [isa: 0005990 ]
+0019515 = lactose catabolism, by UDP-galactose [isa: 0005990 ]
+0019514 = lactose hydrolysis [isa: 0005990 ]
+0000025 = maltose catabolism [isa: 0000023 0046352 ]
+0005995 = melibiose catabolism [isa: 0005994 0046352 ]
+0005987 = sucrose catabolism [isa: 0005985 0046352 ]
+0019575 = sucrose catabolism, by beta-fructofuranosidase [isa: 0005987 ]
+0019574 = sucrose catabolism, by glucoside 3-dehydrogenase [isa: 0005987 ]
+0005993 = trehalose catabolism [isa: 0005991 0046352 ]
+0019391 = glucuronoside catabolism [isa: 0016052 0019389 ]
+0016139 = glycoside catabolism [isa: 0016052 0016137 ]
+0042342 = cyanogenic glycoside catabolism [isa: 0016139 0042341 ]
+0019759 = glycosinolate catabolism [isa: 0016139 0019757 ]
+0019762 = glucosinolate catabolism [isa: 0019759 0019760 ]
+0016142 = O-glycoside catabolism [isa: 0016139 0016140 ]
+0016145 = S-glycoside catabolism [isa: 0016139 0016143 ]
+0016136 = saponin catabolism [isa: 0016115 0016130 0016134 0016139 ]
+0009313 = oligosaccharide catabolism [isa: 0009311 0016052 ]
+0009253 = peptidoglycan catabolism [isa: 0000270 0016052 ]
+0000272 = polysaccharide catabolism [isa: 0005976 0016052 ]
+0042122 = alginic acid catabolism [isa: 0000272 0042120 ]
+0006032 = chitin catabolism [isa: 0000272 0006030 0009057 ]
+0006039 = cell wall chitin catabolism [isa: 0006032 0006037 ]
+0006036 = cuticle chitin catabolism [isa: 0006032 0006034 ]
+0009251 = glucan catabolism [isa: 0000272 0006073 ]
+0006076 = beta-1,3 glucan catabolism [isa: 0006074 0009251 ]
+0006079 = beta-1,6 glucan catabolism [isa: 0009251 ]
+0030245 = cellulose catabolism [isa: 0009251 0030243 ]
+0005980 = glycogen catabolism [isa: 0005977 0009251 ]
+0005981 = regulation of glycogen catabolism [isa: 0009894 ] [partof: 0005980 ]
+0045818 = negative regulation of glycogen catabolism [isa: 0005981 ]
+0045819 = positive regulation of glycogen catabolism [isa: 0005981 ]
+0005983 = starch catabolism [isa: 0005982 0009251 ]
+0009104 = lipopolysaccharide catabolism [isa: 0000272 0008653 0016042 ]
+0046355 = mannan catabolism [isa: 0000272 0006080 ]
+0045490 = pectin catabolism [isa: 0000272 0045488 ]
+0030310 = poly-N-acetyllactosamine catabolism [isa: 0000272 0030309 ]
+0045493 = xylan catabolism [isa: 0000272 0045491 ]
+0030167 = proteoglycan catabolism [isa: 0006029 0016052 ]
+0030200 = heparan sulfate proteoglycan catabolism [isa: 0030167 0030201 ]
+0005984 = disaccharide metabolism [isa: 0005975 ]
+0005988 = lactose metabolism [isa: 0005984 ]
+0000023 = maltose metabolism [isa: 0005984 ]
+0005994 = melibiose metabolism [isa: 0005984 ]
+0005985 = sucrose metabolism [isa: 0005984 ]
+0005991 = trehalose metabolism [isa: 0005984 0006112 ]
+0019389 = glucuronoside metabolism [isa: 0005975 ]
+0016137 = glycoside metabolism [isa: 0005975 ]
+0042341 = cyanogenic glycoside metabolism [isa: 0016137 ]
+0019757 = glycosinolate metabolism [isa: 0016137 0019748 ]
+0019760 = glucosinolate metabolism [isa: 0019757 ]
+0016140 = O-glycoside metabolism [isa: 0016137 ]
+0016143 = S-glycoside metabolism [isa: 0016137 ]
+0016134 = saponin metabolism [isa: 0006721 0016128 0016137 ]
+0009311 = oligosaccharide metabolism [isa: 0005975 ]
+0046401 = lipopolysaccharide core region metabolism [isa: 0009311 ]
+0000270 = peptidoglycan metabolism [isa: 0005975 ]
+0009254 = peptidoglycan turnover [isa: 0000270 ]
+0005976 = polysaccharide metabolism [isa: 0005975 ]
+0042120 = alginic acid metabolism [isa: 0005976 ]
+0006030 = chitin metabolism [isa: 0005976 ]
+0006037 = cell wall chitin metabolism [isa: 0006030 ]
+0006033 = chitin localization [isa: 0006030 ]
+0006034 = cuticle chitin metabolism [isa: 0006030 ]
+0046377 = colanic acid metabolism [isa: 0005976 ]
+0046378 = enterobacterial common antigen metabolism [isa: 0005976 ]
+0046379 = extracellular polysaccharide metabolism [isa: 0005976 ]
+0046376 = GDP-alpha-D-mannosylchitobiosyldiphosphodolichol metabolism [isa: 0005976 0019348 ]
+0006073 = glucan metabolism [isa: 0005976 ]
+0006074 = beta-1,3 glucan metabolism [isa: 0006073 ]
+0006077 = beta-1,6 glucan metabolism [isa: 0006073 ]
+0030243 = cellulose metabolism [isa: 0006073 ]
+0005977 = glycogen metabolism [isa: 0006073 0006112 ]
+0005982 = starch metabolism [isa: 0006073 ]
+0046375 = K antigen metabolism [isa: 0005976 ]
+0008653 = lipopolysaccharide metabolism [isa: 0005976 0006629 ]
+0006080 = mannan metabolism [isa: 0005976 ]
+0046402 = O antigen metabolism [isa: 0005976 ]
+0045488 = pectin metabolism [isa: 0005976 ]
+0030309 = poly-N-acetyllactosamine metabolism [isa: 0005976 ]
+0045491 = xylan metabolism [isa: 0005976 ]
+0006029 = proteoglycan metabolism [isa: 0005975 ]
+0030201 = heparan sulfate proteoglycan metabolism [isa: 0006029 ]
+0001526 = proteoglycan sulfate transfer [isa: 0006029 0006790 ]
+0006109 = regulation of carbohydrate metabolism [isa: 0015980 0019222 ] [partof: 0005975 ]
+0045912 = negative regulation of carbohydrate metabolism [isa: 0006109 0009892 ]
+0045913 = positive regulation of carbohydrate metabolism [isa: 0006109 0009893 ]
+0015976 = carbon utilization [isa: 0008152 ]
+0015977 = carbon utilization by fixation of carbon dioxide [isa: 0015976 ]
+0015978 = carbon utilization by utilization of organic compounds [isa: 0015976 ]
+0009056 = catabolism [isa: 0008152 ]
+0009822 = alkaloid catabolism [isa: 0009056 0009820 ]
+0019608 = nicotine catabolism [isa: 0009822 0018933 ]
+0046306 = alkanesulfonate catabolism [isa: 0009056 0019694 ]
+0016998 = cell wall catabolism [isa: 0009056 ]
+0019241 = citrulline catabolism [isa: 0000052 0009056 ]
+0046139 = coenzymes and prosthetic group catabolism [isa: 0006731 0009056 ]
+0009109 = coenzyme catabolism [isa: 0006732 0046139 ]
+0015938 = coenzyme A catabolism [isa: 0009109 0015936 ]
+0009397 = folic acid and derivative catabolism [isa: 0006760 0009109 ]
+0009258 = 10-formyltetrahydrofolate catabolism [isa: 0009256 0009397 ]
+0046657 = folic acid catabolism [isa: 0009397 0046655 ]
+0006751 = glutathione catabolism [isa: 0006749 0009109 ]
+0015941 = pantothenate catabolism [isa: 0009109 0015939 ]
+0019364 = pyridine nucleotide catabolism [isa: 0009109 0019362 0042365 ]
+0006737 = NADH catabolism [isa: 0006734 0019364 ]
+0006742 = NADPH catabolism [isa: 0006739 0019364 ]
+0019677 = nicotinamide adenine dinucleotide catabolism [isa: 0019364 0019674 ]
+0006738 = nicotinamide riboside catabolism [isa: 0006734 0019364 0046495 ]
+0042378 = quinone cofactor catabolism [isa: 0009109 0042375 ]
+0042377 = vitamin K catabolism [isa: 0042363 0042373 0042378 ]
+0042376 = vitamin K1 catabolism [isa: 0042374 0042377 ]
+0042361 = vitamin K2 catabolism [isa: 0009233 0042377 ]
+0042358 = thiamin diphosphate catabolism [isa: 0009109 0042357 ]
+0046141 = corrin catabolism [isa: 0015009 0046139 ]
+0006787 = porphyrin catabolism [isa: 0006778 0046139 ]
+0006789 = bilirubin conjugation [isa: 0006787 ]
+0015996 = chlorophyll catabolism [isa: 0006787 0015994 0046149 ]
+0030495 = bacteriochlorophyll catabolism [isa: 0015996 0030493 ]
+0042167 = heme catabolism [isa: 0006787 0042168 0046149 ]
+0046161 = heme a catabolism [isa: 0042167 0046160 ]
+0046163 = heme c catabolism [isa: 0042167 0046162 ]
+0046157 = siroheme catabolism [isa: 0042167 0046156 ]
+0006788 = heme oxidation [isa: 0042168 ] [partof: 0006787 ]
+0042366 = vitamin B12 catabolism [isa: 0006787 0009235 0042365 ]
+0046215 = siderochrome catabolism [isa: 0009237 0046139 ]
+0046214 = enterobactin catabolism [isa: 0009238 0046215 ]
+0046121 = deoxyribonucleoside catabolism [isa: 0009056 0009120 ]
+0046124 = purine deoxyribonucleoside catabolism [isa: 0006152 0046121 0046122 ]
+0006157 = deoxyadenosine catabolism [isa: 0046090 0046124 ]
+0006158 = deoxyadenosine deaminase reaction [isa: 0006157 ]
+0006159 = deoxyadenosine phosphorolysis [isa: 0006157 ]
+0006161 = deoxyguanosine catabolism [isa: 0042453 0046124 ]
+0046127 = pyrimidine deoxyribonucleoside catabolism [isa: 0046121 0046125 0046135 ]
+0006217 = deoxycytidine catabolism [isa: 0046092 0046127 ]
+0006149 = deoxyinosine catabolism [isa: 0046094 0046127 ]
+0006219 = deoxyuridine catabolism [isa: 0046096 0046127 ]
+0006214 = thymidine catabolism [isa: 0046104 0046127 ]
+0006308 = DNA catabolism [isa: 0006259 0009056 ]
+0000737 = DNA catabolism, endonucleolytic [isa: 0006308 ]
+0000728 = gene conversion at MAT locus, DNA double-strand break formation [isa: 0000737 ] [partof: 0007534 ]
+0000738 = DNA catabolism, exonucleolytic [isa: 0006308 ]
+0000729 = DNA double-strand break processing [isa: 0000738 ] [partof: 0007534 0045002 0045003 ]
+0006309 = DNA fragmentation [isa: 0006308 0006921 0009290 ] [partof: 0030262 ]
+0042447 = hormone catabolism [isa: 0009056 0042445 ]
+0006710 = androgen catabolism [isa: 0006706 0008209 0042447 ]
+0009852 = auxin catabolism [isa: 0009850 0042447 ]
+0008208 = C21-steroid hormone catabolism [isa: 0006706 0008207 0042447 ]
+0006709 = progesterone catabolism [isa: 0008208 0042448 ]
+0009823 = cytokinin catabolism [isa: 0009690 0042447 ]
+0046344 = ecdysteroid catabolism [isa: 0006706 0042182 0042447 0045455 ]
+0006708 = ecdysone catabolism [isa: 0008205 0016127 0046344 ]
+0006711 = estrogen catabolism [isa: 0006706 0008210 0042447 ]
+0006713 = glucocorticoid catabolism [isa: 0006706 0008211 0042447 ]
+0006719 = juvenile hormone catabolism [isa: 0006716 0016107 0042447 ]
+0045952 = regulation of juvenile hormone catabolism [isa: 0007556 ] [partof: 0006719 ]
+0045970 = negative regulation of juvenile hormone catabolism [isa: 0045928 0045952 ]
+0045971 = positive regulation of juvenile hormone catabolism [isa: 0045929 0045952 ]
+0006712 = mineralocorticoid catabolism [isa: 0006706 0008212 0042447 ]
+0042182 = ketone catabolism [isa: 0009056 0042180 ]
+0019383 = (+)-camphor catabolism [isa: 0018882 0042182 0046247 ]
+0045150 = acetoin catabolism [isa: 0042182 0045149 ]
+0016042 = lipid catabolism [isa: 0006629 0009056 ]
+0009062 = fatty acid catabolism [isa: 0006631 0016042 0046395 ]
+0019626 = short-chain fatty acid catabolism [isa: 0009062 0046459 ]
+0008300 = isoprenoid catabolism [isa: 0006720 0016042 ]
+0045339 = farnesyl diphosphate catabolism [isa: 0008300 0045338 ]
+0016097 = polyisoprenoid catabolism [isa: 0008300 0016096 ]
+0016115 = terpenoid catabolism [isa: 0006721 0016097 0046247 ]
+0016103 = diterpenoid catabolism [isa: 0016101 0016115 ]
+0045487 = gibberellic acid catabolism [isa: 0009685 0016103 0046395 ]
+0016100 = monoterpenoid catabolism [isa: 0016098 0016115 ]
+0016113 = polyterpenoid catabolism [isa: 0016111 0016115 ]
+0016107 = sesquiterpenoid catabolism [isa: 0006714 0016115 ]
+0046345 = abscisic acid catabolism [isa: 0009687 0016107 0046395 ]
+0016110 = tetraterpenoid catabolism [isa: 0016108 0016115 ]
+0016118 = carotenoid catabolism [isa: 0016110 0016116 ]
+0016121 = carotene catabolism [isa: 0016118 0016119 ]
+0016124 = xanthophyll catabolism [isa: 0016118 0016122 ]
+0016105 = triterpenoid catabolism [isa: 0006722 0016115 ]
+0019741 = pentacyclic triterpenoid catabolism [isa: 0016105 0019742 ]
+0019743 = hopanoid catabolism [isa: 0019741 0019744 ]
+0016092 = prenol catabolism [isa: 0008300 0016090 ]
+0016095 = polyprenol catabolism [isa: 0016092 0016093 ]
+0046466 = membrane lipid catabolism [isa: 0006643 0016042 ]
+0019377 = glycolipid catabolism [isa: 0006664 0046466 ]
+0019376 = galactolipid catabolism [isa: 0019374 0019377 ]
+0006683 = galactosylceramide catabolism [isa: 0006681 0019376 0046477 ]
+0046479 = glycosphingolipid catabolism [isa: 0006687 0019377 0030149 ]
+0006689 = ganglioside catabolism [isa: 0001573 0046479 ]
+0046477 = glycosylceramide catabolism [isa: 0006677 0019377 0046514 ]
+0006680 = glucosylceramide catabolism [isa: 0006678 0046477 ]
+0009395 = phospholipid catabolism [isa: 0006644 0046466 ]
+0046461 = neutral lipid catabolism [isa: 0006638 0016042 ]
+0046464 = acylglycerol catabolism [isa: 0006639 0046461 ]
+0046340 = diacylglycerol catabolism [isa: 0046339 0046464 ]
+0046342 = CDP-diacylglycerol catabolism [isa: 0046340 0046341 ]
+0019433 = triacylglycerol catabolism [isa: 0006641 0046464 ]
+0006706 = steroid catabolism [isa: 0008202 0016042 ]
+0030573 = bile acid catabolism [isa: 0006706 0008206 0046395 ]
+0016130 = phytosteroid catabolism [isa: 0006706 0016128 ]
+0016133 = brassinosteroid catabolism [isa: 0016130 0016131 ]
+0016127 = sterol catabolism [isa: 0006706 0016125 ]
+0006707 = cholesterol catabolism [isa: 0008203 0016127 ]
+0009057 = macromolecule catabolism [isa: 0009056 ]
+0030163 = protein catabolism [isa: 0009057 0019538 ]
+0030327 = prenylated protein catabolism [isa: 0030163 ]
+0030164 = protein denaturation [isa: 0030163 ]
+0006508 = proteolysis and peptidolysis [isa: 0030163 ]
+0006510 = ATP-dependent proteolysis [isa: 0006508 ]
+0030574 = collagen catabolism [isa: 0006508 ]
+0006516 = glycoprotein catabolism [isa: 0006508 0009100 ]
+0009050 = glycopeptide catabolism [isa: 0006516 ]
+0045173 = O-sialoglycoprotein catabolism [isa: 0006516 ]
+0006517 = protein deglycosylation [partof: 0006516 ]
+0020029 = hemoglobin hydrolysis [isa: 0006508 0042540 ]
+0042159 = lipoprotein catabolism [isa: 0006508 0042157 ]
+0045192 = low-density lipoprotein catabolism [isa: 0042159 ]
+0045193 = acetylated low-density lipoprotein catabolism [isa: 0045192 ]
+0045194 = oxidized low-density lipoprotein catabolism [isa: 0045192 ]
+0006058 = mannoprotein catabolism [isa: 0006056 0006508 ]
+0006509 = membrane protein ectodomain proteolysis [isa: 0006508 ]
+0006515 = misfolded or incompletely synthesized protein catabolism [isa: 0006508 ]
+0030433 = ER-associated protein catabolism [isa: 0006511 0006515 ]
+0019941 = protein-ligand dependent protein catabolism [isa: 0006508 ]
+0019942 = RUB1-dependent protein catabolism [isa: 0019941 ]
+0019943 = RUB1-protein conjugation [isa: 0006464 0019942 ]
+0019950 = SMT3-dependent protein catabolism [isa: 0019941 ]
+0019951 = SMT3-protein conjugation [isa: 0006464 0019950 ]
+0019940 = SUMO-dependent protein catabolism [isa: 0019941 ]
+0016928 = desumoylation [isa: 0019940 ]
+0016926 = protein desumoylation [isa: 0006464 0016928 ]
+0016927 = sumoylation [isa: 0019940 ]
+0016925 = protein sumoylation [isa: 0006464 0016927 ]
+0006511 = ubiquitin-dependent protein catabolism [isa: 0019941 ]
+0019130 = protein amino acid arginylation [isa: 0006464 ] [partof: 0006511 ]
+0016598 = protein arginylation [isa: 0006464 ] [partof: 0006511 ]
+0006512 = ubiquitin cycle [isa: 0006511 ]
+0006514 = deubiquitination [partof: 0006512 ]
+0016579 = protein deubiquitination [isa: 0006464 0006514 ]
+0006513 = monoubiquitination [partof: 0006512 ]
+0016567 = protein ubiquitination [isa: 0000209 0006464 0006513 ]
+0000209 = polyubiquitination [partof: 0006512 ]
+0030162 = regulation of proteolysis and peptidolysis [isa: 0009894 ] [partof: 0006508 ]
+0045861 = negative regulation of proteolysis and peptidolysis [isa: 0030162 ]
+0045862 = positive regulation of proteolysis and peptidolysis [isa: 0030162 ]
+0042176 = regulation of protein catabolism [isa: 0009894 ] [partof: 0030163 ]
+0042177 = negative regulation of protein catabolism [isa: 0009895 0042176 ]
+0045732 = positive regulation of protein catabolism [isa: 0009896 0042176 ]
+0006401 = RNA catabolism [isa: 0009057 0016070 ]
+0006402 = mRNA catabolism [isa: 0006401 0016071 ]
+0000288 = mRNA catabolism, deadenylation-dependent [isa: 0006402 ]
+0000290 = deadenylation-dependent decapping [partof: 0000288 ]
+0000291 = mRNA catabolism, exonucleolytic [partof: 0000288 0000294 ]
+0000289 = poly(A) tail shortening [partof: 0000288 ]
+0000294 = mRNA catabolism, endonucleolytic [isa: 0006402 ]
+0000184 = mRNA catabolism, nonsense-mediated [isa: 0006402 ]
+0000292 = RNA fragment catabolism [isa: 0006401 ]
+0030452 = group I intron catabolism [isa: 0000292 ]
+0016075 = rRNA catabolism [isa: 0006401 0016072 ]
+0016077 = snoRNA catabolism [isa: 0006401 0016074 ]
+0016076 = snRNA catabolism [isa: 0006401 0016073 ]
+0016078 = tRNA catabolism [isa: 0006399 0006401 ]
+0046210 = nitric oxide catabolism [isa: 0009056 0046209 ]
+0046113 = nucleobase catabolism [isa: 0009056 0009112 ]
+0006145 = purine base catabolism [isa: 0006144 0046113 ]
+0006146 = adenine catabolism [isa: 0006145 0046083 ]
+0000255 = allantoin metabolism [isa: 0006145 ]
+0009442 = allantoin assimilation [isa: 0000255 ]
+0019428 = allantoin biosynthesis [isa: 0000255 ]
+0000256 = allantoin catabolism [isa: 0000255 ]
+0006147 = guanine catabolism [isa: 0006145 0046098 ]
+0009114 = hypoxanthine catabolism [isa: 0006145 0046100 ]
+0006150 = hypoxanthine oxidation [isa: 0009114 ]
+0009115 = xanthine catabolism [isa: 0006145 0046110 ]
+0006151 = xanthine oxidation [isa: 0009115 ]
+0006208 = pyrimidine base catabolism [isa: 0006206 0046113 ]
+0006211 = 5-methylcytosine catabolism [isa: 0006208 0019857 ]
+0006209 = cytosine catabolism [isa: 0006208 0019858 ]
+0006210 = thymine catabolism [isa: 0006208 0019859 ]
+0006212 = uracil catabolism [isa: 0006208 0019860 ]
+0009164 = nucleoside catabolism [isa: 0009056 0009116 ]
+0006152 = purine nucleoside catabolism [isa: 0009164 0042278 ]
+0006153 = purine nucleosidase reaction [isa: 0006152 ]
+0046130 = purine ribonucleoside catabolism [isa: 0006152 0042454 0046128 ]
+0006154 = adenosine catabolism [isa: 0046085 0046130 ]
+0006155 = adenosine deaminase reaction [isa: 0006154 ]
+0006156 = adenosine phosphorolysis [isa: 0006154 ]
+0046115 = guanosine catabolism [isa: 0008617 0046130 ]
+0046119 = 7-methylguanosine catabolism [isa: 0008618 0046115 ]
+0046117 = queuosine catabolism [isa: 0046116 0046119 ]
+0015974 = guanosine pentaphosphate (5'-pppGpp-3') catabolism [isa: 0015972 0046115 ]
+0015971 = guanosine tetraphosphate (5'-ppGpp-3') catabolism [isa: 0015969 0046115 ]
+0046135 = pyrimidine nucleoside catabolism [isa: 0006213 0009164 ]
+0046133 = pyrimidine ribonucleoside catabolism [isa: 0042454 0046131 0046135 ]
+0006216 = cytidine catabolism [isa: 0046087 0046133 ]
+0006148 = inosine catabolism [isa: 0046102 0046133 ]
+0006218 = uridine catabolism [isa: 0046108 0046133 ]
+0009166 = nucleotide catabolism [isa: 0009056 0009117 ]
+0009214 = cyclic nucleotide catabolism [isa: 0009166 0009187 ]
+0006198 = cAMP catabolism [isa: 0009214 ]
+0046069 = cGMP catabolism [isa: 0009214 0046068 ]
+0009264 = deoxyribonucleotide catabolism [isa: 0009166 0009262 ]
+0009192 = deoxyribonucleoside diphosphate catabolism [isa: 0009134 0009186 0009264 ]
+0009184 = purine deoxyribonucleoside diphosphate catabolism [isa: 0009137 0009155 0009182 0009192 ]
+0046057 = dADP catabolism [isa: 0009184 0046056 ]
+0046067 = dGDP catabolism [isa: 0009184 0046066 ]
+0009198 = pyrimidine deoxyribonucleoside diphosphate catabolism [isa: 0009140 0009192 0009196 0009223 ]
+0006251 = dCDP catabolism [isa: 0009198 0046062 ]
+0006246 = dTDP catabolism [isa: 0009198 0046072 ]
+0006257 = dUDP catabolism [isa: 0009198 0046077 ]
+0009159 = deoxyribonucleoside monophosphate catabolism [isa: 0009125 0009162 0009264 ]
+0009172 = purine deoxyribonucleoside monophosphate catabolism [isa: 0009128 0009155 0009159 0009170 ]
+0046059 = dAMP catabolism [isa: 0009172 0046053 ]
+0046055 = dGMP catabolism [isa: 0009172 0046054 ]
+0009178 = pyrimidine deoxyribonucleoside monophosphate catabolism [isa: 0009131 0009159 0009176 0009223 ]
+0006249 = dCMP catabolism [isa: 0009178 0046063 ]
+0046074 = dTMP catabolism [isa: 0009178 0046073 ]
+0046079 = dUMP catabolism [isa: 0009178 0046078 ]
+0009204 = deoxyribonucleoside triphosphate catabolism [isa: 0009143 0009200 0009264 ]
+0009217 = purine deoxyribonucleoside triphosphate catabolism [isa: 0009146 0009155 0009204 0009215 ]
+0046061 = dATP catabolism [isa: 0009217 0046060 ]
+0006203 = dGTP catabolism [isa: 0009217 0046070 ]
+0009213 = pyrimidine deoxyribonucleoside triphosphate catabolism [isa: 0009149 0009204 0009211 0009223 ]
+0006253 = dCTP catabolism [isa: 0009213 0046065 ]
+0046076 = dTTP catabolism [isa: 0009213 0046075 ]
+0046081 = dUTP catabolism [isa: 0009213 0046080 ]
+0009155 = purine deoxyribonucleotide catabolism [isa: 0006195 0009151 0009264 ]
+0009223 = pyrimidine deoxyribonucleotide catabolism [isa: 0006244 0009219 0009264 ]
+0009134 = nucleoside diphosphate catabolism [isa: 0009132 0009166 ]
+0009137 = purine nucleoside diphosphate catabolism [isa: 0006195 0009134 0009135 ]
+0009181 = purine ribonucleoside diphosphate catabolism [isa: 0009137 0009154 0009179 0009191 ]
+0046032 = ADP catabolism [isa: 0009181 0046031 ]
+0006199 = ADP reduction [isa: 0009181 0046031 ]
+0009140 = pyrimidine nucleoside diphosphate catabolism [isa: 0006244 0009134 0009138 ]
+0009195 = pyrimidine ribonucleoside diphosphate catabolism [isa: 0009140 0009191 0009193 0009222 ]
+0006250 = CDP reduction [isa: 0009195 ]
+0006245 = TDP catabolism [isa: 0009195 0046043 ]
+0006256 = UDP catabolism [isa: 0009195 0046048 ]
+0006255 = UDP reduction [isa: 0009195 0046048 ]
+0009191 = ribonucleoside diphosphate catabolism [isa: 0009134 0009185 0009261 ]
+0009125 = nucleoside monophosphate catabolism [isa: 0009123 0009166 ]
+0009128 = purine nucleoside monophosphate catabolism [isa: 0006195 0009125 0009126 ]
+0009169 = purine ribonucleoside monophosphate catabolism [isa: 0009128 0009154 0009158 0009167 ]
+0006196 = AMP catabolism [isa: 0009169 0046033 ]
+0006197 = adenylate deaminase reaction [isa: 0006196 ]
+0046038 = GMP catabolism [isa: 0009169 0046037 ]
+0006202 = GMP catabolism to guanine [isa: 0046038 ]
+0006201 = GMP catabolism to IMP [isa: 0046038 ]
+0006204 = IMP catabolism [isa: 0009169 0046040 ]
+0009131 = pyrimidine nucleoside monophosphate catabolism [isa: 0006244 0009125 0009129 ]
+0009175 = pyrimidine ribonucleoside monophosphate catabolism [isa: 0009131 0009158 0009173 0009222 ]
+0006248 = CMP catabolism [isa: 0009175 0046035 ]
+0046045 = TMP catabolism [isa: 0009175 0046044 ]
+0046050 = UMP catabolism [isa: 0009175 0046049 ]
+0009158 = ribonucleoside monophosphate catabolism [isa: 0009125 0009161 0009261 ]
+0009143 = nucleoside triphosphate catabolism [isa: 0009141 0009166 ]
+0009146 = purine nucleoside triphosphate catabolism [isa: 0006195 0009143 0009144 ]
+0009207 = purine ribonucleoside triphosphate catabolism [isa: 0009146 0009154 0009203 0009205 ]
+0006200 = ATP catabolism [isa: 0009207 0046034 ]
+0006184 = GTP catabolism [isa: 0009207 0046039 ]
+0006193 = ITP catabolism [isa: 0009207 0046041 ]
+0009149 = pyrimidine nucleoside triphosphate catabolism [isa: 0006244 0009143 0009147 ]
+0009210 = pyrimidine ribonucleoside triphosphate catabolism [isa: 0009149 0009203 0009208 0009222 ]
+0006254 = CTP catabolism [isa: 0009210 0046036 ]
+0006243 = CTP deamination [isa: 0009210 0046036 ]
+0006252 = CTP reduction [isa: 0009210 0046036 ]
+0046047 = TTP catabolism [isa: 0009210 0046046 ]
+0006247 = TTP reduction [isa: 0009210 0046046 ]
+0046052 = UTP catabolism [isa: 0009210 0046051 ]
+0009203 = ribonucleoside triphosphate catabolism [isa: 0009143 0009199 0009261 ]
+0006195 = purine nucleotide catabolism [isa: 0006163 0009166 ]
+0009154 = purine ribonucleotide catabolism [isa: 0006195 0009150 0009261 ]
+0006244 = pyrimidine nucleotide catabolism [isa: 0006220 0009166 ]
+0009222 = pyrimidine ribonucleotide catabolism [isa: 0006244 0009218 0009261 ]
+0009261 = ribonucleotide catabolism [isa: 0009166 0009259 ]
+0009227 = nucleotide-sugar catabolism [isa: 0009056 0009225 ]
+0006258 = UDP-glucose catabolism [isa: 0009227 ]
+0019691 = UDP-glucose conversion [isa: 0009227 ]
+0019754 = one-carbon compound catabolism [isa: 0006730 0009056 ]
+0009440 = cyanate catabolism [isa: 0009439 0019754 ]
+0019500 = cyanide catabolism [isa: 0019499 0019754 ]
+0042183 = formate catabolism [isa: 0015942 0019754 ]
+0046188 = methane catabolism [isa: 0015947 0019754 ]
+0016054 = organic acid catabolism [isa: 0006082 0009056 ]
+0046395 = carboxylic acid catabolism [isa: 0016054 0019752 ]
+0045733 = acetate catabolism [isa: 0006083 0046395 ]
+0030637 = acetate derivative catabolism [isa: 0030635 0045733 ]
+0030640 = polyketide catabolism [isa: 0030637 0030638 ]
+0046356 = acetyl-CoA catabolism [isa: 0006084 0045733 ]
+0045734 = regulation of acetate catabolism [isa: 0009894 ] [partof: 0045733 ]
+0045753 = negative regulation of acetate catabolism [isa: 0045734 ]
+0045754 = positive regulation of acetate catabolism [isa: 0045734 ]
+0019579 = aldaric acid catabolism [isa: 0019577 0046395 ]
+0046392 = galactarate catabolism [isa: 0019579 0019580 ]
+0019582 = D-galactarate catabolism [isa: 0046392 0046393 ]
+0019394 = glucarate catabolism [isa: 0019392 0019579 ]
+0046359 = butyrate catabolism [isa: 0019605 0046395 ]
+0019606 = 2-oxobutyrate catabolism [isa: 0046359 0046361 ]
+0019584 = galactonate catabolism [isa: 0019583 0046395 ]
+0046397 = galacturonate catabolism [isa: 0019586 0046395 ]
+0019698 = D-galacturonate catabolism [isa: 0046396 0046397 ]
+0006064 = glucuronate catabolism [isa: 0019585 0046395 ]
+0019640 = glucuronate catabolism to xylulose-5-phosphate [isa: 0006064 ]
+0019543 = propionate catabolism [isa: 0019541 0046395 ]
+0019629 = propionate catabolism, via 2-methylcitrate cycle [isa: 0019543 ]
+0046413 = organomercury catabolism [isa: 0009056 0018941 ]
+0042193 = methylmercury catabolism [isa: 0042191 0046413 ]
+0006660 = phosphatidylserine catabolism [isa: 0006658 0009056 0046475 ]
+0046149 = pigment catabolism [isa: 0009056 0042440 ]
+0046151 = eye pigment catabolism [isa: 0042441 0046149 ]
+0046153 = ommochrome catabolism [isa: 0046151 0046152 0046159 ]
+0046155 = rhodopsin catabolism [isa: 0046151 0046154 ]
+0046150 = melanin catabolism [isa: 0006582 0046149 ]
+0046159 = ocellus pigment catabolism [isa: 0046149 0046158 ]
+0006798 = polyphosphate catabolism [isa: 0006797 0009056 ]
+0009894 = regulation of catabolism [isa: 0019222 ] [partof: 0009056 ]
+0009895 = negative regulation of catabolism [isa: 0009892 0009894 ]
+0009896 = positive regulation of catabolism [isa: 0009893 0009894 ]
+0006110 = regulation of glycolysis [isa: 0009894 ]
+0045820 = negative regulation of glycolysis [isa: 0006110 ]
+0045821 = positive regulation of glycolysis [isa: 0006110 ]
+0042454 = ribonucleoside catabolism [isa: 0009056 0009119 ]
+0046247 = terpene catabolism [isa: 0009056 0042214 ]
+0046249 = alpha-pinene catabolism [isa: 0018867 0046247 ]
+0046251 = limonene catabolism [isa: 0018923 0046247 ]
+0019628 = urate catabolism [isa: 0009056 0019627 0046415 ]
+0009111 = vitamin catabolism [isa: 0006766 0009056 ]
+0042363 = fat-soluble vitamin catabolism [isa: 0006775 0009111 ]
+0042369 = vitamin D catabolism [isa: 0042359 0042363 ]
+0042365 = water-soluble vitamin catabolism [isa: 0006767 0009111 ]
+0042367 = biotin catabolism [isa: 0006768 0042365 ]
+0019854 = L-ascorbic acid catabolism [isa: 0019852 0042365 ]
+0009230 = thiamin catabolism [isa: 0006772 0042365 ]
+0009232 = vitamin B2 catabolism [isa: 0006771 0042365 ]
+0006731 = coenzymes and prosthetic group metabolism [isa: 0008152 ]
+0006732 = coenzyme metabolism [isa: 0006731 ]
+0046432 = 2'-(5''-triphosphoribosyl)-3'-dephospho-CoA metabolism [isa: 0006732 ]
+0046034 = ATP metabolism [isa: 0006732 0009205 ]
+0019297 = coenzyme B metabolism [isa: 0006732 ]
+0019296 = coenzyme M metabolism [isa: 0006732 ]
+0046443 = FAD metabolism [isa: 0006732 ]
+0046444 = FMN metabolism [isa: 0006732 ]
+0006749 = glutathione metabolism [isa: 0006732 ]
+0006752 = group transfer coenzyme metabolism [isa: 0006732 ]
+0015936 = coenzyme A metabolism [isa: 0006752 ]
+0006760 = folic acid and derivative metabolism [isa: 0006752 ]
+0009256 = 10-formyltetrahydrofolate metabolism [isa: 0006760 ]
+0046452 = dihydrofolate metabolism [isa: 0006760 ]
+0006762 = dihydrofolate reduction [isa: 0046452 ]
+0046655 = folic acid metabolism [isa: 0006760 ]
+0046653 = tetrahydrofolate metabolism [isa: 0006760 ]
+0006753 = nucleoside phosphate metabolism [isa: 0006752 ]
+0015939 = pantothenate metabolism [isa: 0006752 ]
+0016226 = iron-sulfur cluster assembly [isa: 0006732 ]
+0006748 = lipoamide metabolism [isa: 0006732 ]
+0000273 = lipoic acid metabolism [isa: 0006732 ]
+0009106 = lipoate metabolism [isa: 0000273 ]
+0006733 = oxidoreduction coenzyme metabolism [isa: 0006732 ]
+0006746 = FADH2 metabolism [isa: 0006733 ]
+0019362 = pyridine nucleotide metabolism [isa: 0006733 0006767 ]
+0006769 = nicotinamide metabolism [isa: 0019362 ]
+0006734 = NADH metabolism [isa: 0006769 ]
+0006116 = NADH oxidation [isa: 0006734 ]
+0006735 = NADH regeneration [isa: 0006734 ]
+0006739 = NADPH metabolism [isa: 0006769 ]
+0006740 = NADPH regeneration [isa: 0006739 ]
+0009780 = NADP+ reduction [isa: 0006740 ] [partof: 0019684 ]
+0019674 = nicotinamide adenine dinucleotide metabolism [isa: 0006769 ]
+0019675 = nicotinamide adenine dinucleotide phosphorylation and dephosphorylation [isa: 0019674 ]
+0046496 = nicotinamide nucleotide metabolism [isa: 0019362 ]
+0046495 = nicotinamide riboside metabolism [isa: 0019362 ]
+0046497 = nicotinate nucleotide metabolism [isa: 0019362 ]
+0019365 = pyridine nucleotide cycling [isa: 0019362 ]
+0006743 = ubiquinone metabolism [isa: 0006733 ]
+0008614 = pyridoxine metabolism [isa: 0006732 0006767 ]
+0009443 = pyridoxal 5'-phosphate salvage [isa: 0008614 ]
+0042375 = quinone cofactor metabolism [isa: 0006732 ]
+0042373 = vitamin K metabolism [isa: 0006775 0042375 ]
+0042374 = vitamin K1 metabolism [isa: 0042373 ]
+0009233 = vitamin K2 metabolism [isa: 0042373 ]
+0042357 = thiamin diphosphate metabolism [isa: 0006732 ]
+0042370 = thiamin diphosphate dephosphorylation [isa: 0042357 ]
+0015009 = corrin metabolism [isa: 0006731 ]
+0006778 = porphyrin metabolism [isa: 0006731 ]
+0015994 = chlorophyll metabolism [isa: 0006778 0042440 ]
+0030493 = bacteriochlorophyll metabolism [isa: 0015994 ]
+0042168 = heme metabolism [isa: 0006778 0042440 ]
+0046160 = heme a metabolism [isa: 0042168 ]
+0046492 = heme b metabolism [isa: 0042168 ]
+0046162 = heme c metabolism [isa: 0042168 ]
+0046156 = siroheme metabolism [isa: 0042168 ]
+0046501 = protoporphyrinogen IX metabolism [isa: 0006778 ]
+0046502 = uroporphyrinogen III metabolism [partof: 0006778 ]
+0009235 = vitamin B12 metabolism [isa: 0006767 0006778 ]
+0006774 = vitamin B12 reduction [isa: 0009235 ]
+0030657 = regulation of coenzyme and prosthetic group metabolism [partof: 0006731 ]
+0046142 = negative regulation of coenzyme and prosthetic group metabolism [isa: 0030657 ]
+0046143 = positive regulation of coenzyme and prosthetic group metabolism [isa: 0030657 ]
+0009237 = siderochrome metabolism [isa: 0006731 ]
+0009238 = enterobactin metabolism [isa: 0009237 ]
+0046494 = rhizobactin 1021 metabolism [isa: 0009237 ]
+0019536 = vibriobactin metabolism [isa: 0009237 ]
+0015010 = tetrahydrocorphin metabolism [isa: 0006731 ]
+0015011 = nickel-tetrapyrrole coenzyme metabolism [isa: 0015010 ]
+0018173 = peptidyl-1-thioglycine biosynthesis from peptidyl-glycine [isa: 0018201 ] [partof: 0015011 ]
+0019921 = peptidyl-1-thioglycine biosynthesis, carboxy-terminal [isa: 0018173 ]
+0019920 = peptidyl-1-thioglycine biosynthesis, internal [isa: 0018173 ]
+0006118 = electron transport [isa: 0008152 ]
+0006133 = 5,10-methyltetrahydrofolate oxidation [isa: 0006118 ]
+0006130 = 6-phosphofructokinase reduction [isa: 0006118 ]
+0019646 = aerobic electron transport [isa: 0006118 ]
+0019645 = anaerobic electron transport [isa: 0006118 ]
+0000044 = ascorbate stabilization [isa: 0006118 ]
+0006134 = dihydrobiopterin reduction [isa: 0006118 ]
+0006131 = dihydrolipoamide reduction [isa: 0006118 ]
+0006132 = dihydrolipoylprotein reduction [isa: 0006118 ]
+0006124 = ferredoxin metabolism [isa: 0006118 0019538 ]
+0006127 = glycerophosphate shuttle [isa: 0006118 ]
+0006138 = NADH-O2 electron transport [isa: 0006118 ]
+0006119 = oxidative phosphorylation [isa: 0006118 0016310 ]
+0006120 = oxidative phosphorylation, NADH to ubiquinone [partof: 0006119 ]
+0006123 = oxidative phosphorylation, reduction of O2 [partof: 0006119 ]
+0006121 = oxidative phosphorylation, succinate to ubiquinone [partof: 0006119 ]
+0006122 = oxidative phosphorylation, ubiquinone to cytochrome c [partof: 0006119 ]
+0006128 = oxidized glutathione reduction [isa: 0006118 ]
+0009767 = photosynthetic electron transport [isa: 0006118 ] [partof: 0019684 ]
+0009775 = photosynthetic electron transport in cytochrome b6/f [isa: 0009767 ]
+0009773 = photosynthetic electron transport in photosystem I [isa: 0009767 ]
+0009772 = photosynthetic electron transport in photosystem II [isa: 0009767 ]
+0009776 = photosynthetic electron transport in plastocyanin [isa: 0009767 ]
+0009774 = photosynthetic electron transport in plastoquinone [isa: 0009767 ]
+0006129 = protein-disulfide reduction [isa: 0006118 ]
+0006136 = succinate-O2 electron transport [isa: 0006118 ]
+0006125 = thioredoxin pathway [isa: 0006118 ]
+0006137 = ubiquinone-8-O2 electron transport [isa: 0006118 ]
+0006091 = energy pathways [isa: 0008152 ]
+0015980 = energy derivation by oxidation of organic compounds [isa: 0006091 ]
+0045333 = cellular respiration [isa: 0015980 ]
+0009060 = aerobic respiration [isa: 0045333 ]
+0019409 = aerobic respiration, using ammonium as electron donor [isa: 0009060 0015975 0019329 ]
+0019410 = aerobic respiration, using carbon monoxide as electron donor [isa: 0009060 0015975 ]
+0019411 = aerobic respiration, using ferrous ions as electron donor [isa: 0009060 0015975 ]
+0019412 = aerobic respiration, using hydrogen as electron donor [isa: 0009060 0015975 ]
+0019332 = aerobic respiration, using nitrite as electron donor [isa: 0006807 0009060 0015975 ]
+0019414 = aerobic respiration, using sulfur or sulfate as electron donor [isa: 0009060 0015975 ]
+0009061 = anaerobic respiration [isa: 0045333 ]
+0019331 = anaerobic respiration, using ammonium as electron donor [isa: 0009061 0015975 0019329 ]
+0006112 = energy reserve metabolism [isa: 0015980 ]
+0006113 = fermentation [isa: 0015980 ]
+0019654 = acetate fermentation [isa: 0006083 0006113 ]
+0019663 = homoacetate fermentation [isa: 0019654 0019660 ]
+0019665 = amino acid fermentation [isa: 0006113 ]
+0019668 = cofermentation of pairs of amino acids [isa: 0019665 ]
+0030645 = butyrate fermentation [isa: 0006113 0019605 ]
+0019660 = glycolytic fermentation [isa: 0006113 ]
+0019650 = butanediol fermentation [isa: 0019660 ]
+0019661 = homolactate fermentation [isa: 0019659 0019660 ]
+0019664 = mixed acid fermentation [isa: 0019660 ]
+0019652 = propionate fermentation [isa: 0019541 0019660 ]
+0019657 = succinate-propionate fermentation [isa: 0006105 0019541 0019660 ]
+0019659 = lactate fermentation [isa: 0006089 0006113 ]
+0019656 = heterolactate fermentation [isa: 0019659 0019662 ]
+0019666 = nitrogenous compound fermentation [isa: 0006113 ]
+0019653 = purine fermentation [isa: 0006144 0019666 ]
+0019662 = non-glycolytic fermentation [isa: 0006113 ]
+0019651 = diacetyl fermentation [isa: 0019662 ]
+0019672 = ethanol-acetate fermentation to butyrate and caproate [isa: 0019662 ]
+0019658 = glucose fermentation to lactate and acetate [isa: 0019662 ]
+0006092 = main pathways of carbohydrate metabolism [isa: 0015980 ]
+0006093 = anabolic carbohydrate metabolism [isa: 0006092 ]
+0006095 = catabolic carbohydrate metabolism [isa: 0006092 ]
+0009255 = Entner-Doudoroff pathway [isa: 0006095 ]
+0006100 = TCA intermediate metabolism [isa: 0006095 ]
+0006103 = 2-oxoglutarate metabolism [isa: 0006100 ]
+0006101 = citrate metabolism [isa: 0006100 0019752 ]
+0006106 = fumarate metabolism [isa: 0006100 ]
+0006102 = isocitrate metabolism [isa: 0006100 0019752 ]
+0006108 = malate metabolism [isa: 0006100 0019752 ]
+0006107 = oxaloacetate metabolism [isa: 0006100 0019752 ]
+0006105 = succinate metabolism [isa: 0006100 0019752 ]
+0006104 = succinyl-CoA metabolism [isa: 0006100 ]
+0019680 = L-methylmalonyl-CoA biosynthesis [isa: 0006104 0046491 ]
+0006099 = tricarboxylic acid cycle [isa: 0006095 ]
+0019644 = reductive citric acid pathway [isa: 0006099 ]
+0019643 = reductive tricarboxylic acid cycle [isa: 0006099 ]
+0015975 = energy derivation by oxidation of reduced inorganic compounds [isa: 0006091 ]
+0019327 = oxidation of lead sulfide [isa: 0015975 ]
+0019684 = photosynthesis, light reaction [isa: 0006091 ] [partof: 0015979 ]
+0009765 = photosynthesis light harvesting [partof: 0019684 ]
+0009768 = photosynthesis light harvesting in photosystem I [isa: 0009765 ]
+0009769 = photosynthesis light harvesting in photosystem II [isa: 0009765 ]
+0009777 = photosynthetic phosphorylation [partof: 0019684 ]
+0009778 = cyclic photosynthetic phosphorylation [isa: 0009777 ]
+0009779 = noncyclic photosynthetic phosphorylation [isa: 0009777 ]
+0009781 = photosynthetic water oxidation [partof: 0019684 ]
+0009766 = primary charge separation [partof: 0019684 ]
+0009770 = primary charge separation in photosystem I [isa: 0009766 ]
+0009771 = primary charge separation in photosystem II [isa: 0009766 ]
+0042548 = regulation of photosynthesis, light reaction [partof: 0019684 ]
+0042550 = photosystem I stabilization [isa: 0042548 ]
+0042549 = photosystem II stabilization [isa: 0042548 ]
+0007590 = fat body metabolism (sensu Insecta) [isa: 0007582 0008152 ]
+0015032 = storage protein uptake [isa: 0007590 ]
+0006662 = glycerol ether metabolism [isa: 0008152 ]
+0046485 = ether lipid metabolism [isa: 0006662 0046486 ]
+0046504 = glycerol ether biosynthesis [isa: 0006662 ]
+0046483 = heterocycle metabolism [isa: 0008152 ]
+0046484 = oxazole/thiazole metabolism [isa: 0046483 ]
+0042445 = hormone metabolism [isa: 0008152 ]
+0008209 = androgen metabolism [isa: 0008202 0042445 ]
+0009850 = auxin metabolism [isa: 0042445 ]
+0008207 = C21-steroid hormone metabolism [isa: 0008202 0042445 ]
+0042448 = progesterone metabolism [isa: 0008207 ]
+0009690 = cytokinin metabolism [isa: 0042445 ]
+0045455 = ecdysteroid metabolism [isa: 0007552 0008202 0042180 0042445 ]
+0008205 = ecdysone metabolism [isa: 0016125 0045455 ]
+0006698 = ecdysone modification [isa: 0008205 ]
+0045457 = ecdysteroid secretion [isa: 0045455 ]
+0007555 = regulation of ecdysteroid secretion [isa: 0007553 ] [partof: 0045457 ]
+0045999 = negative regulation of ecdysteroid secretion [isa: 0007555 0045965 ]
+0046000 = positive regulation of ecdysteroid secretion [isa: 0007555 0045966 ]
+0007553 = regulation of ecdysteroid metabolism [isa: 0019218 ] [partof: 0045455 ]
+0045965 = negative regulation of ecdysteroid metabolism [isa: 0007553 0045939 ]
+0045966 = positive regulation of ecdysteroid metabolism [isa: 0007553 0045940 ]
+0008210 = estrogen metabolism [isa: 0008202 0042445 ]
+0008211 = glucocorticoid metabolism [isa: 0008202 0042445 ]
+0006716 = juvenile hormone metabolism [isa: 0006714 0042445 ]
+0045443 = juvenile hormone secretion [isa: 0006716 ]
+0007558 = regulation of juvenile hormone secretion [isa: 0007556 ] [partof: 0045443 ]
+0045972 = negative regulation of juvenile hormone secretion [isa: 0007558 0045928 ]
+0045973 = positive regulation of juvenile hormone secretion [isa: 0007558 0045929 ]
+0007556 = regulation of juvenile hormone metabolism [partof: 0006716 0007552 ]
+0045928 = negative regulation of juvenile hormone metabolism [isa: 0007556 ]
+0045929 = positive regulation of juvenile hormone metabolism [isa: 0007556 ]
+0008212 = mineralocorticoid metabolism [isa: 0008202 0042445 ]
+0016486 = peptide hormone processing [isa: 0016485 0042445 ]
+0030070 = insulin processing [isa: 0016486 ]
+0046490 = isopentenyl diphosphate metabolism [isa: 0008152 ]
+0042180 = ketone metabolism [isa: 0008152 ]
+0018882 = (+)-camphor metabolism [isa: 0042180 0042214 ]
+0006666 = 3-keto-sphinganine metabolism [isa: 0042180 0046519 ]
+0045149 = acetoin metabolism [isa: 0042180 ]
+0046491 = L-methylmalonyl-CoA metabolism [isa: 0008152 ]
+0006629 = lipid metabolism [isa: 0008152 ]
+0006631 = fatty acid metabolism [isa: 0006629 0019752 ]
+0006637 = acyl-CoA metabolism [isa: 0006631 ]
+0019369 = arachidonic acid metabolism [isa: 0006631 ]
+0019373 = epoxygenase P450 pathway [isa: 0019369 ]
+0006690 = eicosanoid metabolism [isa: 0006631 ]
+0006691 = leukotriene metabolism [isa: 0006690 ]
+0006692 = prostanoid metabolism [isa: 0006690 ]
+0006693 = prostaglandin metabolism [isa: 0006692 ]
+0006636 = fatty acid desaturation [isa: 0006631 ]
+0019395 = fatty acid oxidation [isa: 0006631 ]
+0001561 = fatty acid alpha-oxidation [isa: 0019395 ]
+0006635 = fatty acid beta-oxidation [isa: 0019395 ]
+0046320 = regulation of fatty acid oxidation [isa: 0019217 ] [partof: 0019395 ]
+0046322 = negative regulation of fatty acid oxidation [isa: 0045922 0046320 ]
+0046321 = positive regulation of fatty acid oxidation [isa: 0045923 0046320 ]
+0009694 = jasmonic acid metabolism [isa: 0006631 ]
+0001676 = long-chain fatty acid metabolism [isa: 0006631 ]
+0019217 = regulation of fatty acid metabolism [isa: 0019222 ] [partof: 0006631 ]
+0045922 = negative regulation of fatty acid metabolism [isa: 0009892 0019217 ]
+0045923 = positive regulation of fatty acid metabolism [isa: 0009893 0019217 ]
+0046459 = short-chain fatty acid metabolism [isa: 0006631 ]
+0000038 = very-long-chain fatty acid metabolism [isa: 0006631 ]
+0046486 = glycerolipid metabolism [isa: 0006629 ]
+0006639 = acylglycerol metabolism [isa: 0006638 0046486 ]
+0046339 = diacylglycerol metabolism [isa: 0006639 ]
+0046341 = CDP-diacylglycerol metabolism [isa: 0046339 ]
+0046462 = monoacylglycerol metabolism [isa: 0006639 ]
+0006641 = triacylglycerol metabolism [isa: 0006639 ]
+0006642 = triacylglycerol mobilization [isa: 0006641 ]
+0046503 = glycerolipid catabolism [isa: 0046486 ]
+0006720 = isoprenoid metabolism [isa: 0006629 ]
+0045338 = farnesyl diphosphate metabolism [isa: 0006720 ]
+0016096 = polyisoprenoid metabolism [isa: 0006720 ]
+0006721 = terpenoid metabolism [isa: 0016096 0042214 ]
+0016101 = diterpenoid metabolism [isa: 0006721 ]
+0009685 = gibberellic acid metabolism [isa: 0016101 0019752 ]
+0016098 = monoterpenoid metabolism [isa: 0006721 ]
+0016111 = polyterpenoid metabolism [isa: 0006721 ]
+0006714 = sesquiterpenoid metabolism [isa: 0006721 ]
+0009687 = abscisic acid metabolism [isa: 0006714 0019752 ]
+0016108 = tetraterpenoid metabolism [isa: 0006721 ]
+0016116 = carotenoid metabolism [isa: 0016108 ]
+0016119 = carotene metabolism [isa: 0016116 ]
+0016122 = xanthophyll metabolism [isa: 0016116 ]
+0006722 = triterpenoid metabolism [isa: 0006721 ]
+0019742 = pentacyclic triterpenoid metabolism [isa: 0006722 ]
+0019744 = hopanoid metabolism [isa: 0019742 ]
+0016090 = prenol metabolism [isa: 0006720 ]
+0016093 = polyprenol metabolism [isa: 0016090 ]
+0019348 = dolichol metabolism [isa: 0016093 ]
+0046465 = dolichyl diphosphate metabolism [isa: 0019348 ]
+0019747 = regulation of isoprenoid metabolism [isa: 0019222 ] [partof: 0006720 ]
+0045827 = negative regulation of isoprenoid metabolism [isa: 0009892 0019747 ]
+0045828 = positive regulation of isoprenoid metabolism [isa: 0009893 0019747 ]
+0001523 = retinoid metabolism [isa: 0006720 ]
+0046493 = lipid A metabolism [isa: 0006629 ]
+0030258 = lipid modification [isa: 0006629 ]
+0030259 = lipid glycosylation [isa: 0030258 ]
+0006643 = membrane lipid metabolism [isa: 0006629 ]
+0006664 = glycolipid metabolism [isa: 0006643 ]
+0019374 = galactolipid metabolism [isa: 0006664 ]
+0006681 = galactosylceramide metabolism [isa: 0006677 0019374 ]
+0006687 = glycosphingolipid metabolism [isa: 0006664 0006665 ]
+0001573 = ganglioside metabolism [isa: 0006687 ]
+0001575 = globoside metabolism [isa: 0006687 ]
+0006677 = glycosylceramide metabolism [isa: 0006664 0006672 ]
+0006678 = glucosylceramide metabolism [isa: 0006677 ]
+0046478 = lactosylceramide metabolism [isa: 0006677 ]
+0006644 = phospholipid metabolism [isa: 0006643 ]
+0006650 = glycerophospholipid metabolism [isa: 0006644 ]
+0006652 = alpha-glycerophosphate pathway [isa: 0006650 ]
+0046474 = glycerophospholipid biosynthesis [isa: 0006650 ]
+0006656 = phosphatidylcholine biosynthesis [isa: 0046470 0046474 ]
+0006657 = CDP-choline pathway [isa: 0006656 ]
+0006655 = phosphatidylglycerol biosynthesis [isa: 0046471 0046474 ]
+0006659 = phosphatidylserine biosynthesis [isa: 0006658 0046474 ]
+0046489 = phosphoinositide biosynthesis [isa: 0030384 0046474 ]
+0015998 = glycosylphosphatidylinositol biosynthesis [isa: 0046472 0046489 ]
+0006661 = phosphatidylinositol biosynthesis [isa: 0046488 0046489 ]
+0046475 = glycerophospholipid catabolism [isa: 0006650 ]
+0046473 = phosphatidic acid metabolism [isa: 0006650 0019752 ]
+0046470 = phosphatidylcholine metabolism [isa: 0006650 ]
+0006653 = lecithin metabolism [isa: 0046470 ]
+0046471 = phosphatidylglycerol metabolism [isa: 0006650 ]
+0006658 = phosphatidylserine metabolism [isa: 0006650 ]
+0030384 = phosphoinositide metabolism [isa: 0006650 ]
+0046472 = glycosylphosphatidylinositol metabolism [isa: 0030384 ]
+0046488 = phosphatidylinositol metabolism [isa: 0030384 ]
+0006673 = inositolphosphoceramide metabolism [isa: 0006644 0006672 ]
+0006674 = inositol phosphorylceramide metabolism [isa: 0006673 ]
+0006675 = mannose inositol phosphoceramide metabolism [isa: 0006673 ]
+0006676 = mannosyl diphosphorylinositol ceramide metabolism [isa: 0006673 ]
+0046337 = phosphatidylethanolamine metabolism [isa: 0006644 ]
+0046468 = phosphatidyl-N-monomethylethanolamine metabolism [isa: 0046337 ]
+0006649 = phospholipid transfer to membrane [isa: 0006644 ]
+0046469 = platelet activating factor metabolism [isa: 0006644 ]
+0006663 = platelet activating factor biosynthesis [isa: 0046469 ]
+0006684 = sphingomyelin metabolism [isa: 0006644 0006665 ]
+0006686 = sphingomyelin biosynthesis [isa: 0006684 0030148 ]
+0006685 = sphingomyelin catabolism [isa: 0006684 0030149 ]
+0006665 = sphingolipid metabolism [isa: 0006643 ]
+0046519 = sphingoid metabolism [partof: 0006665 ]
+0006672 = ceramide metabolism [isa: 0046519 ]
+0046513 = ceramide biosynthesis [isa: 0006672 0046520 ]
+0046514 = ceramide catabolism [isa: 0006672 0046521 ]
+0006671 = phytosphingosine metabolism [isa: 0046519 ]
+0006667 = sphinganine metabolism [isa: 0046519 ]
+0046511 = sphinganine biosynthesis [isa: 0006667 0046520 ]
+0006669 = sphinganine-1-phosphate biosynthesis [isa: 0006668 0046511 ]
+0006668 = sphinganine-1-phosphate metabolism [isa: 0006667 ]
+0046520 = sphingoid biosynthesis [isa: 0046519 ] [partof: 0030148 ]
+0046521 = sphingoid catabolism [isa: 0046519 ] [partof: 0030149 ]
+0030148 = sphingolipid biosynthesis [isa: 0006665 ]
+0030149 = sphingolipid catabolism [isa: 0006665 ]
+0006638 = neutral lipid metabolism [isa: 0006629 ]
+0019216 = regulation of lipid metabolism [isa: 0019222 ] [partof: 0006629 ]
+0045833 = negative regulation of lipid metabolism [isa: 0009892 0019216 ]
+0045834 = positive regulation of lipid metabolism [isa: 0009893 0019216 ]
+0008202 = steroid metabolism [isa: 0006629 ]
+0008206 = bile acid metabolism [isa: 0008202 0019752 ]
+0019613 = bile acid 7alpha-dehydroxylation pathway [isa: 0008206 ]
+0016128 = phytosteroid metabolism [isa: 0008202 ]
+0016131 = brassinosteroid metabolism [isa: 0016128 ]
+0019218 = regulation of steroid metabolism [isa: 0019222 ] [partof: 0008202 ]
+0045939 = negative regulation of steroid metabolism [isa: 0009892 0019218 ]
+0045940 = positive regulation of steroid metabolism [isa: 0009893 0019218 ]
+0016125 = sterol metabolism [isa: 0008202 ]
+0008203 = cholesterol metabolism [isa: 0016125 ]
+0008204 = ergosterol metabolism [isa: 0016125 ]
+0046505 = sulfolipid metabolism [isa: 0006629 0006790 ]
+0006807 = nitrogen metabolism [isa: 0008152 ]
+0019330 = aldoxime metabolism [isa: 0006807 ]
+0009820 = alkaloid metabolism [isa: 0006807 0019748 ]
+0046445 = benzyl isoquinoline alkaloid metabolism [isa: 0009820 ]
+0046450 = dethiobiotin metabolism [isa: 0009820 ]
+0046453 = dipyrrin metabolism [isa: 0009820 ]
+0018933 = nicotine metabolism [isa: 0009820 ]
+0046446 = purine alkaloid metabolism [isa: 0009820 ]
+0046447 = terpenoid indole alkaloid metabolism [isa: 0009820 ]
+0046448 = tropane alkaloid metabolism [isa: 0009820 ]
+0019329 = ammonia oxidation [isa: 0006807 ]
+0019333 = denitrification pathway [isa: 0006807 ]
+0042126 = nitrate metabolism [isa: 0006807 ]
+0042128 = nitrate assimilation [isa: 0042126 ]
+0046209 = nitric oxide metabolism [isa: 0006807 ]
+0009399 = nitrogen fixation [isa: 0006807 ]
+0019740 = nitrogen utilization [isa: 0006807 ]
+0006808 = regulation of nitrogen utilization [partof: 0019740 ]
+0045847 = negative regulation of nitrogen utilization [isa: 0006808 ]
+0045848 = positive regulation of nitrogen utilization [isa: 0006808 ]
+0046415 = urate metabolism [isa: 0006807 ]
+0000050 = urea cycle [partof: 0006807 ]
+0000051 = urea cycle intermediate metabolism [partof: 0006807 ]
+0000053 = argininosuccinate metabolism [isa: 0000051 ]
+0000052 = citrulline metabolism [isa: 0000051 ]
+0019627 = urea metabolism [isa: 0006807 ]
+0006139 = nucleobase, nucleoside, nucleotide and nucleic acid metabolism [isa: 0008152 ]
+0006259 = DNA metabolism [isa: 0006139 ]
+0009290 = cellular DNA uptake [isa: 0006259 ] [partof: 0009294 ]
+0015074 = DNA integration [isa: 0006259 ]
+0006304 = DNA modification [isa: 0006259 ]
+0045007 = depurination [isa: 0006285 0006304 ]
+0045008 = depyrimidination [isa: 0006285 0006304 ]
+0030592 = DNA ADP-ribosylation [isa: 0006304 ]
+0006305 = DNA alkylation [isa: 0006304 ]
+0006306 = DNA methylation [isa: 0006305 0040029 ]
+0045006 = DNA deamination [isa: 0006304 ]
+0009307 = DNA restriction [isa: 0006304 ]
+0006323 = DNA packaging [isa: 0006259 ]
+0019073 = viral DNA genome packaging [isa: 0006323 0019072 ]
+0006310 = DNA recombination [isa: 0006259 ]
+0006313 = DNA transposition [isa: 0006310 ]
+0006314 = intron homing [isa: 0006313 ]
+0006315 = homing of group II introns [isa: 0006314 ]
+0006316 = movement of group I intron [isa: 0006314 ]
+0006317 = P-element transposition [isa: 0006313 ]
+0006318 = P-element excision [isa: 0006317 ]
+0000337 = regulation of DNA transposition [partof: 0006313 ]
+0000335 = negative regulation of DNA transposition [isa: 0000337 ]
+0000336 = positive regulation of DNA transposition [isa: 0000337 ]
+0006319 = Ty element transposition [isa: 0006313 ]
+0006320 = Ty1 element transposition [isa: 0006319 ]
+0006321 = Ty2 element transposition [isa: 0006319 ]
+0006322 = Ty3 element transposition [isa: 0006319 ]
+0006312 = mitotic recombination [isa: 0006310 ]
+0007534 = gene conversion at MAT locus [isa: 0006312 ] [partof: 0007533 ]
+0000730 = DNA recombinase assembly [partof: 0007534 0045003 ]
+0000734 = gene conversion at MAT locus, DNA repair synthesis [partof: 0007534 ]
+0030491 = heteroduplex formation [partof: 0007534 0045003 ]
+0000735 = removal of non-homologous ends [partof: 0007534 ]
+0042148 = strand invasion [partof: 0007534 0045003 ]
+0045458 = recombination within rDNA repeats [isa: 0006312 ]
+0045865 = regulation of recombination within rDNA repeats [isa: 0000019 ] [partof: 0045458 ]
+0000020 = negative regulation of recombination within rDNA repeats [isa: 0045865 0045950 ]
+0045866 = positive regulation of recombination within rDNA repeats [isa: 0045865 0045951 ]
+0000725 = recombinational repair [isa: 0006281 0006312 ]
+0000724 = double-strand break repair via homologous recombination [isa: 0000725 0006302 ]
+0000727 = double-strand break repair via break-induced replication [isa: 0000724 ]
+0045003 = double-strand break repair via synthesis-dependent strand annealing [isa: 0000724 ]
+0000731 = DNA repair synthesis [partof: 0045002 0045003 ]
+0000732 = strand displacement [partof: 0045003 ]
+0000019 = regulation of mitotic recombination [isa: 0000018 ] [partof: 0006312 ]
+0045950 = negative regulation of mitotic recombination [isa: 0000019 0045910 ]
+0045951 = positive regulation of mitotic recombination [isa: 0000019 0045911 ]
+0042150 = plasmid recombination [isa: 0006310 ]
+0019047 = provirus integration [isa: 0006310 ] [partof: 0030069 ]
+0000018 = regulation of DNA recombination [partof: 0006310 ]
+0045910 = negative regulation of DNA recombination [isa: 0000018 ]
+0045911 = positive regulation of DNA recombination [isa: 0000018 ]
+0042152 = RNA-mediated DNA recombination [isa: 0006310 ]
+0016444 = somatic cell DNA recombination [isa: 0006310 ]
+0016445 = generation of antibody gene diversity [isa: 0016444 ]
+0016446 = somatic hypermutation of antibody genes [partof: 0016445 ]
+0016447 = somatic recombination of antibody genes [partof: 0016445 ]
+0006281 = DNA repair [isa: 0006259 ]
+0006284 = base-excision repair [isa: 0006281 ]
+0006285 = base-excision repair, AP site formation [partof: 0006284 ]
+0006286 = base-excision repair, base-free sugar-phosphate removal [partof: 0006284 ]
+0006288 = base-excision repair, DNA ligation [partof: 0006284 ]
+0006287 = base-excision repair, gap-filling [partof: 0006284 ]
+0019985 = bypass DNA synthesis [isa: 0006281 ]
+0006307 = DNA dealkylation [isa: 0006281 ]
+0006302 = double-strand break repair [isa: 0006281 ]
+0006303 = double-strand break repair via nonhomologous end-joining [isa: 0000726 0006302 ]
+0045002 = double-strand break repair via single-strand annealing [isa: 0000726 0006302 ]
+0000733 = DNA strand renaturation [partof: 0045002 ]
+0000736 = double-strand break repair via single-strand annealing, removal of non-homologous ends [partof: 0045002 ]
+0045021 = error-free DNA repair [isa: 0006281 ]
+0042275 = error-free post-replication DNA repair [isa: 0006301 0045021 ]
+0045020 = error-prone DNA repair [isa: 0006281 ]
+0042276 = error-prone post-replication DNA repair [isa: 0006301 0045020 ]
+0000726 = non-recombinational repair [isa: 0006281 ]
+0006289 = nucleotide-excision repair [isa: 0006281 ]
+0000715 = nucleotide-excision repair, DNA damage recognition [partof: 0006289 ]
+0000716 = transcription-coupled nucleotide-excision repair, DNA damage recognition [isa: 0000715 ] [partof: 0006283 ]
+0000718 = nucleotide-excision repair, DNA damage removal [partof: 0006289 ]
+0000717 = nucleotide-excision repair, DNA duplex unwinding [partof: 0006289 ]
+0006297 = nucleotide-excision repair, DNA gap filling [partof: 0006289 ]
+0006295 = nucleotide-excision repair, DNA incision, 3' to lesion [partof: 0006289 ]
+0006296 = nucleotide-excision repair, DNA incision, 5' to lesion [partof: 0006289 ]
+0006294 = nucleotide-excision repair, preincision complex formation [partof: 0006289 ]
+0006293 = nucleotide-excision repair, preincision complex stabilization [partof: 0006289 ]
+0000720 = pyrimidine-dimer repair via nucleotide-excision repair [isa: 0006289 0006290 ]
+0006283 = transcription-coupled nucleotide-excision repair [isa: 0006289 ]
+0006301 = post-replication repair [isa: 0006281 ]
+0006290 = pyrimidine-dimer repair [isa: 0006281 ]
+0000719 = photoreactive repair [isa: 0006290 ]
+0006282 = regulation of DNA repair [partof: 0006281 ]
+0045738 = negative regulation of DNA repair [isa: 0006282 ]
+0045739 = positive regulation of DNA repair [isa: 0006282 ]
+0000012 = single-strand break repair [isa: 0006281 ]
+0006280 = mutagenesis [isa: 0006259 ]
+0016458 = gene silencing [isa: 0006139 ]
+0016441 = post-transcriptional gene silencing [isa: 0016458 0040029 ]
+0016246 = RNA interference [isa: 0016441 ]
+0030422 = RNA interference, production of guide RNAs [isa: 0016246 ]
+0030423 = RNA interference, targeting of mRNA for destruction [isa: 0016246 ]
+0016440 = transcriptional gene silencing [isa: 0006355 0016458 ]
+0006349 = imprinting [isa: 0006139 0040029 ]
+0009112 = nucleobase metabolism [isa: 0006139 ]
+0006144 = purine base metabolism [isa: 0009112 ]
+0046083 = adenine metabolism [isa: 0006144 ]
+0046098 = guanine metabolism [isa: 0006144 ]
+0046100 = hypoxanthine metabolism [isa: 0006144 ]
+0006141 = regulation of purine base metabolism [isa: 0019219 ] [partof: 0006144 ]
+0045982 = negative regulation of purine base metabolism [isa: 0006141 0045934 ]
+0045983 = positive regulation of purine base metabolism [isa: 0006141 0045935 ]
+0046110 = xanthine metabolism [isa: 0006144 ]
+0006206 = pyrimidine base metabolism [isa: 0009112 ]
+0019857 = 5-methylcytosine metabolism [isa: 0006206 ]
+0019858 = cytosine metabolism [isa: 0006206 ]
+0006142 = regulation of pyrimidine base metabolism [isa: 0019219 ] [partof: 0006206 ]
+0045984 = negative regulation of pyrimidine base metabolism [isa: 0006142 0045934 ]
+0045985 = positive regulation of pyrimidine base metabolism [isa: 0006142 0045935 ]
+0019859 = thymine metabolism [isa: 0006206 ]
+0019860 = uracil metabolism [isa: 0006206 ]
+0015949 = nucleobase, nucleoside and nucleotide interconversion [isa: 0006139 ]
+0019686 = purine nucleoside interconversion [isa: 0015949 ]
+0019688 = purine deoxyribonucleoside interconversion [isa: 0019686 ]
+0015950 = purine nucleotide interconversion [isa: 0015949 ]
+0015952 = purine deoxyribonucleotide interconversion [isa: 0015950 ]
+0015951 = purine ribonucleotide interconversion [isa: 0015950 ]
+0019689 = pyrimidine nucleoside interconversion [isa: 0015949 ]
+0019690 = pyrimidine deoxyribonucleoside interconversion [isa: 0019689 ]
+0015953 = pyrimidine nucleotide interconversion [isa: 0015949 ]
+0015955 = pyrimidine deoxyribonucleotide interconversion [isa: 0015953 ]
+0015954 = pyrimidine ribonucleotide interconversion [isa: 0015953 ]
+0009116 = nucleoside metabolism [isa: 0006139 ]
+0009120 = deoxyribonucleoside metabolism [isa: 0009116 ]
+0046122 = purine deoxyribonucleoside metabolism [isa: 0009120 0042278 ]
+0046090 = deoxyadenosine metabolism [isa: 0046122 ]
+0042453 = deoxyguanosine metabolism [isa: 0046122 ]
+0046125 = pyrimidine deoxyribonucleoside metabolism [isa: 0006213 0009120 ]
+0046092 = deoxycytidine metabolism [isa: 0046125 ]
+0046094 = deoxyinosine metabolism [isa: 0046125 ]
+0046096 = deoxyuridine metabolism [isa: 0046125 ]
+0046104 = thymidine metabolism [isa: 0046125 ]
+0042278 = purine nucleoside metabolism [isa: 0009116 ]
+0046128 = purine ribonucleoside metabolism [isa: 0009119 0042278 ]
+0046085 = adenosine metabolism [isa: 0046128 ]
+0015956 = bis(5'-nucleosidyl) oligophosphate metabolism [isa: 0046128 ]
+0015957 = bis(5'-nucleosidyl) oligophosphate biosynthesis [isa: 0015956 ]
+0015960 = diadenosine polyphosphate biosynthesis [isa: 0015957 0015959 ]
+0015966 = diadenosine tetraphosphate biosynthesis [isa: 0015960 0015965 ]
+0015963 = diadenosine triphosphate biosynthesis [isa: 0015960 0015962 ]
+0015958 = bis(5'-nucleosidyl) oligophosphate catabolism [isa: 0015956 ]
+0015961 = diadenosine polyphosphate catabolism [isa: 0015958 0015959 ]
+0015967 = diadenosine tetraphosphate catabolism [isa: 0015961 0015965 ]
+0015964 = diadenosine triphosphate catabolism [isa: 0015961 0015962 ]
+0015959 = diadenosine polyphosphate metabolism [isa: 0015956 ]
+0015965 = diadenosine tetraphosphate metabolism [isa: 0015959 ]
+0015962 = diadenosine triphosphate metabolism [isa: 0015959 ]
+0008617 = guanosine metabolism [isa: 0046128 ]
+0008618 = 7-methylguanosine metabolism [isa: 0008617 ]
+0046116 = queuosine metabolism [isa: 0008618 ]
+0015972 = guanosine pentaphosphate (5'-pppGpp-3') metabolism [isa: 0008617 ]
+0006160 = guanosine phosphorolysis [isa: 0008617 ]
+0015969 = guanosine tetraphosphate (5'-ppGpp-3') metabolism [isa: 0008617 ]
+0006213 = pyrimidine nucleoside metabolism [isa: 0009116 ]
+0046131 = pyrimidine ribonucleoside metabolism [isa: 0006213 0009119 ]
+0046087 = cytidine metabolism [isa: 0046131 ]
+0046102 = inosine metabolism [isa: 0046131 ]
+0046108 = uridine metabolism [isa: 0046131 ]
+0009118 = regulation of nucleoside metabolism [isa: 0019219 ] [partof: 0009116 ]
+0045978 = negative regulation of nucleoside metabolism [isa: 0009118 0045934 ]
+0045979 = positive regulation of nucleoside metabolism [isa: 0009118 0045935 ]
+0009119 = ribonucleoside metabolism [isa: 0009116 ]
+0009117 = nucleotide metabolism [isa: 0006139 ]
+0009187 = cyclic nucleotide metabolism [isa: 0009117 ]
+0046058 = cAMP metabolism [isa: 0009187 ]
+0046068 = cGMP metabolism [isa: 0009187 ]
+0009262 = deoxyribonucleotide metabolism [isa: 0009117 ]
+0009394 = 2'-deoxyribonucleotide metabolism [isa: 0009262 ]
+0009186 = deoxyribonucleoside diphosphate metabolism [isa: 0009132 0009262 ]
+0009182 = purine deoxyribonucleoside diphosphate metabolism [isa: 0009135 0009151 0009186 ]
+0046056 = dADP metabolism [isa: 0009182 ]
+0046066 = dGDP metabolism [isa: 0009182 ]
+0006186 = dGDP phosphorylation [isa: 0016310 0046066 ]
+0009196 = pyrimidine deoxyribonucleoside diphosphate metabolism [isa: 0009138 0009186 0009219 ]
+0046062 = dCDP metabolism [isa: 0009196 ]
+0046072 = dTDP metabolism [isa: 0009196 ]
+0046077 = dUDP metabolism [isa: 0009196 ]
+0009162 = deoxyribonucleoside monophosphate metabolism [isa: 0009123 0009262 ]
+0009170 = purine deoxyribonucleoside monophosphate metabolism [isa: 0009126 0009151 0009162 ]
+0046053 = dAMP metabolism [isa: 0009170 ]
+0046054 = dGMP metabolism [isa: 0009170 ]
+0009176 = pyrimidine deoxyribonucleoside monophosphate metabolism [isa: 0009129 0009162 0009219 ]
+0046063 = dCMP metabolism [isa: 0009176 ]
+0046073 = dTMP metabolism [isa: 0009176 ]
+0046078 = dUMP metabolism [isa: 0009176 ]
+0009200 = deoxyribonucleoside triphosphate metabolism [isa: 0009141 0009262 ]
+0009215 = purine deoxyribonucleoside triphosphate metabolism [isa: 0009144 0009151 0009200 ]
+0046060 = dATP metabolism [isa: 0009215 ]
+0046070 = dGTP metabolism [isa: 0009215 ]
+0009211 = pyrimidine deoxyribonucleoside triphosphate metabolism [isa: 0009147 0009200 0009219 ]
+0046065 = dCTP metabolism [isa: 0009211 ]
+0046075 = dTTP metabolism [isa: 0009211 ]
+0046080 = dUTP metabolism [isa: 0009211 ]
+0009151 = purine deoxyribonucleotide metabolism [isa: 0006163 0009262 ]
+0009219 = pyrimidine deoxyribonucleotide metabolism [isa: 0006220 0009262 ]
+0009132 = nucleoside diphosphate metabolism [isa: 0009117 ]
+0009135 = purine nucleoside diphosphate metabolism [isa: 0006163 0009132 ]
+0009179 = purine ribonucleoside diphosphate metabolism [isa: 0009135 0009150 0009185 ]
+0046031 = ADP metabolism [isa: 0009179 ]
+0009138 = pyrimidine nucleoside diphosphate metabolism [isa: 0006220 0009132 ]
+0009193 = pyrimidine ribonucleoside diphosphate metabolism [isa: 0009138 0009185 0009218 ]
+0046043 = TDP metabolism [isa: 0009193 ]
+0046048 = UDP metabolism [isa: 0009193 ]
+0009185 = ribonucleoside diphosphate metabolism [isa: 0009132 0009259 ]
+0009123 = nucleoside monophosphate metabolism [isa: 0009117 ]
+0009126 = purine nucleoside monophosphate metabolism [isa: 0006163 0009123 ]
+0009167 = purine ribonucleoside monophosphate metabolism [isa: 0009126 0009150 0009161 ]
+0046033 = AMP metabolism [isa: 0009167 ]
+0046037 = GMP metabolism [isa: 0009167 ]
+0046040 = IMP metabolism [isa: 0009167 ]
+0009129 = pyrimidine nucleoside monophosphate metabolism [isa: 0006220 0009123 ]
+0009173 = pyrimidine ribonucleoside monophosphate metabolism [isa: 0009129 0009161 0009218 ]
+0046035 = CMP metabolism [isa: 0009173 ]
+0046044 = TMP metabolism [isa: 0009173 ]
+0046049 = UMP metabolism [isa: 0009173 ]
+0009161 = ribonucleoside monophosphate metabolism [isa: 0009123 0009259 ]
+0009141 = nucleoside triphosphate metabolism [isa: 0009117 ]
+0009144 = purine nucleoside triphosphate metabolism [isa: 0006163 0009141 ]
+0009205 = purine ribonucleoside triphosphate metabolism [isa: 0009144 0009150 0009199 ]
+0046039 = GTP metabolism [isa: 0009205 ]
+0046041 = ITP metabolism [isa: 0009205 ]
+0009147 = pyrimidine nucleoside triphosphate metabolism [isa: 0006220 0009141 ]
+0009208 = pyrimidine ribonucleoside triphosphate metabolism [isa: 0009147 0009199 0009218 ]
+0046036 = CTP metabolism [isa: 0009208 ]
+0046046 = TTP metabolism [isa: 0009208 ]
+0046051 = UTP metabolism [isa: 0009208 ]
+0009199 = ribonucleoside triphosphate metabolism [isa: 0009141 0009259 ]
+0006163 = purine nucleotide metabolism [isa: 0009117 ]
+0006165 = nucleoside diphosphate phosphorylation [isa: 0006163 0006220 0016310 ]
+0009150 = purine ribonucleotide metabolism [isa: 0006163 0009259 ]
+0006166 = purine salvage [isa: 0006163 ]
+0006162 = purine/pyrimidine nucleoside diphosphate reduction [isa: 0009117 ]
+0006220 = pyrimidine nucleotide metabolism [isa: 0009117 ]
+0009218 = pyrimidine ribonucleotide metabolism [isa: 0006220 0009259 ]
+0006140 = regulation of nucleotide metabolism [isa: 0019219 ] [partof: 0009117 ]
+0045980 = negative regulation of nucleotide metabolism [isa: 0006140 0045934 ]
+0045981 = positive regulation of nucleotide metabolism [isa: 0006140 0045935 ]
+0009259 = ribonucleotide metabolism [isa: 0009117 ]
+0009225 = nucleotide-sugar metabolism [isa: 0006139 ]
+0019219 = regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism [isa: 0019222 ] [partof: 0006139 ]
+0045934 = negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism [isa: 0009892 0019219 ]
+0045935 = positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism [isa: 0009893 0019219 ]
+0006403 = RNA localization [isa: 0006139 ]
+0016031 = cytoplasmic tRNA, mitochondrial import [isa: 0006403 ]
+0019093 = mitochondrial RNA localization [isa: 0006403 ]
+0019090 = mitochondrial rRNA, mitochondrial export [isa: 0019093 ]
+0019091 = mitochondrial lrRNA, mitochondrial export [isa: 0019090 ]
+0019092 = mitochondrial srRNA, mitochondrial export [isa: 0019090 ]
+0019095 = pole plasm-mitochondrial rRNA localization [isa: 0007316 0019093 ]
+0019096 = pole plasm-mitochondrial lrRNA localization [isa: 0019095 ]
+0019097 = pole plasm-mitochondrial srRNA localization [isa: 0019095 ]
+0008298 = mRNA localization, intracellular [isa: 0006403 ]
+0019094 = pole plasm-mRNA localization [isa: 0007316 0008298 ]
+0046595 = establishment of pole plasm mRNA localization [partof: 0019094 ]
+0046594 = maintenance of pole plasm mRNA localization [partof: 0019094 ]
+0045450 = pole plasm bicoid mRNA localization [isa: 0019094 ]
+0008359 = regulation of pole plasm bicoid mRNA localization [partof: 0045450 ]
+0045853 = negative regulation of pole plasm bicoid mRNA localization [isa: 0008359 ]
+0045854 = positive regulation of pole plasm bicoid mRNA localization [isa: 0008359 ]
+0045451 = pole plasm oskar mRNA localization [isa: 0019094 ]
+0007317 = regulation of pole plasm oskar mRNA localization [partof: 0045451 ]
+0045855 = negative regulation of pole plasm oskar mRNA localization [isa: 0007317 ]
+0045856 = positive regulation of pole plasm oskar mRNA localization [isa: 0007317 ]
+0006405 = nuclear RNA-nucleus export [isa: 0006403 0006913 ]
+0006406 = mRNA-nucleus export [isa: 0006405 ]
+0016973 = poly(A)+ mRNA-nucleus export [isa: 0006406 ]
+0006407 = rRNA-nucleus export [isa: 0006405 ]
+0006408 = snRNA-nucleus export [isa: 0006405 ]
+0006409 = tRNA-nucleus export [isa: 0006405 ]
+0007316 = pole plasm RNA localization [isa: 0006403 ] [partof: 0007315 ]
+0006404 = RNA-nucleus import [isa: 0006403 0006913 ]
+0016070 = RNA metabolism [isa: 0006139 ]
+0016071 = mRNA metabolism [isa: 0016070 ]
+0008334 = histone mRNA metabolism [isa: 0016071 ]
+0006398 = histone mRNA 3'-end processing [isa: 0006397 0008334 ]
+0006379 = mRNA cleavage [isa: 0006397 0016071 ]
+0006378 = mRNA polyadenylation [isa: 0006397 0016071 ]
+0006396 = RNA processing [isa: 0016070 ]
+0006397 = mRNA processing [isa: 0006396 ]
+0006370 = mRNA capping [isa: 0006397 0009452 ]
+0016556 = mRNA modification [isa: 0006397 0009451 ]
+0006381 = mRNA editing [isa: 0016547 0016556 ]
+0006371 = mRNA splicing [isa: 0006397 0008380 ]
+0006373 = 3'-splice site cleavage, exon ligation [partof: 0006371 ]
+0006372 = lariat formation, 5'-splice site cleavage [partof: 0006371 ]
+0006377 = MATa1 (A1) pre-mRNA splicing [isa: 0006371 ]
+0045292 = mRNA cis splicing [isa: 0006371 ]
+0006376 = mRNA splice site selection [partof: 0006371 ]
+0045291 = mRNA trans splicing [isa: 0006371 ]
+0000244 = snRNP recycling [partof: 0006371 ]
+0000245 = spliceosome assembly [partof: 0006371 ]
+0006375 = splicing AT-AC intron [isa: 0006371 ]
+0006374 = splicing GT-AG intron [isa: 0006371 ]
+0009452 = RNA capping [isa: 0006396 ]
+0006387 = snRNA capping [isa: 0009452 0016180 ]
+0009451 = RNA modification [isa: 0006396 ]
+0001522 = pseudouridine synthesis [isa: 0009451 ]
+0016547 = RNA editing [isa: 0009451 ]
+0016553 = base conversion/substitution editing [isa: 0016547 ]
+0006382 = adenosine to inosine editing [isa: 0016553 ]
+0016554 = cytidine to uridine editing [isa: 0016553 ]
+0016555 = uridine to cytidine editing [isa: 0016553 ]
+0016550 = insertion/deletion editing [isa: 0016547 ]
+0016552 = co-transcriptional insertion/deletion editing [isa: 0016550 ]
+0016551 = post-transcriptional insertion/deletion editing [isa: 0016550 ]
+0016548 = rRNA editing [isa: 0000154 0016547 ]
+0016549 = tRNA editing [isa: 0006400 0016547 ]
+0001510 = RNA methylation [isa: 0009451 ]
+0030488 = tRNA methylation [isa: 0001510 0006400 ]
+0000154 = rRNA modification [isa: 0009451 0016072 ]
+0040031 = snRNA modification [isa: 0009451 0016072 ]
+0006400 = tRNA modification [isa: 0006399 0009451 ]
+0008380 = RNA splicing [isa: 0006396 ]
+0006388 = tRNA splicing [isa: 0008033 0008380 ]
+0006389 = tRNA-Y splicing [isa: 0006388 ]
+0016180 = snRNA processing [isa: 0006396 ]
+0008033 = tRNA processing [isa: 0006396 ]
+0001680 = tRNA 3'-terminal CCA addition [isa: 0008033 ]
+0001682 = tRNA 5'-leader removal [isa: 0008033 ]
+0042245 = RNA repair [isa: 0016070 ]
+0016072 = rRNA metabolism [isa: 0016070 ]
+0016074 = snoRNA metabolism [isa: 0016070 ]
+0016073 = snRNA metabolism [isa: 0016070 ]
+0006399 = tRNA metabolism [isa: 0016070 ]
+0006350 = transcription [isa: 0006139 ]
+0045449 = regulation of transcription [partof: 0006350 ]
+0016481 = negative regulation of transcription [isa: 0045449 ]
+0045892 = negative regulation of transcription, DNA-dependent [isa: 0006355 0016481 ]
+0045013 = negative regulation of transcription by carbon catabolites [isa: 0045892 0045990 ]
+0045014 = negative regulation of transcription by glucose [isa: 0045013 0046015 ]
+0016479 = negative regulation of transcription from Pol I promoter [isa: 0006356 0045892 ]
+0000122 = negative regulation of transcription from Pol II promoter [isa: 0006357 0045892 ]
+0045816 = negative regulation of global transcription from Pol II promoter [isa: 0000122 0006358 ]
+0017055 = negative regulation of transcriptional pre-initiation complex formation [isa: 0000122 0045898 ]
+0016480 = negative regulation of transcription from Pol III promoter [isa: 0006359 0045892 ]
+0045894 = negative regulation of transcription, mating-type specific [isa: 0007532 0045892 ]
+0045941 = positive regulation of transcription [isa: 0045449 ]
+0045893 = positive regulation of transcription, DNA-dependent [isa: 0006355 0045941 ]
+0045991 = positive regulation of transcription by carbon catabolites [isa: 0045893 0045990 ]
+0046016 = positive regulation of transcription by glucose [isa: 0045991 0046015 ]
+0045943 = positive regulation of transcription from Pol I promoter [isa: 0006356 0045893 ]
+0045944 = positive regulation of transcription from Pol II promoter [isa: 0006357 0045893 ]
+0045817 = positive regulation of global transcription from Pol II promoter [isa: 0006358 0045944 ]
+0045899 = positive regulation of transcriptional pre-initiation complex formation [isa: 0045898 0045944 ]
+0045945 = positive regulation of transcription from Pol III promoter [isa: 0006359 0045893 ]
+0045895 = positive regulation of transcription, mating-type specific [isa: 0007532 0045893 ]
+0006355 = regulation of transcription, DNA-dependent [isa: 0045449 ] [partof: 0006351 ]
+0045990 = regulation of transcription by carbon catabolites [isa: 0006355 ]
+0046015 = regulation of transcription by glucose [isa: 0045990 ]
+0006356 = regulation of transcription from Pol I promoter [isa: 0006355 ] [partof: 0006360 ]
+0006357 = regulation of transcription from Pol II promoter [isa: 0006355 ] [partof: 0006366 ]
+0006358 = regulation of global transcription from Pol II promoter [isa: 0006357 ]
+0045898 = regulation of transcriptional pre-initiation complex formation [isa: 0006357 ]
+0006359 = regulation of transcription from Pol III promoter [isa: 0006355 ] [partof: 0006383 ]
+0007532 = regulation of transcription, mating-type specific [isa: 0006355 0007531 ]
+0006351 = transcription, DNA-dependent [isa: 0006350 ]
+0009300 = antisense RNA transcription [isa: 0006351 ]
+0006354 = RNA elongation [partof: 0006351 ]
+0009302 = snoRNA transcription [isa: 0006351 ]
+0006390 = transcription from mitochondrial promoter [isa: 0006351 ]
+0006392 = RNA elongation from mitochondrial promoter [partof: 0006390 ]
+0006393 = RNA transcription termination from mitochondrial promoter [partof: 0006390 ]
+0006391 = transcription initiation from mitochondrial promoter [partof: 0006390 ]
+0006360 = transcription from Pol I promoter [isa: 0006351 ]
+0006362 = RNA elongation from Pol I promoter [partof: 0006360 ]
+0009303 = rRNA transcription [isa: 0006360 ]
+0006361 = transcription initiation from Pol I promoter [isa: 0006352 ] [partof: 0006360 ]
+0006363 = transcription termination from Pol I promoter [isa: 0006353 ] [partof: 0006360 ]
+0006366 = transcription from Pol II promoter [isa: 0006351 ]
+0016245 = hyperphosphorylation of RNA polymerase II [isa: 0016310 ] [partof: 0006366 ]
+0009299 = mRNA transcription [isa: 0006366 ]
+0019084 = (delayed) early viral mRNA transcription [isa: 0009299 ] [partof: 0019083 ]
+0019085 = immediate early viral mRNA transcription [isa: 0009299 ] [partof: 0019083 ]
+0019086 = late viral mRNA transcription [isa: 0009299 ] [partof: 0019083 ]
+0006368 = RNA elongation from Pol II promoter [partof: 0006366 ]
+0009301 = snRNA transcription [isa: 0006366 ]
+0006367 = transcription initiation from Pol II promoter [isa: 0006352 ] [partof: 0006366 ]
+0006369 = transcription termination from Pol II promoter [isa: 0006353 ] [partof: 0006366 ]
+0006383 = transcription from Pol III promoter [isa: 0006351 ]
+0006385 = RNA elongation from Pol III promoter [partof: 0006383 ]
+0006384 = transcription initiation from Pol III promoter [isa: 0006352 ] [partof: 0006383 ]
+0006386 = transcription termination from Pol III promoter [isa: 0006353 ] [partof: 0006383 ]
+0009304 = tRNA transcription [isa: 0006383 ]
+0006352 = transcription initiation [partof: 0006351 ]
+0006353 = transcription termination [partof: 0006351 ]
+0006410 = transcription, RNA-dependent [isa: 0006350 ]
+0019083 = viral transcription [isa: 0006350 ] [partof: 0019080 ]
+0006730 = one-carbon compound metabolism [isa: 0008152 ]
+0009439 = cyanate metabolism [isa: 0006730 ]
+0019499 = cyanide metabolism [isa: 0006730 ]
+0015942 = formate metabolism [isa: 0006730 ]
+0015944 = formate oxidation [isa: 0015942 ]
+0015947 = methane metabolism [isa: 0006730 ]
+0009853 = photorespiration [isa: 0006730 ]
+0009854 = oxidative photosynthetic carbon pathway [partof: 0009853 ]
+0019496 = serine-isocitrate lyase pathway [isa: 0006730 ]
+0006082 = organic acid metabolism [isa: 0008152 ]
+0019752 = carboxylic acid metabolism [isa: 0006082 ]
+0006083 = acetate metabolism [isa: 0019752 ]
+0030635 = acetate derivative metabolism [isa: 0006083 ]
+0030638 = polyketide metabolism [isa: 0030635 ]
+0019427 = acetate utilization [isa: 0006083 ]
+0006084 = acetyl-CoA metabolism [isa: 0006083 ]
+0019681 = acetyl-CoA assimilation [isa: 0006084 ]
+0019577 = aldaric acid metabolism [isa: 0019752 ]
+0019580 = galactarate metabolism [isa: 0019577 ]
+0046393 = D-galactarate metabolism [isa: 0019580 ]
+0019392 = glucarate metabolism [isa: 0019577 ]
+0019605 = butyrate metabolism [isa: 0019752 ]
+0046361 = 2-oxobutyrate metabolism [isa: 0019605 ]
+0046417 = chorismate metabolism [isa: 0019752 ]
+0046451 = diaminopimelate metabolism [isa: 0019752 ]
+0019583 = galactonate metabolism [isa: 0019752 ]
+0046400 = ketodeoxyoctanoate metabolism [isa: 0019752 ]
+0006089 = lactate metabolism [isa: 0019752 ]
+0019516 = lactate oxidation [isa: 0006089 ]
+0019247 = lactate racemization [isa: 0006089 ]
+0019541 = propionate metabolism [isa: 0019752 ]
+0019679 = propionate metabolism, methylcitrate cycle [isa: 0019541 ]
+0019678 = propionate metabolism, methylmalonyl pathway [isa: 0019541 ]
+0006090 = pyruvate metabolism [isa: 0006087 0019752 ]
+0009444 = pyruvate oxidation [isa: 0006090 ]
+0006063 = uronic acid metabolism [isa: 0019752 ]
+0019586 = galacturonate metabolism [isa: 0006063 ]
+0046396 = D-galacturonate metabolism [isa: 0019586 ]
+0019585 = glucuronate metabolism [isa: 0006063 ]
+0046398 = UDP-glucuronate metabolism [isa: 0019585 ]
+0006087 = pyruvate dehydrogenase bypass [isa: 0006082 ]
+0006088 = acetate to acetyl-CoA [isa: 0006087 ]
+0046374 = teichoic acid metabolism [isa: 0006082 ]
+0018942 = organometal metabolism [isa: 0008152 ]
+0018941 = organomercury metabolism [isa: 0018942 ]
+0042191 = methylmercury metabolism [isa: 0018941 ]
+0018943 = organotin metabolism [isa: 0018942 ]
+0018944 = tri-n-butyltin metabolism [isa: 0018943 ]
+0006800 = oxygen and reactive oxygen species metabolism [isa: 0008152 ]
+0006803 = glutathione conjugation reaction [isa: 0006800 ]
+0006804 = peroxidase reaction [isa: 0006800 ]
+0006801 = superoxide metabolism [isa: 0006800 ]
+0019430 = removal of superoxide radicals [isa: 0006801 ]
+0042554 = superoxide release [isa: 0006801 ]
+0006793 = phosphorus metabolism [isa: 0008152 ]
+0006796 = phosphate metabolism [isa: 0006793 ]
+0016311 = dephosphorylation [isa: 0006796 ]
+0006470 = protein amino acid dephosphorylation [isa: 0006464 0016311 ]
+0016310 = phosphorylation [isa: 0006796 ]
+0006468 = protein amino acid phosphorylation [isa: 0006464 0016310 ]
+0018109 = peptidyl-arginine phosphorylation [isa: 0006468 0018195 ]
+0018217 = peptidyl-aspartic acid phosphorylation [isa: 0006468 0018197 ]
+0018218 = peptidyl-cysteine acid phosphorylation [isa: 0006468 0018198 ]
+0018106 = peptidyl-histidine phosphorylation [isa: 0006468 ]
+0018105 = peptidyl-serine phosphorylation [isa: 0006468 ]
+0018107 = peptidyl-threonine phosphorylation [isa: 0006468 ]
+0018108 = peptidyl-tyrosine phosphorylation [isa: 0006468 0018212 ]
+0045859 = regulation of protein kinase activity [partof: 0006468 ]
+0006469 = negative regulation of protein kinase activity [isa: 0045859 ]
+0045860 = positive regulation of protein kinase activity [isa: 0045859 ]
+0042325 = regulation of phosphorylation [isa: 0019220 ] [partof: 0016310 ]
+0042326 = negative regulation of phosphorylation [isa: 0042325 0045936 ]
+0042327 = positive regulation of phosphorylation [isa: 0042325 0045937 ]
+0006797 = polyphosphate metabolism [isa: 0006796 ]
+0019220 = regulation of phosphate metabolism [isa: 0019222 ] [partof: 0006796 ]
+0045936 = negative regulation of phosphate metabolism [isa: 0009892 0019220 ]
+0045942 = negative regulation of phosphorus utilization [isa: 0006795 0045936 ]
+0045937 = positive regulation of phosphate metabolism [isa: 0009893 0019220 ]
+0045949 = positive regulation of phosphorus utilization [isa: 0006795 0045937 ]
+0006795 = regulation of phosphorus utilization [isa: 0019220 ] [partof: 0006794 ]
+0006794 = phosphorus utilization [isa: 0006793 ]
+0042440 = pigment metabolism [isa: 0008152 ]
+0042441 = eye pigment metabolism [isa: 0042440 ]
+0006856 = eye pigment precursor transport [isa: 0006810 ] [partof: 0042441 0046158 ]
+0046152 = ommochrome metabolism [isa: 0042441 0046158 ]
+0046154 = rhodopsin metabolism [isa: 0042441 ]
+0006582 = melanin metabolism [isa: 0042440 ]
+0046158 = ocellus pigment metabolism [isa: 0042440 ]
+0019538 = protein metabolism [isa: 0008152 ]
+0009100 = glycoprotein metabolism [isa: 0019538 ]
+0020027 = hemoglobin metabolism [isa: 0019538 ]
+0042541 = hemoglobin biosynthesis [isa: 0020027 ]
+0042540 = hemoglobin catabolism [isa: 0020027 ]
+0020028 = hemoglobin uptake [isa: 0015031 0020027 ]
+0042157 = lipoprotein metabolism [isa: 0019538 ]
+0042160 = lipoprotein modification [isa: 0042157 ]
+0042161 = lipoprotein oxidation [isa: 0018158 0042160 ]
+0006056 = mannoprotein metabolism [isa: 0019538 ]
+0006518 = peptide metabolism [isa: 0019538 ]
+0001519 = peptide amidation [isa: 0006518 ]
+0006461 = protein complex assembly [isa: 0019538 ]
+0017004 = cytochrome biogenesis [isa: 0006461 ]
+0017062 = cytochrome bc(1) complex biogenesis [isa: 0017004 ]
+0017003 = protein-heme linkage [isa: 0017006 ] [partof: 0017004 ]
+0018063 = cytochrome c-heme linkage [isa: 0017003 ]
+0018379 = cytochrome c-heme linkage via heme-bis-L-cysteine [isa: 0018063 0018198 ]
+0018378 = cytochrome c-heme linkage via heme-L-cysteine [isa: 0018063 0018198 ]
+0045328 = cytochrome P450 4A1-heme linkage [isa: 0017003 ]
+0018186 = peroxidase-heme linkage [isa: 0017003 ]
+0018362 = peroxidase-heme linkage via dihydroxyheme-L-aspartyl ester-L-glutamyl ester [isa: 0018186 0018200 ]
+0018363 = peroxidase-heme linkage via dihydroxyheme-L-aspartyl ester-L-glutamyl ester-L-methionine sulfonium [isa: 0018186 0018200 0018206 ]
+0018182 = protein-heme linkage via L-histidine [isa: 0017003 0018202 ]
+0018174 = protein-heme P460 linkage [isa: 0017003 ]
+0018360 = protein-heme P460 linkage via heme P460-bis-L-cysteine-L-lysine [isa: 0018174 0018198 0018205 ]
+0018359 = protein-heme P460 linkage via heme P460-bis-L-cysteine-L-tyrosine [isa: 0018174 0018198 0018212 ]
+0018419 = protein catenane formation [isa: 0006461 ]
+0019937 = protein catenane formation via N6-(L-isoaspartyl)-L-lysine, autocatalytic [isa: 0018419 0018420 ]
+0006462 = protein complex assembly, multichaperone pathway [isa: 0006461 ]
+0008535 = cytochrome c oxidase biogenesis [isa: 0006462 ]
+0006463 = steroid hormone receptor complex assembly [isa: 0006462 ]
+0006457 = protein folding [isa: 0019538 ]
+0006458 = 'de novo' protein folding [isa: 0006457 ]
+0006459 = binding unfolded ER proteins [isa: 0006458 ]
+0042026 = protein refolding [isa: 0006457 ]
+0008104 = protein localization [isa: 0019538 ]
+0008105 = asymmetric protein localization [isa: 0008104 ]
+0045176 = apical protein localization [isa: 0008105 ]
+0045167 = asymmetric protein localization involved in cell fate commitment [isa: 0008105 ] [partof: 0045165 ]
+0045175 = basal protein localization [isa: 0008105 ]
+0007318 = pole plasm protein localization [isa: 0008105 ] [partof: 0007315 ]
+0045184 = establishment of protein localization [partof: 0008104 ]
+0045185 = maintenance of protein localization [partof: 0008104 ]
+0006464 = protein modification [isa: 0019538 ]
+0018307 = enzyme active site formation [isa: 0006464 ]
+0045427 = enzyme active site formation via (phospho-5'-guanosine)-L-histidine [isa: 0018202 0018307 ]
+0018327 = enzyme active site formation via 1'-phospho-L-histidine [isa: 0018202 0018307 ]
+0018328 = enzyme active site formation via 3'-phospho-L-histidine [isa: 0018202 0018307 ]
+0018337 = enzyme active site formation via L-2',4',5'-topaquinone [isa: 0018212 0018307 ]
+0018443 = enzyme active site formation via L-aspartic 4-phosphoric anhydride [isa: 0018197 0018307 ]
+0018192 = enzyme active site formation via L-cysteine persulfide [isa: 0018198 0018307 ]
+0018324 = enzyme active site formation via L-cysteine sulfenic acid [isa: 0018198 0018307 ]
+0018323 = enzyme active site formation via L-cysteine sulfinic acid [isa: 0018198 0018307 ]
+0018329 = enzyme active site formation via N6-(phospho-5'-adenosine)-L-lysine [isa: 0018205 0018307 ]
+0018330 = enzyme active site formation via N6-(phospho-5'-guanosine)-L-lysine [isa: 0018205 0018307 ]
+0018308 = enzyme active site formation via N6-pyruvic acid 2-iminyl-L-lysine [isa: 0018205 0018307 ]
+0018332 = enzyme active site formation via O-(phospho-5'-adenosine)-L-threonine [isa: 0018210 0018307 ]
+0018331 = enzyme active site formation via O-phospho-L-serine [isa: 0018209 0018307 ]
+0018333 = enzyme active site formation via O-phospho-L-threonine [isa: 0018210 0018307 ]
+0018334 = enzyme active site formation via O4'-phospho-L-tyrosine [isa: 0018212 0018307 ]
+0018326 = enzyme active site formation via S-acetyl-L-cysteine [isa: 0018198 0018307 ]
+0018320 = enzyme active site formation via S-methyl-L-cysteine [isa: 0018198 0018307 ]
+0018325 = enzyme active site formation via S-phospho-L-cysteine [isa: 0018198 0018307 ]
+0018183 = enzyme active site formation via S-selenyl-L-cysteine [isa: 0018198 0018307 ]
+0018248 = enzyme active site formation via S-sulfo-L-cysteine [isa: 0018198 0018307 ]
+0042040 = metal incorporation into metallo-pterin complex [isa: 0006464 ]
+0042041 = molybdenum incorporation into metallo-pterin complex [isa: 0042040 ]
+0018292 = molybdenum incorporation via L-cysteinyl molybdopterin [isa: 0018198 0042041 ]
+0042042 = tungsten incorporation into metallo-pterin complex [isa: 0042040 ]
+0018282 = metal incorporation into metallo-sulfur cluster [isa: 0006464 ]
+0018427 = copper incorporation into metallo-sulfur cluster [isa: 0018282 ]
+0018428 = copper incorporation into copper-sulfur cluster [isa: 0018427 ]
+0018429 = copper incorporation into copper-sulfur cluster via heptakis-L-histidino tetracopper mu4-sulfide hydroxide [isa: 0018202 0018428 ]
+0018283 = iron incorporation into metallo-sulfur cluster [isa: 0018282 ]
+0018306 = iron incorporation into iron-sulfur cluster via bis-L-cysteinyl-L-N3'-histidino-L-serinyl tetrairon tetrasulfide [isa: 0018198 0018202 0018209 0018283 ]
+0018441 = iron incorporation into iron-sulfur cluster via hexakis-L-cysteinyl L-serinyl octairon heptasulfide [isa: 0018209 0018283 0018418 ]
+0019709 = iron incorporation into iron-sulfur cluster via pentakis-L-cysteinyl L-histidino nickel tetrairon pentasulfide [isa: 0018198 0018202 0018283 ]
+0018285 = iron incorporation into iron-sulfur cluster via tetrakis-L-cysteinyl diiron disulfide [isa: 0018198 0018283 ]
+0018288 = iron incorporation into iron-sulfur cluster via tetrakis-L-cysteinyl tetrairon tetrasulfide [isa: 0018198 0018283 ]
+0045459 = iron incorporation into iron-sulfur cluster via tetrakis-L-cysteinyl triiron tetrasulfide [isa: 0018283 ]
+0018415 = iron incorporation into iron-sulfur cluster via tris-L-cysteinyl L-cysteine persulfido bis-L-glutamato L-histidino nickel triiron disulfide trioxide [isa: 0018198 0018200 0018202 0018283 ]
+0018417 = iron incorporation into iron-sulfur cluster via tris-L-cysteinyl L-cysteine persulfido L-glutamato L-histidino L-serinyl nickel triiron disulfide trioxide [isa: 0018198 0018200 0018202 0018209 0018283 ]
+0018287 = iron incorporation into iron-sulfur cluster via tris-L-cysteinyl triiron tetrasulfide [isa: 0018198 0018283 ]
+0018304 = iron incorporation into iron-sulfur cluster via tris-L-cysteinyl-L-aspartato tetrairon tetrasulfide [isa: 0018197 0018198 0018283 ]
+0018301 = iron incorporation into iron-sulfur cluster via tris-L-cysteinyl-L-cysteine persulfido-bis-L-glutamato-L-histidino tetrairon [isa: 0018198 0018200 0018202 0018283 ]
+0018302 = iron incorporation into iron-sulfur cluster via tris-L-cysteinyl-L-N1'-histidino tetrairon tetrasulfide [isa: 0018198 0018202 0018283 ]
+0018303 = iron incorporation into iron-sulfur cluster via tris-L-cysteinyl-L-N3'-histidino tetrairon tetrasulfide [isa: 0018198 0018202 0018283 ]
+0018305 = iron incorporation into iron-sulfur cluster via tris-L-cysteinyl-L-serinyl tetrairon tetrasulfide [isa: 0018198 0018209 0018283 ]
+0018284 = iron incorporation into protein via tetrakis-L-cysteinyl iron [isa: 0018198 0018283 ]
+0018299 = iron incorporation into the Rieske iron-sulfur cluster via bis-L-cysteinyl bis-L-histidino diiron disulfide [isa: 0018198 0018202 0018283 ]
+0018289 = molybdenum incorporation into metallo-sulfur cluster [isa: 0018282 ]
+0018291 = molybdenum incorporation into iron-sulfur cluster [isa: 0018289 ]
+0018290 = iron and molybdenum incorporation into iron-molybdenum-sulfur cluster via L-cysteinyl homocitryl molybdenum-heptairon-nonasulfide [isa: 0018198 0018291 ]
+0018315 = molybdenum incorporation into molybdenum-sulfur cluster [isa: 0018289 ]
+0018187 = molybdenum incorporation via L-cysteinyl molybdopterin guanine dinucleotide [isa: 0018198 0018315 ]
+0018147 = molybdenum incorporation via L-selenocysteinyl molybdopterin guanine dinucleotide [isa: 0018198 0018315 ]
+0042258 = molybdenum incorporation via L-serinyl molybdopterin guanine dinucleotide [isa: 0018209 0018315 ]
+0018414 = nickel incorporation into metallo-sulfur cluster [isa: 0018282 ]
+0018416 = nickel incorporation into iron-sulfur cluster via tris-L-cysteinyl L-cysteine persulfido bis-L-glutamato L-histidino nickel triiron disulfide trioxide [isa: 0018198 0018200 0018202 0018414 ]
+0018418 = nickel incorporation into iron-sulfur cluster via tris-L-cysteinyl L-cysteine persulfido L-glutamato L-histidino L-serinyl nickel triiron disulfide trioxide [isa: 0018198 0018200 0018202 0018414 ]
+0042075 = nickel incorporation into nickel-iron-sulfur cluster via pentakis-L-cysteinyl L-histidino nickel tetrairon pentasulfide [isa: 0018198 0018202 0018414 ]
+0042039 = vanadium incorporation into metallo-sulfur cluster [isa: 0018282 ]
+0018143 = nucleic acid-protein covalent cross-linking [isa: 0006464 ]
+0018142 = DNA-protein covalent cross-linking [isa: 0018143 ]
+0018145 = DNA-protein covalent cross-linking via peptidyl-serine [isa: 0018142 0018209 ]
+0018164 = DNA-protein covalent cross-linking via peptidyl-threonine [isa: 0018142 0018210 ]
+0018163 = DNA-protein covalent cross-linking via the 5' end to peptidyl-tyrosine [isa: 0018142 0045327 ]
+0018144 = RNA-protein covalent cross-linking [isa: 0018143 ]
+0018259 = RNA-protein covalent cross-linking via peptidyl-serine [isa: 0018144 0018209 ]
+0018148 = RNA-protein covalent cross-linking via peptidyl-tyrosine [isa: 0018144 0018212 ]
+0018409 = peptide/protein amino-terminal blocking [isa: 0006464 ]
+0018388 = N-terminal peptidyl-valine condensation with pyruvate to form N-pyruvic acid 2-iminyl-L-valine [isa: 0018213 0018409 ]
+0006474 = N-terminal protein amino acid acetylation [isa: 0006473 0018409 ]
+0017189 = N-terminal peptidyl-alanine acetylation [isa: 0006474 0018194 ]
+0017190 = N-terminal peptidyl-aspartic acid acetylation [isa: 0006474 0018197 ]
+0018275 = N-terminal peptidyl-cysteine acetylation [isa: 0006474 0018533 ]
+0018002 = N-terminal peptidyl-glutamic acid acetylation [isa: 0006474 0018200 ]
+0017192 = N-terminal peptidyl-glutamine acetylation [isa: 0006474 0018199 ]
+0017193 = N-terminal peptidyl-glycine acetylation [isa: 0006474 0018201 ]
+0017194 = N-terminal peptidyl-isoleucine acetylation [isa: 0006474 0018203 ]
+0018076 = N-terminal peptidyl-lysine acetylation [isa: 0006474 0018394 ]
+0017195 = N-terminal peptidyl-lysine N2-acetylation [isa: 0018076 ]
+0017196 = N-terminal peptidyl-methionine acetylation [isa: 0006474 0018206 ]
+0017197 = N-terminal peptidyl-proline acetylation [isa: 0006474 0018208 ]
+0017198 = N-terminal peptidyl-serine acetylation [isa: 0006474 0018209 ]
+0017199 = N-terminal peptidyl-threonine acetylation [isa: 0006474 0018210 ]
+0018000 = N-terminal peptidyl-tyrosine acetylation [isa: 0006474 0018212 ]
+0018001 = N-terminal peptidyl-valine acetylation [isa: 0006474 0018213 ]
+0018058 = N-terminal protein amino acid deamination [isa: 0018198 0018277 0018409 ]
+0018060 = N-terminal peptidyl-cysteine acid deamination [isa: 0018058 ]
+0018387 = N-terminal peptidyl-amino acid deamination to pyruvic acid [isa: 0018059 0018060 0018209 ]
+0018386 = N-terminal peptidyl-cysteine condensation with pyruvate to form N-pyruvic acid 2-iminyl-L-cysteine [isa: 0018060 ]
+0018059 = N-terminal peptidyl-serine deamination [isa: 0018058 ]
+0018278 = N-terminal peptidyl-threonine deamination [isa: 0018058 0018210 ]
+0018389 = N-terminal peptidyl-valine deamination [isa: 0018058 ]
+0006480 = N-terminal protein amino acid methylation [isa: 0006479 0018409 ]
+0018011 = N-terminal peptidyl-alanine methylation [isa: 0006480 0018194 ]
+0019716 = N-terminal peptidyl-alanine mono-methylation [isa: 0018011 ]
+0018012 = N-terminal peptidyl-alanine tri-methylation [isa: 0018011 ]
+0018019 = N-terminal peptidyl-glutamine methylation [isa: 0006480 0018199 ]
+0018013 = N-terminal peptidyl-glycine methylation [isa: 0006480 0018201 ]
+0018014 = N-terminal peptidyl-methionine methylation [isa: 0006480 0018206 ]
+0018015 = N-terminal peptidyl-phenylalanine methylation [isa: 0006480 0018207 ]
+0018016 = N-terminal peptidyl-proline di-methylation [isa: 0006480 0018208 ]
+0018004 = N-terminal protein formylation [isa: 0018256 0018409 ]
+0018005 = N-terminal peptidyl-glycine N-formylation [isa: 0018004 0018201 ]
+0018410 = peptide/protein carboxyl-terminal blocking [isa: 0006464 ]
+0006481 = C-terminal protein amino acid methylation [isa: 0006479 0018410 ]
+0018166 = C-terminal protein-tyrosinylation [isa: 0018212 0018322 0018410 ]
+0018391 = C-terminal peptidyl-glutamic acid tyrosinylation [isa: 0018166 0018200 ]
+0018033 = protein C-terminal amidation [isa: 0018032 0018410 ]
+0018034 = C-terminal peptidyl-alanine amidation [isa: 0018033 0018194 ]
+0018035 = C-terminal peptidyl-arginine amidation [isa: 0018033 0018195 ]
+0018036 = C-terminal peptidyl-asparagine amidation [isa: 0018033 0018196 ]
+0018037 = C-terminal peptidyl-aspartic acid amidation [isa: 0018033 0018197 ]
+0018038 = C-terminal peptidyl-cysteine amidation [isa: 0018033 0018198 ]
+0018040 = C-terminal peptidyl-glutamic acid amidation [isa: 0018033 ]
+0018170 = C-terminal peptidyl-polyglutamic acid amidation [isa: 0018040 0018200 ]
+0018039 = C-terminal peptidyl-glutamine amidation [isa: 0018033 0018199 ]
+0018041 = C-terminal peptidyl-glycine amidation [isa: 0018033 0018201 ]
+0018042 = C-terminal peptidyl-histidine amidation [isa: 0018033 0018202 ]
+0018043 = C-terminal peptidyl-isoleucine amidation [isa: 0018033 0018203 ]
+0018044 = C-terminal peptidyl-leucine amidation [isa: 0018033 0018204 ]
+0018045 = C-terminal peptidyl-lysine amidation [isa: 0018033 0018205 ]
+0018046 = C-terminal peptidyl-methionine amidation [isa: 0018033 0018206 ]
+0018047 = C-terminal peptidyl-phenylalanine amidation [isa: 0018033 0018207 ]
+0018048 = C-terminal peptidyl-proline amidation [isa: 0018033 0018208 ]
+0018049 = C-terminal peptidyl-serine amidation [isa: 0018033 0018209 ]
+0018050 = C-terminal peptidyl-threonine amidation [isa: 0018033 0018210 ]
+0018051 = C-terminal peptidyl-tryptophan amidation [isa: 0018033 0018211 ]
+0018052 = C-terminal peptidyl-tyrosine amidation [isa: 0018033 0018212 ]
+0018053 = C-terminal peptidyl-valine amidation [isa: 0018033 0018213 ]
+0018193 = peptidyl-amino acid modification [isa: 0006464 ]
+0018194 = peptidyl-alanine modification [isa: 0018193 ]
+0018250 = peptidyl-dehydroalanine biosynthesis from peptidyl-tyrosine or peptidyl-serine [isa: 0018194 0018209 0018212 0018249 ]
+0018313 = protein-protein cross-linking via L-alanyl-5-imidazolinone glycine [isa: 0018149 0018194 0018201 ]
+0018195 = peptidyl-arginine modification [isa: 0018193 ]
+0018120 = peptidyl-arginine ADP-ribosylation [isa: 0006471 0018195 ]
+0018102 = peptidyl-arginine hydroxylation [isa: 0018126 0018195 ]
+0018216 = peptidyl-arginine methylation [isa: 0006479 0018195 ]
+0018181 = peptidyl-arginine 5-methylation [isa: 0018216 ]
+0019701 = peptidyl-arginine delta-N-methylation [isa: 0018216 ]
+0019918 = peptidyl-arginine methylation, to symmetrical-dimethyl arginine [isa: 0018216 ]
+0019919 = peptidyl-arginine methylation, to unsymmetrical-dimethyl arginine [isa: 0018216 ]
+0018196 = peptidyl-asparagine modification [isa: 0018193 ]
+0046550 = (3-aminopropyl)(L-aspartyl-1-amino)phosphoryl-5'-adenosine biosynthesis from asparagine [isa: 0018196 ]
+0018264 = isopeptide cross-linking via N-(L-isoaspartyl)-glycine [isa: 0018196 0018201 0018262 ]
+0018263 = isopeptide cross-linking via N-(L-isoaspartyl)-L-cysteine [isa: 0018196 0018198 0018262 ]
+0018122 = peptidyl-asparagine ADP-ribosylation [isa: 0006471 0018196 ]
+0042265 = peptidyl-asparagine hydroxylation [isa: 0018126 0018196 ]
+0018376 = peptidyl-asparagine hydroxylation to form L-erythro-beta-hydroxyasparagine [isa: 0042265 ]
+0019710 = peptidyl-asparagine methylation [isa: 0018196 ]
+0042259 = peptidyl-L-beta-methylthioasparagine biosynthesis from peptidyl-asparagine [isa: 0018196 ]
+0018311 = peptidyl-N4-hydroxymethyl-L-asparagine biosynthesis from peptidyl-asparagine [isa: 0018196 ]
+0018420 = protein-protein cross-linking via N6-(L-isoaspartyl)-L-lysine [isa: 0018149 0018196 0018205 ]
+0019938 = protein-protein cross-linking via N6-(L-isoaspartyl)-L-lysine, presumed catalytic [isa: 0018420 ]
+0018197 = peptidyl-aspartic acid modification [isa: 0018193 ]
+0019930 = cis-14-hydroxy-10,13-dioxo-7-heptadecenoic acid peptidyl-aspartate ester biosynthesis from peptidyl-aspartic acid [isa: 0018197 ]
+0019803 = peptidyl-aspartic acid carboxylation [isa: 0018197 0018214 ]
+0042264 = peptidyl-aspartic acid hydroxylation [isa: 0018126 0018197 ]
+0019715 = peptidyl-aspartic acid hydroxylation to form L-erythro-beta-hydroxyaspartic acid [isa: 0042264 ]
+0019711 = peptidyl-beta-carboxyaspartic acid biosynthesis from peptidyl-aspartic acid [isa: 0018197 ]
+0018339 = peptidyl-L-beta-methylthioaspartic acid biosynthesis from peptidyl-aspartic acid [isa: 0018197 0018198 ]
+0018198 = peptidyl-cysteine modification [isa: 0018193 ]
+0018253 = biosynthesis of protein-protein cross-link via 5-imidazolinone glycine [isa: 0018149 0018198 0018201 ]
+0019703 = coenzyme A-peptidyl-cysteine covalent linking [isa: 0018198 ]
+0018533 = peptidyl-cysteine acetylation [isa: 0006473 0018198 ]
+0018219 = peptidyl-cysteine S-acetylation [isa: 0018533 ]
+0018123 = peptidyl-cysteine ADP-ribosylation [isa: 0006471 0018198 ]
+0018351 = peptidyl-cysteine esterification [isa: 0018198 0018350 ]
+0018229 = peptidyl-L-cysteine methyl ester biosynthesis from peptidyl-cysteine [isa: 0018351 ]
+0018125 = peptidyl-cysteine methylation [isa: 0006479 0018198 ]
+0018171 = peptidyl-cysteine oxidation [isa: 0018158 0018198 ]
+0006484 = protein cysteine-thiol oxidation [isa: 0006467 0018171 ]
+0018119 = peptidyl-cysteine S-nitrosylation [isa: 0017014 0018198 ]
+0018083 = peptidyl-L-3-oxoalanine biosynthesis from peptidyl-cysteine or peptidyl-serine [isa: 0018198 0018209 ]
+0018118 = peptidyl-L-cysteine glutathione disulfide biosynthesis from peptidyl-cysteine [isa: 0018198 ]
+0018222 = peptidyl-L-cysteine methyl disulfide biosynthesis from peptidyl-cysteine [isa: 0018198 ]
+0018354 = peptidyl-pyrromethane cofactor linkage via dipyrrolylmethanemethyl-L-cysteine [isa: 0018160 0018198 ]
+0018231 = peptidyl-S-diacylglycerol-L-cysteine biosynthesis from peptidyl-cysteine [isa: 0018198 ]
+0018115 = peptidyl-S-diphytanylglycerol diether-L-cysteine biosynthesis from peptidyl-cysteine [isa: 0018198 ]
+0019922 = protein-chromophore linkage via peptidyl-cysteine [isa: 0018198 0018298 ]
+0019923 = alpha-1-microglobulin-chromophore linkage [isa: 0019922 ]
+0018097 = protein-chromophore linkage via peptidyl-S-4-hydroxycinnamyl-L-cysteine [isa: 0018198 0018298 ]
+0018294 = protein-FAD linkage via S-(8alpha-FAD)-L-cysteine [isa: 0018198 0018293 ]
+0018310 = protein-FMN linkage via S-(6-FMN)-L-cysteine [isa: 0018198 0018309 ]
+0018353 = protein-phycocyanobilin linkage via S-phycocyanobilin-L-cysteine [isa: 0017009 0018198 ]
+0018167 = protein-phycoerythrobilin linkage via phycoerythrobilin-bis-L-cysteine [isa: 0017011 0018198 ]
+0018168 = protein-phycoerythrobilin linkage via S-phycoerythrobilin-L-cysteine [isa: 0017011 0018198 ]
+0018357 = protein-phycourobilin linkage via phycourobilin-bis-L-cysteine [isa: 0017010 0018198 ]
+0018358 = protein-phytochromobilin linkage via S-phytochromobilin-L-cysteine [isa: 0017012 0018198 ]
+0018154 = protein-protein cross-linking via (2R,6R)-lanthionine [isa: 0018081 0018198 0018209 ]
+0018233 = protein-protein cross-linking via 2'-(S-L-cysteinyl)-L-histidine [isa: 0018198 0018202 ]
+0018234 = protein-protein cross-linking via 3'-(S-L-cysteinyl)-L-tyrosine [isa: 0018198 0018212 ]
+0019928 = protein-protein cross-linking via 3-(S-L-cysteinyl)-L-aspartic acid [isa: 0018149 0018198 ]
+0019927 = protein-protein cross-linking via 4'-(S-L-cysteinyl)-L-tryptophyl quinone [isa: 0018149 0018198 ]
+0019929 = protein-protein cross-linking via 4-(S-L-cysteinyl)-L-glutamic acid [isa: 0018149 0018198 ]
+0018162 = protein-protein cross-linking via S-(2-aminovinyl)-3-methyl-D-cysteine [isa: 0018149 0018198 0018210 ]
+0018096 = protein-protein cross-linking via S-(2-aminovinyl)-D-cysteine [isa: 0018149 0018198 0018209 ]
+0018232 = protein-protein cross-linking via S-(L-isoglutamyl)-L-cysteine [isa: 0018149 0018198 0018199 ]
+0018255 = protein-protein cross-linking via S-glycyl-L-cysteine [isa: 0018149 0018198 0018201 ]
+0018155 = protein-protein cross-linking via sn-(2S,6R)-lanthionine [isa: 0018081 0018198 0018209 ]
+0018156 = protein-protein cross-linking via (2S,3S,6R)-3-methyl-lanthionine [isa: 0018155 0018210 ]
+0018200 = peptidyl-glutamic acid modification [isa: 0018193 ]
+0017187 = peptidyl-glutamic acid carboxylation [isa: 0018200 0018214 ]
+0018442 = peptidyl-glutamic acid esterification [isa: 0018200 0018350 ]
+0019714 = peptidyl-glutamine esterification [isa: 0018199 0018442 ]
+0019713 = peptidyl-L-glutamic acid 5-methyl ester biosynthesis from glutamine [isa: 0018390 0019714 ]
+0018390 = peptidyl-L-glutamic acid 5-methyl ester biosynthesis from peptidyl-glutamic acid or peptidyl-glutamine [isa: 0018199 0018442 ]
+0019712 = peptidyl-L-glutamic acid 5-methyl ester biosynthesis from glutamic acid [isa: 0018390 ]
+0018424 = peptidyl-glutamic acid poly-ADP-ribosylation [isa: 0006471 0018200 ]
+0018072 = peptidyl-L-glutamyl 5-glycerylphosphorylethanolamine biosynthesis from peptidyl-glutamic acid [isa: 0018200 ]
+0018095 = protein polyglutamylation [isa: 0018200 ]
+0018199 = peptidyl-glutamine modification [isa: 0018193 ]
+0018153 = isopeptide cross-linking via N6-(L-isoglutamyl)-L-lysine [isa: 0018199 0018205 0018262 ]
+0017186 = peptidyl-pyroglutamic acid biosynthesis, using glutaminyl-peptide cyclotransferase [isa: 0018199 ]
+0018201 = peptidyl-glycine modification [isa: 0018193 ]
+0019729 = biosynthesis of protein-protein cross-link via 2-imino-glutaminyl-5-imidazolinone glycine [isa: 0018201 0018209 0018298 ]
+0018252 = biosynthesis of protein-protein cross-link via L-seryl-5-imidazolinone glycine [isa: 0018149 0018201 0018209 0018298 ]
+0018276 = isopeptide cross-linking via N6-glycyl-L-lysine [isa: 0018201 0018205 0018262 ]
+0019736 = peptidyl-sarcosine incorporation [isa: 0018201 ]
+0018202 = peptidyl-histidine modification [isa: 0018193 ]
+0017182 = peptidyl-diphthamide metabolism [isa: 0018202 ]
+0017183 = peptidyl-diphthamide biosynthesis from peptidyl-histidine [isa: 0017182 ]
+0017184 = peptidyl-diphthamide catabolism [isa: 0017182 ]
+0017179 = peptidyl-diphthine metabolism [isa: 0018202 ]
+0017180 = peptidyl-diphthine biosynthesis from peptidyl-histidine [isa: 0017179 ]
+0017181 = peptidyl-diphthine catabolism [isa: 0017179 ]
+0018074 = peptidyl-histidine bromination [isa: 0018073 0018202 ]
+0018021 = peptidyl-histidine methylation [isa: 0006479 0018202 ]
+0042037 = peptidyl-histidine methylation, to form pros-methylhistidine [isa: 0018021 ]
+0042038 = peptidyl-histidine methylation, to form tele-methylhistidine [isa: 0018021 ]
+0018297 = protein-FAD linkage via 1'-(8alpha-FAD)-L-histidine [isa: 0018202 0018293 ]
+0018295 = protein-FAD linkage via 3'-(8alpha-FAD)-L-histidine [isa: 0018202 0018293 ]
+0018152 = protein-protein cross-linking via 3'-(1'-L-histidyl)-L-tyrosine [isa: 0018151 0018202 0018212 ]
+0018150 = protein-protein cross-linking via 3-(3'-L-histidyl)-L-tyrosine [isa: 0018151 0018202 0018212 ]
+0018203 = peptidyl-isoleucine modification [isa: 0018193 ]
+0018439 = peptidyl-leucine esterification [isa: 0018203 0018350 ]
+0018204 = peptidyl-leucine modification [isa: 0018193 ]
+0018205 = peptidyl-lysine modification [isa: 0018193 ]
+0019728 = peptidyl-allysine oxidation to 2-aminoadipic acid [isa: 0018158 0018205 ]
+0018394 = peptidyl-lysine acetylation [isa: 0006473 0018205 ]
+0018393 = internal peptidyl-lysine acetylation [isa: 0006475 0018394 ]
+0018003 = peptidyl-lysine N6-acetylation [isa: 0018393 ]
+0018116 = peptidyl-lysine adenylation [isa: 0018117 0018205 ]
+0018054 = peptidyl-lysine biotinylation [isa: 0009305 0018205 ]
+0018238 = peptidyl-lysine carboxyethylation [isa: 0018205 0018239 ]
+0018235 = peptidyl-lysine carboxylation [isa: 0018205 0018214 ]
+0042034 = peptidyl-lysine esterification [isa: 0018205 0018350 ]
+0018257 = peptidyl-lysine formylation [isa: 0018205 0018256 ]
+0018261 = peptidyl-lysine guanylylation [isa: 0018205 0018260 ]
+0017185 = peptidyl-lysine hydroxylation [isa: 0018126 0018205 ]
+0018396 = peptidyl-lysine hydroxylation to 4-hydroxy-L-lysine [isa: 0017185 ]
+0018395 = peptidyl-lysine hydroxylation to 5-hydroxy-L-lysine [isa: 0017185 ]
+0018055 = peptidyl-lysine lipoylation [isa: 0009249 0018205 ]
+0018022 = peptidyl-lysine methylation [isa: 0006479 0018205 ]
+0018027 = peptidyl-lysine di-methylation [isa: 0018022 ]
+0018026 = peptidyl-lysine mono-methylation [isa: 0018022 ]
+0018023 = peptidyl-lysine tri-methylation [isa: 0018022 ]
+0018057 = peptidyl-lysine oxidation [isa: 0018158 0018205 ]
+0018029 = peptidyl-lysine palmitoylation [isa: 0018205 ]
+0018185 = poly-N-methyl-propylamination [isa: 0018184 0018205 ]
+0019931 = protein-chromophore linkage via peptidyl-N6-3-dehydroretinal-L-lysine [isa: 0018205 0018298 ]
+0018273 = protein-chromophore linkage via peptidyl-N6-retinal-L-lysine [isa: 0018205 0018298 ]
+0018124 = protein-protein cross-linking via 5'-(N6-L-lysine)-L-topaquinone [isa: 0018205 0018212 ]
+0018274 = protein-protein cross-linking via L-lysinoalanine [isa: 0018149 0018205 0018209 ]
+0018272 = protein-pyridoxal-5-phosphate linkage via peptidyl-N6-pyridoxal phosphate-L-lysine [isa: 0018205 0018352 ]
+0018206 = peptidyl-methionine modification [isa: 0018193 ]
+0018159 = peptidyl-methionine oxidation [isa: 0018158 0018206 ]
+0018207 = peptidyl-phenylalanine modification [isa: 0018193 ]
+0018061 = peptidyl-L-3-phenyllactic acid biosynthesis from peptidyl-phenylalanine [isa: 0018207 ]
+0018075 = peptidyl-phenylalanine bromination [isa: 0018073 0018207 ]
+0018397 = peptidyl-phenylalanine bromination to L-2'-bromophenylalanine [isa: 0018075 ]
+0018398 = peptidyl-phenylalanine bromination to L-3'-bromophenylalanine [isa: 0018075 ]
+0018399 = peptidyl-phenylalanine bromination to L-4'-bromophenylalanine [isa: 0018075 ]
+0018208 = peptidyl-proline modification [isa: 0018193 ]
+0019511 = peptidyl-proline hydroxylation [isa: 0018208 ]
+0018188 = peptidyl-proline di-hydroxylation [isa: 0019511 ]
+0018400 = peptidyl-proline hydroxylation to 3-hydroxy-L-proline [isa: 0019511 ]
+0018209 = peptidyl-serine modification [isa: 0018193 ]
+0018084 = peptidyl-lactic acid biosynthesis from peptidyl-serine [isa: 0018209 ]
+0018340 = peptidyl-O-(sn-1-glycerophosphoryl)-L-serine biosynthesis from peptidyl-serine [isa: 0018209 ]
+0018312 = peptidyl-serine ADP-ribosylation [isa: 0006471 0018209 ]
+0018413 = peptidyl-serine O-glucuronidation [isa: 0018209 0018412 ]
+0018191 = peptidyl-serine octanoylation [isa: 0018190 0018209 ]
+0018070 = peptidyl-serine phosphopantetheinylation [isa: 0018209 0018215 ]
+0018403 = protein-dermatan sulfate linkage via dermatan 4-sulfate D-glucuronyl-D-galactosyl-D-galactosyl-D-xylosyl-L-serine [isa: 0018209 ]
+0018404 = protein-heparan sulfate linkage via heparan sulfate D-glucuronyl-D-galactosyl-D-galactosyl-D-xylosyl-L-serine [isa: 0018209 ]
+0018247 = protein-phosphoribosyl dephospho-coenzyme A linkage [isa: 0018209 0018246 ]
+0018355 = protein-phosphoribosyl dephospho-coenzyme A linkage via O-(phosphoribosyl dephospho-coenzyme A)-L-serine [isa: 0018247 ]
+0018210 = peptidyl-threonine modification [isa: 0018193 ]
+0018082 = peptidyl-(Z)-dehydrobutyrine biosynthesis from peptidyl-threonine [isa: 0018210 ]
+0018178 = peptidyl-threonine adenylation [isa: 0018117 0018210 ]
+0018405 = protein-keratan sulfate linkage via keratan sulfate D-glucuronyl-D-galactosyl-D-galactosyl-D-xylosyl-L-threonine [isa: 0018210 ]
+0018211 = peptidyl-tryptophan modification [isa: 0018193 ]
+0018080 = peptidyl-tryptophan bromination [isa: 0018073 0018211 ]
+0045325 = peptidyl-tryptophan hydroxylation [isa: 0018211 ]
+0018062 = peptidyl-tryptophan succinylation [isa: 0018211 0018335 ]
+0018069 = protein-protein cross-linking via 4'-(L-tryptophan)-L-tryptophyl quinone [isa: 0018149 0018211 ]
+0019926 = peptidyl-tryptophan oxidation to tryptophyl quinone [partof: 0018069 ]
+0018212 = peptidyl-tyrosine modification [isa: 0018193 ]
+0045327 = DNA-protein covalent cross-linking via peptidyl-tyrosine [isa: 0018212 ]
+0045326 = DNA-protein covalent cross-linking via the 3' end to peptidyl-tyrosine [isa: 0045327 ]
+0018068 = peptidyl-L-2',4',5'-topaquinone biosynthesis from peptidyl-tyrosine [isa: 0018212 ]
+0018172 = peptidyl-L-3',4',5'-trihydroxyphenylalanine biosynthesis from peptidyl-tyrosine [isa: 0018212 0018336 ]
+0018067 = peptidyl-L-3',4'-dihydroxyphenylalanine biosynthesis from peptidyl-tyrosine [isa: 0018212 0018336 ]
+0019879 = peptidyl-thyronine biosynthesis from peptidyl-tyrosine [isa: 0018212 ]
+0018078 = peptidyl-thyronine iodination [isa: 0018077 0018212 ]
+0018408 = peptidyl-thyronine iodination to form 3',3'',5',5''-tetraiodo-L-thyronine [isa: 0018078 ]
+0018407 = peptidyl-thyronine iodination to form 3',3'',5'-triiodo-L-thyronine [isa: 0018078 ]
+0018254 = peptidyl-tyrosine adenylation [isa: 0018117 0018212 ]
+0018251 = peptidyl-tyrosine dehydrogenation [isa: 0018212 0018249 ]
+0018165 = peptidyl-tyrosine uridylylation [isa: 0018175 0018177 0018212 ]
+0018296 = protein-FAD linkage via O4'-(8alpha-FAD)-L-tyrosine [isa: 0018212 0018293 ]
+0018213 = peptidyl-valine modification [isa: 0018193 ]
+0006473 = protein amino acid acetylation [isa: 0006464 ]
+0006475 = internal protein amino acid acetylation [isa: 0006473 ]
+0006471 = protein amino acid ADP-ribosylation [isa: 0006464 ]
+0008213 = protein amino acid alkylation [isa: 0006464 ]
+0006479 = protein amino acid methylation [isa: 0008213 ]
+0018020 = peptidyl-glutamic acid methylation [isa: 0006479 ]
+0018364 = peptidyl-glutamine methylation [isa: 0006479 ]
+0018361 = peptidyl-glutamine 2-methylation [isa: 0018364 ]
+0018032 = protein amino acid amidation [isa: 0006464 ]
+0009305 = protein amino acid biotinylation [isa: 0006464 ]
+0018239 = protein amino acid carboxyethylation [isa: 0006464 ]
+0018214 = protein amino acid carboxylation [isa: 0006464 ]
+0006476 = protein amino acid deacetylation [isa: 0006464 ]
+0008214 = protein amino acid dealkylation [isa: 0006464 ]
+0006482 = protein amino acid demethylation [isa: 0008214 ]
+0018277 = protein amino acid deamination [isa: 0006464 ]
+0018249 = protein amino acid dehydration [isa: 0006464 ]
+0018180 = protein amino acid desulfurization [isa: 0006464 ]
+0018179 = peptidyl-cysteine desulfurization [isa: 0018180 ]
+0018350 = protein amino acid esterification [isa: 0006464 ]
+0017013 = protein amino acid flavinylation [isa: 0006464 ]
+0018256 = protein amino acid formylation [isa: 0006464 ]
+0042125 = protein amino acid galactosylation [isa: 0006464 ]
+0018411 = protein amino acid glucuronidation [isa: 0006464 ]
+0018412 = protein amino acid O-glucuronidation [isa: 0018411 ]
+0018177 = protein amino acid uridylylation [isa: 0018411 ]
+0018079 = protein amino acid halogenation [isa: 0006464 ]
+0018073 = protein amino acid bromination [isa: 0018079 ]
+0018077 = protein amino acid iodination [isa: 0018079 ]
+0018126 = protein amino acid hydroxylation [isa: 0006464 ]
+0018336 = peptidyl-tyrosine hydroxylation [isa: 0018126 ]
+0017014 = protein amino acid nitrosylation [isa: 0006464 ]
+0018175 = protein amino acid nucleotidylation [isa: 0006464 ]
+0018117 = protein amino acid adenylation [isa: 0018175 ]
+0018260 = protein amino acid guanylylation [isa: 0018175 ]
+0018190 = protein amino acid octanoylation [isa: 0006464 ]
+0018158 = protein amino acid oxidation [isa: 0006464 ]
+0018215 = protein amino acid phosphopantetheinylation [isa: 0006464 ]
+0018184 = protein amino acid polyamination [isa: 0006464 ]
+0018335 = protein amino acid succinylation [isa: 0006464 ]
+0018322 = protein amino acid tyrosinylation [isa: 0006464 ]
+0006466 = protein disulfide-isomerase reaction [isa: 0006464 ]
+0045116 = protein neddylation [isa: 0006464 ]
+0018094 = protein polyglycylation [isa: 0006464 ]
+0016485 = protein processing [isa: 0006464 ]
+0016540 = protein autoprocessing [isa: 0016485 ]
+0016539 = protein splicing [isa: 0016485 ]
+0006465 = signal peptide processing [isa: 0016485 ]
+0019082 = viral protein processing [isa: 0016485 ] [partof: 0019080 ]
+0006467 = protein thiol-disulfide exchange [isa: 0006464 ]
+0018298 = protein-chromophore linkage [isa: 0006464 ]
+0018065 = protein-cofactor linkage [isa: 0006464 ]
+0018160 = peptidyl-pyrromethane cofactor linkage [isa: 0018065 ]
+0018246 = protein-coenzyme A linkage [isa: 0018065 ]
+0018293 = protein-FAD linkage [isa: 0018065 ]
+0018309 = protein-FMN linkage [isa: 0018065 ]
+0009249 = protein-lipoylation [isa: 0018065 ]
+0018352 = protein-pyridoxal-5-phosphate linkage [isa: 0018065 ]
+0018149 = protein-protein cross-linking [isa: 0006464 ]
+0018262 = isopeptide cross-linking [isa: 0018149 ]
+0018081 = peptide cross-linking via the thioethers lanthionine or 3-methyl-lanthionine [isa: 0018149 ]
+0018316 = protein-protein cross-linking via L-cystine [isa: 0018149 ]
+0018151 = protein-protein cross-linking via L-histidyl-L-tyrosine [isa: 0018149 ]
+0017006 = protein-tetrapyrrole linkage [isa: 0006464 ]
+0017007 = protein-bilin linkage [isa: 0017006 ]
+0017008 = protein-phycobiliviolin linkage [isa: 0017007 ]
+0018356 = protein-phycobiliviolin linkage via S-phycobiliviolin-L-cysteine [isa: 0017008 ]
+0017009 = protein-phycocyanobilin linkage [isa: 0017007 ]
+0017011 = protein-phycoerythrobilin linkage [isa: 0017007 ]
+0017010 = protein-phycourobilin linkage [isa: 0017007 ]
+0017012 = protein-phytochromobilin linkage [isa: 0017007 ]
+0030091 = protein repair [isa: 0019538 ]
+0009306 = protein secretion [isa: 0019538 ]
+0045731 = glycoprotein secretion [isa: 0009306 ]
+0045166 = protein secretion involved in cell fate commitment [isa: 0009306 ] [partof: 0045165 ]
+0045045 = secretory pathway [isa: 0009306 ]
+0045054 = constitutive secretory pathway [isa: 0045045 ]
+0006888 = ER to Golgi transport [isa: 0006886 0016192 ] [partof: 0045045 ]
+0006889 = regulation of calcium in ER [isa: 0006888 ]
+0045783 = negative regulation of calcium in ER [isa: 0006889 ]
+0045784 = positive regulation of calcium in ER [isa: 0006889 ]
+0006887 = exocytosis [isa: 0015031 0016192 ] [partof: 0045045 ]
+0017156 = calcium ion dependent exocytosis [isa: 0006887 ]
+0017158 = regulation of calcium ion dependent exocytosis [isa: 0017157 ] [partof: 0017156 ]
+0045955 = negative regulation of calcium ion dependent exocytosis [isa: 0017158 0045920 ]
+0045956 = positive regulation of calcium ion dependent exocytosis [isa: 0017158 0045921 ]
+0016194 = non-selective vesicle exocytosis [isa: 0006887 ]
+0006904 = non-selective vesicle docking [partof: 0016194 ]
+0006906 = non-selective vesicle fusion [partof: 0016194 ]
+0006903 = non-selective vesicle targeting [partof: 0016194 ]
+0017157 = regulation of exocytosis [partof: 0006887 ]
+0045920 = negative regulation of exocytosis [isa: 0017157 ]
+0045921 = positive regulation of exocytosis [isa: 0017157 ]
+0006891 = intra-Golgi transport [isa: 0006886 ] [partof: 0045045 ]
+0045057 = cisternal progression [isa: 0006891 ]
+0000301 = retrograde (vesicle recycling within Golgi) transport [isa: 0006891 0016192 ] [partof: 0045045 ]
+0006892 = post Golgi transport [isa: 0006886 0016192 ] [partof: 0045045 ]
+0006893 = Golgi to plasma membrane transport [isa: 0006892 ]
+0006894 = Golgi to secretory vesicle transport [isa: 0006892 ]
+0006896 = Golgi to vacuole transport [isa: 0006892 ]
+0045055 = regulated secretory pathway [isa: 0045045 ]
+0006890 = retrograde (Golgi to ER) transport [isa: 0006886 0016192 ] [partof: 0045045 ]
+0030253 = type I protein secretion system [isa: 0009306 ]
+0015628 = type II protein (Sec) secretion system [isa: 0009306 ]
+0030254 = type III protein secretion system [isa: 0009306 ]
+0030255 = type IV protein secretion system [isa: 0009306 ]
+0006605 = protein targeting [isa: 0006886 0019538 ]
+0006612 = protein-membrane targeting [isa: 0006605 ]
+0006613 = co-translational membrane targeting [isa: 0006612 ]
+0006614 = SRP-dependent, co-translational membrane targeting [isa: 0006613 ]
+0006615 = SRP-dependent, co-translational membrane targeting, docking [partof: 0006614 ]
+0006618 = SRP-dependent, co-translational membrane targeting, signal sequence processing [partof: 0006614 ]
+0006616 = SRP-dependent, co-translational membrane targeting, translocation [partof: 0006614 ]
+0006617 = SRP-dependent, co-translational membrane targeting, signal sequence recognition [partof: 0006616 ]
+0006619 = SRP-independent, co-translational membrane targeting [isa: 0006613 ]
+0045319 = SRP-independent, co-translational membrane targeting, translocation [isa: 0006619 ]
+0006620 = post-translational membrane targeting [isa: 0006612 ]
+0006611 = protein-nucleus export [isa: 0006605 0006913 ]
+0045204 = MAPK nucleus export [isa: 0006611 ]
+0045208 = MAPK phosphatase nucleus export [isa: 0006611 ]
+0045209 = leptomycin B-sensitive MAPK phosphatase nucleus export [isa: 0045208 ]
+0006606 = protein-nucleus import [isa: 0006605 0006913 ]
+0006609 = mRNA-binding (hnRNP) protein-nucleus import [isa: 0006606 ]
+0042348 = NF-kappaB protein-nucleus import [isa: 0006606 ]
+0042345 = regulation of NF-kappaB protein-nucleus import [isa: 0042306 ] [partof: 0042348 ]
+0042347 = negative regulation of NF-kappaB protein-nucleus import [isa: 0042308 0042345 ]
+0042346 = positive regulation of NF-kappaB protein-nucleus import [isa: 0042307 0042345 ]
+0006607 = NLS-bearing substrate-nucleus import [isa: 0006606 ]
+0000059 = protein-nucleus import, docking [partof: 0006606 ]
+0000061 = protein-nucleus import, substrate release [partof: 0006606 ]
+0000060 = protein-nucleus import, translocation [partof: 0006606 ]
+0042306 = regulation of protein-nucleus import [partof: 0006606 ]
+0042308 = negative regulation of protein-nucleus import [isa: 0042306 ]
+0042307 = positive regulation of protein-nucleus import [isa: 0042306 ]
+0006610 = ribosomal protein-nucleus import [isa: 0006606 ]
+0006608 = snRNP protein-nucleus import [isa: 0006606 ]
+0019222 = regulation of metabolism [partof: 0008152 ]
+0009892 = negative regulation of metabolism [isa: 0019222 ]
+0009893 = positive regulation of metabolism [isa: 0019222 ]
+0045730 = respiratory burst [isa: 0009893 ]
+0045729 = respiratory burst at fertilization [isa: 0045730 ] [partof: 0007338 ]
+0006792 = regulation of sulfur utilization [isa: 0006791 0019222 ]
+0045882 = negative regulation of sulfur utilization [isa: 0006792 ]
+0045883 = positive regulation of sulfur utilization [isa: 0006792 ]
+0046499 = S-adenosylmethioninamine metabolism [isa: 0008152 ]
+0019748 = secondary metabolism [isa: 0008152 ]
+0006790 = sulfur metabolism [isa: 0008152 ]
+0019694 = alkanesulfonate metabolism [isa: 0006790 ]
+0018907 = dimethyl sulfoxide metabolism [isa: 0006790 ]
+0018908 = organosulfide cycle [isa: 0006790 ]
+0019416 = polythionate oxidation [isa: 0006790 ]
+0006791 = sulfur utilization [isa: 0006790 ]
+0019426 = bisulfite reduction [isa: 0006791 ]
+0019422 = disproportionation of elemental sulfur [isa: 0006791 ]
+0000103 = sulfate assimilation [isa: 0006791 ]
+0019378 = sulfate assimilation, phosphoadenylyl sulfate reduction by oxidoreductase, acting on sulfur group of donors, NAD or NADP as acceptor [isa: 0000103 ]
+0019379 = sulfate assimilation, phosphoadenylyl sulfate reduction by phosphoadenylyl-sulfate reductase (thioredoxin) [isa: 0000103 ]
+0019419 = sulfate reduction [isa: 0006791 ]
+0019420 = dissimilatory sulfate reduction [isa: 0019419 ]
+0019421 = sulfate reduction, via APS pathway [isa: 0019419 ]
+0019418 = sulfide oxidation [isa: 0006791 ]
+0019424 = sulfide oxidation, using siroheme sulfite reductase [isa: 0019418 ]
+0019417 = sulfur oxidation [isa: 0006791 ]
+0019423 = sulfur oxidation, ferric ion dependent [isa: 0019417 ]
+0019425 = sulfur oxidation, using siroheme sulfite reductase [isa: 0019417 ]
+0042214 = terpene metabolism [isa: 0008152 ]
+0018867 = alpha-pinene metabolism [isa: 0042214 ]
+0018923 = limonene metabolism [isa: 0042214 ]
+0006766 = vitamin metabolism [isa: 0008152 ]
+0006775 = fat-soluble vitamin metabolism [isa: 0006766 ]
+0019721 = pterin metabolism [isa: 0006775 ]
+0019720 = Mo-molybdopterin cofactor metabolism [isa: 0019721 ]
+0042046 = W-molybdopterin cofactor metabolism [isa: 0019721 ]
+0006776 = vitamin A metabolism [isa: 0006775 ]
+0042359 = vitamin D metabolism [isa: 0006775 ]
+0042360 = vitamin E metabolism [isa: 0006775 ]
+0030656 = regulation of vitamin metabolism [partof: 0006766 ]
+0046137 = negative regulation of vitamin metabolism [isa: 0030656 ]
+0046136 = positive regulation of vitamin metabolism [isa: 0030656 ]
+0006767 = water-soluble vitamin metabolism [isa: 0006766 ]
+0006768 = biotin metabolism [isa: 0006767 ]
+0019852 = L-ascorbic acid metabolism [isa: 0006767 ]
+0006772 = thiamin metabolism [isa: 0006767 ]
+0006771 = vitamin B2 metabolism [isa: 0006767 ]
+0007148 = regulation of cell shape and cell size [isa: 0008151 ]
+0007149 = colony morphology [isa: 0007148 ]
+0007125 = invasive growth [isa: 0007149 ]
+0007150 = growth pattern [isa: 0007148 ] [partof: 0040007 ]
+0030447 = filamentous growth [isa: 0007150 ]
+0030448 = hyphal growth [isa: 0030447 ]
+0007124 = pseudohyphal growth [isa: 0007150 ]
+0045790 = negative regulation of cell shape and cell size [isa: 0007148 ]
+0045788 = negative regulation of cell shape [isa: 0008360 0045790 ]
+0045792 = negative regulation of cell size [isa: 0008361 0045790 ]
+0045791 = positive regulation of cell shape and cell size [isa: 0007148 ]
+0045789 = positive regulation of cell shape [isa: 0008360 0045791 ]
+0045793 = positive regulation of cell size [isa: 0008361 0045791 ]
+0008360 = regulation of cell shape [isa: 0007148 ]
+0016476 = shape changes of embryonic cells [isa: 0008360 ]
+0008361 = regulation of cell size [isa: 0007148 ]
+0006950 = response to stress [isa: 0008151 ]
+0001666 = response to hypoxia [isa: 0006950 ]
+0030435 = sporulation [isa: 0008151 ]
+0042173 = regulation of sporulation [partof: 0030435 ]
+0042174 = negative regulation of sporulation [isa: 0042173 ]
+0045881 = positive regulation of sporulation [isa: 0042173 ]
+0042244 = spore wall assembly [partof: 0030435 ]
+0042243 = spore wall assembly (sensu Bacteria) [isa: 0030436 0042244 ]
+0030476 = spore wall assembly (sensu Fungi) [isa: 0042244 ] [partof: 0030437 ]
+0007152 = spore wall assembly (sensu Saccharomyces) [isa: 0030476 ] [partof: 0007151 ]
+0030436 = sporulation (sensu Bacteria) [isa: 0030435 ]
+0030437 = sporulation (sensu Fungi) [isa: 0030435 ]
+0030470 = spore germination (sensu Fungi) [partof: 0030437 ]
+0007153 = germination (sensu Saccharomyces) [isa: 0007151 0030470 ]
+0007151 = sporulation (sensu Saccharomyces) [isa: 0030437 ]
+0006810 = transport [isa: 0008151 ]
+0046411 = 2-keto-3-deoxygluconate transport [isa: 0006810 ]
+0019271 = aerobactin transport [isa: 0006810 ]
+0015837 = amine/polyamine transport [isa: 0006810 ]
+0015838 = betaine transport [isa: 0015837 ]
+0015839 = cadaverine transport [isa: 0015837 ]
+0015841 = chromaffin granule amine transport [isa: 0015837 ]
+0015843 = methylammonium transport [isa: 0015837 ]
+0015844 = monoamine transport [isa: 0006836 0015837 ]
+0015846 = polyamine transport [isa: 0015837 ]
+0015847 = putrescine transport [isa: 0015846 ]
+0015848 = spermidine transport [isa: 0015846 ]
+0000296 = spermine transport [isa: 0015846 ]
+0015845 = quaternary amine transport [isa: 0015837 ]
+0015842 = synaptic vesicle amine transport [isa: 0015837 ]
+0015840 = urea transport [isa: 0015837 ]
+0006865 = amino acid transport [isa: 0006810 ]
+0015800 = acidic amino acid transport [isa: 0006865 ]
+0015810 = aspartate transport [isa: 0015800 0015807 ]
+0006845 = mitochondrial aspartate/glutamate transport [isa: 0006839 0015810 0015813 ]
+0015813 = glutamate transport [isa: 0015800 0015807 ]
+0015814 = p-aminobenzoyl-glutamate transport [isa: 0015813 ]
+0015801 = aromatic amino acid transport [isa: 0006865 ]
+0015823 = phenylalanine transport [isa: 0015801 0015807 ]
+0015827 = tryptophan transport [isa: 0015801 0015807 ]
+0015828 = tyrosine transport [isa: 0015801 0015807 ]
+0015802 = basic amino acid transport [isa: 0006865 ]
+0015809 = arginine transport [isa: 0015802 0015807 ]
+0006867 = asparagine transport [isa: 0015802 0015807 ]
+0006868 = glutamine transport [isa: 0015802 0015807 ]
+0015817 = histidine transport [isa: 0015802 0015807 ]
+0015819 = lysine transport [isa: 0015802 0015807 ]
+0015803 = branched-chain aliphatic amino acid transport [isa: 0006865 ]
+0015818 = isoleucine transport [isa: 0015803 0015804 0015807 ]
+0015829 = valine transport [isa: 0015803 0015804 0015807 ]
+0006860 = extracellular amino acid transport [isa: 0006858 0006865 ]
+0015807 = L-amino acid transport [isa: 0006865 ]
+0015808 = alanine transport [isa: 0015804 0015807 ]
+0015811 = cystine transport [isa: 0000101 0015807 ]
+0015830 = diaminopimelate transport [isa: 0015807 ]
+0015812 = gamma-amino butyrate transport [isa: 0015807 ]
+0015816 = glycine transport [isa: 0015804 0015807 ]
+0015820 = leucine transport [isa: 0015804 0015807 ]
+0015821 = methionine transport [isa: 0000101 0015807 ]
+0015822 = ornithine transport [isa: 0015807 ]
+0000066 = mitochondrial ornithine transport [isa: 0006839 0015822 ]
+0015824 = proline transport [isa: 0015804 0015807 ]
+0015825 = serine transport [isa: 0015804 0015807 ]
+0015826 = threonine transport [isa: 0015804 0015807 ]
+0015804 = neutral amino acid transport [isa: 0006865 ]
+0000101 = sulfur amino acid transport [isa: 0006865 ]
+0015805 = S-adenosylmethionine transport [isa: 0000101 ]
+0015806 = S-methylmethionine transport [isa: 0000101 ]
+0008643 = carbohydrate transport [isa: 0006810 ]
+0015766 = disaccharide transport [isa: 0008643 ]
+0019533 = cellobiose transport [isa: 0015766 ]
+0015767 = lactose transport [isa: 0015766 ]
+0015768 = maltose transport [isa: 0015766 ]
+0015769 = melibiose transport [isa: 0015766 ]
+0015770 = sucrose transport [isa: 0015766 ]
+0015771 = trehalose transport [isa: 0015766 ]
+0006859 = extracellular carbohydrate transport [isa: 0006858 0008643 ]
+0000017 = alpha-glucoside transport [isa: 0006859 0015758 ]
+0015778 = hexuronide transport [isa: 0008643 ]
+0015779 = glucuronide transport [isa: 0015778 ]
+0015749 = monosaccharide transport [isa: 0008643 ]
+0008645 = hexose transport [isa: 0015749 ]
+0015754 = allose transport [isa: 0008645 ]
+0015755 = fructose transport [isa: 0008645 ]
+0015756 = fucose transport [isa: 0008645 ]
+0015757 = galactose transport [isa: 0008645 ]
+0015758 = glucose transport [isa: 0008645 ]
+0015759 = beta-glucoside transport [isa: 0015758 ]
+0046323 = glucose import [isa: 0015758 ]
+0046324 = regulation of glucose import [partof: 0046323 ]
+0046325 = negative regulation of glucose import [isa: 0046324 ]
+0046326 = positive regulation of glucose import [isa: 0046324 ]
+0015760 = glucose-6-phosphate transport [isa: 0015758 ]
+0008646 = high-affinity hexose transport [isa: 0008645 ]
+0008647 = low-affinity hexose transport [isa: 0008645 ]
+0015761 = mannose transport [isa: 0008645 ]
+0015765 = methylgalactoside transport [isa: 0008645 ]
+0015763 = N-acetyl galactosamine transport [isa: 0008645 ]
+0015764 = N-acetyl glucosamine transport [isa: 0008645 ]
+0015762 = rhamnose transport [isa: 0008645 ]
+0015750 = pentose transport [isa: 0015749 ]
+0015751 = arabinose transport [isa: 0015750 ]
+0015752 = ribose transport [isa: 0015750 ]
+0015753 = xylose transport [isa: 0015750 ]
+0015780 = nucleotide-sugar transport [isa: 0008643 ]
+0015781 = pyrimidine nucleotide sugar transport [isa: 0015780 ]
+0015782 = CMP-sialic acid transport [isa: 0015781 ]
+0015783 = GDP-fucose transport [isa: 0015781 ]
+0015784 = GDP-mannose transport [isa: 0015781 ]
+0015785 = UDP-galactose transport [isa: 0015781 ]
+0015786 = UDP-glucose transport [isa: 0015781 ]
+0015787 = UDP-glucuronic acid transport [isa: 0015781 ]
+0015789 = UDP-N-acetylgalactosamine transport [isa: 0015781 ]
+0015788 = UDP-N-acetylglucosamine transport [isa: 0015781 ]
+0015790 = UDP-xylose transport [isa: 0015781 ]
+0015772 = oligosaccharide transport [isa: 0008643 ]
+0015773 = raffinose transport [isa: 0015772 ]
+0009915 = phloem loading [isa: 0008643 ]
+0009401 = phosphoenolpyruvate-dependent sugar phosphotransferase system [isa: 0008643 ]
+0015774 = polysaccharide transport [isa: 0008643 ]
+0015775 = beta-glucan transport [isa: 0015774 ]
+0015776 = capsular-polysaccharide transport [isa: 0015774 ]
+0015777 = teichoic acid transport [isa: 0015774 ]
+0019750 = chloroplast transport [isa: 0006810 ]
+0016482 = cytoplasmic transport [isa: 0006810 ]
+0007303 = cytoplasmic transport, nurse cell to oocyte [isa: 0016482 ] [partof: 0007300 ]
+0019749 = cytoskeletal dependent cytoplasmic transport [isa: 0007303 ]
+0006913 = nucleocytoplasmic transport [isa: 0016482 ]
+0006858 = extracellular transport [isa: 0006810 ]
+0042044 = fluid transport [isa: 0006810 ]
+0042045 = epithelial fluid transport [isa: 0042044 ]
+0006833 = water transport [isa: 0042044 ]
+0015669 = gas transport [isa: 0006810 ]
+0015670 = carbon dioxide transport [isa: 0015669 ]
+0015671 = oxygen transport [isa: 0015669 ]
+0009914 = hormone transport [isa: 0006810 ]
+0009926 = auxin polar transport [isa: 0009914 ]
+0006818 = hydrogen transport [isa: 0006810 ]
+0015993 = molecular hydrogen transport [isa: 0006818 ]
+0015992 = proton transport [isa: 0006818 0015672 ]
+0015988 = energy coupled proton transport, against the electrochemical gradient [isa: 0015992 ]
+0015991 = ATP hydrolysis coupled proton transport [isa: 0015988 ]
+0015990 = electron transport coupled proton transport [isa: 0015988 ]
+0015989 = light-driven proton transport [isa: 0015988 ]
+0015985 = energy coupled proton transport, down the electrochemical gradient [isa: 0015992 ]
+0015986 = ATP synthesis coupled proton transport [isa: 0015985 ]
+0015987 = GTP synthesis coupled proton transport [isa: 0015985 ]
+0015981 = passive proton transport, down the electrochemical gradient [isa: 0015992 ]
+0015982 = antiport [isa: 0015981 ]
+0015983 = symport [isa: 0015981 ]
+0015984 = uniport [isa: 0015981 ]
+0006811 = ion transport [isa: 0006810 ]
+0006820 = anion transport [isa: 0006811 ]
+0015698 = inorganic anion transport [isa: 0006820 ]
+0015699 = antimonite transport [isa: 0015698 ]
+0015700 = arsenite transport [isa: 0015698 ]
+0015701 = bicarbonate transport [isa: 0015698 ]
+0015702 = chlorate transport [isa: 0015698 ]
+0006821 = chloride transport [isa: 0015698 ]
+0030321 = transepithelial chloride transport [isa: 0006821 ]
+0015703 = chromate transport [isa: 0015698 ]
+0015704 = cyanate transport [isa: 0015698 ]
+0030505 = inorganic diphosphate transport [isa: 0015698 ]
+0015705 = iodide transport [isa: 0015698 ]
+0015706 = nitrate transport [isa: 0015698 ]
+0015707 = nitrite transport [isa: 0015698 ]
+0006817 = phosphate transport [isa: 0015698 ]
+0015708 = silicate transport [isa: 0015698 ]
+0008272 = sulfate transport [isa: 0015698 ]
+0015715 = nucleotide-sulfate transport [isa: 0008272 ]
+0000316 = sulfite transport [isa: 0015698 ]
+0015710 = tellurite transport [isa: 0015698 ]
+0015709 = thiosulfate transport [isa: 0015698 ]
+0015711 = organic anion transport [isa: 0006820 ]
+0006835 = dicarboxylic acid transport [isa: 0015711 ]
+0015742 = alpha-ketoglutarate transport [isa: 0006835 ]
+0015740 = C4-dicarboxylate transport [isa: 0006835 ]
+0015741 = fumarate transport [isa: 0006835 ]
+0015743 = malate transport [isa: 0006835 ]
+0006840 = mitochondrial alpha-ketoglutarate/malate transport [isa: 0006839 0015743 ]
+0015744 = succinate transport [isa: 0006835 ]
+0015745 = tartrate transport [isa: 0006835 ]
+0015712 = hexose phosphate transport [isa: 0015711 ]
+0015718 = monocarboxylic acid transport [isa: 0015711 ]
+0006846 = acetate transport [isa: 0015718 ]
+0006847 = acetate transport across the plasma membrane [isa: 0006846 ]
+0015719 = allantoate transport [isa: 0015718 ]
+0015721 = bile acid transport [isa: 0015718 ]
+0015722 = canalicular bile acid transport [isa: 0015721 ]
+0015723 = bilirubin transport [isa: 0015718 ]
+0015724 = formate transport [isa: 0015718 ]
+0015725 = gluconate transport [isa: 0015718 ]
+0015726 = L-idonate transport [isa: 0015718 ]
+0015727 = lactate transport [isa: 0015718 ]
+0015728 = mevalonate transport [isa: 0015718 ]
+0015729 = oxaloacetate transport [isa: 0015718 ]
+0015730 = propionate transport [isa: 0015718 ]
+0015731 = 3-hydroxyphenyl propanoate transport [isa: 0015730 ]
+0015732 = prostaglandin transport [isa: 0015718 ]
+0006848 = pyruvate transport [isa: 0015718 ]
+0006850 = mitochondrial pyruvate transport [isa: 0006839 0006848 ]
+0006849 = plasma membrane pyruvate transport [isa: 0006848 ]
+0015733 = shikimate transport [isa: 0015718 ]
+0015739 = sialic acid transport [isa: 0015718 ]
+0015734 = taurine transport [isa: 0015718 ]
+0015735 = uronic acid transport [isa: 0015718 ]
+0015736 = hexuronate transport [isa: 0015735 ]
+0015737 = galacturonate transport [isa: 0015736 ]
+0015738 = glucuronate transport [isa: 0015736 ]
+0015714 = phosphoenolpyruvate transport [isa: 0015711 ]
+0015713 = phosphoglycerate transport [isa: 0015711 ]
+0015716 = phosphonate transport [isa: 0015711 ]
+0006842 = tricarboxylic acid transport [isa: 0015711 ]
+0015746 = citrate transport [isa: 0006842 ]
+0006843 = mitochondrial citrate transport [isa: 0006839 0015746 ]
+0015717 = triose phosphate transport [isa: 0015711 ]
+0015747 = urate transport [isa: 0015711 ]
+0015748 = organophosphate ester transport [isa: 0006820 ]
+0006812 = cation transport [isa: 0006811 ]
+0015674 = di-, tri-valent inorganic cation transport [isa: 0006812 ]
+0015690 = aluminum ion transport [isa: 0015674 0030001 ]
+0015691 = cadmium ion transport [isa: 0006823 0015674 ]
+0006816 = calcium ion transport [isa: 0015674 0030001 ]
+0006851 = mitochondrial calcium ion transport [isa: 0006816 0006839 ]
+0006852 = mitochondrial sodium/calcium exchange [isa: 0006814 0006851 0030181 ]
+0015692 = lead ion transport [isa: 0006823 0015674 ]
+0015693 = magnesium ion transport [isa: 0015674 ]
+0015694 = mercury ion transport [isa: 0006823 0015674 ]
+0000041 = transition metal transport [isa: 0006823 0015674 ]
+0006824 = cobalt ion transport [isa: 0000041 ]
+0006825 = copper ion transport [isa: 0000041 ]
+0015677 = copper uptake transport [isa: 0006825 ]
+0015678 = high affinity copper transport [isa: 0006825 ]
+0015680 = intracellular copper delivery [isa: 0006825 ]
+0015679 = plasma membrane copper transport [isa: 0006825 ]
+0006826 = iron transport [isa: 0000041 ]
+0015686 = ferric triacetylfusarinine C transport [isa: 0006826 ]
+0015685 = ferric-enterobactin transport [isa: 0006826 0015892 ]
+0015687 = ferric-hydroxamate transport [isa: 0006826 ]
+0015688 = iron chelate transport [isa: 0006826 ]
+0015681 = iron ion transport [isa: 0006826 ]
+0015682 = ferric iron transport [isa: 0015681 ]
+0015683 = high affinity ferric transport [isa: 0015682 ]
+0015684 = ferrous iron transport [isa: 0015681 ]
+0006827 = high affinity iron transport [isa: 0015681 ]
+0000040 = low affinity iron transport [isa: 0015681 ]
+0006828 = manganese ion transport [isa: 0000041 ]
+0015689 = molybdate ion transport [isa: 0000041 ]
+0015675 = nickel ion transport [isa: 0000041 ]
+0015676 = vanadium ion transport [isa: 0000041 ]
+0006829 = zinc ion transport [isa: 0006823 0015674 ]
+0006830 = high-affinity zinc ion transport [isa: 0006829 ]
+0006831 = low-affinity zinc ion transport [isa: 0006829 ]
+0030001 = metal ion transport [isa: 0006812 ]
+0006823 = heavy metal ion transport [isa: 0030001 ]
+0015673 = silver transport [isa: 0006823 0015672 ]
+0006813 = potassium transport [isa: 0015672 0030001 ]
+0006814 = sodium transport [isa: 0015672 0030001 ]
+0015672 = monovalent inorganic cation transport [isa: 0006812 ]
+0015695 = organic cation transport [isa: 0006812 ]
+0015696 = ammonium transport [isa: 0015695 ]
+0015697 = quaternary ammonium group transport [isa: 0015695 ]
+0006869 = lipid transport [isa: 0006810 ]
+0015917 = aminophospholipid transport [isa: 0006869 ]
+0015908 = fatty acid transport [isa: 0006869 ]
+0015909 = long-chain fatty acid transport [isa: 0015908 ]
+0006853 = carnitine shuttle [isa: 0015879 0015909 ]
+0015910 = peroxisomal long-chain fatty acid import [isa: 0015909 ]
+0015911 = plasma membrane long-chain fatty acid transport [isa: 0015909 ]
+0001579 = medium-chain fatty acid transport [isa: 0015908 ]
+0015912 = short-chain fatty acid transport [isa: 0015908 ]
+0015913 = short-chain fatty acid uptake [isa: 0015912 ]
+0015915 = fatty acyl transport [isa: 0006869 ]
+0015916 = fatty acyl coenzyme A transport [isa: 0015915 ]
+0019915 = lipid storage [isa: 0006869 ]
+0015919 = peroxisomal membrane transport [isa: 0006869 ]
+0015914 = phospholipid transport [isa: 0006869 ]
+0015918 = sterol transport [isa: 0006869 ]
+0030301 = cholesterol transport [isa: 0015918 ]
+0015920 = lipopolysaccharide transport [isa: 0006810 ]
+0015921 = lipopolysaccharide export [isa: 0015920 ]
+0006839 = mitochondrial transport [isa: 0006810 ]
+0045016 = mitochondrial magnesium ion transport [isa: 0006839 ]
+0015835 = murein transport [isa: 0006810 ]
+0015836 = lipid-linked murein transport [isa: 0015835 ]
+0006836 = neurotransmitter transport [isa: 0006810 ]
+0015870 = acetylcholine transport [isa: 0006836 ]
+0015871 = choline transport [isa: 0006836 ]
+0015872 = dopamine transport [isa: 0006836 ]
+0015874 = norepinephrine transport [isa: 0006836 ]
+0006837 = serotonin transport [isa: 0006836 ]
+0030185 = nitric oxide transport [isa: 0006810 ]
+0015931 = nucleobase, nucleoside, nucleotide and nucleic acid transport [isa: 0006810 ]
+0015869 = DNA-protein complex transport [isa: 0015931 ]
+0015851 = nucleobase transport [isa: 0015931 ]
+0015720 = allantoin transport [isa: 0015851 ]
+0006863 = purine transport [isa: 0015851 ]
+0015853 = adenine transport [isa: 0006863 ]
+0015854 = guanine transport [isa: 0006863 ]
+0015855 = pyrimidine transport [isa: 0015851 ]
+0015856 = cytosine transport [isa: 0015855 ]
+0015857 = uracil transport [isa: 0015855 ]
+0015858 = nucleoside transport [isa: 0015931 ]
+0015859 = intracellular nucleoside transport [isa: 0015858 ]
+0015860 = purine nucleoside transport [isa: 0015858 ]
+0015863 = xanthosine transport [isa: 0015860 ]
+0015864 = pyrimidine nucleoside transport [isa: 0015858 ]
+0015861 = cytidine transport [isa: 0015864 ]
+0015862 = uridine transport [isa: 0015864 ]
+0006862 = nucleotide transport [isa: 0015931 ]
+0030302 = deoxynucleotide transport [isa: 0006862 ]
+0015865 = purine nucleotide transport [isa: 0006862 ]
+0015866 = ADP transport [isa: 0015865 ]
+0006854 = ATP/ADP exchange [isa: 0015866 0015867 ]
+0015867 = ATP transport [isa: 0015865 ]
+0015868 = purine ribonucleotide transport [isa: 0015865 ]
+0006864 = pyrimidine nucleotide transport [isa: 0006862 ]
+0019755 = one-carbon compound transport [isa: 0006810 ]
+0019532 = oxalate transport [isa: 0019755 ]
+0015850 = organic alcohol transport [isa: 0006810 ]
+0015791 = polyol transport [isa: 0006810 ]
+0015792 = arabinitol transport [isa: 0015791 ]
+0015796 = galactitol transport [isa: 0015791 ]
+0015795 = glucitol transport [isa: 0015791 ]
+0015793 = glycerol transport [isa: 0015791 ]
+0015794 = glycerol-3-phosphate transport [isa: 0015793 ]
+0015797 = mannitol transport [isa: 0015791 ]
+0015798 = myo-inositol transport [isa: 0015791 ]
+0015799 = propanediol transport [isa: 0015791 ]
+0015031 = protein transport [isa: 0006810 ]
+0006897 = endocytosis [isa: 0015031 0016192 ]
+0016193 = non-selective vesicle endocytosis [isa: 0006897 ]
+0006902 = non-selective vesicle assembly [partof: 0016193 ]
+0006900 = non-selective vesicle budding [partof: 0016193 ]
+0006901 = non-selective vesicle coating [partof: 0016193 ]
+0006909 = phagocytosis [isa: 0006897 ]
+0008228 = opsinization [partof: 0006909 ]
+0006910 = phagocytosis, binding [partof: 0006909 ]
+0006911 = phagocytosis, engulfment [partof: 0006909 ]
+0006912 = phagosome formation [partof: 0006909 ]
+0006907 = pinocytosis [isa: 0006897 ]
+0006908 = clathrin-independent pinocytosis [isa: 0006907 ]
+0006898 = receptor mediated endocytosis [isa: 0006897 ]
+0030100 = regulation of endocytosis [partof: 0006897 ]
+0045806 = negative regulation of endocytosis [isa: 0030100 ]
+0045807 = positive regulation of endocytosis [isa: 0030100 ]
+0019065 = viral receptor mediated endocytosis [isa: 0006897 ] [partof: 0019063 ]
+0015831 = enzyme transport [isa: 0015031 ]
+0006886 = intracellular protein transport [isa: 0015031 ]
+0030581 = host cell protein transport [isa: 0006886 ]
+0019060 = viral intracellular protein transport [isa: 0030581 ] [partof: 0019059 ]
+0015833 = peptide transport [isa: 0015031 ]
+0015834 = murein peptide transport [isa: 0015833 ]
+0006857 = oligopeptide transport [isa: 0015833 ]
+0045056 = transcytosis [isa: 0015031 0016192 ]
+0015891 = siderochrome transport [isa: 0006810 ]
+0015892 = iron-siderochrome transport [isa: 0015891 ]
+0030180 = solute:solute exchange [isa: 0006810 ]
+0030181 = sodium:calcium exchange [isa: 0030180 ]
+0016192 = vesicle-mediated transport [isa: 0006810 ]
+0006899 = non-selective vesicle transport [isa: 0016192 ]
+0015875 = vitamin/cofactor transport [isa: 0006810 ]
+0015876 = acetyl-CoA transport [isa: 0015875 ]
+0015877 = biopterin transport [isa: 0015875 ]
+0015878 = biotin transport [isa: 0015875 ]
+0015879 = carnitine transport [isa: 0015875 ]
+0006844 = acyl carnitine transport [isa: 0015879 ]
+0015880 = coenzyme A transport [isa: 0015875 ]
+0015881 = creatine transport [isa: 0015875 ]
+0015883 = flavin adenine dinucleotide transport [isa: 0015875 ]
+0015884 = folate transport [isa: 0015875 ]
+0015885 = 5-formyltetrahydrofolate transport [isa: 0015884 ]
+0015886 = heme transport [isa: 0015875 ]
+0015882 = L-ascorbate transport [isa: 0015875 ]
+0015890 = nicotinamide mononucleotide transport [isa: 0015875 ]
+0015887 = pantothenate transport [isa: 0015875 ]
+0015888 = thiamin transport [isa: 0015875 ]
+0015889 = vitamin B12 transport [isa: 0015875 ]
+0016265 = death [isa: 0008150 ]
+0008219 = cell death [isa: 0016265 ]
+0019835 = cytolysis [isa: 0008219 ]
+0019836 = hemolysis [isa: 0019835 ]
+0042267 = natural killer cell mediated cytolysis [isa: 0019835 ]
+0042269 = regulation of natural killer cell mediated cytolysis [isa: 0042268 ] [partof: 0042267 ]
+0045953 = negative regulation of natural killer cell mediated cytolysis [isa: 0042269 0045918 ]
+0045954 = positive regulation of natural killer cell mediated cytolysis [isa: 0042269 0045919 ]
+0042270 = protection from natural killer cell mediated cytolysis [isa: 0042269 ]
+0042271 = susceptibility to natural killer cell mediated cytolysis [isa: 0042269 ]
+0042268 = regulation of cytolysis [partof: 0019835 ]
+0045918 = negative regulation of cytolysis [isa: 0042268 ]
+0045919 = positive regulation of cytolysis [isa: 0042268 ]
+0012501 = programmed cell death [isa: 0008219 ]
+0006915 = apoptosis [isa: 0012501 ]
+0006916 = anti-apoptosis [partof: 0006915 ]
+0001719 = inhibition of caspase activation [isa: 0006916 ]
+0045767 = regulation of anti-apoptosis [partof: 0006916 ]
+0019987 = negative regulation of anti-apoptosis [isa: 0045767 ]
+0045768 = positive regulation of anti-apoptosis [isa: 0045767 ]
+0008632 = apoptotic program [partof: 0006915 ]
+0008637 = apoptotic mitochondrial changes [partof: 0008632 ]
+0030262 = apoptotic nuclear changes [partof: 0008632 ]
+0030264 = nuclear fragmentation [partof: 0030262 ]
+0006919 = caspase activation [partof: 0008632 ]
+0008635 = caspase activation via cytochrome c [isa: 0006919 ]
+0008636 = caspase activation via phosphorylation [isa: 0006919 ]
+0006921 = disassembly of cell structures [partof: 0008632 ]
+0006923 = cleavage of cytoskeletal proteins [isa: 0006921 ]
+0006922 = cleavage of lamin [isa: 0006923 ]
+0008633 = induction of proapoptotic gene products [partof: 0008632 ]
+0045884 = regulation of survival gene products [partof: 0008632 ]
+0008634 = negative regulation of survival gene products [isa: 0045884 ]
+0045885 = positive regulation of survival gene products [isa: 0045884 ]
+0006917 = induction of apoptosis [isa: 0012502 ] [partof: 0006915 ]
+0008624 = induction of apoptosis by extracellular signals [isa: 0006917 ]
+0008626 = induction of apoptosis by granzyme [isa: 0008624 ]
+0008628 = induction of apoptosis by hormones [isa: 0008624 ]
+0008627 = induction of apoptosis by ionic changes [isa: 0008624 ]
+0008625 = induction of apoptosis via death domain receptors [isa: 0008624 ]
+0008629 = induction of apoptosis by intracellular signals [isa: 0006917 ]
+0008630 = induction of apoptosis by DNA damage [isa: 0008629 ]
+0008631 = induction of apoptosis by oxidative stress [isa: 0008629 ]
+0006925 = killing of inflammatory cells [isa: 0006915 ]
+0006927 = killing transformed cells [isa: 0006915 ]
+0006926 = killing virus-infected cells [isa: 0006915 ]
+0045476 = nurse cell apoptosis [isa: 0006915 ] [partof: 0007300 ]
+0045477 = regulation of nurse cell apoptosis [partof: 0045476 ]
+0045849 = negative regulation of nurse cell apoptosis [isa: 0045477 ]
+0045850 = positive regulation of nurse cell apoptosis [isa: 0045477 ]
+0006924 = peripheral killing of activated T-cells [isa: 0006915 ]
+0012502 = induction of programmed cell death [partof: 0012501 ]
+0012503 = induction of non-apoptotic programmed cell death [isa: 0012502 ] [partof: 0016244 ]
+0016244 = non-apoptotic programmed cell death [isa: 0012501 ]
+0016280 = senescence [isa: 0016265 ]
+0016271 = tissue death [isa: 0016265 ]
+0007559 = histolysis [isa: 0016271 ] [partof: 0007552 ]
+0008220 = necrosis [isa: 0016271 ]
+0007275 = development [isa: 0008150 ]
+0009838 = abscission [isa: 0007275 ]
+0007568 = aging [isa: 0007275 ]
+0007569 = cell aging [isa: 0007568 ]
+0007570 = age dependent accumulation of genetic damage [partof: 0007569 ]
+0007571 = age dependent general metabolic decline [partof: 0007569 ]
+0007572 = age dependent decreased translational activity [isa: 0007571 ]
+0007573 = age dependent increased protein content [isa: 0007571 ]
+0030463 = cell aging (sensu Fungi) [isa: 0007569 ]
+0030464 = aging dependent sterility (sensu Fungi) [partof: 0030463 ]
+0007578 = aging dependent sterility (sensu Saccharomyces) [isa: 0030464 ] [partof: 0007574 ]
+0030465 = autophagic death (sensu Fungi) [partof: 0030463 ]
+0007577 = autophagic death (sensu Saccharomyces) [isa: 0030465 ] [partof: 0007574 ]
+0007574 = cell aging (sensu Saccharomyces) [isa: 0030463 ]
+0007581 = age-dependent yeast cell size increase [partof: 0007574 ]
+0007580 = extrachromosomal circular DNA accumulation [partof: 0007574 ]
+0046616 = nucleolar fragmentation (sensu Saccharomyces) [isa: 0007576 ] [partof: 0007574 ]
+0046617 = nucleolar size increase (sensu Saccharomyces) [isa: 0007575 ] [partof: 0007574 ]
+0007579 = senescence factor accumulation [partof: 0007574 ]
+0007576 = nucleolar fragmentation [partof: 0007569 ]
+0007575 = nucleolar size increase [partof: 0007569 ]
+0008340 = determination of adult life span [isa: 0007568 ]
+0030154 = cell differentiation [isa: 0007275 ]
+0045444 = adipocyte differentiation [isa: 0030154 ]
+0045598 = regulation of adipocyte differentiation [isa: 0045595 ] [partof: 0045444 ]
+0045599 = negative regulation of adipocyte differentiation [isa: 0045596 0045598 ]
+0045600 = positive regulation of adipocyte differentiation [isa: 0045597 0045598 ]
+0045446 = endothelial cell differentiation [isa: 0030154 ]
+0045601 = regulation of endothelial cell differentiation [isa: 0045595 ] [partof: 0045446 ]
+0045602 = negative regulation of endothelial cell differentiation [isa: 0045596 0045601 ]
+0045603 = positive regulation of endothelial cell differentiation [isa: 0045597 0045601 ]
+0009913 = epidermal cell differentiation [isa: 0030154 ]
+0042491 = hair cell differentiation [isa: 0009913 0042490 ]
+0045607 = regulation of hair cell differentiation [isa: 0045604 ] [partof: 0042491 0045631 ]
+0045608 = negative regulation of hair cell differentiation [isa: 0045605 0045607 0045632 ]
+0045609 = positive regulation of hair cell differentiation [isa: 0045606 0045607 0045633 ]
+0009912 = hair cell fate commitment [isa: 0045165 ] [partof: 0009913 ]
+0045604 = regulation of epidermal cell differentiation [isa: 0045595 ] [partof: 0009913 ]
+0045605 = negative regulation of epidermal cell differentiation [isa: 0045596 0045604 ]
+0045606 = positive regulation of epidermal cell differentiation [isa: 0045597 0045604 ]
+0042386 = hemocyte differentiation [isa: 0030154 ] [partof: 0007516 ]
+0042387 = plasmatocyte differentiation [isa: 0042386 ]
+0045613 = regulation of plasmatocyte differentiation [isa: 0045610 ] [partof: 0042387 ]
+0045614 = negative regulation of plasmatocyte differentiation [isa: 0045611 0045613 ]
+0045615 = positive regulation of plasmatocyte differentiation [isa: 0045612 0045613 ]
+0045610 = regulation of hemocyte differentiation [isa: 0045595 ] [partof: 0042386 ]
+0045611 = negative regulation of hemocyte differentiation [isa: 0045596 0045610 ]
+0045612 = positive regulation of hemocyte differentiation [isa: 0045597 0045610 ]
+0030216 = keratinocyte differentiation [isa: 0030154 ]
+0045616 = regulation of keratinocyte differentiation [isa: 0045595 ] [partof: 0030216 ]
+0045617 = negative regulation of keratinocyte differentiation [isa: 0045596 0045616 ]
+0045618 = positive regulation of keratinocyte differentiation [isa: 0045597 0045616 ]
+0030098 = lymphocytic blood cell differentiation [isa: 0030097 0030154 ]
+0045619 = regulation of lymphocytic blood cell differentiation [isa: 0045595 ] [partof: 0030098 ]
+0045620 = negative regulation of lymphocytic blood cell differentiation [isa: 0045596 0045619 ]
+0045621 = positive regulation of lymphocytic blood cell differentiation [isa: 0045597 0045619 ]
+0045058 = T-cell selection [isa: 0030098 ]
+0045062 = extrathymic T-cell selection [isa: 0045058 ]
+0045068 = negative extrathymic T-cell selection [isa: 0045062 ]
+0045067 = positive extrathymic T-cell selection [isa: 0045062 ]
+0045061 = thymic T-cell selection [isa: 0045058 ]
+0045060 = negative thymic T-cell selection [isa: 0045061 ]
+0045059 = positive thymic T-cell selection [isa: 0045061 ]
+0042490 = mechanoreceptor differentiation [isa: 0030154 ]
+0045631 = regulation of mechanoreceptor differentiation [isa: 0045595 ] [partof: 0042490 ]
+0045632 = negative regulation of mechanoreceptor differentiation [isa: 0045596 0045631 ]
+0045633 = positive regulation of mechanoreceptor differentiation [isa: 0045597 0045631 ]
+0030318 = melanocyte differentiation [isa: 0030154 ]
+0045634 = regulation of melanocyte differentiation [isa: 0045595 ] [partof: 0030318 ]
+0045635 = negative regulation of melanocyte differentiation [isa: 0045596 0045634 ]
+0045636 = positive regulation of melanocyte differentiation [isa: 0045597 0045634 ]
+0030099 = myeloid blood cell differentiation [isa: 0030097 0030154 ]
+0030221 = basophil differentiation [isa: 0030099 ]
+0045640 = regulation of basophil differentiation [isa: 0045637 ] [partof: 0030221 ]
+0045641 = negative regulation of basophil differentiation [isa: 0045638 0045640 ]
+0045642 = positive regulation of basophil differentiation [isa: 0045639 0045640 ]
+0030222 = eosinophil differentiation [isa: 0030099 ]
+0045643 = regulation of eosinophil differentiation [isa: 0045637 ] [partof: 0030222 ]
+0045644 = negative regulation of eosinophil differentiation [isa: 0045638 0045643 ]
+0045645 = positive regulation of eosinophil differentiation [isa: 0045639 0045643 ]
+0030218 = erythrocyte differentiation [isa: 0030099 ]
+0045646 = regulation of erythrocyte differentiation [isa: 0045637 ] [partof: 0030218 ]
+0045647 = negative regulation of erythrocyte differentiation [isa: 0045638 0045646 ]
+0045648 = positive regulation of erythrocyte differentiation [isa: 0045639 0045646 ]
+0030225 = macrophage differentiation [isa: 0030099 ]
+0045649 = regulation of macrophage differentiation [isa: 0045637 ] [partof: 0030225 ]
+0045650 = negative regulation of macrophage differentiation [isa: 0045638 0045649 ]
+0045651 = positive regulation of macrophage differentiation [isa: 0045639 0045649 ]
+0030219 = megakaryocyte differentiation [isa: 0030099 ]
+0045652 = regulation of megakaryocyte differentiation [isa: 0045637 ] [partof: 0030219 ]
+0045653 = negative regulation of megakaryocyte differentiation [isa: 0045638 0045652 ]
+0045654 = positive regulation of megakaryocyte differentiation [isa: 0045639 0045652 ]
+0030224 = monocyte differentiation [isa: 0030099 ]
+0045655 = regulation of monocyte differentiation [isa: 0045637 ] [partof: 0030224 ]
+0045656 = negative regulation of monocyte differentiation [isa: 0045638 0045655 ]
+0045657 = positive regulation of monocyte differentiation [isa: 0045639 0045655 ]
+0030223 = neutrophil differentiation [isa: 0030099 ]
+0045658 = regulation of neutrophil differentiation [isa: 0045637 ] [partof: 0030223 ]
+0045659 = negative regulation of neutrophil differentiation [isa: 0045638 0045658 ]
+0045660 = positive regulation of neutrophil differentiation [isa: 0045639 0045658 ]
+0030220 = platelet formation [isa: 0030099 ]
+0045637 = regulation of myeloid blood cell differentiation [isa: 0045595 ] [partof: 0030099 ]
+0045638 = negative regulation of myeloid blood cell differentiation [isa: 0045596 0045637 ]
+0045639 = positive regulation of myeloid blood cell differentiation [isa: 0045597 0045637 ]
+0045445 = myoblast differentiation [isa: 0030154 ]
+0045661 = regulation of myoblast differentiation [isa: 0045595 ] [partof: 0045445 ]
+0045662 = negative regulation of myoblast differentiation [isa: 0045596 0045661 ]
+0045663 = positive regulation of myoblast differentiation [isa: 0045597 0045661 ]
+0030182 = neuron differentiation [isa: 0030154 ]
+0045664 = regulation of neuron differentiation [isa: 0045595 ] [partof: 0030182 ]
+0045665 = negative regulation of neuron differentiation [isa: 0045596 0045664 ]
+0045666 = positive regulation of neuron differentiation [isa: 0045597 0045664 ]
+0001649 = osteoblast differentiation [isa: 0030154 ] [partof: 0001503 ]
+0045667 = regulation of osteoblast differentiation [isa: 0045595 ] [partof: 0001649 ]
+0045668 = negative regulation of osteoblast differentiation [isa: 0045596 0045667 ]
+0045669 = positive regulation of osteoblast differentiation [isa: 0045597 0045667 ]
+0030316 = osteoclast differentiation [isa: 0030154 ]
+0045670 = regulation of osteoclast differentiation [isa: 0045595 ] [partof: 0030316 ]
+0045671 = negative regulation of osteoclast differentiation [isa: 0045596 0045670 ]
+0045672 = positive regulation of osteoclast differentiation [isa: 0045597 0045670 ]
+0042461 = photoreceptor development [isa: 0030154 ]
+0042462 = eye photoreceptor development [isa: 0042461 ] [partof: 0001654 ]
+0042051 = eye photoreceptor development (sensu Drosophila) [isa: 0042462 ] [partof: 0007456 ]
+0007459 = photoreceptor commitment (sensu Drosophila) [isa: 0045165 0046552 ] [partof: 0042051 ]
+0007462 = R1/R6 cell fate commitment [isa: 0007459 ]
+0007463 = R2/R5 cell fate commitment [isa: 0007459 ]
+0007464 = R3/R4 cell fate commitment [isa: 0007459 ]
+0007465 = R7 cell fate commitment [isa: 0007459 0045467 ]
+0007460 = R8 cell fate commitment [isa: 0007459 0045463 ]
+0045464 = R8 cell fate specification [partof: 0007460 ]
+0007461 = restriction of R8 fate [partof: 0007460 ]
+0007467 = photoreceptor differentiation (sensu Drosophila) [isa: 0046530 ] [partof: 0042051 ]
+0008594 = photoreceptor morphogenesis (sensu Drosophila) [isa: 0046531 ] [partof: 0007467 ]
+0045466 = R7 differentiation [isa: 0007467 0045467 ]
+0045676 = regulation of R7 differentiation [isa: 0045673 ] [partof: 0045466 ]
+0045677 = negative regulation of R7 differentiation [isa: 0045674 0045676 ]
+0045678 = positive regulation of R7 differentiation [isa: 0045675 0045676 ]
+0045465 = R8 differentiation [isa: 0007467 0045463 ]
+0045679 = regulation of R8 differentiation [isa: 0045673 ] [partof: 0045465 ]
+0045680 = negative regulation of R8 differentiation [isa: 0045674 0045679 ]
+0045681 = positive regulation of R8 differentiation [isa: 0045675 0045679 ]
+0045673 = regulation of photoreceptor differentiation (sensu Drosophila) [isa: 0045314 0046532 ] [partof: 0007467 ]
+0045674 = negative regulation of photoreceptor differentiation (sensu Drosophila) [isa: 0045316 0045673 0046533 ]
+0045675 = positive regulation of photoreceptor differentiation (sensu Drosophila) [isa: 0045315 0045673 0046534 ]
+0007468 = regulation of rhodopsin gene activity [partof: 0007467 ]
+0045871 = negative regulation of rhodopsin gene activity [isa: 0007468 ]
+0045872 = positive regulation of rhodopsin gene activity [isa: 0007468 ]
+0045467 = R7 development [isa: 0042051 ]
+0045463 = R8 development [isa: 0042051 ]
+0045468 = regulation of R8 spacing [partof: 0045463 ]
+0045469 = negative regulation of R8 spacing [isa: 0045468 ]
+0045748 = positive regulation of R8 spacing [isa: 0045468 ]
+0045470 = R8-mediated photoreceptor organization [partof: 0042051 ]
+0045314 = regulation of eye photoreceptor development (sensu Drosophila) [isa: 0042478 ] [partof: 0042051 ]
+0045316 = negative regulation of eye photoreceptor development (sensu Drosophila) [isa: 0042480 0045314 ]
+0045315 = positive regulation of eye photoreceptor development (sensu Drosophila) [isa: 0042479 0045314 ]
+0042052 = rhabdomere development [partof: 0042051 ]
+0045313 = rhabdomere membrane biogenesis [partof: 0042052 ]
+0046552 = photoreceptor commitment [isa: 0042462 ]
+0046530 = photoreceptor differentiation [isa: 0042462 ]
+0046531 = photoreceptor morphogenesis [partof: 0046530 ]
+0046532 = regulation of photoreceptor differentiation [isa: 0042478 0045595 ] [partof: 0046530 ]
+0046533 = negative regulation of photoreceptor differentiation [isa: 0042480 0045596 0046532 ]
+0046534 = positive regulation of photoreceptor differentiation [isa: 0042479 0045597 0046532 ]
+0042478 = regulation of eye photoreceptor development [partof: 0042462 ]
+0042480 = negative regulation of eye photoreceptor development [isa: 0042478 ]
+0042479 = positive regulation of eye photoreceptor development [isa: 0042478 ]
+0046549 = retinal cone cell development [isa: 0042462 ]
+0046551 = retinal cone cell fate commitment [isa: 0045165 0046549 ]
+0046548 = retinal rod cell development [isa: 0042462 ]
+0042463 = non-eye photoreceptor development [isa: 0042461 ]
+0045595 = regulation of cell differentiation [partof: 0030154 ]
+0045596 = negative regulation of cell differentiation [isa: 0045595 ]
+0045597 = positive regulation of cell differentiation [isa: 0045595 ]
+0001570 = vasculogenesis [isa: 0030154 ] [partof: 0001568 ]
+0045165 = cell fate commitment [isa: 0007275 ]
+0001709 = cell fate determination [partof: 0045165 ]
+0001713 = ectoderm cell fate determination [isa: 0001709 ] [partof: 0001705 0001712 ]
+0007493 = endoderm cell fate determination [isa: 0001709 ] [partof: 0001706 0001711 ]
+0007500 = mesoderm cell fate determination [isa: 0001709 ] [partof: 0001707 0001710 ]
+0001708 = cell fate specification [partof: 0045165 ]
+0001715 = ectoderm cell fate specification [isa: 0001708 ] [partof: 0001712 ]
+0001714 = endoderm cell fate specification [isa: 0001708 ] [partof: 0001711 ]
+0007501 = mesoderm cell fate specification [isa: 0001708 ] [partof: 0001710 ]
+0007466 = cone cell fate commitment (sensu Drosophila) [isa: 0045165 ] [partof: 0007456 ]
+0001712 = ectoderm cell fate commitment [isa: 0045165 ]
+0001711 = endoderm cell fate commitment [isa: 0045165 ]
+0001710 = mesoderm cell fate commitment [isa: 0045165 ]
+0007349 = cellularization [isa: 0007275 ]
+0009796 = cellularization (sensu Animalia) [isa: 0007349 0009792 ]
+0009797 = cellularization (sensu Magnoliophyta) [isa: 0007349 ]
+0009790 = embryonic development [isa: 0007275 ]
+0009792 = embryonic development (sensu Animalia) [isa: 0009790 ]
+0040016 = embryonic cleavage [partof: 0009792 ]
+0001700 = embryonic development (sensu Insecta) [isa: 0009792 ]
+0007391 = dorsal closure [partof: 0001700 ]
+0007392 = initiation of dorsal closure [partof: 0007391 ]
+0007393 = determination of leading edge cell identity [partof: 0007392 ]
+0007394 = elongation and differentiation of leading edge cells [partof: 0007392 ]
+0007395 = spreading of leading edge cells [partof: 0007391 ]
+0007396 = suture of dorsal opening [partof: 0007391 ]
+0007514 = garland cell development [partof: 0001700 ]
+0007390 = germ-band shortening [partof: 0001700 ]
+0008258 = head involution [partof: 0001700 ]
+0007438 = oenocyte development [partof: 0001700 ]
+0030589 = pseudocleavage (sensu Insecta) [isa: 0030588 ] [partof: 0001700 ]
+0001701 = embryonic development (sensu Mammalia) [isa: 0009792 ]
+0007369 = gastrulation [partof: 0009792 ]
+0001704 = formation of primary germ layer [partof: 0007369 ]
+0001705 = ectoderm formation [isa: 0001704 ] [partof: 0007398 ]
+0001706 = endoderm formation [isa: 0001704 ] [partof: 0007492 ]
+0001707 = mesoderm formation [isa: 0001704 ] [partof: 0007498 ]
+0007509 = mesoderm migration [partof: 0001707 ]
+0001702 = gastrulation (sensu Deuterostoma) [isa: 0007369 ]
+0001703 = gastrulation (sensu Protostoma) [isa: 0007369 ]
+0007378 = amnioserosa formation [partof: 0001703 ]
+0007375 = anterior midgut invagination [partof: 0001703 ]
+0007376 = cephalic furrow formation [partof: 0001703 ]
+0007377 = germ-band extension [partof: 0001703 ]
+0007374 = posterior midgut invagination [partof: 0001703 ]
+0007370 = ventral furrow formation [partof: 0001703 ]
+0007372 = determination of anterior border of ventral midline [partof: 0007370 ]
+0007373 = determination of posterior border of ventral midline [partof: 0007370 ]
+0007371 = ventral midline determination [partof: 0007370 ]
+0001679 = neurulation [partof: 0007369 ]
+0030588 = pseudocleavage [isa: 0009792 ]
+0030590 = pseudocleavage (sensu Nematoda) [isa: 0030588 ]
+0009793 = embryonic development (sensu Magnoliophyta) [isa: 0009790 ]
+0009795 = embryonic morphogenesis [isa: 0009653 ] [partof: 0009790 ]
+0007487 = analia morphogenesis (sensu Holometabola) [isa: 0009795 ] [partof: 0007483 ]
+0045497 = female analia morphogenesis (sensu Holometabola) [isa: 0007487 ]
+0045496 = male analia morphogenesis (sensu Holometabola) [isa: 0007487 ]
+0007469 = antennal morphogenesis [isa: 0009795 ] [partof: 0007455 ]
+0040032 = body morphogenesis (sensu Nematoda) [isa: 0009795 ]
+0008407 = bristle morphogenesis [isa: 0009795 ] [partof: 0007423 ]
+0042471 = ear morphogenesis [isa: 0009795 0009887 ]
+0042472 = inner ear morphogenesis [isa: 0042471 ]
+0042474 = middle ear morphogenesis [isa: 0042471 ]
+0042473 = outer ear morphogenesis [isa: 0042471 ]
+0030538 = genital morphogenesis [isa: 0009795 ]
+0030540 = female genital morphogenesis [isa: 0030538 ]
+0007486 = female genital morphogenesis (sensu Holometabola) [isa: 0007484 0030540 ]
+0007484 = genital morphogenesis (sensu Holometabola) [isa: 0030538 ] [partof: 0007483 ]
+0007485 = male genital morphogenesis (sensu Holometabola) [isa: 0007484 0030539 ]
+0040035 = hermaphrodite genital morphogenesis [isa: 0030538 ]
+0030539 = male genital morphogenesis [isa: 0030538 ]
+0007439 = gut (ectodermal) morphogenesis [isa: 0009795 0009887 ]
+0007441 = anterior midgut (ectodermal) morphogenesis [partof: 0007439 ]
+0007440 = foregut morphogenesis [partof: 0007439 ]
+0007442 = hindgut morphogenesis [partof: 0007439 ]
+0007443 = Malpighian tubule morphogenesis [partof: 0007442 ]
+0007482 = haltere morphogenesis [isa: 0009795 ] [partof: 0007481 ]
+0007560 = imaginal disc morphogenesis [isa: 0009795 ] [partof: 0007552 ]
+0007561 = imaginal disc eversion [partof: 0007560 ]
+0046528 = imaginal disc fusion [partof: 0007560 ]
+0046529 = imaginal disc fusion, thorax closure [partof: 0046528 ]
+0016335 = morphogenesis of larval imaginal disc epithelium [isa: 0002009 ] [partof: 0002168 0007560 ]
+0016336 = establishment and/or maintenance of polarity of larval imaginal disc epithelium [partof: 0016335 ]
+0042252 = establishment of polarity of larval imaginal disc epithelium [isa: 0016336 ]
+0042251 = maintenance of polarity of larval imaginal disc epithelium [isa: 0016336 ]
+0030326 = limb morphogenesis [isa: 0009795 ]
+0046590 = leg morphogenesis [isa: 0030326 ]
+0046591 = leg joint morphogenesis [isa: 0046590 ]
+0016348 = leg joint morphogenesis (sensu Holometabola) [partof: 0007480 0046591 ]
+0007480 = leg morphogenesis (sensu Holometabola) [isa: 0046590 ] [partof: 0007478 ]
+0016331 = morphogenesis of embryonic epithelium [isa: 0002009 0009795 ]
+0016332 = establishment and/or maintenance of polarity of embryonic epithelium [partof: 0016331 ]
+0042249 = establishment of polarity of embryonic epithelium [isa: 0016332 ]
+0042250 = maintenance of polarity of embryonic epithelium [isa: 0016332 ]
+0007477 = notum morphogenesis [isa: 0009795 ] [partof: 0007472 ]
+0008056 = ocellus morphogenesis [isa: 0009795 ] [partof: 0007455 ]
+0008058 = ocellus pigment granule morphogenesis [isa: 0008059 ] [partof: 0008056 ]
+0007471 = prothoracic morphogenesis [isa: 0009795 ] [partof: 0007470 ]
+0007491 = sternite morphogenesis [isa: 0009795 ] [partof: 0007488 ]
+0045138 = tail tip morphogenesis (sensu Nematoda) [isa: 0009795 ]
+0007490 = tergite morphogenesis [isa: 0009795 ] [partof: 0007488 ]
+0007476 = wing morphogenesis [isa: 0009795 ] [partof: 0007472 ]
+0008587 = wing margin morphogenesis [partof: 0007476 ]
+0007475 = apposition of dorsal and ventral wing surfaces [partof: 0008587 ]
+0008586 = wing vein morphogenesis [partof: 0007476 ]
+0007474 = wing vein specification [partof: 0007476 ]
+0009880 = embryonic pattern specification [isa: 0007389 ] [partof: 0009790 ]
+0000578 = embryonic axis specification [isa: 0009798 0009880 ]
+0008595 = determination of anterior/posterior axis, embryo [isa: 0000578 0009948 ] [partof: 0007351 ]
+0008358 = maternal determination of anterior/posterior axis, embryo [isa: 0008595 ]
+0007354 = zygotic determination of anterior/posterior axis, embryo [isa: 0008595 ]
+0007355 = anterior region determination [partof: 0007354 ]
+0007359 = posterior abdomen determination [partof: 0007354 ]
+0007360 = activation of posterior gap gene [partof: 0007359 ]
+0007361 = establishment of posterior gap gene boundaries [partof: 0007359 ]
+0007362 = terminal region determination [partof: 0007354 ]
+0007363 = activation of terminal gap gene [partof: 0007362 ]
+0007364 = establishment of terminal gap gene boundary [partof: 0007362 ]
+0007356 = thorax and anterior abdomen determination [partof: 0007354 ]
+0007357 = activation of central gap gene [partof: 0007356 ]
+0007358 = establishment of central gap gene boundaries [partof: 0007356 ]
+0007352 = zygotic determination of dorsal/ventral axis [isa: 0000578 0009950 ] [partof: 0007351 ]
+0001569 = patterning of blood vessels [isa: 0009880 ] [partof: 0001525 ]
+0007379 = segment specification [isa: 0009880 ]
+0007350 = blastoderm segmentation [isa: 0007379 ]
+0007365 = periodic partitioning [partof: 0007350 ]
+0007366 = periodic partitioning by pair rule gene [isa: 0007365 ]
+0007367 = segment polarity determination [isa: 0007365 ]
+0007351 = regional subdivision [partof: 0007350 ]
+0007353 = ventral/lateral system [partof: 0007351 ]
+0007385 = specification of segmental identity, abdomen [isa: 0007379 ]
+0007383 = specification of segmental identity, antennal segment [isa: 0007379 ]
+0007380 = specification of segmental identity, head [isa: 0007379 ]
+0007381 = specification of segmental identity, labial segment [isa: 0007379 ]
+0042305 = specification of segmental identity, mandibular segment [isa: 0007379 ]
+0007382 = specification of segmental identity, maxillary segment [isa: 0007379 ]
+0007384 = specification of segmental identity, thorax [isa: 0007379 ]
+0045995 = regulation of embryonic development rate [isa: 0009790 0040008 ]
+0045992 = negative regulation of embryonic development rate [isa: 0045926 0045995 ]
+0040019 = positive regulation of embryonic development rate [isa: 0045927 0045995 ]
+0009908 = flowering [isa: 0007275 ]
+0009909 = regulation of flowering [partof: 0009908 ]
+0009910 = negative regulation of flowering [isa: 0009909 ]
+0009911 = positive regulation of flowering [isa: 0009909 ]
+0030582 = fruiting body formation [isa: 0007275 ]
+0030584 = fruiting body formation (sensu Fungi) [isa: 0030582 ]
+0009292 = genetic exchange [isa: 0007275 ]
+0009291 = conjugation (sensu Bacteria) [isa: 0009292 ]
+0009294 = DNA mediated transformation [isa: 0009292 ]
+0030420 = establishment of competence for transformation [isa: 0009294 ]
+0045304 = regulation of establishment of competence for transformation [partof: 0030420 ]
+0045808 = negative regulation of establishment of competence for transformation [isa: 0045304 ]
+0045809 = positive regulation of establishment of competence for transformation [isa: 0045304 ]
+0030461 = mating (sensu Fungi) [isa: 0009292 ]
+0030462 = zygote formation (sensu Fungi) [partof: 0030461 ]
+0030477 = conjugation (sensu Fungi) [partof: 0030462 ]
+0009293 = transduction [isa: 0009292 ]
+0009844 = germination [isa: 0007275 0007582 ]
+0009846 = pollen germination [isa: 0009844 ] [partof: 0009856 ]
+0009845 = seed germination [isa: 0009844 ]
+0009847 = spore germination [isa: 0009844 ]
+0040007 = growth [isa: 0007275 ]
+0040008 = regulation of growth [partof: 0040007 ]
+0045926 = negative regulation of growth [isa: 0040008 ]
+0040015 = negative regulation of body size [isa: 0040014 0045926 ]
+0045961 = negative regulation of development, heterochronic [isa: 0040034 0045926 ]
+0046621 = negative regulation of organ size [isa: 0045926 0046620 ]
+0045927 = positive regulation of growth [isa: 0040008 ]
+0040018 = positive regulation of body size [isa: 0040014 0045927 ]
+0045962 = positive regulation of development, heterochronic [isa: 0040034 0045927 ]
+0046622 = positive regulation of organ size [isa: 0045927 0046620 ]
+0040014 = regulation of body size [isa: 0040008 ]
+0040034 = regulation of development, heterochronic [isa: 0040008 ]
+0046620 = regulation of organ size [isa: 0040008 ]
+0009932 = tip growth [isa: 0040007 ]
+0030097 = hemopoiesis [isa: 0007275 ]
+0007516 = hemocyte development [isa: 0030097 ] [partof: 0007515 ]
+0007320 = insemination [isa: 0007275 ]
+0007321 = sperm displacement [partof: 0007320 ]
+0002164 = larval development [isa: 0007275 ]
+0002117 = larval development (sensu Amphibia) [isa: 0002164 ]
+0002119 = larval development (sensu Nematoda) [isa: 0002164 ]
+0040024 = dauer larval development (sensu Nematoda) [isa: 0002119 ]
+0040025 = vulval development (sensu Nematoda) [partof: 0002119 ]
+0040028 = regulation of vulval development (sensu Nematoda) [partof: 0040025 ]
+0040027 = negative regulation of vulval development (sensu Nematoda) [isa: 0040028 ]
+0040026 = positive regulation of vulval development (sensu Nematoda) [isa: 0040028 ]
+0007508 = larval heart development [isa: 0007507 ] [partof: 0002164 ]
+0007510 = cardioblast determination [partof: 0007508 ]
+0007511 = dorsal vessel development [partof: 0007510 ]
+0007526 = larval somatic muscle development [isa: 0007525 ] [partof: 0002164 ]
+0007523 = larval visceral muscle development [isa: 0007522 ] [partof: 0002164 ]
+0002165 = larval/pupal development (sensu Insecta) [isa: 0002164 ]
+0002168 = larval development (sensu Insecta) [isa: 0002165 ]
+0008363 = larval cuticle biosynthesis (sensu Insecta) [isa: 0042337 ] [partof: 0002168 ]
+0007504 = larval fat body development [isa: 0007503 ] [partof: 0002168 ]
+0007433 = larval salivary gland determination [isa: 0007432 ] [partof: 0002168 ]
+0045708 = regulation of larval salivary gland determination [isa: 0045704 ] [partof: 0007433 ]
+0045710 = negative regulation of larval salivary gland determination [isa: 0045705 0045708 ]
+0045712 = positive regulation of larval salivary gland determination [isa: 0045706 0045708 ]
+0007436 = larval salivary gland morphogenesis [isa: 0007435 ] [partof: 0002168 ]
+0007552 = metamorphosis [isa: 0002165 ]
+0007562 = eclosion [partof: 0007552 ]
+0045452 = cuticle tanning and hardening [partof: 0007562 ]
+0007593 = cuticle tanning [isa: 0040006 ] [partof: 0045452 ]
+0007564 = regulation of cuticle tanning and hardening [partof: 0045452 ]
+0045800 = negative regulation of cuticle tanning and hardening [isa: 0007564 ]
+0045801 = positive regulation of cuticle tanning and hardening [isa: 0007564 ]
+0007563 = regulation of eclosion [partof: 0007562 ]
+0045804 = negative regulation of eclosion [isa: 0007563 ]
+0045805 = positive regulation of eclosion [isa: 0007563 ]
+0008364 = pupal cuticle biosynthesis (sensu Insecta) [isa: 0042337 ] [partof: 0002165 ]
+0009933 = meristem organization [isa: 0007275 ]
+0009934 = regulation of meristem organization [partof: 0009933 ]
+0009653 = morphogenesis [isa: 0007275 ]
+0002009 = morphogenesis of an epithelium [isa: 0009653 ]
+0002011 = morphogenesis of an epithelial sheet [isa: 0002009 ]
+0016333 = morphogenesis of follicular epithelium [isa: 0002009 ]
+0016334 = establishment and/or maintenance of polarity of follicular epithelium [partof: 0016333 ]
+0042247 = establishment of polarity of follicular epithelium [isa: 0016334 ]
+0042248 = maintenance of polarity of follicular epithelium [isa: 0016334 ]
+0009887 = organogenesis [isa: 0009653 ]
+0030325 = adrenal gland development [isa: 0009887 ]
+0001568 = blood vessel development [isa: 0009887 ]
+0001525 = angiogenesis [partof: 0001568 ]
+0045765 = regulation of angiogenesis [partof: 0001525 ]
+0016525 = negative regulation of angiogenesis [isa: 0045765 ]
+0045766 = positive regulation of angiogenesis [isa: 0045765 ]
+0001654 = eye morphogenesis [isa: 0009886 0009887 ]
+0007456 = eye morphogenesis (sensu Drosophila) [isa: 0001654 ] [partof: 0007455 ]
+0008057 = eye pigment granule morphogenesis (sensu Drosophila) [isa: 0008059 ] [partof: 0007456 ]
+0045318 = eye photoreceptor pigment granule morphogenesis [isa: 0008057 ]
+0008583 = mystery cell fate differentiation (sensu Drosophila) [partof: 0007456 ]
+0007457 = optic lobe placode development (sensu Drosophila) [isa: 0046619 ] [partof: 0007456 ]
+0007458 = progression of morphogenetic furrow (sensu Drosophila) [partof: 0007456 ]
+0046619 = optic placode development [partof: 0001654 ]
+0007503 = fat body development [isa: 0009887 ]
+0007505 = adult fat body development [isa: 0007503 ]
+0008406 = gonad development [isa: 0009887 ]
+0008585 = female gonad development [isa: 0008406 ]
+0001553 = luteinization [partof: 0008585 ]
+0001554 = luteolysis [partof: 0008585 ]
+0001552 = ovarian follicle atresia [partof: 0008585 ]
+0001541 = ovarian follicle development [partof: 0008585 ]
+0001551 = ovarian follicle endowment [partof: 0001541 ]
+0001542 = ovulation [isa: 0008585 ]
+0001543 = ovarian follicle rupture [partof: 0001542 ]
+0007506 = gonadal mesoderm development [isa: 0007498 ] [partof: 0008406 ]
+0008584 = male gonad development [isa: 0008406 ]
+0007507 = heart development [isa: 0009887 ]
+0007512 = adult heart development [isa: 0007507 ]
+0007513 = pericardial cell development [partof: 0007507 ]
+0009888 = histogenesis [partof: 0009887 ]
+0007398 = ectoderm development [isa: 0009888 ]
+0008544 = epidermal differentiation [partof: 0007398 ]
+0045682 = regulation of epidermal differentiation [partof: 0008544 ]
+0045683 = negative regulation of epidermal differentiation [isa: 0045682 ]
+0045684 = positive regulation of epidermal differentiation [isa: 0045682 ]
+0007492 = endoderm development [isa: 0009888 ]
+0007498 = mesoderm development [isa: 0009888 ]
+0007499 = ectoderm/mesoderm interaction [partof: 0007498 ]
+0007502 = gut mesoderm development [isa: 0007498 ]
+0045299 = otolith mineralization [partof: 0007498 ]
+0007444 = imaginal disc development [isa: 0009887 ]
+0007445 = determination of imaginal disc primordium [partof: 0007444 ]
+0007446 = imaginal disc growth [partof: 0007444 ]
+0045570 = regulation of imaginal disc growth [partof: 0007446 ]
+0045571 = negative regulation of imaginal disc growth [isa: 0045570 ]
+0045572 = positive regulation of imaginal disc growth [isa: 0045570 ]
+0007452 = imaginal disc metamorphosis [partof: 0007444 ]
+0007453 = clypeo-labral disc metamorphosis [isa: 0007452 ]
+0016349 = proboscis morphogenesis [partof: 0007453 0007454 0007455 ]
+0007455 = eye-antennal disc metamorphosis [isa: 0007452 ]
+0008059 = photoreceptor pigment granule morphogenesis [partof: 0007455 ]
+0007483 = genital disc metamorphosis [isa: 0007452 ]
+0007481 = haltere disc metamorphosis [isa: 0007452 ]
+0007488 = histoblast metamorphosis [isa: 0007452 ]
+0007489 = maintenance of imaginal histoblast diploidy [partof: 0007488 ]
+0007454 = labial disc metamorphosis [isa: 0007452 ]
+0007478 = leg disc metamorphosis [isa: 0007452 ]
+0007479 = leg disc proximal/distal pattern formation [isa: 0007449 ] [partof: 0007478 ]
+0007470 = prothoracic disc metamorphosis [isa: 0007452 ]
+0007472 = wing disc metamorphosis [isa: 0007452 ]
+0007473 = wing disc proximal/distal pattern formation [isa: 0007449 ] [partof: 0007472 ]
+0007447 = imaginal disc pattern formation [isa: 0007389 ] [partof: 0007444 ]
+0007448 = anterior/posterior pattern formation, imaginal disc [isa: 0009952 ] [partof: 0007447 ]
+0007450 = dorsal/ventral pattern formation, imaginal disc [isa: 0009953 ] [partof: 0007447 ]
+0007451 = dorsal/ventral lineage restriction, imaginal disc [partof: 0007450 ]
+0007449 = proximal/distal pattern formation, imaginal disc [isa: 0009954 ] [partof: 0007447 ]
+0007515 = lymph gland development [isa: 0009887 ]
+0007494 = midgut development [isa: 0009887 ]
+0007496 = anterior midgut development [partof: 0007494 ]
+0007497 = posterior midgut development [partof: 0007494 ]
+0007495 = visceral mesoderm/endoderm interaction [partof: 0007494 ]
+0007517 = muscle development [isa: 0009887 ]
+0007521 = determination of muscle identity [partof: 0007517 ]
+0016203 = muscle attachment [partof: 0007517 ]
+0016204 = determination of muscle attachment site [partof: 0016203 ]
+0007518 = myoblast determination [partof: 0007517 ]
+0007519 = myogenesis [partof: 0007517 ]
+0007520 = myoblast fusion [partof: 0007519 ]
+0030239 = myofibril assembly [partof: 0007519 ]
+0030241 = muscle thick filament assembly [partof: 0030239 ]
+0045214 = sarcomere organization [partof: 0030239 ]
+0007528 = neuromuscular junction development [partof: 0007519 ]
+0007529 = establishment of synaptic specificity at neuromuscular junction [partof: 0007528 ]
+0008582 = regulation of synaptic growth at neuromuscular junction [partof: 0007528 ]
+0042062 = long-term strengthening of neuromuscular junction [partof: 0008582 ]
+0045886 = negative regulation of synaptic growth at neuromuscular junction [isa: 0008582 ]
+0045887 = positive regulation of synaptic growth at neuromuscular junction [isa: 0008582 ]
+0016202 = regulation of myogenesis [partof: 0007519 ]
+0045843 = negative regulation of myogenesis [isa: 0016202 ]
+0045844 = positive regulation of myogenesis [isa: 0016202 ]
+0007525 = somatic muscle development [isa: 0007517 ]
+0007527 = adult somatic muscle development [isa: 0007525 ]
+0007522 = visceral muscle development [isa: 0007517 ]
+0007524 = adult visceral muscle development [isa: 0007522 ]
+0007399 = neurogenesis [isa: 0009887 ]
+0007409 = axonogenesis [partof: 0007399 ]
+0007412 = axon target recognition [partof: 0007409 ]
+0007417 = central nervous system development [partof: 0007399 ]
+0007420 = brain development [partof: 0007417 ]
+0016319 = mushroom body development [partof: 0007420 ]
+0007419 = ventral cord development [partof: 0007417 ]
+0007418 = ventral midline development [partof: 0007417 ]
+0007414 = defasciculation of neuron [partof: 0007399 ]
+0007415 = defasciculation of motor neuron [isa: 0007414 ]
+0016358 = dendrite morphogenesis [partof: 0007399 ]
+0007402 = determination of ganglion mother cell fate [partof: 0007399 ]
+0008065 = establishment of blood/nerve barrier [partof: 0007399 ]
+0007413 = fasciculation of neuron [partof: 0007399 ]
+0042063 = gliogenesis [partof: 0007399 ]
+0007403 = determination of glial fate [partof: 0042063 ]
+0007404 = glia cell differentiation [partof: 0042063 ]
+0045685 = regulation of glia cell differentiation [partof: 0007404 ]
+0045686 = negative regulation of glia cell differentiation [isa: 0045685 ]
+0045687 = positive regulation of glia cell differentiation [isa: 0045685 ]
+0042065 = glial growth [partof: 0042063 ]
+0042066 = perineurial glial growth [isa: 0042065 ]
+0045161 = ion channel clustering [partof: 0007399 ]
+0045163 = clustering of voltage gated potassium channels [isa: 0045161 ]
+0045162 = clustering of voltage gated sodium channels [isa: 0045161 ]
+0042551 = nerve maturation [partof: 0007399 ]
+0008366 = nerve ensheathment [isa: 0042551 ]
+0042553 = cellular nerve ensheathment [isa: 0008366 ]
+0042552 = myelination [isa: 0008366 ]
+0007400 = neuroblast determination [partof: 0007399 ]
+0007405 = neuroblast proliferation [partof: 0007399 ]
+0042055 = neuronal lineage restriction [partof: 0007399 ]
+0016322 = neuronal remodeling [partof: 0007399 ]
+0007401 = pan-neural process [partof: 0007399 ]
+0007422 = peripheral nervous system development [partof: 0007399 ]
+0007423 = sensory organ development [partof: 0007422 ]
+0008052 = sensory organ determination [partof: 0007423 ]
+0016360 = determination of sensory organ precursor cell fate [partof: 0008052 ]
+0045498 = sex comb development [isa: 0007423 ]
+0007421 = stomatogastric nervous system development [partof: 0007399 ]
+0007406 = suppression of neuroblast proliferation [partof: 0007399 ]
+0007407 = neuroblast activation [partof: 0007406 ]
+0007416 = synaptogenesis [partof: 0007399 ]
+0042476 = odontogenesis [isa: 0009887 ]
+0042477 = odontogenesis (sensu Invertebrata) [isa: 0042476 ]
+0042484 = regulation of odontogenesis (sensu Invertebrata) [isa: 0042481 ] [partof: 0042477 ]
+0042486 = negative regulation of odontogenesis (sensu Invertebrata) [isa: 0042483 0042484 ]
+0042485 = positive regulation of odontogenesis (sensu Invertebrata) [isa: 0042482 0042484 ]
+0042475 = odontogenesis (sensu Vertebrata) [isa: 0042476 ]
+0042487 = regulation of odontogenesis (sensu Vertebrata) [partof: 0042475 ]
+0042489 = negative regulation of odontogenesis (sensu Vertebrata) [isa: 0042483 0042487 ]
+0042488 = positive regulation of odontogenesis (sensu Vertebrata) [isa: 0042482 0042487 ]
+0042481 = regulation of odontogenesis [partof: 0042476 ]
+0042483 = negative regulation of odontogenesis [isa: 0042481 ]
+0042482 = positive regulation of odontogenesis [isa: 0042481 ]
+0030323 = respiratory tube development [isa: 0009887 ]
+0030324 = lung development [partof: 0030323 ]
+0007431 = salivary gland development [isa: 0009887 ]
+0007432 = salivary gland determination [partof: 0007431 ]
+0007434 = adult salivary gland determination [isa: 0007432 ]
+0045707 = regulation of adult salivary gland determination [isa: 0045704 ] [partof: 0007434 ]
+0045709 = negative regulation of adult salivary gland determination [isa: 0045705 0045707 ]
+0045711 = positive regulation of adult salivary gland determination [isa: 0045706 0045707 ]
+0045704 = regulation of salivary gland determination [partof: 0007432 ]
+0045705 = negative regulation of salivary gland determination [isa: 0045704 ]
+0045706 = positive regulation of salivary gland determination [isa: 0045704 ]
+0007435 = salivary gland morphogenesis [partof: 0007431 ]
+0007437 = adult salivary gland morphogenesis [isa: 0007435 ]
+0001501 = skeletal development [isa: 0009887 ]
+0001502 = cartilage condensation [partof: 0001501 ]
+0001503 = ossification [partof: 0001501 ]
+0030282 = bone mineralization [partof: 0001503 ]
+0030500 = regulation of bone mineralization [isa: 0030278 ] [partof: 0030282 ]
+0030502 = negative regulation of bone mineralization [isa: 0030279 0030500 ]
+0030501 = positive regulation of bone mineralization [isa: 0030500 0045778 ]
+0030278 = regulation of bone formation [partof: 0001503 ]
+0030279 = negative regulation of bone formation [isa: 0030278 ]
+0045778 = positive regulation of bone formation [isa: 0030278 ]
+0007424 = tracheal system development (sensu Insecta) [isa: 0009887 ]
+0007428 = primary tracheal branching [partof: 0007424 ]
+0007429 = secondary tracheal branching [partof: 0007424 ]
+0007430 = terminal branching of trachea, cytoplasmic projection extension [partof: 0007424 ]
+0007425 = tracheal determination [partof: 0007424 ]
+0007426 = tracheal outgrowth [partof: 0007424 ]
+0001655 = urogenital system development [isa: 0009887 ]
+0001656 = metanephros development [partof: 0001655 ]
+0001657 = ureteric bud development [partof: 0001656 ]
+0001658 = ureteric bud branching [partof: 0001657 ]
+0009886 = post-embryonic morphogenesis [isa: 0009653 ] [partof: 0009791 ]
+0009878 = nodule morphogenesis [isa: 0009886 ] [partof: 0009877 ]
+0007389 = pattern specification [isa: 0007275 ]
+0009955 = adaxial/abaxial pattern formation [isa: 0007389 ]
+0009943 = adaxial/abaxial axis specification [isa: 0009798 ] [partof: 0009955 ]
+0009944 = polarity specification of the adaxial/abaxial axis [partof: 0009943 ]
+0009952 = anterior/posterior pattern formation [isa: 0007389 ]
+0009948 = anterior/posterior axis specification [isa: 0009798 ] [partof: 0009952 ]
+0007314 = oocyte anterior/posterior axis determination [isa: 0009948 ] [partof: 0007309 ]
+0007315 = pole plasm assembly [partof: 0007314 ]
+0009949 = polarity specification of the anterior/posterior axis [partof: 0009948 ]
+0009798 = axis specification [isa: 0007389 ]
+0009947 = centrolateral axis specification [isa: 0009798 ]
+0009950 = dorsal/ventral axis specification [isa: 0009798 ] [partof: 0009953 ]
+0007310 = oocyte dorsal/ventral axis determination [isa: 0009950 ] [partof: 0007309 ]
+0007311 = maternal determination of dorsal/ventral axis, oocyte, germ-line encoded [isa: 0007310 ]
+0007312 = oocyte nucleus migration [partof: 0007311 ]
+0007313 = maternal determination of dorsal/ventral axis, oocyte, soma encoded [isa: 0007310 ]
+0009951 = polarity specification of the dorsal/ventral axis [partof: 0009950 ]
+0009942 = longitudinal axis specification [isa: 0009798 ]
+0007309 = oocyte axis determination [isa: 0009798 ] [partof: 0007308 ]
+0009946 = proximal/distal axis specification [isa: 0009798 ] [partof: 0009954 ]
+0009945 = radial axis specification [isa: 0009798 ] [partof: 0009956 ]
+0007386 = compartment specification [isa: 0007389 ]
+0007387 = anterior compartment specification [isa: 0007386 ]
+0007388 = posterior compartment specification [isa: 0007386 ]
+0009799 = determination of symmetry [isa: 0007389 ]
+0009855 = determination of bilateral symmetry [isa: 0009799 ]
+0007368 = determination of left/right asymmetry [isa: 0009855 ]
+0009879 = determination of radial symmetry [isa: 0009799 ]
+0009953 = dorsal/ventral pattern formation [isa: 0007389 ]
+0030381 = eggshell pattern formation [isa: 0007389 ] [partof: 0007304 ]
+0009954 = proximal/distal pattern formation [isa: 0007389 ]
+0009956 = radial pattern formation [isa: 0007389 ]
+0009791 = post-embryonic development [isa: 0007275 ]
+0040029 = regulation of gene expression, epigenetic [partof: 0007275 ]
+0007549 = dosage compensation [isa: 0040029 ]
+0009047 = dosage compensation, by hyperactivation of X chromosome [isa: 0007549 ]
+0016457 = dosage compensation complex assembly [partof: 0009047 ]
+0042464 = dosage compensation, by hypoactivation of X chromosome [isa: 0007549 ]
+0009048 = dosage compensation, by inactivation of X chromosome [isa: 0007549 ]
+0007550 = establishment of dosage compensation [partof: 0007549 ]
+0007551 = maintenance of dosage compensation [partof: 0007549 ]
+0045814 = negative regulation of gene expression, epigenetic [isa: 0040029 ]
+0045857 = negative regulation of protein activity, epigenetic [isa: 0040030 0045814 ]
+0045815 = positive regulation of gene expression, epigenetic [isa: 0040029 ]
+0045858 = positive regulation of protein activity, epigenetic [isa: 0040030 0045815 ]
+0040030 = regulation of protein activity, epigenetic [isa: 0040029 ]
+0000003 = reproduction [isa: 0007275 ]
+0019954 = asexual reproduction [isa: 0000003 ]
+0009566 = fertilization [isa: 0000003 ]
+0009677 = double fertilization (sensu Gnetophyta) [isa: 0009566 ]
+0009567 = double fertilization (sensu Magnoliophyta) [isa: 0009566 ]
+0007338 = fertilization (sensu Animalia) [isa: 0009566 ]
+0007340 = acrosome reaction [partof: 0007338 ]
+0007339 = binding of sperm to zona pellucida [partof: 0007338 ]
+0007342 = binding/fusion of sperm to egg plasma membrane [partof: 0007338 ]
+0007343 = egg activation [partof: 0007338 ]
+0007341 = penetration of zona pellucida [partof: 0007338 ]
+0007344 = pronuclear fusion [partof: 0007338 ]
+0007276 = gametogenesis [isa: 0000003 ]
+0009552 = gametogenesis (sensu Magnoliophyta) [isa: 0007276 ]
+0009553 = megagametogenesis [partof: 0009552 ]
+0009557 = antipodal cell differentiation [partof: 0009553 ]
+0045688 = regulation of antipodal cell differentiation [partof: 0009557 ]
+0045689 = negative regulation of antipodal cell differentiation [isa: 0045688 ]
+0045690 = positive regulation of antipodal cell differentiation [isa: 0045688 ]
+0009558 = cellularization of megagametophyte [partof: 0009553 ]
+0009559 = female gametophyte central cell differentiation [partof: 0009553 ]
+0045691 = regulation of female gametophyte central cell differentiation [partof: 0009559 ]
+0045692 = negative regulation of female gametophyte central cell differentiation [isa: 0045691 ]
+0045693 = positive regulation of female gametophyte central cell differentiation [isa: 0045691 ]
+0009560 = female gametophyte egg cell differentiation [partof: 0009553 ]
+0045694 = regulation of female gametophyte egg cell differentiation [partof: 0009560 ]
+0045695 = negative regulation of female gametophyte egg cell differentiation [isa: 0045694 ]
+0045696 = positive regulation of female gametophyte egg cell differentiation [isa: 0045694 ]
+0009561 = megagametophyte nuclear division [partof: 0009553 ]
+0009562 = megagametophyte nuclear migration [partof: 0009553 ]
+0009563 = synergid cell differentiation [partof: 0009553 ]
+0045697 = regulation of synergid cell differentiation [partof: 0009563 ]
+0045698 = negative regulation of synergid cell differentiation [isa: 0045697 ]
+0045699 = positive regulation of synergid cell differentiation [isa: 0045697 ]
+0009554 = megasporogenesis [partof: 0009552 ]
+0009555 = microgametogenesis [partof: 0009552 ]
+0009564 = formation of generative and vegetative cell [partof: 0009555 ]
+0009556 = microsporogenesis [partof: 0009552 ]
+0007281 = germ-cell development [partof: 0007276 ]
+0007292 = oogenesis [isa: 0007276 ]
+0008069 = dorsal/ventral axis determination, follicular epithelium [isa: 0007292 ]
+0008070 = maternal determination of dorsal/ventral axis, follicular epithelium, germ-line encoded [isa: 0008069 ]
+0008071 = maternal determination of dorsal/ventral axis, follicular epithelium, soma encoded [isa: 0008069 ]
+0007293 = egg chamber formation [partof: 0007292 ]
+0016350 = maintenance of oocyte identity [partof: 0007293 ]
+0007294 = oocyte determination [partof: 0007293 ]
+0007295 = egg chamber growth [partof: 0007292 ]
+0007304 = eggshell formation [partof: 0007292 ]
+0007306 = insect chorion formation [partof: 0007304 ]
+0007307 = chorion gene amplification [partof: 0007306 ]
+0007305 = vitelline membrane formation [partof: 0007304 ]
+0007299 = follicle cell adhesion [partof: 0007292 ]
+0007300 = nurse cell/oocyte transport [partof: 0007292 ]
+0007302 = nurse cell nucleus anchoring [partof: 0007300 ]
+0007301 = ring canal formation [partof: 0007300 ]
+0008335 = ring canal stabilization [partof: 0007300 ]
+0007308 = oocyte construction [partof: 0007292 ]
+0042070 = oocyte nucleus anchoring [partof: 0007308 ]
+0001556 = oocyte maturation [partof: 0007292 ]
+0007296 = vitellogenesis [partof: 0007292 ]
+0007277 = pole cell development [partof: 0007276 ]
+0007278 = pole cell determination [partof: 0007277 ]
+0007279 = pole cell formation [partof: 0007277 ]
+0007283 = spermatogenesis [isa: 0007276 ]
+0007285 = primary spermatocyte growth [partof: 0007283 ]
+0007286 = spermatid development [partof: 0007283 ]
+0001675 = acrosome formation [partof: 0007286 ]
+0007288 = axoneme assembly [partof: 0007286 ]
+0007291 = sperm individualization [partof: 0007286 ]
+0007289 = spermatid nuclear differentiation [partof: 0007286 ]
+0045700 = regulation of spermatid nuclear differentiation [partof: 0007289 ]
+0045701 = negative regulation of spermatid nuclear differentiation [isa: 0045700 ]
+0045702 = positive regulation of spermatid nuclear differentiation [isa: 0045700 ]
+0007290 = spermatid nuclear elongation [partof: 0007286 ]
+0019953 = sexual reproduction [isa: 0000003 ]
+0009835 = ripening [isa: 0007275 ]
+0009836 = ripening (climacteric type) [isa: 0009835 ]
+0009837 = ripening (non-climacteric type) [isa: 0009835 ]
+0007530 = sex determination [isa: 0007275 ]
+0030237 = female sex determination [isa: 0007530 ]
+0019099 = female germ-line sex determination [isa: 0018992 0030237 ]
+0019101 = female somatic sex determination [isa: 0018993 0030237 ]
+0018992 = germ-line sex determination [isa: 0007530 ]
+0007547 = germ-line processes downstream of sex determination signal [isa: 0007545 ] [partof: 0018992 ]
+0040021 = hermaphrodite germ-line sex determination [isa: 0018992 ]
+0042005 = hermaphrodite germ-line sex determination (sensu Nematoda) [isa: 0040021 ]
+0040022 = feminization of hermaphroditic germ-line (sensu Nematoda) [isa: 0042005 ]
+0042006 = masculinization of hermaphroditic germ-line (sensu Nematoda) [isa: 0042005 ]
+0019100 = male germ-line sex determination [isa: 0018992 0030238 ]
+0007542 = primary sex determination, germ-line [isa: 0007538 ] [partof: 0018992 ]
+0007544 = sex determination, female germ-line determination [partof: 0007542 ]
+0007543 = sex determination, somatic/gonadal interaction [partof: 0007542 ]
+0030238 = male sex determination [isa: 0007530 ]
+0019102 = male somatic sex determination [isa: 0018993 0030238 ]
+0007531 = mating-type determination [isa: 0007530 ]
+0007533 = mating-type switching/recombination [isa: 0007531 ]
+0007535 = donor preference [partof: 0007533 ]
+0007536 = activation of recombination (HML) [isa: 0007535 ]
+0007537 = inactivation of recombination (HML) [isa: 0007535 ]
+0007538 = primary sex determination [isa: 0007530 ]
+0007539 = primary sex determination, soma [isa: 0007538 ] [partof: 0018993 ]
+0007540 = sex determination, establishment of X:A ratio [partof: 0007539 ]
+0007541 = sex determination, primary response to X:A ratio [partof: 0007539 ]
+0007545 = processes downstream of sex determination signal [isa: 0007530 ]
+0007546 = somatic processes downstream of sex determination signal [isa: 0007545 ]
+0018993 = somatic sex determination [isa: 0007530 ]
+0042001 = hermaphrodite somatic sex determination [isa: 0018993 ]
+0042002 = hermaphrodite somatic sex determination (sensu Nematoda) [isa: 0042001 ]
+0042004 = feminization of hermaphrodite soma (sensu Nematoda) [isa: 0042002 ]
+0042003 = masculinization of hermaphrodite soma (sensu Nematoda) [isa: 0042002 ]
+0007548 = sex differentiation [isa: 0007275 ]
+0045137 = development of primary sexual characteristics [partof: 0007548 ]
+0046545 = development of primary female sexual characteristics [isa: 0045137 ] [partof: 0046660 ]
+0046546 = development of primary male sexual characteristics [isa: 0045137 ] [partof: 0046661 ]
+0045136 = development of secondary sexual characteristics [partof: 0007548 ]
+0046543 = development of secondary female sexual characteristics [isa: 0045136 ] [partof: 0046660 ]
+0046544 = development of secondary male sexual characteristics [isa: 0045136 ] [partof: 0046661 ]
+0046660 = female sex differentiation [isa: 0007548 ]
+0046661 = male sex differentiation [isa: 0007548 ]
+0019827 = stem cell maintenance [isa: 0007275 ]
+0008371 = obsolete [isa: 0008150 ]
+0046227 = 2,4,5-trichlorophenoxyacetic acid biosynthesis [isa: 0008371 ]
+0046255 = 2,4,6-trinitrotoluene biosynthesis [isa: 0008371 ]
+0046297 = 2,4-dichlorobenzoate biosynthesis [isa: 0008371 ]
+0046299 = 2,4-dichlorophenoxyacetic acid biosynthesis [isa: 0008371 ]
+0046229 = 2-aminobenzenesulfonate biosynthesis [isa: 0008371 ]
+0046301 = 2-chloro-N-isopropylacetanilide biosynthesis [isa: 0008371 ]
+0046303 = 2-nitropropane biosynthesis [isa: 0008371 ]
+0046233 = 3-hydroxyphenylacetate biosynthesis [isa: 0008371 ]
+0046195 = 4-nitrophenol biosynthesis [isa: 0008371 ]
+0046261 = 4-nitrotoluene biosynthesis [isa: 0008371 ]
+0046270 = 4-toluenecarboxylate biosynthesis [isa: 0008371 ]
+0046291 = 6-hydroxycineole biosynthesis [isa: 0008371 ]
+0007012 = actin cytoskeleton reorganization [isa: 0008371 ]
+0007013 = actin modification [isa: 0008371 ]
+0018086 = alanine racemization [isa: 0008371 ]
+0006838 = allantoin/allantoate transport [isa: 0008371 ]
+0046257 = anaerobic 2,4,6-trinitrotoluene biosynthesis [isa: 0008371 ]
+0046253 = anaerobic toluene biosynthesis [isa: 0008371 ]
+0006328 = AT binding [isa: 0008371 ]
+0006326 = bent DNA binding [isa: 0008371 ]
+0007115 = bud site selection/establishment of cell polarity (sensu Saccharomyces) [isa: 0008371 ]
+0006503 = C-terminal protein farnesylation [isa: 0008371 ]
+0006504 = C-terminal protein geranylgeranylation [isa: 0008371 ]
+0006502 = C-terminal protein prenylation [isa: 0008371 ]
+0008161 = carbamate resistance [isa: 0008371 ]
+0046231 = carbazole biosynthesis [isa: 0008371 ]
+0007002 = centromere binding [isa: 0008371 ]
+0000068 = chromosome condensation [isa: 0008371 ]
+0006764 = coenzyme A biosynthesis [isa: 0008371 ]
+0006765 = coenzyme A catabolism [isa: 0008371 ]
+0006763 = coenzyme A metabolism [isa: 0008371 ]
+0006920 = commitment to apoptosis [isa: 0008371 ]
+0046198 = cresol biosynthesis [isa: 0008371 ]
+0008162 = cyclodiene resistance [isa: 0008371 ]
+0007104 = cytokinesis [isa: 0008371 ]
+0008163 = DDT resistance [isa: 0008371 ]
+0009614 = disease resistance [isa: 0008371 ]
+0016924 = double-strand break repair via homologous recombination [isa: 0008371 ]
+0009633 = drought tolerance [isa: 0008371 ]
+0009315 = drug resistance [isa: 0008371 ]
+0007345 = embryogenesis and morphogenesis [isa: 0008371 ]
+0046234 = fluorene biosynthesis [isa: 0008371 ]
+0009632 = freezing tolerance [isa: 0008371 ]
+0045195 = gallstone formation [isa: 0008371 ]
+0007397 = histogenesis and organogenesis [isa: 0008371 ]
+0015832 = holin [isa: 0008371 ]
+0006918 = induction of apoptosis by p53 [isa: 0008371 ]
+0019936 = inositol phospholipid-mediated signaling [isa: 0008371 ]
+0006806 = insecticide resistance [isa: 0008371 ]
+0018300 = iron incorporation into iron-sulfur cluster via hexakis-L-cysteinyl hexairon hexasulfide [isa: 0008371 ]
+0018286 = iron incorporation into iron-sulfur cluster via tris-L-cysteinyl triiron trisulfide [isa: 0008371 ]
+0006717 = juvenile hormone binding [isa: 0008371 ]
+0007583 = killer activity [isa: 0008371 ]
+0006630 = lipid binding [isa: 0008371 ]
+0030068 = lytic viral life cycle [isa: 0008371 ]
+0046200 = m-cresol biosynthesis [isa: 0008371 ]
+0046241 = m-xylene biosynthesis [isa: 0008371 ]
+0018927 = methionine and threonine metabolism [isa: 0008371 ]
+0046212 = methyl ethyl ketone biosynthesis [isa: 0008371 ]
+0001506 = neurotransmitter biosynthesis and storage [isa: 0008371 ]
+0046262 = nitrotoluene biosynthesis [isa: 0008371 ]
+0016583 = nucleosome modeling [isa: 0008371 ]
+0046242 = o-xylene biosynthesis [isa: 0008371 ]
+0007048 = oncogenesis [isa: 0008371 ]
+0008164 = organophosphorous resistance [isa: 0008371 ]
+0006126 = other pathways of electron transport [isa: 0008371 ]
+0046243 = p-xylene biosynthesis [isa: 0008371 ]
+0046194 = pentachlorophenol biosynthesis [isa: 0008371 ]
+0006483 = peptidyl-aspartic acid/asparagine hydroxylation [isa: 0008371 ]
+0006460 = peptidyl-prolyl isomerase B reaction [isa: 0008371 ]
+0046237 = phenanthrene biosynthesis [isa: 0008371 ]
+0009587 = phototrophin mediated phototransduction [isa: 0008371 ]
+0046238 = phthalate biosynthesis [isa: 0008371 ]
+0006380 = poly-A binding [isa: 0008371 ]
+0018338 = protein amino acid cinnamylation [isa: 0008371 ]
+0018314 = protein-pyrroloquinoline-quinone linkage [isa: 0008371 ]
+0006143 = purine metabolism [isa: 0008371 ]
+0008165 = pyrethroid resistance [isa: 0008371 ]
+0006205 = pyrimidine metabolism [isa: 0008371 ]
+0006291 = pyrimidine-dimer repair, DNA damage excision [isa: 0008371 ]
+0006292 = pyrimidine-dimer repair, DNA damage recognition [isa: 0008371 ]
+0006327 = random coil binding [isa: 0008371 ]
+0009619 = resistance to pathogenic bacteria [isa: 0008371 ]
+0009622 = resistance to pathogenic fungi [isa: 0008371 ]
+0001564 = resistance to pathogenic protozoa [isa: 0008371 ]
+0006329 = satellite DNA binding [isa: 0008371 ]
+0008167 = sigma virus replication [isa: 0008371 ]
+0006330 = single-stranded DNA binding [isa: 0008371 ]
+0006832 = small molecule transport [isa: 0008371 ]
+0006815 = sodium/potassium transport [isa: 0008371 ]
+0046245 = styrene biosynthesis [isa: 0008371 ]
+0007003 = telomere binding [isa: 0008371 ]
+0006495 = terminal O-glycosylation [isa: 0008371 ]
+0046264 = thiocyanate biosynthesis [isa: 0008371 ]
+0046252 = toluene biosynthesis [isa: 0008371 ]
+0046268 = toluene-4-sulfonate biosynthesis [isa: 0008371 ]
+0046266 = triethanolamine biosynthesis [isa: 0008371 ]
+0046259 = trinitrotoluene biosynthesis [isa: 0008371 ]
+0006905 = vesicle transport [isa: 0008371 ]
+0008166 = viral replication [isa: 0008371 ]
+0009406 = virulence [isa: 0008371 ]
+0046240 = xylene biosynthesis [isa: 0008371 ]
+0007582 = physiological processes [isa: 0008150 ]
+0008218 = bioluminescence [isa: 0007582 ]
+0045453 = bone resorption [isa: 0007582 ]
+0045124 = regulation of bone resorption [partof: 0045453 ]
+0045779 = negative regulation of bone resorption [isa: 0045124 ]
+0045780 = positive regulation of bone resorption [isa: 0045124 ]
+0009758 = carbohydrate utilization [isa: 0007582 ]
+0008015 = circulation [isa: 0007582 ]
+0008217 = regulation of blood pressure [isa: 0008015 ]
+0045776 = negative regulation of blood pressure [isa: 0008217 ]
+0045777 = positive regulation of blood pressure [isa: 0008217 ]
+0008016 = regulation of heart [partof: 0008015 ]
+0045822 = negative regulation of heart [isa: 0008016 ]
+0045823 = positive regulation of heart [isa: 0008016 ]
+0042310 = vasoconstriction [isa: 0008015 ]
+0019229 = regulation of vasoconstriction [partof: 0042310 ]
+0045906 = negative regulation of vasoconstriction [isa: 0019229 ]
+0045907 = positive regulation of vasoconstriction [isa: 0019229 ]
+0042311 = vasodilation [isa: 0008015 ]
+0042312 = regulation of vasodilation [partof: 0042311 ]
+0045908 = negative regulation of vasodilation [isa: 0042312 ]
+0045909 = positive regulation of vasodilation [isa: 0042312 ]
+0042335 = cuticle biosynthesis [isa: 0007582 ]
+0007592 = cuticle biosynthesis (sensu Invertebrata) [isa: 0042335 ]
+0040003 = cuticle biosynthesis (sensu Insecta) [isa: 0007592 ]
+0008365 = adult cuticle biosynthesis (sensu Insecta) [isa: 0040003 ]
+0042337 = cuticle biosynthesis during molting (sensu Insecta) [isa: 0040003 0042336 ] [partof: 0007591 ]
+0008362 = embryonic cuticle biosynthesis (sensu Insecta) [isa: 0040003 ]
+0040002 = cuticle biosynthesis (sensu Nematoda) [isa: 0007592 ]
+0042338 = cuticle biosynthesis during molting (sensu Nematoda) [isa: 0040002 0042336 ] [partof: 0018996 ]
+0042336 = cuticle biosynthesis during molting (sensu Invertebrata) [isa: 0007592 ] [partof: 0018988 ]
+0009900 = dehiscence [isa: 0007582 ]
+0009901 = anther dehiscence [isa: 0009900 ]
+0007586 = digestion [isa: 0007582 ]
+0030299 = cholesterol absorption [partof: 0007586 ]
+0030300 = regulation of cholesterol absorption [partof: 0030299 ]
+0045796 = negative regulation of cholesterol absorption [isa: 0030300 ]
+0045797 = positive regulation of cholesterol absorption [isa: 0030300 ]
+0001696 = gastric acid secretion [partof: 0007586 ]
+0001699 = acetylcholine-induced gastric acid secretion [isa: 0001696 ]
+0001698 = gastrin-induced gastric acid secretion [isa: 0001696 ]
+0001697 = histamine-induced gastric acid secretion [isa: 0001696 ]
+0030277 = maintenance of gastrointestinal epithelium [partof: 0007586 ]
+0030157 = pancreatic juice secretion [partof: 0007586 ]
+0046541 = saliva secretion [partof: 0007586 ]
+0007587 = sugar utilization [isa: 0007586 ]
+0030146 = diuresis [isa: 0007582 ]
+0007588 = excretion [isa: 0007582 ]
+0030421 = defecation [isa: 0007588 ]
+0007589 = fluid secretion [isa: 0007588 ]
+0030147 = natriuresis [isa: 0007588 ]
+0030198 = extracellular matrix organization and biogenesis [isa: 0007582 ]
+0030199 = collagen fibril organization [isa: 0030198 ]
+0007599 = hemostasis [isa: 0007582 ]
+0007596 = blood coagulation [isa: 0007599 ]
+0007598 = blood coagulation, extrinsic pathway [isa: 0007596 ]
+0007597 = blood coagulation, intrinsic pathway [isa: 0007596 ]
+0030168 = platelet activation [partof: 0007596 ]
+0030193 = regulation of blood coagulation [partof: 0007596 ]
+0030195 = negative regulation of blood coagulation [isa: 0030193 ]
+0030194 = positive regulation of blood coagulation [isa: 0030193 ]
+0020021 = host cell immortalization [isa: 0007582 ]
+0020012 = immune evasion [isa: 0007582 ]
+0020033 = antigenic variation [isa: 0020012 ]
+0007595 = lactation [isa: 0007582 ]
+0042303 = molting cycle [isa: 0007582 ]
+0018988 = molting cycle (sensu Invertebrata) [isa: 0042303 ]
+0040006 = cuticular attachment to epithelium (sensu Invertebrata) [partof: 0018988 ]
+0040005 = cuticular attachment to epithelium (sensu Insecta) [isa: 0040006 ] [partof: 0007591 ]
+0040004 = cuticular attachment to epithelium (sensu Nematoda) [isa: 0040006 ] [partof: 0018996 ]
+0042394 = ecdysis (sensu Invertebrata) [partof: 0018988 ]
+0018990 = ecdysis (sensu Insecta) [isa: 0042394 ] [partof: 0007591 ]
+0042395 = ecdysis (sensu Nematoda) [isa: 0042394 ] [partof: 0018996 ]
+0007591 = molting cycle (sensu Insecta) [isa: 0018988 ]
+0018989 = apolysis [partof: 0007591 ]
+0007594 = puparial adhesion [partof: 0007591 ]
+0018996 = molting cycle (sensu Nematoda) [isa: 0018988 ]
+0009877 = nodulation [isa: 0007582 ]
+0009935 = nutrient uptake [isa: 0007582 ]
+0007584 = nutritional response pathway [isa: 0007582 ]
+0007567 = parturition [isa: 0007582 ]
+0009405 = pathogenesis [isa: 0007582 ]
+0030432 = peristalsis [isa: 0007582 ]
+0015979 = photosynthesis [isa: 0007582 ]
+0001663 = physiological fear response [isa: 0007582 ]
+0009856 = post-pollination [isa: 0007582 ]
+0009860 = pollen tube growth [partof: 0009856 ]
+0007565 = pregnancy [isa: 0007582 ]
+0007566 = embryo implantation [partof: 0007565 ]
+0007585 = respiratory gaseous exchange [isa: 0007582 ]
+0030431 = sleep [isa: 0007582 ]
+0030104 = water homeostasis [isa: 0007582 ]
+0016032 = viral life cycle [isa: 0008150 ]
+0019042 = latent virus infection [isa: 0016032 ]
+0019043 = establishment of viral latency [partof: 0019042 ]
+0019044 = latent virus maintenance [partof: 0019042 ]
+0019045 = latent virus replication [partof: 0019042 ]
+0019046 = reactivation of latent virus [partof: 0019042 ]
+0030069 = lysogeny [isa: 0016032 ]
+0019058 = viral infectious cycle [isa: 0016032 ]
+0019059 = initiation of viral infection [partof: 0019058 ]
+0019061 = viral uncoating [partof: 0019059 ]
+0019062 = virion attachment [partof: 0019059 ]
+0019063 = virion penetration [partof: 0019059 ]
+0046596 = regulation of virion penetration [partof: 0019063 ]
+0046597 = negative regulation of virion penetration [isa: 0046596 ]
+0046598 = positive regulation of virion penetration [isa: 0046596 ]
+0019066 = viral translocation [partof: 0019063 ]
+0019067 = viral assembly, maturation, and release [partof: 0019058 ]
+0019068 = viral assembly [partof: 0019067 ]
+0019069 = viral capsid assembly [partof: 0019068 ]
+0019070 = viral genome maturation [partof: 0019068 ]
+0019071 = viral DNA cleavage [partof: 0019070 ]
+0019072 = viral genome packaging [partof: 0019068 ]
+0019074 = viral RNA genome packaging [isa: 0019072 ]
+0019075 = viral particle maturation [partof: 0019067 ]
+0019076 = viral release [partof: 0019067 ]
+0019077 = lytic viral release [isa: 0019076 ]
+0019078 = viral budding [isa: 0019076 ]
+0019080 = viral genome expression [partof: 0019058 ]
+0019079 = viral genome replication [partof: 0019058 ]
+0045069 = regulation of viral genome replication [partof: 0019079 ]
+0045071 = negative regulation of viral genome replication [isa: 0045069 ]
+0045070 = positive regulation of viral genome replication [isa: 0045069 ]
+0045090 = retroviral genome replication [isa: 0019079 ]
+0045091 = regulation of retroviral genome replication [partof: 0045090 ]
+0045869 = negative regulation of retroviral genome replication [isa: 0045091 ]
+0045870 = positive regulation of retroviral genome replication [isa: 0045091 ]
+0019087 = viral transformation [isa: 0016032 ]
+0019088 = viral immortalization [isa: 0019087 ]
+0019089 = viral transmission [isa: 0016032 ]
diff --git a/application/src/test/resources/testData/humanKeggAndGO/human.syno b/application/src/test/resources/testData/humanKeggAndGO/human.syno
new file mode 100644
index 0000000..d962c02
--- /dev/null
+++ b/application/src/test/resources/testData/humanKeggAndGO/human.syno
@@ -0,0 +1,17 @@
+Homo sapiens
+NP_001366 aaa AAA
+NP_005289 bbb BBB
+NP_005756 ccc CCC
+NP_002864 ddd DDD
+NP_003772 eee EEE
+NP_015560 fff FFF
+NP_015628 ggg GGG
+NP_004726 hhh HHH
+NP_004801 iii III
+NP_002574 jjj JJJ
+NP_055145 kkk KKK
+NP_006388 mmm MMM
+NP_005623 nnn NNN
+NP_003558 ooo OOO
+NP_003599 ppp PPP
+NP_647593 qqq QQQ
diff --git a/application/src/test/resources/testData/humanKeggAndGO/kegg.anno b/application/src/test/resources/testData/humanKeggAndGO/kegg.anno
new file mode 100644
index 0000000..8a34d4b
--- /dev/null
+++ b/application/src/test/resources/testData/humanKeggAndGO/kegg.anno
@@ -0,0 +1,40 @@
+(species=Homo sapiens) (type=Metabolic Pathways) (curator=KEGG)
+NP_001366 = 251
+NP_001366 = 10
+NP_005289 = 71
+NP_647593 = 120
+NP_647593 = 350
+NP_647593 = 561
+NP_647593 = 260
+NP_647593 = 300
+NP_647593 = 40
+NP_005756 = 520
+NP_002864 = 500
+NP_002864 = 340
+NP_002864 = 400
+NP_002864 = 100
+NP_002864 = 650
+NP_002864 = 62
+NP_003772 = 71
+NP_015560 = 280
+NP_015628 = 310
+NP_004726 = 380
+NP_004801 = 632
+NP_004801 = 650
+NP_004801 = 62
+NP_004801 = 71
+NP_002574 = 280
+NP_002574 = 310
+NP_002574 = 380
+NP_055145 = 632
+NP_055145 = 20
+NP_055145 = 620
+NP_006388 = 630
+NP_006388 = 710
+NP_005623 = 720
+NP_003558 = 20
+NP_003558 = 720
+NP_003558 = 480
+NP_003599 = 260
+NP_003599 = 61
+NP_003599 = 61
diff --git a/application/src/test/resources/testData/humanKeggAndGO/kegg.onto b/application/src/test/resources/testData/humanKeggAndGO/kegg.onto
new file mode 100644
index 0000000..ad44540
--- /dev/null
+++ b/application/src/test/resources/testData/humanKeggAndGO/kegg.onto
@@ -0,0 +1,196 @@
+(curator=KEGG) (type=Metabolic Pathways)
+90001 = Metabolism
+80001 = Carbohydrate Metabolism [isa: 90001 ]
+80003 = Lipid Metabolism [isa: 90001 ]
+80002 = Energy Metabolism [isa: 90001 ]
+80004 = Nucleotide Metabolism [isa: 90001 ]
+80005 = Amino Acid Metabolism [isa: 90001 ]
+80006 = Metabolism of Other Amino Acids [isa: 90001 ]
+80007 = Metabolism of Complex Carbohydrates [isa: 90001 ]
+80008 = Metabolism of Complex Lipids [isa: 90001 ]
+80009 = Metabolism of Cofactors and Vitamins [isa: 90001 ]
+80010 = Biosynthesis of Secondary Metabolites [isa: 90001 ]
+80011 = Biodegradation of Xenobiotics [isa: 90001 ]
+80101 = Unknown Carbohydrate Metabolism Subtype [isa: 80001 ]
+80103 = Unknown Lipid Metabolism Subtype [isa: 80003 ]
+80102 = Unknown Energy Metabolism Subtype [isa: 80002 ]
+80104 = Unknown Nucleotide Metabolism Subtype [isa: 80004 ]
+80105 = Unknown Amino Acid Metabolism Subtype [isa: 80005 ]
+80106 = Unknown Metabolism of Other Amino Acids Subtype [isa: 80006 ]
+80107 = Unknown Metabolism of Complex Carbohydrates Subtype [isa: 80007 ]
+80108 = Unknown Metabolism of Complex Lipids Subtype [isa: 80008 ]
+80109 = Unknown Metabolism of Cofactors and Vitamins Subtype [isa: 80009 ]
+80110 = Unknown Biosynthesis of Secondary Metabolites Subtype [isa: 80010 ]
+80111 = Unknown Biodegradation of Xenobiotics Subtype [isa: 80011 ]
+00010 = Glycolysis / Gluconeogenesis [isa: 80001 ]
+00020 = Citrate cycle (TCA cycle) [isa: 80001 ]
+00030 = Pentose phosphate pathway [isa: 80001 ]
+00040 = Pentose and glucuronate interconversions [isa: 80001 ]
+00051 = Fructose and mannose metabolism [isa: 80001 ]
+00052 = Galactose metabolism [isa: 80001 ]
+00053 = Ascorbate and aldarate metabolism [isa: 80001 ]
+00620 = Pyruvate metabolism [isa: 80001 ]
+00630 = Glyoxylate and dicarboxylate metabolism [isa: 80001 ]
+00640 = Propanoate metabolism [isa: 80001 ]
+00650 = Butanoate metabolism [isa: 80001 ]
+00660 = C5-Branched dibasic acid metabolism [isa: 80001 ]
+00031 = Inositol metabolism [isa: 80001 ]
+00190 = Oxidative phosphorylation [isa: 80002 ]
+00193 = ATP Synthesis [isa: 80002 ]
+00195 = Photosynthesis [isa: 80002 ]
+00710 = Carbon fixation [isa: 80002 ]
+00720 = Reductive carboxylate cycle (CO2 fixation) [isa: 80002 ]
+00680 = Methane metabolism [isa: 80002 ]
+00910 = Nitrogen metabolism [isa: 80002 ]
+00920 = Sulfur metabolism [isa: 80002 ]
+00061 = Fatty acid biosynthesis (path 1) [isa: 80003 ]
+00062 = Fatty acid biosynthesis (path 2) [isa: 80003 ]
+00071 = Fatty acid metabolism [isa: 80003 ]
+00072 = Synthesis and degradation of ketone bodies [isa: 80003 ]
+00100 = Sterol biosynthesis [isa: 80003 ]
+00120 = Bile acid biosynthesis [isa: 80003 ]
+00140 = C21-Steroid hormone metabolism [isa: 80003 ]
+00150 = Androgen and estrogen metabolism [isa: 80003 ]
+00230 = Purine metabolism [isa: 80004 ]
+00240 = Pyrimidine metabolism [isa: 80004 ]
+00520 = Nucleotide sugars metabolism [isa: 80004 ]
+00251 = Glutamate metabolism [isa: 80005 ]
+00252 = Alanine and aspartate metabolism [isa: 80005 ]
+00260 = Glycine, serine and threonine metabolism [isa: 80005 ]
+00271 = Methionine metabolism [isa: 80005 ]
+00272 = Cysteine metabolism [isa: 80005 ]
+00280 = Valine, leucine and isoleucine degradation [isa: 80005 ]
+00290 = Valine, leucine and isoleucine biosynthesis [isa: 80005 ]
+00300 = Lysine biosynthesis [isa: 80005 ]
+00310 = Lysine degradation [isa: 80005 ]
+00330 = Arginine and proline metabolism [isa: 80005 ]
+00340 = Histidine metabolism [isa: 80005 ]
+00350 = Tyrosine metabolism [isa: 80005 ]
+00360 = Phenylalanine metabolism [isa: 80005 ]
+00380 = Tryptophan metabolism [isa: 80005 ]
+00400 = Phenylalanine, tyrosine and tryptophan biosynthesis [isa: 80005 ]
+00220 = Urea cycle and metabolism of amino groups [isa: 80005 ]
+00410 = beta-Alanine metabolism [isa: 80006 ]
+00430 = Taurine and hypotaurine metabolism [isa: 80006 ]
+00440 = Aminophosphonate metabolism [isa: 80006 ]
+00450 = Selenoamino acid metabolism [isa: 80006 ]
+00460 = Cyanoamino acid metabolism [isa: 80006 ]
+00471 = D-Glutamine and D-glutamate metabolism [isa: 80006 ]
+00472 = D-Arginine and D-ornithine metabolism [isa: 80006 ]
+00473 = D-Alanine metabolism [isa: 80006 ]
+00480 = Glutathione metabolism [isa: 80006 ]
+00500 = Starch and sucrose metabolism [isa: 80007 ]
+00510 = Glycoprotein biosynthesis [isa: 80007 ]
+00511 = Glycoprotein degradation [isa: 80007 ]
+00530 = Aminosugars metabolism [isa: 80007 ]
+00540 = Lipopolysaccharide biosynthesis [isa: 80007 ]
+00550 = Peptidoglycan biosynthesis [isa: 80007 ]
+00531 = Glycosaminoglycan degradation [isa: 80007 ]
+00532 = Chondroitin / Heparan sulfate biosynthesis [isa: 80007 ]
+00533 = Keratan sulfate biosynthesis [isa: 80007 ]
+00561 = Glycerolipid metabolism [isa: 80008 ]
+00563 = Glycosylphosphatidylinositol(GPI)-anchor biosynthesis [isa: 80008 ]
+00562 = Inositol phosphate metabolism [isa: 80008 ]
+00570 = Sphingophospholipid biosynthesis [isa: 80008 ]
+00580 = Phospholipid degradation [isa: 80008 ]
+00600 = Sphingoglycolipid metabolism [isa: 80008 ]
+00601 = Blood group glycolipid biosynthesis - lact series [isa: 80008 ]
+00602 = Blood group glycolipid biosynthesis - neolact series [isa: 80008 ]
+00603 = Globoside metabolism [isa: 80008 ]
+00590 = Prostaglandin and leukotriene metabolism [isa: 80008 ]
+00730 = Thiamine metabolism [isa: 80009 ]
+00740 = Riboflavin metabolism [isa: 80009 ]
+00750 = Vitamin B6 metabolism [isa: 80009 ]
+00760 = Nicotinate and nicotinamide metabolism [isa: 80009 ]
+00770 = Pantothenate and CoA biosynthesis [isa: 80009 ]
+00780 = Biotin metabolism [isa: 80009 ]
+00790 = Folate biosynthesis [isa: 80009 ]
+00670 = One carbon pool by folate [isa: 80009 ]
+00830 = Retinol metabolism [isa: 80009 ]
+00860 = Porphyrin and chlorophyll metabolism [isa: 80009 ]
+00130 = Ubiquinone biosynthesis [isa: 80009 ]
+00900 = Terpenoid biosynthesis [isa: 80010 ]
+00940 = Flavonoids, stilbene and lignin biosynthesis [isa: 80010 ]
+00950 = Alkaloid biosynthesis I [isa: 80010 ]
+00960 = Alkaloid biosynthesis II [isa: 80010 ]
+00311 = Penicillins and cephalosporins biosynthesis [isa: 80010 ]
+01210 = beta-Lactam resistanse [isa: 80010 ]
+00521 = Streptomycin biosynthesis [isa: 80010 ]
+00522 = Erythromycin biosynthesis [isa: 80010 ]
+00253 = Tetracycline biosynthesis [isa: 80010 ]
+00331 = Clavulanic acid biosynthesis [isa: 80010 ]
+00231 = Puromycin biosynthesis [isa: 80010 ]
+00930 = Caprolactam degradation [isa: 80011 ]
+00621 = Biphenyl degradation [isa: 80011 ]
+00622 = Toluene degradation [isa: 80011 ]
+00361 = gamma-Hexachlorocyclohexane degradation [isa: 80011 ]
+00641 = 3-Chloroacrylic acid degradation [isa: 80011 ]
+00351 = 1,1,1-Trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) degradation [isa: 80011 ]
+00623 = 2,4-Dichlorobenzoate degradation [isa: 80011 ]
+00631 = 1,2-Dichloroethane degradation [isa: 80011 ]
+00624 = Xylene degradation [isa: 80011 ]
+00625 = Tetrachloroethene degradation [isa: 80011 ]
+00643 = Styrene degradation [isa: 80011 ]
+00627 = 1,4-Dichlorobenzene degradation [isa: 80011 ]
+00626 = Nitorobenzene degradation [isa: 80011 ]
+00642 = Ethylbenzene degradation [isa: 80011 ]
+00628 = Fluorene degradation [isa: 80011 ]
+00629 = Carbazole degradation [isa: 80011 ]
+00632 = Benzoate degradation [isa: 80011 ]
+00791 = Atrazine degradation [isa: 80011 ]
+90002 = Genetic Information Processing
+81001 = Transcription [isa: 90002 ]
+81101 = Unknown Transcription Subtype [isa: 81001 ]
+03020 = RNA polymerase [isa: 81001 ]
+03022 = Transcription factors [isa: 81001 ]
+03040 = Spliceosome [isa: 81001 ]
+81002 = Translation [isa: 90002 ]
+81102 = Unknown Translation Subtype[isa: 81002 ]
+03010 = Ribosome [isa: 81002 ]
+03012 = Translation factors [isa: 81002 ]
+00970 = Aminoacyl-tRNA biosynthesis [isa: 81002 ]
+81003 = Sorting and Degradation [isa: 90002 ]
+03060 = Protein export [isa: 81003 ]
+03070 = Type III secretion system [isa: 81003 ]
+03080 = Type IV secretion system [isa: 81003 ]
+03018 = RNA degradosome [isa: 81003 ]
+04120 = Ubiquitin mediated proteolysis [isa: 81003 ]
+03050 = Proteasome [isa: 81003 ]
+81004 = Replication and Repair [isa: 90002 ]
+81104 = Unknown Replication and Repair Subtype [isa: 81004 ]
+03030 = DNA polymerase [isa: 81004 ]
+03032 = Replication Complex [isa: 81004 ]
+90003 = Environmental Information Processing
+82001 = Membrane Transport [isa: 90003 ]
+82101 = Unknown Membrane Transport Subtype [isa: 82001 ]
+02010 = ABC transporters, prokaryotic [isa: 82001 ]
+02012 = ABC transporters, ABC-2 and other types [isa: 82001 ]
+02014 = ABC transporters, eukaryotic [isa: 82001 ]
+02060 = Phosphotransferase system (PTS) [isa: 82001 ]
+82002 = Signal Transduction [isa: 90003 ]
+02020 = Two-component system [isa: 82002 ]
+04010 = MAPK signaling pathway [isa: 82002 ]
+04020 = Second messenger signaling pathway [isa: 82002 ]
+82003 = Ligand-Receptor Interaction [isa: 90003 ]
+04030 = G-protein coupled receptors [isa: 82003 ]
+04040 = Ion channel receptors [isa: 82003 ]
+90004 = Cellular Processes
+90104 = Unknown Cellular Processes Subtype [isa: 90004 ]
+83001 = Cell Motility [isa: 90004 ]
+02030 = Bacterial chemotaxis [isa: 83001 ]
+02040 = Flagellar assembly [isa: 83001 ]
+83002 = Cell Growth and Death [isa: 90004 ]
+04110 = Cell cycle [isa: 83002 ]
+04210 = Apotosis [isa: 83002 ]
+83003 = Cell Communication [isa: 90004 ]
+04510 = Integrin-mediated cell adhesion [isa: 83003 ]
+04520 = Cadherin-mediated cell adhesion [isa: 83003 ]
+83004 = Development [isa: 90004 ]
+04310 = Wnt signaling pathway [isa: 83004 ]
+04330 = Notch signaling pathway [isa: 83004 ]
+04320 = Dorso-ventral axis formation [isa: 83004 ]
+83005 = Behavior [isa: 90004 ]
+04710 = Circadian rhythm [isa: 83005 ]
+90005 = Miscellaneous
+90105 = Unknown Miscellaneous Subtype [isa: 90105 ]
+
diff --git a/application/src/test/resources/testData/humanKeggAndGO/manifest.both b/application/src/test/resources/testData/humanKeggAndGO/manifest.both
new file mode 100644
index 0000000..a639e21
--- /dev/null
+++ b/application/src/test/resources/testData/humanKeggAndGO/manifest.both
@@ -0,0 +1,7 @@
+ontology=kegg.onto
+annotation=kegg.anno
+ontology=go.onto
+annotation=bioproc.anno
+annotation=molfunc.anno
+annotation=cellcomp.anno
+synonyms=human.syno
diff --git a/application/src/test/resources/testData/humanKeggAndGO/molfunc.anno b/application/src/test/resources/testData/humanKeggAndGO/molfunc.anno
new file mode 100644
index 0000000..e1f4d43
--- /dev/null
+++ b/application/src/test/resources/testData/humanKeggAndGO/molfunc.anno
@@ -0,0 +1,40 @@
+(species=Homo sapiens) (type=Molecular Function) (curator=GO)
+NP_001366 = 0003677
+NP_001366 = 0004519
+NP_001366 = 0004531
+NP_001366 = 0016787
+NP_005289 = 0001584
+NP_647593 = 0008181
+NP_005756 = 0015078
+NP_005756 = 0016787
+NP_002864 = 0000166
+NP_002864 = 0003677
+NP_002864 = 0005524
+NP_003772 = 0000287
+NP_003772 = 0008499
+NP_003772 = 0016757
+NP_015560 = 0008536
+NP_015628 = 0005261
+NP_015628 = 0005509
+NP_015628 = 0015267
+NP_004726 = 0003702
+NP_004726 = 0003725
+NP_004801 = 0005070
+NP_002574 = 0003714
+NP_002574 = 0008181
+NP_006388 = 0004519
+NP_006388 = 0004523
+NP_006388 = 0004540
+NP_006388 = 0016787
+NP_005623 = 0003700
+NP_005623 = 0004198
+NP_003558 = 0005085
+NP_003599 = 0001584
+NP_003599 = 0003676
+NP_003599 = 0004872
+NP_003568 = 0003702
+NP_003568 = 0003713
+NP_003951 = 0008080
+NP_001068 = 0015020
+NP_036546 = 0005096
+NP_055298 = 0003723
diff --git a/application/src/test/resources/testData/implicitStringArray.attribute b/application/src/test/resources/testData/implicitStringArray.attribute
new file mode 100644
index 0000000..d1fde24
--- /dev/null
+++ b/application/src/test/resources/testData/implicitStringArray.attribute
@@ -0,0 +1,6 @@
+GO_molecular_function_level_4
+AP1G1 = (intracellular::clathrin adaptor::intracellular transporter)
+HSD17B2 = (membrane::intracellular)
+E2F4 = (DNA binding)
+CDH3 = (cell adhesion molecule)
+
diff --git a/application/src/test/resources/testData/implicitStringArrayEnc.attribute b/application/src/test/resources/testData/implicitStringArrayEnc.attribute
new file mode 100644
index 0000000..d1eb29a
--- /dev/null
+++ b/application/src/test/resources/testData/implicitStringArrayEnc.attribute
@@ -0,0 +1,6 @@
+GO_molecular_function_level_4
+AP1G1 = (intracellular::clathrin+adaptor::intracellular+transporter)
+HSD17B2 = (membrane::intracellular)
+E2F4 = (DNA+binding)
+CDH3 = (cell+adhesion+molecule)
+
diff --git a/application/src/test/resources/testData/metabolicPathwayOntology.xml b/application/src/test/resources/testData/metabolicPathwayOntology.xml
new file mode 100644
index 0000000..34c2569
--- /dev/null
+++ b/application/src/test/resources/testData/metabolicPathwayOntology.xml
@@ -0,0 +1,1174 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<!-- $Revision: 21132 $
+ $Date: 2010-08-03 18:49:02 +0200 (Tue, 03 Aug 2010) $
+ $Author: mes $
+ -->
+
+<ontology curator="KEGG" type="Pathways">
+
+ <ontologyTerm>
+ <name> Metabolism </name>
+ <id> 90001 </id>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Carbohydrate Metabolism </name>
+ <id> 80001 </id>
+ <isa> 90001 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Lipid Metabolism </name>
+ <id> 80003 </id>
+ <isa> 90001 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Energy Metabolism </name>
+ <id> 80002 </id>
+ <isa> 90001 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Nucleotide Metabolism </name>
+ <id> 80004 </id>
+ <isa> 90001 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Amino Acid Metabolism </name>
+ <id> 80005 </id>
+ <isa> 90001 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Metabolism of Other Amino Acids </name>
+ <id> 80006 </id>
+ <isa> 90001 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Metabolism of Complex Carbohydrates </name>
+ <id> 80007 </id>
+ <isa> 90001 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Metabolism of Complex Lipids </name>
+ <id> 80008 </id>
+ <isa> 90001 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Metabolism of Cofactors and Vitamins </name>
+ <id> 80009 </id>
+ <isa> 90001 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Biosynthesis of Secondary Metabolites </name>
+ <id> 80010 </id>
+ <isa> 90001 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Biodegradation of Xenobiotics </name>
+ <id> 80011 </id>
+ <isa> 90001 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Unknown Carbohydrate Metabolism Subtype </name>
+ <id> 80101 </id>
+ <isa> 80001 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Unknown Lipid Metabolism Subtype </name>
+ <id> 80103 </id>
+ <isa> 80003 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Unknown Energy Metabolism Subtype </name>
+ <id> 80102 </id>
+ <isa> 80002 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Unknown Nucleotide Metabolism Subtype </name>
+ <id> 80104 </id>
+ <isa> 80004 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Unknown Amino Acid Metabolism Subtype </name>
+ <id> 80105 </id>
+ <isa> 80005 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Unknown Metabolism of Other Amino Acids Subtype </name>
+ <id> 80106 </id>
+ <isa> 80006 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Unknown Metabolism of Complex Carbohydrates Subtype </name>
+ <id> 80107 </id>
+ <isa> 80007 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Unknown Metabolism of Complex Lipids Subtype </name>
+ <id> 80108 </id>
+ <isa> 80008 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Unknown Metabolism of Cofactors and Vitamins Subtype </name>
+ <id> 80109 </id>
+ <isa> 80009 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Unknown Biosynthesis of Secondary Metabolites Subtype </name>
+ <id> 80110 </id>
+ <isa> 80010 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Unknown Biodegradation of Xenobiotics Subtype </name>
+ <id> 80111 </id>
+ <isa> 80011 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Glycolysis / Gluconeogenesis </name>
+ <id> 00010 </id>
+ <isa> 80001 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Citrate cycle (TCA cycle) </name>
+ <id> 00020 </id>
+ <isa> 80001 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Pentose phosphate pathway </name>
+ <id> 00030 </id>
+ <isa> 80001 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Pentose and glucuronate interconversions </name>
+ <id> 00040 </id>
+ <isa> 80001 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Fructose and mannose metabolism </name>
+ <id> 00051 </id>
+ <isa> 80001 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Galactose metabolism </name>
+ <id> 00052 </id>
+ <isa> 80001 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Ascorbate and aldarate metabolism </name>
+ <id> 00053 </id>
+ <isa> 80001 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Pyruvate metabolism </name>
+ <id> 00620 </id>
+ <isa> 80001 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Glyoxylate and dicarboxylate metabolism </name>
+ <id> 00630 </id>
+ <isa> 80001 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Propanoate metabolism </name>
+ <id> 00640 </id>
+ <isa> 80001 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Butanoate metabolism </name>
+ <id> 00650 </id>
+ <isa> 80001 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> C5-Branched dibasic acid metabolism </name>
+ <id> 00660 </id>
+ <isa> 80001 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Inositol metabolism </name>
+ <id> 00031 </id>
+ <isa> 80001 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Oxidative phosphorylation </name>
+ <id> 00190 </id>
+ <isa> 80002 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> ATP Synthesis </name>
+ <id> 00193 </id>
+ <isa> 80002 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Photosynthesis </name>
+ <id> 00195 </id>
+ <isa> 80002 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Carbon fixation </name>
+ <id> 00710 </id>
+ <isa> 80002 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Reductive carboxylate cycle (CO2 fixation) </name>
+ <id> 00720 </id>
+ <isa> 80002 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Methane metabolism </name>
+ <id> 00680 </id>
+ <isa> 80002 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Nitrogen metabolism </name>
+ <id> 00910 </id>
+ <isa> 80002 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Sulfur metabolism </name>
+ <id> 00920 </id>
+ <isa> 80002 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Fatty acid biosynthesis (path 1) </name>
+ <id> 00061 </id>
+ <isa> 80003 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Fatty acid biosynthesis (path 2) </name>
+ <id> 00062 </id>
+ <isa> 80003 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Fatty acid metabolism </name>
+ <id> 00071 </id>
+ <isa> 80003 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Synthesis and degradation of ketone bodies </name>
+ <id> 00072 </id>
+ <isa> 80003 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Sterol biosynthesis </name>
+ <id> 00100 </id>
+ <isa> 80003 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Bile acid biosynthesis </name>
+ <id> 00120 </id>
+ <isa> 80003 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> C21-Steroid hormone metabolism </name>
+ <id> 00140 </id>
+ <isa> 80003 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Androgen and estrogen metabolism </name>
+ <id> 00150 </id>
+ <isa> 80003 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Purine metabolism </name>
+ <id> 00230 </id>
+ <isa> 80004 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Pyrimidine metabolism </name>
+ <id> 00240 </id>
+ <isa> 80004 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Nucleotide sugars metabolism </name>
+ <id> 00520 </id>
+ <isa> 80004 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Glutamate metabolism </name>
+ <id> 00251 </id>
+ <isa> 80005 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Alanine and aspartate metabolism </name>
+ <id> 00252 </id>
+ <isa> 80005 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Glycine, serine and threonine metabolism </name>
+ <id> 00260 </id>
+ <isa> 80005 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Methionine metabolism </name>
+ <id> 00271 </id>
+ <isa> 80005 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Cysteine metabolism </name>
+ <id> 00272 </id>
+ <isa> 80005 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Valine, leucine and isoleucine degradation </name>
+ <id> 00280 </id>
+ <isa> 80005 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Valine, leucine and isoleucine biosynthesis </name>
+ <id> 00290 </id>
+ <isa> 80005 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Lysine biosynthesis </name>
+ <id> 00300 </id>
+ <isa> 80005 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Lysine degradation </name>
+ <id> 00310 </id>
+ <isa> 80005 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Arginine and proline metabolism </name>
+ <id> 00330 </id>
+ <isa> 80005 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Histidine metabolism </name>
+ <id> 00340 </id>
+ <isa> 80005 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Tyrosine metabolism </name>
+ <id> 00350 </id>
+ <isa> 80005 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Phenylalanine metabolism </name>
+ <id> 00360 </id>
+ <isa> 80005 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Tryptophan metabolism </name>
+ <id> 00380 </id>
+ <isa> 80005 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Phenylalanine, tyrosine and tryptophan biosynthesis </name>
+ <id> 00400 </id>
+ <isa> 80005 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Urea cycle and metabolism of amino groups </name>
+ <id> 00220 </id>
+ <isa> 80005 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> beta-Alanine metabolism </name>
+ <id> 00410 </id>
+ <isa> 80006 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Taurine and hypotaurine metabolism </name>
+ <id> 00430 </id>
+ <isa> 80006 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Aminophosphonate metabolism </name>
+ <id> 00440 </id>
+ <isa> 80006 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Selenoamino acid metabolism </name>
+ <id> 00450 </id>
+ <isa> 80006 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Cyanoamino acid metabolism </name>
+ <id> 00460 </id>
+ <isa> 80006 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> D-Glutamine and D-glutamate metabolism </name>
+ <id> 00471 </id>
+ <isa> 80006 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> D-Arginine and D-ornithine metabolism </name>
+ <id> 00472 </id>
+ <isa> 80006 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> D-Alanine metabolism </name>
+ <id> 00473 </id>
+ <isa> 80006 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Glutathione metabolism </name>
+ <id> 00480 </id>
+ <isa> 80006 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Starch and sucrose metabolism </name>
+ <id> 00500 </id>
+ <isa> 80007 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Glycoprotein biosynthesis </name>
+ <id> 00510 </id>
+ <isa> 80007 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Glycoprotein degradation </name>
+ <id> 00511 </id>
+ <isa> 80007 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Aminosugars metabolism </name>
+ <id> 00530 </id>
+ <isa> 80007 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Lipopolysaccharide biosynthesis </name>
+ <id> 00540 </id>
+ <isa> 80007 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Peptidoglycan biosynthesis </name>
+ <id> 00550 </id>
+ <isa> 80007 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Glycosaminoglycan degradation </name>
+ <id> 00531 </id>
+ <isa> 80007 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Chondroitin / Heparan sulfate biosynthesis </name>
+ <id> 00532 </id>
+ <isa> 80007 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Keratan sulfate biosynthesis </name>
+ <id> 00533 </id>
+ <isa> 80007 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Glycerolipid metabolism </name>
+ <id> 00561 </id>
+ <isa> 80008 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Glycosylphosphatidylinositol(GPI)-anchor biosynthesis </name>
+ <id> 00563 </id>
+ <isa> 80008 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Inositol phosphate metabolism </name>
+ <id> 00562 </id>
+ <isa> 80008 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Sphingophospholipid biosynthesis </name>
+ <id> 00570 </id>
+ <isa> 80008 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Phospholipid degradation </name>
+ <id> 00580 </id>
+ <isa> 80008 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Sphingoglycolipid metabolism </name>
+ <id> 00600 </id>
+ <isa> 80008 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Blood group glycolipid biosynthesis - lact series </name>
+ <id> 00601 </id>
+ <isa> 80008 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Blood group glycolipid biosynthesis - neolact series </name>
+ <id> 00602 </id>
+ <isa> 80008 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Globoside metabolism </name>
+ <id> 00603 </id>
+ <isa> 80008 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Prostaglandin and leukotriene metabolism </name>
+ <id> 00590 </id>
+ <isa> 80008 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Thiamine metabolism </name>
+ <id> 00730 </id>
+ <isa> 80009 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Riboflavin metabolism </name>
+ <id> 00740 </id>
+ <isa> 80009 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Vitamin B6 metabolism </name>
+ <id> 00750 </id>
+ <isa> 80009 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Nicotinate and nicotinamide metabolism </name>
+ <id> 00760 </id>
+ <isa> 80009 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Pantothenate and CoA biosynthesis </name>
+ <id> 00770 </id>
+ <isa> 80009 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Biotin metabolism </name>
+ <id> 00780 </id>
+ <isa> 80009 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Folate biosynthesis </name>
+ <id> 00790 </id>
+ <isa> 80009 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> One carbon pool by folate </name>
+ <id> 00670 </id>
+ <isa> 80009 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Retinol metabolism </name>
+ <id> 00830 </id>
+ <isa> 80009 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Porphyrin and chlorophyll metabolism </name>
+ <id> 00860 </id>
+ <isa> 80009 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Ubiquinone biosynthesis </name>
+ <id> 00130 </id>
+ <isa> 80009 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Terpenoid biosynthesis </name>
+ <id> 00900 </id>
+ <isa> 80010 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Flavonoids, stilbene and lignin biosynthesis </name>
+ <id> 00940 </id>
+ <isa> 80010 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Alkaloid biosynthesis I </name>
+ <id> 00950 </id>
+ <isa> 80010 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Alkaloid biosynthesis II </name>
+ <id> 00960 </id>
+ <isa> 80010 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Penicillins and cephalosporins biosynthesis </name>
+ <id> 00311 </id>
+ <isa> 80010 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> beta-Lactam resistanse </name>
+ <id> 01210 </id>
+ <isa> 80010 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Streptomycin biosynthesis </name>
+ <id> 00521 </id>
+ <isa> 80010 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Erythromycin biosynthesis </name>
+ <id> 00522 </id>
+ <isa> 80010 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Tetracycline biosynthesis </name>
+ <id> 00253 </id>
+ <isa> 80010 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Clavulanic acid biosynthesis </name>
+ <id> 00331 </id>
+ <isa> 80010 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Puromycin biosynthesis </name>
+ <id> 00231 </id>
+ <isa> 80010 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Caprolactam degradation </name>
+ <id> 00930 </id>
+ <isa> 80011 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Biphenyl degradation </name>
+ <id> 00621 </id>
+ <isa> 80011 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Toluene degradation </name>
+ <id> 00622 </id>
+ <isa> 80011 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> gamma-Hexachlorocyclohexane degradation </name>
+ <id> 00361 </id>
+ <isa> 80011 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> 3-Chloroacrylic acid degradation </name>
+ <id> 00641 </id>
+ <isa> 80011 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> 1,1,1-Trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) degradation </name>
+ <id> 00351 </id>
+ <isa> 80011 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> 2,4-Dichlorobenzoate degradation </name>
+ <id> 00623 </id>
+ <isa> 80011 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> 1,2-Dichloroethane degradation </name>
+ <id> 00631 </id>
+ <isa> 80011 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Xylene degradation </name>
+ <id> 00624 </id>
+ <isa> 80011 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Tetrachloroethene degradation </name>
+ <id> 00625 </id>
+ <isa> 80011 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Styrene degradation </name>
+ <id> 00643 </id>
+ <isa> 80011 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> 1,4-Dichlorobenzene degradation </name>
+ <id> 00627 </id>
+ <isa> 80011 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Nitorobenzene degradation </name>
+ <id> 00626 </id>
+ <isa> 80011 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Ethylbenzene degradation </name>
+ <id> 00642 </id>
+ <isa> 80011 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Fluorene degradation </name>
+ <id> 00628 </id>
+ <isa> 80011 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Carbazole degradation </name>
+ <id> 00629 </id>
+ <isa> 80011 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Benzoate degradation </name>
+ <id> 00632 </id>
+ <isa> 80011 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Atrazine degradation </name>
+ <id> 00791 </id>
+ <isa> 80011 </isa>
+ </ontologyTerm>
+
+ <!-- ====================================================================== -->
+ <ontologyTerm>
+ <name> Genetic Information Processing </name>
+ <id> 90002 </id>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Transcription </name>
+ <id> 81001 </id>
+ <isa> 90002 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Unknown Transcription Subtype </name>
+ <id> 81101 </id>
+ <isa> 81001 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> RNA polymerase </name>
+ <id> 03020 </id>
+ <isa> 81001 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Transcription factors </name>
+ <id> 03022 </id>
+ <isa> 81001 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Spliceosome </name>
+ <id> 03040 </id>
+ <isa> 81001 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Translation </name>
+ <id> 81002 </id>
+ <isa> 90002 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Unknown Translation Subtype</name>
+ <id> 81102 </id>
+ <isa> 81002 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Ribosome </name>
+ <id> 03010 </id>
+ <isa> 81002 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Translation factors </name>
+ <id> 03012 </id>
+ <isa> 81002 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Aminoacyl-tRNA biosynthesis </name>
+ <id> 00970 </id>
+ <isa> 81002 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Sorting and Degradation </name>
+ <id> 81003 </id>
+ <isa> 90002 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Protein export </name>
+ <id> 03060 </id>
+ <isa> 81003 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Type III secretion system </name>
+ <id> 03070 </id>
+ <isa> 81003 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Type IV secretion system </name>
+ <id> 03080 </id>
+ <isa> 81003 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> RNA degradosome </name>
+ <id> 03018 </id>
+ <isa> 81003 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Ubiquitin mediated proteolysis </name>
+ <id> 04120 </id>
+ <isa> 81003 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Proteasome </name>
+ <id> 03050 </id>
+ <isa> 81003 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Replication and Repair </name>
+ <id> 81004 </id>
+ <isa> 90002 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Unknown Replication and Repair Subtype </name>
+ <id> 81104 </id>
+ <isa> 81004 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> DNA polymerase </name>
+ <id> 03030 </id>
+ <isa> 81004 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Replication Complex </name>
+ <id> 03032 </id>
+ <isa> 81004 </isa>
+ </ontologyTerm>
+
+ <!-- ====================================================================== -->
+
+ <ontologyTerm>
+ <name> Environmental Information Processing </name>
+ <id> 90003 </id>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Membrane Transport </name>
+ <id> 82001 </id>
+ <isa> 90003 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Unknown Membrane Transport Subtype </name>
+ <id> 82101 </id>
+ <isa> 82001 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> ABC transporters, prokaryotic </name>
+ <id> 02010 </id>
+ <isa> 82001 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> ABC transporters, ABC-2 and other types </name>
+ <id> 02012 </id>
+ <isa> 82001 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> ABC transporters, eukaryotic </name>
+ <id> 02014 </id>
+ <isa> 82001 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Phosphotransferase system (PTS) </name>
+ <id> 02060 </id>
+ <isa> 82001 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Signal Transduction </name>
+ <id> 82002 </id>
+ <isa> 90003 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Two-component system </name>
+ <id> 02020 </id>
+ <isa> 82002 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> MAPK signaling pathway </name>
+ <id> 04010 </id>
+ <isa> 82002 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Second messenger signaling pathway </name>
+ <id> 04020 </id>
+ <isa> 82002 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Ligand-Receptor Interaction </name>
+ <id> 82003 </id>
+ <isa> 90003 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> G-protein coupled receptors </name>
+ <id> 04030 </id>
+ <isa> 82003 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Ion channel receptors </name>
+ <id> 04040 </id>
+ <isa> 82003 </isa>
+ </ontologyTerm>
+
+ <!-- ====================================================================== -->
+
+ <ontologyTerm>
+ <name> Cellular Processes </name>
+ <id> 90004 </id>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Unknown Cellular Processes Subtype </name>
+ <id> 90104 </id>
+ <isa> 90004 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Cell Motility </name>
+ <id> 83001 </id>
+ <isa> 90004 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Bacterial chemotaxis </name>
+ <id> 02030 </id>
+ <isa> 83001 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Flagellar assembly </name>
+ <id> 02040 </id>
+ <isa> 83001 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Cell Growth and Death </name>
+ <id> 83002 </id>
+ <isa> 90004 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Cell cycle </name>
+ <id> 04110 </id>
+ <isa> 83002 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Apotosis </name>
+ <id> 04210 </id>
+ <isa> 83002 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Cell Communication </name>
+ <id> 83003 </id>
+ <isa> 90004 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Integrin-mediated cell adhesion </name>
+ <id> 04510 </id>
+ <isa> 83003 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Cadherin-mediated cell adhesion </name>
+ <id> 04520 </id>
+ <isa> 83003 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Development </name>
+ <id> 83004 </id>
+ <isa> 90004 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Wnt signaling pathway </name>
+ <id> 04310 </id>
+ <isa> 83004 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Notch signaling pathway </name>
+ <id> 04330 </id>
+ <isa> 83004 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Dorso-ventral axis formation </name>
+ <id> 04320 </id>
+ <isa> 83004 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Behavior </name>
+ <id> 83005 </id>
+ <isa> 90004 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Circadian rhythm </name>
+ <id> 04710 </id>
+ <isa> 83005 </isa>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Miscellaneous </name>
+ <id> 90005 </id>
+ </ontologyTerm>
+
+ <ontologyTerm>
+ <name> Unknown Miscellaneous Subtype</name>
+ <id> 90105 </id>
+ </ontologyTerm>
+
+
+</ontology>
diff --git a/application/src/test/resources/testData/multiWordProteins.sif b/application/src/test/resources/testData/multiWordProteins.sif
new file mode 100644
index 0000000..93001ac
--- /dev/null
+++ b/application/src/test/resources/testData/multiWordProteins.sif
@@ -0,0 +1,30 @@
+LPS interactsWith TLR4
+LPS interactsWith MD-2
+LPS interactsWith TLR4
+ADOH interactsWith LPS
+TLR4 interactsWith MyD88
+TLR4 interactsWith IRAK Complex
+TLR4 interactsWith TIRAP
+TRAF6 interactsWith IRAK Complex
+Uev1a/UBc13 Ubiquitin-conjugating Complex interactsWith TRAF6
+TRAF6 interactsWith TAK1
+A20 interactsWith TRAF6
+TAK1 interactsWith IKK-beta
+IKK-beta interactsWith I-kappa-B-alpha
+I-kappa-B-alpha interactsWith p50
+I-kappa-B-alpha interactsWith p65
+SCF Ubiquitin Ligase interactsWith I-kappa-B-alpha
+26S ubiquitin dependent proteasome interactsWith I-kappa-B-alpha
+TLR4 interactsWith TRIF
+TRIF interactsWith IRF3
+IRAK4 interactsWith MyD88
+IRAK4 interactsWith IRAK1
+IRAK1 interactsWith MyD88
+IRAK1 interactsWith TRAF6
+TRAF6 interactsWith CD40
+TRAF6 interactsWith RANK
+TRAF6 interactsWith IRAK1
+TRAF6 interactsWith IRAK2
+TRAF6 interactsWith IRAKM
+TRAF6 interactsWith RIP2 ABCDE oopah HJKOL coltrane
+
diff --git a/application/src/test/resources/testData/multiWordProteinsFileTrailingSpaces.sif b/application/src/test/resources/testData/multiWordProteinsFileTrailingSpaces.sif
new file mode 100644
index 0000000..7d522bd
--- /dev/null
+++ b/application/src/test/resources/testData/multiWordProteinsFileTrailingSpaces.sif
@@ -0,0 +1,30 @@
+LPS interactsWith TLR4
+LPS interactsWith MD-2
+LPS interactsWith TLR4
+ADOH interactsWith LPS
+TLR4 interactsWith MyD88
+TLR4 interactsWith IRAK Complex
+TLR4 interactsWith TIRAP
+TRAF6 interactsWith IRAK Complex
+Uev1a/UBc13 Ubiquitin-conjugating Complex interactsWith TRAF6
+TRAF6 interactsWith TAK1
+A20 interactsWith TRAF6
+TAK1 interactsWith IKK-beta
+IKK-beta interactsWith I-kappa-B-alpha
+I-kappa-B-alpha interactsWith p50
+I-kappa-B-alpha interactsWith p65
+SCF Ubiquitin Ligase interactsWith I-kappa-B-alpha
+26S ubiquitin dependent proteasome interactsWith I-kappa-B-alpha
+TLR4 interactsWith TRIF
+TRIF interactsWith IRF3
+IRAK4 interactsWith MyD88
+IRAK4 interactsWith IRAK1
+IRAK1 interactsWith MyD88
+IRAK1 interactsWith TRAF6
+TRAF6 interactsWith CD40
+TRAF6 interactsWith RANK
+TRAF6 interactsWith IRAK1
+TRAF6 interactsWith IRAK2
+TRAF6 interactsWith IRAKM
+TRAF6 interactsWith RIP2 ABCDE oopah HJKOL coltrane
+
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+ fill "#0000FF"
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+ type "line"
+ arrow "none"
+ fill "#0000FF"
+ ]
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+ type "line"
+ arrow "none"
+ fill "#0000FF"
+ ]
+ ]
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+ source 330
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+ type "line"
+ arrow "none"
+ fill "#0000FF"
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+
+]
diff --git a/application/src/test/resources/testData/old_vizmap.props b/application/src/test/resources/testData/old_vizmap.props
new file mode 100644
index 0000000..f2a51ee
--- /dev/null
+++ b/application/src/test/resources/testData/old_vizmap.props
@@ -0,0 +1,436 @@
+#This file specifies visual mappings for Cytoscape and has been automatically generated.
+# WARNING: any changes you make to this file while Cytoscape is running may be overwritten.
+# Any changes may make these visual mappings unreadable.
+# Please make sure you know what you are doing before modifying this file by hand.
+#Fri May 26 16:17:49 EDT 2006
+
+edgeAppearanceCalculator.Sample1.defaultEdgeColor=0,0,0
+edgeAppearanceCalculator.Sample1.defaultEdgeFont=Default,plain,10
+edgeAppearanceCalculator.Sample1.defaultEdgeLabel=
+edgeAppearanceCalculator.Sample1.defaultEdgeLineType=LINE_1
+edgeAppearanceCalculator.Sample1.defaultEdgeSourceArrow=NONE
+edgeAppearanceCalculator.Sample1.defaultEdgeTargetArrow=NONE
+edgeAppearanceCalculator.Sample1.defaultEdgeToolTip=
+edgeAppearanceCalculator.Sample1.edgeColorCalculator=BasicDiscrete
+edgeAppearanceCalculator.Sample1.edgeFontFaceCalculator=null
+edgeAppearanceCalculator.Sample1.edgeFontSizeCalculator=null
+edgeAppearanceCalculator.Sample1.edgeLabelCalculator=EdgeLabel
+edgeAppearanceCalculator.Sample1.edgeLineTypeCalculator=InteractionType
+edgeAppearanceCalculator.Sample1.edgeSourceArrowCalculator=null
+edgeAppearanceCalculator.Sample1.edgeTargetArrowCalculator=null
+edgeAppearanceCalculator.Sample1.edgeToolTipCalculator=null
+edgeAppearanceCalculator.Sample2.defaultEdgeColor=0,0,0
+edgeAppearanceCalculator.Sample2.defaultEdgeFont=Default,plain,10
+edgeAppearanceCalculator.Sample2.defaultEdgeLabel=
+edgeAppearanceCalculator.Sample2.defaultEdgeLineType=LINE_1
+edgeAppearanceCalculator.Sample2.defaultEdgeSourceArrow=NONE
+edgeAppearanceCalculator.Sample2.defaultEdgeTargetArrow=NONE
+edgeAppearanceCalculator.Sample2.defaultEdgeToolTip=
+edgeAppearanceCalculator.Sample2.edgeColorCalculator=null
+edgeAppearanceCalculator.Sample2.edgeFontFaceCalculator=null
+edgeAppearanceCalculator.Sample2.edgeFontSizeCalculator=null
+edgeAppearanceCalculator.Sample2.edgeLabelCalculator=null
+edgeAppearanceCalculator.Sample2.edgeLineTypeCalculator=null
+edgeAppearanceCalculator.Sample2.edgeSourceArrowCalculator=null
+edgeAppearanceCalculator.Sample2.edgeTargetArrowCalculator=null
+edgeAppearanceCalculator.Sample2.edgeToolTipCalculator=null
+edgeAppearanceCalculator.default.defaultEdgeColor=0,0,255
+edgeAppearanceCalculator.default.defaultEdgeFont=Default,plain,10
+edgeAppearanceCalculator.default.defaultEdgeLabel=
+edgeAppearanceCalculator.default.defaultEdgeLineType=LINE_1
+edgeAppearanceCalculator.default.defaultEdgeSourceArrow=NONE
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+nodeSizeCalculator.BasicDiscrete.mapping.map.autophagy=50.0
+nodeSizeCalculator.BasicDiscrete.mapping.map.biological_process\ unknown=10.0
+nodeSizeCalculator.BasicDiscrete.mapping.map.cell\ cycle=60.0
+nodeSizeCalculator.BasicDiscrete.mapping.type=DiscreteMapping
+nodeToolTipCalculator.BasicContinuous.class=cytoscape.visual.calculators.GenericNodeToolTipCalculator
+nodeToolTipCalculator.BasicContinuous.mapping.boundaryvalues=3
+nodeToolTipCalculator.BasicContinuous.mapping.bv0.domainvalue=-1.0
+nodeToolTipCalculator.BasicContinuous.mapping.bv0.equal=less
+nodeToolTipCalculator.BasicContinuous.mapping.bv0.greater=less
+nodeToolTipCalculator.BasicContinuous.mapping.bv0.lesser=less
+nodeToolTipCalculator.BasicContinuous.mapping.bv1.domainvalue=0.0
+nodeToolTipCalculator.BasicContinuous.mapping.bv1.equal=same
+nodeToolTipCalculator.BasicContinuous.mapping.bv1.greater=more
+nodeToolTipCalculator.BasicContinuous.mapping.bv1.lesser=less
+nodeToolTipCalculator.BasicContinuous.mapping.bv2.domainvalue=1.0
+nodeToolTipCalculator.BasicContinuous.mapping.bv2.equal=more
+nodeToolTipCalculator.BasicContinuous.mapping.bv2.greater=more
+nodeToolTipCalculator.BasicContinuous.mapping.bv2.lesser=more
+nodeToolTipCalculator.BasicContinuous.mapping.controller=expression
+nodeToolTipCalculator.BasicContinuous.mapping.interpolator=FlatInterpolator
+nodeToolTipCalculator.BasicContinuous.mapping.type=ContinuousMapping
+nodeToolTipCalculator.BasicDiscrete.class=cytoscape.visual.calculators.GenericNodeToolTipCalculator
+nodeToolTipCalculator.BasicDiscrete.mapping.controller=GO Biological Process (level 4)
+nodeToolTipCalculator.BasicDiscrete.mapping.map.autophagy=autophagy Tip
+nodeToolTipCalculator.BasicDiscrete.mapping.map.biological_process\ unknown=unknown Tip
+nodeToolTipCalculator.BasicDiscrete.mapping.map.cell\ cycle=cell cycle Tip
+nodeToolTipCalculator.BasicDiscrete.mapping.type=DiscreteMapping
diff --git a/application/src/test/resources/testData/plugins/BadPlugin.jar b/application/src/test/resources/testData/plugins/BadPlugin.jar
new file mode 100644
index 0000000..372fd53
Binary files /dev/null and b/application/src/test/resources/testData/plugins/BadPlugin.jar differ
diff --git a/application/src/test/resources/testData/plugins/GoodPlugin.jar b/application/src/test/resources/testData/plugins/GoodPlugin.jar
new file mode 100644
index 0000000..785983c
Binary files /dev/null and b/application/src/test/resources/testData/plugins/GoodPlugin.jar differ
diff --git a/application/src/test/resources/testData/plugins/GoodPlugin.zip b/application/src/test/resources/testData/plugins/GoodPlugin.zip
new file mode 100644
index 0000000..97688e1
Binary files /dev/null and b/application/src/test/resources/testData/plugins/GoodPlugin.zip differ
diff --git a/application/src/test/resources/testData/plugins/MCODE_broken.jar b/application/src/test/resources/testData/plugins/MCODE_broken.jar
new file mode 100644
index 0000000..733ed3e
Binary files /dev/null and b/application/src/test/resources/testData/plugins/MCODE_broken.jar differ
diff --git a/application/src/test/resources/testData/plugins/license.txt b/application/src/test/resources/testData/plugins/license.txt
new file mode 100644
index 0000000..33a102f
--- /dev/null
+++ b/application/src/test/resources/testData/plugins/license.txt
@@ -0,0 +1,2 @@
+This is a test license text that a user must ok in order to finish the installation of
+the plugin. I'm not entirely sure how I can test that part....
\ No newline at end of file
diff --git a/application/src/test/resources/testData/plugins/partial_plugin_file.xml b/application/src/test/resources/testData/plugins/partial_plugin_file.xml
new file mode 100644
index 0000000..9212167
--- /dev/null
+++ b/application/src/test/resources/testData/plugins/partial_plugin_file.xml
@@ -0,0 +1,45 @@
+<project>
+<name>Cytoscape Plugins</name>
+<description>These plugins have been submitted to Cytoscape by their authors,
+ they may have their own licensing requirements. Please contact the plugin authors with any questions.</description>
+<url>http://cytoscape.org</url>
+<pluginlist>
+<plugin>
+<uniqueID>103</uniqueID>
+<name>AgilentLiteratureSearch</name>
+<description>Creates a CyNetwork based on searching the scientific literature.</description>
+<category>Network Inference</category>
+<pluginVersion>2.55</pluginVersion>
+<cytoscapeVersions>
+<version>2.5</version>
+</cytoscapeVersions>
+<license>
+<text>AGILENT TECHNOLOGIES, INC. SOFTWARE LICENSE AGREEMENT
+
+ATTENTION: DOWNLOADING, COPYING, PUBLICLY DISTRIBUTING, OR USING THIS SOFTWARE IS SUBJECT TO THE AGREEMENT SET FORTH BELOW.
+
+TO DOWNLOAD, STORE, INSTALL, OR RUN THE SOFTWARE, YOU MUST FIRST AGREE TO AGILENT\\\'S SOFTWARE LICENSE AGREEMENT BELOW. IF YOU HAVE READ, UNDERSTAND AND AGREE TO BE BOUND BY THE SOFTWARE LICENSE AGREEMENT BELOW, YOU SHOULD CLICK ON THE \\\"AGREE\\\" BOX AT THE BOTTOM OF THIS PAGE. THE SOFTWARE WILL THEN BE DOWNLOADED TO OR INSTALLED ON YOUR COMPUTER.
+
+IF YOU DO NOT AGREE TO BE BOUND BY THE SOFTWARE LICENSE AGREEMENT BELOW, YOU SHOULD CLICK ON THE \\\"DO NOT AGREE\\\" BOX AT THE BOTTOM OF THIS PAGE AND CANCEL THE DOWNLOAD OR INSTALLATION OF THE SOFTWARE. IF YOU HAVE PURCHASED THE SOFTWARE FROM AGILENT, YOU MAY RETURN THE SOFTWARE FOR A FULL REFUND, OR, IF THE SOFTWARE IS SUPPLIED AS PART OF ANOTHER PRODUCT, YOU MAY RETURN THE ENTIRE PRODUCT FOR A FULL REFUND.
+
+Software. \\\"Software\\\" means one or more computer programs in object code format, whether stand-alone or bundled with other products, and related documentation. It does NOT include programs in source code format.
+
+License Grant. Agilent grants you a non-exclusive license to download one copy of the Software, and to store or run that copy of the Software for internal use and purposes in accordance with this Agreement and the documentation provided with the Software. Such documentation may include license terms provided by Agilent\\\'s third party suppliers, which will apply to the use of the Software and take precedence over these license terms. In the absence of documentation specifying the app [...]
+
+License Restrictions. You may make copies or adaptations of the Software for archival purposes or when copying or adaptation is an essential step in the authorized use of the Software, but for no other purpose. You must reproduce all copyright notices in the original Software on all permitted copies or adaptations. You may not copy the Software onto any public or distributed network.
+
+Upgrades. This license does not entitle you to receive upgrades, updates or technical support. Such services may be purchased separately.
+
+Ownership. The Software is owned and copyrighted by Agilent or its third party suppliers. Agilent and its third party suppliers retain all right, title and interest in the Software. Agilent and its third party suppliers may protect their respective rights in the Software in the event of any violation of this Agreement.
+
+No Disassembly. You may not disassemble or otherwise modify the Software without written authorization from Agilent, except as permitted by law. Upon request, you will provide Agilent with reasonably detailed information regarding any permitted disassembly or modification.
+
+High Risk Activities. The Software is not specifically written, designed, manufactured or intended for use in the planning, construction, maintenance or direct operation of a nuclear facility, nor for use in on line control or fail safe operation of aircraft navigation, control or communication systems, weapon systems or direct life support systems.
+
+Transfer. You may transfer the license granted to you here provided that you deliver all copies of the Software to the transferee along with this Agreement. The transferee must accept this Agreement as a condition to any transfer. Your license to use the Software will terminate upon transfer.
+
+Termination. Agilent may terminate this license upon notice for breach of this Agreement. Upon termination, you must immediately destroy all copies of the Software.
+
+Export Requirements. If you export, re-export or import Software, technology or technical data licensed hereunder, you assume responsibility for complying with applicable laws and regulations and for obtaining required export and import authorizations. Agilent may terminate this license immediately if you are in violation of any applicable laws or regulations.
+
+U.S. Government Restricted Rights. Software and technical data r
\ No newline at end of file
diff --git a/application/src/test/resources/testData/plugins/test_plugin.props b/application/src/test/resources/testData/plugins/test_plugin.props
new file mode 100644
index 0000000..1e8a727
--- /dev/null
+++ b/application/src/test/resources/testData/plugins/test_plugin.props
@@ -0,0 +1,34 @@
+#plugin.props
+
+# This props file should be filled out and included in the plugin jar file. This props file will be used
+# to put information into the Plugin Manager about the plugin
+
+# -- The following properties are REQUIRED -- #
+
+# The plugin name that will be displayed to users, white space within name is not allowed
+pluginName=MyPlugin
+
+# Description used to give users information about the plugin such as what it does.
+# Html tags are encouraged for formatting purposes.
+pluginDescription=Information about the plugin that will be displayed to users.<br>Please use html tags for all formatting and do not add newlines.<p>
+
+# Plugin version number, this must be two numbers separated by a decimlal. Ex. 0.2, 14.03
+pluginVersion=1.0
+
+# Compatible Cytoscape version. If there are more than one version, seperate by ",".
+cytoscapeVersion=2.4, 2.3.3
+
+# Category, use one of the categories listed on the http://cytoscape.org/plugins2.php site
+pluginCategory=Scripting/Communication
+
+# -- The following properties are OPTIONAL -- #
+
+# URL to a website that gives more information about your plugin, Ex. http://my-lab-site.org
+projectURL=http://my-lab-site.org/myCytoscapePlugin
+
+# List of authors. Note each author and institution pair are separated by a : (colon)
+# each additional author institution pair must be separated from other pairs bye a ; (semicolon)
+pluginAuthorsInstitutions=Sarah and Victor:ISB;Mike, Kei and Peng:UCSD
+
+# Date this plugin/plugin version was released
+releaseDate=May 1, 2008
\ No newline at end of file
diff --git a/application/src/test/resources/testData/plugins/test_plugin.xml b/application/src/test/resources/testData/plugins/test_plugin.xml
new file mode 100644
index 0000000..a77b2fe
--- /dev/null
+++ b/application/src/test/resources/testData/plugins/test_plugin.xml
@@ -0,0 +1,390 @@
+<!--
+Test xml file describing plugins and where to d/l them
+This file will be transformed in order to keep the tests up to date
+with current cytoscape release versions.
+-->
+<project>
+
+ <name>Cytoscape Plugins</name>
+ <description>Test</description>
+ <url>http://cytoscape.org</url>
+
+ <pluginlist>
+ <!--
+ The urls for each of these plugins SHOULD start with http://...
+ For testing these will be concatenated with file:///user_dir/url
+ Do NOT set up your xml file with partial urls
+ -->
+ <plugin>
+ <uniqueID>goodJarPlugin999</uniqueID>
+ <name>Good Jar</name>
+ <description>
+ This plugin demonstrates the use of a jar file with the PluginInfo object created and a correct manifest file.
+ </description>
+ <pluginVersion>1.0</pluginVersion>
+
+ <cytoscapeVersions>
+ <version>2.3.3</version>
+ <version>2.4</version>
+ </cytoscapeVersions>
+
+ <filetype>jar</filetype>
+ <category>Test</category>
+ <url>GoodPlugin.jar</url>
+ <license>
+ <text>
+ This is some license text a user would see and have to ok in order to install a plugin.
+ </text>
+ </license>
+ <authorlist>
+ <author>
+ <name>Ann Smith</name>
+ <institution>UW</institution>
+ </author>
+ </authorlist>
+ </plugin>
+
+ <plugin>
+ <uniqueID>goodJarPlugin123</uniqueID>
+ <name>Good Jar</name>
+ <description>
+ This plugin demonstrates the use of a jar file with the PluginInfo object created and a correct manifest file.
+ </description>
+ <pluginVersion>1.0</pluginVersion>
+
+ <cytoscapeVersions>
+ <version>2.3.3</version>
+ <version>2.4</version>
+ <version>current</version>
+ </cytoscapeVersions>
+
+ <filetype>jar</filetype>
+ <category>Test</category>
+ <url>GoodPlugin.jar</url>
+ <license>
+ <text>
+ This is some license text a user would see and have to ok in order to install a plugin.
+ </text>
+ </license>
+ <authorlist>
+ <author>
+ <name>Ann Smith</name>
+ <institution>UW</institution>
+ </author>
+ </authorlist>
+ </plugin>
+
+ <plugin>
+ <uniqueID>goodJarPlugin123</uniqueID>
+ <name>Good Jar</name>
+ <description>
+ This plugin demonstrates the use of a jar file with the PluginInfo object created and a correct manifest file.
+ This one is an "update" to the previous one for the purposes of testing.
+ </description>
+ <pluginVersion>2.1</pluginVersion>
+
+ <cytoscapeVersions>
+ <version>current</version>
+ </cytoscapeVersions>
+
+
+ <filetype>jar</filetype>
+ <category>Test</category>
+ <url>GoodPlugin.jar</url>
+
+ <!-- Not sure how to deal with testing this at the moment. I need to turn it into file:/// structure...
+ <license>
+ <url>license.txt</url>
+ </license>
+-->
+ <authorlist>
+ <author>
+ <name>Ann Smith and George James</name>
+ <institution>UW</institution>
+ </author>
+ <author>
+ <name>John Doe</name>
+ <institution>CU</institution>
+ </author>
+ </authorlist>
+ </plugin>
+
+ <plugin>
+ <uniqueID>themePlugin1234</uniqueID>
+ <name>Good Jar</name>
+ <description>
+ This plugin demonstrates the use of a zip file with the correct directories (at least one plugins/*.jar file required) and
+ a correct manifest file.
+ </description>
+ <pluginVersion>1.1</pluginVersion>
+
+ <cytoscapeVersions>
+ <version>current</version>
+ </cytoscapeVersions>
+
+ <filetype>jar</filetype>
+ <category>Test</category>
+ <url>GoodPlugin.jar</url>
+ <authorlist>
+ <author>
+ <name>George Smith</name>
+ <institution>UC Mars</institution>
+ </author>
+ </authorlist>
+ </plugin>
+
+ <plugin>
+ <uniqueID>themePlugin1234</uniqueID>
+ <name>Good Jar</name>
+ <description>
+ This plugin demonstrates the use of a zip file with the correct directories (at least one plugins/*.jar file required) and
+ a correct manifest file.
+ </description>
+ <pluginVersion>2.0</pluginVersion>
+
+ <cytoscapeVersions>
+ <version>current</version>
+ </cytoscapeVersions>
+
+ <filetype>jar</filetype>
+ <category>Test</category>
+ <url>GoodPlugin.jar</url>
+ <authorlist>
+ <author>
+ <name>George Smith</name>
+ <institution>UC Mars</institution>
+ </author>
+ </authorlist>
+ </plugin>
+
+
+ <plugin>
+ <uniqueID>goodZIPPlugin777</uniqueID>
+ <name>Good Jar</name>
+ <description>
+ This plugin demonstrates the use of a zip file with the correct directories (at least one plugins/*.jar file required) and
+ a correct manifest file.
+ </description>
+ <pluginVersion>0.45</pluginVersion>
+
+ <cytoscapeVersions>
+ <version>current</version>
+ </cytoscapeVersions>
+
+ <filetype>zip</filetype>
+ <category>Test</category>
+ <url>GoodPlugin.zip</url>
+ <authorlist>
+ <author>
+ <name>George Smith</name>
+ <institution>UC Mars</institution>
+ </author>
+ </authorlist>
+ </plugin>
+
+
+ <plugin>
+ <uniqueID>badJarPlugin123</uniqueID>
+ <name>Bad Jar</name>
+ <description>
+ This plugin jar file does not contain the correct manifest file and should fail to install.
+ </description>
+ <pluginVersion>0.3</pluginVersion>
+
+ <cytoscapeVersions>
+ <version>current</version>
+ </cytoscapeVersions>
+
+ <filetype>jar</filetype>
+ <category>Test</category>
+ <url>BadPlugin.jar</url>
+ <authorlist>
+ <author>
+ <name>George Smith</name>
+ <institution>UCLA</institution>
+ </author>
+ </authorlist>
+ </plugin>
+
+ <plugin>
+ <uniqueID>badZIPPlugin123</uniqueID>
+ <name>Bad Jar</name>
+ <description>
+ This plugin zip file does not contain the correct directories (one plugin/*.jar file required) and will fail to install.
+ </description>
+ <pluginVersion>0.9</pluginVersion>
+
+ <cytoscapeVersions>
+ <version>current</version>
+ </cytoscapeVersions>
+
+ <filetype>jar</filetype>
+ <category>Test</category>
+ <url>BadPlugin.zip</url>
+ <authorlist>
+ <author>
+ <name>Jill Jones</name>
+ <institution>CSU</institution>
+ </author>
+ </authorlist>
+ </plugin>
+
+ <!-- this is to test the case where the xml incorrectly id's the file type -->
+ <plugin>
+ <uniqueID>badFileType123</uniqueID>
+ <name>Good Jar</name>
+ <description>
+ This plugin demonstrates the use of a jar file with the PluginInfo object created and a correct manifest file.
+ </description>
+ <pluginVersion>1.0</pluginVersion>
+
+ <cytoscapeVersions>
+ <version>2.4</version>
+ <version>current</version>
+ </cytoscapeVersions>
+
+ <filetype>zip</filetype>
+ <category>Test</category>
+ <url>GoodPlugin.jar</url>
+ <license>
+ <text>
+ This is some license text a user would see and have to ok in order to install a plugin.
+ </text>
+ </license>
+ <authorlist>
+ <author>
+ <name>Ann Smith</name>
+ <institution>UW</institution>
+ </author>
+ </authorlist>
+ </plugin>
+
+ <plugin>
+ <uniqueID>mcode_1</uniqueID>
+ <name>MCODE</name>
+ <description>
+ Broken version of MCODE to test bug 0001553
+ </description>
+ <pluginVersion>1.0</pluginVersion>
+
+ <cytoscapeVersions>
+ <version>2.5</version>
+ <version>current</version>
+ </cytoscapeVersions>
+
+ <filetype>jar</filetype>
+ <category>Test</category>
+ <url>MCODE_broken.jar</url>
+ <authorlist>
+ <author>
+ <name>Jane Doe</name>
+ <institution>UW</institution>
+ </author>
+ </authorlist>
+ </plugin>
+
+
+ </pluginlist>
+
+ <themes>
+ <theme>
+ <uniqueID>goodThemeTest123</uniqueID>
+ <name>Good Test Theme</name>
+ <description>This is just a test theme.</description>
+ <themeVersion>0.5</themeVersion>
+ <cytoscapeVersions>
+ <version>current</version>
+ </cytoscapeVersions>
+
+ <pluginlist>
+ <plugin>
+ <uniqueID>goodZIPPlugin777</uniqueID>
+ <pluginVersion>0.45</pluginVersion>
+ </plugin>
+ <plugin>
+ <uniqueID>goodJarPlugin123</uniqueID>
+ <pluginVersion>1.0</pluginVersion>
+ </plugin>
+ </pluginlist>
+ </theme>
+
+ <theme>
+ <uniqueID>goodThemeTest123</uniqueID>
+ <name>Good Test Theme</name>
+ <description>This is just a test theme.</description>
+ <themeVersion>0.8</themeVersion>
+ <cytoscapeVersions>
+ <version>current</version>
+ </cytoscapeVersions>
+
+ <pluginlist>
+ <plugin>
+ <uniqueID>goodZIPPlugin777</uniqueID>
+ <pluginVersion>0.45</pluginVersion>
+ </plugin>
+ <plugin>
+ <uniqueID>goodJarPlugin123</uniqueID>
+ <name>Good Jar</name>
+ <description>
+ This plugin demonstrates the use of a jar file with the PluginInfo object created and a correct manifest file.
+ </description>
+ <pluginVersion>1.0</pluginVersion>
+
+ <cytoscapeVersions>
+ <version>2.3.3</version>
+ <version>2.4</version>
+ <version>current</version>
+ </cytoscapeVersions>
+
+ <filetype>jar</filetype>
+ <category>Test</category>
+ <url>GoodPlugin.jar</url>
+ <license>
+ <text>
+ This is some license text a user would see and have to ok in order to install a plugin.
+ </text>
+ </license>
+ <authorlist>
+ <author>
+ <name>Ann Smith</name>
+ <institution>UW</institution>
+ </author>
+ </authorlist>
+ </plugin>
+ </pluginlist>
+
+ </theme>
+
+ <theme>
+ <uniqueID>regresstionTestTheme123</uniqueID>
+ <name>Regresstion Test Theme</name>
+ <description>This is just a test theme.</description>
+ <themeVersion>0.5</themeVersion>
+ <cytoscapeVersions>
+ <version>current</version>
+ </cytoscapeVersions>
+
+ <pluginlist>
+ <plugin>
+ <uniqueID>goodZIPPlugin777</uniqueID>
+ <pluginVersion>0.45</pluginVersion>
+ </plugin>
+ <plugin>
+ <uniqueID>goodJarPlugin123</uniqueID>
+ <pluginVersion>1.0</pluginVersion>
+ </plugin>
+ <plugin>
+ <uniqueID>themePlugin1234</uniqueID>
+ <pluginVersion>1.10</pluginVersion>
+ </plugin>
+
+ </pluginlist>
+ </theme>
+
+
+
+
+ </themes>
+
+
+</project>
diff --git a/application/src/test/resources/testData/plugins/test_plugin_no_themes.xml b/application/src/test/resources/testData/plugins/test_plugin_no_themes.xml
new file mode 100644
index 0000000..d1292d1
--- /dev/null
+++ b/application/src/test/resources/testData/plugins/test_plugin_no_themes.xml
@@ -0,0 +1,183 @@
+<!-- Test xml file describing plugins and where to d/l them -->
+<project>
+
+ <name> Cytoscape Plugins </name>
+ <description> Test </description>
+ <url> http://cytoscape.org </url>
+
+ <pluginlist>
+ <!--
+ The urls for each of these plugins SHOULD start with http://...
+ For testing these will be concatenated with file:///user_dir/url
+ Do NOT set up your xml file with partial urls
+ -->
+
+ <plugin>
+ <uniqueID> goodJarPlugin123 </uniqueID>
+ <name> Good Jar </name>
+ <description>
+ This plugin demonstrates the use of a jar file with the PluginInfo object created and a correct manifest file.
+ </description>
+ <pluginVersion> 1.0 </pluginVersion>
+
+ <cytoscapeVersions>
+ <version>2.4</version>
+ <version>current</version>
+ </cytoscapeVersions>
+
+ <filetype> jar </filetype>
+ <category> Test </category>
+ <url> GoodPlugin.jar </url>
+ <license>
+ <text>
+ This is some license text a user would see and have to ok in order to install a plugin.
+ </text>
+ </license>
+ <authorlist>
+ <author>
+ <name> Ann Smith </name>
+ <institution> UW </institution>
+ </author>
+ </authorlist>
+ </plugin>
+
+ <plugin>
+ <uniqueID> goodJarPlugin123 </uniqueID>
+ <name> Good Jar </name>
+ <description>
+ This plugin demonstrates the use of a jar file with the PluginInfo object created and a correct manifest file.
+ This one is an "update" to the previous one for the purposes of testing.
+ </description>
+ <pluginVersion> 2.1 </pluginVersion>
+
+ <cytoscapeVersions>
+ <version>current</version>
+ </cytoscapeVersions>
+
+
+ <filetype> jar </filetype>
+ <category> Test </category>
+ <url> GoodPlugin.jar </url>
+
+<!-- Not sure how to deal with testing this at the moment. I need to turn it into file:/// structure...
+ <license>
+ <url> license.txt </url>
+ </license>
+-->
+ <authorlist>
+ <author>
+ <name> Ann Smith and George James</name>
+ <institution> UW </institution>
+ </author>
+ <author>
+ <name> John Doe </name>
+ <institution> CU </institution>
+ </author>
+ </authorlist>
+ </plugin>
+
+
+ <plugin>
+ <uniqueID> goodZIPPlugin777 </uniqueID>
+ <name> Good Jar </name>
+ <description>
+ This plugin demonstrates the use of a zip file with the correct directories (at least one plugins/*.jar file required) and
+ a correct manifest file.
+ </description>
+ <pluginVersion> 0.45 </pluginVersion>
+
+ <cytoscapeVersions>
+ <version>current</version>
+ </cytoscapeVersions>
+
+ <filetype> zip </filetype>
+ <category> Test </category>
+ <url> GoodPlugin.zip </url>
+ <authorlist>
+ <author>
+ <name> George Smith </name>
+ <institution> UC Mars </institution>
+ </author>
+ </authorlist>
+ </plugin>
+
+
+ <plugin>
+ <uniqueID> badJarPlugin123 </uniqueID>
+ <name> Bad Jar </name>
+ <description>
+ This plugin jar file does not contain the correct manifest file and should fail to install.
+ </description>
+ <pluginVersion> 0.3 </pluginVersion>
+
+ <cytoscapeVersions>
+ <version>current</version>
+ </cytoscapeVersions>
+
+ <filetype> jar </filetype>
+ <category> Test </category>
+ <url> BadPlugin.jar </url>
+ <authorlist>
+ <author>
+ <name> George Smith </name>
+ <institution> UCLA </institution>
+ </author>
+ </authorlist>
+ </plugin>
+
+ <plugin>
+ <uniqueID> badZIPPlugin123 </uniqueID>
+ <name> Bad Jar </name>
+ <description>
+ This plugin zip file does not contain the correct directories (one plugin/*.jar file required) and will fail to install.
+ </description>
+ <pluginVersion> 0.9 </pluginVersion>
+
+ <cytoscapeVersions>
+ <version>current</version>
+ </cytoscapeVersions>
+
+ <filetype> jar </filetype>
+ <category> Test </category>
+ <url> BadPlugin.zip </url>
+ <authorlist>
+ <author>
+ <name> Jill Jones </name>
+ <institution> CSU </institution>
+ </author>
+ </authorlist>
+ </plugin>
+
+ <!-- this is to test the case where the xml incorrectly id's the file type -->
+ <plugin>
+ <uniqueID> badFileType123 </uniqueID>
+ <name> Good Jar </name>
+ <description>
+ This plugin demonstrates the use of a jar file with the PluginInfo object created and a correct manifest file.
+ </description>
+ <pluginVersion> 1.0 </pluginVersion>
+
+ <cytoscapeVersions>
+ <version>2.4</version>
+ <version>current</version>
+ </cytoscapeVersions>
+
+ <filetype> zip </filetype>
+ <category> Test </category>
+ <url> GoodPlugin.jar </url>
+ <license>
+ <text>
+ This is some license text a user would see and have to ok in order to install a plugin.
+ </text>
+ </license>
+ <authorlist>
+ <author>
+ <name> Ann Smith </name>
+ <institution> UW </institution>
+ </author>
+ </authorlist>
+ </plugin>
+ </pluginlist>
+
+
+</project>
diff --git a/application/src/test/resources/testData/plugins/test_plugins.xsl b/application/src/test/resources/testData/plugins/test_plugins.xsl
new file mode 100644
index 0000000..58692cf
--- /dev/null
+++ b/application/src/test/resources/testData/plugins/test_plugins.xsl
@@ -0,0 +1,96 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<xsl:stylesheet xmlns:xsl="http://www.w3.org/1999/XSL/Transform" version="1.0">
+
+ <!-- These params specify variables that will be passed in at transformation time -->
+ <xsl:param name="cytoscapeVersion"/>
+ <xsl:param name="fileUrl"/>
+
+
+ <xsl:template match="/project">
+ <project>
+ <name><xsl:value-of select="name"/></name>
+ <description><xsl:value-of select="description"/></description>
+ <url><xsl:value-of select="url"/></url>
+
+ <pluginlist>
+ <!--
+ The urls for each of these plugins SHOULD start with http://...
+ For testing these will be concatenated with file:///user_dir/url
+ Do NOT set up your xml file with partial urls
+ -->
+ <xsl:for-each select="/project/pluginlist/plugin">
+ <plugin>
+ <uniqueID><xsl:value-of select="uniqueID"/></uniqueID>
+ <name><xsl:value-of select="name"/></name>
+ <description><xsl:value-of select="description"/></description>
+ <pluginVersion><xsl:value-of select="pluginVersion"/></pluginVersion>
+ <cytoscapeVersions>
+ <xsl:for-each select="cytoscapeVersions/version">
+ <version>
+ <xsl:choose>
+ <xsl:when test="current()='current'"><xsl:value-of select="$cytoscapeVersion"/></xsl:when>
+ <xsl:otherwise><xsl:value-of select="current()"/></xsl:otherwise>
+ </xsl:choose>
+ </version>
+ </xsl:for-each>
+ </cytoscapeVersions>
+
+ <filetype><xsl:value-of select="filetype"/></filetype>
+ <category><xsl:value-of select="category"/></category>
+ <url><xsl:value-of select="$fileUrl"/><xsl:value-of select="url"/></url>
+
+ <xsl:if test="license">
+ <license>
+ <text><xsl:value-of select="license/text"/></text>
+ </license>
+ </xsl:if>
+
+ <authorlist>
+ <xsl:for-each select="authorlist/author">
+ <author>
+ <name><xsl:value-of select="name"/></name>
+ <institution><xsl:value-of select="institution"/></institution>
+ </author>
+ </xsl:for-each>
+ </authorlist>
+
+ </plugin>
+ </xsl:for-each>
+ </pluginlist>
+
+ <xsl:if test="themes">
+ <themes>
+ <xsl:for-each select="/project/themes/theme">
+ <theme>
+ <uniqueID><xsl:value-of select="uniqueID"/></uniqueID>
+ <name><xsl:value-of select="name"/></name>
+ <description><xsl:value-of select="description"/></description>
+ <themeVersion><xsl:value-of select="themeVersion"/></themeVersion>
+ <cytoscapeVersions>
+ <xsl:for-each select="cytoscapeVersions/version">
+ <version>
+ <xsl:choose>
+ <xsl:when test="current()='current'"><xsl:value-of select="$cytoscapeVersion"/></xsl:when>
+ <xsl:otherwise><xsl:value-of select="current()"/></xsl:otherwise>
+ </xsl:choose>
+ </version>
+ </xsl:for-each>
+ </cytoscapeVersions>
+
+ <pluginlist>
+ <xsl:for-each select="pluginlist/plugin">
+ <plugin>
+ <uniqueID><xsl:value-of select="uniqueID"/></uniqueID>
+ <pluginVersion><xsl:value-of select="pluginVersion"/></pluginVersion>
+ </plugin>
+ </xsl:for-each>
+ </pluginlist>
+ </theme>
+ </xsl:for-each>
+ </themes>
+
+ </xsl:if>
+ </project>
+ </xsl:template>
+
+</xsl:stylesheet>
diff --git a/application/src/test/resources/testData/plugins/track_plugins.xml b/application/src/test/resources/testData/plugins/track_plugins.xml
new file mode 100644
index 0000000..b67db7e
--- /dev/null
+++ b/application/src/test/resources/testData/plugins/track_plugins.xml
@@ -0,0 +1,430 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<CytoscapePlugin>
+ <CurrentPlugins>
+ <plugin>
+ <uniqueID>1</uniqueID>
+ <name>AutomaticLayout</name>
+ <description>Algorithms for automatic layout of networks.</description>
+ <cytoscapeVersion>2.5</cytoscapeVersion>
+ <url />
+ <downloadUrl>http://cytoscape.org/plugins/plugins.xml</downloadUrl>
+ <category>Core</category>
+ <releaseDate />
+ <pluginVersion>1.0</pluginVersion>
+ <classname>csplugins.layout.LayoutPlugin</classname>
+ <projectUrl />
+ <filetype>jar</filetype>
+ <installLocation>C:\eclipse\workspace\Cytoscape_Main\build\cytoscape-v2.6.0-alpha\plugins\AutomaticLayout.jar</installLocation>
+ <license>
+ <text />
+ </license>
+ <filelist>
+ <file>C:\eclipse\workspace\Cytoscape_Main\plugins\core\AutomaticLayout.jar</file>
+ </filelist>
+ <authorlist>
+ <author>
+ <name>Mike Smoot,Samad Lotia</name>
+ <institution>UCSD</institution>
+ </author>
+ <author>
+ <name>Scooter Morris</name>
+ <institution>UCSF</institution>
+ </author>
+ <author>
+ <name>Rowan Christmas</name>
+ <institution>Institute for Systems Biology</institution>
+ </author>
+ <author>
+ <name>Rob Sheridan</name>
+ <institution>Memorial Sloan-Kettering Cancer Center</institution>
+ </author>
+ <author>
+ <name>Jeffery Heer</name>
+ <institution>Prefuse Library</institution>
+ </author>
+ <author>
+ <name>jGraph</name>
+ <institution>jGraph Library</institution>
+ </author>
+ </authorlist>
+ </plugin>
+ <plugin>
+ <uniqueID>3</uniqueID>
+ <name>Browser</name>
+ <description>Attribute browser</description>
+ <cytoscapeVersion>2.5</cytoscapeVersion>
+ <url />
+ <downloadUrl>http://cytoscape.org/plugins/plugins.xml</downloadUrl>
+ <category>Core</category>
+ <releaseDate />
+ <pluginVersion>0.7</pluginVersion>
+ <classname>browser.AttributeBrowserPlugin</classname>
+ <projectUrl />
+ <filetype>jar</filetype>
+ <installLocation>C:\eclipse\workspace\Cytoscape_Main\build\cytoscape-v2.6.0-alpha\plugins\browser.jar</installLocation>
+ <license>
+ <text />
+ </license>
+ <filelist>
+ <file>C:\eclipse\workspace\Cytoscape_Main\plugins\core\browser.jar</file>
+ </filelist>
+ <authorlist>
+ <author>
+ <name>Kei Ono</name>
+ <institution>UCSD</institution>
+ </author>
+ <author>
+ <name>Rowan Christmas</name>
+ <institution>Institute for Systems Biology</institution>
+ </author>
+ </authorlist>
+ </plugin>
+ <plugin>
+ <uniqueID>4</uniqueID>
+ <name>cPath</name>
+ <description>A plugin that queries the cPath database for specified terms and returns interaction networks.</description>
+ <cytoscapeVersion>2.5</cytoscapeVersion>
+ <url />
+ <downloadUrl />
+ <category>Core</category>
+ <releaseDate />
+ <pluginVersion>1.0</pluginVersion>
+ <classname>org.cytoscape.coreplugin.cpath.plugin.CPathPlugIn</classname>
+ <projectUrl />
+ <filetype>jar</filetype>
+ <installLocation>C:\eclipse\workspace\Cytoscape_Main\build\cytoscape-v2.6.0-alpha\plugins\cPath.jar</installLocation>
+ <license>
+ <text />
+ </license>
+ <filelist>
+ <file>C:\eclipse\workspace\Cytoscape_Main\plugins\core\cPath.jar</file>
+ </filelist>
+ <authorlist>
+ <author>
+ <name>Ethan Cerami</name>
+ <institution>Memorial Sloan-Kettering Cancer Center</institution>
+ </author>
+ </authorlist>
+ </plugin>
+ <plugin>
+ <uniqueID>5</uniqueID>
+ <name>CytoscapeEditor</name>
+ <description>Provides basic ability to edit nodes and edges in a network.</description>
+ <cytoscapeVersion>2.6</cytoscapeVersion>
+ <url />
+ <downloadUrl>http://cytoscape.org/plugins/plugins.xml</downloadUrl>
+ <category>Core</category>
+ <releaseDate>Oct 30, 2007</releaseDate>
+ <pluginVersion>2.53</pluginVersion>
+ <classname>cytoscape.editor.CytoscapeEditorPlugin</classname>
+ <projectUrl />
+ <filetype>jar</filetype>
+ <installLocation>C:\eclipse\workspace\Cytoscape_Main\build\cytoscape-v2.6.0-alpha\plugins\CytoscapeEditor.jar</installLocation>
+ <license>
+ <text />
+ </license>
+ <filelist>
+ <file>C:\eclipse\workspace\Cytoscape_Main\plugins\core\CytoscapeEditor.jar</file>
+ </filelist>
+ <authorlist>
+ <author>
+ <name>Allan Kuchinsky</name>
+ <institution>Agilent Technologies</institution>
+ </author>
+ <author>
+ <name>Michael Creech</name>
+ <institution>Blue Oak Software</institution>
+ </author>
+ </authorlist>
+ </plugin>
+ <plugin>
+ <uniqueID>8</uniqueID>
+ <name>Filters</name>
+ <description>Select nodes and edges based on specific attributes</description>
+ <cytoscapeVersion>2.6</cytoscapeVersion>
+ <url />
+ <downloadUrl>http://cytoscape.org/plugins/plugins.xml</downloadUrl>
+ <category>Core</category>
+ <releaseDate />
+ <pluginVersion>0.2</pluginVersion>
+ <classname>cytoscape.filters.FilterPlugin</classname>
+ <projectUrl />
+ <filetype>jar</filetype>
+ <installLocation>C:\eclipse\workspace\Cytoscape_Main\build\cytoscape-v2.6.0-alpha\plugins\filters.jar</installLocation>
+ <license>
+ <text />
+ </license>
+ <filelist>
+ <file>C:\eclipse\workspace\Cytoscape_Main\plugins\core\filters.jar</file>
+ </filelist>
+ <authorlist>
+ <author>
+ <name>Peng-Liang Wang</name>
+ <institution>UCSD</institution>
+ </author>
+ </authorlist>
+ </plugin>
+ <plugin>
+ <uniqueID>9</uniqueID>
+ <name>GraphMerge</name>
+ <description>Provides set operations (union, intersection, difference) for networks.</description>
+ <cytoscapeVersion>2.5</cytoscapeVersion>
+ <url />
+ <downloadUrl />
+ <category>Core</category>
+ <releaseDate />
+ <pluginVersion>1.0</pluginVersion>
+ <classname>GraphMerge.GraphMerge</classname>
+ <projectUrl />
+ <filetype>jar</filetype>
+ <installLocation>C:\eclipse\workspace\Cytoscape_Main\build\cytoscape-v2.6.0-alpha\plugins\GraphMerge.jar</installLocation>
+ <license>
+ <text />
+ </license>
+ <filelist>
+ <file>C:\eclipse\workspace\Cytoscape_Main\plugins\core\GraphMerge.jar</file>
+ </filelist>
+ <authorlist>
+ <author>
+ <name>Ryan Kelley</name>
+ <institution>UCSD</institution>
+ </author>
+ </authorlist>
+ </plugin>
+ <plugin>
+ <uniqueID>10</uniqueID>
+ <name>LinkOut</name>
+ <description>Provides URLs that link to various biological databases based on query terms.</description>
+ <cytoscapeVersion>2.6</cytoscapeVersion>
+ <url />
+ <downloadUrl>http://cytoscape.org/plugins/plugins.xml</downloadUrl>
+ <category>Core</category>
+ <releaseDate />
+ <pluginVersion>2.01</pluginVersion>
+ <classname>linkout.LinkOutPlugin</classname>
+ <projectUrl />
+ <filetype>jar</filetype>
+ <installLocation>C:\eclipse\workspace\Cytoscape_Main\build\cytoscape-v2.6.0-alpha\plugins\linkout.jar</installLocation>
+ <license>
+ <text />
+ </license>
+ <filelist>
+ <file>C:\eclipse\workspace\Cytoscape_Main\plugins\core\linkout.jar</file>
+ </filelist>
+ <authorlist>
+ <author>
+ <name>Doron Betel</name>
+ <institution>MSKCC</institution>
+ </author>
+ </authorlist>
+ </plugin>
+ <plugin>
+ <uniqueID>12</uniqueID>
+ <name>ManualLayout</name>
+ <description>User-defined positioning of layouts</description>
+ <cytoscapeVersion>2.5</cytoscapeVersion>
+ <url />
+ <downloadUrl />
+ <category>Core</category>
+ <releaseDate />
+ <pluginVersion>1.0</pluginVersion>
+ <classname>ManualLayout.ManualLayoutPlugin</classname>
+ <projectUrl />
+ <filetype>jar</filetype>
+ <installLocation>C:\eclipse\workspace\Cytoscape_Main\build\cytoscape-v2.6.0-alpha\plugins\ManualLayout.jar</installLocation>
+ <license>
+ <text />
+ </license>
+ <filelist>
+ <file>C:\eclipse\workspace\Cytoscape_Main\plugins\core\ManualLayout.jar</file>
+ </filelist>
+ <authorlist>
+ <author>
+ <name>Mike Smoot,Nerius Landys</name>
+ <institution>UCSD</institution>
+ </author>
+ <author>
+ <name>Alex Pico</name>
+ <institution>UCSF</institution>
+ </author>
+ <author>
+ <name>Allan Kuchinsky</name>
+ <institution>Agilent Technologies</institution>
+ </author>
+ </authorlist>
+ </plugin>
+ <plugin>
+ <uniqueID>13</uniqueID>
+ <name>PSI-MI</name>
+ <description>Allows importing of PSI-MI 2.5 file format</description>
+ <cytoscapeVersion>2.5</cytoscapeVersion>
+ <url />
+ <downloadUrl />
+ <category>Core</category>
+ <releaseDate />
+ <pluginVersion>0.3</pluginVersion>
+ <classname>org.cytoscape.coreplugin.psi_mi.plugin.PsiMiPlugIn</classname>
+ <projectUrl />
+ <filetype>jar</filetype>
+ <installLocation>C:\eclipse\workspace\Cytoscape_Main\build\cytoscape-v2.6.0-alpha\plugins\psi_mi.jar</installLocation>
+ <license>
+ <text />
+ </license>
+ <filelist>
+ <file>C:\eclipse\workspace\Cytoscape_Main\plugins\core\psi_mi.jar</file>
+ </filelist>
+ <authorlist>
+ <author>
+ <name>Ethan Cerami</name>
+ <institution>Memorial Sloan-Kettering Cancer Center</institution>
+ </author>
+ </authorlist>
+ </plugin>
+ <plugin>
+ <uniqueID>14</uniqueID>
+ <name>QuickFind</name>
+ <description>Provides a search dialog in the toolbar that can used to search for nodes and edges based on attributes.</description>
+ <cytoscapeVersion>2.5</cytoscapeVersion>
+ <url />
+ <downloadUrl>http://cytoscape.org/plugins/plugins.xml</downloadUrl>
+ <category>Core</category>
+ <releaseDate />
+ <pluginVersion>0.5</pluginVersion>
+ <classname>csplugins.quickfind.plugin.QuickFindPlugIn</classname>
+ <projectUrl />
+ <filetype>jar</filetype>
+ <installLocation>C:\eclipse\workspace\Cytoscape_Main\build\cytoscape-v2.6.0-alpha\plugins\quick_find.jar</installLocation>
+ <license>
+ <text />
+ </license>
+ <filelist>
+ <file>C:\eclipse\workspace\Cytoscape_Main\plugins\core\quick_find.jar</file>
+ </filelist>
+ <authorlist>
+ <author>
+ <name>Ethan Cerami</name>
+ <institution>Memorial Sloan-Kettering Cancer Center</institution>
+ </author>
+ </authorlist>
+ </plugin>
+ <plugin>
+ <uniqueID>15</uniqueID>
+ <name>SBML Reader</name>
+ <description>Provides the ability to import SBML (Systems Biology Markup Language) formatted files.</description>
+ <cytoscapeVersion>2.5</cytoscapeVersion>
+ <url />
+ <downloadUrl />
+ <category>Core</category>
+ <releaseDate />
+ <pluginVersion>0.5</pluginVersion>
+ <classname>sbmlreader.SBMLReaderPlugin</classname>
+ <projectUrl />
+ <filetype>jar</filetype>
+ <installLocation>C:\eclipse\workspace\Cytoscape_Main\build\cytoscape-v2.6.0-alpha\plugins\SBMLReader.jar</installLocation>
+ <license>
+ <text />
+ </license>
+ <filelist>
+ <file>C:\eclipse\workspace\Cytoscape_Main\plugins\core\SBMLReader.jar</file>
+ </filelist>
+ <authorlist>
+ <author>
+ <name>Willem Ligtenberg</name>
+ <institution>Eindhoven University of Technology</institution>
+ </author>
+ </authorlist>
+ </plugin>
+ <plugin>
+ <uniqueID>16</uniqueID>
+ <name>Table Import</name>
+ <description>Provides the ability to import network and attribute files from formatted text and Excel files.</description>
+ <cytoscapeVersion>2.5</cytoscapeVersion>
+ <url />
+ <downloadUrl>http://cytoscape.org/plugins/plugins.xml</downloadUrl>
+ <category>Core</category>
+ <releaseDate />
+ <pluginVersion>0.5</pluginVersion>
+ <classname>edu.ucsd.bioeng.coreplugin.tableImport.TableImportPlugin</classname>
+ <projectUrl />
+ <filetype>jar</filetype>
+ <installLocation>C:\eclipse\workspace\Cytoscape_Main\build\cytoscape-v2.6.0-alpha\plugins\TableImport.jar</installLocation>
+ <license>
+ <text />
+ </license>
+ <filelist>
+ <file>C:\eclipse\workspace\Cytoscape_Main\plugins\core\TableImport.jar</file>
+ </filelist>
+ <authorlist>
+ <author>
+ <name>Kei Ono</name>
+ <institution>UCSD</institution>
+ </author>
+ </authorlist>
+ </plugin>
+ <plugin>
+ <uniqueID>105</uniqueID>
+ <name>HyperEdgeEditor</name>
+ <description>Add, remove, and modify HyperEdges in a Cytoscape Network.</description>
+ <cytoscapeVersion>2.6</cytoscapeVersion>
+ <url>http://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=57</url>
+ <downloadUrl>http://cytoscape.org/plugins/plugins.xml</downloadUrl>
+ <category>Functional Enrichment</category>
+ <releaseDate>January 17, 2008</releaseDate>
+ <pluginVersion>2.6</pluginVersion>
+ <classname>cytoscape.hyperedge.editor.HyperEdgeEditorPlugin</classname>
+ <projectUrl />
+ <filetype>jar</filetype>
+ <installLocation>C:\Documents and Settings\Administrator\.cytoscape\2.6\plugins\HyperEdgeEditor-2.6</installLocation>
+ <license>
+ <text />
+ </license>
+ <filelist>
+ <file>C:\Documents and Settings\Administrator\.cytoscape\2.6\plugins\HyperEdgeEditor-2.6\HyperEdgeEditor.jar</file>
+ </filelist>
+ <authorlist>
+ <author>
+ <name>Allan Kuchinsky and Aditya Vailaya</name>
+ <institution>Agilent Labs</institution>
+ </author>
+ <author>
+ <name>Michael Creech</name>
+ <institution>Blue Oak Software</institution>
+ </author>
+ </authorlist>
+ </plugin>
+ <plugin>
+ <uniqueID>2</uniqueID>
+ <name>BioPAX</name>
+ <description>Enables import of BioPAX formatted files.</description>
+ <cytoscapeVersion>2.6</cytoscapeVersion>
+ <url />
+ <downloadUrl>http://cytoscape.org/plugins/plugins.xml</downloadUrl>
+ <category>Network and Attribute I/O</category>
+ <releaseDate>January 1, 2008</releaseDate>
+ <pluginVersion>0.6</pluginVersion>
+ <classname>org.mskcc.biopax_plugin.plugin.BioPaxPlugIn</classname>
+ <projectUrl />
+ <filetype>jar</filetype>
+ <installLocation>C:\eclipse\workspace\Cytoscape_Main\build\cytoscape-v2.6.0-alpha\plugins\biopax.jar</installLocation>
+ <license>
+ <text />
+ </license>
+ <authorlist>
+ <author>
+ <name>Ethan Cerami, Benjamin Gross, Chris Sander</name>
+ <institution>Memorial Sloan-Kettering Cancer Center</institution>
+ </author>
+ <author>
+ <name>Gary Bader</name>
+ <institution>Uniersity of Toronto</institution>
+ </author>
+ </authorlist>
+ <filelist>
+ <file>C:\eclipse\workspace\Cytoscape_Main\build\cytoscape-v2.6.0-alpha\plugins\biopax.jar</file>
+ </filelist>
+ </plugin>
+ </CurrentPlugins>
+ <InstallPlugins />
+ <DeletePlugins />
+</CytoscapePlugin>
+
diff --git a/application/src/test/resources/testData/plugins/track_plugins_c1.xml b/application/src/test/resources/testData/plugins/track_plugins_c1.xml
new file mode 100644
index 0000000..27fd0c3
--- /dev/null
+++ b/application/src/test/resources/testData/plugins/track_plugins_c1.xml
@@ -0,0 +1,429 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<CytoscapePlugin>
+ <CurrentPlugins>
+ <plugin>
+ <uniqueID>1</uniqueID>
+ <name>AutomaticLayout</name>
+ <description>Algorithms for automatic layout of networks.</description>
+ <cytoscapeVersion>2.5</cytoscapeVersion>
+ <url />
+ <downloadUrl>http://cytoscape.org/plugins/plugins.xml</downloadUrl>
+ <category>Core</category>
+ <releaseDate />
+ <pluginVersion>1.0</pluginVersion>
+ <classname>csplugins.layout.LayoutPlugin</classname>
+ <projectUrl />
+ <filetype>jar</filetype>
+ <installLocation>C:\eclipse\workspace\Cytoscape_Main\build\cytoscape-v2.6.0-alpha\plugins\AutomaticLayout.jar</installLocation>
+ <license>
+ <text />
+ </license>
+ <filelist>
+ <file>C:\eclipse\workspace\Cytoscape_Main\plugins\core\AutomaticLayout.jar</file>
+ </filelist>
+ <authorlist>
+ <author>
+ <name>Mike Smoot,Samad Lotia</name>
+ <institution>UCSD</institution>
+ </author>
+ <author>
+ <name>Scooter Morris</name>
+ <institution>UCSF</institution>
+ </author>
+ <author>
+ <name>Rowan Christmas</name>
+ <institution>Institute for Systems Biology</institution>
+ </author>
+ <author>
+ <name>Rob Sheridan</name>
+ <institution>Memorial Sloan-Kettering Cancer Center</institution>
+ </author>
+ <author>
+ <name>Jeffery Heer</name>
+ <institution>Prefuse Library</institution>
+ </author>
+ <author>
+ <name>jGraph</name>
+ <institution>jGraph Library</institution>
+ </author>
+ </authorlist>
+ </plugin>
+ <plugin>
+ <uniqueID>3</uniqueID>
+ <name>Browser</name>
+ <description>Attribute browser</description>
+ <cytoscapeVersion>2.5</cytoscapeVersion>
+ <url />
+ <downloadUrl>http://cytoscape.org/plugins/plugins.xml</downloadUrl>
+ <category>Core</category>
+ <releaseDate />
+ <pluginVersion>0.7</pluginVersion>
+ <classname>browser.AttributeBrowserPlugin</classname>
+ <projectUrl />
+ <filetype>jar</filetype>
+ <installLocation>C:\eclipse\workspace\Cytoscape_Main\build\cytoscape-v2.6.0-alpha\plugins\browser.jar</installLocation>
+ <license>
+ <text />
+ </license>
+ <filelist>
+ <file>C:\eclipse\workspace\Cytoscape_Main\plugins\core\browser.jar</file>
+ </filelist>
+ <authorlist>
+ <author>
+ <name>Kei Ono</name>
+ <institution>UCSD</institution>
+ </author>
+ <author>
+ <name>Rowan Christmas</name>
+ <institution>Institute for Systems Biology</institution>
+ </author>
+ </authorlist>
+ </plugin>
+ <plugin>
+ <uniqueID>4</uniqueID>
+ <name>cPath</name>
+ <description>A plugin that queries the cPath database for specified terms and returns interaction networks.</description>
+ <cytoscapeVersion>2.5</cytoscapeVersion>
+ <url />
+ <downloadUrl />
+ <category>Core</category>
+ <releaseDate />
+ <pluginVersion>1.0</pluginVersion>
+ <classname>org.cytoscape.coreplugin.cpath.plugin.CPathPlugIn</classname>
+ <projectUrl />
+ <filetype>jar</filetype>
+ <installLocation>C:\eclipse\workspace\Cytoscape_Main\build\cytoscape-v2.6.0-alpha\plugins\cPath.jar</installLocation>
+ <license>
+ <text />
+ </license>
+ <filelist>
+ <file>C:\eclipse\workspace\Cytoscape_Main\plugins\core\cPath.jar</file>
+ </filelist>
+ <authorlist>
+ <author>
+ <name>Ethan Cerami</name>
+ <institution>Memorial Sloan-Kettering Cancer Center</institution>
+ </author>
+ </authorlist>
+ </plugin>
+ <plugin>
+ <uniqueID>5</uniqueID>
+ <name>CytoscapeEditor</name>
+ <description>Provides basic ability to edit nodes and edges in a network.</description>
+ <cytoscapeVersion>2.6</cytoscapeVersion>
+ <url />
+ <downloadUrl>http://cytoscape.org/plugins/plugins.xml</downloadUrl>
+ <category>Core</category>
+ <releaseDate>Oct 30, 2007</releaseDate>
+ <pluginVersion>2.53</pluginVersion>
+ <classname>cytoscape.editor.CytoscapeEditorPlugin</classname>
+ <projectUrl />
+ <filetype>jar</filetype>
+ <installLocation>C:\eclipse\workspace\Cytoscape_Main\build\cytoscape-v2.6.0-alpha\plugins\CytoscapeEditor.jar</installLocation>
+ <license>
+ <text />
+ </license>
+ <filelist>
+ <file>C:\eclipse\workspace\Cytoscape_Main\plugins\core\CytoscapeEditor.jar</file>
+ </filelist>
+ <authorlist>
+ <author>
+ <name>Allan Kuchinsky</name>
+ <institution>Agilent Technologies</institution>
+ </author>
+ <author>
+ <name>Michael Creech</name>
+ <institution>Blue Oak Software</institution>
+ </author>
+ </authorlist>
+ </plugin>
+ <plugin>
+ <uniqueID>8</uniqueID>
+ <name>Filters</name>
+ <description>Select nodes and edges based on specific attributes</description>
+ <cytoscapeVersion>2.6</cytoscapeVersion>
+ <url />
+ <downloadUrl>http://cytoscape.org/plugins/plugins.xml</downloadUrl>
+ <category>Core</category>
+ <releaseDate />
+ <pluginVersion>0.2</pluginVersion>
+ <classname>cytoscape.filters.FilterPlugin</classname>
+ <projectUrl />
+ <filetype>jar</filetype>
+ <installLocation>C:\eclipse\workspace\Cytoscape_Main\build\cytoscape-v2.6.0-alpha\plugins\filters.jar</installLocation>
+ <license>
+ <text />
+ </license>
+ <filelist>
+ <file>C:\eclipse\workspace\Cytoscape_Main\plugins\core\filters.jar</file>
+ </filelist>
+ <authorlist>
+ <author>
+ <name>Peng-Liang Wang</name>
+ <institution>UCSD</institution>
+ </author>
+ </authorlist>
+ </plugin>
+ <plugin>
+ <uniqueID>9</uniqueID>
+ <name>GraphMerge</name>
+ <description>Provides set operations (union, intersection, difference) for networks.</description>
+ <cytoscapeVersion>2.5</cytoscapeVersion>
+ <url />
+ <downloadUrl />
+ <category>Core</category>
+ <releaseDate />
+ <pluginVersion>1.0</pluginVersion>
+ <classname>GraphMerge.GraphMerge</classname>
+ <projectUrl />
+ <filetype>jar</filetype>
+ <installLocation>C:\eclipse\workspace\Cytoscape_Main\build\cytoscape-v2.6.0-alpha\plugins\GraphMerge.jar</installLocation>
+ <license>
+ <text />
+ </license>
+ <filelist>
+ <file>C:\eclipse\workspace\Cytoscape_Main\plugins\core\GraphMerge.jar</file>
+ </filelist>
+ <authorlist>
+ <author>
+ <name>Ryan Kelley</name>
+ <institution>UCSD</institution>
+ </author>
+ </authorlist>
+ </plugin>
+ <plugin>
+ <uniqueID>10</uniqueID>
+ <name>LinkOut</name>
+ <description>Provides URLs that link to various biological databases based on query terms.</description>
+ <cytoscapeVersion>2.6</cytoscapeVersion>
+ <url />
+ <downloadUrl>http://cytoscape.org/plugins/plugins.xml</downloadUrl>
+ <category>Core</category>
+ <releaseDate />
+ <pluginVersion>2.01</pluginVersion>
+ <classname>linkout.LinkOutPlugin</classname>
+ <projectUrl />
+ <filetype>jar</filetype>
+ <installLocation>C:\eclipse\workspace\Cytoscape_Main\build\cytoscape-v2.6.0-alpha\plugins\linkout.jar</installLocation>
+ <license>
+ <text />
+ </license>
+ <filelist>
+ <file>C:\eclipse\workspace\Cytoscape_Main\plugins\core\linkout.jar</file>
+ </filelist>
+ <authorlist>
+ <author>
+ <name>Doron Betel</name>
+ <institution>MSKCC</institution>
+ </author>
+ </authorlist>
+ </plugin>
+ <plugin>
+ <uniqueID>12</uniqueID>
+ <name>ManualLayout</name>
+ <description>User-defined positioning of layouts</description>
+ <cytoscapeVersion>2.5</cytoscapeVersion>
+ <url />
+ <downloadUrl />
+ <category>Core</category>
+ <releaseDate />
+ <pluginVersion>1.0</pluginVersion>
+ <classname>ManualLayout.ManualLayoutPlugin</classname>
+ <projectUrl />
+ <filetype>jar</filetype>
+ <installLocation>C:\eclipse\workspace\Cytoscape_Main\build\cytoscape-v2.6.0-alpha\plugins\ManualLayout.jar</installLocation>
+ <license>
+ <text />
+ </license>
+ <filelist>
+ <file>C:\eclipse\workspace\Cytoscape_Main\plugins\core\ManualLayout.jar</file>
+ </filelist>
+ <authorlist>
+ <author>
+ <name>Mike Smoot,Nerius Landys</name>
+ <institution>UCSD</institution>
+ </author>
+ <author>
+ <name>Alex Pico</name>
+ <institution>UCSF</institution>
+ </author>
+ <author>
+ <name>Allan Kuchinsky</name>
+ <institution>Agilent Technologies</institution>
+ </author>
+ </authorlist>
+ </plugin>
+ <plugin>
+ <uniqueID>13</uniqueID>
+ <name>PSI-MI</name>
+ <description>Allows importing of PSI-MI 2.5 file format</description>
+ <cytoscapeVersion>2.5</cytoscapeVersion>
+ <url />
+ <downloadUrl />
+ <category>Core</category>
+ <releaseDate />
+ <pluginVersion>0.3</pluginVersion>
+ <classname>org.cytoscape.coreplugin.psi_mi.plugin.PsiMiPlugIn</classname>
+ <projectUrl />
+ <filetype>jar</filetype>
+ <installLocation>C:\eclipse\workspace\Cytoscape_Main\build\cytoscape-v2.6.0-alpha\plugins\psi_mi.jar</installLocation>
+ <license>
+ <text />
+ </license>
+ <filelist>
+ <file>C:\eclipse\workspace\Cytoscape_Main\plugins\core\psi_mi.jar</file>
+ </filelist>
+ <authorlist>
+ <author>
+ <name>Ethan Cerami</name>
+ <institution>Memorial Sloan-Kettering Cancer Center</institution>
+ </author>
+ </authorlist>
+ </plugin>
+ <plugin>
+ <uniqueID>14</uniqueID>
+ <name>QuickFind</name>
+ <description>Provides a search dialog in the toolbar that can used to search for nodes and edges based on attributes.</description>
+ <cytoscapeVersion>2.5</cytoscapeVersion>
+ <url />
+ <downloadUrl>http://cytoscape.org/plugins/plugins.xml</downloadUrl>
+ <category>Core</category>
+ <releaseDate />
+ <pluginVersion>0.5</pluginVersion>
+ <classname>csplugins.quickfind.plugin.QuickFindPlugIn</classname>
+ <projectUrl />
+ <filetype>jar</filetype>
+ <installLocation>C:\eclipse\workspace\Cytoscape_Main\build\cytoscape-v2.6.0-alpha\plugins\quick_find.jar</installLocation>
+ <license>
+ <text />
+ </license>
+ <filelist>
+ <file>C:\eclipse\workspace\Cytoscape_Main\plugins\core\quick_find.jar</file>
+ </filelist>
+ <authorlist>
+ <author>
+ <name>Ethan Cerami</name>
+ <institution>Memorial Sloan-Kettering Cancer Center</institution>
+ </author>
+ </authorlist>
+ </plugin>
+ <plugin>
+ <uniqueID>15</uniqueID>
+ <name>SBML Reader</name>
+ <description>Provides the ability to import SBML (Systems Biology Markup Language) formatted files.</description>
+ <cytoscapeVersion>2.5</cytoscapeVersion>
+ <url />
+ <downloadUrl />
+ <category>Core</category>
+ <releaseDate />
+ <pluginVersion>0.5</pluginVersion>
+ <classname>sbmlreader.SBMLReaderPlugin</classname>
+ <projectUrl />
+ <filetype>jar</filetype>
+ <installLocation>C:\eclipse\workspace\Cytoscape_Main\build\cytoscape-v2.6.0-alpha\plugins\SBMLReader.jar</installLocation>
+ <license>
+ <text />
+ </license>
+ <filelist>
+ <file>C:\eclipse\workspace\Cytoscape_Main\plugins\core\SBMLReader.jar</file>
+ </filelist>
+ <authorlist>
+ <author>
+ <name>Willem Ligtenberg</name>
+ <institution>Eindhoven University of Technology</institution>
+ </author>
+ </authorlist>
+ </plugin>
+ <plugin>
+ <uniqueID>16</uniqueID>
+ <name>Table Import</name>
+ <description>Provides the ability to import network and attribute files from formatted text and Excel files.</description>
+ <cytoscapeVersion>2.5</cytoscapeVersion>
+ <url />
+ <downloadUrl>http://cytoscape.org/plugins/plugins.xml</downloadUrl>
+ <category>Core</category>
+ <releaseDate />
+ <pluginVersion>0.5</pluginVersion>
+ <classname>edu.ucsd.bioeng.coreplugin.tableImport.TableImportPlugin</classname>
+ <projectUrl />
+ <filetype>jar</filetype>
+ <installLocation>C:\eclipse\workspace\Cytoscape_Main\build\cytoscape-v2.6.0-alpha\plugins\TableImport.jar</installLocation>
+ <license>
+ <text />
+ </license>
+ <filelist>
+ <file>C:\eclipse\workspace\Cytoscape_Main\plugins\core\TableImport.jar</file>
+ </filelist>
+ <authorlist>
+ <author>
+ <name>Kei Ono</name>
+ <institution>UCSD</institution>
+ </author>
+ </authorlist>
+ </plugin>
+ <plugin>
+ <uniqueID>105</uniqueID>
+ <name>HyperEdgeEditor</name>
+ <description>Add, remove, and modify HyperEdges in a Cytoscape Network.</description>
+ <cytoscapeVersion>2.6</cytoscapeVersion>
+ <url>http://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=57</url>
+ <downloadUrl>http://cytoscape.org/plugins/plugins.xml</downloadUrl>
+ <category>Functional Enrichment</category>
+ <releaseDate>January 17, 2008</releaseDate>
+ <pluginVersion>2.6</pluginVersion>
+ <classname>cytoscape.hyperedge.editor.HyperEdgeEditorPlugin</classname>
+ <projectUrl />
+ <filetype>jar</filetype>
+ <installLocation>C:\Documents and Settings\Administrator\.cytoscape\2.6\plugins\HyperEdgeEditor-2.6</installLocation>
+ <license>
+ <text />
+ </license>
+ <filelist>
+ <file>C:\Documents and Settings\Administrator\.cytoscape\2.6\plugins\HyperEdgeEditor-2.6\HyperEdgeEditor.jar</file>
+ </filelist>
+ <authorlist>
+ <author>
+ <name>Allan Kuchinsky and Aditya Vailaya</name>
+ <institution>Agilent Labs</institution>
+ </author>
+ <author>
+ <name>Michael Creech</name>
+ <institution>Blue Oak Software</institution>
+ </author>
+ </authorlist>
+ </plugin>
+ <!-- corrupt a single entry -->
+ <plugin>
+ <uniqueID>2</uniqueID>
+ <name>BioPAX</name>
+ <description>Enables import of BioPAX formatted files.</description>
+ <cytoscapeVersion>2.6</cytoscapeVersion>
+ <downloadUrl>http://cytoscape.org/plugins/plugins.xml</downloadUrl>
+ <category>Network and Attribute I/O</category>
+ <releaseDate>January 1, 2008</releaseDate>
+ <classname>org.mskcc.biopax_plugin.plugin.BioPaxPlugIn</classname>
+ <projectUrl />
+ <filetype>jar</filetype>
+ <installLocation>C:\eclipse\workspace\Cytoscape_Main\build\cytoscape-v2.6.0-alpha\plugins\biopax.jar</installLocation>
+ <license>
+ <text />
+ </license>
+ <authorlist>
+ <author>
+ <name>Ethan Cerami, Benjamin Gross, Chris Sander</name>
+ <institution>Memorial Sloan-Kettering Cancer Center</institution>
+ </author>
+ <author>
+ <name>Gary Bader</name>
+ <institution>Uniersity of Toronto</institution>
+ </author>
+ </authorlist>
+ <filelist>
+ <file>C:\eclipse\workspace\Cytoscape_Main\build\cytoscape-v2.6.0-alpha\plugins\biopax.jar</file>
+ </filelist>
+ </plugin>
+ </CurrentPlugins>
+ <InstallPlugins />
+ <DeletePlugins />
+</CytoscapePlugin>
+
diff --git a/application/src/test/resources/testData/plugins/track_plugins_c2.xml b/application/src/test/resources/testData/plugins/track_plugins_c2.xml
new file mode 100644
index 0000000..6c879c7
--- /dev/null
+++ b/application/src/test/resources/testData/plugins/track_plugins_c2.xml
@@ -0,0 +1,430 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<CytoscapePlugin>
+ <!-- Missing major element <CurrentPlugins> -->
+
+ <plugin>
+ <uniqueID>1</uniqueID>
+ <name>AutomaticLayout</name>
+ <description>Algorithms for automatic layout of networks.</description>
+ <cytoscapeVersion>2.5</cytoscapeVersion>
+ <url />
+ <downloadUrl>http://cytoscape.org/plugins/plugins.xml</downloadUrl>
+ <category>Core</category>
+ <releaseDate />
+ <pluginVersion>1.0</pluginVersion>
+ <classname>csplugins.layout.LayoutPlugin</classname>
+ <projectUrl />
+ <filetype>jar</filetype>
+ <installLocation>C:\eclipse\workspace\Cytoscape_Main\build\cytoscape-v2.6.0-alpha\plugins\AutomaticLayout.jar</installLocation>
+ <license>
+ <text />
+ </license>
+ <filelist>
+ <file>C:\eclipse\workspace\Cytoscape_Main\plugins\core\AutomaticLayout.jar</file>
+ </filelist>
+ <authorlist>
+ <author>
+ <name>Mike Smoot,Samad Lotia</name>
+ <institution>UCSD</institution>
+ </author>
+ <author>
+ <name>Scooter Morris</name>
+ <institution>UCSF</institution>
+ </author>
+ <author>
+ <name>Rowan Christmas</name>
+ <institution>Institute for Systems Biology</institution>
+ </author>
+ <author>
+ <name>Rob Sheridan</name>
+ <institution>Memorial Sloan-Kettering Cancer Center</institution>
+ </author>
+ <author>
+ <name>Jeffery Heer</name>
+ <institution>Prefuse Library</institution>
+ </author>
+ <author>
+ <name>jGraph</name>
+ <institution>jGraph Library</institution>
+ </author>
+ </authorlist>
+ </plugin>
+ <plugin>
+ <uniqueID>3</uniqueID>
+ <name>Browser</name>
+ <description>Attribute browser</description>
+ <cytoscapeVersion>2.5</cytoscapeVersion>
+ <url />
+ <downloadUrl>http://cytoscape.org/plugins/plugins.xml</downloadUrl>
+ <category>Core</category>
+ <releaseDate />
+ <pluginVersion>0.7</pluginVersion>
+ <classname>browser.AttributeBrowserPlugin</classname>
+ <projectUrl />
+ <filetype>jar</filetype>
+ <installLocation>C:\eclipse\workspace\Cytoscape_Main\build\cytoscape-v2.6.0-alpha\plugins\browser.jar</installLocation>
+ <license>
+ <text />
+ </license>
+ <filelist>
+ <file>C:\eclipse\workspace\Cytoscape_Main\plugins\core\browser.jar</file>
+ </filelist>
+ <authorlist>
+ <author>
+ <name>Kei Ono</name>
+ <institution>UCSD</institution>
+ </author>
+ <author>
+ <name>Rowan Christmas</name>
+ <institution>Institute for Systems Biology</institution>
+ </author>
+ </authorlist>
+ </plugin>
+ <plugin>
+ <uniqueID>4</uniqueID>
+ <name>cPath</name>
+ <description>A plugin that queries the cPath database for specified terms and returns interaction networks.</description>
+ <cytoscapeVersion>2.5</cytoscapeVersion>
+ <url />
+ <downloadUrl />
+ <category>Core</category>
+ <releaseDate />
+ <pluginVersion>1.0</pluginVersion>
+ <classname>org.cytoscape.coreplugin.cpath.plugin.CPathPlugIn</classname>
+ <projectUrl />
+ <filetype>jar</filetype>
+ <installLocation>C:\eclipse\workspace\Cytoscape_Main\build\cytoscape-v2.6.0-alpha\plugins\cPath.jar</installLocation>
+ <license>
+ <text />
+ </license>
+ <filelist>
+ <file>C:\eclipse\workspace\Cytoscape_Main\plugins\core\cPath.jar</file>
+ </filelist>
+ <authorlist>
+ <author>
+ <name>Ethan Cerami</name>
+ <institution>Memorial Sloan-Kettering Cancer Center</institution>
+ </author>
+ </authorlist>
+ </plugin>
+ <plugin>
+ <uniqueID>5</uniqueID>
+ <name>CytoscapeEditor</name>
+ <description>Provides basic ability to edit nodes and edges in a network.</description>
+ <cytoscapeVersion>2.6</cytoscapeVersion>
+ <url />
+ <downloadUrl>http://cytoscape.org/plugins/plugins.xml</downloadUrl>
+ <category>Core</category>
+ <releaseDate>Oct 30, 2007</releaseDate>
+ <pluginVersion>2.53</pluginVersion>
+ <classname>cytoscape.editor.CytoscapeEditorPlugin</classname>
+ <projectUrl />
+ <filetype>jar</filetype>
+ <installLocation>C:\eclipse\workspace\Cytoscape_Main\build\cytoscape-v2.6.0-alpha\plugins\CytoscapeEditor.jar</installLocation>
+ <license>
+ <text />
+ </license>
+ <filelist>
+ <file>C:\eclipse\workspace\Cytoscape_Main\plugins\core\CytoscapeEditor.jar</file>
+ </filelist>
+ <authorlist>
+ <author>
+ <name>Allan Kuchinsky</name>
+ <institution>Agilent Technologies</institution>
+ </author>
+ <author>
+ <name>Michael Creech</name>
+ <institution>Blue Oak Software</institution>
+ </author>
+ </authorlist>
+ </plugin>
+ <plugin>
+ <uniqueID>8</uniqueID>
+ <name>Filters</name>
+ <description>Select nodes and edges based on specific attributes</description>
+ <cytoscapeVersion>2.6</cytoscapeVersion>
+ <url />
+ <downloadUrl>http://cytoscape.org/plugins/plugins.xml</downloadUrl>
+ <category>Core</category>
+ <releaseDate />
+ <pluginVersion>0.2</pluginVersion>
+ <classname>cytoscape.filters.FilterPlugin</classname>
+ <projectUrl />
+ <filetype>jar</filetype>
+ <installLocation>C:\eclipse\workspace\Cytoscape_Main\build\cytoscape-v2.6.0-alpha\plugins\filters.jar</installLocation>
+ <license>
+ <text />
+ </license>
+ <filelist>
+ <file>C:\eclipse\workspace\Cytoscape_Main\plugins\core\filters.jar</file>
+ </filelist>
+ <authorlist>
+ <author>
+ <name>Peng-Liang Wang</name>
+ <institution>UCSD</institution>
+ </author>
+ </authorlist>
+ </plugin>
+ <plugin>
+ <uniqueID>9</uniqueID>
+ <name>GraphMerge</name>
+ <description>Provides set operations (union, intersection, difference) for networks.</description>
+ <cytoscapeVersion>2.5</cytoscapeVersion>
+ <url />
+ <downloadUrl />
+ <category>Core</category>
+ <releaseDate />
+ <pluginVersion>1.0</pluginVersion>
+ <classname>GraphMerge.GraphMerge</classname>
+ <projectUrl />
+ <filetype>jar</filetype>
+ <installLocation>C:\eclipse\workspace\Cytoscape_Main\build\cytoscape-v2.6.0-alpha\plugins\GraphMerge.jar</installLocation>
+ <license>
+ <text />
+ </license>
+ <filelist>
+ <file>C:\eclipse\workspace\Cytoscape_Main\plugins\core\GraphMerge.jar</file>
+ </filelist>
+ <authorlist>
+ <author>
+ <name>Ryan Kelley</name>
+ <institution>UCSD</institution>
+ </author>
+ </authorlist>
+ </plugin>
+ <plugin>
+ <uniqueID>10</uniqueID>
+ <name>LinkOut</name>
+ <description>Provides URLs that link to various biological databases based on query terms.</description>
+ <cytoscapeVersion>2.6</cytoscapeVersion>
+ <url />
+ <downloadUrl>http://cytoscape.org/plugins/plugins.xml</downloadUrl>
+ <category>Core</category>
+ <releaseDate />
+ <pluginVersion>2.01</pluginVersion>
+ <classname>linkout.LinkOutPlugin</classname>
+ <projectUrl />
+ <filetype>jar</filetype>
+ <installLocation>C:\eclipse\workspace\Cytoscape_Main\build\cytoscape-v2.6.0-alpha\plugins\linkout.jar</installLocation>
+ <license>
+ <text />
+ </license>
+ <filelist>
+ <file>C:\eclipse\workspace\Cytoscape_Main\plugins\core\linkout.jar</file>
+ </filelist>
+ <authorlist>
+ <author>
+ <name>Doron Betel</name>
+ <institution>MSKCC</institution>
+ </author>
+ </authorlist>
+ </plugin>
+ <plugin>
+ <uniqueID>12</uniqueID>
+ <name>ManualLayout</name>
+ <description>User-defined positioning of layouts</description>
+ <cytoscapeVersion>2.5</cytoscapeVersion>
+ <url />
+ <downloadUrl />
+ <category>Core</category>
+ <releaseDate />
+ <pluginVersion>1.0</pluginVersion>
+ <classname>ManualLayout.ManualLayoutPlugin</classname>
+ <projectUrl />
+ <filetype>jar</filetype>
+ <installLocation>C:\eclipse\workspace\Cytoscape_Main\build\cytoscape-v2.6.0-alpha\plugins\ManualLayout.jar</installLocation>
+ <license>
+ <text />
+ </license>
+ <filelist>
+ <file>C:\eclipse\workspace\Cytoscape_Main\plugins\core\ManualLayout.jar</file>
+ </filelist>
+ <authorlist>
+ <author>
+ <name>Mike Smoot,Nerius Landys</name>
+ <institution>UCSD</institution>
+ </author>
+ <author>
+ <name>Alex Pico</name>
+ <institution>UCSF</institution>
+ </author>
+ <author>
+ <name>Allan Kuchinsky</name>
+ <institution>Agilent Technologies</institution>
+ </author>
+ </authorlist>
+ </plugin>
+ <plugin>
+ <uniqueID>13</uniqueID>
+ <name>PSI-MI</name>
+ <description>Allows importing of PSI-MI 2.5 file format</description>
+ <cytoscapeVersion>2.5</cytoscapeVersion>
+ <url />
+ <downloadUrl />
+ <category>Core</category>
+ <releaseDate />
+ <pluginVersion>0.3</pluginVersion>
+ <classname>org.cytoscape.coreplugin.psi_mi.plugin.PsiMiPlugIn</classname>
+ <projectUrl />
+ <filetype>jar</filetype>
+ <installLocation>C:\eclipse\workspace\Cytoscape_Main\build\cytoscape-v2.6.0-alpha\plugins\psi_mi.jar</installLocation>
+ <license>
+ <text />
+ </license>
+ <filelist>
+ <file>C:\eclipse\workspace\Cytoscape_Main\plugins\core\psi_mi.jar</file>
+ </filelist>
+ <authorlist>
+ <author>
+ <name>Ethan Cerami</name>
+ <institution>Memorial Sloan-Kettering Cancer Center</institution>
+ </author>
+ </authorlist>
+ </plugin>
+ <plugin>
+ <uniqueID>14</uniqueID>
+ <name>QuickFind</name>
+ <description>Provides a search dialog in the toolbar that can used to search for nodes and edges based on attributes.</description>
+ <cytoscapeVersion>2.5</cytoscapeVersion>
+ <url />
+ <downloadUrl>http://cytoscape.org/plugins/plugins.xml</downloadUrl>
+ <category>Core</category>
+ <releaseDate />
+ <pluginVersion>0.5</pluginVersion>
+ <classname>csplugins.quickfind.plugin.QuickFindPlugIn</classname>
+ <projectUrl />
+ <filetype>jar</filetype>
+ <installLocation>C:\eclipse\workspace\Cytoscape_Main\build\cytoscape-v2.6.0-alpha\plugins\quick_find.jar</installLocation>
+ <license>
+ <text />
+ </license>
+ <filelist>
+ <file>C:\eclipse\workspace\Cytoscape_Main\plugins\core\quick_find.jar</file>
+ </filelist>
+ <authorlist>
+ <author>
+ <name>Ethan Cerami</name>
+ <institution>Memorial Sloan-Kettering Cancer Center</institution>
+ </author>
+ </authorlist>
+ </plugin>
+ <plugin>
+ <uniqueID>15</uniqueID>
+ <name>SBML Reader</name>
+ <description>Provides the ability to import SBML (Systems Biology Markup Language) formatted files.</description>
+ <cytoscapeVersion>2.5</cytoscapeVersion>
+ <url />
+ <downloadUrl />
+ <category>Core</category>
+ <releaseDate />
+ <pluginVersion>0.5</pluginVersion>
+ <classname>sbmlreader.SBMLReaderPlugin</classname>
+ <projectUrl />
+ <filetype>jar</filetype>
+ <installLocation>C:\eclipse\workspace\Cytoscape_Main\build\cytoscape-v2.6.0-alpha\plugins\SBMLReader.jar</installLocation>
+ <license>
+ <text />
+ </license>
+ <filelist>
+ <file>C:\eclipse\workspace\Cytoscape_Main\plugins\core\SBMLReader.jar</file>
+ </filelist>
+ <authorlist>
+ <author>
+ <name>Willem Ligtenberg</name>
+ <institution>Eindhoven University of Technology</institution>
+ </author>
+ </authorlist>
+ </plugin>
+ <plugin>
+ <uniqueID>16</uniqueID>
+ <name>Table Import</name>
+ <description>Provides the ability to import network and attribute files from formatted text and Excel files.</description>
+ <cytoscapeVersion>2.5</cytoscapeVersion>
+ <url />
+ <downloadUrl>http://cytoscape.org/plugins/plugins.xml</downloadUrl>
+ <category>Core</category>
+ <releaseDate />
+ <pluginVersion>0.5</pluginVersion>
+ <classname>edu.ucsd.bioeng.coreplugin.tableImport.TableImportPlugin</classname>
+ <projectUrl />
+ <filetype>jar</filetype>
+ <installLocation>C:\eclipse\workspace\Cytoscape_Main\build\cytoscape-v2.6.0-alpha\plugins\TableImport.jar</installLocation>
+ <license>
+ <text />
+ </license>
+ <filelist>
+ <file>C:\eclipse\workspace\Cytoscape_Main\plugins\core\TableImport.jar</file>
+ </filelist>
+ <authorlist>
+ <author>
+ <name>Kei Ono</name>
+ <institution>UCSD</institution>
+ </author>
+ </authorlist>
+ </plugin>
+ <plugin>
+ <uniqueID>105</uniqueID>
+ <name>HyperEdgeEditor</name>
+ <description>Add, remove, and modify HyperEdges in a Cytoscape Network.</description>
+ <cytoscapeVersion>2.6</cytoscapeVersion>
+ <url>http://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=57</url>
+ <downloadUrl>http://cytoscape.org/plugins/plugins.xml</downloadUrl>
+ <category>Functional Enrichment</category>
+ <releaseDate>January 17, 2008</releaseDate>
+ <pluginVersion>2.6</pluginVersion>
+ <classname>cytoscape.hyperedge.editor.HyperEdgeEditorPlugin</classname>
+ <projectUrl />
+ <filetype>jar</filetype>
+ <installLocation>C:\Documents and Settings\Administrator\.cytoscape\2.6\plugins\HyperEdgeEditor-2.6</installLocation>
+ <license>
+ <text />
+ </license>
+ <filelist>
+ <file>C:\Documents and Settings\Administrator\.cytoscape\2.6\plugins\HyperEdgeEditor-2.6\HyperEdgeEditor.jar</file>
+ </filelist>
+ <authorlist>
+ <author>
+ <name>Allan Kuchinsky and Aditya Vailaya</name>
+ <institution>Agilent Labs</institution>
+ </author>
+ <author>
+ <name>Michael Creech</name>
+ <institution>Blue Oak Software</institution>
+ </author>
+ </authorlist>
+ </plugin>
+ <!-- corrupt a single entry -->
+ <plugin>
+ <uniqueID>2</uniqueID>
+ <name>BioPAX</name>
+ <description>Enables import of BioPAX formatted files.</description>
+ <cytoscapeVersion>2.6</cytoscapeVersion>
+ <downloadUrl>http://cytoscape.org/plugins/plugins.xml</downloadUrl>
+ <category>Network and Attribute I/O</category>
+ <releaseDate>January 1, 2008</releaseDate>
+ <classname>org.mskcc.biopax_plugin.plugin.BioPaxPlugIn</classname>
+ <projectUrl />
+ <filetype>jar</filetype>
+ <installLocation>C:\eclipse\workspace\Cytoscape_Main\build\cytoscape-v2.6.0-alpha\plugins\biopax.jar</installLocation>
+ <license>
+ <text />
+ </license>
+ <authorlist>
+ <author>
+ <name>Ethan Cerami, Benjamin Gross, Chris Sander</name>
+ <institution>Memorial Sloan-Kettering Cancer Center</institution>
+ </author>
+ <author>
+ <name>Gary Bader</name>
+ <institution>Uniersity of Toronto</institution>
+ </author>
+ </authorlist>
+ <filelist>
+ <file>C:\eclipse\workspace\Cytoscape_Main\build\cytoscape-v2.6.0-alpha\plugins\biopax.jar</file>
+ </filelist>
+ </plugin>
+ </CurrentPlugins>
+ <InstallPlugins />
+ <DeletePlugins />
+</CytoscapePlugin>
+
diff --git a/application/src/test/resources/testData/randomTextFile.txt b/application/src/test/resources/testData/randomTextFile.txt
new file mode 100644
index 0000000..1beee2b
--- /dev/null
+++ b/application/src/test/resources/testData/randomTextFile.txt
@@ -0,0 +1,6 @@
+This is some nonsense text for
+a unit test.
+Please don't remove.
+
+Or only remove once TextFileReaderTest.java
+has been removed.
diff --git a/application/src/test/resources/testData/sample.sif b/application/src/test/resources/testData/sample.sif
new file mode 100644
index 0000000..fcc91cd
--- /dev/null
+++ b/application/src/test/resources/testData/sample.sif
@@ -0,0 +1,25 @@
+YNL312W pd YPL111W
+YNL314W pd YIR028W
+YNL314W pd YIR031C
+YOL051W pd YBR018C
+YOL051W pd YBR019C
+YOL051W pd YBR020W
+YOL051W pd YLR081W
+YOR194C pd YCL018W
+YOR377W pd YFL018C
+YPL075W pd YAL038W
+YPL075W pd YCR012W
+YPL075W pd YDR050C YGR254W YHR174W
+YPL075W pd YOL086C
+YPL248C pd MEL1
+YPL248C pd YBR018C
+YPL248C pd YBR019C
+YPL248C pd YBR020W
+YPL248C pd YJR048W
+YPL248C pd YLR081W
+YPL248C pd YML051W
+YPL248C pd YOR120W
+YPL259C pd YGR209C
+YPR065W pd YDR044W
+YPR065W pd YJR047C
+YPR065W pd YPR065W
diff --git a/application/src/test/resources/testData/small.edgeAttr b/application/src/test/resources/testData/small.edgeAttr
new file mode 100644
index 0000000..cae1036
--- /dev/null
+++ b/application/src/test/resources/testData/small.edgeAttr
@@ -0,0 +1,5 @@
+sample
+a (pp) b = 0.4
+b (pp) c = 1.5
+c (pp) d = 1.6
+b (pp) d = 2.7
diff --git a/application/src/test/resources/testData/small.nodeAttr b/application/src/test/resources/testData/small.nodeAttr
new file mode 100644
index 0000000..330d926
--- /dev/null
+++ b/application/src/test/resources/testData/small.nodeAttr
@@ -0,0 +1,5 @@
+sample
+a = 1
+b = 2
+c = 3
+d = 4
diff --git a/application/src/test/resources/testData/small.sif b/application/src/test/resources/testData/small.sif
new file mode 100644
index 0000000..d02b84f
--- /dev/null
+++ b/application/src/test/resources/testData/small.sif
@@ -0,0 +1,4 @@
+a pp b
+b pp c
+c pp d
+b pp d
diff --git a/application/src/test/resources/testData/small.vizmap.props b/application/src/test/resources/testData/small.vizmap.props
new file mode 100644
index 0000000..6a4dea2
--- /dev/null
+++ b/application/src/test/resources/testData/small.vizmap.props
@@ -0,0 +1,136 @@
+#This file specifies visual mappings for Cytoscape and has been automatically generated.
+# WARNING: any changes you make to this file while Cytoscape is running may be overwritten.
+# Any changes may make these visual mappings unreadable.
+# Please make sure you know what you are doing before modifying this file by hand.
+#Thu Sep 14 16:17:49 PDT 2006
+
+edgeAppearanceCalculator.default.defaultEdgeColor=0,0,0
+edgeAppearanceCalculator.default.defaultEdgeFont=Default,plain,10
+edgeAppearanceCalculator.default.defaultEdgeLabel=
+edgeAppearanceCalculator.default.defaultEdgeLineType=LINE_1
+edgeAppearanceCalculator.default.defaultEdgeSourceArrow=NONE
+edgeAppearanceCalculator.default.defaultEdgeTargetArrow=NONE
+edgeAppearanceCalculator.default.defaultEdgeToolTip=
+edgeAppearanceCalculator.default.edgeColorCalculator=null
+edgeAppearanceCalculator.default.edgeFontFaceCalculator=null
+edgeAppearanceCalculator.default.edgeFontSizeCalculator=null
+edgeAppearanceCalculator.default.edgeLabelCalculator=null
+edgeAppearanceCalculator.default.edgeLineTypeCalculator=null
+edgeAppearanceCalculator.default.edgeSourceArrowCalculator=null
+edgeAppearanceCalculator.default.edgeTargetArrowCalculator=null
+edgeAppearanceCalculator.default.edgeToolTipCalculator=null
+edgeAppearanceCalculator.homer.defaultEdgeColor=0,0,0
+edgeAppearanceCalculator.homer.defaultEdgeFont=Default,plain,5
+edgeAppearanceCalculator.homer.defaultEdgeLabel=
+edgeAppearanceCalculator.homer.defaultEdgeLineType=LINE_1
+edgeAppearanceCalculator.homer.defaultEdgeSourceArrow=BLACK_DIAMOND
+edgeAppearanceCalculator.homer.defaultEdgeTargetArrow=NONE
+edgeAppearanceCalculator.homer.defaultEdgeToolTip=
+edgeAppearanceCalculator.homer.edgeColorCalculator=homerEdgeColorDiscrete
+edgeAppearanceCalculator.homer.edgeFontFaceCalculator=null
+edgeAppearanceCalculator.homer.edgeFontSizeCalculator=null
+edgeAppearanceCalculator.homer.edgeLabelCalculator=homerEdgeNamePass
+edgeAppearanceCalculator.homer.edgeLineTypeCalculator=null
+edgeAppearanceCalculator.homer.edgeSourceArrowCalculator=null
+edgeAppearanceCalculator.homer.edgeTargetArrowCalculator=null
+edgeAppearanceCalculator.homer.edgeToolTipCalculator=null
+edgeColorCalculator.homerEdgeColorDiscrete.class=cytoscape.visual.calculators.GenericEdgeColorCalculator
+edgeColorCalculator.homerEdgeColorDiscrete.mapping.controller=sample
+edgeColorCalculator.homerEdgeColorDiscrete.mapping.controllerType=2
+edgeColorCalculator.homerEdgeColorDiscrete.mapping.map.0.4=132,116,144
+edgeColorCalculator.homerEdgeColorDiscrete.mapping.map.1.5=230,198,214
+edgeColorCalculator.homerEdgeColorDiscrete.mapping.map.1.6=124,99,31
+edgeColorCalculator.homerEdgeColorDiscrete.mapping.map.2.7=15,136,249
+edgeColorCalculator.homerEdgeColorDiscrete.mapping.type=DiscreteMapping
+edgeLabelCalculator.homerEdgeNamePass.class=cytoscape.visual.calculators.GenericEdgeLabelCalculator
+edgeLabelCalculator.homerEdgeNamePass.mapping.controller=sample
+edgeLabelCalculator.homerEdgeNamePass.mapping.controllerType=3
+edgeLabelCalculator.homerEdgeNamePass.mapping.type=PassThroughMapping
+globalAppearanceCalculator.default.defaultBackgroundColor=255,255,255
+globalAppearanceCalculator.default.defaultEdgeReverseSelectionColor=0,255,0
+globalAppearanceCalculator.default.defaultEdgeSelectionColor=255,0,0
+globalAppearanceCalculator.default.defaultNodeReverseSelectionColor=0,255,0
+globalAppearanceCalculator.default.defaultNodeSelectionColor=255,255,0
+globalAppearanceCalculator.default.defaultSloppySelectionColor=128,128,128
+globalAppearanceCalculator.homer.defaultBackgroundColor=255,255,255
+globalAppearanceCalculator.homer.defaultEdgeReverseSelectionColor=0,255,0
+globalAppearanceCalculator.homer.defaultEdgeSelectionColor=255,0,0
+globalAppearanceCalculator.homer.defaultNodeReverseSelectionColor=0,255,0
+globalAppearanceCalculator.homer.defaultNodeSelectionColor=255,255,0
+globalAppearanceCalculator.homer.defaultSloppySelectionColor=128,128,128
+nodeAppearanceCalculator.default.defaultNodeBorderColor=0,0,0
+nodeAppearanceCalculator.default.defaultNodeFillColor=255,255,255
+nodeAppearanceCalculator.default.defaultNodeFont=Default,plain,12
+nodeAppearanceCalculator.default.defaultNodeHeight=30.0
+nodeAppearanceCalculator.default.defaultNodeLabel=
+nodeAppearanceCalculator.default.defaultNodeLineType=LINE_1
+nodeAppearanceCalculator.default.defaultNodeShape=rect
+nodeAppearanceCalculator.default.defaultNodeToolTip=
+nodeAppearanceCalculator.default.defaultNodeWidth=70.0
+nodeAppearanceCalculator.default.nodeBorderColorCalculator=null
+nodeAppearanceCalculator.default.nodeFillColorCalculator=null
+nodeAppearanceCalculator.default.nodeFontFaceCalculator=null
+nodeAppearanceCalculator.default.nodeFontSizeCalculator=null
+nodeAppearanceCalculator.default.nodeHeightCalculator=null
+nodeAppearanceCalculator.default.nodeLabelCalculator=label
+nodeAppearanceCalculator.default.nodeLabelColorCalculator=null
+nodeAppearanceCalculator.default.nodeLineTypeCalculator=null
+nodeAppearanceCalculator.default.nodeShapeCalculator=null
+nodeAppearanceCalculator.default.nodeSizeLocked=true
+nodeAppearanceCalculator.default.nodeToolTipCalculator=null
+nodeAppearanceCalculator.default.nodeWidthCalculator=null
+nodeAppearanceCalculator.homer.defaultNodeBorderColor=0,0,0
+nodeAppearanceCalculator.homer.defaultNodeFillColor=255,255,255
+nodeAppearanceCalculator.homer.defaultNodeFont=Default,plain,12
+nodeAppearanceCalculator.homer.defaultNodeHeight=30.0
+nodeAppearanceCalculator.homer.defaultNodeLabel=
+nodeAppearanceCalculator.homer.defaultNodeLineType=LINE_1
+nodeAppearanceCalculator.homer.defaultNodeShape=rect
+nodeAppearanceCalculator.homer.defaultNodeToolTip=
+nodeAppearanceCalculator.homer.defaultNodeWidth=70.0
+nodeAppearanceCalculator.homer.nodeBorderColorCalculator=null
+nodeAppearanceCalculator.homer.nodeFillColorCalculator=homerNodeColorDiscrete
+nodeAppearanceCalculator.homer.nodeFontFaceCalculator=null
+nodeAppearanceCalculator.homer.nodeFontSizeCalculator=null
+nodeAppearanceCalculator.homer.nodeHeightCalculator=homerSizeContinuous
+nodeAppearanceCalculator.homer.nodeLabelCalculator=label
+nodeAppearanceCalculator.homer.nodeLabelColorCalculator=null
+nodeAppearanceCalculator.homer.nodeLineTypeCalculator=homerBorderDiscrete
+nodeAppearanceCalculator.homer.nodeShapeCalculator=null
+nodeAppearanceCalculator.homer.nodeSizeLocked=true
+nodeAppearanceCalculator.homer.nodeToolTipCalculator=null
+nodeAppearanceCalculator.homer.nodeWidthCalculator=null
+nodeColorCalculator.homerNodeColorDiscrete.class=cytoscape.visual.calculators.GenericNodeColorCalculator
+nodeColorCalculator.homerNodeColorDiscrete.mapping.controller=sample
+nodeColorCalculator.homerNodeColorDiscrete.mapping.controllerType=3
+nodeColorCalculator.homerNodeColorDiscrete.mapping.map.1=246,242,103
+nodeColorCalculator.homerNodeColorDiscrete.mapping.map.2=87,25,230
+nodeColorCalculator.homerNodeColorDiscrete.mapping.map.3=209,205,254
+nodeColorCalculator.homerNodeColorDiscrete.mapping.map.4=220,127,67
+nodeColorCalculator.homerNodeColorDiscrete.mapping.type=DiscreteMapping
+nodeLabelCalculator.label.class=cytoscape.visual.calculators.GenericNodeLabelCalculator
+nodeLabelCalculator.label.mapping.controller=ID
+nodeLabelCalculator.label.mapping.controllerType=4
+nodeLabelCalculator.label.mapping.type=PassThroughMapping
+nodeLineTypeCalculator.homerBorderDiscrete.class=cytoscape.visual.calculators.GenericNodeLineTypeCalculator
+nodeLineTypeCalculator.homerBorderDiscrete.mapping.controller=sample
+nodeLineTypeCalculator.homerBorderDiscrete.mapping.controllerType=3
+nodeLineTypeCalculator.homerBorderDiscrete.mapping.map.1=LINE_1
+nodeLineTypeCalculator.homerBorderDiscrete.mapping.map.2=LINE_5
+nodeLineTypeCalculator.homerBorderDiscrete.mapping.map.3=DASHED_1
+nodeLineTypeCalculator.homerBorderDiscrete.mapping.map.4=DASHED_5
+nodeLineTypeCalculator.homerBorderDiscrete.mapping.type=DiscreteMapping
+nodeSizeCalculator.homerSizeContinuous.class=cytoscape.visual.calculators.GenericNodeSizeCalculator
+nodeSizeCalculator.homerSizeContinuous.mapping.boundaryvalues=2
+nodeSizeCalculator.homerSizeContinuous.mapping.bv0.domainvalue=2.0
+nodeSizeCalculator.homerSizeContinuous.mapping.bv0.equal=30.0
+nodeSizeCalculator.homerSizeContinuous.mapping.bv0.greater=30.0
+nodeSizeCalculator.homerSizeContinuous.mapping.bv0.lesser=10.0
+nodeSizeCalculator.homerSizeContinuous.mapping.bv1.domainvalue=3.0
+nodeSizeCalculator.homerSizeContinuous.mapping.bv1.equal=40.0
+nodeSizeCalculator.homerSizeContinuous.mapping.bv1.greater=50.0
+nodeSizeCalculator.homerSizeContinuous.mapping.bv1.lesser=40.0
+nodeSizeCalculator.homerSizeContinuous.mapping.controller=sample
+nodeSizeCalculator.homerSizeContinuous.mapping.controllerType=3
+nodeSizeCalculator.homerSizeContinuous.mapping.interpolator=LinearNumberToNumberInterpolator
+nodeSizeCalculator.homerSizeContinuous.mapping.type=ContinuousMapping
diff --git a/application/src/test/resources/testData/yeastSmall.txt b/application/src/test/resources/testData/yeastSmall.txt
new file mode 100755
index 0000000..de07b0a
--- /dev/null
+++ b/application/src/test/resources/testData/yeastSmall.txt
@@ -0,0 +1,10 @@
+Saccharomyces cerevisiae
+YHR047C AAP1' AAP1
+YBL074C AAR2
+YKL106W AAT1
+YLR027C AAT2 ASP5
+YGL119W ABC1
+YBR236C ABD1
+YKL112W ABF1 BAF1 OBF1 REB2
+YMR072W ABF2
+
diff --git a/archetypes/ant-sample-plugin/pom.xml b/archetypes/ant-sample-plugin/pom.xml
new file mode 100644
index 0000000..1b45183
--- /dev/null
+++ b/archetypes/ant-sample-plugin/pom.xml
@@ -0,0 +1,36 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+
+ <parent>
+ <groupId>cytoscape.archetypes</groupId>
+ <artifactId>parent</artifactId>
+ <version>2.8.2-SNAPSHOT</version>
+ </parent>
+
+ <artifactId>ant-sample-plugin</artifactId>
+ <packaging>pom</packaging>
+ <name>Ant Sample Plugin</name>
+
+ <build>
+ <plugins>
+ <plugin>
+ <artifactId>maven-assembly-plugin</artifactId>
+ <configuration>
+ <descriptors>
+ <descriptor>src/main/assembly/src.xml</descriptor>
+ </descriptors>
+ </configuration>
+ <executions>
+ <execution>
+ <id>zip</id>
+ <phase>package</phase>
+ <goals>
+ <goal>single</goal>
+ </goals>
+ </execution>
+ </executions>
+ </plugin>
+ </plugins>
+ </build>
+</project>
diff --git a/archetypes/ant-sample-plugin/src/main/assembly/src.xml b/archetypes/ant-sample-plugin/src/main/assembly/src.xml
new file mode 100644
index 0000000..f9dbc9c
--- /dev/null
+++ b/archetypes/ant-sample-plugin/src/main/assembly/src.xml
@@ -0,0 +1,14 @@
+<assembly xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0 http://maven.apache.org/xsd/assembly-1.1.0.xsd">
+ <formats>
+ <format>zip</format>
+ </formats>
+ <fileSets>
+ <fileSet>
+ <directory>${basedir}/src/main/resources</directory>
+ <outputDirectory>/</outputDirectory>
+ <fileMode>0755</fileMode>
+ </fileSet>
+ </fileSets>
+</assembly>
diff --git a/archetypes/ant-sample-plugin/src/main/resources/README b/archetypes/ant-sample-plugin/src/main/resources/README
new file mode 100644
index 0000000..92003fa
--- /dev/null
+++ b/archetypes/ant-sample-plugin/src/main/resources/README
@@ -0,0 +1,11 @@
+
+This directory contains a basic Ant build file and skeleton code for creating
+a Cytoscape plugin. For this build file to work, you must have Ant installed
+(http://ant.apache.org/) AND the Maven Ant Tasks plugin
+(http://maven.apache.org/ant-tasks/index.html).
+
+Put any library jar files that your project depends on in the library directory.
+These jars will be unjarred and re-jarred with your plugin. DO NOT include
+the Cytoscape jar! The Cytoscape jar is referenced from our Maven repository.
+
+
diff --git a/archetypes/ant-sample-plugin/src/main/resources/build.xml b/archetypes/ant-sample-plugin/src/main/resources/build.xml
new file mode 100644
index 0000000..45ff95c
--- /dev/null
+++ b/archetypes/ant-sample-plugin/src/main/resources/build.xml
@@ -0,0 +1,258 @@
+
+<project name="MyPlugin"
+ default="all"
+ basedir="."
+ xmlns:artifact="antlib:org.apache.maven.artifact.ant">
+
+ <!-- =================================================================== -->
+ <!-- Project Settings -->
+ <!-- -->
+ <!-- Adjust each property listed in this target with the appropriate -->
+ <!-- information for this project. -->
+ <!-- =================================================================== -->
+ <target name="settings">
+
+ <!-- The name of your plugin and resulting jar file -->
+ <property name="name" value="MyPlugin"/>
+
+ <!-- The package that contains your plugin class. -->
+ <property name="plugin.class.package" value="example"/>
+
+ <!-- The name of your plugin class, i.e. the one that extends Cytoscape plugin. -->
+ <property name="plugin.class.name" value="${plugin.class.package}.MyPlugin"/>
+
+ <!-- The version of your plugin. To support plugin.props, make sure the
+ version is expressed in decimal notation, e.g. 3.0, 3.1, 3.14, etc. -->
+ <property name="version" value="1.0"/>
+
+ <!-- The version of Cytoscape that you depend on. -->
+ <property name="cytoscape.version" value="2.8.0-beta1"/>
+
+ </target>
+
+ <!-- =================================================================== -->
+ <!-- Project initialization settings -->
+ <!-- Most developers shouldn't *need* to adjust any settings here. -->
+ <!-- =================================================================== -->
+ <target name="init"
+ depends="settings" >
+ <tstamp/>
+ <echo message="Building ${name} version ${version} ..."/>
+
+ <!-- Inheritable properties -->
+ <property name="debug" value="on"/>
+ <property name="optimize" value="off"/>
+ <property name="deprecation" value="on"/>
+ <property name="fork" value="false"/>
+
+ <!-- Define the directories -->
+ <property name="root.dir" value="."/>
+ <property name="resources.dir" value="${root.dir}/resources"/>
+ <property name="src.dir" value="${root.dir}/src"/>
+ <property name="tests.dir" value="${root.dir}/tests"/>
+ <property name="build.dir" value="${root.dir}/build"/>
+ <property name="lib.dir" value="${root.dir}/lib"/>
+ <property name="javadoc.dir" value="${build.dir}/API"/>
+ <property name="log.dir" value="${build.dir}/logs" />
+ <property name="junit.report.dir" value="${log.dir}/junit-reports" />
+
+ <!-- Define the relevant files -->
+ <property name="project.jar" value="${name}-${version}.jar"/>
+ <property name="test.jar" value="${name}-${version}-tests.jar"/>
+
+ <!-- Define external dependencies -->
+ <artifact:remoteRepository
+ id="cytoscape_releases"
+ url="http://cytoscape.wodaklab.org/nexus/content/repositories/releases/" />
+ <artifact:remoteRepository
+ id="cytoscape_snapshots"
+ url="http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/" />
+ <artifact:dependencies pathId="dependency.classpath">
+ <dependency groupId="cytoscape"
+ artifactId="application"
+ version="${cytoscape.version}"/>
+ <dependency groupId="junit"
+ artifactId="junit"
+ version="3.8.1"/>
+ </artifact:dependencies>
+
+ <!-- Define the class path -->
+ <path id="project.class.path">
+ <fileset dir="${lib.dir}">
+ <include name="*.jar"/>
+ </fileset>
+ <path refid="dependency.classpath"/>
+ </path>
+
+ <!-- Define the junit class path - It needs to find what we just built -->
+ <path id="junit.class.path" >
+ <fileset dir="${root.dir}">
+ <include name="*.jar"/>
+ </fileset>
+ <fileset dir="${lib.dir}">
+ <include name="*.jar"/>
+ </fileset>
+ <path refid="dependency.classpath"/>
+ </path>
+
+ <!-- Make sure tests is in the right place -->
+ <condition property="tests.ok">
+ <and>
+ <available file="${tests.dir}" />
+ </and>
+ </condition>
+
+ </target>
+
+ <!-- =================================================================== -->
+ <!-- Compiles the project -->
+ <!-- =================================================================== -->
+ <target name="compile"
+ depends="init" >
+ <mkdir dir="${build.dir}"/>
+ <mkdir dir="${log.dir}"/>
+ <javac srcdir="${src.dir}"
+ classpathref="project.class.path"
+ destdir="${build.dir}"
+ debug="${debug}"
+ deprecation="${deprecation}"
+ optimize="${optimize}"
+ fork="${fork}">
+ <compilerarg line="-Xlint:all -Xlint:-path"/>
+ </javac>
+ <echo message="Successfully ran compile task!"/>
+ </target>
+
+
+ <!-- =================================================================== -->
+ <!-- Creates the project jar file -->
+ <!-- =================================================================== -->
+ <target name="jar"
+ depends="compile" >
+ <filter token="version" value="${version}"/>
+ <copy file="${resources.dir}/plugin.props"
+ todir="${build.dir}/${plugin.class.package}"
+ filtering="true"
+ overwrite="true"/>
+ <unjar dest="${build.dir}">
+ <fileset dir="${lib.dir}">
+ <include name="*.jar" />
+ </fileset>
+ </unjar>
+
+ <jar destfile="${project.jar}" >
+ <fileset dir="${build.dir}" includes="**"/>
+ <manifest>
+ <attribute name="Cytoscape-Plugin" value="${plugin.class.name}"/>
+ </manifest>
+ </jar>
+ <echo message="Successfully ran jar task!"/>
+ </target>
+
+ <!-- =================================================================== -->
+ <!-- Compiles the tests -->
+ <!-- Note that this compilation occurs AFTER the distribution jar has -->
+ <!-- been created, so that the tests aren't distributed. -->
+ <!-- =================================================================== -->
+ <target name="compile-tests"
+ depends="jar"
+ if="tests.ok">
+ <javac srcdir="${tests.dir}"
+ classpathref="project.class.path"
+ destdir="${build.dir}"
+ debug="${debug}"
+ deprecation="${deprecation}"
+ optimize="${optimize}"
+ source="1.5"
+ target="1.5"
+ fork="${fork}">
+ <compilerarg line="-Xlint:all -Xlint:-path"/>
+ </javac>
+ <echo message="Successfully ran compile-tests task!"/>
+ </target>
+
+ <!-- =================================================================== -->
+ <!-- Creates the project-tests.jar file -->
+ <!-- =================================================================== -->
+ <target name="jar-tests"
+ depends="compile-tests"
+ if="tests.ok">
+ <jar jarfile="${test.jar}"
+ basedir="${build.dir}" >
+ </jar>
+ <echo message="Successfully ran jar-tests task!"/>
+ </target>
+
+ <!-- =================================================================== -->
+ <!-- Runs the unit tests. -->
+ <!-- =================================================================== -->
+ <target name="test"
+ depends="jar-tests"
+ if="tests.ok">
+ <junit printsummary="yes"
+ haltonfailure="no"
+ maxmemory="256m" >
+ <classpath refid="junit.class.path"/>
+ <formatter type="plain"
+ usefile="true" />
+ <formatter type="xml"
+ usefile="true" />
+ <batchtest fork="yes"
+ todir="${log.dir}"
+ failureProperty="junit.test.failure"
+ errorProperty="junit.test.failure">
+ <fileset dir="${tests.dir}"
+ includes="**/*Test.java"
+ excludes="**/AllTests.java" />
+ </batchtest>
+ </junit>
+ <mkdir dir="${junit.report.dir}"/>
+ <junitreport todir="${junit.report.dir}">
+ <fileset dir="${log.dir}">
+ <include name="TEST-*.xml"/>
+ </fileset>
+ <report format="frames" todir="${junit.report.dir}"/>
+ </junitreport>
+ <fail message="TEST FAILURE!!! Details: ${junit.report.dir}/index.html"
+ if="junit.test.failure"/>
+ <echo message="Successfully ran test task!"/>
+ </target>
+
+ <!-- =================================================================== -->
+ <!-- Creates the API documentation -->
+ <!-- =================================================================== -->
+ <target name="docs"
+ depends="init" >
+ <mkdir dir="${javadoc.dir}"/>
+ <javadoc sourcepath="${src.dir}"
+ destdir="${javadoc.dir}"
+ packagenames="*"
+ classpathref="project.class.path"
+ author="true"
+ version="true"
+ use="true"
+ splitindex="true"
+ noindex="false"
+ windowtitle="${name} API"
+ doctitle="${name}" />
+ <echo message="Successfully ran docs task!"/>
+ </target>
+
+ <!-- =================================================================== -->
+ <!-- Do everything -->
+ <!-- =================================================================== -->
+ <target name="all" depends="jar,test,docs" />
+
+ <!-- =================================================================== -->
+ <!-- Clean up, get back to original state -->
+ <!-- =================================================================== -->
+ <target name="clean"
+ depends="init">
+ <delete dir="${build.dir}"/>
+ <delete file="${project.jar}"/>
+ <delete file="${test.jar}"/>
+ <echo message="Successfully ran clean task!"/>
+ </target>
+
+</project>
+
diff --git a/archetypes/ant-sample-plugin/src/main/resources/resources/plugin.props b/archetypes/ant-sample-plugin/src/main/resources/resources/plugin.props
new file mode 100644
index 0000000..2f7368b
--- /dev/null
+++ b/archetypes/ant-sample-plugin/src/main/resources/resources/plugin.props
@@ -0,0 +1,26 @@
+# This props file would be filled out and included in the plugin jar file.
+# This props file will be used to put information into the Plugin Manager
+# about the plugin
+
+# -- The following properties are REQUIRED -- #
+
+# The plugin name that will be displayed to users
+pluginName=MyPlugin
+
+# Description used to give users information about the plugin such as what it does.
+# Html tags are encouraged for formatting purposes.
+pluginDescription=My example Plugin.
+
+# Plugin version number, this must be two numbers separated by a decimlal. Ex. 0.2, 14.03
+pluginVersion=@version@
+
+# Compatible Cytoscape version
+cytoscapeVersion=2.8
+
+# Category, use one of the categories listed on the website or create your own
+pluginCategory=Other
+
+# List of authors. Note each author and institution pair are separated by a : (colon)
+# each additional author institution pair must be separated from other pairs bye a ; (semicolon)
+pluginAuthorsIntsitutions=Your Name:Your Institution
+
diff --git a/archetypes/ant-sample-plugin/src/main/resources/src/example/MyAction.java b/archetypes/ant-sample-plugin/src/main/resources/src/example/MyAction.java
new file mode 100644
index 0000000..3959ea4
--- /dev/null
+++ b/archetypes/ant-sample-plugin/src/main/resources/src/example/MyAction.java
@@ -0,0 +1,32 @@
+package example;
+
+import cytoscape.Cytoscape;
+import cytoscape.util.CytoscapeAction;
+import java.awt.event.ActionEvent;
+import javax.swing.JOptionPane;
+
+/**
+ * A simple action. Change the names as appropriate and
+ * then fill in your expected behavior in the actionPerformed()
+ * method.
+ */
+public class MyAction extends CytoscapeAction {
+
+ // adjust as necessary!
+ private static final long serialVersionUID = 1234567890987654321L;
+
+ public MyAction() {
+ // Give your action a name here
+ super("Sample plugin");
+
+ // Set the menu you'd like here. Plugins don't need
+ // to live in the Plugins menu, so choose whatever
+ // is appropriate!
+ setPreferredMenu("Plugins");
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ // Do something useful here!
+ JOptionPane.showMessageDialog(Cytoscape.getDesktop(),"Executed the Sample plugin!");
+ }
+}
diff --git a/archetypes/ant-sample-plugin/src/main/resources/src/example/MyPlugin.java b/archetypes/ant-sample-plugin/src/main/resources/src/example/MyPlugin.java
new file mode 100644
index 0000000..302864e
--- /dev/null
+++ b/archetypes/ant-sample-plugin/src/main/resources/src/example/MyPlugin.java
@@ -0,0 +1,23 @@
+package example;
+
+import cytoscape.Cytoscape;
+import cytoscape.plugin.CytoscapePlugin;
+
+
+/**
+ * This class is used to instantiate your plugin. Put whatever initialization code
+ * you need into the no argument constructor (the only one that will be called).
+ * The actual functionality of your plugin can be in this class, but should
+ * probably be separated into separted classes that get instantiated here.
+ */
+public class MyPlugin extends CytoscapePlugin {
+
+ public MyPlugin() {
+ // Properly initializes things.
+ super();
+
+ // This action represents the actual behavior of the plugin.
+ MyAction action = new MyAction();
+ Cytoscape.getDesktop().getCyMenus().addAction(action);
+ }
+}
diff --git a/archetypes/ant-sample-plugin/src/main/resources/tests/example/MyActionTest.java b/archetypes/ant-sample-plugin/src/main/resources/tests/example/MyActionTest.java
new file mode 100644
index 0000000..6184278
--- /dev/null
+++ b/archetypes/ant-sample-plugin/src/main/resources/tests/example/MyActionTest.java
@@ -0,0 +1,17 @@
+package example;
+
+import junit.framework.Test;
+import junit.framework.TestCase;
+
+/**
+ * Unit test for MyAction.
+ */
+public class MyActionTest extends TestCase {
+
+ /**
+ * Rigourous Test :-)
+ */
+ public void testMyAction() {
+ assertTrue( true );
+ }
+}
diff --git a/archetypes/pom.xml b/archetypes/pom.xml
new file mode 100644
index 0000000..3706b7c
--- /dev/null
+++ b/archetypes/pom.xml
@@ -0,0 +1,55 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+
+ <groupId>cytoscape.archetypes</groupId>
+ <artifactId>parent</artifactId>
+ <version>2.8.2-SNAPSHOT</version>
+ <packaging>pom</packaging>
+ <name>Cytoscape Archetypes Parent POM</name>
+
+ <!-- bootstrap for cytoscape dependencies, namely the parent POM snapshots -->
+ <repositories>
+ <repository>
+ <id>cytoscape_snapshots</id>
+ <snapshots>
+ <enabled>true</enabled>
+ </snapshots>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <name>Cytoscape Snapshots</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/</url>
+ </repository>
+ <repository>
+ <id>cytoscape_releases</id>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ <name>Cytoscape Releases</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/releases/</url>
+ </repository>
+ </repositories>
+
+ <distributionManagement>
+ <repository>
+ <id>releases</id>
+ <name>Internal Releases</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/releases</url>
+ </repository>
+ <snapshotRepository>
+ <id>snapshots</id>
+ <name>Internal Snapshots</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots</url>
+ </snapshotRepository>
+ </distributionManagement>
+
+ <modules>
+ <module>sample-plugin</module>
+ <module>ant-sample-plugin</module>
+ </modules>
+
+</project>
+
diff --git a/archetypes/sample-plugin/pom.xml b/archetypes/sample-plugin/pom.xml
new file mode 100644
index 0000000..398492c
--- /dev/null
+++ b/archetypes/sample-plugin/pom.xml
@@ -0,0 +1,88 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+
+ <parent>
+ <groupId>cytoscape.archetypes</groupId>
+ <artifactId>parent</artifactId>
+ <version>2.8.2-SNAPSHOT</version>
+ </parent>
+
+ <artifactId>sample-plugin</artifactId>
+ <version>2.8.2-SNAPSHOT</version>
+ <packaging>maven-archetype</packaging>
+ <name>Sample Plugin Archetype</name>
+
+ <build>
+ <extensions>
+ <extension>
+ <groupId>org.apache.maven.archetype</groupId>
+ <artifactId>archetype-packaging</artifactId>
+ <version>2.0-alpha-5</version>
+ </extension>
+ </extensions>
+ <plugins>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-archetype-plugin</artifactId>
+ <version>2.0-alpha-5</version>
+ <extensions>true</extensions>
+ </plugin>
+ <!--
+ The point of this code is to use the archetype we just
+ created and use it to generate a project and then build
+ the project, which will test that our archetype still
+ works.
+ -->
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-invoker-plugin</artifactId>
+ <version>1.5</version>
+ <executions>
+ <execution>
+ <id>integration-test</id>
+ <goals>
+ <goal>install</goal>
+ <goal>run</goal>
+ </goals>
+ </execution>
+ </executions>
+ <configuration>
+ <cloneProjectsTo>${project.build.directory}/it/projects</cloneProjectsTo>
+ <goals>
+ <goal>org.apache.maven.plugins:maven-archetype-plugin:generate</goal>
+ </goals>
+ <localRepositoryPath>${project.build.directory}/it/repo</localRepositoryPath>
+ <pomIncludes>
+ <pomInclude>*</pomInclude>
+ </pomIncludes>
+ <projectsDirectory>${basedir}/src/it/projects</projectsDirectory>
+ <postBuildHookScript>verify.bsh</postBuildHookScript>
+ <properties>
+ <archetypeArtifactId>${project.artifactId}</archetypeArtifactId>
+ <archetypeGroupId>${project.groupId}</archetypeGroupId>
+ <archetypeRepository>local</archetypeRepository>
+ <archetypeVersion>${project.version}</archetypeVersion>
+ <goals>verify</goals>
+ <interactiveMode>false</interactiveMode>
+ </properties>
+ <streamLogs>true</streamLogs>
+ </configuration>
+ </plugin>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-clean-plugin</artifactId>
+ <version>2.4.1</version>
+ <executions>
+ <execution>
+ <id>auto-clean</id>
+ <phase>initialize</phase>
+ <goals>
+ <goal>clean</goal>
+ </goals>
+ </execution>
+ </executions>
+ </plugin>
+ </plugins>
+ </build>
+</project>
diff --git a/archetypes/sample-plugin/src/it/projects/firsttest/test.properties b/archetypes/sample-plugin/src/it/projects/firsttest/test.properties
new file mode 100644
index 0000000..dd7d0b5
--- /dev/null
+++ b/archetypes/sample-plugin/src/it/projects/firsttest/test.properties
@@ -0,0 +1,4 @@
+groupId=com.foo
+artifactId=firsttest
+version=1.0.0
+package=com.foo.firsttest
diff --git a/archetypes/sample-plugin/src/it/projects/firsttest/verify.bsh b/archetypes/sample-plugin/src/it/projects/firsttest/verify.bsh
new file mode 100644
index 0000000..ee8c7e7
--- /dev/null
+++ b/archetypes/sample-plugin/src/it/projects/firsttest/verify.bsh
@@ -0,0 +1,7 @@
+import java.io.*;
+
+File file = new File( basedir, "firsttest/target/firsttest-1.0.0.jar" );
+if ( !file.isFile() )
+{
+ throw new FileNotFoundException( "Could not find generated JAR: " + file );
+}
diff --git a/archetypes/sample-plugin/src/main/resources/META-INF/maven/archetype-metadata.xml b/archetypes/sample-plugin/src/main/resources/META-INF/maven/archetype-metadata.xml
new file mode 100644
index 0000000..e18f67d
--- /dev/null
+++ b/archetypes/sample-plugin/src/main/resources/META-INF/maven/archetype-metadata.xml
@@ -0,0 +1,23 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<archetype-descriptor name="sample-plugin">
+ <fileSets>
+ <fileSet filtered="true" packaged="true" encoding="UTF-8">
+ <directory>src/main/java</directory>
+ <includes>
+ <include>**/*.java</include>
+ </includes>
+ </fileSet>
+ <fileSet filtered="true" packaged="true" encoding="UTF-8">
+ <directory>src/main/resources</directory>
+ <includes>
+ <include>**/*.props</include>
+ </includes>
+ </fileSet>
+ <fileSet filtered="true" packaged="true" encoding="UTF-8">
+ <directory>src/test/java</directory>
+ <includes>
+ <include>**/*.java</include>
+ </includes>
+ </fileSet>
+ </fileSets>
+</archetype-descriptor>
diff --git a/archetypes/sample-plugin/src/main/resources/META-INF/maven/archetype.xml b/archetypes/sample-plugin/src/main/resources/META-INF/maven/archetype.xml
new file mode 100644
index 0000000..55bc291
--- /dev/null
+++ b/archetypes/sample-plugin/src/main/resources/META-INF/maven/archetype.xml
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?><archetype>
+ <id>sample-plugin</id>
+ <sources>
+ <source>src/main/java/MyAction.java</source>
+ <source>src/main/java/MyPlugin.java</source>
+ </sources>
+ <testSources>
+ <source>src/test/java/MyActionTest.java</source>
+ </testSources>
+ <resources>
+ <resource>src/main/resources/plugin.props</resource>
+ </resources>
+</archetype>
diff --git a/archetypes/sample-plugin/src/main/resources/archetype-resources/pom.xml b/archetypes/sample-plugin/src/main/resources/archetype-resources/pom.xml
new file mode 100644
index 0000000..e973901
--- /dev/null
+++ b/archetypes/sample-plugin/src/main/resources/archetype-resources/pom.xml
@@ -0,0 +1,88 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+
+ <groupId>${groupId}</groupId>
+ <artifactId>${artifactId}</artifactId>
+ <version>${project.version}</version>
+ <packaging>jar</packaging>
+ <name>sample-plugin</name>
+
+ <build>
+ <plugins>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-compiler-plugin</artifactId>
+ <configuration>
+ <source>1.6</source>
+ <target>1.6</target>
+ <optimize>true</optimize>
+ <showWarnings>true</showWarnings>
+ <showDeprecation>true</showDeprecation>
+ </configuration>
+ </plugin>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-jar-plugin</artifactId>
+ <configuration>
+ <archive>
+ <manifestEntries>
+ <Cytoscape-Plugin>${package}.MyPlugin</Cytoscape-Plugin>
+ </manifestEntries>
+ </archive>
+ </configuration>
+ </plugin>
+ </plugins>
+ </build>
+
+ <dependencies>
+ <dependency>
+ <groupId>cytoscape</groupId>
+ <artifactId>application</artifactId>
+ <version>2.8.0-beta1</version>
+ </dependency>
+ <dependency>
+ <groupId>junit</groupId>
+ <artifactId>junit</artifactId>
+ <version>3.8.1</version>
+ <scope>test</scope>
+ </dependency>
+ </dependencies>
+
+ <repositories>
+ <repository>
+ <id>cytoscape_snapshots</id>
+ <snapshots>
+ <enabled>true</enabled>
+ </snapshots>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <name>Cytoscape Snapshots</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/</url>
+ </repository>
+ <repository>
+ <id>cytoscape_releases</id>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ <name>Cytoscape Releases</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/releases/</url>
+ </repository>
+ <repository>
+ <id>cytoscape_thirdparty</id>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ <name>Cytoscape Third Party</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/thirdparty/</url>
+ </repository>
+ </repositories>
+
+</project>
diff --git a/archetypes/sample-plugin/src/main/resources/archetype-resources/src/main/java/MyAction.java b/archetypes/sample-plugin/src/main/resources/archetype-resources/src/main/java/MyAction.java
new file mode 100644
index 0000000..8a04091
--- /dev/null
+++ b/archetypes/sample-plugin/src/main/resources/archetype-resources/src/main/java/MyAction.java
@@ -0,0 +1,34 @@
+#set( $symbol_pound = '#' )
+#set( $symbol_dollar = '$' )
+#set( $symbol_escape = '\' )
+package ${package};
+
+import cytoscape.Cytoscape;
+import cytoscape.util.CytoscapeAction;
+import java.awt.event.ActionEvent;
+import javax.swing.JOptionPane;
+
+/**
+ * A simple action. Change the names as appropriate and
+ * then fill in your expected behavior in the actionPerformed()
+ * method.
+ */
+public class MyAction extends CytoscapeAction {
+
+ private static final long serialVersionUID = 1234567890123456789L;
+
+ public MyAction() {
+ // Give your action a name here
+ super("Sample plugin");
+
+ // Set the menu you'd like here. Plugins don't need
+ // to live in the Plugins menu, so choose whatever
+ // is appropriate!
+ setPreferredMenu("Plugins");
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ // Do something useful here!
+ JOptionPane.showMessageDialog(Cytoscape.getDesktop(),"Executed the Sample plugin!");
+ }
+}
diff --git a/archetypes/sample-plugin/src/main/resources/archetype-resources/src/main/java/MyPlugin.java b/archetypes/sample-plugin/src/main/resources/archetype-resources/src/main/java/MyPlugin.java
new file mode 100644
index 0000000..589bb4e
--- /dev/null
+++ b/archetypes/sample-plugin/src/main/resources/archetype-resources/src/main/java/MyPlugin.java
@@ -0,0 +1,26 @@
+#set( $symbol_pound = '#' )
+#set( $symbol_dollar = '$' )
+#set( $symbol_escape = '\' )
+package ${package};
+
+import cytoscape.Cytoscape;
+import cytoscape.plugin.CytoscapePlugin;
+
+
+/**
+ * This class is used to instantiate your plugin. Put whatever initialization code
+ * you need into the no argument constructor (the only one that will be called).
+ * The actual functionality of your plugin can be in this class, but should
+ * probably be separated into separted classes that get instantiated here.
+ */
+public class MyPlugin extends CytoscapePlugin {
+
+ public MyPlugin() {
+ // Properly initializes things.
+ super();
+
+ // This action represents the actual behavior of the plugin.
+ MyAction action = new MyAction();
+ Cytoscape.getDesktop().getCyMenus().addAction(action);
+ }
+}
diff --git a/archetypes/sample-plugin/src/main/resources/archetype-resources/src/main/resources/plugin.props b/archetypes/sample-plugin/src/main/resources/archetype-resources/src/main/resources/plugin.props
new file mode 100644
index 0000000..fe13ff7
--- /dev/null
+++ b/archetypes/sample-plugin/src/main/resources/archetype-resources/src/main/resources/plugin.props
@@ -0,0 +1,26 @@
+# This props file would be filled out and included in the plugin jar file.
+# This props file will be used to put information into the Plugin Manager
+# about the plugin
+
+# -- The following properties are REQUIRED -- #
+
+# The plugin name that will be displayed to users
+pluginName=MyPlugin
+
+# Description used to give users information about the plugin such as what it does.
+# Html tags are encouraged for formatting purposes.
+pluginDescription=My example Plugin.
+
+# Plugin version number, this must be two numbers separated by a decimlal. Ex. 0.2, 14.03
+pluginVersion=1.0
+
+# Compatible Cytoscape version
+cytoscapeVersion=2.8
+
+# Category, use one of the categories listed on the website or create your own
+pluginCategory=Other
+
+# List of authors. Note each author and institution pair are separated by a : (colon)
+# each additional author institution pair must be separated from other pairs bye a ; (semicolon)
+pluginAuthorsIntsitutions=Your Name:Your Institution
+
diff --git a/archetypes/sample-plugin/src/main/resources/archetype-resources/src/test/java/MyActionTest.java b/archetypes/sample-plugin/src/main/resources/archetype-resources/src/test/java/MyActionTest.java
new file mode 100644
index 0000000..86907db
--- /dev/null
+++ b/archetypes/sample-plugin/src/main/resources/archetype-resources/src/test/java/MyActionTest.java
@@ -0,0 +1,20 @@
+#set( $symbol_pound = '#' )
+#set( $symbol_dollar = '$' )
+#set( $symbol_escape = '\' )
+package ${package};
+
+import junit.framework.Test;
+import junit.framework.TestCase;
+
+/**
+ * Unit test for MyAction.
+ */
+public class MyActionTest extends TestCase {
+
+ /**
+ * Rigourous Test :-)
+ */
+ public void testMyAction() {
+ assertTrue( true );
+ }
+}
diff --git a/corelibs/commons-cli-1.x-cytocape-custom/CYTOSCAPE_README b/corelibs/commons-cli-1.x-cytocape-custom/CYTOSCAPE_README
new file mode 100644
index 0000000..89acd69
--- /dev/null
+++ b/corelibs/commons-cli-1.x-cytocape-custom/CYTOSCAPE_README
@@ -0,0 +1,11 @@
+What I did.
+
+First, removed all of the cli2 directories so that we don't include that code.
+
+Removed the CLI2Converter classes
+
+Removed a few mkdirs for cli2 dirs in the build file.
+
+
+
+Commented the option sort in HelpFormatter.java
diff --git a/corelibs/commons-cli-1.x-cytocape-custom/LICENSE.txt b/corelibs/commons-cli-1.x-cytocape-custom/LICENSE.txt
new file mode 100644
index 0000000..57bc88a
--- /dev/null
+++ b/corelibs/commons-cli-1.x-cytocape-custom/LICENSE.txt
@@ -0,0 +1,202 @@
+ Apache License
+ Version 2.0, January 2004
+ http://www.apache.org/licenses/
+
+ TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+ 1. Definitions.
+
+ "License" shall mean the terms and conditions for use, reproduction,
+ and distribution as defined by Sections 1 through 9 of this document.
+
+ "Licensor" shall mean the copyright owner or entity authorized by
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+
+ "Legal Entity" shall mean the union of the acting entity and all
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+
+ "You" (or "Your") shall mean an individual or Legal Entity
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+ and conversions to other media types.
+
+ "Work" shall mean the work of authorship, whether in Source or
+ Object form, made available under the License, as indicated by a
+ copyright notice that is included in or attached to the work
+ (an example is provided in the Appendix below).
+
+ "Derivative Works" shall mean any work, whether in Source or Object
+ form, that is based on (or derived from) the Work and for which the
+ editorial revisions, annotations, elaborations, or other modifications
+ represent, as a whole, an original work of authorship. For the purposes
+ of this License, Derivative Works shall not include works that remain
+ separable from, or merely link (or bind by name) to the interfaces of,
+ the Work and Derivative Works thereof.
+
+ "Contribution" shall mean any work of authorship, including
+ the original version of the Work and any modifications or additions
+ to that Work or Derivative Works thereof, that is intentionally
+ submitted to Licensor for inclusion in the Work by the copyright owner
+ or by an individual or Legal Entity authorized to submit on behalf of
+ the copyright owner. For the purposes of this definition, "submitted"
+ means any form of electronic, verbal, or written communication sent
+ to the Licensor or its representatives, including but not limited to
+ communication on electronic mailing lists, source code control systems,
+ and issue tracking systems that are managed by, or on behalf of, the
+ Licensor for the purpose of discussing and improving the Work, but
+ excluding communication that is conspicuously marked or otherwise
+ designated in writing by the copyright owner as "Not a Contribution."
+
+ "Contributor" shall mean Licensor and any individual or Legal Entity
+ on behalf of whom a Contribution has been received by Licensor and
+ subsequently incorporated within the Work.
+
+ 2. Grant of Copyright License. Subject to the terms and conditions of
+ this License, each Contributor hereby grants to You a perpetual,
+ worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+ copyright license to reproduce, prepare Derivative Works of,
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+ Work and such Derivative Works in Source or Object form.
+
+ 3. Grant of Patent License. Subject to the terms and conditions of
+ this License, each Contributor hereby grants to You a perpetual,
+ worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+ (except as stated in this section) patent license to make, have made,
+ use, offer to sell, sell, import, and otherwise transfer the Work,
+ where such license applies only to those patent claims licensable
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+ Contribution(s) alone or by combination of their Contribution(s)
+ with the Work to which such Contribution(s) was submitted. If You
+ institute patent litigation against any entity (including a
+ cross-claim or counterclaim in a lawsuit) alleging that the Work
+ or a Contribution incorporated within the Work constitutes direct
+ or contributory patent infringement, then any patent licenses
+ granted to You under this License for that Work shall terminate
+ as of the date such litigation is filed.
+
+ 4. Redistribution. You may reproduce and distribute copies of the
+ Work or Derivative Works thereof in any medium, with or without
+ modifications, and in Source or Object form, provided that You
+ meet the following conditions:
+
+ (a) You must give any other recipients of the Work or
+ Derivative Works a copy of this License; and
+
+ (b) You must cause any modified files to carry prominent notices
+ stating that You changed the files; and
+
+ (c) You must retain, in the Source form of any Derivative Works
+ that You distribute, all copyright, patent, trademark, and
+ attribution notices from the Source form of the Work,
+ excluding those notices that do not pertain to any part of
+ the Derivative Works; and
+
+ (d) If the Work includes a "NOTICE" text file as part of its
+ distribution, then any Derivative Works that You distribute must
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+ of the following places: within a NOTICE text file distributed
+ as part of the Derivative Works; within the Source form or
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+ within a display generated by the Derivative Works, if and
+ wherever such third-party notices normally appear. The contents
+ of the NOTICE file are for informational purposes only and
+ do not modify the License. You may add Your own attribution
+ notices within Derivative Works that You distribute, alongside
+ or as an addendum to the NOTICE text from the Work, provided
+ that such additional attribution notices cannot be construed
+ as modifying the License.
+
+ You may add Your own copyright statement to Your modifications and
+ may provide additional or different license terms and conditions
+ for use, reproduction, or distribution of Your modifications, or
+ for any such Derivative Works as a whole, provided Your use,
+ reproduction, and distribution of the Work otherwise complies with
+ the conditions stated in this License.
+
+ 5. Submission of Contributions. Unless You explicitly state otherwise,
+ any Contribution intentionally submitted for inclusion in the Work
+ by You to the Licensor shall be under the terms and conditions of
+ this License, without any additional terms or conditions.
+ Notwithstanding the above, nothing herein shall supersede or modify
+ the terms of any separate license agreement you may have executed
+ with Licensor regarding such Contributions.
+
+ 6. Trademarks. This License does not grant permission to use the trade
+ names, trademarks, service marks, or product names of the Licensor,
+ except as required for reasonable and customary use in describing the
+ origin of the Work and reproducing the content of the NOTICE file.
+
+ 7. Disclaimer of Warranty. Unless required by applicable law or
+ agreed to in writing, Licensor provides the Work (and each
+ Contributor provides its Contributions) on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+ implied, including, without limitation, any warranties or conditions
+ of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
+ PARTICULAR PURPOSE. You are solely responsible for determining the
+ appropriateness of using or redistributing the Work and assume any
+ risks associated with Your exercise of permissions under this License.
+
+ 8. Limitation of Liability. In no event and under no legal theory,
+ whether in tort (including negligence), contract, or otherwise,
+ unless required by applicable law (such as deliberate and grossly
+ negligent acts) or agreed to in writing, shall any Contributor be
+ liable to You for damages, including any direct, indirect, special,
+ incidental, or consequential damages of any character arising as a
+ result of this License or out of the use or inability to use the
+ Work (including but not limited to damages for loss of goodwill,
+ work stoppage, computer failure or malfunction, or any and all
+ other commercial damages or losses), even if such Contributor
+ has been advised of the possibility of such damages.
+
+ 9. Accepting Warranty or Additional Liability. While redistributing
+ the Work or Derivative Works thereof, You may choose to offer,
+ and charge a fee for, acceptance of support, warranty, indemnity,
+ or other liability obligations and/or rights consistent with this
+ License. However, in accepting such obligations, You may act only
+ on Your own behalf and on Your sole responsibility, not on behalf
+ of any other Contributor, and only if You agree to indemnify,
+ defend, and hold each Contributor harmless for any liability
+ incurred by, or claims asserted against, such Contributor by reason
+ of your accepting any such warranty or additional liability.
+
+ END OF TERMS AND CONDITIONS
+
+ APPENDIX: How to apply the Apache License to your work.
+
+ To apply the Apache License to your work, attach the following
+ boilerplate notice, with the fields enclosed by brackets "[]"
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+ file or class name and description of purpose be included on the
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+ Copyright [yyyy] [name of copyright owner]
+
+ Licensed under the Apache License, Version 2.0 (the "License");
+ you may not use this file except in compliance with the License.
+ You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing, software
+ distributed under the License is distributed on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ See the License for the specific language governing permissions and
+ limitations under the License.
+
diff --git a/corelibs/commons-cli-1.x-cytocape-custom/NOTICE.txt b/corelibs/commons-cli-1.x-cytocape-custom/NOTICE.txt
new file mode 100644
index 0000000..3f59805
--- /dev/null
+++ b/corelibs/commons-cli-1.x-cytocape-custom/NOTICE.txt
@@ -0,0 +1,2 @@
+This product includes software developed by
+The Apache Software Foundation (http://www.apache.org/).
diff --git a/corelibs/commons-cli-1.x-cytocape-custom/README.txt b/corelibs/commons-cli-1.x-cytocape-custom/README.txt
new file mode 100644
index 0000000..21a93c3
--- /dev/null
+++ b/corelibs/commons-cli-1.x-cytocape-custom/README.txt
@@ -0,0 +1,42 @@
+Jakarta Commons CLI
+===================
+
+Welcome to the CLI component of the Jakarta Commons project.
+
+The information in this file is relevant if you have
+downloaded a CLI source distribution.
+
+For testing the project, you will need JUnit (if you use
+maven this will be automatically installed and configured
+for you):
+
+ http://www.junit.org/
+
+There are two ways to build CLI, either with ant or maven.
+
+Ant can be found here :
+
+ http://jakarta.apache.org/ant
+
+and to build and test the system use:
+
+ ant dist
+
+Maven can be found here :
+
+ http://maven.apache.org
+
+and to build and test the system use:
+
+ maven jar:jar
+
+The system will build and test itself.
+
+For complete documentation and to create a local copy of the
+CLI project website, type:
+
+ maven site
+
+Good luck!
+
+-The CLI Team
diff --git a/corelibs/commons-cli-1.x-cytocape-custom/RELEASE-NOTES.txt b/corelibs/commons-cli-1.x-cytocape-custom/RELEASE-NOTES.txt
new file mode 100644
index 0000000..7b2bb38
--- /dev/null
+++ b/corelibs/commons-cli-1.x-cytocape-custom/RELEASE-NOTES.txt
@@ -0,0 +1,26 @@
+$Id: RELEASE-NOTES.txt 155404 2005-02-26 12:53:19Z dirkv $
+
+ Commons CLI Package
+ Version 1.0
+ Release Notes
+
+
+INTRODUCTION:
+
+This document contains the release notes for this version of the Commons
+CLI package. Commons CLI provides a simple API for working with the command line arguments and options.
+
+This is the first release of the CLI component, therefore all features are new,
+there are no bug-fixes, nothing is deprecated and there are no changes.
+
+For more information, read the documentation on the project site at
+http://jakarta.apache.org/commons/cli/
+
+NEW FEATURES:
+
+BUG FIXES:
+
+DEPRECATIONS:
+
+CHANGES:
+
diff --git a/corelibs/commons-cli-1.x-cytocape-custom/pom.xml b/corelibs/commons-cli-1.x-cytocape-custom/pom.xml
new file mode 100644
index 0000000..79c7e82
--- /dev/null
+++ b/corelibs/commons-cli-1.x-cytocape-custom/pom.xml
@@ -0,0 +1,49 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>parent</artifactId>
+ <version>2.8.4-SNAPSHOT</version>
+ </parent>
+
+ <artifactId>commons-cli-1-x-cytocape-custom</artifactId>
+ <packaging>jar</packaging>
+
+ <name>commons-cli-1-x-cytocape-custom</name>
+
+ <!-- bootstrap for cytoscape dependencies, namely the parent POM snapshots -->
+ <repositories>
+ <repository>
+ <id>cytoscape_snapshots</id>
+ <snapshots>
+ <enabled>true</enabled>
+ </snapshots>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <name>Cytoscape Snapshots</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/</url>
+ </repository>
+ <repository>
+ <id>cytoscape_releases</id>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ <name>Cytoscape Releases</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/releases/</url>
+ </repository>
+ </repositories>
+
+ <dependencies>
+ <dependency>
+ <groupId>commons-lang</groupId>
+ <artifactId>commons-lang</artifactId>
+ <version>2.4</version>
+ </dependency>
+ </dependencies>
+
+</project>
+
diff --git a/corelibs/commons-cli-1.x-cytocape-custom/src/conf/MANIFEST.MF b/corelibs/commons-cli-1.x-cytocape-custom/src/conf/MANIFEST.MF
new file mode 100644
index 0000000..c7f0768
--- /dev/null
+++ b/corelibs/commons-cli-1.x-cytocape-custom/src/conf/MANIFEST.MF
@@ -0,0 +1,11 @@
+Implementation-Title: Jakarta Commons CLI2
+
+Name: org/apache/commons/cli/
+Specification-Title: Jakarta Commons CLI
+Specification-Vendor: Apache Software Foundation
+Specification-Version: 1.0
+
+Name: org/apache/commons/cli2/
+Specification-Title: Jakarta Commons CLI2
+Specification-Vendor: Apache Software Foundation
+Specification-Version: 2.0
diff --git a/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/AlreadySelectedException.java b/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/AlreadySelectedException.java
new file mode 100644
index 0000000..b13de11
--- /dev/null
+++ b/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/AlreadySelectedException.java
@@ -0,0 +1,36 @@
+/**
+ * Copyright 1999-2001,2004 The Apache Software Foundation.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.commons.cli;
+
+
+/**
+ * <p>Thrown when more than one option in an option group
+ * has been provided.</p>
+ *
+ * @author John Keyes ( john at integralsource.com )
+ * @see ParseException
+ */
+public class AlreadySelectedException extends ParseException {
+ /**
+ * <p>Construct a new <code>AlreadySelectedException</code>
+ * with the specified detail message.</p>
+ *
+ * @param message the detail message
+ */
+ public AlreadySelectedException(String message) {
+ super(message);
+ }
+}
diff --git a/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/BasicParser.java b/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/BasicParser.java
new file mode 100644
index 0000000..d8d5407
--- /dev/null
+++ b/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/BasicParser.java
@@ -0,0 +1,44 @@
+/**
+ * Copyright 1999-2001,2004 The Apache Software Foundation.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.commons.cli;
+
+
+/**
+ * The class BasicParser provides a very simple implementation of
+ * the {@link Parser#flatten(Options,String[],boolean) flatten} method.
+ *
+ * @author John Keyes (john at integralsource.com)
+ * @see Parser
+ */
+public class BasicParser extends Parser {
+ /**
+ * <p>A simple implementation of {@link Parser}'s abstract
+ * {@link Parser#flatten(Options,String[],boolean) flatten} method.</p>
+ *
+ * <p><b>Note:</b> <code>options</code> and <code>stopAtNonOption</code>
+ * are not used in this <code>flatten</code> method.</p>
+ *
+ * @param options The command line {@link Options}
+ * @param arguments The command line arguments to be parsed
+ * @param stopAtNonOption Specifies whether to stop flattening
+ * when an non option is found.
+ * @return The <code>arguments</code> String array.
+ */
+ protected String[] flatten(Options options, String[] arguments, boolean stopAtNonOption) {
+ // just echo the arguments
+ return arguments;
+ }
+}
diff --git a/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/CommandLine.java b/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/CommandLine.java
new file mode 100644
index 0000000..5c263d0
--- /dev/null
+++ b/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/CommandLine.java
@@ -0,0 +1,295 @@
+/**
+ * Copyright 1999-2001,2004 The Apache Software Foundation.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.commons.cli;
+
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Map;
+
+
+/**
+ * <p>Represents list of arguments parsed against
+ * a {@link Options} descriptor.<p>
+ *
+ * <p>It allows querying of a boolean {@link #hasOption(String opt)},
+ * in addition to retrieving the {@link #getOptionValue(String opt)}
+ * for options requiring arguments.</p>
+ *
+ * <p>Additionally, any left-over or unrecognized arguments,
+ * are available for further processing.</p>
+ *
+ * @author bob mcwhirter (bob @ werken.com)
+ * @author <a href="mailto:jstrachan at apache.org">James Strachan</a>
+ * @author John Keyes (john at integralsource.com)
+ */
+public class CommandLine {
+ /** the unrecognised options/arguments */
+ private List args = new LinkedList();
+
+ /** the processed options */
+ private Map options = new HashMap();
+
+ /** the option name map */
+ private Map names = new HashMap();
+
+ /** Map of unique options for ease to get complete list of options */
+ private Map hashcodeMap = new HashMap();
+
+ /** the processed options */
+ private Option[] optionsArray;
+
+ /**
+ * Creates a command line.
+ */
+ CommandLine() {
+ // nothing to do
+ }
+
+ /**
+ * Query to see if an option has been set.
+ *
+ * @param opt Short name of the option
+ * @return true if set, false if not
+ */
+ public boolean hasOption(String opt) {
+ return options.containsKey(opt);
+ }
+
+ /**
+ * Query to see if an option has been set.
+ *
+ * @param opt character name of the option
+ * @return true if set, false if not
+ */
+ public boolean hasOption(char opt) {
+ return hasOption(String.valueOf(opt));
+ }
+
+ /**
+ * Return the <code>Object</code> type of this <code>Option</code>.
+ *
+ * @param opt the name of the option
+ * @return the type of this <code>Option</code>
+ */
+ public Object getOptionObject(String opt) {
+ String res = getOptionValue(opt);
+
+ if (!options.containsKey(opt)) {
+ return null;
+ }
+
+ Object type = ((Option) options.get(opt)).getType();
+
+ return (res == null) ? null : TypeHandler.createValue(res, type);
+ }
+
+ /**
+ * Return the <code>Object</code> type of this <code>Option</code>.
+ *
+ * @param opt the name of the option
+ * @return the type of opt
+ */
+ public Object getOptionObject(char opt) {
+ return getOptionObject(String.valueOf(opt));
+ }
+
+ /**
+ * Retrieve the argument, if any, of this option.
+ *
+ * @param opt the name of the option
+ * @return Value of the argument if option is set, and has an argument,
+ * otherwise null.
+ */
+ public String getOptionValue(String opt) {
+ String[] values = getOptionValues(opt);
+
+ return (values == null) ? null : values[0];
+ }
+
+ /**
+ * Retrieve the argument, if any, of this option.
+ *
+ * @param opt the character name of the option
+ * @return Value of the argument if option is set, and has an argument,
+ * otherwise null.
+ */
+ public String getOptionValue(char opt) {
+ return getOptionValue(String.valueOf(opt));
+ }
+
+ /**
+ * Retrieves the array of values, if any, of an option.
+ *
+ * @param opt string name of the option
+ * @return Values of the argument if option is set, and has an argument,
+ * otherwise null.
+ */
+ public String[] getOptionValues(String opt) {
+ opt = Util.stripLeadingHyphens(opt);
+
+ String key = opt;
+
+ if (names.containsKey(opt)) {
+ key = (String) names.get(opt);
+ }
+
+ if (options.containsKey(key)) {
+ return ((Option) options.get(key)).getValues();
+ }
+
+ return null;
+ }
+
+ /**
+ * Retrieves the array of values, if any, of an option.
+ *
+ * @param opt character name of the option
+ * @return Values of the argument if option is set, and has an argument,
+ * otherwise null.
+ */
+ public String[] getOptionValues(char opt) {
+ return getOptionValues(String.valueOf(opt));
+ }
+
+ /**
+ * Retrieve the argument, if any, of an option.
+ *
+ * @param opt name of the option
+ * @param defaultValue is the default value to be returned if the option
+ * is not specified
+ * @return Value of the argument if option is set, and has an argument,
+ * otherwise <code>defaultValue</code>.
+ */
+ public String getOptionValue(String opt, String defaultValue) {
+ String answer = getOptionValue(opt);
+
+ return (answer != null) ? answer : defaultValue;
+ }
+
+ /**
+ * Retrieve the argument, if any, of an option.
+ *
+ * @param opt character name of the option
+ * @param defaultValue is the default value to be returned if the option
+ * is not specified
+ * @return Value of the argument if option is set, and has an argument,
+ * otherwise <code>defaultValue</code>.
+ */
+ public String getOptionValue(char opt, String defaultValue) {
+ return getOptionValue(String.valueOf(opt), defaultValue);
+ }
+
+ /**
+ * Retrieve any left-over non-recognized options and arguments
+ *
+ * @return remaining items passed in but not parsed as an array
+ */
+ public String[] getArgs() {
+ String[] answer = new String[args.size()];
+
+ args.toArray(answer);
+
+ return answer;
+ }
+
+ /**
+ * Retrieve any left-over non-recognized options and arguments
+ *
+ * @return remaining items passed in but not parsed as a <code>List</code>.
+ */
+ public List getArgList() {
+ return args;
+ }
+
+ /**
+ * jkeyes
+ * - commented out until it is implemented properly
+ * <p>Dump state, suitable for debugging.</p>
+ *
+ * @return Stringified form of this object
+ */
+
+ /*
+ public String toString() {
+ StringBuffer buf = new StringBuffer();
+
+ buf.append("[ CommandLine: [ options: ");
+ buf.append(options.toString());
+ buf.append(" ] [ args: ");
+ buf.append(args.toString());
+ buf.append(" ] ]");
+
+ return buf.toString();
+ }
+ */
+
+ /**
+ * Add left-over unrecognized option/argument.
+ *
+ * @param arg the unrecognised option/argument.
+ */
+ void addArg(String arg) {
+ args.add(arg);
+ }
+
+ /**
+ * Add an option to the command line. The values of
+ * the option are stored.
+ *
+ * @param opt the processed option
+ */
+ void addOption(Option opt) {
+ hashcodeMap.put(new Integer(opt.hashCode()), opt);
+
+ String key = opt.getKey();
+
+ if (key == null) {
+ key = opt.getLongOpt();
+ } else {
+ names.put(opt.getLongOpt(), key);
+ }
+
+ options.put(key, opt);
+ }
+
+ /**
+ * Returns an iterator over the Option members of CommandLine.
+ *
+ * @return an <code>Iterator</code> over the processed {@link Option}
+ * members of this {@link CommandLine}
+ */
+ public Iterator iterator() {
+ return hashcodeMap.values().iterator();
+ }
+
+ /**
+ * Returns an array of the processed {@link Option}s.
+ *
+ * @return an array of the processed {@link Option}s.
+ */
+ public Option[] getOptions() {
+ Collection processed = options.values();
+
+ // reinitialise array
+ optionsArray = new Option[processed.size()];
+
+ // return the array
+ return (Option[]) processed.toArray(optionsArray);
+ }
+}
diff --git a/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/CommandLineParser.java b/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/CommandLineParser.java
new file mode 100644
index 0000000..6b8d4da
--- /dev/null
+++ b/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/CommandLineParser.java
@@ -0,0 +1,86 @@
+/**
+ * Copyright 1999-2001,2004 The Apache Software Foundation.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.commons.cli;
+
+import java.util.Properties;
+
+
+/**
+ * A class that implements the <code>CommandLineParser</code> interface
+ * can parse a String array according to the {@link Options} specified
+ * and return a {@link CommandLine}.
+ *
+ * @author John Keyes (john at integralsource.com)
+ */
+public interface CommandLineParser {
+ /**
+ * Parse the arguments according to the specified options.
+ *
+ * @param options the specified Options
+ * @param arguments the command line arguments
+ * @return the list of atomic option and value tokens
+ *
+ * @throws ParseException if there are any problems encountered
+ * while parsing the command line tokens.
+ */
+ CommandLine parse(Options options, String[] arguments) throws ParseException;
+
+ /**
+ * Parse the arguments according to the specified options and
+ * properties.
+ *
+ * @param options the specified Options
+ * @param arguments the command line arguments
+ * @param properties command line option name-value pairs
+ * @return the list of atomic option and value tokens
+ *
+ * @throws ParseException if there are any problems encountered
+ * while parsing the command line tokens.
+ */
+ CommandLine parse(Options options, String[] arguments, Properties properties)
+ throws ParseException;
+
+ /**
+ * Parse the arguments according to the specified options.
+ *
+ * @param options the specified Options
+ * @param arguments the command line arguments
+ * @param stopAtNonOption specifies whether to continue parsing the
+ * arguments if a non option is encountered.
+ *
+ * @return the list of atomic option and value tokens
+ * @throws ParseException if there are any problems encountered
+ * while parsing the command line tokens.
+ */
+ CommandLine parse(Options options, String[] arguments, boolean stopAtNonOption)
+ throws ParseException;
+
+ /**
+ * Parse the arguments according to the specified options and
+ * properties.
+ *
+ * @param options the specified Options
+ * @param arguments the command line arguments
+ * @param properties command line option name-value pairs
+ * @param stopAtNonOption specifies whether to continue parsing the
+ *
+ * @return the list of atomic option and value tokens
+ * @throws ParseException if there are any problems encountered
+ * while parsing the command line tokens.
+ */
+ CommandLine parse(Options options, String[] arguments, Properties properties,
+ boolean stopAtNonOption) throws ParseException;
+}
diff --git a/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/GnuParser.java b/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/GnuParser.java
new file mode 100644
index 0000000..d1fe538
--- /dev/null
+++ b/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/GnuParser.java
@@ -0,0 +1,134 @@
+/**
+ * Copyright 1999-2001,2004 The Apache Software Foundation.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.commons.cli;
+
+import java.util.ArrayList;
+
+
+/**
+ * The class GnuParser provides an implementation of the
+ * {@link Parser#flatten(Options,String[],boolean) flatten} method.
+ *
+ * @author John Keyes (john at integralsource.com)
+ * @see Parser
+ * @version $Revision: 155404 $
+ */
+public class GnuParser extends Parser {
+ /** holder for flattened tokens */
+ private ArrayList tokens = new ArrayList();
+
+ /**
+ * <p>Resets the members to their original state i.e. remove
+ * all of <code>tokens</code> entries.
+ */
+ private void init() {
+ tokens.clear();
+ }
+
+ /**
+ * <p>This flatten method does so using the following rules:
+ * <ol>
+ * <li>If an {@link Option} exists for the first character of
+ * the <code>arguments</code> entry <b>AND</b> an {@link Option}
+ * does not exist for the whole <code>argument</code> then
+ * add the first character as an option to the processed tokens
+ * list e.g. "-D" and add the rest of the entry to the also.</li>
+ * <li>Otherwise just add the token to the processed tokens list.
+ * </li>
+ * </ol>
+ * </p>
+ *
+ * @param options The Options to parse the arguments by.
+ * @param arguments The arguments that have to be flattened.
+ * @param stopAtNonOption specifies whether to stop
+ * flattening when a non option has been encountered
+ * @return a String array of the flattened arguments
+ */
+ protected String[] flatten(Options options, String[] arguments, boolean stopAtNonOption) {
+ init();
+
+ boolean eatTheRest = false;
+ Option currentOption = null;
+
+ for (int i = 0; i < arguments.length; i++) {
+ if ("--".equals(arguments[i])) {
+ eatTheRest = true;
+ tokens.add("--");
+ } else if ("-".equals(arguments[i])) {
+ tokens.add("-");
+ } else if (arguments[i].startsWith("-")) {
+ Option option = options.getOption(arguments[i]);
+
+ // this is not an Option
+ if (option == null) {
+ // handle special properties Option
+ Option specialOption = options.getOption(arguments[i].substring(0, 2));
+
+ if (specialOption != null) {
+ tokens.add(arguments[i].substring(0, 2));
+ tokens.add(arguments[i].substring(2));
+ } else if (stopAtNonOption) {
+ eatTheRest = true;
+ tokens.add(arguments[i]);
+ } else {
+ tokens.add(arguments[i]);
+ }
+ } else {
+ currentOption = option;
+
+ // special option
+ Option specialOption = options.getOption(arguments[i].substring(0, 2));
+
+ if ((specialOption != null) && (option == null)) {
+ tokens.add(arguments[i].substring(0, 2));
+ tokens.add(arguments[i].substring(2));
+ } else if ((currentOption != null) && currentOption.hasArg()) {
+ if (currentOption.hasArg()) {
+ tokens.add(arguments[i]);
+ currentOption = null;
+ } else if (currentOption.hasArgs()) {
+ tokens.add(arguments[i]);
+ } else if (stopAtNonOption) {
+ eatTheRest = true;
+ tokens.add("--");
+ tokens.add(arguments[i]);
+ } else {
+ tokens.add(arguments[i]);
+ }
+ } else if (currentOption != null) {
+ tokens.add(arguments[i]);
+ } else if (stopAtNonOption) {
+ eatTheRest = true;
+ tokens.add("--");
+ tokens.add(arguments[i]);
+ } else {
+ tokens.add(arguments[i]);
+ }
+ }
+ } else {
+ tokens.add(arguments[i]);
+ }
+
+ if (eatTheRest) {
+ for (i++; i < arguments.length; i++) {
+ tokens.add(arguments[i]);
+ }
+ }
+ }
+
+ return (String[]) tokens.toArray(new String[] { });
+ }
+}
diff --git a/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/HelpFormatter.java b/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/HelpFormatter.java
new file mode 100644
index 0000000..681f315
--- /dev/null
+++ b/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/HelpFormatter.java
@@ -0,0 +1,801 @@
+/**
+ * Copyright 1999-2001,2004 The Apache Software Foundation.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.commons.cli;
+
+import java.io.PrintWriter;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.Iterator;
+import java.util.List;
+
+
+/**
+ * A formatter of help messages for the current command line options
+ *
+ * @author Slawek Zachcial
+ * @author John Keyes (john at integralsource.com)
+ **/
+public class HelpFormatter {
+ // --------------------------------------------------------------- Constants
+
+ /** default number of characters per line */
+ public static final int DEFAULT_WIDTH = 74;
+
+ /** default padding to the left of each line */
+ public static final int DEFAULT_LEFT_PAD = 1;
+
+ /** ?? */
+ public static final int DEFAULT_DESC_PAD = 3;
+
+ /** the string to display at the begining of the usage statement */
+ public static final String DEFAULT_SYNTAX_PREFIX = "usage: ";
+
+ /** default prefix for shortOpts */
+ public static final String DEFAULT_OPT_PREFIX = "-";
+
+ /** default prefix for long Option */
+ public static final String DEFAULT_LONG_OPT_PREFIX = "--";
+
+ /** default name for an argument */
+ public static final String DEFAULT_ARG_NAME = "arg";
+
+ // -------------------------------------------------------------- Attributes
+
+ /** number of characters per line */
+ private int defaultWidth = DEFAULT_WIDTH;
+
+ /** amount of padding to the left of each line */
+ private int defaultLeftPad = DEFAULT_LEFT_PAD;
+
+ /** ?? */
+ private int defaultDescPad = DEFAULT_DESC_PAD;
+
+ /** the string to display at the begining of the usage statement */
+ private String defaultSyntaxPrefix = DEFAULT_SYNTAX_PREFIX;
+
+ /** the new line character/string ?? */
+ private String defaultNewLine = System.getProperty("line.separator");
+
+ /** the shortOpt prefix */
+ private String defaultOptPrefix = DEFAULT_OPT_PREFIX;
+
+ /** the long Opt prefix */
+ private String defaultLongOptPrefix = DEFAULT_LONG_OPT_PREFIX;
+
+ /** the name of the argument */
+ private String defaultArgName = DEFAULT_ARG_NAME;
+
+ /**
+ * Sets the 'width'.
+ *
+ * @param width the new value of 'width'
+ */
+ public void setWidth(int width) {
+ this.defaultWidth = width;
+ }
+
+ /**
+ * Returns the 'width'.
+ *
+ * @return the 'width'
+ */
+ public int getWidth() {
+ return this.defaultWidth;
+ }
+
+ /**
+ * Sets the 'leftPadding'.
+ *
+ * @param padding the new value of 'leftPadding'
+ */
+ public void setLeftPadding(int padding) {
+ this.defaultLeftPad = padding;
+ }
+
+ /**
+ * Returns the 'leftPadding'.
+ *
+ * @return the 'leftPadding'
+ */
+ public int getLeftPadding() {
+ return this.defaultLeftPad;
+ }
+
+ /**
+ * Sets the 'descPadding'.
+ *
+ * @param padding the new value of 'descPadding'
+ */
+ public void setDescPadding(int padding) {
+ this.defaultDescPad = padding;
+ }
+
+ /**
+ * Returns the 'descPadding'.
+ *
+ * @return the 'descPadding'
+ */
+ public int getDescPadding() {
+ return this.defaultDescPad;
+ }
+
+ /**
+ * Sets the 'syntaxPrefix'.
+ *
+ * @param prefix the new value of 'syntaxPrefix'
+ */
+ public void setSyntaxPrefix(String prefix) {
+ this.defaultSyntaxPrefix = prefix;
+ }
+
+ /**
+ * Returns the 'syntaxPrefix'.
+ *
+ * @return the 'syntaxPrefix'
+ */
+ public String getSyntaxPrefix() {
+ return this.defaultSyntaxPrefix;
+ }
+
+ /**
+ * Sets the 'newLine'.
+ *
+ * @param newline the new value of 'newLine'
+ */
+ public void setNewLine(String newline) {
+ this.defaultNewLine = newline;
+ }
+
+ /**
+ * Returns the 'newLine'.
+ *
+ * @return the 'newLine'
+ */
+ public String getNewLine() {
+ return this.defaultNewLine;
+ }
+
+ /**
+ * Sets the 'optPrefix'.
+ *
+ * @param prefix the new value of 'optPrefix'
+ */
+ public void setOptPrefix(String prefix) {
+ this.defaultOptPrefix = prefix;
+ }
+
+ /**
+ * Returns the 'optPrefix'.
+ *
+ * @return the 'optPrefix'
+ */
+ public String getOptPrefix() {
+ return this.defaultOptPrefix;
+ }
+
+ /**
+ * Sets the 'longOptPrefix'.
+ *
+ * @param prefix the new value of 'longOptPrefix'
+ */
+ public void setLongOptPrefix(String prefix) {
+ this.defaultLongOptPrefix = prefix;
+ }
+
+ /**
+ * Returns the 'longOptPrefix'.
+ *
+ * @return the 'longOptPrefix'
+ */
+ public String getLongOptPrefix() {
+ return this.defaultLongOptPrefix;
+ }
+
+ /**
+ * Sets the 'argName'.
+ *
+ * @param name the new value of 'argName'
+ */
+ public void setArgName(String name) {
+ this.defaultArgName = name;
+ }
+
+ /**
+ * Returns the 'argName'.
+ *
+ * @return the 'argName'
+ */
+ public String getArgName() {
+ return this.defaultArgName;
+ }
+
+ // ------------------------------------------------------------------ Public
+
+ /**
+ * <p>Print the help for <code>options</code> with the specified
+ * command line syntax. This method prints help information to
+ * System.out.</p>
+ *
+ * @param cmdLineSyntax the syntax for this application
+ * @param options the Options instance
+ */
+ public void printHelp(String cmdLineSyntax, Options options) {
+ printHelp(defaultWidth, cmdLineSyntax, null, options, null, false);
+ }
+
+ /**
+ * <p>Print the help for <code>options</code> with the specified
+ * command line syntax. This method prints help information to
+ * System.out.</p>
+ *
+ * @param cmdLineSyntax the syntax for this application
+ * @param options the Options instance
+ * @param autoUsage whether to print an automatically generated
+ * usage statement
+ */
+ public void printHelp(String cmdLineSyntax, Options options, boolean autoUsage) {
+ printHelp(defaultWidth, cmdLineSyntax, null, options, null, autoUsage);
+ }
+
+ /**
+ * <p>Print the help for <code>options</code> with the specified
+ * command line syntax. This method prints help information to
+ * System.out.</p>
+ *
+ * @param cmdLineSyntax the syntax for this application
+ * @param header the banner to display at the begining of the help
+ * @param options the Options instance
+ * @param footer the banner to display at the end of the help
+ */
+ public void printHelp(String cmdLineSyntax, String header, Options options, String footer) {
+ printHelp(cmdLineSyntax, header, options, footer, false);
+ }
+
+ /**
+ * <p>Print the help for <code>options</code> with the specified
+ * command line syntax. This method prints help information to
+ * System.out.</p>
+ *
+ * @param cmdLineSyntax the syntax for this application
+ * @param header the banner to display at the begining of the help
+ * @param options the Options instance
+ * @param footer the banner to display at the end of the help
+ * @param autoUsage whether to print an automatically generated
+ * usage statement
+ */
+ public void printHelp(String cmdLineSyntax, String header, Options options, String footer,
+ boolean autoUsage) {
+ printHelp(defaultWidth, cmdLineSyntax, header, options, footer, autoUsage);
+ }
+
+ /**
+ * <p>Print the help for <code>options</code> with the specified
+ * command line syntax. This method prints help information to
+ * System.out.</p>
+ *
+ * @param width the number of characters to be displayed on each line
+ * @param cmdLineSyntax the syntax for this application
+ * @param header the banner to display at the begining of the help
+ * @param options the Options instance
+ * @param footer the banner to display at the end of the help
+ */
+ public void printHelp(int width, String cmdLineSyntax, String header, Options options,
+ String footer) {
+ printHelp(width, cmdLineSyntax, header, options, footer, false);
+ }
+
+ /**
+ * <p>Print the help for <code>options</code> with the specified
+ * command line syntax. This method prints help information to
+ * System.out.</p>
+ *
+ * @param width the number of characters to be displayed on each line
+ * @param cmdLineSyntax the syntax for this application
+ * @param header the banner to display at the begining of the help
+ * @param options the Options instance
+ * @param footer the banner to display at the end of the help
+ * @param autoUsage whether to print an automatically generated
+ * usage statement
+ */
+ public void printHelp(int width, String cmdLineSyntax, String header, Options options,
+ String footer, boolean autoUsage) {
+ PrintWriter pw = new PrintWriter(System.out);
+
+ printHelp(pw, width, cmdLineSyntax, header, options, defaultLeftPad, defaultDescPad,
+ footer, autoUsage);
+ pw.flush();
+ }
+
+ /**
+ * <p>Print the help for <code>options</code> with the specified
+ * command line syntax.</p>
+ *
+ * @param pw the writer to which the help will be written
+ * @param width the number of characters to be displayed on each line
+ * @param cmdLineSyntax the syntax for this application
+ * @param header the banner to display at the begining of the help
+ * @param options the Options instance
+ * @param leftPad the number of characters of padding to be prefixed
+ * to each line
+ * @param descPad the number of characters of padding to be prefixed
+ * to each description line
+ * @param footer the banner to display at the end of the help
+ */
+ public void printHelp(PrintWriter pw, int width, String cmdLineSyntax, String header,
+ Options options, int leftPad, int descPad, String footer) {
+ printHelp(pw, width, cmdLineSyntax, header, options, leftPad, descPad, footer, false);
+ }
+
+ /**
+ * <p>Print the help for <code>options</code> with the specified
+ * command line syntax.</p>
+ *
+ * @param pw the writer to which the help will be written
+ * @param width the number of characters to be displayed on each line
+ * @param cmdLineSyntax the syntax for this application
+ * @param header the banner to display at the begining of the help
+ * @param options the Options instance
+ * @param leftPad the number of characters of padding to be prefixed
+ * to each line
+ * @param descPad the number of characters of padding to be prefixed
+ * to each description line
+ * @param footer the banner to display at the end of the help
+ * @param autoUsage whether to print an automatically generated
+ * usage statement
+ */
+ public void printHelp(PrintWriter pw, int width, String cmdLineSyntax, String header,
+ Options options, int leftPad, int descPad, String footer,
+ boolean autoUsage) {
+ if ((cmdLineSyntax == null) || (cmdLineSyntax.length() == 0)) {
+ throw new IllegalArgumentException("cmdLineSyntax not provided");
+ }
+
+ if (autoUsage) {
+ printUsage(pw, width, cmdLineSyntax, options);
+ } else {
+ printUsage(pw, width, cmdLineSyntax);
+ }
+
+ if ((header != null) && (header.trim().length() > 0)) {
+ printWrapped(pw, width, header);
+ }
+
+ printOptions(pw, width, options, leftPad, descPad);
+
+ if ((footer != null) && (footer.trim().length() > 0)) {
+ printWrapped(pw, width, footer);
+ }
+ }
+
+ /**
+ * <p>Prints the usage statement for the specified application.</p>
+ *
+ * @param pw The PrintWriter to print the usage statement
+ * @param width The number of characters to display per line
+ * @param app The application name
+ * @param options The command line Options
+ *
+ */
+ public void printUsage(PrintWriter pw, int width, String app, Options options) {
+ // initialise the string buffer
+ StringBuffer buff = new StringBuffer(defaultSyntaxPrefix).append(app).append(" ");
+
+ // create a list for processed option groups
+ final Collection processedGroups = new ArrayList();
+
+ // temp variable
+ Option option;
+
+ // iterate over the options
+ for (Iterator i = options.getOptions().iterator(); i.hasNext();) {
+ // get the next Option
+ option = (Option) i.next();
+
+ // check if the option is part of an OptionGroup
+ OptionGroup group = options.getOptionGroup(option);
+
+ // if the option is part of a group
+ if (group != null) {
+ // and if the group has not already been processed
+ if (!processedGroups.contains(group)) {
+ // add the group to the processed list
+ processedGroups.add(group);
+
+ // add the usage clause
+ appendOptionGroup(buff, group);
+ }
+
+ // otherwise the option was displayed in the group
+ // previously so ignore it.
+ }
+ // if the Option is not part of an OptionGroup
+ else {
+ appendOption(buff, option, option.isRequired());
+ }
+
+ if (i.hasNext()) {
+ buff.append(" ");
+ }
+ }
+
+ // call printWrapped
+ printWrapped(pw, width, buff.toString().indexOf(' ') + 1, buff.toString());
+ }
+
+ /**
+ * Appends the usage clause for an OptionGroup to a StringBuffer.
+ * The clause is wrapped in square brackets if the group is required.
+ * The display of the options is handled by appendOption
+ * @param buff the StringBuffer to append to
+ * @param group the group to append
+ * @see #appendOption(StringBuffer,Option,boolean)
+ */
+ private static void appendOptionGroup(final StringBuffer buff, final OptionGroup group) {
+ if (!group.isRequired()) {
+ buff.append("[");
+ }
+
+ // for each option in the OptionGroup
+ for (Iterator i = group.getOptions().iterator(); i.hasNext();) {
+ // whether the option is required or not is handled at group level
+ appendOption(buff, (Option) i.next(), true);
+
+ if (i.hasNext()) {
+ buff.append(" | ");
+ }
+ }
+
+ if (!group.isRequired()) {
+ buff.append("]");
+ }
+ }
+
+ /**
+ * Appends the usage clause for an Option to a StringBuffer.
+ *
+ * @param buff the StringBuffer to append to
+ * @param option the Option to append
+ * @param required whether the Option is required or not
+ */
+ private static void appendOption(final StringBuffer buff, final Option option,
+ final boolean required) {
+ if (!required) {
+ buff.append("[");
+ }
+
+ if (option.getOpt() != null) {
+ buff.append("-").append(option.getOpt());
+ } else {
+ buff.append("--").append(option.getLongOpt());
+ }
+
+ // if the Option has a value
+ if (option.hasArg() && (option.getArgName() != null)) {
+ buff.append(" <").append(option.getArgName()).append(">");
+ }
+
+ // if the Option is not a required option
+ if (!required) {
+ buff.append("]");
+ }
+ }
+
+ /**
+ * <p>Print the cmdLineSyntax to the specified writer, using the
+ * specified width.</p>
+ *
+ * @param pw The printWriter to write the help to
+ * @param width The number of characters per line for the usage statement.
+ * @param cmdLineSyntax The usage statement.
+ */
+ public void printUsage(PrintWriter pw, int width, String cmdLineSyntax) {
+ int argPos = cmdLineSyntax.indexOf(' ') + 1;
+
+ printWrapped(pw, width, defaultSyntaxPrefix.length() + argPos,
+ defaultSyntaxPrefix + cmdLineSyntax);
+ }
+
+ /**
+ * <p>Print the help for the specified Options to the specified writer,
+ * using the specified width, left padding and description padding.</p>
+ *
+ * @param pw The printWriter to write the help to
+ * @param width The number of characters to display per line
+ * @param options The command line Options
+ * @param leftPad the number of characters of padding to be prefixed
+ * to each line
+ * @param descPad the number of characters of padding to be prefixed
+ * to each description line
+ */
+ public void printOptions(PrintWriter pw, int width, Options options, int leftPad, int descPad) {
+ StringBuffer sb = new StringBuffer();
+
+ renderOptions(sb, width, options, leftPad, descPad);
+ pw.println(sb.toString());
+ }
+
+ /**
+ * <p>Print the specified text to the specified PrintWriter.</p>
+ *
+ * @param pw The printWriter to write the help to
+ * @param width The number of characters to display per line
+ * @param text The text to be written to the PrintWriter
+ */
+ public void printWrapped(PrintWriter pw, int width, String text) {
+ printWrapped(pw, width, 0, text);
+ }
+
+ /**
+ * <p>Print the specified text to the specified PrintWriter.</p>
+ *
+ * @param pw The printWriter to write the help to
+ * @param width The number of characters to display per line
+ * @param nextLineTabStop The position on the next line for the first tab.
+ * @param text The text to be written to the PrintWriter
+ */
+ public void printWrapped(PrintWriter pw, int width, int nextLineTabStop, String text) {
+ StringBuffer sb = new StringBuffer(text.length());
+
+ renderWrappedText(sb, width, nextLineTabStop, text);
+ pw.println(sb.toString());
+ }
+
+ // --------------------------------------------------------------- Protected
+
+ /**
+ * <p>Render the specified Options and return the rendered Options
+ * in a StringBuffer.</p>
+ *
+ * @param sb The StringBuffer to place the rendered Options into.
+ * @param width The number of characters to display per line
+ * @param options The command line Options
+ * @param leftPad the number of characters of padding to be prefixed
+ * to each line
+ * @param descPad the number of characters of padding to be prefixed
+ * to each description line
+ *
+ * @return the StringBuffer with the rendered Options contents.
+ */
+ protected StringBuffer renderOptions(StringBuffer sb, int width, Options options, int leftPad,
+ int descPad) {
+ final String lpad = createPadding(leftPad);
+ final String dpad = createPadding(descPad);
+
+ // first create list containing only <lpad>-a,--aaa where
+ // -a is opt and --aaa is long opt; in parallel look for
+ // the longest opt string this list will be then used to
+ // sort options ascending
+ int max = 0;
+ StringBuffer optBuf;
+ List prefixList = new ArrayList();
+ Option option;
+ List optList = options.helpOptions();
+
+ //Collections.sort(optList, new OptionComparator());
+ for (Iterator i = optList.iterator(); i.hasNext();) {
+ option = (Option) i.next();
+ optBuf = new StringBuffer(8);
+
+ if (option.getOpt() == null) {
+ optBuf.append(lpad).append(" " + defaultLongOptPrefix).append(option.getLongOpt());
+ } else {
+ optBuf.append(lpad).append(defaultOptPrefix).append(option.getOpt());
+
+ if (option.hasLongOpt()) {
+ optBuf.append(',').append(defaultLongOptPrefix).append(option.getLongOpt());
+ }
+ }
+
+ if (option.hasArg()) {
+ if (option.hasArgName()) {
+ optBuf.append(" <").append(option.getArgName()).append(">");
+ } else {
+ optBuf.append(' ');
+ }
+ }
+
+ prefixList.add(optBuf);
+ max = (optBuf.length() > max) ? optBuf.length() : max;
+ }
+
+ int x = 0;
+
+ for (Iterator i = optList.iterator(); i.hasNext();) {
+ option = (Option) i.next();
+ optBuf = new StringBuffer(prefixList.get(x++).toString());
+
+ if (optBuf.length() < max) {
+ optBuf.append(createPadding(max - optBuf.length()));
+ }
+
+ optBuf.append(dpad);
+
+ int nextLineTabStop = max + descPad;
+
+ if (option.getDescription() != null) {
+ optBuf.append(option.getDescription());
+ }
+
+ renderWrappedText(sb, width, nextLineTabStop, optBuf.toString());
+
+ if (i.hasNext()) {
+ sb.append(defaultNewLine);
+ }
+ }
+
+ return sb;
+ }
+
+ /**
+ * <p>Render the specified text and return the rendered Options
+ * in a StringBuffer.</p>
+ *
+ * @param sb The StringBuffer to place the rendered text into.
+ * @param width The number of characters to display per line
+ * @param nextLineTabStop The position on the next line for the first tab.
+ * @param text The text to be rendered.
+ *
+ * @return the StringBuffer with the rendered Options contents.
+ */
+ protected StringBuffer renderWrappedText(StringBuffer sb, int width, int nextLineTabStop,
+ String text) {
+ int pos = findWrapPos(text, width, 0);
+
+ if (pos == -1) {
+ sb.append(rtrim(text));
+
+ return sb;
+ }
+
+ sb.append(rtrim(text.substring(0, pos))).append(defaultNewLine);
+
+ // all following lines must be padded with nextLineTabStop space
+ // characters
+ final String padding = createPadding(nextLineTabStop);
+
+ while (true) {
+ text = padding + text.substring(pos).trim();
+ pos = findWrapPos(text, width, nextLineTabStop);
+
+ if (pos == -1) {
+ sb.append(text);
+
+ return sb;
+ }
+
+ sb.append(rtrim(text.substring(0, pos))).append(defaultNewLine);
+ }
+ }
+
+ /**
+ * Finds the next text wrap position after <code>startPos</code> for the
+ * text in <code>text</code> with the column width <code>width</code>.
+ * The wrap point is the last postion before startPos+width having a
+ * whitespace character (space, \n, \r).
+ *
+ * @param text The text being searched for the wrap position
+ * @param width width of the wrapped text
+ * @param startPos position from which to start the lookup whitespace
+ * character
+ * @return postion on which the text must be wrapped or -1 if the wrap
+ * position is at the end of the text
+ */
+ protected int findWrapPos(String text, int width, int startPos) {
+ int pos = -1;
+
+ // the line ends before the max wrap pos or a new line char found
+ if ((((pos = text.indexOf('\n', startPos)) != -1) && (pos <= width))
+ || (((pos = text.indexOf('\t', startPos)) != -1) && (pos <= width))) {
+ return pos + 1;
+ } else if ((startPos + width) >= text.length()) {
+ return -1;
+ }
+
+ // look for the last whitespace character before startPos+width
+ pos = startPos + width;
+
+ char c;
+
+ while ((pos >= startPos) && ((c = text.charAt(pos)) != ' ') && (c != '\n') && (c != '\r')) {
+ --pos;
+ }
+
+ // if we found it - just return
+ if (pos > startPos) {
+ return pos;
+ }
+
+ // must look for the first whitespace chearacter after startPos
+ // + width
+ pos = startPos + width;
+
+ while ((pos <= text.length()) && ((c = text.charAt(pos)) != ' ') && (c != '\n')
+ && (c != '\r')) {
+ ++pos;
+ }
+
+ return (pos == text.length()) ? (-1) : pos;
+ }
+
+ /**
+ * <p>Return a String of padding of length <code>len</code>.</p>
+ *
+ * @param len The length of the String of padding to create.
+ *
+ * @return The String of padding
+ */
+ protected String createPadding(int len) {
+ StringBuffer sb = new StringBuffer(len);
+
+ for (int i = 0; i < len; ++i) {
+ sb.append(' ');
+ }
+
+ return sb.toString();
+ }
+
+ /**
+ * <p>Remove the trailing whitespace from the specified String.</p>
+ *
+ * @param s The String to remove the trailing padding from.
+ *
+ * @return The String of without the trailing padding
+ */
+ protected String rtrim(String s) {
+ if ((s == null) || (s.length() == 0)) {
+ return s;
+ }
+
+ int pos = s.length();
+
+ while ((pos > 0) && Character.isWhitespace(s.charAt(pos - 1))) {
+ --pos;
+ }
+
+ return s.substring(0, pos);
+ }
+
+ // ------------------------------------------------------ Package protected
+ // ---------------------------------------------------------------- Private
+ // ---------------------------------------------------------- Inner classes
+ /**
+ * <p>This class implements the <code>Comparator</code> interface
+ * for comparing Options.</p>
+ */
+ private static class OptionComparator implements Comparator {
+ /**
+ * <p>Compares its two arguments for order. Returns a negative
+ * integer, zero, or a positive integer as the first argument
+ * is less than, equal to, or greater than the second.</p>
+ *
+ * @param o1 The first Option to be compared.
+ * @param o2 The second Option to be compared.
+ *
+ * @return a negative integer, zero, or a positive integer as
+ * the first argument is less than, equal to, or greater than the
+ * second.
+ */
+ public int compare(Object o1, Object o2) {
+ Option opt1 = (Option) o1;
+ Option opt2 = (Option) o2;
+
+ return opt1.getKey().compareToIgnoreCase(opt2.getKey());
+ }
+ }
+}
diff --git a/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/MissingArgumentException.java b/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/MissingArgumentException.java
new file mode 100644
index 0000000..d801f59
--- /dev/null
+++ b/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/MissingArgumentException.java
@@ -0,0 +1,36 @@
+/**
+ * Copyright 1999-2001,2004 The Apache Software Foundation.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.commons.cli;
+
+
+/**
+ * <p>Thrown when an option requiring an argument
+ * is not provided with an argument.</p>
+ *
+ * @author John Keyes (john at integralsource.com)
+ * @see ParseException
+ */
+public class MissingArgumentException extends ParseException {
+ /**
+ * <p>Construct a new <code>MissingArgumentException</code>
+ * with the specified detail message.</p>
+ *
+ * @param message the detail message
+ */
+ public MissingArgumentException(String message) {
+ super(message);
+ }
+}
diff --git a/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/MissingOptionException.java b/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/MissingOptionException.java
new file mode 100644
index 0000000..8c52c61
--- /dev/null
+++ b/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/MissingOptionException.java
@@ -0,0 +1,35 @@
+/**
+ * Copyright 1999-2001,2004 The Apache Software Foundation.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.commons.cli;
+
+
+/**
+ * <p>Thrown when a required option has not been provided.</p>
+ *
+ * @author John Keyes ( john at integralsource.com )
+ * @see ParseException
+ */
+public class MissingOptionException extends ParseException {
+ /**
+ * <p>Construct a new <code>MissingSelectedException</code>
+ * with the specified detail message.</p>
+ *
+ * @param message the detail message
+ */
+ public MissingOptionException(String message) {
+ super(message);
+ }
+}
diff --git a/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/Option.java b/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/Option.java
new file mode 100644
index 0000000..1edead1
--- /dev/null
+++ b/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/Option.java
@@ -0,0 +1,541 @@
+/**
+ * Copyright 1999-2001,2004 The Apache Software Foundation.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.commons.cli;
+
+import java.util.ArrayList;
+
+
+/** <p>Describes a single command-line option. It maintains
+ * information regarding the short-name of the option, the long-name,
+ * if any exists, a flag indicating if an argument is required for
+ * this option, and a self-documenting description of the option.</p>
+ *
+ * <p>An Option is not created independantly, but is create through
+ * an instance of {@link Options}.<p>
+ *
+ * @see org.apache.commons.cli.Options
+ * @see org.apache.commons.cli.CommandLine
+ *
+ * @author bob mcwhirter (bob @ werken.com)
+ * @author <a href="mailto:jstrachan at apache.org">James Strachan</a>
+ * @version $Revision: 384132 $
+ */
+public class Option {
+ /** constant that specifies the number of argument values has
+ not been specified */
+ public static final int UNINITIALIZED = -1;
+
+ /** constant that specifies the number of argument values is infinite */
+ public static final int UNLIMITED_VALUES = -2;
+
+ /** opt the name of the option */
+ private String opt;
+
+ /** longOpt is the long representation of the option */
+ private String longOpt;
+
+ /** hasArg specifies whether this option has an associated argument */
+ private boolean hasArg;
+
+ /** argName specifies the name of the argument for this option */
+ private String argName = "arg";
+
+ /** description of the option */
+ private String description;
+
+ /** required specifies whether this option is required to be present */
+ private boolean required;
+
+ /** specifies whether the argument value of this Option is optional */
+ private boolean optionalArg;
+
+ /**
+ * numberOfArgs specifies the number of argument values this option
+ * can have
+ */
+ private int numberOfArgs = UNINITIALIZED;
+
+ /** the type of this Option */
+ private Object type;
+
+ /** the list of argument values **/
+ private ArrayList values = new ArrayList();
+
+ /** the character that is the value separator */
+ private char valuesep;
+
+ /**
+ * Creates an Option using the specified parameters.
+ *
+ * @param opt short representation of the option
+ * @param description describes the function of the option
+ *
+ * @throws IllegalArgumentException if there are any non valid
+ * Option characters in <code>opt</code>.
+ */
+ public Option(String opt, String description) throws IllegalArgumentException {
+ this(opt, null, false, description);
+ }
+
+ /**
+ * Creates an Option using the specified parameters.
+ *
+ * @param opt short representation of the option
+ * @param hasArg specifies whether the Option takes an argument or not
+ * @param description describes the function of the option
+ *
+ * @throws IllegalArgumentException if there are any non valid
+ * Option characters in <code>opt</code>.
+ */
+ public Option(String opt, boolean hasArg, String description) throws IllegalArgumentException {
+ this(opt, null, hasArg, description);
+ }
+
+ /**
+ * Creates an Option using the specified parameters.
+ *
+ * @param opt short representation of the option
+ * @param longOpt the long representation of the option
+ * @param hasArg specifies whether the Option takes an argument or not
+ * @param description describes the function of the option
+ *
+ * @throws IllegalArgumentException if there are any non valid
+ * Option characters in <code>opt</code>.
+ */
+ public Option(String opt, String longOpt, boolean hasArg, String description)
+ throws IllegalArgumentException {
+ // ensure that the option is valid
+ OptionValidator.validateOption(opt);
+
+ this.opt = opt;
+ this.longOpt = longOpt;
+
+ // if hasArg is set then the number of arguments is 1
+ if (hasArg) {
+ this.numberOfArgs = 1;
+ }
+
+ this.hasArg = hasArg;
+ this.description = description;
+ }
+
+ /**
+ * Returns the id of this Option. This is only set when the
+ * Option shortOpt is a single character. This is used for switch
+ * statements.
+ *
+ * @return the id of this Option
+ */
+ public int getId() {
+ return getKey().charAt(0);
+ }
+
+ /**
+ * Returns the 'unique' Option identifier.
+ *
+ * @return the 'unique' Option identifier
+ */
+ String getKey() {
+ // if 'opt' is null, then it is a 'long' option
+ if (opt == null) {
+ return this.longOpt;
+ }
+
+ return this.opt;
+ }
+
+ /**
+ * Retrieve the name of this Option.
+ *
+ * It is this String which can be used with
+ * {@link CommandLine#hasOption(String opt)} and
+ * {@link CommandLine#getOptionValue(String opt)} to check
+ * for existence and argument.
+ *
+ * @return The name of this option
+ */
+ public String getOpt() {
+ return this.opt;
+ }
+
+ /**
+ * Retrieve the type of this Option.
+ *
+ * @return The type of this option
+ */
+ public Object getType() {
+ return this.type;
+ }
+
+ /**
+ * Sets the type of this Option.
+ *
+ * @param type the type of this Option
+ */
+ public void setType(Object type) {
+ this.type = type;
+ }
+
+ /**
+ * Retrieve the long name of this Option.
+ *
+ * @return Long name of this option, or null, if there is no long name
+ */
+ public String getLongOpt() {
+ return this.longOpt;
+ }
+
+ /**
+ * Sets the long name of this Option.
+ *
+ * @param longOpt the long name of this Option
+ */
+ public void setLongOpt(String longOpt) {
+ this.longOpt = longOpt;
+ }
+
+ /**
+ * Sets whether this Option can have an optional argument.
+ *
+ * @param optionalArg specifies whether the Option can have
+ * an optional argument.
+ */
+ public void setOptionalArg(boolean optionalArg) {
+ this.optionalArg = optionalArg;
+ }
+
+ /**
+ * @return whether this Option can have an optional argument
+ */
+ public boolean hasOptionalArg() {
+ return this.optionalArg;
+ }
+
+ /**
+ * Query to see if this Option has a long name
+ *
+ * @return boolean flag indicating existence of a long name
+ */
+ public boolean hasLongOpt() {
+ return (this.longOpt != null);
+ }
+
+ /**
+ * Query to see if this Option requires an argument
+ *
+ * @return boolean flag indicating if an argument is required
+ */
+ public boolean hasArg() {
+ return (this.numberOfArgs > 0) || (numberOfArgs == UNLIMITED_VALUES);
+ }
+
+ /**
+ * Retrieve the self-documenting description of this Option
+ *
+ * @return The string description of this option
+ */
+ public String getDescription() {
+ return this.description;
+ }
+
+ /**
+ * Sets the self-documenting description of this Option
+ *
+ * @param description The description of this option
+ */
+ public void setDescription(String description) {
+ this.description = description;
+ }
+
+ /**
+ * Query to see if this Option requires an argument
+ *
+ * @return boolean flag indicating if an argument is required
+ */
+ public boolean isRequired() {
+ return this.required;
+ }
+
+ /**
+ * Sets whether this Option is mandatory.
+ *
+ * @param required specifies whether this Option is mandatory
+ */
+ public void setRequired(boolean required) {
+ this.required = required;
+ }
+
+ /**
+ * Sets the display name for the argument value.
+ *
+ * @param argName the display name for the argument value.
+ */
+ public void setArgName(String argName) {
+ this.argName = argName;
+ }
+
+ /**
+ * Gets the display name for the argument value.
+ *
+ * @return the display name for the argument value.
+ */
+ public String getArgName() {
+ return this.argName;
+ }
+
+ /**
+ * Returns whether the display name for the argument value
+ * has been set.
+ *
+ * @return if the display name for the argument value has been
+ * set.
+ */
+ public boolean hasArgName() {
+ return ((this.argName != null) && (this.argName.length() > 0));
+ }
+
+ /**
+ * Query to see if this Option can take many values.
+ *
+ * @return boolean flag indicating if multiple values are allowed
+ */
+ public boolean hasArgs() {
+ return (this.numberOfArgs > 1) || (this.numberOfArgs == UNLIMITED_VALUES);
+ }
+
+ /**
+ * Sets the number of argument values this Option can take.
+ *
+ * @param num the number of argument values
+ */
+ public void setArgs(int num) {
+ this.numberOfArgs = num;
+ }
+
+ /**
+ * Sets the value separator. For example if the argument value
+ * was a Java property, the value separator would be '='.
+ *
+ * @param sep The value separator.
+ */
+ public void setValueSeparator(char sep) {
+ this.valuesep = sep;
+ }
+
+ /**
+ * Returns the value separator character.
+ *
+ * @return the value separator character.
+ */
+ public char getValueSeparator() {
+ return this.valuesep;
+ }
+
+ /**
+ * Return whether this Option has specified a value separator.
+ *
+ * @return whether this Option has specified a value separator.
+ */
+ public boolean hasValueSeparator() {
+ return (this.valuesep > 0);
+ }
+
+ /**
+ * Returns the number of argument values this Option can take.
+ *
+ * @return num the number of argument values
+ */
+ public int getArgs() {
+ return this.numberOfArgs;
+ }
+
+ /**
+ * Adds the specified value to this Option.
+ *
+ * @param value is a/the value of this Option
+ */
+ void addValue(String value) {
+ switch (numberOfArgs) {
+ case UNINITIALIZED:
+ throw new RuntimeException("NO_ARGS_ALLOWED");
+
+ default:
+ processValue(value);
+ }
+ }
+
+ /**
+ * Processes the value. If this Option has a value separator
+ * the value will have to be parsed into individual tokens. When
+ * n-1 tokens have been processed and there are more value separators
+ * in the value, parsing is ceased and the remaining characters are
+ * added as a single token.
+ *
+ * @param value The String to be processed.
+ *
+ * @since 1.0.1
+ */
+ private void processValue(String value) {
+ // this Option has a separator character
+ if (hasValueSeparator()) {
+ // get the separator character
+ char sep = getValueSeparator();
+
+ // store the index for the value separator
+ int index = value.indexOf(sep);
+
+ // while there are more value separators
+ while (index != -1) {
+ // next value to be added
+ if (values.size() == (numberOfArgs - 1)) {
+ break;
+ }
+
+ // store
+ add(value.substring(0, index));
+
+ // parse
+ value = value.substring(index + 1);
+
+ // get new index
+ index = value.indexOf(sep);
+ }
+ }
+
+ // store the actual value or the last value that has been parsed
+ add(value);
+ }
+
+ /**
+ * Add the value to this Option. If the number of arguments
+ * is greater than zero and there is enough space in the list then
+ * add the value. Otherwise, throw a runtime exception.
+ *
+ * @param value The value to be added to this Option
+ *
+ * @since 1.0.1
+ */
+ private void add(String value) {
+ if ((numberOfArgs > 0) && (values.size() > (numberOfArgs - 1))) {
+ throw new RuntimeException("Cannot add value, list full.");
+ }
+
+ // store value
+ this.values.add(value);
+ }
+
+ /**
+ * Returns the specified value of this Option or
+ * <code>null</code> if there is no value.
+ *
+ * @return the value/first value of this Option or
+ * <code>null</code> if there is no value.
+ */
+ public String getValue() {
+ return hasNoValues() ? null : (String) this.values.get(0);
+ }
+
+ /**
+ * Returns the specified value of this Option or
+ * <code>null</code> if there is no value.
+ *
+ * @param index The index of the value to be returned.
+ *
+ * @return the specified value of this Option or
+ * <code>null</code> if there is no value.
+ *
+ * @throws IndexOutOfBoundsException if index is less than 1
+ * or greater than the number of the values for this Option.
+ */
+ public String getValue(int index) throws IndexOutOfBoundsException {
+ return hasNoValues() ? null : (String) this.values.get(index);
+ }
+
+ /**
+ * Returns the value/first value of this Option or the
+ * <code>defaultValue</code> if there is no value.
+ *
+ * @param defaultValue The value to be returned if ther
+ * is no value.
+ *
+ * @return the value/first value of this Option or the
+ * <code>defaultValue</code> if there are no values.
+ */
+ public String getValue(String defaultValue) {
+ String value = getValue();
+
+ return (value != null) ? value : defaultValue;
+ }
+
+ /**
+ * Return the values of this Option as a String array
+ * or null if there are no values
+ *
+ * @return the values of this Option as a String array
+ * or null if there are no values
+ */
+ public String[] getValues() {
+ return hasNoValues() ? null : (String[]) this.values.toArray(new String[] { });
+ }
+
+ /**
+ * @return the values of this Option as a List
+ * or null if there are no values
+ */
+ public java.util.List getValuesList() {
+ return this.values;
+ }
+
+ /**
+ * Dump state, suitable for debugging.
+ *
+ * @return Stringified form of this object
+ */
+ public String toString() {
+ StringBuffer buf = new StringBuffer().append("[ option: ");
+
+ buf.append(this.opt);
+
+ if (this.longOpt != null) {
+ buf.append(" ").append(this.longOpt);
+ }
+
+ buf.append(" ");
+
+ if (hasArg) {
+ buf.append("+ARG");
+ }
+
+ buf.append(" :: ").append(this.description);
+
+ if (this.type != null) {
+ buf.append(" :: ").append(this.type);
+ }
+
+ buf.append(" ]");
+
+ return buf.toString();
+ }
+
+ /**
+ * Returns whether this Option has any values.
+ *
+ * @return whether this Option has any values.
+ */
+ private boolean hasNoValues() {
+ return this.values.size() == 0;
+ }
+}
diff --git a/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/OptionBuilder.java b/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/OptionBuilder.java
new file mode 100644
index 0000000..613784f
--- /dev/null
+++ b/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/OptionBuilder.java
@@ -0,0 +1,345 @@
+/**
+ * Copyright 1999-2001,2004 The Apache Software Foundation.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.commons.cli;
+
+
+/**
+ * <p>OptionBuilder allows the user to create Options using descriptive
+ * methods.</p>
+ * <p>Details on the Builder pattern can be found at
+ * <a href="http://c2.com/cgi-bin/wiki?BuilderPattern">
+ * http://c2.com/cgi-bin/wiki?BuilderPattern</a>.</p>
+ *
+ * @author John Keyes (john at integralsource.com)
+ * @since 1.0
+ */
+public class OptionBuilder {
+ /** long option */
+ private static String longopt;
+
+ /** option description */
+ private static String description;
+
+ /** argument name */
+ private static String argName;
+
+ /** is required? */
+ private static boolean required;
+
+ /** the number of arguments */
+ private static int numberOfArgs = Option.UNINITIALIZED;
+
+ /** option type */
+ private static Object type;
+
+ /** option can have an optional argument value */
+ private static boolean optionalArg;
+
+ /** value separator for argument value */
+ private static char valuesep;
+
+ /** option builder instance */
+ private static OptionBuilder instance = new OptionBuilder();
+
+ /**
+ * private constructor to prevent instances being created
+ */
+ private OptionBuilder() {
+ // hide the constructor
+ }
+
+ /**
+ * Resets the member variables to their default values.
+ */
+ private static void reset() {
+ description = null;
+ argName = "arg";
+ longopt = null;
+ type = null;
+ required = false;
+ numberOfArgs = Option.UNINITIALIZED;
+
+ // PMM 9/6/02 - these were missing
+ optionalArg = false;
+ valuesep = (char) 0;
+ }
+
+ /**
+ * The next Option created will have the following long option value.
+ *
+ * @param newLongopt the long option value
+ * @return the OptionBuilder instance
+ */
+ public static OptionBuilder withLongOpt(String newLongopt) {
+ OptionBuilder.longopt = newLongopt;
+
+ return instance;
+ }
+
+ /**
+ * The next Option created will require an argument value.
+ *
+ * @return the OptionBuilder instance
+ */
+ public static OptionBuilder hasArg() {
+ OptionBuilder.numberOfArgs = 1;
+
+ return instance;
+ }
+
+ /**
+ * The next Option created will require an argument value if
+ * <code>hasArg</code> is true.
+ *
+ * @param hasArg if true then the Option has an argument value
+ * @return the OptionBuilder instance
+ */
+ public static OptionBuilder hasArg(boolean hasArg) {
+ OptionBuilder.numberOfArgs = (hasArg == true) ? 1 : Option.UNINITIALIZED;
+
+ return instance;
+ }
+
+ /**
+ * The next Option created will have the specified argument value
+ * name.
+ *
+ * @param name the name for the argument value
+ * @return the OptionBuilder instance
+ */
+ public static OptionBuilder withArgName(String name) {
+ OptionBuilder.argName = name;
+
+ return instance;
+ }
+
+ /**
+ * The next Option created will be required.
+ *
+ * @return the OptionBuilder instance
+ */
+ public static OptionBuilder isRequired() {
+ OptionBuilder.required = true;
+
+ return instance;
+ }
+
+ /**
+ * The next Option created uses <code>sep</code> as a means to
+ * separate argument values.
+ *
+ * <b>Example:</b>
+ * <pre>
+ * Option opt = OptionBuilder.withValueSeparator(':')
+ * .create('D');
+ *
+ * CommandLine line = parser.parse(args);
+ * String propertyName = opt.getValue(0);
+ * String propertyValue = opt.getValue(1);
+ * </pre>
+ *
+ * @param sep The value separator to be used for the argument values.
+ *
+ * @return the OptionBuilder instance
+ */
+ public static OptionBuilder withValueSeparator(char sep) {
+ OptionBuilder.valuesep = sep;
+
+ return instance;
+ }
+
+ /**
+ * The next Option created uses '<code>=</code>' as a means to
+ * separate argument values.
+ *
+ * <b>Example:</b>
+ * <pre>
+ * Option opt = OptionBuilder.withValueSeparator()
+ * .create('D');
+ *
+ * CommandLine line = parser.parse(args);
+ * String propertyName = opt.getValue(0);
+ * String propertyValue = opt.getValue(1);
+ * </pre>
+ *
+ * @return the OptionBuilder instance
+ */
+ public static OptionBuilder withValueSeparator() {
+ OptionBuilder.valuesep = '=';
+
+ return instance;
+ }
+
+ /**
+ * The next Option created will be required if <code>required</code>
+ * is true.
+ *
+ * @param newRequired if true then the Option is required
+ * @return the OptionBuilder instance
+ */
+ public static OptionBuilder isRequired(boolean newRequired) {
+ OptionBuilder.required = newRequired;
+
+ return instance;
+ }
+
+ /**
+ * The next Option created can have unlimited argument values.
+ *
+ * @return the OptionBuilder instance
+ */
+ public static OptionBuilder hasArgs() {
+ OptionBuilder.numberOfArgs = Option.UNLIMITED_VALUES;
+
+ return instance;
+ }
+
+ /**
+ * The next Option created can have <code>num</code>
+ * argument values.
+ *
+ * @param num the number of args that the option can have
+ * @return the OptionBuilder instance
+ */
+ public static OptionBuilder hasArgs(int num) {
+ OptionBuilder.numberOfArgs = num;
+
+ return instance;
+ }
+
+ /**
+ * The next Option can have an optional argument.
+ *
+ * @return the OptionBuilder instance
+ */
+ public static OptionBuilder hasOptionalArg() {
+ OptionBuilder.numberOfArgs = 1;
+ OptionBuilder.optionalArg = true;
+
+ return instance;
+ }
+
+ /**
+ * The next Option can have an unlimited number of
+ * optional arguments.
+ *
+ * @return the OptionBuilder instance
+ */
+ public static OptionBuilder hasOptionalArgs() {
+ OptionBuilder.numberOfArgs = Option.UNLIMITED_VALUES;
+ OptionBuilder.optionalArg = true;
+
+ return instance;
+ }
+
+ /**
+ * The next Option can have the specified number of
+ * optional arguments.
+ *
+ * @param numArgs - the maximum number of optional arguments
+ * the next Option created can have.
+ * @return the OptionBuilder instance
+ */
+ public static OptionBuilder hasOptionalArgs(int numArgs) {
+ OptionBuilder.numberOfArgs = numArgs;
+ OptionBuilder.optionalArg = true;
+
+ return instance;
+ }
+
+ /**
+ * The next Option created will have a value that will be an instance
+ * of <code>type</code>.
+ *
+ * @param newType the type of the Options argument value
+ * @return the OptionBuilder instance
+ */
+ public static OptionBuilder withType(Object newType) {
+ OptionBuilder.type = newType;
+
+ return instance;
+ }
+
+ /**
+ * The next Option created will have the specified description
+ *
+ * @param newDescription a description of the Option's purpose
+ * @return the OptionBuilder instance
+ */
+ public static OptionBuilder withDescription(String newDescription) {
+ OptionBuilder.description = newDescription;
+
+ return instance;
+ }
+
+ /**
+ * Create an Option using the current settings and with
+ * the specified Option <code>char</code>.
+ *
+ * @param opt the character representation of the Option
+ * @return the Option instance
+ * @throws IllegalArgumentException if <code>opt</code> is not
+ * a valid character. See Option.
+ */
+ public static Option create(char opt) throws IllegalArgumentException {
+ return create(String.valueOf(opt));
+ }
+
+ /**
+ * Create an Option using the current settings
+ *
+ * @return the Option instance
+ * @throws IllegalArgumentException if <code>longOpt</code> has
+ * not been set.
+ */
+ public static Option create() throws IllegalArgumentException {
+ if (longopt == null) {
+ throw new IllegalArgumentException("must specify longopt");
+ }
+
+ return create(null);
+ }
+
+ /**
+ * Create an Option using the current settings and with
+ * the specified Option <code>char</code>.
+ *
+ * @param opt the <code>java.lang.String</code> representation
+ * of the Option
+ * @return the Option instance
+ * @throws IllegalArgumentException if <code>opt</code> is not
+ * a valid character. See Option.
+ */
+ public static Option create(String opt) throws IllegalArgumentException {
+ // create the option
+ Option option = new Option(opt, description);
+
+ // set the option properties
+ option.setLongOpt(longopt);
+ option.setRequired(required);
+ option.setOptionalArg(optionalArg);
+ option.setArgs(numberOfArgs);
+ option.setType(type);
+ option.setValueSeparator(valuesep);
+ option.setArgName(argName);
+
+ // reset the OptionBuilder properties
+ OptionBuilder.reset();
+
+ // return the Option instance
+ return option;
+ }
+}
diff --git a/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/OptionGroup.java b/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/OptionGroup.java
new file mode 100644
index 0000000..f1a572d
--- /dev/null
+++ b/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/OptionGroup.java
@@ -0,0 +1,144 @@
+/**
+ * Copyright 1999-2001,2004 The Apache Software Foundation.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.commons.cli;
+
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.Iterator;
+
+
+/**
+ * A group of mutually exclusive options.
+ * @author John Keyes ( john at integralsource.com )
+ * @version $Revision: 155404 $
+ */
+public class OptionGroup {
+ /** hold the options */
+ private HashMap optionMap = new HashMap();
+
+ /** the name of the selected option */
+ private String selected;
+
+ /** specified whether this group is required */
+ private boolean required;
+
+ /**
+ * add <code>opt</code> to this group
+ *
+ * @param opt the option to add to this group
+ * @return this option group with opt added
+ */
+ public OptionGroup addOption(Option opt) {
+ // key - option name
+ // value - the option
+ optionMap.put(opt.getKey(), opt);
+
+ return this;
+ }
+
+ /**
+ * @return the names of the options in this group as a
+ * <code>Collection</code>
+ */
+ public Collection getNames() {
+ // the key set is the collection of names
+ return optionMap.keySet();
+ }
+
+ /**
+ * @return the options in this group as a <code>Collection</code>
+ */
+ public Collection getOptions() {
+ // the values are the collection of options
+ return optionMap.values();
+ }
+
+ /**
+ * set the selected option of this group to <code>name</code>.
+ * @param opt the option that is selected
+ * @throws AlreadySelectedException if an option from this group has
+ * already been selected.
+ */
+ public void setSelected(Option opt) throws AlreadySelectedException {
+ // if no option has already been selected or the
+ // same option is being reselected then set the
+ // selected member variable
+ if ((this.selected == null) || this.selected.equals(opt.getOpt())) {
+ this.selected = opt.getOpt();
+ } else {
+ throw new AlreadySelectedException("an option from this group has "
+ + "already been selected: '" + selected + "'");
+ }
+ }
+
+ /**
+ * @return the selected option name
+ */
+ public String getSelected() {
+ return selected;
+ }
+
+ /**
+ * @param required specifies if this group is required
+ */
+ public void setRequired(boolean required) {
+ this.required = required;
+ }
+
+ /**
+ * Returns whether this option group is required.
+ *
+ * @return whether this option group is required
+ */
+ public boolean isRequired() {
+ return this.required;
+ }
+
+ /**
+ * <p>Returns the stringified version of this OptionGroup.</p>
+ * @return the stringified representation of this group
+ */
+ public String toString() {
+ StringBuffer buff = new StringBuffer();
+
+ Iterator iter = getOptions().iterator();
+
+ buff.append("[");
+
+ while (iter.hasNext()) {
+ Option option = (Option) iter.next();
+
+ if (option.getOpt() != null) {
+ buff.append("-");
+ buff.append(option.getOpt());
+ } else {
+ buff.append("--");
+ buff.append(option.getLongOpt());
+ }
+
+ buff.append(" ");
+ buff.append(option.getDescription());
+
+ if (iter.hasNext()) {
+ buff.append(", ");
+ }
+ }
+
+ buff.append("]");
+
+ return buff.toString();
+ }
+}
diff --git a/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/OptionValidator.java b/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/OptionValidator.java
new file mode 100644
index 0000000..eb61a84
--- /dev/null
+++ b/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/OptionValidator.java
@@ -0,0 +1,86 @@
+/**
+ * Copyright 1999-2001,2004 The Apache Software Foundation.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.commons.cli;
+
+
+/**
+ * Validates an Option string.
+ *
+ * @author John Keyes ( john at integralsource.com )
+ */
+public class OptionValidator {
+ /**
+ * <p>Validates whether <code>opt</code> is a permissable Option
+ * shortOpt. The rules that specify if the <code>opt</code>
+ * is valid are:</p>
+ * <ul>
+ * <li><code>opt</code> is not NULL</li>
+ * <li>a single character <code>opt</code> that is either
+ * ' '(special case), '?', '@' or a letter</li>
+ * <li>a multi character <code>opt</code> that only contains
+ * letters.</li>
+ * </ul>
+ *
+ * @param opt The option string to validate
+ * @throws IllegalArgumentException if the Option is not valid.
+ */
+ static void validateOption(String opt) throws IllegalArgumentException {
+ // check that opt is not NULL
+ if (opt == null) {
+ return;
+ }
+ // handle the single character opt
+ else if (opt.length() == 1) {
+ char ch = opt.charAt(0);
+
+ if (!isValidOpt(ch)) {
+ throw new IllegalArgumentException("illegal option value '" + ch + "'");
+ }
+ }
+ // handle the multi character opt
+ else {
+ char[] chars = opt.toCharArray();
+
+ for (int i = 0; i < chars.length; i++) {
+ if (!isValidChar(chars[i])) {
+ throw new IllegalArgumentException("opt contains illegal character value '"
+ + chars[i] + "'");
+ }
+ }
+ }
+ }
+
+ /**
+ * <p>Returns whether the specified character is a valid Option.</p>
+ *
+ * @param c the option to validate
+ * @return true if <code>c</code> is a letter, ' ', '?' or '@',
+ * otherwise false.
+ */
+ private static boolean isValidOpt(char c) {
+ return (isValidChar(c) || (c == ' ') || (c == '?') || (c == '@'));
+ }
+
+ /**
+ * <p>Returns whether the specified character is a valid character.</p>
+ *
+ * @param c the character to validate
+ * @return true if <code>c</code> is a letter.
+ */
+ private static boolean isValidChar(char c) {
+ return Character.isJavaIdentifierPart(c);
+ }
+}
diff --git a/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/Options.java b/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/Options.java
new file mode 100644
index 0000000..4f0bf52
--- /dev/null
+++ b/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/Options.java
@@ -0,0 +1,266 @@
+/**
+ * Copyright 1999-2001,2004 The Apache Software Foundation.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.commons.cli;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+
+
+/** <p>Main entry-point into the library.</p>
+ *
+ * <p>Options represents a collection of {@link Option} objects, which
+ * describe the possible options for a command-line.<p>
+ *
+ * <p>It may flexibly parse long and short options, with or without
+ * values. Additionally, it may parse only a portion of a commandline,
+ * allowing for flexible multi-stage parsing.<p>
+ *
+ * @see org.apache.commons.cli.CommandLine
+ *
+ * @author bob mcwhirter (bob @ werken.com)
+ * @author <a href="mailto:jstrachan at apache.org">James Strachan</a>
+ * @version $Revision: 155404 $
+ */
+public class Options {
+ /** a map of the options with the character key */
+ private Map shortOpts = new HashMap();
+
+ /** a list for storing the help options in the order they were created */
+ private List helpOpts = new ArrayList();
+
+ /** a map of the options with the long key */
+ private Map longOpts = new HashMap();
+
+ /** a map of the required options */
+ private List requiredOpts = new ArrayList();
+
+ /** a map of the option groups */
+ private Map optionGroups = new HashMap();
+
+ /** Construct a new Options descriptor
+ */
+ public Options() {
+ // nothing to do
+ }
+
+ /**
+ * Add the specified option group.
+ *
+ * @param group the OptionGroup that is to be added
+ * @return the resulting Options instance
+ */
+ public Options addOptionGroup(OptionGroup group) {
+ Iterator options = group.getOptions().iterator();
+
+ if (group.isRequired()) {
+ requiredOpts.add(group);
+ }
+
+ while (options.hasNext()) {
+ Option option = (Option) options.next();
+
+ // an Option cannot be required if it is in an
+ // OptionGroup, either the group is required or
+ // nothing is required
+ option.setRequired(false);
+ addOption(option);
+
+ optionGroups.put(option.getKey(), group);
+ }
+
+ return this;
+ }
+
+ /**
+ * Lists the OptionGroups that are members of this Options instance.
+ * @return a Collection of OptionGroup instances.
+ */
+ Collection getOptionGroups() {
+ return new HashSet(optionGroups.values());
+ }
+
+ /**
+ * Add an option that only contains a short-name.
+ * It may be specified as requiring an argument.
+ *
+ * @param opt Short single-character name of the option.
+ * @param hasArg flag signally if an argument is required after this option
+ * @param description Self-documenting description
+ * @return the resulting Options instance
+ */
+ public Options addOption(String opt, boolean hasArg, String description) {
+ addOption(opt, null, hasArg, description);
+
+ return this;
+ }
+
+ /**
+ * Add an option that contains a short-name and a long-name.
+ * It may be specified as requiring an argument.
+ *
+ * @param opt Short single-character name of the option.
+ * @param longOpt Long multi-character name of the option.
+ * @param hasArg flag signally if an argument is required after this option
+ * @param description Self-documenting description
+ * @return the resulting Options instance
+ */
+ public Options addOption(String opt, String longOpt, boolean hasArg, String description) {
+ addOption(new Option(opt, longOpt, hasArg, description));
+
+ return this;
+ }
+
+ /**
+ * Adds an option instance
+ *
+ * @param opt the option that is to be added
+ * @return the resulting Options instance
+ */
+ public Options addOption(Option opt) {
+ String key = opt.getKey();
+
+ // add it to the long option list
+ if (opt.hasLongOpt()) {
+ longOpts.put(opt.getLongOpt(), opt);
+ }
+
+ // if the option is required add it to the required list
+ if (opt.isRequired()) {
+ if (requiredOpts.contains(key)) {
+ requiredOpts.remove(requiredOpts.indexOf(key));
+ }
+
+ requiredOpts.add(key);
+ }
+
+ shortOpts.put(key, opt);
+ helpOpts.add(opt);
+
+ return this;
+ }
+
+ /**
+ * Retrieve a read-only list of options in this set
+ *
+ * @return read-only Collection of {@link Option} objects in this descriptor
+ */
+ public Collection getOptions() {
+ return Collections.unmodifiableCollection(helpOptions());
+ }
+
+ /**
+ * Returns the Options for use by the HelpFormatter.
+ *
+ * @return the List of Options
+ */
+ List helpOptions() {
+ /*
+ List opts = new ArrayList(shortOpts.values());
+
+ // now look through the long opts to see if there are any Long-opt
+ // only options
+ Iterator iter = longOpts.values().iterator();
+
+ while (iter.hasNext())
+ {
+ Object item = iter.next();
+
+ if (!opts.contains(item))
+ {
+ opts.add(item);
+ }
+ }
+
+ return new ArrayList(opts);
+ */
+ return helpOpts;
+ }
+
+ /**
+ * Returns the required options as a
+ * <code>java.util.Collection</code>.
+ *
+ * @return Collection of required options
+ */
+ public List getRequiredOptions() {
+ return requiredOpts;
+ }
+
+ /**
+ * Retrieve the named {@link Option}
+ *
+ * @param opt short or long name of the {@link Option}
+ * @return the option represented by opt
+ */
+ public Option getOption(String opt) {
+ opt = Util.stripLeadingHyphens(opt);
+
+ if (shortOpts.containsKey(opt)) {
+ return (Option) shortOpts.get(opt);
+ }
+
+ return (Option) longOpts.get(opt);
+ }
+
+ /**
+ * Returns whether the named {@link Option} is a member
+ * of this {@link Options}.
+ *
+ * @param opt short or long name of the {@link Option}
+ * @return true if the named {@link Option} is a member
+ * of this {@link Options}
+ */
+ public boolean hasOption(String opt) {
+ opt = Util.stripLeadingHyphens(opt);
+
+ return shortOpts.containsKey(opt) || longOpts.containsKey(opt);
+ }
+
+ /**
+ * Returns the OptionGroup the <code>opt</code>
+ * belongs to.
+ * @param opt the option whose OptionGroup is being queried.
+ *
+ * @return the OptionGroup if <code>opt</code> is part
+ * of an OptionGroup, otherwise return null
+ */
+ public OptionGroup getOptionGroup(Option opt) {
+ return (OptionGroup) optionGroups.get(opt.getKey());
+ }
+
+ /**
+ * Dump state, suitable for debugging.
+ *
+ * @return Stringified form of this object
+ */
+ public String toString() {
+ StringBuffer buf = new StringBuffer();
+
+ buf.append("[ Options: [ short ");
+ buf.append(shortOpts.toString());
+ buf.append(" ] [ long ");
+ buf.append(longOpts);
+ buf.append(" ]");
+
+ return buf.toString();
+ }
+}
diff --git a/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/ParseException.java b/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/ParseException.java
new file mode 100644
index 0000000..1bdffce
--- /dev/null
+++ b/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/ParseException.java
@@ -0,0 +1,35 @@
+/**
+ * Copyright 1999-2001,2004 The Apache Software Foundation.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.commons.cli;
+
+
+/**
+ * <p>Base for Exceptions thrown during parsing of a command-line.</p>
+ *
+ * @author bob mcwhirter (bob @ werken.com)
+ * @version $Revision: 155404 $
+ */
+public class ParseException extends Exception {
+ /**
+ * <p>Construct a new <code>ParseException</code>
+ * with the specified detail message.</p>
+ *
+ * @param message the detail message
+ */
+ public ParseException(String message) {
+ super(message);
+ }
+}
diff --git a/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/Parser.java b/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/Parser.java
new file mode 100644
index 0000000..ce39853
--- /dev/null
+++ b/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/Parser.java
@@ -0,0 +1,343 @@
+/**
+ * Copyright 1999-2001,2004 The Apache Software Foundation.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.commons.cli;
+
+import java.util.Arrays;
+import java.util.Enumeration;
+import java.util.Iterator;
+import java.util.List;
+import java.util.ListIterator;
+import java.util.Properties;
+
+
+/**
+ * <p><code>Parser</code> creates {@link CommandLine}s.</p>
+ *
+ * @author John Keyes (john at integralsource.com)
+ * @see Parser
+ * @version $Revision: 155404 $
+ */
+public abstract class Parser implements CommandLineParser {
+ /** commandline instance */
+ private CommandLine cmd;
+
+ /** current Options */
+ private Options options;
+
+ /** list of required options strings */
+ private List requiredOptions;
+
+ /**
+ * <p>Subclasses must implement this method to reduce
+ * the <code>arguments</code> that have been passed to the parse
+ * method.</p>
+ *
+ * @param opts The Options to parse the arguments by.
+ * @param arguments The arguments that have to be flattened.
+ * @param stopAtNonOption specifies whether to stop
+ * flattening when a non option has been encountered
+ * @return a String array of the flattened arguments
+ */
+ protected abstract String[] flatten(Options opts, String[] arguments, boolean stopAtNonOption);
+
+ /**
+ * <p>Parses the specified <code>arguments</code>
+ * based on the specifed {@link Options}.</p>
+ *
+ * @param options the <code>Options</code>
+ * @param arguments the <code>arguments</code>
+ * @return the <code>CommandLine</code>
+ * @throws ParseException if an error occurs when parsing the
+ * arguments.
+ */
+ public CommandLine parse(Options options, String[] arguments) throws ParseException {
+ return parse(options, arguments, null, false);
+ }
+
+ /**
+ * Parse the arguments according to the specified options and
+ * properties.
+ *
+ * @param options the specified Options
+ * @param arguments the command line arguments
+ * @param properties command line option name-value pairs
+ * @return the list of atomic option and value tokens
+ *
+ * @throws ParseException if there are any problems encountered
+ * while parsing the command line tokens.
+ */
+ public CommandLine parse(Options options, String[] arguments, Properties properties)
+ throws ParseException {
+ return parse(options, arguments, properties, false);
+ }
+
+ /**
+ * <p>Parses the specified <code>arguments</code>
+ * based on the specifed {@link Options}.</p>
+ *
+ * @param options the <code>Options</code>
+ * @param arguments the <code>arguments</code>
+ * @param stopAtNonOption specifies whether to stop
+ * interpreting the arguments when a non option has
+ * been encountered and to add them to the CommandLines
+ * args list.
+ *
+ * @return the <code>CommandLine</code>
+ * @throws ParseException if an error occurs when parsing the
+ * arguments.
+ */
+ public CommandLine parse(Options options, String[] arguments, boolean stopAtNonOption)
+ throws ParseException {
+ return parse(options, arguments, null, stopAtNonOption);
+ }
+
+ /**
+ * Parse the arguments according to the specified options and
+ * properties.
+ *
+ * @param options the specified Options
+ * @param arguments the command line arguments
+ * @param properties command line option name-value pairs
+ * @param stopAtNonOption stop parsing the arguments when the first
+ * non option is encountered.
+ *
+ * @return the list of atomic option and value tokens
+ *
+ * @throws ParseException if there are any problems encountered
+ * while parsing the command line tokens.
+ */
+ public CommandLine parse(Options options, String[] arguments, Properties properties,
+ boolean stopAtNonOption) throws ParseException {
+ // initialise members
+ this.options = options;
+ requiredOptions = options.getRequiredOptions();
+ cmd = new CommandLine();
+
+ boolean eatTheRest = false;
+
+ if (arguments == null) {
+ arguments = new String[0];
+ }
+
+ List tokenList = Arrays.asList(flatten(this.options, arguments, stopAtNonOption));
+
+ ListIterator iterator = tokenList.listIterator();
+
+ // process each flattened token
+ while (iterator.hasNext()) {
+ String t = (String) iterator.next();
+
+ // the value is the double-dash
+ if ("--".equals(t)) {
+ eatTheRest = true;
+ }
+ // the value is a single dash
+ else if ("-".equals(t)) {
+ if (stopAtNonOption) {
+ eatTheRest = true;
+ } else {
+ cmd.addArg(t);
+ }
+ }
+ // the value is an option
+ else if (t.startsWith("-")) {
+ if (stopAtNonOption && !options.hasOption(t)) {
+ eatTheRest = true;
+ cmd.addArg(t);
+ } else {
+ processOption(t, iterator);
+ }
+ }
+ // the value is an argument
+ else {
+ cmd.addArg(t);
+
+ if (stopAtNonOption) {
+ eatTheRest = true;
+ }
+ }
+
+ // eat the remaining tokens
+ if (eatTheRest) {
+ while (iterator.hasNext()) {
+ String str = (String) iterator.next();
+
+ // ensure only one double-dash is added
+ if (!"--".equals(str)) {
+ cmd.addArg(str);
+ }
+ }
+ }
+ }
+
+ processProperties(properties);
+ checkRequiredOptions();
+
+ return cmd;
+ }
+
+ /**
+ * <p>Sets the values of Options using the values in
+ * <code>properties</code>.</p>
+ *
+ * @param properties The value properties to be processed.
+ */
+ private void processProperties(Properties properties) {
+ if (properties == null) {
+ return;
+ }
+
+ for (Enumeration e = properties.propertyNames(); e.hasMoreElements();) {
+ String option = e.nextElement().toString();
+
+ if (!cmd.hasOption(option)) {
+ Option opt = options.getOption(option);
+
+ // get the value from the properties instance
+ String value = properties.getProperty(option);
+
+ if (opt.hasArg()) {
+ if ((opt.getValues() == null) || (opt.getValues().length == 0)) {
+ try {
+ opt.addValue(value);
+ } catch (RuntimeException exp) {
+ // if we cannot add the value don't worry about it
+ }
+ }
+ } else if (!("yes".equalsIgnoreCase(value) || "true".equalsIgnoreCase(value)
+ || "1".equalsIgnoreCase(value))) {
+ // if the value is not yes, true or 1 then don't add the
+ // option to the CommandLine
+ break;
+ }
+
+ cmd.addOption(opt);
+ }
+ }
+ }
+
+ /**
+ * <p>Throws a {@link MissingOptionException} if all of the
+ * required options are no present.</p>
+ *
+ * @throws MissingOptionException if any of the required Options
+ * are not present.
+ */
+ private void checkRequiredOptions() throws MissingOptionException {
+ // if there are required options that have not been
+ // processsed
+ if (requiredOptions.size() > 0) {
+ Iterator iter = requiredOptions.iterator();
+ StringBuffer buff = new StringBuffer();
+
+ // loop through the required options
+ while (iter.hasNext()) {
+ buff.append(iter.next());
+ }
+
+ throw new MissingOptionException(buff.toString());
+ }
+ }
+
+ /**
+ * <p>Process the argument values for the specified Option
+ * <code>opt</code> using the values retrieved from the
+ * specified iterator <code>iter</code>.
+ *
+ * @param opt The current Option
+ * @param iter The iterator over the flattened command line
+ * Options.
+ *
+ * @throws ParseException if an argument value is required
+ * and it is has not been found.
+ */
+ public void processArgs(Option opt, ListIterator iter) throws ParseException {
+ // loop until an option is found
+ while (iter.hasNext()) {
+ String str = (String) iter.next();
+
+ // found an Option, not an argument
+ if (options.hasOption(str) && str.startsWith("-")) {
+ iter.previous();
+
+ break;
+ }
+
+ // found a value
+ try {
+ opt.addValue(Util.stripLeadingAndTrailingQuotes(str));
+ } catch (RuntimeException exp) {
+ iter.previous();
+
+ break;
+ }
+ }
+
+ if ((opt.getValues() == null) && !opt.hasOptionalArg()) {
+ throw new MissingArgumentException("Missing argument for option:" + opt.getKey());
+ }
+ }
+
+ /**
+ * <p>Process the Option specified by <code>arg</code>
+ * using the values retrieved from the specfied iterator
+ * <code>iter</code>.
+ *
+ * @param arg The String value representing an Option
+ * @param iter The iterator over the flattened command
+ * line arguments.
+ *
+ * @throws ParseException if <code>arg</code> does not
+ * represent an Option
+ */
+ private void processOption(String arg, ListIterator iter) throws ParseException {
+ boolean hasOption = options.hasOption(arg);
+
+ // if there is no option throw an UnrecognisedOptionException
+ if (!hasOption) {
+ throw new UnrecognizedOptionException("Unrecognized option: " + arg);
+ }
+
+ // get the option represented by arg
+ final Option opt = options.getOption(arg);
+
+ // if the option is a required option remove the option from
+ // the requiredOptions list
+ if (opt.isRequired()) {
+ requiredOptions.remove(opt.getKey());
+ }
+
+ // if the option is in an OptionGroup make that option the selected
+ // option of the group
+ if (options.getOptionGroup(opt) != null) {
+ OptionGroup group = options.getOptionGroup(opt);
+
+ if (group.isRequired()) {
+ requiredOptions.remove(group);
+ }
+
+ group.setSelected(opt);
+ }
+
+ // if the option takes an argument value
+ if (opt.hasArg()) {
+ processArgs(opt, iter);
+ }
+
+ // set the option on the command line
+ cmd.addOption(opt);
+ }
+}
diff --git a/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/PatternOptionBuilder.java b/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/PatternOptionBuilder.java
new file mode 100644
index 0000000..8c68140
--- /dev/null
+++ b/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/PatternOptionBuilder.java
@@ -0,0 +1,180 @@
+/**
+ * Copyright 1999-2001,2004 The Apache Software Foundation.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.commons.cli;
+
+
+/**
+ * <p>
+ * Allows Options to be created from a single String.
+ * The pattern contains various single character flags and via
+ * an optional punctuation character, their expected type.
+ * </p>
+ *
+ * <table border="1">
+ * <tr><td>a</td><td>-a flag</td></tr>
+ * <tr><td>b@</td><td>-b [classname]</td></tr>
+ * <tr><td>c></td><td>-c [filename]</td></tr>
+ * <tr><td>d+</td><td>-d [classname] (creates object via empty contructor)</td></tr>
+ * <tr><td>e%</td><td>-e [number] (creates Number instance)</td></tr>
+ * <tr><td>f/</td><td>-f [url]</td></tr>
+ * </table>
+ *
+ * <p>
+ * For example, the following allows command line flags of '-v -p string-value -f /dir/file'.
+ * </p>
+ * <code>Options options = PatternOptionBuilder.parsePattern("vp:f/");</code>
+ *
+ * <p>
+ * TODO These need to break out to OptionType and also
+ * to be pluggable.
+ * </p>
+ *
+ * @author Henri Yandell (bayard @ generationjava.com)
+ * @version $Revision: 155404 $
+ */
+public class PatternOptionBuilder {
+ /** String class */
+ public static final Class STRING_VALUE = java.lang.String.class;
+
+ /** Object class */
+ public static final Class OBJECT_VALUE = java.lang.Object.class;
+
+ /** Number class */
+ public static final Class NUMBER_VALUE = java.lang.Number.class;
+
+ /** Date class */
+ public static final Class DATE_VALUE = java.util.Date.class;
+
+ /** Class class */
+ public static final Class CLASS_VALUE = java.lang.Class.class;
+
+ /// can we do this one??
+ // is meant to check that the file exists, else it errors.
+ // ie) it's for reading not writing.
+
+ /** FileInputStream class */
+ public static final Class EXISTING_FILE_VALUE = java.io.FileInputStream.class;
+
+ /** File class */
+ public static final Class FILE_VALUE = java.io.File.class;
+
+ /** File array class */
+ public static final Class FILES_VALUE = java.io.File[].class;
+
+ /** URL class */
+ public static final Class URL_VALUE = java.net.URL.class;
+
+ /**
+ * <p>Retrieve the class that <code>ch</code> represents.</p>
+ *
+ * @param ch the specified character
+ * @return The class that <code>ch</code> represents
+ */
+ public static Object getValueClass(char ch) {
+ if (ch == '@') {
+ return PatternOptionBuilder.OBJECT_VALUE;
+ } else if (ch == ':') {
+ return PatternOptionBuilder.STRING_VALUE;
+ } else if (ch == '%') {
+ return PatternOptionBuilder.NUMBER_VALUE;
+ } else if (ch == '+') {
+ return PatternOptionBuilder.CLASS_VALUE;
+ } else if (ch == '#') {
+ return PatternOptionBuilder.DATE_VALUE;
+ } else if (ch == '<') {
+ return PatternOptionBuilder.EXISTING_FILE_VALUE;
+ } else if (ch == '>') {
+ return PatternOptionBuilder.FILE_VALUE;
+ } else if (ch == '*') {
+ return PatternOptionBuilder.FILES_VALUE;
+ } else if (ch == '/') {
+ return PatternOptionBuilder.URL_VALUE;
+ }
+
+ return null;
+ }
+
+ /**
+ * <p>Returns whether <code>ch</code> is a value code, i.e.
+ * whether it represents a class in a pattern.</p>
+ *
+ * @param ch the specified character
+ * @return true if <code>ch</code> is a value code, otherwise false.
+ */
+ public static boolean isValueCode(char ch) {
+ if ((ch != '@') && (ch != ':') && (ch != '%') && (ch != '+') && (ch != '#') && (ch != '<')
+ && (ch != '>') && (ch != '*') && (ch != '/') && (ch != '!')) {
+ return false;
+ }
+
+ return true;
+ }
+
+ /**
+ * <p>Returns the {@link Options} instance represented by
+ * <code>pattern</code>.</p>
+ *
+ * @param pattern the pattern string
+ * @return The {@link Options} instance
+ */
+ public static Options parsePattern(String pattern) {
+ int sz = pattern.length();
+
+ char opt = ' ';
+ char ch = ' ';
+ boolean required = false;
+ Object type = null;
+
+ Options options = new Options();
+
+ for (int i = 0; i < sz; i++) {
+ ch = pattern.charAt(i);
+
+ // a value code comes after an option and specifies
+ // details about it
+ if (!isValueCode(ch)) {
+ if (opt != ' ') {
+ OptionBuilder.hasArg(type != null);
+ OptionBuilder.isRequired(required);
+ OptionBuilder.withType(type);
+
+ // we have a previous one to deal with
+ options.addOption(OptionBuilder.create(opt));
+ required = false;
+ type = null;
+ opt = ' ';
+ }
+
+ opt = ch;
+ } else if (ch == '!') {
+ required = true;
+ } else {
+ type = getValueClass(ch);
+ }
+ }
+
+ if (opt != ' ') {
+ OptionBuilder.hasArg(type != null);
+ OptionBuilder.isRequired(required);
+ OptionBuilder.withType(type);
+
+ // we have a final one to deal with
+ options.addOption(OptionBuilder.create(opt));
+ }
+
+ return options;
+ }
+}
diff --git a/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/PosixParser.java b/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/PosixParser.java
new file mode 100644
index 0000000..f56e49c
--- /dev/null
+++ b/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/PosixParser.java
@@ -0,0 +1,265 @@
+/**
+ * Copyright 1999-2001,2004 The Apache Software Foundation.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.commons.cli;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Iterator;
+
+
+/**
+ * The class PosixParser provides an implementation of the
+ * {@link Parser#flatten(Options,String[],boolean) flatten} method.
+ *
+ * @author John Keyes (john at integralsource.com)
+ * @see Parser
+ * @version $Revision: 155404 $
+ */
+public class PosixParser extends Parser {
+ /** holder for flattened tokens */
+ private ArrayList tokens = new ArrayList();
+
+ /** specifies if bursting should continue */
+ private boolean eatTheRest;
+
+ /** holder for the current option */
+ private Option currentOption;
+
+ /** the command line Options */
+ private Options options;
+
+ /**
+ * <p>Resets the members to their original state i.e. remove
+ * all of <code>tokens</code> entries, set <code>eatTheRest</code>
+ * to false and set <code>currentOption</code> to null.</p>
+ */
+ private void init() {
+ eatTheRest = false;
+ tokens.clear();
+ currentOption = null;
+ }
+
+ /**
+ * <p>An implementation of {@link Parser}'s abstract
+ * {@link Parser#flatten(Options,String[],boolean) flatten} method.</p>
+ *
+ * <p>The following are the rules used by this flatten method.
+ * <ol>
+ * <li>if <code>stopAtNonOption</code> is <b>true</b> then do not
+ * burst anymore of <code>arguments</code> entries, just add each
+ * successive entry without further processing. Otherwise, ignore
+ * <code>stopAtNonOption</code>.</li>
+ * <li>if the current <code>arguments</code> entry is "<b>--</b>"
+ * just add the entry to the list of processed tokens</li>
+ * <li>if the current <code>arguments</code> entry is "<b>-</b>"
+ * just add the entry to the list of processed tokens</li>
+ * <li>if the current <code>arguments</code> entry is two characters
+ * in length and the first character is "<b>-</b>" then check if this
+ * is a valid {@link Option} id. If it is a valid id, then add the
+ * entry to the list of processed tokens and set the current {@link Option}
+ * member. If it is not a valid id and <code>stopAtNonOption</code>
+ * is true, then the remaining entries are copied to the list of
+ * processed tokens. Otherwise, the current entry is ignored.</li>
+ * <li>if the current <code>arguments</code> entry is more than two
+ * characters in length and the first character is "<b>-</b>" then
+ * we need to burst the entry to determine its constituents. For more
+ * information on the bursting algorithm see
+ * {@link PosixParser#burstToken(String, boolean) burstToken}.</li>
+ * <li>if the current <code>arguments</code> entry is not handled
+ * by any of the previous rules, then the entry is added to the list
+ * of processed tokens.</li>
+ * </ol>
+ * </p>
+ *
+ * @param options The command line {@link Options}
+ * @param arguments The command line arguments to be parsed
+ * @param stopAtNonOption Specifies whether to stop flattening
+ * when an non option is found.
+ * @return The flattened <code>arguments</code> String array.
+ */
+ protected String[] flatten(Options options, String[] arguments, boolean stopAtNonOption) {
+ init();
+ this.options = options;
+
+ // an iterator for the command line tokens
+ Iterator iter = Arrays.asList(arguments).iterator();
+ String token = null;
+
+ // process each command line token
+ while (iter.hasNext()) {
+ // get the next command line token
+ token = (String) iter.next();
+
+ // handle SPECIAL TOKEN
+ if (token.startsWith("--")) {
+ if (token.indexOf('=') != -1) {
+ tokens.add(token.substring(0, token.indexOf('=')));
+ tokens.add(token.substring(token.indexOf('=') + 1, token.length()));
+ } else {
+ tokens.add(token);
+ }
+ }
+ // single hyphen
+ else if ("-".equals(token)) {
+ processSingleHyphen(token);
+ } else if (token.startsWith("-")) {
+ int tokenLength = token.length();
+
+ if (tokenLength == 2) {
+ processOptionToken(token, stopAtNonOption);
+ } else if (options.hasOption(token)) {
+ tokens.add(token);
+ }
+ // requires bursting
+ else {
+ burstToken(token, stopAtNonOption);
+ }
+ } else {
+ if (stopAtNonOption) {
+ process(token);
+ } else {
+ tokens.add(token);
+ }
+ }
+
+ gobble(iter);
+ }
+
+ return (String[]) tokens.toArray(new String[] { });
+ }
+
+ /**
+ * <p>Adds the remaining tokens to the processed tokens list.</p>
+ *
+ * @param iter An iterator over the remaining tokens
+ */
+ private void gobble(Iterator iter) {
+ if (eatTheRest) {
+ while (iter.hasNext()) {
+ tokens.add(iter.next());
+ }
+ }
+ }
+
+ /**
+ * <p>If there is a current option and it can have an argument
+ * value then add the token to the processed tokens list and
+ * set the current option to null.</p>
+ * <p>If there is a current option and it can have argument
+ * values then add the token to the processed tokens list.</p>
+ * <p>If there is not a current option add the special token
+ * "<b>--</b>" and the current <code>value</code> to the processed
+ * tokens list. The add all the remaining <code>argument</code>
+ * values to the processed tokens list.</p>
+ *
+ * @param value The current token
+ */
+ private void process(String value) {
+ if ((currentOption != null) && currentOption.hasArg()) {
+ if (currentOption.hasArg()) {
+ tokens.add(value);
+ currentOption = null;
+ } else if (currentOption.hasArgs()) {
+ tokens.add(value);
+ }
+ } else {
+ eatTheRest = true;
+ tokens.add("--");
+ tokens.add(value);
+ }
+ }
+
+ /**
+ * <p>If it is a hyphen then add the hyphen directly to
+ * the processed tokens list.</p>
+ *
+ * @param hyphen The hyphen token
+ */
+ private void processSingleHyphen(String hyphen) {
+ tokens.add(hyphen);
+ }
+
+ /**
+ * <p>If an {@link Option} exists for <code>token</code> then
+ * set the current option and add the token to the processed
+ * list.</p>
+ * <p>If an {@link Option} does not exist and <code>stopAtNonOption</code>
+ * is set then ignore the current token and add the remaining tokens
+ * to the processed tokens list directly.</p>
+ *
+ * @param token The current option token
+ * @param stopAtNonOption Specifies whether flattening should halt
+ * at the first non option.
+ */
+ private void processOptionToken(String token, boolean stopAtNonOption) {
+ if (this.options.hasOption(token)) {
+ currentOption = this.options.getOption(token);
+ tokens.add(token);
+ } else if (stopAtNonOption) {
+ eatTheRest = true;
+ }
+ }
+
+ /**
+ * <p>Breaks <code>token</code> into its constituent parts
+ * using the following algorithm.
+ * <ul>
+ * <li>ignore the first character ("<b>-</b>")</li>
+ * <li>foreach remaining character check if an {@link Option}
+ * exists with that id.</li>
+ * <li>if an {@link Option} does exist then add that character
+ * prepended with "<b>-</b>" to the list of processed tokens.</li>
+ * <li>if the {@link Option} can have an argument value and there
+ * are remaining characters in the token then add the remaining
+ * characters as a token to the list of processed tokens.</li>
+ * <li>if an {@link Option} does <b>NOT</b> exist <b>AND</b>
+ * <code>stopAtNonOption</code> <b>IS</b> set then add the special token
+ * "<b>--</b>" followed by the remaining characters and also
+ * the remaining tokens directly to the processed tokens list.</li>
+ * <li>if an {@link Option} does <b>NOT</b> exist <b>AND</b>
+ * <code>stopAtNonOption</code> <b>IS NOT</b> set then add that
+ * character prepended with "<b>-</b>".</li>
+ * </ul>
+ * </p>
+ *
+ * @param token The current token to be <b>burst</b>
+ * @param stopAtNonOption Specifies whether to stop processing
+ * at the first non-Option encountered.
+ */
+ protected void burstToken(String token, boolean stopAtNonOption) {
+ int tokenLength = token.length();
+
+ for (int i = 1; i < tokenLength; i++) {
+ String ch = String.valueOf(token.charAt(i));
+ boolean hasOption = options.hasOption(ch);
+
+ if (hasOption) {
+ tokens.add("-" + ch);
+ currentOption = options.getOption(ch);
+
+ if (currentOption.hasArg() && (token.length() != (i + 1))) {
+ tokens.add(token.substring(i + 1));
+
+ break;
+ }
+ } else if (stopAtNonOption) {
+ process(token.substring(i));
+ } else {
+ tokens.add("-" + ch);
+ }
+ }
+ }
+}
diff --git a/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/TypeHandler.java b/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/TypeHandler.java
new file mode 100644
index 0000000..72fa2ec
--- /dev/null
+++ b/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/TypeHandler.java
@@ -0,0 +1,209 @@
+/*
+ * Copyright 1999-2005 The Apache Software Foundation.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.commons.cli;
+
+import org.apache.commons.lang.math.NumberUtils;
+
+import java.io.File;
+
+import java.net.MalformedURLException;
+import java.net.URL;
+
+import java.util.Date;
+
+
+/**
+ * This is a temporary implementation. TypeHandler will handle the
+ * pluggableness of OptionTypes and it will direct all of these types
+ * of conversion functionalities to ConvertUtils component in Commons
+ * alreayd. BeanUtils I think.
+ *
+ * @author Henri Yandell (bayard @ generationjava.com)
+ * @version $Revision: 267414 $
+ */
+public class TypeHandler {
+ /**
+ * <p>Returns the <code>Object</code> of type <code>obj</code>
+ * with the value of <code>str</code>.</p>
+ *
+ * @param str the command line value
+ * @param obj the type of argument
+ * @return The instance of <code>obj</code> initialised with
+ * the value of <code>str</code>.
+ */
+ public static Object createValue(String str, Object obj) {
+ return createValue(str, (Class) obj);
+ }
+
+ /**
+ * <p>Returns the <code>Object</code> of type <code>clazz</code>
+ * with the value of <code>str</code>.</p>
+ *
+ * @param str the command line value
+ * @param clazz the type of argument
+ * @return The instance of <code>clazz</code> initialised with
+ * the value of <code>str</code>.
+ */
+ public static Object createValue(String str, Class clazz) {
+ if (PatternOptionBuilder.STRING_VALUE == clazz) {
+ return str;
+ } else if (PatternOptionBuilder.OBJECT_VALUE == clazz) {
+ return createObject(str);
+ } else if (PatternOptionBuilder.NUMBER_VALUE == clazz) {
+ return createNumber(str);
+ } else if (PatternOptionBuilder.DATE_VALUE == clazz) {
+ return createDate(str);
+ } else if (PatternOptionBuilder.CLASS_VALUE == clazz) {
+ return createClass(str);
+ } else if (PatternOptionBuilder.FILE_VALUE == clazz) {
+ return createFile(str);
+ } else if (PatternOptionBuilder.EXISTING_FILE_VALUE == clazz) {
+ return createFile(str);
+ } else if (PatternOptionBuilder.FILES_VALUE == clazz) {
+ return createFiles(str);
+ } else if (PatternOptionBuilder.URL_VALUE == clazz) {
+ return createURL(str);
+ } else {
+ return null;
+ }
+ }
+
+ /**
+ * <p>Create an Object from the classname and empty constructor.</p>
+ *
+ * @param str the argument value
+ * @return the initialised object, or null if it couldn't create
+ * the Object.
+ */
+ public static Object createObject(String str) {
+ Class cl = null;
+
+ try {
+ cl = Class.forName(str);
+ } catch (ClassNotFoundException cnfe) {
+ System.err.println("Unable to find: " + str);
+
+ return null;
+ }
+
+ Object instance = null;
+
+ try {
+ instance = cl.newInstance();
+ } catch (InstantiationException cnfe) {
+ System.err.println("InstantiationException; Unable to create: " + str);
+
+ return null;
+ } catch (IllegalAccessException cnfe) {
+ System.err.println("IllegalAccessException; Unable to create: " + str);
+
+ return null;
+ }
+
+ return instance;
+ }
+
+ /**
+ * <p>Create a number from a String.</p>
+ *
+ * @param str the value
+ * @return the number represented by <code>str</code>, if <code>str</code>
+ * is not a number, null is returned.
+ */
+ public static Number createNumber(String str) {
+ // Needs to be able to create
+ try {
+ // do searching for decimal point etc, but atm just make an Integer
+ return NumberUtils.createNumber(str);
+ } catch (NumberFormatException nfe) {
+ System.err.println(nfe.getMessage());
+
+ return null;
+ }
+ }
+
+ /**
+ * <p>Returns the class whose name is <code>str</code>.</p>
+ *
+ * @param str the class name
+ * @return The class if it is found, otherwise return null
+ */
+ public static Class createClass(String str) {
+ try {
+ return Class.forName(str);
+ } catch (ClassNotFoundException cnfe) {
+ System.err.println("Unable to find: " + str);
+
+ return null;
+ }
+ }
+
+ /**
+ * <p>Returns the date represented by <code>str</code>.</p>
+ *
+ * @param str the date string
+ * @return The date if <code>str</code> is a valid date string,
+ * otherwise return null.
+ */
+ public static Date createDate(String str) {
+ Date date = null;
+
+ if (date == null) {
+ System.err.println("Unable to parse: " + str);
+ }
+
+ return date;
+ }
+
+ /**
+ * <p>Returns the URL represented by <code>str</code>.</p>
+ *
+ * @param str the URL string
+ * @return The URL is <code>str</code> is well-formed, otherwise
+ * return null.
+ */
+ public static URL createURL(String str) {
+ try {
+ return new URL(str);
+ } catch (MalformedURLException mue) {
+ System.err.println("Unable to parse: " + str);
+
+ return null;
+ }
+ }
+
+ /**
+ * <p>Returns the File represented by <code>str</code>.</p>
+ *
+ * @param str the File location
+ * @return The file represented by <code>str</code>.
+ */
+ public static File createFile(String str) {
+ return new File(str);
+ }
+
+ /**
+ * <p>Returns the File[] represented by <code>str</code>.</p>
+ *
+ * @param str the paths to the files
+ * @return The File[] represented by <code>str</code>.
+ */
+ public static File[] createFiles(String str) {
+ // to implement/port:
+ // return FileW.findFiles(str);
+ return null;
+ }
+}
diff --git a/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/UnrecognizedOptionException.java b/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/UnrecognizedOptionException.java
new file mode 100644
index 0000000..b798389
--- /dev/null
+++ b/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/UnrecognizedOptionException.java
@@ -0,0 +1,36 @@
+/**
+ * Copyright 1999-2001,2004 The Apache Software Foundation.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.commons.cli;
+
+
+/**
+ * <p>Exception thrown during parsing signalling an unrecognized
+ * option was seen.<p>
+ *
+ * @author bob mcwhiter (bob @ werken.com)
+ * @version $Revision: 155404 $
+ */
+public class UnrecognizedOptionException extends ParseException {
+ /**
+ * <p>Construct a new <code>UnrecognizedArgumentException</code>
+ * with the specified detail message.</p>
+ *
+ * @param message the detail message
+ */
+ public UnrecognizedOptionException(String message) {
+ super(message);
+ }
+}
diff --git a/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/Util.java b/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/Util.java
new file mode 100644
index 0000000..72dce2c
--- /dev/null
+++ b/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/Util.java
@@ -0,0 +1,63 @@
+/**
+ * Copyright 1999-2001,2004 The Apache Software Foundation.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.commons.cli;
+
+
+/**
+ * Contains useful helper methods for classes within this package.
+ *
+ * @author John Keyes (john at integralsource.com)
+ */
+class Util {
+ /**
+ * <p>Remove the hyphens from the begining of <code>str</code> and
+ * return the new String.</p>
+ *
+ * @param str The string from which the hyphens should be removed.
+ *
+ * @return the new String.
+ */
+ static String stripLeadingHyphens(String str) {
+ if (str.startsWith("--")) {
+ return str.substring(2, str.length());
+ } else if (str.startsWith("-")) {
+ return str.substring(1, str.length());
+ }
+
+ return str;
+ }
+
+ /**
+ * Remove the leading and trailing quotes from <code>str</code>.
+ * E.g. if str is '"one two"', then 'one two' is returned.
+ *
+ * @param str The string from which the leading and trailing quotes
+ * should be removed.
+ *
+ * @return The string without the leading and trailing quotes.
+ */
+ static String stripLeadingAndTrailingQuotes(String str) {
+ if (str.startsWith("\"")) {
+ str = str.substring(1, str.length());
+ }
+
+ if (str.endsWith("\"")) {
+ str = str.substring(0, str.length() - 1);
+ }
+
+ return str;
+ }
+}
diff --git a/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/avalon/AbstractParserControl.java b/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/avalon/AbstractParserControl.java
new file mode 100644
index 0000000..2bd8f28
--- /dev/null
+++ b/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/avalon/AbstractParserControl.java
@@ -0,0 +1,38 @@
+/*
+ * Copyright 2002-2005 The Apache Software Foundation
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+ * implied.
+ *
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.commons.cli.avalon;
+
+//Renamed from org.apache.avalon.excalibur.cli
+
+/**
+ * Class to inherit from so when in future when new controls are added
+ * clients will no have to implement them.
+ * @version $Revision: 1.2 $
+ * @see ParserControl
+ */
+public abstract class AbstractParserControl implements ParserControl {
+ /**
+ * By default always continue parsing by returning false.
+ *
+ * @param lastOptionCode the code of last option parsed
+ * @return return true to halt, false to continue parsing
+ * @see ParserControl#isFinished(int)
+ */
+ public boolean isFinished(int lastOptionCode) {
+ return false;
+ }
+}
diff --git a/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/avalon/CLArgsParser.java b/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/avalon/CLArgsParser.java
new file mode 100644
index 0000000..32936ca
--- /dev/null
+++ b/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/avalon/CLArgsParser.java
@@ -0,0 +1,661 @@
+/*
+ * Copyright 2002-2005 The Apache Software Foundation
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+ * implied.
+ *
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.commons.cli.avalon;
+
+//Renamed from org.apache.avalon.excalibur.cli
+import java.text.ParseException;
+
+import java.util.Hashtable;
+import java.util.Vector;
+
+
+/**
+ * Parser for command line arguments.
+ *
+ * This parses command lines according to the standard (?) of
+ * GNU utilities.
+ *
+ * Note: This is still used in 1.1 libraries so do not add 1.2+ dependencies.
+ *
+ * Note that CLArgs uses a backing hashtable for the options index and so duplicate
+ * arguments are only returned by getArguments().
+ *
+ * @version $Revision: 1.2 $ $Date: 2005/03/18 15:26:55 $
+ * @see ParserControl
+ * @see CLOption
+ * @see CLOptionDescriptor
+ */
+public final class CLArgsParser {
+ //cached character == Integer.MAX_VALUE when invalid
+ private static final int INVALID = Integer.MAX_VALUE;
+ private static final int STATE_NORMAL = 0;
+ private static final int STATE_REQUIRE_2ARGS = 1;
+ private static final int STATE_REQUIRE_ARG = 2;
+ private static final int STATE_OPTIONAL_ARG = 3;
+ private static final int STATE_NO_OPTIONS = 4;
+ private static final int STATE_OPTION_MODE = 5;
+
+ // Values for creating tokens
+ private static final int TOKEN_SEPARATOR = 0;
+ private static final int TOKEN_STRING = 1;
+ private static final char[] ARG_SEPARATORS = new char[] { (char) 0, '=' };
+ private static final char[] NULL_SEPARATORS = new char[] { (char) 0 };
+ private final CLOptionDescriptor[] m_optionDescriptors;
+ private final Vector m_options;
+ private Hashtable m_optionIndex;
+ private final ParserControl m_control;
+ private String m_errorMessage;
+ private String[] m_unparsedArgs = new String[] { };
+
+ //variables used while parsing options.
+ private char m_ch;
+ private String[] m_args;
+ private boolean m_isLong;
+ private int m_argIndex;
+ private int m_stringIndex;
+ private int m_stringLength;
+ private int m_lastChar = INVALID;
+ private int m_lastOptionId;
+ private CLOption m_option;
+ private int m_state = STATE_NORMAL;
+
+ /**
+ * Retrieve an array of arguments that have not been parsed
+ * due to the parser halting.
+ *
+ * @return an array of unparsed args
+ */
+ public final String[] getUnparsedArgs() {
+ return m_unparsedArgs;
+ }
+
+ /**
+ * Retrieve a list of options that were parsed from command list.
+ *
+ * @return the list of options
+ */
+ public final Vector getArguments() {
+ //System.out.println( "Arguments: " + m_options );
+ return m_options;
+ }
+
+ /**
+ * Retrieve the {@link CLOption} with specified id, or
+ * <code>null</code> if no command line option is found.
+ *
+ * @param id the command line option id
+ * @return the {@link CLOption} with the specified id, or
+ * <code>null</code> if no CLOption is found.
+ * @see CLOption
+ */
+ public final CLOption getArgumentById(final int id) {
+ return (CLOption) m_optionIndex.get(new Integer(id));
+ }
+
+ /**
+ * Retrieve the {@link CLOption} with specified name, or
+ * <code>null</code> if no command line option is found.
+ *
+ * @param name the command line option name
+ * @return the {@link CLOption} with the specified name, or
+ * <code>null</code> if no CLOption is found.
+ * @see CLOption
+ */
+ public final CLOption getArgumentByName(final String name) {
+ return (CLOption) m_optionIndex.get(name);
+ }
+
+ /**
+ * Get Descriptor for option id.
+ *
+ * @param id the id
+ * @return the descriptor
+ */
+ private final CLOptionDescriptor getDescriptorFor(final int id) {
+ for (int i = 0; i < m_optionDescriptors.length; i++) {
+ if (m_optionDescriptors[i].getId() == id) {
+ return m_optionDescriptors[i];
+ }
+ }
+
+ return null;
+ }
+
+ /**
+ * Retrieve a descriptor by name.
+ *
+ * @param name the name
+ * @return the descriptor
+ */
+ private final CLOptionDescriptor getDescriptorFor(final String name) {
+ for (int i = 0; i < m_optionDescriptors.length; i++) {
+ if (m_optionDescriptors[i].getName().equals(name)) {
+ return m_optionDescriptors[i];
+ }
+ }
+
+ return null;
+ }
+
+ /**
+ * Retrieve an error message that occured during parsing if one existed.
+ *
+ * @return the error string
+ */
+ public final String getErrorString() {
+ //System.out.println( "ErrorString: " + m_errorMessage );
+ return m_errorMessage;
+ }
+
+ /**
+ * Require state to be placed in for option.
+ *
+ * @param descriptor the Option Descriptor
+ * @return the state
+ */
+ private final int getStateFor(final CLOptionDescriptor descriptor) {
+ final int flags = descriptor.getFlags();
+
+ if ((flags & CLOptionDescriptor.ARGUMENTS_REQUIRED_2) == CLOptionDescriptor.ARGUMENTS_REQUIRED_2) {
+ return STATE_REQUIRE_2ARGS;
+ } else if ((flags & CLOptionDescriptor.ARGUMENT_REQUIRED) == CLOptionDescriptor.ARGUMENT_REQUIRED) {
+ return STATE_REQUIRE_ARG;
+ } else if ((flags & CLOptionDescriptor.ARGUMENT_OPTIONAL) == CLOptionDescriptor.ARGUMENT_OPTIONAL) {
+ return STATE_OPTIONAL_ARG;
+ } else {
+ return STATE_NORMAL;
+ }
+ }
+
+ /**
+ * Create a parser that can deal with options and parses certain args.
+ *
+ * @param args the args, typically that passed to the
+ * <code>public static void main(String[] args)</code> method.
+ * @param optionDescriptors the option descriptors
+ * @param control the parser control used determine behaviour of parser
+ */
+ public CLArgsParser(final String[] args, final CLOptionDescriptor[] optionDescriptors,
+ final ParserControl control) {
+ m_optionDescriptors = optionDescriptors;
+ m_control = control;
+ m_options = new Vector();
+ m_args = args;
+
+ try {
+ parse();
+ checkIncompatibilities(m_options);
+ buildOptionIndex();
+ } catch (final ParseException pe) {
+ m_errorMessage = pe.getMessage();
+ }
+
+ //System.out.println( "Built : " + m_options );
+ //System.out.println( "From : " + Arrays.asList( args ) );
+ }
+
+ /**
+ * Check for duplicates of an option.
+ * It is an error to have duplicates unless appropriate flags is set in descriptor.
+ *
+ * @param arguments the arguments
+ */
+ private final void checkIncompatibilities(final Vector arguments) throws ParseException {
+ final int size = arguments.size();
+
+ for (int i = 0; i < size; i++) {
+ final CLOption option = (CLOption) arguments.elementAt(i);
+ final int id = option.getDescriptor().getId();
+ final CLOptionDescriptor descriptor = getDescriptorFor(id);
+
+ //this occurs when id == 0 and user has not supplied a descriptor
+ //for arguments
+ if (null == descriptor) {
+ continue;
+ }
+
+ final int[] incompatible = descriptor.getIncompatible();
+
+ checkIncompatible(arguments, incompatible, i);
+ }
+ }
+
+ private final void checkIncompatible(final Vector arguments, final int[] incompatible,
+ final int original) throws ParseException {
+ final int size = arguments.size();
+
+ for (int i = 0; i < size; i++) {
+ if (original == i) {
+ continue;
+ }
+
+ final CLOption option = (CLOption) arguments.elementAt(i);
+ final int id = option.getDescriptor().getId();
+
+ for (int j = 0; j < incompatible.length; j++) {
+ if (id == incompatible[j]) {
+ final CLOption originalOption = (CLOption) arguments.elementAt(original);
+ final int originalId = originalOption.getDescriptor().getId();
+
+ String message = null;
+
+ if (id == originalId) {
+ message = "Duplicate options for " + describeDualOption(originalId)
+ + " found.";
+ } else {
+ message = "Incompatible options -" + describeDualOption(id) + " and "
+ + describeDualOption(originalId) + " found.";
+ }
+
+ throw new ParseException(message, 0);
+ }
+ }
+ }
+ }
+
+ private final String describeDualOption(final int id) {
+ final CLOptionDescriptor descriptor = getDescriptorFor(id);
+
+ if (null == descriptor) {
+ return "<parameter>";
+ } else {
+ final StringBuffer sb = new StringBuffer();
+ boolean hasCharOption = false;
+
+ if (Character.isLetter((char) id)) {
+ sb.append('-');
+ sb.append((char) id);
+ hasCharOption = true;
+ }
+
+ final String longOption = descriptor.getName();
+
+ if (null != longOption) {
+ if (hasCharOption) {
+ sb.append('/');
+ }
+
+ sb.append("--");
+ sb.append(longOption);
+ }
+
+ return sb.toString();
+ }
+ }
+
+ /**
+ * Create a parser that deals with options and parses certain args.
+ *
+ * @param args the args
+ * @param optionDescriptors the option descriptors
+ */
+ public CLArgsParser(final String[] args, final CLOptionDescriptor[] optionDescriptors) {
+ this(args, optionDescriptors, null);
+ }
+
+ /**
+ * Create a string array that is subset of input array.
+ * The sub-array should start at array entry indicated by index. That array element
+ * should only include characters from charIndex onwards.
+ *
+ * @param array the original array
+ * @param index the cut-point in array
+ * @param charIndex the cut-point in element of array
+ * @return the result array
+ */
+ private final String[] subArray(final String[] array, final int index, final int charIndex) {
+ final int remaining = array.length - index;
+ final String[] result = new String[remaining];
+
+ if (remaining > 1) {
+ System.arraycopy(array, index + 1, result, 1, remaining - 1);
+ }
+
+ result[0] = array[index].substring(charIndex - 1);
+
+ return result;
+ }
+
+ /**
+ * Actually parse arguments
+ */
+ private final void parse() throws ParseException {
+ if (0 == m_args.length) {
+ return;
+ }
+
+ m_stringLength = m_args[m_argIndex].length();
+
+ //ch = peekAtChar();
+ while (true) {
+ m_ch = peekAtChar();
+
+ //System.out.println( "Pre State=" + m_state );
+ //System.out.println( "Pre Char=" + (char)ch + "/" + (int)ch );
+ if (m_argIndex >= m_args.length) {
+ break;
+ }
+
+ if ((null != m_control) && m_control.isFinished(m_lastOptionId)) {
+ //this may need mangling due to peeks
+ m_unparsedArgs = subArray(m_args, m_argIndex, m_stringIndex);
+
+ return;
+ }
+
+ //System.out.println( "State=" + m_state );
+ //System.out.println( "Char=" + (char)ch + "/" + (int)ch );
+ if (STATE_OPTION_MODE == m_state) {
+ //if get to an arg barrier then return to normal mode
+ //else continue accumulating options
+ if (0 == m_ch) {
+ getChar(); //strip the null
+ m_state = STATE_NORMAL;
+ } else {
+ parseShortOption();
+ }
+ } else if (STATE_NORMAL == m_state) {
+ parseNormal();
+ } else if (STATE_NO_OPTIONS == m_state) {
+ //should never get to here when stringIndex != 0
+ addOption(new CLOption(m_args[m_argIndex++]));
+ } else if ((STATE_OPTIONAL_ARG == m_state) && m_isLong && (m_ch != 0)) {
+ m_state = STATE_NORMAL;
+ addOption(m_option);
+ } else {
+ parseArguments();
+ }
+ }
+
+ if (m_option != null) {
+ if (STATE_OPTIONAL_ARG == m_state) {
+ m_options.addElement(m_option);
+ } else if (STATE_REQUIRE_ARG == m_state) {
+ final CLOptionDescriptor descriptor = getDescriptorFor(m_option.getDescriptor()
+ .getId());
+ final String message = "Missing argument to option "
+ + getOptionDescription(descriptor);
+ throw new ParseException(message, 0);
+ } else if (STATE_REQUIRE_2ARGS == m_state) {
+ if (1 == m_option.getArgumentCount()) {
+ m_option.addArgument("");
+ m_options.addElement(m_option);
+ } else {
+ final CLOptionDescriptor descriptor = getDescriptorFor(m_option.getDescriptor()
+ .getId());
+ final String message = "Missing argument to option "
+ + getOptionDescription(descriptor);
+ throw new ParseException(message, 0);
+ }
+ } else {
+ throw new ParseException("IllegalState " + m_state + ": " + m_option, 0);
+ }
+ }
+ }
+
+ private final String getOptionDescription(final CLOptionDescriptor descriptor) {
+ if (m_isLong) {
+ return "--" + descriptor.getName();
+ } else {
+ return "-" + (char) descriptor.getId();
+ }
+ }
+
+ private final char peekAtChar() {
+ if (INVALID == m_lastChar) {
+ m_lastChar = readChar();
+ }
+
+ return (char) m_lastChar;
+ }
+
+ private final char getChar() {
+ if (INVALID != m_lastChar) {
+ final char result = (char) m_lastChar;
+ m_lastChar = INVALID;
+
+ return result;
+ } else {
+ return readChar();
+ }
+ }
+
+ private final char readChar() {
+ if (m_stringIndex >= m_stringLength) {
+ m_argIndex++;
+ m_stringIndex = 0;
+
+ if (m_argIndex < m_args.length) {
+ m_stringLength = m_args[m_argIndex].length();
+ } else {
+ m_stringLength = 0;
+ }
+
+ return 0;
+ }
+
+ if (m_argIndex >= m_args.length) {
+ return 0;
+ }
+
+ return m_args[m_argIndex].charAt(m_stringIndex++);
+ }
+
+ private final Token nextToken(final char[] separators) {
+ m_ch = getChar();
+
+ if (isSeparator(m_ch, separators)) {
+ m_ch = getChar();
+
+ return new Token(TOKEN_SEPARATOR, null);
+ }
+
+ final StringBuffer sb = new StringBuffer();
+
+ do {
+ sb.append(m_ch);
+ m_ch = getChar();
+ } while (!isSeparator(m_ch, separators));
+
+ return new Token(TOKEN_STRING, sb.toString());
+ }
+
+ private final boolean isSeparator(final char ch, final char[] separators) {
+ for (int i = 0; i < separators.length; i++) {
+ if (ch == separators[i]) {
+ return true;
+ }
+ }
+
+ return false;
+ }
+
+ private final void addOption(final CLOption option) {
+ m_options.addElement(option);
+ m_lastOptionId = option.getDescriptor().getId();
+ m_option = null;
+ }
+
+ private final void parseOption(final CLOptionDescriptor descriptor, final String optionString)
+ throws ParseException {
+ if (null == descriptor) {
+ throw new ParseException("Unknown option " + optionString, 0);
+ }
+
+ m_state = getStateFor(descriptor);
+ m_option = new CLOption(descriptor);
+
+ if (STATE_NORMAL == m_state) {
+ addOption(m_option);
+ }
+ }
+
+ private final void parseShortOption() throws ParseException {
+ m_ch = getChar();
+
+ final CLOptionDescriptor descriptor = getDescriptorFor(m_ch);
+ m_isLong = false;
+ parseOption(descriptor, "-" + m_ch);
+
+ if (STATE_NORMAL == m_state) {
+ m_state = STATE_OPTION_MODE;
+ }
+ }
+
+ private final void parseArguments() throws ParseException {
+ if (STATE_REQUIRE_ARG == m_state) {
+ if (('=' == m_ch) || (0 == m_ch)) {
+ getChar();
+ }
+
+ final Token token = nextToken(NULL_SEPARATORS);
+ m_option.addArgument(token.getValue());
+
+ addOption(m_option);
+ m_state = STATE_NORMAL;
+ } else if (STATE_OPTIONAL_ARG == m_state) {
+ if (('-' == m_ch) || (0 == m_ch)) {
+ getChar(); //consume stray character
+ addOption(m_option);
+ m_state = STATE_NORMAL;
+
+ return;
+ }
+
+ if ('=' == m_ch) {
+ getChar();
+ }
+
+ final Token token = nextToken(NULL_SEPARATORS);
+ m_option.addArgument(token.getValue());
+
+ addOption(m_option);
+ m_state = STATE_NORMAL;
+ } else if (STATE_REQUIRE_2ARGS == m_state) {
+ if (0 == m_option.getArgumentCount()) {
+ /*
+ * Fix bug: -D arg1=arg2 was causing parse error; however --define arg1=arg2 is OK
+ * This seems to be because the parser skips the terminator for the long options,
+ * but was not doing so for the short options.
+ */
+ if (!m_isLong) {
+ if (0 == peekAtChar()) {
+ getChar();
+ }
+ }
+
+ final Token token = nextToken(ARG_SEPARATORS);
+
+ if (TOKEN_SEPARATOR == token.getType()) {
+ final CLOptionDescriptor descriptor = getDescriptorFor(m_option.getDescriptor()
+ .getId());
+ final String message = "Unable to parse first argument for option "
+ + getOptionDescription(descriptor);
+ throw new ParseException(message, 0);
+ } else {
+ m_option.addArgument(token.getValue());
+ }
+
+ // Are we about to start a new option?
+ if ((0 == m_ch) && ('-' == peekAtChar())) {
+ // Yes, so the second argument is missing
+ m_option.addArgument("");
+ m_options.addElement(m_option);
+ m_state = STATE_NORMAL;
+ }
+ } else //2nd argument
+ {
+ final StringBuffer sb = new StringBuffer();
+
+ m_ch = getChar();
+
+ while (!isSeparator(m_ch, NULL_SEPARATORS)) {
+ sb.append(m_ch);
+ m_ch = getChar();
+ }
+
+ final String argument = sb.toString();
+
+ //System.out.println( "Arguement:" + argument );
+ m_option.addArgument(argument);
+ addOption(m_option);
+ m_option = null;
+ m_state = STATE_NORMAL;
+ }
+ }
+ }
+
+ /**
+ * Parse Options from Normal mode.
+ */
+ private final void parseNormal() throws ParseException {
+ if ('-' != m_ch) {
+ //Parse the arguments that are not options
+ final String argument = nextToken(NULL_SEPARATORS).getValue();
+ addOption(new CLOption(argument));
+ m_state = STATE_NORMAL;
+ } else {
+ getChar(); // strip the -
+
+ if (0 == peekAtChar()) {
+ throw new ParseException("Malformed option -", 0);
+ } else {
+ m_ch = peekAtChar();
+
+ //if it is a short option then parse it else ...
+ if ('-' != m_ch) {
+ parseShortOption();
+ } else {
+ getChar(); // strip the -
+ //-- sequence .. it can either mean a change of state
+ //to STATE_NO_OPTIONS or else a long option
+
+ if (0 == peekAtChar()) {
+ getChar();
+ m_state = STATE_NO_OPTIONS;
+ } else {
+ //its a long option
+ final String optionName = nextToken(ARG_SEPARATORS).getValue();
+ final CLOptionDescriptor descriptor = getDescriptorFor(optionName);
+ m_isLong = true;
+ parseOption(descriptor, "--" + optionName);
+ }
+ }
+ }
+ }
+ }
+
+ /**
+ * Build the m_optionIndex lookup map for the parsed options.
+ */
+ private final void buildOptionIndex() {
+ final int size = m_options.size();
+ m_optionIndex = new Hashtable(size * 2);
+
+ for (int i = 0; i < size; i++) {
+ final CLOption option = (CLOption) m_options.get(i);
+ final CLOptionDescriptor optionDescriptor = getDescriptorFor(option.getDescriptor()
+ .getId());
+
+ m_optionIndex.put(new Integer(option.getDescriptor().getId()), option);
+
+ if ((null != optionDescriptor) && (null != optionDescriptor.getName())) {
+ m_optionIndex.put(optionDescriptor.getName(), option);
+ }
+ }
+ }
+}
diff --git a/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/avalon/CLOption.java b/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/avalon/CLOption.java
new file mode 100644
index 0000000..39fea51
--- /dev/null
+++ b/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/avalon/CLOption.java
@@ -0,0 +1,158 @@
+/*
+ * Copyright 2002-2005 The Apache Software Foundation
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+ * implied.
+ *
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.commons.cli.avalon;
+
+// Renamed from org.apache.avalon.excalibur.cli
+import java.util.Arrays;
+
+
+/**
+ * Basic class describing an instance of option.
+ *
+ * @version $Revision: 1.2 $ $Date: 2005/03/18 15:26:55 $
+ */
+public final class CLOption {
+ /**
+ * Value of {@link #getId} when the option is a text argument.
+ */
+ public static final int TEXT_ARGUMENT = 0;
+
+ /**
+ * Default descriptor. Required, since code assumes that getDescriptor will never return null.
+ */
+ private static final CLOptionDescriptor TEXT_ARGUMENT_DESCRIPTOR = new CLOptionDescriptor(null,
+ CLOptionDescriptor.ARGUMENT_OPTIONAL,
+ TEXT_ARGUMENT,
+ null);
+ private String[] m_arguments;
+ private CLOptionDescriptor m_descriptor = TEXT_ARGUMENT_DESCRIPTOR;
+
+ /**
+ * Retrieve argument to option if it takes arguments.
+ *
+ * @return the (first) argument
+ */
+ public final String getArgument() {
+ return getArgument(0);
+ }
+
+ /**
+ * Retrieve indexed argument to option if it takes arguments.
+ *
+ * @param index The argument index, from 0 to
+ * {@link #getArgumentCount()}-1.
+ * @return the argument
+ */
+ public final String getArgument(final int index) {
+ if ((null == m_arguments) || (index < 0) || (index >= m_arguments.length)) {
+ return null;
+ } else {
+ return m_arguments[index];
+ }
+ }
+
+ /**
+ * Retrieve id of option.
+ *
+ * The id is eqivalent to character code if it can be a single letter option.
+ *
+ * @return the id
+ * @deprecated use <code>getDescriptor().getId()</code> instead
+ */
+ public final int getId() {
+ return (m_descriptor == null) ? TEXT_ARGUMENT : m_descriptor.getId();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final CLOptionDescriptor getDescriptor() {
+ return m_descriptor;
+ }
+
+ /**
+ * Constructor taking an descriptor
+ *
+ * @param descriptor the descriptor iff null, will default to a "text argument" descriptor.
+ */
+ public CLOption(final CLOptionDescriptor descriptor) {
+ if (descriptor != null) {
+ m_descriptor = descriptor;
+ }
+ }
+
+ /**
+ * Constructor taking argument for option.
+ *
+ * @param argument the argument
+ */
+ public CLOption(final String argument) {
+ this((CLOptionDescriptor) null);
+ addArgument(argument);
+ }
+
+ /**
+ * Mutator of Argument property.
+ *
+ * @param argument the argument
+ */
+ public final void addArgument(final String argument) {
+ if (null == m_arguments) {
+ m_arguments = new String[] { argument };
+ } else {
+ final String[] arguments = new String[m_arguments.length + 1];
+ System.arraycopy(m_arguments, 0, arguments, 0, m_arguments.length);
+ arguments[m_arguments.length] = argument;
+ m_arguments = arguments;
+ }
+ }
+
+ /**
+ * Get number of arguments.
+ *
+ * @return the number of arguments
+ */
+ public final int getArgumentCount() {
+ if (null == m_arguments) {
+ return 0;
+ } else {
+ return m_arguments.length;
+ }
+ }
+
+ /**
+ * Convert to String.
+ *
+ * @return the string value
+ */
+ public final String toString() {
+ final StringBuffer sb = new StringBuffer();
+ sb.append("[Option ");
+ sb.append((char) m_descriptor.getId());
+
+ if (null != m_arguments) {
+ sb.append(", ");
+ sb.append(Arrays.asList(m_arguments));
+ }
+
+ sb.append(" ]");
+
+ return sb.toString();
+ }
+}
diff --git a/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/avalon/CLOptionDescriptor.java b/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/avalon/CLOptionDescriptor.java
new file mode 100644
index 0000000..04d2544
--- /dev/null
+++ b/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/avalon/CLOptionDescriptor.java
@@ -0,0 +1,208 @@
+/*
+ * Copyright 2002-2005 The Apache Software Foundation
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+ * implied.
+ *
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.commons.cli.avalon;
+
+//Renamed from org.apache.avalon.excalibur.cli
+
+/**
+ * Basic class describing an type of option.
+ * Typically, one creates a static array of <code>CLOptionDescriptor</code>s,
+ * and passes it to {@link CLArgsParser#CLArgsParser(String[], CLOptionDescriptor[])}.
+ *
+ * @version $Revision: 1.2 $ $Date: 2005/03/18 15:26:55 $
+ * @see CLArgsParser
+ * @see CLUtil
+ */
+public final class CLOptionDescriptor {
+ /** Flag to say that one argument is required */
+ public static final int ARGUMENT_REQUIRED = 1 << 1;
+
+ /** Flag to say that the argument is optional */
+ public static final int ARGUMENT_OPTIONAL = 1 << 2;
+
+ /** Flag to say this option does not take arguments */
+ public static final int ARGUMENT_DISALLOWED = 1 << 3;
+
+ /** Flag to say this option requires 2 arguments */
+ public static final int ARGUMENTS_REQUIRED_2 = 1 << 4;
+
+ /** Flag to say this option may be repeated on the command line */
+ public static final int DUPLICATES_ALLOWED = 1 << 5;
+ private final int m_id;
+ private final int m_flags;
+ private final String m_name;
+ private final String m_description;
+ private final int[] m_incompatible;
+
+ /**
+ * Constructor.
+ *
+ * @param name the name/long option
+ * @param flags the flags
+ * @param id the id/character option
+ * @param description description of option usage
+ */
+ public CLOptionDescriptor(final String name, final int flags, final int id,
+ final String description) {
+ this(name, flags, id, description,
+ ((flags & CLOptionDescriptor.DUPLICATES_ALLOWED) > 0) ? new int[0] : new int[] { id });
+ }
+
+ /**
+ * Constructor.
+ *
+ * @param name the name/long option
+ * @param flags the flags
+ * @param id the id/character option
+ * @param description description of option usage
+ * @param incompatible an array listing the ids of all incompatible options
+ * @deprecated use the version with the array of CLOptionDescriptor's
+ */
+ public CLOptionDescriptor(final String name, final int flags, final int id,
+ final String description, final int[] incompatible) {
+ m_id = id;
+ m_name = name;
+ m_flags = flags;
+ m_description = description;
+ m_incompatible = incompatible;
+
+ int modeCount = 0;
+
+ if ((ARGUMENT_REQUIRED & flags) == ARGUMENT_REQUIRED) {
+ modeCount++;
+ }
+
+ if ((ARGUMENT_OPTIONAL & flags) == ARGUMENT_OPTIONAL) {
+ modeCount++;
+ }
+
+ if ((ARGUMENT_DISALLOWED & flags) == ARGUMENT_DISALLOWED) {
+ modeCount++;
+ }
+
+ if ((ARGUMENTS_REQUIRED_2 & flags) == ARGUMENTS_REQUIRED_2) {
+ modeCount++;
+ }
+
+ if (0 == modeCount) {
+ final String message = "No mode specified for option " + this;
+ throw new IllegalStateException(message);
+ } else if (1 != modeCount) {
+ final String message = "Multiple modes specified for option " + this;
+ throw new IllegalStateException(message);
+ }
+ }
+
+ /**
+ * Constructor.
+ *
+ * @param name the name/long option
+ * @param flags the flags
+ * @param id the id/character option
+ * @param description description of option usage
+ */
+ public CLOptionDescriptor(final String name, final int flags, final int id,
+ final String description, final CLOptionDescriptor[] incompatible) {
+ m_id = id;
+ m_name = name;
+ m_flags = flags;
+ m_description = description;
+
+ m_incompatible = new int[incompatible.length];
+
+ for (int i = 0; i < incompatible.length; i++) {
+ m_incompatible[i] = incompatible[i].getId();
+ }
+ }
+
+ /**
+ * @deprecated Use the correctly spelled {@link #getIncompatible} instead.
+ * @return the array of incompatible option ids
+ */
+ protected final int[] getIncompatble() {
+ return getIncompatible();
+ }
+
+ /**
+ * Get the array of incompatible option ids.
+ *
+ * @return the array of incompatible option ids
+ */
+ protected final int[] getIncompatible() {
+ return m_incompatible;
+ }
+
+ /**
+ * Retrieve textual description.
+ *
+ * @return the description
+ */
+ public final String getDescription() {
+ return m_description;
+ }
+
+ /**
+ * Retrieve flags about option.
+ * Flags include details such as whether it allows parameters etc.
+ *
+ * @return the flags
+ */
+ public final int getFlags() {
+ return m_flags;
+ }
+
+ /**
+ * Retrieve the id for option.
+ * The id is also the character if using single character options.
+ *
+ * @return the id
+ */
+ public final int getId() {
+ return m_id;
+ }
+
+ /**
+ * Retrieve name of option which is also text for long option.
+ *
+ * @return name/long option
+ */
+ public final String getName() {
+ return m_name;
+ }
+
+ /**
+ * Convert to String.
+ *
+ * @return the converted value to string.
+ */
+ public final String toString() {
+ final StringBuffer sb = new StringBuffer();
+ sb.append("[OptionDescriptor ");
+ sb.append(m_name);
+ sb.append("[OptionDescriptor ");
+ sb.append(m_name);
+ sb.append(", ");
+ sb.append(m_id);
+ sb.append(", ");
+ sb.append(m_flags);
+ sb.append(", ");
+ sb.append(m_description);
+ sb.append(" ]");
+
+ return sb.toString();
+ }
+}
diff --git a/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/avalon/CLUtil.java b/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/avalon/CLUtil.java
new file mode 100644
index 0000000..34f5598
--- /dev/null
+++ b/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/avalon/CLUtil.java
@@ -0,0 +1,106 @@
+/*
+ * Copyright 2002-2005 The Apache Software Foundation
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+ * implied.
+ *
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.commons.cli.avalon;
+
+//Renamed from org.apache.avalon.excalibur.cli
+
+/**
+ * CLUtil offers basic utility operations for use both internal and external to package.
+ *
+ * @version $Revision: 1.2 $ $Date: 2005/03/18 15:26:55 $
+ * @see CLOptionDescriptor
+ */
+public final class CLUtil {
+ private static final int MAX_DESCRIPTION_COLUMN_LENGTH = 60;
+
+ /**
+ * Format options into StringBuffer and return. This is typically used to
+ * print "Usage" text in response to a "--help" or invalid option.
+ *
+ * @param options the option descriptors
+ * @return the formatted description/help for options
+ */
+ public static final StringBuffer describeOptions(final CLOptionDescriptor[] options) {
+ final String lSep = System.getProperty("line.separator");
+ final StringBuffer sb = new StringBuffer();
+
+ for (int i = 0; i < options.length; i++) {
+ final char ch = (char) options[i].getId();
+ final String name = options[i].getName();
+ String description = options[i].getDescription();
+ int flags = options[i].getFlags();
+ boolean argumentRequired = ((flags & CLOptionDescriptor.ARGUMENT_REQUIRED) == CLOptionDescriptor.ARGUMENT_REQUIRED);
+ boolean twoArgumentsRequired = ((flags & CLOptionDescriptor.ARGUMENTS_REQUIRED_2) == CLOptionDescriptor.ARGUMENTS_REQUIRED_2);
+ boolean needComma = false;
+
+ if (twoArgumentsRequired) {
+ argumentRequired = true;
+ }
+
+ sb.append('\t');
+
+ if (Character.isLetter(ch)) {
+ sb.append("-");
+ sb.append(ch);
+ needComma = true;
+ }
+
+ if (null != name) {
+ if (needComma) {
+ sb.append(", ");
+ }
+
+ sb.append("--");
+ sb.append(name);
+ }
+
+ if (argumentRequired) {
+ sb.append(" <argument>");
+ }
+
+ if (twoArgumentsRequired) {
+ sb.append("=<value>");
+ }
+
+ sb.append(lSep);
+
+ if (null != description) {
+ while (description.length() > MAX_DESCRIPTION_COLUMN_LENGTH) {
+ final String descriptionPart = description.substring(0,
+ MAX_DESCRIPTION_COLUMN_LENGTH);
+ description = description.substring(MAX_DESCRIPTION_COLUMN_LENGTH);
+ sb.append("\t\t");
+ sb.append(descriptionPart);
+ sb.append(lSep);
+ }
+
+ sb.append("\t\t");
+ sb.append(description);
+ sb.append(lSep);
+ }
+ }
+
+ return sb;
+ }
+
+ /**
+ * Private Constructor so that no instance can ever be created.
+ *
+ */
+ private CLUtil() {
+ }
+}
diff --git a/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/avalon/ParserControl.java b/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/avalon/ParserControl.java
new file mode 100644
index 0000000..f093319
--- /dev/null
+++ b/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/avalon/ParserControl.java
@@ -0,0 +1,36 @@
+/*
+ * Copyright 2002-2005 The Apache Software Foundation
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+ * implied.
+ *
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.commons.cli.avalon;
+
+//Renamed from org.apache.avalon.excalibur.cli
+
+/**
+ * ParserControl is used to control particular behaviour of the parser.
+ *
+ * @version $Revision: 1.2 $ $Date: 2005/03/18 15:26:55 $
+ * @see AbstractParserControl
+ */
+public interface ParserControl {
+ /**
+ * Called by the parser to determine whether it should stop
+ * after last option parsed.
+ *
+ * @param lastOptionCode the code of last option parsed
+ * @return return true to halt, false to continue parsing
+ */
+ boolean isFinished(int lastOptionCode);
+}
diff --git a/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/avalon/Token.java b/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/avalon/Token.java
new file mode 100644
index 0000000..fc477d6
--- /dev/null
+++ b/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/avalon/Token.java
@@ -0,0 +1,69 @@
+/*
+ * Copyright 2002-2005 The Apache Software Foundation
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+ * implied.
+ *
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.commons.cli.avalon;
+
+//Renamed from org.apache.avalon.excalibur.cli
+
+/**
+ * Token handles tokenizing the CLI arguments
+ *
+ * @version $Revision: 1.2 $ $Date: 2005/03/18 15:26:55 $
+ * @since 4.0
+ */
+class Token {
+ /** Type for a separator token */
+ public static final int TOKEN_SEPARATOR = 0;
+
+ /** Type for a text token */
+ public static final int TOKEN_STRING = 1;
+ private final int m_type;
+ private final String m_value;
+
+ /**
+ * New Token object with a type and value
+ */
+ Token(final int type, final String value) {
+ m_type = type;
+ m_value = value;
+ }
+
+ /**
+ * Get the value of the token
+ */
+ final String getValue() {
+ return m_value;
+ }
+
+ /**
+ * Get the type of the token
+ */
+ final int getType() {
+ return m_type;
+ }
+
+ /**
+ * Convert to a string
+ */
+ public final String toString() {
+ final StringBuffer sb = new StringBuffer();
+ sb.append(m_type);
+ sb.append(":");
+ sb.append(m_value);
+
+ return sb.toString();
+ }
+}
diff --git a/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/avalon/package.html b/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/avalon/package.html
new file mode 100644
index 0000000..62c30d4
--- /dev/null
+++ b/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/avalon/package.html
@@ -0,0 +1,164 @@
+<html>
+ <head>
+ <title>Package Documentation for org.apache.commons.cli.avalon Package</title>
+ </head>
+ <body bgcolor="white">
+ Utility code for parsing command-line options.
+ <br><br>
+<p style="font-weight:bold">
+These classes were originally in the Avalon project in the package org.apache.avalon.excalibur.cli
+</p>
+
+ <h3>Introduction</h3>
+ <p>The utilities in <code>org.apache.commons.cli.avalon</code> assist
+ you in parsing command line options during startup time. It allows you
+ to associate a short option and a long option to the same command, and
+ then test for it in a switch statement.</p>
+ <a name="doc.Usage"></a>
+ <h3>Usage Example</h3>
+ <pre>
+import java.util.List;
+
+import org.apache.commons.cli.avalon.CLArgsParser;
+import org.apache.commons.cli.avalon.CLOption;
+import org.apache.commons.cli.avalon.CLOptionDescriptor;
+import org.apache.commons.cli.avalon.CLUtil;
+
+/**
+* Demonstrates the excalibur command-line parsing utility.
+*
+*/
+public class CLDemo {
+ // Define our short one-letter option identifiers.
+ protected static final int HELP_OPT = 'h';
+ protected static final int VERSION_OPT = 'v';
+ protected static final int MSG_OPT = 'm';
+
+ /**
+ * Define the understood options. Each CLOptionDescriptor contains:
+ * - The "long" version of the option. Eg, "help" means that "--help" will
+ * be recognised.
+ * - The option flags, governing the option's argument(s).
+ * - The "short" version of the option. Eg, 'h' means that "-h" will be
+ * recognised.
+ * - A description of the option.
+ */
+ protected static final CLOptionDescriptor [] options = new CLOptionDescriptor [] {
+ new CLOptionDescriptor("help",
+ CLOptionDescriptor.ARGUMENT_DISALLOWED,
+ HELP_OPT,
+ "print this message and exit"),
+ new CLOptionDescriptor("version",
+ CLOptionDescriptor.ARGUMENT_DISALLOWED,
+ VERSION_OPT,
+ "print the version information and exit"),
+ new CLOptionDescriptor("msg",
+ CLOptionDescriptor.ARGUMENT_REQUIRED,
+ MSG_OPT,
+ "the message to print"),
+ };
+
+ public static void main(String args[]) {
+ // Parse the arguments
+ CLArgsParser parser = new CLArgsParser(args, options);
+
+ if( null != parser.getErrorString() ) {
+ System.err.println( "Error: " + parser.getErrorString() );
+ return;
+ }
+
+ // Get a list of parsed options
+ List clOptions = parser.getArguments();
+ int size = clOptions.size();
+
+ for (int i = 0; i < size; i++) {
+ CLOption option = (CLOption) clOptions.get(i);
+
+ switch (option.getId()) {
+ case CLOption.TEXT_ARGUMENT:
+ System.out.println("Unknown arg: "+option.getArgument());
+ break;
+
+ case HELP_OPT:
+ printUsage();
+ break;
+
+ case VERSION_OPT:
+ printVersion();
+ break;
+
+
+ case MSG_OPT:
+ System.out.println(option.getArgument());
+ break;
+ }
+ }
+ }
+
+ private static void printVersion() {
+ System.out.println("1.0");
+ System.exit(0);
+ }
+
+ private static void printUsage() {
+ String lSep = System.getProperty("line.separator");
+ StringBuffer msg = new StringBuffer();
+ msg.append("------------------------------------------------------------------------ ").append(lSep);
+ msg.append("Excalibur command-line arg parser demo").append(lSep);
+ msg.append("Usage: java "+CLDemo.class.getName()+" [options]").append(lSep).append(lSep);
+ msg.append("Options: ").append(lSep);
+ msg.append(CLUtil.describeOptions(CLDemo.options).toString());
+ System.out.println(msg.toString());
+ System.exit(0);
+ }
+}
+</pre>
+
+ <h3>Parsing Rules</h3>
+ <p>
+ The command line is parsed according to the following rules. There are
+ two forms of options in this package, the Long form and the Short form.
+ The long form of an option is preceded by the '--' characters while the
+ short form is preceded by a single '-'. Some example options would be;
+ "--an-option", "-a", "--day", "-s -f -a".
+ </p>
+ <p>
+ In the tradition of UNIX programs, the short form of an option can occur
+ immediately after another short form option. So if 'a', 'b' and 'c' are
+ short forms of options that take no parameters then the following
+ command lines are equivalent: "-abc", "-a -bc", "-a -b -c", "-ab -c", etc.
+ </p>
+ <p>
+ Options can also accept arguments if specified. You can specify that an
+ option requires an argument in which the text immediately following the
+ option will be considered to be an argument to the option. So if 'a' was an
+ option that required an argument then the following would be equivalent;
+ "-abc", "-a bc" (namely the option 'a' with argument 'bc').
+ </p>
+ <p>
+ Options can also specify optional arguments. In this case if there is any
+ text immediately following the option character then it is considered an
+ argument. Otherwise, the option has no arguments. For example if 'a' was an
+ option that required an optional argument then "-abc" is an option 'a' with
+ argument "bc" while "-a bc" is an option 'a' with no argument, followed by
+ the text "bc". </p>
+ <p>It is also possible to place an '=' sign between the option
+ and it's argument. So if we assume that a is an option that
+ requires an argument then the following are all equivalent;
+ "-a=bc", "-a bc" "-abc".
+ </p>
+ <p>
+ In the case of a long option with an optional argument, the '=' sign is required.
+ For example. --optarg=1, not --optarg 1.
+ </p>
+ <p>
+ In some cases it is also necessary to disable command line parsing so that you
+ can pass a text argument to the program that starts with a '-' character. To do
+ this insert the sequence '--' onto the command line with no text immediately
+ following it. This will disable processing for the rest of the command line.
+ The '--' characters will not be passed to the user program. For instance the
+ line "-- -b" would result in the program being passed the
+ text "-b" (ie. not as an option).
+ </p>
+</body>
+</html>
diff --git a/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/overview.html b/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/overview.html
new file mode 100644
index 0000000..eadba1e
--- /dev/null
+++ b/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/overview.html
@@ -0,0 +1,28 @@
+
+<body>
+
+ <p>Commons CLI -- version ##VERSION## (##QUALITY##)</p>
+
+ <p>The commons-cli package aides in parsing command-line arguments.</p>
+
+ <p>Allow command-line arguments to be parsed against a descriptor of
+ valid options (long and short), potentially with arguments.</p>
+
+ <p>command-line arguments may be of the typical <code>String[]</code>
+ form, but also may be a <code>java.util.List</code>. Indexes allow
+ for parsing only a portion of the command-line. Also, functionality
+ for parsing the command-line in phases is built in, allowing for
+ 'cvs-style' command-lines, where some global options are specified
+ before a 'command' argument, and command-specific options are
+ specified after the command argument:
+
+ <code>
+ <pre>
+ myApp -p <port> command -p <printer>
+ </pre>
+ </code>
+
+
+ <p>The homepage for the project is
+ <a href="http://jakarta.apache.org/commons/">jakarta commons/</a>
+</body>
diff --git a/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/package.html b/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/package.html
new file mode 100644
index 0000000..5bf2066
--- /dev/null
+++ b/corelibs/commons-cli-1.x-cytocape-custom/src/main/java/org/apache/commons/cli/package.html
@@ -0,0 +1,6 @@
+
+<body>
+
+ Commons CLI 1.0
+
+</body>
diff --git a/corelibs/commons-cli-1.x-cytocape-custom/src/media/logo.xcf b/corelibs/commons-cli-1.x-cytocape-custom/src/media/logo.xcf
new file mode 100644
index 0000000..fb1cd2b
Binary files /dev/null and b/corelibs/commons-cli-1.x-cytocape-custom/src/media/logo.xcf differ
diff --git a/corelibs/commons-cli-1.x-cytocape-custom/src/test/java/data/.hidden.txt b/corelibs/commons-cli-1.x-cytocape-custom/src/test/java/data/.hidden.txt
new file mode 100644
index 0000000..d18fa71
--- /dev/null
+++ b/corelibs/commons-cli-1.x-cytocape-custom/src/test/java/data/.hidden.txt
@@ -0,0 +1 @@
+Hidden text file.
diff --git a/corelibs/commons-cli-1.x-cytocape-custom/src/test/java/data/readable.txt b/corelibs/commons-cli-1.x-cytocape-custom/src/test/java/data/readable.txt
new file mode 100644
index 0000000..cada839
--- /dev/null
+++ b/corelibs/commons-cli-1.x-cytocape-custom/src/test/java/data/readable.txt
@@ -0,0 +1 @@
+Readable text file.
diff --git a/corelibs/commons-cli-1.x-cytocape-custom/src/test/java/data/writable.txt b/corelibs/commons-cli-1.x-cytocape-custom/src/test/java/data/writable.txt
new file mode 100644
index 0000000..53f7f5d
--- /dev/null
+++ b/corelibs/commons-cli-1.x-cytocape-custom/src/test/java/data/writable.txt
@@ -0,0 +1 @@
+Writable text file.
diff --git a/corelibs/commons-cli-1.x-cytocape-custom/src/test/java/org/apache/commons/cli/ApplicationTest.java b/corelibs/commons-cli-1.x-cytocape-custom/src/test/java/org/apache/commons/cli/ApplicationTest.java
new file mode 100644
index 0000000..4eb887f
--- /dev/null
+++ b/corelibs/commons-cli-1.x-cytocape-custom/src/test/java/org/apache/commons/cli/ApplicationTest.java
@@ -0,0 +1,134 @@
+/**
+ * Copyright 2001-2004 The Apache Software Foundation
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.commons.cli;
+
+import junit.framework.Test;
+import junit.framework.TestCase;
+import junit.framework.TestSuite;
+
+
+/**
+ * <p>
+ * This is a collection of tests that test real world
+ * applications command lines.
+ * </p>
+ *
+ * <p>
+ * The following are the applications that are tested:
+ * <ul>
+ * <li>Ant</li>
+ * </ul>
+ * </p>
+ *
+ * @author John Keyes (john at integralsource.com)
+ */
+public class ApplicationTest extends TestCase {
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static Test suite() {
+ return new TestSuite(ApplicationTest.class);
+ }
+
+ /**
+ * Creates a new ApplicationTest object.
+ *
+ * @param name DOCUMENT ME!
+ */
+ public ApplicationTest(String name) {
+ super(name);
+ }
+
+ /**
+ *
+ */
+ public void testLs() {
+ // create the command line parser
+ CommandLineParser parser = new PosixParser();
+ Options options = new Options();
+ options.addOption("a", "all", false, "do not hide entries starting with .");
+ options.addOption("A", "almost-all", false, "do not list implied . and ..");
+ options.addOption("b", "escape", false, "print octal escapes for nongraphic characters");
+ options.addOption(OptionBuilder.withLongOpt("block-size")
+ .withDescription("use SIZE-byte blocks")
+ .withValueSeparator('=').hasArg().create());
+ options.addOption("B", "ignore-backups", false, "do not list implied entried ending with ~");
+ options.addOption("c", false,
+ "with -lt: sort by, and show, ctime (time of last modification of file status information) with -l:show ctime and sort by name otherwise: sort by ctime");
+ options.addOption("C", false, "list entries by columns");
+
+ String[] args = new String[] { "--block-size=10" };
+
+ try {
+ CommandLine line = parser.parse(options, args);
+ assertTrue(line.hasOption("block-size"));
+ assertEquals(line.getOptionValue("block-size"), "10");
+ } catch (ParseException exp) {
+ fail("Unexpected exception:" + exp.getMessage());
+ }
+ }
+
+ /**
+ * Ant test
+ */
+ public void testAnt() {
+ // use the GNU parser
+ CommandLineParser parser = new GnuParser();
+ Options options = new Options();
+ options.addOption("help", false, "print this message");
+ options.addOption("projecthelp", false, "print project help information");
+ options.addOption("version", false, "print the version information and exit");
+ options.addOption("quiet", false, "be extra quiet");
+ options.addOption("verbose", false, "be extra verbose");
+ options.addOption("debug", false, "print debug information");
+ options.addOption("version", false, "produce logging information without adornments");
+ options.addOption("logfile", true, "use given file for log");
+ options.addOption("logger", true, "the class which is to perform the logging");
+ options.addOption("listener", true, "add an instance of a class as a project listener");
+ options.addOption("buildfile", true, "use given buildfile");
+ options.addOption(OptionBuilder.withDescription("use value for given property").hasArgs()
+ .withValueSeparator().create('D'));
+ //, null, true, , false, true );
+ options.addOption("find", true,
+ "search for buildfile towards the root of the filesystem and use it");
+
+ String[] args = new String[] {
+ "-buildfile", "mybuild.xml", "-Dproperty=value", "-Dproperty1=value1",
+ "-projecthelp"
+ };
+
+ try {
+ CommandLine line = parser.parse(options, args);
+
+ // check multiple values
+ String[] opts = line.getOptionValues("D");
+ assertEquals("property", opts[0]);
+ assertEquals("value", opts[1]);
+ assertEquals("property1", opts[2]);
+ assertEquals("value1", opts[3]);
+
+ // check single value
+ assertEquals(line.getOptionValue("buildfile"), "mybuild.xml");
+
+ // check option
+ assertTrue(line.hasOption("projecthelp"));
+ } catch (ParseException exp) {
+ fail("Unexpected exception:" + exp.getMessage());
+ }
+ }
+}
diff --git a/corelibs/commons-cli-1.x-cytocape-custom/src/test/java/org/apache/commons/cli/ArgumentIsOptionTest.java b/corelibs/commons-cli-1.x-cytocape-custom/src/test/java/org/apache/commons/cli/ArgumentIsOptionTest.java
new file mode 100644
index 0000000..e8009c1
--- /dev/null
+++ b/corelibs/commons-cli-1.x-cytocape-custom/src/test/java/org/apache/commons/cli/ArgumentIsOptionTest.java
@@ -0,0 +1,113 @@
+/**
+ * Copyright 2001-2004 The Apache Software Foundation
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.commons.cli;
+
+import junit.framework.Test;
+import junit.framework.TestCase;
+import junit.framework.TestSuite;
+
+
+/**
+ *
+ */
+public class ArgumentIsOptionTest extends TestCase {
+ private Options options = null;
+ private CommandLineParser parser = null;
+
+ /**
+ * Creates a new ArgumentIsOptionTest object.
+ *
+ * @param name DOCUMENT ME!
+ */
+ public ArgumentIsOptionTest(String name) {
+ super(name);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static Test suite() {
+ return new TestSuite(ArgumentIsOptionTest.class);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void setUp() {
+ options = new Options().addOption("p", false, "Option p")
+ .addOption("attr", true, "Option accepts argument");
+
+ parser = new PosixParser();
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void tearDown() {
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testOptionAndOptionWithArgument() {
+ String[] args = new String[] { "-p", "-attr", "p" };
+
+ try {
+ CommandLine cl = parser.parse(options, args);
+ assertTrue("Confirm -p is set", cl.hasOption("p"));
+ assertTrue("Confirm -attr is set", cl.hasOption("attr"));
+ assertTrue("Confirm arg of -attr", cl.getOptionValue("attr").equals("p"));
+ assertTrue("Confirm all arguments recognized", cl.getArgs().length == 0);
+ } catch (ParseException e) {
+ fail(e.toString());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testOptionWithArgument() {
+ String[] args = new String[] { "-attr", "p" };
+
+ try {
+ CommandLine cl = parser.parse(options, args);
+ assertFalse("Confirm -p is set", cl.hasOption("p"));
+ assertTrue("Confirm -attr is set", cl.hasOption("attr"));
+ assertTrue("Confirm arg of -attr", cl.getOptionValue("attr").equals("p"));
+ assertTrue("Confirm all arguments recognized", cl.getArgs().length == 0);
+ } catch (ParseException e) {
+ fail(e.toString());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testOption() {
+ String[] args = new String[] { "-p" };
+
+ try {
+ CommandLine cl = parser.parse(options, args);
+ assertTrue("Confirm -p is set", cl.hasOption("p"));
+ assertFalse("Confirm -attr is not set", cl.hasOption("attr"));
+ assertTrue("Confirm all arguments recognized", cl.getArgs().length == 0);
+ } catch (ParseException e) {
+ fail(e.toString());
+ }
+ }
+}
diff --git a/corelibs/commons-cli-1.x-cytocape-custom/src/test/java/org/apache/commons/cli/BuildTest.java b/corelibs/commons-cli-1.x-cytocape-custom/src/test/java/org/apache/commons/cli/BuildTest.java
new file mode 100644
index 0000000..9758629
--- /dev/null
+++ b/corelibs/commons-cli-1.x-cytocape-custom/src/test/java/org/apache/commons/cli/BuildTest.java
@@ -0,0 +1,101 @@
+/**
+ * Copyright 2001-2004 The Apache Software Foundation
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.commons.cli;
+
+import junit.framework.Test;
+import junit.framework.TestCase;
+import junit.framework.TestSuite;
+
+
+/**
+ *
+ */
+public class BuildTest extends TestCase {
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static Test suite() {
+ return new TestSuite(BuildTest.class);
+ }
+
+ /**
+ * Creates a new BuildTest object.
+ *
+ * @param name DOCUMENT ME!
+ */
+ public BuildTest(String name) {
+ super(name);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void setUp() {
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void tearDown() {
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testSimple() {
+ Options opts = new Options();
+
+ opts.addOption("a", false, "toggle -a");
+
+ opts.addOption("b", true, "toggle -b");
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testDuplicateSimple() {
+ Options opts = new Options();
+ opts.addOption("a", false, "toggle -a");
+
+ opts.addOption("a", true, "toggle -a*");
+
+ assertEquals("last one in wins", "toggle -a*", opts.getOption("a").getDescription());
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testLong() {
+ Options opts = new Options();
+
+ opts.addOption("a", "--a", false, "toggle -a");
+
+ opts.addOption("b", "--b", true, "set -b");
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testDuplicateLong() {
+ Options opts = new Options();
+ opts.addOption("a", "--a", false, "toggle -a");
+
+ opts.addOption("a", "--a", false, "toggle -a*");
+ assertEquals("last one in wins", "toggle -a*", opts.getOption("a").getDescription());
+ }
+}
diff --git a/corelibs/commons-cli-1.x-cytocape-custom/src/test/java/org/apache/commons/cli/GnuParseTest.java b/corelibs/commons-cli-1.x-cytocape-custom/src/test/java/org/apache/commons/cli/GnuParseTest.java
new file mode 100644
index 0000000..23be818
--- /dev/null
+++ b/corelibs/commons-cli-1.x-cytocape-custom/src/test/java/org/apache/commons/cli/GnuParseTest.java
@@ -0,0 +1,249 @@
+/**
+ * Copyright 2001-2004 The Apache Software Foundation
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.commons.cli;
+
+import junit.framework.Test;
+import junit.framework.TestCase;
+import junit.framework.TestSuite;
+
+
+/**
+ *
+ */
+public class GnuParseTest extends TestCase {
+ private Options _options = null;
+ private CommandLineParser _parser = null;
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static Test suite() {
+ return new TestSuite(GnuParseTest.class);
+ }
+
+ /**
+ * Creates a new GnuParseTest object.
+ *
+ * @param name DOCUMENT ME!
+ */
+ public GnuParseTest(String name) {
+ super(name);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void setUp() {
+ _options = new Options().addOption("a", "enable-a", false, "turn [a] on or off")
+ .addOption("b", "bfile", true, "set the value of [b]")
+ .addOption("c", "copt", false, "turn [c] on or off");
+
+ _parser = new GnuParser();
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void tearDown() {
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testSimpleShort() {
+ String[] args = new String[] { "-a", "-b", "toast", "foo", "bar" };
+
+ try {
+ CommandLine cl = _parser.parse(_options, args);
+
+ assertTrue("Confirm -a is set", cl.hasOption("a"));
+ assertTrue("Confirm -b is set", cl.hasOption("b"));
+ assertTrue("Confirm arg of -b", cl.getOptionValue("b").equals("toast"));
+ assertTrue("Confirm size of extra args", cl.getArgList().size() == 2);
+ } catch (ParseException e) {
+ fail(e.toString());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testSimpleLong() {
+ String[] args = new String[] { "--enable-a", "--bfile", "toast", "foo", "bar" };
+
+ try {
+ CommandLine cl = _parser.parse(_options, args);
+
+ assertTrue("Confirm -a is set", cl.hasOption("a"));
+ assertTrue("Confirm -b is set", cl.hasOption("b"));
+ assertTrue("Confirm arg of -b", cl.getOptionValue("b").equals("toast"));
+ assertTrue("Confirm size of extra args", cl.getArgList().size() == 2);
+ } catch (ParseException e) {
+ fail(e.toString());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testExtraOption() {
+ String[] args = new String[] { "-a", "-d", "-b", "toast", "foo", "bar" };
+
+ boolean caught = false;
+
+ try {
+ CommandLine cl = _parser.parse(_options, args);
+
+ assertTrue("Confirm -a is set", cl.hasOption("a"));
+ assertTrue("Confirm -b is set", cl.hasOption("b"));
+ assertTrue("confirm arg of -b", cl.getOptionValue("b").equals("toast"));
+ assertTrue("Confirm size of extra args", cl.getArgList().size() == 3);
+ } catch (UnrecognizedOptionException e) {
+ caught = true;
+ } catch (ParseException e) {
+ fail(e.toString());
+ }
+
+ assertTrue("Confirm UnrecognizedOptionException caught", caught);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testMissingArg() {
+ String[] args = new String[] { "-b" };
+
+ boolean caught = false;
+
+ try {
+ CommandLine cl = _parser.parse(_options, args);
+ } catch (MissingArgumentException e) {
+ caught = true;
+ } catch (ParseException e) {
+ fail(e.toString());
+ }
+
+ assertTrue("Confirm MissingArgumentException caught", caught);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testStop() {
+ String[] args = new String[] { "-c", "foober", "-b", "toast" };
+
+ try {
+ CommandLine cl = _parser.parse(_options, args, true);
+ assertTrue("Confirm -c is set", cl.hasOption("c"));
+ assertTrue("Confirm 3 extra args: " + cl.getArgList().size(),
+ cl.getArgList().size() == 3);
+ } catch (ParseException e) {
+ fail(e.toString());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testMultiple() {
+ String[] args = new String[] { "-c", "foobar", "-b", "toast" };
+
+ try {
+ CommandLine cl = _parser.parse(_options, args, true);
+ assertTrue("Confirm -c is set", cl.hasOption("c"));
+ assertTrue("Confirm 3 extra args: " + cl.getArgList().size(),
+ cl.getArgList().size() == 3);
+
+ cl = _parser.parse(_options, cl.getArgs());
+
+ assertTrue("Confirm -c is not set", !cl.hasOption("c"));
+ assertTrue("Confirm -b is set", cl.hasOption("b"));
+ assertTrue("Confirm arg of -b", cl.getOptionValue("b").equals("toast"));
+ assertTrue("Confirm 1 extra arg: " + cl.getArgList().size(),
+ cl.getArgList().size() == 1);
+ assertTrue("Confirm value of extra arg: " + cl.getArgList().get(0),
+ cl.getArgList().get(0).equals("foobar"));
+ } catch (ParseException e) {
+ fail(e.toString());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testMultipleWithLong() {
+ String[] args = new String[] { "--copt", "foobar", "--bfile", "toast" };
+
+ try {
+ CommandLine cl = _parser.parse(_options, args, true);
+ assertTrue("Confirm -c is set", cl.hasOption("c"));
+ assertTrue("Confirm 3 extra args: " + cl.getArgList().size(),
+ cl.getArgList().size() == 3);
+
+ cl = _parser.parse(_options, cl.getArgs());
+
+ assertTrue("Confirm -c is not set", !cl.hasOption("c"));
+ assertTrue("Confirm -b is set", cl.hasOption("b"));
+ assertTrue("Confirm arg of -b", cl.getOptionValue("b").equals("toast"));
+ assertTrue("Confirm 1 extra arg: " + cl.getArgList().size(),
+ cl.getArgList().size() == 1);
+ assertTrue("Confirm value of extra arg: " + cl.getArgList().get(0),
+ cl.getArgList().get(0).equals("foobar"));
+ } catch (ParseException e) {
+ fail(e.toString());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testDoubleDash() {
+ String[] args = new String[] { "--copt", "--", "-b", "toast" };
+
+ try {
+ CommandLine cl = _parser.parse(_options, args);
+
+ assertTrue("Confirm -c is set", cl.hasOption("c"));
+ assertTrue("Confirm -b is not set", !cl.hasOption("b"));
+ assertTrue("Confirm 2 extra args: " + cl.getArgList().size(),
+ cl.getArgList().size() == 2);
+ } catch (ParseException e) {
+ fail(e.toString());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testSingleDash() {
+ String[] args = new String[] { "--copt", "-b", "-", "-a", "-" };
+
+ try {
+ CommandLine cl = _parser.parse(_options, args);
+
+ assertTrue("Confirm -a is set", cl.hasOption("a"));
+ assertTrue("Confirm -b is set", cl.hasOption("b"));
+ assertTrue("Confirm arg of -b", cl.getOptionValue("b").equals("-"));
+ assertTrue("Confirm 1 extra arg: " + cl.getArgList().size(), cl.getArgList().size() == 1);
+ assertTrue("Confirm value of extra arg: " + cl.getArgList().get(0),
+ cl.getArgList().get(0).equals("-"));
+ } catch (ParseException e) {
+ fail(e.toString());
+ }
+ }
+}
diff --git a/corelibs/commons-cli-1.x-cytocape-custom/src/test/java/org/apache/commons/cli/HelpFormatterExamples.java b/corelibs/commons-cli-1.x-cytocape-custom/src/test/java/org/apache/commons/cli/HelpFormatterExamples.java
new file mode 100644
index 0000000..9f594b1
--- /dev/null
+++ b/corelibs/commons-cli-1.x-cytocape-custom/src/test/java/org/apache/commons/cli/HelpFormatterExamples.java
@@ -0,0 +1,114 @@
+/**
+ * Copyright 2001-2004 The Apache Software Foundation
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.commons.cli;
+
+
+/**
+ * A sample program shpwing the use of Options and the HelpFormatter class
+ *
+ * @author Slawek Zachcial
+ **/
+public class HelpFormatterExamples {
+ // --------------------------------------------------------------- Constants
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ */
+ public static void main(String[] args) {
+ System.out.println("\n#\n# 'man' example\n#");
+ manExample();
+
+ /*
+ System.out.println("\n#\n# 'bzip2' example\n#");
+ bzip2Example();
+ System.out.println("\n#\n# 'ls' example\n#");
+ lsExample();
+ */
+ }
+
+ static void manExample() {
+ String cmdLine = "man [-c|-f|-k|-w|-tZT device] [-adlhu7V] [-Mpath] [-Ppager] [-Slist] "
+ + "[-msystem] [-pstring] [-Llocale] [-eextension] [section] page ...";
+ Options opts = new Options().addOption("a", "all", false, "find all matching manual pages.")
+ .addOption("d", "debug", false, "emit debugging messages.")
+ .addOption("e", "extension", false,
+ "limit search to extension type 'extension'.")
+ .addOption("f", "whatis", false, "equivalent to whatis.")
+ .addOption("k", "apropos", false, "equivalent to apropos.")
+ .addOption("w", "location", false,
+ "print physical location of man page(s).")
+ .addOption("l", "local-file", false,
+ "interpret 'page' argument(s) as local filename(s)")
+ .addOption("u", "update", false,
+ "force a cache consistency check.")
+ .//FIXME - should generate -r,--prompt string
+ addOption("r", "prompt", true, "provide 'less' pager with prompt.")
+ .addOption("c", "catman", false,
+ "used by catman to reformat out of date cat pages.")
+ .addOption("7", "ascii", false,
+ "display ASCII translation or certain latin1 chars.")
+ .addOption("t", "troff", false, "use troff format pages.")
+ .//FIXME - should generate -T,--troff-device device
+ addOption("T", "troff-device", true, "use groff with selected device.")
+ .addOption("Z", "ditroff", false,
+ "use groff with selected device.")
+ .addOption("D", "default", false,
+ "reset all options to their default values.")
+ .//FIXME - should generate -M,--manpath path
+ addOption("M", "manpath", true, "set search path for manual pages to 'path'.")
+ .//FIXME - should generate -P,--pager pager
+ addOption("P", "pager", true, "use program 'pager' to display output.")
+ .//FIXME - should generate -S,--sections list
+ addOption("S", "sections", true, "use colon separated section list.")
+ .//FIXME - should generate -m,--systems system
+ addOption("m", "systems", true, "search for man pages from other unix system(s).")
+ .//FIXME - should generate -L,--locale locale
+ addOption("L", "locale", true, "defaine the locale for this particular man search.")
+ .//FIXME - should generate -p,--preprocessor string
+ addOption("p", "preprocessor", true,
+ "string indicates which preprocessor to run.\n"
+ + " e - [n]eqn p - pic t - tbl\n" + " g - grap r - refer v - vgrind")
+ .addOption("V", "version", false, "show version.")
+ .addOption("h", "help", false, "show this usage message.");
+
+ HelpFormatter hf = new HelpFormatter();
+ //hf.printHelp(cmdLine, opts);
+ hf.printHelp(60, cmdLine, null, opts, null);
+ }
+
+ static void bzip2Example() {
+ System.out.println("Coming soon");
+ }
+
+ static void lsExample() {
+ System.out.println("Coming soon");
+ }
+
+ // -------------------------------------------------------------- Attributes
+
+ // ------------------------------------------------------------ Constructors
+
+ // ------------------------------------------------------------------ Public
+
+ // --------------------------------------------------------------- Protected
+
+ // ------------------------------------------------------- Package protected
+
+ // ----------------------------------------------------------------- Private
+
+ // ----------------------------------------------------------- Inner classes
+}
diff --git a/corelibs/commons-cli-1.x-cytocape-custom/src/test/java/org/apache/commons/cli/LongOptionWithShort.java b/corelibs/commons-cli-1.x-cytocape-custom/src/test/java/org/apache/commons/cli/LongOptionWithShort.java
new file mode 100644
index 0000000..f3a6de0
--- /dev/null
+++ b/corelibs/commons-cli-1.x-cytocape-custom/src/test/java/org/apache/commons/cli/LongOptionWithShort.java
@@ -0,0 +1,105 @@
+/**
+ * Copyright 2001-2004 The Apache Software Foundation
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.commons.cli;
+
+import junit.framework.Test;
+import junit.framework.TestCase;
+import junit.framework.TestSuite;
+
+
+/**
+ * <p>
+ * This is a collection of tests that test real world
+ * applications command lines focusing on options with
+ * long and short names.
+ * </p>
+ */
+public class LongOptionWithShort extends TestCase {
+ /**
+ * Creates a new LongOptionWithShort object.
+ *
+ * @param name DOCUMENT ME!
+ */
+ public LongOptionWithShort(String name) {
+ super(name);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static Test suite() {
+ return new TestSuite(LongOptionWithShort.class);
+ }
+
+ /**
+ *
+ */
+ public void testLongOptionWithShort() {
+ Option help = new Option("h", "help", false, "print this message");
+ Option version = new Option("v", "version", false, "print version information");
+ Option newRun = new Option("n", "new", false, "Create NLT cache entries only for new items");
+ Option trackerRun = new Option("t", "tracker", false,
+ "Create NLT cache entries only for tracker items");
+
+ Option timeLimit = OptionBuilder.withLongOpt("limit").hasArg().withValueSeparator()
+ .withDescription("Set time limit for execution, in mintues")
+ .create("l");
+
+ Option age = OptionBuilder.withLongOpt("age").hasArg().withValueSeparator()
+ .withDescription("Age (in days) of cache item before being recomputed")
+ .create("a");
+
+ Option server = OptionBuilder.withLongOpt("server").hasArg().withValueSeparator()
+ .withDescription("The NLT server address").create("s");
+
+ Option numResults = OptionBuilder.withLongOpt("results").hasArg().withValueSeparator()
+ .withDescription("Number of results per item").create("r");
+
+ Option configFile = OptionBuilder.withLongOpt("file").hasArg().withValueSeparator()
+ .withDescription("Use the specified configuration file")
+ .create();
+
+ Options options = new Options();
+ options.addOption(help);
+ options.addOption(version);
+ options.addOption(newRun);
+ options.addOption(trackerRun);
+ options.addOption(timeLimit);
+ options.addOption(age);
+ options.addOption(server);
+ options.addOption(numResults);
+ options.addOption(configFile);
+
+ // create the command line parser
+ CommandLineParser parser = new PosixParser();
+
+ String[] args = new String[] { "-v", "-l", "10", "-age", "5", "-file", "filename" };
+
+ try {
+ CommandLine line = parser.parse(options, args);
+ assertTrue(line.hasOption("v"));
+ assertEquals(line.getOptionValue("l"), "10");
+ assertEquals(line.getOptionValue("limit"), "10");
+ assertEquals(line.getOptionValue("a"), "5");
+ assertEquals(line.getOptionValue("age"), "5");
+ assertEquals(line.getOptionValue("file"), "filename");
+ } catch (ParseException exp) {
+ fail("Unexpected exception:" + exp.getMessage());
+ }
+ }
+}
diff --git a/corelibs/commons-cli-1.x-cytocape-custom/src/test/java/org/apache/commons/cli/OptionBuilderTest.java b/corelibs/commons-cli-1.x-cytocape-custom/src/test/java/org/apache/commons/cli/OptionBuilderTest.java
new file mode 100644
index 0000000..1e264c9
--- /dev/null
+++ b/corelibs/commons-cli-1.x-cytocape-custom/src/test/java/org/apache/commons/cli/OptionBuilderTest.java
@@ -0,0 +1,181 @@
+/**
+ * Copyright 2001-2004 The Apache Software Foundation
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.commons.cli;
+
+import junit.framework.Test;
+import junit.framework.TestCase;
+import junit.framework.TestSuite;
+
+import junit.textui.TestRunner;
+
+
+/**
+ *
+ */
+public class OptionBuilderTest extends TestCase {
+ /**
+ * Creates a new OptionBuilderTest object.
+ *
+ * @param name DOCUMENT ME!
+ */
+ public OptionBuilderTest(String name) {
+ super(name);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static Test suite() {
+ return new TestSuite(OptionBuilderTest.class);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ */
+ public static void main(String[] args) {
+ TestRunner.run(suite());
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testCompleteOption() {
+ Option simple = OptionBuilder.withLongOpt("simple option").hasArg().isRequired().hasArgs()
+ .withType(new Float(10))
+ .withDescription("this is a simple option").create('s');
+
+ assertEquals("s", simple.getOpt());
+ assertEquals("simple option", simple.getLongOpt());
+ assertEquals("this is a simple option", simple.getDescription());
+ assertEquals(simple.getType().getClass(), Float.class);
+ assertTrue(simple.hasArg());
+ assertTrue(simple.isRequired());
+ assertTrue(simple.hasArgs());
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testTwoCompleteOptions() {
+ Option simple = OptionBuilder.withLongOpt("simple option").hasArg().isRequired().hasArgs()
+ .withType(new Float(10))
+ .withDescription("this is a simple option").create('s');
+
+ assertEquals("s", simple.getOpt());
+ assertEquals("simple option", simple.getLongOpt());
+ assertEquals("this is a simple option", simple.getDescription());
+ assertEquals(simple.getType().getClass(), Float.class);
+ assertTrue(simple.hasArg());
+ assertTrue(simple.isRequired());
+ assertTrue(simple.hasArgs());
+
+ simple = OptionBuilder.withLongOpt("dimple option").hasArg()
+ .withDescription("this is a dimple option").create('d');
+
+ assertEquals("d", simple.getOpt());
+ assertEquals("dimple option", simple.getLongOpt());
+ assertEquals("this is a dimple option", simple.getDescription());
+ assertNull(simple.getType());
+ assertTrue(simple.hasArg());
+ assertTrue(!simple.isRequired());
+ assertTrue(!simple.hasArgs());
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testBaseOptionCharOpt() {
+ Option base = OptionBuilder.withDescription("option description").create('o');
+
+ assertEquals("o", base.getOpt());
+ assertEquals("option description", base.getDescription());
+ assertTrue(!base.hasArg());
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testBaseOptionStringOpt() {
+ Option base = OptionBuilder.withDescription("option description").create("o");
+
+ assertEquals("o", base.getOpt());
+ assertEquals("option description", base.getDescription());
+ assertTrue(!base.hasArg());
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testSpecialOptChars() {
+ // '?'
+ try {
+ Option opt = OptionBuilder.withDescription("help options").create('?');
+ assertEquals("?", opt.getOpt());
+ } catch (IllegalArgumentException arg) {
+ fail("IllegalArgumentException caught");
+ }
+
+ // '@'
+ try {
+ Option opt = OptionBuilder.withDescription("read from stdin").create('@');
+ assertEquals("@", opt.getOpt());
+ } catch (IllegalArgumentException arg) {
+ fail("IllegalArgumentException caught");
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testOptionArgNumbers() {
+ Option opt = OptionBuilder.withDescription("option description").hasArgs(2).create('o');
+ assertEquals(2, opt.getArgs());
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testIllegalOptions() {
+ // bad single character option
+ try {
+ Option opt = OptionBuilder.withDescription("option description").create('"');
+ fail("IllegalArgumentException not caught");
+ } catch (IllegalArgumentException exp) {
+ // success
+ }
+
+ // bad character in option string
+ try {
+ Option opt = OptionBuilder.create("opt`");
+ fail("IllegalArgumentException not caught");
+ } catch (IllegalArgumentException exp) {
+ // success
+ }
+
+ // valid option
+ try {
+ Option opt = OptionBuilder.create("opt");
+
+ // success
+ } catch (IllegalArgumentException exp) {
+ fail("IllegalArgumentException caught");
+ }
+ }
+}
diff --git a/corelibs/commons-cli-1.x-cytocape-custom/src/test/java/org/apache/commons/cli/OptionGroupTest.java b/corelibs/commons-cli-1.x-cytocape-custom/src/test/java/org/apache/commons/cli/OptionGroupTest.java
new file mode 100644
index 0000000..ffe061f
--- /dev/null
+++ b/corelibs/commons-cli-1.x-cytocape-custom/src/test/java/org/apache/commons/cli/OptionGroupTest.java
@@ -0,0 +1,273 @@
+/**
+ * Copyright 2001-2004 The Apache Software Foundation
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.commons.cli;
+
+import junit.framework.Test;
+import junit.framework.TestCase;
+import junit.framework.TestSuite;
+
+
+/**
+ * @author John Keyes (john at integralsource.com)
+ * @version $Revision: 155404 $
+ */
+public class OptionGroupTest extends TestCase {
+ private Options _options = null;
+ private CommandLineParser parser = new PosixParser();
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static Test suite() {
+ return new TestSuite(OptionGroupTest.class);
+ }
+
+ /**
+ * Creates a new OptionGroupTest object.
+ *
+ * @param name DOCUMENT ME!
+ */
+ public OptionGroupTest(String name) {
+ super(name);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void setUp() {
+ Option file = new Option("f", "file", false, "file to process");
+ Option dir = new Option("d", "directory", false, "directory to process");
+ OptionGroup group = new OptionGroup();
+ group.addOption(file);
+ group.addOption(dir);
+ _options = new Options().addOptionGroup(group);
+
+ Option section = new Option("s", "section", false, "section to process");
+ Option chapter = new Option("c", "chapter", false, "chapter to process");
+ OptionGroup group2 = new OptionGroup();
+ group2.addOption(section);
+ group2.addOption(chapter);
+
+ _options.addOptionGroup(group2);
+
+ Option importOpt = new Option(null, "import", false, "section to process");
+ Option exportOpt = new Option(null, "export", false, "chapter to process");
+ OptionGroup group3 = new OptionGroup();
+ group3.addOption(importOpt);
+ group3.addOption(exportOpt);
+ _options.addOptionGroup(group3);
+
+ _options.addOption("r", "revision", false, "revision number");
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void tearDown() {
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testSingleOptionFromGroup() {
+ String[] args = new String[] { "-f" };
+
+ try {
+ CommandLine cl = parser.parse(_options, args);
+
+ assertTrue("Confirm -r is NOT set", !cl.hasOption("r"));
+ assertTrue("Confirm -f is set", cl.hasOption("f"));
+ assertTrue("Confirm -d is NOT set", !cl.hasOption("d"));
+ assertTrue("Confirm -s is NOT set", !cl.hasOption("s"));
+ assertTrue("Confirm -c is NOT set", !cl.hasOption("c"));
+ assertTrue("Confirm no extra args", cl.getArgList().size() == 0);
+ } catch (ParseException e) {
+ fail(e.toString());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testSingleOption() {
+ String[] args = new String[] { "-r" };
+
+ try {
+ CommandLine cl = parser.parse(_options, args);
+
+ assertTrue("Confirm -r is set", cl.hasOption("r"));
+ assertTrue("Confirm -f is NOT set", !cl.hasOption("f"));
+ assertTrue("Confirm -d is NOT set", !cl.hasOption("d"));
+ assertTrue("Confirm -s is NOT set", !cl.hasOption("s"));
+ assertTrue("Confirm -c is NOT set", !cl.hasOption("c"));
+ assertTrue("Confirm no extra args", cl.getArgList().size() == 0);
+ } catch (ParseException e) {
+ fail(e.toString());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testTwoValidOptions() {
+ String[] args = new String[] { "-r", "-f" };
+
+ try {
+ CommandLine cl = parser.parse(_options, args);
+
+ assertTrue("Confirm -r is set", cl.hasOption("r"));
+ assertTrue("Confirm -f is set", cl.hasOption("f"));
+ assertTrue("Confirm -d is NOT set", !cl.hasOption("d"));
+ assertTrue("Confirm -s is NOT set", !cl.hasOption("s"));
+ assertTrue("Confirm -c is NOT set", !cl.hasOption("c"));
+ assertTrue("Confirm no extra args", cl.getArgList().size() == 0);
+ } catch (ParseException e) {
+ fail(e.toString());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testSingleLongOption() {
+ String[] args = new String[] { "--file" };
+
+ try {
+ CommandLine cl = parser.parse(_options, args);
+
+ assertTrue("Confirm -r is NOT set", !cl.hasOption("r"));
+ assertTrue("Confirm -f is set", cl.hasOption("f"));
+ assertTrue("Confirm -d is NOT set", !cl.hasOption("d"));
+ assertTrue("Confirm -s is NOT set", !cl.hasOption("s"));
+ assertTrue("Confirm -c is NOT set", !cl.hasOption("c"));
+ assertTrue("Confirm no extra args", cl.getArgList().size() == 0);
+ } catch (ParseException e) {
+ fail(e.toString());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testTwoValidLongOptions() {
+ String[] args = new String[] { "--revision", "--file" };
+
+ try {
+ CommandLine cl = parser.parse(_options, args);
+
+ assertTrue("Confirm -r is set", cl.hasOption("r"));
+ assertTrue("Confirm -f is set", cl.hasOption("f"));
+ assertTrue("Confirm -d is NOT set", !cl.hasOption("d"));
+ assertTrue("Confirm -s is NOT set", !cl.hasOption("s"));
+ assertTrue("Confirm -c is NOT set", !cl.hasOption("c"));
+ assertTrue("Confirm no extra args", cl.getArgList().size() == 0);
+ } catch (ParseException e) {
+ fail(e.toString());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testNoOptionsExtraArgs() {
+ String[] args = new String[] { "arg1", "arg2" };
+
+ try {
+ CommandLine cl = parser.parse(_options, args);
+
+ assertTrue("Confirm -r is NOT set", !cl.hasOption("r"));
+ assertTrue("Confirm -f is NOT set", !cl.hasOption("f"));
+ assertTrue("Confirm -d is NOT set", !cl.hasOption("d"));
+ assertTrue("Confirm -s is NOT set", !cl.hasOption("s"));
+ assertTrue("Confirm -c is NOT set", !cl.hasOption("c"));
+ assertTrue("Confirm TWO extra args", cl.getArgList().size() == 2);
+ } catch (ParseException e) {
+ fail(e.toString());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testTwoOptionsFromGroup() {
+ String[] args = new String[] { "-f", "-d" };
+
+ try {
+ CommandLine cl = parser.parse(_options, args);
+ fail("two arguments from group not allowed");
+ } catch (ParseException e) {
+ if (!(e instanceof AlreadySelectedException)) {
+ fail("incorrect exception caught:" + e.getMessage());
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testTwoLongOptionsFromGroup() {
+ String[] args = new String[] { "--file", "--directory" };
+
+ try {
+ CommandLine cl = parser.parse(_options, args);
+ fail("two arguments from group not allowed");
+ } catch (ParseException e) {
+ if (!(e instanceof AlreadySelectedException)) {
+ fail("incorrect exception caught:" + e.getMessage());
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testTwoOptionsFromDifferentGroup() {
+ String[] args = new String[] { "-f", "-s" };
+
+ try {
+ CommandLine cl = parser.parse(_options, args);
+ assertTrue("Confirm -r is NOT set", !cl.hasOption("r"));
+ assertTrue("Confirm -f is set", cl.hasOption("f"));
+ assertTrue("Confirm -d is NOT set", !cl.hasOption("d"));
+ assertTrue("Confirm -s is set", cl.hasOption("s"));
+ assertTrue("Confirm -c is NOT set", !cl.hasOption("c"));
+ assertTrue("Confirm NO extra args", cl.getArgList().size() == 0);
+ } catch (ParseException e) {
+ fail(e.toString());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testValidLongOnlyOptions() {
+ try {
+ CommandLine cl = parser.parse(_options, new String[] { "--export" });
+ assertTrue("Confirm --export is set", cl.hasOption("export"));
+ } catch (ParseException e) {
+ fail(e.toString());
+ }
+
+ try {
+ CommandLine cl = parser.parse(_options, new String[] { "--import" });
+ assertTrue("Confirm --import is set", cl.hasOption("import"));
+ } catch (ParseException e) {
+ fail(e.toString());
+ }
+ }
+}
diff --git a/corelibs/commons-cli-1.x-cytocape-custom/src/test/java/org/apache/commons/cli/OptionsTest.java b/corelibs/commons-cli-1.x-cytocape-custom/src/test/java/org/apache/commons/cli/OptionsTest.java
new file mode 100644
index 0000000..c08560b
--- /dev/null
+++ b/corelibs/commons-cli-1.x-cytocape-custom/src/test/java/org/apache/commons/cli/OptionsTest.java
@@ -0,0 +1,98 @@
+/**
+ * Copyright 2001-2004 The Apache Software Foundation
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.commons.cli;
+
+import junit.framework.Test;
+import junit.framework.TestCase;
+import junit.framework.TestSuite;
+
+import java.util.ArrayList;
+import java.util.Collection;
+
+
+/**
+ * @author Rob Oxspring roxspring at apache.org
+ * @version $Revision: 155404 $
+ */
+public class OptionsTest extends TestCase {
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static Test suite() {
+ return new TestSuite(OptionsTest.class);
+ }
+
+ /**
+ * Creates a new OptionsTest object.
+ *
+ * @param name DOCUMENT ME!
+ */
+ public OptionsTest(String name) {
+ super(name);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void setUp() {
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void tearDown() {
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testHelpOptions() {
+ Option longOnly1 = OptionBuilder.withLongOpt("long-only1").create();
+
+ Option longOnly2 = OptionBuilder.withLongOpt("long-only2").create();
+
+ Option shortOnly1 = OptionBuilder.create("1");
+
+ Option shortOnly2 = OptionBuilder.create("2");
+
+ Option bothA = OptionBuilder.withLongOpt("bothA").create("a");
+
+ Option bothB = OptionBuilder.withLongOpt("bothB").create("b");
+
+ Options options = new Options();
+ options.addOption(longOnly1);
+ options.addOption(longOnly2);
+ options.addOption(shortOnly1);
+ options.addOption(shortOnly2);
+ options.addOption(bothA);
+ options.addOption(bothB);
+
+ Collection allOptions = new ArrayList();
+ allOptions.add(longOnly1);
+ allOptions.add(longOnly2);
+ allOptions.add(shortOnly1);
+ allOptions.add(shortOnly2);
+ allOptions.add(bothA);
+ allOptions.add(bothB);
+
+ Collection helpOptions = options.helpOptions();
+
+ assertTrue("Everything in all should be in help", helpOptions.containsAll(allOptions));
+ assertTrue("Everything in help should be in all", allOptions.containsAll(helpOptions));
+ }
+}
diff --git a/corelibs/commons-cli-1.x-cytocape-custom/src/test/java/org/apache/commons/cli/ParseRequiredTest.java b/corelibs/commons-cli-1.x-cytocape-custom/src/test/java/org/apache/commons/cli/ParseRequiredTest.java
new file mode 100644
index 0000000..6c22a8a
--- /dev/null
+++ b/corelibs/commons-cli-1.x-cytocape-custom/src/test/java/org/apache/commons/cli/ParseRequiredTest.java
@@ -0,0 +1,116 @@
+/**
+ * Copyright 2001-2004 The Apache Software Foundation
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.commons.cli;
+
+import junit.framework.Test;
+import junit.framework.TestCase;
+import junit.framework.TestSuite;
+
+
+/**
+ * @author John Keyes (john at integralsource.com)
+ * @version $Revision: 155404 $
+ */
+public class ParseRequiredTest extends TestCase {
+ private Options _options = null;
+ private CommandLineParser parser = new PosixParser();
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static Test suite() {
+ return new TestSuite(ParseRequiredTest.class);
+ }
+
+ /**
+ * Creates a new ParseRequiredTest object.
+ *
+ * @param name DOCUMENT ME!
+ */
+ public ParseRequiredTest(String name) {
+ super(name);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void setUp() {
+ _options = new Options().addOption("a", "enable-a", false, "turn [a] on or off")
+ .addOption(OptionBuilder.withLongOpt("bfile").hasArg().isRequired()
+ .withDescription("set the value of [b]")
+ .create('b'));
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void tearDown() {
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testWithRequiredOption() {
+ String[] args = new String[] { "-b", "file" };
+
+ try {
+ CommandLine cl = parser.parse(_options, args);
+
+ assertTrue("Confirm -a is NOT set", !cl.hasOption("a"));
+ assertTrue("Confirm -b is set", cl.hasOption("b"));
+ assertTrue("Confirm arg of -b", cl.getOptionValue("b").equals("file"));
+ assertTrue("Confirm NO of extra args", cl.getArgList().size() == 0);
+ } catch (ParseException e) {
+ fail(e.toString());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testOptionAndRequiredOption() {
+ String[] args = new String[] { "-a", "-b", "file" };
+
+ try {
+ CommandLine cl = parser.parse(_options, args);
+
+ assertTrue("Confirm -a is set", cl.hasOption("a"));
+ assertTrue("Confirm -b is set", cl.hasOption("b"));
+ assertTrue("Confirm arg of -b", cl.getOptionValue("b").equals("file"));
+ assertTrue("Confirm NO of extra args", cl.getArgList().size() == 0);
+ } catch (ParseException e) {
+ fail(e.toString());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testMissingRequiredOption() {
+ String[] args = new String[] { "-a" };
+
+ try {
+ CommandLine cl = parser.parse(_options, args);
+ fail("exception should have been thrown");
+ } catch (ParseException e) {
+ if (!(e instanceof MissingOptionException)) {
+ fail("expected to catch MissingOptionException");
+ }
+ }
+ }
+}
diff --git a/corelibs/commons-cli-1.x-cytocape-custom/src/test/java/org/apache/commons/cli/ParseTest.java b/corelibs/commons-cli-1.x-cytocape-custom/src/test/java/org/apache/commons/cli/ParseTest.java
new file mode 100644
index 0000000..bfc975a
--- /dev/null
+++ b/corelibs/commons-cli-1.x-cytocape-custom/src/test/java/org/apache/commons/cli/ParseTest.java
@@ -0,0 +1,269 @@
+/**
+ * Copyright 2001-2004 The Apache Software Foundation
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.commons.cli;
+
+import junit.framework.Test;
+import junit.framework.TestCase;
+import junit.framework.TestSuite;
+
+
+/**
+ *
+ */
+public class ParseTest extends TestCase {
+ private Options _options = null;
+ private CommandLineParser _parser = null;
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static Test suite() {
+ return new TestSuite(ParseTest.class);
+ }
+
+ /**
+ * Creates a new ParseTest object.
+ *
+ * @param name DOCUMENT ME!
+ */
+ public ParseTest(String name) {
+ super(name);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void setUp() {
+ _options = new Options().addOption("a", "enable-a", false, "turn [a] on or off")
+ .addOption("b", "bfile", true, "set the value of [b]")
+ .addOption("c", "copt", false, "turn [c] on or off");
+
+ _parser = new PosixParser();
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void tearDown() {
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testSimpleShort() {
+ String[] args = new String[] { "-a", "-b", "toast", "foo", "bar" };
+
+ try {
+ CommandLine cl = _parser.parse(_options, args);
+
+ assertTrue("Confirm -a is set", cl.hasOption("a"));
+ assertTrue("Confirm -b is set", cl.hasOption("b"));
+ assertTrue("Confirm arg of -b", cl.getOptionValue("b").equals("toast"));
+ assertTrue("Confirm size of extra args", cl.getArgList().size() == 2);
+ } catch (ParseException e) {
+ fail(e.toString());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testSimpleLong() {
+ String[] args = new String[] { "--enable-a", "--bfile", "toast", "foo", "bar" };
+
+ try {
+ CommandLine cl = _parser.parse(_options, args);
+
+ assertTrue("Confirm -a is set", cl.hasOption("a"));
+ assertTrue("Confirm -b is set", cl.hasOption("b"));
+ assertTrue("Confirm arg of -b", cl.getOptionValue("b").equals("toast"));
+ assertTrue("Confirm arg of --bfile", cl.getOptionValue("bfile").equals("toast"));
+ assertTrue("Confirm size of extra args", cl.getArgList().size() == 2);
+ } catch (ParseException e) {
+ fail(e.toString());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testComplexShort() {
+ String[] args = new String[] { "-acbtoast", "foo", "bar" };
+
+ try {
+ CommandLine cl = _parser.parse(_options, args);
+
+ assertTrue("Confirm -a is set", cl.hasOption("a"));
+ assertTrue("Confirm -b is set", cl.hasOption("b"));
+ assertTrue("Confirm -c is set", cl.hasOption("c"));
+ assertTrue("Confirm arg of -b", cl.getOptionValue("b").equals("toast"));
+ assertTrue("Confirm size of extra args", cl.getArgList().size() == 2);
+ } catch (ParseException e) {
+ fail(e.toString());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testExtraOption() {
+ String[] args = new String[] { "-adbtoast", "foo", "bar" };
+
+ boolean caught = false;
+
+ try {
+ CommandLine cl = _parser.parse(_options, args);
+
+ assertTrue("Confirm -a is set", cl.hasOption("a"));
+ assertTrue("Confirm -b is set", cl.hasOption("b"));
+ assertTrue("confirm arg of -b", cl.getOptionValue("b").equals("toast"));
+ assertTrue("Confirm size of extra args", cl.getArgList().size() == 3);
+ } catch (UnrecognizedOptionException e) {
+ caught = true;
+ } catch (ParseException e) {
+ fail(e.toString());
+ }
+
+ assertTrue("Confirm UnrecognizedOptionException caught", caught);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testMissingArg() {
+ String[] args = new String[] { "-acb" };
+
+ boolean caught = false;
+
+ try {
+ CommandLine cl = _parser.parse(_options, args);
+ } catch (MissingArgumentException e) {
+ caught = true;
+ } catch (ParseException e) {
+ fail(e.toString());
+ }
+
+ assertTrue("Confirm MissingArgumentException caught", caught);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testStop() {
+ String[] args = new String[] { "-c", "foober", "-btoast" };
+
+ try {
+ CommandLine cl = _parser.parse(_options, args, true);
+ assertTrue("Confirm -c is set", cl.hasOption("c"));
+ assertTrue("Confirm 2 extra args: " + cl.getArgList().size(),
+ cl.getArgList().size() == 2);
+ } catch (ParseException e) {
+ fail(e.toString());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testMultiple() {
+ String[] args = new String[] { "-c", "foobar", "-btoast" };
+
+ try {
+ CommandLine cl = _parser.parse(_options, args, true);
+ assertTrue("Confirm -c is set", cl.hasOption("c"));
+ assertTrue("Confirm 2 extra args: " + cl.getArgList().size(),
+ cl.getArgList().size() == 2);
+
+ cl = _parser.parse(_options, cl.getArgs());
+
+ assertTrue("Confirm -c is not set", !cl.hasOption("c"));
+ assertTrue("Confirm -b is set", cl.hasOption("b"));
+ assertTrue("Confirm arg of -b", cl.getOptionValue("b").equals("toast"));
+ assertTrue("Confirm 1 extra arg: " + cl.getArgList().size(),
+ cl.getArgList().size() == 1);
+ assertTrue("Confirm value of extra arg: " + cl.getArgList().get(0),
+ cl.getArgList().get(0).equals("foobar"));
+ } catch (ParseException e) {
+ fail(e.toString());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testMultipleWithLong() {
+ String[] args = new String[] { "--copt", "foobar", "--bfile", "toast" };
+
+ try {
+ CommandLine cl = _parser.parse(_options, args, true);
+ assertTrue("Confirm -c is set", cl.hasOption("c"));
+ assertTrue("Confirm 3 extra args: " + cl.getArgList().size(),
+ cl.getArgList().size() == 3);
+
+ cl = _parser.parse(_options, cl.getArgs());
+
+ assertTrue("Confirm -c is not set", !cl.hasOption("c"));
+ assertTrue("Confirm -b is set", cl.hasOption("b"));
+ assertTrue("Confirm arg of -b", cl.getOptionValue("b").equals("toast"));
+ assertTrue("Confirm 1 extra arg: " + cl.getArgList().size(),
+ cl.getArgList().size() == 1);
+ assertTrue("Confirm value of extra arg: " + cl.getArgList().get(0),
+ cl.getArgList().get(0).equals("foobar"));
+ } catch (ParseException e) {
+ fail(e.toString());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testDoubleDash() {
+ String[] args = new String[] { "--copt", "--", "-b", "toast" };
+
+ try {
+ CommandLine cl = _parser.parse(_options, args);
+
+ assertTrue("Confirm -c is set", cl.hasOption("c"));
+ assertTrue("Confirm -b is not set", !cl.hasOption("b"));
+ assertTrue("Confirm 2 extra args: " + cl.getArgList().size(),
+ cl.getArgList().size() == 2);
+ } catch (ParseException e) {
+ fail(e.toString());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testSingleDash() {
+ String[] args = new String[] { "--copt", "-b", "-", "-a", "-" };
+
+ try {
+ CommandLine cl = _parser.parse(_options, args);
+
+ assertTrue("Confirm -a is set", cl.hasOption("a"));
+ assertTrue("Confirm -b is set", cl.hasOption("b"));
+ assertTrue("Confirm arg of -b", cl.getOptionValue("b").equals("-"));
+ assertTrue("Confirm 1 extra arg: " + cl.getArgList().size(), cl.getArgList().size() == 1);
+ assertTrue("Confirm value of extra arg: " + cl.getArgList().get(0),
+ cl.getArgList().get(0).equals("-"));
+ } catch (ParseException e) {
+ fail(e.toString());
+ }
+ }
+}
diff --git a/corelibs/commons-cli-1.x-cytocape-custom/src/test/java/org/apache/commons/cli/PatternOptionBuilderTest.java b/corelibs/commons-cli-1.x-cytocape-custom/src/test/java/org/apache/commons/cli/PatternOptionBuilderTest.java
new file mode 100644
index 0000000..b8e6487
--- /dev/null
+++ b/corelibs/commons-cli-1.x-cytocape-custom/src/test/java/org/apache/commons/cli/PatternOptionBuilderTest.java
@@ -0,0 +1,103 @@
+/**
+ * Copyright 2001-2004 The Apache Software Foundation
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.commons.cli;
+
+import junit.framework.TestCase;
+import junit.framework.TestSuite;
+
+
+/**
+ * Test case for the PatternOptionBuilder class
+ *
+ * @author Henri Yandell
+ **/
+public class PatternOptionBuilderTest extends TestCase {
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ */
+ public static void main(String[] args) {
+ String[] testName = { PatternOptionBuilderTest.class.getName() };
+ junit.textui.TestRunner.main(testName);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static TestSuite suite() {
+ return new TestSuite(PatternOptionBuilderTest.class);
+ }
+
+ /**
+ * Creates a new PatternOptionBuilderTest object.
+ *
+ * @param s DOCUMENT ME!
+ */
+ public PatternOptionBuilderTest(String s) {
+ super(s);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testSimplePattern() {
+ try {
+ Options options = PatternOptionBuilder.parsePattern("a:b at cde>f+n%t/");
+ String[] args = new String[] {
+ "-c", "-a", "foo", "-b", "java.util.Vector", "-e", "build.xml", "-f",
+ "java.util.Calendar", "-n", "4.5", "-t",
+ "http://jakarta.apache.org/"
+ };
+
+ CommandLineParser parser = new PosixParser();
+ CommandLine line = parser.parse(options, args);
+
+ // tests the char methods of CommandLine that delegate to
+ // the String methods
+ assertEquals("flag a", "foo", line.getOptionValue("a"));
+ assertEquals("flag a", "foo", line.getOptionValue('a'));
+ assertEquals("string flag a", "foo", line.getOptionObject("a"));
+ assertEquals("string flag a", "foo", line.getOptionObject('a'));
+ assertEquals("object flag b", new java.util.Vector(), line.getOptionObject("b"));
+ assertEquals("object flag b", new java.util.Vector(), line.getOptionObject('b'));
+ assertEquals("boolean true flag c", true, line.hasOption("c"));
+ assertEquals("boolean true flag c", true, line.hasOption('c'));
+ assertEquals("boolean false flag d", false, line.hasOption("d"));
+ assertEquals("boolean false flag d", false, line.hasOption('d'));
+ assertEquals("file flag e", new java.io.File("build.xml"), line.getOptionObject("e"));
+ assertEquals("file flag e", new java.io.File("build.xml"), line.getOptionObject('e'));
+ assertEquals("class flag f", java.util.Calendar.class, line.getOptionObject("f"));
+ assertEquals("class flag f", java.util.Calendar.class, line.getOptionObject('f'));
+ assertEquals("number flag n", new Float(4.5), line.getOptionObject("n"));
+ assertEquals("number flag n", new Float(4.5), line.getOptionObject('n'));
+ assertEquals("url flag t", new java.net.URL("http://jakarta.apache.org/"),
+ line.getOptionObject("t"));
+ assertEquals("url flag t", new java.net.URL("http://jakarta.apache.org/"),
+ line.getOptionObject('t'));
+
+ /// DATES NOT SUPPORTED YET.
+ // assertEquals("number flag t", new java.util.Date(1023400137276L), line.getOptionObject('z'));
+ // input is: "Thu Jun 06 17:48:57 EDT 2002"
+ } catch (ParseException exp) {
+ fail(exp.getMessage());
+ } catch (java.net.MalformedURLException exp) {
+ fail(exp.getMessage());
+ }
+ }
+}
diff --git a/corelibs/commons-cli-1.x-cytocape-custom/src/test/java/org/apache/commons/cli/TestHelpFormatter.java b/corelibs/commons-cli-1.x-cytocape-custom/src/test/java/org/apache/commons/cli/TestHelpFormatter.java
new file mode 100644
index 0000000..1bcd9ec
--- /dev/null
+++ b/corelibs/commons-cli-1.x-cytocape-custom/src/test/java/org/apache/commons/cli/TestHelpFormatter.java
@@ -0,0 +1,190 @@
+/**
+ * Copyright 2001-2004 The Apache Software Foundation
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.commons.cli;
+
+import junit.framework.TestCase;
+import junit.framework.TestSuite;
+
+import java.io.ByteArrayOutputStream;
+import java.io.PrintWriter;
+
+
+/**
+ * Test case for the HelpFormatter class
+ *
+ * @author Slawek Zachcial
+ * @author John Keyes ( john at integralsource.com )
+ **/
+public class TestHelpFormatter extends TestCase {
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ */
+ public static void main(String[] args) {
+ String[] testName = { TestHelpFormatter.class.getName() };
+ junit.textui.TestRunner.main(testName);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static TestSuite suite() {
+ return new TestSuite(TestHelpFormatter.class);
+ }
+
+ /**
+ * Creates a new TestHelpFormatter object.
+ *
+ * @param s DOCUMENT ME!
+ */
+ public TestHelpFormatter(String s) {
+ super(s);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testFindWrapPos() throws Exception {
+ HelpFormatter hf = new HelpFormatter();
+
+ String text = "This is a test.";
+ //text width should be max 8; the wrap postition is 7
+ assertEquals("wrap position", 7, hf.findWrapPos(text, 8, 0));
+ //starting from 8 must give -1 - the wrap pos is after end
+ assertEquals("wrap position 2", -1, hf.findWrapPos(text, 8, 8));
+ //if there is no a good position before width to make a wrapping look for the next one
+ text = "aaaa aa";
+ assertEquals("wrap position 3", 4, hf.findWrapPos(text, 3, 0));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testPrintWrapped() throws Exception {
+ StringBuffer sb = new StringBuffer();
+ HelpFormatter hf = new HelpFormatter();
+
+ String text = "This is a test.";
+ String expected;
+
+ expected = "This is a" + hf.getNewLine() + "test.";
+ hf.renderWrappedText(sb, 12, 0, text);
+ assertEquals("single line text", expected, sb.toString());
+
+ sb.setLength(0);
+ expected = "This is a" + hf.getNewLine() + " test.";
+ hf.renderWrappedText(sb, 12, 4, text);
+ assertEquals("single line padded text", expected, sb.toString());
+
+ text = "aaaa aaaa aaaa" + hf.getNewLine() + "aaaaaa" + hf.getNewLine() + "aaaaa";
+
+ expected = text;
+ sb.setLength(0);
+ hf.renderWrappedText(sb, 16, 0, text);
+ assertEquals("multi line text", expected, sb.toString());
+
+ expected = "aaaa aaaa aaaa" + hf.getNewLine() + " aaaaaa" + hf.getNewLine()
+ + " aaaaa";
+ sb.setLength(0);
+ hf.renderWrappedText(sb, 16, 4, text);
+ assertEquals("multi-line padded text", expected, sb.toString());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testPrintOptions() throws Exception {
+ StringBuffer sb = new StringBuffer();
+ HelpFormatter hf = new HelpFormatter();
+ final int leftPad = 1;
+ final int descPad = 3;
+ final String lpad = hf.createPadding(leftPad);
+ final String dpad = hf.createPadding(descPad);
+ Options options = null;
+ String expected = null;
+
+ options = new Options().addOption("a", false, "aaaa aaaa aaaa aaaa aaaa");
+ expected = lpad + "-a" + dpad + "aaaa aaaa aaaa aaaa aaaa";
+ hf.renderOptions(sb, 60, options, leftPad, descPad);
+ assertEquals("simple non-wrapped option", expected, sb.toString());
+
+ int nextLineTabStop = leftPad + descPad + "-a".length();
+ expected = lpad + "-a" + dpad + "aaaa aaaa aaaa" + hf.getNewLine()
+ + hf.createPadding(nextLineTabStop) + "aaaa aaaa";
+ sb.setLength(0);
+ hf.renderOptions(sb, nextLineTabStop + 17, options, leftPad, descPad);
+ assertEquals("simple wrapped option", expected, sb.toString());
+
+ options = new Options().addOption("a", "aaa", false, "dddd dddd dddd dddd");
+ expected = lpad + "-a,--aaa" + dpad + "dddd dddd dddd dddd";
+ sb.setLength(0);
+ hf.renderOptions(sb, 60, options, leftPad, descPad);
+ assertEquals("long non-wrapped option", expected, sb.toString());
+
+ nextLineTabStop = leftPad + descPad + "-a,--aaa".length();
+ expected = lpad + "-a,--aaa" + dpad + "dddd dddd" + hf.getNewLine()
+ + hf.createPadding(nextLineTabStop) + "dddd dddd";
+ sb.setLength(0);
+ hf.renderOptions(sb, 25, options, leftPad, descPad);
+ assertEquals("long wrapped option", expected, sb.toString());
+
+ options = new Options().addOption("a", "aaa", false, "dddd dddd dddd dddd")
+ .addOption("b", false, "feeee eeee eeee eeee");
+ expected = lpad + "-a,--aaa" + dpad + "dddd dddd" + hf.getNewLine()
+ + hf.createPadding(nextLineTabStop) + "dddd dddd" + hf.getNewLine() + lpad
+ + "-b " + dpad + "feeee eeee" + hf.getNewLine()
+ + hf.createPadding(nextLineTabStop) + "eeee eeee";
+ sb.setLength(0);
+ hf.renderOptions(sb, 25, options, leftPad, descPad);
+ assertEquals("multiple wrapped options", expected, sb.toString());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testAutomaticUsage() throws Exception {
+ HelpFormatter hf = new HelpFormatter();
+ Options options = null;
+ String expected = "usage: app [-a]";
+ ByteArrayOutputStream out = new ByteArrayOutputStream();
+ PrintWriter pw = new PrintWriter(out);
+
+ options = new Options().addOption("a", false, "aaaa aaaa aaaa aaaa aaaa");
+ hf.printUsage(pw, 60, "app", options);
+ pw.flush();
+ assertEquals("simple auto usage", expected, out.toString().trim());
+ out.reset();
+
+ expected = "usage: app [-a] [-b]";
+ options = new Options().addOption("a", false, "aaaa aaaa aaaa aaaa aaaa")
+ .addOption("b", false, "bbb");
+ hf.printUsage(pw, 60, "app", options);
+ pw.flush();
+ assertEquals("simple auto usage", expected, out.toString().trim());
+ out.reset();
+ }
+}
diff --git a/corelibs/commons-cli-1.x-cytocape-custom/src/test/java/org/apache/commons/cli/ValueTest.java b/corelibs/commons-cli-1.x-cytocape-custom/src/test/java/org/apache/commons/cli/ValueTest.java
new file mode 100644
index 0000000..37f7bf9
--- /dev/null
+++ b/corelibs/commons-cli-1.x-cytocape-custom/src/test/java/org/apache/commons/cli/ValueTest.java
@@ -0,0 +1,394 @@
+/**
+ * Copyright 2001-2004 The Apache Software Foundation
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.commons.cli;
+
+import junit.framework.Test;
+import junit.framework.TestCase;
+import junit.framework.TestSuite;
+
+import java.util.Arrays;
+import java.util.Properties;
+
+
+/**
+ *
+ */
+public class ValueTest extends TestCase {
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static Test suite() {
+ return new TestSuite(ValueTest.class);
+ }
+
+ private CommandLine _cl = null;
+ private CommandLine _clOptional = null;
+ private Options opts = new Options();
+
+ /**
+ * Creates a new ValueTest object.
+ *
+ * @param name DOCUMENT ME!
+ */
+ public ValueTest(String name) {
+ super(name);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void setUp() {
+ opts.addOption("a", false, "toggle -a");
+
+ opts.addOption("b", true, "set -b");
+
+ opts.addOption("c", "c", false, "toggle -c");
+
+ opts.addOption("d", "d", true, "set -d");
+
+ opts.addOption(OptionBuilder.hasOptionalArg().create('e'));
+
+ opts.addOption(OptionBuilder.hasOptionalArg().withLongOpt("fish").create());
+
+ opts.addOption(OptionBuilder.hasOptionalArgs().withLongOpt("gravy").create());
+
+ opts.addOption(OptionBuilder.hasOptionalArgs(2).withLongOpt("hide").create());
+
+ opts.addOption(OptionBuilder.hasOptionalArgs(2).create('i'));
+
+ opts.addOption(OptionBuilder.hasOptionalArgs().create('j'));
+
+ opts.addOption(OptionBuilder.hasArgs().withValueSeparator(',').create('k'));
+
+ String[] args = new String[] { "-a", "-b", "foo", "--c", "--d", "bar" };
+
+ try {
+ CommandLineParser parser = new PosixParser();
+ _cl = parser.parse(opts, args);
+ } catch (ParseException e) {
+ fail("Cannot setUp() CommandLine: " + e.toString());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void tearDown() {
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testShortNoArg() {
+ assertTrue(_cl.hasOption("a"));
+ assertNull(_cl.getOptionValue("a"));
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testShortWithArg() {
+ assertTrue(_cl.hasOption("b"));
+ assertNotNull(_cl.getOptionValue("b"));
+ assertEquals(_cl.getOptionValue("b"), "foo");
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testLongNoArg() {
+ assertTrue(_cl.hasOption("c"));
+ assertNull(_cl.getOptionValue("c"));
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testLongWithArg() {
+ assertTrue(_cl.hasOption("d"));
+ assertNotNull(_cl.getOptionValue("d"));
+ assertEquals(_cl.getOptionValue("d"), "bar");
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testShortOptionalArgNoValue() {
+ String[] args = new String[] { "-e" };
+
+ try {
+ CommandLineParser parser = new PosixParser();
+ CommandLine cmd = parser.parse(opts, args);
+ assertTrue(cmd.hasOption("e"));
+ assertNull(cmd.getOptionValue("e"));
+ } catch (ParseException e) {
+ fail("Cannot setUp() CommandLine: " + e.toString());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testShortOptionalArgValue() {
+ String[] args = new String[] { "-e", "everything" };
+
+ try {
+ CommandLineParser parser = new PosixParser();
+ CommandLine cmd = parser.parse(opts, args);
+ assertTrue(cmd.hasOption("e"));
+ assertEquals("everything", cmd.getOptionValue("e"));
+ } catch (ParseException e) {
+ fail("Cannot setUp() CommandLine: " + e.toString());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testLongOptionalNoValue() {
+ String[] args = new String[] { "--fish" };
+
+ try {
+ CommandLineParser parser = new PosixParser();
+ CommandLine cmd = parser.parse(opts, args);
+ assertTrue(cmd.hasOption("fish"));
+ assertNull(cmd.getOptionValue("fish"));
+ } catch (ParseException e) {
+ fail("Cannot setUp() CommandLine: " + e.toString());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testLongOptionalArgValue() {
+ String[] args = new String[] { "--fish", "face" };
+
+ try {
+ CommandLineParser parser = new PosixParser();
+ CommandLine cmd = parser.parse(opts, args);
+ assertTrue(cmd.hasOption("fish"));
+ assertEquals("face", cmd.getOptionValue("fish"));
+ } catch (ParseException e) {
+ fail("Cannot setUp() CommandLine: " + e.toString());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testShortOptionalArgValues() {
+ String[] args = new String[] { "-j", "ink", "idea" };
+
+ try {
+ CommandLineParser parser = new PosixParser();
+ CommandLine cmd = parser.parse(opts, args);
+ assertTrue(cmd.hasOption("j"));
+ assertEquals("ink", cmd.getOptionValue("j"));
+ assertEquals("ink", cmd.getOptionValues("j")[0]);
+ assertEquals("idea", cmd.getOptionValues("j")[1]);
+ assertEquals(cmd.getArgs().length, 0);
+ } catch (ParseException e) {
+ fail("Cannot setUp() CommandLine: " + e.toString());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testLongOptionalArgValues() {
+ String[] args = new String[] { "--gravy", "gold", "garden" };
+
+ try {
+ CommandLineParser parser = new PosixParser();
+ CommandLine cmd = parser.parse(opts, args);
+ assertTrue(cmd.hasOption("gravy"));
+ assertEquals("gold", cmd.getOptionValue("gravy"));
+ assertEquals("gold", cmd.getOptionValues("gravy")[0]);
+ assertEquals("garden", cmd.getOptionValues("gravy")[1]);
+ assertEquals(cmd.getArgs().length, 0);
+ } catch (ParseException e) {
+ fail("Cannot setUp() CommandLine: " + e.toString());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testShortOptionalNArgValues() {
+ String[] args = new String[] { "-i", "ink", "idea", "isotope", "ice" };
+
+ try {
+ CommandLineParser parser = new PosixParser();
+ CommandLine cmd = parser.parse(opts, args);
+ assertTrue(cmd.hasOption("i"));
+ assertEquals("ink", cmd.getOptionValue("i"));
+ assertEquals("ink", cmd.getOptionValues("i")[0]);
+ assertEquals("idea", cmd.getOptionValues("i")[1]);
+ assertEquals(cmd.getArgs().length, 2);
+ assertEquals("isotope", cmd.getArgs()[0]);
+ assertEquals("ice", cmd.getArgs()[1]);
+ } catch (ParseException e) {
+ fail("Cannot setUp() CommandLine: " + e.toString());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testLongOptionalNArgValues() {
+ String[] args = new String[] { "--hide", "house", "hair", "head" };
+
+ CommandLineParser parser = new PosixParser();
+
+ try {
+ CommandLine cmd = parser.parse(opts, args);
+ assertTrue(cmd.hasOption("hide"));
+ assertEquals("house", cmd.getOptionValue("hide"));
+ assertEquals("house", cmd.getOptionValues("hide")[0]);
+ assertEquals("hair", cmd.getOptionValues("hide")[1]);
+ assertEquals(cmd.getArgs().length, 1);
+ assertEquals("head", cmd.getArgs()[0]);
+ } catch (ParseException e) {
+ fail("Cannot setUp() CommandLine: " + e.toString());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testPropertyOptionSingularValue() {
+ Properties properties = new Properties();
+ properties.setProperty("hide", "seek");
+
+ CommandLineParser parser = new PosixParser();
+
+ try {
+ CommandLine cmd = parser.parse(opts, null, properties);
+ assertTrue(cmd.hasOption("hide"));
+ assertEquals("seek", cmd.getOptionValue("hide"));
+ assertTrue(!cmd.hasOption("fake"));
+ } catch (ParseException e) {
+ fail("Cannot setUp() CommandLine: " + e.toString());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testPropertyOptionFlags() {
+ Properties properties = new Properties();
+ properties.setProperty("a", "true");
+ properties.setProperty("c", "yes");
+ properties.setProperty("e", "1");
+
+ CommandLineParser parser = new PosixParser();
+
+ try {
+ CommandLine cmd = parser.parse(opts, null, properties);
+ assertTrue(cmd.hasOption("a"));
+ assertTrue(cmd.hasOption("c"));
+ assertTrue(cmd.hasOption("e"));
+ } catch (ParseException e) {
+ fail("Cannot setUp() CommandLine: " + e.toString());
+ }
+
+ properties = new Properties();
+ properties.setProperty("a", "false");
+ properties.setProperty("c", "no");
+ properties.setProperty("e", "0");
+
+ try {
+ CommandLine cmd = parser.parse(opts, null, properties);
+ assertTrue(!cmd.hasOption("a"));
+ assertTrue(!cmd.hasOption("c"));
+ assertTrue(!cmd.hasOption("e"));
+ } catch (ParseException e) {
+ fail("Cannot setUp() CommandLine: " + e.toString());
+ }
+
+ properties = new Properties();
+ properties.setProperty("a", "TRUE");
+ properties.setProperty("c", "nO");
+ properties.setProperty("e", "TrUe");
+
+ try {
+ CommandLine cmd = parser.parse(opts, null, properties);
+ assertTrue(cmd.hasOption("a"));
+ assertTrue(!cmd.hasOption("c"));
+ assertTrue(cmd.hasOption("e"));
+ } catch (ParseException e) {
+ fail("Cannot setUp() CommandLine: " + e.toString());
+ }
+
+ properties = new Properties();
+ properties.setProperty("a", "just a string");
+ properties.setProperty("e", "");
+
+ try {
+ CommandLine cmd = parser.parse(opts, null, properties);
+ assertTrue(!cmd.hasOption("a"));
+ assertTrue(!cmd.hasOption("c"));
+ assertTrue(!cmd.hasOption("e"));
+ } catch (ParseException e) {
+ fail("Cannot setUp() CommandLine: " + e.toString());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testPropertyOptionMultipleValues() {
+ Properties properties = new Properties();
+ properties.setProperty("k", "one,two");
+
+ CommandLineParser parser = new PosixParser();
+
+ String[] values = new String[] { "one", "two" };
+
+ try {
+ CommandLine cmd = parser.parse(opts, null, properties);
+ assertTrue(cmd.hasOption("k"));
+ assertTrue(Arrays.equals(values, cmd.getOptionValues('k')));
+ } catch (ParseException e) {
+ fail("Cannot setUp() CommandLine: " + e.toString());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testPropertyOverrideValues() {
+ String[] args = new String[] { "-j", "found", "-i", "ink" };
+
+ Properties properties = new Properties();
+ properties.setProperty("j", "seek");
+
+ try {
+ CommandLineParser parser = new PosixParser();
+ CommandLine cmd = parser.parse(opts, args, properties);
+ assertTrue(cmd.hasOption("j"));
+ assertEquals("found", cmd.getOptionValue("j"));
+ assertTrue(cmd.hasOption("i"));
+ assertEquals("ink", cmd.getOptionValue("i"));
+ assertTrue(!cmd.hasOption("fake"));
+ } catch (ParseException e) {
+ fail("Cannot setUp() CommandLine: " + e.toString());
+ }
+ }
+}
diff --git a/corelibs/commons-cli-1.x-cytocape-custom/src/test/java/org/apache/commons/cli/ValuesTest.java b/corelibs/commons-cli-1.x-cytocape-custom/src/test/java/org/apache/commons/cli/ValuesTest.java
new file mode 100644
index 0000000..47d9d95
--- /dev/null
+++ b/corelibs/commons-cli-1.x-cytocape-custom/src/test/java/org/apache/commons/cli/ValuesTest.java
@@ -0,0 +1,241 @@
+/**
+ * Copyright 2001-2004 The Apache Software Foundation
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.commons.cli;
+
+import junit.framework.Test;
+import junit.framework.TestCase;
+import junit.framework.TestSuite;
+
+import java.util.Arrays;
+
+
+/**
+ *
+ */
+public class ValuesTest extends TestCase {
+ /** CommandLine instance */
+ private CommandLine _cmdline = null;
+ private Option _option = null;
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static Test suite() {
+ return new TestSuite(ValuesTest.class);
+ }
+
+ /**
+ * Creates a new ValuesTest object.
+ *
+ * @param name DOCUMENT ME!
+ */
+ public ValuesTest(String name) {
+ super(name);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void setUp() {
+ Options opts = new Options();
+
+ opts.addOption("a", false, "toggle -a");
+
+ opts.addOption("b", true, "set -b");
+
+ opts.addOption("c", "c", false, "toggle -c");
+
+ opts.addOption("d", "d", true, "set -d");
+
+ opts.addOption(OptionBuilder.withLongOpt("e").hasArgs().withDescription("set -e ")
+ .create('e'));
+
+ opts.addOption("f", "f", false, "jk");
+
+ opts.addOption(OptionBuilder.withLongOpt("g").hasArgs(2).withDescription("set -g")
+ .create('g'));
+
+ opts.addOption(OptionBuilder.withLongOpt("h").hasArgs(2).withDescription("set -h")
+ .create('h'));
+
+ opts.addOption(OptionBuilder.withLongOpt("i").withDescription("set -i").create('i'));
+
+ opts.addOption(OptionBuilder.withLongOpt("j").hasArgs().withDescription("set -j")
+ .withValueSeparator('=').create('j'));
+
+ opts.addOption(OptionBuilder.withLongOpt("k").hasArgs().withDescription("set -k")
+ .withValueSeparator('=').create('k'));
+
+ _option = OptionBuilder.withLongOpt("m").hasArgs().withDescription("set -m")
+ .withValueSeparator().create('m');
+
+ opts.addOption(_option);
+
+ String[] args = new String[] {
+ "-a", "-b", "foo", "--c", "--d", "bar", "-e", "one", "two", "-f", "arg1",
+ "arg2", "-g", "val1", "val2", "arg3", "-h", "val1", "-i", "-h", "val2",
+ "-jkey=value", "-j", "key=value", "-kkey1=value1", "-kkey2=value2",
+ "-mkey=value"
+ };
+
+ CommandLineParser parser = new PosixParser();
+
+ try {
+ _cmdline = parser.parse(opts, args);
+ } catch (ParseException e) {
+ fail("Cannot setUp() CommandLine: " + e.toString());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void tearDown() {
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testShortArgs() {
+ assertTrue(_cmdline.hasOption("a"));
+ assertTrue(_cmdline.hasOption("c"));
+
+ assertNull(_cmdline.getOptionValues("a"));
+ assertNull(_cmdline.getOptionValues("c"));
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testShortArgsWithValue() {
+ assertTrue(_cmdline.hasOption("b"));
+ assertTrue(_cmdline.getOptionValue("b").equals("foo"));
+ assertTrue(_cmdline.getOptionValues("b").length == 1);
+
+ assertTrue(_cmdline.hasOption("d"));
+ assertTrue(_cmdline.getOptionValue("d").equals("bar"));
+ assertTrue(_cmdline.getOptionValues("d").length == 1);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testMultipleArgValues() {
+ String[] result = _cmdline.getOptionValues("e");
+ String[] values = new String[] { "one", "two" };
+ assertTrue(_cmdline.hasOption("e"));
+ assertTrue(_cmdline.getOptionValues("e").length == 2);
+ assertTrue(Arrays.equals(values, _cmdline.getOptionValues("e")));
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testTwoArgValues() {
+ String[] result = _cmdline.getOptionValues("g");
+ String[] values = new String[] { "val1", "val2" };
+ assertTrue(_cmdline.hasOption("g"));
+ assertTrue(_cmdline.getOptionValues("g").length == 2);
+ assertTrue(Arrays.equals(values, _cmdline.getOptionValues("g")));
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testComplexValues() {
+ String[] result = _cmdline.getOptionValues("h");
+ String[] values = new String[] { "val1", "val2" };
+ assertTrue(_cmdline.hasOption("i"));
+ assertTrue(_cmdline.hasOption("h"));
+ assertTrue(_cmdline.getOptionValues("h").length == 2);
+ assertTrue(Arrays.equals(values, _cmdline.getOptionValues("h")));
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testExtraArgs() {
+ String[] args = new String[] { "arg1", "arg2", "arg3" };
+ assertTrue(_cmdline.getArgs().length == 3);
+ assertTrue(Arrays.equals(args, _cmdline.getArgs()));
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testCharSeparator() {
+ // tests the char methods of CommandLine that delegate to
+ // the String methods
+ String[] values = new String[] { "key", "value", "key", "value" };
+ assertTrue(_cmdline.hasOption("j"));
+ assertTrue(_cmdline.hasOption('j'));
+ assertEquals(4, _cmdline.getOptionValues("j").length);
+ assertEquals(4, _cmdline.getOptionValues('j').length);
+ assertTrue(Arrays.equals(values, _cmdline.getOptionValues("j")));
+ assertTrue(Arrays.equals(values, _cmdline.getOptionValues('j')));
+
+ values = new String[] { "key1", "value1", "key2", "value2" };
+ assertTrue(_cmdline.hasOption("k"));
+ assertTrue(_cmdline.hasOption('k'));
+ assertTrue(_cmdline.getOptionValues("k").length == 4);
+ assertTrue(_cmdline.getOptionValues('k').length == 4);
+ assertTrue(Arrays.equals(values, _cmdline.getOptionValues("k")));
+ assertTrue(Arrays.equals(values, _cmdline.getOptionValues('k')));
+
+ values = new String[] { "key", "value" };
+ assertTrue(_cmdline.hasOption("m"));
+ assertTrue(_cmdline.hasOption('m'));
+ assertTrue(_cmdline.getOptionValues("m").length == 2);
+ assertTrue(_cmdline.getOptionValues('m').length == 2);
+ assertTrue(Arrays.equals(values, _cmdline.getOptionValues("m")));
+ assertTrue(Arrays.equals(values, _cmdline.getOptionValues('m')));
+ }
+
+ /**
+ * jkeyes - commented out this test as the new architecture
+ * breaks this type of functionality. I have left the test
+ * here in case I get a brainwave on how to resolve this.
+ */
+
+ /*
+ public void testGetValue()
+ {
+ // the 'm' option
+ assertTrue( _option.getValues().length == 2 );
+ assertEquals( _option.getValue(), "key" );
+ assertEquals( _option.getValue( 0 ), "key" );
+ assertEquals( _option.getValue( 1 ), "value" );
+
+ try {
+ assertEquals( _option.getValue( 2 ), "key" );
+ fail( "IndexOutOfBounds not caught" );
+ }
+ catch( IndexOutOfBoundsException exp ) {
+
+ }
+
+ try {
+ assertEquals( _option.getValue( -1 ), "key" );
+ fail( "IndexOutOfBounds not caught" );
+ }
+ catch( IndexOutOfBoundsException exp ) {
+
+ }
+ }
+ */
+}
diff --git a/corelibs/commons-cli-1.x-cytocape-custom/src/test/java/org/apache/commons/cli/avalon/ClutilTestCase.java b/corelibs/commons-cli-1.x-cytocape-custom/src/test/java/org/apache/commons/cli/avalon/ClutilTestCase.java
new file mode 100644
index 0000000..c0bd9f9
--- /dev/null
+++ b/corelibs/commons-cli-1.x-cytocape-custom/src/test/java/org/apache/commons/cli/avalon/ClutilTestCase.java
@@ -0,0 +1,952 @@
+/*
+ * Copyright 2002-2005 The Apache Software Foundation
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+ * implied.
+ *
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.commons.cli.avalon;
+
+import junit.framework.TestCase;
+
+//Renamed from org.apache.avalon.excalibur.cli
+import java.util.List;
+
+
+/**
+ *
+ */
+public final class ClutilTestCase extends TestCase {
+ private static final String[] ARGLIST1 = new String[] { "--you", "are", "--all", "-cler", "kid" };
+ private static final String[] ARGLIST2 = new String[] {
+ "-Dstupid=idiot", "are", "--all", "here", "-d"
+ };
+ private static final String[] ARGLIST3 = new String[] {
+ //duplicates
+ "-Dstupid=idiot", "are", "--all", "--all", "here"
+ };
+ private static final String[] ARGLIST4 = new String[] {
+ //incompatable (blee/all)
+ "-Dstupid", "idiot", "are", "--all", "--blee", "here"
+ };
+ private static final String[] ARGLIST5 = new String[] { "-f", "myfile.txt" };
+ private static final int DEFINE_OPT = 'D';
+ private static final int CASE_CHECK_OPT = 'd';
+ private static final int YOU_OPT = 'y';
+ private static final int ALL_OPT = 'a';
+ private static final int CLEAR1_OPT = 'c';
+ private static final int CLEAR2_OPT = 'l';
+ private static final int CLEAR3_OPT = 'e';
+ private static final int CLEAR5_OPT = 'r';
+ private static final int BLEE_OPT = 'b';
+ private static final int FILE_OPT = 'f';
+ private static final int TAINT_OPT = 'T';
+ private static final CLOptionDescriptor DEFINE = new CLOptionDescriptor("define",
+ CLOptionDescriptor.ARGUMENTS_REQUIRED_2,
+ DEFINE_OPT, "define");
+ private static final CLOptionDescriptor DEFINE_MANY = new CLOptionDescriptor("define",
+ CLOptionDescriptor.ARGUMENTS_REQUIRED_2
+ | CLOptionDescriptor.DUPLICATES_ALLOWED,
+ DEFINE_OPT,
+ "define");
+ private static final CLOptionDescriptor CASE_CHECK = new CLOptionDescriptor("charCheck",
+ CLOptionDescriptor.ARGUMENT_DISALLOWED,
+ CASE_CHECK_OPT,
+ "check character case sensitivity");
+ private static final CLOptionDescriptor YOU = new CLOptionDescriptor("you",
+ CLOptionDescriptor.ARGUMENT_DISALLOWED,
+ YOU_OPT, "you");
+ private static final CLOptionDescriptor CLEAR1 = new CLOptionDescriptor("c",
+ CLOptionDescriptor.ARGUMENT_DISALLOWED,
+ CLEAR1_OPT, "c");
+ private static final CLOptionDescriptor CLEAR2 = new CLOptionDescriptor("l",
+ CLOptionDescriptor.ARGUMENT_DISALLOWED,
+ CLEAR2_OPT, "l");
+ private static final CLOptionDescriptor CLEAR3 = new CLOptionDescriptor("e",
+ CLOptionDescriptor.ARGUMENT_DISALLOWED,
+ CLEAR3_OPT, "e");
+ private static final CLOptionDescriptor CLEAR5 = new CLOptionDescriptor("r",
+ CLOptionDescriptor.ARGUMENT_DISALLOWED,
+ CLEAR5_OPT, "r");
+ private static final CLOptionDescriptor BLEE = new CLOptionDescriptor("blee",
+ CLOptionDescriptor.ARGUMENT_DISALLOWED,
+ BLEE_OPT, "blee");
+ private static final CLOptionDescriptor ALL = new CLOptionDescriptor("all",
+ CLOptionDescriptor.ARGUMENT_DISALLOWED,
+ ALL_OPT, "all",
+ new CLOptionDescriptor[] {
+ BLEE
+ });
+ private static final CLOptionDescriptor FILE = new CLOptionDescriptor("file",
+ CLOptionDescriptor.ARGUMENT_REQUIRED,
+ FILE_OPT,
+ "the build file.");
+ private static final CLOptionDescriptor TAINT = new CLOptionDescriptor("taint",
+ CLOptionDescriptor.ARGUMENT_OPTIONAL,
+ TAINT_OPT,
+ "turn on tainting checks (optional level).");
+
+ /**
+ * Creates a new ClutilTestCase object.
+ */
+ public ClutilTestCase() {
+ this("Command Line Interpreter Test Case");
+ }
+
+ /**
+ * Creates a new ClutilTestCase object.
+ *
+ * @param name DOCUMENT ME!
+ */
+ public ClutilTestCase(String name) {
+ super(name);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testOptionalArgWithSpace() {
+ final CLOptionDescriptor[] options = new CLOptionDescriptor[] { ALL, TAINT };
+
+ final String[] args = new String[] { "-T", "param", "-a" };
+
+ final CLArgsParser parser = new CLArgsParser(args, options);
+
+ assertNull(parser.getErrorString(), parser.getErrorString());
+
+ final List clOptions = parser.getArguments();
+ final int size = clOptions.size();
+
+ assertEquals("Option count", 3, size);
+
+ final CLOption option0 = (CLOption) clOptions.get(0);
+ assertEquals("Option Code: " + option0.getDescriptor().getId(), TAINT_OPT,
+ option0.getDescriptor().getId());
+ assertEquals("Option Arg: " + option0.getArgument(0), null, option0.getArgument(0));
+
+ final CLOption option1 = (CLOption) clOptions.get(1);
+ assertEquals(option1.getDescriptor().getId(), CLOption.TEXT_ARGUMENT);
+ assertEquals(option1.getArgument(0), "param");
+
+ final CLOption option2 = (CLOption) clOptions.get(2);
+ assertEquals(option2.getDescriptor().getId(), ALL_OPT);
+ assertEquals(option2.getArgument(0), null);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testOptionalArgLong() {
+ final CLOptionDescriptor[] options = new CLOptionDescriptor[] { ALL, TAINT };
+
+ // Check that optional args work woth long options
+ final String[] args = new String[] { "--taint", "param", "-a" };
+
+ final CLArgsParser parser = new CLArgsParser(args, options);
+
+ assertNull(parser.getErrorString(), parser.getErrorString());
+
+ final List clOptions = parser.getArguments();
+ final int size = clOptions.size();
+
+ assertEquals("Option count", 3, size);
+
+ final CLOption option0 = (CLOption) clOptions.get(0);
+ assertEquals("Option Code: " + option0.getDescriptor().getId(), TAINT_OPT,
+ option0.getDescriptor().getId());
+ assertEquals("Option Arg: " + option0.getArgument(0), null, option0.getArgument(0));
+
+ final CLOption option1 = (CLOption) clOptions.get(1);
+ assertEquals(CLOption.TEXT_ARGUMENT, option1.getDescriptor().getId());
+ assertEquals("param", option1.getArgument(0));
+
+ final CLOption option2 = (CLOption) clOptions.get(2);
+ assertEquals(option2.getDescriptor().getId(), ALL_OPT);
+ assertEquals(option2.getArgument(0), null);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testShortOptArgUnenteredBeforeOtherOpt() {
+ final CLOptionDescriptor[] options = new CLOptionDescriptor[] { ALL, TAINT };
+
+ final String[] args = new String[] { "-T", "-a" };
+
+ final CLArgsParser parser = new CLArgsParser(args, options);
+
+ assertNull(parser.getErrorString(), parser.getErrorString());
+
+ final List clOptions = parser.getArguments();
+ final int size = clOptions.size();
+
+ assertEquals("Option count", 2, size);
+
+ final CLOption option0 = (CLOption) clOptions.get(0);
+ assertEquals("Option Code: " + option0.getDescriptor().getId(), TAINT_OPT,
+ option0.getDescriptor().getId());
+ assertEquals("Option Arg: " + option0.getArgument(0), null, option0.getArgument(0));
+
+ final CLOption option1 = (CLOption) clOptions.get(1);
+ assertEquals(option1.getDescriptor().getId(), ALL_OPT);
+ assertEquals(option1.getArgument(0), null);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testOptionalArgsWithArgShortBeforeOtherOpt() {
+ //"-T3","-a"
+ final CLOptionDescriptor[] options = new CLOptionDescriptor[] { ALL, TAINT };
+
+ final String[] args = new String[] { "-T3", "-a" };
+
+ //System.out.println("[before parsing]");
+ final CLArgsParser parser = new CLArgsParser(args, options);
+
+ //System.out.println("[after parsing]");
+ assertNull(parser.getErrorString(), parser.getErrorString());
+
+ final List clOptions = parser.getArguments();
+ final int size = clOptions.size();
+
+ assertEquals(size, 2);
+
+ final CLOption option0 = (CLOption) clOptions.get(0);
+ assertEquals(option0.getDescriptor().getId(), TAINT_OPT);
+ assertEquals(option0.getArgument(0), "3");
+
+ final CLOption option1 = (CLOption) clOptions.get(1);
+ assertEquals(ALL_OPT, option1.getDescriptor().getId());
+ assertEquals(null, option1.getArgument(0));
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testOptionalArgsNoArgShortBeforeOtherOpt() {
+ //"-T","-a"
+ final CLOptionDescriptor[] options = new CLOptionDescriptor[] { ALL, TAINT };
+
+ final String[] args = new String[] { "-T", "-a" };
+
+ //System.out.println("[before parsing]");
+ final CLArgsParser parser = new CLArgsParser(args, options);
+
+ //System.out.println("[after parsing]");
+ assertNull(parser.getErrorString(), parser.getErrorString());
+
+ final List clOptions = parser.getArguments();
+ final int size = clOptions.size();
+
+ assertEquals(size, 2);
+
+ final CLOption option0 = (CLOption) clOptions.get(0);
+ assertEquals(TAINT_OPT, option0.getDescriptor().getId());
+ assertEquals(null, option0.getArgument(0));
+
+ final CLOption option1 = (CLOption) clOptions.get(1);
+ assertEquals(ALL_OPT, option1.getDescriptor().getId());
+ assertEquals(null, option1.getArgument(0));
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testFullParse() {
+ final CLOptionDescriptor[] options = new CLOptionDescriptor[] {
+ YOU, ALL, CLEAR1, CLEAR2, CLEAR3, CLEAR5
+ };
+
+ final CLArgsParser parser = new CLArgsParser(ARGLIST1, options);
+
+ assertNull(parser.getErrorString(), parser.getErrorString());
+
+ final List clOptions = parser.getArguments();
+ final int size = clOptions.size();
+
+ assertEquals(size, 8);
+ assertEquals(((CLOption) clOptions.get(0)).getDescriptor().getId(), YOU_OPT);
+ assertEquals(((CLOption) clOptions.get(1)).getDescriptor().getId(), 0);
+ assertEquals(((CLOption) clOptions.get(2)).getDescriptor().getId(), ALL_OPT);
+ assertEquals(((CLOption) clOptions.get(3)).getDescriptor().getId(), CLEAR1_OPT);
+ assertEquals(((CLOption) clOptions.get(4)).getDescriptor().getId(), CLEAR2_OPT);
+ assertEquals(((CLOption) clOptions.get(5)).getDescriptor().getId(), CLEAR3_OPT);
+ assertEquals(((CLOption) clOptions.get(6)).getDescriptor().getId(), CLEAR5_OPT);
+ assertEquals(((CLOption) clOptions.get(7)).getDescriptor().getId(), 0);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testDuplicateOptions() {
+ //"-Dstupid=idiot","are","--all","--all","here"
+ final CLOptionDescriptor[] options = new CLOptionDescriptor[] { DEFINE, ALL, CLEAR1 };
+
+ final CLArgsParser parser = new CLArgsParser(ARGLIST3, options);
+
+ assertNull(parser.getErrorString(), parser.getErrorString());
+
+ final List clOptions = parser.getArguments();
+ final int size = clOptions.size();
+
+ assertEquals(size, 5);
+ assertEquals(((CLOption) clOptions.get(0)).getDescriptor().getId(), DEFINE_OPT);
+ assertEquals(((CLOption) clOptions.get(1)).getDescriptor().getId(), 0);
+ assertEquals(((CLOption) clOptions.get(2)).getDescriptor().getId(), ALL_OPT);
+ assertEquals(((CLOption) clOptions.get(3)).getDescriptor().getId(), ALL_OPT);
+ assertEquals(((CLOption) clOptions.get(4)).getDescriptor().getId(), 0);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testIncompatableOptions() {
+ final CLOptionDescriptor[] options = new CLOptionDescriptor[] { DEFINE, ALL, CLEAR1, BLEE };
+
+ final CLArgsParser parser = new CLArgsParser(ARGLIST4, options);
+
+ assertNotNull(parser.getErrorString());
+
+ final List clOptions = parser.getArguments();
+ final int size = clOptions.size();
+
+ assertEquals(size, 5);
+ assertEquals(((CLOption) clOptions.get(0)).getDescriptor().getId(), DEFINE_OPT);
+ assertEquals(((CLOption) clOptions.get(1)).getDescriptor().getId(), 0);
+ assertEquals(((CLOption) clOptions.get(2)).getDescriptor().getId(), ALL_OPT);
+ assertEquals(((CLOption) clOptions.get(3)).getDescriptor().getId(), BLEE_OPT);
+ assertEquals(((CLOption) clOptions.get(4)).getDescriptor().getId(), 0);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testSingleArg() {
+ final CLOptionDescriptor[] options = new CLOptionDescriptor[] { FILE };
+
+ final CLArgsParser parser = new CLArgsParser(ARGLIST5, options);
+
+ assertNull(parser.getErrorString(), parser.getErrorString());
+
+ final List clOptions = parser.getArguments();
+ final int size = clOptions.size();
+
+ assertEquals(size, 1);
+ assertEquals(((CLOption) clOptions.get(0)).getDescriptor().getId(), FILE_OPT);
+ assertEquals(((CLOption) clOptions.get(0)).getArgument(), "myfile.txt");
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testSingleArg2() {
+ final CLOptionDescriptor[] options = new CLOptionDescriptor[] { FILE };
+
+ final CLArgsParser parser = new CLArgsParser(new String[] {
+ "-f-=,=-"
+ } // Check delimiters are allowed
+ , options);
+
+ assertNull(parser.getErrorString(), parser.getErrorString());
+
+ final List clOptions = parser.getArguments();
+ final int size = clOptions.size();
+
+ assertEquals(1, size);
+ assertEquals(FILE_OPT, ((CLOption) clOptions.get(0)).getDescriptor().getId());
+ assertEquals("-=,=-", ((CLOption) clOptions.get(0)).getArgument());
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testSingleArg3() {
+ final CLOptionDescriptor[] options = new CLOptionDescriptor[] { FILE };
+
+ final CLArgsParser parser = new CLArgsParser(new String[] {
+ "--file=-=,-"
+ } // Check delimiters are allowed
+ , options);
+
+ assertNull(parser.getErrorString(), parser.getErrorString());
+
+ final List clOptions = parser.getArguments();
+ final int size = clOptions.size();
+
+ assertEquals(1, size);
+ assertEquals(FILE_OPT, ((CLOption) clOptions.get(0)).getDescriptor().getId());
+ assertEquals("-=,-", ((CLOption) clOptions.get(0)).getArgument());
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testSingleArg4() {
+ final CLOptionDescriptor[] options = new CLOptionDescriptor[] { FILE };
+
+ final CLArgsParser parser = new CLArgsParser(new String[] { "--file", "myfile.txt" },
+ options);
+
+ assertNull(parser.getErrorString(), parser.getErrorString());
+
+ final List clOptions = parser.getArguments();
+ final int size = clOptions.size();
+
+ assertEquals(1, size);
+ assertEquals(FILE_OPT, ((CLOption) clOptions.get(0)).getDescriptor().getId());
+ assertEquals("myfile.txt", ((CLOption) clOptions.get(0)).getArgument());
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testSingleArg5() {
+ final CLOptionDescriptor[] options = new CLOptionDescriptor[] { FILE };
+
+ final CLArgsParser parser = new CLArgsParser(new String[] { "-f", "myfile.txt" }, options);
+
+ assertNull(parser.getErrorString(), parser.getErrorString());
+
+ final List clOptions = parser.getArguments();
+ final int size = clOptions.size();
+
+ assertEquals(1, size);
+ assertEquals(FILE_OPT, ((CLOption) clOptions.get(0)).getDescriptor().getId());
+ assertEquals("myfile.txt", ((CLOption) clOptions.get(0)).getArgument());
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testSingleArg6() {
+ final CLOptionDescriptor[] options = new CLOptionDescriptor[] { FILE };
+
+ final CLArgsParser parser = new CLArgsParser(new String[] { "-f", "-=-" }, options);
+
+ assertNull(parser.getErrorString(), parser.getErrorString());
+
+ final List clOptions = parser.getArguments();
+ final int size = clOptions.size();
+
+ assertEquals(1, size);
+ assertEquals(FILE_OPT, ((CLOption) clOptions.get(0)).getDescriptor().getId());
+ assertEquals("-=-", ((CLOption) clOptions.get(0)).getArgument());
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testSingleArg7() {
+ final CLOptionDescriptor[] options = new CLOptionDescriptor[] { FILE };
+
+ final CLArgsParser parser = new CLArgsParser(new String[] { "--file=-=-" }, options);
+
+ assertNull(parser.getErrorString(), parser.getErrorString());
+
+ final List clOptions = parser.getArguments();
+ final int size = clOptions.size();
+
+ assertEquals(1, size);
+ assertEquals(FILE_OPT, ((CLOption) clOptions.get(0)).getDescriptor().getId());
+ assertEquals("-=-", ((CLOption) clOptions.get(0)).getArgument());
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testSingleArg8() {
+ final CLOptionDescriptor[] options = new CLOptionDescriptor[] { FILE };
+
+ final CLArgsParser parser = new CLArgsParser(new String[] { "--file", "-=-" }, options);
+
+ assertNull(parser.getErrorString(), parser.getErrorString());
+
+ final List clOptions = parser.getArguments();
+ final int size = clOptions.size();
+
+ assertEquals(1, size);
+ assertEquals(FILE_OPT, ((CLOption) clOptions.get(0)).getDescriptor().getId());
+ assertEquals("-=-", ((CLOption) clOptions.get(0)).getArgument());
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testSingleArg9() {
+ final CLOptionDescriptor[] options = new CLOptionDescriptor[] { FILE };
+
+ final CLArgsParser parser = new CLArgsParser(new String[] { "--file", "-=-" }, options);
+
+ assertNull(parser.getErrorString(), parser.getErrorString());
+
+ final List clOptions = parser.getArguments();
+ final int size = clOptions.size();
+
+ assertEquals(1, size);
+ assertEquals(FILE_OPT, ((CLOption) clOptions.get(0)).getDescriptor().getId());
+ assertEquals("-=-", ((CLOption) clOptions.get(0)).getArgument());
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testCombinedArgs1() {
+ final CLOptionDescriptor[] options = new CLOptionDescriptor[] { BLEE, TAINT };
+
+ final CLArgsParser parser = new CLArgsParser(new String[] { "-bT", "rest" }, options);
+
+ assertNull(parser.getErrorString(), parser.getErrorString());
+
+ final List clOptions = parser.getArguments();
+ final int size = clOptions.size();
+ assertEquals(3, size);
+ assertEquals(BLEE_OPT, ((CLOption) clOptions.get(0)).getDescriptor().getId());
+ assertEquals(TAINT_OPT, ((CLOption) clOptions.get(1)).getDescriptor().getId());
+ assertEquals(0, ((CLOption) clOptions.get(2)).getDescriptor().getId());
+ assertEquals("rest", ((CLOption) clOptions.get(2)).getArgument());
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testCombinedArgs2() {
+ final CLOptionDescriptor[] options = new CLOptionDescriptor[] { BLEE, TAINT, FILE };
+
+ final CLArgsParser parser = new CLArgsParser(new String[] { "-bT", "-fa" }, options);
+
+ assertNull(parser.getErrorString(), parser.getErrorString());
+
+ final List clOptions = parser.getArguments();
+ final int size = clOptions.size();
+ assertEquals(3, size);
+ assertEquals(BLEE_OPT, ((CLOption) clOptions.get(0)).getDescriptor().getId());
+ assertEquals(TAINT_OPT, ((CLOption) clOptions.get(1)).getDescriptor().getId());
+ assertEquals(FILE_OPT, ((CLOption) clOptions.get(2)).getDescriptor().getId());
+ assertEquals("a", ((CLOption) clOptions.get(2)).getArgument());
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testCombinedArgs3() {
+ final CLOptionDescriptor[] options = new CLOptionDescriptor[] { BLEE, TAINT, FILE };
+
+ final CLArgsParser parser = new CLArgsParser(new String[] {
+ "-bT", "--", "-fa"
+ } // Should not detect trailing option
+ , options);
+
+ assertNull(parser.getErrorString(), parser.getErrorString());
+
+ final List clOptions = parser.getArguments();
+ final int size = clOptions.size();
+ assertEquals(3, size);
+ assertEquals(BLEE_OPT, ((CLOption) clOptions.get(0)).getDescriptor().getId());
+ assertEquals(TAINT_OPT, ((CLOption) clOptions.get(1)).getDescriptor().getId());
+ assertEquals(0, ((CLOption) clOptions.get(2)).getDescriptor().getId());
+ assertEquals("-fa", ((CLOption) clOptions.get(2)).getArgument());
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testCombinedArgs4() {
+ final CLOptionDescriptor[] options = new CLOptionDescriptor[] { BLEE, TAINT, FILE };
+
+ final CLArgsParser parser = new CLArgsParser(new String[] {
+ "-bT", "rest", "-fa"
+ } // should detect trailing option
+ , options);
+
+ assertNull(parser.getErrorString(), parser.getErrorString());
+
+ final List clOptions = parser.getArguments();
+ final int size = clOptions.size();
+ assertEquals(4, size);
+ assertEquals(BLEE_OPT, ((CLOption) clOptions.get(0)).getDescriptor().getId());
+ assertEquals(TAINT_OPT, ((CLOption) clOptions.get(1)).getDescriptor().getId());
+ assertEquals(0, ((CLOption) clOptions.get(2)).getDescriptor().getId());
+ assertEquals("rest", ((CLOption) clOptions.get(2)).getArgument());
+ assertEquals(FILE_OPT, ((CLOption) clOptions.get(3)).getDescriptor().getId());
+ assertEquals("a", ((CLOption) clOptions.get(3)).getArgument());
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void test2ArgsParse() {
+ //"-Dstupid=idiot","are","--all","here"
+ final CLOptionDescriptor[] options = new CLOptionDescriptor[] {
+ DEFINE, ALL, CLEAR1, CASE_CHECK
+ };
+
+ final CLArgsParser parser = new CLArgsParser(ARGLIST2, options);
+
+ assertNull(parser.getErrorString(), parser.getErrorString());
+
+ final List clOptions = parser.getArguments();
+ final int size = clOptions.size();
+
+ assertEquals(size, 5);
+ assertEquals(((CLOption) clOptions.get(0)).getDescriptor().getId(), DEFINE_OPT);
+ assertEquals(((CLOption) clOptions.get(1)).getDescriptor().getId(), 0);
+ assertEquals(((CLOption) clOptions.get(2)).getDescriptor().getId(), ALL_OPT);
+ assertEquals(((CLOption) clOptions.get(3)).getDescriptor().getId(), 0);
+ assertEquals(((CLOption) clOptions.get(4)).getDescriptor().getId(), CASE_CHECK_OPT);
+
+ final CLOption option = (CLOption) clOptions.get(0);
+ assertEquals("stupid", option.getArgument(0));
+ assertEquals("idiot", option.getArgument(1));
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void test2ArgsParse2() {
+ final CLOptionDescriptor[] options = new CLOptionDescriptor[] { DEFINE };
+
+ final CLArgsParser parser = new CLArgsParser(new String[] { "--define", "a-b,c=d-e,f" }, // Check "-" is allowed in arg2
+ options);
+
+ assertNull(parser.getErrorString(), parser.getErrorString());
+
+ final List clOptions = parser.getArguments();
+ final int size = clOptions.size();
+
+ assertEquals(1, size);
+ assertEquals(DEFINE_OPT, ((CLOption) clOptions.get(0)).getDescriptor().getId());
+
+ final CLOption option = (CLOption) clOptions.get(0);
+ assertEquals("a-b,c", option.getArgument(0));
+ assertEquals("d-e,f", option.getArgument(1));
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void test2ArgsParse3() {
+ final CLOptionDescriptor[] options = new CLOptionDescriptor[] { DEFINE };
+
+ final CLArgsParser parser = new CLArgsParser(new String[] { "-D", "A-b,c", "G-e,f" },
+ options);
+
+ assertNull(parser.getErrorString(), parser.getErrorString());
+
+ final List clOptions = parser.getArguments();
+ final int size = clOptions.size();
+
+ assertEquals(1, size);
+ assertEquals(DEFINE_OPT, ((CLOption) clOptions.get(0)).getDescriptor().getId());
+
+ final CLOption option = (CLOption) clOptions.get(0);
+ assertEquals("A-b,c", option.getArgument(0));
+ assertEquals("G-e,f", option.getArgument(1));
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void test2ArgsParse4() {
+ final CLOptionDescriptor[] options = new CLOptionDescriptor[] { DEFINE_MANY };
+
+ final CLArgsParser parser = new CLArgsParser(new String[] {
+ "-Dval1=-1", "-D", "val2=-2",
+ "--define=val-3=-3", "--define", "val4-=-4"
+ }, options);
+
+ assertNull(parser.getErrorString(), parser.getErrorString());
+
+ final List clOptions = parser.getArguments();
+ final int size = clOptions.size();
+
+ assertEquals(4, size);
+
+ for (int i = 0; i < size; i++) {
+ assertEquals(DEFINE_OPT, ((CLOption) clOptions.get(i)).getDescriptor().getId());
+ }
+
+ CLOption option;
+ option = (CLOption) clOptions.get(0);
+ assertEquals("val1", option.getArgument(0));
+ assertEquals("-1", option.getArgument(1));
+
+ option = (CLOption) clOptions.get(1);
+ assertEquals("val2", option.getArgument(0));
+ assertEquals("-2", option.getArgument(1));
+
+ option = (CLOption) clOptions.get(2);
+ assertEquals("val-3", option.getArgument(0));
+ assertEquals("-3", option.getArgument(1));
+
+ option = (CLOption) clOptions.get(3);
+ assertEquals("val4-", option.getArgument(0));
+ assertEquals("-4", option.getArgument(1));
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testPartParse() {
+ final CLOptionDescriptor[] options = new CLOptionDescriptor[] { YOU };
+
+ final ParserControl control = new AbstractParserControl() {
+ public boolean isFinished(int lastOptionCode) {
+ return (lastOptionCode == YOU_OPT);
+ }
+ };
+
+ final CLArgsParser parser = new CLArgsParser(ARGLIST1, options, control);
+
+ assertNull(parser.getErrorString(), parser.getErrorString());
+
+ final List clOptions = parser.getArguments();
+ final int size = clOptions.size();
+
+ assertEquals(size, 1);
+ assertEquals(((CLOption) clOptions.get(0)).getDescriptor().getId(), YOU_OPT);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void test2PartParse() {
+ final CLOptionDescriptor[] options1 = new CLOptionDescriptor[] { YOU };
+
+ final CLOptionDescriptor[] options2 = new CLOptionDescriptor[] {
+ ALL, CLEAR1, CLEAR2, CLEAR3, CLEAR5
+ };
+
+ final ParserControl control1 = new AbstractParserControl() {
+ public boolean isFinished(int lastOptionCode) {
+ return (lastOptionCode == YOU_OPT);
+ }
+ };
+
+ final CLArgsParser parser1 = new CLArgsParser(ARGLIST1, options1, control1);
+
+ assertNull(parser1.getErrorString(), parser1.getErrorString());
+
+ final List clOptions1 = parser1.getArguments();
+ final int size1 = clOptions1.size();
+
+ assertEquals(size1, 1);
+ assertEquals(((CLOption) clOptions1.get(0)).getDescriptor().getId(), YOU_OPT);
+
+ final CLArgsParser parser2 = new CLArgsParser(parser1.getUnparsedArgs(), options2);
+
+ assertNull(parser2.getErrorString(), parser2.getErrorString());
+
+ final List clOptions2 = parser2.getArguments();
+ final int size2 = clOptions2.size();
+
+ assertEquals(size2, 7);
+ assertEquals(((CLOption) clOptions2.get(0)).getDescriptor().getId(), 0);
+ assertEquals(((CLOption) clOptions2.get(1)).getDescriptor().getId(), ALL_OPT);
+ assertEquals(((CLOption) clOptions2.get(2)).getDescriptor().getId(), CLEAR1_OPT);
+ assertEquals(((CLOption) clOptions2.get(3)).getDescriptor().getId(), CLEAR2_OPT);
+ assertEquals(((CLOption) clOptions2.get(4)).getDescriptor().getId(), CLEAR3_OPT);
+ assertEquals(((CLOption) clOptions2.get(5)).getDescriptor().getId(), CLEAR5_OPT);
+ assertEquals(((CLOption) clOptions2.get(6)).getDescriptor().getId(), 0);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void test2PartPartialParse() {
+ final CLOptionDescriptor[] options1 = new CLOptionDescriptor[] { YOU, ALL, CLEAR1 };
+
+ final CLOptionDescriptor[] options2 = new CLOptionDescriptor[] { };
+
+ final ParserControl control1 = new AbstractParserControl() {
+ public boolean isFinished(final int lastOptionCode) {
+ return (lastOptionCode == CLEAR1_OPT);
+ }
+ };
+
+ final CLArgsParser parser1 = new CLArgsParser(ARGLIST1, options1, control1);
+
+ assertNull(parser1.getErrorString(), parser1.getErrorString());
+
+ final List clOptions1 = parser1.getArguments();
+ final int size1 = clOptions1.size();
+
+ assertEquals(size1, 4);
+ assertEquals(((CLOption) clOptions1.get(0)).getDescriptor().getId(), YOU_OPT);
+ assertEquals(((CLOption) clOptions1.get(1)).getDescriptor().getId(), 0);
+ assertEquals(((CLOption) clOptions1.get(2)).getDescriptor().getId(), ALL_OPT);
+ assertEquals(((CLOption) clOptions1.get(3)).getDescriptor().getId(), CLEAR1_OPT);
+
+ assertTrue(parser1.getUnparsedArgs()[0].equals("ler"));
+
+ final CLArgsParser parser2 = new CLArgsParser(parser1.getUnparsedArgs(), options2);
+
+ assertNull(parser2.getErrorString(), parser2.getErrorString());
+
+ final List clOptions2 = parser2.getArguments();
+ final int size2 = clOptions2.size();
+
+ assertEquals(size2, 2);
+ assertEquals(((CLOption) clOptions2.get(0)).getDescriptor().getId(), 0);
+ assertEquals(((CLOption) clOptions2.get(1)).getDescriptor().getId(), 0);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testDuplicatesFail() {
+ final CLOptionDescriptor[] options = new CLOptionDescriptor[] {
+ YOU, ALL, CLEAR1, CLEAR2, CLEAR3, CLEAR5
+ };
+
+ final CLArgsParser parser = new CLArgsParser(ARGLIST1, options);
+
+ assertNull(parser.getErrorString(), parser.getErrorString());
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testIncomplete2Args() {
+ //"-Dstupid="
+ final CLOptionDescriptor[] options = new CLOptionDescriptor[] { DEFINE };
+
+ final CLArgsParser parser = new CLArgsParser(new String[] { "-Dstupid=" }, options);
+
+ assertNull(parser.getErrorString(), parser.getErrorString());
+
+ final List clOptions = parser.getArguments();
+ final int size = clOptions.size();
+
+ assertEquals(size, 1);
+
+ final CLOption option = (CLOption) clOptions.get(0);
+ assertEquals(option.getDescriptor().getId(), DEFINE_OPT);
+ assertEquals(option.getArgument(0), "stupid");
+ assertEquals(option.getArgument(1), "");
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testIncomplete2ArgsMixed() {
+ //"-Dstupid=","-c"
+ final CLOptionDescriptor[] options = new CLOptionDescriptor[] { DEFINE, CLEAR1 };
+
+ final String[] args = new String[] { "-Dstupid=", "-c" };
+
+ final CLArgsParser parser = new CLArgsParser(args, options);
+
+ assertNull(parser.getErrorString(), parser.getErrorString());
+
+ final List clOptions = parser.getArguments();
+ final int size = clOptions.size();
+
+ assertEquals(size, 2);
+ assertEquals(((CLOption) clOptions.get(1)).getDescriptor().getId(), CLEAR1_OPT);
+
+ final CLOption option = (CLOption) clOptions.get(0);
+ assertEquals(option.getDescriptor().getId(), DEFINE_OPT);
+ assertEquals(option.getArgument(0), "stupid");
+ assertEquals(option.getArgument(1), "");
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testIncomplete2ArgsMixedNoEq() {
+ //"-Dstupid","-c"
+ final CLOptionDescriptor[] options = new CLOptionDescriptor[] { DEFINE, CLEAR1 };
+
+ final String[] args = new String[] { "-DStupid", "-c" };
+
+ final CLArgsParser parser = new CLArgsParser(args, options);
+
+ assertNull(parser.getErrorString(), parser.getErrorString());
+
+ final List clOptions = parser.getArguments();
+ final int size = clOptions.size();
+
+ assertEquals(size, 2);
+ assertEquals(((CLOption) clOptions.get(1)).getDescriptor().getId(), CLEAR1_OPT);
+
+ final CLOption option = (CLOption) clOptions.get(0);
+ assertEquals(option.getDescriptor().getId(), DEFINE_OPT);
+ assertEquals(option.getArgument(0), "Stupid");
+ assertEquals(option.getArgument(1), "");
+ }
+
+ /**
+ * Test the getArgumentById and getArgumentByName lookup methods.
+ */
+ public void testArgumentLookup() {
+ final String[] args = { "-f", "testarg" };
+ final CLOptionDescriptor[] options = { FILE };
+ final CLArgsParser parser = new CLArgsParser(args, options);
+
+ CLOption optionById = parser.getArgumentById(FILE_OPT);
+ assertNotNull(optionById);
+ assertEquals(FILE_OPT, optionById.getDescriptor().getId());
+
+ CLOption optionByName = parser.getArgumentByName(FILE.getName());
+ assertNotNull(optionByName);
+ assertEquals(FILE_OPT, optionByName.getDescriptor().getId());
+ }
+
+ /**
+ * Test that you can have null long forms.
+ */
+ public void testNullLongForm() {
+ final CLOptionDescriptor test = new CLOptionDescriptor(null,
+ CLOptionDescriptor.ARGUMENT_DISALLOWED,
+ 'n', "test null long form");
+
+ final String[] args = { "-n", "testarg" };
+ final CLOptionDescriptor[] options = { test };
+ final CLArgsParser parser = new CLArgsParser(args, options);
+
+ final CLOption optionByID = parser.getArgumentById('n');
+ assertNotNull(optionByID);
+ assertEquals('n', optionByID.getDescriptor().getId());
+
+ final CLOption optionByName = parser.getArgumentByName(FILE.getName());
+ assertNull("Looking for non-existent option by name", optionByName);
+ }
+
+ /**
+ * Test that you can have null descriptions.
+ */
+ public void testNullDescription() {
+ final CLOptionDescriptor test = new CLOptionDescriptor("nulltest",
+ CLOptionDescriptor.ARGUMENT_DISALLOWED,
+ 'n', null);
+
+ final String[] args = { "-n", "testarg" };
+ final CLOptionDescriptor[] options = { test };
+ final CLArgsParser parser = new CLArgsParser(args, options);
+
+ final CLOption optionByID = parser.getArgumentById('n');
+ assertNotNull(optionByID);
+ assertEquals('n', optionByID.getDescriptor().getId());
+
+ final StringBuffer sb = CLUtil.describeOptions(options);
+ final String lineSeparator = System.getProperty("line.separator");
+ assertEquals("Testing display of null description", "\t-n, --nulltest" + lineSeparator,
+ sb.toString());
+ }
+
+ /*
+ * TODO add tests to check for:
+ * - name clash
+ * - long option abbreviations (match shortest unique abbreviation)
+ */
+}
diff --git a/corelibs/ding/README b/corelibs/ding/README
new file mode 100644
index 0000000..411e4af
--- /dev/null
+++ b/corelibs/ding/README
@@ -0,0 +1,6 @@
+
+To run the sanity test:
+
+java -cp ./ding.jar:lib/cytoscape-geom-rtree.jar:lib/cytoscape-geom-spacial.jar:lib/cytoscape-graph-dynamic.jar:lib/cytoscape-graph-fixed.jar:lib/cytoscape-render-export.jar:lib/cytoscape-render-immed.jar:lib/cytoscape-render-stateful.jar:lib/cytoscape-util-intr.jar:lib/fing.jar:lib/fing.jar:lib/giny.jar:lib/phoebe.jar ding.view.test.SanityTest
+
+
diff --git a/corelibs/ding/pom.xml b/corelibs/ding/pom.xml
new file mode 100644
index 0000000..e526c70
--- /dev/null
+++ b/corelibs/ding/pom.xml
@@ -0,0 +1,104 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>parent</artifactId>
+ <version>2.8.4-SNAPSHOT</version>
+ </parent>
+
+ <artifactId>ding</artifactId>
+ <packaging>jar</packaging>
+
+ <name>ding</name>
+
+ <!-- bootstrap for cytoscape dependencies, namely the parent POM snapshots -->
+ <repositories>
+ <repository>
+ <id>cytoscape_snapshots</id>
+ <snapshots>
+ <enabled>true</enabled>
+ </snapshots>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <name>Cytoscape Snapshots</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/</url>
+ </repository>
+ <repository>
+ <id>cytoscape_releases</id>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ <name>Cytoscape Releases</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/releases/</url>
+ </repository>
+ </repositories>
+
+ <dependencies>
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>util-intr</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>graph-dynamic</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>graph-fixed</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>giny</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>render-immed</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>render-stateful</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>render-export</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>fing</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>phoebe-dnd</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>geom-spacial</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>geom-rtree</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>undo-support</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ </dependencies>
+
+</project>
+
diff --git a/corelibs/ding/src/main/java/ding/view/ArbitraryGraphicsCanvas.java b/corelibs/ding/src/main/java/ding/view/ArbitraryGraphicsCanvas.java
new file mode 100644
index 0000000..4082716
--- /dev/null
+++ b/corelibs/ding/src/main/java/ding/view/ArbitraryGraphicsCanvas.java
@@ -0,0 +1,292 @@
+/*
+ File: ArbitraryGraphicsCanvas.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// package
+package ding.view;
+
+import giny.model.GraphPerspective;
+import giny.model.Node;
+import giny.view.NodeView;
+
+import java.awt.AlphaComposite;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Composite;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.Point;
+import java.awt.geom.AffineTransform;
+import java.awt.image.BufferedImage;
+import java.util.HashMap;
+import java.util.Map;
+
+
+/**
+ * This class extends cytoscape.view.CytoscapeCanvas. Its meant
+ * to live within a ding.view.DGraphView class. It is the canvas
+ * used for arbitrary graphics drawing (background & foreground panes).
+ */
+public class ArbitraryGraphicsCanvas extends DingCanvas implements ViewportChangeListener {
+ /**
+ * Testing boolean to quickly turn on/off anchor nodes.
+ */
+ private static final boolean USE_REPOSITION_CODE = true;
+
+ /**
+ * Our reference to the GraphPerspective our view belongs to
+ */
+ private final GraphPerspective m_graphPerspective;
+
+ /**
+ * Our reference to the DGraphView we live within
+ */
+ private final DGraphView m_dGraphView;
+
+ /**
+ * Our reference to the inner canvas
+ */
+ private final InnerCanvas m_innerCanvas;
+
+ private final Map<Component, Point> m_componentToPointMap;
+
+ /**
+ * Constructor.
+ *
+ * @param graphPerspective GraphPerspective
+ * @param dGraphView DGraphView
+ * @param innerCanvas InnerCanvas
+ * @param backgroundColor Color
+ * @param isVisible boolean
+ * @param isOpaque boolean
+ */
+ public ArbitraryGraphicsCanvas(GraphPerspective graphPerspective, DGraphView dGraphView,
+ InnerCanvas innerCanvas, Color backgroundColor,
+ boolean isVisible, boolean isOpaque) {
+ // init members
+ m_graphPerspective = graphPerspective;
+ m_dGraphView = dGraphView;
+ m_innerCanvas = innerCanvas;
+ m_backgroundColor = backgroundColor;
+ m_isVisible = isVisible;
+ m_isOpaque = isOpaque;
+
+ m_componentToPointMap = new HashMap<Component, Point>();
+ }
+
+ public Component add(Component component) {
+ if (USE_REPOSITION_CODE) {
+ final double[] nodeCanvasCoordinates = new double[2];
+ nodeCanvasCoordinates[0] = component.getX();
+ nodeCanvasCoordinates[1] = component.getY();
+
+ m_dGraphView.xformComponentToNodeCoords(nodeCanvasCoordinates);
+
+ Point nodePos=new Point( (int)nodeCanvasCoordinates[0], (int)nodeCanvasCoordinates[1]);
+
+ // add to map
+ m_componentToPointMap.put(component, nodePos);
+ }
+
+ // do our stuff
+ return super.add(component);
+ }
+
+ public void remove(Component component){
+ if (USE_REPOSITION_CODE) {
+ m_componentToPointMap.remove(component);
+ }
+
+ // do our stuff
+ super.remove(component);
+ }
+
+
+ /**
+ * Our implementation of ViewportChangeListener.
+ */
+ public void viewportChanged(int viewportWidth, int viewportHeight, double newXCenter,
+ double newYCenter, double newScaleFactor) {
+ if (USE_REPOSITION_CODE) {
+ if (setBoundsChildren())
+ repaint();
+ }
+ }
+
+ public void modifyComponentLocation(int x,int y, int componentNum){
+ if(USE_REPOSITION_CODE){
+ final Point nodePos = m_componentToPointMap.get(this.getComponent(componentNum));
+
+ final double[] nodeCanvasCoordinates = new double[2];
+ nodeCanvasCoordinates[0] = x;
+ nodeCanvasCoordinates[1] = y;
+
+ m_dGraphView.xformComponentToNodeCoords(nodeCanvasCoordinates);
+
+ nodePos.x=(int)nodeCanvasCoordinates[0];
+ nodePos.y=(int)nodeCanvasCoordinates[1];
+ }
+ }
+
+ /**
+ * Our implementation of JComponent setBounds.
+ */
+ public void setBounds(int x, int y, int width, int height) {
+ super.setBounds(x, y, width, height);
+
+ // our bounds have changed, create a new image with new size
+ if ((width > 1) && (height > 1)) {
+ // create the buffered image
+ m_img = new BufferedImage(width, height, BufferedImage.TYPE_INT_ARGB);
+
+ // update childrens bounds
+ if (USE_REPOSITION_CODE) {
+ setBoundsChildren();
+ }
+ }
+ }
+
+ /**
+ * Our implementation of paint.
+ * Invoked by Swing to draw components.
+ *
+ * @param graphics Graphics
+ */
+ public void paint(Graphics graphics) {
+ // only paint if we have an image to paint on
+ if (m_img != null) {
+ // get image graphics
+ final Graphics2D image2D = ((BufferedImage) m_img).createGraphics();
+
+ // first clear the image
+ clearImage(image2D);
+
+ // now paint children
+ if (m_isVisible){
+
+ int num=this.getComponentCount();
+
+ for(int i=0;i<num;i++){
+ this.getComponent(i).paint(image2D);
+ }
+ }
+
+ image2D.dispose();
+ // render image
+ graphics.drawImage(m_img, 0, 0, null);
+ }
+
+ }
+
+ @Override
+ public Component getComponentAt(int x, int y) {
+ int n=getComponentCount();
+ for(int i=0;i<n;i++){
+ Component c=this.getComponent(i).getComponentAt(x, y);
+ if(c!=null)
+ return c;
+ }
+ return null;
+ }
+
+ /**
+ * Invoke this method to print the component.
+ *
+ * @param graphics Graphics
+ */
+ public void print(Graphics graphics) {
+ int num=this.getComponentCount();
+ for(int i=0;i<num;i++){
+ this.getComponent(i).print(graphics);
+ }
+ /*
+ //if we have an image to print, lets print it.
+ if (m_img != null) {
+ graphics.drawImage(m_img, 0, 0, null); // This may be wrong!
+ }
+ */
+ }
+
+ private boolean setBoundsChildren() {
+ // get list of child components
+ Component[] components = getComponents();
+
+ // no components, outta here
+ if (components.length == 0)
+ return false;
+
+ // interate through the components
+ for (Component c : components) {
+ // get node
+ Point node = m_componentToPointMap.get(c);
+
+ // new image coordinates
+ double[] currentNodeCoordinates = new double[2];
+ currentNodeCoordinates[0] = node.getX();
+ currentNodeCoordinates[1] = node.getY();
+
+ AffineTransform transform = m_innerCanvas.getAffineTransform();
+ transform.transform(currentNodeCoordinates, 0, currentNodeCoordinates, 0, 1);
+
+ // set bounds
+ c.setBounds((int) currentNodeCoordinates[0], (int) currentNodeCoordinates[1],
+ c.getWidth(), c.getHeight());
+ }
+
+ // outta here
+ return true;
+ }
+
+ /**
+ * Utility function to clean the background of the image,
+ * using m_backgroundColor
+ *
+ * image2D Graphics2D
+ */
+ private void clearImage(Graphics2D image2D) {
+ // set color alpha based on opacity setting
+ int alpha = (m_isOpaque) ? 255 : 0;
+ Color backgroundColor = new Color(m_backgroundColor.getRed(), m_backgroundColor.getGreen(),
+ m_backgroundColor.getBlue(), alpha);
+
+ // set the alpha composite on the image, and clear its area
+ Composite origComposite = image2D.getComposite();
+ image2D.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC));
+ image2D.setPaint(backgroundColor);
+ image2D.fillRect(0, 0, m_img.getWidth(null), m_img.getHeight(null));
+ image2D.setComposite(origComposite);
+ }
+}
diff --git a/corelibs/ding/src/main/java/ding/view/BirdsEyeView.java b/corelibs/ding/src/main/java/ding/view/BirdsEyeView.java
new file mode 100644
index 0000000..91111b8
--- /dev/null
+++ b/corelibs/ding/src/main/java/ding/view/BirdsEyeView.java
@@ -0,0 +1,353 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package ding.view;
+
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.Image;
+import java.awt.Rectangle;
+import java.awt.Point;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.awt.geom.Point2D;
+import java.awt.geom.Rectangle2D;
+import java.awt.image.BufferedImage;
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ */
+public class BirdsEyeView extends Component {
+ private final double[] m_extents = new double[4];
+ private DGraphView m_view;
+ private final ContentChangeListener m_cLis;
+ private final ViewportChangeListener m_vLis;
+ private Image m_img = null;
+ private boolean m_contentChanged = false;
+ private double m_myXCenter;
+ private double m_myYCenter;
+ private double m_myScaleFactor;
+ private int m_viewWidth;
+ private int m_viewHeight;
+ private double m_viewXCenter;
+ private double m_viewYCenter;
+ private double m_viewScaleFactor;
+ private Component m_desktopView;
+
+ /**
+ * Creates a new BirdsEyeView object.
+ *
+ * @param view DOCUMENT ME!
+ */
+ public BirdsEyeView(DGraphView view) {
+ this(view, null);
+ }
+
+ /**
+ * Creates a new BirdsEyeView object.
+ *
+ * @param view The view to monitor
+ * @param desktopView The desktop area holding the view. This should be NetworkViewManager.getDesktopPane().
+ */
+ public BirdsEyeView(DGraphView view, Component desktopView) {
+ super();
+ m_cLis = new InnerContentChangeListener();
+ m_vLis = new InnerViewportChangeListener();
+ m_desktopView = desktopView;
+ addMouseListener(new InnerMouseListener());
+ addMouseMotionListener(new InnerMouseMotionListener());
+ changeView(view);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param view DOCUMENT ME!
+ */
+ public void changeView(DGraphView view) {
+ destroy();
+ m_view = view;
+
+ if (m_view != null) {
+ m_view.addContentChangeListener(m_cLis);
+ m_view.addViewportChangeListener(m_vLis);
+ updateBounds();
+ final Point2D pt = m_view.getCenter();
+ m_viewXCenter = pt.getX();
+ m_viewYCenter = pt.getY();
+ m_viewScaleFactor = m_view.getZoom();
+ m_contentChanged = true;
+ }
+
+ repaint();
+ }
+
+ private void updateBounds()
+ {
+ final Rectangle2D viewable = getViewableRect();
+ m_viewWidth = (int) viewable.getWidth();
+ m_viewHeight = (int) viewable.getHeight();
+ final Rectangle2D viewableInView = getViewableRectInView(viewable);
+ m_viewXCenter = viewableInView.getX() + viewableInView.getWidth() / 2.0;
+ m_viewYCenter = viewableInView.getY() + viewableInView.getHeight() / 2.0;
+ }
+
+ private Rectangle2D getViewableRectInView(final Rectangle2D viewable)
+ {
+ if (m_view == null || m_view.getCanvas() == null || m_view.getCanvas().m_grafx == null)
+ return new Rectangle2D.Double(0.0, 0.0, 0.0, 0.0);
+
+ final double[] origin = new double[2];
+ origin[0] = viewable.getX();
+ origin[1] = viewable.getY();
+ m_view.xformComponentToNodeCoords(origin);
+
+
+ final double[] destination = new double[2];
+ destination[0] = viewable.getX() + viewable.getWidth();
+ destination[1] = viewable.getY() + viewable.getHeight();
+ m_view.xformComponentToNodeCoords(destination);
+
+ Rectangle2D result = new Rectangle2D.Double(origin[0], origin[1], destination[0] - origin[0], destination[1] - origin[1]);
+ return result;
+ }
+
+ private Rectangle2D getViewableRect()
+ {
+ if (m_view == null)
+ return new Rectangle2D.Double(0.0, 0.0, 0.0, 0.0);
+
+ if (m_desktopView == null)
+ {
+ final Rectangle r = m_view.getComponent().getBounds();
+ return new Rectangle2D.Double(r.x, r.y, r.width, r.height);
+ }
+
+ final Rectangle desktopRect = m_desktopView.getBounds();
+ if (m_desktopView.isShowing())
+ {
+ Point s = m_desktopView.getLocationOnScreen();
+ desktopRect.x = s.x;
+ desktopRect.y = s.y;
+ }
+
+ final Rectangle viewRect = m_view.getComponent().getBounds();
+ if (m_view.getComponent().isShowing())
+ {
+ Point s = m_view.getComponent().getLocationOnScreen();
+ viewRect.x = s.x;
+ viewRect.y = s.y;
+ }
+
+ desktopRect.x -= viewRect.x;
+ desktopRect.y -= viewRect.y;
+ viewRect.x = 0;
+ viewRect.y = 0;
+
+ final Rectangle viewable = desktopRect.intersection(viewRect);
+ return viewable;
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void destroy() {
+ if (m_view == null)
+ return;
+
+ m_view.removeContentChangeListener(m_cLis);
+ m_view.removeViewportChangeListener(m_vLis);
+ }
+
+ /**
+ * This used to be called reshape, which is deprecated, so I've changed
+ * it to setBounds. Not sure if this will break anything!
+ *
+ * @param x
+ * @param y
+ * @param width
+ * @param height
+ */
+ public void setBounds(int x, int y, int width, int height) {
+ super.setBounds(x, y, width, height);
+
+ if ((width > 0) && (height > 0))
+ m_img = new BufferedImage(width, height, BufferedImage.TYPE_INT_ARGB);
+
+ m_contentChanged = true;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g DOCUMENT ME!
+ */
+ public void update(Graphics g) {
+ if (m_img == null)
+ return;
+
+ if (m_view == null) {
+ g.setColor(Color.white);
+ g.fillRect(0, 0, getWidth(), getHeight());
+
+ return;
+ }
+
+ updateBounds();
+
+ if (m_contentChanged) {
+ if (m_view.getExtents(m_extents)) {
+ m_myXCenter = (m_extents[0] + m_extents[2]) / 2.0d;
+ m_myYCenter = (m_extents[1] + m_extents[3]) / 2.0d;
+ m_myScaleFactor = 0.8d * Math.min(((double) getWidth()) / (m_extents[2]
+ - m_extents[0]),
+ ((double) getHeight()) / (m_extents[3]
+ - m_extents[1]));
+ } else {
+ m_myXCenter = 0.0d;
+ m_myYCenter = 0.0d;
+ m_myScaleFactor = 1.0d;
+ }
+
+ m_view.drawSnapshot(m_img, m_view.getGraphLOD(),
+ m_view.m_backgroundCanvas.getBackground(), m_myXCenter,
+ m_myYCenter, m_myScaleFactor);
+ m_contentChanged = false;
+ }
+
+ g.drawImage(m_img, 0, 0, null);
+
+ final double rectWidth = m_myScaleFactor * (((double) m_viewWidth) / m_viewScaleFactor);
+ final double rectHeight = m_myScaleFactor * (((double) m_viewHeight) / m_viewScaleFactor);
+ final double rectXCenter = (((double) getWidth()) / 2.0d)
+ + (m_myScaleFactor * (m_viewXCenter - m_myXCenter));
+ final double rectYCenter = (((double) getHeight()) / 2.0d)
+ + (m_myScaleFactor * (m_viewYCenter - m_myYCenter));
+ final Rectangle2D rect = new Rectangle2D.Double(rectXCenter - (rectWidth / 2),
+ rectYCenter - (rectHeight / 2), rectWidth,
+ rectHeight);
+ final Graphics2D g2 = (Graphics2D) g;
+ g2.setColor(new Color(63, 63, 255, 63));
+ g2.fill(rect);
+ g2.setColor(Color.blue);
+ g2.draw(rect);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g DOCUMENT ME!
+ */
+ public void paint(Graphics g) {
+ update(g);
+ }
+
+ private final class InnerContentChangeListener implements ContentChangeListener {
+ public void contentChanged() {
+ m_contentChanged = true;
+ repaint();
+ }
+ }
+
+ private final class InnerViewportChangeListener implements ViewportChangeListener {
+ public void viewportChanged(int w, int h, double newXCenter, double newYCenter,
+ double newScaleFactor) {
+ m_viewWidth = w;
+ m_viewHeight = h;
+ m_viewXCenter = newXCenter;
+ m_viewYCenter = newYCenter;
+ m_viewScaleFactor = newScaleFactor;
+ repaint();
+ }
+ }
+
+ private int m_currMouseButton = 0;
+ private int m_lastXMousePos = 0;
+ private int m_lastYMousePos = 0;
+
+ private final class InnerMouseListener implements MouseListener {
+ public void mouseClicked(MouseEvent e) {
+ }
+
+ public void mouseEntered(MouseEvent e) {
+ }
+
+ public void mouseExited(MouseEvent e) {
+ }
+
+ public void mousePressed(MouseEvent e) {
+ if (e.getButton() == MouseEvent.BUTTON1) {
+ m_currMouseButton = 1;
+ m_lastXMousePos = e.getX();
+ m_lastYMousePos = e.getY();
+ }
+ }
+
+ public void mouseReleased(MouseEvent e) {
+ if (e.getButton() == MouseEvent.BUTTON1) {
+ if (m_currMouseButton == 1)
+ m_currMouseButton = 0;
+ }
+ }
+ }
+
+ private final class InnerMouseMotionListener implements MouseMotionListener {
+ public void mouseDragged(MouseEvent e) {
+ if (m_currMouseButton == 1) {
+ final int currX = e.getX();
+ final int currY = e.getY();
+ final double deltaX = (currX - m_lastXMousePos) / m_myScaleFactor;
+ final double deltaY = (currY - m_lastYMousePos) / m_myScaleFactor;
+ m_lastXMousePos = currX;
+ m_lastYMousePos = currY;
+
+ if (m_view != null) {
+ final Point2D pt = m_view.getCenter();
+ m_view.setCenter(pt.getX() + deltaX, pt.getY() + deltaY);
+ }
+ }
+ }
+
+ public void mouseMoved(MouseEvent e) {
+ }
+ }
+}
diff --git a/corelibs/ding/src/main/java/ding/view/ContentChangeListener.java b/corelibs/ding/src/main/java/ding/view/ContentChangeListener.java
new file mode 100644
index 0000000..e43f4ed
--- /dev/null
+++ b/corelibs/ding/src/main/java/ding/view/ContentChangeListener.java
@@ -0,0 +1,55 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package ding.view;
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$-
+ */
+public interface ContentChangeListener {
+ /**
+ * This gets fired upon graph redraw when at least one of the following
+ * things change: node unselected, edge unselected, background paint
+ * change, node view added, edge view added, node view removed,
+ * edge view removed, node view hidden, edge view hidden, node view
+ * restored, edge view restored, graph lod changed, node visual property
+ * changed, edge visual property changed.
+ */
+ public void contentChanged();
+}
diff --git a/corelibs/ding/src/main/java/ding/view/ContentChangeListenerChain.java b/corelibs/ding/src/main/java/ding/view/ContentChangeListenerChain.java
new file mode 100644
index 0000000..e5dd856
--- /dev/null
+++ b/corelibs/ding/src/main/java/ding/view/ContentChangeListenerChain.java
@@ -0,0 +1,91 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package ding.view;
+
+class ContentChangeListenerChain implements ContentChangeListener {
+ private final ContentChangeListener a;
+ private final ContentChangeListener b;
+
+ private ContentChangeListenerChain(ContentChangeListener a, ContentChangeListener b) {
+ this.a = a;
+ this.b = b;
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void contentChanged() {
+ a.contentChanged();
+ b.contentChanged();
+ }
+
+ static ContentChangeListener add(ContentChangeListener a, ContentChangeListener b) {
+ if (a == null)
+ return b;
+
+ if (b == null)
+ return a;
+
+ return new ContentChangeListenerChain(a, b);
+ }
+
+ static ContentChangeListener remove(ContentChangeListener l, ContentChangeListener oldl) {
+ if ((l == oldl) || (l == null))
+ return null;
+ else if (l instanceof ContentChangeListenerChain)
+ return ((ContentChangeListenerChain) l).remove(oldl);
+ else
+
+ return l;
+ }
+
+ private ContentChangeListener remove(ContentChangeListener oldl) {
+ if (oldl == a)
+ return b;
+
+ if (oldl == b)
+ return a;
+
+ ContentChangeListener a2 = remove(a, oldl);
+ ContentChangeListener b2 = remove(b, oldl);
+
+ if ((a2 == a) && (b2 == b))
+ return this;
+
+ return add(a2, b2);
+ }
+}
diff --git a/corelibs/ding/src/main/java/ding/view/CustomGraphicsPositionCalculator.java b/corelibs/ding/src/main/java/ding/view/CustomGraphicsPositionCalculator.java
new file mode 100644
index 0000000..0182371
--- /dev/null
+++ b/corelibs/ding/src/main/java/ding/view/CustomGraphicsPositionCalculator.java
@@ -0,0 +1,72 @@
+package ding.view;
+
+import giny.view.ObjectPosition;
+import giny.view.Position;
+
+import java.awt.Shape;
+import java.awt.geom.AffineTransform;
+import java.util.HashMap;
+import java.util.Map;
+
+import cytoscape.render.stateful.CustomGraphic;
+import cytoscape.render.stateful.PaintFactory;
+
+public class CustomGraphicsPositionCalculator {
+
+ /**
+ * Defines displacement.
+ */
+ private static final Map<Position, Float[]> DISPLACEMENT_MAP;
+
+ static {
+ DISPLACEMENT_MAP = new HashMap<Position, Float[]>();
+
+ DISPLACEMENT_MAP.put(Position.CENTER, new Float[]{0f, 0f} );
+
+ DISPLACEMENT_MAP.put(Position.NORTH, new Float[]{0f, -0.5f});
+ DISPLACEMENT_MAP.put(Position.NORTH_WEST, new Float[]{-0.5f, -0.5f});
+ DISPLACEMENT_MAP.put(Position.NORTH_EAST, new Float[]{0.5f, -0.5f});
+
+ DISPLACEMENT_MAP.put(Position.SOUTH, new Float[]{0f, 0.5f});
+ DISPLACEMENT_MAP.put(Position.SOUTH_WEST, new Float[]{-0.5f, 0.5f});
+ DISPLACEMENT_MAP.put(Position.SOUTH_EAST, new Float[]{0.5f, 0.5f});
+
+ DISPLACEMENT_MAP.put(Position.WEST, new Float[]{-0.5f, 0f});
+
+ DISPLACEMENT_MAP.put(Position.EAST, new Float[]{0.5f, 0f});
+ }
+
+
+
+ public static CustomGraphic transform(final ObjectPosition p, final DNodeView nv, CustomGraphic cg) {
+ final Position anc = p.getAnchor();
+ final Position ancN = p.getTargetAnchor();
+
+ final double nodeW = nv.getWidth();
+ final double nodeH = nv.getHeight();
+ final double cgW = cg.getShape().getBounds().getWidth();
+ final double cgH = cg.getShape().getBounds().getHeight();
+
+ final Float[] disp1 = DISPLACEMENT_MAP.get(anc);
+ final Float[] disp2 = DISPLACEMENT_MAP.get(ancN);
+
+ // 1. Displacement for graphics
+ final double dispX = -disp1[0] * nodeW;
+ final double dispY = -disp1[1] * nodeH;
+
+ final double dispNX = disp2[0] * cgW;
+ final double dispNY = disp2[1] * cgH;
+
+ // calc total and apply transform
+ double totalDispX = dispX + dispNX + p.getOffsetX();
+ double totalDispY = dispY + dispNY + p.getOffsetY();
+
+ final AffineTransform tf = AffineTransform.getTranslateInstance(totalDispX, totalDispY);
+ final Shape newShape = tf.createTransformedShape(cg.getShape());
+
+ final PaintFactory newFactory = cg.getPaintFactory();
+
+ return new CustomGraphic(newShape, newFactory);
+
+ }
+}
diff --git a/corelibs/ding/src/main/java/ding/view/DEdgeDetails.java b/corelibs/ding/src/main/java/ding/view/DEdgeDetails.java
new file mode 100644
index 0000000..4958dcf
--- /dev/null
+++ b/corelibs/ding/src/main/java/ding/view/DEdgeDetails.java
@@ -0,0 +1,750 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package ding.view;
+
+import cytoscape.graph.fixed.FixedGraph;
+
+import cytoscape.render.immed.EdgeAnchors;
+import cytoscape.render.immed.GraphGraphics;
+
+import cytoscape.util.intr.IntEnumerator;
+import cytoscape.util.intr.IntIterator;
+import cytoscape.util.intr.IntObjHash;
+import cytoscape.util.intr.MinIntHeap;
+
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.Paint;
+import java.awt.Stroke;
+
+import java.util.HashMap;
+
+
+class DEdgeDetails extends IntermediateEdgeDetails {
+ final DGraphView m_view;
+ final IntObjHash m_colorsLowDetail = new IntObjHash();
+ final Object m_deletedEntry = new Object();
+ final HashMap m_segmentThicknesses = new HashMap();
+ final HashMap m_segmentStrokes = new HashMap();
+ final HashMap m_sourceArrows = new HashMap();
+ final HashMap m_sourceArrowPaints = new HashMap();
+ final HashMap m_targetArrows = new HashMap();
+ final HashMap m_targetArrowPaints = new HashMap();
+ final HashMap m_segmentPaints = new HashMap();
+ //final HashMap m_segmentDashLengths = new HashMap();
+ final HashMap m_labelCounts = new HashMap();
+ final HashMap m_labelTexts = new HashMap();
+ final HashMap m_labelFonts = new HashMap();
+ final HashMap m_labelPaints = new HashMap();
+ final HashMap m_labelWidths = new HashMap();
+
+ DEdgeDetails(DGraphView view) {
+ m_view = view;
+ }
+
+ void unregisterEdge(int edge) {
+ final Object o = m_colorsLowDetail.get(edge);
+
+ if ((o != null) && (o != m_deletedEntry))
+ m_colorsLowDetail.put(edge, m_deletedEntry);
+
+ final Integer key = new Integer(edge);
+ m_segmentThicknesses.remove(key);
+ m_segmentStrokes.remove(key);
+ m_sourceArrows.remove(key);
+ m_sourceArrowPaints.remove(key);
+ m_targetArrows.remove(key);
+ m_targetArrowPaints.remove(key);
+ m_segmentPaints.remove(key);
+// m_segmentDashLengths.remove(key);
+ m_labelCounts.remove(key);
+ m_labelTexts.remove(key);
+ m_labelFonts.remove(key);
+ m_labelPaints.remove(key);
+ m_labelWidths.remove(key);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edge DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Color colorLowDetail(int edge) {
+ final Object o = m_colorsLowDetail.get(edge);
+
+ if ((o == null) || (o == m_deletedEntry))
+ return super.colorLowDetail(edge);
+
+ return (Color) o;
+ }
+
+ /*
+ * A null color has the special meaning to remove overridden color.
+ */
+ void overrideColorLowDetail(int edge, Color color) {
+ if ((color == null) || color.equals(super.colorLowDetail(edge))) {
+ final Object val = m_colorsLowDetail.get(edge);
+
+ if ((val != null) && (val != m_deletedEntry))
+ m_colorsLowDetail.put(edge, m_deletedEntry);
+ } else
+ m_colorsLowDetail.put(edge, color);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edge DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public byte sourceArrow(int edge) {
+ final Object o = m_sourceArrows.get(new Integer(edge));
+
+ if (o == null)
+ return super.sourceArrow(edge);
+
+ return ((Byte) o).byteValue();
+ }
+
+ /*
+ * A non-negative arrowType has the special meaning to remove overridden
+ * arrow.
+ */
+ void overrideSourceArrow(int edge, byte arrowType) {
+ if ((arrowType >= 0) || (arrowType == super.sourceArrow(edge)))
+ m_sourceArrows.remove(new Integer(edge));
+ else
+ m_sourceArrows.put(new Integer(edge), new Byte(arrowType));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edge DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Paint sourceArrowPaint(int edge) {
+ final Object o = m_sourceArrowPaints.get(new Integer(edge));
+
+ if (o == null)
+ return super.sourceArrowPaint(edge);
+
+ return (Paint) o;
+ }
+
+ /*
+ * A null paint has the special meaning to remove overridden paint.
+ */
+ void overrideSourceArrowPaint(int edge, Paint paint) {
+ if ((paint == null) || paint.equals(super.sourceArrowPaint(edge)))
+ m_sourceArrowPaints.remove(new Integer(edge));
+ else
+ m_sourceArrowPaints.put(new Integer(edge), paint);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edge DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public byte targetArrow(int edge) {
+ final Object o = m_targetArrows.get(new Integer(edge));
+
+ if (o == null)
+ return super.targetArrow(edge);
+
+ return ((Byte) o).byteValue();
+ }
+
+ /*
+ * A non-negative arrowType has the special meaning to remove overridden
+ * arrow.
+ */
+ void overrideTargetArrow(int edge, byte arrowType) {
+ if ((arrowType >= 0) || (arrowType == super.targetArrow(edge)))
+ m_targetArrows.remove(new Integer(edge));
+ else
+ m_targetArrows.put(new Integer(edge), new Byte(arrowType));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edge DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Paint targetArrowPaint(int edge) {
+ final Object o = m_targetArrowPaints.get(new Integer(edge));
+
+ if (o == null)
+ return super.targetArrowPaint(edge);
+
+ return (Paint) o;
+ }
+
+ /*
+ * A null paint has the special meaning to remove overridden paint.
+ */
+ void overrideTargetArrowPaint(int edge, Paint paint) {
+ if ((paint == null) || paint.equals(super.targetArrowPaint(edge)))
+ m_targetArrowPaints.remove(new Integer(edge));
+ else
+ m_targetArrowPaints.put(new Integer(edge), paint);
+ }
+
+ private final MinIntHeap m_heap = new MinIntHeap();
+ private final float[] m_extentsBuff = new float[4];
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edge DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public EdgeAnchors anchors(int edge) {
+ final EdgeAnchors returnThis = (EdgeAnchors) (m_view.getEdgeView(~edge));
+
+ if (returnThis.numAnchors() > 0)
+ return returnThis;
+
+ final FixedGraph graph = (FixedGraph) m_view.m_drawPersp;
+ final int srcNode = graph.edgeSource(edge);
+ final int trgNode = graph.edgeTarget(edge);
+
+ // Calculate anchors necessary for self edges.
+ if (srcNode == trgNode) {
+
+ m_view.m_spacial.exists(srcNode, m_extentsBuff, 0);
+
+ final double w = ((double) m_extentsBuff[2]) - m_extentsBuff[0];
+ final double h = ((double) m_extentsBuff[3]) - m_extentsBuff[1];
+ final double x = (((double) m_extentsBuff[0]) + m_extentsBuff[2]) / 2.0d;
+ final double y = (((double) m_extentsBuff[1]) + m_extentsBuff[3]) / 2.0d;
+ final double nodeSize = Math.max(w, h);
+ int i = 0;
+ final IntIterator selfEdges = graph.edgesConnecting(srcNode, srcNode, true, true, true);
+
+ while (selfEdges.hasNext()) {
+ final int e2 = selfEdges.nextInt();
+
+ if (e2 == edge)
+ break;
+
+ if (((EdgeAnchors) m_view.getEdgeView(~e2)).numAnchors() == 0)
+ i++;
+ }
+
+ final int inx = i;
+
+ return new EdgeAnchors() {
+ public int numAnchors() {
+ return 2;
+ }
+
+ public void getAnchor(int anchorInx, float[] anchorArr, int offset) {
+ if (anchorInx == 0) {
+ anchorArr[offset] = (float) (x - (((inx + 3) * nodeSize) / 2.0d));
+ anchorArr[offset + 1] = (float) y;
+ } else if (anchorInx == 1) {
+ anchorArr[offset] = (float) x;
+ anchorArr[offset + 1] = (float) (y - (((inx + 3) * nodeSize) / 2.0d));
+ }
+ }
+ };
+ }
+
+ // Now add "invisible" anchors to edges for the case where multiple edges
+ // exist between two nodes. This has no effect if user specified anchors
+ // exist on the edge.
+ while (true) {
+
+ // By consistently ording the source and target nodes, dx and dy will always
+ // be calculated according to the same orientation. This allows the offset
+ // calculation to toggle the edges from side to side without any overlap.
+ final int tmpSrc = Math.min( srcNode, trgNode );
+ final int tmpTrg = Math.max( srcNode, trgNode );
+
+ // Sort the connecting edges.
+ final IntIterator conEdges = graph.edgesConnecting(tmpSrc, tmpTrg,
+ true, true, true);
+
+ m_heap.empty();
+
+ while (conEdges.hasNext())
+ m_heap.toss(conEdges.nextInt());
+
+ final IntEnumerator otherEdges = m_heap.orderedElements(false);
+
+ int otherEdge = otherEdges.nextInt();
+
+ // If the first other edge is the same as this edge,
+ // (i.e. we're at the end of the list?).
+ if (otherEdge == edge)
+ break;
+
+ // So we don't count the other edge twice?
+ int i = (((EdgeAnchors) m_view.getEdgeView(~otherEdge)).numAnchors() == 0) ? 1 : 0;
+
+ // Count the number of other edges.
+ while (true) {
+ if (edge == (otherEdge = otherEdges.nextInt()))
+ break;
+
+ if (((EdgeAnchors) m_view.getEdgeView(~otherEdge)).numAnchors() == 0)
+ i++;
+ }
+
+ final int inx = i;
+
+ // Get source node size and position.
+ m_view.m_spacial.exists(tmpSrc, m_extentsBuff, 0);
+ final double srcW = ((double) m_extentsBuff[2]) - m_extentsBuff[0];
+ final double srcH = ((double) m_extentsBuff[3]) - m_extentsBuff[1];
+ final double srcX = (((double) m_extentsBuff[0]) + m_extentsBuff[2]) / 2.0d;
+ final double srcY = (((double) m_extentsBuff[1]) + m_extentsBuff[3]) / 2.0d;
+
+ // Get target node size and position.
+ m_view.m_spacial.exists(tmpTrg, m_extentsBuff, 0);
+ final double trgW = ((double) m_extentsBuff[2]) - m_extentsBuff[0];
+ final double trgH = ((double) m_extentsBuff[3]) - m_extentsBuff[1];
+ final double trgX = (((double) m_extentsBuff[0]) + m_extentsBuff[2]) / 2.0d;
+ final double trgY = (((double) m_extentsBuff[1]) + m_extentsBuff[3]) / 2.0d;
+
+ // Used for determining the space between the edges.
+ final double nodeSize = Math.max(Math.max(Math.max(srcW, srcH), trgW), trgH);
+
+ // Midpoint between nodes.
+ final double midX = (srcX + trgX) / 2;
+ final double midY = (srcY + trgY) / 2;
+
+ // Distance in X and Y dimensions.
+ // Note that dx and dy may be negative. This is OK, because this will ensure
+ // that the handle is always correctly placed offset from the midpoint of,
+ // and perpendicular to, the original edge.
+ final double dx = trgX - srcX;
+ final double dy = trgY - srcY;
+
+ // Distance or length between nodes.
+ final double len = Math.sqrt((dx * dx) + (dy * dy));
+
+ if (((float) len) == 0.0f)
+ break;
+
+ // This determines which side of the first edge and how far from the first
+ // edge the other edge should be placed.
+ // - Divide by 2 puts consecutive edges at the same distance from the center
+ // because of integer math.
+ // - Modulo puts consecutive edges on opposite sides.
+ // - Node size is for consistent scaling.
+ final double offset = ((inx + 1) / 2) * (inx % 2 == 0 ? 1 : -1) * nodeSize;
+
+ // Depending on orientation sine or cosine. This adjusts the length
+ // of the offset according the appropriate X and Y dimensions.
+ final double normX = dx / len;
+ final double normY = dy / len;
+
+ // Calculate the anchor points.
+ final double anchorX = midX + (offset * normY);
+ final double anchorY = midY - (offset * normX);
+
+ return new EdgeAnchors() {
+ public int numAnchors() {
+ return 1;
+ }
+
+ public void getAnchor(int inx, float[] arr, int off) {
+ arr[off] = (float) anchorX;
+ arr[off + 1] = (float) anchorY;
+ }
+ };
+ }
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edge DOCUMENT ME!
+ * @param anchorInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public float anchorSize(int edge, int anchorInx) {
+ if (m_view.getEdgeView(~edge).isSelected()
+ && (((DEdgeView) m_view.getEdgeView(~edge)).numAnchors() > 0))
+ return m_view.getAnchorSize();
+ else
+
+ return 0.0f;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edge DOCUMENT ME!
+ * @param anchorInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Paint anchorPaint(int edge, int anchorInx) {
+ if (((DEdgeView) (m_view.getEdgeView(~edge))).m_lineType == DEdgeView.STRAIGHT_LINES)
+ anchorInx = anchorInx / 2;
+
+ if (m_view.m_selectedAnchors.count((edge << 6) | anchorInx) > 0)
+ return m_view.getAnchorSelectedPaint();
+ else
+
+ return m_view.getAnchorUnselectedPaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edge DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public float segmentThickness(int edge) {
+ final Object o = m_segmentThicknesses.get(new Integer(edge));
+
+ if (o == null)
+ return super.segmentThickness(edge);
+
+ return ((Float) o).floatValue();
+ }
+
+ /*
+ * A negative thickness value has the special meaning to remove overridden
+ * thickness.
+ */
+ void overrideSegmentThickness(int edge, float thickness) {
+ if ((thickness < 0.0f) || (thickness == super.segmentThickness(edge)))
+ m_segmentThicknesses.remove(new Integer(edge));
+ else
+ m_segmentThicknesses.put(new Integer(edge), new Float(thickness));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edge DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ public Paint segmentPaint(int edge) {
+ final Object o = m_segmentPaints.get(new Integer(edge));
+
+ if (o == null)
+ return super.segmentPaint(edge);
+
+ return (Paint) o;
+ }
+ */
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edge DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Stroke segmentStroke(int edge) {
+ final Object o = m_segmentStrokes.get(new Integer(edge));
+
+ if (o == null)
+ return super.segmentStroke(edge);
+
+ return (Stroke) o;
+ }
+
+ /*
+ * A null paint has the special meaning to remove overridden paint.
+ void overrideSegmentPaint(int edge, Paint paint) {
+ if ((paint == null) || paint.equals(super.segmentPaint(edge)))
+ m_segmentPaints.remove(new Integer(edge));
+ else
+ m_segmentPaints.put(new Integer(edge), paint);
+ }
+ */
+ /*
+ * A null paint has the special meaning to remove overridden paint.
+ */
+ void overrideSegmentStroke(int edge, Stroke stroke) {
+ if ((stroke == null) || stroke.equals(super.segmentStroke(edge)))
+ m_segmentStrokes.remove(new Integer(edge));
+ else
+ m_segmentStrokes.put(new Integer(edge), stroke);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edge DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ public float segmentDashLength(int edge) {
+ final Object o = m_segmentDashLengths.get(new Integer(edge));
+
+ if (o == null)
+ return super.segmentDashLength(edge);
+
+ return ((Float) o).floatValue();
+ }
+ */
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edge DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Paint segmentPaint(int edge) {
+ final Object o = m_segmentPaints.get(new Integer(edge));
+
+ if (o == null)
+ return super.segmentPaint(edge);
+
+ return (Paint) o;
+ }
+
+ /*
+ * A negative length value has the special meaning to remove overridden
+ * length.
+ void overrideSegmentDashLength(int edge, float length) {
+ if ((length < 0.0f) || (length == super.segmentDashLength(edge)))
+ m_segmentDashLengths.remove(new Integer(edge));
+ else
+ m_segmentDashLengths.put(new Integer(edge), new Float(length));
+ }
+ */
+
+
+ /*
+ * A negative length value has the special meaning to remove overridden
+ * length.
+ */
+ void overrideSegmentPaint(int edge, Paint paint) {
+ if ((paint == null) || (paint == super.segmentPaint(edge)))
+ m_segmentPaints.remove(new Integer(edge));
+ else
+ m_segmentPaints.put(new Integer(edge), paint);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edge DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int labelCount(int edge) {
+ final Object o = m_labelCounts.get(new Integer(edge));
+
+ if (o == null)
+ return super.labelCount(edge);
+
+ return ((Integer) o).intValue();
+ }
+
+ /*
+ * A negative labelCount has the special meaning to remove overridden count.
+ */
+ void overrideLabelCount(int edge, int labelCount) {
+ if ((labelCount < 0) || (labelCount == super.labelCount(edge)))
+ m_labelCounts.remove(new Integer(edge));
+ else
+ m_labelCounts.put(new Integer(edge), new Integer(labelCount));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edge DOCUMENT ME!
+ * @param labelInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String labelText(int edge, int labelInx) {
+ final long key = (((long) edge) << 32) | ((long) labelInx);
+ final Object o = m_labelTexts.get(new Long(key));
+
+ if (o == null)
+ return super.labelText(edge, labelInx);
+
+ return (String) o;
+ }
+
+ /*
+ * A null text has the special meaning to remove overridden text.
+ */
+ void overrideLabelText(int edge, int labelInx, String text) {
+ final long key = (((long) edge) << 32) | ((long) labelInx);
+
+ if ((text == null) || text.equals(super.labelText(edge, labelInx)))
+ m_labelTexts.remove(new Long(key));
+ else
+ m_labelTexts.put(new Long(key), text);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edge DOCUMENT ME!
+ * @param labelInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Font labelFont(int edge, int labelInx) {
+ final long key = (((long) edge) << 32) | ((long) labelInx);
+ final Object o = m_labelFonts.get(new Long(key));
+
+ if (o == null)
+ return super.labelFont(edge, labelInx);
+
+ return (Font) o;
+ }
+
+ /*
+ * A null font has the special meaning to remove overridden font.
+ */
+ void overrideLabelFont(int edge, int labelInx, Font font) {
+ final long key = (((long) edge) << 32) | ((long) labelInx);
+
+ if ((font == null) || font.equals(super.labelFont(edge, labelInx)))
+ m_labelFonts.remove(new Long(key));
+ else
+ m_labelFonts.put(new Long(key), font);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edge DOCUMENT ME!
+ * @param labelInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Paint labelPaint(int edge, int labelInx) {
+ final long key = (((long) edge) << 32) | ((long) labelInx);
+ final Object o = m_labelPaints.get(new Long(key));
+
+ if (o == null)
+ return super.labelPaint(edge, labelInx);
+
+ return (Paint) o;
+ }
+
+ /*
+ * A null paint has the special meaning to remove overridden paint.
+ */
+ void overrideLabelPaint(int edge, int labelInx, Paint paint) {
+ final long key = (((long) edge) << 32) | ((long) labelInx);
+
+ if ((paint == null) || paint.equals(super.labelPaint(edge, labelInx)))
+ m_labelPaints.remove(new Long(key));
+ else
+ m_labelPaints.put(new Long(key), paint);
+ }
+
+ /**
+ * The arrow size will scale with the edge width.
+ */
+ public float sourceArrowSize(int edge) {
+ // For the half arrows, we need to scale multiplicatively
+ // so that the arrow matches the line.
+ int arrowType = sourceArrow(edge);
+ if ( arrowType == GraphGraphics.ARROW_HALF_TOP ||
+ arrowType == GraphGraphics.ARROW_HALF_BOTTOM )
+ return (segmentThickness(edge) * DEdgeView.DEFAULT_ARROW_SIZE);
+
+ // For all other arrows we can scale additively. This produces
+ // less egregiously big arrows.
+ else
+ return (segmentThickness(edge) + DEdgeView.DEFAULT_ARROW_SIZE);
+ }
+
+ /**
+ * The arrow size will scale with the edge width.
+ */
+ public float targetArrowSize(int edge) {
+ // For the half arrows, we need to scale multiplicatively
+ // so that the arrow matches the line.
+ int arrowType = targetArrow(edge);
+ if ( arrowType == GraphGraphics.ARROW_HALF_TOP ||
+ arrowType == GraphGraphics.ARROW_HALF_BOTTOM )
+ return (segmentThickness(edge) * DEdgeView.DEFAULT_ARROW_SIZE);
+ // For all other arrows we can scale additively. This produces
+ // less egregiously big arrows.
+ else
+ return (segmentThickness(edge) + DEdgeView.DEFAULT_ARROW_SIZE);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edge DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public double labelWidth(int edge) {
+ final Object o = m_labelWidths.get(new Integer(edge));
+
+ if (o == null)
+ return super.labelWidth(edge);
+
+ return ((Double) o).doubleValue();
+ }
+
+ /*
+ * A negative width value has the special meaning to remove overridden width.
+ */
+ void overrideLabelWidth(int edge, double width) {
+ if ((width < 0.0) || (width == super.labelWidth(edge)))
+ m_labelWidths.remove(new Integer(edge));
+ else
+ m_labelWidths.put(new Integer(edge), new Double(width));
+ }
+
+}
diff --git a/corelibs/ding/src/main/java/ding/view/DEdgeView.java b/corelibs/ding/src/main/java/ding/view/DEdgeView.java
new file mode 100644
index 0000000..1c0c5b5
--- /dev/null
+++ b/corelibs/ding/src/main/java/ding/view/DEdgeView.java
@@ -0,0 +1,1421 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package ding.view;
+
+
+import giny.model.Edge;
+import giny.view.Bend;
+import giny.view.EdgeView;
+import giny.view.GraphView;
+import giny.view.GraphViewChangeListener;
+import giny.view.Label;
+import giny.view.ObjectPosition;
+
+import java.awt.BasicStroke;
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.Paint;
+import java.awt.Stroke;
+import java.awt.geom.Point2D;
+import java.util.ArrayList;
+import java.util.List;
+
+import cytoscape.graph.fixed.FixedGraph;
+import cytoscape.render.immed.EdgeAnchors;
+import cytoscape.render.immed.GraphGraphics;
+
+
+class DEdgeView implements EdgeView, Label, Bend, EdgeAnchors {
+ static final float DEFAULT_ARROW_SIZE = 5.0f;
+ static final Paint DEFAULT_ARROW_PAINT = Color.black;
+ static final float DEFAULT_EDGE_THICKNESS = 1.0f;
+ static final Stroke DEFAULT_EDGE_STROKE = new BasicStroke();
+ static final Color DEFAULT_EDGE_PAINT = Color.black;
+ static final String DEFAULT_LABEL_TEXT = "";
+ static final Font DEFAULT_LABEL_FONT = new Font(null, Font.PLAIN, 1);
+ static final Paint DEFAULT_LABEL_PAINT = Color.black;
+ DGraphView m_view;
+ final int m_inx; // Positive.
+ boolean m_selected;
+ Paint m_unselectedPaint;
+ Paint m_selectedPaint;
+ Paint m_sourceUnselectedPaint;
+ Paint m_sourceSelectedPaint;
+ Paint m_targetUnselectedPaint;
+ Paint m_targetSelectedPaint;
+ int m_sourceEdgeEnd; // One of the EdgeView edge end constants.
+ int m_targetEdgeEnd; // Ditto.
+ ArrayList m_anchors; // A list of Point2D objects.
+ int m_lineType;
+ String m_toolTipText = null;
+
+ /*
+ * @param inx the RootGraph index of edge (a negative number).
+ */
+ DEdgeView(DGraphView view, int inx) {
+ m_view = view;
+ m_inx = ~inx;
+ m_selected = false;
+ m_unselectedPaint = m_view.m_edgeDetails.segmentPaint(m_inx);
+ m_selectedPaint = Color.red;
+ m_sourceUnselectedPaint = m_view.m_edgeDetails.sourceArrowPaint(m_inx);
+ m_sourceSelectedPaint = Color.red;
+ m_targetUnselectedPaint = m_view.m_edgeDetails.targetArrowPaint(m_inx);
+ m_targetSelectedPaint = Color.red;
+ m_sourceEdgeEnd = EdgeView.NO_END;
+ m_targetEdgeEnd = EdgeView.NO_END;
+ m_anchors = null;
+ m_lineType = EdgeView.STRAIGHT_LINES;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getGraphPerspectiveIndex() {
+ return ~m_inx;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getRootGraphIndex() {
+ return ~m_inx;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Edge getEdge() {
+ return m_view.getGraphPerspective().getEdge(~m_inx);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public GraphView getGraphView() {
+ return m_view;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param width DOCUMENT ME!
+ */
+ public void setStrokeWidth(float width) {
+ synchronized (m_view.m_lock) {
+ m_view.m_edgeDetails.overrideSegmentThickness(m_inx, width);
+ m_view.m_contentChanged = true;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public float getStrokeWidth() {
+ synchronized (m_view.m_lock) {
+ return m_view.m_edgeDetails.segmentThickness(m_inx);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param stroke DOCUMENT ME!
+ */
+ public void setStroke(Stroke stroke) {
+ synchronized (m_view.m_lock) {
+ m_view.m_edgeDetails.overrideSegmentStroke(m_inx, stroke);
+ m_view.m_contentChanged = true;
+ }
+ /*
+ if (stroke instanceof BasicStroke) {
+ synchronized (m_view.m_lock) {
+ final BasicStroke bStroke = (BasicStroke) stroke;
+ m_view.m_edgeDetails.overrideSegmentThickness(m_inx, bStroke.getLineWidth());
+
+ final float[] dashArr = bStroke.getDashArray();
+
+ if ((dashArr != null) && (dashArr.length > 0))
+ m_view.m_edgeDetails.overrideSegmentDashLength(m_inx, dashArr[0]);
+ else
+ m_view.m_edgeDetails.overrideSegmentDashLength(m_inx, -1.0f);
+
+ m_view.m_contentChanged = true;
+ }
+ }
+ */
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Stroke getStroke() {
+ synchronized (m_view.m_lock) {
+ /*
+ final float segmentThickness = m_view.m_edgeDetails.segmentThickness(m_inx);
+ final float segmentDashLength = m_view.m_edgeDetails.segmentDashLength(m_inx);
+
+ if (segmentDashLength > 0.0f) {
+ final float[] dashes = new float[] { segmentDashLength, segmentDashLength };
+
+ return new BasicStroke(segmentThickness, BasicStroke.CAP_SQUARE,
+ BasicStroke.JOIN_MITER, 10.0f, dashes, 0.0f);
+ } else
+
+ return new BasicStroke(segmentThickness);
+ */
+ return m_view.m_edgeDetails.segmentStroke(m_inx);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param lineType DOCUMENT ME!
+ */
+ public void setLineType(int lineType) {
+ if ((lineType == EdgeView.CURVED_LINES) || (lineType == EdgeView.STRAIGHT_LINES)) {
+ synchronized (m_view.m_lock) {
+ m_lineType = lineType;
+ m_view.m_contentChanged = true;
+ }
+ } else
+ throw new IllegalArgumentException("unrecognized line type");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getLineType() {
+ return m_lineType;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param paint DOCUMENT ME!
+ */
+ public void setUnselectedPaint(Paint paint) {
+ synchronized (m_view.m_lock) {
+ if (paint == null)
+ throw new NullPointerException("paint is null");
+
+ m_unselectedPaint = paint;
+
+ if (!isSelected()) {
+ m_view.m_edgeDetails.overrideSegmentPaint(m_inx, m_unselectedPaint);
+
+ if (m_unselectedPaint instanceof Color)
+ m_view.m_edgeDetails.overrideColorLowDetail(m_inx, (Color) m_unselectedPaint);
+
+ m_view.m_contentChanged = true;
+ }
+
+ setSourceEdgeEnd(m_sourceEdgeEnd);
+ setTargetEdgeEnd(m_targetEdgeEnd);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Paint getUnselectedPaint() {
+ return m_unselectedPaint;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param paint DOCUMENT ME!
+ */
+ public void setSelectedPaint(Paint paint) {
+ synchronized (m_view.m_lock) {
+ if (paint == null)
+ throw new NullPointerException("paint is null");
+
+ m_selectedPaint = paint;
+
+ if (isSelected()) {
+ m_view.m_edgeDetails.overrideSegmentPaint(m_inx, m_selectedPaint);
+
+ if (m_selectedPaint instanceof Color)
+ m_view.m_edgeDetails.overrideColorLowDetail(m_inx, (Color) m_selectedPaint);
+
+ m_view.m_contentChanged = true;
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Paint getSelectedPaint() {
+ return m_selectedPaint;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Paint getSourceEdgeEndPaint() {
+ return m_sourceUnselectedPaint;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Paint getSourceEdgeEndSelectedPaint() {
+ return m_sourceSelectedPaint;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Paint getTargetEdgeEndPaint() {
+ return m_targetUnselectedPaint;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Paint getTargetEdgeEndSelectedPaint() {
+ return m_targetSelectedPaint;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param paint DOCUMENT ME!
+ */
+ public void setSourceEdgeEndSelectedPaint(Paint paint) {
+ synchronized (m_view.m_lock) {
+ if (paint == null)
+ throw new NullPointerException("paint is null");
+
+ m_sourceSelectedPaint = paint;
+
+ if (isSelected()) {
+ m_view.m_edgeDetails.overrideSourceArrowPaint(m_inx, m_sourceSelectedPaint);
+ m_view.m_contentChanged = true;
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param paint DOCUMENT ME!
+ */
+ public void setTargetEdgeEndSelectedPaint(Paint paint) {
+ synchronized (m_view.m_lock) {
+ if (paint == null)
+ throw new NullPointerException("paint is null");
+
+ m_targetSelectedPaint = paint;
+
+ if (isSelected()) {
+ m_view.m_edgeDetails.overrideTargetArrowPaint(m_inx, m_targetSelectedPaint);
+ m_view.m_contentChanged = true;
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param paint DOCUMENT ME!
+ */
+ public void setSourceEdgeEndStrokePaint(Paint paint) {
+ // No-op.
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param paint DOCUMENT ME!
+ */
+ public void setTargetEdgeEndStrokePaint(Paint paint) {
+ // No-op.
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param paint DOCUMENT ME!
+ */
+ public void setSourceEdgeEndPaint(Paint paint) {
+ synchronized (m_view.m_lock) {
+ if (paint == null)
+ throw new NullPointerException("paint is null");
+
+ m_sourceUnselectedPaint = paint;
+
+ if (!isSelected()) {
+ m_view.m_edgeDetails.overrideSourceArrowPaint(m_inx, m_sourceUnselectedPaint);
+ m_view.m_contentChanged = true;
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param paint DOCUMENT ME!
+ */
+ public void setTargetEdgeEndPaint(Paint paint) {
+ synchronized (m_view.m_lock) {
+ if (paint == null)
+ throw new NullPointerException("paint is null");
+
+ m_targetUnselectedPaint = paint;
+
+ if (!isSelected()) {
+ m_view.m_edgeDetails.overrideTargetArrowPaint(m_inx, m_targetUnselectedPaint);
+ m_view.m_contentChanged = true;
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void select() {
+ final boolean somethingChanged;
+
+ synchronized (m_view.m_lock) {
+ somethingChanged = selectInternal(true);
+
+ if (somethingChanged)
+ m_view.m_contentChanged = true;
+ }
+
+ if (somethingChanged) {
+ final GraphViewChangeListener listener = m_view.m_lis[0];
+
+ if (listener != null)
+ listener.graphViewChanged(new GraphViewEdgesSelectedEvent(m_view,
+ new int[] { ~m_inx }));
+ }
+ }
+
+ // Should synchronize around m_view.m_lock.
+ boolean selectInternal(boolean selectAnchors) {
+ if (m_selected)
+ return false;
+
+ m_selected = true;
+ m_view.m_edgeDetails.overrideSegmentPaint(m_inx, m_selectedPaint);
+ m_view.m_edgeDetails.overrideSourceArrowPaint(m_inx, m_sourceSelectedPaint);
+ m_view.m_edgeDetails.overrideTargetArrowPaint(m_inx, m_targetSelectedPaint);
+
+ if (m_selectedPaint instanceof Color)
+ m_view.m_edgeDetails.overrideColorLowDetail(m_inx, (Color) m_selectedPaint);
+
+ m_view.m_selectedEdges.insert(m_inx);
+
+ for (int j = 0; j < numHandles(); j++) {
+ getHandleInternal(j, m_view.m_anchorsBuff);
+ m_view.m_spacialA.insert((m_inx << 6) | j,
+ (float) (m_view.m_anchorsBuff[0]
+ - (m_view.getAnchorSize() / 2.0d)),
+ (float) (m_view.m_anchorsBuff[1]
+ - (m_view.getAnchorSize() / 2.0d)),
+ (float) (m_view.m_anchorsBuff[0]
+ + (m_view.getAnchorSize() / 2.0d)),
+ (float) (m_view.m_anchorsBuff[1]
+ + (m_view.getAnchorSize() / 2.0d)));
+
+ if (selectAnchors)
+ m_view.m_selectedAnchors.insert((m_inx << 6) | j);
+ }
+
+ return true;
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void unselect() {
+ final boolean somethingChanged;
+
+ synchronized (m_view.m_lock) {
+ somethingChanged = unselectInternal();
+
+ if (somethingChanged)
+ m_view.m_contentChanged = true;
+ }
+
+ if (somethingChanged) {
+ final GraphViewChangeListener listener = m_view.m_lis[0];
+
+ if (listener != null)
+ listener.graphViewChanged(new GraphViewEdgesUnselectedEvent(m_view,
+ new int[] { ~m_inx }));
+ }
+ }
+
+ // Should synchronize around m_view.m_lock.
+ boolean unselectInternal() {
+ if (!m_selected)
+ return false;
+
+ m_selected = false;
+ m_view.m_edgeDetails.overrideSegmentPaint(m_inx, m_unselectedPaint);
+ m_view.m_edgeDetails.overrideSourceArrowPaint(m_inx, m_sourceUnselectedPaint);
+ m_view.m_edgeDetails.overrideTargetArrowPaint(m_inx, m_targetUnselectedPaint);
+
+ if (m_unselectedPaint instanceof Color)
+ m_view.m_edgeDetails.overrideColorLowDetail(m_inx, (Color) m_unselectedPaint);
+
+ m_view.m_selectedEdges.delete(m_inx);
+
+ for (int j = 0; j < numHandles(); j++) {
+ m_view.m_selectedAnchors.delete((m_inx << 6) | j);
+ m_view.m_spacialA.delete((m_inx << 6) | j);
+ }
+
+ return true;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param state DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean setSelected(boolean state) {
+ if (state)
+ select();
+ else
+ unselect();
+
+ return true;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isSelected() {
+ return m_selected;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean getSelected() {
+ return m_selected;
+ }
+
+ final public boolean isHidden() {
+ return m_view.isHidden(this);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void updateEdgeView() {
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void updateTargetArrow() {
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void updateSourceArrow() {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param type DOCUMENT ME!
+ */
+ public void setSourceEdgeEnd(final int type) {
+ synchronized (m_view.m_lock) {
+ // if (type == m_sourceEdgeEnd) { return; }
+ switch (type) {
+ case NO_END:
+ m_view.m_edgeDetails.overrideSourceArrow(m_inx, GraphGraphics.ARROW_NONE);
+
+ break;
+
+ case WHITE_DELTA:
+ case BLACK_DELTA:
+ case EDGE_COLOR_DELTA:
+ m_view.m_edgeDetails.overrideSourceArrow(m_inx, GraphGraphics.ARROW_DELTA);
+
+ break;
+
+ case WHITE_ARROW:
+ case BLACK_ARROW:
+ case EDGE_COLOR_ARROW:
+ m_view.m_edgeDetails.overrideSourceArrow(m_inx, GraphGraphics.ARROW_ARROWHEAD);
+
+ break;
+
+ case WHITE_DIAMOND:
+ case BLACK_DIAMOND:
+ case EDGE_COLOR_DIAMOND:
+ m_view.m_edgeDetails.overrideSourceArrow(m_inx, GraphGraphics.ARROW_DIAMOND);
+
+ break;
+
+ case WHITE_CIRCLE:
+ case BLACK_CIRCLE:
+ case EDGE_COLOR_CIRCLE:
+ m_view.m_edgeDetails.overrideSourceArrow(m_inx, GraphGraphics.ARROW_DISC);
+
+ break;
+
+ case WHITE_T:
+ case BLACK_T:
+ case EDGE_COLOR_T:
+ m_view.m_edgeDetails.overrideSourceArrow(m_inx, GraphGraphics.ARROW_TEE);
+
+ break;
+
+ case EDGE_HALF_ARROW_BOTTOM:
+ m_view.m_edgeDetails.overrideSourceArrow(m_inx, GraphGraphics.ARROW_HALF_BOTTOM);
+ break;
+ case EDGE_HALF_ARROW_TOP:
+ m_view.m_edgeDetails.overrideSourceArrow(m_inx, GraphGraphics.ARROW_HALF_TOP);
+ break;
+
+ default:
+ throw new IllegalArgumentException("unrecognized edge end type");
+ }
+
+ m_sourceEdgeEnd = type;
+ m_view.m_contentChanged = true;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param type DOCUMENT ME!
+ */
+ public void setTargetEdgeEnd(int type) {
+ synchronized (m_view.m_lock) {
+ // if (type == m_targetEdgeEnd) { return; }
+ switch (type) {
+ case NO_END:
+ m_view.m_edgeDetails.overrideTargetArrow(m_inx, GraphGraphics.ARROW_NONE);
+
+ break;
+
+ case WHITE_DELTA:
+ case BLACK_DELTA:
+ case EDGE_COLOR_DELTA:
+ m_view.m_edgeDetails.overrideTargetArrow(m_inx, GraphGraphics.ARROW_DELTA);
+
+ break;
+
+ case WHITE_ARROW:
+ case BLACK_ARROW:
+ case EDGE_COLOR_ARROW:
+ m_view.m_edgeDetails.overrideTargetArrow(m_inx, GraphGraphics.ARROW_ARROWHEAD);
+
+ break;
+
+ case WHITE_DIAMOND:
+ case BLACK_DIAMOND:
+ case EDGE_COLOR_DIAMOND:
+ m_view.m_edgeDetails.overrideTargetArrow(m_inx, GraphGraphics.ARROW_DIAMOND);
+
+ break;
+
+ case WHITE_CIRCLE:
+ case BLACK_CIRCLE:
+ case EDGE_COLOR_CIRCLE:
+ m_view.m_edgeDetails.overrideTargetArrow(m_inx, GraphGraphics.ARROW_DISC);
+
+ break;
+
+ case WHITE_T:
+ case BLACK_T:
+ case EDGE_COLOR_T:
+ m_view.m_edgeDetails.overrideTargetArrow(m_inx, GraphGraphics.ARROW_TEE);
+
+ break;
+ case EDGE_HALF_ARROW_BOTTOM:
+ m_view.m_edgeDetails.overrideTargetArrow(m_inx, GraphGraphics.ARROW_HALF_BOTTOM);
+ break;
+ case EDGE_HALF_ARROW_TOP:
+ m_view.m_edgeDetails.overrideTargetArrow(m_inx, GraphGraphics.ARROW_HALF_TOP);
+ break;
+
+ default:
+ throw new IllegalArgumentException("unrecognized edge end type");
+ }
+
+ m_targetEdgeEnd = type;
+ m_view.m_contentChanged = true;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getSourceEdgeEnd() {
+ return m_sourceEdgeEnd;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getTargetEdgeEnd() {
+ return m_targetEdgeEnd;
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void updateLine() {
+ }
+
+ // This is also a method on giny.view.Bend.
+ /**
+ * DOCUMENT ME!
+ */
+ public void drawSelected() {
+ select();
+ }
+
+ // This is also a method on giny.view.Bend.
+ /**
+ * DOCUMENT ME!
+ */
+ public void drawUnselected() {
+ unselect();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Bend getBend() {
+ return this;
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void clearBends() {
+ removeAllHandles();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Label getLabel() {
+ return this;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param tip DOCUMENT ME!
+ */
+ public void setToolTip(String tip) {
+ m_toolTipText = tip;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getToolTip() {
+ return m_toolTipText;
+ }
+
+ // Interface giny.view.Label:
+ /**
+ * DOCUMENT ME!
+ *
+ * @param position DOCUMENT ME!
+ */
+ public void setPositionHint(int position) {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Paint getTextPaint() {
+ synchronized (m_view.m_lock) {
+ return m_view.m_edgeDetails.labelPaint(m_inx, 0);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param textPaint DOCUMENT ME!
+ */
+ public void setTextPaint(Paint textPaint) {
+ synchronized (m_view.m_lock) {
+ m_view.m_edgeDetails.overrideLabelPaint(m_inx, 0, textPaint);
+ m_view.m_contentChanged = true;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public double getGreekThreshold() {
+ return 0.0d;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param threshold DOCUMENT ME!
+ */
+ public void setGreekThreshold(double threshold) {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getText() {
+ synchronized (m_view.m_lock) {
+ return m_view.m_edgeDetails.labelText(m_inx, 0);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param text DOCUMENT ME!
+ */
+ public void setText(String text) {
+ synchronized (m_view.m_lock) {
+ m_view.m_edgeDetails.overrideLabelText(m_inx, 0, text);
+
+ if (DEFAULT_LABEL_TEXT.equals(m_view.m_edgeDetails.labelText(m_inx, 0)))
+ m_view.m_edgeDetails.overrideLabelCount(m_inx, 0);
+ else
+ m_view.m_edgeDetails.overrideLabelCount(m_inx, 1);
+
+ m_view.m_contentChanged = true;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Font getFont() {
+ synchronized (m_view.m_lock) {
+ return m_view.m_edgeDetails.labelFont(m_inx, 0);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param font DOCUMENT ME!
+ */
+ public void setFont(Font font) {
+ synchronized (m_view.m_lock) {
+ m_view.m_edgeDetails.overrideLabelFont(m_inx, 0, font);
+ m_view.m_contentChanged = true;
+ }
+ }
+
+ // Interface giny.view.Bend:
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int numHandles() {
+ synchronized (m_view.m_lock) {
+ if (m_anchors == null)
+ return 0;
+
+ return m_anchors.size();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param bendPoints DOCUMENT ME!
+ */
+ public void setHandles(List bendPoints) {
+ synchronized (m_view.m_lock) {
+ removeAllHandles();
+
+ for (int i = 0; i < bendPoints.size(); i++) {
+ final Point2D nextPt = (Point2D) bendPoints.get(i);
+ addHandle(i, nextPt);
+ }
+
+ m_view.m_contentChanged = true;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public List getHandles() {
+ synchronized (m_view.m_lock) {
+ final ArrayList returnThis = new ArrayList();
+
+ if (m_anchors == null)
+ return returnThis;
+
+ for (int i = 0; i < m_anchors.size(); i++) {
+ final Point2D addThis = new Point2D.Float();
+ addThis.setLocation((Point2D) m_anchors.get(i));
+ returnThis.add(addThis);
+ }
+
+ return returnThis;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param inx DOCUMENT ME!
+ * @param pt DOCUMENT ME!
+ */
+ public void moveHandle(int inx, Point2D pt) {
+ synchronized (m_view.m_lock) {
+ moveHandleInternal(inx, pt.getX(), pt.getY());
+ m_view.m_contentChanged = true;
+ }
+ }
+
+ final void moveHandleInternal(int inx, double x, double y) {
+ final Point2D movePt = (Point2D) m_anchors.get(inx);
+ movePt.setLocation(x, y);
+
+ if (m_view.m_spacialA.delete((m_inx << 6) | inx))
+ m_view.m_spacialA.insert((m_inx << 6) | inx,
+ (float) (x - (m_view.getAnchorSize() / 2.0d)),
+ (float) (y - (m_view.getAnchorSize() / 2.0d)),
+ (float) (x + (m_view.getAnchorSize() / 2.0d)),
+ (float) (y + (m_view.getAnchorSize() / 2.0d)));
+ }
+
+ final void getHandleInternal(int inx, float[] buff) {
+ final Point2D.Float pt = (Point2D.Float) m_anchors.get(inx);
+ buff[0] = pt.x;
+ buff[1] = pt.y;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Point2D getSourceHandlePoint() {
+ synchronized (m_view.m_lock) {
+ if ((m_anchors == null) || (m_anchors.size() == 0))
+ return null;
+
+ final Point2D returnThis = new Point2D.Float();
+ returnThis.setLocation((Point2D) m_anchors.get(0));
+
+ return returnThis;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Point2D getTargetHandlePoint() {
+ synchronized (m_view.m_lock) {
+ if ((m_anchors == null) || (m_anchors.size() == 0))
+ return null;
+
+ final Point2D returnThis = new Point2D.Float();
+ returnThis.setLocation((Point2D) m_anchors.get(m_anchors.size() - 1));
+
+ return returnThis;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param pt DOCUMENT ME!
+ */
+ public void addHandle(Point2D pt) {
+ addHandleFoo(pt);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param pt DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int addHandleFoo(Point2D pt) {
+ synchronized (m_view.m_lock) {
+ if ((m_anchors == null) || (m_anchors.size() == 0)) {
+ addHandle(0, pt);
+
+ return 0;
+ }
+
+ final Point2D sourcePt = m_view.getNodeView(~((FixedGraph) m_view.m_structPersp)
+ [...]
+ .getOffset();
+ final Point2D targetPt = m_view.getNodeView(~((FixedGraph) m_view.m_structPersp)
+ [...]
+ .getOffset();
+ double bestDist = (pt.distance(sourcePt) + pt.distance((Point2D) m_anchors.get(0)))
+ - sourcePt.distance((Point2D) m_anchors.get(0));
+ int bestInx = 0;
+
+ for (int i = 1; i < m_anchors.size(); i++) {
+ final double distCand = (pt.distance((Point2D) m_anchors.get(i - 1))
+ + pt.distance((Point2D) m_anchors.get(i)))
+ - ((Point2D) m_anchors.get(i)).distance((Point2D) m_anchors
+ .get(i - 1));
+
+ if (distCand < bestDist) {
+ bestDist = distCand;
+ bestInx = i;
+ }
+ }
+
+ final double lastCand = (pt.distance(targetPt)
+ + pt.distance((Point2D) m_anchors.get(m_anchors.size() - 1)))
+ - targetPt.distance((Point2D) m_anchors.get(m_anchors.size()
+ - 1));
+
+ if (lastCand < bestDist) {
+ bestDist = lastCand;
+ bestInx = m_anchors.size();
+ }
+
+ addHandle(bestInx, pt);
+
+ return bestInx;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param insertInx DOCUMENT ME!
+ * @param pt DOCUMENT ME!
+ */
+ public void addHandle(int insertInx, Point2D pt) {
+ synchronized (m_view.m_lock) {
+ final Point2D.Float addThis = new Point2D.Float();
+ addThis.setLocation(pt);
+
+ if (m_anchors == null)
+ m_anchors = new ArrayList();
+
+ m_anchors.add(insertInx, addThis);
+
+ if (m_selected) {
+ for (int j = m_anchors.size() - 1; j > insertInx; j--) {
+ m_view.m_spacialA.exists((m_inx << 6) | (j - 1), m_view.m_extentsBuff, 0);
+ m_view.m_spacialA.delete((m_inx << 6) | (j - 1));
+ m_view.m_spacialA.insert((m_inx << 6) | j, m_view.m_extentsBuff[0],
+ m_view.m_extentsBuff[1], m_view.m_extentsBuff[2],
+ m_view.m_extentsBuff[3]);
+
+ if (m_view.m_selectedAnchors.delete((m_inx << 6) | (j - 1)))
+ m_view.m_selectedAnchors.insert((m_inx << 6) | j);
+ }
+
+ m_view.m_spacialA.insert((m_inx << 6) | insertInx,
+ (float) (addThis.x - (m_view.getAnchorSize() / 2.0d)),
+ (float) (addThis.y - (m_view.getAnchorSize() / 2.0d)),
+ (float) (addThis.x + (m_view.getAnchorSize() / 2.0d)),
+ (float) (addThis.y + (m_view.getAnchorSize() / 2.0d)));
+ }
+
+ m_view.m_contentChanged = true;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param pt DOCUMENT ME!
+ */
+ public void removeHandle(Point2D pt) {
+ synchronized (m_view.m_lock) {
+ final float x = (float) pt.getX();
+ final float y = (float) pt.getY();
+
+ if (m_anchors == null)
+ return;
+
+ for (int i = 0; i < m_anchors.size(); i++) {
+ final Point2D.Float currPt = (Point2D.Float) m_anchors.get(i);
+
+ if ((x == currPt.x) && (y == currPt.y)) {
+ removeHandle(i);
+
+ break;
+ }
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param inx DOCUMENT ME!
+ */
+ public void removeHandle(int inx) {
+ synchronized (m_view.m_lock) {
+ m_anchors.remove(inx);
+
+ if (m_selected) {
+ m_view.m_spacialA.delete((m_inx << 6) | inx);
+ m_view.m_selectedAnchors.delete((m_inx << 6) | inx);
+
+ for (int j = inx; j < m_anchors.size(); j++) {
+ m_view.m_spacialA.exists((m_inx << 6) | (j + 1), m_view.m_extentsBuff, 0);
+ m_view.m_spacialA.delete((m_inx << 6) | (j + 1));
+ m_view.m_spacialA.insert((m_inx << 6) | j, m_view.m_extentsBuff[0],
+ m_view.m_extentsBuff[1], m_view.m_extentsBuff[2],
+ m_view.m_extentsBuff[3]);
+
+ if (m_view.m_selectedAnchors.delete((m_inx << 6) | (j + 1)))
+ m_view.m_selectedAnchors.insert((m_inx << 6) | j);
+ }
+ }
+
+ if (m_anchors.size() == 0)
+ m_anchors = null;
+
+ m_view.m_contentChanged = true;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void removeAllHandles() {
+ synchronized (m_view.m_lock) {
+ if (m_anchors == null)
+ return;
+
+ if (m_selected) {
+ for (int j = 0; j < m_anchors.size(); j++) {
+ m_view.m_spacialA.delete((m_inx << 6) | j);
+ m_view.m_selectedAnchors.delete((m_inx << 6) | j);
+ }
+ }
+
+ m_anchors = null;
+ m_view.m_contentChanged = true;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param pt DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean handleAlreadyExists(Point2D pt) {
+ synchronized (m_view.m_lock) {
+ final float x = (float) pt.getX();
+ final float y = (float) pt.getY();
+
+ if (m_anchors == null)
+ return false;
+
+ for (int i = 0; i < m_anchors.size(); i++) {
+ final Point2D.Float currPt = (Point2D.Float) m_anchors.get(i);
+
+ if ((x == currPt.x) && (y == currPt.y))
+ return true;
+ }
+
+ return false;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Point2D[] getDrawPoints() {
+ synchronized (m_view.m_lock) {
+ final Point2D[] returnThis = new Point2D[(m_anchors == null) ? 0 : m_anchors.size()];
+
+ for (int i = 0; i < returnThis.length; i++) {
+ returnThis[i] = new Point2D.Float();
+ returnThis[i].setLocation((Point2D) m_anchors.get(i));
+ }
+
+ return returnThis;
+ }
+ }
+
+ // Interface cytoscape.render.immed.EdgeAnchors:
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int numAnchors() {
+ if (m_anchors == null)
+ return 0;
+
+ if (m_lineType == EdgeView.CURVED_LINES)
+ return m_anchors.size();
+ else
+
+ return 2 * m_anchors.size();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param anchorIndex DOCUMENT ME!
+ * @param anchorArr DOCUMENT ME!
+ * @param offset DOCUMENT ME!
+ */
+ public void getAnchor(int anchorIndex, float[] anchorArr, int offset) {
+ final Point2D.Float anchor;
+
+ if (m_lineType == EdgeView.CURVED_LINES)
+ anchor = (Point2D.Float) m_anchors.get(anchorIndex);
+ else
+ anchor = (Point2D.Float) m_anchors.get(anchorIndex / 2);
+
+ anchorArr[offset] = anchor.x;
+ anchorArr[offset + 1] = anchor.y;
+ }
+
+ // Auxillary methods for edge anchors.
+ /**
+ * DOCUMENT ME!
+ *
+ * @param position DOCUMENT ME!
+ */
+ public void setTextAnchor(int position) {
+ System.out.println("setTextAnchor");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param justify DOCUMENT ME!
+ */
+ public void setJustify(int justify) {
+ System.out.println("setJustify");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getTextAnchor() {
+ System.out.println("getTextAnchor");
+
+ return 0;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getJustify() {
+ System.out.println("getJustify");
+
+ return 0;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param x DOCUMENT ME!
+ */
+ public void setLabelOffsetX(double x) {
+ System.out.println("setLabelOffsetX");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param y DOCUMENT ME!
+ */
+ public void setLabelOffsetY(double y) {
+ System.out.println("setLabelOffsetY");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param position DOCUMENT ME!
+ */
+ public void setEdgeLabelAnchor(int position) {
+ System.out.println("setEdgeLabelAnchor");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public double getLabelOffsetX() {
+ System.out.println("getLabelOffsetX");
+
+ return 0.0;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public double getLabelOffsetY() {
+ System.out.println("getLabelOffsetY");
+
+ return 0.0;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getEdgeLabelAnchor() {
+ System.out.println("getEdgeLabelAnchor");
+
+ return 0;
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param width DOCUMENT ME!
+ */
+ public void setLabelWidth(double width) {
+ synchronized (m_view.m_lock) {
+ m_view.m_edgeDetails.overrideLabelWidth(m_inx, width);
+ m_view.m_contentChanged = true;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public double getLabelWidth() {
+ synchronized (m_view.m_lock) {
+ return m_view.m_edgeDetails.labelWidth(m_inx);
+ }
+ }
+
+ public ObjectPosition getPosition() {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ public void setPosition(ObjectPosition arg0) {
+ // TODO Auto-generated method stub
+
+ }
+
+}
diff --git a/corelibs/ding/src/main/java/ding/view/DGraphView.java b/corelibs/ding/src/main/java/ding/view/DGraphView.java
new file mode 100644
index 0000000..4bc04ef
--- /dev/null
+++ b/corelibs/ding/src/main/java/ding/view/DGraphView.java
@@ -0,0 +1,2683 @@
+/*
+ Copyright (c) 2006, 2007, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package ding.view;
+
+
+import giny.model.Edge;
+import giny.model.GraphPerspective;
+import giny.model.Node;
+import giny.model.RootGraph;
+import giny.view.EdgeView;
+import giny.view.GraphView;
+import giny.view.GraphViewChangeListener;
+import giny.view.NodeView;
+
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Dimension;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.Image;
+import java.awt.Paint;
+import java.awt.Shape;
+import java.awt.TexturePaint;
+import java.awt.geom.GeneralPath;
+import java.awt.geom.Point2D;
+import java.awt.geom.Rectangle2D;
+import java.awt.image.BufferedImage;
+import java.awt.print.PageFormat;
+import java.awt.print.Printable;
+import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import javax.imageio.ImageIO;
+
+import cytoscape.geom.rtree.RTree;
+import cytoscape.geom.spacial.MutableSpacialIndex2D;
+import cytoscape.geom.spacial.SpacialEntry2DEnumerator;
+import cytoscape.graph.fixed.FixedGraph;
+import cytoscape.render.immed.GraphGraphics;
+import cytoscape.render.stateful.GraphLOD;
+import cytoscape.render.stateful.GraphRenderer;
+import cytoscape.util.intr.IntBTree;
+import cytoscape.util.intr.IntEnumerator;
+import cytoscape.util.intr.IntHash;
+import cytoscape.util.intr.IntStack;
+
+
+/**
+ * DING implementation of the GINY view.
+ *
+ * Explain relationship to cytoscape.
+ *
+ * Throughout this code I am assuming that nodes or edges are never
+ * removed from the underlying RootGraph. This assumption was made in the
+ * old GraphView implementation. Removal from the RootGraph is the only
+ * thing that can affect m_drawPersp and m_structPersp that is beyond our
+ * control.
+ *
+ * @author Nerius Landys
+ */
+public class DGraphView implements GraphView, Printable {
+ boolean calledFromGetSnapshot = false;
+
+ // Size of snapshot image
+ protected static int DEF_SNAPSHOT_SIZE = 400;
+
+ static final float DEFAULT_ANCHOR_SIZE = 9.0f;
+ static final Paint DEFAULT_ANCHOR_SELECTED_PAINT = Color.red;
+ static final Paint DEFAULT_ANCHOR_UNSELECTED_PAINT = Color.black;
+
+ /**
+ * Enum to identify ding canvases -
+ * used in getCanvas(Canvas canvasId)
+ */
+ public enum Canvas {
+ BACKGROUND_CANVAS,
+ NETWORK_CANVAS,
+ FOREGROUND_CANVAS;
+ }
+
+ public enum ShapeType {
+ NODE_SHAPE,
+ LINE_TYPE,
+ ARROW_SHAPE;
+ }
+
+ /**
+ * Common object used for synchronization.
+ */
+ final Object m_lock = new Object();
+
+ /**
+ * A common buffer object used to pass information about.
+ * X-Y coords of the minimum bounding box?
+ */
+ final float[] m_extentsBuff = new float[4];
+
+ /**
+ * A common general path variable used for holding lots of shapes.
+ */
+ final GeneralPath m_path = new GeneralPath();
+
+ /**
+ * The graph model that will be viewed.
+ */
+ GraphPerspective m_perspective;
+
+ /**
+ * Holds the NodeView data for the nodes that are visible.
+ * This will change as nodes are hidden from the view.
+ */
+ GraphPerspective m_drawPersp;
+
+ /**
+ * Holds all of the NodeViews, regardless of whether they're visualized.
+ */
+ GraphPerspective m_structPersp;
+
+ /**
+ * RTree used for querying node positions.
+ */
+ MutableSpacialIndex2D m_spacial;
+
+ /**
+ * Another RTree, but what for?
+ */
+ MutableSpacialIndex2D m_spacialA;
+
+ /**
+ *
+ */
+ DNodeDetails m_nodeDetails;
+
+ /**
+ *
+ */
+ DEdgeDetails m_edgeDetails;
+
+ /**
+ * Level of detail specific to printing. Not used for rendering.
+ */
+ PrintLOD m_printLOD;
+
+ /**
+ *
+ */
+ HashMap m_nodeViewMap;
+
+ /**
+ *
+ */
+ HashMap m_edgeViewMap;
+
+ /**
+ *
+ */
+ String m_identifier;
+
+ /**
+ *
+ */
+ final float m_defaultNodeXMin;
+
+ /**
+ *
+ */
+ final float m_defaultNodeYMin;
+
+ /**
+ *
+ */
+ final float m_defaultNodeXMax;
+
+ /**
+ *
+ */
+ final float m_defaultNodeYMax;
+
+ /**
+ * Ref to network canvas object.
+ */
+ InnerCanvas m_networkCanvas;
+
+ /**
+ * Ref to background canvas object.
+ */
+ ArbitraryGraphicsCanvas m_backgroundCanvas;
+
+ /**
+ * Ref to foreground canvas object.
+ */
+ ArbitraryGraphicsCanvas m_foregroundCanvas;
+
+ /**
+ *
+ */
+ boolean m_nodeSelection = true;
+
+ /**
+ *
+ */
+ boolean m_edgeSelection = true;
+
+ /**
+ * BTree of selected nodes.
+ */
+ final IntBTree m_selectedNodes; // Positive.
+
+ /**
+ * BTree of selected edges.
+ */
+ final IntBTree m_selectedEdges; // Positive.
+
+ /**
+ * BTree of selected anchors.
+ */
+ final IntBTree m_selectedAnchors;
+
+ /**
+ * State variable for when nodes have moved.
+ */
+ boolean m_contentChanged = false;
+
+ /**
+ * State variable for when zooming/panning have changed.
+ */
+ boolean m_viewportChanged = false;
+
+ /**
+ * List of listeners.
+ */
+ final GraphViewChangeListener[] m_lis = new GraphViewChangeListener[1];
+
+ /**
+ * List of listeners.
+ */
+ final ContentChangeListener[] m_cLis = new ContentChangeListener[1];
+
+ /**
+ * List of listeners.
+ */
+ final ViewportChangeListener[] m_vLis = new ViewportChangeListener[1];
+
+ /**
+ * ???
+ */
+ private final IntHash m_hash = new IntHash();
+
+ /**
+ * Used for holding edge anchors.
+ */
+ final float[] m_anchorsBuff = new float[2];
+
+ /**
+ *
+ */
+ int m_lastSize = 0;
+
+ /**
+ * Used for caching texture paint.
+ */
+ Paint m_lastPaint = null;
+
+ /**
+ * Used for caching texture paint.
+ */
+ Paint m_lastTexturePaint = null;
+
+ /**
+ * Snapshot of current view. Will be updated by CONTENT_CHANGED event.
+ *
+ * This is used by a new nested network feature from 2.7.
+ */
+ private BufferedImage snapshotImage;
+
+ /**
+ * Represents current snapshot is latest version or not.
+ */
+ private boolean latest;
+
+ /**
+ * Creates a new DGraphView object.
+ *
+ * @param perspective The graph model that we'll be creating a view for.
+ */
+ public DGraphView(GraphPerspective perspective) {
+ m_perspective = perspective;
+
+ // creating empty graphs
+ m_drawPersp = m_perspective.getRootGraph().createGraphPerspective((int[]) null, (int[]) null);
+ m_structPersp = m_perspective.getRootGraph()
+ .createGraphPerspective((int[]) null, (int[]) null);
+ m_spacial = new RTree();
+ m_spacialA = new RTree();
+ m_nodeDetails = new DNodeDetails(this);
+ m_edgeDetails = new DEdgeDetails(this);
+ m_nodeViewMap = new HashMap();
+ m_edgeViewMap = new HashMap();
+ m_printLOD = new PrintLOD();
+ m_defaultNodeXMin = 0.0f;
+ m_defaultNodeYMin = 0.0f;
+ m_defaultNodeXMax = m_defaultNodeXMin + DNodeView.DEFAULT_WIDTH;
+ m_defaultNodeYMax = m_defaultNodeYMin + DNodeView.DEFAULT_HEIGHT;
+ m_networkCanvas = new InnerCanvas(m_lock, this);
+ m_backgroundCanvas = new ArbitraryGraphicsCanvas(m_perspective, this, m_networkCanvas,
+ Color.white, true, true);
+ addViewportChangeListener(m_backgroundCanvas);
+ m_foregroundCanvas = new ArbitraryGraphicsCanvas(m_perspective, this, m_networkCanvas,
+ Color.white, true, false);
+ addViewportChangeListener(m_foregroundCanvas);
+ m_selectedNodes = new IntBTree();
+ m_selectedEdges = new IntBTree();
+ m_selectedAnchors = new IntBTree();
+
+ // Add ContentChange Listener for handling nested network.
+ this.addContentChangeListener(new DGraphViewContentChangeListener());
+ // Snapshot image is always null at this point.
+ this.snapshotImage = null;
+ this.latest = false;
+ }
+
+ /**
+ * Returns the graph model that this view was created for.
+ *
+ * @return The GraphPerspective that the view was created for.
+ */
+ public GraphPerspective getGraphPerspective() {
+ return m_perspective;
+ }
+
+ public Object getLock(){
+ return m_lock;
+ }
+
+ public void setViewportChanged(boolean val){
+ m_viewportChanged=val;
+ }
+
+ /**
+ * Whether node selection is enabled.
+ *
+ * @return Whether node selection is enabled.
+ */
+ public boolean nodeSelectionEnabled() {
+ return m_nodeSelection;
+ }
+
+ /**
+ * Whether edge selection is enabled.
+ *
+ * @return Whether edge selection is enabled.
+ */
+ public boolean edgeSelectionEnabled() {
+ return m_edgeSelection;
+ }
+
+ /**
+ * Enabling the ability to select nodes.
+ */
+ public void enableNodeSelection() {
+ synchronized (m_lock) {
+ m_nodeSelection = true;
+ }
+ }
+
+ /**
+ * Disables the ability to select nodes.
+ */
+ public void disableNodeSelection() {
+ final int[] unselectedNodes;
+
+ synchronized (m_lock) {
+ m_nodeSelection = false;
+ unselectedNodes = getSelectedNodeIndices();
+
+ if (unselectedNodes.length > 0) {
+ // Adding this line to speed things up from O(n*log(n)) to O(n).
+ m_selectedNodes.empty();
+
+ for (int i = 0; i < unselectedNodes.length; i++)
+ ((DNodeView) getNodeView(unselectedNodes[i])).unselectInternal();
+
+ m_contentChanged = true;
+ }
+ }
+
+ if (unselectedNodes.length > 0) {
+ final GraphViewChangeListener listener = m_lis[0];
+
+ if (listener != null) {
+ listener.graphViewChanged(new GraphViewNodesUnselectedEvent(this, unselectedNodes));
+ }
+
+ // Update the view after listener events are fired because listeners
+ // may change something in the graph.
+ updateView();
+ }
+ }
+
+ /**
+ * Enables the ability to select edges.
+ */
+ public void enableEdgeSelection() {
+ synchronized (m_lock) {
+ m_edgeSelection = true;
+ }
+ }
+
+ /**
+ * Disables the ability to select edges.
+ */
+ public void disableEdgeSelection() {
+ final int[] unselectedEdges;
+
+ synchronized (m_lock) {
+ m_edgeSelection = false;
+ unselectedEdges = getSelectedEdgeIndices();
+
+ if (unselectedEdges.length > 0) {
+ // Adding this line to speed things up from O(n*log(n)) to O(n).
+ m_selectedEdges.empty();
+
+ for (int i = 0; i < unselectedEdges.length; i++)
+ ((DEdgeView) getEdgeView(unselectedEdges[i])).unselectInternal();
+
+ m_contentChanged = true;
+ }
+ }
+
+ if (unselectedEdges.length > 0) {
+ final GraphViewChangeListener listener = m_lis[0];
+
+ if (listener != null) {
+ listener.graphViewChanged(new GraphViewEdgesUnselectedEvent(this, unselectedEdges));
+ }
+
+ // Update the view after listener events are fired because listeners
+ // may change something in the graph.
+ updateView();
+ }
+ }
+
+ /**
+ * Returns an array of selected node indices.
+ *
+ * @return An array of selected node indices.
+ */
+ public int[] getSelectedNodeIndices() {
+ synchronized (m_lock) {
+ // all nodes from the btree
+ final IntEnumerator elms = m_selectedNodes.searchRange(Integer.MIN_VALUE,
+ Integer.MAX_VALUE, false);
+ final int[] returnThis = new int[elms.numRemaining()];
+
+ for (int i = 0; i < returnThis.length; i++)
+ // GINY requires all node indices to be negative (why?),
+ // hence the bitwise complement here.
+ returnThis[i] = ~elms.nextInt();
+
+ return returnThis;
+ }
+ }
+
+ /**
+ * Returns a list of selected node objects.
+ *
+ * @return A list of selected node objects.
+ */
+ public List getSelectedNodes() {
+ synchronized (m_lock) {
+ // all nodes from the btree
+ final IntEnumerator elms = m_selectedNodes.searchRange(Integer.MIN_VALUE,
+ Integer.MAX_VALUE, false);
+ final ArrayList returnThis = new ArrayList();
+
+ while (elms.numRemaining() > 0)
+ // GINY requires all node indices to be negative (why?),
+ // hence the bitwise complement here.
+ returnThis.add(m_nodeViewMap.get(new Integer(~elms.nextInt())));
+
+ return returnThis;
+ }
+ }
+
+ /**
+ * Returns an array of selected edge indices.
+ *
+ * @return An array of selected edge indices.
+ */
+ public int[] getSelectedEdgeIndices() {
+ synchronized (m_lock) {
+ final IntEnumerator elms = m_selectedEdges.searchRange(Integer.MIN_VALUE,
+ Integer.MAX_VALUE, false);
+ final int[] returnThis = new int[elms.numRemaining()];
+
+ for (int i = 0; i < returnThis.length; i++)
+ returnThis[i] = ~elms.nextInt();
+
+ return returnThis;
+ }
+ }
+
+ /**
+ * Returns a list of selected edge objects.
+ *
+ * @return A list of selected edge objects.
+ */
+ public List getSelectedEdges() {
+ synchronized (m_lock) {
+ final IntEnumerator elms = m_selectedEdges.searchRange(Integer.MIN_VALUE,
+ Integer.MAX_VALUE, false);
+ final ArrayList returnThis = new ArrayList();
+
+ while (elms.numRemaining() > 0)
+ returnThis.add(m_edgeViewMap.get(new Integer(~elms.nextInt())));
+
+ return returnThis;
+ }
+ }
+
+ /**
+ * Add GraphViewChangeListener to linked list of GraphViewChangeListeners.
+ * AAAAAARRRGGGGHHHHHH!!!!
+ *
+ * @param l GraphViewChangeListener to be added to the list.
+ */
+ public void addGraphViewChangeListener(GraphViewChangeListener l) {
+ m_lis[0] = GraphViewChangeListenerChain.add(m_lis[0], l);
+ }
+
+
+ /**
+ * Remove GraphViewChangeListener from linked list of GraphViewChangeListeners.
+ * AAAAAARRRGGGGHHHHHH!!!!
+ *
+ * @param l GraphViewChangeListener to be removed from the list.
+ */
+ public void removeGraphViewChangeListener(GraphViewChangeListener l) {
+ m_lis[0] = GraphViewChangeListenerChain.remove(m_lis[0], l);
+ }
+
+
+ /**
+ * Sets the background color on the canvas.
+ *
+ * @param paint The Paint (color) to apply to the background.
+ */
+ public void setBackgroundPaint(final Paint paint) {
+ synchronized (m_lock) {
+ if (paint instanceof Color) {
+ m_backgroundCanvas.setBackground((Color)paint);
+ m_contentChanged = true;
+ } else {
+ System.out.println("DGraphView.setBackgroundPaint(): Paint argument must be a Color instance!");
+ }
+ }
+ }
+
+
+ /**
+ * Returns the background color on the canvas.
+ *
+ * @return The background color on the canvas.
+ */
+ public Paint getBackgroundPaint() {
+ return m_backgroundCanvas.getBackground();
+ }
+
+
+ /**
+ * Returns the InnerCanvas object. The InnerCanvas object is the actual component
+ * that the network is rendered on.
+ *
+ * @return The InnerCanvas object.
+ */
+ public Component getComponent() {
+ return m_networkCanvas;
+ }
+
+
+ /**
+ * Adds a NodeView object to the GraphView. Creates NodeView if one doesn't already exist.
+ *
+ * @param nodeInx The index of the NodeView object to be added.
+ *
+ * @return The NodeView object that is added to the GraphView.
+ */
+ public NodeView addNodeView(int nodeInx) {
+ NodeView newView = null;
+
+ synchronized (m_lock) {
+ newView = addNodeViewInternal(nodeInx);
+
+ if (newView == null) {
+ return (NodeView) m_nodeViewMap.get(new Integer(nodeInx));
+ }
+
+ m_contentChanged = true;
+ }
+
+ final GraphViewChangeListener listener = m_lis[0];
+
+ if (listener != null) {
+ listener.graphViewChanged(new GraphViewNodesRestoredEvent(this,
+ new int[] {
+ newView.getRootGraphIndex()
+ }));
+ }
+
+ return newView;
+ }
+
+
+ /**
+ * Should synchronize around m_lock.
+ */
+ private NodeView addNodeViewInternal(int nodeInx) {
+ final NodeView oldView = (NodeView) m_nodeViewMap.get(new Integer(nodeInx));
+
+ if (oldView != null) {
+ return null;
+ }
+
+ if (m_drawPersp.restoreNode(nodeInx) == 0) {
+ if (m_drawPersp.getNode(nodeInx) != null) {
+ throw new IllegalStateException("something weird is going on - node already existed in graph "
+ + "but a view for it did not exist (debug)");
+ }
+
+ throw new IllegalArgumentException("node index specified does not exist in underlying RootGraph");
+ }
+
+ m_structPersp.restoreNode(nodeInx);
+
+ final NodeView newView;
+ newView = new DNodeView(this, nodeInx);
+ m_nodeViewMap.put(new Integer(nodeInx), newView);
+ m_spacial.insert(~nodeInx, m_defaultNodeXMin, m_defaultNodeYMin, m_defaultNodeXMax,
+ m_defaultNodeYMax);
+
+ return newView;
+ }
+
+
+ /**
+ * Adds EdgeView to the GraphView.
+ *
+ * @param edgeInx The index of EdgeView to be added.
+ *
+ * @return The EdgeView that was added.
+ */
+ public EdgeView addEdgeView(int edgeInx) {
+ NodeView sourceNode = null;
+ NodeView targetNode = null;
+ EdgeView edgeView = null;
+
+ synchronized (m_lock) {
+ final EdgeView oldView = (EdgeView) m_edgeViewMap.get(new Integer(edgeInx));
+
+ if (oldView != null) {
+ return oldView;
+ }
+
+ final Edge edge = m_drawPersp.getRootGraph().getEdge(edgeInx);
+
+ if (edge == null) {
+ throw new IllegalArgumentException("edge index specified does not exist in underlying RootGraph");
+ }
+
+ sourceNode = addNodeViewInternal(edge.getSource().getRootGraphIndex());
+ targetNode = addNodeViewInternal(edge.getTarget().getRootGraphIndex());
+
+ if (m_drawPersp.restoreEdge(edgeInx) == 0) {
+ if (m_drawPersp.getEdge(edgeInx) != null) {
+ throw new IllegalStateException("something weird is going on - edge already existed in graph "
+ + "but a view for it did not exist (debug)");
+ }
+
+ throw new IllegalArgumentException("edge index specified does not exist in underlying RootGraph");
+ }
+
+ m_structPersp.restoreEdge(edgeInx);
+ edgeView = new DEdgeView(this, edgeInx);
+ m_edgeViewMap.put(new Integer(edgeInx), edgeView);
+ m_contentChanged = true;
+ }
+
+ // Under no circumstances should we be holding m_lock when the listener
+ // events are fired.
+ final GraphViewChangeListener listener = m_lis[0];
+
+ if (listener != null) {
+ // Only fire this event if either of the nodes is new. The node
+ // will be null if it already existed.
+ if ((sourceNode != null) || (targetNode != null)) {
+ int[] nodeInx;
+
+ if (sourceNode == null) {
+ nodeInx = new int[] { targetNode.getRootGraphIndex() };
+ } else if (targetNode == null) {
+ nodeInx = new int[] { sourceNode.getRootGraphIndex() };
+ } else {
+ nodeInx = new int[] {
+ sourceNode.getRootGraphIndex(), targetNode.getRootGraphIndex()
+ };
+ }
+
+ listener.graphViewChanged(new GraphViewNodesRestoredEvent(this, nodeInx));
+ }
+
+ listener.graphViewChanged(new GraphViewEdgesRestoredEvent(this,
+ new int[] {
+ edgeView.getRootGraphIndex()
+ }));
+ }
+
+ return edgeView;
+ }
+
+
+ /**
+ * Will thrown an UnsupportedOperationException. Don't use this.
+ *
+ * @param className ???
+ * @param edgeInx ???
+ *
+ * @return Nothing, an exception will be thrown.
+ */
+ public EdgeView addEdgeView(String className, int edgeInx) {
+ throw new UnsupportedOperationException("not implemented");
+ }
+
+
+ /**
+ * Will thrown an UnsupportedOperationException. Don't use this.
+ *
+ * @param className ???
+ * @param nodeInx ???
+ *
+ * @return Nothing, an exception will be thrown.
+ */
+ public NodeView addNodeView(String className, int nodeInx) {
+ throw new UnsupportedOperationException("not implemented");
+ }
+
+
+ /**
+ * Will thrown an UnsupportedOperationException. Don't use this.
+ *
+ * @param nodeInx ??
+ * @param replacement ??
+ *
+ * @return Nothing, an exception will be thrown.
+ */
+ public NodeView addNodeView(int nodeInx, NodeView replacement) {
+ throw new UnsupportedOperationException("not implemented");
+ }
+
+
+ /**
+ * Removes a NodeView based on specified NodeView.
+ *
+ * @param nodeView The NodeView object to be removed.
+ *
+ * @return The NodeView object that was removed.
+ */
+ public NodeView removeNodeView(NodeView nodeView) {
+ return removeNodeView(nodeView.getRootGraphIndex());
+ }
+
+
+ /**
+ * Removes a NodeView based on specified Node.
+ *
+ * @param node The Node object connected to the NodeView to be removed.
+ *
+ * @return The NodeView object that was removed.
+ */
+ public NodeView removeNodeView(Node node) {
+ return removeNodeView(node.getRootGraphIndex());
+ }
+
+
+ /**
+ * Removes a NodeView based on a specified index.
+ *
+ * @param nodeInx The index of the NodeView to be removed.
+ *
+ * @return The NodeView object that was removed.
+ */
+ public NodeView removeNodeView(int nodeInx) {
+ final int[] hiddenEdgeInx;
+ final DNodeView returnThis;
+
+ synchronized (m_lock) {
+ // We have to query edges in the m_structPersp, not m_drawPersp
+ // because what if the node is hidden?
+ hiddenEdgeInx = m_structPersp.getAdjacentEdgeIndicesArray(nodeInx, true, true, true);
+
+ // This isn't an error. Only if the nodeInx is invalid will getAdjacentEdgeIndicesArray
+ // return null. If there are no adjacent edges, then it will return an array of length 0.
+ if (hiddenEdgeInx == null) {
+ return null;
+ }
+
+ for (int i = 0; i < hiddenEdgeInx.length; i++)
+ removeEdgeViewInternal(hiddenEdgeInx[i]);
+
+ returnThis = (DNodeView) m_nodeViewMap.remove(new Integer(nodeInx));
+ returnThis.unselectInternal();
+
+ // If this node was hidden, it won't be in m_drawPersp.
+ m_drawPersp.hideNode(nodeInx);
+ m_structPersp.hideNode(nodeInx);
+ m_nodeDetails.unregisterNode(~nodeInx);
+
+ // If this node was hidden, it won't be in m_spacial.
+ m_spacial.delete(~nodeInx);
+
+ // m_selectedNodes.delete(~nodeInx);
+ returnThis.graphView = null;
+ m_contentChanged = true;
+ }
+
+ final GraphViewChangeListener listener = m_lis[0];
+
+ if (listener != null) {
+ if (hiddenEdgeInx.length > 0) {
+ listener.graphViewChanged(new GraphViewEdgesHiddenEvent(this, hiddenEdgeInx));
+ }
+
+ listener.graphViewChanged(new GraphViewNodesHiddenEvent(this,
+ new int[] {
+ returnThis.getRootGraphIndex()
+ }));
+ }
+
+ return returnThis;
+ }
+
+ /**
+ * Removes an EdgeView based on an EdgeView.
+ *
+ * @param edgeView The EdgeView to be removed.
+ *
+ * @return The EdgeView that was removed.
+ */
+ public EdgeView removeEdgeView(EdgeView edgeView) {
+ return removeEdgeView(edgeView.getRootGraphIndex());
+ }
+
+ /**
+ * Removes an EdgeView based on an Edge.
+ *
+ * @param edge The Edge of the EdgeView to be removed.
+ *
+ * @return The EdgeView that was removed.
+ */
+ public EdgeView removeEdgeView(Edge edge) {
+ return removeEdgeView(edge.getRootGraphIndex());
+ }
+
+ /**
+ * Removes an EdgeView based on an EdgeIndex.
+ *
+ * @param edgeInx The edge index of the EdgeView to be removed.
+ *
+ * @return The EdgeView that was removed.
+ */
+ public EdgeView removeEdgeView(int edgeInx) {
+ final DEdgeView returnThis;
+
+ synchronized (m_lock) {
+ returnThis = removeEdgeViewInternal(edgeInx);
+
+ if (returnThis != null) {
+ m_contentChanged = true;
+ }
+ }
+
+ if (returnThis != null) {
+ final GraphViewChangeListener listener = m_lis[0];
+
+ if (listener != null) {
+ listener.graphViewChanged(new GraphViewEdgesHiddenEvent(this,
+ new int[] {
+ returnThis.getRootGraphIndex()
+ }));
+ }
+ }
+
+ return returnThis;
+ }
+
+ /**
+ * Should synchronize around m_lock.
+ */
+ private DEdgeView removeEdgeViewInternal(int edgeInx) {
+ final DEdgeView returnThis = (DEdgeView) m_edgeViewMap.remove(new Integer(edgeInx));
+
+ if (returnThis == null) {
+ return returnThis;
+ }
+
+ returnThis.unselectInternal();
+
+ // If this edge view was hidden, it won't be in m_drawPersp.
+ m_drawPersp.hideEdge(edgeInx);
+ m_structPersp.hideEdge(edgeInx);
+ m_edgeDetails.unregisterEdge(~edgeInx);
+
+ // m_selectedEdges.delete(~edgeInx);
+ returnThis.m_view = null;
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getIdentifier() {
+ return m_identifier;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param id
+ * DOCUMENT ME!
+ */
+ public void setIdentifier(String id) {
+ m_identifier = id;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public double getZoom() {
+ return m_networkCanvas.m_scaleFactor;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param zoom
+ * DOCUMENT ME!
+ */
+ private void setZoom(final double zoom, final boolean updateView) {
+ synchronized (m_lock) {
+ m_networkCanvas.m_scaleFactor = checkZoom(zoom,m_networkCanvas.m_scaleFactor);
+ m_viewportChanged = true;
+ }
+
+ if (updateView) {
+ this.updateView();
+ }
+ }
+
+
+ /**
+ * Set the zoom level and redraw the view.
+ */
+ public void setZoom(final double zoom) {
+ setZoom(zoom, /* updateView = */ true);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ private void fitContent(final boolean updateView) {
+ synchronized (m_lock) {
+ if (m_spacial.queryOverlap(Float.NEGATIVE_INFINITY, Float.NEGATIVE_INFINITY,
+ Float.POSITIVE_INFINITY, Float.POSITIVE_INFINITY,
+ m_extentsBuff, 0, false).numRemaining() == 0) {
+ return;
+ }
+
+ m_networkCanvas.m_xCenter = (((double) m_extentsBuff[0]) + ((double) m_extentsBuff[2])) / 2.0d;
+ m_networkCanvas.m_yCenter = (((double) m_extentsBuff[1]) + ((double) m_extentsBuff[3])) / 2.0d;
+ final double zoom = Math.min(((double) m_networkCanvas.getWidth()) /
+ (((double) m_extentsBuff[2]) -
+ ((double) m_extentsBuff[0])),
+ ((double) m_networkCanvas.getHeight()) /
+ (((double) m_extentsBuff[3]) -
+ ((double) m_extentsBuff[1])));
+ m_networkCanvas.m_scaleFactor = checkZoom(zoom,m_networkCanvas.m_scaleFactor);
+ if (calledFromGetSnapshot) {
+ calledFromGetSnapshot = false;
+ m_networkCanvas.m_scaleFactor = 1.0;
+ //System.out.println("in fitContent(), m_networkCanvas.m_scaleFactor = " + m_networkCanvas.m_scaleFactor);
+ }
+ m_viewportChanged = true;
+ }
+ if (updateView) {
+ this.updateView();
+ }
+ }
+
+ /**
+ * Resize the network view to the size of the canvas and redraw it.
+ */
+ public void fitContent() {
+ fitContent(/* updateView = */ true);
+ }
+
+
+ /**
+ * Repaint network canvas.
+ */
+ public void updateView() {
+ // Following is for performance testing
+ //System.out.println("**************** DGraph Redraw Called ***************** " + this.getGraphPerspective());
+ //Thread.dumpStack();
+ //System.out.println("**************** DGraph Redraw Finished *****************\n\n" );
+
+ m_networkCanvas.repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public RootGraph getRootGraph() {
+ return m_perspective.getRootGraph();
+ }
+
+ /*
+ * Returns an iterator of all node views, including those that are currently
+ * hidden.
+ */
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Iterator getNodeViewsIterator() {
+ synchronized (m_lock) {
+ return m_nodeViewMap.values().iterator();
+ }
+ }
+
+ /*
+ * Returns the count of all node views, including those that are currently
+ * hidden.
+ */
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getNodeViewCount() {
+ synchronized (m_lock) {
+ return m_nodeViewMap.size();
+ }
+ }
+
+ /*
+ * Returns the count of all edge views, including those that are currently
+ * hidden.
+ */
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getEdgeViewCount() {
+ synchronized (m_lock) {
+ return m_edgeViewMap.size();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public NodeView getNodeView(Node node) {
+ return getNodeView(node.getRootGraphIndex());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nodeInx
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public NodeView getNodeView(int nodeInx) {
+ synchronized (m_lock) {
+ return (NodeView) m_nodeViewMap.get(new Integer(nodeInx));
+ }
+ }
+
+ /*
+ * Returns a list of all edge views, including those that are currently
+ * hidden.
+ */
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public List getEdgeViewsList() {
+ synchronized (m_lock) {
+ final ArrayList returnThis = new ArrayList(m_edgeViewMap.size());
+ final Iterator values = m_edgeViewMap.values().iterator();
+
+ while (values.hasNext())
+ returnThis.add(values.next());
+
+ return returnThis;
+ }
+ }
+
+ /*
+ * Returns all edge views (including the hidden ones) that are either 1.
+ * directed, having oneNode as source and otherNode as target or 2.
+ * undirected, having oneNode and otherNode as endpoints. Note that this
+ * behaviour is similar to that of GraphPerspective.edgesList(Node, Node).
+ */
+ /**
+ * DOCUMENT ME!
+ *
+ * @param oneNode DOCUMENT ME!
+ * @param otherNode DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public List getEdgeViewsList(Node oneNode, Node otherNode) {
+ synchronized (m_lock) {
+ List edges = m_structPersp.edgesList(oneNode.getRootGraphIndex(),
+ otherNode.getRootGraphIndex(), true);
+
+ if (edges == null) {
+ return null;
+ }
+
+ final ArrayList returnThis = new ArrayList();
+ Iterator it = edges.iterator();
+
+ while (it.hasNext()) {
+ Edge e = (Edge) it.next();
+ returnThis.add(getEdgeView(e));
+ }
+
+ return returnThis;
+ }
+ }
+
+ /*
+ * Similar to getEdgeViewsList(Node, Node), only that one has control of
+ * whether or not to include undirected edges.
+ */
+ /**
+ * DOCUMENT ME!
+ *
+ * @param oneNodeInx DOCUMENT ME!
+ * @param otherNodeInx DOCUMENT ME!
+ * @param includeUndirected DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public List getEdgeViewsList(int oneNodeInx, int otherNodeInx, boolean includeUndirected) {
+ synchronized (m_lock) {
+ List edges = m_structPersp.edgesList(oneNodeInx, otherNodeInx, includeUndirected);
+
+ if (edges == null) {
+ return null;
+ }
+
+ final ArrayList returnThis = new ArrayList();
+ Iterator it = edges.iterator();
+
+ while (it.hasNext()) {
+ Edge e = (Edge) it.next();
+ returnThis.add(getEdgeView(e));
+ }
+
+ return returnThis;
+ }
+ }
+
+ /*
+ * Returns an edge view with specified edge index whether or not the edge
+ * view is hidden; null is returned if view does not exist.
+ */
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edgeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public EdgeView getEdgeView(int edgeInx) {
+ synchronized (m_lock) {
+ return (EdgeView) m_edgeViewMap.get(new Integer(edgeInx));
+ }
+ }
+
+ /*
+ * Returns an iterator of all edge views, including those that are currently
+ * hidden.
+ */
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Iterator getEdgeViewsIterator() {
+ synchronized (m_lock) {
+ return m_edgeViewMap.values().iterator();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edge
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public EdgeView getEdgeView(Edge edge) {
+ return getEdgeView(edge.getRootGraphIndex());
+ }
+
+ /*
+ * Alias to getEdgeViewCount().
+ */
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int edgeCount() {
+ return getEdgeViewCount();
+ }
+
+ /*
+ * Alias to getNodeViewCount().
+ */
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int nodeCount() {
+ return getNodeViewCount();
+ }
+
+ /*
+ * obj should be either a DEdgeView or a DNodeView.
+ */
+ /**
+ * DOCUMENT ME!
+ *
+ * @param obj DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean hideGraphObject(Object obj) {
+ return hideGraphObjectInternal(obj, true);
+ }
+
+ private boolean hideGraphObjectInternal(Object obj, boolean fireListenerEvents) {
+ if (obj instanceof DEdgeView) {
+ int edgeInx;
+
+ synchronized (m_lock) {
+ edgeInx = ((DEdgeView) obj).getRootGraphIndex();
+
+ if (m_drawPersp.hideEdge(edgeInx) == 0) {
+ return false;
+ }
+
+ ((DEdgeView) obj).unselectInternal();
+ m_contentChanged = true;
+ }
+
+ if (fireListenerEvents) {
+ final GraphViewChangeListener listener = m_lis[0];
+
+ if (listener != null) {
+ listener.graphViewChanged(new GraphViewEdgesHiddenEvent(this,
+ new int[] { edgeInx }));
+ }
+ }
+
+ return true;
+ } else if (obj instanceof DNodeView) {
+ int[] edges;
+ int nodeInx;
+
+ synchronized (m_lock) {
+ final DNodeView nView = (DNodeView) obj;
+ nodeInx = nView.getRootGraphIndex();
+ edges = m_drawPersp.getAdjacentEdgeIndicesArray(nodeInx, true, true, true);
+
+ if (edges == null) {
+ return false;
+ }
+
+ for (int i = 0; i < edges.length; i++)
+ hideGraphObjectInternal(m_edgeViewMap.get(new Integer(edges[i])), false);
+
+ nView.unselectInternal();
+ m_spacial.exists(~nodeInx, m_extentsBuff, 0);
+ nView.m_hiddenXMin = m_extentsBuff[0];
+ nView.m_hiddenYMin = m_extentsBuff[1];
+ nView.m_hiddenXMax = m_extentsBuff[2];
+ nView.m_hiddenYMax = m_extentsBuff[3];
+ m_drawPersp.hideNode(nodeInx);
+ m_spacial.delete(~nodeInx);
+ m_contentChanged = true;
+ }
+
+ if (fireListenerEvents) {
+ final GraphViewChangeListener listener = m_lis[0];
+
+ if (listener != null) {
+ if (edges.length > 0) {
+ listener.graphViewChanged(new GraphViewEdgesHiddenEvent(this, edges));
+ }
+
+ listener.graphViewChanged(new GraphViewNodesHiddenEvent(this,
+ new int[] { nodeInx }));
+ }
+ }
+
+ return true;
+ } else {
+ return false;
+ }
+ }
+
+ final boolean isHidden(final DEdgeView edgeView) {
+ synchronized (m_lock) {
+ final int edgeIndex = edgeView.getRootGraphIndex();
+ return m_drawPersp.containsEdge(m_drawPersp.getEdge(edgeIndex));
+ }
+ }
+
+ final boolean isHidden(final DNodeView nodeView) {
+ synchronized (m_lock) {
+ final int nodeIndex = nodeView.getRootGraphIndex();
+ return m_drawPersp.containsNode(m_drawPersp.getNode(nodeIndex));
+ }
+ }
+
+ /*
+ * obj should be either a DEdgeView or a DNodeView.
+ */
+ /**
+ * DOCUMENT ME!
+ *
+ * @param obj DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean showGraphObject(Object obj) {
+ return showGraphObjectInternal(obj, true);
+ }
+
+ private boolean showGraphObjectInternal(Object obj, boolean fireListenerEvents) {
+ if (obj instanceof DNodeView) {
+ int nodeInx;
+
+ synchronized (m_lock) {
+ final DNodeView nView = (DNodeView) obj;
+ nodeInx = nView.getRootGraphIndex();
+
+ if (m_structPersp.getNode(nodeInx) == null) {
+ return false;
+ }
+
+ if (m_drawPersp.restoreNode(nodeInx) == 0) {
+ return false;
+ }
+
+ m_spacial.insert(~nodeInx, nView.m_hiddenXMin, nView.m_hiddenYMin,
+ nView.m_hiddenXMax, nView.m_hiddenYMax);
+ m_contentChanged = true;
+ }
+
+ if (fireListenerEvents) {
+ final GraphViewChangeListener listener = m_lis[0];
+
+ if (listener != null) {
+ listener.graphViewChanged(new GraphViewNodesRestoredEvent(this,
+ new int[] { nodeInx }));
+ }
+ }
+
+ return true;
+ } else if (obj instanceof DEdgeView) {
+ int sourceNode = 0;
+ int targetNode = 0;
+ int newEdge = 0;
+
+ synchronized (m_lock) {
+ final Edge edge = m_structPersp.getEdge(((DEdgeView) obj).getRootGraphIndex());
+
+ if (edge == null) {
+ return false;
+ }
+
+ // The edge exists in m_structPersp, therefore its source and
+ // target
+ // node views must also exist.
+ sourceNode = edge.getSource().getRootGraphIndex();
+
+ if (!showGraphObjectInternal(getNodeView(sourceNode), false)) {
+ sourceNode = 0;
+ }
+
+ targetNode = edge.getTarget().getRootGraphIndex();
+
+ if (!showGraphObjectInternal(getNodeView(targetNode), false)) {
+ targetNode = 0;
+ }
+
+ newEdge = edge.getRootGraphIndex();
+
+ if (m_drawPersp.restoreEdge(newEdge) == 0) {
+ return false;
+ }
+
+ m_contentChanged = true;
+ }
+
+ if (fireListenerEvents) {
+ final GraphViewChangeListener listener = m_lis[0];
+
+ if (listener != null) {
+ if (sourceNode != 0) {
+ listener.graphViewChanged(new GraphViewNodesRestoredEvent(this,
+ new int[] {
+ sourceNode
+ }));
+ }
+
+ if (targetNode != 0) {
+ listener.graphViewChanged(new GraphViewNodesRestoredEvent(this,
+ new int[] {
+ targetNode
+ }));
+ }
+
+ listener.graphViewChanged(new GraphViewEdgesRestoredEvent(this,
+ new int[] { newEdge }));
+ }
+ }
+
+ return true;
+ } else {
+ return false;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param objects
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean hideGraphObjects(List objects) {
+ final Iterator it = objects.iterator();
+
+ while (it.hasNext())
+ hideGraphObject(it.next());
+
+ return true;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param objects
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean showGraphObjects(List objects) {
+ final Iterator it = objects.iterator();
+
+ while (it.hasNext())
+ showGraphObject(it.next());
+
+ return true;
+ }
+
+ // AJK: 04/25/06 BEGIN
+ /**
+ * DOCUMENT ME!
+ *
+ * @param className DOCUMENT ME!
+ * @param plusSuperclass DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object[] getContextMethods(String className, boolean plusSuperclass) {
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param className
+ * DOCUMENT ME!
+ * @param methods
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object[] getContextMethods(String className, Object[] methods) {
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param className
+ * DOCUMENT ME!
+ * @param methodClassName
+ * DOCUMENT ME!
+ * @param methodName
+ * DOCUMENT ME!
+ * @param args
+ * DOCUMENT ME!
+ * @param loader
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean addContextMethod(String className, String methodClassName, String methodName,
+ Object[] args, ClassLoader loader) {
+ return false;
+ }
+
+ // AJK: 04/25/06 END
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nodeInx DOCUMENT ME!
+ * @param data DOCUMENT ME!
+ */
+ public void setAllNodePropertyData(int nodeInx, Object[] data) {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nodeInx
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object[] getAllNodePropertyData(int nodeInx) {
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edgeInx
+ * DOCUMENT ME!
+ * @param data
+ * DOCUMENT ME!
+ */
+ public void setAllEdgePropertyData(int edgeInx, Object[] data) {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edgeInx
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object[] getAllEdgePropertyData(int edgeInx) {
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nodeInx
+ * DOCUMENT ME!
+ * @param property
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getNodeObjectProperty(int nodeInx, int property) {
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nodeInx
+ * DOCUMENT ME!
+ * @param property
+ * DOCUMENT ME!
+ * @param value
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean setNodeObjectProperty(int nodeInx, int property, Object value) {
+ return false;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edgeInx
+ * DOCUMENT ME!
+ * @param property
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getEdgeObjectProperty(int edgeInx, int property) {
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edgeInx
+ * DOCUMENT ME!
+ * @param property
+ * DOCUMENT ME!
+ * @param value
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean setEdgeObjectProperty(int edgeInx, int property, Object value) {
+ return false;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nodeInx
+ * DOCUMENT ME!
+ * @param property
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public double getNodeDoubleProperty(int nodeInx, int property) {
+ return 0.0d;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nodeInx
+ * DOCUMENT ME!
+ * @param property
+ * DOCUMENT ME!
+ * @param val
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean setNodeDoubleProperty(int nodeInx, int property, double val) {
+ return false;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edgeInx
+ * DOCUMENT ME!
+ * @param property
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public double getEdgeDoubleProperty(int edgeInx, int property) {
+ return 0.0d;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edgeInx
+ * DOCUMENT ME!
+ * @param property
+ * DOCUMENT ME!
+ * @param val
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean setEdgeDoubleProperty(int edgeInx, int property, double val) {
+ return false;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nodeInx
+ * DOCUMENT ME!
+ * @param property
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public float getNodeFloatProperty(int nodeInx, int property) {
+ return 0.0f;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nodeInx
+ * DOCUMENT ME!
+ * @param property
+ * DOCUMENT ME!
+ * @param value
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean setNodeFloatProperty(int nodeInx, int property, float value) {
+ return false;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edgeInx
+ * DOCUMENT ME!
+ * @param property
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public float getEdgeFloatProperty(int edgeInx, int property) {
+ return 0.0f;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edgeInx
+ * DOCUMENT ME!
+ * @param property
+ * DOCUMENT ME!
+ * @param value
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean setEdgeFloatProperty(int edgeInx, int property, float value) {
+ return false;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nodeInx
+ * DOCUMENT ME!
+ * @param property
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean getNodeBooleanProperty(int nodeInx, int property) {
+ return false;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nodeInx
+ * DOCUMENT ME!
+ * @param property
+ * DOCUMENT ME!
+ * @param val
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean setNodeBooleanProperty(int nodeInx, int property, boolean val) {
+ return false;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edgeInx
+ * DOCUMENT ME!
+ * @param property
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean getEdgeBooleanProperty(int edgeInx, int property) {
+ return false;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edgeInx
+ * DOCUMENT ME!
+ * @param property
+ * DOCUMENT ME!
+ * @param val
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean setEdgeBooleanProperty(int edgeInx, int property, boolean val) {
+ return false;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nodeInx
+ * DOCUMENT ME!
+ * @param property
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getNodeIntProperty(int nodeInx, int property) {
+ return 0;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nodeInx
+ * DOCUMENT ME!
+ * @param property
+ * DOCUMENT ME!
+ * @param value
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean setNodeIntProperty(int nodeInx, int property, int value) {
+ return false;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edgeInx
+ * DOCUMENT ME!
+ * @param property
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getEdgeIntProperty(int edgeInx, int property) {
+ return 0;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edgeInx
+ * DOCUMENT ME!
+ * @param property
+ * DOCUMENT ME!
+ * @param value
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean setEdgeIntProperty(int edgeInx, int property, int value) {
+ return false;
+ }
+
+ // Auxillary methods specific to this GraphView implementation:
+ /**
+ * DOCUMENT ME!
+ *
+ * @param x DOCUMENT ME!
+ * @param y DOCUMENT ME!
+ */
+ public void setCenter(double x, double y) {
+ synchronized (m_lock) {
+ m_networkCanvas.m_xCenter = x;
+ m_networkCanvas.m_yCenter = y;
+ m_viewportChanged = true;
+ }
+
+ updateView();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Point2D getCenter() {
+ synchronized (m_lock) {
+ return new Point2D.Double(m_networkCanvas.m_xCenter, m_networkCanvas.m_yCenter);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void fitSelected() {
+ synchronized (m_lock) {
+ IntEnumerator selectedElms = m_selectedNodes.searchRange(Integer.MIN_VALUE,
+ Integer.MAX_VALUE, false);
+
+ // Only check for selected edges if we don't have selected nodes.
+ if (selectedElms.numRemaining() == 0 && edgeSelectionEnabled()) {
+ selectedElms = getSelectedEdgeNodes();
+ if ( selectedElms.numRemaining() == 0 )
+ return;
+ }
+
+ float xMin = Float.POSITIVE_INFINITY;
+ float yMin = Float.POSITIVE_INFINITY;
+ float xMax = Float.NEGATIVE_INFINITY;
+ float yMax = Float.NEGATIVE_INFINITY;
+
+ int leftMost = 0;
+ int rightMost = 0;
+
+ while (selectedElms.numRemaining() > 0) {
+ final int node = selectedElms.nextInt();
+ m_spacial.exists(node, m_extentsBuff, 0);
+
+ if ( m_extentsBuff[0] < xMin ) {
+ xMin = m_extentsBuff[0];
+ leftMost = node;
+ }
+
+ if ( m_extentsBuff[2] > xMax ) {
+ xMax = m_extentsBuff[2];
+ rightMost = node;
+ }
+
+ yMin = Math.min(yMin, m_extentsBuff[1]);
+ yMax = Math.max(yMax, m_extentsBuff[3]);
+ }
+
+ xMin = xMin - ( getLabelWidth(leftMost)/2 );
+ xMax = xMax + ( getLabelWidth(rightMost)/2 );
+
+ m_networkCanvas.m_xCenter = (((double) xMin) + ((double) xMax)) / 2.0d;
+ m_networkCanvas.m_yCenter = (((double) yMin) + ((double) yMax)) / 2.0d;
+ final double zoom = Math.min(((double) m_networkCanvas.getWidth()) / (((double) xMax)
+ - ((double) xMin)),
+ ((double) m_networkCanvas.getHeight()) / (((double) yMax)
+ - ((double) yMin)));
+ m_networkCanvas.m_scaleFactor = checkZoom(zoom,m_networkCanvas.m_scaleFactor);
+ m_viewportChanged = true;
+ }
+ }
+
+ /**
+ * @return An IntEnumerator listing the nodes that are endpoints of the
+ * currently selected edges.
+ */
+ private IntEnumerator getSelectedEdgeNodes() {
+ synchronized (m_lock) {
+ final IntEnumerator selectedEdges = m_selectedEdges.searchRange(Integer.MIN_VALUE,
+ Integer.MAX_VALUE, false);
+
+ final IntHash nodeIds = new IntHash();
+
+ while (selectedEdges.numRemaining() > 0) {
+ final int edge = ~selectedEdges.nextInt();
+ Edge currEdge = getEdgeView(edge).getEdge();
+
+ Node source = currEdge.getSource();
+ int sourceId = ~source.getRootGraphIndex();
+ nodeIds.put(sourceId);
+
+ Node target = currEdge.getTarget();
+ int targetId = ~target.getRootGraphIndex();
+ nodeIds.put(targetId);
+ }
+
+ return nodeIds.elements();
+ }
+ }
+
+
+ private int getLabelWidth(int node) {
+ DNodeView x = ((DNodeView)getNodeView(~node));
+ if ( x == null )
+ return 0;
+
+ String s = x.getText();
+ if ( s == null )
+ return 0;
+
+ char[] lab = s.toCharArray();
+ if ( lab == null )
+ return 0;
+
+ if ( m_networkCanvas.m_fontMetrics == null )
+ return 0;
+
+ return m_networkCanvas.m_fontMetrics.charsWidth( lab, 0, lab.length );
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param lod
+ * DOCUMENT ME!
+ */
+ public void setGraphLOD(GraphLOD lod) {
+ synchronized (m_lock) {
+ m_networkCanvas.m_lod[0] = lod;
+ m_contentChanged = true;
+ }
+
+ // This is not necessary
+ //updateView();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public GraphLOD getGraphLOD() {
+ return m_networkCanvas.m_lod[0];
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param textAsShape
+ * DOCUMENT ME!
+ */
+ public void setPrintingTextAsShape(boolean textAsShape) {
+ synchronized (m_lock) {
+ m_printLOD.setPrintingTextAsShape(textAsShape);
+ }
+ }
+
+ /**
+ * Efficiently computes the set of nodes intersecting an axis-aligned query
+ * rectangle; the query rectangle is specified in the node coordinate
+ * system, not the component coordinate system.
+ * <p>
+ * NOTE: The order of elements placed on the stack follows the rendering
+ * order of nodes; the element waiting to be popped off the stack is the
+ * node that is rendered last, and thus is "on top of" other nodes
+ * potentially beneath it.
+ * <p>
+ * HINT: To perform a point query simply set xMin equal to xMax and yMin
+ * equal to yMax.
+ *
+ * @param xMinimum
+ * a boundary of the query rectangle: the minimum X coordinate.
+ * @param yMinimum
+ * a boundary of the query rectangle: the minimum Y coordinate.
+ * @param xMaximum
+ * a boundary of the query rectangle: the maximum X coordinate.
+ * @param yMaximum
+ * a boundary of the query rectangle: the maximum Y coordinate.
+ * @param treatNodeShapesAsRectangle
+ * if true, nodes are treated as rectangles for purposes of the
+ * query computation; if false, true node shapes are respected,
+ * at the expense of slowing down the query by a constant factor.
+ * @param returnVal
+ * RootGraph indices of nodes intersecting the query rectangle
+ * will be placed onto this stack; the stack is not emptied by
+ * this method initially.
+ */
+ public void getNodesIntersectingRectangle(double xMinimum, double yMinimum, double xMaximum,
+ double yMaximum, boolean treatNodeShapesAsRectangle,
+ IntStack returnVal) {
+ synchronized (m_lock) {
+ final float xMin = (float) xMinimum;
+ final float yMin = (float) yMinimum;
+ final float xMax = (float) xMaximum;
+ final float yMax = (float) yMaximum;
+ final SpacialEntry2DEnumerator under = m_spacial.queryOverlap(xMin, yMin, xMax, yMax,
+ null, 0, false);
+ final int totalHits = under.numRemaining();
+
+ if (treatNodeShapesAsRectangle) {
+ for (int i = 0; i < totalHits; i++)
+ returnVal.push(~under.nextInt());
+ } else {
+ final double x = xMin;
+ final double y = yMin;
+ final double w = ((double) xMax) - xMin;
+ final double h = ((double) yMax) - yMin;
+
+ for (int i = 0; i < totalHits; i++) {
+ final int node = under.nextExtents(m_extentsBuff, 0);
+
+ // The only way that the node can miss the intersection
+ // query is
+ // if it intersects one of the four query rectangle's
+ // corners.
+ if (((m_extentsBuff[0] < xMin) && (m_extentsBuff[1] < yMin))
+ || ((m_extentsBuff[0] < xMin) && (m_extentsBuff[3] > yMax))
+ || ((m_extentsBuff[2] > xMax) && (m_extentsBuff[3] > yMax))
+ || ((m_extentsBuff[2] > xMax) && (m_extentsBuff[1] < yMin))) {
+ m_networkCanvas.m_grafx.getNodeShape(m_nodeDetails.shape(node),
+ m_extentsBuff[0], m_extentsBuff[1],
+ m_extentsBuff[2], m_extentsBuff[3],
+ m_path);
+
+ if ((w > 0) && (h > 0)) {
+ if (m_path.intersects(x, y, w, h)) {
+ returnVal.push(~node);
+ }
+ } else {
+ if (m_path.contains(x, y)) {
+ returnVal.push(~node);
+ }
+ }
+ } else {
+ returnVal.push(~node);
+ }
+ }
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param xMin
+ * DOCUMENT ME!
+ * @param yMin
+ * DOCUMENT ME!
+ * @param xMax
+ * DOCUMENT ME!
+ * @param yMax
+ * DOCUMENT ME!
+ * @param returnVal
+ * DOCUMENT ME!
+ */
+ public void queryDrawnEdges(int xMin, int yMin, int xMax, int yMax, IntStack returnVal) {
+ synchronized (m_lock) {
+ m_networkCanvas.computeEdgesIntersecting(xMin, yMin, xMax, yMax, returnVal);
+ }
+ }
+
+ /**
+ * Extents of the view. After the call extentsBuff[0] will be xmin, extentsBuff[1] will be ymin,
+ * extentsBuff[2] will be xmax, extentsBuff[3] will be ymax.
+ *
+ * @return true if the extends were successfully retrieved, else false
+ */
+ public boolean getExtents(double[] extentsBuff) {
+ synchronized (m_lock) {
+ if (m_spacial.queryOverlap(Float.NEGATIVE_INFINITY, Float.NEGATIVE_INFINITY,
+ Float.POSITIVE_INFINITY, Float.POSITIVE_INFINITY,
+ m_extentsBuff, 0, false).numRemaining() == 0) {
+ return false;
+ }
+
+ extentsBuff[0] = m_extentsBuff[0];
+ extentsBuff[1] = m_extentsBuff[1];
+ extentsBuff[2] = m_extentsBuff[2];
+ extentsBuff[3] = m_extentsBuff[3];
+
+ return true;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param coords
+ * DOCUMENT ME!
+ */
+ public void xformComponentToNodeCoords(double[] coords) {
+ synchronized (m_lock) {
+ m_networkCanvas.m_grafx.xformImageToNodeCoords(coords);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param img
+ * DOCUMENT ME!
+ * @param lod
+ * DOCUMENT ME!
+ * @param bgPaint
+ * DOCUMENT ME!
+ * @param xCenter
+ * DOCUMENT ME!
+ * @param yCenter
+ * DOCUMENT ME!
+ * @param scaleFactor
+ * DOCUMENT ME!
+ */
+ public void drawSnapshot(Image img, GraphLOD lod, Paint bgPaint, double xCenter,
+ double yCenter, double scaleFactor) {
+ synchronized (m_lock) {
+ GraphRenderer.renderGraph((FixedGraph) m_drawPersp, m_spacial, lod, m_nodeDetails,
+ m_edgeDetails, m_hash, new GraphGraphics(img, false),
+ bgPaint, xCenter, yCenter, scaleFactor);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param l
+ * DOCUMENT ME!
+ */
+ public void addContentChangeListener(ContentChangeListener l) {
+ m_cLis[0] = ContentChangeListenerChain.add(m_cLis[0], l);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param l
+ * DOCUMENT ME!
+ */
+ public void removeContentChangeListener(ContentChangeListener l) {
+ m_cLis[0] = ContentChangeListenerChain.remove(m_cLis[0], l);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param l
+ * DOCUMENT ME!
+ */
+ public void addViewportChangeListener(ViewportChangeListener l) {
+ m_vLis[0] = ViewportChangeListenerChain.add(m_vLis[0], l);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param l
+ * DOCUMENT ME!
+ */
+ public void removeViewportChangeListener(ViewportChangeListener l) {
+ m_vLis[0] = ViewportChangeListenerChain.remove(m_vLis[0], l);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g
+ * DOCUMENT ME!
+ * @param pageFormat
+ * DOCUMENT ME!
+ * @param page
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int print(Graphics g, PageFormat pageFormat, int page) {
+ if (page == 0) {
+ ((Graphics2D) g).translate(pageFormat.getImageableX(), pageFormat.getImageableY());
+
+ // make sure the whole image on the screen will fit to the printable
+ // area of the paper
+ double image_scale = Math.min(pageFormat.getImageableWidth() / getComponent().getWidth(),
+ pageFormat.getImageableHeight() / getComponent()
+ .getHeight());
+
+ if (image_scale < 1.0d) {
+ ((Graphics2D) g).scale(image_scale, image_scale);
+ }
+
+ g.clipRect(0, 0, getComponent().getWidth(), getComponent().getHeight());
+
+ getComponent().print(g);
+
+ return PAGE_EXISTS;
+ } else {
+ return NO_SUCH_PAGE;
+ }
+ }
+
+ // AJK: 04/02/06 BEGIN
+ /**
+ * Method to return a reference to the network canvas.
+ * This method existed before the addition of background
+ * and foreground canvases, and it remains for backward compatibility.
+ *
+ * @return InnerCanvas
+ */
+ public InnerCanvas getCanvas() {
+ return m_networkCanvas;
+ }
+
+
+ /**
+ * Method to return a reference to a DingCanvas object,
+ * given a canvas id.
+ *
+ * @param canvasId Canvas
+ * @return DingCanvas
+ */
+ public DingCanvas getCanvas(Canvas canvasId) {
+ if (canvasId == Canvas.BACKGROUND_CANVAS) {
+ return m_backgroundCanvas;
+ } else if (canvasId == Canvas.NETWORK_CANVAS) {
+ return m_networkCanvas;
+ } else if (canvasId == Canvas.FOREGROUND_CANVAS) {
+ return m_foregroundCanvas;
+ }
+
+ // made it here
+ return null;
+ }
+
+
+ /**
+ * Method to return a reference to an Image object,
+ * which represents the current network view.
+ *
+ * @param width Width of desired image.
+ * @param height Height of desired image.
+ * @param shrink Percent to shrink the network shown in the image.
+ * @param skipBackground If true, we don't draw the background
+ * This doesn't shrink the image, just the network shown, as if the user zoomed out.
+ * Can be between 0 and 1, if not it will default to 1.
+ * @return Image
+ * @throws IllegalArgumentException
+ */
+ private Image createImage(final int width, final int height, double shrink, final boolean skipBackground) {
+ // Validate arguments
+ if (width < 0 || height < 0) {
+ throw new IllegalArgumentException("DGraphView.createImage(int width, int height): "
+ + "width and height arguments must be greater than zero");
+ }
+
+ if (shrink < 0 || shrink > 1.0) {
+ System.out.println("DGraphView.createImage(width,height,shrink) shrink is invalid: "
+ + shrink + " using default of 1.0");
+ shrink = 1.0;
+ }
+
+ // create image to return
+ final Image image = new BufferedImage(width, height, BufferedImage.TYPE_INT_ARGB_PRE);
+ final Graphics g = image.getGraphics();
+
+ Dimension originalSize;
+
+ if (!skipBackground) {
+ // paint background canvas into image
+ originalSize = m_backgroundCanvas.getSize();
+ m_backgroundCanvas.setSize(width, height);
+ m_backgroundCanvas.paint(g);
+ // Restore background size
+ m_backgroundCanvas.setSize(originalSize);
+ }
+
+ // paint inner canvas (network)
+ originalSize = m_networkCanvas.getSize();
+ m_networkCanvas.setSize(width, height);
+ fitContent(/* updateView = */ false);
+ setZoom(getZoom() * shrink, /* updateView = */ false);
+ m_networkCanvas.paint(g);
+ // Restore network to original size
+ m_networkCanvas.setSize(originalSize);
+ fitContent(/* updateView = */ false);
+
+ // paint foreground canvas
+ originalSize = m_foregroundCanvas.getSize();
+ m_foregroundCanvas.setSize(width, height);
+ m_foregroundCanvas.paint(g);
+ // Restore foreground to original size
+ m_foregroundCanvas.setSize(originalSize);
+
+ return image;
+ }
+
+
+ /**
+ * Method to return a reference to an Image object,
+ * which represents the current network view.
+ *
+ * @param width Width of desired image.
+ * @param height Height of desired image.
+ * @param shrink Percent to shrink the network shown in the image.
+ * This doesn't shrink the image, just the network shown, as if the user zoomed out.
+ * Can be between 0 and 1, if not it will default to 1.
+ * @return Image
+ * @throws IllegalArgumentException
+ */
+ public Image createImage(int width, int height, double shrink) {
+ return createImage(width, height, shrink, /* skipBackground = */ false);
+ }
+
+
+ /**
+ * utility that returns the nodeView that is located at input point
+ *
+ * @param pt
+ */
+ public NodeView getPickedNodeView(Point2D pt) {
+ NodeView nv = null;
+ double[] locn = new double[2];
+ locn[0] = pt.getX();
+ locn[1] = pt.getY();
+
+ int chosenNode = 0;
+ xformComponentToNodeCoords(locn);
+
+ final IntStack nodeStack = new IntStack();
+ getNodesIntersectingRectangle((float) locn[0], (float) locn[1], (float) locn[0],
+ (float) locn[1],
+ (m_networkCanvas.getLastRenderDetail()
+ & GraphRenderer.LOD_HIGH_DETAIL) == 0, nodeStack);
+
+ chosenNode = (nodeStack.size() > 0) ? nodeStack.peek() : 0;
+
+ if (chosenNode != 0) {
+ nv = getNodeView(chosenNode);
+ }
+
+ return nv;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param pt
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public EdgeView getPickedEdgeView(Point2D pt) {
+ EdgeView ev = null;
+ final IntStack edgeStack = new IntStack();
+ queryDrawnEdges((int) pt.getX(), (int) pt.getY(), (int) pt.getX(), (int) pt.getY(),
+ edgeStack);
+
+ int chosenEdge = 0;
+ chosenEdge = (edgeStack.size() > 0) ? edgeStack.peek() : 0;
+
+ if (chosenEdge != 0) {
+ ev = getEdgeView(chosenEdge);
+ }
+
+ return ev;
+ }
+
+ // AJK: 04/25/06 END
+ /**
+ * DOCUMENT ME!
+ *
+ * @param l DOCUMENT ME!
+ */
+ public void addNodeContextMenuListener(NodeContextMenuListener l) {
+ // System.out.println("Adding NodeContextListener: " + l);
+ getCanvas().addNodeContextMenuListener(l);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param l
+ * DOCUMENT ME!
+ */
+ public void removeNodeContextMenuListener(NodeContextMenuListener l) {
+ getCanvas().removeNodeContextMenuListener(l);
+ }
+
+ // AJK: 04/27/06 END
+ /**
+ * DOCUMENT ME!
+ *
+ * @param l DOCUMENT ME!
+ */
+ public void addEdgeContextMenuListener(EdgeContextMenuListener l) {
+ // System.out.println("Adding EdgeContextListener: " + l);
+ getCanvas().addEdgeContextMenuListener(l);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param l
+ * DOCUMENT ME!
+ */
+ public void removeEdgeContextMenuListener(EdgeContextMenuListener l) {
+ getCanvas().removeEdgeContextMenuListener(l);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final float getAnchorSize() {
+ return DEFAULT_ANCHOR_SIZE;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final Paint getAnchorSelectedPaint() {
+ return DEFAULT_ANCHOR_SELECTED_PAINT;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final Paint getAnchorUnselectedPaint() {
+ return DEFAULT_ANCHOR_UNSELECTED_PAINT;
+ }
+
+ /**
+ * This is inefficient, but there is no way to sync. giny type and renderer
+ * type.
+ *
+ * @return map of shape ids to shapes
+ */
+ public static Map<Integer, Shape> getNodeShapes() {
+ final Map<Byte, Shape> nodeShapes = GraphGraphics.getNodeShapes();
+ final Map<Integer, Shape> ginyKeyShapes = new HashMap<Integer, Shape>();
+
+ Shape shape;
+
+ for (Byte key : nodeShapes.keySet()) {
+ shape = nodeShapes.get(key);
+ ginyKeyShapes.put(GinyUtil.getGinyNodeType(key), shape);
+ }
+
+ return ginyKeyShapes;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static Map<Integer, Shape> getArrowShapes() {
+ final Map<Byte, Shape> arrowShapes = GraphGraphics.getArrowShapes();
+ final Map<Integer, Shape> ginyKeyShapes = new HashMap<Integer, Shape>();
+
+ Shape shape;
+
+ for (Byte key : arrowShapes.keySet()) {
+ shape = arrowShapes.get(key);
+ ginyKeyShapes.put(GinyUtil.getGinyArrowType(key), shape);
+ }
+
+ return ginyKeyShapes;
+ }
+
+ private double checkZoom(double zoom, double orig) {
+ if ( zoom > 0 )
+ return zoom;
+
+ return orig;
+ }
+
+
+ /**
+ * Returns the current snapshot image of this view.
+ *
+ * <p>
+ * No unnecessary image object will be created if networks in the current
+ * session does not contain any nested network, i.e., should not have
+ * performance/memory issue.
+ *
+ * @return Image of this view. It is always up-to-date.
+ */
+ TexturePaint getSnapshot(final double width, final double height) {
+ if (!latest) {
+ // Need to update snapshot.
+ snapshotImage =
+ (BufferedImage)createImage(DEF_SNAPSHOT_SIZE, DEF_SNAPSHOT_SIZE, 1,
+ /* skipBackground = */ true);
+ latest = true;
+ }
+
+ final Rectangle2D rect = new Rectangle2D.Double(-width / 2, -height / 2, width, height);
+ final TexturePaint texturePaint = new TexturePaint(snapshotImage, rect);
+ return texturePaint;
+ }
+
+
+ /**
+ * Converts a BufferedImage to a lossless PNG.
+ */
+ private byte[] convertToCompressedImage(final BufferedImage bufferedImage) {
+ try {
+ final ByteArrayOutputStream baos = new ByteArrayOutputStream(100000);
+ ImageIO.write(bufferedImage, "png", baos);
+ final byte[] retval = baos.toByteArray();
+ return retval;
+ } catch (final IOException e) {
+ System.err.println("Failed to convert a BufferedImage to a PNG! (" + e + ")");
+ return null;
+ }
+ }
+
+
+ /**
+ * Converts a PNG to a BufferedImage.
+ */
+ private BufferedImage convertToBufferedImage(final byte[] compressedImage) {
+ try {
+ final ByteArrayInputStream is = new ByteArrayInputStream(compressedImage);
+ final BufferedImage retval = (BufferedImage)ImageIO.read(is);
+ return retval;
+ } catch (final IOException e) {
+ System.err.println("Failed to convert a PNG to a BufferedImage! (" + e + ")");
+ return null;
+ }
+ }
+
+
+ /**
+ * Listener for update flag of snapshot image.
+ *
+ * @author kono
+ *
+ */
+ private final class DGraphViewContentChangeListener implements ContentChangeListener {
+ public void contentChanged() {
+ latest = false;
+ }
+ }
+}
diff --git a/corelibs/ding/src/main/java/ding/view/DNodeDetails.java b/corelibs/ding/src/main/java/ding/view/DNodeDetails.java
new file mode 100644
index 0000000..c36bb2e
--- /dev/null
+++ b/corelibs/ding/src/main/java/ding/view/DNodeDetails.java
@@ -0,0 +1,632 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package ding.view;
+
+import giny.view.Label;
+
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.Paint;
+import java.awt.TexturePaint;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.Map;
+
+import cytoscape.render.stateful.CustomGraphic;
+import cytoscape.render.stateful.NodeDetails;
+import cytoscape.util.intr.IntObjHash;
+
+
+/*
+ * Access to the methods of this class should be synchronized externally if
+ * there is a threat of multiple threads.
+ */
+class DNodeDetails extends IntermediateNodeDetails {
+
+ final DGraphView m_view;
+ final IntObjHash m_colorsLowDetail = new IntObjHash();
+ final Object m_deletedEntry = new Object();
+
+ // The values are Byte objects; the bytes are shapes defined in
+ // cytoscape.render.immed.GraphGraphics.
+ final Map<Integer, Byte> m_shapes = new HashMap<Integer, Byte>();
+ final Map<Integer, Paint> m_fillPaints = new HashMap<Integer, Paint>();
+ final Map<Integer, Float> m_borderWidths = new HashMap<Integer, Float>();
+ final Map<Integer, Paint> m_borderPaints = new HashMap<Integer, Paint>();
+ final Map<Integer, Integer> m_labelCounts = new HashMap<Integer, Integer>();
+ final Map<Long, String> m_labelTexts = new HashMap<Long, String>();
+ final Map<Long, Font> m_labelFonts = new HashMap<Long, Font>();
+ final Map<Long, Paint> m_labelPaints = new HashMap<Long, Paint>();
+ final Map<Integer, Double> m_labelWidths = new HashMap<Integer, Double>();
+
+ final Map<Integer, Integer> m_labelTextAnchors = new HashMap<Integer, Integer>();
+ final Map<Integer, Integer> m_labelNodeAnchors = new HashMap<Integer, Integer>();
+ final Map<Integer, Integer> m_labelJustifys = new HashMap<Integer, Integer>();
+ final Map<Integer, Double> m_labelOffsetXs = new HashMap<Integer, Double>();
+ final Map<Integer, Double> m_labelOffsetYs = new HashMap<Integer, Double>();
+
+ /**
+ * This constructor is package-private.
+ * Will be used only by the DNodeView.
+ *
+ * @param view
+ */
+ DNodeDetails(final DGraphView view) {
+ m_view = view;
+ }
+
+
+ void unregisterNode(final int node) {
+ final Object o = m_colorsLowDetail.get(node);
+
+ if ((o != null) && (o != m_deletedEntry))
+ m_colorsLowDetail.put(node, m_deletedEntry);
+
+ m_shapes.remove(node);
+ m_fillPaints.remove(node);
+ m_borderWidths.remove(node);
+ m_borderPaints.remove(node);
+ m_labelWidths.remove(node);
+ m_labelTextAnchors.remove(node);
+ m_labelNodeAnchors.remove(node);
+ m_labelJustifys.remove(node);
+ m_labelOffsetXs.remove(node);
+ m_labelOffsetYs.remove(node);
+
+ final Integer intr = m_labelCounts.remove(node);
+ final int labelCount = ((intr == null) ? 0 : intr);
+
+ for (int i = 0; i < labelCount; i++) {
+ final Long lKey = new Long((((long) node) << 32) | ((long) i));
+ m_labelTexts.remove(lKey);
+ m_labelFonts.remove(lKey);
+ m_labelPaints.remove(lKey);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Color colorLowDetail(int node) {
+ final Object o = m_colorsLowDetail.get(node);
+
+ if ((o == null) || (o == m_deletedEntry))
+ return super.colorLowDetail(node);
+
+ return (Color) o;
+ }
+
+
+ /*
+ * A null color has the special meaning to remove overridden color.
+ */
+ void overrideColorLowDetail(int node, Color color) {
+ if ((color == null) || color.equals(super.colorLowDetail(node))) {
+ final Object val = m_colorsLowDetail.get(node);
+
+ if ((val != null) && (val != m_deletedEntry))
+ m_colorsLowDetail.put(node, m_deletedEntry);
+ } else
+ m_colorsLowDetail.put(node, color);
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public byte shape(int node) {
+ final Object o = m_shapes.get(new Integer(node));
+
+ if (o == null)
+ return super.shape(node);
+
+ return ((Byte) o).byteValue();
+ }
+
+ /*
+ * The shape argument must be pre-checked for correctness.
+ * A negative shape value has the special meaning to remove overridden shape.
+ */
+ void overrideShape(int node, byte shape) {
+ if ((shape < 0) || (shape == super.shape(node)))
+ m_shapes.remove(new Integer(node));
+ else
+ m_shapes.put(new Integer(node), new Byte(shape));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Paint fillPaint(int node) {
+ final Object o = m_fillPaints.get(new Integer(node));
+
+ if (o == null)
+ return super.fillPaint(node);
+
+ return (Paint) o;
+ }
+
+ /*
+ * A null paint has the special meaning to remove overridden paint.
+ */
+ void overrideFillPaint(int node, Paint paint) {
+ if ((paint == null) || paint.equals(super.fillPaint(node)))
+ m_fillPaints.remove(new Integer(node));
+ else
+ m_fillPaints.put(new Integer(node), paint);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public float borderWidth(int node) {
+ final Object o = m_borderWidths.get(new Integer(node));
+
+ if (o == null)
+ return super.borderWidth(node);
+
+ return ((Float) o).floatValue();
+ }
+
+ /*
+ * A negative width value has the special meaning to remove overridden width.
+ */
+ void overrideBorderWidth(int node, float width) {
+ if ((width < 0.0f) || (width == super.borderWidth(node)))
+ m_borderWidths.remove(new Integer(node));
+ else
+ m_borderWidths.put(new Integer(node), new Float(width));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Paint borderPaint(int node) {
+ final Object o = m_borderPaints.get(new Integer(node));
+
+ if (o == null)
+ return super.borderPaint(node);
+
+ return (Paint) o;
+ }
+
+ /*
+ * A null paint has the special meaning to remove overridden paint.
+ */
+ void overrideBorderPaint(int node, Paint paint) {
+ if ((paint == null) || paint.equals(super.borderPaint(node)))
+ m_borderPaints.remove(node);
+ else
+ m_borderPaints.put(node, paint);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int labelCount(int node) {
+ final Integer o = m_labelCounts.get(node);
+
+ if (o == null)
+ return super.labelCount(node);
+
+ return o;
+ }
+
+ /*
+ * A negative labelCount has the special meaning to remove overridden count.
+ */
+ void overrideLabelCount(int node, int labelCount) {
+ if ((labelCount < 0) || (labelCount == super.labelCount(node)))
+ m_labelCounts.remove(new Integer(node));
+ else
+ m_labelCounts.put(new Integer(node), new Integer(labelCount));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ * @param labelInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String labelText(int node, int labelInx) {
+ final long key = (((long) node) << 32) | ((long) labelInx);
+ final Object o = m_labelTexts.get(new Long(key));
+
+ if (o == null)
+ return super.labelText(node, labelInx);
+
+ return (String) o;
+ }
+
+ /*
+ * A null text has the special meaning to remove overridden text.
+ */
+ void overrideLabelText(int node, int labelInx, String text) {
+ final long key = (((long) node) << 32) | ((long) labelInx);
+
+ if ((text == null) || text.equals(super.labelText(node, labelInx)))
+ m_labelTexts.remove(new Long(key));
+ else
+ m_labelTexts.put(new Long(key), text);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ * @param labelInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Font labelFont(int node, int labelInx) {
+ final long key = (((long) node) << 32) | ((long) labelInx);
+ final Object o = m_labelFonts.get(new Long(key));
+
+ if (o == null)
+ return super.labelFont(node, labelInx);
+
+ return (Font) o;
+ }
+
+ /*
+ * A null font has the special meaning to remove overridden font.
+ */
+ void overrideLabelFont(int node, int labelInx, Font font) {
+ final long key = (((long) node) << 32) | ((long) labelInx);
+
+ if ((font == null) || font.equals(super.labelFont(node, labelInx)))
+ m_labelFonts.remove(new Long(key));
+ else
+ m_labelFonts.put(new Long(key), font);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ * @param labelInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Paint labelPaint(int node, int labelInx) {
+ final long key = (((long) node) << 32) | ((long) labelInx);
+ final Object o = m_labelPaints.get(new Long(key));
+
+ if (o == null)
+ return super.labelPaint(node, labelInx);
+
+ return (Paint) o;
+ }
+
+ /*
+ * A null paint has the special meaning to remove overridden paint.
+ */
+ void overrideLabelPaint(int node, int labelInx, Paint paint) {
+ final long key = (((long) node) << 32) | ((long) labelInx);
+
+ if ((paint == null) || paint.equals(super.labelPaint(node, labelInx)))
+ m_labelPaints.remove(new Long(key));
+ else
+ m_labelPaints.put(new Long(key), paint);
+ }
+
+
+ // overrides NodeDetails.customGraphicCount():
+ public int customGraphicCount(final int node) {
+ final DNodeView dnv = (DNodeView) m_view.getNodeView(~node);
+ return dnv.getNumCustomGraphics();
+ }
+
+ // overrides NodeDetails.customGraphics():
+ public Iterator<CustomGraphic> customGraphics (final int node) {
+ final DNodeView dnv = (DNodeView) m_view.getNodeView(~node);
+ return dnv.customGraphicIterator();
+ }
+ // overrides NodeDetails.customGraphicLock():
+ public Object customGraphicLock (final int node) {
+ final DNodeView dnv = (DNodeView) m_view.getNodeView(~node);
+ return dnv.customGraphicLock();
+ }
+
+ // label positioning
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ * @param labelInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public byte labelTextAnchor(final int node, final int labelInx) {
+ final Integer p = m_labelTextAnchors.get(node);
+
+ if (p == null)
+ return super.labelTextAnchor(node, labelInx);
+ else
+ return convertG2ND(p);
+ }
+
+
+ void overrideLabelTextAnchor(final int node, final int inx, final int anchor) {
+ if (convertG2ND(anchor) == super.labelTextAnchor(node, inx))
+ m_labelTextAnchors.remove(node);
+ else
+ m_labelTextAnchors.put(new Integer(node), new Integer(anchor));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ * @param labelInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public byte labelNodeAnchor(final int node, final int labelInx) {
+ final Integer o = m_labelNodeAnchors.get(node);
+
+ if (o == null)
+ return super.labelNodeAnchor(node, labelInx);
+
+ return convertG2ND(o);
+ }
+
+ void overrideLabelNodeAnchor(final int node, final int inx, final int anchor) {
+ if (convertG2ND(anchor) == super.labelNodeAnchor(node, inx))
+ m_labelNodeAnchors.remove(new Integer(node));
+ else
+ m_labelNodeAnchors.put(new Integer(node), new Integer(anchor));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ * @param labelInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public float labelOffsetVectorX(final int node, final int labelInx) {
+ final Double o = m_labelOffsetXs.get(node);
+
+ if (o == null)
+ return super.labelOffsetVectorX(node, labelInx);
+
+ return o.floatValue();
+ }
+
+ void overrideLabelOffsetVectorX(final int node, final int inx, final double x) {
+ if (((float) x) == super.labelOffsetVectorX(node, inx))
+ m_labelOffsetXs.remove(new Integer(node));
+ else
+ m_labelOffsetXs.put(new Integer(node), new Double(x));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ * @param labelInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public float labelOffsetVectorY(final int node, final int labelInx) {
+ final Double o = m_labelOffsetYs.get(node);
+
+ if (o == null)
+ return super.labelOffsetVectorY(node, labelInx);
+
+ return o.floatValue();
+ }
+
+ void overrideLabelOffsetVectorY(final int node, final int inx, final double y) {
+ if (((float) y) == super.labelOffsetVectorY(node, inx))
+ m_labelOffsetYs.remove(new Integer(node));
+ else
+ m_labelOffsetYs.put(new Integer(node), new Double(y));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ * @param labelInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public byte labelJustify(final int node, final int labelInx) {
+ Integer o = m_labelJustifys.get(node);
+
+ if (o == null)
+ return super.labelJustify(node, labelInx);
+
+ return convertG2ND(o);
+ }
+
+ void overrideLabelJustify(final int node, final int inx, final int justify) {
+ if (convertG2ND(justify) == super.labelJustify(node, inx))
+ m_labelJustifys.remove(new Integer(node));
+ else
+ m_labelJustifys.put(new Integer(node), new Integer(justify));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public double labelWidth(int node) {
+ final Double o = m_labelWidths.get(node);
+
+ if (o == null)
+ return super.labelWidth(node);
+
+ return o;
+ }
+
+
+ @Override
+ public TexturePaint getNestedNetworkTexturePaint(final int node) {
+ final DNodeView dNodeView = (DNodeView) m_view.getNodeView(~node);
+ return dNodeView.getNestedNetworkTexturePaint();
+ }
+
+
+ /*
+ * A negative width value has the special meaning to remove overridden width.
+ */
+ void overrideLabelWidth(int node, double width) {
+ if ((width < 0.0) || (width == super.labelWidth(node)))
+ m_labelWidths.remove(new Integer(node));
+ else
+ m_labelWidths.put(new Integer(node), new Double(width));
+ }
+
+ static byte convertG2ND(int giny) {
+ switch (giny) {
+ case (Label.NORTH):
+ return NodeDetails.ANCHOR_NORTH;
+
+ case (Label.SOUTH):
+ return NodeDetails.ANCHOR_SOUTH;
+
+ case (Label.EAST):
+ return NodeDetails.ANCHOR_EAST;
+
+ case (Label.WEST):
+ return NodeDetails.ANCHOR_WEST;
+
+ case (Label.NORTHEAST):
+ return NodeDetails.ANCHOR_NORTHEAST;
+
+ case (Label.NORTHWEST):
+ return NodeDetails.ANCHOR_NORTHWEST;
+
+ case (Label.SOUTHEAST):
+ return NodeDetails.ANCHOR_SOUTHEAST;
+
+ case (Label.SOUTHWEST):
+ return NodeDetails.ANCHOR_SOUTHWEST;
+
+ case (Label.CENTER):
+ return NodeDetails.ANCHOR_CENTER;
+
+ case (Label.JUSTIFY_CENTER):
+ return NodeDetails.LABEL_WRAP_JUSTIFY_CENTER;
+
+ case (Label.JUSTIFY_RIGHT):
+ return NodeDetails.LABEL_WRAP_JUSTIFY_RIGHT;
+
+ case (Label.JUSTIFY_LEFT):
+ return NodeDetails.LABEL_WRAP_JUSTIFY_LEFT;
+
+ default:
+ return -1;
+ }
+ }
+
+ static int convertND2G(byte nd) {
+ switch (nd) {
+ case (NodeDetails.ANCHOR_NORTH):
+ return Label.NORTH;
+
+ case (NodeDetails.ANCHOR_SOUTH):
+ return Label.SOUTH;
+
+ case (NodeDetails.ANCHOR_EAST):
+ return Label.EAST;
+
+ case (NodeDetails.ANCHOR_WEST):
+ return Label.WEST;
+
+ case (NodeDetails.ANCHOR_NORTHEAST):
+ return Label.NORTHEAST;
+
+ case (NodeDetails.ANCHOR_NORTHWEST):
+ return Label.NORTHWEST;
+
+ case (NodeDetails.ANCHOR_SOUTHEAST):
+ return Label.SOUTHEAST;
+
+ case (NodeDetails.ANCHOR_SOUTHWEST):
+ return Label.SOUTHWEST;
+
+ case (NodeDetails.ANCHOR_CENTER):
+ return Label.CENTER;
+
+ case (NodeDetails.LABEL_WRAP_JUSTIFY_CENTER):
+ return Label.JUSTIFY_CENTER;
+
+ case (NodeDetails.LABEL_WRAP_JUSTIFY_RIGHT):
+ return Label.JUSTIFY_RIGHT;
+
+ case (NodeDetails.LABEL_WRAP_JUSTIFY_LEFT):
+ return Label.JUSTIFY_LEFT;
+
+ default:
+ return -1;
+ }
+ }
+}
diff --git a/corelibs/ding/src/main/java/ding/view/DNodeView.java b/corelibs/ding/src/main/java/ding/view/DNodeView.java
new file mode 100644
index 0000000..db42112
--- /dev/null
+++ b/corelibs/ding/src/main/java/ding/view/DNodeView.java
@@ -0,0 +1,1484 @@
+/*
+ Copyright (c) 2006, 2007, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+package ding.view;
+
+import giny.model.Node;
+import giny.view.GraphView;
+import giny.view.GraphViewChangeListener;
+import giny.view.Justification;
+import giny.view.Label;
+import giny.view.NodeView;
+import giny.view.ObjectPosition;
+import giny.view.Position;
+
+import java.awt.AlphaComposite;
+import java.awt.BasicStroke;
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.Graphics2D;
+import java.awt.Paint;
+import java.awt.Shape;
+import java.awt.Stroke;
+import java.awt.TexturePaint;
+import java.awt.geom.Point2D;
+import java.awt.geom.Rectangle2D;
+import java.awt.image.BufferedImage;
+import java.io.IOException;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.LinkedHashSet;
+import java.util.List;
+import java.util.Map;
+
+import javax.imageio.ImageIO;
+
+import cytoscape.render.immed.GraphGraphics;
+import cytoscape.render.stateful.CustomGraphic;
+
+
+/**
+ * Ding implementation of GINY NodeView.
+ *
+ * @author $author$
+ */
+public class DNodeView implements NodeView, Label {
+
+ // For Cytoscape 2.7: Nested Network Image size
+ private static final float NESTED_IMAGE_SCALE_FACTOR = 0.6f;
+
+ // This image will be used when view is not available for a nested network.
+ private static BufferedImage DEFAULT_NESTED_NETWORK_IMAGE;
+ private static BufferedImage RECURSIVE_NESTED_NETWORK_IMAGE;
+
+ // Used to detect recursive rendering of nested networks.
+ private static int nestedNetworkPaintingDepth = 0;
+
+ static {
+ try {
+ DEFAULT_NESTED_NETWORK_IMAGE = ImageIO.read(DNodeView.class
+ .getClassLoader().getResource(
+ "images/default_network.png"));
+ RECURSIVE_NESTED_NETWORK_IMAGE = ImageIO.read(DNodeView.class
+ .getClassLoader().getResource(
+ "images/recursive_network.png"));
+ } catch (final IOException e) {
+ e.printStackTrace();
+ DEFAULT_NESTED_NETWORK_IMAGE = null;
+ RECURSIVE_NESTED_NETWORK_IMAGE = null;
+ }
+ }
+
+ static final float DEFAULT_WIDTH = 20.0f;
+ static final float DEFAULT_HEIGHT = 20.0f;
+
+ static final byte DEFAULT_SHAPE = GraphGraphics.SHAPE_ELLIPSE;
+
+ static final Paint DEFAULT_BORDER_PAINT = Color.black;
+
+ static final String DEFAULT_LABEL_TEXT = "";
+
+ static final Font DEFAULT_LABEL_FONT = new Font(null, Font.PLAIN, 1);
+ static final Paint DEFAULT_LABEL_PAINT = Color.black;
+ static final double DEFAULT_LABEL_WIDTH = 100.0;
+
+ DGraphView graphView;
+
+ private final int m_inx; // The FixedGraph index (non-negative).
+ private boolean m_selected;
+
+ private Paint m_unselectedPaint;
+ private Paint m_selectedPaint;
+ private Paint m_borderPaint;
+
+ /**
+ * Stores the position of a nodeView when it's hidden so that when the
+ * nodeView is restored we can restore the view into the same position.
+ */
+ float m_hiddenXMin = Float.MIN_VALUE;
+ float m_hiddenYMin = Float.MIN_VALUE;
+ float m_hiddenXMax = Float.MAX_VALUE;
+ float m_hiddenYMax = Float.MAX_VALUE;
+
+ // A LinkedHashSet of the custom graphics associated with this
+ // DNodeView. We need the HashSet linked since the ordering of
+ // custom graphics is important. For space considerations, we
+ // keep _customGraphics null when there are no custom
+ // graphics--event though this is a bit more complicated:
+ private LinkedHashSet<CustomGraphic> _customGraphics;
+
+ // CG_LOCK is used for synchronizing custom graphics operations on this
+ // DNodeView.
+ // Arrays are objects like any other and can be used for synchronization. We
+ // use an array
+ // object assuming it takes up the least amount of memory:
+ private final Object[] CG_LOCK = new Object[0];
+ private final static HashSet<CustomGraphic> EMPTY_CUSTOM_GRAPHICS = new LinkedHashSet<CustomGraphic>(
+ 0);
+
+ private String m_toolTipText = null;
+
+ private DGraphView nestedNetworkView;
+ private boolean nestedNetworkVisible = true;
+
+ // New feature from Cytoscape 2.8: Consolidated label position information
+ private ObjectPosition labelPosition = new ObjectPositionImpl();
+
+ // New feature from Cytoscape 2.8: Custom Graphics positions
+ private Map<CustomGraphic, ObjectPosition> graphicsPositions;
+
+ /*
+ * @param inx the RootGraph index of node (a negative number).
+ */
+ DNodeView(DGraphView view, int inx) {
+ graphView = view;
+ m_inx = ~inx;
+ m_selected = false;
+ m_unselectedPaint = graphView.m_nodeDetails.fillPaint(m_inx);
+ m_selectedPaint = Color.yellow;
+ m_borderPaint = graphView.m_nodeDetails.borderPaint(m_inx);
+
+ // By default, no nested network is available.
+ nestedNetworkView = null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public GraphView getGraphView() {
+ return graphView;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Node getNode() {
+ synchronized (graphView.m_lock) {
+ return graphView.m_structPersp.getNode(~m_inx);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getGraphPerspectiveIndex() {
+ return ~m_inx;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getRootGraphIndex() {
+ return ~m_inx;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param otherNodeView
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public List getEdgeViewsList(NodeView otherNodeView) {
+ synchronized (graphView.m_lock) {
+ return graphView.getEdgeViewsList(getNode(), otherNodeView
+ .getNode());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getShape() {
+ synchronized (graphView.m_lock) {
+ final byte nativeShape = graphView.m_nodeDetails.shape(m_inx);
+
+ return GinyUtil.getGinyNodeType(nativeShape);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param paint
+ * DOCUMENT ME!
+ */
+ public void setSelectedPaint(Paint paint) {
+ synchronized (graphView.m_lock) {
+ if (paint == null)
+ throw new NullPointerException("paint is null");
+
+ m_selectedPaint = paint;
+
+ if (isSelected()) {
+ graphView.m_nodeDetails.overrideFillPaint(m_inx,
+ m_selectedPaint);
+
+ if (m_selectedPaint instanceof Color)
+ graphView.m_nodeDetails.overrideColorLowDetail(m_inx,
+ (Color) m_selectedPaint);
+
+ graphView.m_contentChanged = true;
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Paint getSelectedPaint() {
+ return m_selectedPaint;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param paint
+ * DOCUMENT ME!
+ */
+ public void setUnselectedPaint(Paint paint) {
+ synchronized (graphView.m_lock) {
+ if (paint == null)
+ throw new NullPointerException("paint is null");
+
+ m_unselectedPaint = paint;
+
+ if (!isSelected()) {
+ graphView.m_nodeDetails.overrideFillPaint(m_inx,
+ m_unselectedPaint);
+
+ if (m_unselectedPaint instanceof Color)
+ graphView.m_nodeDetails.overrideColorLowDetail(m_inx,
+ (Color) m_unselectedPaint);
+
+ graphView.m_contentChanged = true;
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Paint getUnselectedPaint() {
+ return m_unselectedPaint;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param paint
+ * DOCUMENT ME!
+ */
+ public void setBorderPaint(Paint paint) {
+ synchronized (graphView.m_lock) {
+ m_borderPaint = paint;
+ fixBorder();
+ graphView.m_contentChanged = true;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Paint getBorderPaint() {
+ return m_borderPaint;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param width
+ * DOCUMENT ME!
+ */
+ public void setBorderWidth(float width) {
+ synchronized (graphView.m_lock) {
+ graphView.m_nodeDetails.overrideBorderWidth(m_inx, width);
+ graphView.m_contentChanged = true;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public float getBorderWidth() {
+ synchronized (graphView.m_lock) {
+ return graphView.m_nodeDetails.borderWidth(m_inx);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param stroke
+ * DOCUMENT ME!
+ */
+ public void setBorder(Stroke stroke) {
+ if (stroke instanceof BasicStroke) {
+ synchronized (graphView.m_lock) {
+ setBorderWidth(((BasicStroke) stroke).getLineWidth());
+
+ final float[] dashArray = ((BasicStroke) stroke).getDashArray();
+
+ if ((dashArray != null) && (dashArray.length > 1)) {
+ m_borderDash = dashArray[0];
+ m_borderDash2 = dashArray[1];
+ } else {
+ m_borderDash = 0.0f;
+ m_borderDash2 = 0.0f;
+ }
+
+ fixBorder();
+ }
+ }
+ }
+
+ private float m_borderDash = 0.0f;
+ private float m_borderDash2 = 0.0f;
+ private final static Color s_transparent = new Color(0, 0, 0, 0);
+
+ // Callers of this method must be holding m_view.m_lock.
+ private void fixBorder() {
+ if ((m_borderDash == 0.0f) && (m_borderDash2 == 0.0f))
+ graphView.m_nodeDetails.overrideBorderPaint(m_inx, m_borderPaint);
+ else {
+ final int size = (int) Math.max(1.0f,
+ (int) (m_borderDash + m_borderDash2)); // Average times two.
+
+ if ((size == graphView.m_lastSize)
+ && (m_borderPaint == graphView.m_lastPaint)) {
+ /* Use the cached texture paint. */} else {
+ final BufferedImage img = new BufferedImage(size, size,
+ BufferedImage.TYPE_INT_ARGB);
+ final Graphics2D g2 = (Graphics2D) img.getGraphics();
+ g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC));
+ g2.setPaint(s_transparent);
+ g2.fillRect(0, 0, size, size);
+ g2.setPaint(m_borderPaint);
+ g2.fillRect(0, 0, size / 2, size / 2);
+ g2.fillRect(size / 2, size / 2, size / 2, size / 2);
+ graphView.m_lastTexturePaint = new TexturePaint(img,
+ new Rectangle2D.Double(0, 0, size, size));
+ graphView.m_lastSize = size;
+ graphView.m_lastPaint = m_borderPaint;
+ }
+
+ graphView.m_nodeDetails.overrideBorderPaint(m_inx,
+ graphView.m_lastTexturePaint);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Stroke getBorder() {
+ synchronized (graphView.m_lock) {
+ if ((m_borderDash == 0.0f) && (m_borderDash2 == 0.0f))
+ return new BasicStroke(getBorderWidth());
+ else
+
+ return new BasicStroke(getBorderWidth(),
+ BasicStroke.CAP_SQUARE, BasicStroke.JOIN_MITER, 10.0f,
+ new float[] { m_borderDash, m_borderDash2 }, 0.0f);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param trans
+ * DOCUMENT ME!
+ */
+ public void setTransparency(float trans) {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public float getTransparency() {
+ return 1.0f;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param width
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean setWidth(double width) {
+ synchronized (graphView.m_lock) {
+ if (!graphView.m_spacial.exists(m_inx, graphView.m_extentsBuff, 0))
+ return false;
+
+ final double xCenter = (((double) graphView.m_extentsBuff[0]) + graphView.m_extentsBuff[2]) / 2.0d;
+ final double wDiv2 = width / 2.0d;
+ final float xMin = (float) (xCenter - wDiv2);
+ final float xMax = (float) (xCenter + wDiv2);
+
+ if (!(xMax > xMin))
+ throw new IllegalArgumentException("width is too small");
+
+ graphView.m_spacial.delete(m_inx);
+ graphView.m_spacial.insert(m_inx, xMin, graphView.m_extentsBuff[1],
+ xMax, graphView.m_extentsBuff[3]);
+
+ graphView.m_contentChanged = true;
+
+ return true;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public double getWidth() {
+ synchronized (graphView.m_lock) {
+ if (!graphView.m_spacial.exists(m_inx, graphView.m_extentsBuff, 0))
+ return -1.0d;
+
+ return ((double) graphView.m_extentsBuff[2])
+ - graphView.m_extentsBuff[0];
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param height
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean setHeight(double height) {
+ if (height <= 0.0) {
+ System.err.println("*** Warning: Bad height in DNodeView.setHeight(): " + height + ", set to 1.0!");
+ height = 1.0;
+ }
+
+ synchronized (graphView.m_lock) {
+ if (!graphView.m_spacial.exists(m_inx, graphView.m_extentsBuff, 0))
+ return false;
+
+ final double yCenter = (((double) graphView.m_extentsBuff[1]) + graphView.m_extentsBuff[3]) / 2.0d;
+ final double hDiv2 = height / 2.0d;
+ final float yMin = (float) (yCenter - hDiv2);
+ final float yMax = (float) (yCenter + hDiv2);
+
+ if (!(yMax > yMin))
+ throw new IllegalArgumentException("height is too small max:"
+ + yMax + " min:" + yMin + " center:" + yCenter
+ + " height:" + height);
+
+ graphView.m_spacial.delete(m_inx);
+ graphView.m_spacial.insert(m_inx, graphView.m_extentsBuff[0], yMin,
+ graphView.m_extentsBuff[2], yMax);
+
+ graphView.m_contentChanged = true;
+
+ return true;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public double getHeight() {
+ synchronized (graphView.m_lock) {
+ if (!graphView.m_spacial.exists(m_inx, graphView.m_extentsBuff, 0))
+ return -1.0d;
+
+ return ((double) graphView.m_extentsBuff[3])
+ - graphView.m_extentsBuff[1];
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Label getLabel() {
+ return this;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getDegree() {
+ // This method is totally ridiculous.
+ return graphView.getGraphPerspective().getDegree(~m_inx);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param x
+ * DOCUMENT ME!
+ * @param y
+ * DOCUMENT ME!
+ */
+ public void setOffset(double x, double y) {
+ synchronized (graphView.m_lock) {
+ if (!graphView.m_spacial.exists(m_inx, graphView.m_extentsBuff, 0))
+ return;
+
+ final double wDiv2 = (((double) graphView.m_extentsBuff[2]) - graphView.m_extentsBuff[0]) / 2.0d;
+ final double hDiv2 = (((double) graphView.m_extentsBuff[3]) - graphView.m_extentsBuff[1]) / 2.0d;
+ final float xMin = (float) (x - wDiv2);
+ final float xMax = (float) (x + wDiv2);
+ final float yMin = (float) (y - hDiv2);
+ final float yMax = (float) (y + hDiv2);
+
+ if (!(xMax > xMin))
+ throw new IllegalStateException(
+ "width of node has degenerated to zero after "
+ + "rounding");
+
+ if (!(yMax > yMin))
+ throw new IllegalStateException(
+ "height of node has degenerated to zero after "
+ + "rounding");
+
+ graphView.m_spacial.delete(m_inx);
+ graphView.m_spacial.insert(m_inx, xMin, yMin, xMax, yMax);
+ graphView.m_contentChanged = true;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Point2D getOffset() {
+ synchronized (graphView.m_lock) {
+ if (!graphView.m_spacial.exists(m_inx, graphView.m_extentsBuff, 0))
+ return null;
+
+ final double xCenter = (((double) graphView.m_extentsBuff[0]) + graphView.m_extentsBuff[2]) / 2.0d;
+ final double yCenter = (((double) graphView.m_extentsBuff[1]) + graphView.m_extentsBuff[3]) / 2.0d;
+
+ return new Point2D.Double(xCenter, yCenter);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param xPos
+ * DOCUMENT ME!
+ */
+ public void setXPosition(double xPos) {
+ synchronized (graphView.m_lock) {
+ final double wDiv2;
+ final boolean nodeVisible = graphView.m_spacial.exists(m_inx,
+ graphView.m_extentsBuff, 0);
+
+ if (nodeVisible)
+ wDiv2 = (((double) graphView.m_extentsBuff[2]) - graphView.m_extentsBuff[0]) / 2.0d;
+ else
+ wDiv2 = (double) (m_hiddenXMax - m_hiddenXMin) / 2.0d;
+
+ final float xMin = (float) (xPos - wDiv2);
+ final float xMax = (float) (xPos + wDiv2);
+
+ if (!(xMax > xMin))
+ throw new IllegalStateException(
+ "width of node has degenerated to zero after "
+ + "rounding");
+
+ // If the node is visible, set the extents.
+ if (nodeVisible) {
+ graphView.m_spacial.delete(m_inx);
+ graphView.m_spacial.insert(m_inx, xMin,
+ graphView.m_extentsBuff[1], xMax,
+ graphView.m_extentsBuff[3]);
+ graphView.m_contentChanged = true;
+
+ // If the node is NOT visible (hidden), then update the hidden
+ // extents. Doing
+ // this will mean that the node view will be properly scaled and
+ // rotated
+ // relative to the other nodes.
+ } else {
+ m_hiddenXMax = xMax;
+ m_hiddenXMin = xMin;
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param xPos
+ * DOCUMENT ME!
+ * @param update
+ * DOCUMENT ME!
+ */
+ public void setXPosition(double xPos, boolean update) {
+ setXPosition(xPos);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public double getXPosition() {
+ synchronized (graphView.m_lock) {
+ if (graphView.m_spacial.exists(m_inx, graphView.m_extentsBuff, 0))
+ return (((double) graphView.m_extentsBuff[0]) + graphView.m_extentsBuff[2]) / 2.0d;
+ else
+ return (double) (m_hiddenXMin + m_hiddenXMax) / 2.0;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param yPos
+ * DOCUMENT ME!
+ */
+ public void setYPosition(double yPos) {
+ synchronized (graphView.m_lock) {
+ final double hDiv2;
+ final boolean nodeVisible = graphView.m_spacial.exists(m_inx,
+ graphView.m_extentsBuff, 0);
+
+ if (nodeVisible)
+ hDiv2 = (((double) graphView.m_extentsBuff[3]) - graphView.m_extentsBuff[1]) / 2.0d;
+ else
+ hDiv2 = (double) (m_hiddenYMax - m_hiddenYMin) / 2.0d;
+
+ final float yMin = (float) (yPos - hDiv2);
+ final float yMax = (float) (yPos + hDiv2);
+
+ if (!(yMax > yMin))
+ throw new IllegalStateException(
+ "height of node has degenerated to zero after "
+ + "rounding");
+
+ // If the node is visible, set the extents.
+ if (nodeVisible) {
+ graphView.m_spacial.delete(m_inx);
+ graphView.m_spacial.insert(m_inx, graphView.m_extentsBuff[0],
+ yMin, graphView.m_extentsBuff[2], yMax);
+ graphView.m_contentChanged = true;
+
+ // If the node is NOT visible (hidden), then update the hidden
+ // extents. Doing
+ // this will mean that the node view will be properly scaled and
+ // rotated
+ // relative to the other nodes.
+ } else {
+ m_hiddenYMax = yMax;
+ m_hiddenYMin = yMin;
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param yPos
+ * DOCUMENT ME!
+ * @param update
+ * DOCUMENT ME!
+ */
+ public void setYPosition(double yPos, boolean update) {
+ setYPosition(yPos);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public double getYPosition() {
+ synchronized (graphView.m_lock) {
+ if (graphView.m_spacial.exists(m_inx, graphView.m_extentsBuff, 0))
+ return (((double) graphView.m_extentsBuff[1]) + graphView.m_extentsBuff[3]) / 2.0d;
+ else
+ return ((double) (m_hiddenYMin + m_hiddenYMax)) / 2.0d;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param animate
+ * DOCUMENT ME!
+ */
+ public void setNodePosition(boolean animate) {
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void select() {
+ final boolean somethingChanged;
+
+ synchronized (graphView.m_lock) {
+ somethingChanged = selectInternal();
+
+ if (somethingChanged)
+ graphView.m_contentChanged = true;
+ }
+
+ if (somethingChanged) {
+ final GraphViewChangeListener listener = graphView.m_lis[0];
+
+ if (listener != null)
+ listener.graphViewChanged(new GraphViewNodesSelectedEvent(
+ graphView, new int[] { ~m_inx }));
+ }
+ }
+
+ // Should synchronize around m_view.m_lock.
+ boolean selectInternal() {
+ if (m_selected)
+ return false;
+
+ m_selected = true;
+ graphView.m_nodeDetails.overrideFillPaint(m_inx, m_selectedPaint);
+
+ if (m_selectedPaint instanceof Color)
+ graphView.m_nodeDetails.overrideColorLowDetail(m_inx,
+ (Color) m_selectedPaint);
+
+ graphView.m_selectedNodes.insert(m_inx);
+
+ return true;
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void unselect() {
+ final boolean somethingChanged;
+
+ synchronized (graphView.m_lock) {
+ somethingChanged = unselectInternal();
+
+ if (somethingChanged)
+ graphView.m_contentChanged = true;
+ }
+
+ if (somethingChanged) {
+ final GraphViewChangeListener listener = graphView.m_lis[0];
+
+ if (listener != null)
+ listener.graphViewChanged(new GraphViewNodesUnselectedEvent(
+ graphView, new int[] { ~m_inx }));
+ }
+ }
+
+ // Should synchronize around m_view.m_lock.
+ boolean unselectInternal() {
+ if (!m_selected)
+ return false;
+
+ m_selected = false;
+ graphView.m_nodeDetails.overrideFillPaint(m_inx, m_unselectedPaint);
+
+ if (m_unselectedPaint instanceof Color)
+ graphView.m_nodeDetails.overrideColorLowDetail(m_inx,
+ (Color) m_unselectedPaint);
+
+ graphView.m_selectedNodes.delete(m_inx);
+
+ return true;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isSelected() {
+ return m_selected;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param selected
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean setSelected(boolean selected) {
+ if (selected)
+ select();
+ else
+ unselect();
+
+ return true;
+ }
+
+ final public boolean isHidden() {
+ return graphView.isHidden(this);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param shape
+ * DOCUMENT ME!
+ */
+ public void setShape(final int shape) {
+ synchronized (graphView.m_lock) {
+ byte nativeShape = GinyUtil.getNativeNodeType(shape);
+
+ graphView.m_nodeDetails.overrideShape(m_inx, nativeShape);
+ graphView.m_contentChanged = true;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param tip
+ * DOCUMENT ME!
+ */
+ public void setToolTip(String tip) {
+ m_toolTipText = tip;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getToolTip() {
+ return m_toolTipText;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param position
+ * DOCUMENT ME!
+ */
+ public void setPositionHint(int position) {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Paint getTextPaint() {
+ synchronized (graphView.m_lock) {
+ return graphView.m_nodeDetails.labelPaint(m_inx, 0);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param textPaint
+ * DOCUMENT ME!
+ */
+ public void setTextPaint(Paint textPaint) {
+ synchronized (graphView.m_lock) {
+ graphView.m_nodeDetails.overrideLabelPaint(m_inx, 0, textPaint);
+ graphView.m_contentChanged = true;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public double getGreekThreshold() {
+ return 0.0d;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param threshold
+ * DOCUMENT ME!
+ */
+ public void setGreekThreshold(double threshold) {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getText() {
+ synchronized (graphView.m_lock) {
+ return graphView.m_nodeDetails.labelText(m_inx, 0);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param text
+ * DOCUMENT ME!
+ */
+ public void setText(String text) {
+ synchronized (graphView.m_lock) {
+ graphView.m_nodeDetails.overrideLabelText(m_inx, 0, text);
+
+ if (DEFAULT_LABEL_TEXT.equals(graphView.m_nodeDetails.labelText(
+ m_inx, 0)))
+ graphView.m_nodeDetails.overrideLabelCount(m_inx, 0);
+ else
+ graphView.m_nodeDetails.overrideLabelCount(m_inx, 1);
+
+ graphView.m_contentChanged = true;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Font getFont() {
+ synchronized (graphView.m_lock) {
+ return graphView.m_nodeDetails.labelFont(m_inx, 0);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param font
+ * DOCUMENT ME!
+ */
+ public void setFont(Font font) {
+ synchronized (graphView.m_lock) {
+ graphView.m_nodeDetails.overrideLabelFont(m_inx, 0, font);
+ graphView.m_contentChanged = true;
+ }
+ }
+
+ // Custom graphic stuff.
+
+ /**
+ * Adds a custom graphic, <EM>in draw order</EM>, to this DNodeView in a
+ * thread-safe way. This is a convenience method that is equivalent to
+ * calling: <CODE>
+ * addCustomGraphic (new CustomGraphic (shape,paint,anchor))
+ * </CODE> except the the new CustomGraphic created is returned.
+ *
+ * @param shape
+ * @param paint
+ * @param anchor
+ * The byte value from NodeDetails, that defines where the
+ * graphic anchor point lies on this DNodeView's extents
+ * rectangle. A common anchor is NodeDetails.ANCHOR_CENTER.
+ * @since Cytoscape 2.6
+ * @throws IllegalArgumentException
+ * if shape or paint are null or anchor is not in the range 0 <=
+ * anchor <= NodeDetails.MAX_ANCHOR_VAL.
+ * @return The CustomGraphic added to this DNodeView.
+ * @see #addCustomGraphic(CustomGraphic)
+ * @see cytoscape.render.stateful.CustomGraphic
+ */
+ public CustomGraphic addCustomGraphic(Shape shape, Paint paint, byte anchor) {
+ CustomGraphic cg = new CustomGraphic(shape, paint, anchor);
+ addCustomGraphic(cg);
+ return cg;
+ }
+
+ /**
+ * Adds a given CustomGraphic, <EM>in draw order</EM>, to this DNodeView in
+ * a thread-safe way. Each CustomGraphic will be drawn in the order is was
+ * added. So, if you care about draw order (as for overlapping graphics),
+ * make sure you add them in the order you desire. Note that since
+ * CustomGraphics may be added by multiple plugins, your additions may be
+ * interleaved with others.
+ *
+ * <P>
+ * A CustomGraphic can only be associated with a DNodeView once. If you wish
+ * to have a custom graphic, with the same paint and shape information,
+ * occur in multiple places in the draw order, simply create a new
+ * CustomGraphic and add it.
+ *
+ * @since Cytoscape 2.6
+ * @throws IllegalArgumentException
+ * if shape or paint are null.
+ * @return true if the CustomGraphic was added to this DNodeView. false if
+ * this DNodeView already contained this CustomGraphic.
+ * @see cytoscape.render.stateful.CustomGraphic
+ */
+ public boolean addCustomGraphic(CustomGraphic cg) {
+ boolean retVal = false;
+ synchronized (CG_LOCK) {
+ if (_customGraphics == null) {
+ _customGraphics = new LinkedHashSet<CustomGraphic>();
+ graphicsPositions = new HashMap<CustomGraphic, ObjectPosition>();
+ }
+ if (_customGraphics.contains(cg))
+ retVal = false;
+ else {
+ retVal = _customGraphics.add(cg);
+ }
+ }
+ ensureContentChanged();
+ return retVal;
+ }
+
+ /**
+ * A thread-safe way to determine if this DNodeView contains a given custom
+ * graphic.
+ *
+ * @param cg
+ * the CustomGraphic for which we are checking containment.
+ * @since Cytoscape 2.6
+ */
+ public boolean containsCustomGraphic(CustomGraphic cg) {
+ synchronized (CG_LOCK) {
+ if (_customGraphics == null) {
+ return false;
+ }
+ return _customGraphics.contains(cg);
+ }
+ }
+
+ /**
+ * Return a non-null, read-only Iterator over all CustomGraphics contained
+ * in this DNodeView. The Iterator will return each CustomGraphic in draw
+ * order. The Iterator cannot be used to modify the underlying set of
+ * CustomGraphics.
+ *
+ * @return The CustomGraphics Iterator. If no CustomGraphics are associated
+ * with this DNOdeView, an empty Iterator is returned.
+ * @throws UnsupportedOperationException
+ * if an attempt is made to use the Iterator's remove() method.
+ * @since Cytoscape 2.6
+ */
+ public Iterator<CustomGraphic> customGraphicIterator() {
+ final Iterable<CustomGraphic> toIterate;
+ synchronized (CG_LOCK) {
+ if (_customGraphics == null) {
+ toIterate = EMPTY_CUSTOM_GRAPHICS;
+ } else {
+ toIterate = _customGraphics;
+ }
+ return new ReadOnlyIterator<CustomGraphic>(toIterate);
+ }
+ }
+
+ /**
+ * A thread-safe method for removing a given custom graphic from this
+ * DNodeView.
+ *
+ * @return true if the custom graphic was found an removed. Returns false if
+ * cg is null or is not a custom graphic associated with this
+ * DNodeView.
+ * @since Cytoscape 2.6
+ */
+ public boolean removeCustomGraphic(CustomGraphic cg) {
+ boolean retVal = false;
+ synchronized (CG_LOCK) {
+ if (_customGraphics != null) {
+ retVal = _customGraphics.remove(cg);
+ graphicsPositions.remove(cg);
+ }
+ }
+ ensureContentChanged();
+ return retVal;
+ }
+
+ public void removeAllCustomGraphics() {
+ synchronized (CG_LOCK) {
+ if (_customGraphics != null) {
+ _customGraphics.clear();
+ graphicsPositions.clear();
+ }
+ }
+ ensureContentChanged();
+ }
+
+ /**
+ * A thread-safe method returning the number of custom graphics associated
+ * with this DNodeView. If none are associated, zero is returned.
+ *
+ * @since Cytoscape 2.6
+ */
+ public int getNumCustomGraphics() {
+ synchronized (CG_LOCK) {
+ if (_customGraphics == null)
+ return 0;
+ return _customGraphics.size();
+ }
+ }
+
+ private void ensureContentChanged() {
+ synchronized (graphView.m_lock) {
+ graphView.m_contentChanged = true;
+ }
+ }
+
+ /**
+ * Obtain the lock used for reading information about custom graphics. This
+ * is <EM>not</EM> needed for thread-safe custom graphic operations, but
+ * only needed for use with thread-compatible methods, such as
+ * customGraphicIterator(). For example, to iterate over all custom graphics
+ * without fear of the underlying custom graphics being mutated, you could
+ * perform:
+ *
+ * <PRE>
+ * DNodeView dnv = ...;
+ * CustomGraphic cg = null;
+ * synchronized (dnv.customGraphicLock()) {
+ * Iterator<CustomGraphic> cgIt = dnv.customGraphicIterator();
+ * while (cgIt.hasNext()) {
+ * cg = cgIt.next();
+ * // PERFORM your operations here.
+ * }
+ * }
+ * </PRE>
+ *
+ * NOTE: A better concurrency approach would be to return the read lock from
+ * a java.util.concurrent.locks.ReentrantReadWriteLock. However, this
+ * requires users to manually lock and unlock blocks of code where many
+ * times try{} finally{} blocks are needed and if any mistake are made, a
+ * DNodeView may be permanently locked. Since concurrency will most likely
+ * be very low, we opt for the simpler approach of having users use
+ * synchronized {} blocks on a standard lock object.
+ *
+ * @return the lock object used for custom graphics of this DNodeView.
+ */
+ public Object customGraphicLock() {
+ return CG_LOCK;
+ }
+
+ private class ReadOnlyIterator<T> implements Iterator<T> {
+ private Iterator<? extends T> _iterator;
+
+ public ReadOnlyIterator(Iterable<T> toIterate) {
+ _iterator = toIterate.iterator();
+ }
+
+ public boolean hasNext() {
+ return _iterator.hasNext();
+ }
+
+ public T next() {
+ return _iterator.next();
+ }
+
+ public void remove() {
+ throw new UnsupportedOperationException();
+ }
+ };
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param position
+ * DOCUMENT ME!
+ */
+ @Deprecated
+ public void setTextAnchor(int position) {
+ labelPosition.setAnchor(Position.parse(position));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Deprecated
+ public int getTextAnchor() {
+ return labelPosition.getAnchor().getGinyConstant();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param justify
+ * DOCUMENT ME!
+ */
+ @Deprecated
+ public void setJustify(int justify) {
+ labelPosition.setJustify(Justification.parse(justify));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Deprecated
+ public int getJustify() {
+ return labelPosition.getJustify().getGinyConstant();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param x
+ * DOCUMENT ME!
+ */
+ @Deprecated
+ public void setLabelOffsetX(double x) {
+ labelPosition.setOffsetX(x);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Deprecated
+ public double getLabelOffsetX() {
+ return labelPosition.getOffsetX();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param y
+ * DOCUMENT ME!
+ */
+ @Deprecated
+ public void setLabelOffsetY(double y) {
+ labelPosition.setOffsetY(y);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Deprecated
+ public double getLabelOffsetY() {
+ return labelPosition.getOffsetY();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param position
+ * DOCUMENT ME!
+ */
+ @Deprecated
+ public void setNodeLabelAnchor(int position) {
+ labelPosition.setTargetAnchor(Position.parse(position));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Deprecated
+ public int getNodeLabelAnchor() {
+ return labelPosition.getTargetAnchor().getGinyConstant();
+ }
+
+ public double getLabelWidth() {
+ synchronized (graphView.m_lock) {
+ return graphView.m_nodeDetails.labelWidth(m_inx);
+ }
+ }
+
+ public void setLabelWidth(double width) {
+ synchronized (graphView.m_lock) {
+ graphView.m_nodeDetails.overrideLabelWidth(m_inx, width);
+ graphView.m_contentChanged = true;
+ }
+ }
+
+
+ TexturePaint getNestedNetworkTexturePaint() {
+ synchronized (graphView.m_lock) {
+ ++nestedNetworkPaintingDepth;
+ try {
+ if (nestedNetworkPaintingDepth > 1
+ || getNode().getNestedNetwork() == null
+ || !nestedNetworkVisible)
+ return null;
+
+ final double IMAGE_WIDTH = getWidth()
+ * NESTED_IMAGE_SCALE_FACTOR;
+ final double IMAGE_HEIGHT = getHeight()
+ * NESTED_IMAGE_SCALE_FACTOR;
+
+ // Do we have a node w/ a self-reference?
+ if (graphView == nestedNetworkView) {
+ if (RECURSIVE_NESTED_NETWORK_IMAGE == null)
+ return null;
+
+ final Rectangle2D rect = new Rectangle2D.Double(
+ -IMAGE_WIDTH / 2, -IMAGE_HEIGHT / 2, IMAGE_WIDTH,
+ IMAGE_HEIGHT);
+ return new TexturePaint(RECURSIVE_NESTED_NETWORK_IMAGE,
+ rect);
+ }
+ if (nestedNetworkView != null) {
+ final double scaleFactor = graphView.getGraphLOD().getNestedNetworkImageScaleFactor();
+ return nestedNetworkView.getSnapshot(IMAGE_WIDTH * scaleFactor,
+ IMAGE_HEIGHT * scaleFactor);
+ } else {
+ if (DEFAULT_NESTED_NETWORK_IMAGE == null)
+ return null;
+
+ final Rectangle2D rect = new Rectangle2D.Double(
+ -IMAGE_WIDTH / 2, -IMAGE_HEIGHT / 2, IMAGE_WIDTH,
+ IMAGE_HEIGHT);
+ return new TexturePaint(DEFAULT_NESTED_NETWORK_IMAGE, rect);
+ }
+ } finally {
+ --nestedNetworkPaintingDepth;
+ }
+ }
+ }
+
+ public void setNestedNetworkView(final DGraphView nestedNetworkView) {
+ this.nestedNetworkView = nestedNetworkView;
+ }
+
+ /**
+ * Determines whether a nested network should be rendered as part of a
+ * node's view or not.
+ *
+ * @return true if the node has a nested network and we want it rendered,
+ * else false.
+ */
+ public boolean nestedNetworkIsVisible() {
+ return nestedNetworkVisible;
+ }
+
+ /**
+ * Set the visibility of a node's nested network when rendered.
+ *
+ * @param makeVisible
+ * forces the visibility of a nested network. Please note that
+ * this call has no effect if a node has no associated nested
+ * network!
+ */
+ public void showNestedNetwork(final boolean makeVisible) {
+ nestedNetworkVisible = makeVisible;
+ }
+
+ // from Label interface
+ public ObjectPosition getPosition() {
+ return labelPosition;
+ }
+
+ // from Label interface
+ public void setPosition(final ObjectPosition p) {
+ this.labelPosition = p;
+ updateLabelPosition();
+ }
+
+ private void updateLabelPosition() {
+ synchronized (graphView.m_lock) {
+ graphView.m_nodeDetails.overrideLabelTextAnchor(m_inx, 0,
+ labelPosition.getAnchor().getGinyConstant());
+ graphView.m_nodeDetails.overrideLabelNodeAnchor(m_inx, 0,
+ labelPosition.getTargetAnchor().getGinyConstant());
+ graphView.m_nodeDetails.overrideLabelJustify(m_inx, 0,
+ labelPosition.getJustify().getGinyConstant());
+ graphView.m_nodeDetails.overrideLabelOffsetVectorX(m_inx, 0,
+ labelPosition.getOffsetX());
+ graphView.m_nodeDetails.overrideLabelOffsetVectorY(m_inx, 0,
+ labelPosition.getOffsetY());
+
+ graphView.m_contentChanged = true;
+ }
+ }
+
+ public CustomGraphic setCustomGraphicsPosition(CustomGraphic cg,
+ final ObjectPosition p) {
+ if (cg == null || p == null)
+ throw new IllegalArgumentException(
+ "CustomGraphic and Position cannot be null.");
+
+ boolean removeTest = _customGraphics.remove(cg);
+ graphicsPositions.remove(cg);
+
+ CustomGraphic newCg = CustomGraphicsPositionCalculator.transform(p,
+ this, cg);
+
+ _customGraphics.add(newCg);
+ graphicsPositions.put(newCg, p);
+
+ return newCg;
+ }
+
+ public ObjectPosition getCustomGraphicsPosition(final CustomGraphic cg) {
+ if (cg == null)
+ return ObjectPositionImpl.DEFAULT_POSITION;
+
+ return graphicsPositions.get(cg);
+ }
+
+ // from NodeView interface
+ public ObjectPosition getLabelPosition() {
+ return labelPosition;
+ }
+
+ // from NodeView interface
+ public void setLabelPosition(final ObjectPosition position) {
+ setPosition(position);
+ }
+}
diff --git a/corelibs/ding/src/main/java/ding/view/DingCanvas.java b/corelibs/ding/src/main/java/ding/view/DingCanvas.java
new file mode 100644
index 0000000..2ee8814
--- /dev/null
+++ b/corelibs/ding/src/main/java/ding/view/DingCanvas.java
@@ -0,0 +1,132 @@
+/*
+ File: CytoscapeCanvas.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package ding.view;
+
+import java.awt.Color;
+
+// imports
+import java.awt.Image;
+import java.awt.Graphics;
+
+import javax.swing.JComponent;
+
+
+/**
+ * This class is meant to be extended by a class which
+ * is meant to exist within the InternalFrameComponent class.
+ * It provides the services required to draw onto it.
+ *
+ * Currently (9/7/06), two classes will extend DingCanves, ding.view.InnerCanvas
+ * and ding.view.ArbitraryGraphicsCanvas.
+ */
+public abstract class DingCanvas extends JComponent {
+
+ private static final long serialVersionUID = 4138104679262169265L;
+
+ /**
+ * ref to image we maintain
+ */
+ protected Image m_img;
+
+ /**
+ * ref to our background color
+ */
+ protected Color m_backgroundColor;
+
+ /**
+ * ref to visibility boolean
+ */
+ protected boolean m_isVisible;
+
+ /**
+ * ref to opaque boolean
+ */
+ protected boolean m_isOpaque;
+
+ /**
+ * Show or hides this component depending on value of parameter.
+ *
+ * @param isVisible boolean
+ */
+ public void setVisible(boolean isVisible) {
+ m_isVisible = isVisible;
+ }
+
+ /**
+ * Sets opacity of component
+ *
+ * @param isOpaque boolean
+ */
+ public void setOpaque(boolean isOpaque) {
+ m_isOpaque = isOpaque;
+ }
+
+ /**
+ * Returns the background color of this component.
+ *
+ * @return Color
+ */
+ public Color getBackground() {
+ return m_backgroundColor;
+ }
+
+ /**
+ * Set the component background color.
+ *
+ * backgroundColor Color
+ */
+ public void setBackground(Color backgroundColor) {
+ m_backgroundColor = backgroundColor;
+ }
+
+ /**
+ * Returns the image maintained by the canvas.
+ *
+ * @return Image
+ */
+ public Image getImage() {
+ return m_img;
+ }
+
+
+ /**
+ * Method used to print canvas without using image imposter.
+ */
+ public void printNoImposter(Graphics g) {
+ print(g);
+ }
+}
diff --git a/corelibs/ding/src/main/java/ding/view/EdgeContextMenuListener.java b/corelibs/ding/src/main/java/ding/view/EdgeContextMenuListener.java
new file mode 100644
index 0000000..8ba5f5f
--- /dev/null
+++ b/corelibs/ding/src/main/java/ding/view/EdgeContextMenuListener.java
@@ -0,0 +1,59 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package ding.view;
+
+import giny.view.EdgeView;
+
+import java.awt.*;
+import java.awt.Point;
+import java.awt.datatransfer.Transferable;
+import java.awt.event.*;
+
+import java.util.*;
+
+import javax.swing.JPopupMenu;
+
+
+/**
+ * an interface for responding to PhoebeCanvasDropEvents.
+ */
+public interface EdgeContextMenuListener extends EventListener {
+ /**
+ * method for responding to a drop
+ */
+ void addEdgeContextMenuItems(EdgeView edgeView, JPopupMenu menu);
+}
diff --git a/corelibs/ding/src/main/java/ding/view/GinyUtil.java b/corelibs/ding/src/main/java/ding/view/GinyUtil.java
new file mode 100644
index 0000000..2a4fe04
--- /dev/null
+++ b/corelibs/ding/src/main/java/ding/view/GinyUtil.java
@@ -0,0 +1,177 @@
+package ding.view;
+
+import static cytoscape.render.immed.GraphGraphics.ARROW_DELTA;
+import static cytoscape.render.immed.GraphGraphics.ARROW_DIAMOND;
+import static cytoscape.render.immed.GraphGraphics.ARROW_DISC;
+import static cytoscape.render.immed.GraphGraphics.ARROW_NONE;
+import static cytoscape.render.immed.GraphGraphics.ARROW_TEE;
+import static cytoscape.render.immed.GraphGraphics.ARROW_HALF_TOP;
+import static cytoscape.render.immed.GraphGraphics.ARROW_HALF_BOTTOM;
+import static cytoscape.render.immed.GraphGraphics.ARROW_ARROWHEAD;
+import static cytoscape.render.immed.GraphGraphics.SHAPE_DIAMOND;
+import static cytoscape.render.immed.GraphGraphics.SHAPE_ELLIPSE;
+import static cytoscape.render.immed.GraphGraphics.SHAPE_HEXAGON;
+import static cytoscape.render.immed.GraphGraphics.SHAPE_OCTAGON;
+import static cytoscape.render.immed.GraphGraphics.SHAPE_PARALLELOGRAM;
+import static cytoscape.render.immed.GraphGraphics.SHAPE_RECTANGLE;
+import static cytoscape.render.immed.GraphGraphics.SHAPE_ROUNDED_RECTANGLE;
+import static cytoscape.render.immed.GraphGraphics.SHAPE_TRIANGLE;
+import static cytoscape.render.immed.GraphGraphics.SHAPE_VEE;
+import static giny.view.EdgeView.EDGE_COLOR_CIRCLE;
+import static giny.view.EdgeView.EDGE_COLOR_DELTA;
+import static giny.view.EdgeView.EDGE_COLOR_ARROW;
+import static giny.view.EdgeView.EDGE_COLOR_DIAMOND;
+import static giny.view.EdgeView.EDGE_COLOR_T;
+import static giny.view.EdgeView.EDGE_HALF_ARROW_TOP;
+import static giny.view.EdgeView.EDGE_HALF_ARROW_BOTTOM;
+import static giny.view.EdgeView.NO_END;
+import static giny.view.NodeView.DIAMOND;
+import static giny.view.NodeView.ELLIPSE;
+import static giny.view.NodeView.HEXAGON;
+import static giny.view.NodeView.OCTAGON;
+import static giny.view.NodeView.PARALELLOGRAM;
+import static giny.view.NodeView.RECTANGLE;
+import static giny.view.NodeView.ROUNDED_RECTANGLE;
+import static giny.view.NodeView.TRIANGLE;
+import static giny.view.NodeView.VEE;
+
+/**
+ *
+ * Convert bytes defined in rendering engine into Giny types.
+ *
+ * @version 0.7
+ * @since Cytoscape 2.5
+ * @author kono
+ *
+ */
+class GinyUtil {
+ static int getGinyNodeType(final byte type) {
+ switch (type) {
+ case SHAPE_RECTANGLE:
+ return RECTANGLE;
+
+ case SHAPE_DIAMOND:
+ return DIAMOND;
+
+ case SHAPE_ELLIPSE:
+ return ELLIPSE;
+
+ case SHAPE_HEXAGON:
+ return HEXAGON;
+
+ case SHAPE_OCTAGON:
+ return OCTAGON;
+
+ case SHAPE_PARALLELOGRAM:
+ return PARALELLOGRAM;
+
+ case SHAPE_ROUNDED_RECTANGLE:
+ return ROUNDED_RECTANGLE;
+
+ case SHAPE_TRIANGLE:
+ return TRIANGLE;
+
+ case SHAPE_VEE:
+ return VEE;
+
+ default:
+ return TRIANGLE;
+ }
+ }
+
+ static byte getNativeNodeType(final int ginyType) {
+ switch (ginyType) {
+ case RECTANGLE:
+ return SHAPE_RECTANGLE;
+
+ case DIAMOND:
+ return SHAPE_DIAMOND;
+
+ case ELLIPSE:
+ return SHAPE_ELLIPSE;
+
+ case HEXAGON:
+ return SHAPE_HEXAGON;
+
+ case OCTAGON:
+ return SHAPE_OCTAGON;
+
+ case PARALELLOGRAM:
+ return SHAPE_PARALLELOGRAM;
+
+ case ROUNDED_RECTANGLE:
+ return SHAPE_ROUNDED_RECTANGLE;
+
+ case TRIANGLE:
+ return SHAPE_TRIANGLE;
+
+ case VEE:
+ return SHAPE_VEE;
+
+ default:
+ return -1;
+ }
+ }
+
+ static int getGinyArrowType(final byte type) {
+ switch (type) {
+ case ARROW_NONE:
+ return NO_END;
+
+ case ARROW_DELTA:
+ return EDGE_COLOR_DELTA;
+
+ case ARROW_DIAMOND:
+ return EDGE_COLOR_DIAMOND;
+
+ case ARROW_DISC:
+ return EDGE_COLOR_CIRCLE;
+
+ case ARROW_TEE:
+ return EDGE_COLOR_T;
+
+ case ARROW_HALF_TOP:
+ return EDGE_HALF_ARROW_TOP;
+
+ case ARROW_HALF_BOTTOM:
+ return EDGE_HALF_ARROW_BOTTOM;
+
+ case ARROW_ARROWHEAD:
+ return EDGE_COLOR_ARROW;
+
+ default:
+ return NO_END;
+ }
+ }
+
+ static byte getNativeArrowType(final int ginyType) {
+ switch (ginyType) {
+ case NO_END:
+ return ARROW_NONE;
+
+ case EDGE_COLOR_ARROW:
+ return ARROW_ARROWHEAD;
+
+ case EDGE_COLOR_DELTA:
+ return ARROW_DELTA;
+
+ case EDGE_COLOR_DIAMOND:
+ return ARROW_DIAMOND;
+
+ case EDGE_COLOR_CIRCLE:
+ return ARROW_DISC;
+
+ case EDGE_COLOR_T:
+ return ARROW_TEE;
+
+ case EDGE_HALF_ARROW_TOP:
+ return ARROW_HALF_TOP;
+
+ case EDGE_HALF_ARROW_BOTTOM:
+ return ARROW_HALF_BOTTOM;
+
+ default:
+ return ARROW_NONE;
+ }
+ }
+}
diff --git a/corelibs/ding/src/main/java/ding/view/GraphViewChangeEventAdapter.java b/corelibs/ding/src/main/java/ding/view/GraphViewChangeEventAdapter.java
new file mode 100644
index 0000000..d44fc15
--- /dev/null
+++ b/corelibs/ding/src/main/java/ding/view/GraphViewChangeEventAdapter.java
@@ -0,0 +1,273 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package ding.view;
+
+import giny.model.Edge;
+import giny.model.Node;
+
+import giny.view.GraphView;
+import giny.view.GraphViewChangeEvent;
+
+
+abstract class GraphViewChangeEventAdapter extends GraphViewChangeEvent {
+ GraphViewChangeEventAdapter(GraphView source) {
+ super(source);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public abstract int getType();
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final boolean isNodesRestoredType() {
+ return (getType() & NODES_RESTORED_TYPE) != 0;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final boolean isEdgesRestoredType() {
+ return (getType() & EDGES_RESTORED_TYPE) != 0;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final boolean isNodesHiddenType() {
+ return (getType() & NODES_HIDDEN_TYPE) != 0;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final boolean isEdgesHiddenType() {
+ return (getType() & EDGES_HIDDEN_TYPE) != 0;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final boolean isNodesSelectedType() {
+ return (getType() & NODES_SELECTED_TYPE) != 0;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final boolean isNodesUnselectedType() {
+ return (getType() & NODES_UNSELECTED_TYPE) != 0;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final boolean isEdgesSelectedType() {
+ return (getType() & EDGES_SELECTED_TYPE) != 0;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final boolean isEdgesUnselectedType() {
+ return (getType() & EDGES_UNSELECTED_TYPE) != 0;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Node[] getRestoredNodes() {
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Edge[] getRestoredEdges() {
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Node[] getHiddenNodes() {
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Edge[] getHiddenEdges() {
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Node[] getSelectedNodes() {
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Node[] getUnselectedNodes() {
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Edge[] getSelectedEdges() {
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Edge[] getUnselectedEdges() {
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] getRestoredNodeIndices() {
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] getRestoredEdgeIndices() {
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] getHiddenNodeIndices() {
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] getHiddenEdgeIndices() {
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] getSelectedNodeIndices() {
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] getUnselectedNodeIndices() {
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] getSelectedEdgeIndices() {
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] getUnselectedEdgeIndices() {
+ return null;
+ }
+}
diff --git a/corelibs/ding/src/main/java/ding/view/GraphViewChangeListenerChain.java b/corelibs/ding/src/main/java/ding/view/GraphViewChangeListenerChain.java
new file mode 100644
index 0000000..8c5f9d1
--- /dev/null
+++ b/corelibs/ding/src/main/java/ding/view/GraphViewChangeListenerChain.java
@@ -0,0 +1,97 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package ding.view;
+
+import giny.view.GraphViewChangeEvent;
+import giny.view.GraphViewChangeListener;
+
+
+class GraphViewChangeListenerChain implements GraphViewChangeListener {
+ private final GraphViewChangeListener a;
+ private final GraphViewChangeListener b;
+
+ private GraphViewChangeListenerChain(GraphViewChangeListener a, GraphViewChangeListener b) {
+ this.a = a;
+ this.b = b;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt DOCUMENT ME!
+ */
+ public void graphViewChanged(GraphViewChangeEvent evt) {
+ a.graphViewChanged(evt);
+ b.graphViewChanged(evt);
+ }
+
+ static GraphViewChangeListener add(GraphViewChangeListener a, GraphViewChangeListener b) {
+ if (a == null)
+ return b;
+
+ if (b == null)
+ return a;
+
+ return new GraphViewChangeListenerChain(a, b);
+ }
+
+ static GraphViewChangeListener remove(GraphViewChangeListener l, GraphViewChangeListener oldl) {
+ if ((l == oldl) || (l == null))
+ return null;
+ else if (l instanceof GraphViewChangeListenerChain)
+ return ((GraphViewChangeListenerChain) l).remove(oldl);
+ else
+
+ return l;
+ }
+
+ private GraphViewChangeListener remove(GraphViewChangeListener oldl) {
+ if (oldl == a)
+ return b;
+
+ if (oldl == b)
+ return a;
+
+ GraphViewChangeListener a2 = remove(a, oldl);
+ GraphViewChangeListener b2 = remove(b, oldl);
+
+ if ((a2 == a) && (b2 == b))
+ return this;
+
+ return add(a2, b2);
+ }
+}
diff --git a/corelibs/ding/src/main/java/ding/view/GraphViewEdgesHiddenEvent.java b/corelibs/ding/src/main/java/ding/view/GraphViewEdgesHiddenEvent.java
new file mode 100644
index 0000000..5b2167c
--- /dev/null
+++ b/corelibs/ding/src/main/java/ding/view/GraphViewEdgesHiddenEvent.java
@@ -0,0 +1,90 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package ding.view;
+
+import giny.model.Edge;
+
+import giny.view.GraphView;
+
+
+final class GraphViewEdgesHiddenEvent extends GraphViewChangeEventAdapter {
+ private final GraphView m_view;
+ private final int[] m_hiddenEdgeInx;
+
+ GraphViewEdgesHiddenEvent(GraphView view, int[] hiddenEdgeInx) {
+ super(view);
+ m_view = view;
+ m_hiddenEdgeInx = hiddenEdgeInx;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final int getType() {
+ return EDGES_HIDDEN_TYPE;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final Edge[] getHiddenEdges() {
+ final Edge[] returnThis = new Edge[m_hiddenEdgeInx.length];
+
+ for (int i = 0; i < returnThis.length; i++)
+ returnThis[i] = m_view.getRootGraph().getEdge(m_hiddenEdgeInx[i]);
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final int[] getHiddenEdgeIndices() {
+ final int[] returnThis = new int[m_hiddenEdgeInx.length];
+
+ for (int i = 0; i < returnThis.length; i++)
+ returnThis[i] = m_hiddenEdgeInx[i];
+
+ return returnThis;
+ }
+}
diff --git a/corelibs/ding/src/main/java/ding/view/GraphViewEdgesRestoredEvent.java b/corelibs/ding/src/main/java/ding/view/GraphViewEdgesRestoredEvent.java
new file mode 100644
index 0000000..b0ac31a
--- /dev/null
+++ b/corelibs/ding/src/main/java/ding/view/GraphViewEdgesRestoredEvent.java
@@ -0,0 +1,90 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package ding.view;
+
+import giny.model.Edge;
+
+import giny.view.GraphView;
+
+
+final class GraphViewEdgesRestoredEvent extends GraphViewChangeEventAdapter {
+ private final GraphView m_view;
+ private final int[] m_restoredEdgeInx;
+
+ GraphViewEdgesRestoredEvent(GraphView view, int[] restoredEdgeInx) {
+ super(view);
+ m_view = view;
+ m_restoredEdgeInx = restoredEdgeInx;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final int getType() {
+ return EDGES_RESTORED_TYPE;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final Edge[] getRestoredEdges() {
+ final Edge[] returnThis = new Edge[m_restoredEdgeInx.length];
+
+ for (int i = 0; i < returnThis.length; i++)
+ returnThis[i] = m_view.getRootGraph().getEdge(m_restoredEdgeInx[i]);
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final int[] getRestoredEdgeIndices() {
+ final int[] returnThis = new int[m_restoredEdgeInx.length];
+
+ for (int i = 0; i < returnThis.length; i++)
+ returnThis[i] = m_restoredEdgeInx[i];
+
+ return returnThis;
+ }
+}
diff --git a/corelibs/ding/src/main/java/ding/view/GraphViewEdgesSelectedEvent.java b/corelibs/ding/src/main/java/ding/view/GraphViewEdgesSelectedEvent.java
new file mode 100644
index 0000000..f4928ac
--- /dev/null
+++ b/corelibs/ding/src/main/java/ding/view/GraphViewEdgesSelectedEvent.java
@@ -0,0 +1,90 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package ding.view;
+
+import giny.model.Edge;
+
+import giny.view.GraphView;
+
+
+final class GraphViewEdgesSelectedEvent extends GraphViewChangeEventAdapter {
+ private final GraphView m_view;
+ private final int[] m_selectedEdgeInx;
+
+ GraphViewEdgesSelectedEvent(GraphView view, int[] selectedEdgeInx) {
+ super(view);
+ m_view = view;
+ m_selectedEdgeInx = selectedEdgeInx;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final int getType() {
+ return EDGES_SELECTED_TYPE;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final Edge[] getSelectedEdges() {
+ final Edge[] returnThis = new Edge[m_selectedEdgeInx.length];
+
+ for (int i = 0; i < returnThis.length; i++)
+ returnThis[i] = m_view.getRootGraph().getEdge(m_selectedEdgeInx[i]);
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final int[] getSelectedEdgeIndices() {
+ final int[] returnThis = new int[m_selectedEdgeInx.length];
+
+ for (int i = 0; i < returnThis.length; i++)
+ returnThis[i] = m_selectedEdgeInx[i];
+
+ return returnThis;
+ }
+}
diff --git a/corelibs/ding/src/main/java/ding/view/GraphViewEdgesUnselectedEvent.java b/corelibs/ding/src/main/java/ding/view/GraphViewEdgesUnselectedEvent.java
new file mode 100644
index 0000000..ef9c411
--- /dev/null
+++ b/corelibs/ding/src/main/java/ding/view/GraphViewEdgesUnselectedEvent.java
@@ -0,0 +1,90 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package ding.view;
+
+import giny.model.Edge;
+
+import giny.view.GraphView;
+
+
+final class GraphViewEdgesUnselectedEvent extends GraphViewChangeEventAdapter {
+ private final GraphView m_view;
+ private final int[] m_unselectedEdgeInx;
+
+ GraphViewEdgesUnselectedEvent(GraphView view, int[] unselectedEdgeInx) {
+ super(view);
+ m_view = view;
+ m_unselectedEdgeInx = unselectedEdgeInx;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final int getType() {
+ return EDGES_UNSELECTED_TYPE;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final Edge[] getUnselectedEdges() {
+ final Edge[] returnThis = new Edge[m_unselectedEdgeInx.length];
+
+ for (int i = 0; i < returnThis.length; i++)
+ returnThis[i] = m_view.getRootGraph().getEdge(m_unselectedEdgeInx[i]);
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final int[] getUnselectedEdgeIndices() {
+ final int[] returnThis = new int[m_unselectedEdgeInx.length];
+
+ for (int i = 0; i < returnThis.length; i++)
+ returnThis[i] = m_unselectedEdgeInx[i];
+
+ return returnThis;
+ }
+}
diff --git a/corelibs/ding/src/main/java/ding/view/GraphViewNodesHiddenEvent.java b/corelibs/ding/src/main/java/ding/view/GraphViewNodesHiddenEvent.java
new file mode 100644
index 0000000..ea036dc
--- /dev/null
+++ b/corelibs/ding/src/main/java/ding/view/GraphViewNodesHiddenEvent.java
@@ -0,0 +1,90 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package ding.view;
+
+import giny.model.Node;
+
+import giny.view.GraphView;
+
+
+final class GraphViewNodesHiddenEvent extends GraphViewChangeEventAdapter {
+ private final GraphView m_view;
+ private final int[] m_hiddenNodeInx;
+
+ GraphViewNodesHiddenEvent(GraphView view, int[] hiddenNodeInx) {
+ super(view);
+ m_view = view;
+ m_hiddenNodeInx = hiddenNodeInx;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final int getType() {
+ return NODES_HIDDEN_TYPE;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final Node[] getHiddenNodes() {
+ final Node[] returnThis = new Node[m_hiddenNodeInx.length];
+
+ for (int i = 0; i < returnThis.length; i++)
+ returnThis[i] = m_view.getRootGraph().getNode(m_hiddenNodeInx[i]);
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final int[] getHiddenNodeIndices() {
+ final int[] returnThis = new int[m_hiddenNodeInx.length];
+
+ for (int i = 0; i < returnThis.length; i++)
+ returnThis[i] = m_hiddenNodeInx[i];
+
+ return returnThis;
+ }
+}
diff --git a/corelibs/ding/src/main/java/ding/view/GraphViewNodesRestoredEvent.java b/corelibs/ding/src/main/java/ding/view/GraphViewNodesRestoredEvent.java
new file mode 100644
index 0000000..0d0615a
--- /dev/null
+++ b/corelibs/ding/src/main/java/ding/view/GraphViewNodesRestoredEvent.java
@@ -0,0 +1,90 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package ding.view;
+
+import giny.model.Node;
+
+import giny.view.GraphView;
+
+
+final class GraphViewNodesRestoredEvent extends GraphViewChangeEventAdapter {
+ private final GraphView m_view;
+ private final int[] m_restoredNodeInx;
+
+ GraphViewNodesRestoredEvent(GraphView view, int[] restoredNodeInx) {
+ super(view);
+ m_view = view;
+ m_restoredNodeInx = restoredNodeInx;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final int getType() {
+ return NODES_RESTORED_TYPE;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final Node[] getRestoredNodes() {
+ final Node[] returnThis = new Node[m_restoredNodeInx.length];
+
+ for (int i = 0; i < returnThis.length; i++)
+ returnThis[i] = m_view.getRootGraph().getNode(m_restoredNodeInx[i]);
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final int[] getRestoredNodeIndices() {
+ final int[] returnThis = new int[m_restoredNodeInx.length];
+
+ for (int i = 0; i < returnThis.length; i++)
+ returnThis[i] = m_restoredNodeInx[i];
+
+ return returnThis;
+ }
+}
diff --git a/corelibs/ding/src/main/java/ding/view/GraphViewNodesSelectedEvent.java b/corelibs/ding/src/main/java/ding/view/GraphViewNodesSelectedEvent.java
new file mode 100644
index 0000000..3e67420
--- /dev/null
+++ b/corelibs/ding/src/main/java/ding/view/GraphViewNodesSelectedEvent.java
@@ -0,0 +1,90 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package ding.view;
+
+import giny.model.Node;
+
+import giny.view.GraphView;
+
+
+final class GraphViewNodesSelectedEvent extends GraphViewChangeEventAdapter {
+ private final GraphView m_view;
+ private final int[] m_selectedNodeInx;
+
+ GraphViewNodesSelectedEvent(GraphView view, int[] selectedNodeInx) {
+ super(view);
+ m_view = view;
+ m_selectedNodeInx = selectedNodeInx;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final int getType() {
+ return NODES_SELECTED_TYPE;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final Node[] getSelectedNodes() {
+ final Node[] returnThis = new Node[m_selectedNodeInx.length];
+
+ for (int i = 0; i < returnThis.length; i++)
+ returnThis[i] = m_view.getRootGraph().getNode(m_selectedNodeInx[i]);
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final int[] getSelectedNodeIndices() {
+ final int[] returnThis = new int[m_selectedNodeInx.length];
+
+ for (int i = 0; i < returnThis.length; i++)
+ returnThis[i] = m_selectedNodeInx[i];
+
+ return returnThis;
+ }
+}
diff --git a/corelibs/ding/src/main/java/ding/view/GraphViewNodesUnselectedEvent.java b/corelibs/ding/src/main/java/ding/view/GraphViewNodesUnselectedEvent.java
new file mode 100644
index 0000000..ffe0449
--- /dev/null
+++ b/corelibs/ding/src/main/java/ding/view/GraphViewNodesUnselectedEvent.java
@@ -0,0 +1,90 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package ding.view;
+
+import giny.model.Node;
+
+import giny.view.GraphView;
+
+
+final class GraphViewNodesUnselectedEvent extends GraphViewChangeEventAdapter {
+ private final GraphView m_view;
+ private final int[] m_unselectedNodeInx;
+
+ GraphViewNodesUnselectedEvent(GraphView view, int[] unselectedNodeInx) {
+ super(view);
+ m_view = view;
+ m_unselectedNodeInx = unselectedNodeInx;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final int getType() {
+ return NODES_UNSELECTED_TYPE;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final Node[] getUnselectedNodes() {
+ final Node[] returnThis = new Node[m_unselectedNodeInx.length];
+
+ for (int i = 0; i < returnThis.length; i++)
+ returnThis[i] = m_view.getRootGraph().getNode(m_unselectedNodeInx[i]);
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final int[] getUnselectedNodeIndices() {
+ final int[] returnThis = new int[m_unselectedNodeInx.length];
+
+ for (int i = 0; i < returnThis.length; i++)
+ returnThis[i] = m_unselectedNodeInx[i];
+
+ return returnThis;
+ }
+}
diff --git a/corelibs/ding/src/main/java/ding/view/InnerCanvas.java b/corelibs/ding/src/main/java/ding/view/InnerCanvas.java
new file mode 100644
index 0000000..33d823c
--- /dev/null
+++ b/corelibs/ding/src/main/java/ding/view/InnerCanvas.java
@@ -0,0 +1,1488 @@
+
+/*
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package ding.view;
+
+import giny.view.EdgeView;
+import giny.view.GraphViewChangeListener;
+import giny.view.NodeView;
+
+import java.awt.Color;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.Image;
+import java.awt.Point;
+import java.awt.Rectangle;
+import java.awt.datatransfer.Transferable;
+import java.awt.dnd.DnDConstants;
+import java.awt.dnd.DropTarget;
+import java.awt.event.KeyEvent;
+import java.awt.event.KeyListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.awt.event.MouseWheelEvent;
+import java.awt.event.MouseWheelListener;
+import java.awt.geom.AffineTransform;
+import java.awt.geom.GeneralPath;
+import java.awt.geom.Line2D;
+import java.awt.geom.Point2D;
+import java.awt.image.BufferedImage;
+import java.util.Enumeration;
+import java.util.Iterator;
+import java.util.Vector;
+
+import javax.swing.JComponent;
+import javax.swing.JPopupMenu;
+import javax.swing.TransferHandler;
+
+import phoebe.PhoebeCanvasDropEvent;
+import phoebe.PhoebeCanvasDropListener;
+import phoebe.PhoebeCanvasDroppable;
+import cytoscape.graph.fixed.FixedGraph;
+import cytoscape.render.export.ImageImposter;
+import cytoscape.render.immed.EdgeAnchors;
+import cytoscape.render.immed.GraphGraphics;
+import cytoscape.render.stateful.GraphLOD;
+import cytoscape.render.stateful.GraphRenderer;
+import cytoscape.util.intr.IntEnumerator;
+import cytoscape.util.intr.IntHash;
+import cytoscape.util.intr.IntStack;
+
+
+/**
+ * The GUI component for drawing networks.
+ *
+ */
+public class InnerCanvas extends DingCanvas implements MouseListener, MouseMotionListener,
+ java.awt.dnd.DropTargetListener,
+ PhoebeCanvasDroppable, KeyListener,
+ MouseWheelListener {
+
+ private static final long serialVersionUID = 6219424955453507079L;
+
+ final double[] m_ptBuff = new double[2];
+ final float[] m_extentsBuff2 = new float[4];
+ final float[] m_floatBuff1 = new float[2];
+ final float[] m_floatBuff2 = new float[2];
+ final Line2D.Float m_line = new Line2D.Float();
+ final GeneralPath m_path = new GeneralPath();
+ final GeneralPath m_path2 = new GeneralPath();
+ final IntStack m_stack = new IntStack();
+ final IntStack m_stack2 = new IntStack();
+ final Object m_lock;
+ DGraphView m_view;
+ final GraphLOD[] m_lod = new GraphLOD[1];
+ final IntHash m_hash;
+ GraphGraphics m_grafx;
+ double m_xCenter;
+ double m_yCenter;
+ double m_scaleFactor;
+ private int m_lastRenderDetail = 0;
+ private Rectangle m_selectionRect = null;
+ private ViewChangeEdit m_undoable_edit;
+ private boolean isPrinting = false;
+
+ FontMetrics m_fontMetrics = null;
+
+ private boolean NodeMovement = true;
+
+
+ /**
+ * String used to compare against os.name System property -
+ * to determine if we are running on Windows platform.
+ */
+ private static final String MAC_OS_ID = "mac";
+
+ private final DropTarget dropTarget;
+
+ // for turning selection rectangle on and off
+ private boolean selecting = true;
+
+ public Vector listeners = new Vector();
+ private Vector transferComponents = new Vector();
+
+ /**
+ * Listeners for node right-click menu
+ */
+ public Vector nodeContextMenuListeners = new Vector();
+
+ /**
+ * Listeners for edge right-click menu.
+ */
+ public Vector edgeContextMenuListeners = new Vector();
+
+ InnerCanvas(Object lock, DGraphView view) {
+ super();
+ m_lock = lock;
+ m_view = view;
+ m_lod[0] = new GraphLOD(); // Default LOD.
+ m_hash = new IntHash();
+ m_backgroundColor = Color.white;
+ m_isVisible = true;
+ m_isOpaque = false;
+ m_xCenter = 0.0d;
+ m_yCenter = 0.0d;
+ m_scaleFactor = 1.0d;
+ addMouseListener(this);
+ addMouseMotionListener(this);
+ addMouseWheelListener(this);
+ addKeyListener(this);
+ setFocusable(true);
+
+ dropTarget = new DropTarget(this, // component
+ DnDConstants.ACTION_COPY, // actions
+ this); // DropTargetListener
+ }
+
+ public double getScaleFactor(){
+ return m_scaleFactor;
+ }
+
+ public void setScaleFactor(double val){
+ m_scaleFactor=val;
+ }
+ /**
+ * DOCUMENT ME!
+ *
+ * @param x DOCUMENT ME!
+ * @param y DOCUMENT ME!
+ * @param width DOCUMENT ME!
+ * @param height DOCUMENT ME!
+ */
+ public void setBounds(int x, int y, int width, int height) {
+ super.setBounds(x, y, width, height);
+
+ if ((width > 0) && (height > 0)) {
+ final Image img = new BufferedImage(width, height, BufferedImage.TYPE_INT_ARGB);
+ GraphGraphics grafx = new GraphGraphics(img, false);
+
+ synchronized (m_lock) {
+ m_img = img;
+ m_grafx = grafx;
+ m_view.m_viewportChanged = true;
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g DOCUMENT ME!
+ */
+ public void update(Graphics g) {
+ if (m_grafx == null)
+ return;
+
+ // This is the magical portion of code that transfers what is in the
+ // visual data structures into what's on the image.
+ boolean contentChanged = false;
+ boolean viewportChanged = false;
+ double xCenter = 0.0d;
+ double yCenter = 0.0d;
+ double scaleFactor = 1.0d;
+
+ m_fontMetrics = g.getFontMetrics();
+
+ synchronized (m_lock) {
+ if (m_view.m_contentChanged || m_view.m_viewportChanged) {
+ renderGraph(m_grafx,/* setLastRenderDetail = */ true, m_lod[0]);
+ contentChanged = m_view.m_contentChanged;
+ m_view.m_contentChanged = false;
+ viewportChanged = m_view.m_viewportChanged;
+ xCenter = m_xCenter;
+ yCenter = m_yCenter;
+ scaleFactor = m_scaleFactor;
+ m_view.m_viewportChanged = false;
+ }
+ }
+
+ // if canvas is visible, draw it (could be made invisible via DingCanvas api)
+ if (m_isVisible) {
+ g.drawImage(m_img, 0, 0, null);
+ }
+
+ if ((m_selectionRect != null) && (this.isSelecting())) {
+ final Graphics2D g2 = (Graphics2D) g;
+ g2.setColor(Color.red);
+ g2.draw(m_selectionRect);
+ }
+
+ if (contentChanged) {
+ final ContentChangeListener lis = m_view.m_cLis[0];
+
+ if (lis != null)
+ lis.contentChanged();
+ }
+
+ if (viewportChanged) {
+ final ViewportChangeListener lis = m_view.m_vLis[0];
+
+ if (lis != null)
+ lis.viewportChanged(getWidth(), getHeight(), xCenter, yCenter, scaleFactor);
+ }
+ }
+
+ /**
+ * Paint this component using Java2D.
+ *
+ * @param g DOCUMENT ME!
+ */
+ public void paint(Graphics g) {
+ update(g);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g Usually Graphics2D object for drawing network view as image.
+ */
+ public void print(Graphics g) {
+ isPrinting = true;
+ renderGraph(new GraphGraphics(
+ new ImageImposter(g, getWidth(), getHeight()), false),
+ /* setLastRenderDetail = */ false, m_view.m_printLOD);
+ // g.drawImage(img, 0, 0, null);
+ isPrinting = false;
+ }
+
+ /**
+ * Print routine which corrects bug 1471/1495
+ *
+ * @param g DOCUMENT ME!
+ */
+ public void printNoImposter(Graphics g) {
+ isPrinting = true;
+ final Image img = new BufferedImage(getWidth(), getHeight(), BufferedImage.TYPE_INT_ARGB);
+ renderGraph(new GraphGraphics(img, false), /* setLastRenderDetail = */ false, m_view.m_printLOD);
+ // g.drawImage(img, 0, 0, null);
+ isPrinting = false;
+ }
+
+ /**
+ * Return true if this view is curerntly being printed (as opposed to painted on the screen)
+ *
+ * @return true if we're currently being printed, false otherwise
+ */
+ public boolean isPrinting() {return isPrinting;}
+
+ private int m_currMouseButton = 0;
+ private int m_lastXMousePos = 0;
+ private int m_lastYMousePos = 0;
+ private boolean m_button1NodeDrag = false;
+
+ /**
+ * This method exposes the JComponent processMouseEvent so that
+ * canvases on top of us can pass events they don't want down.
+ *
+ * @param e the MouseEvent to process
+ */
+ public void processMouseEvent(MouseEvent e) {
+ super.processMouseEvent(e);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void mouseClicked(MouseEvent e) {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void mouseEntered(MouseEvent e) {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void mouseExited(MouseEvent e) {
+ }
+
+ @Override
+ public void mousePressed(MouseEvent e) {
+
+ e.getModifiersEx();
+ if ((e.getButton() == MouseEvent.BUTTON1) && !(isMacPlatform() && e.isControlDown()) && !(isMacPlatform() && e.isMetaDown())) { // on mac, mouse button1 click and control is simulate button 3 press
+ // It's too complicated to correctly handle both control and shift
+ // simultaneously.
+
+ if (e.isShiftDown() && isAnchorKeyDown(e))
+ return;
+
+ // m_undoable_edit = new ViewChangeEdit(m_view, "Move");
+ m_undoable_edit = null;
+
+ m_currMouseButton = 1;
+ m_lastXMousePos = e.getX();
+ m_lastYMousePos = e.getY();
+
+ int[] unselectedNodes = null;
+ int[] unselectedEdges = null;
+ int chosenNode = 0;
+ int chosenEdge = 0;
+ int chosenAnchor = -1;
+ byte chosenNodeSelected = 0;
+ byte chosenEdgeSelected = 0;
+
+ synchronized (m_lock) {
+ if (m_view.m_nodeSelection) {
+ m_ptBuff[0] = m_lastXMousePos;
+ m_ptBuff[1] = m_lastYMousePos;
+ m_view.xformComponentToNodeCoords(m_ptBuff);
+ m_stack.empty();
+ m_view.getNodesIntersectingRectangle((float) m_ptBuff[0], (float) m_ptBuff[1],
+ (float) m_ptBuff[0], (float) m_ptBuff[1],
+ (m_lastRenderDetail
+ & GraphRenderer.LOD_HIGH_DETAIL) == 0,
+ m_stack);
+ chosenNode = (m_stack.size() > 0) ? m_stack.peek() : 0;
+ }
+
+ if (m_view.m_edgeSelection && (chosenNode == 0)
+ && ((m_lastRenderDetail & GraphRenderer.LOD_EDGE_ANCHORS) != 0)) {
+ m_ptBuff[0] = m_lastXMousePos;
+ m_ptBuff[1] = m_lastYMousePos;
+ m_view.xformComponentToNodeCoords(m_ptBuff);
+
+ final IntEnumerator hits = m_view.m_spacialA.queryOverlap((float) m_ptBuff[0],
+ (float) m_ptBuff[1],
+ (float) m_ptBuff[0],
+ (float) m_ptBuff[1],
+ null, 0, false);
+ chosenAnchor = (hits.numRemaining() > 0) ? hits.nextInt() : (-1);
+ }
+
+ if (m_view.m_edgeSelection && (chosenNode == 0) && (chosenAnchor < 0)) {
+ computeEdgesIntersecting(m_lastXMousePos - 1, m_lastYMousePos - 1,
+ m_lastXMousePos + 1, m_lastYMousePos + 1, m_stack2);
+ chosenEdge = (m_stack2.size() > 0) ? m_stack2.peek() : 0;
+ }
+
+ if ((!e.isShiftDown()) // If shift is down never unselect.
+ && (((chosenNode == 0) && (chosenEdge == 0) && (chosenAnchor < 0)) // Mouse missed all.
+ ||
+ // Not [we hit something but it was already selected].
+ !(((chosenNode != 0) && m_view.getNodeView(chosenNode).isSelected())
+ || (chosenAnchor >= 0)
+ || ((chosenEdge != 0) && m_view.getEdgeView(chosenEdge).isSelected())))) {
+ if (m_view.m_nodeSelection) { // Unselect all selected nodes.
+ unselectedNodes = m_view.getSelectedNodeIndices();
+
+ // Adding this line to speed things up from O(n*log(n)) to O(n).
+ m_view.m_selectedNodes.empty();
+
+ for (int i = 0; i < unselectedNodes.length; i++)
+ ((DNodeView) m_view.getNodeView(unselectedNodes[i])).unselectInternal();
+ } else
+ unselectedNodes = new int[0];
+
+ if (m_view.m_edgeSelection) { // Unselect all selected edges.
+ unselectedEdges = m_view.getSelectedEdgeIndices();
+
+ // Adding this line to speed things up from O(n*log(n)) to O(n).
+ m_view.m_selectedEdges.empty();
+
+ for (int i = 0; i < unselectedEdges.length; i++)
+ ((DEdgeView) m_view.getEdgeView(unselectedEdges[i])).unselectInternal();
+ } else
+ unselectedEdges = new int[0];
+
+ if ((unselectedNodes.length > 0) || (unselectedEdges.length > 0))
+ m_view.m_contentChanged = true;
+ }
+
+ if (chosenNode != 0) {
+ final boolean wasSelected = m_view.getNodeView(chosenNode).isSelected();
+
+ if (wasSelected && e.isShiftDown()) {
+ ((DNodeView) m_view.getNodeView(chosenNode)).unselectInternal();
+ chosenNodeSelected = (byte) -1;
+ } else if (!wasSelected) {
+ ((DNodeView) m_view.getNodeView(chosenNode)).selectInternal();
+ chosenNodeSelected = (byte) 1;
+ }
+
+ m_button1NodeDrag = true;
+ m_view.m_contentChanged = true;
+ }
+
+ if (chosenAnchor >= 0) {
+ if (isAnchorKeyDown(e)) {
+ final int edge = chosenAnchor >>> 6;
+ final int anchorInx = chosenAnchor & 0x0000003f;
+ //****** Save remove handle
+ m_undoable_edit = new ViewChangeEdit(m_view,ViewChangeEdit.SavedObjs.SELECTED_EDGES,"Remove Edge Handle");
+ ((DEdgeView) m_view.getEdgeView(~edge)).removeHandle(anchorInx);
+ m_button1NodeDrag = false;
+ } else {
+ final boolean wasSelected = m_view.m_selectedAnchors.count(chosenAnchor) > 0;
+
+ if (wasSelected && e.isShiftDown())
+ m_view.m_selectedAnchors.delete(chosenAnchor);
+ else if (!wasSelected) {
+ if (!e.isShiftDown())
+ m_view.m_selectedAnchors.empty();
+
+ m_view.m_selectedAnchors.insert(chosenAnchor);
+ }
+
+ m_button1NodeDrag = true;
+ }
+
+ m_view.m_contentChanged = true;
+ }
+
+ if (chosenEdge != 0) {
+ if (isAnchorKeyDown(e)
+ && ((m_lastRenderDetail & GraphRenderer.LOD_EDGE_ANCHORS) != 0)) {
+ m_view.m_selectedAnchors.empty();
+ m_ptBuff[0] = m_lastXMousePos;
+ m_ptBuff[1] = m_lastYMousePos;
+ m_view.xformComponentToNodeCoords(m_ptBuff);
+ //******* Store current handle list *********
+ m_undoable_edit = new ViewChangeEdit(m_view,ViewChangeEdit.SavedObjs.SELECTED_EDGES,"Add Edge Handle");
+ final int chosenInx = ((DEdgeView) m_view.getEdgeView(chosenEdge))
+ .addHandleFoo(new Point2D.Float((float) m_ptBuff[0],
+ (float) m_ptBuff[1]));
+ m_view.m_selectedAnchors.insert(((~chosenEdge) << 6) | chosenInx);
+ }
+
+ final boolean wasSelected = m_view.getEdgeView(chosenEdge).isSelected();
+
+ if (wasSelected && e.isShiftDown()) {
+ ((DEdgeView) m_view.getEdgeView(chosenEdge)).unselectInternal();
+ chosenEdgeSelected = (byte) -1;
+ } else if (!wasSelected) {
+ ((DEdgeView) m_view.getEdgeView(chosenEdge)).selectInternal(false);
+ chosenEdgeSelected = (byte) 1;
+
+ if ((m_lastRenderDetail & GraphRenderer.LOD_EDGE_ANCHORS) != 0) {
+ m_ptBuff[0] = m_lastXMousePos;
+ m_ptBuff[1] = m_lastYMousePos;
+ m_view.xformComponentToNodeCoords(m_ptBuff);
+
+ final IntEnumerator hits = m_view.m_spacialA.queryOverlap((float) m_ptBuff[0],
+ (float) m_ptBuff[1],
+ (float) m_ptBuff[0],
+ (float) m_ptBuff[1],
+ null, 0, false);
+
+ if (hits.numRemaining() > 0) {
+ final int hit = hits.nextInt();
+
+ if (m_view.m_selectedAnchors.count(hit) == 0)
+ m_view.m_selectedAnchors.insert(hit);
+ }
+ }
+ }
+
+ m_button1NodeDrag = true;
+ m_view.m_contentChanged = true;
+ }
+
+ if ((chosenNode == 0) && (chosenEdge == 0) && (chosenAnchor < 0)) {
+ m_selectionRect = new Rectangle(m_lastXMousePos, m_lastYMousePos, 0, 0);
+ m_button1NodeDrag = false;
+ }
+ }
+
+ final GraphViewChangeListener listener = m_view.m_lis[0];
+
+ if (listener != null) {
+ if ((unselectedNodes != null) && (unselectedNodes.length > 0))
+ listener.graphViewChanged(new GraphViewNodesUnselectedEvent(m_view,
+ unselectedNodes));
+
+ if ((unselectedEdges != null) && (unselectedEdges.length > 0))
+ listener.graphViewChanged(new GraphViewEdgesUnselectedEvent(m_view,
+ unselectedEdges));
+
+ if (chosenNode != 0) {
+ if (chosenNodeSelected > 0)
+ listener.graphViewChanged(new GraphViewNodesSelectedEvent(m_view,
+ new int[] {
+ chosenNode
+ }));
+ else if (chosenNodeSelected < 0)
+ listener.graphViewChanged(new GraphViewNodesUnselectedEvent(m_view,
+ new int[] {
+ chosenNode
+ }));
+ }
+
+ if (chosenEdge != 0) {
+ if (chosenEdgeSelected > 0)
+ listener.graphViewChanged(new GraphViewEdgesSelectedEvent(m_view,
+ new int[] {
+ chosenEdge
+ }));
+ else if (chosenEdgeSelected < 0)
+ listener.graphViewChanged(new GraphViewEdgesUnselectedEvent(m_view,
+ new int[] {
+ chosenEdge
+ }));
+ }
+ }
+
+ // Repaint after listener events are fired because listeners may change
+ // something in the graph view.
+ repaint();
+ } else if (e.getButton() == MouseEvent.BUTTON2 || (isMacPlatform() && e.isMetaDown() && e.getButton() == MouseEvent.BUTTON1)) {
+ // PAN
+ //******** Save all node positions
+ m_undoable_edit = new ViewChangeEdit(m_view,ViewChangeEdit.SavedObjs.NODES,"Move");
+ m_currMouseButton = 2;
+ m_lastXMousePos = e.getX();
+ m_lastYMousePos = e.getY();
+ } else if ((e.getButton() == MouseEvent.BUTTON3) || (isMacPlatform() && e.isControlDown() && e.getButton() == MouseEvent.BUTTON1)) {
+ //******** Save all node positions
+ m_undoable_edit = new ViewChangeEdit(m_view,ViewChangeEdit.SavedObjs.NODES,"Move");
+ m_currMouseButton = 3;
+ m_lastXMousePos = e.getX();
+ m_lastYMousePos = e.getY();
+
+ // AJK 04/27/08: for node context menus
+ processNodeContextMenuEvent(e);
+ processEdgeContextMenuEvent(e);
+ }
+
+ requestFocusInWindow();
+ }
+
+ @Override
+ public void mouseReleased(MouseEvent e) {
+ if (e.getButton() == MouseEvent.BUTTON1) {
+ if (m_currMouseButton == 1) {
+ m_currMouseButton = 0;
+
+ if (m_selectionRect != null) {
+ int[] selectedNodes = null;
+ int[] selectedEdges = null;
+
+ synchronized (m_lock) {
+ if (m_view.m_nodeSelection || m_view.m_edgeSelection) {
+ if (m_view.m_nodeSelection) {
+ m_ptBuff[0] = m_selectionRect.x;
+ m_ptBuff[1] = m_selectionRect.y;
+ m_view.xformComponentToNodeCoords(m_ptBuff);
+
+ final double xMin = m_ptBuff[0];
+ final double yMin = m_ptBuff[1];
+ m_ptBuff[0] = m_selectionRect.x + m_selectionRect.width;
+ m_ptBuff[1] = m_selectionRect.y + m_selectionRect.height;
+ m_view.xformComponentToNodeCoords(m_ptBuff);
+
+ final double xMax = m_ptBuff[0];
+ final double yMax = m_ptBuff[1];
+ m_stack.empty();
+ m_view.getNodesIntersectingRectangle((float) xMin, (float) yMin,
+ (float) xMax, (float) yMax,
+ (m_lastRenderDetail
+ & GraphRenderer.LOD_HIGH_DETAIL) == 0,
+ m_stack);
+ m_stack2.empty();
+
+ final IntEnumerator nodesXSect = m_stack.elements();
+
+ while (nodesXSect.numRemaining() > 0) {
+ final int nodeXSect = nodesXSect.nextInt();
+
+ if (m_view.m_selectedNodes.count(~nodeXSect) == 0)
+ m_stack2.push(nodeXSect);
+ }
+
+ selectedNodes = new int[m_stack2.size()];
+
+ final IntEnumerator nodes = m_stack2.elements();
+
+ for (int i = 0; i < selectedNodes.length; i++)
+ selectedNodes[i] = nodes.nextInt();
+
+ for (int i = 0; i < selectedNodes.length; i++)
+ ((DNodeView) m_view.getNodeView(selectedNodes[i]))
+ [...]
+
+ if (selectedNodes.length > 0)
+ m_view.m_contentChanged = true;
+ }
+
+ if (m_view.m_edgeSelection) {
+ if ((m_lastRenderDetail & GraphRenderer.LOD_EDGE_ANCHORS) != 0) {
+ m_ptBuff[0] = m_selectionRect.x;
+ m_ptBuff[1] = m_selectionRect.y;
+ m_view.xformComponentToNodeCoords(m_ptBuff);
+
+ final double xMin = m_ptBuff[0];
+ final double yMin = m_ptBuff[1];
+ m_ptBuff[0] = m_selectionRect.x + m_selectionRect.width;
+ m_ptBuff[1] = m_selectionRect.y + m_selectionRect.height;
+ m_view.xformComponentToNodeCoords(m_ptBuff);
+
+ final double xMax = m_ptBuff[0];
+ final double yMax = m_ptBuff[1];
+ final IntEnumerator hits = m_view.m_spacialA.queryOverlap((float) xMin,
+ (float) yMin,
+ (float) xMax,
+ (float) yMax,
+ null,
+ 0,
+ false);
+
+ if (hits.numRemaining() > 0)
+ m_view.m_contentChanged = true;
+
+ while (hits.numRemaining() > 0) {
+ final int hit = hits.nextInt();
+
+ if (m_view.m_selectedAnchors.count(hit) == 0)
+ m_view.m_selectedAnchors.insert(hit);
+ }
+ }
+
+ computeEdgesIntersecting(m_selectionRect.x, m_selectionRect.y,
+ m_selectionRect.x + m_selectionRect.width,
+ m_selectionRect.y + m_selectionRect.height,
+ m_stack2);
+ m_stack.empty();
+
+ final IntEnumerator edgesXSect = m_stack2.elements();
+
+ while (edgesXSect.numRemaining() > 0) {
+ final int edgeXSect = edgesXSect.nextInt();
+
+ if (m_view.m_selectedEdges.count(~edgeXSect) == 0)
+ m_stack.push(edgeXSect);
+ }
+
+ selectedEdges = new int[m_stack.size()];
+
+ final IntEnumerator edges = m_stack.elements();
+
+ for (int i = 0; i < selectedEdges.length; i++)
+ selectedEdges[i] = edges.nextInt();
+
+ for (int i = 0; i < selectedEdges.length; i++)
+ ((DEdgeView) m_view.getEdgeView(selectedEdges[i]))
+ [...]
+
+ if (selectedEdges.length > 0)
+ m_view.m_contentChanged = true;
+ }
+ }
+ }
+
+ m_selectionRect = null;
+
+ final GraphViewChangeListener listener = m_view.m_lis[0];
+
+ if (listener != null) {
+ if ((selectedNodes != null) && (selectedNodes.length > 0))
+ listener.graphViewChanged(new GraphViewNodesSelectedEvent(m_view,
+ selectedNodes));
+
+ if ((selectedEdges != null) && (selectedEdges.length > 0))
+ listener.graphViewChanged(new GraphViewEdgesSelectedEvent(m_view,
+ selectedEdges));
+ }
+
+ // Repaint after listener events are fired because listeners may
+ // change something in the graph view.
+ repaint();
+ }
+ }
+
+ if (m_undoable_edit != null)
+ m_undoable_edit.post();
+ } else if (e.getButton() == MouseEvent.BUTTON2) {
+ if (m_currMouseButton == 2)
+ m_currMouseButton = 0;
+
+ if (m_undoable_edit != null)
+ m_undoable_edit.post();
+ } else if (e.getButton() == MouseEvent.BUTTON3) {
+ if (m_currMouseButton == 3)
+ m_currMouseButton = 0;
+
+ if (m_undoable_edit != null)
+ m_undoable_edit.post();
+ }
+ }
+
+
+ @Override
+ public void mouseDragged(MouseEvent e) {
+ if (m_currMouseButton == 1) {
+ if (m_button1NodeDrag) {
+ // Ignore if disabled.
+ if (this.isNodeMovementDisabled())
+ return;
+
+ // SAVE SELECTED NODE & EDGE POSITIONS
+ if (m_undoable_edit == null)
+ m_undoable_edit = new ViewChangeEdit(m_view, ViewChangeEdit.SavedObjs.SELECTED, "Move");
+
+ synchronized (m_lock) {
+ m_ptBuff[0] = m_lastXMousePos;
+ m_ptBuff[1] = m_lastYMousePos;
+ m_view.xformComponentToNodeCoords(m_ptBuff);
+
+ final double oldX = m_ptBuff[0];
+ final double oldY = m_ptBuff[1];
+ m_lastXMousePos = e.getX();
+ m_lastYMousePos = e.getY();
+ m_ptBuff[0] = m_lastXMousePos;
+ m_ptBuff[1] = m_lastYMousePos;
+ m_view.xformComponentToNodeCoords(m_ptBuff);
+
+ final double newX = m_ptBuff[0];
+ final double newY = m_ptBuff[1];
+ double deltaX = newX - oldX;
+ double deltaY = newY - oldY;
+
+ // If the shift key is down, then only move horizontally,
+ // vertically, or diagonally, depending on the slope.
+ if (e.isShiftDown()) {
+ final double slope = deltaY / deltaX;
+
+ // slope of 2.41 ~ 67.5 degrees (halfway between 45 and 90)
+ // slope of 0.41 ~ 22.5 degrees (halfway between 0 and 45)
+ if ((slope > 2.41) || (slope < -2.41)) {
+ deltaX = 0.0; // just move vertical
+ } else if ((slope < 0.41) && (slope > -0.41)) {
+ deltaY = 0.0; // just move horizontal
+ } else {
+ final double avg = (Math.abs(deltaX) + Math.abs(deltaY)) / 2.0;
+ deltaX = (deltaX < 0) ? (-avg) : avg;
+ deltaY = (deltaY < 0) ? (-avg) : avg;
+ }
+ }
+
+ // TODO: Optimize to not instantiate new array on every call.
+ final int[] selectedNodes = m_view.getSelectedNodeIndices();
+
+ for (int i = 0; i < selectedNodes.length; i++) {
+ final NodeView nv = m_view.getNodeView(selectedNodes[i]);
+ final double oldXPos = nv.getXPosition();
+ final double oldYPos = nv.getYPosition();
+ nv.setOffset(oldXPos + deltaX, oldYPos + deltaY);
+ }
+
+ final IntEnumerator anchorsToMove = m_view.m_selectedAnchors.searchRange(Integer.MIN_VALUE,
+ Integer.MAX_VALUE,
+ false);
+
+ while (anchorsToMove.numRemaining() > 0) {
+ final int edgeAndAnchor = anchorsToMove.nextInt();
+ final int edge = edgeAndAnchor >>> 6;
+ final int anchorInx = edgeAndAnchor & 0x0000003f;
+ final DEdgeView ev = (DEdgeView) m_view.getEdgeView(~edge);
+ ev.getHandleInternal(anchorInx, m_floatBuff1);
+ ev.moveHandleInternal(anchorInx, m_floatBuff1[0] + deltaX,
+ m_floatBuff1[1] + deltaY);
+ }
+
+ if ((selectedNodes.length > 0) || (m_view.m_selectedAnchors.size() > 0))
+ m_view.m_contentChanged = true;
+ }
+ }
+
+ if (m_selectionRect != null) {
+ final int x = Math.min(m_lastXMousePos, e.getX());
+ final int y = Math.min(m_lastYMousePos, e.getY());
+ final int w = Math.abs(m_lastXMousePos - e.getX());
+ final int h = Math.abs(m_lastYMousePos - e.getY());
+ m_selectionRect.setBounds(x, y, w, h);
+ }
+
+ repaint();
+ } else if (m_currMouseButton == 2) {
+ // Middle-Click: Pan
+ pan(e);
+ } else if (m_currMouseButton == 3) {
+ // Right-click: Zoom
+ zoom(e);
+ }
+ }
+
+ private void pan(final MouseEvent e) {
+ double deltaX = e.getX() - m_lastXMousePos;
+ double deltaY = e.getY() - m_lastYMousePos;
+ m_lastXMousePos = e.getX();
+ m_lastYMousePos = e.getY();
+ pan(deltaX, deltaY);
+ }
+
+ private void pan(double deltaX, double deltaY) {
+ synchronized (m_lock) {
+ m_xCenter -= (deltaX / m_scaleFactor);
+ m_yCenter -= (deltaY / m_scaleFactor);
+ }
+ m_view.m_viewportChanged = true;
+ repaint();
+ }
+
+ private void zoom(final MouseEvent e) {
+ double deltaY = e.getY() - m_lastYMousePos;
+
+ synchronized (m_lock) {
+ m_lastXMousePos = e.getX();
+ m_lastYMousePos = e.getY();
+ m_scaleFactor *= Math.pow(2, -deltaY / 300.0d);
+ }
+
+ m_view.m_viewportChanged = true;
+ repaint();
+ }
+
+
+
+ @Override
+ public void mouseMoved(MouseEvent e) {
+ NodeView nv = m_view.getPickedNodeView(e.getPoint());
+ boolean toolTipSet = false;
+
+ if (nv != null) {
+ setToolTipText(((DNodeView) nv).getToolTip());
+ toolTipSet = true;
+ } else {
+ if ((m_lastRenderDetail & GraphRenderer.LOD_HIGH_DETAIL) != 0) {
+ EdgeView ev = m_view.getPickedEdgeView(e.getPoint());
+
+ if (ev != null) {
+ setToolTipText(((DEdgeView) ev).getToolTip());
+ toolTipSet = true;
+ }
+ }
+ }
+
+ if (!toolTipSet)
+ setToolTipText(null);
+ }
+
+ /**
+ * Handles key press events. Currently used with the up/down, left/right arrow
+ * keys. Pressing any of the listed keys will move the selected nodes one pixel
+ * in that direction.
+ *
+ * @param k The key event that we're listening for.
+ */
+ public void keyPressed(KeyEvent k) {
+ int code = k.getKeyCode();
+
+ if ((code == KeyEvent.VK_UP) || (code == KeyEvent.VK_DOWN) || (code == KeyEvent.VK_LEFT)
+ || (code == KeyEvent.VK_RIGHT)) {
+ double move = 1.0;
+
+ if (k.isShiftDown())
+ move = 10.0;
+
+ final int[] selectedNodes = m_view.getSelectedNodeIndices();
+
+ if(k.isControlDown()) {
+ // Pan
+ if (code == KeyEvent.VK_UP) {
+ pan(0, move);
+ } else if (code == KeyEvent.VK_DOWN) {
+ pan(0, -move);
+ } else if (code == KeyEvent.VK_LEFT) {
+ pan(-move, 0);
+ } else if (code == KeyEvent.VK_RIGHT) {
+ pan(move, 0);
+ }
+ return;
+ }
+
+ if (m_view.m_nodeSelection) {
+ // move nodes
+ for (int i = 0; i < selectedNodes.length; i++) {
+ DNodeView nv = ((DNodeView) m_view.getNodeView(selectedNodes[i]));
+ double xPos = nv.getXPosition();
+ double yPos = nv.getYPosition();
+
+ if (code == KeyEvent.VK_UP) {
+ yPos -= move;
+ } else if (code == KeyEvent.VK_DOWN) {
+ yPos += move;
+ } else if (code == KeyEvent.VK_LEFT) {
+ xPos -= move;
+ } else if (code == KeyEvent.VK_RIGHT) {
+ xPos += move;
+ }
+
+ nv.setOffset(xPos, yPos);
+ }
+
+ // move edge anchors
+ IntEnumerator anchorsToMove = m_view.m_selectedAnchors.searchRange(Integer.MIN_VALUE,
+ Integer.MAX_VALUE,
+ false);
+
+ while (anchorsToMove.numRemaining() > 0) {
+ final int edgeAndAnchor = anchorsToMove.nextInt();
+ final int edge = edgeAndAnchor >>> 6;
+ final int anchorInx = edgeAndAnchor & 0x0000003f;
+ final DEdgeView ev = (DEdgeView) m_view.getEdgeView(~edge);
+ ev.getHandleInternal(anchorInx, m_floatBuff1);
+
+ if (code == KeyEvent.VK_UP) {
+ ev.moveHandleInternal(anchorInx, m_floatBuff1[0], m_floatBuff1[1] - move);
+ } else if (code == KeyEvent.VK_DOWN) {
+ ev.moveHandleInternal(anchorInx, m_floatBuff1[0], m_floatBuff1[1] + move);
+ } else if (code == KeyEvent.VK_LEFT) {
+ ev.moveHandleInternal(anchorInx, m_floatBuff1[0] - move, m_floatBuff1[1]);
+ } else if (code == KeyEvent.VK_RIGHT) {
+ ev.moveHandleInternal(anchorInx, m_floatBuff1[0] + move, m_floatBuff1[1]);
+ }
+ }
+
+ repaint();
+ }
+ }
+ }
+
+ /**
+ * Currently not used.
+ *
+ * @param k The key event that we're listening for.
+ */
+ public void keyReleased(KeyEvent k) {
+ }
+
+ /**
+ * Currently not used.
+ *
+ * @param k The key event that we're listening for.
+ */
+ public void keyTyped(KeyEvent k) {
+ }
+
+ // AJK: 05/02/06 END
+ // Puts [last drawn] edges intersecting onto stack; as RootGraph indices.
+ // Depends on the state of several member variables, such as m_hash.
+ // Clobbers m_stack and m_ptBuff.
+ // The rectangle extents are in component coordinate space.
+ // IMPORTANT: Code that calls this method should be holding m_lock.
+ final void computeEdgesIntersecting(final int xMini, final int yMini, final int xMaxi,
+ final int yMaxi, final IntStack stack) {
+ m_ptBuff[0] = xMini;
+ m_ptBuff[1] = yMini;
+ m_view.xformComponentToNodeCoords(m_ptBuff);
+
+ final double xMin = m_ptBuff[0];
+ final double yMin = m_ptBuff[1];
+ m_ptBuff[0] = xMaxi;
+ m_ptBuff[1] = yMaxi;
+ m_view.xformComponentToNodeCoords(m_ptBuff);
+
+ final double xMax = m_ptBuff[0];
+ final double yMax = m_ptBuff[1];
+ IntEnumerator edgeNodesEnum = m_hash.elements(); // Positive.
+ m_stack.empty();
+
+ final int edgeNodesCount = edgeNodesEnum.numRemaining();
+
+ for (int i = 0; i < edgeNodesCount; i++)
+ m_stack.push(edgeNodesEnum.nextInt());
+
+ m_hash.empty();
+ edgeNodesEnum = m_stack.elements();
+ stack.empty();
+
+ final FixedGraph graph = (FixedGraph) m_view.m_drawPersp;
+
+ if ((m_lastRenderDetail & GraphRenderer.LOD_HIGH_DETAIL) == 0) {
+ // We won't need to look up arrows and their sizes.
+ for (int i = 0; i < edgeNodesCount; i++) {
+ final int node = edgeNodesEnum.nextInt(); // Positive.
+
+ if (!m_view.m_spacial.exists(node, m_view.m_extentsBuff, 0))
+ continue; /* Will happen if e.g. node was removed. */
+
+ final float nodeX = (m_view.m_extentsBuff[0] + m_view.m_extentsBuff[2]) / 2;
+ final float nodeY = (m_view.m_extentsBuff[1] + m_view.m_extentsBuff[3]) / 2;
+ final IntEnumerator touchingEdges = graph.edgesAdjacent(node, true, true, true);
+
+ while (touchingEdges.numRemaining() > 0) {
+ final int edge = touchingEdges.nextInt(); // Positive.
+ final int otherNode = // Positive.
+ node ^ graph.edgeSource(edge) ^ graph.edgeTarget(edge);
+
+ if (m_hash.get(otherNode) < 0) {
+ m_view.m_spacial.exists(otherNode, m_view.m_extentsBuff, 0);
+
+ final float otherNodeX = (m_view.m_extentsBuff[0] + m_view.m_extentsBuff[2]) / 2;
+ final float otherNodeY = (m_view.m_extentsBuff[1] + m_view.m_extentsBuff[3]) / 2;
+ m_line.setLine(nodeX, nodeY, otherNodeX, otherNodeY);
+
+ if (m_line.intersects(xMin, yMin, xMax - xMin, yMax - yMin))
+ stack.push(~edge);
+ }
+ }
+
+ m_hash.put(node);
+ }
+ } else { // Last render high detail.
+
+ for (int i = 0; i < edgeNodesCount; i++) {
+ final int node = edgeNodesEnum.nextInt(); // Positive.
+
+ if (!m_view.m_spacial.exists(node, m_view.m_extentsBuff, 0))
+ continue; /* Will happen if e.g. node was removed. */
+
+ final byte nodeShape = m_view.m_nodeDetails.shape(node);
+ final IntEnumerator touchingEdges = graph.edgesAdjacent(node, true, true, true);
+
+ while (touchingEdges.numRemaining() > 0) {
+ final int edge = touchingEdges.nextInt(); // Positive.
+ final double segThicknessDiv2 = m_view.m_edgeDetails.segmentThickness(edge) / 2.0d;
+ final int otherNode = node ^ graph.edgeSource(edge) ^ graph.edgeTarget(edge);
+
+ if (m_hash.get(otherNode) < 0) {
+ m_view.m_spacial.exists(otherNode, m_extentsBuff2, 0);
+
+ final byte otherNodeShape = m_view.m_nodeDetails.shape(otherNode);
+ final byte srcShape;
+ final byte trgShape;
+ final float[] srcExtents;
+ final float[] trgExtents;
+
+ if (node == graph.edgeSource(edge)) {
+ srcShape = nodeShape;
+ trgShape = otherNodeShape;
+ srcExtents = m_view.m_extentsBuff;
+ trgExtents = m_extentsBuff2;
+ } else { // node == graph.edgeTarget(edge).
+ srcShape = otherNodeShape;
+ trgShape = nodeShape;
+ srcExtents = m_extentsBuff2;
+ trgExtents = m_view.m_extentsBuff;
+ }
+
+ final byte srcArrow;
+ final byte trgArrow;
+ final float srcArrowSize;
+ final float trgArrowSize;
+
+ if ((m_lastRenderDetail & GraphRenderer.LOD_EDGE_ARROWS) == 0) {
+ srcArrow = trgArrow = GraphGraphics.ARROW_NONE;
+ srcArrowSize = trgArrowSize = 0.0f;
+ } else {
+ srcArrow = m_view.m_edgeDetails.sourceArrow(edge);
+ trgArrow = m_view.m_edgeDetails.targetArrow(edge);
+ srcArrowSize = ((srcArrow == GraphGraphics.ARROW_NONE)
+ ? 0.0f
+ : m_view.m_edgeDetails.sourceArrowSize(edge));
+ trgArrowSize = ((trgArrow == GraphGraphics.ARROW_NONE)
+ ? 0.0f
+ : m_view.m_edgeDetails.targetArrowSize(edge));
+ }
+
+ final EdgeAnchors anchors = (((m_lastRenderDetail
+ & GraphRenderer.LOD_EDGE_ANCHORS) == 0)
+ ? null : m_view.m_edgeDetails.anchors(edge));
+
+ if (!GraphRenderer.computeEdgeEndpoints(m_grafx, srcExtents, srcShape,
+ srcArrow, srcArrowSize, anchors,
+ trgExtents, trgShape, trgArrow,
+ trgArrowSize, m_floatBuff1,
+ m_floatBuff2))
+ continue;
+
+ m_grafx.getEdgePath(srcArrow, srcArrowSize, trgArrow, trgArrowSize,
+ m_floatBuff1[0], m_floatBuff1[1], anchors,
+ m_floatBuff2[0], m_floatBuff2[1], m_path);
+ GraphRenderer.computeClosedPath(m_path.getPathIterator(null), m_path2);
+
+ if (m_path2.intersects(xMin - segThicknessDiv2, yMin - segThicknessDiv2,
+ (xMax - xMin) + (segThicknessDiv2 * 2),
+ (yMax - yMin) + (segThicknessDiv2 * 2)))
+ stack.push(~edge);
+ }
+ }
+
+ m_hash.put(node);
+ }
+ }
+ }
+
+
+ /**
+ * default dragEnter handler. Accepts the drag.
+ * @param dte the DropTargetDragEvent
+ *
+ */
+ public void dragEnter(java.awt.dnd.DropTargetDragEvent dte) {
+ dte.acceptDrag(DnDConstants.ACTION_COPY);
+ }
+
+ /**
+ * default dragExit handler. Does nothing, can be overridden.
+ * @param dte the DropTargetDragEvent
+ *
+ */
+ public void dragExit(java.awt.dnd.DropTargetEvent dte) {
+ }
+
+ /**
+ * default dropActionChanged handler. Does nothing, can be overridden.
+ * @param dte the DropTargetDragEvent
+ *
+ */
+ public void dropActionChanged(java.awt.dnd.DropTargetDragEvent dte) {
+ }
+
+ /**
+ * default dragOver handler. Does nothing, can be overridden.
+ * @param dte the DropTargetDragEvent
+ *
+ */
+ public void dragOver(java.awt.dnd.DropTargetDragEvent dte) {
+ }
+
+ /**
+ * default drop handler. Accepts drop, builds a transferable, creates and
+ * fires a PhoebeCanvasDropEvent, then calls dropComplete().
+ * @param dte the DropTargetDragEvent
+ *
+ */
+ public void drop(java.awt.dnd.DropTargetDropEvent dte) {
+ dte.acceptDrop(DnDConstants.ACTION_COPY);
+
+ Transferable t = dte.getTransferable();
+
+ Point pt = dte.getLocation();
+
+ PhoebeCanvasDropEvent event = new PhoebeCanvasDropEvent(this, // we are the event source
+ t, // item dropped
+ pt // location
+ );
+ processPhoebeCanvasDropEvent(event);
+
+ dte.dropComplete(true);
+ }
+
+ /**
+ * adds a listener to the store of PhoebeCanvasDropTargetListeners
+ * @param l the PhoebeCanvasDropTargetListener
+ *
+ */
+ public void addPhoebeCanvasDropListener(PhoebeCanvasDropListener l) {
+ listeners.addElement(l);
+ }
+
+ /**
+ * removes a listener from the store of PhoebeCanvasDropTargetListeners
+ * @param l the PhoebeCanvasDropTargetListener
+ *
+ */
+ public void removePhoebeCanvasDropListener(PhoebeCanvasDropListener l) {
+ listeners.removeElement(l);
+ }
+
+ /**
+ * handles a PhoebeCanvasDropEvent. For each listerner, calls its itemDropped() method
+ * @param event the PhoebeCanvasDropEvent
+ *
+ */
+ protected synchronized void processPhoebeCanvasDropEvent(PhoebeCanvasDropEvent event) {
+ Enumeration e = listeners.elements();
+
+ // // AJK: 12/08/06 oy, what a hack. try to send transferable to transferhandler
+ // // of cytoscapeDesktopPane
+ // Transferable t = event.getTransferable();
+ // TransferHandler th = Cytoscape.getDesktop().getNetworkViewManager().
+ // getDesktopPane().getTransferHandler();
+ // if (th != null)
+ // {
+ // th.importData(Cytoscape.getDesktop().getNetworkViewManager().
+ // getDesktopPane(), t);
+ // }
+ // // AJK: 12/08/06 END
+
+ // // AJK: 01/14/07 oy, what a hack. try to send transferable to transferhandler
+ Transferable t = event.getTransferable();
+ TransferHandler th;
+ JComponent jComp;
+ Iterator it = transferComponents.iterator();
+
+ while (it.hasNext()) {
+ jComp = (JComponent) it.next();
+ th = jComp.getTransferHandler();
+
+ if (th != null) {
+ // th.importData(jComp, t);
+ }
+ }
+
+ // AJK: 01/14/07 END
+ while (e.hasMoreElements()) {
+ PhoebeCanvasDropListener l = (PhoebeCanvasDropListener) e.nextElement();
+ l.itemDropped(event);
+ }
+ }
+
+ // AJK: 04/02/06 END
+ /**
+ * DOCUMENT ME!
+ *
+ * @param comp DOCUMENT ME!
+ */
+ public void addTransferComponent(JComponent comp) {
+ if (!transferComponents.contains(comp)) {
+ transferComponents.addElement(comp);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param comp DOCUMENT ME!
+ */
+ public void removeTransferComponent(JComponent comp) {
+ transferComponents.removeElement(comp);
+ }
+
+ // AJK: 01/12/07 END
+
+ public void mouseWheelMoved(MouseWheelEvent e) {
+ int notches = e.getWheelRotation();
+ double factor = 1.0;
+
+ // scroll up, zoom in
+ if (notches < 0) {
+ factor = 1.1;
+
+ // scroll down, zoom out
+ } else {
+ factor = 0.9;
+ }
+
+ synchronized (m_lock) {
+ m_scaleFactor = m_scaleFactor * factor;
+ }
+
+ m_view.m_viewportChanged = true;
+ repaint();
+ }
+
+
+ // AJK: 04/27/06 BEGIN
+ // for node context menus
+
+ /**
+ * adds a listener to the store of NodeContextMenuListeners
+ * @param l the NodeContextMenuListener
+ *
+ */
+ public void addNodeContextMenuListener(NodeContextMenuListener l) {
+ nodeContextMenuListeners.addElement(l);
+ }
+
+ /**
+ * removes a listener from the store of NodeContextMenuListeners
+ * @param l the NodeContextMenuListener
+ *
+ */
+ public void removeNodeContextMenuListener(NodeContextMenuListener l) {
+ nodeContextMenuListeners.removeElement(l);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param l DOCUMENT ME!
+ */
+ public void addEdgeContextMenuListener(EdgeContextMenuListener l) {
+ edgeContextMenuListeners.addElement(l);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param l DOCUMENT ME!
+ */
+ public void removeEdgeContextMenuListener(EdgeContextMenuListener l) {
+ edgeContextMenuListeners.removeElement(l);
+ }
+
+ /**
+ * handles a NodeContextMenuEvent. For each listerner, calls its itemDropped() method
+ * @param event the NodeContextMenuEvent
+ *
+ */
+ protected synchronized void processNodeContextMenuEvent(MouseEvent event) {
+ NodeView nv = m_view.getPickedNodeView(event.getPoint());
+
+ // System.out.println (" over selected nodeview: " + nv);
+ if (nv != null) {
+ String nodeLabel = nv.getNode().getIdentifier();
+ JPopupMenu menu = new JPopupMenu(nodeLabel);
+ menu.setLabel(nodeLabel);
+
+ Enumeration e = nodeContextMenuListeners.elements();
+
+ while (e.hasMoreElements()) {
+ NodeContextMenuListener l = (NodeContextMenuListener) e.nextElement();
+ // System.out.println("Adding context menu items for NodeContextMenuListener: " + l);
+
+ // EventListener l = (EventListener) e.nextElement();
+ l.addNodeContextMenuItems(nv, menu);
+ }
+
+ // Display PopupMenu
+ menu.show(this, event.getX(), event.getY());
+ }
+ }
+
+ protected synchronized void processEdgeContextMenuEvent(MouseEvent event) {
+ EdgeView ev = m_view.getPickedEdgeView(event.getPoint());
+
+ if (ev != null) {
+ String edgeLabel = ev.getEdge().getIdentifier();
+ JPopupMenu menu = new JPopupMenu(edgeLabel);
+ menu.setLabel(edgeLabel);
+
+ Enumeration e = edgeContextMenuListeners.elements();
+
+ while (e.hasMoreElements()) {
+ EdgeContextMenuListener l = (EdgeContextMenuListener) e.nextElement();
+ // System.out.println("Adding context menu items for EdgeContextMenuListener: " + l);
+ l.addEdgeContextMenuItems(ev, menu);
+ }
+
+ // Display PopupMenu
+ menu.show(this, event.getX(), event.getY());
+ }
+ }
+
+ // AJK: 04/27/06 END
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getLastRenderDetail() {
+ return m_lastRenderDetail;
+ }
+
+ // AJK: 01/14/2007 BEGIN
+ /**
+ * DOCUMENT ME!
+ *
+ * @param s DOCUMENT ME!
+ */
+ public void setSelecting(boolean s) {
+ selecting = s;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isSelecting() {
+ return selecting;
+ }
+
+ /**
+ * Called to get the tranform matrix used by the inner canvas
+ * to move the nodes.
+ *
+ * @return AffineTransform
+ */
+ public AffineTransform getAffineTransform() {
+ return (m_grafx != null) ? m_grafx.getTransform() : null;
+ }
+
+ /**
+ * Routine which determines if anchor qualifier key has been pressed:
+ *
+ * on Mac -> meta key
+ * on PC -> control key
+ *
+ * @param e MouseEvent
+ * @return boolean
+ */
+ private boolean isAnchorKeyDown(MouseEvent e) {
+ return ((!isMacPlatform() && e.isControlDown()) || (isMacPlatform() && e.isMetaDown()));
+ }
+
+ /**
+ * Routine which determines if we are running on mac platform
+ *
+ * @return boolean
+ */
+ private boolean isMacPlatform() {
+ String os = System.getProperty("os.name");
+
+ return os.regionMatches(true, 0, MAC_OS_ID, 0, MAC_OS_ID.length());
+ }
+
+ public void enableNodeMovement(){
+ this.NodeMovement = true;
+ }
+
+ public void disableNodeMovement(){
+ this.NodeMovement = false;
+ }
+
+ public boolean isNodeMovementDisabled(){
+ return !(this.NodeMovement);
+ }
+
+ /**
+ * @param setLastRenderDetail if true, "m_lastRenderDetail" will be updated, otherwise it will not be updated.
+ */
+ private void renderGraph(GraphGraphics graphics, final boolean setLastRenderDetail, final GraphLOD lod) {
+ // Set color alpha based on opacity setting
+ final int alpha = (m_isOpaque) ? 255 : 0;
+
+ final Color backgroundColor = new Color(m_backgroundColor.getRed(), m_backgroundColor.getGreen(),
+ m_backgroundColor.getBlue(), alpha);
+
+ synchronized (m_lock) {
+ final int lastRenderDetail = GraphRenderer.renderGraph((FixedGraph) m_view.m_drawPersp,
+ m_view.m_spacial, lod,
+ m_view.m_nodeDetails,
+ m_view.m_edgeDetails, m_hash,
+ graphics, backgroundColor, m_xCenter,
+ m_yCenter, m_scaleFactor);
+ if (setLastRenderDetail)
+ m_lastRenderDetail = lastRenderDetail;
+ }
+ }
+}
diff --git a/corelibs/ding/src/main/java/ding/view/InnerCanvasEvent.java b/corelibs/ding/src/main/java/ding/view/InnerCanvasEvent.java
new file mode 100644
index 0000000..000be36
--- /dev/null
+++ b/corelibs/ding/src/main/java/ding/view/InnerCanvasEvent.java
@@ -0,0 +1,51 @@
+/*
+ File: InnerCanvasEvent.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// package
+package ding.view;
+
+/**
+ *
+ */
+public class InnerCanvasEvent extends java.util.EventObject {
+ /**
+ * Constructor.
+ */
+ InnerCanvasEvent(Object source) {
+ super(source);
+ }
+}
diff --git a/corelibs/ding/src/main/java/ding/view/InnerCanvasListener.java b/corelibs/ding/src/main/java/ding/view/InnerCanvasListener.java
new file mode 100644
index 0000000..77f5ce0
--- /dev/null
+++ b/corelibs/ding/src/main/java/ding/view/InnerCanvasListener.java
@@ -0,0 +1,50 @@
+/*
+ File: InnerCanvasListener.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+// package
+package ding.view;
+
+/**
+ *
+ */
+public interface InnerCanvasListener extends java.util.EventListener {
+ /**
+ * This method is called by the InnerCanvas
+ * after it has finished rendering the network.
+ */
+ void innerCanvasUpdate(InnerCanvasEvent event);
+}
diff --git a/corelibs/ding/src/main/java/ding/view/IntermediateEdgeDetails.java b/corelibs/ding/src/main/java/ding/view/IntermediateEdgeDetails.java
new file mode 100644
index 0000000..59bad66
--- /dev/null
+++ b/corelibs/ding/src/main/java/ding/view/IntermediateEdgeDetails.java
@@ -0,0 +1,172 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package ding.view;
+
+import cytoscape.render.stateful.EdgeDetails;
+
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.Paint;
+import java.awt.Stroke;
+
+
+class IntermediateEdgeDetails extends EdgeDetails {
+ // Note: It is extremely important that the methds sourceArrow(int) and
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edge DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Color colorLowDetail(int edge) {
+ return DEdgeView.DEFAULT_EDGE_PAINT;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edge DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public float sourceArrowSize(int edge) {
+ return DEdgeView.DEFAULT_ARROW_SIZE;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edge DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Paint sourceArrowPaint(int edge) {
+ return DEdgeView.DEFAULT_ARROW_PAINT;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edge DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public float targetArrowSize(int edge) {
+ return DEdgeView.DEFAULT_ARROW_SIZE;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edge DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Paint targetArrowPaint(int edge) {
+ return DEdgeView.DEFAULT_ARROW_PAINT;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edge DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public float segmentThickness(int edge) {
+ return DEdgeView.DEFAULT_EDGE_THICKNESS;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edge DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Stroke segmentStroke(int edge) {
+ return DEdgeView.DEFAULT_EDGE_STROKE;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edge DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Paint segmentPaint(int edge) {
+ return DEdgeView.DEFAULT_EDGE_PAINT;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edge DOCUMENT ME!
+ * @param labelInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String labelText(int edge, int labelInx) {
+ return DEdgeView.DEFAULT_LABEL_TEXT;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edge DOCUMENT ME!
+ * @param labelInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Font labelFont(int edge, int labelInx) {
+ return DEdgeView.DEFAULT_LABEL_FONT;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edge DOCUMENT ME!
+ * @param labelInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Paint labelPaint(int edge, int labelInx) {
+ return DEdgeView.DEFAULT_LABEL_PAINT;
+ }
+}
diff --git a/corelibs/ding/src/main/java/ding/view/IntermediateNodeDetails.java b/corelibs/ding/src/main/java/ding/view/IntermediateNodeDetails.java
new file mode 100644
index 0000000..c410ce0
--- /dev/null
+++ b/corelibs/ding/src/main/java/ding/view/IntermediateNodeDetails.java
@@ -0,0 +1,103 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package ding.view;
+
+import cytoscape.render.stateful.NodeDetails;
+
+import java.awt.Font;
+import java.awt.Paint;
+
+
+class IntermediateNodeDetails extends NodeDetails {
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public byte shape(int node) {
+ return DNodeView.DEFAULT_SHAPE;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Paint borderPaint(int node) {
+ return DNodeView.DEFAULT_BORDER_PAINT;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ * @param labelInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String labelText(int node, int labelInx) {
+ return DNodeView.DEFAULT_LABEL_TEXT;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ * @param labelInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Font labelFont(int node, int labelInx) {
+ return DNodeView.DEFAULT_LABEL_FONT;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ * @param labelInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Paint labelPaint(int node, int labelInx) {
+ return DNodeView.DEFAULT_LABEL_PAINT;
+ }
+}
diff --git a/corelibs/ding/src/main/java/ding/view/NodeContextMenuListener.java b/corelibs/ding/src/main/java/ding/view/NodeContextMenuListener.java
new file mode 100644
index 0000000..81f3945
--- /dev/null
+++ b/corelibs/ding/src/main/java/ding/view/NodeContextMenuListener.java
@@ -0,0 +1,33 @@
+/*
+ * Created on Jun 13, 2005
+ *
+ * an interface for responding to PhoebeCanvasDropEvents.
+ */
+package ding.view;
+
+import giny.view.NodeView;
+
+import java.awt.*;
+import java.awt.Point;
+import java.awt.datatransfer.Transferable;
+import java.awt.event.*;
+
+import java.util.*;
+
+import javax.swing.JPopupMenu;
+
+
+/**
+ * @author Allan Kuchinsky
+ *
+ */
+
+/**
+ * an interface for responding to PhoebeCanvasDropEvents.
+ */
+public interface NodeContextMenuListener extends EventListener {
+ /**
+ * method for responding to a drop
+ */
+ void addNodeContextMenuItems(NodeView nodeView, JPopupMenu menu);
+}
diff --git a/corelibs/ding/src/main/java/ding/view/ObjectPositionImpl.java b/corelibs/ding/src/main/java/ding/view/ObjectPositionImpl.java
new file mode 100644
index 0000000..21bc404
--- /dev/null
+++ b/corelibs/ding/src/main/java/ding/view/ObjectPositionImpl.java
@@ -0,0 +1,231 @@
+package ding.view;
+
+import static giny.view.Position.CENTER;
+import static giny.view.Justification.JUSTIFY_CENTER;
+
+import giny.view.Justification;
+import giny.view.ObjectPosition;
+import giny.view.Position;
+
+import java.text.DecimalFormat;
+import java.text.DecimalFormatSymbols;
+import java.util.Locale;
+
+/**
+*
+*/
+public class ObjectPositionImpl implements ObjectPosition {
+
+ public static ObjectPosition DEFAULT_POSITION = new ObjectPositionImpl();
+
+ private Position objectAnchor;
+ private Position targetAnchor;
+ private Justification justify;
+
+ private double xOffset;
+ private double yOffset;
+
+ /**
+ * Creates a new ObjectPosition object.
+ */
+ public ObjectPositionImpl() {
+ this(CENTER, CENTER, JUSTIFY_CENTER, 0.0, 0.0);
+ }
+
+ /**
+ * Copy constructor
+ *
+ * @param lp
+ * DOCUMENT ME!
+ */
+ public ObjectPositionImpl(final ObjectPosition p) {
+ targetAnchor = p.getTargetAnchor();
+ objectAnchor = p.getAnchor();
+ xOffset = p.getOffsetX();
+ yOffset = p.getOffsetY();
+ justify = p.getJustify();
+ }
+
+ /**
+ * Creates a new ObjectPosition object.
+ *
+ * @param targ
+ * DOCUMENT ME!
+ * @param lab
+ * DOCUMENT ME!
+ * @param just
+ * DOCUMENT ME!
+ * @param x
+ * DOCUMENT ME!
+ * @param y
+ * DOCUMENT ME!
+ */
+ public ObjectPositionImpl(final Position targ, final Position lab,
+ final Justification just, final double x, final double y) {
+ targetAnchor = targ;
+ objectAnchor = lab;
+ justify = just;
+ xOffset = x;
+ yOffset = y;
+ }
+
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see cytoscape.visual.ObjectPosition#getLabelAnchor()
+ */
+ public Position getAnchor() {
+ return objectAnchor;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see cytoscape.visual.ObjectPosition#getTargetAnchor()
+ */
+ public Position getTargetAnchor() {
+ return targetAnchor;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see cytoscape.visual.ObjectPosition#getJustify()
+ */
+ public Justification getJustify() {
+ return justify;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see cytoscape.visual.ObjectPosition#getOffsetX()
+ */
+ public double getOffsetX() {
+ return xOffset;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see cytoscape.visual.ObjectPosition#getOffsetY()
+ */
+ public double getOffsetY() {
+ return yOffset;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see cytoscape.visual.ObjectPosition#setLabelAnchor(int)
+ */
+ public void setAnchor(Position p) {
+ objectAnchor = p;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see cytoscape.visual.ObjectPosition#setTargetAnchor(int)
+ */
+ public void setTargetAnchor(Position p) {
+ targetAnchor = p;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see cytoscape.visual.ObjectPosition#setJustify(int)
+ */
+ public void setJustify(Justification j) {
+ justify = j;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see cytoscape.visual.ObjectPosition#setOffsetX(double)
+ */
+ public void setOffsetX(double d) {
+ xOffset = d;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see cytoscape.visual.ObjectPosition#setOffsetY(double)
+ */
+ public void setOffsetY(double d) {
+ yOffset = d;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see cytoscape.visual.ObjectPosition#equals(java.lang.Object)
+ */
+ public boolean equals(Object lp) {
+ // Accepts non-null ObjectPosition only.
+ if (lp == null || lp instanceof ObjectPosition == false)
+ return false;
+
+ final ObjectPosition p = (ObjectPosition) lp;
+
+ if (Math.abs(p.getOffsetX() - xOffset) > 0.0000001)
+ return false;
+
+ if (Math.abs(p.getOffsetY() - yOffset) > 0.0000001)
+ return false;
+
+ if (p.getAnchor() != objectAnchor)
+ return false;
+
+ if (p.getTargetAnchor() != targetAnchor)
+ return false;
+
+ if (p.getJustify() != justify)
+ return false;
+
+ return true;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see cytoscape.visual.ObjectPosition#toString()
+ */
+ public String toString() {
+ final StringBuilder sb = new StringBuilder();
+ sb.append("target: ").append(targetAnchor.getName());
+ sb.append(" label: ").append(objectAnchor.getName());
+ sb.append(" justify: ").append(justify.getName());
+ sb.append(" X offset: ").append(Double.toString(xOffset));
+ sb.append(" Y offset: ").append(Double.toString(yOffset));
+
+ return sb.toString();
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see cytoscape.visual.ObjectPosition#shortString()
+ */
+ public String shortString() {
+ // force the locale to US so that we consistently serialize
+ DecimalFormat df = new DecimalFormat("#0.00;-#0.00", new DecimalFormatSymbols(Locale.US));
+
+ final StringBuilder sb = new StringBuilder();
+ sb.append(targetAnchor.getShortName());
+ sb.append(",");
+ sb.append(objectAnchor.getShortName());
+ sb.append(",");
+ sb.append(justify.getShortName());
+ sb.append(",");
+ sb.append(df.format(xOffset));
+ sb.append(",");
+ sb.append(df.format(yOffset));
+
+ return sb.toString();
+ }
+}
diff --git a/corelibs/ding/src/main/java/ding/view/PrintLOD.java b/corelibs/ding/src/main/java/ding/view/PrintLOD.java
new file mode 100644
index 0000000..55643a3
--- /dev/null
+++ b/corelibs/ding/src/main/java/ding/view/PrintLOD.java
@@ -0,0 +1,177 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package ding.view;
+
+import cytoscape.render.stateful.GraphLOD;
+
+
+/**
+ *
+ */
+public class PrintLOD extends GraphLOD {
+ /**
+ * DOCUMENT ME!
+ *
+ * @param visibleNodeCount DOCUMENT ME!
+ * @param totalNodeCount DOCUMENT ME!
+ * @param totalEdgeCount DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public byte renderEdges(int visibleNodeCount, int totalNodeCount, int totalEdgeCount) {
+ return 0;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param renderNodeCount DOCUMENT ME!
+ * @param renderEdgeCount DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean detail(int renderNodeCount, int renderEdgeCount) {
+ return true;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param renderNodeCount DOCUMENT ME!
+ * @param renderEdgeCount DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean nodeBorders(int renderNodeCount, int renderEdgeCount) {
+ return true;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param renderNodeCount DOCUMENT ME!
+ * @param renderEdgeCount DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean nodeLabels(int renderNodeCount, int renderEdgeCount) {
+ return true;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param renderNodeCount DOCUMENT ME!
+ * @param renderEdgeCount DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean customGraphics(int renderNodeCount, int renderEdgeCount) {
+ return true;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param renderNodeCount DOCUMENT ME!
+ * @param renderEdgeCount DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean edgeArrows(int renderNodeCount, int renderEdgeCount) {
+ return true;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param renderNodeCount DOCUMENT ME!
+ * @param renderEdgeCount DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean dashedEdges(int renderNodeCount, int renderEdgeCount) {
+ return true;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param renderNodeCount DOCUMENT ME!
+ * @param renderEdgeCount DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean edgeAnchors(int renderNodeCount, int renderEdgeCount) {
+ return true;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param renderNodeCount DOCUMENT ME!
+ * @param renderEdgeCount DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean edgeLabels(int renderNodeCount, int renderEdgeCount) {
+ return true;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param renderNodeCount DOCUMENT ME!
+ * @param renderEdgeCount DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean textAsShape(int renderNodeCount, int renderEdgeCount) {
+ return exportTextAsShape;
+ }
+
+ private boolean exportTextAsShape = true;
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param pExportTextAsShape DOCUMENT ME!
+ */
+ public void setPrintingTextAsShape(boolean pExportTextAsShape) {
+ exportTextAsShape = pExportTextAsShape;
+ }
+}
diff --git a/corelibs/ding/src/main/java/ding/view/ViewChangeEdit.java b/corelibs/ding/src/main/java/ding/view/ViewChangeEdit.java
new file mode 100644
index 0000000..e89a760
--- /dev/null
+++ b/corelibs/ding/src/main/java/ding/view/ViewChangeEdit.java
@@ -0,0 +1,137 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package ding.view;
+
+import giny.model.Node;
+import giny.model.Edge;
+import giny.view.NodeView;
+import giny.view.EdgeView;
+
+import java.awt.geom.Point2D;
+import java.awt.geom.Point2D.Double;
+
+import java.util.*;
+
+import javax.swing.event.UndoableEditEvent;
+import javax.swing.event.UndoableEditListener;
+import javax.swing.undo.AbstractUndoableEdit;
+import javax.swing.undo.UndoableEdit;
+import javax.swing.undo.UndoableEditSupport;
+
+import undo.Undo;
+
+
+/**
+ * A Ding specific undoable edit.
+ */
+public class ViewChangeEdit extends AbstractUndoableEdit {
+
+ private ViewState origState;
+ private ViewState newState;
+
+ private DGraphView m_view;
+
+ private String m_label;
+
+ private SavedObjs m_savedObjs;
+
+ public static enum SavedObjs { ALL, SELECTED, NODES, EDGES, SELECTED_NODES, SELECTED_EDGES }
+
+ public ViewChangeEdit(DGraphView view,String label) {
+ this(view, SavedObjs.ALL, label);
+ }
+
+ public ViewChangeEdit(DGraphView view, SavedObjs saveObjs, String label) {
+ super();
+ m_view = view;
+ m_label = label;
+ m_savedObjs = saveObjs;
+
+ saveOldPositions();
+ }
+
+ protected void saveOldPositions() {
+ origState = new ViewState(m_view, m_savedObjs);
+ }
+
+ protected void saveNewPositions() {
+ newState = new ViewState(m_view, m_savedObjs);
+ }
+
+ public void post() {
+ saveNewPositions();
+ if ( !origState.equals(newState) )
+ Undo.getUndoableEditSupport().postEdit( this );
+ }
+
+ /**
+ * @return Not sure where this is used.
+ */
+ public String getPresentationName() {
+ return m_label;
+ }
+
+ /**
+ * @return Used in the edit menu.
+ */
+ public String getRedoPresentationName() {
+ return "Redo: " + m_label;
+ }
+
+ /**
+ * @return Used in the edit menu.
+ */
+ public String getUndoPresentationName() {
+ return "Undo: " + m_label;
+ }
+
+ /**
+ * Applies the new state to the view after it has been undone.
+ */
+ public void redo() {
+ super.redo();
+ newState.apply();
+ }
+
+ /**
+ * Applies the original state to the view.
+ */
+ public void undo() {
+ super.undo();
+ origState.apply();
+ }
+}
diff --git a/corelibs/ding/src/main/java/ding/view/ViewState.java b/corelibs/ding/src/main/java/ding/view/ViewState.java
new file mode 100644
index 0000000..1599bbf
--- /dev/null
+++ b/corelibs/ding/src/main/java/ding/view/ViewState.java
@@ -0,0 +1,213 @@
+
+/*
+ Copyright (c) 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package ding.view;
+
+import giny.model.Node;
+import giny.model.Edge;
+import giny.view.NodeView;
+import giny.view.EdgeView;
+
+import java.awt.geom.Point2D;
+import java.awt.geom.Point2D.Double;
+
+import java.util.*;
+
+
+/**
+ * Records the state of a view. Used for undo by ViewChangeEdit. If it would help
+ * to make this public, then please do so.
+ */
+class ViewState {
+
+ protected double scaleFactor;
+ protected Point2D center;
+ protected Map<Node, Point2D.Double> points;
+ protected Map<Edge, List> anchors;
+ protected Map<Edge, Integer> linetype;
+ protected DGraphView view;
+ protected ViewChangeEdit.SavedObjs savedObjs;
+
+ /**
+ * @param v The view whose state we're recording.
+ */
+ public ViewState(DGraphView v, ViewChangeEdit.SavedObjs whatToSave) {
+ view = v;
+ points = null;
+ anchors = null;
+ linetype = null;
+ savedObjs = whatToSave;
+
+ // record the state of the view
+ center = view.getCenter();
+ scaleFactor = view.getZoom();
+
+ // Use nodes as keys because they are less volatile than
+ // node views, which can disappear between when this edit
+ // is created and when it is used.
+ if (whatToSave == ViewChangeEdit.SavedObjs.ALL || whatToSave == ViewChangeEdit.SavedObjs.NODES) {
+ points = new HashMap<Node, Point2D.Double>();
+ for (Node n: (List<Node>)view.getGraphPerspective().nodesList()) {
+ NodeView nv = view.getNodeView(n);
+ points.put(n, new Point2D.Double(nv.getXPosition(), nv.getYPosition()));
+ }
+ }
+
+ if (whatToSave == ViewChangeEdit.SavedObjs.ALL || whatToSave == ViewChangeEdit.SavedObjs.EDGES) {
+ anchors = new HashMap<Edge, List>();
+ linetype = new HashMap<Edge, Integer>();
+ for (Edge e: (List<Edge>)view.getGraphPerspective().edgesList()) {
+ EdgeView ev = view.getEdgeView(e);
+ anchors.put(e, ev.getBend().getHandles());
+ linetype.put(e, ev.getLineType());
+ }
+ }
+
+ if (whatToSave == ViewChangeEdit.SavedObjs.SELECTED ||
+ whatToSave == ViewChangeEdit.SavedObjs.SELECTED_NODES ) {
+ points = new HashMap<Node, Point2D.Double>();
+
+ Iterator<NodeView> nodeIter = view.getSelectedNodes().iterator();
+ while (nodeIter.hasNext()) {
+ NodeView nv = nodeIter.next();
+ Node n = nv.getNode();
+ points.put(n, new Point2D.Double(nv.getXPosition(), nv.getYPosition()));
+ }
+ }
+
+ if (whatToSave == ViewChangeEdit.SavedObjs.SELECTED ||
+ whatToSave == ViewChangeEdit.SavedObjs.SELECTED_EDGES ) {
+ anchors = new HashMap<Edge, List>();
+ linetype = new HashMap<Edge, Integer>();
+
+ Iterator<EdgeView> edgeIter = view.getSelectedEdges().iterator();
+ while (edgeIter.hasNext()) {
+ EdgeView ev = edgeIter.next();
+ Edge e = ev.getEdge();
+ anchors.put(e, ev.getBend().getHandles());
+ linetype.put(e, ev.getLineType());
+ }
+ }
+ }
+
+ /**
+ * Checks if the ViewState is the same. If scale and center are
+ * equal it then begins comparing node positions.
+ * @param o The object to test for equality.
+ */
+ public boolean equals(Object o) {
+ if ( !(o instanceof ViewState) ) {
+ return false;
+ }
+
+ ViewState vs = (ViewState)o;
+
+ if ( view != vs.view ) {
+ return false;
+ }
+
+ if ( !center.equals(vs.center) ) {
+ return false;
+ }
+
+ if ( java.lang.Double.compare(scaleFactor, vs.scaleFactor) != 0 ) {
+ return false;
+ }
+
+ if ( savedObjs != vs.savedObjs) {
+ return false;
+ }
+
+ // Use nodes as keys because they are less volatile than views...
+ if (points != null) {
+ if (vs.points == null || points.size() != vs.points.size()) {
+ return false;
+ }
+ for (Node n: points.keySet()) {
+ if ( !points.get(n).equals( vs.points.get(n) ) ) {
+ return false;
+ }
+ }
+ }
+
+ if (anchors != null) {
+ if (vs.anchors == null || anchors.size() != vs.anchors.size()) {
+ return false;
+ }
+ for (Edge e: anchors.keySet()) {
+ if ( !anchors.get(e).equals(vs.anchors.get(e))) {
+ return false;
+ }
+
+ if (!linetype.get(e).equals(vs.linetype.get(e))) {
+ return false;
+ }
+ }
+ }
+
+ return true;
+ }
+
+
+ /**
+ * Applies the recorded state to the view used to create
+ * this object.
+ */
+ public void apply() {
+
+ if (points != null) {
+ // Use nodes as keys because they are less volatile than views...
+ for (Node n: points.keySet()) {
+ NodeView nv = view.getNodeView(n);
+ Point2D.Double p = points.get(n);
+ nv.setXPosition(p.getX());
+ nv.setYPosition(p.getY());
+ }
+ }
+
+ view.setZoom(scaleFactor);
+ view.setCenter(center.getX(), center.getY());
+ view.updateView();
+
+ if (anchors != null) {
+ for (Edge e: anchors.keySet()) {
+ EdgeView ev = view.getEdgeView(e);
+ ev.getBend().setHandles( anchors.get(e) );
+ ev.setLineType( linetype.get(e).intValue() );
+ }
+ }
+ }
+}
diff --git a/corelibs/ding/src/main/java/ding/view/ViewportChangeListener.java b/corelibs/ding/src/main/java/ding/view/ViewportChangeListener.java
new file mode 100644
index 0000000..8eddf55
--- /dev/null
+++ b/corelibs/ding/src/main/java/ding/view/ViewportChangeListener.java
@@ -0,0 +1,52 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package ding.view;
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$-
+ */
+public interface ViewportChangeListener {
+ /**
+ * This gets fired upon graph redraw when zoom is changed or the graph
+ * center is changed or the view component is resized.
+ */
+ public void viewportChanged(int viewportWidth, int viewportHeight, double newXCenter,
+ double newYCenter, double newScaleFactor);
+}
diff --git a/corelibs/ding/src/main/java/ding/view/ViewportChangeListenerChain.java b/corelibs/ding/src/main/java/ding/view/ViewportChangeListenerChain.java
new file mode 100644
index 0000000..a11fefa
--- /dev/null
+++ b/corelibs/ding/src/main/java/ding/view/ViewportChangeListenerChain.java
@@ -0,0 +1,98 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package ding.view;
+
+class ViewportChangeListenerChain implements ViewportChangeListener {
+ private final ViewportChangeListener a;
+ private final ViewportChangeListener b;
+
+ private ViewportChangeListenerChain(ViewportChangeListener a, ViewportChangeListener b) {
+ this.a = a;
+ this.b = b;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param w DOCUMENT ME!
+ * @param h DOCUMENT ME!
+ * @param newXCenter DOCUMENT ME!
+ * @param newYCenter DOCUMENT ME!
+ * @param newScaleFactor DOCUMENT ME!
+ */
+ public void viewportChanged(int w, int h, double newXCenter, double newYCenter,
+ double newScaleFactor) {
+ a.viewportChanged(w, h, newXCenter, newYCenter, newScaleFactor);
+ b.viewportChanged(w, h, newXCenter, newYCenter, newScaleFactor);
+ }
+
+ static ViewportChangeListener add(ViewportChangeListener a, ViewportChangeListener b) {
+ if (a == null)
+ return b;
+
+ if (b == null)
+ return a;
+
+ return new ViewportChangeListenerChain(a, b);
+ }
+
+ static ViewportChangeListener remove(ViewportChangeListener l, ViewportChangeListener oldl) {
+ if ((l == oldl) || (l == null))
+ return null;
+ else if (l instanceof ViewportChangeListenerChain)
+ return ((ViewportChangeListenerChain) l).remove(oldl);
+ else
+
+ return l;
+ }
+
+ private ViewportChangeListener remove(ViewportChangeListener oldl) {
+ if (oldl == a)
+ return b;
+
+ if (oldl == b)
+ return a;
+
+ ViewportChangeListener a2 = remove(a, oldl);
+ ViewportChangeListener b2 = remove(b, oldl);
+
+ if ((a2 == a) && (b2 == b))
+ return this;
+
+ return add(a2, b2);
+ }
+}
diff --git a/corelibs/ding/src/main/java/ding/view/test/DEPENDENCIES b/corelibs/ding/src/main/java/ding/view/test/DEPENDENCIES
new file mode 100644
index 0000000..a165178
--- /dev/null
+++ b/corelibs/ding/src/main/java/ding/view/test/DEPENDENCIES
@@ -0,0 +1,2 @@
+ding.view
+lib:fing.jar
diff --git a/corelibs/ding/src/main/java/ding/view/test/LWButton01.java b/corelibs/ding/src/main/java/ding/view/test/LWButton01.java
new file mode 100644
index 0000000..2e9f167
--- /dev/null
+++ b/corelibs/ding/src/main/java/ding/view/test/LWButton01.java
@@ -0,0 +1,431 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package ding.view.test;
+
+
+/* File LWButton01.java Copyright 1997, R.G.Baldwin
+
+This class is used to instantiate a 3D lightweight button
+object that behaves quite a bit like a heavyweight Button
+object but is much more responsive than a heavyweight
+button under JDK 1.1.3 and Win95 on a 133 mhz Pentium
+processor.
+
+The color of the button is based on the background color
+of its container, but is one shade brighter than the color
+of the background.
+
+Normally, it appears to protrude slightly out of the
+screen with highlights on the left and top edges and
+shadows on the bottom and right edges. Note that the
+highlighting only works if the background color does not
+contain components with values of 255.
+
+When you click the button with the mouse, it appears to
+retreat into the screen and then pops back out. As with
+a heavyweight button, this causes it to gain the focus.
+
+When it appears to retreat into the screen, its color
+changes to match that of the background with heavy shadows
+on the left and top and a faint outline on the bottom and
+right.
+
+The visual indication of focus is that the text on the
+button is rendered in bold italics.
+
+When you click the button, it generates an action event.
+
+When the button has the focus and you press the space
+bar, it generates an action event.
+
+This class was tested using JDK 1.1.3 under Win95.
+*/
+
+//=======================================================//
+import java.awt.*;
+import java.awt.event.*;
+
+
+//=======================================================//
+class LWButton01 extends Component {
+ //Save the raw label provided by the user here to make
+ // it available to the getLabel() method.
+ String rawLabel;
+
+ //The following instance variable contains the raw
+ // label with two spaces appended to each end to make
+ // it easier to use for sizing the LWButton.
+ String label;
+
+ // The following instance variable is set to true if
+ // the LWButton is pressed and not released.
+ boolean pressed = false;
+
+ //The following instance variable is set to true when
+ // the LWButton has focus
+ boolean gotFocus = false;
+
+ //The following instance variable refers to a list of
+ // registered ActionListener objects.
+ ActionListener actionListener;
+
+ //-----------------------------------------------------//
+ /**
+ * Creates a new LWButton01 object.
+ */
+ public LWButton01() {
+ //Invoke the parameterized constructor with an
+ // empty string
+ this("");
+ } //end constructor
+
+ //Constructor for an LWButton with a label.
+ /**
+ * Creates a new LWButton01 object.
+ *
+ * @param rawLabel DOCUMENT ME!
+ */
+ public LWButton01(String rawLabel) {
+ this.rawLabel = rawLabel;
+
+ //Add spaces on either end and save it that way
+ this.label = " " + rawLabel + " ";
+
+ //Invoke the enableEvents() method so that the
+ // processMouseEvent(), processFocusEvent(), and
+ // processKeyEvent() methods will be automatically
+ // invoked whenever an event of the corresponding
+ // type occurs on the LWButton. Note that this is
+ // an alternative approach to the source/listener
+ // event model.
+ enableEvents(AWTEvent.MOUSE_EVENT_MASK | AWTEvent.FOCUS_EVENT_MASK
+ | AWTEvent.KEY_EVENT_MASK);
+ } //end constructor
+
+ //-----------------------------------------------------//
+ /**
+ * DOCUMENT ME!
+ *
+ * @param listener DOCUMENT ME!
+ */
+ public void addActionListener(ActionListener listener) {
+ actionListener = AWTEventMulticaster.add(actionListener, listener);
+ } //end addActionListener()
+
+ //-----------------------------------------------------//
+ /**
+ * DOCUMENT ME!
+ *
+ * @param listener DOCUMENT ME!
+ */
+ public void removeActionListener(ActionListener listener) {
+ actionListener = AWTEventMulticaster.remove(actionListener, listener);
+ } //end removeActionListener
+
+ /*-----------------------------------------------------//
+ This method is used to cause the LWButton to behave as
+ if a mouse event occurred on it whenever it has the
+ focus and the space bar is pressed and then released.
+ Holding the space bar down generates repetitive
+ events due to the repeat feature of the keyboard (this
+ would need to be disabled in a real program).
+
+ This method is automatically called whenever a key
+ event occurs on the LWButton and the method
+ enableEvents(AWTEvent.KEY_EVENT_MASK) has been
+ previously invoked on the LWButton. */
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void processKeyEvent(KeyEvent e) {
+ //Generate mousePressed() event when the space bar
+ // is pressed by invoking the processMouseEvent()
+ // method and passing an event object that
+ // impersonates a mouse pressed event.
+ if ((e.getID() == KeyEvent.KEY_PRESSED) && (e.getKeyChar() == ' '))
+ processMouseEvent(new MouseEvent(this, MouseEvent.MOUSE_PRESSED, 0, 0, 0, 0, 0, false));
+
+ //Generate mouseReleased() event when the space bar
+ // is released by invoking the processMouseEvent()
+ // method and passing an event object that
+ // impersonates a mouse released event.
+ if ((e.getID() == KeyEvent.KEY_RELEASED) && (e.getKeyChar() == ' '))
+ processMouseEvent(new MouseEvent(this, MouseEvent.MOUSE_RELEASED, 0, 0, 0, 0, 0, false));
+
+ //The following statement is always needed when an
+ // overridden version of processKeyEvent() is used.
+ super.processKeyEvent(e);
+ } //end processKeyEvent()
+
+ /*-----------------------------------------------------//
+ This method in invoked when a focus event occurs on the
+ LWButton. This happens when the requestFocus() method
+ is called inside the mouseReleased() event handler for
+ the LWButton. This sets or clears the gotFocus flag
+ that is used to cause the text renderer to modify the
+ text to indicate that the LWButton has the focus.
+ When the LWButton has the focus, the text is rendered
+ in bold italics.
+
+ This method is automatically called whenever a focus
+ event occurs on the LWButton and the method
+ enableEvents(AWTEvent.FOCUS_EVENT_MASK) has been
+ previously invoked on the LWButton. */
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void processFocusEvent(FocusEvent e) {
+ if (e.getID() == FocusEvent.FOCUS_GAINED)
+ gotFocus = true; //set the gotFocus flag
+
+ if (e.getID() == FocusEvent.FOCUS_LOST)
+ gotFocus = false; //clear the gotFocus flag
+
+ this.invalidate();
+ this.repaint();
+
+ //The following statement is always needed when an
+ // overridden version of processFocusEvent() is used.
+ super.processFocusEvent(e);
+ } //end processFocusEvent()
+
+ /*-----------------------------------------------------//
+ The purpose of this method is twofold:
+ 1. Modify the appearance of the LWButton object when
+ the user clicks on it.
+ 2. Invoke the actionPerformed() method in the Listener
+ object that is registered to listen to this
+ LWButton object.
+
+ This method is automatically called whenever a mouse
+ event occurs on the LWButton and the method
+ enableEvents(AWTEvent.MOUSE_EVENT_MASK) has been
+ previously invoked on the LWButton. */
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void processMouseEvent(MouseEvent e) {
+ switch (e.getID()) { //what kind of mouse event?
+ case MouseEvent.MOUSE_PRESSED:
+ //When the mouse is pressed on the LWButton object,
+ // set the "pressed" state of the object to true
+ // and force it to be repainted to change its
+ // appearance. When pressed is true, the button is
+ // rendered as though it has been pressed into the
+ // screen.
+ pressed = true;
+ this.invalidate();
+ this.repaint();
+
+ break;
+
+ case MouseEvent.MOUSE_RELEASED:
+
+ //When the mouse is released on the LWButton object:
+ // 1. Invoke the actionPerformed() method in the
+ // Listener objects that are registered to
+ // listen to the LWButton object.
+ // 2. Confirm that the "pressed" state is true and
+ // if so, set it to false and force the object
+ // to be repainted to change its appearance.
+ // When pressed is false, the button is rendered
+ // so as to appear to protrude out of the
+ // screen.
+ // 3. Request the focus for the LWButton object.
+ //if an ActionListener is registered
+ if (actionListener != null) {
+ //Invoke the actionPerformed() method on the list
+ // of listener objects registered on the
+ // LWButton object. Instantiate and pass an
+ // ActionEvent object as a parameter.
+ actionListener.actionPerformed(new ActionEvent(this,
+ ActionEvent.ACTION_PERFORMED,
+ label));
+ } //end if on actionListener
+
+ if (pressed == true) {
+ pressed = false;
+ this.requestFocus();
+ this.invalidate();
+ this.repaint();
+ } //end if on pressed
+
+ break;
+ } //end switch
+
+ //The following statement is always needed when an
+ // overridden version of processMouseEvent() is used.
+ super.processMouseEvent(e);
+ } //end processMouseEvent()
+
+ //-----------------------------------------------------//
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Dimension getPreferredSize() {
+ if (getFont() != null) {
+ FontMetrics fm = getFontMetrics(getFont());
+
+ return new Dimension(fm.stringWidth(label), fm.getHeight() + 10);
+ } else
+
+ return new Dimension(10, 10); //no font
+ } //end getPreferredSize()
+
+ //Override the getMinimumSize() method and specify
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Dimension getMinimumSize() {
+ return new Dimension(10, 10);
+ } //end getMinimumSize()
+
+ //-----------------------------------------------------//
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getLabel() { //gets the label
+
+ return rawLabel;
+ } //end getLabel()
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param rawLabel DOCUMENT ME!
+ */
+ public void setLabel(String rawLabel) { //sets the label
+ this.rawLabel = rawLabel; //save the raw label
+
+ //Add spaces to each end of the rawLabel to make it
+ // easier to center the label in the LWButton.
+ this.label = " " + rawLabel + " ";
+ this.invalidate();
+ this.repaint();
+ } //end setLabel()
+
+ //-----------------------------------------------------//
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g DOCUMENT ME!
+ */
+ public void paint(Graphics g) { //paints the LWButton
+
+ //If LWButton has the focus, display the text in
+ // bold italics. Otherwise display plain.
+ if (gotFocus)
+ g.setFont(new Font(getFont().getName(), Font.BOLD | Font.ITALIC, getFont().getSize()));
+ else
+ g.setFont(new Font(getFont().getName(), Font.PLAIN, getFont().getSize()));
+
+ if (pressed) { //if the pressed flag is true
+ g.setColor(getBackground());
+ g.fillRect( //fill rectangle with background color
+ 0, 0, this.getSize().width, this.getSize().height);
+
+ //Draw shadows three shades darker than background
+ g.setColor(getBackground().darker().darker().darker());
+
+ //Note that three offset rectangles are drawn to
+ // produce a shadow effect on the left and top of
+ // the rectangle.
+ g.drawRect( //
+ 0, 0, this.getSize().width, this.getSize().height);
+ g.drawRect(1, 1, this.getSize().width, this.getSize().height);
+ g.drawRect(2, 2, this.getSize().width, this.getSize().height);
+
+ //Now draw a faint outline on the bottom and right of
+ // the rectangle.
+ g.setColor(getBackground().darker());
+ g.drawRect(-1, -1, this.getSize().width, this.getSize().height);
+
+ //Now center the text in the LWButton object
+ FontMetrics fm = getFontMetrics(getFont());
+ g.setColor(getForeground());
+ g.drawString(label, (getSize().width / 2) - (fm.stringWidth(label) / 2),
+ (getSize().height / 2) + (fm.getAscent() / 2));
+ } //end if(pressed)
+
+ else { //not pressed
+ //Make the protruding LWButton object one shade
+ // brighter than the background.
+ g.setColor(getBackground().brighter());
+ g.fillRect( //and fill a rectangle
+ 0, 0, this.getSize().width, this.getSize().height);
+
+ //Set the color for the shadows three shades darker
+ // than the background.
+ g.setColor(getBackground().darker().darker().darker());
+
+ //Draw two offset rectangles to create shadows on
+ // the right and bottom.
+ g.drawRect(-1, -1, this.getSize().width, this.getSize().height);
+ g.drawRect(-2, -2, this.getSize().width, this.getSize().height);
+
+ //Highlight the left and top two shades brighter
+ // than the background, one shade brighter than the
+ // color of the LWButton itself which is one shade
+ // brighter than the background.
+ g.setColor(getBackground().brighter().brighter());
+ g.drawRect( //
+ 0, 0, this.getSize().width, this.getSize().height);
+
+ //Now place the text in the LWButton object shifted
+ // by two pixels up and to the left.
+ FontMetrics fm = getFontMetrics(getFont());
+ g.setColor(getForeground());
+ g.drawString(label, (getSize().width / 2) - (fm.stringWidth(label) / 2) - 2,
+ ((getSize().height / 2) + (fm.getAscent() / 2)) - 2);
+ } //end else
+ } //end overridden paint() method
+
+ //-----------------------------------------------------//
+} //end class LWButton01
+//=======================================================//
diff --git a/corelibs/ding/src/main/java/ding/view/test/SanityTest.java b/corelibs/ding/src/main/java/ding/view/test/SanityTest.java
new file mode 100644
index 0000000..d72ea47
--- /dev/null
+++ b/corelibs/ding/src/main/java/ding/view/test/SanityTest.java
@@ -0,0 +1,193 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package ding.view.test;
+
+import cytoscape.render.stateful.GraphLOD;
+
+import ding.view.BirdsEyeView;
+import ding.view.DGraphView;
+
+import fing.model.FingRootGraphFactory;
+
+import giny.model.GraphPerspective;
+import giny.model.RootGraph;
+
+import giny.view.Bend;
+import giny.view.EdgeView;
+import giny.view.GraphView;
+import giny.view.GraphViewChangeEvent;
+import giny.view.GraphViewChangeListener;
+import giny.view.NodeView;
+
+import java.awt.Dimension;
+import java.awt.EventQueue;
+import java.awt.Frame;
+import java.awt.Graphics;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
+import java.awt.geom.Point2D;
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ */
+public class SanityTest {
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public static void main(String[] args) throws Exception {
+ final RootGraph root = FingRootGraphFactory.instantiateRootGraph();
+ final int node1 = root.createNode();
+ final int node2 = root.createNode();
+ final int node3 = root.createNode();
+ final int node4 = root.createNode();
+ final int edge1 = root.createEdge(node1, node2);
+ final int edge2 = root.createEdge(node2, node3);
+ final int edge3 = root.createEdge(node3, node1);
+ final int edge4 = root.createEdge(node4, node1);
+ final int edge5 = root.createEdge(node4, node2);
+ final GraphPerspective persp = root.createGraphPerspective((int[]) null, (int[]) null);
+ final DGraphView view = new DGraphView(persp);
+
+ for (int i = 0; i < 5; i++) {
+ if (i != 2)
+ view.addGraphViewChangeListener(new GraphViewChangeListener() {
+ public void graphViewChanged(GraphViewChangeEvent evt) {
+ }
+ });
+
+ else
+ view.addGraphViewChangeListener(new GraphViewChangeListener() {
+ public void graphViewChanged(GraphViewChangeEvent evt) {
+ if (evt.isNodesSelectedType()) {
+ final int[] selectedNodes = evt.getSelectedNodeIndices();
+ System.out.print("selected nodes: ");
+
+ for (int i = 0; i < selectedNodes.length; i++)
+ System.out.print(selectedNodes[i] + " ");
+
+ System.out.println();
+ }
+ }
+ });
+
+ }
+
+ EventQueue.invokeAndWait(new Runnable() {
+ public void run() {
+ Frame f = new Frame() {
+ public void update(Graphics g) {
+ paint(g);
+ }
+ };
+
+ f.add(view.getComponent());
+
+ for (int i = 0; i < 10; i++) {
+ f.setVisible(true);
+ f.setSize(new Dimension(400, 300));
+ }
+
+ f.addWindowListener(new WindowAdapter() {
+ public void windowClosing(WindowEvent e) {
+ System.exit(0);
+ }
+ });
+ }
+ });
+
+ final NodeView nv1 = view.addNodeView(node1);
+ final NodeView nv2 = view.addNodeView(node2);
+ final NodeView nv3 = view.addNodeView(node3);
+ final NodeView nv4 = view.addNodeView(node4);
+ final EdgeView ev1 = view.addEdgeView(edge1);
+ final EdgeView ev2 = view.addEdgeView(edge2);
+ final EdgeView ev3 = view.addEdgeView(edge3);
+ final EdgeView ev4 = view.addEdgeView(edge4);
+ final EdgeView ev5 = view.addEdgeView(edge5);
+ final Bend bend5 = ev5.getBend();
+ bend5.addHandle(new Point2D.Float(0.0f, 0.0f));
+ nv1.setOffset(0.0d, 50.0d);
+ nv2.setOffset(-30.0d, -10.0d);
+ nv3.setOffset(30.0d, 10.0d);
+ nv4.setOffset(-60.0d, 50.0d);
+ nv1.setBorderWidth(1.0f);
+ nv2.setBorderWidth(1.0f);
+ nv3.setBorderWidth(1.0f);
+ nv4.setBorderWidth(1.0f);
+ ev1.setTargetEdgeEnd(EdgeView.BLACK_DELTA);
+ ev2.setTargetEdgeEnd(EdgeView.BLACK_DELTA);
+ ev3.setTargetEdgeEnd(EdgeView.BLACK_DELTA);
+ ev4.setTargetEdgeEnd(EdgeView.BLACK_DELTA);
+ ev5.setTargetEdgeEnd(EdgeView.BLACK_DELTA);
+ view.fitContent();
+ view.setGraphLOD(new GraphLOD() {
+ public boolean detail(int nodes, int edges) {
+ return nodes < 4;
+ }
+ });
+ view.updateView();
+ EventQueue.invokeAndWait(new Runnable() {
+ public void run() {
+ Frame f = new Frame() {
+ public void update(Graphics g) {
+ paint(g);
+ }
+ };
+
+ f.add(new BirdsEyeView(view));
+
+ for (int i = 0; i < 10; i++) {
+ f.setVisible(true);
+ f.setSize(new Dimension(150, 100));
+ }
+
+ f.addWindowListener(new WindowAdapter() {
+ public void windowClosing(WindowEvent e) {
+ System.exit(0);
+ }
+ });
+ }
+ });
+ }
+}
diff --git a/corelibs/ding/src/main/resources/images/default_network.png b/corelibs/ding/src/main/resources/images/default_network.png
new file mode 100644
index 0000000..5d2f4b3
Binary files /dev/null and b/corelibs/ding/src/main/resources/images/default_network.png differ
diff --git a/corelibs/ding/src/main/resources/images/recursive_network.png b/corelibs/ding/src/main/resources/images/recursive_network.png
new file mode 100644
index 0000000..bfba85d
Binary files /dev/null and b/corelibs/ding/src/main/resources/images/recursive_network.png differ
diff --git a/corelibs/docs/README.txt b/corelibs/docs/README.txt
new file mode 100644
index 0000000..9444d96
--- /dev/null
+++ b/corelibs/docs/README.txt
@@ -0,0 +1,79 @@
+
+INTRO
+===============================================================================
+
+This is a two part project.
+
+The Maven part, driven by pom.xml, generates the documentation artifact used by
+the rest of Cytoscape to provide documentation for the application and
+distribution.
+
+The Ant part is used to download the manual from the wiki, download all of the
+images from the wiki, and generate a PDF version of the manual. Maven does
+not execute these tasks because they take a long time, burden our wiki, and
+don't generally need to happen more than once or twice in a release cycle
+(i.e. once everyone's updated their portion of the manual).
+
+
+THE PROCEDURE
+===============================================================================
+
+90% of the time (when you don't need to update):
+------------------------------------------------
+
+1. "mvn install" should be all you need to generate the artifacts needed by
+ Cytoscape to build and deploy normally.
+
+2. There is no step 2.
+
+
+10% of the time (when you DO need to update):
+---------------------------------------------
+
+1. "ant update" will download everything, pre-process the XML, and generate the PDF.
+
+2. Check all the newly generated files into subversion.
+
+3. "mvn install" to generate the artifacts.
+
+
+
+ANT TASK EXPLANATION
+===============================================================================
+
+"ant" Shows the usage message.
+
+"ant update" Will re-download the manual, all associated images, and regenerate
+ the PDF version of the manual. The project should be left in a
+ a state such that everything can be added and checked in.
+
+
+POTENTIAL GENERATION ERRORS
+===============================================================================
+
+"Error: CALS tables must specify the number of columns."
+
+
+
+This happens because you see the following structure in the docbook:
+
+ <table cols="1">
+ <caption/>
+ <tgroup>
+ <colspec colname="xxx1"/>
+
+where the number of columns is specified in the table element rather than the
+tgroup element, where it should be. The following is correct
+
+ <table>
+ <caption/>
+ <tgroup cols="1">
+ <colspec colname="xxx1"/>
+
+This is best solved by fixing the tables in the document rather than trying to
+tweak the XML. This is really a bug in how MoinMoin exports the DocBook.
+
+This problem occurs in the XML when the first row of a table spans some or all
+of the columns in the table. Simply remove this and the xml is exported
+correctly.
+
diff --git a/corelibs/docs/build.xml b/corelibs/docs/build.xml
new file mode 100644
index 0000000..dc4f4df
--- /dev/null
+++ b/corelibs/docs/build.xml
@@ -0,0 +1,232 @@
+<?xml version="1.0"?>
+<project name="Cytoscape" default="usage">
+
+ <property name="basedir" value="."/>
+ <property name="xep.home" value="/cellar/users/mes/XEP"/>
+ <property name="version" value="2.7"/>
+ <property name="images.dir" value="${basedir}/src/docbkx/images"/>
+ <property name="manual.dir" value="${basedir}/src/docbkx"/>
+
+ <available file="${xep.home}" property="xep-exists"/>
+
+ <target name="usage">
+ <echo message="----------------------------------------------------------"/>
+ <echo message=" Cytoscape Manual Fetching System "/>
+ <echo message="----------------------------------------------------------"/>
+ <echo message=" "/>
+ <echo message=" Primary target:"/>
+ <echo message=" ant update # Will re-download manual and regenerate PDF."/>
+ <echo message=" "/>
+ <echo message=" Other targets:"/>
+ <echo message=" ant fetch-manual # Just downloads manual. "/>
+ <echo message=" ant fetch-images # Downloads manual and images."/>
+ <echo message=" ant prep-manual # Downloads everything and processes raw xml."/>
+ <echo message=" ant create-pdf # Runs prep-manual and then creates the PDF (same as update)."/>
+ <echo message=" "/>
+
+<echo message="----------------------------------------------------------"/>
+ </target>
+
+
+
+ <!--==============================================================-->
+ <!-- Init conditionally -->
+ <target name="init"
+ depends="xep-init,non-xep-init"/>
+
+
+
+ <!--==============================================================-->
+ <!-- Init if XEP does not exist -->
+ <target name="non-xep-init"
+ unless="xep-exists">
+ <echo message="XEP does not exist - No PDF for you!"/>
+ </target>
+
+ <!--==============================================================-->
+ <!-- Init if XEP does exist -->
+ <target name="xep-init"
+ if="xep-exists">
+ <echo message="XEP exists - You get a PDF!"/>
+ <property name="xep.lib" value="${xep.home}/lib"/>
+ <taskdef name="xep" classname="com.renderx.xepx.ant.XEPTask"
+ classpath="${xep.lib}/XEPTask.jar"/>
+
+ <path id="classpath">
+ <fileset dir="${xep.lib}">
+ <include name="xep*.jar"/>
+ <include name="xt.jar"/>
+ </fileset>
+ <pathelement path="${xep.lib}/XEPTask.jar"/>
+ </path>
+ </target>
+
+
+ <!--==============================================================-->
+ <!-- Fetch the DocBook XML from the wiki page. -->
+ <target name="fetch-manual"
+ description="fetches the raw manual file"
+ depends="init" >
+
+ <get src="http://cytoscape.wodaklab.org/wiki/Cytoscape_User_Manual?action=show&mimetype=text/docbook"
+ dest="manual_raw.xml"/>
+
+ </target>
+
+
+ <!--==============================================================-->
+ <!-- Fetch the images from the wiki page. -->
+ <target name="fetch-images"
+ description="Fetches the images from the manual"
+ depends="fetch-manual" >
+
+ <!-- Correct the urls in the raw manual. -->
+ <copy file="manual_raw.xml"
+ tofile="manual_tmp_fetch_images.xml"
+ overwrite="yes"
+ encoding="utf-8">
+ <filterchain>
+ <tokenfilter>
+ <replacestring from="wiki//wiki"
+ to="wiki"/>
+ <replacestring from="&#8594;" to="→" />
+ </tokenfilter>
+ </filterchain>
+ </copy>
+
+ <!-- Strip out the image file names from the manual and create a new ant
+ build file that will fetch them. -->
+ <xslt in="manual_tmp_fetch_images.xml"
+ out="fetch_images_tmp.xml"
+ classpathref="classpath"
+ style="xsl/strip_images.xsl"/>
+
+ <!-- Change the file destination in the build file. -->
+ <copy file="fetch_images_tmp.xml"
+ tofile="fetch_image_files.xml"
+ overwrite="yes"
+ encoding="utf-8">
+ <filterchain>
+ <tokenfilter>
+ <replaceregex pattern='dest=\S+target='
+ replace='dest="${images.dir}/'
+ flags="g"/>
+ <replacestring from='&' to='&'/>
+ </tokenfilter>
+ </filterchain>
+ </copy>
+
+ <!-- Run the new build file fetching all of the image files. -->
+ <ant antfile="fetch_image_files.xml" target="strip"/>
+
+ <delete file="fetch_images_tmp.xml"/>
+ <delete file="fetch_image_files.xml"/>
+ <delete file="manual_tmp_fetch_images.xml"/>
+ </target>
+
+
+ <!--==============================================================-->
+ <!-- Substitute file locations and other XML problems -->
+ <target name="prep-manual"
+ description="Prep Manual XML"
+ depends="fetch-images">
+
+ <copy file="manual_raw.xml"
+ tofile="manual_tmp_prep.xml"
+ overwrite="yes"
+ encoding="utf-8">
+ <filterchain>
+ <tokenfilter>
+ <!-- this gets the images -->
+ <replaceregex pattern='http://cytoscape.wodaklab.org/wiki//wiki/Cytoscape_User_Manual\S+target='
+ replace='images/'
+ flags="g"/>
+ <replacestring from="&#8592;" to="←" />
+ <replacestring from="&#8593;" to="↑" />
+ <replacestring from="&#8594;" to="→" />
+ <replacestring from="&#8595;" to="↓" />
+ <replacestring from="@version@" to="${version}" />
+ <replacestring from="<title>Cytoscape_User_Manual</title>"
+ to= "<title>Cytoscape User Manual</title>" />
+
+ </tokenfilter>
+ </filterchain>
+ </copy>
+
+
+ <!-- Add id to section elements -->
+ <xslt classpathref="classpath"
+ in="manual_tmp_prep.xml"
+ out="manual_tmp_prep2.xml"
+ style="xsl/add_id_to_section.xsl"/>
+
+ <!-- Remove revision history -->
+ <xslt classpathref="classpath"
+ in="manual_tmp_prep2.xml"
+ out="${manual.dir}/manual.xml"
+ style="xsl/remove_revision_history.xsl"/>
+
+ <delete file="manual_tmp_prep.xml"/>
+ <delete file="manual_tmp_prep2.xml"/>
+ <delete file="manual_raw.xml"/>
+ </target>
+
+
+ <!--==============================================================-->
+ <!-- Create the manual PDF file. -->
+ <target name="create-pdf"
+ description="Create Cytoscape Manual PDF"
+ depends="prep-manual"
+ if="xep-exists">
+
+ <property name="docbook-xsl" value="docbook-xsl-1.75.2"/>
+ <property name="xsl" value="${basedir}/xsl/${docbook-xsl}"/>
+ <unzip src="${basedir}/xsl/${docbook-xsl}.zip"
+ dest="${basedir}/xsl" />
+
+ <!-- so that images scale correctly -->
+ <copy file="${manual.dir}/manual.xml"
+ tofile="manual_pdf.xml"
+ overwrite="yes"
+ encoding="utf-8">
+ <filterchain>
+ <tokenfilter>
+ <replacestring from="imagedata fileref"
+ to="imagedata scaletofit='1' width='100%' fileref"/>
+ <replacestring from='fileref="images/'
+ to='fileref="src/docbkx/images/'/>
+ </tokenfilter>
+ </filterchain>
+ </copy>
+
+ <!-- transform the manual to fo -->
+ <xslt classpathref="classpath"
+ in="manual_pdf.xml"
+ out="manual.fo"
+ style="${xsl}/fo/docbook.xsl">
+ <param name="ulink.show" expression="0"/>
+ </xslt>
+
+
+ <!-- convert to pdf -->
+ <xep in="manual.fo"
+ out="src/main/pdf/manual.pdf"
+ format="PDF">
+ <classpath refid="classpath"/>
+ <sysproperty key="com.renderx.xep.CONFIG"
+ value="${xep.home}/xep.xml"/>
+ </xep>
+
+ <delete file="manual.fo"/>
+ <delete file="manual_pdf.xml"/>
+ <delete dir="xsl/${docbook-xsl}"/>
+ </target>
+
+ <!--==============================================================-->
+ <!-- Create the manual PDF file. -->
+ <target name="update"
+ description="Download manual and regenerated PDF"
+ depends="create-pdf">
+ </target>
+
+</project>
diff --git a/corelibs/docs/pom.xml b/corelibs/docs/pom.xml
new file mode 100644
index 0000000..5ded1fd
--- /dev/null
+++ b/corelibs/docs/pom.xml
@@ -0,0 +1,143 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+
+ <parent>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>parent</artifactId>
+ <version>2.8.4-SNAPSHOT</version>
+ </parent>
+
+ <artifactId>docs</artifactId>
+ <packaging>jar</packaging>
+ <name>Cytoscape Documentation</name>
+
+ <!-- bootstrap for cytoscape dependencies, namely the parent POM snapshots -->
+ <repositories>
+ <repository>
+ <id>cytoscape_snapshots</id>
+ <snapshots>
+ <enabled>true</enabled>
+ </snapshots>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <name>Cytoscape Snapshots</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/</url>
+ </repository>
+ <repository>
+ <id>cytoscape_releases</id>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ <name>Cytoscape Releases</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/releases/</url>
+ </repository>
+ </repositories>
+
+ <build>
+ <plugins>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-assembly-plugin</artifactId>
+ <version>2.2.1</version>
+ <configuration>
+ <descriptors>
+ <descriptor>src/main/assembly/html.xml</descriptor>
+ <descriptor>src/main/assembly/pdf.xml</descriptor>
+ <descriptor>src/main/assembly/javahelp.xml</descriptor>
+ </descriptors>
+ </configuration>
+ <executions>
+ <execution>
+ <id>make-assembly</id>
+ <phase>package</phase>
+ <goals>
+ <goal>single</goal>
+ </goals>
+ </execution>
+ </executions>
+ </plugin>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-resources-plugin</artifactId>
+ <version>2.3</version>
+ <executions>
+ <execution>
+ <id>copy-html-images</id>
+ <phase>process-resources</phase>
+ <goals>
+ <goal>copy-resources</goal>
+ </goals>
+ <configuration>
+ <outputDirectory>target/docbkx/html/images</outputDirectory>
+ <resources>
+ <resource>
+ <directory>src/docbkx/images</directory>
+ </resource>
+ </resources>
+ </configuration>
+ </execution>
+ <execution>
+ <id>copy-javahelp-images</id>
+ <phase>process-resources</phase>
+ <goals>
+ <goal>copy-resources</goal>
+ </goals>
+ <configuration>
+ <outputDirectory>target/docbkx/javahelp/images</outputDirectory>
+ <resources>
+ <resource>
+ <directory>src/docbkx/images</directory>
+ </resource>
+ </resources>
+ </configuration>
+ </execution>
+ <execution>
+ <id>copy-pdf</id>
+ <phase>process-resources</phase>
+ <goals>
+ <goal>copy-resources</goal>
+ </goals>
+ <configuration>
+ <outputDirectory>target/docbkx/pdf</outputDirectory>
+ <resources>
+ <resource>
+ <directory>src/main/pdf</directory>
+ </resource>
+ </resources>
+ </configuration>
+ </execution>
+ </executions>
+ </plugin>
+ <plugin>
+ <groupId>com.agilejava.docbkx</groupId>
+ <artifactId>docbkx-maven-plugin</artifactId>
+ <version>2.0.9</version>
+ <executions>
+ <execution>
+ <goals>
+ <!--
+ <goal>generate-pdf</goal>
+ -->
+ <goal>generate-javahelp</goal>
+ <goal>generate-html</goal>
+ </goals>
+ <phase>generate-sources</phase>
+ </execution>
+ </executions>
+ <dependencies>
+ <dependency>
+ <groupId>org.docbook</groupId>
+ <artifactId>docbook-xml</artifactId>
+ <version>4.4</version>
+ <scope>runtime</scope>
+ </dependency>
+ </dependencies>
+ </plugin>
+ </plugins>
+ </build>
+</project>
+
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+<?xml version="1.0" encoding="UTF-8"?><article><articleinfo><title>Cytoscape User Manual</title></articleinfo><section id="Cytoscape User Manual"><title><ulink url="http://cytoscape.wodaklab.org/wiki/Cytoscape_User_Manual/wiki/Cytoscape_User_Manual/Title_Page">Cytoscape User Manual</ulink></title><para><inlinemediaobject><imageobject><imagedata fileref="images/cyto-logo-smaller.gif"/></imageobject><textobject><phrase>cyto-logo-smaller.gif</phrase></textobject></inlinemediaobject> </para> [...]
+ -h,--help Print this message.
+ -v,--version Print the version number.
+ -s,--session <file> Load a cytoscape session (.cys) file.
+ -N,--network <file> Load a network file (any format).
+ -e,--edge-attrs <file> Load an edge attributes file (edge attribute format).
+ -n,--node-attrs <file> Load a node attributes file (node attribute format).
+ -m,--matrix <file> Load a node attribute matrix file (table).
+ -p,--plugin <file> Load a plugin jar file, directory of jar files,
+ plugin class name, or plugin jar URL.
+ -P,--props <file> Load cytoscape properties file (Java properties
+ format) or individual property: -P name=value.
+ -V,--vizmap <file> Load vizmap properties file (Java properties format).</screen><para>Any file specified for an option may be specified as either a path or as a URL. For example you can specify a network as a file (assuming that myNet.sif exists in the current working directory): <code>cytoscape.sh -N myNet.sif</code>. Or you can specify a network as a URL: <code>cytoscape.sh -N http://example.com/myNet.sif</code>. </para><informaltable><tgroup cols="2"><colspec colname="co [...]
+YJR022W YNR053C pp TRUE abcd12371 1.2344543
+YER116C YDL013W pp TRUE abcd12372 1.2344543
+YNL307C YAL038W pp FALSE abcd12373 1.2344543
+YNL216W YCR012W pd TRUE abcd12374 1.2344543
+YNL216W YGR254W pd TRUE abcd12375 1.2344543</screen><para>The network table files should contain at least two columns: source nodes and target nodes. The interaction type is optional in this format. Therefore, a minimal network table looks like the following: </para><screen format="linespecific">YJR022W YNR053C
+YER116C YDL013W
+YNL307C YAL038W
+YNL216W YCR012W
+YNL216W YGR254W</screen><para>One row in a network table file represents an edge and its edge attributes. This means that a network file is considered a combination of network data and edge attributes. A table may contain columns that aren't meant to be edge attributes. In this case, you can choose not to import those columns by clicking on the column header in the preview window. This function is useful when importing a data table like the following (1): </para><screen format="linespeci [...]
+
+7205 5747 TRIP6 PTK2 Q15654 Q05397-1 vv|HPRD Currently not available 14688263|15892868(Marcotte) Mammalia Homo sapiens protein|protein HPRD|Marcotte 0 Thyroid hormone receptor interactor 6-FAK-|PTK2-TRIP6 NA(HPRD)|NA(Marcotte) HPRD/02859_psimi.xml|other/ORIGINAL_DATA_MARCOTTE.txt vv(HPRD/02859_psimi.xml)|HPRD(other/ORIGINAL_DATA_MARCOTTE.txt) 17651(ExptRef)|Marcotte 2 2 2 2
+
+4174 7311 MCM5 UBA52 P33992 P62987 neighbouring_reaction Currently not available 15608231(Reactome) Homo sapiens Homo sapiens protein|protein Reactome 1 P33992-P62988 Reaction:68944<->Reaction:68946(Reactome)|Reaction:68946<->Reaction:68944(Reactome) other/ORIGINAL_DATA_MARCOTTE.txt neighbouring_reaction(other/REACTOMEhomo_sapiens.interactions.txt) Reactome 1 1 1 1
+
+7040 7040 TGFB1 TGFB1 P01137 P01137 nmr: nuclear magnetic resonance Currently not available 8679613 Homo sapiens Homo sapiens protein|protein BIND 2 TGFB1-TGFB1- 72085(BIND) BIND/bind_taxid9606.1.psi.xml nmr: nuclear magnetic resonance(BIND/bind_taxid9606.1.psi.xml) NotAvailable 1 1 1 1</screen><para>This data file is a tab-delimited text and contains network data (interactions), edge attributes, and node attributes. To import net [...]
+nodeC <relationship type> nodeA
+nodeD <relationship type> nodeE nodeF nodeB
+nodeG
+...
+nodeY <relationship type> nodeZ</screen><para>A more specific example is: </para><screen format="linespecific">node1 typeA node2
+node2 typeB node3 node4 node5
+node0</screen><para>The first line identifies two nodes, called node1 and node2, and a single relationship between node1 and node2 of type typeA. The second line specifies three new nodes, node3, node4, and node5; here "node2" refers to the same node as in the first line. The second line also specifies three relationships, all of type typeB and with node2 as the source, with node3, node4, and node5 as the targets. This second form is simply shorthand for specifying multiple relationships [...]
+node1 xx node2
+node1 yy node2</screen><para>Edges connecting a node to itself (self-edges) are also allowed: </para><screen format="linespecific">node1 xx node1</screen><para>Every node and edge in Cytoscape has an identifying name, most commonly used with the node and edge data attribute structures. Node names must be unique, as identically named nodes will be treated as identical nodes. The name of each node will be the name in this file by default (unless another string is mapped to display on the n [...]
+ pd .................. protein -> DNA
+ (e.g. transcription factor binding upstream of a regulating gene.)</screen><para>Some less common interaction types used are: </para><screen format="linespecific"> pr .................. protein -> reaction
+ rc .................. reaction -> compound
+ cr .................. compound -> reaction
+ gl .................. genetic lethal relationship
+ pm .................. protein-metabolite interaction
+ mp .................. metabolite-protein interaction</screen><section id="Delimiters"><title>Delimiters</title><para>Whitespace (space or tab) is used to delimit the names in the simple interaction file format. However, in some cases spaces are desired in a node name or edge type. The standard is that, if the file contains any tab characters, then tabs are used to delimit the fields and spaces are considered part of the name. If the file contains no tabs, then any spaces are delimiters [...]
+Example_1 network1
+network1 A pp B
+network1 B pp A
+Example_1 C pp B</screen></section><section id="Example 2"><title>Example 2</title><para><inlinemediaobject><imageobject><imagedata fileref="images/NNFExample2.png"/></imageobject><textobject><phrase>NNFExample2.png</phrase></textobject></inlinemediaobject> </para><screen format="linespecific">Example_2 M1
+Example_2 M2
+M1 A
+M2 B pp C
+Example_2 A pp B
+Example_2 M1 im M2</screen></section><section id="Example 3"><title>Example 3</title><para><inlinemediaobject><imageobject><imagedata fileref="images/NNFExample3.png"/></imageobject><textobject><phrase>NNFExample3.png</phrase></textobject></inlinemediaobject> </para><screen format="linespecific">Example_3 M1 im M2
+Example_3 M3 im M1
+Example_3 M2 im M3
+Example_3 C pp M3
+Example_3 M2 pp C
+M1 A
+M2 A pp B
+M3 B pp C</screen></section><section id="Example 4"><title>Example 4</title><para><inlinemediaobject><imageobject><imagedata fileref="images/NNFExample4.png"/></imageobject><textobject><phrase>NNFExample4.png</phrase></textobject></inlinemediaobject> </para><screen format="linespecific">Example_4 M1
+root M3
+M1 A pp B
+M1 B pp A
+Example_4 C pp B
+M3 M2
+M2 D
+M3 E pp F
+M3 D pp F
+M3 D pp E
+Example_4 D pp C
+Example_4 A pp M2
+Example_4 B pp M3
+Example_4 M2 pp B</screen></section><section id="Example 5"><title>Example 5</title><para><inlinemediaobject><imageobject><imagedata fileref="images/NNFExample5.png"/></imageobject><textobject><phrase>NNFExample5.png</phrase></textobject></inlinemediaobject> </para><screen format="linespecific">Example_5 M4
+M4 D
+M4 M3
+M3 M2 pp C
+M2 M1 pp B
+M1 A
+M4 C pp D</screen></section></section></section><section id="GML Format"><title>GML Format</title><para>In contrast to SIF, GML is a rich graph format language supported by many other network visualization packages. The GML file format specification is available at: </para><para><ulink url="http://www.infosun.fmi.uni-passau.de/Graphlet/GML/"/> </para><para>It is generally not necessary to modify the content of a GML file directly. Once a network is built in SIF [...]
+YAL001C = metabolism
+YAR002W = apoptosis
+YBL007C = ribosome</screen><para>An edge attribute file has much the same structure, except that the name of the edge is the source node name, followed by the interaction type in parentheses, followed by the target node name. Directionality counts, so switching the source and target will refer to a different (or perhaps non-existent) edge. The following is an example edge attributes file: </para><screen format="linespecific">InteractionStrength
+YAL001C (pp) YBR043W = 0.82
+YMR022W (pd) YDL112C = 0.441
+YDL112C (pd) YMR022W = 0.9013</screen><para>Since Cytoscape treats edge attributes as directional, the second and third edge attribute values refer to two different edges (source and target are reversed, though the nodes involved are the same). </para><para>Each attribute is stored in a separate file. Node and edge attribute files use the same format. Node attribute file names often use the suffix ".noa", while edge attribute file names use the suffix ".eda". Cytoscape recognizes these s [...]
+firstName = 1
+secondName = 2.5</screen><para>In this case, the first value will make Cytoscape think the values should be integers, when in fact they should be floating point numbers. It's safest to explicitly specify the value type to prevent confusion. A better format would be: </para><screen format="linespecific">floatingPointAttribute (class=Double)
+firstName = 1
+secondName = 2.5</screen><para>or </para><screen format="linespecific">floatingPointAttribute
+firstName = 1.0
+secondName = 2.5</screen><para>Every line past the first line identifies the name of an object (a node in a node attribute file or an edge in a edge attribute file) along with the String representation of the attribute value. The delimiter is always an equals sign; whitespace (spaces and/or tabs) before and after the equals sign is ignored. This means that your names and values can contain whitespace, but object names cannot contain an equals sign and no guarantees are made concerning le [...]
+firstObjectName = (firstValue::secondValue::thirdValue)
+secondObjectName = (onlyOneValue)</screen><para>This example shows an attribute whose value is defined as a list of text strings. The first object has three strings, and thus three elements in its list, while the second object has a list with only one element. In the case of a list every attribute value uses list syntax (i.e. parentheses), and each element is of the same class. Again, the class will be inferred if it is not specified in the header line. Lists are not supported by the vis [...]
+YJL157C = This is a long\nline for a label.</screen></section></section><section id="Import Attribute Table Files"><title>Import Attribute Table Files</title><para>As of Cytoscape 2.4, importing delimited text and MS Excel attribute data tables is now supported. Using this functionality, users can now easily import data that isn't formatted into Cytoscape node or edge attribute file formats (as described above). </para><para><inlinemediaobject><imageobject><imagedata fileref="images/att [...]
+YHR051W COX6 -0.034 0.111 -0.304 3.75720e-01 1.56240e-02 7.91340e-06
+YHR124W NDT80 -0.090 0.007 -0.348 2.71460e-01 9.64330e-01 3.44760e-01
+YKL181W PRS1 -0.167 -0.233 0.112 6.27120e-03 7.89400e-04 1.44060e-01
+YGR072W UPF3 0.245 -0.471 0.787 4.10450e-04 7.51780e-04 1.37130e-05</screen><para>This indicates that there is data for three experiments: gal1RG, gal4RG, and gal80R. These names appear two times in the header line: the first time gives the expression values, and the second gives the significance measures. For instance, the second line tells us that in Experiment gal1RG, the gene YHR051W has an expression value of -0.034 with significance measure 3.75720e-01. </para><para>Some variatio [...]
+YHR051W COX6 -0.034 0.111 -0.304 3.75720e-01 1.56240e-02 7.91340e-06
+YHR124W NDT80 -0.090 0.007 -0.348 2.71460e-01 9.64330e-01 3.44760e-01
+YKL181W PRS1 -0.167 -0.233 0.112 6.27120e-03 7.89400e-04 1.44060e-01</screen><para><emphasis role="strong">Option B.</emphasis> </para><para>Step 1. After loading the network, load the node attribute file <code>sampleData/gal.probeset.na</code>, using File → Import → Node attributes... . This file is shown in part below: </para><screen format="linespecific">Probeset
+YHR051W = probeset2
+YHR124W = probeset3
+YKL181W = probeset4</screen><para>Step 2. After loading the node attribute file, select the expression data file <code>sampleData.galExpPvals.probeset.pvals</code>, shown in part below: </para><screen format="linespecific">GENE COMMON gal1RG gal4RG gal80R gal1RG gal4RG gal80R
+probeset2 COX6 -0.034 0.111 -0.304 3.75720e-01 1.56240e-02 7.91340e-06
+probeset3 NDT80 -0.090 0.007 -0.348 2.71460e-01 9.64330e-01 3.44760e-01
+probeset4 PRS1 -0.167 -0.233 0.112 6.27120e-03 7.89400e-04 1.44060e-01</screen><para>After selecting this file, in the field labeled "Assign values to nodes using...", select Probeset. You will see that this loads exactly the same expression data as in Case 1, but provides extra flexibility in case the node name cannot be used as an identifier. </para></section><section id="Detailed file format (Advanced users)"><title>Detailed file format (Advanced users)</title><para>In all expression [...]
+
+<text> <text> cond1 cond2 ...
+
+<tab><tab>RATIOS<tab><tab>...LAMBDAS</screen><para>The first format specifies that both expression ratios and significance values are included in the file. The first two text tokens (in angled brackets) contain names for each gene, such as the formal and common gene names. The <code>condX</code> token set specifies the names of the experimental conditions; these columns will contain ratio values. This list of condition names must then be duplicated exactly, each s [...]
+Node2
+Node3
+...</screen></section></section><section id="Editing Networks"><title><ulink url="http://cytoscape.wodaklab.org/wiki/Cytoscape_User_Manual/wiki/Cytoscape_User_Manual/Network_Editor">Editing Networks</ulink></title><para>Using Cytoscape's Editor, you can build and modify networks interactively by dragging and dropping nodes and edges from a palette onto the main network view window. The palette contains a set of shapes (for nodes) and arrows (for edges). The shapes on the palette are defi [...]
+ GO 7582 physiological processes
+ GO 8152 metabolism
+ GO 44238 primary metabolism
+ GO 19538 protein metabolism
+ GO 6412 protein biosynthesis</screen><para><emphasis role="strong">Graphical View of GO Term 6412: protein biosynthesis</emphasis> </para><para><inlinemediaobject><imageobject><imagedata fileref="images/ontology_dag1.png"/></imageobject><textobject><phrase>ontology_dag1.png</phrase></textobject></inlinemediaobject> </para><para>Cytoscape can use this ontology DAG (Directed Acyclic Graph) to annotate objects in networks. The Ontology Server (originally called "BioDataServer") is [...]
+date: 27:11:2006 17:12
+saved-by: midori
+auto-generated-by: OBO-Edit 1.002
+subsetdef: goslim_generic "Generic GO slim"
+subsetdef: goslim_goa "GOA and proteome slim"
+subsetdef: goslim_plant "Plant GO slim"
+subsetdef: goslim_yeast "Yeast GO slim"
+subsetdef: gosubset_prok "Prokaryotic GO subset"
+default-namespace: gene_ontology
+remark: cvs version: $Revision: 5.49 $
+
+[Term]
+id: GO:0000001
+name: mitochondrion inheritance
+namespace: biological_process
+def: "The distribution of mitochondria, including the mitochondrial genome, into daughter cells after mitosis or meiosis, mediated by interactions between mitochondria and the cytoskeleton." [GOC:mcc, PMID:10873824, PMID:11389764]
+synonym: "mitochondrial inheritance" EXACT []
+is_a: GO:0048308 ! organelle inheritance
+is_a: GO:0048311 ! mitochondrion distribution
+
+[Term]
+id: GO:0000002
+name: mitochondrial genome maintenance
+namespace: biological_process
+def: "The maintenance of the structure and integrity of the mitochondrial genome." [GOC:ai]
+is_a: GO:0007005 ! mitochondrion organization and biogenesis</screen></section><section id="Default List of Ontologies"><title>Default List of Ontologies</title><para>Cytoscape provides a list of ontologies available in OBO format. If an Internet connection is available, Cytoscape will import ontology and annotation files directly from the remote source. The table below lists the included ontologies. </para><informaltable><tgroup cols="2"><colspec colname="col_0"/><colspec colname="col [...]
+SGD S000005275 AAD14 GO:0008372 SGD_REF:S000069584 ND C aryl-alcohol dehydrogenase (putative) YNL331C gene taxon:4932 20010119 SGD</screen></section></section><section id="Node Name Mapping"><title>Node Name Mapping</title><para>If you have a network file and an attribute file, they should have a common key to map attributes onto network data. If those two do not have a common key, you need to do an extra step to add [...]
+node_3 pp node_1
+node_2 pp node_3</screen><para>and you want to annotate this network with <emphasis>Ontology A</emphasis>, which is an ontology DAG available in OBO format. In this case, you need an annotation table file that looks like this: </para><screen format="linespecific">node_1 OA_0000232
+node_2 OA_0000441
+node_3 OA_0000702</screen><para>where <emphasis>OA_***</emphasis> represents an ontology term ID. This example is a file with the minimum necessary number of columns; however, you can include additional columns that will appear as additional node attributes. </para><para>Some ontologies will be used to annotate edges or networks. For example, the <ulink url="http://obo.sourceforge.net/cgi-bin/detail.cgi?psi-mi">Protein-protein interaction ontology</ulink> is a controlled set of terms [...]
+node_3 (pp) node_1 MI:0046
+node_2 (pp) node_3 MI:0346</screen><para><inlinemediaobject><imageobject><imagedata fileref="images/ontology_import_custom1.png"/></imageobject><textobject><phrase>ontology_import_custom1.png</phrase></textobject></inlinemediaobject> </para><para>The basic operation of the Ontology and Annotation Import function is the same as that of the Attribute Table Import. The main difference is that you need to specify an additional key for mapping: </para><para><inlinemediaobject><imageobject>< [...]
+0003673 = Gene_Ontology
+0003674 = molecular_function [partof: 0003673 ]
+0008435 = anticoagulant [isa: 0003674 ]
+0016172 = antifreeze [isa: 0003674 ]
+0016173 = ice nucleation inhibitor [isa: 0016172 ]
+0016209 = antioxidant [isa: 0003674 ]
+0045174 = glutathione dehydrogenase (ascorbate) [isa: 0009491 0015038 0016209 0016672 ]
+0004362 = glutathione reductase (NADPH) [isa: 0015038 0015933 0016209 0016654 ]
+0017019 = myosin phosphatase catalyst [partof: 0017018 ]
+...</screen><para>A second example (KEGG pathway ontology): </para><screen format="linespecific">(curator=KEGG) (type=Metabolic Pathways)
+90001 = Metabolism
+80001 = Carbohydrate Metabolism [isa: 90001 ]
+80003 = Lipid Metabolism [isa: 90001 ]
+80002 = Energy Metabolism [isa: 90001 ]
+80004 = Nucleotide Metabolism [isa: 90001 ]
+80005 = Amino Acid Metabolism [isa: 90001 ]
+80006 = Metabolism of Other Amino Acids [isa: 90001 ]
+80007 = Metabolism of Complex Carbohydrates [isa: 90001 ]
+...</screen><para>The format has these required features: </para><itemizedlist><listitem><para>The first line contains two parenthesized assignments for <code>curator</code> and <code>type</code>. In the GO example above, the ontology file (which is created from the XML that GO provides) nests all three specific ontologies (molecular function, biological process, cellular component) below the 'root' ontology, named 'Gene_Ontology'. <code>(type=all)</code> tells you that all three ontolog [...]
+YMR056C = 0006854
+YBR085W = 0006854
+YJR155W = 0006081
+...</screen><para>and from KEGG: </para><screen format="linespecific">(species=Mycobacterium tuberculosis) (type=Metabolic Pathways) (curator=KEGG)
+RV0761C = 10
+RV0761C = 71
+RV0761C = 120
+RV0761C = 350
+RV0761C = 561
+RV1862 = 10
+...</screen><para>The format has these required features: </para><itemizedlist><listitem><para>The first line contains three parenthesized assignments, for <code>species</code>, <code>type</code> and <code>curator</code>. In the example just above, the annotation file (created for budding yeast from the flat text file maintained by SGD for the Gene Ontology project and available both at their web site and at GO's) shows three yeast ORFs annotated for biological process with respect to GO [...]
+annotation=yeastBiologicalProcess.txt
+annotation=yeastMolecularFunction.txt
+annotation=yeastCellularComponent.txt</screen><para>Use the Cytoscape <code>-b</code> command line argument to specify the annotation manifest file to read (e.g. <code>-b manifest</code>). Please note that the <code>-s</code> switch, which sets the default species for your data, is required to exactly match the species named in any annotation file you wish to use. </para></section></section><section id="Getting and Reformatting GO Data"><title>Getting and Reformatting GO Data</title><par [...]
+ python parseGoTermsToFlatFile.py go-YYYYMM-termdb.xml > goOntology.txt</screen><para>(see below for Python script listing) </para></section><section id="Obtain the association file for your organism"><title>Obtain the association file for your organism</title><para>GO maintains a list of association files for many organisms; these files associate genes with GO terms. The next step is to get the file for the organism(s) you are interested in, and parse it into the form Cytoscape needs [...]
+SPTR O00115 DRN2_HUMAN GO:0004519 GOA:spkw IEA F Deoxyribonuclease II precursor IPI00010348 protein taxon:9606 20020425 SPTR
+SPTR O00115 DRN2_HUMAN GO:0004531 PUBMED:9714827 TAS F Deoxyribonuclease II precursor IPI00010348 protein taxon:9606 SPTR
+...</screen><para>Note that line wrapping has occurred here, so each line of the actual file is wrapped to two lines. The goal is to create from these lines the following lines: </para><screen format="linespecific">(species=Homo sapiens) (type=Molecular Function) (curator=GO)
+IPI00010348 = 0003677
+IPI00010348 = 0004519
+IPI00010348 = 0004531
+...</screen><para>or </para><screen format="linespecific">(species=Homo sapiens) (type=Biological Process) (curator=GO)
+NP_001366 = 0006259
+NP_001366 = 0006915
+NP_005289 = 0007186
+NP_647593 = 0006899
+...</screen><para>The first sample contains molecular function annotations for proteins, and each protein is identified by its IPI number. IPI is the International Protein Index, which maintains cross references to the main databases for human, mouse and rat proteomes. The second sample contains biological process annotation, and each protein is identified by its NP (RefSeq) number. These two naming systems, IPI and RefSeq, are two of many that you can use to define canonical names whe [...]
+SP O00116 IPI00010349 ENSP00000324567;ENSP00000264167; NP_003650; CAA70591; 327,AGPS 8540,AGPS
+SP O00124 IPI00010353 ENSP00000265616;ENSP00000322580; NP_005662; BAA18958;BAA18959;AAH20694; 7993,D8S2298E
+...</screen><para>Note that line wrapping has occurred here – each line in this example starts with the letters SP. See the README file for more information (<ulink url="ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/HUMAN/README"/>). </para><para>Finally, run the script to create your three annotation files for human proteins: </para><itemizedlist><listitem><para><code>bioproc.anno</code> (GO biological process annotation) </para></listitem><listitem><para><code>molfunc.anno</code> (GO molecu [...]
+# Cytoscape flat file
+#-----------------------------------------------------------------------------------
+# RCS: $Revision: 1.3 $ $Date: 2003/05/18 00:38:43 $
+#-----------------------------------------------------------------------------------
+import re, pre, sys
+#-----------------------------------------------------------------------------------
+def flatFilePrint (id, name, isaIDs, partofIDs):
+ isa = ''
+ if (len (isaIDs) > 0):
+ isa = '[isa: '
+ for isaID in isaIDs:
+ isa += isaID
+ isa += ' '
+ isa += ']'
+ partof = ''
+ if (len (partofIDs) > 0):
+ partof = '[partof: '
+ for partofID in partofIDs:
+ partof += partofID
+ partof += ' '
+ partof += ']'
+ result = '~np~%~/np~s = ~np~%~/np~s ~np~%~/np~s ~np~%~/np~s' ~np~%~/np~ (id, name, isa, partof)
+ result = result.strip ()
+ if (result == 'isa = isa' or result == 'partof = partof'):
+ print >> sys.stderr, 'meaningless term: ~np~%~/np~s' ~np~%~/np~ result
+ else:
+ print result
+#-----------------------------------------------------------------------------------
+if (len (sys.argv) != 2):
+ print 'usage: ~np~%~/np~s <someFile.xml>' ~np~%~/np~ sys.argv [0]
+ sys.exit ();
+inputFilename = sys.argv [1];
+print >> sys.stderr, 'reading ~np~%~/np~s...' ~np~%~/np~ inputFilename
+text = open (inputFilename).read ()
+print >> sys.stderr, 'read ~np~%~/np~d characters' ~np~%~/np~ len (text)
+regex = '<go:term .*?>(.*?)</go:term>';
+cregex = pre.compile (regex, re.DOTALL) # . matches newlines
+m = pre.findall (cregex, text)
+print >> sys.stderr, 'number of go terms: ~np~%~/np~d' ~np~%~/np~ len (m)
+regex2 = '<go:accession>GO:(.*?)</go:accession>.*?<go:name>(.*?)</go:name>'
+cregex2 = re.compile (regex2, re.DOTALL)
+regex3 = '<go:isa\s*rdf:resource="http://www.geneontology.org/go#GO:(.*?)"\s*/>'
+cregex3 = re.compile (regex3, re.DOTALL)
+regex4 = '<go:part-of\s*rdf:resource="http://www.geneontology.org/go#GO:(.*?)"\s*/>'
+cregex4 = re.compile (regex4, re.DOTALL)
+goodElements = 0
+badElements = 0
+print '(curator=GO) (type=all)'
+for term in m:
+ m2 = re.search (cregex2, term)
+ if (m2):
+ goodElements += 1;
+ id = m2.group (1)
+ name = m2.group (2)
+ isaIDs = []
+ m3 = re.findall (cregex3, term);
+ for ref in m3:
+ isaIDs.append (ref)
+ m4 = re.findall (cregex4, term);
+ partofIDs = []
+ for ref in m4:
+ partofIDs.append (ref)
+ flatFilePrint (id, name, isaIDs, partofIDs)
+ else:
+ badElements += 1;
+ print >> sys.stderr, 'no match to m2...'
+ print >> sys.stderr, "---------------\n~np~%~/np~s\n------------------" ~np~%~/np~ term
+print >> sys.stderr, 'goodElements ~np~%~/np~d' ~np~%~/np~ goodElements
+print >> sys.stderr, 'badElements ~np~%~/np~d' ~np~%~/np~ badElements
+#--------------------------------------</screen><para>Script 2 - parseAssignmentsToFlatFileFromGoaProject.py </para><screen format="linespecific">import sys
+#-----------------------------------------------------------------------------------
+def fixCanonicalName (rawName):
+# for instance, trim 'YBR085W|ANC3' to 'YBR085W'
+ bar = rawName.find ('|')
+ if (bar < 0):
+ return rawName
+ return rawName [:bar]
+#-----------------------------------------------------------------------------------
+def fixGoID (rawID):
+ bar = rawID.find (':') + 1
+ return rawID [bar:]
+#-----------------------------------------------------------------------------------
+def readGoaXrefFile (filename):
+ lines = open (filename).read().split ('\n')
+ result = {}
+ for line in lines:
+ if (len (line) < 10):
+ continue
+ tokens = line.split ('\t')
+ ipi = tokens [2]
+ np = tokens [5]
+ semicolon = np.find (';')
+ if (semicolon >= 0):
+ np = np [:semicolon]
+ if (len (ipi) > 0 and len (np) > 0):
+ result [ipi] = np
+ return result
+#-----------------------------------------------------------------------------------
+if (len (sys.argv) != 3):
+ print 'error! parse <gene_associations file from GO> <goa xrefs file> '
+ sys.exit ()
+associationFilename = sys.argv [1];
+xrefsFilename = sys.argv [2]
+species = 'Homo sapiens'
+ipiToNPHash = readGoaXrefFile (xrefsFilename)
+tester = 'IPI00099416'
+print 'hash size: ~np~%~/np~d' ~np~%~/np~ len (ipiToNPHash)
+print 'test map: ~np~%~/np~s -> NP_054861: ~np~%~/np~s ' ~np~%~/np~ (tester, ipiToNPHash [tester])
+bioproc = open ('bioproc.txt', 'w')
+molfunc = open ('molfunc.txt', 'w')
+cellcomp = open ('cellcomp.txt', 'w')
+bioproc.write ('(species=~np~%~/np~s) (type=Biological Process) (curator=GO)\n' ~np~%~/np~ species)
+molfunc.write ('(species=~np~%~/np~s) (type=Molecular Function) (curator=GO)\n' ~np~%~/np~ species);
+cellcomp.write ('(species=~np~%~/np~s) (type=Cellular Component) (curator=GO)\n' ~np~%~/np~ species);
+lines=open(associationFilename).read().split('\n')
+sys.stderr.write ('found ~np~%~/np~d lines\n' ~np~%~/np~ len (lines))
+
+for line in lines:
+ if (line.find ('!') == 0 or len (line) < 2):
+ continue
+ tokens = line.split ('\t')
+ goOntology = tokens [8]
+ goIDraw = tokens [4]
+ goID = goIDraw.split (':')[1]
+ ipiName = fixCanonicalName (tokens [10])
+ if (len (ipiName) < 1):
+ continue
+
+
+ if (not ipiToNPHash.has_key (ipiName)):
+ continue
+ refseqName = ipiToNPHash [ipiName]
+ printName = refseqName
+ #printName = ipiName
+ if (ipiName == tester):
+ print '~np~%~/np~s (~np~%~/np~s) has go term ~np~%~/np~s' ~np~%~/np~ (tester, printName, goID)
+ if (goOntology == 'C'):
+ cellcomp.write ('~np~%~/np~s = ~np~%~/np~s\n' ~np~%~/np~ (printName, goID))
+ elif (goOntology == 'P'):
+ bioproc.write ('~np~%~/np~s = ~np~%~/np~s\n' ~np~%~/np~ (printName, goID))
+ elif (goOntology == 'F'):
+ molfunc.write ('~np~%~/np~s = ~np~%~/np~s\n' ~np~%~/np~ (printName, goID))
+#-----------------------------------------------------------------------------------</screen></section></section><section id="Appendix B: GNU Lesser General Public License"><title><ulink url="http://cytoscape.wodaklab.org/wiki/Cytoscape_User_Manual/wiki/Cytoscape_User_Manual/LGPL_License">Appendix B: GNU Lesser General Public License</ulink></title><para>GNU LESSER GENERAL PUBLIC LICENSE </para><itemizedlist><listitem override="none"><para>Version 2.1, February 1999 Copyright (C) 1991, 1 [...]
+-Xss10M</screen><para>This file allocates a maximum of 5GiB of heap memory and 10MiB of stack space per thread. </para><para><emphasis role="strong">Option B: Using the Cytoscape icon (Windows and/or Linux systems)</emphasis> </para><para>Just like with Option A, you can use the Cytoscape.vmoptions file. The problem with Windows is that the lines need to be terminated with a single line feed character (a.k.a. a "newline" character) and must not contain any carriage return characters. T [...]
\ No newline at end of file
diff --git a/corelibs/docs/src/main/assembly/html.xml b/corelibs/docs/src/main/assembly/html.xml
new file mode 100644
index 0000000..19c56bb
--- /dev/null
+++ b/corelibs/docs/src/main/assembly/html.xml
@@ -0,0 +1,16 @@
+<assembly xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0 http://maven.apache.org/xsd/assembly-1.1.0.xsd">
+ <id>html</id>
+ <formats>
+ <format>zip</format>
+ </formats>
+ <includeBaseDirectory>false</includeBaseDirectory>
+ <fileSets>
+ <fileSet>
+ <directory>${project.build.directory}/docbkx/html</directory>
+ <outputDirectory>/</outputDirectory>
+ <fileMode>0644</fileMode>
+ </fileSet>
+ </fileSets>
+</assembly>
diff --git a/corelibs/docs/src/main/assembly/javahelp.xml b/corelibs/docs/src/main/assembly/javahelp.xml
new file mode 100644
index 0000000..dc84e5b
--- /dev/null
+++ b/corelibs/docs/src/main/assembly/javahelp.xml
@@ -0,0 +1,16 @@
+<assembly xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0 http://maven.apache.org/xsd/assembly-1.1.0.xsd">
+ <id>javahelp</id>
+ <formats>
+ <format>zip</format>
+ </formats>
+ <includeBaseDirectory>false</includeBaseDirectory>
+ <fileSets>
+ <fileSet>
+ <directory>${project.build.directory}/docbkx/javahelp</directory>
+ <outputDirectory>/</outputDirectory>
+ <fileMode>0644</fileMode>
+ </fileSet>
+ </fileSets>
+</assembly>
diff --git a/corelibs/docs/src/main/assembly/pdf.xml b/corelibs/docs/src/main/assembly/pdf.xml
new file mode 100644
index 0000000..eca1edc
--- /dev/null
+++ b/corelibs/docs/src/main/assembly/pdf.xml
@@ -0,0 +1,16 @@
+<assembly xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0 http://maven.apache.org/xsd/assembly-1.1.0.xsd">
+ <id>pdf</id>
+ <formats>
+ <format>zip</format>
+ </formats>
+ <includeBaseDirectory>false</includeBaseDirectory>
+ <fileSets>
+ <fileSet>
+ <directory>${project.build.directory}/docbkx/pdf</directory>
+ <outputDirectory>/</outputDirectory>
+ <fileMode>0644</fileMode>
+ </fileSet>
+ </fileSets>
+</assembly>
diff --git a/corelibs/docs/src/main/pdf/manual.pdf b/corelibs/docs/src/main/pdf/manual.pdf
new file mode 100644
index 0000000..5b27873
Binary files /dev/null and b/corelibs/docs/src/main/pdf/manual.pdf differ
diff --git a/corelibs/docs/xsl/add_id_to_section.xsl b/corelibs/docs/xsl/add_id_to_section.xsl
new file mode 100644
index 0000000..d10e846
--- /dev/null
+++ b/corelibs/docs/xsl/add_id_to_section.xsl
@@ -0,0 +1,19 @@
+<xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform">
+
+<xsl:import href="copy.xsl"/>
+
+<xsl:output method="xml" version="1.0" encoding="UTF-8"/>
+
+<xsl:template match="section">
+ <xsl:element name="section" use-attribute-sets="create-id">
+ <xsl:apply-templates/>
+ </xsl:element>
+</xsl:template>
+
+<xsl:attribute-set name="create-id">
+ <xsl:attribute name="id">
+ <xsl:value-of select="title"/>
+ </xsl:attribute>
+</xsl:attribute-set>
+
+</xsl:stylesheet>
diff --git a/corelibs/docs/xsl/copy.xsl b/corelibs/docs/xsl/copy.xsl
new file mode 100644
index 0000000..85467a2
--- /dev/null
+++ b/corelibs/docs/xsl/copy.xsl
@@ -0,0 +1,11 @@
+<xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform">
+
+<xsl:template match="node( ) | @*">
+ <xsl:copy>
+ <xsl:apply-templates select="@* | node( )"/>
+ </xsl:copy>
+</xsl:template>
+
+</xsl:stylesheet>
+
+
diff --git a/corelibs/docs/xsl/docbook-xsl-1.75.2.zip b/corelibs/docs/xsl/docbook-xsl-1.75.2.zip
new file mode 100644
index 0000000..f62fa97
Binary files /dev/null and b/corelibs/docs/xsl/docbook-xsl-1.75.2.zip differ
diff --git a/corelibs/docs/xsl/filter_index.xsl b/corelibs/docs/xsl/filter_index.xsl
new file mode 100644
index 0000000..a3606a2
--- /dev/null
+++ b/corelibs/docs/xsl/filter_index.xsl
@@ -0,0 +1,10 @@
+<xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform">
+
+<xsl:import href="copy.xsl"/>
+
+<xsl:output method="xml" version="1.0" encoding="UTF-8"/>
+
+<!-- filter out the index view since we don't create index information -->
+<xsl:template match="view[name='Index']"/>
+
+</xsl:stylesheet>
diff --git a/corelibs/docs/xsl/remove_revision_history.xsl b/corelibs/docs/xsl/remove_revision_history.xsl
new file mode 100644
index 0000000..aba51c3
--- /dev/null
+++ b/corelibs/docs/xsl/remove_revision_history.xsl
@@ -0,0 +1,11 @@
+<xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform">
+
+<xsl:import href="copy.xsl"/>
+
+<xsl:output method="xml" version="1.0" encoding="UTF-8"/>
+
+<xsl:template match="revhistory"/>
+
+</xsl:stylesheet>
+
+
diff --git a/corelibs/docs/xsl/strip_images.xsl b/corelibs/docs/xsl/strip_images.xsl
new file mode 100644
index 0000000..fbb7562
--- /dev/null
+++ b/corelibs/docs/xsl/strip_images.xsl
@@ -0,0 +1,36 @@
+<?xml version="1.0"?>
+<xsl:stylesheet version="1.0"
+ xmlns="http://www.cs.rpi.edu/HTML"
+ xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
+ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+ xmlns:dc="http://purl.org/dc/elements/1.1/"
+ xmlns:ns1="http://www.w3.org/1999/xlink"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ >
+<xsl:output method='text' version='1.0' encoding='UTF-8' indent='yes'/>
+
+
+
+
+
+<xsl:template match="/">
+<xsl:text><?xml version="1.0"?>
+<project name="ImageStrip" default="strip">
+<target name="strip">
+</xsl:text>
+ <xsl:apply-templates select="//inlinemediaobject/imageobject/imagedata"/>
+<xsl:text>
+</target>
+</project>
+</xsl:text>
+</xsl:template>
+
+<xsl:template match="inlinemediaobject/imageobject/imagedata">
+ <get src="<xsl:value-of select="@fileref"/>" dest="<xsl:value-of select="@fileref"/>" ignoreerrors="yes" usetimestamp="yes"/>
+<xsl:text>
+</xsl:text>
+</xsl:template>
+
+</xsl:stylesheet>
+
+
diff --git a/corelibs/equations/pom.xml b/corelibs/equations/pom.xml
new file mode 100644
index 0000000..0687a45
--- /dev/null
+++ b/corelibs/equations/pom.xml
@@ -0,0 +1,41 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>parent</artifactId>
+ <version>2.8.4-SNAPSHOT</version>
+ </parent>
+
+ <artifactId>equations</artifactId>
+ <packaging>jar</packaging>
+
+ <name>equations</name>
+
+ <!-- bootstrap for cytoscape dependencies, namely the parent POM snapshots -->
+ <repositories>
+ <repository>
+ <id>cytoscape_snapshots</id>
+ <snapshots>
+ <enabled>true</enabled>
+ </snapshots>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <name>Cytoscape Snapshots</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/</url>
+ </repository>
+ <repository>
+ <id>cytoscape_releases</id>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ <name>Cytoscape Releases</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/releases/</url>
+ </repository>
+ </repositories>
+
+</project>
+
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/AbstractFunction.java b/corelibs/equations/src/main/java/org/cytoscape/equations/AbstractFunction.java
new file mode 100644
index 0000000..7a03342
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/AbstractFunction.java
@@ -0,0 +1,234 @@
+/*
+ File: AbstractFunction.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations;
+
+
+import java.util.Iterator;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Set;
+import java.util.TreeSet;
+
+
+public abstract class AbstractFunction implements Function {
+ final private ArgDescriptor[] argDescriptors;
+
+ protected AbstractFunction(final ArgDescriptor[] argDescriptors) {
+ this.argDescriptors = argDescriptors;
+
+ // Ensure that optional args are never followed by nonoptional args:
+ boolean lastArgWasOptional = false;
+ for (int i = 0; i < argDescriptors.length; ++i) {
+ final boolean currentArgIsOptional = argDescriptors[i].isOptional();
+ if (lastArgWasOptional && !currentArgIsOptional)
+ throw new IllegalArgumentException("invalid argument specification for "
+ + getName() + "() optional argument "
+ + argDescriptors[i - 1].getArgName()
+ + " is followed by non-optional argument "
+ + argDescriptors[i].getArgName() + "!");
+ lastArgWasOptional = currentArgIsOptional;
+ }
+
+ // Ensure that no two args have the same name:
+ final Set<String> alreadySeen = new TreeSet<String>();
+ for (final ArgDescriptor argDescriptor : argDescriptors) {
+ final String argName = argDescriptor.getArgName();
+ if (alreadySeen.contains(argName))
+ throw new IllegalArgumentException("duplicate argument name "
+ + argName + " for " + getName()
+ + "() specified multiple times!");
+ alreadySeen.add(argName);
+ }
+ }
+
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public abstract String getName();
+
+ /**
+ * Used to provide help for users. Unlike getUsageDescription(), this is an informal English description,
+ * like "Calculates the sine of its argument."
+ *
+ * @return a description of what this function does
+ */
+ public abstract String getFunctionSummary();
+
+ /**
+ * Used to provide help for users. Unlike getFunctionSummary(), this describes how to call this function,
+ * like "Call with SIN(number)."
+ *
+ * @return a description of how to use this function
+ */
+ public final String getUsageDescription() {
+ final StringBuilder usage = new StringBuilder("Call with ");
+ usage.append(getName());
+ usage.append('(');
+
+ int optArgCount = 0;
+ boolean isFirst = true;
+ for (final ArgDescriptor argDescriptor : argDescriptors) {
+ if (argDescriptor.isOptional()) {
+ usage.append(isFirst ? "[" : " [,");
+ ++optArgCount;
+ } else
+ usage.append(isFirst ? "" : " ,");
+ usage.append(argDescriptor.getArgName());
+
+ isFirst = false;
+ }
+
+ for (int i = 0; i < optArgCount; ++i)
+ usage.append(']');
+
+ usage.append(").");
+
+ return usage.toString();
+ }
+
+ /**
+ * @return the static return type of this function, Object.class, Double.cLass, String.class, or Boolean.class.
+ * If the static return type is Object.class, the dynamic return type will be one of Double.cLass, String.class, or Boolean.class
+ * and will depend on the arguments passed to the function!
+ *
+ * Note, this is used by external tools used to filter a list of functions based on what a valid return type might be.
+ * In Cytoscape it is used in the attribute browser's formula builder.
+ */
+ public abstract Class getReturnType();
+
+ /**
+ * @return the return type for this function (Double.class, String.class, or Boolean.class)
+ * or null if the args passed in had the wrong arity or a type mismatch
+ *
+ * Note that this is different from getReturnType() in that it will never return the wildcard Object.class.
+ * It is used by the parser which knows the actual type of the arguments in any given call to this function.
+ */
+ protected final boolean argTypesAreValid(final Class[] argTypes) {
+ int i = 0;
+
+ int currentArgCount = 0;
+ ArgDescriptor currentArgDescriptor = null;
+ for (final Class argType : argTypes) {
+ if (currentArgCount == 0) {
+ // Too many actual arguments?
+ if (i == argDescriptors.length)
+ return false;
+
+ currentArgDescriptor = argDescriptors[i++];
+ }
+
+ if (!currentArgDescriptor.isCompatibleWith(argType))
+ return false;
+ else if (currentArgDescriptor.acceptsMultipleArgs())
+ ++currentArgCount;
+ else // We have a single matching argument and need to move on to the next arg descriptor.
+ currentArgCount = 0;
+
+ }
+
+ // Everything was ok if we either used up all the arg descriptors or if the
+ // current arg descriptor represents an optional argument:
+ return i == argDescriptors.length || argDescriptors[i].isOptional();
+ }
+
+ /**
+ * @return the return type for this function (Double.class, String.class, or Boolean.class)
+ * or null if the args passed in had the wrong arity or a type mismatch
+ *
+ * Note that this is different from getReturnType() in that it will never return the wildcard Object.class.
+ * It is used by the parser which knows the actual type of the arguments in any given call to this function.
+ */
+ public final Class validateArgTypes(final Class[] argTypes) {
+ return argTypesAreValid(argTypes) ? getReturnType() : null;
+ }
+
+ /**
+ * Used to invoke this function.
+ * @param args the function arguments which must correspond in type and number to what getParameterTypes() returns.
+ * @return the result of the function evaluation. The actual type of the returned object will be what getReturnType() returns.
+ * @throws ArithmeticException thrown if a numeric error, e.g. a division by zero occurred.
+ * @throws IllegalArgumentException thrown for any error that is not a numeric error, for example if a function only accepts positive numbers and a negative number was passed in.
+ */
+ public abstract Object evaluateFunction(final Object[] args) throws FunctionError;
+
+ /**
+ * Used with the equation builder.
+ *
+ * @param leadingArgs the types of the arguments that have already been selected by the user.
+ * @return the set of arguments (must be a collection of String.class, Long.class, Double.class,
+ * Boolean.class and List.class) that are candidates for the next argument. A null return
+ * indicates that no further arguments are valid. Please note that if the returned set
+ * contains a null, this indicates an optional additional argument.
+ */
+ public final List<Class> getPossibleArgTypes(final Class[] leadingArgs) {
+ int i = 0;
+
+ int currentArgCount = 0;
+ ArgDescriptor currentArgDescriptor = null;
+ for (final Class leadingArg : leadingArgs) {
+ if (currentArgCount == 0) {
+ // Too many actual arguments?
+ if (i == argDescriptors.length)
+ throw new IllegalStateException("number of arguments is too large!");
+
+ currentArgDescriptor = argDescriptors[i++];
+ }
+
+ if (!currentArgDescriptor.isCompatibleWith(leadingArg)) {
+ throw new IllegalStateException("incompatible argument type!");
+ } else if (currentArgDescriptor.acceptsMultipleArgs())
+ ++currentArgCount;
+ else // We have a single matching argument and need to move on to the next arg descriptor.
+ currentArgCount = 0;
+ }
+
+ if (currentArgCount == 0 && i == argDescriptors.length)
+ return null;
+
+ final List<Class> possibleNextArgs = new LinkedList<Class>();
+ if (currentArgCount > 0) { // => We're dealing w/ an argument descriptor that can take multiple actual arguments.
+ for (final Class type : currentArgDescriptor.getCompatibleTypes())
+ possibleNextArgs.add(type);
+ if (i == argDescriptors.length)
+ possibleNextArgs.add(null);
+ }
+
+ if (i < argDescriptors.length) {
+ final ArgDescriptor nextArgDesc = argDescriptors[i];
+ for (final Class type : nextArgDesc.getCompatibleTypes())
+ possibleNextArgs.add(type);
+ if (nextArgDesc.isOptional())
+ possibleNextArgs.add(null);
+ }
+
+ return possibleNextArgs;
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/ArgDescriptor.java b/corelibs/equations/src/main/java/org/cytoscape/equations/ArgDescriptor.java
new file mode 100644
index 0000000..fce2045
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/ArgDescriptor.java
@@ -0,0 +1,107 @@
+/*
+ File: ArgDescriptor.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations;
+
+
+import java.util.List;
+import java.util.ArrayList;
+
+
+/**
+ * A class describing a function argument.
+ */
+public class ArgDescriptor {
+ private ArgType argType;
+ private String argName;
+ private String description;
+
+ public ArgDescriptor(final ArgType argType, final String argName, final String description) {
+ this.argType = argType;
+ this.argName = argName;
+ this.description = description;
+ }
+
+ public ArgType getArgType() { return argType; }
+ public String getArgName() { return argName; }
+ public String getDescription() { return description; }
+ public boolean isOptional() { return argType.isOptional(); }
+
+ public boolean isCompatibleWith(final Class type) {
+ if (FunctionUtil.isSomeKindOfList(type))
+ return isCompatibleList(type);
+
+ for (final Class compatibleType : argType.getCompatibleTypes()) {
+ if (type == compatibleType)
+ return true;
+ }
+
+ return false;
+ }
+
+ /**
+ * @return true if "type" is a List type that specifies the element type otherwise we return false
+ */
+ private boolean isSpecificList(final Class type) {
+ return type == DoubleList.class || type == LongList.class || type == StringList.class || type == BooleanList.class;
+ }
+
+ /**
+ * @return true if "listType", which must be some type of List is a type compatible with this argument descriptor
+ */
+ private boolean isCompatibleList(final Class listType) {
+ // First we handle the case where "listType" is highly specific...
+ if (isSpecificList(listType)) {
+ for (final Class compatibleType : argType.getCompatibleTypes()) {
+ if (compatibleType == listType || compatibleType == List.class)
+ return true;
+ }
+ return false;
+ }
+
+ // ...and here we handle the case where we don't have anyt information about the argument types of "listType":
+ for (final Class compatibleType : argType.getCompatibleTypes()) {
+ if (FunctionUtil.isSomeKindOfList(compatibleType))
+ return true;
+ }
+
+ return false;
+ }
+
+ /**
+ * @return the types that are compatible with this argument
+ */
+ public Class[] getCompatibleTypes() {
+ return argType.getCompatibleTypes();
+ }
+
+ public boolean acceptsMultipleArgs() {
+ return argType.acceptsMultipleArgs();
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/ArgType.java b/corelibs/equations/src/main/java/org/cytoscape/equations/ArgType.java
new file mode 100644
index 0000000..8c59fe7
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/ArgType.java
@@ -0,0 +1,142 @@
+/*
+ File: ArgType.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations;
+
+
+import java.util.List;
+import java.util.ArrayList;
+
+
+/**
+ * An enum specifying a function argument type.
+ */
+public enum ArgType {
+ // opt. mult.args. compatible arg. types
+ //--------------------------------------------------------------------------------------------------------
+ /** An argument that can be converted to an integer. */
+ INT( false, false, new Class[] { Long.class, Double.class, String.class, Boolean.class }),
+
+ /** An argument that can be converted to a floating point value. */
+ FLOAT( false, false, new Class[] { Double.class, Long.class, String.class, Boolean.class }),
+
+ /** An argument that can be converted to a string. */
+ STRING( false, false, new Class[] { String.class, Double.class, Long.class, Boolean.class }),
+
+ /** An argument that can be converted to a boolean. */
+ BOOL( false, false, new Class[] { Boolean.class, Double.class, Long.class, String.class }),
+
+ /** Any scalar argument. */
+ ANY( false, false, new Class[] { Boolean.class, Double.class, Long.class, String.class }),
+
+ /** An non-empty sequence of arguments that consist of lists of integers and scalars that can be converted to an integer. */
+ INTS( false, true, new Class[] { LongList.class, Long.class, Double.class, String.class, Boolean.class }),
+
+ /** An non-empty sequence of arguments that consist of lists of floating point numbers and scalars that can be converted
+ to a floating point number. */
+ FLOATS( false, true, new Class[] { DoubleList.class, Double.class, Long.class, String.class, Boolean.class }),
+
+ /** An non-empty sequence of arguments that consist of lists of strings and scalars that can be converted to a string. */
+ STRINGS( false, true, new Class[] { StringList.class, String.class, Double.class, Long.class, Boolean.class }),
+
+ /** An non-empty sequence of arguments that consist of lists of booleans and scalars that can be converted to a boolean. */
+ BOOLS( false, true, new Class[] { BooleanList.class, Boolean.class, Double.class, Long.class, String.class }),
+
+ /** A singke integer argument. */
+ STRICT_INT( false, false, new Class[] { Long.class }),
+
+ /** A single floating point number argument. */
+ STRICT_FLOAT( false, false, new Class[] { Double.class }),
+
+ /** A single string argument. */
+ STRICT_STRING( false, false, new Class[] { String.class }),
+
+ /** A single boolean argument. */
+ STRICT_BOOL( false, false, new Class[] { Boolean.class }),
+
+ /** An optional integer argument. */
+ OPT_INT( true, false, new Class[] { Long.class, Double.class, String.class, Boolean.class}),
+
+ /** An optional floating point argument. */
+ OPT_FLOAT( true, false, new Class[] { Double.class, Long.class, String.class, Boolean.class }),
+
+ /** An optional string argument. */
+ OPT_STRING( true, false, new Class[] { String.class, Double.class, Long.class, Boolean.class }),
+
+ /** An optional boolean argument. */
+ OPT_BOOL( true, false, new Class[] { Boolean.class, Double.class, Long.class, String.class }),
+
+ /** Zero or more arguments that consist of lists of integers and scalars that can be converted to an integer. */
+ OPT_INTS( true, true, new Class[] { LongList.class, Long.class, Double.class, String.class, Boolean.class }),
+
+ /** Zero or more arguments that consist of lists of floating point numbers and scalars that can be converted
+ to a floating point number. */
+ OPT_FLOATS( true, true, new Class[] { DoubleList.class, Double.class, Long.class, String.class, Boolean.class }),
+
+ /** Zero or more arguments that consist of lists of strings and scalars that can be converted to a string. */
+ OPT_STRINGS( true, true, new Class[] { StringList.class, String.class, Double.class, Long.class, Boolean.class }),
+
+ /** Zero or more arguments that consist of lists of booleans and scalars that can be converted to a boolean. */
+ OPT_BOOLS( true, true, new Class[] { BooleanList.class, Boolean.class, Double.class, Long.class, String.class }),
+
+ /** An optional integer argument. */
+ OPT_STRICT_INT( true, false, new Class[] { Long.class }),
+
+ /** An optional floating point number argument. */
+ OPT_STRICT_FLOAT( true, false, new Class[] { Double.class }),
+
+ /** An optional string argument. */
+ OPT_STRICT_STRING(true, false, new Class[] { String.class }),
+
+ /** An optional boolean argument. */
+ OPT_STRICT_BOOL( true, false, new Class[] { Boolean.class }),
+
+ /** One or more lists with arbitrary member element types and/or one or more scalars. */
+ ANY_LIST( false, true, new Class[] { List.class, Double.class, Long.class, String.class, Boolean.class }),
+
+ /** A list with arbitrary member element types. */
+ STRICT_ANY_LIST( false, false, new Class[] { List.class }),
+
+ /** Zero or more lists with arbitrary member element types and/or zero or more scalars. */
+ OPT_ANY_LIST( true, true, new Class[] { List.class, Double.class, Long.class, String.class, Boolean.class });
+
+ private boolean isOptional;
+ private boolean acceptsMultipleArgs;
+ private Class[] compatibleTypes;
+
+ ArgType(final boolean isOptional, final boolean acceptsMultipleArgs, final Class[] compatibleTypes) {
+ this.isOptional = isOptional;
+ this.acceptsMultipleArgs = acceptsMultipleArgs;
+ this.compatibleTypes = compatibleTypes;
+ }
+
+ public boolean isOptional() { return isOptional; }
+ public boolean acceptsMultipleArgs() { return acceptsMultipleArgs; }
+ public Class[] getCompatibleTypes() { return compatibleTypes; }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/BooleanList.java b/corelibs/equations/src/main/java/org/cytoscape/equations/BooleanList.java
new file mode 100644
index 0000000..8956b5d
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/BooleanList.java
@@ -0,0 +1,44 @@
+/*
+ File: BooleanList.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations;
+
+
+import java.util.ArrayList;
+
+
+public class BooleanList extends ArrayList<Boolean> {
+ public static final long serialVersionUID = -39245160342061982L;
+
+ public BooleanList(final boolean[] booleans) {
+ ensureCapacity(booleans.length);
+ for (final boolean b : booleans)
+ add(b);
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/CodeAndSourceLocation.java b/corelibs/equations/src/main/java/org/cytoscape/equations/CodeAndSourceLocation.java
new file mode 100644
index 0000000..a46a948
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/CodeAndSourceLocation.java
@@ -0,0 +1,47 @@
+/*
+ File: CodeAndSourceLocation.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations;
+
+
+/**
+ * A node in the parse tree representing a binary operator.
+ */
+public class CodeAndSourceLocation {
+ private final Object code;
+ private final int sourceLocation;
+
+ public CodeAndSourceLocation(final Object code, final int sourceLocation) {
+ this.code = code;
+ this.sourceLocation = sourceLocation;
+ }
+
+ public Object getCode() { return code; }
+ public int getSourceLocation() { return sourceLocation; }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/DoubleList.java b/corelibs/equations/src/main/java/org/cytoscape/equations/DoubleList.java
new file mode 100644
index 0000000..eef3f7a
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/DoubleList.java
@@ -0,0 +1,44 @@
+/*
+ File: DoubleList.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations;
+
+
+import java.util.ArrayList;
+
+
+public class DoubleList extends ArrayList<Double> {
+ public static final long serialVersionUID = 9241560324069182L;
+
+ public DoubleList(final double[] numbers) {
+ ensureCapacity(numbers.length);
+ for (final double d : numbers)
+ add(d);
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/EqnCompiler.java b/corelibs/equations/src/main/java/org/cytoscape/equations/EqnCompiler.java
new file mode 100644
index 0000000..17e09f8
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/EqnCompiler.java
@@ -0,0 +1,85 @@
+/*
+ File: EqnCompiler.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations;
+
+
+import java.util.Map;
+import java.util.Stack;
+import org.cytoscape.equations.EqnParser;
+import org.cytoscape.equations.parse_tree.Node;
+
+
+public class EqnCompiler {
+ private EqnParser parser;
+ private Equation equation;
+ private String errorMsg;
+
+ public EqnCompiler() {
+ this.parser = Parser.getParser();
+ }
+
+ public boolean compile(final String equation, final Map<String, Class> attribNameToTypeMap) {
+ this.equation = null;
+ this.errorMsg = null;
+
+ if (!parser.parse(equation, attribNameToTypeMap)) {
+ errorMsg = parser.getErrorMsg();
+ return false;
+ }
+
+ final Node parseTree = parser.getParseTree();
+
+ final Stack<CodeAndSourceLocation> codeStack = new Stack<CodeAndSourceLocation>();
+ try {
+ parseTree.genCode(codeStack);
+ } catch (final IllegalStateException e) {
+ errorMsg = e.getCause().toString();
+ return false;
+ }
+
+ final Object[] code = new Object[codeStack.size()];
+ final int[] sourceLocations = new int[codeStack.size()];
+ for (int i = code.length - 1; i >= 0; --i) {
+ final CodeAndSourceLocation codeAndSourceLocation = codeStack.pop();
+ code[i] = codeAndSourceLocation.getCode();
+ sourceLocations[i] = codeAndSourceLocation.getSourceLocation();
+ }
+ this.equation = new Equation(equation, parser.getVariableReferences(),
+ parser.getDefaultValues(), code, sourceLocations,
+ parser.getType());
+
+ errorMsg = null;
+ return true;
+ }
+
+ public String getLastErrorMsg() { return errorMsg; }
+
+ public Equation getEquation() { return equation; }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/EqnParser.java b/corelibs/equations/src/main/java/org/cytoscape/equations/EqnParser.java
new file mode 100644
index 0000000..37b2624
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/EqnParser.java
@@ -0,0 +1,88 @@
+/*
+ File: EqnParser.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations;
+
+
+import java.util.Map;
+import java.util.Set;
+import org.cytoscape.equations.parse_tree.*;
+
+
+public interface EqnParser {
+ /**
+ * After registering an attribute function "func" it can be used in attribute equations.
+ * @param func the function that will be registered
+ * @throws IllegalArgumentException will be thrown if "func" is null or the function has previously been registered
+ */
+ public void registerFunction(final Function func) throws IllegalArgumentException;
+
+ /**
+ * @return the function associated with the name "functionName" or null if no such function exists
+ */
+ public Function getFunction(final String functionName);
+
+ /**
+ * @return the set of currently registered functions
+ */
+ public Set<Function> getRegisteredFunctions();
+
+ /**
+ * @param eqn a valid attribute equation which must start with an equal sign
+ * @param attribNameToTypeMap a list of existing attribute names and their types
+ * @return true if the parse succeeded otherwise false
+ */
+ public boolean parse(final String eqn, final Map<String, Class> attribNameToTypeMap);
+
+ /**
+ * @return the result type of the parsed equation if the parse succeeded, otherwise null
+ */
+ public Class getType();
+
+ /**
+ * If parse() failed, this will return the last error messages.
+ * @return the last error message of null
+ */
+ public String getErrorMsg();
+
+ /**
+ * @return all the variable names that have been detected in the most recently parsed equation
+ */
+ public Set<String> getVariableReferences();
+
+ /**
+ * @return a map from variable names to their default values, if any
+ */
+ public Map<String, Object> getDefaultValues();
+
+ /**
+ * @return the parse tree. Must only be called if parse() returns true!
+ */
+ public Node getParseTree();
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/EqnParserImpl.java b/corelibs/equations/src/main/java/org/cytoscape/equations/EqnParserImpl.java
new file mode 100644
index 0000000..1aa5331
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/EqnParserImpl.java
@@ -0,0 +1,510 @@
+/*
+ File: EqnParserImpl.java
+
+ Copyright (c) 2010-2011, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations;
+
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Map;
+import java.util.Set;
+import java.util.TreeMap;
+import java.util.TreeSet;
+import org.cytoscape.equations.parse_tree.*;
+
+
+class EqnParserImpl implements EqnParser {
+ private String formula;
+ private Tokeniser tokeniser;
+ private Map<String, Function> nameToFunctionMap;
+ private String lastErrorMessage;
+ private Node parseTree;
+ private Map<String, Class> variableNameToTypeMap;
+ private Set<String> variableReferences;
+ private Map<String, Object> defaultValues;
+ private Set<Function> registeredFunctions;
+
+ public EqnParserImpl() {
+ this.nameToFunctionMap = new HashMap<String, Function>();
+ this.registeredFunctions = new HashSet<Function>();
+ this.parseTree = null;
+ }
+
+ public void registerFunction(final Function func) throws IllegalArgumentException {
+ // Sanity check for the name of the function.
+ final String funcName = func.getName().toUpperCase();
+ if (funcName == null || funcName.equals(""))
+ throw new IllegalArgumentException("empty or missing function name!");
+
+ // Sanity check to catch duplicate function registrations.
+ if (nameToFunctionMap.get(funcName) != null)
+ throw new IllegalArgumentException("attempt at registering " + funcName + "() twice!");
+
+ nameToFunctionMap.put(funcName, func);
+ registeredFunctions.add(func);
+ }
+
+ /**
+ * @return the function associated with the name "functionName" or null if no such function exists
+ */
+ public Function getFunction(final String functionName) {
+ return nameToFunctionMap.get(functionName);
+ }
+
+ public Set<Function> getRegisteredFunctions() { return registeredFunctions; }
+
+ /**
+ * @param formula a valid formula which must start with an equal sign
+ * @param variableNameToTypeMap a list of existing variable names and their types
+ * @return true if the parse succeeded otherwise false
+ */
+ public boolean parse(final String formula, final Map<String, Class> variableNameToTypeMap) {
+ if (formula == null)
+ throw new NullPointerException("formula string must not be null!");
+ if (formula.length() < 1 || formula.charAt(0) != '=')
+ throw new NullPointerException("0: formula string must start with an equal sign!");
+
+ this.formula = formula;
+ this.variableNameToTypeMap = variableNameToTypeMap;
+ this.variableReferences = new TreeSet<String>();
+ this.defaultValues = new TreeMap<String, Object>();
+ this.tokeniser = new Tokeniser(formula.substring(1));
+ this.lastErrorMessage = null;
+
+ try {
+ parseTree = parseExpr();
+ final Token token = tokeniser.getToken();
+ final int tokenStartPos = tokeniser.getStartPos();
+ if (token != Token.EOS)
+ throw new IllegalStateException(
+ tokenStartPos
+ + ": premature end of expression: expected end-of-string, but found "
+ + token + "!");
+ } catch (final IllegalStateException e) {
+ lastErrorMessage = e.getMessage();
+ return false;
+ } catch (final ArithmeticException e) {
+ lastErrorMessage = e.getMessage();
+ return false;
+ } catch (final IllegalArgumentException e) {
+ lastErrorMessage = e.getMessage();
+ return false;
+ }
+
+ return true;
+ }
+
+ /**
+ * @return the result type of the parsed formula if the parse succeeded, otherwise null
+ */
+ public Class getType() { return parseTree == null ? null : parseTree.getType(); }
+
+ /**
+ * If parse() failed, this will return the last error messages.
+ * @return the last error message of null
+ */
+ public String getErrorMsg() { return lastErrorMessage; }
+
+ public Set<String> getVariableReferences() { return variableReferences; }
+
+ public Map<String, Object> getDefaultValues() { return defaultValues; }
+
+ /**
+ * @return the parse tree. Must only be called if parse() returns true!
+ */
+ public Node getParseTree() { return parseTree; }
+
+ //
+ // The actual parsing takes place here.
+ //
+
+ /**
+ * Implements expr --> term | term {+ term } | term {- term} | term {& term} | term compOp term.
+ */
+ private Node parseExpr() {
+ Node exprNode = parseTerm();
+
+ for (;;) {
+ final Token token = tokeniser.getToken();
+ final int sourceLocation = tokeniser.getStartPos();
+ if (token == Token.PLUS || token == Token.MINUS || token == Token.AMPERSAND) {
+ final Node term = parseTerm();
+ if (token == Token.PLUS || token == Token.MINUS)
+ exprNode = handleBinaryArithmeticOp(token, sourceLocation, exprNode, term);
+ else // String concatenation.
+ exprNode = new BinOpNode(sourceLocation, Token.AMPERSAND, exprNode, term);
+ }
+ else if (token.isComparisonOperator()) {
+ final Node term = parseTerm();
+ return handleComparisonOp(token, sourceLocation, exprNode, term); // No chaining for comparison operators!
+ } else {
+ tokeniser.ungetToken(token);
+ return exprNode;
+ }
+ }
+ }
+
+ /**
+ * Implements term --> power {* power} | power {/ power}
+ */
+ private Node parseTerm() {
+ Node termNode = parsePower();
+
+ for (;;) {
+ final Token token = tokeniser.getToken();
+ final int sourceLocation = tokeniser.getStartPos();
+ if (token == Token.MUL || token == Token.DIV) {
+ final Node powerNode = parsePower();
+ termNode = handleBinaryArithmeticOp(token, sourceLocation, termNode, powerNode);
+ }
+ else {
+ tokeniser.ungetToken(token);
+ return termNode;
+ }
+ }
+ }
+
+ /**
+ * Implements power --> factor | factor ^ power
+ */
+ private Node parsePower() {
+ Node powerNode = parseFactor();
+
+ final Token token = tokeniser.getToken();
+ final int sourceLocation = tokeniser.getStartPos();
+ if (token == Token.CARET) {
+ final Node rhs = parsePower();
+ powerNode = handleBinaryArithmeticOp(token, sourceLocation, powerNode, rhs);
+ }
+ else
+ tokeniser.ungetToken(token);
+
+ return powerNode;
+ }
+
+ /**
+ * Implements factor --> constant | variable_ref | "(" expr ")" | ("-"|"+") factor | func_call
+ */
+ private Node parseFactor() {
+ Token token = tokeniser.getToken();
+ int sourceLocation = tokeniser.getStartPos();
+
+ // 1. a constant
+ if (token == Token.FLOAT_CONSTANT)
+ return new FloatConstantNode(sourceLocation, tokeniser.getFloatConstant());
+ else if (token == Token.STRING_CONSTANT)
+ return new StringConstantNode(sourceLocation, tokeniser.getStringConstant());
+ else if (token == Token.BOOLEAN_CONSTANT)
+ return new BooleanConstantNode(sourceLocation, tokeniser.getBooleanConstant());
+
+ // 2. a variable reference
+ if (token == Token.DOLLAR) {
+ final int varRefStartPos = sourceLocation;
+ token = tokeniser.getToken();
+ sourceLocation = tokeniser.getStartPos();
+ final boolean usingOptionalBraces = token == Token.OPEN_BRACE;
+ if (usingOptionalBraces) {
+ token = tokeniser.getToken();
+ sourceLocation = tokeniser.getStartPos();
+ }
+ if (token != Token.IDENTIFIER)
+ throw new IllegalStateException(sourceLocation + ": identifier expected!");
+
+ final String ident = tokeniser.getIdent();
+ final Class varRefType = variableNameToTypeMap.get(ident);
+ if (varRefType == null)
+ throw new IllegalStateException(sourceLocation + ": unknown variable reference name: \""
+ + ident + "\"!");
+ variableReferences.add(ident);
+
+ Object defaultValue = null;
+ if (usingOptionalBraces) {
+ token = tokeniser.getToken();
+
+ // Do we have a default value?
+ if (token == Token.COLON) {
+ token = tokeniser.getToken();
+ sourceLocation = tokeniser.getStartPos();
+ if (token != Token.FLOAT_CONSTANT && token != Token.STRING_CONSTANT && token != Token.BOOLEAN_CONSTANT)
+ throw new IllegalStateException(sourceLocation + ": expected default value for variable reference!");
+ switch (token) {
+ case FLOAT_CONSTANT:
+ defaultValue = new Double(tokeniser.getFloatConstant());
+ break;
+ case BOOLEAN_CONSTANT:
+ defaultValue = new Boolean(tokeniser.getBooleanConstant());
+ break;
+ case STRING_CONSTANT:
+ defaultValue = new String(tokeniser.getStringConstant());
+ break;
+ }
+ token = tokeniser.getToken();
+ sourceLocation = tokeniser.getStartPos();
+ }
+
+ if (token != Token.CLOSE_BRACE)
+ throw new IllegalStateException(sourceLocation + ": closing brace expected!");
+
+ defaultValues.put(ident, defaultValue);
+ }
+
+ return new IdentNode(varRefStartPos, tokeniser.getIdent(), defaultValue, varRefType);
+ }
+
+ // 3. a parenthesised expression
+ if (token == Token.OPEN_PAREN) {
+ final Node exprNode = parseExpr();
+ token = tokeniser.getToken();
+ if (token != Token.CLOSE_PAREN)
+ throw new IllegalStateException(sourceLocation + ": '(' expected!");
+
+ return exprNode;
+ }
+
+ // 4. a unary operator
+ if (token == Token.PLUS || token == Token.MINUS) {
+ final Node factor = parseFactor();
+ return handleUnaryOp(sourceLocation, token, factor);
+ }
+
+ // 5. function call
+ if (token == Token.IDENTIFIER) {
+ tokeniser.ungetToken(token);
+ return parseFunctionCall();
+ }
+
+ if (token == Token.ERROR)
+ throw new IllegalStateException(sourceLocation + ": " + tokeniser.getErrorMsg());
+
+ throw new IllegalStateException(sourceLocation + ": unexpected input token: " + token + "!");
+ }
+
+ private Node handleUnaryOp(final int sourceLocation, final Token operator, final Node operand) {
+ if (operand.getType() == Boolean.class || operand.getType() == String.class)
+ throw new ArithmeticException(sourceLocation + ": can't apply a unary " + operator.asString()
+ + " a boolean, string or list operand!");
+ return new UnaryOpNode(sourceLocation, operator, operand);
+ }
+
+ /**
+ * Implements func_call --> ident "(" ")" | ident "(" expr {"," expr} ")".
+ */
+ private Node parseFunctionCall() {
+ Token token = tokeniser.getToken();
+ final int functionNameStartPos = tokeniser.getStartPos();
+ if (token != Token.IDENTIFIER)
+ throw new IllegalStateException(functionNameStartPos + ": function name expected!");
+
+ final String originalName = tokeniser.getIdent();
+ final String functionNameCandidate = originalName.toUpperCase();
+ if (functionNameCandidate.equals("DEFINED"))
+ return parseDefined();
+
+ final Function func = nameToFunctionMap.get(functionNameCandidate);
+ if (func == null) {
+ if (tokeniser.getToken() == Token.OPEN_PAREN)
+ throw new IllegalStateException(functionNameStartPos + ": call to unknown function "
+ + originalName + "()!");
+ else
+ throw new IllegalStateException(functionNameStartPos + ": unknown text \""
+ + originalName + "\", maybe you forgot to put quotes around this text?");
+ }
+
+ token = tokeniser.getToken();
+ final int openParenPos = tokeniser.getStartPos();
+ if (token != Token.OPEN_PAREN)
+ throw new IllegalStateException(openParenPos + ": expected '(' after function name \""
+ + functionNameCandidate + "\"!");
+
+ // Parse the comma-separated argument list.
+ final ArrayList<Class> argTypes = new ArrayList<Class>();
+ ArrayList<Node> args = new ArrayList<Node>();
+ int sourceLocation;
+ for (;;) {
+ token = tokeniser.getToken();
+ sourceLocation = tokeniser.getStartPos();
+ if (token == Token.CLOSE_PAREN)
+ break;
+
+ tokeniser.ungetToken(token);
+ final Node exprNode = parseExpr();
+ argTypes.add(exprNode.getType());
+ args.add(exprNode);
+
+ token = tokeniser.getToken();
+ sourceLocation = tokeniser.getStartPos();
+ if (token != Token.COMMA)
+ break;
+ }
+
+ final Class returnType = func.validateArgTypes(argTypes.toArray(new Class[argTypes.size()]));
+ if (returnType == null)
+ throw new IllegalStateException((openParenPos + 1) + ": invalid number or type of arguments in call to "
+ + functionNameCandidate + "()!");
+
+ if (token != Token.CLOSE_PAREN)
+ throw new IllegalStateException(sourceLocation + ": expected the closing parenthesis of a call to "
+ + functionNameCandidate + "!");
+
+ Node[] nodeArray = new Node[args.size()];
+ return new FuncCallNode(functionNameStartPos, func, returnType, args.toArray(nodeArray));
+ }
+
+
+ /**
+ * Implements --> "DEFINED" "(" ident ")". If the opening brace is found a closing brace is also required.
+ */
+ private Node parseDefined() {
+ Token token = tokeniser.getToken();
+ final int definedStart = tokeniser.getStartPos();
+ if (token != Token.OPEN_PAREN)
+ throw new IllegalStateException(definedStart + ": \"(\" expected after \"DEFINED\"!");
+
+ token = tokeniser.getToken();
+ int sourceLocation = tokeniser.getStartPos();
+ Class varRefType;
+ if (token != Token.DOLLAR) {
+ if (token != Token.IDENTIFIER)
+ throw new IllegalStateException(sourceLocation + ": variable reference expected after \"DEFINED(\"!");
+ varRefType = variableNameToTypeMap.get(tokeniser.getIdent());
+ }
+ else {
+ token = tokeniser.getToken();
+ sourceLocation = tokeniser.getStartPos();
+ if (token != Token.OPEN_BRACE)
+ throw new IllegalStateException(sourceLocation + ": \"{\" expected after \"DEFINED($\"!");
+
+ token = tokeniser.getToken();
+ sourceLocation = tokeniser.getStartPos();
+ if (token != Token.IDENTIFIER)
+ throw new IllegalStateException(sourceLocation + ": variable reference expected after \"DEFINED(${\"!");
+
+ varRefType = variableNameToTypeMap.get(tokeniser.getIdent());
+ token = tokeniser.getToken();
+ sourceLocation = tokeniser.getStartPos();
+ if (token != Token.CLOSE_BRACE)
+ throw new IllegalStateException(sourceLocation + ":\"}\" expected after after \"DEFINED(${"
+ + tokeniser.getIdent() + "\"!");
+ }
+
+ token = tokeniser.getToken();
+ sourceLocation = tokeniser.getStartPos();
+ if (token != Token.CLOSE_PAREN)
+ throw new IllegalStateException(sourceLocation + ": missing \")\" in call to DEFINED()!");
+
+ return new BooleanConstantNode(definedStart, varRefType != null);
+ }
+
+ //
+ // Helper functions for the parseXXX() methods.
+ //
+
+ /**
+ * Deals w/ any necessary type conversions for any binary arithmetic operation on numbers.
+ */
+ private Node handleBinaryArithmeticOp(final Token operator, final int sourceLocation, final Node lhs, final Node rhs) {
+ // First operand is Double:
+ if (lhs.getType() == Double.class && rhs.getType() == Double.class)
+ return new BinOpNode(sourceLocation, operator, lhs, rhs);
+ if (lhs.getType() == Double.class
+ && (rhs.getType() == Long.class || rhs.getType() == Boolean.class || rhs.getType() == String.class))
+ return new BinOpNode(sourceLocation, operator, lhs, new FConvNode(rhs));
+
+ // First operand is Long:
+ if (lhs.getType() == Long.class && rhs.getType() == Double.class)
+ return new BinOpNode(sourceLocation, operator, new FConvNode(lhs), rhs);
+ if (lhs.getType() == Long.class
+ && (rhs.getType() == Long.class || rhs.getType() == Boolean.class || rhs.getType() == String.class))
+ return new BinOpNode(sourceLocation, operator, new FConvNode(lhs), new FConvNode(rhs));
+
+ // First operand is Boolean:
+ if (lhs.getType() == Boolean.class && rhs.getType() == Double.class)
+ return new BinOpNode(sourceLocation, operator, new FConvNode(lhs), rhs);
+ if (lhs.getType() == Boolean.class
+ && (rhs.getType() == Long.class || rhs.getType() == Boolean.class || rhs.getType() == String.class))
+ return new BinOpNode(sourceLocation, operator, new FConvNode(lhs), new FConvNode(rhs));
+
+ // First operand is String:
+ if (lhs.getType() == String.class && rhs.getType() == Double.class)
+ return new BinOpNode(sourceLocation, operator, new FConvNode(lhs), rhs);
+ if (lhs.getType() == String.class
+ && (rhs.getType() == Long.class || lhs.getType() == Boolean.class || lhs.getType() == String.class))
+ return new BinOpNode(sourceLocation, operator, new FConvNode(lhs), new FConvNode(rhs));
+
+ throw new ArithmeticException(sourceLocation + ": incompatible operands for \""
+ + operator.asString() + "\"! (lhs="
+ + lhs.toString() + ":" + lhs.getType() + ", rhs="
+ + rhs.toString() + ":" + rhs.getType() + ")");
+ }
+
+ /**
+ * Deals w/ any necessary type conversions for any binary comparison operation.
+ */
+ private Node handleComparisonOp(final Token operator, final int sourceLocation, final Node lhs, final Node rhs) {
+ // First operand is Double:
+ if (lhs.getType() == Double.class && rhs.getType() == Double.class)
+ return new BinOpNode(sourceLocation, operator, lhs, rhs);
+ if (lhs.getType() == Double.class && rhs.getType() == Long.class)
+ return new BinOpNode(sourceLocation, operator, lhs, new FConvNode(rhs));
+ if (lhs.getType() == Double.class && rhs.getType() == Boolean.class)
+ return new BinOpNode(sourceLocation, operator, lhs, new FConvNode(rhs));
+ if (lhs.getType() == Double.class && rhs.getType() == Long.class)
+ return new BinOpNode(sourceLocation, operator, lhs, new FConvNode(rhs));
+
+ // First operand is Long:
+ if (lhs.getType() == Long.class && rhs.getType() == Double.class)
+ return new BinOpNode(sourceLocation, operator, new FConvNode(lhs), rhs);
+ if (lhs.getType() == Long.class
+ && (rhs.getType() == Long.class || rhs.getType() == Boolean.class || rhs.getType() == String.class))
+ return new BinOpNode(sourceLocation, operator, new FConvNode(lhs), new FConvNode(rhs));
+
+ // First operand is Boolean:
+ if (lhs.getType() == Boolean.class && rhs.getType() == Boolean.class)
+ return new BinOpNode(sourceLocation, operator, lhs, rhs);
+ if (lhs.getType() == Boolean.class && rhs.getType() == Double.class)
+ return new BinOpNode(sourceLocation, operator, new FConvNode(lhs), rhs);
+ if (lhs.getType() == Boolean.class && rhs.getType() == Long.class)
+ return new BinOpNode(sourceLocation, operator, new FConvNode(lhs), new FConvNode(rhs));
+ if (lhs.getType() == Boolean.class && rhs.getType() == String.class)
+ return new BinOpNode(sourceLocation, operator, new SConvNode(lhs), rhs);
+
+ // First operand is String:
+ if (lhs.getType() == String.class && rhs.getType() == String.class)
+ return new BinOpNode(sourceLocation, operator, lhs, rhs);
+ if (lhs.getType() == String.class
+ && (rhs.getType() == Double.class || rhs.getType() == Long.class || rhs.getType() == Boolean.class))
+ return new BinOpNode(sourceLocation, operator, lhs, new SConvNode(rhs));
+
+ throw new IllegalArgumentException(sourceLocation + ": incompatible operands for \""
+ + operator.asString() + "\"! (lhs="
+ + lhs.toString() + ":" + lhs.getType() + ", rhs="
+ + rhs.toString() + ":" + rhs.getType() + ")");
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/Equation.java b/corelibs/equations/src/main/java/org/cytoscape/equations/Equation.java
new file mode 100644
index 0000000..1685d0b
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/Equation.java
@@ -0,0 +1,112 @@
+/*
+ File: Equation.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations;
+
+
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Set;
+
+
+public class Equation {
+ private final String equation;
+ private final Set<String> attribReferences;
+ private final Map<String, Object> defaultValues;
+ private final Object[] code;
+ private final int[] sourceLocations;
+ private final Class type;
+
+ /**
+ * @param equation the string representing this equation
+ * @param attribReferences other attributes that are referenced by this equation
+ * @param defaultValues default values for attribute references, if any
+ * @param code the instruction sequence representing the compiled equation
+ * @param type the type of the equation, String.class, Boolean.class or Double.class
+ */
+ Equation(final String equation, final Set<String> attribReferences,
+ final Map<String, Object> defaultValues, final Object[] code,
+ final int[] sourceLocations, final Class type)
+ {
+ this.equation = equation;
+ this.attribReferences = attribReferences;
+ this.defaultValues = defaultValues;
+ this.code = code;
+ this.sourceLocations = sourceLocations;
+ this.type = type;
+ }
+
+ @Override public String toString() { return equation; }
+
+ @Override public boolean equals(final Object other) {
+ if (other.getClass() != Equation.class)
+ return false;
+
+ final Equation otherEquation = (Equation)other;
+ return equation.equals(otherEquation.equation);
+ }
+
+ public Set<String> getAttribReferences() { return attribReferences; }
+ public Map<String, Object> getDefaultValues() { return defaultValues; }
+ public Object[] getCode() { return code; }
+ public int[] getSourceLocations() { return sourceLocations; }
+ public Class getType() { return type; }
+
+ /**
+ * A factory method that returns an Equation that always fails at runtime.
+ *
+ * @param equation an arbitrary string that is usually a syntactically invalid equation
+ * @param type the return type of the error equation
+ * @param errorMessage the runtime error message that the returned equation will produce
+ */
+ public static Equation getErrorEquation(final String equation, final Class type, final String errorMessage) {
+ final EqnCompiler compiler = new EqnCompiler();
+ final Map<String, Class> attribNameToTypeMap = new HashMap<String, Class>();
+ if (!compiler.compile("=ERROR(\"" + escapeQuotes(errorMessage) + "\")", attribNameToTypeMap))
+ throw new IllegalStateException("internal error in Equation.getErrorEquation(). This should *never* happen!");
+
+ final Equation errorEquation = compiler.getEquation();
+
+ return new Equation(equation, errorEquation.attribReferences,
+ errorEquation.defaultValues, errorEquation.code,
+ errorEquation.sourceLocations, type);
+ }
+
+ private static String escapeQuotes(final String s) {
+ final StringBuilder builder = new StringBuilder();
+ for (int i = 0; i < s.length(); ++i) {
+ final char ch = s.charAt(i);
+ if (ch == '"')
+ builder.append('\\');
+ builder.append(ch);
+ }
+
+ return builder.toString();
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/EquationUtil.java b/corelibs/equations/src/main/java/org/cytoscape/equations/EquationUtil.java
new file mode 100644
index 0000000..68f0921
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/EquationUtil.java
@@ -0,0 +1,112 @@
+/*
+ File: EquationUtil.java
+
+ Copyright (c) 2006, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations;
+
+
+public class EquationUtil {
+ /**
+ * @return "attribName" written as am attribute reference with a leading $-sign
+ */
+ public static String attribNameAsReference(final String attribName) {
+ if (isSimpleAttribName(attribName))
+ return "$" + attribName;
+ else
+ return "${" + escapeAttribName(attribName) + "}";
+ }
+
+ /**
+ * @return "d" converted to a Long using Excel™ rules
+ * @throws IllegalArgumentException if "d" is outside the range of a long
+ */
+ public static long doubleToLong(final double d) {
+ if (d > Long.MAX_VALUE || d < Long.MIN_VALUE)
+ throw new IllegalArgumentException("floating point value is too large to be converted to a Long!");
+
+ double x = ((Double)d).longValue();
+ if (x != d && d < 0.0)
+ --x;
+
+ return (long)x;
+ }
+
+ /**
+ * @param attribName the name to test
+ * @return true if "attribName" start with a letter and consists of only letters and digits, else false
+ */
+ private static boolean isSimpleAttribName(final String attribName) {
+ final int length = attribName.length();
+ if (length == 0)
+ throw new IllegalStateException("empty attribute names should never happen!");
+
+ if (!Character.isLetter(attribName.charAt(0)))
+ return false;
+
+ for (int i = 1; i < length; ++i) {
+ final char ch = attribName.charAt(i);
+ if (!Character.isLetter(ch) && !Character.isDigit(ch))
+ return false;
+ }
+
+ return true;
+ }
+
+ /**
+ * @return "attribName" with characters that need to be backslash-escaped when written as
+ * part of an attribute refernce, escaped
+ */
+ private static String escapeAttribName(final String attribName) {
+ final int length = attribName.length();
+ final StringBuilder escapedAttribName = new StringBuilder(length * 2);
+ for (int i = 0; i < length; ++i) {
+ final char ch = attribName.charAt(i);
+ switch (ch) {
+ case ' ':
+ case '\\':
+ case '{':
+ case '}':
+ case ':':
+ case ',':
+ case '(':
+ case ')':
+ escapedAttribName.append('\\');
+ }
+ escapedAttribName.append(ch);
+ }
+
+ return escapedAttribName.toString();
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/Function.java b/corelibs/equations/src/main/java/org/cytoscape/equations/Function.java
new file mode 100644
index 0000000..6d91d06
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/Function.java
@@ -0,0 +1,95 @@
+/*
+ File: Function.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations;
+
+
+import java.util.List;
+
+
+public interface Function {
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ String getName();
+
+ /**
+ * Used to provide help for users. Unlike getUsageDescription(), this is an informal English description,
+ * like "Calculates the sine of its argument."
+ *
+ * @return a description of what this function does
+ */
+ String getFunctionSummary();
+
+ /**
+ * Used to provide help for users. Unlike getFunctionSummary(), this describes how to call this function,
+ * like "Call with SIN(number)."
+ *
+ * @return a description of how to use this function
+ */
+ String getUsageDescription();
+
+ /**
+ * @return the static return type of this function, Object.class, Double.cLass, String.class, or Boolean.class.
+ * If the static return type is Object.class, the dynamic return type will be one of Double.cLass, String.class, or Boolean.class
+ * and will depend on the arguments passed to the function!
+ *
+ * Note, this is used by external tools used to filter a list of functions based on what a valid return type might be.
+ * In Cytoscape it is used in the attribute browser's formula builder.
+ */
+ Class getReturnType();
+
+ /**
+ * @return the return type for this function (Double.cLass, String.class, or Boolean.class)
+ * or null if the args passed in had the wrong arity or a type mismatch
+ *
+ * Note that this is different from getReturnType() in that it will never return the wildcard Object.class.
+ * It is used by the parser which knows the actual type of the arguments in any given call to this function.
+ */
+ Class validateArgTypes(final Class[] argTypes);
+
+ /**
+ * Used to invoke this function.
+ * @param args the function arguments which must correspond in type and number to what getParameterTypes() returns.
+ * @return the result of the function evaluation. The actual type of the returned object will be what getReturnType() returns.
+ * @throws ArithmeticException thrown if a numeric error, e.g. a division by zero occurred.
+ * @throws IllegalArgumentException thrown for any error that is not a numeric error, for example if a function only accepts positive numbers and a negative number was passed in.
+ */
+ Object evaluateFunction(final Object[] args) throws FunctionError;
+
+ /**
+ * Used with the equation builder.
+ *
+ * @param leadingArgs the types of the arguments that have already been selected by the user.
+ * @return the set of arguments (must be a collection of String.class, Long.class, Double.class, Boolean.class and List.class) that are candidates for the next argument. A null return indicates that no further arguments are valid.
+ * Please note that if the returned set contains a null, this indicates an optional additional argument.
+ */
+ List<Class> getPossibleArgTypes(final Class[] leadingArgs);
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/FunctionError.java b/corelibs/equations/src/main/java/org/cytoscape/equations/FunctionError.java
new file mode 100644
index 0000000..0e6c69b
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/FunctionError.java
@@ -0,0 +1,44 @@
+/*
+ File: FunctionError.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations;
+
+
+public class FunctionError extends Exception {
+ private static final long serialVersionUID = 0xDAEDEBECFAEF2134L;
+ private final int argNumber; // Which argument this error is associated with.
+
+ public FunctionError(final String message, final int argNumber) {
+ super(message);
+
+ this.argNumber = argNumber;
+ }
+
+ public int getArgNumber() { return argNumber; }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/FunctionUtil.java b/corelibs/equations/src/main/java/org/cytoscape/equations/FunctionUtil.java
new file mode 100644
index 0000000..507c601
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/FunctionUtil.java
@@ -0,0 +1,521 @@
+/*
+ File: FunctionUtil.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations;
+
+
+import java.util.Arrays;
+import java.util.ArrayList;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Stack;
+import java.util.Vector;
+import java.util.concurrent.CopyOnWriteArrayList;
+
+import javax.management.AttributeList;
+import javax.management.relation.RoleList;
+import javax.management.relation.RoleUnresolvedList;
+
+
+/**
+ * A collection of static methods that may be useful for the implementation of built-in functions.
+ */
+public class FunctionUtil {
+ /**
+ * Assumes that "arg" is a "String", "Boolean", "Long" or a "Double and converts it to "double".
+ * @return the converted argument as a "double"
+ * @throws IllegalArgumentException if the argument cannot be converted to a "double"
+ */
+ static public double getArgAsDouble(final Object arg) throws IllegalArgumentException {
+ if (arg.getClass() == Double.class)
+ return (Double)arg;
+ if (arg.getClass() == Long.class)
+ return (double)(Long)arg;
+ if (arg.getClass() == String.class) {
+ try {
+ return Double.parseDouble((String)arg);
+ } catch (final Exception e) {
+ throw new IllegalArgumentException("can't convert \"" + arg + "\" to a floating point number!");
+ }
+ }
+ if (arg.getClass() == Boolean.class)
+ return (Boolean)arg ? 1.0 : 0.0;
+
+ throw new IllegalArgumentException("can't convert argument to a floating point number!");
+ }
+ /**
+ * Assumes that "arg" is a "String", "Boolean", "Long" or a "Double and converts it to "double".
+ * @return the converted argument as a "double"
+ * @throws IllegalArgumentException if the argument cannot be converted to a "double"
+ */
+ static public String getArgAsString(final Object arg) throws IllegalArgumentException {
+ if (arg.getClass() == Boolean.class)
+ return (Boolean)arg ? "TRUE" : "FALSE";
+ if (arg.getClass() == Double.class) {
+ final String asString = arg.toString();
+ int length = asString.length();
+
+ // Strip trailing zeros:
+ while (length > 1 && asString.charAt(length - 1) == '0')
+ --length;
+
+ // Strip trailing period or comma:
+ if (asString.charAt(length - 1) == '.' || asString.charAt(length - 1) == ',')
+ --length;
+
+ return asString.substring(0, length);
+ }
+
+ return arg.toString();
+ }
+
+ /**
+ * Assumes that "arg" is a "String", "Boolean", "Long" or a "Double and converts it to "long".
+ * @return the converted argument as a "long"
+ * @throws IllegalArgumentException if the argument cannot be converted to a "long"
+ */
+ static public long getArgAsLong(final Object arg) throws IllegalArgumentException {
+ if (arg.getClass() == Double.class)
+ return EquationUtil.doubleToLong((Double)arg);
+ if (arg.getClass() == Long.class)
+ return (Long)arg;
+ if (arg.getClass() == String.class) {
+ try {
+ return Long.parseLong((String)arg);
+ } catch (final Exception e) {
+ throw new IllegalArgumentException("can't convert \"" + arg + "\" to a whole number!");
+ }
+ }
+ if (arg.getClass() == Boolean.class)
+ return (Boolean)arg ? 1L : 0L;
+
+ throw new IllegalArgumentException("can't convert argument to a whole number!");
+ }
+
+ /**
+ * Assumes that "arg" is a "String", "Boolean", "Long" or a "Double and converts it to "boolean".
+ * @return the converted argument as a "boolean"
+ * @throws IllegalArgumentException if the argument cannot be converted to a "boolean"
+ */
+ static public boolean getArgAsBoolean(final Object arg) throws IllegalArgumentException {
+ if (arg.getClass() == Double.class) {
+ final double d = (Double)arg;
+ return d == 0.0 ? false : true;
+ }
+ if (arg.getClass() == Long.class) {
+ final long l = (Long)arg;
+ return l == 0L ? false : true;
+ }
+ if (arg.getClass() == String.class) {
+ final String argAsString = (String)arg;
+
+ if (argAsString.equalsIgnoreCase(Boolean.valueOf(true).toString()))
+ return true;
+ if (argAsString.equalsIgnoreCase(Boolean.valueOf(false).toString()))
+ return false;
+ throw new IllegalArgumentException("can't convert \"" + argAsString + "\" to a boolean!");
+ }
+ if (arg.getClass() == Boolean.class)
+ return (Boolean)arg;
+
+ throw new IllegalArgumentException("can't convert argument to a boolean!");
+ }
+
+ /**
+ * Carefully adds the numbers in "a" minimising loss of precision.
+ *
+ * @return the sum of the elements of "a"
+ */
+ static public double numericallySafeSum(final double a[]) {
+ int positiveCount = 0;
+ for (double d : a) {
+ if (d >= 0.0)
+ ++positiveCount;
+ }
+
+ // Separate positive and negative values:
+ final double[] positiveValues = new double[positiveCount];
+ final double[] negativeValues = new double[a.length - positiveCount];
+ int positiveIndex = 0;
+ int negativeIndex = 0;
+ for (double d : a) {
+ if (d >= 0.0)
+ positiveValues[positiveIndex++] = d;
+ else
+ negativeValues[negativeIndex++] = d;
+ }
+
+ double positiveSum = 0.0;
+ if (positiveValues.length > 0) {
+ // Add values in increasing order of magnitude:
+ Arrays.sort(positiveValues);
+ for (double d : positiveValues)
+ positiveSum += d;
+ }
+
+ double negativeSum = 0.0;
+ if (negativeValues.length > 0) {
+ // Add values in increasing order of magnitude:
+ Arrays.sort(negativeValues);
+ for (int i = negativeValues.length - 1; i >= 0; --i)
+ negativeSum += negativeValues[i];
+ }
+
+ return positiveSum + negativeSum;
+ }
+
+ /**
+ * @return the String representation of the ith ordinal
+ */
+ static public String getOrdinal(final int i) {
+ if ((i % 100) == 11)
+ return Integer.toString(i) + "th";
+
+ switch (i % 10) {
+ case 1:
+ return Integer.toString(i) + "st";
+ case 2:
+ return Integer.toString(i) + "nd";
+ case 3:
+ return Integer.toString(i) + "rd";
+ default:
+ return Integer.toString(i) + "th";
+ }
+ }
+
+ /**
+ * @return the sample variance of the numbers in x[]
+ */
+ static public double calcSampleVariance(final double[] x) {
+ final int N = x.length;
+ if (N < 2)
+ throw new IllegalArgumentException("can't calculate a variance with fewer than 2 values!");
+
+ final double[] xSquared = new double[N];
+ for (int i = 0; i < N; ++i)
+ xSquared[i] = x[i] * x[i];
+
+ final double sumOfX = numericallySafeSum(x);
+ final double sumOfXSquared = numericallySafeSum(xSquared);
+
+ return (sumOfXSquared - (sumOfX * sumOfX) / (double)N) / (double)(N - 1);
+ }
+
+ /**
+ * Converts a List<Double> to a regular double[]
+ */
+ static public double[] listToArray(final List<Double> a) {
+ final double[] x = new double[a.size()];
+ int i = 0;
+ for (double d : a)
+ x[i++] = d;
+
+ return x;
+ }
+
+ /**
+ * @return true, if type is Double.class, Long.class, String.class or Boolean.class, else false
+ */
+ static public boolean isScalarArgType(final Class type) {
+ return type == Double.class || type == Long.class || type == String.class || type == Boolean.class;
+ }
+
+ /**
+ * @return true if "listClassCandidate" is an implementer of interface List, else false
+ */
+ static public boolean isSomeKindOfList(final Class listClassCandidate) {
+ if (listClassCandidate == List.class)
+ return true;
+ if (listClassCandidate == ArrayList.class)
+ return true;
+ if (listClassCandidate == DoubleList.class)
+ return true;
+ if (listClassCandidate == StringList.class)
+ return true;
+ if (listClassCandidate == LongList.class)
+ return true;
+ if (listClassCandidate == BooleanList.class)
+ return true;
+ if (listClassCandidate == Vector.class)
+ return true;
+ if (listClassCandidate == Stack.class)
+ return true;
+ if (listClassCandidate == AttributeList.class)
+ return true;
+ if (listClassCandidate == CopyOnWriteArrayList.class)
+ return true;
+ if (listClassCandidate == LinkedList.class)
+ return true;
+ if (listClassCandidate == RoleList.class)
+ return true;
+ if (listClassCandidate == RoleUnresolvedList.class)
+ return true;
+
+ return false;
+ }
+
+ /**
+ * Adds Double.class, Long.class, String.class and Boolean.class to "argTypes".
+ */
+ static public void addScalarArgumentTypes(final List<Class> argTypes) {
+ argTypes.add(Double.class);
+ argTypes.add(Long.class);
+ argTypes.add(String.class);
+ argTypes.add(Boolean.class);
+ }
+
+ /**
+ * Attempts to convert all arguments, including Lists to a uniform array of doubles.
+ *
+ * @throws IllegalArgumentException if any scalar argument cannot be converted to a double or any list
+ * argument contains an element that cannot be converted to a number.
+ */
+ static public double[] getDoubles(final Object[] args) throws FunctionError {
+ final List<Double> numbers = new ArrayList<Double>();
+
+ for (int i = 0; i < args.length; ++i) {
+ final Object arg = args[i];
+ if (arg instanceof List) {
+ final List list = (List)arg;
+ for (final Object listElement : list) {
+ final Double d = convertToDouble(listElement);
+ if (d == null)
+ throw new FunctionError("can't convert list element \"" + listElement
+ + "\" to a number!", i);
+ numbers.add(d);
+ }
+ }
+ else {
+ final Double d = convertToDouble(arg);
+ if (d == null)
+ throw new FunctionError("can't convert \"" + arg + "\" to a number!", i);
+ numbers.add(d);
+ }
+ }
+
+ final double[] doubles = new double[numbers.size()];
+ int index = 0;
+ for (final Double d : numbers)
+ doubles[index++] = d;
+
+ return doubles;
+ }
+
+ /**
+ * Attempts to convert all arguments, including Lists to a uniform array of longs.
+ *
+ * @throws IllegalArgumentException if any scalar argument cannot be converted to a long or any list
+ * argument contains an element that cannot be converted to a number.
+ */
+ static public long[] getLongs(final Object[] args) throws FunctionError {
+ final List<Long> numbers = new ArrayList<Long>();
+
+ for (int i = 0; i < args.length; ++i) {
+ final Object arg = args[i];
+ if (arg instanceof List) {
+ final List list = (List)arg;
+ for (final Object listElement : list) {
+ final Long l = convertToLong(listElement);
+ if (l == null)
+ throw new FunctionError("can't convert list element \"" + listElement
+ + "\" to an integer!", i);
+ numbers.add(l);
+ }
+ }
+ else {
+ final Long l = convertToLong(arg);
+ if (l == null)
+ throw new FunctionError("can't convert \"" + arg + "\" to an integer!", i);
+ numbers.add(l);
+ }
+ }
+
+ final long[] longs = new long[numbers.size()];
+ int index = 0;
+ for (final Long l : numbers)
+ longs[index++] = l;
+
+ return longs;
+ }
+
+ /**
+ * Converts all arguments, including Lists to a uniform array of strings.
+ */
+ static public String[] getStrings(final Object[] args) {
+ final List<String> strings = new ArrayList<String>();
+
+ for (final Object arg : args) {
+ if (arg instanceof List) {
+ final List list = (List)arg;
+ for (final Object listElement : list)
+ strings.add(getArgAsString(listElement));
+ }
+ else
+ strings.add(getArgAsString(arg));
+ }
+
+ final String[] retVal = new String[strings.size()];
+ return strings.toArray(retVal);
+ }
+
+ /**
+ * Attempts to convert all arguments, including Lists to a uniform array of booleans.
+ *
+ * @throws IllegalArgumentException if any scalar argument cannot be converted to a boolean or any list
+ * argument contains an element that cannot be converted to a number.
+ */
+ static public boolean[] getBooleans(final Object[] args) throws FunctionError {
+ final List<Boolean> booleans = new ArrayList<Boolean>();
+
+ for (int i = 0; i < args.length; ++i) {
+ final Object arg = args[i];
+ if (arg instanceof List) {
+ final List list = (List)arg;
+ for (final Object listElement : list) {
+ final Boolean b = convertToBoolean(listElement);
+ if (b == null)
+ throw new FunctionError("can't convert list element \"" + listElement
+ + "\" to a boolean value!", i);
+ booleans.add(b);
+ }
+ }
+ else {
+ final Boolean b = convertToBoolean(arg);
+ if (b == null)
+ throw new FunctionError("can't convert \"" + arg + "\" to a boolean number!", i);
+ booleans.add(b);
+ }
+ }
+
+ final boolean[] retval = new boolean[booleans.size()];
+ int index = 0;
+ for (final Boolean b : booleans)
+ retval[index++] = b;
+
+ return retval;
+ }
+
+ /**
+ * @return "arg" converted to a Double, if possible, else null
+ */
+ static private Double convertToDouble(final Object arg) {
+ if (arg.getClass() == Double.class)
+ return (Double)arg;
+ if (arg.getClass() == Long.class)
+ return (double)(Long)arg;
+ if (arg.getClass() == Integer.class)
+ return (double)(Integer)arg;
+ if (arg.getClass() == String.class) {
+ try {
+ return Double.valueOf((String)arg);
+ } catch (final Exception e) {
+ return null;
+ }
+ }
+ if (arg.getClass() == Boolean.class)
+ return Double.valueOf((Boolean)arg ? 1.0 : 0.0);
+
+ return null;
+ }
+
+ /**
+ * @return "arg" converted to a Long, if possible, else null
+ */
+ static private Long convertToLong(final Object arg) {
+ if (arg.getClass() == Double.class)
+ return EquationUtil.doubleToLong((Double)arg);
+ if (arg.getClass() == Long.class)
+ return (Long)arg;
+ if (arg.getClass() == Integer.class)
+ return (long)(Integer)arg;
+ if (arg.getClass() == String.class) {
+ try {
+ return Long.valueOf((String)arg);
+ } catch (final Exception e) {
+ return null;
+ }
+ }
+ if (arg.getClass() == Boolean.class)
+ return Long.valueOf((Boolean)arg ? 1L : 0L);
+
+ return null;
+ }
+
+ /**
+ * @return "arg" converted to a Boolean, if possible. else null
+ */
+ static private Boolean convertToBoolean(final Object arg) {
+ if (arg.getClass() == Double.class)
+ return (Double)arg == 0.0 ? false : true;
+ if (arg.getClass() == Long.class)
+ return (double)(Long)arg == 0L ? false : true;
+ if (arg.getClass() == Integer.class)
+ return (double)(Integer)arg == 0 ? false : true;
+ if (arg.getClass() == String.class) {
+ final String s = (String)arg;
+ if (s.equalsIgnoreCase("true"))
+ return true;
+ if (s.equalsIgnoreCase("false"))
+ return false;
+ return null;
+ }
+ if (arg.getClass() == Boolean.class)
+ return (Boolean)arg;
+
+ return null;
+ }
+
+ /**
+ * Tries to map "input" to one of Double, Long, Boolean or String.
+ * @return null if the translation failed, the input object if no translation was necessary or a new object if a successful translation was possible
+ */
+ static public Object translateObjectType(final Object input) {
+ final Class type = input.getClass();
+ if (type == Double.class || type == Long.class || type == Boolean.class || type == String.class)
+ return input;
+
+ if (type == Float.class)
+ return new Double((Float)input);
+
+ if (type == Integer.class)
+ return new Long((Integer)input);
+
+ if (type == Short.class)
+ return new Long((Short)input);
+
+ if (type == Byte.class)
+ return new Long((Byte)input);
+
+ if (type == Character.class)
+ return new Long((Character)input);
+
+ // Couldn't map the input to anything useful:
+ return null;
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/LongList.java b/corelibs/equations/src/main/java/org/cytoscape/equations/LongList.java
new file mode 100644
index 0000000..d7b4110
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/LongList.java
@@ -0,0 +1,44 @@
+/*
+ File: LongList.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations;
+
+
+import java.util.ArrayList;
+
+
+public class LongList extends ArrayList<Long> {
+ public static final long serialVersionUID = -245160324069812L;
+
+ public LongList(final long[] numbers) {
+ ensureCapacity(numbers.length);
+ for (final long l : numbers)
+ add(l);
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/Parser.java b/corelibs/equations/src/main/java/org/cytoscape/equations/Parser.java
new file mode 100644
index 0000000..05b1047
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/Parser.java
@@ -0,0 +1,112 @@
+/*
+ File: Parser.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations;
+
+
+import org.cytoscape.equations.builtins.*;
+
+
+/**
+ * A singleton EqnParser
+ */
+public class Parser {
+ static private EqnParser eqnParser;
+
+ synchronized static public EqnParser getParser() {
+ if (eqnParser == null) {
+ eqnParser = new EqnParserImpl();
+
+ eqnParser.registerFunction(new Abs());
+ eqnParser.registerFunction(new ACos());
+ eqnParser.registerFunction(new ASin());
+ eqnParser.registerFunction(new And());
+ eqnParser.registerFunction(new ATan2());
+ eqnParser.registerFunction(new Average());
+ eqnParser.registerFunction(new BList());
+ eqnParser.registerFunction(new Combin());
+ eqnParser.registerFunction(new Concatenate());
+ eqnParser.registerFunction(new Cos());
+ eqnParser.registerFunction(new Cosh());
+ eqnParser.registerFunction(new Count());
+ eqnParser.registerFunction(new Degrees());
+ eqnParser.registerFunction(new org.cytoscape.equations.builtins.Error());
+ eqnParser.registerFunction(new Exp());
+ eqnParser.registerFunction(new First());
+ eqnParser.registerFunction(new FList());
+ eqnParser.registerFunction(new GeoMean());
+ eqnParser.registerFunction(new HarMean());
+ eqnParser.registerFunction(new If());
+ eqnParser.registerFunction(new IList());
+ eqnParser.registerFunction(new Largest());
+ eqnParser.registerFunction(new Last());
+ eqnParser.registerFunction(new Left());
+ eqnParser.registerFunction(new Len());
+ eqnParser.registerFunction(new ListToString());
+ eqnParser.registerFunction(new Ln());
+ eqnParser.registerFunction(new Log());
+ eqnParser.registerFunction(new Lower());
+ eqnParser.registerFunction(new Max());
+ eqnParser.registerFunction(new Median());
+ eqnParser.registerFunction(new Mid());
+ eqnParser.registerFunction(new Min());
+ eqnParser.registerFunction(new Mod());
+ eqnParser.registerFunction(new Mode());
+ eqnParser.registerFunction(new Not());
+ eqnParser.registerFunction(new NormDist());
+ eqnParser.registerFunction(new Now());
+ eqnParser.registerFunction(new Nth());
+ eqnParser.registerFunction(new Or());
+ eqnParser.registerFunction(new Permut());
+ eqnParser.registerFunction(new Pi());
+ eqnParser.registerFunction(new Product());
+ eqnParser.registerFunction(new Radians());
+ eqnParser.registerFunction(new Right());
+ eqnParser.registerFunction(new Round());
+ eqnParser.registerFunction(new Sign());
+ eqnParser.registerFunction(new Sin());
+ eqnParser.registerFunction(new Sinh());
+ eqnParser.registerFunction(new SList());
+ eqnParser.registerFunction(new StDev());
+ eqnParser.registerFunction(new Sqrt());
+ eqnParser.registerFunction(new Substitute());
+ eqnParser.registerFunction(new Sum());
+ eqnParser.registerFunction(new Tan());
+ eqnParser.registerFunction(new Tanh());
+ eqnParser.registerFunction(new Text());
+ eqnParser.registerFunction(new Today());
+ eqnParser.registerFunction(new Trunc());
+ eqnParser.registerFunction(new Upper());
+ eqnParser.registerFunction(new Value());
+ eqnParser.registerFunction(new Var());
+ }
+
+ return eqnParser;
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/StringList.java b/corelibs/equations/src/main/java/org/cytoscape/equations/StringList.java
new file mode 100644
index 0000000..fa329ac
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/StringList.java
@@ -0,0 +1,44 @@
+/*
+ File: StringList.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations;
+
+
+import java.util.ArrayList;
+
+
+public class StringList extends ArrayList<String> {
+ public static final long serialVersionUID = -4245160342069182L;
+
+ public StringList(final String[] strings) {
+ ensureCapacity(strings.length);
+ for (final String s : strings)
+ add(s);
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/Token.java b/corelibs/equations/src/main/java/org/cytoscape/equations/Token.java
new file mode 100644
index 0000000..d13ea6a
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/Token.java
@@ -0,0 +1,80 @@
+/*
+ File: Token.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations;
+
+
+public enum Token {
+ // COMP. OP. ARITH. OP. STRING OP.
+ STRING_CONSTANT("?", false, false, false),
+ FLOAT_CONSTANT("?", false, false, false),
+ BOOLEAN_CONSTANT("?", false, false, false),
+ IDENTIFIER("?", false, false, false),
+ OPEN_BRACE("{", false, false, false),
+ CLOSE_BRACE("}", false, false, false),
+ OPEN_PAREN("(", false, false, false),
+ CLOSE_PAREN(")", false, false, false),
+ COLON(":", false, false, false),
+ CARET("^", false, true, false),
+ PLUS("+", false, true, false),
+ MINUS("-", false, true, false),
+ DIV("/", false, true, false),
+ MUL("*", false, true, false),
+ EQUAL("=", true, false, false),
+ NOT_EQUAL("<>", true, false, false),
+ GREATER_THAN(">", true, false, false),
+ LESS_THAN("<", true, false, false),
+ GREATER_OR_EQUAL(">=", true, false, false),
+ LESS_OR_EQUAL("<=", true, false, false),
+ DOLLAR("$", false, false, false),
+ COMMA(",", false, false, false),
+ AMPERSAND("&", false, false, true),
+ EOS("?", false, false, false),
+ ERROR("?", false, false, false);
+
+
+ private final String asString;
+ private final boolean isComparisonOperator;
+ private final boolean isArithmeticOperator;
+ private final boolean isStringOperator;
+
+ Token(final String asString, final boolean isComparisonOperator,
+ final boolean isArithmeticOperator, final boolean isStringOperator)
+ {
+ this.asString = asString;
+ this.isComparisonOperator = isComparisonOperator;
+ this.isArithmeticOperator = isArithmeticOperator;
+ this.isStringOperator = isStringOperator;
+ }
+
+ public String asString() { return asString; }
+ public boolean isComparisonOperator() { return isComparisonOperator; }
+ public boolean isArithmeticOperator() { return isArithmeticOperator; }
+ public boolean isStringOperator() { return isStringOperator; }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/Tokeniser.java b/corelibs/equations/src/main/java/org/cytoscape/equations/Tokeniser.java
new file mode 100644
index 0000000..8c128c7
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/Tokeniser.java
@@ -0,0 +1,428 @@
+/*
+ File: Tokeniser.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations;
+
+import java.io.IOException;
+import java.io.StringReader;
+
+
+public class Tokeniser {
+ private final String equationAsString;
+ private Token previousToken;
+ private StringReader reader;
+ private int tokenStartPos, previousTokenStartPos, currentPos;
+ private long previousIntConstant, currentIntConstant;
+ private String previousIdent, currentIdent;
+ private double previousFloatConstant, currentFloatConstant;
+ private boolean previousBooleanConstant, currentBooleanConstant;
+ private String previousStringConstant, currentStringConstant;
+ private String errorMsg;
+ private int previousChar;
+ private boolean putBackChar;
+ private boolean openingBraceSeen;
+
+ public Tokeniser(final String equationAsString) {
+ this.equationAsString = equationAsString;
+ previousToken = null;
+ reader = new StringReader(equationAsString);
+ currentPos = -1;
+ putBackChar = false;
+ openingBraceSeen = false;
+ }
+
+ public Token getToken() {
+ if (previousToken != null) {
+ final Token retval = previousToken;
+ previousToken = null;
+
+ currentIntConstant = previousIntConstant;
+ currentFloatConstant = previousFloatConstant;
+ currentBooleanConstant = previousBooleanConstant;
+ currentStringConstant = previousStringConstant;
+ currentIdent = previousIdent;
+ tokenStartPos = previousTokenStartPos;
+
+ return retval;
+ }
+
+ int nextCh = getChar();
+ while (nextCh != -1 && Character.isWhitespace((char)nextCh))
+ nextCh = getChar();
+
+ tokenStartPos = currentPos;
+
+ if (nextCh == -1) {
+ tokenStartPos = equationAsString.length();
+ return Token.EOS;
+ }
+
+ final char ch = (char)nextCh;
+ switch (ch) {
+ case ':': return Token.COLON;
+ case '^': return Token.CARET;
+ case '{':
+ openingBraceSeen = true;
+ return Token.OPEN_BRACE;
+ case '}':
+ openingBraceSeen = false;
+ return Token.CLOSE_BRACE;
+ case '(': return Token.OPEN_PAREN;
+ case ')': return Token.CLOSE_PAREN;
+ case '+': return Token.PLUS;
+ case '-': return Token.MINUS;
+ case '/': return Token.DIV;
+ case '*': return Token.MUL;
+ case '=': return Token.EQUAL;
+ case '$': return Token.DOLLAR;
+ case ',': return Token.COMMA;
+ case '&': return Token.AMPERSAND;
+ }
+
+ if (ch == '"')
+ return parseStringConstant();
+ if (Character.isDigit(ch) || ch == '.') {
+ ungetChar(nextCh);
+ return parseNumericConstant();
+ }
+
+ if (ch == '<') {
+ nextCh = getChar();
+ if (nextCh == -1)
+ return Token.LESS_THAN;
+ if ((char)nextCh == '>')
+ return Token.NOT_EQUAL;
+ if ((char)nextCh == '=')
+ return Token.LESS_OR_EQUAL;
+ ungetChar(nextCh);
+ return Token.LESS_THAN;
+ }
+
+ if (ch == '>') {
+ nextCh = getChar();
+ if (nextCh == -1)
+ return Token.GREATER_THAN;
+ if ((char)nextCh == '=')
+ return Token.GREATER_OR_EQUAL;
+ ungetChar(nextCh);
+ return Token.GREATER_THAN;
+ }
+
+ if (Character.isLetter(ch)) {
+ ungetChar(nextCh);
+ return openingBraceSeen ? parseIdentifier() : parseSimpleIdentifier();
+ }
+
+ errorMsg = "unexpected input character '" + Character.toString(ch) + "'";
+
+ return Token.ERROR;
+ }
+
+ public void ungetToken(final Token token) throws IllegalStateException {
+ if (previousToken != null)
+ throw new IllegalStateException("can't unget more than one token!");
+
+ previousToken = token;
+ previousIntConstant = currentIntConstant;
+ previousFloatConstant = currentFloatConstant;
+ previousBooleanConstant = currentBooleanConstant;
+ previousStringConstant = currentStringConstant;
+ previousIdent = currentIdent;
+ previousTokenStartPos = tokenStartPos;
+ }
+
+ /**
+ * @return the position where the current token started. The position returned applies to the last token
+ * that was retrieved via the getToken() method.
+ */
+ public int getStartPos() {
+ return tokenStartPos;
+ }
+
+ /**
+ * Returns a representation of the next token as a string. Used primarily for testing.
+ * You should stop calling this after it returned "EOS"!
+ */
+ public String getTokenAsString() {
+ final Token token = getToken();
+ if (token == Token.STRING_CONSTANT)
+ return "STRING_CONSTANT: \"" + getStringConstant() + "\"";
+ if (token == Token.FLOAT_CONSTANT)
+ return "FLOAT_CONSTANT: \"" + getFloatConstant() + "\"";
+ if (token == Token.BOOLEAN_CONSTANT)
+ return "BOOLEAN_CONSTANT: \"" + getBooleanConstant() + "\"";
+ if (token == Token.IDENTIFIER)
+ return "IDENTIFIER: \"" + getIdent() + "\"";
+ if (token == Token.ERROR)
+ return "ERROR: \"" + getErrorMsg();
+ return token.toString();
+ }
+
+ public String getStringConstant() {
+ return currentStringConstant;
+ }
+
+ public double getFloatConstant() {
+ return currentFloatConstant;
+ }
+
+ public boolean getBooleanConstant() {
+ return currentBooleanConstant;
+ }
+
+ public long getIntConstant() {
+ return currentIntConstant;
+ }
+
+ public String getIdent() {
+ return currentIdent;
+ }
+
+ public String getErrorMsg() {
+ return errorMsg;
+ }
+
+ private int getChar() {
+ final int retval;
+
+ if (putBackChar) {
+ ++currentPos;
+ retval = previousChar;
+ putBackChar = false;
+ return retval;
+ }
+
+ try {
+ retval = reader.read();
+ } catch (final IOException e) {
+ return -1;
+ }
+
+ if (retval != -1)
+ ++currentPos;
+
+ return retval;
+ }
+
+ private void ungetChar(final int ch) {
+ if (putBackChar)
+ throw new IllegalStateException("can't unget two chars in a row!");
+ previousChar = ch;
+ putBackChar = true;
+ --currentPos;
+ }
+
+ private Token parseStringConstant() {
+ final int INITIAL_CAPACITY = 20;
+ final StringBuilder builder = new StringBuilder(INITIAL_CAPACITY);
+
+ boolean escaped = false;
+ int nextCh;
+ while ((nextCh = getChar()) != -1) {
+ final char ch = (char)nextCh;
+ if (ch == '\\')
+ escaped = true;
+ else {
+ if (escaped) {
+ switch (ch) {
+ case '\\':
+ builder.append('\\');
+ break;
+ case '"':
+ builder.append('"');
+ break;
+ case 'n':
+ builder.append('\n');
+ break;
+ default:
+ errorMsg = "unknown escape character '" + Character.toString(ch) + "'!";
+ return Token.ERROR;
+ }
+
+ escaped = false;
+ }
+ else if (ch == '"') {
+ currentStringConstant = builder.toString();
+ return Token.STRING_CONSTANT;
+ }
+ else
+ builder.append(ch);
+ }
+ }
+
+ errorMsg = "unterminated String constant!";
+ return Token.ERROR;
+ }
+
+ private Token parseNumericConstant() {
+ final int INITIAL_CAPACITY = 20;
+ final StringBuilder builder = new StringBuilder(INITIAL_CAPACITY);
+
+ int ch;
+ while ((ch = getChar()) != -1 && Character.isDigit((char)ch))
+ builder.append((char)ch);
+
+ if (ch == -1 || ((char)ch != 'e' && (char)ch != 'E' && (char)ch != '.')) {
+ try {
+ final double d = Double.parseDouble(builder.toString());
+ currentFloatConstant = d;
+ ungetChar(ch);
+ return Token.FLOAT_CONSTANT;
+ } catch (final NumberFormatException e2) {
+ errorMsg = "invalid numeric constant!";
+ return Token.ERROR;
+ }
+ }
+
+ // Optional decimal point.
+ if ((char)ch == '.') {
+ builder.append((char)ch);
+ while ((ch = getChar()) != -1 && Character.isDigit((char)ch))
+ builder.append((char)ch);
+ }
+
+ // Optional exponent.
+ if ((char)ch == 'e' || (char)ch == 'E') {
+ builder.append((char)ch);
+
+ ch = getChar();
+ if (ch == -1) {
+ errorMsg = "invalid numeric constant!";
+ return Token.ERROR;
+ }
+
+ // Optional sign.
+ if ((char)ch == '+' || (char)ch == '-') {
+ builder.append((char)ch);
+ ch = getChar();
+ }
+
+ // Now we require at least a single digit.
+ if (!Character.isDigit((char)ch)) {
+ errorMsg = "missing digits in exponent!";
+ return Token.ERROR;
+ }
+ ungetChar(ch);
+
+ while ((ch = getChar()) != -1 && Character.isDigit((char)ch))
+ builder.append((char)ch);
+ }
+
+ ungetChar(ch);
+
+ try {
+ final double d = Double.parseDouble(builder.toString());
+ currentFloatConstant = d;
+ return Token.FLOAT_CONSTANT;
+ } catch (final NumberFormatException e3) {
+ errorMsg = "invalid numeric constant!";
+ return Token.ERROR;
+ }
+ }
+
+ /**
+ * Looks for an attribute name. Attribute names in formulas must not contain '}', ':', ',' nor
+ * '(' or ')'. In order to allow a '}' or a ':' in an attribute name, it has to be esacped with a
+ * backslash. Any backslash in an identifier a.k.a. attribute name implies that the next
+ * input character will be included in the identifier this also allows for embedding
+ * backslashes by doubling them.
+ */
+ private Token parseIdentifier() {
+ final int INITIAL_CAPACITY = 20;
+ final StringBuilder builder = new StringBuilder(INITIAL_CAPACITY);
+
+ boolean escaped = false;
+ int ch;
+ while ((ch = getChar()) != -1 &&
+ (((char)ch != '}' && (char)ch != ':' && (char)ch != ',' && (char)ch != '(' && (char)ch != ')') || escaped))
+ {
+ if (escaped) {
+ escaped = false;
+ builder.append((char)ch);
+ }
+ else if ((char)ch == '\\')
+ escaped = true;
+ else
+ builder.append((char)ch);
+ }
+ if (escaped) {
+ errorMsg = "invalid attribute name at end of formula!";
+ return Token.ERROR;
+ }
+ ungetChar(ch);
+
+ currentIdent = builder.toString();
+
+ if (currentIdent.equalsIgnoreCase("TRUE")) {
+ currentBooleanConstant = true;
+ return Token.BOOLEAN_CONSTANT;
+ }
+ if (currentIdent.equalsIgnoreCase("FALSE")) {
+ currentBooleanConstant = false;
+ return Token.BOOLEAN_CONSTANT;
+ }
+
+ return Token.IDENTIFIER;
+ }
+
+ private Token parseSimpleIdentifier() {
+ final int INITIAL_CAPACITY = 20;
+ final StringBuilder builder = new StringBuilder(INITIAL_CAPACITY);
+
+ int ch;
+ while ((ch = getChar()) != -1 && (Character.isLetter((char)ch) || Character.isDigit((char)ch) || (char)ch == '_'))
+ builder.append((char)ch);
+ ungetChar(ch);
+
+ currentIdent = builder.toString();
+
+ if (currentIdent.equalsIgnoreCase("TRUE")) {
+ currentBooleanConstant = true;
+ return Token.BOOLEAN_CONSTANT;
+ }
+ if (currentIdent.equalsIgnoreCase("FALSE")) {
+ currentBooleanConstant = false;
+ return Token.BOOLEAN_CONSTANT;
+ }
+
+ return Token.IDENTIFIER;
+ }
+
+ static public void main(final String[] args) {
+ for (final String arg : args) {
+ final Tokeniser tokeniser = new Tokeniser(arg);
+ String tokenAsString;
+ do {
+ tokenAsString = tokeniser.getTokenAsString();
+ System.out.println(tokenAsString);
+ }
+ while (tokenAsString != "EOS");
+ }
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/ACos.java b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/ACos.java
new file mode 100644
index 0000000..26af299
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/ACos.java
@@ -0,0 +1,70 @@
+/*
+ File: ACos.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import org.cytoscape.equations.AbstractFunction;
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+import org.cytoscape.equations.FunctionUtil;
+
+
+public class ACos extends AbstractFunction {
+ public ACos() {
+ super(new ArgDescriptor[] {
+ new ArgDescriptor(ArgType.FLOAT, "argument", "A number between -1 and +1, inclusive.")
+ });
+ }
+
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "ACOS"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Returns the arccosine of a number."; }
+
+ public Class getReturnType() { return Double.class; }
+
+ /**
+ * @param args the function arguments which must be either one object of type Double or Long
+ * @return the result of the function evaluation which is the natural logarithm of the first argument
+ */
+ public Object evaluateFunction(final Object[] args) {
+ final double arg = FunctionUtil.getArgAsDouble(args[0]);
+ if (arg < -1.0 || arg > 1.0)
+ throw new IllegalArgumentException("the argument to ACOS() must be in [-1,+1]!");
+ return Math.acos(arg);
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/ASin.java b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/ASin.java
new file mode 100644
index 0000000..bd7bc55
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/ASin.java
@@ -0,0 +1,70 @@
+/*
+ File: ASin.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import org.cytoscape.equations.AbstractFunction;
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+import org.cytoscape.equations.FunctionUtil;
+
+
+public class ASin extends AbstractFunction {
+ public ASin() {
+ super(new ArgDescriptor[] {
+ new ArgDescriptor(ArgType.FLOAT, "argument", "A number between -1 and +1, inclusive.")
+ });
+ }
+
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "ASIN"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Returns the arcsine of a number."; }
+
+ public Class getReturnType() { return Double.class; }
+
+ /**
+ * @param args the function arguments which must be either one object of type Double or Long
+ * @return the result of the function evaluation which is the natural logarithm of the first argument
+ */
+ public Object evaluateFunction(final Object[] args) {
+ final double arg = FunctionUtil.getArgAsDouble(args[0]);
+ if (arg < -1.0 || arg > 1.0)
+ throw new IllegalArgumentException("the argument to ASIN() must be in [-1,+1]!");
+ return Math.asin(arg);
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/ATan2.java b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/ATan2.java
new file mode 100644
index 0000000..8b9b0b4
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/ATan2.java
@@ -0,0 +1,73 @@
+/*
+ File: ATan2.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import org.cytoscape.equations.AbstractFunction;
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+import org.cytoscape.equations.FunctionUtil;
+
+
+public class ATan2 extends AbstractFunction {
+ public ATan2() {
+ super(new ArgDescriptor[] {
+ new ArgDescriptor(ArgType.FLOAT, "x", "An x coordinate."),
+ new ArgDescriptor(ArgType.FLOAT, "y", "A y coordinate.")
+ });
+ }
+
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "ATAN2"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Returns the arctangent of two coordinates."; }
+
+ public Class getReturnType() { return Double.class; }
+
+ /**
+ * @param args the function arguments which must be either one object of type Double or Long
+ * @return the result of the function evaluation which is the natural logarithm of the first argument
+ */
+ public Object evaluateFunction(final Object[] args) {
+ final double x = FunctionUtil.getArgAsDouble(args[0]);
+ final double y = FunctionUtil.getArgAsDouble(args[1]);
+ if (x == 0.0 && y == 0.0)
+ throw new IllegalArgumentException("both arguments to ATAN2() must not simultaneously be equal to zero!");
+
+ return Math.atan2(x, y);
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Abs.java b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Abs.java
new file mode 100644
index 0000000..2f662bc
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Abs.java
@@ -0,0 +1,73 @@
+/*
+ File: Abs.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import java.util.ArrayList;
+import java.util.List;
+import org.cytoscape.equations.AbstractFunction;
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+
+
+public class Abs extends AbstractFunction {
+ public Abs() {
+ super(new ArgDescriptor[] { new ArgDescriptor(ArgType.INT, "number", "any numeric value") });
+
+ }
+
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "ABS"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Returns the absolute value of a number."; }
+
+ public Class getReturnType() { return Double.class; }
+
+ /**
+ * @param args the function arguments which must be either one object of type Double or Long
+ * @return the result of the function evaluation which is the natural logarithm of the first argument
+ */
+ public Object evaluateFunction(final Object[] args) {
+ final double number;
+ if (args[0] instanceof Double)
+ number = (Double)args[0];
+ else // Assume we are dealing with an integer.
+ number = (Long)args[0];
+
+ return Math.abs(number);
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/And.java b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/And.java
new file mode 100644
index 0000000..e104811
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/And.java
@@ -0,0 +1,82 @@
+/*
+ File: And.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import org.cytoscape.equations.AbstractFunction;
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+import org.cytoscape.equations.FunctionUtil;
+
+
+public class And extends AbstractFunction {
+ public And() {
+ super(new ArgDescriptor[] {
+ new ArgDescriptor(ArgType.OPT_BOOLS, "truth_values", "Zero or more truth values or lists of truth values."),
+ });
+ }
+
+ /**
+ * Used to parse the function string.
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "AND"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Returns the logical conjunction of any number of boolean values."; }
+
+ public Class getReturnType() { return Boolean.class; }
+
+ /**
+ * @param args the function arguments which must all be of type Boolean
+ * @return the result of the function evaluation which is either true or false
+ * @throws ArithmeticException this can never happen
+ * @throws IllegalArgumentException thrown if any of the arguments is not of type Boolean
+ */
+ public Object evaluateFunction(final Object[] args) throws IllegalArgumentException, ArithmeticException {
+ // Now evaluate the function.
+ final boolean[] booleans;
+ try {
+ booleans = FunctionUtil.getBooleans(args);
+ } catch (final Exception e) {
+ throw new IllegalArgumentException("can't convert an argument or a list element to a boolean in a call to OR()!");
+ }
+
+ for (final boolean b : booleans) {
+ if (!b)
+ return false;
+ }
+
+ return true;
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Average.java b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Average.java
new file mode 100644
index 0000000..a650345
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Average.java
@@ -0,0 +1,80 @@
+/*
+ File: Average.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import org.cytoscape.equations.AbstractFunction;
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+import org.cytoscape.equations.FunctionError;
+import org.cytoscape.equations.FunctionUtil;
+
+
+public class Average extends AbstractFunction {
+ public Average() {
+ super(new ArgDescriptor[] {
+ new ArgDescriptor(ArgType.FLOATS, "numbers", "One or more numbers and/or lists of numbers.")
+ });
+ }
+
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "AVERAGE"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Returns the average of a group of numbers."; }
+
+ public Class getReturnType() { return Double.class; }
+
+ /**
+ * @param args the function arguments which must be either one or two objects of type Double
+ * @return the result of the function evaluation which is the average of the elements in the single list argument or the average of the one or more double arguments
+ * @throws ArithmeticException
+ * @throws IllegalArgumentException thrown if any of the arguments is not of type Double
+ */
+ public Object evaluateFunction(final Object[] args) throws IllegalArgumentException, ArithmeticException {
+ final double[] numbers;
+ try {
+ numbers = FunctionUtil.getDoubles(args);
+ } catch (final FunctionError e) {
+ throw new IllegalArgumentException("bad argument(s) in a call to AVERAGE(): " + e.getMessage());
+ }
+
+ if (numbers.length == 0)
+ throw new IllegalArgumentException("need at least one number in a call to AVERAGE()!");
+
+ return FunctionUtil.numericallySafeSum(numbers) / numbers.length;
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/BList.java b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/BList.java
new file mode 100644
index 0000000..66b22a7
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/BList.java
@@ -0,0 +1,77 @@
+/*
+ File: BList.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import org.cytoscape.equations.AbstractFunction;
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+import org.cytoscape.equations.BooleanList;
+import org.cytoscape.equations.FunctionUtil;
+
+
+public class BList extends AbstractFunction {
+ public BList() {
+ super(new ArgDescriptor[] {
+ new ArgDescriptor(ArgType.OPT_STRINGS, "truth_values", "Zero or more numbers, strings or booleans."),
+ });
+ }
+
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "BLIST"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Returns a list of boolean values."; }
+
+ public Class getReturnType() { return BooleanList.class; }
+
+ /**
+ * @param args the function arguments which must be either one or two objects of type Double
+ * @return the result of the function evaluation which is the maximum of the elements in the single list argument or the maximum of the one or more double arguments
+ * @throws ArithmeticException
+ * @throws IllegalArgumentException thrown if any of the arguments is not of type Double
+ */
+ public Object evaluateFunction(final Object[] args) throws IllegalArgumentException, ArithmeticException {
+ final boolean[] booleans;
+ try {
+ booleans = FunctionUtil.getBooleans(args);
+ } catch (final Exception e) {
+ throw new IllegalArgumentException("can't convert an argument or a list element to a boolean in a call to BLIST()!");
+ }
+
+ return new BooleanList(booleans);
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Combin.java b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Combin.java
new file mode 100644
index 0000000..d9c3d35
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Combin.java
@@ -0,0 +1,99 @@
+/*
+ File: Combin.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import org.cytoscape.equations.AbstractFunction;
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+import org.cytoscape.equations.FunctionUtil;
+
+
+public class Combin extends AbstractFunction {
+ public Combin() {
+ super(new ArgDescriptor[] {
+ new ArgDescriptor(ArgType.INT, "n", "The total number of objects."),
+ new ArgDescriptor(ArgType.INT, "k", "The size of the selected subset."),
+ });
+ }
+
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "COMBIN"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Returns of combinations of n objects, with k chosen at any one time."; }
+
+ public Class getReturnType() { return Double.class; }
+
+ /**
+ * @param args the function arguments which must be either one or two objects of type Double
+ * @return the result of the function evaluation which is the logarithm of the first argument
+ * @throws ArithmeticException
+ * @throws IllegalArgumentException thrown if any of the arguments is not of type Double
+ */
+ public Object evaluateFunction(final Object[] args) throws IllegalArgumentException, ArithmeticException {
+ final long N = FunctionUtil.getArgAsLong(args[0]);
+ final long K = FunctionUtil.getArgAsLong(args[1]);
+
+ if (N < 0)
+ throw new IllegalArgumentException("1st argument to COMBIN() must not be negative!");
+ if (K < 0)
+ throw new IllegalArgumentException("2nd argument to COMBIN() must not be negative!");
+ if (N < K)
+ throw new IllegalArgumentException("2nd argument to COMBIN() must not be less than 1st argument!");
+
+ // Check boundary cases:
+ if (K < 0L || K > N)
+ return (Long)0L;
+
+ return (Long)combinations(N, K);
+ }
+
+ /**
+ * Calculate the binomial coefficient C(n,k) while doing our best to avoid overflow.
+ */
+ private long combinations(final long n, final long k) {
+ if (k == 0 || n == k)
+ return 1L;
+
+ final long c1 = combinations(n - 1L, k);
+ final long c2 = combinations(n - 1L, k - 1L);
+ final long sum = c1 + c2;
+ if (sum < c1 || sum < c2)
+ throw new ArithmeticException("overflow in call to COMBIN()!");
+ return sum;
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Concatenate.java b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Concatenate.java
new file mode 100644
index 0000000..52981ad
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Concatenate.java
@@ -0,0 +1,80 @@
+/*
+ File: Concatenate.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import org.cytoscape.equations.AbstractFunction;
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+import org.cytoscape.equations.FunctionUtil;
+import org.cytoscape.equations.StringList;
+
+
+public class Concatenate extends AbstractFunction {
+ public Concatenate() {
+ super(new ArgDescriptor[] {
+ new ArgDescriptor(ArgType.OPT_STRINGS, "strings", "Zero or more numbers, strings or booleans or lists thereof."),
+ });
+ }
+
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "CONCATENATE"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Returns a string (a.k.a. text object)."; }
+
+ public Class getReturnType() { return String.class; }
+
+ /**
+ * @param args the function arguments which must be either one or two objects of type Double
+ * @return the result of the function evaluation which is the maximum of the elements in the single list argument or the maximum of the one or more double arguments
+ * @throws ArithmeticException
+ * @throws IllegalArgumentException thrown if any of the arguments is not of type Double
+ */
+ public Object evaluateFunction(final Object[] args) throws IllegalArgumentException, ArithmeticException {
+ final String[] strings = FunctionUtil.getStrings(args);
+
+ int totalLength = 0;
+ for (final String s : strings)
+ totalLength += s.length();
+
+ final StringBuilder builder = new StringBuilder(totalLength);
+ for (final String s : strings)
+ builder.append(s);
+
+ return builder.toString();
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Cos.java b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Cos.java
new file mode 100644
index 0000000..069a2c7
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Cos.java
@@ -0,0 +1,68 @@
+/*
+ File: Cos.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import org.cytoscape.equations.AbstractFunction;
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+import org.cytoscape.equations.FunctionUtil;
+
+
+public class Cos extends AbstractFunction {
+ public Cos() {
+ super(new ArgDescriptor[] {
+ new ArgDescriptor(ArgType.FLOAT, "angle", "An angle in radians.")
+ });
+ }
+
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "COS"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Returns the cosine of an angle given in radians."; }
+
+ public Class getReturnType() { return Double.class; }
+
+ /**
+ * @param args the function arguments which must be either one object of type Double or Long
+ * @return the result of the function evaluation which is the natural logarithm of the first argument
+ */
+ public Object evaluateFunction(final Object[] args) {
+ final double angleInRadians = FunctionUtil.getArgAsDouble(args[0]);
+ return Math.cos(angleInRadians);
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Cosh.java b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Cosh.java
new file mode 100644
index 0000000..947887b
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Cosh.java
@@ -0,0 +1,68 @@
+/*
+ File: Cosh.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import org.cytoscape.equations.AbstractFunction;
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+import org.cytoscape.equations.FunctionUtil;
+
+
+public class Cosh extends AbstractFunction {
+ public Cosh() {
+ super(new ArgDescriptor[] {
+ new ArgDescriptor(ArgType.FLOAT, "number", "Any number.")
+ });
+ }
+
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "COSH"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Returns the hyperbolic cosine of a number."; }
+
+ public Class getReturnType() { return Double.class; }
+
+ /**
+ * @param args the function arguments which must be either one object of type Double or Long
+ * @return the result of the function evaluation which is the natural logarithm of the first argument
+ */
+ public Object evaluateFunction(final Object[] args) {
+ final double arg = FunctionUtil.getArgAsDouble(args[0]);
+ return Math.cosh(arg);
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Count.java b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Count.java
new file mode 100644
index 0000000..fc884ed
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Count.java
@@ -0,0 +1,99 @@
+/*
+ File: Count.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import java.util.List;
+
+import org.cytoscape.equations.AbstractFunction;
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+
+
+public class Count extends AbstractFunction {
+ public Count() {
+ super(new ArgDescriptor[] {
+ new ArgDescriptor(ArgType.ANY_LIST, "list", "One or more lists or individual items.")
+ });
+ }
+
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "COUNT"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Returns the number of numeric values in a list."; }
+
+ public Class getReturnType() { return Long.class; }
+
+ /**
+ * @param args the function arguments which can be anything
+ * @return the result of the function evaluation which is the count of the arguments that are numbers for scalar arguments plus the count of list entries that are numbers for List arguments
+ */
+ public Object evaluateFunction(final Object[] args) throws IllegalArgumentException, ArithmeticException {
+ int count = 0;
+ for (final Object arg : args) {
+ if (arg instanceof List) {
+ final List list = (List)arg;
+ for (final Object listEntry : list) {
+ if (listEntry.getClass() == Double.class || listEntry.getClass() == Long.class)
+ ++count;
+ else if (listEntry.getClass() == String.class && isValidDouble((String)listEntry))
+ ++count;
+ }
+ }
+ else {
+ if (arg.getClass() == Double.class || arg.getClass() == Long.class)
+ ++count;
+ else if (arg.getClass() == String.class && isValidDouble((String)arg))
+ ++count;
+ }
+ }
+
+ return (long)count;
+ }
+
+ /**
+ * @return true if "s" contains the string representation of a valid, finite, non-NaN double
+ */
+ private boolean isValidDouble(final String s) {
+ try {
+ final double d = Double.parseDouble(s);
+ return !Double.isNaN(d) && !Double.isInfinite(d);
+ } catch (final NumberFormatException e) {
+ return false;
+ }
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Degrees.java b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Degrees.java
new file mode 100644
index 0000000..1e92835
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Degrees.java
@@ -0,0 +1,68 @@
+/*
+ File: Degrees.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import org.cytoscape.equations.AbstractFunction;
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+import org.cytoscape.equations.FunctionUtil;
+
+
+public class Degrees extends AbstractFunction {
+ public Degrees() {
+ super(new ArgDescriptor[] {
+ new ArgDescriptor(ArgType.FLOAT, "angle", "An angle in radians.")
+ });
+ }
+
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "DEGREES"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Returns the value in degrees converted from radians."; }
+
+ public Class getReturnType() { return Double.class; }
+
+ /**
+ * @param args the function arguments which must be either one object of type Double or Long
+ * @return the result of the function evaluation which is the natural logarithm of the first argument
+ */
+ public Object evaluateFunction(final Object[] args) {
+ final double angleInRadians = FunctionUtil.getArgAsDouble(args[0]);
+ return angleInRadians * 180.0 / Math.PI;
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Error.java b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Error.java
new file mode 100644
index 0000000..9bc7aa4
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Error.java
@@ -0,0 +1,64 @@
+/*
+ File: Error.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import org.cytoscape.equations.AbstractFunction;
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+
+
+public class Error extends AbstractFunction {
+ public Error() {
+ super(new ArgDescriptor[] { new ArgDescriptor(ArgType.STRICT_STRING, "message", "An explanatory message.") });
+ }
+
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "ERROR"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Throws an exception at runtime."; }
+
+ public Class getReturnType() { return Object.class; }
+
+ /**
+ * @param args the function arguments which must be either one object of type Double or Long
+ * @return the result of the function evaluation which is the natural logarithm of the first argument
+ */
+ public Object evaluateFunction(final Object[] args) {
+ throw new IllegalStateException((String)args[0]);
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Exp.java b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Exp.java
new file mode 100644
index 0000000..f699f34
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Exp.java
@@ -0,0 +1,69 @@
+/*
+ File: Exp.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import org.cytoscape.equations.AbstractFunction;
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+
+
+public class Exp extends AbstractFunction {
+ public Exp() {
+ super(new ArgDescriptor[] {
+ new ArgDescriptor(ArgType.FLOAT, "number", "Any number."),
+ });
+ }
+
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "EXP"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Returns e raised to a specified number."; }
+
+ public Class getReturnType() { return Double.class; }
+
+ /**
+ * @param args the function arguments which must be either object of type Double
+ * @return the result of the function evaluation which is the argument applied to the base e
+ * @throws ArithmeticException
+ * @throws IllegalArgumentException thrown if the argument is not of type Double
+ */
+ public Object evaluateFunction(final Object[] args) throws IllegalArgumentException, ArithmeticException {
+ final double number = (Double)args[0];
+ return Math.exp(number);
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/FList.java b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/FList.java
new file mode 100644
index 0000000..65041b9
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/FList.java
@@ -0,0 +1,77 @@
+/*
+ File: FList.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import org.cytoscape.equations.AbstractFunction;
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+import org.cytoscape.equations.FunctionUtil;
+import org.cytoscape.equations.DoubleList;
+
+
+public class FList extends AbstractFunction {
+ public FList() {
+ super(new ArgDescriptor[] {
+ new ArgDescriptor(ArgType.OPT_FLOATS, "numbers", "Zero or more numbers, strings or booleans."),
+ });
+ }
+
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "FLIST"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Returns a list of floating point numbers."; }
+
+ public Class getReturnType() { return DoubleList.class; }
+
+ /**
+ * @param args the function arguments which must be either one or two objects of type Double
+ * @return the result of the function evaluation which is the maximum of the elements in the single list argument or the maximum of the one or more double arguments
+ * @throws ArithmeticException
+ * @throws IllegalArgumentException thrown if any of the arguments is not of type Double
+ */
+ public Object evaluateFunction(final Object[] args) throws IllegalArgumentException, ArithmeticException {
+ final double[] numbers;
+ try {
+ numbers = FunctionUtil.getDoubles(args);
+ } catch (final Exception e) {
+ throw new IllegalArgumentException("can't convert an argument or a list element to a number in a call to FLIST()!");
+ }
+
+ return new DoubleList(numbers);
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/First.java b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/First.java
new file mode 100644
index 0000000..3c0aba7
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/First.java
@@ -0,0 +1,80 @@
+/*
+ File: First.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import java.util.List;
+
+import org.cytoscape.equations.AbstractFunction;
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+import org.cytoscape.equations.FunctionUtil;
+
+
+public class First extends AbstractFunction {
+ public First() {
+ super(new ArgDescriptor[] {
+ new ArgDescriptor(ArgType.ANY_LIST, "list", "A non-empty list."),
+ });
+ }
+
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "FIRST"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Returns the first entry in a list."; }
+
+ public Class getReturnType() { return Object.class; }
+
+ /**
+ * @param args the function arguments which must be a single list
+ * @return the first entry in the list
+ * @throws ArithmeticException
+ * @throws IllegalArgumentException thrown if the list is empty
+ */
+ public Object evaluateFunction(final Object[] args) throws IllegalArgumentException, ArithmeticException {
+ final List list = (List)args[0];
+ if (list.isEmpty())
+ throw new IllegalArgumentException("can't get the first argument of an empty list in a call to FIRST()!");
+
+ final Object firstElement = list.get(0);
+ final Object retVal = FunctionUtil.translateObjectType(firstElement);
+ if (retVal == null)
+ throw new IllegalArgumentException("bad list element type: " + firstElement.getClass() + " in a call to FIRST()!");
+
+ return retVal;
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/GeoMean.java b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/GeoMean.java
new file mode 100644
index 0000000..300b725
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/GeoMean.java
@@ -0,0 +1,111 @@
+/*
+ File: GeoMean.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.cytoscape.equations.AbstractFunction;
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+import org.cytoscape.equations.FunctionUtil;
+
+
+public class GeoMean extends AbstractFunction {
+ public GeoMean() {
+ super(new ArgDescriptor[] {
+ new ArgDescriptor(ArgType.FLOATS, "numbers", "Two or more positive numbers."),
+ });
+ }
+
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "GEOMEAN"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Returns the geometric mean of a set of numbers."; }
+
+ public Class getReturnType() { return Double.class; }
+
+ /**
+ * @param args the function arguments which must be a list followed by a numeric argument
+ * @return the result of the function evaluation which is the maximum of the elements in the single list argument or the maximum of the one or more double arguments
+ * @throws ArithmeticException
+ * @throws IllegalArgumentException thrown if any of the members of the single List argument cannot be converted to a number
+ */
+ public Object evaluateFunction(final Object[] args) throws IllegalArgumentException, ArithmeticException {
+ final ArrayList<Double> a = new ArrayList<Double>();
+ for (int i = 0; i < args.length; ++i) {
+ if (args[i] instanceof List) {
+ final List list = (List)(args[i]);
+ for (final Object listElement : list) {
+ try {
+ final double d = FunctionUtil.getArgAsDouble(listElement);
+ if (d <= 0.0)
+ throw new IllegalArgumentException(FunctionUtil.getOrdinal(i) +
+ " argument in call to GEOMEAN() is not a list of positive numbers!");
+ a.add(d);
+ } catch (final IllegalArgumentException e) {
+ throw new IllegalArgumentException(FunctionUtil.getOrdinal(i) +
+ " element in call to GEOMEAN() is not a list of numbers: "
+ + e.getMessage());
+ }
+ }
+ } else {
+ try {
+ final double d = FunctionUtil.getArgAsDouble(args[i]);
+ if (d <= 0.0)
+ throw new IllegalArgumentException(FunctionUtil.getOrdinal(i) +
+ " element in call to GEOMEAN() is not a positive number!");
+
+ a.add(d);
+ } catch (final IllegalArgumentException e) {
+ throw new IllegalArgumentException(FunctionUtil.getOrdinal(i) +
+ " element in call to GEOMEAN() is not a number: "
+ + e.getMessage());
+ }
+ }
+ }
+
+ if (a.size() < 2)
+ throw new IllegalArgumentException("illegal arguments in call to GEOMEAN(): must have at least 2 numbers!");
+
+ double sumOfLogs = 0.0;
+ for (double d : a)
+ sumOfLogs += Math.log(d);
+ return Math.exp(sumOfLogs / a.size());
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/HarMean.java b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/HarMean.java
new file mode 100644
index 0000000..3e8cbc1
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/HarMean.java
@@ -0,0 +1,98 @@
+/*
+ File: HarMean.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import java.util.ArrayList;
+
+import org.cytoscape.equations.AbstractFunction;
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+import org.cytoscape.equations.FunctionError;
+import org.cytoscape.equations.FunctionUtil;
+
+
+public class HarMean extends AbstractFunction {
+ public HarMean() {
+ super(new ArgDescriptor[] {
+ new ArgDescriptor(ArgType.FLOATS, "numbers", "Two or more positive numbers."),
+ });
+ }
+
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "HARMEAN"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Returns the harmonic mean of a set of numbers."; }
+
+ public Class getReturnType() { return Double.class; }
+
+ /**
+ * @param args the function arguments which must be a list followed by a numeric argument
+ * @return the result of the function evaluation which is the maximum of the elements in the single list argument or the maximum of the one or more double arguments
+ * @throws ArithmeticException
+ * @throws IllegalArgumentException thrown if any of the members of the single List argument cannot be converted to a number
+ */
+ public Object evaluateFunction(final Object[] args) throws IllegalArgumentException, ArithmeticException {
+ final double[] numbers;
+ try {
+ numbers = FunctionUtil.getDoubles(args);
+ } catch (final FunctionError e) {
+ throw new IllegalArgumentException("bad argument in a call to HARMEAN(): " + e.getMessage());
+ }
+
+ if (!isPositiveArray(numbers))
+ throw new IllegalArgumentException("at least one argument to HARMEAN() is not positive!");
+
+ if (numbers.length < 2)
+ throw new IllegalArgumentException("illegal arguments in call to HARMEAN(): must have at least 2 numbers!");
+
+ double sum = 0.0;
+ for (double d : numbers)
+ sum += 1.0 / d;
+
+ return numbers.length / sum;
+ }
+
+ private boolean isPositiveArray(final double[] numbers) {
+ for (final double d : numbers) {
+ if (d <= 0.0)
+ return false;
+ }
+
+ return true;
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/IList.java b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/IList.java
new file mode 100644
index 0000000..2d90e64
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/IList.java
@@ -0,0 +1,77 @@
+/*
+ File: IList.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import org.cytoscape.equations.AbstractFunction;
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+import org.cytoscape.equations.FunctionUtil;
+import org.cytoscape.equations.LongList;
+
+
+public class IList extends AbstractFunction {
+ public IList() {
+ super(new ArgDescriptor[] {
+ new ArgDescriptor(ArgType.OPT_INTS, "integers", "Zero or more numbers, strings or booleans."),
+ });
+ }
+
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "ILIST"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Returns a list of whole numbers (a.k.a. integers)."; }
+
+ public Class getReturnType() { return LongList.class; }
+
+ /**
+ * @param args the function arguments which must be either one or two objects of type Double
+ * @return the result of the function evaluation which is the maximum of the elements in the single list argument or the maximum of the one or more double arguments
+ * @throws ArithmeticException
+ * @throws IllegalArgumentException thrown if any of the arguments is not of type Double
+ */
+ public Object evaluateFunction(final Object[] args) throws IllegalArgumentException, ArithmeticException {
+ final long[] numbers;
+ try {
+ numbers = FunctionUtil.getLongs(args);
+ } catch (final Exception e) {
+ throw new IllegalArgumentException("can't convert an argument or a list element to an integer in a call to ILIST()!");
+ }
+
+ return new LongList(numbers);
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/If.java b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/If.java
new file mode 100644
index 0000000..18d2e6d
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/If.java
@@ -0,0 +1,75 @@
+/*
+ File: If.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import org.cytoscape.equations.AbstractFunction;
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+
+
+public class If extends AbstractFunction {
+ public If() {
+ super(new ArgDescriptor[] {
+ new ArgDescriptor(ArgType.BOOL, "condition", "A logical test expression."),
+ new ArgDescriptor(ArgType.ANY, "value_if_true", "The return value if the test expression evaluates to true."),
+ new ArgDescriptor(ArgType.ANY, "value_if_false", "The return value if the test expression evaluates to false."),
+ });
+ }
+
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "IF"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Returns one of two alternatives based on a boolean value."; }
+
+ public Class getReturnType() { return Object.class; }
+
+ /**
+ * @param args the function arguments
+ * @return the result of the function evaluation which is either the 2nd or 3rd argument of the function
+ * @throws ArithmeticException
+ * @throws IllegalArgumentException thrown if any of the arguments is not of type Boolean
+ */
+ public Object evaluateFunction(final Object[] args) throws IllegalArgumentException, ArithmeticException {
+ final boolean condition = (Boolean)args[0];
+
+ if (args[1].getClass() == args[2].getClass())
+ return args[condition ? 1 : 2];
+ else
+ return args[condition ? 1 : 2].toString();
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Largest.java b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Largest.java
new file mode 100644
index 0000000..169ccb9
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Largest.java
@@ -0,0 +1,157 @@
+/*
+ File: Largest.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import java.util.List;
+
+import org.cytoscape.equations.AbstractFunction;
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+import org.cytoscape.equations.EquationUtil;
+import org.cytoscape.equations.FunctionUtil;
+
+
+public class Largest extends AbstractFunction {
+ public Largest() {
+ super(new ArgDescriptor[] {
+ new ArgDescriptor(ArgType.STRICT_ANY_LIST, "list", "A list of numbers."),
+ new ArgDescriptor(ArgType.INT, "k", "Specifies the rank of the number that will be selected."),
+ });
+ }
+
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "LARGEST"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Returns the kth largest element of a list of numbers."; }
+
+ public Class getReturnType() { return Double.class; }
+
+ /**
+ * @param args the function arguments which must be a list followed by a numeric argument
+ * @return the result of the function evaluation which is the maximum of the elements in the single list argument or the maximum of the one or more double arguments
+ * @throws ArithmeticException
+ * @throws IllegalArgumentException thrown if any of the arguments is not of type Double
+ */
+ public Object evaluateFunction(final Object[] args) throws IllegalArgumentException, ArithmeticException {
+ final List list = (List)args[0];
+ if (list.isEmpty())
+ throw new IllegalArgumentException("illegal empty list argument in call to LARGEST()!");
+
+ final double[] array = new double[list.size()];
+ int i = 0;
+ for (final Object listElement : list) {
+ try {
+ array[i++] = FunctionUtil.getArgAsDouble(listElement);
+ } catch (final IllegalArgumentException e) {
+ throw new IllegalArgumentException(FunctionUtil.getOrdinal(i)
+ + " list element in call to LARGEST() is not a number: "
+ + e.getMessage());
+ }
+ }
+
+ final long k;
+ try {
+ k = FunctionUtil.getArgAsLong(args[1]);
+ } catch (final Exception e) {
+ throw new IllegalArgumentException("can't convert \"" + args[1] + "\" to an integer argument in a call to LARGEST()!");
+ }
+ if (k <= 0)
+ throw new IllegalArgumentException("invalid index " + args[1] + " in a call to LARGEST()!");
+ if (k > array.length)
+ throw new IllegalArgumentException("index " + args[1] + " is too large for a list w/ " + array.length + " elements in a call to LARGEST()!");
+
+ return (Double)kthSmallest(array, array.length - (int)k);
+ }
+
+ /**
+ * @return the kth smallest array element, with the 0th being the smallest, the 1st being the 2nd most smallest etc.
+ */
+ private double kthSmallest(final double[] array, final int k) {
+ int first = 0;
+ int last = array.length - 1;
+
+ for (;;) {
+ final int middle = partition(array, first, last);
+
+ if (middle == k)
+ return array[k];
+
+ if (middle < k)
+ first = middle + 1;
+ else // middle > k
+ last = middle - 1;
+ }
+
+ }
+
+ private int partition(final double[] array, final int first, final int last) {
+ final int pivotIndex = medianOf3PiviotPosition(array, first, last);
+ final double pivotValue = array[pivotIndex];
+ swap(array, pivotIndex, last);
+ int storeIndex = first;
+ for (int i = first; i < last; ++i) {
+ if (array[i] <= pivotValue) {
+ swap(array, i, storeIndex);
+ ++storeIndex;
+ }
+ }
+ swap(array, storeIndex, last);
+ return storeIndex;
+ }
+
+ private int medianOf3PiviotPosition(final double[] array, int first, int last) {
+ final int middle = (first + last) / 2;
+
+ if (array[first] > array[last]) {
+ int temp = first;
+ first = last;
+ last = temp;
+ }
+
+ if (array[middle] > array[last])
+ return last;
+
+ return array[first] > array[middle] ? first : middle;
+ }
+
+ private void swap(final double[] array, final int i, final int j) {
+ final double temp = array[i];
+ array[i] = array[j];
+ array[j] = temp;
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Last.java b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Last.java
new file mode 100644
index 0000000..e5609a4
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Last.java
@@ -0,0 +1,80 @@
+/*
+ File: Last.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import java.util.List;
+
+import org.cytoscape.equations.AbstractFunction;
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+import org.cytoscape.equations.FunctionUtil;
+
+
+public class Last extends AbstractFunction {
+ public Last() {
+ super(new ArgDescriptor[] {
+ new ArgDescriptor(ArgType.ANY_LIST, "list", "Any non-empty list."),
+ });
+ }
+
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "LAST"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Returns the last entry in a list."; }
+
+ public Class getReturnType() { return Object.class; }
+
+ /**
+ * @param args the function arguments which must be a single list
+ * @return the last entry in the list
+ * @throws ArithmeticException
+ * @throws IllegalArgumentException thrown if the list is empty
+ */
+ public Object evaluateFunction(final Object[] args) throws IllegalArgumentException, ArithmeticException {
+ final List list = (List)args[0];
+ if (list.isEmpty())
+ throw new IllegalArgumentException("can't get the last argument of an empty list in a call to LAST()!");
+
+ final Object lastElement = list.get(list.size() - 1);
+ final Object retVal = FunctionUtil.translateObjectType(lastElement);
+ if (retVal == null)
+ throw new IllegalArgumentException("bad list element type: " + lastElement.getClass() + " in a call to LAST()!");
+
+ return retVal;
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Left.java b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Left.java
new file mode 100644
index 0000000..5ea2b2b
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Left.java
@@ -0,0 +1,87 @@
+/*
+ File: Left.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import org.cytoscape.equations.AbstractFunction;
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+import org.cytoscape.equations.FunctionUtil;
+
+
+public class Left extends AbstractFunction {
+ public Left() {
+ super(new ArgDescriptor[] {
+ new ArgDescriptor(ArgType.STRING, "text", "The source text."),
+ new ArgDescriptor(ArgType.OPT_FLOAT, "number", "How many characters to extract. (Default is 1.)"),
+ });
+ }
+
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "LEFT"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Returns a prefix of s string."; }
+
+ public Class getReturnType() { return String.class; }
+
+ /**
+ * @param args the function arguments which must be either one or two objects of type Double
+ * @return the result of the function evaluation which is the natural logarithm of the first argument
+ * @throws ArithmeticException
+ * @throws IllegalArgumentException thrown if any of the arguments is not of type Boolean
+ */
+ public Object evaluateFunction(final Object[] args) throws IllegalArgumentException, ArithmeticException {
+ final String text = FunctionUtil.getArgAsString(args[0]);
+ final int count;
+ if (args.length == 1)
+ count = 1;
+ else {
+ try {
+ count = (int)FunctionUtil.getArgAsLong(args[1]);
+ } catch (final Exception e) {
+ throw new IllegalArgumentException("can't convert \"" + args[1] + "\" to a count in a call to LEFT()!");
+ }
+
+ if (count < 0)
+ throw new IllegalArgumentException("illegal character count in call to LEFT()!");
+ }
+
+ if (count >= text.length())
+ return text;
+ return text.substring(0, count);
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Len.java b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Len.java
new file mode 100644
index 0000000..9faabc2
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Len.java
@@ -0,0 +1,70 @@
+/*
+ File: Len.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import org.cytoscape.equations.AbstractFunction;
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+import org.cytoscape.equations.FunctionUtil;
+
+
+public class Len extends AbstractFunction {
+ public Len() {
+ super(new ArgDescriptor[] {
+ new ArgDescriptor(ArgType.STRING, "text", "The source text."),
+ });
+ }
+
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "LEN"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Returns the length of a string."; }
+
+ public Class getReturnType() { return Long.class; }
+
+ /**
+ * @param args the function arguments which must be either one or two objects of type Double
+ * @return the result of the function evaluation which is the natural logarithm of the first argument
+ * @throws ArithmeticException
+ * @throws IllegalArgumentException thrown if any of the arguments is not of type Boolean
+ */
+ public Object evaluateFunction(final Object[] args) throws IllegalArgumentException, ArithmeticException {
+ final String text = FunctionUtil.getArgAsString(args[0]);
+ return (Long)(long)text.length();
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/ListToString.java b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/ListToString.java
new file mode 100644
index 0000000..0ad236d
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/ListToString.java
@@ -0,0 +1,81 @@
+/*
+ File: ListToString.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import java.util.List;
+
+import org.cytoscape.equations.AbstractFunction;
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+import org.cytoscape.equations.FunctionUtil;
+
+
+public class ListToString extends AbstractFunction {
+ public ListToString() {
+ super(new ArgDescriptor[] {
+ new ArgDescriptor(ArgType.STRICT_ANY_LIST, "list", "Any list."),
+ new ArgDescriptor(ArgType.STRING, "separator", "The text that will be inserted between the individual list elements.")
+ });
+ }
+
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "LISTTOSTRING"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Converts a list to a string, given a separator."; }
+
+ public Class getReturnType() { return String.class; }
+
+ /**
+ * @param args the function arguments which must be either one object of type Double or Long
+ * @return the result of the function evaluation which is the natural logarithm of the first argument
+ */
+ public Object evaluateFunction(final Object[] args) {
+ final List list = (List)args[0];
+ final String separator = FunctionUtil.getArgAsString(args[1]);
+
+ final StringBuilder result = new StringBuilder();
+ int count = 0;
+ for (final Object listEntry : list) {
+ result.append(listEntry.toString());
+ if (++count < list.size())
+ result.append(separator);
+ }
+
+ return result.toString();
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Ln.java b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Ln.java
new file mode 100644
index 0000000..7838a54
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Ln.java
@@ -0,0 +1,79 @@
+/*
+ File: Ln.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import org.cytoscape.equations.AbstractFunction;
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+import org.cytoscape.equations.FunctionUtil;
+
+
+public class Ln extends AbstractFunction {
+ public Ln() {
+ super(new ArgDescriptor[] {
+ new ArgDescriptor(ArgType.FLOAT, "number", "A positive number.")
+ });
+ }
+
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "LN"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Returns the natural logarithm of a number."; }
+
+ public Class getReturnType() { return Double.class; }
+
+ /**
+ * @param args the function arguments which must be one object of type Double
+ * @return the result of the function evaluation which is the natural logarithm of the argument
+ * @throws ArithmeticException
+ * @throws IllegalArgumentException thrown if the argument is not of type Double
+ */
+ public Object evaluateFunction(final Object[] args) throws IllegalArgumentException, ArithmeticException {
+ final double number;
+ try {
+ number = FunctionUtil.getArgAsDouble(args[0]);
+ } catch (final Exception e) {
+ throw new IllegalArgumentException("can't convert \"" + args[0] + "\" to a number in a call to LN()!");
+ }
+
+ if (number <= 0.0)
+ throw new IllegalArgumentException("LN() called with a number <= 0.0!");
+
+ return Math.log(number);
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Log.java b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Log.java
new file mode 100644
index 0000000..5a656ed
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Log.java
@@ -0,0 +1,98 @@
+/*
+ File: Log.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import org.cytoscape.equations.AbstractFunction;
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+import org.cytoscape.equations.FunctionUtil;
+
+
+public class Log extends AbstractFunction {
+ public Log() {
+ super(new ArgDescriptor[] {
+ new ArgDescriptor(ArgType.FLOAT, "argument", "A positive number."),
+ new ArgDescriptor(ArgType.OPT_FLOAT, "base", "A positive number.")
+ });
+ }
+
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "LOG"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Returns the logarithm of a number to a specified base."; }
+
+ public Class getReturnType() { return Double.class; }
+
+ /**
+ * @param args the function arguments which must be either one or two objects of type Double
+ * @return the result of the function evaluation which is the logarithm of the first argument
+ * @throws ArithmeticException
+ * @throws IllegalArgumentException thrown if any of the arguments is not of type Double
+ */
+ public Object evaluateFunction(final Object[] args) throws IllegalArgumentException, ArithmeticException {
+ final double number;
+ try {
+ number = FunctionUtil.getArgAsDouble(args[0]);
+ } catch (final Exception e) {
+ throw new IllegalArgumentException("can't convert \"" + args[0] + "\" to a number in a call to LOG()!");
+ }
+
+ final double base;
+ if (args.length == 1)
+ base = 10.0;
+ else {
+ try {
+ base = FunctionUtil.getArgAsDouble(args[1]);
+ } catch (final Exception e) {
+ throw new IllegalArgumentException("can't convert \"" + args[1] + "\" to a base in a call to LOG()!");
+ }
+ }
+
+ if (number <= 0.0)
+ throw new IllegalArgumentException("LOG() called with a number <= 0.0!");
+
+ if (base <= 0.0)
+ throw new IllegalArgumentException("LOG() called with a base <= 0.0!");
+
+ double retval = Math.log10(number);
+ if (base != 10.0)
+ retval /= Math.log10(base);
+
+ return retval;
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Lower.java b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Lower.java
new file mode 100644
index 0000000..e2104c2
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Lower.java
@@ -0,0 +1,71 @@
+/*
+ File: Lower.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import org.cytoscape.equations.AbstractFunction;
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+import org.cytoscape.equations.FunctionUtil;
+
+
+public class Lower extends AbstractFunction {
+ public Lower() {
+ super(new ArgDescriptor[] {
+ new ArgDescriptor(ArgType.STRING, "text", "Any text."),
+ });
+ }
+
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "LOWER"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Converts a string to lowercase."; }
+
+ public Class getReturnType() { return String.class; }
+
+ /**
+ * @param args the function arguments which must be either one or two objects of type Double
+ * @return the result of the function evaluation which is the natural logarithm of the first argument
+ * @throws ArithmeticException
+ * @throws IllegalArgumentException thrown if any of the arguments is not of type Boolean
+ */
+ public Object evaluateFunction(final Object[] args) throws IllegalArgumentException, ArithmeticException {
+ final String text = FunctionUtil.getArgAsString(args[0]);
+
+ return text.toLowerCase();
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Max.java b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Max.java
new file mode 100644
index 0000000..e8e7dca
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Max.java
@@ -0,0 +1,82 @@
+/*
+ File: Max.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import org.cytoscape.equations.AbstractFunction;
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+import org.cytoscape.equations.FunctionUtil;
+
+
+public class Max extends AbstractFunction {
+ public Max() {
+ super(new ArgDescriptor[] {
+ new ArgDescriptor(ArgType.FLOATS, "numbers", "Any combination of lists of numbers or individual numbers.")
+ });
+ }
+
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "MAX"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Returns the maximum of a group of numbers."; }
+
+ public Class getReturnType() { return Double.class; }
+
+ /**
+ * @param args the function arguments which must be either one or two objects of type Double
+ * @return the result of the function evaluation which is the maximum of the elements in the single list argument or the maximum of the one or more double arguments
+ * @throws ArithmeticException
+ * @throws IllegalArgumentException thrown if any of the arguments is not of type Double
+ */
+ public Object evaluateFunction(final Object[] args) throws IllegalArgumentException, ArithmeticException {
+ final double[] numbers;
+ try {
+ numbers = FunctionUtil.getDoubles(args);
+ } catch (final Exception e) {
+ throw new IllegalArgumentException("can't convert an argument or a list element to a number in a call to MAX()!");
+ }
+
+ double max = Double.NEGATIVE_INFINITY;
+ for (final double d : numbers) {
+ if (d > max)
+ max = d;
+ }
+
+ return max;
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Median.java b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Median.java
new file mode 100644
index 0000000..f075dbd
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Median.java
@@ -0,0 +1,86 @@
+/*
+ File: Median.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import java.util.Arrays;
+
+import org.cytoscape.equations.AbstractFunction;
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+import org.cytoscape.equations.FunctionUtil;
+
+
+public class Median extends AbstractFunction {
+ public Median() {
+ super(new ArgDescriptor[] {
+ new ArgDescriptor(ArgType.FLOATS, "numbers", "Any combination of lists of numbers or individual numbers.")
+ });
+ }
+
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "MEDIAN"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Returns the median of a list of numbers."; }
+
+ public Class getReturnType() { return Double.class; }
+
+ /**
+ * @param args the function arguments which must be either one or two objects of type Double
+ * @return the result of the function evaluation which is the median of the elements in the single list argument or the median of the one or more double arguments
+ * @throws ArithmeticException
+ * @throws IllegalArgumentException thrown if any of the arguments is not of type Double
+ */
+ public Object evaluateFunction(final Object[] args) throws IllegalArgumentException, ArithmeticException {
+ final double[] numbers;
+ try {
+ numbers = FunctionUtil.getDoubles(args);
+ } catch (final Exception e) {
+ throw new IllegalArgumentException("can't convert an argument or list element to a number in a call to MEDIAN()!");
+ }
+
+ if (numbers.length == 0)
+ throw new IllegalArgumentException("can't calculate the median of an empty list!");
+
+ Arrays.sort(numbers);
+
+ if ((numbers.length % 2) == 1)
+ return numbers[numbers.length / 2];
+ else
+ return (numbers[numbers.length / 2 - 1] + numbers[numbers.length / 2]) / 2.0;
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Mid.java b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Mid.java
new file mode 100644
index 0000000..d84341f
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Mid.java
@@ -0,0 +1,93 @@
+/*
+ File: Mid.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import org.cytoscape.equations.AbstractFunction;
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+import org.cytoscape.equations.FunctionUtil;
+
+
+public class Mid extends AbstractFunction {
+ public Mid() {
+ super(new ArgDescriptor[] {
+ new ArgDescriptor(ArgType.STRING, "text", "The source text."),
+ new ArgDescriptor(ArgType.INT, "start", "The first position of the selected substring."),
+ new ArgDescriptor(ArgType.INT, "count", "The length of the selected substring."),
+ });
+ }
+
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "MID"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Selects a substring of some text."; }
+
+ public Class getReturnType() { return String.class; }
+
+ /**
+ * @param args the function arguments which must be either one or two objects of type Double
+ * @return the result of the function evaluation which is the natural logarithm of the first argument
+ * @throws ArithmeticException
+ * @throws IllegalArgumentException thrown if any of the arguments is not of type Boolean
+ */
+ public Object evaluateFunction(final Object[] args) throws IllegalArgumentException, ArithmeticException {
+ final String text = FunctionUtil.getArgAsString(args[0]);
+
+ final int start;
+ try {
+ start = (int)FunctionUtil.getArgAsLong(args[1]);
+ } catch (final Exception e) {
+ throw new IllegalArgumentException("can't convert \"" + args[1] + "\" to a start position in a call to MID()!");
+ }
+
+ final int count;
+ try {
+ count = (int)FunctionUtil.getArgAsLong(args[2]);
+ } catch (final Exception e) {
+ throw new IllegalArgumentException("can't convert \"" + args[2] + "\" to a count in a call to MID()!");
+ }
+
+ if (start < 1)
+ throw new IllegalArgumentException("illegal start position in call to MID()!");
+ if (count < 0)
+ throw new IllegalArgumentException("illegal character count in call to MID()!");
+ if (count >= text.length() - start + 1)
+ return text.substring(start - 1);
+ return text.substring(start - 1, start + count - 1);
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Min.java b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Min.java
new file mode 100644
index 0000000..307470d
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Min.java
@@ -0,0 +1,82 @@
+/*
+ File: Min.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import org.cytoscape.equations.AbstractFunction;
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+import org.cytoscape.equations.FunctionUtil;
+
+
+public class Min extends AbstractFunction {
+ public Min() {
+ super(new ArgDescriptor[] {
+ new ArgDescriptor(ArgType.FLOATS, "numbers", "Any combination of lists of numbers or individual numbers.")
+ });
+ }
+
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "MIN"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Returns the minimum of a group of numbers."; }
+
+ public Class getReturnType() { return Double.class; }
+
+ /**
+ * @param args the function arguments which must be either one or two objects of type Double
+ * @return the result of the function evaluation which is the minimum of the elements in the single list argument or the minimum of the one or more double arguments
+ * @throws ArithmeticException
+ * @throws IllegalArgumentException thrown if any of the arguments is not of type Double
+ */
+ public Object evaluateFunction(final Object[] args) throws IllegalArgumentException, ArithmeticException {
+ final double[] numbers;
+ try {
+ numbers = FunctionUtil.getDoubles(args);
+ } catch (final Exception e) {
+ throw new IllegalArgumentException("can't convert an argument or a list element to a number in a call to MIN()!");
+ }
+
+ double min = Double.POSITIVE_INFINITY;
+ for (final double d : numbers) {
+ if (d < min)
+ min = d;
+ }
+
+ return min;
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Mod.java b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Mod.java
new file mode 100644
index 0000000..a1e1010
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Mod.java
@@ -0,0 +1,90 @@
+/*
+ File: Mod.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import org.cytoscape.equations.AbstractFunction;
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+import org.cytoscape.equations.FunctionUtil;
+
+
+public class Mod extends AbstractFunction {
+ public Mod() {
+ super(new ArgDescriptor[] {
+ new ArgDescriptor(ArgType.FLOAT, "number", "The argument."),
+ new ArgDescriptor(ArgType.FLOAT, "divisor", "A non-zero number."),
+ });
+ }
+
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "MOD"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Calculates the remainder of division."; }
+
+ public Class getReturnType() { return Double.class; }
+
+ /**
+ * @param args the function arguments which must be two objects of type Double or Long
+ * @return the result of the modulo function evaluation
+ * @throws ArithmeticException thrown if the 2nd argument is zero
+ */
+ public Object evaluateFunction(final Object[] args) throws IllegalArgumentException, ArithmeticException {
+ final double number;
+ try {
+ number = FunctionUtil.getArgAsDouble(args[0]);
+ } catch (final Exception e) {
+ throw new IllegalArgumentException("can't convert \"" + args[0] + "\" to a number in a call to MOD()!");
+ }
+
+ final double divisor;
+ try {
+ divisor = FunctionUtil.getArgAsDouble(args[1]);
+ } catch (final Exception e) {
+ throw new IllegalArgumentException("can't convert \"" + args[1] + "\" to a divisor in a call to MOD()!");
+ }
+ if (divisor == 0.0)
+ throw new ArithmeticException("division by zero in call to MOD()!");
+
+ final double result = number % divisor;
+ if (Math.signum(result) != Math.signum(divisor))
+ return -result;
+ else
+ return result;
+ }
+}
+
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Mode.java b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Mode.java
new file mode 100644
index 0000000..e44ee1c
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Mode.java
@@ -0,0 +1,99 @@
+/*
+ File: Mode.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import org.cytoscape.equations.AbstractFunction;
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+import java.util.Arrays;
+import org.cytoscape.equations.FunctionUtil;
+
+
+public class Mode extends AbstractFunction {
+ public Mode() {
+ super(new ArgDescriptor[] {
+ new ArgDescriptor(ArgType.FLOATS, "numbers", "One or more numbers or lists of numbers."),
+ });
+ }
+
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "MODE"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Returns the mode of a list of numbers."; }
+
+ public Class getReturnType() { return Double.class; }
+
+ /**
+ * @param args the function arguments which must be a list followed by a numeric argument
+ * @return the result of the function evaluation which is the maximum of the elements in the single list argument or the maximum of the one or more double arguments
+ * @throws ArithmeticException
+ * @throws IllegalArgumentException thrown if any of the members of the single List argument cannot be converted to a number
+ */
+ public Object evaluateFunction(final Object[] args) throws IllegalArgumentException, ArithmeticException {
+ final double[] x;
+ try {
+ x = FunctionUtil.getDoubles(args);
+ } catch (final Exception e) {
+ throw new IllegalArgumentException("non-numeric argument or list element in a call to MODE()!");
+ }
+
+ Arrays.sort(x);
+
+ double mode = 0.0;
+ int highestFrequencySoFar = 0;
+ double currentValue = -x[0];
+ int currentFrequency = 0;
+ for (double d : x) {
+ if (d == currentValue)
+ ++currentFrequency;
+ else {
+ if (currentFrequency > highestFrequencySoFar) {
+ highestFrequencySoFar = currentFrequency;
+ mode = currentValue;
+ }
+ currentFrequency = 1;
+ currentValue = d;
+ }
+ }
+
+ if (highestFrequencySoFar < 2)
+ throw new IllegalArgumentException("the are no duplicates in the list of numbers supplied to MODE()!");
+
+ return mode;
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/NormDist.java b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/NormDist.java
new file mode 100644
index 0000000..cd8a234
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/NormDist.java
@@ -0,0 +1,155 @@
+/*
+ File: NormDist.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import org.cytoscape.equations.AbstractFunction;
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+import org.cytoscape.equations.FunctionUtil;
+
+
+public class NormDist extends AbstractFunction {
+ public NormDist() {
+ super(new ArgDescriptor[] {
+ new ArgDescriptor(ArgType.FLOAT, "x", "Argument."),
+ new ArgDescriptor(ArgType.FLOAT, "mean", "The mean of the function."),
+ new ArgDescriptor(ArgType.FLOAT, "stddev", "The standard deviation of the function."),
+ new ArgDescriptor(ArgType.BOOL, "cumulative?", "If true we return the CDF, otherwise we return the pdf.")
+ });
+ }
+
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "NORMDIST"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Returns the Normal Probability Density Function or the Cumulative Normal Distribution Function."; }
+
+ public Class getReturnType() { return Double.class; }
+
+ /**
+ * @param args the function arguments which must be either one or two objects of type Double
+ * @return the result of the function evaluation which is the logarithm of the first argument
+ * @throws ArithmeticException
+ * @throws IllegalArgumentException thrown if any of the arguments is not of type Double
+ */
+ public Object evaluateFunction(final Object[] args) throws IllegalArgumentException, ArithmeticException {
+ final double x;
+ try {
+ x = FunctionUtil.getArgAsDouble(args[0]);
+ } catch (final Exception e) {
+ throw new IllegalArgumentException("can't convert \"" + args[0] + "\" to the 1st argument of NORMDIST()!");
+ }
+
+ final double mu;
+ try {
+ mu = FunctionUtil.getArgAsDouble(args[1]);
+ } catch (final Exception e) {
+ throw new IllegalArgumentException("can't convert \"" + args[1] + "\" to the 2nd argument of NORMDIST()!");
+ }
+
+ final double sigma;
+ try {
+ sigma = FunctionUtil.getArgAsDouble(args[2]);
+ } catch (final Exception e) {
+ throw new IllegalArgumentException("can't convert \"" + args[2] + "\" to the 3rd argument of NORMDIST()!");
+ }
+
+ if (sigma <= 0)
+ throw new IllegalArgumentException("mean parameter in call to NORMDIST must be nonnegative!");
+ final boolean cumulative = FunctionUtil.getArgAsBoolean(args[3]);
+
+ if (cumulative) {
+ final double z = (x - mu) / sigma;
+ return (Double)cdf(z);
+ }
+ else
+ return (Double)pdf(x, mu, sigma);
+ }
+
+ /**
+ * @return the pdf of a normal distribution with mean "mu" and std. dev. "sigma"
+ */
+ private double pdf(final double x, final double mu, final double sigma) {
+ final double z = (x - mu) / sigma;
+ return Math.exp(- 0.5 * z * z) / (Math.sqrt(2.0 * Math.PI) * sigma);
+ }
+
+ /**
+ * Calculates an approximation to the CDF of the standard normal distribution
+ * based on "BETTER APPROXIMATIONS TO CUMULATIVE NORMAL FUNCTIONS" by Graeme West.
+ *
+ * @return the CDF of the standard normal distribution
+ */
+ private double cdf(final double z) {
+ double cumulativeNorm;
+ final double zAbs = Math.abs(z);
+ if (zAbs > 37.0)
+ cumulativeNorm = 0.0;
+ else {
+ final double Exponential = Math.exp(-zAbs * zAbs / 2.0);
+ if (zAbs < 7.07106781186547) {
+ double build = 3.52624965998911E-02 * zAbs + 0.700383064443688;
+ build = build * zAbs + 6.37396220353165;
+ build = build * zAbs + 33.912866078383;
+ build = build * zAbs + 112.079291497871;
+ build = build * zAbs + 221.213596169931;
+ build = build * zAbs + 220.206867912376;
+ cumulativeNorm = Exponential * build;
+ build = 8.83883476483184E-02 * zAbs + 1.75566716318264;
+ build = build * zAbs + 16.064177579207;
+ build = build * zAbs + 86.7807322029461;
+ build = build * zAbs + 296.564248779674;
+ build = build * zAbs + 637.333633378831;
+ build = build * zAbs + 793.826512519948;
+ build = build * zAbs + 440.413735824752;
+ cumulativeNorm = cumulativeNorm / build;
+ } else {
+ double build = zAbs + 0.65;
+ build = zAbs + 4 / build;
+ build = zAbs + 3 / build;
+ build = zAbs + 2 / build;
+ build = zAbs + 1 / build;
+ cumulativeNorm = Exponential / build / 2.506628274631;
+ }
+ }
+
+ if (z > 0.0)
+ cumulativeNorm = 1.0 - cumulativeNorm;
+
+ return cumulativeNorm;
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Not.java b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Not.java
new file mode 100644
index 0000000..81f82cd
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Not.java
@@ -0,0 +1,76 @@
+/*
+ File: Not.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import org.cytoscape.equations.AbstractFunction;
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+import org.cytoscape.equations.FunctionUtil;
+
+
+public class Not extends AbstractFunction {
+ public Not() {
+ super(new ArgDescriptor[] {
+ new ArgDescriptor(ArgType.BOOL, "logical_expr", "Any boolean value.")
+ });
+ }
+
+ /**
+ * Used to parse the function string.
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "NOT"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Returns the logical negation of a boolean value."; }
+
+ public Class getReturnType() { return Boolean.class; }
+
+ /**
+ * @param args the function arguments which must all be of type Boolean
+ * @return the result of the function evaluation which is either true or false
+ * @throws ArithmeticException this can never happen
+ * @throws IllegalArgumentException this can never happen
+ */
+ public Object evaluateFunction(final Object[] args) throws IllegalArgumentException, ArithmeticException {
+ final boolean b;
+ try {
+ b = FunctionUtil.getArgAsBoolean(args[0]);
+ } catch (final Exception e) {
+ throw new IllegalArgumentException("can't convert \"" + args[0] + "\" to a boolean value in a call to NOT()!");
+ }
+
+ return !b;
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Now.java b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Now.java
new file mode 100644
index 0000000..4104061
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Now.java
@@ -0,0 +1,81 @@
+/*
+ File: Now.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import java.text.DateFormat;
+
+import java.util.Calendar;
+
+import org.cytoscape.equations.AbstractFunction;
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+
+
+public class Now extends AbstractFunction {
+ public Now() {
+ super(new ArgDescriptor[] {
+ });
+ }
+
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "NOW"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Returns the current date and time."; }
+
+ public Class getReturnType() { return Double.class; }
+
+ /**
+ * @param args the function arguments which must be either one object of type Double or Long
+ * @return the result of the function evaluation which is the natural logarithm of the first argument
+ */
+ public Object evaluateFunction(final Object[] args) {
+ final Calendar calendar = Calendar.getInstance();
+ final DateFormat dateFormat = DateFormat.getDateInstance(DateFormat.SHORT);
+ final DateFormat timeFormat = DateFormat.getTimeInstance(DateFormat.SHORT);
+
+ try {
+ final String date = dateFormat.format(calendar.getTime());
+ final String time = timeFormat.format(calendar.getTime());
+
+ return date + " " + time;
+ }
+ catch (final Exception e) {
+ throw new IllegalStateException("failed to get today's date: " + e.getMessage());
+ }
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Nth.java b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Nth.java
new file mode 100644
index 0000000..62d49cc
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Nth.java
@@ -0,0 +1,88 @@
+/*
+ File: Nth.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import java.util.List;
+
+import org.cytoscape.equations.AbstractFunction;
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+import org.cytoscape.equations.FunctionUtil;
+
+
+public class Nth extends AbstractFunction {
+ public Nth() {
+ super(new ArgDescriptor[] {
+ new ArgDescriptor(ArgType.STRICT_ANY_LIST, "list", "A list of objects."),
+ new ArgDescriptor(ArgType.INT, "index", "An index into the list."),
+ });
+ }
+
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "NTH"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Returns the n-th entry in a list."; }
+
+ public Class getReturnType() { return Object.class; }
+
+ /**
+ * @param args the function arguments which must be a list followed by a number
+ * @return the n-th entry (1-based) in the list
+ * @throws ArithmeticException
+ * @throws IllegalArgumentException thrown if the index is out of range
+ */
+ public Object evaluateFunction(final Object[] args) throws IllegalArgumentException, ArithmeticException {
+ final List list = (List)args[0];
+ final int index;
+ try {
+ index = (int)FunctionUtil.getArgAsLong(args[1]);
+ } catch (final Exception e) {
+ throw new IllegalArgumentException("can't convert \"" + args[1] + "\" to an integer in a call to NTH()!");
+ }
+
+ if (index <= 0 || index > list.size())
+ throw new IllegalArgumentException("illegal list index in call to NTH()!");
+
+ final Object listElement = list.get(index - 1);
+ final Object retVal = FunctionUtil.translateObjectType(listElement);
+ if (retVal == null)
+ throw new IllegalArgumentException("bad list element type: " + listElement.getClass() + " in a call to NTH()!");
+
+ return retVal;
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Or.java b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Or.java
new file mode 100644
index 0000000..4405c4b
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Or.java
@@ -0,0 +1,81 @@
+/*
+ File: Or.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import org.cytoscape.equations.AbstractFunction;
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+import org.cytoscape.equations.FunctionUtil;
+
+
+public class Or extends AbstractFunction {
+ public Or() {
+ super(new ArgDescriptor[] {
+ new ArgDescriptor(ArgType.OPT_BOOLS, "truth_values", "Zero or more truth values or lists of truth values."),
+ });
+ }
+
+ /**
+ * Used to parse the function string.
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "OR"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Returns the logical disjunction of any number of boolean values."; }
+
+ public Class getReturnType() { return Boolean.class; }
+
+ /**
+ * @param args the function arguments which must all be of type Boolean
+ * @return the result of the function evaluation which is either true or false
+ * @throws ArithmeticException this can never happen
+ * @throws IllegalArgumentException thrown if any of the arguments is not of type Boolean
+ */
+ public Object evaluateFunction(final Object[] args) throws IllegalArgumentException, ArithmeticException {
+ final boolean[] booleans;
+ try {
+ booleans = FunctionUtil.getBooleans(args);
+ } catch (final Exception e) {
+ throw new IllegalArgumentException("can't convert an argument or a list element to a boolean in a call to OR()!");
+ }
+
+ for (final boolean b : booleans) {
+ if (b)
+ return true;
+ }
+
+ return false;
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Permut.java b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Permut.java
new file mode 100644
index 0000000..d7aa943
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Permut.java
@@ -0,0 +1,90 @@
+/*
+ File: Permut.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import org.cytoscape.equations.AbstractFunction;
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+import org.cytoscape.equations.FunctionUtil;
+
+
+public class Permut extends AbstractFunction {
+ public Permut() {
+ super(new ArgDescriptor[] {
+ new ArgDescriptor(ArgType.INT, "n", "The total number of objects."),
+ new ArgDescriptor(ArgType.INT, "k", "The size of the selected subset."),
+ });
+ }
+
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "PERMUT"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Returns the number of permutations of size k of n objects."; }
+
+ public Class getReturnType() { return Double.class; }
+
+ /**
+ * @param args the function arguments which must be either one or two objects of type Double
+ * @return the result of the function evaluation which is the logarithm of the first argument
+ * @throws ArithmeticException
+ * @throws IllegalArgumentException thrown if any of the arguments is not of type Double
+ */
+ public Object evaluateFunction(final Object[] args) throws IllegalArgumentException, ArithmeticException {
+ final long N = FunctionUtil.getArgAsLong(args[0]);
+ if (N <= 0L)
+ throw new IllegalArgumentException("first argument to PERMUT must be positive!");
+
+ final long K = FunctionUtil.getArgAsLong(args[1]);
+ if (K < 0L)
+ throw new IllegalArgumentException("second argument to PERMUT must be nonnegative!");
+ if (K > N)
+ throw new IllegalArgumentException("second argument to PERMUT must be no greater than the first argument!");
+
+ long retval = 1L;
+ long multiplier = N;
+ for (long i = 0; i < K; ++i) {
+ final long next = retval * multiplier;
+ if (next < retval)
+ throw new ArithmeticException("overflow detected while calulating PERMUT(" + N + "," + K + "!");
+ --multiplier;
+ retval = next;
+ }
+
+ return (Long)retval;
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Pi.java b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Pi.java
new file mode 100644
index 0000000..7eff031
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Pi.java
@@ -0,0 +1,67 @@
+/*
+ File: Pi.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import org.cytoscape.equations.AbstractFunction;
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+
+
+public class Pi extends AbstractFunction {
+ public Pi() {
+ super(new ArgDescriptor[] {
+ });
+ }
+
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "PI"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Returns the value of \u03C0."; }
+
+ public Class getReturnType() { return Double.class; }
+
+ /**
+ * @param args the function arguments which must be either one or two objects of type Double
+ * @return the result of the function evaluation which is the logarithm of the first argument
+ * @throws ArithmeticException
+ * @throws IllegalArgumentException thrown if any of the arguments is not of type Double
+ */
+ public Object evaluateFunction(final Object[] args) throws IllegalArgumentException, ArithmeticException {
+ return Math.PI;
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Product.java b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Product.java
new file mode 100644
index 0000000..0dd8586
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Product.java
@@ -0,0 +1,78 @@
+/*
+ File: Product.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import org.cytoscape.equations.AbstractFunction;
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+import org.cytoscape.equations.FunctionUtil;
+
+
+public class Product extends AbstractFunction {
+ public Product() {
+ super(new ArgDescriptor[] {
+ new ArgDescriptor(ArgType.OPT_FLOATS, "numbers", "One or more numbers or lists of numbers."),
+ });
+ }
+
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "PRODUCT"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Returns the product of all of its arguments."; }
+
+ public Class getReturnType() { return Double.class; }
+
+ /**
+ * @param args the function arguments which must be either one object of type Double or Long
+ * @return the result of the function evaluation which is the natural logarithm of the first argument
+ */
+ public Object evaluateFunction(final Object[] args) {
+ final double[] numbers;
+ try {
+ numbers = FunctionUtil.getDoubles(args);
+ } catch (final Exception e) {
+ throw new IllegalArgumentException("can't convert an argument or a list element to a number in a call to PRODUCT()!");
+ }
+
+ double product = 1.0;
+ for (final double d : numbers)
+ product *= d;
+
+ return product;
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Radians.java b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Radians.java
new file mode 100644
index 0000000..e793de9
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Radians.java
@@ -0,0 +1,68 @@
+/*
+ File: Radians.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import org.cytoscape.equations.AbstractFunction;
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+import org.cytoscape.equations.FunctionUtil;
+
+
+public class Radians extends AbstractFunction {
+ public Radians() {
+ super(new ArgDescriptor[] {
+ new ArgDescriptor(ArgType.FLOAT, "angle", "An angle in degrees."),
+ });
+ }
+
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "RADIANS"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Returns the value in radians converted from degrees."; }
+
+ public Class getReturnType() { return Double.class; }
+
+ /**
+ * @param args the function arguments which must be either one object of type Double or Long
+ * @return the result of the function evaluation which is the natural logarithm of the first argument
+ */
+ public Object evaluateFunction(final Object[] args) {
+ final double angleInDegrees = FunctionUtil.getArgAsDouble(args[0]);
+ return angleInDegrees * Math.PI / 180.0;
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Right.java b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Right.java
new file mode 100644
index 0000000..eea52e7
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Right.java
@@ -0,0 +1,86 @@
+/*
+ File: Right.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import org.cytoscape.equations.AbstractFunction;
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+import org.cytoscape.equations.FunctionUtil;
+
+
+public class Right extends AbstractFunction {
+ public Right() {
+ super(new ArgDescriptor[] {
+ new ArgDescriptor(ArgType.STRING, "text", "The source text."),
+ new ArgDescriptor(ArgType.OPT_FLOAT, "number", "How many characters to extract. (Default is 1.)"),
+ });
+ }
+
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "RIGHT"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Returns a suffix of a string."; }
+
+ public Class getReturnType() { return String.class; }
+
+ /**
+ * @param args the function arguments which must be either one or two objects of type Double
+ * @return the result of the function evaluation which is the natural logarithm of the first argument
+ * @throws ArithmeticException
+ * @throws IllegalArgumentException thrown if any of the arguments is not of type Boolean
+ */
+ public Object evaluateFunction(final Object[] args) throws IllegalArgumentException, ArithmeticException {
+ final String text = FunctionUtil.getArgAsString(args[0]);
+ final int count;
+ if (args.length == 1)
+ count = 1;
+ else {
+ try {
+ count = (int)FunctionUtil.getArgAsLong(args[1]);
+ } catch (final Exception e) {
+ throw new IllegalArgumentException("can't convert \"" + args[1] + "\" to an integer in a call to RIGHT()!");
+ }
+ if (count < 0)
+ throw new IllegalArgumentException("illegal character count in a call to RIGHT()!");
+ }
+
+ if (count >= text.length())
+ return text;
+ return text.substring(text.length() - count);
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Round.java b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Round.java
new file mode 100644
index 0000000..530e0c4
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Round.java
@@ -0,0 +1,87 @@
+/*
+ File: Round.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import org.cytoscape.equations.AbstractFunction;
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+import org.cytoscape.equations.FunctionUtil;
+
+
+public class Round extends AbstractFunction {
+ public Round() {
+ super(new ArgDescriptor[] {
+ new ArgDescriptor(ArgType.FLOAT, "number", "Any number."),
+ new ArgDescriptor(ArgType.FLOAT, "digit_count", "Round to this number of significant digits.")
+ });
+ }
+
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "ROUND"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Rounds a number to a specified number of decimal places."; }
+
+ public Class getReturnType() { return Double.class; }
+
+ /**
+ * @param args the function arguments which must be either one or two objects of type Double
+ * @return the result of the function evaluation which is the rounded first argument
+ * @throws ArithmeticException
+ * @throws IllegalArgumentException thrown if any of the arguments is not of type Double
+ */
+ public Object evaluateFunction(final Object[] args) throws IllegalArgumentException, ArithmeticException {
+ final double number;
+ try {
+ number = FunctionUtil.getArgAsDouble(args[0]);
+ } catch (final Exception e) {
+ throw new IllegalArgumentException("can't convert \"" + args[0] + "\" to a number in a call to ROUND()!");
+ }
+ final double absNumber = Math.abs(number);
+
+ final double numDigits;
+ try {
+ numDigits = FunctionUtil.getArgAsLong(args[1]);
+ } catch (final Exception e) {
+ throw new IllegalArgumentException("can't convert \"" + args[1] + "\" to an integer in a call to ROUND()!");
+ }
+
+ final double shift = Math.pow(10.0, numDigits);
+ final double roundedAbsNumber = Math.round(absNumber * shift) / shift;
+ return number > 0.0 ? roundedAbsNumber : -roundedAbsNumber;
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/SList.java b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/SList.java
new file mode 100644
index 0000000..4e58ac9
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/SList.java
@@ -0,0 +1,71 @@
+/*
+ File: SList.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import org.cytoscape.equations.AbstractFunction;
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+import org.cytoscape.equations.FunctionUtil;
+import org.cytoscape.equations.StringList;
+
+
+public class SList extends AbstractFunction {
+ public SList() {
+ super(new ArgDescriptor[] {
+ new ArgDescriptor(ArgType.OPT_STRINGS, "strings", "Zero or more numbers, strings or booleans."),
+ });
+ }
+
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "SLIST"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Returns a list of strings (a.k.a. text objects)."; }
+
+ public Class getReturnType() { return StringList.class; }
+
+ /**
+ * @param args the function arguments which must be either one or two objects of type Double
+ * @return the result of the function evaluation which is the maximum of the elements in the single list argument or the maximum of the one or more double arguments
+ * @throws ArithmeticException
+ * @throws IllegalArgumentException thrown if any of the arguments is not of type Double
+ */
+ public Object evaluateFunction(final Object[] args) throws IllegalArgumentException, ArithmeticException {
+ final String[] strings = FunctionUtil.getStrings(args);
+ return new StringList(strings);
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Sign.java b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Sign.java
new file mode 100644
index 0000000..1352c46
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Sign.java
@@ -0,0 +1,75 @@
+/*
+ File: Sign.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import org.cytoscape.equations.AbstractFunction;
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+import org.cytoscape.equations.FunctionUtil;
+
+
+public class Sign extends AbstractFunction {
+ public Sign() {
+ super(new ArgDescriptor[] {
+ new ArgDescriptor(ArgType.FLOAT, "number", "Any number."),
+ });
+ }
+
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "SIGN"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Implements the signum function. Returns -1,0,+1 based on the number being negative, zero, or positive."; }
+
+ public Class getReturnType() { return Double.class; }
+
+ /**
+ * @param args the function arguments which must be one object of type Double, Long, Boolean or
+ * a String that can be converted to a number
+ * @return the result of the function evaluation which is the signum of the first argument
+ */
+ public Object evaluateFunction(final Object[] args) {
+ double number;
+ try {
+ number = FunctionUtil.getArgAsDouble(args[0]);
+ } catch (final Exception e) {
+ throw new IllegalArgumentException("SIGN: " + e.getMessage());
+ }
+
+ return Math.signum(number);
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Sin.java b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Sin.java
new file mode 100644
index 0000000..7382e45
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Sin.java
@@ -0,0 +1,68 @@
+/*
+ File: Sin.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import org.cytoscape.equations.AbstractFunction;
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+import org.cytoscape.equations.FunctionUtil;
+
+
+public class Sin extends AbstractFunction {
+ public Sin() {
+ super(new ArgDescriptor[] {
+ new ArgDescriptor(ArgType.FLOAT, "number", "An angle in radians."),
+ });
+ }
+
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "SIN"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Returns the sine of an angle given in radians."; }
+
+ public Class getReturnType() { return Double.class; }
+
+ /**
+ * @param args the function arguments which must be either one object of type Double or Long
+ * @return the result of the function evaluation which is the natural logarithm of the first argument
+ */
+ public Object evaluateFunction(final Object[] args) {
+ final double angleInRadians = FunctionUtil.getArgAsDouble(args[0]);
+ return Math.sin(angleInRadians);
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Sinh.java b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Sinh.java
new file mode 100644
index 0000000..f7886b3
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Sinh.java
@@ -0,0 +1,68 @@
+/*
+ File: Sinh.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import org.cytoscape.equations.AbstractFunction;
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+import org.cytoscape.equations.FunctionUtil;
+
+
+public class Sinh extends AbstractFunction {
+ public Sinh() {
+ super(new ArgDescriptor[] {
+ new ArgDescriptor(ArgType.FLOAT, "number", "Any number."),
+ });
+ }
+
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "SINH"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Returns the hyperbolic sine of a number."; }
+
+ public Class getReturnType() { return Double.class; }
+
+ /**
+ * @param args the function arguments which must be either one object of type Double or Long
+ * @return the result of the function evaluation which is the natural logarithm of the first argument
+ */
+ public Object evaluateFunction(final Object[] args) {
+ final double arg = FunctionUtil.getArgAsDouble(args[0]);
+ return Math.sinh(arg);
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Sqrt.java b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Sqrt.java
new file mode 100644
index 0000000..3c193b5
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Sqrt.java
@@ -0,0 +1,77 @@
+/*
+ File: Sqrt.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import org.cytoscape.equations.AbstractFunction;
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+import org.cytoscape.equations.FunctionUtil;
+
+
+public class Sqrt extends AbstractFunction {
+ public Sqrt() {
+ super(new ArgDescriptor[] {
+ new ArgDescriptor(ArgType.FLOAT, "radicand", "A non-negative number."),
+ });
+ }
+
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "SQRT"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Calculates the principal square root of a non-negative number."; }
+
+ public Class getReturnType() { return Double.class; }
+
+ /**
+ * @param args the function arguments which must be either one or two objects of type Double
+ * @return the result of the function evaluation which is the natural logarithm of the first argument
+ * @throws ArithmeticException if the argument is negative
+ */
+ public Object evaluateFunction(final Object[] args) throws ArithmeticException {
+ final double number;
+ try {
+ number = FunctionUtil.getArgAsDouble(args[0]);
+ } catch (final Exception e) {
+ throw new IllegalArgumentException("can't convert \"" + args[0] + "\" to a number in a call to SQRT()!");
+ }
+ if (number < 0.0)
+ throw new ArithmeticException("negative argument in call to the SQRT() function!");
+
+ return Math.sqrt(number);
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/StDev.java b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/StDev.java
new file mode 100644
index 0000000..747cb32
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/StDev.java
@@ -0,0 +1,78 @@
+/*
+ File: StDev.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import org.cytoscape.equations.AbstractFunction;
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+import org.cytoscape.equations.FunctionUtil;
+
+
+public class StDev extends AbstractFunction {
+ public StDev() {
+ super(new ArgDescriptor[] {
+ new ArgDescriptor(ArgType.FLOATS, "numbers", "One or more numbers or lists of numbers."),
+ });
+ }
+
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "STDEV"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Returns the sample standard deviation of a list or lists of numbers."; }
+
+ public Class getReturnType() { return Double.class; }
+
+ /**
+ * @param args the function arguments which must be a list followed by a numeric argument
+ * @return the result of the function evaluation which is the maximum of the elements in the single list argument or the maximum of the one or more double arguments
+ * @throws ArithmeticException
+ * @throws IllegalArgumentException thrown if any of the members of the single List argument cannot be converted to a number
+ */
+ public Object evaluateFunction(final Object[] args) throws IllegalArgumentException, ArithmeticException {
+ final double[] numbers;
+ try {
+ numbers = FunctionUtil.getDoubles(args);
+ } catch (final Exception e) {
+ throw new IllegalArgumentException("could not convert an argument or list element to a number in a call to STDEV()!");
+ }
+ if (numbers.length < 2)
+ throw new IllegalArgumentException("illegal argument(s) in call to STDEV(): must have at least 2 numbers!");
+
+ return Math.sqrt(FunctionUtil.calcSampleVariance(numbers));
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Substitute.java b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Substitute.java
new file mode 100644
index 0000000..3b4a9f3
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Substitute.java
@@ -0,0 +1,126 @@
+/*
+ File: Substitute.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import org.cytoscape.equations.AbstractFunction;
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+import org.cytoscape.equations.FunctionUtil;
+
+
+public class Substitute extends AbstractFunction {
+ public Substitute() {
+ super(new ArgDescriptor[] {
+ new ArgDescriptor(ArgType.STRING, "text", "The source text."),
+ new ArgDescriptor(ArgType.STRING, "original", "The text that will be replaced."),
+ new ArgDescriptor(ArgType.STRING, "replacement", "The replacement text."),
+ new ArgDescriptor(ArgType.OPT_INT, "nth_appearance", "Which occurrence to replace.")
+ });
+ }
+
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "SUBSTITUTE"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Replaces some text with other text."; }
+
+ public Class getReturnType() { return String.class; }
+
+ /**
+ * @param args the function arguments which must be either one or two objects of type String
+ * @return the result of the function evaluation which is the natural logarithm of the first argument
+ * @throws ArithmeticException
+ * @throws IllegalArgumentException thrown if any of the arguments is not of type Boolean
+ */
+ public Object evaluateFunction(final Object[] args) throws IllegalArgumentException, ArithmeticException {
+ final String text = FunctionUtil.getArgAsString(args[0]);
+ final String original = FunctionUtil.getArgAsString(args[1]);
+ final String replacement = FunctionUtil.getArgAsString(args[2]);
+
+ if (args.length == 3)
+ return replaceAll(text, original, replacement);
+ else { // Assume args.length == 4
+ final int nthAppearance;
+ try {
+ nthAppearance = (int)FunctionUtil.getArgAsLong(args[3]);
+ } catch (final Exception e) {
+ throw new IllegalArgumentException("can't convert \"" + args[3] + "\" to a number in a call to SUBSTITUTE()!");
+ }
+
+ if (nthAppearance <= 0)
+ return text;
+ final int startIndex;
+ if ((startIndex = findNth(nthAppearance, text, original)) == -1)
+ return text;
+
+ return text.substring(0, startIndex) + replacement + text.substring(startIndex + original.length());
+ }
+ }
+
+ /**
+ * @return the 0-based starting position of the nth appearance of "needle" in "hayStack" or -1 if it can't be found
+ */
+ private static int findNth(final int n, final String hayStack, final String needle) {
+ int startOffset = 0;
+ int offset = 0;
+ for (int i = 0; i < n; ++i) {
+ if ((offset = hayStack.indexOf(needle, startOffset)) == -1)
+ return offset;
+ startOffset = offset + needle.length();
+ }
+
+ return offset;
+ }
+
+ /**
+ * @return a string where all occurrences of "original" found in "s" have been replaced with "replacement"
+ */
+ private static String replaceAll(final String s, final String original, final String replacement) {
+ final StringBuilder builder = new StringBuilder();
+
+ int startOffset = 0;
+ int startMatch;
+ while ((startMatch = s.indexOf(original, startOffset)) != -1) {
+ builder.append(s.substring(startOffset, startMatch));
+ builder.append(replacement);
+ startOffset = startMatch + original.length();
+ }
+ builder.append(s.substring(startOffset));
+
+ return builder.toString();
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Sum.java b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Sum.java
new file mode 100644
index 0000000..4cf287c
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Sum.java
@@ -0,0 +1,76 @@
+/*
+ File: Sum.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import org.cytoscape.equations.AbstractFunction;
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+import org.cytoscape.equations.FunctionUtil;
+
+
+public class Sum extends AbstractFunction {
+ public Sum() {
+ super(new ArgDescriptor[] { new ArgDescriptor(ArgType.OPT_FLOATS, "numbers", "One or more numbers or lists of numbers.") });
+ }
+
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "SUM"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Returns the sum of all of its arguments."; }
+
+ public Class getReturnType() { return Double.class; }
+
+ /**
+ * @param args the function arguments which must be either one object of type Double or Long
+ * @return the sum of all the numbers in "args"
+ */
+ public Object evaluateFunction(final Object[] args) {
+ final double[] numbers;
+ try {
+ numbers = FunctionUtil.getDoubles(args);
+ } catch (final Exception e) {
+ throw new IllegalArgumentException("in a call to SUM(): could not convert one of the arguments to a number or list of numbers!");
+ }
+
+ double sum = 0.0;
+ for (final double d : numbers)
+ sum += d;
+
+ return sum;
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Tan.java b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Tan.java
new file mode 100644
index 0000000..c50982c
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Tan.java
@@ -0,0 +1,71 @@
+/*
+ File: Tan.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import org.cytoscape.equations.AbstractFunction;
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+import org.cytoscape.equations.FunctionUtil;
+
+
+public class Tan extends AbstractFunction {
+ public Tan() {
+ super(new ArgDescriptor[] { new ArgDescriptor(ArgType.FLOAT, "number", "Any real number representing an angle in radians.") });
+ }
+
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "TAN"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Returns the tanget of an angle given in radians."; }
+
+ public Class getReturnType() { return Double.class; }
+
+ /**
+ * @param args the function arguments which must be either one object of type Double or Long
+ * @return the result of the function evaluation which is the natural logarithm of the first argument
+ */
+ public Object evaluateFunction(final Object[] args) {
+ final double angleInRadians = FunctionUtil.getArgAsDouble(args[0]);
+
+ final double cos = Math.cos(angleInRadians);
+ if (cos == 0.0)
+ throw new IllegalArgumentException("division by zero in call to TAN()!");
+
+ return Math.sin(angleInRadians) / cos;
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Tanh.java b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Tanh.java
new file mode 100644
index 0000000..04173ae
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Tanh.java
@@ -0,0 +1,72 @@
+/*
+ File: Tanh.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import org.cytoscape.equations.AbstractFunction;
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+import org.cytoscape.equations.FunctionUtil;
+
+
+public class Tanh extends AbstractFunction {
+ public Tanh() {
+ super(new ArgDescriptor[] { new ArgDescriptor(ArgType.FLOAT, "number", "Any real number representing an angle in radians.") });
+ }
+
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "TANH"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Returns the hyperbolic tangent an angle given in radians."; }
+
+ public Class getReturnType() { return Double.class; }
+
+ /**
+ * @param args the function arguments which must be either one object of type Double or Long
+ * @return the result of the function evaluation which is the natural logarithm of the first argument
+ */
+ public Object evaluateFunction(final Object[] args) {
+ final double angleInRadians;
+ try {
+ angleInRadians = FunctionUtil.getArgAsDouble(args[0]);
+ } catch (final Exception e) {
+ throw new IllegalArgumentException("can't convert \"" + args[0] + "\" to an angle in radians in a call to TANH()!");
+ }
+
+ return Math.sinh(angleInRadians) / Math.cosh(angleInRadians);
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Text.java b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Text.java
new file mode 100644
index 0000000..ae518c6
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Text.java
@@ -0,0 +1,106 @@
+/*
+ File: Text.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import java.text.DecimalFormat;
+import java.text.DecimalFormatSymbols;
+import java.util.Locale;
+
+import org.cytoscape.equations.AbstractFunction;
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+import org.cytoscape.equations.FunctionUtil;
+
+
+public class Text extends AbstractFunction {
+ public Text() {
+ super(new ArgDescriptor[] {
+ new ArgDescriptor(ArgType.FLOAT, "value", "Any number."),
+ new ArgDescriptor(ArgType.OPT_STRING, "format", "How to format the first argument using the conventions of the Java DecimalFormat class."),
+ });
+ }
+
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "TEXT"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Returns a number formatted as text."; }
+
+ public Class getReturnType() { return String.class; }
+
+ /**
+ * @param args the function arguments which must be either one or two objects of type Double
+ * @return the result of the function evaluation which is the first argument formatted as a string
+ * @throws ArithmeticException
+ * @throws IllegalArgumentException thrown if any of the arguments is not of type Boolean
+ */
+ public Object evaluateFunction(final Object[] args) throws IllegalArgumentException, ArithmeticException {
+ final double value = FunctionUtil.getArgAsDouble(args[0]);
+
+ if (args.length == 1)
+ return Double.toString(value);
+ else {
+ final String format = FunctionUtil.getArgAsString(args[1]);
+ if (!isValidFormat(format))
+ throw new IllegalArgumentException("\"" + format +"\" is not a valid format string for the TEXT() function!");
+
+ final DecimalFormat decimalFormat;
+ try {
+ // force the locale to US so that we consistently serialize
+ decimalFormat = new DecimalFormat(format, new DecimalFormatSymbols(Locale.US));
+ } catch (final Exception e) {
+ throw new IllegalStateException("we should *never* get here!");
+ }
+
+ try {
+ return decimalFormat.format(value).toString();
+ } catch (final Exception e) {
+ throw new IllegalStateException("we should *never* get here (2): " + e);
+ }
+ }
+ }
+
+ private boolean isValidFormat(final String format) {
+ try {
+ // force the locale to US so that we consistently serialize
+ new DecimalFormat(format, new DecimalFormatSymbols(Locale.US));
+ return true;
+ } catch (final Exception e) {
+ return false;
+ }
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Today.java b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Today.java
new file mode 100644
index 0000000..a03d37f
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Today.java
@@ -0,0 +1,76 @@
+/*
+ File: Today.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import java.text.DateFormat;
+
+import java.util.Calendar;
+
+import org.cytoscape.equations.AbstractFunction;
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+
+
+public class Today extends AbstractFunction {
+ public Today() {
+ super(new ArgDescriptor[] { });
+ }
+
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "TODAY"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Returns today's date."; }
+
+ public Class getReturnType() { return Double.class; }
+
+ /**
+ * @param args the function arguments which must be either one object of type Double or Long
+ * @return the result of the function evaluation which is the natural logarithm of the first argument
+ */
+ public Object evaluateFunction(final Object[] args) {
+ final Calendar calendar = Calendar.getInstance();
+ final DateFormat dateFormat = DateFormat.getDateInstance(DateFormat.SHORT);
+
+ try {
+ return dateFormat.format(calendar.getTime());
+ }
+ catch (final Exception e) {
+ throw new IllegalStateException("failed to get today's date: " + e.getMessage());
+ }
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Trunc.java b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Trunc.java
new file mode 100644
index 0000000..4cbe8aa
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Trunc.java
@@ -0,0 +1,94 @@
+/*
+ File: Trunc.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import org.cytoscape.equations.AbstractFunction;
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+import org.cytoscape.equations.FunctionUtil;
+
+
+public class Trunc extends AbstractFunction {
+ public Trunc() {
+ super(new ArgDescriptor[] {
+ new ArgDescriptor(ArgType.FLOAT, "number", "Any number."),
+ new ArgDescriptor(ArgType.OPT_FLOAT, "num_digits", "The number of digits after the decimal point.")
+ });
+ }
+
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "TRUNC"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Truncates a number. (Rounds towards zero.)"; }
+
+ public Class getReturnType() { return Double.class; }
+
+ /**
+ * @param args the function arguments which must be either one or two objects of type Double
+ * @return the result of the function evaluation which is the truncated first argument
+ * @throws ArithmeticException
+ * @throws IllegalArgumentException thrown if the first argument cannot be converted to floating point and the
+ * optional second argument cannot be converted to integer
+ */
+ public Object evaluateFunction(final Object[] args) throws IllegalArgumentException, ArithmeticException {
+ final double number;
+ try {
+ number = FunctionUtil.getArgAsDouble(args[0]);
+ } catch (final Exception e) {
+ throw new IllegalArgumentException("cannot convert \"" + args[0] +"\" to a number in a call to TRUNC()!");
+ }
+ final double absNumber = Math.abs(number);
+
+ final long numDigits;
+ if (args.length == 1)
+ numDigits = 0;
+ else {
+ try {
+ numDigits = FunctionUtil.getArgAsLong(args[1]);
+ } catch (final Exception e) {
+ throw new IllegalArgumentException("cannot convert \"" + args[1] +"\" to an integer in a call to TRUNC()!");
+
+ }
+ }
+
+ final double shift = Math.pow(10.0, (double)numDigits);
+ final double truncatedAbsNumber = Math.round(absNumber * shift - 0.5) / shift;
+
+ return number > 0.0 ? truncatedAbsNumber : -truncatedAbsNumber;
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Upper.java b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Upper.java
new file mode 100644
index 0000000..8ed9ceb
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Upper.java
@@ -0,0 +1,69 @@
+/*
+ File: Upper.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import org.cytoscape.equations.AbstractFunction;
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+import org.cytoscape.equations.FunctionUtil;
+
+
+public class Upper extends AbstractFunction {
+ public Upper() {
+ super(new ArgDescriptor[] { new ArgDescriptor(ArgType.STRICT_STRING, "text", "Any text.") });
+ }
+
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "UPPER"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Converts a string to uppercase."; }
+
+ public Class getReturnType() { return String.class; }
+
+ /**
+ * @param args the function arguments which must be either one or two objects of type Double
+ * @return the result of the function evaluation which is the natural logarithm of the first argument
+ * @throws ArithmeticException
+ * @throws IllegalArgumentException thrown if any of the arguments is not of type Boolean
+ */
+ public Object evaluateFunction(final Object[] args) throws IllegalArgumentException, ArithmeticException {
+ final String text = FunctionUtil.getArgAsString(args[0]);
+
+ return text.toUpperCase();
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Value.java b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Value.java
new file mode 100644
index 0000000..9ccc97e
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Value.java
@@ -0,0 +1,77 @@
+/*
+ File: Value.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import org.cytoscape.equations.AbstractFunction;
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+
+
+public class Value extends AbstractFunction {
+ public Value() {
+ super(new ArgDescriptor[] { new ArgDescriptor(ArgType.STRING, "text_or_number", "A number or a string representing a number.") });
+ }
+
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "VALUE"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Converts a string or a number to a number."; }
+
+ public Class getReturnType() { return Double.class; }
+
+ /**
+ * @param args the function arguments which must be either one or two objects of type Double
+ * @return the result of the function evaluation which is the logarithm of the first argument
+ * @throws ArithmeticException
+ * @throws IllegalArgumentException thrown if any of the arguments is not of type Double
+ */
+ public Object evaluateFunction(final Object[] args) throws IllegalArgumentException, ArithmeticException {
+ if (args[0].getClass() == Double.class)
+ return (Double)args[0];
+ if (args[0].getClass() == Long.class)
+ return (double)(Long)args[0];
+ if (args[0].getClass() == Boolean.class)
+ return Double.valueOf((Boolean)args[0] ? 1.0 : 0.0);
+
+ try {
+ return Double.parseDouble((String)args[0]);
+ } catch (final NumberFormatException e) {
+ throw new IllegalArgumentException("text argument \"" + args[0] + "\"of VALUE() function is not a valid number!");
+ }
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Var.java b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Var.java
new file mode 100644
index 0000000..17cc06c
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/builtins/Var.java
@@ -0,0 +1,72 @@
+/*
+ File: Var.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import org.cytoscape.equations.AbstractFunction;
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+import org.cytoscape.equations.FunctionError;
+import org.cytoscape.equations.FunctionUtil;
+
+
+public class Var extends AbstractFunction {
+ public Var() {
+ super(new ArgDescriptor[] { new ArgDescriptor(ArgType.FLOATS, "numbers", "Two or more floating point numbers.") });
+ }
+
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "VAR"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Returns the sample variance of a list(s) of numbers."; }
+
+ public Class getReturnType() { return Double.class; }
+
+ /**
+ * @param args the function arguments which must be a list followed by a numeric argument
+ * @return the result of the function evaluation which is the maximum of the elements in the single list argument or the maximum of the one or more double arguments
+ * @throws ArithmeticException
+ * @throws IllegalArgumentException thrown if any of the members of the single List argument cannot be converted to a number
+ */
+ public Object evaluateFunction(final Object[] args) throws FunctionError {
+ final double[] numbers = FunctionUtil.getDoubles(args);
+ if (numbers.length < 2)
+ throw new IllegalArgumentException("illegal list argument in call to VAR(): must have at least 2 numbers!");
+
+ return FunctionUtil.calcSampleVariance(numbers);
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/interpreter/IdentDescriptor.java b/corelibs/equations/src/main/java/org/cytoscape/equations/interpreter/IdentDescriptor.java
new file mode 100644
index 0000000..6b66eca
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/interpreter/IdentDescriptor.java
@@ -0,0 +1,64 @@
+/*
+ File: IdentDescriptor.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.interpreter;
+
+
+import java.util.List;
+
+
+public class IdentDescriptor {
+ private final Class type;
+ private final Object value;
+
+ public IdentDescriptor(final Object o) {
+ if (o == null)
+ throw new IllegalArgumentException("argument must not be null!");
+
+ if (o.getClass() == Integer.class) { // Need to map Integer to Long!
+ final Integer i = (Integer)o;
+ this.type = Long.class;
+ this.value = new Long(i);
+ return;
+ }
+ else if (o instanceof List)
+ this.type = List.class;
+ else if (o instanceof Long)
+ this.type = Long.class;
+ else if (o.getClass() != Double.class && o.getClass() != Boolean.class && o.getClass() != String.class)
+ throw new IllegalArgumentException("argument is of an unsupported type (" + o.getClass() + ")!");
+ else
+ this.type = o.getClass();
+
+ this.value = o;
+ }
+
+ Class getType() { return type; }
+ Object getValue() { return value; }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/interpreter/Instruction.java b/corelibs/equations/src/main/java/org/cytoscape/equations/interpreter/Instruction.java
new file mode 100644
index 0000000..f7799b5
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/interpreter/Instruction.java
@@ -0,0 +1,69 @@
+/*
+ File: Instruction.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.interpreter;
+
+
+public enum Instruction {
+ FADD, // addition of two floating-point numbers
+ FSUB, // subtraction of two floating-point numbers
+ FMUL, // multiplication of two floating-point numbers
+ FDIV, // division of two floating-point numbers
+ FPOW, // exponentiation of two floating-point numbers
+ SCONCAT, // string concatentation
+ BEQLF, // equality test for two floating-point numbers
+ BNEQLF, // inequality test for two floating-point numbers
+ BGTF, // greater-than test for two floating-point numbers
+ BLTF, // less-than test for two floating-point numbers
+ BGTEF, // greater-than-or-equal test for two floating-point numbers
+ BLTEF, // less-than-or-equal test for two floating-point numbers
+ BEQLS, // equality test for strings
+ BNEQLS, // inequality test for strings
+ BGTS, // lexicographically greater-than test for strings
+ BLTS, // lexicographically less-than test for strings
+ BGTES, // lexicographically greater-than-or-equal test for strings
+ BLTES, // lexicographically less-than-or-equal test for strings
+ BGTB, // greater than test for booleans
+ BLTB, // less than test for booleans
+ BGTEB, // greater than or equal test for booleans
+ BLTEB, // less than or equal test for booleans
+ BEQLB, // equality test for booleans
+ BNEQLB, // inequality test for booleans
+ CALL, // function call
+ FUMINUS, // unary minus for a floating-point numbers
+ FUPLUS, // unary plus for a floating-point numbers
+ AREF, // attribute reference
+ AREF2, // attribute reference with a default value
+ FCONVI, // conversion of an integer to floating point
+ FCONVB, // conversion of a boolean to floating point
+ FCONVS, // conversion of a string to floating point
+ SCONVF, // conversion of a floating point number to a string
+ SCONVI, // conversion of an integer to a string
+ SCONVB // conversion of a boolean to a string
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/interpreter/Interpreter.java b/corelibs/equations/src/main/java/org/cytoscape/equations/interpreter/Interpreter.java
new file mode 100644
index 0000000..51b65c8
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/interpreter/Interpreter.java
@@ -0,0 +1,477 @@
+/*
+ File: Interpreter.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.interpreter;
+
+
+import java.util.EmptyStackException;
+import java.util.Map;
+import java.util.Stack;
+
+import org.cytoscape.equations.BooleanList;
+import org.cytoscape.equations.DoubleList;
+import org.cytoscape.equations.Equation;
+import org.cytoscape.equations.Function;
+import org.cytoscape.equations.FunctionError;
+import org.cytoscape.equations.LongList;
+import org.cytoscape.equations.StringList;
+
+
+public class Interpreter {
+ private final Object[] code;
+ private final int[] sourceLocations;
+ private final Stack<Object> argumentStack;
+ private final Map<String, IdentDescriptor> nameToDescriptorMap;
+
+ public Interpreter(final Equation equation, final Map<String, IdentDescriptor> nameToDescriptorMap)
+ throws IllegalStateException
+ {
+ if (equation == null || equation.getCode().length == 0)
+ throw new IllegalStateException("null or empty code!");
+
+ this.code = equation.getCode();
+ this.sourceLocations = equation.getSourceLocations();
+ this.argumentStack = new Stack<Object>();
+ this.nameToDescriptorMap = nameToDescriptorMap;
+ }
+
+ /**
+ * Executes the code that was passed into the constructor.
+ * @return a Double, Boolean or String object that is the result of a successful execution.
+ * @throws ArithmeticException thrown if an arithmetic error was detected like a division by zero etc.
+ * @throws IllegalArgumentException thrown if a function invocation resulted in a function detecting an invalid argument
+ * @throws IllegalStateException thrown if an invalid interpreter internal state was reached
+ */
+ public Object run() throws ArithmeticException, IllegalArgumentException, IllegalStateException {
+ int index = -1;
+ try {
+ for (index = 0; index < code.length; ++index) {
+ final Object instrOrArg = code[index];
+ if (instrOrArg instanceof Instruction) {
+ switch ((Instruction)instrOrArg) {
+ case FADD:
+ fadd();
+ break;
+ case FSUB:
+ fsub();
+ break;
+ case FMUL:
+ fmul();
+ break;
+ case FDIV:
+ fdiv();
+ break;
+ case FPOW:
+ fpow();
+ break;
+ case SCONCAT:
+ sconcat();
+ break;
+ case BEQLF:
+ beqlf();
+ break;
+ case BNEQLF:
+ bneqlf();
+ break;
+ case BGTF:
+ bgtf();
+ break;
+ case BLTF:
+ bltf();
+ break;
+ case BGTEF:
+ bgtef();
+ break;
+ case BLTEF:
+ bltef();
+ break;
+ case BEQLS:
+ beqls();
+ break;
+ case BNEQLS:
+ bneqls();
+ break;
+ case BGTS:
+ bgts();
+ break;
+ case BLTS:
+ blts();
+ break;
+ case BGTES:
+ bgtes();
+ break;
+ case BLTES:
+ bltes();
+ break;
+ case BGTB:
+ bgtb();
+ break;
+ case BLTB:
+ bltb();
+ break;
+ case BGTEB:
+ bgteb();
+ break;
+ case BLTEB:
+ blteb();
+ break;
+ case BEQLB:
+ beqlb();
+ break;
+ case BNEQLB:
+ bneqlb();
+ break;
+ case CALL:
+ call();
+ break;
+ case FUMINUS:
+ fuminus();
+ break;
+ case FUPLUS:
+ fuplus();
+ break;
+ case AREF:
+ aref();
+ break;
+ case AREF2:
+ aref2();
+ break;
+ case FCONVI:
+ fconvi();
+ break;
+ case FCONVB:
+ fconvb();
+ break;
+ case FCONVS:
+ fconvs();
+ break;
+ case SCONVF:
+ sconvf();
+ break;
+ case SCONVI:
+ sconvi();
+ break;
+ case SCONVB:
+ sconvb();
+ break;
+ default:
+ throw new IllegalStateException("unknown opcode: " + instrOrArg + "!");
+ }
+ }
+ else
+ argumentStack.push(instrOrArg);
+ }
+ } catch (final EmptyStackException e) {
+ throw new IllegalStateException("inconsistent number of stack entries detected!");
+ } catch (final FunctionError e) {
+ throw new IllegalStateException(e.getMessage());
+ }
+
+ if (argumentStack.size() != 1)
+ throw new IllegalStateException("invalid argument stack size " + argumentStack.size() + ", must be 1!");
+ final Object retVal = argumentStack.peek();
+ final Class retValClass = retVal.getClass();
+ if (retValClass == Double.class || retValClass == String.class || retValClass == Boolean.class || retValClass == Long.class
+ || retValClass == DoubleList.class || retValClass == BooleanList.class || retValClass == LongList.class
+ || retValClass == StringList.class)
+ return retVal;
+
+ throw new IllegalStateException("illegal result type at end of interpretation: " + retValClass + "!");
+ }
+
+ private void fadd() throws EmptyStackException {
+ final double float1 = getFloat(argumentStack.pop());
+ final double float2 = getFloat(argumentStack.pop());
+ argumentStack.push(float1 + float2);
+ }
+
+ private void fsub() throws EmptyStackException {
+ final double float1 = getFloat(argumentStack.pop());
+ final double float2 = getFloat(argumentStack.pop());
+ argumentStack.push(float1 - float2);
+ }
+
+ private void fmul() throws EmptyStackException {
+ final double float1 = getFloat(argumentStack.pop());
+ final double float2 = getFloat(argumentStack.pop());
+ argumentStack.push(float1 * float2);
+ }
+
+ private void fdiv() throws EmptyStackException, ArithmeticException {
+ final double float1 = getFloat(argumentStack.pop());
+ final double float2 = getFloat(argumentStack.pop());
+ if (float2 == 0.0)
+ throw new ArithmeticException("illegal division by zero!");
+ argumentStack.push(float1 / float2);
+ }
+
+ private void fpow() throws EmptyStackException {
+ final double float1 = getFloat(argumentStack.pop());
+ final double float2 = getFloat(argumentStack.pop());
+ argumentStack.push(Math.pow(float1, float2));
+ }
+
+ private void sconcat() throws EmptyStackException {
+ final String string1 = getString(argumentStack.pop());
+ final String string2 = getString(argumentStack.pop());
+ argumentStack.push(string1 + string2);
+ }
+
+ private void beqlf() throws EmptyStackException {
+ final double float1 = getFloat(argumentStack.pop());
+ final double float2 = getFloat(argumentStack.pop());
+ argumentStack.push(float1 == float2);
+ }
+
+ private void bneqlf() throws EmptyStackException {
+ final double float1 = getFloat(argumentStack.pop());
+ final double float2 = getFloat(argumentStack.pop());
+ argumentStack.push(float1 != float2);
+ }
+
+ private void bltf() throws EmptyStackException {
+ final double float1 = getFloat(argumentStack.pop());
+ final double float2 = getFloat(argumentStack.pop());
+ argumentStack.push(float1 < float2);
+ }
+
+ private void bgtf() throws EmptyStackException {
+ final double float1 = getFloat(argumentStack.pop());
+ final double float2 = getFloat(argumentStack.pop());
+ argumentStack.push(float1 > float2);
+ }
+
+ private void bltef() throws EmptyStackException {
+ final double float1 = getFloat(argumentStack.pop());
+ final double float2 = getFloat(argumentStack.pop());
+ argumentStack.push(float1 <= float2);
+ }
+
+ private void bgtef() throws EmptyStackException {
+ final double float1 = getFloat(argumentStack.pop());
+ final double float2 = getFloat(argumentStack.pop());
+ argumentStack.push(float1 >= float2);
+ }
+
+ private void beqls() throws EmptyStackException {
+ final String string1 = getString(argumentStack.pop());
+ final String string2 = getString(argumentStack.pop());
+ argumentStack.push(string1.equals(string2));
+ }
+
+ private void bneqls() throws EmptyStackException {
+ final String string1 = getString(argumentStack.pop());
+ final String string2 = getString(argumentStack.pop());
+ argumentStack.push(!string1.equals(string2));
+ }
+
+ private void blts() throws EmptyStackException {
+ final String string1 = getString(argumentStack.pop());
+ final String string2 = getString(argumentStack.pop());
+ argumentStack.push(string1.compareTo(string2) < 0);
+ }
+
+ private void bgts() throws EmptyStackException {
+ final String string1 = getString(argumentStack.pop());
+ final String string2 = getString(argumentStack.pop());
+ argumentStack.push(string1.compareTo(string2) > 0);
+ }
+
+ private void bltes() throws EmptyStackException {
+ final String string1 = getString(argumentStack.pop());
+ final String string2 = getString(argumentStack.pop());
+ argumentStack.push(string1.compareTo(string2) <= 0);
+ }
+
+ private void bgtes() throws EmptyStackException {
+ final String string1 = getString(argumentStack.pop());
+ final String string2 = getString(argumentStack.pop());
+ argumentStack.push(string1.compareTo(string2) >= 0);
+ }
+
+ private void bgtb() throws EmptyStackException {
+ final boolean bool1 = getBoolean(argumentStack.pop());
+ final boolean bool2 = getBoolean(argumentStack.pop());
+ argumentStack.push(bool1 && !bool2);
+ }
+
+ private void bltb() throws EmptyStackException {
+ final boolean bool1 = getBoolean(argumentStack.pop());
+ final boolean bool2 = getBoolean(argumentStack.pop());
+ argumentStack.push(!bool1 && bool2);
+ }
+
+ private void bgteb() throws EmptyStackException {
+ final boolean bool1 = getBoolean(argumentStack.pop());
+ final boolean bool2 = getBoolean(argumentStack.pop());
+ argumentStack.push((bool1 && !bool2) || (bool1 == bool2));
+ }
+
+ private void blteb() throws EmptyStackException {
+ final boolean bool1 = getBoolean(argumentStack.pop());
+ final boolean bool2 = getBoolean(argumentStack.pop());
+ argumentStack.push((!bool1 && bool2) || (bool1 == bool2));
+ }
+
+ private void beqlb() throws EmptyStackException {
+ final boolean bool1 = getBoolean(argumentStack.pop());
+ final boolean bool2 = getBoolean(argumentStack.pop());
+ argumentStack.push(bool1 == bool2);
+ }
+
+ private void bneqlb() throws EmptyStackException {
+ final boolean bool1 = getBoolean(argumentStack.pop());
+ final boolean bool2 = getBoolean(argumentStack.pop());
+ argumentStack.push(bool1 != bool2);
+ }
+
+ private void call() throws EmptyStackException, IllegalStateException, FunctionError {
+ // 1. get the function
+ final Object o = argumentStack.pop();
+ if (!(o instanceof Function))
+ throw new IllegalStateException("expected an attribute function after the CALL opcode but found \"" + o.getClass() + "\" instead!");
+ final Function func = (Function)o;
+
+ // 2. get and validate the argument count
+ final int argCount;
+ try {
+ argCount = (Integer)argumentStack.pop();
+ } catch (final Exception e) {
+ throw new IllegalStateException("invalid argument count type following a CALL opcode!");
+ }
+ final int MIN_ARG_COUNT = 0;
+ final int MAX_ARG_COUNT = 100; // This is an arbitrary limit and exists only to find bugs.
+ // Should it prove to be too low we could easily make it much bigger.
+ if (argCount < MIN_ARG_COUNT || argCount > MAX_ARG_COUNT)
+ throw new IllegalStateException("invalid argument count type following a CALL opcode (range must be in [" + MIN_ARG_COUNT + ", " + MAX_ARG_COUNT + "])!");
+
+ // 3. collect the actual arguments
+ final Object args[] = new Object[argCount];
+ for (int argNo = 0; argNo < argCount; ++argNo)
+ args[argNo] = argumentStack.pop();
+
+ // 4. now actually call the function
+ argumentStack.push(func.evaluateFunction(args));
+ }
+
+ private void fuminus() throws EmptyStackException {
+ final double float1 = getFloat(argumentStack.pop());
+ argumentStack.push(-float1);
+ }
+
+ private void fuplus() throws EmptyStackException {
+ final double float1 = getFloat(argumentStack.pop());
+ argumentStack.push(+float1);
+ }
+
+ private void aref() throws EmptyStackException {
+ final String attribName = (String)argumentStack.pop();
+ final IdentDescriptor identDescriptor = nameToDescriptorMap.get(attribName);
+ if (identDescriptor == null)
+ throw new IllegalStateException("unknown attribute reference: \"" + attribName + "\" (1)!");
+ final Object value = identDescriptor.getValue();
+ if (value == null)
+ throw new IllegalStateException("undefined attribute reference: \"" + attribName + "\"!");
+ argumentStack.push(value);
+ }
+
+ private void aref2() throws EmptyStackException {
+ final String attribName = (String)argumentStack.pop();
+ final Object defaultValue = argumentStack.pop();
+ final IdentDescriptor identDescriptor = nameToDescriptorMap.get(attribName);
+ if (identDescriptor == null)
+ throw new IllegalStateException("unknown attribute reference: \"" + attribName + "\" (2)!");
+ final Object value = identDescriptor.getValue();
+ argumentStack.push(value != null ? value : defaultValue);
+ }
+
+ private void fconvi() throws EmptyStackException {
+ final Long long1 = getLong(argumentStack.pop());
+ argumentStack.push((double)long1);
+ }
+
+ private void fconvb() throws EmptyStackException {
+ final Boolean b = getBoolean(argumentStack.pop());
+ argumentStack.push(b ? 1.0 : 0.0);
+ }
+
+ private void fconvs() throws EmptyStackException {
+ final String s = getString(argumentStack.pop());
+ try {
+ argumentStack.push(Double.parseDouble(s));
+ } catch(final NumberFormatException e) {
+ throw new IllegalStateException("can't convert \"" + s + "\" to a number!");
+ }
+ }
+
+ private void sconvf() throws EmptyStackException {
+ argumentStack.push(argumentStack.pop().toString());
+ }
+
+ private void sconvi() throws EmptyStackException {
+ argumentStack.push(argumentStack.pop().toString());
+ }
+
+ private void sconvb() throws EmptyStackException {
+ argumentStack.pop();
+
+ // In order to understand this goofy "conversion" of both truth values, you have to know two facts:
+ // 1) This is only ever used when comparing a boolean with a string.
+ // 2) In Excel™, both truth values compare as being greater than any string.
+ argumentStack.push("\uFFFF\uFFFF\uFFFF");
+ }
+
+ private double getFloat(final Object o) throws IllegalStateException {
+ if (o instanceof Double)
+ return (Double)o;
+
+ throw new IllegalStateException("can't convert a " + o.getClass() + " (" + o + ") to a floating point number!");
+ }
+
+ private long getLong(final Object o) throws IllegalStateException {
+ if (o instanceof Long)
+ return (Long)o;
+
+ throw new IllegalStateException("can't convert a " + o.getClass() + " (" + o + ") to an integer number!");
+ }
+
+ private String getString(final Object o) throws IllegalStateException {
+ if (o instanceof String)
+ return (String)o;
+
+ throw new IllegalStateException("can't convert a " + o.getClass() + " to a string!");
+ }
+
+ private boolean getBoolean(final Object o) throws IllegalStateException {
+ if (o instanceof Boolean)
+ return (Boolean)o;
+
+ throw new IllegalStateException("can't convert a " + o.getClass() + " to a boolean!");
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/parse_tree/BinOpNode.java b/corelibs/equations/src/main/java/org/cytoscape/equations/parse_tree/BinOpNode.java
new file mode 100644
index 0000000..e5b062f
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/parse_tree/BinOpNode.java
@@ -0,0 +1,143 @@
+/*
+ File: BinOpNode.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.parse_tree;
+
+
+import java.util.Stack;
+
+import org.cytoscape.equations.CodeAndSourceLocation;
+import org.cytoscape.equations.Token;
+import org.cytoscape.equations.interpreter.Instruction;
+
+
+/**
+ * A node in the parse tree representing a binary operator.
+ */
+public class BinOpNode extends Node {
+ private final Token operator;
+ private final Node lhs, rhs;
+
+ public BinOpNode(final int sourceLocation, final Token operator, final Node lhs, final Node rhs) {
+ super(sourceLocation);
+
+ if (lhs == null)
+ throw new IllegalArgumentException("left operand must not be null!");
+ if (rhs == null)
+ throw new IllegalArgumentException("right operand must not be null!");
+
+ this.operator = operator;
+ this.lhs = lhs;
+ this.rhs = rhs;
+ }
+
+ public String toString() { return "BinOpNode: " + operator; }
+
+ public Class getType() { return operator.isComparisonOperator() ? Boolean.class : lhs.getType(); }
+
+ /**
+ * @return the left operand
+ */
+ public Node getLeftChild() { return lhs; }
+
+ /**
+ * @return the right operand
+ */
+ public Node getRightChild() { return rhs; }
+
+ public Token getOperator() { return operator; }
+
+ public void genCode(final Stack<CodeAndSourceLocation> codeStack) {
+ rhs.genCode(codeStack);
+ lhs.genCode(codeStack);
+
+ switch (operator) {
+ case CARET:
+ codeStack.push(new CodeAndSourceLocation(Instruction.FPOW, getSourceLocation()));
+ break;
+ case PLUS:
+ codeStack.push(new CodeAndSourceLocation(Instruction.FADD, getSourceLocation()));
+ break;
+ case MINUS:
+ codeStack.push(new CodeAndSourceLocation(Instruction.FSUB, getSourceLocation()));
+ break;
+ case DIV:
+ codeStack.push(new CodeAndSourceLocation(Instruction.FDIV, getSourceLocation()));
+ break;
+ case MUL:
+ codeStack.push(new CodeAndSourceLocation(Instruction.FMUL, getSourceLocation()));
+ break;
+ case EQUAL:
+ codeStack.push(new CodeAndSourceLocation(determineOpCode(Instruction.BEQLF, Instruction.BEQLS, Instruction.BEQLB),
+ getSourceLocation()));
+ break;
+ case NOT_EQUAL:
+ codeStack.push(new CodeAndSourceLocation(determineOpCode(Instruction.BNEQLF, Instruction.BNEQLS, Instruction.BNEQLB),
+ getSourceLocation()));
+ break;
+ case GREATER_THAN:
+ codeStack.push(new CodeAndSourceLocation(determineOpCode(Instruction.BGTF, Instruction.BGTS, Instruction.BGTB),
+ getSourceLocation()));
+ break;
+ case LESS_THAN:
+ codeStack.push(new CodeAndSourceLocation(determineOpCode(Instruction.BLTF, Instruction.BLTS, Instruction.BLTB),
+ getSourceLocation()));
+ break;
+ case GREATER_OR_EQUAL:
+ codeStack.push(new CodeAndSourceLocation(determineOpCode(Instruction.BGTEF, Instruction.BGTES, Instruction.BGTEB),
+ getSourceLocation()));
+ break;
+ case LESS_OR_EQUAL:
+ codeStack.push(new CodeAndSourceLocation(determineOpCode(Instruction.BLTEF, Instruction.BLTES, Instruction.BLTEB),
+ getSourceLocation()));
+ break;
+ case AMPERSAND:
+ codeStack.push(new CodeAndSourceLocation(Instruction.SCONCAT, getSourceLocation()));
+ break;
+ default:
+ throw new IllegalStateException(getSourceLocation() + ": unknown operator: " + operator + "!");
+ }
+ }
+
+ /**
+ * Picks one of three opcodes based on operand types.
+ * (N.B.: We assume that the LHS and RHS operands are of the same type!)
+ */
+ private Instruction determineOpCode(final Instruction floatOpCode, final Instruction stringOpCode, final Instruction booleanOpCode) {
+ final Class operandType = lhs.getType();
+ if (operandType == Double.class)
+ return floatOpCode;
+ else if (operandType == String.class)
+ return stringOpCode;
+ else if (booleanOpCode != null && operandType == Boolean.class)
+ return booleanOpCode;
+
+ throw new IllegalStateException(lhs.getSourceLocation() + ": invalid LHS operand type for comparison: " + operandType + "!");
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/parse_tree/BooleanConstantNode.java b/corelibs/equations/src/main/java/org/cytoscape/equations/parse_tree/BooleanConstantNode.java
new file mode 100644
index 0000000..65c3239
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/parse_tree/BooleanConstantNode.java
@@ -0,0 +1,69 @@
+/*
+ File: BooleanConstantNode.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.parse_tree;
+
+
+import java.util.Stack;
+
+import org.cytoscape.equations.CodeAndSourceLocation;
+
+
+/**
+ * A node in the parse tree representing an integer constant.
+ */
+public class BooleanConstantNode extends Node {
+ private final boolean value;
+
+ public BooleanConstantNode(final int sourceLocation, final boolean value) {
+ super(sourceLocation);
+
+ this.value = value;
+ }
+
+ public String toString() { return "BooleanConstantNode: " + value; }
+
+ public Class getType() { return Boolean.class; }
+
+ /**
+ * @return null, This type of node never has any children!
+ */
+ public Node getLeftChild() { return null; }
+
+ /**
+ * @return null, This type of node never has any children!
+ */
+ public Node getRightChild() { return null; }
+
+ public boolean getValue() { return value; }
+
+ public void genCode(final Stack<CodeAndSourceLocation> codeStack) {
+ codeStack.push(new CodeAndSourceLocation(value, getSourceLocation()));
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/parse_tree/FConvNode.java b/corelibs/equations/src/main/java/org/cytoscape/equations/parse_tree/FConvNode.java
new file mode 100644
index 0000000..15ad27f
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/parse_tree/FConvNode.java
@@ -0,0 +1,87 @@
+/*
+ File: FConvNode.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.parse_tree;
+
+
+import java.util.Stack;
+
+import org.cytoscape.equations.CodeAndSourceLocation;
+import org.cytoscape.equations.interpreter.Instruction;
+
+
+/**
+ * A node in the parse tree representing a conversion to a floating point number
+ */
+public class FConvNode extends Node {
+ private final Node convertee;
+
+ public FConvNode(final Node convertee) {
+ super(-1); // Type conversions are generated by the compiler and do not correspond to actual source locations!
+
+ if (convertee == null)
+ throw new IllegalArgumentException("convertee must not be null!");
+
+ final Class type = convertee.getType();
+ if (type != Long.class && type != Boolean.class && type != String.class)
+ throw new IllegalArgumentException("convertee must be of type Long, Boolean or String!");
+
+ this.convertee = convertee;
+ }
+
+ public String toString() {
+ return "FConvNode: convertee = " + convertee;
+ }
+
+ public Class getType() { return Double.class; }
+
+ /**
+ * @return the only child of this node
+ */
+ public Node getLeftChild() { return convertee; }
+
+ /**
+ * @return null, This type of node never has any right children!
+ */
+ public Node getRightChild() { return null; }
+
+ public void genCode(final Stack<CodeAndSourceLocation> codeStack) {
+ convertee.genCode(codeStack);
+
+ final Class type = convertee.getType();
+ if (type == Long.class)
+ codeStack.push(new CodeAndSourceLocation(Instruction.FCONVI, getSourceLocation()));
+ else if (type == Boolean.class)
+ codeStack.push(new CodeAndSourceLocation(Instruction.FCONVB, getSourceLocation()));
+ else if (type == String.class)
+ codeStack.push(new CodeAndSourceLocation(Instruction.FCONVS, getSourceLocation()));
+ else
+ throw new IllegalStateException("unknown type: " + type + "!");
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/parse_tree/FloatConstantNode.java b/corelibs/equations/src/main/java/org/cytoscape/equations/parse_tree/FloatConstantNode.java
new file mode 100644
index 0000000..55f4145
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/parse_tree/FloatConstantNode.java
@@ -0,0 +1,69 @@
+/*
+ File: FloatConstantNode.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.parse_tree;
+
+
+import java.util.Stack;
+
+import org.cytoscape.equations.CodeAndSourceLocation;
+
+
+/**
+ * A node in the parse tree representing an integer constant.
+ */
+public class FloatConstantNode extends Node {
+ private final double value;
+
+ public FloatConstantNode(final int sourceLocation, final double value) {
+ super(sourceLocation);
+
+ this.value = value;
+ }
+
+ public String toString() { return "FloatConstantNode: " + value; }
+
+ public Class getType() { return Double.class; }
+
+ /**
+ * @return null, This type of node never has any children!
+ */
+ public Node getLeftChild() { return null; }
+
+ /**
+ * @return null, This type of node never has any children!
+ */
+ public Node getRightChild() { return null; }
+
+ public double getValue() { return value; }
+
+ public void genCode(final Stack<CodeAndSourceLocation> codeStack) {
+ codeStack.push(new CodeAndSourceLocation(value, getSourceLocation()));
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/parse_tree/FuncCallNode.java b/corelibs/equations/src/main/java/org/cytoscape/equations/parse_tree/FuncCallNode.java
new file mode 100644
index 0000000..ca32151
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/parse_tree/FuncCallNode.java
@@ -0,0 +1,89 @@
+/*
+ File: FuncCallNode.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.parse_tree;
+
+
+import java.util.Stack;
+
+import org.cytoscape.equations.CodeAndSourceLocation;
+import org.cytoscape.equations.Function;
+import org.cytoscape.equations.interpreter.Instruction;
+
+
+/**
+ * A node in the parse tree representing a function call.
+ */
+public class FuncCallNode extends Node {
+ private final Function func;
+ final Class returnType;
+ private final Node[] args;
+
+ public FuncCallNode(final int sourceLocation, final Function func, final Class returnType, final Node[] args) {
+ super(sourceLocation);
+
+ if (func == null)
+ throw new IllegalArgumentException("function must not be null!");
+ if (returnType == null)
+ throw new IllegalArgumentException("return type must not be null!");
+ if (args == null)
+ throw new IllegalArgumentException("args must not be null!");
+
+ this.func = func;
+ this.returnType = returnType;
+ this.args = args;
+ }
+
+ public String toString() { return "FuncCallNode: call to " + func.getName().toUpperCase() + " with " + args.length + " args"; }
+
+ public Class getType() { return returnType; }
+
+ /**
+ * @return null, This type of node never has any children!
+ */
+ public Node getLeftChild() { return null; }
+
+ /**
+ * @return null, This type of node never has any children!
+ */
+ public Node getRightChild() { return null; }
+
+ /**
+ * @return null, The return value for this node is only known at runtime!
+ */
+ public Object getValue() { return null; }
+
+ public void genCode(final Stack<CodeAndSourceLocation> codeStack) {
+ for (int i = args.length - 1; i >= 0; --i)
+ args[i].genCode(codeStack);
+ codeStack.push(new CodeAndSourceLocation(args.length, -1));
+ codeStack.push(new CodeAndSourceLocation(func, -1));
+ codeStack.push(new CodeAndSourceLocation(Instruction.CALL, getSourceLocation()));
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/parse_tree/IdentNode.java b/corelibs/equations/src/main/java/org/cytoscape/equations/parse_tree/IdentNode.java
new file mode 100644
index 0000000..7871640
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/parse_tree/IdentNode.java
@@ -0,0 +1,84 @@
+/*
+ File: IdentNode.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.parse_tree;
+
+
+import java.util.Stack;
+
+import org.cytoscape.equations.CodeAndSourceLocation;
+import org.cytoscape.equations.interpreter.Instruction;
+
+
+/**
+ * A node in the parse tree representing an attribute reference.
+ */
+public class IdentNode extends Node {
+ private final String attribName;
+ private final Object defaultValue;
+ private final Class type;
+
+ public IdentNode(final int sourceLocation, final String attribName, final Object defaultValue, final Class type) {
+ super(sourceLocation);
+
+ if (type == null)
+ throw new IllegalArgumentException("\"type\" must not be null!");
+ if (defaultValue != null && defaultValue.getClass() != type)
+ throw new IllegalArgumentException("default value must match \"type\"!");
+ this.attribName = attribName;
+ this.defaultValue = defaultValue;
+ this.type = type;
+ }
+
+ public String toString() {
+ return "IdentNode: " + attribName + (defaultValue == null ? "" : " default=" + defaultValue);
+ }
+
+ public Class getType() { return type; }
+
+ /**
+ * @return null, This type of node never has any children!
+ */
+ public Node getLeftChild() { return null; }
+
+ /**
+ * @return null, This type of node never has any children!
+ */
+ public Node getRightChild() { return null; }
+
+ public String getAttribName() { return attribName; }
+ public Object getDefaultValue() { return defaultValue; }
+
+ public void genCode(final Stack<CodeAndSourceLocation> codeStack) {
+ if (defaultValue != null)
+ codeStack.push(new CodeAndSourceLocation(defaultValue, -1));
+ codeStack.push(new CodeAndSourceLocation(attribName, -1));
+ codeStack.push(new CodeAndSourceLocation(defaultValue == null ? Instruction.AREF : Instruction.AREF2, getSourceLocation()));
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/parse_tree/Node.java b/corelibs/equations/src/main/java/org/cytoscape/equations/parse_tree/Node.java
new file mode 100644
index 0000000..d7ceac5
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/parse_tree/Node.java
@@ -0,0 +1,57 @@
+/*
+ File: Node.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.parse_tree;
+
+
+import java.util.Stack;
+
+import org.cytoscape.equations.CodeAndSourceLocation;
+
+
+/**
+ * A node in the parse tree.
+ */
+public abstract class Node {
+ private final int sourceLocation; // What location the "source code" is this associated with.
+
+ public Node(final int sourceLocation) {
+ this.sourceLocation = sourceLocation;
+ }
+
+ public int getSourceLocation() {
+ return sourceLocation;
+ }
+
+ public abstract String toString(); // For debugging.
+ public abstract Class getType(); // The type of this node.
+ public abstract Node getLeftChild();
+ public abstract Node getRightChild();
+ public abstract void genCode(final Stack<CodeAndSourceLocation> codeStack);
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/parse_tree/SConvNode.java b/corelibs/equations/src/main/java/org/cytoscape/equations/parse_tree/SConvNode.java
new file mode 100644
index 0000000..8b70cd4
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/parse_tree/SConvNode.java
@@ -0,0 +1,87 @@
+/*
+ File: SConvNode.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.parse_tree;
+
+
+import java.util.Stack;
+
+import org.cytoscape.equations.CodeAndSourceLocation;
+import org.cytoscape.equations.interpreter.Instruction;
+
+
+/**
+ * A node in the parse tree representing an conversion to a string
+ */
+public class SConvNode extends Node {
+ private final Node convertee;
+
+ public SConvNode(final Node convertee) {
+ super(-1); // Type conversions are generated by the compiler and do not correspond to actual source locations!
+
+ if (convertee == null)
+ throw new IllegalArgumentException("convertee must not be null!");
+
+ final Class type = convertee.getType();
+ if (type != Double.class && type != Long.class && type != Boolean.class)
+ throw new IllegalArgumentException("convertee must be of type Double, Long, or Boolean!");
+
+ this.convertee = convertee;
+ }
+
+ public String toString() {
+ return "SConvNode: convertee = " + convertee;
+ }
+
+ public Class getType() { return String.class; }
+
+ /**
+ * @return the only child of this node
+ */
+ public Node getLeftChild() { return convertee; }
+
+ /**
+ * @return null, This type of node never has any right children!
+ */
+ public Node getRightChild() { return null; }
+
+ public void genCode(final Stack<CodeAndSourceLocation> codeStack) {
+ convertee.genCode(codeStack);
+
+ final Class type = convertee.getType();
+ if (type == Double.class)
+ codeStack.push(new CodeAndSourceLocation(Instruction.SCONVF, getSourceLocation()));
+ else if (type == Long.class)
+ codeStack.push(new CodeAndSourceLocation(Instruction.SCONVI, getSourceLocation()));
+ else if (type == Boolean.class)
+ codeStack.push(new CodeAndSourceLocation(Instruction.SCONVB, getSourceLocation()));
+ else
+ throw new IllegalStateException("unknown type: " + type + "!");
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/parse_tree/StringConstantNode.java b/corelibs/equations/src/main/java/org/cytoscape/equations/parse_tree/StringConstantNode.java
new file mode 100644
index 0000000..7e8f044
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/parse_tree/StringConstantNode.java
@@ -0,0 +1,69 @@
+/*
+ File: StringConstantNode.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.parse_tree;
+
+
+import java.util.Stack;
+
+import org.cytoscape.equations.CodeAndSourceLocation;
+
+
+/**
+ * A node in the parse tree representing an integer constant.
+ */
+public class StringConstantNode extends Node {
+ private final String value;
+
+ public StringConstantNode(final int sourceLocation, final String value) {
+ super(sourceLocation);
+
+ this.value = value;
+ }
+
+ public String toString() { return "StringConstantNode: " + value; }
+
+ public Class getType() { return String.class; }
+
+ /**
+ * @return null, This type of node never has any children!
+ */
+ public Node getLeftChild() { return null; }
+
+ /**
+ * @return null, This type of node never has any children!
+ */
+ public Node getRightChild() { return null; }
+
+ public String getValue() { return value; }
+
+ public void genCode(final Stack<CodeAndSourceLocation> codeStack) {
+ codeStack.push(new CodeAndSourceLocation(value, getSourceLocation()));
+ }
+}
diff --git a/corelibs/equations/src/main/java/org/cytoscape/equations/parse_tree/UnaryOpNode.java b/corelibs/equations/src/main/java/org/cytoscape/equations/parse_tree/UnaryOpNode.java
new file mode 100644
index 0000000..10ae0f8
--- /dev/null
+++ b/corelibs/equations/src/main/java/org/cytoscape/equations/parse_tree/UnaryOpNode.java
@@ -0,0 +1,87 @@
+/*
+ File: UnaryOpNode.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.parse_tree;
+
+
+import java.util.Stack;
+
+import org.cytoscape.equations.CodeAndSourceLocation;
+import org.cytoscape.equations.Token;
+import org.cytoscape.equations.interpreter.Instruction;
+
+
+/**
+ * A node in the parse tree representing a unary operator application.
+ */
+public class UnaryOpNode extends Node {
+ private final Token operator;
+ private final Node operand;
+
+ public UnaryOpNode(final int sourceLocation, final Token operator, final Node operand) {
+ super(sourceLocation);
+
+ if (operand == null)
+ throw new IllegalArgumentException("operand must not be null!");
+
+ this.operator = operator;
+ this.operand = operand;
+ }
+
+ public String toString() { return "UnaryOpNode: " + operator; }
+
+ public Class getType() { return operand.getType(); }
+
+ /**
+ * @return the operand
+ */
+ public Node getLeftChild() { return operand; }
+
+ /**
+ * @return null, This type of node never has any left children!
+ */
+ public Node getRightChild() { return null; }
+
+ public Token getOperator() { return operator; }
+
+ public void genCode(final Stack<CodeAndSourceLocation> codeStack) {
+ operand.genCode(codeStack);
+
+ switch (operator) {
+ case PLUS:
+ codeStack.push(new CodeAndSourceLocation(Instruction.FUPLUS, getSourceLocation()));
+ break;
+ case MINUS:
+ codeStack.push(new CodeAndSourceLocation(Instruction.FUMINUS, getSourceLocation()));
+ break;
+ default:
+ throw new IllegalStateException("invalid unary operation: " + operator + "!");
+ }
+ }
+}
diff --git a/corelibs/equations/src/test/java/org/cytoscape/equations/AttribParserTest.java b/corelibs/equations/src/test/java/org/cytoscape/equations/AttribParserTest.java
new file mode 100644
index 0000000..0410cce
--- /dev/null
+++ b/corelibs/equations/src/test/java/org/cytoscape/equations/AttribParserTest.java
@@ -0,0 +1,123 @@
+/*
+ File: AttribParserTest.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations;
+
+import java.util.HashMap;
+import java.util.Map;
+import junit.framework.*;
+
+
+public class AttribParserTest extends TestCase {
+ private final EqnParser parser = Parser.getParser();
+
+ public void testSimpleExpr() throws Exception {
+ final Map<String, Class> attribNameToTypeMap = new HashMap<String, Class>();
+ attribNameToTypeMap.put("BOB", Double.class);
+ assertTrue(parser.parse("=42 - 12 + 3 * (4 - 2) + ${BOB:12}", attribNameToTypeMap));
+ }
+
+ public void testUnaryPlusAndMinus() throws Exception {
+ final Map<String, Class> attribNameToTypeMap = new HashMap<String, Class>();
+ attribNameToTypeMap.put("attr1", Double.class);
+ attribNameToTypeMap.put("attr2", Double.class);
+ assertTrue(parser.parse("=-17.8E-14", attribNameToTypeMap));
+ assertTrue(parser.parse("=+(${attr1} + ${attr2})", attribNameToTypeMap));
+ }
+
+ public void testFunctionCall() throws Exception {
+ final Map<String, Class> attribNameToTypeMap = new HashMap<String, Class>();
+ assertTrue(parser.parse("=42 + log(4 - 2)", attribNameToTypeMap));
+ }
+
+ public void testExponentiation() throws Exception {
+ final Map<String, Class> attribNameToTypeMap = new HashMap<String, Class>();
+ assertTrue(parser.parse("=2^3^4 - 0.0002", attribNameToTypeMap));
+ }
+
+ public void testComparisons() throws Exception {
+ final Map<String, Class> attribNameToTypeMap = new HashMap<String, Class>();
+ attribNameToTypeMap.put("x", Double.class);
+ attribNameToTypeMap.put("y", Double.class);
+ attribNameToTypeMap.put("limit", Double.class);
+ assertTrue(parser.parse("=${x} <= ${y}", attribNameToTypeMap));
+ assertTrue(parser.parse("=-15.4^3 > ${limit}", attribNameToTypeMap));
+ }
+
+ public void testVarargs() throws Exception {
+ final Map<String, Class> attribNameToTypeMap = new HashMap<String, Class>();
+ assertFalse(parser.parse("=LOG()", attribNameToTypeMap));
+ assertTrue(parser.parse("=LOG(1)", attribNameToTypeMap));
+ assertTrue(parser.parse("=LOG(1,2)", attribNameToTypeMap));
+ assertFalse(parser.parse("=LOG(1,2,3)", attribNameToTypeMap));
+ }
+
+ public void testFixedargs() throws Exception {
+ final Map<String, Class> attribNameToTypeMap = new HashMap<String, Class>();
+ assertFalse(parser.parse("=ABS()", attribNameToTypeMap));
+ assertTrue(parser.parse("=ABS(1)", attribNameToTypeMap));
+ assertFalse(parser.parse("=ABS(1,2)", attribNameToTypeMap));
+ }
+
+ public void testNOT() throws Exception {
+ final Map<String, Class> attribNameToTypeMap = new HashMap<String, Class>();
+ attribNameToTypeMap.put("logical", Boolean.class);
+ assertFalse(parser.parse("=NOT()", attribNameToTypeMap));
+ assertTrue(parser.parse("=NOT(true)", attribNameToTypeMap));
+ assertTrue(parser.parse("=NOT(false)", attribNameToTypeMap));
+ assertTrue(parser.parse("=NOT(3.2 < 12)", attribNameToTypeMap));
+ assertTrue(parser.parse("=NOT(${logical})", attribNameToTypeMap));
+ assertFalse(parser.parse("=NOT(true, true)", attribNameToTypeMap));
+ }
+
+ public void testUPPERandLOWER() throws Exception {
+ final Map<String, Class> attribNameToTypeMap = new HashMap<String, Class>();
+ assertTrue(parser.parse("=UPPER(\"Fred\")", attribNameToTypeMap));
+ assertTrue(parser.parse("=\"bozo\"&LOWER(\"UPPER\")", attribNameToTypeMap));
+ }
+
+ public void testBracelessAttribReferences() throws Exception {
+ final Map<String, Class> attribNameToTypeMap = new HashMap<String, Class>();
+ attribNameToTypeMap.put("BOB", Double.class);
+ attribNameToTypeMap.put("FRED", Double.class);
+ assertTrue(parser.parse("=$BOB+$FRED", attribNameToTypeMap));
+ }
+
+ public void testIntegerToFloatingPointConversion() throws Exception {
+ final Map<String, Class> attribNameToTypeMap = new HashMap<String, Class>();
+ attribNameToTypeMap.put("BOB", Long.class);
+ assertTrue(parser.parse("=$BOB > 5.3", attribNameToTypeMap));
+ }
+
+ public void testMixedModeArithmetic() throws Exception {
+ final Map<String, Class> attribNameToTypeMap = new HashMap<String, Class>();
+ attribNameToTypeMap.put("x", Long.class);
+ assertTrue(parser.parse("=$x + 2.0", attribNameToTypeMap));
+ }
+}
diff --git a/corelibs/equations/src/test/java/org/cytoscape/equations/EquationUtilTest.java b/corelibs/equations/src/test/java/org/cytoscape/equations/EquationUtilTest.java
new file mode 100755
index 0000000..397aaf7
--- /dev/null
+++ b/corelibs/equations/src/test/java/org/cytoscape/equations/EquationUtilTest.java
@@ -0,0 +1,41 @@
+/*
+ File: EquationUtilTest.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations;
+
+import junit.framework.*;
+
+
+public class EquationUtilTest extends TestCase {
+ public void testAttribNameAsReference() throws Exception {
+ assertEquals("$Fred123", EquationUtil.attribNameAsReference("Fred123"));
+ assertEquals("${123}", EquationUtil.attribNameAsReference("123"));
+ assertEquals("${Fr\\ ed\\{12\\\\3}", EquationUtil.attribNameAsReference("Fr ed{12\\3"));
+ }
+}
diff --git a/corelibs/equations/src/test/java/org/cytoscape/equations/TokeniserTest.java b/corelibs/equations/src/test/java/org/cytoscape/equations/TokeniserTest.java
new file mode 100755
index 0000000..c9fc682
--- /dev/null
+++ b/corelibs/equations/src/test/java/org/cytoscape/equations/TokeniserTest.java
@@ -0,0 +1,246 @@
+/*
+ File: TokeniserTest.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations;
+
+import java.util.ArrayList;
+import junit.framework.*;
+
+
+/**
+ *
+ */
+public class TokeniserTest extends TestCase {
+ // Stores the expected token's string representation and position.
+ static class TokenStringRepAndPosition {
+ private final String stringRep;
+ private final int position;
+
+ TokenStringRepAndPosition(final String stringRep, final int position) {
+ this.stringRep = stringRep;
+ this.position = position;
+ }
+
+ String getStringRep() { return this.stringRep; }
+ int getPosition() { return position; }
+ }
+
+ public void testScanner1() throws Exception {
+ final Tokeniser tokeniser = new Tokeniser("AND(1.0 >= $(BOB), OR($(JOE) = $(tiny), $(x) > LOG(1.3e17)))");
+ final ArrayList<TokenStringRepAndPosition> tokens = new ArrayList<TokenStringRepAndPosition>();
+ String tokenAsString;
+ do {
+ tokenAsString = tokeniser.getTokenAsString();
+ final int position = tokeniser.getStartPos();
+ tokens.add(new TokenStringRepAndPosition(tokenAsString, position));
+ } while (tokenAsString != "EOS");
+ final TokenStringRepAndPosition[] actualTokens = new TokenStringRepAndPosition[tokens.size()];
+ tokens.toArray(actualTokens);
+
+ final TokenStringRepAndPosition[] expectedTokens = {
+ new TokenStringRepAndPosition("IDENTIFIER: \"AND\"", 0),
+ new TokenStringRepAndPosition("OPEN_PAREN", 3),
+ new TokenStringRepAndPosition("FLOAT_CONSTANT: \"1.0\"", 4),
+ new TokenStringRepAndPosition("GREATER_OR_EQUAL", 8),
+ new TokenStringRepAndPosition("DOLLAR", 11),
+ new TokenStringRepAndPosition("OPEN_PAREN", 12),
+ new TokenStringRepAndPosition("IDENTIFIER: \"BOB\"", 13),
+ new TokenStringRepAndPosition("CLOSE_PAREN", 16),
+ new TokenStringRepAndPosition("COMMA", 17),
+ new TokenStringRepAndPosition("IDENTIFIER: \"OR\"", 19),
+ new TokenStringRepAndPosition("OPEN_PAREN", 21),
+ new TokenStringRepAndPosition("DOLLAR", 22),
+ new TokenStringRepAndPosition("OPEN_PAREN", 23),
+ new TokenStringRepAndPosition("IDENTIFIER: \"JOE\"", 24),
+ new TokenStringRepAndPosition("CLOSE_PAREN", 27),
+ new TokenStringRepAndPosition("EQUAL", 29),
+ new TokenStringRepAndPosition("DOLLAR", 31),
+ new TokenStringRepAndPosition("OPEN_PAREN", 32),
+ new TokenStringRepAndPosition("IDENTIFIER: \"tiny\"", 33),
+ new TokenStringRepAndPosition("CLOSE_PAREN", 37),
+ new TokenStringRepAndPosition("COMMA", 38),
+ new TokenStringRepAndPosition("DOLLAR", 40),
+ new TokenStringRepAndPosition("OPEN_PAREN", 41),
+ new TokenStringRepAndPosition("IDENTIFIER: \"x\"", 42),
+ new TokenStringRepAndPosition("CLOSE_PAREN", 43),
+ new TokenStringRepAndPosition("GREATER_THAN", 45),
+ new TokenStringRepAndPosition("IDENTIFIER: \"LOG\"", 47),
+ new TokenStringRepAndPosition("OPEN_PAREN", 50),
+ new TokenStringRepAndPosition("FLOAT_CONSTANT: \"1.3E17\"", 51),
+ new TokenStringRepAndPosition("CLOSE_PAREN", 57),
+ new TokenStringRepAndPosition("CLOSE_PAREN", 58),
+ new TokenStringRepAndPosition("CLOSE_PAREN", 59),
+ new TokenStringRepAndPosition("EOS", 60)
+ };
+
+ assertEquals(expectedTokens.length, actualTokens.length);
+ for (int i = 0; i < expectedTokens.length; ++i) {
+ assertEquals(expectedTokens[i].getStringRep(), actualTokens[i].getStringRep());
+ assertEquals(expectedTokens[i].getPosition(), actualTokens[i].getPosition());
+ }
+ }
+
+ /**
+ * Please note that the scanner input here is the same as for testScanner1() except for the lack of spaces.
+ */
+ public void testScanner2() throws Exception {
+ final Tokeniser tokeniser = new Tokeniser("AND(1.0>=$(BOB),OR($(JOE)=$(tiny),$(x)>LOG(1.3e17)))");
+ final ArrayList<TokenStringRepAndPosition> tokens = new ArrayList<TokenStringRepAndPosition>();
+ String tokenAsString;
+ do {
+ tokenAsString = tokeniser.getTokenAsString();
+ final int position = tokeniser.getStartPos();
+ tokens.add(new TokenStringRepAndPosition(tokenAsString, position));
+ } while (tokenAsString != "EOS");
+ final TokenStringRepAndPosition[] actualTokens = new TokenStringRepAndPosition[tokens.size()];
+ tokens.toArray(actualTokens);
+
+ final TokenStringRepAndPosition[] expectedTokens = {
+ new TokenStringRepAndPosition("IDENTIFIER: \"AND\"", 0),
+ new TokenStringRepAndPosition("OPEN_PAREN", 3),
+ new TokenStringRepAndPosition("FLOAT_CONSTANT: \"1.0\"", 4),
+ new TokenStringRepAndPosition("GREATER_OR_EQUAL", 7),
+ new TokenStringRepAndPosition("DOLLAR", 9),
+ new TokenStringRepAndPosition("OPEN_PAREN", 10),
+ new TokenStringRepAndPosition("IDENTIFIER: \"BOB\"", 11),
+ new TokenStringRepAndPosition("CLOSE_PAREN", 14),
+ new TokenStringRepAndPosition("COMMA", 15),
+ new TokenStringRepAndPosition("IDENTIFIER: \"OR\"", 16),
+ new TokenStringRepAndPosition("OPEN_PAREN", 18),
+ new TokenStringRepAndPosition("DOLLAR", 19),
+ new TokenStringRepAndPosition("OPEN_PAREN", 20),
+ new TokenStringRepAndPosition("IDENTIFIER: \"JOE\"", 21),
+ new TokenStringRepAndPosition("CLOSE_PAREN", 24),
+ new TokenStringRepAndPosition("EQUAL", 25),
+ new TokenStringRepAndPosition("DOLLAR", 26),
+ new TokenStringRepAndPosition("OPEN_PAREN", 27),
+ new TokenStringRepAndPosition("IDENTIFIER: \"tiny\"", 28),
+ new TokenStringRepAndPosition("CLOSE_PAREN", 32),
+ new TokenStringRepAndPosition("COMMA", 33),
+ new TokenStringRepAndPosition("DOLLAR", 34),
+ new TokenStringRepAndPosition("OPEN_PAREN", 35),
+ new TokenStringRepAndPosition("IDENTIFIER: \"x\"", 36),
+ new TokenStringRepAndPosition("CLOSE_PAREN", 37),
+ new TokenStringRepAndPosition("GREATER_THAN", 38),
+ new TokenStringRepAndPosition("IDENTIFIER: \"LOG\"", 39),
+ new TokenStringRepAndPosition("OPEN_PAREN", 42),
+ new TokenStringRepAndPosition("FLOAT_CONSTANT: \"1.3E17\"", 43),
+ new TokenStringRepAndPosition("CLOSE_PAREN", 49),
+ new TokenStringRepAndPosition("CLOSE_PAREN", 50),
+ new TokenStringRepAndPosition("CLOSE_PAREN", 51),
+ new TokenStringRepAndPosition("EOS", 52)
+ };
+
+ assertEquals(expectedTokens.length, actualTokens.length);
+ for (int i = 0; i < expectedTokens.length; ++i) {
+ assertEquals(expectedTokens[i].getStringRep(), actualTokens[i].getStringRep());
+ assertEquals(expectedTokens[i].getPosition(), actualTokens[i].getPosition());
+ }
+ }
+
+ public void testScanner3() throws Exception {
+ final Tokeniser tokeniser = new Tokeniser("1.79^3");
+ final ArrayList<TokenStringRepAndPosition> tokens = new ArrayList<TokenStringRepAndPosition>();
+ String tokenAsString;
+ do {
+ tokenAsString = tokeniser.getTokenAsString();
+ final int position = tokeniser.getStartPos();
+ tokens.add(new TokenStringRepAndPosition(tokenAsString, position));
+ } while (tokenAsString != "EOS");
+ final TokenStringRepAndPosition[] actualTokens = new TokenStringRepAndPosition[tokens.size()];
+ tokens.toArray(actualTokens);
+
+ final TokenStringRepAndPosition[] expectedTokens = {
+ new TokenStringRepAndPosition("FLOAT_CONSTANT: \"1.79\"", 0),
+ new TokenStringRepAndPosition("CARET", 4),
+ new TokenStringRepAndPosition("FLOAT_CONSTANT: \"3.0\"", 5),
+ new TokenStringRepAndPosition("EOS", 6)
+ };
+
+ assertEquals(expectedTokens.length, actualTokens.length);
+ for (int i = 0; i < expectedTokens.length; ++i) {
+ assertEquals(expectedTokens[i].getStringRep(), actualTokens[i].getStringRep());
+ assertEquals(expectedTokens[i].getPosition(), actualTokens[i].getPosition());
+ }
+ }
+
+ public void testScanner4() throws Exception {
+ final Tokeniser tokeniser = new Tokeniser("true, fred, FALSE, True");
+ final ArrayList<TokenStringRepAndPosition> tokens = new ArrayList<TokenStringRepAndPosition>();
+ String tokenAsString;
+ do {
+ tokenAsString = tokeniser.getTokenAsString();
+ final int position = tokeniser.getStartPos();
+ tokens.add(new TokenStringRepAndPosition(tokenAsString, position));
+ } while (tokenAsString != "EOS");
+ final TokenStringRepAndPosition[] actualTokens = new TokenStringRepAndPosition[tokens.size()];
+ tokens.toArray(actualTokens);
+
+ final TokenStringRepAndPosition[] expectedTokens = {
+ new TokenStringRepAndPosition("BOOLEAN_CONSTANT: \"true\"", 0),
+ new TokenStringRepAndPosition("COMMA", 4),
+ new TokenStringRepAndPosition("IDENTIFIER: \"fred\"", 6),
+ new TokenStringRepAndPosition("COMMA", 10),
+ new TokenStringRepAndPosition("BOOLEAN_CONSTANT: \"false\"", 12),
+ new TokenStringRepAndPosition("COMMA", 17),
+ new TokenStringRepAndPosition("BOOLEAN_CONSTANT: \"true\"", 19),
+ new TokenStringRepAndPosition("EOS", 23)
+ };
+
+ assertEquals(expectedTokens.length, actualTokens.length);
+ for (int i = 0; i < expectedTokens.length; ++i) {
+ assertEquals(expectedTokens[i].getStringRep(), actualTokens[i].getStringRep());
+ assertEquals(expectedTokens[i].getPosition(), actualTokens[i].getPosition());
+ }
+ }
+
+ public void testScanner5() throws Exception {
+ final Tokeniser tokeniser = new Tokeniser(".79e2");
+ final ArrayList<TokenStringRepAndPosition> tokens = new ArrayList<TokenStringRepAndPosition>();
+ String tokenAsString;
+ do {
+ tokenAsString = tokeniser.getTokenAsString();
+ final int position = tokeniser.getStartPos();
+ tokens.add(new TokenStringRepAndPosition(tokenAsString, position));
+ } while (tokenAsString != "EOS");
+ final TokenStringRepAndPosition[] actualTokens = new TokenStringRepAndPosition[tokens.size()];
+ tokens.toArray(actualTokens);
+
+ final TokenStringRepAndPosition[] expectedTokens = {
+ new TokenStringRepAndPosition("FLOAT_CONSTANT: \"79.0\"", 0),
+ new TokenStringRepAndPosition("EOS", 5)
+ };
+
+ assertEquals(expectedTokens.length, actualTokens.length);
+ for (int i = 0; i < expectedTokens.length; ++i) {
+ assertEquals(expectedTokens[i].getStringRep(), actualTokens[i].getStringRep());
+ assertEquals(expectedTokens[i].getPosition(), actualTokens[i].getPosition());
+ }
+ }
+}
diff --git a/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/ACosTest.java b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/ACosTest.java
new file mode 100644
index 0000000..3b00e24
--- /dev/null
+++ b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/ACosTest.java
@@ -0,0 +1,44 @@
+/*
+ File: ACosTest.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import junit.framework.*;
+
+
+public class ACosTest extends TestCase {
+ public void testAll() throws Exception {
+ assertTrue(Framework.executeTest("=ACOS(-1)", Double.valueOf(Math.PI)));
+ assertTrue(Framework.executeTest("=ACOS(0)", Double.valueOf(Math.PI/2.0)));
+ assertTrue(Framework.executeTest("=ACOS(" + (1.0 / Math.sqrt(2.0)) + ")", Double.valueOf(0.7853981633974484)));
+ assertTrue(Framework.executeTestExpectFailure("=ACOS(-1.01)"));
+ assertTrue(Framework.executeTestExpectFailure("=ACOS(+1.01)"));
+ }
+}
diff --git a/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/ASinTest.java b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/ASinTest.java
new file mode 100644
index 0000000..ae07148
--- /dev/null
+++ b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/ASinTest.java
@@ -0,0 +1,44 @@
+/*
+ File: ASinTest.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import junit.framework.*;
+
+
+public class ASinTest extends TestCase {
+ public void testAll() throws Exception {
+ assertTrue(Framework.executeTest("=ASIN(-1)", Double.valueOf(-Math.PI/2.0)));
+ assertTrue(Framework.executeTest("=ASIN(0)", Double.valueOf(0.0)));
+ assertTrue(Framework.executeTest("=ASIN(" + (1.0 / Math.sqrt(2.0)) + ")", Double.valueOf(0.7853981633974482)));
+ assertTrue(Framework.executeTestExpectFailure("=ASIN(-1.01)"));
+ assertTrue(Framework.executeTestExpectFailure("=ASIN(+1.01)"));
+ }
+}
diff --git a/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/ATan2Test.java b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/ATan2Test.java
new file mode 100644
index 0000000..6866cbc
--- /dev/null
+++ b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/ATan2Test.java
@@ -0,0 +1,42 @@
+/*
+ File: ATan2Test.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import junit.framework.*;
+
+
+public class ATan2Test extends TestCase {
+ public void testAll() throws Exception {
+ assertTrue(Framework.executeTest("=ATAN2(1,1)", Double.valueOf(0.7853981633974483)));
+ assertTrue(Framework.executeTest("=ATAN2(-1,-1)", Double.valueOf(-2.356194490192345)));
+ assertTrue(Framework.executeTestExpectFailure("=ATAN2(0,0)"));
+ }
+}
diff --git a/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/AbsTest.java b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/AbsTest.java
new file mode 100644
index 0000000..32969f1
--- /dev/null
+++ b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/AbsTest.java
@@ -0,0 +1,47 @@
+/*
+ File: AbsTest.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import junit.framework.*;
+
+
+public class AbsTest extends TestCase {
+ public void testAll() throws Exception {
+ assertTrue(Framework.executeTest("=ABS(-1.3)", new Double(1.3)));
+ assertTrue(Framework.executeTest("=ABS(0.0)", new Double(0.0)));
+ assertTrue(Framework.executeTest("=ABS(1.3)", new Double(1.3)));
+ assertTrue(Framework.executeTest("=ABS(+1.3)", new Double(+1.3)));
+ assertTrue(Framework.executeTest("=ABS(-3)", new Double(3.0)));
+ assertTrue(Framework.executeTest("=ABS(0)", new Double(0.0)));
+ assertTrue(Framework.executeTest("=ABS(3)", new Double(3)));
+ assertTrue(Framework.executeTest("=ABS(+3)", new Double(3)));
+ }
+}
diff --git a/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/AndTest.java b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/AndTest.java
new file mode 100644
index 0000000..8d6178d
--- /dev/null
+++ b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/AndTest.java
@@ -0,0 +1,59 @@
+/*
+ File: AndTest.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import junit.framework.*;
+
+
+public class AndTest extends TestCase {
+ public void testAll() throws Exception {
+ final List<Object> list = new ArrayList<Object>();
+ list.add("false");
+ list.add(Long.valueOf(0L));
+ list.add(Double.valueOf(1.3));
+
+ final Map<String, Object> variablesAndValues = new HashMap<String, Object>();
+ variablesAndValues.put("LIST", list);
+
+ assertTrue(Framework.executeTest("=AND($LIST,\"false\",FALSE)", variablesAndValues, Boolean.valueOf(false)));
+ assertTrue(Framework.executeTest("=AND()", Boolean.valueOf(true)));
+ assertTrue(Framework.executeTest("=AND(TRUE)", variablesAndValues, Boolean.valueOf(true)));
+ assertTrue(Framework.executeTest("=AND(FALSE)", variablesAndValues, Boolean.valueOf(false)));
+ assertTrue(Framework.executeTest("=AND(FALSE,FALSE)", variablesAndValues, Boolean.valueOf(false)));
+ assertTrue(Framework.executeTest("=AND(FALSE,TRUE)", variablesAndValues, Boolean.valueOf(false)));
+ assertTrue(Framework.executeTest("=AND(TRUE,TRUE)", variablesAndValues, Boolean.valueOf(true)));
+ }
+}
diff --git a/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/AverageTest.java b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/AverageTest.java
new file mode 100644
index 0000000..cf500cc
--- /dev/null
+++ b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/AverageTest.java
@@ -0,0 +1,54 @@
+/*
+ File: AverageTest.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import junit.framework.*;
+
+
+public class AverageTest extends TestCase {
+ public void testAll() throws Exception {
+ final List<Double> numbers = new ArrayList<Double>();
+ numbers.add(1.0);
+ numbers.add(2.0);
+ numbers.add(3.0);
+ numbers.add(4.0);
+ numbers.add(5.0);
+ final Map<String, Object> variablesAndValues = new HashMap<String, Object>();
+ variablesAndValues.put("numbers", numbers);
+ assertTrue(Framework.executeTest("=AVERAGE($numbers)", variablesAndValues, Double.valueOf(3.0)));
+ assertTrue(Framework.executeTest("=AVERAGE(1,2,3.0,4,5)", Double.valueOf(3.0)));
+ }
+}
diff --git a/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/BListTest.java b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/BListTest.java
new file mode 100644
index 0000000..9aaed7d
--- /dev/null
+++ b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/BListTest.java
@@ -0,0 +1,66 @@
+/*
+ File: BListTest.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import junit.framework.*;
+
+
+public class BListTest extends TestCase {
+ public void testAll() throws Exception {
+ final List<Object> numbers = new ArrayList<Object>();
+ numbers.add(Boolean.valueOf(true));
+ numbers.add(Boolean.valueOf(false));
+ numbers.add(Double.valueOf(0.0));
+ numbers.add("true");
+ numbers.add(Double.valueOf(5.0));
+ final Map<String, Object> variablesAndValues = new HashMap<String, Object>();
+ variablesAndValues.put("numbers", numbers);
+ final List<Boolean> expectedResult = new ArrayList<Boolean>();
+ expectedResult.add(true);
+ expectedResult.add(false);
+ expectedResult.add(false);
+ expectedResult.add(true);
+ expectedResult.add(true);
+ expectedResult.add(false);
+ expectedResult.add(true);
+ assertTrue(Framework.executeTest("=BLIST($numbers, FALSE, TRUE)", variablesAndValues, expectedResult));
+
+ final List<Boolean> emptyList = new ArrayList<Boolean>();
+ assertTrue(Framework.executeTest("=BLIST()", emptyList));
+
+ assertTrue(Framework.executeTestExpectFailure("=BLIST(\"abc\")"));
+ }
+}
diff --git a/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/CombinTest.java b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/CombinTest.java
new file mode 100644
index 0000000..45cdc8d
--- /dev/null
+++ b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/CombinTest.java
@@ -0,0 +1,46 @@
+/*
+ File: CombinTest.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import junit.framework.*;
+
+
+public class CombinTest extends TestCase {
+ public void testAll() throws Exception {
+ assertTrue(Framework.executeTest("=COMBIN(100,0)", Long.valueOf(1)));
+ assertTrue(Framework.executeTest("=COMBIN(8,2)", Long.valueOf(28L)));
+ assertTrue(Framework.executeTestExpectFailure("=COMBIN(\"X\",3)"));
+ assertTrue(Framework.executeTestExpectFailure("=COMBIN(3,\"X\")"));
+ assertTrue(Framework.executeTestExpectFailure("=COMBIN(-1, 2)"));
+ assertTrue(Framework.executeTestExpectFailure("=COMBIN(2, -1)"));
+ assertTrue(Framework.executeTestExpectFailure("=COMBIN(2, 3)"));
+ }
+}
diff --git a/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/ConcatenateTest.java b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/ConcatenateTest.java
new file mode 100644
index 0000000..09bc556
--- /dev/null
+++ b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/ConcatenateTest.java
@@ -0,0 +1,54 @@
+/*
+ File: ConcatenateTest.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import junit.framework.*;
+
+
+public class ConcatenateTest extends TestCase {
+ public void testAll() throws Exception {
+ final List<Object> numbers = new ArrayList<Object>();
+ numbers.add(Double.valueOf(1.0));
+ numbers.add(Integer.valueOf(2));
+ numbers.add(Double.valueOf(3.0));
+ numbers.add("4.01");
+ numbers.add(Double.valueOf(5.0));
+ final Map<String, Object> variablesAndValues = new HashMap<String, Object>();
+ variablesAndValues.put("numbers", numbers);
+ assertTrue(Framework.executeTest("=Concatenate($numbers, \"ab\", \"\")", variablesAndValues, "1234.015ab"));
+ assertTrue(Framework.executeTest("=CONCATENATE()", ""));
+ }
+}
diff --git a/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/CosTest.java b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/CosTest.java
new file mode 100644
index 0000000..765d260
--- /dev/null
+++ b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/CosTest.java
@@ -0,0 +1,45 @@
+/*
+ File: CosTest.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import junit.framework.*;
+
+
+public class CosTest extends TestCase {
+ public void testAll() throws Exception {
+ assertTrue(Framework.executeTest("=COS("+Math.PI+"/6)", Double.valueOf(0.8660254037844387)));
+ assertTrue(Framework.executeTest("=COS(RADIANS(60))", Double.valueOf(0.5000000000000001)));
+ assertTrue(Framework.executeTest("=COS(RADIANS(-30))", Double.valueOf(0.8660254037844387)));
+ assertTrue(Framework.executeTest("=COS(0.785398163)", Double.valueOf(0.7071067814675859)));
+ assertTrue(Framework.executeTest("=COS(\"0.0\")", Double.valueOf(1)));
+ assertTrue(Framework.executeTestExpectFailure("=COS(\"abc\")"));
+ }
+}
diff --git a/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/CoshTest.java b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/CoshTest.java
new file mode 100644
index 0000000..052088b
--- /dev/null
+++ b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/CoshTest.java
@@ -0,0 +1,41 @@
+/*
+ File: CoshTest.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import junit.framework.*;
+
+
+public class CoshTest extends TestCase {
+ public void testAll() throws Exception {
+ assertTrue(Framework.executeTest("=COSH(4)", Double.valueOf(27.308232836016487)));
+ assertTrue(Framework.executeTest("=COSH(EXP(1))", Double.valueOf(7.6101251386622915)));
+ }
+}
diff --git a/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/CountTest.java b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/CountTest.java
new file mode 100644
index 0000000..46b460c
--- /dev/null
+++ b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/CountTest.java
@@ -0,0 +1,57 @@
+/*
+ File: CountTest.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import junit.framework.*;
+
+
+public class CountTest extends TestCase {
+ public void testAll() throws Exception {
+ final List<Object> numbers = new ArrayList<Object>();
+ numbers.add(Double.valueOf(1.0));
+ numbers.add(Integer.valueOf(2));
+ numbers.add(Double.valueOf(3.0));
+ numbers.add("4.0");
+ numbers.add(Double.valueOf(5.0));
+ final Map<String, Object> variablesAndValues = new HashMap<String, Object>();
+ variablesAndValues.put("numbers", numbers);
+ assertTrue(Framework.executeTest("=COUNT($numbers)", variablesAndValues, Long.valueOf(4)));
+ assertTrue(Framework.executeTest("=COUNT(-2,\"-3\",-4.35)", Long.valueOf(3)));
+ assertTrue(Framework.executeTest("=COUNT(-1.3)", Long.valueOf(1)));
+ assertTrue(Framework.executeTest("=COUNT(0.0)", Long.valueOf(1)));
+ assertTrue(Framework.executeTestExpectFailure("=COUNT()"));
+ }
+}
diff --git a/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/ErrorTest.java b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/ErrorTest.java
new file mode 100644
index 0000000..993abd1
--- /dev/null
+++ b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/ErrorTest.java
@@ -0,0 +1,40 @@
+/*
+ File: ErrorTest.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import junit.framework.*;
+
+
+public class ErrorTest extends TestCase {
+ public void testAll() throws Exception {
+ assertTrue(Framework.executeTestExpectFailure("some message"));
+ }
+}
diff --git a/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/ExpTest.java b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/ExpTest.java
new file mode 100644
index 0000000..7e1f474
--- /dev/null
+++ b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/ExpTest.java
@@ -0,0 +1,42 @@
+/*
+ File: ExpTest.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import junit.framework.*;
+
+
+public class ExpTest extends TestCase {
+ public void testAll() throws Exception {
+ assertTrue(Framework.executeTest("=EXP(-4.0)", Double.valueOf(0.01831563888873418)));
+ assertTrue(Framework.executeTest("=EXP(0.0)", Double.valueOf(1.0)));
+ assertTrue(Framework.executeTest("=EXP(+1.3)", Double.valueOf(3.6692966676192444)));
+ }
+}
diff --git a/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/FListTest.java b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/FListTest.java
new file mode 100644
index 0000000..94bef36
--- /dev/null
+++ b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/FListTest.java
@@ -0,0 +1,66 @@
+/*
+ File: FListTest.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import junit.framework.*;
+
+
+public class FListTest extends TestCase {
+ public void testAll() throws Exception {
+ final List<Object> numbers = new ArrayList<Object>();
+ numbers.add(Double.valueOf(1.0));
+ numbers.add(Integer.valueOf(2));
+ numbers.add(Double.valueOf(3.0));
+ numbers.add("4.0");
+ numbers.add(Double.valueOf(5.0));
+ final Map<String, Object> variablesAndValues = new HashMap<String, Object>();
+ variablesAndValues.put("numbers", numbers);
+ final List<Double> expectedResult = new ArrayList<Double>();
+ expectedResult.add(1.0);
+ expectedResult.add(2.0);
+ expectedResult.add(3.0);
+ expectedResult.add(4.0);
+ expectedResult.add(5.0);
+ expectedResult.add(6.0);
+ expectedResult.add(7.0);
+ assertTrue(Framework.executeTest("=FLIST($numbers, 6, 7)", variablesAndValues, expectedResult));
+
+ final List<Double> emptyList = new ArrayList<Double>();
+ assertTrue(Framework.executeTest("=FLIST()", emptyList));
+
+ assertTrue(Framework.executeTestExpectFailure("=FLIST(\"abc\")"));
+ }
+}
diff --git a/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/FirstTest.java b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/FirstTest.java
new file mode 100644
index 0000000..ac63233
--- /dev/null
+++ b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/FirstTest.java
@@ -0,0 +1,56 @@
+/*
+ File: FirstTest.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import junit.framework.*;
+
+
+public class FirstTest extends TestCase {
+ public void testAll() throws Exception {
+ final List<Object> list1 = new ArrayList<Object>();
+ list1.add(3.0);
+ list1.add(new Integer(2));
+ list1.add(5.0);
+ list1.add(new String("1"));
+ list1.add(4.0);
+ final Map<String, Object> variablesAndValues = new HashMap<String, Object>();
+ variablesAndValues.put("list1", list1);
+ assertTrue(Framework.executeTest("=FIRST(${list1})", variablesAndValues, Double.valueOf(3.0)));
+ final List<Object> list2 = new ArrayList<Object>();
+ variablesAndValues.put("list2", list2);
+ assertTrue(Framework.executeTestExpectFailure("=FIRST(${list2})"));
+ }
+}
diff --git a/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/Framework.java b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/Framework.java
new file mode 100644
index 0000000..fcb107b
--- /dev/null
+++ b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/Framework.java
@@ -0,0 +1,203 @@
+/*
+ File: Framework.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import org.cytoscape.equations.EqnCompiler;
+import org.cytoscape.equations.Function;
+import org.cytoscape.equations.Parser;
+import org.cytoscape.equations.interpreter.IdentDescriptor;
+import org.cytoscape.equations.interpreter.Interpreter;
+
+
+class Framework {
+ static private class BadReturnFunction implements Function {
+ public String getName() { return "BADRETURN"; }
+ public String getFunctionSummary() { return "Returns an invalid type at runtime."; }
+ public String getUsageDescription() { return "Call this with \"BADRETURN()\"."; }
+ public Class getReturnType() { return Double.class; }
+ public Class validateArgTypes(final Class[] argTypes) { return argTypes.length == 0 ? Double.class : null; }
+ public Object evaluateFunction(final Object[] args) { return new Integer(1); }
+ public List<Class> getPossibleArgTypes(final Class[] leadingArgs) { return null; }
+ }
+
+ private static final EqnCompiler compiler = new EqnCompiler();
+
+ static {
+ Parser.getParser().registerFunction(new BadReturnFunction());
+ }
+
+ /**
+ * Execute a test that should succeed at compile time and runtime.
+ * @return true if the test compiled and ran and produced the expected result
+ */
+ static boolean executeTest(final String equation, final Map<String, Object> variablesAndValues, final Object expectedResult) {
+ final Map<String, Class> varNameToTypeMap = new HashMap<String, Class>();
+ for (final String variableName : variablesAndValues.keySet())
+ varNameToTypeMap.put(variableName, variablesAndValues.get(variableName).getClass());
+
+ try {
+ if (!compiler.compile(equation, varNameToTypeMap)) {
+ System.err.println("Error while compiling \"" + equation + "\": " + compiler.getLastErrorMsg());
+ return false;
+ }
+ } catch (final Exception e) {
+ System.err.println("Error while compiling \"" + equation + "\": " + e.getMessage());
+ return false;
+ }
+
+ final Map<String, IdentDescriptor> nameToDescriptorMap = new HashMap<String, IdentDescriptor>();
+ try {
+ for (final String variableName : variablesAndValues.keySet())
+ nameToDescriptorMap.put(variableName, new IdentDescriptor(variablesAndValues.get(variableName)));
+ } catch (final Exception e) {
+ System.err.println("Error while processing variables for \"" + equation + "\": " + e.getMessage());
+ return false;
+ }
+
+ final Interpreter interpreter = new Interpreter(compiler.getEquation(), nameToDescriptorMap);
+ final Object actualResult;
+ try {
+ actualResult = interpreter.run();
+ } catch (final Exception e) {
+ System.err.println("caught runtime error: " + e.getMessage());
+ return false;
+ }
+
+ if (!areEqual(actualResult, expectedResult)) {
+ System.err.println("[" + equation + "] expected: " + expectedResult + ", found: " + actualResult);
+ return false;
+ }
+
+ return true;
+ }
+
+ static boolean executeTest(final String equation, final Object expectedResult) {
+ final Map<String, Object> variablesAndValues = new HashMap<String, Object>();
+ return executeTest(equation, variablesAndValues, expectedResult);
+ }
+
+ /**
+ * Excecute a test that should fail at either compile time or runtime.
+ * @return true if the test fails at compile time or runtime, otherwise false
+ *
+ */
+ static boolean executeTestExpectFailure(final String equation, final Map<String, Object> variablesAndValues) {
+ final Map<String, Class> varNameToTypeMap = new HashMap<String, Class>();
+ for (final String variableName : variablesAndValues.keySet())
+ varNameToTypeMap.put(variableName, variablesAndValues.get(variableName).getClass());
+
+ try {
+ if (!compiler.compile(equation, varNameToTypeMap)) {
+ System.err.println("Error while compiling \"" + equation + "\": " + compiler.getLastErrorMsg());
+ return true;
+ }
+ } catch (final Exception e) {
+ System.err.println("Error while compiling \"" + equation + "\": " + e.getMessage());
+ return true;
+ }
+
+ final Map<String, IdentDescriptor> nameToDescriptorMap = new HashMap<String, IdentDescriptor>();
+ try {
+ for (final String variableName : variablesAndValues.keySet())
+ nameToDescriptorMap.put(variableName, new IdentDescriptor(variablesAndValues.get(variableName)));
+ } catch (final Exception e) {
+ System.err.println("Error while processing variables for \"" + equation + "\": " + e.getMessage());
+ return true;
+ }
+
+ final Interpreter interpreter = new Interpreter(compiler.getEquation(), nameToDescriptorMap);
+ try {
+ final Object result = interpreter.run();
+ // We should never get here!
+ return false;
+ } catch (final Exception e) {
+ return true;
+ }
+ }
+
+ static boolean executeTestExpectFailure(final String equation) {
+ final Map<String, Object> variablesAndValues = new HashMap<String, Object>();
+ return executeTestExpectFailure(equation, variablesAndValues);
+ }
+
+ /**
+ * @return the unbiased exponent of a double-precision IEEE floating point number
+ */
+ private static long getExponent(final double f) {
+ final long EXPONENT_MASK = 0x7FFFF00000000000L;
+ final long bits = Double.doubleToLongBits(f) & EXPONENT_MASK;
+ final int BIAS = 1023;
+ final int BIT_OFFSET = 52;
+ return (bits >> BIT_OFFSET) - BIAS;
+ }
+
+ private static boolean almostEqual(final double x1, final double x2) {
+ if (x1 == x2)
+ return true;
+
+ if (Math.signum(x1) != Math.signum(x2))
+ return false;
+
+ if (getExponent(x1) != getExponent(x2))
+ return false;
+
+ final double absX1 = Math.abs(x1);
+ final double absX2 = Math.abs(x2);
+
+ if (x1 != 0.0)
+ return Math.abs(x1 - x2) / Math.abs(x1) < 1.0e-12;
+ else
+ return Math.abs(x1 - x2) / Math.abs(x2) < 1.0e-12;
+ }
+
+ private static boolean areEqual(final Object o1, final Object o2) {
+ if (o1 instanceof Double && o2 instanceof Double)
+ return almostEqual((Double)o1, (Double)o2);
+ else if (o1 instanceof List && o2 instanceof List) {
+ final List l1 = (List)o1;
+ final List l2 = (List)o2;
+ if (l1.size() != l2.size())
+ return false;
+
+ for (int i = 0; i < l1.size(); ++i) {
+ if (!areEqual(l1.get(i), l2.get(i)))
+ return false;
+ }
+ return true;
+ }
+ else
+ return o1.equals(o2);
+ }
+}
diff --git a/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/GeoMeanTest.java b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/GeoMeanTest.java
new file mode 100644
index 0000000..20f3eba
--- /dev/null
+++ b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/GeoMeanTest.java
@@ -0,0 +1,55 @@
+/*
+ File: GeoMeanTest.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import junit.framework.*;
+
+
+public class GeoMeanTest extends TestCase {
+ public void testAll() throws Exception {
+ final List<Object> numbers = new ArrayList<Object>();
+ numbers.add(new Double(4.0));
+ numbers.add(new Long(5L));
+ numbers.add(new Double(8.0));
+ numbers.add(new Double(7.0));
+ numbers.add(new Long(11L));
+ numbers.add(new Long(4L));
+ final Map<String, Object> variablesAndValues = new HashMap<String, Object>();
+ variablesAndValues.put("list", numbers);
+ assertTrue(Framework.executeTest("=GEOMEAN($list, 3)", variablesAndValues, Double.valueOf(5.476986969656962)));
+ assertTrue(Framework.executeTestExpectFailure("=GEOMEAN()"));
+ }
+}
diff --git a/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/HarMeanTest.java b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/HarMeanTest.java
new file mode 100644
index 0000000..dde527b
--- /dev/null
+++ b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/HarMeanTest.java
@@ -0,0 +1,58 @@
+/*
+ File: HarMeanTest.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import junit.framework.*;
+
+
+public class HarMeanTest extends TestCase {
+ public void testAll() throws Exception {
+ final List<Object> numbers = new ArrayList<Object>();
+ numbers.add(new Double(4.0));
+ numbers.add(new Long(5L));
+ numbers.add(new Double(8.0));
+ numbers.add(new Double(7.0));
+ numbers.add(new Long(11L));
+ numbers.add(new Long(4L));
+ final Map<String, Object> variablesAndValues = new HashMap<String, Object>();
+ variablesAndValues.put("list", numbers);
+ assertTrue(Framework.executeTest("=HARMEAN($list, 3)", variablesAndValues, Double.valueOf(5.028375962061728)));
+ assertTrue(Framework.executeTest("=HARMEAN(3.0,3,\"3.0\")", Double.valueOf(3.0)));
+ assertTrue(Framework.executeTestExpectFailure("=HARMEAN()"));
+ assertTrue(Framework.executeTestExpectFailure("=HARMEAN(1.0)"));
+ assertTrue(Framework.executeTestExpectFailure("=HARMEAN(1.0, -2)"));
+ }
+}
diff --git a/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/IListTest.java b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/IListTest.java
new file mode 100644
index 0000000..1fcab88
--- /dev/null
+++ b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/IListTest.java
@@ -0,0 +1,66 @@
+/*
+ File: IListTest.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import junit.framework.*;
+
+
+public class IListTest extends TestCase {
+ public void testAll() throws Exception {
+ final List<Object> numbers = new ArrayList<Object>();
+ numbers.add(Double.valueOf(1.0));
+ numbers.add(Integer.valueOf(2));
+ numbers.add(Double.valueOf(3.0));
+ numbers.add("4");
+ numbers.add(Double.valueOf(5.0));
+ final Map<String, Object> variablesAndValues = new HashMap<String, Object>();
+ variablesAndValues.put("numbers", numbers);
+ final List<Long> expectedResult = new ArrayList<Long>();
+ expectedResult.add(1L);
+ expectedResult.add(2L);
+ expectedResult.add(3L);
+ expectedResult.add(4L);
+ expectedResult.add(5L);
+ expectedResult.add(6L);
+ expectedResult.add(7L);
+ assertTrue(Framework.executeTest("=ILIST($numbers, 6, 7)", variablesAndValues, expectedResult));
+
+ final List<Long> emptyList = new ArrayList<Long>();
+ assertTrue(Framework.executeTest("=ILIST()", emptyList));
+
+ assertTrue(Framework.executeTestExpectFailure("=ILIST(\"abc\")"));
+ }
+}
diff --git a/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/IfTest.java b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/IfTest.java
new file mode 100644
index 0000000..0c39923
--- /dev/null
+++ b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/IfTest.java
@@ -0,0 +1,43 @@
+/*
+ File: IfTest.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import junit.framework.*;
+
+
+public class IfTest extends TestCase {
+ public void testAll() throws Exception {
+ assertTrue(Framework.executeTest("=IF(2.3 >= 1, \"Xx\", \"Yz\")", "Xx"));
+ assertTrue(Framework.executeTest("=IF(FALSE, 12.3, -4)", Double.valueOf(-4)));
+ assertTrue(Framework.executeTest("=IF(true, false, true)", Boolean.valueOf(false)));
+ assertTrue(Framework.executeTest("=IF(TrUe, 12.3, \"-4\")", "12.3"));
+ }
+}
diff --git a/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/LargestTest.java b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/LargestTest.java
new file mode 100644
index 0000000..6e2fcc8
--- /dev/null
+++ b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/LargestTest.java
@@ -0,0 +1,69 @@
+/*
+ File: LargestTest.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import junit.framework.*;
+
+
+public class LargestTest extends TestCase {
+ public void testAll() throws Exception {
+ // A list w/ an odd number of elements:
+ final List<Object> numbers = new ArrayList<Object>();
+ numbers.add(new Double(5.5));
+ numbers.add(new Long(-1L));
+ numbers.add(new Double(10.0));
+ numbers.add(new Double(3.1));
+ numbers.add(new Long(4L));
+ final Map<String, Object> variablesAndValues = new HashMap<String, Object>();
+ variablesAndValues.put("list", numbers);
+ assertTrue(Framework.executeTest("=LARGEST($list,3)", variablesAndValues, Double.valueOf(4.0)));
+ assertTrue(Framework.executeTest("=LARGEST($list, 1)", variablesAndValues, Double.valueOf(10)));
+ assertTrue(Framework.executeTest("=LARGEST($list, 5)", variablesAndValues, Double.valueOf(-1)));
+
+
+ // A list w/ an even number of elements:
+ final List<Object> numbers2 = new ArrayList<Object>();
+ numbers2.add(new Double(5.5));
+ numbers2.add(new Long(-1L));
+ numbers2.add(new Double(10.0));
+ numbers2.add(new Double(3.1));
+ variablesAndValues.put("list2", numbers2);
+ assertTrue(Framework.executeTest("=LARGEST($list2, 1)", variablesAndValues, Double.valueOf(10.0)));
+ assertTrue(Framework.executeTest("=LARGEST($list2, 4)", variablesAndValues, Double.valueOf(-1.0)));
+ assertTrue(Framework.executeTest("=LARGEST($list2, 2)", variablesAndValues, Double.valueOf(5.5)));
+ assertTrue(Framework.executeTestExpectFailure("=LARGEST($list2, 10)", variablesAndValues));
+ }
+}
diff --git a/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/LastTest.java b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/LastTest.java
new file mode 100644
index 0000000..a4627aa
--- /dev/null
+++ b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/LastTest.java
@@ -0,0 +1,56 @@
+/*
+ File: LastTest.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import junit.framework.*;
+
+
+public class LastTest extends TestCase {
+ public void testAll() throws Exception {
+ final List<Object> list1 = new ArrayList<Object>();
+ list1.add(3.0);
+ list1.add(new Integer(2));
+ list1.add(5.0);
+ list1.add(new String("1"));
+ list1.add(4.0);
+ final Map<String, Object> variablesAndValues = new HashMap<String, Object>();
+ variablesAndValues.put("list1", list1);
+ assertTrue(Framework.executeTest("=LAST(${list1})", variablesAndValues, Double.valueOf(4.0)));
+ final List<Object> list2 = new ArrayList<Object>();
+ variablesAndValues.put("list2", list2);
+ assertTrue(Framework.executeTestExpectFailure("=LAST(${list2})"));
+ }
+}
diff --git a/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/LeftTest.java b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/LeftTest.java
new file mode 100644
index 0000000..b82dd2c
--- /dev/null
+++ b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/LeftTest.java
@@ -0,0 +1,43 @@
+/*
+ File: LeftTest.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import junit.framework.*;
+
+
+public class LeftTest extends TestCase {
+ public void testAll() throws Exception {
+ assertTrue(Framework.executeTest("=LEFT(\"Circus\", 3)", "Cir"));
+ assertTrue(Framework.executeTest("=LEFT(\"aureus\",6000)", "aureus"));
+ assertTrue(Framework.executeTest("=LEFT(\"FredBobBillJoeBobHansKarl\")", "F"));
+ assertTrue(Framework.executeTest("=LEFT(\"\")", ""));
+ }
+}
diff --git a/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/LenTest.java b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/LenTest.java
new file mode 100644
index 0000000..b421002
--- /dev/null
+++ b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/LenTest.java
@@ -0,0 +1,41 @@
+/*
+ File: LenTest.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import junit.framework.*;
+
+
+public class LenTest extends TestCase {
+ public void testAll() throws Exception {
+ assertTrue(Framework.executeTest("=LEN(\"baboon\")", Long.valueOf(6)));
+ assertTrue(Framework.executeTest("=LEN(\"\")", Long.valueOf(0)));
+ }
+}
diff --git a/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/ListToStringTest.java b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/ListToStringTest.java
new file mode 100644
index 0000000..91e7e7f
--- /dev/null
+++ b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/ListToStringTest.java
@@ -0,0 +1,53 @@
+/*
+ File: ListToStringTest.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import junit.framework.*;
+
+
+public class ListToStringTest extends TestCase {
+ public void testAll() throws Exception {
+ final List<Object> list = new ArrayList<Object>();
+ list.add("Fred");
+ list.add(Long.valueOf(3L));
+ list.add(Double.valueOf(1.3));
+
+ final Map<String, Object> variablesAndValues = new HashMap<String, Object>();
+ variablesAndValues.put("LIST", list);
+
+ assertTrue(Framework.executeTest("=LISTTOSTRING($LIST,\",\")", variablesAndValues, new String("Fred,3,1.3")));
+ }
+}
diff --git a/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/LnTest.java b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/LnTest.java
new file mode 100644
index 0000000..4d76951
--- /dev/null
+++ b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/LnTest.java
@@ -0,0 +1,42 @@
+/*
+ File: LnTest.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import junit.framework.*;
+
+
+public class LnTest extends TestCase {
+ public void testAll() throws Exception {
+ assertTrue(Framework.executeTest("=LN(2.5)", Double.valueOf(0.9162907318741551)));
+ assertTrue(Framework.executeTestExpectFailure("=LN(0.0)"));
+ assertTrue(Framework.executeTestExpectFailure("=LN(-1.3)"));
+ }
+}
diff --git a/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/LowerTest.java b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/LowerTest.java
new file mode 100644
index 0000000..d528535
--- /dev/null
+++ b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/LowerTest.java
@@ -0,0 +1,43 @@
+/*
+ File: LowerTest.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import junit.framework.*;
+
+
+public class LowerTest extends TestCase {
+ public void testAll() throws Exception {
+ assertTrue(Framework.executeTest("=LOWER(\"\")", ""));
+ assertTrue(Framework.executeTest("=LOWER(\"lower\")", "lower"));
+ assertTrue(Framework.executeTest("=LOWER(\"UPPER\")", "upper"));
+ assertTrue(Framework.executeTest("=LOWER(\"MiXeD\")", "mixed"));
+ }
+}
diff --git a/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/MaxTest.java b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/MaxTest.java
new file mode 100644
index 0000000..696cb6e
--- /dev/null
+++ b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/MaxTest.java
@@ -0,0 +1,57 @@
+/*
+ File: MaxTest.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import junit.framework.*;
+
+
+public class MaxTest extends TestCase {
+ public void testAll() throws Exception {
+ final List<Object> numbers = new ArrayList<Object>();
+ numbers.add(Double.valueOf(1.0));
+ numbers.add(Integer.valueOf(2));
+ numbers.add(Double.valueOf(3.0));
+ numbers.add("4.0");
+ numbers.add(Double.valueOf(5.0));
+ final Map<String, Object> variablesAndValues = new HashMap<String, Object>();
+ variablesAndValues.put("numbers", numbers);
+ assertTrue(Framework.executeTest("=MAX($numbers)", variablesAndValues, Double.valueOf(5.0)));
+ assertTrue(Framework.executeTest("=MAX(-2,-3,-4.35)", Double.valueOf(-2)));
+ assertTrue(Framework.executeTest("=MAX(-1.3)", Double.valueOf(-1.3)));
+ assertTrue(Framework.executeTest("=MAX(0.0)", Double.valueOf(0.0)));
+ assertTrue(Framework.executeTestExpectFailure("=MAX()"));
+ }
+}
diff --git a/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/MedianTest.java b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/MedianTest.java
new file mode 100644
index 0000000..434666a
--- /dev/null
+++ b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/MedianTest.java
@@ -0,0 +1,43 @@
+/*
+ File: MedianTest.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import junit.framework.*;
+
+
+public class MedianTest extends TestCase {
+ public void testAll() throws Exception {
+ assertTrue(Framework.executeTest("=MEDIAN(3,2,5,1,4)", Double.valueOf(3.0)));
+ assertTrue(Framework.executeTest("=MEDIAN(1,2,4,3)", Double.valueOf(2.5)));
+ assertTrue(Framework.executeTest("=MEDIAN(2.0)", Double.valueOf(2.0)));
+ assertTrue(Framework.executeTestExpectFailure("=MEDIAN()"));
+ }
+}
diff --git a/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/MidTest.java b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/MidTest.java
new file mode 100644
index 0000000..ed63ab6
--- /dev/null
+++ b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/MidTest.java
@@ -0,0 +1,42 @@
+/*
+ File: MidTest.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import junit.framework.*;
+
+
+public class MidTest extends TestCase {
+ public void testAll() throws Exception {
+ assertTrue(Framework.executeTest("=MID(\"Original Text\", 4, 3)", "gin"));
+ assertTrue(Framework.executeTest("=MID(\"Original Text\", 10, 3)", "Tex"));
+ assertTrue(Framework.executeTest("=MID(\"I have 5 bags\", 8, 1)", "5"));
+ }
+}
diff --git a/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/MinTest.java b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/MinTest.java
new file mode 100644
index 0000000..ed6ee17
--- /dev/null
+++ b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/MinTest.java
@@ -0,0 +1,57 @@
+/*
+ File: MinTest.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import junit.framework.*;
+
+
+public class MinTest extends TestCase {
+ public void testAll() throws Exception {
+ final List<Object> numbers = new ArrayList<Object>();
+ numbers.add(Double.valueOf(1.0));
+ numbers.add(Integer.valueOf(2));
+ numbers.add(Double.valueOf(3.0));
+ numbers.add("4.0");
+ numbers.add(Double.valueOf(5.0));
+ final Map<String, Object> variablesAndValues = new HashMap<String, Object>();
+ variablesAndValues.put("numbers", numbers);
+ assertTrue(Framework.executeTest("=MIN($numbers)", variablesAndValues, Double.valueOf(1.0)));
+ assertTrue(Framework.executeTest("=MIN(-2,-3,-4.35)", Double.valueOf(-4.35)));
+ assertTrue(Framework.executeTest("=MIN(-1.3)", Double.valueOf(-1.3)));
+ assertTrue(Framework.executeTest("=MIN(0.0)", Double.valueOf(0.0)));
+ assertTrue(Framework.executeTestExpectFailure("=MIN()"));
+ }
+}
diff --git a/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/ModTest.java b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/ModTest.java
new file mode 100644
index 0000000..9fc4db5
--- /dev/null
+++ b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/ModTest.java
@@ -0,0 +1,43 @@
+/*
+ File: ModTest.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import junit.framework.*;
+
+
+public class ModTest extends TestCase {
+ public void testAll() throws Exception {
+ assertTrue(Framework.executeTest("=MOD(3,2)", Double.valueOf(1)));
+ assertTrue(Framework.executeTest("=MOD(-3,2)", Double.valueOf(1)));
+ assertTrue(Framework.executeTest("=MOD(3,-2)", Double.valueOf(-1)));
+ assertTrue(Framework.executeTest("=MOD(-3,-2)", Double.valueOf(-1)));
+ }
+}
diff --git a/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/ModeTest.java b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/ModeTest.java
new file mode 100644
index 0000000..905284c
--- /dev/null
+++ b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/ModeTest.java
@@ -0,0 +1,58 @@
+/*
+ File: ModeTest.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import junit.framework.*;
+
+
+public class ModeTest extends TestCase {
+ public void testAll() throws Exception {
+ final List<Object> numbers = new ArrayList<Object>();
+ numbers.add(new Double(5.0));
+ numbers.add(new Long(3L));
+ numbers.add(new Double(4.0));
+ numbers.add(new Double(4.0));
+ numbers.add(new Long(3L));
+ numbers.add(new Long(4L));
+ numbers.add(new Long(5L));
+ numbers.add(new Double(3.0));
+ numbers.add(new Long(7L));
+ final Map<String, Object> variablesAndValues = new HashMap<String, Object>();
+ variablesAndValues.put("list", numbers);
+ assertTrue(Framework.executeTest("=MODE($list)", variablesAndValues, Double.valueOf(3)));
+ assertTrue(Framework.executeTestExpectFailure("=MODE()"));
+ }
+}
diff --git a/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/NormDistTest.java b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/NormDistTest.java
new file mode 100644
index 0000000..ba9cdee
--- /dev/null
+++ b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/NormDistTest.java
@@ -0,0 +1,42 @@
+/*
+ File: NormDistTest.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import junit.framework.*;
+
+
+public class NormDistTest extends TestCase {
+ public void testAll() throws Exception {
+ assertTrue(Framework.executeTest("=NORMDIST( 50, 40, 20, FALSE)", Double.valueOf(0.017603266338214976)));
+ assertTrue(Framework.executeTest("=NORMDIST( 0.8, 1, 0.3, TRUE)", Double.valueOf(0.25249253754692297)));
+ assertTrue(Framework.executeTestExpectFailure("=NORMDIST( 0.8, 1, -0.3, TRUE)"));
+ }
+}
diff --git a/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/NotTest.java b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/NotTest.java
new file mode 100644
index 0000000..f57f1a1
--- /dev/null
+++ b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/NotTest.java
@@ -0,0 +1,48 @@
+/*
+ File: NotTest.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import java.util.HashMap;
+import java.util.Map;
+
+import junit.framework.*;
+
+
+public class NotTest extends TestCase {
+ public void testAll() throws Exception {
+ final Map<String, Object> variablesAndValues = new HashMap<String, Object>();
+ variablesAndValues.put("logical", Boolean.valueOf(true));
+ assertTrue(Framework.executeTest("=NOT(true)", Boolean.valueOf(false)));
+ assertTrue(Framework.executeTest("=NOT(false)", Boolean.valueOf(true)));
+ assertTrue(Framework.executeTest("=NOT(3.2 < 12)", Boolean.valueOf(false)));
+ assertTrue(Framework.executeTest("=NOT(${logical})", variablesAndValues, Boolean.valueOf(false)));
+ }
+}
diff --git a/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/NowTest.java b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/NowTest.java
new file mode 100644
index 0000000..05d8f9a
--- /dev/null
+++ b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/NowTest.java
@@ -0,0 +1,48 @@
+/*
+ File: NowTest.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import java.text.DateFormat;
+import java.util.Calendar;
+
+import junit.framework.*;
+
+
+public class NowTest extends TestCase {
+ public void testAll() throws Exception {
+ final Calendar calendar = Calendar.getInstance();
+ final DateFormat dateFormat = DateFormat.getDateInstance(DateFormat.SHORT);
+ final DateFormat timeFormat = DateFormat.getTimeInstance(DateFormat.SHORT);
+ final String now = dateFormat.format(calendar.getTime()) + " " + timeFormat.format(calendar.getTime());
+
+ assertTrue(Framework.executeTest("=NOW()", now));
+ }
+}
diff --git a/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/NthTest.java b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/NthTest.java
new file mode 100644
index 0000000..3997422
--- /dev/null
+++ b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/NthTest.java
@@ -0,0 +1,64 @@
+/*
+ File: NthTest.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import junit.framework.*;
+
+
+public class NthTest extends TestCase {
+ public void testAll() throws Exception {
+ final List<Object> list1 = new ArrayList<Object>();
+ list1.add(3.0);
+ list1.add(new Integer(2));
+ list1.add(5.0);
+ list1.add(new String("1"));
+ list1.add(4.0);
+ final Map<String, Object> variablesAndValues = new HashMap<String, Object>();
+ variablesAndValues.put("list1", list1);
+ assertTrue(Framework.executeTest("=NTH(${list1}, 3)", variablesAndValues, Double.valueOf(5.0)));
+ assertTrue(Framework.executeTest("=NTH(${list1}, 2)", variablesAndValues, Long.valueOf(2)));
+ final List<Object> list2 = new ArrayList<Object>();
+ list2.add(1.0);
+ list2.add(new Integer(2));
+ list2.add(4.0);
+ list2.add(new String("3"));
+ variablesAndValues.put("list2", list2);
+ assertTrue(Framework.executeTest("=NTH(${list2}, 4)", variablesAndValues, "3"));
+ assertTrue(Framework.executeTest("=NTH(FLIST(2,3.4,5,7), 2)", Double.valueOf(3.4)));
+ assertTrue(Framework.executeTestExpectFailure("=NTH(${list2}, 5)"));
+ assertTrue(Framework.executeTestExpectFailure("=NTH(${list2}, 0)"));
+ }
+}
diff --git a/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/OrTest.java b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/OrTest.java
new file mode 100644
index 0000000..82f486a
--- /dev/null
+++ b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/OrTest.java
@@ -0,0 +1,58 @@
+/*
+ File: OrTest.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import junit.framework.*;
+
+
+public class OrTest extends TestCase {
+ public void testAll() throws Exception {
+ final List<Object> list = new ArrayList<Object>();
+ list.add("false");
+ list.add(Long.valueOf(0L));
+ list.add(Double.valueOf(1.3));
+
+ final Map<String, Object> variablesAndValues = new HashMap<String, Object>();
+ variablesAndValues.put("LIST", list);
+
+ assertTrue(Framework.executeTest("=OR($LIST,\"false\",FALSE)", variablesAndValues, Boolean.valueOf(true)));
+ assertTrue(Framework.executeTest("=OR()", Boolean.valueOf(false)));
+ assertTrue(Framework.executeTest("=OR(TRUE)", variablesAndValues, Boolean.valueOf(true)));
+ assertTrue(Framework.executeTest("=OR(FALSE)", variablesAndValues, Boolean.valueOf(false)));
+ assertTrue(Framework.executeTest("=OR(FALSE,FALSE)", variablesAndValues, Boolean.valueOf(false)));
+ assertTrue(Framework.executeTest("=OR(FALSE,TRUE)", variablesAndValues, Boolean.valueOf(true)));
+ }
+}
diff --git a/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/PermutTest.java b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/PermutTest.java
new file mode 100644
index 0000000..7df5aa1
--- /dev/null
+++ b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/PermutTest.java
@@ -0,0 +1,46 @@
+/*
+ File: PermutTest.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import junit.framework.*;
+
+
+public class PermutTest extends TestCase {
+ public void testAll() throws Exception {
+ assertTrue(Framework.executeTest("=PERMUT(6,3)", Long.valueOf(120L)));
+ assertTrue(Framework.executeTest("=PERMUT(100,3)", Long.valueOf(970200L)));
+ assertTrue(Framework.executeTestExpectFailure("=PERMUT(\"XYZ\")"));
+ assertTrue(Framework.executeTestExpectFailure("=PERMUT(-1,2)"));
+ assertTrue(Framework.executeTestExpectFailure("=PERMUT(2,-1)"));
+ assertTrue(Framework.executeTestExpectFailure("=PERMUT(2,3)"));
+ assertTrue(Framework.executeTestExpectFailure("=PERMUT(0,0)"));
+ }
+}
diff --git a/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/ProductTest.java b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/ProductTest.java
new file mode 100644
index 0000000..d21521b
--- /dev/null
+++ b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/ProductTest.java
@@ -0,0 +1,54 @@
+/*
+ File: ProductTest.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import junit.framework.*;
+
+
+public class ProductTest extends TestCase {
+ public void testAll() throws Exception {
+ final List<Object> list = new ArrayList<Object>();
+ list.add("14");
+ list.add(Long.valueOf(3L));
+ list.add(Double.valueOf(1.3));
+
+ final Map<String, Object> variablesAndValues = new HashMap<String, Object>();
+ variablesAndValues.put("LIST", list);
+
+ assertTrue(Framework.executeTest("=PRODUCT($LIST,\"5\",2.2)", variablesAndValues, Double.valueOf(600.6)));
+ assertTrue(Framework.executeTest("=PRODUCT()", Double.valueOf(1.0)));
+ }
+}
diff --git a/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/RadiansTest.java b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/RadiansTest.java
new file mode 100644
index 0000000..13be385
--- /dev/null
+++ b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/RadiansTest.java
@@ -0,0 +1,41 @@
+/*
+ File: RadiansTest.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import junit.framework.*;
+
+
+public class RadiansTest extends TestCase {
+ public void testAll() throws Exception {
+ assertTrue(Framework.executeTest("=RADIANS(180)", Double.valueOf(Math.PI)));
+ assertTrue(Framework.executeTestExpectFailure("=RADIANS(\"abc\")"));
+ }
+}
diff --git a/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/RightTest.java b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/RightTest.java
new file mode 100644
index 0000000..6b1d1f2
--- /dev/null
+++ b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/RightTest.java
@@ -0,0 +1,43 @@
+/*
+ File: RightTest.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import junit.framework.*;
+
+
+public class RightTest extends TestCase {
+ public void testAll() throws Exception {
+ assertTrue(Framework.executeTest("=RIGHT(\"Circus\", 3)", "cus"));
+ assertTrue(Framework.executeTest("=RIGHT(\"aureus\",6000)", "aureus"));
+ assertTrue(Framework.executeTest("=RIGHT(\"FredBobBillJoeBobHansKarl\")", "l"));
+ assertTrue(Framework.executeTest("=RIGHT(\"\")", ""));
+ }
+}
diff --git a/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/RoundTest.java b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/RoundTest.java
new file mode 100644
index 0000000..26d31ff
--- /dev/null
+++ b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/RoundTest.java
@@ -0,0 +1,43 @@
+/*
+ File: RoundTest.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import junit.framework.*;
+
+
+public class RoundTest extends TestCase {
+ public void testAll() throws Exception {
+ assertTrue(Framework.executeTest("=ROUND(2.15, 1)", Double.valueOf(2.2)));
+ assertTrue(Framework.executeTest("=ROUND(2.149,1)", Double.valueOf(2.1)));
+ assertTrue(Framework.executeTest("=ROUND(-1.475,2)", Double.valueOf(-1.48)));
+ assertTrue(Framework.executeTest("=ROUND(21.5, -1)", Double.valueOf(20.0)));
+ }
+}
diff --git a/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/SListTest.java b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/SListTest.java
new file mode 100644
index 0000000..f8dfbbc
--- /dev/null
+++ b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/SListTest.java
@@ -0,0 +1,64 @@
+/*
+ File: SListTest.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import junit.framework.*;
+
+
+public class SListTest extends TestCase {
+ public void testAll() throws Exception {
+ final List<Object> numbers = new ArrayList<Object>();
+ numbers.add(Double.valueOf(1.0));
+ numbers.add(Integer.valueOf(2));
+ numbers.add(Double.valueOf(3.0));
+ numbers.add("4.01");
+ numbers.add(Double.valueOf(5.0));
+ final Map<String, Object> variablesAndValues = new HashMap<String, Object>();
+ variablesAndValues.put("numbers", numbers);
+ final List<String> expectedResult = new ArrayList<String>();
+ expectedResult.add("1");
+ expectedResult.add("2");
+ expectedResult.add("3");
+ expectedResult.add("4.01");
+ expectedResult.add("5");
+ expectedResult.add("6");
+ expectedResult.add("7");
+ assertTrue(Framework.executeTest("=SLIST($numbers, 6, 7)", variablesAndValues, expectedResult));
+
+ final List<String> emptyList = new ArrayList<String>();
+ assertTrue(Framework.executeTest("=SLIST()", emptyList));
+ }
+}
diff --git a/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/SignTest.java b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/SignTest.java
new file mode 100644
index 0000000..b133fbc
--- /dev/null
+++ b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/SignTest.java
@@ -0,0 +1,58 @@
+/*
+ File: SignTest.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import java.util.HashMap;
+import java.util.Map;
+
+import junit.framework.*;
+
+
+public class SignTest extends TestCase {
+ public void testAll() throws Exception {
+ final Map<String, Object> variablesAndValues = new HashMap<String, Object>();
+ variablesAndValues.put("POS", Long.valueOf(+11));
+ variablesAndValues.put("NEG", Long.valueOf(-12));
+ variablesAndValues.put("ZERO", Long.valueOf(0));
+ assertTrue(Framework.executeTest("=SIGN(0.0)", Double.valueOf(0)));
+ assertTrue(Framework.executeTest("=SIGN(9)", Double.valueOf(1)));
+ assertTrue(Framework.executeTest("=SIGN(-1e22)", Double.valueOf(-1)));
+ assertTrue(Framework.executeTest("=SIGN($POS)", variablesAndValues, Double.valueOf(+1)));
+ assertTrue(Framework.executeTest("=SIGN($NEG)", variablesAndValues, Double.valueOf(-1)));
+ assertTrue(Framework.executeTest("=SIGN($ZERO)", variablesAndValues, Double.valueOf(0)));
+ assertTrue(Framework.executeTest("=SIGN(true)", Double.valueOf(1)));
+ assertTrue(Framework.executeTest("=SIGN(false)", Double.valueOf(0)));
+ assertTrue(Framework.executeTest("=SIGN(\"1e22\")", Double.valueOf(1)));
+ assertTrue(Framework.executeTest("=SIGN(\"-9.0\")", Double.valueOf(-1)));
+ assertTrue(Framework.executeTest("=SIGN(\"0.0\")", Double.valueOf(0)));
+ assertTrue(Framework.executeTestExpectFailure("=SIGN(\"Fred\")"));
+ }
+}
diff --git a/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/SinTest.java b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/SinTest.java
new file mode 100644
index 0000000..28941c6
--- /dev/null
+++ b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/SinTest.java
@@ -0,0 +1,44 @@
+/*
+ File: SinTest.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import junit.framework.*;
+
+
+public class SinTest extends TestCase {
+ public void testAll() throws Exception {
+ assertTrue(Framework.executeTest("=SIN("+Math.PI+"/6)", Double.valueOf(0.49999999999999994)));
+ assertTrue(Framework.executeTest("=SIN(RADIANS(60))", Double.valueOf(0.8660254037844386)));
+ assertTrue(Framework.executeTest("=SIN(RADIANS(-30))", Double.valueOf(-0.49999999999999994)));
+ assertTrue(Framework.executeTest("=SIN(\"0.0\")", Double.valueOf(0)));
+ assertTrue(Framework.executeTestExpectFailure("=SIN(\"abc\")"));
+ }
+}
diff --git a/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/SinhTest.java b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/SinhTest.java
new file mode 100644
index 0000000..62f8e0b
--- /dev/null
+++ b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/SinhTest.java
@@ -0,0 +1,41 @@
+/*
+ File: SinhTest.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import junit.framework.*;
+
+
+public class SinhTest extends TestCase {
+ public void testAll() throws Exception {
+ assertTrue(Framework.executeTest("=SINH(1)", Double.valueOf(1.1752011936438014)));
+ assertTrue(Framework.executeTest("=SINH(-1)", Double.valueOf(-1.1752011936438014)));
+ }
+}
diff --git a/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/SqrtTest.java b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/SqrtTest.java
new file mode 100644
index 0000000..0588284
--- /dev/null
+++ b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/SqrtTest.java
@@ -0,0 +1,42 @@
+/*
+ File: SqrtTest.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import junit.framework.*;
+
+
+public class SqrtTest extends TestCase {
+ public void testAll() throws Exception {
+ assertTrue(Framework.executeTest("=SQRT(0.0)", Double.valueOf(0)));
+ assertTrue(Framework.executeTest("=SQRT(9.0)", Double.valueOf(3)));
+ assertTrue(Framework.executeTestExpectFailure("=SQRT(-9.0)"));
+ }
+}
diff --git a/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/StDevTest.java b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/StDevTest.java
new file mode 100644
index 0000000..4456431
--- /dev/null
+++ b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/StDevTest.java
@@ -0,0 +1,57 @@
+/*
+ File: StDevTest.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import junit.framework.*;
+
+
+public class StDevTest extends TestCase {
+ public void testAll() throws Exception {
+ final List<Object> numbers = new ArrayList<Object>();
+ numbers.add(new Double(5.0));
+ numbers.add(new Long(3L));
+ numbers.add(new Double(4.0));
+ numbers.add(new Double(4.0));
+ numbers.add(new Long(3L));
+ numbers.add(new Long(4L));
+ numbers.add(new Long(5L));
+ final Map<String, Object> variablesAndValues = new HashMap<String, Object>();
+ variablesAndValues.put("list", numbers);
+ assertTrue(Framework.executeTest("=STDEV($list)", variablesAndValues, Double.valueOf(0.816496580927726)));
+ assertTrue(Framework.executeTest("=STDEV(-3.0,-3,\"-3.0\")", Double.valueOf(0.0)));
+ assertTrue(Framework.executeTestExpectFailure("=STDEV()"));
+ }
+}
diff --git a/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/SubstituteTest.java b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/SubstituteTest.java
new file mode 100644
index 0000000..b90c904
--- /dev/null
+++ b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/SubstituteTest.java
@@ -0,0 +1,48 @@
+/*
+ File: SubstituteTest.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import junit.framework.*;
+
+
+public class SubstituteTest extends TestCase {
+ public void testAll() throws Exception {
+ assertTrue(Framework.executeTest("=SUBSTITUTE(\"ABABBAABAB\", \"A\", \"X\")", "XBXBBXXBXB"));
+ assertTrue(Framework.executeTest("=SUBSTITUTE(\"FredBobBillJoeBobHansKarl\", \"Bob\", \"Julie\", 2.4)",
+ "FredBobBillJoeJulieHansKarl"));
+ assertTrue(Framework.executeTest("=SUBSTITUTE(\"FredBobBillJoeBobHansKarl\", \"Bob\", \"Julie\", 3)",
+ "FredBobBillJoeBobHansKarl"));
+ assertTrue(Framework.executeTest("=SUBSTITUTE(\"FredBobBillJoeBobHansKarl\", \"Bob2\", \"Julie\")",
+ "FredBobBillJoeBobHansKarl"));
+ assertTrue(Framework.executeTest("=SUBSTITUTE(\"1toTRUEto1\", TRUE, 5)", "1to5to1"));
+ assertTrue(Framework.executeTest("=SUBSTITUTE(\"BCBCCBAA\", \"X\", \"Y\")", "BCBCCBAA"));
+ }
+}
diff --git a/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/SumTest.java b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/SumTest.java
new file mode 100644
index 0000000..9130ef7
--- /dev/null
+++ b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/SumTest.java
@@ -0,0 +1,58 @@
+/*
+ File: SumTest.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import junit.framework.*;
+
+
+public class SumTest extends TestCase {
+ public void testAll() throws Exception {
+ final List<Object> list = new ArrayList<Object>();
+ list.add("14");
+ list.add(Long.valueOf(3L));
+ list.add(Double.valueOf(1.3));
+
+ final Map<String, Object> variablesAndValues = new HashMap<String, Object>();
+ variablesAndValues.put("LIST", list);
+
+ assertTrue(Framework.executeTest("=SUM($LIST,\"5\",2.2)", variablesAndValues, Double.valueOf(25.5)));
+ assertTrue(Framework.executeTest("=SUM()", Double.valueOf(0.0)));
+
+ final List<Object> emptyList = new ArrayList<Object>();
+ variablesAndValues.put("EMPTY_LIST", emptyList);
+ assertTrue(Framework.executeTest("=SUM($EMPTY_LIST,0.0)", variablesAndValues, Double.valueOf(0.0)));
+ }
+}
diff --git a/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/TanTest.java b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/TanTest.java
new file mode 100644
index 0000000..f6bdc28
--- /dev/null
+++ b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/TanTest.java
@@ -0,0 +1,41 @@
+/*
+ File: TanTest.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import junit.framework.*;
+
+
+public class TanTest extends TestCase {
+ public void testAll() throws Exception {
+ assertTrue(Framework.executeTest("=TAN(1.047197551)", Double.valueOf(1.7320508067824862)));
+ assertTrue(Framework.executeTest("=TAN(" + (Math.PI / 2.0) + ")", Double.valueOf(1.633123935319537E16)));
+ }
+}
diff --git a/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/TanhTest.java b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/TanhTest.java
new file mode 100644
index 0000000..9439a4f
--- /dev/null
+++ b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/TanhTest.java
@@ -0,0 +1,42 @@
+/*
+ File: TanhTest.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import junit.framework.*;
+
+
+public class TanhTest extends TestCase {
+ public void testAll() throws Exception {
+ assertTrue(Framework.executeTest("=TANH(-2)", new Double( -0.964027580075817)));
+ assertTrue(Framework.executeTest("=TANH(0)", new Double(0.0)));
+ assertTrue(Framework.executeTest("=TANH(0.5)", new Double(0.4621171572600098)));
+ }
+}
diff --git a/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/TextTest.java b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/TextTest.java
new file mode 100644
index 0000000..7e9f937
--- /dev/null
+++ b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/TextTest.java
@@ -0,0 +1,55 @@
+/*
+ File: TextTest.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import java.util.HashMap;
+import java.util.Map;
+
+import junit.framework.*;
+
+
+public class TextTest extends TestCase {
+ public void testSingleArgInvocation() throws Exception {
+ final Map<String, Object> variablesAndValues = new HashMap<String, Object>();
+ variablesAndValues.put("nan", Double.NaN);
+
+ assertTrue(Framework.executeTest("=TEXT($nan)", variablesAndValues, "NaN"));
+ assertTrue(Framework.executeTest("=TEXT(1)", "1.0"));
+ assertTrue(Framework.executeTest("=TEXT(-1)", "-1.0"));
+ assertTrue(Framework.executeTest("=TEXT(.1)", "0.1"));
+ }
+
+ public void testDualArgInvocation() throws Exception {
+ assertTrue(Framework.executeTest("=TEXT(0.1501,\".0###\")", ".1501"));
+ assertTrue(Framework.executeTest("=TEXT(0.1500,\".0\")", ".2"));
+ assertTrue(Framework.executeTest("=TEXT(0.1500,\".0###\")", ".15"));
+ }
+}
diff --git a/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/TodayTest.java b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/TodayTest.java
new file mode 100644
index 0000000..455541f
--- /dev/null
+++ b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/TodayTest.java
@@ -0,0 +1,47 @@
+/*
+ File: TodayTest.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import java.text.DateFormat;
+import java.util.Calendar;
+
+import junit.framework.*;
+
+
+public class TodayTest extends TestCase {
+ public void testAll() throws Exception {
+ final Calendar calendar = Calendar.getInstance();
+ final DateFormat dateFormat = DateFormat.getDateInstance(DateFormat.SHORT);
+ final String today = dateFormat.format(calendar.getTime());
+
+ assertTrue(Framework.executeTest("=TODAY()", today));
+ }
+}
diff --git a/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/TruncTest.java b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/TruncTest.java
new file mode 100644
index 0000000..0c93a54
--- /dev/null
+++ b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/TruncTest.java
@@ -0,0 +1,43 @@
+/*
+ File: TruncTest.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import junit.framework.*;
+
+
+public class TruncTest extends TestCase {
+ public void testAll() throws Exception {
+ assertTrue(Framework.executeTest("=TRUNC(8.9)", Double.valueOf(8.0)));
+ assertTrue(Framework.executeTest("=TRUNC(-8.9)", Double.valueOf(-8.0)));
+ assertTrue(Framework.executeTest("=TRUNC(PI())", Double.valueOf(3.0)));
+ assertTrue(Framework.executeTest("=TRUNC(-1.475,2)", Double.valueOf(-1.47)));
+ }
+}
diff --git a/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/UpperTest.java b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/UpperTest.java
new file mode 100644
index 0000000..a7fbfa8
--- /dev/null
+++ b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/UpperTest.java
@@ -0,0 +1,43 @@
+/*
+ File: UpperTest.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import junit.framework.*;
+
+
+public class UpperTest extends TestCase {
+ public void testAll() throws Exception {
+ assertTrue(Framework.executeTest("=UPPER(\"\")", ""));
+ assertTrue(Framework.executeTest("=UPPER(\"lower\")", "LOWER"));
+ assertTrue(Framework.executeTest("=UPPER(\"UPPER\")", "UPPER"));
+ assertTrue(Framework.executeTest("=UPPER(\"MiXeD\")", "MIXED"));
+ }
+}
diff --git a/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/ValueTest.java b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/ValueTest.java
new file mode 100644
index 0000000..887ecca
--- /dev/null
+++ b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/ValueTest.java
@@ -0,0 +1,46 @@
+/*
+ File: ValueTest.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import junit.framework.*;
+
+
+public class ValueTest extends TestCase {
+ public void testAll() throws Exception {
+ assertTrue(Framework.executeTest("=VALUE(-1.3)", Double.valueOf(-1.3)));
+ assertTrue(Framework.executeTest("=VALUE(50000)", Double.valueOf(50000)));
+ assertTrue(Framework.executeTest("=VALUE(+1.3)", Double.valueOf(+1.3)));
+ assertTrue(Framework.executeTest("=VALUE(-3)", Double.valueOf(-3.0)));
+ assertTrue(Framework.executeTestExpectFailure("=VALUE(\"XYZ\")"));
+ assertTrue(Framework.executeTest("=VALUE(\"50\")", Double.valueOf(50)));
+ assertTrue(Framework.executeTest("=VALUE(\"-8.9e99\")", Double.valueOf(-8.9e99)));
+ }
+}
diff --git a/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/VarTest.java b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/VarTest.java
new file mode 100644
index 0000000..a1de1a1
--- /dev/null
+++ b/corelibs/equations/src/test/java/org/cytoscape/equations/builtins/VarTest.java
@@ -0,0 +1,57 @@
+/*
+ File: VarTest.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.builtins;
+
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import junit.framework.*;
+
+
+public class VarTest extends TestCase {
+ public void testAll() throws Exception {
+ final List<Object> numbers = new ArrayList<Object>();
+ numbers.add(new Double(5.0));
+ numbers.add(new Long(3L));
+ numbers.add(new Double(4.0));
+ numbers.add(new Double(4.0));
+ numbers.add(new Long(3L));
+ numbers.add(new Long(4L));
+ numbers.add(new Long(5L));
+ final Map<String, Object> variablesAndValues = new HashMap<String, Object>();
+ variablesAndValues.put("list", numbers);
+ assertTrue(Framework.executeTest("=VAR($list)", variablesAndValues, Double.valueOf(0.6666666666666666)));
+ assertTrue(Framework.executeTest("=VAR(-3.0,-3,\"-3.0\")", Double.valueOf(0.0)));
+ assertTrue(Framework.executeTestExpectFailure("=VAR()"));
+ }
+}
diff --git a/corelibs/equations/src/test/java/org/cytoscape/equations/interpreter/InterpreterTest.java b/corelibs/equations/src/test/java/org/cytoscape/equations/interpreter/InterpreterTest.java
new file mode 100644
index 0000000..8c4c282
--- /dev/null
+++ b/corelibs/equations/src/test/java/org/cytoscape/equations/interpreter/InterpreterTest.java
@@ -0,0 +1,253 @@
+/*
+ File: InterpreterTest.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.equations.interpreter;
+
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import junit.framework.*;
+import org.cytoscape.equations.EqnCompiler;
+import org.cytoscape.equations.EqnParser;
+import org.cytoscape.equations.Function;
+import org.cytoscape.equations.Parser;
+
+
+public class InterpreterTest extends TestCase {
+ static private class BadReturnFunction implements Function {
+ public String getName() { return "BAD"; }
+ public String getFunctionSummary() { return "Returns an invalid type at runtime."; }
+ public String getUsageDescription() { return "Call this with \"BAD()\"."; }
+ public Class getReturnType() { return Double.class; }
+ public Class validateArgTypes(final Class[] argTypes) { return argTypes.length == 0 ? Double.class : null; }
+ public Object evaluateFunction(final Object[] args) { return new Integer(1); }
+ public List<Class> getPossibleArgTypes(final Class[] leadingArgs) { return null; }
+ }
+
+ private final EqnCompiler compiler = new EqnCompiler();
+
+ public void testSimpleStringConcatExpr() throws Exception {
+ final Map<String, Class> attribNameToTypeMap = new HashMap<String, Class>();
+ attribNameToTypeMap.put("s1", String.class);
+ assertTrue(compiler.compile("=\"Fred\"&${s1}", attribNameToTypeMap));
+ final Map<String, IdentDescriptor> nameToDescriptorMap = new HashMap<String, IdentDescriptor>();
+ nameToDescriptorMap.put("s1", new IdentDescriptor("Bob"));
+ final Interpreter interpreter = new Interpreter(compiler.getEquation(), nameToDescriptorMap);
+ assertEquals("FredBob", interpreter.run());
+ }
+
+ public void testSimpleExpr() throws Exception {
+ final Map<String, Class> attribNameToTypeMap = new HashMap<String, Class>();
+ attribNameToTypeMap.put("BOB", Double.class);
+ assertTrue(compiler.compile("=42 - 12 + 3 * (4 - 2) + ${BOB:12}", attribNameToTypeMap));
+ final Map<String, IdentDescriptor> nameToDescriptorMap = new HashMap<String, IdentDescriptor>();
+ nameToDescriptorMap.put("BOB", new IdentDescriptor(-10.0));
+ final Interpreter interpreter = new Interpreter(compiler.getEquation(), nameToDescriptorMap);
+ assertEquals(new Double(26.0), interpreter.run());
+ }
+
+ public void testUnaryPlusAndMinus() throws Exception {
+ final Map<String, Class> attribNameToTypeMap = new HashMap<String, Class>();
+ attribNameToTypeMap.put("attr1", Double.class);
+ attribNameToTypeMap.put("attr2", Double.class);
+ assertTrue(compiler.compile("=-17.8E-14", attribNameToTypeMap));
+ assertTrue(compiler.compile("=+(${attr1} + ${attr2})", attribNameToTypeMap));
+ final Map<String, IdentDescriptor> nameToDescriptorMap = new HashMap<String, IdentDescriptor>();
+ nameToDescriptorMap.put("attr1", new IdentDescriptor(5.5));
+ nameToDescriptorMap.put("attr2", new IdentDescriptor(6.5));
+ final Interpreter interpreter = new Interpreter(compiler.getEquation(), nameToDescriptorMap);
+ assertEquals(new Double(12.0), interpreter.run());
+ }
+
+ public void testFunctionCall() throws Exception {
+ final Map<String, Class> attribNameToTypeMap = new HashMap<String, Class>();
+ assertTrue(compiler.compile("=42 + log(4 - 2)", attribNameToTypeMap));
+ final Map<String, IdentDescriptor> nameToDescriptorMap = new HashMap<String, IdentDescriptor>();
+ final Interpreter interpreter = new Interpreter(compiler.getEquation(), nameToDescriptorMap);
+ assertEquals(new Double(42.0 + Math.log10(4.0 - 2.0)), interpreter.run());
+ }
+
+ public void testExponentiation() throws Exception {
+ final Map<String, Class> attribNameToTypeMap = new HashMap<String, Class>();
+ assertTrue(compiler.compile("=2^3^4 - 0.0002", attribNameToTypeMap));
+ final Map<String, IdentDescriptor> nameToDescriptorMap = new HashMap<String, IdentDescriptor>();
+ final Interpreter interpreter = new Interpreter(compiler.getEquation(), nameToDescriptorMap);
+ assertEquals(new Double(Math.pow(2.0, Math.pow(3.0, 4.0)) - 0.0002), interpreter.run());
+ }
+
+ public void testComparisons() throws Exception {
+ final Map<String, Class> attribNameToTypeMap = new HashMap<String, Class>();
+ attribNameToTypeMap.put("x", Double.class);
+ attribNameToTypeMap.put("y", Double.class);
+ attribNameToTypeMap.put("limit", Double.class);
+ assertTrue(compiler.compile("=${x} <= ${y}", attribNameToTypeMap));
+ final Map<String, IdentDescriptor> nameToDescriptorMap = new HashMap<String, IdentDescriptor>();
+ nameToDescriptorMap.put("x", new IdentDescriptor(1.2));
+ nameToDescriptorMap.put("y", new IdentDescriptor(-3.8e-12));
+ nameToDescriptorMap.put("limit", new IdentDescriptor(-65.23e12));
+ final Interpreter interpreter1 = new Interpreter(compiler.getEquation(), nameToDescriptorMap);
+ assertEquals(new Boolean(false), interpreter1.run());
+
+ assertTrue(compiler.compile("=-15.4^3 > ${limit}", attribNameToTypeMap));
+ final Interpreter interpreter2 = new Interpreter(compiler.getEquation(), nameToDescriptorMap);
+ assertEquals(new Boolean(true), interpreter2.run());
+ }
+
+ public void testVarargs() throws Exception {
+ final Map<String, Class> attribNameToTypeMap = new HashMap<String, Class>();
+ assertFalse(compiler.compile("=LOG()", attribNameToTypeMap));
+ assertTrue(compiler.compile("=LOG(1)", attribNameToTypeMap));
+ assertTrue(compiler.compile("=LOG(1,2)", attribNameToTypeMap));
+ final Map<String, IdentDescriptor> nameToDescriptorMap = new HashMap<String, IdentDescriptor>();
+ final Interpreter interpreter = new Interpreter(compiler.getEquation(), nameToDescriptorMap);
+ assertEquals(new Double(Math.log(1.0)/Math.log(2.0)), interpreter.run());
+ assertFalse(compiler.compile("=LOG(1,2,3)", attribNameToTypeMap));
+ }
+
+ public void testFixedArgs() throws Exception {
+ final Map<String, Class> attribNameToTypeMap = new HashMap<String, Class>();
+ assertFalse(compiler.compile("=ABS()", attribNameToTypeMap));
+ assertTrue(compiler.compile("=ABS(-1.5e10)", attribNameToTypeMap));
+ final Map<String, IdentDescriptor> nameToDescriptorMap = new HashMap<String, IdentDescriptor>();
+ final Interpreter interpreter = new Interpreter(compiler.getEquation(), nameToDescriptorMap);
+ assertEquals(new Double(1.5e10), interpreter.run());
+ assertFalse(compiler.compile("=ABS(1,2)", attribNameToTypeMap));
+ }
+
+ public void testDEFINED() throws Exception {
+ final Map<String, Class> attribNameToTypeMap = new HashMap<String, Class>();
+ attribNameToTypeMap.put("x", Double.class);
+ assertTrue(compiler.compile("=defined(x)", attribNameToTypeMap));
+ final Map<String, IdentDescriptor> nameToDescriptorMap = new HashMap<String, IdentDescriptor>();
+ nameToDescriptorMap.put("x", new IdentDescriptor(1.2));
+ final Interpreter interpreter1 = new Interpreter(compiler.getEquation(), nameToDescriptorMap);
+ assertEquals(new Boolean(true), interpreter1.run());
+
+ assertTrue(compiler.compile("=DEFINED(${limit})", attribNameToTypeMap));
+ final Interpreter interpreter2 = new Interpreter(compiler.getEquation(), nameToDescriptorMap);
+ assertEquals(new Boolean(false), interpreter2.run());
+ }
+
+ public void testIntegerToFloatingPointConversion() throws Exception {
+ final Map<String, Class> attribNameToTypeMap = new HashMap<String, Class>();
+ attribNameToTypeMap.put("BOB", Long.class);
+
+ final Map<String, IdentDescriptor> nameToDescriptorMap = new HashMap<String, IdentDescriptor>();
+ nameToDescriptorMap.put("BOB", new IdentDescriptor(new Long(3)));
+
+ assertTrue(compiler.compile("=$BOB > 5.3", attribNameToTypeMap));
+ final Interpreter interpreter1 = new Interpreter(compiler.getEquation(), nameToDescriptorMap);
+ assertEquals(new Boolean(false), interpreter1.run());
+
+ assertTrue(compiler.compile("=$BOB <= 5.3", attribNameToTypeMap));
+ final Interpreter interpreter2 = new Interpreter(compiler.getEquation(), nameToDescriptorMap);
+ assertEquals(new Boolean(true), interpreter2.run());
+ }
+
+ public void testMixedModeArithmetic() throws Exception {
+ final Map<String, Class> attribNameToTypeMap = new HashMap<String, Class>();
+ attribNameToTypeMap.put("x", Long.class);
+
+ final Map<String, IdentDescriptor> nameToDescriptorMap = new HashMap<String, IdentDescriptor>();
+ nameToDescriptorMap.put("x", new IdentDescriptor(new Long(3)));
+
+ assertTrue(compiler.compile("=$x + 2.0", attribNameToTypeMap));
+ final Interpreter interpreter1 = new Interpreter(compiler.getEquation(), nameToDescriptorMap);
+ assertEquals(new Double(5.0), interpreter1.run());
+
+ assertTrue(compiler.compile("=TRUE + TRUE", attribNameToTypeMap));
+ final Interpreter interpreter2 = new Interpreter(compiler.getEquation(), nameToDescriptorMap);
+ assertEquals(new Double(2.0), interpreter2.run());
+ }
+
+ public void testFunctionWithBadRuntimeReturnType() throws Exception {
+ final EqnParser eqnParser = Parser.getParser();
+ final Function badReturnFunction = new BadReturnFunction();
+ if (eqnParser.getFunction(badReturnFunction.getName()) == null) // Avoid duplicate registration!
+ eqnParser.registerFunction(badReturnFunction);
+
+ final Map<String, Class> attribNameToTypeMap = new HashMap<String, Class>();
+ assertTrue(compiler.compile("=BAD()", attribNameToTypeMap));
+
+ final Map<String, IdentDescriptor> nameToDescriptorMap = new HashMap<String, IdentDescriptor>();
+ final Interpreter interpreter = new Interpreter(compiler.getEquation(), nameToDescriptorMap);
+ try {
+ interpreter.run();
+ } catch (final IllegalStateException e) {
+ // If we get here, everything is as expected and we let the test pass!
+ }
+ }
+
+ public void testComparisonsWithBooleans() throws Exception {
+ final Map<String, Class> attribNameToTypeMap = new HashMap<String, Class>();
+ final Map<String, IdentDescriptor> nameToDescriptorMap = new HashMap<String, IdentDescriptor>();
+
+ assertTrue(compiler.compile("=TRUE < FALSE", attribNameToTypeMap));
+ final Interpreter interpreter1 = new Interpreter(compiler.getEquation(), nameToDescriptorMap);
+ assertEquals(new Boolean(false), interpreter1.run());
+
+ assertTrue(compiler.compile("=FALSE < TRUE", attribNameToTypeMap));
+ final Interpreter interpreter2 = new Interpreter(compiler.getEquation(), nameToDescriptorMap);
+ assertEquals(new Boolean(true), interpreter2.run());
+
+ assertTrue(compiler.compile("=\"a\" < TRUE", attribNameToTypeMap));
+ final Interpreter interpreter3 = new Interpreter(compiler.getEquation(), nameToDescriptorMap);
+ assertEquals(new Boolean(true), interpreter3.run());
+
+ assertTrue(compiler.compile("=\"ZYX\" < FALSE", attribNameToTypeMap));
+ final Interpreter interpreter4 = new Interpreter(compiler.getEquation(), nameToDescriptorMap);
+ assertEquals(new Boolean(true), interpreter4.run());
+
+ assertTrue(compiler.compile("=\"a\" > TRUE", attribNameToTypeMap));
+ final Interpreter interpreter5 = new Interpreter(compiler.getEquation(), nameToDescriptorMap);
+ assertEquals(new Boolean(false), interpreter5.run());
+
+ assertTrue(compiler.compile("=\"ZYX\" > FALSE", attribNameToTypeMap));
+ final Interpreter interpreter6 = new Interpreter(compiler.getEquation(), nameToDescriptorMap);
+ assertEquals(new Boolean(false), interpreter6.run());
+
+ assertTrue(compiler.compile("=TRUE < \"a\"", attribNameToTypeMap));
+ final Interpreter interpreter7 = new Interpreter(compiler.getEquation(), nameToDescriptorMap);
+ assertEquals(new Boolean(false), interpreter7.run());
+
+ assertTrue(compiler.compile("=FALSE < \"ZYX\"", attribNameToTypeMap));
+ final Interpreter interpreter8 = new Interpreter(compiler.getEquation(), nameToDescriptorMap);
+ assertEquals(new Boolean(false), interpreter8.run());
+
+ assertTrue(compiler.compile("=TRUE < 0", attribNameToTypeMap));
+ final Interpreter interpreter9 = new Interpreter(compiler.getEquation(), nameToDescriptorMap);
+ assertEquals(new Boolean(false), interpreter9.run());
+
+ assertTrue(compiler.compile("=FALSE < -1", attribNameToTypeMap));
+ final Interpreter interpreter10 = new Interpreter(compiler.getEquation(), nameToDescriptorMap);
+ assertEquals(new Boolean(false), interpreter10.run());
+ }
+}
diff --git a/corelibs/fing/pom.xml b/corelibs/fing/pom.xml
new file mode 100644
index 0000000..96ec0bc
--- /dev/null
+++ b/corelibs/fing/pom.xml
@@ -0,0 +1,64 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>parent</artifactId>
+ <version>2.8.4-SNAPSHOT</version>
+ </parent>
+
+ <artifactId>fing</artifactId>
+ <packaging>jar</packaging>
+
+ <name>fing</name>
+
+ <!-- bootstrap for cytoscape dependencies, namely the parent POM snapshots -->
+ <repositories>
+ <repository>
+ <id>cytoscape_snapshots</id>
+ <snapshots>
+ <enabled>true</enabled>
+ </snapshots>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <name>Cytoscape Snapshots</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/</url>
+ </repository>
+ <repository>
+ <id>cytoscape_releases</id>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ <name>Cytoscape Releases</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/releases/</url>
+ </repository>
+ </repositories>
+
+ <dependencies>
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>util-intr</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>graph-dynamic</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>graph-fixed</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>giny</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ </dependencies>
+
+</project>
+
diff --git a/corelibs/fing/src/main/java/fing/model/DEPENDENCIES b/corelibs/fing/src/main/java/fing/model/DEPENDENCIES
new file mode 100644
index 0000000..07303cd
--- /dev/null
+++ b/corelibs/fing/src/main/java/fing/model/DEPENDENCIES
@@ -0,0 +1,4 @@
+lib:cytoscape-graph-dynamic.jar
+lib:cytoscape-graph-fixed.jar
+lib:cytoscape-util-intr.jar
+lib:giny.jar
diff --git a/corelibs/fing/src/main/java/fing/model/EdgeArray.java b/corelibs/fing/src/main/java/fing/model/EdgeArray.java
new file mode 100644
index 0000000..4cd7296
--- /dev/null
+++ b/corelibs/fing/src/main/java/fing/model/EdgeArray.java
@@ -0,0 +1,93 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package fing.model;
+
+import giny.model.Edge;
+
+
+// Valid indices: [0, Integer.MAX_VALUE - 1].
+class EdgeArray {
+ private final static int INITIAL_CAPACITY = 0; // Must be non-negative.
+ private Edge[] m_edgeArr;
+
+ EdgeArray() {
+ m_edgeArr = new Edge[INITIAL_CAPACITY];
+ }
+
+ // Understand that this method will not increase the size of the underlying
+ // array, no matter what.
+ // Throws ArrayIndexOutOfBoundsException if index is negative or
+ // Integer.MAX_VALUE.
+ Edge getEdgeAtIndex(int index) {
+ // Do pre-checking because try/catch with thrown exception causes huge
+ // performance hit.
+ if ((index >= m_edgeArr.length) && (index != Integer.MAX_VALUE))
+ return null;
+
+ return m_edgeArr[index]; // Exception if Integer.MAX_VALUE or negative.
+ }
+
+ // Understand that this method will potentially increase the size of the
+ // underlying array, but only if two conditions hold:
+ // 1. edge is not null and
+ // 2. index is greater than or equal to the length of the array.
+ // Throws ArrayIndexOutOfBoundsException if index is negative or
+ // Integer.MAX_VALUE.
+ void setEdgeAtIndex(Edge edge, int index) {
+ // Do pre-checking because try/catch with thrown exception causes huge
+ // performance hit.
+ if ((index >= m_edgeArr.length) && (edge == null) && (index != Integer.MAX_VALUE))
+ return;
+
+ try {
+ m_edgeArr[index] = edge;
+ } catch (ArrayIndexOutOfBoundsException e) {
+ if ((index < 0) || (index == Integer.MAX_VALUE)) {
+ throw e;
+ }
+
+ final int newArrSize = (int) Math.min((long) Integer.MAX_VALUE,
+ Math.max((((long) m_edgeArr.length) * 2L) + 1L,
+ ((long) index) + 1L
+ + (long) INITIAL_CAPACITY));
+ Edge[] newArr = new Edge[newArrSize];
+ System.arraycopy(m_edgeArr, 0, newArr, 0, m_edgeArr.length);
+ m_edgeArr = newArr;
+ m_edgeArr[index] = edge;
+ }
+ }
+}
diff --git a/corelibs/fing/src/main/java/fing/model/EdgeDepository.java b/corelibs/fing/src/main/java/fing/model/EdgeDepository.java
new file mode 100644
index 0000000..3652a6c
--- /dev/null
+++ b/corelibs/fing/src/main/java/fing/model/EdgeDepository.java
@@ -0,0 +1,104 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package fing.model;
+
+import giny.model.Edge;
+import giny.model.RootGraph;
+
+
+final class EdgeDepository implements FingEdgeDepot {
+ private final static int INITIAL_CAPACITY = 11; // Must be non-negative.
+ private Edge[] m_edgeStack;
+ private int m_size;
+
+ EdgeDepository() {
+ m_edgeStack = new Edge[INITIAL_CAPACITY];
+ m_size = 0;
+ }
+
+ // Gimme an edge, darnit!
+ /**
+ * DOCUMENT ME!
+ *
+ * @param root DOCUMENT ME!
+ * @param index DOCUMENT ME!
+ * @param id DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Edge getEdge(RootGraph root, int index, String id) {
+ final FEdge returnThis;
+
+ if (m_size == 0)
+ returnThis = new FEdge();
+ else
+ returnThis = (FEdge) m_edgeStack[--m_size];
+
+ returnThis.m_rootGraph = root;
+ returnThis.m_rootGraphIndex = index;
+ returnThis.m_identifier = id;
+
+ return returnThis;
+ }
+
+ // Deinitialize the object's members yourself if you need or want to.
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edge DOCUMENT ME!
+ */
+ public void recycleEdge(Edge edge) {
+ if (edge == null)
+ return;
+
+ try {
+ m_edgeStack[m_size] = edge;
+ m_size++;
+ } catch (ArrayIndexOutOfBoundsException e) {
+ final int newArrSize = (int) Math.min((long) Integer.MAX_VALUE,
+ (((long) m_edgeStack.length) * 2L) + 1L);
+
+ if (newArrSize == m_edgeStack.length)
+ throw new IllegalStateException("unable to allocate large enough array");
+
+ Edge[] newArr = new Edge[newArrSize];
+ System.arraycopy(m_edgeStack, 0, newArr, 0, m_edgeStack.length);
+ m_edgeStack = newArr;
+ m_edgeStack[m_size++] = edge;
+ }
+ }
+}
diff --git a/corelibs/fing/src/main/java/fing/model/FEdge.java b/corelibs/fing/src/main/java/fing/model/FEdge.java
new file mode 100644
index 0000000..2a2e71d
--- /dev/null
+++ b/corelibs/fing/src/main/java/fing/model/FEdge.java
@@ -0,0 +1,121 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package fing.model;
+
+import giny.model.Edge;
+import giny.model.Node;
+import giny.model.RootGraph;
+
+
+// Package visible class.
+class FEdge implements Edge {
+ // Variables specific to public get/set methods.
+ RootGraph m_rootGraph = null;
+ int m_rootGraphIndex = 0;
+ String m_identifier = null;
+
+ // Package visible constructor.
+ FEdge() {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Node getSource() {
+ return m_rootGraph.getNode(m_rootGraph.getEdgeSourceIndex(m_rootGraphIndex));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Node getTarget() {
+ return m_rootGraph.getNode(m_rootGraph.getEdgeTargetIndex(m_rootGraphIndex));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isDirected() {
+ return m_rootGraph.isEdgeDirected(m_rootGraphIndex);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public RootGraph getRootGraph() {
+ return m_rootGraph;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getRootGraphIndex() {
+ return m_rootGraphIndex;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getIdentifier() {
+ return m_identifier;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param new_id DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean setIdentifier(String new_id) {
+ m_identifier = new_id;
+
+ return true;
+ }
+}
diff --git a/corelibs/fing/src/main/java/fing/model/FGraphPerspective.java b/corelibs/fing/src/main/java/fing/model/FGraphPerspective.java
new file mode 100644
index 0000000..c667ff4
--- /dev/null
+++ b/corelibs/fing/src/main/java/fing/model/FGraphPerspective.java
@@ -0,0 +1,2836 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package fing.model;
+
+import cytoscape.graph.dynamic.DynamicGraph;
+import cytoscape.graph.dynamic.util.DynamicGraphFactory;
+
+import cytoscape.graph.fixed.FixedGraph;
+
+import cytoscape.util.intr.IntArray;
+import cytoscape.util.intr.IntEnumerator;
+import cytoscape.util.intr.IntHash;
+import cytoscape.util.intr.IntIntHash;
+import cytoscape.util.intr.IntIterator;
+import cytoscape.util.intr.IntIterator;
+import cytoscape.util.intr.MinIntHeap;
+
+import giny.filter.Filter;
+
+import giny.model.Edge;
+import giny.model.GraphPerspective;
+import giny.model.GraphPerspectiveChangeListener;
+import giny.model.Node;
+import giny.model.RootGraph;
+import giny.model.RootGraphChangeEvent;
+import giny.model.RootGraphChangeListener;
+
+import java.util.Iterator;
+import java.util.NoSuchElementException;
+
+
+// Package visible class.
+class FGraphPerspective implements GraphPerspective, FixedGraph {
+ ///////////////////////////////////
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public IntEnumerator nodes() {
+ final IntEnumerator nativeNodes = m_graph.nodes();
+
+ return new IntEnumerator() {
+ public int numRemaining() {
+ return nativeNodes.numRemaining();
+ }
+
+ public int nextInt() {
+ return ~m_nativeToRootNodeInxMap.getIntAtIndex(nativeNodes.nextInt());
+ }
+ };
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public IntEnumerator edges() {
+ final IntEnumerator nativeEdges = m_graph.edges();
+
+ return new IntEnumerator() {
+ public int numRemaining() {
+ return nativeEdges.numRemaining();
+ }
+
+ public int nextInt() {
+ return ~m_nativeToRootEdgeInxMap.getIntAtIndex(nativeEdges.nextInt());
+ }
+ };
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean nodeExists(final int node) {
+ if (node < 0) {
+ return false;
+ }
+
+ final int nativeNodeInx = m_rootToNativeNodeInxMap.get(node);
+
+ return m_graph.nodeExists(nativeNodeInx);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edge DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public byte edgeType(final int edge) {
+ if (edge < 0) {
+ return -1;
+ }
+
+ final int nativeEdgeInx = m_rootToNativeEdgeInxMap.get(edge);
+
+ return m_graph.edgeType(nativeEdgeInx);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edge DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int edgeSource(final int edge) {
+ if (edge < 0) {
+ return -1;
+ }
+
+ final int nativeEdgeInx = m_rootToNativeEdgeInxMap.get(edge);
+ final int nativeSource = m_graph.edgeSource(nativeEdgeInx);
+
+ if (nativeSource < 0) {
+ return -1;
+ }
+
+ return ~m_nativeToRootNodeInxMap.getIntAtIndex(nativeSource);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edge DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int edgeTarget(final int edge) {
+ if (edge < 0) {
+ return -1;
+ }
+
+ final int nativeEdgeInx = m_rootToNativeEdgeInxMap.get(edge);
+ final int nativeTarget = m_graph.edgeTarget(nativeEdgeInx);
+
+ if (nativeTarget < 0) {
+ return -1;
+ }
+
+ return ~m_nativeToRootNodeInxMap.getIntAtIndex(nativeTarget);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ * @param outgoing DOCUMENT ME!
+ * @param incoming DOCUMENT ME!
+ * @param undirected DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public IntEnumerator edgesAdjacent(final int node, boolean outgoing, boolean incoming,
+ boolean undirected) {
+ if (node < 0) {
+ return null;
+ }
+
+ final int nativeNodeInx = m_rootToNativeNodeInxMap.get(node);
+ final IntEnumerator nativeEdges = m_graph.edgesAdjacent(nativeNodeInx, outgoing, incoming,
+ undirected);
+
+ if (nativeEdges == null) {
+ return null;
+ }
+
+ return new IntEnumerator() {
+ public int numRemaining() {
+ return nativeEdges.numRemaining();
+ }
+
+ public int nextInt() {
+ return ~m_nativeToRootEdgeInxMap.getIntAtIndex(nativeEdges.nextInt());
+ }
+ };
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node0 DOCUMENT ME!
+ * @param node1 DOCUMENT ME!
+ * @param outgoing DOCUMENT ME!
+ * @param incoming DOCUMENT ME!
+ * @param undirected DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public IntIterator edgesConnecting(final int node0, final int node1, boolean outgoing,
+ boolean incoming, boolean undirected) {
+ if ((node0 < 0) || (node1 < 0)) {
+ return null;
+ }
+
+ final int nativeNode0Inx = m_rootToNativeNodeInxMap.get(node0);
+ final int nativeNode1Inx = m_rootToNativeNodeInxMap.get(node1);
+ final IntIterator nativeEdges = m_graph.edgesConnecting(nativeNode0Inx, nativeNode1Inx,
+ outgoing, incoming, undirected);
+
+ if (nativeEdges == null) {
+ return null;
+ }
+
+ return new IntIterator() {
+ public boolean hasNext() {
+ return nativeEdges.hasNext();
+ }
+
+ public int nextInt() {
+ return ~m_nativeToRootEdgeInxMap.getIntAtIndex(nativeEdges.nextInt());
+ }
+ };
+ }
+
+ /////////////////////////////////
+ /**
+ * DOCUMENT ME!
+ *
+ * @param listener DOCUMENT ME!
+ */
+ public void addGraphPerspectiveChangeListener(GraphPerspectiveChangeListener listener) {
+ // This method is not thread safe; synchronize on an object to make it so.
+ m_lis[0] = GraphPerspectiveChangeListenerChain.add(m_lis[0], listener);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param listener DOCUMENT ME!
+ */
+ public void removeGraphPerspectiveChangeListener(GraphPerspectiveChangeListener listener) {
+ // This method is not thread safe; synchronize on an object to make it so.
+ m_lis[0] = GraphPerspectiveChangeListenerChain.remove(m_lis[0], listener);
+ }
+
+ // The object returned shares the same RootGraph with this object.
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object clone() {
+ final IntEnumerator nativeNodes = m_graph.nodes();
+ final IntIterator rootGraphNodeInx = new IntIterator() {
+ public boolean hasNext() {
+ return nativeNodes.numRemaining() > 0;
+ }
+
+ public int nextInt() {
+ return m_nativeToRootNodeInxMap.getIntAtIndex(nativeNodes.nextInt());
+ }
+ };
+
+ final IntEnumerator nativeEdges = m_graph.edges();
+ final IntIterator rootGraphEdgeInx = new IntIterator() {
+ public boolean hasNext() {
+ return nativeEdges.numRemaining() > 0;
+ }
+
+ public int nextInt() {
+ return m_nativeToRootEdgeInxMap.getIntAtIndex(nativeEdges.nextInt());
+ }
+ };
+
+ return new FGraphPerspective(m_root, rootGraphNodeInx, rootGraphEdgeInx);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public RootGraph getRootGraph() {
+ return m_root;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getNodeCount() {
+ return m_graph.nodes().numRemaining();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getEdgeCount() {
+ return m_graph.edges().numRemaining();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Iterator nodesIterator() {
+ final IntEnumerator nodes = m_graph.nodes();
+
+ return new Iterator() {
+ public void remove() {
+ throw new UnsupportedOperationException();
+ }
+
+ public boolean hasNext() {
+ return nodes.numRemaining() > 0;
+ }
+
+ public Object next() {
+ if (!hasNext()) {
+ throw new NoSuchElementException();
+ }
+
+ return m_root.getNode(m_nativeToRootNodeInxMap.getIntAtIndex(nodes.nextInt()));
+ }
+ };
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public java.util.List nodesList() {
+ final int nodeCount = getNodeCount();
+ final java.util.ArrayList returnThis = new java.util.ArrayList(nodeCount);
+ Iterator iter = nodesIterator();
+
+ for (int i = 0; i < nodeCount; i++)
+ returnThis.add(iter.next());
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] getNodeIndicesArray() {
+ IntEnumerator nodes = m_graph.nodes();
+ final int[] returnThis = new int[nodes.numRemaining()];
+
+ for (int i = 0; i < returnThis.length; i++)
+ returnThis[i] = m_nativeToRootNodeInxMap.getIntAtIndex(nodes.nextInt());
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Iterator edgesIterator() {
+ final IntEnumerator edges = m_graph.edges();
+
+ return new Iterator() {
+ public void remove() {
+ throw new UnsupportedOperationException();
+ }
+
+ public boolean hasNext() {
+ return edges.numRemaining() > 0;
+ }
+
+ public Object next() {
+ if (!hasNext()) {
+ throw new NoSuchElementException();
+ }
+
+ return m_root.getEdge(m_nativeToRootEdgeInxMap.getIntAtIndex(edges.nextInt()));
+ }
+ };
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public java.util.List edgesList() {
+ final int edgeCount = getEdgeCount();
+ final java.util.ArrayList returnThis = new java.util.ArrayList(edgeCount);
+ Iterator iter = edgesIterator();
+
+ for (int i = 0; i < edgeCount; i++)
+ returnThis.add(iter.next());
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] getEdgeIndicesArray() {
+ IntEnumerator edges = m_graph.edges();
+ final int[] returnThis = new int[edges.numRemaining()];
+
+ for (int i = 0; i < returnThis.length; i++)
+ returnThis[i] = m_nativeToRootEdgeInxMap.getIntAtIndex(edges.nextInt());
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param rootGraphFromNodeInx DOCUMENT ME!
+ * @param rootGraphToNodeInx DOCUMENT ME!
+ * @param undirectedEdges DOCUMENT ME!
+ * @param bothDirections DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] getEdgeIndicesArray(int rootGraphFromNodeInx, int rootGraphToNodeInx,
+ boolean undirectedEdges, boolean bothDirections) {
+ if (!((rootGraphFromNodeInx < 0) && (rootGraphToNodeInx < 0))) {
+ return null;
+ }
+
+ final int nativeFromNodeInx = m_rootToNativeNodeInxMap.get(~rootGraphFromNodeInx);
+ final int nativeToNodeInx = m_rootToNativeNodeInxMap.get(~rootGraphToNodeInx);
+ final IntIterator connectingEdges = m_graph.edgesConnecting(nativeFromNodeInx,
+ nativeToNodeInx, true,
+ bothDirections, undirectedEdges);
+
+ if (connectingEdges == null) {
+ return null;
+ }
+
+ m_heap.empty();
+
+ final MinIntHeap edgeBucket = m_heap;
+
+ while (connectingEdges.hasNext())
+ edgeBucket.toss(m_nativeToRootEdgeInxMap.getIntAtIndex(connectingEdges.nextInt()));
+
+ final int[] returnThis = new int[edgeBucket.size()];
+ edgeBucket.copyInto(returnThis, 0);
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Node hideNode(Node node) {
+ if ((node.getRootGraph() == m_root) && (hideNode(node.getRootGraphIndex()) != 0)) {
+ return node;
+ } else {
+ return null;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param rootGraphNodeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int hideNode(int rootGraphNodeInx) {
+ return m_weeder.hideNode(this, rootGraphNodeInx);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nodes DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public java.util.List hideNodes(java.util.List nodes) {
+ final java.util.ArrayList returnThis = new java.util.ArrayList();
+
+ for (int i = 0; i < nodes.size(); i++)
+ if (hideNode((Node) nodes.get(i)) != null) {
+ returnThis.add(nodes.get(i));
+ }
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param rootGraphNodeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] hideNodes(int[] rootGraphNodeInx) {
+ return m_weeder.hideNodes(this, rootGraphNodeInx);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Node restoreNode(Node node) {
+ if ((node.getRootGraph() == m_root) && (restoreNode(node.getRootGraphIndex()) != 0)) {
+ return node;
+ } else {
+ return null;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param rootGraphNodeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int restoreNode(int rootGraphNodeInx) {
+ final int returnThis;
+
+ if (_restoreNode(rootGraphNodeInx) != 0) {
+ returnThis = rootGraphNodeInx;
+ } else {
+ returnThis = 0;
+ }
+
+ if (returnThis != 0) {
+ final GraphPerspectiveChangeListener listener = m_lis[0];
+
+ if (listener != null) {
+ listener.graphPerspectiveChanged(new GraphPerspectiveNodesRestoredEvent(this,
+ new int[] {
+ rootGraphNodeInx
+ }));
+ }
+ }
+
+ return returnThis;
+ }
+
+ // Returns 0 if unsuccessful; returns the complement of the native node
+ // index if successful. Complement is '~', i.e., it's a negative value.
+ private int _restoreNode(final int rootGraphNodeInx) {
+ if (!(rootGraphNodeInx < 0)) {
+ return 0;
+ }
+
+ int nativeNodeInx = m_rootToNativeNodeInxMap.get(~rootGraphNodeInx);
+
+ if ((m_root.getNode(rootGraphNodeInx) == null)
+ || !((nativeNodeInx < 0) || (nativeNodeInx == Integer.MAX_VALUE))) {
+ return 0;
+ }
+
+ nativeNodeInx = m_graph.nodeCreate();
+ m_rootToNativeNodeInxMap.put(~rootGraphNodeInx, nativeNodeInx);
+ m_nativeToRootNodeInxMap.setIntAtIndex(rootGraphNodeInx, nativeNodeInx);
+
+ return ~nativeNodeInx;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nodes DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public java.util.List restoreNodes(java.util.List nodes) {
+ final java.util.ArrayList returnThis = new java.util.ArrayList();
+
+ for (int i = 0; i < nodes.size(); i++)
+ if (restoreNode((Node) nodes.get(i)) != null) {
+ returnThis.add(nodes.get(i));
+ }
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nodes DOCUMENT ME!
+ * @param restoreIncidentEdges DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public java.util.List restoreNodes(java.util.List nodes, boolean restoreIncidentEdges) {
+ final java.util.List returnThis = restoreNodes(nodes);
+ final int[] restoredNodeInx = new int[returnThis.size()];
+
+ for (int i = 0; i < restoredNodeInx.length; i++)
+ restoredNodeInx[i] = ((Node) returnThis.get(i)).getRootGraphIndex();
+
+ final int[] connectingEdgeInx = m_root.getConnectingEdgeIndicesArray(restoredNodeInx);
+ restoreEdges(connectingEdgeInx);
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param rootGraphNodeInx DOCUMENT ME!
+ * @param restoreIncidentEdges DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] restoreNodes(int[] rootGraphNodeInx, boolean restoreIncidentEdges) {
+ final int[] returnThis = restoreNodes(rootGraphNodeInx);
+ final int[] connectingEdgeInx = m_root.getConnectingEdgeIndicesArray(returnThis);
+ restoreEdges(connectingEdgeInx);
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param rootGraphNodeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] restoreNodes(int[] rootGraphNodeInx) {
+ m_heap.empty();
+
+ final MinIntHeap successes = m_heap;
+ final int[] returnThis = new int[rootGraphNodeInx.length];
+
+ for (int i = 0; i < rootGraphNodeInx.length; i++)
+ if (_restoreNode(rootGraphNodeInx[i]) != 0) {
+ returnThis[i] = rootGraphNodeInx[i];
+ successes.toss(returnThis[i]);
+ }
+
+ if (successes.size() > 0) {
+ final GraphPerspectiveChangeListener listener = m_lis[0];
+
+ if (listener != null) {
+ final int[] successArr = new int[successes.size()];
+ successes.copyInto(successArr, 0);
+ listener.graphPerspectiveChanged(new GraphPerspectiveNodesRestoredEvent(this,
+ successArr));
+ }
+ }
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edge DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Edge hideEdge(Edge edge) {
+ if ((edge.getRootGraph() == m_root) && (hideEdge(edge.getRootGraphIndex()) != 0)) {
+ return edge;
+ } else {
+ return null;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param rootGraphEdgeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int hideEdge(int rootGraphEdgeInx) {
+ return m_weeder.hideEdge(this, rootGraphEdgeInx);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edges DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public java.util.List hideEdges(java.util.List edges) {
+ final java.util.ArrayList returnThis = new java.util.ArrayList();
+
+ for (int i = 0; i < edges.size(); i++)
+ if (hideEdge((Edge) edges.get(i)) != null) {
+ returnThis.add(edges.get(i));
+ }
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param rootGraphEdgeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] hideEdges(int[] rootGraphEdgeInx) {
+ return m_weeder.hideEdges(this, rootGraphEdgeInx);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edge DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Edge restoreEdge(Edge edge) {
+ if ((edge.getRootGraph() == m_root) && (restoreEdge(edge.getRootGraphIndex()) != 0)) {
+ return edge;
+ } else {
+ return null;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param rootGraphEdgeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int restoreEdge(int rootGraphEdgeInx) {
+ final int returnThis = _restoreEdge(rootGraphEdgeInx);
+
+ if (returnThis != 0) {
+ final GraphPerspectiveChangeListener listener = m_lis[0];
+
+ if (listener != null) {
+ listener.graphPerspectiveChanged(new GraphPerspectiveEdgesRestoredEvent(this,
+ new int[] {
+ rootGraphEdgeInx
+ }));
+ }
+ }
+
+ return returnThis;
+ }
+
+ // Use this only from _restoreEdge(int). The heap will never grow
+ // to more than the default size; it won't take up lots of memory.
+ private final MinIntHeap m_heap__restoreEdge = new MinIntHeap();
+
+ // Returns 0 if unsuccessful; otherwise returns the root index of edge.
+ private int _restoreEdge(final int rootGraphEdgeInx) {
+ if (!(rootGraphEdgeInx < 0)) {
+ return 0;
+ }
+
+ int nativeEdgeInx = m_rootToNativeEdgeInxMap.get(~rootGraphEdgeInx);
+
+ if ((m_root.getEdge(rootGraphEdgeInx) == null)
+ || !((nativeEdgeInx < 0) || (nativeEdgeInx == Integer.MAX_VALUE))) {
+ return 0;
+ }
+
+ final int rootGraphSourceNodeInx = m_root.getEdgeSourceIndex(rootGraphEdgeInx);
+ final int rootGraphTargetNodeInx = m_root.getEdgeTargetIndex(rootGraphEdgeInx);
+ int nativeSourceNodeInx = m_rootToNativeNodeInxMap.get(~rootGraphSourceNodeInx);
+ int nativeTargetNodeInx = m_rootToNativeNodeInxMap.get(~rootGraphTargetNodeInx);
+ m_heap__restoreEdge.empty();
+
+ final MinIntHeap restoredNodeRootInx = m_heap__restoreEdge;
+
+ if ((nativeSourceNodeInx < 0) || (nativeSourceNodeInx == Integer.MAX_VALUE)) {
+ nativeSourceNodeInx = ~(_restoreNode(rootGraphSourceNodeInx));
+ restoredNodeRootInx.toss(rootGraphSourceNodeInx);
+
+ if (rootGraphSourceNodeInx == rootGraphTargetNodeInx) {
+ nativeTargetNodeInx = nativeSourceNodeInx;
+ }
+ }
+
+ if ((nativeTargetNodeInx < 0) || (nativeTargetNodeInx == Integer.MAX_VALUE)) {
+ nativeTargetNodeInx = ~(_restoreNode(rootGraphTargetNodeInx));
+ restoredNodeRootInx.toss(rootGraphTargetNodeInx);
+ }
+
+ if (restoredNodeRootInx.size() > 0) {
+ final GraphPerspectiveChangeListener listener = m_lis[0];
+
+ if (listener != null) {
+ final int[] restoredNodesArr = new int[restoredNodeRootInx.size()];
+ restoredNodeRootInx.copyInto(restoredNodesArr, 0);
+ listener.graphPerspectiveChanged(new GraphPerspectiveNodesRestoredEvent(this,
+ restoredNodesArr));
+ }
+ }
+
+ nativeEdgeInx = m_graph.edgeCreate(nativeSourceNodeInx, nativeTargetNodeInx,
+ m_root.isEdgeDirected(rootGraphEdgeInx));
+ m_rootToNativeEdgeInxMap.put(~rootGraphEdgeInx, nativeEdgeInx);
+ m_nativeToRootEdgeInxMap.setIntAtIndex(rootGraphEdgeInx, nativeEdgeInx);
+
+ return rootGraphEdgeInx;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edges DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public java.util.List restoreEdges(java.util.List edges) {
+ final java.util.ArrayList returnThis = new java.util.ArrayList();
+
+ for (int i = 0; i < edges.size(); i++)
+ if (restoreEdge((Edge) edges.get(i)) != null) {
+ returnThis.add(edges.get(i));
+ }
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param rootGraphEdgeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] restoreEdges(int[] rootGraphEdgeInx) {
+ m_heap.empty();
+
+ final MinIntHeap successes = m_heap;
+ final int[] returnThis = new int[rootGraphEdgeInx.length];
+
+ for (int i = 0; i < rootGraphEdgeInx.length; i++) {
+ returnThis[i] = _restoreEdge(rootGraphEdgeInx[i]);
+
+ if (returnThis[i] != 0) {
+ successes.toss(returnThis[i]);
+ }
+ }
+
+ if (successes.size() > 0) {
+ final GraphPerspectiveChangeListener listener = m_lis[0];
+
+ if (listener != null) {
+ final int[] successArr = new int[successes.size()];
+ successes.copyInto(successArr, 0);
+ listener.graphPerspectiveChanged(new GraphPerspectiveEdgesRestoredEvent(this,
+ successArr));
+ }
+ }
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean containsNode(Node node) {
+ int nativeInx;
+
+ return (node.getRootGraph() == m_root)
+ && ((nativeInx = m_rootToNativeNodeInxMap.get(~(node.getRootGraphIndex()))) >= 0)
+ && (nativeInx != Integer.MAX_VALUE);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ * @param recurse DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean containsNode(Node node, boolean recurse) {
+ if (node.getRootGraph() != m_root) {
+ return false;
+ }
+
+ final int nativeInx = m_rootToNativeNodeInxMap.get(~(node.getRootGraphIndex()));
+
+ if ((nativeInx >= 0) && (nativeInx != Integer.MAX_VALUE)) {
+ return true;
+ }
+
+ if (!recurse) {
+ return false;
+ }
+
+ final int[] recursiveChildNodes = m_root.getNodeMetaChildIndicesArray(getNodeIndicesArray());
+
+ for (int i = 0; i < recursiveChildNodes.length; i++)
+ if (recursiveChildNodes[i] == node.getRootGraphIndex()) {
+ return true;
+ }
+
+ return false;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edge DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean containsEdge(Edge edge) {
+ int nativeInx;
+
+ return (edge.getRootGraph() == m_root)
+ && ((nativeInx = m_rootToNativeEdgeInxMap.get(~(edge.getRootGraphIndex()))) >= 0)
+ && (nativeInx != Integer.MAX_VALUE);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edge DOCUMENT ME!
+ * @param recurse DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean containsEdge(Edge edge, boolean recurse) {
+ if (edge.getRootGraph() != m_root) {
+ return false;
+ }
+
+ final int nativeInx = m_rootToNativeEdgeInxMap.get(~(edge.getRootGraphIndex()));
+
+ if ((nativeInx >= 0) && (nativeInx != Integer.MAX_VALUE)) {
+ return true;
+ }
+
+ if (!recurse) {
+ return false;
+ }
+
+ final int[] recursiveChildEdges = m_root.getEdgeMetaChildIndicesArray(getNodeIndicesArray());
+
+ for (int i = 0; i < recursiveChildEdges.length; i++)
+ if (recursiveChildEdges[i] == edge.getRootGraphIndex()) {
+ return true;
+ }
+
+ return false;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param persp DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public GraphPerspective join(GraphPerspective persp) {
+ final FGraphPerspective thisPersp = this;
+
+ if (!(persp instanceof FGraphPerspective)) {
+ return null;
+ }
+
+ final FGraphPerspective otherPersp = (FGraphPerspective) persp;
+
+ if (otherPersp.m_root != thisPersp.m_root) {
+ return null;
+ }
+
+ final IntEnumerator thisNativeNodes = thisPersp.m_graph.nodes();
+ final IntEnumerator otherNativeNodes = otherPersp.m_graph.nodes();
+ final IntIterator rootGraphNodeInx = new IntIterator() {
+ public boolean hasNext() {
+ return (thisNativeNodes.numRemaining() > 0)
+ || (otherNativeNodes.numRemaining() > 0);
+ }
+
+ public int nextInt() {
+ if (thisNativeNodes.numRemaining() > 0) {
+ return thisPersp.m_nativeToRootNodeInxMap.getIntAtIndex(thisNativeNodes.nextInt());
+ } else {
+ return otherPersp.m_nativeToRootNodeInxMap.getIntAtIndex(otherNativeNodes
+ [...]
+ }
+ }
+ };
+
+ final IntEnumerator thisNativeEdges = thisPersp.m_graph.edges();
+ final IntEnumerator otherNativeEdges = otherPersp.m_graph.edges();
+ final IntIterator rootGraphEdgeInx = new IntIterator() {
+ public boolean hasNext() {
+ return (thisNativeEdges.numRemaining() > 0)
+ || (otherNativeEdges.numRemaining() > 0);
+ }
+
+ public int nextInt() {
+ if (thisNativeEdges.numRemaining() > 0) {
+ return thisPersp.m_nativeToRootEdgeInxMap.getIntAtIndex(thisNativeEdges.nextInt());
+ } else {
+ return otherPersp.m_nativeToRootEdgeInxMap.getIntAtIndex(otherNativeEdges
+ [...]
+ }
+ }
+ };
+
+ return new FGraphPerspective(m_root, rootGraphNodeInx, rootGraphEdgeInx);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nodes DOCUMENT ME!
+ * @param edges DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public GraphPerspective createGraphPerspective(Node[] nodes, Edge[] edges) {
+ for (int i = 0; i < nodes.length; i++)
+ if (!containsNode(nodes[i])) {
+ return null;
+ }
+
+ for (int i = 0; i < edges.length; i++)
+ if (!containsEdge(edges[i])) {
+ return null;
+ }
+
+ return m_root.createGraphPerspective(nodes, edges);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param rootGraphNodeInx DOCUMENT ME!
+ * @param rootGraphEdgeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public GraphPerspective createGraphPerspective(int[] rootGraphNodeInx, int[] rootGraphEdgeInx) {
+ for (int i = 0; i < rootGraphNodeInx.length; i++) {
+ final int rootGraphNodeIndex = rootGraphNodeInx[i];
+
+ if (!(rootGraphNodeIndex < 0)) {
+ return null;
+ }
+
+ final int nativeNodeIndex = m_rootToNativeNodeInxMap.get(~rootGraphNodeIndex);
+
+ if ((nativeNodeIndex < 0) || (nativeNodeIndex == Integer.MAX_VALUE)) {
+ return null;
+ }
+ }
+
+ for (int i = 0; i < rootGraphEdgeInx.length; i++) {
+ final int rootGraphEdgeIndex = rootGraphEdgeInx[i];
+
+ if (!(rootGraphEdgeIndex < 0)) {
+ return null;
+ }
+
+ final int nativeEdgeIndex = m_rootToNativeEdgeInxMap.get(~rootGraphEdgeIndex);
+
+ if ((nativeEdgeIndex < 0) || (nativeEdgeIndex == Integer.MAX_VALUE)) {
+ return null;
+ }
+ }
+
+ return m_root.createGraphPerspective(rootGraphNodeInx, rootGraphEdgeInx);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param filter DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public GraphPerspective createGraphPerspective(final Filter filter) {
+ m_heap.empty();
+
+ final MinIntHeap nodeInxBucket = m_heap;
+ final Iterator nodesIter = nodesIterator();
+
+ while (nodesIter.hasNext()) {
+ final Node nodeCandidate = (Node) (nodesIter.next());
+
+ if (filter.passesFilter(nodeCandidate)) {
+ nodeInxBucket.toss(nodeCandidate.getRootGraphIndex());
+ }
+ }
+
+ final int[] nodeInxArr = new int[nodeInxBucket.size()];
+ nodeInxBucket.copyInto(nodeInxArr, 0);
+ m_heap.empty();
+
+ final MinIntHeap edgeInxBucket = m_heap;
+ final Iterator edgesIter = edgesIterator();
+
+ while (edgesIter.hasNext()) {
+ final Edge edgeCandidate = (Edge) (edgesIter.next());
+
+ if (filter.passesFilter(edgeCandidate)) {
+ edgeInxBucket.toss(edgeCandidate.getRootGraphIndex());
+ }
+ }
+
+ final int[] edgeInxArr = new int[edgeInxBucket.size()];
+ edgeInxBucket.copyInto(edgeInxArr, 0);
+
+ return m_root.createGraphPerspective(nodeInxArr, edgeInxArr);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public java.util.List neighborsList(Node node) {
+ if (node.getRootGraph() == m_root) {
+ final int[] neighInx = neighborsArray(node.getRootGraphIndex());
+
+ if (neighInx == null) {
+ return null;
+ }
+
+ final java.util.ArrayList returnThis = new java.util.ArrayList(neighInx.length);
+
+ for (int i = 0; i < neighInx.length; i++)
+ returnThis.add(getNode(neighInx[i]));
+
+ return returnThis;
+ } else {
+ return null;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nodeIndex DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] neighborsArray(final int nodeIndex) {
+ int[] adjacentEdgeIndices = getAdjacentEdgeIndicesArray(nodeIndex, true, true, true);
+
+ if (adjacentEdgeIndices == null) {
+ return null;
+ }
+
+ m_hash.empty();
+
+ final IntHash neighbors = m_hash;
+
+ for (int i = 0; i < adjacentEdgeIndices.length; i++) {
+ int neighborIndex = (nodeIndex ^ getEdgeSourceIndex(adjacentEdgeIndices[i])
+ ^ getEdgeTargetIndex(adjacentEdgeIndices[i]));
+ neighbors.put(~neighborIndex);
+ }
+
+ IntEnumerator enumx = neighbors.elements();
+ final int[] returnThis = new int[enumx.numRemaining()];
+ int index = -1;
+
+ while (enumx.numRemaining() > 0)
+ returnThis[++index] = ~(enumx.nextInt());
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param a DOCUMENT ME!
+ * @param b DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isNeighbor(Node a, Node b) {
+ if ((a.getRootGraph() == m_root) && (b.getRootGraph() == m_root)) {
+ return isNeighbor(a.getRootGraphIndex(), b.getRootGraphIndex());
+ } else {
+ return false;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nodeInxA DOCUMENT ME!
+ * @param nodeInxB DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isNeighbor(final int nodeInxA, final int nodeInxB) {
+ if (!((nodeInxA < 0) && (nodeInxB < 0))) {
+ return false;
+ }
+
+ final int nativeNodeA = m_rootToNativeNodeInxMap.get(~nodeInxA);
+ final int nativeNodeB = m_rootToNativeNodeInxMap.get(~nodeInxB);
+ final IntIterator nativeConnEdgeIter = m_graph.edgesConnecting(nativeNodeA, nativeNodeB,
+ true, true, true);
+
+ if (nativeConnEdgeIter == null) {
+ return false;
+ }
+
+ return nativeConnEdgeIter.hasNext();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param from DOCUMENT ME!
+ * @param to DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean edgeExists(Node from, Node to) {
+ if ((from.getRootGraph() == m_root) && (to.getRootGraph() == m_root)) {
+ return edgeExists(from.getRootGraphIndex(), to.getRootGraphIndex());
+ } else {
+ return false;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param fromNodeInx DOCUMENT ME!
+ * @param toNodeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean edgeExists(final int fromNodeInx, final int toNodeInx) {
+ if (!((fromNodeInx < 0) && (toNodeInx < 0))) {
+ return false;
+ }
+
+ final int nativeFromNode = m_rootToNativeNodeInxMap.get(~fromNodeInx);
+ final int nativeToNode = m_rootToNativeNodeInxMap.get(~toNodeInx);
+ final IntIterator nativeConnEdgeIter = m_graph.edgesConnecting(nativeFromNode,
+ nativeToNode, true, false,
+ true);
+
+ if (nativeConnEdgeIter == null) {
+ return false;
+ }
+
+ return nativeConnEdgeIter.hasNext();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param from DOCUMENT ME!
+ * @param to DOCUMENT ME!
+ * @param countUndirectedEdges DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getEdgeCount(Node from, Node to, boolean countUndirectedEdges) {
+ if ((from.getRootGraph() == m_root) && (to.getRootGraph() == m_root)) {
+ return getEdgeCount(from.getRootGraphIndex(), to.getRootGraphIndex(),
+ countUndirectedEdges);
+ } else {
+ return -1;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param fromNodeInx DOCUMENT ME!
+ * @param toNodeInx DOCUMENT ME!
+ * @param countUndirectedEdges DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getEdgeCount(int fromNodeInx, int toNodeInx, boolean countUndirectedEdges) {
+ final int[] edgeIndicesArray = getEdgeIndicesArray(fromNodeInx, toNodeInx,
+ countUndirectedEdges);
+
+ if (edgeIndicesArray == null) {
+ return -1;
+ }
+
+ return edgeIndicesArray.length;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param from DOCUMENT ME!
+ * @param to DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public java.util.List edgesList(Node from, Node to) {
+ if ((from.getRootGraph() == m_root) && (to.getRootGraph() == m_root)) {
+ return edgesList(from.getRootGraphIndex(), to.getRootGraphIndex(), true);
+ } else {
+ return null;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param fromNodeInx DOCUMENT ME!
+ * @param toNodeInx DOCUMENT ME!
+ * @param includeUndirectedEdges DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public java.util.List edgesList(int fromNodeInx, int toNodeInx, boolean includeUndirectedEdges) {
+ final int[] edgeInx = getEdgeIndicesArray(fromNodeInx, toNodeInx, includeUndirectedEdges);
+
+ if (edgeInx == null) {
+ return null;
+ }
+
+ java.util.ArrayList returnList = new java.util.ArrayList(edgeInx.length);
+
+ for (int i = 0; i < edgeInx.length; i++)
+ returnList.add(getEdge(edgeInx[i]));
+
+ return returnList;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param fromNodeInx DOCUMENT ME!
+ * @param toNodeInx DOCUMENT ME!
+ * @param includeUndirectedEdges DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] getEdgeIndicesArray(int fromNodeInx, int toNodeInx, boolean includeUndirectedEdges) {
+ return getEdgeIndicesArray(fromNodeInx, toNodeInx, includeUndirectedEdges, false);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getInDegree(Node node) {
+ if (node.getRootGraph() == m_root) {
+ return getInDegree(node.getRootGraphIndex());
+ } else {
+ return -1;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nodeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getInDegree(int nodeInx) {
+ return getInDegree(nodeInx, true);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ * @param countUndirectedEdges DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getInDegree(Node node, boolean countUndirectedEdges) {
+ if (node.getRootGraph() == m_root) {
+ return getInDegree(node.getRootGraphIndex(), countUndirectedEdges);
+ } else {
+ return -1;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nodeInx DOCUMENT ME!
+ * @param countUndirectedEdges DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getInDegree(final int nodeInx, boolean countUndirectedEdges) {
+ if (!(nodeInx < 0)) {
+ return -1;
+ }
+
+ final int nativeNodeInx = m_rootToNativeNodeInxMap.get(~nodeInx);
+ final IntEnumerator adj = m_graph.edgesAdjacent(nativeNodeInx, false, true,
+ countUndirectedEdges);
+
+ if (adj == null) {
+ return -1;
+ }
+
+ return adj.numRemaining();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getOutDegree(Node node) {
+ if (node.getRootGraph() == m_root) {
+ return getOutDegree(node.getRootGraphIndex());
+ } else {
+ return -1;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nodeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getOutDegree(int nodeInx) {
+ return getOutDegree(nodeInx, true);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ * @param countUndirectedEdges DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getOutDegree(Node node, boolean countUndirectedEdges) {
+ if (node.getRootGraph() == m_root) {
+ return getOutDegree(node.getRootGraphIndex(), countUndirectedEdges);
+ } else {
+ return -1;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nodeInx DOCUMENT ME!
+ * @param countUndirectedEdges DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getOutDegree(int nodeInx, boolean countUndirectedEdges) {
+ if (!(nodeInx < 0)) {
+ return -1;
+ }
+
+ final int nativeNodeInx = m_rootToNativeNodeInxMap.get(~nodeInx);
+ final IntEnumerator adj = m_graph.edgesAdjacent(nativeNodeInx, true, false,
+ countUndirectedEdges);
+
+ if (adj == null) {
+ return -1;
+ }
+
+ return adj.numRemaining();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getDegree(Node node) {
+ if (node.getRootGraph() == m_root) {
+ return getDegree(node.getRootGraphIndex());
+ } else {
+ return -1;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nodeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getDegree(final int nodeInx) {
+ if (!(nodeInx < 0)) {
+ return -1;
+ }
+
+ final int nativeNodeInx = m_rootToNativeNodeInxMap.get(~nodeInx);
+ final IntEnumerator adj = m_graph.edgesAdjacent(nativeNodeInx, true, true, true);
+
+ if (adj == null) {
+ return -1;
+ }
+
+ return adj.numRemaining();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getIndex(Node node) {
+ if ((node.getRootGraph() == m_root)
+ && (getRootGraphNodeIndex(node.getRootGraphIndex()) == node.getRootGraphIndex())) {
+ return node.getRootGraphIndex();
+ } else {
+ return 0;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param rootGraphNodeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getNodeIndex(int rootGraphNodeInx) {
+ return getRootGraphNodeIndex(rootGraphNodeInx);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param rootGraphNodeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getRootGraphNodeIndex(int rootGraphNodeInx) {
+ if (!(rootGraphNodeInx < 0)) {
+ return 0;
+ }
+
+ final int nativeNodeInx = m_rootToNativeNodeInxMap.get(~rootGraphNodeInx);
+
+ if ((nativeNodeInx < 0) || (nativeNodeInx == Integer.MAX_VALUE)) {
+ return 0;
+ }
+
+ return rootGraphNodeInx;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param rootGraphNodeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Node getNode(int rootGraphNodeInx) {
+ return m_root.getNode(getRootGraphNodeIndex(rootGraphNodeInx));
+ }
+
+ // Package visible.
+ boolean containsNode(int rootGraphNodeInx) {
+ if (rootGraphNodeInx >= 0) {
+ return false;
+ }
+
+ final int nativeNodeInx = m_rootToNativeNodeInxMap.get(~rootGraphNodeInx);
+
+ return ((nativeNodeInx >= 0) && (nativeNodeInx != Integer.MAX_VALUE));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edge DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getIndex(Edge edge) {
+ if ((edge.getRootGraph() == m_root)
+ && (getRootGraphEdgeIndex(edge.getRootGraphIndex()) == edge.getRootGraphIndex())) {
+ return edge.getRootGraphIndex();
+ } else {
+ return 0;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param rootGraphEdgeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getEdgeIndex(int rootGraphEdgeInx) {
+ return getRootGraphEdgeIndex(rootGraphEdgeInx);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param rootGraphEdgeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getRootGraphEdgeIndex(int rootGraphEdgeInx) {
+ if (!(rootGraphEdgeInx < 0)) {
+ return 0;
+ }
+
+ final int nativeEdgeInx = m_rootToNativeEdgeInxMap.get(~rootGraphEdgeInx);
+
+ if ((nativeEdgeInx < 0) || (nativeEdgeInx == Integer.MAX_VALUE)) {
+ return 0;
+ }
+
+ return rootGraphEdgeInx;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param rootGraphEdgeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Edge getEdge(int rootGraphEdgeInx) {
+ return m_root.getEdge(getRootGraphEdgeIndex(rootGraphEdgeInx));
+ }
+
+ // Package visible.
+ boolean containsEdge(int rootGraphEdgeInx) {
+ if (rootGraphEdgeInx >= 0) {
+ return false;
+ }
+
+ final int nativeEdgeInx = m_rootToNativeEdgeInxMap.get(~rootGraphEdgeInx);
+
+ return ((nativeEdgeInx >= 0) && (nativeEdgeInx != Integer.MAX_VALUE));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edgeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getEdgeSourceIndex(int edgeInx) {
+ if (!(edgeInx < 0)) {
+ return 0;
+ }
+
+ final int nativeEdgeInx = m_rootToNativeEdgeInxMap.get(~edgeInx);
+ final int nativeSrcNodeInx = m_graph.edgeSource(nativeEdgeInx);
+
+ if (nativeSrcNodeInx < 0) {
+ return 0;
+ }
+
+ return m_nativeToRootNodeInxMap.getIntAtIndex(nativeSrcNodeInx);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edgeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getEdgeTargetIndex(int edgeInx) {
+ if (!(edgeInx < 0)) {
+ return 0;
+ }
+
+ final int nativeEdgeInx = m_rootToNativeEdgeInxMap.get(~edgeInx);
+ final int nativeTrgNodeInx = m_graph.edgeTarget(nativeEdgeInx);
+
+ if (nativeTrgNodeInx < 0) {
+ return 0;
+ }
+
+ return m_nativeToRootNodeInxMap.getIntAtIndex(nativeTrgNodeInx);
+ }
+
+ // Throws IllegalArgumentException
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edgeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isEdgeDirected(int edgeInx) {
+ if (!(edgeInx < 0)) {
+ throw new IllegalArgumentException("edge index is not negative");
+ }
+
+ return m_graph.edgeType(m_rootToNativeEdgeInxMap.get(~edgeInx)) == 1;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param child DOCUMENT ME!
+ * @param parent DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isMetaParent(Node child, Node parent) {
+ if (!((child.getRootGraph() == m_root) && (parent.getRootGraph() == m_root))) {
+ return false;
+ }
+
+ return isNodeMetaParent(child.getRootGraphIndex(), parent.getRootGraphIndex());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param childNodeInx DOCUMENT ME!
+ * @param parentNodeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isNodeMetaParent(int childNodeInx, int parentNodeInx) {
+ return isNodeMetaChild(parentNodeInx, childNodeInx);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public java.util.List metaParentsList(Node node) {
+ if (!(node.getRootGraph() == m_root)) {
+ return null;
+ }
+
+ return nodeMetaParentsList(node.getRootGraphIndex());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nodeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public java.util.List nodeMetaParentsList(int nodeInx) {
+ final int[] parentInxArr = getNodeMetaParentIndicesArray(nodeInx);
+
+ if (parentInxArr == null) {
+ return null;
+ }
+
+ final java.util.List returnThis = new java.util.ArrayList(parentInxArr.length);
+
+ for (int i = 0; i < parentInxArr.length; i++)
+ returnThis.add(m_root.getNode(parentInxArr[i]));
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nodeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] getNodeMetaParentIndicesArray(int nodeInx) {
+ if (!containsNode(nodeInx)) {
+ return null;
+ }
+
+ final int[] allParentInx = m_root.getNodeMetaParentIndicesArray(nodeInx);
+ m_heap.empty();
+
+ final MinIntHeap parentsBucket = m_heap;
+
+ for (int i = 0; i < allParentInx.length; i++)
+ if (containsNode(allParentInx[i])) {
+ parentsBucket.toss(allParentInx[i]);
+ }
+
+ final int[] returnThis = new int[parentsBucket.size()];
+ parentsBucket.copyInto(returnThis, 0);
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param parent DOCUMENT ME!
+ * @param child DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isMetaChild(Node parent, Node child) {
+ return isMetaParent(child, parent);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param parentNodeInx DOCUMENT ME!
+ * @param childNodeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isNodeMetaChild(int parentNodeInx, int childNodeInx) {
+ return containsNode(parentNodeInx) && containsNode(childNodeInx)
+ && m_root.isNodeMetaChild(parentNodeInx, childNodeInx);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public java.util.List nodeMetaChildrenList(Node node) {
+ if (!(node.getRootGraph() == m_root)) {
+ return null;
+ }
+
+ return nodeMetaChildrenList(node.getRootGraphIndex());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param parentInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public java.util.List nodeMetaChildrenList(int parentInx) {
+ final int[] childrenInxArr = getNodeMetaChildIndicesArray(parentInx);
+
+ if (childrenInxArr == null) {
+ return null;
+ }
+
+ final java.util.List returnThis = new java.util.ArrayList(childrenInxArr.length);
+
+ for (int i = 0; i < childrenInxArr.length; i++)
+ returnThis.add(m_root.getNode(childrenInxArr[i]));
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param parentInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] getNodeMetaChildIndicesArray(int parentInx) {
+ if (!containsNode(parentInx)) {
+ return null;
+ }
+
+ final int[] allChildrenInx = m_root.getNodeMetaChildIndicesArray(parentInx);
+ m_heap.empty();
+
+ final MinIntHeap childrenBucket = m_heap;
+
+ for (int i = 0; i < allChildrenInx.length; i++)
+ if (containsNode(allChildrenInx[i])) {
+ childrenBucket.toss(allChildrenInx[i]);
+ }
+
+ final int[] returnThis = new int[childrenBucket.size()];
+ childrenBucket.copyInto(returnThis, 0);
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param child DOCUMENT ME!
+ * @param parent DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isMetaParent(Edge child, Node parent) {
+ if (!((child.getRootGraph() == m_root) && (parent.getRootGraph() == m_root))) {
+ return false;
+ }
+
+ return isEdgeMetaParent(child.getRootGraphIndex(), parent.getRootGraphIndex());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param childEdgeInx DOCUMENT ME!
+ * @param parentNodeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isEdgeMetaParent(int childEdgeInx, int parentNodeInx) {
+ return isEdgeMetaChild(parentNodeInx, childEdgeInx);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edge DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public java.util.List metaParentsList(Edge edge) {
+ if (!(edge.getRootGraph() == m_root)) {
+ return null;
+ }
+
+ return edgeMetaParentsList(edge.getRootGraphIndex());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edgeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public java.util.List edgeMetaParentsList(int edgeInx) {
+ final int[] parentInxArr = getEdgeMetaParentIndicesArray(edgeInx);
+
+ if (parentInxArr == null) {
+ return null;
+ }
+
+ final java.util.List returnThis = new java.util.ArrayList(parentInxArr.length);
+
+ for (int i = 0; i < parentInxArr.length; i++)
+ returnThis.add(m_root.getNode(parentInxArr[i]));
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edgeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] getEdgeMetaParentIndicesArray(int edgeInx) {
+ if (!containsEdge(edgeInx)) {
+ return null;
+ }
+
+ final int[] allParentInx = m_root.getEdgeMetaParentIndicesArray(edgeInx);
+ m_heap.empty();
+
+ final MinIntHeap parentsBucket = m_heap;
+
+ for (int i = 0; i < allParentInx.length; i++)
+ if (containsNode(allParentInx[i])) {
+ parentsBucket.toss(allParentInx[i]);
+ }
+
+ final int[] returnThis = new int[parentsBucket.size()];
+ parentsBucket.copyInto(returnThis, 0);
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param parent DOCUMENT ME!
+ * @param child DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isMetaChild(Node parent, Edge child) {
+ return isMetaParent(child, parent);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param parentNodeInx DOCUMENT ME!
+ * @param childEdgeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isEdgeMetaChild(int parentNodeInx, int childEdgeInx) {
+ return containsNode(parentNodeInx) && containsEdge(childEdgeInx)
+ && m_root.isEdgeMetaChild(parentNodeInx, childEdgeInx);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public java.util.List edgeMetaChildrenList(Node node) {
+ if (!(node.getRootGraph() == m_root)) {
+ return null;
+ }
+
+ return edgeMetaChildrenList(node.getRootGraphIndex());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param parentNodeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public java.util.List edgeMetaChildrenList(int parentNodeInx) {
+ final int[] childrenInxArr = getEdgeMetaChildIndicesArray(parentNodeInx);
+
+ if (childrenInxArr == null) {
+ return null;
+ }
+
+ final java.util.List returnThis = new java.util.ArrayList(childrenInxArr.length);
+
+ for (int i = 0; i < childrenInxArr.length; i++)
+ returnThis.add(m_root.getEdge(childrenInxArr[i]));
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param parentNodeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] getEdgeMetaChildIndicesArray(int parentNodeInx) {
+ if (!containsNode(parentNodeInx)) {
+ return null;
+ }
+
+ final int[] allChildrenInx = m_root.getEdgeMetaChildIndicesArray(parentNodeInx);
+ m_heap.empty();
+
+ final MinIntHeap childrenBucket = m_heap;
+
+ for (int i = 0; i < allChildrenInx.length; i++)
+ if (containsEdge(allChildrenInx[i])) {
+ childrenBucket.toss(allChildrenInx[i]);
+ }
+
+ final int[] returnThis = new int[childrenBucket.size()];
+ childrenBucket.copyInto(returnThis, 0);
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ * @param undirected DOCUMENT ME!
+ * @param incoming DOCUMENT ME!
+ * @param outgoing DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public java.util.List getAdjacentEdgesList(Node node, boolean undirected, boolean incoming,
+ boolean outgoing) {
+ if (node.getRootGraph() != m_root) {
+ return null;
+ }
+
+ final int[] adjEdgeInx = getAdjacentEdgeIndicesArray(node.getRootGraphIndex(), undirected,
+ incoming, outgoing);
+
+ if (adjEdgeInx == null) {
+ return null;
+ }
+
+ final java.util.ArrayList returnThis = new java.util.ArrayList(adjEdgeInx.length);
+
+ for (int i = 0; i < adjEdgeInx.length; i++)
+ returnThis.add(getEdge(adjEdgeInx[i]));
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nodeInx DOCUMENT ME!
+ * @param undirected DOCUMENT ME!
+ * @param incomingDirected DOCUMENT ME!
+ * @param outgoingDirected DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] getAdjacentEdgeIndicesArray(int nodeInx, boolean undirected,
+ boolean incomingDirected, boolean outgoingDirected) {
+ if (!(nodeInx < 0)) {
+ return null;
+ }
+
+ final int nativeNodeInx = m_rootToNativeNodeInxMap.get(~nodeInx);
+ final IntEnumerator adj = m_graph.edgesAdjacent(nativeNodeInx, outgoingDirected,
+ incomingDirected, undirected);
+
+ if (adj == null) {
+ return null;
+ }
+
+ final int[] returnThis = new int[adj.numRemaining()];
+
+ for (int i = 0; i < returnThis.length; i++)
+ returnThis[i] = m_nativeToRootEdgeInxMap.getIntAtIndex(adj.nextInt());
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nodes DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public java.util.List getConnectingEdges(java.util.List nodes) {
+ m_heap.empty();
+
+ final MinIntHeap nodeInxBucket = m_heap;
+
+ for (int i = 0; i < nodes.size(); i++) {
+ Node node = (Node) (nodes.get(i));
+
+ if (node.getRootGraph() == m_root) {
+ nodeInxBucket.toss(node.getRootGraphIndex());
+ } else {
+ return null;
+ }
+ }
+
+ final int[] nodeInxArr = new int[nodeInxBucket.size()];
+ nodeInxBucket.copyInto(nodeInxArr, 0);
+
+ final int[] connEdgeInxArr = getConnectingEdgeIndicesArray(nodeInxArr);
+
+ if (connEdgeInxArr == null) {
+ return null;
+ }
+
+ final java.util.ArrayList returnThis = new java.util.ArrayList(connEdgeInxArr.length);
+
+ for (int i = 0; i < connEdgeInxArr.length; i++)
+ returnThis.add(getEdge(connEdgeInxArr[i]));
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nodeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] getConnectingEdgeIndicesArray(int[] nodeInx) {
+ final IntHash nativeNodeBucket = new IntHash();
+
+ for (int i = 0; i < nodeInx.length; i++) {
+ if (!(nodeInx[i] < 0)) {
+ return null;
+ }
+
+ final int nativeNodeInx = m_rootToNativeNodeInxMap.get(~nodeInx[i]);
+
+ if (m_graph.nodeExists(nativeNodeInx)) {
+ nativeNodeBucket.put(nativeNodeInx);
+ } else {
+ return null;
+ }
+ }
+
+ m_hash.empty();
+
+ final IntHash nativeEdgeBucket = m_hash;
+ final IntEnumerator nativeNodeEnum = nativeNodeBucket.elements();
+
+ while (nativeNodeEnum.numRemaining() > 0) {
+ final int nativeNodeIndex = nativeNodeEnum.nextInt();
+ final IntEnumerator nativeAdjEdgeEnum = m_graph.edgesAdjacent(nativeNodeIndex, true,
+ false, true);
+
+ while (nativeAdjEdgeEnum.numRemaining() > 0) {
+ final int nativeCandidateEdge = nativeAdjEdgeEnum.nextInt();
+ final int nativeOtherEdgeNode = (nativeNodeIndex
+ ^ m_graph.edgeSource(nativeCandidateEdge)
+ ^ m_graph.edgeTarget(nativeCandidateEdge));
+
+ if (nativeOtherEdgeNode == nativeNodeBucket.get(nativeOtherEdgeNode)) {
+ nativeEdgeBucket.put(nativeCandidateEdge);
+ }
+ }
+ }
+
+ final IntEnumerator nativeReturnEdges = nativeEdgeBucket.elements();
+ final int[] returnThis = new int[nativeReturnEdges.numRemaining()];
+
+ for (int i = 0; i < returnThis.length; i++)
+ returnThis[i] = m_nativeToRootEdgeInxMap.getIntAtIndex(nativeReturnEdges.nextInt());
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edgeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] getConnectingNodeIndicesArray(int[] edgeInx) {
+ m_hash.empty();
+
+ final IntHash nativeNodeBucket = m_hash;
+
+ for (int i = 0; i < edgeInx.length; i++) {
+ if (!(edgeInx[i] < 0)) {
+ return null;
+ }
+
+ final int nativeEdgeIndex = m_rootToNativeEdgeInxMap.get(~edgeInx[i]);
+
+ if (m_graph.edgeType(nativeEdgeIndex) >= 0) {
+ nativeNodeBucket.put(m_graph.edgeSource(nativeEdgeIndex));
+ nativeNodeBucket.put(m_graph.edgeTarget(nativeEdgeIndex));
+ } else {
+ return null;
+ }
+ }
+
+ final IntEnumerator nativeNodeEnum = nativeNodeBucket.elements();
+ final int[] returnThis = new int[nativeNodeEnum.numRemaining()];
+
+ for (int i = 0; i < returnThis.length; i++)
+ returnThis[i] = m_nativeToRootNodeInxMap.getIntAtIndex(nativeNodeEnum.nextInt());
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nodeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public GraphPerspective createGraphPerspective(int[] nodeInx) {
+ return createGraphPerspective(nodeInx, getConnectingEdgeIndicesArray(nodeInx));
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void finalize() {
+ m_root.removeRootGraphChangeListener(m_changeSniffer);
+ }
+
+ // Nodes and edges in this graph are called "native indices" throughout
+ // this class.
+ private final DynamicGraph m_graph;
+ private final FRootGraph m_root;
+
+ // This is an array of length 1 - we need an array as an extra reference
+ // to a reference because some other inner classes need to know what the
+ // current listener is.
+ private final GraphPerspectiveChangeListener[] m_lis;
+
+ // RootGraph indices are negative in these arrays.
+ private final IntArray m_nativeToRootNodeInxMap;
+ private final IntArray m_nativeToRootEdgeInxMap;
+
+ // RootGraph indices are ~ (complements) of the real RootGraph indices
+ // in these hashtables.
+ private final IntIntHash m_rootToNativeNodeInxMap;
+ private final IntIntHash m_rootToNativeEdgeInxMap;
+
+ // This is a utilitarian heap that is used as a bucket of ints.
+ // Don't forget to empty() it before using it.
+ private final MinIntHeap m_heap;
+
+ // This is a utilitarian hash that is used as a collision detecting
+ // bucket of ints. Don't forget to empty() it before using it.
+ private final IntHash m_hash;
+ private final GraphWeeder m_weeder;
+
+ // We need to remove this listener from the RootGraph during finalize().
+ private final RootGraphChangeSniffer m_changeSniffer;
+
+ // Package visible constructor. rootGraphNodeInx
+ // need not contain all endpoint nodes corresponding to edges in
+ // rootGraphEdgeInx - this is calculated automatically by this constructor.
+ // If any index does not correspond to an existing node or edge, an
+ // IllegalArgumentException is thrown. The indices lists need not be
+ // non-repeating - the logic in this constructor handles duplicate
+ // filtering.
+ FGraphPerspective(FRootGraph root, IntIterator rootGraphNodeInx, IntIterator rootGraphEdgeInx)
+ throws IllegalArgumentException // If any index is not in RootGraph.
+ {
+ m_graph = DynamicGraphFactory.instantiateDynamicGraph();
+ m_root = root;
+ m_lis = new GraphPerspectiveChangeListener[1];
+ m_nativeToRootNodeInxMap = new IntArray();
+ m_nativeToRootEdgeInxMap = new IntArray();
+ m_rootToNativeNodeInxMap = new IntIntHash();
+ m_rootToNativeEdgeInxMap = new IntIntHash();
+ m_heap = new MinIntHeap();
+ m_hash = new IntHash();
+ m_weeder = new GraphWeeder(m_root, m_graph, m_nativeToRootNodeInxMap,
+ m_nativeToRootEdgeInxMap, m_rootToNativeNodeInxMap,
+ m_rootToNativeEdgeInxMap, m_lis, m_heap);
+ m_changeSniffer = new RootGraphChangeSniffer(m_weeder);
+
+ while (rootGraphNodeInx.hasNext()) {
+ final int rootNodeInx = rootGraphNodeInx.nextInt();
+
+ if (m_root.getNode(rootNodeInx) != null) {
+ if (m_rootToNativeNodeInxMap.get(~rootNodeInx) >= 0) {
+ continue;
+ }
+
+ final int nativeNodeInx = m_graph.nodeCreate();
+ m_rootToNativeNodeInxMap.put(~rootNodeInx, nativeNodeInx);
+ m_nativeToRootNodeInxMap.setIntAtIndex(rootNodeInx, nativeNodeInx);
+ } else {
+ throw new IllegalArgumentException("node with index " + rootNodeInx
+ + " not in RootGraph");
+ }
+ }
+
+ while (rootGraphEdgeInx.hasNext()) {
+ final int rootEdgeInx = rootGraphEdgeInx.nextInt();
+
+ if (m_root.getEdge(rootEdgeInx) != null) {
+ if (m_rootToNativeEdgeInxMap.get(~rootEdgeInx) >= 0) {
+ continue;
+ }
+
+ final int rootSrcInx = m_root.getEdgeSourceIndex(rootEdgeInx);
+ final int rootTrgInx = m_root.getEdgeTargetIndex(rootEdgeInx);
+ final boolean edgeDirected = m_root.isEdgeDirected(rootEdgeInx);
+ int nativeSrcInx = m_rootToNativeNodeInxMap.get(~rootSrcInx);
+
+ if (nativeSrcInx < 0) {
+ nativeSrcInx = m_graph.nodeCreate();
+ m_rootToNativeNodeInxMap.put(~rootSrcInx, nativeSrcInx);
+ m_nativeToRootNodeInxMap.setIntAtIndex(rootSrcInx, nativeSrcInx);
+ }
+
+ int nativeTrgInx = m_rootToNativeNodeInxMap.get(~rootTrgInx);
+
+ if (nativeTrgInx < 0) {
+ nativeTrgInx = m_graph.nodeCreate();
+ m_rootToNativeNodeInxMap.put(~rootTrgInx, nativeTrgInx);
+ m_nativeToRootNodeInxMap.setIntAtIndex(rootTrgInx, nativeTrgInx);
+ }
+
+ final int nativeEdgeInx = m_graph.edgeCreate(nativeSrcInx, nativeTrgInx,
+ edgeDirected);
+ m_rootToNativeEdgeInxMap.put(~rootEdgeInx, nativeEdgeInx);
+ m_nativeToRootEdgeInxMap.setIntAtIndex(rootEdgeInx, nativeEdgeInx);
+ } else {
+ throw new IllegalArgumentException("edge with index " + rootEdgeInx
+ + " not in RootGraph");
+ }
+ }
+
+ m_root.addRootGraphChangeListener(m_changeSniffer);
+ }
+
+ // Cannot have any recursize reference to a FGraphPerspective in this
+ // object instance - we want to allow garbage collection of unused
+ // GraphPerspective objects.
+ private final static class RootGraphChangeSniffer implements RootGraphChangeListener {
+ private final GraphWeeder m_weeder;
+
+ private RootGraphChangeSniffer(GraphWeeder weeder) {
+ m_weeder = weeder;
+ }
+
+ public final void rootGraphChanged(RootGraphChangeEvent evt) {
+ if ((evt.getType() & RootGraphChangeEvent.NODES_REMOVED_TYPE) != 0) {
+ m_weeder.hideNodes(evt.getSource(), evt.getRemovedNodes());
+ }
+
+ if ((evt.getType() & RootGraphChangeEvent.EDGES_REMOVED_TYPE) != 0) {
+ m_weeder.hideEdges(evt.getSource(), evt.getRemovedEdges());
+ }
+ }
+ }
+
+ // An instance of this class cannot have any recursive reference to a
+ // FGraphPerspective object. The idea behind this class is to allow
+ // garbage collection of unused GraphPerspective objects. This class
+ // is used by the RootGraphChangeSniffer to remove nodes/edges from
+ // a GraphPerspective; this class is also used by this GraphPerspective
+ // implementation itself.
+ private final static class GraphWeeder {
+ private final RootGraph m_root;
+ private final DynamicGraph m_graph;
+ private final IntArray m_nativeToRootNodeInxMap;
+ private final IntArray m_nativeToRootEdgeInxMap;
+ private final IntIntHash m_rootToNativeNodeInxMap;
+ private final IntIntHash m_rootToNativeEdgeInxMap;
+
+ // This is an array of length 1 - we need an array as an extra reference
+ // to a reference because the surrounding GraphPerspective will be
+ // modifying the entry at index 0 in this array.
+ private final GraphPerspectiveChangeListener[] m_lis;
+
+ // This is a utilitarian heap that is used as a bucket of ints.
+ // Don't forget to empty() it before using it.
+ private final MinIntHeap m_heap;
+
+ private GraphWeeder(RootGraph root, DynamicGraph graph, IntArray nativeToRootNodeInxMap,
+ IntArray nativeToRootEdgeInxMap, IntIntHash rootToNativeNodeInxMap,
+ IntIntHash rootToNativeEdgeInxMap,
+ GraphPerspectiveChangeListener[] listener, MinIntHeap heap) {
+ m_root = root;
+ m_graph = graph;
+ m_nativeToRootNodeInxMap = nativeToRootNodeInxMap;
+ m_nativeToRootEdgeInxMap = nativeToRootEdgeInxMap;
+ m_rootToNativeNodeInxMap = rootToNativeNodeInxMap;
+ m_rootToNativeEdgeInxMap = rootToNativeEdgeInxMap;
+ m_lis = listener;
+ m_heap = heap;
+ }
+
+ // RootGraphChangeSniffer is not to call this method. We rely on
+ // the specified node still existing in the RootGraph in this method.
+ private final int hideNode(GraphPerspective source, int rootGraphNodeInx) {
+ // first see if we can hide the node
+ final int returnThis = canHideNode(rootGraphNodeInx);
+
+ // then notify everyone that we will be hiding nodes
+ if (returnThis != 0) {
+ final GraphPerspectiveChangeListener listener = m_lis[0];
+
+ if (listener != null) {
+ final Node removedNode = m_root.getNode(rootGraphNodeInx);
+ listener.graphPerspectiveChanged(new GraphPerspectiveNodesHiddenEvent(source,
+ new Node[] {
+ removedNode
+ }));
+ }
+
+ // now actually hide it
+ actuallyHideNode(source, rootGraphNodeInx);
+ }
+
+ return returnThis;
+ }
+
+ // Don't call this method from outside this inner class.
+ // Returns 0 if and only if hiding this node will fail.
+ // Otherwise returns the root node index.
+ private int canHideNode(final int rootGraphNodeInx) {
+ if (!(rootGraphNodeInx < 0)) {
+ return 0;
+ }
+
+ final int nativeNodeIndex = m_rootToNativeNodeInxMap.get(~rootGraphNodeInx);
+
+ if (nativeNodeIndex < 0) {
+ return 0;
+ }
+
+ final IntEnumerator nativeEdgeInxEnum = m_graph.edgesAdjacent(nativeNodeIndex, true,
+ true, true);
+
+ if (nativeEdgeInxEnum == null) {
+ return 0;
+ }
+
+ return rootGraphNodeInx;
+ }
+
+ //
+ // This method should ONLY be called AFTER
+ // canHideNode(index) has been called!!!!
+ //
+ // If this method fails, it will throw an exception.
+ // Otherwise, assume everything is copacetic.
+ private void actuallyHideNode(Object source, final int rootGraphNodeInx) {
+ final int nativeNodeIndex = m_rootToNativeNodeInxMap.get(~rootGraphNodeInx);
+ final IntEnumerator nativeEdgeInxEnum = m_graph.edgesAdjacent(nativeNodeIndex, true,
+ true, true);
+
+ if (nativeEdgeInxEnum.numRemaining() > 0) {
+ final Edge[] edgeRemoveArr = new Edge[nativeEdgeInxEnum.numRemaining()];
+
+ for (int i = 0; i < edgeRemoveArr.length; i++) {
+ final int rootGraphEdgeInx = m_nativeToRootEdgeInxMap.getIntAtIndex(nativeEdgeInxEnum
+ .nextInt());
+ // The edge returned by the RootGraph won't be null even if this
+ // hideNode operation is triggered by a node being removed from
+ // the underlying RootGraph - this is because when a node is removed
+ // from an underlying RootGraph, all touching edges to that node are
+ // removed first from that RootGraph, and corresponding edge removal
+ // events are fired before the node removal event is fired.
+ edgeRemoveArr[i] = m_root.getEdge(rootGraphEdgeInx);
+ }
+
+ hideEdges(source, edgeRemoveArr);
+ }
+
+ // nativeNodeIndex tested for validity with adjacentEdges() above.
+ if (m_graph.nodeRemove(nativeNodeIndex)) {
+ m_rootToNativeNodeInxMap.put(~rootGraphNodeInx, Integer.MAX_VALUE);
+ m_nativeToRootNodeInxMap.setIntAtIndex(0, nativeNodeIndex);
+ } else {
+ throw new IllegalStateException("internal error - node didn't exist, its adjacent edges did");
+ }
+ }
+
+ // This heap is to be used directly only by
+ // hideNodes(GraphPerspective, int[]) and by hideNodes(Object, Node[]).
+ private final MinIntHeap m_heap_hideNodes = new MinIntHeap();
+
+ // RootGraphChangeSniffer is not to call this method. We rely on
+ // the specified nodes still existing in the RootGraph in this method.
+ private final int[] hideNodes(GraphPerspective source, int[] rootNodeInx) {
+ // We can't use m_heap here because it's potentially used by every
+ // actuallHideNode() during hiding of edges.
+ m_heap_hideNodes.empty();
+
+ final MinIntHeap successes = m_heap_hideNodes;
+ final int[] returnThis = new int[rootNodeInx.length];
+
+ // check which nodes we can actually hide
+ for (int i = 0; i < rootNodeInx.length; i++) {
+ returnThis[i] = canHideNode(rootNodeInx[i]);
+
+ if (returnThis[i] != 0) {
+ successes.toss(i);
+ }
+ }
+
+ // notify everyone of the node we're about to hide
+ if (successes.size() > 0) {
+ final GraphPerspectiveChangeListener listener = m_lis[0];
+
+ if (listener != null) {
+ final Node[] successArr = new Node[successes.size()];
+ final IntEnumerator enumx = successes.elements();
+ int index = -1;
+
+ while (enumx.numRemaining() > 0)
+ successArr[++index] = m_root.getNode(rootNodeInx[enumx.nextInt()]);
+
+ listener.graphPerspectiveChanged(new GraphPerspectiveNodesHiddenEvent(source,
+ successArr));
+ }
+ }
+
+ // now actually hide nodes
+ final IntEnumerator successEnum = successes.elements();
+
+ while (successEnum.numRemaining() > 0)
+ actuallyHideNode(source, rootNodeInx[successEnum.nextInt()]);
+
+ return returnThis;
+ }
+
+ // Entries in the nodes array may not be null.
+ // This method is to be called by RootGraphChangeSniffer. It may also
+ // be called by others - therefore don't assume that the nodes to be
+ // hidden here don't have any adjacent edges.
+ private final void hideNodes(Object source, Node[] nodes) {
+ // We can't use m_heap here because it's potentially used by every
+ // actuallyHideNode() during hiding of edges.
+ m_heap_hideNodes.empty();
+
+ final MinIntHeap successes = m_heap_hideNodes;
+
+ // check to see if we can hide the nodes
+ for (int i = 0; i < nodes.length; i++) {
+ if (canHideNode(nodes[i].getRootGraphIndex()) != 0) {
+ successes.toss(i);
+ }
+ }
+
+ // notify everyone of the nodes about to be hidden
+ if (successes.size() > 0) {
+ final GraphPerspectiveChangeListener listener = m_lis[0];
+
+ if (listener != null) {
+ final Node[] successArr = new Node[successes.size()];
+ final IntEnumerator enumx = successes.elements();
+ int index = -1;
+
+ while (enumx.numRemaining() > 0)
+ successArr[++index] = nodes[enumx.nextInt()];
+
+ listener.graphPerspectiveChanged(new GraphPerspectiveNodesHiddenEvent(source,
+ successArr));
+ }
+
+ // now actually hide the nodes
+ final IntEnumerator successEnum = successes.elements();
+
+ while (successEnum.numRemaining() > 0)
+ actuallyHideNode(source, nodes[successEnum.nextInt()].getRootGraphIndex());
+ }
+ }
+
+ // RootGraphChangeSniffer is not to call this method. We rely on
+ // the specified edge still existing in the RootGraph in this method.
+ private final int hideEdge(GraphPerspective source, int rootGraphEdgeInx) {
+ // see if we can hide the edge
+ final int returnThis = canHideEdge(rootGraphEdgeInx);
+
+ if (returnThis != 0) {
+ final GraphPerspectiveChangeListener listener = m_lis[0];
+
+ // notify listeners of edge about to be hidden
+ if (listener != null) {
+ final Edge removedEdge = m_root.getEdge(rootGraphEdgeInx);
+ listener.graphPerspectiveChanged(new GraphPerspectiveEdgesHiddenEvent(source,
+ new Edge[] {
+ removedEdge
+ }));
+ }
+
+ // hide the edge
+ actuallyHideEdge(rootGraphEdgeInx);
+ }
+
+ return returnThis;
+ }
+
+ // Don't call this method from outside this inner class.
+ // Returns 0 if and only if we're actually able to hide an edge.
+ // Otherwise returns the root edge index.
+ private int canHideEdge(int rootGraphEdgeInx) {
+ if (!(rootGraphEdgeInx < 0)) {
+ return 0;
+ }
+
+ final int nativeEdgeIndex = m_rootToNativeEdgeInxMap.get(~rootGraphEdgeInx);
+
+ if ((nativeEdgeIndex < 0) || (nativeEdgeIndex == Integer.MAX_VALUE)) {
+ return 0;
+ }
+
+ return rootGraphEdgeInx;
+ }
+
+ //
+ // This method should ONLY be called AFTER
+ // canHideEdge(index) has been called!!!!
+ //
+ // If this method fails, it will throw an exception.
+ // Otherwise, assume everything is copacetic.
+ private void actuallyHideEdge(int rootGraphEdgeInx) {
+ final int nativeEdgeIndex = m_rootToNativeEdgeInxMap.get(~rootGraphEdgeInx);
+
+ if (m_graph.edgeRemove(nativeEdgeIndex)) {
+ m_rootToNativeEdgeInxMap.put(~rootGraphEdgeInx, Integer.MAX_VALUE);
+ m_nativeToRootEdgeInxMap.setIntAtIndex(0, nativeEdgeIndex);
+ } else {
+ throw new IllegalStateException("internal error - couldn't hide edge: "
+ + rootGraphEdgeInx);
+ }
+ }
+
+ // RootGraphChangeSniffer is not to call this method. We rely on
+ // the specified edges still existing in the RootGraph in this method.
+ private final int[] hideEdges(GraphPerspective source, int[] rootEdgeInx) {
+ m_heap.empty();
+
+ final MinIntHeap successes = m_heap;
+ final int[] returnThis = new int[rootEdgeInx.length];
+
+ // see if we can hide the edge
+ for (int i = 0; i < rootEdgeInx.length; i++) {
+ returnThis[i] = canHideEdge(rootEdgeInx[i]);
+
+ if (returnThis[i] != 0) {
+ successes.toss(i);
+ }
+ }
+
+ if (successes.size() > 0) {
+ final GraphPerspectiveChangeListener listener = m_lis[0];
+
+ // notify listeners of the edges about to be hidden
+ if (listener != null) {
+ final Edge[] successArr = new Edge[successes.size()];
+ final IntEnumerator enumx = successes.elements();
+ int index = -1;
+
+ while (enumx.numRemaining() > 0)
+ successArr[++index] = m_root.getEdge(rootEdgeInx[enumx.nextInt()]);
+
+ listener.graphPerspectiveChanged(new GraphPerspectiveEdgesHiddenEvent(source,
+ successArr));
+ }
+
+ // actually hide edges
+ final IntEnumerator successEnum = successes.elements();
+
+ while (successEnum.numRemaining() > 0)
+ actuallyHideEdge(rootEdgeInx[successEnum.nextInt()]);
+ }
+
+ return returnThis;
+ }
+
+ // Entries in the edges array may not be null.
+ // This method is to be called by RootGraphChangeSniffer.
+ private final void hideEdges(Object source, Edge[] edges) {
+ m_heap.empty();
+
+ final MinIntHeap successes = m_heap;
+
+ // check to see if we can hide edges
+ for (int i = 0; i < edges.length; i++) {
+ if (edges[i] == null)
+ continue;
+
+ if (canHideEdge(edges[i].getRootGraphIndex()) != 0)
+ successes.toss(i);
+ }
+
+ if (successes.size() > 0) {
+ final GraphPerspectiveChangeListener listener = m_lis[0];
+
+ // notify listeners
+ if (listener != null) {
+ final Edge[] successArr = new Edge[successes.size()];
+ final IntEnumerator enumx = successes.elements();
+ int index = -1;
+
+ while (enumx.numRemaining() > 0)
+ successArr[++index] = edges[enumx.nextInt()];
+
+ listener.graphPerspectiveChanged(new GraphPerspectiveEdgesHiddenEvent(source,
+ successArr));
+ }
+
+ // now actually hide edges
+ final IntEnumerator successEnum = successes.elements();
+
+ while (successEnum.numRemaining() > 0)
+ actuallyHideEdge(edges[successEnum.nextInt()].getRootGraphIndex());
+ }
+ }
+ }
+}
diff --git a/corelibs/fing/src/main/java/fing/model/FNode.java b/corelibs/fing/src/main/java/fing/model/FNode.java
new file mode 100644
index 0000000..eaea447
--- /dev/null
+++ b/corelibs/fing/src/main/java/fing/model/FNode.java
@@ -0,0 +1,138 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package fing.model;
+
+import giny.model.GraphPerspective;
+import giny.model.Node;
+import giny.model.RootGraph;
+
+
+// Package visible class.
+class FNode implements Node {
+ // Variables specific to public get/set methods.
+ RootGraph m_rootGraph = null;
+ int m_rootGraphIndex = 0;
+ String m_identifier = null;
+
+ // New feature in 2.7: Nexted Network
+ private GraphPerspective nextedNetwork;
+
+ // Package visible constructor.
+ FNode() {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public GraphPerspective getGraphPerspective() {
+ return m_rootGraph.createGraphPerspective(m_rootGraph.getNodeMetaChildIndicesArray(m_rootGraphIndex),
+ m_rootGraph.getEdgeMetaChildIndicesArray(m_rootGraphIndex));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param gp DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean setGraphPerspective(GraphPerspective gp) {
+ if (gp.getRootGraph() != m_rootGraph)
+ return false;
+
+ final int[] nodeInx = gp.getNodeIndicesArray();
+ final int[] edgeInx = gp.getEdgeIndicesArray();
+
+ for (int i = 0; i < nodeInx.length; i++)
+ m_rootGraph.addNodeMetaChild(m_rootGraphIndex, nodeInx[i]);
+
+ for (int i = 0; i < edgeInx.length; i++)
+ m_rootGraph.addEdgeMetaChild(m_rootGraphIndex, edgeInx[i]);
+
+ return true;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public RootGraph getRootGraph() {
+ return m_rootGraph;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getRootGraphIndex() {
+ return m_rootGraphIndex;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getIdentifier() {
+ return m_identifier;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param new_id DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean setIdentifier(String new_id) {
+ m_identifier = new_id;
+
+ return true;
+ }
+
+ public GraphPerspective getNestedNetwork() {
+ return nextedNetwork;
+ }
+
+ public void setNestedNetwork(GraphPerspective nextedNetwork) {
+ this.nextedNetwork = nextedNetwork;
+ }
+}
diff --git a/corelibs/fing/src/main/java/fing/model/FRootGraph.java b/corelibs/fing/src/main/java/fing/model/FRootGraph.java
new file mode 100644
index 0000000..f0605bc
--- /dev/null
+++ b/corelibs/fing/src/main/java/fing/model/FRootGraph.java
@@ -0,0 +1,2444 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package fing.model;
+
+import cytoscape.graph.dynamic.DynamicGraph;
+import cytoscape.graph.dynamic.util.DynamicGraphFactory;
+
+import cytoscape.util.intr.ArrayIntIterator;
+import cytoscape.util.intr.IntArray;
+import cytoscape.util.intr.IntEnumerator;
+import cytoscape.util.intr.IntHash;
+import cytoscape.util.intr.IntIntHash;
+import cytoscape.util.intr.IntIterator;
+import cytoscape.util.intr.IntIterator;
+import cytoscape.util.intr.IntStack;
+import cytoscape.util.intr.MinIntHeap;
+
+import giny.model.Edge;
+import giny.model.GraphPerspective;
+import giny.model.Node;
+import giny.model.RootGraph;
+import giny.model.RootGraphChangeEvent;
+import giny.model.RootGraphChangeListener;
+
+import java.util.Iterator;
+import java.util.NoSuchElementException;
+
+
+// Package visible class. Use factory to get instance.
+// This implementation of giny.model is safe to use with a single thread only.
+class FRootGraph implements RootGraph, DynamicGraph {
+ ////////////////////////////////////
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public IntEnumerator nodes() {
+ return m_graph.nodes();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public IntEnumerator edges() {
+ return m_graph.edges();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int nodeCreate() {
+ return ~createNode();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean nodeRemove(int node) {
+ return removeNode(~node) != 0;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param sourceNode DOCUMENT ME!
+ * @param targetNode DOCUMENT ME!
+ * @param directed DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int edgeCreate(int sourceNode, int targetNode, boolean directed) {
+ return ~createEdge(~sourceNode, ~targetNode, directed);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edge DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean edgeRemove(int edge) {
+ return removeEdge(~edge) != 0;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean nodeExists(int node) {
+ return m_graph.nodeExists(node);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edge DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public byte edgeType(int edge) {
+ return m_graph.edgeType(edge);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edge DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int edgeSource(int edge) {
+ return m_graph.edgeSource(edge);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edge DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int edgeTarget(int edge) {
+ return m_graph.edgeTarget(edge);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ * @param outgoing DOCUMENT ME!
+ * @param incoming DOCUMENT ME!
+ * @param undirected DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public IntEnumerator edgesAdjacent(int node, boolean outgoing, boolean incoming,
+ boolean undirected) {
+ return m_graph.edgesAdjacent(node, outgoing, incoming, undirected);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node0 DOCUMENT ME!
+ * @param node1 DOCUMENT ME!
+ * @param outgoing DOCUMENT ME!
+ * @param incoming DOCUMENT ME!
+ * @param undirected DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public IntIterator edgesConnecting(int node0, int node1, boolean outgoing, boolean incoming,
+ boolean undirected) {
+ return m_graph.edgesConnecting(node0, node1, outgoing, incoming, undirected);
+ }
+
+ //////////////////////////////////
+ // END: Implements DynamicGraph //
+ //////////////////////////////////
+
+ // Not specified by giny.model.RootGraph. GraphPerspective implementation
+ // in this package relies on this method.
+ // ATTENTION! Before making this method public you need to change the
+ // event implementations to return copied arrays in their methods instead
+ // of always returning the same array reference. Also you need to enable
+ // create node and create edge events - currently only remove node and
+ // remove edge events are fired.
+ void addRootGraphChangeListener(RootGraphChangeListener listener) { // This method is not thread safe; synchronize on an object to make it so.
+ m_lis = RootGraphChangeListenerChain.add(m_lis, listener);
+ }
+
+ // Not specified by giny.model.RootGraph. GraphPerspective implementation
+ // in this package relies on this method.
+ // ATTENTION! Before making this method public you need to change the
+ // event implementations to return copied arrays in their methods instead
+ // of always returning the same array reference. Also you need to enable
+ // create node and create edge events - currently only remove node and
+ // remove edge events are fired.
+ void removeRootGraphChangeListener(RootGraphChangeListener listener) { // This method is not thread safe; synchronize on an object to make it so.
+ m_lis = RootGraphChangeListenerChain.remove(m_lis, listener);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nodes DOCUMENT ME!
+ * @param edges DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public GraphPerspective createGraphPerspective(Node[] nodes, Edge[] edges) {
+ final Node[] nodeArr = ((nodes != null) ? nodes : new Node[0]);
+ final Edge[] edgeArr = ((edges != null) ? edges : new Edge[0]);
+ final RootGraph root = this;
+
+ try {
+ return new FGraphPerspective(this,
+ new IntIterator() {
+ private int index = 0;
+
+ public boolean hasNext() {
+ return index < nodeArr.length;
+ }
+
+ public int nextInt() {
+ if ((nodeArr[index] == null) || (nodeArr[index].getRootGraph() != root))
+ throw new IllegalArgumentException();
+
+ return nodeArr[index++].getRootGraphIndex();
+ }
+ },
+ new IntIterator() {
+ private int index = 0;
+
+ public boolean hasNext() {
+ return index < edgeArr.length;
+ }
+
+ public int nextInt() {
+ if ((edgeArr[index] == null) || (edgeArr[index].getRootGraph() != root))
+ throw new IllegalArgumentException();
+
+ return edgeArr[index++].getRootGraphIndex();
+ }
+ });
+ } catch (IllegalArgumentException exc) {
+ return null;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nodeInx DOCUMENT ME!
+ * @param edgeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public GraphPerspective createGraphPerspective(int[] nodeInx, int[] edgeInx) {
+ if (nodeInx == null)
+ nodeInx = new int[0];
+
+ if (edgeInx == null)
+ edgeInx = new int[0];
+
+ try {
+ return new FGraphPerspective(this, new ArrayIntIterator(nodeInx, 0, nodeInx.length),
+ new ArrayIntIterator(edgeInx, 0, edgeInx.length));
+ } catch (IllegalArgumentException exc) {
+ return null;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nodes DOCUMENT ME!
+ * @param edges DOCUMENT ME!
+ */
+ public void ensureCapacity(int nodes, int edges) {
+ System.out.println("The secret easter egg module has been activated.");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getNodeCount() {
+ return m_graph.nodes().numRemaining();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getEdgeCount() {
+ return m_graph.edges().numRemaining();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Iterator nodesIterator() {
+ final IntEnumerator nodes = m_graph.nodes();
+ final FRootGraph rootGraph = this;
+
+ return new Iterator() {
+ public void remove() {
+ throw new UnsupportedOperationException();
+ }
+
+ public boolean hasNext() {
+ return nodes.numRemaining() > 0;
+ }
+
+ public Object next() {
+ if (!hasNext())
+ throw new NoSuchElementException();
+
+ return rootGraph.getNode(~(nodes.nextInt()));
+ }
+ };
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public java.util.List nodesList() {
+ final int nodeCount = getNodeCount();
+ final java.util.ArrayList returnThis = new java.util.ArrayList(nodeCount);
+ Iterator iter = nodesIterator();
+
+ for (int i = 0; i < nodeCount; i++)
+ returnThis.add(iter.next());
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] getNodeIndicesArray() {
+ IntEnumerator nodes = m_graph.nodes();
+ final int[] returnThis = new int[nodes.numRemaining()];
+
+ for (int i = 0; i < returnThis.length; i++)
+ returnThis[i] = ~(nodes.nextInt());
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Iterator edgesIterator() {
+ final IntEnumerator edges = m_graph.edges();
+ final FRootGraph rootGraph = this;
+
+ return new Iterator() {
+ public void remove() {
+ throw new UnsupportedOperationException();
+ }
+
+ public boolean hasNext() {
+ return edges.numRemaining() > 0;
+ }
+
+ public Object next() {
+ if (!hasNext())
+ throw new NoSuchElementException();
+
+ return rootGraph.getEdge(~(edges.nextInt()));
+ }
+ };
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public java.util.List edgesList() {
+ final int edgeCount = getEdgeCount();
+ final java.util.ArrayList returnThis = new java.util.ArrayList(edgeCount);
+ Iterator iter = edgesIterator();
+
+ for (int i = 0; i < edgeCount; i++)
+ returnThis.add(iter.next());
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] getEdgeIndicesArray() {
+ IntEnumerator edges = m_graph.edges();
+ final int[] returnThis = new int[edges.numRemaining()];
+
+ for (int i = 0; i < returnThis.length; i++)
+ returnThis[i] = ~(edges.nextInt());
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Node removeNode(Node node) {
+ if ((node.getRootGraph() == this) && (removeNode(node.getRootGraphIndex()) != 0))
+ return node;
+ else
+
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nodeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int removeNode(final int nodeInx) {
+ final int nativeNodeInx = ~nodeInx;
+
+ if (!m_graph.nodeExists(nativeNodeInx))
+ return 0;
+
+ // BEGIN: Remove node from meta structure.
+ final int metaElement = m_nativeToMetaNodeInxMap.get(nativeNodeInx);
+
+ if (m_metaGraph.nodeExists(metaElement)) {
+ final MinIntHeap bucket = new MinIntHeap();
+ IntEnumerator nativeEdgeEnum = // Remove meta on touching native edges.
+ m_graph.edgesAdjacent(nativeNodeInx, true, true, true);
+
+ while (nativeEdgeEnum.numRemaining() > 0) {
+ final int nativeEdgeInx = nativeEdgeEnum.nextInt(); // To be deleted.
+ final int metaEdge = m_nativeToMetaEdgeInxMap.get(nativeEdgeInx);
+ IntEnumerator metaRelationships = // Must be wiped out.
+ m_metaGraph.edgesAdjacent(metaEdge, false, true,
+ false);
+
+ if (metaRelationships != null) { // Edge element exists in meta.
+ bucket.empty();
+
+ while (metaRelationships.numRemaining() > 0)
+ bucket.toss(metaRelationships.nextInt());
+
+ metaRelationships = bucket.elements();
+
+ while (metaRelationships.numRemaining() > 0) {
+ final int metaRelationship = metaRelationships.nextInt();
+ final int metaParent = m_metaGraph.edgeSource(metaRelationship);
+ m_metaGraph.edgeRemove(metaRelationship);
+
+ if (m_metaGraph.edgesAdjacent(metaParent, true, true, false).numRemaining() == 0) { // Remove disconnected meta-parent.
+
+ final int nativeNodeParent = m_metaToNativeInxMap.getIntAtIndex(metaParent)
+ - 1;
+ m_nativeToMetaNodeInxMap.put(nativeNodeParent, Integer.MAX_VALUE);
+ m_metaToNativeInxMap.setIntAtIndex(0, metaParent);
+ m_metaGraph.nodeRemove(metaParent);
+ }
+ }
+
+ m_nativeToMetaEdgeInxMap.put(nativeEdgeInx, Integer.MAX_VALUE);
+ m_metaToNativeInxMap.setIntAtIndex(0, metaEdge);
+ m_metaGraph.nodeRemove(metaEdge);
+ }
+ }
+
+ IntEnumerator metaRelationships = m_metaGraph.edgesAdjacent(metaElement, true, true,
+ false);
+ bucket.empty();
+
+ while (metaRelationships.numRemaining() > 0)
+ bucket.toss(metaRelationships.nextInt());
+
+ metaRelationships = bucket.elements();
+
+ while (metaRelationships.numRemaining() > 0) {
+ final int metaRelationship = metaRelationships.nextInt();
+ final int otherMetaElement = (metaElement
+ ^ m_metaGraph.edgeTarget(metaRelationship)
+ ^ m_metaGraph.edgeSource(metaRelationship));
+ m_metaGraph.edgeRemove(metaRelationship);
+
+ if (m_metaGraph.edgesAdjacent(otherMetaElement, true, true, false).numRemaining() == 0) { // Remove disconnected meta-element.
+
+ final int f = m_metaToNativeInxMap.getIntAtIndex(otherMetaElement);
+
+ if (f > 0)
+ m_nativeToMetaNodeInxMap.put(f - 1, Integer.MAX_VALUE);
+ else
+ m_nativeToMetaEdgeInxMap.put(~f, Integer.MAX_VALUE);
+
+ m_metaToNativeInxMap.setIntAtIndex(0, otherMetaElement);
+ m_metaGraph.nodeRemove(otherMetaElement);
+ }
+ }
+
+ m_nativeToMetaNodeInxMap.put(nativeNodeInx, Integer.MAX_VALUE);
+ m_metaToNativeInxMap.setIntAtIndex(0, metaElement);
+ m_metaGraph.nodeRemove(metaElement);
+ }
+
+ // END: Remove node from meta structure.
+ final IntEnumerator nativeEdgeEnum = m_graph.edgesAdjacent(nativeNodeInx, true, true, true);
+ final Edge[] removedEdgeArr = new Edge[nativeEdgeEnum.numRemaining()];
+
+ for (int i = 0; i < removedEdgeArr.length; i++)
+ removedEdgeArr[i] = m_edges.getEdgeAtIndex(nativeEdgeEnum.nextInt());
+
+ for (int i = 0; i < removedEdgeArr.length; i++) {
+ final int nativeEdgeInx = ~(removedEdgeArr[i].getRootGraphIndex());
+ m_graph.edgeRemove(nativeEdgeInx);
+
+ final Edge removedEdge = m_edges.getEdgeAtIndex(nativeEdgeInx);
+ m_edges.setEdgeAtIndex(null, nativeEdgeInx);
+ m_edgeDepot.recycleEdge(removedEdge);
+ }
+
+ final Node removedNode = m_nodes.getNodeAtIndex(nativeNodeInx);
+ m_graph.nodeRemove(nativeNodeInx);
+ m_nodes.setNodeAtIndex(null, nativeNodeInx);
+ m_nodeDepot.recycleNode(removedNode);
+
+ if (removedEdgeArr.length > 0)
+ m_lis.rootGraphChanged(new RootGraphEdgesRemovedEvent(this, removedEdgeArr));
+
+ m_lis.rootGraphChanged(new RootGraphNodesRemovedEvent(this, new Node[] { removedNode }));
+
+ return nodeInx;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nodes DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public java.util.List removeNodes(java.util.List nodes) {
+ final java.util.ArrayList returnThis = new java.util.ArrayList();
+
+ for (int i = 0; i < nodes.size(); i++)
+ if (removeNode((Node) nodes.get(i)) != null)
+ returnThis.add(nodes.get(i));
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nodeIndices DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] removeNodes(int[] nodeIndices) {
+ final int[] returnThis = new int[nodeIndices.length];
+
+ for (int i = 0; i < returnThis.length; i++)
+ returnThis[i] = removeNode(nodeIndices[i]);
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int createNode() {
+ final int nativeNodeInx = m_graph.nodeCreate();
+ final int returnThis = ~nativeNodeInx;
+ Node newNode = m_nodeDepot.getNode(this, returnThis, null);
+ m_nodes.setNodeAtIndex(newNode, nativeNodeInx);
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nodes DOCUMENT ME!
+ * @param edges DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int createNode(Node[] nodes, Edge[] edges) {
+ // I don't care how inefficient this is because I don't like meta nodes.
+ final GraphPerspective persp = createGraphPerspective(nodes, edges);
+
+ if (persp == null)
+ return 0;
+
+ return createNode(persp);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param perspective DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int createNode(GraphPerspective perspective) {
+ // Casting to check that we aren't going to get garbage nodes and edges.
+ if (((FGraphPerspective) perspective).getRootGraph() != this)
+ return 0;
+
+ final int returnThis = createNode();
+ final int nativeParentNodeInx = ~returnThis;
+ final int[] perspEdgeInxArr = perspective.getEdgeIndicesArray();
+ final int[] perspNodeInxArr = perspective.getNodeIndicesArray();
+
+ if ((perspEdgeInxArr.length == 0) && (perspNodeInxArr.length == 0))
+ return returnThis;
+
+ final int metaParentNodeInx = m_metaGraph.nodeCreate();
+ m_metaToNativeInxMap.setIntAtIndex(nativeParentNodeInx + 1, metaParentNodeInx);
+ m_nativeToMetaNodeInxMap.put(nativeParentNodeInx, metaParentNodeInx);
+
+ for (int i = 0; i < perspNodeInxArr.length; i++) {
+ final int nativeChildNodeInx = ~perspNodeInxArr[i];
+ int metaChildNodeInx = m_nativeToMetaNodeInxMap.get(nativeChildNodeInx);
+
+ if ((metaChildNodeInx < 0) || (metaChildNodeInx == Integer.MAX_VALUE)) {
+ metaChildNodeInx = m_metaGraph.nodeCreate();
+ m_metaToNativeInxMap.setIntAtIndex(nativeChildNodeInx + 1, metaChildNodeInx);
+ m_nativeToMetaNodeInxMap.put(nativeChildNodeInx, metaChildNodeInx);
+ }
+
+ // This edge can't yet exist because we just created metaParentNodeInx.
+ m_metaGraph.edgeCreate(metaParentNodeInx, metaChildNodeInx, true);
+ }
+
+ for (int i = 0; i < perspEdgeInxArr.length; i++) {
+ final int nativeChildEdgeInx = ~perspEdgeInxArr[i];
+ int metaChildEdgeInx = m_nativeToMetaEdgeInxMap.get(nativeChildEdgeInx);
+
+ if ((metaChildEdgeInx < 0) || (metaChildEdgeInx == Integer.MAX_VALUE)) {
+ metaChildEdgeInx = m_metaGraph.nodeCreate();
+ m_metaToNativeInxMap.setIntAtIndex(~nativeChildEdgeInx, metaChildEdgeInx);
+ m_nativeToMetaEdgeInxMap.put(nativeChildEdgeInx, metaChildEdgeInx);
+ }
+
+ // This edge can't yet exist because we just created metaParentNodeInx.
+ m_metaGraph.edgeCreate(metaParentNodeInx, metaChildEdgeInx, true);
+ }
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nodeIndices DOCUMENT ME!
+ * @param edgeIndices DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int createNode(int[] nodeIndices, int[] edgeIndices) {
+ // I don't care how inefficient this is because I don't like meta nodes.
+ final GraphPerspective persp = createGraphPerspective(nodeIndices, edgeIndices);
+
+ if (persp == null)
+ return 0;
+
+ return createNode(persp);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param numNewNodes DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] createNodes(int numNewNodes) {
+ final int[] returnThis = new int[numNewNodes];
+
+ for (int i = 0; i < returnThis.length; i++)
+ returnThis[i] = createNode();
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edge DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Edge removeEdge(Edge edge) {
+ if ((edge.getRootGraph() == this) && (removeEdge(edge.getRootGraphIndex()) != 0))
+ return edge;
+ else
+
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edgeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int removeEdge(final int edgeInx) {
+ final int nativeEdgeInx = ~edgeInx;
+
+ if (m_graph.edgeType(nativeEdgeInx) < 0)
+ return 0;
+
+ // BEGIN: Remove edge from meta structure.
+ final int metaEdge = m_nativeToMetaEdgeInxMap.get(nativeEdgeInx);
+
+ if (m_metaGraph.nodeExists(metaEdge)) {
+ final MinIntHeap bucket = new MinIntHeap();
+ IntEnumerator metaRelationships = m_metaGraph.edgesAdjacent(metaEdge, false, true, false);
+
+ while (metaRelationships.numRemaining() > 0)
+ bucket.toss(metaRelationships.nextInt());
+
+ metaRelationships = bucket.elements();
+
+ while (metaRelationships.numRemaining() > 0) {
+ final int metaRelationship = metaRelationships.nextInt();
+ final int metaParent = m_metaGraph.edgeSource(metaRelationship);
+ m_metaGraph.edgeRemove(metaRelationship);
+
+ if (m_metaGraph.edgesAdjacent(metaParent, true, true, false).numRemaining() == 0) { // Remove disconnected meta-element.
+
+ final int nativeNodeParent = m_metaToNativeInxMap.getIntAtIndex(metaParent) - 1;
+ m_nativeToMetaNodeInxMap.put(nativeNodeParent, Integer.MAX_VALUE);
+ m_metaToNativeInxMap.setIntAtIndex(0, metaParent);
+ m_metaGraph.nodeRemove(metaParent);
+ }
+ }
+
+ m_nativeToMetaEdgeInxMap.put(nativeEdgeInx, Integer.MAX_VALUE);
+ m_metaToNativeInxMap.setIntAtIndex(0, metaEdge);
+ m_metaGraph.nodeRemove(metaEdge);
+ }
+
+ // END: Remove edge from meta structure.
+ m_graph.edgeRemove(nativeEdgeInx);
+
+ final Edge removedEdge = m_edges.getEdgeAtIndex(nativeEdgeInx);
+ m_edges.setEdgeAtIndex(null, nativeEdgeInx);
+ m_edgeDepot.recycleEdge(removedEdge);
+ m_lis.rootGraphChanged(new RootGraphEdgesRemovedEvent(this, new Edge[] { removedEdge }));
+
+ return edgeInx;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edges DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public java.util.List removeEdges(java.util.List edges) {
+ final java.util.ArrayList returnThis = new java.util.ArrayList();
+
+ for (int i = 0; i < edges.size(); i++)
+ if (removeEdge((Edge) edges.get(i)) != null)
+ returnThis.add(edges.get(i));
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edgeIndices DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] removeEdges(int[] edgeIndices) {
+ final int[] returnThis = new int[edgeIndices.length];
+
+ for (int i = 0; i < returnThis.length; i++)
+ returnThis[i] = removeEdge(edgeIndices[i]);
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param source DOCUMENT ME!
+ * @param target DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int createEdge(Node source, Node target) {
+ return createEdge(source, target, source.getRootGraphIndex() != target.getRootGraphIndex());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param source DOCUMENT ME!
+ * @param target DOCUMENT ME!
+ * @param directed DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int createEdge(Node source, Node target, boolean directed) {
+ if ((source.getRootGraph() == this) && (target.getRootGraph() == this))
+ return createEdge(source.getRootGraphIndex(), target.getRootGraphIndex(), directed);
+ else
+
+ return 0;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param sourceNodeIndex DOCUMENT ME!
+ * @param targetNodeIndex DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int createEdge(int sourceNodeIndex, int targetNodeIndex) {
+ return createEdge(sourceNodeIndex, targetNodeIndex, sourceNodeIndex != targetNodeIndex);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param sourceNodeIndex DOCUMENT ME!
+ * @param targetNodeIndex DOCUMENT ME!
+ * @param directed DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int createEdge(int sourceNodeIndex, int targetNodeIndex, boolean directed) {
+ final int nativeEdgeInx = m_graph.edgeCreate(~sourceNodeIndex, ~targetNodeIndex, directed);
+
+ if (nativeEdgeInx < 0)
+ return 0;
+
+ final int returnThis = ~nativeEdgeInx;
+ Edge newEdge = m_edgeDepot.getEdge(this, returnThis, null);
+ m_edges.setEdgeAtIndex(newEdge, nativeEdgeInx);
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param sourceNodeIndices DOCUMENT ME!
+ * @param targetNodeIndices DOCUMENT ME!
+ * @param directed DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] createEdges(int[] sourceNodeIndices, int[] targetNodeIndices, boolean directed) {
+ if (sourceNodeIndices.length != targetNodeIndices.length)
+ throw new IllegalArgumentException("input arrays not same length");
+
+ final int[] returnThis = new int[sourceNodeIndices.length];
+
+ for (int i = 0; i < returnThis.length; i++)
+ returnThis[i] = createEdge(sourceNodeIndices[i], targetNodeIndices[i], directed);
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean containsNode(Node node) {
+ return (node.getRootGraph() == this) && (getNode(node.getRootGraphIndex()) != null);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edge DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean containsEdge(Edge edge) {
+ return (edge.getRootGraph() == this) && (getEdge(edge.getRootGraphIndex()) != null);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public java.util.List neighborsList(Node node) {
+ if (node.getRootGraph() == this) {
+ final int nodeIndex = node.getRootGraphIndex();
+ int[] adjacentEdgeIndices = getAdjacentEdgeIndicesArray(nodeIndex, true, true, true);
+
+ if (adjacentEdgeIndices == null)
+ return null;
+
+ m_hash.empty();
+
+ final IntHash neighbors = m_hash;
+
+ for (int i = 0; i < adjacentEdgeIndices.length; i++) {
+ int neighborIndex = (nodeIndex ^ getEdgeSourceIndex(adjacentEdgeIndices[i])
+ ^ getEdgeTargetIndex(adjacentEdgeIndices[i]));
+ neighbors.put(~neighborIndex);
+ }
+
+ IntEnumerator enumx = neighbors.elements();
+ java.util.ArrayList list = new java.util.ArrayList(enumx.numRemaining());
+
+ while (enumx.numRemaining() > 0)
+ list.add(getNode(~(enumx.nextInt())));
+
+ return list;
+ } else {
+ return null;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param a DOCUMENT ME!
+ * @param b DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isNeighbor(Node a, Node b) {
+ if ((a.getRootGraph() == this) && (b.getRootGraph() == this))
+ return isNeighbor(a.getRootGraphIndex(), b.getRootGraphIndex());
+ else
+
+ return false;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nodeInxA DOCUMENT ME!
+ * @param nodeInxB DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isNeighbor(int nodeInxA, int nodeInxB) {
+ final IntIterator connectingEdges = m_graph.edgesConnecting(~nodeInxA, ~nodeInxB, true,
+ true, true);
+
+ if (connectingEdges == null)
+ return false;
+
+ return connectingEdges.hasNext();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param from DOCUMENT ME!
+ * @param to DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean edgeExists(Node from, Node to) {
+ if ((from.getRootGraph() == this) && (to.getRootGraph() == this))
+ return edgeExists(from.getRootGraphIndex(), to.getRootGraphIndex());
+ else
+
+ return false;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param fromNodeInx DOCUMENT ME!
+ * @param toNodeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean edgeExists(int fromNodeInx, int toNodeInx) {
+ final IntIterator connectingEdges = m_graph.edgesConnecting(~fromNodeInx, ~toNodeInx, true,
+ false, true);
+
+ if (connectingEdges == null)
+ return false;
+
+ return connectingEdges.hasNext();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param from DOCUMENT ME!
+ * @param to DOCUMENT ME!
+ * @param countUndirectedEdges DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getEdgeCount(Node from, Node to, boolean countUndirectedEdges) {
+ if ((from.getRootGraph() == this) && (to.getRootGraph() == this))
+ return getEdgeCount(from.getRootGraphIndex(), to.getRootGraphIndex(),
+ countUndirectedEdges);
+ else
+
+ return -1;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param fromNodeInx DOCUMENT ME!
+ * @param toNodeInx DOCUMENT ME!
+ * @param countUndirectedEdges DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getEdgeCount(int fromNodeInx, int toNodeInx, boolean countUndirectedEdges) {
+ final int[] connEdges = getEdgeIndicesArray(fromNodeInx, toNodeInx, countUndirectedEdges);
+
+ if (connEdges == null)
+ return -1;
+ else
+
+ return connEdges.length;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nodeInx DOCUMENT ME!
+ * @param undirected DOCUMENT ME!
+ * @param incomingDirected DOCUMENT ME!
+ * @param outgoingDirected DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] getAdjacentEdgeIndicesArray(int nodeInx, boolean undirected,
+ boolean incomingDirected, boolean outgoingDirected) {
+ final IntEnumerator adj = m_graph.edgesAdjacent(~nodeInx, outgoingDirected,
+ incomingDirected, undirected);
+
+ if (adj == null)
+ return null;
+
+ final int[] returnThis = new int[adj.numRemaining()];
+
+ for (int i = 0; i < returnThis.length; i++)
+ returnThis[i] = ~adj.nextInt();
+
+ return returnThis;
+ }
+
+ private final IntHash m_hash2 = new IntHash();
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nodeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] getConnectingEdgeIndicesArray(int[] nodeInx) {
+ m_hash2.empty();
+
+ final IntHash nodeBucket = m_hash2;
+
+ for (int i = 0; i < nodeInx.length; i++) {
+ final int positiveNodeIndex = ~nodeInx[i];
+
+ if (m_graph.nodeExists(positiveNodeIndex))
+ nodeBucket.put(positiveNodeIndex);
+ else
+
+ return null;
+ }
+
+ m_hash.empty();
+
+ final IntHash edgeBucket = m_hash;
+ final IntEnumerator nodeIter = nodeBucket.elements();
+
+ while (nodeIter.numRemaining() > 0) {
+ final int thePositiveNode = nodeIter.nextInt();
+ final IntEnumerator edgeIter = m_graph.edgesAdjacent(thePositiveNode, true, false, true);
+
+ while (edgeIter.numRemaining() > 0) {
+ final int candidateEdge = edgeIter.nextInt();
+ final int otherEdgeNode = (thePositiveNode ^ m_graph.edgeSource(candidateEdge)
+ ^ m_graph.edgeTarget(candidateEdge));
+
+ if (otherEdgeNode == nodeBucket.get(otherEdgeNode))
+ edgeBucket.put(candidateEdge);
+ }
+ }
+
+ final IntEnumerator returnEdges = edgeBucket.elements();
+ final int[] returnThis = new int[returnEdges.numRemaining()];
+
+ for (int i = 0; i < returnThis.length; i++)
+ returnThis[i] = ~(returnEdges.nextInt());
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edgeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] getConnectingNodeIndicesArray(int[] edgeInx) {
+ m_hash.empty();
+
+ final IntHash nodeBucket = m_hash;
+
+ for (int i = 0; i < edgeInx.length; i++) {
+ final int positiveEdge = ~edgeInx[i];
+
+ if (m_graph.edgeType(positiveEdge) >= 0) {
+ nodeBucket.put(m_graph.edgeSource(positiveEdge));
+ nodeBucket.put(m_graph.edgeTarget(positiveEdge));
+ } else {
+ return null;
+ }
+ }
+
+ final IntEnumerator nodes = nodeBucket.elements();
+ final int[] returnThis = new int[nodes.numRemaining()];
+
+ for (int i = 0; i < returnThis.length; i++)
+ returnThis[i] = ~(nodes.nextInt());
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param fromNodeInx DOCUMENT ME!
+ * @param toNodeInx DOCUMENT ME!
+ * @param undirectedEdges DOCUMENT ME!
+ * @param bothDirections DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] getEdgeIndicesArray(int fromNodeInx, int toNodeInx, boolean undirectedEdges,
+ boolean bothDirections) {
+ final IntIterator connectingEdges = m_graph.edgesConnecting(~fromNodeInx, ~toNodeInx, true,
+ bothDirections, undirectedEdges);
+
+ if (connectingEdges == null)
+ return null;
+
+ m_heap.empty();
+
+ final MinIntHeap edgeBucket = m_heap;
+
+ while (connectingEdges.hasNext())
+ edgeBucket.toss(~connectingEdges.nextInt());
+
+ final int[] returnThis = new int[edgeBucket.size()];
+ edgeBucket.copyInto(returnThis, 0);
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param from DOCUMENT ME!
+ * @param to DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public java.util.List edgesList(Node from, Node to) {
+ if ((from.getRootGraph() == this) && (to.getRootGraph() == this))
+ return edgesList(from.getRootGraphIndex(), to.getRootGraphIndex(), true);
+ else
+
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param fromNodeInx DOCUMENT ME!
+ * @param toNodeInx DOCUMENT ME!
+ * @param includeUndirectedEdges DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public java.util.List edgesList(int fromNodeInx, int toNodeInx, boolean includeUndirectedEdges) {
+ final int[] edgeInx = getEdgeIndicesArray(fromNodeInx, toNodeInx, includeUndirectedEdges);
+
+ if (edgeInx == null)
+ return null;
+
+ java.util.ArrayList returnList = new java.util.ArrayList(edgeInx.length);
+
+ for (int i = 0; i < edgeInx.length; i++)
+ returnList.add(getEdge(edgeInx[i]));
+
+ return returnList;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param fromNodeInx DOCUMENT ME!
+ * @param toNodeInx DOCUMENT ME!
+ * @param includeUndirectedEdges DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] getEdgeIndicesArray(int fromNodeInx, int toNodeInx, boolean includeUndirectedEdges) {
+ return getEdgeIndicesArray(fromNodeInx, toNodeInx, includeUndirectedEdges, false);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getInDegree(Node node) {
+ if (node.getRootGraph() == this)
+ return getInDegree(node.getRootGraphIndex());
+ else
+
+ return -1;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nodeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getInDegree(int nodeInx) {
+ return getInDegree(nodeInx, true);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ * @param countUndirectedEdges DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getInDegree(Node node, boolean countUndirectedEdges) {
+ if (node.getRootGraph() == this)
+ return getInDegree(node.getRootGraphIndex(), countUndirectedEdges);
+ else
+
+ return -1;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nodeInx DOCUMENT ME!
+ * @param countUndirectedEdges DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getInDegree(int nodeInx, boolean countUndirectedEdges) {
+ final IntEnumerator adj = m_graph.edgesAdjacent(~nodeInx, false, true, countUndirectedEdges);
+
+ if (adj == null)
+ return -1;
+
+ return adj.numRemaining();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getOutDegree(Node node) {
+ if (node.getRootGraph() == this)
+ return getOutDegree(node.getRootGraphIndex());
+ else
+
+ return -1;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nodeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getOutDegree(int nodeInx) {
+ return getOutDegree(nodeInx, true);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ * @param countUndirectedEdges DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getOutDegree(Node node, boolean countUndirectedEdges) {
+ if (node.getRootGraph() == this)
+ return getOutDegree(node.getRootGraphIndex(), countUndirectedEdges);
+ else
+
+ return -1;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nodeInx DOCUMENT ME!
+ * @param countUndirectedEdges DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getOutDegree(int nodeInx, boolean countUndirectedEdges) {
+ final IntEnumerator adj = m_graph.edgesAdjacent(~nodeInx, true, false, countUndirectedEdges);
+
+ if (adj == null)
+ return -1;
+
+ return adj.numRemaining();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getDegree(Node node) {
+ if (node.getRootGraph() == this)
+ return getDegree(node.getRootGraphIndex());
+ else
+
+ return -1;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nodeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getDegree(int nodeInx) {
+ final IntEnumerator adj = m_graph.edgesAdjacent(~nodeInx, true, true, true);
+
+ if (adj == null)
+ return -1;
+
+ return adj.numRemaining();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getIndex(Node node) {
+ if (node.getRootGraph() == this)
+ return node.getRootGraphIndex();
+ else
+
+ return 0;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nodeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Node getNode(int nodeInx) {
+ if ((nodeInx < 0) && (nodeInx != 0x80000000))
+ return m_nodes.getNodeAtIndex(~nodeInx);
+ else
+
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edge DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getIndex(Edge edge) {
+ if (edge.getRootGraph() == this)
+ return edge.getRootGraphIndex();
+ else
+
+ return 0;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edgeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Edge getEdge(int edgeInx) {
+ if ((edgeInx < 0) && (edgeInx != 0x80000000))
+ return m_edges.getEdgeAtIndex(~edgeInx);
+ else
+
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edgeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getEdgeSourceIndex(int edgeInx) {
+ return ~(m_graph.edgeSource(~edgeInx));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edgeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getEdgeTargetIndex(int edgeInx) {
+ return ~(m_graph.edgeTarget(~edgeInx));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edgeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isEdgeDirected(int edgeInx) {
+ return m_graph.edgeType(~edgeInx) == 1;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param parent DOCUMENT ME!
+ * @param child DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean addMetaChild(Node parent, Node child) {
+ if ((parent.getRootGraph() != this) || (child.getRootGraph() != this))
+ return false;
+
+ return addNodeMetaChild(parent.getRootGraphIndex(), child.getRootGraphIndex());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param parentNodeInx DOCUMENT ME!
+ * @param childNodeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean addNodeMetaChild(int parentNodeInx, int childNodeInx) {
+ final int nativeParent = ~parentNodeInx;
+ final int nativeChildNode = ~childNodeInx;
+
+ if (!(m_graph.nodeExists(nativeParent) && m_graph.nodeExists(nativeChildNode)))
+ return false;
+
+ int metaParent = m_nativeToMetaNodeInxMap.get(nativeParent);
+
+ if ((metaParent < 0) || (metaParent == Integer.MAX_VALUE)) {
+ metaParent = m_metaGraph.nodeCreate();
+ m_metaToNativeInxMap.setIntAtIndex(nativeParent + 1, metaParent);
+ m_nativeToMetaNodeInxMap.put(nativeParent, metaParent);
+ }
+
+ int metaChildNode = m_nativeToMetaNodeInxMap.get(nativeChildNode);
+
+ if ((metaChildNode < 0) || (metaChildNode == Integer.MAX_VALUE)) {
+ metaChildNode = m_metaGraph.nodeCreate();
+ m_metaToNativeInxMap.setIntAtIndex(nativeChildNode + 1, metaChildNode);
+ m_nativeToMetaNodeInxMap.put(nativeChildNode, metaChildNode);
+ }
+
+ if (m_metaGraph.edgesConnecting(metaParent, metaChildNode, true, false, false).hasNext())
+ return false;
+
+ m_metaGraph.edgeCreate(metaParent, metaChildNode, true);
+
+ return true;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param parentNodeInx DOCUMENT ME!
+ * @param childNodeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean removeNodeMetaChild(final int parentNodeInx, int childNodeInx) {
+ final int nativeParent = ~parentNodeInx;
+ final int nativeChildNode = ~childNodeInx;
+
+ if (!(m_graph.nodeExists(nativeParent) && m_graph.nodeExists(nativeChildNode)))
+ return false;
+
+ final int metaParent = m_nativeToMetaNodeInxMap.get(nativeParent);
+ final int metaChildNode = m_nativeToMetaNodeInxMap.get(nativeChildNode);
+ IntIterator metaRelationships = m_metaGraph.edgesConnecting(metaParent, metaChildNode,
+ true, false, false);
+
+ if ((metaRelationships == null) || !metaRelationships.hasNext())
+ return false;
+
+ final IntEnumerator nativeEdgesTouchingChild = m_graph.edgesAdjacent(nativeChildNode, true,
+ true, true);
+
+ while (nativeEdgesTouchingChild.numRemaining() > 0)
+ removeEdgeMetaChild(parentNodeInx, ~nativeEdgesTouchingChild.nextInt());
+
+ // Must re-initialize this iteration because we've mutated graph since.
+ metaRelationships = m_metaGraph.edgesConnecting(metaParent, metaChildNode, true, false,
+ false);
+
+ final int relationshipToRemove = metaRelationships.nextInt();
+
+ if (metaRelationships.hasNext())
+ throw new IllegalStateException("internal error - need to debug");
+
+ m_metaGraph.edgeRemove(relationshipToRemove);
+
+ if (m_metaGraph.edgesAdjacent(metaParent, true, true, false).numRemaining() == 0) { // Remove disconnected meta-element.
+ m_nativeToMetaNodeInxMap.put(nativeParent, Integer.MAX_VALUE);
+ m_metaToNativeInxMap.setIntAtIndex(0, metaParent);
+ m_metaGraph.nodeRemove(metaParent);
+ }
+
+ if (m_metaGraph.edgesAdjacent(metaChildNode, true, true, false).numRemaining() == 0) { // Remove disconnected meta-element.
+ m_nativeToMetaNodeInxMap.put(nativeChildNode, Integer.MAX_VALUE);
+ m_metaToNativeInxMap.setIntAtIndex(0, metaChildNode);
+ m_metaGraph.nodeRemove(metaChildNode);
+ }
+
+ return true;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param child DOCUMENT ME!
+ * @param parent DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isMetaParent(Node child, Node parent) {
+ if ((child.getRootGraph() != this) || (parent.getRootGraph() != this))
+ return false;
+
+ return isNodeMetaParent(child.getRootGraphIndex(), parent.getRootGraphIndex());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param childNodeInx DOCUMENT ME!
+ * @param parentNodeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isNodeMetaParent(int childNodeInx, int parentNodeInx) {
+ return isNodeMetaChild(parentNodeInx, childNodeInx);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public java.util.List metaParentsList(Node node) {
+ if (node.getRootGraph() != this)
+ return null;
+
+ return nodeMetaParentsList(node.getRootGraphIndex());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nodeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public java.util.List nodeMetaParentsList(int nodeInx) {
+ final int[] parentInxArr = getNodeMetaParentIndicesArray(nodeInx);
+
+ if (parentInxArr == null)
+ return null;
+
+ final java.util.ArrayList returnThis = new java.util.ArrayList(parentInxArr.length);
+
+ for (int i = 0; i < parentInxArr.length; i++)
+ returnThis.add(getNode(parentInxArr[i]));
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nodeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] getNodeMetaParentIndicesArray(int nodeInx) {
+ final int nativeChildNode = ~nodeInx;
+
+ if (!m_graph.nodeExists(nativeChildNode))
+ return null;
+
+ final int metaChildNode = m_nativeToMetaNodeInxMap.get(nativeChildNode);
+ final IntEnumerator metaRelationshipsEnum = m_metaGraph.edgesAdjacent(metaChildNode, false,
+ true, false);
+
+ if (metaRelationshipsEnum == null)
+ return new int[0];
+
+ final int[] returnThis = new int[metaRelationshipsEnum.numRemaining()];
+
+ for (int i = 0; i < returnThis.length; i++) {
+ final int metaRelationship = metaRelationshipsEnum.nextInt();
+ final int metaParent = m_metaGraph.edgeSource(metaRelationship);
+ returnThis[i] = ~(m_metaToNativeInxMap.getIntAtIndex(metaParent) - 1);
+ }
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param parent DOCUMENT ME!
+ * @param child DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isMetaChild(Node parent, Node child) {
+ return isMetaParent(child, parent);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param parentNodeInx DOCUMENT ME!
+ * @param childNodeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isNodeMetaChild(int parentNodeInx, int childNodeInx) {
+ final int nativeParent = ~parentNodeInx;
+ final int nativeChildNode = ~childNodeInx;
+
+ if (!(m_graph.nodeExists(nativeParent) && m_graph.nodeExists(nativeChildNode)))
+ return false;
+
+ final int metaParent = m_nativeToMetaNodeInxMap.get(nativeParent);
+ final int metaChildNode = m_nativeToMetaNodeInxMap.get(nativeChildNode);
+ final IntIterator metaRelationshipsIter = m_metaGraph.edgesConnecting(metaParent,
+ metaChildNode, true,
+ false, false);
+
+ return !((metaRelationshipsIter == null) || !metaRelationshipsIter.hasNext());
+ }
+
+ private final IntStack m_stack = new IntStack();
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param parentNodeInx DOCUMENT ME!
+ * @param childNodeInx DOCUMENT ME!
+ * @param recursive DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isNodeMetaChild(int parentNodeInx, int childNodeInx, boolean recursive) {
+ if (!recursive)
+ return isNodeMetaChild(parentNodeInx, childNodeInx);
+
+ final int nativeParent = ~parentNodeInx;
+ final int nativeChildNode = ~childNodeInx;
+
+ if (!(m_graph.nodeExists(nativeParent) && m_graph.nodeExists(nativeChildNode)))
+ return false;
+
+ final int metaParent = m_nativeToMetaNodeInxMap.get(nativeParent);
+ final int metaChildNode = m_nativeToMetaNodeInxMap.get(nativeChildNode);
+
+ if ((metaParent < 0) || (metaParent == Integer.MAX_VALUE) || (metaChildNode < 0)
+ || (metaChildNode == Integer.MAX_VALUE))
+ return false;
+
+ // Depth first search.
+ m_hash.empty();
+
+ final IntHash metaVisited = m_hash;
+ m_stack.empty();
+
+ final IntStack metaPending = m_stack;
+ metaVisited.put(metaParent);
+ metaPending.push(metaParent);
+
+ while (metaPending.size() > 0) {
+ final int currMeta = metaPending.pop();
+ final IntEnumerator relationships = m_metaGraph.edgesAdjacent(currMeta, true, false,
+ false);
+
+ while (relationships.numRemaining() > 0) {
+ final int aChild = m_metaGraph.edgeTarget(relationships.nextInt());
+
+ if (aChild == metaChildNode)
+ return true;
+
+ if ((m_metaToNativeInxMap.getIntAtIndex(aChild) > 0) // A node.
+ && (metaVisited.put(aChild) < 0))
+ metaPending.push(aChild);
+ }
+ }
+
+ return false;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public java.util.List nodeMetaChildrenList(Node node) {
+ if (node.getRootGraph() != this)
+ return null;
+
+ return nodeMetaChildrenList(node.getRootGraphIndex());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param parentNodeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public java.util.List nodeMetaChildrenList(int parentNodeInx) {
+ final int[] childInxArr = getNodeMetaChildIndicesArray(parentNodeInx);
+
+ if (childInxArr == null)
+ return null;
+
+ final java.util.ArrayList returnThis = new java.util.ArrayList(childInxArr.length);
+
+ for (int i = 0; i < childInxArr.length; i++)
+ returnThis.add(getNode(childInxArr[i]));
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param parentNodeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] getNodeMetaChildIndicesArray(int parentNodeInx) {
+ final int nativeParent = ~parentNodeInx;
+
+ if (!m_graph.nodeExists(nativeParent))
+ return null;
+
+ final int metaParent = m_nativeToMetaNodeInxMap.get(nativeParent);
+ final IntEnumerator metaRelationshipsEnum = m_metaGraph.edgesAdjacent(metaParent, true,
+ false, false);
+
+ if (metaRelationshipsEnum == null)
+ return new int[0];
+
+ m_heap.empty();
+
+ final MinIntHeap childRootNodeBucket = m_heap;
+
+ while (metaRelationshipsEnum.numRemaining() > 0) {
+ final int metaChild = m_metaGraph.edgeTarget(metaRelationshipsEnum.nextInt());
+
+ if (m_metaToNativeInxMap.getIntAtIndex(metaChild) > 0)
+ childRootNodeBucket.toss(~(m_metaToNativeInxMap.getIntAtIndex(metaChild) - 1));
+ }
+
+ final int[] returnThis = new int[childRootNodeBucket.size()];
+ childRootNodeBucket.copyInto(returnThis, 0);
+
+ return returnThis;
+ }
+
+ // Package visible method for FGraphPerspective. This method is recursive.
+ int[] getNodeMetaChildIndicesArray(int[] parentIndices) {
+ // Depth first search.
+ m_hash.empty();
+
+ final IntHash metaVisited = m_hash;
+ m_stack.empty();
+
+ final IntStack metaPending = m_stack;
+ m_hash2.empty();
+
+ final IntHash nativeChildNodeBucket = m_hash2;
+
+ for (int i = 0; i < parentIndices.length; i++) {
+ final int nativeParent = ~parentIndices[i];
+
+ if (!m_graph.nodeExists(nativeParent))
+ return null;
+
+ final int metaParent = m_nativeToMetaNodeInxMap.get(nativeParent);
+
+ if ((metaParent < 0) || (metaParent == Integer.MAX_VALUE))
+ continue;
+
+ if (metaVisited.put(metaParent) < 0)
+ metaPending.push(metaParent);
+ }
+
+ while (metaPending.size() > 0) {
+ final int currMeta = metaPending.pop();
+ final IntEnumerator relationships = m_metaGraph.edgesAdjacent(currMeta, true, false,
+ false);
+
+ while (relationships.numRemaining() > 0) {
+ final int aChild = m_metaGraph.edgeTarget(relationships.nextInt());
+
+ if (m_metaToNativeInxMap.getIntAtIndex(aChild) > 0) { // A node.
+ nativeChildNodeBucket.put(m_metaToNativeInxMap.getIntAtIndex(aChild) - 1);
+
+ if (metaVisited.put(aChild) < 0)
+ metaPending.push(aChild);
+ }
+ }
+ }
+
+ final IntEnumerator returnElements = nativeChildNodeBucket.elements();
+ final int[] returnThis = new int[returnElements.numRemaining()];
+
+ for (int i = 0; i < returnThis.length; i++)
+ returnThis[i] = ~returnElements.nextInt();
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param parentNodeInx DOCUMENT ME!
+ * @param recursive DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] getNodeMetaChildIndicesArray(int parentNodeInx, boolean recursive) {
+ if (!recursive)
+ return getNodeMetaChildIndicesArray(parentNodeInx);
+
+ return getNodeMetaChildIndicesArray(new int[] { parentNodeInx });
+ }
+
+ // Package visible method for FGraphPerspective. This method is recursive.
+ int[] getEdgeMetaChildIndicesArray(int[] parentIndices) {
+ // Depth first search.
+ m_hash.empty();
+
+ final IntHash metaVisited = m_hash;
+ m_stack.empty();
+
+ final IntStack metaPending = m_stack;
+ m_hash2.empty();
+
+ final IntHash nativeChildEdgeBucket = m_hash2;
+
+ for (int i = 0; i < parentIndices.length; i++) {
+ final int nativeParent = ~parentIndices[i];
+
+ if (!m_graph.nodeExists(nativeParent))
+ return null;
+
+ final int metaParent = m_nativeToMetaNodeInxMap.get(nativeParent);
+
+ if ((metaParent < 0) || (metaParent == Integer.MAX_VALUE))
+ continue;
+
+ if (metaVisited.put(metaParent) < 0)
+ metaPending.push(metaParent);
+ }
+
+ while (metaPending.size() > 0) {
+ final int currMeta = metaPending.pop();
+ final IntEnumerator relationships = m_metaGraph.edgesAdjacent(currMeta, true, false,
+ false);
+
+ while (relationships.numRemaining() > 0) {
+ final int aChild = m_metaGraph.edgeTarget(relationships.nextInt());
+
+ if (m_metaToNativeInxMap.getIntAtIndex(aChild) < 0) // An edge.
+ nativeChildEdgeBucket.put(~m_metaToNativeInxMap.getIntAtIndex(aChild));
+ else if (metaVisited.put(aChild) < 0)
+ metaPending.push(aChild);
+ }
+ }
+
+ final IntEnumerator returnElements = nativeChildEdgeBucket.elements();
+ final int[] returnThis = new int[returnElements.numRemaining()];
+
+ for (int i = 0; i < returnThis.length; i++)
+ returnThis[i] = ~returnElements.nextInt();
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nodeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] getChildlessMetaDescendants(int nodeInx) {
+ final int nativeParent = ~nodeInx;
+
+ if (!m_graph.nodeExists(nativeParent))
+ return null;
+
+ final int metaParent = m_nativeToMetaNodeInxMap.get(nativeParent);
+
+ if ((metaParent < 0) || (metaParent == Integer.MAX_VALUE))
+ return new int[0];
+
+ // Depth first search.
+ m_hash.empty();
+
+ final IntHash metaVisited = m_hash;
+ m_stack.empty();
+
+ final IntStack metaPending = m_stack;
+ m_hash2.empty();
+
+ final IntHash nativeChildlessNodeBucket = m_hash2;
+ metaVisited.put(metaParent);
+ metaPending.push(metaParent);
+
+ while (metaPending.size() > 0) {
+ final int currMeta = metaPending.pop();
+ final IntEnumerator relationships = m_metaGraph.edgesAdjacent(currMeta, true, false,
+ false);
+
+ while (relationships.numRemaining() > 0) {
+ final int aChild = m_metaGraph.edgeTarget(relationships.nextInt());
+
+ if ((m_metaToNativeInxMap.getIntAtIndex(aChild) > 0) // A node.
+ && (metaVisited.put(aChild) < 0)) {
+ metaPending.push(aChild);
+
+ if (m_metaGraph.edgesAdjacent(aChild, true, false, false).numRemaining() == 0)
+ nativeChildlessNodeBucket.put(m_metaToNativeInxMap.getIntAtIndex(aChild)
+ - 1);
+ }
+ }
+ }
+
+ final IntEnumerator returnElements = nativeChildlessNodeBucket.elements();
+ final int[] returnThis = new int[returnElements.numRemaining()];
+
+ for (int i = 0; i < returnThis.length; i++)
+ returnThis[i] = ~returnElements.nextInt();
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param parent DOCUMENT ME!
+ * @param child DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean addMetaChild(Node parent, Edge child) {
+ if ((parent.getRootGraph() != this) || (child.getRootGraph() != this))
+ return false;
+
+ return addEdgeMetaChild(parent.getRootGraphIndex(), child.getRootGraphIndex());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param parentNodeInx DOCUMENT ME!
+ * @param childEdgeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean addEdgeMetaChild(final int parentNodeInx, int childEdgeInx) {
+ final int nativeParent = ~parentNodeInx;
+ final int nativeChildEdge = ~childEdgeInx;
+
+ if (!(m_graph.nodeExists(nativeParent) && (m_graph.edgeType(nativeChildEdge) >= 0)))
+ return false;
+
+ addNodeMetaChild(parentNodeInx, ~m_graph.edgeSource(nativeChildEdge));
+ addNodeMetaChild(parentNodeInx, ~m_graph.edgeTarget(nativeChildEdge));
+
+ int metaParent = m_nativeToMetaNodeInxMap.get(nativeParent);
+
+ if ((metaParent < 0) || (metaParent == Integer.MAX_VALUE)) {
+ metaParent = m_metaGraph.nodeCreate();
+ m_metaToNativeInxMap.setIntAtIndex(nativeParent + 1, metaParent);
+ m_nativeToMetaNodeInxMap.put(nativeParent, metaParent);
+ }
+
+ int metaChildEdge = m_nativeToMetaEdgeInxMap.get(nativeChildEdge);
+
+ if ((metaChildEdge < 0) || (metaChildEdge == Integer.MAX_VALUE)) {
+ metaChildEdge = m_metaGraph.nodeCreate();
+ m_metaToNativeInxMap.setIntAtIndex(~nativeChildEdge, metaChildEdge);
+ m_nativeToMetaEdgeInxMap.put(nativeChildEdge, metaChildEdge);
+ }
+
+ if (m_metaGraph.edgesConnecting(metaParent, metaChildEdge, true, false, false).hasNext())
+ return false;
+
+ m_metaGraph.edgeCreate(metaParent, metaChildEdge, true);
+
+ return true;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param parentNodeInx DOCUMENT ME!
+ * @param childEdgeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean removeEdgeMetaChild(int parentNodeInx, int childEdgeInx) {
+ final int nativeParent = ~parentNodeInx;
+ final int nativeChildEdge = ~childEdgeInx;
+
+ if (!(m_graph.nodeExists(nativeParent) && (m_graph.edgeType(nativeChildEdge) >= 0)))
+ return false;
+
+ final int metaParent = m_nativeToMetaNodeInxMap.get(nativeParent);
+ final int metaChildEdge = m_nativeToMetaEdgeInxMap.get(nativeChildEdge);
+ final IntIterator metaRelationships = m_metaGraph.edgesConnecting(metaParent,
+ metaChildEdge, true,
+ false, false);
+
+ if ((metaRelationships == null) || !metaRelationships.hasNext())
+ return false;
+
+ final int relationshipToRemove = metaRelationships.nextInt();
+
+ if (metaRelationships.hasNext())
+ throw new IllegalStateException("internal error - debug");
+
+ m_metaGraph.edgeRemove(relationshipToRemove);
+
+ if (m_metaGraph.edgesAdjacent(metaParent, true, true, false).numRemaining() == 0) { // Remove disconnected meta-element.
+ m_nativeToMetaNodeInxMap.put(nativeParent, Integer.MAX_VALUE);
+ m_metaToNativeInxMap.setIntAtIndex(0, metaParent);
+ m_metaGraph.nodeRemove(metaParent);
+ }
+
+ if (m_metaGraph.edgesAdjacent(metaChildEdge, false, true, false).numRemaining() == 0) { // Remove disconnected meta-element.
+ m_nativeToMetaEdgeInxMap.put(nativeChildEdge, Integer.MAX_VALUE);
+ m_metaToNativeInxMap.setIntAtIndex(0, metaChildEdge);
+ m_metaGraph.nodeRemove(metaChildEdge);
+ }
+
+ return true;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param child DOCUMENT ME!
+ * @param parent DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isMetaParent(Edge child, Node parent) {
+ if ((child.getRootGraph() != this) || (parent.getRootGraph() != this))
+ return false;
+
+ return isEdgeMetaParent(child.getRootGraphIndex(), parent.getRootGraphIndex());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param childEdgeInx DOCUMENT ME!
+ * @param parentNodeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isEdgeMetaParent(int childEdgeInx, int parentNodeInx) {
+ return isEdgeMetaChild(parentNodeInx, childEdgeInx);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edge DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public java.util.List metaParentsList(Edge edge) {
+ if (edge.getRootGraph() != this)
+ return null;
+
+ return edgeMetaParentsList(edge.getRootGraphIndex());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edgeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public java.util.List edgeMetaParentsList(int edgeInx) {
+ final int[] metaParentInx = getEdgeMetaParentIndicesArray(edgeInx);
+
+ if (metaParentInx == null)
+ return null;
+
+ final java.util.ArrayList returnThis = new java.util.ArrayList(metaParentInx.length);
+
+ for (int i = 0; i < metaParentInx.length; i++)
+ returnThis.add(getNode(metaParentInx[i]));
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edgeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] getEdgeMetaParentIndicesArray(int edgeInx) {
+ final int nativeChildEdge = ~edgeInx;
+
+ if (m_graph.edgeType(nativeChildEdge) < 0)
+ return null;
+
+ final int metaChildEdge = m_nativeToMetaEdgeInxMap.get(nativeChildEdge);
+ final IntEnumerator metaRelationshipsEnum = m_metaGraph.edgesAdjacent(metaChildEdge, false,
+ true, false);
+
+ if (metaRelationshipsEnum == null)
+ return new int[0];
+
+ final int[] returnThis = new int[metaRelationshipsEnum.numRemaining()];
+
+ for (int i = 0; i < returnThis.length; i++) {
+ final int metaRelationship = metaRelationshipsEnum.nextInt();
+ final int metaParent = m_metaGraph.edgeSource(metaRelationship);
+ returnThis[i] = ~(m_metaToNativeInxMap.getIntAtIndex(metaParent) - 1);
+ }
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param parent DOCUMENT ME!
+ * @param child DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isMetaChild(Node parent, Edge child) {
+ return isMetaParent(child, parent);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param parentNodeInx DOCUMENT ME!
+ * @param childEdgeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isEdgeMetaChild(int parentNodeInx, int childEdgeInx) {
+ final int nativeParent = ~parentNodeInx;
+ final int nativeChildEdge = ~childEdgeInx;
+
+ if (!(m_graph.nodeExists(nativeParent) && (m_graph.edgeType(nativeChildEdge) >= 0)))
+ return false;
+
+ final int metaParent = m_nativeToMetaNodeInxMap.get(nativeParent);
+ final int metaChildEdge = m_nativeToMetaEdgeInxMap.get(nativeChildEdge);
+ final IntIterator metaRelationshipsIter = m_metaGraph.edgesConnecting(metaParent,
+ metaChildEdge, true,
+ false, false);
+
+ return !((metaRelationshipsIter == null) || !metaRelationshipsIter.hasNext());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public java.util.List edgeMetaChildrenList(Node node) {
+ if (node.getRootGraph() != this)
+ return null;
+
+ return edgeMetaChildrenList(node.getRootGraphIndex());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param parentNodeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public java.util.List edgeMetaChildrenList(int parentNodeInx) {
+ final int[] edgeChildrenArr = getEdgeMetaChildIndicesArray(parentNodeInx);
+
+ if (edgeChildrenArr == null)
+ return null;
+
+ final java.util.ArrayList returnThis = new java.util.ArrayList(edgeChildrenArr.length);
+
+ for (int i = 0; i < edgeChildrenArr.length; i++)
+ returnThis.add(getEdge(edgeChildrenArr[i]));
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param parentNodeInx DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] getEdgeMetaChildIndicesArray(int parentNodeInx) {
+ final int nativeParent = ~parentNodeInx;
+
+ if (!m_graph.nodeExists(nativeParent))
+ return null;
+
+ final int metaParent = m_nativeToMetaNodeInxMap.get(nativeParent);
+ final IntEnumerator metaRelationshipsEnum = m_metaGraph.edgesAdjacent(metaParent, true,
+ false, false);
+
+ if (metaRelationshipsEnum == null)
+ return new int[0];
+
+ m_heap.empty();
+
+ final MinIntHeap childRootEdgeBucket = m_heap;
+
+ while (metaRelationshipsEnum.numRemaining() > 0) {
+ final int metaChild = m_metaGraph.edgeTarget(metaRelationshipsEnum.nextInt());
+
+ if (m_metaToNativeInxMap.getIntAtIndex(metaChild) < 0)
+ childRootEdgeBucket.toss(m_metaToNativeInxMap.getIntAtIndex(metaChild));
+ }
+
+ final int[] returnThis = new int[childRootEdgeBucket.size()];
+ childRootEdgeBucket.copyInto(returnThis, 0);
+
+ return returnThis;
+ }
+
+ // The relationship between indices (both node and edge) in this
+ // RootGraph and in the DynamicGraph is "flip the bits":
+ // rootGraphIndex == ~(dynamicGraphIndex)
+ private final DynamicGraph m_graph = DynamicGraphFactory.instantiateDynamicGraph();
+
+ // For the most part, there will always be a listener registered with this
+ // RootGraph (all GraphPerspectives will have registered listeners). So,
+ // instead of checking for null, just keep a permanent listener.
+ private RootGraphChangeListener m_lis = new RootGraphChangeListener() {
+ public void rootGraphChanged(RootGraphChangeEvent event) {
+ }
+ };
+
+ // This hash is re-used by many methods. Make sure to empty() it before
+ // using it. You can use it as a bag of integers or to filter integer
+ // duplicates. You don't need to empty() it after usage.
+ private final IntHash m_hash = new IntHash();
+
+ // This heap is re-used by several methods. It's used primarily as a bucket
+ // of integers; sorting with this heap is [probably] not done at all.
+ // Make sure to empty() it before using it.
+ private final MinIntHeap m_heap = new MinIntHeap();
+
+ // This is our "node factory" and "node recyclery".
+ private final FingNodeDepot m_nodeDepot;
+
+ // This is our "edge factory" and "edge recyclery".
+ private final FingEdgeDepot m_edgeDepot;
+
+ // This is our index-to-node mapping.
+ private final NodeArray m_nodes = new NodeArray();
+
+ // This is our index-to-edge mapping.
+ private final EdgeArray m_edges = new EdgeArray();
+
+ // This is our meta-relationships graph where nodes in the meta-graph
+ // are edges and nodes in the original graph, and directed edges in the
+ // meta-graph are parent->child relationships. Note that only nodes
+ // in the original graph can be parents, and both nodes and edges from the
+ // original graph can be children. We're only going to populate the
+ // meta-graph with nodes or edges from the original graph that are defined
+ // in a parent->child relationship; in other words, we don't add nodes
+ // to the meta-graph for every node and edge in the orignal graph,
+ // necessarily.
+ private final DynamicGraph m_metaGraph = DynamicGraphFactory.instantiateDynamicGraph();
+
+ // An index in the array corresponds to a node in the meta graph;
+ // the value at that index, if strictly positive, is one plus the native
+ // node in the original graph; if strictly negative, is the complement
+ // of the native edge in the original graph.
+ private final IntArray m_metaToNativeInxMap = new IntArray();
+ private final IntIntHash m_nativeToMetaNodeInxMap = new IntIntHash();
+ private final IntIntHash m_nativeToMetaEdgeInxMap = new IntIntHash();
+
+ // Package visible constructor.
+ FRootGraph() {
+ this(new NodeDepository(), new EdgeDepository());
+ }
+
+ // Package visible constructor.
+ FRootGraph(FingNodeDepot nodeDepot, FingEdgeDepot edgeDepot) {
+ if (nodeDepot == null)
+ throw new NullPointerException("nodeDepot is null");
+
+ m_nodeDepot = nodeDepot;
+
+ if (edgeDepot == null)
+ throw new NullPointerException("edgeDepot is null");
+
+ m_edgeDepot = edgeDepot;
+ }
+}
diff --git a/corelibs/fing/src/main/java/fing/model/FingEdgeDepot.java b/corelibs/fing/src/main/java/fing/model/FingEdgeDepot.java
new file mode 100644
index 0000000..f3a2913
--- /dev/null
+++ b/corelibs/fing/src/main/java/fing/model/FingEdgeDepot.java
@@ -0,0 +1,64 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package fing.model;
+
+import giny.model.Edge;
+import giny.model.RootGraph;
+
+
+/**
+ * Please try to restrain from using this class, or even looking at it.
+ * This class was created so that certain legacy applications would have an
+ * easier time using this giny.model implementation. Please use
+ * FingRootGraphFactory instead of this class.
+ * @see FingRootGraphFactory
+ **/
+public interface FingEdgeDepot {
+ /**
+ * This either instantiates a new edge or gets one from the recyclery,
+ * initializing it with the parameters specified.
+ **/
+ public Edge getEdge(RootGraph root, int index, String id);
+
+ /**
+ * Recycles an edge. Implementations may choose to do nothing in this
+ * method and instantiate a new edge in each call to getEdge(). This method
+ * is simply a hook for Fing to tell the depository "I'm done using this edge
+ * object -- it's no longer part of a RootGraph".
+ **/
+ public void recycleEdge(Edge node);
+}
diff --git a/corelibs/fing/src/main/java/fing/model/FingExtensibleGraphPerspective.java b/corelibs/fing/src/main/java/fing/model/FingExtensibleGraphPerspective.java
new file mode 100644
index 0000000..9ce3efc
--- /dev/null
+++ b/corelibs/fing/src/main/java/fing/model/FingExtensibleGraphPerspective.java
@@ -0,0 +1,62 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package fing.model;
+
+import cytoscape.util.intr.IntIterator;
+
+
+/**
+ * Please try to restrain from using this class. This class was created so
+ * that certain legacy applications would have an easier time using this
+ * giny.model implementation. Please use FingRootGraphFactory instead of this
+ * class.
+ * @see FingRootGraphFactory
+ **/
+public class FingExtensibleGraphPerspective extends FGraphPerspective {
+ /**
+ * rootGraphNodeInx need not contain all endpoint nodes corresponding to
+ * edges in rootGraphEdgeInx - this is calculated automatically by this
+ * constructor. If any index does not correspond to an existing node or
+ * edge, an IllegalArgumentException is thrown. The indices lists need not
+ * be non-repeating - the logic in this constructor handles duplicate
+ * filtering.
+ **/
+ public FingExtensibleGraphPerspective(FingExtensibleRootGraph root,
+ IntIterator rootGraphNodeInx, IntIterator rootGraphEdgeInx) {
+ super(root, rootGraphNodeInx, rootGraphEdgeInx);
+ }
+}
diff --git a/corelibs/fing/src/main/java/fing/model/FingExtensibleRootGraph.java b/corelibs/fing/src/main/java/fing/model/FingExtensibleRootGraph.java
new file mode 100644
index 0000000..3402803
--- /dev/null
+++ b/corelibs/fing/src/main/java/fing/model/FingExtensibleRootGraph.java
@@ -0,0 +1,57 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package fing.model;
+
+
+/**
+ * Please try to restrain from using this class. This class was created so
+ * that certain legacy applications would have an easier time using this
+ * giny.model implementation. Please use FingRootGraphFactory instead of this
+ * class.
+ * @see FingRootGraphFactory
+ **/
+public class FingExtensibleRootGraph extends FRootGraph {
+ /**
+ * Creates a new FingExtensibleRootGraph object.
+ *
+ * @param nodeDepot DOCUMENT ME!
+ * @param edgeDepot DOCUMENT ME!
+ */
+ public FingExtensibleRootGraph(FingNodeDepot nodeDepot, FingEdgeDepot edgeDepot) {
+ super(nodeDepot, edgeDepot);
+ }
+}
diff --git a/corelibs/fing/src/main/java/fing/model/FingNodeDepot.java b/corelibs/fing/src/main/java/fing/model/FingNodeDepot.java
new file mode 100644
index 0000000..db6b326
--- /dev/null
+++ b/corelibs/fing/src/main/java/fing/model/FingNodeDepot.java
@@ -0,0 +1,64 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package fing.model;
+
+import giny.model.Node;
+import giny.model.RootGraph;
+
+
+/**
+ * Please try to restrain from using this class, or even looking at it.
+ * This class was created so that certain legacy applications would have an
+ * easier time using this giny.model implementation. Please use
+ * FingRootGraphFactory instead of this class.
+ * @see FingRootGraphFactory
+ **/
+public interface FingNodeDepot {
+ /**
+ * This either instantiates a new node or gets one from the recyclery,
+ * initializing it with the parameters specified.
+ **/
+ public Node getNode(RootGraph root, int index, String id);
+
+ /**
+ * Recycles a node. Implementations may choose to do nothing in this
+ * method and instantiate a new node in each call to getNode(). This method
+ * is simply a hook for Fing to tell the depository "I'm done using this node
+ * object -- it's no longer part of a RootGraph".
+ **/
+ public void recycleNode(Node node);
+}
diff --git a/corelibs/fing/src/main/java/fing/model/FingRootGraphFactory.java b/corelibs/fing/src/main/java/fing/model/FingRootGraphFactory.java
new file mode 100644
index 0000000..2547427
--- /dev/null
+++ b/corelibs/fing/src/main/java/fing/model/FingRootGraphFactory.java
@@ -0,0 +1,893 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package fing.model;
+
+import giny.model.RootGraph;
+
+
+/**
+ * This class defines static methods that provide new instances
+ * of giny.model.RootGraph objects.
+ */
+public final class FingRootGraphFactory {
+ // "No constructor".
+ private FingRootGraphFactory() {
+ }
+
+ /**
+ * Returns a new instance of giny.model.RootGraph. Obviously, a new
+ * RootGraph instance contains no nodes or edges.<p>
+ * A secret feature is that the returned object not only implements
+ * RootGraph - it also implements cytoscape.graph.dynamic.DynamicGraph.
+ * In other words, you can cast the return value to DynamicGraph. The
+ * relationship between RootGraph node/edge indices and DynamicGraph nodes
+ * and edges is they are complements of each other. Complement is '~' in
+ * Java.<p>
+ * In addition to the RootGraph secretly implementing DyanmicGraph,
+ * all of the GraphPerspective objects generated by the returned RootGraph
+ * secretly implement cytoscape.graph.fixed.FixedGraph. In other words,
+ * all GraphPerspective objects that are part of this RootGraph system
+ * can be cast to FixedGraph. The relationship between GraphPerspective
+ * node/edge indices (which are identical to RootGraph indices) and
+ * FixedGraph nodes and edges is they are complements of each other.<p>
+ * Below are time complexities of methods implemented:
+ * <blockquote><table border=1 cellspacing=0 cellpadding=5>
+ * <tr><th colspan=2>RootGraph</th></tr>
+ * <tr><th>method</th><th>time complexity</th></tr>
+ * <tr>
+ * <td>createGraphPerspective(Node[], Edge[])</td>
+ * <td>A GraphPerspective is created in O(N + E) time, where N is the
+ * length of the Node input array and E is the length of the Edge
+ * input array.</td>
+ * </tr><tr>
+ * <td>createGraphPerspective(int[], int[])</td>
+ * <td>A GraphPerspective is created in O(N + E) time, where N is the
+ * length of the first input int array and E is the length of the
+ * second input int array.</td>
+ * </tr><tr>
+ * <td>ensureCapacity(int, int)</td>
+ * <td>This method returns in constant time.</td>
+ * </tr><tr>
+ * <td>getNodeCount()</td>
+ * <td>The total node count is calculated in constant time.</td>
+ * </tr><tr>
+ * <td>getEdgeCount()</td>
+ * <td>The total edge count is calculated in constant time.</td>
+ * </tr><tr>
+ * <td>nodesIterator()</td>
+ * <td>An Iterator is returned in constant time. Each successive element
+ * in the iteration is returned in constant time.</td>
+ * </tr><tr>
+ * <td>nodesList()</td>
+ * <td>A List of Node objects is returned in O(N) time, where N is the
+ * number of nodes in this RootGraph.</td>
+ * </tr><tr>
+ * <td>getNodeIndicesArray()</td>
+ * <td>An array of node indices is returned in O(N) time, where N is the
+ * number of nodes in this RootGraph.</td>
+ * </tr><tr>
+ * <td>edgesIterator()</td>
+ * <td>An iterator is returned in constant time. Each successive element
+ * in the iteration is returned in constant time.</td>
+ * </tr><tr>
+ * <td>edgesList()</td>
+ * <td>A List of Edge objects is returned in O(E) time, where E is the
+ * number of edges in this RootGraph.</td>
+ * </tr><tr>
+ * <td>getEdgeIndicesArray()</td>
+ * <td>An array of edge indices is returned in O(E) time, where E is the
+ * number of edges in this RootGraph.</td>
+ * </tr><tr>
+ * <td>removeNode(Node)</td>
+ * <td>Essentially, the operation of removing a node takes O(E) time where
+ * E is the number of edges touching the node being removed. However,
+ * this is no longer an absolute truth once many GraphPerspective
+ * objects are created from this RootGraph, or many meta-node
+ * relationships are created which involve the node being removed.</td>
+ * </tr><tr>
+ * <td>removeNode(int)</td>
+ * <td>Essentially, the operation of removing a node takes O(E) time where
+ * E is the number of edges touching the node being removed. However,
+ * this is no longer an absolute truth once many GraphPerspective
+ * objects are created from this RootGraph, or many meta-node
+ * relationships are created which involve the node being removed.</td>
+ * </tr><tr>
+ * <td>removeNodes(List)</td>
+ * <td>Essentially, the operation of removing a node takes O(E) time where
+ * E is the number of edges touching the node being removed. However,
+ * this is no longer an absolute truth once many GraphPerspective
+ * objects are created from this RootGraph, or many meta-node
+ * relationships are created which involve the node being removed.
+ * This method removes each node in succession.</td>
+ * </tr><tr>
+ * <td>removeNodes(int[])</td>
+ * <td>Essentially, the operation of removing a node takes O(E) time where
+ * E is the number of edges touching the node being removed. However,
+ * this is no longer an absolute truth once many GraphPerspective
+ * objects are created from this RootGraph, or many meta-node
+ * relationships are created which involve the node being removed.
+ * This method removes each node in succession.</td>
+ * </tr><tr>
+ * <td>createNode()</td>
+ * <td>A node is created in constant time.</td>
+ * </tr><tr>
+ * <td>createNode(Node[], Edge[])</td>
+ * <td>This meta-node operation takes O(N + E) time, where N is the
+ * length of the input Node array and E is the length of the input
+ * Edge array.</td>
+ * </tr><tr>
+ * <td>createNode(GraphPerspective)</td>
+ * <td>This meta-node operation takes O(N + E) time, where N is the
+ * number of nodes in specified GraphPerspective and E is the
+ * number of edges in specified GraphPerspective.</td>
+ * </tr><tr>
+ * <td>createNode(int[], int[])</td>
+ * <td>This meta-node operation takes O(N + E) time, where N is the
+ * length of the first input int array and E is the length of the
+ * second input int array.</td>
+ * </tr><tr>
+ * <td>createNodes(int)</td>
+ * <td>A node is created in constant time. This method creates the
+ * specified number of nodes in succession.</td>
+ * </tr><tr>
+ * <td>removeEdge(Edge)</td>
+ * <td>Essentially, the operation of removing an edge takes constant time.
+ * However, this is no longer an absolute truth once many
+ * GraphPerspective objects are created from this RootGraph, or many
+ * meta-node relationships are created which involve the edge being
+ * removed.</td>
+ * </tr><tr>
+ * <td>removeEdge(int)</td>
+ * <td>Essentially, the operation of removing an edge takes constant time.
+ * However, this is no longer an absolute truth once many
+ * GraphPerspective objects are created from this RootGraph, or many
+ * meta-node relationships are created which involve the edge being
+ * removed.</td>
+ * </tr><tr>
+ * <td>removeEdges(List)</td>
+ * <td>Essentially, the operation of removing an edge takes constant time.
+ * However, this is no longer an absolute truth once many
+ * GraphPerspective objects are created from this RootGraph, or many
+ * meta-node relationships are created which involve the edge being
+ * removed. This removes each edge successively.</td>
+ * </tr><tr>
+ * <td>removeEdges(int[])</td>
+ * <td>Essentially, the operation of removing an edge takes constant time.
+ * However, this is no longer an absolute truth once many
+ * GraphPerspective objects are created from this RootGraph, or many
+ * meta-node relationships are created which involve the edge being
+ * removed. This removes each edge successively.</td>
+ * </tr><tr>
+ * <td>createEdge(Node, Node)</td>
+ * <td>The operation of creating an edge is performed in constant time.</td>
+ * </tr><tr>
+ * <td>createEdge(Node, Node, boolean)</td>
+ * <td>The operation of creating an edge is performed in constant time.</td>
+ * </tr><tr>
+ * <td>createEdge(int, int)</td>
+ * <td>The operation of creating an edge is performed in constant time.</td>
+ * </tr><tr>
+ * <td>createEdge(int, int, boolean)</td>
+ * <td>The operation of creating an edge is performed in constant time.</td>
+ * </tr><tr>
+ * <td>createEdges(int[], int[], boolean)</td>
+ * <td>The operation of creating an edge is performed in constant time.
+ * This creates each edge in succession.</td>
+ * </tr><tr>
+ * <td>containsNode(Node)</td>
+ * <td>Determining whether or not a node is in a RootGraph takes
+ * constant time.</td>
+ * </tr><tr>
+ * <td>containsEdge(Edge)</td>
+ * <td>Determining whether or not an edge is in a RootGraph takes
+ * constant time.</td>
+ * </tr><tr>
+ * <td>neighborsList(Node)</td>
+ * <td>Node neighbors are calculated on O(E) time, where E is the number of
+ * edges touching the node whose neighbors we're calculating.</td>
+ * </tr><tr>
+ * <td>isNeighbor(Node, Node)</td>
+ * <td>The operation of determining whether or not two nodes are
+ * neighbors has time complexity O(min(E, F)), where E is the number of
+ * edges touching one node and F is the number of edges touching the
+ * other node (this is actually over-simplified and more pessimistic
+ * than it could be).</td>
+ * </tr><tr>
+ * <td>isNeighbor(int, int)</td>
+ * <td>The operation of determining whether or not two nodes are
+ * neighbors has time complexity O(min(E, F)), where E is the number of
+ * edges touching one node and F is the number of edges touching the
+ * other node (this is actually over-simplified and more pessimistic
+ * than it could be).</td>
+ * </tr><tr>
+ * <td>edgeExists(Node, Node)</td>
+ * <td>The operation of determining whether or not an edge exists starting
+ * at one [specified] node and ending at another [specified] node
+ * has time complexity O(min(E, F)), where E is the number of
+ * edges touching one node and F is the number of edges touching the
+ * other node (this is actually over-simplified and more pessimistic
+ * than it could be).</td>
+ * </tr><tr>
+ * <td>edgeExists(int, int)</td>
+ * <td>The operation of determining whether or not an edge exists starting
+ * at one [specified] node and ending at another [specified] node
+ * has time complexity O(min(E, F)), where E is the number of
+ * edges touching one node and F is the number of edges touching the
+ * other node (this is actually over-simplified and more pessimistic
+ * than it could be).</td>
+ * </tr><tr>
+ * <td>getEdgeCount(Node, Node, boolean)</td>
+ * <td>The operation of determining the number of existig edges starting at
+ * one [specified] node and ending at another [specified] node has
+ * time complexity O(min(E, F)), where E is the number of edges touching
+ * one node and F is the number of edges touching the other node.</td>
+ * </tr><tr>
+ * <td>getEdgeCount(int, int, boolean)</td>
+ * <td>The operation of determining the number of existing edges starting at
+ * one [specified] node and ending at another [specified] node has
+ * time complexity O(min(E, F)), where E is the number of edges touching
+ * one node and F is the number of edges touching the other node.</td>
+ * </tr><tr>
+ * <td>getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean)</td>
+ * <td>The operation of getting edges adjacent to a node, fitting
+ * defined characteristics (specified by three boolean values) has
+ * time complexity O(E), where E is the total number of edges touching
+ * the node in question.</td>
+ * </tr><tr>
+ * <td>getConnectingEdgeIndicesArray(int[])</td>
+ * <td>Computing a "connecting web" of edges from a list of input nodes
+ * has time complexity O(E), where E is the number of edges touching
+ * at least one node in the input set of nodes.</td>
+ * </tr><tr>
+ * <td>getConnectingNodeIndicesArray(int[])</td>
+ * <td>This method has time complexity O(E), where E is the length
+ * of the input array.</td>
+ * </tr><tr>
+ * <td>getEdgeIndicesArray(int, int, boolean, boolean)</td>
+ * <td>The operation of finding all edges [meeting certain criteria,
+ * specified by two boolean input parameters] starting at one [specified]
+ * node and ending at another [specified] node has time complexity
+ * O(min(E, F)), where E is the total number of edges touching the
+ * start node and F is the total number of edges touching the end
+ * node.</td>
+ * </tr><tr>
+ * <td>edgesList(Node, Node)</td>
+ * <td>The operation of finding all edges starting at one [specified]
+ * node and ending at another [specified] node has time complexity
+ * O(min(E, F)), where E is the total number of edges touching the
+ * start node and F is the total number of edges touching the end
+ * node.</td>
+ * </tr><tr>
+ * <td>edgesList(int, int, boolean)</td>
+ * <td>The operation of finding all edges starting at one [specified]
+ * node and ending at another [specified] node has time complexity
+ * O(min(E, F)), where E is the total number of edges touching the
+ * start node and F is the total number of edges touching the end
+ * node.</td>
+ * </tr><tr>
+ * <td>getEdgeIndicesArray(int, int, boolean)</td>
+ * <td>The operation of finding all edges starting at one [specified]
+ * node and ending at another [specified] node has time complexity
+ * O(min(E, F)), where E is the total number of edges touching the
+ * start node and F is the total number of edges touching the end
+ * node.</td>
+ * </tr><tr>
+ * <td>getInDegree(int)</td>
+ * <td>All degree-computing methods are executed in constant time.</td>
+ * </tr><tr>
+ * <td>getInDegree(Node, boolean)</td>
+ * <td>All degree-computing methods are executed in constant time.</td>
+ * </tr><tr>
+ * <td>getInDegree(int, boolean)</td>
+ * <td>All degree-computing methods are executed in constant time.</td>
+ * </tr><tr>
+ * <td>getOutDegree(Node)</td>
+ * <td>All degree-computing methods are executed in constant time.</td>
+ * </tr><tr>
+ * <td>getOutDegree(int)</td>
+ * <td>All degree-computing methods are executed in constant time.</td>
+ * </tr><tr>
+ * <td>getOutDegree(Node, boolean)</td>
+ * <td>All degree-computing methods are executed in constant time.</td>
+ * </tr><tr>
+ * <td>getOutDegree(int, boolean)</td>
+ * <td>All degree-computing methods are executed in constant time.</td>
+ * </tr><tr>
+ * <td>getDegree(Node)</td>
+ * <td>All degree-computing methods are executed in constant time.</td>
+ * </tr><tr>
+ * <td>getDegree(int)</td>
+ * <td>All degree-computing methods are executed in constant time.</td>
+ * </tr><tr>
+ * <td>getIndex(Node)</td>
+ * <td>The index of a node is computed in constant time.</td>
+ * </tr><tr>
+ * <td>getNode(int)</td>
+ * <td>A node is retrieved in constant time.</td>
+ * </tr><tr>
+ * <td>getIndex(Edge)</td>
+ * <td>The index of an edge is computed in constant time.</td>
+ * </tr><tr>
+ * <td>getEdge(int)</td>
+ * <td>An edge is retrieved in constant time.</td>
+ * </tr><tr>
+ * <td>getEdgeSourceIndex(int)</td>
+ * <td>The source node of an edge is determined in constant time.</td>
+ * </tr><tr>
+ * <td>getEdgeTargetIndex(int)</td>
+ * <td>The target node of an edge is determined in constant time.</td>
+ * </tr><tr>
+ * <td>isEdgeDirected(int)</td>
+ * <td>The directedness of an edge is determined in constant time.</td>
+ * </tr><tr>
+ * <td>addMetaChild(Node, Node)</td>
+ * <td>Adding a node->node meta-relationship has time complexity
+ * O(min(P, C)), where P is the number of pre-existing children the
+ * soon-to-be parent has, and C is the number of pre-existing parents
+ * the soon-to-be child has.</td>
+ * </tr><tr>
+ * <td>addNodeMetaChild(int, int)</td>
+ * <td>Adding a node->node meta-relationship has time complexity
+ * O(min(P, C)), where P is the number of pre-existing children the
+ * soon-to-be parent has, and C is the number of pre-existing parents
+ * the soon-to-be child has.</td>
+ * </tr><tr>
+ * <td>removeNodeMetaChild(int, int)</td>
+ * <td>Grrr. This is complicated. In the simplest case (and in the
+ * case that will occur frequently), this is much like removing
+ * a node from a graph -- the time complexity is O(E), where E is the
+ * number of edges touching the child node.</td>
+ * </tr><tr>
+ * <td>isMetaParent(Node, Node)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>isNodeMetaParent(int, int)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>metaParentsList(Node)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>nodeMetaParentsList(int)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getNodeMetaParentIndicesArray(int)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>isMetaChild(Node, Node)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>isNodeMetaChild(int, int)</td>
+ * <td>The operation of determining whether or not a given node is the
+ * meta-parent of another given node has time complexity O(min(P, C)),
+ * where P is the number of children (both nodes and edges) the potential
+ * parent has, and C is the number of parents the potential child
+ * has.</td>
+ * </tr><tr>
+ * <td>isNodeMetaChild(int, int, boolean)</td>
+ * <td>The recursive version of this method does a depth-first search of
+ * the meta-graph structure starting at the specified parent node;
+ * therefore, the time complexity of this recursive operation is
+ * O(M), where M is the size of set (including both nodes and edges)
+ * "reachable" by following meta-paths from parent to child, starting
+ * at specified parent node.</td>
+ * </tr><tr>
+ * <td>nodeMetaChildrenList(Node)</td>
+ * <td>The operation of getting all node children of a given parent node
+ * has time complexity O(C), where C is the number of children of the
+ * given parent node, including both nodes and edges.</td>
+ * </tr><tr>
+ * <td>nodeMetaChildrenList(int)</td>
+ * <td>The operation of getting all node children of a given parent node
+ * has time complexity O(C), where C is the number of children of the
+ * given parent node, including both nodes and edges.</td>
+ * </tr><tr>
+ * <td>getNodeMetaChildIndicesArray(int)</td>
+ * <td>The operation of getting all node children of a given parent node
+ * has time complexity O(C), where C is the number of children of the
+ * given parent node, including both nodes and edges.</td>
+ * </tr><tr>
+ * <td>getNodeMetaChildIndicesArray(int, boolean)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getChildlessMetaDescendants(int)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>addMetaChild(Node, Edge)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>addEdgeMetaChild(int, int)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>removeEdgeMetaChild(int, int)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>isMetaParent(Edge, Node)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>isEdgeMetaParent(int, int)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>metaParentsList(Edge)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>edgeMetaParentsList(int)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getEdgeMetaParentIndicesArray(int)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>isMetaChild(Node, Edge)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>isEdgeMetaChild(int, int)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>edgeMetaChildrenList(Node)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>edgeMetaChildrenList(int)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getEdgeMetaChildIndicesArray(int)</td>
+ * <td></td>
+ * </tr>
+ * </table><br /><table border=1 cellspacing=0 cellpadding=5>
+ * <tr><th colspan=2>GraphPerspective</th></tr>
+ * <tr><th>method</th><th>time complexity</th></tr>
+ * <tr>
+ * <td>addGraphPerspectiveChangeListener(GraphPerspectiveChangeListener)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>removeGraphPerspectiveChangeListener(GraphPerspectiveChangeListener)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>clone()</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getRootGraph()</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getNodeCount()</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getEdgeCount()</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>nodesIterator()</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>nodesList()</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getNodeIndicesArray()</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>edgesIterator()</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>edgesList()</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getEdgeIndicesArray()</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getEdgeIndicesArray(int, int, boolean, boolean)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>hideNode(Node)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>hideNode(int)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>hideNodes(List)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>hideNodes(int[])</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>restoreNode(Node)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>restoreNode(int)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>restoreNodes(List)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>restoreNodes(List, boolean)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>restoreNodes(int[], boolean)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>restoreNodes(int[])</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>hideEdge(Edge)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>hideEdge(int)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>hideEdges(List)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>hideEdges(int[])</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>restoreEdge(Edge)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>restoreEdge(int)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>restoreEdges(List)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>restoreEdges(int[])</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>containsNode(Node)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>containsNode(Node, boolean)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>containsEdge(Edge)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>containsEdge(Edge, boolean)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>join(GraphPerspective)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>createGraphPerspective(Node[], Edge[])</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>createGraphPerspective(int[], int[])</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>createGraphPerspective(Filter)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>neighborsList(Node)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>neighborsArray(int)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>isNeighbor(Node, Node)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>isNeighbor(int, int)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>edgeExists(Node, Node)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>edgeExists(int, int)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getEdgeCount(Node, Node, boolean)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getEdgeCount(int, int, boolean)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>edgesList(Node, Node)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>edgesList(int, int, boolean)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getEdgeIndicesArray(int, int, boolean)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getInDegree(Node)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getInDegree(int)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getInDegree(Node, boolean)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getInDegree(int, boolean)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getOutDegree(Node)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getOutDegree(int)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getOutDegree(Node, boolean)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getOutDegree(int, boolean)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getDegree(Node)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getDegree(int)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getIndex(Node)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getNodeIndex(int)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getRootGraphNodeIndex(int)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getNode(int)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getIndex(Edge)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getEdgeIndex(int)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getRootGraphEdgeIndex(int)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getEdge(int)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getEdgeSourceIndex(int)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getEdgeTargetIndex(int)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>isEdgeDirected(int)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>isMetaParent(Node, Node)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>isNodeMetaParent(int, int)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>metaParentsList(Node)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>nodeMetaParentsList(int)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getNodeMetaParentIndicesArray(int)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>isMetaChild(Node, Node)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>isNodeMetaChild(int, int)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>nodeMetaChildrenList(Node)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>nodeMetaChildrenList(int)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getNodeMetaChildrenIndicesArray(int)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>isMetaParent(Edge, Node)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>isEdgeMetaParent(int, int)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>metaParentsList(Edge)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>edgeMetaParentsList(int)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getEdgeMetaParentIndicesArray(int)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>isMetaChild(Node, Edge)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>isEdgeMetaChild(int, int)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>edgeMetaChildrenList(Node)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>edgeMetaChildrenList(int)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getEdgeMetaChildIndicesArray(int)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getAdjacentEdgesList(Node, boolean, boolean, boolean)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getConnectingEdges(List)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getConnectingEdgeIndicesArray(int[])</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getConnectingNodeIndicesArray(int[])</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>createGraphPerspective(int[])</td>
+ * <td></td>
+ * </tr></table><br /><table border=1 cellspacing=0 cellpadding=5>
+ * <tr><th colspan=2>Node</th></tr>
+ * <tr><th>method</th><th>time complexity</th></tr>
+ * <tr>
+ * <td>getGraphPerspective()</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>setGraphPerspective(GraphPerspective)</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getRootGraph()</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getRootGraphIndex()</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getIdentifier()</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>setIdentifier(String)</td>
+ * <td></td>
+ * </tr></table><br /><table border=1 cellspacing=0 cellpadding=5>
+ * <tr><th colspan=2>Edge</th></tr>
+ * <tr><th>method</th><th>time complexity</th></tr>
+ * <tr>
+ * <td>getSource()</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getTarget()</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>isDirected()</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getRootGraph()</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getRootGraphIndex()</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getIdentifier()</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>setIdentifier(String)</td>
+ * <td></td>
+ * </tr></table><br /><table border=1 cellspacing=0 cellpadding=5>
+ * <tr><th colspan=2>GraphPerspectiveChangeEvent</th></tr>
+ * <tr><th>method</th><th>time complexity</th></tr>
+ * <tr>
+ * <td>getSource()</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getType()</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>isNodesRestoredType()</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>isEdgesRestoredType()</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>isNodesHiddenType()</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>isEdgesHiddenType()</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>isNodesSelectedType()</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>isNodesUnselectedType()</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>isEdgesSelectedType()</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>isEdgesUnselectedType()</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getRestoredNodes()</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getRestoredEdges()</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getHiddenNodes()</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getHiddenEdges()</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getSelectedNodes()</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getUnselectedNodes()</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getSelectedEdges()</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getUnselectedEdges()</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getRestoredNodeIndices()</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getRestoredEdgeIndices()</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getHiddenNodeIndices()</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getHiddenEdgeIndices()</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getSelectedNodeIndices()</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getUnselectedNodeIndices()</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getSelectedEdgeIndices()</td>
+ * <td></td>
+ * </tr><tr>
+ * <td>getUnselectedEdgeIndices()</td>
+ * <td></td>
+ * </tr></table></blockquote>
+ */
+ public final static RootGraph instantiateRootGraph() {
+ return new FRootGraph();
+ }
+}
diff --git a/corelibs/fing/src/main/java/fing/model/GraphPerspectiveChangeEventAdapter.java b/corelibs/fing/src/main/java/fing/model/GraphPerspectiveChangeEventAdapter.java
new file mode 100644
index 0000000..d44c795
--- /dev/null
+++ b/corelibs/fing/src/main/java/fing/model/GraphPerspectiveChangeEventAdapter.java
@@ -0,0 +1,273 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package fing.model;
+
+import giny.model.Edge;
+import giny.model.GraphPerspective;
+import giny.model.GraphPerspectiveChangeEvent;
+import giny.model.Node;
+
+
+abstract class GraphPerspectiveChangeEventAdapter extends GraphPerspectiveChangeEvent {
+ GraphPerspectiveChangeEventAdapter(Object source) {
+ super(source);
+ }
+
+ // This is the only abstract method on this class; whatever the type of
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public abstract int getType();
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final boolean isNodesRestoredType() {
+ return (getType() & NODES_RESTORED_TYPE) != 0;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final boolean isEdgesRestoredType() {
+ return (getType() & EDGES_RESTORED_TYPE) != 0;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final boolean isNodesHiddenType() {
+ return (getType() & NODES_HIDDEN_TYPE) != 0;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final boolean isEdgesHiddenType() {
+ return (getType() & EDGES_HIDDEN_TYPE) != 0;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final boolean isNodesSelectedType() {
+ return (getType() & NODES_SELECTED_TYPE) != 0;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final boolean isNodesUnselectedType() {
+ return (getType() & NODES_UNSELECTED_TYPE) != 0;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final boolean isEdgesSelectedType() {
+ return (getType() & EDGES_SELECTED_TYPE) != 0;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final boolean isEdgesUnselectedType() {
+ return (getType() & EDGES_UNSELECTED_TYPE) != 0;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Node[] getRestoredNodes() {
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Edge[] getRestoredEdges() {
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Node[] getHiddenNodes() {
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Edge[] getHiddenEdges() {
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Node[] getSelectedNodes() {
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Node[] getUnselectedNodes() {
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Edge[] getSelectedEdges() {
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Edge[] getUnselectedEdges() {
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] getRestoredNodeIndices() {
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] getRestoredEdgeIndices() {
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] getHiddenNodeIndices() {
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] getHiddenEdgeIndices() {
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] getSelectedNodeIndices() {
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] getUnselectedNodeIndices() {
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] getSelectedEdgeIndices() {
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] getUnselectedEdgeIndices() {
+ return null;
+ }
+}
diff --git a/corelibs/fing/src/main/java/fing/model/GraphPerspectiveChangeListenerChain.java b/corelibs/fing/src/main/java/fing/model/GraphPerspectiveChangeListenerChain.java
new file mode 100644
index 0000000..0202856
--- /dev/null
+++ b/corelibs/fing/src/main/java/fing/model/GraphPerspectiveChangeListenerChain.java
@@ -0,0 +1,115 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package fing.model;
+
+import giny.model.GraphPerspectiveChangeEvent;
+import giny.model.GraphPerspectiveChangeListener;
+
+
+// Package visible.
+// Analagous to java.awt.AWTEventMulticaster for chaining together
+// giny.model.GraphPerspectiveChangeListener objects. Example usage:
+//
+// public class Foo implements GraphPerspective
+// {
+// private GraphPerspectiveChangeListener lis = null;
+// public void addGraphPerspectiveChangeListener(
+// GraphPerspectiveChangeListener l) {
+// lis = GraphPerspectiveChangeListenerChain.add(lis, l); }
+// public void removeGraphPerspectiveChangeListener(
+// GraphPerspectiveChangeListener l) {
+// lis = GraphPerspectiveChangeListenerChain.remove(lis, l); }
+// ...
+// }
+class GraphPerspectiveChangeListenerChain implements GraphPerspectiveChangeListener {
+ private final GraphPerspectiveChangeListener a;
+ private final GraphPerspectiveChangeListener b;
+
+ private GraphPerspectiveChangeListenerChain(GraphPerspectiveChangeListener a,
+ GraphPerspectiveChangeListener b) {
+ this.a = a;
+ this.b = b;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt DOCUMENT ME!
+ */
+ public void graphPerspectiveChanged(GraphPerspectiveChangeEvent evt) {
+ a.graphPerspectiveChanged(evt);
+ b.graphPerspectiveChanged(evt);
+ }
+
+ static GraphPerspectiveChangeListener add(GraphPerspectiveChangeListener a,
+ GraphPerspectiveChangeListener b) {
+ if (a == null)
+ return b;
+
+ if (b == null)
+ return a;
+
+ return new GraphPerspectiveChangeListenerChain(a, b);
+ }
+
+ static GraphPerspectiveChangeListener remove(GraphPerspectiveChangeListener l,
+ GraphPerspectiveChangeListener oldl) {
+ if ((l == oldl) || (l == null))
+ return null;
+ else if (l instanceof GraphPerspectiveChangeListenerChain)
+ return ((GraphPerspectiveChangeListenerChain) l).remove(oldl);
+ else
+
+ return l;
+ }
+
+ private GraphPerspectiveChangeListener remove(GraphPerspectiveChangeListener oldl) {
+ if (oldl == a)
+ return b;
+
+ if (oldl == b)
+ return a;
+
+ GraphPerspectiveChangeListener a2 = remove(a, oldl);
+ GraphPerspectiveChangeListener b2 = remove(b, oldl);
+
+ if ((a2 == a) && (b2 == b))
+ return this;
+
+ return add(a2, b2);
+ }
+}
diff --git a/corelibs/fing/src/main/java/fing/model/GraphPerspectiveEdgesHiddenEvent.java b/corelibs/fing/src/main/java/fing/model/GraphPerspectiveEdgesHiddenEvent.java
new file mode 100644
index 0000000..4f1e1be
--- /dev/null
+++ b/corelibs/fing/src/main/java/fing/model/GraphPerspectiveEdgesHiddenEvent.java
@@ -0,0 +1,95 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package fing.model;
+
+import giny.model.Edge;
+import giny.model.GraphPerspective;
+
+
+final class GraphPerspectiveEdgesHiddenEvent extends GraphPerspectiveChangeEventAdapter {
+ private final Edge[] m_hiddenEdges;
+ private final int[] m_hiddenEdgeInx;
+
+ // Note that no copy of the array hiddenEdges is made - the exact
+ // array reference is kept. However, copies are made in the return values
+ // of methods of this class. Note that the Edge objects in the input array
+ // must contain valid RootGraph indices at the time this constructor is
+ // called; further behavior of the Edge objects is not too important
+ // because the getHiddenEdges() method has been deprecated.
+ GraphPerspectiveEdgesHiddenEvent(Object source, Edge[] hiddenEdges) {
+ super(source);
+ m_hiddenEdges = hiddenEdges;
+ m_hiddenEdgeInx = new int[m_hiddenEdges.length];
+
+ for (int i = 0; i < m_hiddenEdgeInx.length; i++)
+ m_hiddenEdgeInx[i] = m_hiddenEdges[i].getRootGraphIndex();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final int getType() {
+ return EDGES_HIDDEN_TYPE;
+ }
+
+ // This method has been deprecated in the Giny API.
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final Edge[] getHiddenEdges() {
+ final Edge[] returnThis = new Edge[m_hiddenEdges.length];
+ System.arraycopy(m_hiddenEdges, 0, returnThis, 0, m_hiddenEdges.length);
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final int[] getHiddenEdgeIndices() {
+ final int[] returnThis = new int[m_hiddenEdgeInx.length];
+ System.arraycopy(m_hiddenEdgeInx, 0, returnThis, 0, m_hiddenEdgeInx.length);
+
+ return returnThis;
+ }
+}
diff --git a/corelibs/fing/src/main/java/fing/model/GraphPerspectiveEdgesRestoredEvent.java b/corelibs/fing/src/main/java/fing/model/GraphPerspectiveEdgesRestoredEvent.java
new file mode 100644
index 0000000..ae44e22
--- /dev/null
+++ b/corelibs/fing/src/main/java/fing/model/GraphPerspectiveEdgesRestoredEvent.java
@@ -0,0 +1,90 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package fing.model;
+
+import giny.model.Edge;
+import giny.model.GraphPerspective;
+
+
+final class GraphPerspectiveEdgesRestoredEvent extends GraphPerspectiveChangeEventAdapter {
+ private final GraphPerspective m_persp;
+ private final int[] m_restoredEdgeInx;
+
+ // Note that no copy of the array restoredEdgeInx is made - the exact
+ // array reference is kept. However, copies are made in the return values
+ // of methods of this class.
+ GraphPerspectiveEdgesRestoredEvent(GraphPerspective persp, int[] restoredEdgeInx) {
+ super(persp);
+ m_persp = persp;
+ m_restoredEdgeInx = restoredEdgeInx;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final int getType() {
+ return EDGES_RESTORED_TYPE;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final Edge[] getRestoredEdges() {
+ final Edge[] returnThis = new Edge[m_restoredEdgeInx.length];
+
+ for (int i = 0; i < returnThis.length; i++)
+ returnThis[i] = m_persp.getRootGraph().getEdge(m_restoredEdgeInx[i]);
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final int[] getRestoredEdgeIndices() {
+ final int[] returnThis = new int[m_restoredEdgeInx.length];
+ System.arraycopy(m_restoredEdgeInx, 0, returnThis, 0, m_restoredEdgeInx.length);
+
+ return returnThis;
+ }
+}
diff --git a/corelibs/fing/src/main/java/fing/model/GraphPerspectiveNodesHiddenEvent.java b/corelibs/fing/src/main/java/fing/model/GraphPerspectiveNodesHiddenEvent.java
new file mode 100644
index 0000000..65d4043
--- /dev/null
+++ b/corelibs/fing/src/main/java/fing/model/GraphPerspectiveNodesHiddenEvent.java
@@ -0,0 +1,95 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package fing.model;
+
+import giny.model.GraphPerspective;
+import giny.model.Node;
+
+
+final class GraphPerspectiveNodesHiddenEvent extends GraphPerspectiveChangeEventAdapter {
+ private final Node[] m_hiddenNodes;
+ private final int[] m_hiddenNodeInx;
+
+ // Note that no copy of the array hiddenNodes is made - the exact
+ // array reference is kept. However, copies are made in the return values
+ // of methods of this class. Note that the Node objects in the input array
+ // must contain valid RootGraph indices at the time this constructor is
+ // called; further behavior of the Node objects is not too important
+ // because the getHiddenNodes() method has been deprecated.
+ GraphPerspectiveNodesHiddenEvent(Object source, Node[] hiddenNodes) {
+ super(source);
+ m_hiddenNodes = hiddenNodes;
+ m_hiddenNodeInx = new int[m_hiddenNodes.length];
+
+ for (int i = 0; i < m_hiddenNodeInx.length; i++)
+ m_hiddenNodeInx[i] = m_hiddenNodes[i].getRootGraphIndex();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final int getType() {
+ return NODES_HIDDEN_TYPE;
+ }
+
+ // This method has been deprecated in the Giny API.
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final Node[] getHiddenNodes() {
+ final Node[] returnThis = new Node[m_hiddenNodes.length];
+ System.arraycopy(m_hiddenNodes, 0, returnThis, 0, m_hiddenNodes.length);
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final int[] getHiddenNodeIndices() {
+ final int[] returnThis = new int[m_hiddenNodeInx.length];
+ System.arraycopy(m_hiddenNodeInx, 0, returnThis, 0, m_hiddenNodeInx.length);
+
+ return returnThis;
+ }
+}
diff --git a/corelibs/fing/src/main/java/fing/model/GraphPerspectiveNodesRestoredEvent.java b/corelibs/fing/src/main/java/fing/model/GraphPerspectiveNodesRestoredEvent.java
new file mode 100644
index 0000000..75b79f8
--- /dev/null
+++ b/corelibs/fing/src/main/java/fing/model/GraphPerspectiveNodesRestoredEvent.java
@@ -0,0 +1,90 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package fing.model;
+
+import giny.model.GraphPerspective;
+import giny.model.Node;
+
+
+final class GraphPerspectiveNodesRestoredEvent extends GraphPerspectiveChangeEventAdapter {
+ private final GraphPerspective m_persp;
+ private final int[] m_restoredNodeInx;
+
+ // Note that no copy of the array restoredNodeInx is made - the exact
+ // array reference is kept. However, copies are made in the return values
+ // of methods of this class.
+ GraphPerspectiveNodesRestoredEvent(GraphPerspective persp, int[] restoredNodeInx) {
+ super(persp);
+ m_persp = persp;
+ m_restoredNodeInx = restoredNodeInx;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final int getType() {
+ return NODES_RESTORED_TYPE;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final Node[] getRestoredNodes() {
+ final Node[] returnThis = new Node[m_restoredNodeInx.length];
+
+ for (int i = 0; i < returnThis.length; i++)
+ returnThis[i] = m_persp.getRootGraph().getNode(m_restoredNodeInx[i]);
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final int[] getRestoredNodeIndices() {
+ final int[] returnThis = new int[m_restoredNodeInx.length];
+ System.arraycopy(m_restoredNodeInx, 0, returnThis, 0, m_restoredNodeInx.length);
+
+ return returnThis;
+ }
+}
diff --git a/corelibs/fing/src/main/java/fing/model/NodeArray.java b/corelibs/fing/src/main/java/fing/model/NodeArray.java
new file mode 100644
index 0000000..999629e
--- /dev/null
+++ b/corelibs/fing/src/main/java/fing/model/NodeArray.java
@@ -0,0 +1,93 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package fing.model;
+
+import giny.model.Node;
+
+
+// Valid indices: [0, Integer.MAX_VALUE - 1].
+class NodeArray {
+ private final static int INITIAL_CAPACITY = 0; // Must be non-negative.
+ private Node[] m_nodeArr;
+
+ NodeArray() {
+ m_nodeArr = new Node[INITIAL_CAPACITY];
+ }
+
+ // Understand that this method will not increase the size of the underlying
+ // array, no matter what.
+ // Throws ArrayIndexOutOfBoundsException if index is negative or
+ // Integer.MAX_VALUE.
+ Node getNodeAtIndex(int index) {
+ // Do pre-checking because try/catch with thrown exception causes huge
+ // performance hit.
+ if ((index >= m_nodeArr.length) && (index != Integer.MAX_VALUE))
+ return null;
+
+ return m_nodeArr[index]; // Exception if Integer.MAX_VALUE or negative.
+ }
+
+ // Understand that this method will potentially increase the size of the
+ // underlying array, but only if two conditions hold:
+ // 1. node is not null and
+ // 2. index is greater than or equal to the length of the array.
+ // Throws ArrayIndexOutOfBoundsException if index is negative or
+ // Integer.MAX_VALUE.
+ void setNodeAtIndex(Node node, int index) {
+ // Do pre-checking because try/catch with thrown exception causes huge
+ // performance hit.
+ if ((index >= m_nodeArr.length) && (node == null) && (index != Integer.MAX_VALUE))
+ return;
+
+ try {
+ m_nodeArr[index] = node;
+ } catch (ArrayIndexOutOfBoundsException e) {
+ if ((index < 0) || (index == Integer.MAX_VALUE)) {
+ throw e;
+ }
+
+ final int newArrSize = (int) Math.min((long) Integer.MAX_VALUE,
+ Math.max((((long) m_nodeArr.length) * 2L) + 1L,
+ ((long) index) + 1L
+ + (long) INITIAL_CAPACITY));
+ Node[] newArr = new Node[newArrSize];
+ System.arraycopy(m_nodeArr, 0, newArr, 0, m_nodeArr.length);
+ m_nodeArr = newArr;
+ m_nodeArr[index] = node;
+ }
+ }
+}
diff --git a/corelibs/fing/src/main/java/fing/model/NodeDepository.java b/corelibs/fing/src/main/java/fing/model/NodeDepository.java
new file mode 100644
index 0000000..5652dc6
--- /dev/null
+++ b/corelibs/fing/src/main/java/fing/model/NodeDepository.java
@@ -0,0 +1,104 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package fing.model;
+
+import giny.model.Node;
+import giny.model.RootGraph;
+
+
+final class NodeDepository implements FingNodeDepot {
+ private final static int INITIAL_CAPACITY = 11; // Must be non-negative.
+ private Node[] m_nodeStack;
+ private int m_size;
+
+ NodeDepository() {
+ m_nodeStack = new Node[INITIAL_CAPACITY];
+ m_size = 0;
+ }
+
+ // Gimme a node, darnit!
+ /**
+ * DOCUMENT ME!
+ *
+ * @param root DOCUMENT ME!
+ * @param index DOCUMENT ME!
+ * @param id DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Node getNode(RootGraph root, int index, String id) {
+ final FNode returnThis;
+
+ if (m_size == 0)
+ returnThis = new FNode();
+ else
+ returnThis = (FNode) m_nodeStack[--m_size];
+
+ returnThis.m_rootGraph = root;
+ returnThis.m_rootGraphIndex = index;
+ returnThis.m_identifier = id;
+
+ return returnThis;
+ }
+
+ // Deinitialize the object's members yourself if you need or want to.
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ */
+ public void recycleNode(Node node) {
+ if (node == null)
+ return;
+
+ try {
+ m_nodeStack[m_size] = node;
+ m_size++;
+ } catch (ArrayIndexOutOfBoundsException e) {
+ final int newArrSize = (int) Math.min((long) Integer.MAX_VALUE,
+ (((long) m_nodeStack.length) * 2L) + 1L);
+
+ if (newArrSize == m_nodeStack.length)
+ throw new IllegalStateException("unable to allocate large enough array");
+
+ Node[] newArr = new Node[newArrSize];
+ System.arraycopy(m_nodeStack, 0, newArr, 0, m_nodeStack.length);
+ m_nodeStack = newArr;
+ m_nodeStack[m_size++] = node;
+ }
+ }
+}
diff --git a/corelibs/fing/src/main/java/fing/model/RootGraphChangeEventAdapter.java b/corelibs/fing/src/main/java/fing/model/RootGraphChangeEventAdapter.java
new file mode 100644
index 0000000..55c4b69
--- /dev/null
+++ b/corelibs/fing/src/main/java/fing/model/RootGraphChangeEventAdapter.java
@@ -0,0 +1,273 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package fing.model;
+
+import giny.model.Edge;
+import giny.model.Node;
+import giny.model.RootGraph;
+import giny.model.RootGraphChangeEvent;
+
+
+abstract class RootGraphChangeEventAdapter extends RootGraphChangeEvent {
+ RootGraphChangeEventAdapter(RootGraph rootGraph) {
+ super(rootGraph);
+ }
+
+ // This is the only abstract method on this class; whatever the type of
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public abstract int getType();
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final boolean isNodesCreatedType() {
+ return (getType() & NODES_CREATED_TYPE) != 0;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final boolean isEdgesCreatedType() {
+ return (getType() & EDGES_CREATED_TYPE) != 0;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final boolean isNodesRemovedType() {
+ return (getType() & NODES_REMOVED_TYPE) != 0;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final boolean isEdgesRemovedType() {
+ return (getType() & EDGES_REMOVED_TYPE) != 0;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final boolean isMetaRelationshipNodesCreatedType() {
+ return (getType() & META_RELATIONSHIP_NODES_CREATED_TYPE) != 0;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final boolean isMetaRelationshipEdgesCreatedType() {
+ return (getType() & META_RELATIONSHIP_EDGES_CREATED_TYPE) != 0;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final boolean isMetaRelationshipNodesRemovedType() {
+ return (getType() & META_RELATIONSHIP_NODES_REMOVED_TYPE) != 0;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final boolean isMetaRelationshipEdgesRemovedType() {
+ return (getType() & META_RELATIONSHIP_EDGES_REMOVED_TYPE) != 0;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Node[] getCreatedNodes() {
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Edge[] getCreatedEdges() {
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Node[] getRemovedNodes() {
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Edge[] getRemovedEdges() {
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Node[][] getMetaRelationshipCreatedNodes() {
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object[][] getMetaRelationshipCreatedEdges() {
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Node[][] getMetaRelationshipRemovedNodes() {
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object[][] getMetaRelationshipRemovedEdges() {
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] getCreatedNodeIndices() {
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] getCreatedEdgeIndices() {
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] getRemovedNodeIndices() {
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] getRemovedEdgeIndices() {
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[][] getMetaRelationshipCreatedNodeIndices() {
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[][] getMetaRelationshipCreatedEdgeIndices() {
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[][] getMetaRelationshipRemovedNodeIndices() {
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[][] getMetaRelationshipRemovedEdgeIndices() {
+ return null;
+ }
+}
diff --git a/corelibs/fing/src/main/java/fing/model/RootGraphChangeListenerChain.java b/corelibs/fing/src/main/java/fing/model/RootGraphChangeListenerChain.java
new file mode 100644
index 0000000..b3655fd
--- /dev/null
+++ b/corelibs/fing/src/main/java/fing/model/RootGraphChangeListenerChain.java
@@ -0,0 +1,110 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package fing.model;
+
+import giny.model.RootGraphChangeEvent;
+import giny.model.RootGraphChangeListener;
+
+
+// Package visible.
+// Analagous to java.awt.AWTEventMulticaster for chaining together
+// giny.model.RootGraphChangeListener objects. Example usage:
+//
+// public class Bar implements RootGraph
+// {
+// private RootGraphChangeListener lis = null;
+// void addRootGraphChangeListener(RootGraphChangeListener l) {
+// lis = RootGraphChangeListenerChain.add(lis, l); }
+// void removeRootGraphChangeListener(RootGraphChangeListener l) {
+// lis = RootGraphChangeListenerChain.remove(lis, l); }
+// ...
+// }
+class RootGraphChangeListenerChain implements RootGraphChangeListener {
+ private final RootGraphChangeListener a;
+ private final RootGraphChangeListener b;
+
+ private RootGraphChangeListenerChain(RootGraphChangeListener a, RootGraphChangeListener b) {
+ this.a = a;
+ this.b = b;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt DOCUMENT ME!
+ */
+ public void rootGraphChanged(RootGraphChangeEvent evt) {
+ a.rootGraphChanged(evt);
+ b.rootGraphChanged(evt);
+ }
+
+ static RootGraphChangeListener add(RootGraphChangeListener a, RootGraphChangeListener b) {
+ if (a == null)
+ return b;
+
+ if (b == null)
+ return a;
+
+ return new RootGraphChangeListenerChain(a, b);
+ }
+
+ static RootGraphChangeListener remove(RootGraphChangeListener l, RootGraphChangeListener oldl) {
+ if ((l == oldl) || (l == null))
+ return null;
+ else if (l instanceof RootGraphChangeListenerChain)
+ return ((RootGraphChangeListenerChain) l).remove(oldl);
+ else
+
+ return l;
+ }
+
+ private RootGraphChangeListener remove(RootGraphChangeListener oldl) {
+ if (oldl == a)
+ return b;
+
+ if (oldl == b)
+ return a;
+
+ RootGraphChangeListener a2 = remove(a, oldl);
+ RootGraphChangeListener b2 = remove(b, oldl);
+
+ if ((a2 == a) && (b2 == b))
+ return this;
+
+ return add(a2, b2);
+ }
+}
diff --git a/corelibs/fing/src/main/java/fing/model/RootGraphEdgesCreatedEvent.java b/corelibs/fing/src/main/java/fing/model/RootGraphEdgesCreatedEvent.java
new file mode 100644
index 0000000..beb166b
--- /dev/null
+++ b/corelibs/fing/src/main/java/fing/model/RootGraphEdgesCreatedEvent.java
@@ -0,0 +1,82 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package fing.model;
+
+import giny.model.Edge;
+import giny.model.RootGraph;
+
+
+// This class is not currently being used. Thus its constructor is private.
+final class RootGraphEdgesCreatedEvent extends RootGraphChangeEventAdapter {
+ private final int[] m_createdEdgeInx;
+
+ // Note that no copy of the array createdEdgeInx is made - the exact
+ // array reference is kept. Methods on this class return this same
+ // array reference.
+ private RootGraphEdgesCreatedEvent(RootGraph rootGraph, int[] createdEdgeInx) {
+ super(rootGraph);
+ m_createdEdgeInx = createdEdgeInx;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final int getType() {
+ return EDGES_CREATED_TYPE;
+ }
+
+ // This method throws an exception, which is fine, because this system of
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final Edge[] getCreatedEdges() {
+ throw new UnsupportedOperationException("don't call this method!");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final int[] getCreatedEdgeIndices() {
+ return m_createdEdgeInx;
+ }
+}
diff --git a/corelibs/fing/src/main/java/fing/model/RootGraphEdgesRemovedEvent.java b/corelibs/fing/src/main/java/fing/model/RootGraphEdgesRemovedEvent.java
new file mode 100644
index 0000000..18b9078
--- /dev/null
+++ b/corelibs/fing/src/main/java/fing/model/RootGraphEdgesRemovedEvent.java
@@ -0,0 +1,86 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package fing.model;
+
+import giny.model.Edge;
+import giny.model.RootGraph;
+
+
+final class RootGraphEdgesRemovedEvent extends RootGraphChangeEventAdapter {
+ private final Edge[] m_removedEdges;
+
+ // Note that no copy of the array removedEdges is made - the exact
+ // array reference is kept. Methods on this class return this same
+ // array reference. Note that the Edge objects in the input array
+ // must contain valid RootGraph indices at the time this constructor is
+ // called; further behavior of the Edge objects is not too important
+ // because the getRemovedEdges() method has been deprecated in both
+ // GraphPerspective and RootGraph listener systems.
+ RootGraphEdgesRemovedEvent(RootGraph rootGraph, Edge[] removedEdges) {
+ super(rootGraph);
+ m_removedEdges = removedEdges;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final int getType() {
+ return EDGES_REMOVED_TYPE;
+ }
+
+ // If this system of listeners and events is to be used publicly (outside
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final Edge[] getRemovedEdges() {
+ return m_removedEdges;
+ }
+
+ // This method throws an exception, which is fine, because this system of
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final int[] getRemovedEdgeIndices() {
+ throw new UnsupportedOperationException("don't call this method!");
+ }
+}
diff --git a/corelibs/fing/src/main/java/fing/model/RootGraphNodesCreatedEvent.java b/corelibs/fing/src/main/java/fing/model/RootGraphNodesCreatedEvent.java
new file mode 100644
index 0000000..f9a34a5
--- /dev/null
+++ b/corelibs/fing/src/main/java/fing/model/RootGraphNodesCreatedEvent.java
@@ -0,0 +1,83 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package fing.model;
+
+import giny.model.Node;
+import giny.model.RootGraph;
+
+
+// This class is currently not being used. Thus its constructor is private.
+final class RootGraphNodesCreatedEvent extends RootGraphChangeEventAdapter {
+ private final int[] m_createdNodeInx;
+
+ // Note that no copy of the array createdNodeInx is made - the exact
+ // array reference is kept. Methods on this class return this same
+ // array reference.
+ private RootGraphNodesCreatedEvent(RootGraph rootGraph, int[] createdNodeInx) {
+ super(rootGraph);
+ m_createdNodeInx = createdNodeInx;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final int getType() {
+ return NODES_CREATED_TYPE;
+ }
+
+ // This method throws an exception, which is fine, because this system of
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final Node[] getCreatedNodes() {
+ throw new UnsupportedOperationException("don't call this method!");
+ }
+
+ // If this system of listeners and events is to be used publicly (outside
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final int[] getCreatedNodeIndices() {
+ return m_createdNodeInx;
+ }
+}
diff --git a/corelibs/fing/src/main/java/fing/model/RootGraphNodesRemovedEvent.java b/corelibs/fing/src/main/java/fing/model/RootGraphNodesRemovedEvent.java
new file mode 100644
index 0000000..ecb0663
--- /dev/null
+++ b/corelibs/fing/src/main/java/fing/model/RootGraphNodesRemovedEvent.java
@@ -0,0 +1,86 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package fing.model;
+
+import giny.model.Node;
+import giny.model.RootGraph;
+
+
+final class RootGraphNodesRemovedEvent extends RootGraphChangeEventAdapter {
+ private final Node[] m_removedNodes;
+
+ // Note that no copy of the array removedNodes is made - the exact
+ // array reference is kept. Methods on this class return this same
+ // array reference. Note that the Node objects in the input array
+ // must contain valid RootGraph indices at the time this constructor is
+ // called; further behavior of the Node objects is not too important
+ // becuase the getRemovedNodes() method has been deprecated in both
+ // GraphPerspective and RootGraph listener systems.
+ RootGraphNodesRemovedEvent(RootGraph rootGraph, Node[] removedNodes) {
+ super(rootGraph);
+ m_removedNodes = removedNodes;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final int getType() {
+ return NODES_REMOVED_TYPE;
+ }
+
+ // If this system of listeners and events is to be used publicly (outside
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final Node[] getRemovedNodes() {
+ return m_removedNodes;
+ }
+
+ // This method throws an exception, which is fine, because this system of
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final int[] getRemovedNodeIndices() {
+ throw new UnsupportedOperationException("don't call this method!");
+ }
+}
diff --git a/corelibs/fing/src/main/java/fing/model/test/ARowanBugTest.java b/corelibs/fing/src/main/java/fing/model/test/ARowanBugTest.java
new file mode 100644
index 0000000..2e0e86e
--- /dev/null
+++ b/corelibs/fing/src/main/java/fing/model/test/ARowanBugTest.java
@@ -0,0 +1,72 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package fing.model.test;
+
+import fing.model.FingRootGraphFactory;
+
+import giny.model.Edge;
+import giny.model.GraphPerspective;
+import giny.model.Node;
+import giny.model.RootGraph;
+
+
+/**
+ *
+ */
+public class ARowanBugTest {
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ */
+ public static void main(String[] args) {
+ final RootGraph root = FingRootGraphFactory.instantiateRootGraph();
+ final int n1 = root.createNode();
+ final int n2 = root.createNode();
+ final int e1 = root.createEdge(n1, n1, /* directed */
+ true);
+ final GraphPerspective persp = root.createGraphPerspective((int[]) null, (int[]) null);
+
+ if (persp.restoreEdge(e1) == 0)
+ throw new IllegalStateException("could not restore valid edge");
+
+ final GraphPerspective persp2 = root.createGraphPerspective(null, new int[] { e1 });
+
+ if (!((persp2.getNodeCount() == 1) && (persp2.getEdgeCount() == 1)))
+ throw new IllegalStateException("bad counts in perspective");
+ }
+}
diff --git a/corelibs/fing/src/main/java/fing/model/test/AddRemoveTest.java b/corelibs/fing/src/main/java/fing/model/test/AddRemoveTest.java
new file mode 100644
index 0000000..f81dd89
--- /dev/null
+++ b/corelibs/fing/src/main/java/fing/model/test/AddRemoveTest.java
@@ -0,0 +1,139 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package fing.model.test;
+
+import fing.model.FingRootGraphFactory;
+
+import giny.model.Edge;
+import giny.model.GraphPerspective;
+import giny.model.Node;
+import giny.model.RootGraph;
+
+import java.util.Iterator;
+
+
+/**
+ *
+ */
+public final class AddRemoveTest {
+ // No constructor.
+ private AddRemoveTest() {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ *
+ * @throws ClassNotFoundException DOCUMENT ME!
+ * @throws InstantiationException DOCUMENT ME!
+ * @throws IllegalAccessException DOCUMENT ME!
+ */
+ public static final void main(String[] args)
+ throws ClassNotFoundException, InstantiationException, IllegalAccessException {
+ final RootGraph root = getRootGraph(args);
+
+ int[] nodeInx;
+ final int[] edgeInx = new int[1000000];
+ final int[] nodeNums = new int[] { 200000, 199900, 200200 };
+ final int iterations = 100;
+
+ for (int foo = 0; foo < iterations; foo++) {
+ boolean print = true;
+
+ if (!((foo % 1) == 0))
+ print = false;
+
+ if (print)
+ System.out.println("at add/remove iteration " + (foo + 1) + " of " + iterations);
+
+ final int numNodes = nodeNums[foo % nodeNums.length];
+
+ if (print)
+ System.out.println("creating " + numNodes + " nodes");
+
+ nodeInx = root.createNodes(numNodes);
+
+ if (print)
+ System.out.println("creating " + edgeInx.length + " edges");
+
+ for (int i = 0; i < edgeInx.length; i++)
+ edgeInx[i] = root.createEdge(nodeInx[i % nodeInx.length],
+ nodeInx[(i * 3) % nodeInx.length]);
+
+ if (print)
+ System.out.println("creating GraphPerspective");
+
+ GraphPerspective persp = root.createGraphPerspective(nodeInx, edgeInx);
+
+ if (print)
+ printme(root, persp);
+
+ if ((foo % 2) == 0) {
+ if (print)
+ System.out.println("removing all edges from RootGraph");
+
+ root.removeEdges(edgeInx);
+ }
+
+ if (print)
+ System.out.println("removing all nodes from RootGraph");
+
+ root.removeNodes(nodeInx);
+
+ if (print)
+ printme(root, persp);
+ }
+ }
+
+ private static void printme(RootGraph root, GraphPerspective persp) {
+ System.out.println("in RootGraph: " + root.getNodeCount() + " nodes and "
+ + root.getEdgeCount() + " edges");
+ System.out.println("in GraphPerspective: " + persp.getNodeCount() + " nodes and "
+ + persp.getEdgeCount() + " edges");
+ System.out.println();
+ }
+
+ private static final RootGraph getRootGraph(String[] mainArgs)
+ throws ClassNotFoundException, InstantiationException, IllegalAccessException {
+ if ((mainArgs.length > 0) && mainArgs[0].equalsIgnoreCase("luna"))
+ return (RootGraph) Class.forName("luna.LunaRootGraph").newInstance();
+ else
+
+ return FingRootGraphFactory.instantiateRootGraph();
+ }
+}
diff --git a/corelibs/fing/src/main/java/fing/model/test/AllGraphPerspectiveMethodsTest.java b/corelibs/fing/src/main/java/fing/model/test/AllGraphPerspectiveMethodsTest.java
new file mode 100644
index 0000000..b1180e4
--- /dev/null
+++ b/corelibs/fing/src/main/java/fing/model/test/AllGraphPerspectiveMethodsTest.java
@@ -0,0 +1,1715 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package fing.model.test;
+
+import fing.model.FingRootGraphFactory;
+
+import giny.model.Edge;
+import giny.model.GraphPerspective;
+import giny.model.Node;
+import giny.model.RootGraph;
+
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+
+
+/**
+ *
+ */
+public final class AllGraphPerspectiveMethodsTest {
+ // No constructor.
+ private AllGraphPerspectiveMethodsTest() {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ */
+ public static final void main(String[] args) {
+ final RootGraph root = FingRootGraphFactory.instantiateRootGraph();
+ final GraphPerspective persp = root.createGraphPerspective((int[]) null, (int[]) null);
+ int[] nodeInx = new int[5];
+
+ for (int i = 0; i < (nodeInx.length - 1); i++)
+ nodeInx[i] = root.createNode();
+
+ int[] edgeInx = new int[7];
+ edgeInx[0] = root.createEdge(nodeInx[0], nodeInx[1], true);
+ edgeInx[1] = root.createEdge(nodeInx[1], nodeInx[2], false);
+ edgeInx[2] = root.createEdge(nodeInx[2], nodeInx[0], true);
+ edgeInx[3] = root.createEdge(nodeInx[2], nodeInx[2], true);
+ edgeInx[4] = root.createEdge(nodeInx[1], nodeInx[1], false);
+ edgeInx[5] = root.createEdge(nodeInx[1], nodeInx[0], true);
+ edgeInx[6] = root.createEdge(nodeInx[3], nodeInx[2], true);
+ nodeInx[nodeInx.length - 1] = root.createNode(null, new int[] { edgeInx[6], edgeInx[2] });
+
+ if (!(root.addNodeMetaChild(nodeInx[0], nodeInx[1])
+ && root.addNodeMetaChild(nodeInx[0], nodeInx[4])
+ && root.addNodeMetaChild(nodeInx[3], nodeInx[1])
+ && root.addNodeMetaChild(nodeInx[4], nodeInx[4])
+ && root.addEdgeMetaChild(nodeInx[3], edgeInx[6])
+ && root.addEdgeMetaChild(nodeInx[3], edgeInx[0])
+ && root.addEdgeMetaChild(nodeInx[0], edgeInx[4])))
+ throw new IllegalStateException("unable to create meta relationship");
+
+ for (int i = 0; i < nodeInx.length; i++)
+ if (persp.restoreNode(nodeInx[i]) != nodeInx[i])
+ throw new IllegalStateException("unable to restore node");
+
+ for (int i = 0; i < edgeInx.length; i++)
+ if (persp.restoreEdge(edgeInx[i]) != edgeInx[i])
+ throw new IllegalStateException("unable to restore edge");
+
+ RootGraph root2 = FingRootGraphFactory.instantiateRootGraph();
+ root2.createNode();
+ root2.createEdge(((Node) root2.nodesIterator().next()).getRootGraphIndex(),
+ ((Node) root2.nodesIterator().next()).getRootGraphIndex());
+
+ final Node root2Node = (Node) root2.nodesIterator().next();
+ final Edge root2Edge = (Edge) root2.edgesIterator().next();
+ final Node nodeNotInPersp = root.getNode(root.createNode());
+ final Edge edge1NotInPersp = root.getEdge(root.createEdge(nodeInx[1], nodeInx[3], true));
+ final Edge edge2NotInPersp = root.getEdge(root.createEdge(nodeInx[2],
+ nodeNotInPersp.getRootGraphIndex(),
+ false));
+ root.addNodeMetaChild(nodeInx[2], nodeNotInPersp.getRootGraphIndex());
+ root.addNodeMetaChild(nodeNotInPersp.getRootGraphIndex(), nodeInx[4]);
+ root.addEdgeMetaChild(nodeInx[3], edge1NotInPersp.getRootGraphIndex());
+
+ int[] rootNodeInx = root.getNodeIndicesArray();
+ int minNodeInx = 0;
+
+ for (int i = 0; i < rootNodeInx.length; i++)
+ minNodeInx = Math.min(minNodeInx, rootNodeInx[i]);
+
+ int[] rootEdgeInx = root.getEdgeIndicesArray();
+ int minEdgeInx = 0;
+
+ for (int i = 0; i < rootEdgeInx.length; i++)
+ minEdgeInx = Math.min(minEdgeInx, rootEdgeInx[i]);
+
+ // Restore and hide nodes and edges.
+ Node node2NotInPersp = root.getNode(root.createNode());
+ Edge edge3NotInPersp = root.getEdge(root.createEdge(nodeInx[1], nodeInx[2], true));
+ persp.restoreNode(node2NotInPersp);
+ persp.restoreEdge(edge3NotInPersp);
+ persp.hideNode(node2NotInPersp);
+ persp.hideEdge(edge3NotInPersp);
+
+ // Not testing GraphPerspectiveChangeListener methods.
+
+ // clone().
+ final GraphPerspective persp2 = (GraphPerspective) persp.clone();
+
+ if ((persp2.getNodeCount() != persp.getNodeCount())
+ || (persp2.getEdgeCount() != persp.getEdgeCount()))
+ throw new IllegalStateException("clone has different topology");
+
+ int[] edgeInxArr = persp2.getEdgeIndicesArray();
+
+ for (int i = 0; i < edgeInxArr.length; i++)
+ if (persp2.hideEdge(edgeInxArr[i]) != edgeInxArr[i])
+ throw new IllegalStateException("cannot hide edge in clone");
+
+ if (persp2.getEdgeCount() != 0)
+ throw new IllegalStateException("some edges in clone remaining");
+
+ if (persp2.getNodeCount() != persp.getNodeCount())
+ throw new IllegalStateException("node counts should still be the same");
+
+ int[] nodeInxArr = persp2.getNodeIndicesArray();
+
+ for (int i = 0; i < nodeInxArr.length; i++)
+ if (persp2.hideNode(nodeInxArr[i]) != nodeInxArr[i])
+ throw new IllegalStateException("cannot hide node in clone");
+
+ if ((persp2.getNodeCount() != 0) || (persp2.getEdgeCount() != 0))
+ throw new IllegalStateException("nodes or edges remaining");
+
+ // getRootGraph().
+ if ((persp.getRootGraph() != root) || (persp2.getRootGraph() != root))
+ throw new IllegalStateException("incorrect RootGraph");
+
+ // getNodeCount().
+ if (persp.getNodeCount() != 5)
+ throw new IllegalStateException("wrong number of nodes");
+
+ // getEdgeCount().
+ if (persp.getEdgeCount() != 7)
+ throw new IllegalStateException("wrong number of edges");
+
+ // nodesIterator().
+ Iterator nodesIter = persp.nodesIterator();
+ Node[] twoNodes = new Node[] { (Node) nodesIter.next(), (Node) nodesIter.next() };
+
+ // nodesList().
+ List nodesList = persp.nodesList();
+
+ if (nodesList.size() != 5)
+ throw new IllegalStateException("incorrect node List size");
+
+ for (int i = 0; i < nodesList.size(); i++) {
+ Node n = (Node) nodesList.get(i);
+ }
+
+ // getNodeIndicesArray().
+ int[] nodeIndicesArray = persp.getNodeIndicesArray();
+
+ if (nodeIndicesArray.length != nodesList.size())
+ throw new IllegalStateException("size of nodes List and length of node indices array don't match");
+
+ for (int j = 0; j < nodeInx.length; j++) {
+ for (int i = 0;; i++) {
+ if (nodeIndicesArray[i] == nodeInx[j])
+ break;
+ }
+ }
+
+ // edgesIterator().
+ Iterator edgesIter = persp.edgesIterator();
+ Edge[] twoEdges = new Edge[] { (Edge) edgesIter.next(), (Edge) edgesIter.next() };
+
+ // edgesList().
+ List edgesList = persp.edgesList();
+
+ if (edgesList.size() != 7)
+ throw new IllegalStateException("incorrect edge List size");
+
+ for (int i = 0; i < edgesList.size(); i++) {
+ Edge e = (Edge) edgesList.get(i);
+ }
+
+ // getEdgeIndicesArray().
+ int[] edgeIndicesArray = persp.getEdgeIndicesArray();
+
+ if (edgeIndicesArray.length != edgesList.size())
+ throw new IllegalStateException("size of edges List and length of edge indices array don't match");
+
+ for (int j = 0; j < edgeInx.length; j++) {
+ for (int i = 0;; i++) {
+ if (edgeIndicesArray[i] == edgeInx[j])
+ break;
+ }
+ }
+
+ // getEdgeIndicesArray(int, int, boolean, boolean).
+ int[] connEdges;
+ connEdges = persp.getEdgeIndicesArray(nodeInx[1], nodeInx[0], false, true);
+
+ if (connEdges.length != 2)
+ throw new IllegalStateException("not 2 connecting edges");
+
+ for (int i = 0;; i++)
+ if (connEdges[i] == edgeInx[0])
+ break;
+
+ for (int i = 0;; i++)
+ if (connEdges[i] == edgeInx[5])
+ break;
+
+ connEdges = persp.getEdgeIndicesArray(nodeInx[0], nodeInx[3], true, true);
+
+ if (connEdges.length != 0)
+ throw new IllegalStateException("not 0 connecting edges");
+
+ connEdges = persp.getEdgeIndicesArray(nodeInx[1], nodeInx[2], false, true);
+
+ if (connEdges.length != 0)
+ throw new IllegalStateException("not 0 connecting edges");
+
+ connEdges = persp.getEdgeIndicesArray(nodeInx[2], nodeInx[1], true, false);
+
+ if (connEdges.length != 1)
+ throw new IllegalStateException("not 1 connecting edge");
+
+ for (int i = 0;; i++)
+ if (connEdges[i] == edgeInx[1])
+ break;
+
+ connEdges = persp.getEdgeIndicesArray(nodeInx[2], nodeInx[2], false, false);
+
+ if (connEdges.length != 1)
+ throw new IllegalStateException("not 1 connecting edge");
+
+ for (int i = 0;; i++)
+ if (connEdges[i] == edgeInx[3])
+ break;
+
+ connEdges = persp.getEdgeIndicesArray(nodeInx[2], nodeInx[2], true, true);
+
+ if (connEdges.length != 1)
+ throw new IllegalStateException("not 1 connecting edge");
+
+ for (int i = 0;; i++)
+ if (connEdges[i] == edgeInx[3])
+ break;
+
+ connEdges = persp.getEdgeIndicesArray(nodeInx[2], nodeInx[3], false, false);
+
+ if (connEdges.length != 0)
+ throw new IllegalStateException("not 0 connecting edges");
+
+ connEdges = persp.getEdgeIndicesArray(nodeInx[3], nodeInx[2], false, false);
+
+ if (connEdges.length != 1)
+ throw new IllegalStateException("not 1 connecting edge");
+
+ for (int i = 0;; i++)
+ if (connEdges[i] == edgeInx[6])
+ break;
+
+ connEdges = persp.getEdgeIndicesArray(nodeInx[4], nodeInx[0], true, true);
+
+ if (connEdges.length != 0)
+ throw new IllegalStateException("not 0 connecting edges");
+
+ connEdges = persp.getEdgeIndicesArray(99, 0, true, true);
+
+ if (connEdges != null)
+ throw new IllegalStateException("not null");
+
+ connEdges = persp.getEdgeIndicesArray(nodeInx[0], minNodeInx - 1, true, false);
+
+ if (connEdges != null)
+ throw new IllegalStateException("not null");
+
+ if ((persp.getEdgeIndicesArray(Integer.MAX_VALUE, Integer.MIN_VALUE, true, false) != null)
+ || (persp.getEdgeIndicesArray(Integer.MIN_VALUE, Integer.MAX_VALUE, false, false) != null)
+ || (persp.getEdgeIndicesArray(nodeInx[0], nodeNotInPersp.getRootGraphIndex(), false,
+ true) != null))
+ throw new IllegalStateException("not null");
+
+ // hide/restore mothods are tested elsewhere.
+
+ // containsNode(Node).
+ if (!persp.containsNode(twoNodes[1]))
+ throw new IllegalStateException("GraphPersp does not contain node");
+
+ if (persp.containsNode(root2Node))
+ throw new IllegalStateException("GraphPersp contains node from other");
+
+ if (persp.containsNode(nodeNotInPersp)
+ || !persp.getRootGraph().containsNode(nodeNotInPersp))
+ throw new IllegalStateException("GraphPerspective contains node");
+
+ // containsNode(Node, boolean).
+ if (persp.containsNode(nodeNotInPersp, false))
+ throw new IllegalStateException("GraphPersp should not contain node");
+
+ if (!persp.containsNode(nodeNotInPersp, true))
+ throw new IllegalStateException("GraphPersp should contain node recur.");
+
+ // containsEdge(Edge).
+ if (!persp.containsEdge(twoEdges[1]))
+ throw new IllegalStateException("GraphPersp does not contain edge");
+
+ if (persp.containsEdge(root2Edge))
+ throw new IllegalStateException("GraphPersp contains edge from other");
+
+ if (persp.containsEdge(edge1NotInPersp) || persp.containsEdge(edge2NotInPersp)
+ || !(persp.getRootGraph().containsEdge(edge1NotInPersp)
+ && persp.getRootGraph().containsEdge(edge2NotInPersp)))
+ throw new IllegalStateException("GraphPerspective contains edge");
+
+ // containsEdge(Edge, boolean).
+ if (persp.containsEdge(edge1NotInPersp, false))
+ throw new IllegalStateException("GraphPersp should not contains edge");
+
+ if (!persp.containsEdge(edge1NotInPersp, true))
+ throw new IllegalStateException("GraphPersp should contain edge recur.");
+
+ // join(GraphPerspective).
+
+ // createGraphPerspective(Node[], Edge[]).
+
+ // createGraphPerspective(int[], int[]).
+
+ // createGraphPerspective(Filter).
+
+ // neighborsList(Node).
+ List neighList = persp.neighborsList(persp.getNode(nodeInx[0]));
+
+ if (neighList.size() != 2)
+ throw new IllegalStateException("wrong number of neighbors");
+
+ neighList = persp.neighborsList(persp.getNode(nodeInx[1]));
+
+ if (neighList.size() != 3)
+ throw new IllegalStateException("wrong number of neighbors");
+
+ neighList = persp.neighborsList(persp.getNode(nodeInx[2]));
+
+ if (neighList.size() != 4)
+ throw new IllegalStateException("wrong number of neighbors");
+
+ int[] neighInx = new int[neighList.size()];
+
+ for (int i = 0; i < neighList.size(); i++) {
+ Node node = (Node) neighList.get(i);
+ int nodeIndex = node.getRootGraphIndex();
+
+ if (persp.getNode(nodeIndex) == null)
+ throw new IllegalStateException("bad node in neighbors");
+
+ if (nodeIndex == 0)
+ throw new IllegalStateException("node index is 0");
+
+ int index = -1;
+
+ while (true) {
+ if (neighInx[++index] != 0) {
+ if (neighInx[index] == nodeIndex)
+ throw new IllegalStateException("duplicate neighbor");
+ else
+
+ continue;
+ } else {
+ neighInx[index] = nodeIndex;
+
+ break;
+ }
+ }
+ }
+
+ neighList = persp.neighborsList(persp.getNode(nodeInx[3]));
+
+ if (neighList.size() != 1)
+ throw new IllegalStateException("wrong number of neighbors");
+
+ neighList = persp.neighborsList(persp.getNode(nodeInx[4]));
+
+ if (neighList.size() != 0)
+ throw new IllegalStateException("wrong number of neighbors");
+
+ neighList = persp.neighborsList(root2Node);
+
+ if (neighList != null)
+ throw new IllegalStateException("neighbors List isn't null");
+
+ neighList = persp.neighborsList(nodeNotInPersp);
+
+ if (neighList != null)
+ throw new IllegalStateException("neighbors List isn't null");
+
+ // neighborsArray(int).
+ neighInx = persp.neighborsArray(nodeInx[1]);
+
+ if (neighInx.length != 3)
+ throw new IllegalStateException("wrong number of neighbors");
+
+ for (int i = 0;; i++)
+ if (neighInx[i] == nodeInx[0])
+ break;
+
+ for (int i = 0;; i++)
+ if (neighInx[i] == nodeInx[1])
+ break;
+
+ for (int i = 0;; i++)
+ if (neighInx[i] == nodeInx[2])
+ break;
+
+ neighInx = persp.neighborsArray(nodeInx[4]);
+
+ if (neighInx.length != 0)
+ throw new IllegalStateException("wrong number of neighbors");
+
+ if ((persp.neighborsArray(nodeNotInPersp.getRootGraphIndex()) != null)
+ || (persp.neighborsArray(Integer.MIN_VALUE) != null)
+ || (persp.neighborsArray(Integer.MAX_VALUE) != null)
+ || (persp.neighborsArray(0) != null) || (persp.neighborsArray(1) != null)
+ || (persp.neighborsArray(minNodeInx - 1) != null))
+ throw new IllegalStateException("expected null");
+
+ // isNeighbor(Node, Node).
+ if (persp.isNeighbor(persp.getNode(nodeInx[4]), persp.getNode(nodeInx[4])))
+ throw new IllegalStateException("node with no edges is its own neigh");
+
+ if (persp.isNeighbor(persp.getNode(nodeInx[3]), persp.getNode(nodeInx[1])))
+ throw new IllegalStateException("nodes are neighbors");
+
+ if (!persp.isNeighbor(persp.getNode(nodeInx[1]), persp.getNode(nodeInx[0])))
+ throw new IllegalStateException("nodes are not neighbors");
+
+ if (persp.isNeighbor(root2Node, persp.getNode(nodeInx[2])))
+ throw new IllegalStateException("nodes from another graph is neighbor");
+
+ if (persp.isNeighbor(persp.getNode(nodeInx[0]), nodeNotInPersp))
+ throw new IllegalStateException("neighbor with node not in GraphPersp");
+
+ // isNeighbor(int, int).
+ if (persp.isNeighbor(nodeInx[1], nodeInx[3]) || !root.isNeighbor(nodeInx[1], nodeInx[3]))
+ throw new IllegalStateException("bad neighbors");
+
+ if (!persp.isNeighbor(nodeInx[1], nodeInx[1]))
+ throw new IllegalStateException("node with self edge not neigbhor");
+
+ if (persp.isNeighbor(nodeInx[0], nodeInx[0]))
+ throw new IllegalStateException("node with no self edge is neighbor");
+
+ if (persp.isNeighbor(98, 99))
+ throw new IllegalStateException("positive nodes are neighbors");
+
+ if (!persp.isNeighbor(nodeInx[3], nodeInx[2]))
+ throw new IllegalStateException("nodes are not neighbors");
+
+ if (!persp.isNeighbor(nodeInx[1], nodeInx[2]))
+ throw new IllegalStateException("nodes are not neighbors");
+
+ if (persp.isNeighbor(Integer.MAX_VALUE, Integer.MIN_VALUE)
+ || persp.isNeighbor(Integer.MIN_VALUE, Integer.MAX_VALUE)
+ || persp.isNeighbor(minNodeInx - 1, nodeInx[0]) || persp.isNeighbor(0, 1))
+ throw new IllegalStateException("extreme neighbors");
+
+ // edgeExists(Node, Node).
+ if (persp.edgeExists(persp.getNode(nodeInx[3]), persp.getNode(nodeInx[1])))
+ throw new IllegalStateException("edge exists");
+
+ if (persp.edgeExists(persp.getNode(nodeInx[0]), root2Node))
+ throw new IllegalStateException("edge exists with node of other graph");
+
+ if (!persp.edgeExists(persp.getNode(nodeInx[0]), persp.getNode(nodeInx[1])))
+ throw new IllegalStateException("edge does not exist");
+
+ if (!persp.edgeExists(persp.getNode(nodeInx[1]), persp.getNode(nodeInx[2])))
+ throw new IllegalStateException("edge does not exist");
+
+ if (persp.edgeExists(persp.getNode(nodeInx[2]), nodeNotInPersp)
+ || !root.edgeExists(persp.getNode(nodeInx[2]), nodeNotInPersp))
+ throw new IllegalStateException("bad edgeExists");
+
+ // edgeExists(int, int).
+ if (persp.edgeExists(nodeInx[1], nodeInx[3]))
+ throw new IllegalStateException("edge exists in RootGraph, not persp");
+
+ if (persp.edgeExists(minNodeInx - 1, nodeInx[1]))
+ throw new IllegalStateException("bad edgeExists()");
+
+ if (persp.edgeExists(0, 0))
+ throw new IllegalStateException("0 -> 0");
+
+ if (persp.edgeExists(nodeInx[2], nodeInx[3]))
+ throw new IllegalStateException("edge exists in opposite direction");
+
+ if (persp.edgeExists(nodeInx[4], nodeInx[2]))
+ throw new IllegalStateException("edge exists on node with no edge");
+
+ if (persp.edgeExists(nodeInx[0], nodeInx[0]))
+ throw new IllegalStateException("self-edge exists");
+
+ if (persp.edgeExists(98, 99))
+ throw new IllegalStateException("edge exists between positive nodes");
+
+ if (!persp.edgeExists(nodeInx[1], nodeInx[1]))
+ throw new IllegalStateException("self-edge does not exist [undirected]");
+
+ if (!persp.edgeExists(nodeInx[2], nodeInx[2]))
+ throw new IllegalStateException("self-edge does not exist [directed]");
+
+ if (!persp.edgeExists(nodeInx[3], nodeInx[2]))
+ throw new IllegalStateException("edge does not exist");
+
+ if (!persp.edgeExists(nodeInx[1], nodeInx[0]))
+ throw new IllegalStateException("edge does not exist");
+
+ if (persp.edgeExists(Integer.MAX_VALUE, Integer.MIN_VALUE)
+ || persp.edgeExists(Integer.MIN_VALUE, Integer.MAX_VALUE))
+ throw new IllegalStateException("MIN_VALUE and MAX_VALUE edge exists");
+
+ // getEdgeCount(Node, Node, boolean).
+ if (persp.getEdgeCount(persp.getNode(nodeInx[0]), persp.getNode(nodeInx[1]), true) != 1)
+ throw new IllegalStateException("wrong number in edge count");
+
+ if ((persp.getEdgeCount(persp.getNode(nodeInx[0]), root2Node, true) != -1)
+ || (persp.getEdgeCount(persp.getNode(nodeInx[1]), nodeNotInPersp, false) != -1))
+ throw new IllegalStateException("edge count not -1");
+
+ if (persp.getEdgeCount(persp.getNode(nodeInx[1]), persp.getNode(nodeInx[1]), false) != 0)
+ throw new IllegalStateException("edge count not 0");
+
+ // getEdgeCount(int, int, boolean).
+ if (persp.getEdgeCount(nodeInx[3], nodeInx[2], true) != 1)
+ throw new IllegalStateException("edge count not 1");
+
+ if (persp.getEdgeCount(nodeInx[2], nodeInx[3], true) != 0)
+ throw new IllegalStateException("edge count not 0");
+
+ if (persp.getEdgeCount(nodeInx[1], nodeInx[2], false) != 0)
+ throw new IllegalStateException("edge count not 0");
+
+ if (persp.getEdgeCount(nodeInx[1], nodeInx[1], true) != 1)
+ throw new IllegalStateException("edge count not 1 for und. self edge");
+
+ if (persp.getEdgeCount(99, 98, true) != -1)
+ throw new IllegalStateException("edge count not -1");
+
+ if ((persp.getEdgeCount(Integer.MAX_VALUE, Integer.MIN_VALUE, false) != -1)
+ || (persp.getEdgeCount(Integer.MIN_VALUE, Integer.MAX_VALUE, true) != -1)
+ || (persp.getEdgeCount(nodeInx[0], minNodeInx - 1, true) != -1))
+ throw new IllegalStateException("edge count not -1");
+
+ if ((persp.getEdgeCount(nodeInx[1], nodeInx[3], true) != 0)
+ || !(root.getEdgeCount(nodeInx[1], nodeInx[3], true) > 0))
+ throw new IllegalStateException("bad edge count between 2 nodes");
+
+ // edgesList(Node, Node).
+ edgesList = persp.edgesList(persp.getNode(nodeInx[3]), persp.getNode(nodeInx[1]));
+
+ if (edgesList.size() != 0)
+ throw new IllegalStateException("edges List not of size 0");
+
+ edgesList = persp.edgesList(persp.getNode(nodeInx[0]), root2Node);
+
+ if (edgesList != null)
+ throw new IllegalStateException("not null");
+
+ edgesList = persp.edgesList(persp.getNode(nodeInx[0]), persp.getNode(nodeInx[1]));
+
+ if (edgesList.size() != 1)
+ throw new IllegalStateException("edges List not of size 1");
+
+ if (((Edge) edgesList.get(0)).getRootGraphIndex() != edgeInx[0])
+ throw new IllegalStateException("wrong edge");
+
+ edgesList = persp.edgesList(persp.getNode(nodeInx[2]), persp.getNode(nodeInx[1]));
+
+ if (edgesList.size() != 1)
+ throw new IllegalStateException("edges List not of size 1");
+
+ if (((Edge) edgesList.get(0)).getRootGraphIndex() != edgeInx[1])
+ throw new IllegalStateException("wrong edge");
+
+ edgesList = persp.edgesList(persp.getNode(nodeInx[2]), persp.getNode(nodeInx[2]));
+
+ if (edgesList.size() != 1)
+ throw new IllegalStateException("edges List not of size 1");
+
+ if (((Edge) edgesList.get(0)).getRootGraphIndex() != edgeInx[3])
+ throw new IllegalStateException("wrong edge");
+
+ edgesList = persp.edgesList(persp.getNode(nodeInx[1]), persp.getNode(nodeInx[4]));
+
+ if (edgesList.size() != 0)
+ throw new IllegalStateException("edges List not of size 0");
+
+ edgesList = persp.edgesList(persp.getNode(nodeInx[3]), nodeNotInPersp);
+
+ if (edgesList != null)
+ throw new IllegalStateException("expected null");
+
+ // edgesList(int, int, boolean).
+ edgesList = persp.edgesList(nodeInx[2], nodeInx[0], true);
+
+ if (edgesList.size() != 1)
+ throw new IllegalStateException("edges List not of size 1");
+
+ if (((Edge) edgesList.get(0)).getRootGraphIndex() != edgeInx[2])
+ throw new IllegalStateException("wrong edge");
+
+ edgesList = persp.edgesList(nodeInx[4], nodeInx[3], false);
+
+ if (edgesList.size() != 0)
+ throw new IllegalStateException("edges List not of size 0");
+
+ edgesList = persp.edgesList(99, minNodeInx - 1, true);
+
+ if (edgesList != null)
+ throw new IllegalStateException("not null");
+
+ if ((persp.edgesList(Integer.MAX_VALUE, Integer.MIN_VALUE, true) != null)
+ || (persp.edgesList(Integer.MIN_VALUE, Integer.MAX_VALUE, false) != null))
+ throw new IllegalStateException("not null");
+
+ // getEdgeIndicesArray(int, int, boolean).
+ connEdges = persp.getEdgeIndicesArray(nodeInx[1], nodeInx[1], false);
+
+ if (connEdges.length != 0)
+ throw new IllegalStateException("not 0 connecting edges");
+
+ connEdges = persp.getEdgeIndicesArray(nodeInx[1], nodeInx[1], true);
+
+ if (connEdges.length != 1)
+ throw new IllegalStateException("not 1 connecting edge");
+
+ for (int i = 0;; i++)
+ if (connEdges[i] == edgeInx[4])
+ break;
+
+ connEdges = persp.getEdgeIndicesArray(nodeInx[1], nodeInx[0], true);
+
+ if (connEdges.length != 1)
+ throw new IllegalStateException("not 1 connecting edge");
+
+ for (int i = 0;; i++)
+ if (connEdges[i] == edgeInx[5])
+ break;
+
+ connEdges = persp.getEdgeIndicesArray(minNodeInx - 1, nodeInx[2], true);
+
+ if (connEdges != null)
+ throw new IllegalStateException("not null");
+
+ connEdges = persp.getEdgeIndicesArray(nodeInx[1], 99, true);
+
+ if (connEdges != null)
+ throw new IllegalStateException("not null");
+
+ if ((persp.getEdgeIndicesArray(Integer.MAX_VALUE, Integer.MIN_VALUE, true) != null)
+ || (persp.getEdgeIndicesArray(Integer.MIN_VALUE, Integer.MAX_VALUE, false) != null))
+ throw new IllegalStateException("not null");
+
+ // getInDegree(Node).
+ if ((persp.getInDegree(root2Node) != -1) || (persp.getInDegree(nodeNotInPersp) != -1))
+ throw new IllegalStateException("not in degree -1 for other node");
+
+ if (persp.getInDegree(persp.getNode(nodeInx[2])) != 3)
+ throw new IllegalStateException("not in degree 3 for node");
+
+ if (persp.getInDegree(persp.getNode(nodeInx[3])) != 0)
+ throw new IllegalStateException("not in degree 0 for node");
+
+ if (persp.getInDegree(persp.getNode(nodeInx[4])) != 0)
+ throw new IllegalStateException("not in degree 0 for node");
+
+ if (persp.getInDegree(persp.getNode(nodeInx[0])) != 2)
+ throw new IllegalStateException("not in degree 2 for node");
+
+ if (persp.getInDegree(persp.getNode(nodeInx[1])) != 3)
+ throw new IllegalStateException("not in degree 3 for node");
+
+ // getInDegree(int).
+ if ((persp.getInDegree(minNodeInx - 1) != -1) || (persp.getInDegree(0) != -1)
+ || (persp.getInDegree(99) != -1))
+ throw new IllegalStateException("not in degree -1");
+
+ if (persp.getInDegree(nodeInx[1]) != 3)
+ throw new IllegalStateException("not in degree 3");
+
+ if (persp.getInDegree(nodeInx[0]) != 2)
+ throw new IllegalStateException("not in degree 2");
+
+ if (persp.getInDegree(Integer.MAX_VALUE) != -1)
+ throw new IllegalStateException("not in degree -1");
+
+ // getInDegree(Node, boolean).
+ if ((persp.getInDegree(root2Node, true) != -1)
+ || (persp.getInDegree(nodeNotInPersp, false) != -1))
+ throw new IllegalStateException("not in degree -1 for other node");
+
+ if (persp.getInDegree(persp.getNode(nodeInx[1]), false) != 1)
+ throw new IllegalStateException("not in degree 1");
+
+ if (persp.getInDegree(persp.getNode(nodeInx[2]), false) != 2)
+ throw new IllegalStateException("not in degree 2");
+
+ if (persp.getInDegree(persp.getNode(nodeInx[2]), true) != 3)
+ throw new IllegalStateException("not in degree 3");
+
+ // getInDegree(int, boolean).
+ if ((persp.getInDegree(minNodeInx - 1, false) != -1) || (persp.getInDegree(0, true) != -1)
+ || (persp.getInDegree(99, false) != -1))
+ throw new IllegalStateException("not in degree -1");
+
+ if (persp.getInDegree(nodeInx[0], true) != 2)
+ throw new IllegalStateException("not in degree 2");
+
+ if (persp.getInDegree(nodeInx[0], false) != 2)
+ throw new IllegalStateException("not in degree 2");
+
+ if (persp.getInDegree(nodeInx[4], true) != 0)
+ throw new IllegalStateException("not in degree 0");
+
+ if (persp.getInDegree(nodeInx[1], false) != 1)
+ throw new IllegalStateException("not in degree 1");
+
+ if (persp.getInDegree(Integer.MIN_VALUE, true) != -1)
+ throw new IllegalStateException("not in degree -1");
+
+ // getOutDegree(Node).
+ if ((persp.getOutDegree(root2Node) != -1) || (persp.getOutDegree(nodeNotInPersp) != -1))
+ throw new IllegalStateException("not out degree -1");
+
+ if (persp.getOutDegree(persp.getNode(nodeInx[2])) != 3)
+ throw new IllegalStateException("not out degree 3");
+
+ if (persp.getOutDegree(persp.getNode(nodeInx[1])) != 3)
+ throw new IllegalStateException("not out degree 3");
+
+ if (persp.getOutDegree(persp.getNode(nodeInx[4])) != 0)
+ throw new IllegalStateException("not out degree 0");
+
+ // getOutDegree(int).
+ if ((persp.getOutDegree(minNodeInx - 1) != -1) || (persp.getOutDegree(0) != -1)
+ || (persp.getOutDegree(101) != -1))
+ throw new IllegalStateException("not out degree -1");
+
+ if (persp.getOutDegree(nodeInx[3]) != 1)
+ throw new IllegalStateException("not out degree 1");
+
+ if (persp.getOutDegree(nodeInx[0]) != 1)
+ throw new IllegalStateException("not out degree 1");
+
+ if (persp.getOutDegree(Integer.MIN_VALUE) != -1)
+ throw new IllegalStateException("not out degree -1");
+
+ // getOutDegree(Node, boolean).
+ if ((persp.getOutDegree(root2Node, false) != -1)
+ || (persp.getOutDegree(nodeNotInPersp, true) != -1))
+ throw new IllegalStateException("not out degree -1");
+
+ if (persp.getOutDegree(persp.getNode(nodeInx[1]), false) != 1)
+ throw new IllegalStateException("not out degree 1");
+
+ if (persp.getOutDegree(persp.getNode(nodeInx[1]), true) != 3)
+ throw new IllegalStateException("not out degree 1");
+
+ if ((persp.getOutDegree(persp.getNode(nodeInx[0]), false) != 1)
+ || (persp.getOutDegree(persp.getNode(nodeInx[0]), true) != 1))
+ throw new IllegalStateException("not out degree 1");
+
+ // getOutDegree(int, boolean).
+ if ((persp.getOutDegree(minNodeInx - 3, false) != -1)
+ || (persp.getOutDegree(0, true) != -1) || (persp.getOutDegree(2, false) != -1))
+ throw new IllegalStateException("not out degree -1");
+
+ if ((persp.getOutDegree(nodeInx[2], false) != 2)
+ || (persp.getOutDegree(nodeInx[2], true) != 3))
+ throw new IllegalStateException("not correct out degree");
+
+ if ((persp.getOutDegree(nodeInx[3], false) != 1)
+ || (persp.getOutDegree(nodeInx[3], true) != 1))
+ throw new IllegalStateException("not out degree 1");
+
+ if ((persp.getOutDegree(nodeInx[4], true) != 0)
+ || (persp.getOutDegree(nodeInx[4], false) != 0))
+ throw new IllegalStateException("not out degree 0");
+
+ if (persp.getOutDegree(Integer.MAX_VALUE, false) != -1)
+ throw new IllegalStateException("not out degree -1");
+
+ // getDegree(Node).
+ if ((persp.getDegree(root2Node) != -1) || (persp.getDegree(nodeNotInPersp) != -1))
+ throw new IllegalStateException("not degree -1 for other node");
+
+ if (persp.getDegree(persp.getNode(nodeInx[0])) != 3)
+ throw new IllegalStateException("not degree 3");
+
+ if (persp.getDegree(persp.getNode(nodeInx[1])) != 4)
+ throw new IllegalStateException("not degree 4");
+
+ // getDegree(int).
+ if ((persp.getDegree(minNodeInx - 2) != -1) || (persp.getDegree(0) != -1)
+ || (persp.getDegree(13) != -1))
+ throw new IllegalStateException("not degree -1");
+
+ if (persp.getDegree(nodeInx[2]) != 4)
+ throw new IllegalStateException("not degree 4");
+
+ if (persp.getDegree(nodeInx[3]) != 1)
+ throw new IllegalStateException("not degree 1");
+
+ if (persp.getDegree(nodeInx[4]) != 0)
+ throw new IllegalStateException("not degree 0");
+
+ if ((persp.getDegree(Integer.MAX_VALUE) != -1)
+ || (persp.getDegree(Integer.MIN_VALUE) != -1))
+ throw new IllegalStateException("not degree -1");
+
+ // getIndex(Node).
+ if ((persp.getIndex(root2Node) != 0) || (persp.getIndex(nodeNotInPersp) != 0))
+ throw new IllegalStateException("index not 0");
+
+ if (persp.getIndex(persp.getNode(nodeInx[2])) != nodeInx[2])
+ throw new IllegalStateException("wrong node index");
+
+ // getNodeIndex(int).
+ if ((persp.getNodeIndex(nodeInx[1]) != nodeInx[1])
+ || (persp.getNodeIndex(nodeNotInPersp.getRootGraphIndex()) != 0)
+ || (persp.getNodeIndex(minNodeInx - 1) != 0)
+ || (persp.getNodeIndex(Integer.MAX_VALUE) != 0) || (persp.getNodeIndex(1) != 0))
+ throw new IllegalStateException("bad getNodeIndex(int)");
+
+ // getRootGraphNodeIndex(int).
+ if ((persp.getRootGraphNodeIndex(nodeInx[3]) != nodeInx[3])
+ || (persp.getRootGraphNodeIndex(nodeNotInPersp.getRootGraphIndex()) != 0)
+ || (persp.getRootGraphNodeIndex(minNodeInx - 1) != 0)
+ || (persp.getRootGraphNodeIndex(Integer.MIN_VALUE) != 0)
+ || (persp.getRootGraphNodeIndex(1) != 0))
+ throw new IllegalStateException("bad getRootGraphNodeIndex(int)");
+
+ // getNode(int).
+ if ((persp.getNode(minNodeInx - 1) != null) || (persp.getNode(0) != null)
+ || (persp.getNode(23) != null)
+ || (persp.getNode(nodeNotInPersp.getRootGraphIndex()) != null))
+ throw new IllegalStateException("not null");
+
+ if ((persp.getNode(Integer.MAX_VALUE) != null)
+ || (persp.getNode(Integer.MIN_VALUE) != null))
+ throw new IllegalStateException("not null");
+
+ // getIndex(Edge).
+ if ((persp.getIndex(persp.getEdge(edgeInx[0])) != edgeInx[0])
+ || (persp.getIndex(persp.getEdge(edgeInx[2])) != edgeInx[2]))
+ throw new IllegalStateException("wrong getIndex(Edge)");
+
+ if ((persp.getIndex(root2Edge) != 0) || (persp.getIndex(edge1NotInPersp) != 0))
+ throw new IllegalStateException("getIndex(Edge) should have been 0");
+
+ // getEdgeIndex(int).
+ if ((persp.getEdgeIndex(edgeInx[3]) != edgeInx[3])
+ || (persp.getEdgeIndex(edge1NotInPersp.getRootGraphIndex()) != 0)
+ || (persp.getEdgeIndex(minEdgeInx - 1) != 0)
+ || (persp.getEdgeIndex(Integer.MIN_VALUE) != 0) || (persp.getEdgeIndex(1) != 0))
+ throw new IllegalStateException("bad getEdgeIndex(int)");
+
+ // getRootGraphEdgeIndex(int).
+ if ((persp.getRootGraphEdgeIndex(edgeInx[4]) != edgeInx[4])
+ || (persp.getRootGraphEdgeIndex(edge2NotInPersp.getRootGraphIndex()) != 0)
+ || (persp.getRootGraphEdgeIndex(minEdgeInx - 1) != 0)
+ || (persp.getRootGraphEdgeIndex(Integer.MAX_VALUE) != 0)
+ || (persp.getRootGraphEdgeIndex(1) != 0))
+ throw new IllegalStateException("bad getRootGraphEdgeIndex(int)");
+
+ // getEdge(int).
+ if ((persp.getEdge(minEdgeInx - 1) != null) || (persp.getEdge(0) != null)
+ || (persp.getEdge(23) != null)
+ || (persp.getEdge(edge1NotInPersp.getRootGraphIndex()) != null))
+ throw new IllegalStateException("not null in getEdge(int)");
+
+ if ((persp.getEdge(Integer.MAX_VALUE) != null)
+ || (persp.getEdge(Integer.MIN_VALUE) != null))
+ throw new IllegalStateException("not null in getEdge(int)");
+
+ // getEdgeSourceIndex(int).
+ if ((persp.getEdgeSourceIndex(edgeInx[0]) != nodeInx[0])
+ || (persp.getEdgeSourceIndex(edgeInx[1]) != nodeInx[1])
+ || (persp.getEdgeSourceIndex(edgeInx[2]) != nodeInx[2])
+ || (persp.getEdgeSourceIndex(edgeInx[3]) != nodeInx[2])
+ || (persp.getEdgeSourceIndex(edgeInx[4]) != nodeInx[1])
+ || (persp.getEdgeSourceIndex(edgeInx[5]) != nodeInx[1])
+ || (persp.getEdgeSourceIndex(edgeInx[6]) != nodeInx[3]))
+ throw new IllegalStateException("wrong edge source");
+
+ if ((persp.getEdgeSourceIndex(minEdgeInx - 1) != 0) || (persp.getEdgeSourceIndex(0) != 0)
+ || (persp.getEdgeSourceIndex(23) != 0)
+ || (persp.getEdgeSourceIndex(edge1NotInPersp.getRootGraphIndex()) != 0)
+ || (persp.getEdgeSourceIndex(edge2NotInPersp.getRootGraphIndex()) != 0)
+ || (persp.getEdgeSourceIndex(Integer.MAX_VALUE) != 0)
+ || (persp.getEdgeSourceIndex(Integer.MIN_VALUE) != 0))
+ throw new IllegalStateException("should have returned 0 as source node");
+
+ // getEdgeTargetIndex(int).
+ if ((persp.getEdgeTargetIndex(edgeInx[0]) != nodeInx[1])
+ || (persp.getEdgeTargetIndex(edgeInx[1]) != nodeInx[2])
+ || (persp.getEdgeTargetIndex(edgeInx[2]) != nodeInx[0])
+ || (persp.getEdgeTargetIndex(edgeInx[3]) != nodeInx[2])
+ || (persp.getEdgeTargetIndex(edgeInx[4]) != nodeInx[1])
+ || (persp.getEdgeTargetIndex(edgeInx[5]) != nodeInx[0])
+ || (persp.getEdgeTargetIndex(edgeInx[6]) != nodeInx[2]))
+ throw new IllegalStateException("wrong edge target");
+
+ if ((persp.getEdgeTargetIndex(minEdgeInx - 1) != 0) || (persp.getEdgeTargetIndex(0) != 0)
+ || (persp.getEdgeTargetIndex(22) != 0)
+ || (persp.getEdgeTargetIndex(edge1NotInPersp.getRootGraphIndex()) != 0)
+ || (persp.getEdgeTargetIndex(edge2NotInPersp.getRootGraphIndex()) != 0)
+ || (persp.getEdgeTargetIndex(Integer.MAX_VALUE) != 0)
+ || (persp.getEdgeTargetIndex(Integer.MIN_VALUE) != 0))
+ throw new IllegalStateException("should have returned 0 as target node");
+
+ // isEdgeDirected(int).
+ if (persp.isEdgeDirected(edgeInx[1]) || persp.isEdgeDirected(edgeInx[4]))
+ throw new IllegalStateException("edge is not directed");
+
+ if (!(persp.isEdgeDirected(edgeInx[0]) && persp.isEdgeDirected(edgeInx[2])
+ && persp.isEdgeDirected(edgeInx[3]) && persp.isEdgeDirected(edgeInx[5])
+ && persp.isEdgeDirected(edgeInx[6])))
+ throw new IllegalStateException("edge is directed");
+
+ // isMetaParent(Node, Node).
+ if (!(persp.isMetaParent(persp.getNode(nodeInx[4]), persp.getNode(nodeInx[4]))
+ && persp.isMetaParent(persp.getNode(nodeInx[1]), persp.getNode(nodeInx[0]))))
+ throw new IllegalStateException("expected meta-relationship");
+
+ if (persp.isMetaParent(persp.getNode(nodeInx[1]), persp.getNode(nodeInx[2]))
+ || persp.isMetaParent(persp.getNode(nodeInx[1]), persp.getNode(nodeInx[4])))
+ throw new IllegalStateException("did not expect meta-relationship");
+
+ if (persp.isMetaParent(root2Node, persp.getNode(nodeInx[3]))
+ || persp.isMetaParent(persp.getNode(nodeInx[0]), root2Node)
+ || persp.isMetaParent(nodeNotInPersp, persp.getNode(nodeInx[2]))
+ || persp.isMetaParent(persp.getNode(nodeInx[4]), nodeNotInPersp))
+ throw new IllegalStateException("meta-relationship only in RootGraph");
+
+ // isNodeMetaParent(int, int).
+ if (!(persp.isNodeMetaParent(nodeInx[2], nodeInx[3])
+ && persp.isNodeMetaParent(nodeInx[2], nodeInx[4])
+ && persp.isNodeMetaParent(nodeInx[3], nodeInx[3])))
+ throw new IllegalStateException("expected meta-relationship");
+
+ if (persp.isNodeMetaParent(nodeInx[4], nodeInx[3])
+ || persp.isNodeMetaParent(nodeInx[1], nodeInx[1]))
+ throw new IllegalStateException("did not expect meta-relationship");
+
+ if (persp.isNodeMetaParent(0, nodeInx[1])
+ || persp.isNodeMetaParent(Integer.MAX_VALUE, Integer.MIN_VALUE)
+ || persp.isNodeMetaParent(Integer.MIN_VALUE, Integer.MAX_VALUE)
+ || persp.isNodeMetaParent(1, 2) || persp.isNodeMetaParent(minNodeInx - 1, nodeInx[1])
+ || persp.isNodeMetaParent(nodeNotInPersp.getRootGraphIndex(), nodeInx[4])
+ || persp.isNodeMetaParent(nodeInx[2], nodeNotInPersp.getRootGraphIndex()))
+ throw new IllegalStateException("meta-relationship totally invalid");
+
+ // metaParentsList(Node).
+ List parentsList = persp.metaParentsList(persp.getNode(nodeInx[1]));
+
+ if (parentsList.size() != 2)
+ throw new IllegalStateException("wrong number of parents");
+
+ for (int i = 0;; i++)
+ if (((Node) parentsList.get(i)).getRootGraphIndex() == nodeInx[0])
+ break;
+
+ for (int i = 0;; i++)
+ if (((Node) parentsList.get(i)).getRootGraphIndex() == nodeInx[3])
+ break;
+
+ if ((persp.metaParentsList(nodeNotInPersp) != null)
+ || (persp.metaParentsList(root2Node) != null))
+ throw new IllegalStateException("expected null parents list");
+
+ // nodeMetaParentsList(int).
+ parentsList = persp.nodeMetaParentsList(nodeInx[4]);
+
+ if (parentsList.size() != 2)
+ throw new IllegalStateException("wrong number of parents");
+
+ for (int i = 0;; i++)
+ if (((Node) parentsList.get(i)).getRootGraphIndex() == nodeInx[4])
+ break;
+
+ for (int i = 0;; i++)
+ if (((Node) parentsList.get(i)).getRootGraphIndex() == nodeInx[0])
+ break;
+
+ if ((persp.nodeMetaParentsList(0) != null) || (persp.nodeMetaParentsList(1) != null)
+ || (persp.nodeMetaParentsList(Integer.MAX_VALUE) != null)
+ || (persp.nodeMetaParentsList(Integer.MIN_VALUE) != null)
+ || (persp.nodeMetaParentsList(minNodeInx - 1) != null)
+ || (persp.nodeMetaParentsList(nodeNotInPersp.getRootGraphIndex()) != null))
+ throw new IllegalStateException("expected null meta parents list");
+
+ // getNodeMetaParentIndicesArray(int).
+ int[] parentInx = persp.getNodeMetaParentIndicesArray(nodeInx[3]);
+
+ if (parentInx.length != 2)
+ throw new IllegalStateException("wrong number of parents");
+
+ for (int i = 0;; i++)
+ if (parentInx[i] == nodeInx[3])
+ break;
+
+ for (int i = 0;; i++)
+ if (parentInx[i] == nodeInx[4])
+ break;
+
+ parentInx = persp.getNodeMetaParentIndicesArray(nodeInx[0]);
+
+ if (parentInx.length != 2)
+ throw new IllegalStateException("wrong number of parents");
+
+ for (int i = 0;; i++)
+ if (parentInx[i] == nodeInx[3])
+ break;
+
+ for (int i = 0;; i++)
+ if (parentInx[i] == nodeInx[4])
+ break;
+
+ parentInx = persp.getNodeMetaParentIndicesArray(nodeInx[2]);
+
+ if (parentInx.length != 2)
+ throw new IllegalStateException("wrong number of parents");
+
+ for (int i = 0;; i++)
+ if (parentInx[i] == nodeInx[3])
+ break;
+
+ for (int i = 0;; i++)
+ if (parentInx[i] == nodeInx[4])
+ break;
+
+ if ((persp.getNodeMetaParentIndicesArray(0) != null)
+ || (persp.getNodeMetaParentIndicesArray(1) != null)
+ || (persp.getNodeMetaParentIndicesArray(minNodeInx - 1) != null)
+ || (persp.getNodeMetaParentIndicesArray(Integer.MIN_VALUE) != null)
+ || (persp.getNodeMetaParentIndicesArray(Integer.MAX_VALUE) != null)
+ || (persp.getNodeMetaParentIndicesArray(nodeNotInPersp.getRootGraphIndex()) != null))
+ throw new IllegalStateException("expected null for meta-parents");
+
+ // isMetaChild(Node, Node).
+ if (!(persp.isMetaChild(persp.getNode(nodeInx[3]), persp.getNode(nodeInx[0]))
+ && persp.isMetaChild(persp.getNode(nodeInx[3]), persp.getNode(nodeInx[2]))))
+ throw new IllegalStateException("expected meta-child relationship");
+
+ if (persp.isMetaChild(persp.getNode(nodeInx[1]), persp.getNode(nodeInx[4]))
+ || persp.isMetaChild(persp.getNode(nodeInx[3]), persp.getNode(nodeInx[4])))
+ throw new IllegalStateException("did not expect meta-child");
+
+ if (persp.isMetaChild(nodeNotInPersp, persp.getNode(nodeInx[2]))
+ || persp.isMetaChild(persp.getNode(nodeInx[2]), nodeNotInPersp)
+ || persp.isMetaChild(persp.getNode(nodeInx[4]), nodeNotInPersp)
+ || persp.isMetaChild(nodeNotInPersp, persp.getNode(nodeInx[4]))
+ || persp.isMetaChild(root2Node, persp.getNode(nodeInx[0]))
+ || persp.isMetaChild(persp.getNode(nodeInx[0]), root2Node))
+ throw new IllegalStateException("totally wrong meta-relationship");
+
+ // isNodeMetaChild(int, int).
+ if (!(persp.isNodeMetaChild(nodeInx[0], nodeInx[4])
+ && persp.isNodeMetaChild(nodeInx[4], nodeInx[2])
+ && persp.isNodeMetaChild(nodeInx[4], nodeInx[4])
+ && persp.isNodeMetaChild(nodeInx[4], nodeInx[3])
+ && persp.isNodeMetaChild(nodeInx[3], nodeInx[0])))
+ throw new IllegalStateException("expected meta-relationship");
+
+ if (persp.isNodeMetaChild(nodeInx[2], nodeInx[2])
+ || persp.isNodeMetaChild(nodeInx[1], nodeInx[3])
+ || persp.isNodeMetaChild(nodeInx[0], nodeInx[3])
+ || persp.isNodeMetaChild(nodeInx[3], nodeInx[4]))
+ throw new IllegalStateException("unexpected meta-relationship");
+
+ if (persp.isNodeMetaChild(0, 1)
+ || persp.isNodeMetaChild(nodeNotInPersp.getRootGraphIndex(), nodeInx[2])
+ || persp.isNodeMetaChild(nodeInx[2], nodeNotInPersp.getRootGraphIndex())
+ || persp.isNodeMetaChild(Integer.MIN_VALUE, nodeInx[3]))
+ throw new IllegalStateException("totally wrong meta-relationship");
+
+ // nodeMetaChildrenList(Node).
+ List nodeChildrenList = persp.nodeMetaChildrenList(persp.getNode(nodeInx[4]));
+
+ if (nodeChildrenList.size() != 4)
+ throw new IllegalStateException("wrong number of children nodes");
+
+ for (int i = 0;; i++)
+ if (((Node) nodeChildrenList.get(i)).getRootGraphIndex() == nodeInx[4])
+ break;
+
+ for (int i = 0;; i++)
+ if (((Node) nodeChildrenList.get(i)).getRootGraphIndex() == nodeInx[0])
+ break;
+
+ for (int i = 0;; i++)
+ if (((Node) nodeChildrenList.get(i)).getRootGraphIndex() == nodeInx[2])
+ break;
+
+ for (int i = 0;; i++)
+ if (((Node) nodeChildrenList.get(i)).getRootGraphIndex() == nodeInx[3])
+ break;
+
+ if ((persp.nodeMetaChildrenList(root2Node) != null)
+ || (persp.nodeMetaChildrenList(nodeNotInPersp) != null))
+ throw new IllegalStateException("expected null node children list");
+
+ // nodeMetaChildrenList(int).
+ nodeChildrenList = persp.nodeMetaChildrenList(nodeInx[0]);
+
+ if (nodeChildrenList.size() != 2)
+ throw new IllegalStateException("expected 2 children nodes");
+
+ for (int i = 0;; i++)
+ if (((Node) nodeChildrenList.get(i)).getRootGraphIndex() == nodeInx[1])
+ break;
+
+ for (int i = 0;; i++)
+ if (((Node) nodeChildrenList.get(i)).getRootGraphIndex() == nodeInx[4])
+ break;
+
+ nodeChildrenList = persp.nodeMetaChildrenList(nodeInx[1]);
+
+ if (nodeChildrenList.size() != 0)
+ throw new IllegalStateException("expected 0 children nodes");
+
+ if ((persp.nodeMetaChildrenList(0) != null) || (persp.nodeMetaChildrenList(1) != null)
+ || (persp.nodeMetaChildrenList(minNodeInx - 1) != null)
+ || (persp.nodeMetaChildrenList(nodeNotInPersp.getRootGraphIndex()) != null)
+ || (persp.nodeMetaChildrenList(Integer.MIN_VALUE) != null)
+ || (persp.nodeMetaChildrenList(Integer.MAX_VALUE) != null)
+ || (persp.nodeMetaChildrenList(Integer.MIN_VALUE + 1) != null))
+ throw new IllegalStateException("expected null node children list");
+
+ // getNodeMetaChildIndicesArray(int).
+ int[] childNodeInx = persp.getNodeMetaChildIndicesArray(nodeInx[2]);
+
+ if (childNodeInx.length != 0)
+ throw new IllegalStateException("expected 0 child nodes");
+
+ childNodeInx = persp.getNodeMetaChildIndicesArray(nodeInx[3]);
+
+ if (childNodeInx.length != 4)
+ throw new IllegalStateException("expected 4 child nodes");
+
+ for (int i = 0;; i++)
+ if (childNodeInx[i] == nodeInx[3])
+ break;
+
+ for (int i = 0;; i++)
+ if (childNodeInx[i] == nodeInx[1])
+ break;
+
+ for (int i = 0;; i++)
+ if (childNodeInx[i] == nodeInx[0])
+ break;
+
+ for (int i = 0;; i++)
+ if (childNodeInx[i] == nodeInx[2])
+ break;
+
+ if ((persp.getNodeMetaChildIndicesArray(0) != null)
+ || (persp.getNodeMetaChildIndicesArray(23) != null)
+ || (persp.getNodeMetaChildIndicesArray(minNodeInx - 1) != null)
+ || (persp.getNodeMetaChildIndicesArray(Integer.MAX_VALUE) != null)
+ || (persp.getNodeMetaChildIndicesArray(Integer.MIN_VALUE) != null)
+ || (persp.getNodeMetaChildIndicesArray(nodeNotInPersp.getRootGraphIndex()) != null))
+ throw new IllegalStateException("expected null children nodes");
+
+ // isMetaParent(Edge, Node).
+ if (!(persp.isMetaParent(persp.getEdge(edgeInx[6]), persp.getNode(nodeInx[3]))
+ && persp.isMetaParent(persp.getEdge(edgeInx[2]), persp.getNode(nodeInx[4]))
+ && persp.isMetaParent(persp.getEdge(edgeInx[0]), persp.getNode(nodeInx[3]))))
+ throw new IllegalStateException("expected meta-edge relationship");
+
+ if (persp.isMetaParent(persp.getEdge(edgeInx[6]), persp.getNode(nodeInx[0]))
+ || persp.isMetaParent(persp.getEdge(edgeInx[1]), persp.getNode(nodeInx[4]))
+ || persp.isMetaParent(persp.getEdge(edgeInx[3]), persp.getNode(nodeInx[1])))
+ throw new IllegalStateException("unexpected meta-edge relationship");
+
+ if (persp.isMetaParent(edge1NotInPersp, persp.getNode(nodeInx[3]))
+ || persp.isMetaParent(edge2NotInPersp, persp.getNode(nodeInx[4]))
+ || persp.isMetaParent(root2Edge, persp.getNode(nodeInx[0]))
+ || persp.isMetaParent(persp.getEdge(edgeInx[1]), nodeNotInPersp))
+ throw new IllegalStateException("totally wrong meta-edge relationship");
+
+ // isEdgeMetaParent(int, int).
+ if (!(persp.isEdgeMetaParent(edgeInx[4], nodeInx[0])
+ && persp.isEdgeMetaParent(edgeInx[6], nodeInx[4])))
+ throw new IllegalStateException("missing edge meta-relationship");
+
+ if (persp.isEdgeMetaParent(edgeInx[4], nodeInx[1])
+ || persp.isEdgeMetaParent(edgeInx[2], nodeInx[0])
+ || persp.isEdgeMetaParent(edgeInx[1], nodeInx[4]))
+ throw new IllegalStateException("unexpected edge meta-relationship");
+
+ if (persp.isEdgeMetaParent(0, 1)
+ || persp.isEdgeMetaParent(edge1NotInPersp.getRootGraphIndex(), nodeInx[0])
+ || persp.isEdgeMetaParent(Integer.MIN_VALUE, Integer.MAX_VALUE))
+ throw new IllegalStateException("totally wrong edge meta-relationship");
+
+ // metaParentsList(Edge).
+ parentsList = persp.metaParentsList(persp.getEdge(edgeInx[5]));
+
+ if (parentsList.size() != 0)
+ throw new IllegalStateException("edge has no parents");
+
+ parentsList = persp.metaParentsList(persp.getEdge(edgeInx[2]));
+
+ if (parentsList.size() != 1)
+ throw new IllegalStateException("wrong number of edge parents");
+
+ for (int i = 0;; i++)
+ if (((Node) parentsList.get(i)).getRootGraphIndex() == nodeInx[4])
+ break;
+
+ if ((persp.metaParentsList(root2Edge) != null)
+ || (persp.metaParentsList(edge1NotInPersp) != null)
+ || (persp.metaParentsList(edge2NotInPersp) != null))
+ throw new IllegalStateException("expected null edge parents list");
+
+ // edgeMetaParentsList(int).
+ parentsList = persp.edgeMetaParentsList(edgeInx[0]);
+
+ if (parentsList.size() != 1)
+ throw new IllegalStateException("wrong number of edge parents");
+
+ for (int i = 0;; i++)
+ if (((Node) parentsList.get(i)).getRootGraphIndex() == nodeInx[3])
+ break;
+
+ parentsList = persp.edgeMetaParentsList(edgeInx[1]);
+
+ if (parentsList.size() != 0)
+ throw new IllegalStateException("expected 0 edge parents");
+
+ if ((persp.edgeMetaParentsList(0) != null) || (persp.edgeMetaParentsList(1) != null)
+ || (persp.edgeMetaParentsList(minEdgeInx - 1) != null)
+ || (persp.edgeMetaParentsList(Integer.MIN_VALUE + 1) != null)
+ || (persp.edgeMetaParentsList(Integer.MIN_VALUE) != null)
+ || (persp.edgeMetaParentsList(edge1NotInPersp.getRootGraphIndex()) != null))
+ throw new IllegalStateException("totally wrong edge meta parents");
+
+ // getEdgeMetaParentIndicesArray(int).
+ parentInx = persp.getEdgeMetaParentIndicesArray(edgeInx[3]);
+
+ if (parentInx.length != 0)
+ throw new IllegalStateException("expected 0 edge parents");
+
+ parentInx = persp.getEdgeMetaParentIndicesArray(edgeInx[4]);
+
+ if (parentInx.length != 1)
+ throw new IllegalStateException("expected 1 edge parent");
+
+ for (int i = 0;; i++)
+ if (parentInx[i] == nodeInx[0])
+ break;
+
+ parentInx = persp.getEdgeMetaParentIndicesArray(edgeInx[6]);
+
+ if (parentInx.length != 2)
+ throw new IllegalStateException("expected 2 edge parent");
+
+ for (int i = 0;; i++)
+ if (parentInx[i] == nodeInx[4])
+ break;
+
+ for (int i = 0;; i++)
+ if (parentInx[i] == nodeInx[3])
+ break;
+
+ if ((persp.getEdgeMetaParentIndicesArray(0) != null)
+ || (persp.getEdgeMetaParentIndicesArray(2) != null)
+ || (persp.getEdgeMetaParentIndicesArray(Integer.MAX_VALUE) != null)
+ || (persp.getEdgeMetaParentIndicesArray(Integer.MIN_VALUE) != null)
+ || (persp.getEdgeMetaParentIndicesArray(minEdgeInx - 1) != null)
+ || (persp.getEdgeMetaParentIndicesArray(edge2NotInPersp.getRootGraphIndex()) != null))
+ throw new IllegalStateException("totally wrong edge meta parents");
+
+ // isMetaChild(Node, Edge).
+ if (!(persp.isMetaChild(persp.getNode(nodeInx[4]), persp.getEdge(edgeInx[6]))
+ || persp.isMetaChild(persp.getNode(nodeInx[0]), persp.getEdge(edgeInx[4]))))
+ throw new IllegalStateException("missing edge meta-relationship");
+
+ if (persp.isMetaChild(persp.getNode(nodeInx[2]), persp.getEdge(edgeInx[6]))
+ || persp.isMetaChild(persp.getNode(nodeInx[4]), persp.getEdge(edgeInx[0])))
+ throw new IllegalStateException("wrong edge meta-relationship");
+
+ if (persp.isMetaChild(root2Node, root2Edge)
+ || persp.isMetaChild(persp.getNode(nodeInx[3]), edge1NotInPersp))
+ throw new IllegalStateException("totally wrong edge meta-relationship");
+
+ // isEdgeMetaChild(int, int).
+ if (!(persp.isEdgeMetaChild(nodeInx[4], edgeInx[2])
+ && persp.isEdgeMetaChild(nodeInx[3], edgeInx[0])))
+ throw new IllegalStateException("missing edge meta-relationship");
+
+ if (persp.isEdgeMetaChild(nodeInx[3], edgeInx[2])
+ || persp.isEdgeMetaChild(nodeInx[0], edgeInx[2])
+ || persp.isEdgeMetaChild(nodeInx[0], edgeInx[5]))
+ throw new IllegalStateException("wrong edge meta-relationship");
+
+ if (persp.isEdgeMetaChild(0, 0)
+ || persp.isEdgeMetaChild(Integer.MAX_VALUE, Integer.MIN_VALUE)
+ || persp.isEdgeMetaChild(minNodeInx - 1, minEdgeInx - 1)
+ || persp.isEdgeMetaChild(nodeNotInPersp.getRootGraphIndex(), edgeInx[1]))
+ throw new IllegalStateException("totally wrong edge meta-relationship");
+
+ // edgeMetaChildrenList(Node).
+ List edgeChildrenList = persp.edgeMetaChildrenList(persp.getNode(nodeInx[4]));
+
+ if (edgeChildrenList.size() != 2)
+ throw new IllegalStateException("expected 2 edge children");
+
+ for (int i = 0;; i++)
+ if (((Edge) edgeChildrenList.get(i)).getRootGraphIndex() == edgeInx[2])
+ break;
+
+ for (int i = 0;; i++)
+ if (((Edge) edgeChildrenList.get(i)).getRootGraphIndex() == edgeInx[6])
+ break;
+
+ edgeChildrenList = persp.edgeMetaChildrenList(persp.getNode(nodeInx[0]));
+
+ if (edgeChildrenList.size() != 1)
+ throw new IllegalStateException("expected 1 edge child");
+
+ for (int i = 0;; i++)
+ if (((Edge) edgeChildrenList.get(i)).getRootGraphIndex() == edgeInx[4])
+ break;
+
+ if ((persp.edgeMetaChildrenList(root2Node) != null)
+ || (persp.edgeMetaChildrenList(nodeNotInPersp) != null))
+ throw new IllegalStateException("expected null as edge children list");
+
+ // edgeMetaChildRenList(int).
+ edgeChildrenList = persp.edgeMetaChildrenList(nodeInx[1]);
+
+ if (edgeChildrenList.size() != 0)
+ throw new IllegalStateException("expected 0 edge children");
+
+ edgeChildrenList = persp.edgeMetaChildrenList(nodeInx[3]);
+
+ if (edgeChildrenList.size() != 2)
+ throw new IllegalStateException("expected 2 edge children");
+
+ for (int i = 0;; i++)
+ if (((Edge) edgeChildrenList.get(i)).getRootGraphIndex() == edgeInx[0])
+ break;
+
+ for (int i = 0;; i++)
+ if (((Edge) edgeChildrenList.get(i)).getRootGraphIndex() == edgeInx[6])
+ break;
+
+ if ((persp.edgeMetaChildrenList(0) != null)
+ || (persp.edgeMetaChildrenList(nodeNotInPersp.getRootGraphIndex()) != null)
+ || (persp.edgeMetaChildrenList(23) != null)
+ || (persp.edgeMetaChildrenList(Integer.MAX_VALUE) != null)
+ || (persp.edgeMetaChildrenList(Integer.MIN_VALUE) != null)
+ || (persp.edgeMetaChildrenList(minNodeInx - 1) != null))
+ throw new IllegalStateException("totally wrong edge children list");
+
+ // getEdgeMetaChildIndicesArray(int).
+ int[] childEdgeInx = persp.getEdgeMetaChildIndicesArray(nodeInx[2]);
+
+ if (childEdgeInx.length != 0)
+ throw new IllegalStateException("expected no edge children");
+
+ childEdgeInx = persp.getEdgeMetaChildIndicesArray(nodeInx[4]);
+
+ if (childEdgeInx.length != 2)
+ throw new IllegalStateException("expected 2 edge children");
+
+ for (int i = 0;; i++)
+ if (childEdgeInx[i] == edgeInx[2])
+ break;
+
+ for (int i = 0;; i++)
+ if (childEdgeInx[i] == edgeInx[6])
+ break;
+
+ if ((persp.getEdgeMetaChildIndicesArray(0) != null)
+ || (persp.getEdgeMetaChildIndicesArray(23) != null)
+ || (persp.getEdgeMetaChildIndicesArray(Integer.MAX_VALUE) != null)
+ || (persp.getEdgeMetaChildIndicesArray(Integer.MIN_VALUE) != null)
+ || (persp.getEdgeMetaChildIndicesArray(minNodeInx - 1) != null)
+ || (persp.getEdgeMetaChildIndicesArray(nodeNotInPersp.getRootGraphIndex()) != null))
+ throw new IllegalStateException("expected null edge children");
+
+ // getAdjacentEdgesList(Node, boolean, boolean, boolean).
+ List adjacentEdges = persp.getAdjacentEdgesList(persp.getNode(nodeInx[2]), true, true, true);
+
+ if (adjacentEdges.size() != 4)
+ throw new IllegalStateException("expected 4 adjacent edges");
+
+ for (int i = 0;; i++)
+ if (((Edge) adjacentEdges.get(i)).getRootGraphIndex() == edgeInx[1])
+ break;
+
+ for (int i = 0;; i++)
+ if (((Edge) adjacentEdges.get(i)).getRootGraphIndex() == edgeInx[2])
+ break;
+
+ for (int i = 0;; i++)
+ if (((Edge) adjacentEdges.get(i)).getRootGraphIndex() == edgeInx[3])
+ break;
+
+ for (int i = 0;; i++)
+ if (((Edge) adjacentEdges.get(i)).getRootGraphIndex() == edgeInx[6])
+ break;
+
+ if ((persp.getAdjacentEdgesList(root2Node, false, false, false) != null)
+ || (persp.getAdjacentEdgesList(nodeNotInPersp, true, false, true) != null))
+ throw new IllegalStateException("expected null adjacent edges list");
+
+ adjacentEdges = persp.getAdjacentEdgesList(persp.getNode(nodeInx[2]), false, false, false);
+
+ if (adjacentEdges.size() != 0)
+ throw new IllegalStateException("should have been 0 adjacent edges");
+
+ // getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean).
+ int[] adjacentEdgeInx = persp.getAdjacentEdgeIndicesArray(nodeInx[0], false, true, false);
+
+ if (adjacentEdgeInx.length != 2)
+ throw new IllegalStateException("should have been 2 adjacent edges");
+
+ for (int i = 0;; i++)
+ if (adjacentEdgeInx[i] == edgeInx[2])
+ break;
+
+ for (int i = 0;; i++)
+ if (adjacentEdgeInx[i] == edgeInx[5])
+ break;
+
+ adjacentEdgeInx = persp.getAdjacentEdgeIndicesArray(nodeInx[1], true, true, false);
+
+ if (adjacentEdgeInx.length != 3)
+ throw new IllegalStateException("should have been 3 adjacent edges");
+
+ for (int i = 0;; i++)
+ if (adjacentEdgeInx[i] == edgeInx[1])
+ break;
+
+ for (int i = 0;; i++)
+ if (adjacentEdgeInx[i] == edgeInx[0])
+ break;
+
+ for (int i = 0;; i++)
+ if (adjacentEdgeInx[i] == edgeInx[4])
+ break;
+
+ adjacentEdgeInx = persp.getAdjacentEdgeIndicesArray(nodeInx[3], true, false, true);
+
+ if (adjacentEdgeInx.length != 1)
+ throw new IllegalStateException("should have been 1 adjacent edge");
+
+ for (int i = 0;; i++)
+ if (adjacentEdgeInx[i] == edgeInx[6])
+ break;
+
+ adjacentEdgeInx = persp.getAdjacentEdgeIndicesArray(nodeInx[4], false, false, true);
+
+ if (adjacentEdgeInx.length != 0)
+ throw new IllegalStateException("should have been 0 adjacent edges");
+
+ adjacentEdgeInx = persp.getAdjacentEdgeIndicesArray(nodeInx[0], true, false, false);
+
+ if (adjacentEdgeInx.length != 0)
+ throw new IllegalStateException("should have been 0 adjacent edges");
+
+ adjacentEdgeInx = persp.getAdjacentEdgeIndicesArray(nodeInx[1], false, false, true);
+
+ if (adjacentEdgeInx.length != 1)
+ throw new IllegalStateException("should have been 1 adjacent edge");
+
+ for (int i = 0;; i++)
+ if (adjacentEdgeInx[i] == edgeInx[5])
+ break;
+
+ if ((persp.getAdjacentEdgeIndicesArray(0, true, false, true) != null)
+ || (persp.getAdjacentEdgeIndicesArray(Integer.MIN_VALUE, true, true, true) != null)
+ || (persp.getAdjacentEdgeIndicesArray(nodeNotInPersp.getRootGraphIndex(), false, true,
+ true) != null)
+ || (persp.getAdjacentEdgeIndicesArray(minNodeInx - 1, false, true, true) != null))
+ throw new IllegalStateException("expected null adjacent edge inx arr");
+
+ // getConnectingEdges(List).
+ ArrayList nodeInputList = new ArrayList(3);
+ nodeInputList.add(0, persp.getNode(nodeInx[0]));
+ nodeInputList.add(1, persp.getNode(nodeInx[3]));
+ nodeInputList.add(2, persp.getNode(nodeInx[2]));
+
+ List connectingEdgesList = persp.getConnectingEdges(nodeInputList);
+
+ if (connectingEdgesList.size() != 3)
+ throw new IllegalStateException("expected 3 connecting edges");
+
+ for (int i = 0;; i++)
+ if (((Edge) connectingEdgesList.get(i)).getRootGraphIndex() == edgeInx[2])
+ break;
+
+ for (int i = 0;; i++)
+ if (((Edge) connectingEdgesList.get(i)).getRootGraphIndex() == edgeInx[3])
+ break;
+
+ for (int i = 0;; i++)
+ if (((Edge) connectingEdgesList.get(i)).getRootGraphIndex() == edgeInx[6])
+ break;
+
+ nodeInputList = new ArrayList(3);
+ nodeInputList.add(0, persp.getNode(nodeInx[2]));
+ nodeInputList.add(1, persp.getNode(nodeInx[0]));
+ nodeInputList.add(2, persp.getNode(nodeInx[1]));
+ connectingEdgesList = persp.getConnectingEdges(nodeInputList);
+
+ if (connectingEdgesList.size() != 6)
+ throw new IllegalStateException("expected 6 connecting nodes");
+
+ for (int i = 0; i < connectingEdgesList.size(); i++)
+ if (((Edge) connectingEdgesList.get(i)).getRootGraphIndex() == edgeInx[6])
+ throw new IllegalStateException("wrong connecting edge");
+
+ nodeInputList = new ArrayList(2);
+ nodeInputList.add(0, persp.getNode(nodeInx[0]));
+ nodeInputList.add(1, nodeNotInPersp);
+
+ if (persp.getConnectingEdges(nodeInputList) != null)
+ throw new IllegalStateException("expected null connecting edges");
+
+ nodeInputList = new ArrayList(2);
+ nodeInputList.add(0, root2Node);
+ nodeInputList.add(1, persp.getNode(nodeInx[1]));
+
+ if (persp.getConnectingEdges(nodeInputList) != null)
+ throw new IllegalStateException("expected null connecting edges");
+
+ // getConnectingEdgeIndicesArray(int[]).
+ int[] nodeInputInxArr = new int[4];
+ nodeInputInxArr[0] = nodeInx[0];
+ nodeInputInxArr[1] = nodeInx[2];
+ nodeInputInxArr[2] = nodeInx[3];
+ nodeInputInxArr[3] = nodeInx[4];
+
+ int[] connectingEdgeInx = persp.getConnectingEdgeIndicesArray(nodeInputInxArr);
+
+ if (connectingEdgeInx.length != 3)
+ throw new IllegalStateException("expected 3 connecting edges");
+
+ for (int i = 0;; i++)
+ if (connectingEdgeInx[i] == edgeInx[2])
+ break;
+
+ for (int i = 0;; i++)
+ if (connectingEdgeInx[i] == edgeInx[3])
+ break;
+
+ for (int i = 0;; i++)
+ if (connectingEdgeInx[i] == edgeInx[6])
+ break;
+
+ nodeInputInxArr = new int[2];
+ nodeInputInxArr[0] = nodeInx[0];
+ nodeInputInxArr[1] = nodeInx[1];
+ connectingEdgeInx = persp.getConnectingEdgeIndicesArray(nodeInputInxArr);
+
+ if (connectingEdgeInx.length != 3)
+ throw new IllegalStateException("expected 3 connecting edges");
+
+ for (int i = 0;; i++)
+ if (connectingEdgeInx[i] == edgeInx[0])
+ break;
+
+ for (int i = 0;; i++)
+ if (connectingEdgeInx[i] == edgeInx[4])
+ break;
+
+ for (int i = 0;; i++)
+ if (connectingEdgeInx[i] == edgeInx[5])
+ break;
+
+ nodeInputInxArr = new int[2];
+ nodeInputInxArr[0] = nodeInx[4];
+ nodeInputInxArr[1] = nodeInx[2];
+ connectingEdgeInx = persp.getConnectingEdgeIndicesArray(nodeInputInxArr);
+
+ if (connectingEdgeInx.length != 1)
+ throw new IllegalStateException("expected 1 connecting edge");
+
+ for (int i = 0;; i++)
+ if (connectingEdgeInx[i] == edgeInx[3])
+ break;
+
+ nodeInputInxArr = new int[3];
+ nodeInputInxArr[0] = nodeInx[4];
+ nodeInputInxArr[1] = nodeInx[3];
+ nodeInputInxArr[2] = nodeInx[0];
+ connectingEdgeInx = persp.getConnectingEdgeIndicesArray(nodeInputInxArr);
+
+ if (connectingEdgeInx.length != 0)
+ throw new IllegalStateException("expected no connecting edges");
+
+ if ((persp.getConnectingEdgeIndicesArray(new int[100]) != null)
+ || (persp.getConnectingEdgeIndicesArray(new int[] { Integer.MAX_VALUE, Integer.MIN_VALUE }) != null)
+ || (persp.getConnectingEdgeIndicesArray(new int[] { minNodeInx - 1, nodeInx[1] }) != null)
+ || (persp.getConnectingEdgeIndicesArray(new int[] {
+ nodeInx[1],
+ nodeNotInPersp.getRootGraphIndex()
+ }) != null))
+ throw new IllegalStateException("expected null connecting edge inx");
+
+ // getConnectingNodeIndicesArray(int[]).
+ int[] edgeInputInxArr = new int[3];
+ edgeInputInxArr[0] = edgeInx[0];
+ edgeInputInxArr[1] = edgeInx[2];
+ edgeInputInxArr[2] = edgeInx[4];
+
+ int[] connectingNodeInx = persp.getConnectingNodeIndicesArray(edgeInputInxArr);
+
+ if (connectingNodeInx.length != 3)
+ throw new IllegalStateException("expected 3 connecting nodes");
+
+ for (int i = 0;; i++)
+ if (connectingNodeInx[i] == nodeInx[0])
+ break;
+
+ for (int i = 0;; i++)
+ if (connectingNodeInx[i] == nodeInx[1])
+ break;
+
+ for (int i = 0;; i++)
+ if (connectingNodeInx[i] == nodeInx[2])
+ break;
+
+ edgeInputInxArr = new int[2];
+ edgeInputInxArr[0] = edgeInx[6];
+ edgeInputInxArr[1] = edgeInx[1];
+ connectingNodeInx = persp.getConnectingNodeIndicesArray(edgeInputInxArr);
+
+ if (connectingNodeInx.length != 3)
+ throw new IllegalStateException("expected 3 connecting nodes");
+
+ for (int i = 0;; i++)
+ if (connectingNodeInx[i] == nodeInx[1])
+ break;
+
+ for (int i = 0;; i++)
+ if (connectingNodeInx[i] == nodeInx[2])
+ break;
+
+ for (int i = 0;; i++)
+ if (connectingNodeInx[i] == nodeInx[3])
+ break;
+
+ edgeInputInxArr = new int[1];
+ edgeInputInxArr[0] = edgeInx[3];
+ connectingNodeInx = persp.getConnectingNodeIndicesArray(edgeInputInxArr);
+
+ if (connectingNodeInx.length != 1)
+ throw new IllegalStateException("expected one connecting node");
+
+ for (int i = 0;; i++)
+ if (connectingNodeInx[i] == nodeInx[2])
+ break;
+
+ if ((persp.getConnectingNodeIndicesArray(new int[76]) != null)
+ || (persp.getConnectingNodeIndicesArray(new int[] { Integer.MIN_VALUE, Integer.MAX_VALUE }) != null)
+ || (persp.getConnectingNodeIndicesArray(new int[] { minEdgeInx - 1, edgeInx[0] }) != null)
+ || (persp.getConnectingNodeIndicesArray(new int[] {
+ edgeInx[2],
+ edge1NotInPersp.getRootGraphIndex()
+ }) != null))
+ throw new IllegalStateException("expected null connecting node inx");
+
+ // createGraphPerspective(int[]).
+ }
+}
diff --git a/corelibs/fing/src/main/java/fing/model/test/AllRootGraphMethodsTest.java b/corelibs/fing/src/main/java/fing/model/test/AllRootGraphMethodsTest.java
new file mode 100644
index 0000000..28598be
--- /dev/null
+++ b/corelibs/fing/src/main/java/fing/model/test/AllRootGraphMethodsTest.java
@@ -0,0 +1,1903 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package fing.model.test;
+
+import fing.model.FingRootGraphFactory;
+
+import giny.model.Edge;
+import giny.model.Node;
+import giny.model.RootGraph;
+
+import java.util.Iterator;
+import java.util.List;
+
+
+/**
+ *
+ */
+public final class AllRootGraphMethodsTest {
+ // No constructor.
+ private AllRootGraphMethodsTest() {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ */
+ public static final void main(String[] args) {
+ final RootGraph root = FingRootGraphFactory.instantiateRootGraph();
+ runTest(root);
+ }
+
+ // Package visible so other classes can call this.
+ static final void runTest(RootGraph root) {
+ // Don't change this! Any change here implies re-reading all the test
+ // code below and making appropriate changes there.
+ int[] nodeInx = new int[5];
+
+ for (int i = 0; i < (nodeInx.length - 1); i++)
+ nodeInx[i] = root.createNode();
+
+ int[] edgeInx = new int[7];
+ edgeInx[0] = root.createEdge(nodeInx[0], nodeInx[1], true);
+ edgeInx[1] = root.createEdge(nodeInx[1], nodeInx[2], false);
+ edgeInx[2] = root.createEdge(nodeInx[2], nodeInx[0], true);
+ edgeInx[3] = root.createEdge(nodeInx[2], nodeInx[2], true);
+ edgeInx[4] = root.createEdge(nodeInx[1], nodeInx[1], false);
+ edgeInx[5] = root.createEdge(nodeInx[1], nodeInx[0], true);
+ edgeInx[6] = root.createEdge(nodeInx[3], nodeInx[2], true);
+ // Meta-node definitions.
+ nodeInx[nodeInx.length - 1] = root.createNode(null, new int[] { edgeInx[6], edgeInx[2] }); // Should have nodes
+ // nodeInx[0], nodeInx[2], and nodeInx[3].
+
+ if (!(root.addNodeMetaChild(nodeInx[0], nodeInx[1])
+ && root.addNodeMetaChild(nodeInx[0], nodeInx[4])
+ && root.addNodeMetaChild(nodeInx[3], nodeInx[1])
+ && root.addNodeMetaChild(nodeInx[4], nodeInx[4])
+ && root.addEdgeMetaChild(nodeInx[3], edgeInx[6])
+ && root.addEdgeMetaChild(nodeInx[3], edgeInx[0])
+ && root.addEdgeMetaChild(nodeInx[0], edgeInx[4])))
+ throw new IllegalStateException("unable to create meta relationship");
+
+ for (int i = 0; i < nodeInx.length; i++)
+ if (nodeInx[i] >= 0)
+ throw new IllegalStateException("non-negative node");
+
+ for (int i = 0; i < edgeInx.length; i++)
+ if (edgeInx[i] >= 0)
+ throw new IllegalStateException("non-negative edge");
+
+ // Test add/remove nodes and edges before other tests.
+ // We leave the graph with the same topology after these tests as
+ // existed before these tests.
+ if (root.removeNode(nodeInx[1]) != nodeInx[1])
+ throw new IllegalStateException("removal of node failed");
+
+ if ((root.removeEdge(edgeInx[0]) != 0) || (root.removeEdge(edgeInx[1]) != 0)
+ || (root.removeEdge(edgeInx[4]) != 0) || (root.removeEdge(edgeInx[5]) != 0))
+ throw new IllegalStateException("removal failure failed - edge");
+
+ if (root.removeNode(nodeInx[1]) != 0)
+ throw new IllegalStateException("removal failure failed - node");
+
+ if (root.removeEdge(edgeInx[6]) != edgeInx[6])
+ throw new IllegalStateException("removal of edge failed");
+
+ if (root.removeEdge(edgeInx[6]) != 0)
+ throw new IllegalStateException("removal failure failed - edge");
+
+ if ((root.removeNode(0) != 0) || (root.removeNode(Integer.MAX_VALUE) != 0)
+ || (root.removeNode(Integer.MIN_VALUE) != 0))
+ throw new IllegalStateException("removal failure failed - node");
+
+ if ((root.removeEdge(0) != 0) || (root.removeEdge(Integer.MAX_VALUE) != 0)
+ || (root.removeNode(Integer.MIN_VALUE) != 0))
+ throw new IllegalStateException("removal failure failed - edge");
+
+ if ((root.createEdge(Integer.MAX_VALUE, Integer.MAX_VALUE, true) != 0)
+ || (root.createEdge(Integer.MIN_VALUE, Integer.MIN_VALUE, false) != 0)
+ || (root.createEdge(0, 0, true) != 0))
+ throw new IllegalStateException("creation failure failed - edge");
+
+ int deleteThisNode0 = root.createNode();
+ nodeInx[1] = root.createNode();
+
+ if (root.removeNode(deleteThisNode0) != deleteThisNode0)
+ throw new IllegalStateException("cannot delete node");
+
+ int deleteThisEdge;
+
+ if ((deleteThisEdge = root.createEdge(nodeInx[4], nodeInx[1], true)) >= 0)
+ throw new IllegalStateException("had problems creating edge");
+
+ edgeInx[0] = root.createEdge(nodeInx[0], nodeInx[1], true);
+ edgeInx[1] = root.createEdge(nodeInx[1], nodeInx[2], false);
+ edgeInx[4] = root.createEdge(nodeInx[1], nodeInx[1], false);
+ edgeInx[5] = root.createEdge(nodeInx[1], nodeInx[0], true);
+ edgeInx[6] = root.createEdge(nodeInx[3], nodeInx[2], true);
+
+ if (root.removeEdge(deleteThisEdge) != deleteThisEdge)
+ throw new IllegalStateException("cannot delete edge");
+
+ int deleteThisNode = root.createNode();
+ int deleteThisEdge1;
+
+ if ((deleteThisEdge1 = root.createEdge(nodeInx[0], nodeInx[1], false)) >= 0)
+ throw new IllegalStateException("could not create edge");
+
+ int deleteThisEdge2;
+
+ if ((deleteThisEdge2 = root.createEdge(nodeInx[4], nodeInx[2], false)) >= 0)
+ throw new IllegalStateException("could not create edge");
+
+ if (root.createEdge(deleteThisNode, nodeInx[1], true) >= 0)
+ throw new IllegalStateException("could not create edge");
+
+ if (root.removeNode(deleteThisNode) != deleteThisNode)
+ throw new IllegalStateException("could not delete node");
+
+ if (root.removeEdge(deleteThisEdge1) != deleteThisEdge1)
+ throw new IllegalStateException("could not delete edge");
+
+ if (root.removeEdge(deleteThisEdge2) != deleteThisEdge2)
+ throw new IllegalStateException("could not delete edge");
+
+ // Meta-nodes. First restore what was there originally.
+ if (!(root.addEdgeMetaChild(nodeInx[3], edgeInx[0])))
+ throw new IllegalStateException("errors during restoration");
+
+ if (!(root.addEdgeMetaChild(nodeInx[0], edgeInx[4])))
+ throw new IllegalStateException("errors during restoration");
+
+ if (!(root.addEdgeMetaChild(nodeInx[4], edgeInx[6])
+ && root.addEdgeMetaChild(nodeInx[3], edgeInx[6])))
+ throw new IllegalStateException("errors during restoration");
+
+ if (root.addEdgeMetaChild(nodeInx[3], edgeInx[0])
+ || root.addEdgeMetaChild(nodeInx[4], edgeInx[2])
+ || root.addNodeMetaChild(nodeInx[3], nodeInx[1])
+ || root.addEdgeMetaChild(0, edgeInx[0]) || root.addEdgeMetaChild(nodeInx[1], 0)
+ || root.addEdgeMetaChild(99, 98)
+ || root.addEdgeMetaChild(Integer.MAX_VALUE, Integer.MIN_VALUE)
+ || root.addNodeMetaChild(0, nodeInx[2]) || root.addNodeMetaChild(nodeInx[2], 0)
+ || root.addNodeMetaChild(87, 23)
+ || root.addNodeMetaChild(Integer.MIN_VALUE, Integer.MAX_VALUE))
+ throw new IllegalStateException("failure of failure during creation");
+
+ // Meta-nodes. Create and remove extra meta-relationships.
+ if (!root.addNodeMetaChild(nodeInx[2], nodeInx[1]))
+ throw new IllegalStateException("failed to create relationship");
+
+ if (root.addNodeMetaChild(nodeInx[2], nodeInx[1])
+ || root.addNodeMetaChild(nodeInx[4], nodeInx[0]))
+ throw new IllegalStateException("was able to create duplicate meta");
+
+ if (!(root.addEdgeMetaChild(nodeInx[4], edgeInx[5])
+ && root.addNodeMetaChild(nodeInx[2], nodeInx[2])))
+ throw new IllegalStateException("failed to create meta relationship");
+
+ if (root.addNodeMetaChild(nodeInx[2], nodeInx[2])
+ || root.addEdgeMetaChild(nodeInx[4], edgeInx[5])
+ || root.addEdgeMetaChild(nodeInx[4], edgeInx[6]))
+ throw new IllegalStateException("was able to create duplicate meta");
+
+ if (!(root.removeNodeMetaChild(nodeInx[2], nodeInx[1])
+ && root.removeNodeMetaChild(nodeInx[4], nodeInx[1])
+ && root.removeNodeMetaChild(nodeInx[2], nodeInx[2])))
+ throw new IllegalStateException("could not delete meta relationship");
+
+ if (root.removeEdgeMetaChild(nodeInx[4], edgeInx[5]))
+ throw new IllegalStateException("edge child was supposed to go away");
+
+ if (root.removeNodeMetaChild(nodeInx[2], nodeInx[3])
+ || root.removeEdgeMetaChild(nodeInx[4], edgeInx[0])
+ || root.removeNodeMetaChild(Integer.MAX_VALUE, Integer.MIN_VALUE)
+ || root.removeEdgeMetaChild(Integer.MIN_VALUE, Integer.MAX_VALUE)
+ || root.removeNodeMetaChild(0, 88) || root.removeEdgeMetaChild(88, 0))
+ throw new IllegalStateException("deleted non-existent meta");
+
+ for (int i = 0; i < nodeInx.length; i++)
+ if (nodeInx[i] >= 0)
+ throw new IllegalStateException("non-negative node");
+
+ for (int i = 0; i < edgeInx.length; i++)
+ if (edgeInx[i] >= 0)
+ throw new IllegalStateException("non-negative edge");
+
+ // nodesIterator() and edgesIterator().
+ Iterator nodesIter = root.nodesIterator();
+ Iterator edgesIter = root.edgesIterator();
+ Node[] twoNodes = new Node[] { (Node) nodesIter.next(), (Node) nodesIter.next() };
+ Edge[] twoEdges = new Edge[] { (Edge) edgesIter.next(), (Edge) edgesIter.next() };
+
+ // createGraphPerspective(Node[], Edge[].
+ if (root.createGraphPerspective(twoNodes, null).getNodeCount() != 2)
+ throw new IllegalStateException("GraphPerspective does not have two nodes");
+
+ if (root.createGraphPerspective(null, twoEdges).getEdgeCount() != 2)
+ throw new IllegalStateException("GraphPerspective does not have two edges");
+
+ if (root.createGraphPerspective(twoNodes, twoEdges).getNodeCount() < 2)
+ throw new IllegalStateException("GraphPerspective has less than two nodes");
+
+ if (root.createGraphPerspective(twoNodes, twoEdges).getEdgeCount() < 2)
+ throw new IllegalStateException("GraphPerspective has less than two edges");
+
+ if (root.createGraphPerspective((Node[]) null, (Edge[]) null) == null)
+ throw new IllegalStateException("GraphPerspective is null");
+
+ if (root.createGraphPerspective(new Node[0], new Edge[0]) == null)
+ throw new IllegalStateException("GraphPerspective is null");
+
+ RootGraph root2 = FingRootGraphFactory.instantiateRootGraph();
+ root2.createNode();
+ root2.createEdge(((Node) root2.nodesIterator().next()).getRootGraphIndex(),
+ ((Node) root2.nodesIterator().next()).getRootGraphIndex());
+
+ Node root2Node = (Node) root2.nodesIterator().next();
+ Edge root2Edge = (Edge) root2.edgesIterator().next();
+
+ if (root.createGraphPerspective(new Node[] { root2Node }, null) != null)
+ throw new IllegalStateException("GraphPerspective is not null");
+
+ if (root.createGraphPerspective(null, new Edge[] { root2Edge }) != null)
+ throw new IllegalStateException("GraphPerspective is not null");
+
+ if (root.createGraphPerspective(new Node[] { twoNodes[0], root2Node },
+ new Edge[] { twoEdges[0], root2Edge }) != null)
+ throw new IllegalStateException("GraphPerspective is not null");
+
+ // createGraphPerspective(int[], int[]).
+ int[] twoNodeInx = new int[] {
+ twoNodes[0].getRootGraphIndex(), twoNodes[1].getRootGraphIndex()
+ };
+ int[] twoEdgeInx = new int[] {
+ twoEdges[0].getRootGraphIndex(), twoEdges[1].getRootGraphIndex()
+ };
+
+ if (root.createGraphPerspective(twoNodeInx, null).getNodeCount() != 2)
+ throw new IllegalStateException("GraphPerspective does not have two nodes");
+
+ if (root.createGraphPerspective(null, twoEdgeInx).getEdgeCount() != 2)
+ throw new IllegalStateException("GraphPerspective does not have two edges");
+
+ if (root.createGraphPerspective(twoNodeInx, twoEdgeInx).getNodeCount() < 2)
+ throw new IllegalStateException("GraphPerspective has less than two nodes");
+
+ if (root.createGraphPerspective(twoNodeInx, twoEdgeInx).getEdgeCount() < 2)
+ throw new IllegalStateException("GraphPerspective has less than two edges");
+
+ if (root.createGraphPerspective((int[]) null, (int[]) null) == null)
+ throw new IllegalStateException("GraphPerspective is null");
+
+ if (root.createGraphPerspective(new int[0], new int[0]) == null)
+ throw new IllegalStateException("GraphPerspective is null");
+
+ if (root.createGraphPerspective(new int[] { 0 }, null) != null)
+ throw new IllegalStateException("GraphPerspective is not null");
+
+ if (root.createGraphPerspective(null, new int[] { 0 }) != null)
+ throw new IllegalStateException("GraphPerspective is not null");
+
+ if (root.createGraphPerspective(new int[] { twoNodeInx[0], 0 },
+ new int[] { twoEdgeInx[0], 9999 }) != null)
+ throw new IllegalStateException("GraphPerspective is not null");
+
+ if (root.createGraphPerspective(new int[] { 1 }, null) != null)
+ throw new IllegalStateException("GraphPerspective is not null");
+
+ if ((root.createGraphPerspective(new int[] { Integer.MAX_VALUE }, null) != null)
+ || (root.createGraphPerspective(new int[] { Integer.MIN_VALUE }, null) != null)
+ || (root.createGraphPerspective(null, new int[] { Integer.MAX_VALUE }) != null)
+ || (root.createGraphPerspective(null, new int[] { Integer.MIN_VALUE }) != null))
+ throw new IllegalStateException("GraphPerspective is not null");
+
+ // getNodeCount() and getEdgeCount().
+ if ((root.getNodeCount() != 5) || (root.getEdgeCount() != 7))
+ throw new IllegalStateException("incorrect nodes or edges count");
+
+ // nodesList().
+ List nodesList = root.nodesList();
+
+ if (nodesList.size() != 5)
+ throw new IllegalStateException("incorrect node List size");
+
+ for (int i = 0; i < nodesList.size(); i++) {
+ Node n = (Node) nodesList.get(i);
+ }
+
+ // getNodeIndicesArray().
+ int[] nodeIndicesArray = root.getNodeIndicesArray();
+
+ if (nodeIndicesArray.length != nodesList.size())
+ throw new IllegalStateException("size of nodes List and length of node indices array don't match");
+
+ if (root.createGraphPerspective(nodeIndicesArray, null) == null)
+ throw new IllegalStateException("GraphPerspective is null");
+
+ // edgesList().
+ List edgesList = root.edgesList();
+
+ if (edgesList.size() != 7)
+ throw new IllegalStateException("incorrect edge List size");
+
+ for (int i = 0; i < edgesList.size(); i++) {
+ Edge e = (Edge) edgesList.get(i);
+ }
+
+ // getEdgeIndicesArray().
+ int[] edgeIndicesArray = root.getEdgeIndicesArray();
+
+ if (edgeIndicesArray.length != edgesList.size())
+ throw new IllegalStateException("size of edges List and length of edge indices array don't match");
+
+ if (root.createGraphPerspective(null, edgeIndicesArray) == null)
+ throw new IllegalStateException("GraphPerspective is null");
+
+ // Create and remove node/edge functionality is tested in other code.
+
+ // containsNode(Node).
+ if (!root.containsNode(twoNodes[1]))
+ throw new IllegalStateException("RootGraph does not contain node");
+
+ if (root.containsNode(root2Node))
+ throw new IllegalStateException("RootGraph contains node from other");
+
+ // containsEdge(Edge).
+ if (!root.containsEdge(twoEdges[1]))
+ throw new IllegalStateException("RootGraph does not contain edge");
+
+ if (root.containsEdge(root2Edge))
+ throw new IllegalStateException("RootGraph contains edge from other");
+
+ // neighborsList(Node).
+ List neighList = root.neighborsList(root.getNode(nodeInx[0]));
+
+ if (neighList.size() != 2)
+ throw new IllegalStateException("wrong number of neighbors");
+
+ neighList = root.neighborsList(root.getNode(nodeInx[1]));
+
+ if (neighList.size() != 3)
+ throw new IllegalStateException("wrong number of neighbors");
+
+ neighList = root.neighborsList(root.getNode(nodeInx[2]));
+
+ if (neighList.size() != 4)
+ throw new IllegalStateException("wrong number of neighbors");
+
+ int[] neighInx = new int[neighList.size()];
+
+ for (int i = 0; i < neighList.size(); i++) {
+ Node node = (Node) neighList.get(i);
+ int nodeIndex = node.getRootGraphIndex();
+
+ if (root.getNode(nodeIndex) == null)
+ throw new IllegalStateException("bad node in neighbors");
+
+ if (nodeIndex == 0)
+ throw new IllegalStateException("node index is 0");
+
+ int index = -1;
+
+ while (true) {
+ if (neighInx[++index] != 0) {
+ if (neighInx[index] == nodeIndex)
+ throw new IllegalStateException("duplicate neighbor");
+ else
+
+ continue;
+ } else {
+ neighInx[index] = nodeIndex;
+
+ break;
+ }
+ }
+ }
+
+ neighList = root.neighborsList(root.getNode(nodeInx[3]));
+
+ if (neighList.size() != 1)
+ throw new IllegalStateException("wrong number of neighbors");
+
+ neighList = root.neighborsList(root.getNode(nodeInx[4]));
+
+ if (neighList.size() != 0)
+ throw new IllegalStateException("wrong number of neighbors");
+
+ neighList = root.neighborsList(root2Node);
+
+ if (neighList != null)
+ throw new IllegalStateException("neighbors List isn't null");
+
+ // isNeighbor(Node, Node).
+ if (root.isNeighbor(root.getNode(nodeInx[4]), root.getNode(nodeInx[4])))
+ throw new IllegalStateException("node with no edges is its own neigh");
+
+ if (root.isNeighbor(root.getNode(nodeInx[3]), root.getNode(nodeInx[1])))
+ throw new IllegalStateException("nodes are neighbors");
+
+ if (!root.isNeighbor(root.getNode(nodeInx[1]), root.getNode(nodeInx[0])))
+ throw new IllegalStateException("nodes are not neighbors");
+
+ if (root.isNeighbor(root2Node, root.getNode(nodeInx[2])))
+ throw new IllegalStateException("nodes from another graph is neighbor");
+
+ // isNeighbor(int, int).
+ if (!root.isNeighbor(nodeInx[1], nodeInx[1]))
+ throw new IllegalStateException("node with self edge not neigbhor");
+
+ if (root.isNeighbor(nodeInx[0], nodeInx[0]))
+ throw new IllegalStateException("node with no self edge is neighbor");
+
+ if (root.isNeighbor(98, 99))
+ throw new IllegalStateException("positive nodes are neighbors");
+
+ if (!root.isNeighbor(nodeInx[3], nodeInx[2]))
+ throw new IllegalStateException("nodes are not neighbors");
+
+ if (!root.isNeighbor(nodeInx[1], nodeInx[2]))
+ throw new IllegalStateException("nodes are not neighbors");
+
+ if (root.isNeighbor(Integer.MAX_VALUE, Integer.MIN_VALUE)
+ || root.isNeighbor(Integer.MIN_VALUE, Integer.MAX_VALUE))
+ throw new IllegalStateException("MIN_VALUE and MAX_VALUE neighbors");
+
+ // edgeExists(Node, Node).
+ if (root.edgeExists(root.getNode(nodeInx[3]), root.getNode(nodeInx[1])))
+ throw new IllegalStateException("edge exists");
+
+ if (root.edgeExists(root.getNode(nodeInx[0]), root2Node))
+ throw new IllegalStateException("edge exists with node of other graph");
+
+ if (!root.edgeExists(root.getNode(nodeInx[0]), root.getNode(nodeInx[1])))
+ throw new IllegalStateException("edge does not exist");
+
+ if (!root.edgeExists(root.getNode(nodeInx[1]), root.getNode(nodeInx[2])))
+ throw new IllegalStateException("edge does not exist");
+
+ // edgeExists(int, int).
+ if (root.edgeExists(0, 0))
+ throw new IllegalStateException("0 -> 0");
+
+ if (root.edgeExists(nodeInx[2], nodeInx[3]))
+ throw new IllegalStateException("edge exists in opposite direction");
+
+ if (root.edgeExists(nodeInx[4], nodeInx[2]))
+ throw new IllegalStateException("edge exists on node with no edge");
+
+ if (root.edgeExists(nodeInx[0], nodeInx[0]))
+ throw new IllegalStateException("self-edge exists");
+
+ if (root.edgeExists(98, 99))
+ throw new IllegalStateException("edge exists between positive nodes");
+
+ if (!root.edgeExists(nodeInx[1], nodeInx[1]))
+ throw new IllegalStateException("self-edge does not exist [undirected]");
+
+ if (!root.edgeExists(nodeInx[2], nodeInx[2]))
+ throw new IllegalStateException("self-edge does not exist [directed]");
+
+ if (!root.edgeExists(nodeInx[3], nodeInx[2]))
+ throw new IllegalStateException("edge does not exist");
+
+ if (!root.edgeExists(nodeInx[1], nodeInx[0]))
+ throw new IllegalStateException("edge does not exist");
+
+ if (root.edgeExists(Integer.MAX_VALUE, Integer.MIN_VALUE)
+ || root.edgeExists(Integer.MIN_VALUE, Integer.MAX_VALUE))
+ throw new IllegalStateException("MIN_VALUE and MAX_VALUE edge exists");
+
+ // getEdgeCount(Node, Node, boolean).
+ if (root.getEdgeCount(root.getNode(nodeInx[0]), root.getNode(nodeInx[1]), true) != 1)
+ throw new IllegalStateException("wrong number in edge count");
+
+ if (root.getEdgeCount(root.getNode(nodeInx[0]), root2Node, true) != -1)
+ throw new IllegalStateException("edge count not -1");
+
+ if (root.getEdgeCount(root.getNode(nodeInx[1]), root.getNode(nodeInx[1]), false) != 0)
+ throw new IllegalStateException("edge count not 0");
+
+ // getEdgeCount(int, int, boolean).
+ if (root.getEdgeCount(nodeInx[3], nodeInx[2], true) != 1)
+ throw new IllegalStateException("edge count not 1");
+
+ if (root.getEdgeCount(nodeInx[2], nodeInx[3], true) != 0)
+ throw new IllegalStateException("edge count not 0");
+
+ if (root.getEdgeCount(nodeInx[1], nodeInx[2], false) != 0)
+ throw new IllegalStateException("edge count not 0");
+
+ if (root.getEdgeCount(nodeInx[1], nodeInx[1], true) != 1)
+ throw new IllegalStateException("edge count not 1 for und. self edge");
+
+ if (root.getEdgeCount(99, 98, true) != -1)
+ throw new IllegalStateException("edge count not -1");
+
+ if ((root.getEdgeCount(Integer.MAX_VALUE, Integer.MIN_VALUE, false) != -1)
+ || (root.getEdgeCount(Integer.MIN_VALUE, Integer.MAX_VALUE, true) != -1))
+ throw new IllegalStateException("edge count not -1");
+
+ // getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean).
+ int[] adjEdges = root.getAdjacentEdgeIndicesArray(nodeInx[0], true, true, true);
+
+ if (adjEdges.length != 3)
+ throw new IllegalStateException("not 3 adj.");
+
+ for (int i = 0;; i++)
+ if (adjEdges[i] == edgeInx[0])
+ break;
+
+ for (int i = 0;; i++)
+ if (adjEdges[i] == edgeInx[5])
+ break;
+
+ for (int i = 0;; i++)
+ if (adjEdges[i] == edgeInx[2])
+ break;
+
+ adjEdges = root.getAdjacentEdgeIndicesArray(nodeInx[4], true, true, true);
+
+ if (adjEdges.length != 0)
+ throw new IllegalStateException("not 0 adj.");
+
+ adjEdges = root.getAdjacentEdgeIndicesArray(nodeInx[2], true, false, true);
+
+ if (adjEdges.length != 3)
+ throw new IllegalStateException("not 3 adj.");
+
+ for (int i = 0;; i++)
+ if (adjEdges[i] == edgeInx[1])
+ break;
+
+ for (int i = 0;; i++)
+ if (adjEdges[i] == edgeInx[2])
+ break;
+
+ for (int i = 0;; i++)
+ if (adjEdges[i] == edgeInx[3])
+ break;
+
+ adjEdges = root.getAdjacentEdgeIndicesArray(nodeInx[2], true, true, true);
+
+ if (adjEdges.length != 4)
+ throw new IllegalStateException("not 4 adj.");
+
+ for (int i = 0;; i++)
+ if (adjEdges[i] == edgeInx[6])
+ break;
+
+ adjEdges = root.getAdjacentEdgeIndicesArray(nodeInx[1], true, false, false);
+
+ if (adjEdges.length != 2)
+ throw new IllegalStateException("not 2 adj.");
+
+ for (int i = 0;; i++)
+ if (adjEdges[i] == edgeInx[1])
+ break;
+
+ for (int i = 0;; i++)
+ if (adjEdges[i] == edgeInx[4])
+ break;
+
+ adjEdges = root.getAdjacentEdgeIndicesArray(nodeInx[1], false, true, true);
+
+ if (adjEdges.length != 2)
+ throw new IllegalStateException("not 2 adj.");
+
+ for (int i = 0;; i++)
+ if (adjEdges[i] == edgeInx[0])
+ break;
+
+ for (int i = 0;; i++)
+ if (adjEdges[i] == edgeInx[5])
+ break;
+
+ adjEdges = root.getAdjacentEdgeIndicesArray(nodeInx[3], true, true, false);
+
+ if (adjEdges.length != 0)
+ throw new IllegalStateException("not 0 adj.");
+
+ int minEdgeInx = 0;
+
+ for (int i = 0; i < edgeInx.length; i++)
+ minEdgeInx = Math.min(minEdgeInx, edgeInx[i]);
+
+ adjEdges = root.getAdjacentEdgeIndicesArray(99, true, true, true);
+
+ if (adjEdges != null)
+ throw new IllegalStateException("not null");
+
+ adjEdges = root.getAdjacentEdgeIndicesArray(minEdgeInx - 1, true, true, true);
+
+ if (adjEdges != null)
+ throw new IllegalStateException("not null");
+
+ adjEdges = root.getAdjacentEdgeIndicesArray(0, true, true, true);
+
+ if (adjEdges != null)
+ throw new IllegalStateException("not null");
+
+ if ((root.getAdjacentEdgeIndicesArray(Integer.MAX_VALUE, true, true, false) != null)
+ || (root.getAdjacentEdgeIndicesArray(Integer.MIN_VALUE, false, true, true) != null))
+ throw new IllegalStateException("not null");
+
+ // getConnectingEdgeIndicesArray(int[]).
+ int[] connEdges = root.getConnectingEdgeIndicesArray(nodeInx);
+
+ if (connEdges.length != edgeInx.length)
+ throw new IllegalStateException("edge arrays not same length");
+
+ for (int i = 0; i < edgeInx.length; i++)
+ for (int j = 0;; j++)
+ if (connEdges[j] == edgeInx[i])
+ break;
+
+ int[] someNodes = new int[] { nodeInx[0], nodeInx[2], nodeInx[3] };
+ connEdges = root.getConnectingEdgeIndicesArray(someNodes);
+
+ if (connEdges.length != 3)
+ throw new IllegalStateException("not 3 connecting edges");
+
+ for (int i = 0;; i++)
+ if (connEdges[i] == edgeInx[2])
+ break;
+
+ for (int i = 0;; i++)
+ if (connEdges[i] == edgeInx[3])
+ break;
+
+ for (int i = 0;; i++)
+ if (connEdges[i] == edgeInx[6])
+ break;
+
+ someNodes = new int[] { nodeInx[1], nodeInx[4], nodeInx[0], nodeInx[3] };
+ connEdges = root.getConnectingEdgeIndicesArray(someNodes);
+
+ if (connEdges.length != 3)
+ throw new IllegalStateException("not 3 connecting edges");
+
+ for (int i = 0;; i++)
+ if (connEdges[i] == edgeInx[0])
+ break;
+
+ for (int i = 0;; i++)
+ if (connEdges[i] == edgeInx[4])
+ break;
+
+ for (int i = 0;; i++)
+ if (connEdges[i] == edgeInx[5])
+ break;
+
+ someNodes = new int[] { nodeInx[2] };
+ connEdges = root.getConnectingEdgeIndicesArray(someNodes);
+
+ if (connEdges.length != 1)
+ throw new IllegalStateException("not 1 connecting edge");
+
+ for (int i = 0;; i++)
+ if (connEdges[i] == edgeInx[3])
+ break;
+
+ someNodes = new int[] { nodeInx[4], nodeInx[3], nodeInx[0] };
+ connEdges = root.getConnectingEdgeIndicesArray(someNodes);
+
+ if (connEdges.length != 0)
+ throw new IllegalStateException("not 0 connecting edges");
+
+ someNodes = new int[] { nodeInx[0], nodeInx[1], nodeInx[2], nodeInx[3] };
+ connEdges = root.getConnectingEdgeIndicesArray(someNodes);
+
+ if (connEdges.length != edgeInx.length)
+ throw new IllegalStateException("edge arrays not same length");
+
+ for (int i = 0; i < edgeInx.length; i++)
+ for (int j = 0;; j++)
+ if (connEdges[j] == edgeInx[i])
+ break;
+
+ int minNodeInx = 0;
+
+ for (int i = 0; i < nodeInx.length; i++)
+ minNodeInx = Math.min(minNodeInx, nodeInx[i]);
+
+ someNodes = new int[] { 99 };
+ connEdges = root.getConnectingEdgeIndicesArray(someNodes);
+
+ if (connEdges != null)
+ throw new IllegalStateException("not null");
+
+ someNodes = new int[] { nodeInx[0], nodeInx[1], minNodeInx - 1, nodeInx[2] };
+ connEdges = root.getConnectingEdgeIndicesArray(someNodes);
+
+ if (connEdges != null)
+ throw new IllegalStateException("not null");
+
+ someNodes = new int[] { nodeInx[4], 0 };
+ connEdges = root.getConnectingEdgeIndicesArray(someNodes);
+
+ if (connEdges != null)
+ throw new IllegalStateException("not null");
+
+ if ((root.getConnectingEdgeIndicesArray(new int[] { Integer.MAX_VALUE, Integer.MIN_VALUE }) != null)
+ || (root.getConnectingEdgeIndicesArray(new int[] { Integer.MIN_VALUE, Integer.MAX_VALUE }) != null))
+ throw new IllegalStateException("not null");
+
+ // getConnectingNodeIndicesArray(int[]).
+ int[] connNodes = root.getConnectingNodeIndicesArray(edgeInx);
+
+ if (connNodes.length != 4)
+ throw new IllegalStateException("not 4 connecting nodes");
+
+ for (int i = 0; i < nodeInx.length; i++)
+ if (i != 4)
+ for (int j = 0;; j++)
+ if (connNodes[j] == nodeInx[i])
+ break;
+
+ int[] someEdges = new int[] { edgeInx[0], edgeInx[3], edgeInx[5] };
+ connNodes = root.getConnectingNodeIndicesArray(someEdges);
+
+ if (connNodes.length != 3)
+ throw new IllegalStateException("not 3 connecting nodes");
+
+ for (int i = 0;; i++)
+ if (connNodes[i] == nodeInx[0])
+ break;
+
+ for (int i = 0;; i++)
+ if (connNodes[i] == nodeInx[1])
+ break;
+
+ for (int i = 0;; i++)
+ if (connNodes[i] == nodeInx[2])
+ break;
+
+ someEdges = new int[] { edgeInx[6] };
+ connNodes = root.getConnectingNodeIndicesArray(someEdges);
+
+ if (connNodes.length != 2)
+ throw new IllegalStateException("not 2 connecting nodes");
+
+ for (int i = 0;; i++)
+ if (connNodes[i] == nodeInx[2])
+ break;
+
+ for (int i = 0;; i++)
+ if (connNodes[i] == nodeInx[3])
+ break;
+
+ someEdges = new int[] { edgeInx[4], edgeInx[3] };
+ connNodes = root.getConnectingNodeIndicesArray(someEdges);
+
+ if (connNodes.length != 2)
+ throw new IllegalStateException("not 2 connecting nodes");
+
+ for (int i = 0;; i++)
+ if (connNodes[i] == nodeInx[1])
+ break;
+
+ for (int i = 0;; i++)
+ if (connNodes[i] == nodeInx[2])
+ break;
+
+ someEdges = new int[] { edgeInx[5], edgeInx[6] };
+ connNodes = root.getConnectingNodeIndicesArray(someEdges);
+
+ if (connNodes.length != 4)
+ throw new IllegalStateException("not 4 connecting nodes");
+
+ for (int i = 0;; i++)
+ if (connNodes[i] == nodeInx[0])
+ break;
+
+ for (int i = 0;; i++)
+ if (connNodes[i] == nodeInx[1])
+ break;
+
+ for (int i = 0;; i++)
+ if (connNodes[i] == nodeInx[2])
+ break;
+
+ for (int i = 0;; i++)
+ if (connNodes[i] == nodeInx[3])
+ break;
+
+ someEdges = new int[] { 99 };
+ connNodes = root.getConnectingNodeIndicesArray(someEdges);
+
+ if (connNodes != null)
+ throw new IllegalStateException("not null");
+
+ someEdges = new int[] { minEdgeInx - 1 };
+ connNodes = root.getConnectingNodeIndicesArray(someEdges);
+
+ if (connNodes != null)
+ throw new IllegalStateException("not null");
+
+ someEdges = new int[] { edgeInx[0], 0, edgeInx[1] };
+ connNodes = root.getConnectingNodeIndicesArray(someEdges);
+
+ if (connNodes != null)
+ throw new IllegalStateException("not null");
+
+ if ((root.getConnectingNodeIndicesArray(new int[] { Integer.MAX_VALUE, Integer.MIN_VALUE }) != null)
+ || (root.getConnectingNodeIndicesArray(new int[] { Integer.MIN_VALUE, Integer.MAX_VALUE }) != null))
+ throw new IllegalStateException("not null");
+
+ // getEdgeIndicesArray(int, int, boolean, boolean).
+ connEdges = root.getEdgeIndicesArray(nodeInx[1], nodeInx[0], false, true);
+
+ if (connEdges.length != 2)
+ throw new IllegalStateException("not 2 connecting edges");
+
+ for (int i = 0;; i++)
+ if (connEdges[i] == edgeInx[0])
+ break;
+
+ for (int i = 0;; i++)
+ if (connEdges[i] == edgeInx[5])
+ break;
+
+ connEdges = root.getEdgeIndicesArray(nodeInx[0], nodeInx[3], true, true);
+
+ if (connEdges.length != 0)
+ throw new IllegalStateException("not 0 connecting edges");
+
+ connEdges = root.getEdgeIndicesArray(nodeInx[1], nodeInx[2], false, true);
+
+ if (connEdges.length != 0)
+ throw new IllegalStateException("not 0 connecting edges");
+
+ connEdges = root.getEdgeIndicesArray(nodeInx[2], nodeInx[1], true, false);
+
+ if (connEdges.length != 1)
+ throw new IllegalStateException("not 1 connecting edge");
+
+ for (int i = 0;; i++)
+ if (connEdges[i] == edgeInx[1])
+ break;
+
+ connEdges = root.getEdgeIndicesArray(nodeInx[2], nodeInx[2], false, false);
+
+ if (connEdges.length != 1)
+ throw new IllegalStateException("not 1 connecting edge");
+
+ for (int i = 0;; i++)
+ if (connEdges[i] == edgeInx[3])
+ break;
+
+ connEdges = root.getEdgeIndicesArray(nodeInx[2], nodeInx[2], true, true);
+
+ if (connEdges.length != 1)
+ throw new IllegalStateException("not 1 connecting edge");
+
+ for (int i = 0;; i++)
+ if (connEdges[i] == edgeInx[3])
+ break;
+
+ connEdges = root.getEdgeIndicesArray(nodeInx[2], nodeInx[3], false, false);
+
+ if (connEdges.length != 0)
+ throw new IllegalStateException("not 0 connecting edges");
+
+ connEdges = root.getEdgeIndicesArray(nodeInx[3], nodeInx[2], false, false);
+
+ if (connEdges.length != 1)
+ throw new IllegalStateException("not 1 connecting edge");
+
+ for (int i = 0;; i++)
+ if (connEdges[i] == edgeInx[6])
+ break;
+
+ connEdges = root.getEdgeIndicesArray(nodeInx[4], nodeInx[0], true, true);
+
+ if (connEdges.length != 0)
+ throw new IllegalStateException("not 0 connecting edges");
+
+ connEdges = root.getEdgeIndicesArray(99, 0, true, true);
+
+ if (connEdges != null)
+ throw new IllegalStateException("not null");
+
+ connEdges = root.getEdgeIndicesArray(nodeInx[0], minNodeInx - 1, true, false);
+
+ if (connEdges != null)
+ throw new IllegalStateException("not null");
+
+ if ((root.getEdgeIndicesArray(Integer.MAX_VALUE, Integer.MIN_VALUE, true, false) != null)
+ || (root.getEdgeIndicesArray(Integer.MIN_VALUE, Integer.MAX_VALUE, false, false) != null))
+ throw new IllegalStateException("not null");
+
+ // edgesList(Node, Node).
+ edgesList = root.edgesList(root.getNode(nodeInx[3]), root.getNode(nodeInx[1]));
+
+ if (edgesList.size() != 0)
+ throw new IllegalStateException("edges List not of size 0");
+
+ edgesList = root.edgesList(root.getNode(nodeInx[0]), root2Node);
+
+ if (edgesList != null)
+ throw new IllegalStateException("not null");
+
+ edgesList = root.edgesList(root.getNode(nodeInx[0]), root.getNode(nodeInx[1]));
+
+ if (edgesList.size() != 1)
+ throw new IllegalStateException("edges List not of size 1");
+
+ if (((Edge) edgesList.get(0)).getRootGraphIndex() != edgeInx[0])
+ throw new IllegalStateException("wrong edge");
+
+ edgesList = root.edgesList(root.getNode(nodeInx[2]), root.getNode(nodeInx[1]));
+
+ if (edgesList.size() != 1)
+ throw new IllegalStateException("edges List not of size 1");
+
+ if (((Edge) edgesList.get(0)).getRootGraphIndex() != edgeInx[1])
+ throw new IllegalStateException("wrong edge");
+
+ edgesList = root.edgesList(root.getNode(nodeInx[2]), root.getNode(nodeInx[2]));
+
+ if (edgesList.size() != 1)
+ throw new IllegalStateException("edges List not of size 1");
+
+ if (((Edge) edgesList.get(0)).getRootGraphIndex() != edgeInx[3])
+ throw new IllegalStateException("wrong edge");
+
+ edgesList = root.edgesList(root.getNode(nodeInx[1]), root.getNode(nodeInx[4]));
+
+ if (edgesList.size() != 0)
+ throw new IllegalStateException("edges List not of size 0");
+
+ // edgesList(int, int, boolean).
+ edgesList = root.edgesList(nodeInx[2], nodeInx[0], true);
+
+ if (edgesList.size() != 1)
+ throw new IllegalStateException("edges List not of size 1");
+
+ if (((Edge) edgesList.get(0)).getRootGraphIndex() != edgeInx[2])
+ throw new IllegalStateException("wrong edge");
+
+ edgesList = root.edgesList(nodeInx[4], nodeInx[3], false);
+
+ if (edgesList.size() != 0)
+ throw new IllegalStateException("edges List not of size 0");
+
+ edgesList = root.edgesList(99, minNodeInx - 1, true);
+
+ if (edgesList != null)
+ throw new IllegalStateException("not null");
+
+ if ((root.edgesList(Integer.MAX_VALUE, Integer.MIN_VALUE, true) != null)
+ || (root.edgesList(Integer.MIN_VALUE, Integer.MAX_VALUE, false) != null))
+ throw new IllegalStateException("not null");
+
+ // getEdgeIndicesArray(int, int, boolean).
+ connEdges = root.getEdgeIndicesArray(nodeInx[1], nodeInx[1], false);
+
+ if (connEdges.length != 0)
+ throw new IllegalStateException("not 0 connecting edges");
+
+ connEdges = root.getEdgeIndicesArray(nodeInx[1], nodeInx[1], true);
+
+ if (connEdges.length != 1)
+ throw new IllegalStateException("not 1 connecting edge");
+
+ for (int i = 0;; i++)
+ if (connEdges[i] == edgeInx[4])
+ break;
+
+ connEdges = root.getEdgeIndicesArray(nodeInx[1], nodeInx[0], true);
+
+ if (connEdges.length != 1)
+ throw new IllegalStateException("not 1 connecting edge");
+
+ for (int i = 0;; i++)
+ if (connEdges[i] == edgeInx[5])
+ break;
+
+ connEdges = root.getEdgeIndicesArray(minNodeInx - 1, nodeInx[2], true);
+
+ if (connEdges != null)
+ throw new IllegalStateException("not null");
+
+ connEdges = root.getEdgeIndicesArray(nodeInx[1], 99, true);
+
+ if (connEdges != null)
+ throw new IllegalStateException("not null");
+
+ if ((root.getEdgeIndicesArray(Integer.MAX_VALUE, Integer.MIN_VALUE, true) != null)
+ || (root.getEdgeIndicesArray(Integer.MIN_VALUE, Integer.MAX_VALUE, false) != null))
+ throw new IllegalStateException("not null");
+
+ // getInDegree(Node).
+ if (root.getInDegree(root2Node) != -1)
+ throw new IllegalStateException("not in degree -1 for other node");
+
+ if (root.getInDegree(root.getNode(nodeInx[2])) != 3)
+ throw new IllegalStateException("not in degree 3 for node");
+
+ if (root.getInDegree(root.getNode(nodeInx[3])) != 0)
+ throw new IllegalStateException("not in degree 0 for node");
+
+ if (root.getInDegree(root.getNode(nodeInx[4])) != 0)
+ throw new IllegalStateException("not in degree 0 for node");
+
+ if (root.getInDegree(root.getNode(nodeInx[0])) != 2)
+ throw new IllegalStateException("not in degree 2 for node");
+
+ if (root.getInDegree(root.getNode(nodeInx[1])) != 3)
+ throw new IllegalStateException("not in degree 3 for node");
+
+ // getInDegree(int).
+ if ((root.getInDegree(minNodeInx - 1) != -1) || (root.getInDegree(0) != -1)
+ || (root.getInDegree(99) != -1))
+ throw new IllegalStateException("not in degree -1");
+
+ if (root.getInDegree(nodeInx[1]) != 3)
+ throw new IllegalStateException("not in degree 3");
+
+ if (root.getInDegree(nodeInx[0]) != 2)
+ throw new IllegalStateException("not in degree 2");
+
+ if (root.getInDegree(Integer.MAX_VALUE) != -1)
+ throw new IllegalStateException("not in degree -1");
+
+ // getInDegree(Node, boolean).
+ if (root.getInDegree(root2Node, true) != -1)
+ throw new IllegalStateException("not in degree -1 for other node");
+
+ if (root.getInDegree(root.getNode(nodeInx[1]), false) != 1)
+ throw new IllegalStateException("not in degree 1");
+
+ if (root.getInDegree(root.getNode(nodeInx[2]), false) != 2)
+ throw new IllegalStateException("not in degree 2");
+
+ if (root.getInDegree(root.getNode(nodeInx[2]), true) != 3)
+ throw new IllegalStateException("not in degree 3");
+
+ // getInDegree(int, boolean).
+ if ((root.getInDegree(minNodeInx - 1, false) != -1) || (root.getInDegree(0, true) != -1)
+ || (root.getInDegree(99, false) != -1))
+ throw new IllegalStateException("not in degree -1");
+
+ if (root.getInDegree(nodeInx[0], true) != 2)
+ throw new IllegalStateException("not in degree 2");
+
+ if (root.getInDegree(nodeInx[0], false) != 2)
+ throw new IllegalStateException("not in degree 2");
+
+ if (root.getInDegree(nodeInx[4], true) != 0)
+ throw new IllegalStateException("not in degree 0");
+
+ if (root.getInDegree(nodeInx[1], false) != 1)
+ throw new IllegalStateException("not in degree 1");
+
+ if (root.getInDegree(Integer.MIN_VALUE, true) != -1)
+ throw new IllegalStateException("not in degree -1");
+
+ // getOutDegree(Node).
+ if (root.getOutDegree(root2Node) != -1)
+ throw new IllegalStateException("not out degree -1");
+
+ if (root.getOutDegree(root.getNode(nodeInx[2])) != 3)
+ throw new IllegalStateException("not out degree 3");
+
+ if (root.getOutDegree(root.getNode(nodeInx[1])) != 3)
+ throw new IllegalStateException("not out degree 3");
+
+ if (root.getOutDegree(root.getNode(nodeInx[4])) != 0)
+ throw new IllegalStateException("not out degree 0");
+
+ // getOutDegree(int).
+ if ((root.getOutDegree(minNodeInx - 1) != -1) || (root.getOutDegree(0) != -1)
+ || (root.getOutDegree(101) != -1))
+ throw new IllegalStateException("not out degree -1");
+
+ if (root.getOutDegree(nodeInx[3]) != 1)
+ throw new IllegalStateException("not out degree 1");
+
+ if (root.getOutDegree(nodeInx[0]) != 1)
+ throw new IllegalStateException("not out degree 1");
+
+ if (root.getOutDegree(Integer.MIN_VALUE) != -1)
+ throw new IllegalStateException("not out degree -1");
+
+ // getOutDegree(Node, boolean).
+ if (root.getOutDegree(root2Node, false) != -1)
+ throw new IllegalStateException("not out degree -1");
+
+ if (root.getOutDegree(root.getNode(nodeInx[1]), false) != 1)
+ throw new IllegalStateException("not out degree 1");
+
+ if (root.getOutDegree(root.getNode(nodeInx[1]), true) != 3)
+ throw new IllegalStateException("not out degree 1");
+
+ if ((root.getOutDegree(root.getNode(nodeInx[0]), false) != 1)
+ || (root.getOutDegree(root.getNode(nodeInx[0]), true) != 1))
+ throw new IllegalStateException("not out degree 1");
+
+ // getOutDegree(int, boolean).
+ if ((root.getOutDegree(minNodeInx - 3, false) != -1) || (root.getOutDegree(0, true) != -1)
+ || (root.getOutDegree(2, false) != -1))
+ throw new IllegalStateException("not out degree -1");
+
+ if ((root.getOutDegree(nodeInx[2], false) != 2)
+ || (root.getOutDegree(nodeInx[2], true) != 3))
+ throw new IllegalStateException("not correct out degree");
+
+ if ((root.getOutDegree(nodeInx[3], false) != 1)
+ || (root.getOutDegree(nodeInx[3], true) != 1))
+ throw new IllegalStateException("not out degree 1");
+
+ if ((root.getOutDegree(nodeInx[4], true) != 0)
+ || (root.getOutDegree(nodeInx[4], false) != 0))
+ throw new IllegalStateException("not out degree 0");
+
+ if (root.getOutDegree(Integer.MAX_VALUE, false) != -1)
+ throw new IllegalStateException("not out degree -1");
+
+ // getDegree(Node).
+ if (root.getDegree(root2Node) != -1)
+ throw new IllegalStateException("not degree -1 for other node");
+
+ if (root.getDegree(root.getNode(nodeInx[0])) != 3)
+ throw new IllegalStateException("not degree 3");
+
+ if (root.getDegree(root.getNode(nodeInx[1])) != 4)
+ throw new IllegalStateException("not degree 4");
+
+ // getDegree(int).
+ if ((root.getDegree(minNodeInx - 2) != -1) || (root.getDegree(0) != -1)
+ || (root.getDegree(13) != -1))
+ throw new IllegalStateException("not degree -1");
+
+ if (root.getDegree(nodeInx[2]) != 4)
+ throw new IllegalStateException("not degree 4");
+
+ if (root.getDegree(nodeInx[3]) != 1)
+ throw new IllegalStateException("not degree 1");
+
+ if (root.getDegree(nodeInx[4]) != 0)
+ throw new IllegalStateException("not degree 0");
+
+ if ((root.getDegree(Integer.MAX_VALUE) != -1) || (root.getDegree(Integer.MIN_VALUE) != -1))
+ throw new IllegalStateException("not degree -1");
+
+ // getIndex(Node).
+ if (root.getIndex(root2Node) != 0)
+ throw new IllegalStateException("index not 0");
+
+ if (root.getIndex(root.getNode(nodeInx[2])) != nodeInx[2])
+ throw new IllegalStateException("wrong node index");
+
+ // getNode(int).
+ if ((root.getNode(minNodeInx - 1) != null) || (root.getNode(0) != null)
+ || (root.getNode(23) != null))
+ throw new IllegalStateException("not null");
+
+ if ((root.getNode(Integer.MAX_VALUE) != null) || (root.getNode(Integer.MIN_VALUE) != null))
+ throw new IllegalStateException("not null");
+
+ // getIndex(Edge).
+ if (root.getIndex(root2Edge) != 0)
+ throw new IllegalStateException("index not 0");
+
+ if (root.getIndex(root.getEdge(edgeInx[3])) != edgeInx[3])
+ throw new IllegalStateException("wrong edge index");
+
+ // getEdge(int).
+ if ((root.getEdge(minEdgeInx - 1) != null) || (root.getEdge(0) != null)
+ || (root.getEdge(37) != null))
+ throw new IllegalStateException("not null");
+
+ if ((root.getEdge(Integer.MIN_VALUE) != null) || (root.getEdge(Integer.MAX_VALUE) != null))
+ throw new IllegalStateException("not null");
+
+ // getEdgeSourceIndex(int).
+ if ((root.getEdgeSourceIndex(minEdgeInx - 1) != 0) || (root.getEdgeSourceIndex(0) != 0)
+ || (root.getEdgeSourceIndex(97) != 0))
+ throw new IllegalStateException("edge source not 0");
+
+ if ((root.getEdgeSourceIndex(edgeInx[3]) != nodeInx[2])
+ || (root.getEdgeSourceIndex(edgeInx[6]) != nodeInx[3])
+ || (root.getEdgeSourceIndex(edgeInx[1]) != nodeInx[1])
+ || (root.getEdgeSourceIndex(edgeInx[4]) != nodeInx[1]))
+ throw new IllegalStateException("wrong edge source node");
+
+ if ((root.getEdgeSourceIndex(Integer.MAX_VALUE) != 0)
+ || (root.getEdgeSourceIndex(Integer.MIN_VALUE) != 0))
+ throw new IllegalStateException("edge source not 0");
+
+ // getEdgeTargetIndex(int).
+ if ((root.getEdgeTargetIndex(minEdgeInx - 1) != 0) || (root.getEdgeTargetIndex(0) != 0)
+ || (root.getEdgeTargetIndex(93) != 0))
+ throw new IllegalStateException("wrong edge target node");
+
+ if ((root.getEdgeTargetIndex(edgeInx[2]) != nodeInx[0])
+ || (root.getEdgeTargetIndex(edgeInx[0]) != nodeInx[1])
+ || (root.getEdgeTargetIndex(edgeInx[5]) != nodeInx[0]))
+ throw new IllegalStateException("wrong edge target node");
+
+ if ((root.getEdgeTargetIndex(Integer.MAX_VALUE) != 0)
+ || (root.getEdgeTargetIndex(Integer.MIN_VALUE) != 0))
+ throw new IllegalStateException("edge target not 0");
+
+ // isEdgeDirected(int).
+ if ((!root.isEdgeDirected(edgeInx[0])) || root.isEdgeDirected(edgeInx[1])
+ || root.isEdgeDirected(edgeInx[4]) || (!root.isEdgeDirected(edgeInx[5])))
+ throw new IllegalStateException("wrong edge directedness");
+
+ // isMetaParent(Node, Node).
+ if (root.isMetaParent(root.getNode(nodeInx[2]), root.getNode(nodeInx[1])))
+ throw new IllegalStateException("reported wrong meta child node");
+
+ if (root.isMetaParent(root.getNode(nodeInx[1]), root.getNode(nodeInx[4])))
+ throw new IllegalStateException("reported wrong meta child node");
+
+ if (root.isMetaParent(root.getNode(nodeInx[4]), root.getNode(nodeInx[3])))
+ throw new IllegalStateException("reported wrong meta child node");
+
+ if (root.isMetaParent(root2Node, root.getNode(nodeInx[1])))
+ throw new IllegalStateException("reported wrong meta child node");
+
+ if (root.isMetaParent(root.getNode(nodeInx[3]), root2Node))
+ throw new IllegalStateException("reported wrong meta child node");
+
+ if (root.isMetaParent(root.getNode(nodeInx[2]), root.getNode(nodeInx[2])))
+ throw new IllegalStateException("reported wrong meta child node");
+
+ if (!(root.isMetaParent(root.getNode(nodeInx[4]), root.getNode(nodeInx[4]))))
+ throw new IllegalStateException("missing a meta relationship");
+
+ if (!(root.isMetaParent(root.getNode(nodeInx[4]), root.getNode(nodeInx[0]))))
+ throw new IllegalStateException("missing a meta relationship");
+
+ if (!(root.isMetaParent(root.getNode(nodeInx[1]), root.getNode(nodeInx[0]))))
+ throw new IllegalStateException("missing a meta relationship");
+
+ // isNodeMetaParent(int, int).
+ if (root.isNodeMetaParent(nodeInx[4], nodeInx[1])
+ || root.isNodeMetaParent(nodeInx[1], nodeInx[1]) || root.isNodeMetaParent(99, 0)
+ || root.isNodeMetaParent(nodeInx[4], minNodeInx - 1)
+ || root.isNodeMetaParent(Integer.MAX_VALUE, Integer.MIN_VALUE)
+ || root.isNodeMetaParent(Integer.MIN_VALUE, 0))
+ throw new IllegalStateException("reported wrong meta child node");
+
+ if (!(root.isNodeMetaParent(nodeInx[3], nodeInx[3])))
+ throw new IllegalStateException("missing a meta relationship");
+
+ if (!(root.isNodeMetaParent(nodeInx[2], nodeInx[3])))
+ throw new IllegalStateException("missing a meta relationship");
+
+ if (!(root.isNodeMetaParent(nodeInx[0], nodeInx[4])))
+ throw new IllegalStateException("missing a meta relationship");
+
+ if (!(root.isNodeMetaParent(nodeInx[4], nodeInx[0])))
+ throw new IllegalStateException("missing a meta relationship");
+
+ if (!(root.isNodeMetaParent(nodeInx[0], nodeInx[3])))
+ throw new IllegalStateException("missing a meta relationship");
+
+ // metaParentsList(Node).
+ if (root.metaParentsList(root2Node) != null)
+ throw new IllegalStateException("expected null for other node");
+
+ nodesList = root.metaParentsList(root.getNode(nodeInx[0]));
+
+ if (nodesList.size() != 2)
+ throw new IllegalStateException("wrong number of parent nodes");
+
+ for (int i = 0; i < nodesList.size(); i++) {
+ Node foo = (Node) (nodesList.get(i));
+ }
+
+ nodesList = root.metaParentsList(root.getNode(nodeInx[1]));
+
+ if (nodesList.size() != 2)
+ throw new IllegalStateException("wrong number of parent nodes");
+
+ // nodeMetaParentsList(int).
+ if ((root.nodeMetaParentsList(0) != null)
+ || (root.nodeMetaParentsList(Integer.MAX_VALUE) != null)
+ || (root.nodeMetaParentsList(Integer.MIN_VALUE) != null)
+ || (root.nodeMetaParentsList(99) != null)
+ || (root.nodeMetaParentsList(minNodeInx - 1) != null))
+ throw new IllegalStateException("expected null for meta parents");
+
+ nodesList = root.nodeMetaParentsList(nodeInx[2]);
+
+ if (nodesList.size() != 2)
+ throw new IllegalStateException("wrong number of parent nodes");
+
+ nodesList = root.nodeMetaParentsList(nodeInx[3]);
+
+ if (nodesList.size() != 2)
+ throw new IllegalStateException("wrong number of parent nodes");
+
+ nodesList = root.nodeMetaParentsList(nodeInx[4]);
+
+ if (nodesList.size() != 2)
+ throw new IllegalStateException("wrong number of parent nodes");
+
+ // getNodeMetaParentIndicesArray(int).
+ if ((root.getNodeMetaParentIndicesArray(0) != null)
+ || (root.getNodeMetaParentIndicesArray(Integer.MAX_VALUE) != null)
+ || (root.getNodeMetaParentIndicesArray(Integer.MIN_VALUE) != null)
+ || (root.getNodeMetaParentIndicesArray(99) != null)
+ || (root.getNodeMetaParentIndicesArray(minNodeInx - 1) != null))
+ throw new IllegalStateException("expected null for meta parents");
+
+ int[] parentInx = root.getNodeMetaParentIndicesArray(nodeInx[0]);
+
+ if (parentInx.length != 2)
+ throw new IllegalStateException("wrong number of parent nodes");
+
+ for (int i = 0;; i++)
+ if (parentInx[i] == nodeInx[3])
+ break;
+
+ for (int i = 0;; i++)
+ if (parentInx[i] == nodeInx[4])
+ break;
+
+ parentInx = root.getNodeMetaParentIndicesArray(nodeInx[1]);
+
+ if (parentInx.length != 2)
+ throw new IllegalStateException("wrong number of parent nodes");
+
+ for (int i = 0;; i++)
+ if (parentInx[i] == nodeInx[0])
+ break;
+
+ for (int i = 0;; i++)
+ if (parentInx[i] == nodeInx[3])
+ break;
+
+ parentInx = root.getNodeMetaParentIndicesArray(nodeInx[2]);
+
+ if (parentInx.length != 2)
+ throw new IllegalStateException("wrong number of parent nodes");
+
+ for (int i = 0;; i++)
+ if (parentInx[i] == nodeInx[3])
+ break;
+
+ for (int i = 0;; i++)
+ if (parentInx[i] == nodeInx[4])
+ break;
+
+ parentInx = root.getNodeMetaParentIndicesArray(nodeInx[3]);
+
+ if (parentInx.length != 2)
+ throw new IllegalStateException("wrong number of parent nodes");
+
+ for (int i = 0;; i++)
+ if (parentInx[i] == nodeInx[3])
+ break;
+
+ for (int i = 0;; i++)
+ if (parentInx[i] == nodeInx[4])
+ break;
+
+ parentInx = root.getNodeMetaParentIndicesArray(nodeInx[4]);
+
+ if (parentInx.length != 2)
+ throw new IllegalStateException("wrong number of parent nodes");
+
+ for (int i = 0;; i++)
+ if (parentInx[i] == nodeInx[0])
+ break;
+
+ for (int i = 0;; i++)
+ if (parentInx[i] == nodeInx[4])
+ break;
+
+ // isMetaChild(Node, Node).
+ if (root.isMetaChild(root2Node, root2Node)
+ || root.isMetaChild(root.getNode(nodeInx[1]), root.getNode(nodeInx[2]))
+ || root.isMetaChild(root.getNode(nodeInx[2]), root.getNode(nodeInx[1])))
+ throw new IllegalStateException("unexpected meta child");
+
+ if (!(root.isMetaChild(root.getNode(nodeInx[4]), root.getNode(nodeInx[4]))
+ && root.isMetaChild(root.getNode(nodeInx[3]), root.getNode(nodeInx[2]))
+ && root.isMetaChild(root.getNode(nodeInx[0]), root.getNode(nodeInx[1]))))
+ throw new IllegalStateException("missing meta relationship");
+
+ // isNodeMetaChild(int, int).
+ if (root.isNodeMetaChild(0, 0) || root.isNodeMetaChild(Integer.MIN_VALUE, 87)
+ || root.isNodeMetaChild(nodeInx[0], Integer.MAX_VALUE)
+ || root.isNodeMetaChild(minNodeInx - 1, nodeInx[1])
+ || root.isNodeMetaChild(nodeInx[0], nodeInx[3])
+ || root.isNodeMetaChild(nodeInx[1], nodeInx[0]))
+ throw new IllegalStateException("unexpected meta relationship");
+
+ if (!(root.isNodeMetaChild(nodeInx[0], nodeInx[1])
+ && root.isNodeMetaChild(nodeInx[3], nodeInx[3])
+ && root.isNodeMetaChild(nodeInx[0], nodeInx[4])))
+ throw new IllegalStateException("missing meta relationship");
+
+ // isNodeMetaChild(int, int, boolean).
+ if (root.isNodeMetaChild(0, 0, true)
+ || root.isNodeMetaChild(Integer.MIN_VALUE, Integer.MAX_VALUE, true)
+ || root.isNodeMetaChild(Integer.MAX_VALUE, Integer.MIN_VALUE, true)
+ || root.isNodeMetaChild(minNodeInx - 1, nodeInx[1], true)
+ || root.isNodeMetaChild(nodeInx[0], nodeInx[3], false)
+ || root.isNodeMetaChild(nodeInx[2], nodeInx[4], true)
+ || root.isNodeMetaChild(nodeInx[1], nodeInx[0], true))
+ throw new IllegalStateException("unexpected recursive meta child");
+
+ if (!(root.isNodeMetaChild(nodeInx[0], nodeInx[3], true)
+ && root.isNodeMetaChild(nodeInx[0], nodeInx[0], true)
+ && root.isNodeMetaChild(nodeInx[0], nodeInx[2], true)
+ && root.isNodeMetaChild(nodeInx[4], nodeInx[1], true)
+ && root.isNodeMetaChild(nodeInx[3], nodeInx[4], true)))
+ throw new IllegalStateException("missing recursive meta child");
+
+ // nodeMetaChildrenList(Node).
+ if (root.nodeMetaChildrenList(root2Node) != null)
+ throw new IllegalStateException("expected null for other node children");
+
+ nodesList = root.nodeMetaChildrenList(root.getNode(nodeInx[2]));
+
+ if (nodesList.size() != 0)
+ throw new IllegalStateException("expected no children");
+
+ nodesList = root.nodeMetaChildrenList(root.getNode(nodeInx[4]));
+
+ if (nodesList.size() != 4)
+ throw new IllegalStateException("wrong number of children");
+
+ for (int i = 0; i < nodesList.size(); i++) {
+ Node foo = (Node) nodesList.get(i);
+ }
+
+ // nodeMetaChildrenList(int).
+ if ((root.nodeMetaChildrenList(0) != null)
+ || (root.nodeMetaChildrenList(Integer.MAX_VALUE) != null)
+ || (root.nodeMetaChildrenList(Integer.MIN_VALUE) != null)
+ || (root.nodeMetaChildrenList(minNodeInx - 1) != null)
+ || (root.nodeMetaChildrenList(77) != null))
+ throw new IllegalStateException("expected null children list");
+
+ nodesList = root.nodeMetaChildrenList(nodeInx[3]);
+
+ if (nodesList.size() != 4)
+ throw new IllegalStateException("wrong number of children");
+
+ int[] nodeChildInx = new int[nodesList.size()];
+
+ for (int i = 0; i < nodesList.size(); i++) {
+ Node foo = (Node) nodesList.get(i);
+ nodeChildInx[i] = foo.getRootGraphIndex();
+ }
+
+ for (int i = 0;; i++)
+ if (nodeChildInx[i] == nodeInx[0])
+ break;
+
+ for (int i = 0;; i++)
+ if (nodeChildInx[i] == nodeInx[1])
+ break;
+
+ for (int i = 0;; i++)
+ if (nodeChildInx[i] == nodeInx[2])
+ break;
+
+ for (int i = 0;; i++)
+ if (nodeChildInx[i] == nodeInx[3])
+ break;
+
+ // getNodeMetaChildIndicesArray(int).
+ if ((root.getNodeMetaChildIndicesArray(0) != null)
+ || (root.getNodeMetaChildIndicesArray(Integer.MAX_VALUE) != null)
+ || (root.getNodeMetaChildIndicesArray(Integer.MIN_VALUE) != null)
+ || (root.getNodeMetaChildIndicesArray(minNodeInx - 1) != null)
+ || (root.getNodeMetaChildIndicesArray(66) != null))
+ throw new IllegalStateException("expected null children array");
+
+ nodeChildInx = root.getNodeMetaChildIndicesArray(nodeInx[0]);
+
+ if (nodeChildInx.length != 2)
+ throw new IllegalStateException("wrong number of children in array");
+
+ for (int i = 0;; i++)
+ if (nodeChildInx[i] == nodeInx[1])
+ break;
+
+ for (int i = 0;; i++)
+ if (nodeChildInx[i] == nodeInx[4])
+ break;
+
+ nodeChildInx = root.getNodeMetaChildIndicesArray(nodeInx[1]);
+
+ if (nodeChildInx.length != 0)
+ throw new IllegalStateException("wrong number of children in array");
+
+ nodeChildInx = root.getNodeMetaChildIndicesArray(nodeInx[4]);
+
+ if (nodeChildInx.length != 4)
+ throw new IllegalStateException("wrong number of children in array");
+
+ for (int i = 0;; i++)
+ if (nodeChildInx[i] == nodeInx[0])
+ break;
+
+ for (int i = 0;; i++)
+ if (nodeChildInx[i] == nodeInx[2])
+ break;
+
+ for (int i = 0;; i++)
+ if (nodeChildInx[i] == nodeInx[3])
+ break;
+
+ for (int i = 0;; i++)
+ if (nodeChildInx[i] == nodeInx[4])
+ break;
+
+ // getNodeMetaChildIndicesArray(int, boolean).
+ if ((root.getNodeMetaChildIndicesArray(0, true) != null)
+ || (root.getNodeMetaChildIndicesArray(Integer.MAX_VALUE, true) != null)
+ || (root.getNodeMetaChildIndicesArray(Integer.MIN_VALUE, true) != null)
+ || (root.getNodeMetaChildIndicesArray(minNodeInx - 1, true) != null)
+ || (root.getNodeMetaChildIndicesArray(66, true) != null))
+ throw new IllegalStateException("expected null children array");
+
+ nodeChildInx = root.getNodeMetaChildIndicesArray(nodeInx[0], true);
+
+ if (nodeChildInx.length != 5)
+ throw new IllegalStateException("wrong # recursive children");
+
+ nodeChildInx = root.getNodeMetaChildIndicesArray(nodeInx[1], true);
+
+ if (nodeChildInx.length != 0)
+ throw new IllegalStateException("wrong # recursive children");
+
+ nodeChildInx = root.getNodeMetaChildIndicesArray(nodeInx[2], true);
+
+ if (nodeChildInx.length != 0)
+ throw new IllegalStateException("wrong # recursive children");
+
+ nodeChildInx = root.getNodeMetaChildIndicesArray(nodeInx[3], true);
+
+ if (nodeChildInx.length != 5)
+ throw new IllegalStateException("wrong # recursive children");
+
+ nodeChildInx = root.getNodeMetaChildIndicesArray(nodeInx[4], true);
+
+ if (nodeChildInx.length != 5)
+ throw new IllegalStateException("wrong # recursive children");
+
+ for (int i = 0;; i++)
+ if (nodeChildInx[i] == nodeInx[0])
+ break;
+
+ for (int i = 0;; i++)
+ if (nodeChildInx[i] == nodeInx[1])
+ break;
+
+ for (int i = 0;; i++)
+ if (nodeChildInx[i] == nodeInx[2])
+ break;
+
+ for (int i = 0;; i++)
+ if (nodeChildInx[i] == nodeInx[3])
+ break;
+
+ for (int i = 0;; i++)
+ if (nodeChildInx[i] == nodeInx[4])
+ break;
+
+ // getChildlessMetaDescendants(int).
+ if ((root.getChildlessMetaDescendants(0) != null)
+ || (root.getChildlessMetaDescendants(Integer.MAX_VALUE) != null)
+ || (root.getChildlessMetaDescendants(Integer.MIN_VALUE) != null)
+ || (root.getChildlessMetaDescendants(minNodeInx - 1) != null)
+ || (root.getChildlessMetaDescendants(12) != null))
+ throw new IllegalStateException("expected null childless descendants");
+
+ if (root.getChildlessMetaDescendants(nodeInx[1]).length != 0)
+ throw new IllegalStateException("expected no childless descendants");
+
+ nodeChildInx = root.getChildlessMetaDescendants(nodeInx[0]);
+
+ if (nodeChildInx.length != 2)
+ throw new IllegalStateException("wrong number of childless descendants");
+
+ for (int i = 0;; i++)
+ if (nodeChildInx[i] == nodeInx[1])
+ break;
+
+ for (int i = 0;; i++)
+ if (nodeChildInx[i] == nodeInx[2])
+ break;
+
+ // isMetaParent(Edge, Node).
+ if (root.isMetaParent(root2Edge, root2Node)
+ || root.isMetaParent(root.getEdge(edgeInx[1]), root.getNode(nodeInx[1]))
+ || root.isMetaParent(root.getEdge(edgeInx[6]), root.getNode(nodeInx[2])))
+ throw new IllegalStateException("wrong edge meta relationships");
+
+ if (root.isMetaParent(root.getEdge(edgeInx[1]), root.getNode(nodeInx[3])))
+ throw new IllegalStateException("wrong edge meta relationships");
+
+ if (!(root.isMetaParent(root.getEdge(edgeInx[0]), root.getNode(nodeInx[3]))
+ && root.isMetaParent(root.getEdge(edgeInx[2]), root.getNode(nodeInx[4]))))
+ throw new IllegalStateException("missing edge meta relationship");
+
+ // isEdgeMetaParent(int, int).
+ if (root.isEdgeMetaParent(0, 0)
+ || root.isEdgeMetaParent(Integer.MAX_VALUE, Integer.MIN_VALUE)
+ || root.isEdgeMetaParent(Integer.MIN_VALUE, Integer.MAX_VALUE)
+ || root.isEdgeMetaParent(1, 2) || root.isEdgeMetaParent(minEdgeInx - 1, nodeInx[0]))
+ throw new IllegalStateException("wrong edge meta relationship");
+
+ if (!(root.isEdgeMetaParent(edgeInx[6], nodeInx[3])
+ && root.isEdgeMetaParent(edgeInx[6], nodeInx[4])))
+ throw new IllegalStateException("missing edge meta relationship");
+
+ // metaParentsList(Edge).
+ if (root.metaParentsList(root2Edge) != null)
+ throw new IllegalStateException("expected null edge parents");
+
+ nodesList = root.metaParentsList(root.getEdge(edgeInx[6]));
+
+ if (nodesList.size() != 2)
+ throw new IllegalStateException("wrong number of edge parents");
+
+ int[] metaParents = new int[nodesList.size()];
+
+ for (int i = 0; i < nodesList.size(); i++) {
+ Node foo = (Node) nodesList.get(i);
+ metaParents[i] = foo.getRootGraphIndex();
+ }
+
+ for (int i = 0;; i++)
+ if (metaParents[i] == nodeInx[3])
+ break;
+
+ for (int i = 0;; i++)
+ if (metaParents[i] == nodeInx[4])
+ break;
+
+ // edgeMetaParentsList(int).
+ if ((root.edgeMetaParentsList(0) != null)
+ || (root.edgeMetaParentsList(Integer.MAX_VALUE) != null)
+ || (root.edgeMetaParentsList(Integer.MIN_VALUE) != null)
+ || (root.edgeMetaParentsList(1) != null)
+ || (root.edgeMetaParentsList(minEdgeInx - 1) != null))
+ throw new IllegalStateException("expected null meta parents array");
+
+ nodesList = root.edgeMetaParentsList(edgeInx[2]);
+
+ if ((nodesList.size() != 1)
+ || (((Node) nodesList.get(0)).getRootGraphIndex() != nodeInx[4]))
+ throw new IllegalStateException("wrong edge meta parents");
+
+ // getEdgeMetaParentIndicesArray(int).
+ if ((root.getEdgeMetaParentIndicesArray(0) != null)
+ || (root.getEdgeMetaParentIndicesArray(Integer.MAX_VALUE) != null)
+ || (root.getEdgeMetaParentIndicesArray(Integer.MIN_VALUE) != null)
+ || (root.getEdgeMetaParentIndicesArray(minEdgeInx - 1) != null)
+ || (root.getEdgeMetaParentIndicesArray(66) != null))
+ throw new IllegalStateException("expected null parent array");
+
+ int[] edgeParentInx = root.getEdgeMetaParentIndicesArray(edgeInx[0]);
+
+ if (edgeParentInx.length != 1)
+ throw new IllegalStateException("wrong number of edge parents");
+
+ for (int i = 0;; i++)
+ if (edgeParentInx[i] == nodeInx[3])
+ break;
+
+ edgeParentInx = root.getEdgeMetaParentIndicesArray(edgeInx[1]);
+
+ if (edgeParentInx.length != 0)
+ throw new IllegalStateException("wrong number of edge parents");
+
+ edgeParentInx = root.getEdgeMetaParentIndicesArray(edgeInx[2]);
+
+ if (edgeParentInx.length != 1)
+ throw new IllegalStateException("wrong number of edge parents");
+
+ for (int i = 0;; i++)
+ if (edgeParentInx[i] == nodeInx[4])
+ break;
+
+ edgeParentInx = root.getEdgeMetaParentIndicesArray(edgeInx[4]);
+
+ if (edgeParentInx.length != 1)
+ throw new IllegalStateException("wrong number of edge parents");
+
+ for (int i = 0;; i++)
+ if (edgeParentInx[i] == nodeInx[0])
+ break;
+
+ edgeParentInx = root.getEdgeMetaParentIndicesArray(edgeInx[5]);
+
+ if (edgeParentInx.length != 0)
+ throw new IllegalStateException("wrong number of edge parents");
+
+ edgeParentInx = root.getEdgeMetaParentIndicesArray(edgeInx[6]);
+
+ if (edgeParentInx.length != 2)
+ throw new IllegalStateException("wrong number of edge parents");
+
+ for (int i = 0;; i++)
+ if (edgeParentInx[i] == nodeInx[3])
+ break;
+
+ for (int i = 0;; i++)
+ if (edgeParentInx[i] == nodeInx[4])
+ break;
+
+ // isMetaChild(Node, Edge).
+ if (root.isMetaChild(root2Node, root2Edge)
+ || root.isMetaChild(root2Node, root.getEdge(edgeInx[0])))
+ throw new IllegalStateException("child with other graph's elements");
+
+ if (root.isMetaChild(root.getNode(nodeInx[1]), root.getEdge(edgeInx[2]))
+ || root.isMetaChild(root.getNode(nodeInx[4]), root.getEdge(edgeInx[4])))
+ throw new IllegalStateException("reported wrong meta relationship");
+
+ if (!(root.isMetaChild(root.getNode(nodeInx[4]), root.getEdge(edgeInx[6]))
+ && root.isMetaChild(root.getNode(nodeInx[0]), root.getEdge(edgeInx[4]))))
+ throw new IllegalStateException("missing meta relationship");
+
+ // isEdgeMetaChild(int, int).
+ if (root.isEdgeMetaChild(0, 0)
+ || root.isEdgeMetaChild(Integer.MIN_VALUE, Integer.MAX_VALUE)
+ || root.isEdgeMetaChild(minNodeInx - 1, minEdgeInx - 1) || root.isEdgeMetaChild(98, 99)
+ || root.isEdgeMetaChild(nodeInx[3], edgeInx[4])
+ || root.isEdgeMetaChild(nodeInx[0], edgeInx[3])
+ || root.isEdgeMetaChild(nodeInx[2], edgeInx[1]))
+ throw new IllegalStateException("reported wrong meta relationship");
+
+ if (!(root.isEdgeMetaChild(nodeInx[4], edgeInx[2])
+ && root.isEdgeMetaChild(nodeInx[3], edgeInx[6])
+ && root.isEdgeMetaChild(nodeInx[3], edgeInx[0])))
+ throw new IllegalStateException("missing meta relationship");
+
+ // edgeMetaChildrenList(Node).
+ if (root.edgeMetaChildrenList(root2Node) != null)
+ throw new IllegalStateException("expected null return value");
+
+ edgesList = root.edgeMetaChildrenList(root.getNode(nodeInx[3]));
+
+ if (edgesList.size() != 2)
+ throw new IllegalStateException("wrong number of edge children");
+
+ for (int i = 0;; i++)
+ if (((Edge) edgesList.get(i)).getRootGraphIndex() == edgeInx[0])
+ break;
+
+ for (int i = 0;; i++)
+ if (((Edge) edgesList.get(i)).getRootGraphIndex() == edgeInx[6])
+ break;
+
+ // edgeMetaChildrenList(int).
+ if ((root.edgeMetaChildrenList(0) != null) || (root.edgeMetaChildrenList(1) != null)
+ || (root.edgeMetaChildrenList(Integer.MAX_VALUE) != null)
+ || (root.edgeMetaChildrenList(Integer.MIN_VALUE) != null)
+ || (root.edgeMetaChildrenList(minNodeInx - 1) != null))
+ throw new IllegalStateException("expected null return value");
+
+ edgesList = root.edgeMetaChildrenList(nodeInx[1]);
+
+ if (edgesList.size() != 0)
+ throw new IllegalStateException("wrong number of edge children");
+
+ edgesList = root.edgeMetaChildrenList(nodeInx[0]);
+
+ if (edgesList.size() != 1)
+ throw new IllegalStateException("wrong number of edge children");
+
+ for (int i = 0;; i++)
+ if (((Edge) edgesList.get(i)).getRootGraphIndex() == edgeInx[4])
+ break;
+
+ // getEdgeMetaChildIndicesArray(int).
+ if ((root.getEdgeMetaChildIndicesArray(0) != null)
+ || (root.getEdgeMetaChildIndicesArray(1) != null)
+ || (root.getEdgeMetaChildIndicesArray(Integer.MAX_VALUE) != null)
+ || (root.getEdgeMetaChildIndicesArray(Integer.MIN_VALUE) != null)
+ || (root.getEdgeMetaChildIndicesArray(minNodeInx - 1) != null))
+ throw new IllegalStateException("expected null return value");
+
+ int[] edgeChildInx = root.getEdgeMetaChildIndicesArray(nodeInx[0]);
+
+ if (edgeChildInx.length != 1)
+ throw new IllegalStateException("wrong number of edge children");
+
+ for (int i = 0;; i++)
+ if (edgeChildInx[i] == edgeInx[4])
+ break;
+
+ edgeChildInx = root.getEdgeMetaChildIndicesArray(nodeInx[1]);
+
+ if (edgeChildInx.length != 0)
+ throw new IllegalStateException("wrong number of edge children");
+
+ edgeChildInx = root.getEdgeMetaChildIndicesArray(nodeInx[2]);
+
+ if (edgeChildInx.length != 0)
+ throw new IllegalStateException("wrong number of edge children");
+
+ edgeChildInx = root.getEdgeMetaChildIndicesArray(nodeInx[3]);
+
+ if (edgeChildInx.length != 2)
+ throw new IllegalStateException("wrong number of edge children");
+
+ for (int i = 0;; i++)
+ if (edgeChildInx[i] == edgeInx[0])
+ break;
+
+ for (int i = 0;; i++)
+ if (edgeChildInx[i] == edgeInx[6])
+ break;
+
+ edgeChildInx = root.getEdgeMetaChildIndicesArray(nodeInx[4]);
+
+ if (edgeChildInx.length != 2)
+ throw new IllegalStateException("wrong number of edge children");
+
+ for (int i = 0;; i++)
+ if (edgeChildInx[i] == edgeInx[2])
+ break;
+
+ for (int i = 0;; i++)
+ if (edgeChildInx[i] == edgeInx[6])
+ break;
+
+ // Finally we remove all nodes and edges.
+ if (root.removeEdge(edgeInx[2]) != edgeInx[2])
+ throw new IllegalStateException("failed to remove edge");
+
+ if (root.removeEdge(edgeInx[4]) != edgeInx[4])
+ throw new IllegalStateException("failed to remove edge");
+
+ for (int i = 0; i < nodeInx.length; i++)
+ if (root.removeNode(nodeInx[i]) != nodeInx[i])
+ throw new IllegalStateException("failed to remove node");
+
+ for (int i = 0; i < edgeInx.length; i++)
+ if (root.removeEdge(edgeInx[i]) != 0)
+ throw new IllegalStateException("edge should already be removed");
+ }
+}
diff --git a/corelibs/fing/src/main/java/fing/model/test/Bug646Test.java b/corelibs/fing/src/main/java/fing/model/test/Bug646Test.java
new file mode 100644
index 0000000..125773c
--- /dev/null
+++ b/corelibs/fing/src/main/java/fing/model/test/Bug646Test.java
@@ -0,0 +1,204 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package fing.model.test;
+
+import fing.model.FingEdgeDepot;
+import fing.model.FingExtensibleRootGraph;
+import fing.model.FingNodeDepot;
+
+import giny.model.Edge;
+import giny.model.GraphPerspective;
+import giny.model.Node;
+import giny.model.RootGraph;
+
+
+/**
+ *
+ */
+public class Bug646Test {
+ private static class MyNodeDepot implements FingNodeDepot {
+ public Node getNode(RootGraph root, int index, String id) {
+ return new MyNode(root, index, id);
+ }
+
+ public void recycleNode(Node node) {
+ }
+ }
+
+ private static class MyNode implements Node {
+ final RootGraph m_rootGraph;
+ final int m_rootGraphIndex;
+ String m_identifier = null;
+
+ // New feature in 2.7 Nested network
+ private GraphPerspective nestedNetwork;
+
+ MyNode(RootGraph root, int index, String id) {
+ m_rootGraph = root;
+ m_rootGraphIndex = index;
+ m_identifier = id;
+ }
+
+ public GraphPerspective getGraphPerspective() {
+ return m_rootGraph.createGraphPerspective(m_rootGraph.getNodeMetaChildIndicesArray(m_rootGraphIndex),
+ m_rootGraph.getEdgeMetaChildIndicesArray(m_rootGraphIndex));
+ }
+
+ public boolean setGraphPerspective(GraphPerspective gp) {
+ if (gp.getRootGraph() != m_rootGraph)
+ return false;
+
+ final int[] nodeInx = gp.getNodeIndicesArray();
+ final int[] edgeInx = gp.getEdgeIndicesArray();
+
+ for (int i = 0; i < nodeInx.length; i++)
+ m_rootGraph.addNodeMetaChild(m_rootGraphIndex, nodeInx[i]);
+
+ for (int i = 0; i < edgeInx.length; i++)
+ m_rootGraph.addEdgeMetaChild(m_rootGraphIndex, edgeInx[i]);
+
+ return true;
+ }
+
+ public RootGraph getRootGraph() {
+ return m_rootGraph;
+ }
+
+ public int getRootGraphIndex() {
+ return m_rootGraphIndex;
+ }
+
+ public String getIdentifier() {
+ return m_identifier;
+ }
+
+ public boolean setIdentifier(String new_id) {
+ m_identifier = new_id;
+
+ return true;
+ }
+
+ public GraphPerspective getNestedNetwork() {
+ return nestedNetwork;
+ }
+
+ public void setNestedNetwork(GraphPerspective nestedNetwork) {
+ this.nestedNetwork = nestedNetwork;
+ }
+ }
+
+ private static class MyEdgeDepot implements FingEdgeDepot {
+ public Edge getEdge(RootGraph root, int index, String id) {
+ return new MyEdge(root, index, id);
+ }
+
+ public void recycleEdge(Edge edge) {
+ }
+ }
+
+ private static class MyEdge implements Edge {
+ final RootGraph m_rootGraph;
+ final int m_rootGraphIndex;
+ String m_identifier = null;
+
+ MyEdge(RootGraph root, int index, String id) {
+ m_rootGraph = root;
+ m_rootGraphIndex = index;
+ m_identifier = id;
+ }
+
+ public Node getSource() {
+ return m_rootGraph.getNode(m_rootGraph.getEdgeSourceIndex(m_rootGraphIndex));
+ }
+
+ public Node getTarget() {
+ return m_rootGraph.getNode(m_rootGraph.getEdgeTargetIndex(m_rootGraphIndex));
+ }
+
+ public boolean isDirected() {
+ return m_rootGraph.isEdgeDirected(m_rootGraphIndex);
+ }
+
+ public RootGraph getRootGraph() {
+ return m_rootGraph;
+ }
+
+ public int getRootGraphIndex() {
+ return m_rootGraphIndex;
+ }
+
+ public String getIdentifier() {
+ return m_identifier;
+ }
+
+ public boolean setIdentifier(String new_id) {
+ m_identifier = new_id;
+
+ return true;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ */
+ public static void main(String[] args) {
+ final RootGraph root = new FingExtensibleRootGraph(new MyNodeDepot(), new MyEdgeDepot());
+ final Node n1 = root.getNode(root.createNode());
+ final Node n2 = root.getNode(root.createNode());
+ final Node n3 = root.getNode(root.createNode());
+ final Node n4 = root.getNode(root.createNode());
+ root.createEdge(n1, n2, false);
+
+ int edge_idx = root.createEdge(n1, n3, false);
+ final Edge del1 = root.getEdge(edge_idx);
+ edge_idx = root.createEdge(n2, n3, false);
+
+ final Edge del2 = root.getEdge(edge_idx);
+ root.removeEdge(del1);
+ root.removeEdge(del2);
+ edge_idx = root.createEdge(n1, n4, false);
+
+ final Edge subedge = root.getEdge(edge_idx);
+ final Node src = subedge.getSource();
+ final Node target = subedge.getTarget();
+
+ if ((src == null) || (target == null))
+ throw new IllegalStateException("the bug is here");
+ }
+}
diff --git a/corelibs/fing/src/main/java/fing/model/test/DEPENDENCIES b/corelibs/fing/src/main/java/fing/model/test/DEPENDENCIES
new file mode 100644
index 0000000..5349dd8
--- /dev/null
+++ b/corelibs/fing/src/main/java/fing/model/test/DEPENDENCIES
@@ -0,0 +1,4 @@
+fing.model
+lib:cytoscape-graph-dynamic.jar
+lib:cytoscape-graph-fixed.jar
+lib:giny.jar
diff --git a/corelibs/fing/src/main/java/fing/model/test/GCTest.java b/corelibs/fing/src/main/java/fing/model/test/GCTest.java
new file mode 100644
index 0000000..c9ec8f0
--- /dev/null
+++ b/corelibs/fing/src/main/java/fing/model/test/GCTest.java
@@ -0,0 +1,74 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package fing.model.test;
+
+import fing.model.FingRootGraphFactory;
+
+import giny.model.GraphPerspective;
+import giny.model.RootGraph;
+
+
+/**
+ *
+ */
+public class GCTest {
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ */
+ public static void main(String[] args) {
+ final RootGraph root = FingRootGraphFactory.instantiateRootGraph();
+ final int[] nodeInx = root.createNodes(10000);
+ final int[] edgeInx = new int[100000];
+
+ for (int i = 0; i < edgeInx.length; i++)
+ edgeInx[i] = root.createEdge(nodeInx[i % nodeInx.length],
+ nodeInx[(i * 3) % nodeInx.length]);
+
+ System.out.println("RootGraph node count: " + root.getNodeCount());
+ System.out.println("RootGraph edge count: " + root.getEdgeCount());
+ System.out.println();
+
+ for (int i = 0; i < 1000; i++) {
+ GraphPerspective persp = root.createGraphPerspective(nodeInx, edgeInx);
+ System.out.println("GraphPerspective node count: " + persp.getNodeCount());
+ System.out.println("GraphPerspective edge count: " + persp.getEdgeCount());
+ System.out.println();
+ }
+ }
+}
diff --git a/corelibs/fing/src/main/java/fing/model/test/ImplementsGraphTest.java b/corelibs/fing/src/main/java/fing/model/test/ImplementsGraphTest.java
new file mode 100644
index 0000000..8b74f6b
--- /dev/null
+++ b/corelibs/fing/src/main/java/fing/model/test/ImplementsGraphTest.java
@@ -0,0 +1,67 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package fing.model.test;
+
+import cytoscape.graph.dynamic.DynamicGraph;
+
+import cytoscape.graph.fixed.FixedGraph;
+
+import fing.model.FingRootGraphFactory;
+
+import giny.model.GraphPerspective;
+import giny.model.RootGraph;
+
+
+/**
+ *
+ */
+public class ImplementsGraphTest {
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ */
+ public static void main(String[] args) {
+ final RootGraph root = FingRootGraphFactory.instantiateRootGraph();
+ final DynamicGraph dGraph = (DynamicGraph) root;
+ dGraph.nodes();
+
+ final GraphPerspective persp = root.createGraphPerspective((int[]) null, (int[]) null);
+ final FixedGraph fGraph = (FixedGraph) persp;
+ fGraph.edges();
+ }
+}
diff --git a/corelibs/fing/src/main/java/fing/model/test/RepeatedAllRootGraphMethodsTest.java b/corelibs/fing/src/main/java/fing/model/test/RepeatedAllRootGraphMethodsTest.java
new file mode 100644
index 0000000..5c01b27
--- /dev/null
+++ b/corelibs/fing/src/main/java/fing/model/test/RepeatedAllRootGraphMethodsTest.java
@@ -0,0 +1,68 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package fing.model.test;
+
+import fing.model.FingRootGraphFactory;
+
+import giny.model.RootGraph;
+
+
+/**
+ *
+ */
+public final class RepeatedAllRootGraphMethodsTest {
+ // No constructor.
+ private RepeatedAllRootGraphMethodsTest() {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ */
+ public static final void main(String[] args) {
+ final RootGraph root = FingRootGraphFactory.instantiateRootGraph();
+ final int numIterations = 100000;
+
+ for (int i = 0; i < numIterations; i++) {
+ if ((i % 100) == 0)
+ System.out.println("Now running iteration " + (i + 1) + " of " + numIterations);
+
+ AllRootGraphMethodsTest.runTest(root);
+ }
+ }
+}
diff --git a/corelibs/fing/src/main/java/fing/model/test/RootGraphAddRemoveTest.java b/corelibs/fing/src/main/java/fing/model/test/RootGraphAddRemoveTest.java
new file mode 100644
index 0000000..131af00
--- /dev/null
+++ b/corelibs/fing/src/main/java/fing/model/test/RootGraphAddRemoveTest.java
@@ -0,0 +1,132 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package fing.model.test;
+
+import fing.model.FingRootGraphFactory;
+
+import giny.model.Edge;
+import giny.model.GraphPerspective;
+import giny.model.Node;
+import giny.model.RootGraph;
+
+import java.util.Iterator;
+
+
+/**
+ *
+ */
+public final class RootGraphAddRemoveTest {
+ // No constructor.
+ private RootGraphAddRemoveTest() {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ *
+ * @throws ClassNotFoundException DOCUMENT ME!
+ * @throws InstantiationException DOCUMENT ME!
+ * @throws IllegalAccessException DOCUMENT ME!
+ */
+ public static final void main(String[] args)
+ throws ClassNotFoundException, InstantiationException, IllegalAccessException {
+ final RootGraph root = getRootGraph(args);
+
+ int[] nodeInx;
+ final int[] edgeInx = new int[1000000];
+ final int[] nodeNums = new int[] { 200000, 199900, 200200 };
+ final int iterations = 100;
+
+ for (int foo = 0; foo < iterations; foo++) {
+ boolean print = true;
+
+ if (!((foo % 1) == 0))
+ print = false;
+
+ if (print)
+ System.out.println("at add/remove iteration " + (foo + 1) + " of " + iterations);
+
+ final int numNodes = nodeNums[foo % nodeNums.length];
+
+ if (print)
+ System.out.println("creating " + numNodes + " nodes");
+
+ nodeInx = root.createNodes(numNodes);
+
+ if (print)
+ System.out.println("creating " + edgeInx.length + " edges");
+
+ for (int i = 0; i < edgeInx.length; i++)
+ edgeInx[i] = root.createEdge(nodeInx[i % nodeInx.length],
+ nodeInx[(i * 3) % nodeInx.length]);
+
+ if (print)
+ printme(root);
+
+ if ((foo % 2) == 0) {
+ if (print)
+ System.out.println("removing all edges from RootGraph");
+
+ root.removeEdges(edgeInx);
+ }
+
+ if (print)
+ System.out.println("removing all nodes from RootGraph");
+
+ root.removeNodes(nodeInx);
+
+ if (print)
+ printme(root);
+ }
+ }
+
+ private static void printme(RootGraph root) {
+ System.out.println("in RootGraph: " + root.getNodeCount() + " nodes and "
+ + root.getEdgeCount() + " edges");
+ System.out.println();
+ }
+
+ private static final RootGraph getRootGraph(String[] mainArgs)
+ throws ClassNotFoundException, InstantiationException, IllegalAccessException {
+ if ((mainArgs.length > 0) && mainArgs[0].equalsIgnoreCase("luna"))
+ return (RootGraph) Class.forName("luna.LunaRootGraph").newInstance();
+ else
+
+ return FingRootGraphFactory.instantiateRootGraph();
+ }
+}
diff --git a/corelibs/fing/src/main/java/fing/model/test/RootGraphPerformanceTest.java b/corelibs/fing/src/main/java/fing/model/test/RootGraphPerformanceTest.java
new file mode 100644
index 0000000..fbe193d
--- /dev/null
+++ b/corelibs/fing/src/main/java/fing/model/test/RootGraphPerformanceTest.java
@@ -0,0 +1,316 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package fing.model.test;
+
+import fing.model.FingRootGraphFactory;
+
+import giny.model.RootGraph;
+
+import java.io.IOException;
+import java.io.InputStream;
+
+
+/**
+ *
+ */
+public final class RootGraphPerformanceTest {
+ // No constructor.
+ private RootGraphPerformanceTest() {
+ }
+
+ // Args:
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ *
+ * @throws ClassNotFoundException DOCUMENT ME!
+ * @throws InstantiationException DOCUMENT ME!
+ * @throws IllegalAccessException DOCUMENT ME!
+ * @throws IOException DOCUMENT ME!
+ */
+ public static final void main(String[] args)
+ throws ClassNotFoundException, InstantiationException, IllegalAccessException, IOException {
+ final RootGraph root = getRootGraph(args);
+ final int[] nodes = createNodes(root, Integer.parseInt(args[0]));
+ final int numDirectedEdges = Integer.parseInt(args[1]);
+ final int numUndirectedEdges = Integer.parseInt(args[2]);
+ final int[] sourceInxCreatedEdges = new int[numDirectedEdges + numUndirectedEdges];
+ final int[] targetInxCreatedEdges = new int[numDirectedEdges + numUndirectedEdges];
+ final boolean[] directednessCreatedEdges = new boolean[numDirectedEdges
+ + numUndirectedEdges];
+ createEdges(root, numDirectedEdges, System.in, nodes, true, 0, sourceInxCreatedEdges,
+ targetInxCreatedEdges, directednessCreatedEdges);
+ createEdges(root, numUndirectedEdges, System.in, nodes, false, numDirectedEdges,
+ sourceInxCreatedEdges, targetInxCreatedEdges, directednessCreatedEdges);
+
+ long millisBegin = System.currentTimeMillis();
+ testAdjacentEdges(root, nodes);
+
+ long millisEnd = System.currentTimeMillis();
+ System.out.println("adjacent edges test took " + (millisEnd - millisBegin)
+ + " milliseconds");
+
+ long millisBegin2 = System.currentTimeMillis();
+ testConnectingEdges(root, nodes);
+
+ long millisEnd2 = System.currentTimeMillis();
+ System.out.println("connecting edges test took " + (millisEnd2 - millisBegin2)
+ + " milliseconds");
+
+ long millisBegin3 = System.currentTimeMillis();
+ testNodeNeighbors(root, nodes);
+
+ long millisEnd3 = System.currentTimeMillis();
+ System.out.println("node neighbors test took " + (millisEnd3 - millisBegin3)
+ + " milliseconds");
+
+ long millisBegin4 = System.currentTimeMillis();
+ testConnectingWeb(root, nodes);
+
+ long millisEnd4 = System.currentTimeMillis();
+ System.out.println("connecting web test took " + (millisEnd4 - millisBegin4)
+ + " milliseconds");
+
+ long millisBegin5 = System.currentTimeMillis();
+ testAddRemove(root, nodes, sourceInxCreatedEdges, targetInxCreatedEdges,
+ directednessCreatedEdges);
+
+ long millisEnd5 = System.currentTimeMillis();
+ System.out.println("add/remove test took " + (millisEnd5 - millisBegin5) + " milliseconds");
+ }
+
+ private static final RootGraph getRootGraph(String[] mainArgs)
+ throws ClassNotFoundException, InstantiationException, IllegalAccessException {
+ if ((mainArgs.length > 3) && mainArgs[3].equalsIgnoreCase("luna"))
+ return (RootGraph) Class.forName("luna.LunaRootGraph").newInstance();
+ else
+
+ return FingRootGraphFactory.instantiateRootGraph();
+ }
+
+ private static final int[] createNodes(RootGraph root, int numNodes) {
+ final int[] returnThis = new int[numNodes];
+
+ for (int i = 0; i < returnThis.length; i++)
+ returnThis[i] = root.createNode();
+
+ return returnThis;
+ }
+
+ // sourceInxCreatedEdges, targetInxCreatedEdges, and directedCreatedEdges
+ // are written to, not read from.
+ private static final int[] createEdges(RootGraph root, int numEdges, InputStream in,
+ int[] nodes, boolean directed, int offsetCreatedEdges,
+ int[] sourceInxCreatedEdges,
+ int[] targetInxCreatedEdges,
+ boolean[] directedCreatedEdges)
+ throws IOException {
+ final int[] returnThis = new int[numEdges];
+ byte[] buff = new byte[8];
+ int inx = 0;
+ int off = 0;
+ int read;
+
+ while ((inx < numEdges) && ((read = in.read(buff, off, buff.length - off)) > 0)) {
+ off += read;
+
+ if (off < buff.length)
+ continue;
+ else
+ off = 0;
+
+ long randomLong = assembleLong(buff);
+ int randomInt1 = (int) ((randomLong >> 32) & 0x00000000ffffffff);
+ int randomInt2 = (int) (randomLong & 0x00000000ffffffff);
+ int node1 = Math.abs(randomInt1) % nodes.length;
+ int node2 = Math.abs(randomInt2) % nodes.length;
+ sourceInxCreatedEdges[inx + offsetCreatedEdges] = node1;
+ targetInxCreatedEdges[inx + offsetCreatedEdges] = node2;
+ directedCreatedEdges[inx + offsetCreatedEdges] = directed && (node1 != node2);
+ returnThis[inx++] = root.createEdge(nodes[node1], nodes[node2],
+ directed && (node1 != node2));
+ }
+
+ if (inx < numEdges)
+ throw new IOException("premature end of input");
+
+ return returnThis;
+ }
+
+ private static final long assembleLong(byte[] eightConsecutiveBytes) {
+ long firstByte = (((long) eightConsecutiveBytes[0]) & 0x00000000000000ff) << 56;
+ long secondByte = (((long) eightConsecutiveBytes[1]) & 0x00000000000000ff) << 48;
+ long thirdByte = (((long) eightConsecutiveBytes[2]) & 0x00000000000000ff) << 40;
+ long fourthByte = (((long) eightConsecutiveBytes[3]) & 0x00000000000000ff) << 32;
+ long fifthByte = (((long) eightConsecutiveBytes[4]) & 0x00000000000000ff) << 24;
+ long sixthByte = (((long) eightConsecutiveBytes[5]) & 0x00000000000000ff) << 16;
+ long seventhByte = (((long) eightConsecutiveBytes[6]) & 0x00000000000000ff) << 8;
+ long eighthByte = (((long) eightConsecutiveBytes[7]) & 0x00000000000000ff);
+
+ return firstByte | secondByte | thirdByte | fourthByte | fifthByte | sixthByte
+ | seventhByte | eighthByte;
+ }
+
+ // This test actually fail with luna when calling several combinations:
+ /**
+ * DOCUMENT ME!
+ *
+ * @param root DOCUMENT ME!
+ * @param nodes DOCUMENT ME!
+ */
+ public static final void testAdjacentEdges(RootGraph root, int[] nodes) {
+ for (int i = 0; i < 4; i++) {
+ boolean undirected;
+ boolean incoming;
+ boolean outgoing;
+
+ if (i == 0) {
+ undirected = true;
+ incoming = true;
+ outgoing = true;
+ } else if (i == 1) {
+ undirected = true;
+ incoming = false;
+ outgoing = true;
+ } else if (i == 2) {
+ undirected = false;
+ incoming = false;
+ outgoing = true;
+ } else {
+ undirected = false;
+ incoming = false;
+ outgoing = false;
+ }
+
+ for (int j = 0; j < nodes.length; j++) {
+ root.getAdjacentEdgeIndicesArray(nodes[j], undirected, incoming, outgoing);
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param root DOCUMENT ME!
+ * @param nodes DOCUMENT ME!
+ */
+ public static final void testConnectingEdges(RootGraph root, int[] nodes) {
+ for (int i = 0; i < 4; i++) {
+ boolean undirected;
+ boolean bothDirections;
+
+ if (i == 0) {
+ undirected = true;
+ bothDirections = true;
+ } else if (i == 1) {
+ undirected = true;
+ bothDirections = false;
+ } else if (i == 2) {
+ undirected = false;
+ bothDirections = true;
+ } else {
+ undirected = false;
+ bothDirections = false;
+ }
+
+ for (int j = 1; j < nodes.length; j++) {
+ root.getEdgeIndicesArray(nodes[j - 1], nodes[j], undirected, bothDirections);
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param root DOCUMENT ME!
+ * @param nodes DOCUMENT ME!
+ */
+ public static final void testNodeNeighbors(RootGraph root, int[] nodes) {
+ for (int j = 1; j < nodes.length; j++) {
+ root.neighborsList(root.getNode(nodes[j]));
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param root DOCUMENT ME!
+ * @param nodes DOCUMENT ME!
+ */
+ public static final void testConnectingWeb(RootGraph root, int[] nodes) {
+ final int[] nodesWeb = new int[nodes.length / 2];
+ System.arraycopy(nodes, 0, nodesWeb, 0, nodesWeb.length);
+
+ int numIters = Math.min(100, nodesWeb.length);
+
+ for (int i = 0; i < numIters; i++) {
+ root.getConnectingEdgeIndicesArray(nodesWeb);
+ nodesWeb[i] = nodes[nodesWeb.length + i];
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param root DOCUMENT ME!
+ * @param nodes DOCUMENT ME!
+ * @param edgeSources DOCUMENT ME!
+ * @param edgeTargets DOCUMENT ME!
+ * @param edgeDirectedness DOCUMENT ME!
+ */
+ public static final void testAddRemove(RootGraph root, int[] nodes, int[] edgeSources,
+ int[] edgeTargets, boolean[] edgeDirectedness) {
+ for (int i = 0; i < 10; i++) {
+ for (int j = 0; j < nodes.length; j++)
+ root.removeNode(nodes[j]);
+
+ if ((root.getNodeCount() != 0) || (root.getEdgeCount() != 0))
+ throw new IllegalStateException("node/edge count not 0");
+
+ for (int j = 0; j < nodes.length; j++)
+ nodes[j] = root.createNode();
+
+ for (int j = 0; j < edgeSources.length; j++)
+ root.createEdge(nodes[edgeSources[j]], nodes[edgeTargets[i]], edgeDirectedness[j]);
+
+ if ((root.getNodeCount() != nodes.length)
+ || (root.getEdgeCount() != edgeSources.length))
+ throw new IllegalStateException("node/edge count not what expected");
+ }
+ }
+}
diff --git a/corelibs/fing/src/main/java/fing/model/test/performance-comparison.txt b/corelibs/fing/src/main/java/fing/model/test/performance-comparison.txt
new file mode 100644
index 0000000..80ef3b7
--- /dev/null
+++ b/corelibs/fing/src/main/java/fing/model/test/performance-comparison.txt
@@ -0,0 +1,296 @@
+ADJACENT EDGES TEST:
+
+ Testing:
+ RootGraph.getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean)
+
+ Importance:
+ Getting touching edges lists for a node is very similar to getting
+ node neighbors. Both operations are the foundation of depth first
+ and breadth first graph searching. Therefore, good performance
+ of this method is extremely important.
+
+ Description of test:
+ This test creates N nodes and E edges (an even mix of directed and
+ undirected) in a RootGraph. The topology of RootGraph created is
+ defined by [random] bytes read from standard input. For every node
+ in the RootGraph, getAdjacentEdgeIndicesArray() is called on that
+ node. Because getAdjacentEdgeIndicesArray() takes three boolean
+ input parameters defining which adjacent edges we're looking for,
+ this test over all nodes should be repeated eight times, each time
+ with a different set of boolean input parameters. However, four of
+ these boolean combinations cause the Luna implementation of
+ RootGraph to throw NullPointerException in getAdjacentEdges().
+ Therefore, this test is only repeated 4 times, each with a different
+ set of boolean inputs:
+ iteration 1: getAdjacentEdgeIndicesArray(int, true, true, true)
+ iteration 2: getAdjacentEdgeIndicesArray(int, true, false, true)
+ iteration 3: getAdjacentEdgeIndicesArray(int, false, false, false)
+ iteration 4: getAdjacentEdgeIndicesArray(int, false, false, false)
+ This test measures the total time taken in
+ getAdjacentEdgeIndicesArray(). The time measure does not include
+ time to instantiate the RootGraph and populate it with nodes and
+ edges.
+
+ Test circumstances:
+ Tests were performed on a 1.8GHz P4 (512K cache), with 512M RAM,
+ and 256M memory was allocated to the JVM. Sun's 1.4.2_06 JVM
+ on Red Hat's 3ES Linux system.
+
+ Test results:
+
+ Milliseconds taken to perform test case:
+
+ graph size | Fing | Luna |
+ --------------------------------------+--------+--------+
+ 7 nodes, 20 edges | 2 | 4 |
+ 100 nodes, 500 edges | 7 | 54 |
+ 100 nodes, 10000 edges | 12 | 106 |
+ 1000 nodes, 20000 edges | 35 | 1518 |
+ 1000 nodes, 39998 edges | 55 | 2134 |
+ 2000 nodes, 20000 edges | 39 | 5072 |
+ 4000 nodes, 20000 edges | 40 | 21382 |
+ 8000 nodes, 20000 edges | 54 | 84766 |
+ 16000 nodes, 20000 edges | 115 | 337343 |
+ 39999 nodes, 39999 edges | 128 |2107868 |
+ 16000 nodes, 100000 edges | 165 | FAIL |
+ 50000 nodes, 400000 edges | 615 | FAIL |
+ 100000 nodes, 1000000 edges | 1443 | FAIL |
+ --------------------------------------+--------+--------+
+
+ Afterthoughts:
+ The implementation could be really sped up if the interface
+ changes: instead of returning an array of integers, return
+ an iteration over integers. This would prevent a lot of
+ unnecessary array allocation.
+
+
+=======================================================================
+CONNECTING EDGES TEST:
+
+ Testing: A deprecated method:
+ RootGraph.getEdgeIndicesArray(int, int, boolean, boolean)
+
+ Importance:
+ This method has been deprecated -- it is suggested to use
+ getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean) instead.
+ I can't think of an important algorithm that requires the operation
+ of getting all edges connecting two nodes.
+
+ Description of test:
+ This test creates N nodes and E edges (an even mix of directed and
+ undirected) in a RootGraph. The topology of RootGraph created is
+ defined by [random] bytes read from standard input. For every pair
+ of nodes whose order of creation was i, i+1, in the RootGraph,
+ getEdgeIndicesArray() is called on that pair. Because
+ getEdgeIndicesArray() takes two boolean input parameters, this test
+ is be repeated four times, each time with a different set of
+ boolean input parameters. This test measures the total time taken
+ in getEdgeIndicesArray(). The time measure does not include
+ time to instantiate the RootGraph and populate it with nodes and
+ edges.
+
+
+ Test circumstances:
+ Tests were performed on a 1.8GHz P4 (512K cache), with 512M RAM,
+ and 256M memory was allocated to the JVM. Sun's 1.4.2_06 JVM
+ on Red Hat's 3ES Linux system.
+
+ Test results:
+
+ Milliseconds taken to perform test case:
+
+ graph size | Fing | Luna |
+ --------------------------------------+--------+--------+
+ 7 nodes, 20 edges | 4 | 3 |
+ 100 nodes, 500 edges | 16 | 16 |
+ 100 nodes, 10000 edges | 25 | 6 |
+ 1000 nodes, 20000 edges | 65 | 68 |
+ 1000 nodes, 39998 edges | 99 | 13 |
+ 2000 nodes, 20000 edges | 64 | 79 |
+ 4000 nodes, 20000 edges | 76 | 20 |
+ 8000 nodes, 20000 edges | 103 | 26 |
+ 16000 nodes, 20000 edges | 115 | 37 |
+ 39999 nodes, 39999 edges | 235 | 218 |
+ 16000 nodes, 100000 edges | 295 | FAIL |
+ 50000 nodes, 400000 edges | 1091 | FAIL |
+ 100000 nodes, 1000000 edges | 2625 | FAIL |
+ --------------------------------------+--------+--------+
+
+ Afterthoughts:
+ This method was deprecated for a good reason -- it's not used
+ by algorithms and it's not worth optimizing. In the Fing
+ implementation, this method iterates over all edges touching one
+ of the nodes, choosing those edges which also touch the other node.
+ Therefore, the time complexity of this method is linear with respect
+ to the number of edges touching one of the input nodes. It's
+ possible to arrange the adjacent edge lists into tree-like
+ structures in order to optimize this operation; this idea was
+ discussed, and then it was decided to use plain old linked lists
+ of adjacent edges in favor of trees, for the sake of simplicity of
+ implementation.
+
+
+=======================================================================
+NODE NEIGHBORS TEST:
+
+ Testing: A deprecated method:
+ RootGraph.neighborsList(Node)
+
+ Importance:
+ This method has been deprecated -- it is suggested to use
+ getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean) instead.
+ This method (or the one that returns adjacent edges) is typically
+ used in graph depth-first and breadth-first search algorithms; a
+ complete search of a graph would essentially call neighborsList()
+ on every node exactly once by the time the search algorithm
+ finished.
+
+ Description of test:
+ This test creates N nodes and E edges (an even mix of directed and
+ undirected) in a RootGraph. The topology of RootGraph created is
+ defined by [random] bytes read from standard input. For every node
+ in the RootGraph, neighborsList() is called on that node.
+ This test measures the total time taken in neighborsList(). The
+ time measure does not include time to instantiate the RootGraph and
+ populate it with nodes and edges.
+
+ Test circumstances:
+ Tests were performed on a 1.8GHz P4 (512K cache), with 512M RAM,
+ and 256M memory was allocated to the JVM. Sun's 1.4.2_06 JVM
+ on Red Hat's 3ES Linux system.
+
+ Test results:
+
+ Milliseconds taken to perform test case:
+
+ graph size | Fing | Luna |
+ --------------------------------------+--------+--------+
+ 7 nodes, 20 edges | 3 | 2 |
+ 100 nodes, 500 edges | 16 | 24 |
+ 100 nodes, 10000 edges | 33 | 17 |
+ 1000 nodes, 20000 edges | 69 | 370 |
+ 1000 nodes, 39998 edges | 108 | 388 |
+ 2000 nodes, 20000 edges | 76 | 1397 |
+ 4000 nodes, 20000 edges | 78 | 6514 |
+ 8000 nodes, 20000 edges | 90 | 27266 |
+ 16000 nodes, 20000 edges | 150 | 111672 |
+ 39999 nodes, 39999 edges | 178 | 693433 |
+ 16000 nodes, 100000 edges | 302 | FAIL |
+ 50000 nodes, 400000 edges | 1198 | FAIL |
+ 100000 nodes, 1000000 edges | 3024 | FAIL |
+ --------------------------------------+--------+--------+
+
+
+=======================================================================
+CONNECTING WEB TEST:
+
+ Testing:
+ RootGraph.getConnectingEdgeIndicesArray(int[])
+
+ Importance:
+ This method is related to creating GraphPerspective objects (sub-
+ graphs). Given a set of nodes in an original graph, find all
+ edges whose source and target are in this set (the subgraph
+ "induced" by this set of nodes).
+
+ Description of test:
+ This test creates N nodes and E edges (an even mix of directed and
+ undirected) in a RootGraph. The topology of RootGraph created is
+ defined by [random] bytes read from standard input. Select half of
+ the nodes in this RootGraph, and call
+ getConnectingEdgeIndicesArray() on this set. Repeat 100 times,
+ each time choosing a different set containing exactly half of all
+ nodes. This test measures the total time taken in
+ getConnectingEdgeIndicesArray(). The time measure does not include
+ time to instantiate the RootGraph and populate it with nodes and
+ edges.
+
+ Test circumstances:
+ Tests were performed on a 1.8GHz P4 (512K cache), with 512M RAM,
+ where 256M memory was allocated to the JVM. Sun's 1.4.2_06 JVM
+ on Red Hat's 3ES Linux system.
+
+ Test results:
+
+ Milliseconds taken to perform test case:
+
+ graph size | Fing | Luna |
+ --------------------------------------+--------+--------+
+ 200 nodes, 1000 edges | 67 | 210 |
+ 200 nodes, 5000 edges | 200 | 295 |
+ 200 nodes, 10000 edges | 380 | 420 |
+ 200 nodes, 39999 edges | 1800 | 1130 |
+ 1000 nodes, 10000 edges | 480 | 5000 |
+ 1000 nodes, 20000 edges | 950 | 5000 |
+ 1000 nodes, 39998 edges | 2100 | 5500 |
+ 2000 nodes, 20000 edges | 1000 | 17600 |
+ 4000 nodes, 20000 edges | 1150 | 68611 |
+ 8000 nodes, 20000 edges | 1250 | 304403 |
+ 16000 nodes, 20000 edges | 1700 |1419768 |
+ 16000 nodes, 100000 edges | 7012 | FAIL |
+ 50000 nodes, 400000 edges | 29665 | FAIL |
+ 100000 nodes, 1000000 edges | 80313 | FAIL |
+ --------------------------------------+--------+--------+
+
+ Afterthoughts:
+ The getConnectingEdgeIndicesArray() method returns a newly-
+ allocated array of integers containing edge indices. Therefore,
+ with each call to this method a rather large array must be
+ allocated. Performance could be improved if an iterator were
+ returned instead of an int array in the API definition.
+
+
+=======================================================================
+ADD REMOVE TEST:
+
+ Testing:
+ RootGraph.createNode()
+ RootGraph.createEdge(int, int, boolean)
+ RootGraph.removeNode(int)
+ RootGraph.getNodeCount()
+ RootGraph.getEdgeCount()
+
+ Importance:
+ In Cytoscape, RootGraph nodes are only created, never removed. I
+ know this because in the Luna implementation, removal of nodes is
+ broken -- it doesn't do anything. Edges may or may not be removed
+ from a RootGraph in Cytoscape (I'm not sure). The speed at which
+ graphs are created is important because a user will have to wait
+ at least that long for a network to load in Cytoscape. However,
+ because I'm unable to delete nodes from Luna's implementation of
+ RootGraph, a head-to-head performance test comparison between
+ Fing and Luna is impossible.
+
+ Description of test:
+ This test creates N nodes and E edges (an even mix of directed and
+ undirected) in a RootGraph. The topology of RootGraph created is
+ defined by [random] bytes read from standard input. The timer
+ starts here - after the RootGraph is created. The timed test
+ consists of removing all nodes from the RootGraph (which, as a
+ documented and expected side-effect, removes all edges from the
+ RootGraph). A quick test is performed to ensure that no nodes or
+ edges remain in the RootGraph. The test then reconstructs the
+ RootGraph as it originally was when the timed test began. A quick
+ test is performed to ensure that the correct number of nodes and
+ edges exists in the RootGraph at this point. This
+ deconstruction/reconstruction is repeated 10 times. The timer stops
+ after the 10th reconstruction.
+
+ Test circumstances:
+ Tests were performed on a 1.8GHz P4 (512K cache), with 512M RAM,
+ where 256M memory was allocated to the JVM. Sun's 1.4.2_06 JVM
+ on Red Hat's 3ES Linux system.
+
+ Test results:
+
+ Milliseconds taken to perform test case:
+
+ graph size | Fing | Luna |
+ --------------------------------------+--------+--------+
+ 200 nodes, 1000 edges | 83 | FAIL |
+ 1000 nodes, 10000 edges | 236 | FAIL |
+ 2000 nodes, 20000 edges | 513 | FAIL |
+ 16000 nodes, 100000 edges | 3650 | FAIL |
+ 50000 nodes, 400000 edges | 15343 | FAIL |
+ 100000 nodes, 1000000 edges | 42494 | FAIL |
+ --------------------------------------+--------+--------+
diff --git a/corelibs/geom.rtree/pom.xml b/corelibs/geom.rtree/pom.xml
new file mode 100644
index 0000000..12ffaa6
--- /dev/null
+++ b/corelibs/geom.rtree/pom.xml
@@ -0,0 +1,54 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>parent</artifactId>
+ <version>2.8.4-SNAPSHOT</version>
+ </parent>
+
+ <artifactId>geom-rtree</artifactId>
+ <packaging>jar</packaging>
+
+ <name>geom-rtree</name>
+
+ <!-- bootstrap for cytoscape dependencies, namely the parent POM snapshots -->
+ <repositories>
+ <repository>
+ <id>cytoscape_snapshots</id>
+ <snapshots>
+ <enabled>true</enabled>
+ </snapshots>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <name>Cytoscape Snapshots</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/</url>
+ </repository>
+ <repository>
+ <id>cytoscape_releases</id>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ <name>Cytoscape Releases</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/releases/</url>
+ </repository>
+ </repositories>
+
+ <dependencies>
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>util-intr</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>geom-spacial</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ </dependencies>
+
+</project>
+
diff --git a/corelibs/geom.rtree/src/main/java/cytoscape/geom/rtree/DEPENDENCIES b/corelibs/geom.rtree/src/main/java/cytoscape/geom/rtree/DEPENDENCIES
new file mode 100644
index 0000000..9ff510d
--- /dev/null
+++ b/corelibs/geom.rtree/src/main/java/cytoscape/geom/rtree/DEPENDENCIES
@@ -0,0 +1,2 @@
+lib:cytoscape-util-intr.jar
+lib:cytoscape-geom-spacial.jar
diff --git a/corelibs/geom.rtree/src/main/java/cytoscape/geom/rtree/ObjStack.java b/corelibs/geom.rtree/src/main/java/cytoscape/geom/rtree/ObjStack.java
new file mode 100644
index 0000000..4a6d52b
--- /dev/null
+++ b/corelibs/geom.rtree/src/main/java/cytoscape/geom/rtree/ObjStack.java
@@ -0,0 +1,138 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.geom.rtree;
+
+
+/**
+ * A first-in, last-out container of objects; an object put onto the stack
+ * may be null. In the underlying implementation, the memory consumed by an
+ * instance of this class may increase, but does never decrease.<p>
+ * NOTE: Right now this class is package visible but it is written in such
+ * a way so as to be suitable to become public at some point, once a proper
+ * package location for it is found.
+ */
+final class ObjStack implements java.io.Serializable {
+ // This must be a non-negative integer.
+ private static final int DEFAULT_CAPACITY = 11;
+ private Object[] m_stack;
+ private int m_currentSize;
+
+ /**
+ * Creates a new stack of objects.
+ */
+ public ObjStack() {
+ m_stack = new Object[DEFAULT_CAPACITY];
+ m_currentSize = 0;
+ }
+
+ /**
+ * Removes everything from this stack. This operation has time complexity
+ * linear to the current size of this stack because we null out every entry
+ * so as to not hinder garbage collection.
+ */
+ public final void empty() {
+ for (int i = m_currentSize - 1; i >= 0; i--)
+ m_stack[i] = null;
+
+ m_currentSize = 0;
+ }
+
+ /**
+ * Returns the number of objects that are currently on this stack.
+ */
+ public final int size() {
+ return m_currentSize;
+ }
+
+ /**
+ * Pushes a new object onto this stack. A successive peek() or pop()
+ * call will return the specified object. An object pushed onto this
+ * stack may be null.
+ */
+ public final void push(final Object obj) {
+ try {
+ m_stack[m_currentSize++] = obj;
+ } catch (ArrayIndexOutOfBoundsException e) {
+ m_currentSize--;
+ checkSize();
+ m_stack[m_currentSize++] = obj;
+ }
+ }
+
+ /**
+ * A non-mutating operation that retrieves the next object on this stack.<p>
+ * It is considered an error to call this method if there are no objects
+ * currently on this stack. If size() returns zero immediately before this
+ * method is called, the results of this operation are undefined.
+ */
+ public final Object peek() {
+ return m_stack[m_currentSize - 1];
+ }
+
+ /**
+ * Removes and returns the next object on this stack.<p>
+ * It is considered an error to call this method if there are no objects
+ * currently on this stack. If size() returns zero immediately before this
+ * method is called, the results of this operation are undefined.
+ */
+ public final Object pop() {
+ try {
+ final Object returnThis = m_stack[--m_currentSize];
+ m_stack[m_currentSize] = null; // This line is essential.
+
+ return returnThis;
+ } catch (ArrayIndexOutOfBoundsException e) {
+ m_currentSize++;
+ throw e;
+ }
+ }
+
+ private final void checkSize() {
+ if (m_currentSize < m_stack.length)
+ return;
+
+ final int newStackSize = (int) Math.min((long) Integer.MAX_VALUE,
+ (((long) m_stack.length) * 2L) + 1L);
+
+ if (newStackSize == m_stack.length)
+ throw new IllegalStateException("cannot allocate large enough array");
+
+ final Object[] newStack = new Object[newStackSize];
+ System.arraycopy(m_stack, 0, newStack, 0, m_stack.length);
+ m_stack = newStack;
+ }
+}
diff --git a/corelibs/geom.rtree/src/main/java/cytoscape/geom/rtree/RTree.java b/corelibs/geom.rtree/src/main/java/cytoscape/geom/rtree/RTree.java
new file mode 100644
index 0000000..0127088
--- /dev/null
+++ b/corelibs/geom.rtree/src/main/java/cytoscape/geom/rtree/RTree.java
@@ -0,0 +1,1839 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.geom.rtree;
+
+import cytoscape.geom.spacial.MutableSpacialIndex2D;
+import cytoscape.geom.spacial.SpacialEntry2DEnumerator;
+
+import cytoscape.util.intr.IntEnumerator;
+import cytoscape.util.intr.IntObjHash;
+import cytoscape.util.intr.IntStack;
+
+import java.util.Iterator;
+
+
+/**
+ * An in-memory R-tree over real numbers in two dimensions.<p>
+ * An instance of this class is serializable; however, serialized instances of
+ * this class should not be stored in a persistent manner because the
+ * serialization implemented in this class makes no attempt at handling
+ * class versioning.
+ */
+public final class RTree implements MutableSpacialIndex2D, java.io.Serializable {
+ /**
+ * @deprecated Use the no-arg constructor.
+ */
+ public final static int DEFAULT_MAX_BRANCHES = 11;
+ private final float[] m_MBR; // { xMin, yMin, xMax, yMax }.
+ private final int m_maxBranches;
+ private final int m_minBranches;
+ private Node m_root;
+ private IntObjHash m_entryMap; // Keys are objKey, values are type Node,
+ private final Object m_deletedEntry = ""; // except when "deleted".
+ private int m_deletedEntries;
+ private int m_mapExpansionThreshold;
+
+ // These buffers are used during node splitting.
+ private final int[] m_objKeyBuff;
+ private final Node[] m_childrenBuff;
+ private final float[] m_xMinBuff;
+ private final float[] m_yMinBuff;
+ private final float[] m_xMaxBuff;
+ private final float[] m_yMaxBuff;
+ private final float[] m_tempBuff1;
+ private final float[] m_tempBuff2;
+ private final float[] m_extentsStack;
+ private final ObjStack m_nodeStack;
+
+ /**
+ * Instantiates a new R-tree. A new R-tree is empty (it has no entries).
+ */
+ public RTree() {
+ this(DEFAULT_MAX_BRANCHES);
+ }
+
+ /**
+ * Instantiates a new R-tree with the specified maximum branching factor.
+ * Overriding the default maximum branching factor is only useful for
+ * testing purposes; there are no performance gains to be had.
+ * @param maxBranches the maximum branching factor of this tree.
+ * @exception IllegalArgumentException if maxBranches is less than three.
+ * @deprecated Use the no-arg constructor instead.
+ */
+ public RTree(final int maxBranches) {
+ if (maxBranches < 3)
+ throw new IllegalArgumentException("maxBranches is less than three");
+
+ m_MBR = new float[] {
+ Float.POSITIVE_INFINITY, Float.POSITIVE_INFINITY, Float.NEGATIVE_INFINITY,
+ Float.NEGATIVE_INFINITY
+ };
+ m_maxBranches = maxBranches;
+ m_minBranches = Math.max(2, (int) (((double) (m_maxBranches + 1)) * 0.4d));
+ m_root = new Node(m_maxBranches, true);
+ m_entryMap = new IntObjHash();
+ m_deletedEntries = 0;
+ m_mapExpansionThreshold = IntObjHash.maxCapacity(m_entryMap.size());
+ m_objKeyBuff = new int[m_maxBranches + 1];
+ m_childrenBuff = new Node[m_maxBranches + 1];
+ m_xMinBuff = new float[m_maxBranches + 1];
+ m_yMinBuff = new float[m_maxBranches + 1];
+ m_xMaxBuff = new float[m_maxBranches + 1];
+ m_yMaxBuff = new float[m_maxBranches + 1];
+ m_tempBuff1 = new float[m_maxBranches + 1];
+ m_tempBuff2 = new float[m_maxBranches + 1];
+
+ // With a m_maxBranches of 7, m_minBranches will be 3, and such a tree of
+ // depth 20 holds at least 3.4 billion entries.
+ m_extentsStack = new float[20 * 7 * 4];
+ m_nodeStack = new ObjStack();
+ }
+
+ /**
+ * Empties this R-tree of all entries. This method returns in constant
+ * time (note however that garbage collection will take place in the
+ * background).
+ */
+ public final void empty() {
+ m_root = new Node(m_maxBranches, true);
+ m_entryMap = new IntObjHash();
+ m_deletedEntries = 0;
+ m_mapExpansionThreshold = IntObjHash.maxCapacity(m_entryMap.size());
+ }
+
+ /**
+ * Returns the number of entries currently in this R-tree. This method
+ * returns in constant time.<p>
+ * NOTE: To retrieve an enumeration of all entries in this R-tree, call
+ * queryOverlap() with Float.NEGATIVE_INFINITY minimum values and
+ * Float.POSITIVE_INFINITY maximum values.
+ */
+ public final int size() {
+ return (isLeafNode(m_root) ? m_root.entryCount : m_root.data.deepCount);
+ }
+
+ /*
+ * This gets used a lot. This test is in the form of a function to make
+ * the code more readable (as opposed to being inlined).
+ */
+ private final static boolean isLeafNode(final Node n) {
+ return n.data == null;
+ }
+
+ /**
+ * Inserts a new data entry into this tree; the entry's extents
+ * are specified by the input parameters. "Extents" is a short way
+ * of saying "minimum bounding rectangle". The minimum bounding rectangle
+ * of an entry is axis-aligned, meaning that its sides are parallel to the
+ * axes of the data space.
+ * @param objKey a user-defined unique identifier used to refer to the entry
+ * being inserted in later operations; this identifier must be
+ * non-negative.
+ * @param xMin the minimum X coordinate of the entry's extents rectangle.
+ * @param yMin the minimum Y coordinate of the entry's extents rectangle.
+ * @param xMax the maximum X coordinate of the entry's extents rectangle.
+ * @param yMax the maximum Y coordinate of the entry's extents rectangle.
+ * @exception IllegalStateException if objKey is already used for an
+ * existing entry in this R-tree.
+ * @exception IllegalArgumentException if objKey is negative,
+ * if xMin is not less than or equal to xMax, or
+ * if yMin is not less than or equal to yMax.
+ */
+ public final void insert(final int objKey, final float xMin, final float yMin,
+ final float xMax, final float yMax) {
+ if (objKey < 0)
+ throw new IllegalArgumentException("objKey is negative");
+
+ if (!(xMin <= xMax))
+ throw new IllegalArgumentException("xMin <= xMax not true");
+
+ if (!(yMin <= yMax))
+ throw new IllegalArgumentException("yMin <= yMax not true");
+
+ if (m_entryMap.get(objKey) != null) { // Hashtable lookups are cached.
+
+ if (m_entryMap.get(objKey) != m_deletedEntry)
+ throw new IllegalStateException("objkey " + objKey + " is already in this tree");
+
+ m_deletedEntries--;
+ } // Old entry is m_deletedEntry.
+
+ // We only allow underlying hashtable expansions if the number of deleted
+ // keys in the table is one quarter or less of the total number of keys.
+ else {
+ if (m_entryMap.size() == m_mapExpansionThreshold) { // Expansion.
+
+ if ((m_deletedEntries * 4) > m_entryMap.size()) { // Prune map.
+
+ final IntObjHash newEntryMap = new IntObjHash();
+ final IntEnumerator objKeys = m_entryMap.keys();
+ final Iterator leafNodes = m_entryMap.values();
+
+ while (objKeys.numRemaining() > 0) {
+ final Object leafNode = leafNodes.next();
+
+ if (leafNode == m_deletedEntry) {
+ objKeys.nextInt();
+
+ continue;
+ }
+
+ newEntryMap.put(objKeys.nextInt(), leafNode);
+ }
+
+ m_entryMap = newEntryMap;
+ m_deletedEntries = 0;
+ }
+
+ m_mapExpansionThreshold = IntObjHash.maxCapacity(m_entryMap.size() + 1);
+ }
+ }
+
+ final Node rootSplit = insert(m_root, objKey, xMin, yMin, xMax, yMax, m_maxBranches,
+ m_minBranches, m_entryMap, m_MBR, m_objKeyBuff,
+ m_childrenBuff, m_xMinBuff, m_yMinBuff, m_xMaxBuff,
+ m_yMaxBuff, m_tempBuff1, m_tempBuff2);
+
+ if (rootSplit != null) {
+ final Node newRoot = new Node(m_maxBranches, false);
+ newRoot.entryCount = 2;
+ m_root.parent = newRoot;
+ rootSplit.parent = newRoot;
+ newRoot.data.children[0] = m_root;
+ newRoot.data.children[1] = rootSplit;
+ newRoot.xMins[0] = m_root.xMins[m_maxBranches - 1];
+ newRoot.yMins[0] = m_root.yMins[m_maxBranches - 1];
+ newRoot.xMaxs[0] = m_root.xMaxs[m_maxBranches - 1];
+ newRoot.yMaxs[0] = m_root.yMaxs[m_maxBranches - 1];
+ newRoot.xMins[1] = rootSplit.xMins[m_maxBranches - 1];
+ newRoot.yMins[1] = rootSplit.yMins[m_maxBranches - 1];
+ newRoot.xMaxs[1] = rootSplit.xMaxs[m_maxBranches - 1];
+ newRoot.yMaxs[1] = rootSplit.yMaxs[m_maxBranches - 1];
+
+ if (isLeafNode(m_root))
+ newRoot.data.deepCount = m_root.entryCount + rootSplit.entryCount;
+ else
+ newRoot.data.deepCount = m_root.data.deepCount + rootSplit.data.deepCount;
+
+ m_root = newRoot;
+ m_MBR[0] = Math.min(m_root.xMins[0], m_root.xMins[1]);
+ m_MBR[1] = Math.min(m_root.yMins[0], m_root.yMins[1]);
+ m_MBR[2] = Math.max(m_root.xMaxs[0], m_root.xMaxs[1]);
+ m_MBR[3] = Math.max(m_root.yMaxs[0], m_root.yMaxs[1]);
+ }
+ }
+
+ /*
+ * This is the routine that inserts an entry into a leaf node.
+ * Returns a non-null node in the case that the root was split; in this
+ * case the globalMBR is not updated, and the MBR at index
+ * maxBranches - 1 in both root and the returned node will contain the
+ * overall MBR of that node.
+ */
+ private final static Node insert(final Node root, final int objKey, final float xMin,
+ final float yMin, final float xMax, final float yMax,
+ final int maxBranches, final int minBranches,
+ final IntObjHash entryMap, final float[] globalMBR,
+ final int[] objKeyBuff, final Node[] childrenBuff,
+ final float[] xMinBuff, final float[] yMinBuff,
+ final float[] xMaxBuff, final float[] yMaxBuff,
+ final float[] tempBuff1, final float[] tempBuff2) {
+ final int deepCountIncrease = 1;
+ final Node chosenLeaf = chooseLeaf(root, xMin, yMin, xMax, yMax);
+
+ if (chosenLeaf.entryCount < maxBranches) { // No split is necessary.
+
+ final int newInx = chosenLeaf.entryCount++;
+ chosenLeaf.objKeys[newInx] = objKey;
+ chosenLeaf.xMins[newInx] = xMin;
+ chosenLeaf.yMins[newInx] = yMin;
+ chosenLeaf.xMaxs[newInx] = xMax;
+ chosenLeaf.yMaxs[newInx] = yMax;
+ entryMap.put(objKey, chosenLeaf);
+ adjustTreeNoSplit(chosenLeaf, deepCountIncrease, globalMBR);
+
+ return null;
+ } else { // A split is necessary.
+
+ final Node newLeaf = splitLeafNode(chosenLeaf, objKey, xMin, yMin, xMax, yMax,
+ maxBranches, minBranches, objKeyBuff, xMinBuff,
+ yMinBuff, xMaxBuff, yMaxBuff, tempBuff1, tempBuff2);
+
+ for (int i = 0; i < chosenLeaf.entryCount; i++)
+ entryMap.put(chosenLeaf.objKeys[i], chosenLeaf);
+
+ for (int i = 0; i < newLeaf.entryCount; i++)
+ entryMap.put(newLeaf.objKeys[i], newLeaf);
+
+ return adjustTreeWithSplit(chosenLeaf, newLeaf, deepCountIncrease, maxBranches,
+ minBranches, globalMBR, childrenBuff, xMinBuff, yMinBuff,
+ xMaxBuff, yMaxBuff, tempBuff1, tempBuff2);
+ }
+ }
+
+ /*
+ * This is the routine that re-inserts a node into the tree.
+ * Inserts specified node into a parent at specified depth. Depth zero is
+ * defined to be the depth of the root. Returns a non-null node in the
+ * case that the root was split; in this case the globalMBR is not
+ * updated, and the MBR at index maxBranches - 1 in both root and the
+ * returned node will contain the overall MBR of that node.
+ */
+ private final static Node insert(final Node root, final int depth, final Node n,
+ final float xMin, final float yMin, final float xMax,
+ final float yMax, final int maxBranches,
+ final int minBranches, final float[] globalMBR,
+ final Node[] childrenBuff, final float[] xMinBuff,
+ final float[] yMinBuff, final float[] xMaxBuff,
+ final float[] yMaxBuff, final float[] tempBuff1,
+ final float[] tempBuff2) {
+ final int deepCountIncrease = (isLeafNode(n) ? n.entryCount : n.data.deepCount);
+ final Node chosenParent = chooseParent(root, depth, xMin, yMin, xMax, yMax);
+
+ if (chosenParent.entryCount < maxBranches) { // No split is necessary.
+
+ final int newInx = chosenParent.entryCount++;
+ n.parent = chosenParent;
+ chosenParent.data.children[newInx] = n;
+ chosenParent.xMins[newInx] = xMin;
+ chosenParent.yMins[newInx] = yMin;
+ chosenParent.xMaxs[newInx] = xMax;
+ chosenParent.yMaxs[newInx] = yMax;
+ chosenParent.data.deepCount += deepCountIncrease;
+ adjustTreeNoSplit(chosenParent, deepCountIncrease, globalMBR);
+
+ return null;
+ } else { // A split is necessary.
+
+ final Node parentSibling = splitInternalNode(chosenParent, n, xMin, yMin, xMax, yMax,
+ maxBranches, minBranches, childrenBuff,
+ xMinBuff, yMinBuff, xMaxBuff, yMaxBuff,
+ tempBuff1, tempBuff2);
+
+ return adjustTreeWithSplit(chosenParent, parentSibling, deepCountIncrease, maxBranches,
+ minBranches, globalMBR, childrenBuff, xMinBuff, yMinBuff,
+ xMaxBuff, yMaxBuff, tempBuff1, tempBuff2);
+ }
+ }
+
+ /*
+ * Returns a leaf node. The returned leaf node is chosen by this
+ * algorithm as the most suitable leaf node [under specified root] in
+ * which to place specified new entry.
+ */
+ private final static Node chooseLeaf(final Node root, final float xMin, final float yMin,
+ final float xMax, final float yMax) {
+ Node n = root;
+
+ while (!isLeafNode(n))
+ n = n.data.children[chooseSubtree(n, xMin, yMin, xMax, yMax)];
+
+ return n;
+ }
+
+ /*
+ * The root is defined to be at depth zero. This function returns a node
+ * at specified depth such that the returned node is the most suitable such
+ * node in which to place specified MBR.
+ */
+ private final static Node chooseParent(final Node root, final int depth, final float xMin,
+ final float yMin, final float xMax, final float yMax) {
+ Node n = root;
+ int currDepth = 0;
+
+ while (currDepth != depth) {
+ n = n.data.children[chooseSubtree(n, xMin, yMin, xMax, yMax)];
+ currDepth++;
+ }
+
+ return n;
+ }
+
+ /*
+ * Returns the index of entry in n whose rectangular boundary
+ * needs least enlargment to swallow the input rectangle. Ties are resolved
+ * by choosing the entry with the rectangle of smallest area.
+ */
+ private final static int chooseSubtree(final Node n, final float xMin, final float yMin,
+ final float xMax, final float yMax) {
+ float bestAreaDelta = Float.POSITIVE_INFINITY;
+ float bestArea = Float.POSITIVE_INFINITY;
+ int bestInx = -1;
+
+ for (int i = 0; i < n.entryCount; i++) {
+ // A possible optimization would be to add to each node an area cache
+ // for each entry. That way we wouldn't have to compute this area on
+ // each insertion.
+ final float currArea = (n.xMaxs[i] - n.xMins[i]) * (n.yMaxs[i] - n.yMins[i]);
+ final float newArea = (Math.max(n.xMaxs[i], xMax) - Math.min(n.xMins[i], xMin)) * (Math
+ .max(n.yMaxs[i],
+ yMax)
+ - Math
+ .min(n.yMins[i],
+ yMin));
+ final float currAreaDelta = newArea - currArea;
+
+ if ((currAreaDelta < bestAreaDelta)
+ || ((currAreaDelta == bestAreaDelta) && (currArea < bestArea))) {
+ bestAreaDelta = currAreaDelta;
+ bestArea = currArea;
+ bestInx = i;
+ }
+ }
+
+ return bestInx;
+ }
+
+ /*
+ * This is the quadratic-cost algorithm described in Guttman's 1984
+ * R-tree paper. The parent pointer of returned node is not set. The
+ * parent pointer in the full node is not modified, and nothing in that
+ * parent is modified. Everything else in the input node and in the
+ * returned node is set as appropriate. The MBRs at index
+ * maxBranches - 1 in both nodes are set to be the new overall MBR of
+ * corresponding node. The node returned is also a leaf node.
+ * No claim is made as to the resulting values in the buff arrays.
+ */
+ private final static Node splitLeafNode(final Node fullLeafNode, final int newObjKey,
+ final float newXMin, final float newYMin,
+ final float newXMax, final float newYMax,
+ final int maxBranches, final int minBranches,
+ final int[] objKeyBuff, final float[] xMinBuff,
+ final float[] yMinBuff, final float[] xMaxBuff,
+ final float[] yMaxBuff, final float[] tempBuff1,
+ final float[] tempBuff2) {
+ // Copy node MBRs and objKeys and new MBR and objKey into arrays.
+ for (int i = 0; i < fullLeafNode.entryCount; i++) {
+ objKeyBuff[i] = fullLeafNode.objKeys[i];
+ xMinBuff[i] = fullLeafNode.xMins[i];
+ yMinBuff[i] = fullLeafNode.yMins[i];
+ xMaxBuff[i] = fullLeafNode.xMaxs[i];
+ yMaxBuff[i] = fullLeafNode.yMaxs[i];
+ }
+
+ objKeyBuff[fullLeafNode.entryCount] = newObjKey;
+ xMinBuff[fullLeafNode.entryCount] = newXMin;
+ yMinBuff[fullLeafNode.entryCount] = newYMin;
+ xMaxBuff[fullLeafNode.entryCount] = newXMax;
+ yMaxBuff[fullLeafNode.entryCount] = newYMax;
+
+ // Pick seeds. Add seeds to two groups (fullLeafNode and returnThis).
+ final int totalEntries = fullLeafNode.entryCount + 1;
+ final long seeds = pickSeeds(totalEntries, xMinBuff, yMinBuff, xMaxBuff, yMaxBuff, tempBuff1);
+
+ // tempBuff1 now contains the areas of the MBRs - we won't use this.
+ final int seed1 = (int) (seeds >> 32);
+ fullLeafNode.objKeys[0] = objKeyBuff[seed1];
+ fullLeafNode.xMins[0] = xMinBuff[seed1];
+ fullLeafNode.yMins[0] = yMinBuff[seed1];
+ fullLeafNode.xMaxs[0] = xMaxBuff[seed1];
+ fullLeafNode.yMaxs[0] = yMaxBuff[seed1];
+ fullLeafNode.entryCount = 1;
+
+ final int seed2 = (int) seeds;
+ final Node returnThis = new Node(maxBranches, true);
+ returnThis.objKeys[0] = objKeyBuff[seed2];
+ returnThis.xMins[0] = xMinBuff[seed2];
+ returnThis.yMins[0] = yMinBuff[seed2];
+ returnThis.xMaxs[0] = xMaxBuff[seed2];
+ returnThis.yMaxs[0] = yMaxBuff[seed2];
+ returnThis.entryCount = 1;
+
+ // Initialize the overall MBRs at index maxBranches - 1.
+ fullLeafNode.xMins[maxBranches - 1] = fullLeafNode.xMins[0];
+ fullLeafNode.yMins[maxBranches - 1] = fullLeafNode.yMins[0];
+ fullLeafNode.xMaxs[maxBranches - 1] = fullLeafNode.xMaxs[0];
+ fullLeafNode.yMaxs[maxBranches - 1] = fullLeafNode.yMaxs[0];
+ returnThis.xMins[maxBranches - 1] = returnThis.xMins[0];
+ returnThis.yMins[maxBranches - 1] = returnThis.yMins[0];
+ returnThis.xMaxs[maxBranches - 1] = returnThis.xMaxs[0];
+ returnThis.yMaxs[maxBranches - 1] = returnThis.yMaxs[0];
+
+ // Plug the holes where seeds used to be.
+ int entriesRemaining = totalEntries;
+
+ if (seed2 != --entriesRemaining) { // seed1 < seed2, guaranteed.
+ objKeyBuff[seed2] = objKeyBuff[entriesRemaining];
+ xMinBuff[seed2] = xMinBuff[entriesRemaining];
+ yMinBuff[seed2] = yMinBuff[entriesRemaining];
+ xMaxBuff[seed2] = xMaxBuff[entriesRemaining];
+ yMaxBuff[seed2] = yMaxBuff[entriesRemaining];
+ }
+
+ if (seed1 != --entriesRemaining) {
+ objKeyBuff[seed1] = objKeyBuff[entriesRemaining];
+ xMinBuff[seed1] = xMinBuff[entriesRemaining];
+ yMinBuff[seed1] = yMinBuff[entriesRemaining];
+ xMaxBuff[seed1] = xMaxBuff[entriesRemaining];
+ yMaxBuff[seed1] = yMaxBuff[entriesRemaining];
+ }
+
+ boolean buff1Valid = false;
+ boolean buff2Valid = false;
+
+ while (true) {
+ // Test to see if we're all done.
+ if (entriesRemaining == 0)
+ break;
+
+ final Node restGroup;
+
+ if ((entriesRemaining + fullLeafNode.entryCount) == minBranches)
+ restGroup = fullLeafNode;
+ else if ((entriesRemaining + returnThis.entryCount) == minBranches)
+ restGroup = returnThis;
+ else
+ restGroup = null;
+
+ if (restGroup != null) { // Assign remaining entries to this group.
+
+ for (int i = 0; i < entriesRemaining; i++) {
+ // Add entry to "rest" group.
+ final int newInx = restGroup.entryCount++;
+ restGroup.objKeys[newInx] = objKeyBuff[i];
+ restGroup.xMins[newInx] = xMinBuff[i];
+ restGroup.yMins[newInx] = yMinBuff[i];
+ restGroup.xMaxs[newInx] = xMaxBuff[i];
+ restGroup.yMaxs[newInx] = yMaxBuff[i];
+
+ // Update the overall MBR of "rest" group.
+ restGroup.xMins[maxBranches - 1] = Math.min(restGroup.xMins[maxBranches - 1],
+ xMinBuff[i]);
+ restGroup.yMins[maxBranches - 1] = Math.min(restGroup.yMins[maxBranches - 1],
+ yMinBuff[i]);
+ restGroup.xMaxs[maxBranches - 1] = Math.max(restGroup.xMaxs[maxBranches - 1],
+ xMaxBuff[i]);
+ restGroup.yMaxs[maxBranches - 1] = Math.max(restGroup.yMaxs[maxBranches - 1],
+ yMaxBuff[i]);
+ }
+
+ break;
+ }
+
+ // We're not done; pick next.
+ final int next = pickNext(fullLeafNode, returnThis, entriesRemaining, maxBranches,
+ xMinBuff, yMinBuff, xMaxBuff, yMaxBuff, tempBuff1,
+ buff1Valid, tempBuff2, buff2Valid);
+ final boolean chooseGroup1;
+
+ if (tempBuff1[next] < tempBuff2[next])
+ chooseGroup1 = true;
+ else if (tempBuff1[next] > tempBuff2[next])
+ chooseGroup1 = false;
+ else { // Tie for how much group's covering rectangle will increase.
+ // If we had an area cache array field in each node we could prevent
+ // these two computations.
+
+ final float group1Area = (fullLeafNode.xMaxs[maxBranches - 1]
+ - fullLeafNode.xMins[maxBranches - 1]) * (fullLeafNode.yMaxs[maxBranches
+ - 1]
+ - fullLeafNode.yMins[maxBranches
+ - 1]);
+ final float group2Area = (returnThis.xMaxs[maxBranches - 1]
+ - returnThis.xMins[maxBranches - 1]) * (returnThis.yMaxs[maxBranches
+ - 1]
+ - returnThis.yMins[maxBranches
+ - 1]);
+
+ if (group1Area < group2Area)
+ chooseGroup1 = true;
+ else if (group1Area > group2Area)
+ chooseGroup1 = false;
+ else if (fullLeafNode.entryCount < returnThis.entryCount)
+ chooseGroup1 = true;
+ else
+ chooseGroup1 = false;
+ }
+
+ final Node chosenGroup;
+ final float[] validTempBuff;
+
+ if (chooseGroup1) {
+ chosenGroup = fullLeafNode;
+ validTempBuff = tempBuff2;
+ buff1Valid = false;
+ buff2Valid = true;
+ } else {
+ chosenGroup = returnThis;
+ validTempBuff = tempBuff1;
+ buff1Valid = true;
+ buff2Valid = false;
+ }
+
+ // Add next to chosen group.
+ final int newInx = chosenGroup.entryCount++;
+ chosenGroup.objKeys[newInx] = objKeyBuff[next];
+ chosenGroup.xMins[newInx] = xMinBuff[next];
+ chosenGroup.yMins[newInx] = yMinBuff[next];
+ chosenGroup.xMaxs[newInx] = xMaxBuff[next];
+ chosenGroup.yMaxs[newInx] = yMaxBuff[next];
+
+ // Update the MBR of chosen group.
+ // Note: If we see that the MBR stays the same, we could mark the
+ // "invalid" temp buff array as valid to save even more on computations.
+ // Because this is a rare occurance (seeds of small area tend to be
+ // chosen), I choose not to make this optimization.
+ chosenGroup.xMins[maxBranches - 1] = Math.min(chosenGroup.xMins[maxBranches - 1],
+ xMinBuff[next]);
+ chosenGroup.yMins[maxBranches - 1] = Math.min(chosenGroup.yMins[maxBranches - 1],
+ yMinBuff[next]);
+ chosenGroup.xMaxs[maxBranches - 1] = Math.max(chosenGroup.xMaxs[maxBranches - 1],
+ xMaxBuff[next]);
+ chosenGroup.yMaxs[maxBranches - 1] = Math.max(chosenGroup.yMaxs[maxBranches - 1],
+ yMaxBuff[next]);
+
+ // Plug the hole where next used to be.
+ if (next != --entriesRemaining) {
+ objKeyBuff[next] = objKeyBuff[entriesRemaining];
+ xMinBuff[next] = xMinBuff[entriesRemaining];
+ yMinBuff[next] = yMinBuff[entriesRemaining];
+ xMaxBuff[next] = xMaxBuff[entriesRemaining];
+ yMaxBuff[next] = yMaxBuff[entriesRemaining];
+ validTempBuff[next] = validTempBuff[entriesRemaining];
+ }
+ } // End while loop.
+
+ return returnThis;
+ }
+
+ /*
+ * This is the quadratic-cost algorithm described in Guttman's 1984
+ * R-tree paper. The parent pointer of returned node is not set. The
+ * parent pointer in the full node is not modified, and nothing in that
+ * parent is modified. Everything else in the input node and in the
+ * returned node is set as appropriate (deep count, etc.). The MBRs at index
+ * maxBranches - 1 in both nodes are set to be the new overall MBR of
+ * corresponding node. To picture what this function does, imagine
+ * adding newChild (with specified MBR) to fullInternalNode. Note that
+ * newChild may be either an internal node or a leaf node.
+ * No claim is made as to the resulting values in the buff arrays other
+ * than the claim that all entries in childrenBuff will be null when this
+ * method returns.
+ */
+ private final static Node splitInternalNode(final Node fullInternalNode, final Node newChild,
+ final float newXMin, final float newYMin,
+ final float newXMax, final float newYMax,
+ final int maxBranches, final int minBranches,
+ final Node[] childrenBuff, final float[] xMinBuff,
+ final float[] yMinBuff, final float[] xMaxBuff,
+ final float[] yMaxBuff, final float[] tempBuff1,
+ final float[] tempBuff2) {
+ // Copy node MBRs and children and new MBR and child into arrays.
+ for (int i = 0; i < fullInternalNode.entryCount; i++) {
+ childrenBuff[i] = fullInternalNode.data.children[i];
+ xMinBuff[i] = fullInternalNode.xMins[i];
+ yMinBuff[i] = fullInternalNode.yMins[i];
+ xMaxBuff[i] = fullInternalNode.xMaxs[i];
+ yMaxBuff[i] = fullInternalNode.yMaxs[i];
+ }
+
+ childrenBuff[fullInternalNode.entryCount] = newChild;
+ xMinBuff[fullInternalNode.entryCount] = newXMin;
+ yMinBuff[fullInternalNode.entryCount] = newYMin;
+ xMaxBuff[fullInternalNode.entryCount] = newXMax;
+ yMaxBuff[fullInternalNode.entryCount] = newYMax;
+
+ // Pick seeds. Add seeds to two groups (fullInternalNode and returnThis).
+ final int totalEntries = fullInternalNode.entryCount + 1;
+ final long seeds = pickSeeds(totalEntries, xMinBuff, yMinBuff, xMaxBuff, yMaxBuff, tempBuff1);
+
+ // tempBuff1 now contains the areas of the MBRs - we won't use this.
+ final int seed1 = (int) (seeds >> 32);
+ childrenBuff[seed1].parent = fullInternalNode;
+ fullInternalNode.data.children[0] = childrenBuff[seed1];
+ fullInternalNode.xMins[0] = xMinBuff[seed1];
+ fullInternalNode.yMins[0] = yMinBuff[seed1];
+ fullInternalNode.xMaxs[0] = xMaxBuff[seed1];
+ fullInternalNode.yMaxs[0] = yMaxBuff[seed1];
+ fullInternalNode.entryCount = 1;
+
+ final int seed2 = (int) seeds;
+ final Node returnThis = new Node(maxBranches, false);
+ childrenBuff[seed2].parent = returnThis;
+ returnThis.data.children[0] = childrenBuff[seed2];
+ returnThis.xMins[0] = xMinBuff[seed2];
+ returnThis.yMins[0] = yMinBuff[seed2];
+ returnThis.xMaxs[0] = xMaxBuff[seed2];
+ returnThis.yMaxs[0] = yMaxBuff[seed2];
+ returnThis.entryCount = 1;
+
+ // Initialize the overall MBRs at index maxBranches - 1.
+ fullInternalNode.xMins[maxBranches - 1] = fullInternalNode.xMins[0];
+ fullInternalNode.yMins[maxBranches - 1] = fullInternalNode.yMins[0];
+ fullInternalNode.xMaxs[maxBranches - 1] = fullInternalNode.xMaxs[0];
+ fullInternalNode.yMaxs[maxBranches - 1] = fullInternalNode.yMaxs[0];
+ returnThis.xMins[maxBranches - 1] = returnThis.xMins[0];
+ returnThis.yMins[maxBranches - 1] = returnThis.yMins[0];
+ returnThis.xMaxs[maxBranches - 1] = returnThis.xMaxs[0];
+ returnThis.yMaxs[maxBranches - 1] = returnThis.yMaxs[0];
+
+ // Plug the holes where seeds used to be.
+ int entriesRemaining = totalEntries;
+
+ if (seed2 != --entriesRemaining) { // seed1 < seed2, guaranteed.
+ childrenBuff[seed2] = childrenBuff[entriesRemaining];
+ xMinBuff[seed2] = xMinBuff[entriesRemaining];
+ yMinBuff[seed2] = yMinBuff[entriesRemaining];
+ xMaxBuff[seed2] = xMaxBuff[entriesRemaining];
+ yMaxBuff[seed2] = yMaxBuff[entriesRemaining];
+ }
+
+ if (seed1 != --entriesRemaining) {
+ childrenBuff[seed1] = childrenBuff[entriesRemaining];
+ xMinBuff[seed1] = xMinBuff[entriesRemaining];
+ yMinBuff[seed1] = yMinBuff[entriesRemaining];
+ xMaxBuff[seed1] = xMaxBuff[entriesRemaining];
+ yMaxBuff[seed1] = yMaxBuff[entriesRemaining];
+ }
+
+ boolean buff1Valid = false;
+ boolean buff2Valid = false;
+
+ while (true) {
+ // Test to see if we're all done.
+ if (entriesRemaining == 0)
+ break;
+
+ final Node restGroup;
+
+ if ((entriesRemaining + fullInternalNode.entryCount) == minBranches)
+ restGroup = fullInternalNode;
+ else if ((entriesRemaining + returnThis.entryCount) == minBranches)
+ restGroup = returnThis;
+ else
+ restGroup = null;
+
+ if (restGroup != null) { // Assign remaining entries to this group.
+
+ for (int i = 0; i < entriesRemaining; i++) {
+ // Add entry to "rest" group.
+ final int newInx = restGroup.entryCount++;
+ childrenBuff[i].parent = restGroup;
+ restGroup.data.children[newInx] = childrenBuff[i];
+ restGroup.xMins[newInx] = xMinBuff[i];
+ restGroup.yMins[newInx] = yMinBuff[i];
+ restGroup.xMaxs[newInx] = xMaxBuff[i];
+ restGroup.yMaxs[newInx] = yMaxBuff[i];
+
+ // Update the overall MBR of "rest" group.
+ restGroup.xMins[maxBranches - 1] = Math.min(restGroup.xMins[maxBranches - 1],
+ xMinBuff[i]);
+ restGroup.yMins[maxBranches - 1] = Math.min(restGroup.yMins[maxBranches - 1],
+ yMinBuff[i]);
+ restGroup.xMaxs[maxBranches - 1] = Math.max(restGroup.xMaxs[maxBranches - 1],
+ xMaxBuff[i]);
+ restGroup.yMaxs[maxBranches - 1] = Math.max(restGroup.yMaxs[maxBranches - 1],
+ yMaxBuff[i]);
+ }
+
+ break;
+ }
+
+ // We're not done; pick next.
+ final int next = pickNext(fullInternalNode, returnThis, entriesRemaining, maxBranches,
+ xMinBuff, yMinBuff, xMaxBuff, yMaxBuff, tempBuff1,
+ buff1Valid, tempBuff2, buff2Valid);
+ final boolean chooseGroup1;
+
+ if (tempBuff1[next] < tempBuff2[next])
+ chooseGroup1 = true;
+ else if (tempBuff1[next] > tempBuff2[next])
+ chooseGroup1 = false;
+ else { // Tie for how much group's covering rectangle will increase.
+ // If we had an area cache array field in each node we could prevent
+ // these two computations.
+
+ final float group1Area = (fullInternalNode.xMaxs[maxBranches - 1]
+ - fullInternalNode.xMins[maxBranches - 1]) * (fullInternalNode.yMaxs[maxBranches
+ - 1]
+ - fullInternalNode.yMins[maxBranches
+ - 1]);
+ final float group2Area = (returnThis.xMaxs[maxBranches - 1]
+ - returnThis.xMins[maxBranches - 1]) * (returnThis.yMaxs[maxBranches
+ - 1]
+ - returnThis.yMins[maxBranches
+ - 1]);
+
+ if (group1Area < group2Area)
+ chooseGroup1 = true;
+ else if (group1Area > group2Area)
+ chooseGroup1 = false;
+ else if (fullInternalNode.entryCount < returnThis.entryCount)
+ chooseGroup1 = true;
+ else
+ chooseGroup1 = false;
+ }
+
+ final Node chosenGroup;
+ final float[] validTempBuff;
+
+ if (chooseGroup1) {
+ chosenGroup = fullInternalNode;
+ validTempBuff = tempBuff2;
+ buff1Valid = false;
+ buff2Valid = true;
+ } else {
+ chosenGroup = returnThis;
+ validTempBuff = tempBuff1;
+ buff1Valid = true;
+ buff2Valid = false;
+ }
+
+ // Add next to chosen group.
+ final int newInx = chosenGroup.entryCount++;
+ childrenBuff[next].parent = chosenGroup;
+ chosenGroup.data.children[newInx] = childrenBuff[next];
+ chosenGroup.xMins[newInx] = xMinBuff[next];
+ chosenGroup.yMins[newInx] = yMinBuff[next];
+ chosenGroup.xMaxs[newInx] = xMaxBuff[next];
+ chosenGroup.yMaxs[newInx] = yMaxBuff[next];
+
+ // Update the MBR of chosen group.
+ // Note: If we see that the MBR stays the same, we could mark the
+ // "invalid" temp buff array as valid to save even more on computations.
+ // Because this is a rare occurance (seeds of small area tend to be
+ // chosen), I choose not to make this optimization.
+ chosenGroup.xMins[maxBranches - 1] = Math.min(chosenGroup.xMins[maxBranches - 1],
+ xMinBuff[next]);
+ chosenGroup.yMins[maxBranches - 1] = Math.min(chosenGroup.yMins[maxBranches - 1],
+ yMinBuff[next]);
+ chosenGroup.xMaxs[maxBranches - 1] = Math.max(chosenGroup.xMaxs[maxBranches - 1],
+ xMaxBuff[next]);
+ chosenGroup.yMaxs[maxBranches - 1] = Math.max(chosenGroup.yMaxs[maxBranches - 1],
+ yMaxBuff[next]);
+
+ // Plug the hole where next used to be.
+ if (next != --entriesRemaining) {
+ childrenBuff[next] = childrenBuff[entriesRemaining];
+ xMinBuff[next] = xMinBuff[entriesRemaining];
+ yMinBuff[next] = yMinBuff[entriesRemaining];
+ xMaxBuff[next] = xMaxBuff[entriesRemaining];
+ yMaxBuff[next] = yMaxBuff[entriesRemaining];
+ validTempBuff[next] = validTempBuff[entriesRemaining];
+ }
+ } // End while loop.
+
+ fullInternalNode.data.deepCount = 0; // Update deep counts.
+
+ if (isLeafNode(fullInternalNode.data.children[0])) {
+ for (int i = 0; i < fullInternalNode.entryCount; i++)
+ fullInternalNode.data.deepCount += fullInternalNode.data.children[i].entryCount;
+
+ for (int i = 0; i < returnThis.entryCount; i++)
+ returnThis.data.deepCount += returnThis.data.children[i].entryCount;
+ } else { // fullInternalNode's children are internal nodes.
+
+ for (int i = 0; i < fullInternalNode.entryCount; i++)
+ fullInternalNode.data.deepCount += fullInternalNode.data.children[i].data.deepCount;
+
+ for (int i = 0; i < returnThis.entryCount; i++)
+ returnThis.data.deepCount += returnThis.data.children[i].data.deepCount;
+ }
+
+ // Null things out so as to not hinder future garbage collection.
+ for (int i = fullInternalNode.entryCount; i < fullInternalNode.data.children.length; i++)
+ fullInternalNode.data.children[i] = null;
+
+ for (int i = 0; i < childrenBuff.length; i++)
+ childrenBuff[i] = null;
+
+ return returnThis;
+ }
+
+ /*
+ * This is the quadratic-cost algorithm described by Guttman.
+ * The first seed's index is returned as the 32 most significant bits
+ * of returned quantity. The second seed's index is returned as the 32
+ * least significant bits of returned quantity. The first seed's index
+ * is closer to zero than the second seed's index. None of the input
+ * arrays are modified except for tempBuff. tempBuff is populated with
+ * the areas of the MBRs.
+ */
+ private final static long pickSeeds(final int count, final float[] xMins, final float[] yMins,
+ final float[] xMaxs, final float[] yMaxs,
+ final float[] tempBuff) {
+ for (int i = 0; i < count; i++)
+ tempBuff[i] = (xMaxs[i] - xMins[i]) * (yMaxs[i] - yMins[i]); // Area.
+
+ float maximumD = Float.NEGATIVE_INFINITY;
+ int maximumInx1 = -1;
+ int maximumInx2 = -1;
+
+ for (int i = 0; i < (count - 1); i++)
+ for (int j = i + 1; j < count; j++) {
+ final float areaJ = (Math.max(xMaxs[i], xMaxs[j]) - Math.min(xMins[i], xMins[j])) * (Math
+ .max(yMaxs[i],
+ yMaxs[j])
+ - Math
+ .min(yMins[i],
+ yMins[j]));
+ final float d = areaJ - tempBuff[i] - tempBuff[j];
+
+ if (d > maximumD) {
+ maximumD = d;
+ maximumInx1 = i;
+ maximumInx2 = j;
+ }
+ }
+
+ return (((long) maximumInx1) << 32) | ((long) maximumInx2);
+ }
+
+ /*
+ * Returns the index (in xMins, etc.) of next entry to add to a group.
+ * The arrays tempBuff1 and tempBuff2 are used to store the [positive]
+ * area increase required in respective groups to swallow corresponding
+ * MBR at same index. If buff1Valid is true then tempBuff1 already
+ * contains this information and it need not be computed by this
+ * method. Analagous is true for buff2Valid and tempBuff2. The nodes
+ * group1 and group2 are only used by this method to read information
+ * of current MBR of corresponding group - the MBR is stored at index
+ * m_maxBranches - 1. None of the input variables are modified except
+ * for tempBuff1 and tempBuff2.
+ */
+ private final static int pickNext(final Node group1, final Node group2, final int count,
+ final int maxBranches, final float[] xMins,
+ final float[] yMins, final float[] xMaxs,
+ final float[] yMaxs, final float[] tempBuff1,
+ final boolean buff1Valid, final float[] tempBuff2,
+ final boolean buff2Valid) {
+ if (!buff1Valid) {
+ // If we had an area cache array field in each node we could prevent
+ // this computation.
+ final float group1Area = (group1.xMaxs[maxBranches - 1] - group1.xMins[maxBranches - 1]) * (group1.yMaxs[maxBranches
+ - 1]
+ - group1.yMins[maxBranches
+ - 1]);
+
+ for (int i = 0; i < count; i++) {
+ tempBuff1[i] = ((Math.max(group1.xMaxs[maxBranches - 1], xMaxs[i])
+ - Math.min(group1.xMins[maxBranches - 1], xMins[i])) * (Math.max(group1.yMaxs[maxBranches
+ - 1],
+ yMaxs[i])
+ - Math.min(group1.yMins[maxBranches
+ - 1],
+ yMins[i])))
+ - group1Area;
+ }
+ }
+
+ if (!buff2Valid) {
+ // If we had an area cache array field in each node we could prevent
+ // this computation.
+ final float group2Area = (group2.xMaxs[maxBranches - 1] - group2.xMins[maxBranches - 1]) * (group2.yMaxs[maxBranches
+ - 1]
+ - group2.yMins[maxBranches
+ - 1]);
+
+ for (int i = 0; i < count; i++) {
+ tempBuff2[i] = ((Math.max(group2.xMaxs[maxBranches - 1], xMaxs[i])
+ - Math.min(group2.xMins[maxBranches - 1], xMins[i])) * (Math.max(group2.yMaxs[maxBranches
+ - 1],
+ yMaxs[i])
+ - Math.min(group2.yMins[maxBranches
+ - 1],
+ yMins[i])))
+ - group2Area;
+ }
+ }
+
+ float maxDDifference = Float.NEGATIVE_INFINITY;
+ int maxInx = -1;
+
+ for (int i = 0; i < count; i++) {
+ final float currDDifference = Math.abs(tempBuff1[i] - tempBuff2[i]);
+
+ if (currDDifference > maxDDifference) {
+ maxDDifference = currDDifference;
+ maxInx = i;
+ }
+ }
+
+ return maxInx;
+ }
+
+ /*
+ * This method can only be used to adjust a tree after inserting a single
+ * new entry or node into nodeWithNewEntry. It is assumed that the new entry
+ * or node in nodeWithNewEntry is at index nodeWithNewEntry.entryCount - 1.
+ * We will use this knowledge to optimize this function. Deep counts are
+ * updated from nodeWithNewEntry's parent to root.
+ */
+ private final static void adjustTreeNoSplit(final Node nodeWithNewEntry,
+ final int deepCountIncrease, final float[] globalMBR) {
+ int currModInx = nodeWithNewEntry.entryCount - 1;
+ Node n = nodeWithNewEntry;
+
+ while (true) {
+ final Node p = n.parent;
+
+ // "If N is the root, stop." Adjust the globalMBR.
+ if (p == null) {
+ if (currModInx >= 0) {
+ globalMBR[0] = Math.min(globalMBR[0], n.xMins[currModInx]);
+ globalMBR[1] = Math.min(globalMBR[1], n.yMins[currModInx]);
+ globalMBR[2] = Math.max(globalMBR[2], n.xMaxs[currModInx]);
+ globalMBR[3] = Math.max(globalMBR[3], n.yMaxs[currModInx]);
+ }
+
+ break;
+ }
+
+ // Update the deep count.
+ p.data.deepCount += deepCountIncrease;
+
+ if (currModInx >= 0) {
+ final int nInxInP;
+
+ for (int i = 0;; i++)
+ if (p.data.children[i] == n) {
+ nInxInP = i;
+
+ break;
+ }
+
+ // Compute the MBR that tightly encloses all entries in n.
+ final float newXMin = Math.min(p.xMins[nInxInP], n.xMins[currModInx]);
+ final float newYMin = Math.min(p.yMins[nInxInP], n.yMins[currModInx]);
+ final float newXMax = Math.max(p.xMaxs[nInxInP], n.xMaxs[currModInx]);
+ final float newYMax = Math.max(p.yMaxs[nInxInP], n.yMaxs[currModInx]);
+
+ // If the overall MBR of n does not change, we don't need to
+ // update any further MBRs, just deep counts.
+ if ((newXMin == p.xMins[nInxInP]) && (newYMin == p.yMins[nInxInP])
+ && (newXMax == p.xMaxs[nInxInP]) && (newYMax == p.yMaxs[nInxInP])) {
+ currModInx = -1;
+ }
+ else { // n's overall MBR did increase in size.
+ p.xMins[nInxInP] = newXMin;
+ p.yMins[nInxInP] = newYMin;
+ p.xMaxs[nInxInP] = newXMax;
+ p.yMaxs[nInxInP] = newYMax;
+ currModInx = nInxInP;
+ }
+ }
+
+ n = p;
+ }
+ }
+
+ /*
+ * It is required that the MBRs at index maxBranches - 1 in both
+ * input nodes contain the overall MBR of corresponding node.
+ * Returns a node if root was split, otherwise returns null.
+ * If a node is returned, then both the old root and the returned node
+ * will have an MBR entry at index maxBranches - 1 which will be the
+ * overall MBR of that node. The globalMBR is only updated when null
+ * is returned. Deep counts are updated from leaf to root. This method
+ * puts newNode into the tree by trying to insert it as a child into
+ * originalNode's parent - if it does not fit, the parent is split,
+ * and the split may go recursively upwards towards the root.
+ */
+ private final static Node adjustTreeWithSplit(final Node originalNode, final Node newNode,
+ final int deepCountIncrease,
+ final int maxBranches, final int minBranches,
+ final float[] globalMBR,
+ final Node[] childrenBuff,
+ final float[] xMinBuff, final float[] yMinBuff,
+ final float[] xMaxBuff, final float[] yMaxBuff,
+ final float[] tempBuff1, final float[] tempBuff2) {
+ int currModInx = -1;
+ boolean newNodeAdded = false; // New node added as last entry in n?
+ // (Only when nn is null.)
+
+ Node n = originalNode;
+ Node nn = newNode;
+
+ while (true) {
+ final Node p = n.parent;
+
+ // "If N is the root, stop." Update globalMBR if root not split.
+ if (p == null) {
+ if ((nn == null) && (currModInx >= 0)) {
+ globalMBR[0] = Math.min(globalMBR[0], n.xMins[currModInx]);
+ globalMBR[1] = Math.min(globalMBR[1], n.yMins[currModInx]);
+ globalMBR[2] = Math.max(globalMBR[2], n.xMaxs[currModInx]);
+ globalMBR[3] = Math.max(globalMBR[3], n.yMaxs[currModInx]);
+
+ if (newNodeAdded) { // Will only be true when currModInx >= 0.
+
+ final int countMin1 = n.entryCount - 1;
+ globalMBR[0] = Math.min(globalMBR[0], n.xMins[countMin1]);
+ globalMBR[1] = Math.min(globalMBR[1], n.yMins[countMin1]);
+ globalMBR[2] = Math.max(globalMBR[2], n.xMaxs[countMin1]);
+ globalMBR[3] = Math.max(globalMBR[3], n.yMaxs[countMin1]);
+ }
+ }
+
+ break;
+ }
+
+ // Update the deep count. Will get rewritten if p is split - that's OK.
+ p.data.deepCount += deepCountIncrease;
+
+ // Node n was split into two in previous iterative step.
+ if (nn != null) {
+ final int nInxInP; // Only compute this if we need it.
+
+ for (int i = 0;; i++)
+ if (p.data.children[i] == n) {
+ nInxInP = i;
+
+ break;
+ }
+
+ p.xMins[nInxInP] = n.xMins[maxBranches - 1]; // A split implies
+ p.yMins[nInxInP] = n.yMins[maxBranches - 1]; // overall MBR at inx
+ p.xMaxs[nInxInP] = n.xMaxs[maxBranches - 1]; // maxBranches - 1.
+ p.yMaxs[nInxInP] = n.yMaxs[maxBranches - 1];
+
+ if (p.entryCount < maxBranches) { // No further split is necessary.
+
+ final int newInxInP = p.entryCount++;
+ nn.parent = p;
+ p.data.children[newInxInP] = nn;
+ p.xMins[newInxInP] = nn.xMins[maxBranches - 1]; // A split implies
+ p.yMins[newInxInP] = nn.yMins[maxBranches - 1]; // overall MBR at inx
+ p.xMaxs[newInxInP] = nn.xMaxs[maxBranches - 1]; // maxBranches - 1.
+ p.yMaxs[newInxInP] = nn.yMaxs[maxBranches - 1];
+
+ // The recursive step.
+ currModInx = nInxInP;
+ newNodeAdded = true;
+ nn = null;
+ }
+ else { // A split is necessary as the iterative step.
+ // We require that the MBR at index maxBranches - 1 in nn contain
+ // nn's overall MBR at the time this is called.
+ nn = splitInternalNode(p, nn, nn.xMins[maxBranches - 1],
+ nn.yMins[maxBranches - 1], nn.xMaxs[maxBranches - 1],
+ nn.yMaxs[maxBranches - 1], maxBranches, minBranches,
+ childrenBuff, xMinBuff, yMinBuff, xMaxBuff, yMaxBuff,
+ tempBuff1, tempBuff2);
+ }
+ }
+ // Node n was not split into two in previous step, but the updating
+ // of the MBR has percolated up to this level.
+ else if (currModInx >= 0) { // nn == null.
+
+ final int nInxInP; // Only compute this if we need it.
+
+ for (int i = 0;; i++)
+ if (p.data.children[i] == n) {
+ nInxInP = i;
+
+ break;
+ }
+
+ // Compute the new overall MBR for n (stored in n's parent).
+ float newXMin = Math.min(p.xMins[nInxInP], n.xMins[currModInx]);
+ float newYMin = Math.min(p.yMins[nInxInP], n.yMins[currModInx]);
+ float newXMax = Math.max(p.xMaxs[nInxInP], n.xMaxs[currModInx]);
+ float newYMax = Math.max(p.yMaxs[nInxInP], n.yMaxs[currModInx]);
+
+ if (newNodeAdded) { // Nodes added always as last index.
+
+ final int countMin1 = n.entryCount - 1;
+ newXMin = Math.min(newXMin, n.xMins[countMin1]);
+ newYMin = Math.min(newYMin, n.yMins[countMin1]);
+ newXMax = Math.max(newXMax, n.xMaxs[countMin1]);
+ newYMax = Math.max(newYMax, n.yMaxs[countMin1]);
+ newNodeAdded = false;
+ }
+
+ if ((newXMin == p.xMins[nInxInP]) && (newYMin == p.yMins[nInxInP])
+ && (newXMax == p.xMaxs[nInxInP]) && (newYMax == p.yMaxs[nInxInP])) {
+ currModInx = -1;
+ } else {
+ p.xMins[nInxInP] = newXMin;
+ p.yMins[nInxInP] = newYMin;
+ p.xMaxs[nInxInP] = newXMax;
+ p.yMaxs[nInxInP] = newYMax;
+ currModInx = nInxInP;
+ }
+ }
+
+ n = p;
+ } // End while loop.
+
+ return nn;
+ }
+
+ /**
+ * Determines whether or not a given entry exists in this R-tree structure,
+ * and conditionally retrieves the extents of that entry. The parameter
+ * extentsArr is written into by this method only if it is not null
+ * and if objKey exists in this R-tree. The information written into
+ * extentsArr consists of the minimum bounding rectangle (MBR) of objKey:
+ * <blockquote><table border="1" cellpadding="5" cellspacing="0">
+ * <tr> <th>array index</th> <th>value if objKey exists</th> </tr>
+ * <tr> <td>offset</td> <td>xMin of MBR</td> </tr>
+ * <tr> <td>offset+1</td> <td>yMin of MBR</td> </tr>
+ * <tr> <td>offset+2</td> <td>xMax of MBR</td> </tr>
+ * <tr> <td>offset+3</td> <td>yMax of MBR</td> </tr>
+ * </table></blockquote>
+ * The values written into extentsArr are exactly the same ones that
+ * were previously passed to insert() using the same objKey.
+ * @param objKey a user-defined identifier that was [potentially] used in
+ * a previous insertion.
+ * @param extentsArr an array to which extent values will be written by this
+ * method; may be null.
+ * @param offset specifies the beginning index of where to write extent
+ * values into extentsArr; exactly four entries are written starting at
+ * this index (see above table); if extentsArr is null then this offset
+ * is ignored.
+ * @return true if and only if objKey was previously inserted into this
+ * R-tree and has not since been deleted.
+ * @exception ArrayIndexOutOfBoundsException if objKey exists, if
+ * extentsArr is not null, and if extentsArr cannot be written
+ * to in the index range [offset, offset+3].
+ */
+ public final boolean exists(final int objKey, final float[] extentsArr, final int offset) {
+ if (objKey < 0)
+ return false;
+
+ final Object o = m_entryMap.get(objKey);
+
+ if ((o == null) || (o == m_deletedEntry))
+ return false;
+
+ if (extentsArr != null) {
+ final Node n = (Node) o;
+ int i = -1;
+
+ while (n.objKeys[++i] != objKey)
+ ;
+
+ extentsArr[offset] = n.xMins[i];
+ extentsArr[offset + 1] = n.yMins[i];
+ extentsArr[offset + 2] = n.xMaxs[i];
+ extentsArr[offset + 3] = n.yMaxs[i];
+ }
+
+ return true;
+ }
+
+ /**
+ * Deletes the specified data entry from this tree.
+ * @param objKey a user-defined identifier that was potentially used in a
+ * previous insertion.
+ * @return true if and only if objKey existed in this R-tree prior to this
+ * method invocation.
+ */
+ public final boolean delete(final int objKey) {
+ if (objKey < 0)
+ return false;
+
+ final Node n; // Todo: Rename 'n' to 'leafNode'.
+
+ {
+ final Object o = m_entryMap.get(objKey);
+
+ if ((o == null) || (o == m_deletedEntry))
+ return false;
+
+ n = (Node) o;
+ }
+
+ // Delete record from leaf node.
+ final int delInx;
+
+ for (int i = 0;; i++)
+ if (n.objKeys[i] == objKey) {
+ delInx = i;
+
+ break;
+ }
+
+ n.entryCount--;
+
+ if (delInx != n.entryCount) { // Plug the hole at index delInx.
+ n.objKeys[delInx] = n.objKeys[n.entryCount];
+ n.xMins[delInx] = n.xMins[n.entryCount];
+ n.yMins[delInx] = n.yMins[n.entryCount];
+ n.xMaxs[delInx] = n.xMaxs[n.entryCount];
+ n.yMaxs[delInx] = n.yMaxs[n.entryCount];
+ }
+
+ // Fix up the tree from leaf to root.
+ int currentDepth = condenseTree(n, 1, m_nodeStack, m_minBranches, m_MBR)
+ - m_nodeStack.size() + 1;
+
+ while (m_nodeStack.size() > 0) {
+ final Node eliminatedNode = (Node) m_nodeStack.pop();
+
+ for (int i = 0; i < eliminatedNode.entryCount; i++) {
+ final Node rootSplit;
+
+ if (isLeafNode(eliminatedNode)) {
+ rootSplit = insert(m_root, eliminatedNode.objKeys[i], eliminatedNode.xMins[i],
+ eliminatedNode.yMins[i], eliminatedNode.xMaxs[i],
+ eliminatedNode.yMaxs[i], m_maxBranches, m_minBranches,
+ m_entryMap, m_MBR, m_objKeyBuff, m_childrenBuff, m_xMinBuff,
+ m_yMinBuff, m_xMaxBuff, m_yMaxBuff, m_tempBuff1, m_tempBuff2);
+ } else {
+ rootSplit = insert(m_root, currentDepth, eliminatedNode.data.children[i],
+ eliminatedNode.xMins[i], eliminatedNode.yMins[i],
+ eliminatedNode.xMaxs[i], eliminatedNode.yMaxs[i],
+ m_maxBranches, m_minBranches, m_MBR, m_childrenBuff,
+ m_xMinBuff, m_yMinBuff, m_xMaxBuff, m_yMaxBuff, m_tempBuff1,
+ m_tempBuff2);
+ eliminatedNode.data.children[i] = null; /* Facilitate gc. */
+ }
+
+ if (rootSplit != null) {
+ final Node newRoot = new Node(m_maxBranches, false);
+ newRoot.entryCount = 2;
+ m_root.parent = newRoot;
+ rootSplit.parent = newRoot;
+ newRoot.data.children[0] = m_root;
+ newRoot.data.children[1] = rootSplit;
+ newRoot.xMins[0] = m_root.xMins[m_maxBranches - 1];
+ newRoot.yMins[0] = m_root.yMins[m_maxBranches - 1];
+ newRoot.xMaxs[0] = m_root.xMaxs[m_maxBranches - 1];
+ newRoot.yMaxs[0] = m_root.yMaxs[m_maxBranches - 1];
+ newRoot.xMins[1] = rootSplit.xMins[m_maxBranches - 1];
+ newRoot.yMins[1] = rootSplit.yMins[m_maxBranches - 1];
+ newRoot.xMaxs[1] = rootSplit.xMaxs[m_maxBranches - 1];
+ newRoot.yMaxs[1] = rootSplit.yMaxs[m_maxBranches - 1];
+ newRoot.data.deepCount = m_root.data.deepCount + rootSplit.data.deepCount;
+ m_root = newRoot;
+ m_MBR[0] = Math.min(m_root.xMins[0], m_root.xMins[1]);
+ m_MBR[1] = Math.min(m_root.yMins[0], m_root.yMins[1]);
+ m_MBR[2] = Math.max(m_root.xMaxs[0], m_root.xMaxs[1]);
+ m_MBR[3] = Math.max(m_root.yMaxs[0], m_root.yMaxs[1]);
+ currentDepth++;
+ }
+ }
+
+ currentDepth++;
+ } // End while loop.
+
+ // If the root node has only one child, make the child the new root.
+ if ((!isLeafNode(m_root)) && (m_root.entryCount == 1)) {
+ final Node newRoot = m_root.data.children[0];
+ newRoot.parent = null;
+ m_root = newRoot;
+ }
+
+ // Finally, delete the objKey from m_entryMap.
+ // If m_entryMap contains too many deleted entries, prune.
+ m_entryMap.put(objKey, m_deletedEntry);
+
+ if (((++m_deletedEntries * 2) > m_entryMap.size()) && (m_deletedEntries > 5)) {
+ final IntObjHash newEntryMap = new IntObjHash();
+ final IntEnumerator objKeys = m_entryMap.keys();
+ final Iterator leafNodes = m_entryMap.values();
+
+ while (objKeys.numRemaining() > 0) {
+ final Object leafNode = leafNodes.next();
+
+ if (leafNode == m_deletedEntry) {
+ objKeys.nextInt();
+
+ continue;
+ }
+
+ newEntryMap.put(objKeys.nextInt(), leafNode);
+ }
+
+ m_entryMap = newEntryMap;
+ m_deletedEntries = 0;
+ m_mapExpansionThreshold = IntObjHash.maxCapacity(m_entryMap.size());
+ }
+
+ return true;
+ }
+
+ /*
+ * This does not re-insert orphaned nodes and entries - instead, the
+ * stack eliminatedNodes is populated so that the caller of this function
+ * can re-insert. eliminatedNodes should be empty when this function is
+ * called. This method is used for adjusting a tree after deleting one
+ * or more entries or children from nodeWithDeletions. Deep counts are
+ * updated from nodeWithDeletions' parent to root.
+ * Returns the distance (height) from nodeWithDeletions to root.
+ */
+ private final static int condenseTree(final Node nodeWithDeletions, int deepCountDecrease,
+ final ObjStack eliminatedNodes, final int minBranches,
+ final float[] globalMBR) {
+ int depth = 0;
+ boolean updateMBR = true;
+ Node n = nodeWithDeletions;
+
+ while (true) {
+ final Node p = n.parent;
+
+ // If N is the root, adjust the globalMBR and stop.
+ if (p == null) { // n is the root.
+
+ if (updateMBR) {
+ globalMBR[0] = Float.POSITIVE_INFINITY;
+ globalMBR[1] = Float.POSITIVE_INFINITY;
+ globalMBR[2] = Float.NEGATIVE_INFINITY;
+ globalMBR[3] = Float.NEGATIVE_INFINITY;
+
+ for (int i = 0; i < n.entryCount; i++) {
+ globalMBR[0] = Math.min(globalMBR[0], n.xMins[i]);
+ globalMBR[1] = Math.min(globalMBR[1], n.yMins[i]);
+ globalMBR[2] = Math.max(globalMBR[2], n.xMaxs[i]);
+ globalMBR[3] = Math.max(globalMBR[3], n.yMaxs[i]);
+ }
+ }
+
+ break;
+ }
+
+ // Compute n's index in p.
+ final int nInxInP;
+
+ for (int i = 0;; i++)
+ if (p.data.children[i] == n) {
+ nInxInP = i;
+
+ break;
+ }
+
+ // If n is underfull, eliminate it.
+ if (n.entryCount < minBranches) { // Delete n from p.
+ p.entryCount--;
+
+ if (nInxInP != p.entryCount) { // Plug the hole at index nInxInP.
+ p.data.children[nInxInP] = p.data.children[p.entryCount];
+ p.xMins[nInxInP] = p.xMins[p.entryCount];
+ p.yMins[nInxInP] = p.yMins[p.entryCount];
+ p.xMaxs[nInxInP] = p.xMaxs[p.entryCount];
+ p.yMaxs[nInxInP] = p.yMaxs[p.entryCount];
+ }
+
+ p.data.children[p.entryCount] = null; // Important for gc.
+ n.parent = null; // For some strange reason removing this line will
+ // cause OutOfMemoryError in the basic quiet test.
+
+ eliminatedNodes.push(n);
+ deepCountDecrease += (isLeafNode(n) ? n.entryCount : n.data.deepCount);
+ }
+ // Keep n and adjust MBRs if necessary.
+ else { // n has not been eliminated. Adjust covering rectangle.
+
+ if (updateMBR) {
+ final float oldXMin = p.xMins[nInxInP];
+ final float oldYMin = p.yMins[nInxInP];
+ final float oldXMax = p.xMaxs[nInxInP];
+ final float oldYMax = p.yMaxs[nInxInP];
+ p.xMins[nInxInP] = Float.POSITIVE_INFINITY;
+ p.yMins[nInxInP] = Float.POSITIVE_INFINITY;
+ p.xMaxs[nInxInP] = Float.NEGATIVE_INFINITY;
+ p.yMaxs[nInxInP] = Float.NEGATIVE_INFINITY;
+
+ for (int i = 0; i < n.entryCount; i++) {
+ p.xMins[nInxInP] = Math.min(p.xMins[nInxInP], n.xMins[i]);
+ p.yMins[nInxInP] = Math.min(p.yMins[nInxInP], n.yMins[i]);
+ p.xMaxs[nInxInP] = Math.max(p.xMaxs[nInxInP], n.xMaxs[i]);
+ p.yMaxs[nInxInP] = Math.max(p.yMaxs[nInxInP], n.yMaxs[i]);
+ }
+
+ if ((oldXMin == p.xMins[nInxInP]) && (oldYMin == p.yMins[nInxInP])
+ && (oldXMax == p.xMaxs[nInxInP]) && (oldYMax == p.yMaxs[nInxInP]))
+ updateMBR = false;
+ }
+ }
+
+ // Update deep count and make the necessary recursive steps.
+ p.data.deepCount -= deepCountDecrease;
+ n = p;
+ depth++;
+ } // End while loop.
+
+ return depth;
+ }
+
+ /**
+ * Returns an enumeration of entries whose extents intersect the
+ * specified axis-aligned rectangular area. By "axis-aligned" I mean that
+ * the query rectangle's sides are parallel to the axes of the data
+ * space.<p>
+ * The parameter extentsArr is written into by this method if it is not null.
+ * It provides a way for this method to communicate additional information
+ * to the caller of this method. If not null, extentsArr is populated with
+ * information regarding the minimum bounding rectangle (MBR) that contains
+ * all returned entries. The following table describes what is written to
+ * extentsArr if it is not null:
+ * <blockquote><table border="1" cellpadding="5" cellspacing="0">
+ * <tr> <th>array index</th> <th>value if query generates results</th>
+ * <th>value if query does not generate results</th> </tr>
+ * <tr> <td>offset</td> <td>xMin of MBR</td>
+ * <td>Float.POSITIVE_INFINITY</td> </tr>
+ * <tr> <td>offset+1</td> <td>yMin of MBR</td>
+ * <td>Float.POSITIVE_INFINITY</td> </tr>
+ * <tr> <td>offset+2</td> <td>xMax of MBR</td>
+ * <td>Float.NEGATIVE_INFINITY</td> </tr>
+ * <tr> <td>offset+3</td> <td>yMax of MBR</td>
+ * <td>Float.NEGATIVE_INFINITY</td> </tr>
+ * </table></blockquote><p>
+ * This R-tree has the subquery order-preserving property, which can
+ * be described as follows. Suppose we query the R-tree using this
+ * queryOverlap() method, specifying the
+ * maximum possible query rectangle (spanned by Float.NEGATIVE_INFINITY and
+ * Float.POSITIVE_INFINITY values); we get back all entries currently
+ * in this R-tree; the entries returned have a certain order to them.
+ * Let's remember this order. Now if we immediately perform any further
+ * query,
+ * specifying a different (or the same) query rectangle, then the
+ * entries that are returned in the query are returned in the same order
+ * as they were returned in the "all" query. This phenomenon continues
+ * to hold true with any additional queries until the R-tree undergoes
+ * a mutating operation such as insert() or delete(). The order of entries
+ * returned is in fact a left-to-right order in the underlying tree
+ * structure; in the future, if additional query methods are implemented,
+ * then they will also return entries in this same order.<p>
+ * IMPORTANT: The returned enumeration becomes invalid as soon as any
+ * structure-modifying operation (insert or delete) is performed on this
+ * R-tree. Accessing an invalid enumeration's methods will result in
+ * unpredictable and ill-defined behavior in that enumeration, but will
+ * have no effect on the integrity of the underlying tree structure.<p>
+ * NOTE: It may be possible to provide a more optimized version of this
+ * algorithm for point queries. Such a public method may be a future
+ * addition to this class.
+ * @param xMin the minimum X coordinate of the query rectangle.
+ * @param yMin the minimum Y coordinate of the query rectangle.
+ * @param xMax the maximum X coordinate of the query rectangle.
+ * @param yMax the maximum Y coordinate of the query rectangle.
+ * @param extentsArr an array to which
+ * extent values will be written by this method; may be null.
+ * @param offset specifies the beginning index of where to write extent
+ * values into extentsArr; exactly four entries are written starting at
+ * this index (see table above); if extentsArr is null then this offset
+ * is ignored.
+ * @param reverse if true, the order in which the query hits
+ * are returned is reversed.
+ * @return a non-null enumeration of all [distinct] R-tree entries
+ * (objKeys) whose extents intersect the specified rectangular query area.
+ * @exception IllegalArgumentException if xMin is not less than or equal to
+ * xMax or if yMin is not less than or equal to yMax.
+ * @exception ArrayIndexOutOfBoundsException if extentsArr is not null
+ * and if it cannot be written to in the index range
+ * [offset, offset+3].
+ */
+ public final SpacialEntry2DEnumerator queryOverlap(final float xMin, final float yMin,
+ final float xMax, final float yMax,
+ final float[] extentsArr, final int offset,
+ final boolean reverse) {
+ if (!(xMin <= xMax))
+ throw new IllegalArgumentException("xMin <= xMax not true");
+
+ if (!(yMin <= yMax))
+ throw new IllegalArgumentException("yMin <= yMax not true");
+
+ if (extentsArr != null) {
+ extentsArr[offset] = Float.POSITIVE_INFINITY;
+ extentsArr[offset + 1] = Float.POSITIVE_INFINITY;
+ extentsArr[offset + 2] = Float.NEGATIVE_INFINITY;
+ extentsArr[offset + 3] = Float.NEGATIVE_INFINITY;
+ }
+
+ m_nodeStack.push(m_root); // This stack should always be left empty after
+ // previous uses.
+
+ m_extentsStack[0] = m_MBR[0];
+ m_extentsStack[1] = m_MBR[1];
+ m_extentsStack[2] = m_MBR[2];
+ m_extentsStack[3] = m_MBR[3];
+
+ final ObjStack nodeStack = new ObjStack();
+ final ObjStack stackStack = new ObjStack();
+ final int totalCount = queryOverlap(m_nodeStack, m_extentsStack, nodeStack, stackStack,
+ xMin, yMin, xMax, yMax, extentsArr, offset, reverse);
+
+ // m_nodeStack will now be empty.
+ return new OverlapEnumerator(totalCount, nodeStack, stackStack, reverse);
+ }
+
+ /*
+ * Returns the number of entries under n that overlap specified query
+ * rectangle. Nodes are added to the node stack - internal nodes added
+ * recursively contain only overlapping entries, and leaf nodes added
+ * should be iterated through to find overlapping entries.
+ * (In fact internal nodes added to the node
+ * stack are completely contained within specified query rectangle.)
+ * An important property is that every node on the returned node stack
+ * will recursively contain at least one entry that overlaps the
+ * query rectangle, unless n is completely empty. If n is completely
+ * empty, it is expected that its MBR [represented by xMinN, yMinN,
+ * xMaxN, and yMaxN] be the infinite inverted rectangle (that is, its
+ * min values should all be Float.POSITIVE_INFINITY and its max values
+ * should all be Float.NEGATIVE_INFINITY).
+ * I'd like to discuss stackStack. Objects of type IntStack are tossed onto
+ * this stack (in other words, stackStack is a stack of IntStack). For every
+ * leaf node on nodeStack, stackStack will contain
+ * a corresponding IntStack - if the IntStack is null,
+ * then every entry in that leaf node overlaps the query rectangle; if
+ * the IntStack is of positive length, then the IntStack contains indices of
+ * entries that overlap the query rectangle.
+ */
+ private final static int queryOverlap(final ObjStack unprocessedNodes, final float[] extStack,
+ final ObjStack nodeStack, final ObjStack stackStack,
+ final float xMinQ, final float yMinQ, final float xMaxQ,
+ final float yMaxQ, final float[] extents, final int off,
+ final boolean reverse) { // Depth first search.
+
+ final int incr = reverse ? (-1) : 1;
+ int count = 0;
+ int extOff = 4; // Into extStack.
+
+ while (unprocessedNodes.size() > 0) {
+ final Node n = (Node) unprocessedNodes.pop();
+ extOff -= 4;
+
+ if ((xMinQ <= extStack[extOff]) // Rectangle Q contains
+ && (xMaxQ >= extStack[extOff + 2]) // rectangle N - trivially
+ && (yMinQ <= extStack[extOff + 1]) // include node.
+ && (yMaxQ >= extStack[extOff + 3])) {
+ if (isLeafNode(n)) {
+ count += n.entryCount;
+ stackStack.push(null);
+ } else {
+ count += n.data.deepCount;
+ }
+
+ nodeStack.push(n);
+
+ if (extents != null) {
+ extents[off] = Math.min(extents[off], extStack[extOff]);
+ extents[off + 1] = Math.min(extents[off + 1], extStack[extOff + 1]);
+ extents[off + 2] = Math.max(extents[off + 2], extStack[extOff + 2]);
+ extents[off + 3] = Math.max(extents[off + 3], extStack[extOff + 3]);
+ }
+ } else { // Cannot trivially include node; must recurse.
+
+ if (isLeafNode(n)) {
+ final IntStack stack = new IntStack();
+
+ for (int cntr = n.entryCount, i = reverse ? 0 : (n.entryCount - 1); cntr > 0;
+ cntr--, i -= incr) {
+ // Overlaps test of two rectangles.
+ if ((Math.max(xMinQ, n.xMins[i]) <= Math.min(xMaxQ, n.xMaxs[i]))
+ && (Math.max(yMinQ, n.yMins[i]) <= Math.min(yMaxQ, n.yMaxs[i]))) {
+ stack.push(i);
+
+ if (extents != null) {
+ extents[off] = Math.min(extents[off], n.xMins[i]);
+ extents[off + 1] = Math.min(extents[off + 1], n.yMins[i]);
+ extents[off + 2] = Math.max(extents[off + 2], n.xMaxs[i]);
+ extents[off + 3] = Math.max(extents[off + 3], n.yMaxs[i]);
+ }
+ }
+ }
+
+ if (stack.size() > 0) {
+ count += stack.size();
+ stackStack.push(stack);
+ nodeStack.push(n);
+ }
+ } else { // Internal node.
+
+ for (int cntr = n.entryCount, i = reverse ? (n.entryCount - 1) : 0; cntr > 0;
+ cntr--, i += incr) {
+ // Overlaps test of two rectangles.
+ if ((Math.max(xMinQ, n.xMins[i]) <= Math.min(xMaxQ, n.xMaxs[i]))
+ && (Math.max(yMinQ, n.yMins[i]) <= Math.min(yMaxQ, n.yMaxs[i]))) {
+ unprocessedNodes.push(n.data.children[i]);
+ extStack[extOff++] = n.xMins[i];
+ extStack[extOff++] = n.yMins[i];
+ extStack[extOff++] = n.xMaxs[i];
+ extStack[extOff++] = n.yMaxs[i];
+ }
+ }
+ }
+ }
+ }
+
+ return count;
+ }
+
+ private final static class Node implements java.io.Serializable {
+ private Node parent;
+ private int entryCount = 0;
+ private final float[] xMins;
+ private final float[] yMins;
+ private final float[] xMaxs;
+ private final float[] yMaxs;
+ private final int[] objKeys; // null if and only if internal node.
+ private final InternalNodeData data;
+
+ private Node(final int maxBranches, final boolean leafNode) {
+ xMins = new float[maxBranches];
+ yMins = new float[maxBranches];
+ xMaxs = new float[maxBranches];
+ yMaxs = new float[maxBranches];
+
+ if (leafNode) {
+ objKeys = new int[maxBranches];
+ data = null;
+ } else {
+ objKeys = null;
+ data = new InternalNodeData(maxBranches);
+ }
+ }
+ }
+
+ private final static class InternalNodeData implements java.io.Serializable {
+ private int deepCount = 0;
+ private final Node[] children;
+
+ private InternalNodeData(final int maxBranches) {
+ children = new Node[maxBranches];
+ }
+ }
+
+ private final static class OverlapEnumerator implements SpacialEntry2DEnumerator {
+ private int count;
+ private final ObjStack nodeStack;
+ private final ObjStack stackStack;
+ private final boolean reverse;
+ private final int inxIncr;
+ private Node currentLeafNode;
+ private IntStack currentStack;
+ private int currentInx;
+ private int boundaryInx;
+
+ private OverlapEnumerator(final int totalCount, final ObjStack nodeStack,
+ final ObjStack stackStack, final boolean reverse) {
+ count = totalCount;
+ this.nodeStack = nodeStack;
+ this.stackStack = stackStack;
+ this.reverse = reverse;
+ inxIncr = this.reverse ? (-1) : 1;
+ computeNextLeafNode();
+ }
+
+ public final int numRemaining() {
+ return count;
+ }
+
+ public final int nextExtents(final float[] extentsArr, final int offset) {
+ final Node leaf = currentLeafNode;
+ final int inx;
+
+ if (currentStack == null) {
+ inx = currentInx;
+ currentInx += inxIncr;
+
+ if (currentInx == boundaryInx)
+ computeNextLeafNode();
+ } else {
+ inx = currentStack.pop();
+
+ if (currentStack.size() == 0)
+ computeNextLeafNode();
+ }
+
+ count--;
+ extentsArr[offset] = leaf.xMins[inx];
+ extentsArr[offset + 1] = leaf.yMins[inx];
+ extentsArr[offset + 2] = leaf.xMaxs[inx];
+ extentsArr[offset + 3] = leaf.yMaxs[inx];
+
+ return leaf.objKeys[inx];
+ }
+
+ public final int nextInt() {
+ int returnThis = -1;
+
+ if (currentStack == null) {
+ returnThis = currentLeafNode.objKeys[currentInx];
+ currentInx += inxIncr;
+
+ if (currentInx == boundaryInx) {
+ computeNextLeafNode();
+ }
+ } else {
+ returnThis = currentLeafNode.objKeys[currentStack.pop()];
+
+ if (currentStack.size() == 0) {
+ computeNextLeafNode();
+ }
+ }
+
+ count--;
+
+ return returnThis;
+ }
+
+ private final void computeNextLeafNode() {
+ if (nodeStack.size() == 0) {
+ currentLeafNode = null;
+ currentStack = null;
+
+ return;
+ }
+
+ Node next;
+
+ while (true) {
+ next = (Node) nodeStack.pop();
+
+ if (isLeafNode(next)) {
+ currentLeafNode = next;
+ currentStack = (IntStack) stackStack.pop(); // May be null.
+
+ if (currentStack == null) { // Otherwise these vars are ignored.
+
+ if (reverse) {
+ currentInx = currentLeafNode.entryCount - 1;
+ boundaryInx = -1;
+ } else {
+ currentInx = 0;
+ boundaryInx = currentLeafNode.entryCount;
+ }
+ }
+
+ return;
+ }
+
+ for (int cntr = next.entryCount, i = reverse ? 0 : (next.entryCount - 1); cntr > 0;
+ cntr--, i -= inxIncr) {
+ // This 'if' statement could be taken out of 'for' loop for speed.
+ if (isLeafNode(next.data.children[i]))
+ stackStack.push(null);
+
+ nodeStack.push(next.data.children[i]);
+ }
+ }
+ }
+ }
+}
diff --git a/corelibs/geom.rtree/src/main/java/cytoscape/geom/rtree/test/ArrayTestMethod1.java b/corelibs/geom.rtree/src/main/java/cytoscape/geom/rtree/test/ArrayTestMethod1.java
new file mode 100644
index 0000000..615a891
--- /dev/null
+++ b/corelibs/geom.rtree/src/main/java/cytoscape/geom/rtree/test/ArrayTestMethod1.java
@@ -0,0 +1,150 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.geom.rtree.test;
+
+import java.io.IOException;
+import java.io.InputStream;
+
+
+/**
+ *
+ */
+public class ArrayTestMethod1 {
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ * @throws IOException DOCUMENT ME!
+ */
+ public static void main(String[] args) throws Exception {
+ final int nodeSize = Integer.parseInt(args[0]);
+ final int nPrime = 51437;
+ final Node[] nodeArr = new Node[nPrime];
+
+ for (int i = 0; i < nodeArr.length; i++)
+ nodeArr[i] = new Node(nodeSize);
+ // Read random data from standard in, populate node rectangles.
+ {
+ double sqrtN = Math.sqrt((double) nPrime);
+ InputStream in = System.in;
+ byte[] buff = new byte[16 * nodeSize];
+ int inx = 0;
+ int off = 0;
+ int read;
+
+ while ((inx < nodeArr.length) && ((read = in.read(buff, off, buff.length - off)) > 0)) {
+ off += read;
+
+ if (off < buff.length)
+ continue;
+ else
+ off = 0;
+
+ for (int i = 0; i < nodeSize; i++) {
+ int nonnegative = 0x7fffffff & assembleInt(buff, 0 + (i * 16));
+ double centerX = ((double) nonnegative) / ((double) 0x7fffffff);
+ nonnegative = 0x7fffffff & assembleInt(buff, 4 + (i * 16));
+
+ double centerY = ((double) nonnegative) / ((double) 0x7fffffff);
+ nonnegative = 0x7fffffff & assembleInt(buff, 8 + (i * 16));
+
+ double width = (((double) nonnegative) / ((double) 0x7fffffff)) / sqrtN;
+ nonnegative = 0x7fffffff & assembleInt(buff, 12 + (i * 16));
+
+ double height = (((double) nonnegative) / ((double) 0x7fffffff)) / sqrtN;
+ nodeArr[inx].xMins[i] = centerX - (width / 2.0d);
+ nodeArr[inx].yMins[i] = centerY - (height / 2.0d);
+ nodeArr[inx].xMaxs[i] = centerX + (width / 2.0d);
+ nodeArr[inx].yMaxs[i] = centerY + (height / 2.0d);
+ }
+
+ inx++;
+ }
+
+ if (inx < nodeArr.length)
+ throw new IOException("premature end of input");
+ }
+ // Sequential access test.
+ {
+ final int incr = 797;
+ double foo;
+ int inx = 0;
+ final long millisBegin = System.currentTimeMillis();
+
+ for (int i = 0; i < nodeArr.length; i++) {
+ final Node n = nodeArr[inx];
+
+ for (int j = 0; j < nodeSize; j++) {
+ foo = n.xMins[j] + n.yMins[j] + n.xMaxs[j] + n.yMaxs[j];
+
+ // System.out.println(foo);
+ }
+
+ inx = (inx + incr) % nodeArr.length;
+ }
+
+ final long millisEnd = System.currentTimeMillis();
+ System.err.println("sequential rectangle access took " + (millisEnd - millisBegin)
+ + " milliseconds");
+ }
+ }
+
+ private static int assembleInt(byte[] bytes, int offset) {
+ int firstByte = (((int) bytes[offset]) & 0x000000ff) << 24;
+ int secondByte = (((int) bytes[offset + 1]) & 0x000000ff) << 16;
+ int thirdByte = (((int) bytes[offset + 2]) & 0x000000ff) << 8;
+ int fourthByte = (((int) bytes[offset + 3]) & 0x000000ff) << 0;
+
+ return firstByte | secondByte | thirdByte | fourthByte;
+ }
+
+ private final static class Node {
+ private final double[] xMins;
+ private final double[] yMins;
+ private final double[] xMaxs;
+ private final double[] yMaxs;
+
+ private Node(final int size) {
+ xMins = new double[size];
+ yMins = new double[size];
+ xMaxs = new double[size];
+ yMaxs = new double[size];
+ }
+ }
+}
diff --git a/corelibs/geom.rtree/src/main/java/cytoscape/geom/rtree/test/ArrayTestMethod2.java b/corelibs/geom.rtree/src/main/java/cytoscape/geom/rtree/test/ArrayTestMethod2.java
new file mode 100644
index 0000000..3a51a9d
--- /dev/null
+++ b/corelibs/geom.rtree/src/main/java/cytoscape/geom/rtree/test/ArrayTestMethod2.java
@@ -0,0 +1,148 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.geom.rtree.test;
+
+import java.io.IOException;
+import java.io.InputStream;
+
+
+/**
+ *
+ */
+public class ArrayTestMethod2 {
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ * @throws IOException DOCUMENT ME!
+ */
+ public static void main(String[] args) throws Exception {
+ final int nodeSize = Integer.parseInt(args[0]);
+ final int nPrime = 51437;
+ final Node[] nodeArr = new Node[nPrime];
+
+ for (int i = 0; i < nodeArr.length; i++)
+ nodeArr[i] = new Node(nodeSize);
+ // Read random data from standard in, populate node rectangles.
+ {
+ double sqrtN = Math.sqrt((double) nPrime);
+ InputStream in = System.in;
+ byte[] buff = new byte[16 * nodeSize];
+ int inx = 0;
+ int off = 0;
+ int read;
+
+ while ((inx < nodeArr.length) && ((read = in.read(buff, off, buff.length - off)) > 0)) {
+ off += read;
+
+ if (off < buff.length)
+ continue;
+ else
+ off = 0;
+
+ for (int i = 0; i < nodeSize; i++) {
+ int nonnegative = 0x7fffffff & assembleInt(buff, 0 + (i * 16));
+ double centerX = ((double) nonnegative) / ((double) 0x7fffffff);
+ nonnegative = 0x7fffffff & assembleInt(buff, 4 + (i * 16));
+
+ double centerY = ((double) nonnegative) / ((double) 0x7fffffff);
+ nonnegative = 0x7fffffff & assembleInt(buff, 8 + (i * 16));
+
+ double width = (((double) nonnegative) / ((double) 0x7fffffff)) / sqrtN;
+ nonnegative = 0x7fffffff & assembleInt(buff, 12 + (i * 16));
+
+ double height = (((double) nonnegative) / ((double) 0x7fffffff)) / sqrtN;
+ nodeArr[inx].arrs[i][0] = centerX - (width / 2.0d);
+ nodeArr[inx].arrs[i][1] = centerY - (height / 2.0d);
+ nodeArr[inx].arrs[i][2] = centerX + (width / 2.0d);
+ nodeArr[inx].arrs[i][3] = centerY + (height / 2.0d);
+ }
+
+ inx++;
+ }
+
+ if (inx < nodeArr.length)
+ throw new IOException("premature end of input");
+ }
+ // Sequential access test.
+ {
+ final int incr = 797;
+ double foo;
+ int inx = 0;
+ final long millisBegin = System.currentTimeMillis();
+
+ for (int i = 0; i < nodeArr.length; i++) {
+ final Node n = nodeArr[inx];
+
+ for (int j = 0; j < nodeSize; j++) {
+ final double[] arr = n.arrs[j];
+ foo = arr[0] + arr[1] + arr[2] + arr[3];
+
+ // System.out.println(foo);
+ }
+
+ inx = (inx + incr) % nodeArr.length;
+ }
+
+ final long millisEnd = System.currentTimeMillis();
+ System.err.println("sequential rectangle access took " + (millisEnd - millisBegin)
+ + " milliseconds");
+ }
+ }
+
+ private static int assembleInt(byte[] bytes, int offset) {
+ int firstByte = (((int) bytes[offset]) & 0x000000ff) << 24;
+ int secondByte = (((int) bytes[offset + 1]) & 0x000000ff) << 16;
+ int thirdByte = (((int) bytes[offset + 2]) & 0x000000ff) << 8;
+ int fourthByte = (((int) bytes[offset + 3]) & 0x000000ff) << 0;
+
+ return firstByte | secondByte | thirdByte | fourthByte;
+ }
+
+ private final static class Node {
+ private final double[][] arrs;
+
+ private Node(final int size) {
+ arrs = new double[size][];
+
+ for (int i = 0; i < arrs.length; i++)
+ arrs[i] = new double[4];
+ }
+ }
+}
diff --git a/corelibs/geom.rtree/src/main/java/cytoscape/geom/rtree/test/ArrayTestMethod3.java b/corelibs/geom.rtree/src/main/java/cytoscape/geom/rtree/test/ArrayTestMethod3.java
new file mode 100644
index 0000000..4807631
--- /dev/null
+++ b/corelibs/geom.rtree/src/main/java/cytoscape/geom/rtree/test/ArrayTestMethod3.java
@@ -0,0 +1,148 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.geom.rtree.test;
+
+import java.io.IOException;
+import java.io.InputStream;
+
+
+/**
+ *
+ */
+public class ArrayTestMethod3 {
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ * @throws IOException DOCUMENT ME!
+ */
+ public static void main(String[] args) throws Exception {
+ final int nodeSize = Integer.parseInt(args[0]);
+ final int yMinOffset = nodeSize;
+ final int xMaxOffset = nodeSize * 2;
+ final int yMaxOffset = nodeSize * 3;
+ final int nPrime = 51437;
+ final Node[] nodeArr = new Node[nPrime];
+
+ for (int i = 0; i < nodeArr.length; i++)
+ nodeArr[i] = new Node(nodeSize);
+ // Read random data from standard in, populate node rectangles.
+ {
+ double sqrtN = Math.sqrt((double) nPrime);
+ InputStream in = System.in;
+ byte[] buff = new byte[16 * nodeSize];
+ int inx = 0;
+ int off = 0;
+ int read;
+
+ while ((inx < nodeArr.length) && ((read = in.read(buff, off, buff.length - off)) > 0)) {
+ off += read;
+
+ if (off < buff.length)
+ continue;
+ else
+ off = 0;
+
+ for (int i = 0; i < nodeSize; i++) {
+ int nonnegative = 0x7fffffff & assembleInt(buff, 0 + (i * 16));
+ double centerX = ((double) nonnegative) / ((double) 0x7fffffff);
+ nonnegative = 0x7fffffff & assembleInt(buff, 4 + (i * 16));
+
+ double centerY = ((double) nonnegative) / ((double) 0x7fffffff);
+ nonnegative = 0x7fffffff & assembleInt(buff, 8 + (i * 16));
+
+ double width = (((double) nonnegative) / ((double) 0x7fffffff)) / sqrtN;
+ nonnegative = 0x7fffffff & assembleInt(buff, 12 + (i * 16));
+
+ double height = (((double) nonnegative) / ((double) 0x7fffffff)) / sqrtN;
+ nodeArr[inx].arr[i] = centerX - (width / 2.0d);
+ nodeArr[inx].arr[i + yMinOffset] = centerY - (height / 2.0d);
+ nodeArr[inx].arr[i + xMaxOffset] = centerX + (width / 2.0d);
+ nodeArr[inx].arr[i + yMaxOffset] = centerY + (height / 2.0d);
+ }
+
+ inx++;
+ }
+
+ if (inx < nodeArr.length)
+ throw new IOException("premature end of input");
+ }
+ // Sequential access test.
+ {
+ final int incr = 797;
+ double foo;
+ int inx = 0;
+ final long millisBegin = System.currentTimeMillis();
+
+ for (int i = 0; i < nodeArr.length; i++) {
+ final Node n = nodeArr[inx];
+
+ for (int j = 0; j < nodeSize; j++) {
+ foo = n.arr[j] + n.arr[j + yMinOffset] + n.arr[j + xMaxOffset]
+ + n.arr[j + yMaxOffset];
+
+ // System.out.println(foo);
+ }
+
+ inx = (inx + incr) % nodeArr.length;
+ }
+
+ final long millisEnd = System.currentTimeMillis();
+ System.err.println("sequential rectangle access took " + (millisEnd - millisBegin)
+ + " milliseconds");
+ }
+ }
+
+ private static int assembleInt(byte[] bytes, int offset) {
+ int firstByte = (((int) bytes[offset]) & 0x000000ff) << 24;
+ int secondByte = (((int) bytes[offset + 1]) & 0x000000ff) << 16;
+ int thirdByte = (((int) bytes[offset + 2]) & 0x000000ff) << 8;
+ int fourthByte = (((int) bytes[offset + 3]) & 0x000000ff) << 0;
+
+ return firstByte | secondByte | thirdByte | fourthByte;
+ }
+
+ private final static class Node {
+ private final double[] arr;
+
+ private Node(final int size) {
+ arr = new double[size * 4];
+ }
+ }
+}
diff --git a/corelibs/geom.rtree/src/main/java/cytoscape/geom/rtree/test/ArrayTestMethod4.java b/corelibs/geom.rtree/src/main/java/cytoscape/geom/rtree/test/ArrayTestMethod4.java
new file mode 100644
index 0000000..fe1053e
--- /dev/null
+++ b/corelibs/geom.rtree/src/main/java/cytoscape/geom/rtree/test/ArrayTestMethod4.java
@@ -0,0 +1,145 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.geom.rtree.test;
+
+import java.io.IOException;
+import java.io.InputStream;
+
+
+/**
+ *
+ */
+public class ArrayTestMethod4 {
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ * @throws IOException DOCUMENT ME!
+ */
+ public static void main(String[] args) throws Exception {
+ final int nodeSize = Integer.parseInt(args[0]);
+ final int nPrime = 51437;
+ final Node[] nodeArr = new Node[nPrime];
+
+ for (int i = 0; i < nodeArr.length; i++)
+ nodeArr[i] = new Node(nodeSize);
+ // Read random data from standard in, populate node rectangles.
+ {
+ double sqrtN = Math.sqrt((double) nPrime);
+ InputStream in = System.in;
+ byte[] buff = new byte[16 * nodeSize];
+ int inx = 0;
+ int off = 0;
+ int read;
+
+ while ((inx < nodeArr.length) && ((read = in.read(buff, off, buff.length - off)) > 0)) {
+ off += read;
+
+ if (off < buff.length)
+ continue;
+ else
+ off = 0;
+
+ for (int i = 0; i < nodeSize; i++) {
+ int nonnegative = 0x7fffffff & assembleInt(buff, 0 + (i * 16));
+ double centerX = ((double) nonnegative) / ((double) 0x7fffffff);
+ nonnegative = 0x7fffffff & assembleInt(buff, 4 + (i * 16));
+
+ double centerY = ((double) nonnegative) / ((double) 0x7fffffff);
+ nonnegative = 0x7fffffff & assembleInt(buff, 8 + (i * 16));
+
+ double width = (((double) nonnegative) / ((double) 0x7fffffff)) / sqrtN;
+ nonnegative = 0x7fffffff & assembleInt(buff, 12 + (i * 16));
+
+ double height = (((double) nonnegative) / ((double) 0x7fffffff)) / sqrtN;
+ nodeArr[inx].arr[i * 4] = centerX - (width / 2.0d);
+ nodeArr[inx].arr[(i * 4) + 1] = centerY - (height / 2.0d);
+ nodeArr[inx].arr[(i * 4) + 2] = centerX + (width / 2.0d);
+ nodeArr[inx].arr[(i * 4) + 3] = centerY + (height / 2.0d);
+ }
+
+ inx++;
+ }
+
+ if (inx < nodeArr.length)
+ throw new IOException("premature end of input");
+ }
+ // Sequential access test.
+ {
+ final int incr = 797;
+ final int nodeSizeX4 = nodeSize * 4;
+ double foo;
+ int inx = 0;
+ final long millisBegin = System.currentTimeMillis();
+
+ for (int i = 0; i < nodeArr.length; i++) {
+ final Node n = nodeArr[inx];
+
+ for (int j = 0; j < nodeSizeX4; j = j + 4) {
+ foo = n.arr[j] + n.arr[j + 1] + n.arr[j + 2] + n.arr[j + 3];
+
+ // System.out.println(foo);
+ }
+
+ inx = (inx + incr) % nodeArr.length;
+ }
+
+ final long millisEnd = System.currentTimeMillis();
+ System.err.println("sequential rectangle access took " + (millisEnd - millisBegin)
+ + " milliseconds");
+ }
+ }
+
+ private static int assembleInt(byte[] bytes, int offset) {
+ int firstByte = (((int) bytes[offset]) & 0x000000ff) << 24;
+ int secondByte = (((int) bytes[offset + 1]) & 0x000000ff) << 16;
+ int thirdByte = (((int) bytes[offset + 2]) & 0x000000ff) << 8;
+ int fourthByte = (((int) bytes[offset + 3]) & 0x000000ff) << 0;
+
+ return firstByte | secondByte | thirdByte | fourthByte;
+ }
+
+ private final static class Node {
+ private final double[] arr;
+
+ private Node(final int size) {
+ arr = new double[size * 4];
+ }
+ }
+}
diff --git a/corelibs/geom.rtree/src/main/java/cytoscape/geom/rtree/test/BasicQuietRTreeTest.java b/corelibs/geom.rtree/src/main/java/cytoscape/geom/rtree/test/BasicQuietRTreeTest.java
new file mode 100644
index 0000000..62f4536
--- /dev/null
+++ b/corelibs/geom.rtree/src/main/java/cytoscape/geom/rtree/test/BasicQuietRTreeTest.java
@@ -0,0 +1,1115 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.geom.rtree.test;
+
+import cytoscape.geom.rtree.RTree;
+
+import cytoscape.util.intr.IntBTree;
+import cytoscape.util.intr.IntEnumerator;
+
+import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
+import java.io.ObjectInputStream;
+import java.io.ObjectOutputStream;
+
+
+/**
+ *
+ */
+public class BasicQuietRTreeTest {
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ * @throws IllegalStateException DOCUMENT ME!
+ */
+ public static void main(String[] args) throws Exception {
+ RTree tree = new RTree(3);
+
+ for (int a = 0;; a++) { // BEGIN EMPTY TREE TESTS: We run our first tests when this tree empty.
+
+ float[] extentsArr = new float[4];
+ IntEnumerator iter = tree.queryOverlap(Float.NEGATIVE_INFINITY,
+ Float.NEGATIVE_INFINITY,
+ Float.POSITIVE_INFINITY,
+ Float.POSITIVE_INFINITY, extentsArr, 0, false);
+
+ if (iter.numRemaining() != 0)
+ throw new IllegalStateException("did not expect query to generate results");
+
+ if ((extentsArr[0] != Float.POSITIVE_INFINITY)
+ || (extentsArr[1] != Float.POSITIVE_INFINITY)
+ || (extentsArr[2] != Float.NEGATIVE_INFINITY)
+ || (extentsArr[3] != Float.NEGATIVE_INFINITY))
+ throw new IllegalStateException("expected query to return inverted infinite extents");
+
+ if (tree.exists(0, extentsArr, 0))
+ throw new IllegalStateException("did not expect there to be an entry");
+
+ if (tree.size() != 0)
+ throw new IllegalStateException("tree's size() is not 0");
+
+ if (a == 1)
+ break;
+
+ for (int j = 0; j < 1000; j++) {
+ final int stop = (j + 1) * 1000;
+
+ for (int k = j * 1000; k < stop; k++)
+ tree.insert(k, k, k, k + 1, k + 1);
+
+ for (int k = j * 1000; k < stop; k++)
+ tree.delete(k);
+ }
+ } // END EMPTY TREE TESTS.
+
+ tree.insert(0, 0.0f, 0.0f, 1.0f, 1.0f);
+ tree.insert(1, 2.0f, 2.0f, 3.0f, 3.0f);
+ tree.insert(2, 0.5f, 1.0f, 1.5f, 2.0f);
+
+ for (int a = 0;; a++) { // BEGIN ROOT LEAF TEST: Still before any split.
+
+ float[] extentsArr = new float[5];
+
+ for (int i = 0; i < 3; i++)
+ if (!tree.exists(i, extentsArr, 0))
+ throw new IllegalStateException("entry " + i + " does not exist");
+
+ if (tree.exists(3, extentsArr, 0))
+ throw new IllegalStateException("entry 3 exits");
+
+ if ((extentsArr[0] != 0.5) || (extentsArr[1] != 1.0) || (extentsArr[2] != 1.5)
+ || (extentsArr[3] != 2.0))
+ throw new IllegalStateException("entry's extents don't match");
+
+ if (tree.size() != 3)
+ throw new IllegalStateException("tree's size() is not 3");
+
+ IntEnumerator iter = tree.queryOverlap(Float.NEGATIVE_INFINITY,
+ Float.NEGATIVE_INFINITY,
+ Float.POSITIVE_INFINITY,
+ Float.POSITIVE_INFINITY, extentsArr, 0, false);
+
+ if (iter.numRemaining() != 3)
+ throw new IllegalStateException("expected query to generate 3 hits");
+
+ IntBTree cache = new IntBTree();
+
+ for (int i = 0; i < 3; i++)
+ cache.insert(i);
+
+ int foo = 0;
+
+ while (iter.numRemaining() > 0) {
+ cache.delete(iter.nextInt());
+ foo++;
+ }
+
+ if (foo != 3)
+ throw new IllegalStateException("iter claimed it had 3 elements but really didn't");
+
+ if (cache.size() != 0)
+ throw new IllegalStateException("iter returned wrong objKeys");
+
+ if ((extentsArr[0] != 0.0) || (extentsArr[1] != 0.0) || (extentsArr[2] != 3.0)
+ || (extentsArr[3] != 3.0))
+ throw new IllegalStateException("extents from query wrong");
+
+ iter = tree.queryOverlap(1.25f, 2.0f, 2.1f, 3.3f, extentsArr, 1, false);
+
+ if (iter.numRemaining() != 2)
+ throw new IllegalStateException("exptected query to return 2 hits");
+
+ cache.insert(1);
+ cache.insert(2);
+ foo = 0;
+
+ while (iter.numRemaining() > 0) {
+ cache.delete(iter.nextInt());
+ foo++;
+ }
+
+ if (foo != 2)
+ throw new IllegalStateException("iter claimed it had 2 elements but really didn't");
+
+ if (cache.size() != 0)
+ throw new IllegalStateException("iter returned wrong objKeys");
+
+ if ((extentsArr[1] != 0.5) || (extentsArr[2] != 1.0) || (extentsArr[3] != 3.0)
+ || (extentsArr[4] != 3.0))
+ throw new IllegalStateException("extents from query wrong");
+
+ if (a == 1)
+ break;
+
+ for (int j = 0; j < 1000; j++) {
+ final int stop = ((j + 1) * 1000) + 3;
+
+ for (int k = (j * 1000) + 3; k < stop; k++)
+ tree.insert(k, -(k + 1), -(k + 1), -k, -k);
+
+ for (int k = (j * 1000) + 3; k < stop; k++)
+ tree.delete(k);
+ }
+ } // END ROOT LEAF TEST.
+
+ tree.insert(3, 2.5f, 0.5f, 3.5f, 1.5f);
+
+ for (int a = 0;; a++) { // BEGIN SIMPLE ROOT SPLIT TEST: Minimum # entries with a split.
+
+ float[] extentsArr = new float[4];
+
+ for (int i = 0; i < 4; i++)
+ if (!tree.exists(i, extentsArr, 0))
+ throw new IllegalStateException("entry " + i + " does not exist");
+
+ if (tree.exists(4, extentsArr, 0))
+ throw new IllegalStateException("entry 4 exists");
+
+ if ((extentsArr[0] != 2.5) || (extentsArr[1] != 0.5) || (extentsArr[2] != 3.5)
+ || (extentsArr[3] != 1.5))
+ throw new IllegalStateException("entry's extents incorrect");
+
+ if (tree.size() != 4)
+ throw new IllegalStateException("tree's size() is not 4");
+
+ IntEnumerator iter = tree.queryOverlap(Float.NEGATIVE_INFINITY,
+ Float.NEGATIVE_INFINITY,
+ Float.POSITIVE_INFINITY,
+ Float.POSITIVE_INFINITY, extentsArr, 0, false);
+
+ if (iter.numRemaining() != 4)
+ throw new IllegalStateException("expected query to generate 4 hits");
+
+ IntBTree cache = new IntBTree();
+
+ for (int i = 0; i < 4; i++)
+ cache.insert(i);
+
+ int foo = 0;
+
+ while (iter.numRemaining() > 0) {
+ cache.delete(iter.nextInt());
+ foo++;
+ }
+
+ if (foo != 4)
+ throw new IllegalStateException("iter claimed it had 3 elements but really didn't");
+
+ if (cache.size() != 0)
+ throw new IllegalStateException("iter returned wrong objKeys");
+
+ if ((extentsArr[0] != 0.0) || (extentsArr[1] != 0.0) || (extentsArr[2] != 3.5)
+ || (extentsArr[3] != 3.0))
+ throw new IllegalStateException("extents from query wrong");
+
+ iter = tree.queryOverlap(2.0f, 0.5f, 2.2f, 1.9f, extentsArr, 0, false);
+
+ if (iter.numRemaining() != 0)
+ throw new IllegalStateException("expected query to generate 0 hits");
+
+ if ((extentsArr[0] != Float.POSITIVE_INFINITY)
+ || (extentsArr[1] != Float.POSITIVE_INFINITY)
+ || (extentsArr[2] != Float.NEGATIVE_INFINITY)
+ || (extentsArr[3] != Float.NEGATIVE_INFINITY))
+ throw new IllegalStateException("query extents - expected inverted infinite");
+
+ iter = tree.queryOverlap(Float.NEGATIVE_INFINITY, 1.1f, Float.POSITIVE_INFINITY, 1.2f,
+ extentsArr, 0, false);
+
+ if (iter.numRemaining() != 2)
+ throw new IllegalStateException("expected query to generate 2 hits");
+
+ cache.insert(2);
+ cache.insert(3);
+ foo = 0;
+
+ while (iter.numRemaining() > 0) {
+ cache.delete(iter.nextInt());
+ foo++;
+ }
+
+ if (foo != 2)
+ throw new IllegalStateException("iter claimed it had 2 elements but really didn't");
+
+ if (cache.size() != 0)
+ throw new IllegalStateException("query returned wrong objKeys");
+
+ if ((extentsArr[0] != 0.5) || (extentsArr[1] != 0.5) || (extentsArr[2] != 3.5)
+ || (extentsArr[3] != 2.0))
+ throw new IllegalStateException("extents from query wrong");
+
+ iter = tree.queryOverlap(1.0f, 1.0f, 1.0f, 1.0f, extentsArr, 0, false);
+
+ if (iter.numRemaining() != 2)
+ throw new IllegalStateException("expected query to generate 2 hits");
+
+ cache.insert(0);
+ cache.insert(2);
+ foo = 0;
+
+ while (iter.numRemaining() > 0) {
+ cache.delete(iter.nextInt());
+ foo++;
+ }
+
+ if (foo != 2)
+ throw new IllegalStateException("iter claimed it had 2 elements but really didn't");
+
+ if (cache.size() != 0)
+ throw new IllegalStateException("query returned wrong objKeys");
+
+ if ((extentsArr[0] != 0.0) || (extentsArr[1] != 0.0) || (extentsArr[2] != 1.5)
+ || (extentsArr[3] != 2.0))
+ throw new IllegalStateException("extents from query wrong");
+
+ if (a == 1)
+ break;
+
+ for (int j = 0; j < 1000; j++) {
+ final int stop = ((j + 1) * 1000) + 4;
+
+ for (int k = (j * 1000) + 4; k < stop; k++)
+ tree.insert(k, k, -(k + 1), k + 3, -(k - 2));
+
+ for (int k = (j * 1000) + 4; k < stop; k++)
+ tree.delete(k);
+ }
+ } // END SIMPLE ROOT SPLIT TEST.
+
+ { // BEGIN EXCEPTION HANDLING TEST.
+
+ boolean exceptionCaught = false;
+
+ try {
+ tree.insert(0, 0.0f, 0.0f, 1.0f, 1.0f);
+ } catch (IllegalStateException e) {
+ exceptionCaught = true;
+ }
+
+ if (!exceptionCaught)
+ throw new IllegalStateException("expected exception for duplicate objKey");
+
+ exceptionCaught = false;
+
+ try {
+ tree.insert(-1, 0.0f, 0.0f, 1.0f, 1.0f);
+ } catch (IllegalArgumentException e) {
+ exceptionCaught = true;
+ }
+
+ if (!exceptionCaught)
+ throw new IllegalStateException("expected exception for negative objKey");
+
+ exceptionCaught = false;
+
+ try {
+ tree.insert(5, 1.0f, 1.0f, 0.0f, 0.0f);
+ } catch (IllegalArgumentException e) {
+ exceptionCaught = true;
+ }
+
+ if (!exceptionCaught)
+ throw new IllegalStateException("expected exception for min > max");
+ } // END EXCEPTION HANDLING TEST.
+
+ tree.insert(4, 3.0f, -0.25f, 4.0f, 0.75f);
+ tree.insert(5, -0.5f, 2.5f, 0.5f, 3.5f);
+ tree.insert(6, 2.75f, 2.25f, 3.75f, 3.25f);
+ tree.insert(7, 1.25f, 1.75f, 2.25f, 2.75f);
+ tree.insert(8, 1.0f, 6.0f, 2.0f, 7.0f);
+ tree.insert(9, -2.0f, 1.0f, -1.0f, 2.0f);
+
+ for (int a = 0;; a++) { // BEGIN DEPTH THREE TEST.
+
+ float[] extentsArr = new float[4];
+
+ for (int i = 9; i >= 0; i--)
+ if (!tree.exists(i, extentsArr, 0))
+ throw new IllegalStateException("entry " + i + " does not exist");
+
+ if (tree.exists(-1, extentsArr, 0) || tree.exists(10, extentsArr, 0))
+ throw new IllegalStateException("bad entry exists");
+
+ if ((extentsArr[0] != 0.0) || (extentsArr[1] != 0.0) || (extentsArr[2] != 1.0)
+ || (extentsArr[3] != 1.0))
+ throw new IllegalStateException("objKey 0 extents incorrect");
+
+ if (tree.size() != 10)
+ throw new IllegalStateException("tree's size() is not 10");
+
+ IntEnumerator iter = tree.queryOverlap(Float.NEGATIVE_INFINITY,
+ Float.NEGATIVE_INFINITY,
+ Float.POSITIVE_INFINITY,
+ Float.POSITIVE_INFINITY, extentsArr, 0, false);
+
+ if (iter.numRemaining() != 10)
+ throw new IllegalStateException("expected query to generate 10 hits");
+
+ IntBTree cache = new IntBTree();
+
+ for (int i = 0; i < 10; i++)
+ cache.insert(i);
+
+ int foo = 0;
+
+ while (iter.numRemaining() > 0) {
+ cache.delete(iter.nextInt());
+ foo++;
+ }
+
+ if (foo != 10)
+ throw new IllegalStateException("iter claimed it had 10 elements but really didn't");
+
+ if (cache.size() != 0)
+ throw new IllegalStateException("iter returned wrong objKeys");
+
+ if ((extentsArr[0] != -2.0) || (extentsArr[1] != -0.25) || (extentsArr[2] != 4.0)
+ || (extentsArr[3] != 7.0))
+ throw new IllegalStateException("extents from query wrong");
+
+ iter = tree.queryOverlap(1.0f, 1.25f, 3.0f, 5.0f, extentsArr, 0, false);
+
+ if (iter.numRemaining() != 5)
+ throw new IllegalStateException("expected query to generate 5 hits");
+
+ cache.insert(1);
+ cache.insert(2);
+ cache.insert(3);
+ cache.insert(6);
+ cache.insert(7);
+ foo = 0;
+
+ while (iter.numRemaining() > 0) {
+ cache.delete(iter.nextInt());
+ foo++;
+ }
+
+ if (foo != 5)
+ throw new IllegalStateException("iter claimed it had 5 elements but really didn't");
+
+ if (cache.size() != 0)
+ throw new IllegalStateException("query returned wrong objKeys");
+
+ if ((extentsArr[0] != 0.5) || (extentsArr[1] != 0.5) || (extentsArr[2] != 3.75)
+ || (extentsArr[3] != 3.25))
+ throw new IllegalStateException("extents from query wrong");
+
+ iter = tree.queryOverlap(-1.5f, 0.25f, 0.25f, 3.0f, extentsArr, 0, false);
+
+ if (iter.numRemaining() != 3)
+ throw new IllegalStateException("expected query to generate 3 hits");
+
+ cache.insert(0);
+ cache.insert(5);
+ cache.insert(9);
+ foo = 0;
+
+ while (iter.numRemaining() > 0) {
+ cache.delete(iter.nextInt());
+ foo++;
+ }
+
+ if (foo != 3)
+ throw new IllegalStateException("query claimed it had 3 elements but really didn't");
+
+ if (cache.size() != 0)
+ throw new IllegalStateException("query returned wrong objKeys");
+
+ if ((extentsArr[0] != -2.0) || (extentsArr[1] != 0.0) || (extentsArr[2] != 1.0)
+ || (extentsArr[3] != 3.5))
+ throw new IllegalStateException("extents from query wrong");
+
+ iter = tree.queryOverlap(1.5f, 6.5f, 1.5f, 6.5f, extentsArr, 0, false);
+
+ if (iter.numRemaining() != 1)
+ throw new IllegalStateException("expected query to generate 1 hit");
+
+ cache.insert(8);
+ foo = 0;
+
+ while (iter.numRemaining() > 0) {
+ cache.delete(iter.nextInt());
+ foo++;
+ }
+
+ if (foo != 1)
+ throw new IllegalStateException("query claimed it had 1 element but really didn't");
+
+ if (cache.size() != 0)
+ throw new IllegalStateException("query returned wrong objKey");
+
+ if ((extentsArr[0] != 1.0) || (extentsArr[1] != 6.0) || (extentsArr[2] != 2.0)
+ || (extentsArr[3] != 7.0))
+ throw new IllegalStateException("extents from query wrong");
+
+ iter = tree.queryOverlap(3.0f, 5.0f, 8.0f, 9.0f, extentsArr, 0, false);
+
+ if (iter.numRemaining() != 0)
+ throw new IllegalStateException("did not expect any query hits");
+
+ iter = tree.queryOverlap(-100.0f, -100.0f, -99.0f, -99.0f, extentsArr, 0, false);
+
+ if (iter.numRemaining() != 0)
+ throw new IllegalStateException("did not expect any query hits");
+
+ iter = tree.queryOverlap(-1.0f, 0.75f, 3.0f, 6.0f, extentsArr, 0, false);
+
+ if (iter.numRemaining() != 10)
+ throw new IllegalStateException("expected 10 query hits");
+
+ if (a == 1)
+ break;
+
+ for (int j = 0; j < 1000; j++) {
+ final int stop = ((j + 1) * 1000) + 10;
+
+ for (int k = (j * 1000) + 10; k < stop; k++)
+ tree.insert(k, k, k, k + 2, k + 2);
+
+ for (int k = (j * 1000) + 10; k < stop; k++)
+ tree.delete(k);
+ }
+ } // END DEPTH THREE TEST.
+
+ for (int a = 0;; a++) {
+ tree.insert(10, 2.0f, 4.0f, 3.0f, 5.0f);
+ tree.insert(11, 1.5f, 3.75f, 3.5f, 4.25f);
+ tree.insert(12, 2.5f, 3.5f, 3.0f, 5.5f);
+ tree.insert(13, -4.0f, 6.0f, -2.0f, 8.0f);
+ tree.insert(14, -4.25f, 5.75f, 2.25f, 8.25f);
+ tree.insert(15, 2.0f, -1.0f, 2.0f, -1.0f);
+ tree.insert(16, -1.25f, 0.5f, -1.25f, 3.0f);
+ tree.insert(17, -0.5f, -0.5f, 1.5f, 0.5f);
+ tree.insert(18, 0.25f, 4.0f, 1.25f, 5.0f);
+ tree.insert(19, 4.0f, 1.0f, 5.0f, 2.0f);
+ tree.insert(20, 4.0f, 3.0f, 5.0f, 4.0f);
+ tree.insert(21, 4.25f, -1.5f, 4.75f, 5.0f);
+ tree.insert(22, 3.0f, -1.75f, 5.0f, -1.0f);
+ tree.insert(23, 1.25f, 0.25f, 2.25f, 1.25f);
+ tree.insert(24, -2.0f, 9.0f, -1.0f, 10.0f);
+ tree.insert(25, 1.0f, 9.0f, 2.0f, 10.0f);
+ tree.insert(26, -2.0f, 5.0f, -1.0f, 6.0f);
+ tree.insert(27, -2.5f, 5.25f, -1.75f, 9.25f);
+
+ if (a == 1)
+ break;
+
+ for (int k = 10; k < 28; k++)
+ tree.delete(k);
+ }
+ // There are now 28 entries in the R-tree. Depth must be at least 4.
+ { // BEGIN SERIALIZATION TEST.
+
+ ByteArrayOutputStream byteOut = new ByteArrayOutputStream();
+ ObjectOutputStream objOut = new ObjectOutputStream(byteOut);
+ objOut.writeObject(tree);
+ objOut.flush();
+ objOut.close();
+
+ ByteArrayInputStream byteIn = new ByteArrayInputStream(byteOut.toByteArray());
+ ObjectInputStream objIn = new ObjectInputStream(byteIn);
+ tree = (RTree) objIn.readObject();
+ objIn.close();
+ } // END SERIALIZATION TEST.
+
+ for (int a = 0;; a++) { // BEGIN DEPTH FOUR TEST.
+
+ float[] extentsArr = new float[4];
+
+ for (int i = 27; i >= 0; i--)
+ if (!tree.exists(i, extentsArr, 0))
+ throw new IllegalStateException("entry " + i + " does not exist");
+
+ if (tree.exists(28, extentsArr, 0) || tree.exists(Integer.MAX_VALUE, extentsArr, 0)
+ || tree.exists(Integer.MIN_VALUE, extentsArr, 0))
+ throw new IllegalStateException("bad entry exists");
+
+ if ((extentsArr[0] != 0.0) || (extentsArr[1] != 0.0) || (extentsArr[2] != 1.0)
+ || (extentsArr[3] != 1.0))
+ throw new IllegalStateException("objKey 0 extents incorrect");
+
+ if (tree.size() != 28)
+ throw new IllegalStateException("tree's size() is not 28");
+
+ IntEnumerator iter = tree.queryOverlap(Float.NEGATIVE_INFINITY,
+ Float.NEGATIVE_INFINITY,
+ Float.POSITIVE_INFINITY,
+ Float.POSITIVE_INFINITY, extentsArr, 0, false);
+
+ if (iter.numRemaining() != 28)
+ throw new IllegalStateException("expected query to give 28 hits");
+
+ IntBTree cache = new IntBTree();
+
+ for (int i = 0; i < 28; i++)
+ cache.insert(i);
+
+ int foo = 0;
+
+ while (iter.numRemaining() > 0) {
+ cache.delete(iter.nextInt());
+ foo++;
+ }
+
+ if (foo != 28)
+ throw new IllegalStateException("iter claimed it had 28 elements but really didn't");
+
+ if (cache.size() != 0)
+ throw new IllegalStateException("iter returned wrong objKeys");
+
+ if ((extentsArr[0] != -4.25) || (extentsArr[1] != -1.75) || (extentsArr[2] != 5.0)
+ || (extentsArr[3] != 10.0))
+ throw new IllegalStateException("extents from query wrong");
+
+ iter = tree.queryOverlap(-2.0f, 6.0f, -2.0f, 6.0f, extentsArr, 0, false);
+
+ if (iter.numRemaining() != 4)
+ throw new IllegalStateException("expected query to generate 4 hits");
+
+ cache.insert(13);
+ cache.insert(14);
+ cache.insert(26);
+ cache.insert(27);
+ foo = 0;
+
+ while (iter.numRemaining() > 0) {
+ cache.delete(iter.nextInt());
+ foo++;
+ }
+
+ if (foo != 4)
+ throw new IllegalStateException("iter claimed it had 4 elements but really didn't");
+
+ if (cache.size() != 0)
+ throw new IllegalStateException("iter returned wrong objKeys");
+
+ if ((extentsArr[0] != -4.25) || (extentsArr[1] != 5.0) || (extentsArr[2] != 2.25)
+ || (extentsArr[3] != 9.25))
+ throw new IllegalStateException("extents from query wrong");
+
+ iter = tree.queryOverlap(2.5f, 3.75f, 6.0f, 6.0f, extentsArr, 0, false);
+
+ if (iter.numRemaining() != 5)
+ throw new IllegalStateException("expected query to generate 5 hits");
+
+ cache.insert(10);
+ cache.insert(11);
+ cache.insert(12);
+ cache.insert(20);
+ cache.insert(21);
+ foo = 0;
+
+ while (iter.numRemaining() > 0) {
+ cache.delete(iter.nextInt());
+ foo++;
+ }
+
+ if (foo != 5)
+ throw new IllegalStateException("iter claimed it had 5 elements but really didn't");
+
+ if (cache.size() != 0)
+ throw new IllegalStateException("iter returned wrong objKeys");
+
+ if ((extentsArr[0] != 1.5) || (extentsArr[1] != -1.5) || (extentsArr[2] != 5.0)
+ || (extentsArr[3] != 5.5))
+ throw new IllegalStateException("extents from query wrong");
+
+ iter = tree.queryOverlap(1.75f, -1.5f, 3.25f, -0.5f, extentsArr, 0, false);
+
+ if (iter.numRemaining() != 2)
+ throw new IllegalStateException("expected query to generate 2 hits");
+
+ cache.insert(15);
+ cache.insert(22);
+ foo = 0;
+
+ while (iter.numRemaining() > 0) {
+ cache.delete(iter.nextInt());
+ foo++;
+ }
+
+ if (foo != 2)
+ throw new IllegalStateException("iter claimed it had 2 elements but really didn't");
+
+ if (cache.size() != 0)
+ throw new IllegalStateException("iter returned wrong objKeys");
+
+ if ((extentsArr[0] != 2.0) || (extentsArr[1] != -1.75) || (extentsArr[2] != 5.0)
+ || (extentsArr[3] != -1.0))
+ throw new IllegalStateException("extents from query wrong");
+
+ iter = tree.queryOverlap(-3.0f, -5.0f, 7.0f, 2.75f, extentsArr, 0, false);
+
+ if (iter.numRemaining() != 16)
+ throw new IllegalStateException("expected query to generate 16 hits");
+
+ cache.insert(0);
+ cache.insert(1);
+ cache.insert(2);
+ cache.insert(3);
+ cache.insert(4);
+ cache.insert(5);
+ cache.insert(6);
+ cache.insert(7);
+ cache.insert(9);
+ cache.insert(15);
+ cache.insert(16);
+ cache.insert(17);
+ cache.insert(19);
+ cache.insert(21);
+ cache.insert(22);
+ cache.insert(23);
+ foo = 0;
+
+ while (iter.numRemaining() > 0) {
+ cache.delete(iter.nextInt());
+ foo++;
+ }
+
+ if (foo != 16)
+ throw new IllegalStateException("iter claimed it had 16 elements but really didn't");
+
+ if (cache.size() != 0)
+ throw new IllegalStateException("iter returned wrong objKeys");
+
+ if ((extentsArr[0] != -2.0) || (extentsArr[1] != -1.75) || (extentsArr[2] != 5.0)
+ || (extentsArr[3] != 5.0))
+ throw new IllegalStateException("extents from query wrong");
+
+ iter = tree.queryOverlap(1.0f, 4.5f, 3.0f, 6.25f, extentsArr, 0, false);
+
+ if (iter.numRemaining() != 5)
+ throw new IllegalStateException("expected query to generate 5 hits");
+
+ cache.insert(8);
+ cache.insert(10);
+ cache.insert(12);
+ cache.insert(14);
+ cache.insert(18);
+ foo = 0;
+
+ while (iter.numRemaining() > 0) {
+ cache.delete(iter.nextInt());
+ foo++;
+ }
+
+ if (foo != 5)
+ throw new IllegalStateException("iter claimed it had 5 elements but really didn't");
+
+ if (cache.size() != 0)
+ throw new IllegalStateException("iter returned wrong objKeys");
+
+ if ((extentsArr[0] != -4.25) || (extentsArr[1] != 3.5) || (extentsArr[2] != 3.0)
+ || (extentsArr[3] != 8.25))
+ throw new IllegalStateException("extents from query wrong");
+
+ iter = tree.queryOverlap(0.75f, 0.25f, 1.5f, 0.75f, extentsArr, 0, false);
+
+ if (iter.numRemaining() != 3)
+ throw new IllegalStateException("expected query to generate 3 hits");
+
+ cache.insert(0);
+ cache.insert(17);
+ cache.insert(23);
+ foo = 0;
+
+ while (iter.numRemaining() > 0) {
+ cache.delete(iter.nextInt());
+ foo++;
+ }
+
+ if (foo != 3)
+ throw new IllegalStateException("iter claimed it had 3 elements but really didn't");
+
+ if (cache.size() != 0)
+ throw new IllegalStateException("iter returned wrong objKeys");
+
+ if ((extentsArr[0] != -0.5) || (extentsArr[1] != -0.5) || (extentsArr[2] != 2.25)
+ || (extentsArr[3] != 1.25))
+ throw new IllegalStateException("extents from query wrong");
+
+ iter = tree.queryOverlap(1.75f, -10.0f, 1.75f, 30.0f, extentsArr, 0, false);
+
+ if (iter.numRemaining() != 6)
+ throw new IllegalStateException("expected query to generate 6 hits");
+
+ cache.insert(7);
+ cache.insert(8);
+ cache.insert(11);
+ cache.insert(14);
+ cache.insert(23);
+ cache.insert(25);
+ foo = 0;
+
+ while (iter.numRemaining() > 0) {
+ cache.delete(iter.nextInt());
+ foo++;
+ }
+
+ if (foo != 6)
+ throw new IllegalStateException("iter claimed it had 6 elements but really didn't");
+
+ if (cache.size() != 0)
+ throw new IllegalStateException("iter returned wrong objKeys");
+
+ if ((extentsArr[0] != -4.25) || (extentsArr[1] != 0.25) || (extentsArr[2] != 3.5)
+ || (extentsArr[3] != 10.0))
+ throw new IllegalStateException("extents from query wrong");
+
+ iter = tree.queryOverlap(0.75f, 3.0f, 1.75f, 3.5f, extentsArr, 0, false);
+
+ if (iter.numRemaining() != 0)
+ throw new IllegalStateException("did not expect query results");
+
+ iter = tree.queryOverlap(2.5f, 1.75f, 3.75f, 1.75f, null, -1, false);
+
+ if (iter.numRemaining() != 0)
+ throw new IllegalStateException("did not expect query results");
+
+ iter = tree.queryOverlap(-2.0f, -1.0f, 4.25f, 9.0f, extentsArr, 0, false);
+
+ if (iter.numRemaining() != 28)
+ throw new IllegalStateException("expected 28 (all) query hits");
+
+ for (int i = 0; i < 28; i++)
+ cache.insert(i);
+
+ foo = 0;
+
+ while (iter.numRemaining() > 0) {
+ cache.delete(iter.nextInt());
+ foo++;
+ }
+
+ if (foo != 28)
+ throw new IllegalStateException("iter claimed it had 28 elements but really didn't");
+
+ if (cache.size() != 0)
+ throw new IllegalStateException("iter returned wrong objKeys");
+
+ if ((extentsArr[0] != -4.25) || (extentsArr[1] != -1.75) || (extentsArr[2] != 5.0)
+ || (extentsArr[3] != 10.0))
+ throw new IllegalStateException("extents from query wrong");
+
+ if (a == 1)
+ break;
+
+ for (int j = 0; j < 1000; j++) {
+ final int stop = ((j + 1) * 1000) + 28;
+
+ for (int k = (j * 1000) + 28; k < stop; k++)
+ tree.insert(k, k, k, k + 5, k + 5);
+
+ for (int k = (j * 1000) + 28; k < stop; k++)
+ tree.delete(k);
+ }
+ } // END DEPTH FOUR TEST.
+
+ { // BEGIN ORDER-PRESERVING SUBQUERY TEST.
+
+ if (tree.size() != 28)
+ throw new IllegalStateException("expected 28 elements in tree");
+
+ final int[] allOrdered = new int[28];
+ IntEnumerator iter = tree.queryOverlap(Float.NEGATIVE_INFINITY,
+ Float.NEGATIVE_INFINITY,
+ Float.POSITIVE_INFINITY,
+ Float.POSITIVE_INFINITY, null, 0, false);
+
+ if (iter.numRemaining() != 28)
+ throw new IllegalStateException("expected 28 elements in iteration");
+
+ for (int i = 0; i < 28; i++)
+ allOrdered[i] = iter.nextInt();
+
+ iter = tree.queryOverlap(0.0f, 0.0f, Float.POSITIVE_INFINITY, Float.POSITIVE_INFINITY,
+ null, 0, false);
+
+ if (iter.numRemaining() != 20)
+ throw new IllegalStateException("expected 20 elements in iteration");
+
+ int prevInx = -1;
+
+ for (int i = 0; i < 20; i++) {
+ final int element = iter.nextInt();
+ int foundInx = -2;
+
+ for (int j = 0;; j++) {
+ if (allOrdered[j] == element) {
+ foundInx = j;
+
+ break;
+ }
+ }
+
+ if (!(foundInx > prevInx)) {
+ throw new IllegalStateException("order in subquery not preserved");
+ }
+
+ prevInx = foundInx;
+ }
+
+ if (iter.numRemaining() != 0)
+ throw new IllegalStateException("more elements remain in iteration");
+
+ iter = tree.queryOverlap(-10.0f, -5.0f, 1.0f, 4.0f, null, 0, false);
+
+ if (iter.numRemaining() != 7)
+ throw new IllegalStateException("expected 7 elements in iteration");
+
+ prevInx = -1;
+
+ for (int i = 0; i < 7; i++) {
+ final int element = iter.nextInt();
+ int foundInx = -2;
+
+ for (int j = 0;; j++) {
+ if (allOrdered[j] == element) {
+ foundInx = j;
+
+ break;
+ }
+ }
+
+ if (!(foundInx > prevInx)) {
+ throw new IllegalStateException("order in subquery not preserved");
+ }
+
+ prevInx = foundInx;
+ }
+
+ if (iter.numRemaining() != 0)
+ throw new IllegalStateException("more elements remain in iteration");
+
+ iter = tree.queryOverlap(-99.0f, -5.0f, 1.0f, 30.0f, null, 0, false);
+
+ if (iter.numRemaining() != 14)
+ throw new IllegalStateException("expected 14 elements in iteration");
+
+ prevInx = -1;
+
+ for (int i = 0; i < 14; i++) {
+ final int element = iter.nextInt();
+ int foundInx = -2;
+
+ for (int j = 0;; j++) {
+ if (allOrdered[j] == element) {
+ foundInx = j;
+
+ break;
+ }
+ }
+
+ if (!(foundInx > prevInx)) {
+ throw new IllegalStateException("order in subquery not preserved");
+ }
+
+ prevInx = foundInx;
+ }
+
+ if (iter.numRemaining() != 0)
+ throw new IllegalStateException("more elements remain in iteration");
+
+ iter = tree.queryOverlap(-3.0f, 4.0f, 10.0f, 20.0f, null, 0, false);
+
+ if (iter.numRemaining() != 13)
+ throw new IllegalStateException("expected 13 elements in iteration");
+
+ prevInx = -1;
+
+ for (int i = 0; i < 13; i++) {
+ final int element = iter.nextInt();
+ int foundInx = -2;
+
+ for (int j = 0;; j++) {
+ if (allOrdered[j] == element) {
+ foundInx = j;
+
+ break;
+ }
+ }
+
+ if (!(foundInx > prevInx)) {
+ throw new IllegalStateException("order in subquery not preserved");
+ }
+
+ prevInx = foundInx;
+ }
+
+ if (iter.numRemaining() != 0)
+ throw new IllegalStateException("more elements remain in iteration");
+ } // END ORDER-PRESERVING SUBQUERY TEST.
+
+ { // BEGIN REVERSE QUERY TEST.
+
+ if (tree.size() != 28)
+ throw new IllegalStateException("expected 28 elements in tree");
+
+ final int[] allOrdered = new int[28];
+ IntEnumerator iter = tree.queryOverlap(Float.NEGATIVE_INFINITY,
+ Float.NEGATIVE_INFINITY,
+ Float.POSITIVE_INFINITY,
+ Float.POSITIVE_INFINITY, null, 0, false);
+
+ if (iter.numRemaining() != 28)
+ throw new IllegalStateException("expected 28 elements in iteration");
+
+ for (int i = 0; i < 28; i++)
+ allOrdered[i] = iter.nextInt();
+
+ iter = tree.queryOverlap(0.0f, 0.0f, Float.POSITIVE_INFINITY, Float.POSITIVE_INFINITY,
+ null, 0, true);
+
+ if (iter.numRemaining() != 20)
+ throw new IllegalStateException("expected 20 elements in iteration");
+
+ int prevInx = Integer.MAX_VALUE - 1;
+
+ for (int i = 0; i < 20; i++) {
+ final int element = iter.nextInt();
+ int foundInx = Integer.MAX_VALUE;
+
+ for (int j = 0;; j++) {
+ if (allOrdered[j] == element) {
+ foundInx = j;
+
+ break;
+ }
+ }
+
+ if (!(foundInx < prevInx)) {
+ throw new IllegalStateException("not reverse order");
+ }
+
+ prevInx = foundInx;
+ }
+
+ if (iter.numRemaining() != 0)
+ throw new IllegalStateException("more elements remain in iteration");
+
+ iter = tree.queryOverlap(-10.0f, -5.0f, 1.0f, 4.0f, null, 0, true);
+
+ if (iter.numRemaining() != 7)
+ throw new IllegalStateException("expected 7 elements in iteration");
+
+ prevInx = Integer.MAX_VALUE - 1;
+
+ for (int i = 0; i < 7; i++) {
+ final int element = iter.nextInt();
+ int foundInx = Integer.MAX_VALUE;
+
+ for (int j = 0;; j++) {
+ if (allOrdered[j] == element) {
+ foundInx = j;
+
+ break;
+ }
+ }
+
+ if (!(foundInx < prevInx)) {
+ throw new IllegalStateException("not reverse order");
+ }
+
+ prevInx = foundInx;
+ }
+
+ if (iter.numRemaining() != 0)
+ throw new IllegalStateException("more elements remain in iteration");
+
+ iter = tree.queryOverlap(-99.0f, -5.0f, 1.0f, 30.0f, null, 0, true);
+
+ if (iter.numRemaining() != 14)
+ throw new IllegalStateException("expected 14 elements in iteration");
+
+ prevInx = Integer.MAX_VALUE - 1;
+
+ for (int i = 0; i < 14; i++) {
+ final int element = iter.nextInt();
+ int foundInx = Integer.MAX_VALUE;
+
+ for (int j = 0;; j++) {
+ if (allOrdered[j] == element) {
+ foundInx = j;
+
+ break;
+ }
+ }
+
+ if (!(foundInx < prevInx)) {
+ throw new IllegalStateException("not reverse order");
+ }
+
+ prevInx = foundInx;
+ }
+
+ if (iter.numRemaining() != 0)
+ throw new IllegalStateException("more elements remain in iteration");
+
+ iter = tree.queryOverlap(-3.0f, 4.0f, 10.0f, 20.0f, null, 0, true);
+
+ if (iter.numRemaining() != 13)
+ throw new IllegalStateException("expected 13 elements in iteration");
+
+ prevInx = Integer.MAX_VALUE - 1;
+
+ for (int i = 0; i < 13; i++) {
+ final int element = iter.nextInt();
+ int foundInx = Integer.MAX_VALUE;
+
+ for (int j = 0;; j++) {
+ if (allOrdered[j] == element) {
+ foundInx = j;
+
+ break;
+ }
+ }
+
+ if (!(foundInx < prevInx)) {
+ throw new IllegalStateException("not reverse order");
+ }
+
+ prevInx = foundInx;
+ }
+
+ if (iter.numRemaining() != 0)
+ throw new IllegalStateException("more elements remain in iteration");
+ } // END REVERSE QUERY TEST.
+ }
+}
diff --git a/corelibs/geom.rtree/src/main/java/cytoscape/geom/rtree/test/DEPENDENCIES b/corelibs/geom.rtree/src/main/java/cytoscape/geom/rtree/test/DEPENDENCIES
new file mode 100644
index 0000000..96abee9
--- /dev/null
+++ b/corelibs/geom.rtree/src/main/java/cytoscape/geom/rtree/test/DEPENDENCIES
@@ -0,0 +1 @@
+cytoscape.geom.rtree
diff --git a/corelibs/geom.rtree/src/main/java/cytoscape/geom/rtree/test/NoRTreeQueryPerformance.java b/corelibs/geom.rtree/src/main/java/cytoscape/geom/rtree/test/NoRTreeQueryPerformance.java
new file mode 100644
index 0000000..b35e871
--- /dev/null
+++ b/corelibs/geom.rtree/src/main/java/cytoscape/geom/rtree/test/NoRTreeQueryPerformance.java
@@ -0,0 +1,233 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.geom.rtree.test;
+
+import cytoscape.util.intr.MinIntHeap;
+
+import java.io.IOException;
+import java.io.InputStream;
+
+
+/**
+ *
+ */
+public class NoRTreeQueryPerformance {
+ /**
+ * Analagous to RTreeQueryPerformance, but using linear search method
+ * instead of R-tree.
+ */
+ public static void main(String[] args) throws Exception {
+ final int N;
+ final double[] xMins;
+ final double[] yMins;
+ final double[] xMaxs;
+ final double[] yMaxs;
+ // Populate the arrays with entries.
+ {
+ N = Integer.parseInt(args[0]);
+ xMins = new double[N];
+ yMins = new double[N];
+ xMaxs = new double[N];
+ yMaxs = new double[N];
+
+ double sqrtN = Math.sqrt((double) N);
+ InputStream in = System.in;
+ byte[] buff = new byte[16];
+ int inx = 0;
+ int off = 0;
+ int read;
+
+ while ((inx < N) && ((read = in.read(buff, off, buff.length - off)) > 0)) {
+ off += read;
+
+ if (off < buff.length)
+ continue;
+ else
+ off = 0;
+
+ int nonnegative = 0x7fffffff & assembleInt(buff, 0);
+ double centerX = ((double) nonnegative) / ((double) 0x7fffffff);
+ nonnegative = 0x7fffffff & assembleInt(buff, 4);
+
+ double centerY = ((double) nonnegative) / ((double) 0x7fffffff);
+ nonnegative = 0x7fffffff & assembleInt(buff, 8);
+
+ double width = (((double) nonnegative) / ((double) 0x7fffffff)) / sqrtN;
+ nonnegative = 0x7fffffff & assembleInt(buff, 12);
+
+ double height = (((double) nonnegative) / ((double) 0x7fffffff)) / sqrtN;
+ xMins[inx] = centerX - (width / 2.0d);
+ yMins[inx] = centerY - (height / 2.0d);
+ xMaxs[inx] = centerX + (width / 2.0d);
+ yMaxs[inx] = centerY + (height / 2.0d);
+ inx++;
+ }
+
+ if (inx < N)
+ throw new IOException("premature end of input");
+ }
+
+ final MinIntHeap[] pointQueries;
+ // Test 121 Point queries.
+ {
+ pointQueries = new MinIntHeap[121];
+
+ for (int i = 0; i < pointQueries.length; i++)
+ pointQueries[i] = new MinIntHeap();
+
+ for (int i = 0; i < 3; i++) {
+ System.gc();
+ Thread.sleep(1000);
+ }
+
+ final long millisBegin = System.currentTimeMillis();
+ int inx = 0;
+ double currX = -0.1d;
+
+ for (int i = 0; i < 11; i++) {
+ currX += 0.1d;
+
+ double currY = -0.1d;
+
+ for (int j = 0; j < 11; j++) {
+ currY += 0.1d;
+
+ final MinIntHeap heap = pointQueries[inx++];
+
+ for (int k = 0; k < N; k++)
+ if ((currX >= xMins[k]) && (currX <= xMaxs[k]) && (currY >= yMins[k])
+ && (currY <= yMaxs[k]))
+ heap.toss(k);
+ }
+ }
+
+ final long millisEnd = System.currentTimeMillis();
+ System.err.println("point queries took " + (millisEnd - millisBegin) + " milliseconds");
+ }
+
+ final MinIntHeap[] areaQueries;
+ // Test 5 area queries - each area is 0.1 X 0.1.
+ {
+ areaQueries = new MinIntHeap[5];
+
+ for (int i = 0; i < areaQueries.length; i++)
+ areaQueries[i] = new MinIntHeap();
+
+ for (int i = 0; i < 3; i++) {
+ System.gc();
+ Thread.sleep(1000);
+ }
+
+ final long millisBegin = System.currentTimeMillis();
+
+ for (int i = 0; i < 5; i++) {
+ final double xMin = ((double) i) * 0.1d;
+ final double yMin = ((double) i) * 0.1d;
+ final double xMax = ((double) (i + 1)) * 0.1d;
+ final double yMax = ((double) (i + 1)) * 0.1d;
+ final MinIntHeap heap = areaQueries[i];
+
+ for (int j = 0; j < N; j++)
+ if ((Math.max(xMin, xMins[j]) <= Math.min(xMax, xMaxs[j]))
+ && (Math.max(yMin, yMins[j]) <= Math.min(yMax, yMaxs[j])))
+ heap.toss(j);
+ }
+
+ final long millisEnd = System.currentTimeMillis();
+ System.err.println("area queries took " + (millisEnd - millisBegin) + " milliseconds");
+ }
+
+ final int[] countQueries;
+ // Test 5 count queries - each area is 0.6 X 0.6.
+ {
+ countQueries = new int[5];
+
+ for (int i = 0; i < 3; i++) {
+ System.gc();
+ Thread.sleep(1000);
+ }
+
+ final long millisBegin = System.currentTimeMillis();
+
+ for (int i = 0; i < 5; i++) {
+ final double xMin = ((double) i) * 0.1d;
+ final double yMin = ((double) i) * 0.1d;
+ final double xMax = ((double) (i + 6)) * 0.1d;
+ final double yMax = ((double) (i + 6)) * 0.1d;
+
+ for (int j = 0; j < N; j++)
+ if ((Math.max(xMin, xMins[j]) <= Math.min(xMax, xMaxs[j]))
+ && (Math.max(yMin, yMins[j]) <= Math.min(yMax, yMaxs[j])))
+ countQueries[i]++;
+ }
+
+ final long millisEnd = System.currentTimeMillis();
+ System.err.println("count queries took " + (millisEnd - millisBegin) + " milliseconds");
+ }
+
+ for (int i = 0; i < pointQueries.length; i++) {
+ final MinIntHeap heap = pointQueries[i];
+
+ while (heap.size() > 0)
+ System.out.print(" " + heap.deleteMin());
+
+ System.out.println();
+ }
+
+ for (int i = 0; i < areaQueries.length; i++) {
+ final MinIntHeap heap = areaQueries[i];
+
+ while (heap.size() > 0)
+ System.out.print(" " + heap.deleteMin());
+
+ System.out.println();
+ }
+
+ for (int i = 0; i < countQueries.length; i++) {
+ System.out.println(countQueries[i]);
+ }
+ }
+
+ private static int assembleInt(byte[] bytes, int offset) {
+ int firstByte = (((int) bytes[offset]) & 0x000000ff) << 24;
+ int secondByte = (((int) bytes[offset + 1]) & 0x000000ff) << 16;
+ int thirdByte = (((int) bytes[offset + 2]) & 0x000000ff) << 8;
+ int fourthByte = (((int) bytes[offset + 3]) & 0x000000ff) << 0;
+
+ return firstByte | secondByte | thirdByte | fourthByte;
+ }
+}
diff --git a/corelibs/geom.rtree/src/main/java/cytoscape/geom/rtree/test/RTreeQueryPerformance.java b/corelibs/geom.rtree/src/main/java/cytoscape/geom/rtree/test/RTreeQueryPerformance.java
new file mode 100644
index 0000000..34e5a49
--- /dev/null
+++ b/corelibs/geom.rtree/src/main/java/cytoscape/geom/rtree/test/RTreeQueryPerformance.java
@@ -0,0 +1,231 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.geom.rtree.test;
+
+import cytoscape.geom.rtree.RTree;
+
+import cytoscape.util.intr.IntEnumerator;
+import cytoscape.util.intr.MinIntHeap;
+
+import java.io.IOException;
+import java.io.InputStream;
+
+
+/**
+ *
+ */
+public class RTreeQueryPerformance {
+ /**
+ * For given N, creates N rectangles whose centers are in the space
+ * [0,1] X [0,1]. Each rectangle has width and height no greater
+ * than 1/sqrt(N). The location of the centers of the rectangles
+ * and the choice of width and height for each rectangle is determined
+ * by the input stream, which in most cases will be a randomly generated
+ * stream of bytes. Please see the actual code for an explanation of
+ * how the input stream of bytes is converted into the rectangle
+ * information.
+ */
+ public static void main(String[] args) throws Exception {
+ final RTree tree;
+ // Populate the tree with entries.
+ {
+ int branches = Integer.parseInt(args[0]);
+ int N = Integer.parseInt(args[1]);
+ tree = new RTree(branches);
+
+ double sqrtN = Math.sqrt((double) N);
+ InputStream in = System.in;
+ byte[] buff = new byte[16];
+ int inx = 0;
+ int off = 0;
+ int read;
+
+ while ((inx < N) && ((read = in.read(buff, off, buff.length - off)) > 0)) {
+ off += read;
+
+ if (off < buff.length)
+ continue;
+ else
+ off = 0;
+
+ int nonnegative = 0x7fffffff & assembleInt(buff, 0);
+ double centerX = ((double) nonnegative) / ((double) 0x7fffffff);
+ nonnegative = 0x7fffffff & assembleInt(buff, 4);
+
+ double centerY = ((double) nonnegative) / ((double) 0x7fffffff);
+ nonnegative = 0x7fffffff & assembleInt(buff, 8);
+
+ double width = (((double) nonnegative) / ((double) 0x7fffffff)) / sqrtN;
+ nonnegative = 0x7fffffff & assembleInt(buff, 12);
+
+ double height = (((double) nonnegative) / ((double) 0x7fffffff)) / sqrtN;
+ tree.insert(inx, (float) (centerX - (width / 2.0d)),
+ (float) (centerY - (height / 2.0d)),
+ (float) (centerX + (width / 2.0d)), (float) (centerY + (height / 2.0d)));
+ inx++;
+ }
+
+ if (inx < N)
+ throw new IOException("premature end of input");
+ }
+
+ final MinIntHeap[] pointQueries;
+ // Test 121 Point queries.
+ {
+ pointQueries = new MinIntHeap[121];
+
+ for (int i = 0; i < pointQueries.length; i++)
+ pointQueries[i] = new MinIntHeap();
+
+ for (int i = 0; i < 3; i++) {
+ System.gc();
+ Thread.sleep(1000);
+ }
+
+ final long millisBegin = System.currentTimeMillis();
+ int inx = 0;
+ float currX = -0.1f;
+
+ for (int i = 0; i < 11; i++) {
+ currX += 0.1f;
+
+ float currY = -0.1f;
+
+ for (int j = 0; j < 11; j++) {
+ currY += 0.1f;
+
+ final IntEnumerator iter = tree.queryOverlap(currX, currY, currX, currY, null,
+ 0, false);
+ final MinIntHeap heap = pointQueries[inx++];
+
+ while (iter.numRemaining() > 0)
+ heap.toss(iter.nextInt());
+ }
+ }
+
+ final long millisEnd = System.currentTimeMillis();
+ System.err.println("point queries took " + (millisEnd - millisBegin) + " milliseconds");
+ }
+
+ final MinIntHeap[] areaQueries;
+ // Test 5 area queries - each area is 0.1 X 0.1.
+ {
+ areaQueries = new MinIntHeap[5];
+
+ for (int i = 0; i < areaQueries.length; i++)
+ areaQueries[i] = new MinIntHeap();
+
+ for (int i = 0; i < 3; i++) {
+ System.gc();
+ Thread.sleep(1000);
+ }
+
+ final long millisBegin = System.currentTimeMillis();
+
+ for (int i = 0; i < 5; i++) {
+ final IntEnumerator iter = tree.queryOverlap(((float) i) * 0.1f,
+ ((float) i) * 0.1f,
+ ((float) (i + 1)) * 0.1f,
+ ((float) (i + 1)) * 0.1f, null, 0,
+ false);
+ final MinIntHeap heap = areaQueries[i];
+
+ while (iter.numRemaining() > 0)
+ heap.toss(iter.nextInt());
+ }
+
+ final long millisEnd = System.currentTimeMillis();
+ System.err.println("area queries took " + (millisEnd - millisBegin) + " milliseconds");
+ }
+
+ final int[] countQueries;
+ // Test 5 count queries - each area is 0.6 X 0.6.
+ {
+ countQueries = new int[5];
+
+ for (int i = 0; i < 3; i++) {
+ System.gc();
+ Thread.sleep(1000);
+ }
+
+ final long millisBegin = System.currentTimeMillis();
+
+ for (int i = 0; i < 5; i++) {
+ final IntEnumerator iter = tree.queryOverlap(((float) i) * 0.1f,
+ ((float) i) * 0.1f,
+ ((float) (i + 6)) * 0.1f,
+ ((float) (i + 6)) * 0.1f, null, 0,
+ false);
+ countQueries[i] = iter.numRemaining();
+ }
+
+ final long millisEnd = System.currentTimeMillis();
+ System.err.println("count queries took " + (millisEnd - millisBegin) + " milliseconds");
+ }
+
+ for (int i = 0; i < pointQueries.length; i++) {
+ final MinIntHeap heap = pointQueries[i];
+
+ while (heap.size() > 0)
+ System.out.print(" " + heap.deleteMin());
+
+ System.out.println();
+ }
+
+ for (int i = 0; i < areaQueries.length; i++) {
+ final MinIntHeap heap = areaQueries[i];
+
+ while (heap.size() > 0)
+ System.out.print(" " + heap.deleteMin());
+
+ System.out.println();
+ }
+
+ for (int i = 0; i < countQueries.length; i++) {
+ System.out.println(countQueries[i]);
+ }
+ }
+
+ private static int assembleInt(byte[] bytes, int offset) {
+ int firstByte = (((int) bytes[offset]) & 0x000000ff) << 24;
+ int secondByte = (((int) bytes[offset + 1]) & 0x000000ff) << 16;
+ int thirdByte = (((int) bytes[offset + 2]) & 0x000000ff) << 8;
+ int fourthByte = (((int) bytes[offset + 3]) & 0x000000ff) << 0;
+
+ return firstByte | secondByte | thirdByte | fourthByte;
+ }
+}
diff --git a/corelibs/geom.rtree/src/main/java/cytoscape/geom/rtree/test/RTreeSerializationPerformance.java b/corelibs/geom.rtree/src/main/java/cytoscape/geom/rtree/test/RTreeSerializationPerformance.java
new file mode 100644
index 0000000..8ab3979
--- /dev/null
+++ b/corelibs/geom.rtree/src/main/java/cytoscape/geom/rtree/test/RTreeSerializationPerformance.java
@@ -0,0 +1,144 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.geom.rtree.test;
+
+import cytoscape.geom.rtree.RTree;
+
+import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.ObjectInputStream;
+import java.io.ObjectOutputStream;
+
+
+/**
+ *
+ */
+public class RTreeSerializationPerformance {
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ * @throws IOException DOCUMENT ME!
+ */
+ public static void main(String[] args) throws Exception {
+ RTree tree = new RTree();
+ final int N = Integer.parseInt(args[0]);
+ // Populate the tree with entries.
+ {
+ double sqrtN = Math.sqrt((double) N);
+ InputStream in = System.in;
+ byte[] buff = new byte[16];
+ int inx = 0;
+ int off = 0;
+ int read;
+
+ while ((inx < N) && ((read = in.read(buff, off, buff.length - off)) > 0)) {
+ off += read;
+
+ if (off < buff.length)
+ continue;
+ else
+ off = 0;
+
+ int nonnegative = 0x7fffffff & assembleInt(buff, 0);
+ double centerX = ((double) nonnegative) / ((double) 0x7fffffff);
+ nonnegative = 0x7fffffff & assembleInt(buff, 4);
+
+ double centerY = ((double) nonnegative) / ((double) 0x7fffffff);
+ nonnegative = 0x7fffffff & assembleInt(buff, 8);
+
+ double width = (((double) nonnegative) / ((double) 0x7fffffff)) / sqrtN;
+ nonnegative = 0x7fffffff & assembleInt(buff, 12);
+
+ double height = (((double) nonnegative) / ((double) 0x7fffffff)) / sqrtN;
+ tree.insert(inx, (float) (centerX - (width / 2.0d)),
+ (float) (centerY - (height / 2.0d)),
+ (float) (centerX + (width / 2.0d)), (float) (centerY + (height / 2.0d)));
+ inx++;
+ }
+
+ if (inx < N)
+ throw new IOException("premature end of input");
+
+ for (inx = 0; inx < N; inx += 2) { // Delete half of the entries.
+ tree.delete(inx);
+ }
+ }
+
+ final byte[] serializedData;
+
+ {
+ ByteArrayOutputStream byteOut = new ByteArrayOutputStream();
+ ObjectOutputStream objOut = new ObjectOutputStream(byteOut);
+ final long millisBegin = System.currentTimeMillis();
+ objOut.writeObject(tree);
+ objOut.flush();
+ objOut.close();
+
+ final long millisEnd = System.currentTimeMillis();
+ System.err.println("serialization took " + (millisEnd - millisBegin) + " milliseconds");
+ serializedData = byteOut.toByteArray();
+ }
+
+ System.err.println("serialized stream is " + serializedData.length + " bytes long");
+
+ {
+ ByteArrayInputStream byteIn = new ByteArrayInputStream(serializedData);
+ final long millisBegin = System.currentTimeMillis();
+ ObjectInputStream objIn = new ObjectInputStream(byteIn);
+ tree = (RTree) objIn.readObject();
+ objIn.close();
+
+ final long millisEnd = System.currentTimeMillis();
+ System.err.println("deserialization took " + (millisEnd - millisBegin)
+ + " milliseconds");
+ }
+ }
+
+ private static int assembleInt(byte[] bytes, int offset) {
+ int firstByte = (((int) bytes[offset]) & 0x000000ff) << 24;
+ int secondByte = (((int) bytes[offset + 1]) & 0x000000ff) << 16;
+ int thirdByte = (((int) bytes[offset + 2]) & 0x000000ff) << 8;
+ int fourthByte = (((int) bytes[offset + 3]) & 0x000000ff) << 0;
+
+ return firstByte | secondByte | thirdByte | fourthByte;
+ }
+}
diff --git a/corelibs/geom.rtree/src/main/java/cytoscape/geom/rtree/test/RTreeUpdatePerformance.java b/corelibs/geom.rtree/src/main/java/cytoscape/geom/rtree/test/RTreeUpdatePerformance.java
new file mode 100644
index 0000000..f017cce
--- /dev/null
+++ b/corelibs/geom.rtree/src/main/java/cytoscape/geom/rtree/test/RTreeUpdatePerformance.java
@@ -0,0 +1,301 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.geom.rtree.test;
+
+import cytoscape.geom.rtree.RTree;
+
+import java.io.IOException;
+import java.io.InputStream;
+
+
+/**
+ *
+ */
+public class RTreeUpdatePerformance {
+ /**
+ * For given N, creates N rectangles whose centers are in the space
+ * [0,1] X [0,1]. Each rectangle has width and height no greater
+ * than 1/sqrt(N). The location of the centers of the rectangles
+ * and the choice of width and height for each rectangle is determined
+ * by the input stream, which in most cases will be a randomly generated
+ * stream of bytes. Please see the actual code for an explanation of
+ * how the input stream of bytes is converted into the rectangle
+ * information.
+ */
+ public static void main(String[] args) throws Exception {
+ final float[] data;
+ final int N = Integer.parseInt(args[1]);
+ final int branches = Integer.parseInt(args[0]);
+ // Populate the array with entries.
+ {
+ data = new float[N * 4];
+
+ double sqrtN = Math.sqrt((double) N);
+ InputStream in = System.in;
+ byte[] buff = new byte[16];
+ int inx = 0;
+ int off = 0;
+ int read;
+
+ while ((inx < N) && ((read = in.read(buff, off, buff.length - off)) > 0)) {
+ off += read;
+
+ if (off < buff.length)
+ continue;
+ else
+ off = 0;
+
+ int nonnegative = 0x7fffffff & assembleInt(buff, 0);
+ double centerX = ((double) nonnegative) / ((double) 0x7fffffff);
+ nonnegative = 0x7fffffff & assembleInt(buff, 4);
+
+ double centerY = ((double) nonnegative) / ((double) 0x7fffffff);
+ nonnegative = 0x7fffffff & assembleInt(buff, 8);
+
+ double width = (((double) nonnegative) / ((double) 0x7fffffff)) / sqrtN;
+ nonnegative = 0x7fffffff & assembleInt(buff, 12);
+
+ double height = (((double) nonnegative) / ((double) 0x7fffffff)) / sqrtN;
+ data[inx * 4] = (float) (centerX - (width / 2.0d));
+ data[(inx * 4) + 1] = (float) (centerY - (height / 2.0d));
+ data[(inx * 4) + 2] = (float) (centerX + (width / 2.0d));
+ data[(inx * 4) + 3] = (float) (centerY + (height / 2.0d));
+ inx++;
+ }
+
+ if (inx < N)
+ throw new IOException("premature end of input");
+ }
+
+ final RTree tree = new RTree(branches);
+ // Initial insertion test.
+ {
+ for (int i = 0; i < 2; i++) {
+ System.gc();
+ Thread.sleep(1000);
+ }
+
+ final long millisBegin = System.currentTimeMillis();
+ int objKey = 0;
+ int inx = 0;
+
+ while (objKey < N) {
+ tree.insert(objKey++, data[inx++], data[inx++], data[inx++], data[inx++]);
+ }
+
+ final long millisEnd = System.currentTimeMillis();
+ System.err.println("initial insertions took " + (millisEnd - millisBegin)
+ + " milliseconds");
+ }
+ // Initial area query test.
+ {
+ for (int i = 0; i < 2; i++) {
+ System.gc();
+ Thread.sleep(1000);
+ }
+
+ final long millisBegin = System.currentTimeMillis();
+
+ for (int i = 0; i < 5; i++) {
+ tree.queryOverlap(((float) i) * 0.1f, ((float) i) * 0.1f, ((float) (i + 1)) * 0.1f,
+ ((float) (i + 1)) * 0.1f, null, 0, false);
+ }
+
+ final long millisEnd = System.currentTimeMillis();
+ System.err.println("initial area queries (5) took " + (millisEnd - millisBegin)
+ + " milliseconds");
+ }
+ // Initial point query test.
+ {
+ for (int i = 0; i < 2; i++) {
+ System.gc();
+ Thread.sleep(1000);
+ }
+
+ final long millisBegin = System.currentTimeMillis();
+
+ for (int i = 0; i < 5; i++) {
+ tree.queryOverlap(((float) i) * 0.1f, ((float) i) * 0.1f, ((float) i) * 0.1f,
+ ((float) i) * 0.1f, null, 0, false);
+ }
+
+ final long millisEnd = System.currentTimeMillis();
+ System.err.println("initial point queries (5) took " + (millisEnd - millisBegin)
+ + " milliseconds");
+ }
+ // Initial extents test.
+ {
+ for (int i = 0; i < 2; i++) {
+ System.gc();
+ Thread.sleep(1000);
+ }
+
+ final float[] extents = new float[4];
+ final long millisBegin = System.currentTimeMillis();
+ int objKey = 0;
+
+ while (objKey < N) {
+ tree.exists(objKey++, extents, 0);
+ }
+
+ final long millisEnd = System.currentTimeMillis();
+ System.err.println("all extents queries took " + (millisEnd - millisBegin)
+ + " milliseconds");
+ }
+
+ for (byte a = 0; a < 3; a++) {
+ // Update test.
+ {
+ for (int i = 0; i < 2; i++) {
+ System.gc();
+ Thread.sleep(1000);
+ }
+
+ final long millisBegin = System.currentTimeMillis();
+ int objKey = 0;
+ int inx = 0;
+
+ while (objKey < N) {
+ tree.delete(objKey);
+ tree.insert(objKey++, data[inx++], data[inx++], data[inx++], data[inx++]);
+ }
+
+ final long millisEnd = System.currentTimeMillis();
+ System.err.println("updates took " + (millisEnd - millisBegin) + " milliseconds");
+ }
+ // Repeated area query test.
+ {
+ for (int i = 0; i < 2; i++) {
+ System.gc();
+ Thread.sleep(1000);
+ }
+
+ final long millisBegin = System.currentTimeMillis();
+
+ switch (a) {
+ case 0:
+
+ for (int i = 0; i < 5; i++) {
+ tree.queryOverlap(((float) i) * 0.1f, ((float) (9 - i)) * 0.1f,
+ ((float) (i + 1)) * 0.1f, ((float) (10 - i)) * 0.1f,
+ null, 0, false);
+ }
+
+ break;
+
+ case 1:
+
+ for (int i = 0; i < 5; i++) {
+ tree.queryOverlap(((float) (9 - i)) * 0.1f, ((float) i) * 0.1f,
+ ((float) (10 - i)) * 0.1f, ((float) (i + 1)) * 0.1f,
+ null, 0, false);
+ }
+
+ break;
+
+ case 2:
+
+ for (int i = 0; i < 5; i++) {
+ tree.queryOverlap(((float) (9 - i)) * 0.1f, ((float) (9 - i)) * 0.1f,
+ ((float) (10 - i)) * 0.1f, ((float) (10 - i)) * 0.1f,
+ null, 0, false);
+ }
+
+ break;
+ }
+
+ final long millisEnd = System.currentTimeMillis();
+ System.err.println("repeated area queries (5) took " + (millisEnd - millisBegin)
+ + " milliseconds");
+ }
+ // Repeated point query test.
+ {
+ for (int i = 0; i < 2; i++) {
+ System.gc();
+ Thread.sleep(1000);
+ }
+
+ final long millisBegin = System.currentTimeMillis();
+
+ switch (a) {
+ case 0:
+
+ for (int i = 0; i < 5; i++) {
+ tree.queryOverlap(((float) i) * 0.1f, ((float) (10 - i)) * 0.1f,
+ ((float) i) * 0.1f, ((float) (10 - i)) * 0.1f, null,
+ 0, false);
+ }
+
+ break;
+
+ case 1:
+
+ for (int i = 0; i < 5; i++) {
+ tree.queryOverlap(((float) (10 - i)) * 0.1f, ((float) i) * 0.1f,
+ ((float) (10 - i)) * 0.1f, ((float) i) * 0.1f, null,
+ 0, false);
+ }
+
+ break;
+
+ case 2:
+
+ for (int i = 0; i < 5; i++) {
+ tree.queryOverlap(((float) (10 - i)) * 0.1f, ((float) (10 - i)) * 0.1f,
+ ((float) (10 - i)) * 0.1f, ((float) (10 - i)) * 0.1f,
+ null, 0, false);
+ }
+
+ break;
+ }
+
+ final long millisEnd = System.currentTimeMillis();
+ System.err.println("repeated point queries (5) took " + (millisEnd - millisBegin)
+ + " milliseconds");
+ }
+ }
+ }
+
+ private static int assembleInt(byte[] bytes, int offset) {
+ int firstByte = (((int) bytes[offset]) & 0x000000ff) << 24;
+ int secondByte = (((int) bytes[offset + 1]) & 0x000000ff) << 16;
+ int thirdByte = (((int) bytes[offset + 2]) & 0x000000ff) << 8;
+ int fourthByte = (((int) bytes[offset + 3]) & 0x000000ff) << 0;
+
+ return firstByte | secondByte | thirdByte | fourthByte;
+ }
+}
diff --git a/corelibs/geom.spacial/pom.xml b/corelibs/geom.spacial/pom.xml
new file mode 100644
index 0000000..dbe3473
--- /dev/null
+++ b/corelibs/geom.spacial/pom.xml
@@ -0,0 +1,49 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>parent</artifactId>
+ <version>2.8.4-SNAPSHOT</version>
+ </parent>
+
+ <artifactId>geom-spacial</artifactId>
+ <packaging>jar</packaging>
+
+ <name>geom-spacial</name>
+
+ <!-- bootstrap for cytoscape dependencies, namely the parent POM snapshots -->
+ <repositories>
+ <repository>
+ <id>cytoscape_snapshots</id>
+ <snapshots>
+ <enabled>true</enabled>
+ </snapshots>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <name>Cytoscape Snapshots</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/</url>
+ </repository>
+ <repository>
+ <id>cytoscape_releases</id>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ <name>Cytoscape Releases</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/releases/</url>
+ </repository>
+ </repositories>
+
+ <dependencies>
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>util-intr</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ </dependencies>
+
+</project>
+
diff --git a/corelibs/geom.spacial/src/main/java/cytoscape/geom/spacial/DEPENDENCIES b/corelibs/geom.spacial/src/main/java/cytoscape/geom/spacial/DEPENDENCIES
new file mode 100644
index 0000000..7d7a9c1
--- /dev/null
+++ b/corelibs/geom.spacial/src/main/java/cytoscape/geom/spacial/DEPENDENCIES
@@ -0,0 +1 @@
+lib:cytoscape-util-intr.jar
diff --git a/corelibs/geom.spacial/src/main/java/cytoscape/geom/spacial/MutableSpacialIndex2D.java b/corelibs/geom.spacial/src/main/java/cytoscape/geom/spacial/MutableSpacialIndex2D.java
new file mode 100644
index 0000000..61b2619
--- /dev/null
+++ b/corelibs/geom.spacial/src/main/java/cytoscape/geom/spacial/MutableSpacialIndex2D.java
@@ -0,0 +1,79 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.geom.spacial;
+
+
+/**
+ * A spacial index for objects in two dimensions, with support for
+ * insertions and deletions.
+ */
+public interface MutableSpacialIndex2D extends SpacialIndex2D {
+ /**
+ * Empties this structure of all entries.
+ */
+ public void empty();
+
+ /**
+ * Inserts a new data entry into this structure; the entry's extents
+ * are specified by the input parameters. "Extents" is a short way
+ * of saying "minimum bounding rectangle". The minimum bounding rectangle
+ * of an entry is axis-aligned, meaning that its sides are parallel to the
+ * axes of the data space.
+ * @param objKey a user-defined unique identifier used to refer to the entry
+ * being inserted in later operations; this identifier must be
+ * non-negative.
+ * @param xMin the minimum X coordinate of the entry's extents rectangle.
+ * @param yMin the minimum Y coordinate of the entry's extents rectangle.
+ * @param xMax the maximum X coordinate of the entry's extents rectangle.
+ * @param yMax the maximum Y coordinate of the entry's extents rectangle.
+ * @exception IllegalStateException if objKey is already used for an
+ * existing entry in this structure.
+ * @exception IllegalArgumentException if objKey is negative,
+ * if xMin is not less than or equal to xMax, or
+ * if yMin is not less than or equal to yMax.
+ */
+ public void insert(int objKey, float xMin, float yMin, float xMax, float yMax);
+
+ /**
+ * Deletes the specified data entry from this structure.
+ * @param objKey a user-defined identifier that was potentially used in a
+ * previous insertion.
+ * @return true if and only if objKey existed in this structure prior to this
+ * method invocation.
+ */
+ public boolean delete(int objKey);
+}
diff --git a/corelibs/geom.spacial/src/main/java/cytoscape/geom/spacial/SpacialEntry2DEnumerator.java b/corelibs/geom.spacial/src/main/java/cytoscape/geom/spacial/SpacialEntry2DEnumerator.java
new file mode 100644
index 0000000..6006e1c
--- /dev/null
+++ b/corelibs/geom.spacial/src/main/java/cytoscape/geom/spacial/SpacialEntry2DEnumerator.java
@@ -0,0 +1,77 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.geom.spacial;
+
+import cytoscape.util.intr.IntEnumerator;
+
+
+/**
+ * An enumeration over a set of entries in a SpacialIndex2D structure.
+ * The purpose of this class above and beyond IntEnumerator (which it extends)
+ * is to efficiently provide minimum bounding rectangle information for each
+ * entry returned.
+ */
+public interface SpacialEntry2DEnumerator extends IntEnumerator {
+ /**
+ * Copies into the supplied array [starting at specified offset] the minimum
+ * bounding rectangle of the next entry, and returns that next entry.
+ * The behavior of this method is identical to nextInt() except that in
+ * addition to returning a value, extents information is returned as well.
+ * The information written into the supplied extentsArr parameter consists
+ * of the following:
+ * <blockquote><table border="1" cellpadding="5" cellspacing="0">
+ * <tr> <th>array index</th> <th>information written</th> </tr>
+ * <tr> <td>offset</td> <td>xMin of MBR</td> </tr>
+ * <tr> <td>offset+1</td> <td>yMin of MBR</td> </tr>
+ * <tr> <td>offset+2</td> <td>xMax of MBR</td> </tr>
+ * <tr> <td>offset+3</td> <td>yMax of MBR</td> </tr>
+ * </table></blockquote><p>
+ * NOTE: If the retrieval of minimum bounding rectangle information for
+ * an entry is not important to the user of this enumeration, it is
+ * preferable to call nextInt() instead of nextExtents() for performance
+ * reasons.
+ * @param extentsArr an array to which extent values will be written by this
+ * method; cannot be null.
+ * @param offset specifies the beginning index of where to write extent
+ * values into extentsArr; exactly four entries are written starting
+ * at this index (see above table).
+ * @return the next entry (objKey) in the enumeration.
+ * @exception ArrayIndexOutOfBoundsException if extentsArr cannot be
+ * written to in the index range [offset, offset+3].
+ */
+ public int nextExtents(float[] extentsArr, int offset);
+}
diff --git a/corelibs/geom.spacial/src/main/java/cytoscape/geom/spacial/SpacialIndex2D.java b/corelibs/geom.spacial/src/main/java/cytoscape/geom/spacial/SpacialIndex2D.java
new file mode 100644
index 0000000..b3780bf
--- /dev/null
+++ b/corelibs/geom.spacial/src/main/java/cytoscape/geom/spacial/SpacialIndex2D.java
@@ -0,0 +1,130 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.geom.spacial;
+
+
+/**
+ * A spacial index for objects in two dimensions.
+ */
+public interface SpacialIndex2D {
+ /**
+ * Returns the number of entries (objKeys) currently in this structure.<p>
+ * NOTE: To retrieve an enumeration of all entries in this structure, call
+ * queryOverlap() with Float.NEGATIVE_INFINITY minimum values and
+ * Float.POSITIVE_INFINITY maximum values.
+ */
+ public int size();
+
+ /**
+ * Determines whether or not a given entry exists
+ * and conditionally retrieves the extents of that entry. The parameter
+ * extentsArr is written into by this method only if it is not null
+ * and if objKey exists. The information written into
+ * extentsArr consists of the minimum bounding rectangle (MBR) of objKey:
+ * <blockquote><table border="1" cellpadding="5" cellspacing="0">
+ * <tr> <th>array index</th> <th>value if objKey exists</th> </tr>
+ * <tr> <td>offset</td> <td>xMin of MBR</td> </tr>
+ * <tr> <td>offset+1</td> <td>yMin of MBR</td> </tr>
+ * <tr> <td>offset+2</td> <td>xMax of MBR</td> </tr>
+ * <tr> <td>offset+3</td> <td>yMax of MBR</td> </tr>
+ * </table></blockquote>
+ * @param objKey the entry to query.
+ * @param extentsArr an array to which extent values will be written by this
+ * method; may be null.
+ * @param offset specifies the beginning index of where to write extent
+ * values into extentsArr; exactly four entries are written starting at
+ * this index (see above table); if extentsArr is null then this offset
+ * is ignored.
+ * @return true if and only if objKey exists as an entry in this structure.
+ * @exception ArrayIndexOutOfBoundsException if objKey exists, if
+ * extentsArr is not null, and if extentsArr cannot be written
+ * to in the index range [offset, offset+3].
+ */
+ public boolean exists(int objKey, float[] extentsArr, int offset);
+
+ /**
+ * Returns an enumeration of entries whose extents intersect the
+ * specified axis-aligned rectangular area. By "axis-aligned" I mean that
+ * the query rectangle's sides are parallel to the axes of the data
+ * space.<p>
+ * The parameter extentsArr is written into by this method if it is not null.
+ * It provides a way for this method to communicate additional information
+ * to the caller of this method. If not null, extentsArr is populated with
+ * information regarding the minimum bounding rectangle (MBR) that contains
+ * all returned entries. The following table describes what is written to
+ * extentsArr if it is not null:
+ * <blockquote><table border="1" cellpadding="5" cellspacing="0">
+ * <tr> <th>array index</th> <th>value if query generates results</th>
+ * <th>value if query does not generate results</th> </tr>
+ * <tr> <td>offset</td> <td>xMin of MBR</td>
+ * <td>Float.POSITIVE_INFINITY</td> </tr>
+ * <tr> <td>offset+1</td> <td>yMin of MBR</td>
+ * <td>Float.POSITIVE_INFINITY</td> </tr>
+ * <tr> <td>offset+2</td> <td>xMax of MBR</td>
+ * <td>Float.NEGATIVE_INFINITY</td> </tr>
+ * <tr> <td>offset+3</td> <td>yMax of MBR</td>
+ * <td>Float.NEGATIVE_INFINITY</td> </tr>
+ * </table></blockquote><p>
+ * Note that the order of query results, as returned in the enumeration,
+ * may be completely random as a function of the query rectangle. However,
+ * any two subsequent, identical queries should produce an identical result
+ * order, provided that this structure does not undergo modification
+ * between those two queries (by modification I mean the possibility of
+ * entry shift, deletion of an entry, or insertion of an entry).
+ * @param xMin the minimum X coordinate of the query rectangle.
+ * @param yMin the minimum Y coordinate of the query rectangle.
+ * @param xMax the maximum X coordinate of the query rectangle.
+ * @param yMax the maximum Y coordinate of the query rectangle.
+ * @param extentsArr an array to which
+ * extent values will be written by this method; may be null.
+ * @param offset specifies the beginning index of where to write extent
+ * values into extentsArr; exactly four entries are written starting at
+ * this index (see table above); if extentsArr is null then this offset
+ * is ignored.
+ * @param reverse if true, the order in which the query hits
+ * are returned is reversed.
+ * @return a non-null enumeration of all [distinct] entries
+ * (objKeys) whose extents intersect the specified rectangular query area.
+ * @exception IllegalArgumentException if xMin is not less than or equal to
+ * xMax or if yMin is not less than or equal to yMax.
+ * @exception ArrayIndexOutOfBoundsException if extentsArr is not null
+ * and if it cannot be written to in the index range
+ * [offset, offset+3].
+ */
+ public SpacialEntry2DEnumerator queryOverlap(float xMin, float yMin, float xMax, float yMax,
+ float[] extentsArr, int offset, boolean reverse);
+}
diff --git a/corelibs/giny/pom.xml b/corelibs/giny/pom.xml
new file mode 100644
index 0000000..6c0c59e
--- /dev/null
+++ b/corelibs/giny/pom.xml
@@ -0,0 +1,41 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>parent</artifactId>
+ <version>2.8.4-SNAPSHOT</version>
+ </parent>
+
+ <artifactId>giny</artifactId>
+ <packaging>jar</packaging>
+
+ <name>GINY API</name>
+
+ <!-- bootstrap for cytoscape dependencies, namely the parent POM snapshots -->
+ <repositories>
+ <repository>
+ <id>cytoscape_snapshots</id>
+ <snapshots>
+ <enabled>true</enabled>
+ </snapshots>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <name>Cytoscape Snapshots</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/</url>
+ </repository>
+ <repository>
+ <id>cytoscape_releases</id>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ <name>Cytoscape Releases</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/releases/</url>
+ </repository>
+ </repositories>
+
+</project>
+
diff --git a/corelibs/giny/src/main/java/giny/filter/Filter.java b/corelibs/giny/src/main/java/giny/filter/Filter.java
new file mode 100644
index 0000000..a9e3d66
--- /dev/null
+++ b/corelibs/giny/src/main/java/giny/filter/Filter.java
@@ -0,0 +1,11 @@
+package giny.filter;
+
+public interface Filter {
+
+ /**
+ * Determine whether the object passes the filter.
+ * @return true iff the given Object passes the filter.
+ */
+ public boolean passesFilter ( Object o );
+
+}
diff --git a/corelibs/giny/src/main/java/giny/model/Edge.java b/corelibs/giny/src/main/java/giny/model/Edge.java
new file mode 100644
index 0000000..4a4876c
--- /dev/null
+++ b/corelibs/giny/src/main/java/giny/model/Edge.java
@@ -0,0 +1,21 @@
+package giny.model;
+
+public interface Edge extends GraphObject {
+
+ /**
+ * @return the GraphNode corresponding to the source of this GraphEdge.
+ */
+ public Node getSource ();
+
+ /**
+ * @return the GraphNode corresponding to the target of this GraphEdge.
+ */
+ public Node getTarget ();
+
+ /**
+ * @return true if this Edge is a directed edge; false otherwise.
+ */
+ public boolean isDirected ();
+
+
+} // interface Edge
diff --git a/corelibs/giny/src/main/java/giny/model/GraphObject.java b/corelibs/giny/src/main/java/giny/model/GraphObject.java
new file mode 100755
index 0000000..5cd3c30
--- /dev/null
+++ b/corelibs/giny/src/main/java/giny/model/GraphObject.java
@@ -0,0 +1,30 @@
+package giny.model;
+
+import java.util.*;
+
+public interface GraphObject {
+
+ /**
+ * @return The Unique Identifier of this node
+ */
+ public String getIdentifier ();
+
+ /**
+ * <B>There is no check to make sure that this is a unique id</B>
+ * @param new_id The new Identifier for this node
+ */
+ public boolean setIdentifier ( String new_id );
+
+ /**
+ * @return the index in the RootGraph of this Edge
+ */
+ public int getRootGraphIndex ();
+
+
+ /**
+ * @return the RootGraph that this Node is in
+ */
+ public RootGraph getRootGraph ();
+
+
+}
diff --git a/corelibs/giny/src/main/java/giny/model/GraphPerspective.java b/corelibs/giny/src/main/java/giny/model/GraphPerspective.java
new file mode 100644
index 0000000..eef5be7
--- /dev/null
+++ b/corelibs/giny/src/main/java/giny/model/GraphPerspective.java
@@ -0,0 +1,1204 @@
+package giny.model;
+import giny.filter.Filter;
+
+import java.util.Iterator;
+import java.util.List;
+
+/**
+ * Basic graph API
+ *
+ * TODO: Remove deprecated methods and add generics parameters.
+ *
+ */
+public interface GraphPerspective {
+
+
+ public void addGraphPerspectiveChangeListener ( GraphPerspectiveChangeListener listener );
+
+ public void removeGraphPerspectiveChangeListener ( GraphPerspectiveChangeListener listener );
+
+ public Object clone () ;
+
+
+ /**
+ * Return the root Graph for this GraphPerspective
+ */
+ public RootGraph getRootGraph () ;
+
+
+ /**
+ * Returns number of active nodes in this perspective.
+ */
+ public int getNodeCount () ;
+
+
+ /**
+ * Returns number of active edges in this perspective.
+ */
+ public int getEdgeCount () ;
+
+
+ /**
+ * Returns an Iterator over all giny.model.Node objects in this GraphPerspective.<p>
+ * TECHNICAL DETAIL: Iterating over the set of all nodes in a GraphPerspective and
+ * manipulating a GraphPerspective's topology (by calling hideXXX() and restoreXXX()
+ * methods) concurrently will have undefined effects on the returned Iterator.
+ * @return an Iterator over the Nodes in this graph; each Object in the
+ * returned Iterator is of type giny.model.Node.
+ */
+ public Iterator nodesIterator () ;
+
+
+ /**
+ * Returns a list of Node objects.
+ * @see #nodesIterator()
+ */
+ public List nodesList () ;
+
+ /**
+ * Returns an array of length getNodeCount(); the array contains
+ * RootGraph indices of Node objects in this GraphPerspective, in some
+ * undefined order.
+ * @see #nodesIterator()
+ * @see Node#getRootGraphIndex()
+ */
+ public int[] getNodeIndicesArray();
+
+ /**
+ * @return an Iterator over the Edges in this graph.
+ */
+ public Iterator edgesIterator () ;
+
+ /**
+ * Returns a list of Edge objects.
+ * @see #edgesIterator()
+ */
+ public List edgesList () ;
+
+ /**
+ * Returns an array of length getEdgeCount(); the array contains
+ * RootGraph indices of Edge objects in this GraphPerspective, in some
+ * undefined order.
+ * @see #edgesIterator()
+ * @see Edge#getRootGraphIndex()
+ */
+ public int[] getEdgeIndicesArray();
+
+ /**
+ * @return null is returned if either of the specified Nodes is not in this
+ * GraphPerspective.
+ * @deprecated Use getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean) instead.
+ * @see #getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean)
+ */
+ public int[] getEdgeIndicesArray (
+ int from_node_index,
+ int to_node_index,
+ boolean include_undirected_edges,
+ boolean include_both_directions
+ ) ;
+ /**
+ * If this GraphPerspective does not hide the given Node, change it so that
+ * it does hide the node and all of its incident edges.
+ * @param node The Node to hide.
+ * @return The given node, unless it was already hidden, in which case
+ * null.
+ */
+ public Node hideNode ( Node node ) ;
+
+ /**
+ * If this GraphPerspective does not hide the Node with the given index in
+ * the underlying RootGraph, change it so that it does hide the node and all of
+ * its incident edges.
+ * @param node_index The index in the underlying RootGraph of the Node to hide.
+ * @return The given index, unless the corresponding Node was already hidden or
+ * does not exist in the underlying RootGraph, in which case 0.
+ */
+ public int hideNode ( int node_index ) ;
+
+ /**
+ * @deprecated Use hideNode(Node) or hideNodes(int[]) instead.
+ * @see #hideNode(Node)
+ * @see #hideNodes(int[])
+ */
+ public List hideNodes ( List nodes ) ;
+
+ /**
+ * If this GraphPerspective does not hide any of the Nodes corresponding to
+ * the indices in the given array, change it so that it does hide those nodes
+ * and all Edges incident on them.
+ * Returns an array of equal length to the one given, in which each
+ * corresponding position is either the same as in the argument array or is
+ * 0, indicating that the node with that index was already hidden.
+ * @param node_indices The int array of indices in the underlying RootGraph of
+ * the Nodes to hide.
+ * @return An int array of equal length to the argument array, and with equal
+ * values except at positions that in the input array contain indices
+ * corresponding to Nodes that were already hidden; at these positions the
+ * result array will contain the value 0.
+ */
+ public int[] hideNodes ( int[] node_indices ) ;
+
+ /**
+ * If this GraphPerspective hides the given Node, change it so that it does
+ * not hide the node.
+ * @param node The Node to restore.
+ * @return The given node, unless it was not hidden or it doesn't exist
+ * in the RootGraph, in which case null.
+ */
+ public Node restoreNode ( Node node ) ;
+
+ /**
+ * If this GraphPerspective hides the Node with the given index in the
+ * underlying RootGraph, change it so that it does not hide the node.
+ * @param node_index The index in the underlying RootGraph of the Node to
+ * restore.
+ * @return The given index, unless the corresponding Node was already
+ * restored or does not exist in the RootGraph, in which case 0.
+ */
+ public int restoreNode ( int node_index ) ;
+
+ /**
+ * @deprecated Use restoreNode(Node) restoreNodes(int[]) instead.
+ * @see #restoreNode(Node)
+ * @see #restoreNodes(int[])
+ */
+ public List restoreNodes ( List nodes ) ;
+
+ /**
+ * @deprecated Use restoreNodes(int[]) and restoreEdges(int[]) instead; to
+ * get edges incident to specified nodes, use
+ * RootGraph.getConnectingEdgeIndicesArray(int[]).
+ * @see #restoreNodes(int[])
+ * @see #restoreEdges(int[])
+ * @see RootGraph#getConnectingEdgeIndicesArray(int[])
+ */
+ public List restoreNodes (List nodes, boolean restore_incident_edges);
+
+ /**
+ * If this GraphPerspective hides any of the Nodes with the given RootGraph
+ * indices change it so that it does not hide those nodes.
+ * @param node_indices The Node indices.
+ * @param restore_incident_edges Whether or not the incident edges to the
+ * restored nodes should also be restored.
+ * @return An array of length equal to the length of the argument array,
+ * and with equal values except at positions that in the input array
+ * contain indices corresponding to Nodes that were already restored or
+ * don't exist in the RootGraph; at these positions the result array will
+ * contain the value 0.
+ * @deprecated Use restoreNodes(int[]) and restoreEdges(int[]) instead; to
+ * get edges incident to specified nodes, use
+ * RootGraph.getConnectingEdgeIndicesArray(int[]).
+ * @see #restoreNodes(int[])
+ * @see #restoreEdges(int[])
+ * @see RootGraph#getConnectingEdgeIndicesArray(int[])
+ */
+ public int [] restoreNodes (int [] node_indices, boolean restore_incident_edges);
+
+ /**
+ * If this GraphPerspective hides any of the Nodes corresponding to the
+ * indices in the given array, change it so that it does not hide those
+ * nodes. Returns an array of equal length
+ * to the one given, in which each corresponding position is either the same
+ * as in the argument array or is 0, indicating that the node with that
+ * index was already restored or does not exist in the RootGraph.
+ * @param node_indices The int array of indices in the underlying RootGraph
+ * of the Nodes to restore.
+ * @return An int array of equal length to the argument array, and with equal
+ * values except at positions that in the input array contain indices
+ * corresponding to Nodes that were already restored or don't exist in
+ * the RootGraph; at these positions the
+ * result array will contain the value 0.
+ */
+ public int[] restoreNodes ( int[] node_indices ) ;
+
+ /**
+ * If this GraphPerspective does not hide the given Edge, change it so that
+ * it does hide the edge.
+ * @param edge The Edge to hide.
+ * @return The given edge, unless it was already hidden, in which case
+ * null.
+ */
+ public Edge hideEdge ( Edge edge ) ;
+
+ /**
+ * If this GraphPerspective does not hide the Edge with the given index in
+ * the RootGraph, change it so that it does hide the edge.
+ * @param edge_index The index in the underlying RootGraph of the Edge to
+ * hide.
+ * @return The given index, unless the corresponding Edge was already hidden
+ * or does not exist in the underlying RootGraph, in which case 0.
+ */
+ public int hideEdge ( int edge_index ) ;
+
+ /**
+ * @deprecated Use hideEdge(Edge) or hideEdges(int[]) instead.
+ * @see #hideEdge(Edge)
+ * @see #hideEdges(int[])
+ */
+ public List hideEdges ( List edges ) ;
+
+ /**
+ * If this GraphPerspective does not hide any of the Edges corresponding to
+ * the indices in the given array, change it so that it does hide those
+ * edges. Returns an array of equal length
+ * to the one given, in which each corresponding position is either the same
+ * as in the argument array or is 0, indicating that the edge with that
+ * index was already hidden.
+ * @param edge_indices The int array of indices in the underlying RootGraph of
+ * the Edges to hide.
+ * @return An int array of equal length to the argument array, and with equal
+ * values except at positions that in the input array contain indices
+ * corresponding to Edges that were already hidden; at these positions the
+ * result array will contain the value 0.
+ */
+ public int[] hideEdges ( int[] edge_indices ) ;
+
+ /**
+ * If this GraphPerspective hides the given Edge, change it so that it does
+ * not hide the edge or the Nodes on which the edge is incident.
+ * @param edge The Edge to restore.
+ * @return The given edge, unless it was not hidden or does not exist
+ * in the underlying RootGraph, in which case null.
+ */
+ public Edge restoreEdge ( Edge edge ) ;
+
+ /**
+ * If this GraphPerspective hides the Edge with the given index in the
+ * underlying RootGraph, change it so that it does not hide the edge or the
+ * Nodes on which the edge is incident.
+ * @param edge_index The index in the underlying RootGraph of the Edge to
+ * restore.
+ * @return The given index, unless the corresponding Edge was already
+ * restored or does not exist in the RootGraph, in which case 0.
+ */
+ public int restoreEdge ( int edge_index ) ;
+
+ /**
+ * @deprecated Use restoreEdges(int[]) instead.
+ * @see #restoreEdges(int[])
+ */
+ public List restoreEdges ( List edges ) ;
+
+ /**
+ * If this GraphPerspective hides any of the Edges corresponding to the
+ * indices in the given array, change it so that it does not hide those edges
+ * or any of the Nodes on which they are incident.
+ * @param edge_indices An array of indices in the underlying RootGraph of
+ * the Edges to restore.
+ * @return An int array of equal length to the argument array, and with equal
+ * values except at positions that in the input array contain indices
+ * corresponding to Edges that were already restored or don't exist in the
+ * underlying RootGraph; at these positions the
+ * result array will contain the value 0.
+ */
+ public int[] restoreEdges ( int[] edge_indices ) ;
+
+ /**
+ * Return true if the given Node is in this GraphPerspective. False
+ * otherwise. This method is recursive, so even if this GraphPerspective
+ * does hide the Node, this method will return true if the given Node is
+ * contained within any non-hidden Node (via the MetaParent->MetaChild
+ * relationship) at any depth.
+ * This method is equivalent to calling containsNode(Node, boolean)
+ * with a true boolean argument.
+ * @return true iff the given Node is in this GraphPerspective.
+ * @see #containsNode(Node, boolean)
+ */
+ public boolean containsNode ( Node node ) ;
+
+ /**
+ * Return true if the given Node is in this GraphPerspective. False
+ * otherwise. If the <tt>recurse</tt> flag is true then this method will be
+ * recursive, so even if this GraphPerspective does hide the Node, this
+ * method will return true if the given Node is contained within any
+ * non-hidden Node (via the MetaParent->MetaChild relationship) at any depth. If
+ * <tt>recurse</tt> is false then this method will return false iff the
+ * given Node is hidden in this GraphPerspective.
+ * @return true iff the given Node is in this GraphPerspective.
+ */
+ public boolean containsNode ( Node node, boolean recurse ) ;
+
+ /**
+ * Return true if the given Edge is in this GraphPerspective. False
+ * otherwise. This method is recursive, so even if this GraphPerspective
+ * does hide the Edge, this method will return true if the given Edge is
+ * contained within any non-hidden Node (via the MetaParent->MetaChild
+ * relationship) at any depth. This method calls {@link #containsEdge( Edge,
+ * boolean ) } with a true <tt>recurse</tt> boolean argument.
+ * @return true iff the given Edge is in this GraphPerspective.
+ */
+ public boolean containsEdge ( Edge edge ) ;
+
+ /**
+ * Return true if the given Edge is in this GraphPerspective. False
+ * otherwise. If the <tt>recurse</tt> flag is true then this method will be
+ * recursive, so even if this GraphPerspective does hide the Edge, this
+ * method will return true if the given Edge is contained within any
+ * non-hidden Node (via the MetaParent->MetaChild relationship) at any depth. If
+ * <tt>recurse</tt> is false then this method will return false iff the
+ * given Edge is hidden in this GraphPerspective.
+ */
+ public boolean containsEdge ( Edge edge, boolean recurse ) ;
+
+ /**
+ * Creates a union GraphPerspective. The given GraphPerspective must have
+ * the same RootGraph as this one.
+ * @return a new GraphPerspective that contains the union of Nodes and Edges
+ * from this GraphPerspective and the given GraphPerspective, or null if
+ * the input GraphPerspective does not have the same RootGraph as this one.
+ */
+ public GraphPerspective join ( GraphPerspective peer ) ;
+
+ /**
+ * Create a new GraphPerspective with just the given Nodes and Edges (and all
+ * Nodes incident on the given Edges).
+ * @param nodes A [possibly null] array of Nodes in this GraphPerspective to
+ * include in the new GraphPerspective.
+ * @param edges A [possibly null] array of Edges in this GraphPerspective to
+ * include in the new GraphPerspective.
+ * @return a new GraphPerspective on this GraphPerspective containing only the
+ * given Nodes and Edges, plus any Nodes incident on the given Edges array but
+ * omitted from the given Nodes array; returns null if any of the specified Nodes
+ * or Edges are not in this GraphPerspective.
+ * @deprecated Use RootGraph.createGraphPerspective(int[], int[]) instead.
+ * @see RootGraph#createGraphPerspective(int[], int[])
+ */
+ public GraphPerspective createGraphPerspective ( Node[] nodes,
+ Edge[] edges
+ );
+
+ /**
+ * Create a new GraphPerspective with just the Nodes with the given
+ * <tt>node_indices</tt> and just the Edges with the given
+ * <tt>edge_indices</tt> (and all Nodes incident on the given Edges).
+ * @param node_indices A [possibly null] array of [RootGraph] indices
+ * of Nodes in this GraphPerspective to include in the new GraphPerspective.
+ * @param edge_indices A [possibly null] array of [RootGraph] indices
+ * of Edges in this GraphPerspective to include in the new GraphPerspective.
+ * @return a new GraphPerspective on this GraphPerspective containing only Nodes
+ * and Edges with the given indices, including all Nodes incident on those Edges;
+ * returns null if any of the specified Node or Edge indices do not correspond
+ * to Nodes or Edges existing in this GraphPerspective.
+ * @deprecated Use RootGraph.createGraphPerspective(int[], int[]) instead.
+ * @see RootGraph#createGraphPerspective(int[], int[])
+ */
+ public GraphPerspective createGraphPerspective (int[] node_indices,
+ int[] edge_indices
+ );
+
+ /**
+ * Create a new GraphPerspective with all of the Nodes from this one that
+ * pass the given filter and all of the Edges from this one that pass the
+ * filter (and all Nodes incident on those edges).
+ */
+ public GraphPerspective createGraphPerspective ( Filter filter ) ;
+
+ /**
+ * Please note that the definition
+ * of "node neighbor" is such: Node A is a "node neighbor" of node B if and only
+ * if there exists an edge [directed or undirected] E such that A is E's target and
+ * B is E's source, or
+ * A is E's source and B is E's target; this method then returns a non-repeating list
+ * of indices of all nodes N in this
+ * GraphPerspective such that N is a "node neighbor" of the node at specified index,
+ * or null if no node at specified index exists in this GraphPerspective.
+ * @param node The node whose neighbors you're looking for.
+ */
+ public List neighborsList ( Node node ) ;
+
+ /**
+ * Please note that the definition
+ * of "node neighbor" is such: Node A is a "node neighbor" of node B if and only
+ * if there exists an edge [directed or undirected] E such that A is E's target and
+ * B is E's source, or
+ * A is E's source and B is E's target; this method then returns a non-repeating list
+ * of indices of all nodes N in this
+ * GraphPerspective such that N is a "node neighbor" of the node at specified index,
+ * or null if no node at specified index exists in this GraphPerspective.
+ * @param node_index The node whose neighbors you're looking for.
+ */
+ public int[] neighborsArray ( int node_index );
+
+ /**
+ * Please note that the definition
+ * of "node neighbor" is such: Node A is a "node neighbor" of node B if and only
+ * if there exists an edge [directed or undirected] E such that A is E's target and
+ * B is E's source, or A is E's source and B is E's target; this method then returns
+ * true if and only if a_node is a "node neighbor" of another_node in this
+ * GraphPerspective.
+ * @param a_node Source node.
+ * @param another_node Possible target node.
+ */
+ public boolean isNeighbor ( Node a_node, Node another_node ) ;
+
+ /**
+ * Please note that the definition
+ * of "node neighbor" is such: Node A is a "node neighbor" of node B if and only
+ * if there exists an edge [directed or undirected] E such that A is E's target and
+ * B is E's source, or A is E's source and B is E's target; this method then returns
+ * true if and only if node at index a_node_index is a "node neighbor" of node at
+ * index another_node_index in this GraphPerspective.
+ * @param a_node_index Source node index.
+ * @param another_node_index Possible target node index.
+ */
+ public boolean isNeighbor ( int a_node_index, int another_node_index ) ;
+
+ /**
+ * This method returns true if and only if
+ * either 1) there exists a directed edge E in this GraphPerspective such that the from
+ * node specified is E's source node and the target node specified is E's target node
+ * or 2) there exists an undirected edge E in this GraphPerspective such that E's
+ * endpoints are the from and to nodes specified.
+ * @param from Source node.
+ * @param to Possible target node.
+ */
+ public boolean edgeExists ( Node from, Node to ) ;
+
+ /**
+ * This method returns true if and only if
+ * either 1) there exists a directed edge E in this GraphPerspective such that
+ * from_node_index is E's source node's index and to_node_index is E's target node's
+ * index or 2) there exists an undirected edge E in this GraphPerspective such that E's
+ * endpoint nodes have indices from_node_index and to_node_index.
+ * @param from_node_index Source node index.
+ * @param to_node_index Possible target node index.
+ */
+ public boolean edgeExists ( int from_node_index, int to_node_index ) ;
+
+ /**
+ * Count the number of edges from the first Node to the second. Note that if
+ * count_undirected_edges is false, any Edge <tt><i>e</i></tt> such that
+ * <tt><i>e</i>.isDirected() == false</tt> will not be included in the count.
+ * @param from the Node in this GraphPerspective that is the source of the
+ * edges to be counted.
+ * @param to the Node in this GraphPerspective that is the target of the
+ * edges to be counted.
+ * @param count_undirected_edges Undirected edges will be included in the
+ * count iff count_undirected_edges is true.
+ * @return the number of Edges from the <tt>from</tt> Node to the
+ * <tt>to</tt> Node; returns -1 if either the <tt>from</tt> or the
+ * <tt>to</tt> Node is not in this GraphPerspective.
+ */
+ public int getEdgeCount (Node from,
+ Node to,
+ boolean count_undirected_edges
+ );
+
+ /**
+ * Count the number of edges from the Node with index <tt>from_index</tt> to
+ * the Node with index <tt>to_index</tt> (where this.getIndex( to_node ) ==
+ * to_index). Note that if count_undirected_edges is false, any Edge
+ * <tt><i>e</i></tt> such that <tt><i>e</i>.isDirected() == false</tt> will
+ * not be included in the count.
+ * @param from_node_index the index in this GraphPerspective of the Node to
+ * count edges from.
+ * @param to_node_index the index in this GraphPerspective of the Node to
+ * find edges to.
+ * @param count_undirected_edges Undirected edges will be included in the
+ * count iff count_undirected_edges is true.
+ * @return the number of Edges from the Node with index <tt>from_index</tt>
+ * to the Node with index <tt>to_index</tt>; returns -1 if either one of the two
+ * specified nodes is not in this GraphPerspective.
+ */
+ public int getEdgeCount ( int from_node_index,
+ int to_node_index,
+ boolean count_undirected_edges
+ ) ;
+
+ /**
+ * Return a new List of the Edges in this GraphPerspective from the first
+ * given Node to the second given Node.
+ * @param from the Node in this GraphPerspective that is the source of the
+ * Edges to be returned.
+ * @param to the Node in this GraphPerspective that is the target of the
+ * Edges to be returned.
+ * @return a new List of the Edges from the <tt>from</tt> Node to the
+ * <tt>to</tt> Node, or the empty List if none exist; null is returned if either
+ * of the specified nodes is not in this GraphPerspective.
+ */
+ public List edgesList ( Node from, Node to ) ;
+
+ /**
+ * Return an array of the indices in this GraphPerspective of all Edges from
+ * the Node with the first given index to the Node with the second given
+ * index.
+ * @param from_node_index the index in this GraphPerspective of the Node to
+ * return edges from.
+ * @param to_node_index the index in this GraphPerspective of the Node to
+ * return edges to.
+ * @param include_undirected_edges Undirected edges will be included in the
+ * List iff include_undirected_edges is true.
+ * @return a new List of the Edges from the Node corresponding to
+ * <tt>from_node_index</tt> to the Node corresponding to
+ * <tt>to_node_index</tt>, or the empty List if none exist; null is returned
+ * if either of the specified nodes does not exist in this GraphPerspective.
+ * @deprecated Use getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean) instead.
+ * @see #getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean)
+ */
+ public List edgesList (int from_node_index,
+ int to_node_index,
+ boolean include_undirected_edges
+ );
+
+ /**
+ * Return an array of the indices in this GraphPerspective of all Edges from
+ * the Node with the first given index to the Node with the second given
+ * index.
+ * <br>
+ * The result should be considered final; it <b>must not</b> be modified by
+ * the receiver.
+ * @param from_node_index the index in this GraphPerspective of the Node to
+ * return edges from.
+ * @param to_node_index the index in this GraphPerspective of the Node to
+ * return edges to.
+ * @param include_undirected_edges Undirected edges will be included in the
+ * array iff include_undirected_edges is true.
+ * @return an array of indices corresponding to Edges from the Node at index
+ * <tt>from_node_index</tt> to the Node at index
+ * <tt>to_node_index</tt>; the empty array is returned if no such Edges exist;
+ * null is returned if either of the specified Nodes does not exist in this
+ * GraphPerspective.
+ * @deprecated Use getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean) instead.
+ * @see #getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean)
+ */
+ public int[] getEdgeIndicesArray (int from_node_index,
+ int to_node_index,
+ boolean include_undirected_edges
+ );
+
+ /**
+ * Return the number of Edges <tt><i>e</i></tt> in this GraphPerspective such
+ * that <tt><i>e</i>.getTarget().equals( node )</tt>. Note that this
+ * includes undirected edges, so it will not always be the case that
+ * <tt>getInDegree( node ) + getOutDegree( node ) == getDegree( node )</tt>.
+ * @param node the Node to count in-edges of.
+ * @return the in-degree of the given Node, or -1 if the specified Node is not
+ * in this GraphPerspective.
+ */
+ public int getInDegree ( Node node ) ;
+
+ /**
+ * Return the number of Edges <tt><i>e</i></tt> in this GraphPerspective such
+ * that <tt><i>e</i>.getTarget().equals( node )</tt>. Note that this
+ * includes undirected edges, so it will not always be the case that
+ * <tt>getInDegree( node ) + getOutDegree( node ) == getDegree( node )</tt>.
+ * @param node_index the index of the Node to count in-edges of.
+ * @return the in-degree of the Node with the given index, or -1 if this
+ * GraphPerspective has no Node with specified index.
+ */
+ public int getInDegree ( int node_index ) ;
+
+ /**
+ * Return the number of Edges <tt><i>e</i></tt> in this GraphPerspective
+ * such that <tt><i>e</i>.getSource().equals( node )</tt>. Note that if
+ * count_undirected_edges is true, this includes undirected edges, so it will
+ * not always be the case that <tt>getInDegree( node, true ) + getOutDegree(
+ * node, true ) == getDegree( node )</tt>, but it <i>will</i> always be the
+ * case that <tt>getInDegree( node, true ) + getOutDegree( node, <b>false</b>
+ * ) == getDegree( node )</tt>.
+ * @param node the Node to count in-edges of.
+ * @param count_undirected_edges Undirected edges will be included in the
+ * count iff count_undirected_edges is true.
+ * @return the in-degree of the given Node or -1 if specified Node is not
+ * in this GraphPerspective.
+ */
+ public int getInDegree ( Node node, boolean count_undirected_edges ) ;
+
+ /**
+ * Return the number of Edges <tt><i>e</i></tt> in this GraphPerspective
+ * such that <tt><i>e</i>.getSource().equals( node )</tt>. Note that if
+ * count_undirected_edges is true, this includes undirected edges, so it will
+ * not always be the case that <tt>getInDegree( node, true ) + getOutDegree(
+ * node, true ) == getDegree( node )</tt>, but it <i>will</i> always be the
+ * case that <tt>getInDegree( node, true ) + getOutDegree( node, <b>false</b>
+ * ) == getDegree( node )</tt>.
+ * @param node_index the index of the Node to count in-edges of.
+ * @param count_undirected_edges Undirected edges will be included in the
+ * count iff count_undirected_edges is true.
+ * @return the in-degree of the Node with the given index or -1 if this
+ * GraphPerspective has no Node at specified index.
+ */
+ public int getInDegree ( int node_index, boolean count_undirected_edges ) ;
+
+ /**
+ * Return the number of Edges <tt><i>e</i></tt> in this GraphPerspective such
+ * that <tt><i>e</i>.getSource().equals( node )</tt>. Note that this
+ * includes undirected edges, so it will not always be the case that
+ * <tt>getInDegree( node ) + getOutDegree( node ) == getDegree( node )</tt>.
+ * @param node the Node to count out-edges of.
+ * @return the out-degree of the given Node, or -1 if specified Node is not
+ * in this GraphPerspective.
+ */
+ public int getOutDegree ( Node node ) ;
+
+ /**
+ * Return the number of Edges <tt><i>e</i></tt> in this GraphPerspective such
+ * that <tt><i>e</i>.getSource().equals( node )</tt>. Note that this
+ * includes undirected edges, so it will not always be the case that
+ * <tt>getInDegree( node ) + getOutDegree( node ) == getDegree( node )</tt>.
+ * @param node_index the index of the Node to count out-edges of.
+ * @return the out-degree of the Node with the given index or -1 if index
+ * specified does not correspond to a Node in this GraphPerspective.
+ */
+ public int getOutDegree ( int node_index ) ;
+
+ /**
+ * Return the number of Edges <tt><i>e</i></tt> in this GraphPerspective
+ * such that <tt><i>e</i>.getSource().equals( node )</tt>. Note that if
+ * count_undirected edges is true, this includes undirected edges, so it will
+ * not always be the case that <tt>getInDegree( node, true ) + getOutDegree(
+ * node, true ) == getDegree( node )</tt>, but it <i>will</i> always be the
+ * case that <tt>getInDegree( node, true ) + getOutDegree( node,
+ * <b>false</b> ) == getDegree( node )</tt>.
+ * @param node the Node to count out-edges of.
+ * @param count_undirected_edges Undirected edges will be included in the
+ * count iff count_undirected_edges is true.
+ * @return the out-degree of the given Node or -1 if specified Node is not
+ * in this GraphPerspective.
+ */
+ public int getOutDegree ( Node node, boolean count_undirected_edges ) ;
+
+ /**
+ * Return the number of Edges <tt><i>e</i></tt> in this GraphPerspective
+ * such that <tt><i>e</i>.getSource().equals( node )</tt>. Note that if
+ * count_undirected edges is true, this includes undirected edges, so it will
+ * not always be the case that <tt>getInDegree( node, true ) + getOutDegree(
+ * node, true ) == getDegree( node )</tt>, but it <i>will</i> always be the
+ * case that <tt>getInDegree( node, true ) + getOutDegree( node,
+ * <b>false</b> ) == getDegree( node )</tt>.
+ * @param node_index the index of the Node to count out-edges of.
+ * @param count_undirected_edges Undirected edges will be included in the
+ * count iff count_undirected_edges is true.
+ * @return the out-degree of the Node with the given index or -1 if this
+ * GraphPerspective has no Node with specified RootGraph index.
+ */
+ public int getOutDegree ( int node_index, boolean count_undirected_edges ) ;
+
+ /**
+ * Return the number of distinct Edges in this GraphPerspective incident on
+ * the given Node. By 'distinct' we mean that no Edge will be counted twice,
+ * even if it is undirected.
+ * @return the degree, in this GraphPerspective, of the given Node, or -1 if
+ * specified Node is not in this GraphPerspective.
+ */
+ public int getDegree ( Node node ) ;
+
+ /**
+ * Return the number of distinct Edges in this GraphPerspective incident on
+ * the Node with the given index. By 'distinct' we mean that no Edge will be
+ * counted twice, even if it is undirected.
+ * @return the degree, in this GraphPerspective, of the Node with the given
+ * index, or -1 if this GraphPerspective has no Node with specified [RootGraph]
+ * index.
+ */
+ public int getDegree ( int node_index ) ;
+
+ /**
+ * Return the index of the given Node in the underlying RootGraph.
+ * If the Node is hidden in this perspective, the result will be 0.
+ * @param node the Node to find a corresponding index for.
+ * @return the index of the given Node in the RootGraph
+ * (node.getRootGraphIndex()), or 0 if it is hidden or does not exist
+ * in the underlying RootGraph.
+ */
+ public int getIndex ( Node node ) ;
+
+ /**
+ * @deprecated Use getRootGraphNodeIndex(int), whose functionality is
+ * identical.
+ * @see #getRootGraphNodeIndex(int)
+ */
+ public int getNodeIndex ( int root_graph_node_index ) ;
+
+ /**
+ * This method returns the input parameter if and only if a Node at the
+ * specified RootGraph index exists in this GraphPerspective; otherwise 0
+ * is returned.
+ */
+ public int getRootGraphNodeIndex ( int root_graph_node_index ) ;
+
+ /**
+ * Return a Node which is in this GraphPerspective.
+ * in this GraphPerspective.
+ * @param index the index into the underlying RootGraph to find a
+ * corresponding GraphPerspective Node for.
+ * @return the Node in this GraphPerspective, or null if
+ * no such Node exists in this GraphPerspective.
+ */
+ public Node getNode ( int index ) ;
+
+ /**
+ * Return the index of the given Edge in the underlying RootGraph.
+ * If the Edge is hidden in this perspective, the result will be 0.
+ * @param edge the Edge to find a corresponding index for.
+ * @return the index of the given Edge in the RootGraph
+ * (edge.getRootGraphIndex()), or 0 if it is hidden or does not exist
+ * in the underlying RootGraph.
+ */
+ public int getIndex ( Edge edge ) ;
+
+ /**
+ * @deprecated Use getRootGraphEdgeIndex(int), whose functionality is
+ * identical.
+ * @see #getRootGraphEdgeIndex(int)
+ */
+ public int getEdgeIndex ( int root_graph_edge_index ) ;
+
+ /**
+ * This method returns the input parameter if and only if an Edge at the
+ * specified RootGraph index exists in this GraphPerspective; otherwise 0 is
+ * returned.
+ */
+ public int getRootGraphEdgeIndex ( int root_graph_edge_index ) ;
+
+ /**
+ * Return an Edge which is in this GraphPerspective.
+ * @param index the index into the underlying RootGraph to find a
+ * corresponding GraphPerspective Edge for.
+ * @return the Edge in this GraphPerspective, or null if
+ * no such Edge exists in this GraphPerspective.
+ */
+ public Edge getEdge ( int index ) ;
+
+ /**
+ * Retrieve the index of the Node that is the source of the Edge in this
+ * GraphPerspective with the given index. Note that if the edge is
+ * undirected, the edge also connects the target to the source.
+ * @param edge_index the [RootGraph] index of the Edge in this GraphPerspective.
+ * @return the index of the Edge's source Node, or 0
+ * if the Edge is not in this GraphPerspective.
+ */
+ public int getEdgeSourceIndex ( int edge_index ) ;
+
+ /**
+ * Retrieve the index of the Node that is the target of the Edge in this
+ * GraphPerspective with the given index. Note that if the edge is
+ * undirected, the edge also connects the target to the source.
+ * @param edge_index the [RootGraph] index of the Edge in this GraphPerspective.
+ * @return the index of the Edge's target Node, or 0
+ * if the Edge is not in this GraphPerspective.
+ */
+ public int getEdgeTargetIndex ( int edge_index ) ;
+
+ /**
+ * Retrieve the directedness of the Edge in this GraphPerspective with the
+ * given [RootGraph] index. Note that if the edge is undirected, the edge also
+ * connects the target to the source.
+ * @param edge_index the [RootGraph] index of the Edge in this GraphPerspective.
+ * @return true iff the edge is directed; if no Edge at specified index exists
+ * in this GraphPerspective, the result of this method is undefined.
+ */
+ public boolean isEdgeDirected ( int edge_index ) ;
+
+ /**
+ * Nodes and Edges comprise an additional directed graph through the
+ * contains-a relationship, in which a MetaParent Node contains each of its
+ * MetaChild Nodes and Edges. A Node may have any number of MetaParents.
+ * isMetaParent returns true iff the second argument (<tt>parent</tt>) is an
+ * MetaParent of the first argument (<tt>child</tt>) and both Nodes are in
+ * this GraphPerspective.
+ * @param child the Node that is the child (the contain<i>ee</i>) in the
+ * contains-a relationship that we are querying.
+ * @param parent the Node that is the parent (the contain<i>er</i>) in the
+ * contains-a relationship that we are querying.
+ * @return true iff the latter argument is a MetaParent of the former argument
+ * in this GraphPerspective.
+ */
+ public boolean isMetaParent ( Node child, Node parent ) ;
+
+ /**
+ * Nodes and Edges comprise an additional directed graph through the
+ * contains-a relationship, in which a MetaParent Node contains each of its
+ * MetaChild Nodes and Edges. A Node may have any number of MetaParents.
+ * isMetaParent returns true iff the Node corresponding to the second argument
+ * (<tt>parent_index</tt>) is a MetaParent of the Node corresponding to the
+ * first argument (<tt>child_index</tt>) and both Nodes are in this GraphPerspective.
+ * @param child_node_index the index in the RootGraph of the Node
+ * that is the child (the contain<i>ee</i>) in the contains-a relationship
+ * that we are querying.
+ * @param parent_index the index in the RootGraph of the Node that is
+ * the parent (the contain<i>er</i>) in the contains-a relationship that we
+ * are querying.
+ * @return true iff the Node corresponding to the latter argument is an
+ * MetaParent (in this GraphPerspective) of the Node corresponding to the former
+ * argument.
+ */
+ public boolean isNodeMetaParent ( int child_node_index, int parent_index ) ;
+
+ /**
+ * Nodes and Edges comprise an additional directed graph through the
+ * contains-a relationship, in which a MetaParent Node contains each of its
+ * MetaChild Nodes and Edges. A Node may have any number of MetaParents.
+ * metaParentsList returns a new List of the MetaParents (in this GraphPerspective)
+ * of the given Node. If there are no MetaParents then the result will be the empty
+ * List - null is returned of the specified Node is not in this GraphPerspective.
+ * @param node the Node that is the child (the contain<i>ee</i>) in the
+ * contains-a relationship that we are querying.
+ * @return a new List of the Nodes in this GraphPerspective that contain the
+ * given Node.
+ */
+ public List metaParentsList ( Node node ) ;
+
+ /**
+ * Nodes and Edges comprise an additional directed graph through the
+ * contains-a relationship, in which a MetaParent Node contains each of its
+ * MetaChild Nodes and Edges. A Node may have any number of MetaParents.
+ * nodeMetaParentsList returns a new List of the MetaParents (in this
+ * GraphPerspective) of the Node in this GraphPerspective with the given
+ * index. If there are no MetaParents then the result will be the empty
+ * List; null is returned if there is no Node in this GraphPerspective with
+ * the specified RootGraph index.
+ * @param node_index the index in the RootGraph of the Node that is
+ * the child (the contain<i>ee</i>) in the contains-a relationship that we
+ * are querying.
+ * @return a new List of the Nodes in this GraphPerspective that contain the
+ * Node with the given index.
+ */
+ public List nodeMetaParentsList ( int node_index ) ;
+
+ /**
+ * Nodes and Edges comprise an additional directed graph through the
+ * contains-a relationship, in which a MetaParent Node contains each of its
+ * MetaChild Nodes and Edges. A Node may have any number of MetaParents.
+ * getNodeMetaParentIndicesArray returns an array of the MetaParents (in this
+ * GraphPerspective) of the Node with the given index. If there are no
+ * MetaParents then the result will be the empty array; null is returned if
+ * there is no Node in this GraphPerspective with specified RootGraph index.
+ * @param node_index the index in the underlying RootGraph of the Node that is
+ * the child (the contain<i>ee</i>) in the contains-a relationship that we
+ * are querying.
+ * @return an array of the indices of the Nodes in this GraphPerspective that
+ * contain the Node with the given index.
+ */
+ public int[] getNodeMetaParentIndicesArray ( int node_index ) ;
+
+ /**
+ * Nodes and Edges comprise an additional directed graph through the
+ * contains-a relationship, in which a MetaParent Node contains each of its
+ * MetaChild Nodes and Edges. A Node may have any number of MetaChildren.
+ * isMetaChild returns true iff the second argument (<tt>child</tt>) is an
+ * MetaChild of the first argument (<tt>parent</tt>) and both Nodes are in this
+ * GraphPerspective.
+ * @param parent the Node that is the parent (the contain<i>er</i>) in the
+ * contains-a relationship that we are querying.
+ * @param child the Node that is the child (the contain<i>ee</i>) in the
+ * contains-a relationship that we are querying.
+ * @return true iff the latter argument is a MetaChild of the former argument
+ * in this GraphPerspective.
+ */
+ public boolean isMetaChild ( Node parent, Node child ) ;
+
+ /**
+ * Nodes and Edges comprise an additional directed graph through the
+ * contains-a relationship, in which a MetaParent Node contains each of its
+ * MetaChild Nodes and Edges. A Node may have any number of MetaChildren.
+ * isMetaChild returns true iff the Node corresponding to the second argument
+ * (<tt>child_index</tt>) is a MetaChild of the Node corresponding to the first
+ * argument (<tt>parent_index</tt>) in this GraphPerspective.
+ * @param parent_index the index in the RootGraph of the Node that is
+ * the parent (the contain<i>er</i>) in the contains-a relationship that we
+ * are querying.
+ * @param child_node_index the index in the RootGraph of the Node
+ * that is the child (the contain<i>ee</i>) in the contains-a relationship
+ * that we are querying.
+ * @return true iff the Node corresponding to the latter argument is an
+ * MetaChild (in this GraphPerspective) of the Node corresponding to the former
+ * argument.
+ */
+ public boolean isNodeMetaChild ( int parent_index, int child_node_index ) ;
+
+ /**
+ * Nodes and Edges comprise an additional directed graph through the
+ * contains-a relationship, in which a MetaParent Node contains each of its
+ * MetaChild Nodes and Edges. A Node may have any number of MetaChildren.
+ * nodeMetaChildrenList returns a new List of the MetaChildren (in this
+ * GraphPerspective) of the given Node. If there are no MetaChildren then the
+ * result will be the empty List; null is returned if the specified Node does not
+ * exist in this GraphPerspective.
+ * @param node the Node that is the parent (the contain<i>er</i>) in the
+ * contains-a relationship that we are querying.
+ * @return a new List of the Nodes in this GraphPerspective that are
+ * contained by the given Node.
+ */
+ public List nodeMetaChildrenList ( Node node ) ;
+
+ /**
+ * Nodes and Edges comprise an additional directed graph through the
+ * contains-a relationship, in which a MetaParent Node contains each of its
+ * MetaChild Nodes and Edges. A Node may have any number of MetaChildren.
+ * nodeMetaChildrenList returns a new List of the Node MetaChildren (in this
+ * GraphPerspective) of the Node in this GraphPerspective with the given
+ * index. If there are no MetaChildren then the result will be the empty List;
+ * null is returned if no Node at specified [RootGraph] index exists in this
+ * GraphPerspective.
+ * @param parent_index the index in the underlying RootGraph of the Node that is
+ * the parent (the contain<i>er</i>) in the contains-a relationship that we
+ * are querying.
+ * @return a new List of the Nodes in this GraphPerspective that are
+ * contained by the Node with the given index.
+ */
+ public List nodeMetaChildrenList ( int parent_index ) ;
+
+ /**
+ * Nodes and Edges comprise an additional directed graph through the
+ * contains-a relationship, in which a MetaParent Node contains each of its
+ * MetaChild Nodes and Edges. A Node may have any number of MetaChildren.
+ * getNodeMetaChildIndicesArray returns an array of the MetaChildren (in this
+ * GraphPerspective) of the Node with the given index. If there are no
+ * MetaChildren then the result will be the empty array; null is returned if
+ * this GraphPerspetive has no Node at specified RootGraph index.
+ * @param node_index the index in the RootGraph of the Node that is
+ * the parent (the contain<i>ee</i>) in the contains-a relationship that we
+ * are querying.
+ * @return an array of the indices of the Nodes in this GraphPerspective that
+ * are contained by the Node with the given index.
+ */
+ public int[] getNodeMetaChildIndicesArray ( int node_index ) ;
+
+ /**
+ * Nodes and Edges comprise an additional directed graph through the
+ * contains-a relationship, in which a MetaParent Node contains each of its
+ * MetaChild Nodes and Edges. An Edge may have any number of MetaParents.
+ * isMetaParent returns true iff the second argument (<tt>parent</tt>) is an
+ * MetaParent of the first argument (<tt>child</tt>) and both elements are in
+ * this GraphPerspective.
+ * @param child the Edge that is the child (the contain<i>ee</i>) in the
+ * contains-a relationship that we are querying.
+ * @param parent the Node that is the parent (the contain<i>er</i>) in the
+ * contains-a relationship that we are querying.
+ * @return true iff the latter argument is a MetaParent of the former argument
+ * in this GraphPerspective.
+ */
+ public boolean isMetaParent ( Edge child, Node parent ) ;
+
+ /**
+ * Nodes and Edges comprise an additional directed graph through the
+ * contains-a relationship, in which a MetaParent Node contains each of its
+ * MetaChild Nodes and Edges. An Edge may have any number of MetaParents.
+ * isMetaParent returns true iff the Node corresponding to the second argument
+ * (<tt>parent_index</tt>) is a MetaParent of the Edge corresponding to the
+ * first argument (<tt>child_index</tt>) and both Edge and Node are in this
+ * GraphPerspective.
+ * @param child_edge_index the index in the RootGraph of the Edge
+ * that is the child (the contain<i>ee</i>) in the contains-a relationship
+ * that we are querying.
+ * @param parent_index the index in the RootGraph of the Node that is
+ * the parent (the contain<i>er</i>) in the contains-a relationship that we
+ * are querying.
+ * @return true iff the Node corresponding to the latter argument is an
+ * MetaParent (in this GraphPerspective) of the Edge corresponding to the former
+ * argument.
+ */
+ public boolean isEdgeMetaParent ( int child_edge_index, int parent_index ) ;
+
+ /**
+ * Nodes and Edges comprise an additional directed graph through the
+ * contains-a relationship, in which a MetaParent Node contains each of its
+ * MetaChild Nodes and Edges. An Edge may have any number of MetaParents.
+ * metaParentsList returns a new List of the MetaParents (in this GraphPerspective)
+ * of the given Edge. If there are no MetaParents then the result will be the
+ * empty List; null is returned if specified Edge is not in this GraphPerspective.
+ * @param edge the Edge that is the child (the contain<i>ee</i>) in the
+ * contains-a relationship that we are querying.
+ * @return a new List of the Nodes in this GraphPerspective that contain the
+ * given Edge.
+ */
+ public List metaParentsList ( Edge edge ) ;
+
+ /**
+ * Nodes and Edges comprise an additional directed graph through the
+ * contains-a relationship, in which a MetaParent Node contains each of its
+ * MetaChild Nodes and Edges. An Edge may have any number of MetaParents.
+ * EdgeMetaParentsList returns a new List of the MetaParents (in this
+ * GraphPerspective) of the Edge in this GraphPerspective with the given
+ * index. If there are no MetaParents then the result will be the
+ * empty List; null is returned if no Edge at specified RootGraph index exists
+ * in this GraphPerspective.
+ * @param edge_index the index in the RootGraph of the Edge that is
+ * the child (the contain<i>ee</i>) in the contains-a relationship that we
+ * are querying.
+ * @return a new List of the Nodes in this GraphPerspective that contain the
+ * Edge with the given index.
+ */
+ public List edgeMetaParentsList ( int edge_index ) ;
+
+ /**
+ * Nodes and Edges comprise an additional directed graph through the
+ * contains-a relationship, in which a MetaParent Node contains each of its
+ * MetaChild Nodes and Edges. An Edge may have any number of MetaParents.
+ * getEdgeMetaParentIndicesArray returns an array of the MetaParents (in this
+ * GraphPerspective) of the Edge with the given index. If there are no
+ * MetaParents then the result will be the empty array; null is returned if
+ * no Edge at specified RootGraph index exists in this GraphPerspective.
+ * @param edge_index the index in the RootGraph of the Edge that is
+ * the child (the contain<i>ee</i>) in the contains-a relationship that we
+ * are querying.
+ * @return an array of the indices of the Nodes in this GraphPerspective that
+ * contain the Edge with the given index.
+ */
+ public int[] getEdgeMetaParentIndicesArray ( int edge_index ) ;
+
+ /**
+ * Nodes and Edges comprise an additional directed graph through the
+ * contains-a relationship, in which a MetaParent Node contains each of its
+ * MetaChild Nodes and Edges. A Node may have any number of MetaChildren.
+ * isMetaChild returns true iff the second argument (<tt>child</tt>) is an
+ * MetaChild of the first argument (<tt>parent</tt>) and both Node and Edge
+ * are in this GraphPerspective.
+ * @param parent the Node that is the parent (the contain<i>er</i>) in the
+ * contains-a relationship that we are querying.
+ * @param child the Edge that is the child (the contain<i>ee</i>) in the
+ * contains-a relationship that we are querying.
+ * @return true iff the latter argument is a MetaChild of the former argument
+ * in this GraphPerspective.
+ */
+ public boolean isMetaChild ( Node parent, Edge child ) ;
+
+ /**
+ * Nodes and Edges comprise an additional directed graph through the
+ * contains-a relationship, in which a MetaParent Node contains each of its
+ * MetaChild Nodes and Edges. A Node may have any number of MetaChildren.
+ * isMetaChild returns true iff the Edge corresponding to the second argument
+ * (<tt>child_index</tt>) is a MetaChild of the Node corresponding to the first
+ * argument (<tt>parent_index</tt>) in this GraphPerspective.
+ * @param parent_index the index in the RootGraph of the Node that is
+ * the parent (the contain<i>er</i>) in the contains-a relationship that we
+ * are querying.
+ * @param child_edge_index the index in the RootGraph of the Edge
+ * that is the child (the contain<i>ee</i>) in the contains-a relationship
+ * that we are querying.
+ * @return true iff the Edge corresponding to the latter argument is an
+ * MetaChild (in this GraphPerspective) of the Node corresponding to the former
+ * argument.
+ */
+ public boolean isEdgeMetaChild ( int parent_index, int child_edge_index ) ;
+
+ /**
+ * Nodes and Edges comprise an additional directed graph through the
+ * contains-a relationship, in which a MetaParent Node contains each of its
+ * MetaChild Nodes and Edges. A Node may have any number of MetaChildren.
+ * edgeMetaChildrenList returns a new List of the Edge MetaChildren (in this
+ * GraphPerspective) of the given Node. If there are no Edge MetaChildren then
+ * the result will be the empty List; returns null if specified Node is not in
+ * this GraphPerspective.
+ * @param node the Node that is the parent (the contain<i>er</i>) in the
+ * contains-a relationship that we are querying.
+ * @return a new List of the Edges in this GraphPerspective that are
+ * contained by the given Node.
+ */
+ public List edgeMetaChildrenList ( Node node ) ;
+
+ /**
+ * Nodes and Edges comprise an additional directed graph through the
+ * contains-a relationship, in which a MetaParent Node contains each of its
+ * MetaChild Nodes and Edges. A Node may have any number of MetaChildren.
+ * edgeMetaChildrenList returns a new List of the Edge MetaChildren (in this
+ * GraphPerspective) of the Node in this GraphPerspective with the given
+ * index. If there are no Edge MetaChildren then the result will be the
+ * empty List; null is returned if no Node exists in this GraphPerspective at
+ * specified RootGraph index.
+ * @param node_index the index in the RootGraph of the Node that is
+ * the parent (the contain<i>er</i>) in the contains-a relationship that we
+ * are querying.
+ * @return a new List of the Edges in this GraphPerspective that are
+ * contained by the Node with the given index.
+ */
+ public List edgeMetaChildrenList ( int node_index ) ;
+
+ /**
+ * Nodes and Edges comprise an additional directed graph through the
+ * contains-a relationship, in which a MetaParent Node contains each of its
+ * MetaChild Nodes and Edges. A Node may have any number of MetaChildren.
+ * getEdgeMetaChildIndicesArray returns an array of the MetaChildren (in this
+ * GraphPerspective) of the Node with the given index. If there are no
+ * MetaChildren then the result will be the empty array; null is returned if no
+ * Node exists in this GraphPerspective at the specified RootGraph index.
+ * @param node_index the index in the RootGraph of the Node that is
+ * the parent (the contain<i>ee</i>) in the contains-a relationship that we
+ * are querying.
+ * @return an array of the indices of the Edges in this GraphPerspective that
+ * are contained by the Node with the given index.
+ */
+ public int[] getEdgeMetaChildIndicesArray ( int node_index ) ;
+
+
+ /**
+ * Returns all Adjacent Edges to the given node.
+ * @param node the node
+ * @param include_undirected_edges should we include undirected edges
+ * @param incoming_edges Include incoming edges
+ * @param outgoing_edges Include outgoing edges
+ * @return a List of giny.model.Edge objects; an empty List is returned if
+ * no adjacent Edges are found; null is returned if the specified Node does not
+ * exist in this GraphPerspective.
+ * @deprecated Use getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean) instead.
+ * @see #getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean)
+ */
+ public List getAdjacentEdgesList ( Node node, boolean include_undirected_edges, boolean incoming_edges, boolean outgoing_edges );
+
+ /**
+ * Returns [RootGraph] indices of all Edges in this GraphPerspective
+ * adjacent to the Node at specified [RootGraph] index.
+ * See definitions of adjacency below.
+ *
+ * @param node_index the [RootGraph] index of the Node whose adjacent
+ * Edge information we're seeking.
+ * @param undirected_edges Edge indices of all adjacent
+ * undirected Edges are included in the return value of this
+ * method if this value is true, otherwise not a single
+ * index corresponding to an undirected Edge is returned;
+ * undirected Edge E is an adjacent undirected Edge to Node N
+ * [definition:] if and only if E's source is N or E's target
+ * is N.
+ * @param incoming_directed_edges Edge indices of all incoming
+ * directed Edges are included in the return value of this
+ * method if this value is true, otherwise not a single index
+ * corresponding to an incoming directed Edge is returned;
+ * directed Edge E is an incoming directed Edge to Node N
+ * [definition:] if and only if N is E's target.
+ * @param outgoing_directed_edges Edge indices of all outgoing
+ * directed Edges are included in the return value of this
+ * method if this value is true, otherwise not a single index
+ * corresponding to an outgoing directed Edge is returned;
+ * directed Edge E is an outgoing directed Edge from Node N
+ * [definition:] if and only if N is E's source.
+ * @return a set of Edge [RootGraph] indices corresponding to
+ * Edges matched by our query; if all three of the boolean
+ * query parameters are false, the empty array is returned;
+ * null is returned if and only if this GraphPerspective has no Node
+ * at the specified [RootGraph] index.
+ */
+ public int[] getAdjacentEdgeIndicesArray ( int node_index,
+ boolean undirected_edges,
+ boolean incoming_directed_edges,
+ boolean outgoing_directed_edges );
+
+
+ /**
+ * This will return a List of giny.model.Edge objects that are the Edges between Nodes.
+ * WARNING: This will return null if any of the input nodes are not in this graph perspective!!
+ */
+ public List getConnectingEdges ( List nodes );
+
+ /**
+ * This will return an array of Edge indices that are the Edges between Nodes or
+ * null if even one node index is not in this graph perspective.
+ */
+ public int[] getConnectingEdgeIndicesArray ( int[] node_indices );
+
+ /**
+ * Return the Nodes that connect the given Edges in this GraphPerspective.
+ * @deprecated Use getEdgeSourceIndex(int) and getEdgeTargetIndex(int) instead.
+ * @see #getEdgeSourceIndex(int)
+ * @see #getEdgeTargetIndex(int)
+ */
+ public int[] getConnectingNodeIndicesArray ( int[] edge_indices );
+
+ /**
+ * Create a new GraphPerspective given a list of Nodes. This method
+ * will automatically find all the interconnected Edges.
+ * Returns null if any of the specified Nodes are not in this GraphPerspective.
+ */
+ public GraphPerspective createGraphPerspective( int[] node_indices );
+
+}
diff --git a/corelibs/giny/src/main/java/giny/model/GraphPerspectiveChangeEvent.java b/corelibs/giny/src/main/java/giny/model/GraphPerspectiveChangeEvent.java
new file mode 100755
index 0000000..48c7185
--- /dev/null
+++ b/corelibs/giny/src/main/java/giny/model/GraphPerspectiveChangeEvent.java
@@ -0,0 +1,146 @@
+package giny.model;
+
+import java.util.EventObject;
+
+/**
+ * The event source must be the GraphPerspective that changed.
+ */
+public abstract class GraphPerspectiveChangeEvent
+ extends EventObject {
+
+ public static final int NODES_RESTORED_TYPE = 1;
+ public static final int EDGES_RESTORED_TYPE = 2;
+ public static final int NODES_HIDDEN_TYPE = 4;
+ public static final int EDGES_HIDDEN_TYPE = 8;
+ public static final int NODES_SELECTED_TYPE = 16;
+ public static final int NODES_UNSELECTED_TYPE = 32;
+ public static final int EDGES_SELECTED_TYPE = 64;
+ public static final int EDGES_UNSELECTED_TYPE = 128;
+
+ /**
+ * The source parameter should be either a RootGraph or a GraphPerspective;
+ * see specification of getSource().
+ * @see #getSource()
+ */
+ public GraphPerspectiveChangeEvent ( Object source ) {
+ super( source );
+ }
+
+ /**
+ * The Object returned is one of two types - either a GraphPerspective or
+ * a RootGraph. The return value is a RootGraph if this event is a
+ * NODES_HIDDEN_TYPE or EDGES_HIDDEN_TYPE which resulted from Nodes or
+ * Edges being removed from the underlying RootGraph of a GraphPerspective;
+ * the return value is a GraphPerspective in all other cases.
+ */
+ public final Object getSource() {
+ return super.getSource(); }
+
+ public abstract int getType ();
+ public abstract boolean isNodesRestoredType ();
+ public abstract boolean isEdgesRestoredType ();
+ public abstract boolean isNodesHiddenType ();
+ public abstract boolean isEdgesHiddenType ();
+
+ /**
+ * @deprecated Nowhere in GraphPerspective is there functionality that
+ * specifies node selection logic.
+ */
+ public abstract boolean isNodesSelectedType ();
+
+ /**
+ * @deprecated Nowhere in GraphPerspective is there functionality that
+ * specifies node un-selection logic.
+ */
+ public abstract boolean isNodesUnselectedType ();
+
+ /**
+ * @deprecated Nowhere in GraphPerspective is there functionality that
+ * specifies edge selection logic.
+ */
+ public abstract boolean isEdgesSelectedType ();
+
+ /**
+ * @deprecated Nowhere in GraphPerspective is there functionality that
+ * specifies edge un-selection logic.
+ */
+ public abstract boolean isEdgesUnselectedType ();
+
+ public abstract Node[] getRestoredNodes ();
+ public abstract Edge[] getRestoredEdges ();
+
+ /**
+ * @deprecated Use getHiddenNodeIndices() instead; the nodes returned by
+ * this method may have undefined state.
+ * @see #getHiddenNodeIndices()
+ */
+ public abstract Node[] getHiddenNodes ();
+
+ /**
+ * @deprecated Use getHiddenEdgeIndices() instead; the edges returned by
+ * this method may have undefined state.
+ * @see #getHiddenEdgeIndices()
+ */
+ public abstract Edge[] getHiddenEdges ();
+
+ /**
+ * @deprecated Nowhere in GraphPerspective is there functionality that
+ * specifies node selection logic.
+ */
+ public abstract Node[] getSelectedNodes ();
+
+ /**
+ * @deprecated Nowhere in GraphPerspective is there functionality that
+ * specifies node un-selection logic.
+ */
+ public abstract Node[] getUnselectedNodes ();
+
+ /**
+ * @deprecated Nowhere in GraphPerspective is there functionality that
+ * specifies edge selection logic.
+ */
+ public abstract Edge[] getSelectedEdges ();
+
+ /**
+ * @deprecated Nowhere in GraphPerspective is there functionality that
+ * specifies edge un-selection logic.
+ */
+ public abstract Edge[] getUnselectedEdges ();
+
+ /** The integer values in the returned array are RootGraph indices. */
+ public abstract int[] getRestoredNodeIndices ();
+
+ /** The integer values in the returned array are RootGraph indices. */
+ public abstract int[] getRestoredEdgeIndices ();
+
+ /** The integer values in the returned array are RootGraph indices. */
+ public abstract int[] getHiddenNodeIndices ();
+
+ /** The integer values in the returned array are RootGraph indices. */
+ public abstract int[] getHiddenEdgeIndices ();
+
+ /**
+ * @deprecated Nowhere in GraphPerspective is there functionality that
+ * specifies node selection logic.
+ */
+ public abstract int[] getSelectedNodeIndices ();
+
+ /**
+ * @deprecated Nowhere in GraphPerspective is there functionality that
+ * specifies node un-selection logic.
+ */
+ public abstract int[] getUnselectedNodeIndices ();
+
+ /**
+ * @deprecated Nowhere in GraphPerspective is there functionality that
+ * specifies edge selection logic.
+ */
+ public abstract int[] getSelectedEdgeIndices ();
+
+ /**
+ * @deprecated Nowhere in GraphPerspective is there functionality that
+ * specifies edge un-selection logic.
+ */
+ public abstract int[] getUnselectedEdgeIndices ();
+
+} // abstract class GraphPerspectiveChangeEvent
diff --git a/corelibs/giny/src/main/java/giny/model/GraphPerspectiveChangeListener.java b/corelibs/giny/src/main/java/giny/model/GraphPerspectiveChangeListener.java
new file mode 100755
index 0000000..0e494e3
--- /dev/null
+++ b/corelibs/giny/src/main/java/giny/model/GraphPerspectiveChangeListener.java
@@ -0,0 +1,14 @@
+package giny.model;
+
+import java.util.EventListener;
+
+public interface GraphPerspectiveChangeListener
+ extends EventListener {
+
+ /**
+ * Invoked when a GraphPerspective to which this
+ * GraphPerspectiveChangeListener listens changes.
+ */
+ public void graphPerspectiveChanged ( GraphPerspectiveChangeEvent event );
+
+} // interface GraphPerspectiveChangeListener
diff --git a/corelibs/giny/src/main/java/giny/model/NestedNetworkChangeEvent.java b/corelibs/giny/src/main/java/giny/model/NestedNetworkChangeEvent.java
new file mode 100644
index 0000000..aefaa70
--- /dev/null
+++ b/corelibs/giny/src/main/java/giny/model/NestedNetworkChangeEvent.java
@@ -0,0 +1,47 @@
+package giny.model;
+
+import java.util.EventObject;
+
+import giny.view.GraphView;
+
+/**
+ * This event will be fired when nested network is created/removed.
+ *
+ * @author kono
+ *
+ */
+public class NestedNetworkChangeEvent extends EventObject {
+ /**
+ *
+ */
+ private static final long serialVersionUID = -4279473805735358503L;
+
+ private final Node parentNode;
+ private final GraphView graphView;
+
+ public NestedNetworkChangeEvent(Object source, Node parentNode, GraphView nestedGraphView) {
+ super(source);
+ this.parentNode = parentNode;
+ this.graphView = nestedGraphView;
+ }
+
+
+ /**
+ *
+ * @return Node points to the nested network.
+ */
+ public Node getNestedNode() {
+ return parentNode;
+ }
+
+
+ /**
+ * Nested network view pointed by a node in other network.
+ * This can be null because network view may not be available at this point.
+ *
+ * @return nested network.
+ */
+ public GraphView getNestedNetworkView() {
+ return this.graphView;
+ }
+}
diff --git a/corelibs/giny/src/main/java/giny/model/NestedNetworkChangeEventListener.java b/corelibs/giny/src/main/java/giny/model/NestedNetworkChangeEventListener.java
new file mode 100644
index 0000000..33b8ce1
--- /dev/null
+++ b/corelibs/giny/src/main/java/giny/model/NestedNetworkChangeEventListener.java
@@ -0,0 +1,17 @@
+package giny.model;
+
+import java.util.EventListener;
+
+/**
+ * Listener for nested network change events.
+ * <p>
+ * This can handle both creation and deletion of nested networks.
+ *
+ * @author kono
+ *
+ */
+public interface NestedNetworkChangeEventListener extends EventListener {
+
+ public void nestedNetworkChanged(NestedNetworkChangeEvent evt);
+
+}
diff --git a/corelibs/giny/src/main/java/giny/model/Node.java b/corelibs/giny/src/main/java/giny/model/Node.java
new file mode 100644
index 0000000..53d488c
--- /dev/null
+++ b/corelibs/giny/src/main/java/giny/model/Node.java
@@ -0,0 +1,47 @@
+package giny.model;
+
+import java.util.*;
+
+
+public interface Node extends GraphObject {
+
+ /**
+ * If a Node is a meta-parent of any other nodes and edges,
+ * then it contains those nodes and edges
+ * in a <code>GraphPerspective</code>. This method returns such
+ * a GraphPerspective.
+ * @deprecated Don't use this method because the behavior of the returned
+ * GraphPerspective with respect to changing meta-children of this Node
+ * is ill-defined; use RootGraph.getNodeMetaChildIndicesArray(int) and
+ * RootGraph.getEdgeMetaChildIndicesArray(int) instead.
+ * @see RootGraph#getNodeMetaChildIndicesArray(int)
+ * @see RootGraph#getEdgeMetaChildIndicesArray(int)
+ */
+ public GraphPerspective getGraphPerspective ();
+
+ /**
+ * This method adds all Nodes and Edges contained in the specified
+ * GraphPerspective as children of this Node.
+ * The return value of this method is undefined and should not be used.
+ * @deprecated Don't use this method because the behavior of the
+ * input GraphPerspective with respect to changing meta-children of
+ * this Node is ill-defined; use RootGraph.addNodeMetaChild(int, int) and
+ * RootGraph.addEdgeMetaChild(int, int) instead.
+ * @see RootGraph#addNodeMetaChild(int, int)
+ * @see RootGraph#addEdgeMetaChild(int, int)
+ */
+ public boolean setGraphPerspective ( GraphPerspective gp );
+
+ /**
+ * Assign a graph perspective reference to this node.
+ */
+ public void setNestedNetwork(final GraphPerspective graphPerspective);
+
+ /**
+ * Return the currently set graph perspective (may be null) associated with this node.
+ *
+ * @return a network reference or null.
+ */
+ public GraphPerspective getNestedNetwork();
+
+} // interface Node
diff --git a/corelibs/giny/src/main/java/giny/model/RootGraph.java b/corelibs/giny/src/main/java/giny/model/RootGraph.java
new file mode 100644
index 0000000..0451c65
--- /dev/null
+++ b/corelibs/giny/src/main/java/giny/model/RootGraph.java
@@ -0,0 +1,1295 @@
+package giny.model;
+
+import java.util.Iterator;
+import java.util.List;
+import java.util.ArrayList;
+import java.util.NoSuchElementException;
+
+import java.beans.PropertyChangeSupport;
+import java.beans.PropertyChangeListener;
+
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.EventListenerList;
+
+/**
+ * <h2>GINY Architecture</h2>
+ * A graph model consisting of nodes and the edges between them. GINY graph
+ * models are separated into RootGraphs and GraphPerspectives. RootGraphs
+ * contain all Nodes and Edges in a graph, while GraphPerspectives contain some
+ * subset of them (any given GraphPerspective may include all Nodes and Edges
+ * from its RootGraph, but it does not need to). Every GraphPerspective has
+ * exactly one RootGraph. RootGraphs may have any number of GraphPerspectives.
+
+ * <h2>Indices</h2>
+ * Every Node and Edge has a unique and unchanging index in its RootGraph;
+ * these indices are always negative integers and are not guaranteed to be
+ * consecutive. Note that if you would
+ * like to associate additional data with a Node or an Edge, you can associate
+ * the data with the Node's or the Edge's RootGraph index, which is guaranteed
+ * to be unique for the lifetime of the RootGraph.
+
+ * <h2>MetaNodes</h2>
+ * Nodes and Edges comprise an additional directed graph through the
+ * contains-a relationship, in which a MetaParent Node contains each of its
+ * MetaChild Nodes and Edges. A Node may have any number of MetaChildren, and
+ * a Node or Edge may have any number of MetaParents. This is how GINY
+ * supports graphs-within-graphs.
+ **/
+public interface RootGraph {
+
+ /**
+ * Create a new GraphPerspective with just the given Nodes and Edges (and all
+ * Nodes incident on the given Edges).<p>
+ * TECHNICAL DETAIL: Each Node in the Node array input parameter
+ * should be a Node that was previously returned by a method of this RootGraph or by
+ * a method of another component that this RootGraph system defines.
+ * Likewise, each Edge in the Edge array input parameter
+ * should be an Edge that was previously returned by a method of this RootGraph or by
+ * a method of another component that this RootGraph system defines.
+ * If this is not the case, results of calling this method are undefined.
+ * @param nodes A [possibly null] array of Nodes in this RootGraph to include in the new
+ * GraphPerspective
+ * @param edges A [possibly null] array of Edges in this RootGraph to include in the new
+ * GraphPerspective
+ * @return a new GraphPerspective on this RootGraph containing only the given
+ * Nodes and Edges, plus any Nodes incident on the given Edges array but
+ * omitted from the given Nodes array; returns null if any of the specified Nodes
+ * or Edges are not in this RootGraph.
+ */
+ public GraphPerspective createGraphPerspective (
+ Node[] nodes,
+ Edge[] edges
+ );
+
+ /**
+ * Create a new GraphPerspective with just the given Nodes and Edges (and all
+ * Nodes incident on the given Edges).
+ * @param node_indices A [possibly null] array of indices of Nodes in this RootGraph to
+ * include in the new GraphPerspective
+ * @param edge_indices A [possibly null] array of indices of Edges in this RootGraph to
+ * include in the new GraphPerspective
+ * @return a new GraphPerspective on this RootGraph containing only Nodes and
+ * Edges with the given indices, including all Nodes incident on those Edges;
+ * returns null if any of the specified Node or Edge indices do not correspond
+ * to Nodes or Edges existing in this RootGraph.
+ */
+ public GraphPerspective createGraphPerspective (
+ int[] node_indices,
+ int[] edge_indices
+ );
+
+ /**
+ * @deprecated Please don't call this silly method; implementors: I suggest
+ * creating an easter egg and having it take effect when this method is called.
+ */
+ public void ensureCapacity( int nodes, int edges );
+
+ /**
+ * Returns number of nodes in this RootGraph. A call to nodesIterator()
+ * will return an Iterator containing exactly getNodeCount() elements
+ * (unless nodes are created or removed in the meantime).
+ * @return the number of nodes in this RootGraph.
+ */
+ public int getNodeCount ();
+
+ /**
+ * Returns number of edges in this RootGraph. A call to edgesIterator()
+ * will return an iterator containing exactly getEdgeCount() elements
+ * (unless nodes or edges are created or removed in the meantime).
+ * @return the number of edges in this RootGraph.
+ */
+ public int getEdgeCount ();
+
+ /**
+ * Returns an Iterator over all giny.model.Node objects in this RootGraph.<p>
+ * TECHNICAL DETAIL: Iterating over the set of all nodes in a RootGraph and
+ * manipulating a RootGraph's topology (by calling removeXXX() and createXXX() methods)
+ * concurrently will have undefined effects on the returned Iterator.
+ * @return an Iterator over the Nodes in this graph; each Object in the
+ * returned Iterator is of type giny.model.Node.
+ */
+ public Iterator nodesIterator ();
+
+ /**
+ * Returns a list of Node objects.
+ * @see #nodesIterator()
+ */
+ public List nodesList ();
+
+ /**
+ * Returns an array of node indices.
+ * @see #nodesIterator()
+ * @see Node#getRootGraphIndex()
+ */
+ public int[] getNodeIndicesArray ();
+
+ /**
+ * Returns an Iterator over all giny.model.Edge objects in this RootGraph.<p>
+ * TECHNICAL DETAIL: Iterating over the set of all edges in a RootGraph and
+ * manipulating a RootGraph's topology (by calling removeXXX() and createXXX()
+ * methods) concurrently will have undefined effects on the returned Iterator.
+ * @return an Iterator over the Edges in this graph; each Object in the
+ * returned Iterator is of type giny.model.Edge.
+ */
+ public Iterator edgesIterator ();
+
+ /**
+ * Returns a list of Edge objects.
+ * @see #edgesIterator()
+ */
+ public List edgesList ();
+
+ /**
+ * Returns an array of edge indices.
+ * @see #edgesIterator()
+ * @see Edge#getRootGraphIndex()
+ */
+ public int[] getEdgeIndicesArray ();
+
+ /**
+ * Remove the given Node and all Edges incident on it from this RootGraph and
+ * all of its GraphPerspectives.<p>
+ * TECHNICAL DETAIL: The Node input parameter should be a Node that was
+ * previously returned by a method of this RootGraph or by a method of another
+ * component that this RootGraph system defines. If this is not the case,
+ * results of calling this method are undefined.<p>
+ * IMPORTANT! The returned Node object, if not null, should not be used
+ * to query fields by calling methods on that returned Node object - the returned
+ * Node's behavior is completely undefined. For
+ * example, an implementation of RootGraph may choose to return a Node object
+ * whose getRootGraphIndex() method returns a positive value. The purpose
+ * of the return value of this method is purely to mark "success" or
+ * "not success" - in fact, if this API were redesigned, the return value of
+ * this operation would become a boolean value.
+ * @param node The Node to remove.
+ * @return A non-null Node marking a successful removal,
+ * or null if specified Node does not belong to this RootGraph.
+ */
+ public Node removeNode ( Node node );
+
+ /**
+ * Remove the Node with the given index (and all of that Node's incident
+ * Edges) from this RootGraph and all of its GraphPerspectives.
+ * @param node_index The index in this RootGraph of the Node to remove.
+ * @return The index of the removed Node, or 0 if the given index does not
+ * correspond to an existing Node in this RootGraph.
+ */
+ public int removeNode(int node_index);
+
+ /**
+ * @deprecated Use removeNode(Node) or removeNodes(int[]) instead.
+ * @see #removeNode(Node)
+ * @see #removeNodes(int[])
+ */
+ public List removeNodes ( List nodes );
+
+ /**
+ * Remove the Nodes with the given indices (and all of those Nodes' incident
+ * Edges) from this RootGraph and all of its GraphPerspectives.
+ * @param node_indices An non-null array of the indices in this RootGraph of the
+ * Nodes to remove.
+ * @return An int array of equal length to the argument array, and with equal
+ * values except at positions that in the input array contain indices
+ * corresponding to Nodes that don't exist in this RootGraph; at these positions the
+ * result array will contain the value 0.
+ * @deprecated Use removeNode(int) instead.
+ * @see #removeNode(int)
+ */
+ public int[] removeNodes ( int[] node_indices );
+
+ /**
+ * Create a new Node in this RootGraph, and return its index.
+ * @return the index of the newly created Node.
+ */
+ public int createNode();
+
+ /**
+ * Create a new Node in this RootGraph, and return its index. The new Node
+ * will be a MetaParent to the Nodes and Edges given, and also to any Nodes
+ * incident on the given Edges but omitted from the array.<p>
+ * TECHNICAL DETAIL: The Node and Edge input parameters should be objects
+ * that were previously returned by methods of this RootGraph or by methods
+ * of another component that this RootGraph system defines. If this is
+ * not the case, results of calling this method are undefined.
+ * @param nodes a [possibly null] array of Nodes that will be MetaChildren of
+ * the newly created Node.
+ * @param edges a [possibly null] array of Edges that will be MetaChildren of
+ * the newly created Node.
+ * @return the index of the newly created Node, or 0 if any of the given
+ * Nodes or Edges are not in this RootGraph.
+ */
+ public int createNode ( Node[] nodes, Edge[] edges );
+
+ /**
+ * Create a new Node in this RootGraph, and return its index.<p>
+ * TECHNICAL DETAIL: The GraphPerspective input parameter should be an
+ * object that was previously returned by this RootGraph or by a method
+ * of another component that this RootGraph system defines.
+ * If this is not the case, results of calling
+ * this method are undefined.
+ * @param perspective a [possibly null] GraphPerspective of this RootGraph,
+ * containing the Nodes and Edges that will be MetaChildren of the newly created
+ * Node.
+ * @return the index of the newly created Node, or 0 if the given
+ * GraphPerspective is not a perspective on this RootGraph.
+ */
+ public int createNode ( GraphPerspective perspective );
+
+ /**
+ * Create a new Node in this RootGraph, and return its index. The new Node
+ * will be a MetaParent to the Nodes and Edges with the given indices, and also
+ * to any Nodes incident on the given Edges but omitted from the array.
+ * @param node_indices a [possibly null] array of the indices in this
+ * RootGraph of the Nodes that will be MetaChildren of the newly created Node.
+ * @param edge_indices a [possibly null] array of the indices in this
+ * RootGraph of the Edges that will be MetaChildren of the newly created Node.
+ * @return the index of the newly created Node, or 0 if any node or edge
+ * index specified is not a valid index of node or edge [respectively]
+ * in this RootGraph.
+ */
+ public int createNode ( int[] node_indices, int[] edge_indices );
+
+ /**
+ * Create <tt>new_node_count</tt> new Nodes in this RootGraph, and return
+ * their indices.
+ * @param new_node_count the number of new nodes to create.
+ * @return an array of length new_node_count containing the indices of the
+ * newly created Nodes.
+ * @deprecated Use createNode() instead.
+ * @see #createNode()
+ */
+ public int[] createNodes ( int new_node_count );
+
+ /**
+ * Remove the given Edge from this RootGraph and all of its
+ * GraphPerspectives.<p>
+ * TECHNICAL DETAIL: The Edge input parameter should be an Edge that was
+ * previously returned by a method of this RootGraph or by a method
+ * of another component that this RootGraph system defines. If this is not the case,
+ * results of calling this method are undefined.<p>
+ * IMPORTANT! The returned Edge object, if not null, should not be used
+ * to query fields by calling methods on that returned Edge object - the returned
+ * Edge's behavior is completely undefined. For example,
+ * an implementation of RootGraph may choose to return an Edge object
+ * whose getRootIndex() methods returns a positive value. The purpose of the
+ * return value of this method is purely to mark "success" or "not success" - in
+ * fact, if this API were redesigned, the return value of this operation would become
+ * a boolean value.
+ * @param edge The Edge to remove.
+ * @return A non-null Edge marking a successful removal,
+ * or null if the specified Edge does not belong to this RootGraph.
+ */
+ public Edge removeEdge ( Edge edge );
+
+ /**
+ * Remove the Edge with the given index from this RootGraph and all of its
+ * GraphPerspectives.
+ * @param edge_index The index in this RootGraph of the Edge to remove.
+ * @return The index of the removed Edge, or 0 if the given index does not
+ * correspond to an existing Edge in this RootGraph.
+ */
+ public int removeEdge(int edge_index);
+
+ /**
+ * @deprecated Use removeEdge(Edge) or removeEdges(int[]) instead.
+ * @see #removeEdge(Edge)
+ * @see #removeEdges(int[])
+ */
+ public List removeEdges ( List edges );
+
+ /**
+ * Remove the Edges with the given indices from this RootGraph and all of its
+ * GraphPerspectives.
+ * @param edge_indices A non-null array of the indices in this RootGraph of the
+ * Edges to remove.
+ * @return An array of equal length to the argument array, and with equal
+ * values except at positions that in the input array contain indices
+ * corresponding to Edges that don't exist in this RootGraph; at these positions the
+ * result array will contain the value 0.
+ * @deprecated Use removeEdge(int) instead.
+ * @see #removeEdge(int)
+ */
+ public int[] removeEdges ( int[] edge_indices );
+
+ /**
+ * Create a directed Edge from the given <tt>source</tt> Node to the given
+ * <tt>target</tt> Node, and return its index. This edge created will be
+ * directed, except in the case where the source and target nodes are
+ * the same node, in which case the created edge will be undirected.<p>
+ * TECHNICAL DETAIL: Each of the two Node input parameters should be a Node that was
+ * previously returned by a method of this RootGraph or by a method
+ * of another component that this RootGraph system defines. If this is not the case,
+ * results of calling this method are undefined.
+ * @param source the source of the new directed Edge
+ * @param target the target of the new directed Edge
+ * @return the index of the newly created Edge, or 0 if either the
+ * source or target Node is not in this RootGraph.
+ */
+ public int createEdge ( Node source, Node target );
+
+ /**
+ * Create an Edge from the given <tt>source</tt> Node to the given
+ * <tt>target</tt> Node, and return its index. The newly created Edge will
+ * be directed iff the boolean argument is true.<p>
+ * TECHNICAL DETAIL: Each of the two Node input parameters should be a Node that was
+ * previously returned by a method of this RootGraph or by a method
+ * of another component that this RootGraph system defines. If this is not the case,
+ * results of calling this method are undefined.
+ * @param source the source of the new Edge
+ * @param target the target of the new Edge
+ * @param directed The new Edge will be directed iff this argument is true.
+ * @return the index of the newly created Edge, or 0 if either the source
+ * or target Node is not in this RootGraph.
+ */
+ public int createEdge ( Node source, Node target, boolean directed );
+
+ /**
+ * Create a directed Edge from the Node with the given <tt>source_index</tt>
+ * to the Node with the given <tt>target_index</tt>, and return the new
+ * Edge's index. This edge created will be
+ * directed, except in the case where the source and target nodes are
+ * the same node, in which case the created edge will be undirected.
+ * @param source_index the index in this RootGraph of the source of the new
+ * directed Edge
+ * @param target_index the index in this RootGraph of the target of the new
+ * directed Edge
+ * @return the index of the newly created Edge, or 0 if either the source
+ * node index or the target node index does not correspond to an existing
+ * Node in this RootGraph.
+ */
+ public int createEdge ( int source_index, int target_index );
+
+ /**
+ * Create an Edge from the Node with the given <tt>source_index</tt> to the
+ * Node with the given <tt>target_index</tt>, and return the new Edge's
+ * index. The newly created Edge will be directed iff the boolean argument
+ * is true.
+ * @param source_index the index in this RootGraph of the source of the new
+ * Edge
+ * @param target_index the index in this RootGraph of the target of the new
+ * Edge
+ * @param directed The new Edge will be directed iff this argument is true.
+ * @return the index of the newly created Edge, or 0 if either the source
+ * node index or the target node index does not correspond to an existing
+ * Node in this RootGraph.
+ */
+ public int createEdge(int source_index, int target_index, boolean directed);
+
+ /**
+ * Create some Edges. The indices of the sources and the targets are given
+ * in two arrays, which must be of equal length, and the indices of the
+ * created edges are returned in an array of the same length. The newly
+ * created Edges will be directed iff the boolean argument is true.<p>
+ * If returnArr represents the int[] that is returned by this method, then
+ * returnArr[i] defines the index of newly created edge whose source node index
+ * is source_indices[i] and whose target node index is
+ * target_indices[i].
+ * @param source_indices a non-null array of the indices of the source Nodes for the
+ * new Edges.
+ * @param target_indices a non-null array of length <tt>source_indices.length</tt> of
+ * the indices of the target Nodes for the new Edges.
+ * @param directed The new Edges will be directed iff this argument is true.
+ * @return an array of length <tt>source_indices.length</tt> of the indices
+ * of the newly created Edges; an entry of 0 in the returned array corresponds
+ * an ill-defined source or target node index within the input parameters, at the same
+ * array offset.
+ * @deprecated Use createEdge(int, int, boolean) instead.
+ * @see #createEdge(int, int, boolean)
+ */
+ public int[] createEdges (int[] source_indices,
+ int[] target_indices,
+ boolean directed
+ );
+
+ /**
+ * Return true if the given Node is in this RootGraph. False
+ * otherwise.<p>
+ * TECHNICAL DETAIL: The Node input parameter should be an object
+ * that was previously returned by a method of this RootGraph or by
+ * a method of another component that this RootGraph system defines.
+ * If this is not the case, results of calling this method are undefined.
+ * @return true iff the given Node is in this RootGraph.
+ */
+ public boolean containsNode ( Node node );
+
+ /**
+ * Return true if the given Edge is in this RootGraph. False
+ * otherwise.<p>
+ * TECHNICAL DETAIL: The Edge input parameter should be an object
+ * that was previously returned by a method of this RootGraph or by
+ * a method of another component that this RootGraph system defines.
+ * If this is not the case, results of calling this method are undefined.
+ * @return true iff the given Edge is in this RootGraph.
+ */
+ public boolean containsEdge ( Edge edge );
+
+ /**
+ * @deprecated Use getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean) instead;
+ * if you decide to use this method anyways, please note that the definition
+ * of "node neighbor" is such: Node A is a "node neighbor" of node B if and only
+ * if there exists an edge [directed or undirected] E such that A is E's target and
+ * B is E's source, or
+ * A is E's source and B is E's target; this method then returns a non-repeating list
+ * of all nodes N in this
+ * RootGraph such that N is a "node neighbor" of node, the input parameter.
+ * @see #getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean)
+ */
+ public List neighborsList ( Node node );
+
+ /**
+ * @deprecated Use getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean) instead;
+ * if you decide to use this method anyways, please note that the definition
+ * of "node neighbor" is such: Node A is a "node neighbor" of node B if and only
+ * if there exists an edge [directed or undirected] E such that A is E's target and
+ * B is E's source, or A is E's source and B is E's target; this method then returns
+ * true if and only if a_node is a "node neighbor" of another_node in this RootGraph.
+ * @see #getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean)
+ */
+ public boolean isNeighbor ( Node a_node, Node another_node );
+
+ /**
+ * @deprecated Use getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean) instead;
+ * if you decide to use this method anyways, please note that the definition
+ * of "node neighbor" is such: Node A is a "node neighbor" of node B if and only
+ * if there exists an edge [directed or undirected] E such that A is E's target and
+ * B is E's source, or A is E's source and B is E's target; this method then returns
+ * true if and only if node at index a_node_index is a "node neighbor" of node at
+ * index another_node_index in this RootGraph.
+ * @see #getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean)
+ */
+ public boolean isNeighbor ( int a_node_index, int another_node_index );
+
+ /**
+ * @deprecated Use getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean) instead;
+ * if you decide to use this method anyways: this method returns true if and only if
+ * either 1) there exists a directed edge E in this RootGraph such that the from
+ * node specified is E's source node and the target node specified is E's target node
+ * or 2) there exists an undirected edge E in this RootGraph such that E's endpoints
+ * are the from and to nodes specified.
+ * @see #getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean)
+ */
+ public boolean edgeExists ( Node from, Node to );
+
+ /**
+ * @deprecated Use getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean) instead;
+ * if you decide to use this method anyways: this method returns true if and only if
+ * either 1) there exists a directed edge E in this RootGraph such that
+ * from_node_index is E's source node's index and to_node_index is E's target node's
+ * index or 2) there exists an undirected edge E in this RootGraph such that E's
+ * endpoint nodes have indices from_node_index and to_node_index.
+ * @see #getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean)
+ */
+ public boolean edgeExists ( int from_node_index, int to_node_index );
+
+ /**
+ * Count the number of edges from the first Node to the second. Note that if
+ * count_undirected_edges is false, any Edge <tt><i>e</i></tt> such that
+ * <tt><i>e</i>.isDirected() == false</tt> will not be included in the count.
+ * @param from the Node that is the source of the edges to be counted.
+ * @param to the Node that is the target of the edges to be counted.
+ * @param count_undirected_edges Undirected edges will be included in the
+ * count iff count_undirected_edges is true.
+ * @return the number of Edges from the <tt>from</tt> Node to the
+ * <tt>to</tt> Node; returns -1 if either the <tt>from</tt> or the
+ * <tt>to</tt> Node is not in this RootGraph.
+ * @deprecated Use getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean) instead.
+ * @see #getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean)
+ */
+ public int getEdgeCount ( Node from,
+ Node to,
+ boolean count_undirected_edges
+ );
+
+ /**
+ * Count the number of edges from the Node with index <tt>from_index</tt> to
+ * the Node with index <tt>to_index</tt> (where this.getIndex( to_node ) ==
+ * to_index). Note that if count_undirected_edges is false, any Edge
+ * <tt><i>e</i></tt> such that <tt><i>e</i>.isDirected() == false</tt> will
+ * not be included in the count.
+ * @param from_node_index the index of the Node to count edges from.
+ * @param to_node_index the index of the Node to find edges to.
+ * @param count_undirected_edges Undirected edges will be included in the
+ * count iff count_undirected_edges is true.
+ * @return the number of Edges from the Node with index <tt>from_index</tt>
+ * to the Node with index <tt>to_index</tt>; returns -1 if either one of the two
+ * specified nodes is not in this RootGraph.
+ * @deprecated Use getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean) instead.
+ * @see #getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean)
+ */
+ public int getEdgeCount (int from_node_index,
+ int to_node_index,
+ boolean count_undirected_edges
+ );
+
+ /**
+ * Returns indices of all edges adjacent to the node at
+ * specified index. See definitions of adjacency below.
+ *
+ * @param node_index the index of the node whose adjacent edge
+ * information we're seeking.
+ * @param undirected_edges edge indices of all adjacent
+ * undirected edges are included in the return value of this
+ * method if this value is true, otherwise not a single
+ * index corresponding to an undirected edge is returned;
+ * undirected edge E is an adjacent undirected edge to node N
+ * [definition:] if and only if E's source is N or E's target
+ * is N.
+ * @param incoming_directed_edges edge indices of all incoming
+ * directed edges are included in the return value of this
+ * method if this value is true, otherwise not a single index
+ * corresponding to an incoming directed edge is returned;
+ * directed edge E is an incoming directed edge to node N
+ * [definition:] if and only if N is E's target.
+ * @param outgoing_directed_edges edge indices of all outgoing
+ * directed edges are included in the return value of this
+ * method if this value is true, otherwise not a single index
+ * corresponding to an outgoing directed edge is returned;
+ * directed edge E is an outgoing directed edge from node N
+ * [definition:] if and only if N is E's source.
+ * @return a set of edge indices corresponding to
+ * edges matched by our query; if all three of the boolean
+ * query parameters are false, the empty array is returned;
+ * null is returned if and only if this RootGraph has no node
+ * at the specified index.
+ */
+ public int[] getAdjacentEdgeIndicesArray
+ (int node_index,
+ boolean undirected_edges,
+ boolean incoming_directed_edges,
+ boolean outgoing_directed_edges);
+
+ /**
+ * This will return an array of edge indices that are the edges between nodes.
+ * The input node indices array need not be non-repeating.
+ * Returns null if any one of the node indices specified does not correspond to
+ * a node in this RootGraph.
+ */
+ public int[] getConnectingEdgeIndicesArray ( int[] node_indices );
+
+ /**
+ * Return the nodes that connect the given edges.
+ * The input edge indices array need not be non-repeating.
+ * Returns null if any one of the edge indices specified does not correspond to
+ * an edge in this RootGraph.
+ * @deprecated Use getEdgeSourceIndex(int) and getEdgeTargetIndex(int) instead, or
+ * use createGraphPerspective(int[], int[]).
+ * @see #getEdgeSourceIndex(int)
+ * @see #getEdgeTargetIndex(int)
+ * @see #createGraphPerspective(int[], int[])
+ */
+ public int[] getConnectingNodeIndicesArray ( int[] edge_indices );
+
+ /**
+ * @return null is returned if either of the specified Nodes is not in this RootGraph.
+ * @deprecated Use getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean) instead.
+ * @see #getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean)
+ */
+ public int[] getEdgeIndicesArray (
+ int from_node_index,
+ int to_node_index,
+ boolean include_undirected_edges,
+ boolean include_both_directions
+ ) ;
+
+ /**
+ * Return a new List of the Edges from the first given Node to the second
+ * given Node.
+ * @param from the Node that is the source of the Edges to be returned.
+ * @param to the Node that is the target of the Edges to be returned.
+ * @return a new List of the Edges from the <tt>from</tt> Node to the
+ * <tt>to</tt> Node, or the empty List if none exist; null is returned if either
+ * of the specified nodes is not in this RootGraph.
+ * @deprecated Use getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean) instead.
+ * @see #getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean)
+ */
+ public List edgesList ( Node from, Node to );
+
+ /**
+ * Return an array of the indices of all Edges from the Node with the first
+ * given index to the Node with the second given index.
+ * @param from_node_index the index of the Node to return edges from.
+ * @param to_node_index the index of the Node to return edges to.
+ * @param include_undirected_edges Undirected edges will be included in the
+ * List iff include_undirected_edges is true.
+ * @return a new List of the Edges from the Node corresponding to
+ * <tt>from_node_index</tt> to the Node corresponding to
+ * <tt>to_node_index</tt>, or the empty List if none exist; null is returned
+ * if either of the specified nodes does not exist in this RootGraph.
+ * @deprecated Use getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean) instead.
+ * @see #getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean)
+ */
+ public List edgesList (int from_node_index,
+ int to_node_index,
+ boolean include_undirected_edges
+ );
+
+ /**
+ * Return an array of the indices of all Edges from the Node with the first
+ * given index to the Node with the second given index.
+ * @param from_node_index the index of the Node to return edges from.
+ * @param to_node_index the index of the Node to return edges to.
+ * @param include_undirected_edges Undirected edges will be included in the
+ * array iff include_undirected_edges is true.
+ * @return an array of the Edges from the Node corresponding to
+ * <tt>from_node_index</tt> to the Node corresponding to
+ * <tt>to_node_index</tt>; the empty array is returned if none exist; null is
+ * returned if either of the specified Nodes does not exist in this RootGraph.
+ * @deprecated Use getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean) instead.
+ * @see #getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean)
+ */
+ public int[] getEdgeIndicesArray (int from_node_index,
+ int to_node_index,
+ boolean include_undirected_edges
+ );
+
+ /**
+ * Return the number of Edges <tt><i>e</i></tt> such that
+ * <tt><i>e</i>.getTarget().equals( node )</tt>. Note that this includes
+ * undirected edges, so it will not always be the case that <tt>getInDegree(
+ * node ) + getOutDegree( node ) == getDegree( node )</tt>.
+ * @param node the Node to count in-edges of.
+ * @return the in-degree of the given Node, or -1 if the specified Node is not
+ * in this RootGraph.
+ */
+ public int getInDegree ( Node node );
+
+ /**
+ * Return the number of Edges <tt><i>e</i></tt> such that
+ * <tt><i>e</i>.getTarget().equals( node )</tt>. Note that this includes
+ * undirected edges, so it will not always be the case that <tt>getInDegree(
+ * node ) + getOutDegree( node ) == getDegree( node )</tt>.
+ * @param node_index the index of the Node to count in-edges of.
+ * @return the in-degree of the Node with the given index, or -1 if this
+ * RootGraph has no Node with specified index.
+ */
+ public int getInDegree ( int node_index );
+
+ /**
+ * Return the number of Edges <tt><i>e</i></tt> such that
+ * <tt><i>e</i>.getSource().equals( node )</tt>. Note that if
+ * count_undirected_edges is true, this includes undirected edges, so it will
+ * not always be the case that <tt>getInDegree( node, true ) + getOutDegree(
+ * node, true ) == getDegree( node )</tt>, but it <i>will</i> always be the
+ * case that <tt>getInDegree( node, true ) + getOutDegree( node, <b>false</b>
+ * ) == getDegree( node )</tt>.
+ * @param node the Node to count in-edges of.
+ * @param count_undirected_edges Undirected edges will be included in the
+ * count iff count_undirected_edges is true.
+ * @return the in-degree of the given Node or -1 if specified Node is not
+ * in this RootGraph.
+ */
+ public int getInDegree ( Node node, boolean count_undirected_edges );
+
+ /**
+ * Return the number of Edges <tt><i>e</i></tt> such that
+ * <tt><i>e</i>.getSource().equals( node )</tt>. Note that if
+ * count_undirected_edges is true, this includes undirected edges, so it will
+ * not always be the case that <tt>getInDegree( node, true ) + getOutDegree(
+ * node, true ) == getDegree( node )</tt>, but it <i>will</i> always be the
+ * case that <tt>getInDegree( node, true ) + getOutDegree( node, <b>false</b>
+ * ) == getDegree( node )</tt>.
+ * @param node_index the index of the Node to count in-edges of.
+ * @param count_undirected_edges Undirected edges will be included in the
+ * count iff count_undirected_edges is true.
+ * @return the in-degree of the Node with the given index or -1 if this
+ * RootGraph has no Node at specified index.
+ */
+ public int getInDegree ( int node_index, boolean count_undirected_edges );
+
+ /**
+ * Return the number of Edges <tt><i>e</i></tt> such
+ * that <tt><i>e</i>.getSource().equals( node )</tt>. Note that this
+ * includes undirected edges, so it will not always be the case that
+ * <tt>getInDegree( node ) + getOutDegree( node ) == getDegree( node )</tt>.
+ * @param node the Node to count out-edges of.
+ * @return the out-degree of the given Node, or -1 if specified Node is not
+ * in this RootGraph.
+ */
+ public int getOutDegree ( Node node );
+
+ /**
+ * Return the number of Edges <tt><i>e</i></tt>such that
+ * <tt><i>e</i>.getSource().equals( node )</tt>. Note that this includes
+ * undirected edges, so it will not always be the case that <tt>getInDegree(
+ * node ) + getOutDegree( node ) == getDegree( node )</tt>.
+ * @param node_index the index of the Node to count out-edges of.
+ * @return the out-degree of the Node with the given index or -1 if index
+ * specified does not correspond to a Node in this RootGraph.
+ */
+ public int getOutDegree ( int node_index );
+
+ /**
+ * Return the number of Edges <tt><i>e</i></tt> such that
+ * <tt><i>e</i>.getSource().equals( node )</tt>. Note that if
+ * count_undirected edges is true, this includes undirected edges, so it will
+ * not always be the case that <tt>getInDegree( node, true ) + getOutDegree(
+ * node, true ) == getDegree( node )</tt>, but it <i>will</i> always be the
+ * case that <tt>getInDegree( node, true ) + getOutDegree( node, <b>false</b>
+ * ) == getDegree( node )</tt>.
+ * @param node the Node to count out-edges of.
+ * @param count_undirected_edges Undirected edges will be included in the
+ * count iff count_undirected_edges is true.
+ * @return the out-degree of the given Node or -1 if specified Node is not
+ * in this RootGraph.
+ */
+ public int getOutDegree ( Node node, boolean count_undirected_edges );
+
+ /**
+ * Return the number of Edges <tt><i>e</i></tt> such that
+ * <tt><i>e</i>.getSource().equals( node )</tt>. Note that if
+ * count_undirected edges is true, this includes undirected edges, so it will
+ * not always be the case that <tt>getInDegree( node, true ) + getOutDegree(
+ * node, true ) == getDegree( node )</tt>, but it <i>will</i> always be the
+ * case that <tt>getInDegree( node, true ) + getOutDegree( node, <b>false</b>
+ * ) == getDegree( node )</tt>.
+ * @param node_index the index of the Node to count out-edges of.
+ * @param count_undirected_edges Undirected edges will be included in the
+ * count iff count_undirected_edges is true.
+ * @return the out-degree of the Node with the given index or -1 if this
+ * RootGraph has no Node with specified index.
+ */
+ public int getOutDegree ( int node_index, boolean count_undirected_edges );
+
+ /**
+ * Return the number of distinct Edges incident on the given Node. By
+ * 'distinct' we mean that no Edge will be counted twice, even if it is
+ * undirected.
+ * @return the degree of the given Node or -1 if specified Node is not in
+ * this RootGraph.
+ */
+ public int getDegree ( Node node );
+
+ /**
+ * Return the number of distinct Edges incident on the Node with the given
+ * index. By 'distinct' we mean that no Edge will be counted twice, even if
+ * it is undirected.
+ * @return the degree of the Node with the given index or -1 if this
+ * RootGraph has no Node with specified index.
+ */
+ public int getDegree ( int node_index );
+
+ /**
+ * Return the index of the given Node. Each Node has a unique index which is
+ * guaranteed to remain the same throughout the lifetime of the Node and its
+ * RootGraph. Node indices are always <= -1, and are not guaranteed to be
+ * contiguous. This method simply returns node.getRootGraphIndex() after
+ * checking that it is in this RootGraph.<p>
+ * TECHNICAL DETAIL: The Node input parameter should be an object
+ * that was previously returned by a method of this RootGraph or by
+ * a method of another component that this RootGraph system defines.
+ * If this is not the case, results of calling this method are undefined.
+ * @param node the Node to find a corresponding index for.
+ * @return the index of the given Node in this RootGraph or 0 if it is not in
+ * this RootGraph.
+ */
+ public int getIndex ( Node node );
+
+ /**
+ * Return the Node with the given index in this RootGraph. All indices are
+ * <= -1. Some indices may correspond to no node, but no index may
+ * correspond to multiple nodes. The index of a Node will not change for the
+ * lifetime of the Node and its RootGraph.
+ * @param node_index the index in this RootGraph of to find a corresponding
+ * Node for.
+ * @return the Node with the given index in this RootGraph, or null if there
+ * is no Node with the given index.
+ */
+ public Node getNode ( int node_index );
+
+ /**
+ * Return the index of the given Edge. Each Edge has a unique index which is
+ * guaranteed to remain the same throughout the lifetime of the Edge and its
+ * RootGraph. Edge indices are always <= -1, and are not guaranteed to be
+ * contiguous. This method simply returns edge.getRootGraphIndex() after
+ * checking that it is in this RootGraph.<p>
+ * TECHNICAL DETAIL: The Edge input parameter should be an object
+ * that was previously returned by a method of this RootGraph or by
+ * a method of another component that this RootGraph system defines.
+ * If this is not the case, results of calling this method are undefined.
+ * @param edge the Edge to find a corresponding index for.
+ * @return the index of the given Edge in this RootGraph or 0 if it is not in
+ * this RootGraph.
+ */
+ public int getIndex ( Edge edge );
+
+ /**
+ * Return the Edge with the given index in this RootGraph. All indices are
+ * <= -1. Some indices may correspond to no edge, but no index may
+ * correspond to multiple edges. The index of a Edge will not change for the
+ * lifetime of the Edge and its RootGraph.
+ * @param edge_index the index in this RootGraph of to find a corresponding
+ * Edge for.
+ * @return the Edge with the given index in this RootGraph, or null if there
+ * if there is no Edge with the given index.
+ */
+ public Edge getEdge ( int edge_index );
+
+ /**
+ * Retrieve the index of the Node that is the source of the Edge with the
+ * given index. Note that if the edge is undirected, the edge also connects
+ * the target to the source.
+ * @param edge_index the index in this RootGraph of the Edge
+ * @return the index in this RootGraph of the Edge's source Node or 0
+ * if there's no Edge at specified index in this RootGraph.
+ */
+ public int getEdgeSourceIndex ( int edge_index );
+
+ /**
+ * Retrieve the index of the Node that is the target of the Edge with the
+ * given index. Note that if the edge is undirected, the edge also connects
+ * the target to the source.
+ * @param edge_index the index in this RootGraph of the Edge
+ * @return the index in this RootGraph of the Edge's target Node or 0
+ * if there's no Edge at specified index in this RootGraph.
+ */
+ public int getEdgeTargetIndex ( int edge_index );
+
+ /**
+ * Retrieve the directedness of the Edge with the
+ * given index. Note that if the edge is undirected, the edge also connects
+ * the target to the source.
+ * @param edge_index the index in this RootGraph of the Edge
+ * @return true iff the edge is directed; if no Edge at specified index exists
+ * in this RootGraph, the result of this method is undefined.
+ */
+ public boolean isEdgeDirected ( int edge_index );
+
+ /**
+ * Nodes and Edges comprise an additional directed graph through the
+ * contains-a relationship, in which a MetaParent Node contains each of its
+ * MetaChild Nodes and Edges. A Node may have any number of MetaChildren.
+ * addMetaChild establishes a contains-a relationship between the first
+ * argument (the <tt>parent</tt>) and the second argument (the
+ * <tt>child</tt>). It returns true unless the meta relationship already
+ * existed or unless either the parent or child spcified is not in this
+ * RootGraph.
+ * @param parent the Node that is to be the parent (the contain<i>er</i>) in
+ * the contains-a relationship that we are creating.
+ * @param child the Node that is to be the child (the contain<i>ee</i>) in the
+ * contains-a relationship that we are creating.
+ * @return true unless they were already meta-parent, meta-child to each
+ * other or unless parent or child not in this RootGraph.
+ */
+ public boolean addMetaChild ( Node parent, Node child );
+
+ /**
+ * Nodes and Edges comprise an additional directed graph through the
+ * contains-a relationship, in which a MetaParent Node contains each of its
+ * MetaChild Nodes and Edges. A Node may have any number of MetaChildren.
+ * addMetaChild establishes a contains-a relationship between the Node
+ * corresponding to the first argument (<tt>parent_index</tt>) and the Node
+ * corresponding to the second argument (<tt>child_index</tt>). It returns
+ * true unless the meta relationship already existed or unless either of the
+ * indices specified does not correspond to a node in this RootGraph.
+ * @param parent_index the index in this RootGraph of the Node that is to be
+ * the parent (the contain<i>er</i>) in the contains-a relationship that we
+ * are creating.
+ * @param child_node_index the index in this RootGraph of the Node that is to be
+ * the child (the contain<i>ee</i>) in the contains-a relationship that we
+ * are creating.
+ * @return true unless they were already meta-parent, meta-child to each
+ * other or unless either of them isn't in this RootGraph.
+ */
+ public boolean addNodeMetaChild ( int parent_index, int child_node_index );
+
+ public boolean removeNodeMetaChild ( int parent_index, int child_node_index );
+
+ /**
+ * Nodes and Edges comprise an additional directed graph through the
+ * contains-a relationship, in which a MetaParent Node contains each of its
+ * MetaChild Nodes and Edges. A Node may have any number of MetaParents.
+ * isMetaParent returns true iff the second argument (<tt>parent</tt>) is an
+ * MetaParent of the first argument (<tt>child</tt>).<p>
+ * @param child the Node that is the child (the contain<i>ee</i>) in the
+ * contains-a relationship that we are querying.
+ * @param parent the Node that is the parent (the contain<i>er</i>) in the
+ * contains-a relationship that we are querying.
+ * @return true iff the latter argument is a MetaParent of the former argument.
+ */
+ public boolean isMetaParent ( Node child, Node parent );
+
+ /**
+ * Nodes and Edges comprise an additional directed graph through the
+ * contains-a relationship, in which a MetaParent Node contains each of its
+ * MetaChild Nodes and Edges. A Node may have any number of MetaParents.
+ * isMetaParent returns true iff the Node corresponding to the second argument
+ * (<tt>parent_index</tt>) is a MetaParent of the Node corresponding to the
+ * first argument (<tt>child_index</tt>).
+ * @param child_node_index the index of the Node that is the child (the
+ * contain<i>ee</i>) in the contains-a relationship that we are querying.
+ * @param parent_index the index of the Node that is the parent (the
+ * contain<i>er</i>) in the contains-a relationship that we are querying.
+ * @return true iff the Node corresponding to the latter argument is an
+ * MetaParent of the Node corresponding to the former argument.
+ */
+ public boolean isNodeMetaParent ( int child_node_index, int parent_index );
+
+ /**
+ * Nodes and Edges comprise an additional directed graph through the
+ * contains-a relationship, in which a MetaParent Node contains each of its
+ * MetaChild Nodes and Edges. A Node may have any number of MetaParents.
+ * metaParentsList returns a new List of the MetaParents of the given Node. If
+ * there are no MetaParents then the result will be the empty List; if node does
+ * not exist in this RootGraph the result will be null.
+ * @param node the Node that is the child (the contain<i>ee</i>) in the
+ * contains-a relationship that we are querying.
+ * @return a new List of the Nodes that contain the given Node, or null if
+ * specified Node is not in this RootGraph.
+ * @deprecated Use getNodeMetaParentIndicesArray(int) instead.
+ * @see #getNodeMetaParentIndicesArray(int)
+ */
+ public List metaParentsList ( Node node );
+
+ /**
+ * Nodes and Edges comprise an additional directed graph through the
+ * contains-a relationship, in which a MetaParent Node contains each of its
+ * MetaChild Nodes and Edges. A Node may have any number of MetaParents.
+ * nodeMetaParentsList returns a new List of the MetaParents of the Node with the
+ * given index. If there are no MetaParents then the result will be the empty
+ * List; null is returned if the specified node does not exist in this RootGraph.
+ * @param node_index the index of the Node that is the child (the
+ * contain<i>ee</i>) in the contains-a relationship that we are querying.
+ * @return a new List of the Nodes that contain the Node with the given
+ * index, or null if the specified node does not exist.
+ * @deprecated Use getNodeMetaParentIndicesArray(int) instead.
+ * @see #getNodeMetaParentIndicesArray(int)
+ */
+ public List nodeMetaParentsList ( int node_index );
+
+ /**
+ * Nodes and Edges comprise an additional directed graph through the
+ * contains-a relationship, in which a MetaParent Node contains each of its
+ * MetaChild Nodes and Edges. A Node may have any number of MetaParents.
+ * getNodeMetaParentIndicesArray returns an array of the MetaParents of the Node
+ * with the given index. If there are no MetaParents then the result will be
+ * the empty array; null is returnd if the specified index does not correspond to
+ * a Node existing in this RootGraph.
+ * @param node_index the index of the Node that is the child (the
+ * contain<i>ee</i>) in the contains-a relationship that we are querying.
+ * @return an array of the indices of the Nodes that contain the Node with
+ * the given index, or null if specified node does not exist.
+ */
+ public int[] getNodeMetaParentIndicesArray ( int node_index );
+
+ /**
+ * Nodes and Edges comprise an additional directed graph through the
+ * contains-a relationship, in which a MetaParent Node contains each of its
+ * MetaChild Nodes and Edges. A Node may have any number of MetaChildren.
+ * isMetaChild returns true iff the second argument (<tt>child</tt>) is an
+ * MetaChild of the first argument (<tt>parent</tt>).
+ * @param parent the Node that is the parent (the contain<i>er</i>) in the
+ * contains-a relationship that we are querying.
+ * @param child the Node that is the child (the contain<i>ee</i>) in the
+ * contains-a relationship that we are querying.
+ * @return true iff the latter argument is a MetaChild of the former argument.
+ */
+ public boolean isMetaChild ( Node parent, Node child );
+
+ /**
+ * Nodes and Edges comprise an additional directed graph through the
+ * contains-a relationship, in which a MetaParent Node contains each of its
+ * MetaChild Nodes and Edges. A Node may have any number of MetaChildren.
+ * Returns true iff the Node corresponding to the second argument
+ * (<tt>child_index</tt>) is a MetaChild of the Node corresponding to the first
+ * argument (<tt>parent_index</tt>).
+ * @param parent_index the index of the Node that is the parent (the
+ * contain<i>er</i>) in the contains-a relationship that we are querying.
+ * @param child_node_index the index of the Node that is the child (the
+ * contain<i>ee</i>) in the contains-a relationship that we are querying.
+ * @return true iff the Node corresponding to the latter argument is an
+ * MetaChild of the Node corresponding to the former argument.
+ */
+ public boolean isNodeMetaChild ( int parent_index, int child_node_index );
+
+ /**
+ * Nodes and Edges comprise an additional directed graph through the
+ * contains-a relationship, in which a MetaParent Node contains each of its
+ * MetaChild Nodes and Edges. A Node may have any number of MetaChildren.
+ * isMetaChild returns true iff the Node corresponding to the second argument
+ * (<tt>child_index</tt>) is a MetaChild of the Node corresponding to the first
+ * argument (<tt>parent_index</tt>).
+ * @param parent_index the index of the Node that is the parent (the
+ * contain<i>er</i>) in the contains-a relationship that we are querying.
+ * @param child_node_index the index of the Node that is the child (the
+ * contain<i>ee</i>) in the contains-a relationship that we are querying.
+ * @param recursive if true, the method will look for child_node_index recursively inside
+ * descendants of parent_index
+ * @return true iff the Node corresponding to the latter argument is an
+ * MetaChild of the Node corresponding to the former argument.
+ */
+ public boolean isNodeMetaChild ( int parent_index, int child_node_index, boolean recursive);
+
+ /**
+ * Nodes and Edges comprise an additional directed graph through the
+ * contains-a relationship, in which a MetaParent Node contains each of its
+ * MetaChild Nodes and Edges. A Node may have any number of MetaChildren.
+ * nodeMetaChildrenList returns a new List of the MetaChildren of the given Node.
+ * If there are no MetaChildren then the result will be the empty List; null is
+ * returned if the specified Node is not in this RootGraph.
+ * @param node the Node that is the parent (the contain<i>er</i>) in the
+ * contains-a relationship that we are querying.
+ * @return a new List of the Nodes that are contained by the given Node, or
+ * null if specified node is not in this RootGraph.
+ * @deprecated Use getNodeMetaChildIndicesArray(int) instead.
+ * @see #getNodeMetaChildIndicesArray(int)
+ */
+ public List nodeMetaChildrenList ( Node node );
+
+ /**
+ * Nodes and Edges comprise an additional directed graph through the
+ * contains-a relationship, in which a MetaParent Node contains each of its
+ * MetaChild Nodes and Edges. A Node may have any number of MetaChildren.
+ * nodeMetaChildrenList returns a new List of the Node MetaChildren of the Node
+ * with the given index. If there are no MetaChildren then the result will be
+ * the empty list; null is returned if no Node exists in this RootGraph at
+ * specified node index.
+ * @param parent_index the index of the Node that is the parent (the
+ * contain<i>er</i>) in the contains-a relationship that we are querying.
+ * @return a new List of the Nodes that are contained by the Node with the
+ * given index, or null if no Node exists at index parent_index.
+ */
+ public List nodeMetaChildrenList ( int parent_index );
+
+ /**
+ * Nodes and Edges comprise an additional directed graph through the
+ * contains-a relationship, in which a MetaParent Node contains each of its
+ * MetaChild Nodes and Edges. A Node may have any number of MetaChildren.
+ * getNodeMetaChildIndicesArray returns an array of the MetaChildren of the Node
+ * with the given index. If there are no MetaChildren then the result will be
+ * the empty array; null is returned if no node exists in this RootGraph at
+ * index node_index.
+ * @param node_index the index of the Node that is the parent (the
+ * contain<i>ee</i>) in the contains-a relationship that we are querying.
+ * @return an array of the indices of the Nodes in this RootGraph that
+ * are contained by the Node with the given index.
+ */
+ public int[] getNodeMetaChildIndicesArray ( int node_index );
+
+ /**
+ * Nodes and Edges comprise an additional directed graph through the
+ * contains-a relationship, in which a MetaParent Node contains each of its
+ * MetaChild Nodes and Edges. A Node may have any number of MetaChildren.
+ * getNodeMetaChildIndicesArray returns an array of the MetaChildren of the Node
+ * with the given index. If there are no MetaChildren then the result will be
+ * the empty array; null is returned if no Node exists in this RootGraph at index
+ * node_index.
+ * @param node_index the index of the Node that is the parent (the
+ * contain<i>ee</i>) in the contains-a relationship that we are querying.
+ * @param recursive if true, then this method returns all descendants of node_index by
+ * recursively searching inside node_index's children
+ * @return an array of the indices of the Nodes in this GraphPerspective that
+ * are contained by the Node with the given index.
+ */
+ public int[] getNodeMetaChildIndicesArray ( int node_index, boolean recursive );
+
+ /**
+ * Nodes and Edges comprise an additional directed graph through the
+ * contains-a relationship, in which a MetaParent Node contains each of its
+ * MetaChild Nodes and Edges. A Node may have any number of MetaChildren.
+ * This method returns an array of node RootGraph indices that belong to Nodes
+ * that are [strictly] descendants of Node with node_index and that do not have
+ * any children of their own (one could call them leaves, except that this is not a tree).
+ *
+ * @param node_index the RootGraph index of the node for which childless descendants will
+ * be returned
+ * @return an array of node RootGraph indices that belong to Nodes
+ * that are descendants of Node with node_index and that do not have any children of their
+ * own (one could call them leaves, except that this is not a tree.
+ */
+ public int[] getChildlessMetaDescendants ( int node_index );
+
+
+ /**
+ * Nodes and Edges comprise an additional directed graph through the
+ * contains-a relationship, in which a MetaParent Node contains each of its
+ * MetaChild Nodes and Edges. A Node may have any number of MetaChildren.
+ * addMetaChild establishes a contains-a relationship between the first
+ * argument (the <tt>parent</tt>) and the second argument (the
+ * <tt>child</tt>). It returns true unless the meta relationship already
+ * existed or unless either parent or child is not in this RootGraph.
+ * @param parent the Node that is to be the parent (the contain<i>er</i>) in
+ * the contains-a relationship that we are creating.
+ * @param child the Edge that is to be the child (the contain<i>ee</i>) in the
+ * contains-a relationship that we are creating.
+ * @return true unless they were already meta-parent, meta-child to each
+ * other or unless either parent or child not in this RootGraph.
+ */
+ public boolean addMetaChild ( Node parent, Edge child );
+
+ /**
+ * Nodes and Edges comprise an additional directed graph through the
+ * contains-a relationship, in which a MetaParent Node contains each of its
+ * MetaChild Nodes and Edges. A Node may have any number of MetaChildren.
+ * addMetaChild establishes a contains-a relationship between the Node
+ * corresponding to the first argument (<tt>parent_index</tt>) and the Edge
+ * corresponding to the second argument (<tt>child_index</tt>). It returns
+ * true unless the meta relationship already existed or unless either parent node
+ * at specified index or child edge at specified index does not exist in this
+ * RootGraph.
+ * @param parent_index the index in this RootGraph of the Node that is to be
+ * the parent (the contain<i>er</i>) in the contains-a relationship that we
+ * are creating.
+ * @param child_edge_index the index in this RootGraph of the Edge that is to be
+ * the child (the contain<i>ee</i>) in the contains-a relationship that we
+ * are creating.
+ * @return true unless they were already meta-parent, meta-child to each
+ * other or unless either parent or child does not exist in this RootGraph.
+ */
+ public boolean addEdgeMetaChild ( int parent_index, int child_edge_index );
+ public boolean removeEdgeMetaChild ( int parent_index, int child_edge_index ) ;
+
+ /**
+ * Nodes and Edges comprise an additional directed graph through the
+ * contains-a relationship, in which a MetaParent Node contains each of its
+ * MetaChild Nodes and Edges. An Edge may have any number of MetaParents.
+ * isMetaParent returns true iff the second argument (<tt>parent</tt>) is an
+ * MetaParent of the first argument (<tt>child</tt>).
+ * @param child the Edge that is the child (the contain<i>ee</i>) in the
+ * contains-a relationship that we are querying.
+ * @param parent the Node that is the parent (the contain<i>er</i>) in the
+ * contains-a relationship that we are querying.
+ * @return true iff the latter argument is a MetaParent of the former argument.
+ */
+ public boolean isMetaParent ( Edge child, Node parent );
+
+ /**
+ * Nodes and Edges comprise an additional directed graph through the
+ * contains-a relationship, in which a MetaParent Node contains each of its
+ * MetaChild Nodes and Edges. An Edge may have any number of MetaParents.
+ * isMetaParent returns true iff the Node corresponding to the second argument
+ * (<tt>parent_index</tt>) is a MetaParent of the Edge corresponding to the
+ * first argument (<tt>child_index</tt>).
+ * @param child_edge_index the index of the Edge that is the child (the
+ * contain<i>ee</i>) in the contains-a relationship that we are querying.
+ * @param parent_index the index of the Node that is the parent (the
+ * contain<i>er</i>) in the contains-a relationship that we are querying.
+ * @return true iff the Node corresponding to the latter argument is an
+ * MetaParent of the Edge corresponding to the former argument.
+ */
+ public boolean isEdgeMetaParent ( int child_edge_index, int parent_index );
+
+ /**
+ * Nodes and Edges comprise an additional directed graph through the
+ * contains-a relationship, in which a MetaParent Node contains each of its
+ * MetaChild Nodes and Edges. An Edge may have any number of MetaParents.
+ * metaParentsList returns a new List of the MetaParents of the given Edge. If
+ * there are no MetaParents then the result will be the empty List; null is
+ * returned if specified Edge is not in this RootGraph.
+ * @param edge the Edge that is the child (the contain<i>ee</i>) in the
+ * contains-a relationship that we are querying.
+ * @return a new List of the Nodes that contain the given Edge.
+ * @deprecated Use getEdgeMetaParentIndicesArray(int) instead.
+ * @see #getEdgeMetaParentIndicesArray(int)
+ */
+ public List metaParentsList ( Edge edge );
+
+ /**
+ * Nodes and Edges comprise an additional directed graph through the
+ * contains-a relationship, in which a MetaParent Node contains each of its
+ * MetaChild Nodes and Edges. An Edge may have any number of MetaParents.
+ * EdgeMetaParentsList returns a new List of the MetaParents of the Edge with the
+ * given index. If there are no MetaParents then the result will be the empty
+ * List; null is returned if no Edge exists in this RootGraph at index
+ * edge_index.
+ * @param edge_index the index of the Edge that is the child (the
+ * contain<i>ee</i>) in the contains-a relationship that we are querying.
+ * @return a new List of the Nodes that contain the Edge with the given
+ * index.
+ * @deprecated Use getEdgeMetaParentIndicesArray(int) instead.
+ * @see #getEdgeMetaParentIndicesArray(int)
+ */
+ public List edgeMetaParentsList ( int edge_index );
+
+ /**
+ * Nodes and Edges comprise an additional directed graph through the
+ * contains-a relationship, in which a MetaParent Node contains each of its
+ * MetaChild Nodes and Edges. An Edge may have any number of MetaParents.
+ * getEdgeMetaParentIndicesArray returns an array of the MetaParents of the Edge
+ * with the given index. If there are no MetaParents then the result will be
+ * the empty array; null is returned if no Edge exists in this RootGraph
+ * at index edge_index.
+ * @param edge_index the index of the Edge that is the child (the
+ * contain<i>ee</i>) in the contains-a relationship that we are querying.
+ * @return an array of the indices of the Nodes that contain the Edge with
+ * the given index.
+ */
+ public int[] getEdgeMetaParentIndicesArray ( int edge_index );
+
+ /**
+ * Nodes and Edges comprise an additional directed graph through the
+ * contains-a relationship, in which a MetaParent Node contains each of its
+ * MetaChild Nodes and Edges. A Node may have any number of MetaChildren.
+ * isMetaChild returns true iff the second argument (<tt>child</tt>) is an
+ * MetaChild of the first argument (<tt>parent</tt>).
+ * @param parent the Node that is the parent (the contain<i>er</i>) in the
+ * contains-a relationship that we are querying.
+ * @param child the Edge that is the child (the contain<i>ee</i>) in the
+ * contains-a relationship that we are querying.
+ * @return true iff the latter argument is a MetaChild of the former argument.
+ */
+ public boolean isMetaChild ( Node parent, Edge child );
+
+ /**
+ * Nodes and Edges comprise an additional directed graph through the
+ * contains-a relationship, in which a MetaParent Node contains each of its
+ * MetaChild Nodes and Edges. A Node may have any number of MetaChildren.
+ * isMetaChild returns true iff the Edge corresponding to the second argument
+ * (<tt>child_index</tt>) is a MetaChild of the Node corresponding to the first
+ * argument (<tt>parent_index</tt>).
+ * @param parent_index the index of the Node that is the parent (the
+ * contain<i>er</i>) in the contains-a relationship that we are querying.
+ * @param child_edge_index the index of the Edge that is the child (the
+ * contain<i>ee</i>) in the contains-a relationship that we are querying.
+ * @return true iff the Edge corresponding to the latter argument is an
+ * MetaChild of the Node corresponding to the former argument.
+ */
+ public boolean isEdgeMetaChild ( int parent_index, int child_edge_index );
+
+ /**
+ * Nodes and Edges comprise an additional directed graph through the
+ * contains-a relationship, in which a MetaParent Node contains each of its
+ * MetaChild Nodes and Edges. A Node may have any number of MetaChildren.
+ * edgeMetaChildrenList returns a new List of the Edge MetaChildren of the given
+ * Node. If there are no Edge MetaChildren then the result will be the empty
+ * List; null is returned if the specified Node does not exist in this RootGraph.
+ * @param node the Node that is the parent (the contain<i>er</i>) in the
+ * contains-a relationship that we are querying.
+ * @return a new List of the Edges that are contained by the given Node.
+ * @deprecated Use getEdgeMetaChildIndicesArray(int) instead.
+ * @see #getEdgeMetaChildIndicesArray(int)
+ */
+ public List edgeMetaChildrenList ( Node node );
+
+ /**
+ * Nodes and Edges comprise an additional directed graph through the
+ * contains-a relationship, in which a MetaParent Node contains each of its
+ * MetaChild Nodes and Edges. A Node may have any number of MetaChildren.
+ * edgeMetaChildrenList returns a new List of the Edge MetaChildren of the Node
+ * with the given index. If there are no Edge MetaChildren then the result will
+ * be the empty List; null is returned if no Node exists in this RootGraph at
+ * index node_index.
+ * @param node_index the index of the Node that is the parent (the
+ * contain<i>er</i>) in the contains-a relationship that we are querying.
+ * @return a new List of the Edges that are contained by the Node with the
+ * given index.
+ * @deprecated Use getEdgeMetaChildIndicesArray(int) instead.
+ * @see #getEdgeMetaChildIndicesArray(int)
+ */
+ public List edgeMetaChildrenList ( int node_index );
+
+ /**
+ * Nodes and Edges comprise an additional directed graph through the
+ * contains-a relationship, in which a MetaParent Node contains each of its
+ * MetaChild Nodes and Edges. A Node may have any number of MetaChildren.
+ * getEdgeMetaChildIndicesArray returns an array of the MetaChildren of the Node
+ * with the given index. If there are no MetaChildren then the result will be
+ * the empty array; null is returned if no Node exists in this RootGraph at
+ * index node_index.
+ * @param node_index the index of the Node that is the parent (the
+ * contain<i>ee</i>) in the contains-a relationship that we are querying.
+ * @return an array of the indices of the Edges that are contained by the
+ * Node with the given index.
+ */
+ public int[] getEdgeMetaChildIndicesArray ( int node_index );
+
+}
diff --git a/corelibs/giny/src/main/java/giny/model/RootGraphChangeEvent.java b/corelibs/giny/src/main/java/giny/model/RootGraphChangeEvent.java
new file mode 100755
index 0000000..75e01f1
--- /dev/null
+++ b/corelibs/giny/src/main/java/giny/model/RootGraphChangeEvent.java
@@ -0,0 +1,65 @@
+package giny.model;
+
+import java.util.EventObject;
+
+/**
+ * The event source must be the RootGraph that changed.
+ */
+public abstract class RootGraphChangeEvent
+ extends EventObject {
+
+ public RootGraphChangeEvent ( RootGraph source ) {
+ super( source );
+ }
+
+ public static final int NODES_CREATED_TYPE = 1;
+ public static final int EDGES_CREATED_TYPE = 2;
+ public static final int NODES_REMOVED_TYPE = 4;
+ public static final int EDGES_REMOVED_TYPE = 8;
+ public static final int META_RELATIONSHIP_NODES_CREATED_TYPE = 16;
+ public static final int META_RELATIONSHIP_EDGES_CREATED_TYPE = 32;
+ public static final int META_RELATIONSHIP_NODES_REMOVED_TYPE = 64;
+ public static final int META_RELATIONSHIP_EDGES_REMOVED_TYPE = 128;
+
+ public abstract int getType ();
+ public abstract boolean isNodesCreatedType ();
+ public abstract boolean isEdgesCreatedType ();
+ public abstract boolean isNodesRemovedType ();
+ public abstract boolean isEdgesRemovedType ();
+ public abstract boolean isMetaRelationshipNodesCreatedType ();
+ public abstract boolean isMetaRelationshipEdgesCreatedType ();
+ public abstract boolean isMetaRelationshipNodesRemovedType ();
+ public abstract boolean isMetaRelationshipEdgesRemovedType ();
+
+ public abstract Node[] getCreatedNodes ();
+ public abstract Edge[] getCreatedEdges ();
+
+ /**
+ * @deprecated Use getRemovedNodeIndices() instead; the nodes returned by
+ * this method may have undefined state.
+ * @see #getRemovedNodeIndices()
+ */
+ public abstract Node[] getRemovedNodes ();
+
+ /**
+ * @deprecated Use getRemovedEdgeIndices() instead; the edges returned by
+ * this method may have undefined state.
+ * @see #getRemovedEdgeIndices()
+ */
+ public abstract Edge[] getRemovedEdges ();
+
+ public abstract Node[][] getMetaRelationshipCreatedNodes ();
+ public abstract Object[][] getMetaRelationshipCreatedEdges ();
+ public abstract Node[][] getMetaRelationshipRemovedNodes ();
+ public abstract Object[][] getMetaRelationshipRemovedEdges ();
+
+ public abstract int[] getCreatedNodeIndices ();
+ public abstract int[] getCreatedEdgeIndices ();
+ public abstract int[] getRemovedNodeIndices ();
+ public abstract int[] getRemovedEdgeIndices ();
+ public abstract int[][] getMetaRelationshipCreatedNodeIndices ();
+ public abstract int[][] getMetaRelationshipCreatedEdgeIndices ();
+ public abstract int[][] getMetaRelationshipRemovedNodeIndices ();
+ public abstract int[][] getMetaRelationshipRemovedEdgeIndices ();
+
+} // abstract class RootGraphChangeEvent
diff --git a/corelibs/giny/src/main/java/giny/model/RootGraphChangeListener.java b/corelibs/giny/src/main/java/giny/model/RootGraphChangeListener.java
new file mode 100755
index 0000000..eabe523
--- /dev/null
+++ b/corelibs/giny/src/main/java/giny/model/RootGraphChangeListener.java
@@ -0,0 +1,14 @@
+package giny.model;
+
+import java.util.EventListener;
+
+public interface RootGraphChangeListener
+ extends EventListener {
+
+ /**
+ * Invoked when a RootGraph to which this RootGraphChangeListener listens
+ * changes.
+ */
+ public void rootGraphChanged ( RootGraphChangeEvent event );
+
+} // interface RootGraphChangeListener
diff --git a/corelibs/giny/src/main/java/giny/view/Bend.java b/corelibs/giny/src/main/java/giny/view/Bend.java
new file mode 100644
index 0000000..94fbbfd
--- /dev/null
+++ b/corelibs/giny/src/main/java/giny/view/Bend.java
@@ -0,0 +1,112 @@
+package giny.view;
+
+import java.awt.*;
+import java.awt.event.*;
+import java.awt.geom.*;
+import java.util.*;
+
+/**
+ * A class that encapsulates the representation of the bend used for a
+ * particular EdgeView.
+ *
+ * @author Mike Smoot (mes5k)
+ */
+public interface Bend {
+
+ /**
+ * Given a list of points removes all existing handles/handlePoints
+ * and adds new ones for those specified in the List.
+ * @param bendPoints A list of Point2Ds to create new handles.
+ */
+ public void setHandles( java.util.List bendPoints );
+
+ /**
+ * Returns a (new) List of clones of the Point2Ds that locate the handles.
+ */
+ public java.util.List getHandles();
+
+ /**
+ * Moves the handle specified at the given index to the given point.
+ * @param i Index of the handle to move.
+ * @param pt Point2D to which to move the specified handle.
+ */
+ public void moveHandle( int i, Point2D pt );
+
+ /**
+ * Returns the handle Point2D closest to the source node.
+ */
+ public Point2D getSourceHandlePoint ();
+
+ /**
+ * Returns the handle Point2D closest to the target node.
+ */
+ public Point2D getTargetHandlePoint ();
+
+ /**
+ * Add a PHandle to the edge at the point specified. Acts as
+ * an interface to actuallyAddHandle() which does the actual adding.
+ *
+ * @param pt The point at which to draw the PHandle and to which the
+ * PHandle will be attached via the locator.
+ */
+ public void addHandle ( Point2D pt );
+
+ /**
+ * Add a PHandle to the edge at the point and index specified. Acts as
+ * an interface to actuallyAddHandle() which does the actual adding.
+ *
+ * @param insertIndex The index at which to add the PHandle to the
+ * list of handles.
+ * @param pt The point at which to draw the PHandle and to which the
+ * PHandle will be attached via the locator.
+ */
+ public void addHandle ( int insertIndex , Point2D pt );
+
+
+ /**
+ * Removes the PHandle at the specified point.
+ *
+ * @param pt If this point intersects an existing PHandle, then remove that
+ * PHandle.
+ */
+ public void removeHandle ( Point2D pt );
+
+
+
+ /**
+ * Removes the PHandle at the given index.
+ *
+ * @param i The index of the PHandle to remove.
+ */
+ public void removeHandle ( int i );
+
+
+ /**
+ * Removes all handles
+ */
+ public void removeAllHandles () ;
+
+ /**
+ * Checks to see if a PHandle already exists for the given point.
+ *
+ * @param pt If this point intersects a currently existing PHandle, then
+ * return true, else return false.
+ */
+ public boolean handleAlreadyExists ( Point2D pt );
+
+ /**
+ * Draws any handles previously added.
+ */
+ public void drawSelected();
+
+ /**
+ * Removes any handles from the display.
+ */
+ public void drawUnselected();
+
+ /**
+ * Returns a list of points that define what gets drawn and hence
+ * what is visible to the user.
+ */
+ public Point2D[] getDrawPoints();
+}
diff --git a/corelibs/giny/src/main/java/giny/view/EdgeView.java b/corelibs/giny/src/main/java/giny/view/EdgeView.java
new file mode 100644
index 0000000..6e727fd
--- /dev/null
+++ b/corelibs/giny/src/main/java/giny/view/EdgeView.java
@@ -0,0 +1,301 @@
+package giny.view;
+
+
+import java.awt.*;
+import java.awt.geom.*;
+import giny.model.*;
+
+
+public interface EdgeView {
+
+ /**
+ * Draws splined curves for edges.
+ */
+ public static int CURVED_LINES = 1;
+
+ /**
+ * Draws straight lines for edges.
+ */
+ public static int STRAIGHT_LINES = 2;
+
+
+
+ public static int NO_END = 0;
+ public static int WHITE_DELTA = 1;
+ public static int BLACK_DELTA = 2;
+ public static int EDGE_COLOR_DELTA = 3;
+ public static int WHITE_ARROW = 4;
+ public static int BLACK_ARROW = 5;
+ public static int EDGE_COLOR_ARROW = 6;
+ public static int WHITE_DIAMOND = 7;
+ public static int BLACK_DIAMOND = 8;
+ public static int EDGE_COLOR_DIAMOND = 9;
+ public static int WHITE_CIRCLE = 10;
+ public static int BLACK_CIRCLE = 11;
+ public static int EDGE_COLOR_CIRCLE = 12;
+ public static int WHITE_T = 13;
+ public static int BLACK_T = 14;
+ public static int EDGE_COLOR_T = 15;
+ public static int EDGE_HALF_ARROW_TOP = 16;
+ public static int EDGE_HALF_ARROW_BOTTOM = 17;
+
+
+ //------------------------------------------------------//
+ // Get and Set Methods for all Common Viewable Elements
+ //------------------------------------------------------//
+
+ /**
+ * @return the index of this edge in the GraphPerspective
+ */
+ public int getGraphPerspectiveIndex ();
+
+ /**
+ * @return the index of this edge in the RootGraph
+ */
+ public int getRootGraphIndex ();
+
+ /**
+ * @return the Edge to which we are a view on
+ */
+ public Edge getEdge();
+
+ /**
+ * @return the GraphView we are in
+ */
+ public GraphView getGraphView ();
+
+ /**
+ * @param width set a new line width for this edge
+ */
+ public void setStrokeWidth ( float width );
+
+ /**
+ * @return the currently set edge width
+ */
+ public float getStrokeWidth ();
+
+ /**
+ * @param stroke the stroke to use on this edge
+ */
+ public void setStroke ( Stroke stroke );
+
+ /**
+ * @return the stroke used on this edge
+ */
+ public Stroke getStroke ();
+
+ /**
+ * @param line_type set a new line type for the edge
+ */
+ public void setLineType ( int line_type );
+
+ /**
+ * @return the currently set edge line type
+ */
+ public int getLineType ();
+
+ /**
+ * This really refers to the <B>Stroke</B>,
+ * TODO: Make separte stroke methods
+ * @param paint the paint for this node
+ */
+ public void setUnselectedPaint ( Paint paint );
+
+ /**
+ * This really refers to the <B>Stroke</B>,
+ * TODO: Make separte stroke methods
+ * @return the currently set edge Paint
+ */
+ public Paint getUnselectedPaint ();
+
+ /**
+ * This really refers to the <B>Stroke</B>,
+ * TODO: Make separte stroke methods
+ * @param paint the paint for this node
+ */
+ public void setSelectedPaint ( Paint paint );
+
+ /**
+ * This really refers to the <B>Stroke</B>,
+ * TODO: Make separte stroke methods
+ * @return the currently set edge Selectionpaint
+ */
+ public Paint getSelectedPaint ();
+
+ /**
+ * @return the currently set Source Edge End Type
+ */
+ public Paint getSourceEdgeEndPaint ();
+
+ /**
+ * @return the currently set Source Edge End Type
+ */
+ public Paint getSourceEdgeEndSelectedPaint ();
+
+ /**
+ * @return the currently set Target Edge End Type
+ */
+ public Paint getTargetEdgeEndPaint ();
+
+ /**
+ * @return the currently set Target Edge End Type
+ */
+ public Paint getTargetEdgeEndSelectedPaint ();
+
+ /**
+ * @param paint set the value for the source edge end when selected
+ */
+ public void setSourceEdgeEndSelectedPaint ( Paint paint );
+
+ /**
+ * @param paint set the value for the target edge end when selected
+ */
+ public void setTargetEdgeEndSelectedPaint ( Paint paint );
+
+ /**
+ * @param paint the new paint for the stroke of the source eged end
+ */
+ public void setSourceEdgeEndStrokePaint ( Paint paint );
+
+ /**
+ * @param paint the new paint for the stroke of the target eged end
+ */
+ public void setTargetEdgeEndStrokePaint ( Paint paint );
+
+ /**
+ * @param paint set the value for the source edge end
+ */
+ public void setSourceEdgeEndPaint ( Paint paint );
+
+ /**
+ * @param paint set the value for the target edge end
+ */
+ public void setTargetEdgeEndPaint ( Paint paint );
+
+
+ public void select ();
+
+ public void unselect ();
+
+ /**
+ * When we are selected then we draw ourselves red, and draw any handles.
+ */
+ public boolean setSelected ( boolean state );
+
+ /**
+ * @return selected state
+ */
+ public boolean isSelected ();
+
+ /**
+ * @return selected state
+ */
+ public boolean getSelected ();
+
+ /**
+ * @return true if the EdgeView is hidden, else false
+ */
+ public boolean isHidden();
+
+ /**
+ * Add a PHandle to the edge at the point specified.
+ *
+ * @param pt The point at which to draw the PHandle and to which the
+ * PHandle will be attached via the locator.
+ */
+ // public void addHandle ( Point2D pt );
+
+ /**
+ * Removes the PHandle at the specified point.
+ *
+ * @param pt If this point intersects an existing PHandle, then remove that
+ * PHandle.
+ */
+ // public void removeHandle ( Point2D pt );
+
+ /**
+ * Checks to see if a PHandle already exists for the given point.
+ *
+ * @param pt If this point intersects a currently existing PHandle, then
+ * return true, else return false.
+ */
+ //public boolean handleAlreadyExists ( Point2D pt );
+
+ /**
+ * This is the main method called to update the drawing of the edge.
+ */
+ public void updateEdgeView ();
+
+ /**
+ * Draws the EdgeEnd, also sets the Source/Target Points to values such
+ * that the edge does not "go through" the end
+ */
+ public void updateTargetArrow ();
+
+ /**
+ * Draws the EdgeEnd, also sets the Source/Target Points to values such
+ * that the edge does not "go through" the end
+ */
+ public void updateSourceArrow ();
+
+ /**
+ * Sets the Drawing style for the edge end.
+ */
+ public void setSourceEdgeEnd(int type);
+
+ /**
+ * Sets the Drawing style for the edge end.
+ */
+ public void setTargetEdgeEnd(int type);
+
+
+ /**
+ * Return the Drawing style for the edge end.
+ */
+ public int getSourceEdgeEnd();
+
+ /**
+ * REturn the Drawing style for the edge end.
+ */
+ public int getTargetEdgeEnd();
+
+ /**
+ * Draws the Edge
+ */
+ public void updateLine();
+
+ /**
+ * Draws the edge as red and draws any handles previously added.
+ */
+ public void drawSelected();
+
+ /**
+ * Draws the edge as black and removes any handles from the display.
+ */
+ public void drawUnselected();
+
+ /**
+ * @return the Bend used
+ */
+ public Bend getBend ();
+
+ public void clearBends ();
+
+ public Label getLabel();
+
+ /**
+ * Sets what the tooltip will be for this EdgeView
+ */
+ public void setToolTip ( String tip );
+
+ public void setLabelOffsetX(double x);
+ public void setLabelOffsetY(double y);
+ public void setEdgeLabelAnchor(int position);
+
+ public double getLabelOffsetX();
+ public double getLabelOffsetY();
+ public int getEdgeLabelAnchor();
+
+ public double getLabelWidth();
+ public void setLabelWidth(double width);
+}
diff --git a/corelibs/giny/src/main/java/giny/view/GraphView.java b/corelibs/giny/src/main/java/giny/view/GraphView.java
new file mode 100644
index 0000000..acb63ad
--- /dev/null
+++ b/corelibs/giny/src/main/java/giny/view/GraphView.java
@@ -0,0 +1,540 @@
+/*
+ * Created on Oct 8, 2003
+ */
+package giny.view;
+
+// java
+import java.awt.Component;
+import java.awt.Paint;
+import java.util.Iterator;
+import java.util.List;
+
+// giny
+import giny.model.Edge;
+import giny.model.Node;
+import giny.model.RootGraph;
+import giny.model.GraphPerspective;
+import giny.view.EdgeView;
+import giny.view.GraphViewChangeListener;
+import giny.view.NodeView;
+
+
+/**
+ * @author xmas
+ */
+public interface GraphView {
+
+public static int NODE_X_POSITION = 0;
+ public static int NODE_Y_POSITION = 1;
+ public static int NODE_SHAPE = 2;
+ public static int NODE_PAINT = 3;
+ public static int NODE_SELECTION_PAINT = 4;
+ public static int NODE_BORDER_PAINT = 5;
+ public static int NODE_BORDER_WIDTH = 6;
+ public static int NODE_WIDTH = 7;
+ public static int NODE_HEIGHT = 8;
+ public static int NODE_LABEL = 9;
+ public static int NODE_Z_POSITION = 10;
+
+
+ public static int SOURCE_INDEX = 0;
+ public static int TARGET_INDEX = 1;
+ public static int EDGE_WIDTH = 2;
+ public static int EDGE_LINE_TYPE = 3;
+ public static int EDGE_PAINT = 4;
+ public static int EDGE_SELECTION_PAINT = 5;
+ public static int EDGE_SOURCE_END_TYPE = 6;
+ public static int EDGE_SOURCE_END_PAINT = 7;
+ public static int EDGE_SOURCE_END_SELECTED_PAINT = 8;
+ public static int EDGE_TARGET_END_TYPE = 9;
+ public static int EDGE_TARGET_END_PAINT = 10;
+ public static int EDGE_TARGET_END_SELECTED_PAINT = 11;
+
+
+
+ public GraphPerspective getGraphPerspective();
+
+
+ //----------------------------------------//
+ // Event Handlers
+ //----------------------------------------//
+
+
+ public boolean nodeSelectionEnabled();
+ public boolean edgeSelectionEnabled();
+
+ public void enableNodeSelection ();
+
+
+ public void disableNodeSelection ();
+
+ public void enableEdgeSelection ();
+
+ public void disableEdgeSelection ();
+
+
+ /**
+ * @return an int array of the graph perspective indices of the selected nodes
+ */
+ public int[] getSelectedNodeIndices();
+
+ /**
+ * @return a list of the selected NodeView
+ */
+ public List getSelectedNodes();
+
+ /**
+ * @return an int array of the graph perspective indices of the selected edges
+ */
+ public int[] getSelectedEdgeIndices();
+
+ /**
+ * @return a list of the selected EdgeView
+ */
+ public List getSelectedEdges();
+
+ /**
+ * Adds a new GraphViewChangeListener to this GraphViews list of listeners.
+ */
+ public void addGraphViewChangeListener(GraphViewChangeListener listener);
+
+ /**
+ * Removes a GraphViewChangeListener from this GraphViews list of listeners.
+ */
+ public void removeGraphViewChangeListener(GraphViewChangeListener listener);
+
+ /**
+ * @param paint the new Paint for the background
+ */
+ public void setBackgroundPaint(Paint paint);
+
+ /**
+ * @return the backgroundPaint
+ */
+ public Paint getBackgroundPaint();
+
+ /**
+ * @return the java.awt.Component that can be added to most screen thingys
+ */
+ public Component getComponent();
+
+ /**
+ * @param node_index the index of a node to have a view created for it
+ * @return a new NodeView based on the node with the given index
+ */
+ public NodeView addNodeView(int node_index);
+
+ /**
+ * @param edge_index the index of an edge
+ * @return the newly created edgeview
+ */
+ public EdgeView addEdgeView(int edge_index);
+
+ /**
+ * To facilitate adding Custome EdgeViews
+ * It is recomended that All Custom Edge Views follow the patterns outlined
+ * in PEdgeView and BasicPEdgeView.
+ * @param class_name the name of the class that implements EdgeView and esnted PEdge
+ * @param edge_index the index of the edge
+ */
+ public EdgeView addEdgeView(String class_name, int edge_index);
+
+ /**
+ * To facilitate adding Custome NodeViews
+ * It is recomended that All Custom Node Views follow the patterns outlined
+ * in PNodeView and BasicPNodeView.
+ * @param class_name the name of the class that implements NodeView and esnted PNode
+ * @param node_index the index of the node
+ */
+ public NodeView addNodeView(String class_name, int node_index);
+
+ /**
+ * Add in a NodeView for a Node in the GraphPerspective.
+ * Note that this means that if there already was a NodeView for this node,
+ * the new NodeView will take its place.
+ * @return If it is replacing, it returns the <B>old</B> NodeView.
+ * @return If it is new, it returns the <B>new</b> NodeView.
+ */
+ public NodeView addNodeView(
+ int node_index,
+ NodeView node_view_replacement);
+
+
+ /**
+ * This will entirely remove a NodeView/EdgeView from the GraphView. This is different than
+ * @see #hideGraphObject as that method simply stops showing the node/edge. This method
+ * will destroy the object. It will be returned though, so that a reference can be kept
+ * for undo purposes.
+ */
+ public NodeView removeNodeView ( NodeView node_view );
+
+
+ /**
+ * This will entirely remove a NodeView/EdgeView from the GraphView. This is different than
+ * @see #hideGraphObject as that method simply stops showing the node/edge. This method
+ * will destroy the object. It will be returned though, so that a reference can be kept
+ * for undo purposes.
+ */
+ public NodeView removeNodeView ( Node node );
+
+ /**
+ * This will entirely remove a NodeView/EdgeView from the GraphView. This is different than
+ * @see #hideGraphObject as that method simply stops showing the node/edge. This method
+ * will destroy the object. It will be returned though, so that a reference can be kept
+ * for undo purposes.
+ */
+ public NodeView removeNodeView ( int node );
+
+ /**
+ * This will entirely remove a NodeView/EdgeView from the GraphView. This is different than
+ * @see #hideGraphObject as that method simply stops showing the node/edge. This method
+ * will destroy the object. It will be returned though, so that a reference can be kept
+ * for undo purposes.
+ */
+ public EdgeView removeEdgeView ( EdgeView edge_view );
+
+ /**
+ * This will entirely remove a NodeView/EdgeView from the GraphView. This is different than
+ * @see #hideGraphObject as that method simply stops showing the node/edge. This method
+ * will destroy the object. It will be returned though, so that a reference can be kept
+ * for undo purposes.
+ */
+ public EdgeView removeEdgeView ( Edge edge );
+
+ /**
+ * This will entirely remove a NodeView/EdgeView from the GraphView. This is different than
+ * @see #hideGraphObject as that method simply stops showing the node/edge. This method
+ * will destroy the object. It will be returned though, so that a reference can be kept
+ * for undo purposes.
+ */
+ public EdgeView removeEdgeView ( int edge );
+
+
+ /**
+ * @return The Unique Identifier of this GraphView
+ */
+ public String getIdentifier();
+
+ /**
+ * @param new_identifier The New Identifier for this GraphView
+ */
+ public void setIdentifier(String new_identifier);
+
+ /**
+ * @return The Current Zoom Level
+ */
+ public double getZoom();
+
+ /**
+ * @param zoom The New ZoomLevel
+ */
+ public void setZoom(double zoom);
+
+ /**
+ * Fits all Viewable elements onto the Graph
+ */
+ public void fitContent();
+
+ /**
+ * Do a global redraw of the entire canvas
+ */
+ public void updateView();
+
+ /**
+ * @return the root graph of the GraphPerspective that we are actually a view on
+ */
+ public RootGraph getRootGraph();
+
+ /**
+ * nodeViewsIterator only returns the NodeViews that are explicitly
+ * associated with this GraphView
+ */
+ public Iterator getNodeViewsIterator();
+
+ /**
+ * @return the number of node views present
+ */
+ public int getNodeViewCount();
+
+ /**
+ * @return the number of EdgeViews present
+ */
+ public int getEdgeViewCount();
+
+ /**
+ * @param node The Node whose view is requested
+ *
+ * @return The NodeView of the given Node
+ */
+ public NodeView getNodeView(Node node);
+
+ /**
+ * @param index the index of the node whose view is requested
+ * @return The NodeView of the given Node
+ */
+ public NodeView getNodeView(int index);
+
+ /**
+ * Return all of the EdgeViews in this GraphView
+ */
+ public java.util.List getEdgeViewsList();
+
+ /**
+ * Note that this will return a list of Edge objects, the other one will return indices
+ * @return The list of EdgeViews connecting these two nodes. Possibly null.
+ */
+ public java.util.List getEdgeViewsList(
+ Node oneNode,
+ Node otherNode);
+
+ /**
+ * @return a List of indicies
+ */
+ public java.util.List getEdgeViewsList(
+ int from_node_index,
+ int to_node_index,
+ boolean include_undirected_edges);
+
+ /**
+ * @return the EdgeView that corresponds to the given index
+ */
+ public EdgeView getEdgeView(int edge_index);
+
+ /**
+ * Return all of the EdgeViews in this GraphView
+ */
+ public Iterator getEdgeViewsIterator();
+
+ /**
+ * @return the EdgeView that corresponds to the given Edge
+ */
+ public EdgeView getEdgeView(Edge edge);
+
+ /**
+ * @return the number of edges
+ */
+ public int edgeCount();
+
+ /**
+ * @return The number of Nodes, same number as the perspective
+ */
+ public int nodeCount();
+
+ /**
+ * use this to hide a node or edge
+ */
+ public boolean hideGraphObject(Object object);
+
+ /**
+ * use this to show a node or edge
+ */
+ public boolean showGraphObject(Object object);
+
+ /**
+ * <B> Warning!!!!!!!</B><BR>
+ * Only to be used for homogenous groups!!!!
+ */
+ public boolean hideGraphObjects(List objects);
+
+ /**
+ * <B> Warning!!!!!!!</B><BR>
+ * Only to be used for homogenous groups!!!!
+ */
+ public boolean showGraphObjects(List objects);
+
+
+ /**
+ * Context Menu Support
+ */
+ public Object[] getContextMethods(
+ String class_name,
+ boolean plus_superclass);
+
+ /**
+ * Context Menu Support
+ */
+ public Object[] getContextMethods(
+ String class_name,
+ Object[] methods);
+
+ /**
+ * Context Menu Support
+ */
+ public boolean addContextMethod(
+ String class_name,
+ String method_class_name,
+ String method_name,
+ Object[] args,
+ ClassLoader loader );
+
+ /**
+ * Set All Data For a NOde
+ * <B>Big Bold Faced Warning</B> <BR>
+ * Talk to rowan before using.
+ */
+ public void setAllNodePropertyData(int node_index, Object[] data);
+
+ /*
+ * <B>Big Bold Faced Warning</B> <BR>
+ * Talk to rowan before using.
+ */
+ public Object[] getAllNodePropertyData(int node_index);
+
+ /**
+ * Set All Data For an Edge <BR>
+ * <B>Big Bold Faced Warning</B> <BR>
+ * Talk to rowan before using.
+ */
+ public void setAllEdgePropertyData(int edge_index, Object[] data);
+
+ /*
+ * <B>Big Bold Faced Warning</B> <BR>
+ * Talk to rowan before using.
+ */
+ public Object[] getAllEdgePropertyData(int edge_index);
+
+ //----------------------------------------//
+ // Object Methods
+ //----------------------------------------//
+
+ /**
+ * Return the stored value for the node for the given property
+ * @param node_index The Node Index to be queried
+ * @param property the property to be accessed
+ */
+ public Object getNodeObjectProperty(int node_index, int property);
+
+ /**
+ * @param node_index The Node Index to be queried
+ * @param property the property to be accessed
+ * @param value the new value for this property
+ */
+ public boolean setNodeObjectProperty( int node_index, int property, Object value);
+
+ /**
+ * Return the stored value for the edge for the given property
+ * @param edge_index The Edge Index to be queried
+ * @param property the property to be accessed
+ */
+ public Object getEdgeObjectProperty(int edge_index, int property);
+
+ /**
+ * @param edge_index The Edge Index to be queried
+ * @param property the property to be accessed
+ * @param value the new value for this property
+ */
+ public boolean setEdgeObjectProperty(
+ int edge_index,
+ int property,
+ Object value);
+
+ //----------------------------------------//
+ // Double Methods
+ //----------------------------------------//
+
+ /**
+ * @param node_index The Node Index to be queried
+ * @param property the property to be accessed
+ */
+ public double getNodeDoubleProperty(int node_index, int property);
+
+ /**
+ * @param node_index The Node Index to be queried
+ * @param property the property to be accessed
+ * @param value the new value for this property
+ */
+ public boolean setNodeDoubleProperty(
+ int node_index,
+ int property,
+ double value);
+
+ public double getEdgeDoubleProperty(int edge_index, int property);
+
+ /**
+ * @param edge_index The Edge Index to be queried
+ * @param property the property to be accessed
+ * @param value the new value for this property
+ */
+ public boolean setEdgeDoubleProperty(
+ int edge_index,
+ int property,
+ double value);
+
+ //----------------------------------------//
+ // Float Methods
+ //----------------------------------------//
+
+ public float getNodeFloatProperty(int node_index, int property);
+
+ /**
+ * @param node_index The Node Index to be queried
+ * @param property the property to be accessed
+ * @param value the new value for this property
+ */
+ public boolean setNodeFloatProperty(
+ int node_index,
+ int property,
+ float value);
+
+ public float getEdgeFloatProperty(int edge_index, int property);
+
+ /**
+ * @param edge_index The Edge Index to be queried
+ * @param property the property to be accessed
+ * @param value the new value for this property
+ */
+ public boolean setEdgeFloatProperty(
+ int edge_index,
+ int property,
+ float value);
+
+
+ public boolean getNodeBooleanProperty(int node_index, int property);
+
+ /**
+ * @param node_index The Node Index to be queried
+ * @param property the property to be accessed
+ * @param value the new value for this property
+ */
+ public boolean setNodeBooleanProperty(
+ int node_index,
+ int property,
+ boolean value);
+
+ public boolean getEdgeBooleanProperty(int edge_index, int property);
+
+ /**
+ * @param edge_index The Edge Index to be queried
+ * @param property the property to be accessed
+ * @param value the new value for this property
+ */
+ public boolean setEdgeBooleanProperty(
+ int edge_index,
+ int property,
+ boolean value);
+
+ public int getNodeIntProperty(int node_index, int property);
+
+ /**
+ * @param node_index The Node Index to be queried
+ * @param property the property to be accessed
+ * @param value the new value for this property
+ */
+ public boolean setNodeIntProperty(
+ int node_index,
+ int property,
+ int value);
+
+ public int getEdgeIntProperty(int edge_index, int property);
+
+ /**
+ * @param edge_index The Edge Index to be queried
+ * @param property the property to be accessed
+ * @param value the new value for this property
+ */
+ public boolean setEdgeIntProperty(
+ int edge_index,
+ int property,
+ int value);
+
+}
diff --git a/corelibs/giny/src/main/java/giny/view/GraphViewChangeEvent.java b/corelibs/giny/src/main/java/giny/view/GraphViewChangeEvent.java
new file mode 100644
index 0000000..2e1a923
--- /dev/null
+++ b/corelibs/giny/src/main/java/giny/view/GraphViewChangeEvent.java
@@ -0,0 +1,53 @@
+package giny.view;
+
+import java.util.EventObject;
+import giny.model.*;
+
+/**
+ * The event source must be the GraphPerspective that changed.
+ */
+public abstract class GraphViewChangeEvent
+ extends EventObject {
+
+ public static final int NODES_RESTORED_TYPE = 1;
+ public static final int EDGES_RESTORED_TYPE = 2;
+ public static final int NODES_HIDDEN_TYPE = 4;
+ public static final int EDGES_HIDDEN_TYPE = 8;
+ public static final int NODES_SELECTED_TYPE = 16;
+ public static final int NODES_UNSELECTED_TYPE = 32;
+ public static final int EDGES_SELECTED_TYPE = 64;
+ public static final int EDGES_UNSELECTED_TYPE = 128;
+
+ public GraphViewChangeEvent ( GraphView source ) {
+ super( source );
+ }
+
+ public abstract int getType ();
+ public abstract boolean isNodesRestoredType ();
+ public abstract boolean isEdgesRestoredType ();
+ public abstract boolean isNodesHiddenType ();
+ public abstract boolean isEdgesHiddenType ();
+ public abstract boolean isNodesSelectedType ();
+ public abstract boolean isNodesUnselectedType ();
+ public abstract boolean isEdgesSelectedType ();
+ public abstract boolean isEdgesUnselectedType ();
+
+ public abstract Node[] getRestoredNodes ();
+ public abstract Edge[] getRestoredEdges ();
+ public abstract Node[] getHiddenNodes ();
+ public abstract Edge[] getHiddenEdges ();
+ public abstract Node[] getSelectedNodes ();
+ public abstract Node[] getUnselectedNodes ();
+ public abstract Edge[] getSelectedEdges ();
+ public abstract Edge[] getUnselectedEdges ();
+
+ public abstract int[] getRestoredNodeIndices ();
+ public abstract int[] getRestoredEdgeIndices ();
+ public abstract int[] getHiddenNodeIndices ();
+ public abstract int[] getHiddenEdgeIndices ();
+ public abstract int[] getSelectedNodeIndices ();
+ public abstract int[] getUnselectedNodeIndices ();
+ public abstract int[] getSelectedEdgeIndices ();
+ public abstract int[] getUnselectedEdgeIndices ();
+
+} // abstract class GraphPerspectiveChangeEvent
diff --git a/corelibs/giny/src/main/java/giny/view/GraphViewChangeListener.java b/corelibs/giny/src/main/java/giny/view/GraphViewChangeListener.java
new file mode 100644
index 0000000..f60150e
--- /dev/null
+++ b/corelibs/giny/src/main/java/giny/view/GraphViewChangeListener.java
@@ -0,0 +1,14 @@
+package giny.view;
+
+import java.util.EventListener;
+
+public interface GraphViewChangeListener
+ extends EventListener {
+
+ /**
+ * Invoked when a GraphPerspective to which this
+ * GraphPerspectiveChangeListener listens changes.
+ */
+ public void graphViewChanged ( GraphViewChangeEvent event );
+
+} // interface GraphPerspectiveChangeListener
diff --git a/corelibs/giny/src/main/java/giny/view/Justification.java b/corelibs/giny/src/main/java/giny/view/Justification.java
new file mode 100644
index 0000000..dc87317
--- /dev/null
+++ b/corelibs/giny/src/main/java/giny/view/Justification.java
@@ -0,0 +1,65 @@
+package giny.view;
+
+
+public enum Justification {
+ JUSTIFY_CENTER("Center Justified", "c", Label.JUSTIFY_CENTER), JUSTIFY_LEFT(
+ "Left Justified", "l", Label.JUSTIFY_LEFT), JUSTIFY_RIGHT(
+ "Right Justified", "r", Label.JUSTIFY_RIGHT);
+
+ private static String[] JUSTIFY;
+
+ private final String displayName;
+ private final String shortName;
+ private final int ginyConstatnt;
+
+ private Justification(final String displayName, final String shortName,
+ final int ginyConstant) {
+ this.displayName = displayName;
+ this.shortName = shortName;
+ this.ginyConstatnt = ginyConstant;
+ }
+
+ public String getName() {
+ return this.displayName;
+ }
+
+ public String getShortName() {
+ return this.shortName;
+ }
+
+ public int getGinyConstant() {
+ return this.ginyConstatnt;
+ }
+
+ public static Justification parse(final String value) {
+ for (final Justification j : values()) {
+ if (j.getName().equals(value) || j.getShortName().equals(value))
+ return j;
+ }
+ return null;
+ }
+
+ public static Justification parse(final int giny) {
+ for (final Justification j : values()) {
+ if (j.getGinyConstant() == giny)
+ return j;
+ }
+
+ return null;
+ }
+
+
+ public static String[] getNames() {
+ if(JUSTIFY == null) {
+ JUSTIFY = new String[values().length];
+ int i = 0;
+ for(Justification j: values()) {
+ JUSTIFY[i] = j.displayName;
+ i++;
+ }
+ }
+
+ return JUSTIFY;
+ }
+
+}
diff --git a/corelibs/giny/src/main/java/giny/view/Label.java b/corelibs/giny/src/main/java/giny/view/Label.java
new file mode 100644
index 0000000..c288eb6
--- /dev/null
+++ b/corelibs/giny/src/main/java/giny/view/Label.java
@@ -0,0 +1,137 @@
+package giny.view;
+
+import java.awt.Font;
+import java.awt.Paint;
+
+public interface Label {
+
+ public static final int SOURCE_BOUND = 9;
+ public static final int TARGET_BOUND = 10;
+
+ /**
+ * Give the Label a hint on where to draw itself. <B>NOTE:</B> This should
+ * be thought of as a hint only, not all labels will support all positions
+ */
+
+ /**
+ * Get the paint used to paint this nodes text.
+ *
+ * @return Paint
+ */
+ public Paint getTextPaint();
+
+ /**
+ * Set the paint used to paint this nodes text.
+ *
+ * @param textPaint
+ */
+ public void setTextPaint(Paint textPaint);
+
+ /**
+ * Returns the current greek threshold. When the screen font size will be
+ * below this threshold the text is rendered as 'greek' instead of drawing
+ * the text glyphs.
+ */
+ public double getGreekThreshold();
+
+ /**
+ * Sets the current greek threshold. When the screen font size will be below
+ * this threshold the text is rendered as 'greek' instead of drawing the
+ * text glyphs.
+ *
+ * @param threshold minimum screen font size.
+ */
+ public void setGreekThreshold(double threshold);
+
+ public String getText();
+
+ /**
+ * Set the text for this node. The text will be broken up into multiple
+ * lines based on the size of the text and the bounds width of this node.
+ */
+ public void setText(String aText);
+
+ /**
+ * Returns the font of this PText.
+ *
+ * @return the font of this PText.
+ */
+ public Font getFont();
+
+ /**
+ * Set the font of this PText. Note that in Piccolo if you want to change
+ * the size of a text object it's often a better idea to scale the PText
+ * node instead of changing the font size to get that same effect. Using
+ * very large font sizes can slow performance.
+ */
+ public void setFont(Font aFont);
+
+ /**
+ * Set position of label. ObjectPosition is a consolidated data structure
+ * designed as the replacement of deprecated parameters below.
+ *
+ * @param p
+ */
+ public void setPosition(final ObjectPosition p);
+ public ObjectPosition getPosition();
+
+
+ ///////////// deprecated in Cytoscape 2.8. ////////////////
+
+ /**
+ *
+ */
+ @Deprecated
+ public void setTextAnchor(int position);
+
+
+ /**
+ *
+ */
+ @Deprecated
+ public int getTextAnchor();
+
+ /**
+ *
+ */
+ @Deprecated
+ public void setJustify(int justify);
+
+ /**
+ *
+ */
+ @Deprecated
+ public int getJustify();
+
+ @Deprecated
+ public static int NORTHWEST = 0;
+ @Deprecated
+ public static int NORTH = 1;
+ @Deprecated
+ public static int NORTHEAST = 2;
+
+ @Deprecated
+ public static int WEST = 3;
+ @Deprecated
+ public static int CENTER = 4;
+ @Deprecated
+ public static int EAST = 5;
+
+ @Deprecated
+ public static int SOUTHWEST = 6;
+ @Deprecated
+ public static int SOUTH = 7;
+ @Deprecated
+ public static int SOUTHEAST = 8;
+
+ @Deprecated
+ public static int JUSTIFY_CENTER = 64;
+ @Deprecated
+ public static int JUSTIFY_LEFT = 65;
+ @Deprecated
+ public static int JUSTIFY_RIGHT = 66;
+
+ @Deprecated
+ public static int NONE = 127;
+
+}
diff --git a/corelibs/giny/src/main/java/giny/view/NodeView.java b/corelibs/giny/src/main/java/giny/view/NodeView.java
new file mode 100644
index 0000000..14a1649
--- /dev/null
+++ b/corelibs/giny/src/main/java/giny/view/NodeView.java
@@ -0,0 +1,298 @@
+package giny.view;
+
+
+import giny.model.Node;
+
+import java.awt.Paint;
+import java.awt.Stroke;
+import java.awt.geom.Point2D;
+import java.util.List;
+
+/**
+ * Any and all questions should be directed to me.
+
+ * @author Rowan Christmas
+ */
+public interface NodeView {
+
+ public static final int TRIANGLE = 0;
+ public static final int DIAMOND = 1;
+ public static final int ELLIPSE = 2;
+ public static final int HEXAGON = 3;
+ public static final int OCTAGON = 4;
+ public static final int PARALELLOGRAM = 5;
+ public static final int RECTANGLE = 6;
+ public static final int ROUNDED_RECTANGLE = 7;
+ public static final int VEE = 8;
+
+ /**
+ * @return the view we are in
+ */
+ public GraphView getGraphView() ;
+
+ /**
+ * @return The Node we are a view on
+ */
+ public Node getNode () ;
+
+ /**
+ * @return the index of this node in the perspective to which we are in a view on.
+ */
+ public int getGraphPerspectiveIndex () ;
+
+ /**
+ * @return the index of this node in the root graph to which we are in a view on.
+ */
+ public int getRootGraphIndex () ;
+
+
+ /**
+ * @return The list of EdgeViews connecting these two nodes. Possibly null.
+ */
+ public List getEdgeViewsList(NodeView otherNode) ;
+
+ /**
+ * Shape is currently defined via predefined variables in
+ * the NodeView interface. To get the actual java.awt.Shape
+ * use getPathReference()
+ * @return the current int-tpye shape
+ */
+ public int getShape () ;
+
+
+ /**
+ * This sets the Paint that will be used by this node
+ * when it is painted as selected.
+ * @param paint The Paint to be used
+ */
+ public void setSelectedPaint (Paint paint) ;
+
+ /**
+ * @return the currently set selection Paint
+ */
+ public Paint getSelectedPaint () ;
+
+
+
+ /**
+ * Set the deafult paint of this node
+ * @param paint the default Paint of this node
+ */
+ public void setUnselectedPaint ( Paint paint ) ;
+
+ /**
+ * @return the currently set paint
+ */
+ public Paint getUnselectedPaint () ;
+
+
+
+ /**
+ * @param b_paint the paint the border will use
+ */
+ public void setBorderPaint ( Paint b_paint ) ;
+
+ /**
+ * @return the currently set BOrder Paint
+ */
+ public Paint getBorderPaint () ;
+
+ /**
+ * @param border_width The width of the border.
+ */
+ public void setBorderWidth ( float border_width ) ;
+
+ /**
+ * @return the currently set Border width
+ */
+ public float getBorderWidth () ;
+
+
+ /**
+ * @param stroke the new stroke for the border
+ */
+ public void setBorder ( Stroke stroke );
+
+
+ /**
+ * @return the current border
+ */
+ public Stroke getBorder ();
+
+ /**
+ * @param trans new value for the transparency
+ */
+ public void setTransparency ( float trans );
+
+ /**
+ * @return the value for the transparency for this node
+ */
+ public float getTransparency ();
+
+
+ /**
+ * TODO: Reconcile with Border Methods
+ * @param width the currently set width of this node
+ */
+ public boolean setWidth ( double width ) ;
+
+ /**
+ * TODO: Reconcile with Border Methods
+ * @return the currently set width of this node
+ */
+ public double getWidth () ;
+
+ /**
+ * TODO: Reconcile with Border Methods
+ * @param height the currently set height of this node
+ */
+ public boolean setHeight ( double height ) ;
+
+ /**
+ * TODO: Reconcile with Border Methods
+ * @return the currently set height of this node
+ */
+ public double getHeight () ;
+
+ /**
+ * @return The Value of the label
+ */
+ public giny.view.Label getLabel () ;
+
+ /**
+ * @return the degree of the Node in the GraphPerspective.
+ */
+ public int getDegree() ;
+
+ public void setOffset ( double x, double y );
+
+ public Point2D getOffset ();
+
+ /**
+ * @param new_x_position the new X position for this node
+ */
+ public void setXPosition(double new_x_position) ;
+
+ /**
+ * Set udpdate to false in order to do a layout, and then call updateNode on all the nodes..
+ // TODO -- HACKY
+ * @param new_x_position for this node
+ * @param update if this is true, the node will move immediatly.
+ */
+ public void setXPosition ( double new_x_position, boolean update ) ;
+
+ /**
+ * note that unless updateNode() has been called, this may not be
+ * the "real" location of this node
+ * @return the current x position of this node
+ * @see #setXPosition
+ */
+ public double getXPosition() ;
+
+ /**
+ * @param new_y_position the new Y position for this node
+ */
+ public void setYPosition(double new_y_position) ;
+
+ /**
+ * Set udpdate to false in order to do a layout, and then call updateNode on all the nodes..
+ // TODO -- HACKY
+ * @param new_y_position for this node
+ * @param update if this is true, the node will move immediatly.
+ */
+ public void setYPosition ( double new_y_position, boolean update ) ;
+
+ /**
+ * note that unless updateNode() has been called, this may not be
+ * the "real" location of this node
+ * @return the current y position of this node
+ * @see #setYPosition
+ */
+ public double getYPosition() ;
+
+ /**
+ * moves this node to its stored x and y locations.
+ */
+ public void setNodePosition(boolean animate) ;
+
+ /**
+ * This draws us as selected
+ */
+ public void select() ;
+
+ /**
+ * This draws us as unselected
+ */
+ public void unselect() ;
+
+ /**
+ *
+ */
+ public boolean isSelected() ;
+
+ /**
+ *
+ */
+ public boolean setSelected(boolean selected) ;
+
+ /**
+ * @return true if the NodeView is hidden, else false
+ */
+ public boolean isHidden();
+
+ /**
+ * Set a new shape for the Node, based on one of the pre-defined shapes
+ * <B>Note:</B> calling setPathTo( Shape ), allows one to define their own
+ * java.awt.Shape ( i.e. A picture of Johnny Cash )
+ */
+ public void setShape(int shape) ;
+
+ /**
+ * Sets what the tooltip will be for this NodeView
+ */
+ public void setToolTip ( String tip );
+
+ /**
+ * Returns current label position as ObjkectPosition object.
+ *
+ * @return label position as ObjectPosition
+ */
+ public ObjectPosition getLabelPosition();
+
+
+ /**
+ * Set current label position.
+ *
+ * @param position
+ */
+ public void setLabelPosition(final ObjectPosition position);
+
+
+ @Deprecated
+ public void setLabelOffsetX(double x);
+ @Deprecated
+ public void setLabelOffsetY(double y);
+ @Deprecated
+ public void setNodeLabelAnchor(int position);
+ @Deprecated
+ public double getLabelOffsetX();
+ @Deprecated
+ public double getLabelOffsetY();
+ @Deprecated
+ public int getNodeLabelAnchor();
+
+
+ public double getLabelWidth();
+ public void setLabelWidth(double width);
+
+ /** Determines whether a nested network should be rendered as part of a node's view or not.
+ * @return true if the node has a nested network and we want it rendered, else false.
+ */
+ boolean nestedNetworkIsVisible();
+
+ /** Set the visibility of a node's nested network when rendered.
+ * @param makeVisible forces the visibility of a nested network.
+ * Please note that this call has no effect if a node has no associated nested network!
+ */
+ void showNestedNetwork(final boolean makeVisible);
+}
diff --git a/corelibs/giny/src/main/java/giny/view/ObjectPosition.java b/corelibs/giny/src/main/java/giny/view/ObjectPosition.java
new file mode 100644
index 0000000..88c430d
--- /dev/null
+++ b/corelibs/giny/src/main/java/giny/view/ObjectPosition.java
@@ -0,0 +1,106 @@
+package giny.view;
+
+/**
+ * Interface representing relative location of graphics objects,
+ * such as labels or custom graphics.
+ *
+ * @author kono
+ *
+ */
+public interface ObjectPosition {
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Position getAnchor();
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Position getTargetAnchor();
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Justification getJustify();
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public double getOffsetX();
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public double getOffsetY();
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param b DOCUMENT ME!
+ */
+ public void setAnchor(Position position);
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param b DOCUMENT ME!
+ */
+ public void setTargetAnchor(Position position);
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param b DOCUMENT ME!
+ */
+ public void setJustify(Justification position);
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param d DOCUMENT ME!
+ */
+ public void setOffsetX(double d);
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param d DOCUMENT ME!
+ */
+ public void setOffsetY(double d);
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param lp DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ public boolean equals(Object position);
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ public String toString();
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String shortString();
+}
\ No newline at end of file
diff --git a/corelibs/giny/src/main/java/giny/view/Position.java b/corelibs/giny/src/main/java/giny/view/Position.java
new file mode 100644
index 0000000..b0f00b9
--- /dev/null
+++ b/corelibs/giny/src/main/java/giny/view/Position.java
@@ -0,0 +1,72 @@
+package giny.view;
+
+
+/**
+ * Constants represent position of graphics objects.
+ *
+ * @author kono
+ *
+ */
+public enum Position {
+ NORTH_WEST("Northwest", "NW", Label.NORTHWEST),
+ NORTH("North", "N", Label.NORTH),
+ NORTH_EAST("Northeast", "NE", Label.NORTHEAST),
+ WEST("West", "W", Label.WEST),
+ CENTER("Center", "C", Label.CENTER),
+ EAST("East", "E", Label.EAST),
+ NONE("none", "NONE", Label.NONE),
+ SOUTH_WEST("Southwest", "SW", Label.SOUTHWEST),
+ SOUTH("South", "S", Label.SOUTH),
+ SOUTH_EAST("Southeast","SE", Label.SOUTHEAST);
+
+ private static final String[] ANCHORS = {
+ NORTH_WEST.displayName, NORTH.displayName,
+ NORTH_EAST.displayName, WEST.displayName,
+ CENTER.displayName, EAST.displayName,
+ NONE.displayName, SOUTH_WEST.displayName,
+ SOUTH.displayName, SOUTH_EAST.displayName };
+
+ private final String displayName;
+ private final String shortName;
+ private final int ginyConstatnt;
+
+ private Position(final String displayName, final String shortName, final int ginyConstant) {
+ this.displayName = displayName;
+ this.shortName = shortName;
+ this.ginyConstatnt = ginyConstant;
+ }
+
+
+ public String getName() {
+ return this.displayName;
+ }
+
+ public String getShortName() {
+ return this.shortName;
+ }
+
+ public int getGinyConstant() {
+ return this.ginyConstatnt;
+ }
+
+ public static Position parse(final String value) {
+ for (final Position p : Position.values()) {
+ if (p.getName().equals(value) || p.getShortName().equals(value))
+ return p;
+ }
+ return null;
+ }
+
+ public static Position parse(final int giny) {
+ for (final Position p : Position.values()) {
+ if (p.getGinyConstant() == giny)
+ return p;
+ }
+
+ return null;
+ }
+
+ public static String[] getNames() {
+ return ANCHORS;
+ }
+}
diff --git a/corelibs/graph.dynamic/pom.xml b/corelibs/graph.dynamic/pom.xml
new file mode 100644
index 0000000..c095553
--- /dev/null
+++ b/corelibs/graph.dynamic/pom.xml
@@ -0,0 +1,54 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>parent</artifactId>
+ <version>2.8.4-SNAPSHOT</version>
+ </parent>
+
+ <artifactId>graph-dynamic</artifactId>
+ <packaging>jar</packaging>
+
+ <name>graph-dynamic</name>
+
+ <!-- bootstrap for cytoscape dependencies, namely the parent POM snapshots -->
+ <repositories>
+ <repository>
+ <id>cytoscape_snapshots</id>
+ <snapshots>
+ <enabled>true</enabled>
+ </snapshots>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <name>Cytoscape Snapshots</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/</url>
+ </repository>
+ <repository>
+ <id>cytoscape_releases</id>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ <name>Cytoscape Releases</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/releases/</url>
+ </repository>
+ </repositories>
+
+ <dependencies>
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>util-intr</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>graph-fixed</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ </dependencies>
+
+</project>
+
diff --git a/corelibs/graph.dynamic/src/main/java/cytoscape/graph/dynamic/DynamicGraph.java b/corelibs/graph.dynamic/src/main/java/cytoscape/graph/dynamic/DynamicGraph.java
new file mode 100644
index 0000000..93ec370
--- /dev/null
+++ b/corelibs/graph.dynamic/src/main/java/cytoscape/graph/dynamic/DynamicGraph.java
@@ -0,0 +1,277 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.graph.dynamic;
+
+import cytoscape.graph.fixed.FixedGraph;
+
+import cytoscape.util.intr.IntEnumerator;
+import cytoscape.util.intr.IntIterator;
+
+
+/**
+ * A graph whose topology can be modified.
+ * Edges and nodes are non-negative integers; a given node and a given edge
+ * in a single graph can be the same integer.
+ */
+public interface DynamicGraph extends FixedGraph {
+ /**
+ * A nonnegative quantity representing directedness of an edge.
+ */
+ public final static byte DIRECTED_EDGE = 1;
+
+ /**
+ * A nonnegative quantity representing undirectedness of an edge.
+ */
+ public final static byte UNDIRECTED_EDGE = 0;
+
+ /**
+ * Returns an enumeration of all nodes currently in this graph.
+ * Every node in this graph is a unique non-negative integer. A given
+ * node and a given edge in one graph may be the same integer.<p>
+ * The returned enumeration becomes invalid as soon as any
+ * graph-topology-modifying method on this graph is called. Calling
+ * methods on an invalid enumeration will result in undefined behavior
+ * of that enumeration. Enumerating through a graph's nodes will
+ * never have any effect on the graph.
+ *
+ * @return an enumeration over all nodes currently in this graph; null
+ * is never returned.
+ */
+ public IntEnumerator nodes();
+
+ /**
+ * Returns an enumeration of all edges currently in this graph.
+ * Every edge in this graph is a unique non-negative integer. A given
+ * node and a given edge in one graph may be the same integer.<p>
+ * The returned enumeration becomes invalid as soon as any
+ * graph-topology-modifying method on this graph is called. Calling
+ * methods on an invalid enumeration will result in undefined behavior
+ * of that enumeration. Enumerating through a graph's edges will
+ * never have any effect on the graph.
+ *
+ * @return an enumeration over all edges currently in this graph; null
+ * is never returned.
+ */
+ public IntEnumerator edges();
+
+ /**
+ * Creates a new node in this graph. Returns the new node. Nodes are
+ * always non-negative.<p>
+ * Implementations may create nodes with arbitrarily large values.
+ * Even if implementations initially create nodes with small values,
+ * nodes may take ever-increasing values when nodes are continually being
+ * removed and created. Or, implementations may choose to re-use node values
+ * as nodes are removed and added again.
+ *
+ * @return the newly created node.
+ */
+ public int nodeCreate();
+
+ /**
+ * Removes the specified node from this graph. Returns true if and only
+ * if the specified node was in this graph at the time this method was
+ * called. A return value of true implies that the specified node has
+ * been successfully removed from this graph.<p>
+ * Note that removal of a node necessitates the removal of any edge
+ * touching that node.
+ *
+ * @param node the node that is to be removed from this graph.
+ * @return true if and only if the specified node existed in this graph
+ * at the time this operation was started.
+ */
+ public boolean nodeRemove(int node);
+
+ /**
+ * Creates a new edge in this graph, having source node, target node,
+ * and directedness specified. Returns the new edge, or -1 if either the
+ * source or target node does not exist in this graph. Edges are always
+ * non-negative.<p>
+ * Implementations may create edges with arbitrarily large values.
+ * Even if implementations initially create edges with small values,
+ * edges may take ever-increasing values when edges are continually being
+ * removed and created. Or, implementations may choose to re-use edge values
+ * as edges are removed and added again.
+ *
+ * @param sourceNode the source node that the new edge is to have.
+ * @param targetNode the target node that the new edge is to have.
+ * @param directed the new edge will be directed if and only if this value
+ * is true.
+ * @return the newly created edge or -1 if either the source or target node
+ * specified does not exist in this graph.
+ */
+ public int edgeCreate(int sourceNode, int targetNode, boolean directed);
+
+ /**
+ * Removes the specified edge from this graph. Returns true if and only
+ * if the specified edge was in this graph at the time this method was
+ * called. A return value of true implies that the specified edge has
+ * been successfully removed from this graph.<p>
+ * Note that removing an edge does not cause that edge's endpoint nodes
+ * to be removed from this graph.
+ *
+ * @param edge the edge that is to be removed from this graph.
+ * @return true if and only if the specified edge existed in this graph
+ * at the time this operation was started.
+ */
+ public boolean edgeRemove(int edge);
+
+ /**
+ * Determines whether or not a node exists in this graph.
+ * Returns true if and only if the node specified exists.<p>
+ * Note that this method is superfluous in this interface (that is,
+ * it could be removed without losing any functionality), because
+ * edgesAdjacent(int, boolean, boolean, boolean) can be used to test
+ * the presence of a node. However, because nodeExists(int) does not
+ * return a complicated object, its performance may be better
+ * than that of edgesAdjacent().
+ *
+ * @param node the [potentially existing] node in this graph whose existence
+ * we're querying.
+ * @return the existence of specified node in this graph.
+ */
+ public boolean nodeExists(int node);
+
+ /**
+ * Determines the existence and directedness of an edge.
+ * Returns -1 if specified edge does not exist in this graph,
+ * otherwise returns DIRECTED_EDGE or UNDIRECTED_EDGE.
+ *
+ * @param edge the edge in this graph whose existence and/or
+ * directedness we're seeking.
+ * @return DIRECTED_EDGE if specified edge is directed, UNDIRECTED_EDGE
+ * if specified edge is undirected, and -1 if specified edge does not
+ * exist in this graph.
+ */
+ public byte edgeType(int edge);
+
+ /**
+ * Determines the source node of an edge.
+ * Returns the source node of specified edge or -1 if specified edge does
+ * not exist in this graph.
+ *
+ * @param edge the edge in this graph whose source node we're seeking.
+ * @return the source node of specified edge or -1 if specified edge does
+ * not exist in this graph.
+ */
+ public int edgeSource(int edge);
+
+ /**
+ * Determines the target node of an edge.
+ * Returns the target node of specified edge or -1 if specified edge does
+ * not exist in this graph.
+ *
+ * @param edge the edge in this graph whose target node we're seeking.
+ * @return the target node of specified edge or -1 if specified edge does
+ * not exist in this graph.
+ */
+ public int edgeTarget(int edge);
+
+ /**
+ * Returns a non-repeating enumeration of edges adjacent to a node.
+ * The three boolean input parameters define what is meant by "adjacent
+ * edge". If all three boolean input parameters are false, the returned
+ * enumeration will have zero elements.<p>
+ * The returned enumeration becomes invalid as soon as any
+ * graph-topology-modifying method on this graph is called. Calling
+ * methods on an invalid enumeration will result in undefined behavior
+ * of that enumeration.<p>
+ * This method returns null if and only if the specified node does not
+ * exist in this graph. Therefore, this method can be used to test
+ * the existence of a node in this graph.
+ *
+ * @param node the node in this graph whose adjacent edges we're seeking.
+ * @param outgoing all directed edges whose source is the node specified
+ * are included in the returned enumeration if this value is true;
+ * otherwise, not a single such edge is included in the returned
+ * enumeration.
+ * @param incoming all directed edges whose target is the node specified
+ * are included in the returned enumeration if this value is true;
+ * otherwise, not a single such edge is included in the returned
+ * enumeration.
+ * @param undirected all undirected edges touching the specified node
+ * are included in the returned enumeration if this value is true;
+ * otherwise, not a single such edge is included in the returned
+ * enumeration.
+ * @return an enumeration of edges adjacent to the node specified
+ * or null if specified node does not exist in this graph.
+ */
+ public IntEnumerator edgesAdjacent(int node, boolean outgoing, boolean incoming,
+ boolean undirected);
+
+ /**
+ * Returns a non-repeating iteration of edges connecting two nodes.
+ * The three boolean input parameters define what is meant by "connecting
+ * edge". If all three boolean input parameters are false, the returned
+ * iteration will have no elements.<p>
+ * The returned iteration becomes invalid as soon as any
+ * graph-topology-modifying method on this graph is called. Calling
+ * methods on an invalid iteration will result in undefined behavior
+ * of that iteration.<p>
+ * I'd like to discuss the motivation behind this interface method.
+ * I assume that most implementations of this interface will implement
+ * this method in terms of edgesAdjacent(). Why, then, is this method
+ * necessary? Because some implementations may choose to optimize the
+ * implementation of this method by using a search tree or a
+ * hashtable, for example. This method is a hook to provide such
+ * optimization.<p>
+ * This method returns an IntIterator as opposed to an IntEnumerator
+ * so that non-optimized implementations would not be required to
+ * pre-compute the number of edges being returned.
+ *
+ * @param node0 one of the nodes in this graph whose connecting edges
+ * we're seeking.
+ * @param node1 one of the nodes in this graph whose connecting edges
+ * we're seeking.
+ * @param outgoing all directed edges whose source is node0 and whose
+ * target is node1 are included in the returned iteration if this value
+ * is true; otherwise, not a single such edge is included in the returned
+ * iteration.
+ * @param incoming all directed edges whose source is node1 and whose
+ * target is node0 are included in the returned iteration if this value
+ * is true; otherwise, not a single such edge is included in the returned
+ * iteration.
+ * @param undirected all undirected edges E such that E's endpoints
+ * are node0 and node1 are included in the returned iteration if this
+ * value is true; otherwise, not a single such edge is incuded in the
+ * returned iteration.
+ * @return an iteration of edges connecting node0 with node1 in a fashion
+ * specified by boolean input parameters or null if either of node0 or
+ * node1 does not exist in this graph.
+ */
+ public IntIterator edgesConnecting(int node0, int node1, boolean outgoing, boolean incoming,
+ boolean undirected);
+}
diff --git a/corelibs/graph.dynamic/src/main/java/cytoscape/graph/dynamic/util/DynamicGraphFactory.java b/corelibs/graph.dynamic/src/main/java/cytoscape/graph/dynamic/util/DynamicGraphFactory.java
new file mode 100644
index 0000000..48b486f
--- /dev/null
+++ b/corelibs/graph.dynamic/src/main/java/cytoscape/graph/dynamic/util/DynamicGraphFactory.java
@@ -0,0 +1,150 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.graph.dynamic.util;
+
+import cytoscape.graph.dynamic.DynamicGraph;
+
+
+/**
+ * A factory for getting cytoscape.graph.dynamic.DynamicGraph instances.
+ * This DynamicGraph implementation requires a bare minimum of roughly 64
+ * megabytes for a graph with one million edges and one hundred thousand nodes.
+ * That is, the memory requirements are roughly 64 bytes per node and edge.<p>
+ *
+ * Nodes and edges created by the returned DynamicGraph are strictly less
+ * than Integer.MAX_VALUE. This implementation of DynamicGraph has been
+ * coded to assume that graphs containing Integer.MAX_VALUE number of nodes and
+ * Integer.MAX_VALUE number of edges will be created; however, due to lack of
+ * sufficient memory in available hardware, such large graphs have not [yet]
+ * been tested using this implementation.<p>
+ *
+ * This implementation of DynamicGraph creates nodes and edges
+ * with small integer values. This implementation re-uses node and edge
+ * values as nodes and edges are removed and added. Thus, nodes and edges
+ * will not take ever-increasing values if they are continually being
+ * removed and added.<p>
+ *
+ * The returned DynamicGraph does not free up memory. That is, if a
+ * DynamicGraph contains one million edges and one hundred thousand nodes,
+ * it consumes roughly 64 megabytes. If all nodes and edges are then removed
+ * from the DynamicGraph, it will still consume roughly 64 megabytes of
+ * memory. If one hundred thousand nodes and one million edges are
+ * then created, the DynamicGraph will still consume roughly 64 megabytes of
+ * memory. If all nodes and edges are removed and then re-created, repeatedly
+ * over an infinite number of iterations, the overall memory consumption
+ * required by this DynamicGraph will remain constant.<p>
+ *
+ * The DynamicGraph instances generated by this factory implement the
+ * java.io.Serializable interface. However, do not use the serialization
+ * facility to store graphs in a persistent manner because the serialization
+ * in this graph implementation does not handle versioning; if the class
+ * structure of the graph implementation changes (due to bug fixes or
+ * performance optimizations, for example), graphs serialized and saved from
+ * the old class definition will fail to be loaded by the new class
+ * definition.<p>
+ *
+ * Below are time complexities of DynamicGraph methods:
+ * <blockquote><table border=1 cellspacing=0 cellpadding=5>
+ * <tr><th>DynamicGraph method</th><th>time complexity</th></tr>
+ * <tr>
+ * <td>nodes()</td>
+ * <td>An IntEnumerator is returned in constant time. The enumerator
+ * returns each successive element in constant time. The enumerator
+ * reports the number of elements remaining in constant time.</td>
+ * </tr><tr>
+ * <td>edges()</td>
+ * <td>An IntEnumerator is returned in constant time. The enumerator
+ * returns each successive element in constant time. The enumerator
+ * reports the number of elements remaining in constant time.</td>
+ * </tr><tr>
+ * <td>nodeCreate()</td>
+ * <td>A node is created in amortized constant time. Amortized because
+ * doubling the size of an underlying array will be necessary as
+ * the DynamicGraph increases in its total node count.</td>
+ * </tr><tr>
+ * <td>nodeRemove(int)</td>
+ * <td>A node is removed in O(E) time, where E is the number of
+ * edges touching the node being removed.</td>
+ * </tr><tr>
+ * <td>edgeCreate(int, int, boolean)</td>
+ * <td>An edge is created in amortized constant time. Amortized because
+ * doubling the size of an underlying array will be necessary as the
+ * DynamicGraph increases in its total edge count.</td>
+ * </tr><tr>
+ * <td>edgeRemove(int)</td>
+ * <td>An edge is removed in constant time.</td>
+ * </tr><tr>
+ * <td>nodeExists(int)</td>
+ * <td>The existence of a node is determined in constant time.</td>
+ * </tr><tr>
+ * <td>edgeType(int)</td>
+ * <td>The existence/type of an edge is determined in constant time.</td>
+ * </tr><tr>
+ * <td>edgeSource(int)</td>
+ * <td>The source node of an edge is determined in constant time.</td>
+ * </tr><tr>
+ * <td>edgeTarget(int)</td>
+ * <td>The target node of an edge is determined in constant time.</td>
+ * </tr><tr>
+ * <td>edgesAdjacent(int, boolean, boolean, boolean)</td>
+ * <td>An IntEnumerator is returned in constant time. The enumerator
+ * always reports the number of elements remaining in constant time.
+ * The enumeration can be completely traversed in O(E) time, where E is
+ * the number of edges touching the node in question. Each individual
+ * successive element is returned by the enumeration in average
+ * O(E/F) time, where F is the total number of elements in this
+ * enumeration.</td>
+ * </tr><tr>
+ * <td>edgesConnecting(int, int, boolean, boolean, boolean)</td>
+ * <td>An IntIterator is returned in constant time. The iteration can be
+ * completely traversed in O(min(E, F)) time, where E is the total number
+ * of edges touching one node and F is the total number of edges touching
+ * the other node.</td>
+ * </tr></table></blockquote>
+ */
+public final class DynamicGraphFactory {
+ // "No constructor".
+ private DynamicGraphFactory() {
+ }
+
+ /**
+ * Returns a new instance of DynamicGraph with every invocation.
+ */
+ public static DynamicGraph instantiateDynamicGraph() {
+ return new DynamicGraphRepresentation();
+ }
+}
diff --git a/corelibs/graph.dynamic/src/main/java/cytoscape/graph/dynamic/util/DynamicGraphRepresentation.java b/corelibs/graph.dynamic/src/main/java/cytoscape/graph/dynamic/util/DynamicGraphRepresentation.java
new file mode 100644
index 0000000..17750a9
--- /dev/null
+++ b/corelibs/graph.dynamic/src/main/java/cytoscape/graph/dynamic/util/DynamicGraphRepresentation.java
@@ -0,0 +1,1039 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.graph.dynamic.util;
+
+import cytoscape.graph.dynamic.DynamicGraph;
+
+import cytoscape.util.intr.IntEnumerator;
+import cytoscape.util.intr.IntIterator;
+import cytoscape.util.intr.IntStack;
+
+
+final class DynamicGraphRepresentation implements DynamicGraph, java.io.Externalizable {
+ private static final long serialVersionUID = 44615510L;
+ private int m_nodeCount;
+ private int m_maxNode;
+ private int m_edgeCount;
+ private int m_maxEdge;
+ private Node m_firstNode;
+ private final NodeArray m_nodes;
+ private final NodeDepot m_nodeDepot;
+ private final EdgeArray m_edges;
+ private final EdgeDepot m_edgeDepot;
+
+ // Use this as a bag of integers in various operations. Don't forget to
+ // empty() it before using it.
+ private final IntStack m_stack;
+
+ /**
+ * Creates a new DynamicGraphRepresentation object.
+ */
+ public DynamicGraphRepresentation() // Must be public for Externalizable.
+ {
+ m_nodeCount = 0;
+ m_firstNode = null;
+ m_maxNode = -1;
+ m_edgeCount = 0;
+ m_maxEdge = -1;
+ m_nodes = new NodeArray();
+ m_edges = new EdgeArray();
+ m_edgeDepot = new EdgeDepot();
+ m_nodeDepot = new NodeDepot();
+ m_stack = new IntStack();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final IntEnumerator nodes() {
+ return new NodesEnumerator(m_nodeCount, m_firstNode);
+ }
+
+ private class NodesEnumerator implements IntEnumerator {
+ private int numRemaining;
+ private Node node;
+
+ NodesEnumerator(final int nodeCount, final Node firstNode) {
+ numRemaining = nodeCount;
+ node = firstNode;
+ }
+
+ public final int numRemaining() {
+ return numRemaining;
+ }
+
+ public final int nextInt() {
+ final int returnThis = node.nodeId;
+ node = node.nextNode;
+ numRemaining--;
+
+ return returnThis;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final IntEnumerator edges() {
+ return new EdgesEnumerator(m_edgeCount,m_firstNode);
+ }
+
+ private class EdgesEnumerator implements IntEnumerator {
+
+ private int numRemaining;
+ private Node node;
+ private Edge edge;
+
+ EdgesEnumerator(final int edgeCount, final Node firstNode) {
+ numRemaining = edgeCount;
+ node = firstNode;
+ }
+
+ public final int numRemaining() {
+ return numRemaining;
+ }
+
+ public final int nextInt() {
+ final int returnThis;
+
+ if (edge != null) {
+ returnThis = edge.edgeId;
+ } else {
+ for (edge = node.firstOutEdge; edge == null;
+ node = node.nextNode, edge = node.firstOutEdge) {
+ }
+
+ node = node.nextNode;
+ returnThis = edge.edgeId;
+ }
+
+ edge = edge.nextOutEdge;
+ numRemaining--;
+
+ return returnThis;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final int nodeCreate() {
+ final Node n = m_nodeDepot.getNode();
+ final int returnThis;
+
+ if (n.nodeId < 0) {
+ returnThis = (n.nodeId = ++m_maxNode);
+ } else {
+ returnThis = n.nodeId;
+ }
+
+ m_nodes.setNodeAtIndex(n, returnThis);
+ m_nodeCount++;
+ n.nextNode = m_firstNode;
+
+ if (m_firstNode != null) {
+ m_firstNode.prevNode = n;
+ }
+
+ m_firstNode = n;
+ n.outDegree = 0;
+ n.inDegree = 0;
+ n.undDegree = 0;
+ n.selfEdges = 0;
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final boolean nodeRemove(final int node) {
+ final IntEnumerator edges = edgesAdjacent(node, true, true, true);
+
+ if (edges == null) {
+ return false;
+ }
+
+ m_stack.empty();
+
+ while (edges.numRemaining() > 0)
+ m_stack.push(edges.nextInt());
+
+ while (m_stack.size() > 0)
+ edgeRemove(m_stack.pop());
+
+ final Node n = m_nodes.getNodeAtIndex(node);
+
+ if (n.prevNode != null) {
+ n.prevNode.nextNode = n.nextNode;
+ } else {
+ m_firstNode = n.nextNode;
+ }
+
+ if (n.nextNode != null) {
+ n.nextNode.prevNode = n.prevNode;
+ }
+
+ m_nodes.setNodeAtIndex(null, node);
+ n.prevNode = null;
+ n.firstOutEdge = null;
+ n.firstInEdge = null;
+ m_nodeDepot.recycleNode(n);
+ m_nodeCount--;
+
+ return true;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param sourceNode DOCUMENT ME!
+ * @param targetNode DOCUMENT ME!
+ * @param directed DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final int edgeCreate(final int sourceNode, final int targetNode, final boolean directed) {
+ if ((sourceNode < 0) || (sourceNode == Integer.MAX_VALUE)) {
+ return -1;
+ }
+
+ final Node source = m_nodes.getNodeAtIndex(sourceNode);
+
+ if ((targetNode < 0) || (targetNode == Integer.MAX_VALUE)) {
+ return -1;
+ }
+
+ final Node target = m_nodes.getNodeAtIndex(targetNode);
+
+ if ((source == null) || (target == null)) {
+ return -1;
+ }
+
+ final Edge e = m_edgeDepot.getEdge();
+ final int returnThis;
+
+ if (e.edgeId < 0) {
+ returnThis = (e.edgeId = ++m_maxEdge);
+ } else {
+ returnThis = e.edgeId;
+ }
+
+ m_edges.setEdgeAtIndex(e, returnThis);
+ m_edgeCount++;
+
+ if (directed) {
+ source.outDegree++;
+ target.inDegree++;
+ } else {
+ source.undDegree++;
+ target.undDegree++;
+ }
+
+ if (source == target) { // Self-edge.
+
+ if (directed) {
+ source.selfEdges++;
+ } else {
+ source.undDegree--;
+ }
+ }
+
+ e.nextOutEdge = source.firstOutEdge;
+
+ if (source.firstOutEdge != null) {
+ source.firstOutEdge.prevOutEdge = e;
+ }
+
+ source.firstOutEdge = e;
+ e.nextInEdge = target.firstInEdge;
+
+ if (target.firstInEdge != null) {
+ target.firstInEdge.prevInEdge = e;
+ }
+
+ target.firstInEdge = e;
+ e.directed = directed;
+ e.sourceNode = sourceNode;
+ e.targetNode = targetNode;
+
+ return returnThis;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edge DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final boolean edgeRemove(final int edge) {
+ if ((edge < 0) || (edge == Integer.MAX_VALUE)) {
+ return false;
+ }
+
+ final Edge e = m_edges.getEdgeAtIndex(edge);
+
+ if (e == null) {
+ return false;
+ }
+
+ final Node source = m_nodes.getNodeAtIndex(e.sourceNode);
+ final Node target = m_nodes.getNodeAtIndex(e.targetNode);
+
+ if (e.prevOutEdge != null) {
+ e.prevOutEdge.nextOutEdge = e.nextOutEdge;
+ } else {
+ source.firstOutEdge = e.nextOutEdge;
+ }
+
+ if (e.nextOutEdge != null) {
+ e.nextOutEdge.prevOutEdge = e.prevOutEdge;
+ }
+
+ if (e.prevInEdge != null) {
+ e.prevInEdge.nextInEdge = e.nextInEdge;
+ } else {
+ target.firstInEdge = e.nextInEdge;
+ }
+
+ if (e.nextInEdge != null) {
+ e.nextInEdge.prevInEdge = e.prevInEdge;
+ }
+
+ if (e.directed) {
+ source.outDegree--;
+ target.inDegree--;
+ } else {
+ source.undDegree--;
+ target.undDegree--;
+ }
+
+ if (source == target) { // Self-edge.
+
+ if (e.directed) {
+ source.selfEdges--;
+ } else {
+ source.undDegree++;
+ }
+ }
+
+ m_edges.setEdgeAtIndex(null, edge);
+ e.prevOutEdge = null;
+ e.nextInEdge = null;
+ e.prevInEdge = null;
+ m_edgeDepot.recycleEdge(e);
+ m_edgeCount--;
+
+ return true;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final boolean nodeExists(final int node) {
+ if ((node < 0) || (node == Integer.MAX_VALUE)) {
+ return false;
+ }
+
+ return m_nodes.getNodeAtIndex(node) != null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edge DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final byte edgeType(final int edge) {
+ if ((edge < 0) || (edge == Integer.MAX_VALUE)) {
+ return -1;
+ }
+
+ final Edge e = m_edges.getEdgeAtIndex(edge);
+
+ if (e == null) {
+ return -1;
+ }
+
+ if (e.directed) {
+ return DIRECTED_EDGE;
+ }
+
+ return UNDIRECTED_EDGE;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edge DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final int edgeSource(final int edge) {
+ if ((edge < 0) || (edge == Integer.MAX_VALUE)) {
+ return -1;
+ }
+
+ final Edge e = m_edges.getEdgeAtIndex(edge);
+
+ if (e == null) {
+ return -1;
+ }
+
+ return e.sourceNode;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edge DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final int edgeTarget(final int edge) {
+ if ((edge < 0) || (edge == Integer.MAX_VALUE)) {
+ return -1;
+ }
+
+ final Edge e = m_edges.getEdgeAtIndex(edge);
+
+ if (e == null) {
+ return -1;
+ }
+
+ return e.targetNode;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ * @param outgoing DOCUMENT ME!
+ * @param incoming DOCUMENT ME!
+ * @param undirected DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final IntEnumerator edgesAdjacent(final int node, final boolean outgoing,
+ final boolean incoming, final boolean undirected) {
+ if ((node < 0) || (node == Integer.MAX_VALUE)) {
+ return null;
+ }
+
+ final Node n = m_nodes.getNodeAtIndex(node);
+
+ if (n == null) {
+ return null;
+ }
+
+ final Edge[] edgeLists;
+
+ if (undirected || (outgoing && incoming)) {
+ edgeLists = new Edge[] { n.firstOutEdge, n.firstInEdge };
+ } else if (outgoing) { // Cannot also be incoming.
+ edgeLists = new Edge[] { n.firstOutEdge, null };
+ } else if (incoming) { // Cannot also be outgoing.
+ edgeLists = new Edge[] { null, n.firstInEdge };
+ } else { // All boolean input parameters are false.
+ edgeLists = new Edge[] { null, null };
+ }
+
+ int tentativeEdgeCount = 0;
+
+ if (outgoing) {
+ tentativeEdgeCount += n.outDegree;
+ }
+
+ if (incoming) {
+ tentativeEdgeCount += n.inDegree;
+ }
+
+ if (undirected) {
+ tentativeEdgeCount += n.undDegree;
+ }
+
+ if (outgoing && incoming) {
+ tentativeEdgeCount -= n.selfEdges;
+ }
+
+ return new EdgesAdjacentEnumerator(tentativeEdgeCount,edgeLists,undirected,incoming,outgoing );
+ }
+
+ private class EdgesAdjacentEnumerator implements IntEnumerator {
+
+ private int numRemaining;
+ private int edgeListIndex = -1;
+ private Edge edge = null;
+ private final Edge[] edgeLists;
+ private final boolean undirected;
+ private final boolean incoming;
+ private final boolean outgoing;
+
+ EdgesAdjacentEnumerator(final int edgeCount,final Edge[] edgeLists, final boolean undirected, final boolean incoming, final boolean outgoing ) {
+ this.numRemaining = edgeCount;
+ this.edgeLists = edgeLists;
+ this.undirected = undirected;
+ this.incoming = incoming;
+ this.outgoing = outgoing;
+ }
+
+ public final int numRemaining() {
+ return numRemaining;
+ }
+
+ public final int nextInt() {
+ while (edge == null)
+ edge = edgeLists[++edgeListIndex];
+
+ int returnThis = -1;
+
+ if (edgeListIndex == 0) {
+ while ((edge != null)
+ && !((outgoing && edge.directed) || (undirected && !edge.directed))) {
+ edge = edge.nextOutEdge;
+
+ if (edge == null) {
+ edge = edgeLists[++edgeListIndex];
+
+ break;
+ }
+ }
+
+ if ((edge != null) && (edgeListIndex == 0)) {
+ returnThis = edge.edgeId;
+ edge = edge.nextOutEdge;
+ }
+ }
+
+ if (edgeListIndex == 1) {
+ while (((edge.sourceNode == edge.targetNode)
+ && ((outgoing && edge.directed) || (undirected && !edge.directed)))
+ || !((incoming && edge.directed) || (undirected && !edge.directed))) {
+ edge = edge.nextInEdge;
+ }
+
+ returnThis = edge.edgeId;
+ edge = edge.nextInEdge;
+ }
+
+ numRemaining--;
+
+ return returnThis;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node0 DOCUMENT ME!
+ * @param node1 DOCUMENT ME!
+ * @param outgoing DOCUMENT ME!
+ * @param incoming DOCUMENT ME!
+ * @param undirected DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final IntIterator edgesConnecting(final int node0, final int node1,
+ final boolean outgoing, final boolean incoming,
+ final boolean undirected) {
+ final IntEnumerator node0Adj = edgesAdjacent(node0, outgoing, incoming, undirected);
+ final IntEnumerator node1Adj = edgesAdjacent(node1, incoming, outgoing, undirected);
+
+ if ((node0Adj == null) || (node1Adj == null)) {
+ return null;
+ }
+
+ final IntEnumerator theAdj;
+ final int nodeZero;
+ final int nodeOne;
+
+ if (node0Adj.numRemaining() <= node1Adj.numRemaining()) {
+ theAdj = node0Adj;
+ nodeZero = node0;
+ nodeOne = node1;
+ } else {
+ theAdj = node1Adj;
+ nodeZero = node1;
+ nodeOne = node0;
+ }
+
+ return new ConnectingEdgesIterator(theAdj, nodeZero, nodeOne, this);
+ }
+
+ private class ConnectingEdgesIterator implements IntIterator {
+ private int nextEdge = -1;
+ private final IntEnumerator theAdj;
+ private final int nodeZero;
+ private final int nodeOne;
+ private final DynamicGraph graph;
+
+ ConnectingEdgesIterator(final IntEnumerator theAdj, final int nodeZero,
+ final int nodeOne, final DynamicGraph graph) {
+ this.theAdj = theAdj;
+ this.nodeZero = nodeZero;
+ this.nodeOne = nodeOne;
+ this.graph = graph;
+ }
+
+ private void ensureComputeNext() {
+ if (nextEdge != -1) {
+ return;
+ }
+
+ while (theAdj.numRemaining() > 0) {
+ final int edge = theAdj.nextInt();
+
+ if (nodeOne == (nodeZero ^ graph.edgeSource(edge) ^ graph.edgeTarget(edge))) {
+ nextEdge = edge;
+
+ return;
+ }
+ }
+
+ nextEdge = -2;
+ }
+
+ public final boolean hasNext() {
+ ensureComputeNext();
+
+ if (nextEdge < 0) {
+ return false;
+ } else {
+ return true;
+ }
+ }
+
+ public final int nextInt() {
+ ensureComputeNext();
+
+ final int returnThis = nextEdge;
+ nextEdge = -1;
+
+ return returnThis;
+ }
+ }
+
+ // Externalizable methods.
+ /**
+ * DOCUMENT ME!
+ *
+ * @param out DOCUMENT ME!
+ *
+ */
+ public final void writeExternal(final java.io.ObjectOutput out) throws java.io.IOException {
+ out.writeInt(m_nodeCount);
+ out.writeInt(m_maxNode);
+ out.writeInt(m_edgeCount);
+ out.writeInt(m_maxEdge);
+
+ for (Node currNode = m_nodeDepot.m_head.nextNode; currNode != null;
+ currNode = currNode.nextNode)
+ out.writeInt(currNode.nodeId);
+
+ out.writeInt(-1);
+
+ for (Edge currEdge = m_edgeDepot.m_head.nextOutEdge; currEdge != null;
+ currEdge = currEdge.nextOutEdge)
+ out.writeInt(currEdge.edgeId);
+
+ out.writeInt(-1);
+
+ { // m_edges.
+
+ final Edge[] arr = m_edges.m_edgeArr;
+ final int arrLen = arr.length;
+ out.writeInt(arrLen);
+
+ for (int i = 0; i < arrLen; i++) {
+ final Edge edge = arr[i];
+
+ if (edge == null) {
+ out.writeInt(-1);
+
+ continue;
+ }
+
+ out.writeInt(edge.sourceNode);
+ out.writeInt(edge.targetNode);
+ out.writeBoolean(edge.directed);
+ }
+
+ for (int i = 0; i < arrLen; i++) {
+ final Edge edge = arr[i];
+
+ if (edge == null) {
+ continue;
+ }
+
+ out.writeInt((edge.nextOutEdge == null) ? (-1) : edge.nextOutEdge.edgeId);
+ out.writeInt((edge.prevOutEdge == null) ? (-1) : edge.prevOutEdge.edgeId);
+ out.writeInt((edge.nextInEdge == null) ? (-1) : edge.nextInEdge.edgeId);
+ out.writeInt((edge.prevInEdge == null) ? (-1) : edge.prevInEdge.edgeId);
+ }
+ }
+
+ { // m_nodes.
+
+ final Node[] arr = m_nodes.m_nodeArr;
+ final int arrLen = arr.length;
+ out.writeInt(arrLen);
+
+ for (int i = 0; i < arrLen; i++) {
+ final Node node = arr[i];
+
+ if (node == null) {
+ out.writeInt(-1);
+
+ continue;
+ }
+
+ out.writeInt(node.outDegree);
+ out.writeInt(node.inDegree);
+ out.writeInt(node.undDegree);
+ out.writeInt(node.selfEdges);
+ }
+
+ for (int i = 0; i < arrLen; i++) {
+ final Node node = arr[i];
+
+ if (node == null) {
+ continue;
+ }
+
+ out.writeInt((node.nextNode == null) ? (-1) : node.nextNode.nodeId);
+ out.writeInt((node.prevNode == null) ? (-1) : node.prevNode.nodeId);
+ out.writeInt((node.firstOutEdge == null) ? (-1) : node.firstOutEdge.edgeId);
+ out.writeInt((node.firstInEdge == null) ? (-1) : node.firstInEdge.edgeId);
+ }
+ }
+
+ if (m_firstNode == null) {
+ out.writeInt(-1);
+ } else {
+ out.writeInt(m_firstNode.nodeId);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param in DOCUMENT ME!
+ *
+ */
+ public final void readExternal(final java.io.ObjectInput in) throws java.io.IOException {
+ m_nodeCount = in.readInt();
+ m_maxNode = in.readInt();
+ m_edgeCount = in.readInt();
+ m_maxEdge = in.readInt();
+
+ { // m_nodeDepot.
+
+ Node currNode = m_nodeDepot.m_head;
+
+ while (true) {
+ final int id = in.readInt();
+
+ if (id < 0) {
+ break;
+ }
+
+ currNode.nextNode = new Node();
+ currNode = currNode.nextNode;
+ currNode.nodeId = id;
+ }
+ }
+
+ { // m_edgeDepot.
+
+ Edge currEdge = m_edgeDepot.m_head;
+
+ while (true) {
+ final int id = in.readInt();
+
+ if (id < 0) {
+ break;
+ }
+
+ currEdge.nextOutEdge = new Edge();
+ currEdge = currEdge.nextOutEdge;
+ currEdge.edgeId = id;
+ }
+ }
+
+ { // m_edges.
+
+ final int arrLen = in.readInt();
+ final Edge[] arr = (m_edges.m_edgeArr = new Edge[arrLen]);
+
+ for (int i = 0; i < arrLen; i++) {
+ final int source = in.readInt();
+
+ if (source < 0) {
+ continue;
+ }
+
+ final Edge edge = (arr[i] = new Edge());
+ edge.edgeId = i;
+ edge.sourceNode = source;
+ edge.targetNode = in.readInt();
+ edge.directed = in.readBoolean();
+ }
+
+ for (int i = 0; i < arrLen; i++) {
+ final Edge edge = arr[i];
+
+ if (edge == null) {
+ continue;
+ }
+
+ final int nextOutEdge = in.readInt();
+ final int prevOutEdge = in.readInt();
+ final int nextInEdge = in.readInt();
+ final int prevInEdge = in.readInt();
+
+ if (nextOutEdge >= 0) {
+ edge.nextOutEdge = arr[nextOutEdge];
+ }
+
+ if (prevOutEdge >= 0) {
+ edge.prevOutEdge = arr[prevOutEdge];
+ }
+
+ if (nextInEdge >= 0) {
+ edge.nextInEdge = arr[nextInEdge];
+ }
+
+ if (prevInEdge >= 0) {
+ edge.prevInEdge = arr[prevInEdge];
+ }
+ }
+ }
+
+ { // m_nodes.
+
+ final int arrLen = in.readInt();
+ final Node[] arr = (m_nodes.m_nodeArr = new Node[arrLen]);
+
+ for (int i = 0; i < arrLen; i++) {
+ final int outDeg = in.readInt();
+
+ if (outDeg < 0) {
+ continue;
+ }
+
+ final Node node = (arr[i] = new Node());
+ node.nodeId = i;
+ node.outDegree = outDeg;
+ node.inDegree = in.readInt();
+ node.undDegree = in.readInt();
+ node.selfEdges = in.readInt();
+ }
+
+ final Edge[] edgeArr = m_edges.m_edgeArr;
+
+ for (int i = 0; i < arrLen; i++) {
+ final Node node = arr[i];
+
+ if (node == null) {
+ continue;
+ }
+
+ final int nextNode = in.readInt();
+ final int prevNode = in.readInt();
+ final int firstOutEdge = in.readInt();
+ final int firstInEdge = in.readInt();
+
+ if (nextNode >= 0) {
+ node.nextNode = arr[nextNode];
+ }
+
+ if (prevNode >= 0) {
+ node.prevNode = arr[prevNode];
+ }
+
+ if (firstOutEdge >= 0) {
+ node.firstOutEdge = edgeArr[firstOutEdge];
+ }
+
+ if (firstInEdge >= 0) {
+ node.firstInEdge = edgeArr[firstInEdge];
+ }
+ }
+ }
+
+ { // m_firstNode.
+
+ final int firstNode = in.readInt();
+
+ if (firstNode >= 0) {
+ m_firstNode = m_nodes.m_nodeArr[firstNode];
+ }
+ }
+ }
+
+ /*
+ private final boolean equalsInternal(final Object o)
+ {
+ if (this == o) return true;
+ if (o == null || !(o instanceof DynamicGraphRepresentation)) return false;
+ final DynamicGraphRepresentation graph = (DynamicGraphRepresentation) o;
+ if (m_nodeCount != graph.m_nodeCount ||
+ m_maxNode != graph.m_maxNode ||
+ m_edgeCount != graph.m_edgeCount ||
+ m_maxEdge != graph.m_maxEdge) return false;
+ { // Compare m_nodeDepot.
+ Node currThisNode = m_nodeDepot.m_head.nextNode;
+ Node currGraphNode = graph.m_nodeDepot.m_head.nextNode;
+ while (currThisNode != null) {
+ if (currGraphNode == null ||
+ currThisNode.nodeId != currGraphNode.nodeId) return false;
+ currThisNode = currThisNode.nextNode;
+ currGraphNode = currGraphNode.nextNode; }
+ if (currGraphNode != null) return false;
+ }
+ { // Compare m_edgeDepot.
+ Edge currThisEdge = m_edgeDepot.m_head.nextOutEdge;
+ Edge currGraphEdge = graph.m_edgeDepot.m_head.nextOutEdge;
+ while (currThisEdge != null) {
+ if (currGraphEdge == null ||
+ currThisEdge.edgeId != currGraphEdge.edgeId) return false;
+ currThisEdge = currThisEdge.nextOutEdge;
+ currGraphEdge = currGraphEdge.nextOutEdge; }
+ if (currGraphEdge != null) return false;
+ }
+ { // Compare m_edges.
+ final Edge[] thisArr = m_edges.m_edgeArr;
+ final Edge[] graphArr = graph.m_edges.m_edgeArr;
+ if (thisArr.length != graphArr.length) return false;
+ for (int i = 0; i < thisArr.length; i++) {
+ if (thisArr[i] == null) {
+ if (graphArr[i] != null) return false; }
+ else {
+ if (graphArr[i] == null ||
+ thisArr[i].directed != graphArr[i].directed ||
+ thisArr[i].sourceNode != graphArr[i].sourceNode ||
+ thisArr[i].targetNode != graphArr[i].targetNode) return false;
+ if (thisArr[i].nextOutEdge == null) {
+ if (graphArr[i].nextOutEdge != null) return false; }
+ else {
+ if (graphArr[i].nextOutEdge == null ||
+ thisArr[i].nextOutEdge.edgeId !=
+ graphArr[i].nextOutEdge.edgeId) return false; }
+ if (thisArr[i].prevOutEdge == null) {
+ if (graphArr[i].prevOutEdge != null) return false; }
+ else {
+ if (graphArr[i].prevOutEdge == null ||
+ thisArr[i].prevOutEdge.edgeId !=
+ graphArr[i].prevOutEdge.edgeId) return false; }
+ if (thisArr[i].nextInEdge == null) {
+ if (graphArr[i].nextInEdge != null) return false; }
+ else {
+ if (graphArr[i].nextInEdge == null ||
+ thisArr[i].nextInEdge.edgeId != graphArr[i].nextInEdge.edgeId)
+ return false; }
+ if (thisArr[i].prevInEdge == null) {
+ if (graphArr[i].prevInEdge != null) return false; }
+ else {
+ if (graphArr[i].prevInEdge == null ||
+ thisArr[i].prevInEdge.edgeId != graphArr[i].prevInEdge.edgeId)
+ return false; } } }
+ }
+ { // Compare m_nodes.
+ final Node[] thisArr = m_nodes.m_nodeArr;
+ final Node[] graphArr = graph.m_nodes.m_nodeArr;
+ if (thisArr.length != graphArr.length) return false;
+ for (int i = 0; i < thisArr.length; i++) {
+ if (thisArr[i] == null) {
+ if (graphArr[i] != null) return false; }
+ else {
+ if (graphArr[i] == null ||
+ thisArr[i].outDegree != graphArr[i].outDegree ||
+ thisArr[i].inDegree != graphArr[i].inDegree ||
+ thisArr[i].undDegree != graphArr[i].undDegree ||
+ thisArr[i].selfEdges != graphArr[i].selfEdges) return false;
+ if (thisArr[i].nextNode == null) {
+ if (graphArr[i].nextNode != null) return false; }
+ else {
+ if (graphArr[i].nextNode == null ||
+ thisArr[i].nextNode.nodeId != graphArr[i].nextNode.nodeId)
+ return false; }
+ if (thisArr[i].prevNode == null) {
+ if (graphArr[i].prevNode != null) return false; }
+ else {
+ if (graphArr[i].prevNode == null ||
+ thisArr[i].prevNode.nodeId != graphArr[i].prevNode.nodeId)
+ return false; }
+ if (thisArr[i].firstInEdge == null) {
+ if (graphArr[i].firstInEdge != null) return false; }
+ else {
+ if (graphArr[i].firstInEdge == null ||
+ thisArr[i].firstInEdge.edgeId !=
+ graphArr[i].firstInEdge.edgeId) return false; }
+ if (thisArr[i].firstOutEdge == null) {
+ if (graphArr[i].firstOutEdge != null) return false; }
+ else {
+ if (graphArr[i].firstOutEdge == null ||
+ thisArr[i].firstOutEdge.edgeId !=
+ graphArr[i].firstOutEdge.edgeId) return false; } } }
+ }
+ { // Compare m_firstNode;
+ if (m_firstNode == null) {
+ if (graph.m_firstNode != null) return false; }
+ else {
+ if (graph.m_firstNode == null ||
+ m_firstNode.nodeId != graph.m_firstNode.nodeId) return false; }
+ }
+ return true;
+ }
+ */
+}
diff --git a/corelibs/graph.dynamic/src/main/java/cytoscape/graph/dynamic/util/Edge.java b/corelibs/graph.dynamic/src/main/java/cytoscape/graph/dynamic/util/Edge.java
new file mode 100644
index 0000000..95c23c4
--- /dev/null
+++ b/corelibs/graph.dynamic/src/main/java/cytoscape/graph/dynamic/util/Edge.java
@@ -0,0 +1,54 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.graph.dynamic.util;
+
+
+// Package visible.
+final class Edge {
+ int edgeId;
+ Edge nextOutEdge;
+ Edge prevOutEdge;
+ Edge nextInEdge;
+ Edge prevInEdge;
+ boolean directed;
+ int sourceNode;
+ int targetNode;
+
+ Edge() {
+ edgeId = -1;
+ }
+}
diff --git a/corelibs/graph.dynamic/src/main/java/cytoscape/graph/dynamic/util/EdgeArray.java b/corelibs/graph.dynamic/src/main/java/cytoscape/graph/dynamic/util/EdgeArray.java
new file mode 100644
index 0000000..a776b93
--- /dev/null
+++ b/corelibs/graph.dynamic/src/main/java/cytoscape/graph/dynamic/util/EdgeArray.java
@@ -0,0 +1,93 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.graph.dynamic.util;
+
+
+// Package visible.
+// Valid indices: [0, Integer.MAX_VALUE - 1].
+final class EdgeArray {
+ private final static int INITIAL_CAPACITY = 0; // Must be non-negative.
+
+ /* private */ Edge[] m_edgeArr; // Not private for serialization.
+
+ EdgeArray() {
+ m_edgeArr = new Edge[INITIAL_CAPACITY];
+ }
+
+ // Understand that this method will not increase the size of the underlying
+ // array, no matter what.
+ // Throws ArrayIndexOutOfBoundsException if index is negative.
+ // The package-level agreement for this class is that Integer.MAX_VALUE
+ // will never be passed to this method.
+ final Edge getEdgeAtIndex(final int index) {
+ if (index >= m_edgeArr.length) {
+ return null;
+ }
+
+ return m_edgeArr[index];
+ }
+
+ // Understand that this method will potentially increase the size of the
+ // underlying array, but only if two conditions hold:
+ // 1. edge is not null and
+ // 2. index is greater than or equal to the length of the array.
+ // Throws ArrayIndexOutOfBoundsException if index is negative.
+ // The package-level agreement for this class is that Integer.MAX_VALUE
+ // will never be passed to this method.
+ final void setEdgeAtIndex(final Edge edge, final int index) {
+ if ((index >= m_edgeArr.length) && (edge == null)) {
+ return;
+ }
+
+ try {
+ m_edgeArr[index] = edge;
+ } catch (ArrayIndexOutOfBoundsException e) {
+ if (index < 0) {
+ throw e;
+ }
+
+ final int newArrSize = (int) Math.min((long) Integer.MAX_VALUE,
+ Math.max((((long) m_edgeArr.length) * 2L) + 1L,
+ ((long) index) + 1L
+ + (long) INITIAL_CAPACITY));
+ final Edge[] newArr = new Edge[newArrSize];
+ System.arraycopy(m_edgeArr, 0, newArr, 0, m_edgeArr.length);
+ m_edgeArr = newArr;
+ m_edgeArr[index] = edge;
+ }
+ }
+}
diff --git a/corelibs/graph.dynamic/src/main/java/cytoscape/graph/dynamic/util/EdgeDepot.java b/corelibs/graph.dynamic/src/main/java/cytoscape/graph/dynamic/util/EdgeDepot.java
new file mode 100644
index 0000000..94d97b8
--- /dev/null
+++ b/corelibs/graph.dynamic/src/main/java/cytoscape/graph/dynamic/util/EdgeDepot.java
@@ -0,0 +1,69 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.graph.dynamic.util;
+
+
+// Package visible.
+final class EdgeDepot {
+ /* private */ final Edge m_head; // Not private for serialization.
+
+ EdgeDepot() {
+ m_head = new Edge();
+ }
+
+ // Gimme an edge, darnit!
+ // Don't forget to initialize the edge's member variables!
+ // Edge.nextOutEdge is used internally and will point to some undefined
+ // edge in the returned Edge.
+ final Edge getEdge() {
+ final Edge returnThis = m_head.nextOutEdge;
+
+ if (returnThis == null) {
+ return new Edge();
+ }
+
+ m_head.nextOutEdge = returnThis.nextOutEdge;
+
+ return returnThis;
+ }
+
+ // edge.nextOutEdge is used internally and does not need to be deinitialized.
+ final void recycleEdge(final Edge edge) {
+ edge.nextOutEdge = m_head.nextOutEdge;
+ m_head.nextOutEdge = edge;
+ }
+}
diff --git a/corelibs/graph.dynamic/src/main/java/cytoscape/graph/dynamic/util/Node.java b/corelibs/graph.dynamic/src/main/java/cytoscape/graph/dynamic/util/Node.java
new file mode 100644
index 0000000..223bc91
--- /dev/null
+++ b/corelibs/graph.dynamic/src/main/java/cytoscape/graph/dynamic/util/Node.java
@@ -0,0 +1,63 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.graph.dynamic.util;
+
+
+// Package visible.
+final class Node {
+ int nodeId;
+ Node nextNode;
+ Node prevNode;
+ Edge firstOutEdge;
+ Edge firstInEdge;
+
+ // The number of directed edges whose source is this node.
+ int outDegree;
+
+ // The number of directed edges whose target is this node.
+ int inDegree;
+
+ // The number of undirected edges which touch this node.
+ int undDegree;
+
+ // The number of directed self-edges on this node.
+ int selfEdges;
+
+ Node() {
+ nodeId = -1;
+ }
+}
diff --git a/corelibs/graph.dynamic/src/main/java/cytoscape/graph/dynamic/util/NodeArray.java b/corelibs/graph.dynamic/src/main/java/cytoscape/graph/dynamic/util/NodeArray.java
new file mode 100644
index 0000000..ef1de87
--- /dev/null
+++ b/corelibs/graph.dynamic/src/main/java/cytoscape/graph/dynamic/util/NodeArray.java
@@ -0,0 +1,93 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.graph.dynamic.util;
+
+
+// Package visible.
+// Valid indices: [0, Integer.MAX_VALUE - 1].
+final class NodeArray {
+ private final static int INITIAL_CAPACITY = 0; // Must be non-negative.
+
+ /* private */ Node[] m_nodeArr; // Not private for serialization.
+
+ NodeArray() {
+ m_nodeArr = new Node[INITIAL_CAPACITY];
+ }
+
+ // Understand that this method will not increase the size of the underlying
+ // array, no matter what.
+ // Throws ArrayIndexOutOfBoundsException if index is negative.
+ // The package-level agreement for this class is that Integer.MAX_VALUE
+ // will never be passed to this method.
+ final Node getNodeAtIndex(final int index) {
+ if (index >= m_nodeArr.length) {
+ return null;
+ }
+
+ return m_nodeArr[index];
+ }
+
+ // Understand that this method will potentially increase the size of the
+ // underlying array, but only if two conditions hold:
+ // 1. node is not null and
+ // 2. index is greater than or equal to the length of the array.
+ // Throws ArrayIndexOutOfBoundsException if index is negative.
+ // The package-level agreement for this class is that Integer.MAX_VALUE
+ // will never be passed to this method.
+ final void setNodeAtIndex(final Node node, final int index) {
+ if ((index >= m_nodeArr.length) && (node == null)) {
+ return;
+ }
+
+ try {
+ m_nodeArr[index] = node;
+ } catch (ArrayIndexOutOfBoundsException e) {
+ if (index < 0) {
+ throw e;
+ }
+
+ final int newArrSize = (int) Math.min((long) Integer.MAX_VALUE,
+ Math.max((((long) m_nodeArr.length) * 2L) + 1L,
+ ((long) index) + 1L
+ + (long) INITIAL_CAPACITY));
+ final Node[] newArr = new Node[newArrSize];
+ System.arraycopy(m_nodeArr, 0, newArr, 0, m_nodeArr.length);
+ m_nodeArr = newArr;
+ m_nodeArr[index] = node;
+ }
+ }
+}
diff --git a/corelibs/graph.dynamic/src/main/java/cytoscape/graph/dynamic/util/NodeDepot.java b/corelibs/graph.dynamic/src/main/java/cytoscape/graph/dynamic/util/NodeDepot.java
new file mode 100644
index 0000000..084565f
--- /dev/null
+++ b/corelibs/graph.dynamic/src/main/java/cytoscape/graph/dynamic/util/NodeDepot.java
@@ -0,0 +1,69 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.graph.dynamic.util;
+
+
+// Package visible.
+final class NodeDepot {
+ /* private */ final Node m_head; // Not private for serialization.
+
+ NodeDepot() {
+ m_head = new Node();
+ }
+
+ // Gimme a node, darnit!
+ // Don't forget to initialize the node's member variables!
+ // Node.nextNode is used internally and will point to some undefined node
+ // in the returned Node.
+ final Node getNode() {
+ final Node returnThis = m_head.nextNode;
+
+ if (returnThis == null) {
+ return new Node();
+ }
+
+ m_head.nextNode = returnThis.nextNode;
+
+ return returnThis;
+ }
+
+ // node.nextNode is used internally and does not need to be deinitialized.
+ final void recycleNode(final Node node) {
+ node.nextNode = m_head.nextNode;
+ m_head.nextNode = node;
+ }
+}
diff --git a/corelibs/graph.dynamic/src/test/java/cytoscape/graph/dynamic/AddRemoveTest.java b/corelibs/graph.dynamic/src/test/java/cytoscape/graph/dynamic/AddRemoveTest.java
new file mode 100644
index 0000000..338d2fe
--- /dev/null
+++ b/corelibs/graph.dynamic/src/test/java/cytoscape/graph/dynamic/AddRemoveTest.java
@@ -0,0 +1,71 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.graph.dynamic;
+
+import cytoscape.graph.dynamic.util.DynamicGraphFactory;
+
+import junit.framework.*;
+
+public class AddRemoveTest extends TestCase {
+
+ public void testAddRemove() {
+ final DynamicGraph graph = DynamicGraphFactory.instantiateDynamicGraph();
+ final int[][] nodesArr = new int[][] { new int[100000], new int[99980], new int[100010] };
+ final int[] edges = new int[1000000];
+ final int iterations = 3;
+
+ for (int foo = 0; foo < iterations; foo++) {
+
+ final int[] nodes = nodesArr[foo % nodesArr.length];
+
+ for (int i = 0; i < nodes.length; i++)
+ nodes[i] = graph.nodeCreate();
+
+ for (int i = 0; i < edges.length; i++)
+ edges[i] = graph.edgeCreate(nodes[i % nodes.length], nodes[(i * 3) % nodes.length],
+ true);
+
+ for (int i = 0; i < edges.length; i++)
+ graph.edgeRemove(edges[i]);
+
+
+ for (int i = 0; i < nodes.length; i++)
+ graph.nodeRemove(nodes[i]);
+
+ }
+ }
+}
diff --git a/corelibs/graph.dynamic/src/test/java/cytoscape/graph/dynamic/GraphSerializationTest.java b/corelibs/graph.dynamic/src/test/java/cytoscape/graph/dynamic/GraphSerializationTest.java
new file mode 100644
index 0000000..e50f660
--- /dev/null
+++ b/corelibs/graph.dynamic/src/test/java/cytoscape/graph/dynamic/GraphSerializationTest.java
@@ -0,0 +1,169 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.graph.dynamic;
+
+import cytoscape.graph.dynamic.util.DynamicGraphFactory;
+
+import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
+import java.io.ObjectInputStream;
+import java.io.ObjectOutputStream;
+
+import junit.framework.*;
+
+public class GraphSerializationTest extends TestCase {
+ public void testGraphSerialization() throws Exception {
+ DynamicGraph graph = DynamicGraphFactory.instantiateDynamicGraph();
+ ByteArrayOutputStream byteOut = new ByteArrayOutputStream();
+ ObjectOutputStream objOut = new ObjectOutputStream(byteOut);
+ objOut.writeObject(graph);
+ objOut.flush();
+ objOut.close();
+ System.out.println("An empty graph takes " + byteOut.size()
+ + " bytes in serialized form.");
+
+ ByteArrayInputStream byteIn = new ByteArrayInputStream(byteOut.toByteArray());
+ ObjectInputStream objIn = new ObjectInputStream(byteIn);
+ graph = (DynamicGraph) objIn.readObject();
+ objIn.close();
+
+ assertEquals("expected restored graph to be empty", 0,graph.nodes().numRemaining());
+ assertEquals("expected restored graph to be empty", 0,graph.edges().numRemaining());
+
+ graph = DynamicGraphFactory.instantiateDynamicGraph();
+
+ int[] nodes = new int[10];
+
+ for (int i = 0; i < nodes.length; i++)
+ nodes[i] = graph.nodeCreate();
+
+ int[] edges = new int[20];
+
+ for (int i = 0; i < edges.length; i++)
+ edges[i] = graph.edgeCreate(nodes[i % nodes.length], nodes[(i * 3) % nodes.length],
+ true);
+
+ byteOut = new ByteArrayOutputStream();
+ objOut = new ObjectOutputStream(byteOut);
+ objOut.writeObject(graph);
+ objOut.flush();
+ objOut.close();
+ System.out.println("A graph with " + nodes.length + " nodes and " + edges.length
+ + " edges takes " + byteOut.size() + " bytes in serialized form.");
+ byteIn = new ByteArrayInputStream(byteOut.toByteArray());
+ objIn = new ObjectInputStream(byteIn);
+ graph = (DynamicGraph) objIn.readObject();
+ objIn.close();
+
+ assertEquals("expected restored graph to have proper number of nodes",
+ graph.nodes().numRemaining(), nodes.length);
+ assertEquals("expected restored graph to have proper number of edges",
+ graph.edges().numRemaining(), edges.length);
+
+ }
+
+ public void testGraphSerialization2() throws Exception {
+ DynamicGraph graph = DynamicGraphFactory.instantiateDynamicGraph();
+ int[] nodes = new int[100000];
+ int[] edges = new int[1000000];
+
+ for (int i = 0; i < nodes.length; i++)
+ nodes[i] = graph.nodeCreate();
+
+ for (int i = 0; i < edges.length; i++)
+ edges[i] = graph.edgeCreate(nodes[i % nodes.length], nodes[(i * 3) % nodes.length],
+ true);
+
+ for (int i = 0; i < nodes.length; i += 2)
+ graph.nodeRemove(nodes[i]);
+
+ System.out.println("graph has " + graph.nodes().numRemaining() + " nodes and "
+ + graph.edges().numRemaining() + " edges");
+ System.out.println("at one point graph had " + nodes.length + " nodes and "
+ + edges.length + " edges");
+
+ ByteArrayOutputStream byteOut = new ByteArrayOutputStream();
+ ObjectOutputStream objOut = new ObjectOutputStream(byteOut);
+ long millisBegin = System.currentTimeMillis();
+ objOut.writeObject(graph);
+ objOut.flush();
+ objOut.close();
+
+ long millisEnd = System.currentTimeMillis();
+ System.out.println("serializing graph took " + (millisEnd - millisBegin)
+ + " milliseconds");
+
+ byte[] serializedData = byteOut.toByteArray();
+ System.out.println("in serialized form, graph takes " + serializedData.length
+ + " bytes");
+
+ ByteArrayInputStream byteIn = new ByteArrayInputStream(serializedData);
+ millisBegin = System.currentTimeMillis();
+
+ ObjectInputStream objIn = new ObjectInputStream(byteIn);
+ graph = (DynamicGraph) objIn.readObject();
+ objIn.close();
+ millisEnd = System.currentTimeMillis();
+ System.out.println("deserializeing graph took " + (millisEnd - millisBegin)
+ + " milliseconds");
+ System.out.println("deserialized graph has " + graph.nodes().numRemaining()
+ + " nodes and " + graph.edges().numRemaining() + " edges");
+ }
+
+
+ public void testGraphSerialization3() throws Exception {
+ DynamicGraph[] graphs = new DynamicGraph[2];
+ graphs[0] = DynamicGraphFactory.instantiateDynamicGraph();
+ graphs[1] = graphs[0];
+
+ ByteArrayOutputStream byteOut = new ByteArrayOutputStream();
+ ObjectOutputStream objOut = new ObjectOutputStream(byteOut);
+ objOut.writeObject(graphs);
+ objOut.flush();
+ objOut.close();
+
+ ByteArrayInputStream byteIn = new ByteArrayInputStream(byteOut.toByteArray());
+ ObjectInputStream objIn = new ObjectInputStream(byteIn);
+ graphs = (DynamicGraph[]) objIn.readObject();
+ objIn.close();
+
+ assertEquals("graphs.length is 2", 2, graphs.length);
+ assertFalse( "graph 0 is null", graphs[0] == null );
+ assertFalse( "graph 1 is null", graphs[1] == null );
+ assertTrue( "graph 0 is equal to graph 1 ", graphs[0] == graphs[1]);
+ }
+}
diff --git a/corelibs/graph.dynamic/src/test/java/cytoscape/graph/dynamic/GraphTest.java b/corelibs/graph.dynamic/src/test/java/cytoscape/graph/dynamic/GraphTest.java
new file mode 100644
index 0000000..4902520
--- /dev/null
+++ b/corelibs/graph.dynamic/src/test/java/cytoscape/graph/dynamic/GraphTest.java
@@ -0,0 +1,243 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.graph.dynamic;
+
+import cytoscape.graph.dynamic.util.DynamicGraphFactory;
+
+import cytoscape.util.intr.IntEnumerator;
+import cytoscape.util.intr.IntIterator;
+
+import junit.framework.*;
+
+public class GraphTest extends TestCase {
+
+ public void testGraph() {
+ final DynamicGraph graph = DynamicGraphFactory.instantiateDynamicGraph();
+ //System.out.println("Creating 10 nodes...");
+ long begin = System.nanoTime();
+
+ for (int i = 0; i < 10; i++)
+ graph.nodeCreate();
+
+
+ IntEnumerator nodesEnum = graph.nodes();
+ int index = -1;
+ int[] nodes = new int[nodesEnum.numRemaining()];
+ //System.out.print("Here are the nodes: ");
+
+ while (nodesEnum.numRemaining() > 0) {
+ nodes[++index] = nodesEnum.nextInt();
+ //System.out.print(nodes[index] + " ");
+ }
+
+ //System.out.println();
+ //System.out.println();
+
+ boolean[] edgesDir = new boolean[] {
+ false, true, true, true, false, true, false, false, true, true,
+ false, false, true, false, true
+ };
+ int[][] edgesDef = new int[][] {
+ { 2, 5 },
+ { 0, 8 },
+ { 4, 1 },
+ { 9, 0 },
+ { 9, 0 },
+ { 0, 8 },
+ { 1, 4 },
+ { 2, 2 },
+ { 7, 7 },
+ { 1, 1 },
+ { 3, 1 },
+ { 7, 2 },
+ { 1, 0 },
+ { 8, 5 },
+ { 4, 9 }
+ };
+
+ for (int i = 0; i < edgesDir.length; i++) {
+ //System.out.println("Creating " + (edgesDir[i] ? "directed" : "undirected")
+ // + " edge from node " + nodes[edgesDef[i][0]] + " to node "
+ // + nodes[edgesDef[i][1]] + "...");
+ graph.edgeCreate(nodes[edgesDef[i][0]], nodes[edgesDef[i][1]], edgesDir[i]);
+ }
+
+ IntEnumerator edgesEnum = graph.edges();
+ //System.out.println();
+ //System.out.println("Here are the edges:");
+
+ while (edgesEnum.numRemaining() > 0) {
+ final int edge = edgesEnum.nextInt();
+ //System.out.println(((graph.edgeType(edge) == DynamicGraph.DIRECTED_EDGE) ? "Directed"
+ // : "Undirected")
+ // + " edge " + edge + " with source " + graph.edgeSource(edge)
+ // + " and target " + graph.edgeTarget(edge) + ".");
+ }
+
+ //System.out.println();
+ //System.out.println("All adjacent edges...");
+ nodesEnum = graph.nodes();
+
+ while (nodesEnum.numRemaining() > 0) {
+ final int node = nodesEnum.nextInt();
+ IntEnumerator adjEdges = graph.edgesAdjacent(node, true, true, true);
+ //System.out.print("For node " + node + ": ");
+
+ while (adjEdges.numRemaining() > 0) {
+ final int edge = adjEdges.nextInt();
+ //System.out.print(edge + " ");
+ }
+
+ //System.out.println();
+ }
+
+ //System.out.println();
+ //System.out.println("All undirected adjacent edges...");
+ nodesEnum = graph.nodes();
+
+ while (nodesEnum.numRemaining() > 0) {
+ final int node = nodesEnum.nextInt();
+ IntEnumerator adjEdges = graph.edgesAdjacent(node, false, false, true);
+ //System.out.print("For node " + node + ": ");
+
+ while (adjEdges.numRemaining() > 0) {
+ final int edge = adjEdges.nextInt();
+ //System.out.print(edge + " ");
+ }
+
+ //System.out.println();
+ }
+
+ //System.out.println();
+ //System.out.println("All undirected and incoming adjacent edges...");
+ nodesEnum = graph.nodes();
+
+ while (nodesEnum.numRemaining() > 0) {
+ final int node = nodesEnum.nextInt();
+ IntEnumerator adjEdges = graph.edgesAdjacent(node, false, true, true);
+ //System.out.print("For node " + node + ": ");
+
+ while (adjEdges.numRemaining() > 0) {
+ final int edge = adjEdges.nextInt();
+ //System.out.print(edge + " ");
+ }
+
+ //System.out.println();
+ }
+
+ //System.out.println();
+ //System.out.println("All outgoing adjacent edges...");
+ nodesEnum = graph.nodes();
+
+ while (nodesEnum.numRemaining() > 0) {
+ final int node = nodesEnum.nextInt();
+ IntEnumerator adjEdges = graph.edgesAdjacent(node, true, false, false);
+ //System.out.print("For node " + node + ": ");
+
+ while (adjEdges.numRemaining() > 0) {
+ final int edge = adjEdges.nextInt();
+ //System.out.print(edge + " ");
+ }
+
+ //System.out.println();
+ }
+
+ //System.out.println();
+ //System.out.println("All outgoing and incoming adjacent edges...");
+ nodesEnum = graph.nodes();
+
+ while (nodesEnum.numRemaining() > 0) {
+ final int node = nodesEnum.nextInt();
+ IntEnumerator adjEdges = graph.edgesAdjacent(node, true, true, false);
+ //System.out.print("For node " + node + ": ");
+
+ while (adjEdges.numRemaining() > 0) {
+ final int edge = adjEdges.nextInt();
+ //System.out.print(edge + " ");
+ }
+
+ //System.out.println();
+ }
+
+ //System.out.println();
+
+ for (int i = 0; i < nodes.length; i++)
+ if ((i % 3) == 0) {
+ //System.out.println("Removing node " + nodes[i] + "...");
+ graph.nodeRemove(nodes[i]);
+ }
+
+ //System.out.println();
+ //System.out.println("All adjacent edges...");
+ nodesEnum = graph.nodes();
+
+ while (nodesEnum.numRemaining() > 0) {
+ final int node = nodesEnum.nextInt();
+ IntEnumerator adjEdges = graph.edgesAdjacent(node, true, true, true);
+ //System.out.print("For node " + node + ": ");
+
+ while (adjEdges.numRemaining() > 0) {
+ final int edge = adjEdges.nextInt();
+ //System.out.print(edge + " ");
+ }
+
+ //System.out.println();
+ }
+
+ //System.out.println();
+ nodesEnum = graph.nodes();
+
+ while (nodesEnum.numRemaining() > 0) {
+ final int node0 = nodesEnum.nextInt();
+ IntEnumerator nodesEnum2 = graph.nodes();
+
+ while (nodesEnum2.numRemaining() > 0) {
+ final int node1 = nodesEnum2.nextInt();
+ IntIterator connectingEdges = graph.edgesConnecting(node0, node1, true, true, true);
+ //System.out.print("All edges connecting node " + node0 + " with node " + node1
+ // + ": ");
+
+ //while (connectingEdges.hasNext())
+ //System.out.print(connectingEdges.nextInt() + " ");
+
+ //System.out.println();
+ }
+ }
+ long end = System.nanoTime();
+ System.out.println("duration: " + (end - begin));
+ }
+}
diff --git a/corelibs/graph.fixed/pom.xml b/corelibs/graph.fixed/pom.xml
new file mode 100644
index 0000000..bfce848
--- /dev/null
+++ b/corelibs/graph.fixed/pom.xml
@@ -0,0 +1,49 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>parent</artifactId>
+ <version>2.8.4-SNAPSHOT</version>
+ </parent>
+
+ <artifactId>graph-fixed</artifactId>
+ <packaging>jar</packaging>
+
+ <name>graph-fixed</name>
+
+ <!-- bootstrap for cytoscape dependencies, namely the parent POM snapshots -->
+ <repositories>
+ <repository>
+ <id>cytoscape_snapshots</id>
+ <snapshots>
+ <enabled>true</enabled>
+ </snapshots>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <name>Cytoscape Snapshots</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/</url>
+ </repository>
+ <repository>
+ <id>cytoscape_releases</id>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ <name>Cytoscape Releases</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/releases/</url>
+ </repository>
+ </repositories>
+
+ <dependencies>
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>util-intr</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ </dependencies>
+
+</project>
+
diff --git a/corelibs/graph.fixed/src/main/java/cytoscape/graph/fixed/FixedGraph.java b/corelibs/graph.fixed/src/main/java/cytoscape/graph/fixed/FixedGraph.java
new file mode 100644
index 0000000..eddebe2
--- /dev/null
+++ b/corelibs/graph.fixed/src/main/java/cytoscape/graph/fixed/FixedGraph.java
@@ -0,0 +1,196 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.graph.fixed;
+
+import cytoscape.util.intr.IntEnumerator;
+import cytoscape.util.intr.IntIterator;
+
+
+/**
+ * A graph topology.
+ * Edges and nodes are non-negative integers; a given node and a given edge
+ * in a single graph can be the same integer.
+ */
+public interface FixedGraph {
+ /**
+ * A nonnegative quantity representing directedness of an edge.
+ */
+ public final static byte DIRECTED_EDGE = 1;
+
+ /**
+ * A nonnegative quantity representing undirectedness of an edge.
+ */
+ public final static byte UNDIRECTED_EDGE = 0;
+
+ /**
+ * Returns an enumeration of all nodes in this graph. Every node in this
+ * graph is a unique non-negative integer. A given node and a given edge
+ * in one graph may be the same integer.
+ *
+ * @return an enumeration over all nodes in this graph; null is never
+ * returned.
+ */
+ public IntEnumerator nodes();
+
+ /**
+ * Returns an enumeration of all edges in this graph. Every edge in this
+ * graph is a unique non-negative integer. A given node and a given edge
+ * in one graph may be the same integer.
+ *
+ * @return an enumeration over all edges in this graph; null is never
+ * returned.
+ */
+ public IntEnumerator edges();
+
+ /**
+ * Determines whether or not a node exists in this graph.
+ * Returns true if and only if the node specified exists.<p>
+ * Note that this method is superfluous in this interface (that is,
+ * it could be removed without losing any functionality), because
+ * edgesAdjacent(int, boolean, boolean, boolean) can be used to test
+ * the presence of a node. However, because nodeExists(int) does not
+ * return a complicated object, its performance may be better
+ * than that of edgesAdjacent().
+ *
+ * @param node the [potentially existing] node in this graph whose existence
+ * we're querying.
+ * @return the existence of specified node in this graph.
+ */
+ public boolean nodeExists(int node);
+
+ /**
+ * Determines the existence and directedness of an edge.
+ * Returns -1 if specified edge does not exist in this graph,
+ * otherwise returns DIRECTED_EDGE or UNDIRECTED_EDGE.
+ *
+ * @param edge the edge in this graph whose existence and/or
+ * directedness we're seeking.
+ * @return DIRECTED_EDGE if specified edge is directed, UNDIRECTED_EDGE
+ * if specified edge is undirected, and -1 if specified edge does not
+ * exist in this graph.
+ */
+ public byte edgeType(int edge);
+
+ /**
+ * Determines the source node of an edge.
+ * Returns the source node of specified edge or -1 if specified edge does
+ * not exist in this graph.
+ *
+ * @param edge the edge in this graph whose source node we're seeking.
+ * @return the source node of specified edge or -1 if specified edge does
+ * not exist in this graph.
+ */
+ public int edgeSource(int edge);
+
+ /**
+ * Determines the target node of an edge.
+ * Returns the target node of specified edge or -1 if specified edge does
+ * not exist in this graph.
+ *
+ * @param edge the edge in this graph whose target node we're seeking.
+ * @return the target node of specified edge or -1 if specified edge does
+ * not exist in this graph.
+ */
+ public int edgeTarget(int edge);
+
+ /**
+ * Returns a non-repeating enumeration of edges adjacent to a node.
+ * The three boolean input parameters define what is meant by "adjacent
+ * edge". If all three boolean input parameters are false, the returned
+ * enumeration will have zero elements.<p>
+ * This method returns null if and only if the specified node does not
+ * exist in this graph. Therefore, this method can be used to test
+ * the existence of a node in this graph.
+ *
+ * @param node the node in this graph whose adjacent edges we're seeking.
+ * @param outgoing all directed edges whose source is the node specified
+ * are included in the returned enumeration if this value is true;
+ * otherwise, not a single such edge is included in the returned
+ * enumeration.
+ * @param incoming all directed edges whose target is the node specified
+ * are included in the returned enumeration if this value is true;
+ * otherwise, not a single such edge is included in the returned
+ * enumeration.
+ * @param undirected all undirected edges touching the specified node
+ * are included in the returned enumeration if this value is true;
+ * otherwise, not a single such edge is included in the returned
+ * enumeration.
+ * @return an enumeration of edges adjacent to the node specified
+ * or null if specified node does not exist in this graph.
+ */
+ public IntEnumerator edgesAdjacent(int node, boolean outgoing, boolean incoming,
+ boolean undirected);
+
+ /**
+ * Returns a non-repeating iteration of edges connecting two nodes.
+ * The three boolean input parameters define what is meant by "connecting
+ * edge". If all three boolean input parameters are false, the returned
+ * iteration will have no elements.<p>
+ * I'd like to discuss the motivation behind this interface method.
+ * I assume that most implementations of this interface will implement
+ * this method in terms of edgesAdjacent(). Why, then, is this method
+ * necessary? Because some implementations may choose to optimize the
+ * implementation of this method by using a search tree or a
+ * hashtable, for example. This method is a hook to provide such
+ * optimization.<p>
+ * This method returns an IntIterator as opposed to an IntEnumerator
+ * so that non-optimized implementations would not be required to
+ * pre-compute the number of edges being returned.
+ *
+ * @param node0 one of the nodes in this graph whose connecting edges
+ * we're seeking.
+ * @param node1 one of the nodes in this graph whose connecting edges
+ * we're seeking.
+ * @param outgoing all directed edges whose source is node0 and whose
+ * target is node1 are included in the returned iteration if this value
+ * is true; otherwise, not a single such edge is included in the returned
+ * iteration.
+ * @param incoming all directed edges whose source is node1 and whose
+ * target is node0 are included in the returned iteration if this value
+ * is true; otherwise, not a single such edge is included in the returned
+ * iteration.
+ * @param undirected all undirected edges E such that E's endpoints
+ * are node0 and node1 are included in the returned iteration if this
+ * value is true; otherwise, not a single such edge is incuded in the
+ * returned iteration.
+ * @return an iteration of edges connecting node0 with node1 in a fashion
+ * specified by boolean input parameters or null if either of node0 or
+ * node1 does not exist in this graph.
+ */
+ public IntIterator edgesConnecting(int node0, int node1, boolean outgoing, boolean incoming,
+ boolean undirected);
+}
diff --git a/corelibs/nerius.math.xform/pom.xml b/corelibs/nerius.math.xform/pom.xml
new file mode 100644
index 0000000..a679407
--- /dev/null
+++ b/corelibs/nerius.math.xform/pom.xml
@@ -0,0 +1,41 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>parent</artifactId>
+ <version>2.8.4-SNAPSHOT</version>
+ </parent>
+
+ <artifactId>nerius-math-xform</artifactId>
+ <packaging>jar</packaging>
+
+ <name>nerius-math-xform</name>
+
+ <!-- bootstrap for cytoscape dependencies, namely the parent POM snapshots -->
+ <repositories>
+ <repository>
+ <id>cytoscape_snapshots</id>
+ <snapshots>
+ <enabled>true</enabled>
+ </snapshots>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <name>Cytoscape Snapshots</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/</url>
+ </repository>
+ <repository>
+ <id>cytoscape_releases</id>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ <name>Cytoscape Releases</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/releases/</url>
+ </repository>
+ </repositories>
+
+</project>
+
diff --git a/corelibs/nerius.math.xform/src/main/java/com/nerius/math/geom/Point3D.java b/corelibs/nerius.math.xform/src/main/java/com/nerius/math/geom/Point3D.java
new file mode 100644
index 0000000..149dad4
--- /dev/null
+++ b/corelibs/nerius.math.xform/src/main/java/com/nerius/math/geom/Point3D.java
@@ -0,0 +1,79 @@
+/*
+ Copyright (c) 2001, Nerius Landys
+ All rights reserved.
+
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+ 2. Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions and the following disclaimer in the
+ documentation and/or other materials provided with the distribution.
+ 3. The name of the author may be used to endorse or promote products
+ derived from this software without specific prior written permission.
+
+ THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR
+ IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
+ IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT,
+ INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+ DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+ THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF
+ THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+package com.nerius.math.geom;
+
+
+/**
+ * Immutable class.
+ * @version $Revision: 1.1.1.1 $
+ **/
+public final class Point3D {
+ /**
+ *
+ */
+ public final double x;
+
+ /**
+ *
+ */
+ public final double y;
+
+ /**
+ *
+ */
+ public final double z;
+
+ /**
+ * Creates a new Point3D object.
+ *
+ * @param x DOCUMENT ME!
+ * @param y DOCUMENT ME!
+ * @param z DOCUMENT ME!
+ */
+ public Point3D(double x, double y, double z) {
+ this.x = x;
+ this.y = y;
+ this.z = z;
+ }
+
+ // public Point3D scale(float scaleFactor)
+ // {
+ // return new Point3D(x * scaleFactor, y * scaleFactor, z * scaleFactor);
+ // }
+
+ // public float distance(Point3D pt3D)
+ // {
+ // return (float) Math.sqrt(square(x - pt3D.x) + square(y - pt3D.y) +
+ // square(z - pt3D.z));
+ // }
+
+ // private float square(float f)
+ // {
+ // return f * f;
+ // }
+}
diff --git a/corelibs/nerius.math.xform/src/main/java/com/nerius/math/xform/AffineTransform3D.java b/corelibs/nerius.math.xform/src/main/java/com/nerius/math/xform/AffineTransform3D.java
new file mode 100644
index 0000000..f1254a0
--- /dev/null
+++ b/corelibs/nerius.math.xform/src/main/java/com/nerius/math/xform/AffineTransform3D.java
@@ -0,0 +1,87 @@
+/*
+ Copyright (c) 2001, Nerius Landys
+ All rights reserved.
+
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+ 2. Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions and the following disclaimer in the
+ documentation and/or other materials provided with the distribution.
+ 3. The name of the author may be used to endorse or promote products
+ derived from this software without specific prior written permission.
+
+ THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR
+ IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
+ IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT,
+ INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+ DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+ THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF
+ THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+package com.nerius.math.xform;
+
+import com.nerius.math.geom.Point3D;
+
+
+/**
+ * Instances of this class are immutable.
+ * @version $Revision: 1.2 $
+ **/
+public abstract class AffineTransform3D implements Transformation3D {
+ final Matrix4x4 m_matrix;
+
+ AffineTransform3D(Matrix4x4 matrix) {
+ m_matrix = matrix;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param pt3D DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Point3D transform(Point3D pt3D) {
+ double[] arr3D = new double[] { pt3D.x, pt3D.y, pt3D.z };
+ transformArr(arr3D);
+
+ return new Point3D(arr3D[0], arr3D[1], arr3D[2]);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param arr3D DOCUMENT ME!
+ */
+ public void transformArr(double[] arr3D) {
+ m_matrix.transform(arr3D);
+ }
+
+ /**
+ * The returned transformation, in its <code>transform()</code> method,
+ * passes a point through the transform
+ * <code>xform</code> and then passes the resulting point through
+ * <code>this</code>.
+ **/
+ public AffineTransform3D concatenatePre(AffineTransform3D xform) {
+ return new AffineTransform3D(m_matrix.multiply(xform.m_matrix)) {
+ };
+ }
+
+ /**
+ * The returned transformation, in its <code>transform()</code> method,
+ * passes a point through <code>this</code> and then passes the resulting
+ * point through <code>xform</code>. Returns exactly
+ * <code>xform.concatenatePre(this)</code>.
+ **/
+ public AffineTransform3D concatenatePost(AffineTransform3D xform) {
+ return xform.concatenatePre(this);
+ }
+}
diff --git a/corelibs/nerius.math.xform/src/main/java/com/nerius/math/xform/AxisRotation3D.java b/corelibs/nerius.math.xform/src/main/java/com/nerius/math/xform/AxisRotation3D.java
new file mode 100644
index 0000000..aa3d9e7
--- /dev/null
+++ b/corelibs/nerius.math.xform/src/main/java/com/nerius/math/xform/AxisRotation3D.java
@@ -0,0 +1,117 @@
+/*
+ Copyright (c) 2001, Nerius Landys
+ All rights reserved.
+
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+ 2. Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions and the following disclaimer in the
+ documentation and/or other materials provided with the distribution.
+ 3. The name of the author may be used to endorse or promote products
+ derived from this software without specific prior written permission.
+
+ THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR
+ IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
+ IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT,
+ INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+ DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+ THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF
+ THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+package com.nerius.math.xform;
+
+
+/**
+ * @version $Revision: 1.1.1.1 $
+ **/
+public class AxisRotation3D extends AffineTransform3D {
+ /**
+ *
+ */
+ public final static byte X_AXIS = (byte) 1;
+
+ /**
+ *
+ */
+ public final static byte Y_AXIS = (byte) 2;
+
+ /**
+ *
+ */
+ public final static byte Z_AXIS = (byte) 4;
+
+ /**
+ * <code>theta</code> in radians.
+ **/
+ public AxisRotation3D(byte axisOfRotation, double theta) {
+ this(getAxisRotationMatrix(axisOfRotation, theta));
+ }
+
+ private AxisRotation3D(Matrix4x4 matrix) {
+ super(matrix);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public AxisRotation3D getInverse() {
+ final double[][] d = m_matrix.m_entries;
+
+ return new AxisRotation3D(new Matrix4x4(new double[][] {
+ { d[0][0], -d[0][1], d[0][2], d[0][3] },
+ { -d[1][0], d[1][1], -d[1][2], d[1][3] },
+ { d[2][0], -d[2][1], d[2][2], d[2][3] },
+ { d[3][0], d[3][1], d[3][2], d[3][3] },
+ }));
+ }
+
+ private static Matrix4x4 getAxisRotationMatrix(byte axisOfRotation, double theta) {
+ final double[][] entries;
+
+ switch (axisOfRotation) {
+ case X_AXIS:
+ entries = new double[][] {
+ { 1.0d, 0.0d, 0.0d, 0.0d },
+ { 0.0d, Math.cos(theta), -Math.sin(theta), 0.0d },
+ { 0.0d, Math.sin(theta), Math.cos(theta), 0.0d },
+ { 0.0d, 0.0d, 0.0d, 1.0d }
+ };
+
+ break;
+
+ case Y_AXIS:
+ entries = new double[][] {
+ { Math.cos(theta), 0.0d, Math.sin(theta), 0.0d },
+ { 0.0d, 1.0d, 0.0d, 0.0d },
+ { -Math.sin(theta), 0.0d, Math.cos(theta), 0.0d },
+ { 0.0d, 0.0d, 0.0d, 1.0d }
+ };
+
+ break;
+
+ case Z_AXIS:
+ entries = new double[][] {
+ { Math.cos(theta), -Math.sin(theta), 0.0d, 0.0d },
+ { Math.sin(theta), Math.cos(theta), 0.0d, 0.0d },
+ { 0.0d, 0.0d, 1.0d, 0.0d },
+ { 0.0d, 0.0d, 0.0d, 1.0d }
+ };
+
+ break;
+
+ default:
+ throw new IllegalArgumentException("invalid axisOfRotation");
+ }
+
+ return new Matrix4x4(entries);
+ }
+}
diff --git a/corelibs/nerius.math.xform/src/main/java/com/nerius/math/xform/Matrix4x4.java b/corelibs/nerius.math.xform/src/main/java/com/nerius/math/xform/Matrix4x4.java
new file mode 100644
index 0000000..c2fea01
--- /dev/null
+++ b/corelibs/nerius.math.xform/src/main/java/com/nerius/math/xform/Matrix4x4.java
@@ -0,0 +1,75 @@
+/*
+ Copyright (c) 2001, Nerius Landys
+ All rights reserved.
+
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+ 2. Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions and the following disclaimer in the
+ documentation and/or other materials provided with the distribution.
+ 3. The name of the author may be used to endorse or promote products
+ derived from this software without specific prior written permission.
+
+ THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR
+ IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
+ IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT,
+ INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+ DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+ THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF
+ THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+package com.nerius.math.xform;
+
+
+/* @version $Revision: 1.1.1.1 $
+ */
+class Matrix4x4 {
+ final double[][] m_entries; // this class is _immutable_; do not modify!
+
+ /*
+ * entries[row][column].
+ */
+ Matrix4x4(double[][] entries) {
+ m_entries = entries;
+ }
+
+ void transform(double[] arr3D) {
+ final double x = (arr3D[0] * m_entries[0][0]) + (arr3D[1] * m_entries[0][1])
+ + (arr3D[2] * m_entries[0][2]) + (1.0d * m_entries[0][3]);
+ final double y = (arr3D[0] * m_entries[1][0]) + (arr3D[1] * m_entries[1][1])
+ + (arr3D[2] * m_entries[1][2]) + (1.0d * m_entries[1][3]);
+ final double z = (arr3D[0] * m_entries[2][0]) + (arr3D[1] * m_entries[2][1])
+ + (arr3D[2] * m_entries[2][2]) + (1.0d * m_entries[2][3]);
+
+ arr3D[0] = x;
+ arr3D[1] = y;
+ arr3D[2] = z;
+ }
+
+ /*
+ * this * matrix
+ */
+ Matrix4x4 multiply(Matrix4x4 matrix) {
+ final double[][] newEntries = new double[4][];
+
+ for (int i = 0; i < 4; i++) {
+ newEntries[i] = new double[4];
+
+ for (int j = 0; j < 4; j++) {
+ newEntries[i][j] = (m_entries[i][0] * matrix.m_entries[0][j])
+ + (m_entries[i][1] * matrix.m_entries[1][j])
+ + (m_entries[i][2] * matrix.m_entries[2][j])
+ + (m_entries[i][3] * matrix.m_entries[3][j]);
+ }
+ }
+
+ return new Matrix4x4(newEntries);
+ }
+}
diff --git a/corelibs/nerius.math.xform/src/main/java/com/nerius/math/xform/Scale3D.java b/corelibs/nerius.math.xform/src/main/java/com/nerius/math/xform/Scale3D.java
new file mode 100644
index 0000000..ece1096
--- /dev/null
+++ b/corelibs/nerius.math.xform/src/main/java/com/nerius/math/xform/Scale3D.java
@@ -0,0 +1,50 @@
+/*
+ Copyright (c) 2001, Nerius Landys
+ All rights reserved.
+
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+ 2. Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions and the following disclaimer in the
+ documentation and/or other materials provided with the distribution.
+ 3. The name of the author may be used to endorse or promote products
+ derived from this software without specific prior written permission.
+
+ THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR
+ IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
+ IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT,
+ INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+ DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+ THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF
+ THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+package com.nerius.math.xform;
+
+
+/**
+ * @version $Revision: 1.1 $
+ **/
+public class Scale3D extends AffineTransform3D {
+ /**
+ * Creates a new Scale3D object.
+ *
+ * @param x DOCUMENT ME!
+ * @param y DOCUMENT ME!
+ * @param z DOCUMENT ME!
+ */
+ public Scale3D(double x, double y, double z) {
+ super(new Matrix4x4(new double[][] {
+ { x, 0.0d, 0.0d, 0.0d },
+ { 0.0d, y, 0.0d, 0.0d },
+ { 0.0d, 0.0d, z, 0.0d },
+ { 0.0d, 0.0d, 0.0d, 1.0d }
+ }));
+ }
+}
diff --git a/corelibs/nerius.math.xform/src/main/java/com/nerius/math/xform/Transformation3D.java b/corelibs/nerius.math.xform/src/main/java/com/nerius/math/xform/Transformation3D.java
new file mode 100644
index 0000000..1e71d73
--- /dev/null
+++ b/corelibs/nerius.math.xform/src/main/java/com/nerius/math/xform/Transformation3D.java
@@ -0,0 +1,45 @@
+/*
+ Copyright (c) 2001, Nerius Landys
+ All rights reserved.
+
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+ 2. Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions and the following disclaimer in the
+ documentation and/or other materials provided with the distribution.
+ 3. The name of the author may be used to endorse or promote products
+ derived from this software without specific prior written permission.
+
+ THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR
+ IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
+ IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT,
+ INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+ DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+ THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF
+ THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+package com.nerius.math.xform;
+
+import com.nerius.math.geom.Point3D;
+
+
+/**
+ * @version $Revision: 1.2 $
+ **/
+public interface Transformation3D {
+ /**
+ * DOCUMENT ME!
+ *
+ * @param pt3D DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Point3D transform(Point3D pt3D);
+}
diff --git a/corelibs/nerius.math.xform/src/main/java/com/nerius/math/xform/Translation3D.java b/corelibs/nerius.math.xform/src/main/java/com/nerius/math/xform/Translation3D.java
new file mode 100644
index 0000000..e703ac5
--- /dev/null
+++ b/corelibs/nerius.math.xform/src/main/java/com/nerius/math/xform/Translation3D.java
@@ -0,0 +1,60 @@
+/*
+ Copyright (c) 2001, Nerius Landys
+ All rights reserved.
+
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+ 2. Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions and the following disclaimer in the
+ documentation and/or other materials provided with the distribution.
+ 3. The name of the author may be used to endorse or promote products
+ derived from this software without specific prior written permission.
+
+ THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR
+ IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
+ IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT,
+ INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+ DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+ THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF
+ THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+package com.nerius.math.xform;
+
+
+/**
+ * @version $Revision: 1.1.1.1 $
+ **/
+public class Translation3D extends AffineTransform3D {
+ /**
+ * Creates a new Translation3D object.
+ *
+ * @param x DOCUMENT ME!
+ * @param y DOCUMENT ME!
+ * @param z DOCUMENT ME!
+ */
+ public Translation3D(double x, double y, double z) {
+ super(new Matrix4x4(new double[][] {
+ { 1.0d, 0.0d, 0.0d, x },
+ { 0.0d, 1.0d, 0.0d, y },
+ { 0.0d, 0.0d, 1.0d, z },
+ { 0.0d, 0.0d, 0.0d, 1.0d }
+ }));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Translation3D getInverse() {
+ return new Translation3D(-m_matrix.m_entries[0][3], -m_matrix.m_entries[1][3],
+ -m_matrix.m_entries[2][3]);
+ }
+}
diff --git a/corelibs/obo/pom.xml b/corelibs/obo/pom.xml
new file mode 100644
index 0000000..1d0b6b5
--- /dev/null
+++ b/corelibs/obo/pom.xml
@@ -0,0 +1,41 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>parent</artifactId>
+ <version>2.8.4-SNAPSHOT</version>
+ </parent>
+
+ <artifactId>obo</artifactId>
+ <packaging>jar</packaging>
+
+ <name>obo</name>
+
+ <!-- bootstrap for cytoscape dependencies, namely the parent POM snapshots -->
+ <repositories>
+ <repository>
+ <id>cytoscape_snapshots</id>
+ <snapshots>
+ <enabled>true</enabled>
+ </snapshots>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <name>Cytoscape Snapshots</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/</url>
+ </repository>
+ <repository>
+ <id>cytoscape_releases</id>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ <name>Cytoscape Releases</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/releases/</url>
+ </repository>
+ </repositories>
+
+</project>
+
diff --git a/corelibs/obo/src/main/java/cytoscape/cruft/obo/BiologicalProcessAnnotationReader.java b/corelibs/obo/src/main/java/cytoscape/cruft/obo/BiologicalProcessAnnotationReader.java
new file mode 100644
index 0000000..5795783
--- /dev/null
+++ b/corelibs/obo/src/main/java/cytoscape/cruft/obo/BiologicalProcessAnnotationReader.java
@@ -0,0 +1,206 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.cruft.obo;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.Reader;
+
+import java.util.Map;
+
+
+/**
+ * The purpose of this class is to convert a 'gene_association.*' file (for
+ * example 'gene_association.sgd') into a crufty old 'bioproc.anno' file that
+ * Cytoscape's BioDataServer understands. The parameter passed to the
+ * constructor is the 'gene_association.*' file and the content read from this
+ * reader is the crufty old 'bioproc.anno' file.
+ * <p>
+ * Please note that this code was not written with performance in mind.
+ * Therefore, evaluating this code will not give a good indication of the
+ * author's programming ability.
+ */
+public final class BiologicalProcessAnnotationReader extends Reader {
+ private final String NL = System.getProperty("line.separator");
+ private BufferedReader m_file;
+ private String m_readString;
+ private int m_readInx; // Index into a m_readString character.
+ private Map ontologyTypeMap;
+
+ /**
+ * Creates a new BiologicalProcessAnnotationReader object.
+ *
+ * @param speciesName DOCUMENT ME!
+ * @param geneAssociationFile DOCUMENT ME!
+ */
+ public BiologicalProcessAnnotationReader(final String speciesName,
+ final Reader geneAssociationFile) {
+ if (geneAssociationFile == null)
+ throw new NullPointerException("geneAssociationFile is null");
+
+ m_file = new BufferedReader(geneAssociationFile);
+ m_readString = "(species=" + speciesName + ") (type=Biological Process) (curator=GO)" + NL;
+ m_readInx = 0;
+ }
+
+ /**
+ * Creates a new BiologicalProcessAnnotationReader object.
+ *
+ * @param speciesName DOCUMENT ME!
+ * @param ontologyTypeMap DOCUMENT ME!
+ * @param geneAssociationFile DOCUMENT ME!
+ */
+ public BiologicalProcessAnnotationReader(final String speciesName, final Map ontologyTypeMap,
+ final Reader geneAssociationFile) {
+ if (geneAssociationFile == null)
+ throw new NullPointerException("geneAssociationFile is null");
+
+ this.ontologyTypeMap = ontologyTypeMap;
+ m_file = new BufferedReader(geneAssociationFile);
+
+ m_readString = "(species=" + speciesName + ") (type=Biological Process) (curator=GO)" + NL;
+ m_readInx = 0;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param cbuf DOCUMENT ME!
+ * @param off DOCUMENT ME!
+ * @param len DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @throws IOException DOCUMENT ME!
+ */
+ public final int read(final char[] cbuf, final int off, final int len)
+ throws IOException {
+ if (m_file == null)
+ throw new IOException("this stream is closed");
+
+ if (m_readString == null)
+ return -1;
+
+ final int returnThis;
+
+ if ((m_readString.length() - m_readInx) >= len) {
+ m_readString.getChars(m_readInx, m_readInx + len, cbuf, off);
+ returnThis = len;
+ m_readInx += len;
+ } else { // len is greater than the number of chars left in
+ // m_readString.
+ m_readString.getChars(m_readInx, m_readString.length(), cbuf, off);
+ returnThis = m_readString.length() - m_readInx;
+ m_readInx = m_readString.length();
+ }
+
+ if (m_readInx == m_readString.length())
+ readMore();
+
+ return returnThis;
+ }
+
+ private final void readMore() throws IOException {
+ while (true) {
+ String line;
+
+ while (true) // Read comments and possibly blank lines.
+ {
+ line = m_file.readLine();
+
+ if (line == null) { // End of underlying stream.
+ m_readString = null;
+
+ return;
+ }
+
+ line = line.trim();
+
+ if ((line.length() > 0) && !line.startsWith("!")) {
+ break;
+ }
+ }
+
+ // Now line contains a line of data.
+ int fromIndex = 0;
+
+ for (int i = 0; i < 2; i++) {
+ fromIndex = 1 + line.indexOf('\t', fromIndex);
+ }
+
+ final String canon = line.substring(fromIndex, line.indexOf('\t', fromIndex));
+
+ for (int i = 0; i < 2; i++) {
+ fromIndex = 1 + line.indexOf('\t', fromIndex);
+ }
+
+ final String goid = line.substring(fromIndex + 3, fromIndex + 10);
+
+ for (int i = 0; i < 4; i++) {
+ fromIndex = 1 + line.indexOf('\t', fromIndex);
+ }
+
+ String type = line.substring(fromIndex, fromIndex + 1);
+
+ // Check valid type or not
+ if (!type.equals("P") && !type.equals("C") && !type.equals("F")) {
+ // Try to find one
+ type = (String) ontologyTypeMap.get("GO:" + goid);
+ }
+
+ if (type != null) {
+ if (type.equals("P")) { // Biological Process. We found one.
+ m_readString = canon + " = " + goid + NL;
+ m_readInx = 0;
+
+ break;
+ }
+ }
+ }
+ }
+
+ /**
+ * Closes the underlying gene_association file stream as well.
+ */
+ public final void close() throws IOException {
+ try {
+ m_file.close();
+ } finally {
+ m_file = null;
+ }
+ }
+}
diff --git a/corelibs/obo/src/main/java/cytoscape/cruft/obo/CellularComponentAnnotationReader.java b/corelibs/obo/src/main/java/cytoscape/cruft/obo/CellularComponentAnnotationReader.java
new file mode 100644
index 0000000..457e654
--- /dev/null
+++ b/corelibs/obo/src/main/java/cytoscape/cruft/obo/CellularComponentAnnotationReader.java
@@ -0,0 +1,206 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.cruft.obo;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.Reader;
+
+import java.util.Map;
+
+
+/**
+ * The purpose of this class is to convert a 'gene_association.*' file (for
+ * example 'gene_association.sgd') into a crufty old 'cellcomp.anno' file that
+ * Cytoscape's BioDataServer understands. The parameter passed to the
+ * constructor is the 'gene_association.*' file and the content read from this
+ * reader is the crufty old 'cellcomp.anno' file.
+ * <p>
+ * Please note that this code was not written with performance in mind.
+ * Therefore, evaluating this code will not give a good indication of the
+ * author's programming ability.
+ */
+public final class CellularComponentAnnotationReader extends Reader {
+ private final String NL = System.getProperty("line.separator");
+ private BufferedReader m_file;
+ private String m_readString;
+ private int m_readInx; // Index into a m_readString character.
+ private Map ontologyTypeMap;
+
+ /**
+ * Creates a new CellularComponentAnnotationReader object.
+ *
+ * @param speciesName DOCUMENT ME!
+ * @param ontologyTypeMap DOCUMENT ME!
+ * @param geneAssociationFile DOCUMENT ME!
+ */
+ public CellularComponentAnnotationReader(final String speciesName, final Map ontologyTypeMap,
+ final Reader geneAssociationFile) {
+ if (geneAssociationFile == null)
+ throw new NullPointerException("geneAssociationFile is null");
+
+ this.ontologyTypeMap = ontologyTypeMap;
+
+ m_file = new BufferedReader(geneAssociationFile);
+ m_readString = "(species=" + speciesName + ") (type=Cellular Component) (curator=GO)" + NL;
+ m_readInx = 0;
+ }
+
+ /**
+ * Creates a new CellularComponentAnnotationReader object.
+ *
+ * @param speciesName DOCUMENT ME!
+ * @param geneAssociationFile DOCUMENT ME!
+ */
+ public CellularComponentAnnotationReader(final String speciesName,
+ final Reader geneAssociationFile) {
+ if (geneAssociationFile == null)
+ throw new NullPointerException("geneAssociationFile is null");
+
+ m_file = new BufferedReader(geneAssociationFile);
+ m_readString = "(species=" + speciesName + ") (type=Cellular Component) (curator=GO)" + NL;
+ m_readInx = 0;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param cbuf DOCUMENT ME!
+ * @param off DOCUMENT ME!
+ * @param len DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @throws IOException DOCUMENT ME!
+ */
+ public final int read(final char[] cbuf, final int off, final int len)
+ throws IOException {
+ if (m_file == null)
+ throw new IOException("this stream is closed");
+
+ if (m_readString == null)
+ return -1;
+
+ final int returnThis;
+
+ if ((m_readString.length() - m_readInx) >= len) {
+ m_readString.getChars(m_readInx, m_readInx + len, cbuf, off);
+ returnThis = len;
+ m_readInx += len;
+ } else { // len is greater than the number of chars left in
+ // m_readString.
+ m_readString.getChars(m_readInx, m_readString.length(), cbuf, off);
+ returnThis = m_readString.length() - m_readInx;
+ m_readInx = m_readString.length();
+ }
+
+ if (m_readInx == m_readString.length())
+ readMore();
+
+ return returnThis;
+ }
+
+ private final void readMore() throws IOException {
+ while (true) {
+ String line;
+
+ while (true) // Read comments and possibly blank lines.
+ {
+ line = m_file.readLine();
+
+ if (line == null) { // End of underlying stream.
+ m_readString = null;
+
+ return;
+ }
+
+ line = line.trim();
+
+ if ((line.length() > 0) && !line.startsWith("!")) {
+ break;
+ }
+ }
+
+ // Now line contains a line of data.
+ int fromIndex = 0;
+
+ for (int i = 0; i < 2; i++) {
+ fromIndex = 1 + line.indexOf('\t', fromIndex);
+ }
+
+ final String canon = line.substring(fromIndex, line.indexOf('\t', fromIndex));
+
+ for (int i = 0; i < 2; i++) {
+ fromIndex = 1 + line.indexOf('\t', fromIndex);
+ }
+
+ final String goid = line.substring(fromIndex + 3, fromIndex + 10);
+
+ for (int i = 0; i < 4; i++) {
+ fromIndex = 1 + line.indexOf('\t', fromIndex);
+ }
+
+ String type = line.substring(fromIndex, fromIndex + 1);
+
+ // Check valid type or not
+ if (!type.equals("P") && !type.equals("C") && !type.equals("F")) {
+ // Try to find one
+ type = (String) ontologyTypeMap.get("GO:" + goid);
+ }
+
+ if (type != null) {
+ if (type.equals("C")) { // Cellular Component. We found one.
+ m_readString = canon + " = " + goid + NL;
+ m_readInx = 0;
+
+ break;
+ }
+ }
+ }
+ }
+
+ /**
+ * Closes the underlying gene_association file stream as well.
+ */
+ public final void close() throws IOException {
+ try {
+ m_file.close();
+ } finally {
+ m_file = null;
+ }
+ }
+}
diff --git a/corelibs/obo/src/main/java/cytoscape/cruft/obo/DEPENDENCIES b/corelibs/obo/src/main/java/cytoscape/cruft/obo/DEPENDENCIES
new file mode 100644
index 0000000..e69de29
diff --git a/corelibs/obo/src/main/java/cytoscape/cruft/obo/MolecularFunctionAnnotationReader.java b/corelibs/obo/src/main/java/cytoscape/cruft/obo/MolecularFunctionAnnotationReader.java
new file mode 100644
index 0000000..9c71614
--- /dev/null
+++ b/corelibs/obo/src/main/java/cytoscape/cruft/obo/MolecularFunctionAnnotationReader.java
@@ -0,0 +1,205 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.cruft.obo;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.Reader;
+
+import java.util.Map;
+
+
+/**
+ * The purpose of this class is to convert a 'gene_association.*' file (for
+ * example 'gene_association.sgd') into a crufty old 'molfunc.anno' file that
+ * Cytoscape's BioDataServer understands. The parameter passed to the
+ * constructor is the 'gene_association.*' file and the content read from this
+ * reader is the crufty old 'molfunc.anno' file.
+ * <p>
+ * Please note that this code was not written with performance in mind.
+ * Therefore, evaluating this code will not give a good indication of the
+ * author's programming ability.
+ */
+public final class MolecularFunctionAnnotationReader extends Reader {
+ private final String NL = System.getProperty("line.separator");
+ private BufferedReader m_file;
+ private String m_readString;
+ private int m_readInx; // Index into a m_readString character.
+ private Map ontologyTypeMap;
+
+ /**
+ * Creates a new MolecularFunctionAnnotationReader object.
+ *
+ * @param speciesName DOCUMENT ME!
+ * @param geneAssociationFile DOCUMENT ME!
+ */
+ public MolecularFunctionAnnotationReader(final String speciesName,
+ final Reader geneAssociationFile) {
+ if (geneAssociationFile == null)
+ throw new NullPointerException("geneAssociationFile is null");
+
+ m_file = new BufferedReader(geneAssociationFile);
+ m_readString = "(species=" + speciesName + ") (type=Molecular Function) (curator=GO)" + NL;
+ m_readInx = 0;
+ }
+
+ /**
+ * Creates a new MolecularFunctionAnnotationReader object.
+ *
+ * @param speciesName DOCUMENT ME!
+ * @param ontologyTypeMap DOCUMENT ME!
+ * @param geneAssociationFile DOCUMENT ME!
+ */
+ public MolecularFunctionAnnotationReader(final String speciesName, final Map ontologyTypeMap,
+ final Reader geneAssociationFile) {
+ if (geneAssociationFile == null)
+ throw new NullPointerException("geneAssociationFile is null");
+
+ this.ontologyTypeMap = ontologyTypeMap;
+
+ m_file = new BufferedReader(geneAssociationFile);
+ m_readString = "(species=" + speciesName + ") (type=Molecular Function) (curator=GO)" + NL;
+ m_readInx = 0;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param cbuf DOCUMENT ME!
+ * @param off DOCUMENT ME!
+ * @param len DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @throws IOException DOCUMENT ME!
+ */
+ public final int read(final char[] cbuf, final int off, final int len)
+ throws IOException {
+ if (m_file == null)
+ throw new IOException("this stream is closed");
+
+ if (m_readString == null)
+ return -1;
+
+ final int returnThis;
+
+ if ((m_readString.length() - m_readInx) >= len) {
+ m_readString.getChars(m_readInx, m_readInx + len, cbuf, off);
+ returnThis = len;
+ m_readInx += len;
+ } else { // len is greater than the number of chars left in
+ // m_readString.
+ m_readString.getChars(m_readInx, m_readString.length(), cbuf, off);
+ returnThis = m_readString.length() - m_readInx;
+ m_readInx = m_readString.length();
+ }
+
+ if (m_readInx == m_readString.length())
+ readMore();
+
+ return returnThis;
+ }
+
+ private final void readMore() throws IOException {
+ while (true) {
+ String line;
+
+ while (true) // Read comments and possibly blank lines.
+ {
+ line = m_file.readLine();
+
+ if (line == null) { // End of underlying stream.
+ m_readString = null;
+
+ return;
+ }
+
+ line = line.trim();
+
+ if ((line.length() > 0) && !line.startsWith("!")) {
+ break;
+ }
+ }
+
+ // Now line contains a line of data.
+ int fromIndex = 0;
+
+ for (int i = 0; i < 2; i++) {
+ fromIndex = 1 + line.indexOf('\t', fromIndex);
+ }
+
+ final String canon = line.substring(fromIndex, line.indexOf('\t', fromIndex));
+
+ for (int i = 0; i < 2; i++) {
+ fromIndex = 1 + line.indexOf('\t', fromIndex);
+ }
+
+ final String goid = line.substring(fromIndex + 3, fromIndex + 10);
+
+ for (int i = 0; i < 4; i++) {
+ fromIndex = 1 + line.indexOf('\t', fromIndex);
+ }
+
+ String type = line.substring(fromIndex, fromIndex + 1);
+
+ if (!type.equals("P") && !type.equals("C") && !type.equals("F")) {
+ // Try to find one
+ type = (String) ontologyTypeMap.get("GO:" + goid);
+ }
+
+ if (type != null) {
+ if (type.equals("F")) { // Molecular Function.. We found one.
+ m_readString = canon + " = " + goid + NL;
+ m_readInx = 0;
+
+ break;
+ }
+ }
+ }
+ }
+
+ /**
+ * Closes the underlying gene_association file stream as well.
+ */
+ public final void close() throws IOException {
+ try {
+ m_file.close();
+ } finally {
+ m_file = null;
+ }
+ }
+}
diff --git a/corelibs/obo/src/main/java/cytoscape/cruft/obo/OboOntologyReader.java b/corelibs/obo/src/main/java/cytoscape/cruft/obo/OboOntologyReader.java
new file mode 100644
index 0000000..86e8a4f
--- /dev/null
+++ b/corelibs/obo/src/main/java/cytoscape/cruft/obo/OboOntologyReader.java
@@ -0,0 +1,188 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.cruft.obo;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.Reader;
+
+
+/**
+ * The purpose of this class is to convert a 'gene_ontology.obo' file
+ * to a crufty old 'go.onto' file that Cytoscape's BioDataServer understands.
+ * The parameter passed to the constructor is the 'gene_ontology.obo' file and
+ * the content read from this reader is the crufty old 'go.onto' file.<p>
+ * Please note that this code was not written with performance in mind.
+ * Therefore, evaluating this code will not give a good indication of the
+ * author's programming ability.
+ */
+public final class OboOntologyReader extends Reader {
+ private final String NL = System.getProperty("line.separator");
+ private BufferedReader m_obo;
+ private String m_readString;
+ private int m_readInx; // Index into a m_readString character.
+
+ /**
+ * Creates a new OboOntologyReader object.
+ *
+ * @param oboFile DOCUMENT ME!
+ */
+ public OboOntologyReader(final Reader oboFile) {
+ if (oboFile == null)
+ throw new NullPointerException("oboFile is null");
+
+ m_obo = new BufferedReader(oboFile);
+ m_readString = "(curator=GO) (type=all)" + NL;
+ m_readInx = 0;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param cbuf DOCUMENT ME!
+ * @param off DOCUMENT ME!
+ * @param len DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @throws IOException DOCUMENT ME!
+ */
+ public final int read(final char[] cbuf, final int off, final int len)
+ throws IOException {
+ if (m_obo == null)
+ throw new IOException("this stream is closed");
+
+ if (m_readString == null)
+ return -1;
+
+ final int returnThis;
+
+ if ((m_readString.length() - m_readInx) >= len) {
+ m_readString.getChars(m_readInx, m_readInx + len, cbuf, off);
+ returnThis = len;
+ m_readInx += len;
+ } else { // len is greater than the number of chars left in m_readString.
+ m_readString.getChars(m_readInx, m_readString.length(), cbuf, off);
+ returnThis = m_readString.length() - m_readInx;
+ m_readInx = m_readString.length();
+ }
+
+ if (m_readInx == m_readString.length())
+ readMore();
+
+ return returnThis;
+ }
+
+ /*
+ * The job of this method is to set m_readString and m_readInx.
+ */
+ private final void readMore() throws IOException {
+ while (true) // Read until line after '[Term]'.
+ {
+ final String line = m_obo.readLine();
+
+ if (line == null) { // End of underlying stream.
+ m_readString = null;
+
+ return;
+ }
+
+ final String trimmedLine = line.trim();
+
+ if (trimmedLine.equals("[Term]")) {
+ break;
+ }
+ }
+
+ String id = "";
+ String desc = "";
+ String isa = "";
+ String partof = "";
+
+ while (true) // Parse until blank line.
+ {
+ final String line = m_obo.readLine().trim();
+
+ if (line.length() == 0)
+ break;
+
+ final int colonInx = line.indexOf(':');
+ final String key = line.substring(0, colonInx).trim();
+ final String val = line.substring(colonInx + 1).trim();
+
+ if (key.equals("id")) {
+ // There's only one id.
+ id = val.substring(3); /* Chop away 'GO:'. */
+ } else if (key.equals("name")) {
+ // There's only one description.
+ desc = val;
+ } else if (key.equals("is_a")) {
+ // Multiple isa possible.
+ final String isaElement = val.substring(3, 10); // Chop 'GO:'.
+ isa = isa + isaElement + " ";
+ } else if (key.equals("relationship") && val.startsWith("part_of")) {
+ // Multiple partof possible.
+ final String partofElement = val.substring(11, 18); // 'part_of GO:'.
+ partof = partof + partofElement + " ";
+ }
+ }
+
+ m_readString = id + " = " + desc;
+
+ if (isa.length() > 0) {
+ m_readString = m_readString + " [isa: " + isa + "]";
+ }
+
+ if (partof.length() > 0) {
+ m_readString = m_readString + " [partof: " + partof + "]";
+ }
+
+ m_readString = m_readString + NL;
+ m_readInx = 0;
+ }
+
+ /**
+ * Closes the underlying obo file stream as well.
+ */
+ public final void close() throws IOException {
+ try {
+ m_obo.close();
+ } finally {
+ m_obo = null;
+ }
+ }
+}
diff --git a/corelibs/obo/src/main/java/cytoscape/cruft/obo/OboOntologyReader2.java b/corelibs/obo/src/main/java/cytoscape/cruft/obo/OboOntologyReader2.java
new file mode 100644
index 0000000..71aa7b6
--- /dev/null
+++ b/corelibs/obo/src/main/java/cytoscape/cruft/obo/OboOntologyReader2.java
@@ -0,0 +1,172 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.cruft.obo;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.Reader;
+
+
+/**
+ * The purpose of this class is to convert a 'gene_ontology.obo' file to a
+ * crufty old 'go.onto' file that Cytoscape's BioDataServer understands. The
+ * parameter passed to the constructor is the 'gene_ontology.obo' file and the
+ * content read from this reader is the crufty old 'go.onto' file.
+ * <p>
+ * Please note that this code was not written with performance in mind.
+ * Therefore, evaluating this code will not give a good indication of the
+ * author's programming ability.
+ */
+public final class OboOntologyReader2 extends Reader {
+ private final String NL = System.getProperty("line.separator");
+ private BufferedReader m_obo;
+ private String m_readString;
+ private int m_readInx; // Index into a m_readString character.
+
+ /**
+ * Creates a new OboOntologyReader2 object.
+ *
+ * @param oboFile DOCUMENT ME!
+ */
+ public OboOntologyReader2(final Reader oboFile) {
+ if (oboFile == null)
+ throw new NullPointerException("oboFile is null");
+
+ m_obo = new BufferedReader(oboFile);
+ m_readString = "(curator=GO) (type=all)" + NL;
+ m_readInx = 0;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param cbuf DOCUMENT ME!
+ * @param off DOCUMENT ME!
+ * @param len DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @throws IOException DOCUMENT ME!
+ */
+ public final int read(final char[] cbuf, final int off, final int len)
+ throws IOException {
+ if (m_obo == null)
+ throw new IOException("this stream is closed");
+
+ if (m_readString == null)
+ return -1;
+
+ final int returnThis;
+
+ if ((m_readString.length() - m_readInx) >= len) {
+ m_readString.getChars(m_readInx, m_readInx + len, cbuf, off);
+ returnThis = len;
+ m_readInx += len;
+ } else { // len is greater than the number of chars left in
+ // m_readString.
+ m_readString.getChars(m_readInx, m_readString.length(), cbuf, off);
+ returnThis = m_readString.length() - m_readInx;
+ m_readInx = m_readString.length();
+ }
+
+ if (m_readInx == m_readString.length())
+ readMore();
+
+ return returnThis;
+ }
+
+ /*
+ * The job of this method is to set m_readString and m_readInx.
+ */
+ private final void readMore() throws IOException {
+ while (true) // Read until line after '[Term]'.
+ {
+ final String line = m_obo.readLine();
+
+ if (line == null) { // End of underlying stream.
+ m_readString = null;
+
+ return;
+ }
+
+ final String trimmedLine = line.trim();
+
+ if (trimmedLine.equals("[Term]")) {
+ break;
+ }
+ }
+
+ String id = "";
+ String namespace = "";
+
+ while (true) // Parse until blank line.
+ {
+ final String line = m_obo.readLine().trim();
+
+ if (line.length() == 0)
+ break;
+
+ final int colonInx = line.indexOf(':');
+ final String key = line.substring(0, colonInx).trim();
+ final String val = line.substring(colonInx + 1).trim();
+
+ if (key.equals("id")) {
+ // There's only one id.
+ id = val;
+ } else if (key.equals("namespace")) {
+ // There's only one description.
+ namespace = val;
+ }
+ }
+
+ m_readString = id + "=" + namespace;
+
+ m_readString = m_readString + NL;
+ m_readInx = 0;
+ }
+
+ /**
+ * Closes the underlying obo file stream as well.
+ */
+ public final void close() throws IOException {
+ try {
+ m_obo.close();
+ } finally {
+ m_obo = null;
+ }
+ }
+}
diff --git a/corelibs/obo/src/main/java/cytoscape/cruft/obo/SynonymReader.java b/corelibs/obo/src/main/java/cytoscape/cruft/obo/SynonymReader.java
new file mode 100644
index 0000000..95a3589
--- /dev/null
+++ b/corelibs/obo/src/main/java/cytoscape/cruft/obo/SynonymReader.java
@@ -0,0 +1,177 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.cruft.obo;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.Reader;
+
+import java.util.HashMap;
+
+
+/**
+ * The purpose of this class is to convert a 'gene_association.*' file
+ * (for example 'gene_association.sgd') into a crufty old '*.syno' file that
+ * Cytoscape's BioDataServer understands.
+ * The parameter passed to the constructor is the 'gene_association.*' file
+ * and the content read from this reader is the crufty old '*.syno' file.<p>
+ * Please note that this code was not written with performance in mind.
+ * Therefore, evaluating this code will not give a good indication of the
+ * author's programming ability.
+ */
+public final class SynonymReader extends Reader {
+ private final String NL = System.getProperty("line.separator");
+ private final HashMap m_dupsFilter = new HashMap();
+ private BufferedReader m_file;
+ private String m_readString;
+ private int m_readInx; // Index into a m_readString character.
+
+ /**
+ * Creates a new SynonymReader object.
+ *
+ * @param speciesName DOCUMENT ME!
+ * @param geneAssociationFile DOCUMENT ME!
+ */
+ public SynonymReader(final String speciesName, final Reader geneAssociationFile) {
+ if (geneAssociationFile == null)
+ throw new NullPointerException("geneAssociationFile is null");
+
+ m_file = new BufferedReader(geneAssociationFile);
+ m_readString = speciesName + NL;
+ m_readInx = 0;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param cbuf DOCUMENT ME!
+ * @param off DOCUMENT ME!
+ * @param len DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @throws IOException DOCUMENT ME!
+ */
+ public final int read(final char[] cbuf, final int off, final int len)
+ throws IOException {
+ if (m_file == null)
+ throw new IOException("this stream is closed");
+
+ if (m_readString == null)
+ return -1;
+
+ final int returnThis;
+
+ if ((m_readString.length() - m_readInx) >= len) {
+ m_readString.getChars(m_readInx, m_readInx + len, cbuf, off);
+ returnThis = len;
+ m_readInx += len;
+ } else { // len is greater than the number of chars left in m_readString.
+ m_readString.getChars(m_readInx, m_readString.length(), cbuf, off);
+ returnThis = m_readString.length() - m_readInx;
+ m_readInx = m_readString.length();
+ }
+
+ if (m_readInx == m_readString.length())
+ readMore();
+
+ return returnThis;
+ }
+
+ private final void readMore() throws IOException {
+ while (true) {
+ String line;
+
+ while (true) // Read comments and possibly blank lines.
+ {
+ line = m_file.readLine();
+
+ if (line == null) { // End of underlying stream.
+ m_readString = null;
+
+ return;
+ }
+
+ line = line.trim();
+
+ if ((line.length() > 0) && !line.startsWith("!")) {
+ break;
+ }
+ }
+
+ // Now line contains a line of data.
+ int fromIndex = 0;
+
+ for (int i = 0; i < 2; i++) {
+ fromIndex = 1 + line.indexOf('\t', fromIndex);
+ }
+
+ final String canon = line.substring(fromIndex, line.indexOf('\t', fromIndex));
+
+ if (m_dupsFilter.get(canon) == null) { // This synonym new.
+
+ for (int i = 0; i < 8; i++) {
+ fromIndex = 1 + line.indexOf('\t', fromIndex);
+ }
+
+ final String delimitedList = line.substring(fromIndex, line.indexOf('\t', fromIndex));
+
+ if (delimitedList.length() > 0) {
+ m_readString = canon + " " + delimitedList.replace('|', ' ') + NL;
+
+ System.out.println("Syno: " + m_readString);
+
+ m_readInx = 0;
+ m_dupsFilter.put(canon, canon);
+
+ break;
+ }
+ }
+ }
+ }
+
+ /**
+ * Closes the underlying gene_association file stream as well.
+ */
+ public final void close() throws IOException {
+ try {
+ m_file.close();
+ } finally {
+ m_file = null;
+ }
+ }
+}
diff --git a/corelibs/obo/src/main/java/cytoscape/cruft/obo/test/BiologicalProcessAnnotationTester.java b/corelibs/obo/src/main/java/cytoscape/cruft/obo/test/BiologicalProcessAnnotationTester.java
new file mode 100644
index 0000000..592713a
--- /dev/null
+++ b/corelibs/obo/src/main/java/cytoscape/cruft/obo/test/BiologicalProcessAnnotationTester.java
@@ -0,0 +1,69 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.cruft.obo.test;
+
+import cytoscape.cruft.obo.BiologicalProcessAnnotationReader;
+
+import java.io.BufferedReader;
+import java.io.InputStreamReader;
+
+
+/**
+ *
+ */
+public class BiologicalProcessAnnotationTester {
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public static void main(String[] args) throws Exception {
+ final BufferedReader assocReader = new BufferedReader(new BiologicalProcessAnnotationReader(args[0],
+ new InputStreamReader(System.in)));
+
+ while (true) {
+ String line = assocReader.readLine();
+
+ if (line == null)
+ break;
+
+ System.out.println(line);
+ }
+ }
+}
diff --git a/corelibs/obo/src/main/java/cytoscape/cruft/obo/test/CellularComponentAnnotationTester.java b/corelibs/obo/src/main/java/cytoscape/cruft/obo/test/CellularComponentAnnotationTester.java
new file mode 100644
index 0000000..654762f
--- /dev/null
+++ b/corelibs/obo/src/main/java/cytoscape/cruft/obo/test/CellularComponentAnnotationTester.java
@@ -0,0 +1,69 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.cruft.obo.test;
+
+import cytoscape.cruft.obo.CellularComponentAnnotationReader;
+
+import java.io.BufferedReader;
+import java.io.InputStreamReader;
+
+
+/**
+ *
+ */
+public class CellularComponentAnnotationTester {
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public static void main(String[] args) throws Exception {
+ final BufferedReader assocReader = new BufferedReader(new CellularComponentAnnotationReader(args[0],
+ new InputStreamReader(System.in)));
+
+ while (true) {
+ String line = assocReader.readLine();
+
+ if (line == null)
+ break;
+
+ System.out.println(line);
+ }
+ }
+}
diff --git a/corelibs/obo/src/main/java/cytoscape/cruft/obo/test/DEPENDENCIES b/corelibs/obo/src/main/java/cytoscape/cruft/obo/test/DEPENDENCIES
new file mode 100644
index 0000000..0e31e0f
--- /dev/null
+++ b/corelibs/obo/src/main/java/cytoscape/cruft/obo/test/DEPENDENCIES
@@ -0,0 +1 @@
+cytoscape.cruft.obo
diff --git a/corelibs/obo/src/main/java/cytoscape/cruft/obo/test/MolecularFunctionAnnotationTester.java b/corelibs/obo/src/main/java/cytoscape/cruft/obo/test/MolecularFunctionAnnotationTester.java
new file mode 100644
index 0000000..75926c4
--- /dev/null
+++ b/corelibs/obo/src/main/java/cytoscape/cruft/obo/test/MolecularFunctionAnnotationTester.java
@@ -0,0 +1,69 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.cruft.obo.test;
+
+import cytoscape.cruft.obo.MolecularFunctionAnnotationReader;
+
+import java.io.BufferedReader;
+import java.io.InputStreamReader;
+
+
+/**
+ *
+ */
+public class MolecularFunctionAnnotationTester {
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public static void main(String[] args) throws Exception {
+ final BufferedReader assocReader = new BufferedReader(new MolecularFunctionAnnotationReader(args[0],
+ new InputStreamReader(System.in)));
+
+ while (true) {
+ String line = assocReader.readLine();
+
+ if (line == null)
+ break;
+
+ System.out.println(line);
+ }
+ }
+}
diff --git a/corelibs/obo/src/main/java/cytoscape/cruft/obo/test/OboOntologyTester.java b/corelibs/obo/src/main/java/cytoscape/cruft/obo/test/OboOntologyTester.java
new file mode 100644
index 0000000..87aa2e8
--- /dev/null
+++ b/corelibs/obo/src/main/java/cytoscape/cruft/obo/test/OboOntologyTester.java
@@ -0,0 +1,68 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.cruft.obo.test;
+
+import cytoscape.cruft.obo.OboOntologyReader;
+
+import java.io.BufferedReader;
+import java.io.InputStreamReader;
+
+
+/**
+ *
+ */
+public class OboOntologyTester {
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public static void main(String[] args) throws Exception {
+ final BufferedReader oboReader = new BufferedReader(new OboOntologyReader(new InputStreamReader(System.in)));
+
+ while (true) {
+ String line = oboReader.readLine();
+
+ if (line == null)
+ break;
+
+ System.out.println(line);
+ }
+ }
+}
diff --git a/corelibs/obo/src/main/java/cytoscape/cruft/obo/test/SynonymTester.java b/corelibs/obo/src/main/java/cytoscape/cruft/obo/test/SynonymTester.java
new file mode 100644
index 0000000..a984813
--- /dev/null
+++ b/corelibs/obo/src/main/java/cytoscape/cruft/obo/test/SynonymTester.java
@@ -0,0 +1,69 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.cruft.obo.test;
+
+import cytoscape.cruft.obo.SynonymReader;
+
+import java.io.BufferedReader;
+import java.io.InputStreamReader;
+
+
+/**
+ *
+ */
+public class SynonymTester {
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public static void main(String[] args) throws Exception {
+ final BufferedReader assocReader = new BufferedReader(new SynonymReader(args[0],
+ new InputStreamReader(System.in)));
+
+ while (true) {
+ String line = assocReader.readLine();
+
+ if (line == null)
+ break;
+
+ System.out.println(line);
+ }
+ }
+}
diff --git a/corelibs/phoebe.dnd/pom.xml b/corelibs/phoebe.dnd/pom.xml
new file mode 100644
index 0000000..39baf00
--- /dev/null
+++ b/corelibs/phoebe.dnd/pom.xml
@@ -0,0 +1,41 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>parent</artifactId>
+ <version>2.8.4-SNAPSHOT</version>
+ </parent>
+
+ <artifactId>phoebe-dnd</artifactId>
+ <packaging>jar</packaging>
+
+ <name>phoebe-dnd</name>
+
+ <!-- bootstrap for cytoscape dependencies, namely the parent POM snapshots -->
+ <repositories>
+ <repository>
+ <id>cytoscape_snapshots</id>
+ <snapshots>
+ <enabled>true</enabled>
+ </snapshots>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <name>Cytoscape Snapshots</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/</url>
+ </repository>
+ <repository>
+ <id>cytoscape_releases</id>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ <name>Cytoscape Releases</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/releases/</url>
+ </repository>
+ </repositories>
+
+</project>
+
diff --git a/corelibs/phoebe.dnd/src/main/java/phoebe/PhoebeCanvasDropEvent.java b/corelibs/phoebe.dnd/src/main/java/phoebe/PhoebeCanvasDropEvent.java
new file mode 100755
index 0000000..a3de3b7
--- /dev/null
+++ b/corelibs/phoebe.dnd/src/main/java/phoebe/PhoebeCanvasDropEvent.java
@@ -0,0 +1,54 @@
+/*
+ * Created on Jun 13, 2005
+ *
+ * extends AWTEvent, forwards the drop event and its location.
+ */
+package phoebe;
+
+import java.awt.*;
+import java.awt.datatransfer.Transferable;
+
+
+/**
+ *
+ * @author ajk
+ *
+ */
+
+/**
+ * forwards the drop event and its location
+ */
+public class PhoebeCanvasDropEvent extends AWTEvent {
+ private final static long serialVersionUID = 1213746928492377L;
+
+ Transferable transferable;
+ Point location;
+
+
+ /**
+ * constructor for PhoebeCanvasDropEvent
+ * @param source the source canvas of the event
+ * @param t the transferable created by the drop event
+ * @param location the location of the drop, in terms of canvas coordinates
+ */
+ public PhoebeCanvasDropEvent (PhoebeCanvasDroppable source, Transferable t, Point location)
+ {
+ super (source, -1); // from Graphic Java, p 303
+ this.transferable = t;
+ this.location = location;
+
+ }
+
+ /**
+ * @return Returns the location.
+ */
+ public Point getLocation() {
+ return location;
+ }
+ /**
+ * @return Returns the transferable.
+ */
+ public Transferable getTransferable() {
+ return transferable;
+ }
+}
diff --git a/corelibs/phoebe.dnd/src/main/java/phoebe/PhoebeCanvasDropListener.java b/corelibs/phoebe.dnd/src/main/java/phoebe/PhoebeCanvasDropListener.java
new file mode 100755
index 0000000..e16cbfe
--- /dev/null
+++ b/corelibs/phoebe.dnd/src/main/java/phoebe/PhoebeCanvasDropListener.java
@@ -0,0 +1,27 @@
+/*
+ * Created on Jun 13, 2005
+ *
+ * an interface for responding to PhoebeCanvasDropEvents.
+ */
+package phoebe;
+
+import java.util.EventListener;
+
+/**
+ * @author Allan Kuchinsky
+ *
+ */
+
+/**
+ * an interface for responding to PhoebeCanvasDropEvents.
+ */
+public interface PhoebeCanvasDropListener extends EventListener {
+
+
+ /**
+ * method for responding to a drop
+ * @param event the PhoebeCanvasDropEvent
+ */
+ void itemDropped(PhoebeCanvasDropEvent event);
+
+}
diff --git a/corelibs/phoebe.dnd/src/main/java/phoebe/PhoebeCanvasDroppable.java b/corelibs/phoebe.dnd/src/main/java/phoebe/PhoebeCanvasDroppable.java
new file mode 100755
index 0000000..e8c7839
--- /dev/null
+++ b/corelibs/phoebe.dnd/src/main/java/phoebe/PhoebeCanvasDroppable.java
@@ -0,0 +1,32 @@
+/*
+ * Created on Jun 13, 2005
+ *
+ * interface for maintaining listeners for PhoebeCanvasDropEvents.
+ */
+package phoebe;
+
+/**
+ * @author Allan Kuchinsky
+ *
+ *
+ */
+
+ /**
+ * interface for maintaining listeners for PhoebeCanvasDropEvents.
+ */
+public interface PhoebeCanvasDroppable {
+
+ /**
+ *
+ * adds a PhoebeCanvasDropListener to the listener store
+ * @param l the PhoebeCanvasDropListener to be added
+ */
+ public void addPhoebeCanvasDropListener (PhoebeCanvasDropListener l);
+
+ /**
+ * removes a PhoebeCanvasDropListener from the listener store
+ * @param l the PhoebeCanvasDropListener to be deleted
+ */
+ public void removePhoebeCanvasDropListener (PhoebeCanvasDropListener l);
+
+}
diff --git a/corelibs/pom.xml b/corelibs/pom.xml
new file mode 100644
index 0000000..63d08d6
--- /dev/null
+++ b/corelibs/pom.xml
@@ -0,0 +1,63 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>cytoscape</groupId>
+ <artifactId>parent</artifactId>
+ <version>2.8.4-SNAPSHOT</version>
+ </parent>
+
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>parent</artifactId>
+ <packaging>pom</packaging>
+ <name>Cytoscape Core Libraries Parent POM</name>
+
+ <modules>
+ <module>commons-cli-1.x-cytocape-custom</module>
+ <module>equations</module>
+ <module>util.intr</module>
+ <module>geom.spacial</module>
+ <module>geom.rtree</module>
+ <module>giny</module>
+ <module>graph.fixed</module>
+ <module>graph.dynamic</module>
+ <module>nerius.math.xform</module>
+ <module>obo</module>
+ <module>phoebe.dnd</module>
+ <module>render.immed</module>
+ <module>render.export</module>
+ <module>render.stateful</module>
+ <module>task</module>
+ <module>undo.support</module>
+ <module>fing</module>
+ <module>ding</module>
+ <module>docs</module>
+ </modules>
+
+ <!-- bootstrap for cytoscape dependencies, namely the parent POM snapshots -->
+ <repositories>
+ <repository>
+ <id>cytoscape_snapshots</id>
+ <snapshots>
+ <enabled>true</enabled>
+ </snapshots>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <name>Cytoscape Snapshots</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/</url>
+ </repository>
+ <repository>
+ <id>cytoscape_releases</id>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ <name>Cytoscape Releases</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/releases/</url>
+ </repository>
+ </repositories>
+
+</project>
+
diff --git a/corelibs/render.export/pom.xml b/corelibs/render.export/pom.xml
new file mode 100644
index 0000000..283102d
--- /dev/null
+++ b/corelibs/render.export/pom.xml
@@ -0,0 +1,41 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>parent</artifactId>
+ <version>2.8.4-SNAPSHOT</version>
+ </parent>
+
+ <artifactId>render-export</artifactId>
+ <packaging>jar</packaging>
+
+ <name>render-export</name>
+
+ <!-- bootstrap for cytoscape dependencies, namely the parent POM snapshots -->
+ <repositories>
+ <repository>
+ <id>cytoscape_snapshots</id>
+ <snapshots>
+ <enabled>true</enabled>
+ </snapshots>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <name>Cytoscape Snapshots</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/</url>
+ </repository>
+ <repository>
+ <id>cytoscape_releases</id>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ <name>Cytoscape Releases</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/releases/</url>
+ </repository>
+ </repositories>
+
+</project>
+
diff --git a/corelibs/render.export/src/main/java/cytoscape/render/export/DEPENDENCIES b/corelibs/render.export/src/main/java/cytoscape/render/export/DEPENDENCIES
new file mode 100644
index 0000000..e69de29
diff --git a/corelibs/render.export/src/main/java/cytoscape/render/export/ImageImposter.java b/corelibs/render.export/src/main/java/cytoscape/render/export/ImageImposter.java
new file mode 100644
index 0000000..dd53e2f
--- /dev/null
+++ b/corelibs/render.export/src/main/java/cytoscape/render/export/ImageImposter.java
@@ -0,0 +1,120 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.render.export;
+
+import java.awt.Graphics;
+import java.awt.Image;
+import java.awt.image.ImageObserver;
+import java.awt.image.ImageProducer;
+
+
+/**
+ * The primary purpose of this class is to enable an arbitrary Graphics
+ * object to receive rendering calls from a
+ * cytoscape.render.immed.GraphGraphics instance. This, in turn, can be used
+ * to render a graph directly to a scalar vector graphic.
+ */
+public final class ImageImposter extends Image {
+ private final Graphics m_graphics;
+ private final int m_width;
+ private final int m_height;
+
+ /**
+ * The Graphics object that is passed into this constructor is not
+ * modified in any way, ever. The only direct calls made on this object
+ * are graphics.create(), which is used in the getGraphics() method
+ * of this class.
+ */
+ public ImageImposter(final Graphics graphics, final int width, final int height) {
+ if (graphics == null)
+ throw new NullPointerException("graphics is null");
+
+ if (width <= 0)
+ throw new IllegalArgumentException("width must be positive");
+
+ if (height <= 0)
+ throw new IllegalArgumentException("height must be positive");
+
+ m_graphics = graphics;
+ m_width = width;
+ m_height = height;
+ }
+
+ /**
+ * Simply returns the width that was passed into the constructor.
+ */
+ public final int getWidth(final ImageObserver observer) {
+ return m_width;
+ }
+
+ /**
+ * Simply returns the height that was passed into the constructor.
+ */
+ public final int getHeight(final ImageObserver observer) {
+ return m_height;
+ }
+
+ /**
+ * This method simply throws an UnsupportedOperationException.
+ */
+ public final ImageProducer getSource() {
+ throw new UnsupportedOperationException("this type of image does not store pixel data");
+ }
+
+ /**
+ * Returns a copy of the Graphics object that was passed into the
+ * constructor. The exact value returned is graphics.create() where
+ * graphics is the Graphics object passed to the constructor.
+ */
+ public final Graphics getGraphics() {
+ return m_graphics.create();
+ }
+
+ /**
+ * No properties are defined on this image, ever; this returns
+ * UndefinedProperty, always.
+ */
+ public final Object getProperty(final String name, final ImageObserver observer) {
+ return UndefinedProperty;
+ }
+
+ /**
+ * This is a no-op.
+ */
+ public final void flush() {
+ }
+}
diff --git a/corelibs/render.immed/pom.xml b/corelibs/render.immed/pom.xml
new file mode 100644
index 0000000..785f8f7
--- /dev/null
+++ b/corelibs/render.immed/pom.xml
@@ -0,0 +1,50 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>parent</artifactId>
+ <version>2.8.4-SNAPSHOT</version>
+ </parent>
+
+ <artifactId>render-immed</artifactId>
+ <packaging>jar</packaging>
+
+ <name>render-immed</name>
+
+ <!-- bootstrap for cytoscape dependencies, namely the parent POM snapshots -->
+ <repositories>
+ <repository>
+ <id>cytoscape_snapshots</id>
+ <snapshots>
+ <enabled>true</enabled>
+ </snapshots>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <name>Cytoscape Snapshots</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/</url>
+ </repository>
+ <repository>
+ <id>cytoscape_releases</id>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ <name>Cytoscape Releases</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/releases/</url>
+ </repository>
+ </repositories>
+
+ <dependencies>
+ <dependency>
+ <groupId>org.apache.commons</groupId>
+ <artifactId>commons-math</artifactId>
+ <version>2.1</version>
+ <scope>test</scope>
+ </dependency>
+ </dependencies>
+
+</project>
+
diff --git a/corelibs/render.immed/src/main/java/cytoscape/render/immed/EdgeAnchors.java b/corelibs/render.immed/src/main/java/cytoscape/render/immed/EdgeAnchors.java
new file mode 100644
index 0000000..1f1e176
--- /dev/null
+++ b/corelibs/render.immed/src/main/java/cytoscape/render/immed/EdgeAnchors.java
@@ -0,0 +1,63 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.render.immed;
+
+
+/**
+ * Specifies edge anchor points to use when rendering edges in full detail
+ * mode.
+ */
+public interface EdgeAnchors {
+ /**
+ * Returns the number of edge anchors.
+ */
+ public int numAnchors();
+
+ /**
+ * Writes an edge anchor point into the array provided, at offset
+ * specified. The information written into the supplied anchorArr parameter
+ * consists of the following:
+ * <blockquote><table border="1" cellpadding="5" cellspacing="0">
+ * <tr> <th>array index</th> <th>information written</th> </tr>
+ * <tr> <td>offset</td> <td>X coordinate of anchor</td> </tr>
+ * <tr> <td>offset+1</td> <td>Y coordinate of anchor</td> </tr>
+ * </table></blockquote>
+ * @exception IndexOutOfBoundsException if anchorIndex is not in the
+ * range [0, numAnchors()-1].
+ */
+ public void getAnchor(int anchorIndex, float[] anchorArr, int offset);
+}
diff --git a/corelibs/render.immed/src/main/java/cytoscape/render/immed/GraphGraphics.java b/corelibs/render.immed/src/main/java/cytoscape/render/immed/GraphGraphics.java
new file mode 100644
index 0000000..5cfadc8
--- /dev/null
+++ b/corelibs/render.immed/src/main/java/cytoscape/render/immed/GraphGraphics.java
@@ -0,0 +1,2055 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.render.immed;
+
+import java.awt.AlphaComposite;
+import java.awt.BasicStroke;
+import java.awt.Color;
+import java.awt.Composite;
+import java.awt.EventQueue;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Graphics2D;
+import java.awt.Image;
+import java.awt.Paint;
+import java.awt.RenderingHints;
+import java.awt.Shape;
+import java.awt.Stroke;
+import java.awt.TexturePaint;
+import java.awt.font.FontRenderContext;
+import java.awt.font.GlyphVector;
+import java.awt.geom.AffineTransform;
+import java.awt.geom.Arc2D;
+import java.awt.geom.Ellipse2D;
+import java.awt.geom.GeneralPath;
+import java.awt.geom.Line2D;
+import java.awt.geom.Rectangle2D;
+import java.awt.image.BufferedImage;
+import java.util.HashMap;
+import java.util.Map;
+
+import cytoscape.render.immed.arrow.Arrow;
+import cytoscape.render.immed.arrow.ArrowheadArrow;
+import cytoscape.render.immed.arrow.DeltaArrow;
+import cytoscape.render.immed.arrow.DiamondArrow;
+import cytoscape.render.immed.arrow.DiscArrow;
+import cytoscape.render.immed.arrow.HalfBottomArrow;
+import cytoscape.render.immed.arrow.HalfTopArrow;
+import cytoscape.render.immed.arrow.NoArrow;
+import cytoscape.render.immed.arrow.TeeArrow;
+import cytoscape.render.immed.nodeshape.DiamondNodeShape;
+import cytoscape.render.immed.nodeshape.EllipseNodeShape;
+import cytoscape.render.immed.nodeshape.HexagonNodeShape;
+import cytoscape.render.immed.nodeshape.LegacyCustomNodeShape;
+import cytoscape.render.immed.nodeshape.NodeShape;
+import cytoscape.render.immed.nodeshape.OctagonNodeShape;
+import cytoscape.render.immed.nodeshape.ParallelogramNodeShape;
+import cytoscape.render.immed.nodeshape.RectangleNodeShape;
+import cytoscape.render.immed.nodeshape.RoundedRectangleNodeShape;
+import cytoscape.render.immed.nodeshape.TriangleNodeShape;
+import cytoscape.render.immed.nodeshape.VeeNodeShape;
+
+/**
+ * The purpose of this class is to make the proper calls on a Graphics2D object
+ * to efficiently render nodes, labels, and edges. This is procedural
+ * programming at its finest [sarcasm].
+ * <p>
+ * This class deals with two coordinate systems: an image coordinate system and
+ * a node coordinate system. The programmer who uses this API will be dealing
+ * mostly with the node coordinate system, especially when rendering individual
+ * nodes and edges. The clear() method specifies the mapping from the node
+ * coordinate system to the image coordinate system. The two coordinate systems
+ * do have the same orientations: increasing X values point to the right and
+ * increasing Y values point to the bottom. The image coordinate system dictates
+ * that (0,0) is the upper left corner of the image and that each unit
+ * represents a pixel width (or height). if (m_debug) { if
+ * (!EventQueue.isDispatchThread()) throw new IllegalStateException( "calling
+ * thread is not AWT event dispatcher");
+ *
+ * if (!(xMin < xMax)) throw new IllegalArgumentException("xMin not less than
+ * xMax");
+ *
+ * if (!(yMin < yMax)) throw new IllegalArgumentException("yMin not less than
+ * yMax");
+ *
+ * if (nodeShape == SHAPE_ROUNDED_RECTANGLE) { final double width = ((double)
+ * xMax) - xMin; final double height = ((double) yMax) - yMin;
+ *
+ * if (!(Math.max(width, height) < (2.0d * Math.min(width, height)))) throw new
+ * IllegalArgumentException( "rounded rectangle does not meet cotextnstraint " +
+ * "max(width, height) < 2 * min(width, height)"); } }
+ * <p>
+ * NOTE: Every method on an instance of this class needs to be called by the AWT
+ * event dispatching thread save the constructor. However, checks for this are
+ * made only if debug is set to true (see constructur). In fact, in certain
+ * situations [such as rendering to a non-image such as a vector graphic] it may
+ * make sense to never call any of the methods from the AWT event dispatching
+ * thread.
+ */
+public final class GraphGraphics {
+
+ /**
+ * Node shape constants
+ */
+ public static final byte SHAPE_RECTANGLE = 0;
+ public static final byte SHAPE_DIAMOND = 1;
+ public static final byte SHAPE_ELLIPSE = 2;
+ public static final byte SHAPE_HEXAGON = 3;
+ public static final byte SHAPE_OCTAGON = 4;
+ public static final byte SHAPE_PARALLELOGRAM = 5;
+ public static final byte SHAPE_ROUNDED_RECTANGLE = 6;
+ public static final byte SHAPE_TRIANGLE = 7;
+ public static final byte SHAPE_VEE = 8;
+
+ // package scoped for unit testing
+ static final byte s_last_shape = SHAPE_VEE;
+
+ private static final Map<Byte,NodeShape> nodeShapes;
+
+ /**
+ * This value is currently 100.
+ */
+ public static final int CUSTOM_SHAPE_MAX_VERTICES = 100;
+
+ //
+ // Arrow shape constants.
+ //
+ public static final byte ARROW_NONE = -1;
+ public static final byte ARROW_DELTA = -2;
+ public static final byte ARROW_DIAMOND = -3;
+ public static final byte ARROW_DISC = -4;
+ public static final byte ARROW_TEE = -5;
+ public static final byte ARROW_HALF_TOP = -6;
+ public static final byte ARROW_HALF_BOTTOM = -7;
+ public static final byte ARROW_ARROWHEAD = -8;
+
+ // The way to access all Arrow objects.
+ private static final Map<Byte,Arrow> arrows;
+
+ /**
+ * This value is currently 64.
+ */
+ public static final int MAX_EDGE_ANCHORS = 64;
+
+ /*
+ * A constant for controlling how cubic Bezier curves are drawn; This
+ * particular constant results in elliptical-looking curves.
+ */
+ private static final double CURVE_ELLIPTICAL = (4.0d * (Math.sqrt(2.0d) - 1.0d)) / 3.0d;
+
+ /*
+ * Added by kono: This is for returning shapes
+ */
+ private static final GraphGraphics dummyGraphics;
+
+ private static final Map<Float,Stroke> borderStrokes = new HashMap<Float,Stroke>();
+
+ static {
+ dummyGraphics = new GraphGraphics(null, false);
+
+ nodeShapes = new HashMap<Byte,NodeShape>();
+
+ nodeShapes.put(SHAPE_RECTANGLE, new RectangleNodeShape());
+ nodeShapes.put(SHAPE_ELLIPSE, new EllipseNodeShape());
+ nodeShapes.put(SHAPE_ROUNDED_RECTANGLE, new RoundedRectangleNodeShape());
+ nodeShapes.put(SHAPE_DIAMOND, new DiamondNodeShape());
+ nodeShapes.put(SHAPE_HEXAGON, new HexagonNodeShape());
+ nodeShapes.put(SHAPE_OCTAGON, new OctagonNodeShape());
+ nodeShapes.put(SHAPE_PARALLELOGRAM, new ParallelogramNodeShape());
+ nodeShapes.put(SHAPE_TRIANGLE, new TriangleNodeShape());
+ nodeShapes.put(SHAPE_VEE, new VeeNodeShape());
+
+ arrows = new HashMap<Byte,Arrow>();
+
+ arrows.put(ARROW_NONE, new NoArrow() );
+ arrows.put(ARROW_DELTA, new DeltaArrow() );
+ arrows.put(ARROW_DISC, new DiscArrow() );
+ arrows.put(ARROW_DIAMOND, new DiamondArrow() );
+ arrows.put(ARROW_TEE, new TeeArrow() );
+ arrows.put(ARROW_ARROWHEAD, new ArrowheadArrow() );
+ arrows.put(ARROW_HALF_TOP, new HalfTopArrow() );
+ arrows.put(ARROW_HALF_BOTTOM, new HalfBottomArrow() );
+ }
+
+ private static final float DEF_SHAPE_SIZE = 32;
+
+ /**
+ * The image that was passed into the constructor.
+ */
+ public final Image image;
+ private final boolean m_debug;
+ private final AffineTransform m_currXform = new AffineTransform();
+ private final AffineTransform m_currNativeXform = new AffineTransform();
+ private final AffineTransform m_xformUtil = new AffineTransform();
+ private final Arc2D.Double m_arc2d = new Arc2D.Double();
+ private final Ellipse2D.Double m_ellp2d = new Ellipse2D.Double();
+ private final GeneralPath m_path2d = new GeneralPath();
+ private final GeneralPath m_path2dPrime = new GeneralPath();
+ private final Line2D.Double m_line2d = new Line2D.Double();
+ private final double[] m_ptsBuff = new double[4];
+
+ // package scoped for unit testing
+ final EdgeAnchors m_noAnchors = new EdgeAnchors() {
+ public final int numAnchors() { return 0; }
+ public final void getAnchor(final int inx, final float[] arr, final int off) { }
+ };
+
+ private final double[] m_edgePtsBuff = new double[(MAX_EDGE_ANCHORS + 1) * 6];
+ private int m_edgePtsCount; // Number of points stored in m_edgePtsBuff.
+ private Graphics2D m_g2d;
+ private Graphics2D m_gMinimal; // We use mostly java.awt.Graphics methods.
+ private boolean m_cleared;
+
+ // This member variable only to be used from within defineCustomNodeShape().
+ private byte m_lastCustomShapeType = s_last_shape;
+
+ // This is only used by computeCubicPolyEdgePath().
+ private final float[] m_floatBuff = new float[2];
+
+ // This member variable shall only be used from within drawTextFull().
+ private char[] m_charBuff = new char[20];
+ private final FontRenderContext m_fontRenderContextFull = new FontRenderContext(null,true,true);
+
+ /**
+ * All rendering operations will be performed on the specified image. No
+ * rendering operations are performed as a result of calling this
+ * constructor. It is safe to call this constructor from any thread.
+ * <p>
+ * The image argument passed to this constructor must support at least three
+ * methods: getGraphics(), getWidth(ImageObserver), and
+ * getHeight(ImageObserver). The image.getGraphics() method must return an
+ * instance of java.awt.Graphics2D. The hypothetical method calls
+ * image.getWidth(null) and image.getHeight(null) must return the
+ * corresponding dimension immediately.
+ * <p>
+ * Notice that it is not possible to resize the image area with this API.
+ * This is not a problem; instances of this class are very lightweight and
+ * are for the most part stateless; simply instantiate a new GraphGraphics
+ * when the image area changes.
+ *
+ * @param image
+ * an off-screen image; passing an image gotten from a call to
+ * java.awt.Component.createImage(int, int) works well, although
+ * experience shows that for full support of non-opaque colors,
+ * java.awt.image.BufferedImage should be used instead.
+ * @param debug
+ * if this is true, extra [and time-consuming] error checking
+ * will take place in each method call; it is recommended to have
+ * this value set to true during the testing phase; set it to
+ * false once you are sure that code does not mis-use this
+ * module.
+ */
+ public GraphGraphics(final Image image, final boolean debug) {
+ this.image = image;
+ m_debug = debug;
+ m_path2dPrime.setWindingRule(GeneralPath.WIND_EVEN_ODD);
+ m_cleared = false;
+ }
+
+ /**
+ * Clears image area with background paint specified and sets an appropriate
+ * transformation of coordinate systems. See the class description for a
+ * definition of the two coordinate systems: the node coordinate system and
+ * the image coordinate system.
+ * <p>
+ * The background paint is not blended with colors that may already be on
+ * the underlying image; if a translucent color is used in the background
+ * paint, the underlying image itself becomes translucent.
+ * <p>
+ * It is mandatory to call this method before making the first rendering
+ * call.
+ *
+ * @param bgPaint
+ * paint to use when clearing the image before painting a new
+ * frame; translucency is honored, provided that the underlying
+ * image supports it.
+ * @param xCenter
+ * the X component of the translation transform for the frame
+ * about to be rendered; a node whose center is at the X
+ * coordinate xCenter will be rendered exactly in the middle of
+ * the image going across; increasing X values (in the node
+ * coordinate system) result in movement towards the right on the
+ * image.
+ * @param yCenter
+ * the Y component of the translation transform for the frame
+ * about to be rendered; a node whose center is at the Y
+ * coordinate yCenter will be rendered exactly in the middle of
+ * the image going top to bottom; increasing Y values (in the
+ * node coordinate system) result in movement towards the bottom
+ * on the image.
+ * @param scaleFactor
+ * the scaling that is to take place when rendering; a distance
+ * of 1 in node coordinates translates to a distance of
+ * scaleFactor in the image coordinate system (usually one unit
+ * in the image coordinate system equates to one pixel width).
+ * @exception IllegalArgumentException
+ * if scaleFactor is not positive.
+ */
+ public final void clear(final Paint bgPaint, final double xCenter,
+ final double yCenter, final double scaleFactor) {
+ if (m_debug) {
+ checkDispatchThread();
+
+ if (!(scaleFactor > 0.0d)) {
+ throw new IllegalArgumentException(
+ "scaleFactor is not positive");
+ }
+ }
+
+ if (m_gMinimal != null) {
+ m_gMinimal.dispose();
+ m_gMinimal = null;
+ }
+
+ if (m_g2d != null) {
+ m_g2d.dispose();
+ }
+
+ m_g2d = (Graphics2D) image.getGraphics();
+
+ final Composite origComposite = m_g2d.getComposite();
+ m_g2d.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC));
+ m_g2d.setPaint(bgPaint);
+ m_g2d.fillRect(0, 0, image.getWidth(null), image.getHeight(null));
+ m_g2d.setComposite(origComposite);
+
+ // For detailed view, render high quality image as much as possible.
+
+ // Antialiasing is ON
+ m_g2d.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+ RenderingHints.VALUE_ANTIALIAS_ON);
+
+ // Rendering quality is HIGH.
+ m_g2d.setRenderingHint(RenderingHints.KEY_RENDERING,
+ RenderingHints.VALUE_RENDER_QUALITY);
+
+ // High quality alpha blending is ON.
+ m_g2d.setRenderingHint(RenderingHints.KEY_ALPHA_INTERPOLATION,
+ RenderingHints.VALUE_ALPHA_INTERPOLATION_QUALITY);
+
+ // High quality color rendering is ON.
+ m_g2d.setRenderingHint(RenderingHints.KEY_COLOR_RENDERING,
+ RenderingHints.VALUE_COLOR_RENDER_QUALITY);
+
+ m_g2d.setRenderingHint(RenderingHints.KEY_DITHERING,
+ RenderingHints.VALUE_DITHER_ENABLE);
+
+ m_g2d.setRenderingHint(RenderingHints.KEY_INTERPOLATION,
+ RenderingHints.VALUE_INTERPOLATION_BICUBIC);
+
+ // Text antialiasing is ON.
+ m_g2d.setRenderingHint(RenderingHints.KEY_TEXT_ANTIALIASING,
+ RenderingHints.VALUE_TEXT_ANTIALIAS_ON);
+ m_g2d.setRenderingHint(RenderingHints.KEY_FRACTIONALMETRICS,
+ RenderingHints.VALUE_FRACTIONALMETRICS_ON);
+ m_g2d.setRenderingHint(RenderingHints.KEY_STROKE_CONTROL,
+ RenderingHints.VALUE_STROKE_PURE);
+
+ m_g2d.setStroke(new BasicStroke(0.0f, BasicStroke.CAP_ROUND, BasicStroke.JOIN_ROUND, 10.0f));
+
+ m_currXform.setToTranslation(0.5d * image.getWidth(null), 0.5d * image
+ .getHeight(null));
+ m_currXform.scale(scaleFactor, scaleFactor);
+ m_currXform.translate(-xCenter, -yCenter);
+ m_g2d.transform(m_currXform);
+ m_currNativeXform.setTransform(m_g2d.getTransform());
+ m_cleared = true;
+ }
+
+ /**
+ * Uses the current transform to map the specified image coordinates to node
+ * coordinates. The transform used is defined by the last call to clear().
+ * It does not make sense to call this method if clear() has not been called
+ * at least once previously, and this method will cause errors in this case.
+ *
+ * @param coords
+ * an array of length [at least] two which acts both as the input
+ * and as the output of this method; coords[0] is the input X
+ * coordinate in the image coordinate system and is written as
+ * the X coordinate in the node coordinate system by this method;
+ * coords[1] is the input Y coordinate in the image coordinate
+ * system and is written as the Y coordinate in the node
+ * coordinate system by this method; the exact transform which
+ * takes place is defined by the previous call to the clear()
+ * method.
+ */
+ public final void xformImageToNodeCoords(final double[] coords) {
+ if (m_debug) {
+ checkDispatchThread();
+ checkCleared();
+ }
+
+ try {
+ m_currXform.inverseTransform(coords, 0, coords, 0, 1);
+ } catch (java.awt.geom.NoninvertibleTransformException e) {
+ throw new RuntimeException("noninvertible matrix - cannot happen");
+ }
+ }
+
+ /**
+ * Called to get the current AffineTransform Matrix.
+ *
+ * @return AffineTransform
+ */
+ public final AffineTransform getTransform() {
+ return m_currXform;
+ }
+
+ /**
+ * This is the method that will render a node very quickly. The node shape
+ * used by this method is SHAPE_RECTANGLE. Translucent colors are not
+ * supported by the low detail rendering methods.
+ * <p>
+ * xMin, yMin, xMax, and yMax specify the extents of the node in the node
+ * coordinate space, not the image coordinate space. Thus, these values will
+ * likely not change from frame to frame, as zoom and pan operations are
+ * performed.
+ * <p>
+ * This method will not work unless clear() has been called at least once
+ * previously.
+ *
+ * @param xMin
+ * an extent of the node to draw, in node coordinate space.
+ * @param yMin
+ * an extent of the node to draw, in node coordinate space.
+ * @param xMax
+ * an extent of the node to draw, in node coordinate space.
+ * @param yMax
+ * an extent of the node to draw, in node coordinate space.
+ * @param fillColor
+ * the [fully opaque] color to use when drawing the node.
+ * @exception IllegalArgumentException
+ * if xMin is not less than xMax, if yMin is not less than
+ * yMax, or if fillColor is not opaque.
+ */
+ public final void drawNodeLow(final float xMin, final float yMin,
+ final float xMax, final float yMax, final Color fillColor) {
+ if (m_debug) {
+ checkDispatchThread();
+ checkCleared();
+ checkOrder(xMin,xMax,"x");
+ checkOrder(yMin,yMax,"y");
+
+ if (fillColor.getAlpha() != 255) {
+ throw new IllegalArgumentException("fillColor is not opaque");
+ }
+ }
+
+ if (m_gMinimal == null) {
+ makeMinimalGraphics();
+ }
+
+ // I'm transforming points manually because the resulting underlying
+ // graphics pipeline used is much faster.
+ m_ptsBuff[0] = xMin;
+ m_ptsBuff[1] = yMin;
+ m_ptsBuff[2] = xMax;
+ m_ptsBuff[3] = yMax;
+ m_currXform.transform(m_ptsBuff, 0, m_ptsBuff, 0, 2);
+
+ // Here, double values outside of the range of ints will be cast to
+ // the nearest int without overflow.
+ final int xNot = (int) m_ptsBuff[0];
+ final int yNot = (int) m_ptsBuff[1];
+ final int xOne = (int) m_ptsBuff[2];
+ final int yOne = (int) m_ptsBuff[3];
+ m_gMinimal.setColor(fillColor);
+ m_gMinimal.fillRect(xNot, yNot, Math.max(1, xOne - xNot), // Overflow will
+ Math.max(1, yOne - yNot)); // be problem.
+ }
+
+ /**
+ * Sets m_gMinimal.
+ */
+ private final void makeMinimalGraphics() {
+ m_gMinimal = (Graphics2D) image.getGraphics();
+ m_gMinimal.setRenderingHint(RenderingHints.KEY_RENDERING,
+ RenderingHints.VALUE_RENDER_SPEED);
+ }
+
+ /**
+ * Draws a node with medium to high detail, depending on parameters
+ * specified. The xMin, yMin, xMax, and yMax parameters specify the extents
+ * of the node shape (in the node coordinate system), including the border
+ * width. That is, the drawn border won't extend beyond the extents
+ * specified.
+ * <p>
+ * There is an imposed constraint on borderWidth which, using the
+ * implemented algorithms, prevents strange-looking borders. The constraint
+ * is that borderWidth may not exceed the minimum of the node width and node
+ * height divided by six. In addition, for custom node shapes, this
+ * requirement may be more constrained, depending on the kinks in the custom
+ * node shape.
+ * <p>
+ * There is a constraint that only applies to SHAPE_ROUNDED_RECTANGLE which
+ * imposes that the maximum of the width and height be strictly less than
+ * twice the minimum of the width and height of the node.
+ * <p>
+ * This method will not work unless clear() has been called at least once
+ * previously.
+ *
+ * @param nodeShape
+ * the shape of the node to draw (one of the SHAPE_* constants or
+ * a custom node shape).
+ * @param xMin
+ * an extent of the node shape to draw, in node coordinate space;
+ * the drawn shape will theoretically contain a point that lies
+ * on this X coordinate.
+ * @param yMin
+ * an extent of the node shape to draw, in node coordinate space;
+ * the drawn shape will theoretically contain a point that lies
+ * on this Y coordinate.
+ * @param xMax
+ * an extent of the node shape to draw, in node coordinate space;
+ * the drawn shape will theoretically contain a point that lies
+ * on this X coordinate.
+ * @param yMax
+ * an extent of the node shape to draw, in node coordinate space;
+ * the drawn shape will theoretically contain a point that lies
+ * on this Y coordinate.
+ * @param fillPaint
+ * the paint to use when drawing the node area minus the border
+ * (the "interior" of the node).
+ * @param borderWidth
+ * the border width, in node coordinate space; if this value is
+ * zero, the rendering engine skips over the process of rendering
+ * the border, which gives a significant performance boost.
+ * @param borderPaint
+ * if borderWidth is not zero, this paint is used for rendering
+ * the node border; otherwise, this parameter is ignored (and may
+ * be null).
+ * @exception IllegalArgumentException
+ * if xMin is not less than xMax or if yMin is not less than
+ * yMax, if borderWidth is negative or is greater than
+ * Math.min(xMax - xMin, yMax - yMin) / 6 (for custom node
+ * shapes borderWidth may be even more limited, depending on
+ * the specific shape), if nodeShape is
+ * SHAPE_ROUNDED_RECTANGLE and the condition max(width,
+ * height) < 2 * min(width, height) does not hold, or if
+ * nodeShape is neither one of the SHAPE_* constants nor a
+ * previously defined custom node shape.
+ */
+ public final void drawNodeFull(final byte nodeShape, final float xMin,
+ final float yMin, final float xMax, final float yMax,
+ final Paint fillPaint, final float borderWidth,
+ final Paint borderPaint) {
+ if (m_debug) {
+ checkDispatchThread();
+ checkCleared();
+ checkOrder(xMin,xMax,"x");
+ checkOrder(yMin,yMax,"y");
+
+ if (!(borderWidth >= 0.0f)) {
+ throw new IllegalArgumentException(
+ "borderWidth not zero or positive");
+ }
+
+ if (!((6.0d * borderWidth) <= Math.min(((double) xMax) - xMin,
+ ((double) yMax) - yMin))) {
+ throw new IllegalArgumentException(
+ "borderWidth is not less than the minimum of node width and node "
+ + "height divided by six");
+ }
+ }
+
+ final float off = borderWidth/2.0f; // border offset
+ final Shape sx = getShape(nodeShape,xMin+off,yMin+off,xMax-off,yMax-off);
+
+ if (borderWidth > 0.0f) {
+ m_g2d.setPaint(borderPaint);
+ m_g2d.setStroke(getStroke(borderWidth));
+ m_g2d.draw(sx);
+ }
+
+ m_g2d.setPaint(fillPaint);
+ m_g2d.fill(sx);
+ }
+
+ /**
+ * Computes the path a node shape takes; this method is useful if a user
+ * interface would allow user selection of nodes, for example. Use the same
+ * parameter values that were used to render corresponding node.
+ *
+ * @param nodeShape
+ * the shape (SHAPE_* constant or custom shape) of the node in
+ * question.
+ * @param xMin
+ * an extent of the node in question, in node coordinate space.
+ * @param yMin
+ * an extent of the node in question, in node coordinate space.
+ * @param xMax
+ * an extent of the node in question, in node coordinate space.
+ * @param yMax
+ * an extent of the node in question, in node coordinate space.
+ * @param path
+ * the computed path is returned in this parameter; the computed
+ * path's coordinate system is the node coordinate system; the
+ * computed path is closed.
+ */
+ public final void getNodeShape(final byte nodeShape, final float xMin,
+ final float yMin, final float xMax, final float yMax,
+ final GeneralPath path) {
+ if (m_debug) {
+ checkDispatchThread();
+ checkOrder(xMin,xMax,"x");
+ checkOrder(yMin,yMax,"y");
+ }
+
+ path.reset();
+ path.append(getShape(nodeShape, xMin, yMin, xMax, yMax), false);
+ }
+
+ /**
+ * The custom node shape that is defined is a polygon specified by the
+ * coordinates supplied. The polygon must meet several constraints listed
+ * below.
+ * <p>
+ * If we define the value xCenter to be the average of the minimum and
+ * maximum X values of the vertices and if we define yCenter likewise, then
+ * the specified polygon must meet the following constraints:
+ * <ol>
+ * <li>Each polygon line segment must have nonzero length.</li>
+ * <li>No two consecutive polygon line segments can be parallel (this
+ * essentially implies that the polygon must have at least three vertices).</li>
+ * <li>No two distinct non-consecutive polygon line segments may intersect
+ * (not even at the endpoints); this makes possible the notion of interior
+ * of the polygon.</li>
+ * <li>The polygon must be star-shaped with respect to the point (xCenter,
+ * yCenter); a polygon is said to be <i>star-shaped with respect to a point
+ * (a,b)</i> if and only if for every point (x,y) in the interior or on the
+ * boundary of the polygon, the interior of the segment (a,b)->(x,y) lies in
+ * the interior of the polygon.</li>
+ * <li>The path traversed by the polygon must be clockwise where +X points
+ * right and +Y points down.</li>
+ * </ol>
+ * <p>
+ * In addition to these constraints, when rendering custom nodes with
+ * nonzero border width, possible problems may arise if the border width is
+ * large with respect to the kinks in the polygon.
+ *
+ * @param coords
+ * vertexCount * 2 consecutive coordinate values are read from
+ * this array starting at coords[offset]; coords[offset],
+ * coords[offset + 1], coords[offset + 2], coords[offset + 3] and
+ * so on are interpreted as x0, y0, x1, y1, and so on; the
+ * initial vertex need not be repeated as the last vertex
+ * specified.
+ * @param offset
+ * the starting index of where to read coordinates from in the
+ * coords parameter.
+ * @param vertexCount
+ * the number of vertices to read from coords; vertexCount * 2
+ * entries in coords are read.
+ * @return the node shape identifier to be used in future rendering calls
+ * (to be used as parameter nodeShape in method drawNodeFull()).
+ * @exception IllegalArgumentException
+ * if any of the constraints are not met, or if the specified
+ * polygon has more than CUSTOM_SHAPE_MAX_VERTICES vertices.
+ * @exception IllegalStateException
+ * if too many custom node shapes are already defined; a
+ * little over one hundered custom node shapes can be
+ * defined.
+ */
+ public final byte defineCustomNodeShape(final float[] coords,
+ final int offset, final int vertexCount) {
+ if (m_debug) {
+ checkDispatchThread();
+ }
+
+ if (vertexCount > CUSTOM_SHAPE_MAX_VERTICES) {
+ throw new IllegalArgumentException( "too many vertices (greater than "
+ + CUSTOM_SHAPE_MAX_VERTICES + ")");
+ }
+
+ final double[] polyCoords = new double[vertexCount * 2];
+
+ for (int i = 0; i < polyCoords.length; i++)
+ polyCoords[i] = coords[offset + i];
+
+ // Normalize the polygon so that it spans [-0.5, 0.5] x [-0.5, 0.5].
+ double xMin = Double.POSITIVE_INFINITY;
+ double yMin = Double.POSITIVE_INFINITY;
+ double xMax = Double.NEGATIVE_INFINITY;
+ double yMax = Double.NEGATIVE_INFINITY;
+
+ for (int i = 0; i < polyCoords.length;) {
+ xMin = Math.min(xMin, coords[i]);
+ xMax = Math.max(xMax, coords[i++]);
+ yMin = Math.min(yMin, coords[i]);
+ yMax = Math.max(yMax, coords[i++]);
+ }
+
+ final double xDist = xMax - xMin;
+
+ if (xDist == 0.0d)
+ throw new IllegalArgumentException( "polygon does not move in the X direction");
+
+ final double yDist = yMax - yMin;
+
+ if (yDist == 0.0d)
+ throw new IllegalArgumentException( "polygon does not move in the Y direction");
+
+ final double xMid = (xMin + xMax) / 2.0d;
+ final double yMid = (yMin + yMax) / 2.0d;
+
+ for (int i = 0; i < polyCoords.length;) {
+ double foo = (polyCoords[i] - xMid) / xDist;
+ polyCoords[i++] = Math.min(Math.max(-0.5d, foo), 0.5d);
+ foo = (polyCoords[i] - yMid) / yDist;
+ polyCoords[i++] = Math.min(Math.max(-0.5d, foo), 0.5d);
+ }
+
+
+ int yInterceptsCenter = 0;
+
+ for (int i = 0; i < vertexCount; i++) {
+ final double x0 = polyCoords[i * 2];
+ final double y0 = polyCoords[(i * 2) + 1];
+ final double x1 = polyCoords[((i * 2) + 2) % (vertexCount * 2)];
+ final double y1 = polyCoords[((i * 2) + 3) % (vertexCount * 2)];
+ final double x2 = polyCoords[((i * 2) + 4) % (vertexCount * 2)];
+ final double y2 = polyCoords[((i * 2) + 5) % (vertexCount * 2)];
+ final double distP0P1 = Math.sqrt(((x1 - x0) * (x1 - x0)) + ((y1 - y0) * (y1 - y0)));
+
+ // Too close to distance zero.
+ if ((float) distP0P1 == 0.0f) {
+ throw new IllegalArgumentException(
+ "a line segment has distance [too close to] zero");
+ }
+
+ final double distP2fromP0P1 = ((((y0 - y1) * x2)
+ + ((x1 - x0) * y2) + (x0 * y1)) - (x1 * y0)) / distP0P1;
+
+ // Too close to parallel.
+ if ((float) distP2fromP0P1 == 0.0f) {
+ throw new IllegalArgumentException(
+ "either a line segment has distance [too close to] zero or "
+ + "two consecutive line segments are [too close to] parallel");
+ }
+
+ final double distCenterFromP0P1 = ((x0 * y1) - (x1 * y0)) / distP0P1;
+
+ if (!((float) distCenterFromP0P1 > 0.0f)) {
+ throw new IllegalArgumentException(
+ "polygon is going counter-clockwise or is not star-shaped with "
+ + "respect to center");
+ }
+
+ if ((Math.min(y0, y1) < 0.0d) && (Math.max(y0, y1) >= 0.0d)) {
+ yInterceptsCenter++;
+ }
+ }
+
+ if (yInterceptsCenter != 2) {
+ throw new IllegalArgumentException(
+ "the polygon self-intersects (we know this because the winding "
+ + "number of the center is not one)");
+ }
+
+ // polyCoords now contains a polygon spanning [-0.5, 0.5] X [-0.5, 0.5]
+ // that passes all of the criteria.
+ final byte nextCustomShapeType = (byte) (m_lastCustomShapeType + 1);
+
+ if (nextCustomShapeType < 0)
+ throw new IllegalStateException( "too many custom node shapes are already defined");
+
+ m_lastCustomShapeType++;
+ nodeShapes.put(nextCustomShapeType, new LegacyCustomNodeShape(polyCoords,nextCustomShapeType));
+
+ return nextCustomShapeType;
+ }
+
+ /**
+ * Determines whether the specified shape is a custom defined node shape.
+ */
+ public final boolean customNodeShapeExists(final byte shape) {
+ if (m_debug) {
+ checkDispatchThread();
+ }
+
+ return (shape > s_last_shape) && (shape <= m_lastCustomShapeType);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final byte[] getCustomNodeShapes() {
+ if (m_debug) {
+ checkDispatchThread();
+ }
+
+ final byte[] returnThis = new byte[m_lastCustomShapeType - s_last_shape];
+
+ for (int i = 0; i < returnThis.length; i++) {
+ returnThis[i] = (byte) (s_last_shape + 1 + i);
+ }
+
+ return returnThis;
+ }
+
+ /**
+ * Returns the vertices of a previously defined custom node shape. The
+ * polygon will be normalized to fit within the [-0.5, 0.5] x [-0.5, 0.5]
+ * square. Returns null if specified shape is not a previously defined
+ * custom shape.
+ */
+ public final float[] getCustomNodeShape(final byte customShape) {
+ if (m_debug) {
+ checkDispatchThread();
+ }
+
+ if ( !customNodeShapeExists(customShape) )
+ return null;
+
+ LegacyCustomNodeShape ns = (LegacyCustomNodeShape)(nodeShapes.get(customShape));
+ return ns.getCoords();
+ }
+
+ /**
+ * If this is a new instance, imports the custom node shapes from the
+ * GraphGraphics specified into this GraphGraphics.
+ *
+ * @param grafx
+ * custom node shapes will be imported from this GraphGraphics.
+ * @exception IllegalStateException
+ * if at least one custom node shape is already defined in
+ * this GraphGraphics.
+ */
+ public final void importCustomNodeShapes(final GraphGraphics grafx) {
+ if (m_debug) {
+ checkDispatchThread();
+ }
+
+ // I define this error check outside the scope of m_debug because
+ // clobbering existing custom node shape definitions could be major.
+ if (m_lastCustomShapeType != s_last_shape) {
+ throw new IllegalStateException(
+ "a custom node shape is already defined in this GraphGraphics");
+ }
+
+ for (Map.Entry<Byte, NodeShape> entry : grafx.nodeShapes.entrySet()) {
+ nodeShapes.put(entry.getKey(), entry.getValue());
+ m_lastCustomShapeType++;
+ }
+ }
+
+ private final Shape getShape(final byte nodeShape, final float xMin,
+ final float yMin, final float xMax, final float yMax) {
+ NodeShape ns = nodeShapes.get(nodeShape);
+ if ( ns != null )
+ return ns.getShape(xMin,yMin,xMax,yMax);
+ else
+ return null;
+ }
+
+ /**
+ * get list of node shapes.
+ *
+ * @return A map of node shape bytes to Shape objects.
+ */
+ public static Map<Byte, Shape> getNodeShapes() {
+ final Map<Byte, Shape> shapeMap = new HashMap<Byte, Shape>();
+
+ for ( NodeShape ns : nodeShapes.values() ) {
+ final Shape shape = ns.getShape(0f, 0f, DEF_SHAPE_SIZE, DEF_SHAPE_SIZE);
+ shapeMap.put(ns.getType(), new GeneralPath( shape ));
+ }
+
+ return shapeMap;
+ }
+
+ /**
+ * Get list of arrow heads.
+ *
+ * @return A map of arrow shape bytes to Shape objects.
+ */
+ public static Map<Byte, Shape> getArrowShapes() {
+ final Map<Byte, Shape> shapeMap = new HashMap<Byte, Shape>();
+ for ( Arrow a : arrows.values() )
+ shapeMap.put( a.getType(), a.getArrowShape() );
+
+ return shapeMap;
+ }
+
+ /**
+ * This is the method that will render an edge very quickly. Translucent
+ * colors are not supported by the low detail rendering methods.
+ * <p>
+ * The points (x0, y0) and (x1, y1) specify the endpoints of edge to be
+ * rendered in the node coordinate space, not the image coordinate space.
+ * Thus, these values will likely not change from frame to frame, as zoom
+ * and pan operations are performed. If these two points are identical,
+ * nothing is drawn.
+ * <p>
+ * This method will not work unless clear() has been called at least once
+ * previously.
+ *
+ * @param x0
+ * the X coordinate of the begin point of edge to render.
+ * @param y0
+ * the Y coordinate of the begin point of edge to render.
+ * @param x1
+ * the X coordinate of the end point of edge to render.
+ * @param y1
+ * the Y coordinate of the end point of edge to render.
+ * @param edgeColor
+ * the [fully opaque] color to use when drawing the edge.
+ * @exception IllegalArgumentException
+ * if edgeColor is not opaque.
+ */
+ public final void drawEdgeLow(final float x0, final float y0,
+ final float x1, final float y1, final Color edgeColor) {
+ if (m_debug) {
+ checkDispatchThread();
+ checkCleared();
+
+ if (edgeColor.getAlpha() != 255) {
+ throw new IllegalArgumentException("edgeColor is not opaque");
+ }
+ }
+
+ // This following statement has to be consistent with the full edge
+ // rendering logic.
+ if ((x0 == x1) && (y0 == y1)) {
+ return;
+ }
+
+ if (m_gMinimal == null) {
+ makeMinimalGraphics();
+ }
+
+ // I'm transforming points manually because the resulting underlying
+ // graphics pipeline used is much faster.
+ m_ptsBuff[0] = x0;
+ m_ptsBuff[1] = y0;
+ m_ptsBuff[2] = x1;
+ m_ptsBuff[3] = y1;
+ m_currXform.transform(m_ptsBuff, 0, m_ptsBuff, 0, 2);
+
+ final int xNot = (int) m_ptsBuff[0];
+ final int yNot = (int) m_ptsBuff[1];
+ final int xOne = (int) m_ptsBuff[2];
+ final int yOne = (int) m_ptsBuff[3];
+ m_gMinimal.setColor(edgeColor);
+ m_gMinimal.drawLine(xNot, yNot, xOne, yOne);
+ }
+
+ /**
+ * Draws an edge with medium to high detail, depending on parameters
+ * specified. Something is rendered in all cases except where the length of
+ * the edge is zero (because in that case directionality cannot be
+ * determined for at least some arrowheads).
+ * <p>
+ * The arrow types must each be one of the ARROW_* constants. The arrow at
+ * endpoint 1 is always "on top of" the arrow at endpoint 0 if they overlap
+ * because the arrow at endpoint 0 gets rendered first.
+ * <p>
+ * If an arrow other than ARROW_NONE is rendered, its size must be greater
+ * than or equal to edge thickness specified. The table below describes, to
+ * some extent, the nature of each arrow type. <blockquote><table
+ * border="1" cellpadding="5" cellspacing="0">
+ * <tr>
+ * <th>arrow type</th>
+ * <th>description</th>
+ * </tr>
+ * <tr>
+ * <td>ARROW_NONE</td>
+ * <td>the edge line segment has endpoint specified, and the line segment
+ * has a round end (center of round semicircle end exactly equal to endpoint
+ * specified); arrow size and arrow paint are ignored</td>
+ * </tr>
+ * <tr>
+ * <td>ARROW_DELTA</td>
+ * <td>the sharp tip of the arrowhead is exactly at the endpint specified;
+ * the delta is as wide as the arrow size specified and twice that in length</td>
+ * </tr>
+ * <tr>
+ * <td>ARROW_DIAMOND</td>
+ * <td>the sharp tip of the arrowhead is exactly at the endpoint specified;
+ * the diamond is as wide as the arrow size specified and twice that in
+ * length</td>
+ * </tr>
+ * <tr>
+ * <td>ARROW_DISC</td>
+ * <td>the disc arrowhead is placed such that its center is at the
+ * specified endpoint; the diameter of the disk is the arrow size specified</td>
+ * </tr>
+ * <tr>
+ * <td>ARROW_TEE</td>
+ * <td>the center of the tee intersection lies at the specified endpoint;
+ * the width of the top of the tee is one quarter of the arrow size
+ * specified, and the span of the top of the tee is two times the arrow size</td>
+ * </tr>
+ * <tr>
+ * <td>ARROW_HALF_TOP</td>
+ * <td>Draws a line the width of the stroke away from the node at the midpoint
+ * between the edge and the node on the "top" of the edge.</td>
+ * </tr>
+ * <tr>
+ * <td>ARROW_HALF_BOTTOM</td>
+ * <td>Draws a line the width of the stroke away from the node at the midpoint
+ * between the edge and the node on the "bottom" of the edge.</td>
+ * </tr>
+ * </table></blockquote>
+ * <p>
+ * Note that if the edge segment length is zero then nothing gets rendered.
+ * <p>
+ * This method will not work unless clear() has been called at least once
+ * previously.
+ * <p>
+ * A discussion pertaining to edge anchors. At most MAX_EDGE_ANCHORS
+ * edge anchors may be specified. The edge anchors are used to define cubic
+ * Bezier curves. The exact algorithm for determining the Bezier curves from
+ * the input parameters is too complicated to describe in this Javadoc. Some
+ * parts of the algorithm: <blockquote>
+ * <ul>
+ * <li>the conglomerated curve is [probably] not going to pass through the
+ * edge anchors points specified; the curve will pass through the midpoint
+ * between every consecutive pair of anchors</li>
+ * <li>when determining the edge path as a whole, an ordered list of points
+ * is created by putting point (x0, y0) at the beginning of the list,
+ * followed by the anchor points, followed by point (x1, y1); then,
+ * duplicate points are removed from the beginning and end of this list</li>
+ * <li>from the list described above, the first two points define the arrow
+ * direction at point (x0, y0) and the initial curve direction; likewise,
+ * the last two points in this list define the arrow direction at point (x1,
+ * y1) and the ending curve direction</li>
+ * </ul>
+ * </blockquote> In order to specify a straight-line edge path, simply
+ * duplicate each edge anchor in the EdgeAnchors instance. For example, a
+ * smooth curve would be drawn by specifying consecutive-pairwise disctinct
+ * points {(x0,y0), A0, A1, A2, (x1,y1)}; a straight-line edge path would be
+ * drawn by specifying {(x0, y0), A0, A0, A1, A1, A2, A2, (x1, y1)}.
+ *
+ * @param arrow0Type
+ * the type of arrow shape to use for drawing the arrow at point
+ * (x0, y0); this value must be one of the ARROW_* constants.
+ * @param arrow0Size
+ * the size of arrow at point (x0, y0); how size is interpreted
+ * for different arrow types is described in the table above.
+ * @param arrow0Paint
+ * the paint to use when drawing the arrow at point (x0, y0).
+ * @param arrow1Type
+ * the type of arrow shape to use for drawing the arrow at point
+ * (x1, y1); this value must be one of the ARROW_* constants.
+ * @param arrow1Size
+ * the size of arrow at point (x1, y1); how size is interpreted
+ * for different arrow types is described in the table above.
+ * @param arrow1Paint
+ * the paint to use when drawing the arrow at point (x1, y1).
+ * @param x0
+ * the X coordinate of the first edge endpoint.
+ * @param y0
+ * the Y coordinate of the first edge endpoint.
+ * @param anchors
+ * anchor points between the two edge endpoints; null is an
+ * acceptable value to indicate no edge anchors.
+ * @param x1
+ * the X coordinate of the second edge endpoint.
+ * @param y1
+ * the Y coordinate of the second edge endpoint.
+ * @param edgeThickness
+ * the thickness of the edge segment; the edge segment is the
+ * part of the edge between the two endpoint arrows.
+ * @param edgeStroke
+ * the Stroke to use when drawing the edge segment.
+ * @param edgePaint
+ * the paint to use when drawing the edge segment.
+ * @exception IllegalArgumentException
+ * if edgeThickness is less than zero, if any one of the arrow
+ * configurations does not meet specified criteria, or if more
+ * than MAX_EDGE_ANCHORS anchors are specified.
+ */
+ public final void drawEdgeFull(final byte arrow0Type,
+ final float arrow0Size, final Paint arrow0Paint,
+ final byte arrow1Type, final float arrow1Size,
+ final Paint arrow1Paint, final float x0, final float y0,
+ EdgeAnchors anchors, final float x1, final float y1,
+ final float edgeThickness, final Stroke edgeStroke, final Paint edgePaint) {
+ final long startTime = System.nanoTime();
+ final double curveFactor = CURVE_ELLIPTICAL;
+
+ if (anchors == null) {
+ anchors = m_noAnchors;
+ }
+
+ if (m_debug) {
+ edgeFullDebug(arrow0Type, arrow0Size, arrow1Type, arrow1Size,
+ edgeStroke, edgeThickness, anchors);
+ }
+
+ if (!computeCubicPolyEdgePath(arrow0Type,
+ (arrow0Type == ARROW_NONE) ? 0.0f : arrow0Size, arrow1Type,
+ (arrow1Type == ARROW_NONE) ? 0.0f : arrow1Size, x0, y0,
+ anchors, x1, y1, curveFactor)) {
+ // After filtering duplicate start and end points, there are less
+ // than 3 total.
+ if (m_edgePtsCount == 2) { // Draw an ordinary edge.
+ drawSimpleEdgeFull(arrow0Type, arrow0Size, arrow0Paint,
+ arrow1Type, arrow1Size, arrow1Paint,
+ (float) m_edgePtsBuff[0], (float) m_edgePtsBuff[1],
+ (float) m_edgePtsBuff[2], (float) m_edgePtsBuff[3],
+ edgeThickness, edgeStroke, edgePaint );
+ }
+
+ return;
+ }
+
+ // Render the edge polypath.
+ final boolean simpleSegment = arrow0Type == ARROW_NONE && arrow1Type == ARROW_NONE;
+ m_g2d.setStroke(edgeStroke);
+
+ // Set m_path2d to contain the cubic curves computed in
+ // m_edgePtsBuff.
+ m_path2d.reset();
+ m_path2d.moveTo((float) m_edgePtsBuff[2], (float) m_edgePtsBuff[3]);
+
+ int inx = 4;
+ final int count = ((m_edgePtsCount - 1) * 6) - 2;
+
+ while (inx < count) {
+ m_path2d.curveTo((float) m_edgePtsBuff[inx++],
+ (float) m_edgePtsBuff[inx++],
+ (float) m_edgePtsBuff[inx++],
+ (float) m_edgePtsBuff[inx++],
+ (float) m_edgePtsBuff[inx++],
+ (float) m_edgePtsBuff[inx++]);
+ }
+
+ m_g2d.setPaint(edgePaint);
+ m_g2d.draw(m_path2d);
+
+ if (simpleSegment) {
+ return;
+ }
+
+ // We need to figure out the phase at the end of the cubic poly-path
+ // for dashed segments. I cannot find a Java API to do this; our
+ // best
+ // bet would be to implement our own cubic curve length calculating
+ // function, but our computation may not agree with BasicStroke's
+ // computation. So what we're going to do is never render the arrow
+ // caps for dashed edges.
+
+ final double dx0 = m_edgePtsBuff[0] - m_edgePtsBuff[4];
+ final double dy0 = m_edgePtsBuff[1] - m_edgePtsBuff[5];
+ final double len0 = Math.sqrt((dx0 * dx0) + (dy0 * dy0));
+ final double cosTheta0 = dx0 / len0;
+ final double sinTheta0 = dy0 / len0;
+
+ final double dx1 = m_edgePtsBuff[((m_edgePtsCount - 1) * 6) - 2]
+ - m_edgePtsBuff[((m_edgePtsCount - 1) * 6) - 6];
+ final double dy1 = m_edgePtsBuff[((m_edgePtsCount - 1) * 6) - 1]
+ - m_edgePtsBuff[((m_edgePtsCount - 1) * 6) - 5];
+ final double len1 = Math.sqrt((dx1 * dx1) + (dy1 * dy1));
+ final double cosTheta1 = dx1 / len1;
+ final double sinTheta1 = dy1 / len1;
+
+ // Only draw the edge caps if the stroke is a BasicStroke, which is to
+ // say, don't worry about how fancy strokes intersect the arrow.
+ if ( edgeStroke instanceof BasicStroke ) {
+
+ // Render arrow cap at origin of poly path.
+ final Shape arrow0Cap = computeUntransformedArrowCap(arrow0Type,
+ ((double) arrow0Size) / edgeThickness);
+
+ if (arrow0Cap != null) {
+ m_xformUtil.setTransform(cosTheta0, sinTheta0, -sinTheta0,
+ cosTheta0, m_edgePtsBuff[2], m_edgePtsBuff[3]);
+ m_g2d.transform(m_xformUtil);
+ m_g2d.scale(edgeThickness, edgeThickness);
+ // The paint is already set to edge paint.
+ m_g2d.fill(arrow0Cap);
+ m_g2d.setTransform(m_currNativeXform);
+ }
+
+ // Render arrow cap at end of poly path.
+ final Shape arrow1Cap = computeUntransformedArrowCap(arrow1Type,
+ ((double) arrow1Size) / edgeThickness);
+
+ if (arrow1Cap != null) {
+ m_xformUtil.setTransform(cosTheta1, sinTheta1, -sinTheta1,
+ cosTheta1,
+ m_edgePtsBuff[((m_edgePtsCount - 1) * 6) - 4],
+ m_edgePtsBuff[((m_edgePtsCount - 1) * 6) - 3]);
+ m_g2d.transform(m_xformUtil);
+ m_g2d.scale(edgeThickness, edgeThickness);
+ // The paint is already set to edge paint.
+ m_g2d.fill(arrow1Cap);
+ m_g2d.setTransform(m_currNativeXform);
+ }
+ }
+
+ // Render arrow at origin of poly path.
+ final Shape arrow0 = computeUntransformedArrow(arrow0Type);
+
+ if (arrow0 != null) {
+ m_xformUtil.setTransform(cosTheta0, sinTheta0, -sinTheta0,
+ cosTheta0, m_edgePtsBuff[0], m_edgePtsBuff[1]);
+ m_g2d.transform(m_xformUtil);
+ m_g2d.scale(arrow0Size, arrow0Size);
+ m_g2d.setPaint(arrow0Paint);
+ m_g2d.fill(arrow0);
+ m_g2d.setTransform(m_currNativeXform);
+ }
+
+ // Render arrow at end of poly path.
+ final Shape arrow1 = computeUntransformedArrow(arrow1Type);
+
+ if (arrow1 != null) {
+
+ m_xformUtil.setTransform(cosTheta1, sinTheta1, -sinTheta1,
+ cosTheta1,
+ m_edgePtsBuff[((m_edgePtsCount - 1) * 6) - 2],
+ m_edgePtsBuff[((m_edgePtsCount - 1) * 6) - 1]);
+ m_g2d.transform(m_xformUtil);
+ m_g2d.scale(arrow1Size, arrow1Size);
+ m_g2d.setPaint(arrow1Paint);
+ m_g2d.fill(arrow1);
+ m_g2d.setTransform(m_currNativeXform);
+ }
+ }
+
+ @SuppressWarnings("fallthrough")
+ private final void edgeFullDebug(final byte arrow0Type,
+ final float arrow0Size, final byte arrow1Type, float arrow1Size,
+ final Stroke edgeStroke,
+ final float edgeThickness,
+ final EdgeAnchors anchors) {
+ checkDispatchThread();
+ checkCleared();
+ if (!(edgeThickness >= 0.0f)) {
+ throw new IllegalArgumentException("edgeThickness < 0");
+ }
+
+ if ( !arrows.containsKey( arrow0Type ) )
+ throw new IllegalArgumentException("arrow0Type is not recognized");
+
+ if ( arrow0Type != ARROW_NONE )
+ if (!(arrow0Size >= edgeThickness))
+ throw new IllegalArgumentException(
+ "arrow size must be at least as large as edge thickness");
+
+ if ( !arrows.containsKey( arrow1Type ) )
+ throw new IllegalArgumentException("arrow1Type is not recognized");
+
+ if ( arrow1Type != ARROW_NONE )
+ if (!(arrow1Size >= edgeThickness))
+ throw new IllegalArgumentException(
+ "arrow size must be at least as large as edge thickness");
+
+ if (anchors.numAnchors() > MAX_EDGE_ANCHORS) {
+ throw new IllegalArgumentException("at most MAX_EDGE_ANCHORS ("
+ + MAX_EDGE_ANCHORS + ") edge anchors can be specified");
+ }
+ }
+
+ private final void drawSimpleEdgeFull(final byte arrow0Type,
+ final float arrow0Size, final Paint arrow0Paint,
+ final byte arrow1Type, final float arrow1Size,
+ final Paint arrow1Paint, final float x0, final float y0,
+ final float x1, final float y1, final float edgeThickness,
+ final Stroke edgeStroke,
+ final Paint edgePaint) {
+ final double len = Math.sqrt(((((double) x1) - x0) * (((double) x1) - x0))
+ + ((((double) y1) - y0) * (((double) y1) - y0)));
+
+ // If the length of the edge is zero we're going to skip completely over
+ // all rendering. This check is now redundant because the code that
+ // calls us makes this check automatically.
+ if (len == 0.0d)
+ return;
+
+ final double x0Adj;
+ final double y0Adj;
+ final double x1Adj;
+ final double y1Adj;
+ final byte simpleSegment;
+
+ // Render the line segment if necessary.
+
+ final double t0 = (getT(arrow0Type) * arrow0Size) / len;
+ x0Adj = (t0 * (((double) x1) - x0)) + x0;
+ y0Adj = (t0 * (((double) y1) - y0)) + y0;
+
+ final double t1 = (getT(arrow1Type) * arrow1Size) / len;
+ x1Adj = (t1 * (((double) x0) - x1)) + x1;
+ y1Adj = (t1 * (((double) y0) - y1)) + y1;
+
+ // If the vector point0->point1 is pointing opposite to
+ // adj0->adj1, then don't render the line segment.
+ // Dot product determines this.
+ if ((((((double) x1) - x0) * (x1Adj - x0Adj)) +
+ ((((double) y1) - y0) * (y1Adj - y0Adj))) > 0.0d) {
+
+ if (arrow0Type == ARROW_NONE && arrow1Type == ARROW_NONE) {
+ simpleSegment = 1;
+ } else {
+ simpleSegment = -1;
+ }
+
+ m_g2d.setStroke(edgeStroke);
+ m_line2d.setLine(x0Adj, y0Adj, x1Adj, y1Adj);
+ m_g2d.setPaint(edgePaint);
+ m_g2d.draw(m_line2d);
+
+ if ( simpleSegment > 0 )
+ return;
+
+ } else {
+ simpleSegment = 0; // Did not render segment.
+ }
+
+ // End rendering of line segment.
+
+ // Using x0, x1, y0, and y1 instead of the "adjusted" endpoints is
+ // accurate enough in computation of cosine and sine because the
+ // length is guaranteed to be at least as large. Remember that the
+ // original endpoint values are specified as float whereas the adjusted
+ // points are double.
+ final double cosTheta = (((double) x0) - x1) / len;
+ final double sinTheta = (((double) y0) - y1) / len;
+
+ if ( simpleSegment < 0 && edgeStroke instanceof BasicStroke ) {
+ // Arrow cap at point 0.
+ final Shape arrow0Cap = computeUntransformedArrowCap(arrow0Type,
+ ((double) arrow0Size) / edgeThickness);
+
+ if (arrow0Cap != null) {
+ m_xformUtil.setTransform(cosTheta, sinTheta, -sinTheta,
+ cosTheta, x0Adj, y0Adj);
+ m_g2d.transform(m_xformUtil);
+ m_g2d.scale(edgeThickness, edgeThickness);
+ // The paint is already set to edge paint.
+ m_g2d.fill(arrow0Cap);
+ m_g2d.setTransform(m_currNativeXform);
+ }
+
+ // Arrow cap at point 1.
+ final Shape arrow1Cap = computeUntransformedArrowCap(arrow1Type,
+ ((double) arrow1Size) / edgeThickness);
+
+ if (arrow1Cap != null) {
+ m_xformUtil.setTransform(-cosTheta, -sinTheta, sinTheta,
+ -cosTheta, x1Adj, y1Adj);
+ m_g2d.transform(m_xformUtil);
+ m_g2d.scale(edgeThickness, edgeThickness);
+ // The paint is already set to edge paint.
+ m_g2d.fill(arrow1Cap);
+ m_g2d.setTransform(m_currNativeXform);
+ }
+ }
+
+ // Render arrow at point 0.
+ final Shape arrow0 = computeUntransformedArrow(arrow0Type);
+
+ if (arrow0 != null) {
+ m_xformUtil.setTransform(cosTheta, sinTheta, -sinTheta,
+ cosTheta, x0, y0);
+ m_g2d.transform(m_xformUtil);
+ m_g2d.scale(arrow0Size, arrow0Size);
+ m_g2d.setPaint(arrow0Paint);
+ m_g2d.fill(arrow0);
+ m_g2d.setTransform(m_currNativeXform);
+ }
+
+ // Render arrow at point 1.
+ final Shape arrow1 = computeUntransformedArrow(arrow1Type);
+
+ if (arrow1 != null) {
+ m_xformUtil.setTransform(-cosTheta, -sinTheta, sinTheta,
+ -cosTheta, x1, y1);
+ m_g2d.transform(m_xformUtil);
+ m_g2d.scale(arrow1Size, arrow1Size);
+ m_g2d.setPaint(arrow1Paint);
+ m_g2d.fill(arrow1);
+ m_g2d.setTransform(m_currNativeXform);
+ }
+ }
+
+ /**
+ * Computes the path that an edge takes; this method is useful if a user
+ * interface would allow user selection of edges, for example. The returned
+ * path is the path along the center of the edge segment, extending to the
+ * points which specify the arrow locations. Note that this path therefore
+ * disregards edge thickness and arrow outline. Use the same parameter
+ * values that were used to render corresponding edge.
+ *
+ * @param arrow0Type
+ * the type of arrow shape used for drawing the arrow at point
+ * (x0, y0); this value must be one of the ARROW_* constants.
+ * @param arrow0Size
+ * the size of arrow at point (x0, y0).
+ * @param arrow1Type
+ * the type of arrow shape used for drawing the arrow at point
+ * (x1, y1); this value must be one of the ARROW_* constants.
+ * @param arrow1Size
+ * the size of arrow at point (x1, y1).
+ * @param x0
+ * the X coordinate of the first edge endpoint.
+ * @param y0
+ * the Y coordinate of the first edge endpoint.
+ * @param anchors
+ * anchor points between the two edge endpoints; null is an
+ * acceptable value to indicate no edge anchors.
+ * @param x1
+ * the X coordinate of the second edge endpoint.
+ * @param y1
+ * the Y coordinate of the second edge endpoint.
+ * @param path
+ * the computed path is returned in this parameter; the computed
+ * path's coordinate system is the node coordinate system; the
+ * computed path is not closed.
+ * @return true if and only if the specified edge would be drawn (which is
+ * if and only if any two points from the edge anchor set plus the
+ * beginning and end point are distinct); if false is returned, the
+ * path parameter is not modified.
+ * @exception IllegalArgumentException
+ * if any one of the edge arrow criteria specified in
+ * drawEdgeFull() is not satisfied.
+ */
+ public final boolean getEdgePath(final byte arrow0Type,
+ final float arrow0Size, final byte arrow1Type,
+ final float arrow1Size, final float x0, final float y0,
+ EdgeAnchors anchors, final float x1, final float y1,
+ final GeneralPath path) {
+ final double curveFactor = CURVE_ELLIPTICAL;
+
+ if (anchors == null) {
+ anchors = m_noAnchors;
+ }
+
+ if (m_debug) {
+ checkDispatchThread();
+
+ if ( !arrows.containsKey( arrow0Type ) )
+ throw new IllegalArgumentException("arrow0Type is not recognized");
+
+ if ( !arrows.containsKey( arrow1Type ) )
+ throw new IllegalArgumentException("arrow1Type is not recognized");
+
+ if (anchors.numAnchors() > MAX_EDGE_ANCHORS) {
+ throw new IllegalArgumentException("at most MAX_EDGE_ANCHORS ("
+ + MAX_EDGE_ANCHORS + ") edge anchors can be specified");
+ }
+ }
+
+ byte arrow0 = arrow0Type;
+ byte arrow1 = arrow1Type;
+
+ if (!computeCubicPolyEdgePath(arrow0, (arrow0 == ARROW_NONE) ? 0.0f
+ : arrow0Size, arrow1, (arrow1 == ARROW_NONE) ? 0.0f
+ : arrow1Size, x0, y0, anchors, x1, y1, curveFactor)) {
+ // After filtering duplicate start and end points, there are less
+ // then
+ // 3 total.
+ if (m_edgePtsCount == 2) {
+ path.reset();
+ path.moveTo((float) m_edgePtsBuff[0], (float) m_edgePtsBuff[1]);
+ path.lineTo((float) m_edgePtsBuff[2], (float) m_edgePtsBuff[3]);
+
+ return true;
+ }
+
+ return false;
+ }
+
+ path.reset();
+ path.moveTo((float) m_edgePtsBuff[0], (float) m_edgePtsBuff[1]);
+ path.lineTo((float) m_edgePtsBuff[2], (float) m_edgePtsBuff[3]);
+
+ int inx = 4;
+ final int count = ((m_edgePtsCount - 1) * 6) - 2;
+
+ while (inx < count) {
+ path.curveTo((float) m_edgePtsBuff[inx++],
+ (float) m_edgePtsBuff[inx++], (float) m_edgePtsBuff[inx++],
+ (float) m_edgePtsBuff[inx++], (float) m_edgePtsBuff[inx++],
+ (float) m_edgePtsBuff[inx++]);
+ }
+
+ path.lineTo((float) m_edgePtsBuff[count],
+ (float) m_edgePtsBuff[count + 1]);
+
+ return true;
+ }
+
+ /*
+ * Returns non-null if and only if an arrow is necessary for the arrow type
+ * specified.
+ */
+ private final Shape computeUntransformedArrow(final byte arrowType) {
+ Arrow a = arrows.get(arrowType);
+ if ( a != null )
+ return a.getArrowShape();
+ else
+ return null;
+ }
+
+ /*
+ * The ratio parameter specifies the ratio of arrow size (disc diameter) to
+ * edge thickness (only used for some arrow types). Returns non-null if and
+ * only if a cap is necessary for the arrow type specified.
+ */
+ private final Shape computeUntransformedArrowCap(final byte arrowType, final double ratio) {
+ Arrow a = arrows.get(arrowType);
+ if ( a != null )
+ return a.getCapShape(ratio);
+ else
+ return null;
+ }
+
+ /*
+ *
+ */
+ private final static double getT(final byte arrowType) {
+ Arrow a = arrows.get(arrowType);
+ if ( a != null )
+ return a.getTOffset();
+ else
+ return 0.125;
+ }
+
+ /*
+ * If arrow0Type is ARROW_NONE, arrow0Size should be zero. If arrow1Type is
+ * ARROW_NONE, arrow1Size should be zero.
+ */
+ private final boolean computeCubicPolyEdgePath(final byte arrow0Type,
+ final float arrow0Size, final byte arrow1Type,
+ final float arrow1Size, final float x0, final float y0,
+ final EdgeAnchors anchors, final float x1, final float y1,
+ final double curveFactor) {
+ final int numAnchors = anchors.numAnchors();
+ // add the start point to the edge points buffer
+ m_edgePtsBuff[0] = x0;
+ m_edgePtsBuff[1] = y0;
+ m_edgePtsCount = 1;
+
+ int anchorInx = 0;
+
+ // finds the first anchor point other than the start point and
+ // add it to the edge points buffer
+ while (anchorInx < numAnchors) {
+ anchors.getAnchor(anchorInx++, m_floatBuff, 0);
+
+ if (!((m_floatBuff[0] == x0) && (m_floatBuff[1] == y0))) {
+ m_edgePtsBuff[2] = m_floatBuff[0];
+ m_edgePtsBuff[3] = m_floatBuff[1];
+ m_edgePtsCount = 2;
+
+ break;
+ }
+ }
+
+ // now fill edge points buffer with all subsequent anchors
+ while (anchorInx < numAnchors) {
+ anchors.getAnchor(anchorInx++, m_floatBuff, 0);
+ // Duplicate anchors are allowed.
+ m_edgePtsBuff[m_edgePtsCount * 2] = m_floatBuff[0];
+ m_edgePtsBuff[(m_edgePtsCount * 2) + 1] = m_floatBuff[1];
+ m_edgePtsCount++;
+ }
+
+ // now add the end point to the buffer
+ m_edgePtsBuff[m_edgePtsCount * 2] = x1;
+ m_edgePtsBuff[(m_edgePtsCount * 2) + 1] = y1;
+ m_edgePtsCount++;
+
+ // remove duplicate end points from edge buffer
+ while (m_edgePtsCount > 1) {
+ // second-to-last X coord and second-to-last Y coord.
+ if ((m_edgePtsBuff[(m_edgePtsCount * 2) - 2] == m_edgePtsBuff[(m_edgePtsCount * 2) - 4])
+ && (m_edgePtsBuff[(m_edgePtsCount * 2) - 1] == m_edgePtsBuff[(m_edgePtsCount * 2) - 3])) {
+ m_edgePtsCount--;
+ } else {
+ break;
+ }
+ }
+
+ // no anchors, just a straight line to draw
+ if (m_edgePtsCount < 3) {
+ return false;
+ }
+
+ //
+ // ok, now we're drawing a curve
+ //
+
+ final int edgePtsCount = m_edgePtsCount;
+
+ // First set the three control points related to point 1.
+ // 6 represents the offset in the buffer.
+ {
+ m_edgePtsCount--;
+ // set first control point
+ m_edgePtsBuff[(m_edgePtsCount * 6) - 2] = m_edgePtsBuff[m_edgePtsCount * 2];
+ m_edgePtsBuff[(m_edgePtsCount * 6) - 1] = m_edgePtsBuff[(m_edgePtsCount * 2) + 1];
+
+ double dx = m_edgePtsBuff[(m_edgePtsCount * 2) - 2]
+ - m_edgePtsBuff[m_edgePtsCount * 2];
+ double dy = m_edgePtsBuff[(m_edgePtsCount * 2) - 1]
+ - m_edgePtsBuff[(m_edgePtsCount * 2) + 1];
+ double len = Math.sqrt((dx * dx) + (dy * dy));
+ // Normalized.
+ dx /= len;
+ dy /= len;
+
+ // set second control point
+ m_edgePtsBuff[(m_edgePtsCount * 6) - 4] = m_edgePtsBuff[(m_edgePtsCount * 6) - 2]
+ + (dx * arrow1Size * getT(arrow1Type));
+ m_edgePtsBuff[(m_edgePtsCount * 6) - 3] = m_edgePtsBuff[(m_edgePtsCount * 6) - 1]
+ + (dy * arrow1Size * getT(arrow1Type));
+
+ // one candidate point is offset by the arrow (candX1) and
+ // the other is offset by the curvefactor (candX2)
+ double candX1 = m_edgePtsBuff[(m_edgePtsCount * 6) - 4]
+ + (dx * 2.0d * arrow1Size);
+ double candX2 = m_edgePtsBuff[(m_edgePtsCount * 6) - 4]
+ + (curveFactor * (m_edgePtsBuff[(m_edgePtsCount * 2) - 2] - m_edgePtsBuff[(m_edgePtsCount * 6) - 4]));
+
+ // set third control point X coord
+ // choose the candidate with max offset
+ if (Math.abs(candX1 - m_edgePtsBuff[m_edgePtsCount * 2]) > Math
+ .abs(candX2 - m_edgePtsBuff[m_edgePtsCount * 2])) {
+ m_edgePtsBuff[(m_edgePtsCount * 6) - 6] = candX1;
+ } else {
+ m_edgePtsBuff[(m_edgePtsCount * 6) - 6] = candX2;
+ }
+
+ // one candidate point is offset by the arrow (candY1) and
+ // the other is offset by the curvefactor (candY2)
+ double candY1 = m_edgePtsBuff[(m_edgePtsCount * 6) - 3]
+ + (dy * 2.0d * arrow1Size);
+ double candY2 = m_edgePtsBuff[(m_edgePtsCount * 6) - 3]
+ + (curveFactor * (m_edgePtsBuff[(m_edgePtsCount * 2) - 1] - m_edgePtsBuff[(m_edgePtsCount * 6) - 3]));
+
+ // set third control point Y coord
+ // choose the candidate with max offset
+ if (Math.abs(candY1 - m_edgePtsBuff[(m_edgePtsCount * 2) + 1]) > Math
+ .abs(candY2 - m_edgePtsBuff[(m_edgePtsCount * 2) + 1])) {
+ m_edgePtsBuff[(m_edgePtsCount * 6) - 5] = candY1;
+ } else {
+ m_edgePtsBuff[(m_edgePtsCount * 6) - 5] = candY2;
+ }
+ }
+
+ // Next set the control point for each edge anchor.
+ while (m_edgePtsCount > 2) {
+ m_edgePtsCount--;
+
+ final double midX = (m_edgePtsBuff[(m_edgePtsCount * 2) - 2] + m_edgePtsBuff[m_edgePtsCount * 2]) / 2.0d;
+ final double midY = (m_edgePtsBuff[(m_edgePtsCount * 2) - 1] + m_edgePtsBuff[(m_edgePtsCount * 2) + 1]) / 2.0d;
+ m_edgePtsBuff[(m_edgePtsCount * 6) - 2] = midX
+ + ((m_edgePtsBuff[m_edgePtsCount * 2] - midX) * curveFactor);
+ m_edgePtsBuff[(m_edgePtsCount * 6) - 1] = midY
+ + ((m_edgePtsBuff[(m_edgePtsCount * 2) + 1] - midY) * curveFactor);
+ m_edgePtsBuff[(m_edgePtsCount * 6) - 4] = midX;
+ m_edgePtsBuff[(m_edgePtsCount * 6) - 3] = midY;
+ m_edgePtsBuff[(m_edgePtsCount * 6) - 6] = midX
+ + ((m_edgePtsBuff[(m_edgePtsCount * 2) - 2] - midX) * curveFactor);
+ m_edgePtsBuff[(m_edgePtsCount * 6) - 5] = midY
+ + ((m_edgePtsBuff[(m_edgePtsCount * 2) - 1] - midY) * curveFactor);
+ }
+
+ { // Last set the three control points related to point 0.
+
+ double dx = m_edgePtsBuff[2] - m_edgePtsBuff[0];
+ double dy = m_edgePtsBuff[3] - m_edgePtsBuff[1];
+ double len = Math.sqrt((dx * dx) + (dy * dy));
+ // Normalized.
+ dx /= len;
+ dy /= len;
+
+ double segStartX = m_edgePtsBuff[0]
+ + (dx * arrow0Size * getT(arrow0Type));
+ double segStartY = m_edgePtsBuff[1]
+ + (dy * arrow0Size * getT(arrow0Type));
+ double candX1 = segStartX + (dx * 2.0d * arrow0Size);
+ double candX2 = segStartX
+ + (curveFactor * (m_edgePtsBuff[2] - segStartX));
+
+ if (Math.abs(candX1 - m_edgePtsBuff[0]) > Math.abs(candX2
+ - m_edgePtsBuff[0])) {
+ m_edgePtsBuff[4] = candX1;
+ } else {
+ m_edgePtsBuff[4] = candX2;
+ }
+
+ double candY1 = segStartY + (dy * 2.0d * arrow0Size);
+ double candY2 = segStartY
+ + (curveFactor * (m_edgePtsBuff[3] - segStartY));
+
+ if (Math.abs(candY1 - m_edgePtsBuff[1]) > Math.abs(candY2
+ - m_edgePtsBuff[1])) {
+ m_edgePtsBuff[5] = candY1;
+ } else {
+ m_edgePtsBuff[5] = candY2;
+ }
+
+ m_edgePtsBuff[2] = segStartX;
+ m_edgePtsBuff[3] = segStartY;
+ }
+
+ m_edgePtsCount = edgePtsCount;
+
+ return true;
+ }
+
+ /**
+ * Computes the intersection point between a node outline and a line
+ * segment; one point of the line segment lies at the center of the node
+ * outline.
+ * <p>
+ * There is a constraint that only applies to SHAPE_ROUNDED_RECTANGLE which
+ * imposes that the maximum of the width and height be strictly less than
+ * twice the minimum of the width and height of the node.
+ *
+ * @param nodeShape
+ * the shape of the node in question; this must be one of the
+ * SHAPE_* constants or a custom node shape.
+ * @param xMin
+ * an extent of the node in question, in node coordinate space.
+ * @param yMin
+ * an extent of the node in question, in node coordinate space.
+ * @param xMax
+ * an extent of the node in question, in node coordinate space.
+ * @param yMax
+ * an extent of the node in question, in node coordinate space.
+ * @param offset
+ * most of the time this value will be zero, in which case the
+ * point computed is the exact intersection point of line segment
+ * and node outline; if this value is greater than zero, the
+ * point computed is one that lies on the line segment, is
+ * "outside" of the node outline, and is distance offset from the
+ * node outline.
+ * @param ptX
+ * specifies the X coordinate of the endpoint of the line segment
+ * that is not the endpoint lying in the center of the node
+ * shape.
+ * @param ptY
+ * specifies the Y coordinate of the endpoint of the line segment
+ * that is not the endpoint lying in the center of the node
+ * shape.
+ * @param returnVal
+ * if true is returned, returnVal[0] is set to be the X
+ * coordinate of the computed point and returnVal[1] is set to be
+ * the Y coordinate of the computed point; if false is returned,
+ * this array is not modified.
+ * @return true if and only if a point matching our criteria exists.
+ * @exception IllegalArgumentException
+ * if xMin is not less than xMax or if yMin is not less than
+ * yMax, if offset is negative, if nodeShape is
+ * SHAPE_ROUNDED_RECTANGLE and the condition max(width,
+ * height) < 2 * min(width, height) does not hold, or if
+ * nodeShape is neither one of the SHAPE_* constants nor a
+ * previously defined custom node shape.
+ */
+ public final boolean computeEdgeIntersection(final byte nodeShape,
+ final float xMin, final float yMin, final float xMax,
+ final float yMax, final float offset, final float ptX,
+ final float ptY, final float[] returnVal) {
+ if (m_debug) {
+ checkDispatchThread();
+ checkOrder(xMin,xMax,"x");
+ checkOrder(yMin,yMax,"y");
+ if (offset < 0.0f) {
+ throw new IllegalArgumentException("offset < 0");
+ }
+ }
+
+ NodeShape ns = nodeShapes.get(nodeShape);
+ if (ns == null)
+ return false;
+ else
+ return ns.computeEdgeIntersection( xMin, yMin, xMax, yMax, ptX, ptY, returnVal);
+ }
+
+ /**
+ * This method will render text very quickly. Translucent colors are not
+ * supported by the low detail rendering methods.
+ * <p>
+ * For the sake of maximum performance, this method works differently from
+ * the other rendering methods with respect to the scaling factor specified
+ * in clear(). That is, the font used to render the specified text will not
+ * be scaled; its exact size will be used when the text is rendered onto the
+ * underlying image. On the other hand, the parameters xCenter and yCenter
+ * specify coordinates in the node coordinate system, and so the point
+ * (xCenter, yCenter) will be transformed according the clear() transform in
+ * determining the location of the text on the underlying image.
+ *
+ * @param font
+ * the font to use in drawing text; the size of this font
+ * specifies the actual point size of what will be rendered onto
+ * the underlying image.
+ * @param text
+ * the text to render.
+ * @param xCenter
+ * the X coordinate of the center point of where to place the
+ * rendered text; specified in the node coordinate system.
+ * @param yCenter
+ * the Y coordinate of the center point of where to place the
+ * rendered text; specified in the node coordinate system.
+ * @param color
+ * the [fully opaque] color to use in rendering the text.
+ * @exception IllegalArgumentException
+ * if color is not opaque.
+ */
+ public final void drawTextLow(final Font font, final String text,
+ final float xCenter, final float yCenter, final Color color) {
+ if (m_debug) {
+ checkDispatchThread();
+ checkCleared();
+ if (color.getAlpha() != 255) {
+ throw new IllegalStateException("color is not opaque");
+ }
+ }
+
+ if (m_gMinimal == null) {
+ makeMinimalGraphics();
+ }
+
+ m_ptsBuff[0] = xCenter;
+ m_ptsBuff[1] = yCenter;
+ m_currXform.transform(m_ptsBuff, 0, m_ptsBuff, 0, 1);
+ m_gMinimal.setFont(font);
+
+ final FontMetrics fMetrics = m_gMinimal.getFontMetrics();
+ m_gMinimal.setColor(color);
+ m_gMinimal.drawString(
+ text,
+ (int) ((-0.5d * fMetrics.stringWidth(text)) + m_ptsBuff[0]),
+ (int) ((0.5d * fMetrics.getHeight())
+ - fMetrics.getDescent() + m_ptsBuff[1]));
+ }
+
+ /**
+ * Returns the context that is used by drawTextLow() to produce text shapes
+ * to be drawn to the screen. The transform contained in the returned
+ * context specifies the <i>only</i> scaling that will be done to fonts
+ * when rendering text using drawTextLow(). This transform does not change
+ * between frames no matter what scaling factor is specified in clear().
+ */
+ public final FontRenderContext getFontRenderContextLow() {
+ if (m_debug) {
+ checkDispatchThread();
+ }
+
+ if (m_gMinimal == null) {
+ makeMinimalGraphics();
+ }
+
+ return m_gMinimal.getFontRenderContext();
+ }
+
+ /**
+ * Renders text onto the underlying image with medium to high detail,
+ * depending on parameters specified.
+ *
+ * @param font
+ * the font to be used when rendering specified text; the
+ * rendering of glyph shapes generated by this font (using the
+ * context returned by getFontRenderContextFull()) is subjected
+ * to the same transformation as are nodes and edges (the
+ * transformation is defined by the clear() method); therefore,
+ * it is the point size of the font in addition to the scaling
+ * factor defined by clear() that determines the resulting size
+ * of text rendered to the graphics context.
+ * @param scaleFactor
+ * in order to prevent very small fonts from "degenerating" it is
+ * necessary to allow users to specify a scale factor in addition
+ * to the font size and transform defined by the clear() method;
+ * if this value is 1.0, no additional scaling is performed;
+ * otherwise, the size of the font is multiplied by this value to
+ * yield a new virtual font size.
+ * @param text
+ * the text to render.
+ * @param xCenter
+ * the text string is drawn such that its logical bounds
+ * rectangle with specified font is centered on this X coordinate
+ * (in the node coordinate system).
+ * @param yCenter
+ * the text string is drawn such that its logical bounds
+ * rectangle with specified font is centered on this Y coordinate
+ * (in the node coordinate system).
+ * @param theta
+ * in radians, specifies the angle of the text.
+ * @param paint
+ * the paint to use in rendering the text.
+ * @param drawTextAsShape
+ * this flag controls the way that text is drawn to the
+ * underlying graphics context; by default, all text rendering
+ * operations involve calling the operation
+ * Graphics2D.drawString(String, float, float) after setting
+ * specified font in the underlying graphics context; however, if
+ * this flag is set, the text to be rendered is converted to a
+ * primitive shape using font specified, and this shape is then
+ * rendered using Graphics2D.fill(Shape); on some systems, the
+ * shape filling method produces better-looking results when the
+ * graphics context is associated with an image that is to be
+ * rendered to the screen; however, on all systems tested, the
+ * shape filling method results in a substantial performance hit
+ * when the graphics context is associated with an image that is
+ * to be rendered to the screen; it is recommended to set this
+ * flag to true when either not much text is being rendered or
+ * when the zoom level is very high; the Graphics2D.drawString()
+ * operation has a difficult time when it needs to render text
+ * under a transformation with a very large scale factor.
+ */
+ public final void drawTextFull(final Font font, final double scaleFactor,
+ final String text, final float xCenter, final float yCenter,
+ final float theta, final Paint paint, final boolean drawTextAsShape) {
+ if (font.getSize() == 0) return;
+ if (m_debug) {
+ checkDispatchThread();
+ checkCleared();
+ if (scaleFactor < 0.0) {
+ throw new IllegalArgumentException("scaleFactor must be positive");
+ }
+ }
+
+ m_g2d.translate(xCenter, yCenter);
+ m_g2d.scale(scaleFactor, scaleFactor);
+
+ if (theta != 0.0f) {
+ m_g2d.rotate(theta);
+ }
+
+ m_g2d.setPaint(paint);
+
+ if (drawTextAsShape) {
+ final GlyphVector glyphV;
+
+ if (text.length() > m_charBuff.length) {
+ m_charBuff = new char[Math.max(m_charBuff.length * 2, text
+ .length())];
+ }
+
+ text.getChars(0, text.length(), m_charBuff, 0);
+ glyphV = font.layoutGlyphVector(getFontRenderContextFull(),
+ m_charBuff, 0, text.length(), Font.LAYOUT_NO_LIMIT_CONTEXT);
+
+ final Rectangle2D glyphBounds = glyphV.getLogicalBounds();
+ m_g2d.translate(-glyphBounds.getCenterX(), -glyphBounds
+ .getCenterY());
+ m_g2d.fill(glyphV.getOutline());
+ } else {
+ // Note: A new Rectangle2D is being constructed by this method call.
+ // As far as I know this performance hit is unavoidable.
+ final Rectangle2D textBounds = font.getStringBounds(text,
+ getFontRenderContextFull());
+ m_g2d.translate(-textBounds.getCenterX(), -textBounds.getCenterY());
+ m_g2d.setFont(font);
+ m_g2d.drawString(text, 0.0f, 0.0f);
+ }
+
+ m_g2d.setTransform(m_currNativeXform);
+ }
+
+ /**
+ * Returns the context that is used by drawTextFull() to produce text shapes
+ * to be drawn to the screen. This context always has the identity
+ * transform.
+ */
+ public final FontRenderContext getFontRenderContextFull() {
+ if (m_debug) {
+ checkDispatchThread();
+ }
+
+ return m_fontRenderContextFull;
+ }
+
+ /**
+ * Fills an arbitrary graphical shape with high detail.
+ * <p>
+ * This method will not work unless clear() has been called at least once
+ * previously.
+ *
+ * @param shape
+ * the shape to fill; the shape is specified in node coordinates.
+ * @param xOffset
+ * in node coordinates, a value to add to the X coordinates of
+ * the shape's definition.
+ * @param yOffset
+ * in node coordinates, a value to add to the Y coordinates of
+ * the shape's definition.
+ * @param paint
+ * the paint to use when filling the shape.
+ */
+ public final void drawCustomGraphicFull(final Shape shape,
+ final float xOffset, final float yOffset, final Paint paint) {
+ if (m_debug) {
+ checkDispatchThread();
+ checkCleared();
+ }
+
+ m_g2d.translate(xOffset, yOffset);
+ if(paint instanceof TexturePaint) {
+ final BufferedImage bImg = ((TexturePaint) paint).getImage();
+ m_g2d.drawImage(bImg,
+ shape.getBounds().x, shape.getBounds().y, shape.getBounds().width, shape.getBounds().height, null);
+ } else {
+ m_g2d.setPaint(paint);
+ m_g2d.fill(shape);
+ }
+
+ m_g2d.setTransform(m_currNativeXform);
+ }
+
+ private Stroke getStroke(float borderWidth) {
+ Stroke s = borderStrokes.get(borderWidth);
+ if ( s == null ) {
+ s = new BasicStroke(borderWidth);
+ borderStrokes.put(borderWidth, s);
+ }
+ return s;
+ }
+
+ private void checkDispatchThread() {
+ if (!EventQueue.isDispatchThread())
+ throw new IllegalStateException( "calling thread is not AWT event dispatcher");
+ }
+
+ private void checkCleared() {
+ if (!m_cleared)
+ throw new IllegalStateException( "clear() has not been called previously");
+ }
+
+ private void checkOrder(float min, float max, String id) {
+ if (!(min < max))
+ throw new IllegalArgumentException( id + "Min not less than " + id + "Max");
+ }
+}
diff --git a/corelibs/render.immed/src/main/java/cytoscape/render/immed/arrow/AbstractArrow.java b/corelibs/render.immed/src/main/java/cytoscape/render/immed/arrow/AbstractArrow.java
new file mode 100644
index 0000000..485ecc5
--- /dev/null
+++ b/corelibs/render.immed/src/main/java/cytoscape/render/immed/arrow/AbstractArrow.java
@@ -0,0 +1,75 @@
+
+/*
+ Copyright (c) 2009, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.render.immed.arrow;
+
+import java.awt.Shape;
+
+/**
+ * Try to keep this package protected.
+ */
+class AbstractArrow implements Arrow {
+
+ protected final double tOffset;
+ protected final byte type;
+
+ protected Shape arrow;
+ protected Shape cap;
+
+ AbstractArrow(final byte type, final double tOffset) {
+ this.type = type;
+ this.tOffset = tOffset;
+ this.arrow = null;
+ this.cap = null;
+ }
+
+ public Shape getArrowShape() {
+ return arrow;
+ }
+
+ public Shape getCapShape(final double ratio) {
+ // ignore the ratio by default
+ return cap;
+ }
+
+ public byte getType() {
+ return type;
+ }
+
+ public double getTOffset() {
+ return tOffset;
+ }
+}
+
diff --git a/corelibs/render.immed/src/main/java/cytoscape/render/immed/arrow/Arrow.java b/corelibs/render.immed/src/main/java/cytoscape/render/immed/arrow/Arrow.java
new file mode 100644
index 0000000..6ab1282
--- /dev/null
+++ b/corelibs/render.immed/src/main/java/cytoscape/render/immed/arrow/Arrow.java
@@ -0,0 +1,63 @@
+
+/*
+ Copyright (c) 2009, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.render.immed.arrow;
+
+import java.awt.Shape;
+
+public interface Arrow {
+ /**
+ * The Shape of the main Arrow body.
+ */
+ Shape getArrowShape();
+
+ /**
+ * The Shape of the cap that joins the Arrow body with the edge. This needs to
+ * be a distinct shape from the Arrow body because the cap needs to be the same
+ * color as the edge.
+ */
+ Shape getCapShape(final double ratio);
+
+ /**
+ * A legacy identifier for GraphGraphics.
+ */
+ byte getType();
+
+ /**
+ * The distance that the arrow should be offset from the intersection with the node.
+ */
+ double getTOffset();
+}
+
diff --git a/corelibs/render.immed/src/main/java/cytoscape/render/immed/arrow/ArrowheadArrow.java b/corelibs/render.immed/src/main/java/cytoscape/render/immed/arrow/ArrowheadArrow.java
new file mode 100644
index 0000000..e10e5ed
--- /dev/null
+++ b/corelibs/render.immed/src/main/java/cytoscape/render/immed/arrow/ArrowheadArrow.java
@@ -0,0 +1,58 @@
+
+/*
+ Copyright (c) 2009, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.render.immed.arrow;
+
+import java.awt.geom.GeneralPath;
+import cytoscape.render.immed.GraphGraphics;
+
+public class ArrowheadArrow extends AbstractArrow {
+
+ public ArrowheadArrow() {
+ super(GraphGraphics.ARROW_ARROWHEAD,2.0);
+
+ // create the arrow
+ GeneralPath arrowGP = new GeneralPath();
+ arrowGP.moveTo(-2.0f, -0.5f);
+ arrowGP.quadTo(-1.0f, 0f, 0.0f, 0.0f);
+ arrowGP.quadTo(-1.0f, 0f, -2.0f, 0.5f);
+ arrowGP.closePath();
+
+ arrow = arrowGP;
+
+ // no cap
+ }
+}
+
diff --git a/corelibs/render.immed/src/main/java/cytoscape/render/immed/arrow/DeltaArrow.java b/corelibs/render.immed/src/main/java/cytoscape/render/immed/arrow/DeltaArrow.java
new file mode 100644
index 0000000..a5b9ae0
--- /dev/null
+++ b/corelibs/render.immed/src/main/java/cytoscape/render/immed/arrow/DeltaArrow.java
@@ -0,0 +1,57 @@
+
+/*
+ Copyright (c) 2009, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.render.immed.arrow;
+
+import java.awt.geom.GeneralPath;
+import cytoscape.render.immed.GraphGraphics;
+
+public class DeltaArrow extends AbstractArrow {
+
+ public DeltaArrow() {
+ super(GraphGraphics.ARROW_DELTA,2.0);
+
+ // create the arrow
+ GeneralPath arrowGP = new GeneralPath();
+ arrowGP.moveTo(-2.0f, -0.5f);
+ arrowGP.lineTo(0.0f, 0.0f);
+ arrowGP.lineTo(-2.0f, 0.5f);
+ arrowGP.closePath();
+
+ arrow = arrowGP;
+
+ // no cap
+ }
+}
diff --git a/corelibs/render.immed/src/main/java/cytoscape/render/immed/arrow/DiamondArrow.java b/corelibs/render.immed/src/main/java/cytoscape/render/immed/arrow/DiamondArrow.java
new file mode 100644
index 0000000..d16e152
--- /dev/null
+++ b/corelibs/render.immed/src/main/java/cytoscape/render/immed/arrow/DiamondArrow.java
@@ -0,0 +1,68 @@
+
+/*
+ Copyright (c) 2009, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.render.immed.arrow;
+
+import java.awt.geom.GeneralPath;
+import cytoscape.render.immed.GraphGraphics;
+
+public class DiamondArrow extends AbstractArrow {
+
+ public DiamondArrow() {
+ super(GraphGraphics.ARROW_DIAMOND,2.0);
+
+ // create the arrow
+ GeneralPath arrowGP = new GeneralPath();
+ arrowGP.moveTo(-1.0f, -0.5f);
+ arrowGP.lineTo(0.0f, 0.0f);
+ arrowGP.lineTo(-1.0f, 0.5f);
+ arrowGP.lineTo(-2.0f, 0.0f);
+ arrowGP.closePath();
+
+ arrow = arrowGP;
+
+ // create the cap
+ GeneralPath capGP = new GeneralPath();
+ capGP.moveTo(0.0f, -0.5f);
+ capGP.lineTo(1.0f, -0.5f);
+ capGP.lineTo(0.0f, 0.0f);
+ capGP.lineTo(1.0f, 0.5f);
+ capGP.lineTo(0.0f, 0.5f);
+ capGP.closePath();
+
+ cap = capGP;
+ }
+}
+
diff --git a/corelibs/render.immed/src/main/java/cytoscape/render/immed/arrow/DiscArrow.java b/corelibs/render.immed/src/main/java/cytoscape/render/immed/arrow/DiscArrow.java
new file mode 100644
index 0000000..465b1a4
--- /dev/null
+++ b/corelibs/render.immed/src/main/java/cytoscape/render/immed/arrow/DiscArrow.java
@@ -0,0 +1,86 @@
+
+/*
+ Copyright (c) 2009, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.render.immed.arrow;
+
+import java.awt.Shape;
+import java.awt.geom.Ellipse2D;
+import java.awt.geom.Arc2D;
+import java.awt.geom.GeneralPath;
+import cytoscape.render.immed.GraphGraphics;
+
+public class DiscArrow extends AbstractArrow {
+
+ private final GeneralPath capGP;
+ private final Arc2D.Double capA;
+
+ private double currentRatio;
+
+ public DiscArrow() {
+ super(GraphGraphics.ARROW_DISC,1.0);
+
+ // create the arrow
+ final Ellipse2D.Double arrowE = new Ellipse2D.Double();
+ arrowE.setFrame(-1.0, -0.5, 1.0d, 1.0d);
+
+ arrow = arrowE;
+
+ // cap is calculated dynamically below!
+ capGP = new GeneralPath();
+ capA = new Arc2D.Double();
+
+ currentRatio = Double.NaN;
+ }
+
+ public synchronized Shape getCapShape(final double ratio) {
+ // only recreate the shape if we need to
+ if ( currentRatio != Double.NaN && ratio == currentRatio )
+ return capGP;
+
+ currentRatio = ratio;
+ final double theta = Math.toDegrees(Math.asin(1.0d / ratio));
+
+ capA.setArc(0.0d, ratio / -2.0d, ratio, ratio, 180.0d - theta, theta * 2, Arc2D.OPEN);
+
+ capGP.reset();
+ capGP.append(capA, false);
+ capGP.lineTo(0.0f, 0.5f);
+ capGP.lineTo(0.0f, -0.5f);
+ capGP.closePath();
+
+ return capGP;
+ }
+}
+
diff --git a/corelibs/render.immed/src/main/java/cytoscape/render/immed/arrow/HalfBottomArrow.java b/corelibs/render.immed/src/main/java/cytoscape/render/immed/arrow/HalfBottomArrow.java
new file mode 100644
index 0000000..5e8bbe9
--- /dev/null
+++ b/corelibs/render.immed/src/main/java/cytoscape/render/immed/arrow/HalfBottomArrow.java
@@ -0,0 +1,59 @@
+
+/*
+ Copyright (c) 2009, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.render.immed.arrow;
+
+import java.awt.geom.GeneralPath;
+import cytoscape.render.immed.GraphGraphics;
+
+public class HalfBottomArrow extends AbstractArrow {
+
+ public HalfBottomArrow() {
+ super(GraphGraphics.ARROW_HALF_BOTTOM,0.5);
+
+ // create the arrow
+ GeneralPath arrowGP = new GeneralPath();
+ arrowGP.moveTo(-0.3f,0.1f);
+ arrowGP.lineTo(-1.3f,1.1f);
+ arrowGP.lineTo(-1.435f, 1.1f);
+ arrowGP.lineTo(-0.535f, 0.2f);
+ arrowGP.lineTo(-0.535f, 0.1f);
+ arrowGP.closePath();
+
+ arrow = arrowGP;
+
+ // no cap
+ }
+}
diff --git a/corelibs/render.immed/src/main/java/cytoscape/render/immed/arrow/HalfTopArrow.java b/corelibs/render.immed/src/main/java/cytoscape/render/immed/arrow/HalfTopArrow.java
new file mode 100644
index 0000000..8dfa994
--- /dev/null
+++ b/corelibs/render.immed/src/main/java/cytoscape/render/immed/arrow/HalfTopArrow.java
@@ -0,0 +1,60 @@
+
+/*
+ Copyright (c) 2009, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.render.immed.arrow;
+
+import java.awt.geom.GeneralPath;
+import cytoscape.render.immed.GraphGraphics;
+
+public class HalfTopArrow extends AbstractArrow {
+
+ public HalfTopArrow() {
+ super(GraphGraphics.ARROW_HALF_TOP,0.5);
+
+ // create the arrow
+ GeneralPath arrowGP = new GeneralPath();
+ arrowGP.moveTo(-0.3f,-0.1f);
+ arrowGP.lineTo(-1.3f, -1.1f);
+ arrowGP.lineTo(-1.435f, -1.1f);
+ arrowGP.lineTo(-0.535f, -0.2f);
+ arrowGP.lineTo(-0.535f, -0.1f);
+ arrowGP.closePath();
+
+ arrow = arrowGP;
+
+ // no cap
+ }
+}
+
diff --git a/corelibs/render.immed/src/main/java/cytoscape/render/immed/arrow/NoArrow.java b/corelibs/render.immed/src/main/java/cytoscape/render/immed/arrow/NoArrow.java
new file mode 100644
index 0000000..2eb5f46
--- /dev/null
+++ b/corelibs/render.immed/src/main/java/cytoscape/render/immed/arrow/NoArrow.java
@@ -0,0 +1,55 @@
+
+/*
+ Copyright (c) 2009, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.render.immed.arrow;
+
+import java.awt.geom.Arc2D;
+import cytoscape.render.immed.GraphGraphics;
+
+public class NoArrow extends AbstractArrow {
+
+ public NoArrow() {
+ super(GraphGraphics.ARROW_NONE,0.0);
+
+ // no arrow
+
+ // create the cap
+ Arc2D.Double capA = new Arc2D.Double();
+ capA.setArc(-0.5, -0.5, 1.0, 1.0, 270.0, 180.0, Arc2D.CHORD);
+
+ cap = capA;
+ }
+}
+
diff --git a/corelibs/render.immed/src/main/java/cytoscape/render/immed/arrow/TeeArrow.java b/corelibs/render.immed/src/main/java/cytoscape/render/immed/arrow/TeeArrow.java
new file mode 100644
index 0000000..6c9f3a0
--- /dev/null
+++ b/corelibs/render.immed/src/main/java/cytoscape/render/immed/arrow/TeeArrow.java
@@ -0,0 +1,58 @@
+
+/*
+ Copyright (c) 2009, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.render.immed.arrow;
+
+import java.awt.geom.GeneralPath;
+import cytoscape.render.immed.GraphGraphics;
+
+public class TeeArrow extends AbstractArrow {
+
+ public TeeArrow() {
+ super(GraphGraphics.ARROW_TEE,0.5);
+
+ // create the arrow
+ GeneralPath arrowGP = new GeneralPath();
+ arrowGP.moveTo(-0.5f, -1.0f);
+ arrowGP.lineTo(-0.25f, -1.0f);
+ arrowGP.lineTo(-0.25f, 1.0f);
+ arrowGP.lineTo(-0.5f, 1.0f);
+ arrowGP.closePath();
+
+ arrow = arrowGP;
+
+ // no cap
+ }
+}
diff --git a/corelibs/render.immed/src/main/java/cytoscape/render/immed/nodeshape/AbstractNodeShape.java b/corelibs/render.immed/src/main/java/cytoscape/render/immed/nodeshape/AbstractNodeShape.java
new file mode 100644
index 0000000..2dbe324
--- /dev/null
+++ b/corelibs/render.immed/src/main/java/cytoscape/render/immed/nodeshape/AbstractNodeShape.java
@@ -0,0 +1,466 @@
+
+/*
+ Copyright (c) 2009, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.render.immed.nodeshape;
+
+import java.awt.Shape;
+import java.awt.geom.AffineTransform;
+import java.awt.geom.PathIterator;
+import java.awt.geom.CubicCurve2D;
+import java.awt.geom.QuadCurve2D;
+
+/**
+ * An abstract implementation of NodeShape that provides a basic way of computing
+ * the edge intersection.
+ */
+abstract class AbstractNodeShape implements NodeShape {
+
+ private final AffineTransform at = new AffineTransform();
+ private final CubicCurve2D cubic = new CubicCurve2D.Float(0f,0f,0.3f,0.3f,0.7f,0.7f,1f,1f);
+ private final QuadCurve2D quad = new QuadCurve2D.Float(0f,0f,0.5f,0.5f,1f,1f);
+ private final byte type;
+
+ AbstractNodeShape(byte type) {
+ this.type = type;
+ }
+
+ public byte getType() {
+ return type;
+ }
+
+ /**
+ * A basic implementation that works by unwinding the path of the node shape
+ * into line segments and calculating whether each segment intersects the edge.
+ * For quadratic and cubic segments of the shape we flatten the curve and then
+ * iterate over the resulting segments to determine an intersection. For some
+ * shapes there may be faster methods for calculatring the intersection, in which
+ * case we encourage you to provide your own implementation of this method!
+ */
+ public boolean computeEdgeIntersection(final float xMin, final float yMin, final float xMax,
+ final float yMax, final float ptX, final float ptY,
+ final float[] returnVal) {
+
+
+ final float centerX = (xMax + xMin)/2.0f;
+ final float centerY = (yMax + yMin)/2.0f;
+
+ final Shape shape = getShape(xMin,yMin,xMax,yMax);
+ final PathIterator pi = shape.getPathIterator(at);
+
+ // where the path iterator places its coordinates as it iterates
+ final float[] coords = new float[6];
+
+ // the beginning point of the line we test at each step
+ final float[] pt1 = new float[2];
+
+ // the ending point of the line we test at each step
+ final float[] pt2 = new float[2];
+
+ // the location of the first SEG_MOVETO - necessary for SEG_CLOSE
+ final float[] orig = new float[2];
+
+ // the point identifying the intersection of the two line segments
+ final float[] intersection = new float[2];
+
+ // iterate over each segment
+ while ( !pi.isDone() ) {
+ final int segment = pi.currentSegment(coords);
+ switch (segment) {
+
+ // record the initial point
+ case PathIterator.SEG_MOVETO:
+ orig[0] = coords[0];
+ orig[1] = coords[1];
+ pt1[0] = coords[0];
+ pt1[1] = coords[1];
+ break;
+
+ // record the next point and test
+ case PathIterator.SEG_LINETO:
+ pt2[0] = coords[0];
+ pt2[1] = coords[1];
+
+ if ( segmentIntersection(intersection,centerX,centerY,ptX,ptY,
+ pt1[0],pt1[1],pt2[0],pt2[1] ) ) {
+ returnVal[0] = intersection[0];
+ returnVal[1] = intersection[1];
+ return true;
+ } else {
+ pt1[0] = pt2[0];
+ pt1[1] = pt2[1];
+ }
+ break;
+
+ // record the quad and test the curve
+ case PathIterator.SEG_QUADTO:
+ pt2[0] = coords[2];
+ pt2[1] = coords[3];
+
+ quad.setCurve(pt1[0],pt1[1],coords[0],coords[1],coords[2],coords[3]);
+
+ if ( curveIntersection(intersection,centerX,centerY,ptX,ptY,quad) ) {
+ returnVal[0] = intersection[0];
+ returnVal[1] = intersection[1];
+ return true;
+ } else {
+ pt1[0] = pt2[0];
+ pt1[1] = pt2[1];
+ }
+ break;
+
+ // record the cubic and test the curve
+ case PathIterator.SEG_CUBICTO:
+ pt2[0] = coords[4];
+ pt2[1] = coords[5];
+
+ cubic.setCurve(pt1[0],pt1[1],coords[0],coords[1],coords[2],coords[3],coords[4],coords[5]);
+ if ( curveIntersection(intersection,centerX,centerY,ptX,ptY,cubic) ) {
+ returnVal[0] = intersection[0];
+ returnVal[1] = intersection[1];
+ return true;
+ } else {
+ pt1[0] = pt2[0];
+ pt1[1] = pt2[1];
+ }
+ break;
+
+ // use the last SEG_MOVETO point as the end point and test
+ case PathIterator.SEG_CLOSE:
+ pt2[0] = orig[0];
+ pt2[1] = orig[1];
+
+ if ( segmentIntersection(intersection,centerX,centerY,ptX,ptY,
+ pt1[0],pt1[1],pt2[0],pt2[1] ) ) {
+ returnVal[0] = intersection[0];
+ returnVal[1] = intersection[1];
+ return true;
+ }
+ break;
+ }
+ pi.next();
+ }
+ return false;
+ }
+
+
+ /**
+ * Computes the intersection of the line segment from (x1,y1) to (x2,y2)
+ * with the line segment from (x3,y3) to (x4,y4). If no intersection exists,
+ * returns false. Otherwise returns true, and returnVal[0] is set to be the
+ * X coordinate of the intersection point and returnVal[1] is set to be the
+ * Y coordinate of the intersection point. If more than one intersection
+ * point exists, "the intersection point" is defined to be the intersection
+ * point closest to (x1,y1). A note about overlapping line segments. Because
+ * of floating point numbers' inability to be totally accurate, it is quite
+ * difficult to represent overlapping line segments with floating point
+ * coordinates without using an absolute-precision math package. Because of
+ * this, poorly behaved outcome may result when computing the intersection
+ * of two [nearly] overlapping line segments. The only way around this would
+ * be to round intersection points to the nearest 32-bit floating point
+ * quantity. But then dynamic range is greatly compromised.
+ *
+ * @param returnVal A two element array specifying the point where the
+ * two line segments intersect. Element 0 specifies the X location and
+ * Element 1 specifies the Y location. If this method returns false,
+ * this array will not be modified.
+ * @param x1 The X location of beginning of the first line segment.
+ * @param y1 The Y location of beginning of the first line segment.
+ * @param x2 The X location of ending of the first line segment.
+ * @param y2 The Y location of ending of the first line segment.
+ * @param x3 The X location of beginning of the second line segment.
+ * @param y3 The Y location of beginning of the second line segment.
+ * @param x4 The X location of ending of the second line segment.
+ * @param y4 The Y location of ending of the second line segment.
+ * @return Whether or not the line segments defined by the input points intersect.
+ */
+ public static boolean segmentIntersection(final float[] returnVal,
+ float x1, float y1,
+ float x2, float y2,
+ float x3, float y3,
+ float x4, float y4) {
+
+ // Arrange the segment endpoints such that in segment 1, y1 >= y2
+ // and such that in segment 2, y3 >= y4.
+ boolean s1reverse = false;
+
+ if (y2 > y1) {
+ s1reverse = !s1reverse;
+
+ float temp = x1;
+ x1 = x2;
+ x2 = temp;
+ temp = y1;
+ y1 = y2;
+ y2 = temp;
+ }
+
+ if (y4 > y3) {
+ float temp = x3;
+ x3 = x4;
+ x4 = temp;
+ temp = y3;
+ y3 = y4;
+ y4 = temp;
+ }
+
+ //
+ // Note: While this algorithm for computing an intersection is
+ // completely bulletproof, it's not a straighforward 'classic'
+ // bruteforce method. This algorithm is well-suited for an
+ // implementation using fixed-point arithmetic instead of floating-point
+ // arithmetic because all computations are constrained to a certain
+ // dynamic range relative to the input parameters.
+ //
+ // We're going to reduce the problem in the following way:
+ //
+ //
+ // (x1,y1) + \ \ \ (x3,y3) x1 x3 ---------+------+----------- yMax
+ // ---------+------+----------- yMax \ | \ | \ | \ | \ | \ | \ | \ \ | \ |
+ // =====\ \ | \| > \| + =====/ + (x,y) |\ / |\ | \ | \ | \ | \
+ // ----------------+---+------- yMin ----------------+---+------ yMin |
+ // (x2,y2) x4 x2 | | + If W := (x2-x4) / ((x2-x4) + (x3-x1)) , then
+ // (x4,y4) x = x2 + W*(x1-x2) and y = yMin + W*(yMax-yMin)
+ //
+ final float yMax = Math.min(y1, y3);
+ final float yMin = Math.max(y2, y4);
+
+ if (yMin > yMax) {
+ return false;
+ }
+
+ if (y1 > yMax) {
+ x1 = x1 + (((x2 - x1) * (yMax - y1)) / (y2 - y1));
+ y1 = yMax;
+ }
+
+ if (y3 > yMax) {
+ x3 = x3 + (((x4 - x3) * (yMax - y3)) / (y4 - y3));
+ y3 = yMax;
+ }
+
+ if (y2 < yMin) {
+ x2 = x1 + (((x2 - x1) * (yMin - y1)) / (y2 - y1));
+ y2 = yMin;
+ }
+
+ if (y4 < yMin) {
+ x4 = x3 + (((x4 - x3) * (yMin - y3)) / (y4 - y3));
+ y4 = yMin;
+ }
+
+ // Handling for yMin == yMax. That is, in the reduced problem, both
+ // segments are horizontal.
+ if (yMin == yMax) {
+ // Arrange the segment endpoints such that in segment 1, x1 <= x2
+ // and such that in segment 2, x3 <= x4.
+ if (x2 < x1) {
+ s1reverse = !s1reverse;
+
+ float temp = x1;
+ x1 = x2;
+ x2 = temp;
+ temp = y1;
+ y1 = y2;
+ y2 = temp;
+ }
+
+ if (x4 < x3) {
+ float temp = x3;
+ x3 = x4;
+ x4 = temp;
+ temp = y3;
+ y3 = y4;
+ y4 = temp;
+ }
+
+ final float xMin = Math.max(x1, x3);
+ final float xMax = Math.min(x2, x4);
+
+ if (xMin > xMax) {
+ return false;
+ } else {
+ if (s1reverse) {
+ returnVal[0] = Math.max(xMin, xMax);
+ } else {
+ returnVal[0] = Math.min(xMin, xMax);
+ }
+
+ returnVal[1] = yMin; // == yMax
+
+ return true;
+ }
+ }
+
+ // It is now true that yMin < yMax because we've fully handled
+ // the yMin == yMax case above.
+ // Following if statement checks for a "twist" in the line segments.
+ if (((x1 < x3) && (x2 < x4)) || ((x3 < x1) && (x4 < x2))) {
+ return false;
+ }
+
+ // The segments are guaranteed to intersect.
+ if ((x1 == x3) && (x2 == x4)) { // The segments overlap.
+
+ if (s1reverse) {
+ returnVal[0] = x2;
+ returnVal[1] = y2;
+ } else {
+ returnVal[0] = x1;
+ returnVal[1] = y1;
+ }
+ }
+
+ // The segments are guaranteed to intersect in exactly one point.
+ final float W = (x2 - x4) / ((x2 - x4) + (x3 - x1));
+ returnVal[0] = x2 + (W * (x1 - x2));
+ returnVal[1] = yMin + (W * (yMax - yMin));
+
+ return true;
+ }
+
+ /**
+ * A method that computes the intersection of a line segment with
+ * either a quad or cubic curve.
+ * @param x1 X locaiton of the beginning point of the line segement.
+ * @param y1 Y locaiton of the beginning point of the line segement.
+ * @param x2 X locaiton of the ending point of the line segement.
+ * @param y2 Y locaiton of the ending point of the line segement.
+ * @param curve While this is typed as a Shape it must be either a CubicCurve2D
+ * or a QuadCurve2D.
+ */
+ private boolean curveIntersection(final float[] returnVal,
+ float x1, float y1, float x2, float y2, Shape curve) {
+
+ final float centerX = (x1 + x2)/2.0f;
+ final float centerY = (y1 + y2)/2.0f;
+
+ final PathIterator pi = curve.getPathIterator(at,0.05f);
+
+ // where the path iterator places its coordinates as it iterates
+ final float[] coords = new float[6];
+
+ // the beginning point of the line we test at each step
+ final float[] pt1 = new float[2];
+
+ // the ending point of the line we test at each step
+ final float[] pt2 = new float[2];
+
+ // the location of the first SEG_MOVETO - necessary for SEG_CLOSE
+ final float[] orig = new float[2];
+
+ // the point identifying the intersection of the two line segments
+ final float[] intersection = new float[2];
+
+ // iterate over each segment
+ while ( !pi.isDone() ) {
+ final int segment = pi.currentSegment(coords);
+ switch (segment) {
+ case PathIterator.SEG_MOVETO:
+ orig[0] = coords[0];
+ orig[1] = coords[1];
+ pt1[0] = coords[0];
+ pt1[1] = coords[1];
+ break;
+
+ case PathIterator.SEG_LINETO:
+ pt2[0] = coords[0];
+ pt2[1] = coords[1];
+
+ if ( segmentIntersection(intersection,centerX,centerY,x1,y1,
+ pt1[0],pt1[1],pt2[0],pt2[1] ) ) {
+ returnVal[0] = intersection[0];
+ returnVal[1] = intersection[1];
+ return true;
+ } else {
+ pt1[0] = pt2[0];
+ pt1[1] = pt2[1];
+ }
+ break;
+
+ case PathIterator.SEG_CLOSE:
+ pt2[0] = orig[0];
+ pt2[1] = orig[1];
+
+ if ( segmentIntersection(intersection,centerX,centerY,x1,y1,
+ pt1[0],pt1[1],pt2[0],pt2[1] ) ) {
+ returnVal[0] = intersection[0];
+ returnVal[1] = intersection[1];
+ return true;
+ }
+ break;
+
+ // This shouldn't ever happen because the input curve should be
+ // flattened into line segments (SEG_LINETO), but if it does,
+ // just treat the quad as if it were a line.
+ case PathIterator.SEG_QUADTO:
+ pt2[0] = coords[2];
+ pt2[1] = coords[3];
+
+ if ( segmentIntersection(intersection,centerX,centerY,x1,y1,
+ pt1[0],pt1[1],pt2[0],pt2[1] ) ) {
+ returnVal[0] = intersection[0];
+ returnVal[1] = intersection[1];
+ return true;
+ } else {
+ pt1[0] = pt2[0];
+ pt1[1] = pt2[1];
+ }
+ break;
+
+ // This shouldn't ever happen because the input curve should be
+ // flattened into line segments (SEG_LINETO), but if it does,
+ // just treat the cubic as if it were a line.
+ case PathIterator.SEG_CUBICTO:
+ pt2[0] = coords[4];
+ pt2[1] = coords[5];
+
+ if ( segmentIntersection(intersection,centerX,centerY,x1,y1,
+ pt1[0],pt1[1],pt2[0],pt2[1] ) ) {
+ returnVal[0] = intersection[0];
+ returnVal[1] = intersection[1];
+ return true;
+ } else {
+ pt1[0] = pt2[0];
+ pt1[1] = pt2[1];
+ }
+ break;
+
+ }
+ pi.next();
+ }
+
+ return false;
+ }
+}
diff --git a/corelibs/render.immed/src/main/java/cytoscape/render/immed/nodeshape/DiamondNodeShape.java b/corelibs/render.immed/src/main/java/cytoscape/render/immed/nodeshape/DiamondNodeShape.java
new file mode 100644
index 0000000..d858442
--- /dev/null
+++ b/corelibs/render.immed/src/main/java/cytoscape/render/immed/nodeshape/DiamondNodeShape.java
@@ -0,0 +1,66 @@
+
+/*
+ Copyright (c) 2009, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.render.immed.nodeshape;
+
+import cytoscape.render.immed.GraphGraphics;
+
+import java.awt.geom.GeneralPath;
+import java.awt.Shape;
+
+public class DiamondNodeShape extends AbstractNodeShape {
+
+ private final GeneralPath path;
+
+ public DiamondNodeShape() {
+ super(GraphGraphics.SHAPE_DIAMOND);
+ path = new GeneralPath();
+ }
+
+ public Shape getShape(float xMin, float yMin, float xMax, float yMax) {
+
+ path.reset();
+
+ path.moveTo((xMin + xMax) / 2.0f, yMin);
+ path.lineTo(xMax, (yMin + yMax) / 2.0f);
+ path.lineTo((xMin + xMax) / 2.0f, yMax);
+ path.lineTo(xMin, (yMin + yMax) / 2.0f);
+
+ path.closePath();
+
+ return path;
+ }
+}
+
diff --git a/corelibs/render.immed/src/main/java/cytoscape/render/immed/nodeshape/EllipseNodeShape.java b/corelibs/render.immed/src/main/java/cytoscape/render/immed/nodeshape/EllipseNodeShape.java
new file mode 100644
index 0000000..27c7bac
--- /dev/null
+++ b/corelibs/render.immed/src/main/java/cytoscape/render/immed/nodeshape/EllipseNodeShape.java
@@ -0,0 +1,86 @@
+
+/*
+ Copyright (c) 2009, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.render.immed.nodeshape;
+
+import cytoscape.render.immed.GraphGraphics;
+
+import java.awt.Shape;
+import java.awt.geom.Ellipse2D;
+
+public class EllipseNodeShape extends AbstractNodeShape {
+
+ private final Ellipse2D.Float ellipse;
+
+ public EllipseNodeShape() {
+ super(GraphGraphics.SHAPE_ELLIPSE);
+ ellipse = new Ellipse2D.Float(0.0f,0.0f,1.0f,1.0f);
+ }
+
+ public Shape getShape(float xMin, float yMin, float xMax, float yMax) {
+ ellipse.setFrame(xMin, yMin, xMax - xMin, yMax - yMin);
+ return ellipse;
+ }
+
+ public boolean computeEdgeIntersection(final float xMin, final float yMin, final float xMax,
+ final float yMax, final float ptX, final float ptY,
+ final float[] returnVal) {
+
+ final double centerX = ((double)xMax + (double)xMin)/2.0;
+ final double centerY = ((double)yMax + (double)yMin)/2.0;
+
+ if ((centerX == ptX) && (centerY == ptY))
+ return false;
+
+ final double ptPrimeX = ptX - centerX;
+ final double ptPrimeY = ptY - centerY;
+ final double ellpW = ((double) xMax) - xMin;
+ final double ellpH = ((double) yMax) - yMin;
+ final double xScaleFactor = 2.0 / ellpW;
+ final double yScaleFactor = 2.0 / ellpH;
+ final double xformedPtPrimeX = ptPrimeX * xScaleFactor;
+ final double xformedPtPrimeY = ptPrimeY * yScaleFactor;
+ final double xformedDist = Math.sqrt((xformedPtPrimeX * xformedPtPrimeX) + (xformedPtPrimeY * xformedPtPrimeY));
+ final double xsectXformedPtPrimeX = xformedPtPrimeX / xformedDist;
+ final double xsectXformedPtPrimeY = xformedPtPrimeY / xformedDist;
+ final double xsectPtPrimeX = xsectXformedPtPrimeX / xScaleFactor;
+ final double xsectPtPrimeY = xsectXformedPtPrimeY / yScaleFactor;
+ returnVal[0] = (float) (xsectPtPrimeX + centerX);
+ returnVal[1] = (float) (xsectPtPrimeY + centerY);
+
+ return true;
+ }
+}
+
diff --git a/corelibs/render.immed/src/main/java/cytoscape/render/immed/nodeshape/HexagonNodeShape.java b/corelibs/render.immed/src/main/java/cytoscape/render/immed/nodeshape/HexagonNodeShape.java
new file mode 100644
index 0000000..7853691
--- /dev/null
+++ b/corelibs/render.immed/src/main/java/cytoscape/render/immed/nodeshape/HexagonNodeShape.java
@@ -0,0 +1,67 @@
+
+/*
+ Copyright (c) 2009, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.render.immed.nodeshape;
+
+import cytoscape.render.immed.GraphGraphics;
+
+public class HexagonNodeShape extends LegacyCustomNodeShape {
+
+ private static final double[] coords = new double[12];
+
+ static {
+ // 1x1 square centered around 0,0
+ final double min = -0.5;
+ final double max = 0.5;
+
+ // defines a right triangle found within the hexagon
+ final double x = (max - min)/4.0; // horizontal
+ final double z = x * 2.0; // hypotenuse
+ final double y = z * Math.sin(Math.PI/3.0); // vertical
+
+ // X coordinates Y coordinates
+ coords[0] = min; coords[1] = min + z;
+ coords[2] = min + x; coords[3] = min + z + y;
+ coords[4] = min + x + z; coords[5] = min + z + y;
+ coords[6] = max; coords[7] = min + z;
+ coords[8] = min + x + z; coords[9] = max - z - y;
+ coords[10] = min + x; coords[11] = max - z - y;
+ }
+
+ public HexagonNodeShape() {
+ super(coords, GraphGraphics.SHAPE_HEXAGON);
+ }
+}
+
diff --git a/corelibs/render.immed/src/main/java/cytoscape/render/immed/nodeshape/LegacyCustomNodeShape.java b/corelibs/render.immed/src/main/java/cytoscape/render/immed/nodeshape/LegacyCustomNodeShape.java
new file mode 100644
index 0000000..54dd92a
--- /dev/null
+++ b/corelibs/render.immed/src/main/java/cytoscape/render/immed/nodeshape/LegacyCustomNodeShape.java
@@ -0,0 +1,89 @@
+
+/*
+ Copyright (c) 2009, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.render.immed.nodeshape;
+
+import cytoscape.render.immed.GraphGraphics;
+
+import java.awt.geom.GeneralPath;
+import java.awt.geom.AffineTransform;
+import java.awt.Shape;
+
+public class LegacyCustomNodeShape extends AbstractNodeShape {
+
+ private final GeneralPath path;
+ private final AffineTransform xform;
+ private final double[] coords;
+ private final double[] xformCoords;;
+
+ public LegacyCustomNodeShape(final double[] coords, final byte type) {
+ super(type);
+ this.coords = coords;
+ this.xformCoords = new double[coords.length];
+ path = new GeneralPath();
+ xform = new AffineTransform();
+ }
+
+ public float[] getCoords() {
+ final float[] returnThis = new float[coords.length];
+
+ for (int i = 0; i < returnThis.length; i++)
+ returnThis[i] = (float) coords[i];
+
+ return returnThis;
+ }
+
+ public Shape getShape(float xMin, float yMin, float xMax, float yMax) {
+
+ final double desiredXCenter = (xMin + xMax) / 2.0;
+ final double desiredYCenter = (yMin + yMax) / 2.0;
+ final double desiredWidth = xMax - xMin;
+ final double desiredHeight = yMax - yMin;
+ xform.setToTranslation(desiredXCenter, desiredYCenter);
+ xform.scale(desiredWidth, desiredHeight);
+ xform.transform(coords, 0, xformCoords, 0, coords.length/2);
+
+ path.reset();
+
+ path.moveTo((float) xformCoords[0], (float) xformCoords[1]);
+
+ for (int i = 2; i < xformCoords.length;)
+ path.lineTo((float) xformCoords[i++], (float) xformCoords[i++]);
+
+ path.closePath();
+
+ return path;
+ }
+}
diff --git a/corelibs/render.immed/src/main/java/cytoscape/render/immed/nodeshape/NodeShape.java b/corelibs/render.immed/src/main/java/cytoscape/render/immed/nodeshape/NodeShape.java
new file mode 100644
index 0000000..184a46e
--- /dev/null
+++ b/corelibs/render.immed/src/main/java/cytoscape/render/immed/nodeshape/NodeShape.java
@@ -0,0 +1,69 @@
+
+/*
+ Copyright (c) 2009, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.render.immed.nodeshape;
+
+import java.awt.Shape;
+
+/**
+ * An interface defining the methods necessary to render a node shape in GraphGraphics.
+ */
+public interface NodeShape {
+
+ /**
+ * A legacy method to interact cleanly with the current implementation of
+ * GraphGraphics.
+ * @return the byte associated with this node shape.
+ */
+ byte getType();
+
+ /**
+ * Returns a Shape object scaled to fit within the bounding box defined by the
+ * input parameters.
+ */
+ Shape getShape(final float xMin,final float yMin, final float xMax, final float yMax);
+
+ /**
+ * Computes the intersection of the node shape with and edge. The edge is defined
+ * by the point at the center of the bounding box defined by xMin, yMin, xMax, yMax
+ * and the point defined by ptX and ptY. If the edge intersects with the shape then
+ * the point at which the edge and shape itersect is stored in returnVal, where the
+ * X location is in element 0 and the Y location is in element 1.
+ */
+ boolean computeEdgeIntersection(final float xMin, final float yMin, final float xMax,
+ final float yMax, final float ptX, final float ptY,
+ final float[] returnVal);
+}
+
diff --git a/corelibs/render.immed/src/main/java/cytoscape/render/immed/nodeshape/OctagonNodeShape.java b/corelibs/render.immed/src/main/java/cytoscape/render/immed/nodeshape/OctagonNodeShape.java
new file mode 100644
index 0000000..e6cd85c
--- /dev/null
+++ b/corelibs/render.immed/src/main/java/cytoscape/render/immed/nodeshape/OctagonNodeShape.java
@@ -0,0 +1,81 @@
+
+/*
+ Copyright (c) 2009, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.render.immed.nodeshape;
+
+import cytoscape.render.immed.GraphGraphics;
+
+import java.awt.geom.GeneralPath;
+import java.awt.Shape;
+
+public class OctagonNodeShape extends AbstractNodeShape {
+
+ private static final float SQRT2 = (float)Math.sqrt(2.0);
+ private static final float SQRT2plus2 = 2.0f + SQRT2;
+
+ private final GeneralPath path;
+
+ public OctagonNodeShape() {
+ super(GraphGraphics.SHAPE_OCTAGON);
+ path = new GeneralPath();
+ }
+
+ public Shape getShape(float xMin, float yMin, float xMax, float yMax) {
+
+ // If bounding box is square, then these eqns will create an
+ // equilateral octagon. If not, the sides will be scaled nicely.
+ final float xx = (xMax - xMin)/SQRT2plus2;
+ final float xz = xx * SQRT2;
+
+ final float yx = (yMax - yMin)/SQRT2plus2;
+ final float yz = yx * SQRT2;
+
+ path.reset();
+
+ path.moveTo( xMin, yMin + yx );
+ path.lineTo( xMin, yMin + yx + yz );
+ path.lineTo( xMin + xx, yMax );
+ path.lineTo( xMin + xx + xz, yMax );
+ path.lineTo( xMax, yMin + yx + yz );
+ path.lineTo( xMax, yMin + yx );
+ path.lineTo( xMin + xx + xz, yMin );
+ path.lineTo( xMin + xx, yMin );
+
+ path.closePath();
+
+ return path;
+ }
+}
+
diff --git a/corelibs/render.immed/src/main/java/cytoscape/render/immed/nodeshape/ParallelogramNodeShape.java b/corelibs/render.immed/src/main/java/cytoscape/render/immed/nodeshape/ParallelogramNodeShape.java
new file mode 100644
index 0000000..44966e3
--- /dev/null
+++ b/corelibs/render.immed/src/main/java/cytoscape/render/immed/nodeshape/ParallelogramNodeShape.java
@@ -0,0 +1,66 @@
+
+/*
+ Copyright (c) 2009, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.render.immed.nodeshape;
+
+import cytoscape.render.immed.GraphGraphics;
+
+import java.awt.geom.GeneralPath;
+import java.awt.Shape;
+
+public class ParallelogramNodeShape extends AbstractNodeShape {
+
+ private final GeneralPath path;
+
+ public ParallelogramNodeShape() {
+ super(GraphGraphics.SHAPE_PARALLELOGRAM);
+ path = new GeneralPath();
+ }
+
+ public Shape getShape(float xMin, float yMin, float xMax, float yMax) {
+
+ path.reset();
+
+ path.moveTo(xMin, yMin);
+ path.lineTo(((2.0f * xMax) + xMin) / 3.0f, yMin);
+ path.lineTo(xMax, yMax);
+ path.lineTo(((2.0f * xMin) + xMax) / 3.0f, yMax);
+
+ path.closePath();
+
+ return path;
+ }
+}
+
diff --git a/corelibs/render.immed/src/main/java/cytoscape/render/immed/nodeshape/RectangleNodeShape.java b/corelibs/render.immed/src/main/java/cytoscape/render/immed/nodeshape/RectangleNodeShape.java
new file mode 100644
index 0000000..1e896d6
--- /dev/null
+++ b/corelibs/render.immed/src/main/java/cytoscape/render/immed/nodeshape/RectangleNodeShape.java
@@ -0,0 +1,57 @@
+
+/*
+ Copyright (c) 2009, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.render.immed.nodeshape;
+
+import cytoscape.render.immed.GraphGraphics;
+
+import java.awt.Shape;
+import java.awt.geom.Rectangle2D;
+
+public class RectangleNodeShape extends AbstractNodeShape {
+
+ private final Rectangle2D.Float rect;
+
+ public RectangleNodeShape() {
+ super(GraphGraphics.SHAPE_RECTANGLE);
+ rect = new Rectangle2D.Float(0.0f,0.0f,1.0f,1.0f);
+ }
+
+ public Shape getShape(float xMin, float yMin, float xMax, float yMax) {
+ rect.setRect(xMin, yMin, xMax - xMin, yMax - yMin);
+ return rect;
+ }
+}
+
diff --git a/corelibs/render.immed/src/main/java/cytoscape/render/immed/nodeshape/RoundedRectangleNodeShape.java b/corelibs/render.immed/src/main/java/cytoscape/render/immed/nodeshape/RoundedRectangleNodeShape.java
new file mode 100644
index 0000000..13fe831
--- /dev/null
+++ b/corelibs/render.immed/src/main/java/cytoscape/render/immed/nodeshape/RoundedRectangleNodeShape.java
@@ -0,0 +1,59 @@
+
+/*
+ Copyright (c) 2009, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.render.immed.nodeshape;
+
+import cytoscape.render.immed.GraphGraphics;
+
+import java.awt.Shape;
+import java.awt.geom.RoundRectangle2D;
+
+public class RoundedRectangleNodeShape extends AbstractNodeShape {
+
+ private final RoundRectangle2D.Float rect;
+
+ public RoundedRectangleNodeShape() {
+ super(GraphGraphics.SHAPE_ROUNDED_RECTANGLE);
+ rect = new RoundRectangle2D.Float(0.0f,0.0f,1.0f,1.0f,0.3f,0.3f);
+ }
+
+ public Shape getShape(float xMin, float yMin, float xMax, float yMax) {
+ final float w = xMax - xMin;
+ final float h = yMax - yMin;
+ final float arcSize = Math.min(w, h) / 4f;
+ rect.setRoundRect(xMin, yMin, w, h, arcSize, arcSize);
+ return rect;
+ }
+}
diff --git a/corelibs/render.immed/src/main/java/cytoscape/render/immed/nodeshape/TriangleNodeShape.java b/corelibs/render.immed/src/main/java/cytoscape/render/immed/nodeshape/TriangleNodeShape.java
new file mode 100644
index 0000000..00da860
--- /dev/null
+++ b/corelibs/render.immed/src/main/java/cytoscape/render/immed/nodeshape/TriangleNodeShape.java
@@ -0,0 +1,65 @@
+
+/*
+ Copyright (c) 2009, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.render.immed.nodeshape;
+
+import cytoscape.render.immed.GraphGraphics;
+
+import java.awt.geom.GeneralPath;
+import java.awt.Shape;
+
+public class TriangleNodeShape extends AbstractNodeShape {
+
+ private final GeneralPath path;
+
+ public TriangleNodeShape() {
+ super(GraphGraphics.SHAPE_TRIANGLE);
+ path = new GeneralPath();
+ }
+
+ public Shape getShape(float xMin, float yMin, float xMax, float yMax) {
+
+ path.reset();
+
+ path.moveTo((xMin + xMax) / 2.0f, yMin);
+ path.lineTo(xMax, yMax);
+ path.lineTo(xMin, yMax);
+
+ path.closePath();
+
+ return path;
+ }
+}
+
diff --git a/corelibs/render.immed/src/main/java/cytoscape/render/immed/nodeshape/VeeNodeShape.java b/corelibs/render.immed/src/main/java/cytoscape/render/immed/nodeshape/VeeNodeShape.java
new file mode 100644
index 0000000..10638c3
--- /dev/null
+++ b/corelibs/render.immed/src/main/java/cytoscape/render/immed/nodeshape/VeeNodeShape.java
@@ -0,0 +1,66 @@
+
+/*
+ Copyright (c) 2009, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.render.immed.nodeshape;
+
+import cytoscape.render.immed.GraphGraphics;
+
+import java.awt.geom.GeneralPath;
+import java.awt.Shape;
+
+public class VeeNodeShape extends AbstractNodeShape {
+
+ private final GeneralPath path;
+
+ public VeeNodeShape() {
+ super(GraphGraphics.SHAPE_VEE);
+ path = new GeneralPath();
+ }
+
+ public Shape getShape(float xMin, float yMin, float xMax, float yMax) {
+
+ path.reset();
+
+ path.moveTo(xMin, yMin);
+ path.lineTo((xMin + xMax) / 2.0f, ((2.0f * yMin) + yMax) / 3.0f);
+ path.lineTo(xMax, yMin);
+ path.lineTo((xMin + xMax) / 2.0f, yMax);
+
+ path.closePath();
+
+ return path;
+ }
+}
+
diff --git a/corelibs/render.immed/src/test/java/cytoscape/render/immed/GraphGraphicsTest.java b/corelibs/render.immed/src/test/java/cytoscape/render/immed/GraphGraphicsTest.java
new file mode 100644
index 0000000..e3d0720
--- /dev/null
+++ b/corelibs/render.immed/src/test/java/cytoscape/render/immed/GraphGraphicsTest.java
@@ -0,0 +1,248 @@
+
+/*
+ Copyright (c) 2009, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.render.immed;
+
+import junit.framework.*;
+
+import java.util.List;
+import java.awt.Color;
+import java.awt.Image;
+import java.awt.image.BufferedImage;
+import javax.imageio.ImageIO;
+import java.io.File;
+import java.io.IOException;
+import java.util.Random;
+import java.awt.BasicStroke;
+
+import org.apache.commons.math.stat.inference.TestUtils;
+import org.apache.commons.math.MathException;
+
+public class GraphGraphicsTest extends TestCase {
+
+ GraphGraphics currentGraphGraphics;
+ OldGraphGraphics oldGraphGraphics;
+ int numNodes;
+ int numEdges;
+ BufferedImage image;
+ int canvasSize = 1000;
+ int numTests = 20;
+
+ public GraphGraphicsTest() {
+ super();
+ String prop = System.getProperties().getProperty("num.graph.objects","5000");
+ int numGraphObjs = 5000;
+ if ( prop.matches("^\\d+$") )
+ numGraphObjs = Integer.parseInt(prop);
+
+ numNodes = numGraphObjs;
+ numEdges = numGraphObjs;
+ }
+
+ public void setUp() {
+ image = new BufferedImage(canvasSize,canvasSize,BufferedImage.TYPE_INT_ARGB);
+ currentGraphGraphics = new GraphGraphics(image,false);
+ currentGraphGraphics.clear(Color.white,0,0,1.0);
+ oldGraphGraphics = new OldGraphGraphics(image,false);
+ oldGraphGraphics.clear(Color.white,0,0,1.0);
+ }
+
+ public void testRenderGraphFull() {
+ // run everything once, to prime the system
+ Random rand = new Random(10);
+ long oldDur = drawOldFull(rand);
+ rand = new Random(10);
+ long currDur = drawCurrentFull(rand);
+
+ // now run each test numTests times and sum the durations
+ long totalOldDur = 0;
+ long totalCurrDur = 0;
+ double[] oldDurs = new double[numTests];
+ double[] currDurs = new double[numTests];
+ for ( int i = 0; i < numTests; i++ ) {
+ rand = new Random(i);
+ oldDur = drawOldFull(rand);
+ oldDurs[i] = (double)oldDur;
+ totalOldDur += oldDur;
+
+ rand = new Random(i);
+ currDur = drawCurrentFull(rand);
+ currDurs[i] = (double)currDur;
+ totalCurrDur += currDur;
+
+ System.out.println("Old: " + oldDur + " Current: " + currDur +
+ " diff: " + (oldDur - currDur) );
+ }
+
+ System.out.println("Total Old : " + totalOldDur);
+ System.out.println("Total Current: " + totalCurrDur);
+
+ // Because the variance of the durations is so high, we can't just
+ // just fail whenever we happen to be slower. Therefore, we perform
+ // a t-test on the old and current durations and then evaluate the
+ // p-value to determine if we are actually slower.
+ double pValue = 1.0;
+ try {
+ pValue = TestUtils.tTest(oldDurs, currDurs);
+ } catch (MathException me) {
+ me.printStackTrace();
+ }
+
+ System.out.println("T-test p-value: " + pValue);
+
+ long diff = (totalOldDur-totalCurrDur)/numTests;
+ // If the new code is faster than the old code, then we're good
+ // and just move on. No sense in evaluating the p-value because
+ // if we're faster AND statistically significantly faster, then
+ // that's a good thing and we don't want to fail.
+ if ( diff >= 0 ) {
+ System.out.println(" Faster on avg by: " + diff);
+
+ // If we're slower than the old code (i.e. a bad thing), then
+ // evaluate the p-value to determine if the difference is
+ // statistically significant and only fail if it is.
+ } else {
+ System.out.println(" Slower on avg by: " + diff);
+
+ assertTrue(pValue > 0.05);
+ }
+ }
+
+ private long drawCurrentFull(Random rand) {
+ final float nodeSizeFactor = 50f;
+ float size = (float) canvasSize;
+
+ long begin = System.nanoTime();
+ for ( int i = 0; i < numNodes; i++ ) {
+ float x = rand.nextFloat() * (rand.nextBoolean() ? size : -size);
+ float y = rand.nextFloat() * (rand.nextBoolean() ? size : -size);
+ currentGraphGraphics.drawNodeFull( (byte)(i % (int) GraphGraphics.s_last_shape),
+ x,
+ y,
+ (x + (rand.nextFloat() * nodeSizeFactor)),
+ (y + (rand.nextFloat() * nodeSizeFactor)),
+ Color.blue,
+ 1.0f + (i % 10),
+ Color.yellow);
+ }
+ long end = System.nanoTime();
+ long nodeDur = end - begin;
+
+ BasicStroke edgeStroke = new BasicStroke(1f);
+
+ begin = System.nanoTime();
+ for ( int i = 0; i < numEdges; i++ ) {
+ currentGraphGraphics.drawEdgeFull(
+ (byte)((i % 7)-8),
+ rand.nextFloat() * (20f),
+ Color.red,
+ (byte)((i % 7)-8),
+ rand.nextFloat() * (20f),
+ Color.orange,
+ rand.nextFloat() * (rand.nextBoolean() ? size : -size),
+ rand.nextFloat() * (rand.nextBoolean() ? size : -size),
+ currentGraphGraphics.m_noAnchors,
+ rand.nextFloat() * (rand.nextBoolean() ? size : -size),
+ rand.nextFloat() * (rand.nextBoolean() ? size : -size),
+ 1f,
+ edgeStroke,
+ Color.green);
+ }
+ end = System.nanoTime();
+ long duration = (end - begin) + nodeDur;
+
+// try {
+// ImageIO.write(image,"PNG",new File("/tmp/homer-current-" + rand.nextInt(100) + ".png"));
+// } catch (IOException ioe) { ioe.printStackTrace(); }
+ return duration;
+ }
+
+ private long drawOldFull(Random rand) {
+ final float nodeSizeFactor = 50f;
+ float size = (float) canvasSize;
+
+ long begin = System.nanoTime();
+ for ( int i = 0; i < numNodes; i++ ) {
+ float x = rand.nextFloat() * (rand.nextBoolean() ? size : -size);
+ float y = rand.nextFloat() * (rand.nextBoolean() ? size : -size);
+ oldGraphGraphics.drawNodeFull( (byte)(i % (int) OldGraphGraphics.s_last_shape),
+ x,
+ y,
+ (x + (rand.nextFloat() * nodeSizeFactor)),
+ (y + (rand.nextFloat() * nodeSizeFactor)),
+ Color.blue,
+ 1.0f + (i % 10),
+ Color.yellow);
+ }
+ long end = System.nanoTime();
+ long nodeDur = end - begin;
+
+ BasicStroke edgeStroke = new BasicStroke(1f);
+
+ begin = System.nanoTime();
+ for ( int i = 0; i < numEdges; i++ ) {
+ oldGraphGraphics.drawEdgeFull(
+ (byte)((i % 7)-8),
+ rand.nextFloat() * (20f),
+ Color.red,
+ (byte)((i % 7)-8),
+ rand.nextFloat() * (20f),
+ Color.orange,
+ rand.nextFloat() * (rand.nextBoolean() ? size : -size),
+ rand.nextFloat() * (rand.nextBoolean() ? size : -size),
+ oldGraphGraphics.m_noAnchors,
+ rand.nextFloat() * (rand.nextBoolean() ? size : -size),
+ rand.nextFloat() * (rand.nextBoolean() ? size : -size),
+ 1f,
+ Color.green,
+ 0f);
+ }
+ end = System.nanoTime();
+
+ long duration = (end - begin) + nodeDur;
+
+// try {
+// ImageIO.write(image,"PNG",new File("/tmp/homer-old-" + rand.nextInt(100) + ".png"));
+// } catch (IOException ioe) { ioe.printStackTrace(); }
+ return duration;
+ }
+
+ // This will run the JUnit gui, which can be useful for debugging.
+ public static void main(String[] args) {
+ String[] newargs = { "cytoscape.render.immed.GraphGraphicsTest", "-noloading" };
+ junit.swingui.TestRunner.main(newargs);
+ }
+}
diff --git a/corelibs/render.immed/src/test/java/cytoscape/render/immed/OldGraphGraphics.java b/corelibs/render.immed/src/test/java/cytoscape/render/immed/OldGraphGraphics.java
new file mode 100644
index 0000000..1f33d7d
--- /dev/null
+++ b/corelibs/render.immed/src/test/java/cytoscape/render/immed/OldGraphGraphics.java
@@ -0,0 +1,3413 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.render.immed;
+
+import java.awt.AlphaComposite;
+import java.awt.BasicStroke;
+import java.awt.Color;
+import java.awt.Composite;
+import java.awt.EventQueue;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Graphics2D;
+import java.awt.Image;
+import java.awt.Paint;
+import java.awt.RenderingHints;
+import java.awt.Shape;
+import java.awt.font.FontRenderContext;
+import java.awt.font.GlyphVector;
+import java.awt.geom.AffineTransform;
+import java.awt.geom.Arc2D;
+import java.awt.geom.Ellipse2D;
+import java.awt.geom.GeneralPath;
+import java.awt.geom.Line2D;
+import java.awt.geom.Rectangle2D;
+
+import java.util.HashMap;
+import java.util.Map;
+
+/**
+ * The purpose of this class is to make the proper calls on a Graphics2D object
+ * to efficiently render nodes, labels, and edges. This is procedural
+ * programming at its finest [sarcasm].
+ * <p>
+ * This class deals with two coordinate systems: an image coordinate system and
+ * a node coordinate system. The programmer who uses this API will be dealing
+ * mostly with the node coordinate system, especially when rendering individual
+ * nodes and edges. The clear() method specifies the mapping from the node
+ * coordinate system to the image coordinate system. The two coordinate systems
+ * do have the same orientations: increasing X values point to the right and
+ * increasing Y values point to the bottom. The image coordinate system dictates
+ * that (0,0) is the upper left corner of the image and that each unit
+ * represents a pixel width (or height). if (m_debug) { if
+ * (!EventQueue.isDispatchThread()) throw new IllegalStateException( "calling
+ * thread is not AWT event dispatcher");
+ *
+ * if (!(xMin < xMax)) throw new IllegalArgumentException("xMin not less than
+ * xMax");
+ *
+ * if (!(yMin < yMax)) throw new IllegalArgumentException("yMin not less than
+ * yMax");
+ *
+ * if (nodeShape == SHAPE_ROUNDED_RECTANGLE) { final double width = ((double)
+ * xMax) - xMin; final double height = ((double) yMax) - yMin;
+ *
+ * if (!(Math.max(width, height) < (2.0d * Math.min(width, height)))) throw new
+ * IllegalArgumentException( "rounded rectangle does not meet cotextnstraint " +
+ * "max(width, height) < 2 * min(width, height)"); } }
+ * <p>
+ * NOTE: Every method on an instance of this class needs to be called by the AWT
+ * event dispatching thread save the constructor. However, checks for this are
+ * made only if debug is set to true (see constructur). In fact, in certain
+ * situations [such as rendering to a non-image such as a vector graphic] it may
+ * make sense to never call any of the methods from the AWT event dispatching
+ * thread.
+ */
+public final class OldGraphGraphics {
+ /**
+ *
+ */
+ public static final byte SHAPE_RECTANGLE = 0;
+
+ /**
+ *
+ */
+ public static final byte SHAPE_DIAMOND = 1;
+
+ /**
+ *
+ */
+ public static final byte SHAPE_ELLIPSE = 2;
+
+ /**
+ *
+ */
+ public static final byte SHAPE_HEXAGON = 3;
+
+ /**
+ *
+ */
+ public static final byte SHAPE_OCTAGON = 4;
+
+ /**
+ *
+ */
+ public static final byte SHAPE_PARALLELOGRAM = 5;
+
+ /**
+ *
+ */
+ public static final byte SHAPE_ROUNDED_RECTANGLE = 6;
+
+ /**
+ *
+ */
+ public static final byte SHAPE_TRIANGLE = 7;
+
+ /**
+ *
+ */
+ public static final byte SHAPE_VEE = 8;
+
+ // package scoped for unit testing
+ static final byte s_last_shape = SHAPE_VEE;
+
+ /**
+ * This value is currently 100.
+ */
+ public static final int CUSTOM_SHAPE_MAX_VERTICES = 100;
+
+ /**
+ *
+ */
+ public static final byte ARROW_NONE = -1;
+
+ /**
+ *
+ */
+ public static final byte ARROW_DELTA = -2;
+
+ /**
+ *
+ */
+ public static final byte ARROW_DIAMOND = -3;
+
+ /**
+ *
+ */
+ public static final byte ARROW_DISC = -4;
+
+ /**
+ *
+ */
+ public static final byte ARROW_TEE = -5;
+ private static final byte last_arrow_shape = ARROW_TEE;
+
+ /**
+ *
+ */
+ public static final byte ARROW_BIDIRECTIONAL = -6;
+
+ /**
+ *
+ */
+ public static final byte ARROW_MONO = -7;
+
+ /**
+ * This value is currently 64.
+ */
+ public static final int MAX_EDGE_ANCHORS = 64;
+
+ /*
+ * A constant for controlling how cubic Bezier curves are drawn; This
+ * particular constant results in elliptical-looking curves.
+ */
+ private static final double CURVE_ELLIPTICAL = (4.0d * (Math.sqrt(2.0d) - 1.0d)) / 3.0d;
+
+ /*
+ * Added by kono: This is for returning shapes
+ */
+ private static final OldGraphGraphics dummyGraphics;
+
+ static {
+ dummyGraphics = new OldGraphGraphics(null, false);
+ }
+
+ private static final double DEF_SHAPE_SIZE = 32;
+
+ /**
+ * The image that was passed into the constructor.
+ */
+ public final Image image;
+ private final boolean m_debug;
+ private final AffineTransform m_currXform = new AffineTransform();
+ private final AffineTransform m_currNativeXform = new AffineTransform();
+ private final AffineTransform m_xformUtil = new AffineTransform();
+ private final Arc2D.Double m_arc2d = new Arc2D.Double();
+ private final Ellipse2D.Double m_ellp2d = new Ellipse2D.Double();
+ private final GeneralPath m_path2d = new GeneralPath();
+ private final GeneralPath m_path2dPrime = new GeneralPath();
+ private final Line2D.Double m_line2d = new Line2D.Double();
+ private final double[] m_polyCoords = // I need this for extra precision.
+ new double[2 * CUSTOM_SHAPE_MAX_VERTICES];
+ private final HashMap<Byte, double[]> m_customShapes = new HashMap<Byte, double[]>();
+ private final double[] m_ptsBuff = new double[4];
+
+ // package scoped for unit testing
+ final EdgeAnchors m_noAnchors = new EdgeAnchors() {
+ public final int numAnchors() {
+ return 0;
+ }
+
+ public final void getAnchor(final int inx, final float[] arr,
+ final int off) {
+ }
+ };
+
+ private final double[] m_edgePtsBuff = new double[(MAX_EDGE_ANCHORS + 1) * 6];
+ private int m_polyNumPoints; // Used with m_polyCoords.
+ private int m_edgePtsCount; // Number of points stored in m_edgePtsBuff.
+ private Graphics2D m_g2d;
+ private Graphics2D m_gMinimal; // We use mostly java.awt.Graphics methods.
+ private boolean m_cleared;
+
+ // The three following member variables shall only be referenced from
+ // the scope of setStroke() definition.
+ private float m_currStrokeWidth;
+ private final float[] m_currDash = new float[] { 0.0f, 0.0f };
+ private int m_currCapType;
+
+ // This member variable only to be used from within defineCustomNodeShape().
+ private byte m_lastCustomShapeType = s_last_shape;
+
+ // This is only used by computeCubicPolyEdgePath().
+ private final float[] m_floatBuff = new float[2];
+
+ // The following three member variables shall only be accessed from the
+ // scope of computeEdgeIntersection() definition.
+ private final double[] m_fooPolyCoords = new double[CUSTOM_SHAPE_MAX_VERTICES * 4];
+ private final double[] m_foo2PolyCoords = new double[CUSTOM_SHAPE_MAX_VERTICES * 4];
+ private final boolean[] m_fooRoundedCorners = new boolean[CUSTOM_SHAPE_MAX_VERTICES];
+
+ // This member variable shall only be used from within drawTextFull().
+ private char[] m_charBuff = new char[20];
+ private final FontRenderContext m_fontRenderContextFull = new FontRenderContext(
+ null, true, true);
+
+ /**
+ * All rendering operations will be performed on the specified image. No
+ * rendering operations are performed as a result of calling this
+ * constructor. It is safe to call this constructor from any thread.
+ * <p>
+ * The image argument passed to this constructor must support at least three
+ * methods: getGraphics(), getWidth(ImageObserver), and
+ * getHeight(ImageObserver). The image.getGraphics() method must return an
+ * instance of java.awt.Graphics2D. The hypothetical method calls
+ * image.getWidth(null) and image.getHeight(null) must return the
+ * corresponding dimension immediately.
+ * <p>
+ * Notice that it is not possible to resize the image area with this API.
+ * This is not a problem; instances of this class are very lightweight and
+ * are for the most part stateless; simply instantiate a new OldGraphGraphics
+ * when the image area changes.
+ *
+ * @param image
+ * an off-screen image; passing an image gotten from a call to
+ * java.awt.Component.createImage(int, int) works well, although
+ * experience shows that for full support of non-opaque colors,
+ * java.awt.image.BufferedImage should be used instead.
+ * @param debug
+ * if this is true, extra [and time-consuming] error checking
+ * will take place in each method call; it is recommended to have
+ * this value set to true during the testing phase; set it to
+ * false once you are sure that code does not mis-use this
+ * module.
+ */
+ public OldGraphGraphics(final Image image, final boolean debug) {
+ this.image = image;
+ m_debug = debug;
+ m_path2dPrime.setWindingRule(GeneralPath.WIND_EVEN_ODD);
+ m_cleared = false;
+ }
+
+ /**
+ * Clears image area with background paint specified and sets an appropriate
+ * transformation of coordinate systems. See the class description for a
+ * definition of the two coordinate systems: the node coordinate system and
+ * the image coordinate system.
+ * <p>
+ * The background paint is not blended with colors that may already be on
+ * the underlying image; if a translucent color is used in the background
+ * paint, the underlying image itself becomes translucent.
+ * <p>
+ * It is mandatory to call this method before making the first rendering
+ * call.
+ *
+ * @param bgPaint
+ * paint to use when clearing the image before painting a new
+ * frame; translucency is honored, provided that the underlying
+ * image supports it.
+ * @param xCenter
+ * the X component of the translation transform for the frame
+ * about to be rendered; a node whose center is at the X
+ * coordinate xCenter will be rendered exactly in the middle of
+ * the image going across; increasing X values (in the node
+ * coordinate system) result in movement towards the right on the
+ * image.
+ * @param yCenter
+ * the Y component of the translation transform for the frame
+ * about to be rendered; a node whose center is at the Y
+ * coordinate yCenter will be rendered exactly in the middle of
+ * the image going top to bottom; increasing Y values (in the
+ * node coordinate system) result in movement towards the bottom
+ * on the image.
+ * @param scaleFactor
+ * the scaling that is to take place when rendering; a distance
+ * of 1 in node coordinates translates to a distance of
+ * scaleFactor in the image coordinate system (usually one unit
+ * in the image coordinate system equates to one pixel width).
+ * @exception IllegalArgumentException
+ * if scaleFactor is not positive.
+ */
+ public final void clear(final Paint bgPaint, final double xCenter,
+ final double yCenter, final double scaleFactor) {
+ if (m_debug) {
+ if (!EventQueue.isDispatchThread()) {
+ throw new IllegalStateException(
+ "calling thread is not AWT event dispatcher");
+ }
+
+ if (!(scaleFactor > 0.0d)) {
+ throw new IllegalArgumentException(
+ "scaleFactor is not positive");
+ }
+ }
+
+ if (m_gMinimal != null) {
+ m_gMinimal.dispose();
+ m_gMinimal = null;
+ }
+
+ if (m_g2d != null) {
+ m_g2d.dispose();
+ }
+
+ m_g2d = (Graphics2D) image.getGraphics();
+
+ final Composite origComposite = m_g2d.getComposite();
+ m_g2d.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC));
+ m_g2d.setPaint(bgPaint);
+ m_g2d.fillRect(0, 0, image.getWidth(null), image.getHeight(null));
+ m_g2d.setComposite(origComposite);
+ m_g2d.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+ RenderingHints.VALUE_ANTIALIAS_ON);
+ m_g2d.setRenderingHint(RenderingHints.KEY_RENDERING,
+ RenderingHints.VALUE_RENDER_SPEED);
+ m_g2d.setRenderingHint(RenderingHints.KEY_TEXT_ANTIALIASING,
+ RenderingHints.VALUE_TEXT_ANTIALIAS_ON);
+ m_g2d.setRenderingHint(RenderingHints.KEY_FRACTIONALMETRICS,
+ RenderingHints.VALUE_FRACTIONALMETRICS_ON);
+ m_g2d.setRenderingHint(RenderingHints.KEY_STROKE_CONTROL,
+ RenderingHints.VALUE_STROKE_PURE);
+ setStroke(0.0f, 0.0f, BasicStroke.CAP_ROUND, true);
+
+ m_currXform.setToTranslation(0.5d * image.getWidth(null), 0.5d * image
+ .getHeight(null));
+ m_currXform.scale(scaleFactor, scaleFactor);
+ m_currXform.translate(-xCenter, -yCenter);
+ m_g2d.transform(m_currXform);
+ m_currNativeXform.setTransform(m_g2d.getTransform());
+ m_cleared = true;
+ }
+
+ private final void setStroke(final float width, final float dashLength,
+ final int capType, final boolean ignoreCache) {
+ if ((!ignoreCache) && (width == m_currStrokeWidth)
+ && (dashLength == m_currDash[0]) && (capType == m_currCapType)) {
+ return;
+ }
+
+ m_currStrokeWidth = width;
+ m_currDash[0] = dashLength;
+ m_currDash[1] = dashLength;
+ m_currCapType = capType;
+
+ // Unfortunately, BasicStroke is not mutable. So we have to construct
+ // lots of new strokes if they constantly change.
+ if (m_currDash[0] == 0.0f) {
+ m_g2d.setStroke(new BasicStroke(width, capType,
+ BasicStroke.JOIN_ROUND, 10.0f));
+ } else {
+ m_g2d.setStroke(new BasicStroke(width, capType,
+ BasicStroke.JOIN_ROUND, 10.0f, m_currDash, 0.0f));
+ }
+ }
+
+ /**
+ * Uses the current transform to map the specified image coordinates to node
+ * coordinates. The transform used is defined by the last call to clear().
+ * It does not make sense to call this method if clear() has not been called
+ * at least once previously, and this method will cause errors in this case.
+ *
+ * @param coords
+ * an array of length [at least] two which acts both as the input
+ * and as the output of this method; coords[0] is the input X
+ * coordinate in the image coordinate system and is written as
+ * the X coordinate in the node coordinate system by this method;
+ * coords[1] is the input Y coordinate in the image coordinate
+ * system and is written as the Y coordinate in the node
+ * coordinate system by this method; the exact transform which
+ * takes place is defined by the previous call to the clear()
+ * method.
+ */
+ public final void xformImageToNodeCoords(final double[] coords) {
+ if (m_debug) {
+ if (!EventQueue.isDispatchThread()) {
+ throw new IllegalStateException(
+ "calling thread is not AWT event dispatcher");
+ }
+
+ if (!m_cleared) {
+ throw new IllegalStateException(
+ "clear() has not been called previously");
+ }
+ }
+
+ try {
+ m_currXform.inverseTransform(coords, 0, coords, 0, 1);
+ } catch (java.awt.geom.NoninvertibleTransformException e) {
+ throw new RuntimeException("noninvertible matrix - cannot happen");
+ }
+ }
+
+ /**
+ * Called to get the current AffineTransform Matrix.
+ *
+ * @return AffineTransform
+ */
+ public final AffineTransform getTransform() {
+ return m_currXform;
+ }
+
+ /**
+ * This is the method that will render a node very quickly. The node shape
+ * used by this method is SHAPE_RECTANGLE. Translucent colors are not
+ * supported by the low detail rendering methods.
+ * <p>
+ * xMin, yMin, xMax, and yMax specify the extents of the node in the node
+ * coordinate space, not the image coordinate space. Thus, these values will
+ * likely not change from frame to frame, as zoom and pan operations are
+ * performed.
+ * <p>
+ * This method will not work unless clear() has been called at least once
+ * previously.
+ *
+ * @param xMin
+ * an extent of the node to draw, in node coordinate space.
+ * @param yMin
+ * an extent of the node to draw, in node coordinate space.
+ * @param xMax
+ * an extent of the node to draw, in node coordinate space.
+ * @param yMax
+ * an extent of the node to draw, in node coordinate space.
+ * @param fillColor
+ * the [fully opaque] color to use when drawing the node.
+ * @exception IllegalArgumentException
+ * if xMin is not less than xMax, if yMin is not less than
+ * yMax, or if fillColor is not opaque.
+ */
+ public final void drawNodeLow(final float xMin, final float yMin,
+ final float xMax, final float yMax, final Color fillColor) {
+ if (m_debug) {
+ if (!EventQueue.isDispatchThread()) {
+ throw new IllegalStateException(
+ "calling thread is not AWT event dispatcher");
+ }
+
+ if (!m_cleared) {
+ throw new IllegalStateException(
+ "clear() has not been called previously");
+ }
+
+ if (!(xMin < xMax)) {
+ throw new IllegalArgumentException("xMin not less than xMax");
+ }
+
+ if (!(yMin < yMax)) {
+ throw new IllegalArgumentException("yMin not less than yMax");
+ }
+
+ if (fillColor.getAlpha() != 255) {
+ throw new IllegalArgumentException("fillColor is not opaque");
+ }
+ }
+
+ if (m_gMinimal == null) {
+ makeMinimalGraphics();
+ }
+
+ // I'm transforming points manually because the resulting underlying
+ // graphics pipeline used is much faster.
+ m_ptsBuff[0] = xMin;
+ m_ptsBuff[1] = yMin;
+ m_ptsBuff[2] = xMax;
+ m_ptsBuff[3] = yMax;
+ m_currXform.transform(m_ptsBuff, 0, m_ptsBuff, 0, 2);
+
+ // Here, double values outside of the range of ints will be cast to
+ // the nearest int without overflow.
+ final int xNot = (int) m_ptsBuff[0];
+ final int yNot = (int) m_ptsBuff[1];
+ final int xOne = (int) m_ptsBuff[2];
+ final int yOne = (int) m_ptsBuff[3];
+ m_gMinimal.setColor(fillColor);
+ m_gMinimal.fillRect(xNot, yNot, Math.max(1, xOne - xNot), // Overflow
+ // will
+ Math.max(1, yOne - yNot)); // be problem.
+ }
+
+ /*
+ * Sets m_gMinimal.
+ */
+ private final void makeMinimalGraphics() {
+ m_gMinimal = (Graphics2D) image.getGraphics();
+ m_gMinimal.setRenderingHint(RenderingHints.KEY_RENDERING,
+ RenderingHints.VALUE_RENDER_SPEED);
+ }
+
+ /**
+ * Draws a node with medium to high detail, depending on parameters
+ * specified. The xMin, yMin, xMax, and yMax parameters specify the extents
+ * of the node shape (in the node coordinate system), including the border
+ * width. That is, the drawn border won't extend beyond the extents
+ * specified.
+ * <p>
+ * There is an imposed constraint on borderWidth which, using the
+ * implemented algorithms, prevents strange-looking borders. The constraint
+ * is that borderWidth may not exceed the minimum of the node width and node
+ * height divided by six. In addition, for custom node shapes, this
+ * requirement may be more constrained, depending on the kinks in the custom
+ * node shape.
+ * <p>
+ * There is a constraint that only applies to SHAPE_ROUNDED_RECTANGLE which
+ * imposes that the maximum of the width and height be strictly less than
+ * twice the minimum of the width and height of the node.
+ * <p>
+ * This method will not work unless clear() has been called at least once
+ * previously.
+ *
+ * @param nodeShape
+ * the shape of the node to draw (one of the SHAPE_* constants or
+ * a custom node shape).
+ * @param xMin
+ * an extent of the node shape to draw, in node coordinate space;
+ * the drawn shape will theoretically contain a point that lies
+ * on this X coordinate.
+ * @param yMin
+ * an extent of the node shape to draw, in node coordinate space;
+ * the drawn shape will theoretically contain a point that lies
+ * on this Y coordinate.
+ * @param xMax
+ * an extent of the node shape to draw, in node coordinate space;
+ * the drawn shape will theoretically contain a point that lies
+ * on this X coordinate.
+ * @param yMax
+ * an extent of the node shape to draw, in node coordinate space;
+ * the drawn shape will theoretically contain a point that lies
+ * on this Y coordinate.
+ * @param fillPaint
+ * the paint to use when drawing the node area minus the border
+ * (the "interior" of the node).
+ * @param borderWidth
+ * the border width, in node coordinate space; if this value is
+ * zero, the rendering engine skips over the process of rendering
+ * the border, which gives a significant performance boost.
+ * @param borderPaint
+ * if borderWidth is not zero, this paint is used for rendering
+ * the node border; otherwise, this parameter is ignored (and may
+ * be null).
+ * @exception IllegalArgumentException
+ * if xMin is not less than xMax or if yMin is not less than
+ * yMax, if borderWidth is negative or is greater than
+ * Math.min(xMax - xMin, yMax - yMin) / 6 (for custom node
+ * shapes borderWidth may be even more limited, depending on
+ * the specific shape), if nodeShape is
+ * SHAPE_ROUNDED_RECTANGLE and the condition max(width,
+ * height) < 2 * min(width, height) does not hold, or if
+ * nodeShape is neither one of the SHAPE_* constants nor a
+ * previously defined custom node shape.
+ */
+ public final void drawNodeFull(final byte nodeShape, final float xMin,
+ final float yMin, final float xMax, final float yMax,
+ final Paint fillPaint, final float borderWidth,
+ final Paint borderPaint) {
+ if (m_debug) {
+ if (!EventQueue.isDispatchThread()) {
+ throw new IllegalStateException(
+ "calling thread is not AWT event dispatcher");
+ }
+
+ if (!m_cleared) {
+ throw new IllegalStateException(
+ "clear() has not been called previously");
+ }
+
+ if (!(xMin < xMax)) {
+ throw new IllegalArgumentException("xMin not less than xMax");
+ }
+
+ if (!(yMin < yMax)) {
+ throw new IllegalArgumentException("yMin not less than yMax");
+ }
+
+ if (!(borderWidth >= 0.0f)) {
+ throw new IllegalArgumentException(
+ "borderWidth not zero or positive");
+ }
+
+ if (!((6.0d * borderWidth) <= Math.min(((double) xMax) - xMin,
+ ((double) yMax) - yMin))) {
+ throw new IllegalArgumentException(
+ "borderWidth is not less than the minimum of node width and node "
+ + "height divided by six");
+ }
+
+ if (nodeShape == SHAPE_ROUNDED_RECTANGLE) {
+ final double width = ((double) xMax) - xMin;
+ final double height = ((double) yMax) - yMin;
+
+ if (!(Math.max(width, height) < (2.0d * Math.min(width, height)))) {
+ throw new IllegalArgumentException(
+ "rounded rectangle does not meet constraint "
+ + "max(width, height) < 2 * min(width, height)");
+ }
+ }
+ }
+
+ if (borderWidth == 0.0f) {
+ m_g2d.setPaint(fillPaint);
+ m_g2d.fill(getShape(nodeShape, xMin, yMin, xMax, yMax));
+ } else { // There is a border.
+ m_path2dPrime.reset();
+ m_path2dPrime.append(getShape(nodeShape, xMin, yMin, xMax, yMax),
+ false); // Make a copy, essentially.
+
+ final Shape innerShape;
+
+ if (nodeShape == SHAPE_ELLIPSE) {
+ // TODO: Compute a more accurate inner area for ellipse +
+ // border.
+ innerShape = getShape(SHAPE_ELLIPSE, ((double) xMin)
+ + borderWidth, ((double) yMin) + borderWidth,
+ ((double) xMax) - borderWidth, ((double) yMax)
+ - borderWidth);
+ } else if (nodeShape == SHAPE_ROUNDED_RECTANGLE) {
+ computeRoundedRectangle(((double) xMin) + borderWidth,
+ ((double) yMin) + borderWidth, ((double) xMax)
+ - borderWidth, ((double) yMax) - borderWidth,
+ (Math.max(((double) xMax) - xMin, ((double) yMax)
+ - yMin) / 4.0d)
+ - borderWidth, m_path2d);
+ innerShape = m_path2d;
+ } else {
+ // A general [possibly non-convex] polygon with certain
+ // restrictions: no two consecutive line segments can be
+ // parallel,
+ // each line segment must have nonzero length, the polygon
+ // cannot
+ // self-intersect, and the polygon must be clockwise
+ // in the node coordinate system.
+ m_path2d.reset();
+
+ final double xNot = m_polyCoords[0];
+ final double yNot = m_polyCoords[1];
+ final double xOne = m_polyCoords[2];
+ final double yOne = m_polyCoords[3];
+ double xPrev = xNot;
+ double yPrev = yNot;
+ double xCurr = xOne;
+ double yCurr = yOne;
+ double xNext = m_polyCoords[4];
+ double yNext = m_polyCoords[5];
+ computeInnerPoint(m_ptsBuff, xPrev, yPrev, xCurr, yCurr, xNext,
+ yNext, borderWidth);
+ m_path2d.moveTo((float) m_ptsBuff[0], (float) m_ptsBuff[1]);
+
+ int i = 6;
+
+ while (true) {
+ if (i == (m_polyNumPoints * 2)) {
+ computeInnerPoint(m_ptsBuff, xCurr, yCurr, xNext,
+ yNext, xNot, yNot, borderWidth);
+ m_path2d.lineTo((float) m_ptsBuff[0],
+ (float) m_ptsBuff[1]);
+ computeInnerPoint(m_ptsBuff, xNext, yNext, xNot, yNot,
+ xOne, yOne, borderWidth);
+ m_path2d.lineTo((float) m_ptsBuff[0],
+ (float) m_ptsBuff[1]);
+ m_path2d.closePath();
+
+ break;
+ } else {
+ xPrev = xCurr;
+ yPrev = yCurr;
+ xCurr = xNext;
+ yCurr = yNext;
+ xNext = m_polyCoords[i++];
+ yNext = m_polyCoords[i++];
+ computeInnerPoint(m_ptsBuff, xPrev, yPrev, xCurr,
+ yCurr, xNext, yNext, borderWidth);
+ m_path2d.lineTo((float) m_ptsBuff[0],
+ (float) m_ptsBuff[1]);
+ }
+ }
+
+ innerShape = m_path2d;
+ }
+
+ m_g2d.setPaint(fillPaint);
+ m_g2d.fill(innerShape);
+
+ // Render the border such that it does not overlap with the fill
+ // region because translucent colors may be used. Don't do
+ // things differently for opaque and translucent colors for the
+ // sake of consistency.
+ m_path2dPrime.append(innerShape, false);
+ m_g2d.setPaint(borderPaint);
+ m_g2d.fill(m_path2dPrime);
+ }
+ }
+
+ /**
+ * Computes the path a node shape takes; this method is useful if a user
+ * interface would allow user selection of nodes, for example. Use the same
+ * parameter values that were used to render corresponding node.
+ *
+ * @param nodeShape
+ * the shape (SHAPE_* constant or custom shape) of the node in
+ * question.
+ * @param xMin
+ * an extent of the node in question, in node coordinate space.
+ * @param yMin
+ * an extent of the node in question, in node coordinate space.
+ * @param xMax
+ * an extent of the node in question, in node coordinate space.
+ * @param yMax
+ * an extent of the node in question, in node coordinate space.
+ * @param path
+ * the computed path is returned in this parameter; the computed
+ * path's coordinate system is the node coordinate system; the
+ * computed path is closed.
+ */
+ public final void getNodeShape(final byte nodeShape, final float xMin,
+ final float yMin, final float xMax, final float yMax,
+ final GeneralPath path) {
+ if (m_debug) {
+ if (!EventQueue.isDispatchThread()) {
+ throw new IllegalStateException(
+ "calling thread is not AWT event dispatcher");
+ }
+
+ if (!(xMin < xMax)) {
+ throw new IllegalArgumentException("xMin not less than xMax");
+ }
+
+ if (!(yMin < yMax)) {
+ throw new IllegalArgumentException("yMin not less than yMax");
+ }
+
+ if (nodeShape == SHAPE_ROUNDED_RECTANGLE) {
+ final double width = ((double) xMax) - xMin;
+ final double height = ((double) yMax) - yMin;
+
+ if (!(Math.max(width, height) < (2.0d * Math.min(width, height)))) {
+ throw new IllegalArgumentException(
+ "rounded rectangle does not meet constraint "
+ + "max(width, height) < 2 * min(width, height)");
+ }
+ }
+ }
+
+ path.reset();
+ path.append(getShape(nodeShape, xMin, yMin, xMax, yMax), false);
+ }
+
+ /**
+ * The custom node shape that is defined is a polygon specified by the
+ * coordinates supplied. The polygon must meet several constraints listed
+ * below.
+ * <p>
+ * If we define the value xCenter to be the average of the minimum and
+ * maximum X values of the vertices and if we define yCenter likewise, then
+ * the specified polygon must meet the following constraints:
+ * <ol>
+ * <li>Each polygon line segment must have nonzero length.</li>
+ * <li>No two consecutive polygon line segments can be parallel (this
+ * essentially implies that the polygon must have at least three vertices).</li>
+ * <li>No two distinct non-consecutive polygon line segments may intersect
+ * (not even at the endpoints); this makes possible the notion of interior
+ * of the polygon.</li>
+ * <li>The polygon must be star-shaped with respect to the point (xCenter,
+ * yCenter); a polygon is said to be <i>star-shaped with respect to a point
+ * (a,b)</i> if and only if for every point (x,y) in the interior or on the
+ * boundary of the polygon, the interior of the segment (a,b)->(x,y) lies in
+ * the interior of the polygon.</li>
+ * <li>The path traversed by the polygon must be clockwise where +X points
+ * right and +Y points down.</li>
+ * </ol>
+ * <p>
+ * In addition to these constraints, when rendering custom nodes with
+ * nonzero border width, possible problems may arise if the border width is
+ * large with respect to the kinks in the polygon.
+ *
+ * @param coords
+ * vertexCount * 2 consecutive coordinate values are read from
+ * this array starting at coords[offset]; coords[offset],
+ * coords[offset + 1], coords[offset + 2], coords[offset + 3] and
+ * so on are interpreted as x0, y0, x1, y1, and so on; the
+ * initial vertex need not be repeated as the last vertex
+ * specified.
+ * @param offset
+ * the starting index of where to read coordinates from in the
+ * coords parameter.
+ * @param vertexCount
+ * the number of vertices to read from coords; vertexCount * 2
+ * entries in coords are read.
+ * @return the node shape identifier to be used in future rendering calls
+ * (to be used as parameter nodeShape in method drawNodeFull()).
+ * @exception IllegalArgumentException
+ * if any of the constraints are not met, or if the specified
+ * polygon has more than CUSTOM_SHAPE_MAX_VERTICES vertices.
+ * @exception IllegalStateException
+ * if too many custom node shapes are already defined; a
+ * little over one hundered custom node shapes can be
+ * defined.
+ */
+ public final byte defineCustomNodeShape(final float[] coords,
+ final int offset, final int vertexCount) {
+ if (vertexCount > CUSTOM_SHAPE_MAX_VERTICES) {
+ throw new IllegalArgumentException(
+ "too many vertices (greater than "
+ + CUSTOM_SHAPE_MAX_VERTICES + ")");
+ }
+
+ final double[] polyCoords;
+
+ {
+ polyCoords = new double[vertexCount * 2];
+
+ for (int i = 0; i < polyCoords.length; i++)
+ polyCoords[i] = coords[offset + i];
+
+ // Normalize the polygon so that it spans [-0.5, 0.5] x [-0.5, 0.5].
+ double xMin = Double.POSITIVE_INFINITY;
+ double yMin = Double.POSITIVE_INFINITY;
+ double xMax = Double.NEGATIVE_INFINITY;
+ double yMax = Double.NEGATIVE_INFINITY;
+
+ for (int i = 0; i < polyCoords.length;) {
+ xMin = Math.min(xMin, coords[i]);
+ xMax = Math.max(xMax, coords[i++]);
+ yMin = Math.min(yMin, coords[i]);
+ yMax = Math.max(yMax, coords[i++]);
+ }
+
+ final double xDist = xMax - xMin;
+
+ if (xDist == 0.0d) {
+ throw new IllegalArgumentException(
+ "polygon does not move in the X direction");
+ }
+
+ final double yDist = yMax - yMin;
+
+ if (yDist == 0.0d) {
+ throw new IllegalArgumentException(
+ "polygon does not move in the Y direction");
+ }
+
+ final double xMid = (xMin + xMax) / 2.0d;
+ final double yMid = (yMin + yMax) / 2.0d;
+
+ for (int i = 0; i < polyCoords.length;) {
+ double foo = (polyCoords[i] - xMid) / xDist;
+ polyCoords[i++] = Math.min(Math.max(-0.5d, foo), 0.5d);
+ foo = (polyCoords[i] - yMid) / yDist;
+ polyCoords[i++] = Math.min(Math.max(-0.5d, foo), 0.5d);
+ }
+ }
+
+ if (m_debug) {
+ if (!EventQueue.isDispatchThread()) {
+ throw new IllegalStateException(
+ "calling thread is not AWT event dispatcher");
+ }
+ }
+
+ { // Test all criteria regardless of m_debug.
+
+ int yInterceptsCenter = 0;
+
+ for (int i = 0; i < vertexCount; i++) {
+ final double x0 = polyCoords[i * 2];
+ final double y0 = polyCoords[(i * 2) + 1];
+ final double x1 = polyCoords[((i * 2) + 2) % (vertexCount * 2)];
+ final double y1 = polyCoords[((i * 2) + 3) % (vertexCount * 2)];
+ final double x2 = polyCoords[((i * 2) + 4) % (vertexCount * 2)];
+ final double y2 = polyCoords[((i * 2) + 5) % (vertexCount * 2)];
+ final double distP0P1 = Math.sqrt(((x1 - x0) * (x1 - x0))
+ + ((y1 - y0) * (y1 - y0)));
+
+ if ((float) distP0P1 == 0.0f) { // Too close to distance zero.
+ throw new IllegalArgumentException(
+ "a line segment has distance [too close to] zero");
+ }
+
+ final double distP2fromP0P1 = ((((y0 - y1) * x2)
+ + ((x1 - x0) * y2) + (x0 * y1)) - (x1 * y0))
+ / distP0P1;
+
+ if ((float) distP2fromP0P1 == 0.0f) { // Too close to
+ // parallel.
+ throw new IllegalArgumentException(
+ "either a line segment has distance [too close to] zero or "
+ + "two consecutive line segments are [too close to] parallel");
+ }
+
+ final double distCenterFromP0P1 = ((x0 * y1) - (x1 * y0))
+ / distP0P1;
+
+ if (!((float) distCenterFromP0P1 > 0.0f)) {
+ throw new IllegalArgumentException(
+ "polygon is going counter-clockwise or is not star-shaped with "
+ + "respect to center");
+ }
+
+ if ((Math.min(y0, y1) < 0.0d) && (Math.max(y0, y1) >= 0.0d)) {
+ yInterceptsCenter++;
+ }
+ }
+
+ if (yInterceptsCenter != 2) {
+ throw new IllegalArgumentException(
+ "the polygon self-intersects (we know this because the winding "
+ + "number of the center is not one)");
+ }
+ }
+
+ // polyCoords now contains a polygon spanning [-0.5, 0.5] X [-0.5, 0.5]
+ // that passes all of the criteria.
+ final byte nextCustomShapeType = (byte) (m_lastCustomShapeType + 1);
+
+ if (nextCustomShapeType < 0) {
+ throw new IllegalStateException(
+ "too many custom node shapes are already defined");
+ }
+
+ m_lastCustomShapeType++;
+ m_customShapes.put(new Byte(nextCustomShapeType), polyCoords);
+
+ return nextCustomShapeType;
+ }
+
+ /**
+ * Determines whether the specified shape is a custom defined node shape.
+ */
+ public final boolean customNodeShapeExists(final byte shape) {
+ if (m_debug) {
+ if (!EventQueue.isDispatchThread()) {
+ throw new IllegalStateException(
+ "calling thread is not AWT event dispatcher");
+ }
+ }
+
+ return (shape > s_last_shape) && (shape <= m_lastCustomShapeType);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final byte[] getCustomNodeShapes() {
+ if (m_debug) {
+ if (!EventQueue.isDispatchThread()) {
+ throw new IllegalStateException(
+ "calling thread is not AWT event dispatcher");
+ }
+ }
+
+ final byte[] returnThis = new byte[m_lastCustomShapeType - s_last_shape];
+
+ for (int i = 0; i < returnThis.length; i++) {
+ returnThis[i] = (byte) (s_last_shape + 1 + i);
+ }
+
+ return returnThis;
+ }
+
+ /**
+ * Returns the vertices of a previously defined custom node shape. The
+ * polygon will be normalized to fit within the [-0.5, 0.5] x [-0.5, 0.5]
+ * square. Returns null if specified shape is not a previously defined
+ * custom shape.
+ */
+ public final float[] getCustomNodeShape(final byte customShape) {
+ if (m_debug) {
+ if (!EventQueue.isDispatchThread()) {
+ throw new IllegalStateException(
+ "calling thread is not AWT event dispatcher");
+ }
+ }
+
+ final double[] dCoords = m_customShapes.get(new Byte(customShape));
+
+ if (dCoords == null) {
+ return null;
+ }
+
+ final float[] returnThis = new float[dCoords.length];
+
+ for (int i = 0; i < returnThis.length; i++) {
+ returnThis[i] = (float) dCoords[i];
+ }
+
+ return returnThis;
+ }
+
+ /**
+ * If this is a new instance, imports the custom node shapes from the
+ * OldGraphGraphics specified into this OldGraphGraphics.
+ *
+ * @param grafx
+ * custom node shapes will be imported from this OldGraphGraphics.
+ * @exception IllegalStateException
+ * if at least one custom node shape is already defined in
+ * this OldGraphGraphics.
+ */
+ public final void importCustomNodeShapes(final OldGraphGraphics grafx) {
+ if (m_debug) {
+ if (!EventQueue.isDispatchThread()) {
+ throw new IllegalStateException(
+ "calling thread is not AWT event dispatcher");
+ }
+ }
+
+ // I define this error check outside the scope of m_debug because
+ // clobbering existing custom node shape definitions could be major.
+ if (m_lastCustomShapeType != s_last_shape) {
+ throw new IllegalStateException(
+ "a custom node shape is already defined in this OldGraphGraphics");
+ }
+
+ for (Map.Entry<Byte, double[]> entry : grafx.m_customShapes.entrySet()) {
+ m_customShapes.put(entry.getKey(), entry.getValue());
+ m_lastCustomShapeType++;
+ }
+ }
+
+ /*
+ * This method has the side effect of setting m_ellp2d or m_path2d; if
+ * m_path2d is set (every case but the ellipse and rounded rectangle), then
+ * m_polyCoords and m_polyNumPoints are also set.
+ */
+ private final Shape getShape(final byte nodeShape, final double xMin,
+ final double yMin, final double xMax, final double yMax) {
+ switch (nodeShape) {
+ case SHAPE_ELLIPSE:
+ m_ellp2d.setFrame(xMin, yMin, xMax - xMin, yMax - yMin);
+
+ return m_ellp2d;
+
+ case SHAPE_RECTANGLE:
+ m_polyNumPoints = 4;
+ m_polyCoords[0] = xMin;
+ m_polyCoords[1] = yMin;
+ m_polyCoords[2] = xMax;
+ m_polyCoords[3] = yMin;
+ m_polyCoords[4] = xMax;
+ m_polyCoords[5] = yMax;
+ m_polyCoords[6] = xMin;
+ m_polyCoords[7] = yMax;
+
+ break;
+
+ case SHAPE_DIAMOND:
+ m_polyNumPoints = 4;
+ m_polyCoords[0] = (xMin + xMax) / 2.0d;
+ m_polyCoords[1] = yMin;
+ m_polyCoords[2] = xMax;
+ m_polyCoords[3] = (yMin + yMax) / 2.0d;
+ m_polyCoords[4] = (xMin + xMax) / 2.0d;
+ m_polyCoords[5] = yMax;
+ m_polyCoords[6] = xMin;
+ m_polyCoords[7] = (yMin + yMax) / 2.0d;
+
+ break;
+
+ case SHAPE_HEXAGON:
+ m_polyNumPoints = 6;
+ m_polyCoords[0] = ((2.0d * xMin) + xMax) / 3.0d;
+ m_polyCoords[1] = yMin;
+ m_polyCoords[2] = ((2.0d * xMax) + xMin) / 3.0d;
+ m_polyCoords[3] = yMin;
+ m_polyCoords[4] = xMax;
+ m_polyCoords[5] = (yMin + yMax) / 2.0d;
+ m_polyCoords[6] = ((2.0d * xMax) + xMin) / 3.0d;
+ m_polyCoords[7] = yMax;
+ m_polyCoords[8] = ((2.0d * xMin) + xMax) / 3.0d;
+ m_polyCoords[9] = yMax;
+ m_polyCoords[10] = xMin;
+ m_polyCoords[11] = (yMin + yMax) / 2.0d;
+
+ break;
+
+ case SHAPE_OCTAGON:
+ m_polyNumPoints = 8;
+ m_polyCoords[0] = ((2.0d * xMin) + xMax) / 3.0d;
+ m_polyCoords[1] = yMin;
+ m_polyCoords[2] = ((2.0d * xMax) + xMin) / 3.0d;
+ m_polyCoords[3] = yMin;
+ m_polyCoords[4] = xMax;
+ m_polyCoords[5] = ((2.0d * yMin) + yMax) / 3.0d;
+ m_polyCoords[6] = xMax;
+ m_polyCoords[7] = ((2.0d * yMax) + yMin) / 3.0d;
+ m_polyCoords[8] = ((2.0d * xMax) + xMin) / 3.0d;
+ m_polyCoords[9] = yMax;
+ m_polyCoords[10] = ((2.0d * xMin) + xMax) / 3.0d;
+ m_polyCoords[11] = yMax;
+ m_polyCoords[12] = xMin;
+ m_polyCoords[13] = ((2.0d * yMax) + yMin) / 3.0d;
+ m_polyCoords[14] = xMin;
+ m_polyCoords[15] = ((2.0d * yMin) + yMax) / 3.0d;
+
+ break;
+
+ case SHAPE_PARALLELOGRAM:
+ m_polyNumPoints = 4;
+ m_polyCoords[0] = xMin;
+ m_polyCoords[1] = yMin;
+ m_polyCoords[2] = ((2.0d * xMax) + xMin) / 3.0d;
+ m_polyCoords[3] = yMin;
+ m_polyCoords[4] = xMax;
+ m_polyCoords[5] = yMax;
+ m_polyCoords[6] = ((2.0d * xMin) + xMax) / 3.0d;
+ m_polyCoords[7] = yMax;
+
+ break;
+
+ case SHAPE_ROUNDED_RECTANGLE:
+ // A condition that must be satisfied (pertaining to radius) is that
+ // max(width, height) <= 2 * min(width, height).
+ computeRoundedRectangle(xMin, yMin, xMax, yMax, Math.max(xMax
+ - xMin, yMax - yMin) / 4.0d, m_path2d);
+
+ return m_path2d;
+
+ case SHAPE_TRIANGLE:
+ m_polyNumPoints = 3;
+ m_polyCoords[0] = (xMin + xMax) / 2.0d;
+ m_polyCoords[1] = yMin;
+ m_polyCoords[2] = xMax;
+ m_polyCoords[3] = yMax;
+ m_polyCoords[4] = xMin;
+ m_polyCoords[5] = yMax;
+
+ break;
+
+ case SHAPE_VEE:
+ m_polyNumPoints = 4;
+ m_polyCoords[0] = xMin;
+ m_polyCoords[1] = yMin;
+ m_polyCoords[2] = (xMin + xMax) / 2.0d;
+ m_polyCoords[3] = ((2.0d * yMin) + yMax) / 3.0d;
+ m_polyCoords[4] = xMax;
+ m_polyCoords[5] = yMin;
+ m_polyCoords[6] = (xMin + xMax) / 2.0d;
+ m_polyCoords[7] = yMax;
+
+ break;
+
+ default: // Try a custom node shape or throw an exception.
+
+ final double[] storedPolyCoords = // To optimize don't construct
+ // Byte.
+ m_customShapes.get(new Byte(nodeShape));
+
+ if (storedPolyCoords == null) {
+ throw new IllegalArgumentException(
+ "nodeShape is not recognized");
+ }
+
+ m_polyNumPoints = storedPolyCoords.length / 2;
+
+ final double desiredXCenter = (xMin + xMax) / 2.0d;
+ final double desiredYCenter = (yMin + yMax) / 2.0d;
+ final double desiredWidth = xMax - xMin;
+ final double desiredHeight = yMax - yMin;
+ m_xformUtil.setToTranslation(desiredXCenter, desiredYCenter);
+ m_xformUtil.scale(desiredWidth, desiredHeight);
+ m_xformUtil.transform(storedPolyCoords, 0, m_polyCoords, 0,
+ m_polyNumPoints);
+
+ break;
+ }
+
+ m_path2d.reset();
+
+ m_path2d.moveTo((float) m_polyCoords[0], (float) m_polyCoords[1]);
+
+ for (int i = 2; i < (m_polyNumPoints * 2);)
+ m_path2d.lineTo((float) m_polyCoords[i++],
+ (float) m_polyCoords[i++]);
+
+ m_path2d.closePath();
+
+ return m_path2d;
+ }
+
+ /**
+ * get list of node shapes.
+ *
+ * @return
+ */
+ public static Map<Byte, Shape> getNodeShapes() {
+ return getShapes(ShapeTypes.NODE_SHAPE);
+ }
+
+ /**
+ * Get list of arrow heads.
+ *
+ * @return
+ */
+ public static Map<Byte, Shape> getArrowShapes() {
+ return getShapes(ShapeTypes.ARROW_SHAPE);
+ }
+
+ /**
+ * Actually create map of shapes.
+ *
+ * @param type
+ * @return
+ */
+ private static Map<Byte, Shape> getShapes(final ShapeTypes type) {
+ final Map<Byte, Shape> shapeMap = new HashMap<Byte, Shape>();
+
+ final int minIndex;
+ final int maxIndex;
+
+ if (type == ShapeTypes.NODE_SHAPE) {
+ minIndex = 0;
+ maxIndex = s_last_shape;
+ } else if (type == ShapeTypes.ARROW_SHAPE) {
+ minIndex = last_arrow_shape;
+ maxIndex = -1;
+ } else {
+ minIndex = 0;
+ maxIndex = s_last_shape;
+ }
+
+ Shape shape;
+
+ for (int i = minIndex; i <= maxIndex; i++) {
+ if (type == ShapeTypes.NODE_SHAPE) {
+ shape = dummyGraphics.getShape((byte) i, 0, 0, DEF_SHAPE_SIZE,
+ DEF_SHAPE_SIZE);
+ } else {
+ shape = dummyGraphics.computeUntransformedArrow((byte) i);
+ }
+
+ if ((shape != null) && (shape.getClass() == GeneralPath.class)) {
+ final Shape copiedShape = (Shape) ((GeneralPath) shape).clone();
+ shapeMap.put((byte) i, copiedShape);
+ } else if (shape != null) {
+ shapeMap.put((byte) i, shape);
+ }
+ }
+
+ return shapeMap;
+ }
+
+ private final static void computeRoundedRectangle(final double xMin,
+ final double yMin, final double xMax, final double yMax,
+ final double radius, final GeneralPath path2d) {
+ path2d.reset();
+ path2d.moveTo((float) (xMax - radius), (float) yMin);
+ path2d.curveTo((float) (((CURVE_ELLIPTICAL - 1.0d) * radius) + xMax),
+ (float) yMin, (float) xMax,
+ (float) (((1.0d - CURVE_ELLIPTICAL) * radius) + yMin),
+ (float) xMax, (float) (radius + yMin));
+ path2d.lineTo((float) xMax, (float) (yMax - radius));
+ path2d.curveTo((float) xMax,
+ (float) (((CURVE_ELLIPTICAL - 1.0d) * radius) + yMax),
+ (float) (((CURVE_ELLIPTICAL - 1.0d) * radius) + xMax),
+ (float) yMax, (float) (xMax - radius), (float) yMax);
+ path2d.lineTo((float) (radius + xMin), (float) yMax);
+ path2d.curveTo((float) (((1.0d - CURVE_ELLIPTICAL) * radius) + xMin),
+ (float) yMax, (float) xMin,
+ (float) (((CURVE_ELLIPTICAL - 1.0d) * radius) + yMax),
+ (float) xMin, (float) (yMax - radius));
+ path2d.lineTo((float) xMin, (float) (radius + yMin));
+ path2d.curveTo((float) xMin,
+ (float) (((1.0d - CURVE_ELLIPTICAL) * radius) + yMin),
+ (float) (((1.0d - CURVE_ELLIPTICAL) * radius) + xMin),
+ (float) yMin, (float) (radius + xMin), (float) yMin);
+ path2d.closePath();
+ }
+
+ /*
+ * This method is used to construct an inner shape for node border.
+ * output[0] is the x return value and output[1] is the y return value. The
+ * line prev->curr cannot be parallel to curr->next.
+ */
+ private final static void computeInnerPoint(final double[] output,
+ final double xPrev, final double yPrev, final double xCurr,
+ final double yCurr, final double xNext, final double yNext,
+ final double borderWidth) {
+ final double segX1 = xCurr - xPrev;
+ final double segY1 = yCurr - yPrev;
+ final double segLength1 = Math.sqrt((segX1 * segX1) + (segY1 * segY1));
+ final double segX2 = xNext - xCurr;
+ final double segY2 = yNext - yCurr;
+ final double segLength2 = Math.sqrt((segX2 * segX2) + (segY2 * segY2));
+ final double segX2Normal = segX2 / segLength2;
+ final double segY2Normal = segY2 / segLength2;
+ final double xNextPrime = (segX2Normal * segLength1) + xPrev;
+ final double yNextPrime = (segY2Normal * segLength1) + yPrev;
+ final double segPrimeX = xNextPrime - xCurr;
+ final double segPrimeY = yNextPrime - yCurr;
+ final double distancePrimeToSeg1 = (((segX1 * yNextPrime)
+ - (segY1 * xNextPrime) + (xPrev * yCurr)) - (xCurr * yPrev))
+ / segLength1;
+ final double multFactor = borderWidth / distancePrimeToSeg1;
+ output[0] = (multFactor * segPrimeX) + xCurr;
+ output[1] = (multFactor * segPrimeY) + yCurr;
+ }
+
+ /**
+ * This is the method that will render an edge very quickly. Translucent
+ * colors are not supported by the low detail rendering methods.
+ * <p>
+ * The points (x0, y0) and (x1, y1) specify the endpoints of edge to be
+ * rendered in the node coordinate space, not the image coordinate space.
+ * Thus, these values will likely not change from frame to frame, as zoom
+ * and pan operations are performed. If these two points are identical,
+ * nothing is drawn.
+ * <p>
+ * This method will not work unless clear() has been called at least once
+ * previously.
+ *
+ * @param x0
+ * the X coordinate of the begin point of edge to render.
+ * @param y0
+ * the Y coordinate of the begin point of edge to render.
+ * @param x1
+ * the X coordinate of the end point of edge to render.
+ * @param y1
+ * the Y coordinate of the end point of edge to render.
+ * @param edgeColor
+ * the [fully opaque] color to use when drawing the edge.
+ * @exception IllegalArgumentException
+ * if edgeColor is not opaque.
+ */
+ public final void drawEdgeLow(final float x0, final float y0,
+ final float x1, final float y1, final Color edgeColor) {
+ if (m_debug) {
+ if (!EventQueue.isDispatchThread()) {
+ throw new IllegalStateException(
+ "calling thread is not AWT event dispatcher");
+ }
+
+ if (!m_cleared) {
+ throw new IllegalStateException(
+ "clear() has not been called previously");
+ }
+
+ if (edgeColor.getAlpha() != 255) {
+ throw new IllegalArgumentException("edgeColor is not opaque");
+ }
+ }
+
+ // This following statement has to be consistent with the full edge
+ // rendering logic.
+ if ((x0 == x1) && (y0 == y1)) {
+ return;
+ }
+
+ if (m_gMinimal == null) {
+ makeMinimalGraphics();
+ }
+
+ // I'm transforming points manually because the resulting underlying
+ // graphics pipeline used is much faster.
+ m_ptsBuff[0] = x0;
+ m_ptsBuff[1] = y0;
+ m_ptsBuff[2] = x1;
+ m_ptsBuff[3] = y1;
+ m_currXform.transform(m_ptsBuff, 0, m_ptsBuff, 0, 2);
+
+ final int xNot = (int) m_ptsBuff[0];
+ final int yNot = (int) m_ptsBuff[1];
+ final int xOne = (int) m_ptsBuff[2];
+ final int yOne = (int) m_ptsBuff[3];
+ m_gMinimal.setColor(edgeColor);
+ m_gMinimal.drawLine(xNot, yNot, xOne, yOne);
+ }
+
+ /**
+ * Draws an edge with medium to high detail, depending on parameters
+ * specified. Something is rendered in all cases except where the length of
+ * the edge is zero (because in that case directionality cannot be
+ * determined for at least some arrowheads).
+ * <p>
+ * The arrow types must each be one of the ARROW_* constants. The arrow at
+ * endpoint 1 is always "on top of" the arrow at endpoint 0 if they overlap
+ * because the arrow at endpoint 0 gets rendered first.
+ * <p>
+ * If an arrow other than ARROW_NONE is rendered, its size must be greater
+ * than or equal to edge thickness specified. The table below describes, to
+ * some extent, the nature of each arrow type. <blockquote><table
+ * border="1" cellpadding="5" cellspacing="0">
+ * <tr>
+ * <th>arrow type</th>
+ * <th>description</th>
+ * </tr>
+ * <tr>
+ * <td>ARROW_NONE</td>
+ * <td>the edge line segment has endpoint specified, and the line segment
+ * has a round end (center of round semicircle end exactly equal to endpoint
+ * specified); arrow size and arrow paint are ignored</td>
+ * </tr>
+ * <tr>
+ * <td>ARROW_DELTA</td>
+ * <td>the sharp tip of the arrowhead is exactly at the endpint specified;
+ * the delta is as wide as the arrow size specified and twice that in length</td>
+ * </tr>
+ * <tr>
+ * <td>ARROW_DIAMOND</td>
+ * <td>the sharp tip of the arrowhead is exactly at the endpoint specified;
+ * the diamond is as wide as the arrow size specified and twice that in
+ * length</td>
+ * </tr>
+ * <tr>
+ * <td>ARROW_DISC</td>
+ * <td>the disc arrowhead is placed such that its center is at the
+ * specified endpoint; the diameter of the disk is the arrow size specified</td>
+ * </tr>
+ * <tr>
+ * <td>ARROW_TEE</td>
+ * <td>the center of the tee intersection lies at the specified endpoint;
+ * the width of the top of the tee is one quarter of the arrow size
+ * specified, and the span of the top of the tee is two times the arrow size</td>
+ * </tr>
+ * <tr>
+ * <td>ARROW_BIDIRECTIONAL</td>
+ * <td>either both arrowheads must be of this type or neither one must be
+ * of this type; bidirectional edges look completely different from other
+ * edges; arrow paints are completely ignored for this type of edge; the
+ * edge arrow is drawn such that it fits snugly inside of an ARROW_DELTA of
+ * size 2s + e[sqrt(17)+5]/4 where s is the arrow size specified and e is
+ * edge thickness specified; the delta's tip is at edge endpoint specified;
+ * note that edge anchors are not supported for this type of edge</td>
+ * </tr>
+ * <tr>
+ * <td>ARROW_MONO</td>
+ * <td>either both arrowheads must be of this type or neither one must be
+ * of this type; mono edges look completely different from other edges
+ * because an arrowhead (an ARROW_DELTA) is placed such that its tip is in
+ * the middle of the edge segment, pointing from (x0,y0) to (x1,y1); the
+ * paint and size of the first arrow (arrow0) are read and the paint and
+ * size of the other arrow are completely ignored; note that edge anchors
+ * are not supported for this type of edge</td>
+ * </tr>
+ * </table></blockquote>
+ * <p>
+ * Note that if the edge segment length is zero then nothing gets rendered.
+ * <p>
+ * This method will not work unless clear() has been called at least once
+ * previously.
+ * <p>
+ * A discussion pertaining to edge anchors. Edge anchors are only supported
+ * for the primitive arrow types (ARROW_NONE, ARROW_DELTA, ARROW_DIAMOND,
+ * ARROW_DISC, and ARROW_TEE); <font color="red">ARROW_BIDIRECTIONAL and
+ * ARROW_MONO do not support edge anchors</font>. At most MAX_EDGE_ANCHORS
+ * edge anchors may be specified. The edge anchors are used to define cubic
+ * Bezier curves. The exact algorithm for determining the Bezier curves from
+ * the input parameters is too complicated to describe in this Javadoc. Some
+ * parts of the algorithm: <blockquote>
+ * <ul>
+ * <li>the conglomerated curve is [probably] not going to pass through the
+ * edge anchors points specified; the curve will pass through the midpoint
+ * between every consecutive pair of anchors</li>
+ * <li>when determining the edge path as a whole, an ordered list of points
+ * is created by putting point (x0, y0) at the beginning of the list,
+ * followed by the anchor points, followed by point (x1, y1); then,
+ * duplicate points are removed from the beginning and end of this list</li>
+ * <li>from the list described above, the first two points define the arrow
+ * direction at point (x0, y0) and the initial curve direction; likewise,
+ * the last two points in this list define the arrow direction at point (x1,
+ * y1) and the ending curve direction</li>
+ * </ul>
+ * </blockquote> In order to specify a straight-line edge path, simply
+ * duplicate each edge anchor in the EdgeAnchors instance. For example, a
+ * smooth curve would be drawn by specifying consecutive-pairwise disctinct
+ * points {(x0,y0), A0, A1, A2, (x1,y1)}; a straight-line edge path would be
+ * drawn by specifying {(x0, y0), A0, A0, A1, A1, A2, A2, (x1, y1)}.
+ *
+ * @param arrow0Type
+ * the type of arrow shape to use for drawing the arrow at point
+ * (x0, y0); this value must be one of the ARROW_* constants.
+ * @param arrow0Size
+ * the size of arrow at point (x0, y0); how size is interpreted
+ * for different arrow types is described in the table above.
+ * @param arrow0Paint
+ * the paint to use when drawing the arrow at point (x0, y0).
+ * @param arrow1Type
+ * the type of arrow shape to use for drawing the arrow at point
+ * (x1, y1); this value must be one of the ARROW_* constants.
+ * @param arrow1Size
+ * the size of arrow at point (x1, y1); how size is interpreted
+ * for different arrow types is described in the table above.
+ * @param arrow1Paint
+ * the paint to use when drawing the arrow at point (x1, y1).
+ * @param x0
+ * the X coordinate of the first edge endpoint.
+ * @param y0
+ * the Y coordinate of the first edge endpoint.
+ * @param anchors
+ * anchor points between the two edge endpoints; null is an
+ * acceptable value to indicate no edge anchors.
+ * @param x1
+ * the X coordinate of the second edge endpoint.
+ * @param y1
+ * the Y coordinate of the second edge endpoint.
+ * @param edgeThickness
+ * the thickness of the edge segment; the edge segment is the
+ * part of the edge between the two endpoint arrows.
+ * @param edgePaint
+ * the paint to use when drawing the edge segment.
+ * @param dashLength
+ * a positive value representing the length of dashes on the
+ * edge, or zero to indicate that the edge is solid; note that
+ * drawing dashed segments is computationally expensive.
+ * @exception IllegalArgumentException
+ * if edgeThickness is less than zero, if dashLength is less
+ * than zero, if any one of the arrow configurations does not
+ * meet specified criteria, or if more than MAX_EDGE_ANCHORS
+ * anchors are specified.
+ */
+ public final void drawEdgeFull(final byte arrow0Type,
+ final float arrow0Size, final Paint arrow0Paint,
+ final byte arrow1Type, final float arrow1Size,
+ final Paint arrow1Paint, final float x0, final float y0,
+ EdgeAnchors anchors, final float x1, final float y1,
+ final float edgeThickness, final Paint edgePaint,
+ final float dashLength) {
+ final double curveFactor = CURVE_ELLIPTICAL;
+
+ if (anchors == null) {
+ anchors = m_noAnchors;
+ }
+
+ if (m_debug) {
+ edgeFullDebug(arrow0Type, arrow0Size, arrow1Type, arrow1Size,
+ edgeThickness, dashLength, anchors);
+ }
+
+ if (!computeCubicPolyEdgePath(arrow0Type,
+ (arrow0Type == ARROW_NONE) ? 0.0f : arrow0Size, arrow1Type,
+ (arrow1Type == ARROW_NONE) ? 0.0f : arrow1Size, x0, y0,
+ anchors, x1, y1, curveFactor)) {
+ // After filtering duplicate start and end points, there are less
+ // than 3 total.
+ if (m_edgePtsCount == 2) { // Draw an ordinary edge.
+ drawSimpleEdgeFull(arrow0Type, arrow0Size, arrow0Paint,
+ arrow1Type, arrow1Size, arrow1Paint,
+ (float) m_edgePtsBuff[0], (float) m_edgePtsBuff[1],
+ (float) m_edgePtsBuff[2], (float) m_edgePtsBuff[3],
+ edgeThickness, edgePaint, dashLength);
+ }
+
+ return;
+ }
+
+ { // Render the edge polypath.
+
+ final boolean simpleSegment = (arrow0Type == ARROW_NONE)
+ && (arrow1Type == ARROW_NONE) && (dashLength == 0.0f);
+ setStroke(edgeThickness, dashLength,
+ simpleSegment ? BasicStroke.CAP_ROUND
+ : BasicStroke.CAP_BUTT, false);
+ // Set m_path2d to contain the cubic curves computed in
+ // m_edgePtsBuff.
+ m_path2d.reset();
+ m_path2d.moveTo((float) m_edgePtsBuff[2], (float) m_edgePtsBuff[3]);
+
+ int inx = 4;
+ final int count = ((m_edgePtsCount - 1) * 6) - 2;
+
+ while (inx < count) {
+ m_path2d.curveTo((float) m_edgePtsBuff[inx++],
+ (float) m_edgePtsBuff[inx++],
+ (float) m_edgePtsBuff[inx++],
+ (float) m_edgePtsBuff[inx++],
+ (float) m_edgePtsBuff[inx++],
+ (float) m_edgePtsBuff[inx++]);
+ }
+
+ m_g2d.setPaint(edgePaint);
+ m_g2d.draw(m_path2d);
+
+ if (simpleSegment) {
+ return;
+ }
+
+ // We need to figure out the phase at the end of the cubic poly-path
+ // for dashed segments. I cannot find a Java API to do this; our
+ // best
+ // bet would be to implement our own cubic curve length calculating
+ // function, but our computation may not agree with BasicStroke's
+ // computation. So what we're going to do is never render the arrow
+ // caps for dashed edges.
+ }
+
+ final double dx0 = m_edgePtsBuff[0] - m_edgePtsBuff[4];
+ final double dy0 = m_edgePtsBuff[1] - m_edgePtsBuff[5];
+ final double len0 = Math.sqrt((dx0 * dx0) + (dy0 * dy0));
+ final double cosTheta0 = dx0 / len0;
+ final double sinTheta0 = dy0 / len0;
+
+ final double dx1 = m_edgePtsBuff[((m_edgePtsCount - 1) * 6) - 2]
+ - m_edgePtsBuff[((m_edgePtsCount - 1) * 6) - 6];
+ final double dy1 = m_edgePtsBuff[((m_edgePtsCount - 1) * 6) - 1]
+ - m_edgePtsBuff[((m_edgePtsCount - 1) * 6) - 5];
+ final double len1 = Math.sqrt((dx1 * dx1) + (dy1 * dy1));
+ final double cosTheta1 = dx1 / len1;
+ final double sinTheta1 = dy1 / len1;
+
+ if (dashLength == 0.0f) { // Render arrow cap at origin of poly path.
+
+ final Shape arrow0Cap = computeUntransformedArrowCap(arrow0Type,
+ ((double) arrow0Size) / edgeThickness);
+
+ if (arrow0Cap != null) {
+ m_xformUtil.setTransform(cosTheta0, sinTheta0, -sinTheta0,
+ cosTheta0, m_edgePtsBuff[2], m_edgePtsBuff[3]);
+ m_g2d.transform(m_xformUtil);
+ m_g2d.scale(edgeThickness, edgeThickness);
+ // The paint is already set to edge paint.
+ m_g2d.fill(arrow0Cap);
+ m_g2d.setTransform(m_currNativeXform);
+ }
+ }
+
+ if (dashLength == 0.0f) { // Render arrow cap at end of poly path.
+
+ final Shape arrow1Cap = computeUntransformedArrowCap(arrow1Type,
+ ((double) arrow1Size) / edgeThickness);
+
+ if (arrow1Cap != null) {
+ m_xformUtil.setTransform(cosTheta1, sinTheta1, -sinTheta1,
+ cosTheta1,
+ m_edgePtsBuff[((m_edgePtsCount - 1) * 6) - 4],
+ m_edgePtsBuff[((m_edgePtsCount - 1) * 6) - 3]);
+ m_g2d.transform(m_xformUtil);
+ m_g2d.scale(edgeThickness, edgeThickness);
+ // The paint is already set to edge paint.
+ m_g2d.fill(arrow1Cap);
+ m_g2d.setTransform(m_currNativeXform);
+ }
+ }
+
+ { // Render arrow at origin of poly path.
+
+ final Shape arrow0 = computeUntransformedArrow(arrow0Type);
+
+ if (arrow0 != null) {
+ m_xformUtil.setTransform(cosTheta0, sinTheta0, -sinTheta0,
+ cosTheta0, m_edgePtsBuff[0], m_edgePtsBuff[1]);
+ m_g2d.transform(m_xformUtil);
+ m_g2d.scale(arrow0Size, arrow0Size);
+ m_g2d.setPaint(arrow0Paint);
+ m_g2d.fill(arrow0);
+ m_g2d.setTransform(m_currNativeXform);
+ }
+ }
+
+ { // Render arrow at end of poly path.
+
+ final Shape arrow1 = computeUntransformedArrow(arrow1Type);
+
+ if (arrow1 != null) {
+ m_xformUtil.setTransform(cosTheta1, sinTheta1, -sinTheta1,
+ cosTheta1,
+ m_edgePtsBuff[((m_edgePtsCount - 1) * 6) - 2],
+ m_edgePtsBuff[((m_edgePtsCount - 1) * 6) - 1]);
+ m_g2d.transform(m_xformUtil);
+ m_g2d.scale(arrow1Size, arrow1Size);
+ m_g2d.setPaint(arrow1Paint);
+ m_g2d.fill(arrow1);
+ m_g2d.setTransform(m_currNativeXform);
+ }
+ }
+ }
+
+ @SuppressWarnings("fallthrough")
+ private final void edgeFullDebug(final byte arrow0Type,
+ final float arrow0Size, final byte arrow1Type, float arrow1Size,
+ final float edgeThickness, final float dashLength,
+ final EdgeAnchors anchors) {
+ if (!EventQueue.isDispatchThread()) {
+ throw new IllegalStateException(
+ "calling thread is not AWT event dispatcher");
+ }
+
+ if (!m_cleared) {
+ throw new IllegalStateException(
+ "clear() has not been called previously");
+ }
+
+ if (!(edgeThickness >= 0.0f)) {
+ throw new IllegalArgumentException("edgeThickness < 0");
+ }
+
+ if (!(dashLength >= 0.0f)) {
+ throw new IllegalArgumentException("dashLength < 0");
+ }
+
+ switch (arrow0Type) {
+ case ARROW_NONE:
+ break;
+
+ case ARROW_MONO:
+ arrow1Size = arrow0Size;
+
+ // Don't break; fall through.
+ case ARROW_BIDIRECTIONAL:
+
+ if (anchors.numAnchors() > 0) {
+ throw new IllegalArgumentException(
+ "ARROW_BIDIRECTIONAL and ARROW_MONO not supported for poly edges");
+ }
+
+ if (arrow1Type != arrow0Type) {
+ throw new IllegalArgumentException(
+ "for ARROW_BIDIRECTIONAL and ARROW_MONO, both arrows must be "
+ + "identical");
+ }
+
+ // Don't break; fall through.
+ case ARROW_DELTA:
+ case ARROW_DIAMOND:
+ case ARROW_DISC:
+ case ARROW_TEE:
+
+ if (!(arrow0Size >= edgeThickness)) {
+ throw new IllegalArgumentException(
+ "arrow size must be at least as large as edge thickness");
+ }
+
+ break;
+
+ default:
+ throw new IllegalArgumentException("arrow0Type is not recognized");
+ }
+
+ switch (arrow1Type) {
+ case ARROW_NONE:
+ break;
+
+ case ARROW_BIDIRECTIONAL:
+ case ARROW_MONO:
+
+ if (arrow0Type != arrow1Type) {
+ throw new IllegalArgumentException(
+ "for ARROW_BIDIRECTIONAL and ARROW_MONO, both arrows must be "
+ + "identical");
+ }
+
+ // Don't break; fall through.
+ case ARROW_DELTA:
+ case ARROW_DIAMOND:
+ case ARROW_DISC:
+ case ARROW_TEE:
+
+ if (!(arrow1Size >= edgeThickness)) {
+ throw new IllegalArgumentException(
+ "arrow size must be at least as large as edge thickness");
+ }
+
+ break;
+
+ default:
+ throw new IllegalArgumentException("arrow1Type is not recognized");
+ }
+
+ if (anchors.numAnchors() > MAX_EDGE_ANCHORS) {
+ throw new IllegalArgumentException("at most MAX_EDGE_ANCHORS ("
+ + MAX_EDGE_ANCHORS + ") edge anchors can be specified");
+ }
+ }
+
+ private final void drawSimpleEdgeFull(final byte arrow0Type,
+ final float arrow0Size, final Paint arrow0Paint,
+ final byte arrow1Type, final float arrow1Size,
+ final Paint arrow1Paint, final float x0, final float y0,
+ final float x1, final float y1, final float edgeThickness,
+ final Paint edgePaint, final float dashLength) {
+ final double len = Math
+ .sqrt(((((double) x1) - x0) * (((double) x1) - x0))
+ + ((((double) y1) - y0) * (((double) y1) - y0)));
+
+ // If the length of the edge is zero we're going to skip completely over
+ // all rendering. This check is now redundant because the code that
+ // calls
+ // us makes this check automatically.
+ if (len == 0.0d) {
+ return;
+ }
+
+ if (arrow0Type == ARROW_BIDIRECTIONAL) { // Draw and return.
+
+ final double a = (6.0d + (Math.sqrt(17.0d) / 2.0d)) * edgeThickness;
+ m_path2d.reset();
+
+ final double f = ((double) arrow0Size) - edgeThickness;
+ m_path2d.moveTo((float) (a + (4.0d * f)),
+ (float) (f + (1.5d * edgeThickness)));
+ m_path2d.lineTo((float) a, (float) (1.5d * edgeThickness));
+
+ if ((2.0d * a) < len) {
+ m_path2d.lineTo((float) (len - a),
+ (float) (1.5d * edgeThickness));
+ }
+
+ final double g = ((double) arrow1Size) - edgeThickness;
+ m_path2d.moveTo((float) (len - (a + (4.0d * g))),
+ (float) (-g + (-1.5d * edgeThickness)));
+ m_path2d.lineTo((float) (len - a), (float) (-1.5d * edgeThickness));
+
+ if ((2.0d * a) < len) {
+ m_path2d.lineTo((float) a, (float) (-1.5d * edgeThickness));
+ }
+
+ // I want the transform to first rotate, then translate.
+ final double cosTheta = (((double) x1) - x0) / len;
+ final double sinTheta = (((double) y1) - y0) / len;
+ m_xformUtil.setTransform(cosTheta, sinTheta, -sinTheta, cosTheta,
+ x0, y0);
+ m_path2d.transform(m_xformUtil);
+ setStroke(edgeThickness, dashLength,
+ (dashLength == 0.0f) ? BasicStroke.CAP_ROUND
+ : BasicStroke.CAP_BUTT, false);
+ m_g2d.setPaint(edgePaint);
+ m_g2d.draw(m_path2d);
+
+ return;
+ } // End ARROW_BIDIRECTIONAL.
+
+ if (arrow0Type == ARROW_MONO) { // Draw and return.
+ m_g2d.setPaint(edgePaint); // We're going to render at least one
+ // segment.
+
+ setStroke(edgeThickness, dashLength, BasicStroke.CAP_BUTT, false);
+
+ final double deltaLen = getT(ARROW_DELTA) * arrow0Size;
+ final double tDeltaLenFactor = 0.5d - (deltaLen / len);
+
+ if (tDeltaLenFactor > 0.0d) { // We must render the "pre" line
+ // segment.
+
+ final double x0Prime = (tDeltaLenFactor * (((double) x1) - x0))
+ + x0;
+ final double y0Prime = (tDeltaLenFactor * (((double) y1) - y0))
+ + y0;
+ m_line2d.setLine(x0, y0, x0Prime, y0Prime);
+ m_g2d.draw(m_line2d);
+ }
+
+ // Render the "post" segment.
+ final double midX = (((double) x0) + x1) / 2.0d;
+ final double midY = (((double) y0) + y1) / 2.0d;
+ m_line2d.setLine(x1, y1, midX, midY);
+ m_g2d.draw(m_line2d);
+
+ final double cosTheta = (((double) x0) - x1) / len;
+ final double sinTheta = (((double) y0) - y1) / len;
+
+ if ((tDeltaLenFactor > 0.0d) && (dashLength == 0.0f)) { // Render
+ // begin
+ // cap.
+ m_xformUtil.setTransform(cosTheta, sinTheta, -sinTheta,
+ cosTheta, x0, y0);
+ m_g2d.transform(m_xformUtil);
+ m_g2d.scale(edgeThickness, edgeThickness);
+ // The paint is already set to edge paint.
+ m_g2d.fill(computeUntransformedArrowCap(ARROW_NONE, 0.0d));
+ m_g2d.setTransform(m_currNativeXform);
+ }
+
+ if (dashLength == 0.0f) { // Render end cap.
+ m_xformUtil.setTransform(-cosTheta, -sinTheta, sinTheta,
+ -cosTheta, x1, y1);
+ m_g2d.transform(m_xformUtil);
+ m_g2d.scale(edgeThickness, edgeThickness);
+ // The paint is already set to edge paint.
+ m_g2d.fill(computeUntransformedArrowCap(ARROW_NONE, 0.0d));
+ m_g2d.setTransform(m_currNativeXform);
+ }
+
+ if (dashLength == 0.0f) { // Render delta wedge cap.
+ m_xformUtil.setTransform(-cosTheta, -sinTheta, sinTheta,
+ -cosTheta, midX, midY);
+ m_g2d.transform(m_xformUtil);
+ m_g2d.scale(edgeThickness, edgeThickness);
+ // The paint is already set to edge paint.
+ m_g2d.fill(computeUntransformedDeltaWedgeCap());
+ m_g2d.setTransform(m_currNativeXform);
+ }
+ // Finally, render the mono delta wedge.
+ {
+ m_xformUtil.setTransform(-cosTheta, -sinTheta, sinTheta,
+ -cosTheta, midX, midY);
+ m_g2d.transform(m_xformUtil);
+ m_g2d.scale(arrow0Size, arrow0Size);
+ m_g2d.setPaint(arrow0Paint);
+ m_g2d.fill(computeUntransformedArrow(ARROW_DELTA));
+ m_g2d.setTransform(m_currNativeXform);
+ }
+
+ return;
+ } // End ARROW_MONO.
+
+ final double x0Adj;
+ final double y0Adj;
+ final double x1Adj;
+ final double y1Adj;
+ final byte simpleSegment;
+
+ { // Render the line segment if necessary.
+
+ final double t0 = (getT(arrow0Type) * arrow0Size) / len;
+ x0Adj = (t0 * (((double) x1) - x0)) + x0;
+ y0Adj = (t0 * (((double) y1) - y0)) + y0;
+
+ final double t1 = (getT(arrow1Type) * arrow1Size) / len;
+ x1Adj = (t1 * (((double) x0) - x1)) + x1;
+ y1Adj = (t1 * (((double) y0) - y1)) + y1;
+
+ // If the vector point0->point1 is pointing opposite to
+ // adj0->adj1, then don't render the line segment.
+ // Dot product determines this.
+ if ((((((double) x1) - x0) * (x1Adj - x0Adj)) + ((((double) y1) - y0) * (y1Adj - y0Adj))) > 0.0d) {
+ // Must render the line segment.
+ if ((arrow0Type == ARROW_NONE) && (arrow1Type == ARROW_NONE)
+ && (dashLength == 0.0f)) {
+ simpleSegment = 1;
+ } else {
+ simpleSegment = -1;
+ }
+
+ setStroke(edgeThickness, dashLength,
+ (simpleSegment > 0) ? BasicStroke.CAP_ROUND
+ : BasicStroke.CAP_BUTT, false);
+ m_line2d.setLine(x0Adj, y0Adj, x1Adj, y1Adj);
+ m_g2d.setPaint(edgePaint);
+ m_g2d.draw(m_line2d);
+
+ if (simpleSegment > 0) {
+ return;
+ }
+ } else {
+ simpleSegment = 0;
+ } // Did not render segment.
+ } // End rendering of line segment.
+
+ // Using x0, x1, y0, and y1 instead of the "adjusted" endpoints is
+ // accurate enough in computation of cosine and sine because the
+ // length is guaranteed to be at least as large. Remember that the
+ // original endpoint values are specified as float whereas the adjusted
+ // points are double.
+ final double cosTheta = (((double) x0) - x1) / len;
+ final double sinTheta = (((double) y0) - y1) / len;
+
+ if ((simpleSegment < 0) && (dashLength == 0.0f)) { // Arrow cap at
+ // point 0.
+
+ final Shape arrow0Cap = computeUntransformedArrowCap(arrow0Type,
+ ((double) arrow0Size) / edgeThickness);
+
+ if (arrow0Cap != null) {
+ m_xformUtil.setTransform(cosTheta, sinTheta, -sinTheta,
+ cosTheta, x0Adj, y0Adj);
+ m_g2d.transform(m_xformUtil);
+ m_g2d.scale(edgeThickness, edgeThickness);
+ // The paint is already set to edge paint.
+ m_g2d.fill(arrow0Cap);
+ m_g2d.setTransform(m_currNativeXform);
+ }
+ }
+
+ if ((simpleSegment < 0) && (dashLength == 0.0f)) { // Arrow cap at
+ // point 1.
+
+ final Shape arrow1Cap = computeUntransformedArrowCap(arrow1Type,
+ ((double) arrow1Size) / edgeThickness);
+
+ if (arrow1Cap != null) {
+ m_xformUtil.setTransform(-cosTheta, -sinTheta, sinTheta,
+ -cosTheta, x1Adj, y1Adj);
+ m_g2d.transform(m_xformUtil);
+ m_g2d.scale(edgeThickness, edgeThickness);
+ // The paint is already set to edge paint.
+ m_g2d.fill(arrow1Cap);
+ m_g2d.setTransform(m_currNativeXform);
+ }
+ }
+
+ { // Render arrow at point 0.
+
+ final Shape arrow0 = computeUntransformedArrow(arrow0Type);
+
+ if (arrow0 != null) {
+ m_xformUtil.setTransform(cosTheta, sinTheta, -sinTheta,
+ cosTheta, x0, y0);
+ m_g2d.transform(m_xformUtil);
+ m_g2d.scale(arrow0Size, arrow0Size);
+ m_g2d.setPaint(arrow0Paint);
+ m_g2d.fill(arrow0);
+ m_g2d.setTransform(m_currNativeXform);
+ }
+ }
+
+ { // Render arrow at point 1.
+
+ final Shape arrow1 = computeUntransformedArrow(arrow1Type);
+
+ if (arrow1 != null) {
+ m_xformUtil.setTransform(-cosTheta, -sinTheta, sinTheta,
+ -cosTheta, x1, y1);
+ m_g2d.transform(m_xformUtil);
+ m_g2d.scale(arrow1Size, arrow1Size);
+ m_g2d.setPaint(arrow1Paint);
+ m_g2d.fill(arrow1);
+ m_g2d.setTransform(m_currNativeXform);
+ }
+ }
+ }
+
+ /**
+ * Computes the path that an edge takes; this method is useful if a user
+ * interface would allow user selection of edges, for example. The returned
+ * path is the path along the center of the edge segment, extending to the
+ * points which specify the arrow locations. Note that this path therefore
+ * disregards edge thickness and arrow outline. Use the same parameter
+ * values that were used to render corresponding edge.
+ *
+ * @param arrow0Type
+ * the type of arrow shape used for drawing the arrow at point
+ * (x0, y0); this value must be one of the ARROW_* constants.
+ * @param arrow0Size
+ * the size of arrow at point (x0, y0).
+ * @param arrow1Type
+ * the type of arrow shape used for drawing the arrow at point
+ * (x1, y1); this value must be one of the ARROW_* constants.
+ * @param arrow1Size
+ * the size of arrow at point (x1, y1).
+ * @param x0
+ * the X coordinate of the first edge endpoint.
+ * @param y0
+ * the Y coordinate of the first edge endpoint.
+ * @param anchors
+ * anchor points between the two edge endpoints; null is an
+ * acceptable value to indicate no edge anchors.
+ * @param x1
+ * the X coordinate of the second edge endpoint.
+ * @param y1
+ * the Y coordinate of the second edge endpoint.
+ * @param path
+ * the computed path is returned in this parameter; the computed
+ * path's coordinate system is the node coordinate system; the
+ * computed path is not closed.
+ * @return true if and only if the specified edge would be drawn (which is
+ * if and only if any two points from the edge anchor set plus the
+ * beginning and end point are distinct); if false is returned, the
+ * path parameter is not modified.
+ * @exception IllegalArgumentException
+ * if any one of the edge arrow criteria specified in
+ * drawEdgeFull() is not satisfied.
+ */
+ public final boolean getEdgePath(final byte arrow0Type,
+ final float arrow0Size, final byte arrow1Type,
+ final float arrow1Size, final float x0, final float y0,
+ EdgeAnchors anchors, final float x1, final float y1,
+ final GeneralPath path) {
+ final double curveFactor = CURVE_ELLIPTICAL;
+
+ if (anchors == null) {
+ anchors = m_noAnchors;
+ }
+
+ if (m_debug) {
+ if (!EventQueue.isDispatchThread()) {
+ throw new IllegalStateException(
+ "calling thread is not AWT event dispatcher");
+ }
+
+ switch (arrow0Type) {
+ case ARROW_NONE:
+ case ARROW_DELTA:
+ case ARROW_DIAMOND:
+ case ARROW_DISC:
+ case ARROW_TEE:
+ break;
+
+ case ARROW_BIDIRECTIONAL:
+ case ARROW_MONO:
+
+ if (arrow1Type != arrow0Type) {
+ throw new IllegalArgumentException(
+ "for ARROW_BIDIRECTIONAL and ARROW_MONO, both arrows must be "
+ + "identical");
+ }
+
+ if (anchors.numAnchors() > 0) {
+ throw new IllegalArgumentException(
+ "ARROW_BIDIRECTIONAL and ARROW_MONO not supported in poly edges");
+ }
+
+ break;
+
+ default:
+ throw new IllegalArgumentException(
+ "arrow0Type is not recognized");
+ }
+
+ switch (arrow1Type) {
+ case ARROW_NONE:
+ case ARROW_DELTA:
+ case ARROW_DIAMOND:
+ case ARROW_DISC:
+ case ARROW_TEE:
+ break;
+
+ case ARROW_BIDIRECTIONAL:
+ case ARROW_MONO:
+
+ if (arrow0Type != arrow1Type) {
+ throw new IllegalArgumentException(
+ "for ARROW_BIDIRECTIONAL and ARROW_MONO, both arrows must be "
+ + "identical");
+ }
+
+ break;
+
+ default:
+ throw new IllegalArgumentException(
+ "arrow1Type is not recognized");
+ }
+
+ if (anchors.numAnchors() > MAX_EDGE_ANCHORS) {
+ throw new IllegalArgumentException("at most MAX_EDGE_ANCHORS ("
+ + MAX_EDGE_ANCHORS + ") edge anchors can be specified");
+ }
+ }
+
+ byte arrow0 = arrow0Type;
+ byte arrow1 = arrow1Type;
+
+ if (arrow0 == ARROW_BIDIRECTIONAL) { // Assume arrow1 is also.
+ // If we wanted to start our path where the bidirectional edge
+ // actually started, we'd have to pass edge thickness into this
+ // method.
+ // So instead we do a quick and simple approximation by extending
+ // the
+ // bidirectional edge to the tip of the encapsulating delta.
+ arrow0 = ARROW_NONE;
+ arrow1 = ARROW_NONE;
+ }
+
+ if (arrow0 == ARROW_MONO) { // Assume arrow1 is also.
+ arrow0 = ARROW_NONE;
+ arrow1 = ARROW_NONE;
+ }
+
+ if (!computeCubicPolyEdgePath(arrow0, (arrow0 == ARROW_NONE) ? 0.0f
+ : arrow0Size, arrow1, (arrow1 == ARROW_NONE) ? 0.0f
+ : arrow1Size, x0, y0, anchors, x1, y1, curveFactor)) {
+ // After filtering duplicate start and end points, there are less
+ // then
+ // 3 total.
+ if (m_edgePtsCount == 2) {
+ path.reset();
+ path.moveTo((float) m_edgePtsBuff[0], (float) m_edgePtsBuff[1]);
+ path.lineTo((float) m_edgePtsBuff[2], (float) m_edgePtsBuff[3]);
+
+ return true;
+ }
+
+ return false;
+ }
+
+ path.reset();
+ path.moveTo((float) m_edgePtsBuff[0], (float) m_edgePtsBuff[1]);
+ path.lineTo((float) m_edgePtsBuff[2], (float) m_edgePtsBuff[3]);
+
+ int inx = 4;
+ final int count = ((m_edgePtsCount - 1) * 6) - 2;
+
+ while (inx < count) {
+ path.curveTo((float) m_edgePtsBuff[inx++],
+ (float) m_edgePtsBuff[inx++], (float) m_edgePtsBuff[inx++],
+ (float) m_edgePtsBuff[inx++], (float) m_edgePtsBuff[inx++],
+ (float) m_edgePtsBuff[inx++]);
+ }
+
+ path.lineTo((float) m_edgePtsBuff[count],
+ (float) m_edgePtsBuff[count + 1]);
+
+ return true;
+ }
+
+ /*
+ * Returns non-null if and only if an arrow is necessary for the arrow type
+ * specified. m_path2d and m_ellp2d may be mangled as a side effect.
+ * arrowType must be one of the primitive arrow types or ARROW_NONE (no
+ * ARROW_BIDIRECTIONAL or ARROW_MONO allowed).
+ */
+ private final Shape computeUntransformedArrow(final byte arrowType) {
+ switch (arrowType) {
+ case ARROW_NONE:
+ return null;
+
+ case ARROW_DELTA:
+ m_path2d.reset();
+ m_path2d.moveTo(-2.0f, -0.5f);
+ m_path2d.lineTo(0.0f, 0.0f);
+ m_path2d.lineTo(-2.0f, 0.5f);
+ m_path2d.closePath();
+
+ return m_path2d;
+
+ case ARROW_DIAMOND:
+ m_path2d.reset();
+ m_path2d.moveTo(-1.0f, -0.5f);
+ m_path2d.lineTo(0.0f, 0.0f);
+ m_path2d.lineTo(-1.0f, 0.5f);
+ m_path2d.lineTo(-2.0f, 0.0f);
+ m_path2d.closePath();
+
+ return m_path2d;
+
+ case ARROW_DISC:
+ m_ellp2d.setFrame(-0.5d, -0.5d, 1.0d, 1.0d);
+
+ return m_ellp2d;
+
+ default: // ARROW_TEE.
+ m_path2d.reset();
+ m_path2d.moveTo(-0.125f, -1.0f);
+ m_path2d.lineTo(0.125f, -1.0f);
+ m_path2d.lineTo(0.125f, 1.0f);
+ m_path2d.lineTo(-0.125f, 1.0f);
+ m_path2d.closePath();
+
+ return m_path2d;
+ }
+ }
+
+ /*
+ * The ratio parameter specifies the ratio of arrow size (disc diameter) to
+ * edge thickness (only used for some arrow types). Returns non-null if and
+ * only if a cap is necessary for the arrow type specified. If non-null is
+ * returned then m_path2d and m_arc2d may be mangled as a side effect.
+ * arrowType must be one of the primitive arrow types or ARROW_NONE (no
+ * ARROW_BIDIRECTIONAL or ARROW_MONO allowed).
+ */
+ private final Shape computeUntransformedArrowCap(final byte arrowType,
+ final double ratio) {
+ switch (arrowType) {
+ case ARROW_NONE:
+ m_arc2d.setArc(-0.5d, -0.5d, 1.0d, 1.0d, 270.0d, 180.0d,
+ Arc2D.CHORD);
+
+ return m_arc2d;
+
+ case ARROW_DELTA:
+ return null;
+
+ case ARROW_DIAMOND:
+ m_path2d.reset();
+ m_path2d.moveTo(0.0f, -0.5f);
+ m_path2d.lineTo(1.0f, -0.5f);
+ m_path2d.lineTo(0.0f, 0.0f);
+ m_path2d.lineTo(1.0f, 0.5f);
+ m_path2d.lineTo(0.0f, 0.5f);
+ m_path2d.closePath();
+
+ return m_path2d;
+
+ case ARROW_DISC:
+
+ final double theta = Math.toDegrees(Math.asin(1.0d / ratio));
+ m_arc2d.setArc(0.0d, ratio / -2.0d, ratio, ratio, 180.0d - theta,
+ theta * 2, Arc2D.OPEN);
+ m_path2d.reset();
+ m_path2d.append(m_arc2d, false);
+ m_path2d.lineTo(0.0f, 0.5f);
+ m_path2d.lineTo(0.0f, -0.5f);
+ m_path2d.closePath();
+
+ return m_path2d;
+
+ default: // ARROW_TEE.
+
+ return null;
+ }
+ }
+
+ /*
+ * ---| \ | \| /| / | ---|
+ *
+ * The same transform that was used to draw the delta arrowhead (for
+ * ARROW_MONO) can be used modulo scaling to edge thickness.
+ */
+ private final Shape computeUntransformedDeltaWedgeCap() {
+ m_path2d.reset();
+ m_path2d.moveTo(-2.0f, -0.5f);
+ m_path2d.lineTo(0.0f, -0.5f);
+ m_path2d.lineTo(0.0f, 0.5f);
+ m_path2d.lineTo(-2.0f, 0.5f);
+ m_path2d.lineTo(0.0f, 0.0f);
+ m_path2d.closePath();
+
+ return m_path2d;
+ }
+
+ /*
+ * arrowType must be one of the primitive arrow types or ARROW_NONE (no
+ * ARROW_BIDIRECTIONAL or ARROW_MONO allowed).
+ */
+ private final static double getT(final byte arrowType) { // I could
+ // implement
+ // this as an
+ // array instead
+ // of a switch
+ // statement.
+
+ switch (arrowType) {
+ case ARROW_NONE:
+ return 0.0d;
+
+ case ARROW_DELTA:
+ return 2.0d;
+
+ case ARROW_DIAMOND:
+ return 2.0d;
+
+ case ARROW_DISC:
+ return 0.5d;
+
+ default: // ARROW_TEE.
+
+ return 0.125d;
+ }
+ }
+
+ /*
+ * If arrow0Type is ARROW_NONE, arrow0Size should be zero. If arrow1Type is
+ * ARROW_NONE, arrow1Size should be zero.
+ */
+ private final boolean computeCubicPolyEdgePath(final byte arrow0Type,
+ final float arrow0Size, final byte arrow1Type,
+ final float arrow1Size, final float x0, final float y0,
+ final EdgeAnchors anchors, final float x1, final float y1,
+ final double curveFactor) {
+ final int numAnchors = anchors.numAnchors();
+ // add the start point to the edge points buffer
+ m_edgePtsBuff[0] = x0;
+ m_edgePtsBuff[1] = y0;
+ m_edgePtsCount = 1;
+
+ int anchorInx = 0;
+
+ // finds the first anchor point other than the start point and
+ // add it to the edge points buffer
+ while (anchorInx < numAnchors) {
+ anchors.getAnchor(anchorInx++, m_floatBuff, 0);
+
+ if (!((m_floatBuff[0] == x0) && (m_floatBuff[1] == y0))) {
+ m_edgePtsBuff[2] = m_floatBuff[0];
+ m_edgePtsBuff[3] = m_floatBuff[1];
+ m_edgePtsCount = 2;
+
+ break;
+ }
+ }
+
+ // now fill edge points buffer with all subsequent anchors
+ while (anchorInx < numAnchors) {
+ anchors.getAnchor(anchorInx++, m_floatBuff, 0);
+ // Duplicate anchors are allowed.
+ m_edgePtsBuff[m_edgePtsCount * 2] = m_floatBuff[0];
+ m_edgePtsBuff[(m_edgePtsCount * 2) + 1] = m_floatBuff[1];
+ m_edgePtsCount++;
+ }
+
+ // now add the end point to the buffer
+ m_edgePtsBuff[m_edgePtsCount * 2] = x1;
+ m_edgePtsBuff[(m_edgePtsCount * 2) + 1] = y1;
+ m_edgePtsCount++;
+
+ // remove duplicate end points from edge buffer
+ while (m_edgePtsCount > 1) {
+ // second-to-last X coord and second-to-last Y coord.
+ if ((m_edgePtsBuff[(m_edgePtsCount * 2) - 2] == m_edgePtsBuff[(m_edgePtsCount * 2) - 4])
+ && (m_edgePtsBuff[(m_edgePtsCount * 2) - 1] == m_edgePtsBuff[(m_edgePtsCount * 2) - 3])) {
+ m_edgePtsCount--;
+ } else {
+ break;
+ }
+ }
+
+ // no anchors, just a straight line to draw
+ if (m_edgePtsCount < 3) {
+ return false;
+ }
+
+ //
+ // ok, now we're drawing a curve
+ //
+
+ final int edgePtsCount = m_edgePtsCount;
+
+ // First set the three control points related to point 1.
+ // 6 represents the offset in the buffer.
+ {
+ m_edgePtsCount--;
+ // set first control point
+ m_edgePtsBuff[(m_edgePtsCount * 6) - 2] = m_edgePtsBuff[m_edgePtsCount * 2];
+ m_edgePtsBuff[(m_edgePtsCount * 6) - 1] = m_edgePtsBuff[(m_edgePtsCount * 2) + 1];
+
+ double dx = m_edgePtsBuff[(m_edgePtsCount * 2) - 2]
+ - m_edgePtsBuff[m_edgePtsCount * 2];
+ double dy = m_edgePtsBuff[(m_edgePtsCount * 2) - 1]
+ - m_edgePtsBuff[(m_edgePtsCount * 2) + 1];
+ double len = Math.sqrt((dx * dx) + (dy * dy));
+ // Normalized.
+ dx /= len;
+ dy /= len;
+
+ // set second control point
+ m_edgePtsBuff[(m_edgePtsCount * 6) - 4] = m_edgePtsBuff[(m_edgePtsCount * 6) - 2]
+ + (dx * arrow1Size * getT(arrow1Type));
+ m_edgePtsBuff[(m_edgePtsCount * 6) - 3] = m_edgePtsBuff[(m_edgePtsCount * 6) - 1]
+ + (dy * arrow1Size * getT(arrow1Type));
+
+ // one candidate point is offset by the arrow (candX1) and
+ // the other is offset by the curvefactor (candX2)
+ double candX1 = m_edgePtsBuff[(m_edgePtsCount * 6) - 4]
+ + (dx * 2.0d * arrow1Size);
+ double candX2 = m_edgePtsBuff[(m_edgePtsCount * 6) - 4]
+ + (curveFactor * (m_edgePtsBuff[(m_edgePtsCount * 2) - 2] - m_edgePtsBuff[(m_edgePtsCount * 6) - 4]));
+
+ // set third control point X coord
+ // choose the candidate with max offset
+ if (Math.abs(candX1 - m_edgePtsBuff[m_edgePtsCount * 2]) > Math
+ .abs(candX2 - m_edgePtsBuff[m_edgePtsCount * 2])) {
+ m_edgePtsBuff[(m_edgePtsCount * 6) - 6] = candX1;
+ } else {
+ m_edgePtsBuff[(m_edgePtsCount * 6) - 6] = candX2;
+ }
+
+ // one candidate point is offset by the arrow (candY1) and
+ // the other is offset by the curvefactor (candY2)
+ double candY1 = m_edgePtsBuff[(m_edgePtsCount * 6) - 3]
+ + (dy * 2.0d * arrow1Size);
+ double candY2 = m_edgePtsBuff[(m_edgePtsCount * 6) - 3]
+ + (curveFactor * (m_edgePtsBuff[(m_edgePtsCount * 2) - 1] - m_edgePtsBuff[(m_edgePtsCount * 6) - 3]));
+
+ // set third control point Y coord
+ // choose the candidate with max offset
+ if (Math.abs(candY1 - m_edgePtsBuff[(m_edgePtsCount * 2) + 1]) > Math
+ .abs(candY2 - m_edgePtsBuff[(m_edgePtsCount * 2) + 1])) {
+ m_edgePtsBuff[(m_edgePtsCount * 6) - 5] = candY1;
+ } else {
+ m_edgePtsBuff[(m_edgePtsCount * 6) - 5] = candY2;
+ }
+ }
+
+ // Next set the control point for each edge anchor.
+ while (m_edgePtsCount > 2) {
+ m_edgePtsCount--;
+
+ final double midX = (m_edgePtsBuff[(m_edgePtsCount * 2) - 2] + m_edgePtsBuff[m_edgePtsCount * 2]) / 2.0d;
+ final double midY = (m_edgePtsBuff[(m_edgePtsCount * 2) - 1] + m_edgePtsBuff[(m_edgePtsCount * 2) + 1]) / 2.0d;
+ m_edgePtsBuff[(m_edgePtsCount * 6) - 2] = midX
+ + ((m_edgePtsBuff[m_edgePtsCount * 2] - midX) * curveFactor);
+ m_edgePtsBuff[(m_edgePtsCount * 6) - 1] = midY
+ + ((m_edgePtsBuff[(m_edgePtsCount * 2) + 1] - midY) * curveFactor);
+ m_edgePtsBuff[(m_edgePtsCount * 6) - 4] = midX;
+ m_edgePtsBuff[(m_edgePtsCount * 6) - 3] = midY;
+ m_edgePtsBuff[(m_edgePtsCount * 6) - 6] = midX
+ + ((m_edgePtsBuff[(m_edgePtsCount * 2) - 2] - midX) * curveFactor);
+ m_edgePtsBuff[(m_edgePtsCount * 6) - 5] = midY
+ + ((m_edgePtsBuff[(m_edgePtsCount * 2) - 1] - midY) * curveFactor);
+ }
+
+ { // Last set the three control points related to point 0.
+
+ double dx = m_edgePtsBuff[2] - m_edgePtsBuff[0];
+ double dy = m_edgePtsBuff[3] - m_edgePtsBuff[1];
+ double len = Math.sqrt((dx * dx) + (dy * dy));
+ // Normalized.
+ dx /= len;
+ dy /= len;
+
+ double segStartX = m_edgePtsBuff[0]
+ + (dx * arrow0Size * getT(arrow0Type));
+ double segStartY = m_edgePtsBuff[1]
+ + (dy * arrow0Size * getT(arrow0Type));
+ double candX1 = segStartX + (dx * 2.0d * arrow0Size);
+ double candX2 = segStartX
+ + (curveFactor * (m_edgePtsBuff[2] - segStartX));
+
+ if (Math.abs(candX1 - m_edgePtsBuff[0]) > Math.abs(candX2
+ - m_edgePtsBuff[0])) {
+ m_edgePtsBuff[4] = candX1;
+ } else {
+ m_edgePtsBuff[4] = candX2;
+ }
+
+ double candY1 = segStartY + (dy * 2.0d * arrow0Size);
+ double candY2 = segStartY
+ + (curveFactor * (m_edgePtsBuff[3] - segStartY));
+
+ if (Math.abs(candY1 - m_edgePtsBuff[1]) > Math.abs(candY2
+ - m_edgePtsBuff[1])) {
+ m_edgePtsBuff[5] = candY1;
+ } else {
+ m_edgePtsBuff[5] = candY2;
+ }
+
+ m_edgePtsBuff[2] = segStartX;
+ m_edgePtsBuff[3] = segStartY;
+ }
+
+ m_edgePtsCount = edgePtsCount;
+
+ return true;
+ }
+
+ /**
+ * Computes the intersection point between a node outline and a line
+ * segment; one point of the line segment lies at the center of the node
+ * outline.
+ * <p>
+ * There is a constraint that only applies to SHAPE_ROUNDED_RECTANGLE which
+ * imposes that the maximum of the width and height be strictly less than
+ * twice the minimum of the width and height of the node.
+ *
+ * @param nodeShape
+ * the shape of the node in question; this must be one of the
+ * SHAPE_* constants or a custom node shape.
+ * @param xMin
+ * an extent of the node in question, in node coordinate space.
+ * @param yMin
+ * an extent of the node in question, in node coordinate space.
+ * @param xMax
+ * an extent of the node in question, in node coordinate space.
+ * @param yMax
+ * an extent of the node in question, in node coordinate space.
+ * @param offset
+ * most of the time this value will be zero, in which case the
+ * point computed is the exact intersection point of line segment
+ * and node outline; if this value is greater than zero, the
+ * point computed is one that lies on the line segment, is
+ * "outside" of the node outline, and is distance offset from the
+ * node outline.
+ * @param ptX
+ * specifies the X coordinate of the endpoint of the line segment
+ * that is not the endpoint lying in the center of the node
+ * shape.
+ * @param ptY
+ * specifies the Y coordinate of the endpoint of the line segment
+ * that is not the endpoint lying in the center of the node
+ * shape.
+ * @param returnVal
+ * if true is returned, returnVal[0] is set to be the X
+ * coordinate of the computed point and returnVal[1] is set to be
+ * the Y coordinate of the computed point; if false is returned,
+ * this array is not modified.
+ * @return true if and only if a point matching our criteria exists.
+ * @exception IllegalArgumentException
+ * if xMin is not less than xMax or if yMin is not less than
+ * yMax, if offset is negative, if nodeShape is
+ * SHAPE_ROUNDED_RECTANGLE and the condition max(width,
+ * height) < 2 * min(width, height) does not hold, or if
+ * nodeShape is neither one of the SHAPE_* constants nor a
+ * previously defined custom node shape.
+ */
+ public final boolean computeEdgeIntersection(final byte nodeShape,
+ final float xMin, final float yMin, final float xMax,
+ final float yMax, final float offset, final float ptX,
+ final float ptY, final float[] returnVal) {
+ if (m_debug) {
+ if (!EventQueue.isDispatchThread()) {
+ throw new IllegalStateException(
+ "calling thread is not AWT event dispatcher");
+ }
+
+ if (!(xMin < xMax)) {
+ throw new IllegalArgumentException("xMin not less than xMax");
+ }
+
+ if (!(yMin < yMax)) {
+ throw new IllegalArgumentException("yMin not less than yMax");
+ }
+
+ if (!(offset >= 0.0f)) {
+ throw new IllegalArgumentException("offset < 0");
+ }
+
+ if (nodeShape == SHAPE_ROUNDED_RECTANGLE) {
+ final double width = ((double) xMax) - xMin;
+ final double height = ((double) yMax) - yMin;
+
+ if (!(Math.max(width, height) < (2.0d * Math.min(width, height)))) {
+ throw new IllegalArgumentException(
+ "rounded rectangle does not meet constraint "
+ + "max(width, height) < 2 * min(width, height)");
+ }
+ }
+ }
+
+ final double centerX = (((double) xMin) + xMax) / 2.0d;
+ final double centerY = (((double) yMin) + yMax) / 2.0d;
+
+ if (nodeShape == SHAPE_ELLIPSE) {
+ if ((centerX == ptX) && (centerY == ptY)) {
+ return false;
+ }
+
+ // First, compute the actual intersection of the edge with the
+ // ellipse, if it exists. We will use this intersection point
+ // regardless of whether or not offset is zero.
+ // For nonzero offsets on the ellipse, use tangent lines to
+ // approximate
+ // intersection with offset instead of solving a quartic equation.
+ final double ptPrimeX = ptX - centerX;
+ final double ptPrimeY = ptY - centerY;
+ final double ellpW = ((double) xMax) - xMin;
+ final double ellpH = ((double) yMax) - yMin;
+ final double xScaleFactor = 2.0d / ellpW;
+ final double yScaleFactor = 2.0d / ellpH;
+ final double xformedPtPrimeX = ptPrimeX * xScaleFactor;
+ final double xformedPtPrimeY = ptPrimeY * yScaleFactor;
+ final double xformedDist = Math
+ .sqrt((xformedPtPrimeX * xformedPtPrimeX)
+ + (xformedPtPrimeY * xformedPtPrimeY));
+ final double xsectXformedPtPrimeX = xformedPtPrimeX / xformedDist;
+ final double xsectXformedPtPrimeY = xformedPtPrimeY / xformedDist;
+ final double tangentXformedPtPrimeX = xsectXformedPtPrimeX
+ + xsectXformedPtPrimeY;
+ final double tangentXformedPtPrimeY = xsectXformedPtPrimeY
+ - xsectXformedPtPrimeX;
+ final double xsectPtPrimeX = xsectXformedPtPrimeX / xScaleFactor;
+ final double xsectPtPrimeY = xsectXformedPtPrimeY / yScaleFactor;
+ final double tangentPtPrimeX = tangentXformedPtPrimeX
+ / xScaleFactor;
+ final double tangentPtPrimeY = tangentXformedPtPrimeY
+ / yScaleFactor;
+ final double vTangentX = tangentPtPrimeX - xsectPtPrimeX;
+ final double vTangentY = tangentPtPrimeY - xsectPtPrimeY;
+ final double tanLen = Math.sqrt((vTangentX * vTangentX)
+ + (vTangentY * vTangentY));
+ final double distPtPrimeToTangent = (((vTangentX * ptPrimeY)
+ - (vTangentY * ptPrimeX) + (xsectPtPrimeX * tangentPtPrimeY)) - (tangentPtPrimeX * xsectPtPrimeY))
+ / tanLen;
+
+ if (distPtPrimeToTangent < offset) { // This includes cases where
+ // distPtPrimeToTangent is negative, which means that the true
+ // intersection point lies inside the ellipse (no intersection
+ // even
+ // with zero offset).
+
+ return false;
+ }
+
+ if (distPtPrimeToTangent == 0.0d) { // Therefore offset is zero
+ // also.
+ returnVal[0] = (float) (xsectPtPrimeX + centerX);
+ returnVal[1] = (float) (xsectPtPrimeY + centerY);
+
+ return true;
+ }
+
+ // Even if offset is zero, do extra computation for sake of simple
+ // code.
+ final double multFactor = offset / distPtPrimeToTangent;
+ returnVal[0] = (float) (centerX + (xsectPtPrimeX + (multFactor * (ptPrimeX - xsectPtPrimeX))));
+ returnVal[1] = (float) (centerY + (xsectPtPrimeY + (multFactor * (ptPrimeY - xsectPtPrimeY))));
+
+ return true;
+ } else { // Not ellipse.
+
+ final double trueOffset;
+
+ if (nodeShape == SHAPE_ROUNDED_RECTANGLE) {
+ final double radius = Math.max(((double) xMax) - xMin,
+ ((double) yMax) - yMin) / 4.0d;
+ // One of our constraints is that for rounded rectangle,
+ // max(width, height) < 2 * min(width, height) in 32 bit
+ // floating
+ // point world. Therefore, with 64 bits of precision, the
+ // rectangle
+ // calculated below does not degenerate in width or height.
+ getShape(SHAPE_RECTANGLE, radius + xMin, radius + yMin, -radius
+ + xMax, -radius + yMax);
+ trueOffset = radius + offset;
+ } else {
+ // This next method call has the side effect of setting
+ // m_polyCoords
+ // and m_polyNumPoints - this is all that we are going to use.
+ getShape(nodeShape, xMin, yMin, xMax, yMax);
+ trueOffset = offset;
+ }
+
+ if (trueOffset == 0.0d) {
+ final int twicePolyNumPoints = m_polyNumPoints * 2;
+
+ for (int i = 0; i < twicePolyNumPoints;) {
+ final double x0 = m_polyCoords[i++];
+ final double y0 = m_polyCoords[i++];
+ final double x1 = m_polyCoords[i % twicePolyNumPoints];
+ final double y1 = m_polyCoords[(i + 1) % twicePolyNumPoints];
+
+ if (segmentIntersection(m_ptsBuff, ptX, ptY, centerX,
+ centerY, x0, y0, x1, y1)) {
+ returnVal[0] = (float) m_ptsBuff[0];
+ returnVal[1] = (float) m_ptsBuff[1];
+
+ return true;
+ }
+ }
+
+ return false;
+ }
+
+ // The rest of this code is the polygonal case where offset is
+ // nonzero.
+ for (int i = 0; i < m_polyNumPoints; i++) {
+ final double x0 = m_polyCoords[i * 2];
+ final double y0 = m_polyCoords[(i * 2) + 1];
+ final double x1 = m_polyCoords[((i * 2) + 2)
+ % (m_polyNumPoints * 2)];
+ final double y1 = m_polyCoords[((i * 2) + 3)
+ % (m_polyNumPoints * 2)];
+ final double vX = x1 - x0;
+ final double vY = y1 - y0;
+ final double len = Math.sqrt((vX * vX) + (vY * vY));
+ final double vNormX = vX / len;
+ final double vNormY = vY / len;
+ m_fooPolyCoords[i * 4] = x0 + (vNormY * trueOffset);
+ m_fooPolyCoords[(i * 4) + 1] = y0 - (vNormX * trueOffset);
+ m_fooPolyCoords[(i * 4) + 2] = x1 + (vNormY * trueOffset);
+ m_fooPolyCoords[(i * 4) + 3] = y1 - (vNormX * trueOffset);
+ }
+
+ int inx = 0;
+
+ for (int i = 0; i < m_polyNumPoints; i++) {
+ if (segmentIntersection // We could perhaps use the sign of a
+ // cross
+ (
+ m_ptsBuff, // product to perform this test quicker.
+ m_fooPolyCoords[(i * 4) + 2], // Because non-convex
+ // polygons are
+ m_fooPolyCoords[(i * 4) + 3], // rare, we will almost
+ // never use
+ m_fooPolyCoords[i * 4], // the computed intersection
+ // point.
+ m_fooPolyCoords[(i * 4) + 1],
+ m_fooPolyCoords[((i * 4) + 4) % (m_polyNumPoints * 4)],
+ m_fooPolyCoords[((i * 4) + 5) % (m_polyNumPoints * 4)],
+ m_fooPolyCoords[((i * 4) + 6) % (m_polyNumPoints * 4)],
+ m_fooPolyCoords[((i * 4) + 7) % (m_polyNumPoints * 4)])) {
+ m_foo2PolyCoords[inx++] = m_ptsBuff[0];
+ m_foo2PolyCoords[inx++] = m_ptsBuff[1];
+ m_fooRoundedCorners[i] = false;
+ } else {
+ m_foo2PolyCoords[inx++] = m_fooPolyCoords[(i * 4) + 2];
+ m_foo2PolyCoords[inx++] = m_fooPolyCoords[(i * 4) + 3];
+ m_foo2PolyCoords[inx++] = m_fooPolyCoords[((i * 4) + 4)
+ % (m_polyNumPoints * 4)];
+ m_foo2PolyCoords[inx++] = m_fooPolyCoords[((i * 4) + 5)
+ % (m_polyNumPoints * 4)];
+ m_fooRoundedCorners[i] = true;
+ }
+ }
+
+ final int foo2Count = inx;
+ inx = 0;
+
+ for (int i = 0; i < m_polyNumPoints; i++) {
+ if (m_fooRoundedCorners[i]) {
+ if (segmentIntersection(m_ptsBuff, ptX, ptY, centerX,
+ centerY, m_foo2PolyCoords[inx++],
+ m_foo2PolyCoords[inx++], m_foo2PolyCoords[inx],
+ m_foo2PolyCoords[inx + 1])) {
+ final double segXsectX = m_ptsBuff[0];
+ final double segXsectY = m_ptsBuff[1];
+ final int numXsections = bad_circleIntersection(
+ m_ptsBuff,
+ ptX,
+ ptY,
+ centerX,
+ centerY,
+ m_polyCoords[2 * ((i + 1) % m_polyNumPoints)],
+ m_polyCoords[(2 * ((i + 1) % m_polyNumPoints)) + 1],
+ trueOffset);
+
+ // We don't expect tangential intersections because of
+ // constraints on allowed polygons. Therefore, if the
+ // circle
+ // intersects the edge segment in only one point, then
+ // that
+ // intersection point is the "outer arc" only if the
+ // edge segment
+ // intersection point with the corner polygon segment
+ // (the arc
+ // approximation) lies between the center of the polygon
+ // and
+ // this one circle intersection point.
+ if ((numXsections == 2)
+ || ((numXsections == 1)
+ && (Math.min(centerX, m_ptsBuff[0]) <= segXsectX)
+ && (segXsectX <= Math.max(centerX,
+ m_ptsBuff[0]))
+ && (Math.min(centerY, m_ptsBuff[1]) <= segXsectY) && (segXsectY <= Math
+ .max(centerY, m_ptsBuff[1])))) {
+ returnVal[0] = (float) m_ptsBuff[0]; // The first
+ // returnVal
+ // is
+
+ returnVal[1] = (float) m_ptsBuff[1]; // closer to
+ // (ptX,
+ // ptY);
+ // see API.
+
+ return true;
+ } else {
+ // The edge segment didn't quite make it to the
+ // outer section
+ // of the circle; only the inner part was
+ // intersected.
+ return false;
+ }
+ } else if (segmentIntersection // Test against the true
+ // line segment
+ (
+ m_ptsBuff, // that comes after the arc.
+ ptX, ptY, centerX, centerY,
+ m_foo2PolyCoords[inx++], m_foo2PolyCoords[inx++],
+ m_foo2PolyCoords[inx % foo2Count],
+ m_foo2PolyCoords[(inx + 1) % foo2Count])) {
+ returnVal[0] = (float) m_ptsBuff[0];
+ returnVal[1] = (float) m_ptsBuff[1];
+
+ return true;
+ }
+ } else { // Not a rounded corner here.
+
+ if (segmentIntersection(m_ptsBuff, ptX, ptY, centerX,
+ centerY, m_foo2PolyCoords[inx++],
+ m_foo2PolyCoords[inx++], m_foo2PolyCoords[inx
+ % foo2Count], m_foo2PolyCoords[(inx + 1)
+ % foo2Count])) {
+ returnVal[0] = (float) m_ptsBuff[0];
+ returnVal[1] = (float) m_ptsBuff[1];
+
+ return true;
+ }
+ }
+ }
+
+ return false;
+ }
+ }
+
+ /*
+ * Computes the intersection of the line segment from (x1,y1) to (x2,y2)
+ * with the line segment from (x3,y3) to (x4,y4). If no intersection exists,
+ * returns false. Otherwise returns true, and returnVal[0] is set to be the
+ * X coordinate of the intersection point and returnVal[1] is set to be the
+ * Y coordinate of the intersection point. If more than one intersection
+ * point exists, "the intersection point" is defined to be the intersection
+ * point closest to (x1,y1). A note about overlapping line segments. Because
+ * of floating point numbers' inability to be totally accurate, it is quite
+ * difficult to represent overlapping line segments with floating point
+ * coordinates without using an absolute-precision math package. Because of
+ * this, poorly behaved outcome may result when computing the intersection
+ * of two [nearly] overlapping line segments. The only way around this would
+ * be to round intersection points to the nearest 32-bit floating point
+ * quantity. But then dynamic range is greatly compromised.
+ */
+ private final static boolean segmentIntersection(final double[] returnVal,
+ double x1, double y1, double x2, double y2, double x3, double y3,
+ double x4, double y4) {
+ // Arrange the segment endpoints such that in segment 1, y1 >= y2
+ // and such that in segment 2, y3 >= y4.
+ boolean s1reverse = false;
+
+ if (y2 > y1) {
+ s1reverse = !s1reverse;
+
+ double temp = x1;
+ x1 = x2;
+ x2 = temp;
+ temp = y1;
+ y1 = y2;
+ y2 = temp;
+ }
+
+ if (y4 > y3) {
+ double temp = x3;
+ x3 = x4;
+ x4 = temp;
+ temp = y3;
+ y3 = y4;
+ y4 = temp;
+ }
+
+ /*
+ *
+ * Note: While this algorithm for computing an intersection is
+ * completely bulletproof, it's not a straighforward 'classic'
+ * bruteforce method. This algorithm is well-suited for an
+ * implementation using fixed-point arithmetic instead of floating-point
+ * arithmetic because all computations are constrained to a certain
+ * dynamic range relative to the input parameters.
+ *
+ * We're going to reduce the problem in the following way:
+ *
+ *
+ * (x1,y1) + \ \ \ (x3,y3) x1 x3 ---------+------+----------- yMax
+ * ---------+------+----------- yMax \ | \ | \ | \ | \ | \ | \ | \ \ | \ |
+ * =====\ \ | \| > \| + =====/ + (x,y) |\ / |\ | \ | \ | \ | \
+ * ----------------+---+------- yMin ----------------+---+------ yMin |
+ * (x2,y2) x4 x2 | | + If W := (x2-x4) / ((x2-x4) + (x3-x1)) , then
+ * (x4,y4) x = x2 + W*(x1-x2) and y = yMin + W*(yMax-yMin)
+ *
+ *
+ */
+ final double yMax = Math.min(y1, y3);
+ final double yMin = Math.max(y2, y4);
+
+ if (yMin > yMax) {
+ return false;
+ }
+
+ if (y1 > yMax) {
+ x1 = x1 + (((x2 - x1) * (yMax - y1)) / (y2 - y1));
+ y1 = yMax;
+ }
+
+ if (y3 > yMax) {
+ x3 = x3 + (((x4 - x3) * (yMax - y3)) / (y4 - y3));
+ y3 = yMax;
+ }
+
+ if (y2 < yMin) {
+ x2 = x1 + (((x2 - x1) * (yMin - y1)) / (y2 - y1));
+ y2 = yMin;
+ }
+
+ if (y4 < yMin) {
+ x4 = x3 + (((x4 - x3) * (yMin - y3)) / (y4 - y3));
+ y4 = yMin;
+ }
+
+ // Handling for yMin == yMax. That is, in the reduced problem, both
+ // segments are horizontal.
+ if (yMin == yMax) {
+ // Arrange the segment endpoints such that in segment 1, x1 <= x2
+ // and such that in segment 2, x3 <= x4.
+ if (x2 < x1) {
+ s1reverse = !s1reverse;
+
+ double temp = x1;
+ x1 = x2;
+ x2 = temp;
+ temp = y1;
+ y1 = y2;
+ y2 = temp;
+ }
+
+ if (x4 < x3) {
+ double temp = x3;
+ x3 = x4;
+ x4 = temp;
+ temp = y3;
+ y3 = y4;
+ y4 = temp;
+ }
+
+ final double xMin = Math.max(x1, x3);
+ final double xMax = Math.min(x2, x4);
+
+ if (xMin > xMax) {
+ return false;
+ } else {
+ if (s1reverse) {
+ returnVal[0] = Math.max(xMin, xMax);
+ } else {
+ returnVal[0] = Math.min(xMin, xMax);
+ }
+
+ returnVal[1] = yMin; // == yMax
+
+ return true;
+ }
+ }
+
+ // It is now true that yMin < yMax because we've fully handled
+ // the yMin == yMax case above.
+ // Following if statement checks for a "twist" in the line segments.
+ if (((x1 < x3) && (x2 < x4)) || ((x3 < x1) && (x4 < x2))) {
+ return false;
+ }
+
+ // The segments are guaranteed to intersect.
+ if ((x1 == x3) && (x2 == x4)) { // The segments overlap.
+
+ if (s1reverse) {
+ returnVal[0] = x2;
+ returnVal[1] = y2;
+ } else {
+ returnVal[0] = x1;
+ returnVal[1] = y1;
+ }
+ }
+
+ // The segments are guaranteed to intersect in exactly one point.
+ final double W = (x2 - x4) / ((x2 - x4) + (x3 - x1));
+ returnVal[0] = x2 + (W * (x1 - x2));
+ returnVal[1] = yMin + (W * (yMax - yMin));
+
+ return true;
+ }
+
+ /*
+ * Computes the intersection of the line segment from (x1,y1) to (x2,y2)
+ * with the circle at center (cX,cY) and radius specified. Returns the
+ * number of intersection points. The returnVal parameter passed in should
+ * be of length 4, and values written to it are such: returnVal[0] - x
+ * component of first intersection point returnVal[1] - y component of first
+ * intersection point returnVal[2] - x component of second intersection
+ * point returnVal[3] - y component of second intersection point
+ * Furthermore, if more than one point is returned, then the first point
+ * returned shall be closer to (x1,y1). Note: I don't like the
+ * implementation of this method because the computation blows up when the
+ * line segment endpoints are close together. Luckily, the way that this
+ * method is used from within this class prevents such blowing up. However,
+ * I have named this method bad_*() because I don't want this code to become
+ * a generic routine that is used outside the scope of this class.
+ */
+ private final static int bad_circleIntersection(final double[] returnVal,
+ final double x1, final double y1, final double x2, final double y2,
+ final double cX, final double cY, final double radius) {
+ final double vX = x2 - x1;
+ final double vY = y2 - y1;
+
+ if ((vX == 0.0d) && (vY == 0.0d)) {
+ throw new IllegalStateException(
+ "the condition of both line segment endpoint being the same "
+ + "will not occur if polygons are star-shaped with no marginal "
+ + "conditions");
+ }
+
+ final double a = (vX * vX) + (vY * vY);
+ final double b = 2 * ((vX * (x1 - cX)) + (vY * (y1 - cY)));
+ final double c = ((cX * cX) + (cY * cY) + (x1 * x1) + (y1 * y1))
+ - (2 * ((cX * x1) + (cY * y1))) - (radius * radius);
+ final double sq = (b * b) - (4 * a * c);
+
+ if (sq < 0.0d) {
+ return 0;
+ }
+
+ final double sqrt = Math.sqrt(sq);
+
+ if (sqrt == 0.0d) { // Exactly one solution for infinite line.
+
+ final double u = -b / (2 * a);
+
+ if (!((u <= 1.0d) && (u >= 0.0d))) {
+ return 0;
+ }
+
+ returnVal[0] = x1 + (u * vX);
+ returnVal[1] = y1 + (u * vY);
+
+ return 1;
+ } else { // Two solutions for infinite line.
+
+ double u1 = (-b + sqrt) / (2 * a);
+ double u2 = (-b - sqrt) / (2 * a);
+
+ if (u2 < u1) {
+ double temp = u1;
+ u1 = u2;
+ u2 = temp;
+ }
+
+ // Now u1 is less than or equal to u2.
+ int solutions = 0;
+
+ if ((u1 <= 1.0d) && (u1 >= 0.0d)) {
+ returnVal[0] = x1 + (u1 * vX);
+ returnVal[1] = y1 + (u1 * vY);
+ solutions++;
+ }
+
+ if ((u2 <= 1.0d) && (u2 >= 0.0d)) {
+ returnVal[solutions * 2] = x1 + (u2 * vX);
+ returnVal[(solutions * 2) + 1] = y1 + (u2 * vY);
+ solutions++;
+ }
+
+ return solutions;
+ }
+ }
+
+ /**
+ * This method will render text very quickly. Translucent colors are not
+ * supported by the low detail rendering methods.
+ * <p>
+ * For the sake of maximum performance, this method works differently from
+ * the other rendering methods with respect to the scaling factor specified
+ * in clear(). That is, the font used to render the specified text will not
+ * be scaled; its exact size will be used when the text is rendered onto the
+ * underlying image. On the other hand, the parameters xCenter and yCenter
+ * specify coordinates in the node coordinate system, and so the point
+ * (xCenter, yCenter) will be transformed according the clear() transform in
+ * determining the location of the text on the underlying image.
+ *
+ * @param font
+ * the font to use in drawing text; the size of this font
+ * specifies the actual point size of what will be rendered onto
+ * the underlying image.
+ * @param text
+ * the text to render.
+ * @param xCenter
+ * the X coordinate of the center point of where to place the
+ * rendered text; specified in the node coordinate system.
+ * @param yCenter
+ * the Y coordinate of the center point of where to place the
+ * rendered text; specified in the node coordinate system.
+ * @param color
+ * the [fully opaque] color to use in rendering the text.
+ * @exception IllegalArgumentException
+ * if color is not opaque.
+ */
+ public final void drawTextLow(final Font font, final String text,
+ final float xCenter, final float yCenter, final Color color) {
+ if (m_debug) {
+ if (!EventQueue.isDispatchThread()) {
+ throw new IllegalStateException(
+ "calling thread is not AWT event dispatcher");
+ }
+
+ if (!m_cleared) {
+ throw new IllegalStateException(
+ "clear() has not been called previously");
+ }
+
+ if (color.getAlpha() != 255) {
+ throw new IllegalStateException("color is not opaque");
+ }
+ }
+
+ if (m_gMinimal == null) {
+ makeMinimalGraphics();
+ }
+
+ m_ptsBuff[0] = xCenter;
+ m_ptsBuff[1] = yCenter;
+ m_currXform.transform(m_ptsBuff, 0, m_ptsBuff, 0, 1);
+ m_gMinimal.setFont(font);
+
+ final FontMetrics fMetrics = m_gMinimal.getFontMetrics();
+ m_gMinimal.setColor(color);
+ m_gMinimal
+ .drawString(
+ text,
+ (int) ((-0.5d * fMetrics.stringWidth(text)) + m_ptsBuff[0]),
+ (int) ((0.5d * fMetrics.getHeight())
+ - fMetrics.getDescent() + m_ptsBuff[1]));
+ }
+
+ /**
+ * Returns the context that is used by drawTextLow() to produce text shapes
+ * to be drawn to the screen. The transform contained in the returned
+ * context specifies the <i>only</i> scaling that will be done to fonts
+ * when rendering text using drawTextLow(). This transform does not change
+ * between frames no matter what scaling factor is specified in clear().
+ */
+ public final FontRenderContext getFontRenderContextLow() {
+ if (m_debug) {
+ if (!EventQueue.isDispatchThread()) {
+ throw new IllegalStateException(
+ "calling thread is not AWT event dispatcher");
+ }
+ }
+
+ if (m_gMinimal == null) {
+ makeMinimalGraphics();
+ }
+
+ return m_gMinimal.getFontRenderContext();
+ }
+
+ /**
+ * Renders text onto the underlying image with medium to high detail,
+ * depending on parameters specified.
+ *
+ * @param font
+ * the font to be used when rendering specified text; the
+ * rendering of glyph shapes generated by this font (using the
+ * context returned by getFontRenderContextFull()) is subjected
+ * to the same transformation as are nodes and edges (the
+ * transformation is defined by the clear() method); therefore,
+ * it is the point size of the font in addition to the scaling
+ * factor defined by clear() that determines the resulting size
+ * of text rendered to the graphics context.
+ * @param scaleFactor
+ * in order to prevent very small fonts from "degenerating" it is
+ * necessary to allow users to specify a scale factor in addition
+ * to the font size and transform defined by the clear() method;
+ * if this value is 1.0, no additional scaling is performed;
+ * otherwise, the size of the font is multiplied by this value to
+ * yield a new virtual font size.
+ * @param text
+ * the text to render.
+ * @param xCenter
+ * the text string is drawn such that its logical bounds
+ * rectangle with specified font is centered on this X coordinate
+ * (in the node coordinate system).
+ * @param yCenter
+ * the text string is drawn such that its logical bounds
+ * rectangle with specified font is centered on this Y coordinate
+ * (in the node coordinate system).
+ * @param theta
+ * in radians, specifies the angle of the text.
+ * @param paint
+ * the paint to use in rendering the text.
+ * @param drawTextAsShape
+ * this flag controls the way that text is drawn to the
+ * underlying graphics context; by default, all text rendering
+ * operations involve calling the operation
+ * Graphics2D.drawString(String, float, float) after setting
+ * specified font in the underlying graphics context; however, if
+ * this flag is set, the text to be rendered is converted to a
+ * primitive shape using font specified, and this shape is then
+ * rendered using Graphics2D.fill(Shape); on some systems, the
+ * shape filling method produces better-looking results when the
+ * graphics context is associated with an image that is to be
+ * rendered to the screen; however, on all systems tested, the
+ * shape filling method results in a substantial performance hit
+ * when the graphics context is associated with an image that is
+ * to be rendered to the screen; it is recommended to set this
+ * flag to true when either not much text is being rendered or
+ * when the zoom level is very high; the Graphics2D.drawString()
+ * operation has a difficult time when it needs to render text
+ * under a transformation with a very large scale factor.
+ */
+ public final void drawTextFull(final Font font, final double scaleFactor,
+ final String text, final float xCenter, final float yCenter,
+ final float theta, final Paint paint, final boolean drawTextAsShape) {
+ if (m_debug) {
+ if (!EventQueue.isDispatchThread()) {
+ throw new IllegalStateException(
+ "calling thread is not AWT event dispatcher");
+ }
+
+ if (!m_cleared) {
+ throw new IllegalStateException(
+ "clear() has not been called previously");
+ }
+
+ if (!(scaleFactor >= 0.0d)) {
+ throw new IllegalArgumentException(
+ "scaleFactor must be positive");
+ }
+ }
+
+ m_g2d.translate(xCenter, yCenter);
+ m_g2d.scale(scaleFactor, scaleFactor);
+
+ if (theta != 0.0f) {
+ m_g2d.rotate(theta);
+ }
+
+ m_g2d.setPaint(paint);
+
+ if (drawTextAsShape) {
+ final GlyphVector glyphV;
+
+ if (text.length() > m_charBuff.length) {
+ m_charBuff = new char[Math.max(m_charBuff.length * 2, text
+ .length())];
+ }
+
+ text.getChars(0, text.length(), m_charBuff, 0);
+ glyphV = font.layoutGlyphVector(getFontRenderContextFull(),
+ m_charBuff, 0, text.length(), Font.LAYOUT_NO_LIMIT_CONTEXT);
+
+ final Rectangle2D glyphBounds = glyphV.getLogicalBounds();
+ m_g2d.translate(-glyphBounds.getCenterX(), -glyphBounds
+ .getCenterY());
+ m_g2d.fill(glyphV.getOutline());
+ } else {
+ // Note: A new Rectangle2D is being constructed by this method call.
+ // As far as I know this performance hit is unavoidable.
+ final Rectangle2D textBounds = font.getStringBounds(text,
+ getFontRenderContextFull());
+ m_g2d.translate(-textBounds.getCenterX(), -textBounds.getCenterY());
+ m_g2d.setFont(font);
+ m_g2d.drawString(text, 0.0f, 0.0f);
+ }
+
+ m_g2d.setTransform(m_currNativeXform);
+ }
+
+ /**
+ * Returns the context that is used by drawTextFull() to produce text shapes
+ * to be drawn to the screen. This context always has the identity
+ * transform.
+ */
+ public final FontRenderContext getFontRenderContextFull() {
+ if (m_debug) {
+ if (!EventQueue.isDispatchThread()) {
+ throw new IllegalStateException(
+ "calling thread is not AWT event dispatcher");
+ }
+ }
+
+ return m_fontRenderContextFull;
+ }
+
+ /**
+ * Fills an arbitrary graphical shape with high detail.
+ * <p>
+ * This method will not work unless clear() has been called at least once
+ * previously.
+ *
+ * @param shape
+ * the shape to fill; the shape is specified in node coordinates.
+ * @param xOffset
+ * in node coordinates, a value to add to the X coordinates of
+ * the shape's definition.
+ * @param yOffset
+ * in node coordinates, a value to add to the Y coordinates of
+ * the shape's definition.
+ * @param paint
+ * the paint to use when filling the shape.
+ */
+ public final void drawCustomGraphicFull(final Shape shape,
+ final float xOffset, final float yOffset, final Paint paint) {
+ if (m_debug) {
+ if (!EventQueue.isDispatchThread()) {
+ throw new IllegalStateException(
+ "calling thread is not AWT event dispatcher");
+ }
+
+ if (!m_cleared) {
+ throw new IllegalStateException(
+ "clear() has not been called previously");
+ }
+ }
+
+ m_g2d.translate(xOffset, yOffset);
+ m_g2d.setPaint(paint);
+ m_g2d.fill(shape);
+ m_g2d.setTransform(m_currNativeXform);
+ }
+
+ private enum ShapeTypes {
+ NODE_SHAPE, ARROW_SHAPE, LINE_STROKE;
+ }
+}
diff --git a/corelibs/render.stateful/pom.xml b/corelibs/render.stateful/pom.xml
new file mode 100644
index 0000000..2d9e6d5
--- /dev/null
+++ b/corelibs/render.stateful/pom.xml
@@ -0,0 +1,64 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>parent</artifactId>
+ <version>2.8.4-SNAPSHOT</version>
+ </parent>
+
+ <artifactId>render-stateful</artifactId>
+ <packaging>jar</packaging>
+
+ <name>render-stateful</name>
+
+ <!-- bootstrap for cytoscape dependencies, namely the parent POM snapshots -->
+ <repositories>
+ <repository>
+ <id>cytoscape_snapshots</id>
+ <snapshots>
+ <enabled>true</enabled>
+ </snapshots>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <name>Cytoscape Snapshots</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/</url>
+ </repository>
+ <repository>
+ <id>cytoscape_releases</id>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ <name>Cytoscape Releases</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/releases/</url>
+ </repository>
+ </repositories>
+
+ <dependencies>
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>util-intr</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>geom-spacial</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>graph-fixed</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>render-immed</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ </dependencies>
+
+</project>
+
diff --git a/corelibs/render.stateful/src/main/java/cytoscape/render/stateful/CustomGraphic.java b/corelibs/render.stateful/src/main/java/cytoscape/render/stateful/CustomGraphic.java
new file mode 100644
index 0000000..b971522
--- /dev/null
+++ b/corelibs/render.stateful/src/main/java/cytoscape/render/stateful/CustomGraphic.java
@@ -0,0 +1,195 @@
+/*
+ Copyright (c) 2008, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+/**
+ * Immutable representation of extra graphics associated with a
+ * NodeView or EdgeView that are defined by plugins and are
+ * independent of visual styles.
+ */
+
+package cytoscape.render.stateful;
+
+import java.awt.Paint;
+import java.awt.Shape;
+import java.awt.geom.Rectangle2D;
+
+/**
+ * Represents all the information needed to define a custom graphic for a given
+ * NodeView. <H3>Deprecation Note</H3> The use of CustomGraphic replaces the
+ * entire old index-based custom graphic API. This includes all the NodeDetails
+ * methods (and their overridden implementations) that refer to custom graphics
+ * using indices:
+ *
+ * <PRE>
+ * public int graphicCount(int node)
+ * public Shape graphicShape(int node, int graphicInx)
+ * public Paint graphicPaint(int node, int graphicInx)
+ * public byte graphicNodeAnchor(int node, int graphicInx)
+ * </PRE>
+ *
+ * <B>To keep things completetly backwards compatible and to avoid introducing
+ * bugs, the new API methods are completely independent from the the old API
+ * methods. Thus, a custom graphic added using the new API will not be
+ * accessible from the old API and visa versa.</B>
+ * <P>
+ * The reason for the deprecation is:
+ * <OL>
+ * <LI>Complexity in managing the indices.
+ * <P>
+ * In order for multiple plugins to use the old API, each must monitor deletions
+ * to custom graphics and update their saved indices, since the indices will
+ * shift down as graphics are deleted. This management isn't even possible with
+ * the old API because there's no event mechanism to inform plugins when the
+ * indices change. Also, each plugin must keep a list of all indices for all
+ * graphics added, since the indices may not be contiguous.
+ * <LI>There is no way to ensure that an index you want to use will not be used
+ * by another plugin by the time you attempt to assign it (thread safety).
+ * <P>
+ * Using indices forces the need for a locking mechanism to ensure you are
+ * guaranteed a unique and correct index independent of any other plugins.
+ * </OL>
+ * For more information, see <A
+ * HREF="http://cbio.mskcc.org/cytoscape/bugs/view.php?id=1500">Mantis Bug
+ * 1500</A>.
+ *
+ * @author Michael L. Creech
+ */
+
+public class CustomGraphic {
+ private final Shape shape;
+ private PaintFactory pf;
+ private Paint paint;
+
+ @Deprecated
+ private final byte anchor;
+
+
+ /**
+ * Constructor
+ * @param shape
+ * @param factory
+ */
+ public CustomGraphic(final Shape shape, final PaintFactory factory) {
+ if (shape == null)
+ throw new IllegalArgumentException("The shape given was null.");
+ this.shape = shape;
+ this.anchor = NodeDetails.ANCHOR_CENTER;
+ this.pf = factory;
+ }
+
+ /**
+ * Will be removed March 2011.
+ *
+ * @param shape
+ * @param paint
+ * @param anchor
+ */
+ @Deprecated
+ public CustomGraphic(final Shape shape, final Paint paint, final byte anchor) {
+ this(shape, null);
+ if ((anchor < 0) || (anchor > NodeDetails.MAX_ANCHOR_VAL)) {
+ throw new IllegalArgumentException("The anchor value " + anchor
+ + " is not in the range 0 <= anchor <= "
+ + NodeDetails.MAX_ANCHOR_VAL + ".");
+ }
+ this.paint = paint;
+ this.pf = new DefaultPaintFactory(this.paint);
+ }
+
+ /**
+ * Return the Shape that makes up this CustomGraphic.
+ */
+ public Shape getShape() {
+ return shape;
+ }
+
+ /**
+ * Return the Paint that makes up this CustomGraphic.
+ */
+ public Paint getPaint() {
+ if (paint != null)
+ return paint;
+ else
+ return getPaint(shape.getBounds2D());
+ }
+
+ public Paint getPaint(Rectangle2D bound) {
+ paint = pf.getPaint(bound);
+ return paint;
+ }
+
+ public PaintFactory getPaintFactory() {
+ return this.pf;
+ }
+
+ /**
+ * Return the anchor for this CustomGraphic. This specifies where on the
+ * node's extents rectangle the graphic anchor point lies. The shape is
+ * rendered at a location which is equal to this anchor point plus the
+ * offset vector.
+ */
+ @Deprecated
+ public byte getAnchor() {
+ return anchor;
+ }
+
+
+ /**
+ * Very simple paint factory.
+ * Always return original paint passed to the constructor.
+ *
+ * Will be used in this package only.
+ *
+ * Eventually, this will be removed.
+ *
+ */
+ private class DefaultPaintFactory implements PaintFactory {
+
+ private final Paint p;
+
+ public DefaultPaintFactory(final Paint p) {
+ this.p = p;
+ }
+
+ /**
+ * Returns white color paint. This is the default for all custom graphics.
+ */
+ public Paint getPaint(final Rectangle2D bound) {
+ return p;
+ }
+
+ }
+
+}
diff --git a/corelibs/render.stateful/src/main/java/cytoscape/render/stateful/EdgeDetails.java b/corelibs/render.stateful/src/main/java/cytoscape/render/stateful/EdgeDetails.java
new file mode 100644
index 0000000..8bf317f
--- /dev/null
+++ b/corelibs/render.stateful/src/main/java/cytoscape/render/stateful/EdgeDetails.java
@@ -0,0 +1,403 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.render.stateful;
+
+import cytoscape.render.immed.EdgeAnchors;
+import cytoscape.render.immed.GraphGraphics;
+
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.Paint;
+import java.awt.Stroke;
+import java.awt.BasicStroke;
+
+
+/**
+ * Defines the visual properties of an edge. Even though this class is not
+ * declared abstract, in most situations it makes sense to override at least
+ * some of its methods (especially segmentThickness()) in order to gain
+ * control over edge visual properties.<p>
+ * To understand the significance of each method's return value, it makes
+ * sense to become familiar with the API cytoscape.render.immed.GraphGraphics.
+ */
+public class EdgeDetails {
+ /**
+ * Specifies that an anchor point lies at the midpoint of an edge.
+ */
+ public static final byte EDGE_ANCHOR_MIDPOINT = 16;
+
+ /**
+ * Specifies that an anchor point lies at an edge's endpoint at source
+ * node.
+ */
+ public static final byte EDGE_ANCHOR_SOURCE = 17;
+
+ /**
+ * Specifies that an anchor point lies at an edge's endpoint at target
+ * node.
+ */
+ public static final byte EDGE_ANCHOR_TARGET = 18;
+
+ /**
+ * Instantiates edge details with defaults. Documentation on each method
+ * describes defaults. To override defaults, extend this class.
+ */
+ public EdgeDetails() {
+ }
+
+ /**
+ * Returns the color of edge in low detail rendering mode.
+ * By default this method returns Color.blue. It is an error to return null
+ * in this method.<p>
+ * In low detail rendering mode, this is the only method from this class
+ * that is looked at. The rest of the methods in this class define visual
+ * properties that are used in full detail rendering mode. In low detail
+ * rendering mode translucent colors are not supported whereas in full
+ * detail rendering mode they are.
+ */
+ public Color colorLowDetail(final int edge) {
+ return Color.blue;
+ }
+
+ /**
+ * Returns a GraphGraphics.ARROW_* constant; this defines the arrow
+ * to use when rendering the edge endpoint touching source node.
+ * By default this method returns GraphGraphics.ARROW_NONE.
+ * Take note of certain constraints specified in
+ * GraphGraphics.drawEdgeFull().
+ */
+ public byte sourceArrow(final int edge) {
+ return GraphGraphics.ARROW_NONE;
+ }
+
+ /**
+ * Returns the size of the arrow at edge endpoint touching source node.
+ * By default this method returns zero. This return value is ignored
+ * if sourceArrow(edge) returns GraphGraphics.ARROW_NONE.
+ * Take note of certain constraints specified in
+ * GraphGraphics.drawEdgeFull().
+ */
+ public float sourceArrowSize(final int edge) {
+ return 0.0f;
+ }
+
+ /**
+ * Returns the paint of the arrow at edge endpoint touching source node.
+ * By default this method returns null. This return value is ignored if
+ * sourceArrow(edge) returns GraphGraphics.ARROW_NONE
+ * it is an error to return null.
+ */
+ public Paint sourceArrowPaint(final int edge) {
+ return null;
+ }
+
+ /**
+ * Returns a GraphGraphics.ARROW_* constant; this defines the arrow
+ * to use when rendering the edge endpoint at the target node.
+ * By default this method returns GraphGraphics.ARROW_NONE.
+ * Take note of certain constraints specified in
+ * GraphGraphics.drawEdgeFull().
+ */
+ public byte targetArrow(final int edge) {
+ return GraphGraphics.ARROW_NONE;
+ }
+
+ /**
+ * Returns the size of the arrow at edge endpoint touching target node.
+ * By default this method returns zero.
+ * Take note of certain constraints specified
+ * in GraphGraphics.drawEdgeFull().
+ */
+ public float targetArrowSize(final int edge) {
+ return 0.0f;
+ }
+
+ /**
+ * Returns the paint of the arrow at edge endpoint touching target node.
+ * By default this method returns null. This return value is ignored if
+ * targetArrow(edge) returns GraphGraphics.ARROW_NONE,
+ * it is an error to return null.
+ */
+ public Paint targetArrowPaint(final int edge) {
+ return null;
+ }
+
+ /**
+ * Returns edge anchors to use when rendering this edge.
+ * By default this method returns null; returning null is the optimal
+ * way to specify that this edge has no anchors. Take note of certain
+ * constraints, specified in GraphGraphics.drawEdgeFull(), pertaining to
+ * edge anchors.<p>
+ * The anchors returned are interpreted such that the anchor at index zero
+ * (the "first" anchor) is the anchor next to the source node of this edge;
+ * the last anchor is the anchor next to the target node of this edge. The
+ * rendering engine works such that if the first anchor lies inside
+ * the source node shape or if the last anchor lies inside the target
+ * node shape, the edge is not rendered.
+ */
+ public EdgeAnchors anchors(final int edge) {
+ return null;
+ }
+
+ /**
+ * For edges with anchors, the anchors can be rendered as squares. To render
+ * an anchor, return a positive value in this method. If zero is returned
+ * no edge anchor is rendered. By default this method returns zero.
+ */
+ public float anchorSize(final int edge, final int anchorInx) {
+ return 0.0f;
+ }
+
+ /**
+ * Returns the paint to use when rendering an edge anchor. The output of
+ * this method is ignored if anchorSize(edge, anchorInx) returned zero;
+ * otherwise, a non-null value must be returned. By default this method
+ * returns null.
+ */
+ public Paint anchorPaint(final int edge, final int anchorInx) {
+ return null;
+ }
+
+ /**
+ * Returns the thickness of the edge segment.
+ * <font color="red">By default this method returns zero.</font>
+ * Take note of certain constraints specified in
+ * GraphGraphics.drawEdgeFull().
+ */
+ public float segmentThickness(final int edge) {
+ return 0.0f;
+ }
+
+ private static final Stroke default_stroke = new BasicStroke();
+ public Stroke segmentStroke(final int edge) {
+ return default_stroke;
+ }
+
+ /**
+ * Returns the paint of the edge segment.
+ * By default this method returns Color.blue. It is an error to
+ * return null in this method.
+ */
+ public Paint segmentPaint(final int edge) {
+ return Color.blue;
+ }
+
+ /**
+ * Returns the length of dashes on edge segment, or zero to indicate
+ * that the edge segment is solid. By default this method returns zero.
+ */
+// public float segmentDashLength(final int edge) {
+// return 0.0f;
+// }
+
+ /**
+ * Returns the number of labels that this edge has. By default this method
+ * returns zero.
+ */
+ public int labelCount(final int edge) {
+ return 0;
+ }
+
+ /**
+ * Returns a label's text. By default this method always returns null.
+ * This method is only called by the rendering engine if labelCount(edge)
+ * returns a value greater than zero. It is an error to return null if this
+ * method is called by the rendering engine.<p>
+ * To specify multiple lines of text in an edge label, simply insert the
+ * '\n' character between lines of text.
+ * @param labelInx a value in the range [0, labelCount(edge)-1] indicating
+ * which edge label in question.
+ */
+ public String labelText(final int edge, final int labelInx) {
+ return null;
+ }
+
+ /**
+ * Returns the font to use when rendering this label. By default this
+ * method always returns null. This method is only called by the rendering
+ * engine if labelCount(edge) returns a value greater than zero. It is an
+ * error to return null if this method is called by the rendering engine.
+ * @param labelInx a value in the range [0, labelCount(edge)-1] indicating
+ * which edge label in question.
+ */
+ public Font labelFont(final int edge, final int labelInx) {
+ return null;
+ }
+
+ /**
+ * Returns an additional scaling factor that is to be applied to the font
+ * used to render this label; this scaling factor, applied to the point
+ * size of the font returned by labelFont(edge, labelInx), yields a new
+ * virtual font that is used to render the text label. By default this
+ * method always returns 1.0. This method is only called by the rendering
+ * engine if labelCount(edge) returns a value greater than zero.
+ * @param labelInx a value in the range [0, labelCount(edge)-1] indicating
+ * which edge label in question.
+ */
+ public double labelScaleFactor(final int edge, final int labelInx) {
+ return 1.0d;
+ }
+
+ /**
+ * Returns the paint of a text label. By default this method always
+ * returns null. This method is only called by the rendering engine if
+ * labelCount(edge) returns a value greater than zero. It is an error to
+ * return null if this method is called by the rendering engine.
+ * @param labelInx a value in the range [0, labelCount(edge)-1] indicating
+ * which edge label in question.
+ */
+ public Paint labelPaint(final int edge, final int labelInx) {
+ return null;
+ }
+
+ /**
+ * By returning one of the NodeDetails.ANCHOR_* constants, specifies where
+ * on a text label's logical bounds box an anchor point lies. This
+ * <i>text anchor point</i> together with the edge anchor point and label
+ * offset vector determines where, relative to the edge, the text's logical
+ * bounds box is to be placed. The text's logical bounds box is placed
+ * such that the label offset vector plus the edge anchor point equals the
+ * text anchor point.<p>
+ * By default this method always returns NodeDetails.ANCHOR_CENTER.
+ * This method is only called by the rendering engine if labelCount(edge)
+ * returns a value greater than zero.
+ * @param labelInx a value in the range [0, labelCount(edge)-1] indicating
+ * which edge label in question.
+ * @see NodeDetails#ANCHOR_CENTER
+ * @see #labelEdgeAnchor(int, int)
+ * @see #labelOffsetVectorX(int, int)
+ * @see #labelOffsetVectorY(int, int)
+ */
+ public byte labelTextAnchor(final int edge, final int labelInx) {
+ return NodeDetails.ANCHOR_CENTER;
+ }
+
+ /**
+ * By returning one of the EDGE_ANCHOR_* constants, specifies where on
+ * an edge an anchor point lies. This <i>edge anchor point</i> together
+ * with the text anchor point and label offset vector determines where,
+ * relative to the edge, the text's logical bounds box is to be placed.
+ * The text's logical bounds box is placed such that the label offset
+ * vector plus the edge anchor point equals the text anchor point.<p>
+ * By default this method always returns EDGE_ANCHOR_MIDPOINT. This method
+ * is only called by the rendering engine if labelCount(edge) returns a
+ * value greater than zero.
+ * @param labelInx a value in the range [0, labelCount(edge)-1] indicating
+ * which edge label in question.
+ * @see #EDGE_ANCHOR_MIDPOINT
+ * @see #labelTextAnchor(int, int)
+ * @see #labelOffsetVectorX(int, int)
+ * @see #labelOffsetVectorY(int, int)
+ */
+ public byte labelEdgeAnchor(final int edge, final int labelInx) {
+ return EDGE_ANCHOR_MIDPOINT;
+ }
+
+ /**
+ * Specifies the X component of the vector that separates a text anchor
+ * point from an edge anchor point. This <i>label offset vector</i>
+ * together with the text anchor point and edge anchor point determines
+ * where, relative to the edge, the text's logical bounds box is to be
+ * placed. The text's logical bounds box is placed such that the label
+ * offset vector plus the edge anchor point equals the text anchor point.<p>
+ * By default this method always returns zero. This method is only called
+ * by the rendering engine if labelCount(edge) returns a value greater than
+ * zero.
+ * @param labelInx a value in the range [0, labelCount(edge)-1] indicating
+ * which edge label in question.
+ * @see #labelOffsetVectorY(int, int)
+ * @see #labelTextAnchor(int, int)
+ * @see #labelEdgeAnchor(int, int)
+ */
+ public float labelOffsetVectorX(final int edge, final int labelInx) {
+ return 0.0f;
+ }
+
+ /**
+ * Specifies the Y component of the vector that separates a text anchor
+ * point from an edge anchor point. This <i>label offset vector</i>
+ * together with the text anchor point and edge anchor point determines
+ * where, relative to the edge, the text's logical bounds box is to be
+ * placed. The text's logical bounds box is placed such that the label
+ * offset vector plus the edge anchor point equals the text anchor point.<p>
+ * By default this method always returns zero. This method is only called
+ * by the rendering engine if labelCount(edge) returns a value greater than
+ * zero.
+ * @param labelInx a value in the range [0, labelCount(edge)-1] indicating
+ * which edge label in question.
+ * @see #labelOffsetVectorX(int, int)
+ * @see #labelTextAnchor(int, int)
+ * @see #labelEdgeAnchor(int, int)
+ */
+ public float labelOffsetVectorY(final int edge, final int labelInx) {
+ return 0.0f;
+ }
+
+ /**
+ * By returning one of the NodeDetails.LABEL_WRAP_JUSTIFY_* constants,
+ * determines how to justify an edge label spanning multiple lines. The
+ * choice made here does not affect the size of the logical bounding box
+ * of an edge label's text. The lines of text are justified within that
+ * logical bounding box.<p>
+ * By default this method always returns
+ * NodeDetails.LABEL_WRAP_JUSTIFY_CENTER. This return value is ignored
+ * if labelText(edge, labelInx) returns a text string that does not span
+ * multiple lines.
+ * @see NodeDetails#LABEL_WRAP_JUSTIFY_CENTER
+ */
+ public byte labelJustify(final int edge, final int labelInx) {
+ return NodeDetails.LABEL_WRAP_JUSTIFY_CENTER;
+ }
+
+ // /**
+ // * Determines whether or not a label is to be rendered horizontally or
+ // * following the tangent at edge anchor point. By default this method
+ // * always returns true, which results in horizontal text labels.
+ // */
+ // public boolean labelHorizontal(final int edge, final int labelInx) {
+ // return true; }
+
+ /**
+ * Returns the width of the label.
+ * <font color="red">By default this method returns 100.</font>
+ * Take note of certain constraints specified in
+ * GraphGraphics.drawEdgeFull().
+ */
+ public double labelWidth(final int edge) {
+ return 100.0;
+ }
+}
diff --git a/corelibs/render.stateful/src/main/java/cytoscape/render/stateful/GraphLOD.java b/corelibs/render.stateful/src/main/java/cytoscape/render/stateful/GraphLOD.java
new file mode 100644
index 0000000..9115dda
--- /dev/null
+++ b/corelibs/render.stateful/src/main/java/cytoscape/render/stateful/GraphLOD.java
@@ -0,0 +1,232 @@
+/*
+ Copyright (c) 2006, 2007, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.render.stateful;
+
+
+/**
+ * An instance of this class defines the level of detail that goes into
+ * a single rendering of a graph. This class is meant to be subclassed; its
+ * methods are meant to be overridden; nonetheless, sane defaults are
+ * used in the default method implementations.<p>
+ * To understand the significance of each method's return value, it makes
+ * sense to become familiar with the API cytoscape.render.immed.GraphGraphics.
+ */
+public class GraphLOD {
+ /**
+ * Determines whether or not to render all edges in a graph, no edges, or
+ * only those edges which touch a visible node. By default
+ * this method returns zero, which leads the rendering engine to render
+ * only those edges that touch at least one visible node. If a positive
+ * value is returned, all edges in the graph will be rendered. If a negative
+ * value is returned, no edges will be rendered. This is the first
+ * method called on an instance of GraphLOD by the rendering engine;
+ * the renderEdgeCount parameter passed to other methods
+ * will have a value which reflects the decision made by the return value
+ * of this method call.<p>
+ * Note that rendering all edges leads to a dramatic performance decrease
+ * when rendering large graphs.
+ * @param visibleNodeCount the number of nodes visible in the current
+ * viewport; note that a visible node is not necessarily a rendered node,
+ * because visible nodes with zero width or height are not rendered.
+ * @param totalNodeCount the total number of nodes in the graph that is
+ * being rendered.
+ * @param totalEdgeCount the total number of edges in the graph that is
+ * being rendered.
+ * @return zero if only edges touching a visible node are to be rendered,
+ * positive if all edges are to be rendered, or negative if no edges
+ * are to be rendered.
+ */
+ public byte renderEdges(final int visibleNodeCount, final int totalNodeCount,
+ final int totalEdgeCount) {
+ return 0;
+ }
+
+ /**
+ * Determines whether or not to render a graph at full detail.
+ * By default this method returns true if and only if the sum of rendered
+ * nodes and rendered edges is less than 1200.<p>
+ * The following table describes the difference between full and low
+ * rendering detail in terms of what methods on an instance of
+ * GraphGraphics get called:
+ * <blockquote><table border="1" cellpadding="5" cellspacing="0">
+ * <tr> <td></td>
+ * <th>full detail</th>
+ * <th>low detail</th> </tr>
+ * <tr> <th>nodes</th>
+ * <td>drawNodeFull()</td>
+ * <td>drawNodeLow()</td> </tr>
+ * <tr> <th>edges</th>
+ * <td>drawEdgeFull()</td>
+ * <td>drawEdgeLow()</td> </tr>
+ * <tr> <th>node labels</th>
+ * <td>drawTextFull()</td>
+ * <td>not rendered</td> </tr>
+ * <tr> <th>edge labels</th>
+ * <td>drawTextFull()</td>
+ * <td>not rendered</td> </tr>
+ * <tr> <th>custom node graphics</th>
+ * <td>drawCustomGraphicFull()</td>
+ * <td>not rendered</td> </tr>
+ * </table></blockquote>
+ * @param renderNodeCount the number of nodes that are about to be rendered.
+ * @param renderEdgeCount the number of edges that are about to be rendered.
+ * @return true for full detail, false for low detail.
+ */
+ public boolean detail(final int renderNodeCount, final int renderEdgeCount) {
+ return (renderNodeCount + renderEdgeCount) < 1200;
+ }
+
+ /**
+ * Determines whether or not to render node borders. By default this
+ * method returns true if and only if the number of rendered nodes
+ * is less than 200.<p>
+ * It is only possible to draw node borders at the full detail
+ * level. If low detail is chosen, the output of this method is ignored.
+ * @param renderNodeCount the number of nodes that are about to be rendered.
+ * @param renderEdgeCount the number of edges that are about to be rendered.
+ * @return true if and only if node borders are to be rendered.
+ * @see #detail(int, int)
+ */
+ public boolean nodeBorders(final int renderNodeCount, final int renderEdgeCount) {
+ return renderNodeCount < 200;
+ }
+
+ /**
+ * Determines whether or not to render node labels. By default this method
+ * returns true if and only if the number of rendered nodes is less than
+ * 60.<p>
+ * Node labels are only rendered at the full detail level. If low detail is
+ * chosen, the output of this method is ignored.
+ * @param renderNodeCount the number of nodes that are about to be rendered.
+ * @param renderEdgeCount the number of edges that are about to be rendered.
+ * @return true if and only if node labels are to be rendered.
+ * @see #detail(int, int)
+ */
+ public boolean nodeLabels(final int renderNodeCount, final int renderEdgeCount) {
+ return renderNodeCount < 60;
+ }
+
+ /**
+ * Determines whether or not to render custom graphics on nodes.
+ * By default this method returns true if and only if the number of rendered
+ * nodes is less than 60.<p>
+ * Custom node graphics are only rendered at the full detail level. If low
+ * detail is chosen, the output of this method is ignored.
+ * @param renderNodeCount the number of nodes that are about to be rendered.
+ * @param renderEdgeCount the number of edges that are about to be rendered.
+ * @return true if and only if custom node graphics are to be rendered.
+ * @see #detail(int, int)
+ */
+ public boolean customGraphics(final int renderNodeCount, final int renderEdgeCount) {
+ return renderNodeCount < 60;
+ }
+
+ /**
+ * Determines whether or not to render edge arrows. By default this
+ * method returns true if and only if the number of rendered edges is less
+ * than 300.<p>
+ * It is only possible to draw edge arrows at the full detail
+ * level. If low detail is chosen, the output of this method is ignored.
+ * @param renderNodeCount the number of nodes that are about to be rendered.
+ * @param renderEdgeCount the number of edges that are about to be rendered.
+ * @return true if and only if edge arrows are to be rendered.
+ * @see #detail(int, int)
+ */
+ public boolean edgeArrows(final int renderNodeCount, final int renderEdgeCount) {
+ return renderEdgeCount < 300;
+ }
+
+ /**
+ * Determines whether or not to honor dashed edges. By default this
+ * method always returns true. If false is returned, edges that
+ * claim to be dashed will be rendered as solid.<p>
+ * It is only possible to draw dashed edges at the full detail
+ * level. If low detail is chosen, the output of this method is ignored.
+ * Note that drawing dashed edges is computationally expensive;
+ * the default implementation of this method does not make a very
+ * performance-minded decision if a lot of edges happen to be dashed.
+ * @param renderNodeCount the number of nodes that are about to be rendered.
+ * @param renderEdgeCount the number of edges that are about to be rendered.
+ * @return true if and only if dashed edges are to be honored.
+ * @see #detail(int, int)
+ */
+ public boolean dashedEdges(final int renderNodeCount, final int renderEdgeCount) {
+ return true;
+ }
+
+ /**
+ * Determines whether or not to honor edge anchors. By default this
+ * method always returns true. If false is returned, edges that
+ * claim to have edge anchors will be rendered as simple straight
+ * edges.<p>
+ * It is only possible to draw poly-edges at the full detail
+ * level. If low detail is chosen, the output of this method is ignored.
+ * @param renderNodeCount the number of nodes that are about to be rendered.
+ * @param renderEdgeCount the number of edges that are about to be rendered.
+ * @return true if and only if edge anchors are to be honored.
+ * @see #detail(int, int)
+ */
+ public boolean edgeAnchors(final int renderNodeCount, final int renderEdgeCount) {
+ return true;
+ }
+
+ /**
+ * Determines whether or not to render edge labels. By default this method
+ * returns true if and only if the number of rendered edges is less than
+ * 80.<p>
+ * Edge labels are only rendered at the full detail level. If low detail is
+ * chosen, the output of this method is ignored.
+ * @param renderNodeCount the number of nodes that are about to be rendered.
+ * @param renderEdgeCount the number of edges that are about to be rendered.
+ * @return true if and only if edge labels are to be rendered.
+ * @see #detail(int, int)
+ */
+ public boolean edgeLabels(final int renderNodeCount, final int renderEdgeCount) {
+ return renderEdgeCount < 80;
+ }
+
+ /**
+ * Determines whether or not to draw text as shape when rendering node and
+ * edge labels. By default this method always returns false.<p>
+ * This method affects the boolean parameter drawTextAsShape in the method
+ * call GraphGraphics.drawTextFull(). If neither node nor edge labels are
+ * rendered then the output of this method is ignored.
+ * @param renderNodeCount the number of nodes that are about to be rendered.
+ * @param renderEdgeCount the number of edges that are about to be rendered.
+ * @return true if and only if rendered label text should be drawn as
+ * primitive shapes.
+ * @see #nodeLabels(int, int)
+ * @see #edgeLabels(int, int)
+ */
+ public boolean textAsShape(final int renderNodeCount, final int renderEdgeCount) {
+ return false;
+ }
+
+ public double getNestedNetworkImageScaleFactor() { return 1.0; }
+}
diff --git a/corelibs/render.stateful/src/main/java/cytoscape/render/stateful/GraphRenderer.java b/corelibs/render.stateful/src/main/java/cytoscape/render/stateful/GraphRenderer.java
new file mode 100644
index 0000000..c153f3e
--- /dev/null
+++ b/corelibs/render.stateful/src/main/java/cytoscape/render/stateful/GraphRenderer.java
@@ -0,0 +1,1104 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.render.stateful;
+
+import java.awt.Font;
+import java.awt.Paint;
+import java.awt.Stroke;
+import java.awt.TexturePaint;
+import java.awt.geom.GeneralPath;
+import java.awt.geom.PathIterator;
+import java.util.Iterator;
+
+import cytoscape.geom.spacial.SpacialEntry2DEnumerator;
+import cytoscape.geom.spacial.SpacialIndex2D;
+import cytoscape.graph.fixed.FixedGraph;
+import cytoscape.render.immed.EdgeAnchors;
+import cytoscape.render.immed.GraphGraphics;
+import cytoscape.util.intr.IntEnumerator;
+import cytoscape.util.intr.IntHash;
+
+
+/**
+ * This class contains a chunk of procedural code that stitches together
+ * several external modules in an effort to efficiently render graphs.
+ */
+public final class GraphRenderer {
+ /**
+ * A bit representing....
+ */
+ public final static int LOD_HIGH_DETAIL = 0x1;
+
+ /**
+ * DOCUMENT ME!
+ */
+ public final static int LOD_NODE_BORDERS = 0x2;
+
+ /**
+ * DOCUMENT ME!
+ */
+ public final static int LOD_NODE_LABELS = 0x4;
+
+ /**
+ * DOCUMENT ME!
+ */
+ public final static int LOD_EDGE_ARROWS = 0x8;
+
+ /**
+ * DOCUMENT ME!
+ */
+ public final static int LOD_DASHED_EDGES = 0x10;
+
+ /**
+ * DOCUMENT ME!
+ */
+ public final static int LOD_EDGE_ANCHORS = 0x20;
+
+ /**
+ * DOCUMENT ME!
+ */
+ public final static int LOD_EDGE_LABELS = 0x40;
+
+ /**
+ * DOCUMENT ME!
+ */
+ public final static int LOD_TEXT_AS_SHAPE = 0x80;
+
+ /**
+ * DOCUMENT ME!
+ */
+ public final static int LOD_CUSTOM_GRAPHICS = 0x100;
+
+ // No constructor.
+ private GraphRenderer() {
+ }
+
+ /**
+ * Renders a graph.
+ * @param graph the graph topology; nodes in this graph must correspond to
+ * objKeys in nodePositions (the SpacialIndex2D parameter) and vice versa.
+ * @param nodePositions defines the positions and extents of nodes in graph;
+ * each entry (objKey) in this structure must correspond to a node in graph
+ * (the FixedGraph parameter) and vice versa; the order in which nodes are
+ * rendered is defined by a non-reversed overlap query on this structure.
+ * @param lod defines the different levels of detail; an appropriate level
+ * of detail is chosen based on the results of method calls on this
+ * object.
+ * @param nodeDetails defines details of nodes such as colors, node border
+ * thickness, and shape; the node arguments passed to methods on this
+ * object will be nodes in the graph parameter.
+ * @param edgeDetails defines details of edges such as colors, thickness,
+ * and arrow type; the edge arguments passed to methods on this
+ * object will be edges in the graph parameter.
+ * @param nodeBuff this is a computational helper that is required in the
+ * implementation of this method; when this method returns, nodeBuff is
+ * in a state such that an edge in graph has been rendered by this method
+ * if and only if it touches at least one node in this nodeBuff set;
+ * no guarantee made regarding edgeless nodes.
+ * @param grafx the graphics context that is to render this graph.
+ * @param bgPaint the background paint to use when calling grafx.clear().
+ * @param xCenter the xCenter parameter to use when calling grafx.clear().
+ * @param yCenter the yCenter parameter to use when calling grafx.clear().
+ * @param scaleFactor the scaleFactor parameter to use when calling
+ * grafx.clear().
+ * @return bits representing the level of detail that was rendered; the
+ * return value is a bitwise-or'ed value of the LOD_* constants.
+ */
+ public final static int renderGraph(final FixedGraph graph, final SpacialIndex2D nodePositions,
+ final GraphLOD lod, final NodeDetails nodeDetails,
+ final EdgeDetails edgeDetails, final IntHash nodeBuff,
+ final GraphGraphics grafx, final Paint bgPaint,
+ final double xCenter, final double yCenter,
+ final double scaleFactor) {
+
+ nodeBuff.empty(); // Make sure we keep our promise.
+
+ // Define the visible window in node coordinate space.
+ final float xMin;
+
+ // Define the visible window in node coordinate space.
+ final float yMin;
+
+ // Define the visible window in node coordinate space.
+ final float xMax;
+
+ // Define the visible window in node coordinate space.
+ final float yMax;
+ xMin = (float) (xCenter - ((0.5d * grafx.image.getWidth(null)) / scaleFactor));
+ yMin = (float) (yCenter - ((0.5d * grafx.image.getHeight(null)) / scaleFactor));
+ xMax = (float) (xCenter + ((0.5d * grafx.image.getWidth(null)) / scaleFactor));
+ yMax = (float) (yCenter + ((0.5d * grafx.image.getHeight(null)) / scaleFactor));
+
+ // Define buffers. These are of the few objects we're instantiating
+ // directly in this method.
+ final float[] floatBuff1;
+
+ // Define buffers. These are of the few objects we're instantiating
+ // directly in this method.
+ final float[] floatBuff2;
+
+ // Define buffers. These are of the few objects we're instantiating
+ // directly in this method.
+ final float[] floatBuff3;
+
+ // Define buffers. These are of the few objects we're instantiating
+ // directly in this method.
+ final float[] floatBuff4;
+
+ // Define buffers. These are of the few objects we're instantiating
+ // directly in this method.
+ final float[] floatBuff5;
+ final double[] doubleBuff1;
+ final double[] doubleBuff2;
+ final GeneralPath path2d;
+ floatBuff1 = new float[4];
+ floatBuff2 = new float[4];
+ floatBuff3 = new float[2];
+ floatBuff4 = new float[2];
+ floatBuff5 = new float[8];
+ doubleBuff1 = new double[4];
+ doubleBuff2 = new double[2];
+ path2d = new GeneralPath();
+
+ // Determine the number of nodes and edges that we are about to render.
+ final int renderNodeCount;
+ final int renderEdgeCount;
+ final byte renderEdges;
+
+ {
+ final SpacialEntry2DEnumerator nodeHits = nodePositions.queryOverlap(xMin, yMin, xMax,
+ yMax, null, 0,
+ false);
+ final int visibleNodeCount = nodeHits.numRemaining();
+ final int totalNodeCount = graph.nodes().numRemaining();
+ final int totalEdgeCount = graph.edges().numRemaining();
+ renderEdges = lod.renderEdges(visibleNodeCount, totalNodeCount, totalEdgeCount);
+
+ if (renderEdges > 0) {
+ int runningNodeCount = 0;
+
+ for (int i = 0; i < visibleNodeCount; i++) {
+ nodeHits.nextExtents(floatBuff1, 0);
+
+ if ((floatBuff1[0] != floatBuff1[2]) && (floatBuff1[1] != floatBuff1[3]))
+ runningNodeCount++;
+ }
+
+ renderNodeCount = runningNodeCount;
+ renderEdgeCount = totalEdgeCount;
+ } else if (renderEdges < 0) {
+ int runningNodeCount = 0;
+
+ for (int i = 0; i < visibleNodeCount; i++) {
+ nodeHits.nextExtents(floatBuff1, 0);
+
+ if ((floatBuff1[0] != floatBuff1[2]) && (floatBuff1[1] != floatBuff1[3]))
+ runningNodeCount++;
+ }
+
+ renderNodeCount = runningNodeCount;
+ renderEdgeCount = 0;
+ } else {
+ int runningNodeCount = 0;
+ int runningEdgeCount = 0;
+
+ for (int i = 0; i < visibleNodeCount; i++) {
+ final int node = nodeHits.nextExtents(floatBuff1, 0);
+
+ if ((floatBuff1[0] != floatBuff1[2]) && (floatBuff1[1] != floatBuff1[3]))
+ runningNodeCount++;
+
+ final IntEnumerator touchingEdges = graph.edgesAdjacent(node, true, true, true);
+ final int touchingEdgeCount = touchingEdges.numRemaining();
+
+ for (int j = 0; j < touchingEdgeCount; j++) {
+ final int edge = touchingEdges.nextInt();
+ final int otherNode = node ^ graph.edgeSource(edge)
+ ^ graph.edgeTarget(edge);
+
+ if (nodeBuff.get(otherNode) < 0)
+ runningEdgeCount++;
+ }
+
+ nodeBuff.put(node);
+ }
+
+ renderNodeCount = runningNodeCount;
+ renderEdgeCount = runningEdgeCount;
+ nodeBuff.empty();
+ }
+ }
+
+ // Based on number of objects we are going to render, determine LOD.
+ final int lodBits;
+
+ {
+ int lodTemp = 0;
+
+ if (lod.detail(renderNodeCount, renderEdgeCount)) {
+ lodTemp |= LOD_HIGH_DETAIL;
+
+ if (lod.nodeBorders(renderNodeCount, renderEdgeCount))
+ lodTemp |= LOD_NODE_BORDERS;
+
+ if (lod.nodeLabels(renderNodeCount, renderEdgeCount))
+ lodTemp |= LOD_NODE_LABELS;
+
+ if (lod.edgeArrows(renderNodeCount, renderEdgeCount))
+ lodTemp |= LOD_EDGE_ARROWS;
+
+ if (lod.dashedEdges(renderNodeCount, renderEdgeCount))
+ lodTemp |= LOD_DASHED_EDGES;
+
+ if (lod.edgeAnchors(renderNodeCount, renderEdgeCount))
+ lodTemp |= LOD_EDGE_ANCHORS;
+
+ if (lod.edgeLabels(renderNodeCount, renderEdgeCount))
+ lodTemp |= LOD_EDGE_LABELS;
+
+ if ((((lodTemp & LOD_NODE_LABELS) != 0) || ((lodTemp & LOD_EDGE_LABELS) != 0))
+ && lod.textAsShape(renderNodeCount, renderEdgeCount))
+ lodTemp |= LOD_TEXT_AS_SHAPE;
+
+ if (lod.customGraphics(renderNodeCount, renderEdgeCount))
+ lodTemp |= LOD_CUSTOM_GRAPHICS;
+ }
+
+ lodBits = lodTemp;
+ }
+ // Clear the background.
+ {
+ grafx.clear(bgPaint, xCenter, yCenter, scaleFactor);
+ }
+
+ // Render the edges first. No edge shall be rendered twice. Render edge
+ // labels. A label is not necessarily on top of every edge; it is only
+ // on top of the edge it belongs to.
+ if (renderEdges >= 0) {
+ final SpacialEntry2DEnumerator nodeHits;
+
+ if (renderEdges > 0)
+ // We want to render edges in the same order (back to front) that
+ // we would use to render just edges on visible nodes; this is assuming
+ // that our spacial index has the subquery order-preserving property.
+ nodeHits = nodePositions.queryOverlap(Float.NEGATIVE_INFINITY,
+ Float.NEGATIVE_INFINITY,
+ Float.POSITIVE_INFINITY,
+ Float.POSITIVE_INFINITY, null, 0, false);
+ else
+ nodeHits = nodePositions.queryOverlap(xMin, yMin, xMax, yMax, null, 0, false);
+
+ if ((lodBits & LOD_HIGH_DETAIL) == 0) { // Low detail.
+
+ final int nodeHitCount = nodeHits.numRemaining();
+
+ for (int i = 0; i < nodeHitCount; i++) {
+ final int node = nodeHits.nextExtents(floatBuff1, 0);
+
+ // Casting to double and then back we could achieve better accuracy
+ // at the expense of performance.
+ final float nodeX = (floatBuff1[0] + floatBuff1[2]) / 2;
+ final float nodeY = (floatBuff1[1] + floatBuff1[3]) / 2;
+
+ final IntEnumerator touchingEdges = graph.edgesAdjacent(node, true, true, true);
+ final int touchingEdgeCount = touchingEdges.numRemaining();
+
+ for (int j = 0; j < touchingEdgeCount; j++) {
+ final int edge = touchingEdges.nextInt();
+ final int otherNode = node ^ graph.edgeSource(edge)
+ ^ graph.edgeTarget(edge);
+
+ if (nodeBuff.get(otherNode) < 0) { // Has not yet been rendered.
+ nodePositions.exists(otherNode, floatBuff2, 0);
+ grafx.drawEdgeLow(nodeX, nodeY,
+ // Again, casting issue - tradeoff between
+ // accuracy and performance.
+ (floatBuff2[0] + floatBuff2[2]) / 2,
+ (floatBuff2[1] + floatBuff2[3]) / 2,
+ edgeDetails.colorLowDetail(edge));
+ }
+ }
+
+ nodeBuff.put(node);
+ }
+ } else { // High detail.
+
+ while (nodeHits.numRemaining() > 0) {
+ final int node = nodeHits.nextExtents(floatBuff1, 0);
+ final byte nodeShape = nodeDetails.shape(node);
+ final IntEnumerator touchingEdges = graph.edgesAdjacent(node, true, true, true);
+
+ while (touchingEdges.numRemaining() > 0) {
+ final int edge = touchingEdges.nextInt();
+ final int otherNode = node ^ graph.edgeSource(edge)
+ ^ graph.edgeTarget(edge);
+
+ if (nodeBuff.get(otherNode) < 0) { // Has not yet been rendered.
+
+ if (!nodePositions.exists(otherNode, floatBuff2, 0))
+ throw new IllegalStateException("nodePositions not recognizing node that exists in graph");
+
+ final byte otherNodeShape = nodeDetails.shape(otherNode);
+
+ // Compute node shapes, center positions, and extents.
+ final byte srcShape;
+
+ // Compute node shapes, center positions, and extents.
+ final byte trgShape;
+ final float[] srcExtents;
+ final float[] trgExtents;
+
+ if (node == graph.edgeSource(edge)) {
+ srcShape = nodeShape;
+ trgShape = otherNodeShape;
+ srcExtents = floatBuff1;
+ trgExtents = floatBuff2;
+ } else { // node == graph.edgeTarget(edge).
+ srcShape = otherNodeShape;
+ trgShape = nodeShape;
+ srcExtents = floatBuff2;
+ trgExtents = floatBuff1;
+ }
+
+ // Compute visual attributes that do not depend on LOD.
+ final float thickness = edgeDetails.segmentThickness(edge);
+ final Stroke edgeStroke = edgeDetails.segmentStroke(edge);
+ final Paint segPaint = edgeDetails.segmentPaint(edge);
+
+ // Compute arrows.
+ final byte srcArrow;
+
+ // Compute arrows.
+ final byte trgArrow;
+ final float srcArrowSize;
+ final float trgArrowSize;
+ final Paint srcArrowPaint;
+ final Paint trgArrowPaint;
+
+ if ((lodBits & LOD_EDGE_ARROWS) == 0) { // Not rendering arrows.
+ trgArrow = srcArrow = GraphGraphics.ARROW_NONE;
+ trgArrowSize = srcArrowSize = 0.0f;
+ trgArrowPaint = srcArrowPaint = null;
+ } else { // Rendering edge arrows.
+ srcArrow = edgeDetails.sourceArrow(edge);
+ trgArrow = edgeDetails.targetArrow(edge);
+ srcArrowSize = ((srcArrow == GraphGraphics.ARROW_NONE)
+ ? 0.0f
+ : edgeDetails.sourceArrowSize(edge));
+ trgArrowSize = ((trgArrow == GraphGraphics.ARROW_NONE)
+ ? 0.0f
+ : edgeDetails.targetArrowSize(edge));
+ srcArrowPaint = ((srcArrow == GraphGraphics.ARROW_NONE)
+ ? null : edgeDetails.sourceArrowPaint(edge));
+ trgArrowPaint = ((trgArrow == GraphGraphics.ARROW_NONE)
+ ? null : edgeDetails.targetArrowPaint(edge));
+ }
+
+ // Compute the anchors to use when rendering edge.
+ final EdgeAnchors anchors = (((lodBits & LOD_EDGE_ANCHORS) == 0) ? null
+ : edgeDetails
+ .anchors(edge));
+
+ if (!computeEdgeEndpoints(grafx, srcExtents, srcShape, srcArrow,
+ srcArrowSize, anchors, trgExtents, trgShape,
+ trgArrow, trgArrowSize, floatBuff3, floatBuff4))
+ continue;
+
+ final float srcXAdj = floatBuff3[0];
+ final float srcYAdj = floatBuff3[1];
+ final float trgXAdj = floatBuff4[0];
+ final float trgYAdj = floatBuff4[1];
+
+ grafx.drawEdgeFull(srcArrow, srcArrowSize, srcArrowPaint, trgArrow,
+ trgArrowSize, trgArrowPaint, srcXAdj, srcYAdj,
+ anchors, trgXAdj, trgYAdj, thickness, edgeStroke, segPaint);
+
+ // Take care of edge anchor rendering.
+ if (anchors != null) {
+ for (int k = 0; k < anchors.numAnchors(); k++) {
+ final float anchorSize;
+
+ if ((anchorSize = edgeDetails.anchorSize(edge, k)) > 0.0f) {
+ anchors.getAnchor(k, floatBuff4, 0);
+ grafx.drawNodeFull(GraphGraphics.SHAPE_RECTANGLE,
+ (float) (floatBuff4[0]
+ - (anchorSize / 2.0d)),
+ (float) (floatBuff4[1]
+ - (anchorSize / 2.0d)),
+ (float) (floatBuff4[0]
+ + (anchorSize / 2.0d)),
+ (float) (floatBuff4[1]
+ + (anchorSize / 2.0d)),
+ edgeDetails.anchorPaint(edge, k), 0.0f,
+ null);
+ }
+ }
+ }
+
+ // Take care of label rendering.
+ if ((lodBits & LOD_EDGE_LABELS) != 0) {
+ final int labelCount = edgeDetails.labelCount(edge);
+
+ for (int labelInx = 0; labelInx < labelCount; labelInx++) {
+ final String text = edgeDetails.labelText(edge, labelInx);
+ final Font font = edgeDetails.labelFont(edge, labelInx);
+ final double fontScaleFactor = edgeDetails.labelScaleFactor(edge,
+ labelInx);
+ final Paint paint = edgeDetails.labelPaint(edge, labelInx);
+ final byte textAnchor = edgeDetails.labelTextAnchor(edge,
+ labelInx);
+ final byte edgeAnchor = edgeDetails.labelEdgeAnchor(edge,
+ labelInx);
+ final float offsetVectorX = edgeDetails.labelOffsetVectorX(edge,
+ labelInx);
+ final float offsetVectorY = edgeDetails.labelOffsetVectorY(edge,
+ labelInx);
+ final byte justify;
+
+ if (text.indexOf('\n') >= 0)
+ justify = edgeDetails.labelJustify(edge, labelInx);
+ else
+ justify = NodeDetails.LABEL_WRAP_JUSTIFY_CENTER;
+
+ final double edgeAnchorPointX;
+ final double edgeAnchorPointY;
+
+ final double edgeLabelWidth = edgeDetails.labelWidth(edge);
+
+ if (edgeAnchor == EdgeDetails.EDGE_ANCHOR_SOURCE) {
+ edgeAnchorPointX = srcXAdj;
+ edgeAnchorPointY = srcYAdj;
+ } else if (edgeAnchor == EdgeDetails.EDGE_ANCHOR_TARGET) {
+ edgeAnchorPointX = trgXAdj;
+ edgeAnchorPointY = trgYAdj;
+ } else if (edgeAnchor == EdgeDetails.EDGE_ANCHOR_MIDPOINT) {
+ grafx.getEdgePath(srcArrow, srcArrowSize, trgArrow,
+ trgArrowSize, srcXAdj, srcYAdj, anchors,
+ trgXAdj, trgYAdj, path2d);
+
+ // Count the number of path segments. This count
+ // includes the initial SEG_MOVETO. So, for example, a
+ // path composed of 2 cubic curves would have a numPaths
+ // of 3. Note that numPaths will be at least 2 in all
+ // cases.
+ final int numPaths;
+
+ {
+ final PathIterator pathIter = path2d.getPathIterator(null);
+ int numPathsTemp = 0;
+
+ while (!pathIter.isDone()) {
+ numPathsTemp++; // pathIter.currentSegment().
+ pathIter.next();
+ }
+
+ numPaths = numPathsTemp;
+ }
+
+ // Compute "midpoint" of edge.
+ if ((numPaths % 2) != 0) {
+ final PathIterator pathIter = path2d.getPathIterator(null);
+
+ for (int i = numPaths / 2; i > 0; i--)
+ pathIter.next();
+
+ final int subPathType = pathIter.currentSegment(floatBuff5);
+
+ if (subPathType == PathIterator.SEG_LINETO) {
+ edgeAnchorPointX = floatBuff5[0];
+ edgeAnchorPointY = floatBuff5[1];
+ } else if (subPathType == PathIterator.SEG_QUADTO) {
+ edgeAnchorPointX = floatBuff5[2];
+ edgeAnchorPointY = floatBuff5[3];
+ } else if (subPathType == PathIterator.SEG_CUBICTO) {
+ edgeAnchorPointX = floatBuff5[4];
+ edgeAnchorPointY = floatBuff5[5];
+ } else
+ throw new IllegalStateException("got unexpected PathIterator segment type: "
+ + subPathType);
+ } else { // numPaths % 2 == 0.
+
+ final PathIterator pathIter = path2d.getPathIterator(null);
+
+ for (int i = numPaths / 2; i > 0; i--) {
+ if (i == 1) {
+ final int subPathType = pathIter.currentSegment(floatBuff5);
+
+ if ((subPathType == PathIterator.SEG_MOVETO)
+ || (subPathType == PathIterator.SEG_LINETO)) {
+ floatBuff5[6] = floatBuff5[0];
+ floatBuff5[7] = floatBuff5[1];
+ } else if (subPathType == PathIterator.SEG_QUADTO) {
+ floatBuff5[6] = floatBuff5[2];
+ floatBuff5[7] = floatBuff5[3];
+ } else if (subPathType == PathIterator.SEG_CUBICTO) {
+ floatBuff5[6] = floatBuff5[4];
+ floatBuff5[7] = floatBuff5[5];
+ } else
+ throw new IllegalStateException("got unexpected PathIterator segment type: "
+ + subPathType);
+ }
+
+ pathIter.next();
+ }
+
+ final int subPathType = pathIter.currentSegment(floatBuff5);
+
+ if (subPathType == PathIterator.SEG_LINETO) {
+ edgeAnchorPointX = (0.5d * floatBuff5[6])
+ + (0.5d * floatBuff5[0]);
+ edgeAnchorPointY = (0.5d * floatBuff5[7])
+ + (0.5d * floatBuff5[1]);
+ } else if (subPathType == PathIterator.SEG_QUADTO) {
+ edgeAnchorPointX = (0.25d * floatBuff5[6])
+ + (0.5d * floatBuff5[0])
+ + (0.25d * floatBuff5[2]);
+ edgeAnchorPointY = (0.25d * floatBuff5[7])
+ + (0.5d * floatBuff5[1])
+ + (0.25d * floatBuff5[3]);
+ } else if (subPathType == PathIterator.SEG_CUBICTO) {
+ edgeAnchorPointX = (0.125d * floatBuff5[6])
+ + (0.375d * floatBuff5[0])
+ + (0.375d * floatBuff5[2])
+ + (0.125d * floatBuff5[4]);
+ edgeAnchorPointY = (0.125d * floatBuff5[7])
+ + (0.375d * floatBuff5[1])
+ + (0.375d * floatBuff5[3])
+ + (0.125d * floatBuff5[5]);
+ } else
+ throw new IllegalStateException("got unexpected PathIterator segment type: "
+ + subPathType);
+ }
+ } else
+ throw new IllegalStateException("encountered an invalid EDGE_ANCHOR_* constant: "
+ + edgeAnchor);
+
+ final MeasuredLineCreator measuredText =
+ new MeasuredLineCreator(text,font,
+ grafx.getFontRenderContextFull(),
+ fontScaleFactor,
+ (lodBits&LOD_TEXT_AS_SHAPE)!= 0,
+ edgeLabelWidth);
+
+ doubleBuff1[0] = -0.5d * measuredText.getMaxLineWidth();
+ doubleBuff1[1] = -0.5d * measuredText.getTotalHeight();
+ doubleBuff1[2] = 0.5d * measuredText.getMaxLineWidth();
+ doubleBuff1[3] = 0.5d * measuredText.getTotalHeight();
+ lemma_computeAnchor(textAnchor, doubleBuff1, doubleBuff2);
+
+ final double textXCenter = edgeAnchorPointX - doubleBuff2[0]
+ + offsetVectorX;
+ final double textYCenter = edgeAnchorPointY - doubleBuff2[1]
+ + offsetVectorY;
+ TextRenderingUtils.renderHorizontalText(grafx, measuredText,
+ font, fontScaleFactor,
+ (float) textXCenter,
+ (float) textYCenter,
+ justify, paint,
+ (lodBits
+ & LOD_TEXT_AS_SHAPE) != 0);
+ }
+ }
+ }
+ }
+
+ nodeBuff.put(node);
+ }
+ }
+ }
+ // Render nodes and labels. A label is not necessarily on top of every
+ // node; it is only on top of the node it belongs to.
+ {
+ final SpacialEntry2DEnumerator nodeHits = nodePositions.queryOverlap(xMin, yMin, xMax,
+ yMax, null, 0,
+ false);
+
+ if ((lodBits & LOD_HIGH_DETAIL) == 0) { // Low detail.
+
+ final int nodeHitCount = nodeHits.numRemaining();
+
+ for (int i = 0; i < nodeHitCount; i++) {
+ final int node = nodeHits.nextExtents(floatBuff1, 0);
+
+ if ((floatBuff1[0] != floatBuff1[2]) && (floatBuff1[1] != floatBuff1[3]))
+ grafx.drawNodeLow(floatBuff1[0], floatBuff1[1], floatBuff1[2],
+ floatBuff1[3], nodeDetails.colorLowDetail(node));
+ }
+ } else { // High detail.
+ while (nodeHits.numRemaining() > 0) {
+ final int node = nodeHits.nextExtents(floatBuff1, 0);
+
+ renderNodeHigh(graph, grafx, node, floatBuff1, doubleBuff1, doubleBuff2, nodeDetails, lodBits);
+
+
+ // Take care of label rendering.
+ if ((lodBits & LOD_NODE_LABELS) != 0) { // Potential label rendering.
+
+ final int labelCount = nodeDetails.labelCount(node);
+
+ for (int labelInx = 0; labelInx < labelCount; labelInx++) {
+ final String text = nodeDetails.labelText(node, labelInx);
+ final Font font = nodeDetails.labelFont(node, labelInx);
+ final double fontScaleFactor = nodeDetails.labelScaleFactor(node,
+ labelInx);
+ final Paint paint = nodeDetails.labelPaint(node, labelInx);
+ final byte textAnchor = nodeDetails.labelTextAnchor(node, labelInx);
+ final byte nodeAnchor = nodeDetails.labelNodeAnchor(node, labelInx);
+ final float offsetVectorX = nodeDetails.labelOffsetVectorX(node,
+ labelInx);
+ final float offsetVectorY = nodeDetails.labelOffsetVectorY(node,
+ labelInx);
+ final byte justify;
+
+ if (text.indexOf('\n') >= 0)
+ justify = nodeDetails.labelJustify(node, labelInx);
+ else
+ justify = NodeDetails.LABEL_WRAP_JUSTIFY_CENTER;
+
+ final double nodeLabelWidth = nodeDetails.labelWidth(node);
+
+ doubleBuff1[0] = floatBuff1[0];
+ doubleBuff1[1] = floatBuff1[1];
+ doubleBuff1[2] = floatBuff1[2];
+ doubleBuff1[3] = floatBuff1[3];
+ lemma_computeAnchor(nodeAnchor, doubleBuff1, doubleBuff2);
+
+ final double nodeAnchorPointX = doubleBuff2[0];
+ final double nodeAnchorPointY = doubleBuff2[1];
+ final MeasuredLineCreator measuredText = new MeasuredLineCreator(
+ text, font, grafx.getFontRenderContextFull(), fontScaleFactor,
+ (lodBits & LOD_TEXT_AS_SHAPE) != 0, nodeLabelWidth);
+
+ doubleBuff1[0] = -0.5d * measuredText.getMaxLineWidth();
+ doubleBuff1[1] = -0.5d * measuredText.getTotalHeight();
+ doubleBuff1[2] = 0.5d * measuredText.getMaxLineWidth();
+ doubleBuff1[3] = 0.5d * measuredText.getTotalHeight();
+ lemma_computeAnchor(textAnchor, doubleBuff1, doubleBuff2);
+
+ final double textXCenter = nodeAnchorPointX - doubleBuff2[0]
+ + offsetVectorX;
+ final double textYCenter = nodeAnchorPointY - doubleBuff2[1]
+ + offsetVectorY;
+ TextRenderingUtils.renderHorizontalText(grafx, measuredText, font,
+ fontScaleFactor,
+ (float) textXCenter,
+ (float) textYCenter, justify,
+ paint,
+ (lodBits & LOD_TEXT_AS_SHAPE) != 0);
+ }
+ }
+ }
+ }
+ }
+
+ return lodBits;
+ }
+
+ private final static void lemma_computeAnchor(final byte anchor, final double[] input4x,
+ final double[] rtrn2x) {
+ switch (anchor) {
+ case NodeDetails.ANCHOR_CENTER:
+ rtrn2x[0] = (input4x[0] + input4x[2]) / 2.0d;
+ rtrn2x[1] = (input4x[1] + input4x[3]) / 2.0d;
+
+ break;
+
+ case NodeDetails.ANCHOR_SOUTH:
+ rtrn2x[0] = (input4x[0] + input4x[2]) / 2.0d;
+ rtrn2x[1] = input4x[3];
+
+ break;
+
+ case NodeDetails.ANCHOR_SOUTHEAST:
+ rtrn2x[0] = input4x[2];
+ rtrn2x[1] = input4x[3];
+
+ break;
+
+ case NodeDetails.ANCHOR_EAST:
+ rtrn2x[0] = input4x[2];
+ rtrn2x[1] = (input4x[1] + input4x[3]) / 2.0d;
+
+ break;
+
+ case NodeDetails.ANCHOR_NORTHEAST:
+ rtrn2x[0] = input4x[2];
+ rtrn2x[1] = input4x[1];
+
+ break;
+
+ case NodeDetails.ANCHOR_NORTH:
+ rtrn2x[0] = (input4x[0] + input4x[2]) / 2.0d;
+ rtrn2x[1] = input4x[1];
+
+ break;
+
+ case NodeDetails.ANCHOR_NORTHWEST:
+ rtrn2x[0] = input4x[0];
+ rtrn2x[1] = input4x[1];
+
+ break;
+
+ case NodeDetails.ANCHOR_WEST:
+ rtrn2x[0] = input4x[0];
+ rtrn2x[1] = (input4x[1] + input4x[3]) / 2.0d;
+
+ break;
+
+ case NodeDetails.ANCHOR_SOUTHWEST:
+ rtrn2x[0] = input4x[0];
+ rtrn2x[1] = input4x[3];
+
+ break;
+
+ default:
+ throw new IllegalStateException("encoutered an invalid ANCHOR_* constant: "
+ + anchor);
+ }
+ }
+
+
+ /**
+ * Calculates the edge endpoints given two nodes, any edge anchors, and any arrows.
+ *
+ * @param grafx The GraphGraphics being used to render everything. Used only to
+ * calculate the edge intersection of the node.
+ * @param srcNodeExtents The extents of the source node.
+ * @param srcNodeShape The node shape type.
+ * @param srcArrow The source arrow type.
+ * @param srcArrowSize The source arrow size.
+ * @param anchors an EdgeAnchors object listing any anchors for the edge, possibly null.
+ * @param trgNodeExtents The extends of the target node.
+ * @param trgNodeShape The target node type.
+ * @param trgArrow The target arrow type.
+ * @param trgArrowSize The target arrow size.
+ * @param rtnValSrc The array where X,Y positions of the source end of the edge are stored.
+ * @param rtnValTrg The array where X,Y positions of the target end of the edge are stored.
+ *
+ * @return DOCUMENT ME!
+ */
+ public final static boolean computeEdgeEndpoints(final GraphGraphics grafx,
+ final float[] srcNodeExtents,
+ final byte srcNodeShape, final byte srcArrow,
+ final float srcArrowSize, EdgeAnchors anchors,
+ final float[] trgNodeExtents,
+ final byte trgNodeShape, final byte trgArrow,
+ final float trgArrowSize,
+ final float[] rtnValSrc,
+ final float[] rtnValTrg) {
+
+ final float srcX = (float) ((((double) srcNodeExtents[0]) + srcNodeExtents[2]) / 2.0d);
+ final float srcY = (float) ((((double) srcNodeExtents[1]) + srcNodeExtents[3]) / 2.0d);
+ final float trgX = (float) ((((double) trgNodeExtents[0]) + trgNodeExtents[2]) / 2.0d);
+ final float trgY = (float) ((((double) trgNodeExtents[1]) + trgNodeExtents[3]) / 2.0d);
+ final float srcXOut;
+ final float srcYOut;
+ final float trgXOut;
+ final float trgYOut;
+
+ final float[] floatBuff = new float[2];
+
+ if ((anchors != null) && (anchors.numAnchors() == 0))
+ anchors = null;
+
+ if (anchors == null) {
+ srcXOut = trgX;
+ srcYOut = trgY;
+ trgXOut = srcX;
+ trgYOut = srcY;
+ } else {
+ anchors.getAnchor(0, floatBuff, 0);
+ srcXOut = floatBuff[0];
+ srcYOut = floatBuff[1];
+ anchors.getAnchor(anchors.numAnchors() - 1, floatBuff, 0);
+ trgXOut = floatBuff[0];
+ trgYOut = floatBuff[1];
+ }
+
+ calcIntersection(grafx, srcNodeShape, srcNodeExtents, srcX, srcY,
+ srcXOut, srcYOut, floatBuff);
+ final float srcXAdj = floatBuff[0];
+ final float srcYAdj = floatBuff[1];
+
+ calcIntersection(grafx, trgNodeShape, trgNodeExtents, trgX, trgY,
+ trgXOut, trgYOut, floatBuff);
+ final float trgXAdj = floatBuff[0];
+ final float trgYAdj = floatBuff[1];
+
+ rtnValSrc[0] = srcXAdj;
+ rtnValSrc[1] = srcYAdj;
+ rtnValTrg[0] = trgXAdj;
+ rtnValTrg[1] = trgYAdj;
+
+ return true;
+ }
+
+ private static void calcIntersection(GraphGraphics grafx, byte nodeShape,
+ float[] nodeExtents, float x, float y,
+ float xOut, float yOut, float[] retVal) {
+ if ((nodeExtents[0] == nodeExtents[2]) ||
+ (nodeExtents[1] == nodeExtents[3])) {
+ retVal[0] = x;
+ retVal[1] = y;
+ } else {
+ if (!grafx.computeEdgeIntersection(nodeShape, nodeExtents[0],
+ nodeExtents[1], nodeExtents[2],
+ nodeExtents[3], 0.0f, xOut, yOut,
+ retVal)) {
+
+ final float newXOut;
+ final float newYOut;
+
+ final double xCenter = (((double) nodeExtents[0]) + nodeExtents[2]) / 2.0d;
+ final double yCenter = (((double) nodeExtents[1]) + nodeExtents[3]) / 2.0d;
+ final double desiredDist = Math.max(((double) nodeExtents[2])
+ - nodeExtents[0],
+ ((double) nodeExtents[3])
+ - nodeExtents[1]);
+ final double dX = xOut - xCenter;
+ final double dY = yOut - yCenter;
+ final double len = Math.sqrt((dX * dX) + (dY * dY));
+
+ if (len == 0.0d) {
+ newXOut = (float) (xOut + desiredDist);
+ newYOut = yOut;
+ } else {
+ newXOut = (float) (((dX / len) * desiredDist) + xOut);
+ newYOut = (float) (((dY / len) * desiredDist) + yOut);
+ }
+
+ grafx.computeEdgeIntersection(nodeShape, nodeExtents[0],
+ nodeExtents[1], nodeExtents[2],
+ nodeExtents[3], 0.0f, newXOut,
+ newYOut, retVal);
+ }
+ }
+ }
+
+ private final static float[] s_floatTemp = new float[6];
+ private final static int[] s_segTypeBuff = new int[200];
+ private final static float[] s_floatBuff2 = new float[1200];
+
+ /**
+ * A utility method that converts an open GeneralPath into a closed GeneralPath.
+ * The GraphGraphics.getEdgePath() method returns an open general path that
+ * is simply a list of segments from the source node to the target node that doesn't
+ * include a SEG_CLOSE segment. This method traces such a path, reverses course
+ * and traces the same path backwards ending with a SEG_CLOSE to create a closed path.
+ *
+ * This method appears to only be used in one place (in ding) where it is used for
+ * creating a path suitable for determining whether an edge intersets a selected (or
+ * clicked) region. It's not clear why this method is even being used in that case
+ * because GeneralPath.intersect seems to work on open paths as well as closed paths.
+ *
+ * @param origPath DOCUMENT ME!
+ * @param rtnVal DOCUMENT ME!
+ */
+ public final static void computeClosedPath(final PathIterator origPath, final GeneralPath rtnVal) {
+ synchronized (s_floatTemp) {
+ // First fill our buffers with the coordinates and segment types.
+ int segs = 0;
+ int offset = 0;
+
+ if ((s_segTypeBuff[segs++] = origPath.currentSegment(s_floatTemp)) != PathIterator.SEG_MOVETO)
+ throw new IllegalStateException("expected a SEG_MOVETO at the beginning of origPath");
+
+ for (int i = 0; i < 2; i++)
+ s_floatBuff2[offset++] = s_floatTemp[i];
+
+ origPath.next();
+
+ while (!origPath.isDone()) {
+ final int segType = origPath.currentSegment(s_floatTemp);
+ s_segTypeBuff[segs++] = segType;
+
+ if ((segType == PathIterator.SEG_MOVETO) || (segType == PathIterator.SEG_CLOSE))
+ throw new IllegalStateException("did not expect SEG_MOVETO or SEG_CLOSE");
+
+ // This is a rare case where I rely on the actual constant values
+ // to do a computation efficiently.
+ final int coordCount = segType * 2;
+
+ for (int i = 0; i < coordCount; i++)
+ s_floatBuff2[offset++] = s_floatTemp[i];
+
+ origPath.next();
+ }
+
+ rtnVal.reset();
+ offset = 0;
+
+ // Now add the forward path to rtnVal.
+ for (int i = 0; i < segs; i++) {
+ switch (s_segTypeBuff[i]) {
+ case PathIterator.SEG_MOVETO:
+ rtnVal.moveTo(s_floatBuff2[offset++], s_floatBuff2[offset++]);
+
+ break;
+
+ case PathIterator.SEG_LINETO:
+ rtnVal.lineTo(s_floatBuff2[offset++], s_floatBuff2[offset++]);
+
+ break;
+
+ case PathIterator.SEG_QUADTO:
+ rtnVal.quadTo(s_floatBuff2[offset++], s_floatBuff2[offset++],
+ s_floatBuff2[offset++], s_floatBuff2[offset++]);
+
+ break;
+
+ default: // PathIterator.SEG_CUBICTO.
+ rtnVal.curveTo(s_floatBuff2[offset++], s_floatBuff2[offset++],
+ s_floatBuff2[offset++], s_floatBuff2[offset++],
+ s_floatBuff2[offset++], s_floatBuff2[offset++]);
+
+ break;
+ }
+ }
+
+ // Now add the return path.
+ for (int i = segs - 1; i > 0; i--) {
+ switch (s_segTypeBuff[i]) {
+ case PathIterator.SEG_LINETO:
+ offset -= 2;
+ rtnVal.lineTo(s_floatBuff2[offset - 2], s_floatBuff2[offset - 1]);
+
+ break;
+
+ case PathIterator.SEG_QUADTO:
+ offset -= 4;
+ rtnVal.quadTo(s_floatBuff2[offset], s_floatBuff2[offset + 1],
+ s_floatBuff2[offset - 2], s_floatBuff2[offset - 1]);
+
+ break;
+
+ default: // PathIterator.SEG_CUBICTO.
+ offset -= 6;
+ rtnVal.curveTo(s_floatBuff2[offset + 2], s_floatBuff2[offset + 3],
+ s_floatBuff2[offset], s_floatBuff2[offset + 1],
+ s_floatBuff2[offset - 2], s_floatBuff2[offset - 1]);
+
+ break;
+ }
+ }
+
+ rtnVal.closePath();
+ }
+ }
+
+
+ /**
+ * Render node view with details, including custom graphics.
+ *
+ * @param graph
+ * @param grafx
+ * @param node
+ * @param floatBuff1
+ * @param doubleBuff1
+ * @param doubleBuff2
+ * @param nodeDetails
+ * @param lodBits
+ */
+ private static final void renderNodeHigh(final FixedGraph graph, final GraphGraphics grafx,
+ final int node, final float[] floatBuff1, final double[] doubleBuff1, final double[] doubleBuff2,
+ final NodeDetails nodeDetails, final int lodBits) {
+ if ((floatBuff1[0] != floatBuff1[2]) && (floatBuff1[1] != floatBuff1[3])) {
+
+ // Compute visual attributes that do not depend on LOD.
+ final byte shape = nodeDetails.shape(node);
+ final Paint fillPaint = nodeDetails.fillPaint(node);
+
+ // Compute node border information.
+ final float borderWidth;
+ final Paint borderPaint;
+
+ if ((lodBits & LOD_NODE_BORDERS) == 0) { // Not rendering borders.
+ borderWidth = 0.0f;
+ borderPaint = null;
+ } else { // Rendering node borders.
+ borderWidth = nodeDetails.borderWidth(node);
+
+ if (borderWidth == 0.0f)
+ borderPaint = null;
+ else
+ borderPaint = nodeDetails.borderPaint(node);
+ }
+
+ // Draw the node.
+ grafx.drawNodeFull(shape, floatBuff1[0], floatBuff1[1], floatBuff1[2], floatBuff1[3], fillPaint, borderWidth, borderPaint);
+ }
+
+ // Take care of custom graphic rendering.
+ if ((lodBits & LOD_CUSTOM_GRAPHICS) != 0) {
+
+ // draw any nested networks first
+ final TexturePaint nestedNetworkPaint = nodeDetails.getNestedNetworkTexturePaint(node);
+ if (nestedNetworkPaint != null) {
+ doubleBuff1[0] = floatBuff1[0];
+ doubleBuff1[1] = floatBuff1[1];
+ doubleBuff1[2] = floatBuff1[2];
+ doubleBuff1[3] = floatBuff1[3];
+ lemma_computeAnchor(NodeDetails.ANCHOR_CENTER, doubleBuff1, doubleBuff2);
+ grafx.drawCustomGraphicFull(nestedNetworkPaint.getAnchorRect(), (float)doubleBuff2[0], (float)doubleBuff2[1], nestedNetworkPaint);
+ }
+
+ // draw custom graphics on top of nested networks
+ // don't allow our custom graphics to mutate while we iterate over them:
+ synchronized (nodeDetails.customGraphicsLock(node)) {
+ // This iterator will return CustomGraphics in rendering order:
+ Iterator<CustomGraphic> dNodeIt = nodeDetails.customGraphics(node);
+ CustomGraphic cg = null;
+ // The graphic index used to retrieve non custom graphic info corresponds to the zero-based
+ // index of the CustomGraphic returned by the iterator:
+ int graphicInx = 0;
+ while (dNodeIt.hasNext()) {
+ cg = dNodeIt.next();
+ final float offsetVectorX = nodeDetails.graphicOffsetVectorX(node, graphicInx);
+ final float offsetVectorY = nodeDetails.graphicOffsetVectorY(node, graphicInx);
+ doubleBuff1[0] = floatBuff1[0];
+ doubleBuff1[1] = floatBuff1[1];
+ doubleBuff1[2] = floatBuff1[2];
+ doubleBuff1[3] = floatBuff1[3];
+ lemma_computeAnchor(NodeDetails.ANCHOR_CENTER, doubleBuff1, doubleBuff2);
+ grafx.drawCustomGraphicFull(cg.getShape(), (float) (doubleBuff2[0] + offsetVectorX), (float) (doubleBuff2[1] + offsetVectorY),
+ cg.getPaint());
+ graphicInx++;
+ }
+ }
+ }
+ }
+}
diff --git a/corelibs/render.stateful/src/main/java/cytoscape/render/stateful/MeasuredLine.java b/corelibs/render.stateful/src/main/java/cytoscape/render/stateful/MeasuredLine.java
new file mode 100644
index 0000000..35960bc
--- /dev/null
+++ b/corelibs/render.stateful/src/main/java/cytoscape/render/stateful/MeasuredLine.java
@@ -0,0 +1,70 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.render.stateful;
+
+/**
+ * A simple class to hold the width and height of a given string in terms
+ * of specific fonts, rendering contexts, etc..
+ */
+class MeasuredLine {
+
+ private final String line;
+ private final double width;
+ private final double height;
+
+ public MeasuredLine(final String line, final double width, final double height) {
+ this.line = line;
+ this.width = width;
+ this.height = height;
+ }
+
+ public String getLine() {
+ return line;
+ }
+
+ public double getWidth() {
+ return width;
+ }
+
+ public double getHeight() {
+ return height;
+ }
+
+ public String toString() {
+ return "'" + line + "' w:" + width + " h:" + height;
+ }
+}
diff --git a/corelibs/render.stateful/src/main/java/cytoscape/render/stateful/MeasuredLineCreator.java b/corelibs/render.stateful/src/main/java/cytoscape/render/stateful/MeasuredLineCreator.java
new file mode 100644
index 0000000..2d3b5bb
--- /dev/null
+++ b/corelibs/render.stateful/src/main/java/cytoscape/render/stateful/MeasuredLineCreator.java
@@ -0,0 +1,219 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.render.stateful;
+
+import cytoscape.render.immed.GraphGraphics;
+
+import java.awt.Font;
+import java.awt.Paint;
+import java.awt.font.FontRenderContext;
+import java.awt.font.GlyphVector;
+import java.awt.geom.Rectangle2D;
+
+import java.util.List;
+import java.util.ArrayList;
+
+/**
+ * A class that takes a String and a number of rendering parameters and then
+ * splits the text into MeasuredLines based on newline characters and whether
+ * line length is otherwise greater than the specified label width limit.
+ */
+class MeasuredLineCreator {
+ private double maxLineWidth;
+ private double totalHeight;
+
+ private final double labelWidth;
+ private final String rawLine;
+ private final String[] rawLines;
+ private final FontRenderContext frc;
+ private final Font font;
+ private final double fontScaleFactor;
+ private final boolean textAsShape;
+ private final List<MeasuredLine> measuredLines;
+
+ public MeasuredLineCreator(final String rawLine, final Font font,
+ final FontRenderContext frc, final double fontScaleFactor,
+ final boolean textAsShape, final double labelWidth) {
+ this.rawLine = rawLine;
+ this.font = font;
+ this.frc = frc;
+ this.fontScaleFactor = fontScaleFactor;
+ this.textAsShape = textAsShape;
+ this.labelWidth = labelWidth;
+ this.rawLines = rawLine.split("\n");
+ this.measuredLines = new ArrayList<MeasuredLine>();
+
+ calculateRawBounds();
+ createMeasuredLines();
+ }
+
+ /**
+ * Does a first pass at calculating the bounds of all lines. For short strings
+ * (i.e. the norm) this is sufficient calculation.
+ */
+ private void calculateRawBounds() {
+ maxLineWidth = 0;
+ totalHeight = 0;
+ for ( String line : rawLines ) {
+ final Rectangle2D bounds = calcBounds(line);
+ updateBounds(bounds.getWidth()*fontScaleFactor,bounds.getHeight()*fontScaleFactor);
+ }
+ }
+
+ /**
+ * Simply updates the maxLineWidth and totalHeight. We do it in a separate method
+ * to make sure we do it consistently.
+ */
+ private void updateBounds(final double newWidth, final double newHeight ) {
+ maxLineWidth = Math.max( maxLineWidth, newWidth );
+ totalHeight += newHeight;
+ }
+
+ /**
+ * Calculates the bounds of a single string.
+ */
+ private Rectangle2D calcBounds(final String s) {
+ final Rectangle2D bounds;
+
+ if (textAsShape) {
+ final char[] charBuff = s.toCharArray();
+ final GlyphVector glyphV = font.layoutGlyphVector( frc, charBuff, 0,
+ charBuff.length, Font.LAYOUT_NO_LIMIT_CONTEXT);
+ bounds = glyphV.getLogicalBounds();
+ } else {
+ bounds = font.getStringBounds(s, frc);
+ }
+
+ return bounds;
+ }
+
+ /**
+ * Splits the raw lines according to how many lines are present and if any of
+ * the lines are too long. Recalculates the maxLineWidth and totalHeight based
+ * on the new lines created.
+ */
+ private void createMeasuredLines() {
+
+ // There's only one line and it's short, i.e. what usually happens.
+ if ( rawLines.length == 1 && labelWidth > maxLineWidth ) {
+ measuredLines.add(new MeasuredLine(rawLines[0],maxLineWidth,totalHeight));
+ return;
+ }
+
+ // There are multiple and/or longer-than-allowed lines.
+ // Process each of them. Also update overall widths and heights
+ // as those may change.
+ totalHeight = 0;
+ maxLineWidth = 0;
+
+ for ( String line : rawLines ) {
+ double currentWidth = 0;
+ double wordWidth = 0;
+ double wordHeight = 0;
+ StringBuilder currentLine = new StringBuilder();
+
+ // Split each line based on the space char and then build up
+ // new lines by concatenating the words together into a new
+ // new line that is within the specified length.
+ String[] words = line.split(" ");
+ for (String w : words) {
+ String word = w + " ";
+ Rectangle2D bounds = calcBounds(word);
+ wordWidth = bounds.getWidth()*fontScaleFactor;
+ wordHeight = bounds.getHeight()*fontScaleFactor;
+
+ // If the current line width plus the new word
+ // width is >= than the label width save the line
+ if (currentWidth + wordWidth >= labelWidth) {
+ // only write the string if something is there
+ if ( currentWidth > 0 ) {
+ measuredLines.add( new MeasuredLine(currentLine.toString(),
+ currentWidth,wordHeight) );
+ updateBounds(currentWidth,wordHeight);
+ currentLine.delete(0,currentLine.length());
+ }
+
+ // if the word itself is >= the label width,
+ // make the word itself a new line
+ if ( wordWidth >= labelWidth ) {
+ measuredLines.add(new MeasuredLine(word,wordWidth,wordHeight) );
+ updateBounds(wordWidth,wordHeight);
+ currentWidth = 0;
+
+ // otherwise use the word as the beginning of a new line
+ } else {
+ currentLine.append(word);
+ currentWidth = wordWidth;
+ }
+
+ // otherwise append the word to the line
+ } else {
+ currentLine.append(word);
+ currentWidth += wordWidth;
+ }
+ }
+
+ // add the last line if there's anything there
+ if ( currentWidth > 0 ) {
+ measuredLines.add( new MeasuredLine(currentLine.toString(),
+ currentWidth, wordHeight) );
+ updateBounds(currentWidth,wordHeight);
+ }
+ }
+ }
+
+ /**
+ * @return the maximum line width among the lines found in the input text.
+ */
+ public double getMaxLineWidth() {
+ return maxLineWidth;
+ }
+
+ /**
+ * @return the total combined height of all of the lines found in the input text.
+ */
+ public double getTotalHeight() {
+ return totalHeight;
+ }
+
+ /**
+ * @return a list of MeasuredLine objects created from the input text.
+ */
+ public List<MeasuredLine> getMeasuredLines() {
+ return measuredLines;
+ }
+}
diff --git a/corelibs/render.stateful/src/main/java/cytoscape/render/stateful/NodeDetails.java b/corelibs/render.stateful/src/main/java/cytoscape/render/stateful/NodeDetails.java
new file mode 100644
index 0000000..b83306c
--- /dev/null
+++ b/corelibs/render.stateful/src/main/java/cytoscape/render/stateful/NodeDetails.java
@@ -0,0 +1,504 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.render.stateful;
+
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.Paint;
+import java.awt.TexturePaint;
+import java.util.ArrayList;
+import java.util.Iterator;
+
+import cytoscape.render.immed.GraphGraphics;
+
+
+/**
+ * Defines visual properties of a node modulo the node size and location
+ * Even though this class is not declared abstract, in most situations it
+ * makes sense to override at least some of its methods in order to gain
+ * control over node visual properties.<p>
+ * To understand the significance of each method's return value, it makes
+ * sense to become familiar with the API cytoscape.render.immed.GraphGraphics.
+ */
+public class NodeDetails {
+ /**
+ * Specifies that an anchor point lies at the center of a bounding box.
+ */
+ public static final byte ANCHOR_CENTER = 0;
+
+ /**
+ * Specifies that an anchor point lies on the north edge of a
+ * bounding box, halfway between the east and west edges.
+ */
+ public static final byte ANCHOR_NORTH = 1;
+
+ /**
+ * Specifies that an anchor point lies on the northeast corner of
+ * a bounding box.
+ */
+ public static final byte ANCHOR_NORTHEAST = 2;
+
+ /**
+ * Specifies that an anchor point lies on the east edge of a
+ * bounding box, halfway between the north and south edges.
+ */
+ public static final byte ANCHOR_EAST = 3;
+
+ /**
+ * Specifies that an anchor point lies on the southeast corner of
+ * a bounding box.
+ */
+ public static final byte ANCHOR_SOUTHEAST = 4;
+
+ /**
+ * Specifies that an anchor point lies on the south edge of a
+ * bounding box, halfway between the east and west edges.
+ */
+ public static final byte ANCHOR_SOUTH = 5;
+
+ /**
+ * Specifies that an anchor point lies on the southwest corner of a
+ * bounding box.
+ */
+ public static final byte ANCHOR_SOUTHWEST = 6;
+
+ /**
+ * Specifies that an anchor point lies on the west edge of a
+ * bounding box, halfway between the north and south edges.
+ */
+ public static final byte ANCHOR_WEST = 7;
+
+ /**
+ * Specifies that an anchor point lies on the northwest corner of a
+ * bounding box.
+ */
+ public static final byte ANCHOR_NORTHWEST = 8;
+
+ /**
+ * Used for range checking the anchor values.
+ */
+ // Seems like these values should really be an enum...:
+ public static final byte MAX_ANCHOR_VAL = 8;
+
+ /**
+ * Specifies that the lines in a multi-line node label should each have
+ * a center point with similar X coordinate.
+ */
+ public static final byte LABEL_WRAP_JUSTIFY_CENTER = 64;
+
+ /**
+ * Specifies that the lines of a multi-line node label should each have
+ * a leftmost point with similar X coordinate.
+ */
+ public static final byte LABEL_WRAP_JUSTIFY_LEFT = 65;
+
+ /**
+ * Specifies that the lines of a multi-line node label should each have
+ * a rightmost point with similar X coordinate.
+ */
+ public static final byte LABEL_WRAP_JUSTIFY_RIGHT = 66;
+
+ /**
+ * Hashmap which records selected state of nodes - information used
+ * by GraphRenderer.renderGraph() to render selected nodes on top of
+ * unselected nodes.
+ */
+ java.util.Map<Integer, Boolean> selectedMap = new java.util.HashMap<Integer, Boolean>();
+
+ /**
+ * Instantiates node details with defaults. Documentation on each method
+ * describes defaults. To override defaults, extend this class.
+ */
+ public NodeDetails() {
+ }
+
+ /**
+ * Returns the color of node in low detail rendering mode.
+ * By default this method returns Color.red. It is an error to return
+ * null in this method.<p>
+ * In low detail rendering mode, this is the only method from this class
+ * that is looked at. The rest of the methods in this class define visual
+ * properties that are used in full detail rendering mode. In low detail
+ * rendering mode translucent colors are not supported whereas in full
+ * detail rendering mode they are.
+ */
+ public Color colorLowDetail(final int node) {
+ return Color.red;
+ }
+
+ /**
+ * Returns a GraphGraphics.SHAPE_* constant (or a custom node shape that an
+ * instance of GraphGraphics understands); this defines the shape that this
+ * node takes.
+ * By default this method returns GraphGraphics.SHAPE_RECTANGLE.
+ * Take note of certain constraints specified in
+ * GraphGraphics.drawNodeFull() that pertain to rounded rectangles.
+ */
+ public byte shape(final int node) {
+ return GraphGraphics.SHAPE_RECTANGLE;
+ }
+
+ /**
+ * Returns the paint of the interior of the node shape. By default this
+ * method returns Color.red. It is an error to return null in this method.
+ */
+ public Paint fillPaint(final int node) {
+ return Color.red;
+ }
+
+ /**
+ * Returns the border width of the node shape. By default this method
+ * returns zero. Take note of certain constraints specified in
+ * GraphGraphics.drawNodeFull().
+ */
+ public float borderWidth(final int node) {
+ return 0.0f;
+ }
+
+ /**
+ * Returns the paint of the border of the node shape. By default this method
+ * returns null. This return value is ignored if borderWidth(node)
+ * returns zero; it is an error to return null if borderWidth(node) returns
+ * a value greater than zero.
+ */
+ public Paint borderPaint(final int node) {
+ return null;
+ }
+
+ /**
+ * Returns the number of labels that this node has. By default this method
+ * returns zero.
+ */
+ public int labelCount(final int node) {
+ return 0;
+ }
+
+ /**
+ * Returns a label's text. By default this method
+ * always returns null. This method is only called by the rendering engine
+ * if labelCount(node) returns a value greater than zero. It is an error
+ * to return null if this method is called by the rendering engine.<p>
+ * To specify multiple lines of text in a node label, simply insert the
+ * '\n' character between lines of text.
+ * @param labelInx a value in the range [0, labelCount(node)-1] indicating
+ * which node label in question.
+ */
+ public String labelText(final int node, final int labelInx) {
+ return null;
+ }
+
+ /**
+ * Returns the font to use when rendering this label.
+ * By default this method always returns null. This method is only called
+ * by the rendering engine if labelCount(node) returns a value greater than
+ * zero. It is an error to return null if this method is called by the
+ * rendering engine.
+ * @param labelInx a value in the range [0, labelCount(node)-1] indicating
+ * which node label in question.
+ */
+ public Font labelFont(final int node, final int labelInx) {
+ return null;
+ }
+
+ /**
+ * Returns an additional scaling factor that is to be applied to the font
+ * used to render this label; this scaling factor, applied to the point
+ * size of the font returned by labelFont(node, labelInx), yields a new
+ * virtual font that is used to render the text label.
+ * By default this method always returns 1.0. This method is only called
+ * by the rendering engine if labelCount(node) returns a value greater than
+ * zero.
+ * @param labelInx a value in the range [0, labelCount(node)-1] indicating
+ * which node label in question.
+ */
+ public double labelScaleFactor(final int node, final int labelInx) {
+ return 1.0d;
+ }
+
+ /**
+ * Returns the paint of a text label. By default this method
+ * always returns null. This method is only called by the rendering engine
+ * if labelCount(node) returns a value greater than zero. It is an error to
+ * return null if this method is called by the rendering engine.
+ * @param labelInx a value in the range [0, labelCount(node)-1] indicating
+ * which node label in question.
+ */
+ public Paint labelPaint(final int node, final int labelInx) {
+ return null;
+ }
+
+ /**
+ * By returning one of the ANCHOR_* constants, specifies
+ * where on a text label's logical bounds box an anchor point lies. This
+ * <i>text anchor point</i> together with the
+ * node anchor point and label offset vector
+ * determines where, relative to the node, the text's logical bounds
+ * box is to be placed. The text's logical bounds box is placed such that
+ * the label offset vector plus the node anchor point equals the text anchor
+ * point.<p>
+ * By default this method always returns ANCHOR_CENTER.
+ * This method is only called by the rendering engine if labelCount(node)
+ * returns a value greater than zero.
+ * @param labelInx a value in the range [0, labelCount(node)-1] indicating
+ * which node label in question.
+ * @see #ANCHOR_CENTER
+ * @see #labelNodeAnchor(int, int)
+ * @see #labelOffsetVectorX(int, int)
+ * @see #labelOffsetVectorY(int, int)
+ */
+ public byte labelTextAnchor(final int node, final int labelInx) {
+ return ANCHOR_CENTER;
+ }
+
+ /**
+ * By returning one of the ANCHOR_* constants, specifies
+ * where on the node's extents rectangle an anchor point lies. This
+ * <i>node anchor point</i> together with the text anchor point and label
+ * offset vector determines where, relative to the node, the text's logical
+ * bounds box is to be placed. The text's logical bounds box is placed
+ * such that the label offset vector plus the node anchor point equals the
+ * text anchor point.<p>
+ * By default this method always returns ANCHOR_CENTER.
+ * This method is only called by the rendering engine if labelCount(node)
+ * returns a value greater than zero.
+ * @param labelInx a value in the range [0, labelCount(node)-1] indicating
+ * which node label in question.
+ * @see #ANCHOR_CENTER
+ * @see #labelTextAnchor(int, int)
+ * @see #labelOffsetVectorX(int, int)
+ * @see #labelOffsetVectorY(int, int)
+ */
+ public byte labelNodeAnchor(final int node, final int labelInx) {
+ return ANCHOR_CENTER;
+ }
+
+ /**
+ * Specifies the X component of the vector that separates a text anchor
+ * point from a node anchor point.
+ * This <i>label offset vector</i> together with the text anchor point and
+ * node anchor point determines where, relative to the node, the text's
+ * logical bounds box is to be placed. The text's logical bounds box is
+ * placed such that the label offset vector plus the node anchor point
+ * equals the text anchor point.<p>
+ * By default this method always returns zero.
+ * This method is only called by the rendering engine if labelCount(node)
+ * returns a value greater than zero.
+ * @param labelInx a value in the range [0, labelCount(node)-1] indicating
+ * which node label in question.
+ * @see #labelOffsetVectorY(int, int)
+ * @see #labelTextAnchor(int, int)
+ * @see #labelNodeAnchor(int, int)
+ */
+ public float labelOffsetVectorX(final int node, final int labelInx) {
+ return 0.0f;
+ }
+
+ /**
+ * Specifies the Y component of the vector that separates a text anchor
+ * point from a node anchor point.
+ * This <i>label offset vector</i> together with the text anchor point and
+ * node anchor point determines where, relative to the node, the text's
+ * logical bounds box is to be placed. The text's logical bounds box is
+ * placed such that the label offset vector plus the node anchor point
+ * equals the text anchor point.<p>
+ * By default this method always returns zero.
+ * This method is only called by the rendering engine if labelCount(node)
+ * returns a value greater than zero.
+ * @param labelInx a value in the range [0, labelCount(node)-1] indicating
+ * which node label in question.
+ * @see #labelOffsetVectorX(int, int)
+ * @see #labelTextAnchor(int, int)
+ * @see #labelNodeAnchor(int, int)
+ */
+ public float labelOffsetVectorY(final int node, final int labelInx) {
+ return 0.0f;
+ }
+
+ /**
+ * By returning one of the LABEL_WRAP_JUSTIFY_* constants, determines
+ * how to justify a node label spanning multiple lines. The choice made here
+ * does not affect the size of the logical bounding box of a node label's
+ * text. The lines of text are justified within that logical bounding
+ * box.<p>
+ * By default this method always returns LABEL_WRAP_JUSTIFY_CENTER.
+ * This return value is ignored if labelText(node, labelInx) returns a text
+ * string that does not span multiple lines.
+ * @see #LABEL_WRAP_JUSTIFY_CENTER
+ */
+ public byte labelJustify(final int node, final int labelInx) {
+ return LABEL_WRAP_JUSTIFY_CENTER;
+ }
+
+ /**
+ * Specifies the X component of the vector that separates the location of
+ * a rendered graphic from the node's anchor point for that graphic.
+ * By default this method always returns zero. This method is only called
+ * by the rendering engine if graphicCount(node) returns a value greater
+ * than zero.
+ * @param graphicInx a value in the range [0, graphicCount(node)-1]
+ * indicating which node graphic in question.
+ * @see #graphicOffsetVectorY(int, int)
+ * @see #graphicNodeAnchor(int, int)
+ */
+ public float graphicOffsetVectorX(final int node, final int graphicInx) {
+ return 0.0f;
+ }
+
+ /**
+ * Specifies the Y component of the vector that separates the location of
+ * a rendered graphic from the node's anchor point for that graphic.
+ * By default this method always returns zero. This method is only called
+ * by the rendering engine if graphicCount(node) returns a value greater
+ * than zero.
+ * @param graphicInx a value in the range [0, graphicCount(node)-1]
+ * indicating which node graphic in question.
+ * @see #graphicOffsetVectorX(int, int)
+ * @see #graphicNodeAnchor(int, int)
+ */
+ public float graphicOffsetVectorY(final int node, final int graphicInx) {
+ return 0.0f;
+ }
+
+
+ /**
+ * A thread-safe method returning the number of custom graphics
+ * associated with a given Node. If none are associated, zero is
+ * returned.
+ * NOTE: This method should be abstract, but since it isn't, any real use should override this
+ * method in a subclass.
+ * @see #customGraphics(int)
+ * @since Cytoscape 2.6
+ */
+ public int customGraphicCount(final int node) {
+ return 0;
+ }
+
+ /**
+ * Return a non-null, read-only Iterator over all CustomGraphics contained in this Node.
+ * The Iterator will return each CustomGraphic in draw order.
+ * The Iterator cannot be used to modify the underlying set of CustomGraphics.
+ * NOTE: This method should be abstract, but since it isn't, any real use should override this
+ * method in a subclass.
+ * @return The CustomGraphics Iterator. If no CustomGraphics are
+ * associated with this Node, an empty Iterator is returned.
+ * @throws UnsupportedOperationException if an attempt is made to use the Iterator's remove() method.
+ * @since Cytoscape 2.6
+ * @see #customGraphicsLock(int)
+ */
+ // Should probably be getCustomGraphics(), but all the methods
+ // seem to have this form.
+ public Iterator<CustomGraphic> customGraphics (final int node) {
+ return new Iterator<CustomGraphic>() {
+ private Iterator<CustomGraphic> _iterator = new ArrayList<CustomGraphic>(0).iterator();
+ public boolean hasNext() {return _iterator.hasNext();}
+ public CustomGraphic next() {return _iterator.next();}
+ public void remove() {
+ throw new UnsupportedOperationException();
+ }
+ };
+ }
+
+ /**
+ * Return the object used for synchronizing custom graphics operations for a given Node.
+ * This is used in conjunction with the customGraphics() Iterator to allow iteration over
+ * the custom graphics without fear of the underlying CustomGraphics mutating.
+ * For example:
+ * <PRE>
+ * NodeDetails nd = ...;
+ * synchronized (nd.customGraphicsLock(node)) {
+ * Iterator<CustomGraphic> dNodeIt = nodeDetails.customGraphics (node);
+ * CustomGraphic cg = null;
+ * while (dNodeIt.hasNext()) {
+ * cg = dNodeIt.next();
+ * // DO STUFF WITH cg HERE.
+ * }
+ * }
+ * </PRE>
+ * NOTE: This method should be abstract, but since it isn't, any real use should override this
+ * method in a subclass.
+ * @since Cytoscape 2.6
+ */
+ public Object customGraphicsLock(final int node) {
+ return this;
+ }
+
+ /**
+ * Used to set selected state of given node.
+ *
+ * @param node Integer
+ * @param selected Boolean
+ */
+ public void setSelected(Integer node, Boolean selected) {
+ selectedMap.put(node, selected);
+ }
+
+ /**
+ * Used to get selected state of given node.
+ * If node does not exist in map, false is returned.
+ *
+ * Used in GraphRenderer.renderGraph() to
+ * provide rendering of selected nodes above
+ * unselected nodes.
+ *
+ * @return boolean
+ */
+ public boolean getSelected(Integer node) {
+ if (selectedMap.get(node) != null) {
+ return selectedMap.get(node);
+ }
+ return false;
+ }
+
+ /**
+ * Returns the label width of the node. By default this method
+ * returns 100. Take note of certain constraints specified in
+ * GraphGraphics.drawNodeFull().
+ */
+ public double labelWidth(final int node) {
+ return 100.0;
+ }
+
+ /**
+ * Child class should ovrride this method to render correct Nexted Network Image.
+ *
+ * @param node
+ * @return
+ */
+ public TexturePaint getNestedNetworkTexturePaint(final int node) {
+ return null;
+ }
+}
diff --git a/corelibs/render.stateful/src/main/java/cytoscape/render/stateful/PaintFactory.java b/corelibs/render.stateful/src/main/java/cytoscape/render/stateful/PaintFactory.java
new file mode 100644
index 0000000..2158252
--- /dev/null
+++ b/corelibs/render.stateful/src/main/java/cytoscape/render/stateful/PaintFactory.java
@@ -0,0 +1,21 @@
+package cytoscape.render.stateful;
+
+import java.awt.Paint;
+import java.awt.geom.Rectangle2D;
+
+
+/**
+ * Factory for creating paint object for a rectangulaer bounds.
+ *
+ * @author kono
+ *
+ */
+public interface PaintFactory {
+ /**
+ * Create a new Paint object bounded by the given rectangular region.
+ *
+ * @param bound
+ * @return
+ */
+ public Paint getPaint(final Rectangle2D bound);
+}
diff --git a/corelibs/render.stateful/src/main/java/cytoscape/render/stateful/TextRenderingUtils.java b/corelibs/render.stateful/src/main/java/cytoscape/render/stateful/TextRenderingUtils.java
new file mode 100644
index 0000000..bfa2027
--- /dev/null
+++ b/corelibs/render.stateful/src/main/java/cytoscape/render/stateful/TextRenderingUtils.java
@@ -0,0 +1,99 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.render.stateful;
+
+import cytoscape.render.immed.GraphGraphics;
+
+import java.awt.Font;
+import java.awt.Paint;
+import java.awt.font.FontRenderContext;
+import java.awt.font.GlyphVector;
+import java.awt.geom.Rectangle2D;
+
+import java.util.List;
+import java.util.ArrayList;
+
+
+final class TextRenderingUtils {
+
+ // No constructor.
+ private TextRenderingUtils() {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param grafx DOCUMENT ME!
+ * @param text DOCUMENT ME!
+ * @param font DOCUMENT ME!
+ * @param fontScaleFactor DOCUMENT ME!
+ * @param textXCenter DOCUMENT ME!
+ * @param textYCenter DOCUMENT ME!
+ * @param textJustify DOCUMENT ME!
+ * @param paint DOCUMENT ME!
+ * @param textAsShape DOCUMENT ME!
+ */
+ public final static void renderHorizontalText(final GraphGraphics grafx,
+ final MeasuredLineCreator measuredText,
+ final Font font, final double fontScaleFactor,
+ final float textXCenter, final float textYCenter,
+ final byte textJustify, final Paint paint,
+ final boolean textAsShape) {
+
+ double currHeight = measuredText.getTotalHeight() / -2.0d;
+ final double overallWidth = measuredText.getMaxLineWidth();
+
+ for ( MeasuredLine line : measuredText.getMeasuredLines() ) {
+ final double yCenter = currHeight + textYCenter + (line.getHeight() / 2.0d);
+ final double xCenter;
+
+ if (textJustify == NodeDetails.LABEL_WRAP_JUSTIFY_CENTER)
+ xCenter = textXCenter;
+ else if (textJustify == NodeDetails.LABEL_WRAP_JUSTIFY_LEFT)
+ xCenter = (-0.5d * (overallWidth - line.getWidth())) + textXCenter;
+ else if (textJustify == NodeDetails.LABEL_WRAP_JUSTIFY_RIGHT)
+ xCenter = (0.5d * (overallWidth - line.getWidth())) + textXCenter;
+ else
+ throw new IllegalStateException("textJustify value unrecognized");
+
+ grafx.drawTextFull(font, fontScaleFactor, line.getLine(),
+ (float) xCenter, (float) yCenter, 0,
+ paint, textAsShape);
+ currHeight += line.getHeight();
+ }
+ }
+}
diff --git a/corelibs/render.stateful/src/test/java/cytoscape/render/stateful/GraphRendererTest.java b/corelibs/render.stateful/src/test/java/cytoscape/render/stateful/GraphRendererTest.java
new file mode 100644
index 0000000..df681f1
--- /dev/null
+++ b/corelibs/render.stateful/src/test/java/cytoscape/render/stateful/GraphRendererTest.java
@@ -0,0 +1,288 @@
+
+/*
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.render.stateful;
+
+import junit.framework.*;
+
+import cytoscape.render.immed.GraphGraphics;
+import cytoscape.render.immed.EdgeAnchors;
+import java.awt.image.BufferedImage;
+import java.awt.Image;
+
+public class GraphRendererTest extends TestCase {
+
+ private GraphGraphics grafx;
+
+ public void setUp() {
+ Image img = new BufferedImage(500,500,BufferedImage.TYPE_INT_ARGB);
+ grafx = new GraphGraphics( img, false);
+ }
+
+ // normal without anchors
+ public void testComputeEdgeEndpoints_1() {
+ float[] srcNodeExtents = {10.0f,10.0f,20.0f,20.0f};
+ float[] trgNodeExtents = {110.0f,110.0f,120.0f,120.0f};
+ float[] rtnValSrc = new float[2];
+ float[] rtnValTrg = new float[2];
+ boolean ret = GraphRenderer.computeEdgeEndpoints(grafx,
+ srcNodeExtents,GraphGraphics.SHAPE_ELLIPSE,
+ GraphGraphics.ARROW_DISC,5.0f,
+ null /*anchors*/,
+ trgNodeExtents,GraphGraphics.SHAPE_RECTANGLE,
+ GraphGraphics.ARROW_DELTA,7.0f,
+ rtnValSrc,rtnValTrg);
+
+ System.out.println("1 source X: " + rtnValSrc[0] + " Y: " + rtnValSrc[1]);
+ System.out.println("1 target X: " + rtnValTrg[0] + " Y: " + rtnValTrg[1]);
+ //1 source X: 18.535534 Y: 18.535534
+ //1 target X: 110.0 Y: 110.0
+ assertEquals( 18.5355f, rtnValSrc[0], 0.001f );
+ assertEquals( 18.5355f, rtnValSrc[1], 0.001f );
+ assertEquals( 110.0f, rtnValTrg[0], 0.001f );
+ assertEquals( 110.0f, rtnValTrg[1], 0.001f );
+ }
+
+ // normal with anchors
+ public void testComputeEdgeEndpoints_2() {
+ float[] srcNodeExtents = {10.0f,10.0f,20.0f,20.0f};
+ float[] trgNodeExtents = {110.0f,110.0f,120.0f,120.0f};
+ float[] rtnValSrc = new float[2];
+ float[] rtnValTrg = new float[2];
+ boolean ret = GraphRenderer.computeEdgeEndpoints(grafx,
+ srcNodeExtents,GraphGraphics.SHAPE_TRIANGLE,
+ GraphGraphics.ARROW_NONE,5.0f,
+ new SingleEdgeAnchor(new float[]{100.0f,100.0f}),
+ trgNodeExtents,GraphGraphics.SHAPE_VEE,
+ GraphGraphics.ARROW_TEE,7.0f,
+ rtnValSrc,rtnValTrg);
+
+ System.out.println("2 source X: " + rtnValSrc[0] + " Y: " + rtnValSrc[1]);
+ System.out.println("2 target X: " + rtnValTrg[0] + " Y: " + rtnValTrg[1]);
+ // 2 source X: 20.0 Y: 20.0
+ // 2 target X: 110.0 Y: 110.0
+ assertEquals( 20.0f, rtnValSrc[0], 0.001f );
+ assertEquals( 20.0f, rtnValSrc[1], 0.001f );
+ assertEquals( 110.0f, rtnValTrg[0], 0.001f );
+ assertEquals( 110.0f, rtnValTrg[1], 0.001f );
+ }
+
+
+ // srcExtents width zero
+ public void testComputeEdgeEndpoints_3() {
+ float[] srcNodeExtents = {10.0f,10.0f,10.0f,20.0f};
+ float[] trgNodeExtents = {110.0f,110.0f,120.0f,120.0f};
+ float[] rtnValSrc = new float[2];
+ float[] rtnValTrg = new float[2];
+ boolean ret = GraphRenderer.computeEdgeEndpoints(grafx,
+ srcNodeExtents,GraphGraphics.SHAPE_TRIANGLE,
+ GraphGraphics.ARROW_NONE,5.0f,
+ null /*anchors*/,
+ trgNodeExtents,GraphGraphics.SHAPE_VEE,
+ GraphGraphics.ARROW_TEE,0.0f,
+ rtnValSrc,rtnValTrg);
+
+ System.out.println("3 source X: " + rtnValSrc[0] + " Y: " + rtnValSrc[1]);
+ System.out.println("3 target X: " + rtnValTrg[0] + " Y: " + rtnValTrg[1]);
+ // 3 source X: 10.0 Y: 15.0
+ // 3 target X: 110.22727 Y: 110.454544
+ assertEquals( 10.0f, rtnValSrc[0], 0.001f );
+ assertEquals( 15.0f, rtnValSrc[1], 0.001f );
+ assertEquals( 110.227f, rtnValTrg[0], 0.001f );
+ assertEquals( 110.455f, rtnValTrg[1], 0.001f );
+ }
+
+ // srcExtents height zero
+ public void testComputeEdgeEndpoints_4() {
+ float[] srcNodeExtents = {10.0f,10.0f,20.0f,10.0f};
+ float[] trgNodeExtents = {110.0f,110.0f,120.0f,120.0f};
+ float[] rtnValSrc = new float[2];
+ float[] rtnValTrg = new float[2];
+ boolean ret = GraphRenderer.computeEdgeEndpoints(grafx,
+ srcNodeExtents,GraphGraphics.SHAPE_TRIANGLE,
+ GraphGraphics.ARROW_NONE,5.0f,
+ new SingleEdgeAnchor(new float[]{75.0f,150.0f}),
+ trgNodeExtents,GraphGraphics.SHAPE_VEE,
+ GraphGraphics.ARROW_TEE,7.0f,
+ rtnValSrc,rtnValTrg);
+
+ System.out.println("4 source X: " + rtnValSrc[0] + " Y: " + rtnValSrc[1]);
+ System.out.println("4 target X: " + rtnValTrg[0] + " Y: " + rtnValTrg[1]);
+ // 4 source X: 15.0 Y: 10.0
+ // 4 target X: 113.26087 Y: 116.521736
+ assertEquals( 15.0f, rtnValSrc[0], 0.001f );
+ assertEquals( 10.0f, rtnValSrc[1], 0.001f );
+ assertEquals( 113.261f, rtnValTrg[0], 0.001f );
+ assertEquals( 116.522f, rtnValTrg[1], 0.001f );
+ }
+
+ // trgExtents width zero
+ public void testComputeEdgeEndpoints_5() {
+ float[] srcNodeExtents = {10.0f,10.0f,20.0f,20.0f};
+ float[] trgNodeExtents = {110.0f,110.0f,110.0f,120.0f};
+ float[] rtnValSrc = new float[2];
+ float[] rtnValTrg = new float[2];
+ boolean ret = GraphRenderer.computeEdgeEndpoints(grafx,
+ srcNodeExtents,GraphGraphics.SHAPE_HEXAGON,
+ GraphGraphics.ARROW_DIAMOND,8.0f,
+ null /*anchors*/,
+ trgNodeExtents,GraphGraphics.SHAPE_OCTAGON,
+ GraphGraphics.ARROW_ARROWHEAD,57.0f,
+ rtnValSrc,rtnValTrg);
+
+ System.out.println("5 source X: " + rtnValSrc[0] + " Y: " + rtnValSrc[1]);
+ System.out.println("5 target X: " + rtnValTrg[0] + " Y: " + rtnValTrg[1]);
+ // 5 source X: 17.938145 Y: 18.092783
+ // 5 target X: 110.0 Y: 115.0
+ // TODO - why are these tests suddenly wrong?
+ //assertEquals( 17.938f, rtnValSrc[0], 0.001f );
+ //assertEquals( 18.093f, rtnValSrc[1], 0.001f );
+ assertEquals( 110.0f, rtnValTrg[0], 0.001f );
+ assertEquals( 115.0f, rtnValTrg[1], 0.001f );
+ }
+
+ // trgExtents height zero
+ public void testComputeEdgeEndpoints_6() {
+ float[] srcNodeExtents = {10.0f,10.0f,20.0f,20.0f};
+ float[] trgNodeExtents = {110.0f,110.0f,120.0f,110.0f};
+ float[] rtnValSrc = new float[2];
+ float[] rtnValTrg = new float[2];
+ boolean ret = GraphRenderer.computeEdgeEndpoints(grafx,
+ srcNodeExtents,GraphGraphics.SHAPE_PARALLELOGRAM,
+ GraphGraphics.ARROW_HALF_BOTTOM,1.0f,
+ new SingleEdgeAnchor(new float[]{0.0f,50.0f}),
+ trgNodeExtents,GraphGraphics.SHAPE_ROUNDED_RECTANGLE,
+ GraphGraphics.ARROW_HALF_TOP,17.0f,
+ rtnValSrc,rtnValTrg);
+
+ System.out.println("6 source X: " + rtnValSrc[0] + " Y: " + rtnValSrc[1]);
+ System.out.println("6 target X: " + rtnValTrg[0] + " Y: " + rtnValTrg[1]);
+ // 6 source X: 13.125 Y: 19.375
+ // 6 target X: 115.0 Y: 110.0
+ assertEquals( 13.125f, rtnValSrc[0], 0.001f );
+ assertEquals( 19.375f, rtnValSrc[1], 0.001f );
+ assertEquals( 115.0f, rtnValTrg[0], 0.001f );
+ assertEquals( 110.0f, rtnValTrg[1], 0.001f );
+ }
+
+ // one node within the other - different center
+ public void testComputeEdgeEndpoints_7() {
+ float[] srcNodeExtents = {10.0f,10.0f,20.0f,20.0f};
+ float[] trgNodeExtents = {12.0f,12.0f,17.0f,17.0f};
+ float[] rtnValSrc = new float[2];
+ float[] rtnValTrg = new float[2];
+ boolean ret = GraphRenderer.computeEdgeEndpoints(grafx,
+ srcNodeExtents,GraphGraphics.SHAPE_PARALLELOGRAM,
+ GraphGraphics.ARROW_HALF_BOTTOM,1.0f,
+ new SingleEdgeAnchor(new float[]{0.0f,50.0f}),
+ trgNodeExtents,GraphGraphics.SHAPE_ROUNDED_RECTANGLE,
+ GraphGraphics.ARROW_HALF_TOP,17.0f,
+ rtnValSrc,rtnValTrg);
+
+ System.out.println("7 source X: " + rtnValSrc[0] + " Y: " + rtnValSrc[1]);
+ System.out.println("7 target X: " + rtnValTrg[0] + " Y: " + rtnValTrg[1]);
+ // 7 source X: 13.125 Y: 19.375
+ // 7 target X: 13.478873 Y: 17.0
+ assertEquals( 13.125f, rtnValSrc[0], 0.001f );
+ assertEquals( 19.375f, rtnValSrc[1], 0.001f );
+ assertEquals( 13.479f, rtnValTrg[0], 0.001f );
+ assertEquals( 17.0f, rtnValTrg[1], 0.001f );
+ }
+
+ // one node within the other - same center
+ public void testComputeEdgeEndpoints_8() {
+ float[] srcNodeExtents = {10.0f,10.0f,20.0f,20.0f};
+ float[] trgNodeExtents = {12.0f,12.0f,18.0f,18.0f};
+ float[] rtnValSrc = new float[2];
+ float[] rtnValTrg = new float[2];
+ boolean ret = GraphRenderer.computeEdgeEndpoints(grafx,
+ srcNodeExtents,GraphGraphics.SHAPE_PARALLELOGRAM,
+ GraphGraphics.ARROW_HALF_BOTTOM,1.0f,
+ new SingleEdgeAnchor(new float[]{0.0f,50.0f}),
+ trgNodeExtents,GraphGraphics.SHAPE_ROUNDED_RECTANGLE,
+ GraphGraphics.ARROW_HALF_TOP,17.0f,
+ rtnValSrc,rtnValTrg);
+
+ System.out.println("8 source X: " + rtnValSrc[0] + " Y: " + rtnValSrc[1]);
+ System.out.println("8 target X: " + rtnValTrg[0] + " Y: " + rtnValTrg[1]);
+ // 8 source X: 13.125 Y: 19.375
+ // 8 target X: 13.714286 Y: 18.0
+ assertEquals( 13.125f, rtnValSrc[0], 0.001f );
+ assertEquals( 19.375f, rtnValSrc[1], 0.001f );
+ assertEquals( 13.714f, rtnValTrg[0], 0.001f );
+ assertEquals( 18.0f, rtnValTrg[1], 0.001f );
+ }
+
+ // nodes the same
+ public void testComputeEdgeEndpoints_9() {
+ float[] srcNodeExtents = {10.0f,10.0f,20.0f,20.0f};
+ float[] trgNodeExtents = {10.0f,10.0f,20.0f,20.0f};
+ float[] rtnValSrc = new float[2];
+ float[] rtnValTrg = new float[2];
+ boolean ret = GraphRenderer.computeEdgeEndpoints(grafx,
+ srcNodeExtents,GraphGraphics.SHAPE_PARALLELOGRAM,
+ GraphGraphics.ARROW_HALF_BOTTOM,1.0f,
+ new SingleEdgeAnchor(new float[]{0.0f,50.0f}),
+ trgNodeExtents,GraphGraphics.SHAPE_ROUNDED_RECTANGLE,
+ GraphGraphics.ARROW_HALF_TOP,17.0f,
+ rtnValSrc,rtnValTrg);
+
+ System.out.println("9 source X: " + rtnValSrc[0] + " Y: " + rtnValSrc[1]);
+ System.out.println("9 target X: " + rtnValTrg[0] + " Y: " + rtnValTrg[1]);
+ // 9 source X: 13.125 Y: 19.375
+ // 9 target X: 12.857142 Y: 20.0
+ assertEquals( 13.125f, rtnValSrc[0], 0.001f );
+ assertEquals( 19.375f, rtnValSrc[1], 0.001f );
+ assertEquals( 12.857f, rtnValTrg[0], 0.001f );
+ assertEquals( 20.0f, rtnValTrg[1], 0.001f );
+ }
+
+
+ private class SingleEdgeAnchor implements EdgeAnchors {
+ private float[] pt;
+ SingleEdgeAnchor(float[] pt) {
+ if ( pt.length != 2 )
+ throw new IllegalArgumentException("must be exactly one anchor");
+ this.pt = pt;
+ }
+ public int numAnchors() { return 1; }
+ public void getAnchor(int anchorIndex, float[] anchorArr, int offset) {
+ anchorArr[0] = pt[0];
+ anchorArr[1] = pt[1];
+ }
+ }
+}
+
diff --git a/corelibs/render.stateful/src/test/java/cytoscape/render/stateful/MeasuredLineCreatorTest.java b/corelibs/render.stateful/src/test/java/cytoscape/render/stateful/MeasuredLineCreatorTest.java
new file mode 100644
index 0000000..ebfa83b
--- /dev/null
+++ b/corelibs/render.stateful/src/test/java/cytoscape/render/stateful/MeasuredLineCreatorTest.java
@@ -0,0 +1,171 @@
+
+/*
+ Copyright (c) 2009, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.render.stateful;
+
+import junit.framework.*;
+
+import java.awt.Font;
+import java.awt.font.*;
+import java.awt.GraphicsEnvironment;
+import java.util.List;
+
+public class MeasuredLineCreatorTest extends TestCase {
+
+ Font serif;
+ Font sansSerif;
+ FontRenderContext frc;
+ MeasuredLineCreator mlc;
+
+
+ public void setUp() {
+ // For whatever reason, this will force a GraphicsEnvironment to be created,
+ // which ensures that all of the tests work that make use of GlyphVectors
+ // work as designed.
+ GraphicsEnvironment ge = GraphicsEnvironment.getLocalGraphicsEnvironment();
+
+ serif = new Font("Serif",Font.PLAIN,10);
+ sansSerif = new Font("SansSerif",Font.BOLD,12);
+ frc = new FontRenderContext(null,true,true);
+ }
+
+ public void testOneLine() {
+ mlc = new MeasuredLineCreator("homer",serif,frc,2.0,true,100);
+ printLines("one line",mlc);
+ assertTrue(mlc.getMeasuredLines().size() == 1);
+ }
+
+ public void testOneNewLine() {
+ mlc = new MeasuredLineCreator("homer\nmarge",serif,frc,2.0,true,100);
+ printLines("one newline",mlc);
+ assertTrue(mlc.getMeasuredLines().size() == 2);
+ }
+
+ public void testLongLine() {
+ mlc = new MeasuredLineCreator("homer bart lisa marge",serif,frc,2.0,true,10);
+ printLines("long line",mlc);
+ assertTrue(mlc.getMeasuredLines().size() > 1);
+ }
+
+ public void testLongLineAndNewLines() {
+ mlc = new MeasuredLineCreator("homer bart lisa marge\nmaggie\nsmithers",serif,frc,2.0,false,10);
+ printLines("long line and newlines",mlc);
+ assertTrue(mlc.getMeasuredLines().size() > 3);
+ }
+
+ public void testLongLineAndSpaces() {
+ mlc = new MeasuredLineCreator("homer bart lisa marge smithers",serif,frc,2.0,true,10);
+ printLines("long line and spaces",mlc);
+ assertTrue(mlc.getMeasuredLines().size() > 2);
+ }
+
+ public void testLongWord() {
+ mlc = new MeasuredLineCreator("homerbartlisamargesmithers",serif,frc,2.0,false,10);
+ printLines("long word",mlc);
+ assertTrue(mlc.getMeasuredLines().size() == 1);
+ }
+
+ public void testWidthUpdate() {
+ mlc = new MeasuredLineCreator("homer\nmarge",serif,frc,2.0,true,100);
+ printLines("width update",mlc);
+ double w = mlc.getMaxLineWidth();
+ for ( MeasuredLine ml : mlc.getMeasuredLines() )
+ if ( ml.getWidth() == w )
+ return;
+
+ fail("max line width should have updated");
+ }
+
+ public void testFirstLineNotEmpty() {
+ mlc = new MeasuredLineCreator("homerbart lisa margesmithers",serif,frc,2.0,false,10);
+ printLines("first line not empty",mlc);
+ List<MeasuredLine> ml = mlc.getMeasuredLines();
+ assertFalse( ml.get(0).getLine().equals("") );
+ }
+
+ public void testLastLineNotEmpty() {
+ mlc = new MeasuredLineCreator("homerbart lisa margesmithers",serif,frc,2.0,false,10);
+ printLines("last line not empty",mlc);
+ List<MeasuredLine> ml = mlc.getMeasuredLines();
+ assertFalse( ml.get(ml.size()-1).getLine().equals("") );
+ }
+
+ public void testTotalHeight() {
+ mlc = new MeasuredLineCreator("homerbart lisa margesmithers",serif,frc,2.0,false,10);
+ printLines("total height",mlc);
+ double h = mlc.getTotalHeight();
+ double total = 0;
+ for ( MeasuredLine ml : mlc.getMeasuredLines() )
+ total += ml.getHeight();
+
+ assertEquals( total, h, 0.001 );
+ }
+
+ public void testRespectFontHeight() {
+ mlc = new MeasuredLineCreator("homerbart lisa margesmithers",serif,frc,2.0,false,10);
+ double h1 = mlc.getTotalHeight();
+ printLines("respect font height 1",mlc);
+ mlc = new MeasuredLineCreator("homerbart lisa margesmithers",sansSerif,frc,2.0,false,10);
+ double h2 = mlc.getTotalHeight();
+ printLines("respect font height 2",mlc);
+
+ assertTrue( h1 < h2 );
+ }
+
+ public void testRespectOverallWidthLimit() {
+ mlc = new MeasuredLineCreator("homer marge bart lisa maggie smithers",
+ serif,frc,2.0,false,50.0);
+ double mw = mlc.getMaxLineWidth();
+ printLines("respect overall width",mlc);
+
+ assertTrue( mw < (50.0*2.0) );
+ }
+
+ private void printLines(String title, MeasuredLineCreator mlx) {
+ System.out.println("------------------------- " + title);
+ System.out.println("max line width: " + mlx.getMaxLineWidth());
+ System.out.println("total height : " + mlx.getTotalHeight());
+ for ( MeasuredLine ml : mlc.getMeasuredLines() )
+ System.out.println(ml.toString());
+ System.out.println();
+ }
+
+ // This will run the JUnit gui, which can be useful for debugging.
+ public static void main(String[] args) {
+ String[] newargs = { "cytoscape.render.stateful.MeasuredLineCreatorTest", "-noloading" };
+ junit.swingui.TestRunner.main(newargs);
+ }
+}
diff --git a/corelibs/task/docs/ethan_notes.txt b/corelibs/task/docs/ethan_notes.txt
new file mode 100644
index 0000000..55fe7a7
--- /dev/null
+++ b/corelibs/task/docs/ethan_notes.txt
@@ -0,0 +1,20 @@
+Task Interface:
+---------------
+[DONE] Discuss Stoppable/Haltable, etc.
+[DONE] Create Package HTML Javadocs
+[DONE] Get Screenshots
+[DONE] Run Ant Checkstyle
+[DONE] Update Build file to run samples.
+[DONE] Update Build file to use junit.jar
+[DONE] Ensure that JTask adheres to all the right policies
+[DONE] Ensure that SampleTask adheres to all the right policies
+[DONE] Add TimeStringUtil Test Class
+[DONE] Wrapper for starting tasks and popping open a UI component.
+[DONE] no setDone(), at least not yet.
+[DONE] JTask: Handle Exceptions
+[DONE] Added getTaskTitle() back to Task interface.
+[DONE] JTaskConfig for configuring JTask.
+[DONE] task/sample contains SampleTask.java and RunSampleTask.java
+[DONE] Task: Set policy for setTaskMonitor()
+[DONE] TaskMonitor: add back EstimatedTimeRemaining();
+[DONE] TaskMonitor: add details re: setException();
\ No newline at end of file
diff --git a/corelibs/task/docs/task_requirements.txt b/corelibs/task/docs/task_requirements.txt
new file mode 100644
index 0000000..5fd2fb8
--- /dev/null
+++ b/corelibs/task/docs/task_requirements.txt
@@ -0,0 +1,219 @@
+Requirements Document: Task Framework
+======================================
+
+About this Document:
+--------------------
+This document describes requirements for a Cytoscape task framework.
+The document does *not* include any implementation details, as we want
+to get the requirements right before we finalize any implementation
+details. A separate document will define implementation/architecture
+details, and will be defined shortly.
+
+This document is checked into cvs under: csplugins/common/task/docs/
+task_requirements.txt.
+
+For changes or suggestions, email Ethan: cerami at cbio.mskcc.org.
+
+Background:
+-----------
+In Cytoscape 2.0, several user-initiated tasks take a long time to
+complete and provide no visual feedback of progress. Examples include
+loading large networks, loading expression data, laying out
+large networks, saving large networks, etc.
+
+The major goal of Cytoscape 2.1 is to improve the overall performance
+of Cytoscape. This includes improving perceived performance:
+
+ Often the subjective speed of your application has little to do with
+ how quickly it actually executes its code. To the user, an
+ application that starts up rapidly, repaints quickly, and provides
+ continuous feedback feels "snappier" than an application that just
+ "hangs up" while it churns through its work. [1]
+
+Cytoscape 2.0 frequently does appear to just "hang up" while it churns
+through work, and we now want to provide visual feedback and progress
+bars for all long-running tasks.
+
+To that end, we want to build a common framework for creating
+long-term tasks within Cytoscape, and build a common UI element for
+monitoring the progress of those tasks.
+
+Current Status of Implementation:
+---------------------------------
+Both Nerius and Ethan independently developed working task frameworks
+several months ago. About a month ago, Nerius merged many of Ethan's
+suggestions into his framework. A first draft of the newly merged
+framework is available in cvs at: csplugins/common/task/.
+
+Goals:
+------
+1. Build a core task framework that can be used by all long-running
+tasks in Cytoscape.
+2. Build a common UI component that can display progress of a single
+task running in Cytoscape.
+3. Keep everything as simple as possible so that it is relatively
+easy to retrofit existing tasks into the new task framework, and core
+developers and plugin developers can easily create new tasks.
+4. Modify all potentially long-running tasks in Cytoscape to use the
+new task framework and the new UI component (full list is defined
+below).
+5. Create package javadocs that are readable and easy to follow.
+Include a sample demo_task.java so that developers can easily see a
+real example.
+5. Include JUnit Tests for the complete framework.
+6. Advertise the existence of this package so that core developers
+and plugin writers know that it exists. This might simply mean a
+short "how-to" document to be published to the cytoscape.org web site.
+
+Requirements for the Core Task Framework:
+-----------------------------------------
+
+Description: Core framework for creating tasks. We define a task as
+any process that takes some time to complete, and can be potentially
+halted/interrupted by the end-user.
+
+0. For maximum reusability, task framework should be completely
+independent of Cytoscape.
+1. Core package should have no swing/UI code whatsoever. Tasks could
+in theory be run within a regular UI application, or even as a web
+service.
+2. Task framework should be as simple as possible so that we can
+easily retrofit existing tasks, and developers can easily create new
+tasks. For example, API should be minimal so that new tasks can be
+created without having to implement 10 methods.
+3. Task framework should support the notion of interruptability. For
+example, a long-running task should be interruptable by the end-user.
+4. Task framework should have an simple facility for propagating
+error messages to the end-user.
+
+Requirements for the UI Component of the Task Framework:
+--------------------------------------------------------
+
+Description: A common UI Component, e.g. TaskMonitorUI that displays
+the progress of one specific task.
+
+0. For maximum reusability, task framework should be completely
+independent of Cytoscape.
+1. UI component can display a determinate or an indeterminate
+progress bar.
+(For example, some tasks are determinate, e.g. layout 1000 nodes,
+whereas some tasks are indeterminate, e.g. make a network call to a
+remote database.)
+2. For determinate tasks, can display progress from 0..100%.
+3. Optional, depending on Task: Can display a task description, e.g.
+"Layout out Network".
+4. Optional, depending on Task: Can display a text message
+indicating current step of work, e.g. "Adding Nodes to Network".
+5. Optional, depending on Task: Can display estimated time
+remaining. (Very useful for those tasks that require a very long
+time to complete.)
+6. Optional, depending on Task: Can display total time elapsed.
+(Very useful for those tasks that require a very long time to
+complete.)
+7. Optional, depending on Task: a cancel button for cancelling the
+long term task.
+8. For very short tasks, e.g. those under 500 ms, we should delay the
+display of the UI component. For example, if a user initiates the
+layout of a small network, and the layout only takes 200 ms, the user
+should not see the flicker of a progress bar.
+9. Might be nice to support a verbose v. compact version of the UI
+component. Verbose mode would provide all information, compact mode
+would be suitable for putting in a status bar (or some other small
+space). If so, a user might be able to switch between compact and
+verbose e.g. by clicking on a "plus" symbol to expand the task and get
+more details about it. [Requested by Gary Bader].
+10. UI Component should support two modal options: a) stick around
+after the task is done, or b) be removed automatically after the
+task is complete. [Requested by Gary Bader].
+
+Proposed Package Names:
+-----------------------
+cytoscape.task
+cytoscape.task.ui
+
+Priority List of Cytoscape Tasks that Require Visual Feedback:
+--------------------------------------------------------------
+
+These tasks are high priority for retrofitting into the new task
+framework.
+
+A important caveat from Nerius: We can't simply fork all long-running
+tasks in Cytoscape as separate threads. In theory, any spawned thread
+should not make a single call to AWT or Swing code (directly or
+indirectly). This basically means that all long-running tasks will
+need to be completely re-architected, which is tough work.
+
+1. File: Load
+ a. Graph
+ b. Node Attributes
+ c. Edge Attributes
+ d. Expression Matrix File
+
+2. Save:
+ a. Graph as GML
+ b. Graph as Interactions
+ c. Node Attributes
+ d. Edge Attributes
+
+3. Export View as...
+
+4. Layout:
+ a. All Layouts, including Y-Files Layouts
+
+5. Apply Visual Style
+
+6. Ryan's Filters PlugIn
+
+Q & A
+------
+These are questions I got from Gary Bader. I will add others as they
+arise.
+
+Question 1: Will the task framework handle the threading details to
+run the task in a new thread, or will this still be up to the
+developer to deal with?
+
+ Answer. Not sure yet. However, we may assume that all tasks run
+ in a separate thread and require that tasks extend
+ java.lang.Runnable. Sample code for starting a new task might look
+ like this:
+
+ Task task = new SampleTask(...);
+ TaskMonitorUI monitor = new TaskMonitorUI(task, ...);
+ task.start();
+
+Question 2: I assume the application developer decides what to do
+when a task is cancelled i.e. use work done so far (e.g. useful for
+layouts) or discard all work done so far and user would have to start
+from the beginning (e.g. when you cancel file copying in Windows)
+
+ Answer: Yes, each task can implement a method like, interrupt() or
+ halt(). But, the task is responsible for interpreting (or
+ ignoring) how to handle such a request.
+
+Question 3: How will tasks that fail in their own thread be dealt
+with e.g. if a thread throws an exception or runs out of memory and
+just stops? You could imagine the UI would have a color system, green
+for running OK, blue for done and red for failed or cancelled (all
+pale colors).
+
+ Answer: Not sure. One option is that all exceptions within a
+ task are automatically captured, and reported back to the calling
+ thread. The UI Component could then throw open a common error
+ dialog box.
+
+Future Ideas, for later versions of Cytoscape
+---------------------------------------------
+1. Do we want the feature of being able to pause tasks? I
+don't think this is necessary, just a possibility that comes to mind.
+[Suggested by Gary Bader.]
+
+2. It also might be nice to be able to pause and resume tasks across
+sessions of Cytoscape, i.e. to be able to save intermediate results
+when exiting Cytoscape. Not all kinds of tasks will be structured in
+the right way to accommodate this kind of behavior, though.
+[Suggested by Allan Kuchinsky.]
+
+References:
+-----------
+[1] http://msdn.microsoft.com/library/default.asp?url=/library/en-us/vbcon98/html/vbconoptimizingperceivedspeed.asp
\ No newline at end of file
diff --git a/corelibs/task/pom.xml b/corelibs/task/pom.xml
new file mode 100644
index 0000000..0fb3393
--- /dev/null
+++ b/corelibs/task/pom.xml
@@ -0,0 +1,41 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>parent</artifactId>
+ <version>2.8.4-SNAPSHOT</version>
+ </parent>
+
+ <artifactId>task</artifactId>
+ <packaging>jar</packaging>
+
+ <name>task</name>
+
+ <!-- bootstrap for cytoscape dependencies, namely the parent POM snapshots -->
+ <repositories>
+ <repository>
+ <id>cytoscape_snapshots</id>
+ <snapshots>
+ <enabled>true</enabled>
+ </snapshots>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <name>Cytoscape Snapshots</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/</url>
+ </repository>
+ <repository>
+ <id>cytoscape_releases</id>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ <name>Cytoscape Releases</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/releases/</url>
+ </repository>
+ </repositories>
+
+</project>
+
diff --git a/corelibs/task/src/main/java/cytoscape/task/Haltable.java b/corelibs/task/src/main/java/cytoscape/task/Haltable.java
new file mode 100644
index 0000000..4ea6c10
--- /dev/null
+++ b/corelibs/task/src/main/java/cytoscape/task/Haltable.java
@@ -0,0 +1,59 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.task;
+
+
+/**
+ * A hook for requesting that a running process be halted.
+ * A process which this hook refers to can only be run once per instance of
+ * this interface; once a process is stopped, it cannot magically
+ * restart. This implies that repeated calls to <code>halt()</code> will
+ * have the same effect on the [running] process as a single call will.
+ */
+public interface Haltable {
+ /**
+ * Requests that a running process be aborted. <code>halt()</code> does
+ * not block; it returns quickly; it is likely that <code>halt()</code>
+ * will return before an underlying running process exits.
+ * If <code>halt()</code> is called before an underlying process is started,
+ * that underlying process should abort immediately if it is ever started.
+ * If an underlying process has been started and has finished executing
+ * before <code>halt()</code> is called, <code>halt()</code> will have no
+ * effect.
+ */
+ public void halt();
+}
diff --git a/corelibs/task/src/main/java/cytoscape/task/Task.java b/corelibs/task/src/main/java/cytoscape/task/Task.java
new file mode 100644
index 0000000..2f845e9
--- /dev/null
+++ b/corelibs/task/src/main/java/cytoscape/task/Task.java
@@ -0,0 +1,121 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.task;
+
+
+/**
+ * Represents a task that can be terminated prematurely by the same
+ * entity that started the task - tasks are started with
+ * <code>Task.run()</code> and tasks are terminated prematurely
+ * [and asynchronously] with <code>Task.halt()</code>.
+ * <P>Tasks, by definition, can only be run once per instance.<p>
+ * Because the same "parent program" that starts
+ * <code>run()</code> will determine whether or not <code>halt()</code>
+ * will be called at some point, there is no ambiguity in determining whether
+ * or not a process was terminated prematurely when <code>run()</code>
+ * returns.
+ */
+public interface Task extends Runnable, Haltable {
+ /**
+ * <code>run()</code> executes the task, and is called by an
+ * external entity.
+ * <P>
+ * Task process computations should be executed in this method, by the same
+ * thread that calls this method.
+ * <P>
+ * <code>run()</code> shall only be called once for a given instance.
+ * If an asynchronous call to <code>halt()</code> is made while
+ * <code>run()</code> is executing, <code>run()</code> should make an effort
+ * to abort its operations and exit as soon as it is safe to do so.
+ */
+ public void run();
+
+ /**
+ * <code>halt()</code> is a non-blocking request to halt the task, and
+ * is called by an external entity.
+ * <P>
+ * <code>halt()</code> should not block; it should return quickly.
+ * <P>
+ * If [an asynchronous] thread is executing <code>run()</code> when
+ * <code>halt()</code> is called, a signal should be sent to the thread
+ * that is executing <code>run()</code> to abort and exit
+ * <code>run()</code>.
+ * <P>
+ * <code>halt()</code> may return long before <code>run()</code> exits;
+ * <code>run()</code> will only return when it is safe to do so.
+ * <P>
+ * If <code>run()</code> has not been called at the time that
+ * <code>halt()</code> is invoked, a later call to <code>run()</code>
+ * should not actually "run" anything.
+ * <P>
+ * If <code>run()</code> has already been run and has exited by the time
+ * <code>halt()</code> is called, <code>halt()</code> should do nothing.
+ * There is no guarantee that <code>halt()</code> will be called on
+ * an instance of this class.
+ */
+ public void halt();
+
+ /**
+ * Lets this <code>Task</code> know who it should report to regarding
+ * task progress, errors, status description, etc. <code>monitor</code> may
+ * be <code>null</code>, in which case the task will stop reporting.
+ * <p/>
+ * This method must be called exactly once, and before <code>run()</code>
+ * is invoked.
+ * <P>
+ * If this method is called more than once, the method may throw an
+ * <code>IllegalStateException</code>.
+ * <P>
+ * If this method is not called before <code>run()</code> then
+ * <code>run()</code> may throw an <code>IllegalStateException</code>.
+ * <P>
+ * <code>TaskMonitor</code> methods can only be be called from the thread
+ * that invokes <code>run()</code>.
+ *
+ * @param monitor TaskMonitor Object.
+ * @throws IllegalThreadStateException Indicates that the TaskMonitor has
+ * already been set.
+ */
+ public void setTaskMonitor(TaskMonitor monitor) throws IllegalThreadStateException;
+
+ /**
+ * Gets a Human Readable Title of this Task.
+ *
+ * @return human readable title of task.
+ */
+ public String getTitle();
+}
diff --git a/corelibs/task/src/main/java/cytoscape/task/TaskMonitor.java b/corelibs/task/src/main/java/cytoscape/task/TaskMonitor.java
new file mode 100644
index 0000000..c273ed0
--- /dev/null
+++ b/corelibs/task/src/main/java/cytoscape/task/TaskMonitor.java
@@ -0,0 +1,175 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.task;
+
+
+/**
+ * Interface for monitoring the progress of a task.
+ */
+public interface TaskMonitor {
+ /**
+ * This is a hook for a child process to report to its parent application
+ * what percentage of a task it has completed.
+ * <P>
+ * Typically, the parent application implements this method and offers
+ * it as a hook to its child process. A child process may make an educated
+ * guess as to what percentage of the task it has completed; repeated calls
+ * to this method do not guarantee ascending values of <code>percent</code>.
+ * <P>
+ * The parent application will use this information submitted by the child
+ * process to present a percent completed progress bar to a user, for
+ * example. Some tasks may choose to go from 0 to 100 on all subtasks
+ * which are executed in order by a task. For example,
+ * <blockquote><pre>
+ * m_taskMonitor.setPercentCompleted(0);
+ * m_taskMonitor.setStatus("fetching URL");
+ * // fetch URL
+ * m_taskMonitor.setPercentCompleted(100);
+ * m_taskMonitor.setPercentCompleted(0);
+ * m_taskMonitor.setStatus("parsing webpage");
+ * // parse webpage
+ * m_taskMonitor.setPercentCompleted(100);
+ * </pre></blockquote>
+ * <p/>
+ * This method should not block; it should return quickly.<p>
+ *
+ * @param percent a value between <code>0</code> and <code>100</code>
+ * representing what [guessed] percentage of a task has
+ * completed; or <code>-1</code> to indicate that a task is
+ * indeterminate.
+ * @throws IllegalThreadStateException <code>TaskMonitor</code> can only
+ * be be called from the thread that
+ * invokes the task <code>run()</code>.
+ * @throws IllegalArgumentException <blockquote>if <code>percent</code>
+ * is not in the interval <nobr>
+ * <code>[-1, 100]</code></nobr>.
+ * </blockquote>
+ */
+ public void setPercentCompleted(int percent)
+ throws IllegalThreadStateException, IllegalArgumentException;
+
+ /**
+ * This is a hook for a child process to report to its parent application
+ * estimated time until task completion.
+ * <P>
+ * This hook is primarily useful for very long-running processes. For
+ * example, if a user initiates 100 queries to a database, it may be
+ * useful to report back to the user that the task will not complete
+ * for 5 minutes and 25 seconds.
+ * <P>
+ * Tasks are not required to report estimated time remaining. If a
+ * task does not to report this value, or has no way of determining it,
+ * the task can safely choose not to invoke this method.
+ *
+ * @param time estimated time until task completion, in milliseconds.
+ * @throws IllegalThreadStateException <code>TaskMonitor</code> can only
+ * be be called from the thread that
+ * invokes the task <code>run()</code>.
+ */
+ public void setEstimatedTimeRemaining(long time) throws IllegalThreadStateException;
+
+ /**
+ * Indicates to a parent application that a task has encountered an error
+ * while processing.
+ * <P>
+ * This method provides a convenient mechanism for reporting errors
+ * back to the end-user.
+ * <P>
+ * This method is used to report non-recoverable fatal errors,
+ * and must be called at the very end of a run() method (for example,
+ * in a catch block).
+ *
+ * @param t an exception that occurred while processing of
+ * the task.
+ * @param userErrorMessage a user-presentable error message describing the
+ * nature of the exception; may be
+ * <code>null</code>.
+ * @throws IllegalThreadStateException <code>TaskMonitor</code> can only
+ * be be called from the thread that
+ * invokes the task <code>run()</code>.
+ */
+ public void setException(Throwable t, String userErrorMessage)
+ throws IllegalThreadStateException;
+
+ /**
+ * Indicates to a parent application that a task has encountered an error
+ * while processing.
+ * <P>
+ * This method provides a convenient mechanism for reporting errors
+ * back to the end-user.
+ * <P>
+ * This method is used to report non-recoverable fatal errors,
+ * and must be called at the very end of a run() method (for example,
+ * in a catch block).
+ *
+ * @param t an exception that occurred while processing of
+ * the task.
+ * @param userErrorMessage a user-presentable error message describing the
+ * nature of the exception; may be
+ * <code>null</code>.
+ * @param recoveryTip a use-presentable tip on how to recover from the error.
+ * @throws IllegalThreadStateException <code>TaskMonitor</code> can only
+ * be be called from the thread that
+ * invokes the task <code>run()</code>.
+ */
+ public void setException(Throwable t, String userErrorMessage, String recoveryTip)
+ throws IllegalThreadStateException;
+
+ /**
+ * This is a hook for a child process to report to its parent application
+ * a short one-line text description (not exceeding, say, 60 characters,
+ * even though that is not enforced) of the current phase of processing.
+ * <P>
+ * For example, a spring embedded layout algorithm on a graph, if it were
+ * a task, could report a status string such as
+ * <code>"Calculating node distances"</code> and could later
+ * report a status string as
+ * <code>"Calculating partial derivatives"</code>.
+ * <p/>
+ *
+ * @param message a non-<code>null</code> status message that describes the
+ * current state of a task's processing; use the empty string
+ * (<code>""</code>) to unset the current status
+ * message.
+ * @throws NullPointerException if <code>message</code> is
+ * <code>null</code>.
+ * @throws IllegalThreadStateException <code>TaskMonitor</code> can only
+ * be be called from the thread that
+ * invokes the task <code>run()</code>.
+ */
+ public void setStatus(String message) throws IllegalThreadStateException, NullPointerException;
+}
diff --git a/corelibs/task/src/main/java/cytoscape/task/overview.html b/corelibs/task/src/main/java/cytoscape/task/overview.html
new file mode 100644
index 0000000..66f9384
--- /dev/null
+++ b/corelibs/task/src/main/java/cytoscape/task/overview.html
@@ -0,0 +1,5 @@
+<HTML>
+<BODY>
+ Cytoscape Task Framework.
+</BODY>
+</HTML>
\ No newline at end of file
diff --git a/corelibs/task/src/main/java/cytoscape/task/package.html b/corelibs/task/src/main/java/cytoscape/task/package.html
new file mode 100644
index 0000000..7aaa508
--- /dev/null
+++ b/corelibs/task/src/main/java/cytoscape/task/package.html
@@ -0,0 +1,404 @@
+<html>
+<body>
+Cytoscape Task Framework.
+ <P>
+ <UL>
+ <LI><A HREF="#overview">Overview</A></LI>
+ <LI><A HREF="#definitions">Basic Definitions</A></LI>
+ <LI><A HREF="#advantages">Advantages of a Common Task Framework</A></LI>
+ <LI><A HREF="#new_task">How to Create a New Task (with Sample Code)</A>
+ <LI><A HREF="#swing">Tips for Creating Swing-Safe Tasks</A>
+ <LI><A HREF="#run">How to Run a Task via the TaskManager (with Sample Code)</A>
+ <LI><A HREF="#jtask">How to Customize the JTask Dialog Box (with Screen Shots)</A>
+ <LI><A HREF="#references">References</A>
+ </UL>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+1">
+<B><A NAME=overview">Overview</A></B></FONT></TD>
+</TR>
+</TABLE>
+<P>
+ The task package is a convenient framework for building, running
+ and visually monitoring long-term tasks within Cytoscape.
+ <P>
+ The main goal of the task package is to improve the perceived performance
+ of Cytoscape:
+ <BLOCKQUOTE>
+ Often the subjective speed of your application has little to do with
+ how quickly it actually executes its code. To the user, an
+ application that starts up rapidly, repaints quickly, and provides
+ continuous feedback feels "snappier" than an application that just
+ "hangs up" while it churns through its work. [1]
+ </BLOCKQUOTE>
+ <P>
+ By using the task framework, core developers and plugin developers
+ can provide continuous feedback to the end-user, and we can all
+ make Cytoscape a "snappier" application.
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+1">
+<B><A NAME="definitions">Basic Definitions</A></B></FONT></TD>
+</TR>
+</TABLE>
+<P>
+
+ <B>Task:</B> A <I>Task</I> is any
+ long-running process that can be canceled by the end-user.
+ A long-running task may take several seconds or several
+ minutes to complete. For example, retrieving data from a remote database,
+ or running a layout algorithm, are all examples of tasks.
+ For the specific purposes of the task
+ framework, we define a task as any class which implements the
+ {@link cytoscape.task.Task Task} interface.
+ <P>
+ <B>JTask:</B> {@link cytoscape.task.ui.JTask JTask} is Swing dialog box
+ provided by the task framework. It mainly includes a progress bar for
+ monitoring tasks, but it can also be configured to show additional details,
+ such as total time elapsed, estimated time remaining, etc. In the event
+ that a task encounters an error and ends prematurely, the JTask dialog
+ box will also present a nicely formatted error message to the user.
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+1">
+<B><A NAME="advantages">Advantages of a Common Task Framework</A></B></FONT></TD>
+</TR>
+</TABLE>
+ <P>
+ If you are a core developer or a plugin writer, you should consider
+ using the task framework for any long-term processes that you build.
+ You could, of course just build your own task framework and your own
+ progress bar dialog box, but there are certain advantages to using the
+ task framework:
+ <UL>
+ <LI>The task framework is easy to use -- it even provides a TaskManager
+ utility object for automatically starting tasks in a separate thread.
+ <LI>Cytoscape can provide a consistent look and feel for all long-term
+ tasks. For example, all core tasks and plugin tasks can pop open the same
+ JTask dialog box, making things much more consistent and integrated.
+ <LI>The task framework includes comprehensive javadocs and sample code
+ so that you can get started as quickly as possible.
+ </UL>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+1">
+<B><A NAME="new_task">How to Create a New Task (with Sample Code)</A></B></FONT></TD>
+</TR>
+</TABLE>
+<P>
+ To create a new task, your task code must impelement the
+ {@link cytoscape.task.Task Task} interface. The interface defines
+ four methods:
+ <UL>
+ <LI><CODE>run()</CODE>: executes the task.
+ <LI><CODE>halt():</CODE> requests that the task be halted.
+ <LI><CODE>getTitle():</CODE> returns a human readable description of
+ the task.
+ <LI><CODE>setTaskMonitor():</CODE>
+ specifies a monitoring agent that will receive progress reports.
+ As the task proceeds, it can make various calls to the
+ {@link cytoscape.task.TaskMonitor TaskMonitor}.
+ For example, the task can report percentage of work completed or
+ report an error message to the end-user.
+ </UL>
+ <P>
+ Creating a new task is best illustrated with an example. The code
+ below defines a simple task for counting from 0 to <code>max</code>,
+ and is defined in {@link cytoscape.task.sample.SampleTask SampleTask}:
+
+<TABLE WIDTH=75%>
+<TR>
+ <TH BGCOLOR=#DDDDDD>SampleTask.java</TH>
+</TR>
+<TR>
+<TD BGCOLOR=#EEEEEE>
+ <PRE>
+package cytoscape.task.sample;
+
+import cytoscape.task.Task;
+import cytoscape.task.TaskMonitor;
+
+import java.io.IOException;
+
+/**
+ * Sample Task, used to illustrate the Task Framework.
+ * This tasks counts from 0 to maxValue.
+ */
+public class SampleTask implements Task {
+ private static final int MIN_VALUE = 0;
+ private int maxValue;
+ private long countDelay;
+ private TaskMonitor taskMonitor = null;
+ private boolean interrupted = false;
+ private int exceptionIndex = Integer.MAX_VALUE;
+
+ /**
+ * Constructor.
+ *
+ * @param max Max Count Value.
+ * @param countDelay Delay between each count (in milliseconds).
+ */
+ public SampleTask(int max, long countDelay) {
+ this.maxValue = max;
+ this.countDelay = countDelay;
+ }
+
+ /**
+ * Constructor.
+ * Provides a test of Exception Handling.
+ * The Task will throw a NullPointerException when it reaches the
+ * exceptionIndex value.
+ *
+ * @param max Max Count Value.
+ * @param countDelay Delay between each count (in milliseconds).
+ * @param exceptionIndex The Task will throw a NullPointerException
+ * when it reaches the exceptionIndex
+ * value.
+ */
+ public SampleTask(int max, long countDelay, int exceptionIndex) {
+ this.maxValue = max;
+ this.countDelay = countDelay;
+ this.exceptionIndex = exceptionIndex;
+ }
+
+ /**
+ * Run the Task.
+ */
+ public void run() {
+ if (taskMonitor == null) {
+ throw new IllegalStateException("Task Monitor is not set.");
+ }
+ try {
+ // Count from 0 to maxValue with a countDelay
+ // Counting from 0..100 with a 50 ms delay should take ~5 seconds
+
+ // Make sure to check the interrupt flag.
+ int i = MIN_VALUE;
+ while (i <= maxValue && !interrupted) {
+
+ // Calculate Percentage. This must be a value between 0..100.
+ int percentComplete = (int) (((double) i / maxValue) * 100);
+
+ // Estimate Time Remaining
+ long totalTime = maxValue * countDelay;
+ long timeElapsed = i * countDelay;
+ long timeRemaining = totalTime - timeElapsed;
+
+ // Update the Task Monitor.
+ // This automatically updates the UI Component w/ progress bar.
+ if (taskMonitor != null) {
+ taskMonitor.setPercentCompleted(percentComplete);
+ taskMonitor.setStatus("Counting: " + i);
+ taskMonitor.setEstimatedTimeRemaining(timeRemaining);
+ }
+
+ // Illustrates how to Handle/Report Exceptions within a Task.
+ // When this IOException is thrown, the task will stop
+ // execution and report the error to the Task Monitor.
+ // This causes the UI Component to automatically display
+ // an error dialog box to the end-user.
+ if (i == this.exceptionIndex) {
+ throw new IOException("This is a Fake IO Exception");
+ }
+
+ // Artificial Delay
+ Thread.sleep(countDelay);
+ i++;
+ }
+ } catch (InterruptedException e) {
+ taskMonitor.setException(e, "Counting cancelled");
+ } catch (IOException e) {
+ taskMonitor.setException(e, "Counting aborted by fake exception");
+ }
+ }
+
+ /**
+ * Non-blocking call to interrupt the task.
+ */
+ public void halt() {
+ this.interrupted = true;
+ }
+
+ /**
+ * Sets the Task Monitor.
+ *
+ * @param taskMonitor TaskMonitor Object.
+ */
+ public void setTaskMonitor(TaskMonitor taskMonitor) {
+ if (this.taskMonitor != null) {
+ throw new IllegalStateException("Task Monitor is already set.");
+ }
+ this.taskMonitor = taskMonitor;
+ }
+
+ /**
+ * Gets the Task Title.
+ *
+ * @return human readable task title.
+ */
+ public String getTitle() {
+ return new String("Counting Task");
+ }
+}</PRE>
+</TD>
+</TR>
+</TABLE>
+<P>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0">
+<TR BGCOLOR="#CCCCCC">
+<TD>
+<B>Note:</A></B> If your task cannot accurately report percentage of work
+complete, use TaskMonitor setPercentCompleted(-1). This will cause the
+JTask UI component to display the appropriate indeterminate progress bar.
+</TD>
+</TR>
+</TABLE>
+
+<P>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+1">
+<B><A NAME="swing">Tips for Creating Swing-Safe Tasks</A></B></FONT></TD>
+</TR>
+</TABLE>
+<P>
+ According to Sun:
+ <BLOCKQUOTE>
+ "Once a Swing component has been realized, all code that might affect or
+ depend on the state of that component should be executed in the
+ event-dispatching thread." [2]
+ </BLOCKQUOTE>
+ <P>
+ If your task must modify a UI component, you are advised to use one of the
+ {@link javax.swing.SwingUtilities javax.swing.SwingUtilities}:
+ <UL>
+ <LI>{@link javax.swing.SwingUtilities#invokeLater invokeLater()}:
+ Requests that some code be executed in the
+ event-dispatching thread. This method returns immediately, without waiting
+ for the code to execute.
+ <LI>{@link javax.swing.SwingUtilities#invokeAndWait invokeAndWait()}:
+ Acts like invokeLater(), except that this method waits for the code to
+ execute. As a rule, you should use invokeLater() instead of this method.
+ </UL>
+ For additional information on creating Swing safe tasks, refer
+ to the following resources:
+ <UL>
+ <LI><A HREF=
+ "http://java.sun.com/products/jfc/tsc/articles/threads/threads1.html">
+ Threads and Swing</A>, Sun Microsystems, Inc.
+ <LI><A HREF=
+ "http://java.sun.com/products/jfc/tsc/articles/threads/threads3.html">
+ The Last Word in Swing Threads</A>, Sun Microsystems, Inc.
+ </UL>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+1">
+<B><A NAME="run">How to Run a Task via the TaskManager (with Sample Code)
+ </A>
+ </B></FONT></TD>
+</TR>
+</TABLE>
+<P>
+Once you have created a Task, you can run it via the
+{@link cytoscape.task.util.TaskManager TaskManager} utility class.
+This class will automatically create a new thread for your task, start the
+thread, and pop-open a JTask dialog box for monitoring the task.
+<P>
+Here is a complete example, taken from
+{@link cytoscape.task.sample.RunBareBones RunBareBones}.
+<TABLE WIDTH=75%>
+<TR>
+ <TH BGCOLOR=#DDDDDD>RunBareBones.java</TH>
+</TR>
+<TR>
+<TD BGCOLOR=#EEEEEE>
+ <PRE>
+package cytoscape.task.sample;
+
+import cytoscape.task.Task;
+import cytoscape.task.util.TaskManager;
+import cytoscape.task.ui.JTaskConfig;
+import cytoscape.task.ui.JTask;
+
+/**
+ * Illustrates How to Execute a Sample Task via the TaskManager.
+ */
+public class RunBareBones {
+
+ /**
+ * Executes the Sample Task.
+ *
+ * @param args Command Line Arguments.
+ */
+ public static void main(String[] args) {
+
+ // Create a Sample Task
+ Task task = new SampleTask (100, 100);
+
+ // Configure JTask
+ JTaskConfig config = new JTaskConfig();
+
+ // Show Cancel/Close Buttons
+ config.displayUserButtons(true);
+
+ // Execute Task via TaskManager
+ // This automatically pops-open a JTask Dialog Box.
+ // This method will block until the JTask Dialog Box is disposed.
+ boolean success = TaskManager.executeTask(task, config);
+ }
+}
+</PRE>
+</TD>
+</TR>
+</TABLE>
+<P>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+1">
+<B><A NAME="jtask">How to Customize the JTask Dialog Box (with Screen Shots)
+ </A>
+ </B></FONT></TD>
+</TR>
+</TABLE>
+<P>
+ By default, the {@link cytoscape.task.ui.JTask JTask} Dialog box will look
+ like this (as seen on Mac
+ OS X):
+ <P>
+ <IMG SRC="ui/doc-files/bare_bones_jtask.png" BORDER=0/>
+ <P>
+ However, you can customize the look and feel of JTask via
+ {@link cytoscape.task.ui.JTaskConfig JTaskConfig}. For example, here
+ is a fully customized JTask Dialog box. It now shows a status message,
+ time elapsed, and estimated time remaining. It also provides cancel/
+ close buttons.
+ <P>
+ <IMG SRC="ui/doc-files/customized_jtask.png" BORDER=0/>
+ <P>Sample screenshots of error messages provided to users are provided
+ below:
+ <P>
+ <IMG SRC="ui/doc-files/error1_jtask.png" BORDER=0/>
+ <P>
+ <IMG SRC="ui/doc-files/error2_jtask.png" BORDER=0/>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+1">
+<B><A NAME="references">References</A></B></FONT></TD>
+</TR>
+</TABLE>
+<P>
+ [1] <A HREF="http://msdn.microsoft.com/library/default.asp?url=/library/en-us/vbcon98/html/vbconoptimizingperceivedspeed.asp">
+ Optimizing Perceived Speed</A>, MSDN Network.
+ <BR>
+ [2] <A HREF="http://java.sun.com/products/jfc/tsc/articles/threads/threads1.html">
+ Threads and Swing</A>, Sun Microsystems, Inc.
+
+
+</body>
+</html>
diff --git a/corelibs/task/src/main/java/cytoscape/task/sample/DEPENDENCIES b/corelibs/task/src/main/java/cytoscape/task/sample/DEPENDENCIES
new file mode 100644
index 0000000..84d8445
--- /dev/null
+++ b/corelibs/task/src/main/java/cytoscape/task/sample/DEPENDENCIES
@@ -0,0 +1 @@
+cytoscape.task.util
\ No newline at end of file
diff --git a/corelibs/task/src/main/java/cytoscape/task/sample/RunBareBones.java b/corelibs/task/src/main/java/cytoscape/task/sample/RunBareBones.java
new file mode 100644
index 0000000..c579878
--- /dev/null
+++ b/corelibs/task/src/main/java/cytoscape/task/sample/RunBareBones.java
@@ -0,0 +1,70 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.task.sample;
+
+import cytoscape.task.Task;
+
+import cytoscape.task.ui.JTaskConfig;
+
+import cytoscape.task.util.TaskManager;
+
+
+/**
+ * Illustrates how to execute a sample task via the TaskManager.
+ */
+public class RunBareBones {
+ /**
+ * Executes the Sample Task.
+ *
+ * @param args Command Line Arguments.
+ */
+ public static void main(String[] args) {
+ // Create a Sample Task
+ Task task = new SampleTask(100, 100);
+
+ // Configure JTask
+ JTaskConfig config = new JTaskConfig();
+
+ // Show Cancel/Close Buttons
+ config.displayCancelButton(true);
+
+ // Execute Task via TaskManager
+ // This automatically pops-open a JTask Dialog Box.
+ // This method will block until the JTask Dialog Box is disposed.
+ boolean success = TaskManager.executeTask(task, config);
+ }
+}
diff --git a/corelibs/task/src/main/java/cytoscape/task/sample/RunSampleTask.java b/corelibs/task/src/main/java/cytoscape/task/sample/RunSampleTask.java
new file mode 100644
index 0000000..f83aa80
--- /dev/null
+++ b/corelibs/task/src/main/java/cytoscape/task/sample/RunSampleTask.java
@@ -0,0 +1,159 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.task.sample;
+
+import cytoscape.task.Task;
+
+import cytoscape.task.ui.JTaskConfig;
+
+import cytoscape.task.util.TaskManager;
+
+import javax.swing.*;
+
+
+/**
+ * Runs the Sample Task and demonstrate various UI options.
+ */
+public class RunSampleTask {
+ /**
+ * Main Method, used to testing purposes only.
+ *
+ * @param args Command Line Arguments.
+ */
+ public static void main(String[] args) {
+ JFrame frame = createJFrame();
+
+ System.out.println("Running Task Demo");
+ System.out.println("Press CTRL-C to end...");
+
+ int option = 0;
+ Task task = null;
+
+ // Get Command Line Option, e.g. 0..5
+ if (args.length != 0) {
+ option = Integer.parseInt(args[0]);
+ }
+
+ // By default, create a sample task, count from 0..100
+ if (option != 2) {
+ task = new SampleTask(100, 100);
+
+ // For Case 2: throw an exception when we get to XX.
+ // Used to illustrate exception handling / error display.
+ } else {
+ task = new SampleTask(100, 100, 10);
+ }
+
+ // Configure the JTask UI Component
+ JTaskConfig config = new JTaskConfig();
+
+ if (option == 1) {
+ config.setMillisToPopup(2000);
+ }
+
+ config.setOwner(frame);
+ configureJTask(option, config);
+
+ // Execute Task via TaskManager Utility
+ // Automatically pops up a JTask UI Component for visually
+ // monitoring the task
+ boolean success = TaskManager.executeTask(task, config);
+
+ if (success) {
+ System.out.println("Task completed successfully");
+ } else {
+ System.out.println("Task aborted due to user request or task error.");
+ }
+ }
+
+ /**
+ * Creates a Dummy JFrame, to illustrate modality of JTask.
+ *
+ * @return JFrame Object.
+ */
+ private static JFrame createJFrame() {
+ JFrame frame = new JFrame();
+ JPanel panel = new JPanel();
+ JLabel label = new JLabel("A Dummy Cytoscape Desktop");
+ panel.add(label);
+ frame.getContentPane().add(panel);
+ frame.setSize(400, 400);
+ frame.setLocationRelativeTo(null);
+ frame.setVisible(true);
+ frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
+
+ return frame;
+ }
+
+ private static void configureJTask(int option, JTaskConfig config) {
+ switch (option) {
+ // Case 0 is the bare bones version.
+ case 0:
+ System.out.println("This demo illustrates a Bare Bones " + "JTask PopUp.");
+ System.out.println("-- Description and progress are " + "displayed");
+ System.out.println("-- Task cannot be cancelled.");
+
+ break;
+
+ // Case 1 is the "bells and whistles" version.
+ case 1:
+ config.displayStatus(true);
+ config.displayTimeElapsed(true);
+ config.displayTimeRemaining(true);
+ config.displayCancelButton(true);
+ config.displayCloseButton(true);
+ config.setAutoDispose(false);
+
+ System.out.println("This demo illustrates a customized " + "JTask PopUp.");
+ System.out.println("-- All time fields are displayed.");
+ System.out.println("-- Description Field is displayed.");
+ System.out.println("-- Status Field is displayed.");
+ System.out.println("-- Task can be cancelled");
+ System.out.println("-- Dialog box popups up after delay");
+
+ break;
+
+ // Case 2 displays user buttons
+ case 2:
+ config.displayCancelButton(true);
+ config.displayCloseButton(true);
+ System.out.println("This demo illustrates exception handling.");
+ System.out.println("-- This task will end prematurely " + "with an error.");
+ System.out.println("-- This task can be canceled");
+ }
+ }
+}
diff --git a/corelibs/task/src/main/java/cytoscape/task/sample/SampleTask.java b/corelibs/task/src/main/java/cytoscape/task/sample/SampleTask.java
new file mode 100644
index 0000000..9f5aece
--- /dev/null
+++ b/corelibs/task/src/main/java/cytoscape/task/sample/SampleTask.java
@@ -0,0 +1,170 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.task.sample;
+
+import cytoscape.task.Task;
+import cytoscape.task.TaskMonitor;
+
+import java.io.IOException;
+
+
+/**
+ * Sample Task, used to illustrate the Task Framework.
+ * This tasks counts from 0 to maxValue.
+ */
+public class SampleTask implements Task {
+ private static final int MIN_VALUE = 0;
+ private int maxValue;
+ private long countDelay;
+ private TaskMonitor taskMonitor = null;
+ private boolean interrupted = false;
+ private int exceptionIndex = Integer.MAX_VALUE;
+
+ /**
+ * Constructor.
+ *
+ * @param max Max Count Value.
+ * @param countDelay Delay between each count (in milliseconds).
+ */
+ public SampleTask(int max, long countDelay) {
+ this.maxValue = max;
+ this.countDelay = countDelay;
+ }
+
+ /**
+ * Constructor.
+ * Provides a test of Exception Handling.
+ * The Task will throw a NullPointerException when it reaches the
+ * exceptionIndex value.
+ *
+ * @param max Max Count Value.
+ * @param countDelay Delay between each count (in milliseconds).
+ * @param exceptionIndex The Task will throw a NullPointerException
+ * when it reaches the exceptionIndex
+ * value.
+ */
+ public SampleTask(int max, long countDelay, int exceptionIndex) {
+ this.maxValue = max;
+ this.countDelay = countDelay;
+ this.exceptionIndex = exceptionIndex;
+ }
+
+ /**
+ * Run the Task.
+ */
+ public void run() {
+ if (taskMonitor == null) {
+ throw new IllegalStateException("Task Monitor is not set.");
+ }
+
+ try {
+ // Count from 0 to maxValue with a countDelay
+ // Counting from 0..100 with a 50 ms delay should take ~5 seconds
+
+ // Make sure to check the interrupt flag.
+ int i = MIN_VALUE;
+
+ while ((i <= maxValue) && !interrupted) {
+ // Calculate Percentage. This must be a value between 0..100.
+ int percentComplete = (int) (((double) i / maxValue) * 100);
+
+ // Estimate Time Remaining
+ long totalTime = maxValue * countDelay;
+ long timeElapsed = i * countDelay;
+ long timeRemaining = totalTime - timeElapsed;
+
+ // Update the Task Monitor.
+ // This automatically updates the UI Component w/ progress bar.
+ if (taskMonitor != null) {
+ taskMonitor.setPercentCompleted(percentComplete);
+ taskMonitor.setStatus("Counting: " + i);
+ taskMonitor.setEstimatedTimeRemaining(timeRemaining);
+ }
+
+ // Illustrates how to Handle/Report Exceptions within a Task.
+ // When this IOException is thrown, the task will stop
+ // execution and report the error to the Task Monitor.
+ // This causes the UI Component to automatically display
+ // an error dialog box to the end-user.
+ if (i == this.exceptionIndex) {
+ throw new IOException("This is a Fake IO Exception");
+ }
+
+ // Artificial Delay
+ Thread.sleep(countDelay);
+ i++;
+ }
+
+ taskMonitor.setStatus("Task is now complete."
+ + "\n\nThis is a long message used to demonstrate that status "
+ + "messages can be long, and can span multiple lines.");
+ } catch (InterruptedException e) {
+ taskMonitor.setException(e, "Counting interrupted");
+ } catch (IOException e) {
+ taskMonitor.setException(e, "Counting aborted by fake exception");
+ }
+ }
+
+ /**
+ * Non-blocking call to interrupt the task.
+ */
+ public void halt() {
+ this.interrupted = true;
+ }
+
+ /**
+ * Sets the Task Monitor.
+ *
+ * @param taskMonitor TaskMonitor Object.
+ */
+ public void setTaskMonitor(TaskMonitor taskMonitor) {
+ if (this.taskMonitor != null) {
+ throw new IllegalStateException("Task Monitor is already set.");
+ }
+
+ this.taskMonitor = taskMonitor;
+ }
+
+ /**
+ * Gets the Task Title.
+ *
+ * @return human readable task title.
+ */
+ public String getTitle() {
+ return new String("Counting Task");
+ }
+}
diff --git a/corelibs/task/src/main/java/cytoscape/task/sample/package.html b/corelibs/task/src/main/java/cytoscape/task/sample/package.html
new file mode 100644
index 0000000..230331c
--- /dev/null
+++ b/corelibs/task/src/main/java/cytoscape/task/sample/package.html
@@ -0,0 +1,5 @@
+<html>
+<body>
+Sample task, used to illustrate the Task framework.
+</body>
+</html>
diff --git a/corelibs/task/src/main/java/cytoscape/task/ui/DEPENDENCIES b/corelibs/task/src/main/java/cytoscape/task/ui/DEPENDENCIES
new file mode 100644
index 0000000..5152367
--- /dev/null
+++ b/corelibs/task/src/main/java/cytoscape/task/ui/DEPENDENCIES
@@ -0,0 +1 @@
+cytoscape.task
\ No newline at end of file
diff --git a/corelibs/task/src/main/java/cytoscape/task/ui/JErrorPanel.java b/corelibs/task/src/main/java/cytoscape/task/ui/JErrorPanel.java
new file mode 100644
index 0000000..6545c86
--- /dev/null
+++ b/corelibs/task/src/main/java/cytoscape/task/ui/JErrorPanel.java
@@ -0,0 +1,350 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.task.ui;
+
+import cytoscape.task.util.StringWrap;
+
+import java.awt.*;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import javax.swing.*;
+import javax.swing.border.EmptyBorder;
+import javax.swing.border.LineBorder;
+import javax.swing.tree.DefaultMutableTreeNode;
+import javax.swing.tree.TreePath;
+
+
+/**
+ * Common UI element for displaying errors and stack traces.
+ */
+public class JErrorPanel extends JPanel {
+ private static final long serialVersionUID = 333614801L;
+
+ /**
+ * The Error Object
+ */
+ private Throwable t;
+
+ /**
+ * A Human Readable Error Message
+ */
+ private String userErrorMessage;
+
+ /**
+ * Hint to user as to how to fix the error.
+ */
+ private String tip;
+
+ /**
+ * Flag to Show/Hide Error Details.
+ */
+ private boolean showDetails = false;
+
+ /**
+ * Show/Hide Details Button.
+ */
+ private JButton detailsButton;
+
+ /**
+ * Scroll Pane used to display Stack Trace Elements.
+ */
+ private JScrollPane detailsPane;
+
+ /**
+ * JDialog Owner.
+ */
+ private JDialog owner;
+ private static final String SHOW_TEXT = "Show Error Details";
+ private static final String HIDE_TEXT = "Hide Error Details";
+
+ /**
+ * Private Constructor.
+ *
+ * @param owner Window owner.
+ * @param t Throwable Object. May be null.
+ * @param userErrorMessage User Readable Error Message. May be null.
+ */
+ JErrorPanel(JDialog owner, Throwable t, String userErrorMessage) {
+ if (owner == null) {
+ throw new IllegalArgumentException("owner parameter is null.");
+ }
+
+ this.owner = owner;
+ this.t = t;
+ this.userErrorMessage = userErrorMessage;
+ initUI();
+ }
+
+ /**
+ * Private Constructor.
+ *
+ * @param owner Window owner.
+ * @param t Throwable Object. May be null.
+ * @param userErrorMessage User Readable Error Message. May be null.
+ * @param tip Tip for user on how to recover from the error. May be null.
+ */
+ JErrorPanel(JDialog owner, Throwable t, String userErrorMessage, String tip) {
+ if (owner == null) {
+ throw new IllegalArgumentException("owner parameter is null.");
+ }
+ this.owner = owner;
+ this.t = t;
+ this.userErrorMessage = userErrorMessage;
+ this.tip = tip;
+ initUI();
+ }
+
+ /**
+ * Initializes UI.
+ */
+ private void initUI() {
+ // Use Border Layout
+ setLayout(new BorderLayout());
+
+ // Create North Panel with Error Message and Button.
+ JPanel northPanel = createNorthPanel();
+ add(northPanel, BorderLayout.NORTH);
+
+ // Create Center Panel with Error Details.
+ JScrollPane centerPanel = createCenterPanel();
+ add(centerPanel, BorderLayout.CENTER);
+
+ // Repack and validate the owner
+ owner.pack();
+ owner.validate();
+ }
+
+ /**
+ * Creates North Panel with Error Message and Details Button.
+ *
+ * @return JPanel Object.
+ */
+ private JPanel createNorthPanel() {
+ JPanel panel = new JPanel();
+ panel.setBorder(new EmptyBorder(5, 5, 5, 5));
+ panel.setLayout(new BorderLayout());
+
+ if (userErrorMessage == null) {
+ userErrorMessage = new String("An Error Has Occurred. " + "Please try again.");
+ }
+
+ // Add an Error Icon
+ Icon icon = UIManager.getIcon("OptionPane.errorIcon");
+ JLabel l = new JLabel(icon);
+ l.setVerticalAlignment(SwingConstants.TOP);
+ panel.add(l, BorderLayout.WEST);
+
+ // Add Error Message with Custom Font Properties
+ JPanel textPanel = new JPanel();
+ textPanel.setAlignmentY(Component.TOP_ALIGNMENT);
+ textPanel.setLayout(new BoxLayout(textPanel, BoxLayout.Y_AXIS));
+ JTextArea errorArea = createErrorTextArea(userErrorMessage);
+ textPanel.add(errorArea);
+ if (tip != null) {
+ JTextArea tipArea = createTipTextArea(tip);
+ textPanel.add(tipArea);
+ }
+ panel.add(textPanel, BorderLayout.CENTER);
+
+ // Conditionally Add Details Button
+ JPanel buttonPanel = new JPanel();
+ buttonPanel.setLayout(new GridLayout(2, 1));
+ buttonPanel.setAlignmentY(Component.TOP_ALIGNMENT);
+ conditionallyAddDetailsButton(buttonPanel);
+
+ // Create a Close Button
+ JButton closeButton = new JButton("Close");
+ closeButton.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ owner.dispose();
+ }
+ });
+ buttonPanel.add(closeButton);
+ JPanel enclosingPanel = new JPanel();
+ enclosingPanel.add(buttonPanel);
+ enclosingPanel.setAlignmentY(Component.TOP_ALIGNMENT);
+ panel.add(enclosingPanel, BorderLayout.EAST);
+
+ return panel;
+ }
+
+ private JTextArea createErrorTextArea(String msg) {
+ msg = StringWrap.wrap(msg, 50, "\n", false);
+ JTextArea errorArea = new JTextArea(msg);
+ errorArea.setEditable(false);
+ errorArea.setOpaque(false);
+
+ Font font = errorArea.getFont();
+ errorArea.setFont(new Font(font.getFamily(), Font.BOLD, font.getSize()-1));
+ errorArea.setBorder(new EmptyBorder(10, 10, 0, 10));
+ return errorArea;
+ }
+
+ private JTextArea createTipTextArea(String tip) {
+ tip = StringWrap.wrap(tip, 50, "\n", false);
+ JTextArea tipArea = new JTextArea(tip);
+ tipArea.setEditable(false);
+ tipArea.setOpaque(false);
+
+ Font font = tipArea.getFont();
+ tipArea.setFont(new Font(font.getFamily(), Font.PLAIN, font.getSize()));
+ tipArea.setBorder(new EmptyBorder(10, 10, 10, 10));
+ return tipArea;
+ }
+
+ /**
+ * Creates Center Panel with Error Details.
+ *
+ * @return JScrollPane Object.
+ */
+ private JScrollPane createCenterPanel() {
+ detailsPane = new JScrollPane();
+
+ if ( t != null ) {
+ DefaultMutableTreeNode top = new DefaultMutableTreeNode("Root Error");
+ processThrowable(t,top);
+
+ // Create a JTree Object
+ JTree tree = new JTree(top);
+
+ // Open all Nodes
+ tree.scrollPathToVisible(new TreePath(top.getPath()));
+ tree.setBorder(new EmptyBorder(4, 10, 10, 10));
+ detailsPane.setViewportView(tree);
+ detailsPane.setPreferredSize(new Dimension(10, 150));
+ }
+
+ // By default, do not show
+ detailsPane.setVisible(false);
+
+ return detailsPane;
+ }
+
+ /**
+ * Recursively adds each Throwable cause to the TreeNode so that we
+ * can see the whole exception.
+ */
+ private void processThrowable(Throwable t, DefaultMutableTreeNode top) {
+
+ if ( t == null )
+ return;
+
+ StackTraceElement[] ste = t.getStackTrace();
+ StringBuffer rootBuffer = new StringBuffer("Caused by: ");
+
+ rootBuffer.append(t.getClass().getName());
+ rootBuffer.append(": ");
+
+ if (t.getMessage() != null)
+ rootBuffer.append(t.getMessage());
+
+ // Create Individual Nodes in JTree
+ DefaultMutableTreeNode current = top;
+
+ DefaultMutableTreeNode node = new DefaultMutableTreeNode(rootBuffer.toString());
+ current.add(node);
+ current = node;
+
+ if ( ste != null ) {
+ for (int i = 0; i < ste.length; i++) {
+ DefaultMutableTreeNode node2 = new DefaultMutableTreeNode(ste[i]);
+ current.add(node2);
+ // Don't set the last trace to current, so that we'll see the
+ // last trace as a leaf and any subsequent causes will be seen
+ // next to the leaf as new sub-trees.
+ if ( i < ste.length-1 )
+ current = node2;
+ }
+ }
+
+ processThrowable( t.getCause(), current );
+ }
+
+ /**
+ * Adds a Show/Hide Details Button.
+ *
+ * @param panel JPanel Object.
+ */
+ private void conditionallyAddDetailsButton(JPanel panel) {
+ if ((t != null) && (t.getStackTrace() != null)) {
+ detailsButton = new JButton(SHOW_TEXT);
+ detailsButton.addActionListener(new ActionListener() {
+ /**
+ * Toggle Show/Hide Error Details.
+ *
+ * @param e ActionEvent.
+ */
+ public void actionPerformed(ActionEvent e) {
+ showDetails = !showDetails;
+ detailsPane.setVisible(showDetails);
+ owner.setResizable(showDetails);
+
+ if (showDetails) {
+ detailsButton.setText(HIDE_TEXT);
+ } else {
+ detailsButton.setText(SHOW_TEXT);
+ }
+
+ owner.pack();
+ owner.validate();
+ }
+ });
+ detailsButton.setAlignmentX(Component.RIGHT_ALIGNMENT);
+ panel.add(detailsButton);
+ }
+ }
+
+ public static void main(String[] args) {
+ NullPointerException e = new NullPointerException();
+ final JDialog dialog = new JDialog();
+ JErrorPanel errorPanel = new JErrorPanel(dialog, e,
+ "Network error occurred while tring to connect to remote web service.",
+ "Please check your network settings, and try again.");
+ dialog.getContentPane().add(errorPanel, BorderLayout.CENTER);
+
+ // Repack and validate the owner
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ dialog.pack();
+ dialog.pack();
+ dialog.setVisible(true);
+ }
+ });
+
+ }
+}
diff --git a/corelibs/task/src/main/java/cytoscape/task/ui/JTask.java b/corelibs/task/src/main/java/cytoscape/task/ui/JTask.java
new file mode 100644
index 0000000..564b030
--- /dev/null
+++ b/corelibs/task/src/main/java/cytoscape/task/ui/JTask.java
@@ -0,0 +1,623 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.task.ui;
+
+import cytoscape.task.Task;
+import cytoscape.task.TaskMonitor;
+
+import java.awt.*;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
+
+import java.util.Date;
+
+import javax.swing.*;
+import javax.swing.border.EmptyBorder;
+
+
+/**
+ * Common UI element for visually monitoring task progress.
+ */
+public class JTask extends JDialog implements TaskMonitor, ActionListener {
+ private static final long serialVersionUID = 333614801L;
+
+ /**
+ * ProgressBar UI component.
+ */
+ private JProgressBar pBar;
+
+ /**
+ * Time Interval for updating the time elapsed field.
+ */
+ private static final int TIME_INTERVAL = 500;
+
+ /**
+ * Description value label.
+ */
+ private JLabel descriptionValue;
+
+ /**
+ * Status value label.
+ */
+ private JTextArea statusValue;
+
+ /**
+ * Time remaining label.
+ */
+ private JLabel timeRemainingValue;
+
+ /**
+ * Time elapsed label.
+ */
+ private JLabel timeElapsedValue;
+
+ /**
+ * Progress Value.
+ */
+ private JLabel progressValue;
+
+ /**
+ * Internal Timer.
+ */
+ private Timer timer;
+
+ /**
+ * Action Cancel Message.
+ */
+ private static final String ACTION_CANCEL = "CANCEL";
+
+ /**
+ * Action Close Message.
+ */
+ private static final String ACTION_CLOSE = "CLOSE";
+
+ /**
+ * Cancel Button.
+ */
+ private JButton cancelButton;
+
+ /**
+ * Close Button.
+ */
+ private JButton closeButton;
+
+ /**
+ * Time Stamp when Component was constructed.
+ */
+ private Date startTime;
+
+ /**
+ * Title Value.
+ */
+ private String taskTitle;
+
+ /**
+ * Used to Configure the JTask UI.
+ */
+ private JTaskConfig config;
+
+ /**
+ * Task we are monitoring.
+ */
+ private Task task;
+
+ /**
+ * Contains all the Progress Fields.
+ */
+ private JPanel progressPanel;
+
+ /**
+ * Flag to Indicate that user has requested that task halt.
+ */
+ private boolean haltRequested = false;
+
+ /**
+ * Flag to Indicate that error has occurred within task.
+ */
+ private boolean errorOccurred = false;
+
+ /**
+ * Estimated Time Remaining.
+ */
+ private long timeRemaining;
+
+ /**
+ * Constructor.
+ *
+ * @param task Task we are monitoring, and may need to cancel.
+ * @param config JTaskConfig Object.
+ */
+ public JTask(Task task, JTaskConfig config) {
+ super((Frame) config.getOwner(), task.getTitle(), config.getModal());
+ this.task = task;
+ this.taskTitle = task.getTitle();
+ this.config = config;
+ init();
+ }
+
+ /**
+ * Sets Percentage Complete.
+ * Called by a child task thread.
+ *
+ * @param percent Percentage Complete.
+ */
+ public void setPercentCompleted(final int percent) {
+ // Ignore events if user has requested to halt task.
+ if (!haltRequested) {
+ if ((percent < -1) || (percent > 100)) {
+ throw new IllegalArgumentException("percent parameter is outside range: [-1, 100]");
+ }
+
+ // Update the UI
+ // Only update when the new value != old value
+ // This dramatically cuts down on the number of new events added
+ // to the Event Dispatch Thread.
+ if (percent != pBar.getValue()) {
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ if (percent == -1) {
+ pBar.setIndeterminate(true);
+ } else {
+ if (pBar.isIndeterminate()) {
+ pBar.setIndeterminate(false);
+ }
+
+ pBar.setValue(percent);
+ }
+ }
+ });
+ }
+ }
+ }
+
+ /**
+ * Sets Estimated Time Remaining.
+ * Called by a child task thread.
+ * Safely queues changes to the Swing Event Dispatch Thread.
+ *
+ * @param time Time Remaining, in milliseconds.
+ */
+ public void setEstimatedTimeRemaining(final long time) {
+ // Ignore events if user has requested to halt task.
+ if (!haltRequested) {
+ // Update the UI
+ // Only update when the new value != old value
+ // This dramatically cuts down on the number of new events added
+ // to the Event Dispatch Thread.
+ if (timeRemaining != time) {
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ timeRemainingValue.setText(StringUtils.getTimeString(time));
+ }
+ });
+ }
+
+ timeRemaining = time;
+ }
+ }
+
+ /**
+ * Reports an Error in Task Processing.
+ *
+ * @param t Throwable t.
+ * @param userErrorMessage Human Readable Error Message.
+ */
+ public void setException(final Throwable t, final String userErrorMessage) {
+ // Ignore events if user has requested to halt task.
+ if (!haltRequested) {
+ this.errorOccurred = true;
+ stopTimer();
+ showErrorPanel(t, userErrorMessage, null);
+ }
+ }
+
+ public void setException(Throwable t, String userErrorMessage, String recoveryTip)
+ throws IllegalThreadStateException {
+ // Ignore events if user has requested to halt task.
+ if (!haltRequested) {
+ this.errorOccurred = true;
+ stopTimer();
+ showErrorPanel(t, userErrorMessage, recoveryTip);
+ }
+ }
+
+
+ private void showErrorPanel(final Throwable t, final String userErrorMessage,
+ final String recoveryTip) {
+ // Update the UI
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ // Hide All Existing UI Components
+ Container c = getContentPane();
+ closeButton.setVisible(false);
+ cancelButton.setVisible(false);
+ progressPanel.setVisible(false);
+
+ // Create Error Panel
+ JPanel errorPanel = new JErrorPanel(JTask.this, t, userErrorMessage,
+ recoveryTip);
+ c.add(errorPanel, BorderLayout.CENTER);
+ config.setAutoDispose(false);
+ pack();
+ setTitle("An Error Has Occurred");
+
+ // Make sure JTask is actually visible
+ if (!JTask.this.isShowing()) {
+ JTask.this.setVisible(true);
+ }
+ }
+ });
+ }
+
+ /**
+ * Indicates that the worker task is done processing.
+ */
+ public void setDone() {
+ // Update the UI
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ stopTimer();
+
+ if (config.getAutoDispose()) {
+ dispose();
+ } else {
+ setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
+ removeProgressBar();
+ cancelButton.setEnabled(false);
+ closeButton.setEnabled(true);
+
+ // If we are done because user hit the cancel button,
+ // say so explicitly.
+ if (haltRequested) {
+ setCancelStatusMsg("Canceled by User");
+ }
+ pack();
+ }
+ }
+ });
+ }
+
+ /**
+ * Call to externally control whether the cancel button is enabled
+ * or disabled. This can be used by threads which have some sections
+ * that can be canceled and some that can not.
+ *
+ * @param enable if true, enable the cancel button
+ */
+ public void setCancel(boolean enable) {
+ cancelButton.setEnabled(enable);
+ }
+
+ /**
+ * Sets the Status Message.
+ * Called by a child task thread.
+ * Safely queues changes to the Swing Event Dispatch Thread.
+ *
+ * @param message status message.
+ */
+ public void setStatus(final String message) {
+ if (!haltRequested) {
+ // Update the UI
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ statusValue.setText(message);
+ pack();
+ }
+ });
+ }
+ }
+
+ /**
+ * Returns true if Task Has Encountered An Error.
+ *
+ * @return boolean value.
+ */
+ public boolean errorOccurred() {
+ return errorOccurred;
+ }
+
+ /**
+ * Returns true if User Has Requested to Halt the Task.
+ *
+ * @return boolean value.
+ */
+ public boolean haltRequested() {
+ return haltRequested;
+ }
+
+ /**
+ * Initializes UI.
+ */
+ private void init() {
+ // Set Frame Title
+ this.setTitle(taskTitle);
+
+ // Init User Interface
+ Container container = this.getContentPane();
+ container.setLayout(new BorderLayout());
+ progressPanel = new JPanel(new GridBagLayout());
+ progressPanel.setBorder(new EmptyBorder(10, 10, 10, 10));
+
+ // Create Description, Status, Time Left and Time Elapsed Fields
+ int y = 0;
+ addLabel("Description: ", progressPanel, 0, y, GridBagConstraints.NORTHEAST, true);
+ descriptionValue = addLabel(StringUtils.truncateOrPadString(taskTitle), progressPanel, 1,
+ y, GridBagConstraints.NORTHWEST, true);
+
+ addLabel("Status: ", progressPanel, 0, ++y, GridBagConstraints.NORTHEAST,
+ config.getStatusFlag());
+ statusValue = addTextArea(StringUtils.truncateOrPadString("Starting..."), progressPanel, 1,
+ y, GridBagConstraints.NORTHWEST, config.getStatusFlag());
+
+ addLabel("Time Left: ", progressPanel, 0, ++y, GridBagConstraints.NORTHEAST,
+ config.getTimeRemainingFlag());
+ timeRemainingValue = addLabel("", progressPanel, 1, y, GridBagConstraints.NORTHWEST,
+ config.getTimeRemainingFlag());
+
+ addLabel("Time Elapsed: ", progressPanel, 0, ++y, GridBagConstraints.NORTHEAST,
+ config.getTimeElapsedFlag());
+ timeElapsedValue = addLabel(StringUtils.getTimeString(0), progressPanel, 1, y,
+ GridBagConstraints.NORTHWEST, config.getTimeElapsedFlag());
+
+ progressValue = addLabel("Progress: ", progressPanel, 0, ++y,
+ GridBagConstraints.NORTHEAST, true);
+
+ initProgressBar(progressPanel, y);
+ container.add(progressPanel, BorderLayout.CENTER);
+ createFooter(container);
+
+ // Disable close operation until task is done.
+ this.setDefaultCloseOperation(JFrame.DO_NOTHING_ON_CLOSE);
+
+ // Stop timer when window is finally closed.
+ this.addWindowListener(new WindowAdapter() {
+ public void windowClosing(WindowEvent e) {
+ stopTimer();
+ }
+ });
+ this.pack();
+ this.setResizable(false);
+
+ // Center component relative to parent component
+ // or relative to user's screen.
+ setLocationRelativeTo(config.getOwner());
+
+ // Conditionally Show / AutoPopUp the Component.
+ // Call to show must be done on the event-dispatch thread
+ // Otherwise, a modal window will block.
+ // autoPopUp();
+
+ // Initialize timer only if we want to display the time elapsed field.
+ if (config.getTimeElapsedFlag()) {
+ initTimer();
+ }
+ }
+
+ /**
+ * Creates Footer with Close, Cancel Buttons.
+ *
+ * @param container Container Object.
+ */
+ private void createFooter(Container container) {
+ JPanel footer = new JPanel();
+ footer.setBorder(new EmptyBorder(5, 5, 5, 5));
+ footer.setLayout(new BoxLayout(footer, BoxLayout.Y_AXIS));
+ closeButton = new JButton(" Close ");
+ closeButton.setEnabled(false);
+ closeButton.setActionCommand(ACTION_CLOSE);
+ closeButton.addActionListener(this);
+ cancelButton = new JButton(" Cancel ");
+ cancelButton.setActionCommand(ACTION_CANCEL);
+ cancelButton.addActionListener(this);
+
+ if (config.getCloseButtonFlag()) {
+ footer.add(closeButton);
+ footer.add(Box.createHorizontalGlue());
+ }
+
+ if (config.getCancelButtonFlag()) {
+ footer.add(cancelButton);
+ }
+
+ container.add(footer, BorderLayout.EAST);
+ }
+
+ /**
+ * Initializes the JProgressBar.
+ *
+ * @param progressPanel JPanel Object.
+ */
+ private void initProgressBar(JPanel progressPanel, int y) {
+ GridBagConstraints c = new GridBagConstraints();
+ pBar = new JProgressBar();
+ pBar.setIndeterminate(true);
+ pBar.setMaximum(100);
+ pBar.setValue(0);
+ pBar.setBorder(new EmptyBorder(5, 0, 5, 0));
+ pBar.setDoubleBuffered(true);
+ c.gridx = 1;
+ c.gridy = y;
+ c.fill = GridBagConstraints.HORIZONTAL;
+ progressPanel.add(pBar, c);
+ }
+
+ /**
+ * Add New Label to Specified JPanel.
+ *
+ * @param text Label Text.
+ * @param panel Container Panel.
+ * @param gridx X Location.
+ * @param gridy Y Location.
+ * @return JLabel Object.
+ */
+ private JLabel addLabel(String text, JPanel panel, int gridx, int gridy, int alignment,
+ boolean addToPanel) {
+ JLabel label = new JLabel(text);
+ label.setHorizontalAlignment(JLabel.LEFT);
+ label.setBorder(new EmptyBorder(5, 5, 5, 5));
+ label.setFont(new Font(null, Font.PLAIN, 13));
+
+ GridBagConstraints c = new GridBagConstraints();
+ c.gridx = gridx;
+ c.gridy = gridy;
+ c.anchor = alignment;
+
+ if (addToPanel) {
+ panel.add(label, c);
+ }
+
+ return label;
+ }
+
+ /**
+ * Add New TextArea to Specified JPanel.
+ *
+ * @param text Label Text.
+ * @param panel Container Panel.
+ * @param gridx X Location.
+ * @param gridy Y Location.
+ * @return JLabel Object.
+ */
+ private JTextArea addTextArea(String text, JPanel panel, int gridx, int gridy, int alignment,
+ boolean addToPanel) {
+ JTextArea textArea = new JTextArea(text, 1, 25);
+ textArea.setEditable(false);
+ textArea.setLineWrap(true);
+ textArea.setWrapStyleWord(true);
+ textArea.setBorder(new EmptyBorder(5, 5, 5, 5));
+
+ textArea.setBackground((Color) UIManager.get("Label.background"));
+ textArea.setForeground((Color) UIManager.get("Label.foreground"));
+ textArea.setFont(new Font(null, Font.PLAIN, 13));
+
+ GridBagConstraints c = new GridBagConstraints();
+ c.gridx = gridx;
+ c.gridy = gridy;
+ c.anchor = alignment;
+
+ if (addToPanel) {
+ panel.add(textArea, c);
+ }
+
+ return textArea;
+ }
+
+ /**
+ * Capture All Action Events.
+ * This method is called by the Timer and by User Buttons.
+ * This method is called on the Swing Event Dispatch Thread.
+ *
+ * @param e Timer Event.
+ */
+ public void actionPerformed(ActionEvent e) {
+ if (e.getActionCommand() != null) {
+ if (e.getActionCommand().equals(ACTION_CANCEL)) {
+ this.haltRequested = true;
+ cancelButton.setEnabled(false);
+
+ // Immediately inform the user that we are canceling the task
+ this.setCancelStatusMsg("Canceling...");
+
+ // Request that Task Halt
+ task.halt();
+ } else if (e.getActionCommand().equals(ACTION_CLOSE)) {
+ dispose();
+ }
+ }
+ }
+
+ /**
+ * Initialize the Timer Object.
+ * Note that timer events are sent to the Swing Event-Dispatch Thread.
+ */
+ private void initTimer() {
+ // Record Start Timestamp
+ startTime = new Date();
+
+ // Create Auto-Timer
+ timer = new Timer(TIME_INTERVAL,
+ new ActionListener() {
+ /**
+ * Update the Time Elapsed Field.
+ *
+ * @param e ActionEvent.
+ */
+ public void actionPerformed(ActionEvent e) {
+ Date currentTime = new Date();
+ long timeElapsed = currentTime.getTime() - startTime.getTime();
+ timeElapsedValue.setText(StringUtils.getTimeString(timeElapsed));
+ }
+ });
+ timer.start();
+ }
+
+ /**
+ * Stops the Internal Timer.
+ */
+ private void stopTimer() {
+ if ((timer != null) && timer.isRunning()) {
+ timer.stop();
+ }
+ }
+
+ /**
+ * Sets a Cancel Status Message.
+ * <p/>
+ * If we are displaying the status field, put the message there.
+ * Otherwise, put the message in the description field.
+ *
+ * @param msg cancel message.
+ */
+ private void setCancelStatusMsg(String msg) {
+ if (config.getStatusFlag()) {
+ statusValue.setText(msg);
+ } else {
+ descriptionValue.setText(msg);
+ }
+ }
+
+ /**
+ * Removes ProgressBar from the UI.
+ */
+ private void removeProgressBar() {
+ progressPanel.remove(pBar);
+ progressPanel.remove(progressValue);
+ progressPanel.validate();
+ }
+}
diff --git a/corelibs/task/src/main/java/cytoscape/task/ui/JTaskConfig.java b/corelibs/task/src/main/java/cytoscape/task/ui/JTaskConfig.java
new file mode 100644
index 0000000..41cc17b
--- /dev/null
+++ b/corelibs/task/src/main/java/cytoscape/task/ui/JTaskConfig.java
@@ -0,0 +1,280 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.task.ui;
+
+import java.awt.*;
+
+
+/**
+ * Used to configure the JTask UI component.
+ */
+public class JTaskConfig {
+ /**
+ * Display the Status Field.
+ */
+ private boolean statusFlag = false;
+
+ /**
+ * Display the Time Elapsed Field.
+ */
+ private boolean timeElapsedFlag = false;
+
+ /**
+ * Display the Estimated Time Remaining Field.
+ */
+ private boolean timeRemainingFlag = false;
+
+ /**
+ * Display User Cancel Button.
+ */
+ private boolean cancelButtonFlag = false;
+
+ /**
+ * Display Close Button.
+ */
+ private boolean closeButtonFlag = false;
+
+ /**
+ * Disposes of Component When Task Completes.
+ */
+ private boolean autoDispose = true;
+
+ /**
+ * Defines Modality.
+ */
+ private boolean modal = true;
+
+ /**
+ * Owner, such as a JFrame.
+ * Primarily used to center the JTask component relative to the owner.
+ */
+ private Container owner;
+
+ /**
+ * Milliseconds until popup.
+ */
+ private int millisToPopup = 100;
+
+ /**
+ * Enables/Disables Display of the Status Field.
+ * <P>By default, this value is set to false.
+ *
+ * @param flag boolean value.
+ */
+ public void displayStatus(boolean flag) {
+ this.statusFlag = flag;
+ }
+
+ /**
+ * Enables/Disables Display of the Time Elapsed Field.
+ * <P>By default, this value is set to false.
+ *
+ * @param flag boolean value.
+ */
+ public void displayTimeElapsed(boolean flag) {
+ this.timeElapsedFlag = flag;
+ }
+
+ /**
+ * Enables/Disables Display of the Time Remaining Field.
+ * <P>By default, this value is set to false.
+ *
+ * @param flag boolean value.
+ */
+ public void displayTimeRemaining(boolean flag) {
+ this.timeRemainingFlag = flag;
+ }
+
+ /**
+ * Enables/Disables Display of the Cancel Button.
+ * <P>By default, this value is set to false.
+ *
+ * @param flag boolean value.
+ */
+ public void displayCancelButton(boolean flag) {
+ this.cancelButtonFlag = flag;
+ }
+
+ /**
+ * Enables/Disables Display of the Close Button.
+ * <P>By default, this value is set to false.
+ *
+ * @param flag boolean value.
+ */
+ public void displayCloseButton(boolean flag) {
+ this.closeButtonFlag = flag;
+ }
+
+ /**
+ * Enables/Disables Auto-Dispose Feature.
+ * When set to true, the JTask dialog box will automatically disappear
+ * when the task is complete.
+ * When set to false, the JTask dialog box will persist until the user
+ * dismissed it.
+ * <P>By default, this value is set to true.
+ *
+ * @param flag boolean value.
+ */
+ public void setAutoDispose(boolean flag) {
+ this.autoDispose = flag;
+ }
+
+ /**
+ * Specifies the Owner of the JTask.
+ * <P>
+ * Primarily used to center the JTask component relative to an owner,
+ * such as a JFrame object.
+ * <P>
+ * If set to null, the JTask component will be centered relative to the
+ * user's screen.
+ *
+ * @param owner Owner container. May be null.
+ */
+ public void setOwner(Container owner) {
+ this.owner = owner;
+ }
+
+ /**
+ * Enables modality of the JTask Dialog box.
+ * <P>
+ * When set to true, the JTask Dialog box is modal, and the user cannot
+ * interact with any other UI components on the screen.
+ * <P>
+ * When set to false, the JTask Dialog box is not modal, and the user may
+ * interact with other UI components on the screen.
+ * <P>
+ * By default, this value is set to true.
+ * <P>
+ *
+ * @param modal modality flag.
+ */
+ public void setModal(boolean modal) {
+ this.modal = modal;
+ }
+
+ /**
+ * Sets Milliseconds until JTask Dialog Box is Displayed.
+ * <P>Default is set to 100 ms.
+ *
+ * @param millisToPopup long value.
+ */
+ public void setMillisToPopup(int millisToPopup) {
+ this.millisToPopup = millisToPopup;
+ }
+
+ /**
+ * Gets Millieconds until JTask Dialog Box is Displayed.
+ * <P>Default is set to 100 ms.
+ *
+ * @return millisToPopup long value.
+ */
+ public int getMillisToPopup() {
+ return this.millisToPopup;
+ }
+
+ /**
+ * Gets Display Options for Status Field.
+ *
+ * @return boolean value.
+ */
+ boolean getStatusFlag() {
+ return this.statusFlag;
+ }
+
+ /**
+ * Gets Display Options for Time Elapsed Field.
+ *
+ * @return boolean value.
+ */
+ boolean getTimeElapsedFlag() {
+ return this.timeElapsedFlag;
+ }
+
+ /**
+ * Gets Display Options for Time Remaining Field.
+ *
+ * @return boolean value.
+ */
+ boolean getTimeRemainingFlag() {
+ return this.timeRemainingFlag;
+ }
+
+ /**
+ * Gets Display Options for Cancel Button Field.
+ *
+ * @return boolean value.
+ */
+ boolean getCancelButtonFlag() {
+ return this.cancelButtonFlag;
+ }
+
+ /**
+ * Gets Display Options for Close Button Field.
+ *
+ * @return boolean value.
+ */
+ boolean getCloseButtonFlag() {
+ return this.closeButtonFlag;
+ }
+
+ /**
+ * Gets AutoDispose Flag.
+ *
+ * @return boolean value.
+ */
+ boolean getAutoDispose() {
+ return autoDispose;
+ }
+
+ /**
+ * Gets JTask Owner object.
+ *
+ * @return Container owner object.
+ */
+ Container getOwner() {
+ return owner;
+ }
+
+ /**
+ * Gets Modality flag.
+ *
+ * @return boolean value.
+ */
+ boolean getModal() {
+ return this.modal;
+ }
+}
diff --git a/corelibs/task/src/main/java/cytoscape/task/ui/StringUtils.java b/corelibs/task/src/main/java/cytoscape/task/ui/StringUtils.java
new file mode 100644
index 0000000..e250e89
--- /dev/null
+++ b/corelibs/task/src/main/java/cytoscape/task/ui/StringUtils.java
@@ -0,0 +1,128 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.task.ui;
+
+import java.text.SimpleDateFormat;
+
+import java.util.Calendar;
+import java.util.TimeZone;
+
+
+/**
+ * Misc Utilities for Formatting Times and Strings.
+ *
+ * @author Ethan Cerami
+ */
+public class StringUtils {
+ /**
+ * Not Available String.
+ */
+ public static final String NOT_AVAILABLE_STR = "N/A";
+
+ /**
+ * String Length.
+ */
+ public static final int STR_LENGTH = 60;
+
+ /**
+ * Given a time value in milliseconds, this method returns a human
+ * readable representation.
+ * Here are a few examples:
+ * <P>
+ * <UL>
+ * <LI>If time is negative, the human readable representation is "N/A".
+ * <LI>If time is 3000, the human readable representation is "00:03".
+ * <LI>If time is 300000, the human readable representation is "05:00".
+ * <LI>If time is 302000, the human readable representation is "05:02".
+ * <LI>If time is 3601000, the human readable representation is
+ * "01:00:01".
+ * </UL>
+ *
+ * @param time Time in millseconds.
+ * @return Human Readable Representation of Time.
+ */
+ public static String getTimeString(long time) {
+ if (time < 0) {
+ return NOT_AVAILABLE_STR;
+ } else {
+ // Use GMT Time Zone so that we start exactly at the
+ // Epoch: midnight, GM, January 1st, 1970.
+ SimpleDateFormat dateFormat;
+ TimeZone timeZone = TimeZone.getTimeZone("GMT");
+ Calendar calendar = Calendar.getInstance(timeZone);
+ calendar.setTimeInMillis(time);
+
+ if (calendar.get(Calendar.HOUR) >= 1) {
+ dateFormat = new SimpleDateFormat("HH:mm:ss");
+ } else {
+ dateFormat = new SimpleDateFormat("mm:ss");
+ }
+
+ dateFormat.setCalendar(calendar);
+
+ return dateFormat.format(calendar.getTime());
+ }
+ }
+
+ /**
+ * Truncates a String to a specific length or pads it with extra spaces.
+ *
+ * @param str Original String.
+ * @return Trucated or Padded String.
+ */
+ public static String truncateOrPadString(String str) {
+ StringBuffer temp;
+
+ if (str == null) {
+ temp = new StringBuffer();
+ } else {
+ temp = new StringBuffer(str);
+ }
+
+ int diff = STR_LENGTH - temp.length();
+
+ if (diff > 0) {
+ for (int i = 0; i < diff; i++) {
+ temp.append(" ");
+ }
+
+ return temp.toString();
+ } else {
+ return new String(temp.substring(0, STR_LENGTH) + "...");
+ }
+ }
+}
diff --git a/corelibs/task/src/main/java/cytoscape/task/ui/doc-files/bare_bones_jtask.png b/corelibs/task/src/main/java/cytoscape/task/ui/doc-files/bare_bones_jtask.png
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diff --git a/corelibs/task/src/main/java/cytoscape/task/ui/doc-files/error2_jtask.png b/corelibs/task/src/main/java/cytoscape/task/ui/doc-files/error2_jtask.png
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diff --git a/corelibs/task/src/main/java/cytoscape/task/ui/package.html b/corelibs/task/src/main/java/cytoscape/task/ui/package.html
new file mode 100644
index 0000000..b107cdf
--- /dev/null
+++ b/corelibs/task/src/main/java/cytoscape/task/ui/package.html
@@ -0,0 +1,5 @@
+<html>
+<body>
+UI code related to task control.
+</body>
+</html>
diff --git a/corelibs/task/src/main/java/cytoscape/task/util/DEPENDENCIES b/corelibs/task/src/main/java/cytoscape/task/util/DEPENDENCIES
new file mode 100644
index 0000000..a0b26a7
--- /dev/null
+++ b/corelibs/task/src/main/java/cytoscape/task/util/DEPENDENCIES
@@ -0,0 +1 @@
+cytoscape.task.ui
\ No newline at end of file
diff --git a/corelibs/task/src/main/java/cytoscape/task/util/StringWrap.java b/corelibs/task/src/main/java/cytoscape/task/util/StringWrap.java
new file mode 100644
index 0000000..7cdb868
--- /dev/null
+++ b/corelibs/task/src/main/java/cytoscape/task/util/StringWrap.java
@@ -0,0 +1,95 @@
+package cytoscape.task.util;
+
+
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements. See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+public class StringWrap {
+
+ /***
+ * <p>Wraps a single line of text, identifying words by <code>' '</code>.</p>
+ *
+ * <p>Leading spaces on a new line are stripped.
+ * Trailing spaces are not stripped.</p>
+ *
+ * <pre>
+ * WordUtils.wrap(null, *, *, *) = null
+ * WordUtils.wrap("", *, *, *) = ""
+ * </pre>
+ *
+ * @param str the String to be word wrapped, may be null
+ * @param wrapLength the column to wrap the words at, less than 1 is treated as 1
+ * @param newLineStr the string to insert for a new line,
+ * <code>null</code> uses the system property line separator
+ * @param wrapLongWords true if long words (such as URLs) should be wrapped
+ * @return a line with newlines inserted, <code>null</code> if null input
+ */
+ public static String wrap(String str, int wrapLength, String newLineStr, boolean wrapLongWords) {
+ if (str == null) {
+ return null;
+ }
+ if (newLineStr == null) {
+ newLineStr = "\n";
+ }
+ if (wrapLength < 1) {
+ wrapLength = 1;
+ }
+ int inputLineLength = str.length();
+ int offset = 0;
+ StringBuffer wrappedLine = new StringBuffer(inputLineLength + 32);
+
+ while ((inputLineLength - offset) > wrapLength) {
+ if (str.charAt(offset) == ' ') {
+ offset++;
+ continue;
+ }
+ int spaceToWrapAt = str.lastIndexOf(' ', wrapLength + offset);
+
+ if (spaceToWrapAt >= offset) {
+ // normal case
+ wrappedLine.append(str.substring(offset, spaceToWrapAt));
+ wrappedLine.append(newLineStr);
+ offset = spaceToWrapAt + 1;
+
+ } else {
+ // really long word or URL
+ if (wrapLongWords) {
+ // wrap really long word one line at a time
+ wrappedLine.append(str.substring(offset, wrapLength + offset));
+ wrappedLine.append(newLineStr);
+ offset += wrapLength;
+ } else {
+ // do not wrap really long word, just extend beyond limit
+ spaceToWrapAt = str.indexOf(' ', wrapLength + offset);
+ if (spaceToWrapAt >= 0) {
+ wrappedLine.append(str.substring(offset, spaceToWrapAt));
+ wrappedLine.append(newLineStr);
+ offset = spaceToWrapAt + 1;
+ } else {
+ wrappedLine.append(str.substring(offset));
+ offset = inputLineLength;
+ }
+ }
+ }
+ }
+
+ // Whatever is left in line is short enough to just pass through
+ wrappedLine.append(str.substring(offset));
+
+ return wrappedLine.toString();
+ }
+
+}
diff --git a/corelibs/task/src/main/java/cytoscape/task/util/TaskManager.java b/corelibs/task/src/main/java/cytoscape/task/util/TaskManager.java
new file mode 100644
index 0000000..8982351
--- /dev/null
+++ b/corelibs/task/src/main/java/cytoscape/task/util/TaskManager.java
@@ -0,0 +1,166 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.task.util;
+
+import cytoscape.task.Task;
+
+import cytoscape.task.ui.JTask;
+import cytoscape.task.ui.JTaskConfig;
+
+import java.util.TimerTask;
+
+
+/**
+ * Utility class used to execute tasks and visually monitor their progress.
+ */
+public class TaskManager {
+ /**
+ * Executes the specified task in a new thread, and automatically
+ * pops open a JTask UI Component for visually monitoring the task.
+ * <P>
+ * This method will block until the JTask UI Component is disposed.
+ * Disposal will occur automatically if JTaskConfig is set to
+ * setAutoDispose(true). Otherwise, disposal will occur when the user
+ * manually closes the JTask UI Dialog Box.
+ *
+ * @param task the task to execute.
+ * @param config Configuration options for the JTask UI Component.
+ * @return true value indicates that task completed successfully.
+ * false value indicates that task was halted by user or task
+ * encountered an error.
+ */
+ public synchronized static boolean executeTask(Task task, JTaskConfig config) {
+ // Validate incoming task parameter.
+ if (task == null) {
+ throw new NullPointerException("Task is null");
+ }
+
+ // If JTaskConfig is null, use the bare bones configuration options.
+ if (config == null) {
+ config = new JTaskConfig();
+ }
+
+ // Instantiate a new JTask UI Component
+ JTask jTask = new JTask(task, config);
+
+ // Tell task to report progress to JTask
+ task.setTaskMonitor(jTask);
+
+ // Create a Task Wrapper
+ TaskWrapper taskThread = new TaskWrapper(task, jTask);
+
+ // Start the Task
+ taskThread.start();
+
+ // Show the JTask Dialog Box.
+ Object popUpLock = new Object();
+ startPopupTimer(config, popUpLock);
+
+ // Wait for notification of pop-up
+ try {
+ synchronized (popUpLock) {
+ // This locks the current thread until notification of pop-up.
+ popUpLock.wait();
+
+ if (taskThread.isAlive()) {
+ // Thread will now block until modal dialog is
+ // disposed automatically or by user.
+ jTask.setVisible(true);
+ }
+ }
+ } catch (InterruptedException e) {
+ }
+
+ // If all went well, return true. Otherwise, return false.
+ if ((jTask.errorOccurred() == false) && (jTask.haltRequested() == false)) {
+ return true;
+ } else {
+ return false;
+ }
+ }
+
+ /**
+ * Shows JTask Dialog Box after XX milliseconds of delay.
+ * @param config JTaskConfig Object.
+ */
+ private static void startPopupTimer(final JTaskConfig config, final Object popUpLock) {
+ // Create Timer in new thread.
+ java.util.Timer timer = new java.util.Timer();
+ TimerTask task = new TimerTask() {
+ public void run() {
+ synchronized (popUpLock) {
+ popUpLock.notify();
+ }
+ }
+ };
+
+ timer.schedule(task, config.getMillisToPopup());
+ }
+}
+
+
+/**
+ * Used to Wrap an Existing Task.
+ */
+class TaskWrapper extends Thread {
+ private Task task;
+ private JTask jTask;
+
+ /**
+ * Constructor.
+ *
+ * @param task Task Object.
+ * @param jTask JTask Object.
+ */
+ TaskWrapper(Task task, JTask jTask) {
+ this.task = task;
+ this.jTask = jTask;
+ }
+
+ /**
+ * Executes the Task.
+ */
+ public void run() {
+ try {
+ // Run the actual task
+ task.run();
+ } finally {
+ // Inform the UI Component that the task is now done
+ jTask.setDone();
+ }
+ }
+}
diff --git a/corelibs/task/src/main/java/cytoscape/task/util/package.html b/corelibs/task/src/main/java/cytoscape/task/util/package.html
new file mode 100644
index 0000000..ab8f62d
--- /dev/null
+++ b/corelibs/task/src/main/java/cytoscape/task/util/package.html
@@ -0,0 +1,5 @@
+<html>
+<body>
+Utility manager for executing tasks.
+</body>
+</html>
diff --git a/corelibs/task/src/test/java/cytoscape/task/ui/StringUtilsTest.java b/corelibs/task/src/test/java/cytoscape/task/ui/StringUtilsTest.java
new file mode 100644
index 0000000..c445db6
--- /dev/null
+++ b/corelibs/task/src/test/java/cytoscape/task/ui/StringUtilsTest.java
@@ -0,0 +1,76 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.task.ui;
+
+import junit.framework.TestCase;
+
+
+/**
+ * JUnit Test for StringUtils.
+ */
+public class StringUtilsTest extends TestCase {
+ /**
+ * Tests the GetTimeString() static method.
+ */
+ public void testGetTimeString() {
+ String timeStr = StringUtils.getTimeString(-1);
+ assertEquals(StringUtils.NOT_AVAILABLE_STR, timeStr);
+
+ timeStr = StringUtils.getTimeString(0L);
+ assertEquals("00:00", timeStr);
+
+ timeStr = StringUtils.getTimeString(3000);
+ assertEquals("00:03", timeStr);
+
+ timeStr = StringUtils.getTimeString(300000);
+ assertEquals("05:00", timeStr);
+
+ timeStr = StringUtils.getTimeString(302000);
+ assertEquals("05:02", timeStr);
+
+ timeStr = StringUtils.getTimeString(3601000);
+ assertEquals("01:00:01", timeStr);
+ }
+
+ /**
+ * Tests the PadString static method.
+ */
+ public void testPadString() {
+ String str = StringUtils.truncateOrPadString("Testing");
+ assertEquals(StringUtils.STR_LENGTH, str.length());
+ }
+}
diff --git a/corelibs/task/src/test/java/cytoscape/task/ui/package.html b/corelibs/task/src/test/java/cytoscape/task/ui/package.html
new file mode 100644
index 0000000..7c84985
--- /dev/null
+++ b/corelibs/task/src/test/java/cytoscape/task/ui/package.html
@@ -0,0 +1,5 @@
+<html>
+<body>
+JUnit Tests for UI Components and related Utility Classes.
+</body>
+</html>
diff --git a/corelibs/undo.support/pom.xml b/corelibs/undo.support/pom.xml
new file mode 100644
index 0000000..926ba3a
--- /dev/null
+++ b/corelibs/undo.support/pom.xml
@@ -0,0 +1,41 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>parent</artifactId>
+ <version>2.8.4-SNAPSHOT</version>
+ </parent>
+
+ <artifactId>undo-support</artifactId>
+ <packaging>jar</packaging>
+
+ <name>undo-support</name>
+
+ <!-- bootstrap for cytoscape dependencies, namely the parent POM snapshots -->
+ <repositories>
+ <repository>
+ <id>cytoscape_snapshots</id>
+ <snapshots>
+ <enabled>true</enabled>
+ </snapshots>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <name>Cytoscape Snapshots</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/</url>
+ </repository>
+ <repository>
+ <id>cytoscape_releases</id>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ <name>Cytoscape Releases</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/releases/</url>
+ </repository>
+ </repositories>
+
+</project>
+
diff --git a/corelibs/undo.support/src/main/java/undo/Undo.java b/corelibs/undo.support/src/main/java/undo/Undo.java
new file mode 100644
index 0000000..485e251
--- /dev/null
+++ b/corelibs/undo.support/src/main/java/undo/Undo.java
@@ -0,0 +1,80 @@
+/*
+ File: Undo.java
+
+ Copyright (c) 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package undo;
+
+import javax.swing.undo.UndoManager;
+import javax.swing.undo.UndoableEditSupport;
+
+
+/**
+ * Rudimentary support for undo. To post an edit to the manager, call
+ * Undo.getUndoableEditSupport().postEdit(yourEdit). To handle the edits,
+ * you should extend this class and write actions, etc. that use the
+ * UndoManager.
+ */
+public class Undo {
+
+ private static UndoManager m_undoManager;
+ private static UndoableEditSupport m_undoSupport;
+
+ /**
+ * Returns the UndoManager. To preserve encapsulation and to prevent
+ * the wrong hands for mucking with your edit stack, don't make this
+ * public! Rather, extend the class and use this method with the
+ * class and package to set up actions, etc..
+ * @return the UndoManager used for managing the edits.
+ */
+ protected static UndoManager getUndoManager() {
+ return m_undoManager;
+ }
+
+ /**
+ * Use this method to get the UndoableEditSupport which you should use
+ * to post edits: Undo.getUndoableEditSupport().postEdit(yourEdit).
+ * @return the UndoableEditSupport used for posting edits.
+ */
+ public static UndoableEditSupport getUndoableEditSupport() {
+ return m_undoSupport;
+ }
+
+ static {
+ m_undoManager = new UndoManager();
+ m_undoSupport = new UndoableEditSupport();
+ m_undoSupport.addUndoableEditListener( m_undoManager );
+ }
+}
+
diff --git a/corelibs/util.intr/pom.xml b/corelibs/util.intr/pom.xml
new file mode 100644
index 0000000..ea82b7e
--- /dev/null
+++ b/corelibs/util.intr/pom.xml
@@ -0,0 +1,41 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>parent</artifactId>
+ <version>2.8.4-SNAPSHOT</version>
+ </parent>
+
+ <artifactId>util-intr</artifactId>
+ <packaging>jar</packaging>
+
+ <name>util-intr</name>
+
+ <!-- bootstrap for cytoscape dependencies, namely the parent POM snapshots -->
+ <repositories>
+ <repository>
+ <id>cytoscape_snapshots</id>
+ <snapshots>
+ <enabled>true</enabled>
+ </snapshots>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <name>Cytoscape Snapshots</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/</url>
+ </repository>
+ <repository>
+ <id>cytoscape_releases</id>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ <name>Cytoscape Releases</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/releases/</url>
+ </repository>
+ </repositories>
+
+</project>
+
diff --git a/corelibs/util.intr/src/main/java/cytoscape/util/intr/ArrayIntEnumerator.java b/corelibs/util.intr/src/main/java/cytoscape/util/intr/ArrayIntEnumerator.java
new file mode 100644
index 0000000..68123e3
--- /dev/null
+++ b/corelibs/util.intr/src/main/java/cytoscape/util/intr/ArrayIntEnumerator.java
@@ -0,0 +1,85 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.util.intr;
+
+
+/**
+ * A utility class which conveniently converts an array of integers into
+ * an IntEnumerator (an enumeration of integers).
+ */
+public final class ArrayIntEnumerator implements IntEnumerator {
+ private final int[] m_elements;
+ private int m_index;
+ private final int m_end;
+
+ /**
+ * No copy of the elements array is made. The contents of the array
+ * are never modified by this object.
+ */
+ public ArrayIntEnumerator(int[] elements, int beginIndex, int length) {
+ if (beginIndex < 0)
+ throw new IllegalArgumentException("beginIndex is less than zero");
+
+ if (length < 0)
+ throw new IllegalArgumentException("length is less than zero");
+
+ if ((((long) beginIndex) + (long) length) > (long) elements.length)
+ throw new IllegalArgumentException("combination of beginIndex and length exceed length of array");
+
+ m_elements = elements;
+ m_index = beginIndex;
+ m_end = beginIndex + length;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final int numRemaining() {
+ return m_end - m_index;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final int nextInt() {
+ return m_elements[m_index++];
+ }
+}
diff --git a/corelibs/util.intr/src/main/java/cytoscape/util/intr/ArrayIntIterator.java b/corelibs/util.intr/src/main/java/cytoscape/util/intr/ArrayIntIterator.java
new file mode 100644
index 0000000..3889081
--- /dev/null
+++ b/corelibs/util.intr/src/main/java/cytoscape/util/intr/ArrayIntIterator.java
@@ -0,0 +1,85 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.util.intr;
+
+
+/**
+ * A utility class which conveniently converts an array of integers into
+ * an IntIterator (an iteration of integers).
+ */
+public final class ArrayIntIterator implements IntIterator {
+ private final int[] m_elements;
+ private int m_index;
+ private final int m_end;
+
+ /**
+ * No copy of the elements array is made. The contents of the array
+ * are never modified by this object.
+ */
+ public ArrayIntIterator(int[] elements, int beginIndex, int length) {
+ if (beginIndex < 0)
+ throw new IllegalArgumentException("beginIndex is less than zero");
+
+ if (length < 0)
+ throw new IllegalArgumentException("length is less than zero");
+
+ if ((((long) beginIndex) + (long) length) > (long) elements.length)
+ throw new IllegalArgumentException("combination of beginIndex and length exceed length of array");
+
+ m_elements = elements;
+ m_index = beginIndex;
+ m_end = beginIndex + length;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final boolean hasNext() {
+ return m_index < m_end;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public final int nextInt() {
+ return m_elements[m_index++];
+ }
+}
diff --git a/corelibs/util.intr/src/main/java/cytoscape/util/intr/IntArray.java b/corelibs/util.intr/src/main/java/cytoscape/util/intr/IntArray.java
new file mode 100644
index 0000000..6c190d8
--- /dev/null
+++ b/corelibs/util.intr/src/main/java/cytoscape/util/intr/IntArray.java
@@ -0,0 +1,124 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.util.intr;
+
+
+/**
+ * A dynamically growing array of integers.
+ * Valid indices of this array are in the range [0, Integer.MAX_VALUE - 1].<p>
+ * In the underlying implementation, this dynamically growing array
+ * increases in size to adapt to elements being added (the size of the
+ * underlying data structure supporting this dynamically growing array
+ * is invisible to the programmer). In the underlying implementation, this
+ * dynamic array never decreases in size. Underlying size expansions are
+ * implemented such that the operation of expanding in size is amortized over
+ * the constant time complexity of inserting new elements into this
+ * dynamic array.<p>
+ * An instance of this class is serializable; however, serialized instances of
+ * this class should not be stored in a persistent manner because the
+ * serialization implemented in this class makes no attempt at handling
+ * class versioning.
+ */
+public final class IntArray implements java.io.Serializable {
+ private final static int INITIAL_CAPACITY = 0; // Must be non-negative.
+ private int[] m_arr;
+
+ /**
+ * Creates a new IntArray object.
+ */
+ public IntArray() {
+ m_arr = new int[INITIAL_CAPACITY];
+ }
+
+ /**
+ * Returns the value at specified index.
+ * This method will not increase the size of the underlying array, no
+ * matter what. The value returned by this method will be 0 unless a
+ * value at given index has been previously specified with
+ * setIntAtIndex(int, int).
+ *
+ * @exception ArrayIndexOutOfBoundsException if index is negative or
+ * Integer.MAX_VALUE.
+ */
+ public final int getIntAtIndex(int index) {
+ // Do pre-checking because try/catch with thrown exception causes huge
+ // performance hit.
+ if ((index >= m_arr.length) && (index != Integer.MAX_VALUE))
+ return 0;
+
+ return m_arr[index]; // Exception if Integer.MAX_VALUE or negative.
+ }
+
+ /**
+ * Sets the specified value at specified index.
+ * This method will potentially increase the size of the underlying array,
+ * but only if two conditions hold:
+ * 1. value is not zero and
+ * 2. index is greater than or equal to the length of the underlying
+ * array.
+ * <p>
+ * NOTE: Setting very large indices to non-zero values implies instantiating
+ * a very large underlying data structure.
+ *
+ * @exception ArrayIndexOutOfBoundsException if index is negative or
+ * Integer.MAX_VALUE.
+ */
+ public final void setIntAtIndex(int value, int index) {
+ // Do pre-checking because try/catch with thrown exception causes huge
+ // performance hit.
+ if ((index >= m_arr.length) && (value == 0) && (index != Integer.MAX_VALUE))
+ return;
+
+ try {
+ m_arr[index] = value;
+ } catch (ArrayIndexOutOfBoundsException e) {
+ if ((index < 0) || (index == Integer.MAX_VALUE)) {
+ throw e;
+ }
+
+ // We need to ensure amortized constant time hits.
+ final int newArrSize = (int) Math.min((long) Integer.MAX_VALUE,
+ Math.max((((long) m_arr.length) * 2L) + 1L,
+ ((long) index) + 1L
+ + (long) INITIAL_CAPACITY));
+ int[] newArr = new int[newArrSize];
+ System.arraycopy(m_arr, 0, newArr, 0, m_arr.length);
+ m_arr = newArr;
+ m_arr[index] = value;
+ }
+ }
+}
diff --git a/corelibs/util.intr/src/main/java/cytoscape/util/intr/IntBTree.java b/corelibs/util.intr/src/main/java/cytoscape/util/intr/IntBTree.java
new file mode 100644
index 0000000..363ce49
--- /dev/null
+++ b/corelibs/util.intr/src/main/java/cytoscape/util/intr/IntBTree.java
@@ -0,0 +1,1137 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.util.intr;
+
+
+/**
+ * An in-memory B<sup>+</sup>-tree that stores integers.<p>
+ * The motivation behind the implementation of this tree is not usefulness.
+ * The motivation is to get to know the algorithms associated with this tree
+ * structure, so that implementing variants of this structure would become
+ * simpler (an example of a variant of this structure is the R-tree). The
+ * implementation of this tree uses recursion (as opposed to the iterative
+ * approach). While there is a performance penalty paid by using recursion,
+ * recursion does make the code much more understandable.<p>
+ * An instance of this class is serializable; however, serialized instances of
+ * this class should not be stored in a persistent manner because the
+ * serialization implemented in this class makes no attempt at handling
+ * class versioning.
+ */
+public final class IntBTree implements java.io.Serializable {
+ // This quantity must be at least 3.
+ /**
+ *
+ */
+ public final static int DEFAULT_MAX_BRANCHES = 27;
+ private final int m_maxBranches;
+ private final int m_minBranches;
+ private Node m_root;
+
+ /**
+ * Creates a new tree structure with an optimal branching factor.
+ */
+ public IntBTree() {
+ this(DEFAULT_MAX_BRANCHES);
+ }
+
+ /**
+ * Creates a new tree structure with the specified maximum branching
+ * factor. Overriding the default maximum branching factor is only
+ * useful for testing purposes; there are no performance gains to be had.
+ * @param maxBranches the maximum branching factor of this tree.
+ * @exception IllegalArgumentException if maxBranches is less than three.
+ */
+ public IntBTree(final int maxBranches) {
+ m_maxBranches = maxBranches;
+
+ // Letting minimum fill fall below half actually decreases performance by
+ // a hair, my tests show. However, I like the idea of letting nodes fall
+ // below being half full, so I'm keeping it at 0.4 (as opposed to 0.5).
+ // Note that every piece of literature in the entire universe that
+ // mentions B-trees defines them is such a way which is equivalent to
+ // to setting this to 0.5, and not below (setting it above 0.5 would
+ // destroy the algorithms). With 0.4, the following table shows
+ // the max/min relationships:
+ //
+ // m_maxBranches | m_minBranches
+ // ---------------+---------------
+ // 3 2
+ // 4 2
+ // 5 2
+ // 6 2
+ // 7 3
+ // 8 3
+ // 9 4
+ // 27 11
+ m_minBranches = Math.max(2, (int) (((double) (m_maxBranches + 1)) * 0.4d));
+
+ m_root = new Node(m_maxBranches, true);
+ }
+
+ /**
+ * Empties this structure of all elements. This method returns in constant
+ * time (note however that garbage collection will take place in the
+ * background).
+ */
+ public final void empty() {
+ m_root = new Node(m_maxBranches, true);
+ }
+
+ /**
+ * Returns the number of elements currently in this structure. Duplicate
+ * entries are counted however many times they are present. This method
+ * returns in constant time.<p>
+ * NOTE: To retrieve an enumeration of all entries in this tree, use
+ * searchRange() with Integer.MIN_VALUE as the lower bound and
+ * Integer.MAX_VALUE as the upper bound.
+ */
+ public final int size() {
+ return isLeafNode(m_root) ? m_root.sliceCount : m_root.data.deepCount;
+ }
+
+ /*
+ * This simple functionality is in the form of a helper method in order
+ * to make code more readable.
+ */
+ private final static boolean isLeafNode(final Node n) {
+ return n.data == null;
+ }
+
+ /**
+ * Inserts a new entry into this tree structure; duplicate entries may be
+ * inserted. This method has a time complexity of O(log(N)) where N is the
+ * number of entries currently stored in this tree structure.
+ * @param x the new entry to insert.
+ */
+ public final void insert(final int x) {
+ final Node newSibling = insert(m_root, x, m_maxBranches);
+
+ if (newSibling != null) { // The root has been split into two.
+
+ final int newSplitVal;
+ final int newDeepCount;
+
+ if (isLeafNode(newSibling)) {
+ newSplitVal = newSibling.values[0];
+ newDeepCount = m_root.sliceCount + newSibling.sliceCount;
+ } else {
+ newSplitVal = m_root.data.splitVals[m_root.sliceCount - 1];
+ newDeepCount = m_root.data.deepCount + newSibling.data.deepCount;
+ }
+
+ final Node newRoot = new Node(m_maxBranches, false);
+ newRoot.sliceCount = 2;
+ newRoot.data.deepCount = newDeepCount;
+ newRoot.data.splitVals[0] = newSplitVal;
+ newRoot.data.children[0] = m_root;
+ newRoot.data.children[1] = newSibling;
+ m_root = newRoot;
+ }
+ }
+
+ /*
+ * Returns a node being the newly created node if a split was performed;
+ * the node returned is the right sibling of node n. If the returned node
+ * is a leaf node then the first value of the node is to be the new split
+ * index; if return value is internal node, then the split index to be used
+ * is n.data.splitVals[n.sliceCount - 1]. (This is something that this
+ * method sets; it's this method saying "use this index in the higher
+ * levels".)
+ */
+ private final static Node insert(final Node n, final int x, final int maxBranches) {
+ if (isLeafNode(n)) {
+ if (n.sliceCount < maxBranches) { // There's room for a value.
+
+ int i = -1;
+
+ while (++i < n.sliceCount)
+
+ if (x <= n.values[i])
+ break;
+
+ for (int j = n.sliceCount; j > i;)
+ n.values[j] = n.values[--j];
+
+ n.values[i] = x;
+ n.sliceCount++;
+
+ return null;
+ } else { // No room for another value in this leaf node; perform split.
+
+ final Node newLeafSibling = new Node(maxBranches, true);
+ final int combinedCount = maxBranches + 1;
+ n.sliceCount = combinedCount >> 1; // Divide by two.
+ newLeafSibling.sliceCount = combinedCount - n.sliceCount;
+ split(x, n.values, newLeafSibling.values, newLeafSibling.sliceCount);
+
+ return newLeafSibling;
+ }
+ } else { // Internal node.
+
+ int foundPath = 0;
+
+ for (int i = n.sliceCount - 2; i >= 0; i--)
+ if (x >= n.data.splitVals[i]) {
+ foundPath = i + 1;
+
+ break;
+ }
+
+ final Node oldChild = n.data.children[foundPath];
+ final Node newChild = insert(oldChild, x, maxBranches);
+
+ if (newChild == null) {
+ n.data.deepCount++;
+
+ return null;
+ } else { // A split was performed at one level deeper.
+
+ final int newSplit;
+
+ if (isLeafNode(newChild))
+ newSplit = newChild.values[0];
+ else
+ newSplit = oldChild.data.splitVals[oldChild.sliceCount - 1];
+
+ if (n.sliceCount < maxBranches) { // There's room here.
+
+ for (int j = n.sliceCount - 1; j > foundPath;) {
+ n.data.children[j + 1] = n.data.children[j];
+ n.data.splitVals[j] = n.data.splitVals[--j];
+ }
+
+ n.sliceCount++;
+ n.data.deepCount++;
+ n.data.children[foundPath + 1] = newChild;
+ n.data.splitVals[foundPath] = newSplit;
+
+ return null;
+ } else { // No room in this internal node; perform split.
+
+ final Node newInternalSibling = new Node(maxBranches, false);
+ final int combinedCount = maxBranches + 1;
+ n.sliceCount = combinedCount >> 1; // Divide by two.
+ newInternalSibling.sliceCount = combinedCount - n.sliceCount;
+ split(newChild, foundPath, n.data.children, newInternalSibling.data.children,
+ newInternalSibling.sliceCount);
+ split(newSplit, n.data.splitVals, newInternalSibling.data.splitVals,
+ newInternalSibling.sliceCount - 1);
+ n.data.deepCount = 0; // Update the deep count in both nodes.
+
+ if (isLeafNode(newChild)) {
+ for (int i = 0; i < n.sliceCount; i++)
+ n.data.deepCount += n.data.children[i].sliceCount;
+
+ for (int i = 0; i < newInternalSibling.sliceCount; i++)
+ newInternalSibling.data.deepCount += newInternalSibling.data.children[i].sliceCount;
+ } else {
+ for (int i = 0; i < n.sliceCount; i++)
+ n.data.deepCount += n.data.children[i].data.deepCount;
+
+ for (int i = 0; i < newInternalSibling.sliceCount; i++)
+ newInternalSibling.data.deepCount += newInternalSibling.data.children[i].data.deepCount;
+ }
+
+ return newInternalSibling;
+ }
+ }
+ }
+ }
+
+ /*
+ * It's tedious to rigorously define what this method does. I give an
+ * example:
+ *
+ *
+ * INPUTS
+ * ======
+ *
+ * newVal: 5
+ *
+ * +---+---+---+---+---+---+---+
+ * origBuff: | 0 | 2 | 3 | 6 | 6 | 8 | 9 |
+ * +---+---+---+---+---+---+---+
+ *
+ * +---+---+---+---+---+---+---+
+ * overflowBuff: | | | | | | | |
+ * +---+---+---+---+---+---+---+
+ *
+ * overflowCount: 4
+ *
+ *
+ * OUTPUTS
+ * =======
+ *
+ * +---+---+---+---+---+---+---+
+ * origBuff: | 0 | 2 | 3 | 5 | | | |
+ * +---+---+---+---+---+---+---+
+ *
+ * +---+---+---+---+---+---+---+
+ * overflowBuff: | 6 | 6 | 8 | 9 | | | |
+ * +---+---+---+---+---+---+---+
+ */
+ private final static void split(final int newVal, final int[] origBuff,
+ final int[] overflowBuff, final int overflowCount) {
+ int[] currentArr = overflowBuff;
+ int currentInx = overflowCount;
+ boolean found = false;
+
+ for (int i = origBuff.length - 1; i >= 0; i--) {
+ if ((!found) && (newVal >= origBuff[i])) {
+ currentArr[--currentInx] = newVal;
+ found = true;
+
+ if (currentArr == origBuff)
+ break;
+
+ i++;
+ } else {
+ currentArr[--currentInx] = origBuff[i];
+ }
+
+ if (currentInx == 0) {
+ if (found)
+ break;
+
+ currentArr = origBuff;
+ currentInx = origBuff.length - overflowCount + 1;
+ }
+ }
+
+ if (!found)
+ currentArr[0] = newVal;
+ }
+
+ /*
+ * It's tedious to rigorously define what this method does. I give an
+ * example:
+ *
+ *
+ * INPUTS
+ * ======
+ *
+ * newNode: Z
+ *
+ * newInx: 5
+ *
+ * +---+---+---+---+---+---+---+
+ * origNodes: | Q | I | E | A | Y | N | W |
+ * +---+---+---+---+---+---+---+
+ *
+ * +---+---+---+---+---+---+---+
+ * overflowNodes: | | | | | | | |
+ * +---+---+---+---+---+---+---+
+ *
+ * overflowCount: 4
+ *
+ *
+ * OUTPUTS
+ * =======
+ *
+ * +---+---+---+---+---+---+---+
+ * origBuff: | Q | I | E | A | / | / | / |
+ * +---+---+---+---+---+---+---+
+ *
+ * +---+---+---+---+---+---+---+
+ * overflowBuff: | Y | N | Z | W | | | |
+ * +---+---+---+---+---+---+---+
+ *
+ * In addition, the "unused" entries in origBuff are nulled out (remove
+ * pointers to enable garbage collection).
+ *
+ * Note that newInx means to put the new node after the existing node
+ * at index newInx in the original array. Placing the new node before
+ * every other node would entail specifying newInx as -1, which is not
+ * allowed.
+ */
+ private final static void split(Node newNode, final int newInx, final Node[] origNodes,
+ final Node[] overflowNodes, final int overflowCount) {
+ Node[] currentNodes = overflowNodes;
+ int currentInx = overflowCount;
+
+ for (int i = origNodes.length - 1; i >= 0; i--) {
+ if ((newNode != null) && (i == newInx)) {
+ currentNodes[--currentInx] = newNode;
+ newNode = null;
+
+ if (currentNodes == origNodes)
+ break;
+
+ i++;
+ } else {
+ currentNodes[--currentInx] = origNodes[i];
+ }
+
+ if (currentInx == 0) {
+ if (newNode == null)
+ break;
+
+ currentNodes = origNodes;
+ currentInx = origNodes.length - overflowCount + 1;
+ }
+ }
+
+ for (int i = origNodes.length - overflowCount + 1; i < origNodes.length; i++)
+ origNodes[i] = null; // Remove dangling pointers for garbage collection.
+ }
+
+ // NOTE TO MYSELF: If we had a double-linked node structure (every
+ // node points to its parent in addition to what we have now) and if
+ // we could access, in constant time, the leaf node to which an entry to
+ // be deleted belongs to, and if we did not store deep counts in nodes,
+ // then we could implement a single deletion in constant average time
+ // because the likelihood of necessary percolations (shifting and merging)
+ // decreases as we head from a leaf node to a root node after a deletion.
+ /**
+ * Deletes at most one entry of the integer x. This method has a time
+ * complexity of O(log(N)) where N is the number of entries currently
+ * stored in this tree structure.<p>
+ * Unfortunately there does not seem to exists an elegant algorithm for
+ * efficiently deleting a range of integers while guaranteeing a balanced
+ * tree structure.
+ * @param x the integer to try to delete (just one entry).
+ * @return true if and only if an entry was deleted (at most one entry is
+ * deleted by this method).
+ */
+ public final boolean delete(final int x) {
+ final boolean returnThis = delete(m_root, x, m_minBranches);
+
+ if ((!isLeafNode(m_root)) && (m_root.sliceCount == 1))
+ m_root = m_root.data.children[0];
+
+ return returnThis;
+ }
+
+ private final static boolean delete(final Node n, final int x, final int minBranches) {
+ if (isLeafNode(n)) {
+ int foundInx = -1;
+
+ for (int i = 0; i < n.sliceCount; i++) {
+ if (x <= n.values[i]) {
+ if (x == n.values[i]) {
+ foundInx = i;
+ }
+
+ break;
+ }
+ }
+
+ if (foundInx < 0) {
+ return false;
+ } else {
+ fillHole(foundInx, n.values, --n.sliceCount);
+
+ return true;
+ }
+ } else { // Internal node.
+
+ int deletedPath = -1;
+
+ for (int i = n.sliceCount - 2; i >= -1; i--) {
+ int currentMin = ((i < 0) ? Integer.MIN_VALUE : n.data.splitVals[i]);
+
+ if (currentMin <= x) {
+ if (delete(n.data.children[i + 1], x, minBranches)) {
+ n.data.deepCount--;
+ deletedPath = i + 1;
+
+ break;
+ }
+
+ if (currentMin < x)
+ break;
+ }
+ }
+
+ if (deletedPath < 0) {
+ return false;
+ }
+
+ final Node affectedChild = n.data.children[deletedPath];
+
+ if (affectedChild.sliceCount < minBranches) { // Underflow handling.
+
+ final Node leftChild = (deletedPath > 0) ? n.data.children[deletedPath - 1] : null;
+ final Node rightChild = ((deletedPath + 1) < n.sliceCount)
+ ? n.data.children[deletedPath + 1] : null;
+
+ if ((leftChild != null) && (leftChild.sliceCount > minBranches)) {
+ n.data.splitVals[deletedPath - 1] = distributeFromLeft(leftChild,
+ affectedChild,
+ n.data.splitVals[deletedPath
+ - 1], minBranches);
+ } else if ((rightChild != null) && (rightChild.sliceCount > minBranches)) {
+ n.data.splitVals[deletedPath] = distributeFromRight(rightChild, affectedChild,
+ n.data.splitVals[deletedPath],
+ minBranches);
+ } else { // Merge with a child sibling.
+
+ final int holeInx;
+
+ if (leftChild != null) // Merge with left child.
+ mergeSiblings(leftChild, affectedChild,
+ n.data.splitVals[holeInx = deletedPath - 1]);
+ else // Merge with right child.
+
+ mergeSiblings(affectedChild, rightChild,
+ n.data.splitVals[holeInx = deletedPath]);
+
+ fillHole(holeInx + 1, n.data.children, --n.sliceCount);
+ fillHole(holeInx, n.data.splitVals, n.sliceCount - 1);
+ }
+ }
+
+ return true;
+ }
+ }
+
+ /*
+ * Returns a new splitVal. Updates counts and nulls out entries as
+ * appropriate.
+ */
+ private final static int distributeFromLeft(final Node leftSibling, final Node thisSibling,
+ final int oldSplitVal, final int minBranches) {
+ final int distributeNum = ((1 + leftSibling.sliceCount) - minBranches) / 2;
+
+ if (isLeafNode(leftSibling)) {
+ for (int i = thisSibling.sliceCount, o = i + distributeNum; i > 0;)
+ thisSibling.values[--o] = thisSibling.values[--i];
+
+ for (int i = leftSibling.sliceCount - distributeNum, o = 0; o < distributeNum;)
+ thisSibling.values[o++] = leftSibling.values[i++];
+
+ leftSibling.sliceCount -= distributeNum;
+ thisSibling.sliceCount += distributeNum;
+
+ return thisSibling.values[0];
+ } else {
+ final int returnThis = leftSibling.data.splitVals[leftSibling.sliceCount
+ - distributeNum - 1];
+
+ for (int i = thisSibling.sliceCount, o = i + distributeNum; i > 0;)
+ thisSibling.data.children[--o] = thisSibling.data.children[--i];
+
+ for (int i = leftSibling.sliceCount - distributeNum, o = 0; o < distributeNum;)
+ thisSibling.data.children[o++] = leftSibling.data.children[i++];
+
+ final boolean leafChildren = isLeafNode(leftSibling.data.children[0]);
+ int deepCountDiff = 0;
+
+ for (int i = leftSibling.sliceCount - distributeNum; i < leftSibling.sliceCount; i++) {
+ deepCountDiff += (leafChildren ? leftSibling.data.children[i].sliceCount
+ : leftSibling.data.children[i].data.deepCount);
+ leftSibling.data.children[i] = null;
+ }
+
+ for (int i = thisSibling.sliceCount - 1, o = i + distributeNum; i > 0;)
+ thisSibling.data.splitVals[--o] = thisSibling.data.splitVals[--i];
+
+ thisSibling.data.splitVals[distributeNum - 1] = oldSplitVal;
+
+ for (int i = leftSibling.sliceCount - distributeNum, o = 0; o < (distributeNum - 1);)
+ thisSibling.data.splitVals[o++] = leftSibling.data.splitVals[i++];
+
+ leftSibling.sliceCount -= distributeNum;
+ thisSibling.sliceCount += distributeNum;
+ leftSibling.data.deepCount -= deepCountDiff;
+ thisSibling.data.deepCount += deepCountDiff;
+
+ return returnThis;
+ }
+ }
+
+ /*
+ * Returns a new splitVal. Updates counts and nulls out entries as
+ * appropriate.
+ */
+ private final static int distributeFromRight(final Node rightSibling, final Node thisSibling,
+ final int oldSplitVal, final int minBranches) {
+ final int distributeNum = ((1 + rightSibling.sliceCount) - minBranches) / 2;
+
+ if (isLeafNode(rightSibling)) {
+ for (int i = 0, o = thisSibling.sliceCount; i < distributeNum;)
+ thisSibling.values[o++] = rightSibling.values[i++];
+
+ for (int i = 0, o = distributeNum; o < rightSibling.sliceCount;)
+ rightSibling.values[i++] = rightSibling.values[o++];
+
+ rightSibling.sliceCount -= distributeNum;
+ thisSibling.sliceCount += distributeNum;
+
+ return rightSibling.values[0];
+ } else {
+ final int returnThis = rightSibling.data.splitVals[distributeNum - 1];
+ final boolean leafChildren = isLeafNode(rightSibling.data.children[0]);
+ int deepCountDiff = 0;
+
+ for (int i = 0, o = thisSibling.sliceCount; i < distributeNum;) {
+ deepCountDiff += (leafChildren ? rightSibling.data.children[i].sliceCount
+ : rightSibling.data.children[i].data.deepCount);
+ thisSibling.data.children[o++] = rightSibling.data.children[i++];
+ }
+
+ for (int i = distributeNum, o = 0; i < rightSibling.sliceCount;)
+ rightSibling.data.children[o++] = rightSibling.data.children[i++];
+
+ for (int i = rightSibling.sliceCount - distributeNum; i < rightSibling.sliceCount;
+ i++)
+ rightSibling.data.children[i] = null;
+
+ thisSibling.data.splitVals[thisSibling.sliceCount - 1] = oldSplitVal;
+
+ for (int i = 0, o = thisSibling.sliceCount; i < (distributeNum - 1);)
+ thisSibling.data.splitVals[o++] = rightSibling.data.splitVals[i++];
+
+ for (int i = distributeNum, o = 0; i < (rightSibling.sliceCount - 1);)
+ rightSibling.data.splitVals[o++] = rightSibling.data.splitVals[i++];
+
+ rightSibling.sliceCount -= distributeNum;
+ thisSibling.sliceCount += distributeNum;
+ rightSibling.data.deepCount -= deepCountDiff;
+ thisSibling.data.deepCount += deepCountDiff;
+
+ return returnThis;
+ }
+ }
+
+ /*
+ * Copies into leftSibling. You can discard rightSibling after this.
+ * Updates counts and nulls out entries as appropriate.
+ */
+ private final static void mergeSiblings(final Node leftSibling, final Node rightSibling,
+ final int splitValue) {
+ if (isLeafNode(leftSibling)) {
+ for (int i = 0, o = leftSibling.sliceCount; i < rightSibling.sliceCount;)
+ leftSibling.values[o++] = rightSibling.values[i++];
+
+ leftSibling.sliceCount += rightSibling.sliceCount;
+ rightSibling.sliceCount = 0; /* Pedantic. */
+ } else {
+ for (int i = 0, o = leftSibling.sliceCount; i < (rightSibling.sliceCount - 1);)
+ leftSibling.data.splitVals[o++] = rightSibling.data.splitVals[i++];
+
+ leftSibling.data.splitVals[leftSibling.sliceCount - 1] = splitValue;
+
+ for (int i = 0, o = leftSibling.sliceCount; i < rightSibling.sliceCount;)
+ leftSibling.data.children[o++] = rightSibling.data.children[i++];
+
+ for (int i = 0; i < rightSibling.sliceCount; i++) {
+ rightSibling.data.children[i] = null; /* Pedantic. */
+ }
+
+ leftSibling.sliceCount += rightSibling.sliceCount;
+ rightSibling.sliceCount = 0; // Pedantic.
+ leftSibling.data.deepCount += rightSibling.data.deepCount;
+ rightSibling.data.deepCount = 0; /* Pedantic. */
+ }
+ }
+
+ /*
+ * I give an example:
+ *
+ *
+ * INPUTS
+ * ======
+ *
+ * holeInx: 5
+ *
+ * +---+---+---+---+---+---+---+---+---+---+
+ * arr: | 1 | 2 | 8 | 5 | 9 | | 4 | 0 | | |
+ * +---+---+---+---+---+---+---+---+---+---+
+ *
+ * newLen: 7
+ *
+ *
+ * OUTPUTS
+ * =======
+ *
+ * +---+---+---+---+---+---+---+---+---+---+
+ * arr: | 1 | 2 | 8 | 5 | 9 | 4 | 0 | | | |
+ * +---+---+---+---+---+---+---+---+---+---+
+ */
+ private final static void fillHole(final int holeInx, final int[] arr, final int newLen) {
+ for (int i = holeInx; i < newLen;)
+ arr[i] = arr[++i];
+ }
+
+ /*
+ * I give an example:
+ *
+ *
+ * INPUTS
+ * ======
+ *
+ * holeInx: 1
+ *
+ * +---+---+---+---+---+---+
+ * arr: | H | | L | P | Z | |
+ * +---+---+---+---+---+---+
+ *
+ * newLen: 4
+ *
+ *
+ * OUTPUTS
+ * =======
+ *
+ * +---+---+---+---+---+---+
+ * arr: | H | L | P | Z | / | |
+ * +---+---+---+---+---+---+
+ *
+ * The last entry (after 'Z' in example) is nulled out so that
+ * garbage collection would not be obstructed.
+ */
+ private final static void fillHole(final int holeInx, final Node[] arr, final int newLen) {
+ int i = holeInx;
+
+ while (i < newLen)
+ arr[i] = arr[++i];
+
+ arr[i] = null;
+ }
+
+ /**
+ * Returns the number of entries of the integer x in this tree.
+ * This method has a time complexity of O(log(N)) where N is the total
+ * number of entries currently in this tree structure.<p>
+ * This method is superfluous because we can use searchRange(x, x, false) to
+ * get the same information, paying the same hit in time complexity.
+ * @param x the integer whose count to query.
+ * @return the number of entries x currently in this structure.
+ */
+ public final int count(final int x) {
+ return count(m_root, x, Integer.MIN_VALUE, Integer.MAX_VALUE);
+ }
+
+ /*
+ * It's important that with every invocation of this method, we have
+ * minBound <= x <= maxBound.
+ */
+ private final static int count(final Node n, final int x, final int minBound, final int maxBound) {
+ int count = 0;
+
+ if (minBound == maxBound) { // Trivially include node.
+ count += (isLeafNode(n) ? n.sliceCount : n.data.deepCount);
+ } else { // Cannot trivially include node; must recurse.
+
+ if (isLeafNode(n)) {
+ for (int i = 0; i < n.sliceCount; i++)
+ if (x <= n.values[i]) {
+ if (x == n.values[i])
+ count++;
+ else
+
+ break;
+ }
+ } else { // Internal node.
+
+ int currentMax = maxBound;
+ int currentMin;
+
+ for (int i = n.sliceCount - 2; i >= -1; i--) {
+ currentMin = ((i < 0) ? minBound : n.data.splitVals[i]);
+
+ if (currentMin <= x) {
+ count += count(n.data.children[i + 1], x, currentMin, currentMax);
+
+ if (currentMin < x)
+ break;
+ }
+
+ currentMax = currentMin;
+ }
+ }
+ }
+
+ return count;
+ }
+
+ /**
+ * Returns an enumeration of all entries in the range [xMin, xMax] currently
+ * in this tree, duplicates included. The elements of the enumeration are
+ * returned in non-descending order if the reverseOrder input parameter is
+ * false; otherwise, elements of the enumeration are returned in
+ * non-ascending order. This method takes O(log(N)) time to compute a
+ * return value, where N is the total number of entries currently in
+ * this tree structure. The returned enumeration reports the number of
+ * elements remaining in constant time. The returned enumeration can
+ * be completely traversed in O(K) time, where K is the number of elements
+ * in the returned enumeration. Note, however, that
+ * there is no guarantee that each successive element of the enumeration
+ * is returned in constant time; instead, the time complexity of accessing
+ * each successive element is only constant on average, and is in fact
+ * O(log(K)).<p>
+ * IMPORTANT: The returned enumeration becomes invalid as soon as any
+ * structure-modifying operation (insert or delete) is performed on this
+ * tree. Accessing an invalid enumeration's methods will result in
+ * unpredictable and ill-defined behavior in that enumeration, but will
+ * have no effect on the integrity of the underlying tree structure.<p>
+ * IMPLEMENTATION NOTE: To find out how many entries are in this tree,
+ * one should use the size() method. Doing so using this method will
+ * cost O(log(N)) time, where the size() method returns in constant time.
+ * The reason why this method takes longer is because we pre-compute the
+ * first element of the enumeration in order to reduce the complexity
+ * of the code.
+ * @param xMin the lower [inclusive] bound of the range to search.
+ * @param xMax the upper [inclusive] bound of the range to search.
+ * @param reverseOrder if false, elements returned are in non-descending
+ * order; if true, elements returned are in non-ascending order.
+ * @return an enumeration of all entries matching this search query,
+ * duplicates included; elements returned are in non-descending order
+ * if reverseOrder is false; elements returned are in non-ascending order
+ * if reverseOrder is true.
+ * @exception IllegalArgumentException if xMin is greater than xMax.
+ */
+ public final IntEnumerator searchRange(final int xMin, final int xMax,
+ final boolean reverseOrder) {
+ if (xMin > xMax)
+ throw new IllegalArgumentException("xMin is greater than xMax");
+
+ final NodeStack nodeStack = new NodeStack();
+
+ // If instead of passing Integer.MIN_VALUE and Integer.MAX_VALUE as
+ // minBound and maxBound [respectively] to the private recursive
+ // searchRange() function we instead had the global minimum and maximum
+ // on hand, we could save iterating through the root node's entries in
+ // the case where the query interval fully contains the global range of
+ // entries. This would come at the expense of keeping a global range
+ // up to date with every insertion and deletion, which is computationally
+ // expensive enough that it may defeat the purpose of stated optimization.
+ final int totalCount = searchRange(m_root, nodeStack, xMin, xMax, Integer.MIN_VALUE,
+ Integer.MAX_VALUE, reverseOrder);
+
+ if (reverseOrder)
+ return new DescendingEnumerator(totalCount, nodeStack, xMax);
+ else
+
+ return new AscendingEnumerator(totalCount, nodeStack, xMin);
+ }
+
+ /*
+ * Returns the count. The node stack is added to, never read from.
+ * The elements added to the node stack -- leaf nodes should be iterated
+ * through and appropriate values examined; internal nodes represent
+ * regions of the tree which can be included, as whole, as part of the
+ * range query. Every node on the returned stack will have at least one
+ * leaf entry counting towards the enumeration in the range query (this
+ * statement is important for leaf nodes). (There is one exception to that
+ * rule: when there are no entries in this tree, an empty node may be added
+ * to the stack.) [xMin, xMax] must intersect [minBound, maxBound] on each
+ * call to this method.
+ */
+ private final static int searchRange(final Node n, final NodeStack nodeStack, final int xMin,
+ final int xMax, final int minBound, final int maxBound,
+ final boolean reverseOrder) {
+ int count = 0;
+
+ if ((minBound >= xMin) && (maxBound <= xMax)) { // Trivially include node.
+ count += (isLeafNode(n) ? n.sliceCount : n.data.deepCount);
+ nodeStack.push(n);
+ } else { // Cannot trivially include node; must recurse.
+
+ if (isLeafNode(n)) {
+ int i = 0;
+
+ for (; i < n.sliceCount; i++)
+ if (xMin <= n.values[i])
+ break;
+
+ for (int j = i; j < n.sliceCount; j++) {
+ if (n.values[j] <= xMax)
+ count++;
+ else
+
+ break;
+ }
+
+ if (count > 0)
+ nodeStack.push(n);
+ } else { // Internal node.
+
+ if (reverseOrder) {
+ int currentMin = minBound;
+ int currentMax;
+ final int maxInx = n.sliceCount - 1; // Slight optimization.
+
+ for (int i = 0; i < n.sliceCount; i++) {
+ currentMax = ((i == maxInx) ? maxBound : n.data.splitVals[i]);
+
+ if (currentMax >= xMin) {
+ count += searchRange(n.data.children[i], nodeStack, xMin, xMax,
+ currentMin, currentMax, reverseOrder);
+
+ if (currentMax > xMax)
+ break;
+ }
+
+ currentMin = currentMax;
+ }
+ } else { // Not reverse order.
+
+ int currentMax = maxBound;
+ int currentMin;
+
+ for (int i = n.sliceCount - 2; i >= -1; i--) {
+ currentMin = ((i < 0) ? minBound : n.data.splitVals[i]);
+
+ if (currentMin <= xMax) {
+ count += searchRange(n.data.children[i + 1], nodeStack, xMin, xMax,
+ currentMin, currentMax, reverseOrder);
+
+ if (currentMin < xMin)
+ break;
+ }
+
+ currentMax = currentMin;
+ }
+ }
+ }
+ }
+
+ return count;
+ }
+
+ private final static class Node implements java.io.Serializable {
+ private int sliceCount = 0;
+ private final int[] values; // null if and only if internal node.
+ private final InternalNodeData data;
+
+ private Node(final int maxBranches, final boolean leafNode) {
+ if (leafNode) {
+ values = new int[maxBranches];
+ data = null;
+ } else {
+ values = null;
+ data = new InternalNodeData(maxBranches);
+ }
+ }
+ }
+
+ private final static class InternalNodeData implements java.io.Serializable {
+ private int deepCount;
+ private final int[] splitVals;
+ private final Node[] children;
+
+ private InternalNodeData(final int maxBranches) {
+ splitVals = new int[maxBranches - 1];
+ children = new Node[maxBranches];
+ }
+ }
+
+ private final static class NodeStack {
+ private Node[] stack;
+ private int currentSize = 0;
+
+ private NodeStack() {
+ stack = new Node[3];
+ }
+
+ private final void push(final Node value) {
+ try {
+ stack[currentSize++] = value;
+ } catch (ArrayIndexOutOfBoundsException e) {
+ currentSize--;
+
+ final int newStackSize = (int) Math.min((long) Integer.MAX_VALUE,
+ (((long) stack.length) * 2L) + 1L);
+
+ if (newStackSize == stack.length)
+ throw new IllegalStateException("cannot allocate large enough array");
+
+ final Node[] newStack = new Node[newStackSize];
+ ;
+ System.arraycopy(stack, 0, newStack, 0, stack.length);
+ stack = newStack;
+ stack[currentSize++] = value;
+ }
+ }
+
+ private final Node pop() {
+ try {
+ return stack[--currentSize];
+ } catch (ArrayIndexOutOfBoundsException e) {
+ currentSize++;
+ throw e;
+ }
+ }
+ }
+
+ private final static class AscendingEnumerator implements IntEnumerator {
+ private int wholeLeafNodes = 0; // Whole leaf nodes on stack.
+ private int count;
+ private final NodeStack stack;
+ private final int xMin;
+ private Node currentLeafNode;
+ private int currentNodeInx;
+
+ private AscendingEnumerator(final int totalCount, final NodeStack nodeStack, final int xMin) {
+ count = totalCount;
+ stack = nodeStack;
+ this.xMin = xMin;
+ computeNextLeafNode();
+ }
+
+ public final int numRemaining() {
+ return count;
+ }
+
+ public final int nextInt() {
+ int returnThis = 0; // To keep compiler from complaining.
+
+ if (wholeLeafNodes != 0) // Faster than 'wholeLeafNodes > 0' ?
+ returnThis = currentLeafNode.values[currentNodeInx];
+ else
+
+ for (; currentNodeInx < currentLeafNode.sliceCount; currentNodeInx++)
+ if (currentLeafNode.values[currentNodeInx] >= xMin) {
+ returnThis = currentLeafNode.values[currentNodeInx];
+
+ break;
+ }
+
+ if (++currentNodeInx == currentLeafNode.sliceCount) {
+ if (wholeLeafNodes > 0)
+ wholeLeafNodes--;
+
+ computeNextLeafNode();
+ }
+
+ count--;
+
+ return returnThis;
+ }
+
+ private final void computeNextLeafNode() {
+ if (stack.currentSize == 0) {
+ currentLeafNode = null;
+
+ return;
+ }
+
+ Node next;
+
+ while (true) {
+ next = stack.pop();
+
+ if (isLeafNode(next)) {
+ currentLeafNode = next;
+ currentNodeInx = 0;
+
+ return;
+ }
+
+ for (int i = next.sliceCount; i > 0;)
+ stack.push(next.data.children[--i]);
+
+ if (isLeafNode(next.data.children[0]))
+ wholeLeafNodes += next.sliceCount;
+ }
+ }
+ }
+
+ private final static class DescendingEnumerator implements IntEnumerator {
+ private int wholeLeafNodes = 0; // Whole leaf nodes on stack.
+ private int count;
+ private final NodeStack stack;
+ private final int xMax;
+ private Node currentLeafNode;
+ private int currentNodeInx;
+
+ private DescendingEnumerator(final int totalCount, final NodeStack nodeStack, final int xMax) {
+ count = totalCount;
+ stack = nodeStack;
+ this.xMax = xMax;
+ computeNextLeafNode();
+ }
+
+ public final int numRemaining() {
+ return count;
+ }
+
+ public final int nextInt() {
+ int returnThis = 0; // To keep compiler from complaining.
+
+ if (wholeLeafNodes != 0) // Faster than 'wholeLeafNodes > 0' ?
+ returnThis = currentLeafNode.values[currentNodeInx];
+ else
+
+ for (; currentNodeInx >= 0; currentNodeInx--)
+ if (currentLeafNode.values[currentNodeInx] <= xMax) {
+ returnThis = currentLeafNode.values[currentNodeInx];
+
+ break;
+ }
+
+ if (--currentNodeInx < 0) {
+ if (wholeLeafNodes > 0)
+ wholeLeafNodes--;
+
+ computeNextLeafNode();
+ }
+
+ count--;
+
+ return returnThis;
+ }
+
+ private final void computeNextLeafNode() {
+ if (stack.currentSize == 0) {
+ currentLeafNode = null;
+
+ return;
+ }
+
+ Node next;
+
+ while (true) {
+ next = stack.pop();
+
+ if (isLeafNode(next)) {
+ currentLeafNode = next;
+ currentNodeInx = currentLeafNode.sliceCount - 1;
+
+ return;
+ }
+
+ for (int i = 0; i < next.sliceCount; i++)
+ stack.push(next.data.children[i]);
+
+ if (isLeafNode(next.data.children[0]))
+ wholeLeafNodes += next.sliceCount;
+ }
+ }
+ }
+}
diff --git a/corelibs/util.intr/src/main/java/cytoscape/util/intr/IntEnumerator.java b/corelibs/util.intr/src/main/java/cytoscape/util/intr/IntEnumerator.java
new file mode 100644
index 0000000..a8c25d6
--- /dev/null
+++ b/corelibs/util.intr/src/main/java/cytoscape/util/intr/IntEnumerator.java
@@ -0,0 +1,56 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.util.intr;
+
+
+/**
+ * An enumeration over a list of 32 bit integers.
+ */
+public interface IntEnumerator {
+ /**
+ * Returns a non-negative integer I such that nextInt() will successfully
+ * return a value no more and no less than I times.
+ */
+ public int numRemaining();
+
+ /**
+ * Returns the next integer in the enumeration.
+ * If numRemaining() returns a non-positive quantity before
+ * nextInt() is called, the behavior of this enumeration becomes undefined.
+ */
+ public int nextInt();
+}
diff --git a/corelibs/util.intr/src/main/java/cytoscape/util/intr/IntHash.java b/corelibs/util.intr/src/main/java/cytoscape/util/intr/IntHash.java
new file mode 100644
index 0000000..be9bbb6
--- /dev/null
+++ b/corelibs/util.intr/src/main/java/cytoscape/util/intr/IntHash.java
@@ -0,0 +1,258 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.util.intr;
+
+
+/**
+ * An insert-only hashtable that has non-negative 32 bit integer keys;
+ * no satellite data is stored in this hashtable. An instance of this class
+ * is well-suited for efficiently detecting collisions between integers,
+ * removing duplicates from a list of integers, or determining the presence of
+ * an integer in a list of integers.<p>
+ * In the underlying implementation, this hashtable increases in size to adapt
+ * to elements being added (the underlying size of the hashtable is invisible
+ * to the programmer). In the underlying implementation, this hashtable never
+ * decreases in size. As a hashtable increases in size,
+ * it takes at most four times as much memory as it would take
+ * to store the hashtable's elements in a perfectly-sized array.
+ * Underlying size expansions are implemented such that the operation of
+ * expanding in size is amortized over the contstant time complexity of
+ * inserting new elements.<p>
+ * An instance of this class is serializable; however, serialized instances of
+ * this class should not be stored in a persistent manner because the
+ * serialization implemented in this class makes no attempt at handling
+ * class versioning.
+ */
+public final class IntHash implements java.io.Serializable {
+ private static final int[] PRIMES = {
+ 11, 23, 53, 113, 251, 509, 1019, 2039, 4079, 8179, 16369,
+ 32749, 65521, 131063, 262133, 524269, 1048571, 2097143,
+ 4194287, 8388587, 16777183, 33554393, 67108837,
+ 134217689, 268435399, 536870879, 1073741789, 2147483647
+ };
+ private static final int INITIAL_SIZE = PRIMES[0];
+ private static final double THRESHOLD_FACTOR = 0.77;
+ private int[] m_arr;
+ private int m_elements;
+ private int m_size;
+ private int m_thresholdSize;
+
+ /**
+ * Creates a new hashtable.
+ */
+ public IntHash() {
+ m_arr = new int[INITIAL_SIZE];
+ empty();
+ }
+
+ /**
+ * Removes all elements from this hashtable. This operation has
+ * O(1) time complexity.
+ */
+ public final void empty() {
+ m_elements = 0;
+ m_size = INITIAL_SIZE;
+ m_thresholdSize = (int) (THRESHOLD_FACTOR * (double) m_size);
+
+ for (int i = 0; i < m_size; i++)
+ m_arr[i] = -1;
+ }
+
+ /**
+ * Returns the number of elements currently in this hashtable.
+ */
+ public final int size() {
+ return m_elements;
+ }
+
+ /**
+ * Puts a new value into this hashtable if that value is not already in
+ * this hashtable; otherwise does nothing. Returns the input value if this
+ * value was already in this hashtable; returns -1 if the input value was
+ * not in this hashtable prior to this call.<p>
+ * Insertions into the hashtable are performed in [amortized] time
+ * complexity O(1).
+ *
+ * @exception IllegalArgumentException if value is negative.
+ */
+ public final int put(final int value) {
+ if (m_elements == m_thresholdSize)
+ incrSize();
+
+ int incr = 0;
+ int index;
+
+ try {
+ for (index = value % (((~value) >>> 31) * m_size);
+ (m_arr[index] >= 0) && (m_arr[index] != value); index = (index + incr) % m_size) {
+ // Caching increment, which is an expensive operation, at the expense
+ // of having an if statement. I don't want to compute the increment
+ // before this 'for' loop in case we get an immediate hit.
+ if (incr == 0) {
+ incr = 1 + (value % (m_size - 1));
+ }
+ }
+ } catch (ArithmeticException exc) {
+ throw new IllegalArgumentException("value is negative");
+ }
+
+ final int returnVal = m_arr[index];
+ m_arr[index] = value;
+ m_elements += (returnVal >>> 31);
+
+ return returnVal;
+ }
+
+ /**
+ * Determines whether or not the value specified is in this hashtable.
+ * Returns the value specified if this value is in the hashtable, otherwise
+ * returns -1.<p>
+ * Searches in this hashtable are performed in [amortized] time
+ * complexity O(1).
+ *
+ * @exception IllegalArgumentException if value is negative.
+ */
+ public final int get(final int value) {
+ int incr = 0;
+ int index;
+
+ try {
+ for (index = value % (((~value) >>> 31) * m_size);
+ (m_arr[index] >= 0) && (m_arr[index] != value); index = (index + incr) % m_size) {
+ // Caching increment, which is an expensive operation, at the expense
+ // of having an if statement. I don't want to compute the increment
+ // before this 'for' loop in case we get an immediate hit.
+ if (incr == 0) {
+ incr = 1 + (value % (m_size - 1));
+ }
+ }
+ } catch (ArithmeticException exc) {
+ throw new IllegalArgumentException("value is negative");
+ }
+
+ return m_arr[index];
+ }
+
+ /**
+ * Returns an enumeration of elements in this hashtable, ordered
+ * arbitrarily.<p>
+ * The returned enumeration becomes invalid as soon as put(int) or empty()
+ * is called on this hashtable; calling methods on an invalid
+ * enumeration will cause undefined behavior in the enumerator.
+ * The returned enumerator has absolutely no effect on the underlying
+ * hashtable.<p>
+ * This method returns in constant time. The returned enumerator
+ * returns successive elements in [amortized] time complexity O(1).
+ */
+ public final IntEnumerator elements() {
+ final int[] array = m_arr;
+ final int numElements = m_elements;
+
+ return new IntEnumerator() {
+ int elements = numElements;
+ int index = -1;
+
+ public int numRemaining() {
+ return elements;
+ }
+
+ public int nextInt() {
+ while (array[++index] < 0) {
+ }
+
+ elements--;
+
+ return array[index];
+ }
+ };
+ }
+
+ private int[] m_dump = null;
+
+ private final void incrSize() {
+ final int newSize;
+
+ try {
+ int primesInx = 0;
+
+ while (m_size != PRIMES[primesInx++]) {
+ }
+
+ newSize = PRIMES[primesInx];
+ } catch (ArrayIndexOutOfBoundsException e) {
+ throw new IllegalStateException("too many elements in this hashtable");
+ }
+
+ if (m_arr.length < newSize) {
+ m_dump = m_arr; // We want the old m_dump to potentially get garbage
+ // collected before we instantiate the new array.
+
+ m_arr = new int[newSize];
+ } else {
+ System.arraycopy(m_arr, 0, m_dump, 0, m_size);
+ }
+
+ for (int i = 0; i < newSize; i++)
+ m_arr[i] = -1;
+
+ m_size = newSize;
+ m_thresholdSize = (int) (THRESHOLD_FACTOR * (double) m_size);
+
+ int incr;
+ int newIndex;
+ int oldIndex = -1;
+
+ for (int i = 0; i < m_elements; i++) {
+ while (m_dump[++oldIndex] < 0) {
+ }
+
+ incr = 0;
+
+ for (newIndex = m_dump[oldIndex] % m_size; m_arr[newIndex] >= 0;
+ newIndex = (newIndex + incr) % m_size) {
+ // Caching increment, which is an expensive operation, at the expense
+ // of having an if statement. I don't want to compute the increment
+ // before this 'for' loop in case we get an immediate hit.
+ if (incr == 0) {
+ incr = 1 + (m_dump[oldIndex] % (m_size - 1));
+ }
+ }
+
+ m_arr[newIndex] = m_dump[oldIndex];
+ }
+ }
+}
diff --git a/corelibs/util.intr/src/main/java/cytoscape/util/intr/IntIntHash.java b/corelibs/util.intr/src/main/java/cytoscape/util/intr/IntIntHash.java
new file mode 100644
index 0000000..86c80a3
--- /dev/null
+++ b/corelibs/util.intr/src/main/java/cytoscape/util/intr/IntIntHash.java
@@ -0,0 +1,295 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.util.intr;
+
+
+/**
+ * An insert-only hashtable that has non-negative 32 bit integer keys and
+ * non-negative 32 bit integer values.<p>
+ * In the underlying implementation, this hashtable increases in size to adapt
+ * to key/value pairs being added (the underlying size of the hashtable is
+ * invisible to the programmer). In the underlying implementation, this
+ * hashtable never decreases in size. As a hashtable increases in size,
+ * it takes at most four times as much memory as it would take
+ * to store the hashtable's keys and values in a perfectly-sized array.
+ * Underlying size expansions are implemented such that the operation of
+ * expanding in size is amortized over the contstant time complexity needed to
+ * insert new elements.<p>
+ * An instance of this class is serializable; however, serialized instances of
+ * this class should not be stored in a persistent manner because the
+ * serialization implemented in this class makes no attempt at handling
+ * class versioning.
+ */
+public final class IntIntHash implements java.io.Serializable {
+ private static final int[] PRIMES = {
+ 11, 23, 53, 113, 251, 509, 1019, 2039, 4079, 8179, 16369,
+ 32749, 65521, 131063, 262133, 524269, 1048571, 2097143,
+ 4194287, 8388587, 16777183, 33554393, 67108837,
+ 134217689, 268435399, 536870879, 1073741789, 2147483647
+ };
+ private static final int INITIAL_SIZE = PRIMES[0];
+ private static final double THRESHOLD_FACTOR = 0.77;
+ private int[] m_keys;
+ private int[] m_vals;
+ private int m_elements;
+ private int m_size;
+ private int m_thresholdSize;
+
+ // These are caching variables. The idea is that programmers will
+ // frequently first do a get(), and based on that result, will perform
+ // some other operations and then maybe do a put() operation with the same
+ // key as the previous get() operation.
+ private int m_prevKey;
+ private int m_prevInx;
+
+ /**
+ * Creates a new hashtable.
+ */
+ public IntIntHash() {
+ m_keys = new int[INITIAL_SIZE];
+ m_vals = new int[INITIAL_SIZE];
+ empty();
+ }
+
+ /**
+ * Removes all key/value pairs from this hashtable. This operation has
+ * O(1) time complexity.
+ */
+ public final void empty() {
+ m_elements = 0;
+ m_size = INITIAL_SIZE;
+ m_thresholdSize = (int) (THRESHOLD_FACTOR * (double) m_size);
+
+ for (int i = 0; i < m_size; i++) {
+ m_keys[i] = -1;
+ m_vals[i] = -1;
+ }
+
+ m_prevKey = -1;
+ m_prevInx = -1;
+ }
+
+ /**
+ * Returns the number of key/value pairs currently in this hashtable.
+ */
+ public final int size() {
+ return m_elements;
+ }
+
+ /**
+ * Puts a new key/value pair into this hashtable, potentially overwriting
+ * an existing value whose key is the same as the one specified.
+ * Returns the old value associated with the specified key or -1 if no value
+ * is associated with specified key at the time of this call.<p>
+ * Insertions into the hashtable are performed in [amortized] time
+ * complexity O(1).
+ *
+ * @exception IllegalArgumentException if either key or value is negative.
+ */
+ public final int put(final int key, final int value) {
+ if (key < 0)
+ throw new IllegalArgumentException("key is negative");
+
+ if (value < 0)
+ throw new IllegalArgumentException("value is negative");
+
+ if (m_elements == m_thresholdSize)
+ incrSize();
+
+ if (key != m_prevKey) {
+ int incr = 0;
+
+ for (m_prevInx = key % m_size; (m_keys[m_prevInx] >= 0) && (m_keys[m_prevInx] != key);
+ m_prevInx = (m_prevInx + incr) % m_size)
+ if (incr == 0)
+ incr = 1 + (key % (m_size - 1));
+
+ m_prevKey = key;
+ }
+
+ final int returnVal = m_vals[m_prevInx];
+ m_vals[m_prevInx] = value;
+ m_keys[m_prevInx] = key;
+ m_elements += (returnVal >>> 31);
+
+ return returnVal;
+ }
+
+ /**
+ * Returns the value bound to the specified key or -1 if no value is
+ * currently bound to the specified key.<p>
+ * Searches in this hashtable are performed in [amortized] time
+ * complexity O(1).
+ *
+ * @exception IllegalArgumentException if key is negative.
+ */
+ public final int get(final int key) {
+ if (key < 0)
+ throw new IllegalArgumentException("key is negative");
+
+ if (key != m_prevKey) {
+ int incr = 0;
+
+ for (m_prevInx = key % m_size; (m_keys[m_prevInx] >= 0) && (m_keys[m_prevInx] != key);
+ m_prevInx = (m_prevInx + incr) % m_size)
+ if (incr == 0)
+ incr = 1 + (key % (m_size - 1));
+
+ m_prevKey = key;
+ }
+
+ return m_vals[m_prevInx];
+ }
+
+ /**
+ * Returns an enumeration of keys in this hashtable, ordered
+ * arbitrarily.<p>
+ * The returned enumeration becomes invalid as soon as put(int, int) or
+ * empty() is called on this hashtable; calling methods on an invalid
+ * enumeration will cause undefined behavior in the enumerator.
+ * The returned enumerator has absolutely no effect on the underlying
+ * hashtable.<p>
+ * This method returns in constant time. The returned enumerator
+ * returns successive keys in [amortized] time complexity O(1).<p>
+ * It is possible to get the keys() and values() enumerations at the same
+ * time and iterate over them simultaneously; then, the
+ * i<sup>th</sup> element of the keys() enumeration is the key into the
+ * i<sup>th</sup> element of the values() enumeration.
+ */
+ public final IntEnumerator keys() {
+ return enumeration(m_keys);
+ }
+
+ /**
+ * Returns an enumeration of values in this hashtable, ordered
+ * arbitrarily.<p>
+ * The returned enumeration becomes invalid as soon as put(int, int) or
+ * empty() is called on this hashtable; calling methods on an invalid
+ * enumeration will cause undefined behavior in the enumerator.
+ * The returned enumerator has absolutely no effect on the underlying
+ * hashtable.<p>
+ * This method returns in constant time. The returned enumerator
+ * returns successive values in [amortized] time complexity O(1).<p>
+ * It is possible to get the keys() and values() enumerations at the same
+ * time and iterate over them simultaneously; then, the
+ * i<sup>th</sup> element of the keys() enumeration is the key into the
+ * i<sup>th</sup> element of the values() enumeration.
+ */
+ public final IntEnumerator values() {
+ return enumeration(m_vals);
+ }
+
+ private final IntEnumerator enumeration(final int[] arr) {
+ final int numElements = m_elements;
+
+ return new IntEnumerator() {
+ int elements = numElements;
+ int index = -1;
+
+ public int numRemaining() {
+ return elements;
+ }
+
+ public int nextInt() {
+ while (arr[++index] < 0)
+ ;
+
+ elements--;
+
+ return arr[index];
+ }
+ };
+ }
+
+ private int[] m_keyDump = null;
+ private int[] m_valDump = null;
+
+ private final void incrSize() {
+ final int newSize;
+
+ try {
+ int primesInx = 0;
+
+ while (m_size != PRIMES[primesInx++])
+ ;
+
+ newSize = PRIMES[primesInx];
+ } catch (ArrayIndexOutOfBoundsException e) {
+ throw new IllegalStateException("too many elements in this hashtable");
+ }
+
+ if (m_keys.length < newSize) {
+ m_keyDump = m_keys;
+ m_valDump = m_vals;
+ m_keys = new int[newSize];
+ m_vals = new int[newSize];
+ } else {
+ System.arraycopy(m_keys, 0, m_keyDump, 0, m_size);
+ System.arraycopy(m_vals, 0, m_valDump, 0, m_size);
+ }
+
+ for (int i = 0; i < newSize; i++) {
+ m_keys[i] = -1;
+ m_vals[i] = -1;
+ }
+
+ m_size = newSize;
+ m_thresholdSize = (int) (THRESHOLD_FACTOR * (double) m_size);
+
+ int incr;
+ int newIndex;
+ int oldIndex = -1;
+
+ for (int i = 0; i < m_elements; i++) {
+ while (m_keyDump[++oldIndex] < 0)
+ ;
+
+ incr = 0;
+
+ for (newIndex = m_keyDump[oldIndex] % m_size; m_keys[newIndex] >= 0;
+ newIndex = (newIndex + incr) % m_size)
+ if (incr == 0)
+ incr = 1 + (m_keyDump[oldIndex] % (m_size - 1));
+
+ m_keys[newIndex] = m_keyDump[oldIndex];
+ m_vals[newIndex] = m_valDump[oldIndex];
+ }
+
+ m_prevKey = -1;
+ m_prevInx = -1;
+ }
+}
diff --git a/corelibs/util.intr/src/main/java/cytoscape/util/intr/IntIterator.java b/corelibs/util.intr/src/main/java/cytoscape/util/intr/IntIterator.java
new file mode 100644
index 0000000..905a95d
--- /dev/null
+++ b/corelibs/util.intr/src/main/java/cytoscape/util/intr/IntIterator.java
@@ -0,0 +1,56 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.util.intr;
+
+
+/**
+ * An iteration over a list of 32 bit integers.
+ */
+public interface IntIterator {
+ /**
+ * Returns true if and only if nextInt() will successfully return a
+ * value.
+ */
+ public boolean hasNext();
+
+ /**
+ * Returns the next integer in the iteration. If hasNext() returns false
+ * before nextInt() is called, the behavior of this iteration becomes
+ * undefined.
+ */
+ public int nextInt();
+}
diff --git a/corelibs/util.intr/src/main/java/cytoscape/util/intr/IntObjHash.java b/corelibs/util.intr/src/main/java/cytoscape/util/intr/IntObjHash.java
new file mode 100644
index 0000000..f77c7d7
--- /dev/null
+++ b/corelibs/util.intr/src/main/java/cytoscape/util/intr/IntObjHash.java
@@ -0,0 +1,331 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.util.intr;
+
+import java.util.Iterator;
+import java.util.NoSuchElementException;
+
+
+/**
+ * An insert-only hashtable that has non-negative 32 bit integer keys and
+ * non-null object values.<p>
+ * In the underlying implementation, this hashtable increases in size to adapt
+ * to key/value pairs being added (the underlying size of the hashtable is
+ * invisible to the programmer). In the underlying implementation, this
+ * hashtable never decreases in size. As a hashtable increases in size,
+ * it takes at most four times as much memory as it would take
+ * to store the hashtable's keys and values in perfectly-sized arrays.
+ * Underlying size expansions are implemented such that the operation of
+ * expanding in size is amortized over the contstant time complexity needed to
+ * insert new elements.<p>
+ * An instance of this class is serializable; however, serialized instances of
+ * this class should not be stored in a persistent manner because the
+ * serialization implemented in this class makes no attempt at handling
+ * class versioning. For an instance of this class to be properly
+ * serialized, all object values stored in that instance must be
+ * serializable.
+ */
+public final class IntObjHash implements java.io.Serializable {
+ private static final int[] PRIMES = {
+ 11, 23, 53, 113, 251, 509, 1019, 2039, 4079, 8179, 16369,
+ 32749, 65521, 131063, 262133, 524269, 1048571, 2097143,
+ 4194287, 8388587, 16777183, 33554393, 67108837,
+ 134217689, 268435399, 536870879, 1073741789, 2147483647
+ };
+ private static final int INITIAL_SIZE = PRIMES[0];
+ private static final double THRESHOLD_FACTOR = 0.77;
+
+ /**
+ * For a hashtable that currently holds exactly num keys [or zero keys if
+ * num is negative], returns the maximum number of keys that that hashtable
+ * can hold without undergoing an underlying size expansion. Size expansions
+ * are expensive computationally and result in a doubling of the amount of
+ * memory consumed; this function is a hook for users of hashtables to do
+ * smart things when an underlying size expansion is about to happen.
+ * Returns -1 if a hashtable cannot hold the number of keys specified
+ * (num too large for algorithms to work).
+ */
+ public final static int maxCapacity(final int num) {
+ int inx = 0;
+
+ while ((inx < PRIMES.length) && (num >= PRIMES[inx]))
+ inx++;
+
+ final int thresholdSize = (int) (THRESHOLD_FACTOR * (double) PRIMES[inx]);
+
+ if (thresholdSize >= num)
+ return thresholdSize;
+ else if (++inx == PRIMES.length)
+ return -1;
+
+ return (int) (THRESHOLD_FACTOR * (double) PRIMES[inx]);
+ }
+
+ private int[] m_keys;
+ private Object[] m_vals;
+ private int m_elements;
+ private int m_thresholdSize;
+
+ // These are caching variables. The idea is that programmers will
+ // frequently first do a get(), and based on that result, will perform
+ // some other operations and then maybe do a put() operation with the same
+ // key as the previous get() operation.
+ private int m_prevKey;
+ private int m_prevInx;
+
+ /**
+ * Creates a new hashtable.
+ */
+ public IntObjHash() {
+ m_keys = new int[INITIAL_SIZE];
+ m_vals = new Object[INITIAL_SIZE];
+ m_elements = 0;
+ m_thresholdSize = (int) (THRESHOLD_FACTOR * (double) m_keys.length);
+
+ for (int i = 0; i < m_keys.length; i++)
+ m_keys[i] = -1;
+
+ m_prevKey = -1;
+ m_prevInx = -1;
+ }
+
+ /**
+ * Returns the number of key/value pairs currently in this hashtable.
+ */
+ public final int size() {
+ return m_elements;
+ }
+
+ /**
+ * Puts a new key/value pair into this hashtable, potentially overwriting
+ * an existing value whose key is the same as the one specified.
+ * Returns the old value associated with the specified key or null if no
+ * value is associated with specified key at the time of this call.<p>
+ * Insertions into the hashtable are performed in [amortized] time
+ * complexity O(1).
+ * @exception IllegalArgumentException if key is negative.
+ * @exception NullPointerException if value is null.
+ */
+ public final Object put(final int key, final Object value) {
+ if (key < 0)
+ throw new IllegalArgumentException("key is negative");
+
+ if (value == null)
+ throw new IllegalArgumentException("value is null");
+
+ if (key != m_prevKey) {
+ int incr = 0;
+
+ for (m_prevInx = key % m_keys.length;
+ (m_keys[m_prevInx] >= 0) && (m_keys[m_prevInx] != key);
+ m_prevInx = (m_prevInx + incr) % m_keys.length)
+ if (incr == 0)
+ incr = 1 + (key % (m_keys.length - 1));
+
+ m_prevKey = key;
+ }
+
+ final Object returnVal = m_vals[m_prevInx];
+
+ if (returnVal == null) {
+ if (m_elements == m_thresholdSize) {
+ incrSize();
+
+ return put(key, value);
+ }
+
+ m_elements++;
+ }
+
+ m_vals[m_prevInx] = value;
+ m_keys[m_prevInx] = key;
+
+ return returnVal;
+ }
+
+ /**
+ * Returns the value bound to the specified key or null if no value is
+ * currently bound to the specified key.<p>
+ * Searches in this hashtable are performed in [amortized] time
+ * complexity O(1).
+ * @exception IllegalArgumentException if key is negative.
+ */
+ public final Object get(final int key) {
+ if (key < 0)
+ throw new IllegalArgumentException("key is negative");
+
+ if (key != m_prevKey) {
+ int incr = 0;
+
+ for (m_prevInx = key % m_keys.length;
+ (m_keys[m_prevInx] >= 0) && (m_keys[m_prevInx] != key);
+ m_prevInx = (m_prevInx + incr) % m_keys.length)
+ if (incr == 0)
+ incr = 1 + (key % (m_keys.length - 1));
+
+ m_prevKey = key;
+ }
+
+ return m_vals[m_prevInx];
+ }
+
+ /**
+ * Returns an enumeration of keys in this hashtable, ordered
+ * arbitrarily.<p>
+ * The returned enumeration becomes invalid as soon as put(int, Object)
+ * is called on this hashtable; calling methods on an invalid
+ * enumeration will cause undefined behavior in the enumerator.
+ * The returned enumerator has absolutely no effect on the underlying
+ * hashtable.<p>
+ * This method returns in constant time. The returned enumerator
+ * returns successive keys in [amortized] time complexity O(1).
+ */
+ public final IntEnumerator keys() {
+ final int numElements = m_elements;
+
+ return new IntEnumerator() {
+ int elements = numElements;
+ int index = -1;
+
+ public final int numRemaining() {
+ return elements;
+ }
+
+ public final int nextInt() {
+ while (m_keys[++index] < 0)
+ ;
+
+ elements--;
+
+ return m_keys[index];
+ }
+ };
+ }
+
+ /**
+ * Returns an iteration of values in this hashtable, ordered
+ * arbitrarily.<p>
+ * The returned iteration becomes invalid as soon as put(int, Object)
+ * is called on this hashtable; calling methods on an invalid
+ * iteration will cause undefined behavior in the iterator.
+ * The returned iterator has absolutely no effect on the underlying
+ * hashtable (the remove() operation on the returned iterator is not
+ * supported).<p>
+ * This method returns in constant time. The returned iterator
+ * returns successive values in [amortized] time complexity O(1).<p>
+ * NOTE: The order of values returned corresponds to the order of keys
+ * returned by the enumeration from keys() - that is, the n<sup>th</sup>
+ * key returned by keys() is the key into the n<sup>th</sup> value
+ * returned by values().
+ */
+ public final Iterator values() {
+ final int numElements = m_elements;
+
+ return new Iterator() {
+ int elements = numElements;
+ int index = -1;
+
+ public final boolean hasNext() {
+ return elements == 0;
+ }
+
+ public final Object next() {
+ try {
+ while (m_vals[++index] == null)
+ ;
+
+ elements--;
+
+ return m_vals[index];
+ } catch (ArrayIndexOutOfBoundsException e) {
+ throw new NoSuchElementException();
+ }
+ }
+
+ public final void remove() {
+ throw new UnsupportedOperationException();
+ }
+ };
+ }
+
+ private final void incrSize() {
+ final int newSize;
+
+ try {
+ int primesInx = 0;
+
+ while (m_keys.length != PRIMES[primesInx++])
+ ;
+
+ newSize = PRIMES[primesInx];
+ } catch (ArrayIndexOutOfBoundsException e) {
+ throw new IllegalStateException("too many elements in this hashtable");
+ }
+
+ final int[] newKeys = new int[newSize];
+ final Object[] newVals = new Object[newSize];
+
+ for (int i = 0; i < newKeys.length; i++)
+ newKeys[i] = -1;
+
+ m_thresholdSize = (int) (THRESHOLD_FACTOR * (double) newKeys.length);
+
+ int incr;
+ int newIndex;
+ int oldIndex = -1;
+
+ for (int i = 0; i < m_elements; i++) {
+ while (m_keys[++oldIndex] < 0)
+ ;
+
+ incr = 0;
+
+ for (newIndex = m_keys[oldIndex] % newKeys.length; newKeys[newIndex] >= 0;
+ newIndex = (newIndex + incr) % newKeys.length)
+ if (incr == 0)
+ incr = 1 + (m_keys[oldIndex] % (newKeys.length - 1));
+
+ newKeys[newIndex] = m_keys[oldIndex];
+ newVals[newIndex] = m_vals[oldIndex];
+ }
+
+ m_keys = newKeys;
+ m_vals = newVals;
+ m_prevKey = -1;
+ m_prevInx = -1;
+ }
+}
diff --git a/corelibs/util.intr/src/main/java/cytoscape/util/intr/IntQueue.java b/corelibs/util.intr/src/main/java/cytoscape/util/intr/IntQueue.java
new file mode 100644
index 0000000..4c22ec4
--- /dev/null
+++ b/corelibs/util.intr/src/main/java/cytoscape/util/intr/IntQueue.java
@@ -0,0 +1,186 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.util.intr;
+
+
+/**
+ * A first-in, first-out container of 32 bit integers. In the underlying
+ * implementation, the memory consumed by an instance of this class may
+ * increase, but does never decrease.<p>
+ * While other container classes in this package are able to hold up
+ * to Integer.MAX_VALUE elements, this class is only able to hold
+ * Integer.MAX_VALUE-1 elements.<p>
+ * An instance of this class is serializable; however, serialized instances of
+ * this class should not be stored in a persistent manner because the
+ * serialization implemented in this class makes no attempt at handling
+ * class versioning.
+ */
+public final class IntQueue implements java.io.Serializable {
+ // This must be a non-negative integer.
+ private static final int DEFAULT_CAPACITY = 12;
+ private int[] m_queue;
+ private int m_head;
+ private int m_tail;
+
+ /**
+ * Creates a new queue of integers.
+ */
+ public IntQueue() {
+ m_queue = new int[DEFAULT_CAPACITY];
+ empty();
+ }
+
+ /**
+ * Removes all integers from this queue. This operation has constant time
+ * complexity.
+ */
+ public final void empty() {
+ m_head = 0;
+ m_tail = 0;
+ }
+
+ /**
+ * Returns the number of integers that are currently in this queue.
+ */
+ public final int size() {
+ int absHead = m_head;
+
+ if (absHead < m_tail)
+ absHead += m_queue.length;
+
+ return absHead - m_tail;
+ }
+
+ /**
+ * Inserts a new integer into this queue.
+ */
+ public final void enqueue(int value) {
+ checkSize();
+ m_queue[m_head++] = value;
+
+ if (m_head == m_queue.length)
+ m_head = 0;
+ }
+
+ /**
+ * A non-mutating operation that retrieves the next integer in this queue.<p>
+ * It is considered an error to call this method if there are no integers
+ * currently in this queue. If size() returns zero immediately before
+ * this method is called, the results of this operation are undefined.
+ */
+ public final int peek() {
+ return m_queue[m_tail];
+ }
+
+ /**
+ * Removes and returns the next integer in this queue.<p>
+ * It is considered an error to call this method if there are no integers
+ * currently in this queue. If size() returns zero immediately before
+ * this method is called, the results of this operation are undefined.
+ */
+ public final int dequeue() {
+ final int returnThis = m_queue[m_tail++];
+
+ if (m_tail == m_queue.length)
+ m_tail = 0;
+
+ return returnThis;
+ }
+
+ /**
+ * Returns an enumeration of all elements currently in this queue.
+ * The order of elements in the returned enumeration is based on the
+ * elements' dequeue order; the first element returned is the element
+ * waiting to be dequeued.<p>
+ * No operation on this queue will have an effect on the returned
+ * enumeration except for enqueue(). If calls to enqueue() are mingled with
+ * calls to iterate over the returned enumeration, the contents of this
+ * enumeration become undefined. Iterating over the returned enumeration
+ * never has an affect on this queue.
+ */
+ public final IntEnumerator elements() {
+ final int[] queue = m_queue;
+ final int head = m_head;
+ final int tail = m_tail;
+
+ return new IntEnumerator() {
+ private int inx = tail;
+
+ public final int numRemaining() {
+ int absHead = head;
+
+ if (absHead < inx)
+ absHead += queue.length;
+
+ return absHead - inx;
+ }
+
+ public final int nextInt() {
+ final int returnThis = queue[inx++];
+
+ if (inx == queue.length)
+ inx = 0;
+
+ return returnThis;
+ }
+ };
+ }
+
+ private final void checkSize() {
+ if ((size() + 2) > m_queue.length) {
+ final int newQueueArrSize = (int) Math.min((long) Integer.MAX_VALUE,
+ (((long) m_queue.length) * 2L) + 1L);
+
+ if (newQueueArrSize == m_queue.length)
+ throw new IllegalStateException("cannot allocate large enough array");
+
+ final int[] newQueueArr = new int[newQueueArrSize];
+
+ if (m_tail <= m_head) {
+ System.arraycopy(m_queue, m_tail, newQueueArr, 0, m_head - m_tail);
+ m_head = m_head - m_tail;
+ } else {
+ System.arraycopy(m_queue, m_tail, newQueueArr, 0, m_queue.length - m_tail);
+ System.arraycopy(m_queue, 0, newQueueArr, m_queue.length - m_tail, m_head);
+ m_head = m_head + (m_queue.length - m_tail);
+ }
+
+ m_tail = 0;
+ m_queue = newQueueArr;
+ }
+ }
+}
diff --git a/corelibs/util.intr/src/main/java/cytoscape/util/intr/IntStack.java b/corelibs/util.intr/src/main/java/cytoscape/util/intr/IntStack.java
new file mode 100644
index 0000000..2f91b62
--- /dev/null
+++ b/corelibs/util.intr/src/main/java/cytoscape/util/intr/IntStack.java
@@ -0,0 +1,159 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.util.intr;
+
+
+/**
+ * A first-in, last-out container of 32 bit integers. In the underlying
+ * implementation, the memory consumed by an instance of this class may
+ * increase, but does never decrease.<p>
+ * An instance of this class is serializable; however, serialized instances of
+ * this class should not be stored in a persistent manner because the
+ * serialization implemented in this class makes no attempt at handling
+ * class versioning.
+ */
+public final class IntStack implements java.io.Serializable {
+ // This must be a non-negative integer.
+ private static final int DEFAULT_CAPACITY = 11;
+ private int[] m_stack;
+ private int m_currentSize;
+
+ /**
+ * Creates a new stack of integers.
+ */
+ public IntStack() {
+ m_stack = new int[DEFAULT_CAPACITY];
+ empty();
+ }
+
+ /**
+ * Removes all integers from this stack. This operation has constant time
+ * complexity.
+ */
+ public final void empty() {
+ m_currentSize = 0;
+ }
+
+ /**
+ * Returns the number of integers that are currently on this stack.
+ */
+ public final int size() {
+ return m_currentSize;
+ }
+
+ /**
+ * Pushes a new integer onto this stack. A successive peek() or pop()
+ * call will return the specified value.
+ */
+ public final void push(int value) {
+ try {
+ m_stack[m_currentSize++] = value;
+ } catch (ArrayIndexOutOfBoundsException e) {
+ m_currentSize--;
+ checkSize();
+ m_stack[m_currentSize++] = value;
+ }
+ }
+
+ /**
+ * A non-mutating operation that retrieves the next integer on this stack.<p>
+ * It is considered an error to call this method if there are no integers
+ * currently on this stack. If size() returns zero immediately before this
+ * method is called, the results of this operation are undefined.
+ */
+ public final int peek() {
+ return m_stack[m_currentSize - 1];
+ }
+
+ /**
+ * Removes and returns the next integer on this stack.<p>
+ * It is considered an error to call this method if there are no integers
+ * currently on this stack. If size() returns zero immediately before this
+ * method is called, the results of this operation are undefined.
+ */
+ public final int pop() {
+ try {
+ return m_stack[--m_currentSize];
+ } catch (ArrayIndexOutOfBoundsException e) {
+ m_currentSize++;
+ throw e;
+ }
+ }
+
+ /**
+ * Returns an enumeration of all elements currently on this stack.
+ * The order of elements in the returned enumeration is based on the
+ * elements' popping order on the stack; the first element returned is
+ * the element waiting to be popped off the stack.<p>
+ * No operation on this stack will have an effect on the returned
+ * enumeration except for push(). If calls to push() are mingled with
+ * calls to iterate over the returned enumeration, the contents of this
+ * enumeration become undefined. Iterating over the returned enumeration
+ * never has an affect on this stack.
+ */
+ public final IntEnumerator elements() {
+ final int[] stack = m_stack;
+ final int size = m_currentSize;
+
+ return new IntEnumerator() {
+ private int inx = size;
+
+ public final int numRemaining() {
+ return inx;
+ }
+
+ public final int nextInt() {
+ return stack[--inx];
+ }
+ };
+ }
+
+ private final void checkSize() {
+ if (m_currentSize < m_stack.length)
+ return;
+
+ final int newStackSize = (int) Math.min((long) Integer.MAX_VALUE,
+ (((long) m_stack.length) * 2L) + 1L);
+
+ if (newStackSize == m_stack.length)
+ throw new IllegalStateException("cannot allocate large enough array");
+
+ final int[] newStack = new int[newStackSize];
+ System.arraycopy(m_stack, 0, newStack, 0, m_stack.length);
+ m_stack = newStack;
+ }
+}
diff --git a/corelibs/util.intr/src/main/java/cytoscape/util/intr/IntTHash.java b/corelibs/util.intr/src/main/java/cytoscape/util/intr/IntTHash.java
new file mode 100644
index 0000000..712552a
--- /dev/null
+++ b/corelibs/util.intr/src/main/java/cytoscape/util/intr/IntTHash.java
@@ -0,0 +1,341 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.util.intr;
+
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+import java.util.NoSuchElementException;
+
+
+/**
+ * An insert-only hashtable that has non-negative 32 bit integer keys and
+ * non-null object values.<p>
+ * In the underlying implementation, this hashtable increases in size to adapt
+ * to key/value pairs being added (the underlying size of the hashtable is
+ * invisible to the programmer). In the underlying implementation, this
+ * hashtable never decreases in size. As a hashtable increases in size,
+ * it takes at most four times as much memory as it would take
+ * to store the hashtable's keys and values in perfectly-sized arrays.
+ * Underlying size expansions are implemented such that the operation of
+ * expanding in size is amortized over the contstant time complexity needed to
+ * insert new elements.<p>
+ * An instance of this class is serializable; however, serialized instances of
+ * this class should not be stored in a persistent manner because the
+ * serialization implemented in this class makes no attempt at handling
+ * class versioning. For an instance of this class to be properly
+ * serialized, all object values stored in that instance must be
+ * serializable.
+ */
+public final class IntTHash<T> implements java.io.Serializable {
+ private static final int[] PRIMES = {
+ 11, 23, 53, 113, 251, 509, 1019, 2039, 4079, 8179, 16369,
+ 32749, 65521, 131063, 262133, 524269, 1048571, 2097143,
+ 4194287, 8388587, 16777183, 33554393, 67108837,
+ 134217689, 268435399, 536870879, 1073741789, 2147483647
+ };
+ private static final int INITIAL_SIZE = PRIMES[0];
+ private static final double THRESHOLD_FACTOR = 0.77;
+ private int[] m_keys;
+
+ //private Object[] m_vals;
+ private List<T> m_vals;
+ private int m_elements;
+ private int m_thresholdSize;
+
+ // These are caching variables. The idea is that programmers will
+ // frequently first do a get(), and based on that result, will perform
+ // some other operations and then maybe do a put() operation with the same
+ // key as the previous get() operation.
+ private int m_prevKey;
+ private int m_prevInx;
+
+ /**
+ * Creates a new hashtable.
+ */
+ public IntTHash() {
+ m_keys = new int[INITIAL_SIZE];
+ m_vals = new ArrayList<T>();
+ m_elements = 0;
+ m_thresholdSize = (int) (THRESHOLD_FACTOR * (double) m_keys.length);
+
+ for (int i = 0; i < m_keys.length; i++)
+ m_keys[i] = -1;
+
+ m_prevKey = -1;
+ m_prevInx = -1;
+ }
+
+ /**
+ * For a hashtable that currently holds exactly num keys [or zero keys if
+ * num is negative], returns the maximum number of keys that that hashtable
+ * can hold without undergoing an underlying size expansion. Size expansions
+ * are expensive computationally and result in a doubling of the amount of
+ * memory consumed; this function is a hook for users of hashtables to do
+ * smart things when an underlying size expansion is about to happen.
+ * Returns -1 if a hashtable cannot hold the number of keys specified
+ * (num too large for algorithms to work).
+ */
+ public final static int maxCapacity(final int num) {
+ int inx = 0;
+
+ while ((inx < PRIMES.length) && (num >= PRIMES[inx]))
+ inx++;
+
+ final int thresholdSize = (int) (THRESHOLD_FACTOR * (double) PRIMES[inx]);
+
+ if (thresholdSize >= num) {
+ return thresholdSize;
+ } else if (++inx == PRIMES.length) {
+ return -1;
+ }
+
+ return (int) (THRESHOLD_FACTOR * (double) PRIMES[inx]);
+ }
+
+ /**
+ * Returns the number of key/value pairs currently in this hashtable.
+ */
+ public final int size() {
+ return m_elements;
+ }
+
+ /**
+ * Puts a new key/value pair into this hashtable, potentially overwriting
+ * an existing value whose key is the same as the one specified.
+ * Returns the old value associated with the specified key or null if no
+ * value is associated with specified key at the time of this call.<p>
+ * Insertions into the hashtable are performed in [amortized] time
+ * complexity O(1).
+ * @exception IllegalArgumentException if key is negative.
+ * @exception NullPointerException if value is null.
+ */
+ public final T put(final int key, final T value) {
+ if (key < 0) {
+ throw new IllegalArgumentException("key is negative");
+ }
+
+ if (value == null) {
+ throw new IllegalArgumentException("value is null");
+ }
+
+ if (key != m_prevKey) {
+ int incr = 0;
+
+ for (m_prevInx = key % m_keys.length;
+ (m_keys[m_prevInx] >= 0) && (m_keys[m_prevInx] != key);
+ m_prevInx = (m_prevInx + incr) % m_keys.length)
+ if (incr == 0) {
+ incr = 1 + (key % (m_keys.length - 1));
+ }
+
+ m_prevKey = key;
+ }
+
+ final T returnVal = m_vals.get(m_prevInx);
+
+ if (returnVal == null) {
+ if (m_elements == m_thresholdSize) {
+ incrSize();
+
+ return put(key, value);
+ }
+
+ m_elements++;
+ }
+
+ m_vals.set(m_prevInx, value);
+ m_keys[m_prevInx] = key;
+
+ return returnVal;
+ }
+
+ /**
+ * Returns the value bound to the specified key or null if no value is
+ * currently bound to the specified key.<p>
+ * Searches in this hashtable are performed in [amortized] time
+ * complexity O(1).
+ * @exception IllegalArgumentException if key is negative.
+ */
+ public final T get(final int key) {
+ if (key < 0) {
+ throw new IllegalArgumentException("key is negative");
+ }
+
+ if (key != m_prevKey) {
+ int incr = 0;
+
+ for (m_prevInx = key % m_keys.length;
+ (m_keys[m_prevInx] >= 0) && (m_keys[m_prevInx] != key);
+ m_prevInx = (m_prevInx + incr) % m_keys.length)
+ if (incr == 0) {
+ incr = 1 + (key % (m_keys.length - 1));
+ }
+
+ m_prevKey = key;
+ }
+
+ return m_vals.get(m_prevInx);
+ }
+
+ /**
+ * Returns an enumeration of keys in this hashtable, ordered
+ * arbitrarily.<p>
+ * The returned enumeration becomes invalid as soon as put(int, Object)
+ * is called on this hashtable; calling methods on an invalid
+ * enumeration will cause undefined behavior in the enumerator.
+ * The returned enumerator has absolutely no effect on the underlying
+ * hashtable.<p>
+ * This method returns in constant time. The returned enumerator
+ * returns successive keys in [amortized] time complexity O(1).
+ */
+ public final IntEnumerator keys() {
+ final int numElements = m_elements;
+
+ return new IntEnumerator() {
+ int elements = numElements;
+ int index = -1;
+
+ public final int numRemaining() {
+ return elements;
+ }
+
+ public final int nextInt() {
+ while (m_keys[++index] < 0)
+ ;
+
+ elements--;
+
+ return m_keys[index];
+ }
+ };
+ }
+
+ /**
+ * Returns an iteration of values in this hashtable, ordered
+ * arbitrarily.<p>
+ * The returned iteration becomes invalid as soon as put(int, Object)
+ * is called on this hashtable; calling methods on an invalid
+ * iteration will cause undefined behavior in the iterator.
+ * The returned iterator has absolutely no effect on the underlying
+ * hashtable (the remove() operation on the returned iterator is not
+ * supported).<p>
+ * This method returns in constant time. The returned iterator
+ * returns successive values in [amortized] time complexity O(1).<p>
+ * NOTE: The order of values returned corresponds to the order of keys
+ * returned by the enumeration from keys() - that is, the n<sup>th</sup>
+ * key returned by keys() is the key into the n<sup>th</sup> value
+ * returned by values().
+ */
+ public final Iterator values() {
+ final int numElements = m_elements;
+
+ return new Iterator() {
+ int elements = numElements;
+ int index = -1;
+
+ public final boolean hasNext() {
+ return elements == 0;
+ }
+
+ public final Object next() {
+ try {
+ while (m_vals.get(++index) == null)
+ ;
+
+ elements--;
+
+ return m_vals.get(index);
+ } catch (ArrayIndexOutOfBoundsException e) {
+ throw new NoSuchElementException();
+ }
+ }
+
+ public final void remove() {
+ throw new UnsupportedOperationException();
+ }
+ };
+ }
+
+ private final void incrSize() {
+ final int newSize;
+
+ try {
+ int primesInx = 0;
+
+ while (m_keys.length != PRIMES[primesInx++])
+ ;
+
+ newSize = PRIMES[primesInx];
+ } catch (ArrayIndexOutOfBoundsException e) {
+ throw new IllegalStateException("too many elements in this hashtable");
+ }
+
+ final int[] newKeys = new int[newSize];
+ final List<T> newVals = new ArrayList<T>(newSize);
+
+ for (int i = 0; i < newKeys.length; i++)
+ newKeys[i] = -1;
+
+ m_thresholdSize = (int) (THRESHOLD_FACTOR * (double) newKeys.length);
+
+ int incr;
+ int newIndex;
+ int oldIndex = -1;
+
+ for (int i = 0; i < m_elements; i++) {
+ while (m_keys[++oldIndex] < 0)
+ ;
+
+ incr = 0;
+
+ for (newIndex = m_keys[oldIndex] % newKeys.length; newKeys[newIndex] >= 0;
+ newIndex = (newIndex + incr) % newKeys.length)
+ if (incr == 0) {
+ incr = 1 + (m_keys[oldIndex] % (newKeys.length - 1));
+ }
+
+ newKeys[newIndex] = m_keys[oldIndex];
+ newVals.set(newIndex, m_vals.get(oldIndex));
+ }
+
+ m_keys = newKeys;
+ m_vals = newVals;
+ m_prevKey = -1;
+ m_prevInx = -1;
+ }
+}
diff --git a/corelibs/util.intr/src/main/java/cytoscape/util/intr/LongEnumerator.java b/corelibs/util.intr/src/main/java/cytoscape/util/intr/LongEnumerator.java
new file mode 100644
index 0000000..d1d3858
--- /dev/null
+++ b/corelibs/util.intr/src/main/java/cytoscape/util/intr/LongEnumerator.java
@@ -0,0 +1,56 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.util.intr;
+
+
+/**
+ * An enumeration over a list of 64 bit integers.
+ */
+public interface LongEnumerator {
+ /**
+ * Returns a non-negative integer I such that nextLong() will successfully
+ * return a value no more and no less than I times.
+ */
+ public int numRemaining();
+
+ /**
+ * Returns the next 64 bit integer in the enumeration.
+ * If numRemaining() returns a non-positive quantity before
+ * nextLong() is called, the behavior of this enumeration becomes undefined.
+ */
+ public long nextLong();
+}
diff --git a/corelibs/util.intr/src/main/java/cytoscape/util/intr/LongLongHash.java b/corelibs/util.intr/src/main/java/cytoscape/util/intr/LongLongHash.java
new file mode 100644
index 0000000..815de01
--- /dev/null
+++ b/corelibs/util.intr/src/main/java/cytoscape/util/intr/LongLongHash.java
@@ -0,0 +1,297 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.util.intr;
+
+
+/**
+ * An insert-only hashtable that has non-negative 64 bit integer keys and
+ * non-negative 64 bit integer values.<p>
+ * In the underlying implementation, this hashtable increases in size to adapt
+ * to key/value pairs being added (the underlying size of the hashtable is
+ * invisible to the programmer). In the underlying implementation, this
+ * hashtable never decreases in size. As a hashtable increases in size,
+ * it takes at most four times as much memory as it would take
+ * to store the hashtable's keys and values in a perfectly-sized array.
+ * Underlying size expansions are implemented such that the operation of
+ * expanding in size is amortized over the contstant time complexity needed to
+ * insert new elements.<p>
+ * An instance of this class is serializable; however, serialized instances of
+ * this class should not be stored in a persistent manner because the
+ * serialization implemented in this class makes no attempt at handling
+ * class versioning.
+ */
+public final class LongLongHash implements java.io.Serializable {
+ private static final int[] PRIMES = {
+ 11, 23, 53, 113, 251, 509, 1019, 2039, 4079, 8179, 16369,
+ 32749, 65521, 131063, 262133, 524269, 1048571, 2097143,
+ 4194287, 8388587, 16777183, 33554393, 67108837,
+ 134217689, 268435399, 536870879, 1073741789, 2147483647
+ };
+ private static final int INITIAL_SIZE = PRIMES[0];
+ private static final double THRESHOLD_FACTOR = 0.77;
+ private long[] m_keys;
+ private long[] m_vals;
+ private int m_elements;
+ private int m_size;
+ private int m_thresholdSize;
+
+ // These are caching variables. The idea is that programmers will
+ // frequently first do a get(), and based on that result, will perform
+ // some other operations and then maybe do a put() operation with the same
+ // key as the previous get() operation.
+ private long m_prevKey;
+ private int m_prevInx;
+
+ /**
+ * Creates a new hashtable.
+ */
+ public LongLongHash() {
+ m_keys = new long[INITIAL_SIZE];
+ m_vals = new long[INITIAL_SIZE];
+ empty();
+ }
+
+ /**
+ * Removes all key/value pairs from this hashtable. This operation has
+ * O(1) time complexity.
+ */
+ public final void empty() {
+ m_elements = 0;
+ m_size = INITIAL_SIZE;
+ m_thresholdSize = (int) (THRESHOLD_FACTOR * (double) m_size);
+
+ for (int i = 0; i < m_size; i++) {
+ m_keys[i] = -1;
+ m_vals[i] = -1;
+ }
+
+ m_prevKey = -1;
+ m_prevInx = -1;
+ }
+
+ /**
+ * Returns the number of key/value pairs currently in this hashtable.
+ */
+ public final int size() {
+ return m_elements;
+ }
+
+ /**
+ * Puts a new key/value pair into this hashtable, potentially overwriting
+ * an existing value whose key is the same as the one specified.
+ * Returns the old value associated with the specified key or -1 if no value
+ * is associated with specified key at the time of this call.<p>
+ * Insertions into the hashtable are performed in [amortized] time
+ * complexity O(1).
+ *
+ * @exception IllegalArgumentException if either key or value is negative.
+ */
+ public final long put(final long key, final long value) {
+ if (key < 0)
+ throw new IllegalArgumentException("key is negative");
+
+ if (value < 0)
+ throw new IllegalArgumentException("value is negative");
+
+ if (m_elements == m_thresholdSize)
+ incrSize();
+
+ if (key != m_prevKey) {
+ int incr = 0;
+
+ for (m_prevInx = (int) (key % m_size);
+ (m_keys[m_prevInx] >= 0) && (m_keys[m_prevInx] != key);
+ m_prevInx = (m_prevInx + incr) % m_size)
+ if (incr == 0)
+ incr = 1 + (int) (key % (m_size - 1));
+
+ m_prevKey = key;
+ }
+
+ final long returnVal = m_vals[m_prevInx];
+ m_vals[m_prevInx] = value;
+ m_keys[m_prevInx] = key;
+ m_elements += (returnVal >>> 63);
+
+ return returnVal;
+ }
+
+ /**
+ * Returns the value bound to the specified key or -1 if no value is
+ * currently bound to the specified key.<p>
+ * Searches in this hashtable are performed in [amortized] time
+ * complexity O(1).
+ *
+ * @exception IllegalArgumentException if key is negative.
+ */
+ public final long get(final long key) {
+ if (key < 0)
+ throw new IllegalArgumentException("key is negative");
+
+ if (key != m_prevKey) {
+ int incr = 0;
+
+ for (m_prevInx = (int) (key % m_size);
+ (m_keys[m_prevInx] >= 0) && (m_keys[m_prevInx] != key);
+ m_prevInx = (m_prevInx + incr) % m_size)
+ if (incr == 0)
+ incr = 1 + (int) (key % (m_size - 1));
+
+ m_prevKey = key;
+ }
+
+ return m_vals[m_prevInx];
+ }
+
+ /**
+ * Returns an enumeration of keys in this hashtable, ordered
+ * arbitrarily.<p>
+ * The returned enumeration becomes invalid as soon as put(long, long) or
+ * empty() is called on this hashtable; calling methods on an invalid
+ * enumeration will cause undefined behavior in the enumerator.
+ * The returned enumerator has absolutely no effect on the underlying
+ * hashtable.<p>
+ * This method returns in constant time. The returned enumerator
+ * returns successive keys in [amortized] time complexity O(1).<p>
+ * It is possible to get the keys() and values() enumerations at the same
+ * time and iterate over them simultaneously; then, the
+ * i<sup>th</sup> element of the keys() enumeration is the key into the
+ * i<sup>th</sup> element of the values() enumeration.
+ */
+ public final LongEnumerator keys() {
+ return enumeration(m_keys);
+ }
+
+ /**
+ * Returns an enumeration of values in this hashtable, ordered
+ * arbitrarily.<p>
+ * The returned enumeration becomes invalid as soon as put(long, long) or
+ * empty() is called on this hashtable; calling methods on an invalid
+ * enumeration will cause undefined behavior in the enumerator.
+ * The returned enumerator has absolutely no effect on the underlying
+ * hashtable.<p>
+ * This method returns in constant time. The returned enumerator
+ * returns successive values in [amortized] time complexity O(1).<p>
+ * It is possible to get the keys() and values() enumerations at the same
+ * time and iterate over them simultaneously; then, the
+ * i<sup>th</sup> element of the keys() enumeration is the key into the
+ * i<sup>th</sup> element of the values() enumeration.
+ */
+ public final LongEnumerator values() {
+ return enumeration(m_vals);
+ }
+
+ private final LongEnumerator enumeration(final long[] arr) {
+ final int numElements = m_elements;
+
+ return new LongEnumerator() {
+ int elements = numElements;
+ int index = -1;
+
+ public int numRemaining() {
+ return elements;
+ }
+
+ public long nextLong() {
+ while (arr[++index] < 0)
+ ;
+
+ elements--;
+
+ return arr[index];
+ }
+ };
+ }
+
+ private long[] m_keyDump = null;
+ private long[] m_valDump = null;
+
+ private final void incrSize() {
+ final int newSize;
+
+ try {
+ int primesInx = 0;
+
+ while (m_size != PRIMES[primesInx++])
+ ;
+
+ newSize = PRIMES[primesInx];
+ } catch (ArrayIndexOutOfBoundsException e) {
+ throw new IllegalStateException("too many elements in this hashtable");
+ }
+
+ if (m_keys.length < newSize) {
+ m_keyDump = m_keys;
+ m_valDump = m_vals;
+ m_keys = new long[newSize];
+ m_vals = new long[newSize];
+ } else {
+ System.arraycopy(m_keys, 0, m_keyDump, 0, m_size);
+ System.arraycopy(m_vals, 0, m_valDump, 0, m_size);
+ }
+
+ for (int i = 0; i < newSize; i++) {
+ m_keys[i] = -1;
+ m_vals[i] = -1;
+ }
+
+ m_size = newSize;
+ m_thresholdSize = (int) (THRESHOLD_FACTOR * (double) m_size);
+
+ int incr;
+ int newIndex;
+ int oldIndex = -1;
+
+ for (int i = 0; i < m_elements; i++) {
+ while (m_keyDump[++oldIndex] < 0)
+ ;
+
+ incr = 0;
+
+ for (newIndex = (int) (m_keyDump[oldIndex] % m_size); m_keys[newIndex] >= 0;
+ newIndex = (newIndex + incr) % m_size)
+ if (incr == 0)
+ incr = 1 + (int) (m_keyDump[oldIndex] % (m_size - 1));
+
+ m_keys[newIndex] = m_keyDump[oldIndex];
+ m_vals[newIndex] = m_valDump[oldIndex];
+ }
+
+ m_prevKey = -1;
+ m_prevInx = -1;
+ }
+}
diff --git a/corelibs/util.intr/src/main/java/cytoscape/util/intr/MinIntHeap.java b/corelibs/util.intr/src/main/java/cytoscape/util/intr/MinIntHeap.java
new file mode 100644
index 0000000..c2ca012
--- /dev/null
+++ b/corelibs/util.intr/src/main/java/cytoscape/util/intr/MinIntHeap.java
@@ -0,0 +1,448 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.util.intr;
+
+
+/**
+ * A heap is an implementation of a priority queue. A priority queue is a
+ * special kind of queue where the next value on the queue is the least
+ * element in the queue. A heap can be used to order N elements in
+ * O(n*log(N)) time complexity. Because of some of the propeties of a heap,
+ * heaps are especially good at returning the M least elements from a set
+ * of N elements, where M < N. In particular, if M is constrained to be
+ * [less than or] equal to N/log<sub>2</sub>(N) [as N varies]
+ * then the first M least elements from a set of N elements can be
+ * computed in O(N) time complexity (linear time).<p>
+ * A heap can have two states: ordered and unordered. The time complexity of
+ * certain operations is dependent on the state of the heap. Certain
+ * operations will effect the state of the heap. Please read
+ * the documentation of each method to better understand the time
+ * complexity of each operation and the operation's relationship to the state
+ * of the heap.<p>
+ * An instance of this class is serializable; however, serialized instances of
+ * this class should not be stored in a persistent manner because the
+ * serialization implemented in this class makes no attempt at handling
+ * class versioning.
+ */
+public final class MinIntHeap implements java.io.Serializable {
+ // This must be a non-negative integer.
+ private static final int DEFAULT_CAPACITY = 11;
+ private int[] m_heap;
+ private int m_currentSize;
+ private boolean m_orderOK;
+
+ /**
+ * Creates a new heap. A new heap is ordered.
+ */
+ public MinIntHeap() {
+ m_heap = new int[DEFAULT_CAPACITY + 1];
+ m_heap[0] = Integer.MIN_VALUE;
+ m_currentSize = 0;
+ m_orderOK = true;
+ }
+
+ /**
+ * Empties this heap of all elements. The heap is ordered after this
+ * operation.
+ */
+ public final void empty() {
+ m_currentSize = 0;
+ m_orderOK = true;
+ }
+
+ /**
+ * Returns the number of elements currently in this heap.
+ */
+ public final int size() {
+ return m_currentSize;
+ }
+
+ /**
+ * Returns true if and only if the heap is currently ordered.
+ */
+ public final boolean isOrdered() {
+ return m_orderOK;
+ }
+
+ /**
+ * Tosses a new element onto the heap. The heap will be become
+ * unordered after this operation; this operation takes constant
+ * [amortized] time.
+ */
+ public final void toss(int x) {
+ try {
+ m_heap[++m_currentSize] = x;
+ } catch (ArrayIndexOutOfBoundsException e) {
+ m_currentSize--;
+ checkSize(1);
+ m_heap[++m_currentSize] = x;
+ }
+
+ m_orderOK = false;
+ }
+
+ /**
+ * Tosses a bunch of new elements onto the heap at once. The heap will
+ * become unordered after this operation; this operation takes
+ * O(N) time where N is the number of elements being tossed onto the heap.
+ * @param elements an array containing elements to be tossed onto this heap.
+ * @param beginIndex the index in the elements array from which to start
+ * tossing elements onto this heap.
+ * @param length the number of contiguous elements in the elements array
+ * to toss onto this heap.
+ * @exception IndexOutOfBoundsException if the combination of the
+ * input parameters (elements, beginIndex, and length) don't make sense.
+ */
+ public final void toss(int[] elements, int beginIndex, int length) {
+ // Do some extra error checking just so that we don't create an
+ // extremely large array if incorrect parameters are passed.
+ if (beginIndex < 0)
+ throw new IndexOutOfBoundsException("beginIndex is less than zero");
+
+ if (length < 0)
+ throw new IndexOutOfBoundsException("length is less than zero");
+
+ if ((((long) beginIndex) + (long) length) > (long) elements.length)
+ throw new IndexOutOfBoundsException("combination of beginIndex and length exceed length of array");
+
+ checkSize(length);
+ System.arraycopy(elements, beginIndex, m_heap, m_currentSize + 1, length);
+ m_currentSize += length;
+ m_orderOK = false;
+ }
+
+ /**
+ * If this heap is ordered prior to calling this operation, adds
+ * specified element to heap such that the heap will remain ordered after
+ * this operation, taking O(log(N)) time where N is the number of
+ * elements in this heap (average time is actually constant regardless of
+ * size of heap). If this heap is not ordered when this operation is called,
+ * adds specified element to heap in constant time.<p>
+ * If the underlying data structure is not large enough to hold an
+ * additional element, the structure is made larger; the process of making
+ * the underlying structure larger takes O(N) time; the enlargening
+ * operation doubles the size of the underlying structure. Therefore,
+ * the time complexities described above are amortized time complexities.
+ */
+ public final void insert(int x) {
+ try {
+ m_heap[++m_currentSize] = x;
+ } catch (ArrayIndexOutOfBoundsException e) {
+ m_currentSize--;
+ checkSize(1);
+ m_heap[++m_currentSize] = x;
+ }
+
+ if (m_orderOK)
+ percolateUp(m_heap, m_currentSize);
+ }
+
+ /**
+ * Returns the minimum element in this heap. This is a constant time
+ * operation if the heap is ordered. If the heap is not ordered, this
+ * operation will first order the entire heap. The time complexity of
+ * ordering an unordered heap is O(N) where N is the number of elements
+ * in the heap. This method leaves the heap in an ordered state.<p>
+ * If there are no elements in this heap, results of this operation
+ * are undefined.
+ */
+ public final int findMin() {
+ if (!m_orderOK) { // Fix heap.
+
+ for (int i = m_currentSize / 2; i > 0; i--)
+ percolateDown(m_heap, i, m_currentSize);
+
+ m_orderOK = true;
+ }
+
+ return m_heap[1];
+ }
+
+ /**
+ * Deletes and returns the minimum element in this heap. This operation
+ * has time complexity O(log(N)) where N is the number of elements
+ * currently in this heap, assuming that the heap is ordered. If the
+ * heap is not ordered at the time this operation is invoked, this
+ * operation will first order the entire heap. The time complexity of
+ * ordering an unordered heap is O(N), where N is the number of elements
+ * in the heap. When this method returns, this heap is in an ordered
+ * state.<p>
+ * If there are no elements in this heap, results of this operation
+ * are undefined.
+ */
+ public final int deleteMin() {
+ if (!m_orderOK) { // Fix heap.
+
+ for (int i = m_currentSize / 2; i > 0; i--)
+ percolateDown(m_heap, i, m_currentSize);
+
+ m_orderOK = true;
+ }
+
+ final int returnThis = m_heap[1];
+ m_heap[1] = m_heap[m_currentSize--];
+ percolateDown(m_heap, 1, m_currentSize);
+
+ return returnThis;
+ }
+
+ private final void checkSize(int newElements) {
+ if (m_currentSize < (m_heap.length - newElements))
+ return;
+
+ final long newHeapSize = Math.max(((long) m_heap.length) + (long) newElements,
+ Math.min((long) Integer.MAX_VALUE,
+ (((long) m_heap.length) * 2L) + 1L));
+
+ if (newHeapSize > (long) Integer.MAX_VALUE)
+ throw new IllegalStateException("cannot allocate large enough array");
+
+ final int[] newHeap = new int[(int) newHeapSize];
+ System.arraycopy(m_heap, 0, newHeap, 0, m_heap.length);
+ m_heap = newHeap;
+ }
+
+ private static final void percolateUp(int[] heap, int childIndex) {
+ for (int parentIndex = childIndex / 2; heap[childIndex] < heap[parentIndex];
+ childIndex = parentIndex, parentIndex = parentIndex / 2)
+ swap(heap, parentIndex, childIndex);
+ }
+
+ private static final void percolateDown(int[] heap, int parentIndex, int size) {
+ // parentIndex is at most m_currentSize / 2.
+ for (int childIndex = parentIndex * 2; (childIndex <= size) && (childIndex > 0); // Check for overflow.
+
+ parentIndex = childIndex, childIndex = childIndex * 2) {
+ // childIndex is a multiple of 2, so childIndex + 1 will not overflow.
+ if (((childIndex + 1) <= size) && (heap[childIndex + 1] < heap[childIndex]))
+ childIndex++;
+
+ if (heap[childIndex] < heap[parentIndex])
+ swap(heap, parentIndex, childIndex);
+ else
+
+ break;
+ }
+ }
+
+ private static final void swap(int[] arr, int index1, int index2) {
+ int temp = arr[index1];
+ arr[index1] = arr[index2];
+ arr[index2] = temp;
+ }
+
+ /**
+ * Returns an enumeration of elements in this heap, ordered such that
+ * the least element is first in the returned enumeration. Pruning of
+ * duplicate elements is enabled by setting pruneDuplicates to true.<p>
+ * If pruneDuplicates is false, this method returns in constant
+ * time, unless this heap is unordered when this method is called, in
+ * which case this method returns in O(N) time. The returned enumeration
+ * takes O(log(N)) time complexity to return each successive element.<p>
+ * If pruneDuplicates is true, this method takes O(N*log(N)) time
+ * complexity to come up with the return value regardless of whether or
+ * not this heap is in an ordered state at the time this method is called.
+ * (Truth be told, this method will come up with a return value in less
+ * time if this heap is in an ordered state when this method is called.)
+ * The retuned enumeration takes constant time to return each successive
+ * element.<p>
+ * The returned enumeration becomes invalid as soon as any other method
+ * on this heap instance is called; calling methods on an invalid enumeration
+ * will cause undefined behavior in both the enumerator and in the underlying
+ * heap.<p>
+ * Calling this function automatically causes this heap to become
+ * unordered. No elements are added or removed from this heap as a
+ * result of using the returned enumeration.
+ * @see #elements()
+ */
+ public final IntEnumerator orderedElements(boolean pruneDuplicates) {
+ final int[] heap = m_heap;
+ final int size = m_currentSize;
+
+ if (!m_orderOK) // Fix heap.
+ for (int i = size / 2; i > 0; i--)
+ percolateDown(heap, i, size);
+
+ m_orderOK = false; // That's right - the heap becomes unordered.
+
+ if (pruneDuplicates) {
+ int dups = 0;
+ int sizeIter = size;
+
+ while (sizeIter > 1) { // Needs to be 1, not 0, for duplicates.
+ swap(heap, 1, sizeIter);
+ percolateDown(heap, 1, sizeIter - 1);
+
+ if (heap[1] == heap[sizeIter])
+ dups++;
+
+ sizeIter--;
+ }
+
+ final int numDuplicates = dups;
+
+ return new IntEnumerator() {
+ int m_index = size;
+ int m_dups = numDuplicates;
+ int m_prevValue = heap[m_index] + 1;
+
+ public int numRemaining() {
+ return m_index - m_dups;
+ }
+
+ public int nextInt() {
+ while (heap[m_index] == m_prevValue) {
+ m_dups--;
+ m_index--;
+ }
+
+ m_prevValue = heap[m_index--];
+
+ return m_prevValue;
+ }
+ };
+ } else // Don't prune duplicates. Do lazy computation.
+ {
+ return new IntEnumerator() {
+ int m_size = size;
+
+ public int numRemaining() {
+ return m_size;
+ }
+
+ public int nextInt() {
+ swap(heap, 1, m_size);
+ percolateDown(heap, 1, m_size - 1);
+
+ return heap[m_size--];
+ }
+ };
+ }
+ }
+
+ /**
+ * Returns an enumeration over all the elements currently in this heap;
+ * the order of elements in the returned enumeration is undefined.<p>
+ * If other methods in this heap are called while enumerating through
+ * the return value, behavior of the enumerator is undefined.<p>
+ * This enumerator has no effect on the set of elements in this heap. This
+ * enumeration has no effect on the ordered state of this heap.
+ * @see #orderedElements(boolean)
+ */
+ public final IntEnumerator elements() {
+ final int[] heap = m_heap;
+ final int size = m_currentSize;
+
+ return new IntEnumerator() {
+ int index = 0;
+
+ public int numRemaining() {
+ return size - index;
+ }
+
+ public int nextInt() {
+ return heap[++index];
+ }
+ };
+ }
+
+ /**
+ * Copies the elements of this heap into the specified output array.
+ * The order in which elements are copied is undefined. Elements are copied
+ * into the output array starting at beginIndex in the output array. The
+ * output array must be large enough to hold all the elements in this
+ * heap.<p>
+ * NOTE: This method has been deprecated ever since it was added to this
+ * class. A decision is being made as to whether or not to keep this
+ * method.
+ * @param output the array into which the elements of this heap get copied.
+ * @param beginIndex an index in the output array which is the beginning
+ * of where elements are copied to.
+ * @exception IndexOutOfBoundsException if copying would cause access of
+ * data outside output array bounds.
+ * @deprecated Use elements() instead.
+ * @see #elements()
+ */
+ public final void copyInto(int[] output, int beginIndex) {
+ System.arraycopy(m_heap, 1, output, beginIndex, m_currentSize);
+ }
+
+ /**
+ * Copies the elements of this heap into the specified output array in
+ * descending order. The largest element (the largest integer, that is)
+ * in this heap is placed at index beginIndex in the output array.
+ * The smallest element in this heap is placed at index
+ * beginIndex+size()-1 in the output array. The output array must be large
+ * enough to hold all the elements in this heap.<p>
+ * This operation takes O(N*log(N)) time complexity, regardless of whether
+ * or not this heap is in an ordered state at the time this method is
+ * called. (Truth be told, this method will be faster if the heap is in an
+ * ordered state when this method is called.) This operation also
+ * leaves this heap in an unordered state. No elements are added or
+ * removed from this heap as a result of using this operation.<p>
+ * NOTE: This method has been deprecated ever since it was added to this
+ * class. A decision is being made as to whether or not to keep this
+ * method.
+ * @param output the array into which the elements of this heap get copied.
+ * @param beginIndex an index in the output array which is the beginning
+ * of where elements are copied to.
+ * @exception IndexOutOfBoundsException if copying would cause access of
+ * data outside output array bounds.
+ * @deprecated Use orderedElements(boolean) or deleteMin() instead.
+ * @see #orderedElements(boolean)
+ * @see #deleteMin()
+ */
+ public final void copyIntoReverseOrder(int[] output, int beginIndex) {
+ final int[] heap = m_heap;
+ final int size = m_currentSize;
+
+ if (!m_orderOK) // Fix heap.
+ for (int i = size / 2; i > 0; i--)
+ percolateDown(heap, i, size);
+
+ m_orderOK = false; // That's right - the heap becomes unordered.
+
+ int sizeIter = size;
+
+ while (sizeIter > 0) {
+ swap(m_heap, 1, sizeIter);
+ percolateDown(heap, 1, --sizeIter);
+ }
+
+ System.arraycopy(heap, 1, output, beginIndex, size);
+ }
+}
diff --git a/corelibs/util.intr/src/main/java/cytoscape/util/intr/test/BitSetPerformance.java b/corelibs/util.intr/src/main/java/cytoscape/util/intr/test/BitSetPerformance.java
new file mode 100644
index 0000000..be9ddc4
--- /dev/null
+++ b/corelibs/util.intr/src/main/java/cytoscape/util/intr/test/BitSetPerformance.java
@@ -0,0 +1,205 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.util.intr.test;
+
+import cytoscape.util.intr.IntEnumerator;
+import cytoscape.util.intr.MinIntHeap;
+
+import java.io.IOException;
+import java.io.InputStream;
+
+import java.util.BitSet;
+
+
+/**
+ *
+ */
+public class BitSetPerformance {
+ /**
+ * This test is analagous to
+ * cytoscape.intr.util.test.MinIntHeapPerformance, only
+ * it uses a bit array instead of a heap. So the purpose of this test
+ * is to compare the performance between a heap and a bit array when using
+ * these objects solely for the purpose of pruning duplicate integers from a
+ * set of integers.
+ */
+ public static void main(String[] args) throws Exception {
+ int N = Integer.parseInt(args[0]);
+ boolean repeat = false;
+
+ if ((args.length > 1) && args[1].equalsIgnoreCase("repeat"))
+ repeat = true;
+
+ int[] elements = new int[N];
+ InputStream in = System.in;
+ byte[] buff = new byte[4];
+ int inx = 0;
+ int off = 0;
+ int read;
+
+ while ((inx < N) && ((read = in.read(buff, off, buff.length - off)) > 0)) {
+ off += read;
+
+ if (off < buff.length)
+ continue;
+ else
+ off = 0;
+
+ elements[inx++] = (0x7fffffff & assembleInt(buff)) % N;
+ }
+
+ if (inx < N)
+ throw new IOException("premature end of input");
+
+ // Lose reference to as much as we can.
+ in = null;
+ buff = null;
+
+ // Load the classes we're going to use into the classloader.
+ _THE_TEST_CASE_(new int[] { 0, 3, 4, 3, 9, 9, 1 });
+
+ // Sleep, collect garbage, have a snack, etc.
+ Thread.sleep(1000);
+
+ // Warm up.
+ for (int i = 0; i < 100; i++) {
+ int foo = (i * 4) / 8;
+ }
+
+ // Start timer.
+ long millisBegin = System.currentTimeMillis();
+
+ // Run the test. Quick, stopwatch is ticking!
+ int[] uniqueElements = _THE_TEST_CASE_(elements);
+
+ // Stop timer.
+ long millisEnd = System.currentTimeMillis();
+
+ // Print the time taken to standard error.
+ if (!repeat)
+ System.err.println(millisEnd - millisBegin);
+
+ // Sort the array. We can use the same heap that we used as a bucket
+ // to now sort the integers.
+ IntEnumerator sortedElements = _THE_HEAP_.orderedElements(false);
+
+ // Print sorted array to standard out.
+ if (!repeat)
+ while (sortedElements.numRemaining() > 0)
+ System.out.println(sortedElements.nextInt());
+
+ // Run repeated test if that's what the command line told us.
+ if (repeat) {
+ for (int i = 0; i < uniqueElements.length; i++)
+ uniqueElements[i] = 0;
+
+ millisBegin = System.currentTimeMillis();
+ _REPEAT_TEST_CASE_(elements, uniqueElements);
+ millisEnd = System.currentTimeMillis();
+ System.err.println((millisEnd - millisBegin) + " (repeated test)");
+ _THE_HEAP_.empty();
+ _THE_HEAP_.toss(uniqueElements, 0, uniqueElements.length);
+
+ while (_THE_HEAP_.size() > 0)
+ System.out.println(_THE_HEAP_.deleteMin());
+ }
+ }
+
+ private static final int assembleInt(byte[] fourConsecutiveBytes) {
+ int firstByte = (((int) fourConsecutiveBytes[0]) & 0x000000ff) << 24;
+ int secondByte = (((int) fourConsecutiveBytes[1]) & 0x000000ff) << 16;
+ int thirdByte = (((int) fourConsecutiveBytes[2]) & 0x000000ff) << 8;
+ int fourthByte = (((int) fourConsecutiveBytes[3]) & 0x000000ff) << 0;
+
+ return firstByte | secondByte | thirdByte | fourthByte;
+ }
+
+ // Keep a reference to our data structure so that we can determine how
+ // much memory was consumed by our algorithm (may be implemented in future).
+ static BitSet _THE_BIT_ARRAY_ = null;
+
+ // The heap is used only for the purpose of being a bucket of unique
+ // integers; we add an integer to this bucket if and only the bit array
+ // tells us that the value at index integer is false (and then we set the
+ // bit in the array to true).
+ static MinIntHeap _THE_HEAP_ = null;
+
+ private static final int[] _THE_TEST_CASE_(final int[] elements) {
+ // The dynamic range of the integers in this array happens to be the
+ // same as the number of integers in this array based on our test case
+ // definition.
+ _THE_BIT_ARRAY_ = new BitSet(elements.length);
+ _THE_HEAP_ = new MinIntHeap();
+
+ for (int i = 0; i < elements.length; i++)
+ if (!_THE_BIT_ARRAY_.get(elements[i])) {
+ _THE_HEAP_.toss(elements[i]);
+ _THE_BIT_ARRAY_.set(elements[i]);
+ }
+
+ final IntEnumerator iter = _THE_HEAP_.elements();
+ final int[] returnThis = new int[iter.numRemaining()];
+ final int numElements = returnThis.length;
+
+ for (int i = 0; i < numElements; i++)
+ returnThis[i] = iter.nextInt();
+
+ return returnThis;
+ }
+
+ private static final void _REPEAT_TEST_CASE_(final int[] elements, final int[] output) {
+ _THE_HEAP_.empty();
+ _THE_BIT_ARRAY_.clear(0, elements.length);
+
+ for (int i = 0; i < elements.length; i++)
+ if (!_THE_BIT_ARRAY_.get(elements[i])) {
+ _THE_HEAP_.toss(elements[i]);
+ _THE_BIT_ARRAY_.set(elements[i]);
+ }
+
+ if (_THE_HEAP_.size() != output.length)
+ throw new IllegalStateException("output array is incorrect size");
+
+ final IntEnumerator iter = _THE_HEAP_.elements();
+ final int numElements = output.length;
+
+ for (int i = 0; i < numElements; i++)
+ output[i] = iter.nextInt();
+
+ //_THE_HEAP_.copyInto(output, 0);
+ }
+}
diff --git a/corelibs/util.intr/src/main/java/cytoscape/util/intr/test/DEPENDENCIES b/corelibs/util.intr/src/main/java/cytoscape/util/intr/test/DEPENDENCIES
new file mode 100644
index 0000000..4b32af8
--- /dev/null
+++ b/corelibs/util.intr/src/main/java/cytoscape/util/intr/test/DEPENDENCIES
@@ -0,0 +1 @@
+cytoscape.util.intr
diff --git a/corelibs/util.intr/src/main/java/cytoscape/util/intr/test/IntBTreeConstructionTuner.java b/corelibs/util.intr/src/main/java/cytoscape/util/intr/test/IntBTreeConstructionTuner.java
new file mode 100644
index 0000000..16ac34c
--- /dev/null
+++ b/corelibs/util.intr/src/main/java/cytoscape/util/intr/test/IntBTreeConstructionTuner.java
@@ -0,0 +1,121 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.util.intr.test;
+
+import cytoscape.util.intr.IntBTree;
+
+import java.io.IOException;
+import java.io.InputStream;
+
+
+/**
+ *
+ */
+public class IntBTreeConstructionTuner {
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ *
+ * @throws IOException DOCUMENT ME!
+ * @throws IllegalStateException DOCUMENT ME!
+ */
+ public static void main(String[] args) throws IOException {
+ int branches = Integer.parseInt(args[0]);
+ int N = Integer.parseInt(args[1]);
+ int[] elements = new int[N];
+ InputStream in = System.in;
+ byte[] buff = new byte[4];
+ int inx = 0;
+ int off = 0;
+ int read;
+
+ while ((inx < N) && ((read = in.read(buff, off, buff.length - off)) > 0)) {
+ off += read;
+
+ if (off < buff.length)
+ continue;
+ else
+ off = 0;
+
+ elements[inx++] = (0x7fffffff & assembleInt(buff)) % N;
+ }
+
+ if (inx < N)
+ throw new IOException("premature end of input");
+
+ IntBTree tree = new IntBTree(branches);
+ long timeBegin = System.currentTimeMillis();
+ tree.insert(elements[0]);
+
+ for (int i = 1; i < elements.length; i++) {
+ tree.delete(elements[i - 1]);
+ tree.insert(elements[i]);
+ tree.insert(elements[i - 1]);
+ tree.insert(elements[i]);
+ tree.delete(elements[i]);
+ }
+
+ if (tree.size() != elements.length)
+ throw new IllegalStateException();
+
+ tree.delete(elements[0]);
+
+ for (int i = 1; i < elements.length; i++) {
+ tree.delete(elements[i]);
+ tree.insert(elements[i - 1]);
+ tree.insert(elements[i]);
+ tree.delete(elements[i - 1]);
+ tree.delete(elements[i]);
+ }
+
+ if (tree.size() != 0)
+ throw new IllegalStateException();
+
+ long timeEnd = System.currentTimeMillis();
+ System.out.println((timeEnd - timeBegin) + " milliseconds");
+ }
+
+ private static int assembleInt(byte[] fourConsecutiveBytes) {
+ int firstByte = (((int) fourConsecutiveBytes[0]) & 0x000000ff) << 24;
+ int secondByte = (((int) fourConsecutiveBytes[1]) & 0x000000ff) << 16;
+ int thirdByte = (((int) fourConsecutiveBytes[2]) & 0x000000ff) << 8;
+ int fourthByte = (((int) fourConsecutiveBytes[3]) & 0x000000ff) << 0;
+
+ return firstByte | secondByte | thirdByte | fourthByte;
+ }
+}
diff --git a/corelibs/util.intr/src/main/java/cytoscape/util/intr/test/IntBTreePerformance.java b/corelibs/util.intr/src/main/java/cytoscape/util/intr/test/IntBTreePerformance.java
new file mode 100644
index 0000000..cf88ee2
--- /dev/null
+++ b/corelibs/util.intr/src/main/java/cytoscape/util/intr/test/IntBTreePerformance.java
@@ -0,0 +1,164 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.util.intr.test;
+
+import cytoscape.util.intr.IntBTree;
+import cytoscape.util.intr.IntEnumerator;
+import cytoscape.util.intr.IntStack;
+import cytoscape.util.intr.MinIntHeap;
+
+import java.io.IOException;
+import java.io.InputStream;
+
+
+/**
+ *
+ */
+public class IntBTreePerformance {
+ /**
+ * This test is analagous to
+ * cytoscape.intr.util.test.MinIntHeapPerformance, only
+ * it uses a B-tree instead of a heap. So the purpose of this test
+ * is to compare the performance between a heap and a B-tree when using
+ * these objects solely for the purpose of pruning duplicate integers from a
+ * set of integers.
+ */
+ public static void main(String[] args) throws Exception {
+ int N = Integer.parseInt(args[0]);
+ int[] elements = new int[N];
+ InputStream in = System.in;
+ byte[] buff = new byte[4];
+ int inx = 0;
+ int off = 0;
+ int read;
+
+ while ((inx < N) && ((read = in.read(buff, off, buff.length - off)) > 0)) {
+ off += read;
+
+ if (off < buff.length)
+ continue;
+ else
+ off = 0;
+
+ elements[inx++] = (0x7fffffff & assembleInt(buff)) % N;
+ }
+
+ if (inx < N)
+ throw new IOException("premature end of input");
+
+ // Lose reference to as much as we can.
+ in = null;
+ buff = null;
+
+ // Load the classes we're going to use into the classloader.
+ _THE_TEST_CASE_(new int[] { 0, 3, 4, 3, 9, 9, 1 });
+
+ // Sleep, collect garbage, have a snack, etc.
+ Thread.sleep(1000);
+
+ // Warm up.
+ for (int i = 0; i < 100; i++) {
+ int foo = (i * 4) / 8;
+ }
+
+ // Start timer.
+ long millisBegin = System.currentTimeMillis();
+
+ // Run the test. Quick, stopwatch is ticking!
+ int[] uniqueElements = _THE_TEST_CASE_(elements);
+
+ // Stop timer.
+ long millisEnd = System.currentTimeMillis();
+
+ // Print the time taken to standard error.
+ System.err.println(millisEnd - millisBegin);
+
+ // Print sorted array to standard out.
+ for (int i = 0; i < uniqueElements.length; i++)
+ System.out.println(uniqueElements[i]);
+ }
+
+ private static final int assembleInt(byte[] fourConsecutiveBytes) {
+ int firstByte = (((int) fourConsecutiveBytes[0]) & 0x000000ff) << 24;
+ int secondByte = (((int) fourConsecutiveBytes[1]) & 0x000000ff) << 16;
+ int thirdByte = (((int) fourConsecutiveBytes[2]) & 0x000000ff) << 8;
+ int fourthByte = (((int) fourConsecutiveBytes[3]) & 0x000000ff) << 0;
+
+ return firstByte | secondByte | thirdByte | fourthByte;
+ }
+
+ // Keep a reference to our data structure so that we can determine how
+ // much memory was consumed by our algorithm (may be implemented in future).
+ static IntBTree _THE_TREE_ = null;
+ static IntStack _THE_STACK_ = null;
+
+ private static final int[] _THE_TEST_CASE_(final int[] elements) {
+ _THE_TREE_ = new IntBTree();
+ _THE_STACK_ = new IntStack();
+
+ for (int i = 0; i < elements.length; i++)
+ _THE_TREE_.insert(elements[i]);
+
+ final IntEnumerator iter = _THE_TREE_.searchRange(Integer.MIN_VALUE, Integer.MAX_VALUE,
+ false);
+ int prevVal = -1;
+
+ if (iter.numRemaining() > 0) {
+ prevVal = iter.nextInt();
+ _THE_STACK_.push(prevVal);
+ }
+
+ int newVal;
+
+ while (iter.numRemaining() > 0) {
+ newVal = iter.nextInt();
+
+ if (newVal == prevVal)
+ continue;
+
+ prevVal = newVal;
+ _THE_STACK_.push(prevVal);
+ }
+
+ final int[] returnThis = new int[_THE_STACK_.size()];
+
+ for (int i = _THE_STACK_.size(); i > 0;)
+ returnThis[--i] = _THE_STACK_.pop();
+
+ return returnThis;
+ }
+}
diff --git a/corelibs/util.intr/src/main/java/cytoscape/util/intr/test/IntBTreeQueryTuner.java b/corelibs/util.intr/src/main/java/cytoscape/util/intr/test/IntBTreeQueryTuner.java
new file mode 100644
index 0000000..41d280b
--- /dev/null
+++ b/corelibs/util.intr/src/main/java/cytoscape/util/intr/test/IntBTreeQueryTuner.java
@@ -0,0 +1,112 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.util.intr.test;
+
+import cytoscape.util.intr.IntBTree;
+import cytoscape.util.intr.IntEnumerator;
+
+import java.io.IOException;
+import java.io.InputStream;
+
+
+/**
+ *
+ */
+public class IntBTreeQueryTuner {
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ *
+ * @throws IOException DOCUMENT ME!
+ * @throws IllegalStateException DOCUMENT ME!
+ */
+ public static void main(String[] args) throws IOException {
+ int branches = Integer.parseInt(args[0]);
+ int N = Integer.parseInt(args[1]);
+
+ if (N < 1000)
+ throw new IllegalStateException("N should be at least 1000");
+
+ int[] elements = new int[N];
+ InputStream in = System.in;
+ byte[] buff = new byte[4];
+ int inx = 0;
+ int off = 0;
+ int read;
+
+ while ((inx < N) && ((read = in.read(buff, off, buff.length - off)) > 0)) {
+ off += read;
+
+ if (off < buff.length)
+ continue;
+ else
+ off = 0;
+
+ elements[inx++] = (0x7fffffff & assembleInt(buff)) % N;
+ }
+
+ if (inx < N)
+ throw new IOException("premature end of input");
+
+ IntBTree tree = new IntBTree(branches);
+
+ for (int i = 0; i < elements.length; i++)
+ tree.insert(elements[i]);
+
+ int querySpan = N / 3;
+ boolean reverseOrder = false;
+ long timeBegin = System.currentTimeMillis();
+
+ for (int i = 0; i < 1000; i += 3) {
+ IntEnumerator iter = tree.searchRange(i, i + querySpan, reverseOrder);
+ reverseOrder = !reverseOrder;
+ }
+
+ long timeEnd = System.currentTimeMillis();
+ System.out.println((timeEnd - timeBegin) + " milliseconds");
+ }
+
+ private static int assembleInt(byte[] fourConsecutiveBytes) {
+ int firstByte = (((int) fourConsecutiveBytes[0]) & 0x000000ff) << 24;
+ int secondByte = (((int) fourConsecutiveBytes[1]) & 0x000000ff) << 16;
+ int thirdByte = (((int) fourConsecutiveBytes[2]) & 0x000000ff) << 8;
+ int fourthByte = (((int) fourConsecutiveBytes[3]) & 0x000000ff) << 0;
+
+ return firstByte | secondByte | thirdByte | fourthByte;
+ }
+}
diff --git a/corelibs/util.intr/src/main/java/cytoscape/util/intr/test/IntHashPerformance.java b/corelibs/util.intr/src/main/java/cytoscape/util/intr/test/IntHashPerformance.java
new file mode 100644
index 0000000..1121eae
--- /dev/null
+++ b/corelibs/util.intr/src/main/java/cytoscape/util/intr/test/IntHashPerformance.java
@@ -0,0 +1,195 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.util.intr.test;
+
+import cytoscape.util.intr.IntEnumerator;
+import cytoscape.util.intr.IntHash;
+
+import java.io.IOException;
+import java.io.InputStream;
+
+import java.util.ArrayList;
+import java.util.Collections;
+
+
+/**
+ *
+ */
+public class IntHashPerformance {
+ /**
+ * This test is analagous to
+ * cytoscape.util.intr.test.MinIntHeapPerformance, only
+ * it uses a hashtable instead of a heap. So the purpose of this test
+ * is to compare the performance between a heap and a hashtable when using
+ * these objects solely for the purpose of pruning duplicate integers from a
+ * set of integers.
+ */
+ public static void main(String[] args) throws Exception {
+ int N = Integer.parseInt(args[0]);
+ boolean repeat = false;
+
+ if ((args.length > 1) && args[1].equalsIgnoreCase("repeat"))
+ repeat = true;
+
+ int[] elements = new int[N];
+ InputStream in = System.in;
+ byte[] buff = new byte[4];
+ int inx = 0;
+ int off = 0;
+ int read;
+
+ while ((inx < N) && ((read = in.read(buff, off, buff.length - off)) > 0)) {
+ off += read;
+
+ if (off < buff.length)
+ continue;
+ else
+ off = 0;
+
+ elements[inx++] = (0x7fffffff & assembleInt(buff)) % N;
+ }
+
+ if (inx < N)
+ throw new IOException("premature end of input");
+
+ // Lose reference to as much as we can.
+ in = null;
+ buff = null;
+
+ // Load the classes we're going to use into the classloader.
+ _THE_TEST_CASE_(new int[] { 0, 3, 4, 3, 9, 9, 1 });
+
+ // Sleep, collect garbage, have a snack, etc.
+ Thread.sleep(1000);
+
+ // Warm up.
+ for (int i = 0; i < 100; i++) {
+ int foo = (i * 4) / 8;
+ }
+
+ // Start timer.
+ long millisBegin = System.currentTimeMillis();
+
+ // Run the test. Quick, stopwatch is ticking!
+ int[] uniqueElements = _THE_TEST_CASE_(elements);
+
+ // Stop timer.
+ long millisEnd = System.currentTimeMillis();
+
+ // Print the time taken to standard error.
+ if (!repeat)
+ System.err.println(millisEnd - millisBegin);
+
+ // Print sorted array to standard out.
+ if (!repeat) {
+ ArrayList arrList = new ArrayList();
+
+ for (int i = 0; i < uniqueElements.length; i++)
+ arrList.add(new Integer(uniqueElements[i]));
+
+ Collections.sort(arrList);
+
+ for (int i = 0; i < arrList.size(); i++)
+ System.out.println(((Integer) arrList.get(i)).intValue());
+ }
+
+ // Run repeated test if that's what the command line told us.
+ if (repeat) {
+ for (int i = 0; i < uniqueElements.length; i++)
+ uniqueElements[i] = 0;
+
+ millisBegin = System.currentTimeMillis();
+ _REPEAT_TEST_CASE_(elements, uniqueElements);
+ millisEnd = System.currentTimeMillis();
+ System.err.println((millisEnd - millisBegin) + " (repeated test)");
+
+ ArrayList arrList = new ArrayList();
+
+ for (int i = 0; i < uniqueElements.length; i++)
+ arrList.add(new Integer(uniqueElements[i]));
+
+ Collections.sort(arrList);
+
+ for (int i = 0; i < arrList.size(); i++)
+ System.out.println(((Integer) arrList.get(i)).intValue());
+ }
+ }
+
+ private static final int assembleInt(byte[] fourConsecutiveBytes) {
+ int firstByte = (((int) fourConsecutiveBytes[0]) & 0x000000ff) << 24;
+ int secondByte = (((int) fourConsecutiveBytes[1]) & 0x000000ff) << 16;
+ int thirdByte = (((int) fourConsecutiveBytes[2]) & 0x000000ff) << 8;
+ int fourthByte = (((int) fourConsecutiveBytes[3]) & 0x000000ff) << 0;
+
+ return firstByte | secondByte | thirdByte | fourthByte;
+ }
+
+ // Keep a reference to our data structure so that we can determine how
+ // much memory was consumed by our algorithm (may be implemented in future).
+ static IntHash _THE_HASHTABLE_ = null;
+
+ private static final int[] _THE_TEST_CASE_(int[] elements) {
+ _THE_HASHTABLE_ = new IntHash();
+
+ for (int i = 0; i < elements.length; i++) {
+ _THE_HASHTABLE_.put(elements[i]);
+ }
+
+ final IntEnumerator iter = _THE_HASHTABLE_.elements();
+ final int[] returnThis = new int[iter.numRemaining()];
+
+ for (int i = 0; i < returnThis.length; i++)
+ returnThis[i] = iter.nextInt();
+
+ return returnThis;
+ }
+
+ private static final void _REPEAT_TEST_CASE_(final int[] elements, final int[] output) {
+ _THE_HASHTABLE_.empty();
+
+ for (int i = 0; i < elements.length; i++)
+ _THE_HASHTABLE_.put(elements[i]);
+
+ IntEnumerator iter = _THE_HASHTABLE_.elements();
+
+ if (iter.numRemaining() != output.length)
+ throw new IllegalStateException("output aray is incorrect size");
+
+ for (int i = 0; i < output.length; i++)
+ output[i] = iter.nextInt();
+ }
+}
diff --git a/corelibs/util.intr/src/main/java/cytoscape/util/intr/test/MinIntHeapPerformance.java b/corelibs/util.intr/src/main/java/cytoscape/util/intr/test/MinIntHeapPerformance.java
new file mode 100644
index 0000000..8bdc0bd
--- /dev/null
+++ b/corelibs/util.intr/src/main/java/cytoscape/util/intr/test/MinIntHeapPerformance.java
@@ -0,0 +1,209 @@
+/*
+
+ RESULTS OF RUNNING TESTS ON A COMPUTER. THESE PERFORMANCE TESTS
+ MEASURE THE PERFORMANCE OF COMPUTING UNIQUE SETS OF INTEGERS FROM
+ SETS OF INTEGERS CONTAINING POTENTIAL DUPLICATES, USING 4 DIFFERENT
+ ALGORITHMIC STRATEGIES. THE PROBLEM IS: GIVEN A SET OF N INTEGERS
+ IN THE RANGE [0,N-1], RETURN A SUBSET WITH DUPLICATES REMOVED.
+
+ Giving the JVM half a gig of memory, against the same random
+ bytes file, under "same conditions". Note: the set of unique
+ integers returned by the heap and tree test is ordered as a result
+ of the nature of the algorithm.
+
+ Milliseconds taken to perform test case:
+
+ N | MinIntHeap | IntHash | BitSet | IntBTree |
+ ----------+------+------+------+------+------+------+------+------+
+ | init |repeat| init |repeat| init |repeat| init |repeat|
+ +------+------+------+------+------+------+------+------+
+ 1| 0 0| 0 0| 0 0| 0 N/A|
+ 100| 0 1| 0 0| 0 1| 10 |
+ 1000| 3 3| 5 1| 2 2| 12 |
+ 10000| 13 6| 11 5| 12 3| 28 |
+ 50000| 36 26| 31 18| 25 9| 73 |
+ 100000| 61 53| 48 47| 33 16| 133 |
+ 200000| 134 117| 111 90| 57 26| 260 |
+ 500000| 410 375| 300 230| 133 57| 754 |
+ 1000000| 950 920| 600 500| 227 113| 1670 |
+ 2000000| 2210 2190| 1200 1030| 450 220| 3751 |
+ 5000000| 6700 6550| 3200 2800| 1180 718| 11103 |
+ 10000000| 15000 15000| 6400 5775| 2740 1920| 24402 |
+ 15000000| 24000 | 8925 8220| 4500 | 38500 |
+ 20000000| 34500 | 12875 | 6000 | N/A |
+ 30000000| 55000 | X | 9620 | |
+ 40000000| 81000 | | 12150 | |
+ 50000000| X | | X | |
+ | (out of | | | |
+ | memory) | | | |
+
+*/
+package cytoscape.util.intr.test;
+
+import cytoscape.util.intr.IntEnumerator;
+import cytoscape.util.intr.MinIntHeap;
+
+import java.io.IOException;
+import java.io.InputStream;
+
+
+/**
+ *
+ */
+public class MinIntHeapPerformance {
+ /**
+ * Argument at index 0: a number representing the number of elements to be
+ * tossed onto a heap. If N elements are tossed onto a heap, each element
+ * shall be in the range [0, N-1].<p>
+ * Standard input is read, and should contain bytes [read: binary data] of
+ * input defining
+ * integer elements to be tossed onto the heap, with enough
+ * bytes to define N integers (each integer is 4 bytes of standard input).
+ * Integers are
+ * defined from the input by taking groups of 4 consecutive bytes from input,
+ * each group defining a single integer by interpreting the first byte in
+ * a group to be the most significant bits of the integer etc. The
+ * range [0, N-1] of each integer is satisifed by dividing the positized
+ * value of each assembled
+ * four-byte integer by N, and taking the remainder as the element to be
+ * tossed onto the heap.<p>
+ * Writes to standard out the ordered set of input integers with
+ * duplicates pruned, such that each output integer is followed by the
+ * system's newline separator character sequence. The integers written are
+ * in plaintext, unlike the format of the input.<p>
+ * Output to standard error is the time taken to use the heap to order
+ * the input, with duplicates removed. The output format is simply a
+ * plaintext
+ * integer representing the number of milliseconds required for this
+ * test case, followed by the system's newline separator character
+ * sequence. Basically, a timer starts
+ * right before calling the MinIntHeap constructor with an array of
+ * input integers; the timer stops after we've instantiated a new array to
+ * contain the ordered list of elements with duplicates removed, and after
+ * we've completely filled the array with these elements. Note that
+ * the process of instantiating this array is time consuming and has nothing
+ * to do with the algorithm we're trying to test; this operation is
+ * included in this time trial anyways.<p>
+ * An optional second argument to this program is the string 'repeat' -
+ * this command-line option will run a first test, and then a repeated test
+ * using the same objects that were used in the first test (basically, the
+ * purpose of the repeated test is to not instantiate anything) - all
+ * output information is based off of the repeated test.
+ */
+ public static void main(String[] args) throws Exception {
+ int N = Integer.parseInt(args[0]);
+ boolean repeat = false;
+
+ if ((args.length > 1) && args[1].equalsIgnoreCase("repeat"))
+ repeat = true;
+
+ int[] elements = new int[N];
+ InputStream in = System.in;
+ byte[] buff = new byte[4];
+ int inx = 0;
+ int off = 0;
+ int read;
+
+ while ((inx < N) && ((read = in.read(buff, off, buff.length - off)) > 0)) {
+ off += read;
+
+ if (off < buff.length)
+ continue;
+ else
+ off = 0;
+
+ elements[inx++] = (0x7fffffff & assembleInt(buff)) % N;
+ }
+
+ if (inx < N)
+ throw new IOException("premature end of input");
+
+ // Lose reference to as much as we can.
+ in = null;
+ buff = null;
+
+ // Load the classes we're going to use into the classloader.
+ _THE_TEST_CASE_(new int[] { 0, 3, 4, 3, 9, 9, 1 });
+
+ // Sleep, collect garbage, have a snack, etc.
+ Thread.sleep(1000);
+
+ // Wake up. Warm up. Get up on your feet.
+ for (int i = 0; i < 100; i++) {
+ int foo = (i * 4) / 8;
+ }
+
+ // Start timer.
+ long millisBegin = System.currentTimeMillis();
+
+ // Run the test. Quick, stopwatch is ticking!
+ int[] uniqueElements = _THE_TEST_CASE_(elements);
+
+ // Stop timer.
+ long millisEnd = System.currentTimeMillis();
+
+ // Print the time taken to standard error.
+ if (!repeat)
+ System.err.println(millisEnd - millisBegin);
+
+ // Print sorted array to standard out.
+ if (!repeat)
+ for (int i = 0; i < uniqueElements.length; i++)
+ System.out.println(uniqueElements[i]);
+
+ // Run repeated test if that's what the command line told us.
+ if (repeat) {
+ for (int i = 0; i < uniqueElements.length; i++)
+ uniqueElements[i] = 0;
+
+ millisBegin = System.currentTimeMillis();
+ _REPEAT_TEST_CASE_(elements, uniqueElements);
+ millisEnd = System.currentTimeMillis();
+ System.err.println((millisEnd - millisBegin) + " (repeated test)");
+
+ for (int i = 0; i < uniqueElements.length; i++)
+ System.out.println(uniqueElements[i]);
+ }
+ }
+
+ private static final int assembleInt(byte[] fourConsecutiveBytes) {
+ int firstByte = (((int) fourConsecutiveBytes[0]) & 0x000000ff) << 24;
+ int secondByte = (((int) fourConsecutiveBytes[1]) & 0x000000ff) << 16;
+ int thirdByte = (((int) fourConsecutiveBytes[2]) & 0x000000ff) << 8;
+ int fourthByte = (((int) fourConsecutiveBytes[3]) & 0x000000ff) << 0;
+
+ return firstByte | secondByte | thirdByte | fourthByte;
+ }
+
+ // Keep a reference to our data structure so that we can determine how
+ // much memory was consumed by our algorithm (may be implemented in future).
+ static MinIntHeap _THE_HEAP_ = null;
+
+ private static final int[] _THE_TEST_CASE_(final int[] elements) {
+ _THE_HEAP_ = new MinIntHeap();
+ _THE_HEAP_.toss(elements, 0, elements.length);
+
+ final IntEnumerator iter = _THE_HEAP_.orderedElements(true);
+ final int[] returnThis = new int[iter.numRemaining()];
+ final int numElements = returnThis.length;
+
+ for (int i = 0; i < numElements; i++)
+ returnThis[i] = iter.nextInt();
+
+ return returnThis;
+ }
+
+ private static final void _REPEAT_TEST_CASE_(final int[] elements, final int[] output) {
+ _THE_HEAP_.empty();
+ _THE_HEAP_.toss(elements, 0, elements.length);
+
+ final IntEnumerator iter = _THE_HEAP_.orderedElements(true);
+ final int numElements = iter.numRemaining();
+
+ if (numElements != output.length)
+ throw new IllegalStateException("output array is incorrect size");
+
+ for (int i = 0; i < numElements; i++)
+ output[i] = iter.nextInt();
+ }
+}
diff --git a/corelibs/util.intr/src/main/java/cytoscape/util/intr/test/PrimesGenerator.java b/corelibs/util.intr/src/main/java/cytoscape/util/intr/test/PrimesGenerator.java
new file mode 100644
index 0000000..9f44c1b
--- /dev/null
+++ b/corelibs/util.intr/src/main/java/cytoscape/util/intr/test/PrimesGenerator.java
@@ -0,0 +1,68 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.util.intr.test;
+
+import cytoscape.util.intr.IntStack;
+
+import java.math.BigInteger;
+
+
+/**
+ *
+ */
+public class PrimesGenerator {
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ */
+ public static void main(String[] args) {
+ final IntStack stack = new IntStack();
+ int currSeed = Integer.MAX_VALUE;
+
+ while (currSeed > 10) {
+ while (!((new BigInteger(String.valueOf(currSeed))).isProbablePrime(64)))
+ currSeed--;
+
+ stack.push(currSeed);
+ currSeed = currSeed / 2;
+ }
+
+ while (stack.size() > 0)
+ System.out.println(stack.pop());
+ }
+}
diff --git a/corelibs/util.intr/src/test/java/cytoscape/util/intr/IntBTreeTest.java b/corelibs/util.intr/src/test/java/cytoscape/util/intr/IntBTreeTest.java
new file mode 100644
index 0000000..e5d25aa
--- /dev/null
+++ b/corelibs/util.intr/src/test/java/cytoscape/util/intr/IntBTreeTest.java
@@ -0,0 +1,199 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.util.intr;
+
+import cytoscape.util.intr.IntBTree;
+import cytoscape.util.intr.IntEnumerator;
+
+import junit.framework.*;
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ */
+public class IntBTreeTest extends TestCase {
+ IntBTree tree;
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void setUp() {
+ tree = new IntBTree(3);
+ System.out.println("Instantiated new IntBTree.");
+
+ final int[] arr = new int[] { 8, 1, 3, 8, 3, 0, 9, 1, 7, 3, 3, 0, 4, 3, 1, 3, 3 };
+
+ System.out.print("My int[] is: { ");
+
+ for (int i = 0; i < (arr.length - 1); i++) {
+ tree.insert(arr[i]);
+ System.out.print(arr[i] + ", ");
+ }
+
+ System.out.println(arr[arr.length - 1] + " }.");
+
+ System.out.println("Inserted all elements of array into tree.");
+ }
+
+ // tests the order of the iterator
+ /**
+ * DOCUMENT ME!
+ */
+ public void testOrder() {
+ IntEnumerator iter = tree.searchRange(Integer.MIN_VALUE, Integer.MAX_VALUE, false);
+ System.out.println("Here are the ordered elements:");
+ System.out.print(" ");
+
+ int curr = -1;
+ int last = -1;
+
+ while (iter.numRemaining() > 0) {
+ curr = iter.nextInt();
+ System.out.print(curr + " ");
+ assertTrue(last <= curr);
+ last = curr;
+ }
+
+ System.out.println(".");
+ }
+
+ // tests the counting of the number of occurrances in the btree
+ /**
+ * DOCUMENT ME!
+ */
+ public void testCount() {
+ final int[] countThese = new int[] {
+ Integer.MIN_VALUE, -1, 0, 1, 3, 4, 6, 7, 8, 9, 10, 99,
+ Integer.MAX_VALUE
+ };
+
+ for (int i = 0; i < countThese.length; i++)
+ System.out.println("The count of integer " + countThese[i] + " is "
+ + tree.count(countThese[i]) + ".");
+
+ assertEquals(0, tree.count(Integer.MIN_VALUE));
+ assertEquals(0, tree.count(-1));
+ assertEquals(2, tree.count(0));
+ assertEquals(3, tree.count(1));
+ //assertEquals( 7, tree.count(3));// bug!
+ assertEquals(1, tree.count(4));
+ assertEquals(0, tree.count(6));
+ assertEquals(1, tree.count(7));
+ assertEquals(2, tree.count(8));
+ assertEquals(1, tree.count(9));
+ assertEquals(0, tree.count(10));
+ assertEquals(0, tree.count(99));
+ assertEquals(0, tree.count(Integer.MAX_VALUE));
+ }
+
+ /**
+ * Tests the values returned within specified min and max ranges.
+ */
+ public void testMinMaxRange() {
+ IntEnumerator iter = tree.searchRange(Integer.MIN_VALUE, Integer.MAX_VALUE, false);
+
+ final int[] xMins = new int[] {
+ Integer.MIN_VALUE, Integer.MIN_VALUE, -23, 1, 3, 2, 3, 8, 4, 4, 5, 6,
+ -1, 11
+ };
+ final int[] xMaxs = new int[] {
+ Integer.MAX_VALUE, 3, 99, 2, Integer.MAX_VALUE, 6, 4, 8, 4, 8, 6, 6,
+ -1, 11
+ };
+
+ for (int i = 0; i < xMins.length; i++) {
+ System.out.println("In range [" + xMins[i] + ", " + xMaxs[i] + "]:");
+ System.out.print(" ascending: ");
+ iter = tree.searchRange(xMins[i], xMaxs[i], false);
+
+ while (iter.numRemaining() > 0) {
+ int n = iter.nextInt();
+ assertTrue(n <= xMaxs[i]);
+ assertTrue(n >= xMins[i]);
+ System.out.print(n + " ");
+ }
+
+ System.out.println(".");
+ System.out.print(" descending: ");
+ iter = tree.searchRange(xMins[i], xMaxs[i], true);
+
+ while (iter.numRemaining() > 0) {
+ int n = iter.nextInt();
+ assertTrue(n <= xMaxs[i]);
+ assertTrue(n >= xMins[i]);
+ System.out.print(n + " ");
+ }
+
+ System.out.println(".");
+ }
+ }
+
+ /**
+ * tests the deletion operation
+ */
+ public void testDelete() {
+ IntEnumerator iter = tree.searchRange(Integer.MIN_VALUE, Integer.MAX_VALUE, false);
+
+ System.out.println("Now going to delete some random entries.");
+
+ assertTrue(tree.delete(8));
+ assertTrue(!tree.delete(-1));
+ assertTrue(tree.delete(3));
+ assertTrue(!tree.delete(2));
+ assertTrue(tree.delete(9));
+ assertTrue(tree.delete(3));
+ assertTrue(tree.delete(0));
+ assertTrue(tree.delete(3));
+
+ System.out.println("Now going to delete remaining entries.");
+
+ iter = tree.searchRange(Integer.MIN_VALUE, Integer.MAX_VALUE, false);
+
+ final int[] intsRemaining = new int[iter.numRemaining()];
+
+ for (int i = 0; i < intsRemaining.length; i++)
+ intsRemaining[i] = iter.nextInt();
+
+ for (int i = 0; i < intsRemaining.length; i++) {
+ final int delInt = intsRemaining[(i + (intsRemaining.length / 2)) % intsRemaining.length];
+ System.out.println("deleting " + delInt);
+ assertTrue(tree.delete(delInt));
+ }
+ }
+}
diff --git a/corelibs/util.intr/src/test/java/cytoscape/util/intr/MinIntHeapTest.java b/corelibs/util.intr/src/test/java/cytoscape/util/intr/MinIntHeapTest.java
new file mode 100644
index 0000000..dcef955
--- /dev/null
+++ b/corelibs/util.intr/src/test/java/cytoscape/util/intr/MinIntHeapTest.java
@@ -0,0 +1,125 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.util.intr;
+
+import cytoscape.util.intr.IntEnumerator;
+import cytoscape.util.intr.MinIntHeap;
+
+import junit.framework.*;
+
+
+/**
+ *
+ */
+public class MinIntHeapTest extends TestCase {
+ MinIntHeap heap;
+ int[] arr;
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void setUp() {
+ heap = new MinIntHeap();
+ System.out.println("Instantiated new MinIntHeap.");
+
+ arr = new int[] { 5, 8, 1, 3, 8, 3, 0, 9, 1, 2, 7, 3 };
+ System.out.println("Defined my int[] to be: { 5, 8, 1, 3, 8, 3, 0, 9, 1, 2, 7, 3 }.");
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testToss() {
+ int last = -1;
+ int size = 0;
+
+ for (int i = 0; i < arr.length; i++) {
+ heap.toss(arr[i]);
+ size = heap.size();
+ assertTrue(size > last);
+ last = size;
+ }
+
+ System.out.println("Tossed all elements of array onto heap.");
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testIterator() {
+ // doh!
+ testToss();
+
+ IntEnumerator iter = heap.orderedElements(true);
+ assertNotNull(iter);
+
+ System.out.println("Got an IntEnumerator by calling orderedElements(true) on heap.");
+ System.out.println("The enumerator's numRemaining() method returns " + iter.numRemaining()
+ + ".");
+
+ assertEquals(8, iter.numRemaining());
+
+ System.out.print("The enumerator looks like this: { ");
+
+ while (iter.numRemaining() > 1)
+ System.out.print(iter.nextInt() + ", ");
+
+ System.out.println(iter.nextInt() + " }.");
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void testOrder() {
+ // doh!
+ testToss();
+
+ IntEnumerator iter = heap.orderedElements(false);
+ assertNotNull(iter);
+ System.out.println("Got an IntEnumerator by calling orderedElements(false) on heap.");
+ System.out.println("The enumerator's numRemaining() method returns " + iter.numRemaining()
+ + ".");
+
+ assertEquals(12, iter.numRemaining());
+ System.out.print("The enumerator looks like this: { ");
+
+ while (iter.numRemaining() > 1)
+ System.out.print(iter.nextInt() + ", ");
+
+ System.out.println(iter.nextInt() + " }.");
+ }
+}
diff --git a/corelibs/util.intr/src/test/java/cytoscape/util/intr/SerializationTest.java b/corelibs/util.intr/src/test/java/cytoscape/util/intr/SerializationTest.java
new file mode 100644
index 0000000..08e50d5
--- /dev/null
+++ b/corelibs/util.intr/src/test/java/cytoscape/util/intr/SerializationTest.java
@@ -0,0 +1,151 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.util.intr;
+
+import cytoscape.util.intr.IntArray;
+import cytoscape.util.intr.IntBTree;
+import cytoscape.util.intr.IntHash;
+import cytoscape.util.intr.IntIntHash;
+import cytoscape.util.intr.IntObjHash;
+import cytoscape.util.intr.IntQueue;
+import cytoscape.util.intr.IntStack;
+import cytoscape.util.intr.MinIntHeap;
+
+import junit.framework.*;
+
+import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
+import java.io.ObjectInputStream;
+import java.io.ObjectOutputStream;
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ */
+public class SerializationTest extends TestCase {
+ /**
+ * DOCUMENT ME!
+ */
+ public void testSerialize() {
+ try {
+ IntArray intArray = new IntArray();
+ intArray.setIntAtIndex(-3, 5);
+
+ IntBTree intBTree = new IntBTree();
+
+ for (int i = 0; i < 200; i++)
+ intBTree.insert((i * 77) % 1001);
+
+ IntHash intHash = new IntHash();
+ intHash.put(23);
+
+ IntIntHash intIntHash = new IntIntHash();
+ intIntHash.put(2, 3);
+
+ IntObjHash intObjHash = new IntObjHash();
+ intObjHash.put(1, "foo");
+
+ IntQueue intQueue = new IntQueue();
+ intQueue.enqueue(-43);
+
+ IntStack intStack = new IntStack();
+ intStack.push(72);
+
+ MinIntHeap minIntHeap = new MinIntHeap();
+ minIntHeap.insert(4);
+
+ ByteArrayOutputStream byteOut = new ByteArrayOutputStream();
+ ObjectOutputStream objOut = new ObjectOutputStream(byteOut);
+ objOut.writeObject(intArray);
+ objOut.writeObject(intBTree);
+ objOut.writeObject(intHash);
+ objOut.writeObject(intIntHash);
+ objOut.writeObject(intObjHash);
+ objOut.writeObject(intQueue);
+ objOut.writeObject(intStack);
+ objOut.writeObject(minIntHeap);
+ objOut.flush();
+ objOut.close();
+
+ ByteArrayInputStream byteIn = new ByteArrayInputStream(byteOut.toByteArray());
+ ObjectInputStream objIn = new ObjectInputStream(byteIn);
+ intArray = (IntArray) objIn.readObject();
+ intBTree = (IntBTree) objIn.readObject();
+ intHash = (IntHash) objIn.readObject();
+ intIntHash = (IntIntHash) objIn.readObject();
+ intObjHash = (IntObjHash) objIn.readObject();
+ intQueue = (IntQueue) objIn.readObject();
+ intStack = (IntStack) objIn.readObject();
+ minIntHeap = (MinIntHeap) objIn.readObject();
+ objIn.close();
+
+ assertEquals(-3, intArray.getIntAtIndex(5));
+ assertEquals(0, intArray.getIntAtIndex(4));
+
+ assertEquals(200, intBTree.size());
+ assertTrue(intBTree.delete(154));
+ assertTrue(intBTree.delete(77));
+ assertEquals(198, intBTree.size());
+
+ assertEquals(1, intHash.size());
+ assertEquals(23, intHash.get(23));
+ assertEquals(-1, intHash.get(7));
+
+ assertEquals(1, intIntHash.size());
+ assertEquals(3, intIntHash.get(2));
+ assertEquals(-1, intIntHash.get(0));
+
+ assertEquals(1, intObjHash.size());
+ assertTrue("foo".equals(intObjHash.get(1)));
+ assertNull(intObjHash.get(2));
+
+ assertEquals(-43, intQueue.dequeue());
+ assertEquals(0, intQueue.size());
+
+ assertEquals(72, intStack.pop());
+ assertEquals(0, intStack.size());
+
+ assertEquals(4, minIntHeap.deleteMin());
+ assertEquals(0, minIntHeap.size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail();
+ }
+ }
+}
diff --git a/coreplugins/AdvancedNetworkMerge/pom.xml b/coreplugins/AdvancedNetworkMerge/pom.xml
new file mode 100644
index 0000000..daaaa7a
--- /dev/null
+++ b/coreplugins/AdvancedNetworkMerge/pom.xml
@@ -0,0 +1,64 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>parent</artifactId>
+ <version>2.8.4-SNAPSHOT</version>
+ </parent>
+
+ <artifactId>advanced-network-merge</artifactId>
+ <packaging>jar</packaging>
+
+ <name>Advanced Network Merge</name>
+
+ <!-- bootstrap for cytoscape dependencies, namely the parent POM snapshots -->
+ <repositories>
+ <repository>
+ <id>cytoscape_snapshots</id>
+ <snapshots>
+ <enabled>true</enabled>
+ </snapshots>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <name>Cytoscape Snapshots</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/</url>
+ </repository>
+ <repository>
+ <id>cytoscape_releases</id>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ <name>Cytoscape Releases</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/releases/</url>
+ </repository>
+ </repositories>
+
+ <build>
+ <plugins>
+ <plugin>
+ <artifactId>maven-assembly-plugin</artifactId>
+ <configuration>
+ <archive>
+ <manifestEntries>
+ <Cytoscape-Plugin>csplugins.network.merge.NetworkMergePlugin</Cytoscape-Plugin>
+ </manifestEntries>
+ </archive>
+ </configuration>
+ </plugin>
+ </plugins>
+ </build>
+
+ <dependencies>
+ <dependency>
+ <groupId>cytoscape-temp</groupId>
+ <artifactId>cythesaurus-service</artifactId>
+ <version>1.0</version>
+ </dependency>
+ </dependencies>
+
+</project>
+
diff --git a/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/AbstractNetworkMerge.java b/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/AbstractNetworkMerge.java
new file mode 100644
index 0000000..d019995
--- /dev/null
+++ b/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/AbstractNetworkMerge.java
@@ -0,0 +1,405 @@
+/* File: AbstractNetworkMerge.java
+
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+package csplugins.network.merge;
+
+import java.util.List;
+import java.util.Vector;
+import java.util.Iterator;
+import java.util.Set;
+import java.util.HashSet;
+import java.util.Map;
+import java.util.HashMap;
+
+import cytoscape.Cytoscape;
+import cytoscape.CyNetwork;
+import cytoscape.data.CyAttributes;
+import cytoscape.data.Semantics;
+import cytoscape.task.TaskMonitor;
+
+import giny.model.GraphObject;
+import giny.model.Node;
+import giny.model.Edge;
+/**
+ * NetworkMerge implement
+ *
+ *
+ */
+public abstract class AbstractNetworkMerge implements NetworkMerge {
+ protected final NetworkMergeParameter parameter;
+ protected TaskMonitor taskMonitor;
+ protected boolean interrupted; // to enable cancel of the network merge operation
+
+ public AbstractNetworkMerge(final NetworkMergeParameter parameter) {
+ if (parameter==null) {
+ throw new NullPointerException();
+ }
+
+ this.parameter = parameter;
+ taskMonitor = null;
+ interrupted = false;
+ }
+
+ public void interrupt() {
+ interrupted = true;
+ }
+
+ public void setTaskMonitor(final TaskMonitor taskMonitor) {
+ this.taskMonitor = taskMonitor;
+ }
+
+ /**
+ * Check whether two nodes match
+ *
+ * @param net1,net2 two networks
+ * @param n1,n2 two nodes belongs to net1 and net2 respectively
+ *
+ * @return true if n1 and n2 matches
+ */
+ public abstract boolean matchNode(CyNetwork net1, Node n1, CyNetwork net2, Node n2);
+
+ /**
+ * Merge (matched) nodes into one
+ *
+ * @param mapNetNode
+ * map of network to node, node in the network to be merged
+ *
+ * @return merged Node
+ */
+ public abstract Node mergeNode(Map<CyNetwork,Set<GraphObject>> mapNetNode);
+
+ /**
+ * Merge (matched) nodes into one. This method will be refactored in Cytoscape3
+ *
+ * @param mapNetEdge
+ * map from network to Edge, Edge in the network to be merged
+ * @param source, target
+ * source and target nodes in the merge network
+ *
+ * @return merged Node
+ */
+ public abstract Edge mergeEdge(Map<CyNetwork,Set<GraphObject>> mapNetEdge, Node source,
+ Node target, String interaction, boolean directed);
+
+ /**
+ * Check whether two edges match
+ *
+ * @param net1,net2 two networks
+ * @param e1,e2 two edges belongs to net1 and net2 respectively
+ *
+ * @return true if n1 and n2 matches
+ */
+ public boolean matchEdge(final CyNetwork net1, Edge e1, final CyNetwork net2, Edge e2) {
+ if (net1==null || e1==null || e2==null) {
+ throw new java.lang.NullPointerException();
+ }
+
+ //TODO should interaction be considered or not?
+ final CyAttributes attributes = Cytoscape.getEdgeAttributes();
+
+ Object i1 = attributes.getAttribute(e1.getIdentifier(),Semantics.INTERACTION);
+ Object i2 = attributes.getAttribute(e2.getIdentifier(),Semantics.INTERACTION);
+
+ if ((i1==null&&i2!=null) || (i1!=null&&i2==null)) {
+ return false;
+ }
+
+ if (i1!=null && !i1.equals(i2))
+ return false;
+
+ if (e1.isDirected()) { // directed
+ if (!e2.isDirected()) return false;
+ return matchNode(net1, e1.getSource(), net2, e2.getSource())
+ && matchNode(net1, e1.getTarget(), net2, e2.getTarget());
+ } else { //non directed
+ if (e2.isDirected()) return false;
+ if (matchNode(net1, e1.getSource(), net2, e2.getSource())
+ && matchNode(net1, e1.getTarget(), net2, e2.getTarget()))
+ return true;
+ if (matchNode(net1, e1.getSource(), net2, e2.getTarget())
+ && matchNode(net1, e1.getTarget(), net2, e2.getSource()))
+ return true;
+ return false;
+ }
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ public CyNetwork mergeNetwork(final List<CyNetwork> networks, final Operation op, final String title) {
+ if (networks==null || op==null || title==null) {
+ throw new java.lang.NullPointerException();
+ }
+
+ if (networks.isEmpty()) {
+ throw new java.lang.IllegalArgumentException("No merging network");
+ }
+
+ if (title.length()==0) {
+ throw new java.lang.IllegalArgumentException("Empty title");
+ }
+
+ // get node matching list
+ List<Map<CyNetwork,Set<GraphObject>>> matchedNodeList = getMatchedList(networks,true);
+
+ matchedNodeList = selectMatchedGOList(matchedNodeList, op, networks);
+
+ final Map<Node,Node> mapNN = new HashMap<Node,Node>(); // save information on mapping from original nodes to merged nodes
+ // to use when merge edges
+
+ // merge nodes in the list
+ final int nNode = matchedNodeList.size();
+ List<Node> nodes = new Vector<Node>(nNode);
+ for (int i=0; i<nNode; i++) {
+ if (interrupted) return null;
+ updateTaskMonitor("Merging nodes...\n"+i+"/"+nNode,(i+1)*100/nNode);
+
+ final Map<CyNetwork,Set<GraphObject>> mapNetNode = matchedNodeList.get(i);
+ final Node node = mergeNode(mapNetNode);
+ nodes.add(node);
+
+ final Iterator<Set<GraphObject>> itNodes = mapNetNode.values().iterator();
+ while (itNodes.hasNext()) {
+ final Set<GraphObject> nodes_ori = itNodes.next();
+ final Iterator<GraphObject> itNode = nodes_ori.iterator();
+ while (itNode.hasNext()) {
+ final Node node_ori = (Node) itNode.next();
+ mapNN.put(node_ori, node);
+ }
+ }
+ }
+ updateTaskMonitor("Merging nodes completed",100);
+
+ // match edges
+ List<Map<CyNetwork,Set<GraphObject>>> matchedEdgeList = getMatchedList(networks,false);
+
+ matchedEdgeList = selectMatchedGOList(matchedEdgeList, op, networks);
+
+ // merge edges
+ final int nEdge = matchedEdgeList.size();
+ final List<Edge> edges = new Vector<Edge>(nEdge);
+ for (int i=0; i<nEdge; i++) {
+ if (interrupted) return null;
+ updateTaskMonitor("Merging edges...\n"+i+"/"+nEdge,(i+1)*100/nEdge);
+
+ final Map<CyNetwork,Set<GraphObject>> mapNetEdge = matchedEdgeList.get(i);
+
+ // get the source and target nodes in merged network
+ final Iterator<Set<GraphObject>> itEdges = mapNetEdge.values().iterator();
+
+ final Set<GraphObject> edgeSet = itEdges.next();
+ if (edgeSet==null||edgeSet.isEmpty()) {
+ throw new java.lang.IllegalStateException("Null or empty edge set");
+ }
+
+ final Edge edge_ori = (Edge) edgeSet.iterator().next();
+ final Node source = mapNN.get(edge_ori.getSource());
+ final Node target = mapNN.get(edge_ori.getTarget());
+ if (source==null||target==null) { // some of the node may be exluded when intersection or difference
+ continue;
+ }
+
+ final boolean directed = edge_ori.isDirected();
+ final CyAttributes attributes = Cytoscape.getEdgeAttributes();
+ final String interaction = (String)attributes.getAttribute(edge_ori.getIdentifier(),Semantics.INTERACTION);
+
+ final Edge edge = mergeEdge(mapNetEdge,source,target,interaction,directed);
+ edges.add(edge);
+ }
+ updateTaskMonitor("Merging edges completed",100);
+
+ // create new network
+ final CyNetwork network = Cytoscape.createNetwork(nodes, edges, title);
+
+ updateTaskMonitor("Successfully merged the selected "+networks.size()+" networks into network "+title+" with "+nNode+" nodes and "+nEdge+" edges",100);
+
+ return network;
+ }
+
+ /**
+ * Get a list of matched nodes/edges
+ *
+ * @param networks
+ * Networks to be merged
+ *
+ * @return list of map from network to node/edge
+ */
+ protected List<Map<CyNetwork,Set<GraphObject>>> getMatchedList(final List<CyNetwork> networks, final boolean isNode) {
+ if (networks==null) {
+ throw new java.lang.NullPointerException();
+ }
+
+ if (networks.isEmpty()) {
+ throw new java.lang.IllegalArgumentException("No merging network");
+ }
+
+ final List<Map<CyNetwork,Set<GraphObject>>> matchedList = new Vector<Map<CyNetwork,Set<GraphObject>>>();
+
+ final int nNet = networks.size();
+
+ // Get the total number nodes/edge to calculate the status
+ int totalGO=0, processedGO=0;
+ for (int i=0; i<nNet; i++) {
+ final CyNetwork net = networks.get(i);
+ totalGO += isNode?net.getNodeCount():net.getEdgeCount();
+ }
+
+ for (int i=0; i<nNet; i++) {
+
+
+ final CyNetwork net1 = networks.get(i);
+ final Iterator<GraphObject> it;
+ if (isNode) {
+ it = (Iterator<GraphObject>)net1.nodesIterator();
+ } else { //edge
+ it = net1.edgesIterator();
+ }
+
+ while (it.hasNext()) {
+ if (interrupted) return null;
+ updateTaskMonitor("Matching "+(isNode?"nodes":"edges")+"...\n"+processedGO+"/"+totalGO,processedGO*100/totalGO);
+ processedGO++;
+
+ final GraphObject go1 = it.next();
+
+ // chech whether any nodes in the matchedNodeList match with this node
+ // if yes, add to the list, else add a new map to the list
+ boolean matched = false;
+ final int n = matchedList.size();
+ int j=0;
+ for (; j<n; j++) {
+ final Map<CyNetwork,Set<GraphObject>> matchedGO = matchedList.get(j);
+ final Iterator<CyNetwork> itNet = matchedGO.keySet().iterator();
+ while (itNet.hasNext()) {
+ final CyNetwork net2 = itNet.next();
+ //if (net1==net2) continue; // assume the same network don't have nodes match to each other
+ if (!parameter.inNetworkMergeEnabled() && net1==net2) continue;
+
+ final Set<GraphObject> gos2 = matchedGO.get(net2);
+ if (gos2!=null) {
+ GraphObject go2 = gos2.iterator().next();
+ if (isNode) { //NODE
+ matched = matchNode(net1,(Node)go1,net2,(Node)go2);
+ } else {// EDGE
+ matched = matchEdge(net1,(Edge)go1,net2,(Edge)go2);
+ }
+ if (matched) {
+ Set<GraphObject> gos1 = matchedGO.get(net1);
+ if (gos1==null) {
+ gos1 = new HashSet<GraphObject>();
+ matchedGO.put(net1, gos1);
+ }
+ gos1.add(go1);
+ break;
+ }
+ }
+ }
+ if (matched) {
+ break;
+ }
+ }
+ if (!matched) { //no matched node found, add new map to the list
+ final Map<CyNetwork,Set<GraphObject>> matchedGO = new HashMap<CyNetwork,Set<GraphObject>>();
+ Set<GraphObject> gos1 = new HashSet<GraphObject>();
+ gos1.add(go1);
+ matchedGO.put(net1, gos1);
+ matchedList.add(matchedGO);
+ }
+
+ }
+
+ }
+
+ updateTaskMonitor("Matching "+(isNode?"nodes":"edges")+" completed",100);
+
+ return matchedList;
+ }
+ /**
+ * Select nodes for merge according to different op
+ *
+ * @param networks
+ * Networks to be merged
+ * @param op
+ * Operation
+ * @param size
+ * Number of networks
+ *
+ * @return list of matched nodes
+ */
+ protected List<Map<CyNetwork,Set<GraphObject>>> selectMatchedGOList(final List<Map<CyNetwork,Set<GraphObject>>> matchedGOList,
+ final Operation op,
+ final List<CyNetwork> networks) {
+ if (matchedGOList==null || op==null) {
+ throw new java.lang.NullPointerException();
+ }
+
+ int nnet = networks.size();
+
+ if (op==Operation.UNION) {
+ return matchedGOList;
+ } else if (op==Operation.INTERSECTION) {
+ List<Map<CyNetwork,Set<GraphObject>>> list = new Vector<Map<CyNetwork,Set<GraphObject>>>();
+ for (Map<CyNetwork,Set<GraphObject>> map:matchedGOList) {
+ if (map.size()==nnet) {// if contained in all the networks
+ list.add(map);
+ }
+ }
+
+ return list;
+ } else { //if (op==Operation.DIFFERENCE)
+ List<Map<CyNetwork,Set<GraphObject>>> list = new Vector<Map<CyNetwork,Set<GraphObject>>>();
+ if (nnet<2) return list;
+
+ CyNetwork net1 = networks.get(0);
+ CyNetwork net2 = networks.get(1);
+
+ for (Map<CyNetwork,Set<GraphObject>> map:matchedGOList) {
+ if (map.containsKey(net1)&&!map.containsKey(net2)) {
+ list.add(map);
+ }
+ }
+
+ return list;
+ }
+ }
+
+ private void updateTaskMonitor(String status, int percentage) {
+ if (this.taskMonitor!=null) {
+ taskMonitor.setStatus(status);
+ taskMonitor.setPercentCompleted(percentage);
+ }
+ }
+}
diff --git a/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/AttributeBasedNetworkMerge.java b/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/AttributeBasedNetworkMerge.java
new file mode 100644
index 0000000..f188dde
--- /dev/null
+++ b/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/AttributeBasedNetworkMerge.java
@@ -0,0 +1,369 @@
+/* File: AttributeBasedNetworkMerge.java
+
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+package csplugins.network.merge;
+
+import csplugins.network.merge.util.AttributeValueMatcher;
+import csplugins.network.merge.util.DefaultAttributeValueMatcher;
+import csplugins.network.merge.model.AttributeMapping;
+import csplugins.network.merge.model.MatchingAttribute;
+import csplugins.network.merge.util.AttributeMerger;
+import csplugins.network.merge.util.AttributeValueCastUtils;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Iterator;
+import java.util.Set;
+import java.util.HashSet;
+import java.util.Map;
+import java.util.HashMap;
+import java.util.Arrays;
+import java.util.Collections;
+
+import cytoscape.Cytoscape;
+import cytoscape.CyNetwork;
+import cytoscape.data.CyAttributes;
+import cytoscape.data.Semantics;
+import cytoscape.data.attr.MultiHashMapDefinition;
+
+import giny.model.Node;
+import giny.model.Edge;
+import giny.model.GraphObject;
+
+/**
+ * Attribute based Network merge
+ *
+ *
+ */
+public class AttributeBasedNetworkMerge extends AbstractNetworkMerge{
+ protected final MatchingAttribute matchingAttribute;
+ protected final AttributeMapping nodeAttributeMapping;
+ protected final AttributeMapping edgeAttributeMapping;
+ protected final AttributeValueMatcher attributeValueMatcher;
+ protected final AttributeMerger attributeMerger;
+
+ /**
+ * Constucter for regular attribute based network merge
+ * @param matchingAttribute
+ * @param nodeAttributeMapping
+ * @param edgeAttributeMapping
+ */
+ public AttributeBasedNetworkMerge(
+ final NetworkMergeParameter parameter,
+ final MatchingAttribute matchingAttribute,
+ final AttributeMapping nodeAttributeMapping,
+ final AttributeMapping edgeAttributeMapping,
+ final AttributeMerger attributeMerger) {
+ this(parameter,
+ matchingAttribute,
+ nodeAttributeMapping,
+ edgeAttributeMapping,
+ attributeMerger,
+ new DefaultAttributeValueMatcher());
+ }
+
+ /**
+ * Constucter for attribute based network merge with assigned comparator
+ * @param matchingAttribute
+ * @param nodeAttributeMapping
+ * @param edgeAttributeMapping
+ * @param attributeValueMatcher
+ * compare whether two attributes of nodes
+ */
+ public AttributeBasedNetworkMerge(
+ final NetworkMergeParameter parameter,
+ final MatchingAttribute matchingAttribute,
+ final AttributeMapping nodeAttributeMapping,
+ final AttributeMapping edgeAttributeMapping,
+ final AttributeMerger attributeMerger,
+ AttributeValueMatcher attributeValueMatcher) {
+ super(parameter);
+ if (matchingAttribute==null
+ || nodeAttributeMapping==null
+ || edgeAttributeMapping==null
+ || attributeMerger==null
+ || attributeValueMatcher==null) {
+ throw new java.lang.NullPointerException();
+ }
+ this.matchingAttribute = matchingAttribute;
+ this.nodeAttributeMapping = nodeAttributeMapping;
+ this.edgeAttributeMapping = edgeAttributeMapping;
+ this.attributeMerger = attributeMerger;
+ this.attributeValueMatcher = attributeValueMatcher;
+ }
+
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public boolean matchNode(final CyNetwork net1,
+ final Node n1,
+ final CyNetwork net2,
+ final Node n2) {
+ if (net1==null || net2==null || n1==null || n2==null) {
+ throw new java.lang.NullPointerException();
+ }
+
+ //TODO: should it match if n1==n2?
+ if (n1==n2) {
+ return true;
+ }
+
+ String attr1 = matchingAttribute.getAttributeForMatching(net1.getIdentifier());
+ String attr2 = matchingAttribute.getAttributeForMatching(net2.getIdentifier());
+
+ if (attr1==null || attr2==null) {
+ throw new java.lang.IllegalArgumentException("No such network selected");
+ }
+
+ //TODO: remove in cytoscape3
+ if (attr1.compareTo("ID")==0) {
+ attr1 = Semantics.CANONICAL_NAME;
+ }
+ if (attr1.compareTo("ID")==0) {
+ attr1 = Semantics.CANONICAL_NAME;
+ }//TODO: remove in cytoscape3
+
+ final CyAttributes attributes = Cytoscape.getNodeAttributes();
+ final String id1 = n1.getIdentifier();
+ final String id2 = n2.getIdentifier();
+
+ if (!attributes.hasAttribute(id1, attr1)
+ ||!attributes.hasAttribute(id2, attr2)) { //ignore null attribute
+ return false;
+ }
+
+ return attributeValueMatcher.matched(id1, attr1, id2, attr2, attributes);
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public Node mergeNode(final Map<CyNetwork,Set<GraphObject>> mapNetNode) {
+ //TODO: refactor in Cytoscape3,
+ // in 2.x node with the same identifier be the same node
+ // and different nodes must have different identifier.
+ // Is this true in 3.0?
+ if (mapNetNode==null||mapNetNode.isEmpty()) {
+ return null;
+ }
+
+ // Assign ID and canonicalName in resulting network
+ // remove in Cytoscape3
+ final Iterator<Set<GraphObject>> itNodes = mapNetNode.values().iterator();
+ Set<GraphObject> nodes = new HashSet<GraphObject>();
+ while (itNodes.hasNext()) {
+ nodes.addAll(itNodes.next());
+ }
+
+ final Iterator<GraphObject> itNode = nodes.iterator();
+ String id = new String(itNode.next().getIdentifier());
+
+ if (nodes.size()>1) { // if more than 1 nodes to be merged, assign the id
+ // as the combination of all identifiers
+ List<String> nodeIds = new ArrayList<String>(nodes.size());
+ nodeIds.add(id);
+ while (itNode.hasNext()) {
+ final Node node = (Node) itNode.next();
+ nodeIds.add(node.getIdentifier());
+ }
+
+ Collections.sort(nodeIds);
+
+ StringBuilder sb = new StringBuilder();
+ for (String nodeId : nodeIds) {
+ sb.append(nodeId+"-");
+ }
+ sb.deleteCharAt(sb.length()-1);
+
+ id = sb.toString();
+
+ // if node with this id exist, get new one
+ String appendix = "";
+ int app = 0;
+ while (Cytoscape.getCyNode(id+appendix)!=null) {
+ appendix = ""+ ++app;
+ }
+ id += appendix;
+ }
+
+ // Get the node with id or create a new node
+ // for attribute confilict handling, introduce a conflict node here?
+ final Node node = Cytoscape.getCyNode(id, true);
+
+ // set other attributes as indicated in attributeMapping
+ setAttribute(id,mapNetNode,nodeAttributeMapping);
+
+ return node;
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public Edge mergeEdge(final Map<CyNetwork,Set<GraphObject>> mapNetEdge,
+ final Node source,
+ final Node target,
+ final String interaction,
+ final boolean directed) {
+ //TODO: refactor in Cytoscape3
+ if (mapNetEdge==null||mapNetEdge.isEmpty()||source==null||target==null) {
+ return null;
+ }
+
+ // Get the edge or create a new one
+ // attribute confilict handling?
+ final Edge edge = Cytoscape.getCyEdge(source, target,
+ Semantics.INTERACTION, interaction, true, directed); // ID and canonicalName set when created
+ final String id = edge.getIdentifier();
+
+ // set other attributes as indicated in attributeMapping
+ setAttribute(id,mapNetEdge,edgeAttributeMapping);
+
+ return edge;
+ }
+
+ /*
+ * set attribute for the merge node/edge according to attribute mapping
+ *
+ */
+ protected void setAttribute(final String id,
+ final Map<CyNetwork,Set<GraphObject>> mapNetGOs,
+ final AttributeMapping attributeMapping) {
+ if (id==null || mapNetGOs==null || attributeMapping==null) {
+ throw new java.lang.NullPointerException();
+ }
+
+ CyAttributes cyAttributes = attributeMapping.getCyAttributes();
+
+ final int nattr = attributeMapping.getSizeMergedAttributes();
+ for (int i=0; i<nattr; i++) {
+ final String attr_merged = attributeMapping.getMergedAttribute(i);
+ if (attr_merged==null||attr_merged.length()==0) {
+ throw new java.lang.IllegalStateException("Null or empty name for the merged attribute");
+ }
+
+ // define the attribute first
+ final Set<String> attrNames = new HashSet<String>(attributeMapping.getOriginalAttributeMap(i).values());
+ final String attr_mc = AttributeValueCastUtils.getMostCompatibleAttribute(attrNames, cyAttributes);
+
+ if (attr_mc!=null) { // if compatible type
+ if (!AttributeValueCastUtils.isAttributeTypeConvertable(attr_mc, attr_merged, cyAttributes)) {
+ throw new java.lang.IllegalStateException("'"+attr_mc+"' cannot be converted to '"+attr_merged+"'");
+ }
+
+ // if attr_merged is a new attribute, define it first
+ if (!Arrays.asList(cyAttributes.getAttributeNames()).contains(attr_merged)) {
+ final byte type_to = attributeMapping.getMergedAttributeType(i);
+ final MultiHashMapDefinition mmapDef = cyAttributes.getMultiHashMapDefinition();
+
+ byte type;
+ byte[] keyTypes;
+ if (type_to==CyAttributes.TYPE_STRING) {
+ type = CyAttributes.TYPE_STRING;
+ keyTypes = null;
+ } else if (type_to==CyAttributes.TYPE_SIMPLE_LIST ) {
+ type = cyAttributes.getType(attr_mc);
+ if (type<0) { //TODO: improve
+ type = MultiHashMapDefinition.TYPE_STRING;
+ }
+ keyTypes = new byte[] { MultiHashMapDefinition.TYPE_INTEGER };
+ } else {
+ type = mmapDef.getAttributeValueType(attr_mc);
+ keyTypes = mmapDef.getAttributeKeyspaceDimensionTypes(attr_mc);
+ }
+
+ mmapDef.defineAttribute(attr_merged,
+ type,
+ keyTypes);
+ //TODO: collecte new attribute here
+ // if exception occur or user choose to cancel, undefine
+ }
+ } else { // if incompatible type
+ if (!Arrays.asList(cyAttributes.getAttributeNames()).contains(attr_merged)) {
+ final byte type = attributeMapping.getMergedAttributeType(i);
+ final MultiHashMapDefinition mmapDef = cyAttributes.getMultiHashMapDefinition();
+
+ final byte[] keyTypes;
+ if (type==CyAttributes.TYPE_STRING) {
+ keyTypes = null;
+ } else if (type==CyAttributes.TYPE_SIMPLE_LIST ) {
+ keyTypes = new byte[] { MultiHashMapDefinition.TYPE_INTEGER };
+ } else {
+ keyTypes = null;
+ }
+
+ mmapDef.defineAttribute(attr_merged,
+ MultiHashMapDefinition.TYPE_STRING,
+ keyTypes);
+ //TODO: collecte new attribute here
+ // if exception occur or user choose to cancel, undefine
+ } else {
+ if (cyAttributes.getType(attr_merged)==CyAttributes.TYPE_STRING) {
+ throw new java.lang.IllegalStateException("Incompatible type can only be converted into String");
+ }
+ }
+ }
+
+ // merge
+ Map<String,String> mapGOAttr = new HashMap<String,String>();
+ final Iterator<Map.Entry<CyNetwork,Set<GraphObject>>> itEntryNetGOs = mapNetGOs.entrySet().iterator();
+ while (itEntryNetGOs.hasNext()) {
+ final Map.Entry<CyNetwork,Set<GraphObject>> entryNetGOs = itEntryNetGOs.next();
+ final String idNet = entryNetGOs.getKey().getIdentifier();
+ final String attrName = attributeMapping.getOriginalAttribute(idNet, i);
+ if (attrName!=null) {
+ final Iterator<GraphObject> itGO = entryNetGOs.getValue().iterator();
+ while (itGO.hasNext()) {
+ final String idGO = itGO.next().getIdentifier();
+ mapGOAttr.put(idGO, attrName);
+ }
+ }
+ }
+
+ try {
+ attributeMerger.mergeAttribute(mapGOAttr, id, attr_merged, cyAttributes);
+ } catch (Exception e) {
+ e.printStackTrace();
+ continue;
+ }
+ }
+ }
+
+
+}
diff --git a/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/NetworkMerge.java b/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/NetworkMerge.java
new file mode 100644
index 0000000..c085993
--- /dev/null
+++ b/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/NetworkMerge.java
@@ -0,0 +1,73 @@
+/*
+ File: NetworkMerge.java
+
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+package csplugins.network.merge;
+
+import java.util.List;
+
+import cytoscape.CyNetwork;
+
+/**
+ * Interface of merging networks
+ *
+ *
+ */
+
+public interface NetworkMerge {
+
+ public enum Operation {
+ UNION("union"),INTERSECTION("intersection"),DIFFERENCE("difference");
+ private String opName;
+
+ private Operation(final String opName) {
+ this.opName = opName;
+ }
+
+ public String toString() {
+ return opName;
+ }
+ }
+
+ /**
+ * Merge networks into one.
+ * @param networks networks to be merged
+ * @param op operation
+ * @param title title of the merged network
+ * @return the merged network.
+ */
+ public CyNetwork mergeNetwork(List<CyNetwork> networks, Operation op, String title);
+}
diff --git a/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/NetworkMergeParameter.java b/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/NetworkMergeParameter.java
new file mode 100644
index 0000000..227001c
--- /dev/null
+++ b/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/NetworkMergeParameter.java
@@ -0,0 +1,48 @@
+/* File: NetworkMergeParameter.java
+
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+package csplugins.network.merge;
+
+/**
+ *
+ *
+ */
+public interface NetworkMergeParameter {
+
+ public boolean inNetworkMergeEnabled();
+
+ public void enableInNetworkMerge(boolean enabled);
+}
diff --git a/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/NetworkMergeParameterImpl.java b/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/NetworkMergeParameterImpl.java
new file mode 100644
index 0000000..5b5d1fb
--- /dev/null
+++ b/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/NetworkMergeParameterImpl.java
@@ -0,0 +1,60 @@
+/* File: NetworkMergeParameterImpl.java
+
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+package csplugins.network.merge;
+
+/**
+ *
+ * @author gjj
+ */
+public class NetworkMergeParameterImpl implements NetworkMergeParameter {
+ private boolean inNetworkMerge;
+
+ public NetworkMergeParameterImpl() {
+ }
+
+ public NetworkMergeParameterImpl(boolean inNetworkMerge) {
+ this.inNetworkMerge = inNetworkMerge;
+ }
+
+ public boolean inNetworkMergeEnabled() {
+ return inNetworkMerge;
+ }
+
+ public void enableInNetworkMerge(boolean enabled) {
+ inNetworkMerge = enabled;
+ }
+}
diff --git a/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/NetworkMergePlugin.java b/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/NetworkMergePlugin.java
new file mode 100644
index 0000000..0923e7f
--- /dev/null
+++ b/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/NetworkMergePlugin.java
@@ -0,0 +1,130 @@
+/* File: NetworkMergePlugin.java
+
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+package csplugins.network.merge;
+
+import csplugins.network.merge.ui.NetworkMergeFrame;
+
+import cytoscape.plugin.CytoscapePlugin;
+import cytoscape.Cytoscape;
+import cytoscape.data.CyAttributes;
+import cytoscape.data.Semantics;
+import cytoscape.util.CytoscapeAction;
+
+import giny.model.Node;
+
+import java.awt.event.ActionEvent;
+
+import java.util.List;
+import java.util.Arrays;
+
+/**
+ * Plugin to merge networks
+ *
+ * @since Cytoscape 2.7.0
+ */
+public class NetworkMergePlugin extends CytoscapePlugin {
+
+ private static final CytoscapeAction action = new NetworkMergeAction();
+
+ /**
+ * Add new menu item under "Plugins"
+ */
+ public NetworkMergePlugin() {
+ Cytoscape.getDesktop().getCyMenus().getOperationsMenu().add(
+ action);
+ }
+
+ /**
+ * Call the action directly.
+ * This feature used by other plugins.
+ *
+ * @return
+ */
+ public static void invokeAction() {
+ action.actionPerformed(null);
+ }
+
+ private static class NetworkMergeAction extends CytoscapeAction {
+ public NetworkMergeAction() {
+ super("Advanced Network Merge");
+ }
+
+ /**
+ * This method is called when the user selects the menu item.
+ */
+ @Override
+ public void actionPerformed(final ActionEvent ae) {
+ prepare(); // TODO: remove in Cytoscape3
+
+ final NetworkMergeFrame frame = new NetworkMergeFrame();
+ frame.setLocationRelativeTo(Cytoscape.getDesktop());
+ frame.setVisible(true);
+ // TODO: make this value user-editable (always on top or not).
+ frame.setAlwaysOnTop(true);
+ }
+
+ // TODO: remove in Cytoscape3
+ /*
+ * Copy node ID to canonicalName if canonicalName does not exist
+ */
+ private void prepare() {
+ CyAttributes cyAttributes = Cytoscape.getNodeAttributes();
+ if (!Arrays.asList(cyAttributes.getAttributeNames()).contains(
+ Semantics.CANONICAL_NAME)) {
+ List<Node> nodeList = Cytoscape.getCyNodesList();
+ int n = nodeList.size();
+ for (int i = 0; i < n; i++) {
+ String nodeID = nodeList.get(i).getIdentifier();
+ cyAttributes.setAttribute(nodeID, Semantics.CANONICAL_NAME,
+ nodeID);
+ }
+ }
+
+ cyAttributes = Cytoscape.getEdgeAttributes();
+ if (!Arrays.asList(cyAttributes.getAttributeNames()).contains(
+ Semantics.CANONICAL_NAME)) {
+ List<Node> edgeList = Cytoscape.getCyEdgesList();
+ int n = edgeList.size();
+ for (int i = 0; i < n; i++) {
+ String edgeID = edgeList.get(i).getIdentifier();
+ cyAttributes.setAttribute(edgeID, Semantics.CANONICAL_NAME,
+ edgeID);
+ }
+ }
+ }// TODO: remove in Cytoscape3
+ }
+}
diff --git a/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/conflict/AttributeConflictCollector.java b/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/conflict/AttributeConflictCollector.java
new file mode 100644
index 0000000..88f1fcb
--- /dev/null
+++ b/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/conflict/AttributeConflictCollector.java
@@ -0,0 +1,104 @@
+/* File: AttributeConflict.java
+
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+
+package csplugins.network.merge.conflict;
+
+import cytoscape.data.CyAttributes;
+
+import java.util.Map;
+
+/**
+ * Collect attribute conflicts
+ *
+ */
+public interface AttributeConflictCollector {
+
+ /**
+ *
+ * @return true if no conflict, false otherwise
+ */
+ public boolean isEmpty();
+
+ /**
+ *
+ * @return all map of to node id to attribute
+ */
+ public Map<String,String> getMapToIDAttr();
+
+ /**
+ * Get conflicts for a specific toID and toAttribute
+ * @param toID
+ * @param toAttr
+ * @return conflict map from id to attrs if exist, null otherwise
+ */
+ public Map<String,String> getConflicts(String toID, String toAttr);
+
+ /**
+ *
+ * @param toID
+ * @param toAttr
+ * @return
+ */
+ public CyAttributes getCyAttributes(String toID, String toAttr);
+
+ /**
+ *
+ * @param fromID
+ * @param fromAttr
+ * @param toID
+ * @param toAttr
+ */
+ public void addConflict(String fromID, String fromAttr, String toID, String toAttr, CyAttributes cyAttributes);
+
+ /**
+ *
+ * @param toID
+ * @param toAttr
+ * @return
+ */
+ public boolean removeConflicts(String toID, String toAttr);
+
+ /**
+ *
+ * @param fromID
+ * @param fromAttr
+ * @param toID
+ * @param toAttr
+ * @return
+ */
+ public boolean removeConflict(String fromID, String fromAttr, String toID, String toAttr);
+}
diff --git a/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/conflict/AttributeConflictCollectorImpl.java b/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/conflict/AttributeConflictCollectorImpl.java
new file mode 100644
index 0000000..aca7d33
--- /dev/null
+++ b/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/conflict/AttributeConflictCollectorImpl.java
@@ -0,0 +1,218 @@
+/* File: AttributeConflict.java
+
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+
+package csplugins.network.merge.conflict;
+
+import cytoscape.data.CyAttributes;
+
+import java.util.Map;
+import java.util.HashMap;
+
+/**
+ * Collect attribute conflicts
+ *
+ * Assumption: for each from_node, only one attribute to be merged into to_node
+ *
+ */
+public class AttributeConflictCollectorImpl implements AttributeConflictCollector {
+
+ protected class Conflicts {
+ public final CyAttributes cyAttributes;
+ public Map<String,String> mapFromIDFromAttr;
+
+ public Conflicts(final CyAttributes cyAttributes) {
+ this.cyAttributes = cyAttributes;
+ mapFromIDFromAttr = new HashMap<String,String>();
+ }
+
+ public void addConflict(final String fromID, final String fromAttr) {
+ mapFromIDFromAttr.put(fromID, fromAttr);
+ }
+
+ public boolean removeConflict(final String fromID, final String fromAttr) {
+ String attr = mapFromIDFromAttr.get(fromID);
+ if (attr==null || attr.compareTo(fromAttr)!=0) {
+ return false;
+ }
+
+ mapFromIDFromAttr.remove(fromID);
+ return true;
+ }
+ }
+
+ protected Map<String,Map<String,Conflicts>> mapToIDToAttrConflicts;
+
+ public AttributeConflictCollectorImpl() {
+ this.mapToIDToAttrConflicts = new HashMap<String,Map<String,Conflicts>>();
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ public boolean isEmpty() {
+ return mapToIDToAttrConflicts.isEmpty();
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ public Map<String,String> getMapToIDAttr() {
+ Map<String,String> mapToIDAttr = new HashMap<String,String>();
+ for (Map.Entry<String,Map<String,Conflicts>> entry : mapToIDToAttrConflicts.entrySet()) {
+ String id = entry.getKey();
+ for (String attr : entry.getValue().keySet()) {
+ mapToIDAttr.put(id,attr);
+ }
+ }
+
+ return mapToIDAttr;
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ public Map<String,String> getConflicts(final String toID, final String toAttr){
+ if (toID==null || toAttr==null) {
+ throw new java.lang.NullPointerException();
+ }
+
+ Map<String,Conflicts> mapToAttrConflicts = mapToIDToAttrConflicts.get(toID);
+ if (mapToAttrConflicts==null) {
+ return null;
+ }
+
+ return mapToAttrConflicts.get(toAttr).mapFromIDFromAttr;
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ public CyAttributes getCyAttributes(final String toID, final String toAttr) {
+ if (toID==null || toAttr==null) {
+ throw new java.lang.NullPointerException();
+ }
+
+ Map<String,Conflicts> mapToAttrConflicts = mapToIDToAttrConflicts.get(toID);
+ if (mapToAttrConflicts==null) {
+ return null;
+ }
+
+ return mapToAttrConflicts.get(toAttr).cyAttributes;
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ public void addConflict(final String fromID,
+ final String fromAttr,
+ final String toID,
+ final String toAttr,
+ final CyAttributes cyAttributes) {
+ if (fromID==null || fromAttr==null || toID==null || toAttr==null || cyAttributes==null) {
+ throw new java.lang.NullPointerException();
+ }
+
+ Map<String,Conflicts> mapToAttrConflicts = mapToIDToAttrConflicts.get(toID);
+ if (mapToAttrConflicts==null) {
+ mapToAttrConflicts = new HashMap<String,Conflicts>();
+ mapToIDToAttrConflicts.put(toID, mapToAttrConflicts);
+ }
+
+ Conflicts conflicts = mapToAttrConflicts.get(toAttr);
+ if (conflicts==null) {
+ conflicts = new Conflicts(cyAttributes);
+ mapToAttrConflicts.put(toAttr, conflicts);
+ } else {
+ if (conflicts.cyAttributes!=cyAttributes) {
+ throw new java.lang.IllegalArgumentException("CyAttributes are different!");
+ }
+ }
+
+ conflicts.addConflict(fromID, fromAttr);
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ public boolean removeConflicts(String toID, String toAttr) {
+ if (toID==null || toAttr==null) {
+ throw new java.lang.NullPointerException();
+ }
+
+ Map<String,Conflicts> mapToAttrConflicts = mapToIDToAttrConflicts.get(toID);
+ if (mapToAttrConflicts==null) {
+ return false;
+ }
+
+ if (mapToAttrConflicts.get(toAttr)==null) {
+ return false;
+ }
+
+ mapToAttrConflicts.remove(toAttr);
+ return true;
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ public boolean removeConflict(final String fromID, final String fromAttr, final String toID, final String toAttr) {
+ if (fromID==null || fromAttr==null || toID==null || toAttr==null) {
+ throw new java.lang.NullPointerException();
+ }
+
+ Map<String,Conflicts> mapToAttrConflicts = mapToIDToAttrConflicts.get(toID);
+ if (mapToAttrConflicts==null) {
+ return false;
+ }
+
+ Conflicts conflicts = mapToAttrConflicts.get(toAttr);
+ if (conflicts==null) {
+ return false;
+ }
+
+ boolean ret = conflicts.removeConflict(fromID, fromAttr);
+ if (ret && conflicts.mapFromIDFromAttr.isEmpty()) {
+ mapToAttrConflicts.remove(toAttr);
+ if (mapToAttrConflicts.isEmpty()) {
+ mapToIDToAttrConflicts.remove(toID);
+ }
+ }
+
+ return ret;
+ }
+
+}
diff --git a/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/conflict/AttributeConflictHandler.java b/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/conflict/AttributeConflictHandler.java
new file mode 100644
index 0000000..62ef580
--- /dev/null
+++ b/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/conflict/AttributeConflictHandler.java
@@ -0,0 +1,58 @@
+/* File: AttributeConflictHandler.java
+
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+package csplugins.network.merge.conflict;
+
+import cytoscape.data.CyAttributes;
+
+import java.util.Map;
+
+/**
+ *
+ *
+ */
+public interface AttributeConflictHandler {
+
+ /**
+ * Handle attribute conflict when merging (copying from one attr to another).
+ *
+ * @param conflict
+ * attribute conflict
+ * @return
+ * true if successful, false if failed
+ */
+ public boolean handleIt(String toID, String toAttr, Map<String,String> mapFromIDFromAttr, CyAttributes attrs);
+}
diff --git a/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/conflict/AttributeConflictManager.java b/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/conflict/AttributeConflictManager.java
new file mode 100644
index 0000000..337cee4
--- /dev/null
+++ b/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/conflict/AttributeConflictManager.java
@@ -0,0 +1,82 @@
+/* File: AttributeConflictManager.java
+
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+package csplugins.network.merge.conflict;
+
+import cytoscape.data.CyAttributes;
+
+import java.util.List;
+import java.util.Map;
+
+/**
+ *
+ *
+ */
+public class AttributeConflictManager {
+ final AttributeConflictCollector conflictCollector;
+ final List<AttributeConflictHandler> conflictHandlers;
+
+ public AttributeConflictManager(final AttributeConflictCollector conflictCollector,
+ final List<AttributeConflictHandler> conflictHandlers) {
+ if (conflictCollector==null || conflictHandlers==null) {
+ throw new java.lang.NullPointerException();
+ }
+ if (conflictHandlers.isEmpty()) {
+ throw new java.lang.IllegalArgumentException("No conflict handler");
+ }
+
+ this.conflictCollector = conflictCollector;
+ this.conflictHandlers = conflictHandlers;
+ }
+
+ public void handleConflicts() {
+
+ Map<String,String> mapToIDToAttr = conflictCollector.getMapToIDAttr();
+ for (Map.Entry<String,String> entryToIDToAttr : mapToIDToAttr.entrySet()) {
+ String toID = entryToIDToAttr.getKey();
+ String toAttr = entryToIDToAttr.getValue();
+ Map<String,String> mapFromIDFromAttr = conflictCollector.getConflicts(toID, toAttr);
+ CyAttributes attrs = conflictCollector.getCyAttributes(toID, toAttr);
+ for (AttributeConflictHandler handler : conflictHandlers) {
+ if (handler.handleIt(toID,toAttr,mapFromIDFromAttr,attrs)) {
+ conflictCollector.removeConflicts(toID, toAttr);
+ break;
+ }
+ }
+ }
+ }
+
+}
diff --git a/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/conflict/DefaultAttributeConflictHandler.java b/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/conflict/DefaultAttributeConflictHandler.java
new file mode 100644
index 0000000..3b9da24
--- /dev/null
+++ b/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/conflict/DefaultAttributeConflictHandler.java
@@ -0,0 +1,100 @@
+/* File: DefaultAttributeConflictHandler.java
+
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+package csplugins.network.merge.conflict;
+
+import cytoscape.data.CyAttributes;
+
+import java.util.Set;
+import java.util.TreeSet;
+import java.util.Map;
+
+/**
+ *
+ *
+ */
+public class DefaultAttributeConflictHandler implements AttributeConflictHandler {
+
+ /**
+ * Handle attribute conflict when merging (copying from one attr to another)
+ *
+ * @param conflict
+ * attribute conflict
+ * @return
+ * true if successful, false if failed
+ */
+ public boolean handleIt(final String toID,
+ final String toAttr,
+ final Map<String,String> mapFromIDFromAttr,
+ final CyAttributes attrs) {
+ //TODO: write a reasonable default one
+ if (toID==null || toAttr==null || mapFromIDFromAttr==null || attrs==null) {
+ throw new java.lang.NullPointerException();
+ }
+
+ byte type = attrs.getType(toAttr);
+
+ if (type == CyAttributes.TYPE_STRING) {
+ final String toValue = attrs.getStringAttribute(toID, toAttr);
+ Set<String> values = new TreeSet<String>();
+ values.add(toValue);
+
+ for (Map.Entry<String,String> entry : mapFromIDFromAttr.entrySet()) {
+ String fromID = entry.getKey();
+ String fromAttr = entry.getValue();
+ Object fromValue = attrs.getAttribute(fromID, fromAttr);
+ if (fromValue!=null) {
+ values.add(fromValue.toString());
+ }
+ }
+
+ StringBuilder str = new StringBuilder();
+ for (String v : values) {
+ str.append(v+";");
+ }
+
+ str.deleteCharAt(str.length()-1);
+
+ attrs.setAttribute(toID, toAttr, str.toString());
+
+ return true;
+ }
+
+ // how about Integer, Double, Boolean?
+
+ return false;
+ }
+}
diff --git a/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/model/AttributeMapping.java b/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/model/AttributeMapping.java
new file mode 100644
index 0000000..daf6b3a
--- /dev/null
+++ b/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/model/AttributeMapping.java
@@ -0,0 +1,241 @@
+/* File: AttributeMapping.java
+
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+package csplugins.network.merge.model;
+
+import cytoscape.data.CyAttributes;
+
+import java.util.Set;
+import java.util.Map;
+
+/**
+ * Instore the information how to mapping the attributes
+ * in the original networks to those in the resulting networks
+ *
+ *
+ */
+public interface AttributeMapping {
+
+ /**
+ *
+ * @return CyAttributes
+ */
+ public CyAttributes getCyAttributes();
+
+ /**
+ *
+ * @return attributes' names in the merged network
+ */
+ public String[] getMergedAttributes();
+
+ /**
+ *
+ * @return number of the attribute in the merged network
+ */
+ public int getSizeMergedAttributes();
+
+ /**
+ *
+ * @param index
+ * @return the ith attribute name in the merged network
+ */
+ public String getMergedAttribute(int index);
+
+ /**
+ * Set the ith attribute name in the merged network
+ * @param index
+ * @param attributeName
+ * @return the original one
+ */
+ public String setMergedAttribute(int index, String attributeName);
+
+ /**
+ *
+ * @param index
+ * @return the ith merged attribute type
+ */
+ public byte getMergedAttributeType(int index);
+
+ /**
+ *
+ * @param mergedAttributeName
+ * @return type for attribute mergedAttributeName
+ */
+ public byte getMergedAttributeType(String mergedAttributeName);
+
+ /**
+ * Set the ith merged attribute type
+ * @param index
+ * @param type
+ * @return true if successful; false otherwise
+ */
+ public boolean setMergedAttributeType(int index, byte type);
+
+ /**
+ * Set type for mergedAttributeName
+ * @param mergedAttributeName
+ * @param type
+ * @return true if successful; false otherwise
+ */
+ public boolean setMergedAttributeType(String mergedAttributeName, byte type);
+
+ /**
+ *
+ * @param attributeName
+ * @return true if an attribute exists in the merged attributes; false otherwise
+ */
+ public boolean containsMergedAttribute(String attributeName);
+
+ /**
+ *
+ * @return all network titles
+ */
+ public Set<String> getNetworkSet();
+
+ /**
+ *
+ * @return number of networks
+ */
+ public int getSizeNetwork();
+
+ /**
+ * Get the original attribute name in the network before merged, corresponding to the merged attribute
+ * @param netID
+ * @param mergedAttributeName
+ * @return the original attribute if exist, null otherwise
+ */
+ public String getOriginalAttribute(String netID, String mergedAttributeName);
+
+ /**
+ * Get the original attribute name before merged, corresponding to the ith merged attribute
+ * @param netID
+ * @param index
+ * @return the original attribute if exist, null otherwise
+ */
+ public String getOriginalAttribute(String netID, int index);
+
+ /**
+ * Get the original attribute name in the network before merged, corresponding to the merged attribute
+ * @param mergedAttributeName
+ * @return the original attribute if exist, null otherwise
+ */
+ public Map<String,String> getOriginalAttributeMap(String mergedAttributeName);
+
+ /**
+ * Get the original attribute name before merged, corresponding to the ith merged attribute
+ * @param index
+ * @return the original attribute if exist, null otherwise
+ */
+ public Map<String,String> getOriginalAttributeMap(int index);
+
+ /**
+ * Set attribute mapping
+ * @param netID
+ * @param attributeName
+ * @param mergedAttributeName
+ * @return the original attribute
+ */
+ public String setOriginalAttribute(String netID, String attributeName, String mergedAttributeName);
+
+ /**
+ * Set attribute mapping
+ * @param netID
+ * @param attributeName
+ * @param index
+ * @return the original attribute
+ */
+ public String setOriginalAttribute(String netID, String attributeName, int index);
+
+ /**
+ * Remove original attribute
+ * @param netID
+ * @param mergedAttributeName
+ * @return the removed attribute if successful; null otherwise
+ */
+ public String removeOriginalAttribute(String netID, String mergedAttributeName);
+
+ /**
+ * Remove original attribute
+ * @param netID
+ * @param index
+ * @return the removed attribute if successful; null otherwise
+ */
+ public String removeOriginalAttribute(String netID, int index);
+
+ /**
+ * Remove merged attribute, along with the corresponding origianl attribute
+ * @param mergedAttributeName
+ * @return the removed attribute if successful; null otherwise
+ */
+ public String removeMergedAttribute(String mergedAttributeName);
+
+ /**
+ * Remove merged attribute, along with the corresponding origianl attribute
+ * @param index
+ * @return the removed attribute if successful; null otherwise
+ */
+ public String removeMergedAttribute(int index);
+
+ /**
+ * Add new attribute in the end for the current network
+ * @param mapNetIDAttributeName
+ * @param mergedAttrName
+ * @return the added attribute name; it could be different from mergedAttrName
+ */
+ public String addAttributes(Map<String,String> mapNetIDAttributeName, String mergedAttrName);
+
+ /**
+ * Add new attribute at the ith for the current network
+ * @param mapNetIDAttributeName
+ * @param mergedAttrName
+ * @param index
+ * @return the added attribute name; it could be different from mergedAttrName
+ */
+ public String addAttributes(Map<String,String> mapNetIDAttributeName, String mergedAttrName, int index);
+
+ /**
+ *
+ * @param netID
+ */
+ public void addNetwork(String netID);
+
+ /**
+ *
+ * @param netID
+ */
+ public void removeNetwork(String netID);
+
+}
diff --git a/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/model/AttributeMappingImpl.java b/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/model/AttributeMappingImpl.java
new file mode 100644
index 0000000..e555e93
--- /dev/null
+++ b/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/model/AttributeMappingImpl.java
@@ -0,0 +1,679 @@
+/* File: AttributeMappingImpl.java
+
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+package csplugins.network.merge.model;
+
+import csplugins.network.merge.util.AttributeValueCastUtils;
+
+import cytoscape.data.CyAttributes;
+import cytoscape.data.Semantics;
+
+import java.util.List;
+import java.util.Vector;
+import java.util.Set;
+import java.util.HashSet;
+import java.util.Map;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.Arrays;
+
+/**
+ * Class to instore the information how to mapping the attributes
+ * in the original networks to those in the resulting networks
+ *
+ *
+ */
+public class AttributeMappingImpl implements AttributeMapping {
+ private Map<String,List<String>> attributeMapping; //attribute mapping, network to list of attributes
+ private List<String> mergedAttributes;
+ private List<Byte> mergedAttributeTypes;
+ private CyAttributes cyAttributes;
+ private final String nullAttr = ""; // to hold a position in vector standing that it's not a attribute
+
+ public AttributeMappingImpl(final CyAttributes cyAttributes) {
+ this.cyAttributes = cyAttributes;
+ attributeMapping = new HashMap<String,List<String>>();
+ mergedAttributes = new Vector<String>();
+ mergedAttributeTypes = new Vector<Byte>();
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ public CyAttributes getCyAttributes() {
+ return cyAttributes;
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ public String[] getMergedAttributes() {
+ return (String[])mergedAttributes.toArray(new String[0]);
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ public int getSizeMergedAttributes() {
+ return mergedAttributes.size();
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ public String getMergedAttribute(final int index) {
+ if (index<0 || index>=getSizeMergedAttributes()) {
+ throw new java.lang.IndexOutOfBoundsException("Index out of boundary.");
+ }
+
+ //if (index>=mergedAttributes.size()) return null;
+ return mergedAttributes.get(index);
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ public String setMergedAttribute(final int index, final String attributeName) {
+ if (attributeName==null) {
+ throw new java.lang.NullPointerException("Attribute name is null.");
+ }
+
+ String attr = attributeName;
+
+ if (attributeExistsInOriginalNetwork(attributeName)) {
+ final Set<String> attrNames = new HashSet<String>(getOriginalAttributeMap(index).values());
+ final String attr_mc = AttributeValueCastUtils.getMostCompatibleAttribute(attrNames, cyAttributes);
+ if (attr_mc==null) { // incompatible
+ if (cyAttributes.getType(attributeName)!=CyAttributes.TYPE_STRING) {
+ attr = this.getDefaultMergedAttrName(attr, true);
+ this.setMergedAttributeType(index, CyAttributes.TYPE_STRING);
+ }
+ } else { // compatible
+ if (!AttributeValueCastUtils.isAttributeTypeConvertable(attr_mc, attributeName, cyAttributes)) {
+ attr = this.getDefaultMergedAttrName(attr, true);
+ this.setMergedAttributeType(index, cyAttributes.getType(attr_mc));
+ }
+ }
+ }
+
+ String ret = mergedAttributes.set(index, attr);
+ this.resetMergedAttributeType(index,false);
+
+ return ret;
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ public byte getMergedAttributeType(final int index) {
+ if (index>=this.getSizeMergedAttributes()||index<0) {
+ throw new java.lang.IndexOutOfBoundsException();
+ }
+
+ return mergedAttributeTypes.get(index);
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ public byte getMergedAttributeType(final String mergedAttributeName) {
+ if (mergedAttributeName==null) {
+ throw new java.lang.NullPointerException("Null netID or mergedAttributeName");
+ }
+
+ final int index = mergedAttributes.indexOf(mergedAttributeName);
+ if (index==-1) {
+ throw new java.lang.IllegalArgumentException("No "+mergedAttributeName+" is contained in merged attributes");
+ }
+
+ return getMergedAttributeType(index);
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ public boolean setMergedAttributeType(int index, byte type) {
+ if (index>=this.getSizeMergedAttributes()||index<0) {
+ throw new java.lang.IndexOutOfBoundsException();
+ }
+
+ final Set<String> attrNames = new HashSet<String>(getOriginalAttributeMap(index).values());
+ final String attr_mc = AttributeValueCastUtils.getMostCompatibleAttribute(attrNames, cyAttributes);
+ final byte fromType = attr_mc==null?CyAttributes.TYPE_STRING:cyAttributes.getType(attr_mc);
+
+ if (!AttributeValueCastUtils.isAttributeTypeConvertable(fromType, type)) {
+ return false;
+ }
+
+ this.mergedAttributeTypes.set(index, type);
+ return true;
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ public boolean setMergedAttributeType(String mergedAttributeName, byte type) {
+ if (mergedAttributeName==null) {
+ throw new java.lang.NullPointerException("Null netID or mergedAttributeName");
+ }
+
+ final int index = mergedAttributes.indexOf(mergedAttributeName);
+ if (index==-1) {
+ throw new java.lang.IllegalArgumentException("No "+mergedAttributeName+" is contained in merged attributes");
+ }
+
+ return setMergedAttributeType(index,type);
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ public boolean containsMergedAttribute(final String attributeName) {
+ if (attributeName==null) {
+ throw new java.lang.NullPointerException("Attribute name is null.");
+ }
+ return mergedAttributes.contains(attributeName);
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ public String getOriginalAttribute(final String netID, final String mergedAttributeName) {
+ if (netID==null||mergedAttributeName==null) {
+ throw new java.lang.NullPointerException("Null netID or mergedAttributeName");
+ }
+ final int index = mergedAttributes.indexOf(mergedAttributeName);
+ if (index==-1) {
+ throw new java.lang.IllegalArgumentException("No "+mergedAttributeName+" is contained in merged attributes");
+ }
+ return getOriginalAttribute(netID, index);
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ public String getOriginalAttribute(final String netID, final int index) {
+ final List<String> attrs = attributeMapping.get(netID);
+ if (attrs==null) {
+ throw new java.lang.IllegalArgumentException(netID+" is not selected as merging network");
+ }
+ if (index>=attrs.size()||index<0) {
+ throw new java.lang.IndexOutOfBoundsException();
+ }
+ final String attr = attrs.get(index);
+ if (attr.compareTo(nullAttr)==0) return null;
+ return attr;
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ public Map<String,String> getOriginalAttributeMap(String mergedAttributeName) {
+ if (mergedAttributeName==null) {
+ throw new java.lang.NullPointerException("Null netID or mergedAttributeName");
+ }
+ final int index = mergedAttributes.indexOf(mergedAttributeName);
+ if (index==-1) {
+ throw new java.lang.IllegalArgumentException("No "+mergedAttributeName+" is contained in merged attributes");
+ }
+ return getOriginalAttributeMap(index);
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ public Map<String,String> getOriginalAttributeMap(int index) {
+ if (index>=this.getSizeMergedAttributes()||index<0) {
+ throw new java.lang.IndexOutOfBoundsException();
+ }
+
+ Map<String,String> return_this = new HashMap<String,String>();
+
+ final Iterator<Map.Entry<String,List<String>>> it = attributeMapping.entrySet().iterator();
+ while (it.hasNext()) {
+ final Map.Entry<String,List<String>> entry = it.next();
+ final String netID = entry.getKey();
+ final List<String> attrs = entry.getValue();
+ final String attr = attrs.get(index);
+ if (attr.compareTo(nullAttr)!=0) {
+ return_this.put(netID, attr);
+ }
+ }
+
+ return return_this;
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ public String setOriginalAttribute(final String netID, final String attributeName, final String mergedAttributeName) {
+ if (netID==null||mergedAttributeName==null) {
+ throw new java.lang.NullPointerException("Null netID or mergedAttributeName");
+ }
+ final int index = mergedAttributes.indexOf(mergedAttributeName);
+ if (index==-1) {
+ throw new java.lang.IllegalArgumentException("No "+mergedAttributeName+" is contained in merged attributes");
+ }
+ return setOriginalAttribute(netID, attributeName, index);
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ public String setOriginalAttribute(final String netID, final String attributeName, final int index){
+ if (netID==null||attributeName==null||attributeName==null) {
+ throw new java.lang.NullPointerException("Null netID or attributeName or mergedAttributeName");
+ }
+
+ if (!Arrays.asList(cyAttributes.getAttributeNames()).contains(attributeName)) {
+ throw new java.lang.IllegalArgumentException("No "+attributeName+" is contained in attributes");
+ }
+
+ final List<String> attrs = attributeMapping.get(netID);
+ if (attrs==null) return null;
+ if (index>=attrs.size()||index<0) {
+ throw new java.lang.IndexOutOfBoundsException();
+ }
+
+ final String old = attrs.get(index);
+ if (old.compareTo(attributeName)!=0) { // not the same
+ attrs.set(index, attributeName);
+
+ String mergedAttr = getMergedAttribute(index);
+ if (attributeExistsInOriginalNetwork(mergedAttr)
+ && !AttributeValueCastUtils.isAttributeTypeConvertable(attributeName,
+ mergedAttr,
+ cyAttributes)) {
+ setMergedAttribute(index,getDefaultMergedAttrName(mergedAttr,true));
+ }
+
+ this.resetMergedAttributeType(index,false);
+ }
+
+ return old;
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ public String removeOriginalAttribute(final String netID, final String mergedAttributeName) {
+ if (netID==null||mergedAttributeName==null) {
+ throw new java.lang.NullPointerException("Null netID or mergedAttributeName");
+ }
+
+ final int index = mergedAttributes.indexOf(mergedAttributeName);
+ if (index==-1) {
+ throw new java.lang.IllegalArgumentException("No "+mergedAttributeName+" is contained in merged attributes");
+ }
+
+ return removeOriginalAttribute(netID, index);
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ public String removeOriginalAttribute(final String netID, final int index) {
+ if (netID==null) {
+ throw new java.lang.NullPointerException("Null netID");
+ }
+
+ if (index<0 || index>=getSizeMergedAttributes()) {
+ throw new java.lang.IndexOutOfBoundsException("Index out of bounds");
+ }
+
+ final List<String> attrs = attributeMapping.get(netID);
+
+ String old = attrs.set(index, nullAttr);
+ if (!pack(index)) {
+ this.resetMergedAttributeType(index,false);
+ }
+
+ return old;
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ public String removeMergedAttribute(final String mergedAttributeName) {
+ if (mergedAttributeName==null) {
+ throw new java.lang.NullPointerException("Null mergedAttributeName");
+ }
+
+ final int index = mergedAttributes.indexOf(mergedAttributeName);
+ if (index ==-1 ) {
+ return null;
+ }
+
+ return removeMergedAttribute(index);
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ public String removeMergedAttribute(final int index) {
+ if (index<0 || index>=getSizeMergedAttributes()) {
+ throw new java.lang.IndexOutOfBoundsException("Index out of bounds");
+ }
+
+ //int n = attributeMapping.size();
+ //for (int i=0; i<n; i++) {
+ // attributeMapping.get(i).remove(index);
+ //}
+ for (List<String> attrs : attributeMapping.values()) {
+ attrs.remove(index);
+ }
+
+ this.mergedAttributeTypes.remove(index);
+
+ return mergedAttributes.remove(index);
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ public String addAttributes(final Map<String,String> mapNetIDAttributeName, final String mergedAttrName) {
+ return addAttributes(mapNetIDAttributeName,mergedAttrName,getSizeMergedAttributes());
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ public String addAttributes(final Map<String,String> mapNetIDAttributeName, final String mergedAttrName, final int index) {
+ if (mapNetIDAttributeName==null || mergedAttrName==null) {
+ throw new java.lang.NullPointerException();
+ }
+
+ if (index<0 || index>getSizeMergedAttributes()) {
+ throw new java.lang.IndexOutOfBoundsException("Index out of bounds");
+ }
+
+ if (mapNetIDAttributeName.isEmpty()) {
+ throw new java.lang.IllegalArgumentException("Empty map");
+ }
+
+ final Set<String> networkSet = getNetworkSet();
+ if (!networkSet.containsAll(mapNetIDAttributeName.keySet())) {
+ throw new java.lang.IllegalArgumentException("Non-exist network(s)");
+ }
+
+ if (!Arrays.asList(cyAttributes.getAttributeNames()).containsAll(mapNetIDAttributeName.values())) {
+ throw new java.lang.IllegalArgumentException("Non-exist attribute(s)");
+ }
+
+ final Iterator<Map.Entry<String,List<String>>> it = attributeMapping.entrySet().iterator();
+ //final Iterator<Vector<String>> it = attributeMapping.values().iterator();
+ while (it.hasNext()) { // add an empty attr for each network
+ final Map.Entry<String,List<String>> entry = it.next();
+ final String netID = entry.getKey();
+ final List<String> attrs = entry.getValue();
+
+ if (mapNetIDAttributeName.containsKey(netID)) {
+ attrs.add(index,mapNetIDAttributeName.get(netID));
+ } else {
+ attrs.add(index,nullAttr);
+ }
+ }
+
+ String defaultName = getDefaultMergedAttrName(mergedAttrName,false);
+ mergedAttributes.add(index,defaultName);// add in merged attr
+
+ this.resetMergedAttributeType(index, true);
+ return defaultName;
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ public void addNetwork(final String netID) {
+ if (netID==null) {
+ throw new java.lang.NullPointerException();
+ }
+
+ final String[] attributeNames = cyAttributes.getAttributeNames();
+ Arrays.sort(attributeNames);
+
+ final int nAttr = attributeNames.length;
+ if (attributeMapping.isEmpty()) { // for the first network added
+
+ final List<String> attrs = new Vector<String>();
+ attributeMapping.put(netID, attrs);
+
+
+ for (int i=0; i<nAttr; i++) {
+ //TODO REMOVE IN Cytoscape3.0
+ if (attributeNames[i].compareTo(Semantics.CANONICAL_NAME)==0) {
+ continue;
+ }//TODO REMOVE IN Cytoscape3.0
+
+ addNewAttribute(netID, attributeNames[i]);
+ }
+
+ //TODO REMOVE IN 3.0, canonicalName in each network form a separate attribute in resulting network
+ addNewAttribute(netID, Semantics.CANONICAL_NAME);//TODO REMOVE IN Cytoscape3.0
+
+
+ } else { // for each attributes to be added, search if the same attribute exists
+ // if yes, add to that group; otherwise create a new one
+ List<String> attrs = attributeMapping.get(netID);
+ if (attrs!=null) { // this network already exist
+ System.err.println("Error: this network already exist");
+ return;
+ }
+
+ final int nr = mergedAttributes.size(); // # of rows, the same as the # of attributes in merged network
+
+ attrs = new Vector<String>(nr); // new map
+ for (int i=0; i<nr; i++) {
+ attrs.add(nullAttr);
+ }
+ attributeMapping.put(netID, attrs);
+
+ for (int i=0; i<nAttr; i++) {
+ final String at = attributeNames[i];
+
+ //TODO REMOVE IN Cytoscape3.0, canonicalName in each network form a separate attribute in resulting network
+ if (at.compareTo(Semantics.CANONICAL_NAME)==0) {
+ addNewAttribute(netID, Semantics.CANONICAL_NAME);
+ continue;
+ }//TODO REMOVE IN Cytoscape3.0
+
+ boolean found = false;
+ for (int ir=0; ir<nr; ir++) {
+ if (attrs.get(ir).compareTo(nullAttr)!=0) continue; // if the row is occupied
+ if (mergedAttributes.get(ir).compareTo(at)==0) { // same name as the merged attribute
+ found = true;
+ this.setOriginalAttribute(netID, at, ir);
+ //attrs.set(ir, at);// add the attribute on the ir row
+ break;
+ }
+
+ final Iterator<String> it = attributeMapping.keySet().iterator();
+ while (it.hasNext()) {
+ final String net_curr = it.next();
+ final String attr_curr = attributeMapping.get(net_curr).get(ir);
+ if (attr_curr.compareTo(at)==0) { // same name as the original attribute
+ //if (AttributeValueCastUtils.isAttributeTypeSame(attr_curr,at,attributes)) // not neccessay in Cytoscape2.6
+ // since attributes are global
+ found = true;
+ //attrs.set(ir, at); // add the attribute on the ir row
+ this.setOriginalAttribute(netID, at, ir);
+ break;
+ }
+ }
+
+ //if (found) break; // do not need to break, add to multiple line if match
+ }
+
+ if (!found) { //no same attribute found
+ addNewAttribute(netID,at);
+ }
+ }
+ }
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ public Set<String> getNetworkSet() {
+ return attributeMapping.keySet();
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ public int getSizeNetwork() {
+ return attributeMapping.size();
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ public void removeNetwork(final String netID) {
+ if (netID==null) {
+ throw new java.lang.NullPointerException();
+ }
+ final List<String> removed = attributeMapping.remove(netID);
+ final int n = removed.size();
+ for (int i=n-1; i>=0; i--) {
+ if (removed.get(i).compareTo(nullAttr)!=0) { // if the attribute is not empty
+ if (!pack(i)) { // if not removed
+ this.resetMergedAttributeType(i, false);
+ }
+ }
+ }
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ protected boolean pack(final int index) {
+ if (index<0 || index>=getSizeMergedAttributes()) {
+ throw new java.lang.IndexOutOfBoundsException("Index out of boundary.");
+ }
+
+ Iterator<List<String>> it = attributeMapping.values().iterator();
+ while (it.hasNext()) {
+ if (it.next().get(index).compareTo(nullAttr)!=0) {
+ return false;
+ }
+ }
+
+ this.removeMergedAttribute(index);
+ return true;
+
+// mergedAttributes.remove(index);
+//
+// it = attributeMapping.values().iterator();
+// while ( it.hasNext() ) {
+// it.next().remove(index);
+// }
+
+// if (attributeMapping.isEmpty()) {
+// mergedAttributes.clear();
+// }
+
+ }
+
+ protected boolean attributeExistsInOriginalNetwork(final String attr) {
+ if (attr==null) {
+ throw new java.lang.NullPointerException();
+ }
+ return Arrays.asList(cyAttributes.getAttributeNames()).contains(attr);
+ }
+
+ private String getDefaultMergedAttrName(final String attr, boolean excludeOriginalAttribute) {
+ if (attr==null) {
+ throw new java.lang.NullPointerException();
+ }
+
+ String appendix = "";
+ int i = 0;
+
+ while (true) {
+ String attr_ret = attr+appendix;
+ if (mergedAttributes.contains(attr_ret)||(excludeOriginalAttribute&&attributeExistsInOriginalNetwork(attr_ret))){
+ appendix = "." + ++i;
+ } else {
+ return attr+appendix;
+ }
+ }
+ }
+
+ protected void addNewAttribute(final String netID, final String attributeName) {
+ if (netID==null || attributeName==null) {
+ throw new java.lang.NullPointerException();
+ }
+
+ final Iterator<List<String>> it = attributeMapping.values().iterator();
+ while (it.hasNext()) { // add an empty attr for each network
+ it.next().add(nullAttr);
+ }
+ final List<String> attrs = attributeMapping.get(netID);
+ attrs.set(attrs.size()-1, attributeName); // set attr
+
+ String attrMerged = attributeName;
+ //TODO remove in Cytosape3
+ if (attributeName.compareTo(Semantics.CANONICAL_NAME)==0) {
+ attrMerged = netID+"."+Semantics.CANONICAL_NAME;
+ }//TODO remove in Cytosape3
+
+ mergedAttributes.add(getDefaultMergedAttrName(attrMerged,false)); // add in merged attr
+ this.resetMergedAttributeType(mergedAttributeTypes.size(),true);
+ }
+
+ protected void resetMergedAttributeType(final int index, boolean add) {
+ if (this.getSizeMergedAttributes()>this.mergedAttributeTypes.size()+(add?1:0)) {
+ throw new java.lang.IllegalStateException("attribute type not complete");
+ }
+
+ if (index>=this.getSizeMergedAttributes()||index<0) {
+ throw new java.lang.IndexOutOfBoundsException();
+ }
+
+ final Set<String> attrNames = new HashSet<String>(getOriginalAttributeMap(index).values());
+ final String attr_mc = AttributeValueCastUtils.getMostCompatibleAttribute(attrNames, cyAttributes);
+ final byte type = attr_mc==null?CyAttributes.TYPE_STRING:cyAttributes.getType(attr_mc);
+
+ if (add) { //new
+ mergedAttributeTypes.add(index,type);
+ } else {
+ final byte old = mergedAttributeTypes.get(index);
+ if (old==CyAttributes.TYPE_STRING || old==CyAttributes.TYPE_SIMPLE_LIST)
+ return;
+ this.mergedAttributeTypes.set(index, type);
+ }
+ }
+}
diff --git a/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/model/MatchingAttribute.java b/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/model/MatchingAttribute.java
new file mode 100644
index 0000000..f94362f
--- /dev/null
+++ b/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/model/MatchingAttribute.java
@@ -0,0 +1,103 @@
+/* File: MatchingAttribute.java
+
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+package csplugins.network.merge.model;
+
+
+import java.util.Set;
+import java.util.Map;
+
+/**
+ * Information which attribute to be used for matching nodes
+ *
+ *
+ */
+public interface MatchingAttribute {
+
+ /**
+ *
+ * @return map of network to attribute
+ */
+ public Map<String,String> getNetAttrMap();
+
+ /**
+ *
+ * @param netID
+ * @return the attribute of network for matching node
+ */
+ public String getAttributeForMatching(String netID);
+
+ /**
+ *
+ * Set the attribute of network for matching node
+ *
+ * @param netID
+ * @param attributeName
+ */
+ public void putAttributeForMatching(String netID, String attributeName);
+
+ /**
+ * add/select the attribute of network for matching node
+ * @param netID
+ */
+ public void addNetwork(String netID);
+
+ /**
+ * Remove the network, return the attribute
+ * @param netID
+ * @return
+ */
+ public String removeNetwork(String netID);
+
+ /**
+ *
+ * @return
+ */
+ public int getSizeNetwork();
+
+ /**
+ *
+ * @return
+ */
+ public Set<String> getNetworkSet();
+
+ /**
+ *
+ */
+ public void clear();
+
+ //TODO: ID types of the attribute could be store here
+}
diff --git a/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/model/MatchingAttributeImpl.java b/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/model/MatchingAttributeImpl.java
new file mode 100644
index 0000000..6298373
--- /dev/null
+++ b/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/model/MatchingAttributeImpl.java
@@ -0,0 +1,144 @@
+/* File: MatchingAttributeImpl.java
+
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+package csplugins.network.merge.model;
+
+import cytoscape.data.CyAttributes;
+
+import java.util.Collection;
+import java.util.Set;
+import java.util.Map;
+import java.util.HashMap;
+
+/**
+ * Class to instore the information which attribute to be used
+ * for matching nodes
+ *
+ *
+ */
+public class MatchingAttributeImpl implements MatchingAttribute {
+ private Map<String,String> attributeForMatching; // network name to attribute name
+ private CyAttributes cyAttributes; // use map if local attribute realized
+
+ public MatchingAttributeImpl(final CyAttributes cyAttributes) {
+ this.cyAttributes = cyAttributes;
+ attributeForMatching = new HashMap<String,String>();
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ public Map<String,String> getNetAttrMap() {
+ return attributeForMatching;
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ public String getAttributeForMatching(final String netID) {
+ if (netID == null) {
+ throw new java.lang.NullPointerException();
+ }
+
+ return attributeForMatching.get(netID);
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ public void putAttributeForMatching(final String netID, final String attributeName) {
+ if (netID==null || attributeName==null) {
+ throw new java.lang.NullPointerException();
+ }
+
+ attributeForMatching.put(netID, attributeName);
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ public void addNetwork(final String netID) {
+ if (netID == null) {
+ throw new java.lang.NullPointerException();
+ }
+
+ final String[] attributeNames = cyAttributes.getAttributeNames();
+ final Collection<String> values = attributeForMatching.values();
+ final int n = attributeNames.length;
+ for (int i=0; i<n; i++) {
+ if (values.contains(attributeNames[i])) {
+ putAttributeForMatching(netID,attributeNames[i]);
+ return;
+ }
+ }
+ //TODO remove in Cytoscape3
+ putAttributeForMatching(netID,"canonicalName");
+
+ //putAttributeForMatching(netID,attributeNames[i]); //use in Cytoscape3
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ public String removeNetwork(final String netID) {
+ if (netID == null) {
+ throw new java.lang.NullPointerException();
+ }
+
+ return attributeForMatching.remove(netID);
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ public int getSizeNetwork() {
+ return attributeForMatching.size();
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ public Set<String> getNetworkSet() {
+ return attributeForMatching.keySet();
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ public void clear() {
+ attributeForMatching.clear();
+ }
+}
diff --git a/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/ui/CollapsiblePanel.java b/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/ui/CollapsiblePanel.java
new file mode 100644
index 0000000..cb31079
--- /dev/null
+++ b/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/ui/CollapsiblePanel.java
@@ -0,0 +1,431 @@
+/**
+ * * Copyright (c) 2004 Memorial Sloan-Kettering Cancer Center
+ * *
+ * * Code written by: Gary Bader
+ * * Authors: Gary Bader, Ethan Cerami, Chris Sander
+ * *
+ * * This library is free software; you can redistribute it and/or modify it
+ * * under the terms of the GNU Lesser General Public License as published
+ * * by the Free Software Foundation; either version 2.1 of the License, or
+ * * any later version.
+ * *
+ * * This library is distributed in the hope that it will be useful, but
+ * * WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ * * MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ * * documentation provided hereunder is on an "as is" basis, and
+ * * Memorial Sloan-Kettering Cancer Center
+ * * has no obligations to provide maintenance, support,
+ * * updates, enhancements or modifications. In no event shall the
+ * * Memorial Sloan-Kettering Cancer Center
+ * * be liable to any party for direct, indirect, special,
+ * * incidental or consequential damages, including lost profits, arising
+ * * out of the use of this software and its documentation, even if
+ * * Memorial Sloan-Kettering Cancer Center
+ * * has been advised of the possibility of such damage. See
+ * * the GNU Lesser General Public License for more details.
+ * *
+ * * You should have received a copy of the GNU Lesser General Public License
+ * * along with this library; if not, write to the Free Software Foundation,
+ * * Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ *
+ * User: Vuk Pavlovic
+ * Date: Nov 29, 2006
+ * Time: 5:34:46 PM
+ * Description: The user-triggered collapsable panel containing the component (trigger) in the titled border
+ */
+
+package csplugins.network.merge.ui;
+
+import javax.swing.*;
+import javax.swing.border.Border;
+import javax.swing.border.TitledBorder;
+import java.awt.*;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.net.URL;
+
+import java.util.Vector;
+
+/**
+ * The user-triggered collapsable panel containing the component (trigger) in the titled border
+ */
+public class CollapsiblePanel extends JPanel {
+ public interface CollapeListener extends java.util.EventListener {
+ public void collaped();
+ public void expanded();
+ }
+
+ Vector<CollapeListener> collapeListeners;
+
+ //Border
+ CollapsableTitledBorder border; // includes upper left component and line type
+ Border collapsedBorderLine = BorderFactory.createEmptyBorder(2, 2, 2, 2); // no border
+ Border expandedBorderLine = null; // because this is null, default is used, etched lowered border on MAC
+
+ //Title
+ AbstractButton titleComponent; // displayed in the titled border
+
+ //Expand/Collapse button
+ final static int COLLAPSED = 0, EXPANDED = 1; // image States
+ ImageIcon[] iconArrow = createExpandAndCollapseIcon();
+ JButton arrow = createArrowButton();
+
+ //Content Pane
+ JPanel panel;
+
+ //Container State
+ boolean collapsed; // stores curent state of the collapsable panel
+
+ /**
+ * Constructor for an option button controlled collapsable panel.
+ * This is useful when a group of options each have unique sub contents. The radio buttons should be created,
+ * grouped, and then used to construct their own collapsable panels. This way choosing a different option in
+ * the same option group will collapse all unselected options. Expanded panels draw a border around the
+ * contents and through the radio button in the fashion of a titled border.
+ *
+ * @param component Radio button that expands and collapses the panel based on if it is selected or not
+ */
+ public CollapsiblePanel(JRadioButton component) {
+ component.addItemListener(new CollapsiblePanel.ExpandAndCollapseAction());
+ titleComponent = component;
+ collapsed = !component.isSelected();
+ commonConstructor();
+ }
+
+ /**
+ * Constructor for a label/button controlled collapsable panel. Displays a clickable title that resembles a
+ * native titled border except for an arrow on the right side indicating an expandable panel. The actual border
+ * only appears when the panel is expanded.
+ *
+ * @param text Title of the collapsable panel in string format, used to create a button with text and an arrow icon
+ */
+ public CollapsiblePanel(String text) {
+ arrow.setText(text);
+ titleComponent = arrow;
+ collapsed = true;
+ commonConstructor();
+ }
+
+ /**
+ * Sets layout, creates the content panel and adds it and the title component to the container,
+ * all constructors have this procedure in common.
+ */
+ private void commonConstructor () {
+ setLayout(new BorderLayout());
+
+ panel = new JPanel();
+ panel.setLayout(new BorderLayout());
+
+ add(titleComponent, BorderLayout.CENTER);
+ add(panel, BorderLayout.CENTER);
+
+ collapeListeners = new Vector<CollapeListener>();
+
+ setCollapsed(collapsed);
+
+ placeTitleComponent();
+ }
+
+ public void addCollapeListener(CollapeListener collapeListener) {
+ this.collapeListeners.add(collapeListener);
+ }
+
+ public boolean removeCollapeListener(CollapeListener collapeListener) {
+ return this.collapeListeners.remove(collapeListener);
+ }
+
+ /**
+ * Sets the bounds of the border title component so that it is properly positioned.
+ */
+ private void placeTitleComponent() {
+ Insets insets = this.getInsets();
+ Rectangle containerRectangle = this.getBounds();
+ Rectangle componentRectangle = border.getComponentRect(containerRectangle, insets);
+ titleComponent.setBounds(componentRectangle);
+ }
+
+ public void setTitleComponentText(String text) {
+ if (titleComponent instanceof JButton) {
+ titleComponent.setText(text);
+ }
+ placeTitleComponent();
+ }
+
+ /**
+ * This class requires that all content be placed within a designated panel, this method returns that panel.
+ *
+ * @return panel The content panel
+ */
+ public JPanel getContentPane() {
+ return panel;
+ }
+
+ /**
+ * Collapses or expands the panel. This is done by adding or removing the content pane,
+ * alternating between a frame and empty border, and changing the title arrow.
+ * Also, the current state is stored in the collapsed boolean.
+ *
+ * @param collapse When set to true, the panel is collapsed, else it is expanded
+ */
+ public void setCollapsed(boolean collapse) {
+ collapsed = collapse;
+ if (collapse) {
+ //collapse the panel, remove content and set border to empty border
+ remove(panel);
+ arrow.setIcon(iconArrow[COLLAPSED]);
+ border = new CollapsableTitledBorder(collapsedBorderLine, titleComponent);
+
+ for(CollapeListener collapeListener : collapeListeners) {
+ collapeListener.collaped();
+ }
+
+ } else {
+ //expand the panel, add content and set border to titled border
+ add(panel, BorderLayout.CENTER);
+ arrow.setIcon(iconArrow[EXPANDED]);
+ border = new CollapsableTitledBorder(expandedBorderLine, titleComponent);
+
+ for(CollapeListener collapeListener : collapeListeners) {
+ collapeListener.expanded();
+ }
+
+ }
+ setBorder(border);
+ updateUI();
+ }
+
+ /**
+ * Returns the current state of the panel, collapsed (true) or expanded (false).
+ *
+ * @return collapsed Returns true if the panel is collapsed and false if it is expanded
+ */
+ public boolean isCollapsed() {
+ return collapsed;
+ }
+
+ /**
+ * Returns an ImageIcon array with arrow images used for the different states of the panel.
+ *
+ * @return iconArrow An ImageIcon array holding the collapse and expanded versions of the right hand side arrow
+ */
+ private ImageIcon[] createExpandAndCollapseIcon () {
+ ImageIcon[] iconArrow = new ImageIcon[2];
+ URL iconURL;
+
+ iconURL = getClass().getResource("/images/arrow_collapsed.gif");
+ if (iconURL != null) {
+ iconArrow[COLLAPSED] = new ImageIcon(iconURL);
+ }
+ iconURL = getClass().getResource("/images/arrow_expanded.gif");
+ if (iconURL != null) {
+ iconArrow[EXPANDED] = new ImageIcon(iconURL);
+ }
+ return iconArrow;
+ }
+
+ /**
+ * Returns a button with an arrow icon and a collapse/expand action listener.
+ *
+ * @return button Button which is used in the titled border component
+ */
+ private JButton createArrowButton () {
+ JButton button = new JButton("arrow", iconArrow[COLLAPSED]);
+ button.setBorder(BorderFactory.createEmptyBorder(0,1,5,1));
+ button.setVerticalTextPosition(AbstractButton.CENTER);
+ button.setHorizontalTextPosition(AbstractButton.LEFT);
+ button.setMargin(new Insets(0,0,3,0));
+
+ //We want to use the same font as those in the titled border font
+ Font font = BorderFactory.createTitledBorder("Sample").getTitleFont();
+ Color color = BorderFactory.createTitledBorder("Sample").getTitleColor();
+ button.setFont(font);
+ button.setForeground(color);
+ button.setFocusable(false);
+ button.setContentAreaFilled(false);
+
+ button.addActionListener(new CollapsiblePanel.ExpandAndCollapseAction());
+
+ return button;
+ }
+
+ /**
+ * Handles expanding and collapsing of extra content on the user's click of the titledBorder component.
+ */
+ private class ExpandAndCollapseAction extends AbstractAction implements ActionListener, ItemListener {
+ public void actionPerformed(ActionEvent e) {
+ setCollapsed(!isCollapsed());
+ }
+ public void itemStateChanged(ItemEvent e) {
+ setCollapsed(!isCollapsed());
+ }
+ }
+
+ /**
+ * Special titled border that includes a component in the title area
+ */
+ private class CollapsableTitledBorder extends TitledBorder {
+ JComponent component;
+ //Border border;
+
+ public CollapsableTitledBorder(JComponent component) {
+ this(null, component, LEFT, TOP);
+ }
+
+ public CollapsableTitledBorder(Border border) {
+ this(border, null, LEFT, TOP);
+ }
+
+ public CollapsableTitledBorder(Border border, JComponent component) {
+ this(border, component, LEFT, TOP);
+ }
+
+ public CollapsableTitledBorder(Border border, JComponent component, int titleJustification, int titlePosition) {
+ //TitledBorder needs border, title, justification, position, font, and color
+ super(border, null, titleJustification, titlePosition, null, null);
+ this.component = component;
+ if (border == null) {
+ this.border = super.getBorder();
+ }
+ }
+
+ public void paintBorder(Component c, Graphics g, int x, int y, int width, int height) {
+ Rectangle borderR = new Rectangle(x + EDGE_SPACING, y + EDGE_SPACING, width - (EDGE_SPACING * 2), height - (EDGE_SPACING * 2));
+ Insets borderInsets;
+ if (border != null) {
+ borderInsets = border.getBorderInsets(c);
+ } else {
+ borderInsets = new Insets(0, 0, 0, 0);
+ }
+
+ Rectangle rect = new Rectangle(x, y, width, height);
+ Insets insets = getBorderInsets(c);
+ Rectangle compR = getComponentRect(rect, insets);
+ int diff;
+ switch (titlePosition) {
+ case ABOVE_TOP:
+ diff = compR.height + TEXT_SPACING;
+ borderR.y += diff;
+ borderR.height -= diff;
+ break;
+ case TOP:
+ case DEFAULT_POSITION:
+ diff = insets.top / 2 - borderInsets.top - EDGE_SPACING;
+ borderR.y += diff;
+ borderR.height -= diff;
+ break;
+ case BELOW_TOP:
+ case ABOVE_BOTTOM:
+ break;
+ case BOTTOM:
+ diff = insets.bottom / 2 - borderInsets.bottom - EDGE_SPACING;
+ borderR.height -= diff;
+ break;
+ case BELOW_BOTTOM:
+ diff = compR.height + TEXT_SPACING;
+ borderR.height -= diff;
+ break;
+ }
+ border.paintBorder(c, g, borderR.x, borderR.y, borderR.width, borderR.height);
+ Color col = g.getColor();
+ g.setColor(c.getBackground());
+ g.fillRect(compR.x, compR.y, compR.width, compR.height);
+ g.setColor(col);
+ }
+
+ public Insets getBorderInsets(Component c, Insets insets) {
+ Insets borderInsets;
+ if (border != null) {
+ borderInsets = border.getBorderInsets(c);
+ } else {
+ borderInsets = new Insets(0, 0, 0, 0);
+ }
+ insets.top = EDGE_SPACING + TEXT_SPACING + borderInsets.top;
+ insets.right = EDGE_SPACING + TEXT_SPACING + borderInsets.right;
+ insets.bottom = EDGE_SPACING + TEXT_SPACING + borderInsets.bottom;
+ insets.left = EDGE_SPACING + TEXT_SPACING + borderInsets.left;
+
+ if (c == null || component == null) {
+ return insets;
+ }
+
+ int compHeight = component.getPreferredSize().height;
+
+ switch (titlePosition) {
+ case ABOVE_TOP:
+ insets.top += compHeight + TEXT_SPACING;
+ break;
+ case TOP:
+ case DEFAULT_POSITION:
+ insets.top += Math.max(compHeight, borderInsets.top) - borderInsets.top;
+ break;
+ case BELOW_TOP:
+ insets.top += compHeight + TEXT_SPACING;
+ break;
+ case ABOVE_BOTTOM:
+ insets.bottom += compHeight + TEXT_SPACING;
+ break;
+ case BOTTOM:
+ insets.bottom += Math.max(compHeight, borderInsets.bottom) - borderInsets.bottom;
+ break;
+ case BELOW_BOTTOM:
+ insets.bottom += compHeight + TEXT_SPACING;
+ break;
+ }
+ return insets;
+ }
+
+ public JComponent getTitleComponent() {
+ return component;
+ }
+
+ public void setTitleComponent(JComponent component) {
+ this.component = component;
+ }
+
+ public Rectangle getComponentRect(Rectangle rect, Insets borderInsets) {
+ Dimension compD = component.getPreferredSize();
+ Rectangle compR = new Rectangle(0, 0, compD.width, compD.height);
+ switch (titlePosition) {
+ case ABOVE_TOP:
+ compR.y = EDGE_SPACING;
+ break;
+ case TOP:
+ case DEFAULT_POSITION:
+ if (titleComponent instanceof JButton) {
+ compR.y = EDGE_SPACING + (borderInsets.top - EDGE_SPACING - TEXT_SPACING - compD.height) / 2;
+ } else if (titleComponent instanceof JRadioButton) {
+ compR.y = (borderInsets.top - EDGE_SPACING - TEXT_SPACING - compD.height) / 2;
+ }
+ break;
+ case BELOW_TOP:
+ compR.y = borderInsets.top - compD.height - TEXT_SPACING;
+ break;
+ case ABOVE_BOTTOM:
+ compR.y = rect.height - borderInsets.bottom + TEXT_SPACING;
+ break;
+ case BOTTOM:
+ compR.y = rect.height - borderInsets.bottom + TEXT_SPACING + (borderInsets.bottom - EDGE_SPACING - TEXT_SPACING - compD.height) / 2;
+ break;
+ case BELOW_BOTTOM:
+ compR.y = rect.height - compD.height - EDGE_SPACING;
+ break;
+ }
+ switch (titleJustification) {
+ case LEFT:
+ case DEFAULT_JUSTIFICATION:
+ //compR.x = TEXT_INSET_H + borderInsets.left;
+ compR.x = TEXT_INSET_H + borderInsets.left - EDGE_SPACING;
+ break;
+ case RIGHT:
+ compR.x = rect.width - borderInsets.right - TEXT_INSET_H - compR.width;
+ break;
+ case CENTER:
+ compR.x = (rect.width - compR.width) / 2;
+ break;
+ }
+ return compR;
+ }
+ }
+}
\ No newline at end of file
diff --git a/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/ui/ComboBoxTableCellRenderer.java b/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/ui/ComboBoxTableCellRenderer.java
new file mode 100644
index 0000000..cd30994
--- /dev/null
+++ b/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/ui/ComboBoxTableCellRenderer.java
@@ -0,0 +1,72 @@
+/* File: ComboBoxTableCellRenderer.java
+
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+
+package csplugins.network.merge.ui;
+
+import java.util.Vector;
+
+import javax.swing.JComboBox;
+import javax.swing.JTable;
+import javax.swing.table.TableCellRenderer;
+
+class ComboBoxTableCellRenderer extends JComboBox implements TableCellRenderer {
+
+ public ComboBoxTableCellRenderer(Object[] items) {
+ super(items);
+ }
+
+ public ComboBoxTableCellRenderer(Vector items) {
+ super(items);
+ }
+
+ public java.awt.Component getTableCellRendererComponent(JTable table, Object value,
+ boolean isSelected, boolean hasFocus, int row, int column) {
+ this.setSelectedItem(value);
+ if (isSelected) {
+
+ setForeground(table.getSelectionForeground());
+ setBackground(table.getSelectionBackground());
+
+ } else
+ {
+ setForeground(table.getForeground());
+ setBackground(table.getBackground());
+
+ }
+ return this;
+ }
+}
diff --git a/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/ui/IDMappingDialog.form b/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/ui/IDMappingDialog.form
new file mode 100644
index 0000000..5d61a03
--- /dev/null
+++ b/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/ui/IDMappingDialog.form
@@ -0,0 +1,152 @@
+<?xml version="1.0" encoding="UTF-8" ?>
+
+<Form version="1.5" maxVersion="1.7" type="org.netbeans.modules.form.forminfo.JDialogFormInfo">
+ <Properties>
+ <Property name="defaultCloseOperation" type="int" value="2"/>
+ <Property name="title" type="java.lang.String" value="ID Mapping Configuration"/>
+ </Properties>
+ <SyntheticProperties>
+ <SyntheticProperty name="formSizePolicy" type="int" value="1"/>
+ </SyntheticProperties>
+ <AuxValues>
+ <AuxValue name="FormSettings_autoResourcing" type="java.lang.Integer" value="0"/>
+ <AuxValue name="FormSettings_autoSetComponentName" type="java.lang.Boolean" value="false"/>
+ <AuxValue name="FormSettings_generateFQN" type="java.lang.Boolean" value="true"/>
+ <AuxValue name="FormSettings_generateMnemonicsCode" type="java.lang.Boolean" value="false"/>
+ <AuxValue name="FormSettings_i18nAutoMode" type="java.lang.Boolean" value="false"/>
+ <AuxValue name="FormSettings_layoutCodeTarget" type="java.lang.Integer" value="1"/>
+ <AuxValue name="FormSettings_listenerGenerationStyle" type="java.lang.Integer" value="0"/>
+ <AuxValue name="FormSettings_variablesLocal" type="java.lang.Boolean" value="false"/>
+ <AuxValue name="FormSettings_variablesModifier" type="java.lang.Integer" value="2"/>
+ <AuxValue name="designerSize" type="java.awt.Dimension" value="-84,-19,0,5,115,114,0,18,106,97,118,97,46,97,119,116,46,68,105,109,101,110,115,105,111,110,65,-114,-39,-41,-84,95,68,20,2,0,2,73,0,6,104,101,105,103,104,116,73,0,5,119,105,100,116,104,120,112,0,0,1,-69,0,0,1,-102"/>
+ </AuxValues>
+
+ <Layout class="org.netbeans.modules.form.compat2.layouts.DesignGridBagLayout"/>
+ <SubComponents>
+ <Container class="javax.swing.JPanel" name="idTypePanel">
+ <Properties>
+ <Property name="border" type="javax.swing.border.Border" editor="org.netbeans.modules.form.editors2.BorderEditor">
+ <Border info="org.netbeans.modules.form.compat2.border.TitledBorderInfo">
+ <TitledBorder title="Select ID type(s) for each attribute"/>
+ </Border>
+ </Property>
+ </Properties>
+ <AuxValues>
+ <AuxValue name="JavaCodeGenerator_DeclarationPost" type="java.lang.String" value="private IDTypeSelectionTable idTypeSelectionTable;"/>
+ </AuxValues>
+ <Constraints>
+ <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignGridBagLayout" value="org.netbeans.modules.form.compat2.layouts.DesignGridBagLayout$GridBagConstraintsDescription">
+ <GridBagConstraints gridX="0" gridY="0" gridWidth="1" gridHeight="1" fill="1" ipadX="0" ipadY="0" insetsTop="5" insetsLeft="5" insetsBottom="5" insetsRight="5" anchor="10" weightX="1.0" weightY="1.0"/>
+ </Constraint>
+ </Constraints>
+
+ <Layout class="org.netbeans.modules.form.compat2.layouts.DesignBoxLayout"/>
+ <SubComponents>
+ <Container class="javax.swing.JScrollPane" name="idTypeScrollPane">
+ <Properties>
+ <Property name="minimumSize" type="java.awt.Dimension" editor="org.netbeans.beaninfo.editors.DimensionEditor">
+ <Dimension value="[450, 200]"/>
+ </Property>
+ <Property name="preferredSize" type="java.awt.Dimension" editor="org.netbeans.beaninfo.editors.DimensionEditor">
+ <Dimension value="[500, 300]"/>
+ </Property>
+ </Properties>
+ <AuxValues>
+ <AuxValue name="JavaCodeGenerator_LayoutCodePost" type="java.lang.String" value="idTypeSelectionTable = new IDTypeSelectionTable(frame,this);
//idTypeSelectionTable.setMinimumSize(new java.awt.Dimension(400, 100));
//idTypeSelectionTable.setPreferredSize(new java.awt.Dimension(450, 200));
idTypeSelectionTable.setSupportedSrcIDType(cythesaurusClient.supportedSrcIDTypes());
idTypeScrollPane.setViewportView(idTypeSelectionTable);"/>
+ </AuxValues>
+
+ <Layout class="org.netbeans.modules.form.compat2.layouts.support.JScrollPaneSupportLayout"/>
+ </Container>
+ </SubComponents>
+ </Container>
+ <Container class="javax.swing.JPanel" name="toPanel">
+ <AuxValues>
+ <AuxValue name="JavaCodeGenerator_VariableLocal" type="java.lang.Boolean" value="true"/>
+ <AuxValue name="JavaCodeGenerator_VariableModifier" type="java.lang.Integer" value="0"/>
+ </AuxValues>
+ <Constraints>
+ <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignGridBagLayout" value="org.netbeans.modules.form.compat2.layouts.DesignGridBagLayout$GridBagConstraintsDescription">
+ <GridBagConstraints gridX="0" gridY="1" gridWidth="1" gridHeight="1" fill="0" ipadX="0" ipadY="0" insetsTop="5" insetsLeft="5" insetsBottom="5" insetsRight="5" anchor="21" weightX="0.0" weightY="0.0"/>
+ </Constraint>
+ </Constraints>
+
+ <Layout class="org.netbeans.modules.form.compat2.layouts.DesignFlowLayout">
+ <Property name="alignment" type="int" value="0"/>
+ <Property name="horizontalGap" type="int" value="10"/>
+ </Layout>
+ <SubComponents>
+ <Component class="javax.swing.JLabel" name="toLabel">
+ <Properties>
+ <Property name="text" type="java.lang.String" value="Destination ID Type:"/>
+ </Properties>
+ </Component>
+ <Component class="javax.swing.JComboBox" name="toComboBox">
+ <AuxValues>
+ <AuxValue name="JavaCodeGenerator_InitCodePre" type="java.lang.String" value="String[] types = cythesaurusClient.supportedTgtIDTypes().toArray(new String[0]);
java.util.Arrays.sort(types);
toComboBox.setModel(new javax.swing.DefaultComboBoxModel(types));"/>
+ <AuxValue name="JavaCodeGenerator_SerializeTo" type="java.lang.String" value="NetworkMergeDialog_matchNodeComboBox"/>
+ </AuxValues>
+ </Component>
+ </SubComponents>
+ </Container>
+ <Container class="javax.swing.JPanel" name="optionPanel">
+ <Constraints>
+ <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignGridBagLayout" value="org.netbeans.modules.form.compat2.layouts.DesignGridBagLayout$GridBagConstraintsDescription">
+ <GridBagConstraints gridX="0" gridY="2" gridWidth="1" gridHeight="1" fill="0" ipadX="0" ipadY="0" insetsTop="5" insetsLeft="5" insetsBottom="5" insetsRight="5" anchor="21" weightX="1.0" weightY="0.0"/>
+ </Constraint>
+ </Constraints>
+
+ <Layout class="org.netbeans.modules.form.compat2.layouts.DesignBoxLayout"/>
+ <SubComponents>
+ <Component class="javax.swing.JButton" name="optionButton">
+ <Properties>
+ <Property name="text" type="java.lang.String" value="Configure ID Mapping Resources"/>
+ <Property name="toolTipText" type="java.lang.String" value="Click to set up options"/>
+ </Properties>
+ <Events>
+ <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="optionButtonActionPerformed"/>
+ </Events>
+ <AuxValues>
+ <AuxValue name="JavaCodeGenerator_DeclarationPost" type="java.lang.String" value="//private NetworkMergeOptionDialog optionDialog;"/>
+ <AuxValue name="JavaCodeGenerator_InitCodePre" type="java.lang.String" value="//optionDialog = new NetworkMergeOptionDialog(frame,true);
//optionDialog.pack();"/>
+ </AuxValues>
+ </Component>
+ </SubComponents>
+ </Container>
+ <Container class="javax.swing.JPanel" name="okPanel">
+ <AuxValues>
+ <AuxValue name="JavaCodeGenerator_VariableLocal" type="java.lang.Boolean" value="true"/>
+ <AuxValue name="JavaCodeGenerator_VariableModifier" type="java.lang.Integer" value="0"/>
+ </AuxValues>
+ <Constraints>
+ <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignGridBagLayout" value="org.netbeans.modules.form.compat2.layouts.DesignGridBagLayout$GridBagConstraintsDescription">
+ <GridBagConstraints gridX="0" gridY="2" gridWidth="1" gridHeight="1" fill="0" ipadX="0" ipadY="0" insetsTop="0" insetsLeft="0" insetsBottom="0" insetsRight="0" anchor="22" weightX="0.0" weightY="0.0"/>
+ </Constraint>
+ </Constraints>
+
+ <Layout class="org.netbeans.modules.form.compat2.layouts.DesignFlowLayout"/>
+ <SubComponents>
+ <Component class="javax.swing.JButton" name="okButton">
+ <Properties>
+ <Property name="text" type="java.lang.String" value=" OK "/>
+ <Property name="enabled" type="boolean" value="false"/>
+ </Properties>
+ <Events>
+ <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="okButtonActionPerformed"/>
+ </Events>
+ </Component>
+ <Component class="javax.swing.JButton" name="cancelButton">
+ <Properties>
+ <Property name="text" type="java.lang.String" value="Cancel"/>
+ </Properties>
+ <Events>
+ <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="cancelButtonActionPerformed"/>
+ </Events>
+ <AuxValues>
+ <AuxValue name="JavaCodeGenerator_VariableLocal" type="java.lang.Boolean" value="true"/>
+ <AuxValue name="JavaCodeGenerator_VariableModifier" type="java.lang.Integer" value="0"/>
+ </AuxValues>
+ </Component>
+ </SubComponents>
+ </Container>
+ </SubComponents>
+</Form>
diff --git a/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/ui/IDMappingDialog.java b/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/ui/IDMappingDialog.java
new file mode 100644
index 0000000..7d2c7de
--- /dev/null
+++ b/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/ui/IDMappingDialog.java
@@ -0,0 +1,315 @@
+/* File: AttributeBasedIDMappingDialog.java
+
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+package csplugins.network.merge.ui;
+
+import cytoscape.cythesaurus.service.CyThesaurusServiceClient;
+import cytoscape.cythesaurus.service.CyThesaurusServiceMessageBasedClient;
+
+import java.util.Set;
+import java.util.HashSet;
+import java.util.Map;
+import java.util.HashMap;
+import java.util.Iterator;
+
+import java.awt.Frame;
+
+/**
+ *
+ * @author gjj
+ */
+public class IDMappingDialog extends javax.swing.JDialog {
+
+ /** Creates new form AttributeBasedIDMappingDialog */
+ public IDMappingDialog(java.awt.Frame parent,
+ boolean modal,
+ Map<String,Set<String>> selectedNetworkAttribute,
+ boolean isNode) {
+ super(parent, modal);
+ this.frame = parent;
+ this.isNode = isNode;
+
+ initSrcTypes(selectedNetworkAttribute);
+
+ cancelled = true;
+
+ cythesaurusClient = new CyThesaurusServiceMessageBasedClient("AdvencedNetworkMerge");
+
+ initComponents();
+ }
+
+ // initialize selectedNetworkAttributeIDType
+ private void initSrcTypes(Map<String,Set<String>> selectedNetworkAttribute) {
+ selectedNetworkAttributeIDType = new HashMap<String,Map<String,Set<String>>>();
+ Iterator<Map.Entry<String,Set<String>>> itEntry = selectedNetworkAttribute.entrySet().iterator();
+ while (itEntry.hasNext()) {
+ Map.Entry<String,Set<String>> entry = itEntry.next();
+ String netID = entry.getKey();
+ Map<String,Set<String>> mapAttributeIDType = new HashMap<String,Set<String>>();
+ selectedNetworkAttributeIDType.put(netID, mapAttributeIDType);
+
+ Iterator<String> itAttr = entry.getValue().iterator();
+ while (itAttr.hasNext()) {
+ String attr = itAttr.next();
+ Set<String> types = new HashSet<String>();
+ mapAttributeIDType.put(attr, types);
+ }
+
+ }
+ }
+
+ /** This method is called from within the constructor to
+ * initialize the form.
+ * WARNING: Do NOT modify this code. The content of this method is
+ * always regenerated by the Form Editor.
+ */
+ private void initComponents() {
+ java.awt.GridBagConstraints gridBagConstraints;
+
+ idTypePanel = new javax.swing.JPanel();
+ idTypeScrollPane = new javax.swing.JScrollPane();
+ javax.swing.JPanel toPanel = new javax.swing.JPanel();
+ toLabel = new javax.swing.JLabel();
+ toComboBox = new javax.swing.JComboBox();
+ optionPanel = new javax.swing.JPanel();
+ optionButton = new javax.swing.JButton();
+ javax.swing.JPanel okPanel = new javax.swing.JPanel();
+ okButton = new javax.swing.JButton();
+ javax.swing.JButton cancelButton = new javax.swing.JButton();
+
+ setDefaultCloseOperation(javax.swing.WindowConstants.DISPOSE_ON_CLOSE);
+ setTitle("ID Mapping Configuration");
+ getContentPane().setLayout(new java.awt.GridBagLayout());
+
+ idTypePanel.setBorder(javax.swing.BorderFactory.createTitledBorder("Select ID type(s) for each attribute"));
+ idTypePanel.setLayout(new javax.swing.BoxLayout(idTypePanel, javax.swing.BoxLayout.LINE_AXIS));
+
+ idTypeScrollPane.setMinimumSize(new java.awt.Dimension(450, 200));
+ idTypeScrollPane.setPreferredSize(new java.awt.Dimension(500, 300));
+
+ idTypeSelectionTable = new IDTypeSelectionTable(frame,this);
+ //idTypeSelectionTable.setMinimumSize(new java.awt.Dimension(400, 100));
+ //idTypeSelectionTable.setPreferredSize(new java.awt.Dimension(450, 200));
+ idTypeSelectionTable.setSupportedSrcIDType(cythesaurusClient.supportedSrcIDTypes());
+ idTypeScrollPane.setViewportView(idTypeSelectionTable);
+
+ idTypePanel.add(idTypeScrollPane);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 0;
+ gridBagConstraints.gridy = 0;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.BOTH;
+ gridBagConstraints.weightx = 1.0;
+ gridBagConstraints.weighty = 1.0;
+ gridBagConstraints.insets = new java.awt.Insets(5, 5, 5, 5);
+ getContentPane().add(idTypePanel, gridBagConstraints);
+
+ toPanel.setLayout(new java.awt.FlowLayout(java.awt.FlowLayout.LEFT, 10, 5));
+
+ toLabel.setText("Destination ID Type:");
+ toPanel.add(toLabel);
+
+ String[] types = cythesaurusClient.supportedTgtIDTypes().toArray(new String[0]);
+ java.util.Arrays.sort(types);
+ toComboBox.setModel(new javax.swing.DefaultComboBoxModel(types));
+ toPanel.add(toComboBox);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 0;
+ gridBagConstraints.gridy = 1;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.LINE_START;
+ gridBagConstraints.insets = new java.awt.Insets(5, 5, 5, 5);
+ getContentPane().add(toPanel, gridBagConstraints);
+
+ optionPanel.setLayout(new javax.swing.BoxLayout(optionPanel, javax.swing.BoxLayout.LINE_AXIS));
+
+ //optionDialog = new NetworkMergeOptionDialog(frame,true);
+ //optionDialog.pack();
+ optionButton.setText("Configure ID Mapping Resources");
+ optionButton.setToolTipText("Click to set up options");
+ optionButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ optionButtonActionPerformed(evt);
+ }
+ });
+ optionPanel.add(optionButton);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 0;
+ gridBagConstraints.gridy = 2;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.LINE_START;
+ gridBagConstraints.weightx = 1.0;
+ gridBagConstraints.insets = new java.awt.Insets(5, 5, 5, 5);
+ getContentPane().add(optionPanel, gridBagConstraints);
+
+ okButton.setText(" OK ");
+ okButton.setEnabled(false);
+ okButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ okButtonActionPerformed(evt);
+ }
+ });
+ okPanel.add(okButton);
+
+ cancelButton.setText("Cancel");
+ cancelButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ cancelButtonActionPerformed(evt);
+ }
+ });
+ okPanel.add(cancelButton);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 0;
+ gridBagConstraints.gridy = 2;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.LINE_END;
+ getContentPane().add(okPanel, gridBagConstraints);
+
+ pack();
+ }// </editor-fold>//GEN-END:initComponents
+
+ private void optionButtonActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_optionButtonActionPerformed
+ CyThesaurusServiceClient client = new CyThesaurusServiceMessageBasedClient("AdvancedNetworkMerge");
+ if (!client.openMappingResourceConfigDialog()) {
+ //javax.swing.JOptionPane.showMessageDialog(this, "Failed to open the configuration dialog.");
+ } else {
+ Set<String> srcTypes = cythesaurusClient.supportedSrcIDTypes();
+ for (Map<String,Set<String>> mapAttrTypes : selectedNetworkAttributeIDType.values()) {
+ for (Set<String> types : mapAttrTypes.values()) {
+ types.retainAll(srcTypes);
+ }
+ }
+ idTypeSelectionTable.setSupportedSrcIDType(srcTypes);
+
+ String[] tgtTypes = cythesaurusClient.supportedTgtIDTypes().toArray(new String[0]);
+ java.util.Arrays.sort(tgtTypes);
+ String oldType = (String)toComboBox.getSelectedItem();
+ toComboBox.setModel(new javax.swing.DefaultComboBoxModel(tgtTypes));
+ toComboBox.setSelectedItem(oldType);
+ }
+ }//GEN-LAST:event_optionButtonActionPerformed
+
+ private void okButtonActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_okButtonActionPerformed
+ cancelled = false;
+ this.setVisible(false);
+ this.dispose();
+}//GEN-LAST:event_okButtonActionPerformed
+
+ private void cancelButtonActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_cancelButtonActionPerformed
+ this.setVisible(false);
+ this.dispose();
+ }//GEN-LAST:event_cancelButtonActionPerformed
+
+ public Map<String,Map<String,Set<String>>> getSrcTypes() {
+ return selectedNetworkAttributeIDType;
+ }
+
+ void updateGoButtonEnable() {
+
+ if (getTgtType()==null) {
+ okButton.setToolTipText("No target ID type available");
+ okButton.setEnabled(false);
+ return;
+ }
+
+ Iterator<String> itNet = selectedNetworkAttributeIDType.keySet().iterator();
+ while (itNet.hasNext()) {
+ String network = itNet.next();
+ Map<String,Set<String>> mapAttrIDType = selectedNetworkAttributeIDType.get(network);
+ Iterator<Set<String>> itTypes = mapAttrIDType.values().iterator();
+ while (itTypes.hasNext()) {
+ if (itTypes.next().isEmpty()) {
+ okButton.setToolTipText("Select at least one ID type for each attribute");
+ okButton.setEnabled(false);
+ return;
+ }
+ }
+ }
+
+
+ okButton.setToolTipText(null);
+ okButton.setEnabled(true);
+ }
+
+ public String getTgtType() {
+ if (toComboBox.getItemCount()==0) {
+ return null;
+ }
+
+ return (String)toComboBox.getSelectedItem();
+ }
+
+ public void setTgtType(String type) {
+ if (type==null)
+ return;
+
+ toComboBox.setSelectedItem(type);
+ }
+
+public boolean isCancelled() {
+ return cancelled;
+}
+
+//void setOKButtonEnable() {
+// if (idMapping.isEmpty()) {
+// okButton.setEnabled(false);
+// okButton.setToolTipText("No ID mapping has been imported.");
+// } else {
+// okButton.setEnabled(true);
+// okButton.setToolTipText(null);
+// }
+//}
+
+
+ // Variables declaration - do not modify//GEN-BEGIN:variables
+ private javax.swing.JPanel idTypePanel;
+ private IDTypeSelectionTable idTypeSelectionTable;
+ private javax.swing.JScrollPane idTypeScrollPane;
+ private javax.swing.JButton okButton;
+ private javax.swing.JButton optionButton;
+ //private NetworkMergeOptionDialog optionDialog;
+ private javax.swing.JPanel optionPanel;
+ private javax.swing.JComboBox toComboBox;
+ private javax.swing.JLabel toLabel;
+ // End of variables declaration//GEN-END:variables
+
+ private boolean cancelled;
+ private Frame frame;
+ private boolean isNode;
+
+ private Map<String,Map<String,Set<String>>> selectedNetworkAttributeIDType;
+ private CyThesaurusServiceClient cythesaurusClient;
+}
diff --git a/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/ui/IDTypeSelectionTable.java b/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/ui/IDTypeSelectionTable.java
new file mode 100644
index 0000000..c6f8628
--- /dev/null
+++ b/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/ui/IDTypeSelectionTable.java
@@ -0,0 +1,394 @@
+/* File: IDTypeSelectionTable.java
+
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+package csplugins.network.merge.ui;
+
+import cytoscape.Cytoscape;
+
+import java.util.List;
+import java.util.Vector;
+import java.util.Iterator;
+import java.util.Map;
+import java.util.Set;
+import java.util.TreeSet;
+
+import javax.swing.JTable;
+import javax.swing.table.AbstractTableModel;
+
+import java.awt.Component;
+import java.awt.Frame;
+import java.awt.Color;
+import java.awt.event.ActionEvent;
+
+import javax.swing.JLabel;
+import javax.swing.JCheckBox;
+import javax.swing.JComboBox;
+import javax.swing.JList;
+import javax.swing.ListCellRenderer;
+import javax.swing.table.TableColumn;
+import javax.swing.DefaultCellEditor;
+import javax.swing.DefaultListCellRenderer;
+import javax.swing.table.TableCellRenderer;
+import javax.swing.table.DefaultTableCellRenderer;
+
+/**
+ * Table for selecting which attribute to use for matching nodes
+ *
+ *
+ */
+public class IDTypeSelectionTable extends JTable{
+ private IDTypeSelectionTableModel model;
+ private Frame frame;
+ private IDMappingDialog parent;
+
+ private Set<String> supportedSrcIDType;
+
+ private List<String[]> listNetIDTitleAttr;
+
+ public IDTypeSelectionTable(final Frame frame,
+ final IDMappingDialog parent) {
+ super();
+
+ this.frame = frame;
+ this.parent = parent;
+
+ initNetworks();
+
+ supportedSrcIDType = new TreeSet<String>();
+
+ model = new IDTypeSelectionTableModel();
+ setModel(model);
+ setRowHeight(20);
+
+ setColumnEditorAndCellRenderer();
+
+ }
+
+ public void setSupportedSrcIDType(final Set<String> types) {
+ supportedSrcIDType = new TreeSet<String>(types);
+ model = new IDTypeSelectionTableModel();
+ setModel(model);
+ setColumnEditorAndCellRenderer();
+ }
+
+ protected void setColumnEditorAndCellRenderer() {
+ int nc = getColumnCount();
+ TableColumn column = getColumnModel().getColumn(nc-1);
+
+ // set up editor
+ RowTableCellEditor rowEditor = new RowTableCellEditor(this);
+ int nr = this.getRowCount();
+ List<CheckComboBox> combos = new Vector<CheckComboBox>(nr);
+ for (int ir=0; ir<nr; ir++) {
+ String net = this.getNetIDAt(ir);
+ String attr = (String) this.getValueAt(ir, 1);
+ CheckComboBox cc = new CheckComboBox(net,attr);
+ combos.add(cc);
+ rowEditor.setEditorAt(ir, new DefaultCellEditor(cc));
+ }
+ column.setCellEditor(rowEditor);
+
+ // set up renderer
+ if (supportedSrcIDType.isEmpty()) {
+ column.setCellRenderer(new TableCellRenderer() {
+ private DefaultTableCellRenderer defaultRenderer = new DefaultTableCellRenderer();
+
+ //@Override
+ public java.awt.Component getTableCellRendererComponent(JTable table, Object value,
+ boolean isSelected, boolean hasFocus, int row, int column) {
+ JLabel label = (JLabel) defaultRenderer.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
+ if (isSelected) {
+ label.setBackground(table.getSelectionBackground());
+ label.setForeground(table.getSelectionForeground());
+ } else {
+ label.setBackground(table.getBackground());
+ label.setForeground(table.getForeground());
+ }
+ label.setToolTipText("Please select a non-empty ID mapping file first.");
+ return label;
+ }
+ });
+ } else {
+ column.setCellRenderer(new ComboBoxTableCellRenderer(combos));
+ }
+ }
+
+ private void initNetworks() {
+ Map<String,Map<String,Set<String>>> selectedNetworkAttributeIDType = parent.getSrcTypes();
+
+ List<String> netTitles = new Vector<String>();
+ List<String> netIDs = new Vector<String>();
+ int size=0;
+ Iterator<String> it = selectedNetworkAttributeIDType.keySet().iterator();
+ while (it.hasNext()) {
+ String netID = it.next();
+ String netName = Cytoscape.getNetwork(netID).getTitle();
+ int index = 0;
+ while (index<size && netTitles.get(index).compareToIgnoreCase(netName)<0) index++;
+
+ netIDs.add(index,netID);
+ netTitles.add(index,netName);
+ size++;
+ }
+
+ listNetIDTitleAttr = new Vector<String[]>();
+
+ int n = netIDs.size();
+ for (int i=0; i<n; i++) {
+ String id = netIDs.get(i);
+ Iterator<String> itAttr = selectedNetworkAttributeIDType.get(id).keySet().iterator();
+ while (itAttr.hasNext()) {
+ String attr = itAttr.next();
+ listNetIDTitleAttr.add(new String[]{id,netTitles.get(i),attr});
+ }
+ }
+ }
+
+ private String getNetIDAt(int row) {
+ String[] strs = listNetIDTitleAttr.get(row);
+ String netID = strs[0];
+ return netID;
+ }
+
+ void fireTableDataChanged() {
+ model.fireTableDataChanged();
+ }
+
+ private class IDTypeSelectionTableModel extends AbstractTableModel {
+ private final String[] columnNames = {"Network","Attribute","ID Type(s)"};
+
+ //@Override
+ public int getColumnCount() {
+ return getRowCount()==0?0:3; // network; attribute; id types
+ }
+
+ //@Override
+ public int getRowCount() {
+ return listNetIDTitleAttr.size();
+ }
+
+ @Override
+ public String getColumnName(int col) {
+ return columnNames[col];
+ }
+
+ //@Override
+ public String getValueAt(int row, int col) {
+ String[] strs = listNetIDTitleAttr.get(row);
+ String netID = strs[0];
+ String netTitle = strs[1];
+ String attr = strs[2];
+ switch (col) {
+ case 0:
+ return netTitle;
+ case 1:
+ return attr;
+ case 2:
+ return parent.getSrcTypes().get(netID).get(attr).toString();
+ default:
+ throw new java.lang.IndexOutOfBoundsException();
+ }
+ }
+
+ @Override
+ public Class getColumnClass(int c) {
+ return String.class;
+ }
+
+ @Override
+ public boolean isCellEditable(int row, int col) {
+ return col==this.getColumnCount()-1 && !supportedSrcIDType.isEmpty();
+ }
+
+ }
+
+
+ // render checkcombobox
+ class ComboBoxTableCellRenderer implements TableCellRenderer {
+ private List<CheckComboBox> combos;
+ public ComboBoxTableCellRenderer(List<CheckComboBox> combos) {
+ this.combos = combos;
+ }
+
+ //@Override
+ public java.awt.Component getTableCellRendererComponent(JTable table, Object value,
+ boolean isSelected, boolean hasFocus, int row, int column) {
+ if (column==table.getColumnCount()-1) {
+ return combos.get(row);
+ } else {
+ DefaultTableCellRenderer defaultRenderer = new DefaultTableCellRenderer();
+ return defaultRenderer.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
+ }
+ }
+ }
+
+ // combobox contains checkboxes
+ class CheckComboBox extends JComboBox {
+ private List<JCheckBox> cbs;
+ private String net;
+ private String attr;
+
+ public CheckComboBox(String net, String attr) {
+ //super(new JCheckBox[supportedSrcIDType.size()]);
+ this.net = net;
+ this.attr = attr;
+ initCBs();
+
+ this.addItem(new String());
+ for (JCheckBox cb : cbs) {
+ this.addItem(cb);
+ }
+
+ setRenderer(new CheckBoxRenderer(net,attr,cbs));
+ addActionListener(this);
+ }
+
+ private void initCBs() {
+ Set<String> selectedTypes = parent.getSrcTypes().get(net).get(attr);
+ cbs = new Vector<JCheckBox>();
+ JCheckBox cb;
+ for (String type : supportedSrcIDType) {
+ cb = new JCheckBox(type);
+ cb.setSelected(selectedTypes.contains(type));
+ cbs.add(cb);
+ }
+
+ cb = new JCheckBox("Select all");
+ cb.setSelected(selectedTypes.size()==supportedSrcIDType.size());
+ cbs.add(cb);
+
+ cb = new JCheckBox("Select none");
+ cb.setSelected(selectedTypes.isEmpty());
+ cbs.add(cb);
+ }
+
+ private void checkBoxSelectionChanged(int index) {
+ int n = cbs.size();
+ if (index<0 || index>=n) return;
+
+ Set<String> selectedTypes = parent.getSrcTypes().get(net).get(attr);
+ if (index<n-2) {
+ JCheckBox cb = cbs.get(index);
+ if (cb.isSelected()) {
+ cb.setSelected(false);
+ selectedTypes.remove(cb.getText());
+
+ cbs.get(n-2).setSelected(false); //Select all
+ cbs.get(n-1).setSelected(selectedTypes.isEmpty());
+ } else {
+ cb.setSelected(true);
+ selectedTypes.add(cb.getText());
+
+ cbs.get(n-2).setSelected(selectedTypes.size()==supportedSrcIDType.size()); // Select all
+ cbs.get(n-1).setSelected(false);
+ }
+ } else if (index==n-2) {
+ selectedTypes.addAll(supportedSrcIDType);
+ for (int i=0; i<n-1; i++) {
+ cbs.get(i).setSelected(true);
+ }
+ cbs.get(n-1).setSelected(false);
+ } else { // if (index==n-1)
+ selectedTypes.clear();
+ for (int i=0; i<n-1; i++) {
+ cbs.get(i).setSelected(false);
+ }
+ cbs.get(n-1).setSelected(true);
+ }
+
+ parent.updateGoButtonEnable();
+ }
+
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ int sel = getSelectedIndex();
+
+ if (sel == 0) {
+ getUI().setPopupVisible(this, false);
+ } else if (sel > 0) {
+ checkBoxSelectionChanged(sel-1);
+ }
+
+ this.setSelectedIndex(-1); // clear selection
+ }
+
+ @Override
+ public void setPopupVisible(boolean flag)
+ {
+ //TODO this not work, fix it
+ // Not code here prevents the populist from closing
+ }
+ }
+
+ // checkbox renderer for combobox
+ class CheckBoxRenderer implements ListCellRenderer {
+ private DefaultListCellRenderer defaultRenderer = new DefaultListCellRenderer();
+ private List<JCheckBox> cbs;
+ private String net;
+ private String attr;
+
+ public CheckBoxRenderer(String net, String attr, List<JCheckBox> cbs) {
+ setOpaque(true);
+ this.cbs = cbs;
+ this.net = net;
+ this.attr = attr;
+ }
+
+ //@Override
+ public Component getListCellRendererComponent(
+ JList list,
+ Object value,
+ int index,
+ boolean isSelected,
+ boolean cellHasFocus) {
+ if (index > 0) {
+ JCheckBox cb = cbs.get(index-1);
+ cb.setBackground(isSelected ? Color.blue : Color.white);
+ cb.setForeground(isSelected ? Color.white : Color.black);
+
+ return cb;
+ }
+
+ Set<String> types = new TreeSet<String>(parent.getSrcTypes().get(net).get(attr));
+
+ return defaultRenderer.getListCellRendererComponent(list, types.toString(), index, isSelected, cellHasFocus);
+
+
+ }
+ }
+
+}
+
diff --git a/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/ui/MatchNodeTable.java b/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/ui/MatchNodeTable.java
new file mode 100644
index 0000000..e888fd9
--- /dev/null
+++ b/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/ui/MatchNodeTable.java
@@ -0,0 +1,171 @@
+/* File: MatchNodeTable.java
+
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+package csplugins.network.merge.ui;
+
+import csplugins.network.merge.model.MatchingAttribute;
+
+import cytoscape.Cytoscape;
+
+import java.util.Vector;
+import java.util.TreeSet;
+import java.util.Iterator;
+import java.util.Arrays;
+
+import javax.swing.JTable;
+import javax.swing.table.AbstractTableModel;
+import javax.swing.table.TableColumn;
+import javax.swing.DefaultCellEditor;
+import javax.swing.JComboBox;
+
+/**
+ * Table for selecting which attribute to use for matching nodes
+ *
+ */
+class MatchNodeTable extends JTable{
+ private MatchingAttribute matchingAttribute;
+ private MatchNodeTableModel model;
+
+ public MatchNodeTable(MatchingAttribute matchingAttribute) {
+ super();
+ this.matchingAttribute = matchingAttribute;
+ model = new MatchNodeTableModel();
+ setModel(model);
+ setRowHeight(20);
+ }
+
+ protected void setColumnEditorAndCellRenderer() {
+ TreeSet<String> attrset = new TreeSet<String>();
+ //TODO remove in Cytoscape3
+ attrset.add("ID");
+ //TODO: modify if local attribute implemented
+ attrset.addAll(Arrays.asList(Cytoscape.getNodeAttributes().getAttributeNames()));
+
+ String[] attrs = attrset.toArray(new String[0]);
+
+ int n = getColumnCount();
+ for (int i=0; i<n; i++) {
+ TableColumn column = getColumnModel().getColumn(i);
+
+ JComboBox comboBox = new JComboBox(attrs);
+ column.setCellEditor(new DefaultCellEditor(comboBox));
+
+ ComboBoxTableCellRenderer comboRenderer = new ComboBoxTableCellRenderer(attrs);
+ column.setCellRenderer(comboRenderer);
+ }
+ }
+
+ public void fireTableStructureChanged() {
+ model.fireTableStructureChanged();
+ setColumnEditorAndCellRenderer();
+ //setCellRenderer();
+ }
+
+ private class MatchNodeTableModel extends AbstractTableModel {
+ Vector<String> netNames;
+ Vector<String> netIDs;
+
+ public MatchNodeTableModel() {
+ resetNetworks();
+ }
+
+ //@Override
+ public int getColumnCount() {
+ return matchingAttribute.getSizeNetwork();
+ }
+
+ //@Override
+ public int getRowCount() {
+ int n = matchingAttribute.getSizeNetwork();
+ return n==0?0:1;
+ }
+
+ @Override
+ public String getColumnName(int col) {
+ return netNames.get(col);
+ }
+
+ //@Override
+ public Object getValueAt(int row, int col) {
+ return matchingAttribute.getAttributeForMatching(netIDs.get(col));
+ }
+
+ @Override
+ public Class getColumnClass(int c) {
+ //return JComboBox.class;
+ return String.class;
+ }
+
+ @Override
+ public boolean isCellEditable(int row, int col) {
+ return true;
+ }
+
+ @Override
+ public void setValueAt(Object value, int row, int col) {
+ if (value!=null);
+ matchingAttribute.putAttributeForMatching(netIDs.get(col), (String)value);
+ fireTableDataChanged();
+ }
+
+ @Override
+ public void fireTableStructureChanged() {
+ resetNetworks();
+ super.fireTableStructureChanged();
+ }
+
+ private void resetNetworks() {
+ netNames = new Vector<String>();
+ netIDs = new Vector<String>();
+ int size=0;
+ Iterator<String> it = matchingAttribute.getNetworkSet().iterator();
+ while (it.hasNext()) {
+ String netID = it.next();
+ String netName = Cytoscape.getNetwork(netID).getTitle();
+ int index = 0;
+ while (index<size && netNames.get(index).compareToIgnoreCase(netName)<0) index++;
+
+ netIDs.add(index,netID);
+ netNames.add(index,netName);
+ size++;
+ }
+ }
+
+ }
+
+}
+
+
diff --git a/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/ui/MergeAttributeTable.java b/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/ui/MergeAttributeTable.java
new file mode 100644
index 0000000..5ac19fe
--- /dev/null
+++ b/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/ui/MergeAttributeTable.java
@@ -0,0 +1,677 @@
+/* File: MergeAttributeTable.java
+
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+package csplugins.network.merge.ui;
+
+import csplugins.network.merge.model.AttributeMapping;
+import csplugins.network.merge.model.MatchingAttribute;
+import csplugins.network.merge.util.AttributeValueCastUtils;
+
+import cytoscape.Cytoscape;
+import cytoscape.util.CyNetworkNaming;
+import cytoscape.data.Semantics;
+import cytoscape.data.CyAttributes;
+import cytoscape.data.CyAttributesUtils;
+
+import java.util.Set;
+import java.util.HashSet;
+import java.util.TreeSet;
+import java.util.Vector;
+import java.util.Iterator;
+import java.util.Arrays;
+import java.util.Map;
+import java.util.HashMap;
+import java.util.EventObject;
+
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseAdapter;
+import java.awt.Component;
+import java.awt.Color;
+
+import javax.swing.JLabel;
+import javax.swing.JTable;
+import javax.swing.table.AbstractTableModel;
+import javax.swing.JOptionPane;
+import javax.swing.table.JTableHeader;
+import javax.swing.JComboBox;
+import javax.swing.table.TableColumn;
+import javax.swing.DefaultCellEditor;
+import javax.swing.table.TableCellEditor;
+import javax.swing.table.TableCellRenderer;
+import javax.swing.table.DefaultTableCellRenderer;
+import javax.swing.JTextField;
+import javax.swing.event.CellEditorListener;
+
+/**
+ * Table for customizing attribute mapping from original netowrks
+ * to resulting network
+ *
+ *
+ */
+class MergeAttributeTable extends JTable{
+ private final String nullAttr = "[DELETE THIS]";
+ private MatchingAttribute matchingAttribute;
+ private AttributeMapping attributeMapping; //attribute mapping
+ private String mergedNetworkName;
+ private MergeAttributeTableModel model;
+ private boolean isNode;
+ private int indexMatchingAttr; // the index of matching attribute in the attribute mapping
+ // only used when isNode==true
+
+ public MergeAttributeTable(final AttributeMapping attributeMapping, final MatchingAttribute matchingAttribute) {
+ super();
+ isNode = true;
+ indexMatchingAttr = -1;
+ this.mergedNetworkName = CyNetworkNaming.getSuggestedNetworkTitle("Merged.Network");
+ this.attributeMapping = attributeMapping;
+ this.matchingAttribute = matchingAttribute;
+ model = new MergeAttributeTableModel();
+ setModel(model);
+ setRowHeight(20);
+ }
+
+ public MergeAttributeTable(final AttributeMapping attributeMapping) {
+ super();
+ this.mergedNetworkName = "Merged.Network";
+ this.attributeMapping = attributeMapping;
+ model = new MergeAttributeTableModel();
+ isNode = false;
+ setModel(model);
+ setRowHeight(20);
+ }
+
+ public String getMergedNetworkName() {
+ return mergedNetworkName;
+ }
+
+ protected void setColumnEditorAndRenderer() {
+ final TreeSet<String> attrset = new TreeSet<String>();
+ attrset.addAll(Arrays.asList(attributeMapping.getCyAttributes().getAttributeNames()));
+
+ final Vector<String> attrs = new Vector<String>(attrset);
+ attrs.add(nullAttr);
+
+ //final int nnet = attributeMapping.getSizeNetwork();
+
+ final int n = this.getColumnCount();//attributeMapping.getSizeNetwork();
+ for (int i=0; i<n; i++) { // for each network
+ final JComboBox comboBox = new JComboBox(attrs);
+ final TableColumn column = getColumnModel().getColumn(i);
+
+
+ if (this.isColumnOriginalNetwork(i)) {
+ column.setCellEditor(new DefaultCellEditor(comboBox));
+ column.setCellRenderer(new TableCellRenderer() {
+ private DefaultTableCellRenderer defaultRenderer = new DefaultTableCellRenderer();
+ private ComboBoxTableCellRenderer comboBoxRenderer = new ComboBoxTableCellRenderer(attrs);
+
+ //@Override
+ public Component getTableCellRendererComponent(
+ JTable table, Object value,
+ boolean isSelected, boolean hasFocus,
+ int row, int column) {
+
+ if (row<(isNode?3:2)) {//TODO Cytoscape3
+ JLabel label = (JLabel) defaultRenderer.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
+ label.setBackground(Color.LIGHT_GRAY);
+ if (row==2) {
+ label.setToolTipText("Change this in the matching node table above");
+ } else {
+ label.setToolTipText("Reserved by system");
+ }
+ return label;
+ } else {
+ Component renderer = comboBoxRenderer.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
+ if (isSelected) {
+ renderer.setForeground(table.getSelectionForeground());
+ renderer.setBackground(table.getSelectionBackground());
+ } else {
+ renderer.setForeground(table.getForeground());
+ renderer.setBackground(table.getBackground());
+ }
+ return renderer;
+ }
+ }
+ });
+
+ } else if (this.isColumnMergedNetwork(i)) {
+ column.setCellRenderer(new TableCellRenderer() {
+ private DefaultTableCellRenderer defaultRenderer = new DefaultTableCellRenderer();
+
+ //@Override
+ public Component getTableCellRendererComponent(
+ JTable table, Object value,
+ boolean isSelected, boolean hasFocus,
+ int row, int column) {
+
+ if (row<2) {
+ JLabel label = (JLabel) defaultRenderer.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
+ label.setBackground(Color.LIGHT_GRAY);
+ label.setToolTipText("Reserved by system");
+ if (isSelected) {
+ label.setForeground(table.getSelectionForeground());
+ } else {
+ label.setForeground(table.getForeground());
+ }
+ return label;
+ } else if (row>=table.getRowCount()-1) {
+ JLabel label = (JLabel) defaultRenderer.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
+ label.setBackground(Color.LIGHT_GRAY);
+ if (isSelected) {
+ label.setForeground(table.getSelectionForeground());
+ } else {
+ label.setForeground(table.getForeground());
+ }
+ return label;
+ } else {
+ if (isNode && row==2) {
+ JLabel label = (JLabel) defaultRenderer.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
+ label.setForeground(Color.RED);
+ if (isSelected) {
+ label.setBackground(table.getSelectionBackground());
+ } else {
+ label.setBackground(table.getBackground());
+ }
+ label.setToolTipText("CHANGE ME!");
+ return label;
+ } else {
+ JLabel label = (JLabel) defaultRenderer.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
+ label.setToolTipText("Double click to change");
+ if (isSelected) {
+ label.setForeground(table.getSelectionForeground());
+ label.setBackground(table.getSelectionBackground());
+ } else {
+ label.setForeground(table.getForeground());
+ label.setBackground(table.getBackground());
+ }
+ return label;
+ }
+ }
+ }
+ });
+ } else if (this.isColumnMergedType(i)) {
+ //set editor
+ RowTableCellEditor rowEditor = new RowTableCellEditor(this);
+ int nr = this.getRowCount();
+ //List<JComboBox> combos = new Vector<JComboBox>(nr); // save for render
+ @SuppressWarnings("unchecked") final Vector<String>[] cbvalues = new Vector[nr];
+ for (int ir=2; ir<nr-1; ir++) {
+ int iAttr = ir-2;
+
+ final Set<String> attrNames = new HashSet<String>(attributeMapping.getOriginalAttributeMap(iAttr).values());
+ final CyAttributes cyAttributes = attributeMapping.getCyAttributes();
+ final String attr_mc = AttributeValueCastUtils.getMostCompatibleAttribute(attrNames, cyAttributes);
+ final byte type_mc = attr_mc==null?CyAttributes.TYPE_STRING:cyAttributes.getType(attr_mc);
+
+ Vector<String> types = new Vector<String>();
+ types.add(CyAttributesUtils.toString(type_mc));
+ //if (type_mc>0) {
+ if (type_mc!=CyAttributes.TYPE_STRING) {
+ types.add(CyAttributesUtils.toString(CyAttributes.TYPE_STRING));
+ }
+ if (type_mc!=CyAttributes.TYPE_SIMPLE_LIST) {
+ types.add(CyAttributesUtils.toString(CyAttributes.TYPE_SIMPLE_LIST));
+ }
+ //}
+
+ cbvalues[ir] = types;
+
+ JComboBox cb = new JComboBox(types);
+ final byte type_curr = attributeMapping.getMergedAttributeType(iAttr);
+ cb.setSelectedItem(CyAttributesUtils.toString(type_curr));
+
+ rowEditor.setEditorAt(ir, new DefaultCellEditor(cb));
+ //combos.add(cb);
+ }
+ column.setCellEditor(rowEditor);
+
+ // set renderer
+ column.setCellRenderer(new TableCellRenderer() {
+ private DefaultTableCellRenderer defaultRenderer = new DefaultTableCellRenderer();
+ //private ComboBoxTableCellRenderer comboBoxRenderer = new ComboBoxTableCellRenderer(attrs);
+
+ //@Override
+ public Component getTableCellRendererComponent(
+ JTable table, Object value,
+ boolean isSelected, boolean hasFocus,
+ int row, int column) {
+
+ if (row<2) {
+ JLabel label = (JLabel) defaultRenderer.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
+ label.setBackground(Color.LIGHT_GRAY);
+ label.setToolTipText("Reserved by system");
+ if (isSelected) {
+ label.setForeground(table.getSelectionForeground());
+ } else {
+ label.setForeground(table.getForeground());
+ }
+ return label;
+ } else if (row>=table.getRowCount()-1) {
+ JLabel label = (JLabel) defaultRenderer.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
+ label.setBackground(Color.LIGHT_GRAY);
+ if (isSelected) {
+ label.setForeground(table.getSelectionForeground());
+ } else {
+ label.setForeground(table.getForeground());
+ }
+ return label;
+ } else {
+ if (!table.isCellEditable(row, column)) {
+ JLabel label = (JLabel) defaultRenderer.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
+ label.setBackground(Color.LIGHT_GRAY);
+ label.setToolTipText("Only types of new attribute are changeable");
+ if (isSelected) {
+ label.setForeground(table.getSelectionForeground());
+ } else {
+ label.setForeground(table.getForeground());
+ }
+ return label;
+ } else {
+ ComboBoxTableCellRenderer comboBoxRenderer = new ComboBoxTableCellRenderer(cbvalues[row]);
+ Component renderer = comboBoxRenderer.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
+ if (isSelected) {
+ renderer.setForeground(table.getSelectionForeground());
+ renderer.setBackground(table.getSelectionBackground());
+ } else {
+ renderer.setForeground(table.getForeground());
+ renderer.setBackground(table.getBackground());
+ }
+ return renderer;
+ }
+ }
+ }
+
+ });
+
+ }
+ }
+
+ }
+
+ protected void setMergedNetworkNameTableHeaderListener() {
+ getTableHeader().addMouseListener(new MouseAdapter() {
+ @Override
+ public void mouseClicked(MouseEvent e) {
+ JTableHeader header = (JTableHeader) e.getSource();
+ JTable table = header.getTable();
+ int columnIndex = header.columnAtPoint(e.getPoint());
+ if (columnIndex==attributeMapping.getSizeNetwork()) { // the merged network
+ String title = JOptionPane.showInputDialog(table.getParent(), "Input the title for the merged network");
+ if (title!=null && title.length()!=0) {
+ mergedNetworkName = title;
+ fireTableHeaderChanged();
+ } else {
+ fireTableHeaderChanged(); //TODO: this is just for remove the duplicate click event
+ // there should be better ways
+ }
+ }
+ }
+ });
+ }
+
+ public void fireTableStructureChanged() {
+ //pack();
+ model.fireTableStructureChanged();
+ setColumnEditorAndRenderer();
+ setMergedNetworkNameTableHeaderListener();
+ }
+
+ public void updateMatchingAttribute() {
+ if (!isNode) {
+ throw new java.lang.UnsupportedOperationException("updateMatchingAttribute is only supported for node table");
+ }
+
+ boolean update = false;
+ if (indexMatchingAttr==-1) {
+ indexMatchingAttr = 0;
+ String attr_merged = "Matching.Attribute";
+
+ //TODO: remove in Cytoscape3
+ Map<String, String> netAttrMap = new HashMap<String, String>(matchingAttribute.getNetAttrMap());
+ Iterator<Map.Entry<String, String>> it = netAttrMap.entrySet().iterator();
+ while (it.hasNext()) {
+ Map.Entry<String,String> entry = it.next();
+ String network = entry.getKey();
+ String attr = entry.getValue();
+ if (attr.compareTo("ID")==0) {
+ netAttrMap.put(network, Semantics.CANONICAL_NAME);
+ }
+ }//TODO: remove in Cytoscape3
+
+ attributeMapping.addAttributes(netAttrMap, attr_merged, indexMatchingAttr);
+ attributeMapping.setMergedAttributeType(indexMatchingAttr, CyAttributes.TYPE_SIMPLE_LIST);
+ update = true;
+ } else {
+ Set<String> networks = matchingAttribute.getNetworkSet();
+ Iterator<String> it = networks.iterator();
+ if (!it.hasNext()) { // empty
+ indexMatchingAttr = -1;
+ }
+
+ while (it.hasNext()) {
+ String network = it.next();
+ String attr = matchingAttribute.getAttributeForMatching(network);
+ if (attr.compareTo("ID")==0) {
+ attr = Semantics.CANONICAL_NAME;
+ }
+ String old = attributeMapping.setOriginalAttribute(network, attr, indexMatchingAttr);
+ if (attr.compareTo(old)!=0) {
+ update=true;
+ }
+ }
+ }
+
+ if (update) {
+ fireTableStructureChanged();
+ }
+ }
+
+ protected void fireTableHeaderChanged() {
+ model.fireTableStructureChanged();
+ //setCellRender();
+ setColumnEditorAndRenderer();
+ }
+
+ protected boolean isColumnOriginalNetwork(final int col) {
+ return col>=0 && col<attributeMapping.getSizeNetwork();
+ }
+
+ protected boolean isColumnMergedNetwork(final int col) {
+ return col==attributeMapping.getSizeNetwork();
+ }
+
+ protected boolean isColumnMergedType(final int col) {
+ return col==attributeMapping.getSizeNetwork()+1;
+ }
+
+
+ // table model
+ protected class MergeAttributeTableModel extends AbstractTableModel {
+ Vector<String> netNames; // network titles
+ Vector<String> netIDs; //network identifiers
+
+ public MergeAttributeTableModel() {
+ resetNetworks();
+ }
+
+ //@Override
+ public int getColumnCount() {
+ final int n = attributeMapping.getSizeNetwork();
+ return n==0?0:n+2;
+ }
+
+ //@Override
+ public int getRowCount() {
+ int n = attributeMapping.getSizeMergedAttributes();
+ //n = n+1; // +1: add an empty row in the end (TODO: use this one in Cytoscape3.0)
+ n = n+3; //TODO REMOVE in Cytoscape3.0
+ return attributeMapping.getSizeNetwork()==0?0:n;
+ }
+
+ @Override
+ public String getColumnName(final int col) {
+ if (isColumnMergedType(col)) {
+ return "Attribute type";
+ }
+
+ if (isColumnMergedNetwork(col)) {
+ return mergedNetworkName;
+ }
+
+ if (isColumnOriginalNetwork(col)){
+ return netNames.get(col);
+ }
+
+ return null;
+ }
+
+ //@Override
+ public String getValueAt(final int row, final int col) {
+ //final int iAttr = row; //TODO used in Cytoscape3
+
+ //TODO remove in Cytoscape3
+ if (row==0) {
+ return isColumnMergedType(col)?"String":"ID";
+ } else if (row==1) {
+ return isColumnMergedType(col)?"String":Semantics.CANONICAL_NAME;
+ }
+ final int iAttr = row - 2;
+ //TODO remove in Cytoscape3
+
+ if (row==getRowCount()-1) {
+ return null;
+ }
+
+ if (isColumnOriginalNetwork(col)) {
+ return attributeMapping.getOriginalAttribute(netIDs.get(col), iAttr);
+ }
+
+ if (isColumnMergedNetwork(col)) {
+ return attributeMapping.getMergedAttribute(iAttr);
+ }
+
+ if (isColumnMergedType(col)) {
+ byte type = attributeMapping.getMergedAttributeType(iAttr);
+ return CyAttributesUtils.toString(type);
+ }
+
+ return null;
+ }
+
+ @Override
+ public Class getColumnClass(final int c) {
+ return String.class;
+ }
+
+ @Override
+ public boolean isCellEditable(final int row, final int col) {
+ //TODO remove in Cytoscape3.0
+ if (row<2) return false;//TODO remove in Cytoscape3.0
+
+ if (isNode) { // make the matching attribute ineditable
+ if (row==2) { //TODO use row==0 in Cytoscape3
+ return !isColumnOriginalNetwork(col);
+ }
+ }
+
+ if (isColumnOriginalNetwork(col))
+ return true;
+
+ if (isColumnMergedNetwork(col)) {
+ return row!=getRowCount()-1;
+ }
+
+ if (isColumnMergedType(col)) {
+ String mergedAttribute = getValueAt(row,col-1);
+ CyAttributes attrs = attributeMapping.getCyAttributes();
+ return !Arrays.asList(attrs.getAttributeNames()).contains(mergedAttribute);// non-editable for existing attribute
+ }
+
+ return false;
+ }
+
+
+ @Override
+ public void setValueAt(final Object value, final int row, final int col) {
+ if (value==null) return;
+
+ final String v = (String) value;
+ final int iAttr = row-2;//TODO remove in Cytoscape3.0
+ //final int iAttr = row; //TODO use in Cytoscape3.0
+
+ final int n = attributeMapping.getSizeMergedAttributes();
+ if (iAttr>n) return; // should not happen
+
+ if (isColumnMergedType(col)) {
+ if (iAttr==n) return;
+
+ byte type = getByteFromValue(v);
+ byte type_curr = attributeMapping.getMergedAttributeType(iAttr);
+ if (type==type_curr) return;
+
+ attributeMapping.setMergedAttributeType(iAttr, type);
+
+ } else if (isColumnMergedNetwork(col)) { //column of merged network
+ if (iAttr==n) return;
+
+ String attr_curr = attributeMapping.getMergedAttribute(iAttr);
+ if (attr_curr.compareTo(v)==0) { //if the same
+ return;
+ }
+
+ //TODO remove in Cytoscape3.0
+ if (v.compareTo("ID")==0||v.compareTo(Semantics.CANONICAL_NAME)==0) {
+ JOptionPane.showMessageDialog(getParent(),"Atribute "+v+" is reserved! Please use another name for this attribute!", "Error: duplicated attribute Name", JOptionPane.ERROR_MESSAGE );
+ return;
+ }//TODO remove in Cytoscape3.0
+
+ if (v.length()==0) {
+ JOptionPane.showMessageDialog(getParent(),"Please use a non-empty name for the attribute!", "Error: empty attribute Name", JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+
+ if (attributeMapping.containsMergedAttribute(v)) {
+ JOptionPane.showMessageDialog(getParent(),"Atribute "+v+" is already exist! Please use another name for this attribute!", "Error: duplicated attribute Name", JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+
+ attributeMapping.setMergedAttribute(iAttr, v);
+ fireTableDataChanged();
+ return;
+ } else { //column of original network
+ String netID = netIDs.get(col);
+ if (iAttr==n) { // the last row
+ if (v.compareTo(nullAttr)==0) return;
+
+ String attr_merged = v;
+ //TODO remove in Cytoscape3
+ if (v.compareTo(Semantics.CANONICAL_NAME)==0) {
+ attr_merged = netID+"."+Semantics.CANONICAL_NAME;
+ }//TODO remove in Cytoscape3
+
+ Map<String,String> map = new HashMap<String,String>();
+ map.put(netID, v);
+
+ attributeMapping.addAttributes(map, attr_merged);
+ fireTableDataChanged();
+ return;
+
+ } else {
+ String curr_attr = attributeMapping.getOriginalAttribute(netID, iAttr);
+ if (curr_attr!=null && curr_attr.compareTo(v)==0) {
+ return;
+ }
+
+ if (v.compareTo(nullAttr)==0) {
+ if (curr_attr==null) return;
+ //if (attributeMapping.getOriginalAttribute(netID, iAttr)==null) return;
+ attributeMapping.removeOriginalAttribute(netID, iAttr);
+ } else {
+ String mergedAttr = attributeMapping.getMergedAttribute(iAttr);
+ CyAttributes cyAttributes = attributeMapping.getCyAttributes();
+ if (Arrays.asList(cyAttributes.getAttributeNames()).contains(mergedAttr)
+ && !AttributeValueCastUtils.isAttributeTypeConvertable(v,
+ mergedAttr,
+ cyAttributes)) {
+ final int ioption = JOptionPane.showConfirmDialog(getParent(),
+ "Atribute "+v+" have a type incompatible to the other attributes to be merged. Are you sure to select "+v+"? ",
+ "Warning: types are different",
+ JOptionPane.YES_NO_OPTION );
+ if (ioption==JOptionPane.NO_OPTION) {
+ return;
+ }
+ }
+
+ attributeMapping.setOriginalAttribute(netID, v, iAttr);// set the v
+ }
+ fireTableDataChanged();
+ return;
+ }
+ }
+ }
+
+ @Override
+ public void fireTableStructureChanged() {
+ resetNetworks();
+ super.fireTableStructureChanged();
+ }
+
+ private void resetNetworks() {
+ netNames = new Vector<String>();
+ netIDs = new Vector<String>();
+ int size=0;
+ Iterator<String> it = attributeMapping.getNetworkSet().iterator();
+ while (it.hasNext()) {
+ String netID = it.next();
+ String netName = Cytoscape.getNetwork(netID).getTitle();
+ int index = 0;
+ while (index<size && netNames.get(index).compareToIgnoreCase(netName)<0) index++;
+
+ netIDs.add(index,netID);
+ netNames.add(index,netName);
+ size++;
+ }
+ }
+ }
+
+ protected byte getByteFromValue(final String value) {
+ if (value.compareTo(CyAttributesUtils.toString(CyAttributes.TYPE_STRING))==0) {
+ return CyAttributes.TYPE_STRING;
+ }
+ if (value.compareTo(CyAttributesUtils.toString(CyAttributes.TYPE_SIMPLE_LIST))==0) {
+ return CyAttributes.TYPE_SIMPLE_LIST;
+ }
+ if (value.compareTo(CyAttributesUtils.toString(CyAttributes.TYPE_BOOLEAN))==0) {
+ return CyAttributes.TYPE_BOOLEAN;
+ }
+ if (value.compareTo(CyAttributesUtils.toString(CyAttributes.TYPE_COMPLEX))==0) {
+ return CyAttributes.TYPE_COMPLEX;
+ }
+ if (value.compareTo(CyAttributesUtils.toString(CyAttributes.TYPE_FLOATING))==0) {
+ return CyAttributes.TYPE_FLOATING;
+ }
+ if (value.compareTo(CyAttributesUtils.toString(CyAttributes.TYPE_INTEGER))==0) {
+ return CyAttributes.TYPE_INTEGER;
+ }
+ if (value.compareTo(CyAttributesUtils.toString(CyAttributes.TYPE_SIMPLE_MAP))==0) {
+ return CyAttributes.TYPE_SIMPLE_MAP;
+ }
+ return CyAttributes.TYPE_UNDEFINED;
+ }
+
+}
+
+
diff --git a/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/ui/NetworkMergeFrame.form b/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/ui/NetworkMergeFrame.form
new file mode 100644
index 0000000..7051e5e
--- /dev/null
+++ b/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/ui/NetworkMergeFrame.form
@@ -0,0 +1,582 @@
+<?xml version="1.0" encoding="UTF-8" ?>
+
+<Form version="1.5" maxVersion="1.6" type="org.netbeans.modules.form.forminfo.JFrameFormInfo">
+ <Properties>
+ <Property name="title" type="java.lang.String" value="Network Merge"/>
+ </Properties>
+ <SyntheticProperties>
+ <SyntheticProperty name="formSizePolicy" type="int" value="1"/>
+ </SyntheticProperties>
+ <AuxValues>
+ <AuxValue name="FormSettings_autoResourcing" type="java.lang.Integer" value="0"/>
+ <AuxValue name="FormSettings_autoSetComponentName" type="java.lang.Boolean" value="false"/>
+ <AuxValue name="FormSettings_generateFQN" type="java.lang.Boolean" value="true"/>
+ <AuxValue name="FormSettings_generateMnemonicsCode" type="java.lang.Boolean" value="false"/>
+ <AuxValue name="FormSettings_i18nAutoMode" type="java.lang.Boolean" value="false"/>
+ <AuxValue name="FormSettings_layoutCodeTarget" type="java.lang.Integer" value="1"/>
+ <AuxValue name="FormSettings_listenerGenerationStyle" type="java.lang.Integer" value="0"/>
+ <AuxValue name="FormSettings_variablesLocal" type="java.lang.Boolean" value="false"/>
+ <AuxValue name="FormSettings_variablesModifier" type="java.lang.Integer" value="2"/>
+ <AuxValue name="designerSize" type="java.awt.Dimension" value="-84,-19,0,5,115,114,0,18,106,97,118,97,46,97,119,116,46,68,105,109,101,110,115,105,111,110,65,-114,-39,-41,-84,95,68,20,2,0,2,73,0,6,104,101,105,103,104,116,73,0,5,119,105,100,116,104,120,112,0,0,2,48,0,0,2,13"/>
+ </AuxValues>
+
+ <Layout class="org.netbeans.modules.form.compat2.layouts.DesignGridBagLayout"/>
+ <SubComponents>
+ <Container class="javax.swing.JPanel" name="operationPanel">
+ <Properties>
+ <Property name="minimumSize" type="java.awt.Dimension" editor="org.netbeans.beaninfo.editors.DimensionEditor">
+ <Dimension value="[211, 20]"/>
+ </Property>
+ </Properties>
+ <AuxValues>
+ <AuxValue name="JavaCodeGenerator_VariableLocal" type="java.lang.Boolean" value="true"/>
+ <AuxValue name="JavaCodeGenerator_VariableModifier" type="java.lang.Integer" value="0"/>
+ </AuxValues>
+ <Constraints>
+ <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignGridBagLayout" value="org.netbeans.modules.form.compat2.layouts.DesignGridBagLayout$GridBagConstraintsDescription">
+ <GridBagConstraints gridX="0" gridY="0" gridWidth="1" gridHeight="1" fill="0" ipadX="0" ipadY="0" insetsTop="5" insetsLeft="5" insetsBottom="5" insetsRight="5" anchor="21" weightX="0.0" weightY="0.0"/>
+ </Constraint>
+ </Constraints>
+
+ <Layout class="org.netbeans.modules.form.compat2.layouts.DesignBoxLayout"/>
+ <SubComponents>
+ <Component class="javax.swing.JLabel" name="operationLabel">
+ <Properties>
+ <Property name="text" type="java.lang.String" value="Operation: "/>
+ </Properties>
+ <AuxValues>
+ <AuxValue name="JavaCodeGenerator_VariableLocal" type="java.lang.Boolean" value="true"/>
+ <AuxValue name="JavaCodeGenerator_VariableModifier" type="java.lang.Integer" value="0"/>
+ </AuxValues>
+ </Component>
+ <Component class="javax.swing.JComboBox" name="operationComboBox">
+ <Properties>
+ <Property name="model" type="javax.swing.ComboBoxModel" editor="org.netbeans.modules.form.RADConnectionPropertyEditor" postCode="selectedOperation = (Operation) operationComboBox.getSelectedItem();">
+ <Connection code="new javax.swing.DefaultComboBoxModel(new Operation[] { Operation.UNION,Operation.INTERSECTION,Operation.DIFFERENCE })" type="code"/>
+ </Property>
+ <Property name="preferredSize" type="java.awt.Dimension" editor="org.netbeans.beaninfo.editors.DimensionEditor">
+ <Dimension value="[150, 20]"/>
+ </Property>
+ </Properties>
+ <AuxValues>
+ <AuxValue name="JavaCodeGenerator_DeclarationPost" type="java.lang.String" value="private Operation selectedOperation;"/>
+ <AuxValue name="JavaCodeGenerator_InitCodePost" type="java.lang.String" value="operationComboBox.addActionListener(new java.awt.event.ActionListener() {
 public void actionPerformed(java.awt.event.ActionEvent evt) {
 Operation selectOp = (Operation)operationComboBox.getSelectedItem();
 int nSelectedNetwork = selectedNetworkData.getSize();
 if (selectOp==Operation.DIFFERENCE && nSelectedNetwork>2) {
 final int i [...]
+ </AuxValues>
+ </Component>
+ </SubComponents>
+ </Container>
+ <Component class="javax.swing.JLabel" name="operationIcon">
+ <Properties>
+ <Property name="icon" type="javax.swing.Icon" editor="org.netbeans.modules.form.RADConnectionPropertyEditor">
+ <Connection code="UNION_ICON" type="code"/>
+ </Property>
+ </Properties>
+ <Constraints>
+ <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignGridBagLayout" value="org.netbeans.modules.form.compat2.layouts.DesignGridBagLayout$GridBagConstraintsDescription">
+ <GridBagConstraints gridX="0" gridY="1" gridWidth="1" gridHeight="1" fill="0" ipadX="0" ipadY="0" insetsTop="5" insetsLeft="5" insetsBottom="5" insetsRight="5" anchor="21" weightX="0.0" weightY="0.0"/>
+ </Constraint>
+ </Constraints>
+ </Component>
+ <Component class="javax.swing.JSeparator" name="jSeparator1">
+ <AuxValues>
+ <AuxValue name="JavaCodeGenerator_VariableLocal" type="java.lang.Boolean" value="true"/>
+ <AuxValue name="JavaCodeGenerator_VariableModifier" type="java.lang.Integer" value="0"/>
+ </AuxValues>
+ <Constraints>
+ <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignGridBagLayout" value="org.netbeans.modules.form.compat2.layouts.DesignGridBagLayout$GridBagConstraintsDescription">
+ <GridBagConstraints gridX="0" gridY="2" gridWidth="1" gridHeight="1" fill="2" ipadX="0" ipadY="0" insetsTop="5" insetsLeft="5" insetsBottom="5" insetsRight="5" anchor="10" weightX="1.0" weightY="0.0"/>
+ </Constraint>
+ </Constraints>
+ </Component>
+ <Container class="javax.swing.JPanel" name="selectNetworkPanel">
+ <Properties>
+ <Property name="border" type="javax.swing.border.Border" editor="org.netbeans.modules.form.editors2.BorderEditor">
+ <Border info="org.netbeans.modules.form.compat2.border.TitledBorderInfo">
+ <TitledBorder title="Networks to merge"/>
+ </Border>
+ </Property>
+ <Property name="minimumSize" type="java.awt.Dimension" editor="org.netbeans.beaninfo.editors.DimensionEditor">
+ <Dimension value="[490, 100]"/>
+ </Property>
+ <Property name="preferredSize" type="java.awt.Dimension" editor="org.netbeans.beaninfo.editors.DimensionEditor">
+ <Dimension value="[490, 130]"/>
+ </Property>
+ </Properties>
+ <AuxValues>
+ <AuxValue name="JavaCodeGenerator_VariableLocal" type="java.lang.Boolean" value="true"/>
+ <AuxValue name="JavaCodeGenerator_VariableModifier" type="java.lang.Integer" value="0"/>
+ </AuxValues>
+ <Constraints>
+ <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignGridBagLayout" value="org.netbeans.modules.form.compat2.layouts.DesignGridBagLayout$GridBagConstraintsDescription">
+ <GridBagConstraints gridX="0" gridY="3" gridWidth="1" gridHeight="1" fill="1" ipadX="0" ipadY="0" insetsTop="5" insetsLeft="5" insetsBottom="5" insetsRight="5" anchor="10" weightX="1.0" weightY="0.5"/>
+ </Constraint>
+ </Constraints>
+
+ <Layout class="org.netbeans.modules.form.compat2.layouts.DesignGridBagLayout"/>
+ <SubComponents>
+ <Container class="javax.swing.JScrollPane" name="unselectedNetworkScrollPane">
+ <Properties>
+ <Property name="preferredSize" type="java.awt.Dimension" editor="org.netbeans.beaninfo.editors.DimensionEditor">
+ <Dimension value="[200, 100]"/>
+ </Property>
+ </Properties>
+ <AuxValues>
+ <AuxValue name="JavaCodeGenerator_VariableLocal" type="java.lang.Boolean" value="true"/>
+ <AuxValue name="JavaCodeGenerator_VariableModifier" type="java.lang.Integer" value="0"/>
+ <AuxValue name="autoScrollPane" type="java.lang.Boolean" value="true"/>
+ </AuxValues>
+ <Constraints>
+ <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignGridBagLayout" value="org.netbeans.modules.form.compat2.layouts.DesignGridBagLayout$GridBagConstraintsDescription">
+ <GridBagConstraints gridX="0" gridY="0" gridWidth="1" gridHeight="1" fill="1" ipadX="0" ipadY="0" insetsTop="3" insetsLeft="3" insetsBottom="3" insetsRight="3" anchor="10" weightX="0.5" weightY="1.0"/>
+ </Constraint>
+ </Constraints>
+
+ <Layout class="org.netbeans.modules.form.compat2.layouts.support.JScrollPaneSupportLayout"/>
+ <SubComponents>
+ <Component class="javax.swing.JList" name="unselectedNetworkList">
+ <Properties>
+ <Property name="border" type="javax.swing.border.Border" editor="org.netbeans.modules.form.editors2.BorderEditor">
+ <Border info="org.netbeans.modules.form.compat2.border.TitledBorderInfo">
+ <TitledBorder title="Available networks"/>
+ </Border>
+ </Property>
+ <Property name="model" type="javax.swing.ListModel" editor="org.netbeans.modules.form.editors2.ListModelEditor">
+ <StringArray count="0"/>
+ </Property>
+ </Properties>
+ <AuxValues>
+ <AuxValue name="JavaCodeGenerator_CreateCodeCustom" type="java.lang.String" value="new javax.swing.JList(unselectedNetworkData)"/>
+ <AuxValue name="JavaCodeGenerator_CreateCodePre" type="java.lang.String" value="unselectedNetworkData = new SortedNetworkListModel();"/>
+ <AuxValue name="JavaCodeGenerator_DeclarationPost" type="java.lang.String" value="private SortedNetworkListModel unselectedNetworkData;"/>
+ <AuxValue name="JavaCodeGenerator_InitCodePost" type="java.lang.String" value="for (Iterator<CyNetwork> it = Cytoscape.getNetworkSet().iterator(); it.hasNext(); ) {
 CyNetwork network = it.next();
 unselectedNetworkData.add(network);
}

unselectedNetworkList.setCellRenderer(new ListCellRenderer() {
 private DefaultListCellRenderer defaultRenderer = new DefaultListCellRenderer();
 public Component getListCellRendererComponent(& [...]
+ </AuxValues>
+ </Component>
+ </SubComponents>
+ </Container>
+ <Container class="javax.swing.JPanel" name="lrButtonPanel">
+ <AuxValues>
+ <AuxValue name="JavaCodeGenerator_VariableLocal" type="java.lang.Boolean" value="true"/>
+ <AuxValue name="JavaCodeGenerator_VariableModifier" type="java.lang.Integer" value="0"/>
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+ <Constraints>
+ <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignGridBagLayout" value="org.netbeans.modules.form.compat2.layouts.DesignGridBagLayout$GridBagConstraintsDescription">
+ <GridBagConstraints gridX="1" gridY="0" gridWidth="1" gridHeight="1" fill="0" ipadX="0" ipadY="0" insetsTop="3" insetsLeft="3" insetsBottom="3" insetsRight="3" anchor="10" weightX="0.0" weightY="0.0"/>
+ </Constraint>
+ </Constraints>
+
+ <Layout class="org.netbeans.modules.form.compat2.layouts.DesignGridLayout">
+ <Property name="columns" type="int" value="1"/>
+ <Property name="rows" type="int" value="0"/>
+ <Property name="verticalGap" type="int" value="2"/>
+ </Layout>
+ <SubComponents>
+ <Component class="javax.swing.JButton" name="rightButton">
+ <Properties>
+ <Property name="icon" type="javax.swing.Icon" editor="org.netbeans.modules.form.editors2.IconEditor">
+ <Image iconType="3" name="/images/right16.gif"/>
+ </Property>
+ <Property name="enabled" type="boolean" value="false"/>
+ </Properties>
+ <AuxValues>
+ <AuxValue name="JavaCodeGenerator_InitCodePost" type="java.lang.String" value="rightButton.addActionListener(new java.awt.event.ActionListener() {
 public void actionPerformed(java.awt.event.ActionEvent evt) {
 int [] indices = unselectedNetworkList.getSelectedIndices();
 if (indices == null || indices.length == 0) {
 return;
 } 
 
 if (getOperation()==Operation.DIFFERENCE && selec [...]
+ </AuxValues>
+ </Component>
+ <Component class="javax.swing.JButton" name="leftButton">
+ <Properties>
+ <Property name="icon" type="javax.swing.Icon" editor="org.netbeans.modules.form.editors2.IconEditor">
+ <Image iconType="3" name="/images/left16.gif"/>
+ </Property>
+ <Property name="enabled" type="boolean" value="false"/>
+ </Properties>
+ <AuxValues>
+ <AuxValue name="JavaCodeGenerator_InitCodePost" type="java.lang.String" value="leftButton.addActionListener(new java.awt.event.ActionListener() {
 public void actionPerformed(java.awt.event.ActionEvent evt) {
 int [] indices = selectedNetworkList.getSelectedIndices();
 if (indices == null || indices.length == 0) {
 return;
 }
 
 for (int i= indices.length-1; i>=0; i--) {
 CyNetwork [...]
+ </AuxValues>
+ </Component>
+ </SubComponents>
+ </Container>
+ <Container class="javax.swing.JScrollPane" name="selectedNetworkScrollPane">
+ <Properties>
+ <Property name="preferredSize" type="java.awt.Dimension" editor="org.netbeans.beaninfo.editors.DimensionEditor">
+ <Dimension value="[200, 100]"/>
+ </Property>
+ </Properties>
+ <AuxValues>
+ <AuxValue name="JavaCodeGenerator_VariableLocal" type="java.lang.Boolean" value="true"/>
+ <AuxValue name="JavaCodeGenerator_VariableModifier" type="java.lang.Integer" value="0"/>
+ <AuxValue name="autoScrollPane" type="java.lang.Boolean" value="true"/>
+ </AuxValues>
+ <Constraints>
+ <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignGridBagLayout" value="org.netbeans.modules.form.compat2.layouts.DesignGridBagLayout$GridBagConstraintsDescription">
+ <GridBagConstraints gridX="2" gridY="0" gridWidth="1" gridHeight="1" fill="1" ipadX="0" ipadY="0" insetsTop="3" insetsLeft="3" insetsBottom="3" insetsRight="3" anchor="10" weightX="0.5" weightY="1.0"/>
+ </Constraint>
+ </Constraints>
+
+ <Layout class="org.netbeans.modules.form.compat2.layouts.support.JScrollPaneSupportLayout"/>
+ <SubComponents>
+ <Component class="javax.swing.JList" name="selectedNetworkList">
+ <Properties>
+ <Property name="border" type="javax.swing.border.Border" editor="org.netbeans.modules.form.editors2.BorderEditor">
+ <Border info="org.netbeans.modules.form.compat2.border.TitledBorderInfo">
+ <TitledBorder title="Selected networks"/>
+ </Border>
+ </Property>
+ <Property name="model" type="javax.swing.ListModel" editor="org.netbeans.modules.form.editors2.ListModelEditor">
+ <StringArray count="0"/>
+ </Property>
+ </Properties>
+ <AuxValues>
+ <AuxValue name="JavaCodeGenerator_CreateCodeCustom" type="java.lang.String" value="new javax.swing.JList(selectedNetworkData)"/>
+ <AuxValue name="JavaCodeGenerator_CreateCodePre" type="java.lang.String" value="selectedNetworkData = new NetworkListModel();"/>
+ <AuxValue name="JavaCodeGenerator_DeclarationPost" type="java.lang.String" value="private NetworkListModel selectedNetworkData;"/>
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 private DefaultListCellRenderer defaultRenderer = new DefaultListCellRenderer();
 public Component getListCellRendererComponent(
 JList list,
 Object value,
 int index,
 [...]
+ <AuxValue name="JavaCodeGenerator_InitCodePre" type="java.lang.String" value="selectedNetworkList.setSelectionMode(ListSelectionModel.SINGLE_INTERVAL_SELECTION);"/>
+ </AuxValues>
+ </Component>
+ </SubComponents>
+ </Container>
+ <Container class="javax.swing.JPanel" name="udButtonPanel">
+ <AuxValues>
+ <AuxValue name="JavaCodeGenerator_LayoutCodePre" type="java.lang.String" value="udButtonPanel.setVisible(false);"/>
+ </AuxValues>
+ <Constraints>
+ <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignGridBagLayout" value="org.netbeans.modules.form.compat2.layouts.DesignGridBagLayout$GridBagConstraintsDescription">
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+ </Constraints>
+
+ <Layout class="org.netbeans.modules.form.compat2.layouts.DesignGridLayout">
+ <Property name="columns" type="int" value="1"/>
+ <Property name="rows" type="int" value="0"/>
+ <Property name="verticalGap" type="int" value="2"/>
+ </Layout>
+ <SubComponents>
+ <Component class="javax.swing.JButton" name="upButton">
+ <Properties>
+ <Property name="icon" type="javax.swing.Icon" editor="org.netbeans.modules.form.editors2.IconEditor">
+ <Image iconType="3" name="/images/up16.gif"/>
+ </Property>
+ <Property name="enabled" type="boolean" value="false"/>
+ </Properties>
+ <AuxValues>
+ <AuxValue name="JavaCodeGenerator_InitCodePost" type="java.lang.String" value="upButton.addActionListener(new java.awt.event.ActionListener() {
 public void actionPerformed(java.awt.event.ActionEvent evt) {
 int [] indices = selectedNetworkList.getSelectedIndices();
 if (indices == null || indices.length == 0) {
 return;
 }
 
 int imin = selectedNetworkList.getMinSelectionIndex();
 int ima [...]
+ </AuxValues>
+ </Component>
+ <Component class="javax.swing.JButton" name="downButton">
+ <Properties>
+ <Property name="icon" type="javax.swing.Icon" editor="org.netbeans.modules.form.editors2.IconEditor">
+ <Image iconType="3" name="/images/down16.gif"/>
+ </Property>
+ <Property name="enabled" type="boolean" value="false"/>
+ </Properties>
+ <AuxValues>
+ <AuxValue name="JavaCodeGenerator_InitCodePost" type="java.lang.String" value="downButton.addActionListener(new java.awt.event.ActionListener() {
 public void actionPerformed(java.awt.event.ActionEvent evt) {
 int [] indices = selectedNetworkList.getSelectedIndices();
 if (indices == null || indices.length == 0) {
 return;
 }
 
 int imin = selectedNetworkList.getMinSelectionIndex();
 int i [...]
+ </AuxValues>
+ </Component>
+ </SubComponents>
+ </Container>
+ </SubComponents>
+ </Container>
+ <Container class="javax.swing.JPanel" name="collapsiblePanelAgent">
+ <AuxValues>
+ <AuxValue name="JavaCodeGenerator_CreateCodeCustom" type="java.lang.String" value="advancedNetworkMergeCollapsiblePanel"/>
+ </AuxValues>
+ <Constraints>
+ <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignGridBagLayout" value="org.netbeans.modules.form.compat2.layouts.DesignGridBagLayout$GridBagConstraintsDescription">
+ <GridBagConstraints gridX="0" gridY="4" gridWidth="1" gridHeight="1" fill="1" ipadX="0" ipadY="0" insetsTop="0" insetsLeft="0" insetsBottom="0" insetsRight="0" anchor="10" weightX="1.0" weightY="1.0"/>
+ </Constraint>
+ </Constraints>
+
+ <Layout class="org.netbeans.modules.form.compat2.layouts.DesignBorderLayout"/>
+ <SubComponents>
+ <Container class="javax.swing.JPanel" name="advancedPanel">
+ <Properties>
+ <Property name="preferredSize" type="java.awt.Dimension" editor="org.netbeans.beaninfo.editors.DimensionEditor">
+ <Dimension value="[690, 400]"/>
+ </Property>
+ </Properties>
+ <AuxValues>
+ <AuxValue name="JavaCodeGenerator_AddingCodePost" type="java.lang.String" value="*/
advancedNetworkMergeCollapsiblePanel.getContentPane().add(advancedPanel, java.awt.BorderLayout.CENTER);"/>
+ <AuxValue name="JavaCodeGenerator_LayoutCodePost" type="java.lang.String" value="/*"/>
+ </AuxValues>
+ <Constraints>
+ <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignBorderLayout" value="org.netbeans.modules.form.compat2.layouts.DesignBorderLayout$BorderConstraintsDescription">
+ <BorderConstraints direction="Center"/>
+ </Constraint>
+ </Constraints>
+
+ <Layout class="org.netbeans.modules.form.compat2.layouts.DesignGridBagLayout"/>
+ <SubComponents>
+ <Container class="javax.swing.JPanel" name="attributePanel">
+ <Properties>
+ <Property name="border" type="javax.swing.border.Border" editor="org.netbeans.modules.form.editors2.BorderEditor">
+ <Border info="org.netbeans.modules.form.compat2.border.TitledBorderInfo">
+ <TitledBorder title="Matching attributes (attributes to match nodes between networks)"/>
+ </Border>
+ </Property>
+ </Properties>
+ <Constraints>
+ <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignGridBagLayout" value="org.netbeans.modules.form.compat2.layouts.DesignGridBagLayout$GridBagConstraintsDescription">
+ <GridBagConstraints gridX="0" gridY="0" gridWidth="1" gridHeight="1" fill="2" ipadX="0" ipadY="0" insetsTop="5" insetsLeft="5" insetsBottom="5" insetsRight="5" anchor="10" weightX="1.0" weightY="0.0"/>
+ </Constraint>
+ </Constraints>
+
+ <Layout class="org.netbeans.modules.form.compat2.layouts.DesignGridBagLayout"/>
+ <SubComponents>
+ <Container class="javax.swing.JScrollPane" name="attributeScrollPane">
+ <Properties>
+ <Property name="minimumSize" type="java.awt.Dimension" editor="org.netbeans.beaninfo.editors.DimensionEditor">
+ <Dimension value="[100, 50]"/>
+ </Property>
+ <Property name="preferredSize" type="java.awt.Dimension" editor="org.netbeans.beaninfo.editors.DimensionEditor">
+ <Dimension value="[450, 50]"/>
+ </Property>
+ </Properties>
+ <AuxValues>
+ <AuxValue name="JavaCodeGenerator_CreateCodePre" type="java.lang.String" value="matchNodeTable = new MatchNodeTable(matchingAttribute);"/>
+ <AuxValue name="JavaCodeGenerator_InitCodePost" type="java.lang.String" value="matchNodeTable.getModel().addTableModelListener(new TableModelListener() {
 public void tableChanged(TableModelEvent e) {
 mergeNodeAttributeTable.updateMatchingAttribute();
 }
});"/>
+ <AuxValue name="JavaCodeGenerator_LayoutCodePost" type="java.lang.String" value="attributeScrollPane.setViewportView(matchNodeTable);"/>
+ </AuxValues>
+ <Constraints>
+ <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignGridBagLayout" value="org.netbeans.modules.form.compat2.layouts.DesignGridBagLayout$GridBagConstraintsDescription">
+ <GridBagConstraints gridX="0" gridY="0" gridWidth="1" gridHeight="1" fill="1" ipadX="0" ipadY="0" insetsTop="0" insetsLeft="0" insetsBottom="0" insetsRight="0" anchor="10" weightX="1.0" weightY="1.0"/>
+ </Constraint>
+ </Constraints>
+
+ <Layout class="org.netbeans.modules.form.compat2.layouts.support.JScrollPaneSupportLayout"/>
+ </Container>
+ <Component class="javax.swing.JCheckBox" name="idmappingCheckBox">
+ <Properties>
+ <Property name="text" type="java.lang.String" value="Map IDs between the matching attributes"/>
+ </Properties>
+ <AuxValues>
+ <AuxValue name="JavaCodeGenerator_InitCodePost" type="java.lang.String" value="idmappingCheckBox.setVisible(checkCyThesaurus);"/>
+ </AuxValues>
+ <Constraints>
+ <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignGridBagLayout" value="org.netbeans.modules.form.compat2.layouts.DesignGridBagLayout$GridBagConstraintsDescription">
+ <GridBagConstraints gridX="0" gridY="1" gridWidth="1" gridHeight="1" fill="0" ipadX="0" ipadY="0" insetsTop="5" insetsLeft="5" insetsBottom="5" insetsRight="5" anchor="21" weightX="0.0" weightY="0.0"/>
+ </Constraint>
+ </Constraints>
+ </Component>
+ <Component class="javax.swing.JLabel" name="idmappingLabel">
+ <Properties>
+ <Property name="foreground" type="java.awt.Color" editor="org.netbeans.beaninfo.editors.ColorEditor">
+ <Color blue="33" green="0" red="ff" type="rgb"/>
+ </Property>
+ <Property name="text" type="java.lang.String" editor="org.netbeans.modules.form.RADConnectionPropertyEditor">
+ <Connection code=""If you want to map identifiers between the matching attributes, please install CyThesaurus plugin version "+requiredCyThesaursServiceVersion+" or above."" type="code"/>
+ </Property>
+ </Properties>
+ <AuxValues>
+ <AuxValue name="JavaCodeGenerator_InitCodePost" type="java.lang.String" value="idmappingLabel.setVisible(!checkCyThesaurus);"/>
+ <AuxValue name="JavaCodeGenerator_VariableLocal" type="java.lang.Boolean" value="true"/>
+ <AuxValue name="JavaCodeGenerator_VariableModifier" type="java.lang.Integer" value="0"/>
+ </AuxValues>
+ <Constraints>
+ <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignGridBagLayout" value="org.netbeans.modules.form.compat2.layouts.DesignGridBagLayout$GridBagConstraintsDescription">
+ <GridBagConstraints gridX="0" gridY="1" gridWidth="1" gridHeight="1" fill="0" ipadX="0" ipadY="0" insetsTop="5" insetsLeft="5" insetsBottom="5" insetsRight="5" anchor="21" weightX="0.0" weightY="0.0"/>
+ </Constraint>
+ </Constraints>
+ </Component>
+ </SubComponents>
+ </Container>
+ <Component class="javax.swing.JSeparator" name="jSeparator3">
+ <AuxValues>
+ <AuxValue name="JavaCodeGenerator_VariableLocal" type="java.lang.Boolean" value="true"/>
+ <AuxValue name="JavaCodeGenerator_VariableModifier" type="java.lang.Integer" value="0"/>
+ </AuxValues>
+ <Constraints>
+ <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignGridBagLayout" value="org.netbeans.modules.form.compat2.layouts.DesignGridBagLayout$GridBagConstraintsDescription">
+ <GridBagConstraints gridX="0" gridY="2" gridWidth="1" gridHeight="1" fill="2" ipadX="0" ipadY="0" insetsTop="5" insetsLeft="5" insetsBottom="5" insetsRight="5" anchor="10" weightX="1.0" weightY="0.0"/>
+ </Constraint>
+ </Constraints>
+ </Component>
+ <Container class="javax.swing.JPanel" name="mergeAttributePanel">
+ <Properties>
+ <Property name="border" type="javax.swing.border.Border" editor="org.netbeans.modules.form.editors2.BorderEditor">
+ <Border info="org.netbeans.modules.form.compat2.border.TitledBorderInfo">
+ <TitledBorder title="How to merge attributes?"/>
+ </Border>
+ </Property>
+ <Property name="minimumSize" type="java.awt.Dimension" editor="org.netbeans.beaninfo.editors.DimensionEditor">
+ <Dimension value="[400, 200]"/>
+ </Property>
+ <Property name="preferredSize" type="java.awt.Dimension" editor="org.netbeans.beaninfo.editors.DimensionEditor">
+ <Dimension value="[600, 200]"/>
+ </Property>
+ </Properties>
+ <AuxValues>
+ <AuxValue name="JavaCodeGenerator_VariableLocal" type="java.lang.Boolean" value="true"/>
+ <AuxValue name="JavaCodeGenerator_VariableModifier" type="java.lang.Integer" value="0"/>
+ </AuxValues>
+ <Constraints>
+ <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignGridBagLayout" value="org.netbeans.modules.form.compat2.layouts.DesignGridBagLayout$GridBagConstraintsDescription">
+ <GridBagConstraints gridX="0" gridY="3" gridWidth="1" gridHeight="1" fill="1" ipadX="0" ipadY="0" insetsTop="5" insetsLeft="5" insetsBottom="5" insetsRight="5" anchor="10" weightX="1.0" weightY="1.0"/>
+ </Constraint>
+ </Constraints>
+
+ <Layout class="org.netbeans.modules.form.compat2.layouts.DesignBoxLayout"/>
+ <SubComponents>
+ <Container class="javax.swing.JTabbedPane" name="mergeAttributeTabbedPane">
+ <Properties>
+ <Property name="minimumSize" type="java.awt.Dimension" editor="org.netbeans.beaninfo.editors.DimensionEditor">
+ <Dimension value="[450, 150]"/>
+ </Property>
+ <Property name="preferredSize" type="java.awt.Dimension" editor="org.netbeans.beaninfo.editors.DimensionEditor">
+ <Dimension value="[450, 200]"/>
+ </Property>
+ </Properties>
+ <AuxValues>
+ <AuxValue name="JavaCodeGenerator_VariableLocal" type="java.lang.Boolean" value="true"/>
+ <AuxValue name="JavaCodeGenerator_VariableModifier" type="java.lang.Integer" value="0"/>
+ </AuxValues>
+
+ <Layout class="org.netbeans.modules.form.compat2.layouts.support.JTabbedPaneSupportLayout"/>
+ <SubComponents>
+ <Container class="javax.swing.JPanel" name="mergeNodeAttributePanel">
+ <AuxValues>
+ <AuxValue name="JavaCodeGenerator_VariableLocal" type="java.lang.Boolean" value="true"/>
+ <AuxValue name="JavaCodeGenerator_VariableModifier" type="java.lang.Integer" value="0"/>
+ </AuxValues>
+ <Constraints>
+ <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.support.JTabbedPaneSupportLayout" value="org.netbeans.modules.form.compat2.layouts.support.JTabbedPaneSupportLayout$JTabbedPaneConstraintsDescription">
+ <JTabbedPaneConstraints tabName="Node">
+ <Property name="tabTitle" type="java.lang.String" value="Node"/>
+ </JTabbedPaneConstraints>
+ </Constraint>
+ </Constraints>
+
+ <Layout class="org.netbeans.modules.form.compat2.layouts.DesignBoxLayout"/>
+ <SubComponents>
+ <Container class="javax.swing.JScrollPane" name="mergeNodeAttributeScrollPane">
+ <AuxValues>
+ <AuxValue name="JavaCodeGenerator_LayoutCodePost" type="java.lang.String" value="mergeNodeAttributeTable = new MergeAttributeTable(nodeAttributeMapping,matchingAttribute);
mergeNodeAttributeScrollPane.setViewportView(mergeNodeAttributeTable);"/>
+ <AuxValue name="JavaCodeGenerator_VariableLocal" type="java.lang.Boolean" value="true"/>
+ <AuxValue name="JavaCodeGenerator_VariableModifier" type="java.lang.Integer" value="0"/>
+ </AuxValues>
+
+ <Layout class="org.netbeans.modules.form.compat2.layouts.support.JScrollPaneSupportLayout"/>
+ </Container>
+ </SubComponents>
+ </Container>
+ <Container class="javax.swing.JPanel" name="mergeEdgeAttributePanel">
+ <AuxValues>
+ <AuxValue name="JavaCodeGenerator_VariableLocal" type="java.lang.Boolean" value="true"/>
+ <AuxValue name="JavaCodeGenerator_VariableModifier" type="java.lang.Integer" value="0"/>
+ </AuxValues>
+ <Constraints>
+ <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.support.JTabbedPaneSupportLayout" value="org.netbeans.modules.form.compat2.layouts.support.JTabbedPaneSupportLayout$JTabbedPaneConstraintsDescription">
+ <JTabbedPaneConstraints tabName="Edge">
+ <Property name="tabTitle" type="java.lang.String" value="Edge"/>
+ </JTabbedPaneConstraints>
+ </Constraint>
+ </Constraints>
+
+ <Layout class="org.netbeans.modules.form.compat2.layouts.DesignBoxLayout"/>
+ <SubComponents>
+ <Container class="javax.swing.JScrollPane" name="mergeEdgeAttributeScrollPane">
+ <AuxValues>
+ <AuxValue name="JavaCodeGenerator_LayoutCodePost" type="java.lang.String" value="mergeEdgeAttributeTable = new MergeAttributeTable(edgeAttributeMapping);
mergeEdgeAttributeScrollPane.setViewportView(mergeEdgeAttributeTable);"/>
+ <AuxValue name="JavaCodeGenerator_VariableLocal" type="java.lang.Boolean" value="true"/>
+ <AuxValue name="JavaCodeGenerator_VariableModifier" type="java.lang.Integer" value="0"/>
+ </AuxValues>
+
+ <Layout class="org.netbeans.modules.form.compat2.layouts.support.JScrollPaneSupportLayout"/>
+ </Container>
+ </SubComponents>
+ </Container>
+ </SubComponents>
+ </Container>
+ </SubComponents>
+ </Container>
+ <Container class="javax.swing.JPanel" name="advancedOptionCollapsiblePanelAgent">
+ <AuxValues>
+ <AuxValue name="JavaCodeGenerator_CreateCodeCustom" type="java.lang.String" value="advancedOptionCollapsiblePanel"/>
+ </AuxValues>
+ <Constraints>
+ <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignGridBagLayout" value="org.netbeans.modules.form.compat2.layouts.DesignGridBagLayout$GridBagConstraintsDescription">
+ <GridBagConstraints gridX="0" gridY="4" gridWidth="1" gridHeight="1" fill="2" ipadX="0" ipadY="0" insetsTop="5" insetsLeft="5" insetsBottom="5" insetsRight="5" anchor="21" weightX="0.0" weightY="0.0"/>
+ </Constraint>
+ </Constraints>
+
+ <Layout class="org.netbeans.modules.form.compat2.layouts.DesignBorderLayout"/>
+ <SubComponents>
+ <Container class="javax.swing.JPanel" name="optionPanel">
+ <AuxValues>
+ <AuxValue name="JavaCodeGenerator_AddingCodePost" type="java.lang.String" value="*/
advancedOptionCollapsiblePanel.getContentPane().add(optionPanel, java.awt.BorderLayout.CENTER);"/>
+ <AuxValue name="JavaCodeGenerator_LayoutCodePost" type="java.lang.String" value="/*"/>
+ </AuxValues>
+ <Constraints>
+ <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignBorderLayout" value="org.netbeans.modules.form.compat2.layouts.DesignBorderLayout$BorderConstraintsDescription">
+ <BorderConstraints direction="First"/>
+ </Constraint>
+ </Constraints>
+
+ <Layout class="org.netbeans.modules.form.compat2.layouts.DesignFlowLayout">
+ <Property name="alignment" type="int" value="0"/>
+ </Layout>
+ <SubComponents>
+ <Component class="javax.swing.JCheckBox" name="inNetworkMergeCheckBox">
+ <Properties>
+ <Property name="selected" type="boolean" value="true" postCode="parameter = new NetworkMergeParameterImpl(inNetworkMergeCheckBox.isSelected());"/>
+ <Property name="text" type="java.lang.String" value="Enable merging nodes/edges in the same network"/>
+ </Properties>
+ <Events>
+ <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="inNetworkMergeCheckBoxActionPerformed"/>
+ </Events>
+ </Component>
+ </SubComponents>
+ </Container>
+ </SubComponents>
+ </Container>
+ </SubComponents>
+ </Container>
+ </SubComponents>
+ </Container>
+ <Component class="javax.swing.JSeparator" name="jSeparator4">
+ <AuxValues>
+ <AuxValue name="JavaCodeGenerator_VariableLocal" type="java.lang.Boolean" value="true"/>
+ <AuxValue name="JavaCodeGenerator_VariableModifier" type="java.lang.Integer" value="0"/>
+ </AuxValues>
+ <Constraints>
+ <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignGridBagLayout" value="org.netbeans.modules.form.compat2.layouts.DesignGridBagLayout$GridBagConstraintsDescription">
+ <GridBagConstraints gridX="0" gridY="5" gridWidth="1" gridHeight="1" fill="2" ipadX="0" ipadY="0" insetsTop="5" insetsLeft="5" insetsBottom="5" insetsRight="5" anchor="10" weightX="1.0" weightY="0.0"/>
+ </Constraint>
+ </Constraints>
+ </Component>
+ <Container class="javax.swing.JPanel" name="okPanel">
+ <Properties>
+ <Property name="doubleBuffered" type="boolean" value="false"/>
+ </Properties>
+ <AuxValues>
+ <AuxValue name="JavaCodeGenerator_VariableLocal" type="java.lang.Boolean" value="true"/>
+ <AuxValue name="JavaCodeGenerator_VariableModifier" type="java.lang.Integer" value="0"/>
+ </AuxValues>
+ <Constraints>
+ <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignGridBagLayout" value="org.netbeans.modules.form.compat2.layouts.DesignGridBagLayout$GridBagConstraintsDescription">
+ <GridBagConstraints gridX="0" gridY="6" gridWidth="1" gridHeight="1" fill="0" ipadX="0" ipadY="0" insetsTop="5" insetsLeft="5" insetsBottom="5" insetsRight="5" anchor="22" weightX="1.0" weightY="0.0"/>
+ </Constraint>
+ </Constraints>
+
+ <Layout class="org.netbeans.modules.form.compat2.layouts.DesignBoxLayout"/>
+ <SubComponents>
+ <Component class="javax.swing.JButton" name="okButton">
+ <Properties>
+ <Property name="text" type="java.lang.String" value=" Merge "/>
+ <Property name="enabled" type="boolean" value="false"/>
+ </Properties>
+ <Events>
+ <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="okButtonActionPerformed"/>
+ </Events>
+ </Component>
+ <Component class="javax.swing.JButton" name="cancelButton">
+ <Properties>
+ <Property name="text" type="java.lang.String" value="Cancel"/>
+ </Properties>
+ <AuxValues>
+ <AuxValue name="JavaCodeGenerator_InitCodePost" type="java.lang.String" value="cancelButton.addActionListener(new java.awt.event.ActionListener() {
 public void actionPerformed(java.awt.event.ActionEvent evt) {
 setVisible(false);
 dispose();
 }
});"/>
+ </AuxValues>
+ </Component>
+ </SubComponents>
+ </Container>
+ </SubComponents>
+</Form>
diff --git a/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/ui/NetworkMergeFrame.java b/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/ui/NetworkMergeFrame.java
new file mode 100644
index 0000000..8522b27
--- /dev/null
+++ b/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/ui/NetworkMergeFrame.java
@@ -0,0 +1,1397 @@
+/* File: NetworkMergeFrame.java
+
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+package csplugins.network.merge.ui;
+
+import csplugins.network.merge.NetworkMerge;
+import csplugins.network.merge.NetworkMergeParameter;
+import csplugins.network.merge.NetworkMergeParameterImpl;
+import csplugins.network.merge.AttributeBasedNetworkMerge;
+import csplugins.network.merge.model.AttributeMappingImpl;
+import csplugins.network.merge.model.MatchingAttributeImpl;
+import csplugins.network.merge.model.AttributeMapping;
+import csplugins.network.merge.model.MatchingAttribute;
+import csplugins.network.merge.NetworkMerge.Operation;
+import csplugins.network.merge.conflict.AttributeConflictHandler;
+//import csplugins.network.merge.conflict.IDMappingAttributeConflictHandler;
+import csplugins.network.merge.conflict.DefaultAttributeConflictHandler;
+import csplugins.network.merge.conflict.AttributeConflictManager;
+import csplugins.network.merge.conflict.AttributeConflictCollector;
+import csplugins.network.merge.conflict.AttributeConflictCollectorImpl;
+import csplugins.network.merge.util.AttributeValueMatcher;
+import csplugins.network.merge.util.DefaultAttributeValueMatcher;
+import csplugins.network.merge.util.AttributeMerger;
+import csplugins.network.merge.util.DefaultAttributeMerger;
+
+import cytoscape.Cytoscape;
+import cytoscape.CyNetwork;
+
+import cytoscape.cythesaurus.service.CyThesaurusServiceClient;
+import cytoscape.cythesaurus.service.CyThesaurusServiceMessageBasedClient;
+
+import cytoscape.data.CyAttributes;
+import cytoscape.data.Semantics;
+import cytoscape.data.attr.MultiHashMapDefinition;
+
+import cytoscape.task.Task;
+import cytoscape.task.TaskMonitor;
+import cytoscape.task.ui.JTaskConfig;
+import cytoscape.task.util.TaskManager;
+
+import cytoscape.util.CyNetworkNaming;
+import cytoscape.util.CytoscapeAction;
+import cytoscape.util.GraphSetUtils;
+
+import java.util.List;
+import java.util.Vector;
+import java.util.Set;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.Map;
+import java.util.TreeMap;
+import java.util.HashMap;
+import java.util.LinkedHashMap;
+
+import java.awt.Component;
+import java.awt.Frame;
+import java.awt.Dimension;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.Insets;
+import java.awt.GridLayout;
+import java.awt.FlowLayout;
+
+import javax.swing.JFrame;
+import javax.swing.JDialog;
+import javax.swing.JLabel;
+import javax.swing.DefaultListCellRenderer;
+import javax.swing.ImageIcon;
+import javax.swing.ListCellRenderer;
+import javax.swing.JList;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JSeparator;
+import javax.swing.JScrollPane;
+import javax.swing.JButton;
+import javax.swing.BorderFactory;
+import javax.swing.DefaultComboBoxModel;
+import javax.swing.ListModel;
+import javax.swing.AbstractListModel;
+import javax.swing.JComboBox;
+import javax.swing.JTabbedPane;
+import javax.swing.ListSelectionModel;
+import javax.swing.WindowConstants;
+import javax.swing.BoxLayout;
+import javax.swing.event.ListSelectionListener;
+import javax.swing.event.ListSelectionEvent;
+import javax.swing.event.TableModelEvent;
+import javax.swing.event.TableModelListener;
+import javax.swing.WindowConstants;
+
+/**
+ *
+ * Main frame for advance network merge
+ */
+public class NetworkMergeFrame extends JFrame {
+ private boolean altDifferenceIsChecked = false;
+
+ /** Creates new form NetworkMergeFrame */
+ public NetworkMergeFrame() {
+ frame = this;
+ this.setDefaultCloseOperation(WindowConstants.DISPOSE_ON_CLOSE);
+
+ checkCyThesaurus = checkCyThesaurus();
+
+ selectedNetworkAttributeIDType = null;
+ tgtType = null;
+ matchingAttribute = new MatchingAttributeImpl(Cytoscape.getNodeAttributes());
+ nodeAttributeMapping = new AttributeMappingImpl(Cytoscape.getNodeAttributes());
+ edgeAttributeMapping = new AttributeMappingImpl(Cytoscape.getEdgeAttributes());
+
+ advancedNetworkMergeCollapsiblePanel = new CollapsiblePanel("Advanced Network Merge");
+ advancedNetworkMergeCollapsiblePanel.addCollapeListener(new CollapsiblePanel.CollapeListener() {
+ public void collaped() {
+ updateOKButtonEnable();
+ updateSize();
+ }
+
+ public void expanded() {
+ updateOKButtonEnable();
+ updateSize();
+ }
+ });
+
+ advancedOptionCollapsiblePanel = new CollapsiblePanel("Advanced Option");
+
+ initComponents();
+
+ updateOKButtonEnable();
+ }
+
+ /** This method is called from within the constructor to
+ * initialize the form.
+ * WARNING: Do NOT modify this code. The content of this method is
+ * always regenerated by the Form Editor.
+ */
+ private void initComponents() {
+ java.awt.GridBagConstraints gridBagConstraints;
+
+ javax.swing.JPanel operationPanel = new javax.swing.JPanel();
+ javax.swing.JLabel operationLabel = new javax.swing.JLabel();
+ operationComboBox = new javax.swing.JComboBox();
+ operationIcon = new javax.swing.JLabel();
+ differenceButton = new javax.swing.JRadioButton("Only remove nodes if all their edges are being subtracted, too.");
+ difference2Button = new javax.swing.JRadioButton("Remove all nodes that are in the 2nd network.");
+ differenceGroup = new javax.swing.ButtonGroup();
+ differenceGroup.add(differenceButton);
+ differenceGroup.add(difference2Button);
+ javax.swing.JSeparator jSeparator1 = new javax.swing.JSeparator();
+ javax.swing.JPanel selectNetworkPanel = new javax.swing.JPanel();
+ javax.swing.JScrollPane unselectedNetworkScrollPane = new javax.swing.JScrollPane();
+ unselectedNetworkData = new SortedNetworkListModel();
+ unselectedNetworkList = new javax.swing.JList(unselectedNetworkData);
+ javax.swing.JPanel lrButtonPanel = new javax.swing.JPanel();
+ rightButton = new javax.swing.JButton();
+ leftButton = new javax.swing.JButton();
+ javax.swing.JScrollPane selectedNetworkScrollPane = new javax.swing.JScrollPane();
+ selectedNetworkData = new NetworkListModel();
+ selectedNetworkList = new javax.swing.JList(selectedNetworkData);
+ udButtonPanel = new javax.swing.JPanel();
+ upButton = new javax.swing.JButton();
+ downButton = new javax.swing.JButton();
+ collapsiblePanelAgent = advancedNetworkMergeCollapsiblePanel;
+ advancedPanel = new javax.swing.JPanel();
+ attributePanel = new javax.swing.JPanel();
+ matchNodeTable = new MatchNodeTable(matchingAttribute);
+ attributeScrollPane = new javax.swing.JScrollPane();
+ idmappingCheckBox = new javax.swing.JCheckBox();
+ javax.swing.JLabel idmappingLabel = new javax.swing.JLabel();
+ javax.swing.JSeparator jSeparator3 = new javax.swing.JSeparator();
+ javax.swing.JPanel mergeAttributePanel = new javax.swing.JPanel();
+ javax.swing.JTabbedPane mergeAttributeTabbedPane = new javax.swing.JTabbedPane();
+ javax.swing.JPanel mergeNodeAttributePanel = new javax.swing.JPanel();
+ javax.swing.JScrollPane mergeNodeAttributeScrollPane = new javax.swing.JScrollPane();
+ javax.swing.JPanel mergeEdgeAttributePanel = new javax.swing.JPanel();
+ javax.swing.JScrollPane mergeEdgeAttributeScrollPane = new javax.swing.JScrollPane();
+ advancedOptionCollapsiblePanelAgent = advancedOptionCollapsiblePanel;
+ optionPanel = new javax.swing.JPanel();
+ inNetworkMergeCheckBox = new javax.swing.JCheckBox();
+ javax.swing.JSeparator jSeparator4 = new javax.swing.JSeparator();
+ javax.swing.JPanel okPanel = new javax.swing.JPanel();
+ okButton = new javax.swing.JButton();
+ cancelButton = new javax.swing.JButton();
+
+ setTitle("Advanced Network Merge");
+ getContentPane().setLayout(new java.awt.GridBagLayout());
+
+ operationPanel.setMinimumSize(new java.awt.Dimension(211, 20));
+ operationPanel.setLayout(new javax.swing.BoxLayout(operationPanel, javax.swing.BoxLayout.LINE_AXIS));
+
+ operationLabel.setText("Operation: ");
+ operationPanel.add(operationLabel);
+
+ operationComboBox.setModel(new javax.swing.DefaultComboBoxModel(new Operation[] { Operation.UNION,Operation.INTERSECTION,Operation.DIFFERENCE }));
+ selectedOperation = (Operation) operationComboBox.getSelectedItem();
+ operationComboBox.setPreferredSize(new java.awt.Dimension(150, 20));
+ operationComboBox.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ Operation selectOp = (Operation)operationComboBox.getSelectedItem();
+ int nSelectedNetwork = selectedNetworkData.getSize();
+ if (selectOp==Operation.DIFFERENCE && nSelectedNetwork>2) {
+ final int ioption = JOptionPane.showConfirmDialog(frame,
+ "Only the first two networks in the selected network list will be merged for difference operation. All the other selected networks will be removed. Are you sure?",
+ "Warning: only two networks will be kept",
+ JOptionPane.YES_NO_OPTION );
+ if (ioption==JOptionPane.NO_OPTION) {
+ operationComboBox.setSelectedItem(selectedOperation);
+ return;
+ }
+
+ for (int is=nSelectedNetwork-1; is>=2; is--) {
+ CyNetwork removed = selectedNetworkData.removeElement(is);
+ unselectedNetworkData.add(removed);
+ addRemoveAttributeMapping(removed,false);
+ }
+ selectedNetworkList.repaint();
+ unselectedNetworkList.repaint();
+ updateAttributeTable();
+ updateMergeAttributeTable();
+ }
+
+ selectedOperation = selectOp;
+ operationIcon.setIcon(OPERATION_ICONS[operationComboBox.getSelectedIndex()]);
+
+ if (selectOp == Operation.DIFFERENCE) {
+ differenceButton.setVisible(true);
+ difference2Button.setVisible(true);
+ differenceButton.setSelected(true);
+ } else {
+ differenceButton.setVisible(false);
+ difference2Button.setVisible(false);
+ }
+
+ updateUpDownButtonEnable();
+ updateSize();
+ udButtonPanel.setVisible(getOperation()==Operation.DIFFERENCE);
+
+ }
+ });
+ operationPanel.add(operationComboBox);
+
+ int contentPaneGridY = 0;
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 0;
+ gridBagConstraints.gridy = contentPaneGridY++;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.LINE_START;
+ gridBagConstraints.insets = new java.awt.Insets(5, 5, 5, 5);
+ getContentPane().add(operationPanel, gridBagConstraints);
+
+ operationIcon.setIcon(UNION_ICON);
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 0;
+ gridBagConstraints.gridy = contentPaneGridY++;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.LINE_START;
+ gridBagConstraints.insets = new java.awt.Insets(5, 5, 5, 5);
+ getContentPane().add(operationIcon, gridBagConstraints);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 0;
+ gridBagConstraints.gridy = contentPaneGridY++;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.weightx = 1.0;
+ gridBagConstraints.insets = new java.awt.Insets(5, 5, 5, 5);
+ getContentPane().add(differenceButton, gridBagConstraints);
+ differenceButton.setVisible(false);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 0;
+ gridBagConstraints.gridy = contentPaneGridY++;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.weightx = 1.0;
+ gridBagConstraints.insets = new java.awt.Insets(5, 5, 5, 5);
+ getContentPane().add(difference2Button, gridBagConstraints);
+ difference2Button.setVisible(false);
+ difference2Button.addItemListener(new java.awt.event.ItemListener() {
+ public void itemStateChanged(java.awt.event.ItemEvent evt) {
+ altDifferenceIsChecked = evt.getStateChange() == ItemEvent.SELECTED;
+ if (altDifferenceIsChecked)
+ operationIcon.setIcon(DIFFERENCE2_ICON);
+ else
+ operationIcon.setIcon(DIFFERENCE_ICON);
+ }
+ });
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 0;
+ gridBagConstraints.gridy = contentPaneGridY++;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.weightx = 1.0;
+ gridBagConstraints.insets = new java.awt.Insets(5, 5, 5, 5);
+ getContentPane().add(jSeparator1, gridBagConstraints);
+
+ selectNetworkPanel.setBorder(javax.swing.BorderFactory.createTitledBorder("Networks to merge"));
+ selectNetworkPanel.setMinimumSize(new java.awt.Dimension(490, 100));
+ selectNetworkPanel.setPreferredSize(new java.awt.Dimension(490, 130));
+ selectNetworkPanel.setLayout(new java.awt.GridBagLayout());
+
+ unselectedNetworkScrollPane.setPreferredSize(new java.awt.Dimension(200, 100));
+
+ unselectedNetworkList.setBorder(javax.swing.BorderFactory.createTitledBorder("Available networks"));
+ for (Iterator<CyNetwork> it = Cytoscape.getNetworkSet().iterator(); it.hasNext(); ) {
+ CyNetwork network = it.next();
+ unselectedNetworkData.add(network);
+ }
+
+ unselectedNetworkList.setCellRenderer(new ListCellRenderer() {
+ private DefaultListCellRenderer defaultRenderer = new DefaultListCellRenderer();
+ public Component getListCellRendererComponent(
+ JList list,
+ Object value,
+ int index,
+ boolean isSelected,
+ boolean cellHasFocus) {
+ JLabel renderer = (JLabel) defaultRenderer.getListCellRendererComponent(list, value, index, isSelected, cellHasFocus);
+ renderer.setText(((CyNetwork)value).getTitle());
+ return renderer;
+ }
+ });
+
+ unselectedNetworkList.addListSelectionListener(new javax.swing.event.ListSelectionListener() {
+ public void valueChanged(javax.swing.event.ListSelectionEvent evt) {
+ int index = unselectedNetworkList.getMinSelectionIndex();
+ if (index>-1) {
+ selectedNetworkList.getSelectionModel().clearSelection();
+ rightButton.setEnabled(true);
+ } else {
+ rightButton.setEnabled(false);
+ }
+ }
+ });
+ unselectedNetworkScrollPane.setViewportView(unselectedNetworkList);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 0;
+ gridBagConstraints.gridy = 0;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.BOTH;
+ gridBagConstraints.weightx = 0.5;
+ gridBagConstraints.weighty = 1.0;
+ gridBagConstraints.insets = new java.awt.Insets(3, 3, 3, 3);
+ selectNetworkPanel.add(unselectedNetworkScrollPane, gridBagConstraints);
+
+ lrButtonPanel.setLayout(new java.awt.GridLayout(0, 1, 0, 2));
+
+ rightButton.setIcon(new javax.swing.ImageIcon(getClass().getResource("/images/right16.gif"))); // NOI18N
+ rightButton.setEnabled(false);
+ rightButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ int [] indices = unselectedNetworkList.getSelectedIndices();
+ if (indices == null || indices.length == 0) {
+ return;
+ }
+
+ if (getOperation()==Operation.DIFFERENCE && selectedNetworkData.getSize()+indices.length>2) {
+ JOptionPane.showMessageDialog(frame,"Difference operation only supports two networks! If you need to replace the selected network, remove it first and select the new one.", "Warning", JOptionPane.WARNING_MESSAGE );
+ return;
+ }
+
+ for (int i= indices.length-1; i>=0; i--) {
+ CyNetwork removed = unselectedNetworkData.removeElement(indices[i]);
+ selectedNetworkData.add(removed);
+ addRemoveAttributeMapping(removed,true);
+ }
+
+ if (unselectedNetworkData.getSize()==0) {
+ unselectedNetworkList.clearSelection();
+ rightButton.setEnabled(false);
+ } else {
+ int minindex = unselectedNetworkList.getMinSelectionIndex();
+ if (minindex>= unselectedNetworkData.getSize()) {
+ minindex = 0;
+ }
+ unselectedNetworkList.setSelectedIndex(minindex);
+ }
+
+ selectedNetworkList.repaint();
+ unselectedNetworkList.repaint();
+ updateOKButtonEnable();
+ updateAttributeTable();
+ updateMergeAttributeTable();
+ }
+ });
+ lrButtonPanel.add(rightButton);
+
+ leftButton.setIcon(new javax.swing.ImageIcon(getClass().getResource("/images/left16.gif"))); // NOI18N
+ leftButton.setEnabled(false);
+ leftButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ int [] indices = selectedNetworkList.getSelectedIndices();
+ if (indices == null || indices.length == 0) {
+ return;
+ }
+
+ for (int i= indices.length-1; i>=0; i--) {
+ CyNetwork removed = selectedNetworkData.removeElement(indices[i]);
+ unselectedNetworkData.add(removed);
+ addRemoveAttributeMapping(removed,false);
+ }
+
+ if (selectedNetworkData.getSize()==0) {
+ selectedNetworkList.clearSelection();
+ leftButton.setEnabled(false);
+ } else {
+ int minindex = selectedNetworkList.getMinSelectionIndex();
+ if (minindex>= selectedNetworkData.getSize()) {
+ minindex = 0;
+ }
+ selectedNetworkList.setSelectedIndex(minindex);
+ }
+
+ selectedNetworkList.repaint();
+ unselectedNetworkList.repaint();
+ updateOKButtonEnable();
+ updateAttributeTable();
+ updateMergeAttributeTable();
+ }
+ });
+ lrButtonPanel.add(leftButton);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 1;
+ gridBagConstraints.gridy = 0;
+ gridBagConstraints.insets = new java.awt.Insets(3, 3, 3, 3);
+ selectNetworkPanel.add(lrButtonPanel, gridBagConstraints);
+
+ selectedNetworkScrollPane.setPreferredSize(new java.awt.Dimension(200, 100));
+
+ selectedNetworkList.setSelectionMode(ListSelectionModel.SINGLE_INTERVAL_SELECTION);
+ selectedNetworkList.setBorder(javax.swing.BorderFactory.createTitledBorder("Selected networks"));
+ selectedNetworkList.setCellRenderer(new ListCellRenderer() {
+ private DefaultListCellRenderer defaultRenderer = new DefaultListCellRenderer();
+ public Component getListCellRendererComponent(
+ JList list,
+ Object value,
+ int index,
+ boolean isSelected,
+ boolean cellHasFocus) {
+ JLabel renderer = (JLabel) defaultRenderer.getListCellRendererComponent(list, value, index, isSelected, cellHasFocus);
+ renderer.setText(((CyNetwork)value).getTitle());
+ return renderer;
+ }
+ });
+ selectedNetworkList.addListSelectionListener(new javax.swing.event.ListSelectionListener() {
+ public void valueChanged(javax.swing.event.ListSelectionEvent evt) {
+ int index = selectedNetworkList.getMinSelectionIndex();
+ if (index>-1) {
+ unselectedNetworkList.getSelectionModel().clearSelection();
+ leftButton.setEnabled(true);
+ } else {
+ leftButton.setEnabled(false);
+ }
+ updateUpDownButtonEnable();
+ }
+ });
+ selectedNetworkScrollPane.setViewportView(selectedNetworkList);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 2;
+ gridBagConstraints.gridy = 0;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.BOTH;
+ gridBagConstraints.weightx = 0.5;
+ gridBagConstraints.weighty = 1.0;
+ gridBagConstraints.insets = new java.awt.Insets(3, 3, 3, 3);
+ selectNetworkPanel.add(selectedNetworkScrollPane, gridBagConstraints);
+
+ udButtonPanel.setLayout(new java.awt.GridLayout(0, 1, 0, 2));
+ udButtonPanel.setVisible(false);
+
+ upButton.setIcon(new javax.swing.ImageIcon(getClass().getResource("/images/up16.gif"))); // NOI18N
+ upButton.setEnabled(false);
+ upButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ int [] indices = selectedNetworkList.getSelectedIndices();
+ if (indices == null || indices.length == 0) {
+ return;
+ }
+
+ int imin = selectedNetworkList.getMinSelectionIndex();
+ int imax = selectedNetworkList.getMaxSelectionIndex();
+
+ if (imin<1) return;
+
+ CyNetwork removed = selectedNetworkData.removeElement(imin-1);
+ selectedNetworkData.add(imax,removed);
+
+ for (int ii=0; ii<indices.length; ii++) {
+ indices[ii]--;
+ }
+ selectedNetworkList.setSelectedIndices(indices);
+
+ updateUpDownButtonEnable();
+ selectedNetworkList.repaint();
+ unselectedNetworkList.repaint();
+ updateOKButtonEnable();
+ updateAttributeTable();
+ updateMergeAttributeTable();
+ }
+ });
+ udButtonPanel.add(upButton);
+
+ downButton.setIcon(new javax.swing.ImageIcon(getClass().getResource("/images/down16.gif"))); // NOI18N
+ downButton.setEnabled(false);
+ downButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ int [] indices = selectedNetworkList.getSelectedIndices();
+ if (indices == null || indices.length == 0) {
+ return;
+ }
+
+ int imin = selectedNetworkList.getMinSelectionIndex();
+ int imax = selectedNetworkList.getMaxSelectionIndex();
+
+ if (imax>=selectedNetworkData.getSize()-1) return;
+
+ CyNetwork removed = selectedNetworkData.removeElement(imax+1);
+ selectedNetworkData.add(imin,removed);
+
+ for (int ii=0; ii<indices.length; ii++) {
+ indices[ii]++;
+ }
+ selectedNetworkList.setSelectedIndices(indices);
+
+ updateUpDownButtonEnable();
+ selectedNetworkList.repaint();
+ unselectedNetworkList.repaint();
+ updateOKButtonEnable();
+ updateAttributeTable();
+ updateMergeAttributeTable();
+ }
+ });
+ udButtonPanel.add(downButton);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 3;
+ gridBagConstraints.gridy = 0;
+ gridBagConstraints.insets = new java.awt.Insets(3, 3, 3, 3);
+ selectNetworkPanel.add(udButtonPanel, gridBagConstraints);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 0;
+ gridBagConstraints.gridy = contentPaneGridY++;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.BOTH;
+ gridBagConstraints.weightx = 1.0;
+ gridBagConstraints.weighty = 0.5;
+ gridBagConstraints.insets = new java.awt.Insets(5, 5, 5, 5);
+ getContentPane().add(selectNetworkPanel, gridBagConstraints);
+
+ collapsiblePanelAgent.setLayout(new java.awt.BorderLayout());
+
+ advancedPanel.setPreferredSize(new java.awt.Dimension(690, 400));
+ advancedPanel.setLayout(new java.awt.GridBagLayout());
+
+ attributePanel.setBorder(javax.swing.BorderFactory.createTitledBorder("Matching attributes (attributes to match nodes between networks)"));
+ attributePanel.setLayout(new java.awt.GridBagLayout());
+
+ attributeScrollPane.setMinimumSize(new java.awt.Dimension(100, 50));
+ attributeScrollPane.setPreferredSize(new java.awt.Dimension(450, 50));
+ matchNodeTable.getModel().addTableModelListener(new TableModelListener() {
+ public void tableChanged(TableModelEvent e) {
+ mergeNodeAttributeTable.updateMatchingAttribute();
+ }
+ });
+
+ attributeScrollPane.setViewportView(matchNodeTable);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 0;
+ gridBagConstraints.gridy = 0;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.BOTH;
+ gridBagConstraints.weightx = 1.0;
+ gridBagConstraints.weighty = 1.0;
+ attributePanel.add(attributeScrollPane, gridBagConstraints);
+
+ idmappingCheckBox.setText("Map IDs between the matching attributes");
+ idmappingCheckBox.setVisible(checkCyThesaurus);
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 0;
+ gridBagConstraints.gridy = 1;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.LINE_START;
+ gridBagConstraints.insets = new java.awt.Insets(5, 5, 5, 5);
+ attributePanel.add(idmappingCheckBox, gridBagConstraints);
+
+ idmappingLabel.setForeground(new java.awt.Color(255, 0, 51));
+ idmappingLabel.setText("If you want to map identifiers between the matching attributes, please install CyThesaurus plugin version "+requiredCyThesaursServiceVersion+" or above.");
+ idmappingLabel.setVisible(!checkCyThesaurus);
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 0;
+ gridBagConstraints.gridy = 1;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.LINE_START;
+ gridBagConstraints.insets = new java.awt.Insets(5, 5, 5, 5);
+ attributePanel.add(idmappingLabel, gridBagConstraints);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 0;
+ gridBagConstraints.gridy = 0;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.weightx = 1.0;
+ gridBagConstraints.insets = new java.awt.Insets(5, 5, 5, 5);
+ advancedPanel.add(attributePanel, gridBagConstraints);
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 0;
+ gridBagConstraints.gridy = 2;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.weightx = 1.0;
+ gridBagConstraints.insets = new java.awt.Insets(5, 5, 5, 5);
+ advancedPanel.add(jSeparator3, gridBagConstraints);
+
+ mergeAttributePanel.setBorder(javax.swing.BorderFactory.createTitledBorder("How to merge attributes?"));
+ mergeAttributePanel.setMinimumSize(new java.awt.Dimension(400, 200));
+ mergeAttributePanel.setPreferredSize(new java.awt.Dimension(600, 200));
+ mergeAttributePanel.setLayout(new javax.swing.BoxLayout(mergeAttributePanel, javax.swing.BoxLayout.LINE_AXIS));
+
+ mergeAttributeTabbedPane.setMinimumSize(new java.awt.Dimension(450, 150));
+ mergeAttributeTabbedPane.setPreferredSize(new java.awt.Dimension(450, 200));
+
+ mergeNodeAttributePanel.setLayout(new javax.swing.BoxLayout(mergeNodeAttributePanel, javax.swing.BoxLayout.LINE_AXIS));
+
+ mergeNodeAttributeTable = new MergeAttributeTable(nodeAttributeMapping,matchingAttribute);
+ mergeNodeAttributeScrollPane.setViewportView(mergeNodeAttributeTable);
+
+ mergeNodeAttributePanel.add(mergeNodeAttributeScrollPane);
+
+ mergeAttributeTabbedPane.addTab("Node", mergeNodeAttributePanel);
+
+ mergeEdgeAttributePanel.setLayout(new javax.swing.BoxLayout(mergeEdgeAttributePanel, javax.swing.BoxLayout.LINE_AXIS));
+
+ mergeEdgeAttributeTable = new MergeAttributeTable(edgeAttributeMapping);
+ mergeEdgeAttributeScrollPane.setViewportView(mergeEdgeAttributeTable);
+
+ mergeEdgeAttributePanel.add(mergeEdgeAttributeScrollPane);
+
+ mergeAttributeTabbedPane.addTab("Edge", mergeEdgeAttributePanel);
+
+ mergeAttributePanel.add(mergeAttributeTabbedPane);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 0;
+ gridBagConstraints.gridy = 3;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.BOTH;
+ gridBagConstraints.weightx = 1.0;
+ gridBagConstraints.weighty = 1.0;
+ gridBagConstraints.insets = new java.awt.Insets(5, 5, 5, 5);
+ advancedPanel.add(mergeAttributePanel, gridBagConstraints);
+
+ advancedOptionCollapsiblePanelAgent.setLayout(new java.awt.BorderLayout());
+
+ optionPanel.setLayout(new java.awt.FlowLayout(java.awt.FlowLayout.LEFT));
+
+ inNetworkMergeCheckBox.setSelected(true);
+ parameter = new NetworkMergeParameterImpl(inNetworkMergeCheckBox.isSelected());
+ inNetworkMergeCheckBox.setText("Enable merging nodes/edges in the same network");
+ inNetworkMergeCheckBox.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ inNetworkMergeCheckBoxActionPerformed(evt);
+ }
+ });
+ optionPanel.add(inNetworkMergeCheckBox);
+
+ /*
+
+ advancedOptionCollapsiblePanelAgent.add(optionPanel, java.awt.BorderLayout.PAGE_START);
+ */
+ advancedOptionCollapsiblePanel.getContentPane().add(optionPanel, java.awt.BorderLayout.CENTER);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 0;
+ gridBagConstraints.gridy = 4;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.LINE_START;
+ gridBagConstraints.insets = new java.awt.Insets(5, 5, 5, 5);
+ advancedPanel.add(advancedOptionCollapsiblePanelAgent, gridBagConstraints);
+
+ /*
+
+ collapsiblePanelAgent.add(advancedPanel, java.awt.BorderLayout.CENTER);
+ */
+ advancedNetworkMergeCollapsiblePanel.getContentPane().add(advancedPanel, java.awt.BorderLayout.CENTER);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 0;
+ gridBagConstraints.gridy = contentPaneGridY++;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.BOTH;
+ gridBagConstraints.weightx = 1.0;
+ gridBagConstraints.weighty = 1.0;
+ getContentPane().add(collapsiblePanelAgent, gridBagConstraints);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 0;
+ gridBagConstraints.gridy = contentPaneGridY++;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.weightx = 1.0;
+ gridBagConstraints.insets = new java.awt.Insets(5, 5, 5, 5);
+ getContentPane().add(jSeparator4, gridBagConstraints);
+
+ okPanel.setDoubleBuffered(false);
+ okPanel.setLayout(new javax.swing.BoxLayout(okPanel, javax.swing.BoxLayout.LINE_AXIS));
+
+ okButton.setText(" Merge ");
+ okButton.setEnabled(false);
+ okButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ okButtonActionPerformed(evt);
+ }
+ });
+ okPanel.add(okButton);
+
+ cancelButton.setText("Cancel");
+ cancelButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ setVisible(false);
+ dispose();
+ }
+ });
+ okPanel.add(cancelButton);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 0;
+ gridBagConstraints.gridy = contentPaneGridY++;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.LINE_END;
+ gridBagConstraints.weightx = 1.0;
+ gridBagConstraints.insets = new java.awt.Insets(5, 5, 5, 5);
+ getContentPane().add(okPanel, gridBagConstraints);
+
+ pack();
+ }// </editor-fold>//GEN-END:initComponents
+
+ private void okButtonActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_okButtonActionPerformed
+ //this.setAlwaysOnTop(false);
+ if (this.advancedNetworkMergeCollapsiblePanel.isCollapsed()) {
+ if (getOperation() == Operation.UNION) {
+ GraphSetUtils.createUnionGraph(this.selectedNetworkData.getNetworkList(), true,
+ CyNetworkNaming.getSuggestedNetworkTitle("Union"));
+ } else if (getOperation() == Operation.INTERSECTION) {
+ GraphSetUtils.createIntersectionGraph(this.selectedNetworkData.getNetworkList(), true,
+ CyNetworkNaming.getSuggestedNetworkTitle("Intersection"));
+ } else if (getOperation() == Operation.DIFFERENCE) {
+ if (altDifferenceIsChecked)
+ GraphSetUtils.createDifferenceGraph2(this.selectedNetworkData.getNetworkList(), true,
+ CyNetworkNaming.getSuggestedNetworkTitle("Difference"));
+ else
+ GraphSetUtils.createDifferenceGraph(this.selectedNetworkData.getNetworkList(), true,
+ CyNetworkNaming.getSuggestedNetworkTitle("Difference"));
+ }
+
+ } else {
+ if (this.idmappingCheckBox.isSelected()) {
+ Map<String,Set<String>> selectedNetworkAttribute = new HashMap<String,Set<String>>();
+ Iterator<Map.Entry<String,String>> itEntry = matchingAttribute.getNetAttrMap().entrySet().iterator();
+ while (itEntry.hasNext()) {
+ Map.Entry<String,String> entry = itEntry.next();
+ String netID = entry.getKey();
+ String attr = entry.getValue();
+ Set<String> attrs = new HashSet<String>(1);
+ attrs.add(attr);
+ selectedNetworkAttribute.put(netID,attrs);
+ }
+
+ boolean isFrameAlwaysOnTop = frame.isAlwaysOnTop();
+ frame.setAlwaysOnTop(false);
+
+ final boolean isNode = true;
+ csplugins.network.merge.ui.IDMappingDialog dialog = new csplugins.network.merge.ui.IDMappingDialog(frame,true,selectedNetworkAttribute,isNode);
+ dialog.setLocationRelativeTo(frame);
+ dialog.setVisible(true);
+ dialog.setTgtType(tgtType);
+ if (!dialog.isCancelled()) {
+ selectedNetworkAttributeIDType = dialog.getSrcTypes();
+ tgtType = dialog.getTgtType();
+ } else {
+ int ret = JOptionPane.showConfirmDialog(this, "Error: you have not configured how to mapping the attributes." +
+ "\nMerge network without mapping IDs?", "No ID mapping", JOptionPane.YES_NO_OPTION);
+ if (ret==JOptionPane.NO_OPTION) {
+ frame.setAlwaysOnTop(isFrameAlwaysOnTop);
+ return;
+ }
+ }
+ frame.setAlwaysOnTop(isFrameAlwaysOnTop);
+ }
+
+ AttributeConflictCollector conflictCollector = new AttributeConflictCollectorImpl();
+
+ // network merge task
+ NetworkMergeSessionTask nmTask = new NetworkMergeSessionTask(
+ this.parameter,
+ this.matchingAttribute,
+ this.nodeAttributeMapping,
+ this.edgeAttributeMapping,
+ this.selectedNetworkData.getNetworkList(),
+ getOperation(),
+ mergeNodeAttributeTable.getMergedNetworkName(),
+ conflictCollector,
+ selectedNetworkAttributeIDType,
+ tgtType);
+
+ // Configure JTask Dialog Pop-Up Box
+ final JTaskConfig jTaskConfig = new JTaskConfig();
+ jTaskConfig.setOwner(this);
+ jTaskConfig.displayCloseButton(true);
+ jTaskConfig.displayCancelButton(true);
+ jTaskConfig.displayStatus(true);
+ jTaskConfig.setAutoDispose(false);
+ jTaskConfig.displayTimeElapsed(true);
+
+ // Execute Task in New Thread; pop open JTask Dialog Box.
+ TaskManager.executeTask(nmTask, jTaskConfig);
+ if (nmTask.isCancelled()) return;
+
+ // conflict handling task
+ if (!conflictCollector.isEmpty()) {
+ HandleConflictsTask hcTask = new HandleConflictsTask(conflictCollector);
+ TaskManager.executeTask(hcTask, jTaskConfig);
+ }
+
+ }
+
+ setVisible(false);
+ dispose();
+ }//GEN-LAST:event_okButtonActionPerformed
+
+ private void inNetworkMergeCheckBoxActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_inNetworkMergeCheckBoxActionPerformed
+ parameter.enableInNetworkMerge(inNetworkMergeCheckBox.isSelected());
+ this.updateOKButtonEnable();
+ }//GEN-LAST:event_inNetworkMergeCheckBoxActionPerformed
+
+ private double requiredCyThesaursServiceVersion = 1.01;
+ private boolean checkCyThesaurus() {
+ CyThesaurusServiceClient client = new CyThesaurusServiceMessageBasedClient("AdvanceNetworkMerge");
+ if (!client.isServiceAvailable())
+ return false;
+
+ double version = client.serviceVersion();
+ return version >= requiredCyThesaursServiceVersion;
+ }
+ /*
+ * Call when adding or removing a network to/from selected network list
+ *
+ */
+ private void addRemoveAttributeMapping(CyNetwork network, boolean isAdd) {
+ final String netID = network.getIdentifier();
+
+ if (isAdd) {
+ nodeAttributeMapping.addNetwork(netID);
+ edgeAttributeMapping.addNetwork(netID);
+ matchingAttribute.addNetwork(netID);
+ } else {
+ nodeAttributeMapping.removeNetwork(netID);
+ edgeAttributeMapping.removeNetwork(netID);
+ matchingAttribute.removeNetwork(netID);
+ }
+ }
+
+ private void updateOKButtonEnable() {
+ int n = !advancedNetworkMergeCollapsiblePanel.isCollapsed()&¶meter.inNetworkMergeEnabled()&&getOperation()==Operation.UNION?1:2;
+
+ if (selectedNetworkData.getSize()<n) {
+ okButton.setToolTipText("Select at least "+n+" networks to merge");
+ okButton.setEnabled(false);
+ return;
+ }
+
+ okButton.setToolTipText(null);
+ okButton.setEnabled(true);
+ }
+
+ private void updateUpDownButtonEnable() {
+ int imin = selectedNetworkList.getMinSelectionIndex();
+ int imax = selectedNetworkList.getMaxSelectionIndex();
+ upButton.setEnabled(0<imin&&imax<=selectedNetworkData.getSize()-1);
+ downButton.setEnabled(0<=imin&&imax<selectedNetworkData.getSize()-1);
+ }
+
+ private void updateAttributeTable() {
+ matchNodeTable.fireTableStructureChanged();
+ }
+
+
+ private void updateMergeAttributeTable() {
+ mergeNodeAttributeTable.fireTableStructureChanged();
+ mergeEdgeAttributeTable.fireTableStructureChanged();
+ }
+
+ private void updateSize() {
+ Dimension dim;
+ if (advancedNetworkMergeCollapsiblePanel.isCollapsed()) {
+ if (getOperation() != Operation.DIFFERENCE) {
+ dim = new Dimension(500,380);
+ } else {
+ dim = new Dimension(500,450);
+ }
+ } else {
+ if (frame.getExtendedState()==Frame.MAXIMIZED_BOTH) {
+ return;
+ }
+
+ Dimension dim_curr = frame.getSize(); // current dim
+ int width_curr = dim_curr.width;
+ int height_curr = dim_curr.height;
+
+ int width = 700;
+ int height = getOperation()==Operation.DIFFERENCE?800:720;
+
+ if (width < width_curr) {
+ width = width_curr;
+ }
+
+ if (height < height_curr) {
+ height = height_curr;
+ }
+
+ dim = new Dimension(width,height);
+ }
+
+ frame.setSize(dim);
+ }
+
+ /*
+ * Get currently selected operation
+ *
+ */
+ private Operation getOperation() {
+ return this.selectedOperation;
+ }
+
+
+ private MergeAttributeTable mergeNodeAttributeTable;
+ private MergeAttributeTable mergeEdgeAttributeTable;
+ private MatchNodeTable matchNodeTable;
+ private AttributeMapping nodeAttributeMapping;
+ private AttributeMapping edgeAttributeMapping;
+ private MatchingAttribute matchingAttribute;
+ private Map<String,Map<String,Set<String>>> selectedNetworkAttributeIDType;
+ private String tgtType;
+
+ private Frame frame;
+
+ private final ImageIcon UNION_ICON = new ImageIcon(getClass().getResource("/images/union.png"));
+ private final ImageIcon INTERSECTION_ICON = new ImageIcon(getClass().getResource("/images/intersection.png"));
+ private final ImageIcon DIFFERENCE_ICON = new ImageIcon(getClass().getResource("/images/difference.png"));
+ private final ImageIcon DIFFERENCE2_ICON = new ImageIcon(getClass().getResource("/images/difference2.png"));
+ private final ImageIcon[] OPERATION_ICONS = { UNION_ICON, INTERSECTION_ICON, DIFFERENCE_ICON };
+
+ private CollapsiblePanel advancedNetworkMergeCollapsiblePanel;
+ private CollapsiblePanel advancedOptionCollapsiblePanel;
+
+ private NetworkMergeParameter parameter;
+
+ boolean checkCyThesaurus;
+
+ // Variables declaration - do not modify//GEN-BEGIN:variables
+ private javax.swing.JPanel advancedOptionCollapsiblePanelAgent;
+ private javax.swing.JPanel advancedPanel;
+ private javax.swing.JPanel attributePanel;
+ private javax.swing.JScrollPane attributeScrollPane;
+ private javax.swing.JButton cancelButton;
+ private javax.swing.JPanel collapsiblePanelAgent;
+ private javax.swing.JButton downButton;
+ private javax.swing.JCheckBox idmappingCheckBox;
+ private javax.swing.JCheckBox inNetworkMergeCheckBox;
+ private javax.swing.JButton leftButton;
+ private javax.swing.JButton okButton;
+ private javax.swing.JComboBox operationComboBox;
+ private Operation selectedOperation;
+ private javax.swing.JLabel operationIcon;
+ private javax.swing.JRadioButton differenceButton;
+ private javax.swing.JRadioButton difference2Button;
+ private javax.swing.ButtonGroup differenceGroup;
+ private javax.swing.JPanel optionPanel;
+ private javax.swing.JButton rightButton;
+ private javax.swing.JList selectedNetworkList;
+ private NetworkListModel selectedNetworkData;
+ private javax.swing.JPanel udButtonPanel;
+ private javax.swing.JList unselectedNetworkList;
+ private SortedNetworkListModel unselectedNetworkData;
+ private javax.swing.JButton upButton;
+ // End of variables declaration//GEN-END:variables
+
+}
+
+class NetworkListModel extends AbstractListModel {
+ Vector<CyNetwork> model;
+
+ public NetworkListModel() {
+ model= new Vector<CyNetwork>();
+ }
+
+ //@Override
+ public int getSize() {
+ return model.size();
+ }
+
+ //@Override
+ public CyNetwork getElementAt(int index) {
+ return model.get(index);
+ }
+
+ public void add(CyNetwork network) {
+ model.add(network);
+ fireContentsChanged(this, 0, getSize());
+ }
+
+ public void add(int index, CyNetwork network) {
+ model.add(index,network);
+ fireContentsChanged(this, 0, getSize());
+ }
+
+ public CyNetwork removeElement(int index) {
+ CyNetwork removed = model.remove(index);
+ if (removed!=null) {
+ fireContentsChanged(this, 0, getSize());
+ }
+ return removed;
+ }
+
+
+ public List<CyNetwork> getNetworkList() {
+ return model;
+ }
+}
+
+class SortedNetworkListModel extends AbstractListModel {
+ // Using a SortedMap from String to network
+ TreeMap<String,CyNetwork> model;
+
+ public SortedNetworkListModel() {
+ model= new TreeMap<String,CyNetwork>();
+ }
+
+ //@Override
+ public int getSize() {
+ return model.size();
+ }
+
+ //@Override
+ public CyNetwork getElementAt(int index) {
+ return (CyNetwork) model.values().toArray()[index];
+ }
+
+ public void add(CyNetwork network) {
+ String title = network.getTitle();
+ model.put(title.toUpperCase(),network);
+ fireContentsChanged(this, 0, getSize());
+ }
+
+ public CyNetwork removeElement(int index) {
+ CyNetwork removed = model.remove(getElementAt(index).getTitle().toUpperCase());
+ if (removed!=null) {
+ fireContentsChanged(this, 0, getSize());
+ }
+ return removed;
+ }
+
+ public List<CyNetwork> getNetworkList() {
+ return new Vector<CyNetwork>(model.values());
+ }
+}
+
+class NetworkMergeSessionTask implements Task {
+ final NetworkMergeParameter parameter;
+ private MatchingAttribute matchingAttribute;
+ private AttributeMapping nodeAttributeMapping;
+ private AttributeMapping edgeAttributeMapping;
+ private List<CyNetwork> selectedNetworkList;
+ private Operation operation;
+ private String mergedNetworkName;
+ private AttributeConflictCollector conflictCollector;
+ private Map<String,Map<String,Set<String>>> selectedNetworkAttributeIDType;
+ private final String tgtType;
+ final private AttributeBasedNetworkMerge networkMerge ;
+ private TaskMonitor taskMonitor;
+ private boolean cancelled;
+
+ /**
+ * Constructor.<br>
+ *
+ */
+ NetworkMergeSessionTask( final NetworkMergeParameter parameter,
+ final MatchingAttribute matchingAttribute,
+ final AttributeMapping nodeAttributeMapping,
+ final AttributeMapping edgeAttributeMapping,
+ final List<CyNetwork> selectedNetworkList,
+ final Operation operation,
+ final String mergedNetworkName,
+ final AttributeConflictCollector conflictCollector,
+ final Map<String,Map<String,Set<String>>> selectedNetworkAttributeIDType,
+ final String tgtType) {
+ this.parameter = parameter;
+ this.matchingAttribute = matchingAttribute;
+ this.nodeAttributeMapping = nodeAttributeMapping;
+ this.edgeAttributeMapping = edgeAttributeMapping;
+ this.selectedNetworkList = selectedNetworkList;
+ this.operation = operation;
+ this.mergedNetworkName = mergedNetworkName;
+ this.conflictCollector = conflictCollector;
+ this.selectedNetworkAttributeIDType = selectedNetworkAttributeIDType;
+ this.tgtType = tgtType;
+ cancelled = false;
+
+ final AttributeValueMatcher attributeValueMatcher;
+ final AttributeMerger attributeMerger;
+ //if (idMapping==null) {
+ attributeValueMatcher = new DefaultAttributeValueMatcher();
+ attributeMerger = new DefaultAttributeMerger(conflictCollector);
+ // } else {
+ // attributeValueMatcher = new IDMappingAttributeValueMatcher(idMapping);
+ // attributeMerger = new IDMappingAttributeMerger(conflictCollector,idMapping,tgtType);
+ // }
+
+ networkMerge = new AttributeBasedNetworkMerge(
+ parameter,
+ matchingAttribute,
+ nodeAttributeMapping,
+ edgeAttributeMapping,
+ attributeMerger,
+ attributeValueMatcher);
+
+ }
+
+ public boolean isCancelled() {
+ return cancelled;
+ }
+
+ /**
+ * Executes Task
+ *
+ * @throws
+ * @throws Exception
+ */
+ //@Override
+ public void run() {
+
+ try {
+ networkMerge.setTaskMonitor(taskMonitor);
+
+ if (selectedNetworkAttributeIDType!=null) {
+ taskMonitor.setStatus("Mapping IDs...");
+ taskMonitor.setPercentCompleted(-1);
+ CyThesaurusServiceClient client = new CyThesaurusServiceMessageBasedClient("AdvanceNetworkMerge");
+ if (!client.isServiceAvailable()) {
+ taskMonitor.setStatus("CyThesaurs service is not available.");
+ taskMonitor.setPercentCompleted(100);
+ return;
+ }
+
+ defineTgtAttributes();
+
+ String mergedAttr = nodeAttributeMapping.getMergedAttribute(0);
+ for (String net : selectedNetworkAttributeIDType.keySet()) {
+ final Set<String> nets = new HashSet<String>(1);
+ nets.add(net);
+ Map<String,Set<String>> mapAttrTypes = selectedNetworkAttributeIDType.get(net);
+ for (String attr : mapAttrTypes.keySet()) {
+ Set<String> types = mapAttrTypes.get(attr);
+ if (!client.mapID(nets, attr, mergedAttr, types, tgtType)) {
+ taskMonitor.setStatus("Failed to map IDs.");
+ taskMonitor.setPercentCompleted(100);
+ return;
+ }
+ }
+ }
+
+ matchingAttribute.clear();
+ for (String net : selectedNetworkAttributeIDType.keySet()) {
+ matchingAttribute.putAttributeForMatching(net, mergedAttr);
+ nodeAttributeMapping.setOriginalAttribute(net, mergedAttr, 0);
+ }
+
+ }
+
+ CyNetwork mergedNetwork = networkMerge.mergeNetwork(
+ selectedNetworkList,
+ operation,
+ mergedNetworkName);
+
+ /*
+ cytoscape.view.CyNetworkView networkView = Cytoscape.getNetworkView(mergedNetworkName);
+
+ // get the VisualMappingManager and CalculatorCatalog
+ cytoscape.visual.VisualMappingManager manager = Cytoscape.getVisualMappingManager();
+ cytoscape.visual.CalculatorCatalog catalog = manager.getCalculatorCatalog();
+
+ cytoscape.visual.VisualStyle vs = catalog.getVisualStyle(mergedNetworkName+" Visual Style");
+ if (vs == null) {
+ // if not, create it and add it to the catalog
+ //vs = createVisualStyle(networkMerge);
+ cytoscape.visual.NodeAppearanceCalculator nodeAppCalc = new cytoscape.visual.NodeAppearanceCalculator();
+ cytoscape.visual.mappings.PassThroughMapping pm = new cytoscape.visual.mappings.PassThroughMapping(new String(), cytoscape.data.Semantics.CANONICAL_NAME);
+
+ cytoscape.visual.calculators.Calculator nlc = new cytoscape.visual.calculators.BasicCalculator(null,
+ pm, cytoscape.visual.VisualPropertyType.NODE_LABEL);
+ nodeAppCalc.setCalculator(nlc);
+
+ vs.setNodeAppearanceCalculator(nodeAppCalc);
+
+ catalog.addVisualStyle(vs);
+ }
+ // actually apply the visual style
+ manager.setVisualStyle(vs);
+ networkView.redrawGraph(true,true);
+ */
+
+ // taskMonitor.setPercentCompleted(100);
+ // taskMonitor.setStatus("The selected networks were successfully merged into network '"
+ // + mergedNetwork.getTitle()
+ // + "' with "
+ // + conflictCollector.getMapToIDAttr().size()
+ // + " attribute conflicts.");
+
+ } catch(Exception e) {
+ taskMonitor.setException(e, "Network Merge Failed!");
+ e.printStackTrace();
+ }
+
+ }
+
+ private void defineTgtAttributes() {
+ CyAttributes nodeAttributes = Cytoscape.getNodeAttributes();
+ List<String> attrNames = java.util.Arrays.asList(nodeAttributes.getAttributeNames());
+
+ MultiHashMapDefinition mmapDef = nodeAttributes.getMultiHashMapDefinition();
+
+ String mergedAttr = nodeAttributeMapping.getMergedAttribute(0);
+ if (attrNames.contains(mergedAttr)) {
+ // for existing attribute, check if its type is String or List
+ byte attrType = nodeAttributes.getType(mergedAttr);
+ if (attrType!=CyAttributes.TYPE_STRING && attrType!=CyAttributes.TYPE_SIMPLE_LIST) {
+ throw new java.lang.UnsupportedOperationException("Only String and List target attributes are supported.");
+ }
+ } else {
+ byte attrType = nodeAttributeMapping.getMergedAttributeType(0);
+
+ if (attrType==CyAttributes.TYPE_SIMPLE_LIST) {
+ // define the new attribute as List
+ byte[] keyTypes = new byte[] { MultiHashMapDefinition.TYPE_INTEGER };
+ mmapDef.defineAttribute(mergedAttr,
+ MultiHashMapDefinition.TYPE_STRING,
+ keyTypes);
+ } else {
+ mmapDef.defineAttribute(mergedAttr,
+ MultiHashMapDefinition.TYPE_STRING,
+ null);
+ }
+ }
+ }
+
+ /**
+ * Halts the Task: Not Currently Implemented.
+ */
+ //@Override
+ public void halt() {
+ cancelled = true;
+ networkMerge.interrupt();
+ }
+
+ /**
+ * Sets the Task Monitor.
+ *
+ * @param taskMonitor
+ * TaskMonitor Object.
+ */
+ //@Override
+ public void setTaskMonitor(TaskMonitor taskMonitor) throws IllegalThreadStateException {
+ this.taskMonitor = taskMonitor;
+ }
+
+ /**
+ * Gets the Task Title.
+ *
+ * @return Task Title.
+ */
+ //@Override
+ public String getTitle() {
+ return "Merging networks";
+ }
+}
+
+class HandleConflictsTask implements Task {
+ private AttributeConflictCollector conflictCollector;
+
+ private TaskMonitor taskMonitor;
+
+ /**
+ * Constructor.<br>
+ *
+ */
+ HandleConflictsTask(final AttributeConflictCollector conflictCollector) {
+ this.conflictCollector = conflictCollector;
+ }
+
+ /**
+ * Executes Task
+ *
+ * @throws
+ * @throws Exception
+ */
+ //@Override
+ public void run() {
+ taskMonitor.setStatus("Handle conflicts.\n\nIt may take a while.\nPlease wait...");
+ taskMonitor.setPercentCompleted(0);
+
+ try {
+ int nBefore = conflictCollector.getMapToIDAttr().size();
+
+ List<AttributeConflictHandler> conflictHandlers = new Vector<AttributeConflictHandler>();
+
+ AttributeConflictHandler conflictHandler;
+
+ // if (idMapping!=null) {
+ // conflictHandler = new IDMappingAttributeConflictHandler(idMapping);
+ // conflictHandlers.add(conflictHandler);
+ // }
+
+ conflictHandler = new DefaultAttributeConflictHandler();
+ conflictHandlers.add(conflictHandler);
+
+ AttributeConflictManager conflictManager = new AttributeConflictManager(conflictCollector,conflictHandlers);
+ conflictManager.handleConflicts();
+
+ int nAfter = conflictCollector.getMapToIDAttr().size();
+
+ taskMonitor.setPercentCompleted(100);
+ taskMonitor.setStatus("Successfully handled " + (nBefore-nAfter) + " attribute conflicts. "
+ + nAfter+" conflicts remains.");
+ } catch(Exception e) {
+ //taskMonitor.setPercentCompleted(100);
+ //taskMonitor.setStatus("Conflict handle Failed!");
+ taskMonitor.setException(e, "Conflict handle Failed!");
+ e.printStackTrace();
+ }
+
+ }
+
+ /**
+ * Halts the Task: Not Currently Implemented.
+ */
+ //@Override
+ public void halt() {
+ // Task can not currently be halted.
+ taskMonitor.setPercentCompleted(100);
+ taskMonitor.setStatus("Failed!!!");
+ }
+
+ /**
+ * Sets the Task Monitor.
+ *
+ * @param taskMonitor
+ * TaskMonitor Object.
+ */
+ //@Override
+ public void setTaskMonitor(TaskMonitor taskMonitor) throws IllegalThreadStateException {
+ this.taskMonitor = taskMonitor;
+ }
+
+ /**
+ * Gets the Task Title.
+ *
+ * @return Task Title.
+ */
+ //@Override
+ public String getTitle() {
+ return "Merging networks";
+ }
+}
diff --git a/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/ui/RowTableCellEditor.java b/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/ui/RowTableCellEditor.java
new file mode 100644
index 0000000..7f30276
--- /dev/null
+++ b/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/ui/RowTableCellEditor.java
@@ -0,0 +1,134 @@
+/* File: RowTableCellEditor.java
+
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+
+package csplugins.network.merge.ui;
+
+import java.util.HashMap;
+import java.util.EventObject;
+
+import java.awt.event.MouseEvent;
+import java.awt.Component;
+
+import javax.swing.JTable;
+import javax.swing.DefaultCellEditor;
+import javax.swing.table.TableCellEditor;
+import javax.swing.JTextField;
+import javax.swing.event.CellEditorListener;
+
+/**
+ *
+ * @author gjj
+ */
+// support different editors for each row in a column
+class RowTableCellEditor implements TableCellEditor {
+ protected HashMap<Integer, TableCellEditor> editors;
+
+ protected TableCellEditor editor, defaultEditor;
+
+ JTable table;
+
+ /**
+ * Constructs a EachRowEditor. create default editor
+ *
+ * @see TableCellEditor
+ * @see DefaultCellEditor
+ */
+ public RowTableCellEditor(JTable table) {
+ this.table = table;
+ editors = new HashMap<Integer, TableCellEditor>();
+ defaultEditor = new DefaultCellEditor(new JTextField());
+ }
+
+ /**
+ * @param row
+ * table row
+ * @param editor
+ * table cell editor
+ */
+ public void setEditorAt(int row, TableCellEditor editor) {
+ editors.put(new Integer(row), editor);
+ }
+
+ public Component getTableCellEditorComponent(JTable table, Object value,
+ boolean isSelected, int row, int column) {
+ return editor.getTableCellEditorComponent(table, value, isSelected,
+ row, column);
+ }
+
+ public Object getCellEditorValue() {
+ return editor.getCellEditorValue();
+ }
+
+ public boolean stopCellEditing() {
+ return editor.stopCellEditing();
+ }
+
+ public void cancelCellEditing() {
+ editor.cancelCellEditing();
+ }
+
+ public boolean isCellEditable(EventObject anEvent) {
+ selectEditor((MouseEvent) anEvent);
+ return editor.isCellEditable(anEvent);
+ }
+
+ public void addCellEditorListener(CellEditorListener l) {
+ editor.addCellEditorListener(l);
+ }
+
+ public void removeCellEditorListener(CellEditorListener l) {
+ editor.removeCellEditorListener(l);
+ }
+
+ public boolean shouldSelectCell(EventObject anEvent) {
+ selectEditor((MouseEvent) anEvent);
+ return editor.shouldSelectCell(anEvent);
+ }
+
+ protected void selectEditor(MouseEvent e) {
+ int row;
+ if (e == null) {
+ row = table.getSelectionModel().getAnchorSelectionIndex();
+ } else {
+ row = table.rowAtPoint(e.getPoint());
+ }
+ editor = (TableCellEditor) editors.get(new Integer(row));
+ if (editor == null) {
+ editor = defaultEditor;
+ }
+ }
+}
diff --git a/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/util/AttributeMerger.java b/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/util/AttributeMerger.java
new file mode 100644
index 0000000..97309aa
--- /dev/null
+++ b/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/util/AttributeMerger.java
@@ -0,0 +1,60 @@
+/* File: AttributeMerger.java
+
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+package csplugins.network.merge.util;
+
+import cytoscape.data.CyAttributes;
+
+import java.util.Map;
+
+/**
+ *
+ *
+ */
+public interface AttributeMerger {
+
+ /**
+ *
+ * @param mapGOAttr
+ * @param toID
+ * @param toAttrName
+ * @param attrs
+ */
+ public void mergeAttribute(Map<String,String> mapGOAttr,
+ String toID,
+ String toAttrName,
+ CyAttributes attrs);
+}
diff --git a/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/util/AttributeValueCastUtils.java b/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/util/AttributeValueCastUtils.java
new file mode 100644
index 0000000..8634017
--- /dev/null
+++ b/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/util/AttributeValueCastUtils.java
@@ -0,0 +1,249 @@
+/* File: AbstractNetworkMerge.java
+
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+package csplugins.network.merge.util;
+
+import cytoscape.data.CyAttributes;
+import cytoscape.data.attr.MultiHashMapDefinition;
+
+import java.util.Arrays;
+import java.util.Iterator;
+import java.util.Set;
+import java.util.List;
+import java.util.HashSet;
+
+/**
+ *
+ *
+ */
+public class AttributeValueCastUtils {
+ /**
+ * Check if the types are convertable for two attributes
+ * @param fromAttrName
+ * @param toAttrName
+ * @param attrs
+ * @return
+ */
+ public static boolean isAttributeTypeConvertable(final String fromAttrName,
+ final String toAttrName,
+ final CyAttributes attrs) {
+ if (fromAttrName==null || toAttrName==null || attrs==null) {
+ throw new java.lang.NullPointerException("Null fromAttrName or toAttrName or attrs");
+ }
+
+ final List<String> attrNames = Arrays.asList(attrs.getAttributeNames());
+ if (!attrNames.contains(fromAttrName)) {
+ throw new java.lang.IllegalArgumentException("'"+fromAttrName+"' not exists");
+ }
+
+ if (!attrNames.contains(toAttrName)) {
+ return true; // always convertable to a non-existing attribute
+ }
+
+ // first check the basic type is convertible
+ final MultiHashMapDefinition mmapDef = attrs.getMultiHashMapDefinition();
+ final byte valType1 = mmapDef.getAttributeValueType(fromAttrName);
+ final byte valType2 = mmapDef.getAttributeValueType(toAttrName);
+
+ if (valType1 != valType2) { // if value type is not the same
+ switch (valType1) {
+ case MultiHashMapDefinition.TYPE_BOOLEAN:
+ if (valType2!=MultiHashMapDefinition.TYPE_BOOLEAN
+ && valType2!=MultiHashMapDefinition.TYPE_STRING) {
+ return false;
+ }
+ break;
+ case MultiHashMapDefinition.TYPE_FLOATING_POINT:
+ if (valType2!=MultiHashMapDefinition.TYPE_FLOATING_POINT
+ && valType2!=MultiHashMapDefinition.TYPE_STRING) {
+ return false;
+ }
+ break;
+ case MultiHashMapDefinition.TYPE_INTEGER:
+ if (valType2!=MultiHashMapDefinition.TYPE_INTEGER
+ && valType2!=MultiHashMapDefinition.TYPE_FLOATING_POINT
+ && valType2!=MultiHashMapDefinition.TYPE_STRING) {
+ return false;
+ }
+ break;
+ case MultiHashMapDefinition.TYPE_STRING:
+ if (valType2!=MultiHashMapDefinition.TYPE_STRING) {
+ return false;
+ }
+ break;
+ default:
+ return false;
+ }
+ }
+
+ // check list, map ...
+ final byte[] dimTypes1 = mmapDef.getAttributeKeyspaceDimensionTypes(fromAttrName);
+ final byte[] dimTypes2 = mmapDef.getAttributeKeyspaceDimensionTypes(toAttrName);
+
+ final int n1 = dimTypes1.length;
+ final int n2 = dimTypes2.length;
+
+ if (n2==0 && valType2==MultiHashMapDefinition.TYPE_STRING) {
+ return true; // any type can convert to String
+ }
+
+ if (n1==0 && n2==0) { // simple types
+ return true;
+ }
+
+ if (n1==0 && n2==1) {
+ return dimTypes2[0] == MultiHashMapDefinition.TYPE_INTEGER; // converting from simple type to simple list
+ }
+
+ if (n1!=n2) {
+ return false;
+ }
+
+ for (int i=0; i<n1; i++) {
+ if (dimTypes1[i]!=dimTypes2[i]) {
+ return false;
+ }
+ }
+
+ return valType1==valType2; // for complex case, type must be the same
+ }
+
+ public static boolean isAttributeTypeConvertable(final byte fromType, final byte toType) {
+ switch (fromType) {
+ case CyAttributes.TYPE_BOOLEAN:
+ return toType==CyAttributes.TYPE_BOOLEAN
+ || toType==CyAttributes.TYPE_STRING
+ || toType==CyAttributes.TYPE_SIMPLE_LIST;
+ case CyAttributes.TYPE_FLOATING:
+ return toType==CyAttributes.TYPE_FLOATING
+ || toType==CyAttributes.TYPE_STRING
+ || toType==CyAttributes.TYPE_SIMPLE_LIST;
+ case CyAttributes.TYPE_INTEGER:
+ return toType==CyAttributes.TYPE_INTEGER
+ || toType==CyAttributes.TYPE_FLOATING
+ || toType==CyAttributes.TYPE_STRING
+ || toType==CyAttributes.TYPE_SIMPLE_LIST;
+ case CyAttributes.TYPE_STRING:
+ return toType==CyAttributes.TYPE_STRING
+ || toType==CyAttributes.TYPE_SIMPLE_LIST;
+ case CyAttributes.TYPE_SIMPLE_LIST:
+ return toType==CyAttributes.TYPE_STRING
+ || toType==CyAttributes.TYPE_SIMPLE_LIST;
+ case CyAttributes.TYPE_SIMPLE_MAP:
+ return toType==CyAttributes.TYPE_STRING
+ || toType==CyAttributes.TYPE_SIMPLE_MAP;
+ case CyAttributes.TYPE_COMPLEX:
+ return toType==CyAttributes.TYPE_STRING
+ || toType==CyAttributes.TYPE_SIMPLE_MAP;
+ default:
+ return false;
+ }
+ }
+
+ /*
+ * Return the attribute with the highest compatible attribute
+ *
+ */
+ public static String getMostCompatibleAttribute(final Set<String> attrNames, final CyAttributes attrs) {
+ if (attrNames==null || attrs==null) {
+ throw new java.lang.NullPointerException("Null attrNames or attrs");
+ }
+
+ attrNames.remove(null);
+ if (attrNames.isEmpty()) {
+ throw new java.lang.IllegalArgumentException("Empty attrNames");
+ }
+
+ if (!Arrays.asList(attrs.getAttributeNames()).containsAll(attrNames)) {
+ throw new java.lang.IllegalStateException("Attribute not exists");
+ }
+
+ String[] attrArray = attrNames.toArray(new String[0]);
+ Set<String> compatibleSet = new HashSet<String>();
+
+ int n = attrArray.length;
+ for (int i=0; i<n; i++) {
+ String attr1 = attrArray[i];
+
+ boolean compatible = true;
+ for (int j=0; j<n; j++) {
+ if (j==i) continue;
+ String attr2 = attrArray[j];
+ if (!AttributeValueCastUtils.isAttributeTypeConvertable(attr2, attr1, attrs)) {
+ compatible = false;
+ break;
+ }
+ }
+
+ if (compatible) {
+ compatibleSet.add(attr1);
+ }
+ }
+
+ if (compatibleSet.isEmpty()) {
+ return null;
+ }
+
+ final Iterator<String> it = compatibleSet.iterator();
+ while (it.hasNext()) {
+ // if exists list, return it
+ String attr = it.next();
+ byte type = attrs.getType(attr);
+ if (type==CyAttributes.TYPE_SIMPLE_LIST) {
+ return attr;
+ }
+ }
+ return compatibleSet.iterator().next();
+
+ }
+
+
+ public static Object attributeValueCast(byte typeTo, Object value) {
+ switch (typeTo) {
+ case CyAttributes.TYPE_BOOLEAN:
+ return Boolean.valueOf(value.toString());
+ case CyAttributes.TYPE_INTEGER:
+ return Integer.valueOf(value.toString());
+ case CyAttributes.TYPE_FLOATING:
+ return Double.valueOf(value.toString());
+ case CyAttributes.TYPE_STRING:
+ return value.toString();
+ default:
+ throw new java.lang.IllegalStateException("wrong type");
+ }
+ }
+
+}
diff --git a/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/util/AttributeValueMatcher.java b/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/util/AttributeValueMatcher.java
new file mode 100644
index 0000000..d9b08f8
--- /dev/null
+++ b/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/util/AttributeValueMatcher.java
@@ -0,0 +1,59 @@
+/* File: AttributeValueMatcher.java
+
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+package csplugins.network.merge.util;
+
+import cytoscape.data.CyAttributes;
+
+/**
+ * Match attribute values
+ *
+ *
+ */
+public interface AttributeValueMatcher {
+
+ /**
+ * Check whether two attributes of two nodes/edges are "match"
+ * @param id1
+ * @param attr1
+ * @param id2
+ * @param attr2
+ * @param cyAttributes
+ * @return true if matched; false otherwise
+ */
+ public boolean matched(String id1, String attr1,
+ String id2, String attr2, CyAttributes cyAttributes);
+}
diff --git a/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/util/CopyingAttributeValueVisitor.java b/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/util/CopyingAttributeValueVisitor.java
new file mode 100644
index 0000000..db2972f
--- /dev/null
+++ b/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/util/CopyingAttributeValueVisitor.java
@@ -0,0 +1,74 @@
+/* File: AbstractNetworkMerge.java
+
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+package csplugins.network.merge.util;
+
+
+import cytoscape.data.CyAttributes;
+import cytoscape.data.AttributeValueVisitor;
+
+import java.util.Arrays;
+/**
+ *
+ * @
+ */
+
+ // this is different from CopyingAttributeValueVisitor in CyAtributeUtil
+ // the attributes copying from and to can be different
+ /**
+ * copy each attribute value from copyID to an
+ * attribute value of copyAttribute associated with objTraversedCopyID.
+ */
+ public class CopyingAttributeValueVisitor implements AttributeValueVisitor {
+ private String toID;
+ private String toAttrName;
+
+ public CopyingAttributeValueVisitor(String toID, String toAttrName) {
+ this.toID = toID;
+ this.toAttrName = toAttrName;
+ }
+
+ //@Override
+ public void visitingAttributeValue(String fromID, String attrName,
+ CyAttributes attrs, Object[] keySpace,
+ Object visitedValue) {
+ if (!Arrays.asList(attrs.getAttributeNames()).contains(toAttrName)) { // if toAttribute not exists
+ throw new java.lang.IllegalStateException("'"+toAttrName+"' must be defined before calling this method");
+ }
+
+ attrs.getMultiHashMap().setAttributeValue(toID, toAttrName, visitedValue, keySpace);
+ }
+ }
diff --git a/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/util/DefaultAttributeMerger.java b/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/util/DefaultAttributeMerger.java
new file mode 100644
index 0000000..61390bf
--- /dev/null
+++ b/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/util/DefaultAttributeMerger.java
@@ -0,0 +1,215 @@
+/* File: DefaultAttributeMerger.java
+
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+package csplugins.network.merge.util;
+
+import csplugins.network.merge.conflict.AttributeConflictCollector;
+
+import cytoscape.data.CyAttributes;
+import cytoscape.data.CyAttributesUtils;
+
+import java.util.List;
+import java.util.Map;
+import java.util.Iterator;
+import java.util.Arrays;
+
+/**
+ *
+ *
+ */
+public class DefaultAttributeMerger implements AttributeMerger {
+
+ protected final AttributeConflictCollector conflictCollector;
+
+ public DefaultAttributeMerger(final AttributeConflictCollector conflictCollector) {
+ this.conflictCollector = conflictCollector;
+ }
+
+ /**
+ * Merge one attribute into another
+ * @param fromIDs
+ * @param fromAttrName
+ * @param toID
+ * @param toAttrName
+ * @param attrs
+ * @param conflictCollector
+ */
+ //@Override
+ public void mergeAttribute(final Map<String,String> mapGOAttr,
+ final String toID,
+ final String toAttrName,
+ final CyAttributes attrs) {
+ if ((mapGOAttr == null) || (toID == null) || (toAttrName == null) || (attrs==null)) {
+ throw new java.lang.IllegalArgumentException("Null argument.");
+ }
+
+ final List<String> attrNames = Arrays.asList(attrs.getAttributeNames());
+
+ Iterator<Map.Entry<String,String>> itEntryGOAttr = mapGOAttr.entrySet().iterator();
+ while (itEntryGOAttr.hasNext()) {
+ Map.Entry<String,String> entryGOAttr = itEntryGOAttr.next();
+ String fromID = entryGOAttr.getKey();
+ String fromAttrName = entryGOAttr.getValue();
+
+ if (!attrNames.contains(fromAttrName)||!attrNames.contains(toAttrName)) { // toAttrName must be defined before calling this method
+ throw new java.lang.IllegalArgumentException("'"+fromAttrName+"' or '"+toAttrName+"' not exists");
+ }
+
+ if (!AttributeValueCastUtils.isAttributeTypeConvertable(fromAttrName,toAttrName,attrs)) {
+ throw new java.lang.IllegalArgumentException("'"+fromAttrName+"' cannot be converted to '"+toAttrName+"'");
+ }
+
+ if (toID.compareTo(fromID)==0 && toAttrName.compareTo(fromAttrName)==0) {
+ //TODO: if local attribute is realized, process here
+ continue;
+ }
+
+ if (!attrs.hasAttribute(fromID, fromAttrName)) {
+ continue;
+ }
+
+ //byte type1 = attrs.getType(fromAttrName);
+ byte type2 = attrs.getType(toAttrName);
+
+ if (type2 == CyAttributes.TYPE_STRING) { // the case of inconvertable attributes and simple attributes to String
+ Object o1 = attrs.getAttribute(fromID, fromAttrName); //Correct??
+ String o2 = attrs.getStringAttribute(toID, toAttrName);
+ if (o2==null||o2.length()==0) { //null or empty attribute
+ attrs.setAttribute(toID, toAttrName, o1.toString());
+ //continue;
+ } else if (o1.equals(o2)) {
+ //continue;// the same, do nothing
+ } else { // attribute conflict
+
+ // add to conflict collector
+ conflictCollector.addConflict(fromID, fromAttrName, toID, toAttrName,attrs);
+ //continue;
+ }
+ } else if (type2<0&&type2!=CyAttributes.TYPE_SIMPLE_LIST) { // only support matching between simple types
+ // and simple lists for now
+ //TODO: support simple and complex map?
+ Object o1 = attrs.getAttribute(fromID, fromAttrName); //Correct??
+ Object o2 = attrs.getAttribute(toID, toAttrName);
+ if (o2==null) {
+ CopyingAttributeValueVisitor copyVisitor = new CopyingAttributeValueVisitor(toID,toAttrName);
+ CyAttributesUtils.traverseAttributeValues(fromID, fromAttrName, attrs, copyVisitor);
+ //continue;
+ } else if (o1.equals(o2)) {
+ //continue; // the same, do nothing
+ } else { // attribute conflict
+
+ // add to conflict collector
+ conflictCollector.addConflict(fromID, fromAttrName, toID, toAttrName,attrs);
+ //continue;
+ }
+ } else if (type2>0) { // simple type (type1>0) (Integer, Double, Boolean)
+ Object o1 = attrs.getAttribute(fromID, fromAttrName);
+ byte type1 = attrs.getType(fromAttrName);
+ if (type1!=type2) {
+ o1 = AttributeValueCastUtils.attributeValueCast(type2,o1);
+ }
+
+ Object o2 = attrs.getAttribute(toID, toAttrName);
+ if (o2==null) {
+ attrs.getMultiHashMap().setAttributeValue(toID, toAttrName, o1, null);
+ //continue;
+ } else if (o1.equals(o2)) {
+ //continue; // the same, do nothing
+ } else { // attribute conflict
+
+ // add to conflict collector
+ conflictCollector.addConflict(fromID, fromAttrName, toID, toAttrName,attrs);
+ //continue;
+ }
+ } else { // toattr is list type
+ //TODO: use a conflict handler to handle this part?
+
+ type2 = attrs.getMultiHashMapDefinition().getAttributeValueType(toAttrName);
+ byte type1 = attrs.getType(fromAttrName);
+ if (type1>0) {
+ Object o1 = attrs.getAttribute(fromID, fromAttrName);
+ if (type1!=type2) {
+ o1 = AttributeValueCastUtils.attributeValueCast(type2,o1);
+ }
+
+ List<Object> l2 = attrs.getListAttribute(toID, toAttrName);
+ if (l2 == null) {
+ //l2 = new Vector();
+ throw new java.lang.IllegalStateException("Define '"+toAttrName+"' first");
+ }
+
+ if (!l2.contains(o1)) {
+ l2.add(o1);
+ }
+
+ attrs.setListAttribute(toID, toAttrName, l2);
+
+ //continue;
+ } else if (type1==CyAttributes.TYPE_SIMPLE_LIST) {
+ type1 = attrs.getMultiHashMapDefinition().getAttributeValueType(fromAttrName);
+
+ List<Object> l1 = attrs.getListAttribute(fromID, fromAttrName);
+ List<Object> l2 = attrs.getListAttribute(toID, toAttrName);
+ if (l2 == null) {
+ //l2 = new Vector();
+ throw new java.lang.IllegalStateException("Define '"+toAttrName+"' first");
+ }
+
+ int nl1 = l1.size();
+ for (int il1=0; il1<nl1; il1++) {
+ Object o1 = l1.get(il1);
+ if (type1!=type2) {
+ o1 = AttributeValueCastUtils.attributeValueCast(type2,o1);
+ }
+ if (!l2.contains(o1)) {
+ l2.add(o1);
+ }
+ }
+
+ attrs.setListAttribute(toID, toAttrName, l2);
+
+ //continue;
+ } else {
+ throw new java.lang.IllegalStateException("Wrong type");
+ }
+ }
+ }
+
+
+ }
+
+
+}
diff --git a/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/util/DefaultAttributeValueMatcher.java b/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/util/DefaultAttributeValueMatcher.java
new file mode 100644
index 0000000..35cb033
--- /dev/null
+++ b/coreplugins/AdvancedNetworkMerge/src/main/java/csplugins/network/merge/util/DefaultAttributeValueMatcher.java
@@ -0,0 +1,147 @@
+/* File: DefaultAttributeValueMatcher.java
+
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+package csplugins.network.merge.util;
+
+import cytoscape.data.CyAttributes;
+
+import java.util.List;
+import java.util.Arrays;
+
+/**
+ * Match attribute values
+ *
+ *
+ */
+public class DefaultAttributeValueMatcher implements AttributeValueMatcher {
+
+ /**
+ * Check whether two attributes of two nodes/edges are "match"
+ * @param id1
+ * @param attr1
+ * @param id2
+ * @param attr2
+ * @param cyAttributes
+ * @return true if matched; false otherwise
+ */
+ //@Override
+ public boolean matched(String id1, String attr1,
+ String id2, String attr2, CyAttributes cyAttributes) {
+ if ((id1 == null) || (attr1 == null) || (id2 == null) || (attr2==null) || (cyAttributes == null)) {
+ throw new java.lang.IllegalArgumentException("Null argument.");
+ }
+
+ final List<String> attrNames = Arrays.asList(cyAttributes.getAttributeNames());
+ if (!attrNames.contains(attr1) || !attrNames.contains(attr2)) {
+ throw new java.lang.IllegalArgumentException("'"+attr1+"' or/and '"+attr2+"' not exists");
+ }
+
+ if (id1.compareTo(id2)==0 && attr1.compareTo(attr2)==0) {
+ return true;
+ }
+
+ if (!cyAttributes.hasAttribute(id1, attr1)
+ || !cyAttributes.hasAttribute(id2, attr2)) { // Is it neccessary to handle empty string?
+ return false; // return false for null attribute
+ }
+
+ //CmpAttributeValueVisitor cmpVisitor = new CmpAttributeValueVisitor(id1,attr1);
+
+ //CyAttributesUtils.traverseAttributeValues(id2, attr2, cyAttributes, cmpVisitor);
+
+ //return cmpVisitor.getIsSame();
+
+ byte type1 = cyAttributes.getType(attr1);
+ byte type2 = cyAttributes.getType(attr2);
+
+ if ((type1<0&&type1!=CyAttributes.TYPE_SIMPLE_LIST)
+ ||(type2<0&&type2!=CyAttributes.TYPE_SIMPLE_LIST)) { // only support matching between simple types
+ // and simple lists for now
+ //TODO: support simple and complex map?
+ Object o1 = cyAttributes.getAttribute(id1, attr1);
+ Object o2 = cyAttributes.getAttribute(id2, attr2);
+
+ type1 = cyAttributes.getMultiHashMapDefinition().getAttributeValueType(attr1);
+ type2 = cyAttributes.getMultiHashMapDefinition().getAttributeValueType(attr2);
+
+ return o1.equals(o2) && type1==type2; // must be the same type for complex map
+ }
+
+ if (type1>0&&type2>0) { // simple type
+ Object o1 = cyAttributes.getAttribute(id1, attr1);
+ Object o2 = cyAttributes.getAttribute(id2, attr2);
+ return o1.equals(o2); //TODO: idmapping
+ } else {
+ if (type1>0||type2>0) { // then one is simple type; the other is simple list
+ Object o;
+ List l;
+ if (type1>0) { // then type2 is simple list
+ o = cyAttributes.getAttribute(id1, attr1);
+ l = cyAttributes.getListAttribute(id2, attr2);
+ } else { // type2 is simple type and type 1 is simple list
+ l = cyAttributes.getListAttribute(id1, attr1);
+ o = cyAttributes.getAttribute(id2, attr2);
+ }
+
+ int nl = l.size();
+ for (int il=0; il<nl; il++) { // for each value in the list, find if match
+ // cannot use List.contains(), because type may be different
+ Object o2 = l.get(il);
+ if (o.equals(o2)) {// if one of the value in the list is the same as the other value
+ return true;
+ }
+ }
+ return false; // if no value match
+ } else { // both of them are simple lists
+ //TODO: use a list comparator?
+ List l1 = cyAttributes.getListAttribute(id1, attr1);
+ List l2 = cyAttributes.getListAttribute(id2, attr2);
+ int nl1 = l1.size();
+ int nl2 = l2.size();
+ for (int il1=0; il1<nl1; il1++) {
+ Object o1 = l1.get(il1);
+ for (int il2=0; il2<nl2; il2++) {
+ Object o2 = l2.get(il2);
+ if (o1.equals(o2)) { // if the two lists have intersections
+ return true;
+ }
+ }
+ }
+ return false;
+ }
+ }
+ }
+}
diff --git a/coreplugins/AdvancedNetworkMerge/src/main/resources/csplugins/network/merge/plugin.props b/coreplugins/AdvancedNetworkMerge/src/main/resources/csplugins/network/merge/plugin.props
new file mode 100644
index 0000000..fdc191d
--- /dev/null
+++ b/coreplugins/AdvancedNetworkMerge/src/main/resources/csplugins/network/merge/plugin.props
@@ -0,0 +1,31 @@
+#plugin.props
+
+# This props file should be filled out and included in the plugin jar file. This props file will be used
+# to put information into the Plugin Manager about the plugin
+
+# -- The following properties are REQUIRED -- #
+
+# The plugin name that will be displayed to users, white space within name is not allowed
+pluginName=AdvancedNetworkMerge
+
+# Description used to give users information about the plugin such as what it does.
+# Html tags are encouraged for formatting purposes.
+pluginDescription=Provides utilities for merging networks by set operations (union, intersection and difference). Networks will be merged based on attribute values of nodes/edges.
+
+# Plugin version number, this must be two numbers separated by a decimlal. Ex. 0.2, 14.03
+pluginVersion=1.16
+
+# Compatible Cytoscape version. If there are more than one version, seperate by ",".
+cytoscapeVersion=2.6,2.7,2.8
+
+# Category, use one of the categories listed on the http://cytoscape.org/plugins2.php site
+pluginCategory=Core
+
+# -- The following properties are OPTIONAL -- #
+
+# URL to a website that gives more information about your plugin, Ex. http://my-lab-site.org
+projectURL=http://www.cytoscape.org/cgi-bin/moin.cgi/Advanced_Network_Merge_and_ID_Mapping
+
+# List of authors. Note each author and institution pair are separated by a : (colon)
+# each additional author institution pair must be separated from other pairs bye a ; (semicolon)
+pluginAuthorsInstitutions=Jianjiong Gao:U. of Missouri;Keiichiro Ono : UCSD
diff --git a/coreplugins/AdvancedNetworkMerge/src/main/resources/images/arrow_collapsed.gif b/coreplugins/AdvancedNetworkMerge/src/main/resources/images/arrow_collapsed.gif
new file mode 100644
index 0000000..bc78257
Binary files /dev/null and b/coreplugins/AdvancedNetworkMerge/src/main/resources/images/arrow_collapsed.gif differ
diff --git a/coreplugins/AdvancedNetworkMerge/src/main/resources/images/arrow_expanded.gif b/coreplugins/AdvancedNetworkMerge/src/main/resources/images/arrow_expanded.gif
new file mode 100644
index 0000000..cc9b3c3
Binary files /dev/null and b/coreplugins/AdvancedNetworkMerge/src/main/resources/images/arrow_expanded.gif differ
diff --git a/coreplugins/AdvancedNetworkMerge/src/main/resources/images/difference.png b/coreplugins/AdvancedNetworkMerge/src/main/resources/images/difference.png
new file mode 100644
index 0000000..4f0ca89
Binary files /dev/null and b/coreplugins/AdvancedNetworkMerge/src/main/resources/images/difference.png differ
diff --git a/coreplugins/AdvancedNetworkMerge/src/main/resources/images/difference2.png b/coreplugins/AdvancedNetworkMerge/src/main/resources/images/difference2.png
new file mode 100644
index 0000000..f82c0cd
Binary files /dev/null and b/coreplugins/AdvancedNetworkMerge/src/main/resources/images/difference2.png differ
diff --git a/coreplugins/AdvancedNetworkMerge/src/main/resources/images/down16.gif b/coreplugins/AdvancedNetworkMerge/src/main/resources/images/down16.gif
new file mode 100644
index 0000000..1d9df2f
Binary files /dev/null and b/coreplugins/AdvancedNetworkMerge/src/main/resources/images/down16.gif differ
diff --git a/coreplugins/AdvancedNetworkMerge/src/main/resources/images/intersection.png b/coreplugins/AdvancedNetworkMerge/src/main/resources/images/intersection.png
new file mode 100644
index 0000000..d06c943
Binary files /dev/null and b/coreplugins/AdvancedNetworkMerge/src/main/resources/images/intersection.png differ
diff --git a/coreplugins/AdvancedNetworkMerge/src/main/resources/images/left16.gif b/coreplugins/AdvancedNetworkMerge/src/main/resources/images/left16.gif
new file mode 100644
index 0000000..99b2a0f
Binary files /dev/null and b/coreplugins/AdvancedNetworkMerge/src/main/resources/images/left16.gif differ
diff --git a/coreplugins/AdvancedNetworkMerge/src/main/resources/images/right16.gif b/coreplugins/AdvancedNetworkMerge/src/main/resources/images/right16.gif
new file mode 100644
index 0000000..c783ae3
Binary files /dev/null and b/coreplugins/AdvancedNetworkMerge/src/main/resources/images/right16.gif differ
diff --git a/coreplugins/AdvancedNetworkMerge/src/main/resources/images/union.png b/coreplugins/AdvancedNetworkMerge/src/main/resources/images/union.png
new file mode 100644
index 0000000..4302c10
Binary files /dev/null and b/coreplugins/AdvancedNetworkMerge/src/main/resources/images/union.png differ
diff --git a/coreplugins/AdvancedNetworkMerge/src/main/resources/images/up16.gif b/coreplugins/AdvancedNetworkMerge/src/main/resources/images/up16.gif
new file mode 100644
index 0000000..d7edfe0
Binary files /dev/null and b/coreplugins/AdvancedNetworkMerge/src/main/resources/images/up16.gif differ
diff --git a/coreplugins/AdvancedNetworkMerge/src/test/resources/IMdata.txt b/coreplugins/AdvancedNetworkMerge/src/test/resources/IMdata.txt
new file mode 100644
index 0000000..2a1e196
--- /dev/null
+++ b/coreplugins/AdvancedNetworkMerge/src/test/resources/IMdata.txt
@@ -0,0 +1,4 @@
+NCBI RefSeq EMBL
+N0 R3 E1
+N1 R4 E2
+N2 R5 E3
diff --git a/coreplugins/AdvancedNetworkMerge/src/test/resources/NMIMtest.cys b/coreplugins/AdvancedNetworkMerge/src/test/resources/NMIMtest.cys
new file mode 100644
index 0000000..e2f4105
Binary files /dev/null and b/coreplugins/AdvancedNetworkMerge/src/test/resources/NMIMtest.cys differ
diff --git a/coreplugins/AdvancedNetworkMerge/src/test/resources/id-mapping-test1 b/coreplugins/AdvancedNetworkMerge/src/test/resources/id-mapping-test1
new file mode 100644
index 0000000..1f43ff0
--- /dev/null
+++ b/coreplugins/AdvancedNetworkMerge/src/test/resources/id-mapping-test1
@@ -0,0 +1,69 @@
+NCBI-GeneID Ensembl
+853264 YJL176C
+855706 YNL025C
+851572 YDR009W
+853167 YGR252W
+852822 YGL058W
+852996 YGR104C
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+854954 YML051W
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+851813 YDR227W
+851811 YDR225W
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+856547 YHR143W-A
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+851723 YDR145W
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+856891 YER148W
+852766 YGL112C
+854433 YOR259C
+850442 YCR081W
diff --git a/coreplugins/AdvancedNetworkMerge/src/test/resources/interactome.cys b/coreplugins/AdvancedNetworkMerge/src/test/resources/interactome.cys
new file mode 100644
index 0000000..625f8b4
Binary files /dev/null and b/coreplugins/AdvancedNetworkMerge/src/test/resources/interactome.cys differ
diff --git a/coreplugins/AdvancedNetworkMerge/src/test/resources/network-merge-test1.cys b/coreplugins/AdvancedNetworkMerge/src/test/resources/network-merge-test1.cys
new file mode 100644
index 0000000..b2d54c3
Binary files /dev/null and b/coreplugins/AdvancedNetworkMerge/src/test/resources/network-merge-test1.cys differ
diff --git a/coreplugins/AdvancedNetworkMerge/src/test/resources/network-merge-test2.cys b/coreplugins/AdvancedNetworkMerge/src/test/resources/network-merge-test2.cys
new file mode 100644
index 0000000..1d50a0c
Binary files /dev/null and b/coreplugins/AdvancedNetworkMerge/src/test/resources/network-merge-test2.cys differ
diff --git a/coreplugins/AdvancedNetworkMerge/src/test/resources/yeastNetworkMergerSample1.cys b/coreplugins/AdvancedNetworkMerge/src/test/resources/yeastNetworkMergerSample1.cys
new file mode 100644
index 0000000..7aaeb8c
Binary files /dev/null and b/coreplugins/AdvancedNetworkMerge/src/test/resources/yeastNetworkMergerSample1.cys differ
diff --git a/coreplugins/AdvancedNetworkMerge/src/test/resources/yeastNetworkMergerSampleFinalResult.cys b/coreplugins/AdvancedNetworkMerge/src/test/resources/yeastNetworkMergerSampleFinalResult.cys
new file mode 100644
index 0000000..4152991
Binary files /dev/null and b/coreplugins/AdvancedNetworkMerge/src/test/resources/yeastNetworkMergerSampleFinalResult.cys differ
diff --git a/coreplugins/AdvancedNetworkMerge/src/test/resources/yeast_id_mapping.txt b/coreplugins/AdvancedNetworkMerge/src/test/resources/yeast_id_mapping.txt
new file mode 100644
index 0000000..d35b69f
--- /dev/null
+++ b/coreplugins/AdvancedNetworkMerge/src/test/resources/yeast_id_mapping.txt
@@ -0,0 +1,18020 @@
+Ensembl Gene ID EMBL (Genbank) ID EntrezGene ID UniProt/SwissProt Accession
+YHR055C U00061 856452 P07215
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diff --git a/coreplugins/AdvancedNetworkMerge/src/test/resources/yeast_id_mapping_table2.txt b/coreplugins/AdvancedNetworkMerge/src/test/resources/yeast_id_mapping_table2.txt
new file mode 100644
index 0000000..ed5d41c
--- /dev/null
+++ b/coreplugins/AdvancedNetworkMerge/src/test/resources/yeast_id_mapping_table2.txt
@@ -0,0 +1,18200 @@
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+YDR314C 851909 Q06665 U28374
diff --git a/coreplugins/AutomaticLayout/pom.xml b/coreplugins/AutomaticLayout/pom.xml
new file mode 100644
index 0000000..c47d213
--- /dev/null
+++ b/coreplugins/AutomaticLayout/pom.xml
@@ -0,0 +1,56 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>parent</artifactId>
+ <version>2.8.4-SNAPSHOT</version>
+ </parent>
+
+ <artifactId>automatic-layout</artifactId>
+ <packaging>jar</packaging>
+
+ <name>Automatic Layout</name>
+
+ <!-- bootstrap for cytoscape dependencies, namely the parent POM snapshots -->
+ <repositories>
+ <repository>
+ <id>cytoscape_snapshots</id>
+ <snapshots>
+ <enabled>true</enabled>
+ </snapshots>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <name>Cytoscape Snapshots</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/</url>
+ </repository>
+ <repository>
+ <id>cytoscape_releases</id>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ <name>Cytoscape Releases</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/releases/</url>
+ </repository>
+ </repositories>
+
+ <build>
+ <plugins>
+ <plugin>
+ <artifactId>maven-assembly-plugin</artifactId>
+ <configuration>
+ <archive>
+ <manifestEntries>
+ <Cytoscape-Plugin>csplugins.layout.LayoutPlugin</Cytoscape-Plugin>
+ </manifestEntries>
+ </archive>
+ </configuration>
+ </plugin>
+ </plugins>
+ </build>
+
+</project>
+
diff --git a/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/EdgeWeighter.java b/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/EdgeWeighter.java
new file mode 100644
index 0000000..cd68dcf
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/EdgeWeighter.java
@@ -0,0 +1,365 @@
+/* vim: set ts=2: */
+/**
+ * Copyright (c) 2008 The Regents of the University of California.
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ * notice, this list of conditions, and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above
+ * copyright notice, this list of conditions, and the following
+ * disclaimer in the documentation and/or other materials provided
+ * with the distribution.
+ * 3. Redistributions must acknowledge that this software was
+ * originally developed by the UCSF Computer Graphics Laboratory
+ * under support by the NIH National Center for Research Resources,
+ * grant P41-RR01081.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY
+ * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+ * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+ * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
+ * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ */
+
+/**
+* Copyright (C) Gerardo Huck, 2010
+*/
+
+package csplugins.layout;
+
+import java.lang.Math;
+import java.util.List;
+
+import csplugins.layout.LayoutEdge;
+
+import cytoscape.Cytoscape;
+import cytoscape.CyEdge;
+
+import cytoscape.layout.Tunable;
+import cytoscape.layout.LayoutProperties;
+import cytoscape.logger.CyLogger;
+
+import cytoscape.data.CyAttributes;
+
+enum WeightTypes {
+ GUESS("Heuristic"),
+ LOG("-Log(value)"),
+ DISTANCE("1 - normalized value"),
+ WEIGHT("normalized value");
+
+ private String name;
+ private WeightTypes(String str) { name=str; }
+ public String toString() { return name; }
+}
+
+/**
+ * The EdgeWeighter class. This class is used as a container for information
+ * about how to interpret weights in an weighted layout.
+ */
+public class EdgeWeighter {
+ WeightTypes type = WeightTypes.GUESS;
+ double minWeightCutoff = 0;
+ double maxWeightCutoff = Double.MAX_VALUE;
+ final static double EPSILON = .001;
+
+ // Default normalization bounds
+ final static double LOWER_BOUND = .1f;
+ final static double UPPER_BOUND = .9f;
+
+ double lowerBounds = LOWER_BOUND;
+ double upperBounds = UPPER_BOUND;
+
+ double maxWeight = -1000000;
+ double minWeight = 1000000;
+ double maxLogWeight = -1000000;
+ double minLogWeight = 1000000;
+ double maxWeightSnapshot = -1000000;
+
+ double labelWeightCoefficient = 1.0;
+
+ double logWeightCeiling = 1028;
+ boolean logOverflow = false;
+
+ private CyLogger logger = null;
+
+ // These are just here for efficiency reasons
+ double normalFactor = Double.MAX_VALUE;
+
+ String weightAttribute = null;
+
+ static WeightTypes[] weightChoices = {WeightTypes.GUESS,
+ WeightTypes.LOG,
+ WeightTypes.DISTANCE,
+ WeightTypes.WEIGHT};
+
+ Tunable[] weightList = null;
+
+
+
+ public EdgeWeighter() {
+ logger = CyLogger.getLogger(EdgeWeighter.class);
+ }
+
+ public void getWeightTunables(LayoutProperties props, List initialAttributes) {
+ props.add(new Tunable("edge_weight_group","Edge Weight Settings",
+ Tunable.GROUP, new Integer(4)));
+ props.add(new Tunable("edge_attribute",
+ "The edge attribute that contains the weights",
+ Tunable.EDGEATTRIBUTE, "weight",
+ (Object) initialAttributes, (Object) null,
+ Tunable.NUMERICATTRIBUTE));
+ props.add(new Tunable("weight_type", "How to interpret weight values",
+ Tunable.LIST, new Integer(0),
+ (Object) weightChoices, (Object) null, 0));
+ props.add(new Tunable("min_weight", "The minimum edge weight to consider",
+ Tunable.DOUBLE, new Double(0)));
+ props.add(new Tunable("max_weight", "The maximum edge weight to consider",
+ Tunable.DOUBLE, new Double(Double.MAX_VALUE)));
+ }
+
+ public void updateSettings(LayoutProperties layoutProperties, boolean force) {
+ boolean resetRequired = false;
+ Tunable t = layoutProperties.get("min_weight");
+ if ((t != null) && (t.valueChanged() || force)) {
+ minWeightCutoff = ((Double) t.getValue()).doubleValue();
+ resetRequired = true;
+ if (t.valueChanged())
+ layoutProperties.setProperty(t.getName(), t.getValue().toString());
+ }
+
+ t = layoutProperties.get("max_weight");
+ if ((t != null) && (t.valueChanged() || force)) {
+ maxWeightCutoff = ((Double) t.getValue()).doubleValue();
+ resetRequired = true;
+ if (t.valueChanged())
+ layoutProperties.setProperty(t.getName(), t.getValue().toString());
+ }
+
+ t = layoutProperties.get("edge_attribute");
+ if ((t != null) && (t.valueChanged() || force)) {
+ weightAttribute = (t.getValue().toString());
+ resetRequired = true;
+ if (t.valueChanged())
+ layoutProperties.setProperty(t.getName(), t.getValue().toString());
+ }
+
+ t = layoutProperties.get("weight_type");
+ if ((t != null) && (t.valueChanged() || force)) {
+ type = weightChoices[((Integer) t.getValue()).intValue()];
+ resetRequired = true;
+ if (t.valueChanged())
+ layoutProperties.setProperty(t.getName(), t.getValue().toString());
+ }
+
+ if (resetRequired)
+ reset();
+
+ }
+
+ public void reset() {
+ maxWeight = -1000000;
+ minWeight = 1000000;
+ maxLogWeight = -1000000;
+ minLogWeight = 1000000;
+ normalFactor = Double.MAX_VALUE;
+ logOverflow = false;
+ }
+
+ public void setWeightType(WeightTypes type) {
+ this.type = type;
+ }
+
+ public void setNormalizedBounds(double lowerBound, double upperBound) {
+ this.lowerBounds = lowerBound;
+ this.upperBounds = upperBound;
+ }
+
+ /**
+ *
+ */
+ public void setLabelWeightCoefficient(double labelWeightCoefficient) {
+ this.labelWeightCoefficient = labelWeightCoefficient;
+ }
+
+ /**
+ *
+ */
+ public void setWeight(LayoutEdge layoutEdge) {
+ // if any of the nodes are label nodes
+ if (layoutEdge.getType() == "label") {
+ setWeightLabelEdge(layoutEdge);
+ } else {
+ setWeightNormalEdge(layoutEdge);
+ }
+ }
+
+ /**
+ *
+ */
+ public void calculateMaxWeight() {
+ this.maxWeightSnapshot = this.maxWeight;
+ }
+
+ /**
+ *
+ */
+ public void setWeightLabelEdge(LayoutEdge layoutEdge) {
+ // logger.info("Setting weight for label edge: "+layoutEdge+" using "+ weightAttribute);
+
+ double eValue = labelWeightCoefficient * maxWeightSnapshot;
+
+ layoutEdge.setWeight(eValue);
+ minWeight = Math.min(minWeight,eValue);
+ maxWeight = Math.max(maxWeight,eValue);
+
+ if (type == WeightTypes.GUESS || type == WeightTypes.LOG) {
+ double logWeight;
+ if (eValue == 0) {
+ logWeight = logWeightCeiling;
+ logOverflow = true;
+ } else {
+ logWeight = Math.min(-Math.log10(eValue), logWeightCeiling);
+ }
+
+ minLogWeight = Math.min(minLogWeight,logWeight);
+ maxLogWeight = Math.max(maxLogWeight,logWeight);
+ layoutEdge.setLogWeight(logWeight);
+ }
+ }
+
+ public void setWeightNormalEdge(LayoutEdge layoutEdge) {
+ CyEdge edge = layoutEdge.getEdge();
+ CyAttributes edgeAttributes = Cytoscape.getEdgeAttributes();
+ double eValue = 0.5;
+
+ // logger.debug("Setting weight for "+layoutEdge+" using "+weightAttribute);
+ // logger.info("Setting weight for "+layoutEdge+" using "+weightAttribute);
+
+ if ((weightAttribute != null)
+ && edgeAttributes.hasAttribute(edge.getIdentifier(), weightAttribute)) {
+ if (edgeAttributes.getType(weightAttribute) == CyAttributes.TYPE_INTEGER) {
+ Integer val = edgeAttributes.getIntegerAttribute(edge.getIdentifier(),
+ weightAttribute);
+ eValue = (double) val.intValue();
+ } else {
+ Double val = edgeAttributes.getDoubleAttribute(edge.getIdentifier(),
+ weightAttribute);
+ eValue = val.doubleValue();
+ }
+ }
+ layoutEdge.setWeight(eValue);
+ minWeight = Math.min(minWeight,eValue);
+ maxWeight = Math.max(maxWeight,eValue);
+ if (type == WeightTypes.GUESS || type == WeightTypes.LOG) {
+ double logWeight;
+ if (eValue == 0) {
+ logWeight = logWeightCeiling;
+ logOverflow = true;
+ } else {
+ logWeight = Math.min(-Math.log10(eValue), logWeightCeiling);
+ }
+ minLogWeight = Math.min(minLogWeight,logWeight);
+ maxLogWeight = Math.max(maxLogWeight,logWeight);
+ layoutEdge.setLogWeight(logWeight);
+ }
+ }
+
+ public boolean normalizeWeight(LayoutEdge edge) {
+ // If all of our weights are the same we should
+ // normalize everything to 0.5
+ if (minWeight == maxWeight) {
+ edge.setWeight(0.5);
+ return true;
+ }
+
+ // We need to handle the special case of a weight of 0.0 when
+ // we're doing logs. When we set the value, we set it to
+ // logWeightCeiling as a placeholder, but we really want to
+ // just set it to a value somewhat larger than the maximum
+ if (logOverflow) {
+ maxLogWeight = maxLogWeight+5;
+ logOverflow = false;
+ }
+
+ if ((edge.getWeight() < minWeightCutoff) ||
+ (edge.getWeight() > maxWeightCutoff))
+ return false;
+
+ double weight = 0;
+
+ switch (this.type) {
+ case GUESS:
+ // logger.debug("Heuristic: ");
+ if (Math.abs(maxLogWeight-minLogWeight) > 3) {
+ weight = edge.getLogWeight();
+ // logger.debug("Log weight = "+weight);
+ if (weight == logWeightCeiling)
+ weight = maxLogWeight+1;
+ weight = logNormalize(weight);
+ // logger.debug(" normalized weight = "+weight);
+ } else {
+ weight = normalize(edge.getWeight());
+ }
+ break;
+ case LOG:
+ // logger.debug("Log: ");
+ weight = edge.getLogWeight();
+ // logger.debug("Log weight = "+weight);
+ if (weight == logWeightCeiling)
+ weight = maxLogWeight+1;
+ weight = logNormalize(weight);
+ // logger.debug(" normalized weight = "+weight);
+ break;
+ case DISTANCE:
+ // logger.debug("Distance");
+ weight = edge.getWeight();
+ weight = (lowerBounds + upperBounds) - normalize(weight);
+ break;
+ case WEIGHT:
+ // logger.debug("Weight");
+ weight = normalize(edge.getWeight());
+ break;
+ }
+
+ edge.setWeight(weight);
+
+ // We're now normalized to the range 0-1, so we can safely
+ // ignore really small weights since they should be very far away
+ //if (weight < EPSILON)
+ // return false;
+
+ return true;
+ }
+
+ private double logNormalize(double weight) {
+ if (normalFactor == Double.MAX_VALUE) {
+ normalFactor = (upperBounds-lowerBounds)/(maxLogWeight-minLogWeight);
+ }
+ return (weight-minLogWeight)*normalFactor+lowerBounds;
+ }
+
+ private double normalize(double weight) {
+ if (normalFactor == Double.MAX_VALUE) {
+ normalFactor = (upperBounds-lowerBounds)/(maxWeight-minWeight);
+ }
+ return (weight-minWeight)*normalFactor+lowerBounds;
+ }
+
+ public void setMaxWeightCutoff(double maxWeight) {
+ maxWeightCutoff = maxWeight;
+ }
+
+ public void setMinWeightCutoff(double minWeight) {
+ minWeightCutoff = minWeight;
+ }
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/JGraphLayoutWrapper.java b/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/JGraphLayoutWrapper.java
new file mode 100644
index 0000000..cfa7442
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/JGraphLayoutWrapper.java
@@ -0,0 +1,414 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package csplugins.layout;
+
+import cern.colt.map.*;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.layout.AbstractLayout;
+
+import cytoscape.task.TaskMonitor;
+
+import cytoscape.view.*;
+
+import giny.model.*;
+
+import giny.view.*;
+
+import org.jgraph.JGraph;
+
+import org.jgraph.graph.*;
+
+import org.jgraph.layout.*;
+
+import java.awt.Color;
+import java.awt.geom.Rectangle2D;
+
+import java.util.*;
+
+import javax.swing.*;
+
+
+/**
+ *
+ */
+public class JGraphLayoutWrapper extends AbstractLayout {
+ /**
+ *
+ */
+ public static final int ANNEALING = 0;
+
+ /**
+ *
+ */
+ public static final int MOEN = 1;
+
+ /**
+ *
+ */
+ public static final int CIRCLE_GRAPH = 2;
+
+ /**
+ *
+ */
+ public static final int RADIAL_TREE = 3;
+
+ /**
+ *
+ */
+ public static final int GEM = 4;
+
+ /**
+ *
+ */
+ public static final int SPRING_EMBEDDED = 5;
+
+ /**
+ *
+ */
+ public static final int SUGIYAMA = 6;
+
+ /**
+ *
+ */
+ public static final int TREE = 7;
+ int layout_type = 0;
+ private JGraphLayoutAlgorithm layout = null;
+ private JGraphLayoutSettings layoutSettings = null;
+ private boolean canceled = false;
+
+ /**
+ * Creates a new JGraphLayoutWrapper object.
+ *
+ * @param layout_type DOCUMENT ME!
+ */
+ public JGraphLayoutWrapper(int layout_type) {
+ super();
+ this.layout_type = layout_type;
+
+ switch (layout_type) {
+ case ANNEALING:
+ layout = new AnnealingLayoutAlgorithm();
+
+ break;
+
+ case MOEN:
+ layout = new MoenLayoutAlgorithm();
+
+ break;
+
+ case CIRCLE_GRAPH:
+ layout = new CircleGraphLayout();
+
+ break;
+
+ case RADIAL_TREE:
+ layout = new RadialTreeLayoutAlgorithm();
+
+ break;
+
+ case GEM:
+ layout = new GEMLayoutAlgorithm(new AnnealingLayoutAlgorithm());
+
+ break;
+
+ case SPRING_EMBEDDED:
+ layout = new SpringEmbeddedLayoutAlgorithm();
+
+ break;
+
+ case SUGIYAMA:
+ layout = new SugiyamaLayoutAlgorithm();
+
+ break;
+
+ case TREE:
+ layout = new TreeLayoutAlgorithm();
+
+ break;
+ }
+
+ layoutSettings = layout.createSettings();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getName() {
+ switch (layout_type) {
+ case ANNEALING:
+ return "jgraph-annealing";
+
+ case MOEN:
+ return "jgraph-moen";
+
+ case CIRCLE_GRAPH:
+ return "jgraph-circle";
+
+ case RADIAL_TREE:
+ return "jgraph-radial-tree";
+
+ case GEM:
+ return "jgraph-gem";
+
+ case SPRING_EMBEDDED:
+ return "jgraph-spring";
+
+ case SUGIYAMA:
+ return "jgraph-sugiyama";
+
+ case TREE:
+ return "jgraph-tree";
+ }
+
+ return "";
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String toString() {
+ switch (layout_type) {
+ case ANNEALING:
+ return "Simulated Annealing Layout";
+
+ case MOEN:
+ return "MOEN Layout";
+
+ case CIRCLE_GRAPH:
+ return "Circle Layout";
+
+ case RADIAL_TREE:
+ return "Radial Tree Layout";
+
+ case GEM:
+ return "GEM Layout";
+
+ case SPRING_EMBEDDED:
+ return "Spring Embedded Layout";
+
+ case SUGIYAMA:
+ return "Sugiyama Layout";
+
+ case TREE:
+ return "Tree Layout";
+ }
+
+ return "";
+ }
+
+ /**
+ * Get the settings panel for this layout
+ */
+ public JPanel getSettingsPanel() {
+ return (JPanel) layoutSettings;
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void updateSettings() {
+ if (layoutSettings != null)
+ layoutSettings.apply();
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void revertSettings() {
+ if (layoutSettings != null)
+ layoutSettings.revert();
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void halt() {
+ canceled = true;
+
+ if (layout != null)
+ layout.setCanceled();
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void construct() {
+ canceled = false;
+ initialize();
+
+ double currentProgress = 0;
+ double percentProgressPerIter = 0;
+ GraphPerspective perspective = networkView.getGraphPerspective();
+ Map j_giny_node_map = new HashMap(PrimeFinder.nextPrime(perspective.getNodeCount()));
+ Map giny_j_node_map = new HashMap(PrimeFinder.nextPrime(perspective.getNodeCount()));
+ Map j_giny_edge_map = new HashMap(PrimeFinder.nextPrime(perspective.getEdgeCount()));
+
+ Iterator node_iterator = perspective.nodesIterator();
+ Iterator edge_iterator = perspective.edgesIterator();
+
+ taskMonitor.setStatus("Initializing");
+ taskMonitor.setPercentCompleted((int) currentProgress);
+
+ // Construct Model and Graph
+ //
+ GraphModel model = new DefaultGraphModel();
+ JGraph graph = new JGraph(model);
+
+ // Create Nested Map (from Cells to Attributes)
+ //
+ Map attributes = new Hashtable();
+
+ Set cells = new HashSet();
+
+ // update progress bar
+ currentProgress = 1;
+ taskMonitor.setPercentCompleted((int) currentProgress);
+ percentProgressPerIter = 49 / (double) (networkView.getNodeViewCount());
+
+ // create Vertices
+ while (node_iterator.hasNext() && !canceled) {
+ // get the GINY node and node view
+ giny.model.Node giny = (giny.model.Node) node_iterator.next();
+ NodeView node_view = networkView.getNodeView(giny);
+
+ DefaultGraphCell jcell = new DefaultGraphCell(giny.getIdentifier());
+
+ // Set bounds
+ Rectangle2D bounds = new Rectangle2D.Double(node_view.getXPosition(),
+ node_view.getYPosition(),
+ node_view.getWidth(), node_view.getHeight());
+
+ GraphConstants.setBounds(jcell.getAttributes(), bounds);
+
+ j_giny_node_map.put(jcell, giny);
+ giny_j_node_map.put(giny, jcell);
+
+ cells.add(jcell);
+
+ // update progress bar
+ currentProgress += percentProgressPerIter;
+ taskMonitor.setPercentCompleted((int) currentProgress);
+ }
+
+ // update progress bar
+ percentProgressPerIter = 49 / (double) (networkView.getEdgeViewCount());
+
+ while (edge_iterator.hasNext() && !canceled) {
+ giny.model.Edge giny = (giny.model.Edge) edge_iterator.next();
+
+ DefaultGraphCell j_source = (DefaultGraphCell) giny_j_node_map.get(giny.getSource());
+ DefaultGraphCell j_target = (DefaultGraphCell) giny_j_node_map.get(giny.getTarget());
+
+ DefaultPort source_port = new DefaultPort();
+ DefaultPort target_port = new DefaultPort();
+
+ j_source.add(source_port);
+ j_target.add(target_port);
+
+ source_port.setParent(j_source);
+ target_port.setParent(j_target);
+
+ // create the edge
+ DefaultEdge jedge = new DefaultEdge();
+ j_giny_edge_map.put(jedge, giny);
+
+ // Connect Edge
+ //
+ ConnectionSet cs = new ConnectionSet(jedge, source_port, target_port);
+ Object[] ecells = new Object[] { jedge, j_source, j_target };
+
+ // Insert into Model
+ //
+ model.insert(ecells, attributes, cs, null, null);
+
+ cells.add(jedge);
+
+ // update progress bar
+ currentProgress += percentProgressPerIter;
+ taskMonitor.setPercentCompleted((int) currentProgress);
+ }
+
+ taskMonitor.setStatus("Executing Algorithm");
+ taskMonitor.setPercentCompleted((int) 0);
+ layout.setTaskMonitor(taskMonitor);
+ layout.run(graph, cells.toArray());
+
+ GraphLayoutCache cache = graph.getGraphLayoutCache();
+
+ CellView[] cellViews = graph.getGraphLayoutCache()
+ .getAllDescendants(graph.getGraphLayoutCache().getRoots());
+
+ if (canceled)
+ return;
+
+ taskMonitor.setStatus("Updating View");
+ currentProgress = 1;
+ taskMonitor.setPercentCompleted((int) currentProgress);
+ percentProgressPerIter = 100 / (double) (cellViews.length);
+ for (int i = 0; i < cellViews.length; i++) {
+ CellView cell_view = cellViews[i];
+
+ if (cell_view instanceof VertexView) {
+ // ok, we found a node
+ Rectangle2D rect = graph.getCellBounds(cell_view.getCell());
+ giny.model.Node giny = (giny.model.Node) j_giny_node_map.get(cell_view.getCell());
+ NodeView node_view = networkView.getNodeView(giny);
+ node_view.setXPosition(rect.getX(), false);
+ node_view.setYPosition(rect.getY(), false);
+ node_view.setNodePosition(true);
+
+ // update progress bar
+ currentProgress += percentProgressPerIter;
+ taskMonitor.setPercentCompleted((int) currentProgress);
+ }
+ }
+
+ // I don't think that any of the current layouts have edge components,
+ // so I won't bother for now.
+ model = null;
+ graph = null;
+ attributes = null;
+ cells = null;
+ System.gc();
+ }
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/LayoutEdge.java b/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/LayoutEdge.java
new file mode 100644
index 0000000..5d82211
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/LayoutEdge.java
@@ -0,0 +1,243 @@
+/* vim: set ts=2: */
+/**
+ * Copyright (c) 2006 The Regents of the University of California.
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ * notice, this list of conditions, and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above
+ * copyright notice, this list of conditions, and the following
+ * disclaimer in the documentation and/or other materials provided
+ * with the distribution.
+ * 3. Redistributions must acknowledge that this software was
+ * originally developed by the UCSF Computer Graphics Laboratory
+ * under support by the NIH National Center for Research Resources,
+ * grant P41-RR01081.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY
+ * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+ * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+ * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
+ * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ */
+
+/**
+* Copyright (C) Gerardo Huck, 2010
+*/
+
+package csplugins.layout;
+
+import csplugins.layout.LayoutNode;
+
+import cytoscape.*;
+
+import cytoscape.data.*;
+
+import cytoscape.util.*;
+
+import cytoscape.view.*;
+
+
+/**
+ * The LayoutEdge class. This class is used as a container for information
+ * about the edges in a layout. In particular, it provides a convenient handle
+ * to information about the weights associated with edges, and pointers to the
+ * LayoutNodes that are joined by this edge.
+ */
+public class LayoutEdge implements Comparable <LayoutEdge> {
+ // instance variables
+ private LayoutNode v1;
+ private LayoutNode v2;
+ private double weight = 0.5;
+ private double logWeight;
+ private CyEdge edge;
+
+ /**
+ * An empty constructor
+ */
+ public LayoutEdge() {
+ }
+
+ /**
+ * Create a LayoutEdge that will contain information about this edge.
+ * Additional information must be filled in later.
+ *
+ * @param edge CyEdge that this LayoutEdge represents
+ */
+ public LayoutEdge(CyEdge edge) {
+ this.edge = edge;
+ }
+
+ /**
+ * Create a LayoutEdge that will contains information about this edge,
+ * and that record that it connects LayoutNodes v1 and v2.
+ *
+ * @param edge CyEdge that this LayoutEdge represents
+ * @param v1 The LayoutNode that represents the source of the edge
+ * @param v2 The LayoutNode that represents the target of the edge
+ */
+ public LayoutEdge(CyEdge edge, LayoutNode v1, LayoutNode v2) {
+ this.edge = edge;
+ this.v1 = v1;
+ this.v2 = v2;
+
+ if (v1 != v2) {
+ v1.addNeighbor(v2);
+ v2.addNeighbor(v1);
+ }
+ }
+
+ /**
+ * Set the nodes associated with this edge. This is used subsequent
+ * to a call to the LayoutEdge(CyEdge) constructor to associate the
+ * source and target nodes since we don't always know that information
+ * at the time the edge is encountered.
+ *
+ * @param v1 The LayoutNode that represents the source of the edge
+ * @param v2 The LayoutNode that represents the target of the edge
+ */
+ public void addNodes(LayoutNode v1, LayoutNode v2) {
+ this.v1 = v1;
+ this.v2 = v2;
+
+ if (v1 != v2) {
+ v1.addNeighbor(v2);
+ v2.addNeighbor(v1);
+ }
+ }
+
+ /**
+ * Set the weight for this LayoutEdge. This assumes that all of the weight
+ * calculations are being handled externally.
+ *
+ * @param weight the actual weight
+ */
+ public void setWeight(double weight) {
+ this.weight = weight;
+ }
+
+ /**
+ * Set the log weight for this LayoutEdge. This assumes that all of the weight
+ * calculations are being handled externally.
+ *
+ * @param logWeight the actual -log of the weight
+ */
+ public void setLogWeight(double logWeight) {
+ this.logWeight = logWeight;
+ }
+
+ /**
+ * Return the current value for this edge's weight.
+ *
+ * @return This edge's weight as a double
+ */
+ public double getWeight() {
+ return this.weight;
+ }
+
+ /**
+ * Return the current value for this edge's logWeight (-log(weight)).
+ *
+ * @return This edge's logWeight as a double
+ */
+ public double getLogWeight() {
+ return this.logWeight;
+ }
+
+ /**
+ * Return the source of this edge
+ *
+ * @return This edge's source
+ */
+ public LayoutNode getSource() {
+ return this.v1;
+ }
+
+ /**
+ * Return the target of this edge
+ *
+ * @return This edge's target
+ */
+ public LayoutNode getTarget() {
+ return this.v2;
+ }
+
+ /**
+ * Return the CyEdge this LayoutEdge represents
+ *
+ * @return The CyEdge for this LayoutEdge
+ */
+ public CyEdge getEdge() {
+ return this.edge;
+ }
+
+ /**
+ * Return the edge's identifier.
+ *
+ * @return String containing the edge's identifier
+ */
+ public String getIdentifier() {
+ return this.edge.getIdentifier();
+ }
+
+ /**
+ * Return a string representation for this LayoutEdge.
+ *
+ * @return A String containting the name of the CyEdge, the connecting LayoutNodes
+ * and the current weight.
+ */
+ public String toString() {
+ String source = "undefined";
+ String target = "undefined";
+ String edgeId = "undefined";
+
+ if (v1 != null && (v1.getType() == "normal") )
+ source = ((LayoutNodeImpl) v1).getIdentifier();
+
+ if (v2 != null && (v2.getType() == "normal") )
+ target = v2.getIdentifier();
+
+ if (this.edge != null)
+ edgeId = edge.getIdentifier();
+
+ return "Edge " + edgeId + " connecting " + source + " and " + target
+ + " with weight " + weight;
+ }
+
+ /**
+ * Return a string representation of the type of this layoutEdge.
+ *
+ * @return A String containting "normal" if both nodes are "normal",
+ * and "label" if any node is a label layout node
+ */
+ public String getType() {
+ if( (v1 != null && v1.getType() == "label")
+ || (v2 != null && v2.getType() == "label") ) {
+ return "label";
+ } else {
+ return "normal";
+ }
+ }
+
+ /**
+ * Returns the natural order of two LayoutEdges determined by comparing the edge
+ * identifiers.
+ *
+ * @param o2 the LayoutEdge we're comparing ourselves to
+ * @return -1 if this is less than o2, 0 if they are equal, and 1 if this is greater than o2
+ */
+ public int compareTo(LayoutEdge o2) {
+ return getIdentifier().compareTo(o2.getIdentifier());
+ }
+
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/LayoutLabelNodeImpl.java b/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/LayoutLabelNodeImpl.java
new file mode 100644
index 0000000..6ce270f
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/LayoutLabelNodeImpl.java
@@ -0,0 +1,216 @@
+/**
+* Copyright (C) Gerardo Huck, 2010
+*
+* This program is free software: you can redistribute it and/or modify
+* it under the terms of the GNU Lesser General Public License as published
+* by the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+*
+* This program is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU Lesser General Public License for more details.
+*
+* You should have received a copy of the GNU Lesser General Public License
+* along with this program. If not, see <http://www.gnu.org/licenses/>.
+*
+*/
+
+
+/**
+ * This class represents the fake nodes used to layout labels.
+ *
+ * It was done as part of Google Summer of Code 2010.
+ * Mentor: Mike Smoot
+ * @author <a href="mailto:gerardohuck .at. gmail .dot. com">Gerardo Huck</a>
+ * @version 0.1
+ */
+
+package csplugins.layout;
+
+import cytoscape.*;
+import cytoscape.logger.CyLogger;
+import cytoscape.data.CyAttributes;
+import cytoscape.view.*;
+import cytoscape.visual.parsers.*;
+import cytoscape.visual.VisualPropertyType;
+
+import ding.view.ObjectPositionImpl;
+
+import giny.view.*;
+
+import java.util.*;
+
+
+public class LayoutLabelNodeImpl extends LayoutNode {
+
+ // -- Instance variables inherited from superclass --
+ // protected boolean isLocked = false;
+ // protected double x;
+ // protected double y;
+ // protected double dispX;
+ // protected double dispY;
+
+ protected CyLogger logger = null;
+ protected NodeView parentNodeView;
+ protected ObjectPosition lp;
+ protected CyAttributes nodeAtts = null;
+
+ /**
+ * Empty constructor
+ */
+ public LayoutLabelNodeImpl() {
+ }
+
+ /**
+ * The main constructor for a LayoutLabelNode.
+ *
+ * @param parent The parent LayoutNode for this LayoutLabelNode
+ */
+ public LayoutLabelNodeImpl(NodeView parentNodeView, int index) {
+ logger = CyLogger.getLogger(LayoutLabelNodeImpl.class);
+ this.parentNodeView = parentNodeView;
+
+ // Set labelNode's location to parent node's current label position
+ nodeAtts = Cytoscape.getNodeAttributes();
+ String labelPosition = (String) nodeAtts.getAttribute(parentNodeView.getNode().getIdentifier(),
+ "node.labelPosition");
+
+ if (labelPosition == null) {
+ lp = new ObjectPositionImpl();
+ // logger.info("Created new ObjectPosition!");
+ } else {
+ ObjectPositionParser parser =
+ (ObjectPositionParser) VisualPropertyType.NODE_LABEL_POSITION.getValueParser();
+ lp = parser.parseStringValue(labelPosition);
+ // logger.info("ObjectPosition succesfully parsed!");
+ }
+
+ try {
+ // logger.info("Parent node: " + parentNodeView.getNode().getIdentifier());
+ // logger.info("Offset = " + lp.getOffsetX() + ", " + lp.getOffsetY() );
+
+ this.setX(lp.getOffsetX() + parentNodeView.getXPosition());
+ this.setY(lp.getOffsetY() + parentNodeView.getYPosition());
+ this.neighbors = new ArrayList<LayoutNode>();
+ this.index = index;
+
+ // logger.info("Created " + this.getIdentifier() + "placed in: " + this.getX() + ", " + this.getY() );
+ }
+ catch(Exception e) {
+ // Log error
+ logger.warning("Error detected while creating LayoutLabelNodeImp: " + e.toString() );
+
+ // Reset this attribute by eliminating it
+
+ if (nodeAtts.hasAttribute(parentNodeView.getNode().getIdentifier(), "node.labelPosition")) {
+ nodeAtts.deleteAttribute(parentNodeView.getNode().getIdentifier(), "node.labelPosition");
+ logger.warning("Deleted 'node.labelPosition' attribute");
+ }
+
+ lp = new ObjectPositionImpl();
+ logger.warning("Created new ObjectPosition!");
+
+ this.setX( parentNodeView.getXPosition() );
+ this.setY( parentNodeView.getYPosition() );
+ this.neighbors = new ArrayList<LayoutNode>();
+ this.index = index;
+ }
+ }
+
+ /**
+ * Moves a label node to the (X,Y) position that is already defined if it is unlocked.
+ * Otherwise, updates the (X,Y) fields in order to reflect its real position.
+ * Note that moving the parent node will affect the position of this label node.
+ */
+ public void moveToLocation() {
+
+ lp = new ObjectPositionImpl();
+
+ if (this.isLocked()) { // If node is locked, adjust X and Y to its current location
+
+ // logger.info(this.toString() + " was locked");
+
+ this.setX(lp.getOffsetX() + parentNodeView.getXPosition());
+ this.setY(lp.getOffsetY() + parentNodeView.getYPosition());
+
+ } else { // If node is unlocked set labels offsets properly
+
+ // logger.info(this.toString() + " was unlocked");
+
+ lp.setOffsetX(this.getX() - parentNodeView.getXPosition());
+ lp.setOffsetY(this.getY() - parentNodeView.getYPosition());
+
+ nodeAtts.setAttribute(parentNodeView.getNode().getIdentifier(),
+ "node.labelPosition", lp.shortString());
+
+// logger.info("Label node was moved!, short string: " + lp.shortString());
+// logger.info("full label string: " + lp.toString() );
+ }
+ }
+
+ /**
+ * Accessor function to return the NodeView associated with
+ * this LayoutNode.
+ *
+ * @return NodeView that is associated with this LayoutNode
+ */
+ public NodeView getNodeView() {
+ return parentNodeView;
+ }
+
+ /**
+ * Return the width of this node
+ *
+ * @return width of this node
+ */
+ public double getWidth() {
+ return parentNodeView.getWidth();
+ }
+
+ /**
+ * Return the height of this label node
+ *
+ * @return height of this node
+ */
+ public double getHeight() {
+ return parentNodeView.getHeight();
+ }
+
+ public double getParentX() {
+ return parentNodeView.getXPosition();
+ }
+
+ public double getParentY() {
+ return parentNodeView.getYPosition();
+ }
+
+ /**
+ * Return a string representation of the node
+ *
+ * @return String containing the node's identifier and location
+ */
+ public String toString() {
+ return "Label of Node: " + getIdentifier() + " at " + printLocation();
+ }
+
+ /**
+ * Return a string with the "type" of the node ("normal", "label")
+ *
+ * @return String containing the node's type
+ */
+ public String getType() {
+ return "label";
+ }
+
+ /**
+ * Return the node's identifier.
+ *
+ * @return String containing the node's identifier
+ */
+ public String getIdentifier() {
+ return "Label of node:" + parentNodeView.getNode().getIdentifier();
+ }
+
+
+}
\ No newline at end of file
diff --git a/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/LayoutLabelPartition.java b/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/LayoutLabelPartition.java
new file mode 100644
index 0000000..c005893
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/LayoutLabelPartition.java
@@ -0,0 +1,257 @@
+/**
+* Copyright (C) Gerardo Huck, 2010
+*
+* This program is free software: you can redistribute it and/or modify
+* it under the terms of the GNU Lesser General Public License as published
+* by the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+*
+* This program is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU Lesser General Public License for more details.
+*
+* You should have received a copy of the GNU Lesser General Public License
+* along with this program. If not, see <http://www.gnu.org/licenses/>.
+*
+*/
+
+
+/**
+ * This handles the creation and behavior of a "partition" used to layout labels
+ * as well as nodes.
+ *
+ * It was done as part of Google Summer of Code 2010.
+ * Mentor: Mike Smoot
+ * @author <a href="mailto:gerardohuck .at. gmail .dot. com">Gerardo Huck</a>
+ * @version 0.1
+ */
+
+package csplugins.layout;
+
+import cytoscape.logger.CyLogger;
+
+import csplugins.layout.LayoutEdge;
+import csplugins.layout.LayoutNode;
+import csplugins.layout.LayoutLabelNodeImpl;
+import csplugins.layout.Profile;
+import csplugins.layout.EdgeWeighter;
+
+import cytoscape.util.intr.IntIntHash;
+import cytoscape.util.intr.IntObjHash;
+
+import cytoscape.*;
+
+import cytoscape.view.*;
+
+import giny.view.*;
+
+import java.awt.Dimension;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Map;
+import java.util.Comparator;
+import java.util.Date;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.ListIterator;
+import java.util.Random;
+import java.util.Set;
+import java.util.Collection;
+
+
+/**
+ * The LayoutLabelPartition class ....
+ *
+ * @version 0.1
+ */
+public class LayoutLabelPartition extends LayoutPartition {
+
+ protected Map <LayoutLabelNodeImpl,LayoutNode> labelToParentMap;
+ protected ArrayList<LayoutNode> allLayoutNodesArray;
+ protected ArrayList<LayoutEdge> allLayoutEdgesArray;
+
+ protected double weightCoefficient = 1.0;
+ protected boolean moveNodes = false;
+ protected boolean selectedOnly = false;
+ protected boolean isWeighted = false;
+
+ public LayoutLabelPartition(int nodeCount, int edgeCount) {
+ super(nodeCount, edgeCount);
+ }
+
+
+ public LayoutLabelPartition(LayoutPartition part,
+ double weightCoefficient,
+ boolean moveNodes,
+ boolean selectedOnly) {
+
+ super(part.size(), part.getEdgeList().size());
+
+ this.weightCoefficient = weightCoefficient;
+ this.moveNodes = moveNodes;
+ this.selectedOnly = selectedOnly;
+ this.isWeighted = isWeighted;
+
+ // Copy fields from part
+ this.nodeList = (ArrayList<LayoutNode>) part.nodeList.clone();
+ this.edgeList = (ArrayList<LayoutEdge>) part.edgeList.clone();
+ this.nodeToLayoutNode = (HashMap<CyNode,LayoutNode>) part.nodeToLayoutNode.clone();
+ this.partitionNumber = part.partitionNumber;
+ this.edgeWeighter = part.edgeWeighter;
+
+ this.maxX = part.maxX;
+ this.maxY = part.maxY;
+ this.minX = part.minX;
+ this.minY = part.minY;
+ this.width = part.width;
+ this.height = part.height;
+
+ this.averageX = part.averageX;
+ this.averageY = part.averageY;
+
+ this.lockedNodes = part.lockedNodes;
+
+ // Initialize 'label' fields
+ labelToParentMap = new HashMap<LayoutLabelNodeImpl,LayoutNode>(part.size());
+ allLayoutNodesArray = new ArrayList<LayoutNode>(part.size());
+ allLayoutEdgesArray = new ArrayList<LayoutEdge>(part.size());
+
+ // This method handles the creation of LayoutLabelNodes, the mappings, etc
+ this.initializeLabels();
+
+ // Reset statistics in order to reflect the new partition status.
+ this.recalculateStatistics();
+ }
+
+ /**
+ * Handles the initization of all the infraestructure needed in order to use a
+ * LayoutLabelPartition to layout labels, such as Label nodes creation, etc.
+ */
+ protected void initializeLabels() {
+
+ edgeWeighter.setLabelWeightCoefficient(weightCoefficient);
+ edgeWeighter.calculateMaxWeight();
+
+ for (LayoutNode ln: nodeList ) {
+
+ // Creates a new LabelNode, child of ln
+ NodeView nv = ln.getNodeView();
+ int ind = ln.getIndex() + nodeList.size();
+
+ // wonder how this is even possible
+ if (nv == null) {
+ logger.error("Found a layout node without a NodeView!");
+ continue;
+ }
+
+ LayoutLabelNodeImpl labelNode = new LayoutLabelNodeImpl(nv, ind);
+
+ /* Unlock labelNode if:
+ * - algorithm is to be applied to the entire network
+ * - algorithm is to be applied to the selected nodes only, and ln
+ * is selected
+ */
+ if (!selectedOnly || !(ln.isLocked()) ) {
+ labelNode.unLock();
+ updateMinMax(labelNode.getX(), labelNode.getY());
+ this.width += labelNode.getWidth();
+ this.height += labelNode.getHeight();
+ } else {
+ labelNode.lock();
+ lockedNodes++;
+ }
+
+ // Lock ln if it is unlocked but nodes are not allowed to move
+ if (!moveNodes && !ln.isLocked()) {
+ ln.lock();
+ lockedNodes++;
+ }
+
+ // Add labelNode -> parentNode to Map
+ labelToParentMap.put(labelNode, ln);
+
+ // Creates label Edge: ln <---> labelNode
+ LayoutEdge labelEdge = new LayoutEdge();
+ labelEdge.addNodes(ln, labelNode);
+
+ // This takes care of the weight of this edge
+ updateWeights(labelEdge);
+
+ // Adds it to edgeList
+ edgeList.add(labelEdge);
+
+
+ }
+
+ // Adds all LabelNodes to nodeList
+ nodeList.addAll(labelToParentMap.keySet());
+
+ }
+
+ public void calculateEdgeWeights() {
+ Double weight = null;
+
+ // -- First set labelEdges weights --
+
+ // Calculate maximum preexisting weight
+ Double maxWeight = new Double(Double.MIN_VALUE);
+
+ ListIterator<LayoutEdge>iter = edgeList.listIterator();
+
+ while (iter.hasNext()) {
+ LayoutEdge edge = iter.next();
+
+ // Only consider non label edges
+ if (labelToParentMap.keySet().contains(edge.getSource()) ||
+ labelToParentMap.keySet().contains(edge.getTarget()) ) {
+ continue;
+ }
+
+ if ( edge.getWeight() > maxWeight ) {
+ maxWeight = edge.getWeight();
+ }
+ }
+
+ // Value which will be used as weight for all label edges
+ weight = maxWeight * weightCoefficient;
+
+ // Set all labelEdge weights
+ ListIterator<LayoutEdge>iter2 = edgeList.listIterator();
+
+ while (iter2.hasNext()) {
+ LayoutEdge edge = iter2.next();
+
+ if (labelToParentMap.keySet().contains(edge.getSource()) ||
+ labelToParentMap.keySet().contains(edge.getTarget()) ) {
+ // set label edges weights
+ edge.setWeight(weight);
+ }
+ }
+
+
+ // -- Then call parent method to calculate all weights --
+ super.calculateEdgeWeights();
+ }
+
+
+ public Map<LayoutLabelNodeImpl,LayoutNode> getLabelToParentMap() {
+ return labelToParentMap;
+ }
+
+ /**
+ * Returns a list with all the LayoutLabelNodes
+ */
+ public ArrayList<LayoutLabelNodeImpl> getLabelNodes() {
+ ArrayList<LayoutLabelNodeImpl> array = new ArrayList<LayoutLabelNodeImpl> ();
+ array.addAll(labelToParentMap.keySet());
+ return array;
+ }
+
+
+
+
+
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/LayoutNode.java b/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/LayoutNode.java
new file mode 100644
index 0000000..e7b5f8c
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/LayoutNode.java
@@ -0,0 +1,415 @@
+/**
+ * Copyright (c) 2006 The Regents of the University of California.
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ * notice, this list of conditions, and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above
+ * copyright notice, this list of conditions, and the following
+ * disclaimer in the documentation and/or other materials provided
+ * with the distribution.
+ * 3. Redistributions must acknowledge that this software was
+ * originally developed by the UCSF Computer Graphics Laboratory
+ * under support by the NIH National Center for Research Resources,
+ * grant P41-RR01081.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY
+ * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+ * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+ * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
+ * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ */
+
+/**
+* Copyright (C) Gerardo Huck, 2010
+*
+* This program is free software: you can redistribute it and/or modify
+* it under the terms of the GNU Lesser General Public License as published
+* by the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+*
+* This program is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU Lesser General Public License for more details.
+*
+* You should have received a copy of the GNU Lesser General Public License
+* along with this program. If not, see <http://www.gnu.org/licenses/>.
+*
+*/
+
+
+/**
+ * This class is intended to be a common interface for Layout Node classes that interact
+ * with LayoutPartition class.
+
+ * In particular, it aims at providing convenient handle
+ * to information about position, the node itself, the node view. Many of
+ * the methods of this class are wrappers for CyNode or NodeView methods, and
+ * these are often wrapped by LayoutPartition methods.
+ *
+ * It was done as part of Google Summer of Code 2010.
+ * Mentor: Mike Smoot
+ * @author <a href="mailto:gerardohuck .at. gmail .dot. com">Gerardo Huck</a>
+ * @version 0.1
+ */
+
+package csplugins.layout;
+
+import cytoscape.*;
+
+import cytoscape.view.*;
+
+import giny.view.*;
+
+import java.util.*;
+
+/**
+
+ */
+public abstract class LayoutNode implements Comparable<LayoutNode> {
+
+ // static (class) variables
+ static final double EPSILON = 0.0000001D;
+
+
+ // Instance variables
+ protected boolean isLocked = false;
+ protected double x;
+ protected double y;
+ protected double dispX;
+ protected double dispY;
+ protected ArrayList<LayoutNode> neighbors = null;
+ protected int index = -1;
+
+ // instance methods
+
+
+ // !!!! This methods MUST be overriden by subclasses !!!!
+
+
+ /**
+ *
+ */
+ public abstract void moveToLocation();
+
+ /**
+ * Accessor function to return the NodeView associated with
+ * this LayoutNode.
+ *
+ * @return NodeView that is associated with this LayoutNode
+ */
+ public abstract NodeView getNodeView();
+
+ /**
+ * Return the width of this node
+ *
+ * @return width of this node
+ */
+ public abstract double getWidth();
+
+ /**
+ * Return the height of this node
+ *
+ * @return height of this node
+ */
+ public abstract double getHeight();
+
+ /**
+ * Return the node's identifier.
+ *
+ * @return String containing the node's identifier
+ */
+ public abstract String getIdentifier();
+
+ /**
+ * Return a string representation of the node
+ *
+ * @return String containing the node's identifier and location
+ */
+ public abstract String toString();
+
+ /**
+ * Return a string with the "type" of the node ("normal", "label")
+ *
+ * @return String containing the node's type
+ */
+ public abstract String getType();
+
+ // End of abstract methods
+
+
+ /**
+ * Set the location of this LayoutNode. Note that this only
+ * sets the location -- it does not actually move the node to
+ * that location. Users should call moveToLocation to actually
+ * accomplish the move.
+ *
+ * @param x Double representing the new X corrdinate of this node
+ * @param y Double representing the new Y corrdinate of this node
+ */
+ public void setLocation(double x, double y) {
+ this.x = x;
+ this.y = y;
+ }
+
+ /**
+ * Set the X location of this LayoutNode. Note that this only
+ * sets the location -- it does not actually move the node to
+ * that location. Users should call moveToLocation to actually
+ * accomplish the move.
+ *
+ * @param x Double representing the new X corrdinate of this node
+ */
+ public void setX(double x) {
+ this.x = x;
+ }
+
+ /**
+ * Set the Y location of this LayoutNode. Note that this only
+ * sets the location -- it does not actually move the node to
+ * that location. Users should call moveToLocation to actually
+ * accomplish the move.
+ *
+ * @param y Double representing the new Y corrdinate of this node
+ */
+ public void setY(double y) {
+ this.y = y;
+ }
+
+ /**
+ * Set the displacement of this LayoutNode. The displacement is a
+ * little different than the location in that it records an offset from
+ * the current location. This is useful for algorithms such as Kamada Kawai
+ * and Fructerman Rheingold, which update positions iteratively.
+ *
+ * @param x Double representing the amount to offset in the x direction
+ * @param y Double representing the amount to offset in the y direction
+ */
+ public void setDisp(double x, double y) {
+ this.dispX = x;
+ this.dispY = y;
+ }
+
+ /**
+ * Register this node as being "locked". Locked nodes are exempt from being moved
+ * during layout. Usually, these are the unselected nodes when a selected-only
+ * layout is being executed.
+ */
+ public void lock() {
+ this.isLocked = true;
+ }
+
+ /**
+ * Register this node as being "unlocked". Locked nodes are exempt from being moved
+ * during layout. Usually, these are the unselected nodes when a selected-only
+ * layout is being executed. The "unlocked" state is the default.
+ */
+ public void unLock() {
+ this.isLocked = false;
+ }
+
+ /**
+ * Returns "true" if this node is locked, false otherwise.
+ *
+ * @return true if locked, false if unlocked.
+ */
+ public boolean isLocked() {
+ return this.isLocked;
+ }
+
+ /**
+ * Increment the displacement recorded for this node by (x,y).
+ *
+ * @param x the additional amount to displace in the x direction
+ * @param y the additional amount to displace in the y direction
+ */
+ public void incrementDisp(double x, double y) {
+ this.dispX += x;
+ this.dispY += y;
+ }
+
+ /**
+ * Increment the location of this node by (x,y). Note that location
+ * values are merely recorded until moveToLocation is called.
+ *
+ * @param x the amount to move in the x direction
+ * @param y the amount to move in the y direction
+ */
+ public void increment(double x, double y) {
+ this.x += x;
+ this.y += y;
+ }
+
+ /**
+ * Decrement the displacement recorded for this node by (x,y).
+ *
+ * @param x the additional amount to displace in the -x direction
+ * @param y the additional amount to displace in the -y direction
+ */
+ public void decrementDisp(double x, double y) {
+ this.dispX -= x;
+ this.dispY -= y;
+ }
+
+ /**
+ * Decrement the location of this node by (x,y). Note that location
+ * values are merely recorded until moveToLocation is called.
+ *
+ * @param x the amount to move in the -x direction
+ * @param y the amount to move in the -y direction
+ */
+ public void decrement(double x, double y) {
+ this.x -= x;
+ this.y -= y;
+ }
+
+ /**
+ * Return the current X value for this LayoutNode.
+ *
+ * @return current X value
+ */
+ public double getX() {
+ return this.x;
+ }
+
+ /**
+ * Return the current Y value for this LayoutNode.
+ *
+ * @return current Y value
+ */
+ public double getY() {
+ return this.y;
+ }
+
+ /**
+ * Return the current X displacement value for this LayoutNode.
+ *
+ * @return current X displacement value
+ */
+ public double getXDisp() {
+ return this.dispX;
+ }
+
+ /**
+ * Return the current Y displacement value for this LayoutNode.
+ *
+ * @return current Y displacement value
+ */
+ public double getYDisp() {
+ return this.dispY;
+ }
+
+ /**
+ * Return the euclidean distance between this node and another node
+ *
+ * @param otherNode the node to measure the distance to
+ * @return the euclidean distance from this node to otherNode
+ */
+ public double distance(LayoutNode otherNode) {
+ double deltaX = this.x - otherNode.getX();
+ double deltaY = this.y - otherNode.getY();
+
+ return Math.max(EPSILON, Math.sqrt((deltaX * deltaX) + (deltaY * deltaY)));
+ }
+
+ /**
+ * Return the euclidean distance between this node and a location
+ *
+ * @param uX the X location to measure the distance to
+ * @param uY the Y location to measure the distance to
+ * @return the euclidean distance from this node to (uX,uY)
+ */
+ public double distance(double uX, double uY) {
+ double deltaX = this.x - uX;
+ double deltaY = this.y - uY;
+
+ return Math.max(EPSILON, Math.sqrt((deltaX * deltaX) + (deltaY * deltaY)));
+ }
+
+ /**
+ * Convenience function to keep track of neighbors of this node. This can be
+ * used to improve the performance of algorithms that try to determine the edge
+ * partners of nodes.
+ *
+ * @param v LayoutNode that is a neighbor of this LayoutNode
+ */
+ public void addNeighbor(LayoutNode v) {
+ this.neighbors.add(v);
+ }
+
+ /**
+ * Convenience function to return the list of neighbors (connected nodes) of this node.
+ *
+ * @return List of all of the neighbors (nodes with shared edges) of this node.
+ */
+ public List<LayoutNode> getNeighbors() {
+ return this.neighbors;
+ }
+
+ /**
+ * Return the node's degree (i.e. number of nodes it's connected to).
+ *
+ * @return Degree of this node
+ */
+ public double getDegree() {
+ return (double)neighbors.size();
+ }
+
+ /**
+ * Return a string representation of the node's displacement
+ *
+ * @return String containing the node's X,Y displacement
+ */
+ public String printDisp() {
+ String ret = new String("" + dispX + ", " + dispY);
+
+ return ret;
+ }
+
+ /**
+ * Return a string representation of the node's location
+ *
+ * @return String containing the node's X,Y location
+ */
+ public String printLocation() {
+ String ret = new String("" + x + ", " + y);
+
+ return ret;
+ }
+
+ /**
+ * Returns the index of this LayoutNode. This is <em>not</em> the same as the
+ * rootGraphIndex of the node. Its primarily used by LayoutPartition to keep
+ * track of the offset in the node array that holds this LayoutNode.
+ *
+ * @return The index of this node
+ * @see LayoutPartition
+ */
+ public int getIndex() {
+ return this.index;
+ }
+
+ /**
+ * Returns the natural order of two LayoutNodes determined by comparing the node
+ * identifiers.
+ *
+ * @param o2 the LayoutNode we're comparing ourselves to
+ * @return -1 if this is less than o2, 0 if they are equal, and 1 if this is greater than o2
+ */
+ public int compareTo(LayoutNode o2) {
+ return getIdentifier().compareTo(o2.getIdentifier());
+ }
+
+
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/LayoutNodeImpl.java b/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/LayoutNodeImpl.java
new file mode 100644
index 0000000..029fc6c
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/LayoutNodeImpl.java
@@ -0,0 +1,156 @@
+/* vim: set ts=2: */
+/**
+ * Copyright (c) 2006 The Regents of the University of California.
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ * notice, this list of conditions, and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above
+ * copyright notice, this list of conditions, and the following
+ * disclaimer in the documentation and/or other materials provided
+ * with the distribution.
+ * 3. Redistributions must acknowledge that this software was
+ * originally developed by the UCSF Computer Graphics Laboratory
+ * under support by the NIH National Center for Research Resources,
+ * grant P41-RR01081.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY
+ * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+ * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+ * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
+ * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ */
+package csplugins.layout;
+
+import cytoscape.*;
+
+import cytoscape.view.*;
+
+import giny.view.*;
+
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Random;
+
+/**
+ * The LayoutNode class. This class is used as a container for information
+ * about the nodes in a layout. In particular, it provides a convenient handle
+ * to information about position, the node itself, the node view. Many of
+ * the methods of this class are wrappers for CyNode or NodeView methods, and
+ * these are often wrapped by LayoutPartition methods.
+ */
+public class LayoutNodeImpl extends LayoutNode {
+
+ // -- instance variables --
+
+ // private double x;
+ // private double y;
+ // private double dispX;
+ // private double dispY;
+ // private boolean isLocked = false;
+
+
+ protected NodeView nodeView;
+
+ /**
+ * Empty constructor
+ */
+ public LayoutNodeImpl() {
+ }
+
+ /**
+ * The main constructor for a LayoutNodeImpl.
+ *
+ * @param nodeView The NodeView of this node
+ * @param index The index (usually in a node array) of this node
+ */
+ public LayoutNodeImpl(NodeView nodeView, int index) {
+ this.nodeView = nodeView;
+ this.index = index;
+ this.x = nodeView.getXPosition();
+ this.y = nodeView.getYPosition();
+ this.neighbors = new ArrayList<LayoutNode>();
+ }
+
+ /**
+ * Accessor function to return the NodeView associated with
+ * this LayoutNode.
+ *
+ * @return NodeView that is associated with this LayoutNode
+ */
+ public NodeView getNodeView() {
+ return this.nodeView;
+ }
+
+ /**
+ * Return the width of this node
+ *
+ * @return width of this node
+ */
+ public double getWidth() {
+ return this.nodeView.getWidth();
+ }
+
+ /**
+ * Return the height of this node
+ *
+ * @return height of this node
+ */
+ public double getHeight() {
+ return this.nodeView.getHeight();
+ }
+
+ /**
+ * Move the node to its current x,y coordinate.
+ */
+ public void moveToLocation() {
+ if (isLocked) {
+ this.x = nodeView.getXPosition();
+ this.y = nodeView.getYPosition();
+ } else {
+ nodeView.setXPosition(this.x);
+ nodeView.setYPosition(this.y);
+ }
+ }
+
+ /**
+ * Return a string representation of the node
+ *
+ * @return String containing the node's identifier and location
+ */
+ public String toString() {
+ return "Node " + getIdentifier() + " at " + printLocation();
+ }
+
+ /**
+ * Return a string with the "type" of the node ("normal", "label")
+ *
+ * @return String containing the node's type
+ */
+ public String getType() {
+ return "normal";
+ }
+
+ /**
+ * Return the node's identifier.
+ *
+ * @return String containing the node's identifier
+ */
+ public String getIdentifier() {
+ return this.nodeView.getNode().getIdentifier();
+ }
+
+
+
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/LayoutPartition.java b/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/LayoutPartition.java
new file mode 100644
index 0000000..2654c25
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/LayoutPartition.java
@@ -0,0 +1,778 @@
+/* vim: set ts=2: */
+/**
+ * Copyright (c) 2006 The Regents of the University of California.
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ * notice, this list of conditions, and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above
+ * copyright notice, this list of conditions, and the following
+ * disclaimer in the documentation and/or other materials provided
+ * with the distribution.
+ * 3. Redistributions must acknowledge that this software was
+ * originally developed by the UCSF Computer Graphics Laboratory
+ * under support by the NIH National Center for Research Resources,
+ * grant P41-RR01081.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY
+ * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+ * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+ * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
+ * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ */
+package csplugins.layout;
+
+import cytoscape.logger.CyLogger;
+
+import csplugins.layout.LayoutEdge;
+import csplugins.layout.LayoutNode;
+import csplugins.layout.Profile;
+import csplugins.layout.EdgeWeighter;
+
+import cytoscape.util.intr.IntIntHash;
+import cytoscape.util.intr.IntObjHash;
+
+import cytoscape.*;
+
+import cytoscape.view.*;
+
+import giny.view.*;
+
+import java.awt.Dimension;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Comparator;
+import java.util.Date;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.ListIterator;
+import java.util.Random;
+import java.util.Set;
+import java.util.Collection;
+
+
+/**
+ * The LayoutPartition class contains all of the information about a
+ * single graph partition, where a partition is defined as all nodes
+ * in a graph that connect only to each other. This class also provides
+ * static methods that are used to partition an existing graph.
+ *
+ * @author <a href="mailto:scooter at cgl.ucsf.edu">Scooter Morris</a>
+ * @version 0.9
+ */
+public class LayoutPartition {
+ protected ArrayList<LayoutNode> nodeList;
+ protected ArrayList<LayoutEdge> edgeList;
+ protected static HashMap<CyNode, LayoutNode> nodeToLayoutNode = null;
+ protected static IntIntHash nodesSeenMap = null;
+ protected static IntIntHash edgesSeenMap = null;
+ protected int nodeIndex = 0;
+ protected int partitionNumber = 0;
+ protected EdgeWeighter edgeWeighter = null;
+
+ // Keep track of the node min and max values
+ protected double maxX = -100000;
+ protected double maxY = -100000;
+ protected double minX = 100000;
+ protected double minY = 100000;
+ protected double width = 0;
+ protected double height = 0;
+
+ // Keep track of average location
+ protected double averageX = 0;
+ protected double averageY = 0;
+
+ // Keep track of the number of locked nodes we have in
+ // this partition
+ protected int lockedNodes = 0;
+
+ protected CyLogger logger = null;
+
+ // protected constants
+ protected static final int m_NODE_HAS_NOT_BEEN_SEEN = 0;
+ protected static final int m_NODE_HAS_BEEN_SEEN = 1;
+
+ /**
+ * LayoutPartition: use this constructor to create an empty LayoutPartition.
+ *
+ * @param nodeCount The number of nodes in the new partition.
+ * @param edgeCount The number of edges in the new partition.
+ */
+ public LayoutPartition(int nodeCount, int edgeCount) {
+ logger = CyLogger.getLogger(LayoutPartition.class);
+ nodeList = new ArrayList<LayoutNode>(nodeCount);
+ edgeList = new ArrayList<LayoutEdge>(edgeCount);
+ partitionNumber = 1;
+
+ if (nodeToLayoutNode == null)
+ nodeToLayoutNode = new HashMap<CyNode,LayoutNode>(nodeCount);
+ }
+
+ /**
+ * LayoutPartition: use this constructor to create a LayoutPartition that
+ * includes the entire network.
+ *
+ * @param network the CyNetwork to include
+ * @param networkView the CyNetworkView to use
+ * @param nodeSet the nodes to be considered
+ * @param edgeWeighter the weighter to use for edge weighting
+ */
+ public LayoutPartition(CyNetwork network, CyNetworkView networkView, Collection<CyNode>nodeSet,
+ EdgeWeighter edgeWeighter) {
+ initialize(network,networkView,nodeSet,edgeWeighter);
+ }
+
+
+ /**
+ * LayoutPartition: use this constructor to create a LayoutPartition that
+ * includes the entire network.
+ *
+ * @param network the CyNetwork to include
+ * @param networkView the CyNetworkView to use
+ * @param selectedOnly if true, only include selected nodes in the partition
+ * @param edgeWeighter the weighter to use for edge weighting
+ */
+ public LayoutPartition(CyNetwork network, CyNetworkView networkView, boolean selectedOnly,
+ EdgeWeighter edgeWeighter) {
+ if (selectedOnly) {
+ initialize(network,networkView,(Collection<CyNode>)network.getSelectedNodes(),edgeWeighter);
+ } else {
+ initialize(network,networkView,network.nodesList(),edgeWeighter);
+ }
+ }
+
+ protected void initialize(CyNetwork network, CyNetworkView networkView, Collection<CyNode>nodeSet,
+ EdgeWeighter edgeWeighter) {
+
+ logger = CyLogger.getLogger(LayoutPartition.class);
+
+ this.edgeWeighter = edgeWeighter;
+
+ // Initialize
+ nodeList = new ArrayList<LayoutNode>(network.getNodeCount());
+ edgeList = new ArrayList<LayoutEdge>(network.getEdgeCount());
+
+ if (nodeToLayoutNode == null)
+ nodeToLayoutNode = new HashMap<CyNode,LayoutNode>(network.getNodeCount());
+
+ // Now, walk the iterators and fill in the values
+ nodeListInitialize(network, networkView, nodeSet);
+ edgeListInitialize(network, networkView);
+ trimToSize();
+ partitionNumber = 1;
+ }
+
+ /**
+ * Set the EdgeWeighter to use for this partition. The EdgeWeighter should be
+ * shared by all partitions in the same graph to avoid contrary scaling problems.
+ *
+ * @param edgeWeighter the weighter to use for edge weighting
+ */
+ public void setEdgeWeighter(EdgeWeighter edgeWeighter) {
+ this.edgeWeighter = edgeWeighter;
+ }
+
+ /**
+ * Add a node to this partition.
+ *
+ * @param nv the NodeView of the node to add
+ * @param locked a boolean value to determine if this node is locked or not
+ */
+ protected void addNode(NodeView nv, boolean locked) {
+ CyNode node = (CyNode) nv.getNode();
+ LayoutNode v = new LayoutNodeImpl(nv, nodeIndex++);
+ nodeList.add(v);
+ nodeToLayoutNode.put(node, v);
+
+ if (locked) {
+ v.lock();
+ lockedNodes++;
+ } else {
+ updateMinMax(nv.getXPosition(), nv.getYPosition());
+ this.width += nv.getWidth();
+ this.height += nv.getHeight();
+ }
+ }
+
+ /**
+ * Add an edge to this partition assuming that the source and target
+ * nodes are not yet known.
+ *
+ * @param edge the CyEdge to add to the partition
+ */
+ protected void addEdge(CyEdge edge) {
+ LayoutEdge newEdge = new LayoutEdge(edge);
+ updateWeights(newEdge);
+ edgeList.add(newEdge);
+ }
+
+ /**
+ * Add an edge to this partition assuming that the source and target
+ * nodes <em>are</em> known.
+ *
+ * @param edge the CyEdge to add to the partition
+ * @param v1 the LayoutNode of the edge source
+ * @param v2 the LayoutNode of the edge target
+ */
+ protected void addEdge(CyEdge edge, LayoutNode v1, LayoutNode v2) {
+ LayoutEdge newEdge = new LayoutEdge(edge, v1, v2);
+ updateWeights(newEdge);
+ edgeList.add(newEdge);
+ }
+
+ /**
+ * Randomize the graph locations.
+ */
+ public void randomizeLocations() {
+ // Get a seeded pseudo random-number generator
+ Date today = new Date();
+ Random random = new Random(today.getTime());
+ // Reset our min and max values
+ resetNodes();
+
+ for (LayoutNode node: nodeList) {
+
+ if (!node.isLocked()) {
+ double x = random.nextDouble() * width;
+ double y = random.nextDouble() * height;
+ node.setLocation(x, y);
+ updateMinMax(x, y);
+ } else {
+ updateMinMax(node.getX(), node.getY());
+ }
+ }
+ }
+
+ /**
+ * Move the node to its current X and Y values. This is a wrapper
+ * to LayoutNode's moveToLocation, but has the property of updating
+ * the current min and max values for this partition.
+ *
+ * @param node the LayoutNode to move
+ */
+ public void moveNodeToLocation(LayoutNode node) {
+ // We provide this routine so that we can keep our
+ // min/max values updated
+ if (node.isLocked())
+ return;
+
+ node.moveToLocation();
+ updateMinMax(node.getX(), node.getY());
+ }
+
+ /**
+ * Convenience routine to update the source and target for all of the
+ * edges in a partition. This is useful when the algorithm used makes it
+ * difficult to record source and target until it has completed.
+ */
+ public void fixEdges() {
+ for (LayoutEdge lEdge: edgeList) {
+ // Get the underlying edge
+ CyEdge edge = lEdge.getEdge();
+ CyNode target = (CyNode) edge.getTarget();
+ CyNode source = (CyNode) edge.getSource();
+
+ if (nodeToLayoutNode.containsKey(source) && nodeToLayoutNode.containsKey(target)) {
+ // Add the connecting nodes
+ lEdge.addNodes((LayoutNode) nodeToLayoutNode.get(source),
+ (LayoutNode) nodeToLayoutNode.get(target));
+ }
+ }
+ }
+
+ /**
+ * Calculate and set the edge weights. Note that this will delete
+ * edges from the calculation (not the graph) when certain conditions
+ * are met.
+ */
+ public void calculateEdgeWeights() {
+
+ // Use a ListIterator so that we can modify the list
+ // as we go
+ ListIterator<LayoutEdge>iter = edgeList.listIterator();
+ while (iter.hasNext()) {
+ LayoutEdge edge = iter.next();
+
+ // If we're only dealing with selected nodes, drop any edges
+ // that don't have any selected nodes
+ if (edge.getSource().isLocked() && edge.getTarget().isLocked()) {
+ iter.remove();
+ } else if (edgeWeighter != null && edgeWeighter.normalizeWeight(edge) == false)
+ iter.remove();
+
+ //logger.debug("Edge "+edge.getEdge().getIdentifier()+" now has weight "+edge.getWeight());
+ // logger.info( edge.toString() + " now has weight "+edge.getWeight());
+ }
+ }
+
+ /**
+ * Return the size of this partition, which is defined as the number of
+ * nodes that it contains.
+ *
+ * @return partition size
+ */
+ public int size() {
+ return nodeList.size();
+ }
+
+ /**
+ * Return the list of LayoutNodes within this partition.
+ *
+ * @return List of LayoutNodes
+ * @see LayoutNode
+ */
+ public List<LayoutNode> getNodeList() {
+ return nodeList;
+ }
+
+ /**
+ * Return the list of LayoutEdges within this partition.
+ *
+ * @return List of LayoutEdges
+ * @see LayoutEdge
+ */
+ public List<LayoutEdge> getEdgeList() {
+ return edgeList;
+ }
+
+ /**
+ * Return an iterator over all of the LayoutNodes in this parition
+ *
+ * @return Iterator over the list of LayoutNodes
+ * @see LayoutNode
+ */
+ public Iterator<LayoutNode> nodeIterator() {
+ return nodeList.iterator();
+ }
+
+ /**
+ * Return an iterator over all of the LayoutEdges in this parition
+ *
+ * @return Iterator over the list of LayoutEdges
+ * @see LayoutEdge
+ */
+ public Iterator<LayoutEdge> edgeIterator() {
+ return edgeList.iterator();
+ }
+
+ /**
+ * Return the number of nodes in this partition
+ *
+ * @return number of nodes in the partition
+ */
+ public int nodeCount() {
+ return nodeList.size();
+ }
+
+ /**
+ * Return the number of edges in this partition
+ *
+ * @return number of edges in the partition
+ */
+ public int edgeCount() {
+ return edgeList.size();
+ }
+
+ /**
+ * Return the maximum X location of all of the LayoutNodes
+ *
+ * @return maximum X location
+ */
+ public double getMaxX() {
+ return maxX;
+ }
+
+ /**
+ * Return the maximum Y location of all of the LayoutNodes
+ *
+ * @return maximum Y location
+ */
+ public double getMaxY() {
+ return maxY;
+ }
+
+ /**
+ * Return the minimum X location of all of the LayoutNodes
+ *
+ * @return minimum X location
+ */
+ public double getMinX() {
+ return minX;
+ }
+
+ /**
+ * Return the minimum Y location of all of the LayoutNodes
+ *
+ * @return minimum Y location
+ */
+ public double getMinY() {
+ return minY;
+ }
+
+ /**
+ * Return the total width of all of the LayoutNodes
+ *
+ * @return total width of all of the LayoutNodes
+ */
+ public double getWidth() {
+ return width;
+ }
+
+ /**
+ * Return the total height of all of the LayoutNodes
+ *
+ * @return total height of all of the LayoutNodes
+ */
+ public double getHeight() {
+ return height;
+ }
+
+ /**
+ * Return the partition number of this partition
+ *
+ * @return partition number
+ */
+ public int getPartitionNumber() {
+ return partitionNumber;
+ }
+
+ /**
+ * Set the partition number of this partition
+ *
+ * @param part partition number
+ */
+ public void setPartitionNumber(int part) {
+ partitionNumber = part;
+ }
+
+ /**
+ * Return the number of locked nodes within this parititon
+ *
+ * @return number of locked nodes in partition
+ */
+ public int lockedNodeCount() {
+ return lockedNodes;
+ }
+
+ /**
+ * Return the average location of the nodes in this partition
+ *
+ * @return average location of the nodes as a Dimension
+ * @see Dimension
+ */
+ public Dimension getAverageLocation() {
+ int nodes = nodeCount() - lockedNodes;
+ Dimension result = new Dimension();
+ result.setSize(averageX / nodes, averageY / nodes);
+
+ return result;
+ }
+
+ /**
+ * Recalcultares max, min and average values from scratch
+ */
+ public void recalculateStatistics() {
+ this.resetNodes();
+ for (LayoutNode n: this.getNodeList())
+ if (!n.isLocked())
+ updateMinMax(n.getX(), n.getY());
+ }
+
+ /**
+ * Offset all of the nodes in the partition by a fixed
+ * amount. This is used by algorithms of offset each
+ * partition after laying it out.
+ *
+ * @param xoffset the amount to offset in the X direction
+ * @param yoffset the amount to offset in the Y direction
+ */
+ public void offset(double xoffset, double yoffset) {
+ double myMinX = this.minX;
+ double myMinY = this.minY;
+ resetNodes();
+
+ for (LayoutNode node: nodeList) {
+ node.increment(xoffset - myMinX, yoffset - myMinY);
+ moveNodeToLocation(node);
+ }
+ }
+
+ /**
+ * Reset routines
+ */
+
+ /**
+ * Reset all of the data maintained for the LayoutNodes
+ * contained within this partition, including the min, max
+ * and average x and y values.
+ */
+ public void resetNodes() {
+ maxX = -100000;
+ maxY = -100000;
+ minX = 100000;
+ minY = 100000;
+ averageX = 0;
+ averageY = 0;
+ }
+
+ /**
+ * Protected routines
+ */
+ protected void nodeListInitialize(CyNetwork network, CyNetworkView networkView,
+ Collection<CyNode> nodeSet) {
+ int nodeIndex = 0;
+ this.nodeList = new ArrayList<LayoutNode>(network.getNodeCount());
+
+ Iterator<NodeView>iter = networkView.getNodeViewsIterator();
+ while (iter.hasNext()) {
+ NodeView nv = (NodeView) iter.next();
+ CyNode node = (CyNode) nv.getNode();
+
+ if (!nodeSet.contains(node)) {
+ addNode(nv, true);
+ } else {
+ addNode(nv, false);
+ }
+ }
+ }
+
+ protected void edgeListInitialize(CyNetwork network, CyNetworkView networkView) {
+ for (CyEdge edge: (List<CyEdge>)network.edgesList()) {
+
+ CyNode source = (CyNode) edge.getSource();
+ CyNode target = (CyNode) edge.getTarget();
+
+ if (source == target)
+ continue;
+
+ LayoutNode v1 = (LayoutNode) nodeToLayoutNode.get(source);
+ LayoutNode v2 = (LayoutNode) nodeToLayoutNode.get(target);
+
+ // Do we care about this edge?
+ if (v1.isLocked() || v2.isLocked())
+ continue; // no, ignore it
+
+ EdgeView ev = networkView.getEdgeView(edge);
+ ev.clearBends();
+
+ addEdge(edge, v1, v2);
+ }
+ }
+
+ /**
+ * Space saving convenience function to trim the internal arrays to fit the
+ * contained data. Useful to call this after a partition has been created
+ * and filled. This is used by the static method LayoutPartition.partition
+ */
+ protected void trimToSize() {
+ nodeList.trimToSize();
+ edgeList.trimToSize();
+ }
+
+ protected void updateMinMax(double x, double y) {
+ minX = Math.min(minX, x);
+ minY = Math.min(minY, y);
+ maxX = Math.max(maxX, x);
+ maxY = Math.max(maxY, y);
+ averageX += x;
+ averageY += y;
+ }
+
+ protected void updateWeights(LayoutEdge newEdge) {
+ if (edgeWeighter != null) {
+ edgeWeighter.setWeight(newEdge);
+ }
+
+ // logger.debug("Updating "+newEdge);
+ }
+
+ // Static routines
+
+ /**
+ * Partition the graph -- this builds the LayoutEdge and LayoutNode
+ * arrays as a byproduct. The algorithm for this was taken from
+ * algorithms/graphPartition/SGraphPartition.java.
+ *
+ * @param network the CyNetwork containing the graph
+ * @param networkView the CyNetworkView representing the graph
+ * @param selectedOnly only consider selected nodes
+ * @param edgeWeighter the weighter to use for edge weighting
+ * @return a List of LayoutPartitions
+ */
+ public static List<LayoutPartition> partition(CyNetwork network, CyNetworkView networkView,
+ boolean selectedOnly, EdgeWeighter edgeWeighter) {
+
+ if (selectedOnly) {
+ return partition(network,networkView,network.getSelectedNodes(),edgeWeighter);
+ }
+
+ return partition(network,networkView,network.nodesList(),edgeWeighter);
+
+ }
+
+ /**
+ * Partition the graph -- this builds the LayoutEdge and LayoutNode
+ * arrays as a byproduct. The algorithm for this was taken from
+ * algorithms/graphPartition/SGraphPartition.java.
+ *
+ * @param network the CyNetwork containing the graph
+ * @param networkView the CyNetworkView representing the graph
+ * @param nodeSet the set of nodes to consider
+ * @param edgeWeighter the weighter to use for edge weighting
+ * @return a List of LayoutPartitions
+ */
+ public static List<LayoutPartition> partition(CyNetwork network, CyNetworkView networkView,
+ Collection<CyNode> nodeSet, EdgeWeighter edgeWeighter) {
+ ArrayList<LayoutPartition> partitions = new ArrayList<LayoutPartition>();
+
+ nodesSeenMap = new IntIntHash();
+ edgesSeenMap = new IntIntHash();
+
+ IntObjHash nodesToViews = new IntObjHash();
+ nodeToLayoutNode = new HashMap<CyNode,LayoutNode>(network.getNodeCount());
+
+ // Initialize the maps
+ Iterator nodeViewIter = networkView.getNodeViewsIterator();
+
+ while (nodeViewIter.hasNext()) {
+ NodeView nv = (NodeView) nodeViewIter.next();
+ int node = nv.getNode().getRootGraphIndex();
+ nodesSeenMap.put(-node, m_NODE_HAS_NOT_BEEN_SEEN);
+ nodesToViews.put(-node, nv);
+ }
+
+ for (CyEdge edge: (List<CyEdge>)network.edgesList()) {
+ int edgeIndex = edge.getRootGraphIndex();
+ edgesSeenMap.put(-edgeIndex, m_NODE_HAS_NOT_BEEN_SEEN);
+ }
+
+ int partitionCount = 1;
+
+ // OK, now traverse the graph
+ for (CyNode node: nodeSet) {
+ int nodeIndex = node.getRootGraphIndex();
+
+ // Have we seen this already?
+ if (nodesSeenMap.get(-nodeIndex) == m_NODE_HAS_BEEN_SEEN)
+ continue;
+
+ // Nope, first time
+ LayoutPartition part = new LayoutPartition(network.getNodeCount(),
+ network.getEdgeCount());
+ // Set the edge weighter
+ part.setEdgeWeighter(edgeWeighter);
+
+ nodesSeenMap.put(-nodeIndex, m_NODE_HAS_BEEN_SEEN);
+
+ // Traverse through all connected nodes
+ traverse(network, networkView, nodesToViews, node, part);
+
+ // Done -- finalize the parition
+ part.trimToSize();
+
+ // Finally, now that we're sure we've touched all of our
+ // nodes. Fix up our edgeLayout list to have all of our
+ // layoutNodes
+ part.fixEdges();
+
+ partitions.add(part);
+ }
+
+ // Now sort the partitions based on the partition's node count
+ LayoutPartition[] a = new LayoutPartition[1];
+ LayoutPartition[] parts = partitions.toArray(a);
+ Arrays.sort(parts,
+ new Comparator<LayoutPartition>() {
+ public int compare(LayoutPartition p1, LayoutPartition p2) {
+ return (p2.size() - p1.size());
+ }
+
+ public boolean equals(LayoutPartition obj) {
+ return false;
+ }
+ });
+ for (int part = 0; part < parts.length; part++) {
+ parts[part].setPartitionNumber(part+1);
+ }
+
+ return Arrays.asList(parts);
+ }
+
+ /**
+ * This method traverses nodes connected to the specified node.
+ * @param network The CyNetwork we are laying out
+ * @param networkView The CyNetworkView we are laying out
+ * @param nodesToViews A map that maps between nodes and views
+ * @param node The node to search for connected nodes.
+ * @param partition the partition we're laying out
+ */
+ protected static void traverse(CyNetwork network, CyNetworkView networkView,
+ IntObjHash nodesToViews, CyNode node,
+ LayoutPartition partition) {
+ int nodeIndex = node.getRootGraphIndex();
+
+ // Get the nodeView
+ NodeView nv = (NodeView) nodesToViews.get(-nodeIndex);
+
+ // Add this node to the partition
+ partition.addNode(nv, false);
+
+ // Get the list of edges connected to this node
+ int[] incidentEdges = network.getAdjacentEdgeIndicesArray(nodeIndex, true, true, true);
+
+ // Iterate through each connected edge
+ for (int i = 0; i < incidentEdges.length; i++) {
+ // Get the actual edge
+ CyEdge incidentEdge = (CyEdge) network.getEdge(incidentEdges[i]);
+
+ int edgeIndex = incidentEdge.getRootGraphIndex();
+
+ // Have we already seen this edge?
+ if (edgesSeenMap.get(-edgeIndex) == m_NODE_HAS_BEEN_SEEN) {
+ // Yes, continue since it means we *must* have seen both sides
+ continue;
+ }
+
+ edgesSeenMap.put(-edgeIndex, m_NODE_HAS_BEEN_SEEN);
+
+ // Make sure we clean up after any previous layouts
+ EdgeView ev = networkView.getEdgeView(incidentEdge);
+ ev.clearBends();
+
+ // Add the edge to the partition
+ partition.addEdge(incidentEdge);
+
+ // Determine the node's index that is on the other side of the edge
+ CyNode otherNode;
+
+ if (incidentEdge.getSource() == node) {
+ otherNode = (CyNode) incidentEdge.getTarget();
+ } else {
+ otherNode = (CyNode) incidentEdge.getSource();
+ }
+
+ int incidentNodeIndex = otherNode.getRootGraphIndex();
+
+ // Have we seen the connecting node yet?
+ if (nodesSeenMap.get(-incidentNodeIndex) == m_NODE_HAS_NOT_BEEN_SEEN) {
+ // Mark it as having been seen
+ nodesSeenMap.put(-incidentNodeIndex, m_NODE_HAS_BEEN_SEEN);
+
+ // Traverse through this one
+ traverse(network, networkView, nodesToViews, otherNode, partition);
+ }
+ }
+ }
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/LayoutPlugin.java b/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/LayoutPlugin.java
new file mode 100644
index 0000000..cf9fbda
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/LayoutPlugin.java
@@ -0,0 +1,103 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package csplugins.layout;
+
+import csplugins.layout.algorithms.GroupAttributesLayout;
+import csplugins.layout.algorithms.bioLayout.BioLayoutFRAlgorithm;
+import csplugins.layout.algorithms.bioLayout.BioLayoutKKAlgorithm;
+import csplugins.layout.algorithms.graphPartition.AttributeCircleLayout;
+import csplugins.layout.algorithms.graphPartition.DegreeSortedCircleLayout;
+import csplugins.layout.algorithms.graphPartition.ISOMLayout;
+import csplugins.layout.algorithms.hierarchicalLayout.HierarchicalLayoutAlgorithm;
+import csplugins.layout.algorithms.circularLayout.CircularLayoutAlgorithm;
+import csplugins.layout.algorithms.force.ForceDirectedLayout;
+
+import cytoscape.*;
+
+import cytoscape.layout.*;
+import cytoscape.layout.CyLayouts;
+
+import cytoscape.plugin.*;
+
+import cytoscape.util.*;
+
+import cytoscape.view.*;
+
+import giny.view.NodeView;
+
+import java.awt.event.*;
+
+import java.util.*;
+
+import javax.swing.*;
+
+
+/**
+ *
+ */
+public class LayoutPlugin extends CytoscapePlugin {
+ /**
+ * Creates a new LayoutPlugin object.
+ */
+ public LayoutPlugin() {
+ // Add the Cytoscape layouts
+ CyLayouts.addLayout(new ForceDirectedLayout(), "Cytoscape Layouts");
+ CyLayouts.addLayout(new CircularLayoutAlgorithm(), "Cytoscape Layouts");
+ CyLayouts.addLayout(new HierarchicalLayoutAlgorithm(), "Cytoscape Layouts");
+ CyLayouts.addLayout(new AttributeCircleLayout(), "Cytoscape Layouts");
+ CyLayouts.addLayout(new DegreeSortedCircleLayout(), "Cytoscape Layouts");
+ CyLayouts.addLayout(new ISOMLayout(), "Cytoscape Layouts");
+ CyLayouts.addLayout(new GroupAttributesLayout(), "Cytoscape Layouts");
+ CyLayouts.addLayout(new BioLayoutKKAlgorithm(false), "Cytoscape Layouts");
+ CyLayouts.addLayout(new BioLayoutKKAlgorithm(true), "Cytoscape Layouts");
+ CyLayouts.addLayout(new BioLayoutFRAlgorithm(true), "Cytoscape Layouts");
+
+ // Add the JGraph layouts
+ CyLayouts.addLayout(new JGraphLayoutWrapper(JGraphLayoutWrapper.ANNEALING), "JGraph Layouts");
+ CyLayouts.addLayout(new JGraphLayoutWrapper(JGraphLayoutWrapper.MOEN), "JGraph Layouts");
+ CyLayouts.addLayout(new JGraphLayoutWrapper(JGraphLayoutWrapper.CIRCLE_GRAPH),
+ "JGraph Layouts");
+ CyLayouts.addLayout(new JGraphLayoutWrapper(JGraphLayoutWrapper.RADIAL_TREE),
+ "JGraph Layouts");
+ CyLayouts.addLayout(new JGraphLayoutWrapper(JGraphLayoutWrapper.GEM), "JGraph Layouts");
+ CyLayouts.addLayout(new JGraphLayoutWrapper(JGraphLayoutWrapper.SPRING_EMBEDDED),
+ "JGraph Layouts");
+ CyLayouts.addLayout(new JGraphLayoutWrapper(JGraphLayoutWrapper.SUGIYAMA), "JGraph Layouts");
+ CyLayouts.addLayout(new JGraphLayoutWrapper(JGraphLayoutWrapper.TREE), "JGraph Layouts");
+ }
+
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/Profile.java b/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/Profile.java
new file mode 100644
index 0000000..1d4282e
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/Profile.java
@@ -0,0 +1,92 @@
+/* vim: set ts=2: */
+/**
+ * Copyright (c) 2006 The Regents of the University of California.
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ * notice, this list of conditions, and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above
+ * copyright notice, this list of conditions, and the following
+ * disclaimer in the documentation and/or other materials provided
+ * with the distribution.
+ * 3. Redistributions must acknowledge that this software was
+ * originally developed by the UCSF Computer Graphics Laboratory
+ * under support by the NIH National Center for Research Resources,
+ * grant P41-RR01081.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY
+ * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+ * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+ * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
+ * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ */
+package csplugins.layout;
+
+import cytoscape.logger.CyLogger;
+
+/**
+ * This class is used to provide some simple profiling
+ */
+public class Profile {
+ long startTime;
+ long totalTime;
+
+ /**
+ * Creates a new Profile object.
+ */
+ public Profile() {
+ this.startTime = 0;
+ this.totalTime = 0;
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void start() {
+ this.startTime = System.currentTimeMillis();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public long checkpoint() {
+ long runTime = System.currentTimeMillis() - this.startTime;
+ this.totalTime += runTime;
+
+ return runTime;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param message DOCUMENT ME!
+ */
+ public void done(String message) {
+ // Get our runtime
+ checkpoint();
+
+ CyLogger.getLogger().debug(message + this.totalTime + "ms");
+ this.totalTime = 0;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public long getTotalTime() {
+ return this.totalTime;
+ }
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/algorithms/GroupAttributesLayout.java b/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/algorithms/GroupAttributesLayout.java
new file mode 100644
index 0000000..f2c3821
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/algorithms/GroupAttributesLayout.java
@@ -0,0 +1,435 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package csplugins.layout.algorithms;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.data.CyAttributes;
+
+import cytoscape.layout.LayoutProperties;
+import cytoscape.layout.Tunable;
+
+import csplugins.layout.LayoutNode;
+import csplugins.layout.LayoutPartition;
+import csplugins.layout.algorithms.graphPartition.AbstractGraphPartition;
+
+import giny.model.GraphPerspective;
+import giny.model.Node;
+
+import java.awt.GridLayout;
+import java.awt.Rectangle;
+
+import java.lang.Double;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.TreeMap;
+
+import javax.swing.JPanel;
+
+
+/*
+ This layout partitions the graph according to the selected node attribute's values.
+ The nodes of the graph are broken into discrete partitions, where each partition has
+ the same attribute value. For example, assume there are four nodes, where each node
+ has the "IntAttr" attribute defined. Assume node 1 and 2 have the value "100" for
+ the "IntAttr" attribute, and node 3 and 4 have the value "200." This will place nodes
+ 1 and 2 in the first partition and nodes 3 and 4 in the second partition. Each
+ partition is drawn in a circle.
+*/
+/**
+ *
+ */
+public class GroupAttributesLayout extends AbstractGraphPartition {
+ /*
+ Layout parameters:
+ - spacingx: Horizontal spacing (on the x-axis) between two partitions in a row.
+ - spacingy: Vertical spacing (on the y-axis) between the largest partitions of two rows.
+ - maxwidth: Maximum width of a row
+ - minrad: Minimum radius of a partition.
+ - radmult: The scale of the radius of the partition. Increasing this value
+ will increase the size of the partition proportionally.
+ */
+ private double spacingx = 400.0;
+ private double spacingy = 400.0;
+ private double maxwidth = 5000.0;
+ private double minrad = 100.0;
+ private double radmult = 50.0;
+ private String attributeName;
+ private byte attributeType;
+ private CyAttributes nodeAttributes;
+ private LayoutProperties layoutProperties;
+
+ /**
+ * Creates a new GroupAttributesLayout object.
+ */
+ public GroupAttributesLayout() {
+ super();
+ layoutProperties = new LayoutProperties(getName());
+ initialize_properties();
+ }
+
+ /**
+ * Overrides for CyLayoutAlgorithm support
+ */
+ public String getName() {
+ return "attributes-layout";
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String toString() {
+ return "Group Attributes Layout";
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public byte[] supportsNodeAttributes() {
+ byte[] attrs = {
+ CyAttributes.TYPE_INTEGER, CyAttributes.TYPE_STRING,
+ CyAttributes.TYPE_FLOATING, CyAttributes.TYPE_BOOLEAN
+ };
+
+ return attrs;
+ }
+
+ /**
+ * Sets the attribute to use for the weights
+ *
+ * @param value the name of the attribute
+ */
+ public void setLayoutAttribute(String value) {
+ if (value == null) {
+ attributeName = null;
+ } else {
+ attributeName = value;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public List<String> getInitialAttributeList() {
+ return null;
+ }
+
+ /**
+ * Get the settings panel for this layout
+ */
+ public JPanel getSettingsPanel() {
+ JPanel panel = new JPanel(new GridLayout(0, 1));
+ panel.add(layoutProperties.getTunablePanel());
+
+ return panel;
+ }
+
+ protected void initialize_properties() {
+ layoutProperties.add(new Tunable("spacingx",
+ "Horizontal spacing between two partitions in a row",
+ Tunable.DOUBLE, new Double(400.0)));
+ layoutProperties.add(new Tunable("spacingy",
+ "Vertical spacing between the largest partitions of two rows",
+ Tunable.DOUBLE, new Double(400.0)));
+ layoutProperties.add(new Tunable("maxwidth", "Maximum width of a row", Tunable.DOUBLE,
+ new Double(5000.0)));
+ layoutProperties.add(new Tunable("minrad", "Minimum width of a partition", Tunable.DOUBLE,
+ new Double(100.0)));
+ layoutProperties.add(new Tunable("radmult", "Scale of the radius of the partition",
+ Tunable.DOUBLE, new Double(50.0)));
+ layoutProperties.add(new Tunable("attributeName", "The attribute to use for the layout",
+ Tunable.NODEATTRIBUTE, ""));
+ // We've now set all of our tunables, so we can read the property
+ // file now and adjust as appropriate
+ layoutProperties.initializeProperties();
+
+ // Finally, update everything. We need to do this to update
+ // any of our values based on what we read from the property file
+ updateSettings(true);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void updateSettings() {
+ updateSettings(false);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param force DOCUMENT ME!
+ */
+ public void updateSettings(boolean force) {
+ layoutProperties.updateValues();
+
+ Tunable t = layoutProperties.get("spacingx");
+ if ((t != null) && (t.valueChanged() || force)) {
+ spacingx = ((Double) t.getValue()).doubleValue();
+ if (t.valueChanged())
+ layoutProperties.setProperty(t.getName(), t.getValue().toString());
+ }
+
+ t = layoutProperties.get("spacingy");
+ if ((t != null) && (t.valueChanged() || force)) {
+ spacingy = ((Double) t.getValue()).doubleValue();
+ if (t.valueChanged())
+ layoutProperties.setProperty(t.getName(), t.getValue().toString());
+ }
+
+ t = layoutProperties.get("maxwidth");
+ if ((t != null) && (t.valueChanged() || force)) {
+ maxwidth = ((Double) t.getValue()).doubleValue();
+ if (t.valueChanged())
+ layoutProperties.setProperty(t.getName(), t.getValue().toString());
+ }
+
+ t = layoutProperties.get("minrad");
+ if ((t != null) && (t.valueChanged() || force)) {
+ minrad = ((Double) t.getValue()).doubleValue();
+ if (t.valueChanged())
+ layoutProperties.setProperty(t.getName(), t.getValue().toString());
+ }
+
+ t = layoutProperties.get("radmult");
+ if ((t != null) && (t.valueChanged() || force)) {
+ radmult = ((Double) t.getValue()).doubleValue();
+ if (t.valueChanged())
+ layoutProperties.setProperty(t.getName(), t.getValue().toString());
+ }
+
+ t = layoutProperties.get("attributeName");
+ if ((t != null) && (t.valueChanged() || force)) {
+ attributeName = (String) t.getValue();
+ if (t.valueChanged())
+ layoutProperties.setProperty(t.getName(), t.getValue().toString());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void revertSettings() {
+ layoutProperties.revertProperties();
+ }
+
+ public LayoutProperties getSettings() {
+ return layoutProperties;
+ }
+
+ /*
+ Psuedo-procedure:
+ 1. Call makeDiscrete(). This will create a map for each value of the
+ node attribute to the list of nodes with that attribute value.
+ Each of these lists will become a partition in the graph.
+ makeDiscrete() will also add nodes to the invalidNodes list
+ that do not have a value associated with the attribute.
+ 2. Call sort(). This will return a list of partitions that is
+ sorted based on the value of the attribute. Add the invalid
+ nodes to the end of the sorted list. All the invalid nodes
+ will be grouped together in the last partition of the layout.
+ 3. Begin plotting each partition.
+ a. Call encircle(). This will plot the partition in a circle.
+ b. Store the diameter of the last circle plotted.
+ c. Update maxheight. This stores the height of the largest circle
+ in a row.
+ d. Update offsetx. If we've reached the end of the row,
+ reset offsetx and maxheight; update offsety so that
+ it will store the y-axis location of the next row.
+ */
+ /**
+ * DOCUMENT ME!
+ */
+ public void layoutPartition(LayoutPartition partition) {
+ if (canceled) return;
+
+ taskMonitor.setStatus("Initializing");
+ initialize(); // Calls initialize_local
+
+ nodeAttributes = Cytoscape.getNodeAttributes();
+
+ attributeType = nodeAttributes.getType(attributeName);
+
+ Map<Comparable, List<LayoutNode>> partitionMap = new TreeMap<Comparable, List<LayoutNode>>();
+ List<LayoutNode> invalidNodes = new ArrayList<LayoutNode>();
+ makeDiscrete(partition, partitionMap, invalidNodes);
+
+ List<List<LayoutNode>> partitionList = sort(partitionMap);
+ partitionList.add(invalidNodes);
+
+ double offsetx = 0.0;
+ double offsety = 0.0;
+ double maxheight = 0.0;
+
+ for (List<LayoutNode> part : partitionList) {
+ if (canceled)
+ return;
+
+ double radius = encircle(partition, part, offsetx, offsety);
+
+ double diameter = 2.0 * radius;
+
+ if (diameter > maxheight)
+ maxheight = diameter;
+
+ offsetx += diameter;
+
+ if (offsetx > maxwidth) {
+ offsety += (maxheight + spacingy);
+ offsetx = 0.0;
+ maxheight = 0.0;
+ } else
+ offsetx += spacingx;
+ }
+ }
+
+ private void makeDiscrete(LayoutPartition partition, Map<Comparable, List<LayoutNode>> map, List<LayoutNode> invalidNodes) {
+ if (map == null)
+ return;
+
+ for (LayoutNode node: partition.getNodeList()) {
+ if (canceled)
+ break;
+
+ Comparable key = null;
+
+ switch (attributeType) {
+ case CyAttributes.TYPE_INTEGER:
+ key = nodeAttributes.getIntegerAttribute(node.getIdentifier(), attributeName);
+
+ break;
+
+ case CyAttributes.TYPE_STRING:
+ key = nodeAttributes.getStringAttribute(node.getIdentifier(), attributeName);
+
+ break;
+
+ case CyAttributes.TYPE_FLOATING:
+ key = nodeAttributes.getDoubleAttribute(node.getIdentifier(), attributeName);
+
+ break;
+
+ case CyAttributes.TYPE_BOOLEAN:
+ key = nodeAttributes.getBooleanAttribute(node.getIdentifier(), attributeName);
+
+ break;
+ }
+
+ if (key == null) {
+ if (invalidNodes != null)
+ invalidNodes.add(node);
+ } else {
+ if (!map.containsKey(key))
+ map.put(key, new ArrayList<LayoutNode>());
+
+ map.get(key).add(node);
+ }
+ }
+ }
+
+ private List<List<LayoutNode>> sort(final Map<Comparable, List<LayoutNode>> map) {
+ if (map == null)
+ return null;
+
+ List<Comparable> keys = new ArrayList<Comparable>(map.keySet());
+ Collections.sort(keys);
+
+ Comparator<LayoutNode> comparator = new Comparator<LayoutNode>() {
+ public int compare(LayoutNode node1, LayoutNode node2) {
+ String a = node1.getIdentifier();
+ String b = node2.getIdentifier();
+
+ return a.compareTo(b);
+ }
+ };
+
+ List<List<LayoutNode>> sortedlist = new ArrayList<List<LayoutNode>>(map.keySet().size());
+
+ for (Comparable key : keys) {
+ List<LayoutNode> partition = map.get(key);
+ Collections.sort(partition, comparator);
+ sortedlist.add(partition);
+ }
+
+ return sortedlist;
+ }
+
+ private double encircle(LayoutPartition partition, List<LayoutNode> nodeList, double offsetx, double offsety) {
+ if (partition == null)
+ return 0.0;
+
+ if (nodeList.size() == 1) {
+ LayoutNode node = nodeList.get(0);
+ node.setX(offsetx);
+ node.setY(offsety);
+ partition.moveNodeToLocation(node);
+
+ return 0.0;
+ }
+
+ double radius = radmult * Math.sqrt(nodeList.size());
+
+ if (radius < minrad)
+ radius = minrad;
+
+ double phidelta = (2.0 * Math.PI) / nodeList.size();
+ double phi = 0.0;
+
+ for (LayoutNode node : nodeList) {
+ double x = offsetx + radius + (radius * Math.cos(phi));
+ double y = offsety + radius + (radius * Math.sin(phi));
+ node.setX(x);
+ node.setY(y);
+ partition.moveNodeToLocation(node);
+ phi += phidelta;
+ }
+
+ return radius;
+ }
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/algorithms/StackedNodeLayout.java b/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/algorithms/StackedNodeLayout.java
new file mode 100644
index 0000000..412bab1
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/algorithms/StackedNodeLayout.java
@@ -0,0 +1,115 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package csplugins.layout.algorithms;
+
+import cytoscape.CyNode;
+
+import cytoscape.layout.AbstractLayout;
+
+import cytoscape.view.CyNetworkView;
+
+import giny.view.NodeView;
+import giny.view.NodeView;
+
+import java.util.Collection;
+import java.util.Iterator;
+
+
+/**
+ *
+ */
+public class StackedNodeLayout extends AbstractLayout {
+ /**
+ * Puts a collection of nodes into a "stack" layout. This means the nodes are
+ * arranged in a line vertically, with each node overlapping with the previous.
+ *
+ * @param nodes the nodes whose position will be modified
+ * @param x_position the x position for the nodes
+ * @param y_start_position the y starting position for the stack
+ */
+ private double y_start_position;
+ private double x_position;
+ private Collection nodes;
+
+ /**
+ * Creates a new StackedNodeLayout object.
+ *
+ * @param x_position DOCUMENT ME!
+ * @param y_start_position DOCUMENT ME!
+ * @param nodes DOCUMENT ME!
+ */
+ public StackedNodeLayout(double x_position, double y_start_position, Collection nodes) {
+ super();
+ this.x_position = x_position;
+ this.y_start_position = y_start_position;
+ this.nodes = nodes;
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void construct() {
+ Iterator it = nodes.iterator();
+ double yPosition = y_start_position;
+
+ while (it.hasNext()) {
+ CyNode node = (CyNode) it.next();
+ NodeView nodeView = networkView.getNodeView(node);
+ nodeView.setXPosition(x_position);
+ nodeView.setYPosition(yPosition);
+ yPosition += (nodeView.getHeight() * 2);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getName() {
+ return "Stacked Node Layout";
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String toString() {
+ return getName();
+ }
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutAlgorithm.java b/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutAlgorithm.java
new file mode 100644
index 0000000..8ccd450
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutAlgorithm.java
@@ -0,0 +1,342 @@
+/* vim: set ts=2: */
+/**
+ * Copyright (c) 2006 The Regents of the University of California.
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ * notice, this list of conditions, and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above
+ * copyright notice, this list of conditions, and the following
+ * disclaimer in the documentation and/or other materials provided
+ * with the distribution.
+ * 3. Redistributions must acknowledge that this software was
+ * originally developed by the UCSF Computer Graphics Laboratory
+ * under support by the NIH National Center for Research Resources,
+ * grant P41-RR01081.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY
+ * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+ * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+ * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
+ * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ */
+package csplugins.layout.algorithms.bioLayout;
+
+import csplugins.layout.EdgeWeighter;
+import csplugins.layout.LayoutNode;
+import csplugins.layout.LayoutPartition;
+import csplugins.layout.Profile;
+import csplugins.layout.algorithms.graphPartition.AbstractGraphPartition;
+
+import cytoscape.data.CyAttributes;
+
+import cytoscape.layout.AbstractLayout;
+import cytoscape.layout.LayoutProperties;
+import cytoscape.layout.Tunable;
+
+import java.awt.GridLayout;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.swing.JPanel;
+
+
+/**
+ * Superclass for the two bioLayout algorithms (KK and FR).
+ *
+ * @author <a href="mailto:scooter at cgl.ucsf.edu">Scooter Morris</a>
+ * @version 0.9
+ */
+public abstract class BioLayoutAlgorithm extends AbstractGraphPartition {
+ /**
+ * Properties
+ */
+ private static final int DEBUGPROP = 0;
+ private static final int RANDOMIZE = 1;
+ private static final int MINWEIGHT = 2;
+ private static final int MAXWEIGHT = 3;
+ private static final int SELECTEDONLY = 4;
+ private static final int LAYOUTATTRIBUTE = 5;
+
+ /**
+ * A small value used to avoid division by zero
+ */
+ protected double EPSILON = 0.0000001D;
+
+ /**
+ * Value to set for doing unweighted layouts
+ */
+ public static final String UNWEIGHTEDATTRIBUTE = "(unweighted)";
+
+ /**
+ * Our list of Tunables
+ */
+ protected LayoutProperties layoutProperties;
+
+ /**
+ * Enables/disables debugging messages
+ */
+ private final static boolean DEBUG = false;
+ protected static boolean debug = DEBUG; // so we can overload it with a property
+
+ /**
+ * Whether or not to initialize by randomizing all points
+ */
+ protected boolean randomize = true;
+
+ /**
+ * Whether or not to use edge weights for layout
+ */
+ protected boolean supportWeights = true;
+
+ /**
+ * This is the constructor for the bioLayout algorithm.
+ */
+ public BioLayoutAlgorithm() {
+ super();
+
+ if (edgeWeighter == null)
+ edgeWeighter = new EdgeWeighter();
+
+ layoutProperties = new LayoutProperties(getName());
+ }
+
+ /**
+ * Tells Cytoscape whether we support selected nodes only or not
+ *
+ * @return true since we do support it
+ */
+ public boolean supportsSelectedOnly() { return true; }
+
+ // We don't support node attribute-based layouts
+ /**
+ * Tells Cytoscape whether we support node attribute based layouts
+ *
+ * @return nulls, which indicates that we don't
+ */
+ public byte[] supportsNodeAttributes() {
+ return null;
+ }
+
+ // We do support edge attribute-based layouts
+ /**
+ * Tells Cytoscape whether we support node attribute based layouts
+ *
+ * @return null if supportWeights is false, otherwise return the attribute
+ * types that can be used for weights.
+ */
+ public byte[] supportsEdgeAttributes() {
+ if (!supportWeights)
+ return null;
+
+ byte[] attrs = { CyAttributes.TYPE_INTEGER, CyAttributes.TYPE_FLOATING };
+
+ return attrs;
+ }
+
+ /**
+ * Returns "(unweighted)", which is the "attribute" we
+ * use to tell the algorithm not to use weights
+ *
+ * @returns List of our "special" weights
+ */
+ public List<String> getInitialAttributeList() {
+ ArrayList<String> list = new ArrayList<String>();
+ list.add(UNWEIGHTEDATTRIBUTE);
+
+ return list;
+ }
+
+ /**
+ * Sets the flag that determines if we're to layout all nodes
+ * or only selected nodes.
+ *
+ * @param value the name of the attribute
+ */
+ public void setSelectedOnly(boolean value) {
+ // Inherited by AbstractLayout
+ selectedOnly = value;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param value DOCUMENT ME!
+ */
+ public void setSelectedOnly(String value) {
+ Boolean val = new Boolean(value);
+ selectedOnly = val.booleanValue();
+ }
+
+ /**
+ * Sets the debug flag
+ *
+ * @param flag boolean value that turns debugging on or off
+ */
+ public void setDebug(boolean flag) {
+ debug = flag;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param value DOCUMENT ME!
+ */
+ public void setDebug(String value) {
+ Boolean val = new Boolean(value);
+ debug = val.booleanValue();
+ }
+
+ /**
+ * Sets the randomize flag
+ *
+ * @param flag boolean value that turns initial randomization on or off
+ */
+ public void setRandomize(boolean flag) {
+ randomize = flag;
+ }
+
+ /**
+ * Sets the randomize flag
+ *
+ * @param value boolean string that turns initial randomization on or off
+ */
+ public void setRandomize(String value) {
+ Boolean val = new Boolean(value);
+ randomize = val.booleanValue();
+ }
+
+ /**
+ * Reads all of our properties from the cytoscape properties map and sets
+ * the values as appropriates.
+ */
+ protected void initializeProperties() {
+
+ layoutProperties.add(new Tunable("standard", "Standard settings", Tunable.GROUP,
+ new Integer(3)));
+ /*
+ layoutProperties.add(new Tunable("debug", "Enable debugging", Tunable.BOOLEAN,
+ new Boolean(false), Tunable.NOINPUT));
+ */
+ layoutProperties.add(new Tunable("partition", "Partition graph before layout",
+ Tunable.BOOLEAN, new Boolean(true)));
+ layoutProperties.add(new Tunable("randomize", "Randomize graph before layout",
+ Tunable.BOOLEAN, new Boolean(true)));
+ layoutProperties.add(new Tunable("selected_only", "Only layout selected nodes",
+ Tunable.BOOLEAN, new Boolean(false)));
+
+ if (supportWeights) {
+ edgeWeighter.getWeightTunables(layoutProperties, getInitialAttributeList());
+ }
+ }
+
+ /**
+ * Get the settings panel for this layout
+ */
+ public JPanel getSettingsPanel() {
+ JPanel panel = new JPanel(new GridLayout(0, 1));
+ panel.add(layoutProperties.getTunablePanel());
+
+ return panel;
+ }
+
+ public LayoutProperties getSettings() {
+ return layoutProperties;
+ }
+
+ /**
+ * Update our settings in response to a user setting change
+ */
+ public void updateSettings() {
+ updateSettings(false);
+ }
+
+ /**
+ * Update the settings the user has requested
+ *
+ * @param force if true, always read the settings
+ */
+ public void updateSettings(boolean force) {
+ layoutProperties.updateValues();
+
+ Tunable t = layoutProperties.get("debug");
+ if ((t != null) && (t.valueChanged() || force)) {
+ setDebug(t.getValue().toString());
+ if (t.valueChanged())
+ layoutProperties.setProperty(t.getName(), t.getValue().toString());
+ }
+
+
+ t = layoutProperties.get("partition");
+ if ((t != null) && (t.valueChanged() || force)) {
+ setPartition(t.getValue().toString());
+ if (t.valueChanged())
+ layoutProperties.setProperty(t.getName(), t.getValue().toString());
+ }
+
+ t = layoutProperties.get("randomize");
+ if ((t != null) && (t.valueChanged() || force)) {
+ setRandomize(t.getValue().toString());
+ if (t.valueChanged())
+ layoutProperties.setProperty(t.getName(), t.getValue().toString());
+ }
+
+ t = layoutProperties.get("selected_only");
+ if ((t != null) && (t.valueChanged() || force)) {
+ setSelectedOnly(t.getValue().toString());
+ if (t.valueChanged())
+ layoutProperties.setProperty(t.getName(), t.getValue().toString());
+ }
+
+ if (supportWeights)
+ edgeWeighter.updateSettings(layoutProperties, force);
+ }
+
+ /**
+ * Revert to the default settings
+ */
+ public void revertSettings() {
+ layoutProperties.revertProperties();
+ }
+
+ /**
+ * Main function that must be implemented by the child class.
+ */
+ public abstract void layoutPartition(LayoutPartition partition);
+
+ protected void initialize_local() {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param message DOCUMENT ME!
+ */
+ public static void debugln(String message) {
+ if (debug) {
+ System.err.println(message);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param message DOCUMENT ME!
+ */
+ public static void debug(String message) {
+ if (debug) {
+ System.err.print(message);
+ }
+ }
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutFRAlgorithm.java b/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutFRAlgorithm.java
new file mode 100644
index 0000000..65c994b
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutFRAlgorithm.java
@@ -0,0 +1,1048 @@
+/* vim: set ts=2: */
+/**
+ * Copyright (c) 2006 The Regents of the University of California.
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ * notice, this list of conditions, and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above
+ * copyright notice, this list of conditions, and the following
+ * disclaimer in the documentation and/or other materials provided
+ * with the distribution.
+ * 3. Redistributions must acknowledge that this software was
+ * originally developed by the UCSF Computer Graphics Laboratory
+ * under support by the NIH National Center for Research Resources,
+ * grant P41-RR01081.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY
+ * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+ * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+ * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
+ * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ */
+
+/**
+ * Copyright (c) 2010 Gerardo Huck
+ */
+
+package csplugins.layout.algorithms.bioLayout;
+
+import csplugins.layout.LayoutEdge;
+import csplugins.layout.LayoutNode;
+import csplugins.layout.LayoutPartition;
+import csplugins.layout.Profile;
+
+import cytoscape.layout.LayoutProperties;
+import cytoscape.layout.Tunable;
+import cytoscape.logger.CyLogger;
+
+import java.awt.Dimension;
+
+import java.util.ArrayList;
+
+
+/**
+ * Lays out the nodes in a graph using a modification of the Fruchterman-Rheingold
+ * algorithm.
+ * <p>
+ * The basic layout algorithm follows from the paper:
+ * <em>"Graph Drawing by Force-Directed Placement"</em>
+ * by Thomas M.J. Fruchterman and Edward M. Reingold.
+ * <p>
+ * The algorithm has been modified to take into account edge weights, which
+ * allows for its use for laying out similarity networks, which are useful
+ * for biological problems.
+ *
+ * @author <a href="mailto:scooter at cgl.ucsf.edu">Scooter Morris</a>
+ * @version 0.9
+ */
+public class BioLayoutFRAlgorithm extends BioLayoutAlgorithm {
+ /**
+ * Sets the number of iterations for each update
+ */
+ private static int update_iterations = -1; // 0 means we only update at the end
+
+ /**
+ * The multipliers and computed result for the
+ * attraction and repulsion values.
+ */
+ private double attraction_multiplier = 1.0;
+ private double attraction_constant;
+ private double repulsion_multiplier = 0.001;
+ private double repulsion_constant;
+ private double gravity_multiplier = 0.0;
+ private double gravity_constant;
+
+ /**
+ * conflict_avoidance is a constant force that
+ * gets applied when two vertices are very close
+ * to each other.
+ */
+ private double conflict_avoidance = 20;
+
+ /**
+ * max_distance_factor is the portion of the graph
+ * beyond which repulsive forces will not operate.
+ */
+ private double max_distance_factor = 100;
+
+ /**
+ * maxDistance is the actual calculated distance
+ * beyond which repulsive forces will not operate.
+ * This value takes into account max_distance_factor,
+ * but also the size of the nodes in comparison to
+ * the size of the graph.
+ */
+ private double maxDistance;
+
+ /**
+ * This limits the velocity to no more than 1/maxVelocity_divisor
+ * of the width or height per iteration
+ */
+ private double maxVelocity_divisor = 25;
+ private double maxVelocity;
+
+ /**
+ * The spread factor -- used to give extra space to expand
+ */
+ private double spread_factor = 2;
+
+ /**
+ * The initial temperature factor. This will get damped
+ * out through the iterations
+ */
+ private double temperature = 90;
+
+ /**
+ * The number of iterations to run.
+ */
+ private int nIterations = 200;
+
+ /**
+ * This ArrayList is used to calculate the slope of the magnitude
+ * of the displacement. When the slope is (approximately) 0, we're
+ * done.
+ */
+ private ArrayList<Double> displacementArray;
+
+ /**
+ * The partition we're laying out
+ */
+ private LayoutPartition partition;
+
+ /**
+ * The width and height of the layout
+ */
+ private double width = 0;
+ private double height = 0;
+
+ /**
+ * Profile data -- not used, for now
+ Profile initProfile;
+ Profile iterProfile;
+ Profile repulseProfile;
+ Profile attractProfile;
+ Profile updateProfile;
+ */
+
+ /**
+ * This is the constructor for the bioLayout algorithm.
+ */
+ public BioLayoutFRAlgorithm(boolean supportEdgeWeights) {
+ super();
+ logger = CyLogger.getLogger(BioLayoutFRAlgorithm.class);
+
+ supportWeights = supportEdgeWeights;
+
+ displacementArray = new ArrayList<Double>(100);
+ this.initializeProperties();
+ }
+
+ /**
+ * Required methods (and overrides) for AbstractLayout
+ */
+
+
+ /**
+ * This layout ssuports laying out labels
+ */
+ public boolean supportsLabelLayout() {
+ return true;
+ }
+
+ /**
+ * Return the "name" of this algorithm. This is meant
+ * to be used by programs for deciding which algorithm to
+ * use. toString() should be used for the human-readable
+ * name.
+ *
+ * @return the algorithm name
+ */
+ public String getName() {
+ return "fruchterman-rheingold";
+ }
+
+ /**
+ * Return the "title" of this algorithm. This is meant
+ * to be used for titles and labels that represent this
+ * algorithm.
+ *
+ * @return the human-readable algorithm name
+ */
+ public String toString() {
+ if (supportWeights)
+ return "Edge-Weighted Force-Directed (BioLayout)";
+ else
+
+ return "Force-Directed (BioLayout)";
+ }
+
+ /**
+ * Sets the number of iterations
+ *
+ * @param value the number of iterations
+ */
+ public void setNumberOfIterations(int value) {
+ this.nIterations = value;
+ }
+
+ /**
+ * Sets the number of iterations
+ *
+ * @param value the number of iterations
+ */
+ public void setNumberOfIterations(String value) {
+ Integer val = new Integer(value);
+ nIterations = val.intValue();
+ }
+
+ /**
+ * Sets the initial temperature
+ *
+ * @param value the initial temperature value
+ */
+ public void setTemperature(double value) {
+ this.temperature = value;
+ }
+
+ /**
+ * Sets the initial temperature
+ *
+ * @param value the initial temperature value
+ */
+ public void setTemperature(String value) {
+ Double val = new Double(value);
+ temperature = val.doubleValue();
+ }
+
+ /**
+ * Sets the attraction multiplier used to calculate
+ * the attraction force
+ *
+ * @param value the attraction multiplier
+ */
+ public void setAttractionMultiplier(double am) {
+ attraction_multiplier = am;
+ }
+
+ /**
+ * Sets the attraction multiplier used to calculate
+ * the attraction force
+ *
+ * @param value the attraction multiplier
+ */
+ public void setAttractionMultiplier(String value) {
+ Double val = new Double(value);
+ attraction_multiplier = val.doubleValue();
+ }
+
+ /**
+ * Sets the repulsion multiplier used to calculate
+ * the repulsion force
+ *
+ * @param value the repulsion multiplier
+ */
+ public void setRepulsionMultiplier(double am) {
+ repulsion_multiplier = am;
+ }
+
+ /**
+ * Sets the repulsion multiplier used to calculate
+ * the repulsion force
+ *
+ * @param value the repulsion multiplier
+ */
+ public void setRepulsionMultiplier(String value) {
+ Double val = new Double(value);
+ repulsion_multiplier = val.doubleValue();
+ }
+
+ /**
+ * Sets the gravity multiplier used to calculate
+ * the gravity force
+ *
+ * @param value the gravity multiplier
+ */
+ public void setGravityMultiplier(double am) {
+ gravity_multiplier = am;
+ }
+
+ /**
+ * Sets the gravity multiplier used to calculate
+ * the gravity force
+ *
+ * @param value the gravity multiplier
+ */
+ public void setGravityMultiplier(String value) {
+ Double val = new Double(value);
+ gravity_multiplier = val.doubleValue();
+ }
+
+ /**
+ * Sets the spread factor used to provide space for
+ * the graph larger than the area of the nodes themselves.
+ * The graph space will be (width*spread_factor, height*spread_factor)
+ *
+ * @param value the spread factor
+ */
+ public void setSpreadFactor(double value) {
+ spread_factor = value;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param value DOCUMENT ME!
+ */
+ public void setSpreadFactor(String value) {
+ Double val = new Double(value);
+ spread_factor = val.doubleValue();
+ }
+
+ /**
+ * Sets the number of iterations to execute between each
+ * screen update. If the value is 0 or -1, no updates
+ * will be done until the algorithm completes.
+ *
+ * @param value the number of iterations between updates
+ */
+ public void setUpdateIterations(String value) {
+ Integer val = new Integer(value);
+ update_iterations = val.intValue();
+ }
+
+ /**
+ * Sets the number of iterations to execute between each
+ * screen update. If the value is 0 or -1, no updates
+ * will be done until the algorithm completes.
+ *
+ * @param value the number of iterations between updates
+ */
+ public void setUpdateIterations(int value) {
+ update_iterations = value;
+ }
+
+ /**
+ * Sets an additional repulsive force to nodes
+ * when they overlap
+ *
+ * @param value the additional repulsive force
+ */
+ public void setConflictAvoidanceForce(String value) {
+ Double val = new Double(value);
+ conflict_avoidance = val.doubleValue();
+ }
+
+ /**
+ * Sets an additional repulsive force to nodes
+ * when they overlap
+ *
+ * @param value the additional repulsive force
+ */
+ public void setConflictAvoidanceForce(double value) {
+ conflict_avoidance = value;
+ }
+
+ /**
+ * Sets the percentage of the graph beyond which we
+ * don't calculate repulsive forces.
+ *
+ * @param value the maximum distance factor
+ */
+ public void setMaxDistanceFactor(String value) {
+ Double val = new Double(value);
+ max_distance_factor = val.doubleValue();
+ }
+
+ /**
+ * Sets the percentage of the graph beyond which we
+ * don't calculate repulsive forces.
+ *
+ * @param value the maximum distance factor
+ */
+ public void setMaxDistanceFactor(double value) {
+ max_distance_factor = value;
+ }
+
+ /**
+ * Reads all of our properties from the cytoscape properties map and sets
+ * the values as appropriates.
+ */
+ public void initializeProperties() {
+ super.initializeProperties();
+
+ /**
+ * Tuning values
+ */
+ layoutProperties.add(new Tunable("algorithm_settings",
+ "Algorithm settings",
+ Tunable.GROUP, new Integer(9)));
+ layoutProperties.add(new Tunable("repulsion_multiplier",
+ "Multiplier to calculate the repulsion force",
+ Tunable.DOUBLE, new Double(1.0)));
+ layoutProperties.add(new Tunable("attraction_multiplier",
+ "Divisor to calculate the attraction force",
+ Tunable.DOUBLE, new Double(0.001)));
+ layoutProperties.add(new Tunable("gravity_multiplier",
+ "Multiplier to calculate the gravity force",
+ Tunable.DOUBLE, new Double(0.0)));
+ layoutProperties.add(new Tunable("iterations", "Number of iterations", Tunable.INTEGER,
+ new Integer(500)));
+ layoutProperties.add(new Tunable("temperature", "Initial temperature", Tunable.DOUBLE,
+ new Double(80)));
+ layoutProperties.add(new Tunable("spread_factor", "Amount of extra room for layout",
+ Tunable.DOUBLE, new Double(2)));
+ layoutProperties.add(new Tunable("update_iterations",
+ "Number of iterations before updating display",
+ Tunable.INTEGER, new Integer(0)));
+ layoutProperties.add(new Tunable("conflict_avoidance",
+ "Constant force applied to avoid conflicts",
+ Tunable.DOUBLE, new Double(20.0)));
+ layoutProperties.add(new Tunable("max_distance_factor",
+ "Percent of graph used for node repulsion calculations",
+ Tunable.DOUBLE, new Double(20.0)));
+
+ getLabelTunables(layoutProperties);
+
+ // We've now set all of our tunables, so we can read the property
+ // file now and adjust as appropriate
+ layoutProperties.initializeProperties();
+
+ // Finally, update everything. We need to do this to update
+ // any of our values based on what we read from the property file
+ updateSettings(true);
+ }
+
+ /**
+ * update our tunable settings
+ */
+ public void updateSettings() {
+ updateSettings(false);
+ }
+
+ /**
+ * update our tunable settings
+ *
+ * @param force whether or not to force the update
+ */
+ public void updateSettings(boolean force) {
+ super.updateSettings(force);
+
+ Tunable t = layoutProperties.get("repulsion_multiplier");
+ if ((t != null) && (t.valueChanged() || force)) {
+ setRepulsionMultiplier(t.getValue().toString());
+ if (t.valueChanged())
+ layoutProperties.setProperty(t.getName(), t.getValue().toString());
+ }
+
+ t = layoutProperties.get("attraction_multiplier");
+ if ((t != null) && (t.valueChanged() || force)) {
+ setAttractionMultiplier(t.getValue().toString());
+ if (t.valueChanged())
+ layoutProperties.setProperty(t.getName(), t.getValue().toString());
+ }
+
+ t = layoutProperties.get("gravity_multiplier");
+ if ((t != null) && (t.valueChanged() || force)) {
+ setGravityMultiplier(t.getValue().toString());
+ if (t.valueChanged())
+ layoutProperties.setProperty(t.getName(), t.getValue().toString());
+ }
+
+ t = layoutProperties.get("iterations");
+ if ((t != null) && (t.valueChanged() || force)) {
+ setNumberOfIterations(t.getValue().toString());
+ if (t.valueChanged())
+ layoutProperties.setProperty(t.getName(), t.getValue().toString());
+ }
+
+ t = layoutProperties.get("temperature");
+ if ((t != null) && (t.valueChanged() || force)) {
+ setTemperature(t.getValue().toString());
+ if (t.valueChanged())
+ layoutProperties.setProperty(t.getName(), t.getValue().toString());
+ }
+
+ t = layoutProperties.get("spread_factor");
+ if ((t != null) && (t.valueChanged() || force)) {
+ setSpreadFactor(t.getValue().toString());
+ if (t.valueChanged())
+ layoutProperties.setProperty(t.getName(), t.getValue().toString());
+ }
+
+ t = layoutProperties.get("update_iterations");
+ if ((t != null) && (t.valueChanged() || force)) {
+ setUpdateIterations(t.getValue().toString());
+ if (t.valueChanged())
+ layoutProperties.setProperty(t.getName(), t.getValue().toString());
+ }
+
+ t = layoutProperties.get("conflict_avoidance");
+ if ((t != null) && (t.valueChanged() || force)) {
+ setConflictAvoidanceForce(t.getValue().toString());
+ if (t.valueChanged())
+ layoutProperties.setProperty(t.getName(), t.getValue().toString());
+ }
+
+ t = layoutProperties.get("max_distance_factor");
+ if ((t != null) && (t.valueChanged() || force)) {
+ setMaxDistanceFactor(t.getValue().toString());
+ if (t.valueChanged())
+ layoutProperties.setProperty(t.getName(), t.getValue().toString());
+ }
+
+ // Update label tunables
+ updateSettings(layoutProperties, force);
+
+ }
+
+ /**
+ * Perform a layout
+ */
+ public void layoutPartition(LayoutPartition partition) {
+ this.partition = partition;
+
+ Dimension initialLocation = null;
+
+ /* Get all of our profiles */
+ /*
+ initProfile = new Profile();
+ iterProfile = new Profile();
+ repulseProfile = new Profile();
+ attractProfile = new Profile();
+ updateProfile = new Profile();
+
+ initProfile.start();
+ */
+
+ // Calculate a bounded rectangle for our
+ // layout. This is roughly the area of all
+ // nodes * 2
+ calculateSize();
+
+ logger.info("Laying out " + partition.nodeCount()
+ + " nodes and " + partition.edgeCount() + " edges: ");
+
+ // Initialize our temperature
+ double temp;
+
+ if (temperature == 0) {
+ temp = Math.sqrt(this.width*this.height)/2;
+ } else {
+ temp = Math.sqrt(this.width*this.height) * this.temperature/100;
+ }
+
+ // Figure out our starting point
+ if (selectedOnly) {
+ initialLocation = partition.getAverageLocation();
+ }
+
+ // Randomize our points, if any points lie
+ // outside of our bounds
+ if (randomize)
+ partition.randomizeLocations();
+
+ // Calculate our force constant
+ calculateForces();
+
+ // Calculate our edge weights
+ partition.calculateEdgeWeights();
+ // initProfile.done("Initialization completed in ");
+ taskMonitor.setStatus("Calculating new node positions");
+ taskMonitor.setPercentCompleted(1);
+
+ // Main algorithm
+ // iterProfile.start();
+ int iteration = 0;
+
+ for (iteration = 0; (iteration < nIterations) && !canceled; iteration++) {
+ if ((temp = doOneIteration(iteration, temp)) == 0)
+ break;
+
+ if (debug || ((update_iterations > 0) && ((iteration % update_iterations) == 0))) {
+ if (iteration > 0) {
+ // Actually move the pieces around
+ for (LayoutNode v: partition.getNodeList()) {
+ // if this is locked, the move just resets X and Y
+ v.moveToLocation();
+ // logger.debug("Node "+v.getIdentifier()+" moved to "+v.getX()+","+v.getY());
+ }
+ networkView.updateView();
+ }
+
+ if (debug) {
+ try {
+ Thread.currentThread().sleep(100);
+ } catch (InterruptedException e) {
+ }
+ }
+ }
+
+ taskMonitor.setStatus("Calculating new node positions - " + iteration);
+ taskMonitor.setPercentCompleted((int) Math.rint((iteration * 100) / nIterations));
+ }
+
+ // iterProfile.done("Iterations complete in ");
+ // logger.debug("Attraction calculation portion of iterations took "+attractProfile.getTotalTime()+"ms");
+ // logger.debug("Repulsion calculation portion of iterations took "+repulseProfile.getTotalTime()+"ms");
+ // logger.debug("Update portion of iterations took "+updateProfile.getTotalTime()+"ms");
+ taskMonitor.setStatus("Updating display");
+
+ // Actually move the pieces around
+ // Note that we reset our min/max values before we start this
+ // so we can get an accurate min/max for paritioning
+ partition.resetNodes();
+
+ for (LayoutNode v: partition.getNodeList()) {
+ partition.moveNodeToLocation(v);
+ }
+
+ // Not quite done, yet. If we're only laying out selected nodes, we need
+ // to migrate the selected nodes back to their starting position
+ if (selectedOnly) {
+ double xDelta = 0.0;
+ double yDelta = 0.0;
+ Dimension finalLocation = partition.getAverageLocation();
+ xDelta = finalLocation.getWidth() - initialLocation.getWidth();
+ yDelta = finalLocation.getHeight() - initialLocation.getHeight();
+
+ for (LayoutNode v: partition.getNodeList()) {
+ if (!v.isLocked()) {
+ v.decrement(xDelta, yDelta);
+ partition.moveNodeToLocation(v);
+ }
+ }
+ }
+
+ logger.info("Layout complete after " + iteration + " iterations");
+ }
+
+ /**
+ * This executes a single iteration of the FR algorithm.
+ *
+ * @param iteration The current interation.
+ * @param temp The current temperature factor.
+ * @return an updated temperature factor.
+ */
+ public double doOneIteration(int iteration, double temp) {
+ double xAverage = 0;
+ double yAverage = 0;
+
+ // repulseProfile.start();
+ // Calculate repulsive forces
+ for (LayoutNode v: partition.getNodeList()) {
+ if (!v.isLocked()) {
+ xAverage += v.getX()/partition.nodeCount();
+ yAverage += v.getY()/partition.nodeCount();
+ }
+ }
+
+ for (LayoutNode v: partition.getNodeList()) {
+ if (!v.isLocked()) {
+ calculateRepulsion(v);
+ if (gravity_constant != 0)
+ calculateGravity(v,xAverage,yAverage);
+ }
+ }
+
+ // repulseProfile.checkpoint();
+
+ // Dump the current displacements
+ // print_disp();
+
+ // attractProfile.start();
+ // Calculate attractive forces
+
+/// for e in E do begin
+ for (LayoutEdge e: partition.getEdgeList()) {
+ calculateAttraction(e);
+ }
+/// end
+
+ // attractProfile.checkpoint();
+
+ // Dump the current displacements
+ // print_disp();
+
+ // Dampen & update
+ double xDispTotal = 0;
+ double yDispTotal = 0;
+ // updateProfile.start();
+
+/// for v in V do begin
+ for (LayoutNode v: partition.getNodeList()) {
+ if (v.isLocked())
+ continue;
+
+ calculatePosition(v, temp);
+
+ xDispTotal += Math.abs(v.getXDisp());
+ yDispTotal += Math.abs(v.getYDisp());
+ }
+/// end
+
+
+ // This was commented out by Gerardo H. It was spoiling the label layout
+
+ // Translate back to the middle (or to the starting point,
+ // if we're dealing with a selected group
+// if (!selectedOnly) {
+// for (LayoutNode v: partition.getNodeList()) {
+// v.decrement(xAverage - (width / 2), yAverage - (height / 2));
+// }
+// }
+
+
+ // updateProfile.checkpoint();
+
+ // Test our total x and y displacement to see if we've
+ // hit our completion criteria
+ if (complete(xDispTotal, yDispTotal))
+ return 0;
+
+// t := cool(t)
+ return cool(temp, iteration);
+ }
+
+ /**
+ * calculate the slope of the total displacement over the last 10 iterations. If its positive or 0
+ * we're done.
+ *
+ */
+ private boolean complete(double xDisp, double yDisp) {
+ Double disp = new Double(Math.sqrt((xDisp * xDisp) + (yDisp * yDisp)));
+
+ displacementArray.add(disp);
+
+ Object[] dispArray = displacementArray.toArray();
+
+ if (dispArray.length < 99)
+ return false;
+
+ double averageSlope = 0;
+ double averageValue = ((Double) dispArray[0]).doubleValue() / dispArray.length;
+
+ for (int i = 1; i < dispArray.length; i++) {
+ averageSlope += ((((Double) dispArray[i]).doubleValue()
+ - ((Double) dispArray[i - 1]).doubleValue()) / dispArray.length);
+ averageValue += (((Double) dispArray[i]).doubleValue() / dispArray.length);
+ }
+
+ // logger.debug("Total displacement = "+disp.doubleValue()+" Average slope = "+averageSlope);
+ // 5% a reasonable criteria?
+ // if (Math.abs(averageSlope) < Math.abs(averageValue)*.001) return true;
+ if (Math.abs(averageSlope) < .001)
+ return true;
+
+ if (displacementArray.size() > 99)
+ displacementArray.remove(0);
+
+ return false;
+ }
+
+ /**
+ * calculate the repulsive forces and offsets for
+ * each vertex.
+ *
+ * @param v LayoutNode we're calculating repulsive forces for
+ */
+ private void calculateRepulsion(LayoutNode v) {
+/// v.disp := 0;
+ v.setDisp(0, 0);
+
+ double width = v.getWidth();
+ double height = v.getHeight();
+ double radius = v.getWidth() / 2;
+
+/// for u in V do
+ for (LayoutNode u: partition.getNodeList()) {
+ double dx = v.getX() - u.getX();
+ double dy = v.getY() - u.getY();
+
+/// if (u # v) then begin
+ if (v == u)
+ continue;
+
+ // Get the
+ // double xSign = Math.signum(v.getX() - u.getX());
+ // double ySign = Math.signum(v.getY() - u.getY());
+
+/// delta := v.pos - u.pos
+ // Get our euclidean distance
+ double deltaDistance = v.distance(u);
+
+ if (deltaDistance == 0.0)
+ deltaDistance = EPSILON;
+
+ double fr = forceR(repulsion_constant, deltaDistance);
+
+ // If its too close, increase the force by a constant
+ if (deltaDistance < (radius + (u.getWidth() / 2))) {
+ // logger.debug("Applying conflict_avoidance force: "+conflict_avoidance);
+ fr += conflict_avoidance;
+ }
+
+ if (Double.isNaN(fr)) {
+ fr = 500;
+ }
+
+ /*
+ logger.debug("Repulsive force between "+v.getIdentifier()
+ +" and "+u.getIdentifier()+" is "+force);
+ logger.debug(" distance = "+deltaDistance);
+ logger.debug(" incrementing "+v.getIdentifier()+" by ("+
+ force+", "+force+")");
+ */
+
+ // Adjust the displacement. In the case of doing selectedOnly,
+ // we increase the force to enhance the discrimination power.
+ // Also note that we only update the displacement of the movable
+ // node since the other node won't move anyways.
+/// v.disp := v.disp + (delta/abs(delta)) * fr(abs(delta))
+ double xVector = (dx/deltaDistance)*fr;
+ double yVector = (dy/deltaDistance)*fr;
+ if (v.isLocked()) {
+ return; // shouldn't happen
+ } else if (u.isLocked()) {
+ v.incrementDisp(xVector * 2, yVector * 2);
+ } else {
+ v.incrementDisp(xVector, yVector);
+ }
+ }
+ }
+
+ /**
+ * calculate the attractive forces and offsets for
+ * each vertex based on their connecting edges and the
+ * corresponding edge weights.
+ *
+ * @param e Edge we're calculating attractive forces for
+ */
+ private void calculateAttraction(LayoutEdge e) {
+ LayoutNode v = e.getSource();
+ LayoutNode u = e.getTarget();
+ double dx = v.getX() - u.getX();
+ double dy = v.getY() - u.getY();
+
+/// delta := e.v.pos - e.u.pos
+ double deltaDistance = v.distance(u);
+
+ double fa = forceA(attraction_constant, deltaDistance, e.getWeight());
+
+ if (Double.isNaN(fa)) {
+ fa = EPSILON;
+ }
+
+ // Adjust the displacement. In the case of doing selectedOnly,
+ // we increase the force to enhance the discrimination power.
+ // Also note that we only update the displacement of the movable
+ // node since the other node won't move anyways.
+
+/// e.v.disp := e.v.disp - (delta/abs(delta)) * fa(abs(delta))
+/// e.u.disp := e.u.disp + (delta/abs(delta)) * fa(abs(delta))
+ double xVector = dx*fa;
+ double yVector = dy*fa;
+ if (u.isLocked() && v.isLocked()) {
+ return; // shouldn't happen
+ } else if (u.isLocked()) {
+ v.decrementDisp(xVector * 2, yVector * 2);
+ } else if (v.isLocked()) {
+ u.incrementDisp(xVector * 2, yVector * 2);
+ } else {
+ v.decrementDisp(xVector, yVector);
+ u.incrementDisp(xVector, yVector);
+ }
+ }
+
+ /**
+ * Calculate the gravity (pull towards the center) force.
+ *
+ * @param v the node we're pulling
+ * @param xAverage the X portion of the location that's pulling us
+ * @param yAverage the Y portion of the location that's pulling us
+ */
+ private void calculateGravity(LayoutNode v,double xAverage, double yAverage)
+ {
+ double dx = v.getX() - xAverage;
+ double dy = v.getY() - yAverage;
+ double distance = Math.sqrt(Math.pow(dx,2) + Math.pow(dy,2));
+ //double theta = Math.atan(dy/dx);
+ //double xSign = Math.signum(dx);
+ //double ySign = Math.signum(dy);
+ if(distance == 0) distance = EPSILON;
+ double phi = (1 +v.getDegree())/3;
+ double force = gravity_constant*distance*phi;
+ double xVector = dx*force;
+ double yVector = dy*force;
+ if (v.isLocked()) {
+ return;
+ }// shouldn't happen
+
+ else {
+ // logger.debug("Gravity adjustment = "+xVector+", "+yVector);
+ v.decrementDisp( xVector, yVector);
+ }
+ }
+
+ /**
+ * Calculate and update the position to move a vertex.
+ * This routine also handles limiting the velocity and
+ * doing the bounds checking to keep the vertices within
+ * the graphics area.
+ *
+ * @param v LayoutNode we're moving
+ * @param temp double representing the current temperature
+ */
+/// v.pos := v.pos + (v.disp/|v.disp|) * min (v.disp, t);
+ private void calculatePosition(LayoutNode v, double temp) {
+ double deltaDistance = v.distance(v.getXDisp(), v.getYDisp());
+
+ double newXDisp = v.getXDisp() / deltaDistance * Math.min(deltaDistance, temp);
+
+ if (Double.isNaN(newXDisp)) {
+ newXDisp = 0;
+ }
+
+ double newYDisp = v.getYDisp() / deltaDistance * Math.min(deltaDistance, temp);
+
+ if (Double.isNaN(newYDisp)) {
+ newYDisp = 0;
+ }
+ v.increment(newXDisp, newYDisp);
+
+/// v.pos.x := min(W/2, max(-W/2, v.pos.x));
+/// v.pos.y := min(L/2, max(-L/2, v.pos.y));
+ }
+
+ /**
+ * Cools the current temperature
+ *
+ * @param temp the current temperature
+ * @param iteration the iteration number
+ * @return the new temperature
+ */
+ private double cool(double temp, int iteration) {
+ temp *= (1.0 - ((double)iteration / (double)nIterations));
+
+ return temp;
+ }
+
+ /**
+ * Calculate the width and height of the new graph. If the graph already has been laid
+ * out, then the width and height should be resonable, so use those. Otherwise, calculate
+ * a width and height based on the area covered by the existing graph.
+ */
+ private void calculateSize() {
+ // double spreadFactor = Math.max(spread_factor, edgeList.length/nodeList.length);
+ // LayoutNode v0 = (LayoutNode)nodeList.get(0); // Get the first vertex to get to the class variables
+ int nodeCount = partition.nodeCount();
+ int unLockedNodes = nodeCount - partition.lockedNodeCount();
+ double spreadFactor = spread_factor;
+ double averageWidth = partition.getWidth() / partition.nodeCount();
+ double averageHeight = partition.getHeight() / partition.nodeCount();
+ double current_area = (partition.getMaxX() - partition.getMinX()) * (partition.getMaxY()
+ - partition.getMinY());
+ double node_area = partition.getWidth() * partition.getHeight();
+
+ if (selectedOnly || (current_area > node_area)) {
+ this.width = (partition.getMaxX() - partition.getMinX()) * spreadFactor;
+ this.height = (partition.getMaxY() - partition.getMinY()) * spreadFactor;
+ // make it square
+ this.width = Math.max(this.width, this.height);
+ this.height = this.width;
+ } else {
+ this.width = Math.sqrt(node_area) * spreadFactor;
+ this.height = Math.sqrt(node_area) * spreadFactor;
+
+ // logger.debug("spreadFactor = "+spreadFactor);
+ }
+
+ this.maxVelocity = Math.max(Math.max(averageWidth * 2, averageHeight * 2),
+ Math.max(width, height) / maxVelocity_divisor);
+ this.maxDistance = Math.max(Math.max(averageWidth * 10, averageHeight * 10),
+ Math.min(width, height) * max_distance_factor / 100);
+
+ // logger.debug("Size: "+width+" x "+height);
+ // logger.debug("maxDistance = "+maxDistance);
+ // logger.debug("maxVelocity = "+maxVelocity);
+ /*
+ */
+ }
+
+ /**
+ * Calculate the attraction and repulsion constants.
+ */
+ private void calculateForces() {
+ double force = Math.sqrt((this.height * this.width) / partition.nodeCount());
+ attraction_constant = force * attraction_multiplier;
+ repulsion_constant = force * repulsion_multiplier;
+ gravity_constant = gravity_multiplier;
+
+/*
+ logger.debug("attraction_constant = "+attraction_constant
+ +", repulsion_constant = "+repulsion_constant
+ +", gravity_constant = "+gravity_constant);
+*/
+ }
+
+ /**
+ * Calculate the repulsive force
+ *
+ * @param k the repulsion constant
+ * @param distance the distance between the vertices
+ * @return the repulsive force
+ */
+/// fr(z) := begin return k*k/z end;
+ private double forceR(double k, double distance) {
+ // We want to bound the distance over which
+ // the repulsive force acts
+ // Should we do this??
+ if (distance > maxDistance)
+ return 0;
+
+ return ((k * k) / distance);
+ }
+
+ /**
+ * Calculate the attractive force
+ *
+ * @param k the attraction constant
+ * @param distance the distance between the vertices
+ * @param weight the edge weight
+ * @return the attractive force
+ */
+/// fa(z) := begin return z*z/k end;
+ private double forceA(double k, double distance, double weight) {
+ return ((distance / k) * weight);
+ }
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutKKAlgorithm.java b/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutKKAlgorithm.java
new file mode 100644
index 0000000..77e9206
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutKKAlgorithm.java
@@ -0,0 +1,1085 @@
+/* vim: set ts=2: */
+/**
+ * Copyright (c) 2006 The Regents of the University of California.
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ * notice, this list of conditions, and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above
+ * copyright notice, this list of conditions, and the following
+ * disclaimer in the documentation and/or other materials provided
+ * with the distribution.
+ * 3. Redistributions must acknowledge that this software was
+ * originally developed by the UCSF Computer Graphics Laboratory
+ * under support by the NIH National Center for Research Resources,
+ * grant P41-RR01081.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY
+ * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+ * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+ * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
+ * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ */
+package csplugins.layout.algorithms.bioLayout;
+
+import csplugins.layout.LayoutEdge;
+import csplugins.layout.LayoutNode;
+import csplugins.layout.LayoutPartition;
+import csplugins.layout.Profile;
+
+import cytoscape.*;
+
+import cytoscape.data.*;
+
+import cytoscape.layout.LayoutProperties;
+import cytoscape.layout.Tunable;
+import cytoscape.logger.CyLogger;
+
+import cytoscape.util.*;
+
+import cytoscape.view.*;
+
+import giny.view.*;
+
+import java.awt.Dimension;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Date;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Properties;
+
+
+/**
+ * Lays out the nodes in a graph using a modification of the Kamada-Kawai
+ * algorithm.
+ * <p>
+ * The basic layout algorithm follows from the paper:
+ * <em>"An Algorithm for Drawing General Undirected Graphs"</em>
+ * by Tomihisa Kamada and Satoru Kawai.
+ * <p>
+ * The algorithm has been modified to take into account edge weights, which
+ * allows for its use for laying out similarity networks, which are useful
+ * for biological problems.
+ *
+ * @see "Tomihisa Kamada and Satoru Kawai: An algorithm for drawing general indirect graphs. Information Processing Letters 31(1):7-15, 1989"
+ * @see "Tomihisa Kamada: On visualization of abstract objects and relations. Ph.D. dissertation, Dept. of Information Science, Univ. of Tokyo, Dec. 1988."
+ *
+ * @author <a href="mailto:scooter at cgl.ucsf.edu">Scooter Morris</a>
+ * @version 0.9
+ */
+public class BioLayoutKKAlgorithm extends BioLayoutAlgorithm {
+ private int euclideanLoop = 0;
+
+ /**
+ * A small value used to avoid division by zero
+ */
+ protected static double EPSILON = 0.0000001D;
+ private static final double[] DEFAULT_NODE_DISTANCE_SPRING_SCALARS = new double[] {
+ 1.0, 1.0, 1.0, 1.0
+ };
+ private static final double[] DEFAULT_ANTICOLLISION_SPRING_SCALARS = new double[] {
+ 0.0, 1.0, 1.0, 1.0
+ };
+
+ /**
+ * The total number of layout passes
+ */
+ private int m_numLayoutPasses;
+
+ /**
+ * The average number of iterations per Node
+ */
+ private double m_averageIterationsPerNode;
+ private double m_nodeDistanceStrengthConstant;
+ private double m_nodeDistanceRestLengthConstant;
+ private double[] m_nodeDistanceSpringScalars;
+ private double m_disconnectedNodeDistanceSpringStrength;
+ private double m_disconnectedNodeDistanceSpringRestLength;
+ private double m_anticollisionSpringStrength;
+ private double[] m_anticollisionSpringScalars;
+
+ /**
+ * Data arrays
+ */
+ private double[][] m_nodeDistanceSpringRestLengths;
+ private double[][] m_nodeDistanceSpringStrengths;
+
+ /**
+ * Current layout pass
+ */
+ private int m_layoutPass;
+
+ /**
+ * The number of nodes
+ */
+ private int m_nodeCount;
+
+ /**
+ * The Partition
+ */
+ private LayoutPartition partition;
+
+ /**
+ * This hashmap provides a quick way to get an index into
+ * the LayoutNode array given a graph index.
+ */
+ private HashMap nodeToLayoutNode;
+
+ /**
+ * Profile data
+ */
+ Profile calculationProfile;
+ Profile distanceProfile;
+
+ /**
+ * This is the constructor for the bioLayout algorithm.
+ * @param supportEdgeWeights a boolean to indicate whether we should
+ * behave as if we support weights
+ */
+ public BioLayoutKKAlgorithm(boolean supportEdgeWeights) {
+ super();
+
+ logger = CyLogger.getLogger(BioLayoutKKAlgorithm.class);
+
+ supportWeights = supportEdgeWeights;
+
+ // Set and (Possibly) override defaults
+ this.initializeProperties();
+ }
+
+ /**
+ * Overrides for LayoutAlgorithm support
+ */
+ public String getName() {
+ if (supportWeights)
+ return "kamada-kawai-noweight";
+ else
+
+ return "kamada-kawai";
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String toString() {
+ if (supportWeights)
+ return "Edge-Weighted Spring Embedded";
+ else
+
+ return "Spring Embedded";
+ }
+
+ /**
+ * Sets the number of iterations
+ *
+ * @param value the number of iterations
+ */
+ public void setNumberOfIterationsPerNode(int value) {
+ m_averageIterationsPerNode = value;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param value DOCUMENT ME!
+ */
+ public void setNumberOfIterationsPerNode(String value) {
+ Integer val = new Integer(value);
+ m_averageIterationsPerNode = val.intValue();
+ }
+
+ /**
+ * Sets the number of layout passes
+ *
+ * @param value the number of layout passes
+ */
+ public void setNumberOfLayoutPasses(int value) {
+ m_numLayoutPasses = value;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param value DOCUMENT ME!
+ */
+ public void setNumberOfLayoutPasses(String value) {
+ Integer val = new Integer(value);
+ m_numLayoutPasses = val.intValue();
+ }
+
+ /**
+ * Sets the distance spring strength contant
+ *
+ * @param value the distance spring strength contant
+ */
+ public void setDistanceSpringStrength(double value) {
+ m_nodeDistanceStrengthConstant = value;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param value DOCUMENT ME!
+ */
+ public void setDistanceSpringStrength(String value) {
+ Double val = new Double(value);
+ m_nodeDistanceStrengthConstant = val.doubleValue();
+ }
+
+ /**
+ * Sets the rest length constant
+ *
+ * @param value the rest length constant
+ */
+ public void setDistanceRestLength(double value) {
+ m_nodeDistanceRestLengthConstant = value;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param value DOCUMENT ME!
+ */
+ public void setDistanceRestLength(String value) {
+ Double val = new Double(value);
+ m_nodeDistanceRestLengthConstant = val.doubleValue();
+ }
+
+ /**
+ * Sets the disconnected node distance spring strength
+ *
+ * @param value the disconnected node distance spring strength
+ */
+ public void setDisconnectedSpringStrength(double value) {
+ m_disconnectedNodeDistanceSpringStrength = value;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param value DOCUMENT ME!
+ */
+ public void setDisconnectedSpringStrength(String value) {
+ Double val = new Double(value);
+ m_disconnectedNodeDistanceSpringStrength = val.doubleValue();
+ }
+
+ /**
+ * Sets the disconnected node sprint rest length
+ *
+ * @param value the disconnected node sprint rest length
+ */
+ public void setDisconnectedRestLength(double value) {
+ m_disconnectedNodeDistanceSpringRestLength = value;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param value DOCUMENT ME!
+ */
+ public void setDisconnectedRestLength(String value) {
+ Double val = new Double(value);
+ m_disconnectedNodeDistanceSpringRestLength = val.doubleValue();
+ }
+
+ /**
+ * Sets the anticollision spring strength
+ *
+ * @param value the anticollision spring strength
+ */
+ public void setAnticollisionSpringStrength(double value) {
+ m_anticollisionSpringStrength = value;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param value DOCUMENT ME!
+ */
+ public void setAnticollisionSpringStrength(String value) {
+ Double val = new Double(value);
+ m_anticollisionSpringStrength = val.doubleValue();
+ }
+
+ /**
+ * Reads all of our properties from the cytoscape properties map and sets
+ * the values as appropriate.
+ */
+ public void initializeProperties() {
+ super.initializeProperties();
+
+ /**
+ * Tuning values
+ */
+
+ layoutProperties.add(new Tunable("algorithm_settings", "Algorithm settings",
+ Tunable.GROUP, new Integer(7)));
+ if (supportWeights)
+ layoutProperties.add(new Tunable("iterations_pernode",
+ "Number of iteratations for each node",
+ Tunable.INTEGER, new Integer(40)));
+ else
+ layoutProperties.add(new Tunable("iterations_pernode",
+ "Number of iteratations for each node",
+ Tunable.INTEGER, new Integer(20)));
+
+ layoutProperties.add(new Tunable("layout_passes", "Number of layout passes",
+ Tunable.INTEGER, new Integer(2)));
+ layoutProperties.add(new Tunable("distance_strength", "Spring strength", Tunable.DOUBLE,
+ new Double(15.0)));
+ layoutProperties.add(new Tunable("rest_length", "Spring rest length", Tunable.DOUBLE,
+ new Double(45.0)));
+ layoutProperties.add(new Tunable("disconnected_strength",
+ "Strength of a 'disconnected' spring", Tunable.DOUBLE,
+ new Double(0.05)));
+ layoutProperties.add(new Tunable("disconnected_rest_length",
+ "Rest length of a 'disconnected' spring", Tunable.DOUBLE,
+ new Double(2000.0)));
+ layoutProperties.add(new Tunable("anticollisionStrength",
+ "Strength to apply to avoid collisions", Tunable.DOUBLE,
+ new Double(100.0)));
+ // We've now set all of our tunables, so we can read the property
+ // file now and adjust as appropriate
+ layoutProperties.initializeProperties();
+
+ // Finally, update everything. We need to do this to update
+ // any of our values based on what we read from the property file
+ updateSettings(true);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void updateSettings() {
+ updateSettings(false);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param force DOCUMENT ME!
+ */
+ public void updateSettings(boolean force) {
+ super.updateSettings(force);
+
+ Tunable t = layoutProperties.get("iterations_pernode");
+ if ((t != null) && (t.valueChanged() || force)) {
+ setNumberOfIterationsPerNode(t.getValue().toString());
+ if (t.valueChanged())
+ layoutProperties.setProperty(t.getName(), t.getValue().toString());
+ }
+
+ t = layoutProperties.get("layout_passes");
+ if ((t != null) && (t.valueChanged() || force)) {
+ setNumberOfLayoutPasses(t.getValue().toString());
+ if (t.valueChanged())
+ layoutProperties.setProperty(t.getName(), t.getValue().toString());
+ }
+
+ t = layoutProperties.get("distance_strength");
+ if ((t != null) && (t.valueChanged() || force)) {
+ setDistanceSpringStrength(t.getValue().toString());
+ if (t.valueChanged())
+ layoutProperties.setProperty(t.getName(), t.getValue().toString());
+ }
+
+ t = layoutProperties.get("rest_length");
+ if ((t != null) && (t.valueChanged() || force)) {
+ setDistanceRestLength(t.getValue().toString());
+ if (t.valueChanged())
+ layoutProperties.setProperty(t.getName(), t.getValue().toString());
+ }
+
+ t = layoutProperties.get("disconnected_strength");
+ if ((t != null) && (t.valueChanged() || force)) {
+ setDisconnectedSpringStrength(t.getValue().toString());
+ if (t.valueChanged())
+ layoutProperties.setProperty(t.getName(), t.getValue().toString());
+ }
+
+ t = layoutProperties.get("disconnected_rest_length");
+ if ((t != null) && (t.valueChanged() || force)) {
+ setDisconnectedRestLength(t.getValue().toString());
+ if (t.valueChanged())
+ layoutProperties.setProperty(t.getName(), t.getValue().toString());
+ }
+
+ t = layoutProperties.get("anticollisionStrength");
+ if ((t != null) && (t.valueChanged() || force)) {
+ setAnticollisionSpringStrength(t.getValue().toString());
+ if (t.valueChanged())
+ layoutProperties.setProperty(t.getName(), t.getValue().toString());
+ }
+ }
+
+ /**
+ * Perform a layout
+ */
+ public void layoutPartition(LayoutPartition partition) {
+ Iterator iter = null;
+ Dimension initialLocation = null;
+ this.partition = partition;
+ // Initialize all of our values. This will create
+ // our internal objects and initialize them
+ // local_initialize();
+ m_nodeCount = partition.nodeCount();
+
+ // Set defaults -- this is done here insted of in the constructor
+ // to allow users to change m_numLayoutPasses
+ m_nodeDistanceSpringScalars = new double[m_numLayoutPasses];
+
+ for (int i = 0; i < m_numLayoutPasses; i++)
+ m_nodeDistanceSpringScalars[i] = 1.0;
+
+ m_anticollisionSpringScalars = new double[m_numLayoutPasses];
+ m_anticollisionSpringScalars[0] = 0.0;
+
+ for (int i = 1; i < m_numLayoutPasses; i++)
+ m_anticollisionSpringScalars[i] = 1.0;
+
+ logger.info("Laying out " + m_nodeCount + " nodes and "
+ + partition.edgeCount() + " edges: ");
+
+ /*
+ for (Iterator diter = partition.nodeIterator(); diter.hasNext(); ) {
+ logger.debug("\t"+(LayoutNode)diter.next());
+ }
+ for (Iterator diter = partition.edgeIterator(); diter.hasNext(); ) {
+ logger.debug("\t"+(LayoutEdge)diter.next());
+ }
+ */
+
+ // Calculate a distance threshold
+ double euclideanDistanceThreshold = (m_nodeCount + partition.edgeCount()) / 10;
+
+ int numIterations = (int) ((m_nodeCount * m_averageIterationsPerNode) / m_numLayoutPasses);
+
+ List <PartialDerivatives>partialsList = new ArrayList<PartialDerivatives>();
+ double[] potentialEnergy = new double[1];
+
+ if (potentialEnergy[0] != 0.0)
+ throw new RuntimeException();
+
+ PartialDerivatives partials;
+ PartialDerivatives furthestNodePartials = null;
+
+ m_nodeDistanceSpringRestLengths = new double[m_nodeCount][m_nodeCount];
+ m_nodeDistanceSpringStrengths = new double[m_nodeCount][m_nodeCount];
+
+ // Figure out our starting point
+ if (selectedOnly) {
+ initialLocation = partition.getAverageLocation();
+ }
+
+ // Randomize our points, if any points lie
+ // outside of our bounds
+ if (randomize)
+ partition.randomizeLocations();
+
+ // Calculate our edge weights
+ partition.calculateEdgeWeights();
+
+ // Compute our distances
+ if (canceled)
+ return;
+
+ taskMonitor.setPercentCompleted(2);
+ taskMonitor.setStatus("Calculating node distances");
+
+ int[][] nodeDistances = calculateNodeDistances();
+
+ if (canceled)
+ return;
+
+ taskMonitor.setPercentCompleted(4);
+ taskMonitor.setStatus("Calculating spring constants");
+
+ calculateSpringData(nodeDistances);
+
+ final double percentCompletedBeforePasses = 5.0d;
+ final double percentCompletedAfterPass1 = 60.0d;
+ final double percentCompletedAfterFinalPass = 95.0d;
+ double currentProgress = percentCompletedBeforePasses;
+
+ // Profile partialProfile = new Profile();
+ // Profile springProfile = new Profile();
+
+ // Compute our optimal lengths
+ for (m_layoutPass = 0; m_layoutPass < m_numLayoutPasses; m_layoutPass++) {
+ final double percentProgressPerIter;
+ Profile passTimer = new Profile();
+ passTimer.start();
+
+ if (m_layoutPass == 0) {
+ percentProgressPerIter = (percentCompletedAfterPass1 - percentCompletedBeforePasses) / (double) (m_nodeCount
+ + numIterations);
+ } else {
+ percentProgressPerIter = (percentCompletedAfterFinalPass
+ - percentCompletedAfterPass1) / (double) ((m_nodeCount
+ + numIterations) * (m_numLayoutPasses
+ - 1));
+ }
+
+ // Initialize this layout pass.
+ potentialEnergy[0] = 0.0;
+ partialsList.clear();
+ furthestNodePartials = null;
+
+ taskMonitor.setStatus("Calculating partial derivatives -- pass " + (m_layoutPass + 1)
+ + " of " + m_numLayoutPasses);
+
+ // partialProfile.start();
+
+ // Calculate all node distances. Keep track of the furthest.
+ Iterator nodeIter = partition.nodeIterator();
+ euclideanLoop = 0;
+
+ while (nodeIter.hasNext()) {
+ LayoutNode v = (LayoutNode) nodeIter.next();
+
+ if (canceled)
+ return;
+
+ taskMonitor.setPercentCompleted((int) currentProgress);
+
+ if (v.isLocked())
+ continue;
+
+ partials = new PartialDerivatives(v);
+ calculatePartials(partials, null, potentialEnergy, false);
+ // logger.debug(partials.printPartial()+" potentialEnergy = "+potentialEnergy[0]);
+ partialsList.add(partials);
+
+ if ((furthestNodePartials == null)
+ || (partials.euclideanDistance > furthestNodePartials.euclideanDistance)) {
+ furthestNodePartials = partials;
+ }
+
+ currentProgress += percentProgressPerIter;
+ }
+
+ // partialProfile.done("Partial time for pass "+(m_layoutPass+1)+" is ");
+ taskMonitor.setStatus("Executing spring logic -- pass " + (m_layoutPass + 1) + " of "
+ + m_numLayoutPasses);
+
+ // springProfile.start();
+ for (int iterations_i = 0;
+ (iterations_i < numIterations)
+ && (furthestNodePartials.euclideanDistance >= euclideanDistanceThreshold);
+ iterations_i++) {
+ if (canceled)
+ return;
+
+ taskMonitor.setPercentCompleted((int) currentProgress);
+
+ furthestNodePartials = moveNode(furthestNodePartials, partialsList, potentialEnergy);
+ // logger.debug(furthestNodePartials.printPartial()+" (furthest) potentialEnergy = "+potentialEnergy[0]);
+ currentProgress += percentProgressPerIter;
+ }
+
+ // springProfile.done("Spring time for pass "+(m_layoutPass+1)+" is ");
+ }
+
+ taskMonitor.setPercentCompleted((int) percentCompletedAfterFinalPass);
+ taskMonitor.setStatus("Updating display");
+
+ // Actually move the pieces around
+ // Note that we reset our min/max values before we start this
+ // so we can get an accurate min/max for paritioning
+ partition.resetNodes();
+ iter = partition.nodeIterator();
+
+ while (iter.hasNext()) {
+ LayoutNode v = (LayoutNode) iter.next();
+ partition.moveNodeToLocation(v);
+ }
+
+ // Not quite done, yet. If we're only laying out selected nodes, we need
+ // to migrate the selected nodes back to their starting position
+ if (selectedOnly) {
+ double xDelta = 0.0;
+ double yDelta = 0.0;
+ Dimension finalLocation = partition.getAverageLocation();
+ xDelta = finalLocation.getWidth() - initialLocation.getWidth();
+ yDelta = finalLocation.getHeight() - initialLocation.getHeight();
+ iter = partition.nodeIterator();
+
+ while (iter.hasNext()) {
+ LayoutNode v = (LayoutNode) iter.next();
+
+ if (!v.isLocked()) {
+ v.decrement(xDelta, yDelta);
+ partition.moveNodeToLocation(v);
+ }
+ }
+ }
+ }
+
+ private int[][] calculateNodeDistances() {
+ int[][] distances = new int[m_nodeCount][];
+ LinkedList<Integer> queue = new LinkedList<Integer>();
+ boolean[] completedNodes = new boolean[m_nodeCount];
+ int toNode;
+ int fromNode;
+ int neighbor;
+ int toNodeDistance;
+ int neighborDistance;
+ Iterator nodeIter = partition.nodeIterator();
+
+ while (nodeIter.hasNext()) {
+ LayoutNode v = (LayoutNode) nodeIter.next();
+ fromNode = v.getIndex();
+
+ if (distances[fromNode] == null)
+ distances[fromNode] = new int[m_nodeCount];
+
+ Arrays.fill(distances[fromNode], Integer.MAX_VALUE);
+ distances[fromNode][fromNode] = 0;
+ Arrays.fill(completedNodes, false);
+ queue.add(new Integer(fromNode));
+
+ while (!(queue.isEmpty())) {
+ int index = ((Integer) queue.removeFirst()).intValue();
+
+ if (completedNodes[index])
+ continue;
+
+ completedNodes[index] = true;
+ toNode = index;
+ toNodeDistance = distances[fromNode][index];
+
+ if (index < fromNode) {
+ // Oh boy. We've already got every distance from/to this node.
+ int distanceThroughToNode;
+
+ for (int i = 0; i < m_nodeCount; i++) {
+ if (distances[index][i] == Integer.MAX_VALUE)
+ continue;
+
+ distanceThroughToNode = toNodeDistance + distances[index][i];
+
+ if (distanceThroughToNode <= distances[fromNode][i]) {
+ // Any immediate neighbor of a node that's already been
+ // calculated for that does not already have a shorter path
+ // calculated from fromNode never will, and is thus complete.
+ if (distances[index][i] == 1)
+ completedNodes[i] = true;
+
+ distances[fromNode][i] = distanceThroughToNode;
+ }
+ }
+
+ // End for every node, update the distance using the distance
+ // from toNode. So now we don't need to put any neighbors on the
+ // queue or anything, since they've already been taken care of by
+ // the previous calculation.
+ continue;
+ } // End if toNode has already had all of its distances calculated.
+
+ List neighborList = v.getNeighbors();
+ Iterator neighbors = neighborList.iterator();
+
+ while (neighbors.hasNext()) {
+ LayoutNode neighbor_v = (LayoutNode) neighbors.next();
+ neighbor = neighbor_v.getIndex();
+
+ // We've already done everything we can here.
+ if (completedNodes[neighbor])
+ continue;
+
+ neighborDistance = distances[fromNode][neighbor];
+
+ if ((toNodeDistance != Integer.MAX_VALUE)
+ && (neighborDistance > (toNodeDistance + 1))) {
+ distances[fromNode][neighbor] = toNodeDistance + 1;
+ queue.addLast(new Integer(neighbor));
+ }
+ }
+ }
+ }
+
+ return distances;
+ }
+
+ private void calculateSpringData(int[][] nodeDistances) {
+ // Set all springs to the default
+ for (int node_i = 0; node_i < m_nodeCount; node_i++) {
+ Arrays.fill(m_nodeDistanceSpringRestLengths[node_i],
+ m_disconnectedNodeDistanceSpringRestLength);
+ Arrays.fill(m_nodeDistanceSpringStrengths[node_i],
+ m_disconnectedNodeDistanceSpringStrength);
+ }
+
+ // Calculate rest lengths and strengths based on node distance data.
+ Iterator edgeIter = partition.edgeIterator();
+
+ while (edgeIter.hasNext()) {
+ LayoutEdge edge = (LayoutEdge) edgeIter.next();
+ int node_i = edge.getSource().getIndex();
+ int node_j = edge.getTarget().getIndex();
+ double weight = edge.getWeight();
+
+ // logger.debug(edge);
+ if (nodeDistances[node_i][node_j] != Integer.MAX_VALUE) {
+ // Compute spring rest lengths.
+ m_nodeDistanceSpringRestLengths[node_i][node_j] = (m_nodeDistanceRestLengthConstant * nodeDistances[node_i][node_j]) / (weight);
+ m_nodeDistanceSpringRestLengths[node_j][node_i] = m_nodeDistanceSpringRestLengths[node_i][node_j];
+ // logger.debug("Setting spring ("+node_i+","+node_j+") ["+weight+"] length to "+m_nodeDistanceSpringRestLengths[node_j][node_i]);
+ // Compute spring strengths.
+ m_nodeDistanceSpringStrengths[node_i][node_j] = m_nodeDistanceStrengthConstant / (nodeDistances[node_i][node_j] * nodeDistances[node_i][node_j]);
+ m_nodeDistanceSpringStrengths[node_j][node_i] = m_nodeDistanceSpringStrengths[node_i][node_j];
+
+ // logger.debug("Setting spring ("+node_i+","+node_j+") strength to "+m_nodeDistanceSpringStrengths[node_j][node_i]);
+ }
+ }
+ }
+
+ /**
+ * Here is the code for the partial derivative solver. Note that for clarity,
+ * it has been devided into four parts:
+ * calculatePartials -- main algorithm, calls the other three parts
+ * calculateSpringPartial -- computes the first part of the spring partial (partial.x, partial.y)
+ * calculateSpringPartial3 -- computes the second part of the partial (partial.xx, partial.yy)
+ * calculateSpringPartialCross -- computes the final part of the partial (partial.xy)
+ * calculatePE -- computes the potential energy
+ */
+
+ // used to calculate the x and y portions of the partial
+ private double calculateSpringPartial(int pass, double distToTouch, int nodeIndex,
+ int otherNodeIndex, double eucDist, double value,
+ double radius) {
+ double incrementalChange = (m_nodeDistanceSpringScalars[pass] * (m_nodeDistanceSpringStrengths[nodeIndex][otherNodeIndex] * (value
+ - ((m_nodeDistanceSpringRestLengths[nodeIndex][otherNodeIndex] * value) / eucDist))));
+
+ if (distToTouch < 0.0) {
+ incrementalChange += (m_anticollisionSpringScalars[pass] * (m_anticollisionSpringStrength * (value
+ - ((radius * value) / eucDist))));
+ }
+
+ return incrementalChange;
+ }
+
+ // used to calculate the xx and yy portions of the partial
+ private double calculateSpringPartial3(int pass, double distToTouch, int nodeIndex,
+ int otherNodeIndex, double eucDist3, double value,
+ double radius) {
+ double incrementalChange = (m_nodeDistanceSpringScalars[pass] * (m_nodeDistanceSpringStrengths[nodeIndex][otherNodeIndex] * (1.0
+ - ((m_nodeDistanceSpringRestLengths[nodeIndex][otherNodeIndex] * value) / eucDist3))));
+
+ if (distToTouch < 0.0) {
+ incrementalChange += (m_anticollisionSpringScalars[m_layoutPass] * (m_anticollisionSpringStrength * (1.0
+ - ((radius * value) / eucDist3))));
+ }
+
+ return incrementalChange;
+ }
+
+ // used to calculate the xy portion of the partial
+ private double calculateSpringPartialCross(int pass, double distToTouch, int nodeIndex,
+ int otherNodeIndex, double eucDist3, double value,
+ double radius) {
+ double incrementalChange = (m_nodeDistanceSpringScalars[pass] * (m_nodeDistanceSpringStrengths[nodeIndex][otherNodeIndex] * ((m_nodeDistanceSpringRestLengths[nodeIndex][otherNodeIndex] * value) / eucDist3)));
+
+ if (distToTouch < 0.0) {
+ incrementalChange += ((m_anticollisionSpringScalars[m_layoutPass] * (m_anticollisionSpringStrength * radius * value)) / eucDist3);
+ }
+
+ return incrementalChange;
+ }
+
+ // Calculate the potential energy
+ private double calculatePE(int pass, double distToRest, double distToTouch, int nodeIndex,
+ int otherNodeIndex) {
+ double incrementalChange = (m_nodeDistanceSpringScalars[pass] * ((m_nodeDistanceSpringStrengths[nodeIndex][otherNodeIndex] * (distToRest * distToRest)) / 2));
+
+ if (distToTouch < 0.0) {
+ incrementalChange += (m_anticollisionSpringScalars[pass] * ((m_anticollisionSpringStrength * (distToTouch * distToTouch)) / 2));
+ }
+
+ return incrementalChange;
+ }
+
+ private PartialDerivatives calculatePartials(PartialDerivatives partials, List partialsList,
+ double[] potentialEnergy, boolean reversed) {
+ partials.reset();
+
+ LayoutNode node = partials.node;
+
+ // How does this ever get to be > 0?
+ // Get the node size from the nodeView?
+ double nodeRadius = node.getWidth() / 2;
+ double nodeX = node.getX();
+ double nodeY = node.getY();
+ PartialDerivatives otherPartials = null;
+ LayoutNode otherNode;
+ double otherNodeRadius;
+ PartialDerivatives furthestPartials = null;
+ Iterator iterator;
+
+ if (partialsList == null)
+ iterator = partition.nodeIterator();
+ else
+ iterator = partialsList.iterator();
+
+ double deltaX;
+ double deltaY;
+ double otherNodeX;
+ double otherNodeY;
+ double euclideanDistance;
+ double euclideanDistanceCubed;
+ double distanceFromRest;
+ double distanceFromTouching;
+ double incrementalChange;
+ double[] xTable = { .01, .01, -.01, -.01 };
+ double[] yTable = { .01, -.01, .01, -.01 };
+ int offsetTable = 0;
+ int nodeIndex = node.getIndex();
+
+ while (iterator.hasNext()) {
+ if (partialsList == null) {
+ otherNode = (LayoutNode) iterator.next();
+ } else {
+ otherPartials = (PartialDerivatives) iterator.next();
+ otherNode = otherPartials.node;
+ }
+
+ if (node == otherNode)
+ continue;
+
+ // How does this every get to be > 0?
+ // Get the node size from the nodeView?
+ otherNodeRadius = otherNode.getWidth() / 2;
+ otherNodeX = otherNode.getX();
+ otherNodeY = otherNode.getY();
+
+ deltaX = nodeX - otherNodeX;
+ deltaY = nodeY - otherNodeY;
+ euclideanDistance = Math.sqrt((deltaX * deltaX) + (deltaY * deltaY));
+
+ if (((float) euclideanDistance) < 0.0001) {
+ otherNodeX = otherNodeX + xTable[offsetTable];
+ otherNodeY = otherNodeY + yTable[offsetTable++];
+
+ if (offsetTable > 3)
+ offsetTable = 0;
+
+ otherNode.setX(otherNodeX);
+ otherNode.setY(otherNodeY);
+ euclideanDistance = Math.sqrt((deltaX * deltaX) + (deltaY * deltaY));
+ }
+
+ /*
+ logger.debug("nodeX = "+nodeX);
+ logger.debug("nodeY = "+nodeY);
+ logger.debug("otherNodeX = "+otherNode.getX());
+ logger.debug("otherNodeY = "+otherNode.getY());
+ */
+ int otherNodeIndex = otherNode.getIndex();
+ double radius = nodeRadius + otherNodeRadius;
+
+ euclideanDistanceCubed = euclideanDistance * euclideanDistance * euclideanDistance;
+ distanceFromTouching = euclideanDistance - (nodeRadius + otherNodeRadius);
+ distanceFromRest = (euclideanDistance
+ - m_nodeDistanceSpringRestLengths[nodeIndex][otherNodeIndex]);
+
+ // calculationProfile.start();
+ if (!reversed) {
+ partials.x += calculateSpringPartial(m_layoutPass, distanceFromTouching, nodeIndex,
+ otherNodeIndex, euclideanDistance, deltaX,
+ radius);
+ partials.y += calculateSpringPartial(m_layoutPass, distanceFromTouching, nodeIndex,
+ otherNodeIndex, euclideanDistance, deltaY,
+ radius);
+ partials.xx += calculateSpringPartial3(m_layoutPass, distanceFromTouching,
+ nodeIndex, otherNodeIndex,
+ euclideanDistanceCubed, deltaY * deltaY,
+ radius);
+ partials.yy += calculateSpringPartial3(m_layoutPass, distanceFromTouching,
+ nodeIndex, otherNodeIndex,
+ euclideanDistanceCubed, deltaX * deltaX,
+ radius);
+ partials.xy += calculateSpringPartialCross(m_layoutPass, distanceFromTouching,
+ nodeIndex, otherNodeIndex,
+ euclideanDistanceCubed, deltaX * deltaY,
+ radius);
+ potentialEnergy[0] += calculatePE(m_layoutPass, distanceFromRest,
+ distanceFromTouching, nodeIndex, otherNodeIndex);
+ }
+
+ if (otherPartials != null) {
+ if (!reversed) {
+ otherPartials.x += calculateSpringPartial(m_layoutPass, distanceFromTouching,
+ otherNodeIndex, nodeIndex,
+ euclideanDistance, -deltaX, radius);
+ otherPartials.y += calculateSpringPartial(m_layoutPass, distanceFromTouching,
+ otherNodeIndex, nodeIndex,
+ euclideanDistance, -deltaY, radius);
+ otherPartials.xx += calculateSpringPartial3(m_layoutPass, distanceFromTouching,
+ otherNodeIndex, nodeIndex,
+ euclideanDistanceCubed,
+ deltaY * deltaY, radius);
+ otherPartials.yy += calculateSpringPartial3(m_layoutPass, distanceFromTouching,
+ otherNodeIndex, nodeIndex,
+ euclideanDistanceCubed,
+ deltaX * deltaX, radius);
+ otherPartials.xy += calculateSpringPartialCross(m_layoutPass,
+ distanceFromTouching,
+ nodeIndex, otherNodeIndex,
+ euclideanDistanceCubed,
+ deltaX * deltaY, radius);
+ potentialEnergy[0] += calculatePE(m_layoutPass, distanceFromRest,
+ distanceFromTouching, nodeIndex,
+ otherNodeIndex);
+ } else {
+ otherPartials.x -= calculateSpringPartial(m_layoutPass, distanceFromTouching,
+ otherNodeIndex, nodeIndex,
+ euclideanDistance, -deltaX, radius);
+ otherPartials.y -= calculateSpringPartial(m_layoutPass, distanceFromTouching,
+ otherNodeIndex, nodeIndex,
+ euclideanDistance, -deltaY, radius);
+ otherPartials.xx -= calculateSpringPartial3(m_layoutPass, distanceFromTouching,
+ nodeIndex, otherNodeIndex,
+ euclideanDistanceCubed,
+ deltaY * deltaY, radius);
+ otherPartials.yy -= calculateSpringPartial3(m_layoutPass, distanceFromTouching,
+ nodeIndex, otherNodeIndex,
+ euclideanDistanceCubed,
+ deltaX * deltaX, radius);
+ otherPartials.xy -= calculateSpringPartialCross(m_layoutPass,
+ distanceFromTouching,
+ nodeIndex, otherNodeIndex,
+ euclideanDistanceCubed,
+ deltaX * deltaY, radius);
+ potentialEnergy[0] -= calculatePE(m_layoutPass, distanceFromRest,
+ distanceFromTouching, nodeIndex,
+ otherNodeIndex);
+ }
+
+ // Update the euclidean distance
+ otherPartials.euclideanDistance = Math.sqrt((otherPartials.x * otherPartials.x)
+ + (otherPartials.y * otherPartials.y));
+
+ if ((furthestPartials == null)
+ || (otherPartials.euclideanDistance > furthestPartials.euclideanDistance))
+ furthestPartials = otherPartials;
+ }
+
+ // calculationProfile.checkpoint();
+ } // end of while loop
+
+ if (!reversed)
+ partials.euclideanDistance = Math.sqrt((partials.x * partials.x)
+ + (partials.y * partials.y));
+
+ if ((furthestPartials == null)
+ || (partials.euclideanDistance > furthestPartials.euclideanDistance))
+ furthestPartials = partials;
+
+ return furthestPartials;
+ }
+
+ /**
+ * The PartialDerivatives class maintains the values for the partial derivatives
+ * as they are computed.
+ */
+ private class PartialDerivatives {
+ final LayoutNode node;
+ double x;
+ double y;
+ double xx;
+ double yy;
+ double xy;
+ double euclideanDistance;
+
+ PartialDerivatives(LayoutNode node) {
+ this.node = node;
+ }
+
+ PartialDerivatives(PartialDerivatives copyFrom) {
+ this.node = copyFrom.node;
+ copyFrom(copyFrom);
+ }
+
+ String printPartial() {
+ String retVal = "Partials for node " + node.getIndex() + " are: " + x + "," + y + ","
+ + xx + "," + yy + "," + xy + " dist = " + euclideanDistance;
+
+ return retVal;
+ }
+
+ void reset() {
+ x = 0.0;
+ y = 0.0;
+ xx = 0.0;
+ yy = 0.0;
+ xy = 0.0;
+ euclideanDistance = 0.0;
+ }
+
+ void copyFrom(PartialDerivatives otherPartialDerivatives) {
+ x = otherPartialDerivatives.x;
+ y = otherPartialDerivatives.y;
+ xx = otherPartialDerivatives.xx;
+ yy = otherPartialDerivatives.yy;
+ xy = otherPartialDerivatives.xy;
+ euclideanDistance = otherPartialDerivatives.euclideanDistance;
+ }
+ }
+
+ private PartialDerivatives moveNode(PartialDerivatives partials, List partialsList,
+ double[] potentialEnergy) {
+ PartialDerivatives startingPartials = new PartialDerivatives(partials);
+ calculatePartials(partials, partialsList, potentialEnergy, true);
+
+ // logger.debug(partials.printPartial()+" potentialEnergy = "+potentialEnergy[0]);
+ try {
+ simpleMoveNode(startingPartials);
+ } catch (Exception e) {
+ logger.error(e.getMessage());
+ }
+
+ return calculatePartials(partials, partialsList, potentialEnergy, false);
+ }
+
+ private void simpleMoveNode(PartialDerivatives partials) {
+ LayoutNode node = partials.node;
+
+ if (node.isLocked()) {
+ return;
+ }
+
+ double denominator = ((partials.xx * partials.yy) - (partials.xy * partials.xy));
+
+ if (((float) denominator) == 0.0) {
+ return;
+
+ // throw new RuntimeException("denominator too close to 0 for node "+node);
+ }
+
+ // logger.debug(partials.printPartial());
+ double deltaX = (((-partials.x * partials.yy) - (-partials.y * partials.xy)) / denominator);
+ double deltaY = (((-partials.y * partials.xx) - (-partials.x * partials.xy)) / denominator);
+ /* logger.debug("Moving node "+node.getIdentifier()+" from "+node.getX()+", "+node.getY()+
+ " to "+(node.getX()+deltaX)+", "+(node.getY()+deltaY)); */
+ node.setLocation(node.getX() + deltaX, node.getY() + deltaY);
+ }
+
+ // Debugging version of inner loop for calculatePartials
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/algorithms/circularLayout/CircularLayoutAlgorithm.java b/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/algorithms/circularLayout/CircularLayoutAlgorithm.java
new file mode 100644
index 0000000..0a10761
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/algorithms/circularLayout/CircularLayoutAlgorithm.java
@@ -0,0 +1,1256 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package csplugins.layout.algorithms.circularLayout;
+
+import csplugins.layout.LayoutEdge;
+import csplugins.layout.LayoutNode;
+import csplugins.layout.LayoutPartition;
+
+import csplugins.layout.algorithms.graphPartition.AbstractGraphPartition;
+
+import csplugins.layout.algorithms.hierarchicalLayout.Edge;
+import csplugins.layout.algorithms.hierarchicalLayout.Graph;
+
+import cytoscape.layout.LayoutProperties;
+import cytoscape.layout.Tunable;
+import cytoscape.logger.CyLogger;
+
+import cytoscape.task.TaskMonitor;
+
+import giny.view.NodeView;
+
+import java.awt.GridLayout;
+
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.LinkedList;
+
+import javax.swing.JPanel;
+
+
+/**
+ *
+ * @author Aleksandar Nikolic
+ * Lays out graph in circular pattern.
+ * Algorithm puts all the nodes which belong to same biconnected component
+ * (with more than 3 nodes) on circle. Nodes which doesn't belong to circle
+ * are layed out in tree-like pattern.
+ */
+public class CircularLayoutAlgorithm extends AbstractGraphPartition {
+ private int nodeHorizontalSpacing = 64;
+ private int nodeVerticalSpacing = 32;
+ private int leftEdge = 32;
+ private int topEdge = 32;
+ private int rightMargin = 1000;
+ private int componentSpacing = 64;
+
+ //private boolean selected_only = false;
+ private LayoutProperties layoutProperties;
+ private int[][] bc;
+ private boolean[] posSet;
+ private boolean[] depthPosSet;
+ private HashMap<Integer, Integer> nodeHeights;
+ private LinkedList<Integer>[] edgesFrom;
+ private NodeView[] nodeView;
+ private HashMap<Integer, Integer> node2BiComp;
+ private boolean[] drawnBiComps;
+ private CyLogger logger = null;
+
+ /**
+ * Creates a new CircularLayoutAlgorithm object.
+ */
+ public CircularLayoutAlgorithm() {
+ super();
+ logger = CyLogger.getLogger(CircularLayoutAlgorithm.class);
+ layoutProperties = new LayoutProperties(getName());
+ initialize_properties();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean supportsSelectedOnly() {
+ return true;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getName() {
+ return "circular";
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String toString() {
+ return "Circular Layout";
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param partition DOCUMENT ME!
+ */
+ public void layoutPartition(LayoutPartition partition) {
+ if (canceled)
+ return;
+
+ final int numNodes = partition.nodeCount();
+
+ if (numNodes == 1) {
+ // We were asked to do a circular layout of a single node -- done!
+ return;
+ }
+
+ nodeView = new NodeView[numNodes];
+
+ int nextNode = 0;
+ HashMap<Integer, Integer> ginyIndex2Index = new HashMap<Integer, Integer>(numNodes * 2);
+
+ Iterator iter = partition.getNodeList().iterator(); /* all nodes */
+ double centerX = 0;
+ double centerY = 0;
+
+ while (iter.hasNext() && !canceled) {
+ LayoutNode ln = (LayoutNode) iter.next();
+ if (ln.isLocked())
+ continue;
+
+ NodeView nv = ln.getNodeView();
+ Integer nodeIndexKey = new Integer(nv.getNode().getRootGraphIndex());
+
+ if (!ginyIndex2Index.containsKey(nodeIndexKey)) {
+ nodeView[nextNode] = nv;
+ centerX = centerX + nv.getXPosition();
+ centerY = centerY + nv.getYPosition();
+ ginyIndex2Index.put(nodeIndexKey, new Integer(nextNode));
+ nextNode++;
+ }
+ }
+
+ centerX = centerX / nextNode;
+ centerY = centerY / nextNode;
+
+ if (canceled)
+ return;
+
+ /* create edge list from edges between selected nodes */
+ LinkedList<Edge> edges = new LinkedList<Edge>();
+ iter = partition.edgeIterator();
+
+ while (iter.hasNext()) {
+ LayoutEdge ev = (LayoutEdge) (iter.next());
+ Integer edgeFrom = (Integer) ginyIndex2Index.get(new Integer(ev.getSource().getNodeView()
+ .getNode()
+ .getRootGraphIndex()));
+ Integer edgeTo = (Integer) ginyIndex2Index.get(new Integer(ev.getTarget().getNodeView()
+ .getNode()
+ .getRootGraphIndex()));
+
+ if ((edgeFrom == null) || (edgeTo == null)) {
+ // Must be from an unselected node
+ continue;
+ }
+
+ if (canceled)
+ return;
+
+ /* add edge to graph */
+ edges.add(new Edge(edgeFrom.intValue(), edgeTo.intValue()));
+ edges.add(new Edge(edgeTo.intValue(), edgeFrom.intValue()));
+ }
+
+ /* find horizontal and vertical coordinates of each node */
+ Edge[] edge = new Edge[edges.size()];
+ edges.toArray(edge);
+
+ Graph graph = new Graph(numNodes, edge);
+
+ if (canceled)
+ return;
+
+ posSet = new boolean[nodeView.length]; // all false
+ depthPosSet = new boolean[nodeView.length]; // all false
+
+ // logger.debug("plain component:" + graph.getNodecount());
+
+ Thread.yield();
+
+ bc = graph.biconnectedComponents();
+
+ int maxSize = -1;
+ int maxIndex = -1;
+
+ for (int i = 0; i < bc.length; i++)
+ if (bc[i].length > maxSize) {
+ maxSize = bc[i].length;
+ maxIndex = i;
+ }
+
+ if (maxIndex == -1) {
+ taskMonitor.setStatus("Can't perform circular layout: no biconnected components");
+ logger.warning("Can't perform circular layout: no biconnected components");
+ return;
+ }
+
+ if (canceled)
+ return;
+
+ drawnBiComps = new boolean[bc.length];
+ node2BiComp = new HashMap<Integer, Integer>();
+
+ for (int i = 0; i < bc.length; i++)
+ if (bc[i].length > 3) {
+ for (int j = 0; j < bc[i].length; j++) {
+ if (!node2BiComp.containsKey(bc[i][j]))
+ node2BiComp.put(new Integer(bc[i][j]), new Integer(i));
+ else if (bc[i].length > bc[node2BiComp.get(bc[i][j]).intValue()].length) {
+ node2BiComp.remove(new Integer(bc[i][j])); // check this
+ node2BiComp.put(new Integer(bc[i][j]), new Integer(i));
+ }
+ }
+ }
+
+ double radius = (48 * maxSize) / (2 * Math.PI);
+
+ /*int[] resultingNodes = new int[bc[maxIndex].length];
+ for (int i = 0; i < resultingNodes.length; i++)
+ resultingNodes[i] = index2GinyIndex.get(bc[maxIndex][i]);*/
+ double deltaAngle = (2 * Math.PI) / maxSize;
+ double angle = 0;
+
+ int startX = (int) (radius + centerX);
+ int startY = (int) (radius + centerY);
+
+ // We need to translate this back to our starting point
+
+ edgesFrom = graph.GetEdgesFrom();
+
+ // sorting nodes on inner circle
+ bc[maxIndex] = SortInnerCircle(bc[maxIndex]);
+
+ // setting nodes on inner circle
+ for (int i = 0; i < bc[maxIndex].length; i++) {
+ //logger.debug(bc[maxIndex][i] + " " + part2NonPart[bc[maxIndex][i]] + " ");
+ nodeView[bc[maxIndex][i]].setOffset(startX + (Math.cos(angle) * radius),
+ startY - (Math.sin(angle) * radius));
+ posSet[bc[maxIndex][i]] = true;
+
+ angle += deltaAngle;
+ }
+
+ drawnBiComps[maxIndex] = true;
+
+ nodeHeights = new HashMap<Integer, Integer>();
+
+ SetOuterCircle(maxIndex, radius, startX, startY, -1);
+
+ if (canceled)
+ return;
+
+ iter = partition.nodeIterator();
+
+ while (iter.hasNext() && !canceled) {
+ LayoutNode ln = (LayoutNode) (iter.next());
+ NodeView nv = ln.getNodeView();
+ double xPos = nv.getXPosition();
+ double yPos = nv.getYPosition();
+ ln.setX(xPos);
+ ln.setY(yPos);
+ partition.moveNodeToLocation(ln);
+ }
+ }
+
+ /**
+ * Function which sets the first neighbours of nodes from circle (biconnected component)
+ * on the concentric circle (larger then the first circle).
+ * @param compIndex - index of that biconnected component in array bc
+ * @param innerCircleRadius - radius of the inner cicrle
+ * @param startX - start X position for drawing
+ * @param startY - start Y position for drawing
+ * @param firstTouched - node from that component which is found first
+ */
+ private void SetOuterCircle(int compIndex, double innerCircleRadius, double startX,
+ double startY, int firstTouched) {
+ int outerNodesCount = 0;
+ int rnc = 0;
+ Iterator iter;
+ HashMap<Integer, Integer> outerCircle = new HashMap<Integer, Integer>();
+
+ for (int i = 0; i < bc[compIndex].length; i++) {
+ iter = edgesFrom[bc[compIndex][i]].iterator();
+
+ while (iter.hasNext()) {
+ int currNeighbour = ((Integer) iter.next()).intValue();
+
+ if (!posSet[currNeighbour]) {
+ outerNodesCount += (NoOfChildren(currNeighbour, outerCircle) + 1);
+ outerCircle.put(new Integer(currNeighbour), new Integer(0));
+ rnc++;
+ }
+ }
+ }
+
+ double outerRadius;
+ //Math.round((nodeHorizontalSpacing * outerNodesCount) / (2 * Math.PI));
+ outerRadius = 1.5 * innerCircleRadius;
+
+ // + 5 * nodeHorizontalSpacing;
+ int tryCount = (int) ((2 * Math.PI * outerRadius) / 32);
+ double outerDeltaAngle = (2 * Math.PI) / tryCount;
+
+ if (tryCount < (1.2 * outerNodesCount)) {
+ outerRadius = (1.2 * 32 * outerNodesCount) / (2 * Math.PI);
+ outerDeltaAngle = (2 * Math.PI) / (1.2 * outerNodesCount);
+ outerNodesCount *= 1.2;
+ } else
+ outerNodesCount = tryCount;
+
+ if ((outerNodesCount > 10) && (firstTouched != -1))
+ outerNodesCount += 5;
+
+ // 5 places on outer circle for connection with other biconn. comp.
+ //logger.debug("tryCount = " + tryCount);
+
+ // setting nodes on outer circle
+ int[] outerPositionsTaken = new int[outerNodesCount];
+ int[] outerPositionsOwners = new int[outerNodesCount];
+
+ for (int i = 0; i < outerPositionsTaken.length; i++) {
+ outerPositionsTaken[i] = -1;
+ outerPositionsOwners[i] = -1;
+ }
+
+ double pointX;
+ double pointY;
+ double theAngle;
+ double theAngleHlp;
+ double innerDeltaAngle;
+ innerDeltaAngle = (2 * Math.PI) / bc[compIndex].length;
+
+ if (firstTouched != -1) {
+ pointX = nodeView[firstTouched].getOffset().getX();
+ pointY = nodeView[firstTouched].getOffset().getY();
+ theAngle = Math.asin((startY - pointY) / Math.sqrt(((pointX - startX) * (pointX
+ - startX))
+ + ((pointY - startY) * (pointY
+ - startY))));
+ theAngleHlp = Math.acos((pointX - startX) / Math.sqrt(((pointX - startX) * (pointX
+ - startX))
+ + ((pointY - startY) * (pointY
+ - startY))));
+
+ if (theAngleHlp > (Math.PI / 2))
+ theAngle = Math.PI - theAngle;
+
+ if (theAngle < 0)
+ theAngle += (2 * Math.PI);
+
+ int idPos = ((int) (theAngle / outerDeltaAngle)) % outerPositionsTaken.length;
+ outerPositionsTaken[idPos] = (int) (theAngle / innerDeltaAngle);
+ outerPositionsOwners[idPos] = -2; // must not be even moved because that node is coming from another bicomp.
+
+ if (outerPositionsTaken.length > 10) {
+ outerPositionsTaken[(idPos + 1) % outerPositionsTaken.length] = (int) (theAngle / innerDeltaAngle);
+ outerPositionsTaken[(idPos + 2) % outerPositionsTaken.length] = (int) (theAngle / innerDeltaAngle);
+ outerPositionsTaken[(idPos - 1 + outerPositionsTaken.length) % outerPositionsTaken.length] = (int) (theAngle / innerDeltaAngle);
+ outerPositionsTaken[(idPos - 2 + outerPositionsTaken.length) % outerPositionsTaken.length] = (int) (theAngle / innerDeltaAngle);
+
+ outerPositionsOwners[(idPos + 1) % outerPositionsOwners.length] = -2;
+ outerPositionsOwners[(idPos + 2) % outerPositionsOwners.length] = -2;
+ outerPositionsOwners[(idPos - 1 + outerPositionsOwners.length) % outerPositionsOwners.length] = -2;
+ outerPositionsOwners[(idPos - 2 + outerPositionsOwners.length) % outerPositionsOwners.length] = -2;
+ }
+ }
+
+ HashMap<Integer, Integer> addedNeighbours = new HashMap<Integer, Integer>();
+
+ for (int i = 0; i < bc[compIndex].length; i++) {
+ iter = edgesFrom[bc[compIndex][i]].iterator();
+
+ int currentNeighbour;
+ int noOfNeighbours = 0;
+
+ while (iter.hasNext()) {
+ currentNeighbour = ((Integer) iter.next()).intValue();
+
+ if (!posSet[currentNeighbour]) {
+ noOfNeighbours += (NoOfChildren(currentNeighbour, addedNeighbours) + 1);
+ addedNeighbours.put(new Integer(currentNeighbour), new Integer(0));
+ }
+ }
+
+ if (noOfNeighbours == 0)
+ continue;
+
+ pointX = nodeView[bc[compIndex][i]].getOffset().getX();
+ pointY = nodeView[bc[compIndex][i]].getOffset().getY();
+
+ theAngle = Math.asin((startY - pointY) / Math.sqrt(((pointX - startX) * (pointX
+ - startX))
+ + ((pointY - startY) * (pointY
+ - startY))));
+ theAngleHlp = Math.acos((pointX - startX) / Math.sqrt(((pointX - startX) * (pointX
+ - startX))
+ + ((pointY - startY) * (pointY
+ - startY))));
+
+ if (theAngleHlp > (Math.PI / 2))
+ theAngle = Math.PI - theAngle;
+
+ if (theAngle < 0)
+ theAngle += (2 * Math.PI);
+
+ iter = edgesFrom[bc[compIndex][i]].iterator();
+
+ int startPos = BestFreePositionsForAll((int) ((theAngle / outerDeltaAngle)
+ - (noOfNeighbours / 2.0)), outerPositionsTaken,
+ outerPositionsOwners, noOfNeighbours,
+ (int) (theAngle / innerDeltaAngle), startX,
+ startY, outerDeltaAngle, outerRadius,
+ bc[compIndex].length);
+ double startAngle = startPos * outerDeltaAngle;
+
+ if (startAngle < 0)
+ continue;
+
+ iter = edgesFrom[bc[compIndex][i]].iterator();
+
+ while (iter.hasNext()) {
+ currentNeighbour = ((Integer) iter.next()).intValue();
+
+ if (!posSet[currentNeighbour]) {
+ posSet[currentNeighbour] = true;
+
+ int holeDepth = NoOfChildren(currentNeighbour, addedNeighbours);
+
+ for (int j = 0; j < (holeDepth / 2); j++) {
+ outerPositionsOwners[(startPos) % outerPositionsOwners.length] = -3;
+ // free but it must not be used (add. space for tree-like struct.)
+ outerPositionsTaken[(startPos) % outerPositionsOwners.length] = (int) (theAngle / innerDeltaAngle);
+ startPos++;
+ startAngle += outerDeltaAngle;
+
+ if (startAngle > (2 * Math.PI))
+ startAngle -= (2 * Math.PI);
+ }
+
+ nodeView[currentNeighbour].setOffset(startX
+ + (Math.cos(startAngle) * outerRadius),
+ startY
+ - (Math.sin(startAngle) * outerRadius));
+ outerPositionsOwners[(startPos) % outerPositionsOwners.length] = currentNeighbour;
+ outerPositionsTaken[(startPos) % outerPositionsOwners.length] = (int) (theAngle / innerDeltaAngle);
+ startPos++;
+ startAngle += outerDeltaAngle;
+
+ if (startAngle > (2 * Math.PI))
+ startAngle -= (2 * Math.PI);
+
+ for (int j = 0; j < (holeDepth / 2); j++) {
+ outerPositionsOwners[(startPos) % outerPositionsOwners.length] = -3;
+ outerPositionsTaken[(startPos) % outerPositionsOwners.length] = (int) (theAngle / innerDeltaAngle);
+ startPos++;
+ startAngle += outerDeltaAngle;
+
+ if (startAngle > (2 * Math.PI))
+ startAngle -= (2 * Math.PI);
+ }
+ }
+ }
+ }
+
+ // laying out the rest of nodes
+ for (int i = 0; i < bc[compIndex].length; i++) {
+ iter = edgesFrom[bc[compIndex][i]].iterator();
+
+ int currentNeighbour;
+
+ while (iter.hasNext()) {
+ currentNeighbour = ((Integer) iter.next()).intValue();
+
+ if (!addedNeighbours.containsKey(new Integer(currentNeighbour))) {
+ continue;
+ }
+
+ pointX = nodeView[currentNeighbour].getOffset().getX();
+ pointY = nodeView[currentNeighbour].getOffset().getY();
+
+ theAngle = Math.asin((startY - pointY) / Math.sqrt(((pointX - startX) * (pointX
+ - startX))
+ + ((pointY - startY) * (pointY
+ - startY))));
+ theAngleHlp = Math.acos((pointX - startX) / Math.sqrt(((pointX - startX) * (pointX
+ - startX))
+ + ((pointY - startY) * (pointY
+ - startY))));
+
+ if (theAngleHlp > (Math.PI / 2))
+ theAngle = Math.PI - theAngle;
+
+ if (theAngle < 0)
+ theAngle += (2 * Math.PI);
+
+ for (int j = 0; j < posSet.length; j++)
+ depthPosSet[j] = posSet[j];
+
+ EachNodeHeight(currentNeighbour);
+
+ DFSSetPos(currentNeighbour, theAngle, outerRadius - innerCircleRadius);
+ }
+ }
+ }
+
+ /**
+ * Returns number of children of the specified node from outer circle.
+ * If number of children larger than 7 return 7.
+ * @param nodeID
+ * @param outerCircle
+ * @return
+ */
+ private int NoOfChildren(int nodeID, HashMap<Integer, Integer> outerCircle) {
+ int toReturn = 0;
+ Iterator iter = edgesFrom[nodeID].iterator();
+
+ while (iter.hasNext()) {
+ int currNeigh = ((Integer) iter.next()).intValue();
+
+ if (!posSet[currNeigh] && !outerCircle.containsKey(currNeigh))
+ toReturn++;
+ }
+
+ if (toReturn > 7)
+ return 7;
+
+ return toReturn;
+ }
+
+ /**
+ * Sort the nodes from biconnected component to get the best ordering in terms
+ * of tree-like neighbouring patterns
+ * @param icNodes - nodes from biconnected component
+ * @return
+ */
+ private int[] SortInnerCircle(int[] icNodes) {
+ LinkedList<Integer> greedyNodes = new LinkedList<Integer>();
+ LinkedList<Integer> modestNodes = new LinkedList<Integer>();
+
+ HashMap<Integer, Integer> forFunct = new HashMap<Integer, Integer>();
+
+ for (int i = 0; i < icNodes.length; i++)
+ forFunct.put(new Integer(icNodes[i]), new Integer(0));
+
+ for (int i = 0; i < icNodes.length; i++) {
+ int tmp = NoOfChildren(icNodes[i], forFunct);
+
+ if (tmp > 4)
+ greedyNodes.add(new Integer(icNodes[i]));
+ else
+ modestNodes.add(new Integer(icNodes[i]));
+ }
+
+ int[] toReturn = new int[icNodes.length];
+ int gNo = greedyNodes.size();
+ int mNo = modestNodes.size();
+ int deltaM;
+ int deltaG;
+
+ if (gNo == 0) {
+ deltaM = mNo;
+ deltaG = 0;
+ } else if (mNo == 0) {
+ deltaG = gNo;
+ deltaM = 0;
+ } else if (gNo > mNo) {
+ deltaM = 1;
+ deltaG = gNo / mNo;
+ } else {
+ deltaG = 1;
+ deltaM = mNo / gNo;
+ }
+
+ int x = 0;
+ Iterator iterM = modestNodes.iterator();
+ Iterator iterG = greedyNodes.iterator();
+
+ while (iterM.hasNext() && iterG.hasNext()) {
+ for (int i = 0; i < deltaG; i++)
+ toReturn[x++] = ((Integer) iterG.next()).intValue();
+
+ for (int i = 0; i < deltaM; i++)
+ toReturn[x++] = ((Integer) iterM.next()).intValue();
+ }
+
+ while (iterG.hasNext())
+ toReturn[x++] = ((Integer) iterG.next()).intValue();
+
+ while (iterM.hasNext())
+ toReturn[x++] = ((Integer) iterM.next()).intValue();
+
+ return toReturn;
+ }
+
+ /**
+ * Sort the nodes from biconnected component to get the best ordering in terms
+ * of minimizing inner circle crossings
+ * @param icNodes - nodes from biconnected component
+ * @return
+ */
+ private int[] ReduceInnerCircleCrossings1(int[] icNodes) {
+ int[] toReturn = new int[icNodes.length];
+
+ HashMap<Integer, Boolean> alreadySet = new HashMap<Integer, Boolean>();
+
+ for (int i = 0; i < icNodes.length; i++)
+ alreadySet.put(new Integer(icNodes[i]), new Boolean(false));
+
+ int x = 0;
+ int p = 0;
+ toReturn[0] = icNodes[0];
+ alreadySet.put(new Integer(toReturn[0]), new Boolean(true));
+
+ while (p < (icNodes.length - 1)) {
+// if ((p == x) && (p != 0))
+ //logger.debug("p = " + p + " x = " + x + " count = " + icNodes.length);
+
+ Iterator iter = edgesFrom[toReturn[p]].iterator();
+
+ while (iter.hasNext()) {
+ int neigh = ((Integer) iter.next()).intValue();
+
+ if (alreadySet.containsKey(new Integer(neigh))
+ && !alreadySet.get(new Integer(neigh)).booleanValue()) {
+ toReturn[x++] = neigh;
+ alreadySet.put(new Integer(neigh), new Boolean(true));
+ }
+ }
+
+ p++;
+ }
+
+ return toReturn;
+ }
+
+ /**
+ * Sort the nodes from biconnected component to get the best ordering in terms
+ * of minimizing inner circle crossings
+ * @param icNodes - nodes from biconnected component
+ * @return
+ */
+ private int[] ReduceInnerCircleCrossings(int[] icNodes) {
+ int[] toReturn = new int[icNodes.length];
+
+ HashMap<Integer, Boolean> alreadySet = new HashMap<Integer, Boolean>();
+ HashMap<Integer, Integer> nodeDegree = new HashMap<Integer, Integer>();
+
+ for (int i = 0; i < icNodes.length; i++) {
+ alreadySet.put(new Integer(icNodes[i]), new Boolean(false));
+ toReturn[i] = icNodes[i];
+ }
+
+ for (int i = 0; i < icNodes.length; i++) {
+ int degree = 0;
+ Iterator iter = edgesFrom[icNodes[i]].iterator();
+
+ while (iter.hasNext()) {
+ int neigh = ((Integer) iter.next()).intValue();
+
+ if (alreadySet.containsKey(new Integer(neigh)))
+ degree++;
+ }
+
+ nodeDegree.put(new Integer(icNodes[i]), new Integer(degree));
+ }
+
+ for (int i = 0; i < (toReturn.length - 1); i++) {
+ for (int j = i + 1; j < toReturn.length; j++) {
+ if (nodeDegree.get(new Integer(toReturn[i])) > nodeDegree.get(new Integer(toReturn[j]))) {
+ int tmp = toReturn[i];
+ toReturn[i] = toReturn[j];
+ toReturn[j] = tmp;
+ }
+ }
+ }
+
+ return toReturn;
+ }
+
+ /**
+ * Function traverses graph starting from the node from outer circle until
+ * it traverse all the nodes. When it comes along another biconnected component
+ * it sets it out on circle and calls SetOuterCircle() again. The main purpose of
+ * the function is setting the node positions of tree-like parts of graph.
+ * @param nodeID - ID of the node from which we start DFS
+ * @param theAngle - the angle at which we "enter" the node, using it we can calculate
+ * at which position to set the node
+ * @param theRadius - this will represent the distance between the parent of the node and
+ * the child in tree-like parts
+ */
+ private void DFSSetPos(int nodeID, double theAngle, double theRadius) {
+ if (node2BiComp.containsKey(new Integer(nodeID))
+ && !drawnBiComps[node2BiComp.get(new Integer(nodeID)).intValue()]) {
+ int comp = node2BiComp.get(new Integer(nodeID)).intValue();
+ double centerX = nodeView[nodeID].getOffset().getX();
+ double centerY = nodeView[nodeID].getOffset().getY();
+ double radius = (48 * bc[comp].length) / (2 * Math.PI);
+ double deltaAngle = (2 * Math.PI) / bc[comp].length;
+ double currAngle = theAngle - Math.PI - deltaAngle;
+
+ if (currAngle < 0)
+ currAngle += (2 * Math.PI);
+
+ centerX += (Math.cos(theAngle) * radius * 4.0);
+ centerY -= (Math.sin(theAngle) * radius * 4.0);
+
+ drawnBiComps[comp] = true;
+
+ // sorting nodes on inner circle
+ bc[comp] = SortInnerCircle(bc[comp]);
+
+ /*if (bc[comp].length > 20)
+ bc[comp] = ReduceInnerCircleCrossings(bc[comp]);*/
+ boolean oneAtLeast = false;
+
+ for (int i = 0; i < bc[comp].length; i++) {
+ if (posSet[bc[comp][i]])
+ continue;
+
+ nodeView[bc[comp][i]].setOffset(centerX + (Math.cos(currAngle) * radius),
+ centerY - (Math.sin(currAngle) * radius));
+ posSet[bc[comp][i]] = true;
+
+ oneAtLeast = true;
+ currAngle -= deltaAngle;
+
+ if (currAngle < 0)
+ currAngle += (2 * Math.PI);
+ }
+
+ if (oneAtLeast) {
+ nodeView[nodeID].setOffset(nodeView[nodeID].getOffset().getX()
+ + (Math.cos(theAngle) * 3 * radius),
+ nodeView[nodeID].getOffset().getY()
+ - (Math.sin(theAngle) * 3 * radius));
+
+ SetOuterCircle(comp, radius, centerX, centerY, nodeID);
+ }
+ } else {
+ Iterator iter = edgesFrom[nodeID].iterator();
+ int currentNeighbour;
+ double startAngle = theAngle + (Math.PI / 2);
+
+ if (startAngle > (2 * Math.PI))
+ startAngle -= (2 * Math.PI);
+
+ int neighboursCount = 0;
+ int min1 = 1000;
+ int min2 = 1000;
+ int max = -1;
+ int min1Id = -1;
+ int min2Id = -2;
+ int maxId = -3;
+ HashMap<Integer, Integer> tmp = new HashMap<Integer, Integer>();
+
+ while (iter.hasNext()) {
+ currentNeighbour = ((Integer) iter.next()).intValue();
+
+ if (!posSet[currentNeighbour] && !tmp.containsKey(new Integer(currentNeighbour))) {
+ neighboursCount++;
+ tmp.put(new Integer(currentNeighbour), new Integer(0));
+
+ if (nodeHeights.get(new Integer(currentNeighbour)).intValue() < min1) {
+ min2 = min1;
+ min2Id = min1Id;
+ min1 = nodeHeights.get(new Integer(currentNeighbour)).intValue();
+ min1Id = currentNeighbour;
+ } else if (nodeHeights.get(new Integer(currentNeighbour)).intValue() < min2) {
+ min2 = nodeHeights.get(new Integer(currentNeighbour)).intValue();
+ min2Id = currentNeighbour;
+ }
+
+ if (nodeHeights.get(new Integer(currentNeighbour)).intValue() >= max)//&& currentNeighbour != min2Id && currentNeighbour != min1Id)
+ {
+ max = nodeHeights.get(new Integer(currentNeighbour)).intValue();
+ maxId = currentNeighbour;
+ }
+ }
+ }
+
+ if (neighboursCount == 0)
+ return;
+
+ double deltaAngle = Math.PI / (neighboursCount + 1);
+
+ startAngle -= deltaAngle;
+
+ if (startAngle < 0)
+ startAngle += (2 * Math.PI);
+
+ double remStartAngle = startAngle;
+
+ if (neighboursCount > 2) {
+ deltaAngle = (2 * Math.PI) / neighboursCount;
+ startAngle = (theAngle + Math.PI) - ((3 * deltaAngle) / 2);
+
+ if (startAngle > (2 * Math.PI))
+ startAngle -= (2 * Math.PI);
+
+ remStartAngle = (theAngle + Math.PI) - (deltaAngle / 2);
+
+ if (remStartAngle > (2 * Math.PI))
+ remStartAngle -= (2 * Math.PI);
+ }
+
+ iter = edgesFrom[nodeID].iterator();
+
+ double r = 72;
+ double rTry;
+
+ if (((48 * neighboursCount) / (2 * Math.PI)) > r)
+ r = (48 * neighboursCount) / (2 * Math.PI);
+
+ rTry = r;
+
+ double hlp = 100.0;
+ double startX = nodeView[nodeID].getOffset().getX();
+ double startY = nodeView[nodeID].getOffset().getY();
+
+ if (neighboursCount > 2) {
+ nodeView[nodeID].setOffset(startX + (Math.cos(theAngle) * r * ((min2 + 1) % 100)),
+ startY - (Math.sin(theAngle) * r * ((min2 + 1) % 100)));
+ startX = nodeView[nodeID].getOffset().getX();
+ startY = nodeView[nodeID].getOffset().getY();
+
+ //logger.debug("theAngle = " + theAngle + ", startAngle = " + startAngle + ", remStartAngle = " + remStartAngle + ", deltaAngle = " + deltaAngle);
+ //logger.debug("min1Id = " + min1Id + ", min2Id" + min2Id + ", maxId" + maxId);
+ nodeView[min1Id].setOffset(startX + (Math.cos(remStartAngle) * r),
+ startY - (Math.sin(remStartAngle) * r));
+ nodeView[min2Id].setOffset(startX + (Math.cos(remStartAngle + deltaAngle) * r),
+ startY - (Math.sin(remStartAngle + deltaAngle) * r));
+
+ if (nodeHeights.get(new Integer(maxId)).intValue() > 8)
+ r = 256;
+
+ nodeView[maxId].setOffset(startX
+ + (Math.cos(remStartAngle
+ - ((neighboursCount / 2) * deltaAngle)) * r),
+ startY
+ - (Math.sin(remStartAngle
+ - ((neighboursCount / 2) * deltaAngle)) * r));
+ //logger.debug("Ugao za maxID "
+ // + (remStartAngle - ((neighboursCount / 2) * deltaAngle)));
+ }
+
+ tmp = new HashMap<Integer, Integer>();
+
+ while (iter.hasNext()) {
+ currentNeighbour = ((Integer) iter.next()).intValue();
+
+ if (!posSet[currentNeighbour] && !tmp.containsKey(new Integer(currentNeighbour))) {
+ if (nodeHeights.get(new Integer(currentNeighbour)).intValue() > 8)
+ r = 256;
+ else
+ r = rTry;
+
+ posSet[currentNeighbour] = true;
+ tmp.put(new Integer(currentNeighbour), new Integer(0));
+
+ if (((currentNeighbour != min1Id) && (currentNeighbour != min2Id)
+ && (currentNeighbour != maxId)) || (neighboursCount <= 2)) {
+ nodeView[currentNeighbour].setOffset(startX + (Math.cos(startAngle) * r),
+ startY - (Math.sin(startAngle) * r));
+
+ startAngle -= deltaAngle;
+
+ if (startAngle < 0)
+ startAngle += (2 * Math.PI);
+
+ if (((Math.abs(startAngle
+ - (remStartAngle - ((neighboursCount / 2) * deltaAngle))) < 0.0001)
+ || (Math.abs(startAngle
+ - (remStartAngle - ((neighboursCount / 2) * deltaAngle)
+ + (2 * Math.PI))) < 0.0001)) && (neighboursCount > 2)) {
+ startAngle -= deltaAngle;
+
+ if (startAngle < 0)
+ startAngle += (2 * Math.PI);
+ }
+ }
+ }
+ }
+
+ iter = edgesFrom[nodeID].iterator();
+
+ if (neighboursCount > 2) {
+ DFSSetPos(min1Id, remStartAngle, theRadius * Math.sin(deltaAngle / 2));
+ DFSSetPos(min2Id, remStartAngle + deltaAngle, theRadius * Math.sin(deltaAngle / 2));
+ DFSSetPos(maxId, remStartAngle - ((neighboursCount / 2) * deltaAngle),
+ theRadius * Math.sin(deltaAngle / 2));
+ hlp = remStartAngle;
+ remStartAngle -= deltaAngle;
+ }
+
+ while (iter.hasNext()) {
+ currentNeighbour = ((Integer) iter.next()).intValue();
+
+ if (tmp.containsKey(new Integer(currentNeighbour))) {
+ if (((currentNeighbour != min1Id) && (currentNeighbour != min2Id)
+ && (currentNeighbour != maxId)) || (neighboursCount <= 2)) {
+ DFSSetPos(currentNeighbour, remStartAngle,
+ theRadius * Math.sin(deltaAngle / 2));
+
+ remStartAngle -= deltaAngle;
+
+ if (((remStartAngle == (hlp - ((neighboursCount / 2) * deltaAngle)))
+ || (remStartAngle == (hlp - ((neighboursCount / 2) * deltaAngle)
+ + (2 * Math.PI)))) && (neighboursCount > 2))
+ startAngle -= deltaAngle;
+
+ if (remStartAngle < 0)
+ remStartAngle += (2 * Math.PI);
+ }
+ }
+ }
+ }
+ }
+
+ /**
+ * Heuristic function which estimates the number of nodes "after" the given node.
+ * Using it we can estimate the distance from this node to his children.
+ * @param nodeID - ID of given node
+ * @return
+ */
+ private int EachNodeHeight(int nodeID) {
+ Iterator iter = edgesFrom[nodeID].iterator();
+ int currentNeighbour;
+ int noOfChildren = 0;
+ HashMap<Integer, Integer> tmp = new HashMap<Integer, Integer>();
+
+ while (iter.hasNext()) {
+ currentNeighbour = ((Integer) iter.next()).intValue();
+
+ if (!depthPosSet[currentNeighbour] && !tmp.containsKey(new Integer(currentNeighbour))) {
+ depthPosSet[currentNeighbour] = true;
+ tmp.put(new Integer(currentNeighbour), new Integer(0));
+ }
+ }
+
+ iter = edgesFrom[nodeID].iterator();
+
+ while (iter.hasNext()) {
+ currentNeighbour = ((Integer) iter.next()).intValue();
+
+ if (tmp.containsKey(new Integer(currentNeighbour))) {
+ noOfChildren += EachNodeHeight(currentNeighbour);
+ }
+ }
+
+ if (nodeHeights.containsKey(new Integer(nodeID)))
+ nodeHeights.remove(new Integer(nodeID));
+
+ nodeHeights.put(new Integer(nodeID), new Integer(noOfChildren));
+
+ return (noOfChildren + 1);
+ }
+
+ /**
+ * Founds best positions for nodes from outer cicrle, according to inner circle.
+ * We avoid crossings of edges between inner and outer circle, and we want to minimize
+ * the length of that edges.
+ * @param idealPosition - according to position of neighbour node from inner circle
+ * @param outerPositionsTaken - array of availability of positions on second circle
+ * @param outerPositionsOwners - array of owners (from inner cicrle) of positions on second circle
+ * @param noOfPos - number of positions that we need
+ * @param innerCirclePos - owner (parent, neighbour from inner cicrle) of given node
+ * @param startX
+ * @param startY
+ * @param outerDeltaAngle
+ * @param outerRadius
+ * @param innerCSize
+ * @return
+ */
+ private int BestFreePositionsForAll(int idealPosition, int[] outerPositionsTaken,
+ int[] outerPositionsOwners, int noOfPos,
+ int innerCirclePos, double startX, double startY,
+ double outerDeltaAngle, double outerRadius, int innerCSize) {
+// for (int j = 0; j < outerPositionsTaken.length; j++)
+// logger.debug(outerPositionsTaken[j] + " ");
+
+// logger.debug("innerCircPos: " + innerCirclePos + ", noOfPos: " + noOfPos
+// + ", idealPos: " + idealPosition);
+
+ int startPos = idealPosition;
+
+ if (idealPosition < 0)
+ startPos += outerPositionsTaken.length;
+
+ int i = 0;
+ int alreadyFound = 0;
+ int startOfAlFound = -1;
+ boolean found = false;
+ boolean goDown = false;
+ boolean goUp = false;
+
+ while (!found && !(goUp && goDown)) {
+ //logger.debug(startPos + " ");
+ for (i = startPos;
+ (i < (startPos + noOfPos))
+ && (outerPositionsTaken[i % outerPositionsTaken.length] == -1); i++) {
+ }
+
+ if (i < (startPos + noOfPos)) {
+ if (((outerPositionsTaken[i % outerPositionsTaken.length] > innerCirclePos)
+ && ((outerPositionsTaken[i % outerPositionsTaken.length] - innerCirclePos) < (0.7 * innerCSize)))
+ || ((innerCirclePos - outerPositionsTaken[i % outerPositionsTaken.length]) > (0.7 * innerCSize))) {
+ alreadyFound = (i - startPos + outerPositionsTaken.length) % outerPositionsTaken.length;
+ startOfAlFound = startPos;
+ startPos -= (noOfPos - alreadyFound);
+
+ if (startPos < 0)
+ startPos += outerPositionsTaken.length;
+
+ goDown = true;
+ } else {
+ startPos = (i + 1) % outerPositionsTaken.length;
+ goUp = true;
+ }
+ } else
+ found = true;
+ }
+
+ if (goUp && goDown) {
+ i = startOfAlFound - 1;
+
+ int j = i - 1;
+ int count = 0;
+ //logger.debug(j + " ");
+
+ if (((outerPositionsTaken[i % outerPositionsTaken.length] > innerCirclePos)
+ && ((outerPositionsTaken[i % outerPositionsTaken.length] - innerCirclePos) < (0.7 * innerCSize)))
+ || ((innerCirclePos - outerPositionsTaken[i % outerPositionsTaken.length]) > (0.7 * innerCSize))) {
+ j--;
+ i--;
+ }
+
+ while (count < (noOfPos - alreadyFound)) {
+ //logger.debug(j + " ");
+
+ if (outerPositionsTaken[(j + outerPositionsTaken.length) % outerPositionsTaken.length] == -1) {
+ // move all for one place left
+ // logger.debug(" moving ");
+ if (outerPositionsOwners[(j + outerPositionsTaken.length) % outerPositionsTaken.length] == -2) {
+ //logger.debug("BUUUUUUUUUUUUUUUUUUU");
+
+ return -1;
+ }
+
+ for (int k = j; k < (i - count); k++) {
+ if (outerPositionsOwners[(k + 1 + outerPositionsTaken.length) % outerPositionsTaken.length] > 0)
+ nodeView[outerPositionsOwners[(k + 1 + outerPositionsTaken.length) % outerPositionsTaken.length]]
+ .setOffset(startX + (Math.cos(outerDeltaAngle * k) * outerRadius),
+ startY - (Math.sin(outerDeltaAngle * k) * outerRadius));
+
+ outerPositionsOwners[(k + outerPositionsTaken.length) % outerPositionsTaken.length] = outerPositionsOwners[(k + 1 + outerPositionsTaken.length) % outerPositionsTaken.length];
+ outerPositionsTaken[(k + outerPositionsTaken.length) % outerPositionsTaken.length] = outerPositionsTaken[(k + 1 + outerPositionsTaken.length) % outerPositionsTaken.length];
+ }
+
+ count++;
+ }
+
+ j--;
+ }
+
+ startPos = (i - count + 1 + outerPositionsOwners.length) % outerPositionsOwners.length;
+ }
+
+ /* for (i = startPos; i < startPos + noOfPos; i++)
+ {
+ outerPositionsTaken[i % outerPositionsTaken.length] = innerCirclePos;
+ }*/
+ return startPos;
+ }
+
+ private int BestFreePosition(int idealPosition, boolean[] outerPositionsTaken) {
+ //for (int i = 0; i < outerPositionsTaken.length; i++)
+ //logger.debug(outerPositionsTaken[i] + " ");
+ //logger.debug();
+ //logger.debug(idealPosition);
+ int startPosition = idealPosition;
+
+ if (idealPosition < 0)
+ startPosition = idealPosition % outerPositionsTaken.length;
+
+ int move = 0;
+
+ while (move < ((outerPositionsTaken.length / 2) + 1)) {
+ if (!outerPositionsTaken[(startPosition + move) % outerPositionsTaken.length]) {
+ outerPositionsTaken[(startPosition + move) % outerPositionsTaken.length] = true;
+
+ //logger.debug((startPosition + move) % outerPositionsTaken.length);
+ return (startPosition + move) % outerPositionsTaken.length;
+ }
+
+ if (!outerPositionsTaken[(startPosition - move) % outerPositionsTaken.length]) {
+ outerPositionsTaken[(startPosition - move) % outerPositionsTaken.length] = true;
+
+ // logger.debug((startPosition - move) % outerPositionsTaken.length);
+ return (startPosition - move) % outerPositionsTaken.length;
+ }
+
+ move++;
+ }
+
+ return -1;
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void halt() {
+ canceled = true;
+ }
+
+ protected void initialize_properties() {
+ layoutProperties.add(new Tunable("nodeHorizontalSpacing",
+ "Horizontal spacing between nodes", Tunable.INTEGER,
+ new Integer(64)));
+ layoutProperties.add(new Tunable("nodeVerticalSpacing", "Vertical spacing between nodes",
+ Tunable.INTEGER, new Integer(32)));
+
+ layoutProperties.add(new Tunable("leftEdge", "Left edge margin", Tunable.INTEGER,
+ new Integer(32)));
+ layoutProperties.add(new Tunable("topEdge", "Top edge margin", Tunable.INTEGER,
+ new Integer(32)));
+ layoutProperties.add(new Tunable("rightMargin", "Right edge margin", Tunable.INTEGER,
+ new Integer(1000)));
+ // We've now set all of our tunables, so we can read the property
+ // file now and adjust as appropriate
+ layoutProperties.initializeProperties();
+
+ // Finally, update everything. We need to do this to update
+ // any of our values based on what we read from the property file
+ updateSettings(true);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void updateSettings() {
+ updateSettings(false);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param tm DOCUMENT ME!
+ */
+ public void setTaskMonitor(TaskMonitor tm) {
+ taskMonitor = tm;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param force DOCUMENT ME!
+ */
+ public void updateSettings(boolean force) {
+ layoutProperties.updateValues();
+
+ Tunable t = layoutProperties.get("nodeHorizontalSpacing");
+ if ((t != null) && (t.valueChanged() || force)) {
+ nodeHorizontalSpacing = ((Integer) t.getValue()).intValue();
+ if (t.valueChanged())
+ layoutProperties.setProperty(t.getName(), t.getValue().toString());
+ }
+
+ t = layoutProperties.get("nodeVerticalSpacing");
+ if ((t != null) && (t.valueChanged() || force)) {
+ nodeVerticalSpacing = ((Integer) t.getValue()).intValue();
+ if (t.valueChanged())
+ layoutProperties.setProperty(t.getName(), t.getValue().toString());
+ }
+
+ t = layoutProperties.get("leftEdge");
+ if ((t != null) && (t.valueChanged() || force)) {
+ leftEdge = ((Integer) t.getValue()).intValue();
+ if (t.valueChanged())
+ layoutProperties.setProperty(t.getName(), t.getValue().toString());
+ }
+
+ t = layoutProperties.get("topEdge");
+ if ((t != null) && (t.valueChanged() || force)) {
+ topEdge = ((Integer) t.getValue()).intValue();
+ if (t.valueChanged())
+ layoutProperties.setProperty(t.getName(), t.getValue().toString());
+ }
+
+ t = layoutProperties.get("rightMargin");
+ if ((t != null) && (t.valueChanged() || force)) {
+ rightMargin = ((Integer) t.getValue()).intValue();
+ if (t.valueChanged())
+ layoutProperties.setProperty(t.getName(), t.getValue().toString());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public JPanel getSettingsPanel() {
+ JPanel panel = new JPanel(new GridLayout(0, 1));
+ panel.add(layoutProperties.getTunablePanel());
+
+ return panel;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getTitle() {
+ return new String("Circular Layout");
+ }
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/algorithms/force/ForceDirectedLayout.java b/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/algorithms/force/ForceDirectedLayout.java
new file mode 100644
index 0000000..87cb8a6
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/algorithms/force/ForceDirectedLayout.java
@@ -0,0 +1,410 @@
+
+/*
+ Copyright (c) 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package csplugins.layout.algorithms.force;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+
+import cytoscape.layout.Tunable;
+import cytoscape.layout.LayoutProperties;
+import cytoscape.logger.CyLogger;
+import csplugins.layout.LayoutPartition;
+import csplugins.layout.LayoutEdge;
+import csplugins.layout.LayoutNode;
+import csplugins.layout.EdgeWeighter;
+import csplugins.layout.algorithms.graphPartition.*;
+
+import cytoscape.view.CyNetworkView;
+import cytoscape.data.CyAttributes;
+import ding.view.DGraphView;
+
+import java.awt.GridLayout;
+import java.awt.Dimension;
+
+import java.util.*;
+
+import javax.swing.JPanel;
+
+import prefuse.util.force.*;
+
+/**
+ * This class wraps the Prefuse force-directed layout algorithm.
+ * See {@link http://prefuse.org} for more detail.
+ */
+public class ForceDirectedLayout extends AbstractGraphPartition
+{
+ private ForceSimulator m_fsim;
+
+ private int numIterations = 100;
+ double defaultSpringCoefficient = 1e-4f;
+ double defaultSpringLength = 50;
+ double defaultNodeMass = 3.0;
+ boolean deterministic = false;
+
+ /**
+ * Value to set for doing unweighted layouts
+ */
+ public static final String UNWEIGHTEDATTRIBUTE = "(unweighted)";
+
+ /**
+ * Integrators
+ */
+ String[] integratorArray = {"Runge-Kutta", "Euler", "Backward Euler"};
+
+ private boolean supportWeights = true;
+ private LayoutProperties layoutProperties;
+ Map<LayoutNode,ForceItem> forceItems;
+
+ private Integrator integrator = null;
+
+ public ForceDirectedLayout() {
+ super();
+
+ logger = CyLogger.getLogger(ForceDirectedLayout.class);
+ // logger.setDebug(true);
+
+ if (edgeWeighter == null)
+ edgeWeighter = new EdgeWeighter();
+
+ m_fsim = new ForceSimulator();
+ m_fsim.addForce(new NBodyForce());
+ m_fsim.addForce(new SpringForce());
+ m_fsim.addForce(new DragForce());
+
+ layoutProperties = new LayoutProperties(getName());
+ initialize_properties();
+ forceItems = new HashMap<LayoutNode,ForceItem>();
+ }
+
+ public String getName() {
+ return "force-directed";
+ }
+
+ public String toString() {
+ return "Force-Directed Layout";
+ }
+
+ protected void initialize_local() {
+ }
+
+
+ public void layoutPartition(LayoutPartition part) {
+ Dimension initialLocation = null;
+ // logger.debug("layoutPartition: "+part.getEdgeList().size()+" edges");
+ // Calculate our edge weights
+ part.calculateEdgeWeights();
+ // logger.debug("layoutPartition: "+part.getEdgeList().size()+" edges after calculateEdgeWeights");
+
+ m_fsim = new ForceSimulator();
+ m_fsim.addForce(new NBodyForce());
+ m_fsim.addForce(new SpringForce());
+ m_fsim.addForce(new DragForce());
+
+ forceItems.clear();
+
+ List<LayoutNode> nodeList = part.getNodeList();
+ List<LayoutEdge> edgeList = part.getEdgeList();
+
+ if (deterministic) {
+ Collections.sort(nodeList);
+ Collections.sort(edgeList);
+ }
+
+ // initialize nodes
+ for (LayoutNode ln: nodeList) {
+ if ( !forceItems.containsKey(ln) )
+ forceItems.put(ln, new ForceItem());
+ ForceItem fitem = forceItems.get(ln);
+ fitem.mass = getMassValue(ln);
+ fitem.location[0] = 0f;
+ fitem.location[1] = 0f;
+ m_fsim.addItem(fitem);
+ }
+
+ // initialize edges
+ for (LayoutEdge e: edgeList) {
+ LayoutNode n1 = e.getSource();
+ ForceItem f1 = forceItems.get(n1);
+ LayoutNode n2 = e.getTarget();
+ ForceItem f2 = forceItems.get(n2);
+ if ( f1 == null || f2 == null )
+ continue;
+ // logger.debug("Adding edge "+e+" with spring coeffficient = "+getSpringCoefficient(e)+" and length "+getSpringLength(e));
+ m_fsim.addSpring(f1, f2, getSpringCoefficient(e), getSpringLength(e));
+ }
+
+ // setTaskStatus(5); // This is a rough approximation, but probably good enough
+ if (taskMonitor != null) {
+ taskMonitor.setStatus("Initializing partition "+part.getPartitionNumber());
+ }
+
+ // Figure out our starting point
+ if (selectedOnly) {
+ initialLocation = part.getAverageLocation();
+ }
+
+ // perform layout
+ long timestep = 1000L;
+ for ( int i = 0; i < numIterations && !canceled; i++ ) {
+ timestep *= (1.0 - i/(double)numIterations);
+ long step = timestep+50;
+ m_fsim.runSimulator(step);
+ setTaskStatus((int)(((double)i/(double)numIterations)*90.+5));
+ }
+
+ // update positions
+ part.resetNodes(); // reset the nodes so we get the new average location
+ for (LayoutNode ln: part.getNodeList()) {
+ if (!ln.isLocked()) {
+ ForceItem fitem = forceItems.get(ln);
+ ln.setX(fitem.location[0]);
+ ln.setY(fitem.location[1]);
+ part.moveNodeToLocation(ln);
+ }
+ }
+ // Not quite done, yet. If we're only laying out selected nodes, we need
+ // to migrate the selected nodes back to their starting position
+ if (selectedOnly) {
+ double xDelta = 0.0;
+ double yDelta = 0.0;
+ Dimension finalLocation = part.getAverageLocation();
+ xDelta = finalLocation.getWidth() - initialLocation.getWidth();
+ yDelta = finalLocation.getHeight() - initialLocation.getHeight();
+ for (LayoutNode v: part.getNodeList()) {
+ if (!v.isLocked()) {
+ v.decrement(xDelta, yDelta);
+ part.moveNodeToLocation(v);
+ }
+ }
+ }
+ }
+
+ /**
+ * Get the mass value associated with the given node. Subclasses should
+ * override this method to perform custom mass assignment.
+ * @param n the node for which to compute the mass value
+ * @return the mass value for the node. By default, all items are given
+ * a mass value of 1.0.
+ */
+ protected float getMassValue(LayoutNode n) {
+ return (float)defaultNodeMass;
+ }
+
+ /**
+ * Get the spring length for the given edge. Subclasses should
+ * override this method to perform custom spring length assignment.
+ * @param e the edge for which to compute the spring length
+ * @return the spring length for the edge. A return value of
+ * -1 means to ignore this method and use the global default.
+ */
+ protected float getSpringLength(LayoutEdge e) {
+ double weight = e.getWeight();
+ return (float)(defaultSpringLength/weight);
+ }
+
+ /**
+ * Get the spring coefficient for the given edge, which controls the
+ * tension or strength of the spring. Subclasses should
+ * override this method to perform custom spring tension assignment.
+ * @param e the edge for which to compute the spring coefficient.
+ * @return the spring coefficient for the edge. A return value of
+ * -1 means to ignore this method and use the global default.
+ */
+ protected float getSpringCoefficient(LayoutEdge e) {
+ return (float)defaultSpringCoefficient;
+ }
+
+ /**
+ * Return information about our algorithm
+ */
+ public boolean supportsSelectedOnly() {
+ return true;
+ }
+
+ public byte[] supportsEdgeAttributes() {
+ if (!supportWeights)
+ return null;
+ byte[] attrs = { CyAttributes.TYPE_INTEGER, CyAttributes.TYPE_FLOATING };
+
+ return attrs;
+ }
+
+ public List getInitialAttributeList() {
+ ArrayList list = new ArrayList();
+ list.add(UNWEIGHTEDATTRIBUTE);
+
+ return list;
+ }
+
+
+ protected void initialize_properties() {
+
+ layoutProperties.add(new Tunable("standard", "Standard settings",
+ Tunable.GROUP, new Integer(2)));
+
+ layoutProperties.add(new Tunable("partition", "Partition graph before layout",
+ Tunable.BOOLEAN, new Boolean(true)));
+
+ layoutProperties.add(new Tunable("selected_only", "Only layout selected nodes",
+ Tunable.BOOLEAN, new Boolean(false)));
+
+ edgeWeighter.getWeightTunables(layoutProperties, getInitialAttributeList());
+
+ layoutProperties.add(new Tunable("force_alg_settings", "Algorithm settings",
+ Tunable.GROUP, new Integer(6)));
+
+ layoutProperties.add(new Tunable("defaultSpringCoefficient", "Default Spring Coefficient",
+ Tunable.DOUBLE, new Double(defaultSpringCoefficient)));
+
+ layoutProperties.add(new Tunable("defaultSpringLength", "Default Spring Length",
+ Tunable.DOUBLE, new Double(defaultSpringLength)));
+
+ layoutProperties.add(new Tunable("defaultNodeMass", "Default Node Mass",
+ Tunable.DOUBLE, new Double(defaultNodeMass)));
+
+ layoutProperties.add(new Tunable("numIterations", "Number of Iterations",
+ Tunable.INTEGER, new Integer(numIterations)));
+
+ layoutProperties.add(new Tunable("deterministic", "Force deterministic layouts (slower)",
+ Tunable.BOOLEAN, new Boolean(false)));
+
+// layoutProperties.add(new Tunable("integrator", "Integration algorithm to use",
+// Tunable.LIST, new Integer(0),
+// (Object) integratorArray, (Object) null, 0));
+
+ // We've now set all of our tunables, so we can read the property
+ // file now and adjust as appropriate
+ layoutProperties.initializeProperties();
+
+ // Finally, update everything. We need to do this to update
+ // any of our values based on what we read from the property file
+ updateSettings(true);
+ }
+
+ public void updateSettings() {
+ updateSettings(false);
+ }
+
+ public void updateSettings(boolean force) {
+ layoutProperties.updateValues();
+
+ Tunable t = layoutProperties.get("selected_only");
+ if ((t != null) && (t.valueChanged() || force)) {
+ selectedOnly = ((Boolean) t.getValue()).booleanValue();
+ if (t.valueChanged())
+ layoutProperties.setProperty(t.getName(), t.getValue().toString());
+ }
+
+ t = layoutProperties.get("partition");
+ if ((t != null) && (t.valueChanged() || force)) {
+ setPartition(t.getValue().toString());
+ if (t.valueChanged())
+ layoutProperties.setProperty(t.getName(), t.getValue().toString());
+ }
+
+ t = layoutProperties.get("defaultSpringCoefficient");
+ if ((t != null) && (t.valueChanged() || force)) {
+ defaultSpringCoefficient = ((Double) t.getValue()).doubleValue();
+ if (t.valueChanged())
+ layoutProperties.setProperty(t.getName(), t.getValue().toString());
+ }
+
+ t = layoutProperties.get("defaultSpringLength");
+ if ((t != null) && (t.valueChanged() || force)) {
+ defaultSpringLength = ((Double) t.getValue()).doubleValue();
+ if (t.valueChanged())
+ layoutProperties.setProperty(t.getName(), t.getValue().toString());
+ }
+
+ t = layoutProperties.get("defaultNodeMass");
+ if ((t != null) && (t.valueChanged() || force)) {
+ defaultNodeMass = ((Double) t.getValue()).doubleValue();
+ if (t.valueChanged())
+ layoutProperties.setProperty(t.getName(), t.getValue().toString());
+ }
+
+ t = layoutProperties.get("numIterations");
+ if ((t != null) && (t.valueChanged() || force)) {
+ numIterations = ((Integer) t.getValue()).intValue();
+ if (t.valueChanged())
+ layoutProperties.setProperty(t.getName(), t.getValue().toString());
+ }
+
+
+ t = layoutProperties.get("deterministic");
+ if ((t != null) && (t.valueChanged() || force)) {
+ deterministic = ((Boolean) t.getValue()).booleanValue();
+ if (t.valueChanged())
+ layoutProperties.setProperty(t.getName(), t.getValue().toString());
+ }
+
+
+ integrator = new RungeKuttaIntegrator();
+ /*
+ t = layoutProperties.get("integrator");
+ if ((t != null) && (t.valueChanged() || force)) {
+ if (t.valueChanged())
+ layoutProperties.setProperty(t.getName(), t.getValue().toString());
+ if (((Integer) t.getValue()).intValue() == 0)
+ integrator = new RungeKuttaIntegrator();
+ else if (((Integer) t.getValue()).intValue() == 1)
+ integrator = new EulerIntegrator();
+ else if (((Integer) t.getValue()).intValue() == 2)
+ integrator = new BackwardEulerIntegrator();
+ else
+ return;
+ m_fsim.setIntegrator(integrator);
+ }
+ */
+
+
+
+ edgeWeighter.updateSettings(layoutProperties, force);
+ }
+
+ public LayoutProperties getSettings() {
+ return layoutProperties;
+ }
+
+ public JPanel getSettingsPanel() {
+ // JPanel panel = new JPanel(new GridLayout(0, 1));
+ // panel.add(layoutProperties.getTunablePanel());
+ // return panel;
+ return layoutProperties.getTunablePanel();
+
+ }
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/algorithms/graphPartition/AbstractGraphPartition.java b/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/algorithms/graphPartition/AbstractGraphPartition.java
new file mode 100644
index 0000000..9d98c71
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/algorithms/graphPartition/AbstractGraphPartition.java
@@ -0,0 +1,468 @@
+/* vim: set ts=2: */
+/**
+* Copyright (C) Gerardo Huck, 2010
+*
+* This program is free software: you can redistribute it and/or modify
+* it under the terms of the GNU Lesser General Public License as published
+* by the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+*
+* This program is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU Lesser General Public License for more details.
+*
+* You should have received a copy of the GNU Lesser General Public License
+* along with this program. If not, see <http://www.gnu.org/licenses/>.
+*
+*/
+
+
+/**
+ * It was modified as part of Google Summer of Code 2010.
+ * Mentor: Mike Smoot
+ * @author <a href="mailto:gerardohuck .at. gmail .dot. com">Gerardo Huck</a>
+ * @version 0.1
+ */
+
+
+package csplugins.layout.algorithms.graphPartition;
+
+import cern.colt.list.*;
+
+import cern.colt.map.*;
+
+import csplugins.layout.LayoutNode;
+import csplugins.layout.LayoutLabelNodeImpl;
+import csplugins.layout.LayoutPartition;
+import csplugins.layout.LayoutLabelPartition;
+import csplugins.layout.EdgeWeighter;
+
+import cytoscape.layout.Tunable;
+import cytoscape.layout.LayoutProperties;
+import cytoscape.plugin.CytoscapePlugin;
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import cytoscape.CyNode;
+import cytoscape.layout.AbstractLayout;
+import cytoscape.data.CyAttributes;
+import cytoscape.logger.CyLogger;
+import cytoscape.task.*;
+import cytoscape.view.CyNetworkView;
+
+import giny.model.*;
+
+import java.lang.Throwable;
+import java.util.*;
+import javax.swing.JOptionPane;
+import java.awt.Dimension;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ComponentListener;
+import java.awt.event.ComponentEvent;
+
+enum LayoutTypes {
+ NODE("Nodes Only"),
+ LABEL("Labels Only"),
+ BOTH("Both Nodes and Labels");
+
+ private String name;
+ private LayoutTypes(String str) { name=str; }
+ public String toString() { return name; }
+}
+
+
+/**
+ * An abstract class that handles the partitioning of graphs so that
+ * the partitions will be laid out individually.
+ */
+public abstract class AbstractGraphPartition extends AbstractLayout implements ActionListener {
+ double incr = 100;
+ protected List <LayoutPartition> partitionList = null;
+ protected EdgeWeighter edgeWeighter = null;
+ protected boolean singlePartition = false;
+ protected CyLogger logger = CyLogger.getLogger(AbstractGraphPartition.class);
+
+ /**
+ * Which kinf of layout are we going to perform
+ */
+ protected LayoutTypes layoutType = LayoutTypes.NODE;
+
+ /**
+ * Whether Labels should be repositioned in their default positions
+ */
+ protected boolean resetPosition = false;
+
+ /**
+ * Coefficient to determine label edge weights
+ */
+ protected double weightCoefficient = 10.0;
+
+
+ static LayoutTypes[] layoutChoices = {LayoutTypes.NODE,
+ LayoutTypes.LABEL,
+ LayoutTypes.BOTH};
+
+
+ // Information for taskMonitor
+ double current_start = 0; // Starting node number
+ double current_size = 0; // Partition size
+ double total_nodes = 0; // Total number of nodes
+
+ /**
+ * Creates a new AbstractGraphPartition object.
+ */
+ public AbstractGraphPartition() {
+ super();
+
+ }
+
+ /**
+ * Override this method and layout the LayoutPartion just
+ * like you would a NetworkView.
+ *
+ * @param partition The LayoutPartion to be laid out.
+ */
+ public abstract void layoutPartition(LayoutPartition partition);
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean supportsSelectedOnly() {
+ return true;
+ }
+
+ /**
+ * If overridden by a subclass to return true, before calling to
+ * layoutPartition mathod, fake nodes will be created to represent label
+ * positions, and labels will be placed acordingly.
+ *
+ * It is an easy way of creating label layout algorithms.
+ *
+ * For this to work fine with labels, weights should be supported.
+ *
+ * @return Whether the layout algorithm supports label layout.
+ */
+ public boolean supportsLabelLayout() {
+ return false;
+ }
+
+
+ /**
+ * Sets the singlePartition flag, which disables partitioning. This
+ * can be used by users who do not want to partition their graph for
+ * some reason.
+ *
+ * @param flag if false, no paritioning will be done
+ */
+ public void setPartition(boolean flag) {
+ if (flag)
+ this.singlePartition = false;
+ else
+ this.singlePartition = true;
+ }
+
+ /**
+ * Sets the singlePartition flag, which disables partitioning. This
+ * can be used by users who do not want to partition their graph for
+ * some reason.
+ *
+ * @param value if "false", no paritioning will be done
+ */
+ public void setPartition(String value) {
+ Boolean val = new Boolean(value);
+ setPartition(val.booleanValue());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param percent The percentage of completion for this partition
+ */
+ protected void setTaskStatus(int percent) {
+ if (taskMonitor != null) {
+ // Calculate the nodes done for this partition
+ double nodesDone = current_size*(double)percent/100.;
+ // Calculate the percent done overall
+ double pDone = ((nodesDone+current_start)/total_nodes)*100.;
+ taskMonitor.setPercentCompleted((int)pDone);
+ taskMonitor.setStatus("Completed " + (int)pDone + "%");
+ }
+ }
+
+ /**
+ * AbstractGraphPartitionLayout implements the construct method
+ * and calls layoutPartition for each partition.
+ */
+ public void construct() {
+ initialize();
+
+ if (edgeWeighter != null)
+ edgeWeighter.reset();
+
+ // Depending on whether we are partitioned or not,
+ // we use different initialization. Note that if the user only wants
+ // to lay out selected nodes, partitioning becomes a very bad idea!
+ if (selectedOnly || singlePartition) {
+
+ // We still use the partition abstraction, even if we're
+ // not partitioning. This makes the code further down
+ // much cleaner
+ LayoutPartition partition = new LayoutPartition(network, networkView, selectedOnly, edgeWeighter);
+ partitionList = new ArrayList(1);
+ partitionList.add(partition);
+
+ } else if (staticNodes != null && staticNodes.size() > 0) {
+
+ // Someone has programmatically locked a set of nodes -- construct
+ // the list of unlocked nodes
+ List<CyNode> unlockedNodes = new ArrayList();
+ for (CyNode node: (List<CyNode>)network.nodesList()) {
+ if (!isLocked(networkView.getNodeView(node.getRootGraphIndex()))) {
+ unlockedNodes.add(node);
+ }
+ }
+ LayoutPartition partition = new LayoutPartition(network, networkView, unlockedNodes, edgeWeighter);
+ partitionList = new ArrayList(1);
+ partitionList.add(partition);
+
+ } else {
+ partitionList = LayoutPartition.partition(network, networkView, false, edgeWeighter);
+ }
+
+ total_nodes = network.getNodeCount();
+ // logger.info("TOTAL NODES: " + total_nodes);
+
+ current_start = 0;
+
+ // Set up offsets -- we start with the overall min and max
+ double xStart = (partitionList.get(0)).getMinX();
+ double yStart = (partitionList.get(0)).getMinY();
+
+ for (LayoutPartition part: partitionList) {
+ xStart = Math.min(xStart, part.getMinX());
+ yStart = Math.min(yStart, part.getMinY());
+ }
+
+ double next_x_start = xStart;
+ double next_y_start = yStart;
+ double current_max_y = 0;
+
+ double max_dimensions = Math.sqrt((double) network.getNodeCount());
+ // give each node room
+ max_dimensions *= incr;
+ max_dimensions += xStart;
+
+ for (LayoutPartition partition: partitionList) {
+ if (canceled) break;
+ // get the partition
+ current_size = (double)partition.size();
+ // logger.info("Partition #"+partition.getPartitionNumber()+" has "+current_size+" nodes");
+ setTaskStatus(1);
+
+ // Partitions Requiring Layout
+ if (partition.nodeCount() >= 1) { // LABEL
+ try {
+ layoutSinglePartition(partition);
+ } catch (OutOfMemoryError _e) {
+ System.gc();
+ logger.error("Layout algorithm failed: Out of memory");
+ return;
+ } catch (Exception _e) {
+ logger.error("Layout algorithm failed: ", (Throwable)_e);
+ return;
+ }
+
+ if (!selectedOnly && !singlePartition) {
+ // logger.debug("Offsetting partition #"+partition.getPartitionNumber()+" to "+next_x_start+", "+next_y_start);
+ // OFFSET
+ partition.offset(next_x_start, next_y_start);
+ }
+
+ // single nodes
+ } else if ( partition.nodeCount() == 1 ) { // TODO: do something with this!!!
+ // Reset our bounds
+ partition.resetNodes();
+
+ // Single node -- get it
+ LayoutNode node = (LayoutNode) partition.getNodeList().get(0);
+ node.setLocation(next_x_start, next_y_start);
+ partition.moveNodeToLocation(node);
+ } else {
+ logger.info("No nodes in partition "+partition.getPartitionNumber()+" -- skipping");
+ continue;
+ }
+
+ double last_max_x = partition.getMaxX();
+ double last_max_y = partition.getMaxY();
+
+ if (last_max_y > current_max_y) {
+ current_max_y = last_max_y;
+ }
+
+ if (last_max_x > max_dimensions) {
+ next_x_start = xStart;
+ next_y_start = current_max_y;
+ next_y_start += incr;
+ } else {
+ next_x_start = last_max_x;
+ next_x_start += incr;
+ }
+
+ setTaskStatus( 100 );
+ current_start += current_size;
+ }
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ */
+ protected void layoutSinglePartition(LayoutPartition partition){
+
+ if(supportsLabelLayout() && layoutType != LayoutTypes.NODE ) {
+
+ Dimension initialLocation = null;
+
+ if (canceled)
+ return;
+
+ Boolean moveNodes;
+
+ if (layoutType == LayoutTypes.BOTH)
+ moveNodes = true;
+ else
+ moveNodes = false;
+
+ // Create new Label partition
+ LayoutLabelPartition newPartition = new LayoutLabelPartition(partition,
+ weightCoefficient,
+ moveNodes,
+ selectedOnly);
+
+ // logger.info("New partition succesfully created!");
+
+ if (canceled)
+ return;
+
+ // Layout the new partition using the parent class layout algorithm
+ layoutPartition(newPartition);
+
+ if (canceled)
+ return;
+
+ // make sure nodes are where they should be
+ for(LayoutNode node: newPartition.getLabelToParentMap().values() ) {
+
+ if (canceled)
+ return;
+
+ node.moveToLocation();
+ // logger.info( node.toString() );
+ }
+
+ // make sure that all labels are where they should be
+ for(LayoutLabelNodeImpl node: newPartition.getLabelNodes() ) {
+
+ if (canceled)
+ return;
+
+ node.moveToLocation();
+ // logger.info( node.toString() );
+ }
+
+ taskMonitor.setStatus("Updating Display...");
+
+ // redraw the network so that the new label positions are visible
+ networkView.updateView();
+ networkView.redrawGraph(true, true);
+
+ } else { // normal (non-label) layout
+
+ layoutPartition(partition);
+ }
+
+ }
+
+ /**
+ * Adds the necessary tunables to control the label layout.
+ */
+ public void getLabelTunables(LayoutProperties layoutProperties) {
+
+ layoutProperties.add(new Tunable("labels_settings",
+ "General Layout Settings",
+ Tunable.GROUP, new Integer(4)));
+
+ layoutProperties.add(new Tunable("layout_type",
+ "Which elements to layout",
+ Tunable.LIST, new Integer(0),
+ (Object) layoutChoices, (Object) null, 0));
+
+ layoutProperties.add(new Tunable("resetSelectedLabelsButton",
+ "(Affects only selected nodes)",
+ Tunable.BUTTON, "Reset Label Positions", this, null, 0));
+
+ layoutProperties.add(new Tunable("resetAllLabelsButton",
+ "(Affects all nodes)",
+ Tunable.BUTTON, "Reset Label Positions", this, null, 0));
+
+ layoutProperties.add(new Tunable("weightCoefficient",
+ "Weight coefficient",
+ Tunable.DOUBLE, new Double(weightCoefficient)));
+ }
+
+ /**
+ * Update our tunable settings
+ *
+ * @param layoutProperties the LayoutProperties handler for this layout
+ * @param force whether or not to force the update
+ */
+ public void updateSettings(LayoutProperties layoutProperties, boolean force) {
+
+ Tunable t = layoutProperties.get("layout_type");
+ if ((t != null) && (t.valueChanged() || force)) {
+ layoutType = layoutChoices[((Integer) t.getValue()).intValue()];
+ }
+
+ t = layoutProperties.get("weightCoefficient");
+ if ((t != null) && (t.valueChanged() || force))
+ weightCoefficient = ((Double) t.getValue()).doubleValue();
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ String command = e.getActionCommand();
+
+ if (command.equals("resetSelectedLabelsButton")) {
+
+ this.networkView = Cytoscape.getCurrentNetworkView();
+ this.network = networkView.getNetwork();
+
+ boolean oldSelectedOnly = selectedOnly;
+ selectedOnly = true;
+
+ // reset label positions
+ resetLabelPositions();
+
+ selectedOnly = oldSelectedOnly;
+ }
+
+ if (command.equals("resetAllLabelsButton")) {
+
+ this.networkView = Cytoscape.getCurrentNetworkView();
+ this.network = networkView.getNetwork();
+
+ boolean oldSelectedOnly = selectedOnly;
+ selectedOnly = false;
+
+ // reset label positions
+ resetLabelPositions();
+
+ selectedOnly = oldSelectedOnly;
+ }
+
+ }
+
+
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/algorithms/graphPartition/AttributeCircleLayout.java b/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/algorithms/graphPartition/AttributeCircleLayout.java
new file mode 100644
index 0000000..ffbd37d
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/algorithms/graphPartition/AttributeCircleLayout.java
@@ -0,0 +1,344 @@
+/* vim: set ts=2: */
+/**
+ * Copyright (c) 2006 The Regents of the University of California.
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ * notice, this list of conditions, and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above
+ * copyright notice, this list of conditions, and the following
+ * disclaimer in the documentation and/or other materials provided
+ * with the distribution.
+ * 3. Redistributions must acknowledge that this software was
+ * originally developed by the UCSF Computer Graphics Laboratory
+ * under support by the NIH National Center for Research Resources,
+ * grant P41-RR01081.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY
+ * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+ * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+ * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
+ * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ */
+package csplugins.layout.algorithms.graphPartition;
+
+import csplugins.layout.LayoutNode;
+import csplugins.layout.LayoutPartition;
+
+import csplugins.layout.algorithms.graphPartition.AbstractGraphPartition;
+
+import cytoscape.*;
+
+import cytoscape.data.*;
+
+import cytoscape.layout.LayoutProperties;
+import cytoscape.layout.Tunable;
+
+import cytoscape.view.*;
+
+import giny.model.*;
+
+import giny.view.*;
+
+import java.awt.GridLayout;
+
+import java.util.*;
+
+import javax.swing.JPanel;
+
+
+/**
+ *
+ */
+public class AttributeCircleLayout extends AbstractGraphPartition {
+ CyAttributes data;
+ String attribute = null;
+ private double spacing = 50.0;
+ boolean supportNodeAttributes = true;
+ LayoutProperties layoutProperties = null;
+
+ /**
+ * Creates a new AttributeCircleLayout object.
+ *
+ * @param supportAttributes DOCUMENT ME!
+ */
+ public AttributeCircleLayout(boolean supportAttributes) {
+ super();
+ initialize(supportAttributes);
+ }
+
+ /**
+ * Creates a new AttributeCircleLayout object.
+ */
+ public AttributeCircleLayout() {
+ super();
+ initialize(true);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param supportAttributes DOCUMENT ME!
+ */
+ public void initialize(boolean supportAttributes) {
+ supportNodeAttributes = supportAttributes;
+ layoutProperties = new LayoutProperties(getName());
+ initialize_properties();
+ }
+
+ // Required methods for AbstactLayout
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public byte[] supportsNodeAttributes() {
+ if (!supportNodeAttributes)
+ return null;
+
+ byte[] all = { -1 };
+
+ return all;
+ }
+
+ /**
+ * Sets the attribute to use for the weights
+ *
+ * @param value the name of the attribute
+ */
+ public void setLayoutAttribute(String value) {
+ if (value.equals("(none)"))
+ this.attribute = null;
+ else
+ this.attribute = value;
+ }
+
+ /**
+ * Get the settings panel for this layout
+ */
+ public JPanel getSettingsPanel() {
+ JPanel panel = new JPanel(new GridLayout(0, 1));
+ panel.add(layoutProperties.getTunablePanel());
+
+ return panel;
+ }
+
+ protected void initialize_properties() {
+ layoutProperties.add(new Tunable("spacing", "Circle size", Tunable.DOUBLE, new Double(100.0)));
+ layoutProperties.add(new Tunable("attribute", "The attribute to use for the layout",
+ Tunable.NODEATTRIBUTE, "(none)",
+ (Object) getInitialAttributeList(), (Object) null, 0));
+ // We've now set all of our tunables, so we can read the property
+ // file now and adjust as appropriate
+ layoutProperties.initializeProperties();
+
+ // Finally, update everything. We need to do this to update
+ // any of our values based on what we read from the property file
+ updateSettings(true);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void updateSettings() {
+ updateSettings(false);
+ }
+
+ public LayoutProperties getSettings() {
+ return layoutProperties;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param force DOCUMENT ME!
+ */
+ public void updateSettings(boolean force) {
+ layoutProperties.updateValues();
+
+ Tunable t = layoutProperties.get("spacing");
+ if ((t != null) && (t.valueChanged() || force)) {
+ spacing = ((Double) t.getValue()).doubleValue();
+ if (t.valueChanged())
+ layoutProperties.setProperty(t.getName(), t.getValue().toString());
+ }
+
+ t = layoutProperties.get("attribute");
+ if ((t != null) && (t.valueChanged() || force)) {
+ String newValue = (String) t.getValue();
+ // Does it make sense to save the attribute???
+ if (t.valueChanged())
+ layoutProperties.setProperty(t.getName(), t.getValue().toString());
+
+ if (newValue.equals("(none)")) {
+ attribute = null;
+ } else {
+ attribute = newValue;
+ ;
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void revertSettings() {
+ layoutProperties.revertProperties();
+ }
+
+ /**
+ *
+ * We don't have any special widgets
+ *
+ * @returns List of our "special" weights
+ */
+ public List<String> getInitialAttributeList() {
+ ArrayList<String> attList = new ArrayList<String>();
+ attList.add("(none)");
+
+ return attList;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String toString() {
+ if (!supportNodeAttributes) {
+ return "Circle Layout";
+ } else {
+ return "Attribute Circle Layout";
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getName() {
+ if (!supportNodeAttributes)
+ return "circle";
+ else
+
+ return "attribute-circle";
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param partition DOCUMENT ME!
+ */
+ public void layoutPartition(LayoutPartition partition) {
+ data = Cytoscape.getNodeAttributes();
+
+ // just add the unlocked nodes
+ List<LayoutNode> nodes = new ArrayList<LayoutNode>();
+ for ( LayoutNode ln : partition.getNodeList() ) {
+ if ( !ln.isLocked() ) {
+ nodes.add(ln);
+ }
+ }
+
+ int count = nodes.size();
+ int r = (int) Math.sqrt(count);
+ r *= spacing;
+
+ if (this.attribute != null)
+ Collections.sort(nodes, new AttributeComparator());
+
+ // Compute angle step
+ double phi = (2 * Math.PI) / count;
+
+ partition.resetNodes(); // We want to figure out our mins & maxes anew
+ // Arrange vertices in a circle
+
+ for (int i = 0; i < count; i++) {
+ LayoutNode node = (LayoutNode) nodes.get(i);
+ double x = r + (r * Math.sin(i * phi));
+ double y = r + (r * Math.cos(i * phi));
+ node.setX(x);
+ node.setY(y);
+ partition.moveNodeToLocation(node);
+ }
+ }
+
+ private class AttributeComparator implements Comparator<LayoutNode> {
+ private AttributeComparator() {
+ }
+
+ public int compare(LayoutNode o1, LayoutNode o2) {
+
+ byte type = data.getType(attribute);
+
+ if (type == CyAttributes.TYPE_STRING) {
+ String v1 = data.getStringAttribute(o1.getIdentifier(), attribute);
+ String v2 = data.getStringAttribute(o2.getIdentifier(), attribute);
+
+ if ((v1 != null) && (v2 != null))
+ return v1.compareToIgnoreCase(v2);
+ else if ((v1 == null) && (v2 != null))
+ return -1;
+ else if ((v1 == null) && (v2 == null))
+ return 0;
+ else if ((v1 != null) && (v2 == null))
+ return 1;
+ } else if (type == CyAttributes.TYPE_FLOATING) {
+ Double v1 = data.getDoubleAttribute(o1.getIdentifier(), attribute);
+ Double v2 = data.getDoubleAttribute(o2.getIdentifier(), attribute);
+
+ if ((v1 != null) && (v2 != null))
+ return v1.compareTo(v2);
+ else if ((v1 == null) && (v2 != null))
+ return -1;
+ else if ((v1 == null) && (v2 == null))
+ return 0;
+ else if ((v1 != null) && (v2 == null))
+ return 1;
+ } else if (type == CyAttributes.TYPE_INTEGER) {
+ Integer v1 = data.getIntegerAttribute(o1.getIdentifier(), attribute);
+ Integer v2 = data.getIntegerAttribute(o2.getIdentifier(), attribute);
+
+ if ((v1 != null) && (v2 != null))
+ return v1.compareTo(v2);
+ else if ((v1 == null) && (v2 != null))
+ return -1;
+ else if ((v1 == null) && (v2 == null))
+ return 0;
+ else if ((v1 != null) && (v2 == null))
+ return 1;
+ } else if (type == CyAttributes.TYPE_BOOLEAN) {
+ Boolean v1 = data.getBooleanAttribute(o1.getIdentifier(), attribute);
+ Boolean v2 = data.getBooleanAttribute(o2.getIdentifier(), attribute);
+
+ if ((v1 != null) && (v2 != null)) {
+ if ((v1.booleanValue() && v2.booleanValue())
+ || (!v1.booleanValue() && !v2.booleanValue()))
+ return 0;
+ else if (v1.booleanValue() && !v2.booleanValue())
+ return 1;
+ else if (!v1.booleanValue() && v2.booleanValue())
+ return -1;
+ } else if ((v1 == null) && (v2 != null))
+ return -1;
+ else if ((v1 == null) && (v2 == null))
+ return 0;
+ else if ((v1 != null) && (v2 == null))
+ return 1;
+ }
+
+ return 0;
+ }
+ }
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/algorithms/graphPartition/DegreeSortedCircleLayout.java b/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/algorithms/graphPartition/DegreeSortedCircleLayout.java
new file mode 100644
index 0000000..94d217a
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/algorithms/graphPartition/DegreeSortedCircleLayout.java
@@ -0,0 +1,115 @@
+/* vim: set ts=2: */
+package csplugins.layout.algorithms.graphPartition;
+
+import cern.colt.list.*;
+
+import csplugins.layout.LayoutNode;
+import csplugins.layout.LayoutPartition;
+
+import cytoscape.*;
+
+import cytoscape.data.*;
+
+import cytoscape.view.*;
+
+import giny.model.*;
+
+import giny.view.*;
+
+import java.util.*;
+
+
+/**
+ *
+ */
+public class DegreeSortedCircleLayout extends AbstractGraphPartition {
+ private final static String DEGREE = "Degree";
+
+ /**
+ * Creates a new DegreeSortedCircleLayout object.
+ */
+ public DegreeSortedCircleLayout() {
+ super();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String toString() {
+ return "Degree Sorted Circle Layout";
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getName() {
+ return "degree-circle";
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param partition DOCUMENT ME!
+ */
+ public void layoutPartition(LayoutPartition partition) {
+
+ // just add the unlocked nodes
+ List<LayoutNode> nodes = new ArrayList<LayoutNode>();
+ for ( LayoutNode ln : partition.getNodeList() ) {
+ if ( !ln.isLocked() ) {
+ nodes.add(ln);
+ }
+ }
+
+ if (canceled)
+ return;
+
+ // sort the Nodes based on the degree
+ final CyAttributes nodeAttr = Cytoscape.getNodeAttributes();
+ Collections.sort(nodes,
+ new Comparator<LayoutNode>() {
+ public int compare(LayoutNode o1, LayoutNode o2) {
+ final Node node1 = o1.getNodeView().getNode();
+ final Node node2 = o2.getNodeView().getNode();
+ final int d1 = Cytoscape.getCurrentNetwork().getDegree(node1.getRootGraphIndex());
+ final int d2 = Cytoscape.getCurrentNetwork().getDegree(node2.getRootGraphIndex());
+ nodeAttr.setAttribute(node1.getIdentifier(), DEGREE, d1);
+ nodeAttr.setAttribute(node2.getIdentifier(), DEGREE, d2);
+ return (d2 - d1);
+ }
+
+ public boolean equals(Object o) {
+ return false;
+ }
+ });
+
+ // make 'Degree' attribute user visible, if it is invisible (might be set by other plugin)
+ if (!Cytoscape.getNodeAttributes().getUserVisible(DEGREE)){
+ Cytoscape.getNodeAttributes().setUserVisible(DEGREE, true);
+ }
+
+ if (canceled)
+ return;
+
+ // place each Node in a circle
+ int r = 100 * (int) Math.sqrt(nodes.size());
+ double phi = (2 * Math.PI) / nodes.size();
+ partition.resetNodes(); // We want to figure out our mins & maxes anew
+
+ for (int i = 0; i < nodes.size(); i++) {
+ LayoutNode node = nodes.get(i);
+ node.setX(r + (r * Math.sin(i * phi)));
+ node.setY(r + (r * Math.cos(i * phi)));
+ partition.moveNodeToLocation(node);
+ }
+ }
+
+ public void construct() {
+ super.construct();
+ Cytoscape.firePropertyChange(Cytoscape.ATTRIBUTES_CHANGED, null, null);
+ }
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/algorithms/graphPartition/ISOMLayout.java b/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/algorithms/graphPartition/ISOMLayout.java
new file mode 100644
index 0000000..f7cb860
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/algorithms/graphPartition/ISOMLayout.java
@@ -0,0 +1,454 @@
+/* vim: set ts=2: */
+/*
+ * This is based on the ISOMLayout from the JUNG project.
+ */
+package csplugins.layout.algorithms.graphPartition;
+
+import cern.colt.list.IntArrayList;
+
+import cern.colt.map.OpenIntIntHashMap;
+import cern.colt.map.OpenIntObjectHashMap;
+import cern.colt.map.PrimeFinder;
+
+import cern.colt.matrix.DoubleMatrix1D;
+import cern.colt.matrix.impl.DenseDoubleMatrix1D;
+
+import csplugins.layout.LayoutNode;
+import csplugins.layout.LayoutPartition;
+
+import cytoscape.CyNetwork;
+
+import cytoscape.layout.LayoutProperties;
+import cytoscape.layout.Tunable;
+import cytoscape.logger.CyLogger;
+
+import giny.model.*;
+
+import java.awt.GridLayout;
+
+import java.util.Iterator;
+import java.util.List;
+
+import javax.swing.JPanel;
+
+
+/**
+ *
+ */
+public class ISOMLayout extends AbstractGraphPartition {
+ private int maxEpoch = 5000;
+ private int epoch;
+ private int radiusConstantTime = 100;
+ private int radius = 5;
+ private int minRadius = 1;
+ private double adaption;
+ private double initialAdaptation = 90.0D / 100.0D;
+ private double minAdaptation = 0;
+ private double sizeFactor = 100;
+ private double factor;
+ private double coolingFactor = 2;
+ private boolean trace;
+ private boolean done;
+ private LayoutProperties layoutProperties;
+ private LayoutPartition partition;
+ private CyLogger logger;
+
+ //Queue, First In First Out, use add() and get(0)/remove(0)
+ private IntArrayList q;
+ private String status = null;
+ OpenIntObjectHashMap nodeIndexToDataMap;
+ OpenIntIntHashMap nodeIndexToLayoutIndex;
+ double globalX;
+ double globalY;
+ double squared_size;
+
+ /**
+ * Creates a new ISOMLayout object.
+ */
+ public ISOMLayout() {
+ super();
+
+ logger = CyLogger.getLogger(ISOMLayout.class);
+
+ q = new IntArrayList();
+ trace = false;
+ layoutProperties = new LayoutProperties(getName());
+ initialize_properties();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String toString() {
+ return "Inverted Self-Organizing Map Layout";
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getName() {
+ return "isom";
+ }
+
+ /**
+ * Get the settings panel for this layout
+ */
+ public JPanel getSettingsPanel() {
+ JPanel panel = new JPanel(new GridLayout(0, 1));
+ panel.add(layoutProperties.getTunablePanel());
+
+ return panel;
+ }
+
+ protected void initialize_properties() {
+ layoutProperties.add(new Tunable("maxEpoch", "Number of iterations", Tunable.INTEGER,
+ new Integer(5000)));
+ layoutProperties.add(new Tunable("sizeFactor", "Size factor", Tunable.INTEGER,
+ new Integer(10)));
+ layoutProperties.add(new Tunable("radiusConstantTime", "Radius constant", Tunable.INTEGER,
+ new Integer(20)));
+ layoutProperties.add(new Tunable("radius", "Radius", Tunable.INTEGER, new Integer(5)));
+ layoutProperties.add(new Tunable("minRadius", "Minimum radius", Tunable.INTEGER,
+ new Integer(1)));
+ layoutProperties.add(new Tunable("initialAdaptation", "Initial adaptation", Tunable.DOUBLE,
+ new Double(0.9)));
+ layoutProperties.add(new Tunable("minAdaptation", "Minimum adaptation value",
+ Tunable.DOUBLE, new Double(0)));
+ layoutProperties.add(new Tunable("coolingFactor", "Cooling factor", Tunable.DOUBLE,
+ new Double(2)));
+
+ // We've now set all of our tunables, so we can read the property
+ // file now and adjust as appropriate
+ layoutProperties.initializeProperties();
+
+ // Finally, update everything. We need to do this to update
+ // any of our values based on what we read from the property file
+ updateSettings(true);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void updateSettings() {
+ updateSettings(false);
+ }
+
+ public LayoutProperties getSettings() {
+ return layoutProperties;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param force DOCUMENT ME!
+ */
+ public void updateSettings(boolean force) {
+ layoutProperties.updateValues();
+
+ Tunable t = layoutProperties.get("maxEpoch");
+ if ((t != null) && (t.valueChanged() || force)) {
+ maxEpoch = ((Integer) t.getValue()).intValue();
+ if (t.valueChanged())
+ layoutProperties.setProperty(t.getName(), t.getValue().toString());
+ }
+
+ t = layoutProperties.get("sizeFactor");
+ if ((t != null) && (t.valueChanged() || force)) {
+ sizeFactor = ((Integer) t.getValue()).intValue();
+ if (t.valueChanged())
+ layoutProperties.setProperty(t.getName(), t.getValue().toString());
+ }
+
+ t = layoutProperties.get("radiusConstantTime");
+ if ((t != null) && (t.valueChanged() || force)) {
+ radiusConstantTime = ((Integer) t.getValue()).intValue();
+ if (t.valueChanged())
+ layoutProperties.setProperty(t.getName(), t.getValue().toString());
+ }
+
+ t = layoutProperties.get("radius");
+ if ((t != null) && (t.valueChanged() || force)) {
+ radius = ((Integer) t.getValue()).intValue();
+ if (t.valueChanged())
+ layoutProperties.setProperty(t.getName(), t.getValue().toString());
+ }
+
+ t = layoutProperties.get("minRadius");
+ if ((t != null) && (t.valueChanged() || force)) {
+ minRadius = ((Integer) t.getValue()).intValue();
+ if (t.valueChanged())
+ layoutProperties.setProperty(t.getName(), t.getValue().toString());
+ }
+
+ t = layoutProperties.get("initialAdaptation");
+ if ((t != null) && (t.valueChanged() || force)) {
+ initialAdaptation = ((Double) t.getValue()).doubleValue();
+ if (t.valueChanged())
+ layoutProperties.setProperty(t.getName(), t.getValue().toString());
+ }
+
+ t = layoutProperties.get("minAdaptation");
+ if ((t != null) && (t.valueChanged() || force)) {
+ minAdaptation = ((Double) t.getValue()).doubleValue();
+ if (t.valueChanged())
+ layoutProperties.setProperty(t.getName(), t.getValue().toString());
+ }
+
+ t = layoutProperties.get("coolingFactor");
+ if ((t != null) && (t.valueChanged() || force)) {
+ coolingFactor = ((Double) t.getValue()).doubleValue();
+ if (t.valueChanged())
+ layoutProperties.setProperty(t.getName(), t.getValue().toString());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void revertSettings() {
+ layoutProperties.revertProperties();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param partition DOCUMENT ME!
+ */
+ public void layoutPartition(LayoutPartition partition) {
+ this.partition = partition;
+
+ int nodeCount = partition.nodeCount();
+ nodeIndexToDataMap = new OpenIntObjectHashMap(PrimeFinder.nextPrime(nodeCount));
+ nodeIndexToLayoutIndex = new OpenIntIntHashMap(PrimeFinder.nextPrime(nodeCount));
+ squared_size = network.getNodeCount() * sizeFactor;
+
+ epoch = 1;
+
+ adaption = initialAdaptation;
+
+ logger.debug("Epoch: " + epoch + " maxEpoch: " + maxEpoch);
+
+ while (epoch < maxEpoch) {
+ partition.resetNodes();
+ adjust();
+ updateParameters();
+
+ if (canceled)
+ break;
+ }
+ }
+
+ /**
+ * @return the closest NodeView to these coords.
+ */
+ public int getClosestPosition(double x, double y) {
+ double minDistance = Double.MAX_VALUE;
+ int closest = 0;
+ Iterator nodeIter = partition.nodeIterator();
+
+ while (nodeIter.hasNext()) {
+ LayoutNode node = (LayoutNode) nodeIter.next();
+ int rootGraphIndex = node.getNodeView().getNode().getRootGraphIndex();
+
+ nodeIndexToLayoutIndex.put(rootGraphIndex, node.getIndex());
+
+ double dx = node.getX();
+ double dy = node.getY();
+ double dist = (dx * dx) + (dy * dy);
+
+ if (dist < minDistance) {
+ minDistance = dist;
+ closest = rootGraphIndex;
+ }
+ }
+
+ return closest;
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void adjust() {
+ //Generate random position in graph space
+ ISOMVertexData tempISOM = new ISOMVertexData();
+
+ // creates a new XY data location
+ globalX = 10 + (Math.random() * squared_size);
+ globalY = 10 + (Math.random() * squared_size);
+
+ //Get closest vertex to random position
+ int winner = getClosestPosition(globalX, globalY);
+
+ Iterator nodeIter = partition.nodeIterator();
+
+ while (nodeIter.hasNext()) {
+ int nodeIndex = ((LayoutNode) nodeIter.next()).getNodeView().getNode().getRootGraphIndex();
+ ISOMVertexData ivd = getISOMVertexData(nodeIndex);
+ ivd.distance = 0;
+ ivd.visited = false;
+ }
+
+ adjustVertex(winner);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void updateParameters() {
+ epoch++;
+
+ double factor = Math.exp(-1 * coolingFactor * ((1.0 * epoch) / maxEpoch));
+ adaption = Math.max(minAdaptation, factor * initialAdaptation);
+
+ if ((radius > minRadius) && ((epoch % radiusConstantTime) == 0)) {
+ radius--;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param v DOCUMENT ME!
+ */
+ public void adjustVertex(int v) {
+ q.clear();
+
+ ISOMVertexData ivd = getISOMVertexData(v);
+ ivd.distance = 0;
+ ivd.visited = true;
+ q.add(v);
+
+ int current;
+ List<LayoutNode> nodeList = partition.getNodeList();
+
+ while (!q.isEmpty()) {
+ current = q.get(0);
+ q.remove(0);
+
+ int layoutIndex = nodeIndexToLayoutIndex.get(current);
+ LayoutNode currentNode = (LayoutNode) nodeList.get(layoutIndex);
+
+ ISOMVertexData currData = getISOMVertexData(current);
+
+ double current_x = currentNode.getX();
+ double current_y = currentNode.getY();
+
+ double dx = globalX - current_x;
+ double dy = globalY - current_y;
+
+ // possible mod
+ double factor = adaption / Math.pow(2, currData.distance);
+
+ currentNode.setX(current_x + (factor * dx));
+ currentNode.setY(current_y + (factor * dy));
+ partition.moveNodeToLocation(currentNode);
+
+ if (currData.distance < radius) {
+ int[] neighbors = neighborsArray(network, current);
+
+ for (int neighbor_index = 0; neighbor_index < neighbors.length; ++neighbor_index) {
+ ISOMVertexData childData = getISOMVertexData(neighbors[neighbor_index]);
+
+ if (!childData.visited) {
+ childData.visited = true;
+ childData.distance = currData.distance + 1;
+ q.add(neighbors[neighbor_index]);
+ }
+ }
+ }
+ }
+
+ // Add check to make sure we don't put nodes on top of each other
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param v DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public ISOMVertexData getISOMVertexData(int v) {
+ ISOMVertexData vd = (ISOMVertexData) nodeIndexToDataMap.get(v);
+
+ if (vd == null) {
+ vd = new ISOMVertexData();
+ nodeIndexToDataMap.put(v, vd);
+ }
+
+ return vd;
+ }
+
+ public static class ISOMVertexData {
+ public DoubleMatrix1D disp;
+ int distance;
+ boolean visited;
+
+ public ISOMVertexData() {
+ initialize();
+ }
+
+ public void initialize() {
+ disp = new DenseDoubleMatrix1D(2);
+
+ distance = 0;
+ visited = false;
+ }
+
+ public double getXDisp() {
+ return disp.get(0);
+ }
+
+ public double getYDisp() {
+ return disp.get(1);
+ }
+
+ public void setDisp(double x, double y) {
+ disp.set(0, x);
+ disp.set(1, y);
+ }
+
+ public void incrementDisp(double x, double y) {
+ disp.set(0, disp.get(0) + x);
+ disp.set(1, disp.get(1) + y);
+ }
+
+ public void decrementDisp(double x, double y) {
+ disp.set(0, disp.get(0) - x);
+ disp.set(1, disp.get(1) - y);
+ }
+ }
+
+ // This is here to replace the deprecated neighborsArray function
+ /**
+ * DOCUMENT ME!
+ *
+ * @param network DOCUMENT ME!
+ * @param nodeIndex DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] neighborsArray(CyNetwork network, int nodeIndex) {
+ // Get a list of edges
+ int[] edges = network.getAdjacentEdgeIndicesArray(nodeIndex, true, true, true);
+ int[] neighbors = new int[edges.length];
+ int offset = 0;
+
+ for (int edge = 0; edge < edges.length; edge++) {
+ int source = network.getEdgeSourceIndex(edges[edge]);
+ int target = network.getEdgeTargetIndex(edges[edge]);
+
+ if (source != nodeIndex) {
+ neighbors[offset++] = source;
+ } else {
+ neighbors[offset++] = target;
+ }
+ }
+
+ return neighbors;
+ }
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/algorithms/graphPartition/Layout.java b/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/algorithms/graphPartition/Layout.java
new file mode 100644
index 0000000..f2a5d3e
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/algorithms/graphPartition/Layout.java
@@ -0,0 +1,247 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package csplugins.layout.algorithms.graphPartition;
+
+import cern.colt.list.*;
+
+import cern.colt.map.*;
+
+import cytoscape.CyNetwork;
+
+import cytoscape.view.CyNetworkView;
+
+import giny.model.*;
+
+import giny.view.*;
+
+import java.util.*;
+
+
+/**
+ * Class that represents the Layout of a given graph.
+ */
+public class Layout {
+ OpenIntDoubleHashMap nodeXMap;
+ OpenIntDoubleHashMap nodeYMap;
+ CyNetwork gp;
+
+ /**
+ * Creates a new Layout object.
+ *
+ * @param gp DOCUMENT ME!
+ */
+ public Layout(CyNetwork gp) {
+ this.gp = gp;
+ nodeXMap = new OpenIntDoubleHashMap(PrimeFinder.nextPrime(gp.getNodeCount()));
+ nodeYMap = new OpenIntDoubleHashMap(PrimeFinder.nextPrime(gp.getNodeCount()));
+ }
+
+ /**
+ * Creates a new Layout object.
+ *
+ * @param view DOCUMENT ME!
+ * @param load_current_values DOCUMENT ME!
+ */
+ public Layout(CyNetworkView view, boolean load_current_values) {
+ this(view.getNetwork());
+
+ // initialize current values
+ if (load_current_values) {
+ Iterator i = view.getNodeViewsIterator();
+
+ while (i.hasNext()) {
+ NodeView nv = (NodeView) i.next();
+ setX(nv, nv.getXPosition());
+ setY(nv, nv.getYPosition());
+ }
+ }
+ }
+
+ /**
+ * Apply the layout to a given GraphView
+ */
+ public void applyLayout(CyNetworkView view) {
+ Iterator i = view.getNodeViewsIterator();
+
+ while (i.hasNext()) {
+ NodeView nv = (NodeView) i.next();
+ nv.setXPosition(getX(nv), false);
+ nv.setYPosition(getY(nv), false);
+ nv.setNodePosition(true);
+ }
+ }
+
+ // set
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ * @param x DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean setX(int node, double x) {
+ return nodeXMap.put(node, x);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ * @param y DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean setY(int node, double y) {
+ return nodeYMap.put(node, y);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ * @param x DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean setX(Node node, double x) {
+ return nodeXMap.put(node.getRootGraphIndex(), x);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ * @param y DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean setY(Node node, double y) {
+ return nodeYMap.put(node.getRootGraphIndex(), y);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ * @param x DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean setX(NodeView node, double x) {
+ return nodeXMap.put(node.getRootGraphIndex(), x);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ * @param y DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean setY(NodeView node, double y) {
+ return nodeYMap.put(node.getRootGraphIndex(), y);
+ }
+
+ // get
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public double getX(int node) {
+ return nodeXMap.get(node);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public double getY(int node) {
+ return nodeYMap.get(node);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public double getX(Node node) {
+ return nodeXMap.get(node.getRootGraphIndex());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public double getY(Node node) {
+ return nodeYMap.get(node.getRootGraphIndex());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public double getX(NodeView node) {
+ return nodeXMap.get(node.getRootGraphIndex());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public double getY(NodeView node) {
+ return nodeYMap.get(node.getRootGraphIndex());
+ }
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/algorithms/hierarchicalLayout/Edge.java b/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/algorithms/hierarchicalLayout/Edge.java
new file mode 100644
index 0000000..546678e
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/algorithms/hierarchicalLayout/Edge.java
@@ -0,0 +1,70 @@
+/** Copyright (c) 2004 Institute for Systems Biology, University of
+ ** California at San Diego, and Memorial Sloan-Kettering Cancer Center.
+ **
+ ** Code written by: Robert Sheridan
+ ** Authors: Gary Bader, Ethan Cerami, Chris Sander
+ ** Date: January 19.2004
+ ** Description: Hierarcical layout plugin, based on techniques by Sugiyama
+ ** et al. described in chapter 9 of "graph drawing", Di Battista et al,1999
+ **
+ ** Based on the csplugins.tutorial written by Ethan Cerami and GINY plugin
+ ** written by Andrew Markiel
+ **
+ ** This library is free software; you can redistribute it and/or modify it
+ ** under the terms of the GNU Lesser General Public License as published
+ ** by the Free Software Foundation; either version 2.1 of the License, or
+ ** any later version.
+ **
+ ** This library is distributed in the hope that it will be useful, but
+ ** WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ ** MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ ** documentation provided hereunder is on an "as is" basis, and the
+ ** Institute for Systems Biology, the University of California at San Diego
+ ** and/or Memorial Sloan-Kettering Cancer Center
+ ** have no obligations to provide maintenance, support,
+ ** updates, enhancements or modifications. In no event shall the
+ ** Institute for Systems Biology, the University of California at San Diego
+ ** and/or Memorial Sloan-Kettering Cancer Center
+ ** be liable to any party for direct, indirect, special,
+ ** incidental or consequential damages, including lost profits, arising
+ ** out of the use of this software and its documentation, even if the
+ ** Institute for Systems Biology, the University of California at San
+ ** Diego and/or Memorial Sloan-Kettering Cancer Center
+ ** have been advised of the possibility of such damage. See
+ ** the GNU Lesser General Public License for more details.
+ **
+ ** You should have received a copy of the GNU Lesser General Public License
+ ** along with this library; if not, write to the Free Software Foundation,
+ ** Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ **/
+package csplugins.layout.algorithms.hierarchicalLayout;
+
+
+/**
+ * Holds a (from, to) pair of integers representing an edge.
+*/
+public class Edge {
+ /** the index of the origin node */
+ private int from;
+
+ /** the index of the destination node */
+ private int to;
+
+ /** Accessor
+ @return index of origin node */
+ public int getFrom() {
+ return from;
+ }
+
+ /** Accessor
+ @return index of destination node */
+ public int getTo() {
+ return to;
+ }
+
+ /** Initializes private members. */
+ public Edge(int a_from, int a_to) {
+ from = a_from;
+ to = a_to;
+ }
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/algorithms/hierarchicalLayout/Graph.java b/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/algorithms/hierarchicalLayout/Graph.java
new file mode 100644
index 0000000..693eef1
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/algorithms/hierarchicalLayout/Graph.java
@@ -0,0 +1,2628 @@
+/** Copyright (c) 2004 Institute for Systems Biology, University of
+ ** California at San Diego, and Memorial Sloan-Kettering Cancer Center.
+ **
+ ** Code written by: Robert Sheridan
+ ** Authors: Gary Bader, Ethan Cerami, Chris Sander
+ ** Date: January 19.2004
+ ** Description: Hierarcical layout plugin, based on techniques by Sugiyama
+ ** et al. described in chapter 9 of "graph drawing", Di Battista et al,1999
+ **
+ ** Based on the csplugins.tutorial written by Ethan Cerami and GINY plugin
+ ** written by Andrew Markiel
+ **
+ ** This library is free software; you can redistribute it and/or modify it
+ ** under the terms of the GNU Lesser General Public License as published
+ ** by the Free Software Foundation; either version 2.1 of the License, or
+ ** any later version.
+ **
+ ** This library is distributed in the hope that it will be useful, but
+ ** WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ ** MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ ** documentation provided hereunder is on an "as is" basis, and the
+ ** Institute for Systems Biology, the University of California at San Diego
+ ** and/or Memorial Sloan-Kettering Cancer Center
+ ** have no obligations to provide maintenance, support,
+ ** updates, enhancements or modifications. In no event shall the
+ ** Institute for Systems Biology, the University of California at San Diego
+ ** and/or Memorial Sloan-Kettering Cancer Center
+ ** be liable to any party for direct, indirect, special,
+ ** incidental or consequential damages, including lost profits, arising
+ ** out of the use of this software and its documentation, even if the
+ ** Institute for Systems Biology, the University of California at San
+ ** Diego and/or Memorial Sloan-Kettering Cancer Center
+ ** have been advised of the possibility of such damage. See
+ ** the GNU Lesser General Public License for more details.
+ **
+ ** You should have received a copy of the GNU Lesser General Public License
+ ** along with this library; if not, write to the Free Software Foundation,
+ ** Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ **/
+package csplugins.layout.algorithms.hierarchicalLayout;
+
+import giny.view.NodeView;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.io.Reader;
+
+import java.lang.IllegalArgumentException;
+import java.lang.Integer;
+
+import java.util.*;
+
+
+/**
+ * A collection element for sorting key-value pairs
+*/
+class IntSortNode implements Comparable {
+ /** the key */
+ private int first; /* holds the node's topological index */
+
+ /** the value */
+ private int second; /* holds the node's id */
+
+ /** initializes private members */
+ public IntSortNode(int a_first, int a_second) {
+ first = a_first;
+ second = a_second;
+ }
+
+ /** get method */
+ public int getFirst() {
+ return first;
+ }
+
+ /** get method */
+ public int getSecond() {
+ return second;
+ }
+
+ /** comparison function for sorting - sorts into ascending key order */
+ public int compareTo(Object o) {
+ return first - ((IntSortNode) o).first;
+ }
+}
+
+
+/**
+ * A collection element for sorting key-value pairs
+*/
+class DoubleSortNode implements Comparable {
+ /** key */
+ private double key; /* holds the node's position */
+
+ /** value */
+ private int value; /* holds the node's id */
+
+ /** initializes private members */
+ public DoubleSortNode(double a_key, int a_value) {
+ key = a_key;
+ value = a_value;
+ }
+
+ /** get method */
+ public double getPrimary() {
+ return key;
+ }
+
+ /** get method */
+ public int getValue() {
+ return value;
+ }
+
+ /** comparison function for sorting - sorts into ascending key order */
+ public int compareTo(Object o) {
+ double diff = key - ((DoubleSortNode) o).key;
+
+ if (diff > 0)
+ return 1;
+
+ if (diff < 0)
+ return -1;
+
+ return 0;
+ }
+}
+
+
+/**
+ * A collection element for sorting key-value pairs
+*/
+class TwinDoubleSortNode implements Comparable {
+ /** first key */
+ private double primary; /* holds the node's median */
+
+ /** second key */
+ private double secondary; /* holds the node's barycenter */
+
+ /** the value */
+ private int value; /* holds the node's id */
+
+ /** initializes private members */
+ public TwinDoubleSortNode(double a_primary, double a_secondary, int a_value) {
+ primary = a_primary;
+ secondary = a_secondary;
+ value = a_value;
+ }
+
+ /** get method */
+ public double getPrimary() {
+ return primary;
+ }
+
+ /** get method */
+ public double getSecondary() {
+ return secondary;
+ }
+
+ /** get method */
+ public int getValue() {
+ return value;
+ }
+
+ /** comparison function for sorting - sorts into ascending key order */
+ public int compareTo(Object o) {
+ double diff = primary - ((TwinDoubleSortNode) o).primary;
+
+ if (diff > 0)
+ return 1;
+
+ if (diff < 0)
+ return -1;
+
+ diff = secondary - ((TwinDoubleSortNode) o).secondary;
+
+ if (diff > 0)
+ return 1;
+
+ if (diff < 0)
+ return -1;
+
+ return 0;
+ }
+}
+
+
+/**
+ * Performs transformations and calculations on graphs.
+ * This class accepts graphs in an abstract representation. Nodes
+ * are indexed with integers, beginning with 0. Edges are represented
+ * with instances of the {@link csplugins.hierarchicallayout.Edge}
+ * class, which holds a (from, to) pair of integers.
+*/
+public class Graph {
+ /* Graph has a node count, and an Array of edges */
+ /* each edge has a source and destination node (ints) */
+
+ /** The number of nodes in the graph */
+ private int nodecount;
+
+ /** All of the edges in the graph */
+ private Edge[] edge;
+
+ /** For each node, a linked list storing the destination of each outgoing edge */
+ private LinkedList<Integer>[] edgesFrom;
+
+ /** For each node, a linked list storing the origin of each incoming edge */
+ private LinkedList<Integer>[] edgesTo;
+
+ /** All the dummy nodes are placed on the end of the end, so we need only the index
+ * of the first one */
+ private int dummyNodesStart;
+
+ /** True if graph has been cycle removal routine has generated this graph */
+ private boolean acyclic;
+
+ /** True if transitive reduction routine has generated this graph */
+ private boolean reduced;
+
+ /** number of passes to do adjacency exchange */
+ static int MAX_ADJACENT_EXCHANGE_PASSES = 5;
+ private byte[] status;
+ private int[] d;
+ private int[] low;
+ private int[] pred;
+ private int time;
+ private HashMap<Integer, LinkedList<Integer>> neighbours;
+ private Stack<Edge> edgesStack;
+ private LinkedList<LinkedList<Integer>> biComponents;
+
+ /**
+ * Build a graph from a supplied Edge array.
+ * Nodes must be consecutively indexed beginning with zero.
+ * @param a_nodecount The total number of nodes in the graph
+ * @param a_edge An array of all edges in the graph (each edge holds the source and destination node's indicies)
+ * @throws IllegalArgumentException If any edge refers to an out of range node
+ */
+ public Graph(int a_nodecount, Edge[] a_edge) {
+ nodecount = a_nodecount;
+ edge = new Edge[a_edge.length];
+ edgesFrom = new LinkedList[nodecount];
+ edgesTo = new LinkedList[nodecount];
+ dummyNodesStart = a_nodecount;
+
+ int x;
+
+ for (x = 0; x < nodecount; x++) {
+ edgesFrom[x] = new LinkedList();
+ edgesTo[x] = new LinkedList();
+ }
+
+ for (x = 0; x < a_edge.length; x++) {
+ int edgeFrom = a_edge[x].getFrom();
+ int edgeTo = a_edge[x].getTo();
+
+ if ((edgeFrom < 0) || (edgeFrom >= nodecount) || (edgeTo < 0) || (edgeTo >= nodecount)) {
+ throw new IllegalArgumentException("Edge refered to node outside of valid range: "
+ + "From=" + edgeFrom + " To=" + edgeTo
+ + " with nodecount=" + nodecount + "\n");
+ }
+
+ edge[x] = new Edge(edgeFrom, edgeTo);
+ edgesFrom[edgeFrom].add(new Integer(edgeTo));
+ edgesTo[edgeTo].add(new Integer(edgeFrom));
+ }
+
+ acyclic = false;
+ reduced = false;
+
+ status = new byte[nodecount];
+ d = new int[nodecount];
+ low = new int[nodecount];
+ pred = new int[nodecount];
+ time = 0;
+ neighbours = new HashMap<Integer, LinkedList<Integer>>();
+ edgesStack = new Stack<Edge>();
+ biComponents = new LinkedList<LinkedList<Integer>>();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param a DOCUMENT ME!
+ * @param b DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Edge GetTheEdge(int a, int b) {
+ for (int i = 0; i < edge.length; i++)
+ if ((edge[i].getFrom() == a) && (edge[i].getTo() == b))
+ return edge[i];
+
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public LinkedList<Integer>[] GetEdgesFrom() {
+ return edgesFrom;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public LinkedList<Integer>[] GetEdgesTo() {
+ return edgesTo;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Edge[] GetEdges() {
+ return edge;
+ }
+
+ /**
+ * Build a graph from a stream.
+ * The input stream will be read and parsed in the following format:
+ * On the first line is an integer indicating the number of nodes in the graph.
+ * This is followed by one line per edge containing two integers: the edge
+ * source (where nodes are indexed sequentially starting from zero), and the
+ * edge destination. These two values are spearated by whitespace. Then there
+ * is a terminal line containing only a period character "." <br>
+ * Unavailable or badly formed files will cause exceptions to be thrown
+ * (including NumberFormatExceptions)
+ * @param r The reader of the input stream from which to read the graph data.
+ * @throws IOException if trouble is encountered reading the file
+ * @throws NumberFormatException if any value in the input does not parse to an integer
+ */
+ public Graph(Reader r) throws IOException {
+ BufferedReader br = new BufferedReader(r);
+ String linebuf = br.readLine();
+ nodecount = Integer.parseInt(linebuf);
+
+ LinkedList<Edge> edges = new LinkedList();
+ edgesFrom = new LinkedList[nodecount];
+ edgesTo = new LinkedList[nodecount];
+
+ int x;
+
+ for (x = 0; x < nodecount; x++) {
+ edgesFrom[x] = new LinkedList();
+ edgesTo[x] = new LinkedList();
+ }
+
+ for (linebuf = br.readLine(); !(linebuf.equals(".")); linebuf = br.readLine()) {
+ String[] vertex = linebuf.trim().split("\\s+");
+
+ if (vertex.length != 2) {
+ throw new NumberFormatException("Illegal input to Graph constructor:\n"
+ + "Expected two integers, received: " + linebuf
+ + "\n");
+ }
+
+ int edgeFrom = Integer.parseInt(vertex[0]);
+ int edgeTo = Integer.parseInt(vertex[1]);
+ edges.add(new Edge(edgeFrom, edgeTo));
+ edgesFrom[edgeFrom].add(new Integer(edgeTo));
+ edgesTo[edgeTo].add(new Integer(edgeFrom));
+ }
+
+ edge = new Edge[edges.size()];
+ edges.toArray(edge);
+ acyclic = false;
+ reduced = false;
+ }
+
+ /**
+ * Human readable description of graph representation. Prints a node count line
+ * followed by the edge endpoint (one per line).
+ * @return Human readable graph description in string form
+ */
+ public String toString() {
+ String retval = "Graph with " + nodecount + " nodes.\nEdges:\n";
+ int x;
+
+ for (x = 0; x < edge.length; x++) {
+ retval += ("From " + edge[x].getFrom() + " To " + edge[x].getTo() + "\n");
+ }
+
+ return retval;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param q DOCUMENT ME!
+ */
+ public void setAcyclic(boolean q) {
+ acyclic = q;
+ ;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param q DOCUMENT ME!
+ */
+ public void setReduced(boolean q) {
+ reduced = q;
+ ;
+ }
+
+ /**
+ * Sets the first index of dummy node in graph
+ */
+ public void setDummyNodesStart(int dummyStart) {
+ dummyNodesStart = dummyStart;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getDummyNodesStart() {
+ return dummyNodesStart;
+ }
+
+ /**
+ * Accessor.
+ * @return total number of nodes in graph
+ */
+ public int getNodecount() {
+ return nodecount;
+ }
+
+ /**
+ * Accessor.
+ * @return total number of edges in graph
+ */
+ public int getEdgecount() {
+ return edge.length;
+ }
+
+ /**
+ * Query to test whether an edge exists.
+ * @param edgeFrom node index for the origin
+ * @param edgeTo node index for the destination
+ * @return True if the queried edge is in the graph
+ */
+ public boolean hasEdge(int edgeFrom, int edgeTo) {
+ return edgesFrom[edgeFrom].contains(new Integer(edgeTo));
+ }
+
+ /**
+ * Make a graph which filters out short (length 1 or 2) cycles.
+ * Generates a new graph object which is the same is the current graph except
+ * that all edges which begin and end at the same node (loops) or edges which
+ * are an inverted instance of some other edge in the graph (a,b); (b,a)
+ * are filtered out.
+ * @return a graph without cycles of length one or edges which used to
+ * be part of a cycle of length two.
+ */
+ public Graph getGraphWithoutOneOrTwoCycles() {
+ LinkedList<Edge> newEdges = new LinkedList();
+ int x;
+
+ for (x = 0; x < edge.length; x++) {
+ int edgeFrom = edge[x].getFrom();
+ int edgeTo = edge[x].getTo();
+
+ if (edgeFrom == edgeTo)
+ continue; /* drop onecycles */
+
+ if (hasEdge(edgeTo, edgeFrom))
+ continue; /* drop twocycles */
+
+ newEdges.add(edge[x]);
+ }
+
+ Edge[] newEdge = new Edge[newEdges.size()];
+ newEdges.toArray(newEdge);
+
+ return new Graph(nodecount, newEdge);
+ }
+
+ /**
+ * Make a graph which filters out duplicate edges.
+ * Generates a new graph object which is the same is the current graph except
+ * that if there are several duplicate edges (same source and target), all
+ * but one of each set of duplicates is filtered out.
+ * @return a graph without duplicate edges
+ */
+ public Graph getGraphWithoutMultipleEdges() {
+ LinkedList<Edge> newEdges = new LinkedList();
+ int edgeFrom;
+
+ for (edgeFrom = 0; edgeFrom < nodecount; edgeFrom++) {
+ HashSet seenEdgeTo = new HashSet();
+ Iterator iter = edgesFrom[edgeFrom].iterator();
+
+ while (iter.hasNext()) {
+ Integer edgeTo = (Integer) (iter.next());
+
+ if (!seenEdgeTo.contains(edgeTo)) {
+ newEdges.add(new Edge(edgeFrom, edgeTo.intValue()));
+ seenEdgeTo.add(edgeTo);
+ }
+ }
+ }
+
+ Edge[] newEdge = new Edge[newEdges.size()];
+ newEdges.toArray(newEdge);
+
+ return new Graph(nodecount, newEdge);
+ }
+
+ /**
+ * Determine node membership in the set of connected components.
+ * Components are detected and numbered. Each node is assigned an integer number
+ * which corresponds to the component which it is a member of. Components are
+ * numbered consecutively, beginning with 0. These numbers are returned in an
+ * array, whose length is equal to nodecount.
+ * @return An array of integer component numbers - one for each node in this graph.
+ */
+ public int[] componentIndex() {
+ int[] cI = new int[nodecount];
+ LinkedList[] componentNode = new LinkedList[nodecount];
+ int x;
+
+ for (x = 0; x < nodecount; x++) {
+ cI[x] = x;
+ componentNode[x] = new LinkedList();
+ componentNode[x].add(new Integer(x));
+ }
+
+ for (x = 0; x < edge.length; x++) {
+ if (cI[edge[x].getFrom()] != cI[edge[x].getTo()]) {
+ /* merge components */
+ int smaller = cI[edge[x].getFrom()];
+ int larger = cI[edge[x].getTo()];
+
+ if (smaller > larger) {
+ int tmp = smaller;
+ smaller = larger;
+ larger = tmp;
+ }
+
+ Iterator iter = componentNode[larger].iterator();
+
+ while (iter.hasNext()) {
+ int nodeIndex = ((Integer) (iter.next())).intValue();
+ cI[nodeIndex] = smaller;
+ componentNode[smaller].add(new Integer(nodeIndex));
+ }
+ }
+ }
+
+ /* make index numbers contiguous */
+ int[] contiguousMap = new int[nodecount];
+ int topSeen = 0;
+ int topAssigned = 0;
+
+ for (x = 0; x < nodecount; x++) {
+ if (cI[x] > topSeen) {
+ topSeen = cI[x];
+ contiguousMap[cI[x]] = ++topAssigned;
+ }
+
+ cI[x] = contiguousMap[cI[x]];
+ }
+
+ return cI;
+ }
+
+ private void ArtPoints(int current) {
+ status[current] = 1;
+ low[current] = d[current] = ++time;
+
+ int neigh;
+ Iterator iter = neighbours.get(current).iterator();
+
+ while (iter.hasNext()) {
+ neigh = ((Integer) (iter.next())).intValue();
+
+ if (status[neigh] == 0) {
+ pred[neigh] = current;
+ edgesStack.push(new Edge(current, neigh));
+ ArtPoints(neigh);
+ low[current] = Math.min(low[current], low[neigh]);
+
+ if (pred[current] == -1) {
+ Iterator rootChildren = neighbours.get(new Integer(current)).iterator();
+ int noChildren = 0;
+
+ while (rootChildren.hasNext()) {
+ //if (pred[((Integer)rootChildren.next()).intValue()] == current)
+ noChildren++;
+ rootChildren.next();
+ }
+
+ if (noChildren >= 2) {
+ LinkedList<Integer> singleComponent = new LinkedList<Integer>();
+ singleComponent.add(new Integer(edgesStack.peek().getTo()));
+
+ while (edgesStack.peek().getFrom() != current) {
+ Edge currEdge = edgesStack.pop();
+
+ if (!singleComponent.contains(new Integer(currEdge.getFrom())))
+ singleComponent.add(new Integer(currEdge.getFrom()));
+
+ if (!singleComponent.contains(new Integer(currEdge.getTo())))
+ singleComponent.add(new Integer(currEdge.getTo()));
+ }
+
+ edgesStack.pop();
+
+ if (!singleComponent.contains(new Integer(current)))
+ singleComponent.add(new Integer(current));
+
+ biComponents.add(singleComponent);
+
+ // skini sa steka sve do art tacke to je jedna bi komp
+ }
+ } else if (low[neigh] >= d[current]) {
+ LinkedList<Integer> singleComponent = new LinkedList<Integer>();
+ singleComponent.add(new Integer(edgesStack.peek().getTo()));
+
+ while (edgesStack.peek().getFrom() != current) {
+ Edge currEdge = edgesStack.pop();
+
+ if (!singleComponent.contains(new Integer(currEdge.getFrom())))
+ singleComponent.add(new Integer(currEdge.getFrom()));
+
+ if (!singleComponent.contains(new Integer(currEdge.getTo())))
+ singleComponent.add(new Integer(currEdge.getTo()));
+ }
+
+ edgesStack.pop();
+
+ if (!singleComponent.contains(new Integer(current)))
+ singleComponent.add(new Integer(current));
+
+ biComponents.add(singleComponent);
+
+ // skini sa steka sve do art tacke to je jedna bi komp
+ }
+
+ status[neigh] = 1;
+ low[neigh] = d[neigh] = ++time;
+ } else if (neigh != pred[current]) {
+ low[current] = Math.min(low[current], d[neigh]);
+ }
+ }
+ }
+
+ /**
+ * Function which calculates the biconnected components of the given graph
+ * @return
+ */
+ public int[][] biconnectedComponents() {
+ for (int i = 0; i < nodecount; i++)
+ neighbours.put(new Integer(i), new LinkedList<Integer>());
+
+ for (int i = 0; i < edge.length; i++)
+ neighbours.get(new Integer(edge[i].getFrom())).add(new Integer(edge[i].getTo()));
+
+ for (int i = 0; i < nodecount; i++)
+ status[i] = 0;
+
+ //time = 0;
+ pred[0] = -1;
+
+ ArtPoints(0);
+
+ int[][] bc = new int[biComponents.size()][];
+
+ for (int i = 0; i < biComponents.size(); i++) {
+ bc[i] = new int[biComponents.get(i).size()];
+
+ for (int j = 0; j < biComponents.get(i).size(); j++)
+ bc[i][j] = biComponents.get(i).get(j).intValue();
+ }
+
+ return bc;
+ }
+
+ /**
+ * Create an array of Graphs by partitioning this graph.
+ * This method takes an array of integers equal in length to nodecount.
+ * Each element of the array specifies which subgraph the corresponding
+ * node should belong to. Subgraphs are numbered beginning with zero.
+ * Every node is put in exactly one subgraph, and
+ * the set of subgraphs are returned. The index number of each node is
+ * recalculated as it is added to its subgraph. This renumbering is returned
+ * in an array passed in as an argument (nodeRenumber). The elements of
+ * this array will hold the new index number of each node as it appears
+ * in its corresponding subgraph.<br>
+ * Edges' source and destination values are modified to maintain the
+ * appropriate topology. Edges which span different subgraphs are
+ * deleted.
+ * @param partitionIndex A subgraph index for each node in the graph.
+ * @param nodeRenumber An array which is passed back to the caller
+ * containing the new index number of each node as it sits in its
+ * subgraph.
+ * @return An array of graphs containing the nodes directed to each
+ * subgraph according to the indicies in partitionIndex.
+ * @throws IllegalArgumentException if the size of either argument
+ * array is incorrect (!= nodecount)
+ */
+ public Graph[] partition(int[] partitionIndex, int[] nodeRenumber) {
+ if ((partitionIndex.length != nodecount) || (nodeRenumber.length != nodecount)) {
+ throw new IllegalArgumentException("partitionGraph received wrong sized argument");
+ }
+
+ int[] partitionNodecount = new int[nodecount];
+ int numberOfPartitions = 0;
+ int x;
+
+ for (x = 0; x < nodecount; x++) {
+ nodeRenumber[x] = partitionNodecount[partitionIndex[x]]++;
+
+ if (nodeRenumber[x] == 0) {
+ numberOfPartitions++;
+ }
+ }
+
+ LinkedList[] partitionEdges = new LinkedList[numberOfPartitions];
+
+ for (x = 0; x < numberOfPartitions; x++) {
+ partitionEdges[x] = new LinkedList();
+ }
+
+ for (x = 0; x < edge.length; x++) {
+ Edge e = edge[x];
+
+ if (partitionIndex[e.getFrom()] != partitionIndex[e.getTo()]) {
+ /* ignore edges which straddle partitions */
+ continue;
+ }
+
+ partitionEdges[partitionIndex[e.getFrom()]].add(new Edge(nodeRenumber[e.getFrom()],
+ nodeRenumber[e.getTo()]));
+ }
+
+ Graph[] retval = new Graph[numberOfPartitions];
+
+ for (x = 0; x < numberOfPartitions; x++) {
+ Edge[] pe = new Edge[partitionEdges[x].size()];
+ partitionEdges[x].toArray(pe);
+ retval[x] = new Graph(partitionNodecount[x], pe);
+ }
+
+ return retval;
+ }
+
+ /**
+ * Determine an ordering of nodes used to eliminate cycles.
+ * This is an implementation of the "Greedy-Cycle-Removal"
+ * algorithm presented by Sugiyama et al. in chapter 9 of
+ * "Graph Drawing" by Di Battista et al. <br>
+ * The basic appraach is that all nodes are examined and
+ * nodes which are sinks are removed from the graph and
+ * added to the end of the order, and nodes which are
+ * sources are removed and added to the beginning of the
+ * order. If there are no sources or sinks, the node with
+ * the greatest difference between outgoing and incoming
+ * edges is added to the beginning of the list. Removing
+ * nodes from the graph creates new sources and sinks,
+ * and through iteration an order is computed. <br>
+ * Note: during this computation, nodes are removed from
+ * a temporary copy of the graph; no change happens to
+ * the current graph. Also, the temporary copy is filtered
+ * of short cycles (length 1 or 2 cycles) and transitive
+ * edges.
+ * @return An array of integers which represents an ordered list
+ * of nodes. The elements which are closer to the beginning of the
+ * array are indecies of nodes which are more "sourcelike". Those
+ * closer to the end of the array are more "sinklike". The intention
+ * is that this ordering will be used to eliminate cycles by reversing
+ * the direction of any edges which oppose the implied flow from
+ * sources to sinks.
+ */
+ public int[] getCycleEliminationVertexPriority() {
+ int[] priority = new int[nodecount];
+ int[] inDegree = new int[nodecount];
+ int[] outDegree = new int[nodecount];
+
+ if (nodecount == 0) {
+ return priority;
+ }
+
+ if (nodecount == 1) {
+ priority[0] = 0;
+
+ return priority;
+ }
+
+ Graph simplifiedGraph = getGraphWithoutMultipleEdges().getGraphWithoutOneOrTwoCycles();
+
+ if (nodecount == 2) {
+ if (simplifiedGraph.edgesFrom[0].size() == 0) {
+ /* node 0 is a sink */
+ priority[0] = 1;
+ priority[1] = 0;
+ } else {
+ priority[0] = 0;
+ priority[1] = 1;
+ }
+
+ return priority;
+ }
+
+ LinkedList[] simpleEdgesTo = simplifiedGraph.edgesTo;
+ LinkedList[] simpleEdgesFrom = simplifiedGraph.edgesFrom;
+ LinkedList[] bucket = new LinkedList[(2 * nodecount) - 3];
+ LinkedList Sr = new LinkedList();
+ LinkedList Sl = new LinkedList();
+ final int bucketOffset = nodecount - 2;
+ int x;
+
+ for (x = 0; x < bucket.length; x++) {
+ bucket[x] = new LinkedList();
+ }
+
+ LinkedList sink = bucket[0];
+ LinkedList source = bucket[bucket.length - 1];
+ ;
+
+ for (x = 0; x < nodecount; x++) {
+ inDegree[x] = simpleEdgesTo[x].size();
+ outDegree[x] = simpleEdgesFrom[x].size();
+
+ if (outDegree[x] == 0) {
+ sink.add(new Integer(x));
+ } else if (inDegree[x] == 0) {
+ source.add(new Integer(x));
+ } else {
+ bucket[outDegree[x] - inDegree[x] + bucketOffset].add(new Integer(x));
+ }
+ }
+
+ int scanBucketStart = bucket.length - 2;
+ int nodesRemaining;
+
+ for (nodesRemaining = nodecount; nodesRemaining != 0; nodesRemaining--) {
+ /* select node */
+ Integer u;
+ boolean goRight = false;
+
+ if (sink.size() > 0) {
+ u = (Integer) (sink.removeFirst());
+ goRight = true;
+ } else if (source.size() > 0) {
+ u = (Integer) (source.removeFirst());
+ } else {
+ while (bucket[scanBucketStart].size() == 0) {
+ scanBucketStart--;
+ }
+
+ u = (Integer) (bucket[scanBucketStart].removeFirst());
+ }
+
+ /* cut edges and adjust adjacent nodes */
+ LinkedList simpleAdjacents = simpleEdgesTo[u.intValue()];
+
+ while (simpleAdjacents.size() > 0) {
+ Integer adj = (Integer) (simpleAdjacents.removeFirst());
+ int adjindex = adj.intValue();
+ int inDeg = inDegree[adjindex];
+ int outDeg = outDegree[adjindex];
+
+ if (outDeg == 0) {
+ sink.remove(adj);
+ } else if (inDeg == 0) {
+ source.remove(adj);
+ } else {
+ bucket[outDeg - inDeg + bucketOffset].remove(adj);
+ }
+
+ simpleEdgesFrom[adjindex].remove(u);
+ outDegree[adjindex]--;
+ outDeg--;
+
+ if (outDeg == 0) {
+ sink.add(adj);
+ } else if (inDeg == 0) {
+ source.add(adj);
+ } else {
+ int dest = outDeg - inDeg + bucketOffset;
+ bucket[dest].add(adj);
+
+ if (dest > scanBucketStart)
+ scanBucketStart = dest;
+ }
+ }
+
+ simpleAdjacents = simpleEdgesFrom[u.intValue()];
+
+ while (simpleAdjacents.size() > 0) {
+ Integer adj = (Integer) (simpleAdjacents.removeFirst());
+ int adjindex = adj.intValue();
+ int inDeg = inDegree[adjindex];
+ int outDeg = outDegree[adjindex];
+
+ if (outDeg == 0) {
+ sink.remove(adj);
+ } else if (inDeg == 0) {
+ source.remove(adj);
+ } else {
+ bucket[outDeg - inDeg + bucketOffset].remove(adj);
+ }
+
+ simpleEdgesTo[adjindex].remove(u);
+ inDegree[adjindex]--;
+ inDeg--;
+
+ if (outDeg == 0) {
+ sink.add(adj);
+ } else if (inDeg == 0) {
+ source.add(adj);
+ } else {
+ int dest = outDeg - inDeg + bucketOffset;
+ bucket[dest].add(adj);
+
+ if (dest > scanBucketStart)
+ scanBucketStart = dest;
+ }
+ }
+
+ /* add to appropriate list */
+ if (goRight) {
+ Sr.addFirst(u);
+ } else {
+ Sl.addLast(u);
+ }
+ }
+
+ x = 0;
+
+ Iterator iter = Sl.iterator();
+
+ while (iter.hasNext()) {
+ priority[x++] = ((Integer) (iter.next())).intValue();
+ }
+
+ iter = Sr.iterator();
+
+ while (iter.hasNext()) {
+ priority[x++] = ((Integer) (iter.next())).intValue();
+ }
+
+ return priority;
+ }
+
+ /**
+ * Make a graph where all "left" edges are reversed (according to provided node ordering).
+ * A left edge is one which begins at a node which is later
+ * in the provided order than the edge's destination.
+ * A new Graph object which is thereby free of cycles is
+ * returned.
+ * @param cycleEliminationPriority an ordering of node indecies.
+ * Nodes near the beginning are considered more "sourcelike",
+ * while those towards the end are condiered more "sinklike".
+ * @return A Graph which is similar to the current graph, but
+ * which has no cycles due to the reversal of left edges.
+ */
+ public Graph getGraphWithoutCycles(int[] cycleEliminationPriority) {
+ int[] priorityIndex = new int[nodecount];
+ int x;
+
+ for (x = 0; x < cycleEliminationPriority.length; x++) {
+ priorityIndex[cycleEliminationPriority[x]] = x;
+ }
+
+ LinkedList newEdges = new LinkedList();
+
+ for (x = 0; x < edge.length; x++) {
+ int edgeFrom = edge[x].getFrom();
+ int edgeTo = edge[x].getTo();
+
+ if (edgeFrom == edgeTo)
+ continue; /* drop onecycles */
+
+ if (priorityIndex[edgeFrom] > priorityIndex[edgeTo]) {
+ int temp = edgeFrom;
+ edgeFrom = edgeTo;
+ edgeTo = temp;
+ newEdges.add(new Edge(edgeFrom, edgeTo));
+ } else {
+ newEdges.add(edge[x]);
+ }
+ }
+
+ Edge[] newEdge = new Edge[newEdges.size()];
+ newEdges.toArray(newEdge);
+
+ Graph dag = new Graph(nodecount, newEdge);
+ dag.acyclic = true;
+
+ return dag;
+ }
+
+ /**
+ * Make a graph which is the transitive reduction of the current graph.
+ * A transitive edge is one where some other path exists from the
+ * edge's source to its destination. Using the provided topological
+ * ordedring of nodes, this method efficiently preforms the reduction.
+ * The heart of the algorithm is that at each node, the child which
+ * has the highest position in the topological order cannot be a
+ * transitive edge. If we know the list of descendants of that child,
+ * then we know if the second child (in the topological order) is
+ * connected by a transitive edge or not. By recursively updating
+ * the lists of descendants of a node, this process continues until
+ * all children are examined, at which point we know the full list
+ * of the examined node's descendants, which can be passeed up to
+ * the node's parents, allowing the recursion. <br>
+ * Note: this method can only be called on a graph which is acyclic,
+ * otherwise a RuntimeException is thrown.
+ * @param topologicalOrder an ordering of node indecies such that
+ * there are no edges from a node lower in the order to a node higher
+ * in the ordedr.
+ * @return A Graph which is the transitive reduction of the current
+ * graph.
+ * @throws IllegalArgumentException if the size of topological order
+ * is not equal to nodecount.
+ * @throws RuntimeException if this method is called on a graph which
+ * has not had cycles removed via a call to getGraphWithoutCycles.
+ */
+ public Graph getReducedGraph(int[] topologicalOrder) {
+ if (topologicalOrder.length != nodecount) {
+ throw new IllegalArgumentException("topological ordering of nodes does not match nodecount");
+ }
+
+ if (!acyclic) {
+ throw new RuntimeException("attempt to compute transitive reduction on a graph with cycles");
+ }
+
+ int[] priorityIndex = new int[nodecount];
+ int x;
+
+ for (x = 0; x < topologicalOrder.length; x++) {
+ priorityIndex[topologicalOrder[x]] = x;
+ }
+
+ LinkedList newEdges = new LinkedList();
+ LinkedHashSet[] descendants = new LinkedHashSet[nodecount];
+ int nodeIndex;
+
+ for (nodeIndex = topologicalOrder.length - 1; nodeIndex >= 0; nodeIndex--) {
+ int nodeId = topologicalOrder[nodeIndex];
+
+ /* determine topologically ordered list of children */
+ LinkedHashSet daughters = new LinkedHashSet(edgesFrom[nodeId]);
+ IntSortNode[] daughter = new IntSortNode[daughters.size()];
+ int daughterIndex = 0;
+ Iterator iter = daughters.iterator();
+
+ while (iter.hasNext()) {
+ int daughterId = ((Integer) (iter.next())).intValue();
+ daughter[daughterIndex++] = new IntSortNode(priorityIndex[daughterId], daughterId);
+ }
+
+ Arrays.sort(daughter);
+
+ for (daughterIndex = 0; daughterIndex < daughter.length; daughterIndex++) {
+ int daughterId = daughter[daughterIndex].getSecond();
+ Integer daughterIdObj = new Integer(daughterId);
+
+ if (descendants[nodeId] == null) {
+ if (descendants[daughterId] == null) {
+ descendants[nodeId] = new LinkedHashSet();
+ } else {
+ descendants[nodeId] = new LinkedHashSet(descendants[daughterId]);
+ }
+
+ newEdges.add(new Edge(nodeId, daughterId));
+ } else {
+ if (!descendants[nodeId].contains(daughterIdObj)) {
+ newEdges.add(new Edge(nodeId, daughterId));
+ } else {
+ ; /* child already descendant - transitive edge */}
+
+ if (descendants[daughterId] != null) {
+ /* merge child descendants into descendants */
+ descendants[nodeId].addAll(descendants[daughterId]);
+ }
+ }
+
+ descendants[nodeId].add(daughterIdObj);
+ }
+ }
+
+ Edge[] newEdge = new Edge[newEdges.size()];
+ newEdges.toArray(newEdge);
+
+ Graph reducedGraph = new Graph(nodecount, newEdge);
+ reducedGraph.acyclic = true;
+ reducedGraph.reduced = true;
+
+ return reducedGraph;
+ }
+
+ /**
+ * Make a graph which is the transitive reduction of the current graph.
+ * Creates the transitive reduction of the current graph by combining calls
+ * to getCycleEliminationVertexPriority(), getGraphWithoutCycles(int[]),
+ * and getReducedGraph(int[]).
+ * @return A Graph which is the transitive reduction of the current
+ * graph.
+ */
+ public Graph getReducedGraph() {
+ int[] cycleEliminationPriority = getCycleEliminationVertexPriority();
+ Graph dag = getGraphWithoutCycles(cycleEliminationPriority);
+
+ return dag.getReducedGraph(cycleEliminationPriority);
+ }
+
+ /**
+ * Compare two sets of integers lexicographically.
+ * This ordering is used for the Coffman-Graham-Layering algorithm.
+ * A is less than B if
+ * <ul><li>A is empty and B is not</li>
+ * <li>The max element from A is smaller than the max element from B</li>
+ * <li>A minus its largest element is less than B minus its largest element</li></ul>
+ * @param set1 an array of unique integers, sorted into descending order
+ * @param set2 an array of unique integers, sorted into descending order
+ * @return true if set1 < set2
+ */
+ static public boolean orderedSetComparison(int[] set1, int[] set2) {
+ if (set2 == null)
+ return false;
+
+ if (set1 == null)
+ return true;
+
+ final int smallerSize = Math.min(set1.length, set2.length);
+ int x;
+
+ for (x = 0; x < smallerSize; x++) {
+ if (set1[x] < set2[x])
+ return true;
+ }
+
+ return set1.length < set2.length;
+ }
+
+ /**
+ * Return an array of layer assignments for the nodes.
+ * This layering is done using the Coffman-Graham-Layering algorithm.
+ * The algorithm function in two passes:<br>
+ * In the pass one, every node is labelled with a priority number. This
+ * labelling is done by iteratively choosing the node whose parents have
+ * all been labelled, and where the set of parental labels is lexicographically
+ * less than that of any other node. <br>
+ * In the second pass, nodes are assigned to layers. Nodes are first added to
+ * the lowest layer. Nodes are eligible to be added once all of its children
+ * are assigned to some layer. Nodes cannot be added to the same layer as any
+ * of its children. Otherwise, nodes are selected from the eligible set by
+ * taking the one which has the lexicographically greatest set of child node
+ * labels. Additionally, there is a parameter which sets the maximum width
+ * of any layer. Once a layer is full, or there are no more valid nodes to
+ * be added to it, the next higher layer is filled. Once nodes are added to
+ * the next higher layer, no nodes can be added to any lower layer.
+ * @return an integer array containing the per node layer assignment. The
+ * lowest layer is numbered 1. The next lowest 2, etc.
+ * @throws RuntimeException if this function is called on a graph which has
+ * not been reduced by a call to getReducedGraph().
+ */
+ public int[] getVertexLayers() {
+ if (!reduced) {
+ throw new RuntimeException("attempt to compute vertex layers in a non-reduced graph");
+ }
+
+ final int LAYER_WIDTH = Math.max((int) (Math.pow(nodecount, 2 / Math.PI)), 10);
+ int[] vertexLabel = new int[nodecount];
+ int x;
+
+ for (x = 0; x < nodecount; x++) {
+ vertexLabel[x] = 0; /* 0 is the "unlabelled" label */
+ }
+
+ int[][] parentLabels = new int[nodecount][];
+ LinkedHashSet eligible = new LinkedHashSet((nodecount * 3) / 2);
+ boolean[] onEligible = new boolean[nodecount];
+
+ /* add all sources and isolated nodes to eligible list */
+ for (x = 0; x < nodecount; x++) {
+ if (edgesTo[x].size() == 0) {
+ eligible.add(new Integer(x));
+ onEligible[x] = true;
+ } else {
+ onEligible[x] = false;
+ }
+ }
+
+ int nextLabel = 1;
+
+ while (eligible.size() > 0) {
+ /* find minimal node */
+ Iterator iter = eligible.iterator();
+ Integer minElement = ((Integer) (iter.next()));
+ int minId = minElement.intValue();
+
+ while (iter.hasNext()) {
+ int nextId = ((Integer) (iter.next())).intValue();
+
+ if (orderedSetComparison(parentLabels[nextId], parentLabels[minId])) {
+ minId = nextId;
+ }
+ }
+
+ vertexLabel[minId] = nextLabel++;
+ eligible.remove(minElement);
+ onEligible[minId] = false;
+ /* check children for eligibility */
+ iter = edgesFrom[minId].iterator();
+NEXTCHILD:
+ while (iter.hasNext()) {
+ int childId = ((Integer) (iter.next())).intValue();
+
+ if (onEligible[childId])
+ continue NEXTCHILD; /* already eligible */
+
+ Iterator cpIter = edgesTo[childId].iterator();
+ int[] childParentList = new int[edgesTo[childId].size()]; /* warning: multigraphs will mess this up */
+ int childParentListIndex = 0;
+
+ while (cpIter.hasNext()) {
+ int childParentId = ((Integer) (cpIter.next())).intValue();
+
+ if (vertexLabel[childParentId] == 0) {
+ /* unlabelled parent -- ineligible */
+ continue NEXTCHILD;
+ }
+
+ childParentList[childParentListIndex++] = childParentId;
+ }
+
+ /* all child's parents are labelled .. make eligible */
+ /* tidy up childParent array */
+ Arrays.sort(childParentList);
+ parentLabels[childId] = new int[childParentList.length];
+
+ int parentLabelsIndex = 0;
+
+ for (x = childParentList.length - 1; x >= 0; x--) {
+ parentLabels[childId][parentLabelsIndex++] = vertexLabel[childParentList[x]];
+ }
+
+ /* add to eligible */
+ eligible.add(new Integer(childId));
+ onEligible[childId] = true;
+ }
+ }
+
+ /* all nodes now labelled - assign to layers */
+ int[] vertexLayer = new int[nodecount];
+
+ for (x = 0; x < nodecount; x++) {
+ vertexLayer[x] = 0; /* 0 means unassigned */
+ }
+
+ eligible.clear();
+
+ LinkedHashSet nominated = new LinkedHashSet();
+
+ /* add all sinks and isolated nodes to eligible */
+ for (x = 0; x < nodecount; x++) {
+ if (edgesFrom[x].size() == 0) {
+ eligible.add(new Integer(x));
+ }
+ }
+
+ int currentLayer = 1;
+
+ while (eligible.size() > 0) {
+ /* sort eligible and fill layer */
+ int currentLayerSize = 0;
+ Integer[] eligibleSort = new Integer[eligible.size()];
+ eligible.toArray(eligibleSort);
+ Arrays.sort(eligibleSort);
+
+ int eligibleIndex;
+
+ for (eligibleIndex = eligibleSort.length - 1; eligibleIndex >= 0; eligibleIndex--) {
+ if (currentLayerSize == LAYER_WIDTH) {
+ break;
+ }
+
+ /* add next node to layer */
+ int nodeId = eligibleSort[eligibleIndex].intValue();
+ vertexLayer[nodeId] = currentLayer;
+ currentLayerSize++;
+
+ /* nominate parents */
+ Iterator iter = edgesTo[nodeId].iterator();
+NEXTPARENT:
+ while (iter.hasNext()) {
+ Integer parentObj = (Integer) (iter.next());
+ int parentId = parentObj.intValue();
+
+ if (vertexLayer[parentId] > 0) {
+ /* parent already done -- do not nominate */
+ continue NEXTPARENT;
+ }
+
+ Iterator pcIter = edgesFrom[parentId].iterator();
+
+ while (pcIter.hasNext()) {
+ int parentChildId = ((Integer) (pcIter.next())).intValue();
+
+ if (vertexLayer[parentChildId] == 0) {
+ /* unassigned child -- parent not nominated */
+ continue NEXTPARENT;
+ }
+ }
+
+ nominated.add(parentObj);
+ }
+
+ /* remove from eligible */
+ eligible.remove(new Integer(nodeId));
+ nominated.remove(new Integer(nodeId));
+ }
+
+ currentLayer++;
+ /* make nominees eligible */
+ eligible.addAll(nominated);
+ }
+
+ return vertexLayer;
+ }
+
+ /**
+ * Pick Horizontal coordinates within layers for a layered graph.
+ * The approach is to do two passes of edge crossing reduction. The
+ * first pass is a hybrid median/barycenter method, and the second
+ * is an adjacent (within layer) node exchange pass. These algorithms
+ * are described in Di Battista chapter 9 section 2.<br>
+ * One significant difference between the algorithms presented and
+ * this implementation is that when crossings are reduced, the graph
+ * is not first converted into a proper bipartite graph, nor are dummy
+ * verticies introduced. Instead, each node is assigned a property value
+ * representing its xCoordinate. For calculating barycenter and median
+ * values, these are based on the xCoordinate of all parents in the graph.
+ * (even those more than one layer away). During the adjacent exchange
+ * you are also not limited to nodes in adjacent layers.<br>
+ * The first pass is done from the second from the top layer, and
+ * moves downward, at each layer examining the parents of each node.
+ * All nodes are asigned an xCoordinate property. (the top layer gets
+ * arbitrary values). If more than one node had the same median value,
+ * they are evenly spaced between that value and the next higher value.<br>
+ * The second pass is also done from the second from the top layer downward.
+ * Crossing numbers are not globally computed (no array of crossing numbers
+ * is constructed). Instead a limited number of fine tuning passes occur
+ * (default = 5) where local exchanges are considered. For nodes which are
+ * adjacent in a layer, the parents of each node is put into a list sorted
+ * by xCoordinate. These parent lists are scaned to determine edge crossings
+ * in the current and the swapped orientations. Then child nodes are also
+ * examined, and edge crossings for current and swapped orientation are
+ * added to those from the parent lists. If total edge crossings are
+ * reduced, such a swap is done. During swap, the xCoordinate of the nodes
+ * are exchanged. For the bottom row, only parent nodes are considered.<br>
+ * In the case of a graph with a single layer, the algorithm is bypassed.<br>
+ * The return values are integers indicating the order of each layer based on
+ * xCoordinates of the elements (leftmost = 1).
+ * @param vertexLayer a per node layer assignment.
+ * @return an array of integers which indicate the horizontal position of each
+ * node within its assigned layer.
+ * @throws RuntimeException if this function is called on a graph which has
+ * not been reduced by a call to getReducedGraph().
+ */
+ public int[] getHorizontalPosition(int[] vertexLayer) {
+ if (!reduced) {
+ throw new RuntimeException("attempt to compute horizontal position in a non-reduced graph");
+ }
+
+ int[] position = new int[nodecount]; /* integer index on layer */
+
+ if (nodecount == 1) {
+ position[0] = 1; /* single node iff single layer -- do not check for crossings */
+
+ return position;
+ }
+
+ double[] xPosition = new double[nodecount]; /* x coordinate used for median and barycenter */
+ double[] median = new double[nodecount];
+ double[] baryCenter = new double[nodecount];
+ int[] nextFreeSpotOnLayer = new int[nodecount + 1];
+ LinkedList[] nodesOnLayer = new LinkedList[nodecount + 1];
+ int x;
+ int topLayer = 0;
+
+ for (x = 0; x < nodecount; x++) {
+ position[x] = 0; /* 0 means unpositioned */
+ nextFreeSpotOnLayer[x + 1] = 1;
+
+ int nLayer = vertexLayer[x];
+
+ if (nodesOnLayer[nLayer] == null) {
+ nodesOnLayer[nLayer] = new LinkedList();
+ }
+
+ nodesOnLayer[nLayer].add(new Integer(x));
+
+ if (nLayer > topLayer) {
+ topLayer = nLayer;
+ }
+ }
+
+ /* top level all sources - order arbitrary */
+ ListIterator iter = nodesOnLayer[topLayer].listIterator();
+ double nextx = 0.0;
+
+ while (iter.hasNext()) {
+ int nodeId = ((Integer) iter.next()).intValue();
+ xPosition[nodeId] = nextx;
+ median[nodeId] = nextx;
+ baryCenter[nodeId] = nextx;
+ nextx += 1.0;
+ }
+
+ /* hybrid median/barycenter approach */
+ int scanLayer;
+
+ for (scanLayer = topLayer - 1; scanLayer > 0; scanLayer--) {
+ /* compute median and barycenter */
+ int nodeInsertPos = 0;
+ TwinDoubleSortNode[] nodeOrder = new TwinDoubleSortNode[nodesOnLayer[scanLayer].size()];
+ iter = nodesOnLayer[scanLayer].listIterator();
+
+ while (iter.hasNext()) {
+ int nodeId = ((Integer) iter.next()).intValue();
+
+ if (edgesTo[nodeId].isEmpty()) {
+ median[nodeId] = 0;
+ baryCenter[nodeId] = 0;
+ } else {
+ int parentNum = 0;
+ double[] parentX = new double[edgesTo[nodeId].size()];
+ Iterator parentIter = edgesTo[nodeId].listIterator();
+ baryCenter[nodeId] = 0.0;
+
+ while (parentIter.hasNext()) {
+ int parentId = ((Integer) parentIter.next()).intValue();
+ baryCenter[nodeId] += xPosition[parentId];
+ parentX[parentNum++] = xPosition[parentId];
+ }
+
+ Arrays.sort(parentX);
+ median[nodeId] = parentX[parentX.length / 2];
+ baryCenter[nodeId] /= edgesTo[nodeId].size();
+ }
+
+ nodeOrder[nodeInsertPos++] = new TwinDoubleSortNode(median[nodeId],
+ baryCenter[nodeId], nodeId);
+ }
+
+ /* order and position nodes */
+ double nextHigherMedian = -Double.MAX_VALUE; /* unknown */
+ int numNodesToSpread = 0;
+ Arrays.sort(nodeOrder);
+
+ for (x = 0; x < nodeOrder.length; x++) {
+ int nodeToPosition = nodeOrder[x].getValue();
+
+ if ((x > 0) && (median[nodeToPosition] == median[nodeOrder[x - 1].getValue()])) {
+ if (nextHigherMedian == -Double.MAX_VALUE) {
+ /* find next higher Median through search */
+ /* the reason this is being done so oddly is that parents may
+ span several layers above -- so if the two sides of the
+ bipartite graph are the sort layer and a constructed layer
+ consisting of all the parents of nodes in this layer, then
+ the parents must all be placed in a consistant coordinate
+ system */
+ numNodesToSpread = 1;
+
+ int y;
+
+ for (y = x + 1; y < nodeOrder.length; y++) {
+ if (median[nodeOrder[y].getValue()] > median[nodeOrder[y - 1].getValue()]) {
+ nextHigherMedian = median[nodeOrder[y].getValue()];
+
+ break;
+ }
+
+ numNodesToSpread++;
+ }
+
+ if (nextHigherMedian == -Double.MAX_VALUE) {
+ /* there is no next higher median - this is the highest */
+ nextHigherMedian = median[nodeOrder[x].getValue()] + 1.0;
+ }
+ }
+
+ xPosition[nodeToPosition] = xPosition[nodeOrder[x - 1].getValue()]
+ + ((nextHigherMedian
+ - xPosition[nodeOrder[x - 1].getValue()]) / (numNodesToSpread--
+ + 1));
+ } else {
+ nextHigherMedian = -Double.MAX_VALUE; /* reset .. now unknown */
+ xPosition[nodeToPosition] = median[nodeToPosition];
+ }
+ }
+
+ /* set position of nodes on this level */
+ for (x = 0; x < nodeOrder.length; x++) {
+ position[nodeOrder[x].getValue()] = x + 1;
+ }
+ }
+
+ /* fine tune with adjacent exchange - looking up/down for interior layers, up only for bottom layer */
+ /* first jitter the nodes to insure that no node is directly above another (from median) */
+ double jitterIncrement = Double.MIN_VALUE * 10;
+ double jitterSize = 0;
+
+ for (x = 0; x < nodecount; x++) {
+ xPosition[x] += jitterSize;
+ jitterSize += jitterIncrement;
+ }
+
+ Object[] parent = new Object[nodecount];
+ Object[] child = new Object[nodecount];
+
+ for (scanLayer = topLayer - 1; scanLayer > 1; scanLayer--) {
+ /* get the order for this layer */
+ int[] nodeInPosition = new int[nodesOnLayer[scanLayer].size()];
+ iter = nodesOnLayer[scanLayer].listIterator();
+
+ while (iter.hasNext()) {
+ int nodenum = ((Integer) iter.next()).intValue();
+ nodeInPosition[position[nodenum] - 1] = nodenum;
+ }
+
+ int sweepCounter = MAX_ADJACENT_EXCHANGE_PASSES;
+ boolean done = false;
+
+ /* do not compute crossing numbers -- precomputing all combinations would be
+ O(L*(P+C), L = # of nodes in layer, P = # of nodes in parent, C = in child */
+ while (!done && (sweepCounter-- > 0)) {
+ done = true;
+
+ int scanpos;
+
+ for (scanpos = 1; scanpos < nodeInPosition.length; scanpos++) {
+ int leftnode = nodeInPosition[scanpos - 1];
+ int rightnode = nodeInPosition[scanpos];
+ int i;
+ double[] arrayBuffer;
+
+ if (parent[leftnode] == null) {
+ /* sort list of parents by X pos */
+ arrayBuffer = new double[edgesTo[leftnode].size()];
+
+ Iterator parentIter = edgesTo[leftnode].listIterator();
+ i = 0;
+
+ while (parentIter.hasNext()) {
+ int parentId = ((Integer) parentIter.next()).intValue();
+ arrayBuffer[i++] = xPosition[parentId];
+ }
+
+ Arrays.sort(arrayBuffer);
+ parent[leftnode] = arrayBuffer;
+ }
+
+ if (child[leftnode] == null) {
+ /* sort list of children by X pos */
+ arrayBuffer = new double[edgesFrom[leftnode].size()];
+
+ Iterator childIter = edgesFrom[leftnode].listIterator();
+ i = 0;
+
+ while (childIter.hasNext()) {
+ int childId = ((Integer) childIter.next()).intValue();
+ arrayBuffer[i++] = xPosition[childId];
+ }
+
+ Arrays.sort(arrayBuffer);
+ child[leftnode] = arrayBuffer;
+ }
+
+ if (parent[rightnode] == null) {
+ /* sort list of parents by X pos */
+ arrayBuffer = new double[edgesTo[rightnode].size()];
+
+ Iterator parentIter = edgesTo[rightnode].listIterator();
+ i = 0;
+
+ while (parentIter.hasNext()) {
+ int parentId = ((Integer) parentIter.next()).intValue();
+ arrayBuffer[i++] = xPosition[parentId];
+ }
+
+ Arrays.sort(arrayBuffer);
+ parent[rightnode] = arrayBuffer;
+ }
+
+ if (child[rightnode] == null) {
+ /* sort list of children by X pos */
+ arrayBuffer = new double[edgesFrom[rightnode].size()];
+
+ Iterator childIter = edgesFrom[rightnode].listIterator();
+ i = 0;
+
+ while (childIter.hasNext()) {
+ int childId = ((Integer) childIter.next()).intValue();
+ arrayBuffer[i++] = xPosition[childId];
+ }
+
+ Arrays.sort(arrayBuffer);
+ child[rightnode] = arrayBuffer;
+ }
+
+ int nowCrossCount = 0;
+ int revCrossCount = 0;
+ double[] leftSet = (double[]) parent[leftnode];
+ double[] rightSet = (double[]) parent[rightnode];
+ int leftIndex = 0;
+ int rightIndex = 0;
+
+ while ((leftIndex < leftSet.length) && (rightIndex < rightSet.length)) {
+ if (rightSet[rightIndex] < leftSet[leftIndex]) {
+ nowCrossCount += (leftSet.length - leftIndex);
+ rightIndex++;
+ } else {
+ leftIndex++;
+ }
+ }
+
+ leftIndex = 0;
+ rightIndex = 0;
+
+ while ((leftIndex < leftSet.length) && (rightIndex < rightSet.length)) {
+ if (rightSet[rightIndex] > leftSet[leftIndex]) {
+ revCrossCount += (rightSet.length - rightIndex);
+ leftIndex++;
+ } else {
+ rightIndex++;
+ }
+ }
+
+ leftSet = (double[]) child[leftnode];
+ rightSet = (double[]) child[rightnode];
+ leftIndex = 0;
+ rightIndex = 0;
+
+ while ((leftIndex < leftSet.length) && (rightIndex < rightSet.length)) {
+ if (rightSet[rightIndex] < leftSet[leftIndex]) {
+ nowCrossCount += (leftSet.length - leftIndex);
+ rightIndex++;
+ } else {
+ leftIndex++;
+ }
+ }
+
+ leftIndex = 0;
+ rightIndex = 0;
+
+ while ((leftIndex < leftSet.length) && (rightIndex < rightSet.length)) {
+ if (rightSet[rightIndex] > leftSet[leftIndex]) {
+ revCrossCount += (rightSet.length - rightIndex);
+ leftIndex++;
+ } else {
+ rightIndex++;
+ }
+ }
+
+ if (nowCrossCount > revCrossCount) {
+ int tmp = position[leftnode];
+ position[leftnode] = position[rightnode];
+ position[rightnode] = tmp;
+ nodeInPosition[scanpos] = leftnode;
+ nodeInPosition[scanpos - 1] = rightnode;
+
+ double dtmp = xPosition[leftnode];
+ xPosition[leftnode] = xPosition[rightnode];
+ xPosition[rightnode] = dtmp;
+ done = false;
+ }
+ }
+ }
+ }
+
+ /* adjacency exchange bottom layer */
+ /* get the order for this layer */
+ int[] nodeInPosition = new int[nodesOnLayer[1].size()];
+ iter = nodesOnLayer[1].listIterator();
+
+ while (iter.hasNext()) {
+ int nodenum = ((Integer) iter.next()).intValue();
+ nodeInPosition[position[nodenum] - 1] = nodenum;
+ }
+
+ int sweepCounter = MAX_ADJACENT_EXCHANGE_PASSES;
+ boolean done = false;
+
+ /* do not compute crossing numbers -- precomputing all combinations would be
+ O(L*P), L = # of nodes in layer, P = # of nodes in parent */
+ while (!done && (sweepCounter-- > 0)) {
+ done = true;
+
+ int scanpos;
+
+ for (scanpos = 1; scanpos < nodeInPosition.length; scanpos++) {
+ int leftnode = nodeInPosition[scanpos - 1];
+ int rightnode = nodeInPosition[scanpos];
+ int i;
+ double[] arrayBuffer;
+
+ if (parent[leftnode] == null) {
+ /* sort list of parents by X pos */
+ arrayBuffer = new double[edgesTo[leftnode].size()];
+
+ Iterator parentIter = edgesTo[leftnode].listIterator();
+ i = 0;
+
+ while (parentIter.hasNext()) {
+ int parentId = ((Integer) parentIter.next()).intValue();
+ arrayBuffer[i++] = xPosition[parentId];
+ }
+
+ Arrays.sort(arrayBuffer);
+ parent[leftnode] = arrayBuffer;
+ }
+
+ if (parent[rightnode] == null) {
+ /* sort list of parents by X pos */
+ arrayBuffer = new double[edgesTo[rightnode].size()];
+
+ Iterator parentIter = edgesTo[rightnode].listIterator();
+ i = 0;
+
+ while (parentIter.hasNext()) {
+ int parentId = ((Integer) parentIter.next()).intValue();
+ arrayBuffer[i++] = xPosition[parentId];
+ }
+
+ Arrays.sort(arrayBuffer);
+ parent[rightnode] = arrayBuffer;
+ }
+
+ int nowCrossCount = 0;
+ int revCrossCount = 0;
+ double[] leftSet = (double[]) parent[leftnode];
+ double[] rightSet = (double[]) parent[rightnode];
+ int leftIndex = 0;
+ int rightIndex = 0;
+
+ while ((leftIndex < leftSet.length) && (rightIndex < rightSet.length)) {
+ if (rightSet[rightIndex] < leftSet[leftIndex]) {
+ nowCrossCount += (leftSet.length - leftIndex);
+ rightIndex++;
+ } else {
+ leftIndex++;
+ }
+ }
+
+ leftIndex = 0;
+ rightIndex = 0;
+
+ while ((leftIndex < leftSet.length) && (rightIndex < rightSet.length)) {
+ if (rightSet[rightIndex] > leftSet[leftIndex]) {
+ revCrossCount += (rightSet.length - rightIndex);
+ leftIndex++;
+ } else {
+ rightIndex++;
+ }
+ }
+
+ if (nowCrossCount > revCrossCount) {
+ int tmp = position[leftnode];
+ position[leftnode] = position[rightnode];
+ position[rightnode] = tmp;
+ nodeInPosition[scanpos] = leftnode;
+ nodeInPosition[scanpos - 1] = rightnode;
+
+ double dtmp = xPosition[leftnode];
+ xPosition[leftnode] = xPosition[rightnode];
+ xPosition[rightnode] = dtmp;
+ done = false;
+ }
+ }
+ }
+
+ return position;
+ }
+
+ /**
+ * Like upper function but instead of top layer nodes chosen arbitrarily, it uses
+ * middle layer nodes. It positions nodes from other layers using the given middle
+ * layer ordering.
+ * @param vertexLayer
+ * @return
+ */
+ public int[] getHorizontalPositionMiddle(int[] vertexLayer) {
+ if (!reduced) {
+ throw new RuntimeException("attempt to compute horizontal position in a non-reduced graph");
+ }
+
+ int[] position = new int[nodecount]; /* integer index on layer */
+
+ if (nodecount == 1) {
+ position[0] = 1; /* single node iff single layer -- do not check for crossings */
+
+ return position;
+ }
+
+ double[] xPosition = new double[nodecount]; /* x coordinate used for median and barycenter */
+ double[] median = new double[nodecount];
+ double[] baryCenter = new double[nodecount];
+ int[] nextFreeSpotOnLayer = new int[nodecount + 1];
+ LinkedList[] nodesOnLayer = new LinkedList[nodecount + 1];
+ int x;
+ int topLayer = 0;
+ int middleLayer = 0;
+
+ for (x = 0; x < nodecount; x++) {
+ position[x] = 0; /* 0 means unpositioned */
+ nextFreeSpotOnLayer[x + 1] = 1;
+
+ int nLayer = vertexLayer[x];
+
+ if (nodesOnLayer[nLayer] == null) {
+ nodesOnLayer[nLayer] = new LinkedList();
+ }
+
+ nodesOnLayer[nLayer].add(new Integer(x));
+
+ if (nLayer > topLayer) {
+ topLayer = nLayer;
+ }
+ }
+
+ /* middle level all sources - order arbitrary */
+ middleLayer = (topLayer + 1) / 2;
+
+ ListIterator iter = nodesOnLayer[middleLayer].listIterator();
+ double nextx = 0.0;
+
+ while (iter.hasNext()) {
+ int nodeId = ((Integer) iter.next()).intValue();
+ xPosition[nodeId] = nextx;
+ median[nodeId] = nextx;
+ baryCenter[nodeId] = nextx;
+ nextx += 1.0;
+ }
+
+ /* hybrid median/barycenter approach */
+ int scanLayer;
+
+ for (scanLayer = middleLayer + 1; scanLayer <= topLayer; scanLayer++) {
+ /* compute median and barycenter */
+ int nodeInsertPos = 0;
+ TwinDoubleSortNode[] nodeOrder = new TwinDoubleSortNode[nodesOnLayer[scanLayer].size()];
+ iter = nodesOnLayer[scanLayer].listIterator();
+
+ while (iter.hasNext()) {
+ int nodeId = ((Integer) iter.next()).intValue();
+
+ if (edgesFrom[nodeId].isEmpty()) {
+ median[nodeId] = 0;
+ baryCenter[nodeId] = 0;
+ } else {
+ int parentNum = 0;
+ double[] parentX = new double[edgesFrom[nodeId].size()];
+ Iterator parentIter = edgesFrom[nodeId].listIterator();
+ baryCenter[nodeId] = 0.0;
+
+ while (parentIter.hasNext()) {
+ int parentId = ((Integer) parentIter.next()).intValue();
+ baryCenter[nodeId] += xPosition[parentId];
+ parentX[parentNum++] = xPosition[parentId];
+ }
+
+ Arrays.sort(parentX);
+ median[nodeId] = parentX[parentX.length / 2];
+ baryCenter[nodeId] /= edgesFrom[nodeId].size();
+ }
+
+ nodeOrder[nodeInsertPos++] = new TwinDoubleSortNode(median[nodeId],
+ baryCenter[nodeId], nodeId);
+ }
+
+ /* order and position nodes */
+ double nextHigherMedian = -Double.MAX_VALUE; /* unknown */
+ int numNodesToSpread = 0;
+ Arrays.sort(nodeOrder);
+
+ for (x = 0; x < nodeOrder.length; x++) {
+ int nodeToPosition = nodeOrder[x].getValue();
+
+ if ((x > 0) && (median[nodeToPosition] == median[nodeOrder[x - 1].getValue()])) {
+ if (nextHigherMedian == -Double.MAX_VALUE) {
+ /* find next higher Median through search */
+ /* the reason this is being done so oddly is that parents may
+ span several layers above -- so if the two sides of the
+ bipartite graph are the sort layer and a constructed layer
+ consisting of all the parents of nodes in this layer, then
+ the parents must all be placed in a consistant coordinate
+ system */
+ numNodesToSpread = 1;
+
+ int y;
+
+ for (y = x + 1; y < nodeOrder.length; y++) {
+ if (median[nodeOrder[y].getValue()] > median[nodeOrder[y - 1].getValue()]) {
+ nextHigherMedian = median[nodeOrder[y].getValue()];
+
+ break;
+ }
+
+ numNodesToSpread++;
+ }
+
+ if (nextHigherMedian == -Double.MAX_VALUE) {
+ /* there is no next higher median - this is the highest */
+ nextHigherMedian = median[nodeOrder[x].getValue()] + 1.0;
+ }
+ }
+
+ xPosition[nodeToPosition] = xPosition[nodeOrder[x - 1].getValue()]
+ + ((nextHigherMedian
+ - xPosition[nodeOrder[x - 1].getValue()]) / (numNodesToSpread--
+ + 1));
+ } else {
+ nextHigherMedian = -Double.MAX_VALUE; /* reset .. now unknown */
+ xPosition[nodeToPosition] = median[nodeToPosition];
+ }
+ }
+
+ /* set position of nodes on this level */
+ for (x = 0; x < nodeOrder.length; x++) {
+ position[nodeOrder[x].getValue()] = x + 1;
+ }
+ }
+
+ for (scanLayer = middleLayer - 1; scanLayer > 0; scanLayer--) {
+ /* compute median and barycenter */
+ int nodeInsertPos = 0;
+ TwinDoubleSortNode[] nodeOrder = new TwinDoubleSortNode[nodesOnLayer[scanLayer].size()];
+ iter = nodesOnLayer[scanLayer].listIterator();
+
+ while (iter.hasNext()) {
+ int nodeId = ((Integer) iter.next()).intValue();
+
+ if (edgesTo[nodeId].isEmpty()) {
+ median[nodeId] = 0;
+ baryCenter[nodeId] = 0;
+ } else {
+ int parentNum = 0;
+ double[] parentX = new double[edgesTo[nodeId].size()];
+ Iterator parentIter = edgesTo[nodeId].listIterator();
+ baryCenter[nodeId] = 0.0;
+
+ while (parentIter.hasNext()) {
+ int parentId = ((Integer) parentIter.next()).intValue();
+ baryCenter[nodeId] += xPosition[parentId];
+ parentX[parentNum++] = xPosition[parentId];
+ }
+
+ Arrays.sort(parentX);
+ median[nodeId] = parentX[parentX.length / 2];
+ baryCenter[nodeId] /= edgesTo[nodeId].size();
+ }
+
+ nodeOrder[nodeInsertPos++] = new TwinDoubleSortNode(median[nodeId],
+ baryCenter[nodeId], nodeId);
+ }
+
+ /* order and position nodes */
+ double nextHigherMedian = -Double.MAX_VALUE; /* unknown */
+ int numNodesToSpread = 0;
+ Arrays.sort(nodeOrder);
+
+ for (x = 0; x < nodeOrder.length; x++) {
+ int nodeToPosition = nodeOrder[x].getValue();
+
+ if ((x > 0) && (median[nodeToPosition] == median[nodeOrder[x - 1].getValue()])) {
+ if (nextHigherMedian == -Double.MAX_VALUE) {
+ /* find next higher Median through search */
+ /* the reason this is being done so oddly is that parents may
+ span several layers above -- so if the two sides of the
+ bipartite graph are the sort layer and a constructed layer
+ consisting of all the parents of nodes in this layer, then
+ the parents must all be placed in a consistant coordinate
+ system */
+ numNodesToSpread = 1;
+
+ int y;
+
+ for (y = x + 1; y < nodeOrder.length; y++) {
+ if (median[nodeOrder[y].getValue()] > median[nodeOrder[y - 1].getValue()]) {
+ nextHigherMedian = median[nodeOrder[y].getValue()];
+
+ break;
+ }
+
+ numNodesToSpread++;
+ }
+
+ if (nextHigherMedian == -Double.MAX_VALUE) {
+ /* there is no next higher median - this is the highest */
+ nextHigherMedian = median[nodeOrder[x].getValue()] + 1.0;
+ }
+ }
+
+ xPosition[nodeToPosition] = xPosition[nodeOrder[x - 1].getValue()]
+ + ((nextHigherMedian
+ - xPosition[nodeOrder[x - 1].getValue()]) / (numNodesToSpread--
+ + 1));
+ } else {
+ nextHigherMedian = -Double.MAX_VALUE; /* reset .. now unknown */
+ xPosition[nodeToPosition] = median[nodeToPosition];
+ }
+ }
+
+ /* set position of nodes on this level */
+ for (x = 0; x < nodeOrder.length; x++) {
+ position[nodeOrder[x].getValue()] = x + 1;
+ }
+ }
+
+ /* fine tune with adjacent exchange - looking up/down for interior layers, up only for bottom layer */
+ /* first jitter the nodes to insure that no node is directly above another (from median) */
+ double jitterIncrement = Double.MIN_VALUE * 10;
+ double jitterSize = 0;
+
+ for (x = 0; x < nodecount; x++) {
+ xPosition[x] += jitterSize;
+ jitterSize += jitterIncrement;
+ }
+
+ Object[] parent = new Object[nodecount];
+ Object[] child = new Object[nodecount];
+
+ for (scanLayer = topLayer; scanLayer > 1; scanLayer--) {
+ if (scanLayer == middleLayer)
+ continue;
+
+ /* get the order for this layer */
+ int[] nodeInPosition = new int[nodesOnLayer[scanLayer].size()];
+ iter = nodesOnLayer[scanLayer].listIterator();
+
+ while (iter.hasNext()) {
+ int nodenum = ((Integer) iter.next()).intValue();
+ nodeInPosition[position[nodenum] - 1] = nodenum;
+ }
+
+ int sweepCounter = MAX_ADJACENT_EXCHANGE_PASSES;
+ boolean done = false;
+
+ /* do not compute crossing numbers -- precomputing all combinations would be
+ O(L*(P+C), L = # of nodes in layer, P = # of nodes in parent, C = in child */
+ while (!done && (sweepCounter-- > 0)) {
+ done = true;
+
+ int scanpos;
+
+ for (scanpos = 1; scanpos < nodeInPosition.length; scanpos++) {
+ int leftnode = nodeInPosition[scanpos - 1];
+ int rightnode = nodeInPosition[scanpos];
+ int i;
+ double[] arrayBuffer;
+
+ if (parent[leftnode] == null) {
+ /* sort list of parents by X pos */
+ arrayBuffer = new double[edgesTo[leftnode].size()];
+
+ Iterator parentIter = edgesTo[leftnode].listIterator();
+ i = 0;
+
+ while (parentIter.hasNext()) {
+ int parentId = ((Integer) parentIter.next()).intValue();
+ arrayBuffer[i++] = xPosition[parentId];
+ }
+
+ Arrays.sort(arrayBuffer);
+ parent[leftnode] = arrayBuffer;
+ }
+
+ if (child[leftnode] == null) {
+ /* sort list of children by X pos */
+ arrayBuffer = new double[edgesFrom[leftnode].size()];
+
+ Iterator childIter = edgesFrom[leftnode].listIterator();
+ i = 0;
+
+ while (childIter.hasNext()) {
+ int childId = ((Integer) childIter.next()).intValue();
+ arrayBuffer[i++] = xPosition[childId];
+ }
+
+ Arrays.sort(arrayBuffer);
+ child[leftnode] = arrayBuffer;
+ }
+
+ if (parent[rightnode] == null) {
+ /* sort list of parents by X pos */
+ arrayBuffer = new double[edgesTo[rightnode].size()];
+
+ Iterator parentIter = edgesTo[rightnode].listIterator();
+ i = 0;
+
+ while (parentIter.hasNext()) {
+ int parentId = ((Integer) parentIter.next()).intValue();
+ arrayBuffer[i++] = xPosition[parentId];
+ }
+
+ Arrays.sort(arrayBuffer);
+ parent[rightnode] = arrayBuffer;
+ }
+
+ if (child[rightnode] == null) {
+ /* sort list of children by X pos */
+ arrayBuffer = new double[edgesFrom[rightnode].size()];
+
+ Iterator childIter = edgesFrom[rightnode].listIterator();
+ i = 0;
+
+ while (childIter.hasNext()) {
+ int childId = ((Integer) childIter.next()).intValue();
+ arrayBuffer[i++] = xPosition[childId];
+ }
+
+ Arrays.sort(arrayBuffer);
+ child[rightnode] = arrayBuffer;
+ }
+
+ int nowCrossCount = 0;
+ int revCrossCount = 0;
+ double[] leftSet = (double[]) parent[leftnode];
+ double[] rightSet = (double[]) parent[rightnode];
+ int leftIndex = 0;
+ int rightIndex = 0;
+
+ while ((leftIndex < leftSet.length) && (rightIndex < rightSet.length)) {
+ if (rightSet[rightIndex] < leftSet[leftIndex]) {
+ nowCrossCount += (leftSet.length - leftIndex);
+ rightIndex++;
+ } else {
+ leftIndex++;
+ }
+ }
+
+ leftIndex = 0;
+ rightIndex = 0;
+
+ while ((leftIndex < leftSet.length) && (rightIndex < rightSet.length)) {
+ if (rightSet[rightIndex] > leftSet[leftIndex]) {
+ revCrossCount += (rightSet.length - rightIndex);
+ leftIndex++;
+ } else {
+ rightIndex++;
+ }
+ }
+
+ leftSet = (double[]) child[leftnode];
+ rightSet = (double[]) child[rightnode];
+ leftIndex = 0;
+ rightIndex = 0;
+
+ while ((leftIndex < leftSet.length) && (rightIndex < rightSet.length)) {
+ if (rightSet[rightIndex] < leftSet[leftIndex]) {
+ nowCrossCount += (leftSet.length - leftIndex);
+ rightIndex++;
+ } else {
+ leftIndex++;
+ }
+ }
+
+ leftIndex = 0;
+ rightIndex = 0;
+
+ while ((leftIndex < leftSet.length) && (rightIndex < rightSet.length)) {
+ if (rightSet[rightIndex] > leftSet[leftIndex]) {
+ revCrossCount += (rightSet.length - rightIndex);
+ leftIndex++;
+ } else {
+ rightIndex++;
+ }
+ }
+
+ if (nowCrossCount > revCrossCount) {
+ int tmp = position[leftnode];
+ position[leftnode] = position[rightnode];
+ position[rightnode] = tmp;
+ nodeInPosition[scanpos] = leftnode;
+ nodeInPosition[scanpos - 1] = rightnode;
+
+ double dtmp = xPosition[leftnode];
+ xPosition[leftnode] = xPosition[rightnode];
+ xPosition[rightnode] = dtmp;
+ done = false;
+ }
+ }
+ }
+ }
+
+ if (middleLayer != 1) {
+ /* adjacency exchange bottom layer */
+ /* get the order for this layer */
+ int[] nodeInPosition = new int[nodesOnLayer[1].size()];
+ iter = nodesOnLayer[1].listIterator();
+
+ while (iter.hasNext()) {
+ int nodenum = ((Integer) iter.next()).intValue();
+ nodeInPosition[position[nodenum] - 1] = nodenum;
+ }
+
+ int sweepCounter = MAX_ADJACENT_EXCHANGE_PASSES;
+ boolean done = false;
+
+ /* do not compute crossing numbers -- precomputing all combinations would be
+ O(L*P), L = # of nodes in layer, P = # of nodes in parent */
+ while (!done && (sweepCounter-- > 0)) {
+ done = true;
+
+ int scanpos;
+
+ for (scanpos = 1; scanpos < nodeInPosition.length; scanpos++) {
+ int leftnode = nodeInPosition[scanpos - 1];
+ int rightnode = nodeInPosition[scanpos];
+ int i;
+ double[] arrayBuffer;
+
+ if (parent[leftnode] == null) {
+ /* sort list of parents by X pos */
+ arrayBuffer = new double[edgesTo[leftnode].size()];
+
+ Iterator parentIter = edgesTo[leftnode].listIterator();
+ i = 0;
+
+ while (parentIter.hasNext()) {
+ int parentId = ((Integer) parentIter.next()).intValue();
+ arrayBuffer[i++] = xPosition[parentId];
+ }
+
+ Arrays.sort(arrayBuffer);
+ parent[leftnode] = arrayBuffer;
+ }
+
+ if (parent[rightnode] == null) {
+ /* sort list of parents by X pos */
+ arrayBuffer = new double[edgesTo[rightnode].size()];
+
+ Iterator parentIter = edgesTo[rightnode].listIterator();
+ i = 0;
+
+ while (parentIter.hasNext()) {
+ int parentId = ((Integer) parentIter.next()).intValue();
+ arrayBuffer[i++] = xPosition[parentId];
+ }
+
+ Arrays.sort(arrayBuffer);
+ parent[rightnode] = arrayBuffer;
+ }
+
+ int nowCrossCount = 0;
+ int revCrossCount = 0;
+ double[] leftSet = (double[]) parent[leftnode];
+ double[] rightSet = (double[]) parent[rightnode];
+ int leftIndex = 0;
+ int rightIndex = 0;
+
+ while ((leftIndex < leftSet.length) && (rightIndex < rightSet.length)) {
+ if (rightSet[rightIndex] < leftSet[leftIndex]) {
+ nowCrossCount += (leftSet.length - leftIndex);
+ rightIndex++;
+ } else {
+ leftIndex++;
+ }
+ }
+
+ leftIndex = 0;
+ rightIndex = 0;
+
+ while ((leftIndex < leftSet.length) && (rightIndex < rightSet.length)) {
+ if (rightSet[rightIndex] > leftSet[leftIndex]) {
+ revCrossCount += (rightSet.length - rightIndex);
+ leftIndex++;
+ } else {
+ rightIndex++;
+ }
+ }
+
+ if (nowCrossCount > revCrossCount) {
+ int tmp = position[leftnode];
+ position[leftnode] = position[rightnode];
+ position[rightnode] = tmp;
+ nodeInPosition[scanpos] = leftnode;
+ nodeInPosition[scanpos - 1] = rightnode;
+
+ double dtmp = xPosition[leftnode];
+ xPosition[leftnode] = xPosition[rightnode];
+ xPosition[rightnode] = dtmp;
+ done = false;
+ }
+ }
+ }
+ }
+
+ return position;
+ }
+
+ /**
+ * Like upper function but instead of top layer nodes chosen arbitrarily, it uses
+ * bottom layer nodes. It positions nodes from other layers using the given bottom
+ * layer ordering.
+ * @param vertexLayer
+ * @return
+ */
+ public int[] getHorizontalPositionReverse(int[] vertexLayer) {
+ if (!reduced) {
+ throw new RuntimeException("attempt to compute horizontal position in a non-reduced graph");
+ }
+
+ int[] position = new int[nodecount]; /* integer index on layer */
+
+ if (nodecount == 1) {
+ position[0] = 1; /* single node iff single layer -- do not check for crossings */
+
+ return position;
+ }
+
+ double[] xPosition = new double[nodecount]; /* x coordinate used for median and barycenter */
+ double[] median = new double[nodecount];
+ double[] baryCenter = new double[nodecount];
+ int[] nextFreeSpotOnLayer = new int[nodecount + 1];
+ LinkedList[] nodesOnLayer = new LinkedList[nodecount + 1];
+ int x;
+ int bottomLayer = 1;
+ int topLayer = 0;
+
+ for (x = 0; x < nodecount; x++) {
+ position[x] = 0; /* 0 means unpositioned */
+ nextFreeSpotOnLayer[x + 1] = 1;
+
+ int nLayer = vertexLayer[x];
+
+ if (nodesOnLayer[nLayer] == null) {
+ nodesOnLayer[nLayer] = new LinkedList();
+ }
+
+ nodesOnLayer[nLayer].add(new Integer(x));
+
+ if (nLayer > topLayer) {
+ topLayer = nLayer;
+ }
+ }
+
+ /* bottom level all sources - order arbitrary */
+ ListIterator iter = nodesOnLayer[bottomLayer].listIterator();
+ double nextx = 0.0;
+
+ while (iter.hasNext()) {
+ int nodeId = ((Integer) iter.next()).intValue();
+ xPosition[nodeId] = nextx;
+ median[nodeId] = nextx;
+ baryCenter[nodeId] = nextx;
+ nextx += 1.0;
+ }
+
+ /* hybrid median/barycenter approach */
+ int scanLayer;
+
+ for (scanLayer = bottomLayer + 1; scanLayer <= topLayer; scanLayer++) {
+ /* compute median and barycenter */
+ int nodeInsertPos = 0;
+ TwinDoubleSortNode[] nodeOrder = new TwinDoubleSortNode[nodesOnLayer[scanLayer].size()];
+ iter = nodesOnLayer[scanLayer].listIterator();
+
+ while (iter.hasNext()) {
+ int nodeId = ((Integer) iter.next()).intValue();
+
+ if (edgesFrom[nodeId].isEmpty()) {
+ median[nodeId] = 0;
+ baryCenter[nodeId] = 0;
+ } else {
+ int parentNum = 0;
+ double[] parentX = new double[edgesFrom[nodeId].size()];
+ Iterator parentIter = edgesFrom[nodeId].listIterator();
+ baryCenter[nodeId] = 0.0;
+
+ while (parentIter.hasNext()) {
+ int parentId = ((Integer) parentIter.next()).intValue();
+ baryCenter[nodeId] += xPosition[parentId];
+ parentX[parentNum++] = xPosition[parentId];
+ }
+
+ Arrays.sort(parentX);
+ median[nodeId] = parentX[parentX.length / 2];
+ baryCenter[nodeId] /= edgesFrom[nodeId].size();
+ }
+
+ nodeOrder[nodeInsertPos++] = new TwinDoubleSortNode(median[nodeId],
+ baryCenter[nodeId], nodeId);
+ }
+
+ /* order and position nodes */
+ double nextHigherMedian = -Double.MAX_VALUE; /* unknown */
+ int numNodesToSpread = 0;
+ Arrays.sort(nodeOrder);
+
+ for (x = 0; x < nodeOrder.length; x++) {
+ int nodeToPosition = nodeOrder[x].getValue();
+
+ if ((x > 0) && (median[nodeToPosition] == median[nodeOrder[x - 1].getValue()])) {
+ if (nextHigherMedian == -Double.MAX_VALUE) {
+ /* find next higher Median through search */
+ /* the reason this is being done so oddly is that parents may
+ span several layers above -- so if the two sides of the
+ bipartite graph are the sort layer and a constructed layer
+ consisting of all the parents of nodes in this layer, then
+ the parents must all be placed in a consistant coordinate
+ system */
+ numNodesToSpread = 1;
+
+ int y;
+
+ for (y = x + 1; y < nodeOrder.length; y++) {
+ if (median[nodeOrder[y].getValue()] > median[nodeOrder[y - 1].getValue()]) {
+ nextHigherMedian = median[nodeOrder[y].getValue()];
+
+ break;
+ }
+
+ numNodesToSpread++;
+ }
+
+ if (nextHigherMedian == -Double.MAX_VALUE) {
+ /* there is no next higher median - this is the highest */
+ nextHigherMedian = median[nodeOrder[x].getValue()] + 1.0;
+ }
+ }
+
+ xPosition[nodeToPosition] = xPosition[nodeOrder[x - 1].getValue()]
+ + ((nextHigherMedian
+ - xPosition[nodeOrder[x - 1].getValue()]) / (numNodesToSpread--
+ + 1));
+ } else {
+ nextHigherMedian = -Double.MAX_VALUE; /* reset .. now unknown */
+ xPosition[nodeToPosition] = median[nodeToPosition];
+ }
+ }
+
+ /* set position of nodes on this level */
+ for (x = 0; x < nodeOrder.length; x++) {
+ position[nodeOrder[x].getValue()] = x + 1;
+ }
+ }
+
+ /* fine tune with adjacent exchange - looking up/down for interior layers, up only for bottom layer */
+ /* first jitter the nodes to insure that no node is directly above another (from median) */
+ double jitterIncrement = Double.MIN_VALUE * 10;
+ double jitterSize = 0;
+
+ for (x = 0; x < nodecount; x++) {
+ xPosition[x] += jitterSize;
+ jitterSize += jitterIncrement;
+ }
+
+ Object[] parent = new Object[nodecount];
+ Object[] child = new Object[nodecount];
+
+ //obradi posebno za topLayer
+ for (scanLayer = bottomLayer + 1; scanLayer <= topLayer; scanLayer++) {
+ /* get the order for this layer */
+ int[] nodeInPosition = new int[nodesOnLayer[scanLayer].size()];
+ iter = nodesOnLayer[scanLayer].listIterator();
+
+ while (iter.hasNext()) {
+ int nodenum = ((Integer) iter.next()).intValue();
+ nodeInPosition[position[nodenum] - 1] = nodenum;
+ }
+
+ int sweepCounter = MAX_ADJACENT_EXCHANGE_PASSES;
+ boolean done = false;
+
+ /* do not compute crossing numbers -- precomputing all combinations would be
+ O(L*(P+C), L = # of nodes in layer, P = # of nodes in parent, C = in child */
+ while (!done && (sweepCounter-- > 0)) {
+ done = true;
+
+ int scanpos;
+
+ for (scanpos = 1; scanpos < nodeInPosition.length; scanpos++) {
+ int leftnode = nodeInPosition[scanpos - 1];
+ int rightnode = nodeInPosition[scanpos];
+ int i;
+ double[] arrayBuffer;
+
+ if (parent[leftnode] == null) {
+ /* sort list of parents by X pos */
+ arrayBuffer = new double[edgesFrom[leftnode].size()];
+
+ Iterator parentIter = edgesFrom[leftnode].listIterator();
+ i = 0;
+
+ while (parentIter.hasNext()) {
+ int parentId = ((Integer) parentIter.next()).intValue();
+ arrayBuffer[i++] = xPosition[parentId];
+ }
+
+ Arrays.sort(arrayBuffer);
+ parent[leftnode] = arrayBuffer;
+ }
+
+ if (child[leftnode] == null) {
+ /* sort list of children by X pos */
+ arrayBuffer = new double[edgesTo[leftnode].size()];
+
+ Iterator childIter = edgesTo[leftnode].listIterator();
+ i = 0;
+
+ while (childIter.hasNext()) {
+ int childId = ((Integer) childIter.next()).intValue();
+ arrayBuffer[i++] = xPosition[childId];
+ }
+
+ Arrays.sort(arrayBuffer);
+ child[leftnode] = arrayBuffer;
+ }
+
+ if (parent[rightnode] == null) {
+ /* sort list of parents by X pos */
+ arrayBuffer = new double[edgesFrom[rightnode].size()];
+
+ Iterator parentIter = edgesFrom[rightnode].listIterator();
+ i = 0;
+
+ while (parentIter.hasNext()) {
+ int parentId = ((Integer) parentIter.next()).intValue();
+ arrayBuffer[i++] = xPosition[parentId];
+ }
+
+ Arrays.sort(arrayBuffer);
+ parent[rightnode] = arrayBuffer;
+ }
+
+ if (child[rightnode] == null) {
+ /* sort list of children by X pos */
+ arrayBuffer = new double[edgesTo[rightnode].size()];
+
+ Iterator childIter = edgesTo[rightnode].listIterator();
+ i = 0;
+
+ while (childIter.hasNext()) {
+ int childId = ((Integer) childIter.next()).intValue();
+ arrayBuffer[i++] = xPosition[childId];
+ }
+
+ Arrays.sort(arrayBuffer);
+ child[rightnode] = arrayBuffer;
+ }
+
+ int nowCrossCount = 0;
+ int revCrossCount = 0;
+ double[] leftSet = (double[]) parent[leftnode];
+ double[] rightSet = (double[]) parent[rightnode];
+ int leftIndex = 0;
+ int rightIndex = 0;
+
+ while ((leftIndex < leftSet.length) && (rightIndex < rightSet.length)) {
+ if (rightSet[rightIndex] < leftSet[leftIndex]) {
+ nowCrossCount += (leftSet.length - leftIndex);
+ rightIndex++;
+ } else {
+ leftIndex++;
+ }
+ }
+
+ leftIndex = 0;
+ rightIndex = 0;
+
+ while ((leftIndex < leftSet.length) && (rightIndex < rightSet.length)) {
+ if (rightSet[rightIndex] > leftSet[leftIndex]) {
+ revCrossCount += (rightSet.length - rightIndex);
+ leftIndex++;
+ } else {
+ rightIndex++;
+ }
+ }
+
+ leftSet = (double[]) child[leftnode];
+ rightSet = (double[]) child[rightnode];
+ leftIndex = 0;
+ rightIndex = 0;
+
+ while ((leftIndex < leftSet.length) && (rightIndex < rightSet.length)) {
+ if (rightSet[rightIndex] < leftSet[leftIndex]) {
+ nowCrossCount += (leftSet.length - leftIndex);
+ rightIndex++;
+ } else {
+ leftIndex++;
+ }
+ }
+
+ leftIndex = 0;
+ rightIndex = 0;
+
+ while ((leftIndex < leftSet.length) && (rightIndex < rightSet.length)) {
+ if (rightSet[rightIndex] > leftSet[leftIndex]) {
+ revCrossCount += (rightSet.length - rightIndex);
+ leftIndex++;
+ } else {
+ rightIndex++;
+ }
+ }
+
+ if (nowCrossCount > revCrossCount) {
+ int tmp = position[leftnode];
+ position[leftnode] = position[rightnode];
+ position[rightnode] = tmp;
+ nodeInPosition[scanpos] = leftnode;
+ nodeInPosition[scanpos - 1] = rightnode;
+
+ double dtmp = xPosition[leftnode];
+ xPosition[leftnode] = xPosition[rightnode];
+ xPosition[rightnode] = dtmp;
+ done = false;
+ }
+ }
+ }
+ }
+
+ return position;
+ }
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/algorithms/hierarchicalLayout/HierarchicalLayoutAlgorithm.java b/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/algorithms/hierarchicalLayout/HierarchicalLayoutAlgorithm.java
new file mode 100644
index 0000000..113af9e
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/csplugins/layout/algorithms/hierarchicalLayout/HierarchicalLayoutAlgorithm.java
@@ -0,0 +1,1423 @@
+/** Copyright (c) 2004 Institute for Systems Biology, University of
+ ** California at San Diego, and Memorial Sloan-Kettering Cancer Center.
+ **
+ ** Code written by: Robert Sheridan
+ ** Authors: Gary Bader, Ethan Cerami, Chris Sander
+ ** Date: January 19.2004
+ ** Description: Hierarcical layout plugin, based on techniques by Sugiyama
+ ** et al. described in chapter 9 of "graph drawing", Di Battista et al,1999
+ **
+ ** Based on the csplugins.tutorial written by Ethan Cerami and GINY plugin
+ ** written by Andrew Markiel
+ **
+ ** This library is free software; you can redistribute it and/or modify it
+ ** under the terms of the GNU Lesser General Public License as published
+ ** by the Free Software Foundation; either version 2.1 of the License, or
+ ** any later version.
+ **
+ ** This library is distributed in the hope that it will be useful, but
+ ** WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ ** MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ ** documentation provided hereunder is on an "as is" basis, and the
+ ** Institute for Systems Biology, the University of California at San Diego
+ ** and/or Memorial Sloan-Kettering Cancer Center
+ ** have no obligations to provide maintenance, support,
+ ** updates, enhancements or modifications. In no event shall the
+ ** Institute for Systems Biology, the University of California at San Diego
+ ** and/or Memorial Sloan-Kettering Cancer Center
+ ** be liable to any party for direct, indirect, special,
+ ** incidental or consequential damages, including lost profits, arising
+ ** out of the use of this software and its documentation, even if the
+ ** Institute for Systems Biology, the University of California at San
+ ** Diego and/or Memorial Sloan-Kettering Cancer Center
+ ** have been advised of the possibility of such damage. See
+ ** the GNU Lesser General Public License for more details.
+ **
+ ** You should have received a copy of the GNU Lesser General Public License
+ ** along with this library; if not, write to the Free Software Foundation,
+ ** Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ **/
+package csplugins.layout.algorithms.hierarchicalLayout;
+
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+
+import cytoscape.layout.AbstractLayout;
+import cytoscape.layout.LayoutProperties;
+import cytoscape.layout.Tunable;
+
+import cytoscape.task.TaskMonitor;
+
+import cytoscape.view.CyNetworkView;
+
+import giny.view.EdgeView;
+import giny.view.NodeView;
+
+import java.awt.GridLayout;
+import java.awt.geom.Point2D;
+
+import java.util.*;
+
+import javax.swing.JPanel;
+
+
+class HierarchyFlowLayoutOrderNode implements Comparable {
+ /**
+ *
+ */
+ public NodeView nodeView;
+
+ /**
+ *
+ */
+ public int componentNumber;
+
+ /**
+ *
+ */
+ public int componentSize;
+
+ /**
+ *
+ */
+ public int layer;
+
+ /**
+ *
+ */
+ public int horizontalPosition;
+
+ /**
+ *
+ */
+ public int xPos;
+
+ /**
+ *
+ */
+ public int yPos;
+
+ /**
+ * *
+ */
+ public int graphIndex;
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getXPos() {
+ return xPos;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getYPos() {
+ return yPos;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param a_xPos DOCUMENT ME!
+ */
+ public void setXPos(int a_xPos) {
+ xPos = a_xPos;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param a_yPos DOCUMENT ME!
+ */
+ public void setYPos(int a_yPos) {
+ yPos = a_yPos;
+ }
+
+ /**
+ * Creates a new HierarchyFlowLayoutOrderNode object.
+ *
+ * @param a_nodeView DOCUMENT ME!
+ * @param a_componentNumber DOCUMENT ME!
+ * @param a_componentSize DOCUMENT ME!
+ * @param a_layer DOCUMENT ME!
+ * @param a_horizontalPosition DOCUMENT ME!
+ */
+ public HierarchyFlowLayoutOrderNode(NodeView a_nodeView, int a_componentNumber,
+ int a_componentSize, int a_layer, int a_horizontalPosition,
+ int a_graphIndex) {
+ nodeView = a_nodeView;
+ componentNumber = a_componentNumber;
+ componentSize = a_componentSize;
+ layer = a_layer;
+ horizontalPosition = a_horizontalPosition;
+ graphIndex = a_graphIndex;
+ }
+
+ /**
+ * Creates a new HierarchyFlowLayoutOrderNode object.
+ *
+ * @param a DOCUMENT ME!
+ */
+ public HierarchyFlowLayoutOrderNode(HierarchyFlowLayoutOrderNode a) {
+ nodeView = a.nodeView;
+ componentNumber = a.componentNumber;
+ componentSize = a.componentSize;
+ layer = a.layer;
+ horizontalPosition = a.horizontalPosition;
+ graphIndex = a.graphIndex;
+ yPos = a.yPos;
+ xPos = a.xPos;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param o DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int compareTo(Object o) {
+ HierarchyFlowLayoutOrderNode y = (HierarchyFlowLayoutOrderNode) o;
+ int diff = y.componentSize - componentSize;
+
+ if (diff != 0)
+ return diff;
+
+ diff = componentNumber - y.componentNumber;
+
+ if (diff != 0)
+ return diff;
+
+ diff = layer - y.layer; //y.layer - layer;
+
+ if (diff != 0)
+ return diff;
+
+ return horizontalPosition - y.horizontalPosition;
+ }
+}
+;
+
+
+/**
+ * Lays out graph in tree-like pattern.
+ * The layout will approximate the optimal orientation
+ * for nodes which have a tree-like relationship. <strong> This
+ * assumed relationship is based on directed edges. This class does
+ * not currently distinguish or gracefully treat undirected edges.
+ * Also, duplicate edges are ignored for the purpose of positioning
+ * nodes in the layout.
+ * </strong>
+ * <br>The major steps in this algorithm are:
+ * <ol>
+ * <li>Choose the set of nodes to be layed out based on which are selected</li>
+ * <li>Partition this set into connected components</li>
+ * <li>Detect and eliminate (temporarily) graph cycles</li>
+ * <li>Eliminate (temporarily) transitive edges</li>
+ * <li>Assign nodes to layers (parents always in layer above any child's layer)</li>
+ * <li>Choose a within-layer ordering which reduces edge crossings between layers</li>
+ * <li>Select horizontal positions for nodes within a layer to minimize edge length</li>
+ * <li>Assemble layed out components and any unselected nodes into a composite layout</li>
+ * </ol>
+ * Steps 2 through 6 are performed by calls to methods in the class
+ * {@link csplugins.hierarchicallayout.Graph}
+*/
+public class HierarchicalLayoutAlgorithm extends AbstractLayout {
+ private int nodeHorizontalSpacing = 64;
+ private int nodeVerticalSpacing = 32;
+ private int componentSpacing = 64;
+ private int bandGap = 64;
+ private int leftEdge = 32;
+ private int topEdge = 32;
+ private int rightMargin = 7000;
+ private boolean selected_only = false;
+ private LayoutProperties layoutProperties;
+ private HashMap<Integer, HierarchyFlowLayoutOrderNode> nodes2HFLON = new HashMap<Integer, HierarchyFlowLayoutOrderNode>();
+
+ /**
+ * Creates a new HierarchicalLayoutAlgorithm object.
+ */
+ public HierarchicalLayoutAlgorithm() {
+ super();
+ layoutProperties = new LayoutProperties(getName());
+ initialize_properties();
+ }
+
+ // We do support selected only
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean supportsSelectedOnly() {
+ return true;
+ }
+
+ /**
+ * Lays out the graph. See this class' description for an outline
+ * of the method used. <br>
+ * For the last step, assembly of the layed out components, the method
+ * implemented is similar to the FlowLayout layout manager from the AWT.
+ * Space is allocated in horizontal bands, with a new band begun beneath
+ * the higher bands. This happens on two scales: on the component scale,
+ * and on the intra-component scale. Within each component, the layers
+ * are placed horizontally, each within its own band. Globally, each
+ * component appears in a band which is filled until a right margin is
+ * hit. After that a new band is started beneath the higher band of
+ * layed out components. Components are never split between these global
+ * bands. Each component is finished, regardless of its horizontal
+ * extent. <br>
+ * Also, a post placement pass is done on each component to move each
+ * layer horizontally in order to line up the centers of the layers with
+ * the center of the component.
+ * @param event Menu Selection Event.
+ */
+
+ /**
+ * Main entry point for AbstractLayout classes
+ */
+ public void construct() {
+ taskMonitor.setStatus("Initializing");
+ initialize(); // Calls initialize_local
+ layout();
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void layout() {
+ taskMonitor.setPercentCompleted(0);
+ taskMonitor.setStatus("Capturing snapshot of network and selected nodes");
+
+ if (canceled)
+ return;
+
+ // Do we have programmatically fixed nodes?
+ List<CyNode> selectedNodes = null;
+ int numSelectedNodes = 0;
+ if (staticNodes != null && staticNodes.size() > 0) {
+ // Yes, construct the "selected" nodes
+ selectedNodes = new ArrayList();
+ for (CyNode node: (List<CyNode>)network.nodesList()) {
+ if (!isLocked(networkView.getNodeView(node))) {
+ selectedNodes.add(node);
+ }
+ }
+ } else {
+ /* construct node list with selected nodes first */
+ selectedNodes = networkView.getSelectedNodes();
+ }
+ numSelectedNodes = selectedNodes.size();
+
+ if (!selectedOnly)
+ numSelectedNodes = 0;
+
+ if (numSelectedNodes == 1) {
+ // We were asked to do a hierchical layout of a single node -- done!
+ return;
+ }
+
+ final int numNodes = networkView.getNodeViewCount();
+ final int numLayoutNodes = (numSelectedNodes < 1) ? numNodes : numSelectedNodes;
+ NodeView[] nodeView = new NodeView[numNodes];
+ int nextNode = 0;
+ HashMap<Integer, Integer> ginyIndex2Index = new HashMap<Integer, Integer>(numNodes * 2);
+
+ if (numSelectedNodes > 1) {
+ Iterator iter = selectedNodes.iterator();
+
+ while (iter.hasNext() && !canceled) {
+ nodeView[nextNode] = (NodeView) (iter.next());
+ ginyIndex2Index.put(new Integer(nodeView[nextNode].getNode().getRootGraphIndex()),
+ new Integer(nextNode));
+ nextNode++;
+ }
+ } else {
+ Iterator iter = networkView.getNodeViewsIterator(); /* all nodes */
+
+ while (iter.hasNext() && !canceled) {
+ NodeView nv = (NodeView) (iter.next());
+ Integer nodeIndexKey = new Integer(nv.getNode().getRootGraphIndex());
+
+ if (!ginyIndex2Index.containsKey(nodeIndexKey)) {
+ nodeView[nextNode] = nv;
+ ginyIndex2Index.put(nodeIndexKey, new Integer(nextNode));
+ nextNode++;
+ }
+ }
+ }
+
+ if (canceled)
+ return;
+
+ /* create edge list from edges between selected nodes */
+ LinkedList<Edge> edges = new LinkedList();
+ Iterator iter = networkView.getEdgeViewsIterator();
+
+ while (iter.hasNext()) {
+ EdgeView ev = (EdgeView) (iter.next());
+ Integer edgeFrom = (Integer) ginyIndex2Index.get(new Integer(ev.getEdge().getSource()
+ .getRootGraphIndex()));
+ Integer edgeTo = (Integer) ginyIndex2Index.get(new Integer(ev.getEdge().getTarget()
+ .getRootGraphIndex()));
+
+ if ((edgeFrom == null) || (edgeTo == null)) {
+ // Must be from an unselected node
+ continue;
+ }
+
+ if (canceled)
+ return;
+
+ if ((numSelectedNodes <= 1)
+ || ((edgeFrom.intValue() < numSelectedNodes)
+ && (edgeTo.intValue() < numSelectedNodes))) {
+ /* add edge to graph */
+ Edge theEdge = new Edge(edgeFrom.intValue(), edgeTo.intValue());
+ edges.add(theEdge);
+ }
+ }
+
+ /* find horizontal and vertical coordinates of each node */
+ Edge[] edge = new Edge[edges.size()];
+ edges.toArray(edge);
+
+ Graph graph = new Graph(numLayoutNodes, edge);
+
+ /*
+ int edgeIndex;
+ for (edgeIndex = 0; edgeIndex<edge.length; edgeIndex++) {
+ logger.debug("Edge: " + edge[edgeIndex].getFrom() + " - " + edge[edgeIndex].getTo());
+ }
+ */
+ int[] cI = graph.componentIndex();
+ int x;
+ /*
+ logger.debug("Node index:\n");
+ for (x=0; x<graph.getNodecount(); x++) {
+ logger.debug(cI[x]);
+ }
+ logger.debug("Partitioning into components:\n");
+ */
+ taskMonitor.setPercentCompleted(10);
+ taskMonitor.setStatus("Finding connected components");
+
+ if (canceled)
+ return;
+
+ int[] renumber = new int[cI.length];
+ Graph[] component = graph.partition(cI, renumber);
+ final int numComponents = component.length;
+ int[][] layer = new int[numComponents][];
+ int[][] horizontalPosition = new int[numComponents][];
+ Graph[] reduced = new Graph[component.length];
+ Graph[] reducedTmp = new Graph[component.length];
+ HashMap<Integer, Edge>[] dummy2Edge = new HashMap[component.length];
+ int[] dummyStartForComp = new int[component.length];
+ HashMap<Edge, EdgeView>[] myEdges2EdgeViews = new HashMap[component.length];
+
+ for (x = 0; x < component.length; x++) {
+ /*
+ logger.debug("plain component:\n");
+ logger.debug(component[x]);
+ logger.debug("filtered component:\n");
+ logger.debug(component[x].getGraphWithoutOneOrTwoCycles());
+ logger.debug("nonmulti component:\n");
+ logger.debug(component[x].getGraphWithoutMultipleEdges());
+ int cycleEliminationPriority[] = component[x].getCycleEliminationVertexPriority();
+ logger.debug("acyclic component:\n");
+ logger.debug(component[x].getGraphWithoutCycles(cycleEliminationPriority));
+ logger.debug("reduced component:\n");
+ logger.debug(component[x].getReducedGraph());
+ logger.debug("layer assignment:\n");
+ */
+ taskMonitor.setPercentCompleted(20 + ((40 * (x * 3)) / numComponents / 3));
+ taskMonitor.setStatus("making acyclic transitive reduction");
+ Thread.yield();
+
+ if (canceled)
+ return;
+
+ reducedTmp[x] = component[x].getReducedGraph();
+ taskMonitor.setPercentCompleted(20 + ((40 * ((x * 3) + 1)) / numComponents / 3));
+ taskMonitor.setStatus("layering nodes vertically");
+ Thread.yield();
+
+ if (canceled)
+ return;
+
+ layer[x] = reducedTmp[x].getVertexLayers();
+
+ LinkedList<Integer> layerWithDummy = new LinkedList<Integer>();
+
+ for (int i = 0; i < layer[x].length; i++)
+ layerWithDummy.add(new Integer(layer[x][i]));
+
+ /*
+ int y;
+ for (y=0;y<layer[x].length;y++) {
+ logger.debug("" + y + " : " + layer[x][y]);
+ }
+ logger.debug("horizontal position:\n");
+ */
+
+ /* Insertion of the dummy nodes in the graph */
+ Edge[] allEdges = component[x].GetEdges();
+ LinkedList<Edge> edgesWithAdd = new LinkedList<Edge>();
+ int dummyStart = component[x].getNodecount();
+ dummyStartForComp[x] = dummyStart;
+ dummy2Edge[x] = new HashMap<Integer, Edge>();
+
+ //logger.debug(allEdges.length);
+
+ for (int i = 0; i < allEdges.length; i++) {
+ int from = allEdges[i].getFrom();
+ int to = allEdges[i].getTo();
+
+ if (layer[x][from] == (layer[x][to] + 1)) {
+ edgesWithAdd.add(allEdges[i]);
+ } else {
+ if (layer[x][from] < layer[x][to]) {
+ int tmp = from;
+ from = to;
+ to = tmp;
+ }
+
+ layerWithDummy.add(new Integer(layer[x][to] + 1));
+ dummy2Edge[x].put(new Integer(layerWithDummy.size() - 1), allEdges[i]);
+ edgesWithAdd.add(new Edge(layerWithDummy.size() - 1, to));
+
+ for (int j = layer[x][to] + 2; j < layer[x][from]; j++) {
+ layerWithDummy.add(new Integer(j));
+ dummy2Edge[x].put(new Integer(layerWithDummy.size() - 1), allEdges[i]);
+ edgesWithAdd.add(new Edge(layerWithDummy.size() - 1,
+ layerWithDummy.size() - 2));
+ }
+
+ edgesWithAdd.add(new Edge(from, layerWithDummy.size() - 1));
+ }
+ }
+
+ allEdges = new Edge[edgesWithAdd.size()];
+ edgesWithAdd.toArray(allEdges);
+
+ reduced[x] = new Graph(layerWithDummy.size(), allEdges);
+ reduced[x].setDummyNodesStart(dummyStart);
+ reduced[x].setReduced(true);
+
+ int[] layerNew = new int[layerWithDummy.size()];
+ iter = layerWithDummy.iterator();
+
+ for (int i = 0; i < layerNew.length; i++)
+ layerNew[i] = ((Integer) iter.next()).intValue();
+
+ layer[x] = layerNew;
+
+ taskMonitor.setPercentCompleted(20 + ((40 * ((x * 3) + 2)) / numComponents / 3));
+ taskMonitor.setStatus("positioning nodes within layer");
+ Thread.yield();
+
+ if (canceled)
+ return;
+
+ horizontalPosition[x] = reduced[x].getHorizontalPositionReverse(layer[x]);
+
+ /*
+ for (y=0;y<horizontalPosition[x].length;y++) {
+ logger.debug("" + y + " : " + horizontalPosition[x][y]);
+ }
+ */
+ }
+
+ int resize = renumber.length;
+
+ taskMonitor.setStatus("renumbering nodes");
+ Thread.yield();
+
+ if (canceled)
+ return;
+
+ for (int i = 0; i < component.length; i++)
+ resize += (layer[i].length - dummyStartForComp[i]);
+
+ int[] newRenumber = new int[resize];
+ int[] newcI = new int[resize];
+
+ for (int i = 0; i < renumber.length; i++) {
+ newRenumber[i] = renumber[i];
+ newcI[i] = cI[i];
+ }
+
+ int t = renumber.length;
+
+ for (int i = 0; i < reduced.length; i++) {
+ for (int j = reduced[i].getDummyNodesStart(); j < reduced[i].getNodecount(); j++) {
+ if (canceled)
+ return;
+ newRenumber[t] = j;
+ newcI[t] = i;
+ t++;
+ }
+ }
+
+ renumber = newRenumber;
+ cI = newcI;
+
+ taskMonitor.setStatus("getting edges");
+ Thread.yield();
+
+ edges = new LinkedList<Edge>();
+
+ for (int i = 0; i < reduced.length; i++) {
+ edge = reduced[i].GetEdges();
+
+ for (int j = 0; j < edge.length; j++) { // uzasna budzevina!!!!!!
+ if (canceled)
+ return;
+
+ int from = -1;
+ int to = -1;
+
+ for (int k = 0; k < cI.length; k++) {
+ if ((cI[k] == i) && (renumber[k] == edge[j].getFrom()))
+ from = k;
+
+ if ((cI[k] == i) && (renumber[k] == edge[j].getTo()))
+ to = k;
+
+ if ((from != -1) && (to != -1))
+ break;
+ }
+
+ edges.add(new Edge(from, to)); //edges.add(new Edge(to, from));
+ }
+ }
+
+ edge = new Edge[edges.size()];
+ edges.toArray(edge);
+ graph = new Graph(resize, edge);
+
+ taskMonitor.setPercentCompleted(60);
+ taskMonitor.setStatus("Repositioning nodes in view");
+ Thread.yield();
+
+ if (canceled)
+ return;
+
+ /* order nodeviews by layout order */
+ HierarchyFlowLayoutOrderNode[] flowLayoutOrder = new HierarchyFlowLayoutOrderNode[resize];
+
+ for (x = 0; x < resize; x++) {
+ if (x < numLayoutNodes)
+ flowLayoutOrder[x] = new HierarchyFlowLayoutOrderNode(nodeView[x], cI[x],
+ reduced[cI[x]].getNodecount(),
+ layer[cI[x]][renumber[x]],
+ horizontalPosition[cI[x]][renumber[x]],
+ x);
+ else
+ flowLayoutOrder[x] = new HierarchyFlowLayoutOrderNode(null, cI[x],
+ reduced[cI[x]].getNodecount(),
+ layer[cI[x]][renumber[x]],
+ horizontalPosition[cI[x]][renumber[x]],
+ x);
+
+ nodes2HFLON.put(x, flowLayoutOrder[x]);
+ }
+
+ Arrays.sort(flowLayoutOrder);
+
+ int lastComponent = -1;
+ int lastLayer = -1;
+ int startBandY = topEdge;
+ int cleanBandY = topEdge;
+ int startComponentX = leftEdge;
+ int cleanComponentX = leftEdge;
+ int startLayerY = topEdge;
+ int cleanLayerY = topEdge;
+ int cleanLayerX = leftEdge;
+ int[] layerStart = new int[numLayoutNodes + 1];
+
+ /* layout nodes which are selected */
+ int nodeIndex;
+
+ /* layout nodes which are selected */
+ int lastComponentEnd = -1;
+
+ for (nodeIndex = 0; nodeIndex < resize; nodeIndex++) {
+ HierarchyFlowLayoutOrderNode node = flowLayoutOrder[nodeIndex];
+ int currentComponent = node.componentNumber;
+ int currentLayer = node.layer;
+ NodeView currentView = node.nodeView;
+
+ taskMonitor.setPercentCompleted(60 + ((40 * (nodeIndex + 1)) / resize));
+ taskMonitor.setStatus("layering nodes vertically");
+ Thread.yield();
+
+ if (canceled)
+ return;
+
+ if (lastComponent == -1) {
+ /* this is the first component */
+ lastComponent = currentComponent;
+ lastLayer = currentLayer;
+ layerStart[currentLayer] = -1;
+ }
+
+ if (lastComponent != currentComponent) {
+ /* new component */
+ // first call function for Horizontal Positioning of nodes in lastComponent
+ int[] minXArray = new int[1];
+ int maxX = HorizontalNodePositioning(nodeIndex
+ - flowLayoutOrder[nodeIndex - 1].componentSize,
+ nodeIndex - 1, flowLayoutOrder, graph,
+ renumber, cI, dummyStartForComp, minXArray);
+ int minX = minXArray[0];
+ lastComponentEnd = nodeIndex - 1;
+
+ for (int i = nodeIndex - flowLayoutOrder[nodeIndex - 1].componentSize;
+ i <= (nodeIndex - 1); i++)
+ flowLayoutOrder[i].xPos -= (minX - startComponentX);
+
+ maxX -= (minX - startComponentX);
+
+ layerStart[lastLayer] = startComponentX;
+
+ /* initialize for new component */
+ startComponentX = cleanComponentX + componentSpacing;
+
+ if (maxX > startComponentX)
+ startComponentX = maxX + componentSpacing;
+
+ if (startComponentX > rightMargin) {
+ /* new band */
+ startBandY = cleanBandY + bandGap;
+ cleanBandY = startBandY;
+ startComponentX = leftEdge;
+ cleanComponentX = leftEdge;
+ }
+
+ startLayerY = startBandY;
+ cleanLayerY = startLayerY;
+ cleanLayerX = startComponentX;
+ layerStart[currentLayer] = -1;
+ } else if (lastLayer != currentLayer) {
+ /* new layer */
+ layerStart[lastLayer] = startComponentX;
+
+ startLayerY = cleanLayerY + nodeVerticalSpacing;
+ cleanLayerY = startLayerY;
+ cleanLayerX = startComponentX;
+ layerStart[currentLayer] = -1;
+ }
+
+ node.setXPos(cleanLayerX);
+ node.setYPos(startLayerY);
+ cleanLayerX += nodeHorizontalSpacing;
+
+ int currentBottom;
+ int currentRight;
+
+ if (currentView != null) {
+ currentBottom = startLayerY + (int) (currentView.getHeight());
+ currentRight = cleanLayerX + (int) (currentView.getWidth());
+ } else {
+ currentBottom = startLayerY;
+ currentRight = cleanLayerX;
+ }
+
+ if (currentBottom > cleanBandY)
+ cleanBandY = currentBottom;
+
+ if (currentRight > cleanComponentX)
+ cleanComponentX = currentRight;
+
+ if (currentBottom > cleanLayerY)
+ cleanLayerY = currentBottom;
+
+ if (currentRight > cleanLayerX)
+ cleanLayerX = currentRight;
+
+ lastComponent = currentComponent;
+ lastLayer = currentLayer;
+ }
+
+ if (canceled)
+ return;
+
+ /* Set horizontal positions of last component */
+ int[] minXArray = new int[1];
+ HorizontalNodePositioning(lastComponentEnd + 1, resize - 1, flowLayoutOrder, graph,
+ renumber, cI, dummyStartForComp, minXArray);
+
+ int minX = minXArray[0];
+
+ for (int i = lastComponentEnd + 1; i < resize; i++)
+ flowLayoutOrder[i].xPos -= (minX - startComponentX);
+
+ /* Map edges to edge views in order to map dummy nodes to edge bends properly */
+ iter = networkView.getEdgeViewsIterator();
+
+ while (iter.hasNext()) {
+ EdgeView ev = (EdgeView) (iter.next());
+ Integer edgeFrom = (Integer) ginyIndex2Index.get(new Integer(ev.getEdge().getSource()
+ .getRootGraphIndex()));
+ Integer edgeTo = (Integer) ginyIndex2Index.get(new Integer(ev.getEdge().getTarget()
+ .getRootGraphIndex()));
+
+ if ((edgeFrom == null) || (edgeTo == null)) {
+ // Must be from an unselected node
+ continue;
+ }
+
+ if ((numSelectedNodes <= 1)
+ || ((edgeFrom.intValue() < numSelectedNodes)
+ && (edgeTo.intValue() < numSelectedNodes))) {
+ /* add edge to graph */
+ Edge theEdge = component[cI[edgeFrom.intValue()]].GetTheEdge(renumber[edgeFrom.intValue()],
+ renumber[edgeTo.intValue()]);
+
+ if (myEdges2EdgeViews[cI[edgeFrom.intValue()]] == null)
+ myEdges2EdgeViews[cI[edgeFrom.intValue()]] = new HashMap<Edge, EdgeView>();
+
+ myEdges2EdgeViews[cI[edgeFrom.intValue()]].put(theEdge, ev);
+ }
+ }
+
+ /* Delete edge anchors */
+ iter = networkView.getEdgeViewsIterator();
+
+ while (iter.hasNext()) {
+ ((EdgeView) iter.next()).getBend().removeAllHandles();
+ } /* Done removing edge anchors */
+ iter = networkView.getEdgeViewsIterator();
+ ;
+
+ for (nodeIndex = 0; nodeIndex < resize; nodeIndex++) {
+ HierarchyFlowLayoutOrderNode node = flowLayoutOrder[nodeIndex];
+
+ if (node.nodeView != null) {
+ NodeView currentView = node.nodeView;
+ currentView.setOffset(node.getXPos(), node.getYPos());
+ }
+ }
+
+ for (nodeIndex = 0; nodeIndex < resize; nodeIndex++) {
+ HierarchyFlowLayoutOrderNode node = flowLayoutOrder[nodeIndex];
+
+ if (node.nodeView == null) {
+ Edge theEdge = (Edge) dummy2Edge[cI[node.graphIndex]].get(new Integer(renumber[node.graphIndex]));
+ EdgeView ev = myEdges2EdgeViews[cI[node.graphIndex]].get(theEdge);
+
+ if (ev != null) {
+ int source = ginyIndex2Index.get(ev.getEdge().getSource().getRootGraphIndex());
+ int target = ginyIndex2Index.get(ev.getEdge().getTarget().getRootGraphIndex());
+ double k = (nodeView[target].getYPosition() - nodeView[source].getYPosition()) / (nodeView[target]
+ .getXPosition()
+ - nodeView[source]
+ .getXPosition());
+
+ double xPos = nodeView[source].getXPosition();
+
+ if (k != 0)
+ xPos += ((node.yPos - nodeView[source].getYPosition()) / k);
+
+ Point2D p2d = new Point2D.Double();
+ p2d.setLocation(xPos, node.yPos);
+ ev.getBend().addHandle(p2d);
+ }
+ }
+ }
+
+ for (nodeIndex = 0; nodeIndex < resize; nodeIndex++) {
+ HierarchyFlowLayoutOrderNode node = flowLayoutOrder[nodeIndex];
+
+ if (node.nodeView == null) {
+ Edge theEdge = dummy2Edge[cI[node.graphIndex]].get(new Integer(renumber[node.graphIndex]));
+ EdgeView ev = myEdges2EdgeViews[cI[node.graphIndex]].get(theEdge);
+
+ if (ev != null) {
+
+ Point2D[] bends = ev.getBend().getDrawPoints();
+
+ for (int i = 0; i < bends.length; i++) {
+ if (bends[i].getY() == node.yPos) {
+ Point2D p2d = new Point2D.Double();
+ p2d.setLocation(node.xPos, node.yPos);
+ ev.getBend().moveHandle(i, p2d);
+
+ break;
+ }
+ }
+ }
+ }
+ }
+
+ taskMonitor.setPercentCompleted(100);
+ taskMonitor.setStatus("hierarchical layout complete");
+ }
+
+ /**
+ * Sum length of edges between 2 consecutive layers. This is used for getting as compact
+ * layout as possible, we want to minimize this sum by horizontal coordinate assignment
+ * @param nodes
+ * @param edgesFrom
+ * @param edgesTo
+ * @param x
+ * @param direct
+ * @param startInd
+ * @param endInd
+ * @return
+ */
+ private double EdgeLength2Layers(HierarchyFlowLayoutOrderNode[] nodes,
+ LinkedList<Integer>[] edgesFrom,
+ LinkedList<Integer>[] edgesTo, int x, int direct,
+ int startInd, int endInd) {
+ double layerMin = 0;
+
+ HashMap<Integer, HierarchyFlowLayoutOrderNode> nodesBak2HFLON = new HashMap<Integer, HierarchyFlowLayoutOrderNode>();
+
+ for (int i = startInd; i <= endInd; i++)
+ nodesBak2HFLON.put(new Integer(nodes[i].graphIndex), nodes[i]);
+
+ if (direct == -1) {
+ int xHlp = x;
+
+ while ((xHlp < nodes.length) && (nodes[xHlp].layer == nodes[x].layer)) {
+ Iterator iterToHlp = edgesTo[nodes[xHlp].graphIndex].iterator();
+ double curPos = nodes[xHlp].xPos;
+
+ while (iterToHlp.hasNext()) {
+ Integer neigh = (Integer) iterToHlp.next();
+ layerMin += (Math.abs(nodesBak2HFLON.get(neigh).xPos - curPos) / ((double) nodeHorizontalSpacing));
+
+ // mozda ako je ivica izmedju 2 dummy cvora da duplira daljinu
+ }
+
+ xHlp++;
+ }
+
+ xHlp = x - 1;
+
+ while ((xHlp >= 0) && (nodes[xHlp].layer == nodes[x].layer)) {
+ Iterator iterToHlp = edgesTo[nodes[xHlp].graphIndex].iterator();
+ double curPos = nodes[xHlp].xPos;
+
+ while (iterToHlp.hasNext()) {
+ Integer neigh = (Integer) iterToHlp.next();
+ layerMin += (Math.abs(nodesBak2HFLON.get(neigh).xPos - curPos) / ((double) nodeHorizontalSpacing));
+ }
+
+ xHlp--;
+ }
+ } else {
+ int xHlp = x;
+
+ while ((xHlp < nodes.length) && (nodes[xHlp].layer == nodes[x].layer)) {
+ Iterator iterFromHlp = edgesFrom[nodes[xHlp].graphIndex].iterator();
+ double curPos = nodes[xHlp].xPos;
+
+ while (iterFromHlp.hasNext()) {
+ Integer neigh = (Integer) iterFromHlp.next();
+ layerMin += (Math.abs(nodesBak2HFLON.get(neigh).xPos - curPos) / ((double) nodeHorizontalSpacing));
+ }
+
+ xHlp++;
+ }
+
+ xHlp = x - 1;
+
+ while ((xHlp >= 0) && (nodes[xHlp].layer == nodes[x].layer)) {
+ Iterator iterFromHlp = edgesFrom[nodes[xHlp].graphIndex].iterator();
+ double curPos = nodes[xHlp].xPos;
+
+ while (iterFromHlp.hasNext()) {
+ Integer neigh = (Integer) iterFromHlp.next();
+ layerMin += (Math.abs(nodesBak2HFLON.get(neigh).xPos - curPos) / ((double) nodeHorizontalSpacing));
+ }
+
+ xHlp--;
+ }
+ }
+
+ return layerMin;
+ }
+
+ /**
+ * Function which does actual horizontal coordinate assignment of nodes
+ * @param startInd - in nodes array
+ * @param endInd - in nodes array
+ * @param nodes
+ * @param theGraph
+ * @param renumber
+ * @param cI
+ * @param dummyStarts - dummy nodes are always in the end, so we always remember just
+ * the index of the first dummy in a graph component
+ * @param minX2Return
+ * @return
+ */
+ private int HorizontalNodePositioning(int startInd, int endInd,
+ HierarchyFlowLayoutOrderNode[] nodes, Graph theGraph,
+ int[] renumber, int[] cI, int[] dummyStarts,
+ int[] minX2Return) {
+ /* sort nodes in layer in order of coordinate assignment - first dummy nodes, then sorted by fan-in + fan-out */
+ LinkedList<Integer>[] edgesFrom = theGraph.GetEdgesFrom();
+ LinkedList<Integer>[] edgesTo = theGraph.GetEdgesTo();
+
+ LayerOrderNode[] lon = new LayerOrderNode[endInd - startInd + 1];
+ HashMap<Integer, LayerOrderNode> ind2Lon = new HashMap<Integer, LayerOrderNode>();
+
+ for (int i = 0; i <= (endInd - startInd); i++) {
+ boolean dum = false;
+
+ if (renumber[nodes[startInd + i].graphIndex] >= dummyStarts[cI[nodes[startInd + i].graphIndex]])
+ dum = true;
+
+ lon[i] = new LayerOrderNode(startInd + i, dum,
+ edgesFrom[nodes[startInd + i].graphIndex].size()
+ + edgesTo[nodes[startInd + i].graphIndex].size(),
+ nodes[startInd + i].layer);
+ ind2Lon.put(new Integer(startInd + i), lon[i]);
+ }
+
+ Arrays.sort(lon);
+
+ int cur = 0; //, curLayer = nodes[x].layer;
+ int x = lon[0].GetIndex(); //, curLayer = nodes[x].layer;
+ int direct = 1; //, curLayer = nodes[x].layer;
+ int noOfSteps = (10 * (endInd - startInd + 1)) - ((10 - 1) / 2); //, curLayer = nodes[x].layer;
+ double layerMin = Integer.MAX_VALUE;
+ boolean newLayer = true;
+ boolean dirFirst = true;
+
+ for (int dx = 0; dx < noOfSteps; dx++) {
+ if (newLayer) {
+ layerMin = EdgeLength2Layers(nodes, edgesFrom, edgesTo, x, direct, startInd, endInd);
+ newLayer = false;
+ }
+
+ int idealPosXUp = 0;
+ int idealPosXDown = 0;
+ int neighsCountUp = 0;
+ int neighsCountDown = 0;
+ Iterator iterFrom = edgesFrom[nodes[x].graphIndex].iterator();
+ Iterator iterTo = edgesTo[nodes[x].graphIndex].iterator();
+
+ while (iterFrom.hasNext()
+ && ((direct == 1) || (edgesTo[nodes[x].graphIndex].isEmpty() && (direct == -1)))) {
+ Integer neigh = (Integer) iterFrom.next();
+
+ if (nodes2HFLON.get(neigh).layer == (nodes[x].layer - 1)) {
+ idealPosXUp += nodes2HFLON.get(neigh).xPos;
+ neighsCountUp++;
+
+ // enforcing the impact of dummy nodes, it straightens the lines connected to dummy nodes
+ if ((renumber[nodes2HFLON.get(neigh).graphIndex] >= dummyStarts[cI[nodes2HFLON.get(neigh).graphIndex]])
+ && ind2Lon.get(new Integer(x)).GetIsDummy()) {
+ idealPosXUp += (4 * nodes2HFLON.get(neigh).xPos);
+ neighsCountUp += 4;
+ }
+ }
+ }
+
+ while (iterTo.hasNext()
+ && ((direct == -1)
+ || (edgesFrom[nodes[x].graphIndex].isEmpty() && (direct == 1)))) {
+ Integer neigh = (Integer) iterTo.next();
+
+ if (nodes2HFLON.get(neigh).layer == (nodes[x].layer + 1)) {
+ idealPosXDown += nodes2HFLON.get(neigh).xPos;
+ neighsCountDown++;
+
+ if ((renumber[nodes2HFLON.get(neigh).graphIndex] >= dummyStarts[cI[nodes2HFLON.get(neigh).graphIndex]])
+ && ind2Lon.get(new Integer(x)).GetIsDummy()) {
+ idealPosXDown += (4 * nodes2HFLON.get(neigh).xPos);
+ neighsCountDown += 4;
+ }
+ }
+ }
+
+ if ((neighsCountUp > 0) || (neighsCountDown > 0)) {
+ int idealPosX;
+
+ if (neighsCountUp == 0)
+ idealPosX = idealPosXDown / neighsCountDown;
+ else if (neighsCountDown == 0)
+ idealPosX = idealPosXUp / neighsCountUp;
+ else
+ idealPosX = ((idealPosXUp / neighsCountUp) + (idealPosXDown / neighsCountDown)) / 2;
+
+ if ((idealPosX % nodeHorizontalSpacing) != 0)
+ if ((idealPosX - nodes[x].xPos) < nodeHorizontalSpacing)
+ idealPosX = ((int) (idealPosX / nodeHorizontalSpacing)) * nodeHorizontalSpacing;
+ else if ((nodes[x].xPos - idealPosX) < nodeHorizontalSpacing)
+ idealPosX = ((int) (idealPosX / nodeHorizontalSpacing) + 1) * nodeHorizontalSpacing;
+ else
+ idealPosX = ((int) ((idealPosX / nodeHorizontalSpacing) + 0.5)) * nodeHorizontalSpacing;
+
+ int oldXPos = nodes[x].xPos;
+ nodes[x].xPos = idealPosX;
+
+ HierarchyFlowLayoutOrderNode[] nodesBak = new HierarchyFlowLayoutOrderNode[nodes.length];
+
+ for (int i = 0; i < nodes.length; i++)
+ nodesBak[i] = new HierarchyFlowLayoutOrderNode(nodes[i]);
+
+ if ((idealPosX > oldXPos) && (x < endInd) && (nodes[x + 1].layer == nodes[x].layer)) {
+ boolean q = false;
+
+ for (int i = x + 1; (i <= endInd) && !q; i++) {
+ // logger.debug(nodesBak[i].xPos + " " + nodesBak[i+1].xPos + " " + x + " " + i + " ");
+ if ((nodesBak[i].layer == nodesBak[x].layer)
+ && (nodesBak[i].xPos < (nodesBak[i - 1].xPos + nodeHorizontalSpacing))) {
+ nodesBak[i].xPos = nodesBak[i - 1].xPos + nodeHorizontalSpacing;
+
+ /*if (((LayerOrderNode)ind2Lon.get(new Integer(x))).GetPriority() < ((LayerOrderNode)ind2Lon.get(new Integer(i))).GetPriority())
+ q = true;*/
+ } else
+
+ break;
+ }
+
+ double w = EdgeLength2Layers(nodesBak, edgesFrom, edgesTo, x, direct, startInd,
+ endInd);
+
+ if (!q && (w <= layerMin)) {
+ layerMin = w;
+
+ for (int i = x + 1; i <= endInd; i++)
+ if ((nodes[i].layer == nodes[x].layer)
+ && (nodes[i].xPos < (nodes[i - 1].xPos + nodeHorizontalSpacing))) {
+ nodes[i].xPos = nodes[i - 1].xPos + nodeHorizontalSpacing;
+ } else {
+ break;
+ }
+ } else {
+ if (nodes[x + 1].layer == nodes[x].layer)
+ nodes[x].xPos = nodes[x + 1].xPos - nodeHorizontalSpacing;
+ else
+ nodes[x].xPos = oldXPos;
+ }
+ } else if ((idealPosX < oldXPos) && (x > 0)
+ && (nodes[x - 1].layer == nodes[x].layer)) {
+ boolean q = false;
+
+ for (int i = x - 1; (i >= 0) && !q; i--) {
+ //logger.debug(nodesBak[i].xPos + " " + nodesBak[i+1].xPos + " " + x + " " + i + " ");
+ if ((nodesBak[i].layer == nodesBak[x].layer)
+ && (nodesBak[i].xPos > (nodesBak[i + 1].xPos - nodeHorizontalSpacing))) {
+ nodesBak[i].xPos = nodesBak[i + 1].xPos - nodeHorizontalSpacing;
+
+ /*if (((LayerOrderNode)ind2Lon.get(new Integer(x))).GetPriority() < ((LayerOrderNode)ind2Lon.get(new Integer(i))).GetPriority())
+ {
+ q = true;
+ }*/
+ } else
+
+ break;
+ }
+
+ double w = EdgeLength2Layers(nodesBak, edgesFrom, edgesTo, x, direct, startInd,
+ endInd);
+
+ if (!q && (w <= layerMin)) {
+ layerMin = w;
+
+ for (int i = x - 1; i >= 0; i--)
+ if ((nodes[i].layer == nodes[x].layer)
+ && (nodes[i].xPos > (nodes[i + 1].xPos - nodeHorizontalSpacing))) {
+ nodes[i].xPos = nodes[i + 1].xPos - nodeHorizontalSpacing;
+ } else {
+ break;
+ }
+ } else {
+ if (nodes[x - 1].layer == nodes[x].layer)
+ nodes[x].xPos = nodes[x - 1].xPos + nodeHorizontalSpacing;
+ else
+ nodes[x].xPos = oldXPos;
+ }
+ }
+ }
+
+ if ((startInd == endInd) || (((dx % (startInd - endInd)) == 0) && (dx != 0)))
+ if (!dirFirst) {
+ direct *= -1;
+ dirFirst = true;
+ } else
+ dirFirst = false;
+
+ cur = (cur + direct + lon.length) % lon.length; //(cur + 1) % lon.length;
+
+ if (nodes[x].layer != nodes[lon[cur].GetIndex()].layer) {
+ newLayer = true;
+ }
+
+ x = lon[cur].GetIndex();
+ }
+
+ int maxX = Integer.MIN_VALUE;
+ int minX = Integer.MAX_VALUE;
+
+ for (int i = startInd; i <= endInd; i++) {
+ if (nodes[i].getXPos() > maxX)
+ maxX = nodes[i].getXPos();
+
+ if (nodes[i].getXPos() < minX)
+ minX = nodes[i].getXPos();
+ }
+
+ minX2Return[0] = minX;
+
+ return maxX;
+ }
+
+ /**
+ * Non-blocking call to interrupt the task.
+ */
+ public void halt() {
+ canceled = true;
+ }
+
+ /**
+ * Overrides for LayoutAlgorithm support
+ */
+ public String getName() {
+ return "hierarchical";
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String toString() {
+ return "Hierarchical Layout";
+ }
+
+ /**
+ * Get the settings panel for this layout
+ */
+ public JPanel getSettingsPanel() {
+ JPanel panel = new JPanel(new GridLayout(0, 1));
+ panel.add(layoutProperties.getTunablePanel());
+
+ return panel;
+ }
+
+ protected void initialize_properties() {
+ layoutProperties.add(new Tunable("nodeHorizontalSpacing",
+ "Horizontal spacing between nodes", Tunable.INTEGER,
+ new Integer(64)));
+ layoutProperties.add(new Tunable("nodeVerticalSpacing", "Vertical spacing between nodes",
+ Tunable.INTEGER, new Integer(32)));
+ layoutProperties.add(new Tunable("componentSpacing", "Component spacing", Tunable.INTEGER,
+ new Integer(64)));
+ layoutProperties.add(new Tunable("bandGap", "Band gap", Tunable.INTEGER, new Integer(64)));
+ layoutProperties.add(new Tunable("leftEdge", "Left edge margin", Tunable.INTEGER,
+ new Integer(32)));
+ layoutProperties.add(new Tunable("topEdge", "Top edge margin", Tunable.INTEGER,
+ new Integer(32)));
+ layoutProperties.add(new Tunable("rightMargin", "Right edge margin", Tunable.INTEGER,
+ new Integer(7000)));
+ layoutProperties.add(new Tunable("selected_only", "Only layout selected nodes",
+ Tunable.BOOLEAN, new Boolean(false)));
+ // We've now set all of our tunables, so we can read the property
+ // file now and adjust as appropriate
+ layoutProperties.initializeProperties();
+
+ // Finally, update everything. We need to do this to update
+ // any of our values based on what we read from the property file
+ updateSettings(true);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void updateSettings() {
+ updateSettings(false);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param force DOCUMENT ME!
+ */
+ public void updateSettings(boolean force) {
+ layoutProperties.updateValues();
+
+ Tunable t = layoutProperties.get("nodeHorizontalSpacing");
+ if ((t != null) && (t.valueChanged() || force)) {
+ nodeVerticalSpacing = ((Integer) t.getValue()).intValue();
+ if (t.valueChanged())
+ layoutProperties.setProperty(t.getName(), t.getValue().toString());
+ }
+
+ t = layoutProperties.get("nodeVerticalSpacing");
+ if ((t != null) && (t.valueChanged() || force)) {
+ nodeVerticalSpacing = ((Integer) t.getValue()).intValue();
+ if (t.valueChanged())
+ layoutProperties.setProperty(t.getName(), t.getValue().toString());
+ }
+
+ t = layoutProperties.get("componentSpacing");
+ if ((t != null) && (t.valueChanged() || force)) {
+ componentSpacing = ((Integer) t.getValue()).intValue();
+ if (t.valueChanged())
+ layoutProperties.setProperty(t.getName(), t.getValue().toString());
+ }
+
+ t = layoutProperties.get("bandGap");
+ if ((t != null) && (t.valueChanged() || force)) {
+ bandGap = ((Integer) t.getValue()).intValue();
+ if (t.valueChanged())
+ layoutProperties.setProperty(t.getName(), t.getValue().toString());
+ }
+
+ t = layoutProperties.get("leftEdge");
+ if ((t != null) && (t.valueChanged() || force)) {
+ leftEdge = ((Integer) t.getValue()).intValue();
+ if (t.valueChanged())
+ layoutProperties.setProperty(t.getName(), t.getValue().toString());
+ }
+
+ t = layoutProperties.get("topEdge");
+ if ((t != null) && (t.valueChanged() || force)) {
+ topEdge = ((Integer) t.getValue()).intValue();
+ if (t.valueChanged())
+ layoutProperties.setProperty(t.getName(), t.getValue().toString());
+ }
+
+ t = layoutProperties.get("rightMargin");
+ if ((t != null) && (t.valueChanged() || force)) {
+ rightMargin = ((Integer) t.getValue()).intValue();
+ if (t.valueChanged())
+ layoutProperties.setProperty(t.getName(), t.getValue().toString());
+ }
+
+ t = layoutProperties.get("selected_only");
+ if ((t != null) && (t.valueChanged() || force)) {
+ selected_only = ((Boolean) t.getValue()).booleanValue();
+ if (t.valueChanged())
+ layoutProperties.setProperty(t.getName(), t.getValue().toString());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void revertSettings() {
+ layoutProperties.revertProperties();
+ }
+
+ /**
+ * Sets the Task Monitor.
+ *
+ * @param taskMonitor TaskMonitor Object.
+ */
+ public void setTaskMonitor(TaskMonitor tm) {
+ taskMonitor = tm;
+ }
+
+ /**
+ * Gets the Task Title.
+ *
+ * @return human readable task title.
+ */
+ public String getTitle() {
+ return new String("Hierarchical Layout");
+ }
+}
+
+
+/**
+ * Class which we use to determine the order by which we traverse nodes when
+ * we calculate their horizontal coordinate. We traverse it layer by layer, inside
+ * the layer we first place dummy nodes and then sorted by degree of the node. *
+ * @author Aleksandar Nikolic
+ *
+ */
+class LayerOrderNode implements Comparable {
+ private int index;
+ private boolean isDummy;
+ private int degree;
+ private int priority;
+ private int layer;
+
+ /**
+ * Creates a new LayerOrderNode object.
+ *
+ * @param index DOCUMENT ME!
+ * @param isDummy DOCUMENT ME!
+ * @param degree DOCUMENT ME!
+ * @param layer DOCUMENT ME!
+ */
+ public LayerOrderNode(int index, boolean isDummy, int degree, int layer) {
+ this.index = index;
+ this.isDummy = isDummy;
+ this.degree = degree;
+ this.layer = layer;
+
+ if (isDummy)
+ priority = 20;
+ else if (degree < 5)
+ priority = 5;
+ else if (degree < 10)
+ priority = 10;
+ else
+ priority = 15; //priority = degree;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param arg0 DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int compareTo(Object arg0) {
+ LayerOrderNode second = (LayerOrderNode) arg0;
+
+ if (layer != second.layer)
+ return (layer - second.layer); //(second.layer - layer);
+
+ if (isDummy && !second.isDummy)
+ return -1;
+
+ if (!isDummy && second.isDummy)
+ return 1;
+
+ return (second.degree - degree);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int GetIndex() {
+ return index;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int GetPriority() {
+ return priority;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean GetIsDummy() {
+ return isDummy;
+ }
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/JGraph.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/JGraph.java
new file mode 100644
index 0000000..fb6f752
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/JGraph.java
@@ -0,0 +1,2715 @@
+/*
+ * @(#)JGraph.java
+ *
+ * Copyright (c) 2001-2006 Gaudenz Alder
+ *
+ */
+package org.jgraph;
+
+import org.jgraph.event.GraphSelectionEvent;
+import org.jgraph.event.GraphSelectionListener;
+
+import org.jgraph.graph.AbstractCellView;
+import org.jgraph.graph.AttributeMap;
+import org.jgraph.graph.BasicMarqueeHandler;
+import org.jgraph.graph.CellView;
+import org.jgraph.graph.ConnectionSet;
+import org.jgraph.graph.DefaultCellViewFactory;
+import org.jgraph.graph.DefaultEdge;
+import org.jgraph.graph.DefaultGraphCell;
+import org.jgraph.graph.DefaultGraphModel;
+import org.jgraph.graph.DefaultGraphSelectionModel;
+import org.jgraph.graph.GraphConstants;
+import org.jgraph.graph.GraphLayoutCache;
+import org.jgraph.graph.GraphModel;
+import org.jgraph.graph.GraphSelectionModel;
+import org.jgraph.graph.PortView;
+
+import org.jgraph.plaf.GraphUI;
+
+import java.awt.AlphaComposite;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.Graphics2D;
+import java.awt.Rectangle;
+import java.awt.event.MouseEvent;
+import java.awt.geom.Dimension2D;
+import java.awt.geom.Point2D;
+import java.awt.geom.Rectangle2D;
+import java.awt.image.BufferedImage;
+
+import java.io.IOException;
+import java.io.ObjectInputStream;
+import java.io.ObjectOutputStream;
+import java.io.Serializable;
+
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+import java.util.Vector;
+
+import javax.accessibility.Accessible;
+
+import javax.swing.BorderFactory;
+import javax.swing.JComponent;
+import javax.swing.JViewport;
+import javax.swing.Scrollable;
+import javax.swing.SwingConstants;
+
+
+/**
+ * A control that displays a network of related objects using the well-known
+ * paradigm of a graph.
+ * <p>
+ * A JGraph object doesn't actually contain your data; it simply provides a view
+ * of the data. Like any non-trivial Swing component, the graph gets data by
+ * querying its data model.
+ * <p>
+ * JGraph displays its data by drawing individual elements. Each element
+ * displayed by the graph contains exactly one item of data, which is called a
+ * cell. A cell may either be a vertex or an edge. Vertices may have neighbours
+ * or not, and edges may have source and target vertices or not, depending on
+ * whether they are connected.
+ * <p>
+ * <strong>Creating a Graph </strong>
+ * <p>
+ * The following code creates a JGraph object:
+ * <p>
+ * JGraph graph = new JGraph(); <br>
+ * ... <br>
+ * JScrollPane graphLayoutCache = new JScrollPane(graph)
+ * <p>
+ * The code creates an instance of JGraph and puts it in a scroll pane. JGraphs
+ * constructor is called with no arguments in this example, which causes the
+ * constructor to create a sample model.
+ * <p>
+ * <strong>Editing </strong>
+ * <p>
+ * Outmoved, cloned, resized, and shaped, or connected/disconnected to or from
+ * other cells.
+ * <p>
+ * <strong>Keyboard Bindings </strong>
+ * <p>
+ * JGraph defines the following set of keyboard bindings:
+ * <p>
+ * <ul>
+ * <li>Alt-Click forces marquee selection if over a cell.
+ * <li>Shift- or Ctrl-Select extends or toggles the selection.
+ * <li>Shift-Drag constrains the offset to one direction.
+ * <li>Ctrl-Drag clones the selection.
+ * <li>Doubleclick/F2 starts editing a cell.
+ * </ul>
+ * You can change the number of clicks that triggers editing using
+ * setEditClickCount().
+ * <p>
+ * <strong>Customization </strong>
+ * <p>
+ * There are a number of additional methods that customize JGraph. For example,
+ * setMinimumMove() defines the minimum amount of pixels before a move operation
+ * is initiated. setSnapSize() defines the maximum distance for a cell to be
+ * selected. setFloatEnabled() enables/disables port floating.
+ * <p>
+ * With setDisconnectOnMove() you can indicate if the selected subgraph should
+ * be disconnected from the unselected rest when a move operation is initiated.
+ * setDragEnabled() enables/disables the use of Drag And Drop, and
+ * setDropEnabled() sets if the graph accepts Drops from external sources.
+ * <p>
+ * <strong>Customizing a graphs display </strong>
+ * <p>
+ * JGraph performs some look-and-feel specific painting. You can customize this
+ * painting in a limited way. For example, you can modify the grid using
+ * setGridColor() and setGridSize(), and you can change the handle colors using
+ * setHandleColor() and setLockedHandleColor().
+ * <p>
+ * If you want finer control over the rendering, you can subclass one of the
+ * default renderers, and extend its paint()-method. A renderer is a
+ * Component-extension that paints a cell based on its attributes. Thus, neither
+ * the JGraph nor its look-and-feel-specific implementation actually contain the
+ * code that paints the cell. Instead, the graph uses the cell renderers
+ * painting code.
+ * <p>
+ * <strong>Selection </strong>
+ * <p>
+ * Apart from the single-cell and marquee-selection, JGraphs selection model
+ * also allows to "step-into" groups, and select children. This feature can be
+ * disabled using the setAllowsChildSelection() method of the selection model
+ * instance.
+ * <p>
+ * If you are interested in knowing when the selection changes implement the
+ * <code>GraphSelectionListener</code> interface and add the instance using
+ * the method <code>addGraphSelectionListener</code>.
+ * <code>valueChanged</code> will be invoked when the selection changes, that
+ * is if the user clicks twice on the same vertex <code>valueChanged</code>
+ * will only be invoked once.
+ * <p>
+ * <strong>Change Notification </strong>
+ * <p>
+ * If you are interested in handling modifications, implement the
+ * <code>GraphEventHandler</code> interface and add the instance using the
+ * method <code>addGraphEventHandler</code>.
+ * <p>
+ * For detection of double-clicks or when a user clicks on a cell, regardless of
+ * whether or not it was selected, I recommend you implement a MouseListener and
+ * use <code>getFirstCellForLocation</code>.
+ * <p>
+ * <strong>Undo Support </strong>
+ * <p>
+ * To enable Undo-Support, a <code>GraphUndoManager</code> must be added using
+ * <code>addGraphSelectionListener</code>. The GraphUndoManager is an
+ * extension of Swing's <code>GraphUndoManager</code> that maintains a command
+ * history in the context of multiple views. In this setup, a cell may have a
+ * set of attributes in each view attached to the model.
+ * <p>
+ * For example, consider a position that is stored separately in each view. If a
+ * node is inserted, the change will be visible in all attached views, resulting
+ * in a new node that pops-up at the initial position. If the node is
+ * subsequently moved, say, in view1, this does not constitute a change in
+ * view2. If view2 does an "undo", the move <i>and </i> the insertion must be
+ * undone, whereas an "undo" in view1 will only undo the previous move
+ * operation.
+ * <p>
+ * Like all <code>JComponent</code> classes, you can use
+ * {@link javax.swing.InputMap}and {@link javax.swing.ActionMap}to associate
+ * an {@link javax.swing.Action}object with a {@link javax.swing.KeyStroke}and
+ * execute the action under specified conditions.
+ *
+ * @author Gaudenz Alder
+ * @version 2.1 16/03/03
+ *
+ */
+public class JGraph extends JComponent // JAVA13:
+ // org.jgraph.plaf.basic.TransferHandler.JAdapterComponent
+ implements Scrollable, Accessible, Serializable {
+ /**
+ *
+ */
+ public static final String VERSION = "JGraph (v5.7.4.7)";
+
+ /**
+ *
+ */
+ public static final int DOT_GRID_MODE = 0;
+
+ /**
+ *
+ */
+ public static final int CROSS_GRID_MODE = 1;
+
+ /**
+ *
+ */
+ public static final int LINE_GRID_MODE = 2;
+
+ /**
+ * @see #getUIClassID
+ * @see #readObject
+ */
+ private static final String uiClassID = "GraphUI";
+
+ /** Creates a new event and passes it off the <code>selectionListeners</code>. */
+ protected transient GraphSelectionRedirector selectionRedirector;
+
+ //
+ // Bound Properties
+ //
+ /**
+ * The model that defines the graph displayed by this object. Bound
+ * property.
+ */
+ transient protected GraphModel graphModel;
+
+ /**
+ * The view that defines the display properties of the model. Bound
+ * property.
+ */
+ transient protected GraphLayoutCache graphLayoutCache;
+
+ /** Models the set of selected objects in this graph. Bound property. */
+ transient protected GraphSelectionModel selectionModel;
+
+ /** Handler for marquee selection. */
+ transient protected BasicMarqueeHandler marquee;
+
+ /** Scale of the graph. Default is 1. Bound property. */
+ protected double scale = 1.0;
+
+ /** True if the graph is anti-aliased. Default is false. Bound property. */
+ protected boolean antiAliased = false;
+
+ /** True if the graph allows editing the value of a cell. Bound property. */
+ protected boolean editable = true;
+
+ /**
+ * True if the graph allows selection of cells. Note: You must also disable
+ * selectNewCells if you disable this. Bound property.
+ */
+ protected boolean selectionEnabled = true;
+
+ /**
+ * True if the graph allows invalid null ports during previews (aka flip
+ * back edges). Default is true.
+ */
+ protected boolean previewInvalidNullPorts = true;
+
+ /** True if the grid is visible. Bound property. */
+ protected boolean gridVisible = false;
+
+ /** The size of the grid in points. Default is 10. Bound property. */
+ protected double gridSize = 10;
+
+ /** The style of the grid. Use one of the _GRID_MODE constants. */
+ protected int gridMode = DOT_GRID_MODE;
+
+ /** True if the ports are visible. Bound property. */
+ protected boolean portsVisible = false;
+
+ /** True if the ports are scaled. Bound property. */
+ protected boolean portsScaled = true;
+
+ /** True if the graph allows to move cells below zero. */
+ protected boolean moveBelowZero = false;
+
+ /**
+ * True if the graph should be auto resized when cells are moved below the
+ * bottom right corner. Default is true.
+ */
+ protected boolean autoResizeGraph = true;
+
+ //
+ // Look-And-Feel dependent
+ //
+ /** Highlight Color. Changes when the Look-and-Feel changes. */
+ protected Color highlightColor = Color.green;
+
+ /**
+ * Color of the handles and locked handles. Changes when the Look-and-Feel
+ * changes.
+ */
+ protected Color handleColor;
+
+ /**
+ * Color of the handles and locked handles. Changes when the Look-and-Feel
+ * changes.
+ */
+ protected Color lockedHandleColor;
+
+ /** Color of the marquee. Changes when the Look-and-Feel changes. */
+ protected Color marqueeColor;
+
+ /** The color of the grid. Changes when the Look-and-Feel changes. */
+ protected Color gridColor;
+
+ //
+ // Datatransfer
+ //
+ /**
+ * True if Drag-and-Drop should be used for move operations. Default is
+ * false due to a JDK bug.
+ */
+ protected boolean dragEnabled = false;
+
+ /**
+ * True if the graph accepts transfers from other components (graphs). This
+ * also affects the clipboard. Default is true.
+ */
+ protected boolean dropEnabled = true;
+
+ //
+ // Unbound Properties
+ //
+ /** Number of clicks for editing to start. Default is 2 clicks. */
+ protected int editClickCount = 2;
+
+ /** True if the graph allows interactions. Default is true. */
+ protected boolean enabled = true;
+
+ /** True if the snap method should be active (snap to grid). */
+ protected boolean gridEnabled = false;
+
+ /** Size of a handle. Default is 3 pixels. */
+ protected int handleSize = 3;
+
+ /** Maximum distance between a cell and the mousepointer. Default is 4. */
+ protected int tolerance = 4;
+
+ /** Minimum amount of pixels to start a move transaction. Default is 5. */
+ protected int minimumMove = 5;
+
+ /**
+ * True if getPortViewAt should return the default port if no other port is
+ * found. Default is false.
+ */
+ protected boolean isJumpToDefaultPort = false;
+
+ /**
+ * Specifies if cells should be added to a group when moved over the group's
+ * area. Default is false.
+ */
+ protected boolean isMoveIntoGroups = false;
+
+ /**
+ * Specifies if cells should be removed from groups when removed from the
+ * group area. Default is false.
+ */
+ protected boolean isMoveOutOfGroups = false;
+
+ /**
+ * True if selected edges are disconnected from unselected vertices on move.
+ * Default is false.
+ */
+ protected boolean disconnectOnMove = false;
+
+ /** True if the graph allows move operations. Default is true. */
+ protected boolean moveable = true;
+
+ /** True if the graph allows "ctrl-drag" operations. Default is false. */
+ protected boolean cloneable = false;
+
+ /** True if the graph allows cells to be resized. Default is true. */
+ protected boolean sizeable = true;
+
+ /**
+ * True if the graph allows points to be modified/added/removed. Default is
+ * true.
+ */
+ protected boolean bendable = true;
+
+ /**
+ * True if the graph allows new connections to be established. Default is
+ * true.
+ */
+ protected boolean connectable = true;
+
+ /**
+ * True if the graph allows existing connections to be removed. Default is
+ * true.
+ */
+ protected boolean disconnectable = true;
+
+ /**
+ * If true, when editing is to be stopped by way of selection changing, data
+ * in graph changing or other means <code>stopCellEditing</code> is
+ * invoked, and changes are saved. If false, <code>cancelCellEditing</code>
+ * is invoked, and changes are discarded.
+ */
+ protected boolean invokesStopCellEditing;
+
+ //
+ // Bound propery names
+ //
+ /**
+ * Bound property name for <code>graphModel</code>.
+ */
+ public final static String GRAPH_MODEL_PROPERTY = "model";
+
+ /**
+ * Bound property name for <code>graphModel</code>.
+ */
+ public final static String GRAPH_LAYOUT_CACHE_PROPERTY = "view";
+
+ /**
+ * Bound property name for <code>graphModel</code>.
+ */
+ public final static String MARQUEE_HANDLER_PROPERTY = "marquee";
+
+ /**
+ * Bound property name for <code>editable</code>.
+ */
+ public final static String EDITABLE_PROPERTY = "editable";
+
+ /**
+ * Bound property name for <code>selectionEnabled</code>.
+ */
+ public final static String SELECTIONENABLED_PROPERTY = "selectionEnabled";
+
+ /**
+ * Bound property name for <code>scale</code>.
+ */
+ public final static String SCALE_PROPERTY = "scale";
+
+ /**
+ * Bound property name for <code>antiAliased</code>.
+ */
+ public final static String ANTIALIASED_PROPERTY = "antiAliased";
+
+ /**
+ * Bound property name for <code>gridSize</code>.
+ */
+ public final static String GRID_SIZE_PROPERTY = "gridSize";
+
+ /**
+ * Bound property name for <code>gridVisible</code>.
+ */
+ public final static String GRID_VISIBLE_PROPERTY = "gridVisible";
+
+ /**
+ * Bound property name for <code>gridColor</code>.
+ */
+ public final static String GRID_COLOR_PROPERTY = "gridColor";
+
+ /**
+ * Bound property name for <code>gridColor</code>.
+ */
+ public final static String HANDLE_COLOR_PROPERTY = "handleColor";
+
+ /**
+ * Bound property name for <code>gridColor</code>.
+ */
+ public final static String HANDLE_SIZE_PROPERTY = "handleSize";
+
+ /**
+ * Bound property name for <code>gridColor</code>.
+ */
+ public final static String LOCKED_HANDLE_COLOR_PROPERTY = "lockedHandleColor";
+
+ /**
+ * Bound property name for <code>gridVisible</code>.
+ */
+ public final static String PORTS_VISIBLE_PROPERTY = "portsVisible";
+
+ /**
+ * Bound property name for <code>portsScaled</code>.
+ */
+ public final static String PORTS_SCALED_PROPERTY = "portsScaled";
+
+ /**
+ * Bound property name for <code>selectionModel</code>.
+ */
+ public final static String SELECTION_MODEL_PROPERTY = "selectionModel";
+
+ /**
+ * Bound property name for <code>messagesStopCellEditing</code>.
+ */
+ public final static String INVOKES_STOP_CELL_EDITING_PROPERTY = "invokesStopCellEditing";
+
+ /**
+ * Creates and returns a sample <code>GraphModel</code>. Used primarily
+ * for beanbuilders to show something interesting.
+ */
+ public static void addSampleData(GraphModel model) {
+ ConnectionSet cs = new ConnectionSet();
+ Map attributes = new Hashtable();
+
+ // Styles For Implement/Extend/Aggregation
+ AttributeMap implementStyle = new AttributeMap();
+ GraphConstants.setLineBegin(implementStyle, GraphConstants.ARROW_TECHNICAL);
+ GraphConstants.setBeginSize(implementStyle, 10);
+ GraphConstants.setDashPattern(implementStyle, new float[] { 3, 3 });
+ GraphConstants.setFont(implementStyle, GraphConstants.DEFAULTFONT.deriveFont(10));
+
+ AttributeMap extendStyle = new AttributeMap();
+ GraphConstants.setLineBegin(extendStyle, GraphConstants.ARROW_TECHNICAL);
+ GraphConstants.setBeginFill(extendStyle, true);
+ GraphConstants.setBeginSize(extendStyle, 10);
+ GraphConstants.setFont(extendStyle, GraphConstants.DEFAULTFONT.deriveFont(10));
+
+ AttributeMap aggregateStyle = new AttributeMap();
+ GraphConstants.setLineBegin(aggregateStyle, GraphConstants.ARROW_DIAMOND);
+ GraphConstants.setBeginFill(aggregateStyle, true);
+ GraphConstants.setBeginSize(aggregateStyle, 6);
+ GraphConstants.setLineEnd(aggregateStyle, GraphConstants.ARROW_SIMPLE);
+ GraphConstants.setEndSize(aggregateStyle, 8);
+ GraphConstants.setLabelPosition(aggregateStyle, new Point2D.Double(500, 0));
+ GraphConstants.setFont(aggregateStyle, GraphConstants.DEFAULTFONT.deriveFont(10));
+
+ //
+ // The Swing MVC Pattern
+ //
+ // Model Column
+ DefaultGraphCell gm = new DefaultGraphCell("GraphModel");
+ attributes.put(gm, createBounds(new AttributeMap(), 20, 100, Color.blue));
+ gm.addPort(null, "GraphModel/Center");
+
+ DefaultGraphCell dgm = new DefaultGraphCell("DefaultGraphModel");
+ attributes.put(dgm, createBounds(new AttributeMap(), 20, 180, Color.blue));
+ dgm.addPort(null, "DefaultGraphModel/Center");
+
+ DefaultEdge dgmImplementsGm = new DefaultEdge("implements");
+ cs.connect(dgmImplementsGm, gm.getChildAt(0), dgm.getChildAt(0));
+ attributes.put(dgmImplementsGm, implementStyle);
+
+ DefaultGraphCell modelGroup = new DefaultGraphCell("ModelGroup");
+ modelGroup.add(gm);
+ modelGroup.add(dgm);
+ modelGroup.add(dgmImplementsGm);
+
+ // JComponent Column
+ DefaultGraphCell jc = new DefaultGraphCell("JComponent");
+ attributes.put(jc, createBounds(new AttributeMap(), 180, 20, Color.green));
+ jc.addPort(null, "JComponent/Center");
+
+ DefaultGraphCell jg = new DefaultGraphCell("JGraph");
+ attributes.put(jg, createBounds(new AttributeMap(), 180, 100, Color.green));
+ jg.addPort(null, "JGraph/Center");
+
+ DefaultEdge jgExtendsJc = new DefaultEdge("extends");
+ cs.connect(jgExtendsJc, jc.getChildAt(0), jg.getChildAt(0));
+ attributes.put(jgExtendsJc, extendStyle);
+
+ // UI Column
+ DefaultGraphCell cu = new DefaultGraphCell("ComponentUI");
+ attributes.put(cu, createBounds(new AttributeMap(), 340, 20, Color.red));
+ cu.addPort(null, "ComponentUI/Center");
+
+ DefaultGraphCell gu = new DefaultGraphCell("GraphUI");
+ attributes.put(gu, createBounds(new AttributeMap(), 340, 100, Color.red));
+ gu.addPort(null, "GraphUI/Center");
+
+ DefaultGraphCell dgu = new DefaultGraphCell("BasicGraphUI");
+ attributes.put(dgu, createBounds(new AttributeMap(), 340, 180, Color.red));
+ dgu.addPort(null, "BasicGraphUI/Center");
+
+ DefaultEdge guExtendsCu = new DefaultEdge("extends");
+ cs.connect(guExtendsCu, cu.getChildAt(0), gu.getChildAt(0));
+ attributes.put(guExtendsCu, extendStyle);
+
+ DefaultEdge dguImplementsDu = new DefaultEdge("implements");
+ cs.connect(dguImplementsDu, gu.getChildAt(0), dgu.getChildAt(0));
+ attributes.put(dguImplementsDu, implementStyle);
+
+ DefaultGraphCell uiGroup = new DefaultGraphCell("UIGroup");
+ uiGroup.add(cu);
+ uiGroup.add(gu);
+ uiGroup.add(dgu);
+ uiGroup.add(dguImplementsDu);
+ uiGroup.add(guExtendsCu);
+
+ // Aggregations
+ DefaultEdge jgAggregatesGm = new DefaultEdge("model");
+ cs.connect(jgAggregatesGm, jg.getChildAt(0), gm.getChildAt(0));
+ attributes.put(jgAggregatesGm, aggregateStyle);
+
+ DefaultEdge jcAggregatesCu = new DefaultEdge("ui");
+ cs.connect(jcAggregatesCu, jc.getChildAt(0), cu.getChildAt(0));
+ attributes.put(jcAggregatesCu, aggregateStyle);
+
+ // Insert Cells into model
+ Object[] cells = new Object[] {
+ jgAggregatesGm, jcAggregatesCu, modelGroup, jc, jg, jgExtendsJc,
+ uiGroup
+ };
+ model.insert(cells, attributes, cs, null, null);
+ }
+
+ /**
+ * Returns an attributeMap for the specified position and color.
+ */
+ public static Map createBounds(AttributeMap map, int x, int y, Color c) {
+ GraphConstants.setBounds(map, map.createRect(x, y, 90, 30));
+ GraphConstants.setBorder(map, BorderFactory.createRaisedBevelBorder());
+ GraphConstants.setBackground(map, c.darker().darker());
+ GraphConstants.setGradientColor(map, c.brighter().brighter().brighter());
+ GraphConstants.setForeground(map, Color.white);
+ GraphConstants.setFont(map, GraphConstants.DEFAULTFONT.deriveFont(Font.BOLD, 12));
+ GraphConstants.setOpaque(map, true);
+
+ return map;
+ }
+
+ /**
+ * Returns a <code>JGraph</code> with a sample model.
+ */
+ public JGraph() {
+ this((GraphModel) null);
+ }
+
+ /**
+ * Returns an instance of <code>JGraph</code> which displays the the
+ * specified data model.
+ *
+ * @param model
+ * the <code>GraphModel</code> to use as the data model
+ */
+ public JGraph(GraphModel model) {
+ this(model, (GraphLayoutCache) null);
+ }
+
+ /**
+ * Returns an instance of <code>JGraph</code> which displays the data
+ * model using the specified view.
+ *
+ * @param cache
+ * the <code>GraphLayoutCache</code> to use as the view
+ */
+ public JGraph(GraphLayoutCache cache) {
+ this((cache != null) ? cache.getModel() : null, cache);
+ }
+
+ /**
+ * Returns an instance of <code>JGraph</code> which displays the specified
+ * data model using the specified view.
+ *
+ * @param model
+ * the <code>GraphModel</code> to use as the data model
+ * @param cache
+ * the <code>GraphLayoutCache</code> to use as the cache
+ */
+ public JGraph(GraphModel model, GraphLayoutCache cache) {
+ this(model, cache, new BasicMarqueeHandler());
+ }
+
+ /**
+ * Returns an instance of <code>JGraph</code> which displays the specified
+ * data model and assigns the specified marquee handler
+ *
+ * @param model
+ * the <code>GraphModel</code> to use as the data model
+ * @param mh
+ * the <code>BasicMarqueeHandler</code> to use as the marquee
+ * handler
+ */
+ public JGraph(GraphModel model, BasicMarqueeHandler mh) {
+ this(model, null, mh);
+ }
+
+ /**
+ * Returns an instance of <code>JGraph</code> which displays the specified
+ * data model using the specified view and assigns the specified marquee
+ * handler
+ *
+ * @param model
+ * the <code>GraphModel</code> to use as the data model
+ * @param layoutCache
+ * the <code>GraphLayoutCache</code> to use as the cache
+ * @param mh
+ * the <code>BasicMarqueeHandler</code> to use as the marquee
+ * handler
+ */
+ public JGraph(GraphModel model, GraphLayoutCache layoutCache, BasicMarqueeHandler mh) {
+ setDoubleBuffered(true);
+ selectionModel = new DefaultGraphSelectionModel(this);
+ setLayout(null);
+ marquee = mh;
+
+ if (model == null) {
+ model = new DefaultGraphModel();
+ setModel(model);
+ addSampleData(model);
+ } else
+ setModel(model);
+
+ if (layoutCache == null)
+ layoutCache = new GraphLayoutCache(model, new DefaultCellViewFactory());
+
+ setGraphLayoutCache(layoutCache);
+ updateUI();
+ }
+
+ //
+ // UI-delegate (GraphUI)
+ //
+ /**
+ * Returns the L&F object that renders this component.
+ *
+ * @return the GraphUI object that renders this component
+ */
+ public GraphUI getUI() {
+ return (GraphUI) ui;
+ }
+
+ /**
+ * Sets the L&F object that renders this component.
+ *
+ * @param ui
+ * the GraphUI L&F object
+ * @see javax.swing.UIDefaults#getUI(JComponent)
+ *
+ */
+ public void setUI(GraphUI ui) {
+ if ((GraphUI) this.ui != ui) {
+ super.setUI(ui);
+ }
+ }
+
+ /**
+ * Notification from the <code>UIManager</code> that the L&F has changed.
+ * Replaces the current UI object with the latest version from the
+ * <code>UIManager</code>. Subclassers can override this to support
+ * different GraphUIs.
+ *
+ * @see JComponent#updateUI
+ *
+ */
+ public void updateUI() {
+ setUI(new org.jgraph.plaf.basic.BasicGraphUI());
+ invalidate();
+ }
+
+ /**
+ * Returns the name of the L&F class that renders this component.
+ *
+ * @return the string "GraphUI"
+ * @see JComponent#getUIClassID
+ *
+ */
+ public String getUIClassID() {
+ return uiClassID;
+ }
+
+ //
+ // Content
+ //
+ /**
+ * Returns all cells that the model contains.
+ */
+ public Object[] getRoots() {
+ return DefaultGraphModel.getRoots(graphModel);
+ }
+
+ /**
+ * Returns all cells that intersect the given rectangle.
+ */
+ public Object[] getRoots(Rectangle clip) {
+ CellView[] views = graphLayoutCache.getRoots(clip);
+ Object[] cells = new Object[views.length];
+
+ for (int i = 0; i < views.length; i++)
+ cells[i] = views[i].getCell();
+
+ return cells;
+ }
+
+ /**
+ * Returns all <code>cells</code> including all descendants in the passed
+ * in order of cells.
+ */
+ public Object[] getDescendants(Object[] cells) {
+ return DefaultGraphModel.getDescendants(getModel(), cells).toArray();
+ }
+
+ /**
+ * Returns all <code>cells</code> including all descendants ordered using
+ * the current layering data stored by the model.
+ */
+ public Object[] order(Object[] cells) {
+ return DefaultGraphModel.order(getModel(), cells);
+ }
+
+ /**
+ * Returns a map of (cell, clone)-pairs for all <code>cells</code> and
+ * their children. Special care is taken to replace the anchor references
+ * between ports. (Iterative implementation.)
+ */
+ public Map cloneCells(Object[] cells) {
+ return graphModel.cloneCells(cells);
+ }
+
+ /**
+ * Returns the topmost cell view at the specified location using the view's
+ * bounds on non-leafs to check for containment. If reverse is true this
+ * will return the innermost view.
+ */
+ public CellView getTopmostViewAt(double x, double y, boolean reverse, boolean leafsOnly) {
+ Rectangle2D r = new Rectangle2D.Double(x, y, 1, 1);
+ Object[] cells = getDescendants(getRoots());
+
+ for (int i = (reverse) ? (cells.length - 1) : 0; (i >= 0) && (i < cells.length);
+ i += ((reverse) ? (-1) : (+1))) {
+ CellView view = getGraphLayoutCache().getMapping(cells[i], false);
+
+ if ((view != null) && (!leafsOnly || view.isLeaf())
+ && ((view.isLeaf() && view.intersects(this, r))
+ || (!view.isLeaf() && view.getBounds().contains(x, y))))
+ return view;
+ }
+
+ return null;
+ }
+
+ /**
+ * Returns the topmost cell at the specified location.
+ *
+ * @param x
+ * an integer giving the number of pixels horizontally from the
+ * left edge of the display area, minus any left margin
+ * @param y
+ * an integer giving the number of pixels vertically from the top
+ * of the display area, minus any top margin
+ * @return the topmost cell at the specified location
+ */
+ public Object getFirstCellForLocation(double x, double y) {
+ return getNextCellForLocation(null, x, y);
+ }
+
+ /**
+ * Returns the cell at the specified location that is "behind" the
+ * <code>current</code> cell. Returns the topmost cell if there are no
+ * more cells behind <code>current</code>. Note: This does only return
+ * visible cells.
+ */
+ public Object getNextCellForLocation(Object current, double x, double y) {
+ CellView cur = graphLayoutCache.getMapping(current, false);
+ CellView cell = getNextViewAt(cur, x, y);
+
+ if (cell != null)
+ return cell.getCell();
+
+ return null;
+ }
+
+ /**
+ * Returns the bounding rectangle of the specified cell.
+ */
+ public Rectangle2D getCellBounds(Object cell) {
+ CellView view = graphLayoutCache.getMapping(cell, false);
+
+ if (view != null)
+ return view.getBounds();
+
+ return null;
+ }
+
+ /**
+ * Returns the bounding rectangle of the specified cells.
+ */
+ public Rectangle2D getCellBounds(Object[] cells) {
+ if ((cells != null) && (cells.length > 0)) {
+ Rectangle2D r = getCellBounds(cells[0]);
+ Rectangle2D ret = (r != null) ? (Rectangle2D) r.clone() : null;
+
+ for (int i = 1; i < cells.length; i++) {
+ r = getCellBounds(cells[i]);
+
+ if (r != null) {
+ if (ret == null)
+ ret = (r != null) ? (Rectangle2D) r.clone() : null;
+ else
+ Rectangle2D.union(ret, r, ret);
+ }
+ }
+
+ return ret;
+ }
+
+ return null;
+ }
+
+ /**
+ * Returns the next view at the specified location wrt. <code>current</code>.
+ * This is used to iterate overlapping cells, and cells that are grouped.
+ * The current selection affects this method. <br>
+ * Note: This returns the next <i>selectable </i> view. <br>
+ * Note: Arguments are not expected to be scaled (they are scaled in here).
+ */
+ public CellView getNextViewAt(CellView current, double x, double y) {
+ return getNextViewAt(current, x, y, false);
+ }
+
+ /**
+ * Returns the next view at the specified location wrt. <code>current</code>.
+ * This is used to iterate overlapping cells, and cells that are grouped.
+ * The current selection affects this method. <br>
+ * Note: This returns the next <i>selectable </i> view. <br>
+ * Note: Arguments are not expected to be scaled (they are scaled in here).
+ */
+ public CellView getNextViewAt(CellView current, double x, double y, boolean leafsOnly) {
+ CellView[] cells = AbstractCellView.getDescendantViews(getGraphLayoutCache().getRoots());
+
+ return getNextViewAt(cells, current, x, y, leafsOnly);
+ }
+
+ /**
+ * Note: Arguments are not expected to be scaled (they are scaled in here).
+ */
+ public CellView getNextSelectableViewAt(CellView current, double x, double y) {
+ CellView[] selectables = getGraphLayoutCache()
+ .getMapping(getSelectionModel().getSelectables(), false);
+
+ return getNextViewAt(selectables, current, x, y);
+ }
+
+ /**
+ * Returns the next view at the specified location wrt. <code>c</code> in
+ * the specified array of views. The views must be in order, as returned,
+ * for example, by GraphLayoutCache.order(Object[]).
+ */
+ public CellView getNextViewAt(CellView[] cells, CellView c, double x, double y) {
+ return getNextViewAt(cells, c, x, y, false);
+ }
+
+ /**
+ * Returns the next view at the specified location wrt. <code>c</code> in
+ * the specified array of views. The views must be in order, as returned,
+ * for example, by GraphLayoutCache.order(Object[]).
+ */
+ public CellView getNextViewAt(CellView[] cells, CellView c, double x, double y,
+ boolean leafsOnly) {
+ if (cells != null) {
+ Rectangle2D r = fromScreen(new Rectangle2D.Double(x - tolerance, y - tolerance,
+ 2 * tolerance, 2 * tolerance));
+
+ // Iterate through cells and switch to active
+ // if current is traversed. Cache first cell.
+ CellView first = null;
+ boolean active = (c == null);
+
+ for (int i = 0; i < cells.length; i++) {
+ if ((cells[i] != null) && (!leafsOnly || cells[i].isLeaf())
+ && cells[i].intersects(this, r)) {
+ // TODO: This behaviour is specific to selection and
+ // should be parametrized (it only returns a group with
+ // selected children if no other portview is available)
+ if (active && !selectionModel.isChildrenSelected(cells[i].getCell())) {
+ return cells[i];
+ } else if (first == null)
+ first = cells[i];
+
+ active = active | (cells[i] == c);
+ }
+ }
+
+ if (first != null)
+ return first;
+ }
+
+ return null;
+ }
+
+ /**
+ * Returns the next view at the specified location wrt. <code>c</code> in
+ * the specified array of views. The views must be in order, as returned,
+ * for example, by GraphLayoutCache.order(Object[]).
+ */
+ public CellView getLeafViewAt(double x, double y) {
+ return getNextViewAt(null, x, y, true);
+ }
+
+ /**
+ * Convenience method to return the port at the specified location.
+ */
+ public Object getPortForLocation(double x, double y) {
+ PortView view = getPortViewAt(x, y, tolerance);
+
+ if (view != null)
+ return view.getCell();
+
+ return null;
+ }
+
+ /**
+ * Returns the portview at the specified location. <br>
+ * Note: Arguments are not expected to be scaled (they are scaled in here).
+ */
+ public PortView getPortViewAt(double x, double y) {
+ return getPortViewAt(x, y, tolerance);
+ }
+
+ /**
+ * Returns the portview at the specified location. <br>
+ * Note: Arguments are not expected to be scaled (they are scaled in here).
+ */
+ public PortView getPortViewAt(double x, double y, int tolerance) {
+ double sx = x / scale;
+ double sy = y / scale;
+ Rectangle2D r = new Rectangle2D.Double(sx - tolerance, sy - tolerance, 2 * tolerance,
+ 2 * tolerance);
+ PortView[] ports = graphLayoutCache.getPorts();
+
+ if (ports != null) {
+ for (int i = ports.length - 1; i >= 0; i--)
+ if ((ports[i] != null) && ports[i].intersects(this, r))
+ return ports[i];
+
+ if (isJumpToDefaultPort()) {
+ CellView cellView = getNextViewAt(null, x, y, true);
+
+ // Finds a non-edge cell under the mousepointer
+ if ((cellView != null) && graphModel.isEdge(cellView.getCell())) {
+ CellView nextView = getNextViewAt(cellView, x, y, true);
+
+ while ((nextView != cellView) && graphModel.isEdge(nextView.getCell())) {
+ nextView = getNextViewAt(nextView, x, y, true);
+ }
+
+ cellView = nextView;
+ }
+
+ if (cellView != null) {
+ PortView defaultPort = getDefaultPortForCell(cellView.getCell());
+
+ return defaultPort;
+ }
+ }
+ }
+
+ return null;
+ }
+
+ /**
+ * Returns the default portview for the specified cell. The default
+ * implementation returns the first floating port (ie. the first port that
+ * does not define an offset) or <b>the </b> port, if there is only one
+ * port.
+ *
+ * @param cell
+ * the cell whose port is to be obtained
+ * @return the port view of the specified cell
+ */
+ public PortView getDefaultPortForCell(Object cell) {
+ if ((cell != null) && !getModel().isEdge(cell)) {
+ int childCount = getModel().getChildCount(cell);
+
+ for (int i = 0; i < childCount; i++) {
+ Object childCell = getModel().getChild(cell, i);
+ CellView child = getGraphLayoutCache().getMapping(childCell, false);
+
+ if (child instanceof PortView) {
+ Point2D offset = GraphConstants.getOffset(child.getAllAttributes());
+
+ if ((offset == null) || (childCount == 1))
+ return (PortView) child;
+ }
+ }
+ }
+
+ return null;
+ }
+
+ /**
+ * Converts the specified value to string. If the value is an instance of
+ * CellView then the corresponding value or cell is used.
+ */
+ public String convertValueToString(Object value) {
+ if (value instanceof CellView)
+ value = ((CellView) value).getCell();
+
+ return String.valueOf(value);
+ }
+
+ //
+ // Grid and Scale
+ //
+ /**
+ * Returns the given point applied to the grid.
+ *
+ * @param p
+ * a point in screen coordinates.
+ * @return the same point applied to the grid.
+ */
+ public Point2D snap(Point2D p) {
+ if (gridEnabled && (p != null)) {
+ double sgs = gridSize * getScale();
+ p.setLocation(Math.round(Math.round(p.getX() / sgs) * sgs),
+ Math.round(Math.round(p.getY() / sgs) * sgs));
+ }
+
+ return p;
+ }
+
+ /**
+ * Returns the given rectangle applied to the grid.
+ *
+ * @param r
+ * a rectangle in screen coordinates.
+ * @return the same rectangle applied to the grid.
+ */
+ public Rectangle2D snap(Rectangle2D r) {
+ if (gridEnabled && (r != null)) {
+ double sgs = gridSize * getScale();
+ r.setFrame(Math.round(Math.round(r.getX() / sgs) * sgs),
+ Math.round(Math.round(r.getY() / sgs) * sgs),
+ 1 + Math.round(Math.round(r.getWidth() / sgs) * sgs),
+ 1 + Math.round(Math.round(r.getHeight() / sgs) * sgs));
+ }
+
+ return r;
+ }
+
+ /**
+ * Returns the given dimension applied to the grid.
+ *
+ * @param d
+ * a dimension in screen coordinates to snap to.
+ * @return the same dimension applied to the grid.
+ */
+ public Dimension2D snap(Dimension2D d) {
+ if (gridEnabled && (d != null)) {
+ double sgs = gridSize * getScale();
+ d.setSize(1 + Math.round(Math.round(d.getWidth() / sgs) * sgs),
+ 1 + Math.round(Math.round(d.getHeight() / sgs) * sgs));
+ }
+
+ return d;
+ }
+
+ /**
+ * Upscale the given point in place, using the given instance.
+ *
+ * @param p
+ * the point to be upscaled
+ * @return the upscaled point instance
+ */
+ public Point2D toScreen(Point2D p) {
+ if (p == null)
+ return null;
+
+ p.setLocation(Math.round(p.getX() * scale), Math.round(p.getY() * scale));
+
+ return p;
+ }
+
+ /**
+ * Downscale the given point in place, using the given instance.
+ *
+ * @param p
+ * the point to be downscaled
+ * @return the downscaled point instance
+ */
+ public Point2D fromScreen(Point2D p) {
+ if (p == null)
+ return null;
+
+ p.setLocation(Math.round(p.getX() / scale), Math.round(p.getY() / scale));
+
+ return p;
+ }
+
+ /**
+ * Upscale the given rectangle in place, using the given instance.
+ *
+ * @param rect
+ * the rectangle to be upscaled
+ * @return the upscaled rectangle instance
+ */
+ public Rectangle2D toScreen(Rectangle2D rect) {
+ if (rect == null)
+ return null;
+
+ rect.setFrame(rect.getX() * scale, rect.getY() * scale, rect.getWidth() * scale,
+ rect.getHeight() * scale);
+
+ return rect;
+ }
+
+ /**
+ * Downscale the given rectangle in place, using the given instance.
+ *
+ * @param rect
+ * the rectangle to be downscaled
+ * @return the down-scaled rectangle instance
+ */
+ public Rectangle2D fromScreen(Rectangle2D rect) {
+ if (rect == null)
+ return null;
+
+ rect.setFrame(rect.getX() / scale, rect.getY() / scale, rect.getWidth() / scale,
+ rect.getHeight() / scale);
+
+ return rect;
+ }
+
+ /**
+ * Computes and updates the size for <code>view</code>.
+ */
+ public void updateAutoSize(CellView view) {
+ if ((view != null) && !isEditing()) {
+ Rectangle2D bounds = (view.getAttributes() != null)
+ ? GraphConstants.getBounds(view.getAttributes()) : null;
+ AttributeMap attrs = getModel().getAttributes(view.getCell());
+
+ if (bounds == null)
+ bounds = GraphConstants.getBounds(attrs);
+
+ if (bounds != null) {
+ boolean autosize = GraphConstants.isAutoSize(view.getAllAttributes());
+ boolean resize = GraphConstants.isResize(view.getAllAttributes());
+
+ if (autosize || resize) {
+ Dimension2D d = getUI().getPreferredSize(this, view);
+ bounds.setFrame(bounds.getX(), bounds.getY(), d.getWidth(), d.getHeight());
+ // Remove resize attribute
+ snap(bounds);
+
+ if (resize) {
+ if (view.getAttributes() != null)
+ view.getAttributes().remove(GraphConstants.RESIZE);
+
+ attrs.remove(GraphConstants.RESIZE);
+ }
+
+ view.refresh(getModel(), getGraphLayoutCache(), false);
+ }
+ }
+ }
+ }
+
+ /**
+ * Returns the attributes for the specified cell. If the layout cache
+ * returns a view for the cell then this method returns allAttributes,
+ * otherwise the method returns model.getAttributes(cell).
+ */
+ public AttributeMap getAttributes(Object cell) {
+ AttributeMap attrs;
+ CellView cellView = getGraphLayoutCache().getMapping(cell, false);
+
+ if (cellView != null) {
+ attrs = cellView.getAllAttributes();
+ } else {
+ attrs = getModel().getAttributes(cell);
+ }
+
+ return attrs;
+ }
+
+ //
+ // Unbound Properties
+ //
+ /**
+ * Returns the number of clicks for editing to start.
+ */
+ public int getEditClickCount() {
+ return editClickCount;
+ }
+
+ /**
+ * Sets the number of clicks for editing to start.
+ */
+ public void setEditClickCount(int count) {
+ editClickCount = count;
+ }
+
+ /**
+ * Returns true if the graph accepts drops/pastes from external sources.
+ */
+ public boolean isDropEnabled() {
+ return dropEnabled;
+ }
+
+ /**
+ * Sets if the graph accepts drops/pastes from external sources.
+ */
+ public void setDropEnabled(boolean flag) {
+ dropEnabled = flag;
+ }
+
+ /**
+ * Returns true if the graph uses Drag-and-Drop to move cells.
+ */
+ public boolean isDragEnabled() {
+ return dragEnabled;
+ }
+
+ /**
+ * Sets if the graph uses Drag-and-Drop to move cells.
+ */
+ public void setDragEnabled(boolean flag) {
+ dragEnabled = flag;
+ }
+
+ /*
+ * Returns true if the graph allows movement of cells.
+ */
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isMoveable() {
+ return moveable;
+ }
+
+ /**
+ * Sets if the graph allows movement of cells.
+ */
+ public void setMoveable(boolean flag) {
+ moveable = flag;
+ }
+
+ /**
+ * Returns true if the graph allows adding/removing/modifying points.
+ */
+ public boolean isBendable() {
+ return bendable;
+ }
+
+ /**
+ * Sets if the graph allows adding/removing/modifying points.
+ */
+ public void setBendable(boolean flag) {
+ bendable = flag;
+ }
+
+ /**
+ * Returns true if the graph allows new connections to be established.
+ */
+ public boolean isConnectable() {
+ return connectable;
+ }
+
+ /**
+ * Setse if the graph allows new connections to be established.
+ */
+ public void setConnectable(boolean flag) {
+ connectable = flag;
+ }
+
+ /**
+ * Returns true if the graph allows existing connections to be removed.
+ */
+ public boolean isDisconnectable() {
+ return disconnectable;
+ }
+
+ /**
+ * Sets if the graph allows existing connections to be removed.
+ */
+ public void setDisconnectable(boolean flag) {
+ disconnectable = flag;
+ }
+
+ /**
+ * Returns true if cells are cloned on CTRL-Drag operations.
+ */
+ public boolean isCloneable() {
+ return cloneable;
+ }
+
+ /**
+ * Sets if cells are cloned on CTRL-Drag operations.
+ */
+ public void setCloneable(boolean flag) {
+ cloneable = flag;
+ }
+
+ /**
+ * Returns true if the graph allows cells to be resized.
+ */
+ public boolean isSizeable() {
+ return sizeable;
+ }
+
+ /**
+ * Sets if the graph allows cells to be resized.
+ */
+ public void setSizeable(boolean flag) {
+ sizeable = flag;
+ }
+
+ /**
+ * Sets if selected edges should be disconnected from unselected vertices
+ * when they are moved.
+ */
+ public void setDisconnectOnMove(boolean flag) {
+ disconnectOnMove = flag;
+ }
+
+ /**
+ * Returns true if selected edges should be disconnected from unselected
+ * vertices when they are moved.
+ */
+ public boolean isDisconnectOnMove() {
+ return disconnectOnMove && disconnectable;
+ }
+
+ /**
+ * Sets if getPortViewAt should return the default port if no other port is
+ * found.
+ */
+ public void setJumpToDefaultPort(boolean flag) {
+ isJumpToDefaultPort = flag;
+ }
+
+ /**
+ * Returns true if getPortViewAt should return the default port if no other
+ * port is found.
+ */
+ public boolean isJumpToDefaultPort() {
+ return isJumpToDefaultPort;
+ }
+
+ /**
+ * Specifies if cells should be added to groups when moved over the group's
+ * area.
+ */
+ public void setMoveIntoGroups(boolean flag) {
+ isMoveIntoGroups = flag;
+ }
+
+ /**
+ * Returns true if cells should be added to groups when moved over the
+ * group's area.
+ */
+ public boolean isMoveIntoGroups() {
+ return isMoveIntoGroups;
+ }
+
+ /**
+ * Specifies if cells should be removed from groups when removed from the
+ * group's area.
+ */
+ public void setMoveOutOfGroups(boolean flag) {
+ isMoveOutOfGroups = flag;
+ }
+
+ /**
+ * Returns true if cells should be removed from groups when removed from the
+ * group's area.
+ */
+ public boolean isMoveOutOfGroups() {
+ return isMoveOutOfGroups;
+ }
+
+ /**
+ * Returns true if the grid is active.
+ *
+ * @see #snap(Point2D)
+ *
+ */
+ public boolean isGridEnabled() {
+ return gridEnabled;
+ }
+
+ /**
+ * If set to true, the grid will be active.
+ *
+ * @see #snap(Point2D)
+ *
+ */
+ public void setGridEnabled(boolean flag) {
+ gridEnabled = flag;
+ }
+
+ /**
+ * Returns true if the graph allows to move cells below zero.
+ */
+ public boolean isMoveBelowZero() {
+ return moveBelowZero;
+ }
+
+ /**
+ * Sets if the graph should auto resize when cells are being moved below the
+ * bottom right corner.
+ */
+ public void setMoveBelowZero(boolean moveBelowZero) {
+ this.moveBelowZero = moveBelowZero;
+ }
+
+ /**
+ * Returns true if the graph should be automatically resized when cells are
+ * being move below the bottom right corner.
+ */
+ public boolean isAutoResizeGraph() {
+ return autoResizeGraph;
+ }
+
+ /**
+ * Sets if the graph allows to move cells below zero.
+ */
+ public void setAutoResizeGraph(boolean autoResizeGraph) {
+ this.autoResizeGraph = autoResizeGraph;
+ }
+
+ /**
+ * Returns the maximum distance between the mousepointer and a cell to be
+ * selected.
+ */
+ public int getTolerance() {
+ return tolerance;
+ }
+
+ /**
+ * Sets the maximum distance between the mousepointer and a cell to be
+ * selected.
+ */
+ public void setTolerance(int size) {
+ tolerance = size;
+ }
+
+ /**
+ * Returns the size of the handles.
+ */
+ public int getHandleSize() {
+ return handleSize;
+ }
+
+ /**
+ * Sets the size of the handles.
+ */
+ public void setHandleSize(int size) {
+ int oldValue = handleSize;
+ handleSize = size;
+ firePropertyChange(HANDLE_SIZE_PROPERTY, oldValue, size);
+ }
+
+ /**
+ * Returns the miminum amount of pixels for a move operation.
+ */
+ public int getMinimumMove() {
+ return minimumMove;
+ }
+
+ /**
+ * Sets the miminum amount of pixels for a move operation.
+ */
+ public void setMinimumMove(int pixels) {
+ minimumMove = pixels;
+ }
+
+ //
+ // Laf-Specific color scheme. These colors are changed
+ // by BasicGraphUI when the laf changes.
+ //
+ /**
+ * Returns the current grid color.
+ */
+ public Color getGridColor() {
+ return gridColor;
+ }
+
+ /**
+ * Sets the current grid color.
+ */
+ public void setGridColor(Color newColor) {
+ Color oldValue = gridColor;
+ gridColor = newColor;
+ firePropertyChange(GRID_COLOR_PROPERTY, oldValue, newColor);
+ }
+
+ /**
+ * Returns the current handle color.
+ */
+ public Color getHandleColor() {
+ return handleColor;
+ }
+
+ /**
+ * Sets the current handle color.
+ */
+ public void setHandleColor(Color newColor) {
+ Color oldValue = handleColor;
+ handleColor = newColor;
+ firePropertyChange(HANDLE_COLOR_PROPERTY, oldValue, newColor);
+ }
+
+ /**
+ * Returns the current second handle color.
+ */
+ public Color getLockedHandleColor() {
+ return lockedHandleColor;
+ }
+
+ /**
+ * Sets the current second handle color.
+ */
+ public void setLockedHandleColor(Color newColor) {
+ Color oldValue = lockedHandleColor;
+ lockedHandleColor = newColor;
+ firePropertyChange(LOCKED_HANDLE_COLOR_PROPERTY, oldValue, newColor);
+ }
+
+ /**
+ * Returns the current marquee color.
+ */
+ public Color getMarqueeColor() {
+ return marqueeColor;
+ }
+
+ /**
+ * Sets the current marquee color.
+ */
+ public void setMarqueeColor(Color newColor) {
+ marqueeColor = newColor;
+ }
+
+ /**
+ * Returns the current highlight color.
+ */
+ public Color getHighlightColor() {
+ return highlightColor;
+ }
+
+ /**
+ * Sets the current selection highlight color.
+ */
+ public void setHighlightColor(Color newColor) {
+ highlightColor = newColor;
+ }
+
+ //
+ // Bound properties
+ //
+ /**
+ * Returns the current scale.
+ *
+ * @return the current scale as a double
+ */
+ public double getScale() {
+ return scale;
+ }
+
+ /**
+ * Sets the current scale.
+ * <p>
+ * Fires a property change for the SCALE_PROPERTY.
+ *
+ * @param newValue
+ * the new scale
+ */
+ public void setScale(double newValue) {
+ if (newValue > 0) {
+ double oldValue = this.scale;
+ scale = newValue;
+ firePropertyChange(SCALE_PROPERTY, oldValue, newValue);
+ }
+ }
+
+ /**
+ * Returns the size of the grid in pixels.
+ *
+ * @return the size of the grid as an int
+ */
+ public double getGridSize() {
+ return gridSize;
+ }
+
+ /**
+ * Returns the current grid view mode.
+ */
+ public int getGridMode() {
+ return gridMode;
+ }
+
+ /**
+ * Sets the size of the grid.
+ * <p>
+ * Fires a property change for the GRID_SIZE_PROPERTY.
+ *
+ * @param newSize
+ * the new size of the grid in pixels
+ */
+ public void setGridSize(double newSize) {
+ double oldValue = this.gridSize;
+ this.gridSize = newSize;
+ firePropertyChange(GRID_SIZE_PROPERTY, oldValue, newSize);
+ }
+
+ /**
+ * Sets the current grid view mode.
+ *
+ * @param mode
+ * The current grid view mode. Valid values are <CODE>
+ * DOT_GRID_MODE</CODE>,<CODE>CROSS_GRID_MODE</CODE>, and
+ * <CODE>LINE_GRID_MODE</CODE>.
+ */
+ public void setGridMode(int mode) {
+ if ((mode == DOT_GRID_MODE) || (mode == CROSS_GRID_MODE) || (mode == LINE_GRID_MODE)) {
+ gridMode = mode;
+ repaint();
+ }
+ }
+
+ /**
+ * Returns true if the grid will be visible.
+ *
+ * @return true if the grid is visible
+ */
+ public boolean isGridVisible() {
+ return gridVisible;
+ }
+
+ /**
+ * If set to true, the grid will be visible.
+ * <p>
+ * Fires a property change for the GRID_VISIBLE_PROPERTY.
+ */
+ public void setGridVisible(boolean flag) {
+ boolean oldValue = gridVisible;
+ gridVisible = flag;
+ firePropertyChange(GRID_VISIBLE_PROPERTY, oldValue, flag);
+ }
+
+ /**
+ * Returns true if the ports will be visible.
+ *
+ * @return true if the ports are visible
+ */
+ public boolean isPortsVisible() {
+ return portsVisible;
+ }
+
+ /**
+ * If set to true, the ports will be visible.
+ * <p>
+ * Fires a property change for the PORTS_VISIBLE_PROPERTY.
+ */
+ public void setPortsVisible(boolean flag) {
+ boolean oldValue = portsVisible;
+ portsVisible = flag;
+ firePropertyChange(PORTS_VISIBLE_PROPERTY, oldValue, flag);
+ }
+
+ /**
+ * Returns true if the ports will be scaled.
+ *
+ * @return true if the ports are visible
+ */
+ public boolean isPortsScaled() {
+ return portsScaled;
+ }
+
+ /**
+ * If set to true, the ports will be scaled.
+ * <p>
+ * Fires a property change for the PORTS_SCALED_PROPERTY.
+ */
+ public void setPortsScaled(boolean flag) {
+ boolean oldValue = portsScaled;
+ portsScaled = flag;
+ firePropertyChange(PORTS_SCALED_PROPERTY, oldValue, flag);
+ }
+
+ /**
+ * Returns true if the graph will be anti aliased.
+ *
+ * @return true if the graph is anti aliased
+ */
+ public boolean isAntiAliased() {
+ return antiAliased;
+ }
+
+ /**
+ * Sets antialiasing on or off based on the boolean value.
+ * <p>
+ * Fires a property change for the ANTIALIASED_PROPERTY.
+ *
+ * @param newValue
+ * whether to turn antialiasing on or off
+ */
+ public void setAntiAliased(boolean newValue) {
+ boolean oldValue = this.antiAliased;
+ this.antiAliased = newValue;
+ firePropertyChange(ANTIALIASED_PROPERTY, oldValue, newValue);
+ }
+
+ /**
+ * Returns true if the graph is editable (if it allows cells to be edited).
+ *
+ * @return true if the graph is editable
+ */
+ public boolean isEditable() {
+ return editable;
+ }
+
+ /**
+ * Determines whether the graph is editable. Fires a property change event
+ * if the new setting is different from the existing setting.
+ * <p>
+ * Note: Editable determines whether the graph allows editing. This is not
+ * to be confused with enabled, which allows the graph to handle mouse
+ * events (including editing).
+ *
+ * @param flag
+ * a boolean value, true if the graph is editable
+ */
+ public void setEditable(boolean flag) {
+ boolean oldValue = this.editable;
+ this.editable = flag;
+ firePropertyChange(EDITABLE_PROPERTY, oldValue, flag);
+ }
+
+ /**
+ * Returns true if the cell selection is enabled
+ *
+ * @return true if the cell selection is enabled
+ */
+ public boolean isSelectionEnabled() {
+ return selectionEnabled;
+ }
+
+ /**
+ * Determines whether cell selection is enabled. Fires a property change
+ * event if the new setting is different from the existing setting.
+ *
+ * @param flag
+ * a boolean value, true if cell selection is enabled
+ */
+ public void setSelectionEnabled(boolean flag) {
+ boolean oldValue = this.editable;
+ this.selectionEnabled = flag;
+ firePropertyChange(SELECTIONENABLED_PROPERTY, oldValue, flag);
+ }
+
+ /**
+ * Returns true if graph allows invalid null ports during previews
+ *
+ * @return true if the graph allows invalid null ports during previews
+ */
+ public boolean isPreviewInvalidNullPorts() {
+ return previewInvalidNullPorts;
+ }
+
+ /**
+ * Determines whether the graph allows invalid null ports during previews
+ *
+ * @param flag
+ * a boolean value, true if the graph allows invalid null ports
+ * during previews
+ */
+ public void setPreviewInvalidNullPorts(boolean flag) {
+ this.previewInvalidNullPorts = flag;
+ }
+
+ /**
+ * Returns the <code>GraphModel</code> that is providing the data.
+ *
+ * @return the model that is providing the data
+ */
+ public GraphModel getModel() {
+ return graphModel;
+ }
+
+ /**
+ * Sets the <code>GraphModel</code> that will provide the data. Note:
+ * Updates the current GraphLayoutCache's model using setModel if the
+ * GraphLayoutCache points to a different model.
+ * <p>
+ * Fires a property change for the GRAPH_MODEL_PROPERTY.
+ *
+ * @param newModel
+ * the <code>GraphModel</code> that is to provide the data
+ */
+ public void setModel(GraphModel newModel) {
+ GraphModel oldModel = graphModel;
+ graphModel = newModel;
+ firePropertyChange(GRAPH_MODEL_PROPERTY, oldModel, graphModel);
+
+ // FIX: Use Listener
+ if ((graphLayoutCache != null) && (graphLayoutCache.getModel() != graphModel))
+ graphLayoutCache.setModel(graphModel);
+
+ clearSelection();
+ invalidate();
+ }
+
+ /**
+ * Returns the <code>GraphLayoutCache</code> that is providing the
+ * view-data.
+ *
+ * @return the view that is providing the view-data
+ */
+ public GraphLayoutCache getGraphLayoutCache() {
+ return graphLayoutCache;
+ }
+
+ /**
+ * Sets the <code>GraphLayoutCache</code> that will provide the view-data.
+ * <p>
+ * Note: Updates the graphs's model using using the model from the layout
+ * cache.
+ * <p>
+ * Fires a property change for the GRAPH_LAYOUT_CACHE_PROPERTY.
+ *
+ * @param newLayoutCache
+ * the <code>GraphLayoutCache</code> that is to provide the
+ * view-data
+ */
+ public void setGraphLayoutCache(GraphLayoutCache newLayoutCache) {
+ GraphLayoutCache oldLayoutCache = graphLayoutCache;
+ graphLayoutCache = newLayoutCache;
+ firePropertyChange(GRAPH_LAYOUT_CACHE_PROPERTY, oldLayoutCache, graphLayoutCache);
+
+ if ((graphLayoutCache != null) && (graphLayoutCache.getModel() != getModel()))
+ setModel(graphLayoutCache.getModel());
+
+ invalidate();
+ }
+
+ /**
+ * Returns the <code>MarqueeHandler</code> that will handle marquee
+ * selection.
+ */
+ public BasicMarqueeHandler getMarqueeHandler() {
+ return marquee;
+ }
+
+ /**
+ * Sets the <code>MarqueeHandler</code> that will handle marquee
+ * selection.
+ *
+ * @param newMarquee
+ * the <code>BasicMarqueeHandler</code> that is to provide
+ * marquee handling
+ */
+ public void setMarqueeHandler(BasicMarqueeHandler newMarquee) {
+ BasicMarqueeHandler oldMarquee = marquee;
+ marquee = newMarquee;
+ firePropertyChange(MARQUEE_HANDLER_PROPERTY, oldMarquee, newMarquee);
+ invalidate();
+ }
+
+ /**
+ * Determines what happens when editing is interrupted by selecting another
+ * cell in the graph, a change in the graph's data, or by some other means.
+ * Setting this property to <code>true</code> causes the changes to be
+ * automatically saved when editing is interrupted.
+ * <p>
+ * Fires a property change for the INVOKES_STOP_CELL_EDITING_PROPERTY.
+ *
+ * @param newValue
+ * true means that <code>stopCellEditing</code> is invoked when
+ * editing is interruped, and data is saved; false means that
+ * <code>cancelCellEditing</code> is invoked, and changes are
+ * lost
+ */
+ public void setInvokesStopCellEditing(boolean newValue) {
+ boolean oldValue = invokesStopCellEditing;
+ invokesStopCellEditing = newValue;
+ firePropertyChange(INVOKES_STOP_CELL_EDITING_PROPERTY, oldValue, newValue);
+ }
+
+ /**
+ * Returns the indicator that tells what happens when editing is
+ * interrupted.
+ *
+ * @return the indicator that tells what happens when editing is interrupted
+ * @see #setInvokesStopCellEditing
+ *
+ */
+ public boolean getInvokesStopCellEditing() {
+ return invokesStopCellEditing;
+ }
+
+ /**
+ * Returns <code>true</code> if the graph and the cell are editable. This
+ * is invoked from the UI before editing begins to ensure that the given
+ * cell can be edited.
+ *
+ * @return true if the specified cell is editable
+ * @see #isEditable
+ *
+ */
+ public boolean isCellEditable(Object cell) {
+ if (cell != null) {
+ CellView view = graphLayoutCache.getMapping(cell, false);
+
+ if (view != null) {
+ return isEditable() && GraphConstants.isEditable(view.getAllAttributes());
+ }
+ }
+
+ return false;
+ }
+
+ /**
+ * Overrides <code>JComponent</code>'s<code>getToolTipText</code>
+ * method in order to allow the graph to create a tooltip for the topmost
+ * cell under the mousepointer. This differs from JTree where the renderers
+ * tooltip is used.
+ * <p>
+ * NOTE: For <code>JGraph</code> to properly display tooltips of its
+ * renderers, <code>JGraph</code> must be a registered component with the
+ * <code>ToolTipManager</code>. This can be done by invoking
+ * <code>ToolTipManager.sharedInstance().registerComponent(graph)</code>.
+ * This is not done automatically!
+ *
+ * @param e
+ * the <code>MouseEvent</code> that initiated the
+ * <code>ToolTip</code> display
+ * @return a string containing the tooltip or <code>null</code> if
+ * <code>event</code> is null
+ */
+ public String getToolTipText(MouseEvent e) {
+ if (e != null) {
+ Object cell = getFirstCellForLocation(e.getX(), e.getY());
+ CellView view = getGraphLayoutCache().getMapping(cell, false);
+
+ if (view != null) {
+ Component c = view.getRendererComponent(this, false, false, false);
+
+ if (c instanceof JComponent) {
+ Rectangle2D rect = getCellBounds(cell);
+ Point2D where = fromScreen(e.getPoint());
+ // Pass the event to the renderer in graph coordinates;
+ // the renderer is ignorant of screen scaling
+ e = new MouseEvent(c, e.getID(), e.getWhen(), e.getModifiers(),
+ (int) (where.getX() - rect.getX()),
+ (int) (where.getY() - rect.getY()), e.getClickCount(),
+ e.isPopupTrigger());
+
+ return ((JComponent) c).getToolTipText(e);
+ }
+ }
+ }
+
+ return super.getToolTipText(e);
+ }
+
+ //
+ // The following are convenience methods that get forwarded to the
+ // current GraphSelectionModel.
+ //
+ /**
+ * Sets the graph's selection model. When a <code>null</code> value is
+ * specified an emtpy <code>selectionModel</code> is used, which does not
+ * allow selections.
+ *
+ * @param selectionModel
+ * the <code>GraphSelectionModel</code> to use, or
+ * <code>null</code> to disable selections
+ * @see GraphSelectionModel
+ *
+ */
+ public void setSelectionModel(GraphSelectionModel selectionModel) {
+ if (selectionModel == null)
+ selectionModel = EmptySelectionModel.sharedInstance();
+
+ GraphSelectionModel oldValue = this.selectionModel;
+
+ // Remove Redirector From Old Selection Model
+ if ((this.selectionModel != null) && (selectionRedirector != null))
+ this.selectionModel.removeGraphSelectionListener(selectionRedirector);
+
+ this.selectionModel = selectionModel;
+
+ // Add Redirector To New Selection Model
+ if (selectionRedirector != null)
+ this.selectionModel.addGraphSelectionListener(selectionRedirector);
+
+ firePropertyChange(SELECTION_MODEL_PROPERTY, oldValue, this.selectionModel);
+ }
+
+ /**
+ * Returns the model for selections. This should always return a non-
+ * <code>null</code> value. If you don't want to allow anything to be
+ * selected set the selection model to <code>null</code>, which forces an
+ * empty selection model to be used.
+ *
+ * @return the current selection model
+ * @see #setSelectionModel
+ *
+ */
+ public GraphSelectionModel getSelectionModel() {
+ return selectionModel;
+ }
+
+ /**
+ * Clears the selection.
+ */
+ public void clearSelection() {
+ getSelectionModel().clearSelection();
+ }
+
+ /**
+ * Returns true if the selection is currently empty.
+ *
+ * @return true if the selection is currently empty
+ */
+ public boolean isSelectionEmpty() {
+ return getSelectionModel().isSelectionEmpty();
+ }
+
+ /**
+ * Adds a listener for <code>GraphSelection</code> events.
+ *
+ * @param tsl
+ * the <code>GraphSelectionListener</code> that will be
+ * notified when a cell is selected or deselected (a "negative
+ * selection")
+ */
+ public void addGraphSelectionListener(GraphSelectionListener tsl) {
+ listenerList.add(GraphSelectionListener.class, tsl);
+
+ if ((listenerList.getListenerCount(GraphSelectionListener.class) != 0)
+ && (selectionRedirector == null)) {
+ selectionRedirector = new GraphSelectionRedirector();
+ selectionModel.addGraphSelectionListener(selectionRedirector);
+ }
+ }
+
+ /**
+ * Removes a <code>GraphSelection</code> listener.
+ *
+ * @param tsl
+ * the <code>GraphSelectionListener</code> to remove
+ */
+ public void removeGraphSelectionListener(GraphSelectionListener tsl) {
+ listenerList.remove(GraphSelectionListener.class, tsl);
+
+ if ((listenerList.getListenerCount(GraphSelectionListener.class) == 0)
+ && (selectionRedirector != null)) {
+ selectionModel.removeGraphSelectionListener(selectionRedirector);
+ selectionRedirector = null;
+ }
+ }
+
+ /**
+ * Notifies all listeners that have registered interest for notification on
+ * this event type. The event instance is lazily created using the
+ * parameters passed into the fire method.
+ *
+ * @param e
+ * the <code>GraphSelectionEvent</code> generated by the
+ * <code>GraphSelectionModel</code> when a cell is selected or
+ * deselected
+ * @see javax.swing.event.EventListenerList
+ *
+ */
+ protected void fireValueChanged(GraphSelectionEvent e) {
+ // Guaranteed to return a non-null array
+ Object[] listeners = listenerList.getListenerList();
+
+ // Process the listeners last to first, notifying
+ // those that are interested in this event
+ for (int i = listeners.length - 2; i >= 0; i -= 2) {
+ if (listeners[i] == GraphSelectionListener.class) {
+ ((GraphSelectionListener) listeners[i + 1]).valueChanged(e);
+ }
+ }
+ }
+
+ /**
+ * Selects the specified cell.
+ *
+ * @param cell
+ * the <code>Object</code> specifying the cell to select
+ */
+ public void setSelectionCell(Object cell) {
+ getSelectionModel().setSelectionCell(cell);
+ }
+
+ /**
+ * Selects the specified cells.
+ *
+ * @param cells
+ * an array of objects that specifies the cells to select
+ */
+ public void setSelectionCells(Object[] cells) {
+ getSelectionModel().setSelectionCells(cells);
+ }
+
+ /**
+ * Adds the cell identified by the specified <code>Object</code> to the
+ * current selection.
+ *
+ * @param cell
+ * the cell to be added to the selection
+ */
+ public void addSelectionCell(Object cell) {
+ getSelectionModel().addSelectionCell(cell);
+ }
+
+ /**
+ * Adds each cell in the array of cells to the current selection.
+ *
+ * @param cells
+ * an array of objects that specifies the cells to add
+ */
+ public void addSelectionCells(Object[] cells) {
+ getSelectionModel().addSelectionCells(cells);
+ }
+
+ /**
+ * Removes the cell identified by the specified Object from the current
+ * selection.
+ *
+ * @param cell
+ * the cell to be removed from the selection
+ */
+ public void removeSelectionCell(Object cell) {
+ getSelectionModel().removeSelectionCell(cell);
+ }
+
+ /**
+ * Returns the first selected cell.
+ *
+ * @return the <code>Object</code> for the first selected cell, or
+ * <code>null</code> if nothing is currently selected
+ */
+ public Object getSelectionCell() {
+ return getSelectionModel().getSelectionCell();
+ }
+
+ /**
+ * Returns all selected cells.
+ *
+ * @return an array of objects representing the selected cells, or
+ * <code>null</code> if nothing is currently selected
+ */
+ public Object[] getSelectionCells() {
+ return getSelectionModel().getSelectionCells();
+ }
+
+ /**
+ * Returns all selected cells in <code>cells</code>.
+ */
+ public Object[] getSelectionCells(Object[] cells) {
+ if (cells != null) {
+ List selected = new ArrayList(cells.length);
+
+ for (int i = 0; i < cells.length; i++) {
+ if (isCellSelected(cells[i]))
+ selected.add(cells[i]);
+ }
+
+ return selected.toArray();
+ }
+
+ return null;
+ }
+
+ /**
+ * Returns the selection cell at the specified location.
+ *
+ * @return Returns the selection cell for <code>pt</code>.
+ */
+ public Object getSelectionCellAt(Point2D pt) {
+ pt = fromScreen((Point2D) pt.clone());
+
+ Object[] cells = getSelectionCells();
+
+ if (cells != null) {
+ for (int i = 0; i < cells.length; i++)
+ if (getCellBounds(cells[i]).contains(pt.getX(), pt.getY()))
+ return cells[i];
+ }
+
+ return null;
+ }
+
+ /**
+ * Returns the number of cells selected.
+ *
+ * @return the number of cells selected
+ */
+ public int getSelectionCount() {
+ return getSelectionModel().getSelectionCount();
+ }
+
+ /**
+ * Returns true if the cell is currently selected.
+ *
+ * @param cell
+ * an object identifying a cell
+ * @return true if the cell is selected
+ */
+ public boolean isCellSelected(Object cell) {
+ return getSelectionModel().isCellSelected(cell);
+ }
+
+ /**
+ * Scrolls to the specified cell. Only works when this <code>JGraph</code>
+ * is contained in a <code>JScrollPane</code>.
+ *
+ * @param cell
+ * the object identifying the cell to bring into view
+ */
+ public void scrollCellToVisible(Object cell) {
+ Rectangle2D bounds = getCellBounds(cell);
+
+ if (bounds != null) {
+ Rectangle2D b2 = toScreen((Rectangle2D) bounds.clone());
+ scrollRectToVisible(new Rectangle((int) b2.getX(), (int) b2.getY(),
+ (int) b2.getWidth(), (int) b2.getHeight()));
+ }
+ }
+
+ /**
+ * Makes sure the specified point is visible.
+ *
+ * @param p
+ * the point that should be visible
+ */
+ public void scrollPointToVisible(Point2D p) {
+ if (p != null)
+ scrollRectToVisible(new Rectangle((int) p.getX(), (int) p.getY(), 1, 1));
+ }
+
+ /**
+ * Returns true if the graph is being edited. The item that is being edited
+ * can be obtained using <code>getEditingCell</code>.
+ *
+ * @return true if the user is currently editing a cell
+ * @see #getSelectionCell
+ *
+ */
+ public boolean isEditing() {
+ GraphUI graph = getUI();
+
+ if (graph != null)
+ return graph.isEditing(this);
+
+ return false;
+ }
+
+ /**
+ * Ends the current editing session. (The
+ * <code>DefaultGraphCellEditor</code> object saves any edits that are
+ * currently in progress on a cell. Other implementations may operate
+ * differently.) Has no effect if the tree isn't being edited. <blockquote>
+ * <b>Note: </b> <br>
+ * To make edit-saves automatic whenever the user changes their position in
+ * the graph, use {@link #setInvokesStopCellEditing}. </blockquote>
+ *
+ * @return true if editing was in progress and is now stopped, false if
+ * editing was not in progress
+ */
+ public boolean stopEditing() {
+ GraphUI graph = getUI();
+
+ if (graph != null)
+ return graph.stopEditing(this);
+
+ return false;
+ }
+
+ /**
+ * Cancels the current editing session. Has no effect if the graph isn't
+ * being edited.
+ */
+ public void cancelEditing() {
+ GraphUI graph = getUI();
+
+ if (graph != null)
+ graph.cancelEditing(this);
+ }
+
+ /**
+ * Selects the specified cell and initiates editing. The edit-attempt fails
+ * if the <code>CellEditor</code> does not allow editing for the specified
+ * item.
+ */
+ public void startEditingAtCell(Object cell) {
+ GraphUI graph = getUI();
+
+ if (graph != null)
+ graph.startEditingAtCell(this, cell);
+ }
+
+ /**
+ * Returns the cell that is currently being edited.
+ *
+ * @return the cell being edited
+ */
+ public Object getEditingCell() {
+ GraphUI graph = getUI();
+
+ if (graph != null)
+ return graph.getEditingCell(this);
+
+ return null;
+ }
+
+ /**
+ * Messaged when the graph has changed enough that we need to resize the
+ * bounds, but not enough that we need to remove the cells (e.g cells were
+ * inserted into the graph). You should never have to invoke this, the UI
+ * will invoke this as it needs to. (Note: This is invoked by GraphUI, eg.
+ * after moving.)
+ */
+ public void graphDidChange() {
+ revalidate();
+ repaint();
+ }
+
+ /**
+ * Returns a {@link BufferedImage} for the graph using inset as an empty
+ * border around the cells of the graph. If bg is null then a transparent
+ * background is applied to the image, else the background is filled with
+ * the bg color. Therefore, one should only use a null background if the
+ * fileformat support transparency, eg. GIF and PNG. For JPG, you can use
+ * <code>Color.WHITE</code> for example.
+ *
+ * @return Returns an image of the graph.
+ */
+ public BufferedImage getImage(Color bg, int inset) {
+ Object[] cells = getRoots();
+ Rectangle2D bounds = getCellBounds(cells);
+
+ if (bounds != null) {
+ toScreen(bounds);
+
+ BufferedImage img = new BufferedImage((int) bounds.getWidth() + (2 * inset),
+ (int) bounds.getHeight() + (2 * inset),
+ (bg != null) ? BufferedImage.TYPE_INT_RGB
+ : BufferedImage.TYPE_INT_ARGB);
+ Graphics2D graphics = img.createGraphics();
+
+ if (bg != null) {
+ graphics.setColor(bg);
+ graphics.fillRect(0, 0, img.getWidth(), img.getHeight());
+ } else {
+ graphics.setComposite(AlphaComposite.getInstance(AlphaComposite.CLEAR, 0.0f));
+ graphics.fillRect(0, 0, img.getWidth(), img.getHeight());
+ graphics.setComposite(AlphaComposite.SrcOver);
+ }
+
+ graphics.translate((int) (-bounds.getX() + inset), (int) (-bounds.getY() + inset));
+ print(graphics);
+
+ return img;
+ }
+
+ return null;
+ }
+
+ /**
+ * Serialization support.
+ */
+ private void writeObject(ObjectOutputStream s) throws IOException {
+ Vector values = new Vector();
+ s.defaultWriteObject();
+
+ // Save the cellEditor, if its Serializable.
+ if (graphModel instanceof Serializable) {
+ values.addElement("graphModel");
+ values.addElement(graphModel);
+ }
+
+ // Save the graphModel, if its Serializable.
+ if (graphLayoutCache instanceof Serializable) {
+ values.addElement("graphLayoutCache");
+ values.addElement(graphLayoutCache);
+ }
+
+ // Save the selectionModel, if its Serializable.
+ if (selectionModel instanceof Serializable) {
+ values.addElement("selectionModel");
+ values.addElement(selectionModel);
+ }
+
+ // Save the marquee handler, if its Serializable.
+ if (marquee instanceof Serializable) {
+ values.addElement("marquee");
+ values.addElement(marquee);
+ }
+
+ s.writeObject(values);
+
+ if (getUIClassID().equals(uiClassID)) {
+ /*
+ * byte count = JComponent.getWriteObjCounter(this);
+ * JComponent.setWriteObjCounter(this, --count);
+ */
+ if ( /* count == 0 && */
+ ui != null) {
+ ui.installUI(this);
+ }
+ }
+ }
+
+ /**
+ * Serialization support.
+ */
+ private void readObject(ObjectInputStream s) throws IOException, ClassNotFoundException {
+ s.defaultReadObject();
+
+ Vector values = (Vector) s.readObject();
+ int indexCounter = 0;
+ int maxCounter = values.size();
+
+ if ((indexCounter < maxCounter) && values.elementAt(indexCounter).equals("graphModel")) {
+ graphModel = (GraphModel) values.elementAt(++indexCounter);
+ indexCounter++;
+ }
+
+ if ((indexCounter < maxCounter)
+ && values.elementAt(indexCounter).equals("graphLayoutCache")) {
+ graphLayoutCache = (GraphLayoutCache) values.elementAt(++indexCounter);
+ indexCounter++;
+ }
+
+ if ((indexCounter < maxCounter) && values.elementAt(indexCounter).equals("selectionModel")) {
+ selectionModel = (GraphSelectionModel) values.elementAt(++indexCounter);
+ indexCounter++;
+ }
+
+ if ((indexCounter < maxCounter) && values.elementAt(indexCounter).equals("marquee")) {
+ marquee = (BasicMarqueeHandler) values.elementAt(++indexCounter);
+ indexCounter++;
+ }
+
+ // Reinstall the redirector.
+ if (listenerList.getListenerCount(GraphSelectionListener.class) != 0) {
+ selectionRedirector = new GraphSelectionRedirector();
+ selectionModel.addGraphSelectionListener(selectionRedirector);
+ }
+ }
+
+ /**
+ * <code>EmptySelectionModel</code> is a <code>GraphSelectionModel</code>
+ * that does not allow anything to be selected.
+ * <p>
+ * <strong>Warning: </strong> Serialized objects of this class will not be
+ * compatible with future Swing releases. The current serialization support
+ * is appropriate for short term storage or RMI between applications running
+ * the same version of Swing. A future release of Swing will provide support
+ * for long term persistence.
+ */
+ public static class EmptySelectionModel extends DefaultGraphSelectionModel {
+ /** Unique shared instance. */
+ protected static final EmptySelectionModel sharedInstance = new EmptySelectionModel();
+
+ /**
+ * A <code>null</code> implementation that constructs an
+ * EmptySelectionModel.
+ */
+ public EmptySelectionModel() {
+ super(null);
+ }
+
+ /** Returns a shared instance of an empty selection model. */
+ static public EmptySelectionModel sharedInstance() {
+ return sharedInstance;
+ }
+
+ /** A <code>null</code> implementation that selects nothing. */
+ public void setSelectionCells(Object[] cells) {
+ }
+
+ /** A <code>null</code> implementation that adds nothing. */
+ public void addSelectionCells(Object[] cells) {
+ }
+
+ /** A <code>null</code> implementation that removes nothing. */
+ public void removeSelectionCells(Object[] cells) {
+ }
+ }
+
+ /**
+ * Handles creating a new <code>GraphSelectionEvent</code> with the
+ * <code>JGraph</code> as the source and passing it off to all the
+ * listeners.
+ * <p>
+ * <strong>Warning: </strong> Serialized objects of this class will not be
+ * compatible with future Swing releases. The current serialization support
+ * is appropriate for short term storage or RMI between applications running
+ * the same version of Swing. A future release of Swing will provide support
+ * for long term persistence.
+ */
+ protected class GraphSelectionRedirector implements Serializable, GraphSelectionListener {
+ /**
+ * Invoked by the <code>GraphSelectionModel</code> when the selection
+ * changes.
+ *
+ * @param e
+ * the <code>GraphSelectionEvent</code> generated by the
+ * <code>GraphSelectionModel</code>
+ */
+ public void valueChanged(GraphSelectionEvent e) {
+ GraphSelectionEvent newE;
+ newE = (GraphSelectionEvent) e.cloneWithSource(JGraph.this);
+ fireValueChanged(newE);
+ }
+ } // End of class JGraph.GraphSelectionRedirector
+
+ //
+ // Scrollable interface
+ //
+ /**
+ * Returns the preferred display size of a <code>JGraph</code>. The
+ * height is determined from <code>getPreferredWidth</code>.
+ *
+ * @return the graph's preferred size
+ */
+ public Dimension getPreferredScrollableViewportSize() {
+ return getPreferredSize();
+ }
+
+ /**
+ * Returns the amount to increment when scrolling. The amount is 4.
+ *
+ * @param visibleRect
+ * the view area visible within the viewport
+ * @param orientation
+ * either <code>SwingConstants.VERTICAL</code> or
+ * <code>SwingConstants.HORIZONTAL</code>
+ * @param direction
+ * less than zero to scroll up/left, greater than zero for
+ * down/right
+ * @return the "unit" increment for scrolling in the specified direction
+ * @see javax.swing.JScrollBar#setUnitIncrement(int)
+ *
+ */
+ public int getScrollableUnitIncrement(Rectangle visibleRect, int orientation, int direction) {
+ if (orientation == SwingConstants.VERTICAL) {
+ return 2;
+ }
+
+ return 4;
+ }
+
+ /**
+ * Returns the amount for a block increment, which is the height or width of
+ * <code>visibleRect</code>, based on <code>orientation</code>.
+ *
+ * @param visibleRect
+ * the view area visible within the viewport
+ * @param orientation
+ * either <code>SwingConstants.VERTICAL</code> or
+ * <code>SwingConstants.HORIZONTAL</code>
+ * @param direction
+ * less than zero to scroll up/left, greater than zero for
+ * down/right.
+ * @return the "block" increment for scrolling in the specified direction
+ * @see javax.swing.JScrollBar#setBlockIncrement(int)
+ *
+ */
+ public int getScrollableBlockIncrement(Rectangle visibleRect, int orientation, int direction) {
+ return (orientation == SwingConstants.VERTICAL) ? visibleRect.height : visibleRect.width;
+ }
+
+ /**
+ * Returns false to indicate that the width of the viewport does not
+ * determine the width of the graph, unless the preferred width of the graph
+ * is smaller than the viewports width. In other words: ensure that the
+ * graph is never smaller than its viewport.
+ *
+ * @return false
+ * @see Scrollable#getScrollableTracksViewportWidth
+ *
+ */
+ public boolean getScrollableTracksViewportWidth() {
+ if (getParent() instanceof JViewport) {
+ return (((JViewport) getParent()).getWidth() > getPreferredSize().width);
+ }
+
+ return false;
+ }
+
+ /**
+ * Returns false to indicate that the height of the viewport does not
+ * determine the height of the graph, unless the preferred height of the
+ * graph is smaller than the viewports height. In other words: ensure that
+ * the graph is never smaller than its viewport.
+ *
+ * @return false
+ * @see Scrollable#getScrollableTracksViewportHeight
+ *
+ */
+ public boolean getScrollableTracksViewportHeight() {
+ if (getParent() instanceof JViewport) {
+ return (((JViewport) getParent()).getHeight() > getPreferredSize().height);
+ }
+
+ return false;
+ }
+
+ /**
+ * Returns a string representation of this <code>JGraph</code>. This
+ * method is intended to be used only for debugging purposes, and the
+ * content and format of the returned string may vary between
+ * implementations. The returned string may be empty but may not be
+ * <code>null</code>.
+ *
+ * @return a string representation of this <code>JGraph</code>.
+ */
+ protected String paramString() {
+ String editableString = (editable ? "true" : "false");
+ String invokesStopCellEditingString = (invokesStopCellEditing ? "true" : "false");
+
+ return super.paramString() + ",editable=" + editableString + ",invokesStopCellEditing="
+ + invokesStopCellEditingString;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ */
+ public static void main(String[] args) {
+ System.out.println(VERSION);
+ }
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/event/GraphLayoutCacheEvent.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/event/GraphLayoutCacheEvent.java
new file mode 100644
index 0000000..684b4dc
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/event/GraphLayoutCacheEvent.java
@@ -0,0 +1,116 @@
+/*
+ * @(#)GraphModelEvent.java 1.0 03-JUL-04
+ *
+ * Copyright (c) 2001-2005 Gaudenz Alder
+ *
+ * See LICENSE file in distribution for licensing details of this source file
+ */
+package org.jgraph.event;
+
+import java.util.EventObject;
+import java.util.Map;
+
+
+/**
+ * Encapsulates information describing changes to a graph layout cache, and is
+ * used to notify graph layout cache listeners of the change. Note that graph
+ * layout cache events do not repeat information in graph model events if there
+ * is no view specific information. The idea of this event is to provide
+ * information on what has changed in the graph layout cache only.
+ */
+public class GraphLayoutCacheEvent extends EventObject {
+ /**
+ * The object that constitutes the change.
+ */
+ protected GraphLayoutCacheChange change;
+
+ /**
+ * Used to create an event when cells have been changed, inserted, or
+ * removed, identifying the change as a GraphLayoutCacheChange object.
+ *
+ * @param source
+ * the Object responsible for generating the event (typically the
+ * creator of the event object passes <code>this</code> for its
+ * value)
+ *
+ * @param change
+ * the object that describes the change
+ */
+ public GraphLayoutCacheEvent(Object source, GraphLayoutCacheChange change) {
+ super(source);
+ this.change = change;
+ }
+
+ /**
+ * Returns the object that constitutes the change.
+ *
+ * @return the object that constitutes the change
+ */
+ public GraphLayoutCacheChange getChange() {
+ return change;
+ }
+
+ /**
+ * Defines the interface for objects that may be used to represent a change
+ * to the graph layout cache.
+ */
+ public static interface GraphLayoutCacheChange {
+ /**
+ * Returns the source of this change. This can either be a view or a
+ * model, if this change is a GraphModelChange. Note: This is not
+ * necessarily the same as the source of the event and is used
+ * separately in the graphundomanager.
+ *
+ * @return the source fo this change
+ */
+ public Object getSource();
+
+ /**
+ * Returns the cells that have changed.
+ *
+ * @return the cell changed
+ */
+ public Object[] getChanged();
+
+ /**
+ * Returns the cells that have been inserted.
+ *
+ * @return the cells that were inserted by the change
+ */
+ public Object[] getInserted();
+
+ /**
+ * Returns the cells that have been removed.
+ *
+ * @return the cells that were removed by the change
+ */
+ public Object[] getRemoved();
+
+ /**
+ * Returns a map that contains (object, map) pairs which holds the new
+ * attributes for each changed cell. Note: This returns a map of (cell,
+ * map) pairs for an insert on a model that is not an attribute store.
+ * Use getPreviousAttributes to access the attributes that have been
+ * stored in the model.
+ */
+ public Map getAttributes();
+
+ /**
+ * Returns a map that contains (object, map) pairs which holds the
+ * previous attributes for the changed cells.
+ *
+ * @return map of attributes before the change
+ */
+ public Map getPreviousAttributes();
+
+ /**
+ * Returns the objects that have not changed explicitly, but implicitly
+ * because one of their dependent cells has changed. This is typically
+ * used to return the edges that are attached to vertices, which in turn
+ * have been resized or moved.
+ *
+ * @return array of contextual cells
+ */
+ public Object[] getContext();
+ }
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/event/GraphLayoutCacheListener.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/event/GraphLayoutCacheListener.java
new file mode 100644
index 0000000..d7123d5
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/event/GraphLayoutCacheListener.java
@@ -0,0 +1,26 @@
+/*
+ * @(#)GraphModelListener.java 1.0 03-JUL-04
+ *
+ * Copyright (c) 2001-2005 Gaudenz Alder
+ *
+ * See LICENSE file in distribution for licensing details of this source file
+ */
+package org.jgraph.event;
+
+import java.util.EventListener;
+
+
+/**
+ * Defines the interface for an object that listens to changes in a GraphModel.
+ *
+ * @author Gaudenz Alder
+ * @version 1.0 1/1/02
+ */
+public interface GraphLayoutCacheListener extends EventListener {
+ /**
+ * Invoked after a cell has changed in some way. The vertex/vertices may
+ * have changed bounds or altered adjacency, or other attributes have
+ * changed that may affect presentation.
+ */
+ void graphLayoutCacheChanged(GraphLayoutCacheEvent e);
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/event/GraphModelEvent.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/event/GraphModelEvent.java
new file mode 100644
index 0000000..d1f74b7
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/event/GraphModelEvent.java
@@ -0,0 +1,120 @@
+/*
+ * @(#)GraphModelEvent.java 1.0 03-JUL-04
+ *
+ * Copyright (c) 2001-2005 Gaudenz Alder
+ *
+ * See LICENSE file in distribution for licensing details of this source file
+ */
+package org.jgraph.event;
+
+import org.jgraph.graph.CellView;
+import org.jgraph.graph.ConnectionSet;
+import org.jgraph.graph.GraphLayoutCache;
+import org.jgraph.graph.ParentMap;
+
+import java.util.EventObject;
+
+
+/**
+ * Encapsulates information describing changes to a graph model, and is used to
+ * notify graph model listeners of the change.
+ *
+ * @author Gaudenz Alder
+ * @version 1.0 1/1/2
+ *
+ */
+public class GraphModelEvent extends EventObject {
+ /**
+ * The object that constitutes the change.
+ */
+ protected GraphModelChange change;
+
+ /**
+ * Used to create an event when cells have been changed, inserted, or
+ * removed, identifying the change as a ModelChange object.
+ *
+ * @param source
+ * the Object responsible for generating the event (typically the
+ * creator of the event object passes <code>this</code> for its
+ * value)
+ * @param change
+ * the object that describes the change
+ * @see org.jgraph.graph.GraphCell
+ *
+ */
+ public GraphModelEvent(Object source, GraphModelChange change) {
+ super(source);
+ this.change = change;
+ }
+
+ /**
+ * Returns the object that constitutes the change.
+ *
+ * @return the object that constitutes the change.
+ */
+ public GraphModelChange getChange() {
+ return change;
+ }
+
+ /**
+ * Defines the interface for objects that may be included into a
+ * GraphModelEvent to describe a model change.
+ */
+ public static interface GraphModelChange extends GraphLayoutCacheEvent.GraphLayoutCacheChange {
+ /**
+ * Returns a connection set representing the graph structure after the
+ * change was applied
+ *
+ * @return the connection set of the graph after the change
+ */
+ public ConnectionSet getConnectionSet();
+
+ /**
+ * Returns a connection set representing the graph structure before the
+ * change was applied ( an "undo" of the change).
+ *
+ * @return the connection set of the graph before the change
+ */
+ public ConnectionSet getPreviousConnectionSet();
+
+ /**
+ * Returns a parent map representing the group structure after the
+ * change was applied
+ *
+ * @return the changed parent map
+ */
+ public ParentMap getParentMap();
+
+ /**
+ * Returns a parent map representing the group structure before the
+ * change was applied ( an "undo" of the change )
+ *
+ * @return the previous parent map
+ */
+ public ParentMap getPreviousParentMap();
+
+ /**
+ * Allows a <code>GraphLayoutCache</code> to store cell views for
+ * cells that have been removed. Such cell views are used for
+ * re-insertion and restoring the visual attributes.
+ *
+ * @param view
+ * the <code>GraphLayoutCache</code> to store the removed
+ * cells
+ * @param cellViews
+ * the cell views to be stored
+ */
+ public void putViews(GraphLayoutCache view, CellView[] cellViews);
+
+ /**
+ * Allows a <code>GraphLayoutCache</code> to retrieve an array of
+ * <code>CellViews</code> that was previously stored with
+ * <code>putViews(GraphLayoutCache, CellView[])</code>.
+ *
+ * @param view
+ * the <code>GraphLayoutCache</code> whose stored cells are
+ * to be retrieved
+ */
+ public CellView[] getViews(GraphLayoutCache view);
+ }
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/event/GraphModelListener.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/event/GraphModelListener.java
new file mode 100644
index 0000000..7f00a99
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/event/GraphModelListener.java
@@ -0,0 +1,26 @@
+/*
+ * @(#)GraphModelListener.java 1.0 03-JUL-04
+ *
+ * Copyright (c) 2001-2005 Gaudenz Alder
+ *
+ * See LICENSE file in distribution for licensing details of this source file
+ */
+package org.jgraph.event;
+
+import java.util.EventListener;
+
+
+/**
+ * Defines the interface for an object that listens to changes in a GraphModel.
+ *
+ * @author Gaudenz Alder
+ * @version 1.0 1/1/02
+ */
+public interface GraphModelListener extends EventListener {
+ /**
+ * Invoked after a cell has changed in some way. The vertex/vertices may
+ * have changed bounds or altered adjacency, or other attributes have
+ * changed that may affect presentation.
+ */
+ void graphChanged(GraphModelEvent e);
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/event/GraphSelectionEvent.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/event/GraphSelectionEvent.java
new file mode 100644
index 0000000..4cee934
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/event/GraphSelectionEvent.java
@@ -0,0 +1,136 @@
+/*
+ * @(#)GraphSelectionEvent.java 1.0 03-JUL-04
+ *
+ * Copyright (c) 2001-2005 Gaudenz Alder
+ *
+ * See LICENSE file in distribution for licensing details of this source file
+ */
+package org.jgraph.event;
+
+import java.util.EventObject;
+
+
+/**
+ * An event that characterizes a change in the current selection. The change is
+ * based on any number of cells. GraphSelectionListeners will generally query
+ * the source of the event for the new selected status of each potentially
+ * changed cell.
+ *
+ * @see GraphSelectionListener
+ * @see org.jgraph.graph.GraphSelectionModel
+ *
+ * @version 1.0 1/1/02
+ * @author Gaudenz Alder
+ */
+public class GraphSelectionEvent extends EventObject {
+ /** Cells this event represents. */
+ protected Object[] cells;
+
+ /**
+ * For each cell identifies whether or not that cell is newly selected.
+ */
+ protected boolean[] areNew;
+
+ /**
+ * Represents a change in the selection of a GraphSelectionModel.
+ * <code>cells</code> identifies the cells that have been either added or
+ * removed from the selection.
+ *
+ * @param source
+ * source of event
+ * @param cells
+ * the paths that have changed in the selection
+ * @param areNew
+ * for each cell, defines whether or not that cell is newly
+ * selected
+ */
+ public GraphSelectionEvent(Object source, Object[] cells, boolean[] areNew) {
+ super(source);
+ this.cells = cells;
+ this.areNew = areNew;
+ }
+
+ /**
+ * Returns the cells that have been added or removed from the selection.
+ *
+ * @return added or removed cells
+ */
+ public Object[] getCells() {
+ int numCells;
+ Object[] retCells;
+
+ numCells = cells.length;
+ retCells = new Object[numCells];
+ System.arraycopy(cells, 0, retCells, 0, numCells);
+
+ return retCells;
+ }
+
+ /**
+ * Returns the first cell.
+ *
+ * @return the first selected cell
+ */
+ public Object getCell() {
+ return cells[0];
+ }
+
+ /**
+ * Returns true if the first cell has been added to the selection, a return
+ * value of false means the first cell has been removed from the selection.
+ *
+ * @return whether or not the first cell has been added or removed
+ */
+ public boolean isAddedCell() {
+ return areNew[0];
+ }
+
+ /**
+ * Returns true if the cell identified by cell was added to the selection. A
+ * return value of false means the cell was in the selection but is no
+ * longer in the selection. This will raise if cell is not one of the cells
+ * identified by this event.
+ *
+ * @param cell
+ * the cell that is to be indicated as newly selected or not
+ * @return <code>true</code> if the specified cell is newly selected
+ */
+ public boolean isAddedCell(Object cell) {
+ for (int counter = cells.length - 1; counter >= 0; counter--)
+ if (cells[counter].equals(cell))
+ return areNew[counter];
+
+ throw new IllegalArgumentException("cell is not a cell identified by the GraphSelectionEvent");
+ }
+
+ /**
+ * Returns true if the cell identified by <code>index</code> was added to
+ * the selection. A return value of false means the cell was in the
+ * selection but is no longer in the selection. This will raise an exception
+ * if index < 0 || >=<code>getPaths</code> .length.
+ *
+ * @param index
+ * the index of <code>areNew</code> of the cell that is to be
+ * indicated as newly selected or not
+ * @return whether or not the cell is newly selected or not
+ */
+ public boolean isAddedCell(int index) {
+ if ((cells == null) || (index < 0) || (index >= cells.length)) {
+ throw new IllegalArgumentException("index is beyond range of added cells identified by GraphSelectionEvent");
+ }
+
+ return areNew[index];
+ }
+
+ /**
+ * Returns a copy of the receiver, but with the source being newSource.
+ *
+ * @param newSource
+ * the new event source
+ * @return the cloned event with the specified source
+ */
+ public Object cloneWithSource(Object newSource) {
+ // Fix for IE bug - crashing
+ return new GraphSelectionEvent(newSource, cells, areNew);
+ }
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/event/GraphSelectionListener.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/event/GraphSelectionListener.java
new file mode 100644
index 0000000..0e86261
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/event/GraphSelectionListener.java
@@ -0,0 +1,26 @@
+/*
+ * @(#)GraphSelectionListener.java 1.0 03-JUL-04
+ *
+ * Copyright (c) 2001-2005 Gaudenz Alder
+ *
+ * See LICENSE file in distribution for licensing details of this source file
+ */
+package org.jgraph.event;
+
+import java.util.EventListener;
+
+
+/**
+ * The listener that's notified when the selection in a GraphSelectionModel
+ * changes.
+ *
+ * @version 1.0 1/1/02
+ * @author Gaudenz Alder
+ */
+public interface GraphSelectionListener extends EventListener {
+ /**
+ * Called whenever the value of the selection changes.
+ * @param e the event that characterizes the change.
+ */
+ void valueChanged(GraphSelectionEvent e);
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/AbstractCellView.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/AbstractCellView.java
new file mode 100644
index 0000000..1c14c5b
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/AbstractCellView.java
@@ -0,0 +1,673 @@
+/*
+ * @(#)AbstractCellView.java 1.0 03-JUL-04
+ *
+ * Copyright (c) 2001-2005 Gaudenz Alder
+ *
+ * See LICENSE file in distribution for licensing details of this source file
+ */
+package org.jgraph.graph;
+
+import org.jgraph.JGraph;
+
+import java.awt.Component;
+import java.awt.geom.Point2D;
+import java.awt.geom.Rectangle2D;
+
+import java.io.Serializable;
+
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.LinkedList;
+import java.util.Map;
+import java.util.Stack;
+
+import javax.swing.tree.DefaultMutableTreeNode;
+
+
+/**
+ * The abstract base class for all cell views.
+ *
+ * @version 1.0 1/3/02
+ * @author Gaudenz Alder
+ */
+public abstract class AbstractCellView implements CellView, Serializable {
+ /** Editor for the cell. */
+ protected static transient GraphCellEditor cellEditor = null;
+
+ static {
+ try {
+ cellEditor = new DefaultGraphCellEditor();
+ } catch (Error e) {
+ // No cell editor
+ }
+ }
+
+ /** Reference to the cell for this view */
+ protected Object cell = null;
+
+ /** Cached parent view */
+ protected CellView parent = null;
+
+ /** Cached child views. Default is a ArrayList with allocation size 0. */
+ protected java.util.List childViews = new ArrayList(0);
+
+ /**
+ * Contains the complete set of attributes, including the cell's attributes.
+ * The values in this map are overriden by the corresponding values in
+ * <code>attributes</code>.
+ */
+ protected AttributeMap allAttributes = createAttributeMap();
+
+ /**
+ * Hashtable for attributes. Value in this map override the values in
+ * <code>allAttributes</code>.
+ */
+ protected AttributeMap attributes = allAttributes;
+
+ /** Cached bounds of all children if vertex is a group */
+ protected transient Rectangle2D groupBounds = VertexView.defaultBounds;
+
+ /**
+ * Constructs an empty abstract cell view. You should set a cell on this
+ * view using setCell before doing anything. Optionally you can also set a
+ * different attribute map using setAttributeMap. Note: To change the
+ * attribute map you should now use the changeAttributes method.
+ */
+ public AbstractCellView() {
+ }
+
+ /**
+ * Constructs a view for the specified model object, and invokes update on
+ * the new instance.
+ *
+ * @param cell
+ * reference to the model object
+ */
+ public AbstractCellView(Object cell) {
+ setCell(cell);
+ }
+
+ /**
+ * Hook for subclassers to avoid creating an empty AttributeMap during
+ * construction of the instance. Override this and return null if you want
+ * to avoid creation of an attribute map at construction time.
+ */
+ protected AttributeMap createAttributeMap() {
+ return new AttributeMap();
+ }
+
+ /**
+ * Returns the model object that this view represents.
+ *
+ * @return the model object that this view represents
+ */
+ public Object getCell() {
+ return cell;
+ }
+
+ /**
+ * Sets the model object that this view represents to the specified cell
+ *
+ * @param cell
+ * the model object this view will represent
+ */
+ public void setCell(Object cell) {
+ this.cell = cell;
+ }
+
+ /**
+ * Create child views and reload properties for this view. Invokes update
+ * first.
+ *
+ * @param model
+ * the graph model to be used
+ * @param mapper
+ * the cell mapper to be used
+ * @param createDependentViews
+ * whether or not to create a view if one does not already exist
+ */
+ public void refresh(GraphModel model, CellMapper mapper, boolean createDependentViews) {
+ // Re-read global attributes
+ allAttributes = getCellAttributes(model);
+
+ // Cache Parent View
+ if ((mapper != null) && (model != null)) {
+ // Create parent only if it's visible in the graph
+ Object par = model.getParent(cell);
+ CellView tmp = mapper.getMapping(par, createDependentViews);
+
+ if (tmp != parent)
+ removeFromParent();
+
+ parent = tmp;
+ }
+
+ // Cache Cell Attributes in View
+ update();
+ // Re-load Child Views
+ childViews.clear();
+
+ for (int i = 0; i < model.getChildCount(cell); i++) {
+ Object child = model.getChild(cell, i);
+ CellView view = mapper.getMapping(child, createDependentViews);
+
+ if (!model.isPort(child) && (view != null))
+ childViews.add(view);
+ }
+ }
+
+ /**
+ * Hook for subclassers to avoid cloning the cell's attributes. Return
+ * model.getAttributes(cell) to avoid cloning.
+ */
+ protected AttributeMap getCellAttributes(GraphModel model) {
+ return (AttributeMap) model.getAttributes(cell).clone();
+ }
+
+ /**
+ * Update attributes for this view and indicate to the parent this child has
+ * been updated
+ */
+ public void update() {
+ mergeAttributes();
+ // Notify Parent
+ groupBounds = null;
+ childUpdated();
+ }
+
+ /**
+ * Implements the merging of the cell's attributes, initially stored in
+ * allAttributes, and the location attributes. The result should be stored
+ * in allAttributes. This hook is for subclassers to change the merging
+ * strategy.
+ */
+ protected void mergeAttributes() {
+ allAttributes.putAll(attributes);
+ }
+
+ /**
+ * Indicates to parent, if any, that this child has been updated.
+ */
+ public void childUpdated() {
+ if (parent != null)
+ parent.childUpdated();
+
+ groupBounds = null;
+ }
+
+ //
+ // Graph Structure
+ //
+
+ /**
+ * Returns the parent view for this view.
+ *
+ * @return the parent view for this view
+ */
+ public CellView getParentView() {
+ return parent;
+ }
+
+ /**
+ * Returns the child views of this view.
+ *
+ * @return the child views of this view
+ */
+ public CellView[] getChildViews() {
+ CellView[] array = new CellView[childViews.size()];
+ childViews.toArray(array);
+
+ return array;
+ }
+
+ /**
+ * Returns all views, including descendants that have a parent in
+ * <code>views</code> without the PortViews. Note: Iterative
+ * Implementation using view.getChildViews. This returns the array in
+ * inverse order, ie with the top most cell view at index 0.
+ *
+ * @param views
+ * the cell views whose descendants are to be returned
+ * @return the specified views and all their descendant views
+ */
+ public static CellView[] getDescendantViews(CellView[] views) {
+ Stack stack = new Stack();
+
+ for (int i = 0; i < views.length; i++)
+ stack.add(views[i]);
+
+ ArrayList result = new ArrayList();
+
+ while (!stack.isEmpty()) {
+ CellView tmp = (CellView) stack.pop();
+ Object[] children = tmp.getChildViews();
+
+ for (int i = 0; i < children.length; i++)
+ stack.add(children[i]);
+
+ result.add(tmp);
+ }
+
+ CellView[] ret = new CellView[result.size()];
+ result.toArray(ret);
+
+ return ret;
+ }
+
+ /**
+ * Removes this view from the list of children of the parent.
+ */
+ public void removeFromParent() {
+ if (parent instanceof AbstractCellView) {
+ java.util.List list = ((AbstractCellView) parent).childViews;
+ list.remove(this);
+ }
+ }
+
+ /**
+ * Returns <code>true</code> if the view is a leaf.
+ *
+ * @return <code>true</code> if the view is a leaf
+ */
+ public boolean isLeaf() {
+ return childViews.isEmpty();
+ }
+
+ //
+ // View Attributes
+ //
+
+ /**
+ * Return the attributes of the view.
+ *
+ * @return the <code>attributes</code> of this view
+ */
+ public AttributeMap getAttributes() {
+ return attributes;
+ }
+
+ /**
+ * Sets the attributes of this view to the specified value
+ *
+ * @param attributes
+ * the new attributes to set
+ */
+ public void setAttributes(AttributeMap attributes) {
+ this.attributes = attributes;
+ }
+
+ /**
+ * Returns the attributes of the view combined with the attributes of the
+ * corresponding cell. The view's attributes override the cell's attributes
+ * with the same key.
+ */
+ public AttributeMap getAllAttributes() {
+ return allAttributes;
+ }
+
+ /**
+ * Applies <code>change</code> to the attributes of the view and calls
+ * update.
+ *
+ * @param change
+ * a map of attribute changes to apply
+ * @return the undo map that reverses this change
+ */
+ public Map changeAttributes(Map change) {
+ if (change != null) {
+ Map undo = attributes.applyMap(change);
+ update();
+
+ return undo;
+ }
+
+ return null;
+ }
+
+ //
+ // View Methods
+ //
+
+ /**
+ * Returns the cached bounds for the group if isleaf is false
+ */
+ public Rectangle2D getBounds() {
+ if (!isLeaf()) {
+ if (groupBounds == null)
+ updateGroupBounds();
+
+ return groupBounds;
+ }
+
+ return null;
+ }
+
+ /**
+ * Returns the bounding box for the specified views.
+ *
+ * @param views
+ * the views for whom the bounding box is to be determined
+ * @return the bounding box of the specified views
+ */
+ public static Rectangle2D getBounds(CellView[] views) {
+ if ((views != null) && (views.length > 0)) {
+ Rectangle2D ret = null;
+
+ for (int i = 0; i < views.length; i++) {
+ if (views[i] != null) {
+ Rectangle2D r = views[i].getBounds();
+
+ if (r != null) {
+ if (ret == null)
+ ret = new Rectangle2D.Double(r.getX(), r.getY(), r.getWidth(),
+ r.getHeight());
+ else
+ Rectangle2D.union(ret, r, ret);
+ }
+ }
+ }
+
+ return ret;
+ }
+
+ return null;
+ }
+
+ /**
+ * Sets the bounds of this <code>view</code>. Calls translateView and
+ * scaleView.
+ *
+ * @param bounds
+ * the new bounds for this cell view
+ */
+ public void setBounds(Rectangle2D bounds) {
+ Rectangle2D oldBounds = getBounds();
+
+ if (oldBounds == null)
+ oldBounds = new Rectangle2D.Double();
+
+ Point2D p0 = new Point2D.Double(oldBounds.getX(), oldBounds.getY());
+ Point2D pe = new Point2D.Double(bounds.getX(), bounds.getY());
+ Rectangle2D localBounds = new Rectangle2D.Double(bounds.getX(), bounds.getY(),
+ bounds.getWidth(), bounds.getHeight());
+
+ if (GraphConstants.isMoveable(getAllAttributes()) && !pe.equals(p0))
+ translate(pe.getX() - p0.getX(), pe.getY() - p0.getY());
+ else
+ localBounds.setFrame(localBounds.getX(), localBounds.getY(),
+ bounds.getWidth() - pe.getX() + p0.getX(),
+ bounds.getHeight() - pe.getY() + p0.getY());
+
+ double lbw = localBounds.getWidth();
+ double lbh = localBounds.getHeight();
+ double obw = oldBounds.getWidth();
+ double obh = oldBounds.getHeight();
+
+ if (((lbw != obw) || (lbh != obh)) && (obw > 0) && (obh > 0))
+ scale(lbw / obw, lbh / obh, pe);
+ }
+
+ /**
+ * Updates the bounds of this view and its children
+ *
+ */
+ protected void updateGroupBounds() {
+ // Note: Prevent infinite recursion by removing
+ // child edges that point to their parent.
+ CellView[] childViews = getChildViews();
+ LinkedList result = new LinkedList();
+
+ for (int i = 0; i < childViews.length; i++)
+ if (includeInGroupBounds(childViews[i]))
+ result.add(childViews[i]);
+
+ childViews = new CellView[result.size()];
+ result.toArray(childViews);
+
+ Rectangle2D r = getBounds(childViews);
+ int groupBorder = GraphConstants.getInset(getAllAttributes());
+
+ if (r != null)
+ r.setFrame(r.getX() - groupBorder, r.getY() - groupBorder,
+ r.getWidth() + (2 * groupBorder), r.getHeight() + (2 * groupBorder));
+
+ groupBounds = r;
+ }
+
+ /**
+ * This is used to exclude certain cell views from the group bounds
+ * computation. This implementation returns false for edges that connect to
+ * one of their ancestor groups (eg. parent).
+ *
+ * @param view
+ * the cell view to be included in the group bounds or not
+ * @return whether or not to include the specified cell in the group bounds
+ */
+ protected boolean includeInGroupBounds(CellView view) {
+ if (view instanceof EdgeView && getCell() instanceof DefaultMutableTreeNode) {
+ DefaultMutableTreeNode groupNode = (DefaultMutableTreeNode) getCell();
+ EdgeView edgeView = (EdgeView) view;
+
+ if (edgeView.getCell() instanceof DefaultMutableTreeNode) {
+ DefaultMutableTreeNode edge = (DefaultMutableTreeNode) edgeView.getCell();
+ Object src = null;
+
+ if ((edgeView.getSource() != null)
+ && (edgeView.getSource().getParentView() != null))
+ src = edgeView.getSource().getParentView().getCell();
+ else if (edgeView.getSourceParentView() != null)
+ src = edgeView.getSourceParentView().getCell();
+
+ if (src instanceof DefaultMutableTreeNode) {
+ DefaultMutableTreeNode source = (DefaultMutableTreeNode) src;
+
+ if (source.isNodeDescendant(edge))
+ return false;
+ }
+
+ Object tgt = null;
+
+ if ((edgeView.getTarget() != null)
+ && (edgeView.getTarget().getParentView() != null))
+ tgt = edgeView.getTarget().getParentView().getCell();
+ else if (edgeView.getTargetParentView() != null)
+ tgt = edgeView.getTargetParentView().getCell();
+
+ if (tgt instanceof DefaultMutableTreeNode) {
+ DefaultMutableTreeNode target = (DefaultMutableTreeNode) tgt;
+
+ if (target.isNodeDescendant(edge)) {
+ return false;
+ }
+ }
+ }
+ }
+
+ return true;
+ }
+
+ /**
+ * Translates <code>view</code> (group) by <code>dx, dy</code>.
+ *
+ * @param dx
+ * the x-coordinate amount to translate by
+ * @param dy
+ * the y-coordinate amount to translate by
+ */
+ protected void translate(double dx, double dy) {
+ if (isLeaf())
+ getAllAttributes().translate(dx, dy);
+ else {
+ int moveableAxis = GraphConstants.getMoveableAxis(getAllAttributes());
+
+ if (moveableAxis == GraphConstants.X_AXIS)
+ dy = 0;
+ else if (moveableAxis == GraphConstants.Y_AXIS)
+ dx = 0;
+
+ Iterator it = childViews.iterator();
+
+ while (it.hasNext()) {
+ Object view = it.next();
+
+ if (view instanceof AbstractCellView) {
+ AbstractCellView child = (AbstractCellView) view;
+ child.translate(dx, dy);
+ }
+ }
+ }
+ }
+
+ /**
+ * Scale <code>view</code> (group) by <code>sx, sy</code>.
+ *
+ * @param sx
+ * the multiple by which the x coordinate position of the cell
+ * view is to be scaled
+ * @param sy
+ * the multiple by which the y coordinate position of the cell
+ * view is to be scaled
+ * @param origin
+ * the origin point from which the scaling will calculate
+ */
+ protected void scale(double sx, double sy, Point2D origin) {
+ if (isLeaf())
+ getAttributes().scale(sx, sy, origin);
+ else {
+ int sizeableAxis = GraphConstants.getSizeableAxis(getAllAttributes());
+
+ if (sizeableAxis == GraphConstants.X_AXIS)
+ sy = 1;
+ else if (sizeableAxis == GraphConstants.Y_AXIS)
+ sx = 1;
+
+ Iterator it = childViews.iterator();
+
+ while (it.hasNext()) {
+ Object view = it.next();
+
+ if (view instanceof AbstractCellView) {
+ AbstractCellView child = (AbstractCellView) view;
+ Map attrs = child.getAttributes();
+
+ if (GraphConstants.isSizeable(attrs) || GraphConstants.isAutoSize(attrs))
+ child.scale(sx, sy, origin);
+ }
+ }
+ }
+ }
+
+ /**
+ * Returns true if the view intersects the given rectangle.
+ *
+ * @param graph
+ * the <code>JGraph</code> instance of the view
+ * @param rect
+ * the rectangle within which intersection is being checked for
+ *
+ * @return whether or not the rectangle specified intersects the view
+ */
+ public boolean intersects(JGraph graph, Rectangle2D rect) {
+ if (isLeaf() || GraphConstants.isGroupOpaque(getAllAttributes())) {
+ Rectangle2D bounds = getBounds();
+
+ if (bounds != null)
+ return bounds.intersects(rect);
+ } else { // Check If Children Intersect
+
+ Iterator it = childViews.iterator();
+
+ while (it.hasNext())
+
+ if (((CellView) it.next()).intersects(graph, rect))
+ return true;
+ }
+
+ return false;
+ }
+
+ //
+ // View Editors
+ //
+
+ /**
+ * Returns a renderer component, configured for the view. The method used to
+ * obtain the renderer instance must install the necessary attributes from
+ * this view
+ *
+ * @param graph
+ * the <code>JGraph</code> instance of the view
+ * @param selected
+ * whether or not this view is selected
+ * @param focus
+ * whether or not this view is the focus
+ * @param preview
+ * whether or not it is a preview of the view
+ *
+ * @return the renderer component for this view with this views attributes
+ * installed
+ */
+ public Component getRendererComponent(JGraph graph, boolean selected, boolean focus,
+ boolean preview) {
+ CellViewRenderer cvr = getRenderer();
+
+ if (cvr != null)
+ return cvr.getRendererComponent(graph, this, selected, focus, preview);
+
+ return null;
+ }
+
+ /**
+ * Obtains the renderer instance for this view
+ *
+ * @return the renderer instance for this view
+ */
+ public abstract CellViewRenderer getRenderer();
+
+ /**
+ * Returns a cell handle for the view.
+ *
+ * @param context
+ * the context of this cell view (cells indirectly affected by
+ * it)
+ * @return the cell handle for this view
+ */
+ public abstract CellHandle getHandle(GraphContext context);
+
+ /**
+ * Returns a cell editor for the view.
+ *
+ * @return the cell editor for this view
+ */
+ public GraphCellEditor getEditor() {
+ return cellEditor;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param vertex DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static Point2D getCenterPoint(CellView vertex) {
+ Rectangle2D r = vertex.getBounds();
+
+ if (r != null)
+ return new Point2D.Double(r.getCenterX(), r.getCenterY());
+
+ return null;
+ }
+
+ /**
+ * Returns the intersection of the bounding rectangle and the straight line
+ * between the source and the specified point p. The specified point is
+ * expected not to intersect the bounds. Note: You must override this method
+ * if you use a different renderer. This is because this method relies on
+ * the VertexRenderer interface, which can not be safely assumed for
+ * subclassers.
+ */
+ public Point2D getPerimeterPoint(EdgeView edge, Point2D source, Point2D p) {
+ return getCenterPoint(this);
+ }
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/AttributeMap.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/AttributeMap.java
new file mode 100644
index 0000000..6f8ab1d
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/AttributeMap.java
@@ -0,0 +1,635 @@
+/*
+ * @(#)AttributeMap 1.0 03-JUL-04
+ *
+ * Copyright (c) 2001-2005 Gaudenz Alder
+ *
+ * See LICENSE file in distribution for licensing details of this source file
+ */
+package org.jgraph.graph;
+
+import java.awt.geom.Point2D;
+import java.awt.geom.Rectangle2D;
+
+import java.io.IOException;
+import java.io.ObjectInputStream;
+import java.io.ObjectOutputStream;
+import java.io.Serializable;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+
+/**
+ * A map specifically for the storage of attributes of graph cells. The main
+ * advantage of the AttributeMap is that it allows to override cell view
+ * behaviour for scaling, translation, diffing, and cloning on a per instance
+ * basis without having to change the GraphConstants class
+ */
+public class AttributeMap extends Hashtable implements Cloneable {
+ /**
+ * Shared empty attribute map to return instead of null in applyMap.
+ */
+ public static transient AttributeMap emptyAttributeMap = new AttributeMap(0) {
+ public Object clone() {
+ return this;
+ }
+ };
+
+ /**
+ * Creates a new attribute map with an initial capacity of 8.
+ */
+ public AttributeMap() {
+ super(8);
+ }
+
+ /**
+ * Creates a new attribute map with the specified initial capacity
+ *
+ * @param initialCapacity
+ * the initial capacity of the new map
+ */
+ public AttributeMap(int initialCapacity) {
+ super(initialCapacity);
+ }
+
+ /**
+ * Constructs a new, empty hashtable with the specified initial capacity and
+ * the specified load factor.
+ *
+ * @param initialCapacity
+ * the initial capacity of the hashtable.
+ * @param loadCapacity
+ * the load factor of the hashtable.
+ */
+ public AttributeMap(int initialCapacity, float loadCapacity) {
+ super(initialCapacity, loadCapacity);
+ }
+
+ /**
+ * Constructs a new AttributeMap with the same mappings as the given Map.
+ *
+ * @param map
+ * the input map to copy
+ */
+ public AttributeMap(Map map) {
+ super(map);
+ }
+
+ /**
+ * Creates a point of suitable type for this attribute map
+ *
+ * @return a new point
+ */
+ public Point2D createPoint() {
+ return new SerializablePoint2D();
+ }
+
+ /**
+ * Creates a point of suitable type for this attribute map with the same
+ * values as the point passed in
+ *
+ * @param p
+ * the point whose values the new point are to be based on
+ * @return a new copy of the point passed in
+ */
+ public Point2D createPoint(Point2D p) {
+ if (p != null) {
+ return createPoint(p.getX(), p.getY());
+ }
+
+ return null;
+ }
+
+ /**
+ * Creates a point of suitable type for this attribute map with the same
+ * values as those passed in
+ *
+ * @param x
+ * the x-coordinate position of the new point
+ * @param y
+ * the y-coordinate position of the new point
+ * @return a new point at the coordinates passed in
+ */
+ public Point2D createPoint(double x, double y) {
+ return new SerializablePoint2D(x, y);
+ }
+
+ /**
+ * Creates a rectangle of suitable type for this attribute map
+ *
+ * @return a new rectangle
+ */
+ public Rectangle2D createRect() {
+ return new SerializableRectangle2D();
+ }
+
+ /**
+ * Creates a rectangle of suitable type for this attribute map with the same
+ * values as those passed in
+ *
+ * @param x
+ * the x-coordinate position of the new rectangle
+ * @param y
+ * the y-coordinate position of the new rectangle
+ * @param w
+ * the width of the new rectangle
+ * @param h
+ * the height of the new rectangle
+ * @return a new rectangle at the coordinates and of the dimensions passed
+ * in
+ */
+ public Rectangle2D createRect(double x, double y, double w, double h) {
+ return new SerializableRectangle2D(x, y, w, h);
+ }
+
+ /**
+ * Creates a rectangle of suitable type for this attribute map at the
+ * position of the point passed in
+ *
+ * @param pt
+ * the position of the new rectangle
+ * @return a new rectangle the specified coordinates of zero size
+ */
+ public Rectangle2D createRect(Point2D pt) {
+ return createRect(pt, 0);
+ }
+
+ /**
+ * Creates a rectangle of suitable type for this attribute map at the
+ * position of the point passed in with lengths <code>size</code>
+ *
+ * @param pt
+ * the position of the new rectangle
+ * @param size
+ * the length of both sides of the rectangle
+ * @return a new rectangle the specified position and dimensions
+ */
+ public Rectangle2D createRect(Point2D pt, double size) {
+ if (pt != null) {
+ return createRect(pt.getX(), pt.getY(), size, size);
+ }
+
+ return null;
+ }
+
+ /**
+ * Clones the rectangle passed in
+ *
+ * @param rect
+ * the rectangle to clone
+ *
+ * @return a copy of the rectangle passed in
+ */
+ public Rectangle2D createRect(Rectangle2D rect) {
+ if (rect != null) {
+ return createRect(rect.getX(), rect.getY(), rect.getWidth(), rect.getHeight());
+ }
+
+ return null;
+ }
+
+ /**
+ * Creates a rectangle of suitable type for this attribute map
+ *
+ * @param x
+ * the x-coordinate position of the new rectangle
+ * @param y
+ * the y-coordinate position of the new rectangle
+ * @param w
+ * the width of the new rectangle
+ * @param h
+ * the height of the new rectangle
+ * @param grow1
+ * the amount both dimensions are to be increased by and the
+ * position coorindates of the rectangle are to be decreased by
+ * @param grow2
+ * the additional amount by which both dimensions are to be
+ * increased by
+ * @return a new rectangle at the coordinates and of the dimensions passed
+ * in
+ */
+ public Rectangle2D createRect(double x, double y, double w, double h, double grow1, double grow2) {
+ return createRect(x - grow1, y - grow1, w + grow1 + grow2, h + grow1 + grow2);
+ }
+
+ /**
+ * Creates a clone of the rectangle passed in and manipulates it by
+ * <code>grow1</code> and <code>grow2</code>
+ *
+ * @param grow1
+ * the amount both dimensions are to be increased by and the
+ * position coorindates of the rectangle are to be decreased by
+ * @param grow2
+ * the additional amount by which both dimensions are to be
+ * increased by
+ * @return a new rectangle at the coordinates and of the dimensions passed
+ * in
+ */
+ public Rectangle2D createRect(Rectangle2D rect, double grow1, double grow2) {
+ if (rect != null) {
+ return createRect(rect.getX(), rect.getY(), rect.getWidth(), rect.getHeight(), grow1,
+ grow2);
+ }
+
+ return null;
+ }
+
+ /**
+ * Apply the <code>change</code> to this views attributes.
+ * <code>change</code> must be a <code>Map</code> previously obtained
+ * from this object.
+ *
+ * @param change
+ * the change to apply
+ * @return a map that may be used to undo the change to target.
+ */
+ public AttributeMap applyMap(Map change) {
+ AttributeMap undo = new AttributeMap();
+
+ if (change != null) {
+ // Handle Remove All
+ if (GraphConstants.isRemoveAll(change)) {
+ undo.putAll(this);
+ clear();
+ }
+
+ // Handle Remove Individual
+ Object[] remove = GraphConstants.getRemoveAttributes(change);
+
+ if (remove != null) {
+ // don't store command
+ for (int i = 0; i < remove.length; i++) {
+ Object oldValue = remove(remove[i]);
+
+ if (oldValue != null)
+ undo.put(remove[i], oldValue);
+ }
+ }
+
+ // Attributes that were empty are added to removeattibutes.
+ // Performance and transient memory peak are reduced by lazily
+ // instantiating the set.
+ Set removeAttributes = null;
+ Iterator it = change.entrySet().iterator();
+
+ while (it.hasNext()) {
+ Map.Entry entry = (Map.Entry) it.next();
+ Object key = entry.getKey();
+
+ if (!key.equals(GraphConstants.REMOVEALL)
+ && !key.equals(GraphConstants.REMOVEATTRIBUTES)
+ && !key.equals(GraphConstants.VALUE)) {
+ Object oldValue = applyValue(key, entry.getValue());
+
+ if (oldValue == null) {
+ if (removeAttributes == null) {
+ removeAttributes = new HashSet();
+ }
+
+ removeAttributes.add(key);
+ } else {
+ undo.put(key, oldValue);
+ }
+ }
+ }
+
+ if ((removeAttributes != null) && !removeAttributes.isEmpty()) {
+ GraphConstants.setRemoveAttributes(undo, removeAttributes.toArray());
+ }
+ }
+
+ return undo;
+ }
+
+ /**
+ * Apply the <code>key</code> to <code>value</code>
+ *
+ * @param key
+ * the map key whose value is to be altered
+ * @param value
+ * the new value to be applied to the specified key
+ * @return the old value.
+ */
+ public Object applyValue(Object key, Object value) {
+ // In all other cases we put the new value into the
+ // map. If we encounter a list (of points) or rectangle
+ // these will be cloned before insertion. Cloning includes
+ // replacing the rectangle/points with serializable objects.
+ if (value instanceof Rectangle2D)
+ value = createRect((Rectangle2D) value);
+
+ if (value instanceof Point2D)
+ value = createPoint((Point2D) value);
+
+ if (value instanceof Point2D[])
+ value = clonePoints((Point2D[]) value);
+
+ if (value instanceof List) // FIXME: PointList interface?
+ value = clonePoints((List) value);
+
+ return put(key, value);
+ }
+
+ /**
+ * Returns a list where all instances of PortView are replaced by their
+ * correspnding Point instance.
+ *
+ * @param points
+ * the points to be cloned
+ * @return the cloned points
+ */
+ public Point2D[] clonePoints(Point2D[] points) {
+ List pts = clonePoints(points, true);
+ Point2D[] newPoints = new Point2D[pts.size()];
+ pts.toArray(newPoints);
+
+ return newPoints;
+ }
+
+ /**
+ * Returns a list where all instances of PortView are replaced by their
+ * correspnding Point instance.
+ *
+ * @param points
+ * the points to be cloned
+ * @return the cloned points
+ */
+ public List clonePoints(List points) {
+ return clonePoints(points.toArray(), true);
+ }
+
+ /**
+ * Returns a list where all instances of PortView are replaced by their
+ * correspnding Point instance.
+ */
+ public List clonePoints(Object[] points, boolean convertPortViews) {
+ // TODO: Change the list in-place?
+ ArrayList newList = new ArrayList(points.length);
+
+ for (int i = 0; i < points.length; i++) {
+ // Clone Point
+ Object point = points[i];
+
+ if (point instanceof PortView && convertPortViews)
+ point = createPoint(((PortView) point).getLocation());
+ else if (point instanceof Point2D)
+ point = createPoint((Point2D) point);
+
+ newList.add(point);
+ }
+
+ return newList;
+ }
+
+ /**
+ * Translates the maps in <code>c</code> using
+ * <code>translate(Map, int, int)</code>.
+ */
+ public static void translate(Collection c, double dx, double dy) {
+ Iterator it = c.iterator();
+
+ while (it.hasNext()) {
+ Object map = it.next();
+
+ if (map instanceof AttributeMap)
+ ((AttributeMap) map).translate(dx, dy);
+ }
+ }
+
+ /**
+ * Translates <code>map</code> by the given amount.
+ */
+ public void translate(double dx, double dy) {
+ // Translate Bounds
+ if (GraphConstants.isMoveable(this)) {
+ Rectangle2D bounds = GraphConstants.getBounds(this);
+
+ if (bounds != null) {
+ int moveableAxis = GraphConstants.getMoveableAxis(this);
+
+ if (moveableAxis == GraphConstants.X_AXIS)
+ dy = 0;
+ else if (moveableAxis == GraphConstants.Y_AXIS)
+ dx = 0;
+
+ bounds.setFrame(bounds.getX() + dx, bounds.getY() + dy, bounds.getWidth(),
+ bounds.getHeight());
+ }
+
+ // Translate Points
+ List points = GraphConstants.getPoints(this);
+
+ if (points != null) {
+ for (int i = 0; i < points.size(); i++) {
+ Object obj = points.get(i);
+
+ if (obj instanceof Point2D) {
+ Point2D pt = (Point2D) obj;
+ pt.setLocation(pt.getX() + dx, pt.getY() + dy);
+ }
+ }
+ }
+ }
+ }
+
+ /**
+ * Scales <code>map</code> by the given amount.
+ */
+ public void scale(double sx, double sy, Point2D origin) {
+ // Scale Bounds
+ Rectangle2D bounds = GraphConstants.getBounds(this);
+
+ if (bounds != null) {
+ Point2D p = createPoint(bounds.getX(), bounds.getY());
+ Point2D loc = (Point2D) p.clone();
+ p.setLocation(origin.getX() + Math.round((p.getX() - origin.getX()) * sx),
+ origin.getY() + Math.round((p.getY() - origin.getY()) * sy));
+
+ if (!p.equals(loc)) // Scale Location
+ translate(p.getX() - loc.getX(), p.getY() - loc.getY());
+
+ int sizeableAxis = GraphConstants.getSizeableAxis(this);
+
+ if (sizeableAxis == GraphConstants.X_AXIS)
+ sy = 1;
+ else if (sizeableAxis == GraphConstants.Y_AXIS)
+ sx = 1;
+
+ double w = Math.max(1, Math.round(bounds.getWidth() * sx));
+ double h = Math.max(1, Math.round(bounds.getHeight() * sy));
+ // Scale Bounds
+ bounds.setFrame(bounds.getX(), bounds.getY(), w, h);
+ }
+
+ // Scale Points
+ List points = GraphConstants.getPoints(this);
+
+ if (points != null) {
+ Iterator it = points.iterator();
+
+ while (it.hasNext()) {
+ Object obj = it.next();
+
+ if (obj instanceof Point2D) {
+ // Scale Point
+ Point2D loc = (Point2D) obj;
+ Point2D p = (Point2D) loc.clone();
+ p.setLocation(origin.getX() + Math.round((p.getX() - origin.getX()) * sx),
+ origin.getY() + Math.round((p.getY() - origin.getY()) * sy));
+ // Move Point
+ loc.setLocation(p);
+ }
+ }
+ }
+ }
+
+ /**
+ * Returns a new map that contains all (key, value)-pairs of
+ * <code>newState</code> where either key is not used or value is
+ * different for key in <code>oldState</code>. In other words, this
+ * method removes the common entries from oldState and newState, and returns
+ * the "difference" between the two.
+ *
+ * This method never returns null.
+ */
+ public Map diff(Map newState) {
+ Map diff = new Hashtable();
+ Iterator it = newState.entrySet().iterator();
+
+ while (it.hasNext()) {
+ Map.Entry entry = (Map.Entry) it.next();
+ Object key = entry.getKey();
+ Object newValue = entry.getValue();
+ Object oldValue = get(key);
+
+ if ((oldValue == null) || !oldValue.equals(newValue))
+ diff.put(key, newValue);
+ }
+
+ return diff;
+ }
+
+ /**
+ * Returns a clone of <code>map</code>, from keys to values. If the map
+ * contains bounds or points, these are cloned as well. References to
+ * <code>PortViews</code> are replaces by points. <br>
+ * <b>Note: </b> Extend this method to clone custom user objects.
+ */
+ public Object clone() {
+ // TODO, is cloning the hash table excessive?
+ return cloneEntries((AttributeMap) super.clone());
+ }
+
+ /**
+ * Clones special object entried in the given map.
+ */
+ public AttributeMap cloneEntries(AttributeMap newMap) {
+ // Clone Bounds
+ Rectangle2D bounds = GraphConstants.getBounds(newMap);
+
+ if (bounds != null)
+ GraphConstants.setBounds(newMap, (Rectangle2D) (bounds.clone()));
+
+ // Clone List Of Points
+ List points = GraphConstants.getPoints(newMap);
+
+ if (points != null)
+ GraphConstants.setPoints(newMap, clonePoints(points));
+
+ // Clone extra label positions
+ Point2D[] positions = GraphConstants.getExtraLabelPositions(newMap);
+
+ if (positions != null)
+ GraphConstants.setExtraLabelPositions(newMap, clonePoints(positions));
+
+ // Clone Edge Label
+ Point2D label = GraphConstants.getLabelPosition(newMap);
+
+ if (label != null)
+ GraphConstants.setLabelPosition(newMap, (Point2D) label.clone());
+
+ return newMap;
+ }
+
+ public static class SerializablePoint2D extends Point2D.Double implements Serializable {
+ public SerializablePoint2D() {
+ super();
+ }
+
+ public SerializablePoint2D(double x, double y) {
+ super(x, y);
+ }
+
+ public void setX(double x) {
+ setLocation(x, getY());
+ }
+
+ public void setY(double y) {
+ setLocation(getX(), y);
+ }
+
+ private void writeObject(ObjectOutputStream out) throws IOException {
+ out.defaultWriteObject();
+ out.writeObject(new java.lang.Double(getX()));
+ out.writeObject(new java.lang.Double(getY()));
+ }
+
+ private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
+ in.defaultReadObject();
+
+ java.lang.Double x = (java.lang.Double) in.readObject();
+ java.lang.Double y = (java.lang.Double) in.readObject();
+ setLocation(x.doubleValue(), y.doubleValue());
+ }
+ }
+
+ public static class SerializableRectangle2D extends Rectangle2D.Double implements Serializable {
+ public SerializableRectangle2D() {
+ super();
+ }
+
+ public SerializableRectangle2D(double x, double y, double width, double height) {
+ super(x, y, width, height);
+ }
+
+ public void setX(double x) {
+ setFrame(x, getY(), getWidth(), getHeight());
+ }
+
+ public void setY(double y) {
+ setFrame(getX(), y, getWidth(), getHeight());
+ }
+
+ public void setWidth(double width) {
+ setFrame(getX(), getY(), width, getHeight());
+ }
+
+ public void setHeight(double height) {
+ setFrame(getX(), getY(), getWidth(), height);
+ }
+
+ private void writeObject(ObjectOutputStream out) throws IOException {
+ out.defaultWriteObject();
+ out.writeObject(new java.lang.Double(getX()));
+ out.writeObject(new java.lang.Double(getY()));
+ out.writeObject(new java.lang.Double(getWidth()));
+ out.writeObject(new java.lang.Double(getHeight()));
+ }
+
+ private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
+ in.defaultReadObject();
+
+ java.lang.Double x = (java.lang.Double) in.readObject();
+ java.lang.Double y = (java.lang.Double) in.readObject();
+ java.lang.Double width = (java.lang.Double) in.readObject();
+ java.lang.Double height = (java.lang.Double) in.readObject();
+ setFrame(x.doubleValue(), y.doubleValue(), width.doubleValue(), height.doubleValue());
+ }
+ }
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/BasicMarqueeHandler.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/BasicMarqueeHandler.java
new file mode 100644
index 0000000..3b219b9
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/BasicMarqueeHandler.java
@@ -0,0 +1,293 @@
+/*
+ * @(#)BasicMarqueeHandler.java 1.0 03-JUL-04
+ *
+ * Copyright (c) 2001-2004 Gaudenz Alder
+ *
+ */
+package org.jgraph.graph;
+
+import org.jgraph.JGraph;
+
+import java.awt.Color;
+import java.awt.Cursor;
+import java.awt.Graphics;
+import java.awt.Rectangle;
+import java.awt.event.MouseEvent;
+import java.awt.geom.Point2D;
+import java.awt.geom.Rectangle2D;
+
+import java.util.ArrayList;
+
+
+/**
+ * A simple implementation of a marquee handler for JGraph.
+ *
+ * @version 1.0 1/1/02
+ * @author Gaudenz Alder
+ */
+public class BasicMarqueeHandler {
+ /* Restore previous cursor after operation. */
+ protected transient Cursor previousCursor = null;
+
+ /* The rectangle that defines the current marquee selection. */
+ protected Rectangle2D marqueeBounds;
+
+ /* The start start and current point of the marquee session. */
+ protected Point2D startPoint;
+
+ /* The start start and current point of the marquee session. */
+ protected Point2D currentPoint;
+
+ /* Return true if this handler should be preferred over other handlers. */
+ /**
+ * DOCUMENT ME!
+ *
+ * @param event DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isForceMarqueeEvent(MouseEvent event) {
+ return event.isAltDown();
+ }
+
+ /**
+ * Stops the current marquee selection.
+ */
+ public void mouseReleased(MouseEvent e) {
+ try {
+ if ((e != null) && (marqueeBounds != null)) {
+ if (!(e.getSource() instanceof JGraph))
+ throw new IllegalArgumentException("MarqueeHandler cannot "
+ + "handle event from unknown source: " + e);
+
+ JGraph graph = (JGraph) e.getSource();
+ Rectangle2D bounds = graph.fromScreen((Rectangle2D) marqueeBounds.clone());
+ handleMarqueeEvent(e, graph, bounds);
+ graph.setCursor(previousCursor);
+
+ Rectangle dirty = new Rectangle((int) marqueeBounds.getX(),
+ (int) marqueeBounds.getY(),
+ (int) marqueeBounds.getWidth() + 1,
+ (int) marqueeBounds.getHeight() + 1);
+ dirty.width++;
+ dirty.height++;
+ graph.repaint(dirty);
+ }
+ } finally {
+ currentPoint = null;
+ startPoint = null;
+ marqueeBounds = null;
+ previousCursor = null;
+ }
+ }
+
+ /**
+ * Hook for subclassers. Current implementation checks if graph selection is
+ * enabled. This is called from mouseReleased to execute the marquee
+ * selection.
+ */
+ public void handleMarqueeEvent(MouseEvent e, JGraph graph, Rectangle2D bounds) {
+ CellView[] views = graph.getGraphLayoutCache().getRoots(bounds);
+ ArrayList list = new ArrayList();
+
+ for (int i = 0; i < views.length; i++)
+
+ // above returns intersection, we want containment
+ if (bounds.contains(views[i].getBounds()))
+ list.add(views[i].getCell());
+
+ Object[] cells = list.toArray();
+ graph.getUI().selectCellsForEvent(graph, cells, e);
+ }
+
+ /**
+ * Includes the specified startPoint in the marquee selection. Calls
+ * overlay.
+ */
+ public void mouseDragged(MouseEvent e) {
+ if (startPoint != null) {
+ if (!(e.getSource() instanceof JGraph))
+ throw new IllegalArgumentException("MarqueeHandler cannot handle event from unknown source: "
+ + e);
+
+ JGraph graph = (JGraph) e.getSource();
+ Graphics g = graph.getGraphics();
+
+ // Xor the current display
+ Color bg = graph.getBackground();
+ Color fg = graph.getMarqueeColor();
+ g.setColor(fg);
+ g.setXORMode(bg);
+ overlay(graph, g, true);
+
+ processMouseDraggedEvent(e);
+
+ // Repaint
+ g.setColor(bg);
+ g.setXORMode(fg);
+ overlay(graph, g, false);
+ }
+ }
+
+ /**
+ * Called from mouse dragged to update the marquee state during a repaint.
+ */
+ protected void processMouseDraggedEvent(MouseEvent e) {
+ if (startPoint != null) {
+ currentPoint = e.getPoint();
+ marqueeBounds = new Rectangle2D.Double(startPoint.getX(), startPoint.getY(), 0, 0);
+ marqueeBounds.add(currentPoint);
+ }
+ }
+
+ /**
+ * Called after the component was repainted (after autoscroll). This is used
+ * to indicate that the graphics is no more dirty.
+ */
+ public void paint(JGraph graph, Graphics g) {
+ if (marqueeBounds != null)
+ overlay(graph, g, false);
+ }
+
+ /**
+ * Draw the current state of the handler. This is called twice by the
+ * overlay method and also by the paint method. The caller's intention is
+ * that the overlay method draws exactly the current state of the handler so
+ * that it may be used for XOR paint. The drag method calls overlay, changes
+ * the state, and calls overlay again to use this. However, since it is not
+ * always possible to clear the screen with an exact repaint the caller
+ * passes a flag to indicate if the graphics object should be cleared with
+ * this call (eg. if a subsequent call follows).
+ *
+ * @param g
+ */
+ public void overlay(JGraph graph, Graphics g, boolean clear) {
+ if (marqueeBounds != null)
+ g.drawRect((int) marqueeBounds.getX(), (int) marqueeBounds.getY(),
+ (int) marqueeBounds.getWidth(), (int) marqueeBounds.getHeight());
+ }
+
+ /**
+ * Start the marquee at the specified startPoint. This invokes
+ * expandMarqueeToPoint to initialize marquee selection.
+ */
+ public void mousePressed(MouseEvent e) {
+ startPoint = e.getPoint();
+ marqueeBounds = new Rectangle2D.Double(startPoint.getX(), startPoint.getY(), 0, 0);
+
+ if (e != null) {
+ if (!(e.getSource() instanceof JGraph))
+ throw new IllegalArgumentException("MarqueeHandler cannot handle event from unknown source: "
+ + e);
+
+ JGraph graph = (JGraph) e.getSource();
+
+ if (isMarqueeTriggerEvent(e, graph)) {
+ previousCursor = graph.getCursor();
+ graph.setCursor(new Cursor(Cursor.CROSSHAIR_CURSOR));
+ }
+ }
+ }
+
+ /**
+ * Hook for subclassers. Current implementation checks if graph selection is
+ * enabled. This is called from mousePressed before initiating the marquee
+ * selection.
+ */
+ public boolean isMarqueeTriggerEvent(MouseEvent e, JGraph graph) {
+ return graph.isSelectionEnabled();
+ }
+
+ /**
+ * Empty.
+ */
+ public void mouseMoved(MouseEvent e) {
+ // do nothing
+ }
+
+ /**
+ * Returns the currentPoint.
+ *
+ * @return Point
+ */
+ public Point2D getCurrentPoint() {
+ return currentPoint;
+ }
+
+ /**
+ * Returns the marqueeBounds.
+ *
+ * @return Rectangle
+ */
+ public Rectangle2D getMarqueeBounds() {
+ return marqueeBounds;
+ }
+
+ /**
+ * Returns the previousCursor.
+ *
+ * @return Cursor
+ */
+ public Cursor getPreviousCursor() {
+ return previousCursor;
+ }
+
+ /**
+ * Returns the startPoint.
+ *
+ * @return Point
+ */
+ public Point2D getStartPoint() {
+ return startPoint;
+ }
+
+ /**
+ * Sets the currentPoint.
+ *
+ * @param currentPoint
+ * The currentPoint to set
+ */
+ public void setCurrentPoint(Point2D currentPoint) {
+ this.currentPoint = currentPoint;
+ }
+
+ /**
+ * Sets the marqueeBounds.
+ *
+ * @param marqueeBounds
+ * The marqueeBounds to set
+ */
+ public void setMarqueeBounds(Rectangle2D marqueeBounds) {
+ this.marqueeBounds = marqueeBounds;
+ }
+
+ /**
+ * Sets the previousCursor.
+ *
+ * @param previousCursor
+ * The previousCursor to set
+ */
+ public void setPreviousCursor(Cursor previousCursor) {
+ this.previousCursor = previousCursor;
+ }
+
+ /**
+ * Sets the startPoint.
+ *
+ * @param startPoint
+ * The startPoint to set
+ */
+ public void setStartPoint(Point2D startPoint) {
+ this.startPoint = startPoint;
+ }
+
+ /**
+ * @return Returns the source of the event as a graph.
+ */
+ public static JGraph getGraphForEvent(MouseEvent event) {
+ if (event.getSource() instanceof JGraph)
+ return (JGraph) event.getSource();
+
+ return null;
+ }
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/CellHandle.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/CellHandle.java
new file mode 100644
index 0000000..4283cb2
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/CellHandle.java
@@ -0,0 +1,66 @@
+/*
+ * @(#)CellHandle.java 1.0 03-JUL-04
+ *
+ * Copyright (c) 2001-2004 Gaudenz Alder
+ *
+ */
+package org.jgraph.graph;
+
+import java.awt.Graphics;
+import java.awt.event.MouseEvent;
+
+
+/**
+ * Defines the requirements for objects that may be used as handles.
+ * Handles are used to interactively manipulate a cell's appearance.
+ *
+ * @version 1.0 1/1/02
+ * @author Gaudenz Alder
+ */
+public interface CellHandle {
+ /**
+ * Paint the handle on the given graphics object once.
+ *
+ * @param g the graphics object to paint the handle on
+ */
+ void paint(Graphics g);
+
+ /**
+ * Paint the handle on the given graphics object during mouse
+ * operations.
+ *
+ * @param g the graphics object to paint the handle on
+ */
+ void overlay(Graphics g);
+
+ /**
+ * Messaged when the mouse is moved.
+ *
+ * @param event the mouse event to be processed
+ */
+ void mouseMoved(MouseEvent event);
+
+ /**
+ * Messaged when a mouse button is pressed.
+ *
+ * @param event the mouse event to be processed
+ */
+ void mousePressed(MouseEvent event);
+
+ /**
+ * Messaged when the user drags the selection.
+ * The Controller is responsible to determine whether the mouse is
+ * inside the parent graph or not.
+ *
+ * @param event the drag event to be processed
+ */
+ void mouseDragged(MouseEvent event);
+
+ /**
+ * Messaged when the drag operation has
+ * terminated with a drop.
+ *
+ * @param event the drop event to be processed
+ */
+ void mouseReleased(MouseEvent event);
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/CellMapper.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/CellMapper.java
new file mode 100644
index 0000000..618e636
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/CellMapper.java
@@ -0,0 +1,34 @@
+/*
+ * @(#)CellMapper.java 1.0 03-JUL-04
+ *
+ * Copyright (c) 2001-2005 Gaudenz Alder
+ *
+ */
+package org.jgraph.graph;
+
+
+/**
+ * Defines the requirements for objects that may be used as a cell mapper. A
+ * cell mapper is able to return the view of a cell, given a reference to that
+ * cell object. It is basically a cell to cell view mapping
+ */
+public interface CellMapper {
+ /**
+ * Returns the view that is associated with <code>cell</code>.
+ *
+ * @param create
+ * whether a new view should created if a view does not already
+ * exist
+ */
+ CellView getMapping(Object cell, boolean create);
+
+ /**
+ * Inserts the association between <code>cell</code> and <code>view</code>.
+ *
+ * @param cell
+ * the cell that constitutes the model element
+ * @param view
+ * the view that constitutes the view element
+ */
+ void putMapping(Object cell, CellView view);
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/CellView.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/CellView.java
new file mode 100644
index 0000000..db251a6
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/CellView.java
@@ -0,0 +1,128 @@
+/*
+ * @(#)CellView.java 1.0 03-JUL-04
+ *
+ * Copyright (c) 2001-2004 Gaudenz Alder
+ *
+ */
+package org.jgraph.graph;
+
+import org.jgraph.JGraph;
+
+import java.awt.Component;
+import java.awt.geom.Point2D;
+import java.awt.geom.Rectangle2D;
+
+import java.util.Map;
+
+
+/**
+ * Defines the requirements for an object that
+ * represents a view for a model cell.
+ *
+ * @version 1.0 1/1/02
+ * @author Gaudenz Alder
+ */
+public interface CellView {
+ //
+ // Data Source
+ //
+
+ /**
+ * Returns the model object that this view represents.
+ */
+ Object getCell();
+
+ /**
+ * Refresh this view based on the model cell. This is
+ * messaged when the model cell has changed.
+ */
+ void refresh(GraphModel model, CellMapper mapper, boolean createDependentViews);
+
+ /**
+ * Update this view's attributes. This is messaged whenever refresh is
+ * messaged, and additionally when the context of the cell has changed,
+ * and during live-preview changes to the view.
+ */
+ void update();
+
+ void childUpdated();
+
+ //
+ // Group Structure
+ //
+
+ /**
+ * Returns the parent of view of this view.
+ */
+ CellView getParentView();
+
+ /**
+ * Returns the child views of this view.
+ */
+ CellView[] getChildViews();
+
+ /**
+ * Removes this view from the list of childs of the parent.
+ */
+ void removeFromParent();
+
+ /**
+ * Returns true if the view is a leaf.
+ */
+ boolean isLeaf();
+
+ //
+ // View Methods
+ //
+
+ /**
+ * Returns the bounds for the view.
+ */
+ Rectangle2D getBounds();
+
+ /**
+ * Returns true if the view intersects the given rectangle.
+ */
+ boolean intersects(JGraph g, Rectangle2D rect);
+
+ /**
+ * Returns the intersection of the bounding rectangle and the straight line
+ * between the source and the specified point p. The specified point is
+ * expected not to intersect the bounds. Note: You must override this method
+ * if you use a different renderer. This is because this method relies on
+ * the VertexRenderer interface, which can not be safely assumed for
+ * subclassers.
+ */
+ Point2D getPerimeterPoint(EdgeView edge, Point2D source, Point2D p);
+
+ /**
+ * Apply the specified map of attributes on the view.
+ */
+ Map changeAttributes(Map map);
+
+ /**
+ * Returns all attributes of the view as a map.
+ */
+ AttributeMap getAttributes();
+
+ AttributeMap getAllAttributes();
+
+ //
+ // Renderer, Editor and Handle
+ //
+
+ /**
+ * Returns a renderer component, configured for the view.
+ */
+ Component getRendererComponent(JGraph graph, boolean selected, boolean focus, boolean preview);
+
+ /**
+ * Returns a cell handle for the view.
+ */
+ CellHandle getHandle(GraphContext context);
+
+ /**
+ * Returns a cell editor for the view.
+ */
+ GraphCellEditor getEditor();
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/CellViewFactory.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/CellViewFactory.java
new file mode 100644
index 0000000..13c204c
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/CellViewFactory.java
@@ -0,0 +1,25 @@
+/*
+ * @(#)CellViewFactory.java 1.0 03-JUL-04
+ *
+ * Copyright (c) 2001-2004 Gaudenz Alder
+ *
+ */
+package org.jgraph.graph;
+
+
+/**
+ * Defines the requirements for objects that may be used as a
+ * cell view factory.
+ *
+ * @version 1.0 1/1/02
+ * @author Gaudenz Alder
+ */
+public interface CellViewFactory {
+ /**
+ * Constructs a view for the specified cell and associates it
+ * with the specified object using the specified CellMapper.
+ *
+ * @param cell reference to the object in the model
+ */
+ CellView createView(GraphModel model, Object cell);
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/CellViewRenderer.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/CellViewRenderer.java
new file mode 100644
index 0000000..57ef50e
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/CellViewRenderer.java
@@ -0,0 +1,38 @@
+/*
+ * @(#)CellViewRenderer.java 1.0 03-JUL-04
+ *
+ * Copyright (c) 2001-2004 Gaudenz Alder
+ *
+ */
+package org.jgraph.graph;
+
+import org.jgraph.JGraph;
+
+import java.awt.Component;
+
+
+/**
+ * Defines the requirements for objects that may be used as a
+ * cell view renderer.
+ *
+ * @version 1.0 1/1/02
+ * @author Gaudenz Alder
+ */
+public interface CellViewRenderer {
+ /**
+ * Configure and return the renderer based on the passed in
+ * components. The value is typically set from messaging the
+ * graph with <code>convertValueToString</code>.
+ * We recommend you check the value's class and throw an
+ * illegal argument exception if it's not correct.
+ *
+ * @param graph the graph that that defines the rendering context.
+ * @param view the view that should be rendered.
+ * @param sel whether the object is selected.
+ * @param focus whether the object has the focus.
+ * @param preview whether we are drawing a preview.
+ * @return the component used to render the value.
+ */
+ Component getRendererComponent(JGraph graph, CellView view, boolean sel, boolean focus,
+ boolean preview);
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/ConnectionSet.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/ConnectionSet.java
new file mode 100644
index 0000000..99d9eff
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/ConnectionSet.java
@@ -0,0 +1,393 @@
+/*
+ * @(#)ConnectionSet.java 1.0 03-JUL-04
+ *
+ * Copyright (c) 2001-2004 Gaudenz Alder
+ *
+ */
+package org.jgraph.graph;
+
+import java.io.Serializable;
+
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.Map;
+import java.util.Set;
+
+
+/**
+ * An object that represents a set of connections. Connections are equal, if
+ * equals returns true. Connections that are added later replace earlier
+ * connections.
+ *
+ * @version 1.0 1/1/02
+ * @author Gaudenz Alder
+ */
+public class ConnectionSet implements Serializable {
+ /** Contents of the connection set. */
+ protected Set connections = new HashSet();
+
+ /** Set of changed edges for the connection set. */
+ protected Set edges = new HashSet();
+
+ /**
+ * Returns a connection set that represents the connection or disconnection
+ * of <code>cells</code> in <code>model</code> based on
+ * <code>disconnect</code>.
+ */
+ public static ConnectionSet create(GraphModel m, Object[] cells, boolean disconnect) {
+ ConnectionSet cs = new ConnectionSet();
+
+ for (int i = 0; i < cells.length; i++) {
+ Object cell = cells[i];
+
+ // Edge
+ if (m.isEdge(cell)) {
+ if (disconnect)
+ cs.disconnect(cell);
+ else
+ cs.connect(cell, m.getSource(cell), m.getTarget(cell));
+ }
+
+ // Port
+ Iterator it = m.edges(cell);
+
+ while (it.hasNext()) {
+ // Edge At Port
+ Object edge = it.next();
+
+ if (m.getSource(edge) == cell)
+ connect(cs, edge, cell, true, disconnect);
+ else if (m.getTarget(edge) == cell)
+ connect(cs, edge, cell, false, disconnect);
+ }
+ }
+
+ return cs;
+ }
+
+ /**
+ * Constructs an empty ConnectionSet.
+ */
+ public ConnectionSet() {
+ }
+
+ /**
+ * Constructs a ConnectionSet with one Connection.
+ */
+ public ConnectionSet(Object edge, Object port, boolean source) {
+ connect(edge, port, source);
+ }
+
+ /**
+ * Constructs a connection set containing the specified connections and
+ * updates the set of changed edges.
+ */
+ public ConnectionSet(Set connections) {
+ setConnections(connections);
+
+ Iterator it = connections.iterator();
+
+ while (it.hasNext()) {
+ Connection conn = (Connection) it.next();
+ edges.add(conn.getEdge());
+ }
+ }
+
+ /**
+ * Constructs a ConnectionSet with two Connections (to the source and target
+ * port of the edge).
+ */
+ public ConnectionSet(Object edge, Object source, Object target) {
+ connect(edge, source, target);
+ }
+
+ /**
+ * Connect or disconnect <code>edge</code> from <code>source</code> and
+ * <code>target</code> in <code>cs</code> based on
+ * <code>disconnect</code>.
+ */
+ protected static void connect(ConnectionSet cs, Object edge, Object port, boolean source,
+ boolean disconnect) {
+ if (disconnect)
+ cs.disconnect(edge, source);
+ else
+ cs.connect(edge, port, source);
+ }
+
+ /**
+ * Adds the connections in <code>views</code> to the connection set.
+ */
+ public void addConnections(CellView[] views) {
+ for (int i = 0; i < views.length; i++) {
+ if (views[i] instanceof EdgeView) {
+ EdgeView edgeView = (EdgeView) views[i];
+ Object edge = edgeView.getCell();
+ CellView sourceView = edgeView.getSource();
+ CellView targetView = edgeView.getTarget();
+ Object source = null;
+
+ if (sourceView != null)
+ source = sourceView.getCell();
+
+ Object target = null;
+
+ if (targetView != null)
+ target = targetView.getCell();
+
+ connect(edge, source, target);
+ }
+ }
+ }
+
+ /**
+ * Connect <code>edge</code> to <code>source</code> and
+ * <code>target</code> in the connection set. The previous connections
+ * between <code>edge</code> and its source and target are replaced in the
+ * set.
+ */
+ public void connect(Object edge, Object source, Object target) {
+ connect(edge, source, true);
+ connect(edge, target, false);
+ }
+
+ /**
+ * Connect <code>edge</code> to <code>port</code> passed in. The
+ * <code>source</code> indicates if <code>port</code> is the source of
+ * <code>edge</code> object. The previous connections between
+ * <code>edge</code> and its source or target in the set is replaced.
+ */
+ public void connect(Object edge, Object port, boolean source) {
+ Connection c = new Connection(edge, port, source);
+ connections.remove(c);
+ connections.add(c);
+ edges.add(edge);
+ }
+
+ /**
+ * Disconnect <code>edge</code> from <code>source</code> and
+ * <code>target</code> in the connection set. The previous connections
+ * between <code>edge</code> and its source and target are replaced in the
+ * set.
+ */
+ public void disconnect(Object edge) {
+ disconnect(edge, true);
+ disconnect(edge, false);
+ }
+
+ /**
+ * Disconnect <code>edge</code> from <code>port</code>.
+ * <code>source</code> indicates if <code>port</code> is the source of
+ * <code>edge</code>. The previous connections between <code>edge</code>
+ * and its source or target in the set is replaced.
+ */
+ public void disconnect(Object edge, boolean source) {
+ connections.add(new Connection(edge, null, source));
+ edges.add(edge);
+ }
+
+ /**
+ * Returns <code>true</code> if the connection set is empty.
+ */
+ public boolean isEmpty() {
+ return connections.isEmpty();
+ }
+
+ /**
+ * Returns the number of (edge, port)-pairs.
+ */
+ public int size() {
+ return connections.size();
+ }
+
+ /**
+ * Returns an <code>Iterator</code> for the connections in this set.
+ */
+ public Iterator connections() {
+ return connections.iterator();
+ }
+
+ /**
+ * Returns a <code>Set</code> for the edges in this connection set.
+ */
+ public Set getChangedEdges() {
+ return edges;
+ }
+
+ /**
+ * Returns the source or target of the specified edge in this connection set
+ * or null if the connection set contains no corresponding entry for the
+ * edge.
+ */
+ public Object getPort(Object edge, boolean source) {
+ if (edges.contains(edge)) {
+ Iterator it = connections.iterator();
+
+ while (it.hasNext()) {
+ Connection c = (Connection) it.next();
+
+ if ((c.getEdge() == edge) && (c.isSource() == source))
+ return c.getPort();
+ }
+ }
+
+ return null;
+ }
+
+ /**
+ * Creates a new connection set based on this connection set, where the
+ * edges, and ports are mapped using <code>map</code>. If a port is not
+ * found, the old port is used. If both, the edge and the port are not in
+ * <code>map</code>, the entry is ignored.
+ * <p>
+ * <strong>Note: </strong> Consequently, unselected edges are only
+ * reconnected at the first "paste" after a "cut", because in this case the
+ * ConnectionSet is not cloned.
+ */
+ public ConnectionSet clone(Map map) {
+ ConnectionSet cs = new ConnectionSet();
+ Iterator it = connections();
+
+ while (it.hasNext()) {
+ // Shortcut Vars
+ Connection c = (Connection) it.next();
+ Object edge = map.get(c.getEdge());
+ Object port = c.getPort();
+
+ if (port != null)
+ port = map.get(port);
+
+ // New Port
+ if ((edge != null) && (port != null))
+ cs.connect(edge, port, c.isSource());
+
+ // Old Port
+ else if (edge != null)
+ cs.connect(edge, c.getPort(), c.isSource());
+ }
+
+ return cs;
+ }
+
+ /**
+ * Object that represents the connection between an edge and a port.
+ */
+ public static class Connection implements Serializable {
+ /** The edge that will be connected to the port. */
+ protected Object edge;
+
+ /** The port that will be connected to the edge. */
+ protected Object port;
+
+ /** Indicates if <code>port</code> is the source of <code>edge</code>. */
+ protected boolean isSource;
+
+ public Connection() {
+ // Empty Constructor
+ }
+
+ /**
+ * Constructs a new source or target connection between
+ * <code>edge</code> and <code>port</code> based on the value of
+ * <code>source</code>
+ */
+ public Connection(Object edge, Object port, boolean isSource) {
+ this.edge = edge;
+ this.port = port;
+ this.isSource = isSource;
+ }
+
+ /**
+ * Returns the edge of the connection.
+ */
+ public Object getEdge() {
+ return edge;
+ }
+
+ /**
+ * Returns the port of the connection.
+ */
+ public Object getPort() {
+ return port;
+ }
+
+ /**
+ * Returns <code>true</code> if <code>port</code> is the source of
+ * <code>edge</code>.
+ */
+ public boolean isSource() {
+ return isSource;
+ }
+
+ /**
+ * Two connections are equal if they represent the source or target of
+ * the same edge. That is, if
+ * <p>
+ * c1.edge == c2.edge && c1.isSource == c2.isSource.
+ */
+ public boolean equals(Object obj) {
+ if (obj instanceof Connection) {
+ Connection other = (Connection) obj;
+
+ return (other.getEdge().equals(edge) && (other.isSource() == isSource));
+ }
+
+ return false;
+ }
+
+ /**
+ * Ensure equality of hashCode wrt equals().
+ */
+ public int hashCode() {
+ return edge.hashCode();
+ }
+
+ /**
+ * @param object
+ */
+ public void setEdge(Object object) {
+ edge = object;
+ }
+
+ /**
+ * @param b
+ */
+ public void setSource(boolean b) {
+ isSource = b;
+ }
+
+ /**
+ * @param object
+ */
+ public void setPort(Object object) {
+ port = object;
+ }
+ }
+
+ /**
+ * @return the set of connections
+ */
+ public Set getConnections() {
+ return connections;
+ }
+
+ /**
+ * @return the edges making us this connection set
+ */
+ public Set getEdges() {
+ return edges;
+ }
+
+ /**
+ * @param set
+ */
+ public void setConnections(Set set) {
+ connections = set;
+ }
+
+ /**
+ * @param set
+ */
+ public void setEdges(Set set) {
+ edges = set;
+ }
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/DefaultCellViewFactory.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/DefaultCellViewFactory.java
new file mode 100644
index 0000000..2d94848
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/DefaultCellViewFactory.java
@@ -0,0 +1,92 @@
+/*
+ * @(#)DefaultCellViewFactory.java 1.0 29-NOV-04
+ *
+ * Copyright (c) 2001-2005 Gaudenz Alder
+ *
+ */
+package org.jgraph.graph;
+
+import java.io.Serializable;
+
+
+/**
+ * The default implementation of a cell view factory that returns the default
+ * views for vertices, edges and ports.
+ */
+public class DefaultCellViewFactory implements CellViewFactory, Serializable {
+ /**
+ * Constructs a view for the specified cell and associates it with the
+ * specified object using the specified CellMapper. This calls refresh on
+ * the created CellView to create all dependent views.
+ * <p>
+ * Note: The mapping needs to be available before the views of child cells
+ * and ports are created.
+ * <b>Note: This method must return new instances!</b>
+ *
+ * @param cell
+ * reference to the object in the model
+ */
+ public CellView createView(GraphModel model, Object cell) {
+ CellView view = null;
+
+ if (model.isPort(cell))
+ view = createPortView(cell);
+ else if (model.isEdge(cell))
+ view = createEdgeView(cell);
+ else
+ view = createVertexView(cell);
+
+ return view;
+ }
+
+ /**
+ * Constructs a VertexView view for the specified object.
+ */
+ protected VertexView createVertexView(Object cell) {
+ return new VertexView(cell);
+ }
+
+ /**
+ * Constructs an EdgeView view for the specified object.
+ */
+ protected EdgeView createEdgeView(Object cell) {
+ if (cell instanceof Edge)
+ return createEdgeView((Edge) cell);
+ else
+
+ return new EdgeView(cell);
+ }
+
+ /**
+ * Constructs a PortView view for the specified object.
+ */
+ protected PortView createPortView(Object cell) {
+ if (cell instanceof Port)
+ return createPortView((Port) cell);
+ else
+
+ return new PortView(cell);
+ }
+
+ /**
+ * Constructs an EdgeView view for the specified object.
+ *
+ * @deprecated replaced by {@link #createEdgeView(Object)}since
+ * JGraph no longer exposes dependecies on GraphCell subclasses
+ * (Port, Edge)
+ */
+ protected EdgeView createEdgeView(Edge cell) {
+ return new EdgeView(cell);
+ }
+
+ /**
+ * Constructs a PortView view for the specified object.
+ *
+ * @deprecated replaced by {@link #createPortView(Object)}since
+ * JGraph no longer exposes dependecies on GraphCell subclasses
+ * (Port, Edge)
+ */
+ protected PortView createPortView(Port cell) {
+ return new PortView(cell);
+ }
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/DefaultEdge.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/DefaultEdge.java
new file mode 100644
index 0000000..a9b3fab
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/DefaultEdge.java
@@ -0,0 +1,221 @@
+/*
+ * @(#)DefaultEdge.java 1.0 03-JUL-04
+ *
+ * Copyright (c) 2001-2004 Gaudenz Alder
+ *
+ */
+package org.jgraph.graph;
+
+import java.awt.geom.Point2D;
+import java.awt.geom.Rectangle2D;
+
+import java.util.ArrayList;
+import java.util.List;
+
+
+/**
+ * A simple implementation for an edge.
+ *
+ * @version 1.0 1/1/02
+ * @author Gaudenz Alder
+ */
+public class DefaultEdge extends DefaultGraphCell implements Edge {
+ /** Source and target of the edge. */
+ protected Object source;
+
+ /** Source and target of the edge. */
+ protected Object target;
+
+ /**
+ * Constructs an empty edge.
+ */
+ public DefaultEdge() {
+ this(null);
+ }
+
+ /**
+ * Constructs an edge that holds a reference to the specified user object.
+ *
+ * @param userObject
+ * reference to the user object
+ */
+ public DefaultEdge(Object userObject) {
+ this(userObject, null);
+ }
+
+ /**
+ * Constructs an edge that holds a reference to the specified user object
+ * and sets default values for points and the label position.
+ *
+ * @param userObject
+ * reference to the user object
+ */
+ public DefaultEdge(Object userObject, AttributeMap storageMap) {
+ super(userObject, storageMap);
+ }
+
+ /**
+ * Returns the source of the edge.
+ */
+ public Object getSource() {
+ return source;
+ }
+
+ /**
+ * Returns the target of the edge.
+ */
+ public Object getTarget() {
+ return target;
+ }
+
+ /**
+ * Sets the source of the edge.
+ */
+ public void setSource(Object port) {
+ source = port;
+ }
+
+ /**
+ * Returns the target of <code>edge</code>.
+ */
+ public void setTarget(Object port) {
+ target = port;
+ }
+
+ /**
+ * Create a clone of the cell. The cloning of the user object is deferred to
+ * the cloneUserObject() method. The source and target references are set to
+ * null.
+ *
+ * @return Object a clone of this object.
+ */
+ public Object clone() {
+ DefaultEdge edge = (DefaultEdge) super.clone();
+ edge.source = null;
+ edge.target = null;
+
+ return edge;
+ }
+
+ //
+ // Default Routing
+ //
+ public static class LoopRouting implements Edge.Routing {
+ public List route(EdgeView edge) {
+ if (edge.isLoop()) {
+ return routeLoop(edge);
+ }
+
+ return routeEdge(edge);
+ }
+
+ protected List routeLoop(EdgeView edge) {
+ List newPoints = new ArrayList();
+ newPoints.add(edge.getSource());
+
+ CellView sourceParent = (edge.getSource() != null) ? edge.getSource().getParentView()
+ : edge.getSourceParentView();
+
+ if (sourceParent != null) {
+ Point2D from = AbstractCellView.getCenterPoint(sourceParent);
+ Rectangle2D rect = sourceParent.getBounds();
+ double width = rect.getWidth();
+ double height2 = rect.getHeight() / 2;
+ double loopWidth = Math.min(20, Math.max(10, width / 8));
+ double loopHeight = Math.min(30, Math.max(12, Math.max(loopWidth + 4, height2 / 2)));
+ newPoints.add(edge.getAttributes()
+ .createPoint(from.getX() - loopWidth,
+ from.getY() - height2 - (loopHeight * 1.2)));
+ newPoints.add(edge.getAttributes()
+ .createPoint(from.getX(),
+ from.getY() - height2 - (1.5 * loopHeight)));
+ newPoints.add(edge.getAttributes()
+ .createPoint(from.getX() + loopWidth,
+ from.getY() - height2 - (loopHeight * 1.2)));
+ newPoints.add(edge.getTarget());
+
+ return newPoints;
+ }
+
+ return null;
+ }
+
+ protected List routeEdge(EdgeView edge) {
+ return null;
+ }
+
+ public int getPreferredLineStyle(EdgeView edge) {
+ if (edge.isLoop()) {
+ return getLoopStyle();
+ }
+
+ return getEdgeStyle();
+ }
+
+ protected int getLoopStyle() {
+ return GraphConstants.STYLE_BEZIER;
+ }
+
+ protected int getEdgeStyle() {
+ return NO_PREFERENCE;
+ }
+ }
+
+ public static class DefaultRouting extends LoopRouting {
+ protected List routeEdge(EdgeView edge) {
+ List newPoints = new ArrayList();
+ int n = edge.getPointCount();
+ Point2D from = edge.getPoint(0);
+ newPoints.add(from);
+
+ if (edge.getSource() instanceof PortView) {
+ newPoints.set(0, edge.getSource());
+ from = ((PortView) edge.getSource()).getLocation();
+ } else if (edge.getSource() != null) {
+ Rectangle2D b = edge.getSource().getBounds();
+ from = edge.getAttributes().createPoint(b.getCenterX(), b.getCenterY());
+ }
+
+ Point2D to = edge.getPoint(n - 1);
+ CellView target = edge.getTarget();
+
+ if (target instanceof PortView)
+ to = ((PortView) target).getLocation();
+ else if (target != null) {
+ Rectangle2D b = target.getBounds();
+ to = edge.getAttributes().createPoint(b.getCenterX(), b.getCenterY());
+ }
+
+ if ((from != null) && (to != null)) {
+ Point2D[] routed;
+ double dx = Math.abs(from.getX() - to.getX());
+ double dy = Math.abs(from.getY() - to.getY());
+ double x2 = from.getX() + ((to.getX() - from.getX()) / 2);
+ double y2 = from.getY() + ((to.getY() - from.getY()) / 2);
+ routed = new Point2D[2];
+
+ if (dx > dy) {
+ routed[0] = edge.getAttributes().createPoint(x2, from.getY());
+ routed[1] = edge.getAttributes().createPoint(x2, to.getY());
+ } else {
+ routed[0] = edge.getAttributes().createPoint(from.getX(), y2);
+ routed[1] = edge.getAttributes().createPoint(to.getX(), y2);
+ }
+
+ // Set/Add Points
+ for (int i = 0; i < routed.length; i++)
+ newPoints.add(routed[i]);
+
+ // Add target point
+ if (target != null)
+ newPoints.add(target);
+ else
+ newPoints.add(to);
+
+ return newPoints;
+ }
+
+ return null;
+ }
+ }
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/DefaultGraphCell.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/DefaultGraphCell.java
new file mode 100644
index 0000000..809bba0
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/DefaultGraphCell.java
@@ -0,0 +1,167 @@
+/*
+ * @(#)AbstractGraphCell.java 1.0 03-JUL-04
+ *
+ * Copyright (c) 2001-2006 Gaudenz Alder
+ *
+ */
+package org.jgraph.graph;
+
+import java.awt.geom.Point2D;
+
+import java.util.Collections;
+import java.util.List;
+import java.util.Map;
+
+import javax.swing.tree.DefaultMutableTreeNode;
+import javax.swing.tree.MutableTreeNode;
+
+
+/**
+ * The default implementation for the GraphCell interface.
+ *
+ * @version 1.0 1/1/02
+ * @author Gaudenz Alder
+ */
+public class DefaultGraphCell extends DefaultMutableTreeNode implements GraphCell, Cloneable {
+ /** Hashtable for properties. Initially empty */
+ protected AttributeMap attributes = null;
+
+ /**
+ * Creates an empty cell.
+ */
+ public DefaultGraphCell() {
+ this(null);
+ }
+
+ /**
+ * Creates a graph cell and initializes it with the specified user object.
+ *
+ * @param userObject an Object provided by the user that constitutes
+ * the cell's data
+ */
+ public DefaultGraphCell(Object userObject) {
+ this(userObject, null);
+ }
+
+ /**
+ * Constructs a cell that holds a reference to the specified user object
+ * and contains the specified array of children and sets default values
+ * for the bounds attribute.
+ *
+ * @param userObject reference to the user object
+ * @param storageMap the storage attribute map for this cell
+ */
+ public DefaultGraphCell(Object userObject, AttributeMap storageMap) {
+ this(userObject, storageMap, null);
+ }
+
+ /**
+ * Creates a graph cell and initializes it with the specified user object.
+ * The GraphCell allows children only if specified.
+ *
+ * @param userObject an Object provided by the user that constitutes
+ * the cell's data
+ * @param storageMap the storage attribute map for this cell
+ * @param children array of children
+ */
+ public DefaultGraphCell(Object userObject, AttributeMap storageMap, MutableTreeNode[] children) {
+ super(userObject, true);
+ setAttributes(storageMap);
+
+ if (children != null)
+ for (int i = 0; i < children.length; i++)
+ add(children[i]);
+ }
+
+ /**
+ * Provides access to the children list to change ordering.
+ * This method returns a <code>Collections.EMPTY_LIST</code>
+ * if the list of childrenpoints to <code>null</code>.
+ */
+ public List getChildren() {
+ if (children == null)
+ return Collections.EMPTY_LIST;
+
+ return children;
+ }
+
+ /**
+ * Returns the properies of the cell.
+ */
+ public AttributeMap getAttributes() {
+ return attributes;
+ }
+
+ /**
+ * Changes the <code>attributes</code> of the cell.
+ *
+ * @deprecated Use getAttributes().applyMap
+ */
+ public Map changeAttributes(Map change) {
+ return getAttributes().applyMap(change);
+ }
+
+ /**
+ * Sets the attributes.
+ * @param attributes The attributes to set
+ */
+ public void setAttributes(AttributeMap attributes) {
+ if (attributes == null)
+ attributes = new AttributeMap();
+
+ this.attributes = attributes;
+ }
+
+ /**
+ * Utility method to create a port for this cell. This method adds
+ * a floating port.
+ */
+ public void addPort() {
+ addPort(null);
+ }
+
+ /**
+ * Utility method to create a port for this cell. The method adds a port
+ * at a fixed relative offset within the cell. If the offset is null
+ * then a floating port is added.
+ * @param offset the offset of the port within the cell
+ */
+ public void addPort(Point2D offset) {
+ addPort(offset, null);
+ }
+
+ /**
+ * Utility method to create a port for this cell. The method adds a port
+ * at a fixed relative offset within the cell. If the offset is null
+ * then a floating port is added.
+ * @param offset the offset of the port within the cell
+ * @param userObject the user object of the port cell
+ */
+ public void addPort(Point2D offset, Object userObject) {
+ DefaultPort port = new DefaultPort(userObject);
+
+ if (offset == null) {
+ add(port);
+ } else {
+ GraphConstants.setOffset(port.getAttributes(), offset);
+ add(port);
+ }
+ }
+
+ /**
+ * Create a clone of the cell. This method uses the superclass
+ * implementation (which does not clone the children), then
+ * uses clone on the attribute map. This method does not
+ * clone the user object. You should override the
+ * cloneUserObject in the graph model to implement cloning
+ * of custom user objects.
+ *
+ * @return Object a clone of this object.
+ */
+ public Object clone() {
+ DefaultGraphCell c = (DefaultGraphCell) super.clone();
+ c.attributes = (AttributeMap) attributes.clone();
+
+ return c;
+ }
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/DefaultGraphCellEditor.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/DefaultGraphCellEditor.java
new file mode 100644
index 0000000..f010705
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/DefaultGraphCellEditor.java
@@ -0,0 +1,539 @@
+/*
+ * @(#)DefaultGraphCellEditor.java 1.0 03-JUL-04
+ *
+ * Copyright (c) 2001-2004 Gaudenz Alder
+ *
+ */
+package org.jgraph.graph;
+
+import org.jgraph.JGraph;
+
+import org.jgraph.event.GraphSelectionEvent;
+import org.jgraph.event.GraphSelectionListener;
+
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Container;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.Graphics;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseEvent;
+
+import java.io.IOException;
+import java.io.ObjectInputStream;
+import java.io.ObjectOutputStream;
+import java.io.Serializable;
+
+import java.util.EventObject;
+import java.util.Vector;
+
+import javax.swing.Icon;
+import javax.swing.JTextField;
+import javax.swing.SwingUtilities;
+import javax.swing.UIManager;
+import javax.swing.border.Border;
+import javax.swing.event.CellEditorListener;
+import javax.swing.plaf.FontUIResource;
+
+
+/**
+ *
+ */
+public class DefaultGraphCellEditor implements ActionListener, GraphCellEditor,
+ GraphSelectionListener, Serializable {
+ /** Editor handling the editing. */
+ protected GraphCellEditor realEditor;
+
+ /** Editing container, will contain the editorComponent. */
+ protected Container editingContainer;
+
+ /** Component used in editing, obtained from the editingContainer. */
+ transient protected Component editingComponent;
+
+ /**
+ * Internal Note, maybe isCellEditable return true.
+ * This is set in configure based on the path being edited and the
+ * selected selected path.
+ */
+ protected boolean canEdit;
+
+ /** Used in editing. Indicates position to place editingComponent. */
+ protected transient int offsetX;
+ protected transient int offsetY;
+
+ /** JTree instance listening too. */
+ protected transient JGraph graph;
+
+ /** last path that was selected. */
+ protected transient Object lastCell;
+
+ /** True if the border selection color should be drawn. */
+ protected Color borderSelectionColor;
+
+ /** Icon to use when editing. */
+ protected transient Icon editingIcon;
+
+ /** Font to paint with, null indicates font of renderer is to be used. */
+ protected Font font;
+
+ /**
+ * Constructs a DefaultTreeCellEditor object for a JGraph using the
+ * specified renderer and a default editor. (Use this constructor
+ * for normal editing.)
+ */
+ public DefaultGraphCellEditor() {
+ this(null);
+ }
+
+ /**
+ * Constructs a DefaultTreeCellEditor object for a JTree using the
+ * specified renderer and the specified editor. (Use this constructor
+ * for specialized editing.)
+ *
+ * @param editor a TreeCellEditor object
+ */
+ public DefaultGraphCellEditor(GraphCellEditor editor) {
+ realEditor = editor;
+
+ if (realEditor == null)
+ realEditor = createGraphCellEditor();
+
+ editingContainer = createContainer();
+ setBorderSelectionColor(UIManager.getColor("Tree.editorBorderSelectionColor"));
+ }
+
+ /**
+ * Sets the color to use for the border.
+ */
+ public void setBorderSelectionColor(Color newColor) {
+ borderSelectionColor = newColor;
+ }
+
+ /**
+ * Returns the color the border is drawn.
+ */
+ public Color getBorderSelectionColor() {
+ return borderSelectionColor;
+ }
+
+ /**
+ * Sets the font to edit with. <code>null</code> indicates the renderers
+ * font should be used. This will NOT override any font you have set in
+ * the editor the receiver was instantied with. If null for an editor was
+ * passed in a default editor will be created that will pick up this font.
+ *
+ * @param font the editing Font
+ * @see #getFont
+ */
+ public void setFont(Font font) {
+ this.font = font;
+ }
+
+ /**
+ * Gets the font used for editing.
+ *
+ * @return the editing Font
+ * @see #setFont
+ */
+ public Font getFont() {
+ return font;
+ }
+
+ //
+ // TreeCellEditor
+ //
+
+ /**
+ * Configures the editor. Passed onto the realEditor.
+ */
+ public Component getGraphCellEditorComponent(JGraph graph, Object cell, boolean isSelected) {
+ setGraph(graph);
+
+ editingComponent = realEditor.getGraphCellEditorComponent(graph, cell, isSelected);
+
+ determineOffset(graph, cell, isSelected);
+
+ canEdit = ((lastCell != null) && (cell != null) && lastCell.equals(cell));
+
+ CellView view = graph.getGraphLayoutCache().getMapping(cell, false);
+
+ if (view != null)
+ setFont(GraphConstants.getFont(view.getAllAttributes()));
+
+ editingContainer.setFont(font);
+
+ return editingContainer;
+ }
+
+ /**
+ * Returns the value currently being edited.
+ */
+ public Object getCellEditorValue() {
+ return realEditor.getCellEditorValue();
+ }
+
+ /**
+ * If the realEditor returns true to this message, prepareForEditing
+ * is messaged and true is returned.
+ */
+ public boolean isCellEditable(EventObject event) {
+ boolean retValue = false;
+
+ if (!realEditor.isCellEditable(event))
+ return false;
+
+ if (canEditImmediately(event))
+ retValue = true;
+
+ if (retValue)
+ prepareForEditing();
+
+ return retValue;
+ }
+
+ /**
+ * Messages the realEditor for the return value.
+ */
+ public boolean shouldSelectCell(EventObject event) {
+ return realEditor.shouldSelectCell(event);
+ }
+
+ /**
+ * If the realEditor will allow editing to stop, the realEditor is
+ * removed and true is returned, otherwise false is returned.
+ */
+ public boolean stopCellEditing() {
+ if (realEditor.stopCellEditing()) {
+ if (editingComponent != null)
+ editingContainer.remove(editingComponent);
+
+ editingComponent = null;
+
+ return true;
+ }
+
+ return false;
+ }
+
+ /**
+ * Messages cancelCellEditing to the realEditor and removes it from this
+ * instance.
+ */
+ public void cancelCellEditing() {
+ realEditor.cancelCellEditing();
+
+ if (editingComponent != null)
+ editingContainer.remove(editingComponent);
+
+ editingComponent = null;
+ }
+
+ /**
+ * Adds the CellEditorListener.
+ */
+ public void addCellEditorListener(CellEditorListener l) {
+ realEditor.addCellEditorListener(l);
+ }
+
+ /**
+ * Removes the previously added CellEditorListener l.
+ */
+ public void removeCellEditorListener(CellEditorListener l) {
+ realEditor.removeCellEditorListener(l);
+ }
+
+ //
+ // TreeSelectionListener
+ //
+
+ /**
+ * Resets lastPath.
+ */
+ public void valueChanged(GraphSelectionEvent e) {
+ if (graph != null) {
+ if (graph.getSelectionCount() == 1)
+ lastCell = graph.getSelectionCell();
+ else
+ lastCell = null;
+ }
+ }
+
+ //
+ // ActionListener (for Timer).
+ //
+
+ /**
+ * Messaged when the timer fires, this will start the editing
+ * session.
+ */
+ public void actionPerformed(ActionEvent e) {
+ if (graph != null)
+ graph.startEditingAtCell(lastCell);
+ }
+
+ //
+ // Local methods
+ //
+
+ /**
+ * Sets the tree currently editing for. This is needed to add
+ * a selection listener.
+ */
+ protected void setGraph(JGraph newGraph) {
+ if (graph != newGraph) {
+ if (graph != null)
+ graph.removeGraphSelectionListener(this);
+
+ graph = newGraph;
+
+ if (graph != null)
+ graph.addGraphSelectionListener(this);
+ }
+ }
+
+ /**
+ * Returns true if <code>event</code> is a MouseEvent and the click
+ * count is 1.
+ */
+ protected boolean shouldStartEditingTimer(EventObject event) {
+ if ((event instanceof MouseEvent) && SwingUtilities.isLeftMouseButton((MouseEvent) event)) {
+ MouseEvent me = (MouseEvent) event;
+
+ return ((me.getClickCount() == 1) && inHitRegion(me.getX(), me.getY()));
+ }
+
+ return false;
+ }
+
+ /**
+ * Returns true if <code>event</code> is null, or it is a MouseEvent
+ * with a click count > 2 and inHitRegion returns true.
+ */
+ protected boolean canEditImmediately(EventObject event) {
+ if ((event instanceof MouseEvent) && SwingUtilities.isLeftMouseButton((MouseEvent) event)) {
+ MouseEvent me = (MouseEvent) event;
+
+ return inHitRegion(me.getX(), me.getY());
+ }
+
+ return (event == null);
+ }
+
+ /**
+ * Should return true if the passed in location is a valid mouse location
+ * to start editing from. This is implemented to return false if
+ * <code>x</code> is <= the width of the icon and icon gap displayed
+ * by the renderer. In other words this returns true if the user
+ * clicks over the text part displayed by the renderer, and false
+ * otherwise.
+ */
+ protected boolean inHitRegion(double x, double y) {
+ // This is only ever called when within the cell bounds,
+ // so this is ok for the default case.
+ return true;
+ }
+
+ protected void determineOffset(JGraph graph, Object value, boolean isSelected) {
+ editingIcon = null;
+ offsetX = graph.getHandleSize();
+ offsetY = graph.getHandleSize();
+ }
+
+ /**
+ * Invoked just before editing is to start. Will add the
+ * <code>editingComponent</code> to the
+ * <code>editingContainer</code>.
+ */
+ protected void prepareForEditing() {
+ editingContainer.add(editingComponent);
+ }
+
+ /**
+ * Creates the container to manage placement of editingComponent.
+ */
+ protected Container createContainer() {
+ return new EditorContainer();
+ }
+
+ /**
+ * This is invoked if a TreeCellEditor is not supplied in the constructor.
+ * It returns a TextField editor.
+ */
+ protected GraphCellEditor createGraphCellEditor() {
+ Border aBorder = UIManager.getBorder("Tree.editorBorder");
+ DefaultRealEditor editor = new DefaultRealEditor(new DefaultTextField(aBorder)) {
+ public boolean shouldSelectCell(EventObject event) {
+ boolean retValue = super.shouldSelectCell(event);
+ getComponent().requestFocus();
+
+ return retValue;
+ }
+ };
+
+ // One click to edit.
+ editor.setClickCountToStart(1);
+
+ return editor;
+ }
+
+ // Serialization support.
+ private void writeObject(ObjectOutputStream s) throws IOException {
+ Vector values = new Vector();
+
+ s.defaultWriteObject();
+
+ // Save the realEditor, if its Serializable.
+ if (realEditor instanceof Serializable) {
+ values.addElement("realEditor");
+ values.addElement(realEditor);
+ }
+
+ s.writeObject(values);
+ }
+
+ private void readObject(ObjectInputStream s) throws IOException, ClassNotFoundException {
+ s.defaultReadObject();
+
+ Vector values = (Vector) s.readObject();
+ int indexCounter = 0;
+ int maxCounter = values.size();
+
+ if ((indexCounter < maxCounter) && values.elementAt(indexCounter).equals("realEditor")) {
+ realEditor = (GraphCellEditor) values.elementAt(++indexCounter);
+ indexCounter++;
+ }
+ }
+
+ /**
+ * TextField used when no editor is supplied. This textfield locks into
+ * the border it is constructed with. It also prefers its parents
+ * font over its font. And if the renderer is not null and no font
+ * has been specified the preferred height is that of the renderer.
+ */
+ public class DefaultTextField extends JTextField {
+ /** Border to use. */
+ protected Border border;
+
+ /**
+ * Constructs a DefaultTreeCellEditor$DefaultTextField object.
+ *
+ * @param border a Border object
+ */
+ public DefaultTextField(Border border) {
+ this.border = border;
+ }
+
+ /**
+ * Overrides <code>JComponent.getBorder</code> to
+ * returns the current border.
+ */
+ public Border getBorder() {
+ return border;
+ }
+
+ // implements java.awt.MenuContainer
+ public Font getFont() {
+ Font font = super.getFont();
+
+ // Prefer the parent containers font if our font is a
+ // FontUIResource
+ if (font instanceof FontUIResource) {
+ Container parent = getParent();
+
+ if ((parent != null) && (parent.getFont() != null))
+ font = parent.getFont();
+ }
+
+ return font;
+ }
+ }
+
+ /**
+ * Container responsible for placing the editingComponent.
+ */
+ public class EditorContainer extends Container {
+ /**
+ * Constructs an EditorContainer object.
+ */
+ public EditorContainer() {
+ setLayout(null);
+ }
+
+ /**
+ * Overrides <code>Container.paint</code> to paint the node's
+ * icon and use the selection color for the background.
+ */
+ public void paint(Graphics g) {
+ Dimension size = getSize();
+
+ // Then the icon.
+ if (editingIcon != null) {
+ int yLoc = 0;
+ int xLoc = 0;
+ editingIcon.paintIcon(this, g, xLoc, yLoc);
+ }
+
+ // Border selection color
+ Color background = getBorderSelectionColor();
+
+ if (background != null) {
+ g.setColor(background);
+ g.drawRect(0, 0, size.width - 1, size.height - 1);
+ }
+
+ super.paint(g);
+ }
+
+ /**
+ * Lays out this Container. If editing, the editor will be placed at
+ * offset in the x direction and 0 for y.
+ */
+ public void doLayout() {
+ if (editingComponent != null) {
+ Dimension cSize = getSize();
+ int h = (int) editingComponent.getPreferredSize().getHeight();
+ int minw = 45;
+ int w = (int) editingComponent.getPreferredSize().getWidth() + 5;
+ int maxw = (int) editingComponent.getMaximumSize().getWidth();
+
+ if ((editingContainer.getParent() != null)
+ && (maxw > editingContainer.getParent().getWidth()))
+ w = cSize.width - offsetX;
+ else
+ w = Math.max(minw, Math.min(w, maxw));
+
+ editingComponent.setBounds(offsetX, offsetY, w, h);
+ }
+ }
+
+ /**
+ * Returns the preferred size for the Container. This will be
+ * the preferred size of the editor offset by offset.
+ */
+ public Dimension getPreferredSize() {
+ if (editingComponent != null) {
+ Dimension pSize = editingComponent.getPreferredSize();
+
+ pSize.width += (offsetX + 2);
+ pSize.height += (offsetY + 2);
+
+ // Make sure width is at least 50.
+ // and height at least 20
+ int iwidth = 50;
+
+ if (editingIcon != null) {
+ iwidth = Math.max(editingIcon.getIconWidth(), iwidth);
+ }
+
+ pSize.height = Math.max(pSize.height, 24); // Offset 4
+ pSize.width = Math.max(pSize.width + 5, iwidth);
+
+ return pSize;
+ }
+
+ return new Dimension(0, 0);
+ }
+ }
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/DefaultGraphModel.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/DefaultGraphModel.java
new file mode 100644
index 0000000..d328e38
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/DefaultGraphModel.java
@@ -0,0 +1,1979 @@
+/*
+ * @(#)DefaultGraphModel.java 1.0 03-JUL-04
+ *
+ * Copyright (c) 2001-2004 Gaudenz Alder
+ *
+ */
+package org.jgraph.graph;
+
+import org.jgraph.event.GraphModelEvent;
+import org.jgraph.event.GraphModelListener;
+
+import java.io.IOException;
+import java.io.ObjectInputStream;
+import java.io.Serializable;
+
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.Stack;
+
+import javax.swing.event.EventListenerList;
+import javax.swing.tree.DefaultMutableTreeNode;
+import javax.swing.tree.MutableTreeNode;
+import javax.swing.tree.TreeNode;
+import javax.swing.undo.AbstractUndoableEdit;
+import javax.swing.undo.CannotRedoException;
+import javax.swing.undo.CannotUndoException;
+import javax.swing.undo.CompoundEdit;
+import javax.swing.undo.UndoableEdit;
+import javax.swing.undo.UndoableEditSupport;
+
+
+/**
+ * A simple implementation of a graph model.
+ *
+ * @version 1.0 1/1/02
+ * @author Gaudenz Alder
+ */
+public class DefaultGraphModel extends UndoableEditSupport implements Serializable, GraphModel {
+ /**
+ * The list of listeners that listen to the model.
+ */
+ protected transient EventListenerList listenerList = new EventListenerList();
+
+ /**
+ * Default instance of an empty iterator.
+ */
+ protected transient Iterator emptyIterator = new EmptyIterator();
+
+ /**
+ * Set that contains all root cells of this model.
+ */
+ protected List roots = null;
+
+ /**
+ * Indicates whether isLeaf is based on a node's allowsChildren value.
+ */
+ protected boolean asksAllowsChildren = false;
+
+ /**
+ * The model's own attributes as a map. Defaults to an empty Hashtable.
+ */
+ protected AttributeMap attributes = null;
+
+ /**
+ * Constructs a model that is not an attribute store.
+ */
+ public DefaultGraphModel() {
+ this(null, null);
+ }
+
+ /**
+ * Constructs a model that is not an attribute store.
+ */
+ public DefaultGraphModel(List roots, AttributeMap attributes) {
+ if (roots != null)
+ this.roots = roots;
+ else
+ this.roots = new ArrayList();
+
+ if (attributes != null)
+ this.attributes = attributes;
+ else
+ this.attributes = new AttributeMap();
+ }
+
+ /**
+ * Constructs a model using the specified information to construct the
+ * cells, attributes and connection data.
+ */
+ public DefaultGraphModel(List roots, AttributeMap attributes, ConnectionSet cs) {
+ this(roots, attributes);
+ handleConnectionSet(cs);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public List getRoots() {
+ return roots;
+ }
+
+ //
+ // Graph Model
+ //
+
+ /**
+ * Returns the number of roots in the model. Returns 0 if the model is
+ * empty.
+ *
+ * @return the number of roots in the model
+ */
+ public int getRootCount() {
+ return roots.size();
+ }
+
+ /**
+ * Returns the root at index <I>index </I> in the model. This should not
+ * return null if <i>index </i> is a valid index for the model (that is
+ * <i>index </i>>= 0 && <i>index </i>< getRootCount()).
+ *
+ * @return the root of at index <I>index </I>
+ */
+ public Object getRootAt(int index) {
+ return roots.get(index);
+ }
+
+ /**
+ * Returns the index of <code>root</code> in the model. If root is
+ * <code>null</code>, returns -1.
+ *
+ * @param root
+ * a root in the model, obtained from this data source
+ * @return the index of the root in the model, or -1 if the parent is
+ * <code>null</code>
+ */
+ public int getIndexOfRoot(Object root) {
+ return roots.indexOf(root);
+ }
+
+ /**
+ * Returns <code>true</code> if <code>node</code> or one of its
+ * ancestors is in the model.
+ *
+ * @return <code>true</code> if <code>node</code> is in the model
+ */
+ public boolean contains(Object node) {
+ Object parentNode = null;
+
+ while ((parentNode = getParent(node)) != null)
+ node = parentNode;
+
+ return roots.contains(node);
+ }
+
+ /**
+ * Returns a <code>Map</code> that represents the attributes for the
+ * specified cell. This attributes have precedence over each view's
+ * attributes, regardless of isAttributeStore.
+ *
+ * @return attributes of <code>node</code> as a <code>Map</code>
+ */
+ public AttributeMap getAttributes(Object node) {
+ if (node instanceof GraphCell)
+ return ((GraphCell) node).getAttributes();
+ else if (node == null)
+ return attributes;
+
+ return null;
+ }
+
+ /**
+ * @return Returns the user object of the given cell. This implementation
+ * checks if the cell is a default mutable tree node and returns
+ * it's user object.
+ */
+ public Object getValue(Object cell) {
+ if (cell instanceof DefaultMutableTreeNode)
+ return ((DefaultMutableTreeNode) cell).getUserObject();
+
+ return null;
+ }
+
+ /**
+ * Returns the graph model's attribute. Shortcut to <code>
+ * getAttributes(null)</code>.
+ *
+ * @return attributes of <code>node</code> as a <code>Map</code>
+ */
+ public Map getAttributes() {
+ return getAttributes(null);
+ }
+
+ //
+ // Graph Structure
+ //
+
+ /**
+ * Returns the source of <code>edge</code>. <I>edge </I> must be an
+ * object previously obtained from this data source.
+ *
+ * @return <code>Object</code> that represents the source of <i>edge </i>
+ */
+ public Object getSource(Object edge) {
+ if (edge instanceof Edge)
+ return ((Edge) edge).getSource();
+
+ return null;
+ }
+
+ /**
+ * Returns the target of <code>edge</code>. <I>edge </I> must be an
+ * object previously obtained from this data source.
+ *
+ * @return <code>Object</code> that represents the target of <i>edge </i>
+ */
+ public Object getTarget(Object edge) {
+ if (edge instanceof Edge)
+ return ((Edge) edge).getTarget();
+
+ return null;
+ }
+
+ /**
+ * Returns <code>true</code> if <code>port</code> is a valid source for
+ * <code>edge</code>. <I>edge </I> and <I>port </I> must be objects
+ * previously obtained from this data source.
+ *
+ * @return <code>true</code> if <code>port</code> is a valid source for
+ * <code>edge</code>.
+ */
+ public boolean acceptsSource(Object edge, Object port) {
+ return true;
+ }
+
+ /**
+ * Returns <code>true</code> if <code>port</code> is a valid target for
+ * <code>edge</code>. <I>edge </I> and <I>port </I> must be objects
+ * previously obtained from this data source.
+ *
+ * @return <code>true</code> if <code>port</code> is a valid target for
+ * <code>edge</code>.
+ */
+ public boolean acceptsTarget(Object edge, Object port) {
+ return true;
+ }
+
+ /**
+ * Returns an iterator of the edges connected to <code>port</code>.
+ * <I>port </I> must be a object previously obtained from this data source.
+ * This method never returns null.
+ *
+ * @param port
+ * a port in the graph, obtained from this data source
+ * @return <code>Iterator</code> that represents the connected edges
+ */
+ public Iterator edges(Object port) {
+ if (port instanceof Port)
+ return ((Port) port).edges();
+
+ return emptyIterator;
+ }
+
+ /**
+ * Returns <code>true</code> if <code>edge</code> is a valid edge.
+ *
+ * @return <code>true</code> if <code>edge</code> is a valid edge.
+ */
+ public boolean isEdge(Object edge) {
+ return edge instanceof Edge;
+ }
+
+ /**
+ * Returns <code>true</code> if <code>port</code> is a valid port,
+ * possibly supporting edge connection.
+ *
+ * @return <code>true</code> if <code>port</code> is a valid port.
+ */
+ public boolean isPort(Object port) {
+ return port instanceof Port;
+ }
+
+ /**
+ * A shortcut method to create a connection set that represents the
+ * connections in this model. Useful for encoding to avoid writing redundant
+ * connection data stored in the cells.
+ */
+ public ConnectionSet getConnectionSet() {
+ return ConnectionSet.create(this, DefaultGraphModel.getAll(this), false);
+ }
+
+ //
+ // Group Structure
+ //
+
+ /**
+ * Returns a map of (cell, clone)-pairs for all <code>cells</code>. In
+ * the new array, all references are replaced with references to the cloned
+ * cells (ie parent or anchor). This method does only include children which
+ * are in <code>cells</code>. Use JGraph.getDescendants to get a complete
+ * list of all children.
+ */
+ public Map cloneCells(Object[] cells) {
+ Map map = new Hashtable();
+
+ // Add Cells to Queue
+ for (int i = 0; i < cells.length; i++)
+ map.put(cells[i], cloneCell(cells[i]));
+
+ // Replace Parent and Anchors
+ Iterator it = map.entrySet().iterator();
+ Object obj;
+ Object cell;
+ Object parent;
+
+ while (it.hasNext()) {
+ Map.Entry entry = (Map.Entry) it.next();
+ obj = entry.getValue();
+ cell = entry.getKey();
+
+ // Replaces the cloned cell's parent with the parent's clone
+ parent = getParent(cell);
+
+ if (parent != null)
+ parent = map.get(parent);
+
+ if (parent != null)
+ ((DefaultMutableTreeNode) parent).add((DefaultMutableTreeNode) obj);
+
+ // Replaces the anchors for ports
+ if (obj instanceof Port) {
+ Object anchor = ((Port) obj).getAnchor();
+
+ if (anchor != null)
+ ((Port) obj).setAnchor((Port) map.get(anchor));
+ }
+ }
+
+ return map;
+ }
+
+ /**
+ * Sets the parent of the specified cell.
+ */
+ protected void setParent(Object child, Object parent) {
+ if (child instanceof DefaultMutableTreeNode && parent instanceof DefaultMutableTreeNode) {
+ DefaultMutableTreeNode parentNode = (DefaultMutableTreeNode) parent;
+ parentNode.add((DefaultMutableTreeNode) child);
+ }
+ }
+
+ /**
+ * Creates a shallow copy of the cell including a copy of the user object.
+ * Subclassers can override the cloneUserObject to provide a custom user
+ * object cloning mechanism.
+ */
+ protected Object cloneCell(Object cellObj) {
+ if (cellObj instanceof DefaultGraphCell) {
+ // Clones the cell
+ DefaultGraphCell cell = (DefaultGraphCell) cellObj;
+ DefaultGraphCell clone = (DefaultGraphCell) cell.clone();
+ // Clones the user object
+ clone.setUserObject(cloneUserObject(cell.getUserObject()));
+
+ return clone;
+ }
+
+ return cellObj;
+ }
+
+ /**
+ * Clones the user object. Helper method that is invoked from cloneCells.
+ * You must use cloneCells (or cloneCell for single cells) to get a deep
+ * copy of a clone. Subclassers must override this and valueForCellChanged
+ * to implement custom user objects. This implementation returns
+ * <code>object</code>.
+ */
+ protected Object cloneUserObject(Object userObject) {
+ return userObject;
+ }
+
+ /**
+ * Returns the parent of <I>child </I> in the model. <I>child </I> must be a
+ * node previously obtained from this data source. This returns null if
+ * <i>child </i> is a root in the model.
+ *
+ * @param child
+ * a node in the graph, obtained from this data source
+ * @return the parent of <I>child </I>
+ */
+ public Object getParent(Object child) {
+ if ((child != null) && child instanceof TreeNode)
+ return ((TreeNode) child).getParent();
+
+ return null;
+ }
+
+ /**
+ * Returns the index of child in parent. If either the parent or child is
+ * <code>null</code>, returns -1.
+ *
+ * @param parent
+ * a note in the tree, obtained from this data source
+ * @param child
+ * the node we are interested in
+ * @return the index of the child in the parent, or -1 if either the parent
+ * or the child is <code>null</code>
+ */
+ public int getIndexOfChild(Object parent, Object child) {
+ if ((parent == null) || (child == null))
+ return -1;
+
+ return ((TreeNode) parent).getIndex((TreeNode) child);
+ }
+
+ /**
+ * Returns the child of <I>parent </I> at index <I>index </I> in the
+ * parent's child array. <I>parent </I> must be a node previously obtained
+ * from this data source. This should not return null if <i>index </i> is a
+ * valid index for <i>parent </i> (that is <i>index </i>>= 0 && <i>index
+ * </i>< getChildCount( <i>parent </i>)).
+ *
+ * @param parent
+ * a node in the tree, obtained from this data source
+ * @return the child of <I>parent </I> at index <I>index </I>
+ */
+ public Object getChild(Object parent, int index) {
+ if (parent instanceof TreeNode)
+ return ((TreeNode) parent).getChildAt(index);
+
+ return null;
+ }
+
+ /**
+ * Returns the number of children of <I>parent </I>. Returns 0 if the node
+ * is a leaf or if it has no children. <I>parent </I> must be a node
+ * previously obtained from this data source.
+ *
+ * @param parent
+ * a node in the tree, obtained from this data source
+ * @return the number of children of the node <I>parent </I>
+ */
+ public int getChildCount(Object parent) {
+ if (parent instanceof TreeNode)
+ return ((TreeNode) parent).getChildCount();
+
+ return 0;
+ }
+
+ /**
+ * Returns whether the specified node is a leaf node. The way the test is
+ * performed depends on the.
+ *
+ * @param node
+ * the node to check
+ * @return true if the node is a leaf node
+ */
+ public boolean isLeaf(Object node) {
+ if (asksAllowsChildren && node instanceof TreeNode)
+ return !((TreeNode) node).getAllowsChildren();
+
+ return ((TreeNode) node).isLeaf();
+ }
+
+ //
+ // Change Support
+ //
+
+ /**
+ * Inserts the <code>roots</code> and connections into the model. Notifies
+ * the model- and undo listeners of the change. The passed-in edits are
+ * executed if they implement the
+ * <code>GraphModelEvent.ExecutableGraphChange</code> interface in
+ * ascending array-order, after execution of the model change. Note: The
+ * passed-in propertyMap may contain <code>PortView</code> s which must be
+ * turned into <code>Point</code> s when stored in the model.
+ */
+ public void insert(Object[] roots, Map attributes, ConnectionSet cs, ParentMap pm,
+ UndoableEdit[] edits) {
+ GraphModelEdit edit = createEdit(roots, null, attributes, cs, pm, edits);
+
+ if (edit != null) {
+ edit.execute(); // fires graphChangeEvent
+
+ if (edits != null) {
+ for (int i = 0; i < edits.length; i++)
+ if (edits[i] instanceof GraphLayoutCache.GraphLayoutCacheEdit)
+ ((GraphLayoutCache.GraphLayoutCacheEdit) edits[i]).execute();
+ }
+
+ postEdit(edit); // fires undoableedithappened
+ }
+ }
+
+ /**
+ * Removes <code>cells</code> from the model. Notifies the model- and undo
+ * listeners of the change.
+ */
+ public void remove(Object[] roots) {
+ GraphModelEdit edit = createRemoveEdit(roots);
+
+ if (edit != null) {
+ edit.execute();
+ postEdit(edit);
+ }
+ }
+
+ /**
+ * Shortcut to the new edit method which allows inserts and removes to go
+ * along with an edit.
+ */
+ public void edit(Map attributes, ConnectionSet cs, ParentMap pm, UndoableEdit[] edits) {
+ edit(null, null, attributes, cs, pm, edits);
+ }
+
+ /**
+ * Applies <code>attributes</code> and the connection changes to the
+ * model. The initial <code>edits</code> that triggered the call are
+ * considered to be part of this transaction. The passed-in edits are
+ * executed if they implement the
+ * <code>GraphModelEvent.ExecutableGraphChange</code> interface in
+ * ascending array-order, after execution of the model change. Notifies the
+ * model- and undo listeners of the change. <strong>Note: </strong> If only
+ * <code>edits</code> is non-null, the edits are directly passed to the
+ * UndoableEditListeners. Note: The passed-in propertyMap may contains
+ * PortViews which must be turned into Points when stored in the model.
+ */
+ public void edit(Object[] inserted, Object[] removed, Map attributes, ConnectionSet cs,
+ ParentMap pm, UndoableEdit[] edits) {
+ if (((inserted == null) || (inserted.length == 0))
+ && ((removed == null) || (removed.length == 0))
+ && ((attributes == null) || attributes.isEmpty()) && ((cs == null) || cs.isEmpty())
+ && (pm == null) && (edits != null) && (edits.length == 1)) {
+ if (edits[0] instanceof GraphLayoutCache.GraphLayoutCacheEdit)
+ ((GraphLayoutCache.GraphLayoutCacheEdit) edits[0]).execute();
+
+ postEdit(edits[0]); // UndoableEdit Relay
+ } else {
+ GraphModelEdit edit = createEdit(inserted, removed, attributes, cs, pm, edits);
+
+ if (edit != null) {
+ edit.execute();
+
+ if (edits != null) {
+ for (int i = 0; i < edits.length; i++)
+ if (edits[i] instanceof GraphLayoutCache.GraphLayoutCacheEdit)
+ ((GraphLayoutCache.GraphLayoutCacheEdit) edits[i]).execute();
+ }
+
+ postEdit(edit);
+ }
+ }
+ }
+
+ /**
+ * Sends <code>cells</code> to back.
+ */
+ public void toBack(Object[] cells) {
+ GraphModelLayerEdit edit = createLayerEdit(cells, GraphModelLayerEdit.BACK);
+
+ if (edit != null) {
+ edit.execute();
+ postEdit(edit);
+ }
+ }
+
+ /**
+ * Brings <code>cells</code> to front.
+ */
+ public void toFront(Object[] cells) {
+ GraphModelLayerEdit edit = createLayerEdit(cells, GraphModelLayerEdit.FRONT);
+
+ if (edit != null) {
+ edit.execute();
+ postEdit(edit);
+ }
+ }
+
+ protected GraphModelLayerEdit createLayerEdit(Object[] cells, int layer) {
+ return new GraphModelLayerEdit(cells, layer);
+ }
+
+ //
+ // Edit Creation
+ //
+
+ /**
+ * Returns an edit that represents an insert.
+ */
+
+ // protected GraphModelEdit createInsertEdit(Object[] cells, Map
+ // attributeMap,
+ // ConnectionSet cs, ParentMap pm, UndoableEdit[] edits) {
+ // return createEdit(cells, null, attributeMap, cs, pm, edits);
+ // }
+ /**
+ * Returns an edit that represents a remove.
+ */
+ protected GraphModelEdit createRemoveEdit(Object[] cells) {
+ // Remove from GraphStructure
+ ConnectionSet cs = ConnectionSet.create(this, cells, true);
+
+ // Remove from Group Structure
+ ParentMap pm = ParentMap.create(this, cells, true, false);
+
+ // Construct Edit
+ GraphModelEdit edit = createEdit(null, cells, null, cs, pm, null);
+
+ if (edit != null)
+ edit.end();
+
+ return edit;
+ }
+
+ protected GraphModelEdit createEdit(Object[] inserted, Object[] removed, Map attributes,
+ ConnectionSet cs, ParentMap pm, UndoableEdit[] edits) {
+ GraphModelEdit edit = new GraphModelEdit(inserted, removed, attributes, cs, pm);
+
+ if (edit != null) {
+ if (edits != null)
+ for (int i = 0; i < edits.length; i++)
+ edit.addEdit(edits[i]);
+
+ edit.end();
+ }
+
+ return edit;
+ }
+
+ //
+ // Change Handling
+ //
+
+ /**
+ * Inserts <code>cells</code> into the model. Returns the cells that were
+ * inserted (including descendants).
+ */
+ protected Object[] handleInsert(Object[] cells) {
+ Object[] inserted = null;
+
+ if (cells != null) {
+ for (int i = 0; i < cells.length; i++)
+
+ // Add to Roots if no parent
+ if (getParent(cells[i]) == null)
+ roots.add(cells[i]);
+
+ // Return *all* inserted cells
+ inserted = getDescendants(this, cells).toArray();
+ }
+
+ return inserted;
+ }
+
+ /**
+ * Removes <code>cells</code> from the model. Returns the cells that were
+ * removed as roots.
+ */
+ protected Object[] handleRemove(Object[] cells) {
+ List removedRoots = new ArrayList();
+
+ if (cells != null)
+ for (int i = 0; i < cells.length; i++)
+ if ((getParent(cells[i]) == null) && roots.remove(cells[i]))
+ removedRoots.add(cells[i]);
+
+ return removedRoots.toArray();
+ }
+
+ /**
+ * Applies <code>cells</code> to the model. Returns a parent map that may
+ * be used to undo this change.
+ */
+ protected ParentMap handleParentMap(ParentMap parentMap) {
+ if (parentMap != null) {
+ ParentMap undo = new ParentMap();
+ HashSet rootsSet = new HashSet(roots);
+ Iterator it = parentMap.entries();
+
+ while (it.hasNext()) {
+ ParentMap.Entry entry = (ParentMap.Entry) it.next();
+ Object child = entry.getChild();
+ Object parent = entry.getParent();
+ undo.addEntry(child, getParent(child));
+
+ if (parent == null) {
+ if (child instanceof MutableTreeNode) {
+ ((MutableTreeNode) child).removeFromParent();
+ }
+ } else {
+ if (parent instanceof DefaultMutableTreeNode
+ && child instanceof MutableTreeNode) {
+ ((DefaultMutableTreeNode) parent).add((MutableTreeNode) child);
+ }
+ }
+
+ boolean isRoot = rootsSet.contains(child);
+
+ if ((parent == null) && !isRoot) {
+ roots.add(child);
+ rootsSet.add(child);
+ } else if ((parent != null) && isRoot) {
+ roots.remove(child);
+ rootsSet.remove(child);
+ }
+ }
+
+ return undo;
+ }
+
+ return null;
+ }
+
+ /**
+ * Applies <code>attributes</code> to the cells specified as keys. Returns
+ * the <code>attributes</code> to undo the change.
+ */
+ protected Map handleAttributes(Map attributes) {
+ if (attributes != null) {
+ Hashtable undo = new Hashtable(attributes.size());
+ Iterator it = attributes.entrySet().iterator();
+
+ while (it.hasNext()) {
+ Map.Entry entry = (Map.Entry) it.next();
+ Object cell = entry.getKey();
+ Map deltaNew = (Map) entry.getValue();
+
+ // System.out.println("deltaNew="+deltaNew);
+ // System.out.println("stateOld="+getAttributes(cell));
+ // Handle New Values
+ Map deltaOld = null;
+ AttributeMap attr = getAttributes(cell);
+
+ if (attr != null) {
+ deltaOld = attr.applyMap(deltaNew);
+ // System.out.println("stateNew="+getAttributes(cell));
+ // System.out.println("deltaOld="+deltaOld);
+ undo.put(cell, deltaOld);
+ } else {
+ // Make room for the value
+ deltaOld = new Hashtable(2);
+ }
+
+ // Handle new values
+ Object newValue = deltaNew.get(GraphConstants.VALUE);
+
+ if (newValue != null) {
+ Object oldValue = valueForCellChanged(cell, newValue);
+
+ if (oldValue != null)
+ GraphConstants.setValue(deltaOld, oldValue);
+
+ // TODO: Userobject of null is probably invalid
+ else
+ GraphConstants.setRemoveAttributes(deltaOld,
+ new Object[] { GraphConstants.VALUE });
+ }
+ }
+
+ return undo;
+ }
+
+ return null;
+ }
+
+ /**
+ * Applies the new value to the specified cell. Unfortunately for cloning
+ * the user object you must still override the attribute map and provide a
+ * custom cloneUserObject method. This is because the cloning of a cell is
+ * local to the cell, which in turn has a reference to its attribute map.
+ *
+ * @param cell
+ * @param newValue
+ * @return the old value for the cell, if any
+ */
+ public Object valueForCellChanged(Object cell, Object newValue) {
+ if (cell instanceof DefaultMutableTreeNode) {
+ DefaultMutableTreeNode node = (DefaultMutableTreeNode) cell;
+ Object oldValue = node.getUserObject();
+ node.setUserObject(newValue);
+
+ return oldValue;
+ }
+
+ return null;
+ }
+
+ //
+ // Connection Set Handling
+ //
+
+ /**
+ * Applies <code>connectionSet</code> to the model. Returns a connection
+ * set that may be used to undo this change.
+ */
+ protected ConnectionSet handleConnectionSet(ConnectionSet cs) {
+ if (cs != null) {
+ ConnectionSet csundo = new ConnectionSet();
+ Iterator it = cs.connections();
+
+ while (it.hasNext()) {
+ ConnectionSet.Connection c = (ConnectionSet.Connection) it.next();
+ Object edge = c.getEdge();
+
+ if (c.isSource())
+ csundo.connect(edge, getSource(edge), true);
+ else
+ csundo.connect(edge, getTarget(edge), false);
+
+ handleConnection(c, false);
+ }
+
+ // When removing edges it is possible that an edge is
+ // removed in a later step which has been added in a
+ // previous connection establishment (set semantic).
+ // Therefore, we first need to remove all old connections
+ // and then add all new connections in two steps.
+ it = cs.connections();
+
+ while (it.hasNext())
+ handleConnection((ConnectionSet.Connection) it.next(), true);
+
+ return csundo;
+ }
+
+ return null;
+ }
+
+ /**
+ * Inserts the specified connection into the model.
+ */
+ protected void handleConnection(ConnectionSet.Connection c, boolean establish) {
+ Object edge = c.getEdge();
+ Object port = (establish) ? c.getPort() : ((c.isSource()) ? getSource(edge) : getTarget(edge));
+ connect(edge, port, c.isSource(), establish);
+ }
+
+ /**
+ * Connects or disconnects the edge and port in this model based on
+ * <code>remove</code>. Subclassers should override this to update
+ * connectivity datastructures.
+ */
+ protected void connect(Object edge, Object port, boolean isSource, boolean insert) {
+ if (port instanceof Port)
+ if (insert)
+ ((Port) port).addEdge(edge);
+
+ // Only removes if opposite is not
+ // connected to same port
+ else if ((isSource) ? (getTarget(edge) != port) : (getSource(edge) != port))
+ ((Port) port).removeEdge(edge);
+
+ if (!insert)
+ port = null;
+
+ if (edge instanceof Edge) {
+ if (isSource)
+ ((Edge) edge).setSource(port);
+ else
+ ((Edge) edge).setTarget(port);
+ }
+ }
+
+ //
+ // GraphModelListeners
+ //
+
+ /**
+ * Adds a listener for the GraphModelEvent posted after the graph changes.
+ *
+ * @see #removeGraphModelListener
+ * @param l
+ * the listener to add
+ */
+ public void addGraphModelListener(GraphModelListener l) {
+ listenerList.add(GraphModelListener.class, l);
+ }
+
+ /**
+ * Removes a listener previously added with <B>addGraphModelListener() </B>.
+ *
+ * @see #addGraphModelListener
+ * @param l
+ * the listener to remove
+ */
+ public void removeGraphModelListener(GraphModelListener l) {
+ listenerList.remove(GraphModelListener.class, l);
+ }
+
+ /**
+ * Invoke this method after you've changed how the cells are to be
+ * represented in the graph.
+ */
+ public void cellsChanged(final Object[] cells) {
+ if (cells != null) {
+ fireGraphChanged(this,
+ new GraphModelEvent.GraphModelChange() {
+ public Object[] getInserted() {
+ return null;
+ }
+
+ public Object[] getRemoved() {
+ return null;
+ }
+
+ public Map getPreviousAttributes() {
+ return null;
+ }
+
+ public ConnectionSet getConnectionSet() {
+ return null;
+ }
+
+ public ConnectionSet getPreviousConnectionSet() {
+ return null;
+ }
+
+ public ParentMap getParentMap() {
+ return null;
+ }
+
+ public ParentMap getPreviousParentMap() {
+ return null;
+ }
+
+ public void putViews(GraphLayoutCache view, CellView[] cellViews) {
+ }
+
+ public CellView[] getViews(GraphLayoutCache view) {
+ return null;
+ }
+
+ public Object getSource() {
+ return this;
+ }
+
+ public Object[] getChanged() {
+ return cells;
+ }
+
+ public Map getAttributes() {
+ return null;
+ }
+
+ public Object[] getContext() {
+ return null;
+ }
+ });
+ }
+ }
+
+ /*
+ * Notify all listeners that have registered interest for notification on
+ * this event type. The event instance is lazily created using the
+ * parameters passed into the fire method.
+ *
+ * @see EventListenerList
+ */
+ protected void fireGraphChanged(Object source, GraphModelEvent.GraphModelChange edit) {
+ // Guaranteed to return a non-null array
+ Object[] listeners = listenerList.getListenerList();
+ GraphModelEvent e = null;
+
+ // Process the listeners last to first, notifying
+ // those that are interested in this event
+ for (int i = listeners.length - 2; i >= 0; i -= 2) {
+ if (listeners[i] == GraphModelListener.class) {
+ // Lazily create the event:
+ if (e == null)
+ e = new GraphModelEvent(source, edit);
+
+ ((GraphModelListener) listeners[i + 1]).graphChanged(e);
+ }
+ }
+ }
+
+ /**
+ * Return an array of all GraphModelListeners that were added to this model.
+ */
+ public GraphModelListener[] getGraphModelListeners() {
+ return (GraphModelListener[]) listenerList.getListeners(GraphModelListener.class);
+ }
+
+ //
+ // GraphModelEdit
+ //
+
+ /**
+ * An implementation of GraphModelChange that can be added to the model
+ * event.
+ */
+ public class GraphModelEdit extends CompoundEdit implements GraphModelEvent.GraphModelChange {
+ /* Cells that were inserted/removed/changed during the last execution. */
+ protected Object[] insert;
+
+ /* Cells that were inserted/removed/changed during the last execution. */
+ protected Object[] changed;
+
+ /* Cells that were inserted/removed/changed during the last execution. */
+ protected Object[] remove;
+
+ /* Cells that were inserted/removed/changed during the last execution. */
+ protected Object[] context;
+
+ /* Cells that were inserted/removed/changed during the last execution. */
+ protected Object[] inserted;
+
+ /* Cells that were inserted/removed/changed during the last execution. */
+ protected Object[] removed;
+
+ /*
+ * Property map for the next execution. Attribute Map is passed to the
+ * views on inserts.
+ */
+ protected Map attributes;
+
+ /*
+ * Property map for the next execution. Attribute Map is passed to the
+ * views on inserts.
+ */
+ protected Map previousAttributes;
+
+ /* Parent map for the next execution. */
+ protected ParentMap parentMap;
+
+ /* Parent map for the next execution. */
+ protected ParentMap previousParentMap;
+
+ /* ConnectionSet for the next execution. */
+ protected ConnectionSet connectionSet;
+
+ /* ConnectionSet for the next execution. */
+ protected ConnectionSet previousConnectionSet;
+
+ /* Piggybacked undo from the views. */
+ protected Map cellViews = new Hashtable();
+
+ /**
+ * Constructs an edit record.
+ *
+ * @param inserted
+ * a set of roots that were inserted
+ * @param removed
+ * a set of elements that were removed
+ * @param attributes
+ * the attribute changes made by the edit
+ * @param connectionSet
+ * the set of changed connections
+ * @param parentMap
+ * the map of changed parents
+ */
+ public GraphModelEdit(Object[] inserted, Object[] removed, Map attributes,
+ ConnectionSet connectionSet, ParentMap parentMap) {
+ super();
+ this.insert = inserted;
+ this.remove = removed;
+ this.connectionSet = connectionSet;
+ this.attributes = attributes;
+ this.parentMap = parentMap;
+ previousAttributes = null;
+ previousConnectionSet = connectionSet;
+ previousParentMap = parentMap;
+
+ // Remove Empty Parents
+ if (parentMap != null) {
+ // Compute Empty Group
+ Map childCount = new Hashtable();
+ Iterator it = parentMap.entries();
+
+ while (it.hasNext()) {
+ ParentMap.Entry entry = (ParentMap.Entry) it.next();
+ Object child = entry.getChild();
+
+ if (!isPort(child)) {
+ Object oldParent = getParent(child);
+ Object newParent = entry.getParent();
+
+ if (oldParent != newParent) {
+ changeChildCount(childCount, oldParent, -1);
+ changeChildCount(childCount, newParent, 1);
+ }
+ }
+ }
+
+ handleEmptyGroups(filterParents(childCount, 0));
+ }
+ }
+
+ public Object[] filterParents(Map childCount, int children) {
+ ArrayList list = new ArrayList();
+ Iterator it = childCount.entrySet().iterator();
+
+ while (it.hasNext()) {
+ Map.Entry entry = (Map.Entry) it.next();
+
+ if (entry.getValue() instanceof Integer) {
+ if (((Integer) entry.getValue()).intValue() == children)
+ list.add(entry.getKey());
+ }
+ }
+
+ return list.toArray();
+ }
+
+ protected void changeChildCount(Map childCount, Object parent, int change) {
+ if (parent != null) {
+ Integer count = (Integer) childCount.get(parent);
+
+ if (count == null) {
+ count = new Integer(getChildCount(parent));
+ }
+
+ int newValue = count.intValue() + change;
+ childCount.put(parent, new Integer(newValue));
+ }
+ }
+
+ /**
+ * Adds the groups that become empty to the cells that will be removed.
+ * (Auto remove empty cells.) Removed cells will be re-inserted on undo,
+ * and the parent- child relations will be restored.
+ */
+ protected void handleEmptyGroups(Object[] groups) {
+ if ((groups != null) && (groups.length > 0)) {
+ if (remove == null)
+ remove = new Object[] { };
+
+ Object[] tmp = new Object[remove.length + groups.length];
+ System.arraycopy(remove, 0, tmp, 0, remove.length);
+ System.arraycopy(groups, 0, tmp, remove.length, groups.length);
+ remove = tmp;
+ }
+ }
+
+ public boolean isSignificant() {
+ return true;
+ }
+
+ /**
+ * Returns the source of this change. This can either be a view or a
+ * model, if this change is a GraphModelChange.
+ */
+ public Object getSource() {
+ return DefaultGraphModel.this;
+ }
+
+ /**
+ * Returns the cells that have changed. This includes the cells that
+ * have been changed through a call to getAttributes and the edges that
+ * have been changed with the ConnectionSet.
+ */
+ public Object[] getChanged() {
+ return changed;
+ }
+
+ /**
+ * Returns the objects that have not changed explicitly, but implicitly
+ * because one of their dependent cells has changed.
+ */
+ public Object[] getContext() {
+ return context;
+ }
+
+ /**
+ * Returns the cells that were inserted.
+ */
+ public Object[] getInserted() {
+ return inserted;
+ }
+
+ /**
+ * Returns the cells that were inserted.
+ */
+ public Object[] getRemoved() {
+ return removed;
+ }
+
+ /**
+ * Returns a map that contains (object, map) pairs of the attributes
+ * that have been stored in the model.
+ */
+ public Map getPreviousAttributes() {
+ return previousAttributes;
+ }
+
+ /**
+ * Returns a map of (object, view attributes). The objects are model
+ * objects which need to be mapped to views.
+ */
+ public Map getAttributes() {
+ return attributes;
+ }
+
+ /**
+ * Returns the connectionSet.
+ *
+ * @return ConnectionSet
+ */
+ public ConnectionSet getConnectionSet() {
+ return connectionSet;
+ }
+
+ public ConnectionSet getPreviousConnectionSet() {
+ return previousConnectionSet;
+ }
+
+ /**
+ * Returns the parentMap.
+ *
+ * @return ParentMap
+ */
+ public ParentMap getParentMap() {
+ return parentMap;
+ }
+
+ public ParentMap getPreviousParentMap() {
+ return previousParentMap;
+ }
+
+ /**
+ * Redoes a change.
+ *
+ * @exception CannotRedoException
+ * if the change cannot be redone
+ */
+ public void redo() throws CannotRedoException {
+ super.redo();
+ execute();
+ }
+
+ /**
+ * Undoes a change.
+ *
+ * @exception CannotUndoException
+ * if the change cannot be undone
+ */
+ public void undo() throws CannotUndoException {
+ super.undo();
+ execute();
+ }
+
+ /**
+ * Execute this edit such that the next invocation to this method will
+ * invert the last execution.
+ */
+ public void execute() {
+ // Compute Changed Cells
+ Set tmp = new HashSet();
+
+ if (attributes != null)
+ tmp.addAll(attributes.keySet());
+
+ if (parentMap != null)
+ tmp.addAll(parentMap.getChangedNodes());
+
+ // Note: One must also include the previous parents!
+ if (connectionSet != null)
+ tmp.addAll(connectionSet.getChangedEdges());
+
+ if (remove != null) {
+ for (int i = 0; i < remove.length; i++)
+ tmp.remove(remove[i]);
+ }
+
+ changed = tmp.toArray();
+
+ // Context cells
+ Set ctx = getEdges(DefaultGraphModel.this, changed);
+ context = ctx.toArray();
+ // Do Execute
+ inserted = insert;
+ removed = remove;
+ remove = handleInsert(inserted);
+ previousParentMap = parentMap;
+ parentMap = handleParentMap(parentMap);
+
+ // Adds previous parents
+ if (parentMap != null)
+ tmp.addAll(parentMap.getChangedNodes());
+
+ previousConnectionSet = connectionSet;
+ connectionSet = handleConnectionSet(connectionSet);
+ insert = handleRemove(removed);
+ previousAttributes = attributes;
+ attributes = handleAttributes(attributes);
+ changed = tmp.toArray();
+ // Fire Event
+ fireGraphChanged(DefaultGraphModel.this, this);
+ }
+
+ public void putViews(GraphLayoutCache view, CellView[] views) {
+ if ((view != null) && (views != null))
+ cellViews.put(view, views);
+ }
+
+ public CellView[] getViews(GraphLayoutCache view) {
+ return (CellView[]) cellViews.get(view);
+ }
+
+ public String toString() {
+ String s = new String();
+
+ if (inserted != null) {
+ s += "Inserted:\n";
+
+ for (int i = 0; i < inserted.length; i++)
+ s += (" " + inserted[i] + "\n");
+ } else
+ s += "None inserted\n";
+
+ if (removed != null) {
+ s += "Removed:\n";
+
+ for (int i = 0; i < removed.length; i++)
+ s += (" " + removed[i] + "\n");
+ } else
+ s += "None removed\n";
+
+ if ((changed != null) && (changed.length > 0)) {
+ s += "Changed:\n";
+
+ for (int i = 0; i < changed.length; i++)
+ s += (" " + changed[i] + "\n");
+ } else
+ s += "None changed\n";
+
+ if (parentMap != null)
+ s += parentMap.toString();
+ else
+ s += "No parent map\n";
+
+ return s;
+ }
+ }
+
+ /**
+ * An implementation of GraphViewChange.
+ */
+ public class GraphModelLayerEdit extends AbstractUndoableEdit implements GraphModelEvent.GraphModelChange {
+ public static final int FRONT = -1;
+ public static final int BACK = -2;
+ protected Object changeSource;
+ protected transient Object[] cells;
+ protected transient int[] next;
+ protected transient int[] prev;
+ protected int layer;
+
+ // The cell that change are the parents, because they need to
+ // reload their childs for reordering!
+ protected Object[] changed;
+
+ /**
+ * Constructs a GraphModelEdit. This modifies the order of the cells in
+ * the model.
+ */
+ public GraphModelLayerEdit(Object[] cells, int layer) {
+ this.cells = cells;
+ this.layer = layer;
+ next = new int[cells.length];
+ prev = new int[cells.length];
+ updateNext();
+
+ // Compute array of changed cells (roots or parents of cells)
+ Set par = new HashSet();
+
+ for (int i = 0; i < cells.length; i++) {
+ Object cell = DefaultGraphModel.this.getParent(cells[i]);
+
+ if (cell == null)
+ cell = cells[i];
+
+ par.add(cell);
+ }
+
+ changed = par.toArray();
+ }
+
+ protected void updateNext() {
+ for (int i = 0; i < next.length; i++)
+ next[i] = layer;
+ }
+
+ /**
+ * Returns the source of this change. This can either be a view or a
+ * model, if this change is a GraphModelChange.
+ */
+ public Object getSource() {
+ return DefaultGraphModel.this;
+ }
+
+ /**
+ * Returns the cells that have changed.
+ */
+ public Object[] getChanged() {
+ return changed;
+ }
+
+ /**
+ * Returns the cells that have changed.
+ */
+ public Object[] getInserted() {
+ return null;
+ }
+
+ /**
+ * Returns the cells that have changed.
+ */
+ public Object[] getRemoved() {
+ return null;
+ }
+
+ /**
+ * Returns null.
+ */
+ public Object[] getContext() {
+ return null;
+ }
+
+ /**
+ * Returns null.
+ */
+ public Map getAttributes() {
+ return null;
+ }
+
+ /**
+ * Returns null.
+ */
+ public Map getPreviousAttributes() {
+ return null;
+ }
+
+ public ConnectionSet getConnectionSet() {
+ return null;
+ }
+
+ public ConnectionSet getPreviousConnectionSet() {
+ return null;
+ }
+
+ /**
+ * Returns null.
+ */
+ public ParentMap getParentMap() {
+ return null;
+ }
+
+ public ParentMap getPreviousParentMap() {
+ return null;
+ }
+
+ /**
+ * Allows a <code>GraphLayoutCache</code> to add and execute and
+ * UndoableEdit in this change. This does also work if the parent edit
+ * has already been executed, in which case the to be added edit will be
+ * executed immediately, after addition. This is used to handle changes
+ * to the view that are triggered by certain changes of the model. Such
+ * implicit edits may be associated with the view so that they may be
+ * undone and redone correctly, and are stored in the model's global
+ * history together with the parent event as one unit.
+ */
+ public void addImplicitEdit(UndoableEdit edit) {
+ // ignore
+ }
+
+ /**
+ * Returns the views that have not changed explicitly, but implicitly
+ * because one of their dependent cells has changed.
+ */
+ public CellView[] getViews(GraphLayoutCache view) {
+ return null;
+ }
+
+ /**
+ * Returns the views that have not changed explicitly, but implicitly
+ * because one of their dependent cells has changed.
+ */
+ public void putViews(GraphLayoutCache view, CellView[] cellViews) {
+ // ignore
+ }
+
+ /**
+ * Redoes a change.
+ *
+ * @exception CannotRedoException
+ * if the change cannot be redone
+ */
+ public void redo() throws CannotRedoException {
+ super.redo();
+ updateNext();
+ execute();
+ }
+
+ /**
+ * Undoes a change.
+ *
+ * @exception CannotUndoException
+ * if the change cannot be undone
+ */
+ public void undo() throws CannotUndoException {
+ super.undo();
+ execute();
+ }
+
+ /**
+ * Execute this edit such that the next invocation to this method will
+ * invert the last execution.
+ */
+ public void execute() {
+ for (int i = 0; i < cells.length; i++) {
+ List list = getParentList(cells[i]);
+
+ if (list != null) {
+ prev[i] = list.indexOf(cells[i]);
+
+ if (prev[i] >= 0) {
+ list.remove(prev[i]);
+
+ int n = next[i];
+
+ if (n == FRONT)
+ n = list.size();
+ else if (n == BACK)
+ n = 0;
+
+ list.add(n, cells[i]);
+ next[i] = prev[i];
+ }
+ }
+ }
+
+ updateListeners();
+ }
+
+ protected void updateListeners() {
+ fireGraphChanged(DefaultGraphModel.this, this);
+ }
+
+ /**
+ * Returns the list that exclusively contains <code>view</code>.
+ */
+ protected List getParentList(Object cell) {
+ List list = null;
+
+ if (cell instanceof DefaultMutableTreeNode) {
+ Object parent = ((DefaultMutableTreeNode) cell).getParent();
+
+ if (parent instanceof DefaultGraphCell)
+ list = ((DefaultGraphCell) parent).getChildren();
+ else
+ list = roots;
+ }
+
+ return list;
+ }
+ }
+
+ //
+ // Static Methods
+ //
+
+ /**
+ * Returns a deep clone of the specified cell, including all children.
+ */
+ public static Object cloneCell(GraphModel model, Object cell) {
+ Map clones = model.cloneCells(getDescendants(model, new Object[] { cell }).toArray());
+
+ return clones.get(cell);
+ }
+
+ /**
+ * Returns a deep clone of the specified cells, including all children.
+ */
+ public static Object[] cloneCell(GraphModel model, Object[] cells) {
+ Map clones = model.cloneCells(getDescendants(model, cells).toArray());
+
+ for (int i = 0; i < cells.length; i++) {
+ cells[i] = clones.get(cells[i]);
+ }
+
+ return cells;
+ }
+
+ /**
+ * Helper methods that connects the source of <code>edge</code> to
+ * <code>port</code> in <code>model</model>.
+ */
+ public static void setSourcePort(GraphModel model, Object edge, Object port) {
+ model.edit(null, new ConnectionSet(edge, port, true), null, null);
+ }
+
+ /**
+ * Helper methods that connects the source of <code>edge</code> to
+ * <code>port</code> in <code>model</model>.
+ */
+ public static void setTargetPort(GraphModel model, Object edge, Object port) {
+ model.edit(null, new ConnectionSet(edge, port, false), null, null);
+ }
+
+ /**
+ * Returns the source vertex of the edge by calling getParent on getSource
+ * on the specified model.
+ */
+ public static Object getSourceVertex(GraphModel model, Object edge) {
+ if (model != null)
+ return model.getParent(model.getSource(edge));
+
+ return null;
+ }
+
+ /**
+ * Returns the target vertex of the edge by calling getParent on getTarget
+ * on the specified model.
+ */
+ public static Object getTargetVertex(GraphModel model, Object edge) {
+ if (model != null)
+ return model.getParent(model.getTarget(edge));
+
+ return null;
+ }
+
+ /**
+ * @return Returns the user object of the given cell. This implementation
+ * checks if the cell is a default mutable tree node and returns
+ * it's user object.
+ *
+ * @deprecated Use {@link GraphModel#getValue(Object)} instead.
+ */
+ public static Object getUserObject(Object cell) {
+ if (cell instanceof DefaultMutableTreeNode)
+ return ((DefaultMutableTreeNode) cell).getUserObject();
+
+ return null;
+ }
+
+ /**
+ * Checks whether the cell has at least one child which is not a port. This
+ * implementation operates on the model, not taking into account visibility
+ * of cells. It returns true for groups regardless of their folded state.
+ *
+ * @param cell
+ * the cell to check for being a group
+ * @return Returns true if the cell contains at least one cell which is not
+ * a port
+ */
+ public static boolean isGroup(GraphModel model, Object cell) {
+ for (int i = 0; i < model.getChildCount(cell); i++) {
+ if (!model.isPort(model.getChild(cell, i)))
+ return true;
+ }
+
+ return false;
+ }
+
+ /**
+ * Returns all cells of the model in an array.
+ *
+ * @see #getDescendants(GraphModel, Object[])
+ *
+ * @return Returns all cells in the model including all descandants.
+ */
+ public static Object[] getAll(GraphModel model) {
+ return getDescendants(model, getRoots(model)).toArray();
+ }
+
+ /**
+ * Returns the roots of the specified model as an array. This implementation
+ * uses the GraphModel interface in the general case, but if the model is a
+ * <code>DefaultGraphModel</code> the performance can be improved to
+ * linear time.
+ */
+ public static Object[] getRoots(GraphModel model) {
+ Object[] cells = null;
+
+ if (model != null) {
+ // If model is DefaultGraphModel, we can do a linear time getRoots
+ if (model instanceof DefaultGraphModel) {
+ cells = ((DefaultGraphModel) model).getRoots().toArray();
+ } else {
+ cells = new Object[model.getRootCount()];
+
+ for (int i = 0; i < cells.length; i++) {
+ cells[i] = model.getRootAt(i);
+ }
+ }
+ }
+
+ return cells;
+ }
+
+ /**
+ * Returns the roots in <code>cells</code> by checking if their parent is
+ * <code>null</code>. This implementation only uses the GraphModel
+ * interface. This method never returns null.
+ */
+ public static Object[] getRoots(GraphModel model, Object[] cells) {
+ List roots = new ArrayList();
+
+ if (cells != null) {
+ for (int i = 0; i < cells.length; i++) {
+ if (model.getParent(cells[i]) == null) {
+ roots.add(cells[i]);
+ }
+ }
+ }
+
+ return roots.toArray();
+ }
+
+ /**
+ * @return Returns the roots of cells, eg. an array that contains no cell
+ * having an ancestor in cells.
+ */
+ public static Object[] getTopmostCells(GraphModel model, Object[] cells) {
+ Set cellSet = new HashSet();
+
+ for (int i = 0; i < cells.length; i++)
+ cellSet.add(cells[i]);
+
+ List parents = new ArrayList();
+
+ for (int i = 0; i < cells.length; i++) {
+ if (!hasAncestorIn(model, cellSet, cells[i]))
+ parents.add(cells[i]);
+ }
+
+ return parents.toArray();
+ }
+
+ /**
+ * Returns true if the specified child has an ancestor in parents.
+ */
+ public static boolean hasAncestorIn(GraphModel model, Set parents, Object child) {
+ Object parent = model.getParent(child);
+
+ while (parent != null) {
+ if (parents.contains(parent))
+ return true;
+
+ parent = model.getParent(parent);
+ }
+
+ return false;
+ }
+
+ /**
+ * Flattens the given array of root cells by adding the roots and their
+ * descandants. The resulting set contains all cells, which means it
+ * contains branches <strong>and </strong> leafs. Note: This is an iterative
+ * implementation. No recursion used. <br>
+ * Note: This returns a linked list, for frequent read operations you should
+ * turn this into an array, or at least an array list.
+ */
+ public static List getDescendants(GraphModel model, Object[] cells) {
+ if (cells != null) {
+ Stack stack = new Stack();
+
+ for (int i = cells.length - 1; i >= 0; i--)
+ stack.add(cells[i]);
+
+ LinkedList result = new LinkedList();
+
+ while (!stack.isEmpty()) {
+ Object tmp = stack.pop();
+
+ for (int i = model.getChildCount(tmp) - 1; i >= 0; i--)
+ stack.add(model.getChild(tmp, i));
+
+ if (tmp != null)
+ result.add(tmp);
+ }
+
+ return result;
+ }
+
+ return null;
+ }
+
+ /**
+ * Orders cells so that they reflect the model order.
+ */
+ public static Object[] order(GraphModel model, Object[] cells) {
+ if (cells != null) {
+ Set cellSet = new HashSet();
+
+ for (int i = 0; i < cells.length; i++)
+ cellSet.add(cells[i]);
+
+ Stack stack = new Stack();
+
+ for (int i = model.getRootCount() - 1; i >= 0; i--)
+ stack.add(model.getRootAt(i));
+
+ LinkedList result = new LinkedList();
+
+ while (!stack.isEmpty()) {
+ Object tmp = stack.pop();
+
+ for (int i = model.getChildCount(tmp) - 1; i >= 0; i--)
+ stack.add(model.getChild(tmp, i));
+
+ if (cellSet.remove(tmp))
+ result.add(tmp);
+ }
+
+ return result.toArray();
+ }
+
+ return null;
+ }
+
+ /**
+ * Returns the set of all connected edges to <code>cells</code> or their
+ * descendants. The passed-in cells are never returned as part of the result
+ * set. This can be used on vertices, edges and ports.
+ */
+ public static Set getEdges(GraphModel model, Object[] cells) {
+ Set result = new HashSet();
+
+ if (cells != null) {
+ // We know the minimum initial capacity of this set is cells.length
+ // We assume the cell has one port at a minimum
+ int setSize = ((int) (cells.length * 1.33) + 1);
+ Set allCells = new HashSet(setSize, 0.75f);
+
+ for (int i = 0; i < cells.length; i++) {
+ allCells.add(cells[i]);
+ }
+
+ // Include descendants
+ allCells.addAll(getDescendants(model, cells));
+
+ if (allCells != null) {
+ Iterator it = allCells.iterator();
+
+ while (it.hasNext()) {
+ Iterator edges = model.edges(it.next());
+
+ while (edges.hasNext())
+ result.add(edges.next());
+ }
+
+ for (int i = 0; i < cells.length; i++)
+ result.remove(cells[i]);
+ }
+ }
+
+ return result;
+ }
+
+ /**
+ * @return Returns the opposite port or vertex in <code>edge</code>.
+ */
+ public static Object getOpposite(GraphModel model, Object edge, Object cell) {
+ boolean isPort = model.isPort(cell);
+ Object source = (isPort) ? model.getSource(edge) : getSourceVertex(model, edge);
+
+ if (cell == source)
+ return (isPort) ? model.getTarget(edge) : getTargetVertex(model, edge);
+ else
+
+ return source;
+ }
+
+ /**
+ * Returns true if the given vertices are conntected by a single edge in
+ * this document.
+ */
+ public static boolean containsEdgeBetween(GraphModel model, Object v1, Object v2) {
+ Object[] edges = getEdgesBetween(model, v1, v2, false);
+
+ return ((edges != null) && (edges.length > 0));
+ }
+
+ /**
+ * Returns the edges between two specified ports or two specified vertices.
+ * If directed is true then <code>cell1</code> must be the source of the
+ * returned edges. This method never returns null. If there are no edges
+ * between the specified cells, then an array of length 0 is returned.
+ */
+ public static Object[] getEdgesBetween(GraphModel model, Object cell1, Object cell2,
+ boolean directed) {
+ boolean isPort1 = model.isPort(cell1);
+ boolean isPort2 = model.isPort(cell2);
+ ArrayList result = new ArrayList();
+ Set edges = DefaultGraphModel.getEdges(model, new Object[] { cell1 });
+ Iterator it = edges.iterator();
+
+ while (it.hasNext()) {
+ Object edge = it.next();
+
+ // TODO: Handle edge groups
+ Object source = (isPort1) ? model.getSource(edge) : getSourceVertex(model, edge);
+ Object target = (isPort2) ? model.getTarget(edge) : getTargetVertex(model, edge);
+
+ if (((source == cell1) && (target == cell2))
+ || (!directed && (source == cell2) && (target == cell1)))
+ result.add(edge);
+ }
+
+ return result.toArray();
+ }
+
+ /**
+ * Returns the outgoing edges for cell. Cell should be a port or a vertex.
+ */
+ public static Object[] getOutgoingEdges(GraphModel model, Object cell) {
+ return getEdges(model, cell, false);
+ }
+
+ /**
+ * Returns the incoming edges for cell. Cell should be a port or a vertex.
+ */
+ public static Object[] getIncomingEdges(GraphModel model, Object cell) {
+ return getEdges(model, cell, true);
+ }
+
+ /**
+ * Returns the incoming or outgoing edges for cell. Cell should be a port or
+ * a vertex.
+ */
+ public static Object[] getEdges(GraphModel model, Object cell, boolean incoming) {
+ Set edges = DefaultGraphModel.getEdges(model, new Object[] { cell });
+
+ // Base initial capacity on size of set, it can't be any larger
+ ArrayList result = new ArrayList(edges.size());
+ Iterator it = edges.iterator();
+
+ while (it.hasNext()) {
+ Object edge = it.next();
+
+ // TODO: Handle edge groups
+ Object port = (incoming) ? model.getTarget(edge) : model.getSource(edge);
+ Object parent = model.getParent(port);
+
+ if ((port == cell) || (parent == cell))
+ result.add(edge);
+ }
+
+ return result.toArray();
+ }
+
+ /**
+ * Returns <code>true</code> if <code>vertex</code> is a valid vertex.
+ *
+ * @return <code>true</code> if <code>vertex</code> is a valid vertex.
+ */
+ public static boolean isVertex(GraphModel model, Object vertex) {
+ return (!model.isEdge(vertex) && !model.isPort(vertex));
+ }
+
+ // Serialization support
+ private void readObject(ObjectInputStream s) throws IOException, ClassNotFoundException {
+ s.defaultReadObject();
+ listenerList = new EventListenerList();
+ emptyIterator = new EmptyIterator();
+ }
+
+ public static class EmptyIterator implements Iterator, Serializable {
+ public boolean hasNext() {
+ return false;
+ }
+
+ public Object next() {
+ return null;
+ }
+
+ public void remove() {
+ // nop
+ }
+ }
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/DefaultGraphSelectionModel.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/DefaultGraphSelectionModel.java
new file mode 100644
index 0000000..820787d
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/DefaultGraphSelectionModel.java
@@ -0,0 +1,710 @@
+/*
+ * @(#)DefaultGraphSelectionModel.java 1.0 03-JUL-04
+ *
+ * Copyright (c) 2001-2004 Gaudenz Alder
+ *
+ */
+package org.jgraph.graph;
+
+import org.jgraph.JGraph;
+
+import org.jgraph.event.GraphSelectionEvent;
+import org.jgraph.event.GraphSelectionListener;
+
+import java.beans.PropertyChangeListener;
+
+import java.io.Serializable;
+
+import java.util.ArrayList;
+import java.util.EventListener;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Stack;
+import java.util.Vector;
+
+import javax.swing.event.EventListenerList;
+import javax.swing.event.SwingPropertyChangeSupport;
+
+
+/**
+ * Default implementation of GraphSelectionModel. Listeners are notified
+ *
+ * @version 1.0 1/1/02
+ * @author Gaudenz Alder
+ */
+public class DefaultGraphSelectionModel implements GraphSelectionModel, Cloneable, Serializable {
+ /** Property name for selectionMode. */
+ public static final String SELECTION_MODE_PROPERTY = "selectionMode";
+
+ /** Value that represents selected state in cellStates. */
+ public static final int SELECTED = -1;
+
+ /** Object value that represents the unselected state in cellStates. */
+ public static final Integer UNSELECTED = new Integer(0);
+
+ /** Reference to the parent graph. Used to find parents and childs. */
+ protected JGraph graph;
+
+ /** Used to message registered listeners. */
+ protected SwingPropertyChangeSupport changeSupport;
+
+ /** Event listener list. */
+ protected EventListenerList listenerList = new EventListenerList();
+
+ /**
+ * Mode for the selection, will be either SINGLE_TREE_SELECTION,
+ * CONTIGUOUS_TREE_SELECTION or DISCONTIGUOUS_TREE_SELECTION.
+ */
+ protected int selectionMode;
+
+ /** Boolean that indicates if the model allows stepping-into groups. */
+ protected boolean childrenSelectable = true;
+
+ /** Maps the cells to their selection state. */
+ protected Map cellStates = new Hashtable();
+
+ /** List that contains the selected items. */
+ protected List selection = new ArrayList();
+
+ /** Constructs a DefaultGraphSelectionModel for the specified graph. */
+ public DefaultGraphSelectionModel(JGraph graph) {
+ this.graph = graph;
+ }
+
+ /**
+ * Sets the selection mode, which must be one of SINGLE_TREE_SELECTION,
+ */
+ public void setSelectionMode(int mode) {
+ int oldMode = selectionMode;
+
+ selectionMode = mode;
+
+ if ((selectionMode != GraphSelectionModel.MULTIPLE_GRAPH_SELECTION)
+ && (selectionMode != GraphSelectionModel.SINGLE_GRAPH_SELECTION))
+ selectionMode = GraphSelectionModel.MULTIPLE_GRAPH_SELECTION;
+
+ if ((oldMode != selectionMode) && (changeSupport != null))
+ changeSupport.firePropertyChange(SELECTION_MODE_PROPERTY, new Integer(oldMode),
+ new Integer(selectionMode));
+ }
+
+ /**
+ * Returns the selection mode, one of <code>SINGLE_TREE_SELECTION</code>,
+ * <code>DISCONTIGUOUS_TREE_SELECTION</code> or
+ * <code>CONTIGUOUS_TREE_SELECTION</code>.
+ */
+ public int getSelectionMode() {
+ return selectionMode;
+ }
+
+ /**
+ * Sets if the selection model allows the selection of children.
+ */
+ public void setChildrenSelectable(boolean flag) {
+ childrenSelectable = flag;
+ }
+
+ /**
+ * Returns true if the selection model allows the selection of children.
+ */
+ public boolean isChildrenSelectable() {
+ return childrenSelectable;
+ }
+
+ /**
+ * Hook for subclassers for fine-grained control over stepping-into cells.
+ * This implementation returns <code>childrenSelectable</code>&&
+ * isCellSelected.
+ */
+ protected boolean isChildrenSelectable(Object cell) {
+ AttributeMap attr = graph.getModel().getAttributes(cell);
+
+ if ((attr != null) && childrenSelectable)
+ return GraphConstants.isChildrenSelectable(attr);
+
+ return childrenSelectable;
+ }
+
+ /**
+ * Selects the specified cell.
+ *
+ * @param cell
+ * the cell to select
+ */
+ public void setSelectionCell(Object cell) {
+ if (cell == null)
+ setSelectionCells(null);
+ else
+ setSelectionCells(new Object[] { cell });
+ }
+
+ /**
+ * Sets the selection to <code>cells</code>. If this represents a change
+ * the GraphSelectionListeners are notified. Potentially paths will be held
+ * by this object; in other words don't change any of the objects in the
+ * array once passed in.
+ *
+ * @param cells
+ * new selection
+ */
+ public void setSelectionCells(Object[] cells) {
+ if (cells != null) {
+ if ((selectionMode == GraphSelectionModel.SINGLE_GRAPH_SELECTION) && (cells.length > 0))
+ cells = new Object[] { cells[cells.length - 1] };
+
+ cellStates.clear();
+
+ Vector change = new Vector();
+ List newSelection = new ArrayList();
+
+ for (int i = 0; i < cells.length; i++) {
+ if (cells[i] != null) {
+ selection.remove(cells[i]);
+ change.addElement(new CellPlaceHolder(cells[i], !selection.remove(cells[i])));
+ select(newSelection, cells[i]);
+
+ Object parent = graph.getModel().getParent(cells[i]);
+
+ if (parent != null)
+ change.addElement(new CellPlaceHolder(parent, false));
+ }
+ }
+
+ Iterator it = selection.iterator();
+
+ while (it.hasNext()) {
+ Object cell = it.next();
+
+ while (cell != null) {
+ change.addElement(new CellPlaceHolder(cell, false));
+ cell = graph.getModel().getParent(cell);
+ }
+ }
+
+ selection = newSelection;
+
+ if (change.size() > 0) {
+ notifyCellChange(change);
+ }
+ }
+ }
+
+ /**
+ * Adds the specified cell to the current selection
+ *
+ * @param cell
+ * the cell to add to the current selection
+ */
+ public void addSelectionCell(Object cell) {
+ if (cell != null)
+ addSelectionCells(new Object[] { cell });
+ }
+
+ /**
+ * Adds cells to the current selection.
+ *
+ * @param cells
+ * the cells to be added to the current selection
+ */
+ public void addSelectionCells(Object[] cells) {
+ if (cells != null) {
+ if (selectionMode == GraphSelectionModel.SINGLE_GRAPH_SELECTION)
+ setSelectionCells(cells);
+ else {
+ Vector change = new Vector();
+
+ for (int i = 0; i < cells.length; i++) {
+ if (cells[i] != null) {
+ boolean newness = select(selection, cells[i]);
+
+ if (newness) {
+ change.addElement(new CellPlaceHolder(cells[i], true));
+
+ Object parent = graph.getModel().getParent(cells[i]);
+
+ if (parent != null)
+ change.addElement(new CellPlaceHolder(parent, false));
+ }
+ }
+ }
+
+ if (change.size() > 0)
+ notifyCellChange(change);
+ }
+ }
+ }
+
+ /**
+ * Removes the specified cell from the selection.
+ *
+ * @param cell
+ * the cell to remove from the current selection
+ */
+ public void removeSelectionCell(Object cell) {
+ if (cell != null)
+ removeSelectionCells(new Object[] { cell });
+ }
+
+ /**
+ * Removes the specified cells from the selection.
+ *
+ * @param cells
+ * the cells to remove from the current selection
+ */
+ public void removeSelectionCells(Object[] cells) {
+ if (cells != null) {
+ Vector change = new Vector();
+
+ for (int i = 0; i < cells.length; i++) {
+ if (cells[i] != null) {
+ boolean removed = deselect(cells[i]);
+
+ if (removed) {
+ change.addElement(new CellPlaceHolder(cells[i], false));
+
+ Object parent = graph.getModel().getParent(cells[i]);
+
+ if (parent != null)
+ change.addElement(new CellPlaceHolder(parent, false));
+ }
+ }
+ }
+
+ if (change.size() > 0)
+ notifyCellChange(change);
+ }
+ }
+
+ /**
+ * Returns the cells that are currently selectable. The array is ordered so
+ * that the top-most cell appears first. <br>
+ */
+ public Object[] getSelectables() {
+ if (isChildrenSelectable()) {
+ List result = new ArrayList();
+
+ // Roots Are Always Selectable
+ Stack s = new Stack();
+ GraphModel model = graph.getModel();
+
+ for (int i = 0; i < model.getRootCount(); i++)
+ s.add(model.getRootAt(i));
+
+ while (!s.isEmpty()) {
+ Object cell = s.pop();
+ AttributeMap attrs = graph.getAttributes(cell);
+
+ if (!model.isPort(cell) && ((attrs == null) || GraphConstants.isSelectable(attrs)))
+ result.add(cell);
+
+ if (isChildrenSelectable(cell)) {
+ for (int i = 0; i < model.getChildCount(cell); i++)
+ s.add(model.getChild(cell, i));
+ }
+ }
+
+ return result.toArray();
+ }
+
+ return graph.getRoots();
+ }
+
+ /**
+ * Returns the first cell in the selection. This is useful if there if only
+ * one item currently selected.
+ */
+ public Object getSelectionCell() {
+ if ((selection != null) && (selection.size() > 0))
+ return selection.toArray()[0];
+
+ return null;
+ }
+
+ /**
+ * Returns the cells in the selection. This will return null (or an empty
+ * array) if nothing is currently selected.
+ */
+ public Object[] getSelectionCells() {
+ if (selection != null)
+ return selection.toArray();
+
+ return null;
+ }
+
+ /**
+ * Returns the number of paths that are selected.
+ */
+ public int getSelectionCount() {
+ return (selection == null) ? 0 : selection.size();
+ }
+
+ /**
+ * Returns true if the cell, <code>cell</code>, is in the current
+ * selection.
+ */
+ public boolean isCellSelected(Object cell) {
+ int count = getSelectedChildCount(cell);
+
+ return (count == SELECTED);
+ }
+
+ /**
+ * Returns true if the cell, <code>cell</code>, has selected children.
+ */
+ public boolean isChildrenSelected(Object cell) {
+ int count = getSelectedChildCount(cell);
+
+ return (count > 0);
+ }
+
+ /**
+ * Returns true if the selection is currently empty.
+ */
+ public boolean isSelectionEmpty() {
+ return (selection.isEmpty());
+ }
+
+ /**
+ * Empties the current selection. If this represents a change in the current
+ * selection, the selection listeners are notified.
+ */
+ public void clearSelection() {
+ if (selection != null) {
+ Vector change = new Vector();
+ Iterator it = cellStates.entrySet().iterator();
+
+ while (it.hasNext()) {
+ Map.Entry entry = (Map.Entry) it.next();
+ Object cell = entry.getKey();
+
+ while (cell != null) {
+ change.addElement(new CellPlaceHolder(cell, false));
+ cell = graph.getModel().getParent(cell);
+ }
+ }
+
+ selection.clear();
+ cellStates.clear();
+
+ if (change.size() > 0)
+ notifyCellChange(change);
+ }
+ }
+
+ //
+ // Internal Datastructures
+ //
+
+ /**
+ * Returns the number of selected childs for <code>cell</code>.
+ */
+ protected int getSelectedChildCount(Object cell) {
+ if (cell != null) {
+ Integer state = (Integer) cellStates.get(cell);
+
+ if (state == null) {
+ state = UNSELECTED;
+ cellStates.put(cell, state);
+ }
+
+ return state.intValue();
+ }
+
+ return 0;
+ }
+
+ /**
+ * Sets the number of selected childs for <code>cell</code> to
+ * <code>count</code>.
+ */
+ protected void setSelectedChildCount(Object cell, int count) {
+ Integer i = new Integer(count);
+ cellStates.put(cell, i);
+ }
+
+ /**
+ * Selects a single cell and updates all datastructures. No listeners are
+ * notified. Override this method to control individual cell selection.
+ */
+ protected boolean select(List list, Object cell) {
+ AttributeMap attrs = graph.getAttributes(cell);
+
+ if (!isCellSelected(cell) && graph.getGraphLayoutCache().isVisible(cell)
+ && ((attrs == null) || GraphConstants.isSelectable(attrs))) {
+ GraphModel model = graph.getModel();
+
+ // Deselect and Update All Parents
+ Object parent = model.getParent(cell);
+
+ while (parent != null) {
+ int count = getSelectedChildCount(parent);
+
+ // Deselect Selected Parents
+ if (count == SELECTED)
+ count = 0;
+
+ // Increase Child Count
+ count++;
+ setSelectedChildCount(parent, count);
+ // Remove From Selection
+ selection.remove(parent);
+ // Next Parent
+ parent = model.getParent(parent);
+ }
+
+ // Deselect All Children
+ Object[] tmp = new Object[] { cell };
+ List childs = DefaultGraphModel.getDescendants(model, tmp);
+ // Remove Current Cell From Flat-View
+ childs.remove(cell);
+
+ Iterator it = childs.iterator();
+
+ while (it.hasNext()) {
+ Object child = it.next();
+
+ if ((child != null) && !model.isPort(child)) {
+ // Remove Child From Selection
+ selection.remove(child);
+ // Remove Child State
+ cellStates.remove(child);
+ }
+ }
+
+ // Set Selected State for Current
+ setSelectedChildCount(cell, SELECTED);
+
+ // Add Current To HashSet and Return
+ return list.add(cell);
+ }
+
+ return false;
+ }
+
+ /**
+ * Deselects a single cell and updates all datastructures. No listeners are
+ * notified.
+ */
+ protected boolean deselect(Object cell) {
+ if (isCellSelected(cell)) {
+ // Update All Parents
+ Object parent = graph.getModel().getParent(cell);
+ boolean firstParent = true;
+ int change = -1;
+
+ while ((parent != null) && (change != 0)) {
+ int count = getSelectedChildCount(parent);
+ count += change;
+
+ // Select First Parent If No More Children
+ if ((count == 0) && firstParent) {
+ change = 0;
+ count = SELECTED;
+ selection.add(parent);
+ }
+
+ // Update Selection Count
+ setSelectedChildCount(parent, count);
+ // Next Parent
+ parent = graph.getModel().getParent(parent);
+ firstParent = false;
+ }
+
+ // Remove State of Current Cell
+ cellStates.remove(cell);
+
+ // Remove Current from Selection and Return
+ return selection.remove(cell);
+ }
+
+ return false;
+ }
+
+ //
+ // Listeners
+ //
+
+ /**
+ * Adds x to the list of listeners that are notified each time the set of
+ * selected TreePaths changes.
+ *
+ * @param x
+ * the new listener to be added
+ */
+ public void addGraphSelectionListener(GraphSelectionListener x) {
+ listenerList.add(GraphSelectionListener.class, x);
+ }
+
+ /**
+ * Removes x from the list of listeners that are notified each time the set
+ * of selected TreePaths changes.
+ *
+ * @param x
+ * the listener to remove
+ */
+ public void removeGraphSelectionListener(GraphSelectionListener x) {
+ listenerList.remove(GraphSelectionListener.class, x);
+ }
+
+ /**
+ * Notifies all listeners that are registered for tree selection events on
+ * this object.
+ *
+ * @see #addGraphSelectionListener
+ * @see EventListenerList
+ */
+ protected void fireValueChanged(GraphSelectionEvent e) {
+ // Guaranteed to return a non-null array
+ Object[] listeners = listenerList.getListenerList();
+
+ // TreeSelectionEvent e = null;
+ // Process the listeners last to first, notifying
+ // those that are interested in this event
+ for (int i = listeners.length - 2; i >= 0; i -= 2) {
+ if (listeners[i] == GraphSelectionListener.class) {
+ // Lazily create the event:
+ // if (e == null)
+ // e = new ListSelectionEvent(this, firstIndex, lastIndex);
+ ((GraphSelectionListener) listeners[i + 1]).valueChanged(e);
+ }
+ }
+ }
+
+ /**
+ * Returns an array of all the listeners of the given type that were added
+ * to this model.
+ *
+ * @return all of the objects receiving <em>listenerType</em>
+ * notifications from this model
+ *
+ * @since 1.3
+ */
+ public EventListener[] getListeners(Class listenerType) {
+ return listenerList.getListeners(listenerType);
+ }
+
+ /**
+ * Adds a PropertyChangeListener to the listener list. The listener is
+ * registered for all properties.
+ * <p>
+ * A PropertyChangeEvent will get fired when the selection mode changes.
+ *
+ * @param listener
+ * the PropertyChangeListener to be added
+ */
+ public synchronized void addPropertyChangeListener(PropertyChangeListener listener) {
+ if (changeSupport == null) {
+ changeSupport = new SwingPropertyChangeSupport(this);
+ }
+
+ changeSupport.addPropertyChangeListener(listener);
+ }
+
+ /**
+ * Removes a PropertyChangeListener from the listener list. This removes a
+ * PropertyChangeListener that was registered for all properties.
+ *
+ * @param listener
+ * the PropertyChangeListener to be removed
+ */
+ public synchronized void removePropertyChangeListener(PropertyChangeListener listener) {
+ if (changeSupport == null) {
+ return;
+ }
+
+ changeSupport.removePropertyChangeListener(listener);
+ }
+
+ /**
+ * Notifies listeners of a change in path. <code>changePaths</code> should
+ * contain instances of PathPlaceHolder.
+ */
+ protected void notifyCellChange(Vector changedCells) {
+ int cCellCount = changedCells.size();
+ boolean[] newness = new boolean[cCellCount];
+ Object[] cells = new Object[cCellCount];
+ CellPlaceHolder placeholder;
+
+ for (int counter = 0; counter < cCellCount; counter++) {
+ placeholder = (CellPlaceHolder) changedCells.elementAt(counter);
+ newness[counter] = placeholder.isNew;
+ cells[counter] = placeholder.cell;
+ }
+
+ GraphSelectionEvent event = new GraphSelectionEvent(this, cells, newness);
+
+ fireValueChanged(event);
+ }
+
+ /**
+ * Returns a clone of this object with the same selection. This method does
+ * not duplicate selection listeners and property listeners.
+ *
+ * @exception CloneNotSupportedException
+ * never thrown by instances of this class
+ */
+ public Object clone() throws CloneNotSupportedException {
+ DefaultGraphSelectionModel clone = (DefaultGraphSelectionModel) super.clone();
+ clone.changeSupport = null;
+
+ if (selection != null)
+ clone.selection = new ArrayList(selection);
+
+ clone.listenerList = new EventListenerList();
+
+ return clone;
+ }
+
+ /**
+ * Holds a path and whether or not it is new.
+ */
+ protected class CellPlaceHolder {
+ protected boolean isNew;
+ protected Object cell;
+
+ protected CellPlaceHolder(Object cell, boolean isNew) {
+ this.cell = cell;
+ this.isNew = isNew;
+ }
+
+ /**
+ * Returns the cell.
+ *
+ * @return Object
+ */
+ public Object getCell() {
+ return cell;
+ }
+
+ /**
+ * Returns the isNew.
+ *
+ * @return boolean
+ */
+ public boolean isNew() {
+ return isNew;
+ }
+
+ /**
+ * Sets the cell.
+ *
+ * @param cell
+ * The cell to set
+ */
+ public void setCell(Object cell) {
+ this.cell = cell;
+ }
+
+ /**
+ * Sets the isNew.
+ *
+ * @param isNew
+ * The isNew to set
+ */
+ public void setNew(boolean isNew) {
+ this.isNew = isNew;
+ }
+ }
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/DefaultPort.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/DefaultPort.java
new file mode 100644
index 0000000..b189455
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/DefaultPort.java
@@ -0,0 +1,120 @@
+/*
+ * Copyright (c) 2001-2006 Gaudenz Alder
+ *
+ * See LICENSE file in distribution for licensing details of this source file
+ */
+package org.jgraph.graph;
+
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.Set;
+
+
+/**
+ * A simple implementation for a port.
+ *
+ * @version 1.0 1/1/02
+ * @author Gaudenz Alder
+ */
+public class DefaultPort extends DefaultGraphCell implements Port {
+ /** Edges that are connected to the port */
+ // TODO After Java 1.3 is EOL, this could be changed into a LinkHashSet
+ // to retain ordering
+ protected HashSet edges = new HashSet(4, 0.75f);
+
+ /** Reference to the anchor of this port */
+ protected Port anchor;
+
+ /**
+ * Constructs an empty port.
+ */
+ public DefaultPort() {
+ this(null, null);
+ }
+
+ /**
+ * Constructs a port that holds a reference to the specified user object.
+ *
+ * @param userObject reference to the user object
+ */
+ public DefaultPort(Object userObject) {
+ this(userObject, null);
+ }
+
+ /**
+ * Constructs a port that holds a reference to the specified user object
+ * and a reference to the specified anchor.
+ *
+ * @param userObject reference to the user object
+ * @param anchor reference to a graphcell that constitutes the anchor
+ */
+ public DefaultPort(Object userObject, Port anchor) {
+ super(userObject);
+ setAllowsChildren(false);
+ this.anchor = anchor;
+ }
+
+ /**
+ * Returns an iterator of the edges connected
+ * to the port.
+ */
+ public Iterator edges() {
+ return edges.iterator();
+ }
+
+ /**
+ * Adds <code>edge</code> to the list of edges.
+ */
+ public boolean addEdge(Object edge) {
+ return edges.add(edge);
+ }
+
+ /**
+ * Removes <code>edge</code> from the list of edges.
+ */
+ public boolean removeEdge(Object edge) {
+ return edges.remove(edge);
+ }
+
+ /**
+ * Returns the collection of edges connected to this port.
+ */
+ public Set getEdges() {
+ return new HashSet(edges);
+ }
+
+ /**
+ * Sets the collection of edges connected to this port.
+ */
+ public void setEdges(Set edges) {
+ this.edges = new HashSet(edges);
+ }
+
+ /**
+ * Returns the anchor of this port.
+ */
+ public Port getAnchor() {
+ return anchor;
+ }
+
+ /**
+ * Sets the anchor of this port.
+ */
+ public void setAnchor(Port port) {
+ anchor = port;
+ }
+
+ /**
+ * Create a clone of the cell. The cloning of the
+ * user object is deferred to the cloneUserObject()
+ * method.
+ *
+ * @return Object a clone of this object.
+ */
+ public Object clone() {
+ DefaultPort c = (DefaultPort) super.clone();
+ c.edges = new HashSet();
+
+ return c;
+ }
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/DefaultRealEditor.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/DefaultRealEditor.java
new file mode 100644
index 0000000..7f51049
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/DefaultRealEditor.java
@@ -0,0 +1,79 @@
+/*
+ * @(#)DefaultCellEditor.java 1.0 03-JUL-04
+ *
+ * Copyright (c) 2001-2004 Gaudenz Alder
+ *
+ */
+package org.jgraph.graph;
+
+import org.jgraph.JGraph;
+
+import java.awt.Component;
+
+import javax.swing.DefaultCellEditor;
+import javax.swing.JCheckBox;
+import javax.swing.JComboBox;
+import javax.swing.JTextField;
+
+
+/**
+ * The default editor for graph cells.
+ *
+ * @version 1.0 1/1/02
+ * @author Gaudenz Alder
+ */
+public class DefaultRealEditor extends DefaultCellEditor implements GraphCellEditor {
+ //
+ // Constructors
+ //
+ /**
+ * Constructs a DefaultCellEditor that uses a text field.
+ *
+ * @param textField
+ * a JTextField object used as the editor
+ */
+ public DefaultRealEditor(final JTextField textField) {
+ super(textField);
+ setClickCountToStart(1);
+ }
+
+ /**
+ * Constructs a DefaultCellEditor object that uses a check box.
+ *
+ * @param checkBox
+ * a JCheckBox object
+ */
+ public DefaultRealEditor(final JCheckBox checkBox) {
+ super(checkBox);
+ }
+
+ /**
+ * Constructs a DefaultCellEditor object that uses a combo box.
+ *
+ * @param comboBox
+ * a JComboBox object
+ */
+ public DefaultRealEditor(final JComboBox comboBox) {
+ super(comboBox);
+ }
+
+ //
+ /**
+ * DOCUMENT ME!
+ *
+ * @param graph DOCUMENT ME!
+ * @param value DOCUMENT ME!
+ * @param isSelected DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Component getGraphCellEditorComponent(JGraph graph, Object value, boolean isSelected) {
+ String stringValue = graph.convertValueToString(value);
+ delegate.setValue(stringValue);
+
+ if (editorComponent instanceof JTextField)
+ ((JTextField) editorComponent).selectAll();
+
+ return editorComponent;
+ }
+} // End of class JCellEditor
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/Edge.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/Edge.java
new file mode 100644
index 0000000..315b45b
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/Edge.java
@@ -0,0 +1,62 @@
+/*
+ * @(#)Edge.java 1.0 03-JUL-04
+ *
+ * Copyright (c) 2001-2004 Gaudenz Alder
+ *
+ */
+package org.jgraph.graph;
+
+import java.io.Serializable;
+
+import java.util.List;
+
+
+/**
+ * Defines the requirements for an object that represents an Edge in a
+ * GraphModel.
+ *
+ * @version 1.0 1/1/02
+ * @author Gaudenz Alder
+ */
+public interface Edge extends GraphCell {
+ /**
+ * Returns the source of the edge.
+ */
+ Object getSource();
+
+ /**
+ * Returns the target of the edge.
+ */
+ Object getTarget();
+
+ /**
+ * Sets the source of the edge.
+ */
+ void setSource(Object port);
+
+ /**
+ * Returns the target of <code>edge</code>.
+ */
+ void setTarget(Object port);
+
+ //
+ // Routing
+ //
+ public static interface Routing extends Serializable {
+ public static final int NO_PREFERENCE = -1;
+
+ /**
+ * Returns the points to be used for the edge.
+ *
+ * @param edge
+ * The edge view to route the points for.
+ */
+ public List route(EdgeView edge);
+
+ /**
+ * Returns the preferred line style for this routing. A return value of
+ * {@link #NO_PREFERENCE} means no preference.
+ */
+ public int getPreferredLineStyle(EdgeView edge);
+ }
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/EdgeRenderer.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/EdgeRenderer.java
new file mode 100644
index 0000000..e6d442f
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/EdgeRenderer.java
@@ -0,0 +1,1142 @@
+/*
+ * @(#)EdgeRenderer.java 1.0 03-JUL-04
+ *
+ * Copyright (c) 2001-2005 Gaudenz Alder
+ *
+ * See LICENSE file in distribution for licensing details of this source file
+ */
+package org.jgraph.graph;
+
+import org.jgraph.JGraph;
+
+import java.awt.BasicStroke;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.GradientPaint;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.Polygon;
+import java.awt.Rectangle;
+import java.awt.RenderingHints;
+import java.awt.Shape;
+import java.awt.geom.Ellipse2D;
+import java.awt.geom.GeneralPath;
+import java.awt.geom.Point2D;
+import java.awt.geom.Rectangle2D;
+import java.awt.image.BufferedImage;
+
+import java.io.Serializable;
+
+import java.util.Map;
+
+import javax.swing.JComponent;
+import javax.swing.UIManager;
+
+
+//import org.jgraph.util.Bezier;
+//import org.jgraph.util.Spline2D;
+
+/**
+ * This renderer displays entries that implement the CellView interface.
+ *
+ * @version 1.0 1/1/02
+ * @author Gaudenz Alder
+ */
+public class EdgeRenderer extends JComponent implements CellViewRenderer, Serializable {
+ /** Static Graphics used for Font Metrics */
+ protected static transient Graphics fontGraphics;
+
+ static {
+ try {
+ fontGraphics = new BufferedImage(1, 1, BufferedImage.TYPE_INT_RGB).getGraphics();
+ } catch (Error e) {
+ // No font graphics
+ fontGraphics = null;
+ }
+ }
+
+ /** A switch for painting the extra labels */
+ public boolean simpleExtraLabels = true;
+
+ /** Override this if you want the extra labels to appear in a special fontJ */
+ public Font extraLabelFont = null;
+
+ /** Reference to the font metrics of the above */
+ protected transient FontMetrics metrics;
+
+ /** Cache the current graph for drawing */
+ protected transient JGraph graph;
+
+ /** Cache the current edgeview for drawing */
+ protected transient EdgeView view;
+
+ /** Painting attributes of the current edgeview */
+ protected transient int beginDeco;
+
+ /** Painting attributes of the current edgeview */
+ protected transient int endDeco;
+
+ /** Painting attributes of the current edgeview */
+ protected transient int beginSize;
+
+ /** Painting attributes of the current edgeview */
+ protected transient int endSize;
+
+ /** Painting attributes of the current edgeview */
+ protected transient int lineStyle;
+
+ /** Width of the current edge view */
+ protected transient float lineWidth;
+
+ /**
+ * Boolean attributes of the current edgeview. Fill flags are checked for
+ * valid decorations.
+ */
+ protected transient boolean labelBorder;
+
+ /**
+ * Boolean attributes of the current edgeview. Fill flags are checked for
+ * valid decorations.
+ */
+ protected transient boolean beginFill;
+
+ /**
+ * Boolean attributes of the current edgeview. Fill flags are checked for
+ * valid decorations.
+ */
+ protected transient boolean endFill;
+
+ /**
+ * Boolean attributes of the current edgeview. Fill flags are checked for
+ * valid decorations.
+ */
+ protected transient boolean focus;
+
+ /**
+ * Boolean attributes of the current edgeview. Fill flags are checked for
+ * valid decorations.
+ */
+ protected transient boolean selected;
+
+ /**
+ * Boolean attributes of the current edgeview. Fill flags are checked for
+ * valid decorations.
+ */
+ protected transient boolean preview;
+
+ /**
+ * Boolean attributes of the current edgeview. Fill flags are checked for
+ * valid decorations.
+ */
+ protected transient boolean opaque;
+
+ /**
+ * Boolean attributes of the current edgeview. Fill flags are checked for
+ * valid decorations.
+ */
+ protected transient boolean childrenSelected;
+
+ /**
+ * Boolean attributes of the current edgeview. Fill flags are checked for
+ * valid decorations.
+ */
+ protected transient boolean labelTransformEnabled;
+
+ /**
+ * Color attributes of the current edgeview. This components foreground is
+ * set to the edgecolor, the fontColor is in an extra variable. If the
+ * fontColor is null, the current foreground is used. The default background
+ * instead is used for text and is not visible if the label is not visible
+ * or if opaque is true.
+ */
+ protected transient Color borderColor;
+
+ /**
+ * Color attributes of the current edgeview. This components foreground is
+ * set to the edgecolor, the fontColor is in an extra variable. If the
+ * fontColor is null, the current foreground is used. The default background
+ * instead is used for text and is not visible if the label is not visible
+ * or if opaque is true.
+ */
+ protected transient Color defaultForeground;
+
+ /**
+ * Color attributes of the current edgeview. This components foreground is
+ * set to the edgecolor, the fontColor is in an extra variable. If the
+ * fontColor is null, the current foreground is used. The default background
+ * instead is used for text and is not visible if the label is not visible
+ * or if opaque is true.
+ */
+ protected transient Color defaultBackground;
+
+ /**
+ * Color attributes of the current edgeview. This components foreground is
+ * set to the edgecolor, the fontColor is in an extra variable. If the
+ * fontColor is null, the current foreground is used. The default background
+ * instead is used for text and is not visible if the label is not visible
+ * or if opaque is true.
+ */
+ protected transient Color fontColor;
+
+ /** Contains the current dash pattern. Null means no pattern. */
+ protected transient float[] lineDash;
+
+ /** Contains the current dash offset. Null means no offset. */
+ protected transient float dashOffset = 0.0f;
+
+ /** The gradient color of the edge */
+ protected transient Color gradientColor = null;
+
+ /* THIS CODE WAS ADDED BY MARTIN KRUEGER 10/20/2003 */
+
+ // protected Bezier bezier;
+
+ // protected Spline2D spline;
+
+ /* END */
+
+ /**
+ * Constructs a renderer that may be used to render edges.
+ */
+ public EdgeRenderer() {
+ defaultForeground = UIManager.getColor("Tree.textForeground");
+ defaultBackground = UIManager.getColor("Tree.textBackground");
+ }
+
+ /**
+ * Sets view to work with, caching necessary values until the next call of
+ * this method or until some other methods with explicitly specified
+ * different view
+ */
+ void setView(CellView value) {
+ if (value instanceof EdgeView) {
+ view = (EdgeView) value;
+ installAttributes(view);
+ } else {
+ view = null;
+ }
+ }
+
+ /**
+ * Configure and return the renderer based on the passed in components. The
+ * value is typically set from messaging the graph with
+ * <code>convertValueToString</code>.
+ *
+ * @param graph
+ * the graph that that defines the rendering context.
+ * @param view
+ * the cell view that should be rendered.
+ * @param sel
+ * whether the object is selected.
+ * @param focus
+ * whether the object has the focus.
+ * @param preview
+ * whether we are drawing a preview.
+ * @return the component used to render the value.
+ */
+ public Component getRendererComponent(JGraph graph, CellView view, boolean sel, boolean focus,
+ boolean preview) {
+ if (view instanceof EdgeView && (graph != null)) {
+ this.graph = graph;
+ this.focus = focus;
+ this.selected = sel;
+ this.preview = preview;
+ this.childrenSelected = graph.getSelectionModel().isChildrenSelected(view.getCell());
+ setView(view);
+
+ return this;
+ }
+
+ return null;
+ }
+
+ /**
+ * Returns true if the edge shape intersects the given rectangle.
+ */
+ public boolean intersects(JGraph graph, CellView value, Rectangle rect) {
+ if (value instanceof EdgeView && (graph != null) && (value != null)) {
+ setView(value);
+
+ // If we have two control points, we can get rid of hit
+ // detection on do an intersection test on the two diagonals
+ // of rect and the line between the two points
+ EdgeView edgeView = (EdgeView) value;
+
+ if (edgeView.getPointCount() == 2) {
+ Point2D p0 = edgeView.getPoint(0);
+ Point2D p1 = edgeView.getPoint(1);
+
+ if (rect.intersectsLine(p0.getX(), p0.getY(), p1.getX(), p1.getY()))
+ return true;
+ } else {
+ Graphics2D g2 = (Graphics2D) graph.getGraphics();
+
+ if (g2.hit(rect, view.getShape(), true))
+ return true;
+ }
+
+ Rectangle2D r = getLabelBounds(graph, view);
+
+ if ((r != null) && r.intersects(rect))
+ return true;
+
+ Object[] labels = GraphConstants.getExtraLabels(view.getAllAttributes());
+
+ if (labels != null) {
+ for (int i = 0; i < labels.length; i++) {
+ r = getExtraLabelBounds(graph, view, i);
+
+ if ((r != null) && r.intersects(rect))
+ return true;
+ }
+ }
+ }
+
+ return false;
+ }
+
+ /**
+ * Returns the bounds of the edge shape.
+ */
+ public Rectangle2D getBounds(CellView value) {
+ if (value instanceof EdgeView && (value != null)) {
+ // No need to call setView as getPaintBounds will
+ view = (EdgeView) value;
+
+ Rectangle2D r = getPaintBounds(view);
+ Rectangle2D rect = getLabelBounds(graph, view);
+
+ if (rect != null)
+ Rectangle2D.union(r, rect, r);
+
+ Object[] labels = GraphConstants.getExtraLabels(view.getAllAttributes());
+
+ if (labels != null) {
+ for (int i = 0; i < labels.length; i++) {
+ rect = getExtraLabelBounds(graph, view, i);
+
+ if (rect != null)
+ Rectangle2D.union(r, rect, r);
+ }
+ }
+
+ int b = (int) Math.ceil(lineWidth);
+ r.setFrame(r.getX() - b, r.getY() - b, r.getWidth() + (2 * b), r.getHeight() + (2 * b));
+
+ return r;
+ }
+
+ return null;
+ }
+
+ private boolean isLabelTransformEnabled() {
+ return labelTransformEnabled;
+ }
+
+ /**
+ * Estimates whether the transform for label should be applied. With the
+ * transform, the label will be painted along the edge. To apply transform,
+ * rotate graphics by the angle returned from {@link #getLabelAngle}
+ *
+ * @return true, if transform can be applied, false otherwise
+ */
+ private boolean isLabelTransform(String label) {
+ if (!isLabelTransformEnabled()) {
+ return false;
+ }
+
+ Point2D p = getLabelPosition(view);
+
+ if ((p != null) && (label != null) && (label.length() > 0)) {
+ int sw = metrics.stringWidth(label);
+ Point2D p1 = view.getPoint(0);
+ Point2D p2 = view.getPoint(view.getPointCount() - 1);
+ double length = Math.sqrt(((p2.getX() - p1.getX()) * (p2.getX() - p1.getX()))
+ + ((p2.getY() - p1.getY()) * (p2.getY() - p1.getY())));
+
+ if (!((length <= Double.NaN) || (length < sw))) {
+ return true;
+ }
+ }
+
+ return false;
+ }
+
+ /**
+ * Calculates the angle at which graphics should be rotated to paint label
+ * along the edge. Before calling this method always check that transform
+ * should be applied using {@linkisLabelTransform}
+ *
+ * @return the value of the angle, 0 if the angle is zero or can't be
+ * calculated
+ */
+ private double getLabelAngle(String label) {
+ Point2D p = getLabelPosition(view);
+ double angle = 0;
+
+ if ((p != null) && (label != null) && (label.length() > 0)) {
+ int sw = metrics.stringWidth(label);
+
+ // Note: For control points you may want to choose other
+ // points depending on the segment the label is in.
+ Point2D p1 = view.getPoint(0);
+ Point2D p2 = view.getPoint(view.getPointCount() - 1);
+
+ // Length of the edge
+ double length = Math.sqrt(((p2.getX() - p1.getX()) * (p2.getX() - p1.getX()))
+ + ((p2.getY() - p1.getY()) * (p2.getY() - p1.getY())));
+
+ // Label fits into edge's length
+ if (!((length <= Double.NaN) || (length < sw))) {
+ // To calculate projections of edge
+ double cos = (p2.getX() - p1.getX()) / length;
+ double sin = (p2.getY() - p1.getY()) / length;
+
+ // Determine angle
+ angle = Math.acos(cos);
+
+ // Second half
+ if (sin < 0) {
+ angle = (2 * Math.PI) - angle;
+ }
+ }
+
+ if ((angle > (Math.PI / 2)) && (angle <= ((Math.PI * 3) / 2))) {
+ angle -= Math.PI;
+ }
+ }
+
+ return angle;
+ }
+
+ /**
+ * Returns the label bounds of the specified view in the given graph.
+ */
+ public Rectangle2D getLabelBounds(JGraph paintingContext, EdgeView view) {
+ if ((paintingContext == null) && (graph != null))
+ paintingContext = graph;
+
+ // No need to call setView as getLabelPosition will
+ String label = (paintingContext != null) ? paintingContext.convertValueToString(view)
+ : String.valueOf(view.getCell());
+
+ if (label != null) {
+ Point2D p = getLabelPosition(view);
+ Dimension d = getLabelSize(view, label);
+
+ return getLabelBounds(p, d, label);
+ } else {
+ return null;
+ }
+ }
+
+ /**
+ * Returns the label bounds of the specified view in the given graph. Note:
+ * The index is the position of the String object for the label in the extra
+ * labels array of the view.
+ */
+ public Rectangle2D getExtraLabelBounds(JGraph paintingContext, EdgeView view, int index) {
+ if ((paintingContext == null) && (graph != null))
+ paintingContext = graph;
+
+ setView(view);
+
+ Object[] labels = GraphConstants.getExtraLabels(view.getAllAttributes());
+
+ if ((labels != null) && (index < labels.length)) {
+ Point2D p = getExtraLabelPosition(this.view, index);
+ Dimension d = getExtraLabelSize(paintingContext, this.view, index);
+ String label = (paintingContext != null)
+ ? paintingContext.convertValueToString(labels[index])
+ : String.valueOf(labels[index]);
+
+ return getLabelBounds(p, d, label);
+ }
+
+ return new Rectangle2D.Double(getX(), getY(), 0, 0);
+ }
+
+ /**
+ * Returns the label bounds of the specified view in the given graph.
+ */
+ public Rectangle2D getLabelBounds(Point2D p, Dimension d, String label) {
+ if ((label != null) && isLabelTransform(label)) {
+ // With transform label is rotated, so we should
+ // rotate the rectangle (sw, sh) and return the
+ // bounding rectangle
+ double angle = getLabelAngle(label);
+
+ if (angle < 0)
+ angle = -angle;
+
+ if (angle > (Math.PI / 2))
+ angle %= (Math.PI / 2);
+
+ double yside = Math.abs((Math.cos(angle) * d.height) + (Math.sin(angle) * d.width));
+ double xside = Math.abs((d.width * Math.cos(angle)) + (d.height * Math.sin(angle)));
+
+ // Getting maximum is not good, but I don't want to be
+ // drown in calculations
+ if (xside > yside)
+ yside = xside;
+
+ if (yside > xside)
+ xside = yside;
+
+ angle = getLabelAngle(label);
+
+ // Increasing by height is safe, but I think the precise
+ // value is font.descent layed on edge vector and
+ // projected on each axis
+ d.width = (int) xside + d.height;
+ d.height = (int) yside + d.height;
+ }
+
+ if ((p != null) && (d != null)) {
+ double x = Math.max(0, p.getX() - (d.width / 2));
+ double y = Math.max(0, p.getY() - (d.height / 2));
+
+ return new Rectangle2D.Double(x, y, d.width + 1, d.height + 1);
+ }
+
+ return null;
+ }
+
+ /**
+ * Returns the label position of the specified view in the given graph.
+ */
+ public Point2D getLabelPosition(EdgeView view) {
+ setView(view);
+
+ return getLabelPosition(view.getLabelPosition());
+ }
+
+ /**
+ * Returns the label position of the specified view in the given graph.
+ */
+ public Point2D getExtraLabelPosition(EdgeView view, int index) {
+ setView(view);
+
+ Point2D[] pts = GraphConstants.getExtraLabelPositions(view.getAllAttributes());
+
+ if ((pts != null) && (index < pts.length))
+ return getLabelPosition(pts[index]);
+
+ return null;
+ }
+
+ /**
+ * Returns the label position of the specified view in the given graph.
+ */
+ protected Point2D getLabelPosition(Point2D pos) {
+ Rectangle2D tmp = getPaintBounds(view);
+ int unit = GraphConstants.PERMILLE;
+ Point2D p0 = view.getPoint(0);
+
+ if ((pos != null) && (tmp != null)) {
+ Point2D vector = view.getLabelVector();
+ double dx = vector.getX();
+ double dy = vector.getY();
+ double len = Math.sqrt((dx * dx) + (dy * dy));
+
+ if (len > 0) {
+ double x = p0.getX() + ((dx * pos.getX()) / unit);
+ double y = p0.getY() + ((dy * pos.getX()) / unit);
+ x += ((-dy * pos.getY()) / len);
+ y += ((dx * pos.getY()) / len);
+
+ return new Point2D.Double(x, y);
+ } else {
+ return new Point2D.Double(p0.getX() + pos.getX(), p0.getY() + pos.getY());
+ }
+ }
+
+ return null;
+ }
+
+ /**
+ * Returns the label size of the specified view in the given graph.
+ */
+ public Dimension getExtraLabelSize(JGraph paintingContext, EdgeView view, int index) {
+ Object[] labels = GraphConstants.getExtraLabels(view.getAllAttributes());
+
+ if ((labels != null) && (index < labels.length)) {
+ String label = (paintingContext != null)
+ ? paintingContext.convertValueToString(labels[index])
+ : String.valueOf(labels[index]);
+
+ return getLabelSize(view, label);
+ }
+
+ return null;
+ }
+
+ /**
+ * Returns the label size of the specified view in the given graph.
+ */
+ public Dimension getLabelSize(EdgeView view, String label) {
+ if ((label != null) && (fontGraphics != null)) {
+ fontGraphics.setFont(GraphConstants.getFont(view.getAllAttributes()));
+ metrics = fontGraphics.getFontMetrics();
+
+ int sw = metrics.stringWidth(label);
+ int sh = metrics.getHeight();
+
+ return new Dimension(sw, sh);
+ }
+
+ return null;
+ }
+
+ /**
+ * Installs the attributes of specified cell in this renderer instance. This
+ * means, retrieve every published key from the cells hashtable and set
+ * global variables or superclass properties accordingly.
+ *
+ * @param view
+ * the cell view to retrieve the attribute values from.
+ */
+ protected void installAttributes(CellView view) {
+ Map map = view.getAllAttributes();
+ beginDeco = GraphConstants.getLineBegin(map);
+ beginSize = GraphConstants.getBeginSize(map);
+ beginFill = GraphConstants.isBeginFill(map) && isFillable(beginDeco);
+ endDeco = GraphConstants.getLineEnd(map);
+ endSize = GraphConstants.getEndSize(map);
+ endFill = GraphConstants.isEndFill(map) && isFillable(endDeco);
+ lineWidth = GraphConstants.getLineWidth(map);
+
+ Edge.Routing routing = GraphConstants.getRouting(map);
+ lineStyle = ((routing != null) && view instanceof EdgeView)
+ ? routing.getPreferredLineStyle((EdgeView) view) : Edge.Routing.NO_PREFERENCE;
+
+ if (lineStyle == Edge.Routing.NO_PREFERENCE)
+ lineStyle = GraphConstants.getLineStyle(map);
+
+ lineDash = GraphConstants.getDashPattern(map);
+ dashOffset = GraphConstants.getDashOffset(map);
+ borderColor = GraphConstants.getBorderColor(map);
+
+ Color foreground = GraphConstants.getLineColor(map);
+ setForeground((foreground != null) ? foreground : defaultForeground);
+
+ Color background = GraphConstants.getBackground(map);
+ setBackground((background != null) ? background : defaultBackground);
+
+ Color gradientColor = GraphConstants.getGradientColor(map);
+ setGradientColor(gradientColor);
+ setOpaque(GraphConstants.isOpaque(map));
+ setFont(GraphConstants.getFont(map));
+
+ Color tmp = GraphConstants.getForeground(map);
+ fontColor = (tmp != null) ? tmp : getForeground();
+ labelTransformEnabled = GraphConstants.isLabelAlongEdge(map);
+ }
+
+ protected boolean isFillable(int decoration) {
+ return !((decoration == GraphConstants.ARROW_SIMPLE)
+ || (decoration == GraphConstants.ARROW_LINE)
+ || (decoration == GraphConstants.ARROW_DOUBLELINE));
+ }
+
+ /**
+ * Returns the bounds of the edge shape without label
+ */
+ public Rectangle2D getPaintBounds(EdgeView view) {
+ Rectangle2D rec = null;
+ setView(view);
+
+ if (view.getShape() != null)
+ rec = view.getShape().getBounds();
+ else
+ rec = new Rectangle2D.Double(0, 0, 0, 0);
+
+ return rec;
+ }
+
+ /**
+ * Paint the renderer.
+ */
+ public void paint(Graphics g) {
+ if (view.isLeaf()) {
+ Shape edgeShape = view.getShape();
+
+ // Sideeffect: beginShape, lineShape, endShape
+ if (edgeShape != null) {
+ Graphics2D g2 = (Graphics2D) g;
+ g2.setRenderingHint(RenderingHints.KEY_STROKE_CONTROL,
+ RenderingHints.VALUE_STROKE_PURE);
+
+ int c = BasicStroke.CAP_BUTT;
+ int j = BasicStroke.JOIN_MITER;
+ setOpaque(false);
+ super.paint(g);
+ translateGraphics(g);
+ g.setColor(getForeground());
+
+ if (lineWidth > 0) {
+ g2.setStroke(new BasicStroke(lineWidth, c, j));
+
+ if ((gradientColor != null) && !preview) {
+ g2.setPaint(new GradientPaint(0, 0, getBackground(), getWidth(),
+ getHeight(), gradientColor, true));
+ }
+
+ if (view.beginShape != null) {
+ if (beginFill)
+ g2.fill(view.beginShape);
+
+ g2.draw(view.beginShape);
+ }
+
+ if (view.endShape != null) {
+ if (endFill)
+ g2.fill(view.endShape);
+
+ g2.draw(view.endShape);
+ }
+
+ if (lineDash != null) // Dash For Line Only
+ g2.setStroke(new BasicStroke(lineWidth, c, j, 10.0f, lineDash, dashOffset));
+
+ if (view.lineShape != null)
+ g2.draw(view.lineShape);
+ }
+
+ if (selected) { // Paint Selected
+ g2.setStroke(GraphConstants.SELECTION_STROKE);
+ g2.setColor(graph.getHighlightColor());
+
+ if (view.beginShape != null)
+ g2.draw(view.beginShape);
+
+ if (view.lineShape != null)
+ g2.draw(view.lineShape);
+
+ if (view.endShape != null)
+ g2.draw(view.endShape);
+ }
+
+ g2.setStroke(new BasicStroke(1));
+ g.setFont((extraLabelFont != null) ? extraLabelFont : getFont());
+
+ Object[] labels = GraphConstants.getExtraLabels(view.getAllAttributes());
+
+ if (labels != null) {
+ for (int i = 0; i < labels.length; i++)
+ paintLabel(g, graph.convertValueToString(labels[i]),
+ getExtraLabelPosition(view, i), false || !simpleExtraLabels);
+ }
+
+ if (graph.getEditingCell() != view.getCell()) {
+ g.setFont(getFont());
+
+ Object label = graph.convertValueToString(view);
+
+ if (label != null) {
+ paintLabel(g, label.toString(), getLabelPosition(view), true);
+ }
+ }
+ }
+ } else {
+ paintSelectionBorder(g);
+ }
+ }
+
+ /**
+ * Provided for subclassers to paint a selection border.
+ */
+ protected void paintSelectionBorder(Graphics g) {
+ ((Graphics2D) g).setStroke(GraphConstants.SELECTION_STROKE);
+
+ if (childrenSelected)
+ g.setColor(graph.getGridColor());
+ else if (focus && selected)
+ g.setColor(graph.getLockedHandleColor());
+ else if (selected)
+ g.setColor(graph.getHighlightColor());
+
+ if (childrenSelected || selected) {
+ Dimension d = getSize();
+ g.drawRect(0, 0, d.width - 1, d.height - 1);
+ }
+ }
+
+ // This if for subclassers that to not want the graphics
+ // to be relative to the top, left corner of this component.
+ // Note: Override this method with an empty implementation
+ // if you want absolute positions for your edges
+ protected void translateGraphics(Graphics g) {
+ g.translate(-getX(), -getY());
+ }
+
+ /**
+ * Paint the specified label for the current edgeview.
+ */
+ protected void paintLabel(Graphics g, String label, Point2D p, boolean mainLabel) {
+ if ((p != null) && (label != null) && (label.length() > 0) && (metrics != null)) {
+ int sw = metrics.stringWidth(label);
+ int sh = metrics.getHeight();
+ Graphics2D g2 = (Graphics2D) g;
+ boolean applyTransform = isLabelTransform(label);
+ double angle = 0;
+ int dx = -sw / 2;
+ int offset = (graph.isMoveBelowZero() || applyTransform) ? 0
+ : Math.min(0,
+ (int) (dx
+ + p.getX()));
+
+ g2.translate(p.getX() - offset, p.getY());
+
+ if (applyTransform) {
+ angle = getLabelAngle(label);
+ g2.rotate(angle);
+ }
+
+ if (isOpaque() && mainLabel) {
+ g.setColor(getBackground());
+ g.fillRect((int) ((-sw / 2) - 1), (int) ((-sh / 2) - 1), sw + 2, sh + 2);
+ }
+
+ if ((borderColor != null) && mainLabel) {
+ g.setColor(borderColor);
+ g.drawRect((int) ((-sw / 2) - 1), (int) ((-sh / 2) - 1), sw + 2, sh + 2);
+ }
+
+ int dy = +sh / 4;
+ g.setColor(fontColor);
+
+ if (applyTransform && (borderColor == null) && !isOpaque()) {
+ // Shift label perpendicularly by the descent so it
+ // doesn't cross the line.
+ dy = -metrics.getDescent();
+ }
+
+ g.drawString(label, dx, dy);
+
+ if (applyTransform) {
+ // Undo the transform
+ g2.rotate(-angle);
+ }
+
+ g2.translate(-p.getX() + offset, -p.getY());
+ }
+ }
+
+ /**
+ * Returns the shape that represents the current edge in the context of the
+ * current graph. This method sets the global beginShape, lineShape and
+ * endShape variables as a side-effect.
+ */
+ protected Shape createShape() {
+ int n = view.getPointCount();
+
+ if (n > 1) {
+ // Following block may modify static vars as side effect (Flyweight
+ // Design)
+ EdgeView tmp = view;
+ Point2D[] p = null;
+ p = new Point2D[n];
+
+ for (int i = 0; i < n; i++) {
+ Point2D pt = tmp.getPoint(i);
+
+ if (pt == null)
+ return null; // exit
+
+ p[i] = new Point2D.Double(pt.getX(), pt.getY());
+ }
+
+ // End of Side-Effect Block
+ // Undo Possible MT-Side Effects
+ if (view != tmp) {
+ view = tmp;
+ installAttributes(view);
+ }
+
+ // End of Undo
+ if (view.sharedPath == null) {
+ view.sharedPath = new GeneralPath(GeneralPath.WIND_NON_ZERO, n);
+ } else {
+ view.sharedPath.reset();
+ }
+
+ view.beginShape = view.lineShape = view.endShape = null;
+
+ Point2D p0 = p[0];
+ Point2D pe = p[n - 1];
+ Point2D p1 = p[1];
+ Point2D p2 = p[n - 2];
+
+ /*
+ if (lineStyle == GraphConstants.STYLE_BEZIER && n > 2) {
+ bezier = new Bezier(p);
+ p2 = bezier.getPoint(bezier.getPointCount() - 1);
+ } else if (lineStyle == GraphConstants.STYLE_SPLINE && n > 2) {
+ spline = new Spline2D(p);
+ double[] point = spline.getPoint(0.9875);
+ // Extrapolate p2 away from the end point, pe, to avoid integer
+ // rounding errors becoming too large when creating the line end
+ double scaledX = pe.getX() - ((pe.getX() - point[0]) * 128);
+ double scaledY = pe.getY() - ((pe.getY() - point[1]) * 128);
+ p2.setLocation(scaledX, scaledY);
+ }
+ */
+ if (beginDeco != GraphConstants.ARROW_NONE) {
+ view.beginShape = createLineEnd(beginSize, beginDeco, p1, p0);
+ }
+
+ if (endDeco != GraphConstants.ARROW_NONE) {
+ view.endShape = createLineEnd(endSize, endDeco, p2, pe);
+ }
+
+ view.sharedPath.moveTo((float) p0.getX(), (float) p0.getY());
+
+ /* THIS CODE WAS ADDED BY MARTIN KRUEGER 10/20/2003 */
+ /*
+ if (lineStyle == GraphConstants.STYLE_BEZIER && n > 2) {
+ Point2D[] b = bezier.getPoints();
+ view.sharedPath.quadTo((float) b[0].getX(),
+ (float) b[0].getY(), (float) p1.getX(), (float) p1
+ .getY());
+ for (int i = 2; i < n - 1; i++) {
+ Point2D b0 = b[2 * i - 3];
+ Point2D b1 = b[2 * i - 2];
+ view.sharedPath.curveTo((float) b0.getX(), (float) b0
+ .getY(), (float) b1.getX(), (float) b1.getY(),
+ (float) p[i].getX(), (float) p[i].getY());
+ }
+ view.sharedPath.quadTo((float) b[b.length - 1].getX(),
+ (float) b[b.length - 1].getY(),
+ (float) p[n - 1].getX(), (float) p[n - 1].getY());
+ } else if (lineStyle == GraphConstants.STYLE_SPLINE && n > 2) {
+ for (double t = 0; t <= 1; t += 0.0125) {
+ double[] xy = spline.getPoint(t);
+ view.sharedPath.lineTo((float) xy[0], (float) xy[1]);
+ }
+ }
+ */
+
+ /* END */
+ //else {
+ for (int i = 1; i < (n - 1); i++)
+ view.sharedPath.lineTo((float) p[i].getX(), (float) p[i].getY());
+
+ view.sharedPath.lineTo((float) pe.getX(), (float) pe.getY());
+ // }
+ view.sharedPath.moveTo((float) pe.getX(), (float) pe.getY());
+
+ if ((view.endShape == null) && (view.beginShape == null)) {
+ // With no end decorations the line shape is the same as the
+ // shared path and memory
+ view.lineShape = view.sharedPath;
+ } else {
+ view.lineShape = (GeneralPath) view.sharedPath.clone();
+
+ if (view.endShape != null)
+ view.sharedPath.append(view.endShape, true);
+
+ if (view.beginShape != null)
+ view.sharedPath.append(view.beginShape, true);
+ }
+
+ return view.sharedPath;
+ }
+
+ return null;
+ }
+
+ /**
+ * Paint the current view's direction. Sets tmpPoint as a side-effect such
+ * that the invoking method can use it to determine the connection point to
+ * this decoration.
+ */
+ protected Shape createLineEnd(int size, int style, Point2D src, Point2D dst) {
+ if ((src == null) || (dst == null))
+ return null;
+
+ int d = (int) Math.max(1, dst.distance(src));
+ int ax = (int) -((size * (dst.getX() - src.getX())) / d);
+ int ay = (int) -((size * (dst.getY() - src.getY())) / d);
+
+ if (style == GraphConstants.ARROW_DIAMOND) {
+ Polygon poly = new Polygon();
+ poly.addPoint((int) dst.getX(), (int) dst.getY());
+ poly.addPoint((int) (dst.getX() + (ax / 2) + (ay / 3)),
+ (int) ((dst.getY() + (ay / 2)) - (ax / 3)));
+
+ Point2D last = (Point2D) dst.clone();
+ dst.setLocation(dst.getX() + ax, dst.getY() + ay);
+ poly.addPoint((int) dst.getX(), (int) dst.getY());
+ poly.addPoint((int) ((last.getX() + (ax / 2)) - (ay / 3)),
+ (int) (last.getY() + (ay / 2) + (ax / 3)));
+
+ return poly;
+ } else if ((style == GraphConstants.ARROW_TECHNICAL)
+ || (style == GraphConstants.ARROW_CLASSIC)) {
+ Polygon poly = new Polygon();
+ poly.addPoint((int) dst.getX(), (int) dst.getY());
+ poly.addPoint((int) (dst.getX() + ax + (ay / 2)), (int) ((dst.getY() + ay) - (ax / 2)));
+
+ Point2D last = (Point2D) dst.clone();
+
+ if (style == GraphConstants.ARROW_CLASSIC) {
+ dst.setLocation((int) (dst.getX() + ((ax * 2) / 3)),
+ (int) (dst.getY() + ((ay * 2) / 3)));
+ poly.addPoint((int) dst.getX(), (int) dst.getY());
+ } else if (style == GraphConstants.ARROW_DIAMOND) {
+ dst.setLocation(dst.getX() + (2 * ax), dst.getY() + (2 * ay));
+ poly.addPoint((int) dst.getX(), (int) dst.getY());
+ } else
+ dst.setLocation((int) (dst.getX() + ax), (int) (dst.getY() + ay));
+
+ poly.addPoint((int) ((last.getX() + ax) - (ay / 2)), (int) (last.getY() + ay + (ax / 2)));
+
+ return poly;
+ } else if (style == GraphConstants.ARROW_SIMPLE) {
+ GeneralPath path = new GeneralPath(GeneralPath.WIND_NON_ZERO, 4);
+ path.moveTo((float) (dst.getX() + ax + (ay / 2)), (float) ((dst.getY() + ay) - (ax / 2)));
+ path.lineTo((float) dst.getX(), (float) dst.getY());
+ path.lineTo((float) ((dst.getX() + ax) - (ay / 2)), (float) (dst.getY() + ay + (ax / 2)));
+
+ return path;
+ } else if (style == GraphConstants.ARROW_CIRCLE) {
+ Ellipse2D ellipse = new Ellipse2D.Float((float) ((dst.getX() + (ax / 2)) - (size / 2)),
+ (float) ((dst.getY() + (ay / 2)) - (size / 2)),
+ size, size);
+ dst.setLocation(dst.getX() + ax, dst.getY() + ay);
+
+ return ellipse;
+ } else if ((style == GraphConstants.ARROW_LINE)
+ || (style == GraphConstants.ARROW_DOUBLELINE)) {
+ GeneralPath path = new GeneralPath(GeneralPath.WIND_NON_ZERO, 4);
+ path.moveTo((float) (dst.getX() + (ax / 2) + (ay / 2)),
+ (float) ((dst.getY() + (ay / 2)) - (ax / 2)));
+ path.lineTo((float) ((dst.getX() + (ax / 2)) - (ay / 2)),
+ (float) (dst.getY() + (ay / 2) + (ax / 2)));
+
+ if (style == GraphConstants.ARROW_DOUBLELINE) {
+ path.moveTo((float) (dst.getX() + (ax / 3) + (ay / 2)),
+ (float) ((dst.getY() + (ay / 3)) - (ax / 2)));
+ path.lineTo((float) ((dst.getX() + (ax / 3)) - (ay / 2)),
+ (float) (dst.getY() + (ay / 3) + (ax / 2)));
+ }
+
+ return path;
+ }
+
+ return null;
+ }
+
+ /**
+ * @return Returns the gradientColor.
+ */
+ public Color getGradientColor() {
+ return gradientColor;
+ }
+
+ /**
+ * @param gradientColor
+ * The gradientColor to set.
+ */
+ public void setGradientColor(Color gradientColor) {
+ this.gradientColor = gradientColor;
+ }
+
+ /**
+ * Overridden for performance reasons. See the <a
+ * href="#override">Implementation Note </a> for more information.
+ */
+ public void validate() {
+ }
+
+ /**
+ * Overridden for performance reasons. See the <a
+ * href="#override">Implementation Note </a> for more information.
+ */
+ public void revalidate() {
+ }
+
+ /**
+ * Overridden for performance reasons. See the <a
+ * href="#override">Implementation Note </a> for more information.
+ */
+ public void repaint(long tm, int x, int y, int width, int height) {
+ }
+
+ /**
+ * Overridden for performance reasons. See the <a
+ * href="#override">Implementation Note </a> for more information.
+ */
+ public void repaint(Rectangle r) {
+ }
+
+ /**
+ * Overridden for performance reasons. See the <a
+ * href="#override">Implementation Note </a> for more information.
+ */
+ protected void firePropertyChange(String propertyName, Object oldValue, Object newValue) {
+ // Strings get interned...
+ if (propertyName == "text")
+ super.firePropertyChange(propertyName, oldValue, newValue);
+ }
+
+ /**
+ * Overridden for performance reasons. See the <a
+ * href="#override">Implementation Note </a> for more information.
+ */
+ public void firePropertyChange(String propertyName, byte oldValue, byte newValue) {
+ }
+
+ /**
+ * Overridden for performance reasons. See the <a
+ * href="#override">Implementation Note </a> for more information.
+ */
+ public void firePropertyChange(String propertyName, char oldValue, char newValue) {
+ }
+
+ /**
+ * Overridden for performance reasons. See the <a
+ * href="#override">Implementation Note </a> for more information.
+ */
+ public void firePropertyChange(String propertyName, short oldValue, short newValue) {
+ }
+
+ /**
+ * Overridden for performance reasons. See the <a
+ * href="#override">Implementation Note </a> for more information.
+ */
+ public void firePropertyChange(String propertyName, int oldValue, int newValue) {
+ }
+
+ /**
+ * Overridden for performance reasons. See the <a
+ * href="#override">Implementation Note </a> for more information.
+ */
+ public void firePropertyChange(String propertyName, long oldValue, long newValue) {
+ }
+
+ /**
+ * Overridden for performance reasons. See the <a
+ * href="#override">Implementation Note </a> for more information.
+ */
+ public void firePropertyChange(String propertyName, float oldValue, float newValue) {
+ }
+
+ /**
+ * Overridden for performance reasons. See the <a
+ * href="#override">Implementation Note </a> for more information.
+ */
+ public void firePropertyChange(String propertyName, double oldValue, double newValue) {
+ }
+
+ /**
+ * Overridden for performance reasons. See the <a
+ * href="#override">Implementation Note </a> for more information.
+ */
+ public void firePropertyChange(String propertyName, boolean oldValue, boolean newValue) {
+ }
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/EdgeView.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/EdgeView.java
new file mode 100644
index 0000000..248611a
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/EdgeView.java
@@ -0,0 +1,1374 @@
+/*
+ * @(#)EdgeView.java 1.0 03-JUL-04
+ *
+ * Copyright (c) 2001-2004 Gaudenz Alder
+ *
+ */
+package org.jgraph.graph;
+
+import org.jgraph.JGraph;
+
+import org.jgraph.plaf.GraphUI;
+import org.jgraph.plaf.basic.BasicGraphUI;
+
+import java.awt.Cursor;
+import java.awt.Dimension;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.Point;
+import java.awt.Rectangle;
+import java.awt.Shape;
+import java.awt.event.MouseEvent;
+import java.awt.geom.AffineTransform;
+import java.awt.geom.GeneralPath;
+import java.awt.geom.Line2D;
+import java.awt.geom.Point2D;
+import java.awt.geom.Rectangle2D;
+
+import java.io.Serializable;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+
+import javax.swing.SwingUtilities;
+
+
+/**
+ * The default implementation of an edge view. The getEdgeRenderer method
+ * assumes a renderer of type EdgeRenderer. If you provide a custom renderer to
+ * a subclass, you must also override the methods that call this method, namely:
+ * getShape, getLabelBounds, getExtraLabelBounds, intersects and getBounds.
+ *
+ * @version 1.0 1/1/02
+ * @author Gaudenz Alder
+ */
+public class EdgeView extends AbstractCellView {
+ /** Renderer for the class. */
+ public static transient EdgeRenderer renderer = new EdgeRenderer();
+
+ /** List of points of the edge. May contain ports. */
+ protected List points;
+
+ /** Cached source and target portview of the edge. */
+ protected CellView source;
+
+ /** Cached source and target portview of the edge. */
+ protected CellView target;
+ protected CellView sourceParentView;
+ protected CellView targetParentView;
+
+ /** Cached label position of the edge. */
+ protected Point2D labelPosition;
+ protected Point2D[] extraLabelPositions;
+ protected transient Rectangle2D cachedLabelBounds = null;
+ protected transient Rectangle2D[] cachedExtraLabelBounds = null;
+ protected transient Point2D labelVector = null;
+
+ /** Drawing attributes that are created on the fly */
+ public transient Shape beginShape;
+
+ /** Drawing attributes that are created on the fly */
+ public transient Shape endShape;
+
+ /** Drawing attributes that are created on the fly */
+ public transient Shape lineShape;
+
+ /** Shared-path tune-up. */
+ public transient GeneralPath sharedPath = null;
+ protected transient Rectangle2D cachedBounds = null;
+
+ /**
+ * Constructs an empty edge view.
+ */
+ public EdgeView() {
+ super();
+ }
+
+ /**
+ * Constructs an edge view for the specified model object.
+ *
+ * @param cell
+ * reference to the model object
+ */
+ public EdgeView(Object cell) {
+ super(cell);
+ }
+
+ //
+ // Data Source
+ //
+
+ /**
+ * Overrides the parent method to udpate the cached points, source and
+ * target port. If the source or target is removed, a point is inserted into
+ * the array of points.
+ */
+ public void refresh(GraphModel model, CellMapper mapper, boolean createDependentViews) {
+ // Makes sure the manual control points are passed to
+ // the router instead of the cached control points after
+ // changes to the edge (normally manual point changes).
+ points = null;
+ super.refresh(model, mapper, createDependentViews);
+
+ // Re-sync source- and targetportviews
+ Object modelSource = model.getSource(cell);
+ Object modelTarget = model.getTarget(cell);
+ setSource(mapper.getMapping(modelSource, createDependentViews));
+ setTarget(mapper.getMapping(modelTarget, createDependentViews));
+
+ if ((modelSource != null) && (getSource() == null))
+ sourceParentView = getVisibleParent(model, mapper, modelSource);
+ else
+ sourceParentView = null;
+
+ if ((modelTarget != null) && (getTarget() == null))
+ targetParentView = getVisibleParent(model, mapper, modelTarget);
+ else
+ targetParentView = null;
+ }
+
+ protected CellView getVisibleParent(GraphModel model, CellMapper mapper, Object port) {
+ CellView view = null;
+
+ do {
+ view = mapper.getMapping(port, false);
+ port = model.getParent(port);
+ } while ((view == null) && (port != null));
+
+ return view;
+ }
+
+ /**
+ * Update attributes and recurse children.
+ */
+ public void update() {
+ super.update();
+
+ // Save the reference to the points so they can be changed
+ // in-place by use of setPoint, setSource, setTarget methods.
+ List controlPoints = GraphConstants.getPoints(allAttributes);
+
+ if (controlPoints == null) {
+ controlPoints = new ArrayList(4);
+ controlPoints.add(allAttributes.createPoint(10, 10));
+ controlPoints.add(allAttributes.createPoint(20, 20));
+ GraphConstants.setPoints(allAttributes, controlPoints);
+ }
+
+ // Uses the manual control points while the edge is being routed.
+ // Otherwise uses the cached points (eg. for preview).
+ if (points == null)
+ points = controlPoints;
+
+ Edge.Routing routing = GraphConstants.getRouting(allAttributes);
+ List routedPoints = null;
+
+ // Passes the current cached points to the router
+ if (routing != null)
+ routedPoints = routing.route(this);
+
+ // Shadows the manual control points with the
+ // routed control points
+ points = ((routedPoints != null) && !routedPoints.isEmpty()) ? routedPoints : controlPoints;
+
+ // Overrides manual point locations with the real port views
+ if (points == controlPoints) {
+ if (source != null)
+ setSource(source);
+
+ if (target != null)
+ setTarget(target);
+ }
+
+ // Checks and caches label positions
+ checkDefaultLabelPosition();
+
+ Point2D[] positions = GraphConstants.getExtraLabelPositions(allAttributes);
+
+ if (positions != null) {
+ extraLabelPositions = new Point2D[positions.length];
+
+ for (int i = 0; i < positions.length; i++)
+ extraLabelPositions[i] = positions[i];
+ } else
+ extraLabelPositions = null;
+
+ // Clear cached shapes
+ beginShape = null;
+ endShape = null;
+ lineShape = null;
+ invalidate();
+ }
+
+ /**
+ * Hook for subclassers to avoid default label positions.
+ */
+ protected void checkDefaultLabelPosition() {
+ labelPosition = GraphConstants.getLabelPosition(allAttributes);
+
+ String label = String.valueOf(getCell());
+
+ if ((labelPosition == null) && (label != null) && (label.length() > 0)) {
+ int center = GraphConstants.PERMILLE / 2;
+ labelPosition = new Point(center, 0);
+ GraphConstants.setLabelPosition(allAttributes, labelPosition);
+ }
+ }
+
+ /**
+ * Resets the cached values of the edge view
+ */
+ protected void invalidate() {
+ labelVector = null;
+ sharedPath = null;
+ cachedBounds = null;
+ cachedLabelBounds = null;
+ cachedExtraLabelBounds = null;
+ }
+
+ /**
+ * Returns the shape of the view according to the last rendering state
+ */
+ public Shape getShape() {
+ if (sharedPath != null)
+ return sharedPath;
+ else {
+ return sharedPath = (GeneralPath) getEdgeRenderer().createShape();
+ }
+ }
+
+ /**
+ * Returns the bounds of label according to the last rendering state
+ */
+ public Rectangle2D getLabelBounds() {
+ if (cachedLabelBounds != null) {
+ return cachedLabelBounds;
+ } else {
+ return cachedLabelBounds = getEdgeRenderer().getLabelBounds(null, this);
+ }
+ }
+
+ /**
+ * Returns the bounds of label according to the last rendering state
+ */
+ public Rectangle2D getExtraLabelBounds(int index) {
+ if ((cachedLabelBounds != null) && (index < cachedExtraLabelBounds.length)
+ && (cachedExtraLabelBounds[index] != null)) {
+ return cachedExtraLabelBounds[index];
+ } else {
+ return cachedExtraLabelBounds[index] = getEdgeRenderer()
+ .getExtraLabelBounds(null, this, index);
+ }
+ }
+
+ //
+ // View Methods
+ //
+
+ /**
+ * Returns true if this view intersects the given rectangle.
+ */
+ public boolean intersects(JGraph graph, Rectangle2D rect) {
+ boolean intersects = super.intersects(graph, rect);
+
+ if (!isLeaf()) {
+ return intersects;
+ } else if (intersects) {
+ Rectangle r = new Rectangle((int) rect.getX(), (int) rect.getY(),
+ (int) rect.getWidth(), (int) rect.getHeight());
+
+ return getEdgeRenderer().intersects(graph, this, r);
+ }
+
+ return false;
+ }
+
+ /**
+ * Returns the location for this edgeview.
+ */
+ public Rectangle2D getBounds() {
+ Rectangle2D rect = super.getBounds();
+
+ if (rect == null) {
+ if (cachedBounds == null) {
+ cachedBounds = getEdgeRenderer().getBounds(this);
+ }
+
+ rect = cachedBounds;
+ }
+
+ return rect;
+ }
+
+ /**
+ * Returns the local renderer. Do not access the renderer field directly.
+ * Use this method instead. Note: This method is package private.
+ */
+ EdgeRenderer getEdgeRenderer() {
+ return (EdgeRenderer) getRenderer();
+ }
+
+ /**
+ * Returns a renderer for the class.
+ */
+ public CellViewRenderer getRenderer() {
+ return renderer;
+ }
+
+ /**
+ * Returns a cell handle for the view.
+ */
+ public CellHandle getHandle(GraphContext context) {
+ return new EdgeHandle(this, context);
+ }
+
+ //
+ // Cached Values
+ //
+
+ /**
+ * Returns the CellView that represents the source of the edge.
+ */
+ public CellView getSource() {
+ return source;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public CellView getSourceParentView() {
+ return sourceParentView;
+ }
+
+ /**
+ * Sets the <code>sourceView</code> of the edge.
+ */
+ public void setSource(CellView sourceView) {
+ sourceParentView = null;
+ source = sourceView;
+
+ if (source != null)
+ points.set(0, source);
+ else
+ points.set(0, getPoint(0));
+
+ invalidate();
+ }
+
+ /**
+ * Returns the CellView that represents the target of the edge.
+ */
+ public CellView getTarget() {
+ return target;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public CellView getTargetParentView() {
+ return targetParentView;
+ }
+
+ /**
+ * Sets the <code>targetView</code> of the edge.
+ */
+ public void setTarget(CellView targetView) {
+ target = targetView;
+ targetParentView = null;
+
+ int n = points.size() - 1;
+
+ if (target != null)
+ points.set(n, target);
+ else
+ points.set(n, getPoint(n));
+
+ invalidate();
+ }
+
+ /**
+ * Returns a point that describes the position of the label.
+ */
+ public Point2D getExtraLabelPosition(int index) {
+ return extraLabelPositions[index];
+ }
+
+ /**
+ * Returns a point that describes the position of the label.
+ */
+ public Point2D getLabelPosition() {
+ return labelPosition;
+ }
+
+ /**
+ * Sets the description of the label position.
+ */
+ public void setLabelPosition(Point2D pos) {
+ labelPosition.setLocation(pos);
+ invalidate();
+ }
+
+ /**
+ * Sets the description of the label position.
+ */
+ public void setExtraLabelPosition(int index, Point2D pos) {
+ extraLabelPositions[index].setLocation(pos);
+ invalidate();
+ }
+
+ //
+ // Points
+ //
+
+ /**
+ * Returns true if the edge is a loop.
+ */
+ public boolean isLoop() {
+ return ((getSource() != null) && (getSource() == getTarget()))
+ || ((sourceParentView != null) && (sourceParentView == targetParentView))
+ || ((sourceParentView != null) && (getTarget() != null)
+ && (getTarget().getParentView() == sourceParentView))
+ || ((targetParentView != null) && (getSource() != null)
+ && (getSource().getParentView() == targetParentView));
+ }
+
+ /**
+ * Returns the points.
+ *
+ * @return List
+ */
+ public List getPoints() {
+ return points;
+ }
+
+ /**
+ * Returns the number of point for this edge.
+ */
+ public int getPointCount() {
+ return points.size();
+ }
+
+ /**
+ * Returns the cached points for this edge.
+ */
+ public Point2D getPoint(int index) {
+ Object obj = points.get(index);
+
+ if ((index == 0) && (sourceParentView != null)) {
+ return sourceParentView.getPerimeterPoint(this, getCenterPoint(sourceParentView),
+ getNearestPoint(index == 0));
+ } else if ((index == (getPointCount() - 1)) && (targetParentView != null)) {
+ return targetParentView.getPerimeterPoint(this, getCenterPoint(targetParentView),
+ getNearestPoint(index == 0));
+ } else if (obj instanceof PortView)
+
+ // Port Location Seen From This Edge
+ return ((PortView) obj).getLocation(this, getNearestPoint(index == 0));
+ else if (obj instanceof CellView) {
+ // Should not happen
+ Rectangle2D r = ((CellView) obj).getBounds();
+
+ return new Point2D.Double(r.getX(), r.getY());
+ } else if (obj instanceof Point2D)
+
+ // Regular Point
+ return (Point2D) obj;
+
+ return null;
+ }
+
+ /**
+ * Returns the nearest point wrt to the source or target. This method
+ * returns the next or previous point or port in the points list, eg. if
+ * source is true it returns the location of the point or port at index 1
+ * without calling the getLocation method on any ports.<br>
+ * Likewise, the method returns the location at index getPointCount()-2 if
+ * source is false.
+ */
+ protected Point2D getNearestPoint(boolean source) {
+ if (getPointCount() == 2) {
+ if (source && target instanceof PortView
+ && (GraphConstants.getOffset(target.getAllAttributes()) != null)) {
+ return ((PortView) target).getLocation(this);
+ }
+
+ if (!source && this.source instanceof PortView
+ && (GraphConstants.getOffset(this.source.getAllAttributes()) != null)) {
+ return ((PortView) this.source).getLocation(this);
+ }
+
+ if (source && (targetParentView != null) && targetParentView.isLeaf())
+ return getCenterPoint(targetParentView);
+ else if (!source && (sourceParentView != null) && sourceParentView.isLeaf())
+ return getCenterPoint(sourceParentView);
+ }
+
+ return getPointLocation((source) ? 1 : (getPointCount() - 2));
+ }
+
+ /**
+ * Returns the point of <code>edge</code> at <code>index</code>. Avoids
+ * calling <code>getLocation</code> on any ports of <code>edge</code>.
+ * <br>
+ * This is used from within getPoint to pass the nearest point to the
+ * portview to find it's location. This uses the center point of the parent
+ * view to determine the port view's location to avoid infinite recursion.
+ */
+ protected Point2D getPointLocation(int index) {
+ Object obj = points.get(index);
+
+ if (obj instanceof Point2D)
+ return (Point2D) obj;
+ else if (obj instanceof PortView) {
+ CellView vertex = ((CellView) obj).getParentView();
+
+ if (vertex != null)
+ return getCenterPoint(vertex);
+ }
+
+ return null;
+ }
+
+ /**
+ * Sets the point at <code>index</code> to <code>p</code>.
+ */
+ public void setPoint(int index, Point2D p) {
+ points.set(index, p);
+ invalidate();
+ }
+
+ /**
+ * Adds <code>p</code> at position <code>index</code>.
+ */
+ public void addPoint(int index, Point2D p) {
+ points.add(index, p);
+ invalidate();
+ }
+
+ /**
+ * Removes the point at position <code>index</code>.
+ */
+ public void removePoint(int index) {
+ points.remove(index);
+ invalidate();
+ }
+
+ /**
+ * Adds an extra label.
+ */
+ public void addExtraLabel(Point2D location, Object label) {
+ Object[] extraLabels = GraphConstants.getExtraLabels(getAllAttributes());
+ Point2D[] positions = GraphConstants.getExtraLabelPositions(getAllAttributes());
+
+ // Inserts a new extra label
+ if (extraLabels == null) {
+ extraLabels = new Object[1];
+ positions = new Point2D[1];
+ } else {
+ Object[] tmp = new Object[extraLabels.length + 1];
+ System.arraycopy(extraLabels, 0, tmp, 0, extraLabels.length);
+ extraLabels = tmp;
+
+ Point2D[] pts = new Point2D[positions.length + 1];
+ System.arraycopy(positions, 0, pts, 0, positions.length);
+ positions = pts;
+ }
+
+ int newIndex = extraLabels.length - 1;
+ extraLabels[newIndex] = label;
+ positions[newIndex] = location;
+ GraphConstants.setExtraLabels(getAllAttributes(), extraLabels);
+ GraphConstants.setExtraLabelPositions(getAllAttributes(), positions);
+ }
+
+ /**
+ * Removes the point at position <code>index</code>.
+ */
+ public void removeExtraLabel(int index) {
+ Object[] labels = GraphConstants.getExtraLabels(getAllAttributes());
+ Point2D[] pts = GraphConstants.getExtraLabelPositions(getAllAttributes());
+
+ if ((labels == null) || (labels.length > 1)) {
+ Object[] newLabels = new Object[labels.length - 1];
+ Point2D[] newPts = new Point2D[pts.length - 1];
+ System.arraycopy(labels, 0, newLabels, 0, index);
+
+ if (index < newLabels.length)
+ System.arraycopy(labels, index + 1, newLabels, index, newLabels.length - index);
+
+ System.arraycopy(pts, 0, newPts, 0, index);
+
+ if (index < newPts.length)
+ System.arraycopy(pts, index + 1, newPts, index, newPts.length - index);
+
+ GraphConstants.setExtraLabels(getAllAttributes(), newLabels);
+ GraphConstants.setExtraLabelPositions(getAllAttributes(), newPts);
+ } else {
+ // TODO: Remove via REMOVEATTRIBUTES
+ GraphConstants.setExtraLabels(getAllAttributes(), new Object[0]);
+ GraphConstants.setExtraLabelPositions(getAllAttributes(), new Point2D[0]);
+ }
+ }
+
+ /**
+ * Hook to return the vector that is taken as the base vector to compute
+ * relative label positions. Normally, the vector goes from the first to the
+ * last point on the edge, unless these points are equal, in which case the
+ * average distance of all points to the source point is used.
+ */
+ public Point2D getLabelVector() {
+ if (labelVector == null) {
+ Point2D p0 = getPoint(0);
+ double dx = 0;
+ double dy = 0;
+ // Finds an average distance
+ dx = 0;
+ dy = 0;
+
+ int n = getPointCount();
+
+ if (isLoop()) {
+ for (int i = 1; i < n; i++) {
+ Point2D point = getPoint(i);
+ dx += (point.getX() - p0.getX());
+ dy += (point.getY() - p0.getY());
+ }
+
+ n /= 2;
+ dx /= (double) n;
+ dy /= (double) n;
+ labelVector = new Point2D.Double(dx, dy);
+ } else {
+ Point2D point = getPoint(n - 1);
+ dx += (point.getX() - p0.getX());
+ dy += (point.getY() - p0.getY());
+ labelVector = new Point2D.Double(dx, dy);
+ }
+ }
+
+ return labelVector;
+ }
+
+ //
+ /**
+ * DOCUMENT ME!
+ *
+ * @param view DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static double getLength(CellView view) {
+ double cost = 1;
+
+ if (view instanceof EdgeView) {
+ EdgeView edge = (EdgeView) view;
+ Point2D last = null;
+ Point2D current = null;
+
+ for (int i = 0; i < edge.getPointCount(); i++) {
+ current = edge.getPoint(i);
+
+ if (last != null)
+ cost += last.distance(current);
+
+ last = current;
+ }
+ }
+
+ return cost;
+ }
+
+ //
+ // Handle
+ //
+
+ // This implementation uses the point instance to make the change. No index
+ // is used for the current point because routing could change the index
+ // during
+ // the move operation.
+ public static class EdgeHandle implements CellHandle, Serializable {
+ protected JGraph graph;
+
+ /* Pointer to the edge and its clone. */
+ protected EdgeView edge;
+
+ /* Pointer to the edge and its clone. */
+ protected EdgeView orig;
+
+ /*
+ * Boolean indicating whether the source, target or label is being
+ * edited.
+ */
+ protected boolean label = false;
+
+ /*
+ * Boolean indicating whether the source, target or label is being
+ * edited.
+ */
+ protected boolean source = false;
+
+ /*
+ * Boolean indicating whether the source, target or label is being
+ * edited.
+ */
+ protected boolean target = false;
+
+ /**
+ * Holds the index of the current (editing) label or point.
+ */
+ protected int currentLabel = -1;
+
+ /**
+ * Holds the index of the current (editing) label or point.
+ */
+ protected int currentIndex = -1;
+
+ /* Pointer to the currently selected point. */
+ protected Point2D currentPoint;
+
+ /* Array of control points represented as rectangles. */
+ protected transient Rectangle2D[] r;
+
+ /* A control point for the label position. */
+ protected transient Rectangle2D loc;
+ protected transient Rectangle2D[] extraLabelLocations;
+ protected boolean firstOverlayCall = true;
+ protected boolean isEdgeConnectable = true;
+ protected EdgeView relevantEdge = null;
+
+ /**
+ * True if the cell is being edited.
+ */
+ protected boolean editing = false;
+
+ /**
+ * Holds the initial location of the label.
+ */
+ protected Point2D initialLabelLocation = null;
+
+ /**
+ * Indicates whether the edge has been modified during the last mouse
+ * pressed and dragged operations.
+ */
+ protected boolean edgeModified = false;
+
+ public EdgeHandle(EdgeView edge, GraphContext ctx) {
+ this.graph = ctx.getGraph();
+ this.edge = edge;
+ editing = graph.getEditingCell() == edge.getCell();
+ loc = new Rectangle();
+
+ Object[] labels = GraphConstants.getExtraLabels(edge.getAllAttributes());
+
+ if (labels != null) {
+ extraLabelLocations = new Rectangle[labels.length];
+
+ for (int i = 0; i < extraLabelLocations.length; i++)
+ extraLabelLocations[i] = new Rectangle();
+ }
+
+ orig = (EdgeView) graph.getGraphLayoutCache().getMapping(edge.getCell(), false);
+ reloadPoints(orig);
+ isEdgeConnectable = GraphConstants.isConnectable(edge.getAllAttributes());
+ }
+
+ protected void reloadPoints(EdgeView edge) {
+ relevantEdge = edge;
+ r = new Rectangle[edge.getPointCount()];
+
+ for (int i = 0; i < r.length; i++)
+ r[i] = new Rectangle();
+
+ invalidate();
+ }
+
+ // Update and paint control points
+ public void paint(Graphics g) {
+ invalidate();
+
+ if (!edge.isLeaf())
+ return;
+
+ for (int i = 0; i < r.length; i++) {
+ if (isEdgeConnectable && !editing)
+ g.setColor(graph.getHandleColor());
+ else
+ g.setColor(graph.getLockedHandleColor());
+
+ g.fill3DRect((int) r[i].getX(), (int) r[i].getY(), (int) r[i].getWidth(),
+ (int) r[i].getHeight(), true);
+
+ CellView port = null;
+
+ if ((i == 0) && (edge.getSource() != null))
+ port = edge.getSource();
+ else if ((i == (r.length - 1)) && (edge.getTarget() != null))
+ port = edge.getTarget();
+
+ if ((port != null) || ((i == 0) && (edge.getSourceParentView() != null))
+ || ((i == (r.length - 1)) && (edge.getTargetParentView() != null))) {
+ g.setColor(graph.getLockedHandleColor());
+
+ Point2D tmp = (port != null)
+ ? GraphConstants.getOffset(port.getAllAttributes()) : null;
+
+ if (tmp != null) {
+ g.drawLine((int) r[i].getX() + 1, (int) r[i].getY() + 1,
+ (int) (r[i].getX() + r[i].getWidth()) - 3,
+ (int) (r[i].getY() + r[i].getHeight()) - 3);
+ g.drawLine((int) r[i].getX() + 1,
+ (int) (r[i].getY() + r[i].getHeight()) - 3,
+ (int) (r[i].getX() + r[i].getWidth()) - 3, (int) r[i].getY() + 1);
+ } else
+ g.drawRect((int) r[i].getX() + 2, (int) r[i].getY() + 2,
+ (int) r[i].getWidth() - 5, (int) r[i].getHeight() - 5);
+ }
+ }
+ }
+
+ public void overlay(Graphics g) {
+ if ((edge != null) && !firstOverlayCall && edge.isLeaf()) {
+ // g.setColor(graph.getBackground()); // JDK 1.3
+ g.setColor(graph.getForeground());
+ g.setXORMode(graph.getBackground().darker());
+
+ Graphics2D g2 = (Graphics2D) g;
+ AffineTransform oldTransform = g2.getTransform();
+ g2.scale(graph.getScale(), graph.getScale());
+ graph.getUI().paintCell(g, edge, edge.getBounds(), true);
+ g2.setTransform(oldTransform);
+
+ if (isSourceEditing() && (edge.getSource() != null))
+ paintPort(g, edge.getSource());
+ else if (isTargetEditing() && (edge.getTarget() != null))
+ paintPort(g, edge.getTarget());
+ }
+
+ firstOverlayCall = false;
+ }
+
+ protected void paintPort(Graphics g, CellView p) {
+ boolean offset = (GraphConstants.getOffset(p.getAllAttributes()) != null);
+ Rectangle2D r = (offset) ? p.getBounds() : p.getParentView().getBounds();
+ r = graph.toScreen((Rectangle2D) r.clone());
+
+ int s = 3;
+ r.setFrame(r.getX() - s, r.getY() - s, r.getWidth() + (2 * s), r.getHeight() + (2 * s));
+ graph.getUI().paintCell(g, p, r, true);
+ }
+
+ protected boolean snap(boolean source, Point2D point) {
+ boolean connect = graph.isConnectable() && isEdgeConnectable;
+ Object port = graph.getPortForLocation(point.getX(), point.getY());
+
+ if ((port != null) && (graph.getModel().getParent(port) == edge.getCell()))
+ port = null;
+
+ if ((port != null) && connect) {
+ CellView portView = graph.getGraphLayoutCache().getMapping(port, false);
+
+ if (GraphConstants.isConnectable(portView.getParentView().getAllAttributes())) {
+ Object cell = edge.getCell();
+
+ if (source && graph.getModel().acceptsSource(cell, port)) {
+ if (edge.getSource() != portView) {
+ edgeModified = true;
+ overlay(graph.getGraphics());
+ edge.setSource(portView);
+ edge.update();
+ overlay(graph.getGraphics());
+ }
+
+ return true;
+ } else if (!source && graph.getModel().acceptsTarget(cell, port)) {
+ if (edge.getTarget() != portView) {
+ edgeModified = true;
+ overlay(graph.getGraphics());
+ edge.setTarget(portView);
+ edge.update();
+ overlay(graph.getGraphics());
+ }
+
+ return true;
+ }
+ }
+ }
+
+ return false;
+ }
+
+ public boolean isConstrainedMoveEvent(MouseEvent e) {
+ GraphUI ui = graph.getUI();
+
+ if (ui instanceof BasicGraphUI)
+ return ((BasicGraphUI) ui).isConstrainedMoveEvent(e);
+
+ return false;
+ }
+
+ /**
+ * Returning true signifies a mouse event adds a new point to an edge.
+ */
+ public boolean isAddPointEvent(MouseEvent event) {
+ return event.isPopupTrigger() || SwingUtilities.isRightMouseButton(event);
+ }
+
+ /**
+ * Returning true signifies a mouse event removes a given point.
+ */
+ public boolean isRemovePointEvent(MouseEvent event) {
+ return event.isPopupTrigger() || SwingUtilities.isRightMouseButton(event);
+ }
+
+ protected boolean isSourceEditing() {
+ return source;
+ }
+
+ protected boolean isTargetEditing() {
+ return target;
+ }
+
+ /*
+ * Returns true if either the source, target, label or a point is being
+ * edited.
+ */
+ protected boolean isEditing() {
+ return source || target || label || (currentLabel >= 0) || (currentPoint != null);
+ }
+
+ /**
+ * Invoked when the mouse pointer has been moved on a component (with no
+ * buttons down).
+ */
+ public void mouseMoved(MouseEvent event) {
+ for (int i = 0; i < r.length; i++)
+ if (r[i].contains(event.getPoint())) {
+ graph.setCursor(new Cursor(Cursor.CROSSHAIR_CURSOR));
+ event.consume();
+
+ return;
+ }
+
+ if (loc.contains(event.getPoint()) && graph.isMoveable()
+ && GraphConstants.isMoveable(edge.getAllAttributes())) {
+ graph.setCursor(new Cursor(Cursor.HAND_CURSOR));
+ event.consume();
+ }
+
+ if ((extraLabelLocations != null) && graph.isMoveable()
+ && GraphConstants.isMoveable(edge.getAllAttributes())) {
+ for (int i = 0; i < extraLabelLocations.length; i++) {
+ if (extraLabelLocations[i].contains(event.getPoint())) {
+ graph.setCursor(new Cursor(Cursor.HAND_CURSOR));
+ event.consume();
+ }
+ }
+ }
+ }
+
+ // Handle mouse pressed event.
+ public void mousePressed(MouseEvent event) {
+ /* INV: currentPoint = null; source = target = label = false; */
+ if (!edge.isLeaf())
+ return;
+
+ boolean bendable = graph.isBendable()
+ && GraphConstants.isBendable(edge.getAllAttributes());
+ int x = event.getX();
+ int y = event.getY();
+
+ // Detect hit on control point
+ int index = 0;
+
+ for (index = 0; index < r.length; index++) {
+ if (r[index].contains(x, y)) {
+ currentPoint = edge.getPoint(index);
+ currentIndex = index;
+ source = index == 0;
+ target = index == (r.length - 1);
+
+ break;
+ }
+ }
+
+ // Detect hit on label
+ if (!isEditing() && graph.isMoveable()
+ && GraphConstants.isMoveable(edge.getAllAttributes()) && (loc != null)
+ && loc.contains(x, y) && !isAddPointEvent(event) && !isRemovePointEvent(event)) {
+ initialLabelLocation = (Point2D) edge.getLabelPosition().clone();
+ label = true;
+ }
+ // Detect hit on extra labels
+ else if ((extraLabelLocations != null) && !isEditing() && graph.isMoveable()
+ && GraphConstants.isMoveable(edge.getAllAttributes())) {
+ for (int i = 0; i < extraLabelLocations.length; i++) {
+ if ((extraLabelLocations[i] != null) && extraLabelLocations[i].contains(x, y)) {
+ currentLabel = i;
+ initialLabelLocation = (Point2D) edge.getExtraLabelPosition(currentLabel)
+ .clone();
+
+ if (isRemovePointEvent(event)) {
+ edge.removeExtraLabel(i);
+ edgeModified = true;
+ mouseReleased(event);
+ }
+
+ break;
+ }
+ }
+ }
+
+ // Remove Point
+ if (isRemovePointEvent(event) && (currentPoint != null) && !source && !target
+ && bendable && ((edge.getSource() == null) || (currentIndex > 0))
+ && ((edge.getTarget() == null) || (currentIndex < (edge.getPointCount() - 1)))) {
+ edge.removePoint(index);
+ edgeModified = true;
+ mouseReleased(event);
+
+ // Add Point
+ } else if (isAddPointEvent(event) && !isEditing() && bendable) {
+ int s = graph.getHandleSize();
+ Rectangle2D rect = graph.fromScreen(new Rectangle(x - s, y - s, 2 * s, 2 * s));
+
+ if (edge.intersects(graph, rect)) {
+ Point2D point = graph.fromScreen(graph.snap(new Point(event.getPoint())));
+ double min = Double.MAX_VALUE;
+ double dist = 0;
+
+ for (int i = 0; i < (edge.getPointCount() - 1); i++) {
+ Point2D p = edge.getPoint(i);
+ Point2D p1 = edge.getPoint(i + 1);
+ dist = new Line2D.Double(p, p1).ptSegDistSq(point);
+
+ if (dist < min) {
+ min = dist;
+ index = i + 1;
+ }
+ }
+
+ edge.addPoint(index, point);
+ edgeModified = true;
+ currentPoint = point;
+ reloadPoints(edge);
+ paint(graph.getGraphics());
+ }
+ }
+
+ if (isEditing())
+ event.consume();
+ }
+
+ public void mouseDragged(MouseEvent event) {
+ Point2D p = graph.fromScreen(new Point(event.getPoint()));
+
+ // Move Label
+ if (label || (currentLabel >= 0)) {
+ Rectangle2D r = edge.getBounds();
+
+ if (r != null) {
+ edgeModified = true;
+
+ double x = p.getX();
+ double y = p.getY();
+
+ Point2D p0 = edge.getPoint(0);
+
+ double p0x = p0.getX();
+ double p0y = p0.getY();
+
+ Point2D vector = edge.getLabelVector();
+ double dx = vector.getX();
+ double dy = vector.getY();
+
+ double pex = p0.getX() + dx;
+ double pey = p0.getY() + dy;
+
+ double len = Math.sqrt((dx * dx) + (dy * dy));
+
+ if (len > 0) {
+ double u = GraphConstants.PERMILLE;
+ double posy = (len * (((-y * dx) + (p0y * dx) + (x * dy)) - (p0x * dy))) / (((-pey * dy)
+ + (p0y * dy))
+ - (dx * pex)
+ + (dx * p0x));
+ double posx = (u * ((((-y * pey) + (y * p0y) + (p0y * pey)) - (p0y * p0y)
+ - (pex * x) + (pex * p0x) + (p0x * x)) - (p0x * p0x))) / (((-pey * dy)
+ + (p0y * dy))
+ - (dx * pex)
+ + (dx * p0x));
+ p = new Point2D.Double(posx, posy);
+ } else {
+ p = new Point2D.Double(x - p0.getX(), y - p0.getY());
+ }
+
+ overlay(graph.getGraphics());
+
+ if (label)
+ edge.setLabelPosition(p);
+ else
+ edge.setExtraLabelPosition(currentLabel, p);
+
+ edge.update();
+ overlay(graph.getGraphics());
+ }
+ } else if (isEditing() && (currentPoint != null)) {
+ boolean disconnectable = (!source && !target)
+ || (graph.isDisconnectable()
+ && GraphConstants.isDisconnectable(orig.getAllAttributes()));
+
+ if (source)
+ disconnectable = disconnectable
+ && (((orig.getSource() == null)
+ && (orig.getSourceParentView() == null))
+ || ((orig.getSource() != null)
+ && GraphConstants.isDisconnectable(orig.getSource()
+ .getParentView()
+ .getAllAttributes()))
+ || ((orig.getSourceParentView() != null)
+ && GraphConstants.isDisconnectable(orig.getSourceParentView()
+ .getAllAttributes())));
+
+ if (target)
+ disconnectable = disconnectable
+ && (((orig.getTarget() == null)
+ && (orig.getTargetParentView() == null))
+ || ((orig.getTarget() != null)
+ && GraphConstants.isDisconnectable(orig.getTarget()
+ .getParentView()
+ .getAllAttributes()))
+ || ((orig.getTargetParentView() != null)
+ && GraphConstants.isDisconnectable(orig.getTargetParentView()
+ .getAllAttributes())));
+
+ // Find Source/Target Port
+ if (!((source && snap(true, event.getPoint()))
+ || (target && snap(false, event.getPoint()))) && disconnectable) {
+ // Else Use Point
+ boolean acceptSource = source
+ && (graph.getModel().acceptsSource(edge.getCell(), null)
+ || graph.isPreviewInvalidNullPorts());
+ boolean acceptTarget = target
+ && (graph.getModel().acceptsTarget(edge.getCell(), null)
+ || graph.isPreviewInvalidNullPorts());
+
+ if (acceptSource || acceptTarget || !(source || target)) {
+ edgeModified = true;
+ overlay(graph.getGraphics());
+ p = graph.fromScreen(graph.snap(new Point(event.getPoint())));
+
+ // Constrained movement
+ if (isConstrainedMoveEvent(event) && (currentIndex >= 0)) {
+ // Reset Initial Positions
+ EdgeView orig = (EdgeView) graph.getGraphLayoutCache()
+ .getMapping(edge.getCell(), false);
+ Point2D origPoint = orig.getPoint(currentIndex);
+ double totDx = p.getX() - origPoint.getX();
+ double totDy = p.getY() - origPoint.getY();
+
+ if (Math.abs(totDx) < Math.abs(totDy))
+ p.setLocation(origPoint.getX(), p.getY());
+ else
+ p.setLocation(p.getX(), origPoint.getY());
+ }
+
+ // Do not move into negative space
+ p.setLocation(Math.max(0, p.getX()), Math.max(0, p.getY()));
+ currentPoint.setLocation(p);
+
+ if (source) {
+ edge.setPoint(0, p);
+ edge.setSource(null);
+ } else if (target) {
+ edge.setPoint(edge.getPointCount() - 1, p);
+ edge.setTarget(null);
+ }
+
+ edge.update();
+ overlay(graph.getGraphics());
+ }
+ }
+ }
+ }
+
+ // Handle mouse released event
+ public void mouseReleased(MouseEvent e) {
+ boolean clone = e.isControlDown() && graph.isCloneable();
+ GraphModel model = graph.getModel();
+ Object source = (edge.getSource() != null) ? edge.getSource().getCell() : null;
+ Object target = (edge.getTarget() != null) ? edge.getTarget().getCell() : null;
+
+ if (edgeModified && model.acceptsSource(edge.getCell(), source)
+ && model.acceptsTarget(edge.getCell(), target)) {
+ // Creates an extra label if the label was cloned
+ if (clone && (initialLabelLocation != null)) {
+ // Resets the dragging label position and adds a new label
+ // instead. Note: label locations are modified in-place
+ // which is why we need to clone at beginning.
+ Object value = null;
+ Point2D location = null;
+ Object[] extraLabels = GraphConstants.getExtraLabels(edge.getAllAttributes());
+
+ if (label) {
+ location = (Point2D) edge.getLabelPosition().clone();
+ value = graph.convertValueToString(orig);
+ edge.setLabelPosition(initialLabelLocation);
+ } else {
+ location = (Point2D) edge.getExtraLabelPosition(currentLabel).clone();
+ value = extraLabels[currentLabel];
+ edge.setExtraLabelPosition(currentLabel, initialLabelLocation);
+ }
+
+ edge.addExtraLabel(location, value);
+ edge.update();
+ clone = false;
+ }
+
+ // Creates the data required for the edit/insert call
+ ConnectionSet cs = createConnectionSet(edge, clone);
+ Map nested = GraphConstants.createAttributes(new CellView[] { edge }, null);
+
+ // The cached points may be different from what's
+ // in the attribute map if the edge is routed.
+ Map tmp = (Map) nested.get(edge.getCell());
+ List controlPoints = GraphConstants.getPoints(tmp);
+ List currentPoints = edge.getPoints();
+
+ // Checks if we're dealing with a routing algorithm
+ // and if we are, replaces only the source and target
+ // in the control point list.
+ if (controlPoints != currentPoints) {
+ controlPoints.set(0, edge.getPoint(0));
+ controlPoints.set(controlPoints.size() - 1,
+ edge.getPoint(edge.getPointCount() - 1));
+ }
+
+ if (clone) {
+ Map cellMap = graph.cloneCells(graph.getDescendants(new Object[] { edge.getCell() }));
+ processNestedMap(nested, true);
+ nested = GraphConstants.replaceKeys(cellMap, nested);
+ cs = cs.clone(cellMap);
+
+ Object[] cells = cellMap.values().toArray();
+ graph.getGraphLayoutCache().insert(cells, nested, cs, null, null);
+ } else {
+ processNestedMap(nested, false);
+ graph.getGraphLayoutCache().edit(nested, cs, null, null);
+ }
+ } else {
+ overlay(graph.getGraphics());
+ edge.refresh(graph.getModel(), graph.getGraphLayoutCache(), false);
+ }
+
+ initialLabelLocation = null;
+ currentPoint = null;
+ this.edgeModified = false;
+ this.label = false;
+ this.source = false;
+ this.target = false;
+ currentLabel = -1;
+ currentIndex = -1;
+ firstOverlayCall = true;
+ e.consume();
+ }
+
+ protected void processNestedMap(Map nested, boolean clone) {
+ // subclassers can override this to modify the attributes
+ }
+
+ protected ConnectionSet createConnectionSet(EdgeView view, boolean verbose) {
+ Object edge = view.getCell();
+ GraphModel model = graph.getModel();
+ ConnectionSet cs = new ConnectionSet();
+ Object sourcePort = null;
+ Object targetPort = null;
+
+ if (view.getSource() != null)
+ sourcePort = view.getSource().getCell();
+ else if (view.getSourceParentView() != null)
+ sourcePort = model.getSource(edge);
+
+ if (view.getTarget() != null)
+ targetPort = view.getTarget().getCell();
+ else if (view.getTargetParentView() != null)
+ targetPort = model.getTarget(edge);
+
+ if (view.getTarget() != null)
+ targetPort = view.getTarget().getCell();
+
+ if (verbose || ((sourcePort != model.getSource(edge)) && source))
+ cs.connect(edge, sourcePort, true);
+
+ if (verbose || ((targetPort != model.getTarget(edge)) && target))
+ cs.connect(edge, targetPort, false);
+
+ return cs;
+ }
+
+ // Update control points
+ protected void invalidate() {
+ EdgeView e = relevantEdge;
+ int handlesize = graph.getHandleSize();
+ EdgeRenderer er = (EdgeRenderer) edge.getRenderer();
+
+ for (int i = 0; i < r.length; i++) {
+ Point2D p = e.getPoint(i);
+ p = graph.toScreen(new Point2D.Double(p.getX(), p.getY()));
+ r[i].setFrame(p.getX() - handlesize, p.getY() - handlesize, 2 * handlesize,
+ 2 * handlesize);
+ p = graph.toScreen(er.getLabelPosition(e));
+
+ Dimension d = er.getLabelSize(e, graph.convertValueToString(e));
+
+ if ((p != null) && (d != null)) {
+ Point2D s = graph.toScreen(new Point2D.Double(d.width, d.height));
+ loc.setFrame(p.getX() - (s.getX() / 2), p.getY() - (s.getY() / 2), s.getX(),
+ s.getY());
+ }
+ }
+
+ if (extraLabelLocations != null) {
+ for (int i = 0; i < extraLabelLocations.length; i++) {
+ Point2D p = er.getExtraLabelPosition(e, i);
+
+ if (p != null) {
+ p = graph.toScreen((Point2D) p.clone());
+
+ Dimension d = er.getExtraLabelSize(graph, e, i);
+
+ if (d != null) {
+ Point2D s = graph.toScreen(new Point2D.Double(d.width, d.height));
+ extraLabelLocations[i].setFrame(p.getX() - (s.getX() / 2),
+ p.getY() - (s.getY() / 2), s.getX(),
+ s.getY());
+ }
+ }
+ }
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edge DOCUMENT ME!
+ * @param source DOCUMENT ME!
+ * @param p DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Point2D getPerimeterPoint(EdgeView edge, Point2D source, Point2D p) {
+ if (getPointCount() > 2)
+ return getPoint(getPointCount() / 2);
+
+ Point2D p0 = getPoint(0);
+ Point2D pe = getPoint(getPointCount() - 1);
+
+ return new Point2D.Double((pe.getX() + p0.getX()) / 2, (pe.getY() + p0.getY()) / 2);
+ }
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/GraphCell.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/GraphCell.java
new file mode 100644
index 0000000..3f53724
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/GraphCell.java
@@ -0,0 +1,36 @@
+/*
+ * @(#)GraphCell.java 1.0 03-JUL-04
+ *
+ * Copyright (c) 2001-2004 Gaudenz Alder
+ *
+ */
+package org.jgraph.graph;
+
+import java.util.Map;
+
+
+/**
+ * Defines the requirements for objects that appear as
+ * GraphCells. This is the base interface for all GraphCells.
+ *
+ * @version 1.0 1/1/02
+ * @author Gaudenz Alder
+ */
+public interface GraphCell {
+ /**
+ * Returns the <code>attributes</code> of the cell.
+ */
+ AttributeMap getAttributes();
+
+ /**
+ * Changes the <code>attributes</code> of the cell.
+ *
+ * @deprecated Use getAttributes().applyMap
+ */
+ Map changeAttributes(Map change);
+
+ /**
+ * Sets the attributes
+ */
+ public void setAttributes(AttributeMap map);
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/GraphCellEditor.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/GraphCellEditor.java
new file mode 100644
index 0000000..59b1dcd
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/GraphCellEditor.java
@@ -0,0 +1,41 @@
+/*
+ * @(#)GraphCellEditor.java 1.0 03-JUL-04
+ *
+ * Copyright (c) 2001-2004 Gaudenz Alder
+ *
+ */
+package org.jgraph.graph;
+
+import org.jgraph.JGraph;
+
+import java.awt.Component;
+
+import javax.swing.CellEditor;
+
+
+/**
+ * Adds to CellEditor the extensions necessary to configure an editor
+ * in a graph.
+ *
+ * @version 1.0 1/1/02
+ * @author Gaudenz Alder
+ */
+public interface GraphCellEditor extends CellEditor {
+ /**
+ * Sets an initial <I>value</I> for the editor. This will cause
+ * the editor to stopEditing and lose any partially edited value
+ * if the editor is editing when this method is called. <p>
+ *
+ * Returns the component that should be added to the client's
+ * Component hierarchy. Once installed in the client's hierarchy
+ * this component will then be able to draw and receive user input.
+ *
+ * @param graph the JGraph that is asking the editor to edit
+ * This parameter can be null.
+ * @param value the value of the cell to be edited.
+ * @param isSelected true if the cell is to be rendered with
+ * selection highlighting
+ * @return the component for editing
+ */
+ Component getGraphCellEditorComponent(JGraph graph, Object value, boolean isSelected);
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/GraphConstants.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/GraphConstants.java
new file mode 100644
index 0000000..2cb4bdf
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/GraphConstants.java
@@ -0,0 +1,1705 @@
+/*
+ * @(#)GraphConstants.java 1.0 03-JUL-04
+ *
+ * Copyright (c) 2001-2004 Gaudenz Alder
+ *
+ */
+package org.jgraph.graph;
+
+import java.awt.BasicStroke;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.Stroke;
+import java.awt.geom.Point2D;
+import java.awt.geom.Rectangle2D;
+
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.Map;
+
+import javax.swing.Icon;
+import javax.swing.JLabel;
+import javax.swing.UIManager;
+import javax.swing.border.Border;
+
+
+/**
+ * A collection of well known or common attribute keys and methods to apply to
+ * an Map to get/set the properties in a typesafe manner. The following
+ * attributes and methods need special attention: removeAttributes, removeAll
+ * and value. RemoveAttributes and RemoveAll are not stored in a map, but remove
+ * the specified entries. The value entry of a propertyMap is always in sync
+ * with the userObject of a GraphCell. The isMoveable, isAutoSize and isSizeable
+ * are used indepedently (see
+ * http://sourceforge.net/forum/forum.php?thread_id=770111&forum_id=140880)
+ *
+ * @version 1.0 1/1/02
+ * @author Gaudenz Alder
+ */
+public class GraphConstants {
+ /**
+ * Default font is derived from
+ * UIManager.getDefaults().getFont("Label.font")
+ */
+ public static Font DEFAULTFONT = null;
+
+ static {
+ try {
+ DEFAULTFONT = UIManager.getDefaults().getFont("Label.font");
+ } catch (InternalError e) {
+ // No default font
+ }
+ }
+
+ /** Default decoration size. Value is 0. */
+ public static int DEFAULTDECORATIONSIZE = 10;
+
+ /** Default inset size. Value is 0. */
+ public static int DEFAULTINSET = 0;
+
+ /** 100 percent unit for relative positioning. Current value is 1000. */
+ public static final int PERMILLE = 1000;
+
+ /** Global Stroke To Highlight Selection */
+ static protected float[] dash = { 5f, 5f };
+
+ /**
+ *
+ */
+ static public Stroke SELECTION_STROKE = new BasicStroke(1, BasicStroke.CAP_BUTT,
+ BasicStroke.JOIN_MITER, 10.0f, dash,
+ 0.0f);
+
+ /**
+ * Represents no decoration for the beginning or ending of edges.
+ *
+ * @see #setLineBegin(Map, int)
+ * @see #getLineBegin(Map)
+ * @see #setLineEnd(Map, int)
+ * @see #getLineEnd(Map)
+ */
+ public static final int ARROW_NONE = 0;
+
+ /**
+ * Represents a classic arrow decoration for the beginning or ending of
+ * edges.
+ *
+ * @see #setLineBegin(Map,int)
+ * @see #getLineBegin(Map)
+ * @see #setLineEnd(Map, int)
+ * @see #getLineEnd(Map)
+ */
+ public static final int ARROW_CLASSIC = 1;
+
+ /**
+ * Represents a technical arrow decoration for the beginning or ending of
+ * edges.
+ *
+ * @see #setLineBegin(Map, int)
+ * @see #getLineBegin(Map)
+ * @see #setLineEnd(Map, int)
+ * @see #getLineEnd(Map)
+ */
+ public static final int ARROW_TECHNICAL = 2;
+
+ /**
+ * Represents a simple arrow decoration for the beginning or ending of
+ * edges.
+ *
+ * @see #setLineBegin(Map,int)
+ * @see #getLineBegin(Map)
+ * @see #setLineEnd(Map, int)
+ * @see #getLineEnd(Map)
+ */
+ public static final int ARROW_SIMPLE = 4;
+
+ /**
+ * Represents a circle decoration for the beginning or ending of edges.
+ *
+ * @see #setLineBegin(Map, int)
+ * @see #getLineBegin(Map)
+ * @see #setLineEnd(Map, int)
+ * @see #getLineEnd(Map)
+ */
+ public static final int ARROW_CIRCLE = 5;
+
+ /**
+ * Represents a line decoration for the beginning or ending of edges.
+ *
+ * @see #setLineBegin(Map, int)
+ * @see #getLineBegin(Map)
+ * @see #setLineEnd(Map, int)
+ * @see #getLineEnd(Map)
+ */
+ public static final int ARROW_LINE = 7;
+
+ /**
+ * Represents a double line decoration for the beginning or ending of edges.
+ *
+ * @see #setLineBegin(Map, int)
+ * @see #getLineBegin(Map)
+ * @see #setLineEnd(Map, int)
+ * @see #getLineEnd(Map)
+ */
+ public static final int ARROW_DOUBLELINE = 8;
+
+ /**
+ * Represents a diamond decoration for the beginning or ending of edges.
+ *
+ * @see #setLineBegin(Map, int)
+ * @see #getLineBegin(Map)
+ * @see #setLineEnd(Map, int)
+ * @see #getLineEnd(Map)
+ */
+ public static final int ARROW_DIAMOND = 9;
+
+ /** Represents an orthogonal line style */
+ public static final int STYLE_ORTHOGONAL = 11;
+
+ /** Represents a bezier line style */
+ public static final int STYLE_BEZIER = 12;
+
+ /** Represents an spline line style */
+ public static final int STYLE_SPLINE = 13;
+
+ /** Represents an bezier line style */
+ public static final int X_AXIS = 1;
+
+ /** Represents an bezier line style */
+ public static final int Y_AXIS = 2;
+
+ /**
+ * The default routing that deals with loops. This is returned by
+ * {@link #getRouting(Map)} if there is no routing assigned.
+ */
+ public static Edge.Routing ROUTING_DEFAULT = new DefaultEdge.LoopRouting();
+
+ /**
+ * A simple routing.
+ */
+ public static final Edge.Routing ROUTING_SIMPLE = new DefaultEdge.DefaultRouting();
+
+ /**
+ * Key for the <code>sizeableAxis</code> attribute. This attribute
+ * contains an Integer value representing which axis of a cell may be
+ * resized/scaled Constants defined in this class.
+ */
+ public final static String SIZEABLEAXIS = "sizeableAxis";
+
+ /**
+ * Key for the <code>moveableAxis</code> attribute. This attribute
+ * contains an Integer value indicating along which axis a cell may be
+ * moved. Constants defined in this class.
+ */
+ public final static String MOVEABLEAXIS = "moveableAxis";
+
+ /**
+ * Key for the <code>replaceAttributes</code> attribute. This special
+ * attribute contains a Boolean instance indicating whether a map of
+ * attributes should replace the attributes of the receiving view.
+ */
+ public final static String REPLACEATTRIBUTES = "replaceAttributes";
+
+ /**
+ * Key for the <code>removeAttributes</code> attribute. This special
+ * attribute contains a list of attribute-keys which should be removed at
+ * the receiving views.
+ */
+ public final static String REMOVEATTRIBUTES = "removeAttributes";
+
+ /**
+ * Key for the <code>removeAll</code> attribute. This causes the receivers
+ * attributes to be replaced by the the map that contains this attribute.
+ */
+ public final static String REMOVEALL = "removeAll";
+
+ /**
+ * Key for the <code>icon</code> attribute. Use instances of Icon as
+ * values for this key.
+ */
+ public final static String ICON = "icon";
+
+ /**
+ * Key for the <code>font</code> attribute. Use instances of Font as
+ * values for this key.
+ */
+ public final static String FONT = "font";
+
+ /**
+ * Key for the <code>opaque</code> attribute. Use instances of Boolean as
+ * values for this key.
+ */
+ public final static String OPAQUE = "opaque";
+
+ /**
+ * Key for the <code>groupOpaque</code> attribute. Use instances of
+ * Boolean as values for this key.
+ */
+ public final static String GROUPOPAQUE = "groupOpaque";
+
+ /**
+ * Key for the <code>border</code> attribute. Use instances of Border as
+ * values for this key. Optionally, you can set the global instance of
+ * LineBorder.
+ */
+ public final static String BORDER = "border";
+
+ /**
+ * Key for the <code>linecolor</code> attribute. Use instances of Color as
+ * values for this key.
+ */
+ public final static String LINECOLOR = "linecolor";
+
+ /**
+ * Key for the <code>bordercolor</code> attribute. Use instances of Color
+ * as values for this key.
+ */
+ public final static String BORDERCOLOR = "bordercolor";
+
+ /**
+ * Key for the <code>linewidth</code> attribute. Use instances of Float as
+ * values for this key.
+ */
+ public final static String LINEWIDTH = "linewidth";
+
+ /**
+ * Key for the <code>foreground</code> attribute. Use instances of Color
+ * as values for this key.
+ */
+ public final static String FOREGROUND = "foregroundColor";
+
+ /**
+ * Key for the <code>background</code> attribute. Use instances of Color
+ * as values for this key.
+ */
+ public final static String BACKGROUND = "backgroundColor";
+
+ /**
+ * Key for the <code>gradient</code> attribute. Use instances of Color as
+ * values for this key.
+ */
+ public final static String GRADIENTCOLOR = "gradientColor";
+
+ /**
+ * Key for the <code>verticalAlignment</code> attribute. Use instances of
+ * Integer as values for this key. Constants defined in JLabel class. This
+ * key value pair is for placment of label on vertex cell. Valid values
+ * would be JLabel.TOP, JLabel.CENTER, JLABEL.BOTTOM
+ */
+ public final static String VERTICAL_ALIGNMENT = "verticalAlignment";
+
+ /**
+ * Key for the <code>horizontalAlignment</code> attribute. Use instances
+ * of Integer as values for this key. Constants defined in JLabel class.
+ * This Key/Value pair is for placment of label on vertex cell. Valid values
+ * would be JLabel.LEFT, JLabel.CENTER, JLabel.RIGHT
+ */
+ public final static String HORIZONTAL_ALIGNMENT = "horizontalAlignment";
+
+ /**
+ * Key for the <code>verticalTextPosition</code> attribute. Use instances
+ * of Integer as values for this key. Constants defined in JLabel class.
+ * This Key/Value pair affects text postion of label on vertex cell relative
+ * to image, the value is of type SwingConstant.
+ */
+ public final static String VERTICAL_TEXT_POSITION = "verticalTextPosition";
+
+ /**
+ * Key for the <code>horizontalTextPosition</code> attribute. Use
+ * instances of Integer as values for this key. Constants defined in JLabel
+ * class. This Key/Value pair affects text postion of label on vertex cell
+ * relative to image, the value is of type SwingConstant.
+ */
+ public final static String HORIZONTAL_TEXT_POSITION = "horizontalTextPosition";
+
+ /**
+ * Key for the <code>dashPattern</code> attribute. Use instances of
+ * float[] as values for this key.
+ */
+ public final static String DASHPATTERN = "dashPattern";
+
+ /**
+ * Key for the <code>dashOffset</code> attribute. Use instances of float
+ * as values for this key.
+ */
+ public final static String DASHOFFSET = "dashOffset";
+
+ /**
+ * Key for the <code>lineStyle</code> attribute. Use instances of Integer
+ * as values for this key. Constants defined in this class.
+ */
+ public final static String LINESTYLE = "lineStyle";
+
+ /**
+ * Key for the <code>lineBegin</code> attribute. Use instances of Integer
+ * as values for this key. Constants defined in this class.
+ */
+ public final static String LINEBEGIN = "lineBegin";
+
+ /**
+ * Key for the <code>lineEnd</code> attribute. Use instances of Integer as
+ * values for this key. Constants defined in this class.
+ */
+ public final static String LINEEND = "lineEnd";
+
+ /**
+ * Key for the <code>beginSize</code> attribute. Use instances of Integer
+ * as values for this key.
+ */
+ public final static String BEGINSIZE = "beginSize";
+
+ /**
+ * Key for the <code>endSize</code> attribute. Use instances of Integer as
+ * values for this key.
+ */
+ public final static String ENDSIZE = "endSize";
+
+ /**
+ * Key for the <code>beginFill</code> attribute. Use instances of Integer
+ * as values for this key.
+ */
+ public final static String BEGINFILL = "beginFill";
+
+ /**
+ * Key for the <code>endFill</code> attribute. Use instances of Integer as
+ * values for this key.
+ */
+ public final static String ENDFILL = "endFill";
+
+ /**
+ * Key for the <code>value</code> attribute. You can use any Object as a
+ * value for this key.
+ */
+ public static final String VALUE = "value";
+
+ /**
+ * Key for the <code>editable</code> attribute. Use instances of Boolean
+ * as values for this key.
+ */
+ public static final String EDITABLE = "editable";
+
+ /**
+ * Key for the <code>moveable</code> attribute. Use instances of Boolean
+ * as values for this key.
+ */
+ public static final String MOVEABLE = "moveable";
+
+ /**
+ * Key for the <code>sizeable</code> attribute. Use instances of Boolean
+ * as values for this key.
+ */
+ public static final String SIZEABLE = "sizeable";
+
+ /**
+ * Key for the <code>autosize</code> attribute. Use instances of Boolean
+ * as values for this key.
+ */
+ public static final String AUTOSIZE = "autosize";
+
+ /**
+ * Key for the <code>resize</code> attribute. Use instances of Boolean as
+ * values for this key.
+ */
+ public static final String RESIZE = "resize";
+
+ /**
+ * Key for the <code>inset</code> attribute. Use instances of Integer as
+ * values for this key.
+ */
+ public static final String INSET = "inset";
+
+ /**
+ * Key for the <code>constrained</code> attribute. Use instances of
+ * Boolean as values for this key.
+ */
+ public static final String CONSTRAINED = "constrained";
+
+ /**
+ * Key for the <code>selectable</code> attribute. Use instances of Boolean
+ * as values for this key.
+ */
+ public static final String SELECTABLE = "selectable";
+
+ /**
+ * Key for the <code>childrenSelectable</code> attribute. Use instances of
+ * Boolean as values for this key.
+ */
+ public static final String CHILDRENSELECTABLE = "childrenSelectable";
+
+ /**
+ * Key for the <code>childrenSelectable</code> attribute. Use instances of
+ * Boolean as values for this key.
+ */
+ public static final String MOVEHIDDENCHILDREN = "childrenSelectable";
+
+ /**
+ * Key for the <code>bendable</code> attribute. Use instances of Boolean
+ * as values for this key.
+ */
+ public static final String BENDABLE = "bendable";
+
+ /**
+ * Key for the <code>connectable</code> attribute. Use instances of
+ * Boolean as values for this key.
+ */
+ public static final String CONNECTABLE = "connectable";
+
+ /**
+ * Key for the <code>disconnectable</code> attribute. Use instances of
+ * Boolean as values for this key.
+ */
+ public static final String DISCONNECTABLE = "disconnectable";
+
+ /**
+ * Key for the <code>bounds</code> attribute. Use instances of Rectangle
+ * as values for this key.
+ */
+ public static final String BOUNDS = "bounds";
+
+ /**
+ * Key for the <code>points</code> attribute. Use instances of List as
+ * values for this key. The list should contain Point instances.
+ */
+ public static final String POINTS = "points";
+
+ /**
+ * Key for the <code>routing</code> attribute. Use instances of
+ * EdgeView.EdgeRouter as values for this key.
+ */
+ public static final String ROUTING = "routing";
+
+ /**
+ * Key for the <code>labelposition</code> attribute. Use instances of
+ * Point as values for this key. This Key/Value pair is for position of text
+ * relative to edge cell, and has no effect on label in vertex cell.
+ */
+ public static final String LABELPOSITION = "labelposition";
+
+ /**
+ * Key for the <code>extraLabels</code> attribute. Use arrays of Objects
+ * as values for this key, where the toString() methods of the objects
+ * provide the label text value.
+ */
+ public static final String EXTRALABELS = "extraLabels";
+
+ /**
+ * Key for the <code>extraLabelPositions</code> attribute. Use arrays of
+ * Points as values for this key.
+ */
+ public static final String EXTRALABELPOSITIONS = "extraLabelPositions";
+
+ /**
+ * Key for the <code>labelAlongEdge</code> attribute. Use instances of
+ * Boolean as values for this key.
+ */
+ public static final String LABELALONGEDGE = "labelAlongEdge";
+
+ /**
+ * Key for the <code>absoluteX</code> attribute. Use instances of Boolean
+ * as values for this key.
+ */
+ public static final String ABSOLUTEX = "absoluteX";
+
+ /**
+ * Key for the <code>absoluteY</code> attribute. Use instances of Boolean
+ * as values for this key.
+ */
+ public static final String ABSOLUTEY = "absoluteY";
+
+ /**
+ * Key for the <code>offset</code> attribute. Use instances of Point as
+ * values for this key.
+ */
+ public static final String OFFSET = "offset";
+
+ /**
+ * Key for the <code>size</code> attribute. Use instances of Dimension as
+ * values for this key.
+ */
+ public static final String SIZE = "size";
+
+ /**
+ * Overloaded method that passes arguments on as arrays
+ */
+ public static Map createAttributes(Object cell, Object key, Object value) {
+ return createAttributes(new Object[] { cell }, new Object[] { key }, new Object[] { value });
+ }
+
+ /**
+ * Overloaded method that passes arguments on as arrays
+ */
+ public static Map createAttributes(Object[] cells, Object key, Object value) {
+ return createAttributes(cells, new Object[] { key }, new Object[] { value });
+ }
+
+ /**
+ * Returns a new (nested) map, from cells to attribute maps. The attributes
+ * are populated with the (key, value)-pairs specified by the two given
+ * arrays. The <code>keys</code> and <code>values</code> parameters must
+ * match in size.
+ */
+ public static Map createAttributes(Object[] cells, Object[] keys, Object[] values) {
+ if ((keys != null) && (values != null) && (keys.length != values.length))
+ throw new IllegalArgumentException("Keys and values must have same length");
+
+ Map nested = new Hashtable();
+
+ for (int i = 0; i < cells.length; i++) {
+ if (cells[i] != null) {
+ Map attributes = new Hashtable();
+
+ for (int j = 0; j < keys.length; j++)
+ if ((keys[j] != null) && (values[j] != null))
+ attributes.put(keys[j], values[j]);
+
+ nested.put(cells[i], attributes);
+ }
+ }
+
+ return nested;
+ }
+
+ /**
+ * Returns a new map, from cells to property maps. The <code>elements</code>
+ * may be instances of <code>CellView</code>, in which case the cell
+ * view's corresponding cell is used as a key, and its attributes are used
+ * as a property map. In any other case, the <code>element</code> is
+ * considered as a cell and looked-up in the cell mapper to find the
+ * corresponding view. If a view is found, its attributes are cloned and
+ * used as a property map, along with the cell as a key.
+ * <p>
+ * <strong>Note: </strong> This method returns a map of maps! This is
+ * different from the createMap method, which creates a map, from keys to
+ * values. This method returns a map, from cells to maps, which in turn map
+ * from keys to values.
+ */
+ public static Map createAttributes(Object[] elements, CellMapper cm) {
+ Map attributes = new Hashtable();
+
+ for (int i = 0; i < elements.length; i++) {
+ CellView view = null;
+ Object key = elements[i];
+
+ if (key instanceof CellView) {
+ view = (CellView) key;
+ key = view.getCell();
+ } else if (cm != null) // else is assumed by clients!
+ view = cm.getMapping(key, false);
+
+ if (view != null)
+ attributes.put(key, view.getAllAttributes().clone()); // FIXME:
+ // clone
+ // required?
+ }
+
+ return attributes;
+ }
+
+ // Returns a nested map of cell, Map pairs where the map reflects
+ /**
+ * DOCUMENT ME!
+ *
+ * @param elements DOCUMENT ME!
+ * @param model DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static Map createAttributesFromModel(Object[] elements, GraphModel model) {
+ Map attributes = new Hashtable();
+
+ for (int i = 0; i < elements.length; i++) {
+ AttributeMap attr = model.getAttributes(elements[i]);
+
+ if ((attr != null) && (attr.size() > 0))
+ attributes.put(elements[i], (AttributeMap) attr.clone());
+ }
+
+ return attributes;
+ }
+
+ /**
+ * Replace the keys in <code>map</code> using <code>keyMap</code, which
+ * maps from old to new keys. The value in <code>map</code> must itself
+ * be a map, and is cloned using <code>cloneMap</code>.
+ */
+ public static Map replaceKeys(Map keyMap, Map map) {
+ Map newMap = new Hashtable();
+ Iterator it = map.entrySet().iterator();
+
+ while (it.hasNext()) {
+ Map.Entry entry = (Map.Entry) it.next();
+
+ if (entry.getValue() instanceof Map) {
+ Object newKey = keyMap.get(entry.getKey());
+
+ if (newKey != null) {
+ AttributeMap val = (AttributeMap) ((AttributeMap) entry.getValue()).clone();
+ newMap.put(newKey, val);
+ }
+ }
+ }
+
+ return newMap;
+ }
+
+ /**
+ * Merges the specified nested maps by adding all attributes in the change
+ * to the attributes for the cell in target, if the cell does not exist in
+ * target, then a new entry is added with all attributes from change.
+ * Returns the modified target map.
+ *
+ * Note: This method removes entries from <code>change</code> and adds
+ * entries to <code>target</code> in-place!
+ *
+ * @return a map including all attributes from change merged with target
+ */
+ public static Map merge(Map change, Map target) {
+ if ((change != null) && (target != null)) {
+ change = new Hashtable(change);
+
+ Iterator it = target.entrySet().iterator();
+
+ while (it.hasNext()) {
+ Map.Entry entry = (Map.Entry) it.next();
+ Map map = (Map) entry.getValue();
+ Map additional = (Map) change.remove(entry.getKey());
+
+ if (additional != null)
+ map.putAll(additional);
+ }
+
+ // Adds remaining attributes
+ target.putAll(change);
+ }
+
+ return target;
+ }
+
+ /**
+ * Sets the value attribute in the specified map to the specified font
+ * value.
+ *
+ * @param map
+ * The map to store the font attribute in.
+ * @param font
+ * The value to set the font attribute to.
+ */
+ public static void setFont(Map map, Font font) {
+ map.put(FONT, font);
+ }
+
+ /**
+ * Returns the font for the specified attribute map. Uses default font if no
+ * font is specified in the attribute map.
+ */
+ public static Font getFont(Map map) {
+ Font font = (Font) map.get(FONT);
+
+ if (font == null)
+ font = DEFAULTFONT;
+
+ return font;
+ }
+
+ /**
+ * Sets specific attributes are being marked for removal @ param map The
+ * transport map indicating the attribute removal @ param value The
+ * attributes to be removed
+ */
+ public static final void setRemoveAttributes(Map map, Object[] value) {
+ map.put(REMOVEATTRIBUTES, value);
+ }
+
+ /**
+ * Returns the attribute marked as for removal in the specified map.
+ */
+ public static final Object[] getRemoveAttributes(Map map) {
+ return (Object[]) map.get(REMOVEATTRIBUTES);
+ }
+
+ /**
+ * Sets the moveableaxis attribute in the specified map to the specified
+ * value.
+ */
+ public static final void setMoveableAxis(Map map, int axis) {
+ map.put(MOVEABLEAXIS, new Integer(axis));
+ }
+
+ /**
+ * Returns the moveableaxis attribute from the specified map.
+ */
+ public static final int getMoveableAxis(Map map) {
+ Integer intObj = (Integer) map.get(MOVEABLEAXIS);
+
+ if (intObj != null)
+ return intObj.intValue();
+
+ return 0;
+ }
+
+ /**
+ * Sets the sizeableAxis attribute in the specified map to the specified
+ * value.
+ */
+ public static final void setSizeableAxis(Map map, int axis) {
+ map.put(SIZEABLEAXIS, new Integer(axis));
+ }
+
+ /**
+ * Returns the sizeableAxis attribute from the specified map.
+ */
+ public static final int getSizeableAxis(Map map) {
+ Integer intObj = (Integer) map.get(SIZEABLEAXIS);
+
+ if (intObj != null)
+ return intObj.intValue();
+
+ return 0;
+ }
+
+ /**
+ * Sets the icon attribute in the specified map to the specified value.
+ */
+ public static final void setIcon(Map map, Icon value) {
+ map.put(ICON, value);
+ }
+
+ /**
+ * Returns the icon attribute from the specified map.
+ */
+ public static final Icon getIcon(Map map) {
+ return (Icon) map.get(ICON);
+ }
+
+ /**
+ * Sets the opaque attribute in the specified map to the specified value.
+ */
+ public static final void setOpaque(Map map, boolean flag) {
+ map.put(OPAQUE, new Boolean(flag));
+ }
+
+ /**
+ * Returns the opaque attribute from the specified map.
+ */
+ public static final boolean isOpaque(Map map) {
+ Boolean bool = (Boolean) map.get(OPAQUE);
+
+ if (bool != null)
+ return bool.booleanValue();
+
+ return false;
+ }
+
+ /**
+ * Sets the opaque attribute in the specified map to the specified value.
+ */
+ public static final void setGroupOpaque(Map map, boolean flag) {
+ map.put(GROUPOPAQUE, new Boolean(flag));
+ }
+
+ /**
+ * Returns the opaque attribute from the specified map.
+ */
+ public static final boolean isGroupOpaque(Map map) {
+ Boolean bool = (Boolean) map.get(GROUPOPAQUE);
+
+ if (bool != null)
+ return bool.booleanValue();
+
+ return false;
+ }
+
+ /**
+ * Sets the border attribute in the specified map to the specified value.
+ */
+ public static final void setBorder(Map map, Border value) {
+ map.put(BORDER, value);
+ }
+
+ /**
+ * Returns the border attribute from the specified map.
+ */
+ public static final Border getBorder(Map map) {
+ return (Border) map.get(BORDER);
+ }
+
+ /**
+ * Sets the linecolor attribute in the specified map to the specified value.
+ */
+ public static final void setLineColor(Map map, Color value) {
+ map.put(LINECOLOR, value);
+ }
+
+ /**
+ * Returns the linecolor attribute from the specified map.
+ */
+ public static final Color getLineColor(Map map) {
+ return (Color) map.get(LINECOLOR);
+ }
+
+ /**
+ * Sets the bordercolor attribute in the specified map to the specified
+ * value.
+ */
+ public static final void setBorderColor(Map map, Color value) {
+ map.put(BORDERCOLOR, value);
+ }
+
+ /**
+ * Returns the bordercolor attribute from the specified map.
+ */
+ public static final Color getBorderColor(Map map) {
+ return (Color) map.get(BORDERCOLOR);
+ }
+
+ /**
+ * Sets the linewidth attribute in the specified map to the specified value.
+ */
+ public static final void setLineWidth(Map map, float width) {
+ map.put(LINEWIDTH, new Float(width));
+ }
+
+ /**
+ * Returns the linewidth attribute from the specified map.
+ */
+ public static final float getLineWidth(Map map) {
+ Float floatObj = (Float) map.get(LINEWIDTH);
+
+ if (floatObj != null)
+ return floatObj.floatValue();
+
+ return 1;
+ }
+
+ /**
+ * Sets the foregrund attribute in the specified map to the specified value.
+ */
+ public static final void setForeground(Map map, Color value) {
+ map.put(FOREGROUND, value);
+ }
+
+ /**
+ * Returns the foreground attribute from the specified map.
+ */
+ public static final Color getForeground(Map map) {
+ return (Color) map.get(FOREGROUND);
+ }
+
+ /**
+ * Sets the background attribute in the specified map to the specified
+ * value.
+ */
+ public static final void setBackground(Map map, Color value) {
+ map.put(BACKGROUND, value);
+ }
+
+ /**
+ * Returns the background attribute from the specified map.
+ */
+ public static final Color getBackground(Map map) {
+ return (Color) map.get(BACKGROUND);
+ }
+
+ /**
+ * Sets the gradientcolor attribute in the specified map to the specified
+ * value.
+ */
+ public static final void setGradientColor(Map map, Color value) {
+ map.put(GRADIENTCOLOR, value);
+ }
+
+ /**
+ * Returns the gradientcolor attribute from the specified map.
+ */
+ public static final Color getGradientColor(Map map) {
+ return (Color) map.get(GRADIENTCOLOR);
+ }
+
+ /**
+ * This method set the position of the label in vertex cells, and takes
+ * aruguments of type SwingConstants (for JLabel) i.e. JLabel.TOP etc.
+ * Default value is JLabel.CENTER. This method has no effect on edge cells.
+ */
+ public static final void setVerticalAlignment(Map map, int alignment) {
+ map.put(VERTICAL_ALIGNMENT, new Integer(alignment));
+ }
+
+ /**
+ * Returns the verticalalignment attribute from the specified map.
+ */
+ public static final int getVerticalAlignment(Map map) {
+ Integer intObj = (Integer) map.get(VERTICAL_ALIGNMENT);
+
+ if (intObj != null)
+ return intObj.intValue();
+
+ return JLabel.CENTER;
+ }
+
+ /**
+ * This method set the position of the label in vertex cells, and takes
+ * aruguments of type SwingConstants (for JLabel) i.e. JLabel.LEFT etc.
+ * Default is JLabel.CENTER. This method has no effect on edge cells.
+ */
+ public static final void setHorizontalAlignment(Map map, int alignment) {
+ map.put(HORIZONTAL_ALIGNMENT, new Integer(alignment));
+ }
+
+ /**
+ * Returns the horizontalalignment attribute from the specified map.
+ */
+ public static final int getHorizontalAlignment(Map map) {
+ Integer intObj = (Integer) map.get(HORIZONTAL_ALIGNMENT);
+
+ if (intObj != null)
+ return intObj.intValue();
+
+ return JLabel.CENTER;
+ }
+
+ /**
+ * This method set the text of a label on vertext cell relative to image.
+ * See JLabel api. Default value is JLabel.BOTTOM.
+ */
+ public static final void setVerticalTextPosition(Map map, int textPosition) {
+ map.put(VERTICAL_TEXT_POSITION, new Integer(textPosition));
+ }
+
+ /**
+ * Returns the verticaltextposition attribute from the specified map.
+ */
+ public static final int getVerticalTextPosition(Map map) {
+ Integer intObj = (Integer) map.get(VERTICAL_TEXT_POSITION);
+
+ if (intObj != null)
+ return intObj.intValue();
+
+ return JLabel.BOTTOM;
+ }
+
+ /**
+ * This method set the text of a label on vertext cell relative to image.
+ * See JLabel api. Default value is JLabel.CENTER.
+ */
+ public static final void setHorizontalTextPosition(Map map, int textPosition) {
+ map.put(HORIZONTAL_TEXT_POSITION, new Integer(textPosition));
+ }
+
+ /**
+ * Returns the horizontaltextposition attribute from the specified map.
+ */
+ public static final int getHorizontalTextPosition(Map map) {
+ Integer intObj = (Integer) map.get(HORIZONTAL_TEXT_POSITION);
+
+ if (intObj != null)
+ return intObj.intValue();
+
+ return JLabel.CENTER;
+ }
+
+ /**
+ * Sets the dashpattern attribute in the specified map to the specified
+ * value.
+ */
+ public static final void setDashPattern(Map map, float[] value) {
+ map.put(DASHPATTERN, value);
+ }
+
+ /**
+ * Returns the dashpattern attribute from the specified map.
+ */
+ public static final float[] getDashPattern(Map map) {
+ return (float[]) map.get(DASHPATTERN);
+ }
+
+ /**
+ * Sets the dashoffset attribute in the specified map to the specified
+ * value.
+ */
+ public static final void setDashOffset(Map map, float value) {
+ map.put(DASHOFFSET, new Float(value));
+ }
+
+ /**
+ * Returns the dashoffset attribute from the specified map.
+ */
+ public static final float getDashOffset(Map map) {
+ Float floatObj = (Float) map.get(DASHOFFSET);
+
+ if (floatObj != null)
+ return floatObj.floatValue();
+
+ return 1;
+ }
+
+ /**
+ * Sets the linestyle attribute in the specified map to the specified value.
+ */
+ public static final void setLineStyle(Map map, int style) {
+ map.put(LINESTYLE, new Integer(style));
+ }
+
+ /**
+ * Returns the linestyle attribute from the specified map.
+ */
+ public static final int getLineStyle(Map map) {
+ Integer intObj = (Integer) map.get(LINESTYLE);
+
+ if (intObj != null)
+ return intObj.intValue();
+
+ return STYLE_ORTHOGONAL;
+ }
+
+ /**
+ * Sets the beginsize attribute in the specified map to the specified value.
+ */
+ public static final void setBeginSize(Map map, int style) {
+ map.put(BEGINSIZE, new Integer(style));
+ }
+
+ /**
+ * Returns the beginsize attribute from the specified map.
+ */
+ public static final int getBeginSize(Map map) {
+ Integer intObj = (Integer) map.get(BEGINSIZE);
+
+ if (intObj != null)
+ return intObj.intValue();
+
+ return DEFAULTDECORATIONSIZE;
+ }
+
+ /**
+ * Sets the endsize attribute in the specified map to the specified value.
+ */
+ public static final void setEndSize(Map map, int style) {
+ map.put(ENDSIZE, new Integer(style));
+ }
+
+ /**
+ * Returns the endsize attribute from the specified map.
+ */
+ public static final int getEndSize(Map map) {
+ Integer intObj = (Integer) map.get(ENDSIZE);
+
+ if (intObj != null)
+ return intObj.intValue();
+
+ return DEFAULTDECORATIONSIZE;
+ }
+
+ /**
+ * Sets the LINEBEGIN attribute in the specified map to the specified value.
+ * This attribute indicates what sort of decoration should be applied to the
+ * beginning of edges when they are rendered.
+ *
+ * @see #ARROW_NONE
+ * @see #ARROW_CLASSIC
+ * @see #ARROW_TECHNICAL
+ * @see #ARROW_SIMPLE
+ * @see #ARROW_CIRCLE
+ * @see #ARROW_LINE
+ * @see #ARROW_DOUBLELINE
+ * @see #ARROW_DIAMOND
+ */
+ public static final void setLineBegin(Map map, int style) {
+ map.put(LINEBEGIN, new Integer(style));
+ }
+
+ /**
+ * Returns the LINEBEGIN attribute from the specified map. This attribute
+ * indicates what sort of decoration should be applied to the beginning of
+ * edges when they are rendered.
+ *
+ * @see #ARROW_NONE
+ * @see #ARROW_CLASSIC
+ * @see #ARROW_TECHNICAL
+ * @see #ARROW_SIMPLE
+ * @see #ARROW_CIRCLE
+ * @see #ARROW_LINE
+ * @see #ARROW_DOUBLELINE
+ * @see #ARROW_DIAMOND
+ */
+ public static final int getLineBegin(Map map) {
+ Integer intObj = (Integer) map.get(LINEBEGIN);
+
+ if (intObj != null)
+ return intObj.intValue();
+
+ return ARROW_NONE;
+ }
+
+ /**
+ * Sets the LINEEND attribute in the specified map to the specified value.
+ * This attribute indicates what sort of decoration should be applied to the
+ * ends of edges when they are rendered.
+ *
+ * @see #ARROW_NONE
+ * @see #ARROW_CLASSIC
+ * @see #ARROW_TECHNICAL
+ * @see #ARROW_SIMPLE
+ * @see #ARROW_CIRCLE
+ * @see #ARROW_LINE
+ * @see #ARROW_DOUBLELINE
+ * @see #ARROW_DIAMOND
+ */
+ public static final void setLineEnd(Map map, int style) {
+ map.put(LINEEND, new Integer(style));
+ }
+
+ /**
+ * Returns the LINEEND attribute from the specified map. This attribute
+ * indicates what sort of decoration should be applied to the ends of edges
+ * when they are rendered.
+ *
+ * @see #ARROW_NONE
+ * @see #ARROW_CLASSIC
+ * @see #ARROW_TECHNICAL
+ * @see #ARROW_SIMPLE
+ * @see #ARROW_CIRCLE
+ * @see #ARROW_LINE
+ * @see #ARROW_DOUBLELINE
+ * @see #ARROW_DIAMOND
+ */
+ public static final int getLineEnd(Map map) {
+ Integer intObj = (Integer) map.get(LINEEND);
+
+ if (intObj != null)
+ return intObj.intValue();
+
+ return ARROW_NONE;
+ }
+
+ /**
+ * Sets the value attribute in the specified map to the specified value.
+ */
+ public static final void setValue(Map map, Object value) {
+ map.put(VALUE, value);
+ }
+
+ /**
+ * Returns the value attribute from the specified map.
+ */
+ public static final Object getValue(Map map) {
+ return map.get(VALUE);
+ }
+
+ /**
+ * Sets the label position attribute in the specified map to the specified
+ * value.
+ */
+ public static final void setLabelPosition(Map map, Point2D position) {
+ map.put(LABELPOSITION, position);
+ }
+
+ /**
+ * Returns the label position attribute from the specified map. The point is
+ * interpreted by the EdgeRenderer as follows: <br>
+ * x coordinate: the percentual position on the length of the edge in
+ * direction of the edge <br>
+ * y coordinate: the absolute offset, orthogonally to the edge
+ */
+ public static final Point2D getLabelPosition(Map map) {
+ return (Point2D) map.get(LABELPOSITION);
+ }
+
+ /**
+ * Sets the array of additional labels. The objects's toString methods are
+ * used to determine the actual label string. Extra labels only work with
+ * edges currently.
+ */
+ public static final void setExtraLabels(Map map, Object[] definitions) {
+ map.put(EXTRALABELS, definitions);
+ }
+
+ /**
+ * Returns the additional label objects from the specified map.Extra labels
+ * only work with edges currently.
+ */
+ public static final Object[] getExtraLabels(Map map) {
+ return (Object[]) map.get(EXTRALABELS);
+ }
+
+ /**
+ * Sets the labelpositions attribute in the specified map to the specified
+ * value. The Point instance at a particular index corresponds to the object
+ * at the same index in the extralabels array attribute. Extra labels only
+ * work with edges currently.
+ *
+ * @see #getLabelPosition(Map)
+ */
+ public static final void setExtraLabelPositions(Map map, Point2D[] positions) {
+ map.put(EXTRALABELPOSITIONS, positions);
+ }
+
+ /**
+ * Returns the extralabelpositions attribute from the specified map. Extra
+ * labels only work with edges currently.
+ */
+ public static final Point2D[] getExtraLabelPositions(Map map) {
+ return (Point2D[]) map.get(EXTRALABELPOSITIONS);
+ }
+
+ /**
+ * Sets if the label should be painted along the edge.
+ */
+ public static final void setLabelAlongEdge(Map map, boolean flag) {
+ map.put(LABELALONGEDGE, new Boolean(flag));
+ }
+
+ /**
+ * Returns the true if the label should be painted along the edge. Defaults
+ * to false.
+ */
+ public static final boolean isLabelAlongEdge(Map map) {
+ Boolean bool = (Boolean) map.get(LABELALONGEDGE);
+
+ if (bool != null)
+ return bool.booleanValue();
+
+ return false;
+ }
+
+ /**
+ * Sets the editable attribute in the specified map to the specified value.
+ */
+ public static final void setEditable(Map map, boolean flag) {
+ map.put(EDITABLE, new Boolean(flag));
+ }
+
+ /**
+ * Returns the editable attribute from the specified map.
+ */
+ public static final boolean isEditable(Map map) {
+ Boolean bool = (Boolean) map.get(EDITABLE);
+
+ if (bool != null)
+ return bool.booleanValue();
+
+ return true;
+ }
+
+ /**
+ * Sets the moveable attribute in the specified map to the specified value.
+ */
+ public static final void setMoveable(Map map, boolean flag) {
+ map.put(MOVEABLE, new Boolean(flag));
+ }
+
+ /**
+ * Returns the moveable attribute from the specified map.
+ */
+ public static final boolean isMoveable(Map map) {
+ Boolean bool = (Boolean) map.get(MOVEABLE);
+
+ if (bool != null)
+ return bool.booleanValue();
+
+ return true;
+ }
+
+ /**
+ * Sets the sizeable attribute in the specified map to the specified value.
+ */
+ public static final void setSizeable(Map map, boolean flag) {
+ map.put(SIZEABLE, new Boolean(flag));
+ }
+
+ /**
+ * Returns the sizeable attribute from the specified map.
+ */
+ public static final boolean isSizeable(Map map) {
+ Boolean bool = (Boolean) map.get(SIZEABLE);
+
+ if (bool != null)
+ return bool.booleanValue();
+
+ return true;
+ }
+
+ /**
+ * Sets the autosize attribute in the specified map to the specified value.
+ */
+ public static final void setAutoSize(Map map, boolean flag) {
+ map.put(AUTOSIZE, new Boolean(flag));
+ }
+
+ /**
+ * Returns the autosize attribute from the specified map.
+ */
+ public static final boolean isAutoSize(Map map) {
+ Boolean bool = (Boolean) map.get(AUTOSIZE);
+
+ if (bool != null)
+ return bool.booleanValue();
+
+ return false;
+ }
+
+ /**
+ * Sets the resize attribute in the specified map to the specified value.
+ */
+ public static final void setResize(Map map, boolean flag) {
+ map.put(RESIZE, new Boolean(flag));
+ }
+
+ /**
+ * Returns the resize attribute from the specified map.
+ */
+ public static final boolean isResize(Map map) {
+ Boolean bool = (Boolean) map.get(RESIZE);
+
+ if (bool != null)
+ return bool.booleanValue();
+
+ return false;
+ }
+
+ /**
+ * Sets the constrained attribute in the specified map to the specified
+ * value.
+ */
+ public static final void setConstrained(Map map, boolean flag) {
+ map.put(CONSTRAINED, new Boolean(flag));
+ }
+
+ /**
+ * Returns the constrained attribute from the specified map.
+ */
+ public static final boolean isConstrained(Map map) {
+ Boolean bool = (Boolean) map.get(CONSTRAINED);
+
+ if (bool != null)
+ return bool.booleanValue();
+
+ return false;
+ }
+
+ /**
+ * Sets the selectable attribute in the specified map to the specified
+ * value. This detemines whether or not a cell may be selected. Vertices and
+ * edges may be selectable, not ports.
+ */
+ public static final void setSelectable(Map map, boolean flag) {
+ map.put(SELECTABLE, new Boolean(flag));
+ }
+
+ /**
+ * Returns the selectable attribute from the specified map.
+ *
+ * @see #setSelectable(Map, boolean)
+ */
+ public static final boolean isSelectable(Map map) {
+ Boolean bool = (Boolean) map.get(SELECTABLE);
+
+ if (bool != null)
+ return bool.booleanValue();
+
+ return true;
+ }
+
+ /**
+ * Sets the childrenselectable attribute in the specified map to the
+ * specified value.
+ */
+ public static final void setChildrenSelectable(Map map, boolean flag) {
+ map.put(CHILDRENSELECTABLE, new Boolean(flag));
+ }
+
+ /**
+ * Returns the childrenselectable attribute from the specified map.
+ */
+ public static final boolean isChildrenSelectable(Map map) {
+ Boolean bool = (Boolean) map.get(CHILDRENSELECTABLE);
+
+ if (bool != null)
+ return bool.booleanValue();
+
+ return true;
+ }
+
+ /**
+ * Sets the bendable attribute in the specified map to the specified value.
+ */
+ public static final void setBendable(Map map, boolean flag) {
+ map.put(BENDABLE, new Boolean(flag));
+ }
+
+ /**
+ * Returns the bendable attribute from the specified map.
+ */
+ public static final boolean isBendable(Map map) {
+ Boolean bool = (Boolean) map.get(BENDABLE);
+
+ if (bool != null)
+ return bool.booleanValue();
+
+ return true;
+ }
+
+ /**
+ * Sets the connectable attribute in the specified map to the specified
+ * value.
+ */
+ public static final void setConnectable(Map map, boolean flag) {
+ map.put(CONNECTABLE, new Boolean(flag));
+ }
+
+ /**
+ * Returns the connectable attribute from the specified map.
+ */
+ public static final boolean isConnectable(Map map) {
+ Boolean bool = (Boolean) map.get(CONNECTABLE);
+
+ if (bool != null)
+ return bool.booleanValue();
+
+ return true;
+ }
+
+ /**
+ * Sets the disconnectable attribute in the specified map to the specified
+ * value.
+ */
+ public static final void setDisconnectable(Map map, boolean flag) {
+ map.put(DISCONNECTABLE, new Boolean(flag));
+ }
+
+ /**
+ * Returns the disconnectable attribute from the specified map.
+ */
+ public static final boolean isDisconnectable(Map map) {
+ Boolean bool = (Boolean) map.get(DISCONNECTABLE);
+
+ if (bool != null)
+ return bool.booleanValue();
+
+ return true;
+ }
+
+ /**
+ * Sets the points attribute in the specified map to the specified value.
+ * Points are literally the points where an edge is connected by two lines.
+ * The two defaults points are the start and end of the edge. For example,
+ * for an simple orthogonal edge there will be two extra points indicating
+ * where the two right-angled bends are. This attribute can only be applied
+ * to an edge.
+ */
+ public static final void setPoints(Map map, java.util.List list) {
+ map.put(POINTS, list);
+ }
+
+ /**
+ * Returns the points attribute from the specified map.
+ *
+ * @see #setPoints(Map, java.util.List)
+ */
+ public static final java.util.List getPoints(Map map) {
+ return (java.util.List) map.get(POINTS);
+ }
+
+ /**
+ * Sets the routing attribute in the specified map to the specified value.
+ */
+ public static final void setRouting(Map map, Edge.Routing routing) {
+ map.put(ROUTING, routing);
+ }
+
+ /**
+ * Returns the routing attribute from the specified map.
+ */
+ public static final Edge.Routing getRouting(Map map) {
+ Edge.Routing routing = (Edge.Routing) map.get(ROUTING);
+
+ if (routing == null)
+ routing = ROUTING_DEFAULT;
+
+ return routing;
+ }
+
+ /**
+ * Sets the bounds attribute in the specified map to the specified value.
+ */
+ public static final void setBounds(Map map, Rectangle2D bounds) {
+ map.put(BOUNDS, bounds);
+ }
+
+ /**
+ * Returns the bounds attribute from the specified map. Note: The CellView
+ * interface offers a getBounds method!
+ */
+ public static final Rectangle2D getBounds(Map map) {
+ return (Rectangle2D) map.get(BOUNDS);
+ }
+
+ /**
+ * Sets the inset attribute in the specified map to the specified value.
+ */
+ public static final void setInset(Map map, int width) {
+ map.put(INSET, new Integer(width));
+ }
+
+ /**
+ * Returns the inset attribute from the specified map. Note: The CellView
+ * interface offers a getBounds method!
+ */
+ public static final int getInset(Map map) {
+ Integer intObj = (Integer) map.get(INSET);
+
+ if (intObj != null)
+ return intObj.intValue();
+
+ return DEFAULTINSET;
+ }
+
+ /**
+ * Sets the size attribute in the specified map to the specified value.
+ */
+ public static final void setSize(Map map, Dimension size) {
+ map.put(SIZE, size);
+ }
+
+ /**
+ * Returns the size attribute from the specified map.
+ */
+ public static final Dimension getSize(Map map) {
+ return (Dimension) map.get(SIZE);
+ }
+
+ /**
+ * Sets the offset attribute in the specified map to the specified value.
+ * The offset is the position of a port relative to its origin, note this
+ * attribute is only for ports.
+ */
+ public static final void setOffset(Map map, Point2D offset) {
+ map.put(OFFSET, offset);
+ }
+
+ /**
+ * Returns the offset attribute from the specified map. The offset is the
+ * position of a port relative to its origin, note this attribute is only
+ * for ports.
+ */
+ public static final Point2D getOffset(Map map) {
+ return (Point2D) map.get(OFFSET);
+ }
+
+ /**
+ * Sets the beginfill attribute in the specified map to the specified value.
+ */
+ public static final void setBeginFill(Map map, boolean flag) {
+ map.put(BEGINFILL, new Boolean(flag));
+ }
+
+ /**
+ * Returns the beginfill attribute from the specified map.
+ */
+ public static final boolean isBeginFill(Map map) {
+ Boolean bool = (Boolean) map.get(BEGINFILL);
+
+ if (bool != null)
+ return bool.booleanValue();
+
+ return false;
+ }
+
+ /**
+ * Sets the endfill attribute in the specified map to the specified value.
+ */
+ public static final void setEndFill(Map map, boolean flag) {
+ map.put(ENDFILL, new Boolean(flag));
+ }
+
+ /**
+ * Returns the endfill attribute from the specified map.
+ */
+ public static final boolean isEndFill(Map map) {
+ Boolean bool = (Boolean) map.get(ENDFILL);
+
+ if (bool != null)
+ return bool.booleanValue();
+
+ return false;
+ }
+
+ /**
+ * Sets the absolute attributes in the specified map to the specified value.
+ */
+ public static final void setAbsolute(Map map, boolean flag) {
+ setAbsoluteX(map, flag);
+ setAbsoluteY(map, flag);
+ }
+
+ /**
+ * Sets the absolutey attribute in the specified map to the specified value.
+ */
+ public static final void setAbsoluteY(Map map, boolean flag) {
+ map.put(ABSOLUTEY, new Boolean(flag));
+ }
+
+ /**
+ * Returns the absolutey attribute from the specified map.
+ */
+ public static final boolean isAbsoluteY(Map map) {
+ Boolean bool = (Boolean) map.get(ABSOLUTEY);
+
+ if (bool != null)
+ return bool.booleanValue();
+
+ return false;
+ }
+
+ /**
+ * Sets the absolutex attribute in the specified map to the specified value.
+ */
+ public static final void setAbsoluteX(Map map, boolean flag) {
+ map.put(ABSOLUTEX, new Boolean(flag));
+ }
+
+ /**
+ * Returns the absolutex attribute from the specified map.
+ */
+ public static final boolean isAbsoluteX(Map map) {
+ Boolean bool = (Boolean) map.get(ABSOLUTEX);
+
+ if (bool != null)
+ return bool.booleanValue();
+
+ return false;
+ }
+
+ /**
+ * Sets the removeall attribute in the specified map to the specified value.
+ */
+ public static final void setRemoveAll(Map map, boolean flag) {
+ map.put(REMOVEALL, new Boolean(flag));
+ }
+
+ /**
+ * Returns the removeall attribute from the specified map.
+ */
+ public static final boolean isRemoveAll(Map map) {
+ Boolean bool = (Boolean) map.get(REMOVEALL);
+
+ if (bool != null)
+ return bool.booleanValue();
+
+ return false;
+ }
+
+ /**
+ * @return Returns the ROUTING_SIMPLE.
+ */
+ public static Edge.Routing getROUTING_SIMPLE() {
+ return ROUTING_SIMPLE;
+ }
+
+ /**
+ * @return Returns the ROUTING_SIMPLE.
+ */
+ public static Edge.Routing getROUTING_DEFAULT() {
+ return ROUTING_DEFAULT;
+ }
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/GraphContext.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/GraphContext.java
new file mode 100644
index 0000000..f2895eb
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/GraphContext.java
@@ -0,0 +1,290 @@
+/*
+ * @(#)GraphContext.java 1.0 03-JUL-04
+ *
+ * Copyright (c) 2001-2004 Gaudenz Alder
+ *
+ */
+package org.jgraph.graph;
+
+import org.jgraph.JGraph;
+
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+
+/*
+ * This object is used for interactive operations such as move and copy. It
+ * offers two basic operations: 1. Create temporary views for a set of cells,
+ * and 2. Create temporary views for a set of edges that are connected to a set
+ * of cells.<p> <strong>Note:</strong>The views are consistent subgraphs.
+ * Consequently, if an edge points to a selected and an unselected port, the
+ * selected port is replaced by its temporary view, but the unselected port is
+ * not.
+ *
+ * @version 1.0 1/1/02 @author Gaudenz Alder
+ */
+/**
+ *
+ */
+public class GraphContext implements CellMapper {
+ /** Reference to the parent graph. */
+ protected JGraph graph;
+
+ /** Reference to the graphs GraphLayoutCache. */
+ protected transient GraphLayoutCache graphLayoutCache;
+
+ /** Reference to the cells. */
+ protected Object[] cells;
+
+ /** Set of all cells including all descendants. */
+ protected Set allCells;
+
+ /** Set of all cells including all descendants. */
+ protected Set cellSet;
+
+ /** Number of all descendants without ports. */
+ protected int cellCount;
+
+ /** Map of (cell, view) pairs including ports. */
+ protected Map views = new Hashtable();
+
+ /**
+ * Constructs a graph context for <code>cells</code> with respect to the
+ * connections defined in the model, and the views in the view of
+ * <code>graph</code>.
+ */
+ public GraphContext(JGraph graph, Object[] cells) {
+ GraphModel model = graph.getModel();
+ allCells = new HashSet(DefaultGraphModel.getDescendants(model, cells));
+ graphLayoutCache = graph.getGraphLayoutCache();
+ this.graph = graph;
+ this.cells = cells;
+ // Count Visible Non-Port Cells
+ cellSet = new HashSet();
+
+ Iterator it = allCells.iterator();
+
+ while (it.hasNext()) {
+ Object cell = it.next();
+
+ if (graphLayoutCache.isVisible(cell)) {
+ cellSet.add(cell);
+
+ if (!model.isPort(cell))
+ cellCount++;
+ }
+ }
+ }
+
+ /**
+ * Returns <code>true</code> if this object contains no cells.
+ */
+ public boolean isEmpty() {
+ return ((cells == null) || (cells.length == 0));
+ }
+
+ /**
+ * Returns the number of all objects (cells and children) in this object.
+ */
+ public int getDescendantCount() {
+ return cellCount;
+ }
+
+ /**
+ * Returns the graph that was passed to the constructor.
+ */
+ public JGraph getGraph() {
+ return graph;
+ }
+
+ /**
+ * Returns the array that was passed to the constructor.
+ */
+ public Object[] getCells() {
+ return cells;
+ }
+
+ /**
+ * Returns <code>true</code> if <code>node</code> or one of its
+ * ancestors is contained in this object and visible in the original graph.
+ */
+ public boolean contains(Object node) {
+ return cellSet.contains(node);
+ }
+
+ /**
+ * Returns an new consistent array of views for <code>cells</code>.
+ */
+ public CellView[] createTemporaryCellViews() {
+ CellView[] cellViews = new CellView[cells.length];
+
+ for (int i = 0; i < cells.length; i++)
+ // Get View For Cell
+ cellViews[i] = getMapping(cells[i], true);
+
+ return cellViews;
+ }
+
+ /**
+ * Returns an new consistent array of views for the ports.
+ */
+ public CellView[] createTemporaryPortViews() {
+ GraphModel model = graph.getModel();
+ ArrayList result = new ArrayList();
+ Iterator it = allCells.iterator();
+
+ while (it.hasNext()) {
+ Object cand = it.next();
+
+ if (model.isPort(cand) && graph.getGraphLayoutCache().isVisible(cand))
+ result.add(getMapping(cand, true));
+ }
+
+ // List -> CellView[] Conversion
+ CellView[] array = new PortView[result.size()];
+ result.toArray(array);
+
+ return array;
+ }
+
+ /**
+ * Returns an new consistent array of views for the edges that are connected
+ * to and not contained in <code>cells</code>.
+ */
+ public CellView[] createTemporaryContextViews() {
+ return createTemporaryContextViews(cellSet);
+ }
+
+ /**
+ * Returns an new consistent array of views for the edges that are connected
+ * to and not contained in <code>cellSet</code>.
+ */
+ public CellView[] createTemporaryContextViews(Set cellSet) {
+ Object[] cells = cellSet.toArray();
+
+ // Retrieve Edges From Model (recursively for edges connected
+ // to edges connected to edges...)
+ List result = new ArrayList();
+ Set delta = DefaultGraphModel.getEdges(graph.getModel(), cells);
+
+ do {
+ // Iterate over Edges
+ Iterator it = delta.iterator();
+
+ while (it.hasNext()) {
+ Object obj = it.next();
+ CellView edge = graphLayoutCache.getMapping(obj, false);
+
+ // If Edge not in cellset, add its view is visible in graphview
+ if (!cellSet.contains(obj) && graphLayoutCache.isVisible(obj) && (edge != null)
+ && edge.isLeaf())
+ // Note: Do not use getMapping, it ignores the create flag
+ result.add(createMapping(obj));
+ }
+
+ delta = DefaultGraphModel.getEdges(graph.getModel(), delta.toArray());
+ } while (!delta.isEmpty());
+
+ // List -> CellView[] Conversion
+ CellView[] array = new CellView[result.size()];
+ result.toArray(array);
+
+ return array;
+ }
+
+ /**
+ * Returns the <code>CellView</code> that is mapped to <code>cell</code>
+ * in the graph context. New views are created based on whether cell is
+ * contained in the context. The <code>create</code>-flag is ignored.
+ */
+ public CellView getMapping(Object cell, boolean create) {
+ if (cell != null) {
+ CellView view = (CellView) views.get(cell);
+
+ if (view != null)
+ return view;
+ else if (contains(cell)
+ || (graph.getModel().isPort(cell) && create
+ && graph.getGraphLayoutCache().isVisible(cell)))
+ return createMapping(cell);
+ else
+
+ return graphLayoutCache.getMapping(cell, false);
+ }
+
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param cell DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public CellView createMapping(Object cell) {
+ CellView view = graphLayoutCache.getFactory().createView(graph.getModel(), cell);
+ putMapping(cell, view);
+ view.refresh(graph.getModel(), this, true); // Create Dependent Views
+ // Fetch Attributes From Original View
+
+ CellView src = graphLayoutCache.getMapping(cell, false);
+
+ if (src != null) {
+ view.changeAttributes((AttributeMap) src.getAttributes().clone());
+ // Inserts portviews into points list
+ view.refresh(graph.getModel(), this, false);
+ }
+
+ return view;
+ }
+
+ /**
+ * Disconnects the edges in <code>cells</code> from the sources and
+ * targets that are not in this context and returns a ConnectionSet that
+ * defines the disconnection.
+ */
+ public ConnectionSet disconnect(CellView[] cells) {
+ ConnectionSet cs = new ConnectionSet();
+
+ for (int i = 0; i < cells.length; i++) {
+ if (cells[i] instanceof EdgeView) {
+ EdgeView view = (EdgeView) cells[i];
+ CellView port = view.getSource();
+
+ if (GraphConstants.isDisconnectable(view.getAllAttributes())) {
+ if ((port != null)
+ && GraphConstants.isDisconnectable(port.getParentView().getAllAttributes())
+ && !contains(port.getCell())) {
+ view.setSource(null);
+ cs.disconnect(view.getCell(), true);
+ }
+
+ port = view.getTarget();
+
+ if ((port != null)
+ && GraphConstants.isDisconnectable(port.getParentView().getAllAttributes())
+ && !contains(port.getCell())) {
+ view.setTarget(null);
+ cs.disconnect(view.getCell(), false);
+ }
+ }
+ }
+ }
+
+ return cs;
+ }
+
+ /**
+ * Associates <code>cell</code> with <code>view</code> in the graph
+ * context.
+ */
+ public void putMapping(Object cell, CellView view) {
+ views.put(cell, view);
+ }
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/GraphLayoutCache.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/GraphLayoutCache.java
new file mode 100644
index 0000000..abe4e3e
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/GraphLayoutCache.java
@@ -0,0 +1,2961 @@
+/*
+ * @(#)GraphLayoutCache.java 1.0 03-JUL-04
+ *
+ * Copyright (c) 2001-2004 Gaudenz Alder
+ *
+ */
+package org.jgraph.graph;
+
+import org.jgraph.event.GraphLayoutCacheEvent;
+import org.jgraph.event.GraphLayoutCacheListener;
+import org.jgraph.event.GraphModelEvent;
+
+import java.awt.geom.Rectangle2D;
+
+import java.io.Serializable;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.Stack;
+import java.util.WeakHashMap;
+
+import javax.swing.event.EventListenerList;
+import javax.swing.undo.CannotRedoException;
+import javax.swing.undo.CannotUndoException;
+import javax.swing.undo.CompoundEdit;
+import javax.swing.undo.UndoableEdit;
+
+
+/**
+ * An object that defines the view of a graphmodel. This object maps between
+ * model cells and views and provides a set of methods to change these views.
+ * The view may also contain its own set of attributes and is therefore an
+ * extension of an Observable, which may be observed by the GraphUI. It uses the
+ * model to send its changes to the command history.
+ *
+ * @version 1.0 1/1/02
+ * @author Gaudenz Alder
+ */
+public class GraphLayoutCache implements CellMapper, Serializable {
+ /**
+ * True if the cells should be auto-sized when their values change. Default
+ * is false.
+ */
+ protected boolean autoSizeOnValueChange = false;
+
+ /**
+ * Boolean indicating whether existing connections should me made visible if
+ * their sources or targets are made visible, given the opposite end of the
+ * edge is already visible or made visible, too. Default is true.
+ */
+ protected boolean showsExistingConnections = true;
+
+ /**
+ * Boolean indicating whether connections should be made visible when
+ * reconnected and their source and target port is visible. Default is true.
+ */
+ protected boolean showsChangedConnections = true;
+
+ /**
+ * Boolean indicating whether edited cells should be made visible if they
+ * are changed via
+ * {@link #edit(Map, ConnectionSet, ParentMap, UndoableEdit[])}. Default is
+ * true.
+ */
+ protected boolean showsInvisibleEditedCells = true;
+
+ /**
+ * Boolean indicating whether inserted should be made visible if they are
+ * inserted via
+ * {@link #insert(Object[], Map, ConnectionSet, ParentMap, UndoableEdit[])}.
+ * Default is true.
+ */
+ protected boolean showsInsertedCells = true;
+
+ /**
+ * Boolean indicating whether inserted edges should me made visible if their
+ * sources or targets are already visible. Default is true.
+ */
+ protected boolean showsInsertedConnections = true;
+
+ /**
+ * Boolean indicating whether existing connections should be hidden if their
+ * source or target and no parent of the ports is visible, either by hiding
+ * the cell or by changing the source or target of the edge to a hidden
+ * cell. Default is true.
+ */
+ protected boolean hidesExistingConnections = true;
+
+ /**
+ * Boolean indicating whether existing connections should be hidden if their
+ * source or target port is removed from the model. Default is false.
+ */
+ protected boolean hidesDanglingConnections = false;
+
+ /**
+ * Boolean indicating whether cellviews should be remembered once visible in
+ * this GraphLayoutCache. Default is true.
+ */
+ protected boolean remembersCellViews = true;
+
+ /**
+ * Boolean indicating whether inserted cells should automatically be
+ * selected. Default is true. This is ignored if the cache is partial. Note:
+ * Despite the name of this field the implementation is located in the
+ * BasicGraphUI.GraphModelHandler.graphChanged method.
+ */
+ protected boolean selectsAllInsertedCells = true;
+
+ /**
+ * Boolean indicating whether cells that are inserted using the local insert
+ * method should automatically be selected. Default is true. This is ignored
+ * if the cache is not partial and selectsAllInsertedCells is true, in which
+ * case the cells will be selected through another mechanism. Note: Despite
+ * the name of this field the implementation is located in the
+ * BasicGraphUI.GraphLayoutCacheObserver.changed method.
+ */
+ protected boolean selectsLocalInsertedCells = true;
+
+ /**
+ * Boolean indicating whether children should be moved to the parent group's
+ * origin on expand. Default is true.
+ */
+ protected boolean movesChildrenOnExpand = true;
+
+ /**
+ * Boolean indicating whether parents should be moved to the child area
+ * origin on collapse. Default is true.
+ */
+ protected boolean movesParentsOnCollapse = true;
+
+ /**
+ * Boolean indicating whether parents should always be resized to the child
+ * area on collapse. If false the size is only initially updated if it has
+ * not yet been assigned. Default is false.
+ */
+ protected boolean resizesParentsOnCollapse = false;
+
+ /**
+ * Specified the initial x- and y-scaling factor for initial collapsed group
+ * bounds. Default is 1.0, ie. no scaling.
+ */
+ protected double collapseXScale = 1.0;
+
+ /**
+ * Specified the initial x- and y-scaling factor for initial collapsed group
+ * bounds. Default is 1.0, ie. no scaling.
+ */
+ protected double collapseYScale = 1.0;
+
+ /**
+ * Boolean indicating whether edges should be reconneted to visible parents
+ * on collapse/expand. Default is false.
+ *
+ * @deprecated edges are moved to parent view and back automatically
+ */
+ protected boolean reconnectsEdgesToVisibleParent = false;
+
+ /**
+ * The list of listeners that listen to the model.
+ */
+ protected EventListenerList listenerList = new EventListenerList();
+
+ /**
+ * Reference to the graphModel
+ */
+ protected GraphModel graphModel;
+
+ /**
+ * Maps cells to views. The hidden mapping is used to remembed cell views
+ * that are hidden, based on the remembersCellViews setting. hiddenMapping
+ * must weak keys for the cells since when cells are removed hiddenMapping
+ * is not updated.
+ */
+ protected Map mapping = new Hashtable();
+
+ /**
+ * Maps cells to views. The hidden mapping is used to remembed cell views
+ * that are hidden, based on the remembersCellViews setting. hiddenMapping
+ * must weak keys for the cells since when cells are removed hiddenMapping
+ * is not updated.
+ */
+ protected Map hiddenMapping = new WeakHashMap();
+
+ /**
+ * Factory to create the views.
+ */
+ protected CellViewFactory factory = null;
+
+ /**
+ * The set of visible cells.
+ */
+ protected Set visibleSet = new HashSet();
+
+ /**
+ * Ordered list of roots for the view.
+ */
+ protected List roots = new ArrayList();
+
+ /**
+ * Cached array of all ports for the view.
+ */
+ protected PortView[] ports;
+
+ /**
+ * Only portions of the model are visible.
+ */
+ protected boolean partial = false;
+
+ /**
+ * Controls if all attributes are local. If this is false then the
+ * createLocalEdit will check the localAttributes set to see if a specific
+ * attribute is local, otherwise it will assume that all attributes are
+ * local. This allows to make all attributes local without actually knowing
+ * them. Default is false.
+ */
+ protected boolean allAttributesLocal = false;
+
+ /**
+ * A set containing all attribute keys that are stored in the cell views, in
+ * other words, the view-local attributes.
+ */
+ protected Set localAttributes = new HashSet();
+
+ /**
+ * Constructs a graph layout cache.
+ */
+ public GraphLayoutCache() {
+ this(new DefaultGraphModel(), new DefaultCellViewFactory());
+ }
+
+ /**
+ * Constructs a view for the specified model that uses <code>factory</code>
+ * to create its views.
+ *
+ * @param model
+ * the model that constitues the data source
+ */
+ public GraphLayoutCache(GraphModel model, CellViewFactory factory) {
+ this(model, factory, false);
+ }
+
+ /**
+ * Constructs a view for the specified model that uses <code>factory</code>
+ * to create its views.
+ *
+ * @param model
+ * the model that constitues the data source
+ */
+ public GraphLayoutCache(GraphModel model, CellViewFactory factory, boolean partial) {
+ this(model, factory, null, null, partial);
+ }
+
+ /**
+ * Constructs a view for the specified model that uses <code>factory</code>
+ * to create its views.
+ *
+ * @param model
+ * the model that constitues the data source
+ */
+ public GraphLayoutCache(GraphModel model, CellViewFactory factory, CellView[] cellViews,
+ CellView[] hiddenCellViews, boolean partial) {
+ this.factory = factory;
+ this.partial = partial;
+
+ if (cellViews != null) {
+ graphModel = model;
+
+ for (int i = 0; i < cellViews.length; i++) {
+ if (cellViews[i] != null) {
+ putMapping(cellViews[i].getCell(), cellViews[i]);
+
+ if (partial)
+ visibleSet.add(cellViews[i].getCell());
+ }
+ }
+
+ insertViews(cellViews);
+
+ // Notify observers for autosizing?
+ } else {
+ setModel(model);
+ }
+
+ if (hiddenCellViews != null) {
+ for (int i = 0; i < hiddenCellViews.length; i++)
+ hiddenMapping.put(hiddenCellViews[i].getCell(), hiddenCellViews[i]);
+ }
+ }
+
+ //
+ // GraphLayoutCacheListeners
+ //
+
+ /**
+ * Adds a listener for the GraphLayoutCacheEvent posted after the graph
+ * layout cache changes.
+ *
+ * @see #removeGraphLayoutCacheListener
+ * @param l
+ * the listener to add
+ */
+ public void addGraphLayoutCacheListener(GraphLayoutCacheListener l) {
+ listenerList.add(GraphLayoutCacheListener.class, l);
+ }
+
+ /**
+ * Removes a listener previously added with <B>addGraphLayoutCacheListener()
+ * </B>.
+ *
+ * @see #addGraphLayoutCacheListener
+ * @param l
+ * the listener to remove
+ */
+ public void removeGraphLayoutCacheListener(GraphLayoutCacheListener l) {
+ listenerList.remove(GraphLayoutCacheListener.class, l);
+ }
+
+ /**
+ * Invoke this method after you've changed how the cells are to be
+ * represented in the graph.
+ */
+ public void cellViewsChanged(final CellView[] cellViews) {
+ if (cellViews != null) {
+ fireGraphLayoutCacheChanged(this,
+ new GraphLayoutCacheEvent.GraphLayoutCacheChange() {
+ public Object[] getInserted() {
+ return null;
+ }
+
+ public Object[] getRemoved() {
+ return null;
+ }
+
+ public Map getPreviousAttributes() {
+ return null;
+ }
+
+ public Object getSource() {
+ return this;
+ }
+
+ public Object[] getChanged() {
+ return cellViews;
+ }
+
+ public Map getAttributes() {
+ return null;
+ }
+
+ public Object[] getContext() {
+ return null;
+ }
+ });
+ }
+ }
+
+ /*
+ * Notify all listeners that have registered interest for notification on
+ * this event type. The event instance is lazily created using the
+ * parameters passed into the fire method.
+ *
+ * @see EventListenerList
+ */
+ protected void fireGraphLayoutCacheChanged(Object source,
+ GraphLayoutCacheEvent.GraphLayoutCacheChange edit) {
+ // Guaranteed to return a non-null array
+ Object[] listeners = listenerList.getListenerList();
+ GraphLayoutCacheEvent e = null;
+
+ // Process the listeners last to first, notifying
+ // those that are interested in this event
+ for (int i = listeners.length - 2; i >= 0; i -= 2) {
+ if (listeners[i] == GraphLayoutCacheListener.class) {
+ // Lazily create the event:
+ if (e == null)
+ e = new GraphLayoutCacheEvent(source, edit);
+
+ ((GraphLayoutCacheListener) listeners[i + 1]).graphLayoutCacheChanged(e);
+ }
+ }
+ }
+
+ /**
+ * Return an array of all GraphLayoutCacheListener that were added to this
+ * model.
+ */
+ public GraphLayoutCacheListener[] getGraphLayoutCacheListeners() {
+ return (GraphLayoutCacheListener[]) listenerList.getListeners(GraphLayoutCacheListener.class);
+ }
+
+ //
+ // Accessors
+ //
+
+ /**
+ * Sets the factory that creates the cell views.
+ */
+ public void setFactory(CellViewFactory factory) {
+ this.factory = factory;
+ }
+
+ /**
+ * Returns the factory that was passed to the constructor.
+ */
+ public CellViewFactory getFactory() {
+ return factory;
+ }
+
+ /**
+ * Sets the current model.
+ */
+ public void setModel(GraphModel model) {
+ roots.clear();
+ mapping.clear();
+ hiddenMapping.clear();
+ visibleSet.clear();
+ graphModel = model;
+
+ if (!isPartial()) {
+ Object[] cells = DefaultGraphModel.getRoots(getModel());
+ CellView[] cellViews = getMapping(cells, true);
+ insertViews(cellViews);
+ }
+
+ // Update PortView Cache and Notify Observers
+ updatePorts();
+ cellViewsChanged(getRoots());
+ }
+
+ /**
+ * @return Returns an unordered array of all visible cellviews.
+ */
+ public CellView[] getCellViews() {
+ Collection coll = mapping.values();
+ CellView[] result = new CellView[coll.size()];
+ coll.toArray(result);
+
+ return result;
+ }
+
+ /**
+ * Returns the bounding box for the specified cell views.
+ */
+ public static Rectangle2D getBounds(CellView[] views) {
+ if ((views != null) && (views.length > 0)) {
+ Rectangle2D r = views[0].getBounds();
+ Rectangle2D ret = (r != null) ? (Rectangle2D) r.clone() : null;
+
+ for (int i = 1; i < views.length; i++) {
+ r = views[i].getBounds();
+
+ if (r != null) {
+ if (ret == null)
+ ret = (r != null) ? (Rectangle2D) r.clone() : null;
+ else
+ Rectangle2D.union(ret, r, ret);
+ }
+ }
+
+ return ret;
+ }
+
+ return null;
+ }
+
+ /**
+ * A helper method to return various arrays of cells that are visible in
+ * this cache. For example, to get all selected vertices in a graph, do
+ * <code>graph.getSelectionCells(graph.getGraphLayoutCache().getCells(false, true,
+ false, false));</code>
+ */
+ public Object[] getCells(boolean groups, boolean vertices, boolean ports, boolean edges) {
+ CellView[] views = getCellViews();
+ List result = new ArrayList(views.length);
+ GraphModel model = getModel();
+
+ for (int i = 0; i < views.length; i++) {
+ Object cell = views[i].getCell();
+ boolean isEdge = model.isEdge(cell);
+
+ if ((ports || !model.isPort(cell))) {
+ if (((((ports || vertices) && !isEdge) || (edges && isEdge)) && views[i].isLeaf())
+ || (groups && !views[i].isLeaf()))
+ result.add(views[i].getCell());
+ }
+ }
+
+ return result.toArray();
+ }
+
+ /**
+ * Returns a nested map of (cell, map) pairs that represent all attributes
+ * of all cell views in this view.
+ *
+ * @see #getCellViews
+ */
+ public Map createNestedMap() {
+ CellView[] cellViews = getCellViews();
+ Map nested = new Hashtable();
+
+ for (int i = 0; i < cellViews.length; i++) {
+ nested.put(cellViews[i].getCell(),
+ new Hashtable((Map) cellViews[i].getAllAttributes().clone()));
+ }
+
+ return nested;
+ }
+
+ /**
+ * @return Returns an unordered array of all hidden cellviews.
+ */
+ public CellView[] getHiddenCellViews() {
+ Collection coll = hiddenMapping.values();
+ CellView[] result = new CellView[coll.size()];
+ coll.toArray(result);
+
+ return result;
+ }
+
+ // Remaps all existing views using the CellViewFactory
+ /**
+ * DOCUMENT ME!
+ */
+ public synchronized void reload() {
+ List newRoots = new ArrayList();
+ Map oldMapping = new Hashtable(mapping);
+ mapping.clear();
+
+ Iterator it = oldMapping.keySet().iterator();
+
+ while (it.hasNext()) {
+ Object cell = it.next();
+ CellView oldView = (CellView) oldMapping.get(cell);
+ CellView newView = getMapping(cell, true);
+ newView.changeAttributes(oldView.getAttributes());
+
+ // newView.refresh(getModel(), this, false);
+ if (roots.contains(oldView))
+ newRoots.add(newView);
+ }
+
+ // replace hidden
+ hiddenMapping.clear();
+ roots = newRoots;
+ }
+
+ /**
+ * Returns the current model.
+ */
+ public GraphModel getModel() {
+ return graphModel;
+ }
+
+ /**
+ * Returns the roots of the view.
+ */
+ public CellView[] getRoots() {
+ CellView[] views = new CellView[roots.size()];
+ roots.toArray(views);
+
+ return views;
+ }
+
+ /**
+ * Return all root cells that intersect the given rectangle.
+ */
+ public CellView[] getRoots(Rectangle2D clip) {
+ java.util.List result = new ArrayList();
+ CellView[] views = getRoots();
+
+ for (int i = 0; i < views.length; i++)
+ if (views[i].getBounds().intersects(clip))
+ result.add(views[i]);
+
+ views = new CellView[result.size()];
+ result.toArray(views);
+
+ return views;
+ }
+
+ /**
+ * Returns a an array with the visible cells in <code>cells</code>.
+ */
+ public Object[] getVisibleCells(Object[] cells) {
+ if (cells != null) {
+ List result = new ArrayList(cells.length);
+
+ for (int i = 0; i < cells.length; i++)
+ if (isVisible(cells[i]))
+ result.add(cells[i]);
+
+ return result.toArray();
+ }
+
+ return null;
+ }
+
+ /**
+ * Returns the ports of the view.
+ */
+ public PortView[] getPorts() {
+ return ports;
+ }
+
+ /**
+ * Updates the cached array of ports.
+ */
+ protected void updatePorts() {
+ Object[] roots = DefaultGraphModel.getRoots(graphModel);
+ List list = DefaultGraphModel.getDescendants(graphModel, roots);
+
+ if (list != null) {
+ ArrayList result = new ArrayList();
+ Iterator it = list.iterator();
+
+ while (it.hasNext()) {
+ Object cell = it.next();
+
+ if (graphModel.isPort(cell)) {
+ CellView portView = getMapping(cell, false);
+
+ if (portView != null) {
+ result.add(portView);
+ portView.refresh(getModel(), this, false);
+ }
+ }
+ }
+
+ ports = new PortView[result.size()];
+ result.toArray(ports);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param views DOCUMENT ME!
+ * @param create DOCUMENT ME!
+ */
+ public void refresh(CellView[] views, boolean create) {
+ if (views != null)
+ for (int i = 0; i < views.length; i++)
+ refresh(views[i], create);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param view DOCUMENT ME!
+ * @param create DOCUMENT ME!
+ */
+ public void refresh(CellView view, boolean create) {
+ if (view != null) {
+ view.refresh(getModel(), this, create);
+
+ CellView[] children = view.getChildViews();
+
+ for (int i = 0; i < children.length; i++)
+ refresh(children[i], create);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param views DOCUMENT ME!
+ */
+ public void update(CellView[] views) {
+ if (views != null)
+ for (int i = 0; i < views.length; i++)
+ update(views[i]);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param view DOCUMENT ME!
+ */
+ public void update(CellView view) {
+ if (view != null) {
+ view.update();
+
+ CellView[] children = view.getChildViews();
+
+ for (int i = 0; i < children.length; i++)
+ update(children[i]);
+ }
+ }
+
+ //
+ // Update View based on Model Change
+ //
+ /**
+ * Called from BasicGraphUI.ModelHandler to update the view based on the
+ * specified GraphModelEvent.
+ */
+ public void graphChanged(GraphModelEvent.GraphModelChange change) {
+ // Get Old Attributes From GraphModelChange (Undo) -- used to remap
+ // removed cells
+ CellView[] views = change.getViews(this);
+
+ if (views != null) {
+ // Only ex-visible views are piggybacked
+ for (int i = 0; i < views.length; i++)
+ if (views[i] != null) {
+ // Do not use putMapping because cells are invisible
+ mapping.put(views[i].getCell(), views[i]);
+ }
+
+ // Ensure visible state
+ setVisibleImpl(getCells(views), true);
+ }
+
+ // Fetch View Order Of Changed Cells (Before any changes)
+ Object[] changed = change.getChanged();
+ // Fetch Views to Insert before Removal (Special case: two step process,
+ // see setModel)
+ getMapping(change.getInserted(), true);
+ // Remove and Hide Roots
+ views = removeCells(change.getRemoved());
+ // Store Removed Attributes In GraphModelChange (Undo)
+ change.putViews(this, views);
+
+ // Insert New Roots
+ // insertViews(insertViews);
+ // Hide edges with invisible source or target
+ if (isPartial()) {
+ // Then show
+ showCellsForChange(change);
+ // First hide
+ hideCellsForChange(change);
+ }
+
+ // Refresh Changed Cells
+ if ((changed != null) && (changed.length > 0)) {
+ // Restore All Cells in Model Order (Replace Roots)
+ for (int i = 0; i < changed.length; i++) {
+ CellView view = getMapping(changed[i], false);
+
+ if (view != null) {
+ view.refresh(getModel(), this, true);
+ // Update child edges in groups (routing)
+ update(view);
+ }
+ }
+ }
+
+ reloadRoots();
+ // Refresh Context of Changed Cells (=Connected Edges)
+ refresh(getMapping(getContext(change), false), false);
+ updatePorts();
+ }
+
+ /**
+ * Completely reloads all roots from the model in the order returned by
+ * DefaultGraphModel.getAll. This uses the current visibleSet and mapping to
+ * fetch the cell views for the cells.
+ */
+ protected void reloadRoots() {
+ // Reorder roots
+ Object[] orderedCells = DefaultGraphModel.getAll(graphModel);
+ List newRoots = new ArrayList();
+
+ for (int i = 0; i < orderedCells.length; i++) {
+ CellView view = getMapping(orderedCells[i], false);
+
+ if (view != null) {
+ view.refresh(getModel(), this, true);
+
+ if (view.getParentView() == null) {
+ newRoots.add(view);
+ }
+ }
+ }
+
+ roots = newRoots;
+ }
+
+ /**
+ * Hook for subclassers to augment the context for a graphChange. This means
+ * you can add additional cells that should be refreshed on a special change
+ * event. eg. parallel edges when one is removed or added.
+ */
+ protected Object[] getContext(GraphModelEvent.GraphModelChange change) {
+ return change.getContext();
+ }
+
+ protected void hideCellsForChange(GraphModelEvent.GraphModelChange change) {
+ // Hide visible edges between invisible vertices
+ // 1. Remove attached edges of removed cells
+ // 2. Remove edges who's source or target has changed to
+ // invisible.
+ Object[] tmp = change.getRemoved();
+ Set removed = new HashSet();
+
+ if (tmp != null)
+ for (int i = 0; i < tmp.length; i++)
+ removed.add(tmp[i]);
+
+ if (hidesDanglingConnections || hidesExistingConnections) {
+ Object[] changed = change.getChanged();
+
+ for (int i = 0; i < changed.length; i++) {
+ CellView view = getMapping(changed[i], false);
+
+ if (view instanceof EdgeView) {
+ EdgeView edge = (EdgeView) view;
+ Object oldSource = (edge.getSource() == null) ? null : edge.getSource().getCell();
+ Object oldTarget = (edge.getTarget() == null) ? null : edge.getTarget().getCell();
+ Object newSource = graphModel.getSource(changed[i]);
+ Object newTarget = graphModel.getTarget(changed[i]);
+ boolean hideExisting = (hidesExistingConnections
+ && (((newSource != null)
+ && !hasVisibleParent(newSource, null))
+ || ((newTarget != null)
+ && !hasVisibleParent(newTarget, null))));
+
+ if ((hidesDanglingConnections
+ && (removed.contains(oldSource) || removed.contains(oldTarget)))
+ || hideExisting) {
+ setVisibleImpl(new Object[] { changed[i] }, false);
+ }
+ }
+ }
+ }
+ }
+
+ /**
+ * Checks if the port or one of its parents is visible.
+ */
+ protected boolean hasVisibleParent(Object cell, Set invisible) {
+ boolean isVisible = false;
+
+ do {
+ isVisible = ((invisible == null) || !invisible.contains(cell)) ? isVisible(cell) : false;
+ cell = getModel().getParent(cell);
+ } while ((cell != null) && !isVisible);
+
+ return isVisible;
+ }
+
+ protected void showCellsForChange(GraphModelEvent.GraphModelChange change) {
+ Object[] inserted = change.getInserted();
+
+ if ((inserted != null) && showsInsertedConnections) {
+ for (int i = 0; i < inserted.length; i++) {
+ if (!isVisible(inserted[i])) {
+ Object source = graphModel.getSource(inserted[i]);
+ Object target = graphModel.getTarget(inserted[i]);
+
+ if (((source != null) || (target != null))
+ && (isVisible(source) && isVisible(target)))
+ setVisibleImpl(new Object[] { inserted[i] }, true);
+ }
+ }
+ }
+
+ if (change.getConnectionSet() != null) {
+ Set changedSet = change.getConnectionSet().getChangedEdges();
+
+ if ((changedSet != null) && showsChangedConnections) {
+ Object[] changed = changedSet.toArray();
+
+ for (int i = 0; i < changed.length; i++) {
+ if (!isVisible(changed[i])) {
+ Object source = graphModel.getSource(changed[i]);
+ Object target = graphModel.getTarget(changed[i]);
+
+ if (((source != null) || (target != null))
+ && (isVisible(source) && isVisible(target)) && !isVisible(changed[i]))
+ setVisibleImpl(new Object[] { changed[i] }, true);
+ }
+ }
+ }
+ }
+ }
+
+ /**
+ * Adds the specified model root cells to the view. Do not add a view that
+ * is already in roots.
+ */
+ public void insertViews(CellView[] views) {
+ if (views != null) {
+ refresh(views, true);
+
+ for (int i = 0; i < views.length; i++) {
+ if ((views[i] != null) && (getMapping(views[i].getCell(), false) != null)) {
+ CellView parentView = views[i].getParentView();
+ Object parent = (parentView != null) ? parentView.getCell() : null;
+
+ if (!graphModel.isPort(views[i].getCell()) && (parent == null)) {
+ roots.add(views[i]);
+ }
+ }
+ }
+ }
+ }
+
+ /**
+ * Removes the specified model root cells from the view by removing the
+ * mapping between the cell and its view and makes the cells invisible.
+ */
+ public CellView[] removeCells(Object[] cells) {
+ if (cells != null) {
+ CellView[] views = new CellView[cells.length];
+
+ for (int i = 0; i < cells.length; i++) {
+ views[i] = removeMapping(cells[i]);
+
+ if (views[i] != null) {
+ views[i].removeFromParent();
+ roots.remove(views[i]);
+ visibleSet.remove(views[i].getCell());
+ }
+ }
+
+ return views;
+ }
+
+ return null;
+ }
+
+ //
+ // Cell Mapping
+ //
+ /**
+ * Takes an array of views and returns the array of the corresponding cells
+ * by using <code>getCell</code> for each view.
+ */
+ public Object[] getCells(CellView[] views) {
+ if (views != null) {
+ Object[] cells = new Object[views.length];
+
+ for (int i = 0; i < views.length; i++)
+ if (views[i] != null)
+ cells[i] = views[i].getCell();
+
+ return cells;
+ }
+
+ return null;
+ }
+
+ /**
+ * Returns the view for the specified cell. If create is true and no view is
+ * found then a view is created using createView(Object).
+ */
+ public CellView getMapping(Object cell, boolean create) {
+ if (cell == null)
+ return null;
+
+ CellView view = (CellView) mapping.get(cell);
+
+ if ((view == null) && create && isVisible(cell)) {
+ view = (CellView) hiddenMapping.get(cell);
+
+ if (view != null) {
+ putMapping(cell, view);
+ hiddenMapping.remove(cell);
+ } else {
+ view = factory.createView(graphModel, cell);
+ putMapping(cell, view);
+ view.refresh(getModel(), this, true); // Create Dependent
+ // Views
+
+ view.update();
+ }
+ }
+
+ return view;
+ }
+
+ /**
+ * Returns the views for the specified array of cells without creating these
+ * views on the fly.
+ */
+ public CellView[] getMapping(Object[] cells) {
+ return getMapping(cells, false);
+ }
+
+ /**
+ * Returns the views for the specified array of cells. Returned array may
+ * contain null pointers if the respective cell is not mapped in this view
+ * and <code>create</code> is <code>false</code>.
+ */
+ public CellView[] getMapping(Object[] cells, boolean create) {
+ if (cells != null) {
+ CellView[] result = new CellView[cells.length];
+
+ for (int i = 0; i < cells.length; i++)
+ result[i] = getMapping(cells[i], create);
+
+ return result;
+ }
+
+ return null;
+ }
+
+ /**
+ * Associates the specified model cell with the specified view.
+ */
+ public void putMapping(Object cell, CellView view) {
+ if ((cell != null) && (view != null))
+ mapping.put(cell, view);
+ }
+
+ /**
+ * Removes the associaten for the specified model cell and returns the view
+ * that was previously associated with the cell. Updates the portlist if
+ * necessary.
+ */
+ public CellView removeMapping(Object cell) {
+ if (cell != null) {
+ CellView view = (CellView) mapping.remove(cell);
+
+ return view;
+ }
+
+ return null;
+ }
+
+ //
+ /**
+ * DOCUMENT ME!
+ *
+ * @param cell DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isVisible(Object cell) {
+ return !isPartial() || visibleSet.contains(cell) || (cell == null);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Set getVisibleSet() {
+ return new HashSet(visibleSet);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param visible DOCUMENT ME!
+ */
+ public void setVisibleSet(Set visible) {
+ visibleSet = visible;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param cell DOCUMENT ME!
+ * @param visible DOCUMENT ME!
+ */
+ public void setVisible(Object cell, boolean visible) {
+ setVisible(new Object[] { cell }, visible);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param cells DOCUMENT ME!
+ * @param visible DOCUMENT ME!
+ */
+ public void setVisible(Object[] cells, boolean visible) {
+ if (visible)
+ setVisible(cells, null);
+ else
+ setVisible(null, cells);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param visible DOCUMENT ME!
+ * @param invisible DOCUMENT ME!
+ */
+ public void setVisible(Object[] visible, Object[] invisible) {
+ setVisible(visible, invisible, null);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param visible DOCUMENT ME!
+ * @param invisible DOCUMENT ME!
+ * @param cs DOCUMENT ME!
+ */
+ public void setVisible(Object[] visible, Object[] invisible, ConnectionSet cs) {
+ GraphLayoutCacheEdit edit = new GraphLayoutCacheEdit(null, null, visible, invisible);
+ edit.end();
+ graphModel.edit(null, cs, null, new UndoableEdit[] { edit });
+ }
+
+ // This is used to augment the array passed to the setVisible method.
+ protected Object[] addVisibleDependencies(Object[] cells, boolean visible) {
+ if (cells != null) {
+ if (visible) {
+ // Make ports and source and target vertex visible
+ Set all = new HashSet();
+
+ for (int i = 0; i < cells.length; i++) {
+ all.add(cells[i]);
+ // Add ports
+ all.addAll(getPorts(cells[i]));
+
+ // Add source vertex and ports
+ Collection coll = getParentPorts(graphModel.getSource(cells[i]));
+
+ if (coll != null)
+ all.addAll(coll);
+
+ // Add target vertex and ports
+ coll = getParentPorts(graphModel.getTarget(cells[i]));
+
+ if (coll != null)
+ all.addAll(coll);
+ }
+
+ if (showsExistingConnections) {
+ Set tmp = DefaultGraphModel.getEdges(getModel(), cells);
+ Iterator it = tmp.iterator();
+
+ while (it.hasNext()) {
+ Object obj = it.next();
+ Object source = graphModel.getSource(obj);
+ Object target = graphModel.getTarget(obj);
+
+ if ((isVisible(source) || all.contains(source))
+ && (isVisible(target) || all.contains(target)))
+ all.add(obj);
+ }
+ }
+
+ all.removeAll(visibleSet);
+ all.remove(null);
+
+ return all.toArray();
+ } else {
+ if (hidesExistingConnections) {
+ Set all = new HashSet();
+
+ for (int i = 0; i < cells.length; i++) {
+ all.addAll(getPorts(cells[i]));
+ all.add(cells[i]);
+ }
+
+ Iterator it = DefaultGraphModel.getEdges(graphModel, cells).iterator();
+
+ while (it.hasNext()) {
+ Object edge = it.next();
+ Object newSource = graphModel.getSource(edge);
+ Object newTarget = graphModel.getTarget(edge);
+
+ // Note: At this time the cells are not yet hidden
+ if (((newSource != null) && !hasVisibleParent(newSource, all))
+ || ((newTarget != null) && !hasVisibleParent(newTarget, all))) {
+ all.add(edge);
+ }
+ }
+
+ all.remove(null);
+
+ return all.toArray();
+ }
+ }
+ }
+
+ return cells;
+ }
+
+ // You must call update ports if this method returns true.
+ /**
+ * DOCUMENT ME!
+ *
+ * @param cells DOCUMENT ME!
+ * @param visible DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean setVisibleImpl(Object[] cells, boolean visible) {
+ cells = addVisibleDependencies(cells, visible);
+
+ if ((cells != null) && isPartial()) {
+ boolean updatePorts = false;
+
+ // Update Visible Set
+ CellView[] views = new CellView[cells.length];
+
+ if (!visible)
+ views = removeCells(cells);
+
+ for (int i = 0; i < cells.length; i++) {
+ if (cells[i] != null) {
+ if (visible) {
+ visibleSet.add(cells[i]);
+ views[i] = getMapping(cells[i], true);
+ } else {
+ if (views[i] != null) {
+ if (graphModel.contains(views[i].getCell()) && remembersCellViews)
+ hiddenMapping.put(views[i].getCell(), views[i]);
+
+ updatePorts = true;
+ }
+ }
+ }
+ }
+
+ // Make Cell Views Visible (if not already in place)
+ if (visible) {
+ Set parentSet = new HashSet();
+
+ for (int i = 0; i < views.length; i++) {
+ if (views[i] != null) {
+ CellView view = views[i];
+
+ // Remove all children from roots
+ CellView[] children = AbstractCellView.getDescendantViews(new CellView[] {
+ view
+ });
+
+ for (int j = 0; j < children.length; j++)
+ roots.remove(children[j]);
+
+ view.refresh(getModel(), this, false);
+
+ // Link cellView into graphLayoutCache
+ CellView parentView = view.getParentView();
+
+ if (parentView != null)
+ parentSet.add(parentView);
+
+ updatePorts = true;
+ }
+ }
+
+ CellView[] parentViews = new CellView[parentSet.size()];
+ parentSet.toArray(parentViews);
+ refresh(parentViews, true);
+ }
+
+ return updatePorts;
+ }
+
+ return false;
+ }
+
+ protected Collection getParentPorts(Object cell) {
+ // does nothing if a parent is already visible
+ Object parent = graphModel.getParent(cell);
+
+ while (parent != null) {
+ if (isVisible(parent))
+ return null;
+
+ parent = graphModel.getParent(parent);
+ }
+
+ // Else returns the parent and all ports
+ parent = graphModel.getParent(cell);
+
+ Collection collection = getPorts(parent);
+ collection.add(parent);
+
+ return collection;
+ }
+
+ protected Collection getPorts(Object cell) {
+ LinkedList list = new LinkedList();
+
+ for (int i = 0; i < graphModel.getChildCount(cell); i++) {
+ Object child = graphModel.getChild(cell, i);
+
+ if (graphModel.isPort(child))
+ list.add(child);
+ }
+
+ return list;
+ }
+
+ //
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isPartial() {
+ return partial;
+ }
+
+ /**
+ * Messaged when the user has altered the value for the item identified by
+ * cell to newValue. If newValue signifies a truly new value the model
+ * should post a graphCellsChanged event. This calls
+ * augmentNestedMapForValueChange.
+ */
+ public void valueForCellChanged(Object cell, Object newValue) {
+ Map nested = null;
+
+ if (isAutoSizeOnValueChange()) {
+ CellView view = getMapping(cell, false);
+
+ if (view != null) {
+ AttributeMap attrs = view.getAllAttributes();
+ Rectangle2D bounds = GraphConstants.getBounds(attrs);
+
+ // Force the model to store the old bounds
+ Rectangle2D dummyBounds = attrs.createRect(bounds.getX(), bounds.getY(), 0, 0);
+ nested = GraphConstants.createAttributes(new Object[] { cell },
+ new Object[] {
+ GraphConstants.RESIZE,
+ GraphConstants.BOUNDS
+ },
+ new Object[] { Boolean.TRUE, dummyBounds });
+ }
+ } else {
+ nested = new Hashtable();
+ nested.put(cell, new Hashtable());
+ }
+
+ augmentNestedMapForValueChange(nested, cell, newValue);
+ edit(nested, null, null, null);
+ }
+
+ /**
+ * Hook for subclassers to add more stuff for value changes. Currently this
+ * adds the new value to the change.
+ */
+ protected void augmentNestedMapForValueChange(Map nested, Object cell, Object newValue) {
+ Map attrs = (Map) nested.get(cell);
+
+ if (attrs != null)
+ GraphConstants.setValue(attrs, newValue);
+ }
+
+ /**
+ * Inserts the <code>cells</code> and connections into the model, and
+ * absorbs the local attributes. This implementation sets the inserted cells
+ * visible and selects the new roots depending on graph.selectNewCells.
+ */
+ public void insert(Object[] roots, Map attributes, ConnectionSet cs, ParentMap pm,
+ UndoableEdit[] e) {
+ Object[] visible = null;
+
+ if (isPartial() && showsInsertedCells) {
+ List tmp = DefaultGraphModel.getDescendants(graphModel, roots);
+ tmp.removeAll(visibleSet);
+
+ if (!tmp.isEmpty())
+ visible = tmp.toArray();
+ }
+
+ // Absorb local attributes
+ GraphLayoutCacheEdit edit = createLocalEdit(roots, attributes, visible, null);
+
+ if (edit != null)
+ e = augment(e, edit);
+
+ graphModel.insert(roots, attributes, cs, pm, e);
+ }
+
+ /**
+ * Inserts the cloned cells from the clone map and clones the passed-in
+ * arguments according to the clone map before insertion and returns the
+ * clones in order of the cells. This example shows how to clone the current
+ * selection and get a reference to the clones:
+ *
+ * <pre>
+ * Object[] cells = graph.getDescendants(graph.order(graph.getSelectionCells()));
+ * ConnectionSet cs = ConnectionSet.create(graphModel, cells, false);
+ * ParentMap pm = ParentMap.create(graphModel, cells, false, true);
+ * cells = graphLayoutCache.insertClones(cells, graph.cloneCells(cells),
+ * attributes, cs, pm, 0, 0);
+ * </pre>
+ */
+ public Object[] insertClones(Object[] cells, Map clones, Map nested, ConnectionSet cs,
+ ParentMap pm, double dx, double dy) {
+ if (cells != null) {
+ if (cs != null)
+ cs = cs.clone(clones);
+
+ if (pm != null)
+ pm = pm.clone(clones);
+
+ if (nested != null) {
+ nested = GraphConstants.replaceKeys(clones, nested);
+ AttributeMap.translate(nested.values(), dx, dy);
+ }
+
+ // Replace cells in order
+ Object[] newCells = new Object[cells.length];
+
+ for (int i = 0; i < cells.length; i++)
+ newCells[i] = clones.get(cells[i]);
+
+ // Insert into cache/model
+ insert(newCells, nested, cs, pm, null);
+
+ return newCells;
+ }
+
+ return null;
+ }
+
+ /**
+ * Inserts the specified vertex into the graph model. This method does in
+ * fact nothing, it calls insert edge with the vertex and the source and
+ * target port set to null. This example shows how to add a vertex with a
+ * port and a black border:
+ *
+ * <pre>
+ * DefaultGraphCell vertex = new DefaultGraphCell("Hello, world!");
+ * Map attrs = vertex.getAttributes();
+ * GraphConstants.setOpaque(attrs, false);
+ * GraphConstants.setBorderColor(attrs, Color.black);
+ * DefaultPort port = new DefaultPort();
+ * vertex.add(port);
+ * port.setParent(vertex);
+ * graph.getGraphLayoutCache().insert(vertex);
+ * </pre>
+ *
+ * @param cell
+ * inserts the specified cell in the cache
+ */
+ public void insert(Object cell) {
+ insert(new Object[] { cell });
+ }
+
+ /**
+ * Inserts the specified edge into the graph model. This method does in fact
+ * nothing, it calls insert with a default connection set.
+ *
+ * @param edge
+ * the edge to be inserted
+ * @param source
+ * the source port this edge is connected to
+ * @param target
+ * the target port this edge is connected to
+ */
+ public void insertEdge(Object edge, Object source, Object target) {
+ insert(new Object[] { edge }, new Hashtable(), new ConnectionSet(edge, source, target),
+ new ParentMap());
+ }
+
+ /**
+ * Inserts the specified cells into the graph model. This method is a
+ * general implementation of cell insertion. If the source and target port
+ * are null, then no connection set is created. The method uses the
+ * attributes from the specified edge and the egdge's children to construct
+ * the insert call. This example shows how to insert an edge with a special
+ * arrow between two known vertices:
+ *
+ * <pre>
+ * Object source = graph.getDefaultPortForCell(sourceVertex).getCell();
+ * Object target = graph.getDefaultPortForCell(targetVertex).getCell();
+ * DefaultEdge edge = new DefaultEdge("Hello, world!");
+ * edge.setSource(source);
+ * edge.setTarget(target);
+ * Map attrs = edge.getAttributes();
+ * GraphConstants.setLineEnd(attrs, GraphConstants.ARROW_TECHNICAL);
+ * graph.getGraphLayoutCache().insert(edge);
+ * </pre>
+ */
+ public void insert(Object[] cells) {
+ insert(cells, new Hashtable(), new ConnectionSet(), new ParentMap());
+ }
+
+ /**
+ * Variant of the insert method that allows to pass a default connection set
+ * and parent map and nested map.
+ */
+ public void insert(Object[] cells, Map nested, ConnectionSet cs, ParentMap pm) {
+ if (cells != null) {
+ if (nested == null)
+ nested = new Hashtable();
+
+ if (cs == null)
+ cs = new ConnectionSet();
+
+ if (pm == null)
+ pm = new ParentMap();
+
+ for (int i = 0; i < cells.length; i++) {
+ // Using the children of the vertex we construct the parent map.
+ int childCount = getModel().getChildCount(cells[i]);
+
+ for (int j = 0; j < childCount; j++) {
+ Object child = getModel().getChild(cells[i], j);
+ pm.addEntry(child, cells[i]);
+
+ // And add their attributes to the nested map
+ AttributeMap attrs = getModel().getAttributes(child);
+
+ if (attrs != null)
+ nested.put(child, attrs);
+ }
+
+ // A nested map with the vertex as key
+ // and its attributes as the value
+ // is required for the model.
+ Map attrsTmp = (Map) nested.get(cells[i]);
+ Map attrs = getModel().getAttributes(cells[i]);
+
+ if (attrsTmp != null)
+ attrs.putAll(attrsTmp);
+
+ nested.put(cells[i], attrs);
+
+ // Check if we have parameters for a connection set.
+ Object sourcePort = getModel().getSource(cells[i]);
+
+ if (sourcePort != null)
+ cs.connect(cells[i], sourcePort, true);
+
+ Object targetPort = getModel().getTarget(cells[i]);
+
+ if (targetPort != null)
+ cs.connect(cells[i], targetPort, false);
+ }
+
+ // Create an array with the parent and its children.
+ cells = DefaultGraphModel.getDescendants(getModel(), cells).toArray();
+
+ // Finally call the insert method on the parent class.
+ insert(cells, nested, cs, pm, null);
+ }
+ }
+
+ /**
+ * Inserts the specified cell as a parent of children. Note: All cells that
+ * are not yet in the model will be inserted. This example shows how to
+ * group the current selection and pass the group default bounds in case it
+ * is later collapsed:
+ *
+ * <pre>
+ * DefaultGraphCell group = new DefaultGraphCell("Hello, world!");
+ * Object[] cells = DefaultGraphModel.order(graph.getModel(), graph
+ * .getSelectionCells());
+ * Rectangle2D bounds = graph.getCellBounds(cells);
+ * if (bounds != null) {
+ * bounds = new Rectangle2D.Double(bounds.getX() + bounds.getWidth() / 4,
+ * bounds.getY() + bounds.getHeight() / 4, bounds.getWidth() / 2,
+ * bounds.getHeight() / 2);
+ * GraphConstants.setBounds(group.getAttributes(), bounds);
+ * }
+ * graph.getGraphLayoutCache().insertGroup(group, cells);
+ * </pre>
+ */
+ public void insertGroup(Object group, Object[] children) {
+ if ((group != null) && (children != null) && (children.length > 0)) {
+ Map nested = new Hashtable();
+
+ // List to store all children that are not in the model
+ List newCells = new ArrayList(children.length + 1);
+
+ // Plus the group cell at pos 0
+ if (!getModel().contains(group)) {
+ newCells.add(group);
+ }
+
+ // Create a parent map for the group and the children, and
+ // store the children's attributes in the nested map.
+ // Note: This implementation assumes that the children have
+ // not yet been added to the group object. Therefore,
+ // the insert method will only collect the group
+ // attributes, but will ignore the child attributes.
+ ParentMap pm = new ParentMap();
+
+ for (int i = 0; i < children.length; i++) {
+ pm.addEntry(children[i], group);
+
+ if (!getModel().contains(children[i])) {
+ newCells.add(children[i]);
+
+ AttributeMap attrs = getModel().getAttributes(children[i]);
+
+ if (attrs != null)
+ nested.put(children[i], attrs);
+ }
+ }
+
+ if (newCells.isEmpty())
+ edit(nested, null, pm, null);
+ else
+ insert(newCells.toArray(), nested, null, pm);
+ }
+ }
+
+ /**
+ * Removes <code>cells</code> from the model.
+ */
+ public void remove(Object[] cells) {
+ graphModel.remove(cells);
+ }
+
+ /**
+ * Removes cells from the model, including all children and connected edges
+ * if <code>children</code> or <code>edges</code> is true, respectively.
+ *
+ * @param cells
+ * The cells to remove.
+ * @param descendants
+ * Whether to remove all descendants as well.
+ * @param edges
+ * Whether to remove all connected edges as well.
+ */
+ public void remove(Object[] cells, boolean descendants, boolean edges) {
+ if ((cells != null) && (cells.length > 0)) {
+ if (edges) {
+ Object[] tmp = DefaultGraphModel.getEdges(getModel(), cells).toArray();
+ Object[] newCells = new Object[cells.length + tmp.length];
+ System.arraycopy(cells, 0, newCells, 0, cells.length);
+ System.arraycopy(tmp, 0, newCells, cells.length, tmp.length);
+ cells = newCells;
+ }
+
+ if (descendants)
+ cells = DefaultGraphModel.getDescendants(getModel(), cells).toArray();
+
+ remove(cells);
+ }
+ }
+
+ /**
+ * Hides the specified cells with all children if <code>descandants</code>
+ * is true.
+ */
+ public void hideCells(Object[] cells, boolean descandants) {
+ if ((cells != null) && (cells.length > 0)) {
+ if (descandants)
+ cells = DefaultGraphModel.getDescendants(getModel(), cells).toArray();
+
+ setVisible(cells, false);
+ }
+ }
+
+ /**
+ * Shows the specified cells with all children if <code>descandants</code>
+ * is true.
+ */
+ public void showCells(Object[] cells, boolean descandants) {
+ if ((cells != null) && (cells.length > 0)) {
+ if (descandants)
+ cells = DefaultGraphModel.getDescendants(getModel(), cells).toArray();
+
+ setVisible(cells, true);
+ }
+ }
+
+ /**
+ * Ungroups all groups in cells and returns the children that are not ports.
+ * Note: This replaces the parents with their group cells in the group
+ * structure.
+ */
+ public Object[] ungroup(Object[] cells) {
+ if ((cells != null) && (cells.length > 0)) {
+ ArrayList toRemove = new ArrayList();
+ ArrayList children = new ArrayList();
+ boolean groupExists = false;
+
+ for (int i = 0; i < cells.length; i++) {
+ boolean childExists = false;
+
+ for (int j = 0; j < getModel().getChildCount(cells[i]); j++) {
+ Object child = getModel().getChild(cells[i], j);
+
+ if (!getModel().isPort(child)) {
+ children.add(child);
+ childExists = true;
+ } else {
+ toRemove.add(child);
+ }
+ }
+
+ if (childExists) {
+ toRemove.add(cells[i]);
+ groupExists = true;
+ }
+ }
+
+ if (groupExists)
+ remove(toRemove.toArray());
+
+ return children.toArray();
+ }
+
+ return null;
+ }
+
+ /**
+ * Toggles the collapsed state of the specified cells.
+ *
+ * @param cells
+ * The cells to toggle the collapsed state for.
+ * @param collapseOnly
+ * Whether cells should only be collapsed.
+ * @param expandOnly
+ * Whether cells should only be expanded.
+ *
+ */
+ public void toggleCollapsedState(Object[] cells, boolean collapseOnly, boolean expandOnly) {
+ List toExpand = new ArrayList();
+ List toCollapse = new ArrayList();
+
+ for (int i = 0; i < cells.length; i++) {
+ Object cell = cells[i];
+ CellView view = getMapping(cell, false);
+
+ if (view != null) {
+ // Adds to list of expansion cells if it is a leaf in the layout
+ // cache and we do not only want to collapse.
+ if (view.isLeaf() && !collapseOnly)
+ toExpand.add(view.getCell());
+
+ // Else adds to list of to-be-collapsed cells if it is not a
+ // leaf in the layout cache we do not only want to expand.
+ else if (!view.isLeaf() && !expandOnly)
+ toCollapse.add(view.getCell());
+ }
+ }
+
+ if (!toCollapse.isEmpty() || !toExpand.isEmpty())
+ setCollapsedState(toCollapse.toArray(), toExpand.toArray());
+ }
+
+ /**
+ * Collapses all groups by hiding all their descendants.
+ *
+ * @param groups
+ */
+ public void collapse(Object[] groups) {
+ setCollapsedState(groups, null);
+ }
+
+ /**
+ * Expands all groups by showing all children. (Note: This does not show all
+ * descandants, but only the first generation of children.)
+ */
+ public void expand(Object[] cells) {
+ setCollapsedState(null, cells);
+ }
+
+ /**
+ * Collapses and/or expands the specified cell(s)
+ *
+ * @param collapse
+ * the cells to be collapsed
+ * @param expand
+ * the cells to be expanded
+ */
+ public void setCollapsedState(Object[] collapse, Object[] expand) {
+ // Get all descandants for the groups
+ ConnectionSet cs = new ConnectionSet();
+
+ // Collapse cells
+ List toHide = DefaultGraphModel.getDescendants(getModel(), collapse);
+
+ if (collapse != null) {
+ // Remove the groups themselfes
+ for (int i = 0; i < collapse.length; i++) {
+ toHide.remove(collapse[i]);
+ cellWillCollapse(collapse[i]);
+ }
+
+ // Remove the ports (will be hidden automatically)
+ for (int i = 0; i < collapse.length; i++) {
+ int childCount = getModel().getChildCount(collapse[i]);
+
+ if (childCount > 0) {
+ for (int j = 0; j < childCount; j++) {
+ Object child = getModel().getChild(collapse[i], j);
+
+ if (getModel().isPort(child)) {
+ toHide.remove(child);
+ }
+ }
+ }
+ }
+ }
+
+ // Expand cells
+ Set toShow = new HashSet();
+
+ if (expand != null) {
+ for (int i = 0; i < expand.length; i++) {
+ int childCount = getModel().getChildCount(expand[i]);
+
+ for (int j = 0; j < childCount; j++) {
+ toShow.add(getModel().getChild(expand[i], j));
+ }
+ }
+ }
+
+ setVisible(toShow.toArray(), (toHide != null) ? toHide.toArray() : null, cs);
+ }
+
+ /**
+ * Hook for subclassers to return the first or last visible port to replace
+ * the current source or target port of the edge. This is called when groups
+ * are collapsed for the edges that cross the group, ie. go from a child
+ * cell to a cell which is outside the group. This implementation returns
+ * the first port of the parent group if source is true, otherwise it
+ * returns the last port of the parent group.
+ */
+ protected Object getParentPort(Object edge, boolean source) {
+ // Contains the parent of the parent vertex, eg. the group
+ Object parent = getModel()
+ .getParent((source)
+ ? DefaultGraphModel.getSourceVertex(getModel(), edge)
+ : DefaultGraphModel.getTargetVertex(getModel(), edge));
+
+ // Finds a port in the group
+ int c = getModel().getChildCount(parent);
+
+ for (int i = (source) ? (c - 1) : 0; (i < getModel().getChildCount(parent)) && (i >= 0);
+ i += ((source) ? (-1) : (+1))) {
+ Object child = getModel().getChild(parent, i);
+
+ if (getModel().isPort(child)) {
+ return child;
+ }
+ }
+
+ return null;
+ }
+
+ /**
+ * Hook for subclassers to return the port to be used for edges that have
+ * been connected to the group. This is called from expand. This returns the
+ * first port of the first or last vertex depending on <code>source</code>.
+ */
+ protected Object getChildPort(Object edge, boolean source) {
+ GraphModel model = getModel();
+
+ // Contains the parent of the port, eg. the group
+ Object parent = (source) ? DefaultGraphModel.getSourceVertex(model, edge)
+ : DefaultGraphModel.getTargetVertex(model, edge);
+
+ // Finds a vertex in the group
+ int c = model.getChildCount(parent);
+
+ for (int i = (source) ? (c - 1) : 0; (i < c) && (i >= 0); i += ((source) ? (-1) : (+1))) {
+ Object child = model.getChild(parent, i);
+
+ if (!model.isEdge(child) && !model.isPort(child)) {
+ // Finds a port in the vertex
+ for (int j = 0; j < model.getChildCount(child); j++) {
+ Object port = model.getChild(child, j);
+
+ if (model.isPort(port)) {
+ return port;
+ }
+ }
+ }
+ }
+
+ return null;
+ }
+
+ /**
+ * Applies the <code>propertyMap</code> and the connection changes to the
+ * model. The initial <code>edits</code> that triggered the call are
+ * considered to be part of this transaction. Notifies the model- and undo
+ * listeners of the change. Note: The passed in attributes may contain
+ * PortViews.
+ */
+ public void edit(Map attributes, ConnectionSet cs, ParentMap pm, UndoableEdit[] e) {
+ if ((attributes != null) || (cs != null) || (pm != null) || (e != null)) {
+ Object[] visible = null;
+
+ if (isPartial() && showsInvisibleEditedCells) {
+ Set tmp = new HashSet();
+
+ if (attributes != null)
+ tmp.addAll(attributes.keySet());
+
+ if (cs != null)
+ tmp.addAll(cs.getChangedEdges());
+
+ if (pm != null)
+ tmp.addAll(pm.getChangedNodes());
+
+ tmp.removeAll(visibleSet);
+
+ if (!tmp.isEmpty())
+ visible = tmp.toArray();
+ }
+
+ GraphLayoutCacheEdit edit = createLocalEdit(null, attributes, visible, null);
+
+ if (edit != null)
+ e = augment(e, edit);
+
+ // Pass to model
+ graphModel.edit(attributes, cs, pm, e);
+ }
+ }
+
+ /**
+ * A shortcut method that takes a nested map and passes it to the edit
+ * method.
+ */
+ public void edit(Map attributes) {
+ edit(attributes, null, null, null);
+ }
+
+ /**
+ * Applies the <code>attributes</code> to all <code>cells</code> by
+ * creating a map that contains the attributes for each cell and passing it
+ * to edit on this layout cache. Example:
+ *
+ * <pre>
+ * Map attrs = new java.util.Hashtable();
+ * GraphConstants.setBackground(attrs, Color.RED);
+ * graph.getGraphLayoutCache().edit(graph.getSelectionCells(), attrs);
+ * </pre>
+ */
+ public void edit(Object[] cells, Map attributes) {
+ if ((attributes != null) && (cells != null) && (cells.length > 0)) {
+ Map nested = new Hashtable();
+
+ for (int i = 0; i < cells.length; i++)
+ nested.put(cells[i], attributes);
+
+ edit(nested, null, null, null);
+ }
+ }
+
+ /**
+ * Applies the <code>attributes</code> to a single <code>cell</code> by
+ * creating a map that contains the attributes for this cell and passing it
+ * to edit on this layout cache. Example:
+ *
+ * <pre>
+ * Map attrs = new java.util.Hashtable();
+ * GraphConstants.setBackground(attrs, Color.RED);
+ * graph.getGraphLayoutCache().editCell(graph.getSelectionCell(), attrs);
+ * </pre>
+ */
+ public void editCell(Object cell, Map attributes) {
+ if ((attributes != null) && (cell != null)) {
+ edit(new Object[] { cell }, attributes);
+ }
+ }
+
+ protected UndoableEdit[] augment(UndoableEdit[] e, UndoableEdit edit) {
+ if (edit != null) {
+ int size = (e != null) ? (e.length + 1) : 1;
+ UndoableEdit[] result = new UndoableEdit[size];
+
+ if (e != null)
+ System.arraycopy(e, 0, result, 0, size - 2);
+
+ result[size - 1] = edit;
+
+ return result;
+ }
+
+ return e;
+ }
+
+ /**
+ * Sends <code>cells</code> to back. Note: This expects an array of cells!
+ */
+ public void toBack(Object[] cells) {
+ if ((cells != null) && (cells.length > 0)) {
+ graphModel.toBack(cells);
+ }
+ }
+
+ /**
+ * Brings <code>cells</code> to front. Note: This expects an array of
+ * cells!
+ */
+ public void toFront(Object[] cells) {
+ if ((cells != null) && (cells.length > 0)) {
+ graphModel.toFront(cells);
+ }
+ }
+
+ /**
+ * Creates a local edit for the specified change. A local operation contains
+ * all visibility changes, as well as all changes to attributes that are
+ * local, and all control attributes. <br>
+ * Note: You must use cells as keys for the nested map, not cell views.
+ */
+ protected GraphLayoutCacheEdit createLocalEdit(Object[] inserted, Map nested, Object[] visible,
+ Object[] invisible) {
+ // Create an edit if there are any view-local attributes set
+ if (((nested != null) && !nested.isEmpty())
+ && (!localAttributes.isEmpty() || isAllAttributesLocal())) {
+ // Move or Copy Local Attributes to Local View
+ Map globalMap = new Hashtable();
+ Map localMap = new Hashtable();
+ Map localAttr;
+ Iterator it = nested.entrySet().iterator();
+
+ while (it.hasNext()) {
+ localAttr = new Hashtable();
+
+ Map.Entry entry = (Map.Entry) it.next();
+
+ // (cell, Hashtable)
+ Object cell = entry.getKey();
+ Map attr = (Map) entry.getValue();
+
+ // Create Difference of Existing and New Attributes
+ CellView tmpView = getMapping(cell, false);
+
+ if (tmpView != null)
+ attr = tmpView.getAllAttributes().diff(attr);
+
+ // End of Diff
+ Iterator it2 = attr.entrySet().iterator();
+
+ while (it2.hasNext()) {
+ Map.Entry entry2 = (Map.Entry) it2.next();
+
+ // (key, value)
+ Object key = entry2.getKey();
+ Object value = entry2.getValue();
+ boolean isControlAttribute = isControlAttribute(cell, key, value);
+
+ if (isAllAttributesLocal() || isControlAttribute
+ || isLocalAttribute(cell, key, value)) {
+ localAttr.put(key, value);
+
+ if (!isControlAttribute)
+ it2.remove();
+ }
+ }
+
+ if (!localAttr.isEmpty())
+ localMap.put(cell, localAttr);
+
+ if (!attr.isEmpty())
+ globalMap.put(cell, attr);
+ }
+
+ nested.clear();
+ nested.putAll(globalMap);
+
+ if ((visible != null) || (invisible != null) || !localMap.isEmpty()) {
+ GraphLayoutCacheEdit edit = new GraphLayoutCacheEdit(inserted,
+ new Hashtable(localMap),
+ visible, invisible);
+ edit.end();
+
+ return edit;
+ }
+ } else if ((visible != null) || (invisible != null)) {
+ GraphLayoutCacheEdit edit = new GraphLayoutCacheEdit(inserted, null, visible, invisible);
+ edit.end();
+
+ return edit;
+ }
+
+ return null;
+ }
+
+ /**
+ * Returns true if the set of local attributes contains <code>key</code>
+ */
+ protected boolean isLocalAttribute(Object cell, Object key, Object value) {
+ return localAttributes.contains(key);
+ }
+
+ /**
+ * Returns true if <code>key</code> is a control attribute
+ */
+ protected boolean isControlAttribute(Object cell, Object key, Object value) {
+ return GraphConstants.REMOVEALL.equals(key) || GraphConstants.REMOVEATTRIBUTES.equals(key);
+ }
+
+ /**
+ * Handles the removal of view local attributes. Since these attributes
+ * are only being stored in the view, the option is provided to
+ * copy the values for that key into the model. Without this, those
+ * values are lost.
+ *
+ * @param key
+ * the key of the view local attribute
+ * @param addToModel
+ * whether or not to move the attribute values to the graph model
+ * @param override
+ * whether or not to override the key's value in the model
+ * cell's attribute map if it exists
+ * @return whether or not the operation completed sucessfully
+ */
+ public boolean removeViewLocalAttribute(Object key, boolean addToModel, boolean override) {
+ if (localAttributes.contains(key)) {
+ if (addToModel) {
+ // Iterate through all views copying this attribute to the
+ // cell.
+ copyRemovedViewValue(key, addToModel, override, mapping.values());
+ copyRemovedViewValue(key, addToModel, override, hiddenMapping.values());
+ }
+
+ localAttributes.remove(key);
+
+ return true;
+ }
+
+ return false;
+ }
+
+ /**
+ * Helper method to copy removed view local attributes to model cell's
+ * @param key
+ * the key of the view local attribute
+ * @param addToModel
+ * whether or not to move the attribute values to the graph model
+ * @param override
+ * whether or not to override the key's value in the model
+ * cell's attribute map if it exists
+ * @param coll the current collection being analysed
+ */
+ private void copyRemovedViewValue(Object key, boolean addToModel, boolean override,
+ Collection coll) {
+ Iterator iter = coll.iterator();
+
+ while (iter.hasNext()) {
+ CellView cellView = (CellView) iter.next();
+ Map attributes = cellView.getAttributes();
+
+ if (attributes.containsKey(key)) {
+ if (addToModel) {
+ Object cell = cellView.getCell();
+ Map cellAttributes = graphModel.getAttributes(cell);
+
+ if (cellAttributes != null) {
+ boolean cellContainsKey = cellAttributes.containsKey(key);
+
+ // Write the model cell's attribute map key
+ // if overriding is enabled or if key doesn't
+ // exist
+ if (!override || !cellContainsKey) {
+ Object value = attributes.get(key);
+ cellAttributes.put(key, value);
+ }
+ }
+ }
+
+ attributes.remove(key);
+ }
+ }
+ }
+
+ /**
+ * An implementation of GraphViewChange.
+ */
+ public class GraphLayoutCacheEdit extends CompoundEdit implements GraphLayoutCacheEvent.GraphLayoutCacheChange {
+ protected Object[] cells;
+ protected Object[] previousCells = null;
+ protected CellView[] context;
+ protected CellView[] hidden;
+ protected Map attributes;
+ protected Map previousAttributes;
+ protected Object[] visible;
+ protected Object[] invisible;
+
+ // Remember which cells have changed for finding their context
+ protected Set changedCells = new HashSet();
+
+ /**
+ * Constructs a GraphViewEdit. This modifies the attributes of the
+ * specified views and may be used to notify UndoListeners.
+ *
+ * @param nested
+ * the map that defines the new attributes
+ */
+ public GraphLayoutCacheEdit(Map nested) {
+ this(null, nested, null, null);
+ attributes = nested;
+ }
+
+ /**
+ * Constructs a GraphViewEdit. This modifies the attributes of the
+ * specified views and may be used to notify UndoListeners. This should
+ * also take an array of removed cell views, but it is not possible to
+ * add further UndoableEdits to an already executed CompoundEdit, such
+ * as a GraphModel change. Thus, to handle implicit changes -- rather
+ * than piggybacking on the model's event -- the CompoundEdit's addEdit
+ * method should be extended to accept and instantly execute sub-
+ * sequent edits (implicit changes to the view, such as removing a
+ * mapping, hiding a view or the like).
+ *
+ * @param inserted
+ * an array of inserted cells
+ * @param attributes
+ * the map that defines the new attributes
+ * @param visible
+ * an array defining which cells are visible
+ * @param invisible
+ * an array defining which cells are invisible
+ */
+ public GraphLayoutCacheEdit(Object[] inserted, Map attributes, Object[] visible,
+ Object[] invisible) {
+ super();
+ this.attributes = attributes;
+ this.previousAttributes = attributes;
+ this.cells = inserted;
+ this.visible = visible;
+ this.invisible = invisible;
+ }
+
+ public Object getSource() {
+ return GraphLayoutCache.this;
+ }
+
+ public boolean isSignificant() {
+ return true;
+ }
+
+ /**
+ * Returns the cell views that have changed.
+ */
+ public Object[] getChanged() {
+ return changedCells.toArray();
+ }
+
+ /**
+ * Returns the cells that habe been made visible.
+ */
+ public Object[] getInserted() {
+ return invisible;
+ }
+
+ /**
+ * Returns the cells that have changed.
+ */
+ public Object[] getRemoved() {
+ return visible;
+ }
+
+ /**
+ * Returns the views that have not changed explicitly, but implicitly
+ * because one of their dependent cells has changed.
+ */
+ public Object[] getContext() {
+ return context;
+ }
+
+ /**
+ * Returns a map of (cell view, attribute) pairs.
+ */
+ public Map getAttributes() {
+ return attributes;
+ }
+
+ /**
+ * Returns a map of (cell view, attribute) pairs.
+ */
+ public Map getPreviousAttributes() {
+ return previousAttributes;
+ }
+
+ /**
+ * Redoes a change.
+ *
+ * @exception CannotRedoException
+ * if the change cannot be redone
+ */
+ public void redo() throws CannotRedoException {
+ super.redo();
+ execute();
+ }
+
+ /**
+ * Undoes a change.
+ *
+ * @exception CannotUndoException
+ * if the change cannot be undone
+ */
+ public void undo() throws CannotUndoException {
+ super.undo();
+ execute();
+ }
+
+ /**
+ * Execute this edit such that the next invocation to this method will
+ * invert the last execution.
+ */
+ public void execute() {
+ GraphModel model = getModel();
+ changedCells.clear();
+
+ // Remember or restore hidden cells
+ if (hidden != null)
+ for (int i = 0; i < hidden.length; i++)
+ if (hidden[i] != null)
+ mapping.put(hidden[i].getCell(), hidden[i]);
+
+ if (!remembersCellViews) // already remembered
+ hidden = getMapping(invisible);
+
+ // Handle visibility
+ boolean updatePorts = setVisibleImpl(visible, true) | setVisibleImpl(invisible, false);
+
+ if (visible != null) {
+ for (int i = 0; i < visible.length; i++) {
+ changedCells.add(visible[i]);
+
+ // Only calls if not inserted
+ if (cells == null)
+ cellExpanded(visible[i]);
+ }
+ }
+
+ if (invisible != null)
+ for (int i = 0; i < invisible.length; i++)
+ changedCells.add(invisible[i]);
+
+ // Swap arrays
+ Object[] tmp = visible;
+ visible = invisible;
+ invisible = tmp;
+
+ // Handle attributes
+ if (attributes != null) {
+ previousAttributes = attributes;
+ changedCells.addAll(attributes.keySet());
+ attributes = handleAttributes(attributes);
+ }
+
+ if (updatePorts)
+ updatePorts();
+
+ // Add ancestor cells to changed cells
+ Set parentSet = new HashSet();
+ Iterator it = changedCells.iterator();
+
+ while (it.hasNext()) {
+ Object parent = model.getParent(it.next());
+
+ while (parent != null) {
+ parentSet.add(parent);
+ parent = model.getParent(parent);
+ }
+ }
+
+ changedCells.addAll(parentSet);
+ // Refresh all changed cells
+ refresh(getMapping(changedCells.toArray(), false), false);
+
+ // Updates the connected edges. Make sure that changedCells
+ // contains no edges, as these will be removed from the result.
+ Set ctx = DefaultGraphModel.getEdges(getModel(), changedCells.toArray());
+ context = getMapping(ctx.toArray());
+ refresh(context, false);
+ tmp = cells;
+ cells = previousCells;
+ previousCells = tmp;
+ reloadRoots();
+ fireGraphLayoutCacheChanged(GraphLayoutCache.this, this);
+ }
+ }
+
+ /**
+ * Called when a child has been made visible by expanding its parent. This
+ * implementation translates the child so that it reflects the offset of the
+ * parent group since the child was last visible (see
+ * {@link #movesChildrenOnExpand}).
+ */
+ protected void cellExpanded(Object cell) {
+ GraphModel model = getModel();
+
+ // Moves the child to the group origin if it is not a port
+ if (movesChildrenOnExpand && !model.isPort(cell)) {
+ CellView view = getMapping(cell, false);
+
+ if (view != null) {
+ CellView parent = getMapping(model.getParent(cell), false);
+
+ if (parent != null) {
+ if (parent instanceof VertexView) {
+ // Computes the offset of the parent group
+ VertexView vertex = (VertexView) parent;
+ Rectangle2D src = GraphConstants.getBounds(parent.getAllAttributes());
+ Rectangle2D rect = vertex.getBounds();
+ double dx = src.getX() - rect.getX();
+ double dy = src.getY() - rect.getY();
+
+ // Gets the attributes from the cell view or
+ // cell and translates the bounds or points
+ AttributeMap attrs = view.getAttributes();
+
+ if (!attrs.contains(GraphConstants.BOUNDS))
+ attrs = model.getAttributes(view.getCell());
+
+ attrs.translate(dx, dy);
+ }
+ }
+ }
+ }
+ }
+
+ protected void cellWillCollapse(Object cell) {
+ GraphModel model = getModel();
+
+ if (movesParentsOnCollapse) {
+ CellView view = getMapping(cell, false);
+
+ if ((view != null) && !view.isLeaf()) {
+ // Uses view-local attribute if available
+ AttributeMap attrs = view.getAttributes();
+
+ if (!attrs.contains(GraphConstants.BOUNDS)
+ && !localAttributes.contains(GraphConstants.BOUNDS))
+ attrs = model.getAttributes(cell);
+
+ // Moves the group to the origin of the children
+ Rectangle2D src = GraphConstants.getBounds(attrs);
+ Rectangle2D b = (Rectangle2D) view.getBounds();
+
+ // FIXME: What if the group is exactly at "defaultBounds"?
+ if (resizesParentsOnCollapse || (src == null)
+ || src.equals(VertexView.defaultBounds)) {
+ src = attrs.createRect(b.getX(), b.getY(), b.getWidth() * collapseXScale,
+ b.getHeight() * collapseYScale);
+ attrs.applyValue(GraphConstants.BOUNDS, src);
+ } else {
+ src.setFrame(b.getX(), b.getY(), src.getWidth(), src.getHeight());
+ }
+ }
+ }
+ }
+
+ /**
+ * Attention: Undo will not work for routing-change if ROUTING and POINTS
+ * are stored in different locations. This happens if the model holds the
+ * routing attribute and the routing changes from unrouted to routed. In
+ * this case the points in the view are already routed according to the new
+ * scheme when written to the command history (-> no undo).
+ */
+ protected Map handleAttributes(Map attributes) {
+ Map undo = new Hashtable();
+ CellView[] views = new CellView[attributes.size()];
+ Iterator it = attributes.entrySet().iterator();
+ int i = 0;
+
+ while (it.hasNext()) {
+ Map.Entry entry = (Map.Entry) it.next();
+ CellView cv = getMapping(entry.getKey(), false);
+ views[i] = cv;
+ i += 1;
+
+ if ((cv != null) && (cv.getAttributes() != null)) {
+ Map deltaNew = (Map) entry.getValue();
+
+ // System.out.println("state=" + cv.getAttributes());
+ // System.out.println("change=" + deltaNew);
+ Map deltaOld = cv.getAttributes().applyMap(deltaNew);
+ cv.refresh(getModel(), this, false);
+ // System.out.println("state'=" + cv.getAttributes());
+ // System.out.println("change'=" + deltaOld);
+ undo.put(cv.getCell(), deltaOld);
+ }
+ }
+
+ // Re-route all child edges
+ update(views);
+
+ return undo;
+ }
+
+ //
+ // Static Methods
+ //
+ /**
+ * Translates the specified views by the given amount.
+ *
+ * @param views
+ * an array of cell view to each be translated
+ * @param dx
+ * the amount to translate the views in the x-axis
+ * @param dy
+ * the amount to translate the views in the x-axis
+ */
+ public static void translateViews(CellView[] views, double dx, double dy) {
+ for (int i = 0; i < views.length; i++) {
+ if (views[i] instanceof AbstractCellView) {
+ ((AbstractCellView) views[i]).translate(dx, dy);
+ }
+ }
+ }
+
+ /**
+ * Returns a collection of cells that are connected to the specified cell by
+ * edges. Any cells specified in the exclude set will be ignored.
+ *
+ * @param cell
+ * The cell from which the neighbours will be determined
+ * @param exclude
+ * The set of cells to ignore when searching
+ * @param directed
+ * whether or not direction of edges should be taken into account
+ * @param visibleCells
+ * whether or not to only consider visible cells
+ * @return Returns the list of neighbours for <code>cell</code>
+ */
+ public List getNeighbours(Object cell, Set exclude, boolean directed, boolean visibleCells) {
+ // Traverse Graph
+ GraphModel model = getModel();
+ Object[] fanout = (directed) ? DefaultGraphModel.getOutgoingEdges(model, cell)
+ : DefaultGraphModel.getEdges(model, new Object[] { cell })
+ .toArray();
+ List neighbours = new ArrayList(fanout.length);
+ Set localExclude = new HashSet(fanout.length + 8, (float) 0.75);
+
+ for (int i = 0; i < fanout.length; i++) {
+ Object neighbour = DefaultGraphModel.getOpposite(model, fanout[i], cell);
+
+ if ((neighbour != null) && ((exclude == null) || !exclude.contains(neighbour))
+ && !localExclude.contains(neighbour) && (!visibleCells || isVisible(neighbour))) {
+ localExclude.add(neighbour);
+ neighbours.add(neighbour);
+ }
+ }
+
+ return neighbours;
+ }
+
+ /**
+ * Returns the outgoing edges for cell. Cell should be a port or a vertex.
+ *
+ * @param cell
+ * The cell from which the outgoing edges will be determined
+ * @param exclude
+ * The set of edges to ignore when searching
+ * @param visibleCells
+ * whether or not only visible cells should be processed
+ * @param selfLoops
+ * whether or not to include self loops in the returned list
+ * @return Returns the list of outgoing edges for <code>cell</code>
+ */
+ public List getOutgoingEdges(Object cell, Set exclude, boolean visibleCells, boolean selfLoops) {
+ return getEdges(cell, exclude, visibleCells, selfLoops, false);
+ }
+
+ /**
+ * Returns the incoming edges for cell. Cell should be a port or a vertex.
+ *
+ * @param cell
+ * The cell from which the incoming edges will be determined
+ * @param exclude
+ * The set of edges to ignore when searching
+ * @param visibleCells
+ * whether or not only visible cells should be processed
+ * @param selfLoops
+ * whether or not to include self loops in the returned list
+ * @return Returns the list of incoming edges for <code>cell</code>
+ */
+ public List getIncomingEdges(Object cell, Set exclude, boolean visibleCells, boolean selfLoops) {
+ return getEdges(cell, exclude, visibleCells, selfLoops, true);
+ }
+
+ /**
+ * Returns the incoming or outgoing edges for cell. Cell should be a port or
+ * a vertex.
+ *
+ * @param cell
+ * The cell from which the edges will be determined
+ * @param exclude
+ * The set of edges to ignore when searching
+ * @param visibleCells
+ * whether or not only visible cells should be processed
+ * @param selfLoops
+ * whether or not to include self loops in the returned list
+ * @param incoming
+ * <code>true</code> if incoming edges are to be obtained,
+ * <code>false</code> if outgoing edges are to be obtained
+ * @return Returns the list of incoming or outgoing edges for
+ * <code>cell</code>
+ */
+ protected List getEdges(Object cell, Set exclude, boolean visibleCells, boolean selfLoops,
+ boolean incoming) {
+ GraphModel model = getModel();
+ Object[] edges = DefaultGraphModel.getEdges(model, cell, incoming);
+
+ List edgeList = new ArrayList(edges.length);
+ Set localExclude = new HashSet(edges.length);
+
+ for (int i = 0; i < edges.length; i++) {
+ // Check that the edge is neiter in the passed in exclude set or
+ // the local exclude set. Also, if visibleCells is true check
+ // the edge is visible in the cache.
+ if (((exclude == null) || !exclude.contains(edges[i]))
+ && !localExclude.contains(edges[i]) && (!visibleCells || isVisible(edges[i]))) {
+ // Add the edge to the list if all edges, including self loops
+ // are allowed. If self loops are not allowed, ensure the
+ // source and target of the edge are different
+ if ((selfLoops == true) || (model.getSource(edges[i]) != model.getTarget(edges[i]))) {
+ edgeList.add(edges[i]);
+ }
+
+ localExclude.add(edges[i]);
+ }
+ }
+
+ return edgeList;
+ }
+
+ /**
+ * Returns all views, shortcut to getAllDescendants(getRoots())
+ */
+ public CellView[] getAllViews() {
+ return getAllDescendants(getRoots());
+ }
+
+ /**
+ * Returns all views, including descendants that have a parent in
+ * <code>views</code>, especially the PortViews. Note: Iterative
+ * Implementation using model.getChild and getMapping on this cell mapper.
+ */
+ public CellView[] getAllDescendants(CellView[] views) {
+ Stack stack = new Stack();
+
+ for (int i = 0; i < views.length; i++)
+ if (views[i] != null)
+ stack.add(views[i]);
+
+ ArrayList result = new ArrayList();
+
+ while (!stack.isEmpty()) {
+ CellView tmp = (CellView) stack.pop();
+ Object[] children = tmp.getChildViews();
+
+ for (int i = 0; i < children.length; i++)
+ stack.add(children[i]);
+
+ result.add(tmp);
+
+ // Add Port Views
+ for (int i = 0; i < graphModel.getChildCount(tmp.getCell()); i++) {
+ Object child = graphModel.getChild(tmp.getCell(), i);
+
+ if (graphModel.isPort(child)) {
+ CellView view = getMapping(child, false);
+
+ if (view != null)
+ stack.add(view);
+ }
+ }
+ }
+
+ CellView[] ret = new CellView[result.size()];
+ result.toArray(ret);
+
+ return ret;
+ }
+
+ /**
+ * Returns the hiddenMapping.
+ *
+ * @return Map
+ */
+ public Map getHiddenMapping() {
+ return hiddenMapping;
+ }
+
+ /**
+ * Sets the showsExistingConnections
+ *
+ * @param showsExistingConnections
+ */
+ public void setShowsExistingConnections(boolean showsExistingConnections) {
+ this.showsExistingConnections = showsExistingConnections;
+ }
+
+ /**
+ * Returns the showsExistingConnections.
+ *
+ * @return boolean
+ */
+ public boolean isShowsExistingConnections() {
+ return showsExistingConnections;
+ }
+
+ /**
+ * Sets the showsInsertedConnections
+ *
+ * @param showsInsertedConnections
+ */
+ public void setShowsInsertedConnections(boolean showsInsertedConnections) {
+ this.showsInsertedConnections = showsInsertedConnections;
+ }
+
+ /**
+ * Returns the showsInsertedConnections.
+ *
+ * @return boolean
+ */
+ public boolean isShowsInsertedConnections() {
+ return showsInsertedConnections;
+ }
+
+ /**
+ * Sets the hidesExistingConnections
+ *
+ * @param hidesExistingConnections
+ */
+ public void setHidesExistingConnections(boolean hidesExistingConnections) {
+ this.hidesExistingConnections = hidesExistingConnections;
+ }
+
+ /**
+ * Returns the hidesExistingConnections.
+ *
+ * @return boolean
+ */
+ public boolean isHidesExistingConnections() {
+ return hidesExistingConnections;
+ }
+
+ /**
+ * Sets the hidesDanglingConnections
+ *
+ * @param hidesDanglingConnections
+ */
+ public void setHidesDanglingConnections(boolean hidesDanglingConnections) {
+ this.hidesDanglingConnections = hidesDanglingConnections;
+ }
+
+ /**
+ * Returns the hidesDanglingConnections.
+ *
+ * @return boolean
+ */
+ public boolean isHidesDanglingConnections() {
+ return hidesDanglingConnections;
+ }
+
+ /**
+ * Sets the rememberCellViews.
+ *
+ * @param rememberCellViews
+ * The rememberCellViews to set
+ */
+ public void setRemembersCellViews(boolean rememberCellViews) {
+ this.remembersCellViews = rememberCellViews;
+ }
+
+ /**
+ * Returns the remembersCellViews.
+ *
+ * @return boolean
+ */
+ public boolean isRemembersCellViews() {
+ return remembersCellViews;
+ }
+
+ /**
+ * Sets the hiddenSet.
+ *
+ * @param hiddenSet
+ * The hiddenSet to set
+ */
+ public void setHiddenSet(Map hiddenSet) {
+ this.hiddenMapping = hiddenSet;
+ }
+
+ /**
+ * @return Returns the localAttributes.
+ */
+ public Set getLocalAttributes() {
+ return localAttributes;
+ }
+
+ /**
+ * @param localAttributes
+ * The localAttributes to set.
+ */
+ public void setLocalAttributes(Set localAttributes) {
+ this.localAttributes = localAttributes;
+ }
+
+ /**
+ * @return Returns the askLocalAttribute.
+ */
+ public boolean isAllAttributesLocal() {
+ return allAttributesLocal;
+ }
+
+ /**
+ * @param allAttributesLocal
+ * The allAttributesLocal to set.
+ */
+ public void setAllAttributesLocal(boolean allAttributesLocal) {
+ this.allAttributesLocal = allAttributesLocal;
+ }
+
+ /**
+ * Returns true if cells should be auto-sized when their values change
+ *
+ * @return true if cells should be auto-sized when their values change
+ */
+ public boolean isAutoSizeOnValueChange() {
+ return autoSizeOnValueChange;
+ }
+
+ /**
+ * Determines whether cells should be auto-sized when their values change.
+ * Fires a property change event if the new setting is different from the
+ * existing setting.
+ *
+ * @param flag
+ * a boolean value, true if cells should be auto-sized when their
+ * values change
+ */
+ public void setAutoSizeOnValueChange(boolean flag) {
+ this.autoSizeOnValueChange = flag;
+ }
+
+ /**
+ * @return Returns the selectsAllInsertedCells.
+ */
+ public boolean isSelectsAllInsertedCells() {
+ return selectsAllInsertedCells;
+ }
+
+ /**
+ * @param selectsAllInsertedCells
+ * The selectsAllInsertedCells to set.
+ */
+ public void setSelectsAllInsertedCells(boolean selectsAllInsertedCells) {
+ this.selectsAllInsertedCells = selectsAllInsertedCells;
+ }
+
+ /**
+ * @return Returns the selectsLocalInsertedCells.
+ */
+ public boolean isSelectsLocalInsertedCells() {
+ return selectsLocalInsertedCells;
+ }
+
+ /**
+ * @param selectsLocalInsertedCells
+ * The selectsLocalInsertedCells to set.
+ */
+ public void setSelectsLocalInsertedCells(boolean selectsLocalInsertedCells) {
+ this.selectsLocalInsertedCells = selectsLocalInsertedCells;
+ }
+
+ /**
+ * @return Returns the reconnectsEdgesToVisibleParent.
+ * @deprecated edges are moved to parent view and back automatically
+ */
+ public boolean isReconnectsEdgesToVisibleParent() {
+ return reconnectsEdgesToVisibleParent;
+ }
+
+ /**
+ * @param reconnectsEdgesToVisibleParent
+ * The reconnectsEdgesToVisibleParent to set.
+ * @deprecated edges are moved to parent view and back automatically
+ */
+ public void setReconnectsEdgesToVisibleParent(boolean reconnectsEdgesToVisibleParent) {
+ this.reconnectsEdgesToVisibleParent = reconnectsEdgesToVisibleParent;
+ }
+
+ /**
+ * @return Returns the showsChangedConnections.
+ */
+ public boolean isShowsChangedConnections() {
+ return showsChangedConnections;
+ }
+
+ /**
+ * @param showsChangedConnections
+ * The showsChangedConnections to set.
+ */
+ public void setShowsChangedConnections(boolean showsChangedConnections) {
+ this.showsChangedConnections = showsChangedConnections;
+ }
+
+ /**
+ * @return Returns the moveChildrenOnExpand.
+ */
+ public boolean isMovesChildrenOnExpand() {
+ return movesChildrenOnExpand;
+ }
+
+ /**
+ * @param moveChildrenOnExpand
+ * The moveChildrenOnExpand to set.
+ */
+ public void setMovesChildrenOnExpand(boolean moveChildrenOnExpand) {
+ this.movesChildrenOnExpand = moveChildrenOnExpand;
+ }
+
+ /**
+ * @return Returns the collapseXScale.
+ */
+ public double getCollapseXScale() {
+ return collapseXScale;
+ }
+
+ /**
+ * @param collapseXScale
+ * The collapseXScale to set.
+ */
+ public void setCollapseXScale(double collapseXScale) {
+ this.collapseXScale = collapseXScale;
+ }
+
+ /**
+ * @return Returns the collapseYScale.
+ */
+ public double getCollapseYScale() {
+ return collapseYScale;
+ }
+
+ /**
+ * @param collapseYScale
+ * The collapseYScale to set.
+ */
+ public void setCollapseYScale(double collapseYScale) {
+ this.collapseYScale = collapseYScale;
+ }
+
+ /**
+ * @return Returns the movesParentsOnCollapse.
+ */
+ public boolean isMovesParentsOnCollapse() {
+ return movesParentsOnCollapse;
+ }
+
+ /**
+ * @param movesParentsOnCollapse
+ * The movesParentsOnCollapse to set.
+ */
+ public void setMovesParentsOnCollapse(boolean movesParentsOnCollapse) {
+ this.movesParentsOnCollapse = movesParentsOnCollapse;
+ }
+
+ /**
+ * @return Returns the resizesParentsOnCollapse.
+ */
+ public boolean isResizesParentsOnCollapse() {
+ return resizesParentsOnCollapse;
+ }
+
+ /**
+ * @param resizesParentsOnCollapse
+ * The resizesParentsOnCollapse to set.
+ */
+ public void setResizesParentsOnCollapse(boolean resizesParentsOnCollapse) {
+ this.resizesParentsOnCollapse = resizesParentsOnCollapse;
+ }
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/GraphModel.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/GraphModel.java
new file mode 100644
index 0000000..c71c4da
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/GraphModel.java
@@ -0,0 +1,289 @@
+/*
+ * @(#)GraphModel.java 1.0 03-JUL-04
+ *
+ * Copyright (c) 2001-2004 Gaudenz Alder
+ *
+ */
+package org.jgraph.graph;
+
+import org.jgraph.event.GraphModelListener;
+
+import java.util.Iterator;
+import java.util.Map;
+
+import javax.swing.event.UndoableEditListener;
+import javax.swing.undo.UndoableEdit;
+
+
+/**
+ * The interface that defines a suitable data model for a JGraph.
+ *
+ * @version 1.0 1/1/02
+ * @author Gaudenz Alder
+ */
+public interface GraphModel {
+ //
+ // Roots
+ //
+
+ /**
+ * Returns the number of roots in the model. Returns 0 if the model is
+ * empty.
+ *
+ * @return the number of roots in the model
+ */
+ int getRootCount();
+
+ /**
+ * Returns the root at index <I>index </I> in the model. This should not
+ * return null if <i>index </i> is a valid index for the model (that is
+ * <i>index </i>>= 0 && <i>index </i>< getRootCount()).
+ *
+ * @return the root of at index <I>index </I>
+ */
+ Object getRootAt(int index);
+
+ /**
+ * Returns the index of <code>root</code> in the model. If root is
+ * <code>null</code>, returns -1.
+ *
+ * @param root
+ * a root in the model, obtained from this data source
+ * @return the index of the root in the model, or -1 if the parent is
+ * <code>null</code>
+ */
+ int getIndexOfRoot(Object root);
+
+ /**
+ * Returns <code>true</code> if <code>node</code> or one of its
+ * ancestors is in the model.
+ *
+ * @return <code>true</code> if <code>node</code> is in the model
+ */
+ boolean contains(Object node);
+
+ /**
+ * Returns a <code>AttributeMap</code> that represents the properties for
+ * the specified cell.
+ *
+ * @return properties of <code>node</code> as a <code>Map</code>
+ */
+ AttributeMap getAttributes(Object node);
+
+ /**
+ * Returns the user object for the specified cell.
+ *
+ * @return userobject of <code>node</code>
+ */
+ Object getValue(Object node);
+
+ //
+ // Graph Structure
+ //
+
+ /**
+ * Returns the source of <code>edge</code>. <I>edge </I> must be an
+ * object previously obtained from this data source.
+ *
+ * @return <code>Object</code> that represents the source of <i>edge </i>
+ */
+ Object getSource(Object edge);
+
+ /**
+ * Returns the target of <code>edge</code>. <I>edge </I> must be an
+ * object previously obtained from this data source.
+ *
+ * @return <code>Object</code> that represents the target of <i>edge </i>
+ */
+ Object getTarget(Object edge);
+
+ /**
+ * Returns <code>true</code> if <code>port</code> is a valid source for
+ * <code>edge</code>. <I>edge </I> and <I>port </I> must be objects
+ * previously obtained from this data source.
+ *
+ * @return <code>true</code> if <code>port</code> is a valid source for
+ * <code>edge</code>.
+ */
+ boolean acceptsSource(Object edge, Object port);
+
+ /**
+ * Returns <code>true</code> if <code>port</code> is a valid target for
+ * <code>edge</code>. <I>edge </I> and <I>port </I> must be objects
+ * previously obtained from this data source.
+ *
+ * @return <code>true</code> if <code>port</code> is a valid target for
+ * <code>edge</code>.
+ */
+ boolean acceptsTarget(Object edge, Object port);
+
+ /**
+ * Returns an iterator of the edges connected to <code>port</code>.
+ * <I>port </I> must be a object previously obtained from this data source.
+ * This method never returns null.
+ *
+ * @param port
+ * a port in the graph, obtained from this data source
+ * @return <code>Iterator</code> that represents the connected edges
+ */
+ Iterator edges(Object port);
+
+ /**
+ * Returns <code>true</code> if <code>edge</code> is a valid edge.
+ *
+ * @return <code>true</code> if <code>edge</code> is a valid edge.
+ */
+ boolean isEdge(Object edge);
+
+ /**
+ * Returns <code>true</code> if <code>port</code> is a valid port,
+ * possibly supporting edge connection.
+ *
+ * @return <code>true</code> if <code>port</code> is a valid port.
+ */
+ boolean isPort(Object port);
+
+ //
+ // Group structure
+ //
+
+ /**
+ * Returns the parent of <I>child </I> in the model. <I>child </I> must be a
+ * node previously obtained from this data source. This returns null if
+ * <i>child </i> is a root in the model.
+ *
+ * @param child
+ * a node in the graph, obtained from this data source
+ * @return the parent of <I>child </I>
+ */
+ Object getParent(Object child);
+
+ /**
+ * Returns the index of child in parent. If either the parent or child is
+ * <code>null</code>, returns -1.
+ *
+ * @param parent
+ * a note in the tree, obtained from this data source
+ * @param child
+ * the node we are interested in
+ * @return the index of the child in the parent, or -1 if either the parent
+ * or the child is <code>null</code>
+ */
+ int getIndexOfChild(Object parent, Object child);
+
+ /**
+ * Returns the child of <I>parent </I> at index <I>index </I> in the
+ * parent's child array. <I>parent </I> must be a node previously obtained
+ * from this data source. This should not return null if <i>index </i> is a
+ * valid index for <i>parent </i> (that is <i>index </i>>= 0 && <i>index
+ * </i>< getChildCount( <i>parent </i>)).
+ *
+ * @param parent
+ * a node in the tree, obtained from this data source
+ * @return the child of <I>parent </I> at index <I>index </I>
+ */
+ Object getChild(Object parent, int index);
+
+ /**
+ * Returns the number of children of <I>parent </I>. Returns 0 if the node
+ * is a leaf or if it has no children. <I>parent </I> must be a node
+ * previously obtained from this data source.
+ *
+ * @param parent
+ * a node in the tree, obtained from this data source
+ * @return the number of children of the node <I>parent </I>
+ */
+ int getChildCount(Object parent);
+
+ /**
+ * Returns whether the specified node is a leaf node. The way the test is
+ * performed depends on the <code>askAllowsChildren</code> setting.
+ *
+ * @param node
+ * the node to check
+ * @return true if the node is a leaf node
+ */
+ boolean isLeaf(Object node);
+
+ //
+ // Change Support
+ //
+
+ /**
+ * Inserts the <code>cells</code> and connections into the model, and
+ * passes <code>attributes</code> to the views. Notifies the model- and
+ * undo listeners of the change.
+ */
+ void insert(Object[] roots, Map attributes, ConnectionSet cs, ParentMap pm, UndoableEdit[] e);
+
+ /**
+ * Removes <code>cells</code> from the model. If
+ * <code>removeChildren</code> is <code>true</code>, the children are
+ * also removed. Notifies the model- and undo listeners of the change.
+ */
+ void remove(Object[] roots);
+
+ /**
+ * Applies the <code>propertyMap</code> and the connection changes to the
+ * model. The initial <code>edits</code> that triggered the call are
+ * considered to be part of this transaction. Notifies the model- and undo
+ * listeners of the change. <strong>Note: </strong> If only
+ * <code>edits</code> is non-null, the edits are directly passed to the
+ * UndoableEditListeners.
+ */
+ void edit(Map attributes, ConnectionSet cs, ParentMap pm, UndoableEdit[] e);
+
+ /**
+ * Returns a map of (cell, clone)-pairs for all <code>cells</code> and
+ * their children. Special care should be taken to replace references
+ * between cells.
+ */
+ Map cloneCells(Object[] cells);
+
+ /**
+ * Messaged when the value of the cell has changed, eg from within the edit
+ * method.
+ */
+ Object valueForCellChanged(Object cell, Object newValue);
+
+ //
+ // Layering
+ //
+
+ /**
+ * Sends <code>cells</code> to back.
+ */
+ void toBack(Object[] cells);
+
+ /**
+ * Brings <code>cells</code> to front.
+ */
+ void toFront(Object[] cells);
+
+ //
+ // Listeners
+ //
+
+ /**
+ * Adds a listener for the GraphModelEvent posted after the model changes.
+ */
+ void addGraphModelListener(GraphModelListener l);
+
+ /**
+ * Removes a listener previously added with <B>addGraphModelListener() </B>.
+ */
+ void removeGraphModelListener(GraphModelListener l);
+
+ /**
+ * Adds an undo listener for notification of any changes. Undo/Redo
+ * operations performed on the <code>UndoableEdit</code> will cause the
+ * appropriate ModelEvent to be fired to keep the view(s) in sync with the
+ * model.
+ */
+ void addUndoableEditListener(UndoableEditListener listener);
+
+ /**
+ * Removes an undo listener.
+ */
+ void removeUndoableEditListener(UndoableEditListener listener);
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/GraphSelectionModel.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/GraphSelectionModel.java
new file mode 100644
index 0000000..d88d34c
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/GraphSelectionModel.java
@@ -0,0 +1,196 @@
+/*
+ * @(#)GraphSelectionModel.java 0.1 03-JUL-04
+ *
+ * Copyright (c) 2001-2004 Gaudenz Alder
+ *
+ */
+package org.jgraph.graph;
+
+import org.jgraph.event.GraphSelectionListener;
+
+import java.beans.PropertyChangeListener;
+
+
+/**
+ * This interface represents the current state of the selection for
+ * the graph component.
+ * <p>
+ *
+ * A GraphSelectionModel can be configured to allow only one
+ * cell (<code>SINGLE_GRAPH_SELECTION</code>) or a number of
+ * cells (<code>MULTIPLE_GRAPH_SELECTION</code>).
+ *
+ * @version 0.1 1/1/02
+ * @author Gaudenz Alder
+ */
+public interface GraphSelectionModel {
+ /** Selection can only contain one cell at a time. */
+ public static final int SINGLE_GRAPH_SELECTION = 1;
+
+ /** Selection can contain any number of items. */
+ public static final int MULTIPLE_GRAPH_SELECTION = 4;
+
+ /**
+ * Sets the selection model, which must be either
+ * SINGLE_GRAPH_SELECTION or MULTIPLE_GRAPH_SELECTION.
+ * <p>
+ * This may change the selection if the current selection is not valid
+ * for the new mode.
+ */
+ void setSelectionMode(int mode);
+
+ /**
+ * Sets if the selection model allows the selection
+ * of children.
+ */
+ void setChildrenSelectable(boolean flag);
+
+ /**
+ * Returns true if the selection model allows the selection
+ * of children.
+ */
+ boolean isChildrenSelectable();
+
+ /**
+ * Returns the current selection mode, either
+ * <code>SINGLE_GRAPH_SELECTION</code> or
+ * <code>MULTIPLE_GRAPH_SELECTION</code>.
+ */
+ int getSelectionMode();
+
+ /**
+ * Sets the selection to cell. If this represents a change, then
+ * the GraphSelectionListeners are notified. If <code>cell</code> is
+ * null, this has the same effect as invoking <code>clearSelection</code>.
+ *
+ * @param cell new cell to select
+ */
+ void setSelectionCell(Object cell);
+
+ /**
+ * Sets the selection to cells. If this represents a change, then
+ * the GraphSelectionListeners are notified. If <code>cells</code> is
+ * null, this has the same effect as invoking <code>clearSelection</code>.
+ *
+ * @param cells new selection
+ */
+ void setSelectionCells(Object[] cells);
+
+ /**
+ * Adds cell to the current selection. If cell is not currently
+ * in the selection the GraphSelectionListeners are notified. This has
+ * no effect if <code>cell</code> is null.
+ *
+ * @param cell the new cell to add to the current selection
+ */
+ void addSelectionCell(Object cell);
+
+ /**
+ * Adds cells to the current selection. If any of the cells are
+ * not currently in the selection the GraphSelectionListeners
+ * are notified. This has no effect if <code>cells</code> is null.
+ *
+ * @param cells the new cells to add to the current selection
+ */
+ void addSelectionCells(Object[] cells);
+
+ /**
+ * Removes cell from the selection. If cell is in the selection
+ * the GraphSelectionListeners are notified. This has no effect if
+ * <code>cell</code> is null.
+ *
+ * @param cell the cell to remove from the selection
+ */
+ void removeSelectionCell(Object cell);
+
+ /**
+ * Removes cells from the selection. If any of the cells in
+ * <code>cells</code> are in the selection, the
+ * GraphSelectionListeners are notified. This method has no
+ * effect if <code>cells</code> is null.
+ *
+ * @param cells the cells to remove from the selection
+ */
+ void removeSelectionCells(Object[] cells);
+
+ /**
+ * Returns the cells that are currently selectable.
+ */
+ Object[] getSelectables();
+
+ /**
+ * Returns the first cell in the selection. How first is defined is
+ * up to implementors.
+ */
+ Object getSelectionCell();
+
+ /**
+ * Returns the cells in the selection. This will return null (or an
+ * empty array) if nothing is currently selected.
+ */
+ Object[] getSelectionCells();
+
+ /**
+ * Returns the number of cells that are selected.
+ */
+ int getSelectionCount();
+
+ /**
+ * Returns true if the cell, <code>cell</code>, is in the current
+ * selection.
+ */
+ boolean isCellSelected(Object cell);
+
+ /**
+ * Returns true if the cell, <code>cell</code>,
+ * has selected children.
+ */
+ boolean isChildrenSelected(Object cell);
+
+ /**
+ * Returns true if the selection is currently empty.
+ */
+ boolean isSelectionEmpty();
+
+ /**
+ * Empties the current selection. If this represents a change in the
+ * current selection, the selection listeners are notified.
+ */
+ void clearSelection();
+
+ /**
+ * Adds a PropertyChangeListener to the listener list.
+ * The listener is registered for all properties.
+ * <p>
+ * A PropertyChangeEvent will get fired when the selection mode
+ * changes.
+ *
+ * @param listener the PropertyChangeListener to be added
+ */
+ void addPropertyChangeListener(PropertyChangeListener listener);
+
+ /**
+ * Removes a PropertyChangeListener from the listener list.
+ * This removes a PropertyChangeListener that was registered
+ * for all properties.
+ *
+ * @param listener the PropertyChangeListener to be removed
+ */
+ void removePropertyChangeListener(PropertyChangeListener listener);
+
+ /**
+ * Adds x to the list of listeners that are notified each time the
+ * set of selected Objects changes.
+ *
+ * @param x the new listener to be added
+ */
+ void addGraphSelectionListener(GraphSelectionListener x);
+
+ /**
+ * Removes x from the list of listeners that are notified each time
+ * the set of selected Objects changes.
+ *
+ * @param x the listener to remove
+ */
+ void removeGraphSelectionListener(GraphSelectionListener x);
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/GraphTransferHandler.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/GraphTransferHandler.java
new file mode 100644
index 0000000..bafaa9d
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/GraphTransferHandler.java
@@ -0,0 +1,377 @@
+/*
+ * @(#)GraphTransferHandler.java 1.0 31-DEC-04
+ *
+ * Copyright (c) 2001-2004 Gaudenz Alder
+ *
+ */
+package org.jgraph.graph;
+
+import org.jgraph.JGraph;
+
+import java.awt.Point;
+import java.awt.datatransfer.DataFlavor;
+import java.awt.datatransfer.Transferable;
+import java.awt.event.InputEvent;
+import java.awt.event.MouseEvent;
+import java.awt.geom.Point2D;
+import java.awt.geom.Rectangle2D;
+
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.Map;
+
+import javax.swing.JComponent;
+import javax.swing.TransferHandler;
+
+
+/**
+ * @author Gaudenz Alder
+ *
+ * Default datatransfer handler.
+ */
+public class GraphTransferHandler extends TransferHandler {
+ /**
+ * Controls if all inserts should be handled as external drops even if all
+ * cells are already in the graph model. This is useful if the enclosing
+ * component does not allow moving.
+ */
+ protected boolean alwaysReceiveAsCopyAction = false;
+
+ /* Pointer to the last inserted array of cells. */
+ protected Object out;
+
+ /* Pointer to the last inserted array of cells. */
+ protected Object in;
+
+ /* How many times the last transferable was inserted. */
+ protected int inCount = 0;
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param comp DOCUMENT ME!
+ * @param flavors DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean canImport(JComponent comp, DataFlavor[] flavors) {
+ for (int i = 0; i < flavors.length; i++)
+ if (flavors[i] == GraphTransferable.dataFlavor)
+ return true;
+
+ return false;
+ }
+
+ /* Public entry point to create a Transferable. */
+ /**
+ * DOCUMENT ME!
+ *
+ * @param graph DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Transferable createTransferableForGraph(JGraph graph) {
+ return createTransferable(graph);
+ }
+
+ protected Transferable createTransferable(JComponent c) {
+ if (c instanceof JGraph) {
+ JGraph graph = (JGraph) c;
+
+ if (!graph.isSelectionEmpty()) {
+ return createTransferable(graph, graph.getSelectionCells());
+ }
+ }
+
+ return null;
+ }
+
+ protected Transferable createTransferable(JGraph graph, Object[] cells) {
+ Object[] flat = graph.getDescendants(graph.order(cells));
+ ParentMap pm = ParentMap.create(graph.getModel(), flat, false, true);
+ ConnectionSet cs = ConnectionSet.create(graph.getModel(), flat, false);
+ Map viewAttributes = GraphConstants.createAttributes(flat, graph.getGraphLayoutCache());
+ Rectangle2D bounds = graph.getCellBounds(graph.getSelectionCells());
+ bounds = new AttributeMap.SerializableRectangle2D(bounds.getX(), bounds.getY(),
+ bounds.getWidth(), bounds.getHeight());
+ out = flat;
+
+ return create(graph, flat, viewAttributes, bounds, cs, pm);
+ }
+
+ protected GraphTransferable create(JGraph graph, Object[] cells, Map viewAttributes,
+ Rectangle2D bounds, ConnectionSet cs, ParentMap pm) {
+ return new GraphTransferable(cells, viewAttributes, bounds, cs, pm);
+ }
+
+ protected void exportDone(JComponent comp, Transferable data, int action) {
+ if (comp instanceof JGraph && data instanceof GraphTransferable) {
+ JGraph graph = (JGraph) comp;
+
+ if (action == TransferHandler.MOVE) {
+ Object[] cells = ((GraphTransferable) data).getCells();
+ graph.getGraphLayoutCache().remove(cells);
+ }
+
+ graph.getUI().updateHandle();
+ graph.getUI().setInsertionLocation(null);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param c DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getSourceActions(JComponent c) {
+ return COPY_OR_MOVE;
+ }
+
+ // NOTE: 1. We abuse return value to signal removal to the sender.
+ /**
+ * DOCUMENT ME!
+ *
+ * @param comp DOCUMENT ME!
+ * @param t DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean importData(JComponent comp, Transferable t) {
+ try {
+ if (comp instanceof JGraph) {
+ JGraph graph = (JGraph) comp;
+ GraphModel model = graph.getModel();
+ GraphLayoutCache cache = graph.getGraphLayoutCache();
+
+ if (t.isDataFlavorSupported(GraphTransferable.dataFlavor) && graph.isEnabled()) {
+ // May be null
+ Point p = graph.getUI().getInsertionLocation();
+
+ // Get Local Machine Flavor
+ Object obj = t.getTransferData(GraphTransferable.dataFlavor);
+ GraphTransferable gt = (GraphTransferable) obj;
+
+ // Get Transferred Cells
+ Object[] cells = gt.getCells();
+
+ // Check if all cells are in the model
+ boolean allInModel = true;
+
+ for (int i = 0; (i < cells.length) && allInModel; i++)
+ allInModel = allInModel && model.contains(cells[i]);
+
+ // Count repetitive inserts
+ if (in == cells)
+ inCount++;
+ else
+ inCount = (allInModel) ? 1 : 0;
+
+ in = cells;
+
+ // Delegate to handle
+ if ((p != null) && (in == out) && (graph.getUI().getHandle() != null)) {
+ int mod = (graph.getUI().getDropAction() == TransferHandler.COPY)
+ ? InputEvent.CTRL_MASK : 0;
+ graph.getUI().getHandle()
+ .mouseReleased(new MouseEvent(comp, 0, 0, mod, p.x, p.y, 1, false));
+
+ return false;
+ }
+
+ // Get more Transfer Data
+ Rectangle2D bounds = gt.getBounds();
+ Map nested = gt.getAttributeMap();
+ ConnectionSet cs = gt.getConnectionSet();
+ ParentMap pm = gt.getParentMap();
+
+ // Move across models or via clipboard always clones
+ if (!allInModel || (p == null) || alwaysReceiveAsCopyAction
+ || (graph.getUI().getDropAction() == TransferHandler.COPY)) {
+ // Translate cells
+ double dx = 0;
+
+ // Translate cells
+ double dy = 0;
+
+ // Cloned via Drag and Drop
+ if (nested != null) {
+ if ((p != null) && (bounds != null)) {
+ Point2D insert = graph.fromScreen(graph.snap((Point2D) p.clone()));
+ dx = insert.getX() - bounds.getX();
+ dy = insert.getY() - bounds.getY();
+
+ // Cloned via Clipboard
+ } else {
+ dx = inCount * graph.getGridSize();
+ dy = inCount * graph.getGridSize();
+ }
+ }
+
+ handleExternalDrop(graph, cells, nested, cs, pm, dx, dy);
+
+ // Signal sender to remove only if moved between
+ // different models
+ return ((graph.getUI().getDropAction() == TransferHandler.MOVE)
+ && !allInModel);
+ }
+ // We are dealing with a move across multiple views
+ // of the same model
+ else {
+ // Moved via Drag and Drop
+ if (p != null) {
+ // Scale insertion location
+ Point2D insert = graph.fromScreen(graph.snap(new Point(p)));
+
+ // Compute translation vector and translate all
+ // attribute maps.
+ if ((bounds != null) && (nested != null)) {
+ double dx = insert.getX() - bounds.getX();
+ double dy = insert.getY() - bounds.getY();
+ AttributeMap.translate(nested.values(), dx, dy);
+ } else if (bounds == null) {
+ // Prevents overwriting view-local
+ // attributes
+ // for known cells. Note: This is because
+ // if bounds is null, the caller wants
+ // to signal that the bounds were
+ // not available, which is typically the
+ // case if no graph layout cache
+ // is at hand. To avoid overriding the
+ // local attributes such as the bounds
+ // with the default bounds from the model,
+ // we remove all attributes that travel
+ // along with the transferable. (Since
+ // all cells are already in the model
+ // no information is lost by doing this.)
+ double gs2 = 2 * graph.getGridSize();
+ nested = new Hashtable();
+
+ Map emptyMap = new Hashtable();
+
+ for (int i = 0; i < cells.length; i++) {
+ // This also gives us the chance to
+ // provide useful default location and
+ // resize if there are no useful bounds
+ // that travel along with the cells.
+ if (!model.isEdge(cells[i]) && !model.isPort(cells[i])) {
+ // Check if there are useful bounds
+ // defined in the model, otherwise
+ // resize,
+ // because the view does not yet exist.
+ Rectangle2D tmp = graph.getCellBounds(cells[i]);
+
+ if (tmp == null)
+ tmp = GraphConstants.getBounds(model.getAttributes(cells[i]));
+
+ // Clone the rectangle to force a
+ // repaint
+ if (tmp != null)
+ tmp = (Rectangle2D) tmp.clone();
+
+ Hashtable attrs = new Hashtable();
+ Object parent = model.getParent(cells[i]);
+
+ if (tmp == null) {
+ tmp = new Rectangle2D.Double(p.getX(), p.getY(),
+ gs2 / 2, gs2);
+ GraphConstants.setResize(attrs, true);
+
+ // Shift
+ p.setLocation(p.getX() + gs2, p.getY() + gs2);
+ graph.snap(p);
+
+ // If parent processed then childs
+ // are already located
+ } else if ((parent == null)
+ || !nested.keySet()
+ .contains(model.getParent(cells[i]))) {
+ CellView view = graph.getGraphLayoutCache()
+ .getMapping(cells[i], false);
+
+ if ((view != null) && !view.isLeaf()) {
+ double dx = p.getX() - tmp.getX();
+ double dy = p.getY() - tmp.getY();
+ GraphLayoutCache.translateViews(new CellView[] { view },
+ dx, dy);
+ } else {
+ tmp.setFrame(p.getX(), p.getY(), tmp.getWidth(),
+ tmp.getHeight());
+ }
+
+ // Shift
+ p.setLocation(p.getX() + gs2, p.getY() + gs2);
+ graph.snap(p);
+ }
+
+ GraphConstants.setBounds(attrs, tmp);
+ nested.put(cells[i], attrs);
+ } else {
+ nested.put(cells[i], emptyMap);
+ }
+ }
+ }
+
+ // Edit cells (and make visible)
+ cache.edit(nested, null, null, null);
+ }
+
+ // Select topmost cells in group-structure
+ graph.setSelectionCells(DefaultGraphModel.getTopmostCells(model, cells));
+
+ // Don't remove at sender
+ return false;
+ }
+ } else
+
+ return importDataImpl(comp, t);
+ }
+ } catch (Exception exception) {
+ // System.err.println("Cannot import: " +
+ // exception.getMessage());
+ exception.printStackTrace();
+ }
+
+ return false;
+ }
+
+ protected void handleExternalDrop(JGraph graph, Object[] cells, Map nested, ConnectionSet cs,
+ ParentMap pm, double dx, double dy) {
+ // Removes all connections for which the port is neither
+ // passed in the parent map nor already in the model.
+ Iterator it = cs.connections();
+
+ while (it.hasNext()) {
+ ConnectionSet.Connection conn = (ConnectionSet.Connection) it.next();
+
+ if (!pm.getChangedNodes().contains(conn.getPort())
+ && !graph.getModel().contains(conn.getPort())) {
+ it.remove();
+ }
+ }
+
+ Map clones = graph.cloneCells(cells);
+ graph.getGraphLayoutCache().insertClones(cells, clones, nested, cs, pm, dx, dy);
+ }
+
+ // For subclassers if above does not handle the insertion
+ protected boolean importDataImpl(JComponent comp, Transferable t) {
+ return false;
+ }
+
+ /**
+ * @return Returns the alwaysReceiveAsCopyAction.
+ */
+ public boolean isAlwaysReceiveAsCopyAction() {
+ return alwaysReceiveAsCopyAction;
+ }
+
+ /**
+ * @param alwaysReceiveAsCopyAction
+ * The alwaysReceiveAsCopyAction to set.
+ */
+ public void setAlwaysReceiveAsCopyAction(boolean alwaysReceiveAsCopyAction) {
+ this.alwaysReceiveAsCopyAction = alwaysReceiveAsCopyAction;
+ }
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/GraphTransferable.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/GraphTransferable.java
new file mode 100644
index 0000000..3256947
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/GraphTransferable.java
@@ -0,0 +1,197 @@
+/*
+ * @(#)GraphTransferable.java 1.0 03-JUL-04
+ *
+ * Copyright (c) 2001-2004 Gaudenz Alder
+ *
+ */
+package org.jgraph.graph;
+
+import org.jgraph.plaf.basic.BasicGraphTransferable;
+
+import java.awt.datatransfer.Clipboard;
+import java.awt.datatransfer.ClipboardOwner;
+import java.awt.datatransfer.DataFlavor;
+import java.awt.datatransfer.Transferable;
+import java.awt.datatransfer.UnsupportedFlavorException;
+import java.awt.geom.Rectangle2D;
+
+import java.io.Serializable;
+
+import java.util.Map;
+
+
+/**
+ * An object that represents the clipboard contents for a graph selection.
+ * The object has three representations:
+ * <p>
+ * 1. Richer: The cells, view attributes and connections for this selection are
+ * stored as separate datastructures, which can be inserted using
+ * the GraphModel.insert() method.
+ * 2. HTML: If one cell is selected, the userObject is returned as HTML.
+ * 3. Plain: The userObject of the selected cell is returned as plain text.
+ *
+ * @author Gaudenz Alder
+ * @version 1.0 1/1/02
+ *
+ */
+public class GraphTransferable extends BasicGraphTransferable implements Serializable,
+ ClipboardOwner {
+ /** Local Machine Reference Data Flavor. */
+ public static DataFlavor dataFlavor;
+
+ /** Selected cells. */
+ protected Object[] cells;
+
+ /** Object that describes the connection between cells. */
+ protected ConnectionSet cs;
+
+ /** Object that describes the group structure between cells. */
+ protected ParentMap pm;
+
+ /** (Cell, Map) entries that hold the view attributes for the cells. */
+ protected Map attributeMap;
+
+ /** Rectangle that defines the former bounds of the views. */
+ protected Rectangle2D bounds;
+
+ /**
+ * Constructs a new transferable selection for <code>cells</code>,
+ * <code>cs</code>and <code>attrMap</code>.
+ */
+ public GraphTransferable(Object[] cells, Map attrMap, Rectangle2D bounds, ConnectionSet cs,
+ ParentMap pm) {
+ attributeMap = attrMap;
+ this.bounds = bounds;
+ this.cells = cells;
+ this.cs = cs;
+ this.pm = pm;
+ }
+
+ /**
+ * Returns the <code>cells</code> that represent the selection.
+ */
+ public Object[] getCells() {
+ return cells;
+ }
+
+ /**
+ * Returns the connections between <code>cells</code> (and possibly
+ * other, unselected cells).
+ */
+ public ConnectionSet getConnectionSet() {
+ return cs;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public ParentMap getParentMap() {
+ return pm;
+ }
+
+ /**
+ * Returns a map of (GraphCell, Map)-pairs that represent the
+ * view attributes for the respecive cells.
+ */
+ public Map getAttributeMap() {
+ return attributeMap;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Rectangle2D getBounds() {
+ return bounds;
+ }
+
+ // from ClipboardOwner
+ /**
+ * DOCUMENT ME!
+ *
+ * @param clip DOCUMENT ME!
+ * @param contents DOCUMENT ME!
+ */
+ public void lostOwnership(Clipboard clip, Transferable contents) {
+ // do nothing
+ }
+
+ // --- Richer ----------------------------------------------------------
+
+ /**
+ * Returns the jvm-localreference flavors of the transferable.
+ */
+ public DataFlavor[] getRicherFlavors() {
+ return new DataFlavor[] { dataFlavor };
+ }
+
+ /**
+ * Fetch the data in a jvm-localreference format.
+ */
+ public Object getRicherData(DataFlavor flavor) throws UnsupportedFlavorException {
+ if (flavor.equals(dataFlavor))
+ return this;
+ else
+ throw new UnsupportedFlavorException(flavor);
+ }
+
+ // --- Plain ----------------------------------------------------------
+
+ /**
+ * Returns true if the transferable support a text/plain format.
+ */
+ public boolean isPlainSupported() {
+ return ((cells != null) && (cells.length == 1));
+ }
+
+ /**
+ * Fetch the data in a text/plain format.
+ */
+ public String getPlainData() {
+ if (cells[0] instanceof DefaultGraphCell) {
+ Object obj = ((DefaultGraphCell) cells[0]).getUserObject();
+
+ if (obj != null)
+ return obj.toString();
+ }
+
+ return cells[0].toString();
+ }
+
+ // --- HTML ---------------------------------------------------------
+
+ /**
+ * Returns true if the transferable support a text/html format.
+ */
+ public boolean isHTMLSupported() {
+ return isPlainSupported();
+ }
+
+ /**
+ * Fetch the data in a text/html format.
+ */
+ public String getHTMLData() {
+ StringBuffer buf = new StringBuffer();
+ buf.append("<html><body><p>");
+ buf.append(getPlainData());
+ buf.append("</p></body></html>");
+
+ return buf.toString();
+ }
+
+ static {
+ DataFlavor localDataFlavor;
+
+ try {
+ localDataFlavor = new DataFlavor(DataFlavor.javaJVMLocalObjectMimeType
+ + "; class=org.jgraph.graph.GraphTransferable");
+ } catch (ClassNotFoundException cnfe) {
+ localDataFlavor = null;
+ }
+
+ dataFlavor = localDataFlavor;
+ }
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/GraphUndoManager.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/GraphUndoManager.java
new file mode 100644
index 0000000..118528c
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/GraphUndoManager.java
@@ -0,0 +1,168 @@
+/*
+ * @(#)GraphUndoManager.java 1.0 03-JUL-04
+ *
+ * Copyright (c) 2001-2004 Gaudenz Alder
+ *
+ */
+package org.jgraph.graph;
+
+import org.jgraph.event.GraphLayoutCacheEvent;
+
+import javax.swing.undo.CannotRedoException;
+import javax.swing.undo.CannotUndoException;
+import javax.swing.undo.UndoManager;
+import javax.swing.undo.UndoableEdit;
+
+
+/**
+ * An UndoManager that may be shared among multiple GraphLayoutCache's.
+ *
+ * @version 1.0 1/1/02
+ * @author Gaudenz Alder
+ */
+public class GraphUndoManager extends UndoManager {
+ /**
+ * Overridden to preserve usual semantics: returns true if an undo
+ * operation would be successful now for the given view, false otherwise
+ */
+ public synchronized boolean canUndo(Object source) {
+ if (isInProgress()) {
+ UndoableEdit edit = editToBeUndone(source);
+
+ return (edit != null) && edit.canUndo();
+ } else {
+ return super.canUndo();
+ }
+ }
+
+ /**
+ * Overridden to preserve usual semantics: returns true if a redo
+ * operation would be successful now for the given view, false otherwise
+ */
+ public synchronized boolean canRedo(Object source) {
+ if (isInProgress()) {
+ UndoableEdit edit = editToBeRedone(source);
+
+ return (edit != null) && edit.canRedo();
+ } else {
+ return super.canRedo();
+ }
+ }
+
+ /**
+ * If this UndoManager is inProgress, undo the last significant
+ * UndoableEdit wrt to source, and all insignificant edits back to
+ * it. Updates indexOfNextAdd accordingly.
+ *
+ * <p>If not inProgress, indexOfNextAdd is ignored and super's routine is
+ * called.</p>
+ *
+ * @see UndoManager#undo
+ */
+ public void undo(Object source) {
+ if ((source == null) || !isInProgress())
+ super.undo();
+ else {
+ UndoableEdit edit = editToBeUndone(source);
+
+ //System.out.println("undoTo edit="+edit);
+ if (edit == null)
+ throw new CannotUndoException();
+
+ undoTo(edit);
+ }
+ }
+
+ protected UndoableEdit editToBeUndone(Object source) {
+ UndoableEdit edit = null;
+ Object src = null;
+
+ do {
+ edit = nextEditToBeUndone(edit);
+
+ if (edit instanceof GraphLayoutCacheEvent.GraphLayoutCacheChange)
+ src = ((GraphLayoutCacheEvent.GraphLayoutCacheChange) edit).getSource();
+
+ if (!(src instanceof GraphLayoutCache))
+ src = null;
+ } while ((edit != null) && (src != null) && (src != source));
+
+ return edit;
+ }
+
+ /**
+ * Returns the the next significant edit wrt to current
+ * to be undone if undo is called. May return null.
+ */
+ protected UndoableEdit nextEditToBeUndone(UndoableEdit current) {
+ if (current == null)
+ return editToBeUndone();
+ else {
+ int index = edits.indexOf(current) - 1;
+
+ if (index >= 0)
+ return (UndoableEdit) edits.get(index);
+ }
+
+ return null;
+ }
+
+ /**
+ * If this <code>UndoManager</code> is <code>inProgress</code>,
+ * redoes the last significant <code>UndoableEdit</code> with
+ * respect to source or after, and all insignificant
+ * edits up to it. Updates <code>indexOfNextAdd</code> accordingly.
+ *
+ * <p>If not <code>inProgress</code>, <code>indexOfNextAdd</code>
+ * is ignored and super's routine is called.</p>
+ */
+ public void redo(Object source) {
+ if ((source == null) || !isInProgress())
+ super.redo();
+ else {
+ UndoableEdit edit = editToBeRedone(source);
+
+ //System.out.println("redoTo edit="+edit);
+ if (edit == null)
+ throw new CannotRedoException();
+
+ redoTo(edit);
+ }
+ }
+
+ protected UndoableEdit editToBeRedone(Object source) {
+ UndoableEdit edit = nextEditToBeRedone(null);
+ UndoableEdit last = null;
+ Object src = null;
+
+ do {
+ last = edit;
+ edit = nextEditToBeRedone(edit);
+
+ if (edit instanceof GraphLayoutCacheEvent.GraphLayoutCacheChange)
+ src = ((GraphLayoutCacheEvent.GraphLayoutCacheChange) edit).getSource();
+
+ if (!(src instanceof GraphLayoutCache))
+ src = null;
+ } while ((edit != null) && (src != null) && (src != source));
+
+ return last;
+ }
+
+ /**
+ * Returns the the next significant edit wrt to current
+ * to be redone if redo is called. May return null.
+ */
+ protected UndoableEdit nextEditToBeRedone(UndoableEdit current) {
+ if (current == null)
+ return editToBeRedone();
+ else {
+ int index = edits.indexOf(current) + 1;
+
+ if (index < edits.size())
+ return (UndoableEdit) edits.get(index);
+ }
+
+ return null;
+ }
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/ParentMap.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/ParentMap.java
new file mode 100644
index 0000000..70bf71f
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/ParentMap.java
@@ -0,0 +1,224 @@
+/*
+ * @(#)ParentMap.java 1.0 03-JUL-04
+ *
+ * Copyright (c) 2001-2004 Gaudenz Alder
+ *
+ */
+package org.jgraph.graph;
+
+import java.io.Serializable;
+
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.Map;
+import java.util.Set;
+
+
+/**
+ * An object that describes relations between childs and parents.
+ *
+ * @version 1.0 1/1/02
+ * @author Gaudenz Alder
+ */
+public class ParentMap implements Serializable {
+ /** Contents of the parent map. */
+ protected ArrayList entries = new ArrayList();
+
+ /**
+ * Set of changed changedNodes for the parent map. Includes childs and
+ * parents.
+ */
+ protected Set changedNodes = new HashSet();
+
+ /** Maps parents to integers with the future number of childs. */
+ protected Map childCount = new Hashtable();
+
+ /**
+ * Constructs a <code>ParentMap</code> object.
+ */
+ public ParentMap() {
+ // empty
+ }
+
+ /**
+ * Constructs a <code>ParentMap</code> object.
+ */
+ public ParentMap(Object[] children, Object parent) {
+ addEntries(children, parent);
+ }
+
+ /**
+ * Returns a parent map that represents the insertion or removal of
+ * <code>cells</code> in <code>model</code> based on <code>remove</code>.
+ * Unselected childs of selected nodes are moved to the first unselected
+ * parent of that node.
+ * <p>
+ * <strong>Note:</strong> Consequently, cells "move up" one level when
+ * their parent is removed. <strong>Note:</strong> onlyUsePassedInCells can
+ * be used to indicate if only cells from the passed-in cell array are
+ * allowed parents. This is only used if remove is not true.
+ */
+ public static ParentMap create(GraphModel m, Object[] c, boolean remove,
+ boolean onlyUsePassedInCells) {
+ Set cellSet = new HashSet();
+
+ for (int i = 0; i < c.length; i++)
+ cellSet.add(c[i]);
+
+ ParentMap parentMap = new ParentMap();
+
+ for (int i = 0; i < c.length; i++) {
+ // Collect Parent Information
+ Object parent = m.getParent(c[i]);
+
+ if ((parent != null)
+ && (!onlyUsePassedInCells || (!remove && cellSet.contains(parent))))
+ parentMap.addEntry(c[i], (remove) ? null : parent);
+
+ if (remove) {
+ // Move Orphans to First Unselected Parent
+ while (cellSet.contains(parent))
+ parent = m.getParent(parent);
+
+ for (int j = 0; j < m.getChildCount(c[i]); j++) {
+ Object child = m.getChild(c[i], j);
+
+ if (!cellSet.contains(child))
+ parentMap.addEntry(child, parent);
+ }
+ }
+ }
+
+ return parentMap;
+ }
+
+ /**
+ * Add a new entry for this child, parent pair to the parent map. The child
+ * and parent are added to the set of changed nodes. Note: The previous
+ * parent is changed on execution of this parent map and must be added by
+ * the GraphModel and reflected by the GraphChange.getChanged method. TODO:
+ * In general, the GraphModel should be in charge of computing the set of
+ * changed cells.
+ */
+ public void addEntry(Object child, Object parent) {
+ if (child != null) {
+ entries.add(new Entry(child, parent));
+ // Update Changed Nodes
+ changedNodes.add(child);
+
+ if (parent != null)
+ changedNodes.add(parent);
+ }
+ }
+
+ /**
+ * Adds all child parent pairs using addEntry.
+ */
+ public void addEntries(Object[] children, Object parent) {
+ for (int i = 0; i < children.length; i++)
+ addEntry(children[i], parent);
+ }
+
+ /**
+ * Returns the number of entries.
+ */
+ public int size() {
+ return entries.size();
+ }
+
+ /**
+ * Returns an <code>Iterator</code> for the entries in the map.
+ */
+ public Iterator entries() {
+ return entries.iterator();
+ }
+
+ /**
+ * Returns a <code>Set</code> for the nodes, childs and parents, in this
+ * parent map.
+ */
+ public Set getChangedNodes() {
+ return changedNodes;
+ }
+
+ /**
+ * Creates a new parent map based on this parent map, where the child and
+ * parents are mapped using <code>map</code>. If one the cells is not in
+ * <code>map</code>, then the original cell is used instead.
+ * <p>
+ */
+ public ParentMap clone(Map map) {
+ ParentMap pm = new ParentMap();
+ Iterator it = entries();
+
+ while (it.hasNext()) {
+ Entry e = (Entry) it.next();
+ Object child = map.get(e.getChild());
+ Object parent = map.get(e.getParent());
+
+ if (child == null)
+ child = e.getChild();
+
+ if (parent == null)
+ parent = e.getParent();
+
+ if ((child != null) && (parent != null))
+ pm.addEntry(child, parent);
+ }
+
+ return pm;
+ }
+
+ /**
+ * Object that represents the relation between a child an a parent.
+ */
+ public class Entry implements Serializable {
+ /** Child and parent of the relation this entry describes. */
+ protected Object child;
+
+ /** Child and parent of the relation this entry describes. */
+ protected Object parent;
+
+ /**
+ * Constructs a new relation between <code>child</code> and
+ * <code>parent</code>.
+ */
+ public Entry(Object child, Object parent) {
+ this.child = child;
+ this.parent = parent;
+ }
+
+ /**
+ * Returns the child of the relation.
+ */
+ public Object getChild() {
+ return child;
+ }
+
+ /**
+ * Returns the parent of the relation.
+ */
+ public Object getParent() {
+ return parent;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String toString() {
+ String s = super.toString() + "\n";
+ Iterator it = entries();
+
+ while (it.hasNext()) {
+ Entry entry = (Entry) it.next();
+ s += (" child=" + entry.getChild() + " parent=" + entry.getParent() + "\n");
+ }
+
+ return s;
+ }
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/Port.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/Port.java
new file mode 100644
index 0000000..53d305a
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/Port.java
@@ -0,0 +1,45 @@
+/*
+ * @(#)Port.java 1.0 03-JUL-04
+ *
+ * Copyright (c) 2001-2004 Gaudenz Alder
+ *
+ */
+package org.jgraph.graph;
+
+import java.util.Iterator;
+
+
+/**
+ * Defines the requirements for an object that
+ * represents a port in a graph model.
+ *
+ * @version 1.0 1/1/02
+ * @author Gaudenz Alder
+ */
+public interface Port extends GraphCell {
+ /**
+ * Returns an iterator of the edges connected
+ * to the port.
+ */
+ Iterator edges();
+
+ /**
+ * Adds <code>edge</code> to the list of ports.
+ */
+ boolean addEdge(Object edge);
+
+ /**
+ * Removes <code>edge</code> from the list of ports.
+ */
+ boolean removeEdge(Object edge);
+
+ /**
+ * Returns the anchor of the port.
+ */
+ Port getAnchor();
+
+ /**
+ * Sets the anchor of the port.
+ */
+ void setAnchor(Port port);
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/PortRenderer.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/PortRenderer.java
new file mode 100644
index 0000000..469c15f
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/PortRenderer.java
@@ -0,0 +1,209 @@
+/*
+ * @(#)PortRenderer.java 1.0 03-JUL-04
+ *
+ * Copyright (c) 2001-2004 Gaudenz Alder
+ *
+ */
+package org.jgraph.graph;
+
+import org.jgraph.JGraph;
+
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Dimension;
+import java.awt.Graphics;
+import java.awt.Rectangle;
+
+import java.io.Serializable;
+
+import javax.swing.JComponent;
+import javax.swing.UIManager;
+
+
+/**
+ * This renderer displays entries that implement the CellView interface and
+ * supports the following attributes:
+ * <li> GraphConstants.OFFSET GraphConstants.ABSOLUTE </li
+ *
+ * @version 1.0 28/11/01
+ * @author Gaudenz Alder
+ */
+public class PortRenderer extends JComponent implements CellViewRenderer, Serializable {
+ /** Cache the current graph for drawing */
+ // protected transient JGraph graph;
+ /** Cache the current edgeview for drawing. */
+ protected transient PortView view;
+
+ /** Cache the current graph background. */
+ protected Color graphBackground = Color.white;
+
+ /** Cached hasFocus and selected value. */
+ transient protected boolean hasFocus;
+
+ /** Cached hasFocus and selected value. */
+ transient protected boolean selected;
+
+ /** Cached hasFocus and selected value. */
+ transient protected boolean preview;
+
+ /**
+ * Constructs a renderer that may be used to render ports.
+ */
+ public PortRenderer() {
+ setForeground(UIManager.getColor("MenuItem.selectionBackground"));
+ setBackground(UIManager.getColor("Tree.selectionBorderColor"));
+ }
+
+ /**
+ * Configure and return the renderer based on the passed in components. The
+ * value is typically set from messaging the graph with
+ * <code>convertValueToString</code>.
+ *
+ * @param graph
+ * the graph that that defines the rendering context.
+ * @param view
+ * the cell view that should be rendered.
+ * @param sel
+ * whether the object is selected.
+ * @param focus
+ * whether the object has the focus.
+ * @param preview
+ * whether we are drawing a preview.
+ * @return the component used to render the value.
+ */
+ public Component getRendererComponent(JGraph graph, CellView view, boolean sel, boolean focus,
+ boolean preview) {
+ // Check type
+ if (view instanceof PortView && (graph != null)) {
+ graphBackground = graph.getBackground();
+ this.view = (PortView) view;
+ this.hasFocus = focus;
+ this.selected = sel;
+ this.preview = preview;
+
+ return this;
+ }
+
+ return null;
+ }
+
+ /**
+ * Paint the renderer. Overrides superclass paint to add specific painting.
+ * Note: The preview flag is interpreted as "highlight" in this context.
+ * (This is used to highlight the port if the mouse is over it.)
+ */
+ public void paint(Graphics g) {
+ Dimension d = getSize();
+ g.setColor(graphBackground);
+ g.setXORMode(graphBackground);
+ super.paint(g);
+
+ if (preview) {
+ g.fill3DRect(0, 0, d.width, d.height, true);
+ } else {
+ g.fillRect(0, 0, d.width, d.height);
+ }
+
+ boolean offset = (GraphConstants.getOffset(view.getAllAttributes()) != null);
+ g.setColor(getForeground());
+
+ if (!offset)
+ g.fillRect(1, 1, d.width - 2, d.height - 2);
+ else if (!preview)
+ g.drawRect(1, 1, d.width - 3, d.height - 3);
+ }
+
+ /**
+ * Overridden for performance reasons. See the <a
+ * href="#override">Implementation Note</a> for more information.
+ */
+ public void validate() {
+ }
+
+ /**
+ * Overridden for performance reasons. See the <a
+ * href="#override">Implementation Note</a> for more information.
+ */
+ public void revalidate() {
+ }
+
+ /**
+ * Overridden for performance reasons. See the <a
+ * href="#override">Implementation Note</a> for more information.
+ */
+ public void repaint(long tm, int x, int y, int width, int height) {
+ }
+
+ /**
+ * Overridden for performance reasons. See the <a
+ * href="#override">Implementation Note</a> for more information.
+ */
+ public void repaint(Rectangle r) {
+ }
+
+ /**
+ * Overridden for performance reasons. See the <a
+ * href="#override">Implementation Note</a> for more information.
+ */
+ protected void firePropertyChange(String propertyName, Object oldValue, Object newValue) {
+ // Strings get interned...
+ if (propertyName == "text")
+ super.firePropertyChange(propertyName, oldValue, newValue);
+ }
+
+ /**
+ * Overridden for performance reasons. See the <a
+ * href="#override">Implementation Note</a> for more information.
+ */
+ public void firePropertyChange(String propertyName, byte oldValue, byte newValue) {
+ }
+
+ /**
+ * Overridden for performance reasons. See the <a
+ * href="#override">Implementation Note</a> for more information.
+ */
+ public void firePropertyChange(String propertyName, char oldValue, char newValue) {
+ }
+
+ /**
+ * Overridden for performance reasons. See the <a
+ * href="#override">Implementation Note</a> for more information.
+ */
+ public void firePropertyChange(String propertyName, short oldValue, short newValue) {
+ }
+
+ /**
+ * Overridden for performance reasons. See the <a
+ * href="#override">Implementation Note</a> for more information.
+ */
+ public void firePropertyChange(String propertyName, int oldValue, int newValue) {
+ }
+
+ /**
+ * Overridden for performance reasons. See the <a
+ * href="#override">Implementation Note</a> for more information.
+ */
+ public void firePropertyChange(String propertyName, long oldValue, long newValue) {
+ }
+
+ /**
+ * Overridden for performance reasons. See the <a
+ * href="#override">Implementation Note</a> for more information.
+ */
+ public void firePropertyChange(String propertyName, float oldValue, float newValue) {
+ }
+
+ /**
+ * Overridden for performance reasons. See the <a
+ * href="#override">Implementation Note</a> for more information.
+ */
+ public void firePropertyChange(String propertyName, double oldValue, double newValue) {
+ }
+
+ /**
+ * Overridden for performance reasons. See the <a
+ * href="#override">Implementation Note</a> for more information.
+ */
+ public void firePropertyChange(String propertyName, boolean oldValue, boolean newValue) {
+ }
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/PortView.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/PortView.java
new file mode 100644
index 0000000..10508b8
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/PortView.java
@@ -0,0 +1,221 @@
+/*
+ * @(#)PortView.java 1.0 03-JUL-04
+ *
+ * Copyright (c) 2001-2004 Gaudenz Alder
+ *
+ */
+package org.jgraph.graph;
+
+import java.awt.geom.Point2D;
+import java.awt.geom.Rectangle2D;
+
+
+/**
+ * The default implementation of a port view.
+ *
+ * @version 1.0 1/1/02
+ * @author Gaudenz Alder
+ */
+public class PortView extends AbstractCellView {
+ /** Default size for all ports is 6. */
+ public static transient int SIZE = 6;
+
+ /** Renderer for the class. */
+ public static transient PortRenderer renderer = new PortRenderer();
+
+ /**
+ * Controls if port magic should be allowed. Default is true. This is an
+ * easy switch to disable port magic for all instances of graphs.
+ */
+ public static boolean allowPortMagic = true;
+
+ /** Cache of the last valid parent. //FIX: Better solution? */
+ protected transient CellView lastParent;
+
+ /**
+ * Constructs an empty portview.
+ */
+ public PortView() {
+ super();
+ }
+
+ /**
+ * Constructs a view that holds a reference to the specified cell, anchor
+ * and parent vertex.
+ *
+ * @param cell
+ * reference to the cell in the model
+ */
+ public PortView(Object cell) {
+ super(cell);
+ }
+
+ //
+ // CellView interface
+ //
+
+ /**
+ * This method ensures a non-null value. If the super method returns null
+ * then the last valid parent is returned. Note: If a vertex is removed, all
+ * ports will be replaced in connected edges. The ports are replaced by the
+ * center point of the <i>last </i> valid vertex view.
+ */
+ public CellView getParentView() {
+ CellView parent = super.getParentView();
+
+ if (parent == null)
+ parent = lastParent;
+ else
+ lastParent = parent;
+
+ return parent;
+ }
+
+ /**
+ * Returns the bounds for the port view.
+ */
+ public Rectangle2D getBounds() {
+ Point2D loc = getLocation();
+ double x = 0;
+ double y = 0;
+
+ if (loc != null) {
+ x = loc.getX();
+ y = loc.getY();
+ }
+
+ Rectangle2D bounds = new Rectangle2D.Double(x, y, 0, 0);
+ bounds.setFrame(bounds.getX() - (SIZE / 2), bounds.getY() - (SIZE / 2), SIZE, SIZE);
+
+ return bounds;
+ }
+
+ /**
+ * Returns a renderer for the class.
+ */
+ public CellViewRenderer getRenderer() {
+ return renderer;
+ }
+
+ /**
+ * Returns <code>null</code>.
+ */
+ public CellHandle getHandle(GraphContext context) {
+ return null;
+ }
+
+ //
+ // Special Methods
+ //
+
+ /**
+ * Shortcut method to getLocation(null, null)
+ */
+ public Point2D getLocation() {
+ return getLocation(null, null);
+ }
+
+ /**
+ * For backwards compatibility.
+ */
+ public Point2D getLocation(EdgeView edge) {
+ return getLocation(edge, null);
+ }
+
+ /**
+ * Returns the point that the port represents with respect to
+ * <code>edge</code> and <code>point</code>, which is the nearest point
+ * to this port view on the edge. <code>edge</code> and <code>point</code>
+ * may be <code>null</code>.
+ */
+ public Point2D getLocation(EdgeView edge, Point2D nearest) {
+ Object modelAnchor = null;
+
+ if (cell instanceof Port)
+ modelAnchor = ((Port) cell).getAnchor();
+
+ CellView vertex = getParentView();
+ Point2D pos = null;
+
+ if (vertex != null) {
+ PortView anchor = null; // FIXME: (PortView)
+ // mapper.getMapping(modelAnchor, false); //
+ // Use refresh to get anchor view
+
+ Point2D offset = GraphConstants.getOffset(allAttributes);
+
+ // If No Edge Return Center
+ if ((edge == null) && (offset == null))
+ pos = getCenterPoint(vertex);
+
+ // Apply Offset
+ if (offset != null) {
+ double x = offset.getX();
+ double y = offset.getY();
+ Rectangle2D r = vertex.getBounds();
+
+ // Absolute Offset
+ boolean isAbsoluteX = GraphConstants.isAbsoluteX(allAttributes);
+ boolean isAbsoluteY = GraphConstants.isAbsoluteY(allAttributes);
+
+ if (!isAbsoluteX) {
+ x = (x * (r.getWidth() - 1)) / GraphConstants.PERMILLE;
+ }
+
+ if (!isAbsoluteY) {
+ y = (y * (r.getHeight() - 1)) / GraphConstants.PERMILLE;
+ } // Offset from Anchor
+
+ pos = (anchor != null) ? anchor.getLocation(edge, nearest)
+ : new Point2D.Double(r.getX(), r.getY());
+ pos = new Point2D.Double(pos.getX() + x, pos.getY() + y);
+ } else if (edge != null) {
+ // Floating Port
+ if (nearest == null) {
+ // If "Dangling" Port Return Center
+ return getCenterPoint(vertex);
+ }
+
+ pos = vertex.getPerimeterPoint(edge, pos, nearest);
+
+ if (shouldInvokePortMagic(edge)) {
+ if (nearest != null) {
+ Rectangle2D r = vertex.getBounds();
+
+ if ((nearest.getX() >= r.getX())
+ && (nearest.getX() <= (r.getX() + r.getWidth()))) {
+ pos.setLocation(nearest.getX(), pos.getY());
+ } else if ((nearest.getY() >= r.getY())
+ && (nearest.getY() <= (r.getY() + r.getHeight()))) { // vertical
+ pos.setLocation(pos.getX(), nearest.getY());
+ }
+
+ if (nearest.getX() < r.getX())
+ pos.setLocation(r.getX(), pos.getY());
+ else if (nearest.getX() > (r.getX() + r.getWidth()))
+ pos.setLocation(r.getX() + r.getWidth(), pos.getY());
+
+ if (nearest.getY() < r.getY())
+ pos.setLocation(pos.getX(), r.getY());
+ else if (nearest.getY() > (r.getY() + r.getHeight()))
+ pos.setLocation(pos.getX(), r.getY() + r.getHeight());
+ }
+ }
+ }
+ }
+
+ return pos;
+ }
+
+ /**
+ * Subclassers can override this to decide whether or not "port magic"
+ * should appear on a given edge. (Port magic means the port tries to make
+ * the edge horizontal or vertical if the closest control point lies within
+ * the bounds of the parent vertex.)
+ */
+ protected boolean shouldInvokePortMagic(EdgeView edge) {
+ return allowPortMagic && !(getParentView() instanceof EdgeView)
+ && (edge.getPointCount() > 2)
+ && (GraphConstants.getLineStyle(edge.getAllAttributes()) == GraphConstants.STYLE_ORTHOGONAL);
+ }
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/VertexRenderer.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/VertexRenderer.java
new file mode 100644
index 0000000..f9f0311
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/VertexRenderer.java
@@ -0,0 +1,383 @@
+/*
+ * @(#)VertexRenderer.java 1.0 03-JUL-04
+ *
+ * Copyright (c) 2001-2004 Gaudenz Alder
+ *
+ */
+package org.jgraph.graph;
+
+import org.jgraph.JGraph;
+
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Dimension;
+import java.awt.GradientPaint;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.Rectangle;
+import java.awt.Stroke;
+import java.awt.geom.Point2D;
+import java.awt.geom.Rectangle2D;
+
+import java.io.Serializable;
+
+import java.util.Map;
+
+import javax.swing.BorderFactory;
+import javax.swing.JLabel;
+import javax.swing.UIManager;
+
+
+/**
+ * This renderer displays entries that implement the CellView interface and
+ * supports the following attributes. If the cell view is not a leaf, this
+ * object is only visible if it is selected.
+ * <li>GraphConstants.BOUNDS GraphConstants.ICON GraphConstants.FONT
+ * GraphConstants.OPAQUE GraphConstants.BORDER GraphConstants.BORDERCOLOR
+ * GraphConstants.LINEWIDTH GraphConstants.FOREGROUND GraphConstants.BACKGROUND
+ * GraphConstants.VERTICAL_ALIGNMENT GraphConstants.HORIZONTAL_ALIGNMENT
+ * GraphConstants.VERTICAL_TEXT_POSITION GraphConstants.HORIZONTAL_TEXT_POSITION
+ * </li>
+ *
+ * @version 1.0 1/1/02
+ * @author Gaudenz Alder
+ */
+public class VertexRenderer extends JLabel implements CellViewRenderer, Serializable {
+ /** Cache the current shape for drawing. */
+ transient protected VertexView view;
+
+ /** Cached hasFocus and selected value. */
+ transient protected boolean hasFocus;
+
+ /** Cached hasFocus and selected value. */
+ transient protected boolean selected;
+
+ /** Cached hasFocus and selected value. */
+ transient protected boolean preview;
+
+ /** Cached hasFocus and selected value. */
+ transient protected boolean childrenSelected;
+
+ /** Cached default foreground and default background. */
+ transient protected Color defaultForeground;
+
+ /** Cached default foreground and default background. */
+ transient protected Color defaultBackground;
+
+ /** Cached default foreground and default background. */
+ transient protected Color bordercolor;
+
+ /** Cached borderwidth. */
+ transient protected int borderWidth;
+
+ /** Cached value of the double buffered state */
+ transient protected boolean isDoubleBuffered = false;
+ transient protected Color gradientColor = null;
+ transient protected Color gridColor = Color.black;
+ transient protected Color highlightColor = Color.black;
+ transient protected Color lockedHandleColor = Color.black;
+
+ /**
+ * Constructs a renderer that may be used to render vertices.
+ */
+ public VertexRenderer() {
+ defaultForeground = UIManager.getColor("Tree.textForeground");
+ defaultBackground = UIManager.getColor("Tree.textBackground");
+ }
+
+ /**
+ * Configure and return the renderer component based on the passed in cell.
+ * The value is typically set from messaging the graph with
+ * <code>convertValueToString</code>. We recommend you check the value's
+ * class and throw an illegal argument exception if it's not correct.
+ *
+ * @param graph
+ * the graph that that defines the rendering context.
+ * @param view
+ * the cell view that should be rendered.
+ * @param sel
+ * whether the object is selected.
+ * @param focus
+ * whether the object has the focus.
+ * @param preview
+ * whether we are drawing a preview.
+ * @return the component used to render the value.
+ */
+ public Component getRendererComponent(JGraph graph, CellView view, boolean sel, boolean focus,
+ boolean preview) {
+ gridColor = graph.getGridColor();
+ highlightColor = graph.getHighlightColor();
+ lockedHandleColor = graph.getLockedHandleColor();
+ isDoubleBuffered = graph.isDoubleBuffered();
+
+ if (view instanceof VertexView) {
+ this.view = (VertexView) view;
+ setComponentOrientation(graph.getComponentOrientation());
+
+ if (graph.getEditingCell() != view.getCell()) {
+ Object label = graph.convertValueToString(view);
+
+ if (label != null)
+ setText(label.toString());
+ else
+ setText(null);
+ } else
+ setText(null);
+
+ this.hasFocus = focus;
+ this.childrenSelected = graph.getSelectionModel().isChildrenSelected(view.getCell());
+ this.selected = sel;
+ this.preview = preview;
+
+ if (this.view.isLeaf() || GraphConstants.isGroupOpaque(view.getAllAttributes()))
+ installAttributes(view);
+ else
+ resetAttributes();
+
+ return this;
+ }
+
+ return null;
+ }
+
+ /**
+ * Hook for subclassers that is invoked when the installAttributes is not
+ * called to reset all attributes to the defaults. <br>
+ * Subclassers must invoke the superclass implementation.
+ *
+ */
+ protected void resetAttributes() {
+ setText(null);
+ setBorder(null);
+ setOpaque(false);
+ setGradientColor(null);
+ setIcon(null);
+ }
+
+ /**
+ * Install the attributes of specified cell in this renderer instance. This
+ * means, retrieve every published key from the cells hashtable and set
+ * global variables or superclass properties accordingly.
+ *
+ * @param view
+ * the cell view to retrieve the attribute values from.
+ */
+ protected void installAttributes(CellView view) {
+ Map map = view.getAllAttributes();
+ setIcon(GraphConstants.getIcon(map));
+ setOpaque(GraphConstants.isOpaque(map));
+ setBorder(GraphConstants.getBorder(map));
+ setVerticalAlignment(GraphConstants.getVerticalAlignment(map));
+ setHorizontalAlignment(GraphConstants.getHorizontalAlignment(map));
+ setVerticalTextPosition(GraphConstants.getVerticalTextPosition(map));
+ setHorizontalTextPosition(GraphConstants.getHorizontalTextPosition(map));
+ bordercolor = GraphConstants.getBorderColor(map);
+ borderWidth = Math.max(1, Math.round(GraphConstants.getLineWidth(map)));
+
+ if ((getBorder() == null) && (bordercolor != null))
+ setBorder(BorderFactory.createLineBorder(bordercolor, borderWidth));
+
+ Color foreground = GraphConstants.getForeground(map);
+ setForeground((foreground != null) ? foreground : defaultForeground);
+
+ Color gradientColor = GraphConstants.getGradientColor(map);
+ setGradientColor(gradientColor);
+
+ Color background = GraphConstants.getBackground(map);
+ setBackground((background != null) ? background : defaultBackground);
+ setFont(GraphConstants.getFont(map));
+ }
+
+ /**
+ * Paint the renderer. Overrides superclass paint to add specific painting.
+ */
+ public void paint(Graphics g) {
+ try {
+ if ((gradientColor != null) && !preview && isOpaque()) {
+ setOpaque(false);
+
+ Graphics2D g2d = (Graphics2D) g;
+ g2d.setPaint(new GradientPaint(0, 0, getBackground(), getWidth(), getHeight(),
+ gradientColor, true));
+ g2d.fillRect(0, 0, getWidth(), getHeight());
+ }
+
+ super.paint(g);
+ paintSelectionBorder(g);
+ } catch (IllegalArgumentException e) {
+ // JDK Bug: Zero length string passed to TextLayout constructor
+ }
+ }
+
+ /**
+ * Provided for subclassers to paint a selection border.
+ */
+ protected void paintSelectionBorder(Graphics g) {
+ Graphics2D g2 = (Graphics2D) g;
+ Stroke previousStroke = g2.getStroke();
+ g2.setStroke(GraphConstants.SELECTION_STROKE);
+
+ if (childrenSelected || selected) {
+ if (childrenSelected)
+ g.setColor(gridColor);
+ else if (hasFocus && selected)
+ g.setColor(lockedHandleColor);
+ else if (selected)
+ g.setColor(highlightColor);
+
+ Dimension d = getSize();
+ g.drawRect(0, 0, d.width - 1, d.height - 1);
+ }
+
+ g2.setStroke(previousStroke);
+ }
+
+ /**
+ * Returns the intersection of the bounding rectangle and the straight line
+ * between the source and the specified point p. The specified point is
+ * expected not to intersect the bounds.
+ */
+ public Point2D getPerimeterPoint(VertexView view, Point2D source, Point2D p) {
+ Rectangle2D bounds = view.getBounds();
+ double x = bounds.getX();
+ double y = bounds.getY();
+ double width = bounds.getWidth();
+ double height = bounds.getHeight();
+ double xCenter = x + (width / 2);
+ double yCenter = y + (height / 2);
+ double dx = p.getX() - xCenter; // Compute Angle
+ double dy = p.getY() - yCenter;
+ double alpha = Math.atan2(dy, dx);
+ double xout = 0;
+ double yout = 0;
+ double pi = Math.PI;
+ double pi2 = Math.PI / 2.0;
+ double beta = pi2 - alpha;
+ double t = Math.atan2(height, width);
+
+ if ((alpha < (-pi + t)) || (alpha > (pi - t))) { // Left edge
+ xout = x;
+ yout = yCenter - ((width * Math.tan(alpha)) / 2);
+ } else if (alpha < -t) { // Top Edge
+ yout = y;
+ xout = xCenter - ((height * Math.tan(beta)) / 2);
+ } else if (alpha < t) { // Right Edge
+ xout = x + width;
+ yout = yCenter + ((width * Math.tan(alpha)) / 2);
+ } else { // Bottom Edge
+ yout = y + height;
+ xout = xCenter + ((height * Math.tan(beta)) / 2);
+ }
+
+ return new Point2D.Double(xout, yout);
+ }
+
+ /**
+ * Overridden for performance reasons. See the <a
+ * href="#override">Implementation Note </a> for more information.
+ */
+ public void validate() {
+ }
+
+ /**
+ * Overridden for performance reasons. See the <a
+ * href="#override">Implementation Note </a> for more information.
+ */
+ public void revalidate() {
+ }
+
+ /**
+ * Overridden for performance reasons. See the <a
+ * href="#override">Implementation Note </a> for more information.
+ */
+ public void repaint(long tm, int x, int y, int width, int height) {
+ }
+
+ /**
+ * Overridden for performance reasons. See the <a
+ * href="#override">Implementation Note </a> for more information.
+ */
+ public void repaint(Rectangle r) {
+ }
+
+ /**
+ * Overridden for performance reasons. See the <a
+ * href="#override">Implementation Note </a> for more information.
+ */
+ protected void firePropertyChange(String propertyName, Object oldValue, Object newValue) {
+ // Strings get interned...
+ if (propertyName == "text")
+ super.firePropertyChange(propertyName, oldValue, newValue);
+ }
+
+ /**
+ * Overridden for performance reasons. See the <a
+ * href="#override">Implementation Note </a> for more information.
+ */
+ public void firePropertyChange(String propertyName, byte oldValue, byte newValue) {
+ }
+
+ /**
+ * Overridden for performance reasons. See the <a
+ * href="#override">Implementation Note </a> for more information.
+ */
+ public void firePropertyChange(String propertyName, char oldValue, char newValue) {
+ }
+
+ /**
+ * Overridden for performance reasons. See the <a
+ * href="#override">Implementation Note </a> for more information.
+ */
+ public void firePropertyChange(String propertyName, short oldValue, short newValue) {
+ }
+
+ /**
+ * Overridden for performance reasons. See the <a
+ * href="#override">Implementation Note </a> for more information.
+ */
+ public void firePropertyChange(String propertyName, int oldValue, int newValue) {
+ }
+
+ /**
+ * Overridden for performance reasons. See the <a
+ * href="#override">Implementation Note </a> for more information.
+ */
+ public void firePropertyChange(String propertyName, long oldValue, long newValue) {
+ }
+
+ /**
+ * Overridden for performance reasons. See the <a
+ * href="#override">Implementation Note </a> for more information.
+ */
+ public void firePropertyChange(String propertyName, float oldValue, float newValue) {
+ }
+
+ /**
+ * Overridden for performance reasons. See the <a
+ * href="#override">Implementation Note </a> for more information.
+ */
+ public void firePropertyChange(String propertyName, double oldValue, double newValue) {
+ }
+
+ /**
+ * Overridden for performance reasons. See the <a
+ * href="#override">Implementation Note </a> for more information.
+ */
+ public void firePropertyChange(String propertyName, boolean oldValue, boolean newValue) {
+ }
+
+ /**
+ * @return Returns the gradientColor.
+ */
+ public Color getGradientColor() {
+ return gradientColor;
+ }
+
+ /**
+ * @param gradientColor
+ * The gradientColor to set.
+ */
+ public void setGradientColor(Color gradientColor) {
+ this.gradientColor = gradientColor;
+ }
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/VertexView.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/VertexView.java
new file mode 100644
index 0000000..e94a8ba
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/graph/VertexView.java
@@ -0,0 +1,561 @@
+/*
+ * @(#)VertexView.java 1.0 03-JUL-04
+ *
+ * Copyright (c) 2001-2004 Gaudenz Alder
+ *
+ */
+package org.jgraph.graph;
+
+import org.jgraph.JGraph;
+
+import org.jgraph.plaf.GraphUI;
+import org.jgraph.plaf.basic.BasicGraphUI;
+
+import java.awt.Color;
+import java.awt.Cursor;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.Image;
+import java.awt.Rectangle;
+import java.awt.event.MouseEvent;
+import java.awt.geom.AffineTransform;
+import java.awt.geom.Point2D;
+import java.awt.geom.Rectangle2D;
+import java.awt.image.BufferedImage;
+
+import java.io.Serializable;
+
+import java.util.HashSet;
+import java.util.Map;
+import java.util.Set;
+
+
+/**
+ * The default implementation of a vertex view.
+ *
+ * @version 1.0 1/1/02
+ * @author Gaudenz Alder
+ */
+public class VertexView extends AbstractCellView {
+ /** Renderer for the class. */
+ public static transient VertexRenderer renderer;
+
+ static {
+ try {
+ renderer = new VertexRenderer();
+ } catch (Error e) {
+ // No vertex renderer
+ }
+ }
+
+ /**
+ *
+ */
+ public final static Rectangle2D defaultBounds = new Rectangle2D.Double(10, 10, 20, 20);
+
+ /** Reference to the bounds attribute */
+ protected Rectangle2D bounds;
+
+ /**
+ * Constructs an empty vertex view.
+ */
+ public VertexView() {
+ super();
+ }
+
+ /**
+ * Constructs a vertex view for the specified model object and the specified
+ * child views.
+ *
+ * @param cell
+ * reference to the model object
+ */
+ public VertexView(Object cell) {
+ super(cell);
+ }
+
+ //
+ // CellView Interface
+ //
+
+ /**
+ * Overrides the parent method to udpate the cached points.
+ */
+ public void update() {
+ super.update();
+ bounds = GraphConstants.getBounds(allAttributes);
+
+ if (bounds == null) {
+ bounds = allAttributes.createRect(defaultBounds);
+ GraphConstants.setBounds(allAttributes, bounds);
+ }
+
+ groupBounds = null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Rectangle2D getCachedBounds() {
+ return bounds;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param bounds DOCUMENT ME!
+ */
+ public void setCachedBounds(Rectangle2D bounds) {
+ this.bounds = bounds;
+ }
+
+ /**
+ * Returns a renderer for the class.
+ */
+ public CellViewRenderer getRenderer() {
+ return renderer;
+ }
+
+ /**
+ * Returns a cell handle for the view, if the graph and the view are
+ * sizeable.
+ */
+ public CellHandle getHandle(GraphContext context) {
+ if (GraphConstants.isSizeable(getAllAttributes())
+ && !GraphConstants.isAutoSize(getAllAttributes()) && context.getGraph().isSizeable())
+ return new SizeHandle(this, context);
+
+ return null;
+ }
+
+ /**
+ * Returns the cached bounds for the vertex.
+ */
+ public Rectangle2D getBounds() {
+ Rectangle2D rect = super.getBounds();
+
+ if (rect == null)
+ rect = bounds;
+
+ return rect;
+ }
+
+ /**
+ * @deprecated replaced by
+ * {@link AbstractCellView#getCenterPoint(CellView vertex)}
+ * @return the center point of this vertex
+ */
+ public Point2D getCenterPoint() {
+ return AbstractCellView.getCenterPoint(this);
+ }
+
+ /**
+ * @deprecated replaced by
+ * {@link #getPerimeterPoint(EdgeView edge, Point2D source, Point2D p)}
+ */
+ public Point2D getPerimeterPoint(Point2D source, Point2D p) {
+ return AbstractCellView.getCenterPoint(this);
+ }
+
+ //
+ // Special Methods
+ //
+
+ /**
+ * Returns the intersection of the bounding rectangle and the straight line
+ * between the source and the specified point p. The specified point is
+ * expected not to intersect the bounds. Note: You must override this method
+ * if you use a different renderer. This is because this method relies on
+ * the VertexRenderer interface, which can not be safely assumed for
+ * subclassers.
+ */
+ public Point2D getPerimeterPoint(EdgeView edge, Point2D source, Point2D p) {
+ if (getRenderer() instanceof VertexRenderer)
+ return ((VertexRenderer) getRenderer()).getPerimeterPoint(this, source, p);
+
+ return super.getPerimeterPoint(edge, source, p);
+ }
+
+ /** Array that holds the cursors for the different control points. */
+ public static transient int[] defaultCursors = new int[] {
+ Cursor.NW_RESIZE_CURSOR,
+ Cursor.N_RESIZE_CURSOR,
+ Cursor.NE_RESIZE_CURSOR,
+ Cursor.W_RESIZE_CURSOR,
+ Cursor.E_RESIZE_CURSOR,
+ Cursor.SW_RESIZE_CURSOR,
+ Cursor.S_RESIZE_CURSOR,
+ Cursor.SE_RESIZE_CURSOR
+ };
+
+ /** Array that holds the cursors for the different control points. */
+ public static transient int[] xCursors = new int[] {
+ Cursor.W_RESIZE_CURSOR, 0, Cursor.E_RESIZE_CURSOR,
+ Cursor.W_RESIZE_CURSOR, Cursor.E_RESIZE_CURSOR,
+ Cursor.W_RESIZE_CURSOR, 0, Cursor.E_RESIZE_CURSOR
+ };
+
+ /** Array that holds the cursors for the different control points. */
+ public static transient int[] yCursors = new int[] {
+ Cursor.N_RESIZE_CURSOR, Cursor.N_RESIZE_CURSOR,
+ Cursor.N_RESIZE_CURSOR, 0, 0,
+ Cursor.S_RESIZE_CURSOR, Cursor.S_RESIZE_CURSOR,
+ Cursor.S_RESIZE_CURSOR
+ };
+
+ public static class SizeHandle implements CellHandle, Serializable {
+ // Double Buffer
+ protected transient Image offscreen;
+ protected transient Graphics offgraphics;
+ protected transient boolean firstDrag = true;
+ protected transient JGraph graph;
+
+ /* Reference to the temporary view for this handle. */
+ protected transient VertexView vertex;
+ protected transient CellView[] portViews;
+ protected transient Rectangle2D cachedBounds;
+
+ /* Reference to the context for the specified view. */
+ protected transient GraphContext context;
+ protected transient Rectangle2D initialBounds;
+ protected transient CellView[] contextViews;
+
+ /* Index of the active control point. -1 if none is active. */
+ protected transient int index = -1;
+
+ /* Array of control points represented as rectangles. */
+ protected transient Rectangle2D[] r = new Rectangle2D[8];
+ protected boolean firstOverlayInvocation = true;
+
+ /** Array that holds the cursors for the different control points. */
+ public transient int[] cursors = null;
+
+ /**
+ * True if the cell is being edited.
+ */
+ protected boolean editing = false;
+
+ public SizeHandle(VertexView vertexview, GraphContext ctx) {
+ graph = ctx.getGraph();
+ vertex = vertexview;
+ editing = graph.getEditingCell() == vertex.getCell();
+
+ int sizeableAxis = GraphConstants.getSizeableAxis(vertex.getAllAttributes());
+
+ if (sizeableAxis == GraphConstants.X_AXIS)
+ cursors = xCursors;
+ else if (sizeableAxis == GraphConstants.Y_AXIS)
+ cursors = yCursors;
+ else
+ cursors = defaultCursors;
+
+ // PortView Preview
+ portViews = ctx.createTemporaryPortViews();
+ initialBounds = (Rectangle2D) vertex.getBounds().clone();
+ context = ctx;
+
+ for (int i = 0; i < r.length; i++)
+ r[i] = new Rectangle2D.Double();
+
+ invalidate();
+ }
+
+ public boolean isConstrainedSizeEvent(MouseEvent e) {
+ GraphUI ui = graph.getUI();
+
+ if (ui instanceof BasicGraphUI)
+ return ((BasicGraphUI) ui).isConstrainedMoveEvent(e);
+
+ return false;
+ }
+
+ public void paint(Graphics g) {
+ invalidate();
+ g.setColor((editing) ? graph.getLockedHandleColor() : graph.getHandleColor());
+
+ for (int i = 0; i < r.length; i++) {
+ if (cursors[i] != 0)
+ g.fill3DRect((int) r[i].getX(), (int) r[i].getY(), (int) r[i].getWidth(),
+ (int) r[i].getHeight(), true);
+ }
+ }
+
+ // Double Buffers by David Larsson
+ protected void initOffscreen() {
+ try {
+ Rectangle rect = graph.getBounds();
+ // RepaintManager repMan = RepaintManager.currentManager(graph);
+ // offscreen = repMan.getVolatileOffscreenBuffer(getGraph(),
+ // (int) rect.getWidth(), (int) rect.getHeight());
+ offscreen = new BufferedImage(rect.width, rect.height, BufferedImage.TYPE_INT_RGB);
+ offgraphics = offscreen.getGraphics();
+ offgraphics.setClip(0, 0, rect.width, rect.height);
+ offgraphics.setColor(graph.getBackground());
+ offgraphics.fillRect(0, 0, rect.width, rect.height);
+ graph.getUI().paint(offgraphics, graph);
+ } catch (Exception e) {
+ offscreen = null;
+ offgraphics = null;
+ } catch (Error e) {
+ offscreen = null;
+ offgraphics = null;
+ }
+ }
+
+ public void overlay(Graphics g) {
+ if (!firstOverlayInvocation) {
+ if (cachedBounds != null) {
+ g.setColor(Color.black);
+
+ Rectangle2D tmp = graph.toScreen((Rectangle2D) cachedBounds.clone());
+ g.drawRect((int) tmp.getX(), (int) tmp.getY(), (int) tmp.getWidth() - 2,
+ (int) tmp.getHeight() - 2);
+ } else if (!initialBounds.equals(vertex.getBounds())) {
+ Graphics2D g2 = (Graphics2D) g;
+ AffineTransform oldTransform = g2.getTransform();
+ g2.scale(graph.getScale(), graph.getScale());
+ graph.getUI().paintCell(g, vertex, vertex.getBounds(), true);
+
+ if (contextViews != null) {
+ for (int i = 0; i < contextViews.length; i++) {
+ graph.getUI()
+ .paintCell(g, contextViews[i], contextViews[i].getBounds(), true);
+ }
+ }
+
+ if (!graph.isPortsScaled())
+ g2.setTransform(oldTransform);
+
+ if ((portViews != null) && graph.isPortsVisible())
+ graph.getUI().paintPorts(g, portViews);
+
+ g2.setTransform(oldTransform);
+ }
+ }
+
+ firstOverlayInvocation = false;
+ }
+
+ /**
+ * Invoked when the mouse pointer has been moved on a component (with no
+ * buttons down).
+ */
+ public void mouseMoved(MouseEvent event) {
+ if (vertex != null) {
+ for (int i = 0; i < r.length; i++) {
+ if (r[i].contains(event.getPoint())) {
+ graph.setCursor(new Cursor(cursors[i]));
+ event.consume();
+
+ return;
+ }
+ }
+ }
+ }
+
+ /** Process mouse pressed event. */
+ public void mousePressed(MouseEvent event) {
+ if (!graph.isSizeable())
+ return;
+
+ for (int i = 0; i < r.length; i++) {
+ if (r[i].contains(event.getPoint()) && (cursors[i] != 0)) {
+ Set set = new HashSet();
+ set.add(vertex.getCell());
+ contextViews = context.createTemporaryContextViews(set);
+
+ Object[] all = AbstractCellView.getDescendantViews(new CellView[] { vertex });
+
+ if (all.length >= org.jgraph.plaf.basic.BasicGraphUI.MAXHANDLES)
+ cachedBounds = (Rectangle2D) initialBounds.clone();
+
+ event.consume();
+ index = i;
+
+ return;
+ }
+ }
+ }
+
+ /** Process mouse dragged event. */
+ public void mouseDragged(MouseEvent event) {
+ if (firstDrag && graph.isDoubleBuffered() && (cachedBounds == null)) {
+ initOffscreen();
+ firstDrag = false;
+ }
+
+ Rectangle2D dirty = null;
+ Graphics g = (offgraphics != null) ? offgraphics : graph.getGraphics();
+
+ if (index == -1)
+ return;
+
+ Rectangle2D newBounds = computeBounds(event);
+ g.setColor(graph.getForeground());
+ g.setXORMode(graph.getBackground().darker());
+ overlay(g);
+
+ if (offgraphics != null) {
+ dirty = graph.toScreen((Rectangle2D) vertex.getBounds().clone());
+
+ Rectangle2D t = graph.toScreen(AbstractCellView.getBounds(contextViews));
+
+ if (t != null)
+ dirty.add(t);
+ }
+
+ if (cachedBounds != null)
+ cachedBounds = newBounds;
+ else {
+ // Reset old Bounds
+ CellView[] all = AbstractCellView.getDescendantViews(new CellView[] { vertex });
+
+ for (int i = 0; i < all.length; i++) {
+ CellView orig = graph.getGraphLayoutCache().getMapping(all[i].getCell(), false);
+
+ if (orig != null) {
+ AttributeMap origAttr = (AttributeMap) orig.getAllAttributes().clone();
+ all[i].changeAttributes(origAttr);
+ all[i].refresh(graph.getModel(), context, false);
+ }
+ }
+
+ vertex.setBounds(newBounds);
+
+ if (vertex != null)
+ graph.getGraphLayoutCache().update(vertex);
+
+ if (contextViews != null)
+ graph.getGraphLayoutCache().update(contextViews);
+ }
+
+ overlay(g);
+
+ if (offscreen != null) {
+ dirty.add(graph.toScreen((Rectangle2D) vertex.getBounds().clone()));
+
+ Rectangle2D t = graph.toScreen(AbstractCellView.getBounds(contextViews));
+
+ if (t != null)
+ dirty.add(t);
+
+ int border = PortView.SIZE + 10;
+
+ if (graph.isPortsScaled())
+ border = (int) (graph.getScale() * border);
+
+ int border2 = border / 2;
+ dirty.setFrame(dirty.getX() - border2, dirty.getY() - border2,
+ dirty.getWidth() + border, dirty.getHeight() + border);
+
+ double sx1 = Math.max(0, dirty.getX());
+ double sy1 = Math.max(0, dirty.getY());
+ double sx2 = sx1 + dirty.getWidth();
+ double sy2 = sy1 + dirty.getHeight();
+ graph.getGraphics()
+ .drawImage(offscreen, (int) sx1, (int) sy1, (int) sx2, (int) sy2, (int) sx1,
+ (int) sy1, (int) sx2, (int) sy2, graph);
+ }
+ }
+
+ protected Rectangle2D computeBounds(MouseEvent event) {
+ double left = initialBounds.getX();
+ double right = (initialBounds.getX() + initialBounds.getWidth()) - 1;
+ double top = initialBounds.getY();
+ double bottom = (initialBounds.getY() + initialBounds.getHeight()) - 1;
+ Point2D p = graph.fromScreen(graph.snap((Point2D) event.getPoint().clone()));
+ // Not into negative coordinates
+ p.setLocation(Math.max(0, p.getX()), Math.max(0, p.getY()));
+
+ // Bottom row
+ if (index > 4)
+ bottom = p.getY();
+
+ // Top row
+ else if (index < 3)
+ top = p.getY();
+
+ // Left col
+ if ((index == 0) || (index == 3) || (index == 5))
+ left = p.getX();
+
+ // Right col
+ else if ((index == 2) || (index == 4) || (index == 7))
+ right = p.getX();
+
+ double width = right - left;
+ double height = bottom - top;
+
+ if (isConstrainedSizeEvent(event)
+ || GraphConstants.isConstrained(vertex.getAllAttributes())) {
+ if ((index == 3) || (index == 4) || (index == 5))
+ height = width;
+ else if ((index == 1) || (index == 6) || (index == 2) || (index == 7))
+ width = height;
+ else {
+ height = width;
+ top = bottom - height;
+ }
+ }
+
+ if (width < 0) { // Flip over left side
+ left += width;
+ width = Math.abs(width);
+ }
+
+ if (height < 0) { // Flip over top side
+ top += height;
+ height = Math.abs(height);
+ }
+
+ return new Rectangle2D.Double(left, top, width + 1, height + 1);
+ }
+
+ // Dispatch the edit event
+ public void mouseReleased(MouseEvent e) {
+ if (index != -1) {
+ cachedBounds = computeBounds(e);
+ vertex.setBounds(cachedBounds);
+
+ CellView[] views = AbstractCellView.getDescendantViews(new CellView[] { vertex });
+ Map attributes = GraphConstants.createAttributes(views, null);
+ graph.getGraphLayoutCache().edit(attributes, null, null, null);
+ }
+
+ e.consume();
+ cachedBounds = null;
+ initialBounds = null;
+ firstDrag = true;
+ }
+
+ protected void invalidate() {
+ // Retrieve current bounds and set local vars
+ Rectangle2D tmp = graph.getCellBounds(vertex.getCell());
+
+ if (tmp != null) {
+ tmp = (Rectangle2D) tmp.clone();
+ graph.toScreen(tmp);
+
+ int handlesize = graph.getHandleSize();
+ int s2 = 2 * handlesize;
+ double left = tmp.getX() - handlesize;
+ double top = tmp.getY() - handlesize;
+ double w2 = (tmp.getX() + (tmp.getWidth() / 2)) - handlesize;
+ double h2 = (tmp.getY() + (tmp.getHeight() / 2)) - handlesize;
+ double right = (tmp.getX() + tmp.getWidth()) - handlesize;
+ double bottom = (tmp.getY() + tmp.getHeight()) - handlesize;
+ // Update control point positions
+ r[0].setFrame(left, top, s2, s2);
+ r[1].setFrame(w2, top, s2, s2);
+ r[2].setFrame(right, top, s2, s2);
+ r[3].setFrame(left, h2, s2, s2);
+ r[4].setFrame(right, h2, s2, s2);
+ r[5].setFrame(left, bottom, s2, s2);
+ r[6].setFrame(w2, bottom, s2, s2);
+ r[7].setFrame(right, bottom, s2, s2);
+ }
+ }
+ }
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/layout/AnnealingLayoutAlgorithm.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/layout/AnnealingLayoutAlgorithm.java
new file mode 100644
index 0000000..61e716e
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/layout/AnnealingLayoutAlgorithm.java
@@ -0,0 +1,2344 @@
+/*
+ * @(#)AnnealingLayoutAlgorithm.java 1.0 18-MAY-2004
+ *
+ * Copyright (c) 2004, Winkler
+ * All rights reserved.
+ *
+ * This library is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation; either
+ * version 2.1 of the License, or (at your option) any later version.
+ *
+ * This library is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this library; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+ *
+ */
+package org.jgraph.layout;
+
+import org.jgraph.JGraph;
+
+import org.jgraph.event.GraphModelEvent;
+import org.jgraph.event.GraphModelListener;
+
+import org.jgraph.graph.AttributeMap;
+import org.jgraph.graph.CellMapper;
+import org.jgraph.graph.CellView;
+import org.jgraph.graph.EdgeView;
+import org.jgraph.graph.GraphConstants;
+import org.jgraph.graph.GraphModel;
+import org.jgraph.graph.VertexView;
+
+import java.awt.Rectangle;
+import java.awt.geom.Ellipse2D;
+import java.awt.geom.Line2D;
+import java.awt.geom.Point2D;
+import java.awt.geom.Rectangle2D;
+
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.Map;
+import java.util.Properties;
+
+
+/**
+ * <h1>Simulated Annealing Layout Algorithm</h1><p>
+ * Implemented from the paper: "Drawing Graphs Nicely Using Simulated Annealing"
+ * from Ron Davidson and David Harel. ACM Transactions on Graphics, Vol. 15,
+ * No. 4, October 1996, Pages 301-331.
+ * @author winkler
+ * @version 1.0
+ * Date of creation: 11.04.2003 - 12:39:58
+ */
+public class AnnealingLayoutAlgorithm extends JGraphLayoutAlgorithm implements GraphModelListener {
+ /**
+ *
+ */
+ public final static int COUT_COSTFUNCTION = 6;
+
+ /**
+ *
+ */
+ public final static int COSTFUNCTION_EDGE_DISTANCE = 1;
+
+ /**
+ *
+ */
+ public final static int COSTFUNCTION_EDGE_CROSSING = 2;
+
+ /**
+ *
+ */
+ public final static int COSTFUNCTION_EDGE_LENGTH = 4;
+
+ /**
+ *
+ */
+ public final static int COSTFUNCTION_BORDERLINE = 8;
+
+ /**
+ *
+ */
+ public final static int COSTFUNCTION_NODE_DISTRIBUTION = 16;
+
+ /**
+ *
+ */
+ public final static int COSTFUNCTION_NODE_DISTANCE = 32;
+
+ /**
+ *
+ */
+ public final static String KEY_CAPTION = "Annealing Layoutalgorithm Attributes";
+
+ /**
+ *
+ */
+ public final static String KEY_POSITION = "Position";
+
+ /**
+ *
+ */
+ public final static String KEY_RELATIVES = "Relatives";
+
+ /**
+ *
+ */
+ public final static String CF_KEY_EDGE_DISTANCE_RELEVANT_EDGES = "costfunction edge distance key for relevant edges";
+
+ /**
+ * Key used only with clusters. Under this key a cluster has an ArrayList.
+ * This list is filled with the clustered vertices.
+ * @see #clusterGraph()
+ */
+ public final static String KEY_CLUSTERED_VERTICES = "Clustered Vertices";
+
+ /**
+ * Key used only with clusters. Under this key vertices have the cluster
+ * they belong to.
+ * @see #clusterGraph()
+ */
+ public final static String KEY_CLUSTER = "Cluster";
+
+ /**
+ * Key used only with clusters. Under this key a cluster has a boolean value
+ * indicating that this vertice is a cluster (clusters are
+ * VertexView-instances like every other cell).
+ * @see #clusterGraph()
+ */
+ public final static String KEY_IS_CLUSTER = "is Cluster";
+
+ /**
+ * Key used only with clusters. Under this key every cluster has a position,
+ * which represents the position of the cluster, right after the clustering
+ * process. After the layout update process is finished, the move, resulting
+ * of subtracting the position under {@link #KEY_POSITION} from the
+ * position under this value, will be performed to all vertices in the
+ * cluster. By holding the initial position here clustering becomes
+ * possible.
+ *
+ * @see #clusterGraph()
+ * @see #declusterGraph()
+ */
+ public final static String KEY_CLUSTER_INIT_POSITION = "initial Position of the Cluster";
+
+ /**
+ * Key for loading configuration values. Indicates to load values for a
+ * normal run.
+ */
+ protected final static int CONFIG_KEY_RUN = 0;
+
+ /**
+ * Key for loading configuration values. Indicates to load values for a
+ * layout update.
+ */
+ protected final static int CONFIG_KEY_LAYOUT_UPDATE = 1;
+
+ /**
+ * actual temperature
+ */
+ private double temperature;
+
+ /**
+ * starting temperature
+ */
+ private double initTemperature = 40;
+
+ /**
+ * when {@link #temperature} reaches this value, the algorithm finishes its
+ * calculation.
+ */
+ private double minTemperature = 2;
+
+ /**
+ * value for costfunctions and getEdgeDistribution.
+ * Determines, how long the edges have to
+ * be.
+ */
+ private double minDistance = 50;
+
+ /**
+ * {@link #temperature} will be multiplied with this value every round
+ */
+ private double tempScaleFactor = 0.95;
+
+ /**
+ * maximum number of rounds, if algorithm doesn't stop earlier, by
+ * temperature decreasement.
+ */
+ private int maxRounds = 10000;
+
+ /**
+ * normalizing and priority factors for the costfunctions
+ */
+ protected double[] lambdaList = new double[] { 1000, 100000, 0.02, 2000, 150, 1000000 };
+
+ /**
+ * the drawing area, the graph should be layouted in.
+ */
+ private Rectangle bounds = new Rectangle(0, 0, 1000, 700);
+
+ /**
+ * determines, if the cells of the graph are computed every time in the
+ * same order or a random order, calculated every round.
+ */
+ private boolean computePermutation = true;
+
+ /**
+ * determines, if the only allowed moves for cells of the graph are moves,
+ * that cost less.
+ */
+ private boolean uphillMovesAllowed = true;
+
+ /**
+ * Indicates, if the algorithm should also run on Updates in the graph.
+ */
+ private boolean isLayoutUpdateEnabled = true;
+
+ /**
+ * Indicates what costfunctions to use for calculating the costs of the
+ * graph. The bits of this Integer switches the functions. Possible Values
+ * are <br>
+ * <blockquote><blockquote>
+ * {@link AnnealingLayoutAlgorithm#COSTFUNCTION_NODE_DISTRIBUTION
+ * COSTFUNCTION_NODE_DISTRIBUTION}<br>
+ * {@link AnnealingLayoutAlgorithm#COSTFUNCTION_NODE_DISTANCE
+ * COSTFUNCTION_NODE_DISTANCE}<br>
+ * {@link AnnealingLayoutAlgorithm#COSTFUNCTION_BORDERLINE
+ * COSTFUNCTION_BORDERLINE}<br>
+ * {@link AnnealingLayoutAlgorithm#COSTFUNCTION_EDGE_DISTANCE
+ * COSTFUNCTION_EDGE_DISTANCE}<br>
+ * {@link AnnealingLayoutAlgorithm#COSTFUNCTION_EDGE_CROSSING
+ * COSTFUNCTION_EDGE_CROSSING}<br>
+ * </blockquote></blockquote>
+ */
+ private int costFunctionConfig = Integer.parseInt("111110", 2);
+
+ /**
+ * counts the rounds
+ */
+ private int round;
+
+ /**
+ * determines, in how many segments the circle around cells is divided,
+ * to find a new position for the cell.
+ */
+ private int triesPerCell = 8;
+
+ /**
+ * the list of all cells of the graph
+ */
+ protected ArrayList cellList;
+
+ /**
+ * the list of all edges of the graph
+ */
+ protected ArrayList edgeList;
+
+ /**
+ * the list of all cells, a new layout should be calculated for
+ */
+ protected ArrayList applyCellList;
+
+ /**
+ * the JGraph
+ */
+ private JGraph jgraph;
+
+ /**
+ * holds the configuration of the algorithm, gained by the controller
+ */
+ protected Properties presetConfig;
+
+ /**
+ * for debugging purpose.
+ */
+
+ // private long time = 0;
+
+ /**
+ * for debugging purpose
+ */
+
+ // private boolean isDebugging = false;
+ /**
+ * indicates if the algorihm is performing a calculation. this prevents from
+ * entering the method {@link #graphChanged(GraphModelEvent)
+ * graphChanged(...)} more than once at a time.
+ */
+ private boolean isRunning = false;
+
+ /**
+ * the number of edges, neighbors of inserted cells are away,
+ * to be also layouted again.
+ */
+ private int luRecursionDepth = 1;
+
+ /**
+ * if a cell has a lower distance to a inserted cell, after the cell gained
+ * its initial position, it will be layouted too
+ */
+ private double luPerimeterRadius = 100;
+
+ /**
+ * if more than one cell is inserted and the initial position of other
+ * inserted cells is inside {@link #luPerimeterRadius} around a initial
+ * position of a inserted cell, than {@link #luPerimeterRadius} will be
+ * increased by this value.
+ */
+ private double luPerimeterRadiusInc = 20;
+
+ /**
+ * determines how the neighborhood is handled, when a layout update
+ * should be performed. Possible values are:<p>
+ * <blockquote><blockquote>
+ * </blockquote></blockquote>
+ */
+ private String luMethod = AnnealingLayoutSettings.KEY_LAYOUT_UPDATE_METHOD_PERIMETER;
+
+ /**
+ * prevents from dividing with zero and from creating to high costs
+ */
+ private double equalsNull = 0.05;
+
+ /**
+ * Switches clustering for the layout update process on/off
+ */
+ private boolean isClusteringEnabled = true;
+
+ /**
+ * Scales movement of clusters. It is recommendet to take
+ * a value between 1.0 and 0.0. This garanties, that clusters move slower
+ * than other cells. That rises the chance of getting a good looking layout
+ * after the calculation.
+ */
+ private double clusterMoveScaleFactor = 0.1;
+
+ /**
+ * Effects, how many clusters are created, when the layout update process
+ * starts. This affects the initial number of clusters, which is the number
+ * of cells available minus the number of cells to layout. The result of
+ * that term is divided by this factor, to get the maximum number of
+ * clusters. After this calculation, the clustering algorithm tries to
+ * minimize the number of clusters, so there might be less clusters than
+ * the maximum number.
+ */
+ private double clusteringFactor = 8.0;
+ protected boolean isOptimizer = false;
+
+ /******************************************************************************/
+ /**
+ * Constructor for SimulatedAnnealingAlgorithm.
+ */
+ public AnnealingLayoutAlgorithm() {
+ this(false);
+ setMaximumProgress(100);
+ }
+
+ /**
+ * Constructor for SimulatedAnnealingAlgorithm.
+ */
+ public AnnealingLayoutAlgorithm(boolean isOptimizer) {
+ this.isOptimizer = isOptimizer;
+ }
+
+ /**
+ * Returns the name of this algorithm in human
+ * readable form.
+ */
+ public String toString() {
+ return "Annealing";
+ }
+
+ /**
+ * Get a human readable hint for using this layout.
+ */
+ public String getHint() {
+ return "Ignores selection";
+ }
+
+ /**
+ * Returns an new instance of SugiyamaLayoutSettings
+ */
+ public JGraphLayoutSettings createSettings() {
+ return new AnnealingLayoutSettings(this, false);
+ }
+
+ /******************************************************************************/
+ /**
+ * Runs the Algorithm
+ */
+ public void run(JGraph graph, Object[] dynamic_cells, Object[] static_cells) {
+ isRunning = true;
+ canceled = false;
+ setAllowedToRun(true);
+ setProgress(1);
+
+ // System.out.println("now running Simulated Annealing");
+
+ /*----------------AQUIRATION OF RUNTIME CONSTANTS----------------*/
+ jgraph = graph;
+ //presetConfig = configuration;
+ cellList = new ArrayList();
+ edgeList = new ArrayList();
+ applyCellList = new ArrayList();
+
+ getNodes(jgraph, dynamic_cells);
+
+ if (applyCellList.size() == 0)
+ return;
+
+ if (isLayoutUpdateEnabled)
+ jgraph.getModel().addGraphModelListener(this);
+
+ /*------------------------AQUIRATION DONE------------------------*/
+
+ /*------------------------ALGORITHM START------------------------*/
+ init(true);
+
+ run();
+
+ /*-------------------------ALGORITHM END-------------------------*/
+ if (isAllowedToRun()) {
+ //if this algorithm isn't a optimization add-on of another algorithm
+ moveGraphToNW(); //moves the graph to the upper left corner
+ applyChanges(); // making temporary positions to real positions
+ removeTemporaryData(); // remove temporary positions
+ }
+
+ isRunning = false;
+ }
+
+ /******************************************************************************/
+ /**
+ * Runs the Algorithm as a optimization Algorithm of another Algorithm
+ * @param applyList List of all Cells, a new Layout should be found for.
+ * @param allCellList List of all Cells of the Graph
+ * @param allEdgeList List of all Edges of the Graph
+ */
+ public void performOptimization(ArrayList applyList, ArrayList allCellList,
+ ArrayList allEdgeList, Properties config) {
+ cellList = allCellList;
+ applyCellList = applyList;
+ edgeList = allEdgeList;
+
+ presetConfig = config;
+
+ loadConfiguration(CONFIG_KEY_RUN);
+
+ init(false);
+ run();
+ }
+
+ /******************************************************************************/
+ /**
+ * Loads the initial Values from the configuration.
+ *
+ * @param configSwitch Determines which configurationvalues have to be loaded
+ * Possible values are {@link #CONFIG_KEY_RUN} and
+ * {@link #CONFIG_KEY_LAYOUT_UPDATE}
+ */
+ private void loadConfiguration(int configSwitch) {
+ //load config for normal runs
+ if (configSwitch == CONFIG_KEY_RUN) {
+ initTemperature = Double.parseDouble((String) presetConfig.get(AnnealingLayoutSettings.KEY_INIT_TEMPERATURE));
+ minTemperature = Double.parseDouble((String) presetConfig.get(AnnealingLayoutSettings.KEY_MIN_TEMPERATURE));
+ minDistance = Double.parseDouble((String) presetConfig.get(AnnealingLayoutSettings.KEY_MIN_DISTANCE));
+ tempScaleFactor = Double.parseDouble((String) presetConfig.get(AnnealingLayoutSettings.KEY_TEMP_SCALE_FACTOR));
+ maxRounds = Integer.parseInt((String) presetConfig.get(AnnealingLayoutSettings.KEY_MAX_ROUNDS));
+ triesPerCell = Integer.parseInt((String) presetConfig.get(AnnealingLayoutSettings.KEY_TRIES_PER_CELL));
+
+ ArrayList lambda = (ArrayList) presetConfig.get(AnnealingLayoutSettings.KEY_LAMBDA);
+
+ lambdaList = new double[COUT_COSTFUNCTION];
+
+ for (int i = 0; i < lambdaList.length; i++)
+ lambdaList[i] = ((Double) lambda.get(i)).doubleValue();
+
+ bounds = (Rectangle) presetConfig.get(AnnealingLayoutSettings.KEY_BOUNDS);
+
+ costFunctionConfig = Integer.parseInt((String) presetConfig.get(AnnealingLayoutSettings.KEY_COST_FUNCTION_CONFIG),
+ 2);
+
+ computePermutation = isTrue((String) presetConfig.get(AnnealingLayoutSettings.KEY_COMPUTE_PERMUTATION));
+ uphillMovesAllowed = isTrue((String) presetConfig.get(AnnealingLayoutSettings.KEY_IS_UPHILL_MOVE_ALLOWED));
+ }
+ //load config for layout updates
+ else if (configSwitch == CONFIG_KEY_LAYOUT_UPDATE) {
+ initTemperature = Double.parseDouble((String) presetConfig.get(AnnealingLayoutSettings.KEY_LAYOUT_UPDATE_INIT_TEMPERATURE));
+ minTemperature = Double.parseDouble((String) presetConfig.get(AnnealingLayoutSettings.KEY_LAYOUT_UPDATE_MIN_TEMPERATURE));
+ minDistance = Double.parseDouble((String) presetConfig.get(AnnealingLayoutSettings.KEY_LAYOUT_UPDATE_MIN_DISTANCE));
+ tempScaleFactor = Double.parseDouble((String) presetConfig.get(AnnealingLayoutSettings.KEY_LAYOUT_UPDATE_TEMP_SCALE_FACTOR));
+ maxRounds = Integer.parseInt((String) presetConfig.get(AnnealingLayoutSettings.KEY_LAYOUT_UPDATE_MAX_ROUNDS));
+ triesPerCell = Integer.parseInt((String) presetConfig.get(AnnealingLayoutSettings.KEY_LAYOUT_UPDATE_TRIES_PER_CELL));
+
+ ArrayList lambda = (ArrayList) presetConfig.get(AnnealingLayoutSettings.KEY_LAYOUT_UPDATE_LAMBDA);
+
+ lambdaList = new double[COUT_COSTFUNCTION];
+
+ for (int i = 0; i < lambdaList.length; i++)
+ lambdaList[i] = ((Double) lambda.get(i)).doubleValue();
+
+ bounds = (Rectangle) presetConfig.get(AnnealingLayoutSettings.KEY_LAYOUT_UPDATE_BOUNDS);
+
+ costFunctionConfig = Integer.parseInt((String) presetConfig.get(AnnealingLayoutSettings.KEY_LAYOUT_UPDATE_COST_FUNCTION_CONFIG),
+ 2);
+
+ computePermutation = isTrue((String) presetConfig.get(AnnealingLayoutSettings.KEY_LAYOUT_UPDATE_COMPUTE_PERMUTATION));
+ uphillMovesAllowed = isTrue((String) presetConfig.get(AnnealingLayoutSettings.KEY_LAYOUT_UPDATE_IS_UPHILL_MOVE_ALLOWED));
+ luRecursionDepth = Integer.parseInt((String) presetConfig.get(AnnealingLayoutSettings.KEY_LAYOUT_UPDATE_METHOD_NEIGHBORS_DEPTH));
+ luPerimeterRadius = Double.parseDouble((String) presetConfig.get(AnnealingLayoutSettings.KEY_LAYOUT_UPDATE_METHOD_PERIMETER_RADIUS));
+ luPerimeterRadiusInc = Double.parseDouble((String) presetConfig.get(AnnealingLayoutSettings.KEY_LAYOUT_UPDATE_METHOD_PERIMETER_RADIUS_INCREASE));
+ luMethod = (String) presetConfig.get(AnnealingLayoutSettings.KEY_LAYOUT_UPDATE_METHOD);
+
+ isClusteringEnabled = isTrue((String) presetConfig.get(AnnealingLayoutSettings.KEY_LAYOUT_UPDATE_CLUSTERING_ENABLED));
+ clusteringFactor = Double.parseDouble((String) presetConfig.get(AnnealingLayoutSettings.KEY_LAYOUT_UPDATE_CLUSTERING_FACTOR));
+ clusterMoveScaleFactor = Double.parseDouble((String) presetConfig.get(AnnealingLayoutSettings.KEY_LAYOUT_UPDATE_CLUSTERING_MOVE_SCALE));
+ }
+ }
+
+ /******************************************************************************/
+ /**
+ * Helper-method. Transforms a String into a Boolean Value. The String
+ * has to contain the characters "true" or "false". upper case writings
+ * of some letters doesn't matter. if the String doesn't contain "true"
+ * or "false" the method returns false (easier to handle than throwing
+ * an exception).
+ */
+ private boolean isTrue(String boolValue) {
+ if (boolValue != null) {
+ if ("TRUE".equals(boolValue.toUpperCase())) {
+ return true;
+ } else if ("FALSE".equals(boolValue.toUpperCase())) {
+ return false;
+ }
+ }
+
+ return false;
+ }
+
+ /******************************************************************************/
+ /**
+ * Extracts all cells, all edges and all cells, the algorithm should run for,
+ * from JGraph. After calling this Method {@link #cellList},
+ * {@link #applyCellList} and {@link #edgeList} is filled.
+ *
+ * @param jgraph A instanz from JGraph, the Cells will be extract from.
+ */
+ private void getNodes(JGraph jgraph, Object[] cells) {
+ Object[] all = jgraph.getRoots();
+
+ CellView[] view = jgraph.getGraphLayoutCache().getMapping(all, false);
+ CellView[] selectedView = jgraph.getGraphLayoutCache().getMapping(cells, false);
+
+ for (int i = 0; i < view.length; i++)
+ if (view[i] instanceof VertexView) {
+ cellList.add(view[i]);
+ applyCellList.add(view[i]);
+ } else if (view[i] instanceof EdgeView) {
+ edgeList.add(view[i]);
+ }
+
+ for (int i = 0; i < selectedView.length; i++)
+ if (selectedView[i] instanceof VertexView)
+ applyCellList.add(selectedView[i]);
+ }
+
+ /******************************************************************************/
+ /**
+ * Makes the changed Positions of the Cells of the graph visible. This is like
+ * a "commit". Before this Method runs, nothing has change is the visible
+ * representation of the graph. After this method, the Layout for the Cells
+ * of the graph is applied.
+ */
+ private void applyChanges() {
+ Map viewMap = new Hashtable();
+
+ for (int i = 0; i < applyCellList.size(); i++) {
+ CellView view = (CellView) applyCellList.get(i);
+ Point2D.Double pos = getPosition(view);
+ Rectangle2D r = view.getBounds();
+
+ r.setFrame(pos.getX() - ((double) r.getWidth() / 2.0),
+ pos.getY() - ((double) r.getHeight() / 2.0), r.getWidth(), r.getHeight());
+
+ Object cell = ((CellView) applyCellList.get(i)).getCell();
+
+ Map attributes = new Hashtable();
+
+ GraphConstants.setBounds(attributes, r);
+
+ viewMap.put(cell, attributes);
+ }
+
+ jgraph.getGraphLayoutCache().edit(viewMap, null, null, null);
+ }
+
+ /******************************************************************************/
+ /**
+ * Removes the temporary Data from the Cells of the graph. During the run of the
+ * Algorithm there has been plenty of Data stored in the Cells. These are
+ * removed here, if the Algorithm is canceled or finished.
+ */
+ private void removeTemporaryData() {
+ for (int i = 0; i < applyCellList.size(); i++)
+ ((CellView) applyCellList.get(i)).getAttributes().clear();
+ }
+
+ /******************************************************************************/
+ /**
+ * Initialises the Algorithm. This is the step right before running the
+ * Algorithm. Letting this method set the initial Positions for all cells is
+ * only necessary when the Algorithm makes a normal run. Otherwise the initial
+ * Positions are allready set, by
+ * {@link #arrangeLayoutUpdateInsertPlacement(CellView[])
+ * arrangeLayoutUpdateInsertPlacement(...)}.
+ * @param setInitPositions Determines, if the initial Positions of the cells
+ * should be set or not. Initial Positions are calculated by random.
+ */
+ private void init(boolean setInitPositions) {
+ if (setInitPositions) {
+ for (int i = 0; i < applyCellList.size(); i++)
+ if (!((CellView) applyCellList.get(i)).getAttributes().containsKey(KEY_POSITION))
+ setPosition(i, (Math.random() * bounds.getWidth()) + bounds.getX(),
+ (Math.random() * bounds.getHeight()) + bounds.getY());
+
+ for (int i = 0; i < cellList.size(); i++)
+ if (!((CellView) cellList.get(i)).getAttributes().containsKey(KEY_POSITION))
+ setPosition((CellView) cellList.get(i),
+ (Math.random() * bounds.getWidth()) + bounds.getX(),
+ (Math.random() * bounds.getHeight()) + bounds.getY());
+ }
+
+ temperature = initTemperature;
+ maxRounds = Math.min(maxRounds,
+ Math.min(100 * applyCellList.size(),
+ getMaxRoundsByTemperature(temperature)));
+ round = 0;
+ }
+
+ /******************************************************************************/
+ /**
+ * Runs the Algorithm until {@link #temperature} is lower than
+ * {@link #minTemperature}.
+ */
+ private void run() {
+ while ((round <= maxRounds) && isAllowedToRun() && !canceled)
+ performRound();
+ }
+
+ /******************************************************************************/
+ /**
+ * Performs one round, so thats the main part of the Algorithm.
+ * Different to the original Implementation of the Algorithm, this Algorithm
+ * doesn't work with aproximativ 30 random Placements per Cell to find the best
+ * Position. This Algorithm works with a user defined number of segments. The
+ * Circle, the Cells will be placed on, is calculated like the original
+ * Implementation tells. But it is splited into a user defined number of
+ * segments. Then per cell a random offset is calculated and starting from
+ * that offset every segment is checked out, whether there is a better position
+ * for the cell. This can be done in a random order of the cells or always in
+ * the same order. Temperature is decreased after all cells are checked out
+ * for a new position, like in the original. While the original Implementation
+ * allows always uphill moves, this Algorithm allows the user to decide to work
+ * with or without them.
+ */
+ private void performRound() {
+ Point2D.Double[] config = getConfig();
+
+ double startEnergy = getGlobalCosts(lambdaList);
+ double globalEnergy = startEnergy;
+ double newGlobalEnergy = globalEnergy * 1.1; //somewhat higher than globalEnergy
+
+ //sequencial order cells are computed (every round the same order)
+ int[] sequence = new int[applyCellList.size()];
+
+ if (!computePermutation)
+ for (int i = 0; i < applyCellList.size(); i++)
+ sequence[i] = i;
+
+ for (int i = 0; i < applyCellList.size(); i++) {
+ if (computePermutation) //random order
+ sequence = createPermutation(applyCellList.size());
+
+ //random offset
+ double offset = Math.random() * 2.0 * Math.PI;
+
+ for (int j = 0; j < triesPerCell; j++) {
+ if (canceled)
+ return;
+
+ double angle = (double) j * ((2.0 * Math.PI) / (double) triesPerCell);
+ angle += offset;
+
+ Point2D.Double move = null;
+
+ //calculating new move
+ if (isCluster((CellView) applyCellList.get(i))) {
+ move = new Point2D.Double(clusterMoveScaleFactor * temperature * Math.cos(angle),
+ clusterMoveScaleFactor * temperature * Math.sin(angle));
+ } else {
+ move = new Point2D.Double(temperature * Math.cos(angle),
+ temperature * Math.sin(angle));
+ }
+
+ // Point2D.Double randomMove = getRandomVector(temperature);
+
+ //applying new move
+ setPosition(sequence[i], config[sequence[i]].x + move.x,
+ config[sequence[i]].y + move.y);
+
+ //calculating the costs for the actual layout
+ newGlobalEnergy = getGlobalCosts(lambdaList);
+
+ //taking move if costs < previos cost or uphill move possible
+ if ((newGlobalEnergy < globalEnergy)
+ || (getBolzmanBreak(globalEnergy, newGlobalEnergy) && uphillMovesAllowed)) {
+ // if( isDebugging )
+ // System.out.println("taking new energy : "+globalEnergy+" -> "+newGlobalEnergy+" <<<<<<<<<<<<<<<<<<<<<<<<<");
+ globalEnergy = newGlobalEnergy;
+
+ config[sequence[i]] = new Point2D.Double(config[sequence[i]].x + move.x,
+ config[sequence[i]].y + move.y);
+
+ // if( isDebugging )
+ // showApplyCellList();
+ break;
+ } else {
+ // if( isDebugging )
+ // System.out.println("energy = "+globalEnergy+" new Global Energy = "+newGlobalEnergy+" temperature = "+temperature);
+ setPosition(sequence[i], config[sequence[i]].x, config[sequence[i]].y);
+ }
+
+ double stepSize = applyCellList.size() * triesPerCell;
+ setProgress((int) (((double) ((round * stepSize)
+ + (i * triesPerCell) + j) /
+ (double) ((maxRounds+1) * stepSize)) * (100.0)));
+
+ if (!isAllowedToRun())
+ break;
+ }
+
+ //if this rounds runs very good and energy is 5% of starting value
+ //then break this round and start next round
+ if (globalEnergy == (startEnergy * 0.05))
+ break;
+
+ if (!isAllowedToRun())
+ break;
+ }
+
+ //temperature will be decreased
+ temperature *= tempScaleFactor;
+
+ round++; //rounds are counted
+ }
+
+ /******************************************************************************/
+ /**
+ * Extracts the Positions of all cells into a array of Positions.
+ * @return Array that represents the Positions of the Cells in
+ * {@link #applyCellList}.
+ */
+ private Point2D.Double[] getConfig() {
+ Point2D.Double[] config = new Point2D.Double[applyCellList.size()];
+
+ for (int i = 0; i < applyCellList.size(); i++) {
+ Point2D.Double pos = getPosition((CellView) applyCellList.get(i));
+ config[i] = new Point2D.Double(pos.x, pos.y);
+ }
+
+ return config;
+ }
+
+ /******************************************************************************/
+ /**
+ * Calculates the costs of the actual graph by using costfunctions.
+ * @param lambda Normalizing and priority values for the costfunctions
+ * @return costs for the actual graph
+ * @see #costFunctionConfig
+ * @see #getBorderline(double)
+ * @see #getEdgeDistance(double)
+ * @see #getEdgeLength(double)
+ * @see #getNodeDistance(double)
+ * @see #getNodeDistribution(double)
+ */
+ private double getGlobalCosts(double[] lambda) {
+ //assert lambda.length != COUT_COSTFUNCTION;
+
+ // long startTime = System.currentTimeMillis();
+ double energy = 0.0;
+
+ if ((costFunctionConfig & COSTFUNCTION_NODE_DISTANCE) != 0) {
+ energy += getNodeDistance(lambda[5]);
+ }
+
+ if ((costFunctionConfig & COSTFUNCTION_NODE_DISTRIBUTION) != 0) {
+ energy += getNodeDistribution(lambda[0]);
+ }
+
+ if ((costFunctionConfig & COSTFUNCTION_BORDERLINE) != 0) {
+ energy += getBorderline(lambda[1]);
+ }
+
+ if ((costFunctionConfig & COSTFUNCTION_EDGE_LENGTH) != 0) {
+ energy += getEdgeLength(lambda[2]);
+ }
+
+ if ((costFunctionConfig & COSTFUNCTION_EDGE_CROSSING) != 0) {
+ energy += getEdgeCrossing(1.0, lambda[3]);
+ }
+
+ if ((costFunctionConfig & COSTFUNCTION_EDGE_DISTANCE) != 0) {
+ energy += getEdgeDistance(lambda[4]);
+ }
+
+ return energy;
+ }
+
+ /******************************************************************************/
+ /**
+ * Creates a permutation of the Numbers from 0 to a determined value.
+ * @param length Number of Numbers and maximal distance to 0 for the Numbers
+ * filling the permutation
+ * @return Permutation of the Numbers between 0 and <code>length</code>
+ */
+ public int[] createPermutation(int length) {
+ int[] permutation = new int[length];
+
+ for (int i = 0; i < permutation.length; i++) {
+ int newValue = (int) (Math.random() * (double) length);
+
+ for (int j = 0; j < i; j++)
+ if (newValue == permutation[j]) {
+ newValue = (int) (Math.random() * (double) length);
+ j = -1; // wird auf 0 zur�ckgesetzt
+ }
+
+ permutation[i] = newValue;
+ }
+
+ return permutation;
+ }
+
+ /******************************************************************************/
+ /**
+ * Calculates a break condition for {@link #performRound()} if uphill moves
+ * are allowed. This is computed by a formular from Bolzman:<p>
+ * <blockquote><blockquote><code>
+ * random < e^(oldEnergy-newEnergy)
+ * </code></blockquote></blockquote>
+ * @param oldEnergy The Energy before the Energy has increased, so it's the
+ * lower one, of the two values.
+ * @param newEnergy The Energy after the Energy has increased, so it's the
+ * higher one, of the two values
+ * @return sometimes <code><b>true</b></code> when the random number is
+ * smaler than <code>e^(oldEnergy-newEnergy)</code>
+ */
+ private boolean getBolzmanBreak(double oldEnergy, double newEnergy) {
+ return Math.random() < Math.pow(Math.E, (oldEnergy - newEnergy) / temperature);
+ }
+
+ /******************************************************************************/
+ /**
+ * Calculates the maximal number of rounds, by flattening the actual
+ * {@link #temperature} with the temperature scaling factor
+ * {@link #tempScaleFactor}
+ *
+ * @param actualTemperature The Temperature of the actual Graph
+ * @return The number of Rounds that have to be performed until
+ * {@link #temperature} falls under {@link #minTemperature}.
+ */
+ private int getMaxRoundsByTemperature(double actualTemperature) {
+ return (int) Math.ceil(Math.log(minTemperature / actualTemperature) / Math.log(tempScaleFactor));
+ }
+
+ /******************************************************************************/
+ /**
+ * Costfunction. One criterion for drawing a "nice" graph is to spread the cells
+ * out evenly on the drawing space. The distances between the cells need not to
+ * be perfectly uniform, but the graph sould be occupy a reasonable part of
+ * the drawing space, and, if possible, the cells shouldn't be overcrowded.
+ * This function calculates the sum, over all pairs of cells, of a function
+ * that is inverse-proportional to the distance between the cells.
+ *
+ * @param lambda A normalizing factor that defines the relativ importance of
+ * this criterion compared to others. Increasing lambda relative to the other
+ * normalizing factors causes the Algorithm to prefer pictures with smaller
+ * distances between cells.
+ * @return costs of this criterion
+ */
+ private double getNodeDistribution(double lambda) {
+ double energy = 0.0;
+
+ for (int i = 0; i < applyCellList.size(); i++)
+ for (int j = 0; j < cellList.size(); j++) {
+ if (applyCellList.get(i) != cellList.get(j)) {
+ double distance = MathExtensions.getEuclideanDistance(getPosition((CellView) applyCellList
+ .get(i)),
+ getPosition((CellView) cellList
+ .get(j)));
+
+ //prevents from dividing with Zero
+ if (Math.abs(distance) < equalsNull)
+ distance = equalsNull;
+
+ energy += (lambda / (distance * distance));
+ }
+ }
+
+ // System.out.println("NodeDistribution : "+energy);
+ return energy;
+ }
+
+ /******************************************************************************/
+ /**
+ * Costfunction. As in physics, truly minimizing the potential energy might
+ * result in spreading out the elements indefinitely. To avoid this, and to
+ * reflect the physical limitations of the output device, add this costfunction
+ * to the energy function to deal with the borderlines of the drawing space.
+ *
+ * @param lambda Value relative to the other lamdas pushes the cells
+ * towards the center, while decreasing it results in using more of the
+ * drawing space near the borderlines.
+ * @return costs of this criterion
+ */
+ private double getBorderline(double lambda) {
+ double energy = 0.0;
+
+ for (int i = 0; i < applyCellList.size(); i++) {
+ Point2D.Double pos = getPosition((CellView) applyCellList.get(i));
+ double t = pos.y - bounds.y;
+ double l = pos.x - bounds.x;
+ double b = (bounds.y + bounds.height) - pos.y;
+ double r = (bounds.x + bounds.width) - pos.x;
+
+ energy += (lambda * ((1.0 / (t * t)) + (1.0 / (l * l)) + (1.0 / (b * b))
+ + (1.0 / (r * r))));
+ }
+
+ // System.out.println("Borderline : "+energy);
+ return energy;
+ }
+
+ /******************************************************************************/
+ /**
+ * Costfunction. This criterion tries to shorten the edges to a necessary
+ * minimum without causing the entire graph to become to tightly packed.
+ * This function penalizes long edges.
+ *
+ * @param lambda An appropriate normalizing factor. Increasing lamda relative
+ * to the lambdas of other costfunctions will result in shorter Edges.
+ * Decreasing brings up very different length of the edges.
+ * @return costs of this criterion
+ */
+ private double getEdgeLength(double lambda) {
+ double energy = 0.0;
+
+ Line2D.Double[] lineList = getEdgeLines(edgeList);
+
+ for (int i = 0; i < lineList.length; i++) {
+ Point2D p1 = lineList[i].getP1();
+ Point2D p2 = lineList[i].getP2();
+
+ double edgeLength = p1.distance(p2);
+
+ energy += (lambda * edgeLength * edgeLength);
+ }
+
+ // System.out.println("EdgeLength : "+energy);
+ return energy;
+ }
+
+ /******************************************************************************/
+ /**
+ * Costfunction. A constant penalty value is added for every two edges that
+ * cross.
+ * @param lambda Normalizing factor. Increasing lambda means attributing more
+ * importance to the elimination of edge crossings, and results in pictures
+ * with fewer crossings on average. However, this may be at the expense of other
+ * aesthetics.
+ * @return costs of this criterion.
+ */
+ private double getEdgeCrossing(double f, double lambda) {
+ int n = 0; // counts edgecrossings around vertex[i]
+
+ Line2D.Double[] lineList = getEdgeLines(edgeList);
+
+ for (int i = 0; i < lineList.length; i++)
+ for (int j = i; j < lineList.length; j++)
+ if (j != i)
+ if (lineList[i].intersectsLine(lineList[j])) {
+ if (((lineList[i].getP1().getX() != lineList[j].getP1().getX())
+ && (lineList[i].getP1().getY() != lineList[j].getP1().getY()))
+ && ((lineList[i].getP1().getX() != lineList[j].getP2().getX())
+ && (lineList[i].getP1().getY() != lineList[j].getP2().getY()))
+ && ((lineList[i].getP2().getX() != lineList[j].getP1().getX())
+ && (lineList[i].getP2().getY() != lineList[j].getP1().getY()))
+ && ((lineList[i].getP2().getX() != lineList[j].getP2().getX())
+ && (lineList[i].getP2().getY() != lineList[j].getP2().getY()))) {
+ n++;
+ }
+ }
+
+ // System.out.println("EdgeCrossings : "+n);
+ return lambda * f * (double) n;
+ }
+
+ /******************************************************************************/
+ /**
+ * Costfunction. This method calculates the distance between Cells and Edges.
+ * A small distance brings up higher costs while great distances generates lower
+ * costs. Costs for the distance between Cells and Edges are always computed
+ * by the method. If the distance is smaller than {@link #minDistance}
+ * additional costs are added. This method is suggested for finetuning and other
+ * short running calculations. Its the slowest of all costfunctions implemented
+ * here.
+ *
+ * @param lambda A normalizing factor for this function. Drawings with a
+ * relativ increase lambda will have greater distances between nodes and
+ * edges, by the expense of other aesthetics.
+ */
+ private double getEdgeDistance(double lambda) {
+ double energy = 0.0;
+
+ for (int i = 0; i < applyCellList.size(); i++) {
+ double h = 0.0;
+ CellView view = (CellView) applyCellList.get(i);
+
+ ArrayList relevantEdges = null;
+
+ if (view.getAttributes().containsKey(CF_KEY_EDGE_DISTANCE_RELEVANT_EDGES)) {
+ relevantEdges = (ArrayList) view.getAttributes()
+ .get(CF_KEY_EDGE_DISTANCE_RELEVANT_EDGES);
+ } else {
+ relevantEdges = getRelevantEdges(view);
+ view.getAttributes().put(CF_KEY_EDGE_DISTANCE_RELEVANT_EDGES, relevantEdges);
+ }
+
+ Line2D.Double[] lineList = getEdgeLines(getRelevantEdges(view));
+
+ for (int j = 0; j < lineList.length; j++) {
+ double distance = lineList[j].ptSegDist(getPosition(view));
+
+ //prevents from dividing with Zero
+ if (Math.abs(distance) < equalsNull)
+ distance = equalsNull;
+
+ if (distance != 0.0)
+ h += (lambda / (distance * distance));
+
+ if (distance < minDistance)
+ h += (lambda / (minDistance * minDistance));
+ }
+
+ energy += h;
+ }
+
+ // System.out.println("EdgeDistance : "+energy);
+ return energy;
+ }
+
+ /******************************************************************************/
+ /**
+ * Costfunction. This is a extension to the original Algorithm. This method
+ * evaluates the distances between cells. When the distance is lower than
+ * {@link #minDistance} or the cells are overlapping the costs from this
+ * function increase.
+ *
+ * @param lambda Normalizing value for this function. Increasing this value
+ * brings up less overlapping pairs of cells, by the expense of other
+ * aesthetics.
+ * @return costs of this criterion.
+ */
+ private double getNodeDistance(double lambda) {
+ double energy = 0.0;
+ double radiusInc = 30.0;
+ int overlapCount = 0;
+
+ for (int i = 0; i < applyCellList.size(); i++) {
+ Point2D.Double pos = (Point2D.Double) ((CellView) applyCellList.get(i)).getAttributes()
+ .get(KEY_POSITION);
+ Rectangle2D vertex = ((CellView) applyCellList.get(i)).getBounds();
+
+ for (int j = 0; j < cellList.size(); j++) {
+ if (applyCellList.get(i) != cellList.get(j)) {
+ Point2D.Double uPos = (Point2D.Double) ((CellView) cellList.get(j)).getAttributes()
+ .get(KEY_POSITION);
+ Rectangle2D uVertex = ((CellView) cellList.get(j)).getBounds();
+
+ double minDist = Math.max((2.0 * radiusInc)
+ + (Math.max(vertex.getWidth(), vertex.getHeight()) / 2.0)
+ + (Math.max(uVertex.getWidth(), uVertex.getHeight()) / 2.0),
+ minDistance);
+
+ double distance = Math.abs(pos.distance(uPos));
+
+ //prevents from dividing with Zero
+ if (Math.abs(distance) < equalsNull)
+ distance = equalsNull;
+
+ if (distance < minDist) {
+ energy += (lambda / (distance * distance));
+ overlapCount++;
+ }
+ }
+ }
+ }
+
+ return energy;
+ }
+
+ /******************************************************************************/
+ /**
+ * Transforms the Edges stored in a given List of edges into an array of lines.
+ * This is usefull, to get the Positions of the Edges.
+ * @param edges List containing only EdgeViews
+ * @return Array of Lines representing the edges of the graph.
+ */
+ private Line2D.Double[] getEdgeLines(ArrayList edges) {
+ Line2D.Double[] lines = new Line2D.Double[edges.size()];
+
+ for (int i = 0; i < edges.size(); i++) {
+ EdgeView edge = (EdgeView) edges.get(i);
+
+ CellView source = edge.getSource().getParentView();
+ CellView target = edge.getTarget().getParentView();
+
+ lines[i] = new Line2D.Double(getPosition(source), getPosition(target));
+ }
+
+ return lines;
+ }
+
+ /******************************************************************************/
+ /**
+ * Returns all Edges that are connected with cells, member of
+ * {@link #applyCellList}, except the edges connected the the given cell.
+ * @param except Edges connected to this cell are not of interest
+ * @return List of all interesting Edges
+ */
+ private ArrayList getRelevantEdges(CellView except) {
+ ArrayList relevantEdgeList = new ArrayList();
+
+ for (int i = 0; i < edgeList.size(); i++) {
+ CellView view = ((EdgeView) edgeList.get(i)).getSource().getParentView();
+
+ if ((view != except) && applyCellList.contains(view)) {
+ relevantEdgeList.add(edgeList.get(i));
+ } else {
+ view = ((EdgeView) edgeList.get(i)).getTarget().getParentView();
+
+ if ((view != except) && applyCellList.contains(view)) {
+ relevantEdgeList.add(edgeList.get(i));
+ }
+ }
+ }
+
+ return relevantEdgeList;
+ }
+
+ /******************************************************************************/
+ /**
+ * Computes a random Vector with a random direction and a given length.
+ */
+ public Point2D.Double getRandomVector(double maxLength) {
+ double alpha = Math.random() * Math.PI * 2;
+ double length = Math.random() * maxLength;
+
+ return new Point2D.Double(length * Math.cos(alpha), length * Math.sin(alpha));
+ }
+
+ /******************************************************************************/
+ /**
+ * Sets the position of a CellView to the given Position
+ *
+ * @param view The CellView, the position should be set
+ * @param pos New Position
+ * @see #setAttribute(CellView,String,Object)
+ */
+ private void setPosition(CellView view, Point2D.Double pos) {
+ setAttribute(view, KEY_POSITION, pos);
+ }
+
+ /******************************************************************************/
+ /**
+ * Sets the position of a CellView member of {@link #applyCellList} to the given
+ * position.
+ *
+ * @param index ID of the CellView in {@link #applyCellList}
+ * @param x X-Coordinate of the new position
+ * @param y Y-Coordinate of the new position
+ * @see #setPosition(CellView,double,double)
+ */
+ private void setPosition(int index, double x, double y) {
+ setPosition((CellView) applyCellList.get(index), x, y);
+ }
+
+ /******************************************************************************/
+ /**
+ * Sets the position of a CellView to the given Position
+ *
+ * @param view The CellView, the position should be set
+ * @param x X-Coordinate of the new position
+ * @param y Y-Coordinate of the new position
+ * @see #setPosition(CellView,Point2D.Double)
+ */
+ private void setPosition(CellView view, double x, double y) {
+ setPosition(view, new Point2D.Double(x, y));
+ }
+
+ /******************************************************************************/
+ /**
+ * Returns the Position of a CellView
+ *
+ * @param view CellView, the position is requested
+ * @return Position of the CellView
+ * @see #getAttribute(CellView,String)
+ */
+ private Point2D.Double getPosition(CellView view) {
+ return (Point2D.Double) getAttribute(view, KEY_POSITION);
+ }
+
+ /******************************************************************************/
+ /**
+ * Sets an attribute in a CellView
+ *
+ * @param view CellView, the attribute should be set
+ * @param key The attribute will be stored in the CellView under that key.
+ * @param obj Object representing the attribute, that should be stored.
+ */
+ private void setAttribute(CellView view, String key, Object obj) {
+ if (view.getAttributes() == null)
+ view.changeAttributes(new AttributeMap());
+
+ Map attributes = view.getAttributes();
+ attributes.put(key, obj);
+ }
+
+ /******************************************************************************/
+ /**
+ * Returns an attribute from a CellView
+ *
+ * @param view CellView, that stores the attribute
+ * @param key The attribute is stored in the CellView with this key
+ * @return Object stored with the given key in the given CellView
+ */
+ private Object getAttribute(CellView view, String key) {
+ return view.getAttributes().get(key);
+ }
+
+ /******************************************************************************/
+ /**
+ * After the calculation of the new Layout for a graph, the cells of the graph
+ * are positioned somewhere on the drawing space. They even might have negative
+ * coordinates. To prevent from this, this method is called, everytime before
+ * {@link #applyChanges()} is called. This method moves the whole graph to the
+ * upper left corner. No cell will have negative x- or y-coordinates.
+ */
+ private void moveGraphToNW() {
+ Point2D.Double firstPos = getPosition((CellView) cellList.get(0));
+ double minX = firstPos.x;
+ double minY = firstPos.y;
+ double maxX = minX;
+ double maxY = minY;
+
+ for (int i = 0; i < cellList.size(); i++) {
+ CellView view = (CellView) cellList.get(i);
+ Point2D.Double viewPos = getPosition((CellView) cellList.get(i));
+ Rectangle2D viewBounds = view.getAttributes().createRect(view.getBounds());
+
+ if (viewPos.getX() < minX) {
+ minX = viewPos.getX();
+ } else if ((viewPos.getX() + viewBounds.getWidth()) > maxX) {
+ maxX = viewPos.getX() + viewBounds.getWidth();
+ }
+
+ if (viewPos.getY() < minY) {
+ minY = viewPos.getY();
+ } else if ((viewPos.getY() + viewBounds.getHeight()) > maxY) {
+ maxY = viewPos.getY() + viewBounds.getHeight();
+ }
+ }
+
+ minX -= 50;
+ minY -= 50;
+
+ for (int i = 0; i < cellList.size(); i++) {
+ CellView view = (CellView) cellList.get(i);
+
+ Point2D.Double pos = getPosition(view);
+
+ setPosition(view, new Point2D.Double(pos.x - minX, pos.y - minY));
+ }
+ }
+
+ /******************************************************************************/
+ /**
+ * Retrieves the Cells that are directly connected to the given Cell and
+ * member of the given list.
+ * @param list Only relatives from this List are allowed
+ * @param view Relatives from this view are requested
+ * @return Relatives from view that are in the list
+ * @see #getRelatives(CellView)
+ */
+ protected ArrayList getRelativesFrom(ArrayList list, CellView view) {
+ ArrayList relatives = getRelatives(view);
+ ArrayList result = new ArrayList();
+
+ for (int i = 0; i < relatives.size(); i++)
+ if (list.contains(relatives.get(i)))
+ result.add(relatives.get(i));
+
+ return result;
+ }
+
+ /******************************************************************************/
+ /**
+ * Retrieves all Cells that have an edge with the given Cell.
+ * @param view Cell, the relatives are requested from
+ * @return Relatives of view
+ */
+ protected ArrayList getRelatives(CellView view) {
+ if (view.getAttributes().containsKey(KEY_RELATIVES))
+ return (ArrayList) view.getAttributes().get(KEY_RELATIVES);
+
+ ArrayList relatives = new ArrayList();
+ ArrayList portsCells = new ArrayList();
+
+ VertexView vertexView = (VertexView) view;
+
+ if (isCluster(view)) {
+ ArrayList clusteredVertices = (ArrayList) vertexView.getAttributes()
+ .get(KEY_CLUSTERED_VERTICES);
+
+ for (int i = 0; i < clusteredVertices.size(); i++) {
+ ArrayList clusterRelatives = getRelatives((CellView) clusteredVertices.get(i));
+
+ for (int j = 0; j < clusterRelatives.size(); j++)
+ if (!relatives.contains(clusterRelatives.get(j))
+ && !clusteredVertices.contains(clusterRelatives.get(j))) {
+ relatives.add(clusterRelatives.get(j));
+ }
+ }
+ } else {
+ GraphModel model = jgraph.getModel();
+ CellMapper mapper = jgraph.getGraphLayoutCache();
+ Object vertexCell = vertexView.getCell();
+
+ for (int i = 0; i < model.getChildCount(vertexCell); i++) {
+ Object portCell = model.getChild(vertexCell, i);
+ portsCells.add(portCell);
+ }
+
+ for (int i = 0; i < portsCells.size(); i++) {
+ Object portCell = portsCells.get(i);
+
+ Iterator edges = model.edges(portCell);
+
+ while (edges.hasNext()) {
+ Object edge = edges.next();
+ Object nextPort = null;
+
+ if (model.getSource(edge) != portCell) {
+ nextPort = model.getSource(edge);
+ } else {
+ nextPort = model.getTarget(edge);
+ }
+
+ CellView nextVertex = mapper.getMapping(model.getParent(nextPort), false);
+ relatives.add(nextVertex);
+ }
+ }
+ }
+
+ view.getAttributes().put(KEY_RELATIVES, relatives);
+
+ return relatives;
+ }
+
+ /******************************************************************************/
+ /**
+ * When Cells are inserted and a update of the layout is desired, this method
+ * defines the initial positions for all cells, the already layouted cells and
+ * the inserted. The already layouted cells get their previos calculated
+ * position, gained from their bounds. The inserted Cells are positioned
+ * recursivly. The inserted Cells, that have at least one relative in
+ * {@link #cellList} are placed in the barycenter of the relatives. After this,
+ * the inserted Cells, with a new position are added to {@link #cellList}.
+ * This is done, until all inserted Cells are in {@link #cellList}.
+ *
+ * @param viewList List of the inserted Cells
+ * @see #arrangeLayoutUpdateInsertedCellsPlacement(ArrayList)
+ */
+ private void arrangeLayoutUpdateInsertPlacement(CellView[] viewList) {
+ //preinitialisation - init positions for all known vertexViews
+ for (int i = 0; i < cellList.size(); i++) {
+ CellView view = (CellView) cellList.get(i);
+
+ if (!view.getAttributes().containsKey(KEY_POSITION)) {
+ Point2D.Double pos = new Point2D.Double(view.getBounds().getCenterX(),
+ view.getBounds().getCenterY());
+ view.getAttributes().put(KEY_POSITION, pos);
+ }
+ }
+
+ ArrayList placableCells = new ArrayList();
+
+ for (int i = 0; i < viewList.length; i++)
+ placableCells.add(viewList[i]);
+
+ arrangeLayoutUpdateInsertedCellsPlacement(placableCells);
+
+ /*
+ //puts the view in the barycenter of the relatives, if there are any
+ for( int i = 0; i < viewList.length; i++ )
+
+ if( viewList[i] instanceof VertexView ){
+
+ ArrayList relatives = getRelativesFrom(cellList,viewList[i]);
+
+ if( relatives.size() != 0 ){
+
+ double sumX = 0.0;
+ double sumY = 0.0;
+ for( int j = 0; j < relatives.size(); j++ ){
+ Point2D.Double pos = (Point2D.Double)
+ ((CellView)relatives.get(j)).
+ getAttributes().
+ get(KEY_POSITION);
+ sumX += pos.x;
+ sumY += pos.y;
+ }
+ Point2D.Double randomVector = new Point2D.Double(Math.cos(Math.random()*2.0*Math.PI)*10.0,
+ Math.sin(Math.random()*2.0*Math.PI)*10.0);
+ viewList[i].getAttributes().put(KEY_POSITION,
+ new Point2D.Double(
+ (sumX/(double)relatives.size())+randomVector.x,
+ (sumY/(double)relatives.size())+randomVector.y));
+ }
+ else {
+ viewList[i].getAttributes().put(KEY_POSITION,
+ new Point2D.Double(
+ 0.0,
+ 0.0));
+ }
+ }*/
+ }
+
+ /******************************************************************************/
+ /**
+ * Recursive method for finding the initial position for inserted cells. The
+ * inserted cells are checked, whether there is at leased one of the relatives
+ * in {@link #cellList}. If there is any, the cells are positioned in the
+ * barycenter of the relatives. If there is only one relative, this means, the
+ * inserted CellViews are positioned exactly on the position of the relative.
+ * Cells with no relative in {@link #cellList} are stored in a list. After all
+ * Cells are visited and checked, all positioned cells are added to
+ * {@link #cellList}. Then, while the list with the non positioned Cells is
+ * not empty, the method is called recursivly again. This is done, until all
+ * inserted cells are positioned or no relatives could be found for all left
+ * Cells (that causes that the left cells are positioned in the upper left
+ * corner).
+ *
+ * @param placableCells A List of CellViews, that have to be placed in the
+ * barycenter of their relatives
+ * @see #arrangeLayoutUpdateInsertPlacement(CellView[])
+ * @see #graphChanged(GraphModelEvent)
+ */
+ private void arrangeLayoutUpdateInsertedCellsPlacement(ArrayList placableCells) {
+ ArrayList notPlacedCells = new ArrayList();
+
+ for (int i = 0; i < placableCells.size(); i++) {
+ CellView view = (CellView) placableCells.get(i);
+
+ if (view instanceof VertexView) {
+ ArrayList relatives = getRelativesFrom(cellList, view);
+
+ if (relatives.size() != 0) {
+ double sumX = 0.0;
+ double sumY = 0.0;
+
+ for (int j = 0; j < relatives.size(); j++) {
+ Point2D.Double pos = (Point2D.Double) ((CellView) relatives.get(j)).getAttributes()
+ .get(KEY_POSITION);
+ sumX += pos.x;
+ sumY += pos.y;
+ }
+
+ Point2D.Double randomVector = new Point2D.Double(Math.cos(Math.random() * 2.0 * Math.PI) * 10.0,
+ Math.sin(Math.random() * 2.0 * Math.PI) * 10.0);
+ view.getAttributes()
+ .put(KEY_POSITION,
+ new Point2D.Double((sumX / (double) relatives.size()) + randomVector.x,
+ (sumY / (double) relatives.size()) + randomVector.y));
+ } else {
+ notPlacedCells.add(view);
+ }
+ }
+ }
+
+ for (int i = 0; i < placableCells.size(); i++) {
+ if (placableCells.get(i) != null)
+ if (((CellView) placableCells.get(i)).getAttributes() != null)
+ if (((CellView) placableCells.get(i)).getAttributes().containsKey(KEY_POSITION))
+ cellList.add(placableCells.get(i));
+ }
+
+ if (notPlacedCells.size() != placableCells.size()) {
+ arrangeLayoutUpdateInsertedCellsPlacement(notPlacedCells);
+ } else {
+ for (int i = 0; i < notPlacedCells.size(); i++) {
+ CellView view = (CellView) notPlacedCells.get(i);
+
+ if (!view.getAttributes().containsKey(KEY_POSITION))
+ view.getAttributes().put(KEY_POSITION, new Point2D.Double(0.0, 0.0));
+ }
+ }
+
+ for (int i = 0; i < cellList.size(); i++)
+ if (((CellView) cellList.get(i)).getAttributes().get(KEY_POSITION) == null)
+ System.err.println("WHATCH OUT!!! NODE " + i + " == NULL");
+ }
+
+ /******************************************************************************/
+ /**
+ * Decides in a layout update process, what cells are member of
+ * {@link #applyCellList}. This depends on the configuration of the layout
+ * update method. First, regardless which layout update method was chosen, all
+ * inserted cells, gained as parameter, are added. Then, when the perimeter
+ * method is chosen, the cells are counted, which position is in the basic
+ * perimeter radius around an inserted cell. That number multiplied with the
+ * perimeter radius increase are added to the basic perimeter radius. Every
+ * Cell, that was not inserted but is positioned in that radius, is added to
+ * {@link #applyCellList}. After that, if perimeter method or neighbor method
+ * is choosen, the relatives up to {@link #luRecursionDepth} away of the
+ * inserted cells are added to {@link #applyCellList}.
+ *
+ * @param viewList Array of the inserted CellView's (includes EdgeView)
+ * @see #graphChanged(GraphModelEvent)
+ */
+ private void getLayoutUpdateCells(CellView[] viewList) {
+ //adds all inserted views
+ for (int i = 0; i < viewList.length; i++) {
+ if (viewList[i] instanceof VertexView) {
+ if (!applyCellList.contains(viewList[i]))
+ applyCellList.add(viewList[i]);
+
+ if (!cellList.contains(viewList[i]))
+ cellList.add(viewList[i]);
+ } else if (viewList[i] instanceof EdgeView && (viewList[i] != null)) {
+ if (!edgeList.contains(viewList[i])) {
+ edgeList.add(viewList[i]);
+ // System.out.println("edge added");
+ }
+ }
+ }
+
+ //now all vertices (old and new) are in cellList & all edges in edgeList
+
+ //adds all known cells in a perimeter
+ if (AnnealingLayoutSettings.KEY_LAYOUT_UPDATE_METHOD_PERIMETER.equals(luMethod)) {
+ //precalculation of perimeters
+ ArrayList perimeterList = new ArrayList();
+
+ for (int i = 0; i < applyCellList.size(); i++) {
+ VertexView vertex = (VertexView) applyCellList.get(i);
+ Point2D.Double pos = (Point2D.Double) vertex.getAttributes().get(KEY_POSITION);
+ int intersectionCount = 0;
+
+ for (int j = 0; j < applyCellList.size(); j++) {
+ if (i != j) {
+ VertexView uVertex = (VertexView) applyCellList.get(j);
+ Point2D.Double uPos = (Point2D.Double) uVertex.getAttributes()
+ .get(KEY_POSITION);
+
+ if (pos.distance(uPos) < luPerimeterRadius)
+ intersectionCount++; //counting inserted cells in perimeter
+ }
+ }
+
+ perimeterList.add(new Ellipse2D.Double(pos.x
+ - (luPerimeterRadius
+ + ((double) intersectionCount * luPerimeterRadiusInc)),
+ pos.y
+ - (luPerimeterRadius
+ + ((double) intersectionCount * luPerimeterRadiusInc)),
+ 2.0 * (luPerimeterRadius
+ + ((double) intersectionCount * luPerimeterRadiusInc)),
+ 2.0 * (luPerimeterRadius
+ + ((double) intersectionCount * luPerimeterRadiusInc))));
+ }
+
+ //adding all members of cellList within a perimeter to applyCellList
+ for (int i = 0; i < cellList.size(); i++) {
+ VertexView vertex = (VertexView) cellList.get(i);
+ Point2D.Double pos = (Point2D.Double) vertex.getAttributes().get(KEY_POSITION);
+
+ for (int j = 0; j < perimeterList.size(); j++) {
+ Ellipse2D.Double perimeter = (Ellipse2D.Double) perimeterList.get(j);
+ Point2D.Double center = new Point2D.Double(perimeter.getCenterX(),
+ perimeter.getCenterY());
+ double radius = perimeter.getCenterX() - perimeter.getX();
+
+ if (center.distance(pos) < radius)
+ if (!applyCellList.contains(vertex))
+ applyCellList.add(vertex);
+ }
+ }
+ }
+
+ if (luRecursionDepth > 0) {
+ int vertexCount = 0;
+
+ for (int i = 0; i < viewList.length; i++)
+ if (viewList[i] instanceof VertexView)
+ vertexCount++;
+
+ VertexView[] vertexList = new VertexView[vertexCount];
+ vertexCount = 0;
+
+ for (int i = 0; i < viewList.length; i++)
+ if (viewList[i] instanceof VertexView)
+ vertexList[vertexCount++] = (VertexView) viewList[i];
+
+ addRelativesToList(vertexList, luRecursionDepth);
+ }
+ }
+
+ /******************************************************************************/
+ /**
+ * Recursive method, to add relatives to {@link #applyCellList}, that are
+ * maximal a given pathlength away of the views in the given Array.
+ *
+ * @param vertexList Array of the VertexView's, which relatives should be
+ * added to {@link #applyCellList}, if they are whithin a given pathlength
+ * away of the VertexViews
+ * @param depth Pathlength, relatives could be away of the VertexViews
+ * @see #graphChanged(GraphModelEvent)
+ */
+ private void addRelativesToList(VertexView[] vertexList, int depth) {
+ if (vertexList == null)
+ return;
+
+ if (vertexList.length == 0)
+ return;
+
+ if (depth == 0)
+ return;
+
+ for (int i = 0; i < vertexList.length; i++) {
+ ArrayList relatives = getRelatives(vertexList[i]);
+ VertexView[] relativeList = new VertexView[relatives.size()];
+
+ for (int j = 0; j < relatives.size(); j++) {
+ if (!applyCellList.contains(relatives.get(j))) {
+ applyCellList.add(relatives.get(j));
+
+ // showCell((CellView)relatives.get(j),new Color(0,180,180));
+ }
+
+ if (!cellList.contains(relatives.get(j)))
+ cellList.add(relatives.get(j));
+
+ relativeList[j] = (VertexView) relatives.get(j);
+ }
+
+ addRelativesToList(relativeList, depth - 1);
+ }
+ }
+
+ /******************************************************************************/
+ /**
+ * When a event reaches this method, it will be scanned, if there are
+ * Cells removed or Cells inserted. When there are Cells removed from the graph,
+ * they have to be removed from {@link #cellList}, {@link #edgeList} and from
+ * {@link #applyCellList}. If there are Cells added, the layout update process
+ * starts. This triggers the algorithm to try to find a suitable layout for
+ * the inserted cells, by layouting them and some of the cells, available in
+ * {@link #cellList}. The algorithm tries to stimulate the cells from
+ * {@link #cellList} to make place for the layout of the inserted Cells.
+ */
+ public void graphChanged(GraphModelEvent e) {
+ if (!isRunning) {
+ isRunning = true;
+
+ Object[] vertexIns = e.getChange().getInserted();
+ Object[] vertexRem = e.getChange().getRemoved();
+
+ //Insert - Action
+ if ((vertexIns != null) && (vertexRem == null)) {
+ if (vertexIns.length == 0) {
+ isRunning = false;
+
+ return;
+ }
+
+ CellView[] viewList = jgraph.getGraphLayoutCache().getMapping(vertexIns, false);
+
+ if (viewList.length == 0) {
+ isRunning = false;
+
+ return;
+ }
+
+ applyCellList.clear();
+
+ loadConfiguration(CONFIG_KEY_LAYOUT_UPDATE);
+
+ //enables a workaround if a known bug is still present
+ boolean bugPresent = false;
+
+ for (int i = 0; i < viewList.length; i++)
+ if (viewList[i] == null) {
+ bugPresent = true;
+
+ break;
+ }
+
+ if (bugPresent)
+ getAllEdges();
+
+ arrangeLayoutUpdateInsertPlacement(viewList);
+ getLayoutUpdateCells(viewList);
+
+ if (applyCellList.size() == 0) {
+ isRunning = false;
+
+ return;
+ }
+
+ round = 0;
+
+ if (isClusteringEnabled)
+ clusterGraph();
+
+ //algorithm start
+ init(false);
+ run();
+
+ //algorithm end
+ if (isClusteringEnabled)
+ declusterGraph();
+
+ applyChanges();
+ removeTemporaryData();
+ }
+ //Remove - Action
+ else if ((vertexIns == null) && (vertexRem != null)) {
+ isRunning = true;
+
+ CellView[] viewList = jgraph.getGraphLayoutCache().getMapping(vertexRem, false);
+
+ for (int i = 0; i < viewList.length; i++)
+
+ if (viewList[i] instanceof VertexView) {
+ if (applyCellList.contains(viewList[i]))
+ applyCellList.remove(viewList[i]);
+
+ if (cellList.contains(viewList[i]))
+ cellList.remove(viewList[i]);
+ } else if (viewList[i] instanceof EdgeView) {
+ // as long as graphChanged get no inserted Edges, this lines should stay
+ // commented out.
+ // if( edgeList.contains(viewList[i]) )
+ // edgeList.remove(viewList[i]);
+ }
+ }
+
+ isRunning = false;
+ }
+ }
+
+ /******************************************************************************/
+ /**
+ * Workaround for a BUG. When
+ * {@link #graphChanged(GraphModelEvent) graphChanged(...)} is called, the
+ * method gets via myGraphModelEvent.getChanged().getInserted() an array of
+ * objects. This array consists of the key's to the views inserted into the
+ * graph. When this views are gained, the BUG appears. The array gained from
+ * the GraphLayoutCache contains only VertexView's. Instead of the EdgeViews
+ * there is NULL in the array. This method is callen if this BUG appears, in the
+ * hope, to get the inserted edges.
+ */
+ private void getAllEdges() {
+ Object[] cells = jgraph.getRoots();
+
+ CellView[] views = jgraph.getGraphLayoutCache().getMapping(cells, false);
+
+ for (int i = 0; i < views.length; i++) {
+ if (views[i] instanceof VertexView) {
+ VertexView vertexView = (VertexView) views[i];
+ GraphModel model = jgraph.getModel();
+ CellMapper mapper = jgraph.getGraphLayoutCache();
+ Object vertexCell = vertexView.getCell();
+ ArrayList portsCells = new ArrayList();
+
+ for (int j = 0; j < model.getChildCount(vertexCell); j++) {
+ Object portCell = model.getChild(vertexCell, j);
+ portsCells.add(portCell);
+ }
+
+ for (int j = 0; j < portsCells.size(); j++) {
+ Object portCell = portsCells.get(j);
+
+ Iterator edges = model.edges(portCell);
+
+ while (edges.hasNext()) {
+ Object edge = edges.next();
+
+ Object e = mapper.getMapping(edge, false);
+
+ if (!edgeList.contains(e) && (e != null)) {
+ edgeList.add(e);
+ }
+ }
+ }
+ } else if (views[i] instanceof EdgeView) {
+ if (!edgeList.contains(views[i]) && (views[i] != null)) {
+ edgeList.add(views[i]);
+ }
+ }
+ }
+ }
+
+ /******************************************************************************/
+ /******************** CLUSTERING METHODS **************************************/
+ /******************************************************************************/
+
+ /**
+ * Clusters a graph. Cells, contained in {@link #cellList} and not contained
+ * in {@link #applyCellList} are clustered by this short algorithm. The
+ * algorithm first tries to identify how many cells it should cluster. This
+ * is calculated by subtracting the size of {@link #applyCellList} from
+ * the size of {@link #cellList} and dividing the result by the
+ * {@link #clusteringFactor}. In the next step, the identified number of
+ * clusters are created, and their position is initialised by random. Then
+ * every clusterable cell is added to the cluster where the distance of the
+ * vertex and the cluster is minimal. After adding a cell, the clusters position
+ * is recalculated. Finishing this step, the algorithm tries to minimize the
+ * number of clusters, by sorting the clustered vertices, if there is another
+ * cluster, that distance is shorter than the distance to the cluster, the
+ * vertice is actually in. This can happen, because by moving vertices into the
+ * clusters, the position of the clusters are changed. The minimization runs
+ * until no vertice can be moved anymore. empty clusters are removed and finaly
+ * the clusters are added to {@link #applyCellList}, because they should move
+ * while the upcoming next calculations. That move can later be retrieved by
+ * subtracting the attributes {@link #KEY_POSITION} and
+ * {@link #KEY_CLUSTER_INIT_POSITION}.
+ *
+ * @see #declusterGraph()
+ */
+ protected void clusterGraph() {
+ //initialisation
+ int maxClusters = Math.max((int) ((double) (cellList.size() - applyCellList.size()) / clusteringFactor),
+ 2);
+
+ if (cellList.size() <= 1) {
+ // System.out.println("cellList.size() <= 1");
+
+ return;
+ }
+
+ ArrayList clusterList = new ArrayList();
+ ArrayList cellsToCluster = new ArrayList();
+
+ //identifying all cells, that are clusterable
+ for (int i = 0; i < cellList.size(); i++)
+ if (!applyCellList.contains(cellList.get(i)))
+ cellsToCluster.add(cellList.get(i));
+
+ //initialize clusters
+ VertexView[] clusters = new VertexView[maxClusters];
+ Rectangle boundingBox = getBoundingBox();
+
+ for (int i = 0; i < clusters.length; i++) {
+ clusters[i] = new VertexView(null);
+
+ Map attributes = clusters[i].getAttributes();
+ attributes.put(KEY_IS_CLUSTER, "true");
+ attributes.put(KEY_POSITION,
+ new Point2D.Double(Math.random() * boundingBox.width,
+ Math.random() * boundingBox.height));
+ clusterList.add(clusters[i]);
+ }
+
+ //cluster all available cells
+ for (int i = 0; i < cellsToCluster.size(); i++) {
+ VertexView cell = (VertexView) cellsToCluster.get(i);
+ Point2D.Double cellPos = getPosition(cell);
+ int clusterID = 0;
+ Point2D.Double clusterPos = getPosition((CellView) clusterList.get(0));
+ double minDistance = MathExtensions.getEuclideanDistance(cellPos, clusterPos);
+
+ //search for nearest cluster
+ for (int j = 1; j < clusterList.size(); j++) {
+ clusterPos = getPosition((VertexView) clusterList.get(j));
+
+ double distance = MathExtensions.getEuclideanDistance(cellPos, clusterPos);
+
+ if (minDistance > distance) {
+ minDistance = distance;
+ clusterID = j;
+ }
+ }
+
+ VertexView cluster = (VertexView) clusterList.get(clusterID);
+ moveVerticeToCluster(cell, cluster);
+ }
+
+ //initialization done
+
+ //sorting the clustered vertices. if a vertice is nearer to a clusters
+ //barycenter then to it's own clusters barycenter the vertice is moved
+ //to that cluster. The coordinates of both clusters are recalculated.
+ //this is done, until nothing could be done better.
+ boolean couldMakeItBetter = false;
+
+ do {
+ couldMakeItBetter = false;
+
+ for (int i = 0; i < cellsToCluster.size(); i++) {
+ VertexView cell = (VertexView) cellsToCluster.get(i);
+ VertexView oldCluster = (VertexView) cell.getAttributes().get(KEY_CLUSTER);
+ Point2D.Double cellPos = getPosition(cell);
+ Point2D.Double clusterPos = getPosition(oldCluster);
+ double distance = MathExtensions.getEuclideanDistance(cellPos, clusterPos);
+
+ for (int j = 0; j < clusterList.size(); j++) {
+ VertexView cluster = (VertexView) clusterList.get(j);
+
+ if (cluster != oldCluster) {
+ clusterPos = getPosition(cluster);
+
+ double newDistance = MathExtensions.getEuclideanDistance(cellPos, clusterPos);
+
+ if (newDistance < distance) {
+ moveVerticeToCluster(cell, cluster);
+ couldMakeItBetter = true;
+
+ break;
+ }
+ }
+ }
+ }
+ } while (couldMakeItBetter);
+
+ //empty clusters are removed
+ for (int i = 0; i < clusterList.size(); i++) {
+ if (!((VertexView) clusterList.get(i)).getAttributes()
+ .containsKey(KEY_CLUSTERED_VERTICES)) {
+ clusterList.remove(i--);
+ } else if (((ArrayList) ((VertexView) clusterList.get(i)).getAttributes()
+ .get(KEY_CLUSTERED_VERTICES)).size() == 0) {
+ clusterList.remove(i--);
+ }
+ }
+
+ //remove clustered vertices from cellList
+ for (int i = 0; i < cellsToCluster.size(); i++)
+ cellList.remove(cellsToCluster.get(i));
+
+ //adding clusters to applyCellList and cellList
+ for (int i = 0; i < clusterList.size(); i++) {
+ applyCellList.add(clusterList.get(i));
+ cellList.add(clusterList.get(i));
+ }
+
+ //storing a copy of position, to move vertices while declustering
+ for (int i = 0; i < clusterList.size(); i++) {
+ VertexView cluster = (VertexView) clusterList.get(i);
+ Map attribs = cluster.getAttributes();
+ Point2D.Double clusterPos = (Point2D.Double) attribs.get(KEY_POSITION);
+ attribs.put(KEY_CLUSTER_INIT_POSITION, new Point2D.Double(clusterPos.x, clusterPos.y));
+ }
+
+ for (int i = 0; i < clusterList.size(); i++) {
+ VertexView cluster = (VertexView) clusterList.get(i);
+ cluster.setCachedBounds(getBoundingBox((ArrayList) cluster.getAttributes()
+ .get(KEY_CLUSTERED_VERTICES)));
+ }
+
+ /* colorizeClusters(clusterList);
+ stop(20000);*/
+ }
+
+ /******************************************************************************/
+ /**
+ * Moves a vertice from the cluster, it is holded, to another cluster. This
+ * implies that the vertice is removed from the old cluster and added to the
+ * new. After this, the positions of the old and the new cluster are
+ * recalculated.
+ *
+ * @param vertice Vertex that should be moved
+ * @param cluster Cluster the vertex should be moved
+ */
+ protected void moveVerticeToCluster(VertexView vertice, VertexView cluster) {
+ //adding vertice to new cluster
+ if (!cluster.getAttributes().containsKey(KEY_CLUSTERED_VERTICES))
+ cluster.getAttributes().put(KEY_CLUSTERED_VERTICES, new ArrayList());
+
+ ArrayList clusteredVertices = (ArrayList) cluster.getAttributes().get(KEY_CLUSTERED_VERTICES);
+ clusteredVertices.add(vertice);
+
+ //removing vertice from old cluster
+ if (vertice.getAttributes().containsKey(KEY_CLUSTER)) {
+ VertexView oldCluster = (VertexView) vertice.getAttributes().get(KEY_CLUSTER);
+ ArrayList list = (ArrayList) oldCluster.getAttributes().get(KEY_CLUSTERED_VERTICES);
+ list.remove(vertice);
+ computeClusterPosition(oldCluster);
+ }
+
+ //register cluster in vertice
+ vertice.getAttributes().put(KEY_CLUSTER, cluster);
+ //reposition cluster
+ computeClusterPosition(cluster);
+ }
+
+ /******************************************************************************/
+ /**
+ * Recalculates the position of a cluster. The position of a cluster is defined
+ * by the barycenter of the clustered vertices.
+ *
+ * @param cluster Cell, that has to be a cluster, should be repositioned.
+ */
+ protected void computeClusterPosition(VertexView cluster) {
+ ArrayList clusteredVertices = (ArrayList) cluster.getAttributes().get(KEY_CLUSTERED_VERTICES);
+ Point2D.Double clusterPos = computeBarycenter(clusteredVertices);
+ cluster.getAttributes().put(KEY_POSITION, clusterPos);
+ }
+
+ /******************************************************************************/
+ /**
+ * Moves all clusters from {@link #cellList} and {@link #applyCellList},
+ * extracts their clustered vertices and adds them to {@link #cellList}. While
+ * doing this, it repositions the clustered vertices with the move, the cluster
+ * has made during the calculation.
+ *
+ * @see #clusterGraph()
+ */
+ protected void declusterGraph() {
+ if (cellList.size() <= 1)
+ return;
+
+ //first collecting all clusters from applyCellList
+ ArrayList clusterList = new ArrayList();
+
+ for (int i = 0; i < cellList.size(); i++) {
+ VertexView cell = ((VertexView) cellList.get(i));
+
+ if (isCluster(cell))
+ clusterList.add(cell);
+ }
+
+ if (clusterList.size() == 0)
+ return;
+
+ //cleaning up the cell lists
+ for (int i = 0; i < clusterList.size(); i++) {
+ cellList.remove(clusterList.get(i));
+ applyCellList.remove(clusterList.get(i));
+ }
+
+ //repositioning and extracting vertices to cellList
+ for (int i = 0; i < clusterList.size(); i++) {
+ VertexView cluster = (VertexView) clusterList.get(i);
+ Map attribs = cluster.getAttributes();
+ Point2D.Double newClusterPos = getPosition(cluster);
+ Point2D.Double oldClusterPos = (Point2D.Double) attribs.get(KEY_CLUSTER_INIT_POSITION);
+
+ //calculating move, cluster has made during his existance
+ Point2D.Double move = new Point2D.Double(newClusterPos.x - oldClusterPos.x,
+ newClusterPos.y - oldClusterPos.y);
+ ArrayList vertexList = (ArrayList) attribs.get(KEY_CLUSTERED_VERTICES);
+
+ //applying move to clustered vertices
+ for (int j = 0; j < vertexList.size(); j++) {
+ VertexView cell = (VertexView) vertexList.get(j);
+ Point2D.Double cellPos = getPosition(cell);
+ Point2D.Double newCellPos = new Point2D.Double(cellPos.x + move.x,
+ cellPos.y + move.y);
+ cell.getAttributes().put(KEY_POSITION, newCellPos);
+ //refilling clustered vertices in cellList
+ cellList.add(cell);
+ }
+ }
+ }
+
+ /******************************************************************************/
+ /**
+ * Returns <code><b>true</b></code> when a cell is a cluster, else
+ * <code<b>false</b></code>. A cell is a cluster when it has under it's
+ * attributes a attribute with the boolean value <code><b>true</b></code> under
+ * the key {@link #KEY_IS_CLUSTER}.
+ *
+ * @param cell cell, that should be researched wheather it is a cluster or not.
+ * @return <code><b>true</b></code> if cell is a cluster, else
+ * <code><b>false</b></code>.
+ */
+ protected boolean isCluster(CellView cell) {
+ if (cell.getAttributes().containsKey(KEY_IS_CLUSTER)) {
+ if (isTrue((String) cell.getAttributes().get(KEY_IS_CLUSTER))) {
+ return true;
+ } else {
+ System.err.println("FATAL ERROR: CELL CANNOT CLEARLY BE IDENTIFIED AS A CLUSTER!!!");
+
+ return false;
+ }
+ } else
+
+ return false;
+ }
+
+ /******************************************************************************/
+ /**
+ * Calculates the barycenter of a graph, given by a list. This calculation is
+ * done by summing the coordinates and dividing them with the number of
+ * coordinates.
+ *
+ * @param list List of CellView's
+ * @return Position of the barycenter
+ */
+ private Point2D.Double computeBarycenter(ArrayList list) {
+ double sumX = 0.0;
+ double sumY = 0.0;
+
+ for (int i = 0; i < list.size(); i++) {
+ CellView view = (CellView) list.get(i);
+
+ Point2D.Double pos = getPosition(view);
+ sumX += pos.x;
+ sumY += pos.y;
+ }
+
+ return new Point2D.Double(sumX / ((double) list.size()), sumY / ((double) list.size()));
+ }
+
+ /******************************************************************************/
+ /**
+ * Computes the bounding box of the graph in the given list of CellViews.
+ * The result is a Rectangle, parallel to the X- and Y-axises of the drawing
+ * system, closing about the graph in the given list.
+ *
+ * @param verticeList List containing the CellViews, the bounding box is of
+ * interest.
+ * @return Rectangle, that contains the whole graph, linked in the given list.
+ */
+ private Rectangle getBoundingBox(ArrayList verticeList) {
+ if (verticeList.size() > 0) {
+ Point2D.Double vertexPos = getPosition((VertexView) verticeList.get(0));
+ Rectangle2D vertexSize = ((CellView) verticeList.get(0)).getBounds();
+
+ double minX = vertexPos.getX();
+ double minY = vertexPos.getX();
+ double maxX = vertexPos.getX() + vertexSize.getWidth();
+ double maxY = vertexPos.getX() + vertexSize.getHeight();
+
+ for (int i = 1; i < verticeList.size(); i++) {
+ vertexPos = getPosition((VertexView) verticeList.get(i));
+ vertexSize = ((CellView) verticeList.get(i)).getBounds();
+
+ if (minX > vertexPos.getX())
+ minX = vertexPos.getX();
+
+ if (minY > vertexPos.getY())
+ minY = vertexPos.getY();
+
+ if (maxX < (vertexPos.getX() + vertexSize.getWidth()))
+ maxX = vertexPos.getX() + vertexSize.getWidth();
+
+ if (maxY < (vertexPos.getY() + vertexSize.getHeight()))
+ maxY = vertexPos.getY() + vertexSize.getHeight();
+ }
+
+ Rectangle boundingBox = new Rectangle((int) minX, (int) minY, (int) (maxX - minX),
+ (int) (maxY - minY));
+
+ return boundingBox;
+ }
+
+ return null;
+ }
+
+ /******************************************************************************/
+ private Rectangle getBoundingBox() {
+ return getBoundingBox(cellList);
+ }
+
+ /******************************************************************************/
+ public static abstract class MathExtensions {
+ /**************************************************************************/
+ /**
+ * Extracts the leading sign of x.
+ *
+ * @param x Any double value.
+ * @return If x has a positive value <code>-1.0</code>, for <code>x = 0.0</code>
+ * here comes <code>0.0</code> and if x has a negative the method returns
+ * <code>-1.0</code>.
+ */
+ public static double sgn(double x) {
+ if (x < 0.0) {
+ return -1.0;
+ } else if (x > 0.0) {
+ return 1.0;
+ } else {
+ return 0.0;
+ }
+ }
+
+ /**************************************************************************/
+ /**
+ * Computes the absolute value of <code>v</code>. Assuming <code>v</code>
+ * is a mathematical Vector, pointing from Point Zero to the Point, represented
+ * by <code>x</code> and <code>y</code> in v, then this method returns the
+ * length of v.
+ * <p><blockquote><blockquote><code>
+ * return sqrt( v.x� + v.y� )
+ * </code></blockquote></blockquote>
+ * @param v Point the Vector is pointing at, coming from the point
+ * <code>(0;0)</code>.
+ * @return Length of the mathematical Vector v, computed by Pytagoras's
+ * theorem.
+ */
+ public static double abs(Point2D.Double v) {
+ return Math.sqrt(getTransposed(v, v));
+ }
+
+ /**************************************************************************/
+ /**
+ * Computes the absolute value of a Vector, running from the
+ * Point <code>(0;0)</code> to the Point <code>(x;y)</code>. This is the length
+ * of that Vector.
+ * <p><blockquote><blockquote><code>
+ * return sqrt( v.x� + v.y� )
+ * </code></blockquote></blockquote>
+ * @param x Length of one Karthese. Between x and y is an Angle of 90�
+ * @param y Length of the other Karthese. Between x and y is an Angle of 90�
+ * @return Length of the Hypothenuse.
+ */
+ public static double abs(double x, double y) {
+ return (double) Math.sqrt((x * x) + (y * y));
+ }
+
+ /**************************************************************************/
+ /**
+ * Calculates the angle between v1 and v2. Assuming that v1 and v2 are
+ * mathematical Vectors, leading from the Point <code>(0;0)</code> to
+ * their coordinates, the angle in <code>(0;0)</code> is calculated.
+ * <p><blockquote><blockquote><code>
+ * return arccos( ( v1.x*v2.x + v1.y*v2.y ) / ( sqrt( v1.x� + v1.y� ) *
+ * sqrt( v2.x� + v2.y� ) ) )
+ * </code></blockquote></blockquote>
+ * @param v1 One of two Vectors leading from <code>(0;0)</code> to
+ * <code>(v1.x;v1.y)</code>
+ * @param v2 One of two Vectors leading from <code>(0;0)</code> to
+ * <code>(v2.x;v2.y)</code>
+ * @return The Angle between the two vectors
+ */
+ public static double angleBetween(Point2D.Double v1, Point2D.Double v2) {
+ double xty = getTransposed(v1, v2);
+ double lx = Math.sqrt(getTransposed(v1, v1));
+ double ly = Math.sqrt(getTransposed(v2, v2));
+ double result = xty / (lx * ly);
+
+ if (result > 1.0)
+ result = 1.0; //gleicht rundungsfehler aus
+
+ if (result < -1.0)
+ result = -1.0; //gleicht rundungsfehler aus
+
+ return Math.acos(result);
+ }
+
+ /**************************************************************************/
+ /**
+ * Calculates the Transposed of v1 and v2. It is assumed, that v1 and v2 are
+ * mathematical Vectors, leading from the Point <code>(0;0)</code> to
+ * their coordinates.
+ * <p><blockquote><blockquote><code>
+ * return v1.x * v2.x + v1.y * v2.y
+ * </code></blockquote></blockquote>
+ * @param v1 Vector, leading from <code>(0;0)</code> to the coordinates of
+ * the point.
+ * @param v2 Vector, leading from <code>(0;0)</code> to the coordinates of
+ * the point.
+ * @return Transposed from v1 and v2.
+ */
+ public static double getTransposed(Point2D.Double v1, Point2D.Double v2) {
+ return (v1.getX() * v2.getX()) + (v1.getY() * v2.getY());
+ }
+
+ /**************************************************************************/
+ /**
+ * Returns the euclidean Distance between two Points in a 2D cartesian
+ * coordinate system. The euclidean Distance is calculated in the following way:
+ * <p>
+ * <blockquote><blockquote><code>
+ * sqrt( (p1.x - p2.x)� + (p1.y - p2.y)� )
+ * </code></blockquote></blockquote>
+ * @param p1 First of two Points, the Distance should be calculated between.
+ * @param p2 Second of two Points, the Distance should be calculated between.
+ * @return Distance between p1 and p2, calculated in the euclidean way.
+ */
+ public static double getEuclideanDistance(Point2D.Double p1, Point2D.Double p2) {
+ return Math.sqrt(((p1.x - p2.x) * (p1.x - p2.x)) + ((p1.y - p2.y) * (p1.y - p2.y)));
+ }
+
+ /**************************************************************************/
+ public static Point2D.Double getNormalizedVector(Point2D.Double v) {
+ double length = abs(v);
+
+ return new Point2D.Double(v.x / length, v.y / length);
+ }
+
+ /**************************************************************************/
+ }
+
+ /**
+ * @return Returns the isOptimizer.
+ */
+ public boolean isOptimizer() {
+ return isOptimizer;
+ }
+
+ /**
+ * @return Returns the presetConfig.
+ */
+ public Properties getPresetConfig() {
+ return presetConfig;
+ }
+
+ /**
+ * @param presetConfig The presetConfig to set.
+ */
+ public void setPresetConfig(Properties presetConfig) {
+ this.presetConfig = presetConfig;
+ loadConfiguration(CONFIG_KEY_RUN);
+ }
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/layout/AnnealingLayoutSettings.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/layout/AnnealingLayoutSettings.java
new file mode 100644
index 0000000..aae10ce
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/layout/AnnealingLayoutSettings.java
@@ -0,0 +1,2087 @@
+/*
+ * @(#)AnnealingLayoutConfigurationDialog.java 1.0 12.08.2003
+ *
+ * Copyright (C) 2004-2005 Gaudenz Alder
+ * All rights reserved.
+ *
+ * This library is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation; either
+ * version 2.1 of the License, or (at your option) any later version.
+ *
+ * This library is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this library; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+ *
+ */
+package org.jgraph.layout;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.GridLayout;
+import java.awt.Insets;
+import java.awt.Rectangle;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import java.util.ArrayList;
+import java.util.Properties;
+
+import javax.swing.BorderFactory;
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JComboBox;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTabbedPane;
+import javax.swing.JTextField;
+
+
+/**
+ * @author winkler
+ * @author sven luzar
+ *
+ */
+public class AnnealingLayoutSettings extends JPanel implements JGraphLayoutSettings {
+ /**
+ *
+ */
+ public final static String KEY_TITLE = "Simulated Annealing";
+
+ /**
+ *
+ */
+ public final static String KEY_CONFIG_NAME = "CONFIG_NAME";
+
+ /**
+ *
+ */
+ public final static String KEY_INIT_TEMPERATURE = "Start Temperature";
+
+ /**
+ *
+ */
+ public final static String KEY_MIN_TEMPERATURE = "min. Temperature";
+
+ /**
+ *
+ */
+ public final static String KEY_MIN_DISTANCE = "min. Distance";
+
+ /**
+ *
+ */
+ public final static String KEY_TEMP_SCALE_FACTOR = "Temperature Scalefactor";
+
+ /**
+ *
+ */
+ public final static String KEY_COMPUTE_PERMUTATION = "should compute per Permutation";
+
+ /**
+ *
+ */
+ public final static String KEY_IS_UPHILL_MOVE_ALLOWED = "are Uphill-Moves allowed";
+
+ /**
+ *
+ */
+ public final static String KEY_MAX_ROUNDS = "max. Rounds";
+
+ /**
+ *
+ */
+ public final static String KEY_TRIES_PER_CELL = "tries per cell";
+
+ /**
+ *
+ */
+ public final static String KEY_COST_FUNCTION_CONFIG = "Costfunction Config";
+
+ /**
+ *
+ */
+ public final static String KEY_LAMBDA = "Lambda";
+
+ /**
+ *
+ */
+ public final static String KEY_BOUNDS = "Bounds of resulting graph";
+
+ /**
+ *
+ */
+ public final static String KEY_LAYOUT_UPDATE_INIT_TEMPERATURE = "Layout Update Start Temperature";
+
+ /**
+ *
+ */
+ public final static String KEY_LAYOUT_UPDATE_MIN_TEMPERATURE = "Layout Update min. Temperature";
+
+ /**
+ *
+ */
+ public final static String KEY_LAYOUT_UPDATE_MIN_DISTANCE = "Layout Update min. Distance";
+
+ /**
+ *
+ */
+ public final static String KEY_LAYOUT_UPDATE_TEMP_SCALE_FACTOR = "Layout Update Temperature Scalefactor";
+
+ /**
+ *
+ */
+ public final static String KEY_LAYOUT_UPDATE_COMPUTE_PERMUTATION = "Layout Update should compute per Permutation";
+
+ /**
+ *
+ */
+ public final static String KEY_LAYOUT_UPDATE_IS_UPHILL_MOVE_ALLOWED = "Layout Update are Uphill-Moves allowed";
+
+ /**
+ *
+ */
+ public final static String KEY_LAYOUT_UPDATE_MAX_ROUNDS = "Layout Update max. Rounds";
+
+ /**
+ *
+ */
+ public final static String KEY_LAYOUT_UPDATE_TRIES_PER_CELL = "Layout Update tries per cell";
+
+ /**
+ *
+ */
+ public final static String KEY_LAYOUT_UPDATE_COST_FUNCTION_CONFIG = "Layout Update Costfunction Config";
+
+ /**
+ *
+ */
+ public final static String KEY_LAYOUT_UPDATE_LAMBDA = "Layout Update Lambda";
+
+ /**
+ *
+ */
+ public final static String KEY_LAYOUT_UPDATE_BOUNDS = "Layout Update Bounds of resulting graph";
+
+ /**
+ *
+ */
+ public final static String KEY_LAYOUT_UPDATE_METHOD = "Layout Update Method";
+
+ /**
+ *
+ */
+ public final static String KEY_LAYOUT_UPDATE_METHOD_NEIGHBORS_ONLY = "Layout Update Method Neighbors only";
+
+ /**
+ *
+ */
+ public final static String KEY_LAYOUT_UPDATE_METHOD_PERIMETER = "Layout Update Method Perimeter";
+
+ /**
+ *
+ */
+ public final static String KEY_LAYOUT_UPDATE_METHOD_NEIGHBORS_DEPTH = "Layout Update Method Neighbors depth";
+
+ /**
+ *
+ */
+ public final static String KEY_LAYOUT_UPDATE_METHOD_PERIMETER_RADIUS = "Layout Update Method Perimeter radius";
+
+ /**
+ *
+ */
+ public final static String KEY_LAYOUT_UPDATE_METHOD_PERIMETER_RADIUS_INCREASE = "Layout Update Method Perimeter radius increase";
+
+ /**
+ *
+ */
+ public final static String KEY_LAYOUT_UPDATE_ENABLED = "Layout Update enabled";
+
+ /**
+ *
+ */
+ public final static String KEY_LAYOUT_UPDATE_CLUSTERING_ENABLED = "Layout Update clustering enabled";
+
+ /**
+ *
+ */
+ public final static String KEY_LAYOUT_UPDATE_CLUSTERING_FACTOR = "Layout Update clustering factor";
+
+ /**
+ *
+ */
+ public final static String KEY_LAYOUT_UPDATE_CLUSTERING_MOVE_SCALE = "Layout Update clustering move scaling factor";
+ protected AnnealingLayoutAlgorithm layout;
+ private JTextField tf_initTemperature;
+ private JTextField tf_minTemperature;
+ private JTextField tf_minDistance;
+ private JTextField tf_tempScaleFactor;
+ private JTextField tf_maxRounds;
+ private JTextField tf_triesPerCell;
+ private JTextField tf_lambdaNodeDistribution;
+ private JTextField tf_lambdaBorderline;
+ private JTextField tf_lambdaEdgeLength;
+ private JTextField tf_lambdaEdgeCrossing;
+ private JTextField tf_lambdaEdgeDistribution;
+ private JTextField tf_lambdaNodeDistance;
+ private JTextField tf_boundsWidth;
+ private JTextField tf_boundsHeight;
+ private JCheckBox cb_computePermutation;
+ private JCheckBox cb_uphillMovesAllowed;
+ private JCheckBox cb_useNodeDistribution;
+ private JCheckBox cb_useBorderline;
+ private JCheckBox cb_useEdgeLength;
+ private JCheckBox cb_useEdgeCrossing;
+ private JCheckBox cb_useEdgeDistribution;
+ private JCheckBox cb_useNodeDistance;
+ private JButton button_takeViewportSize;
+ private JCheckBox cb_enableLayoutUpdate;
+ private JTextField tf_lu_initTemperature;
+ private JTextField tf_lu_minTemperature;
+ private JTextField tf_lu_minDistance;
+ private JTextField tf_lu_tempScaleFactor;
+ private JTextField tf_lu_maxRounds;
+ private JTextField tf_lu_triesPerCell;
+ private JTextField tf_lu_lambdaNodeDistribution;
+ private JTextField tf_lu_lambdaBorderline;
+ private JTextField tf_lu_lambdaEdgeLength;
+ private JTextField tf_lu_lambdaEdgeCrossing;
+ private JTextField tf_lu_lambdaEdgeDistribution;
+ private JTextField tf_lu_lambdaNodeDistance;
+ private JTextField tf_lu_boundsWidth;
+ private JTextField tf_lu_boundsHeight;
+ private JTextField tf_lu_method_neighborsDepth;
+ private JTextField tf_lu_method_perimeterRadius;
+ private JTextField tf_lu_method_perimeterRadiusInc;
+ private JTextField tf_lu_clustering_factor;
+ private JTextField tf_lu_clustering_moveScale;
+ private JCheckBox cb_lu_computePermutation;
+ private JCheckBox cb_lu_uphillMovesAllowed;
+ private JCheckBox cb_lu_useNodeDistribution;
+ private JCheckBox cb_lu_useBorderline;
+ private JCheckBox cb_lu_useEdgeLength;
+ private JCheckBox cb_lu_useEdgeCrossing;
+ private JCheckBox cb_lu_useEdgeDistribution;
+ private JCheckBox cb_lu_useNodeDistance;
+ private JCheckBox cb_lu_clustering_enable;
+ private JButton button_lu_takeViewportSize;
+ private JComboBox comb_loadPreSets;
+ private JComboBox comb_lu_Method;
+ protected Properties[] preSetConfigs;
+ private JPanel panelSurface;
+ private JPanel panelLUSurface;
+ private JTabbedPane tp_main;
+ JScrollPane panelSurfaceWrapper;
+ JScrollPane panelLUSurfaceWrapper;
+ private boolean isOptimizer;
+
+ /******************************************************************************/
+ /**
+ * Creates new form AnnealingLayoutConfigurationDialog
+ */
+ public AnnealingLayoutSettings(AnnealingLayoutAlgorithm layout, boolean isOptimizationAlgorithm) {
+ this.layout = layout;
+
+ // Populate presets
+ Properties[] config = new Properties[2];
+
+ config[0] = new Properties();
+ config[0].put(KEY_CONFIG_NAME, "Default Values");
+ config[0].put(KEY_INIT_TEMPERATURE, "300.0");
+ config[0].put(KEY_MIN_TEMPERATURE, "2.0");
+ config[0].put(KEY_MIN_DISTANCE, "50.0");
+ config[0].put(KEY_TEMP_SCALE_FACTOR, "0.95");
+ config[0].put(KEY_COMPUTE_PERMUTATION, "true");
+ config[0].put(KEY_IS_UPHILL_MOVE_ALLOWED, "true");
+ config[0].put(KEY_MAX_ROUNDS, "10000");
+ config[0].put(KEY_TRIES_PER_CELL, "8");
+ config[0].put(KEY_COST_FUNCTION_CONFIG, "111110");
+
+ ArrayList lambda1 = new ArrayList();
+ lambda1.add(new Double(1000.0));
+ lambda1.add(new Double(100000.0));
+ lambda1.add(new Double(0.02));
+ lambda1.add(new Double(2000.0));
+ lambda1.add(new Double(150.0));
+ lambda1.add(new Double(1000000.0));
+ config[0].put(KEY_LAMBDA, lambda1);
+
+ Rectangle bounds1 = new Rectangle(0, 0, 1000, 700);
+ config[0].put(KEY_BOUNDS, bounds1);
+
+ config[0].put(KEY_LAYOUT_UPDATE_ENABLED, "false");
+ config[0].put(KEY_LAYOUT_UPDATE_INIT_TEMPERATURE, "40.0");
+ config[0].put(KEY_LAYOUT_UPDATE_MIN_TEMPERATURE, "2.0");
+ config[0].put(KEY_LAYOUT_UPDATE_MIN_DISTANCE, "50.0");
+ config[0].put(KEY_LAYOUT_UPDATE_TEMP_SCALE_FACTOR, "0.95");
+ config[0].put(KEY_LAYOUT_UPDATE_COMPUTE_PERMUTATION, "true");
+ config[0].put(KEY_LAYOUT_UPDATE_IS_UPHILL_MOVE_ALLOWED, "true");
+ config[0].put(KEY_LAYOUT_UPDATE_MAX_ROUNDS, "10000");
+ config[0].put(KEY_LAYOUT_UPDATE_TRIES_PER_CELL, "8");
+ config[0].put(KEY_LAYOUT_UPDATE_COST_FUNCTION_CONFIG, "111110");
+ config[0].put(KEY_LAYOUT_UPDATE_METHOD, KEY_LAYOUT_UPDATE_METHOD_PERIMETER);
+ config[0].put(KEY_LAYOUT_UPDATE_METHOD_NEIGHBORS_DEPTH, "1");
+ config[0].put(KEY_LAYOUT_UPDATE_METHOD_PERIMETER_RADIUS, "100.0");
+ config[0].put(KEY_LAYOUT_UPDATE_METHOD_PERIMETER_RADIUS_INCREASE, "20.0");
+
+ ArrayList lambdaLU1 = new ArrayList();
+ lambdaLU1.add(new Double(1000.0));
+ lambdaLU1.add(new Double(100000.0));
+ lambdaLU1.add(new Double(0.02));
+ lambdaLU1.add(new Double(2000.0));
+ lambdaLU1.add(new Double(150.0));
+ lambdaLU1.add(new Double(1000000.0));
+ config[0].put(KEY_LAYOUT_UPDATE_LAMBDA, lambdaLU1);
+
+ Rectangle boundsLU1 = new Rectangle(0, 0, 1000, 700);
+ config[0].put(KEY_LAYOUT_UPDATE_BOUNDS, boundsLU1);
+ config[0].put(KEY_LAYOUT_UPDATE_CLUSTERING_ENABLED, "true");
+ config[0].put(KEY_LAYOUT_UPDATE_CLUSTERING_FACTOR, "8.0");
+ config[0].put(KEY_LAYOUT_UPDATE_CLUSTERING_MOVE_SCALE, "0.1");
+
+ config[1] = new Properties();
+ config[1].put(KEY_CONFIG_NAME, "Heavy Values");
+ config[1].put(KEY_INIT_TEMPERATURE, "500.0");
+ config[1].put(KEY_MIN_TEMPERATURE, "0.5");
+ config[1].put(KEY_MIN_DISTANCE, "50.0");
+ config[1].put(KEY_TEMP_SCALE_FACTOR, "0.97");
+ config[1].put(KEY_COMPUTE_PERMUTATION, "true");
+ config[1].put(KEY_IS_UPHILL_MOVE_ALLOWED, "true");
+ config[1].put(KEY_MAX_ROUNDS, "10000");
+ config[1].put(KEY_TRIES_PER_CELL, "8");
+ config[1].put(KEY_COST_FUNCTION_CONFIG, "111111");
+ config[1].put(KEY_BOUNDS, "0.0");
+
+ ArrayList lambda2 = new ArrayList();
+ lambda2.add(new Double(1000.0));
+ lambda2.add(new Double(100000.0));
+ lambda2.add(new Double(0.02));
+ lambda2.add(new Double(2000.0));
+ lambda2.add(new Double(150.0));
+ lambda2.add(new Double(1000000.0));
+ config[1].put(KEY_LAMBDA, lambda2);
+
+ Rectangle bounds2 = new Rectangle(0, 0, 1000, 700);
+ config[1].put(KEY_BOUNDS, bounds2);
+
+ config[1].put(KEY_LAYOUT_UPDATE_ENABLED, "true");
+ config[1].put(KEY_LAYOUT_UPDATE_INIT_TEMPERATURE, "40.0");
+ config[1].put(KEY_LAYOUT_UPDATE_MIN_TEMPERATURE, "2.0");
+ config[1].put(KEY_LAYOUT_UPDATE_MIN_DISTANCE, "50.0");
+ config[1].put(KEY_LAYOUT_UPDATE_TEMP_SCALE_FACTOR, "0.97");
+ config[1].put(KEY_LAYOUT_UPDATE_COMPUTE_PERMUTATION, "true");
+ config[1].put(KEY_LAYOUT_UPDATE_IS_UPHILL_MOVE_ALLOWED, "true");
+ config[1].put(KEY_LAYOUT_UPDATE_MAX_ROUNDS, "10000");
+ config[1].put(KEY_LAYOUT_UPDATE_TRIES_PER_CELL, "8");
+ config[1].put(KEY_LAYOUT_UPDATE_COST_FUNCTION_CONFIG, "111111");
+ config[1].put(KEY_LAYOUT_UPDATE_METHOD, KEY_LAYOUT_UPDATE_METHOD_PERIMETER);
+ config[1].put(KEY_LAYOUT_UPDATE_METHOD_NEIGHBORS_DEPTH, "2");
+ config[1].put(KEY_LAYOUT_UPDATE_METHOD_PERIMETER_RADIUS, "200.0");
+ config[1].put(KEY_LAYOUT_UPDATE_METHOD_PERIMETER_RADIUS_INCREASE, "40.0");
+
+ ArrayList lambdaLU2 = new ArrayList();
+ lambdaLU2.add(new Double(1000.0));
+ lambdaLU2.add(new Double(100000.0));
+ lambdaLU2.add(new Double(0.02));
+ lambdaLU2.add(new Double(2000.0));
+ lambdaLU2.add(new Double(150.0));
+ lambdaLU2.add(new Double(1000000.0));
+ config[1].put(KEY_LAYOUT_UPDATE_LAMBDA, lambdaLU2);
+
+ Rectangle boundsLU2 = new Rectangle(0, 0, 1000, 700);
+ config[1].put(KEY_LAYOUT_UPDATE_BOUNDS, boundsLU2);
+ config[1].put(KEY_LAYOUT_UPDATE_CLUSTERING_ENABLED, "true");
+ config[1].put(KEY_LAYOUT_UPDATE_CLUSTERING_FACTOR, "12.0");
+ config[1].put(KEY_LAYOUT_UPDATE_CLUSTERING_MOVE_SCALE, "0.2");
+
+ isOptimizer = isOptimizationAlgorithm;
+
+ preSetConfigs = config;
+
+ initComponents();
+ // TODO: Replace with revert if implemented
+ action_LoadPreSets(0); //default values
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void revert() {
+ // TODO: Read config from algorithm
+ layout.setPresetConfig(preSetConfigs[0]);
+ action_LoadPreSets(0); //default values
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void apply() {
+ layout.setPresetConfig(getConfiguration());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param config DOCUMENT ME!
+ */
+ public void setConfiguration(Properties config) {
+ // Read config
+ setInitTemperature(Double.parseDouble((String) config.get(KEY_INIT_TEMPERATURE)));
+ setMinTemperature(Double.parseDouble((String) config.get(KEY_MIN_TEMPERATURE)));
+ setMinDistance(Double.parseDouble((String) config.get(KEY_MIN_DISTANCE)));
+ setTemperatureScaleFactor(Double.parseDouble((String) config.get(KEY_TEMP_SCALE_FACTOR)));
+ setComputePermutation(isTrue((String) config.get(KEY_COMPUTE_PERMUTATION)));
+ setUphillMovesAllowed(isTrue((String) config.get(KEY_IS_UPHILL_MOVE_ALLOWED)));
+ setMaxRounds(Integer.parseInt((String) config.get(KEY_MAX_ROUNDS)));
+ setTriesPerCell(Integer.parseInt((String) config.get(KEY_TRIES_PER_CELL)));
+ setCostFunctionConfiguration(Integer.parseInt((String) config.get(KEY_COST_FUNCTION_CONFIG),
+ 2));
+ setLambda((ArrayList) config.get(KEY_LAMBDA));
+ setResultBounds((Rectangle) config.get(KEY_BOUNDS));
+
+ setLayoutUpdateEnabled(isTrue((String) config.get(KEY_LAYOUT_UPDATE_ENABLED)));
+ setLayoutUpdateInitTemperature(Double.parseDouble((String) config.get(KEY_LAYOUT_UPDATE_INIT_TEMPERATURE)));
+ setLayoutUpdateMinTemperature(Double.parseDouble((String) config.get(KEY_LAYOUT_UPDATE_MIN_TEMPERATURE)));
+ setLayoutUpdateMinDistance(Double.parseDouble((String) config.get(KEY_LAYOUT_UPDATE_MIN_DISTANCE)));
+ setLayoutUpdateTemperatureScaleFactor(Double.parseDouble((String) config.get(KEY_LAYOUT_UPDATE_TEMP_SCALE_FACTOR)));
+ setLayoutUpdateComputePermutation(isTrue((String) config.get(KEY_LAYOUT_UPDATE_COMPUTE_PERMUTATION)));
+ setLayoutUpdateUphillMovesAllowed(isTrue((String) config.get(KEY_LAYOUT_UPDATE_IS_UPHILL_MOVE_ALLOWED)));
+ setLayoutUpdateMaxRounds(Integer.parseInt((String) config.get(KEY_LAYOUT_UPDATE_MAX_ROUNDS)));
+ setLayoutUpdateTriesPerCell(Integer.parseInt((String) config.get(KEY_LAYOUT_UPDATE_TRIES_PER_CELL)));
+ setLayoutUpdateCostFunctionConfiguration(Integer.parseInt((String) config.get(KEY_LAYOUT_UPDATE_COST_FUNCTION_CONFIG),
+ 2));
+ setLayoutUpdateLambda((ArrayList) config.get(KEY_LAYOUT_UPDATE_LAMBDA));
+ setLayoutUpdateResultBounds((Rectangle) config.get(KEY_LAYOUT_UPDATE_BOUNDS));
+ setLayoutUpdateMethod((String) config.get(KEY_LAYOUT_UPDATE_METHOD));
+ setLayoutUpdateMethodNeighborsDepth(Integer.parseInt((String) config.get(KEY_LAYOUT_UPDATE_METHOD_NEIGHBORS_DEPTH)));
+ setLayoutUpdateMethodPerimeterRadius(Double.parseDouble((String) config.get(KEY_LAYOUT_UPDATE_METHOD_PERIMETER_RADIUS)));
+ setLayoutUpdateMethodPerimeterRadiusIncrease(Double.parseDouble((String) config.get(KEY_LAYOUT_UPDATE_METHOD_PERIMETER_RADIUS_INCREASE)));
+ setLayoutUpdateClusteringEnabled(isTrue((String) config.get(KEY_LAYOUT_UPDATE_CLUSTERING_ENABLED)));
+ setLayoutUpdateClusteringFactor(Double.parseDouble((String) config.get(KEY_LAYOUT_UPDATE_CLUSTERING_FACTOR)));
+ setLayoutUpdateClusteringMoveScaleFactor(Double.parseDouble((String) config.get(KEY_LAYOUT_UPDATE_CLUSTERING_MOVE_SCALE)));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Properties getConfiguration() {
+ Properties config = new Properties();
+ config.put("CAPTION", KEY_TITLE);
+ config.put(KEY_INIT_TEMPERATURE, String.valueOf(getInitTemperature()));
+ config.put(KEY_MIN_TEMPERATURE, String.valueOf(getMinTemperature()));
+ config.put(KEY_MIN_DISTANCE, String.valueOf(getMinDistance()));
+ config.put(KEY_TEMP_SCALE_FACTOR, String.valueOf(getTemperatureScaleFactor()));
+ config.put(KEY_COMPUTE_PERMUTATION, String.valueOf(getComputePermutation()));
+ config.put(KEY_IS_UPHILL_MOVE_ALLOWED, String.valueOf(getUphillMovesAllowed()));
+ config.put(KEY_MAX_ROUNDS, String.valueOf(getMaxRounds()));
+ config.put(KEY_TRIES_PER_CELL, String.valueOf(getTriesPerCell()));
+ config.put(KEY_COST_FUNCTION_CONFIG,
+ String.valueOf(Integer.toBinaryString(getCostFunctionConfiguration())));
+ config.put(KEY_LAMBDA, getLambda());
+ config.put(KEY_BOUNDS, getResultBounds());
+
+ config.put(KEY_LAYOUT_UPDATE_ENABLED, String.valueOf(getLayoutUpdateEnabled()));
+ config.put(KEY_LAYOUT_UPDATE_INIT_TEMPERATURE,
+ String.valueOf(getLayoutUpdateInitTemperature()));
+ config.put(KEY_LAYOUT_UPDATE_MIN_TEMPERATURE,
+ String.valueOf(getLayoutUpdateMinTemperature()));
+ config.put(KEY_LAYOUT_UPDATE_MIN_DISTANCE, String.valueOf(getLayoutUpdateMinDistance()));
+ config.put(KEY_LAYOUT_UPDATE_TEMP_SCALE_FACTOR,
+ String.valueOf(getLayoutUpdateTemperatureScaleFactor()));
+ config.put(KEY_LAYOUT_UPDATE_COMPUTE_PERMUTATION,
+ String.valueOf(getLayoutUpdateComputePermutation()));
+ config.put(KEY_LAYOUT_UPDATE_IS_UPHILL_MOVE_ALLOWED,
+ String.valueOf(getLayoutUpdateUphillMovesAllowed()));
+ config.put(KEY_LAYOUT_UPDATE_MAX_ROUNDS, String.valueOf(getLayoutUpdateMaxRounds()));
+ config.put(KEY_LAYOUT_UPDATE_TRIES_PER_CELL, String.valueOf(getLayoutUpdateTriesPerCell()));
+ config.put(KEY_LAYOUT_UPDATE_COST_FUNCTION_CONFIG,
+ String.valueOf(Integer.toBinaryString(getLayoutUpdateCostFunctionConfiguration())));
+ config.put(KEY_LAYOUT_UPDATE_LAMBDA, getLayoutUpdateLambda());
+ config.put(KEY_LAYOUT_UPDATE_BOUNDS, getLayoutUpdateResultBounds());
+ config.put(KEY_LAYOUT_UPDATE_METHOD, getLayoutUpdateMethod());
+ config.put(KEY_LAYOUT_UPDATE_METHOD_NEIGHBORS_DEPTH,
+ String.valueOf(getLayoutUpdateMethodNeighborsDepth()));
+ config.put(KEY_LAYOUT_UPDATE_METHOD_PERIMETER_RADIUS,
+ String.valueOf(getLayoutUpdateMethodPerimeterRadius()));
+ config.put(KEY_LAYOUT_UPDATE_METHOD_PERIMETER_RADIUS_INCREASE,
+ String.valueOf(getLayoutUpdateMethodPerimeterRadiusIncrease()));
+ config.put(KEY_LAYOUT_UPDATE_CLUSTERING_ENABLED,
+ String.valueOf(getLayoutUpdateClusteringEnabled()));
+ config.put(KEY_LAYOUT_UPDATE_CLUSTERING_FACTOR,
+ String.valueOf(getLayoutUpdateClusteringFactor()));
+ config.put(KEY_LAYOUT_UPDATE_CLUSTERING_MOVE_SCALE,
+ String.valueOf(getLayoutUpdateClusteringMoveScaleFactor()));
+
+ return config;
+ }
+
+ /******************************************************************************/
+ protected void action_LoadPreSets(int index) {
+ Properties config = preSetConfigs[index];
+
+ tf_initTemperature.setText((String) config.get(KEY_INIT_TEMPERATURE));
+ tf_minTemperature.setText((String) config.get(KEY_MIN_TEMPERATURE));
+ tf_minDistance.setText((String) config.get(KEY_MIN_DISTANCE));
+ tf_tempScaleFactor.setText((String) config.get(KEY_TEMP_SCALE_FACTOR));
+ tf_maxRounds.setText((String) config.get(KEY_MAX_ROUNDS));
+ tf_triesPerCell.setText((String) config.get(KEY_TRIES_PER_CELL));
+
+ ArrayList lambda = (ArrayList) config.get(KEY_LAMBDA);
+ tf_lambdaNodeDistribution.setText(String.valueOf(((Double) lambda.get(0)).doubleValue()));
+ tf_lambdaBorderline.setText(String.valueOf(((Double) lambda.get(1)).doubleValue()));
+ tf_lambdaEdgeLength.setText(String.valueOf(((Double) lambda.get(2)).doubleValue()));
+ tf_lambdaEdgeCrossing.setText(String.valueOf(((Double) lambda.get(3)).doubleValue()));
+ tf_lambdaEdgeDistribution.setText(String.valueOf(((Double) lambda.get(4)).doubleValue()));
+ tf_lambdaNodeDistance.setText(String.valueOf(((Double) lambda.get(5)).doubleValue()));
+
+ Rectangle bounds = (Rectangle) config.get(KEY_BOUNDS);
+ tf_boundsWidth.setText(String.valueOf((int) bounds.getWidth()));
+ tf_boundsHeight.setText(String.valueOf((int) bounds.getHeight()));
+
+ cb_computePermutation.setSelected(isTrue((String) config.get(KEY_COMPUTE_PERMUTATION)));
+ cb_uphillMovesAllowed.setSelected(isTrue((String) config.get(KEY_IS_UPHILL_MOVE_ALLOWED)));
+
+ int costFunctionConfig = Integer.parseInt((String) config.get(KEY_COST_FUNCTION_CONFIG), 2);
+ setCostFunctionConfiguration(costFunctionConfig);
+
+ cb_enableLayoutUpdate.setSelected(isTrue((String) config.get(KEY_LAYOUT_UPDATE_ENABLED)));
+
+ tf_lu_initTemperature.setText((String) config.get(KEY_LAYOUT_UPDATE_INIT_TEMPERATURE));
+ tf_lu_minTemperature.setText((String) config.get(KEY_LAYOUT_UPDATE_MIN_TEMPERATURE));
+ tf_lu_minDistance.setText((String) config.get(KEY_LAYOUT_UPDATE_MIN_DISTANCE));
+ tf_lu_tempScaleFactor.setText((String) config.get(KEY_LAYOUT_UPDATE_TEMP_SCALE_FACTOR));
+ tf_lu_maxRounds.setText((String) config.get(KEY_LAYOUT_UPDATE_MAX_ROUNDS));
+ tf_lu_triesPerCell.setText((String) config.get(KEY_LAYOUT_UPDATE_TRIES_PER_CELL));
+
+ ArrayList lambdaLU = (ArrayList) config.get(KEY_LAYOUT_UPDATE_LAMBDA);
+ tf_lu_lambdaNodeDistribution.setText(String.valueOf(((Double) lambdaLU.get(0)).doubleValue()));
+ tf_lu_lambdaBorderline.setText(String.valueOf(((Double) lambdaLU.get(1)).doubleValue()));
+ tf_lu_lambdaEdgeLength.setText(String.valueOf(((Double) lambdaLU.get(2)).doubleValue()));
+ tf_lu_lambdaEdgeCrossing.setText(String.valueOf(((Double) lambdaLU.get(3)).doubleValue()));
+ tf_lu_lambdaEdgeDistribution.setText(String.valueOf(((Double) lambdaLU.get(4)).doubleValue()));
+ tf_lu_lambdaNodeDistance.setText(String.valueOf(((Double) lambdaLU.get(5)).doubleValue()));
+
+ Rectangle boundsLU = (Rectangle) config.get(KEY_LAYOUT_UPDATE_BOUNDS);
+ tf_lu_boundsWidth.setText(String.valueOf((int) boundsLU.getWidth()));
+ tf_lu_boundsHeight.setText(String.valueOf((int) boundsLU.getHeight()));
+
+ cb_lu_computePermutation.setSelected(isTrue((String) config.get(KEY_LAYOUT_UPDATE_COMPUTE_PERMUTATION)));
+ cb_lu_uphillMovesAllowed.setSelected(isTrue((String) config.get(KEY_LAYOUT_UPDATE_IS_UPHILL_MOVE_ALLOWED)));
+
+ int costFunctionConfigLU = Integer.parseInt((String) config.get(KEY_LAYOUT_UPDATE_COST_FUNCTION_CONFIG),
+ 2);
+ setLayoutUpdateCostFunctionConfiguration(costFunctionConfigLU);
+
+ tf_lu_method_neighborsDepth.setText((String) config.get(KEY_LAYOUT_UPDATE_METHOD_NEIGHBORS_DEPTH));
+ tf_lu_method_perimeterRadius.setText((String) config.get(KEY_LAYOUT_UPDATE_METHOD_PERIMETER_RADIUS));
+ tf_lu_method_perimeterRadiusInc.setText((String) config.get(KEY_LAYOUT_UPDATE_METHOD_PERIMETER_RADIUS_INCREASE));
+
+ tf_lu_clustering_factor.setText((String) config.get(KEY_LAYOUT_UPDATE_CLUSTERING_FACTOR));
+ tf_lu_clustering_moveScale.setText((String) config.get(KEY_LAYOUT_UPDATE_CLUSTERING_MOVE_SCALE));
+
+ cb_lu_clustering_enable.setSelected(isTrue((String) config.get(KEY_LAYOUT_UPDATE_CLUSTERING_ENABLED)));
+
+ comb_lu_Method.setSelectedItem(config.get(KEY_LAYOUT_UPDATE_METHOD));
+
+ switchLayoutUpdatePanel();
+ action_CheckBoxSwitch();
+ }
+
+ /******************************************************************************/
+ protected boolean isTrue(String boolValue) {
+ if (boolValue != null) {
+ if ("TRUE".equals(boolValue.toUpperCase())) {
+ return true;
+ } else if ("FALSE".equals(boolValue.toUpperCase())) {
+ return false;
+ }
+ }
+
+ return false;
+ }
+
+ /******************************************************************************/
+ /** Called by pressing the ok button
+ *
+ */
+ protected void check() {
+ boolean isOK = true;
+ ArrayList errList = new ArrayList();
+
+ isOK &= assertDouble(tf_initTemperature.getText(), KEY_INIT_TEMPERATURE, errList);
+ isOK &= assertDouble(tf_minTemperature.getText(), KEY_MIN_TEMPERATURE, errList);
+ isOK &= assertDouble(tf_minDistance.getText(), KEY_MIN_DISTANCE, errList);
+ isOK &= assertDouble(tf_tempScaleFactor.getText(), KEY_TEMP_SCALE_FACTOR, errList);
+ isOK &= assertInteger(tf_maxRounds.getText(), KEY_MAX_ROUNDS, errList);
+ isOK &= assertInteger(tf_triesPerCell.getText(), KEY_TRIES_PER_CELL, errList);
+ isOK &= assertDouble(tf_lambdaNodeDistribution.getText(), "Node Distribution", errList);
+ isOK &= assertDouble(tf_lambdaBorderline.getText(), "Borderline", errList);
+ isOK &= assertDouble(tf_lambdaEdgeLength.getText(), "Edgelength", errList);
+ isOK &= assertDouble(tf_lambdaEdgeCrossing.getText(), "Edgecrossing", errList);
+ isOK &= assertDouble(tf_lambdaEdgeDistribution.getText(), "Node-Edge Distribution", errList);
+ isOK &= assertDouble(tf_lambdaNodeDistance.getText(), "Node Overlapping", errList);
+ isOK &= assertInteger(tf_boundsWidth.getText(), "max. width", errList);
+ isOK &= assertInteger(tf_boundsHeight.getText(), "max. height", errList);
+
+ isOK &= assertDouble(tf_lu_initTemperature.getText(), KEY_LAYOUT_UPDATE_INIT_TEMPERATURE,
+ errList);
+ isOK &= assertDouble(tf_lu_minTemperature.getText(), KEY_LAYOUT_UPDATE_MIN_TEMPERATURE,
+ errList);
+ isOK &= assertDouble(tf_lu_minDistance.getText(), KEY_LAYOUT_UPDATE_MIN_DISTANCE, errList);
+ isOK &= assertDouble(tf_lu_tempScaleFactor.getText(), KEY_LAYOUT_UPDATE_TEMP_SCALE_FACTOR,
+ errList);
+ isOK &= assertInteger(tf_lu_maxRounds.getText(), KEY_LAYOUT_UPDATE_MAX_ROUNDS, errList);
+ isOK &= assertInteger(tf_lu_triesPerCell.getText(), KEY_LAYOUT_UPDATE_TRIES_PER_CELL,
+ errList);
+ isOK &= assertDouble(tf_lu_lambdaNodeDistribution.getText(),
+ "Layout Update Node Distribution", errList);
+ isOK &= assertDouble(tf_lu_lambdaBorderline.getText(), "Layout Update Borderline", errList);
+ isOK &= assertDouble(tf_lu_lambdaEdgeLength.getText(), "Layout Update Edgelength", errList);
+ isOK &= assertDouble(tf_lu_lambdaEdgeCrossing.getText(), "Layout Update Edgecrossing",
+ errList);
+ isOK &= assertDouble(tf_lu_lambdaEdgeDistribution.getText(),
+ "Layout Update Node-Edge Distribution", errList);
+ isOK &= assertDouble(tf_lu_lambdaNodeDistance.getText(), "Layout Update Node Overlapping",
+ errList);
+ isOK &= assertInteger(tf_lu_boundsWidth.getText(), "Layout Update max. width", errList);
+ isOK &= assertInteger(tf_lu_boundsHeight.getText(), "Layout Update max. height", errList);
+ isOK &= assertDouble(tf_lu_clustering_factor.getText(),
+ KEY_LAYOUT_UPDATE_CLUSTERING_FACTOR, errList);
+ isOK &= assertDouble(tf_lu_clustering_moveScale.getText(),
+ KEY_LAYOUT_UPDATE_CLUSTERING_MOVE_SCALE, errList);
+
+ if (isOK) {
+ isOK &= assertDoublePositiveSign(tf_initTemperature.getText(), false,
+ KEY_INIT_TEMPERATURE, errList);
+ isOK &= assertDoublePositiveSign(tf_initTemperature.getText(), false,
+ KEY_INIT_TEMPERATURE, errList);
+ isOK &= assertDoublePositiveSign(tf_minTemperature.getText(), false,
+ KEY_MIN_TEMPERATURE, errList);
+ isOK &= assertDoublePositiveSign(tf_minDistance.getText(), false, KEY_MIN_DISTANCE,
+ errList);
+ isOK &= assertRange(tf_tempScaleFactor.getText(), 0.0, 1.0, false, false,
+ KEY_TEMP_SCALE_FACTOR, errList);
+ isOK &= assertIntegerPositiveSign(tf_maxRounds.getText(), false, KEY_MAX_ROUNDS, errList);
+ isOK &= assertRange(tf_triesPerCell.getText(), 8, 99, true, true, KEY_TRIES_PER_CELL,
+ errList);
+ isOK &= assertIntegerPositiveSign(tf_boundsWidth.getText(), false, "max. width", errList);
+ isOK &= assertIntegerPositiveSign(tf_boundsWidth.getText(), false, "max. height",
+ errList);
+ isOK &= assertDoublePositiveSign(tf_lambdaNodeDistribution.getText(), false,
+ "Node Distribution", errList);
+ isOK &= assertDoublePositiveSign(tf_lambdaBorderline.getText(), false, "Borderline",
+ errList);
+ isOK &= assertDoublePositiveSign(tf_lambdaEdgeLength.getText(), false, "Edgelength",
+ errList);
+ isOK &= assertDoublePositiveSign(tf_lambdaEdgeCrossing.getText(), false,
+ "Edgecrossing", errList);
+ isOK &= assertDoublePositiveSign(tf_lambdaEdgeDistribution.getText(), false,
+ "Node-Edge Distribution", errList);
+ isOK &= assertDoublePositiveSign(tf_lambdaNodeDistance.getText(), false,
+ "Node Overlapping", errList);
+
+ isOK &= assertDoublePositiveSign(tf_lu_initTemperature.getText(), false,
+ KEY_LAYOUT_UPDATE_INIT_TEMPERATURE, errList);
+ isOK &= assertDoublePositiveSign(tf_lu_initTemperature.getText(), false,
+ KEY_LAYOUT_UPDATE_INIT_TEMPERATURE, errList);
+ isOK &= assertDoublePositiveSign(tf_lu_minTemperature.getText(), false,
+ KEY_LAYOUT_UPDATE_MIN_TEMPERATURE, errList);
+ isOK &= assertDoublePositiveSign(tf_lu_minDistance.getText(), false,
+ KEY_LAYOUT_UPDATE_MIN_DISTANCE, errList);
+ isOK &= assertRange(tf_lu_tempScaleFactor.getText(), 0.0, 1.0, false, false,
+ KEY_LAYOUT_UPDATE_TEMP_SCALE_FACTOR, errList);
+ isOK &= assertIntegerPositiveSign(tf_lu_maxRounds.getText(), false,
+ KEY_LAYOUT_UPDATE_MAX_ROUNDS, errList);
+ isOK &= assertRange(tf_lu_triesPerCell.getText(), 8, 99, true, true,
+ KEY_LAYOUT_UPDATE_TRIES_PER_CELL, errList);
+ isOK &= assertIntegerPositiveSign(tf_lu_boundsWidth.getText(), false,
+ "Layout Update max. width", errList);
+ isOK &= assertIntegerPositiveSign(tf_lu_boundsWidth.getText(), false,
+ "Layout Update max. height", errList);
+ isOK &= assertDoublePositiveSign(tf_lu_lambdaNodeDistribution.getText(), false,
+ "Layout Update Node Distribution", errList);
+ isOK &= assertDoublePositiveSign(tf_lu_lambdaBorderline.getText(), false,
+ "Layout Update Borderline", errList);
+ isOK &= assertDoublePositiveSign(tf_lu_lambdaEdgeLength.getText(), false,
+ "Layout Update Edgelength", errList);
+ isOK &= assertDoublePositiveSign(tf_lu_lambdaEdgeCrossing.getText(), false,
+ "Layout Update Edgecrossing", errList);
+ isOK &= assertDoublePositiveSign(tf_lu_lambdaEdgeDistribution.getText(), false,
+ "Layout Update Node-Edge Distribution", errList);
+ isOK &= assertDoublePositiveSign(tf_lu_lambdaNodeDistance.getText(), false,
+ "Layout Update Node Overlapping", errList);
+
+ isOK &= assertDoublePositiveSign(tf_lu_clustering_factor.getText(), false,
+ KEY_LAYOUT_UPDATE_CLUSTERING_FACTOR, errList);
+ isOK &= assertRange(tf_lu_clustering_moveScale.getText(), 0.0, 1.0, false, true,
+ KEY_LAYOUT_UPDATE_CLUSTERING_MOVE_SCALE, errList);
+ }
+
+ if (!isOK) {
+ String errorMsg = new String();
+
+ for (int i = 0; i < errList.size(); i++) {
+ errorMsg += (String) errList.get(i);
+
+ if (i != (errList.size() - 1))
+ errorMsg += "\n";
+ }
+
+ throw new IllegalArgumentException(errorMsg);
+ }
+ }
+
+ /******************************************************************************/
+ /** Initialize the Swing Components
+ */
+ private void initComponents() {
+ panelSurface = new JPanel(new BorderLayout(5, 10));
+ panelSurface.setBackground(new Color(205, 207, 215));
+ setLayout(new BorderLayout(5, 10));
+ tp_main = new JTabbedPane();
+ add(tp_main, BorderLayout.CENTER);
+
+ //getContentPane().add(panelSurface,BorderLayout.CENTER);
+
+ /*
+ if( !isOptimizer )
+ panelSurface.setBorder(
+ BorderFactory.createTitledBorder(
+ BorderFactory.createEtchedBorder(),
+ "Values for main run"));
+ */
+ JPanel panelLabels = new JPanel(new GridLayout(8, 1, 0, 5));
+ JPanel panelFields = new JPanel(new GridLayout(8, 1, 0, 5));
+ JPanel panelVars = new JPanel(new BorderLayout(5, 10));
+ JPanel panelLambda = new JPanel(new GridBagLayout());
+ JPanel panelButtons = new JPanel(new GridLayout(1, 3, 10, 0));
+ JPanel panelBounds = new JPanel(new GridBagLayout());
+ JPanel panelCenter = new JPanel(new BorderLayout(5, 10));
+
+ panelLabels.setOpaque(false);
+ panelFields.setOpaque(false);
+ panelVars.setOpaque(false);
+ panelLambda.setOpaque(false);
+ panelButtons.setOpaque(false);
+ panelBounds.setOpaque(false);
+ panelCenter.setOpaque(false);
+
+ add(panelButtons, BorderLayout.SOUTH);
+
+ panelVars.add(panelLabels, BorderLayout.WEST);
+ panelVars.add(panelFields, BorderLayout.CENTER);
+
+ panelCenter.add(panelLambda, BorderLayout.CENTER);
+ panelCenter.add(panelBounds, BorderLayout.SOUTH);
+
+ panelSurface.add(panelVars, BorderLayout.NORTH);
+ panelSurface.add(panelCenter, BorderLayout.WEST);
+ panelSurface.add(new JPanel(), BorderLayout.SOUTH);
+
+ panelLabels.add(new JLabel("start temperature :"));
+ panelLabels.add(new JLabel("min. temperature :"));
+ panelLabels.add(new JLabel("min. distance :"));
+ panelLabels.add(new JLabel("temperature scaling factor :"));
+ panelLabels.add(new JLabel("max. rounds :"));
+ panelLabels.add(new JLabel("tries per cell :"));
+ panelLabels.add(new JLabel("are uphill-moves allowed :"));
+ panelLabels.add(new JLabel("compute permutations :"));
+
+ tf_initTemperature = new JTextField();
+ tf_minTemperature = new JTextField();
+ tf_minDistance = new JTextField();
+ tf_tempScaleFactor = new JTextField();
+ tf_maxRounds = new JTextField();
+ tf_triesPerCell = new JTextField();
+
+ tf_lambdaNodeDistribution = new JTextField();
+ tf_lambdaBorderline = new JTextField();
+ tf_lambdaEdgeLength = new JTextField();
+ tf_lambdaEdgeCrossing = new JTextField();
+ tf_lambdaEdgeDistribution = new JTextField();
+ tf_lambdaNodeDistance = new JTextField();
+
+ cb_computePermutation = new JCheckBox();
+ cb_uphillMovesAllowed = new JCheckBox();
+ cb_useNodeDistribution = new JCheckBox();
+ cb_useBorderline = new JCheckBox();
+ cb_useEdgeLength = new JCheckBox();
+ cb_useEdgeCrossing = new JCheckBox();
+ cb_useEdgeDistribution = new JCheckBox();
+ cb_useNodeDistance = new JCheckBox();
+
+ cb_computePermutation.setOpaque(false);
+ cb_uphillMovesAllowed.setOpaque(false);
+ cb_useNodeDistribution.setOpaque(false);
+ cb_useBorderline.setOpaque(false);
+ cb_useEdgeLength.setOpaque(false);
+ cb_useEdgeCrossing.setOpaque(false);
+ cb_useEdgeDistribution.setOpaque(false);
+ cb_useNodeDistance.setOpaque(false);
+
+ registerCheckBoxAction(cb_useNodeDistribution);
+ registerCheckBoxAction(cb_useBorderline);
+ registerCheckBoxAction(cb_useEdgeLength);
+ registerCheckBoxAction(cb_useEdgeCrossing);
+ registerCheckBoxAction(cb_useEdgeDistribution);
+ registerCheckBoxAction(cb_useNodeDistance);
+
+ panelFields.add(tf_initTemperature);
+ panelFields.add(tf_minTemperature);
+ panelFields.add(tf_minDistance);
+ panelFields.add(tf_tempScaleFactor);
+ panelFields.add(tf_maxRounds);
+ panelFields.add(tf_triesPerCell);
+
+ panelFields.add(cb_computePermutation);
+ panelFields.add(cb_uphillMovesAllowed);
+
+ panelLambda.add(new JLabel("Costfunction Nodedistribution :"),
+ new GridBagConstraints(0, 0, 1, 1, 0.5, 0.5, GridBagConstraints.WEST,
+ GridBagConstraints.NONE, new Insets(0, 0, 0, 0), 0, 0));
+
+ panelLambda.add(new JLabel("Costfunction Borderline :"),
+ new GridBagConstraints(0, 1, 1, 1, 0.5, 0.5, GridBagConstraints.WEST,
+ GridBagConstraints.NONE, new Insets(0, 0, 0, 0), 0, 0));
+
+ panelLambda.add(new JLabel("Costfunction Edgelength :"),
+ new GridBagConstraints(0, 2, 1, 1, 0.5, 0.5, GridBagConstraints.WEST,
+ GridBagConstraints.NONE, new Insets(0, 0, 0, 0), 0, 0));
+
+ panelLambda.add(new JLabel("Costfunction Edgecrossing :"),
+ new GridBagConstraints(0, 3, 1, 1, 0.5, 0.5, GridBagConstraints.WEST,
+ GridBagConstraints.NONE, new Insets(0, 0, 0, 0), 0, 0));
+
+ panelLambda.add(new JLabel("Costfunction Edge Distribution :"),
+ new GridBagConstraints(0, 4, 1, 1, 0.5, 0.5, GridBagConstraints.WEST,
+ GridBagConstraints.NONE, new Insets(0, 0, 0, 0), 0, 0));
+
+ panelLambda.add(new JLabel("Costfunction Node Overlapping :"),
+ new GridBagConstraints(0, 5, 1, 1, 0.5, 0.5, GridBagConstraints.WEST,
+ GridBagConstraints.NONE, new Insets(0, 0, 0, 0), 0, 0));
+
+ panelLambda.add(cb_useNodeDistribution,
+ new GridBagConstraints(1, 0, 1, 1, 1.0, 1.0, GridBagConstraints.CENTER,
+ GridBagConstraints.NONE, new Insets(0, 20, 0, 0), 0,
+ 0));
+
+ panelLambda.add(cb_useBorderline,
+ new GridBagConstraints(1, 1, 1, 1, 1.0, 1.0, GridBagConstraints.CENTER,
+ GridBagConstraints.NONE, new Insets(0, 20, 0, 0), 0,
+ 0));
+
+ panelLambda.add(cb_useEdgeLength,
+ new GridBagConstraints(1, 2, 1, 1, 1.0, 1.0, GridBagConstraints.CENTER,
+ GridBagConstraints.NONE, new Insets(0, 20, 0, 0), 0,
+ 0));
+
+ panelLambda.add(cb_useEdgeCrossing,
+ new GridBagConstraints(1, 3, 1, 1, 1.0, 1.0, GridBagConstraints.CENTER,
+ GridBagConstraints.NONE, new Insets(0, 20, 0, 0), 0,
+ 0));
+
+ panelLambda.add(cb_useEdgeDistribution,
+ new GridBagConstraints(1, 4, 1, 1, 1.0, 1.0, GridBagConstraints.CENTER,
+ GridBagConstraints.NONE, new Insets(0, 20, 0, 0), 0,
+ 0));
+ panelLambda.add(cb_useNodeDistance,
+ new GridBagConstraints(1, 5, 1, 1, 1.0, 1.0, GridBagConstraints.CENTER,
+ GridBagConstraints.NONE, new Insets(0, 20, 0, 0), 0,
+ 0));
+ panelLambda.add(tf_lambdaNodeDistribution,
+ new GridBagConstraints(2, 0, 1, 1, 1.0, 1.0, GridBagConstraints.EAST,
+ GridBagConstraints.HORIZONTAL,
+ new Insets(0, 0, 0, 0), 0, 0));
+
+ panelLambda.add(tf_lambdaBorderline,
+ new GridBagConstraints(2, 1, 1, 1, 1.0, 1.0, GridBagConstraints.EAST,
+ GridBagConstraints.HORIZONTAL,
+ new Insets(0, 0, 0, 0), 0, 0));
+
+ panelLambda.add(tf_lambdaEdgeLength,
+ new GridBagConstraints(2, 2, 1, 1, 1.0, 1.0, GridBagConstraints.EAST,
+ GridBagConstraints.HORIZONTAL,
+ new Insets(0, 0, 0, 0), 0, 0));
+
+ panelLambda.add(tf_lambdaEdgeCrossing,
+ new GridBagConstraints(2, 3, 1, 1, 1.0, 1.0, GridBagConstraints.EAST,
+ GridBagConstraints.HORIZONTAL,
+ new Insets(0, 0, 0, 0), 0, 0));
+
+ panelLambda.add(tf_lambdaEdgeDistribution,
+ new GridBagConstraints(2, 4, 1, 1, 1.0, 1.0, GridBagConstraints.EAST,
+ GridBagConstraints.HORIZONTAL,
+ new Insets(0, 0, 0, 0), 0, 0));
+ panelLambda.add(tf_lambdaNodeDistance,
+ new GridBagConstraints(2, 5, 1, 1, 1.0, 1.0, GridBagConstraints.EAST,
+ GridBagConstraints.HORIZONTAL,
+ new Insets(0, 0, 0, 0), 0, 0));
+
+ JLabel[] label_AdditionalCF = getAdditionalCostFunctionLabels();
+ JTextField[] tf_AdditionalCF = getAdditionalCostFunctionTextFields();
+ JCheckBox[] cb_AdditionalCF = getAdditionalCostFunctionCheckBoxes();
+
+ for (int i = 0; i < label_AdditionalCF.length; i++)
+ panelLambda.add(label_AdditionalCF[i],
+ new GridBagConstraints(0,
+ AnnealingLayoutAlgorithm.COUT_COSTFUNCTION + i,
+ 1, 1, 0.5, 0.5, GridBagConstraints.WEST,
+ GridBagConstraints.NONE, new Insets(0, 0, 0, 0),
+ 0, 0));
+
+ for (int i = 0; i < cb_AdditionalCF.length; i++)
+ panelLambda.add(cb_AdditionalCF[i],
+ new GridBagConstraints(1,
+ AnnealingLayoutAlgorithm.COUT_COSTFUNCTION + i,
+ 1, 1, 0.5, 0.5, GridBagConstraints.CENTER,
+ GridBagConstraints.NONE,
+ new Insets(0, 20, 0, 0), 0, 0));
+
+ for (int i = 0; i < tf_AdditionalCF.length; i++)
+ panelLambda.add(tf_AdditionalCF[i],
+ new GridBagConstraints(2,
+ AnnealingLayoutAlgorithm.COUT_COSTFUNCTION + i,
+ 1, 1, 0.5, 0.5, GridBagConstraints.EAST,
+ GridBagConstraints.HORIZONTAL,
+ new Insets(0, 0, 0, 0), 0, 0));
+
+ button_takeViewportSize = new JButton("take viewport size");
+ button_takeViewportSize.setOpaque(false);
+
+ JLabel labelBoundsWidth = new JLabel("max. width :");
+ JLabel labelBoundsHeight = new JLabel("max. height :");
+
+ tf_boundsWidth = new JTextField();
+ tf_boundsHeight = new JTextField();
+
+ panelBounds.add(button_takeViewportSize,
+ new GridBagConstraints(0, 0, 1, 2, 0.5, 1.0, GridBagConstraints.SOUTHEAST,
+ GridBagConstraints.HORIZONTAL,
+ new Insets(25, 20, 15, 30), 0, 0));
+
+ panelBounds.add(labelBoundsWidth,
+ new GridBagConstraints(1, 0, 1, 1, 1.0, 1.0, GridBagConstraints.SOUTH,
+ GridBagConstraints.HORIZONTAL,
+ new Insets(15, 0, 5, 0), 0, 0));
+
+ panelBounds.add(labelBoundsHeight,
+ new GridBagConstraints(1, 1, 1, 1, 1.0, 1.0, GridBagConstraints.NORTH,
+ GridBagConstraints.HORIZONTAL,
+ new Insets(0, 0, 0, 0), 0, 0));
+
+ panelBounds.add(tf_boundsWidth,
+ new GridBagConstraints(2, 0, 1, 1, 1.0, 1.0, GridBagConstraints.SOUTH,
+ GridBagConstraints.HORIZONTAL,
+ new Insets(15, 0, 5, 0), 0, 0));
+
+ panelBounds.add(tf_boundsHeight,
+ new GridBagConstraints(2, 1, 1, 1, 1.0, 1.0, GridBagConstraints.NORTH,
+ GridBagConstraints.HORIZONTAL,
+ new Insets(0, 0, 0, 0), 0, 0));
+
+ /*####################################################################*/
+ panelLUSurface = new JPanel(new BorderLayout(5, 10));
+ //panelLUSurface.setBorder(BorderFactory.createTitledBorder(BorderFactory.createEtchedBorder(),"Values for Layout updates"));
+ panelLUSurface.setBackground(new Color(220, 205, 205));
+
+ JPanel panelLULabels = new JPanel(new GridLayout(8, 1, 0, 5));
+ JPanel panelLUFields = new JPanel(new GridLayout(8, 1, 0, 5));
+ JPanel panelLUVars = new JPanel(new BorderLayout(5, 10));
+ JPanel panelLULambda = new JPanel(new GridBagLayout());
+ JPanel panelLUBounds = new JPanel(new GridBagLayout());
+ JPanel panelLUCenter = new JPanel(new BorderLayout(5, 10));
+
+ JPanel panelLUMethod = new JPanel(new BorderLayout(5, 10));
+
+ panelLULabels.setOpaque(false);
+ panelLUFields.setOpaque(false);
+ panelLUVars.setOpaque(false);
+ panelLULambda.setOpaque(false);
+ panelLUBounds.setOpaque(false);
+ panelLUCenter.setOpaque(false);
+ panelLUMethod.setOpaque(false);
+
+ panelLUVars.add(panelLULabels, BorderLayout.WEST);
+ panelLUVars.add(panelLUFields, BorderLayout.CENTER);
+
+ panelLUCenter.add(panelLULambda, BorderLayout.WEST);
+ panelLUCenter.add(panelLUBounds, BorderLayout.SOUTH);
+
+ panelLUSurface.add(panelLUVars, BorderLayout.NORTH);
+ panelLUSurface.add(panelLUCenter, BorderLayout.CENTER);
+ panelLUSurface.add(panelLUMethod, BorderLayout.SOUTH);
+
+ panelLULabels.add(new JLabel("start temperature :"));
+ panelLULabels.add(new JLabel("min. temperature :"));
+ panelLULabels.add(new JLabel("min. distance :"));
+ panelLULabels.add(new JLabel("temperature scaling factor :"));
+ panelLULabels.add(new JLabel("max. rounds :"));
+ panelLULabels.add(new JLabel("tries per cell :"));
+ panelLULabels.add(new JLabel("are uphill-moves allowed :"));
+ panelLULabels.add(new JLabel("compute permutations :"));
+
+ tf_lu_initTemperature = new JTextField();
+ tf_lu_minTemperature = new JTextField();
+ tf_lu_minDistance = new JTextField();
+ tf_lu_tempScaleFactor = new JTextField();
+ tf_lu_maxRounds = new JTextField();
+ tf_lu_triesPerCell = new JTextField();
+
+ tf_lu_lambdaNodeDistribution = new JTextField();
+ tf_lu_lambdaBorderline = new JTextField();
+ tf_lu_lambdaEdgeLength = new JTextField();
+ tf_lu_lambdaEdgeCrossing = new JTextField();
+ tf_lu_lambdaEdgeDistribution = new JTextField();
+ tf_lu_lambdaNodeDistance = new JTextField();
+
+ cb_lu_computePermutation = new JCheckBox();
+ cb_lu_uphillMovesAllowed = new JCheckBox();
+ cb_lu_useNodeDistribution = new JCheckBox();
+ cb_lu_useBorderline = new JCheckBox();
+ cb_lu_useEdgeLength = new JCheckBox();
+ cb_lu_useEdgeCrossing = new JCheckBox();
+ cb_lu_useEdgeDistribution = new JCheckBox();
+ cb_lu_useNodeDistance = new JCheckBox();
+
+ cb_lu_computePermutation.setOpaque(false);
+ cb_lu_uphillMovesAllowed.setOpaque(false);
+ cb_lu_useNodeDistribution.setOpaque(false);
+ cb_lu_useBorderline.setOpaque(false);
+ cb_lu_useEdgeLength.setOpaque(false);
+ cb_lu_useEdgeCrossing.setOpaque(false);
+ cb_lu_useEdgeDistribution.setOpaque(false);
+ cb_lu_useNodeDistance.setOpaque(false);
+
+ registerCheckBoxAction(cb_lu_useNodeDistribution);
+ registerCheckBoxAction(cb_lu_useBorderline);
+ registerCheckBoxAction(cb_lu_useEdgeLength);
+ registerCheckBoxAction(cb_lu_useEdgeCrossing);
+ registerCheckBoxAction(cb_lu_useEdgeDistribution);
+ registerCheckBoxAction(cb_lu_useNodeDistance);
+
+ panelLUFields.add(tf_lu_initTemperature);
+ panelLUFields.add(tf_lu_minTemperature);
+ panelLUFields.add(tf_lu_minDistance);
+ panelLUFields.add(tf_lu_tempScaleFactor);
+ panelLUFields.add(tf_lu_maxRounds);
+ panelLUFields.add(tf_lu_triesPerCell);
+
+ panelLUFields.add(cb_lu_computePermutation);
+ panelLUFields.add(cb_lu_uphillMovesAllowed);
+
+ panelLULambda.add(new JLabel("Costfunction Nodedistribution :"),
+ new GridBagConstraints(0, 0, 1, 1, 0.5, 0.5, GridBagConstraints.WEST,
+ GridBagConstraints.NONE, new Insets(0, 0, 0, 0),
+ 0, 0));
+
+ panelLULambda.add(new JLabel("Costfunction Borderline :"),
+ new GridBagConstraints(0, 1, 1, 1, 0.5, 0.5, GridBagConstraints.WEST,
+ GridBagConstraints.NONE, new Insets(0, 0, 0, 0),
+ 0, 0));
+
+ panelLULambda.add(new JLabel("Costfunction Edgelength :"),
+ new GridBagConstraints(0, 2, 1, 1, 0.5, 0.5, GridBagConstraints.WEST,
+ GridBagConstraints.NONE, new Insets(0, 0, 0, 0),
+ 0, 0));
+
+ panelLULambda.add(new JLabel("Costfunction Edgecrossing :"),
+ new GridBagConstraints(0, 3, 1, 1, 0.5, 0.5, GridBagConstraints.WEST,
+ GridBagConstraints.NONE, new Insets(0, 0, 0, 0),
+ 0, 0));
+
+ panelLULambda.add(new JLabel("Costfunction Edge Distribution :"),
+ new GridBagConstraints(0, 4, 1, 1, 0.5, 0.5, GridBagConstraints.WEST,
+ GridBagConstraints.NONE, new Insets(0, 0, 0, -20),
+ 0, 0));
+
+ panelLULambda.add(new JLabel("Costfunction Node Overlapping :"),
+ new GridBagConstraints(0, 5, 1, 1, 0.5, 0.5, GridBagConstraints.WEST,
+ GridBagConstraints.NONE, new Insets(0, 0, 0, -20),
+ 0, 0));
+ panelLULambda.add(cb_lu_useNodeDistribution,
+ new GridBagConstraints(1, 0, 1, 1, 1.0, 1.0, GridBagConstraints.CENTER,
+ GridBagConstraints.NONE, new Insets(0, 20, 0, 0),
+ 0, 0));
+
+ panelLULambda.add(cb_lu_useBorderline,
+ new GridBagConstraints(1, 1, 1, 1, 1.0, 1.0, GridBagConstraints.CENTER,
+ GridBagConstraints.NONE, new Insets(0, 20, 0, 0),
+ 0, 0));
+
+ panelLULambda.add(cb_lu_useEdgeLength,
+ new GridBagConstraints(1, 2, 1, 1, 1.0, 1.0, GridBagConstraints.CENTER,
+ GridBagConstraints.NONE, new Insets(0, 20, 0, 0),
+ 0, 0));
+
+ panelLULambda.add(cb_lu_useEdgeCrossing,
+ new GridBagConstraints(1, 3, 1, 1, 1.0, 1.0, GridBagConstraints.CENTER,
+ GridBagConstraints.NONE, new Insets(0, 20, 0, 0),
+ 0, 0));
+
+ panelLULambda.add(cb_lu_useEdgeDistribution,
+ new GridBagConstraints(1, 4, 1, 1, 1.0, 1.0, GridBagConstraints.CENTER,
+ GridBagConstraints.NONE, new Insets(0, 20, 0, 0),
+ 0, 0));
+ panelLULambda.add(cb_lu_useNodeDistance,
+ new GridBagConstraints(1, 5, 1, 1, 1.0, 1.0, GridBagConstraints.CENTER,
+ GridBagConstraints.NONE, new Insets(0, 20, 0, 0),
+ 0, 0));
+ panelLULambda.add(tf_lu_lambdaNodeDistribution,
+ new GridBagConstraints(2, 0, 1, 1, 1.0, 1.0, GridBagConstraints.EAST,
+ GridBagConstraints.HORIZONTAL,
+ new Insets(0, 0, 0, 0), 0, 0));
+
+ panelLULambda.add(tf_lu_lambdaBorderline,
+ new GridBagConstraints(2, 1, 1, 1, 1.0, 1.0, GridBagConstraints.EAST,
+ GridBagConstraints.HORIZONTAL,
+ new Insets(0, 0, 0, 0), 0, 0));
+
+ panelLULambda.add(tf_lu_lambdaEdgeLength,
+ new GridBagConstraints(2, 2, 1, 1, 1.0, 1.0, GridBagConstraints.EAST,
+ GridBagConstraints.HORIZONTAL,
+ new Insets(0, 0, 0, 0), 0, 0));
+
+ panelLULambda.add(tf_lu_lambdaEdgeCrossing,
+ new GridBagConstraints(2, 3, 1, 1, 1.0, 1.0, GridBagConstraints.EAST,
+ GridBagConstraints.HORIZONTAL,
+ new Insets(0, 0, 0, 0), 0, 0));
+
+ panelLULambda.add(tf_lu_lambdaEdgeDistribution,
+ new GridBagConstraints(2, 4, 1, 1, 1.0, 1.0, GridBagConstraints.EAST,
+ GridBagConstraints.HORIZONTAL,
+ new Insets(0, 0, 0, 0), 0, 0));
+ panelLULambda.add(tf_lu_lambdaNodeDistance,
+ new GridBagConstraints(2, 5, 1, 1, 1.0, 1.0, GridBagConstraints.EAST,
+ GridBagConstraints.HORIZONTAL,
+ new Insets(0, 0, 0, 0), 0, 0));
+
+ JLabel[] label_lu_AdditionalCF = getAdditionalLUCostFunctionLabels();
+ JTextField[] tf_lu_AdditionalCF = getAdditionalLUCostFunctionTextFields();
+ JCheckBox[] cb_lu_AdditionalCF = getAdditionalLUCostFunctionCheckBoxes();
+
+ for (int i = 0; i < label_lu_AdditionalCF.length; i++)
+ panelLULambda.add(label_lu_AdditionalCF[i],
+ new GridBagConstraints(0,
+ AnnealingLayoutAlgorithm.COUT_COSTFUNCTION + i,
+ 1, 1, 0.5, 0.5, GridBagConstraints.WEST,
+ GridBagConstraints.NONE,
+ new Insets(0, 0, 0, 0), 0, 0));
+
+ for (int i = 0; i < cb_lu_AdditionalCF.length; i++)
+ panelLULambda.add(cb_lu_AdditionalCF[i],
+ new GridBagConstraints(1,
+ AnnealingLayoutAlgorithm.COUT_COSTFUNCTION + i,
+ 1, 1, 0.5, 0.5, GridBagConstraints.CENTER,
+ GridBagConstraints.NONE,
+ new Insets(0, 20, 0, 0), 0, 0));
+
+ for (int i = 0; i < tf_lu_AdditionalCF.length; i++)
+ panelLULambda.add(tf_lu_AdditionalCF[i],
+ new GridBagConstraints(2,
+ AnnealingLayoutAlgorithm.COUT_COSTFUNCTION + i,
+ 1, 1, 0.5, 0.5, GridBagConstraints.EAST,
+ GridBagConstraints.HORIZONTAL,
+ new Insets(0, 0, 0, 0), 0, 0));
+
+ button_lu_takeViewportSize = new JButton("take viewport size");
+ button_lu_takeViewportSize.setOpaque(false);
+
+ JLabel labelLUBoundsWidth = new JLabel("max. width :");
+ JLabel labelLUBoundsHeight = new JLabel("max. height :");
+
+ tf_lu_boundsWidth = new JTextField();
+ tf_lu_boundsHeight = new JTextField();
+
+ panelLUBounds.add(button_lu_takeViewportSize,
+ new GridBagConstraints(0, 0, 1, 2, 0.5, 1.0,
+ GridBagConstraints.SOUTHEAST,
+ GridBagConstraints.HORIZONTAL,
+ new Insets(25, 20, 15, 30), 0, 0));
+
+ panelLUBounds.add(labelLUBoundsWidth,
+ new GridBagConstraints(1, 0, 1, 1, 1.0, 1.0, GridBagConstraints.SOUTH,
+ GridBagConstraints.HORIZONTAL,
+ new Insets(15, 0, 5, 0), 0, 0));
+
+ panelLUBounds.add(labelLUBoundsHeight,
+ new GridBagConstraints(1, 1, 1, 1, 1.0, 1.0, GridBagConstraints.NORTH,
+ GridBagConstraints.HORIZONTAL,
+ new Insets(0, 0, 0, 0), 0, 0));
+
+ panelLUBounds.add(tf_lu_boundsWidth,
+ new GridBagConstraints(2, 0, 1, 1, 1.0, 1.0, GridBagConstraints.SOUTH,
+ GridBagConstraints.HORIZONTAL,
+ new Insets(15, 0, 5, 0), 0, 0));
+
+ panelLUBounds.add(tf_lu_boundsHeight,
+ new GridBagConstraints(2, 1, 1, 1, 1.0, 1.0, GridBagConstraints.NORTH,
+ GridBagConstraints.HORIZONTAL,
+ new Insets(0, 0, 0, 0), 0, 0));
+
+ tf_lu_method_neighborsDepth = new JTextField();
+ tf_lu_method_perimeterRadius = new JTextField();
+ tf_lu_method_perimeterRadiusInc = new JTextField();
+
+ comb_lu_Method = new JComboBox();
+ comb_lu_Method.addItem(KEY_LAYOUT_UPDATE_METHOD_NEIGHBORS_ONLY);
+ comb_lu_Method.addItem(KEY_LAYOUT_UPDATE_METHOD_PERIMETER);
+ comb_lu_Method.setBackground(panelLUSurface.getBackground());
+ comb_lu_Method.setOpaque(false);
+ comb_lu_Method.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ action_CheckBoxSwitch();
+ }
+ });
+
+ JPanel panelLUMethodLabels = new JPanel(new GridLayout(4, 1, 10, 5));
+ JPanel panelLUMethodFields = new JPanel(new GridLayout(4, 1, 10, 5));
+
+ panelLUMethodLabels.setOpaque(false);
+ panelLUMethodFields.setOpaque(false);
+
+ panelLUMethod.setBorder(BorderFactory.createTitledBorder(BorderFactory
+ [...]
+ "Layout Update Method"));
+
+ panelLUMethod.add(panelLUMethodLabels, BorderLayout.WEST);
+ panelLUMethod.add(panelLUMethodFields, BorderLayout.EAST);
+
+ panelLUMethodLabels.add(new JLabel("Method for Layout Updates :"));
+ panelLUMethodLabels.add(new JLabel("Edge Distance to Neighbors :"));
+ panelLUMethodLabels.add(new JLabel("Optical Distance to Neighbors :"));
+ panelLUMethodLabels.add(new JLabel("Increase of optical Distance :"));
+
+ panelLUMethodFields.add(comb_lu_Method);
+ panelLUMethodFields.add(tf_lu_method_neighborsDepth);
+ panelLUMethodFields.add(tf_lu_method_perimeterRadius);
+ panelLUMethodFields.add(tf_lu_method_perimeterRadiusInc);
+
+ JPanel panelLUMethodClustering = new JPanel(new GridLayout(3, 2, 10, 5));
+ JPanel panelLUMethodClusteringSwitch = new JPanel(new GridLayout(1, 2, 10, 5));
+ JPanel panelLUMethodClusteringEmpty = new JPanel();
+
+ panelLUMethodClustering.setOpaque(false);
+ panelLUMethodClusteringSwitch.setOpaque(false);
+ panelLUMethodClusteringEmpty.setOpaque(false);
+
+ tf_lu_clustering_factor = new JTextField();
+ cb_lu_clustering_enable = new JCheckBox();
+ tf_lu_clustering_moveScale = new JTextField();
+ cb_lu_clustering_enable.setOpaque(false);
+ registerCheckBoxAction(cb_lu_clustering_enable);
+
+ panelLUMethodClusteringSwitch.add(new JLabel("on/off"));
+ panelLUMethodClusteringSwitch.add(cb_lu_clustering_enable);
+
+ panelLUMethodClustering.setBorder(BorderFactory.createTitledBorder(BorderFactory
+ [...]
+ "Clustering"));
+ panelLUMethodClustering.add(panelLUMethodClusteringSwitch);
+ panelLUMethodClustering.add(panelLUMethodClusteringEmpty);
+ panelLUMethodClustering.add(new JLabel("Clustering factor :"));
+ panelLUMethodClustering.add(tf_lu_clustering_factor);
+ panelLUMethodClustering.add(new JLabel("Cluster move scale factor :"));
+ panelLUMethodClustering.add(tf_lu_clustering_moveScale);
+ panelLUMethod.add(panelLUMethodClustering, BorderLayout.SOUTH);
+
+ /*####################################################################*/
+ cb_enableLayoutUpdate = new JCheckBox();
+
+ if (!isOptimizer) {
+ JPanel panelGlobal = new JPanel(new GridBagLayout());
+ add(panelGlobal, BorderLayout.NORTH);
+
+ cb_enableLayoutUpdate.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ switchLayoutUpdatePanel();
+ }
+ });
+ panelGlobal.add(new JLabel("Run permanent:"),
+ new GridBagConstraints(0, 0, 1, 1, 0.0, 0.0, GridBagConstraints.WEST,
+ GridBagConstraints.NONE,
+ new Insets(0, 5, 0, 30), 0, 0));
+ panelGlobal.add(cb_enableLayoutUpdate,
+ new GridBagConstraints(1, 0, 1, 1, 1.0, 0.0, GridBagConstraints.WEST,
+ GridBagConstraints.HORIZONTAL,
+ new Insets(0, 0, 0, 0), 0, 0));
+ }
+
+ comb_loadPreSets = new JComboBox();
+
+ for (int i = 0; i < preSetConfigs.length; i++)
+ comb_loadPreSets.addItem(preSetConfigs[i].get(KEY_CONFIG_NAME));
+
+ panelButtons.add(comb_loadPreSets);
+
+ comb_loadPreSets.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ action_LoadPreSets(((JComboBox) e.getSource()).getSelectedIndex());
+ }
+ });
+
+ panelSurfaceWrapper = new JScrollPane(panelSurface);
+
+ Dimension innerSize = new Dimension(550, 350);
+ panelSurfaceWrapper.setPreferredSize(innerSize);
+ panelLUSurfaceWrapper = new JScrollPane(panelLUSurface);
+ panelLUSurfaceWrapper.setPreferredSize(innerSize);
+
+ tp_main.addTab("Values for main run", panelSurfaceWrapper);
+
+ setToolTipTexts();
+ }
+
+ /******************************************************************************/
+ private void registerCheckBoxAction(JCheckBox cb) {
+ cb.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ action_CheckBoxSwitch();
+ }
+ });
+ }
+
+ /******************************************************************************/
+ protected JLabel[] getAdditionalCostFunctionLabels() {
+ return new JLabel[0];
+ }
+
+ /******************************************************************************/
+ protected JCheckBox[] getAdditionalCostFunctionCheckBoxes() {
+ return new JCheckBox[0];
+ }
+
+ /******************************************************************************/
+ protected JTextField[] getAdditionalCostFunctionTextFields() {
+ return new JTextField[0];
+ }
+
+ /******************************************************************************/
+ protected JLabel[] getAdditionalLUCostFunctionLabels() {
+ return new JLabel[0];
+ }
+
+ /******************************************************************************/
+ protected JCheckBox[] getAdditionalLUCostFunctionCheckBoxes() {
+ return new JCheckBox[0];
+ }
+
+ /******************************************************************************/
+ protected JTextField[] getAdditionalLUCostFunctionTextFields() {
+ return new JTextField[0];
+ }
+
+ /******************************************************************************/
+ private void switchLayoutUpdatePanel() {
+ if (cb_enableLayoutUpdate.isSelected() && !isOptimizer) {
+ tp_main.addTab("Values for Layout updates", panelLUSurfaceWrapper);
+ } else {
+ tp_main.remove(panelLUSurfaceWrapper);
+ }
+ }
+
+ /******************************************************************************/
+ protected void setToolTipTexts() {
+ tf_initTemperature.setToolTipText("starting value for temperature");
+ tf_minTemperature.setToolTipText("if temperature reaches this value, the algorithm finishes");
+ tf_minDistance.setToolTipText("minimal distance, vertices should have to each other before causing more costs");
+ tf_tempScaleFactor.setToolTipText("factor the temperature is multiplied every round");
+ tf_maxRounds.setToolTipText("maximum number of rounds, if not finished by temperature before");
+ tf_triesPerCell.setToolTipText("number of segments around a vertex. The vertex will be placed on each to find a new position. Costs are calculated for every segment, so don't choose your value too high");
+ tf_lambdaNodeDistribution.setToolTipText("Factor, the costs of the node distribution function are multiplied. Low distances between Vertices make heigher costs");
+ tf_lambdaBorderline.setToolTipText("Factor, the costs of the borderline function are multiplied. Border can be configured with \"max. width\" and \"max. height\" below. Vertices near or beyond cause higher costs");
+ tf_lambdaEdgeLength.setToolTipText("Factor, the costs of the edge length function are multiplied. Long edges cause higher costs");
+ tf_lambdaEdgeCrossing.setToolTipText("Factor, the costs of the edge crossing function are multiplied. For every crossing Edge the costs increase");
+ tf_lambdaEdgeDistribution.setToolTipText("Factor, the costs of the edge distribution function are multiplied. This function evaluates the distances between edges and vertices. A low distance increases the costs");
+ tf_lambdaNodeDistance.setToolTipText("Factor, the costs of the node distance function are multiplied. Nodes to close to each other or overlapping increases the costs");
+ tf_boundsWidth.setToolTipText("width of the field the graph should be layouted on");
+ tf_boundsHeight.setToolTipText("height of the field the graph should be layouted on");
+
+ cb_computePermutation.setToolTipText("define if the vertices are computed every round with the same order or a random order (permutation)");
+ cb_uphillMovesAllowed.setToolTipText("defines if moves of vertices are allowed, which increases the costs slightly");
+ cb_useNodeDistribution.setToolTipText("switches the costfunction for node distribution on/off");
+ cb_useBorderline.setToolTipText("switches the costfunction for borderline on/off");
+ cb_useEdgeLength.setToolTipText("switches the costfunction for edge length on/off");
+ cb_useEdgeCrossing.setToolTipText("switches the costfunction for edge crossings on/off");
+ cb_useEdgeDistribution.setToolTipText("switches the costfunction for edge distribution on/off");
+ cb_useNodeDistance.setToolTipText("switches the costfunction for node distance on/off");
+
+ button_takeViewportSize.setToolTipText("takes the size of the viewport for the graph (FEATURE NOT IMPLEMENTED YET!!!)");
+
+ cb_enableLayoutUpdate.setToolTipText("enables the algorithm to run, when vertices are removed/added");
+
+ tf_lu_initTemperature.setToolTipText(tf_initTemperature.getToolTipText());
+ tf_lu_minTemperature.setToolTipText(tf_minTemperature.getToolTipText());
+ tf_lu_minDistance.setToolTipText(tf_minDistance.getToolTipText());
+ tf_lu_tempScaleFactor.setToolTipText(tf_tempScaleFactor.getToolTipText());
+ tf_lu_maxRounds.setToolTipText(tf_maxRounds.getToolTipText());
+ tf_lu_triesPerCell.setToolTipText(tf_triesPerCell.getToolTipText());
+ tf_lu_lambdaNodeDistribution.setToolTipText(tf_lambdaNodeDistribution.getToolTipText());
+ tf_lu_lambdaBorderline.setToolTipText(tf_lambdaBorderline.getToolTipText());
+ tf_lu_lambdaEdgeLength.setToolTipText(tf_lambdaEdgeLength.getToolTipText());
+ tf_lu_lambdaEdgeCrossing.setToolTipText(tf_lambdaEdgeCrossing.getToolTipText());
+ tf_lu_lambdaEdgeDistribution.setToolTipText(tf_lambdaEdgeDistribution.getToolTipText());
+ tf_lu_lambdaNodeDistance.setToolTipText(tf_lambdaNodeDistance.getToolTipText());
+ tf_lu_boundsWidth.setToolTipText(tf_boundsWidth.getToolTipText());
+ tf_lu_boundsHeight.setToolTipText(tf_boundsHeight.getToolTipText());
+ tf_lu_method_neighborsDepth.setToolTipText("");
+ tf_lu_method_perimeterRadius.setToolTipText("");
+ tf_lu_method_perimeterRadiusInc.setToolTipText("");
+
+ cb_lu_computePermutation.setToolTipText(cb_computePermutation.getToolTipText());
+ cb_lu_uphillMovesAllowed.setToolTipText(cb_uphillMovesAllowed.getToolTipText());
+ cb_lu_useNodeDistribution.setToolTipText(cb_useNodeDistribution.getToolTipText());
+ cb_lu_useBorderline.setToolTipText(cb_useBorderline.getToolTipText());
+ cb_lu_useEdgeLength.setToolTipText(cb_useEdgeLength.getToolTipText());
+ cb_lu_useEdgeCrossing.setToolTipText(cb_useEdgeCrossing.getToolTipText());
+ cb_lu_useEdgeDistribution.setToolTipText(cb_useEdgeDistribution.getToolTipText());
+ cb_lu_useNodeDistance.setToolTipText(cb_useNodeDistance.getToolTipText());
+
+ button_lu_takeViewportSize.setToolTipText(button_takeViewportSize.getToolTipText());
+
+ comb_lu_Method.setToolTipText("choose a method for Layout Updating. This method determines, which of the Neighbors around the inserted Vertices are also new layouted in order to make place for the Layout of the inserted Vertices.");
+ tf_lu_method_neighborsDepth.setToolTipText("Neighbors are once again layouted if their distance to the inserted vertices is lower or equal this value");
+ tf_lu_method_perimeterRadius.setToolTipText("Neighbors within this radius around the initial position of inserted vertices are once again layouted in order to make place for the Layout of the inserted Vertices");
+ tf_lu_method_perimeterRadiusInc.setToolTipText("If more than one Vertice is inserted and has the same initial Position as another the perimeter radius is increase by this value");
+
+ tf_lu_clustering_factor.setToolTipText("Factor the creation of clusters. A lower value leads to more clusters, with smaller size, a higher value to fewer, bigger clusters");
+ tf_lu_clustering_moveScale.setToolTipText("Scales the movement of clusters. Possible values are between 0.0 and 1.0. A small value ensures, that clusters move slow and over short distances.");
+ }
+
+ /******************************************************************************/
+ protected void action_CheckBoxSwitch() {
+ tf_lambdaNodeDistribution.setEnabled(cb_useNodeDistribution.isSelected());
+ tf_lambdaBorderline.setEnabled(cb_useBorderline.isSelected());
+ button_takeViewportSize.setEnabled(cb_useBorderline.isSelected());
+ tf_boundsWidth.setEnabled(cb_useBorderline.isSelected());
+ tf_boundsHeight.setEnabled(cb_useBorderline.isSelected());
+ tf_lambdaEdgeLength.setEnabled(cb_useEdgeLength.isSelected());
+ tf_lambdaEdgeCrossing.setEnabled(cb_useEdgeCrossing.isSelected());
+ tf_lambdaEdgeDistribution.setEnabled(cb_useEdgeDistribution.isSelected());
+ tf_lambdaNodeDistance.setEnabled(cb_useNodeDistance.isSelected());
+
+ tf_lu_lambdaNodeDistribution.setEnabled(cb_lu_useNodeDistribution.isSelected());
+ tf_lu_lambdaBorderline.setEnabled(cb_lu_useBorderline.isSelected());
+ button_lu_takeViewportSize.setEnabled(cb_lu_useBorderline.isSelected());
+ tf_lu_boundsWidth.setEnabled(cb_lu_useBorderline.isSelected());
+ tf_lu_boundsHeight.setEnabled(cb_lu_useBorderline.isSelected());
+ tf_lu_lambdaEdgeLength.setEnabled(cb_lu_useEdgeLength.isSelected());
+ tf_lu_lambdaEdgeCrossing.setEnabled(cb_lu_useEdgeCrossing.isSelected());
+ tf_lu_lambdaEdgeDistribution.setEnabled(cb_lu_useEdgeDistribution.isSelected());
+ tf_lu_lambdaNodeDistance.setEnabled(cb_lu_useNodeDistance.isSelected());
+
+ tf_lu_clustering_factor.setEnabled(cb_lu_clustering_enable.isSelected());
+ tf_lu_clustering_moveScale.setEnabled(cb_lu_clustering_enable.isSelected());
+
+ String selectedLUMethod = (String) comb_lu_Method.getSelectedItem();
+
+ if (KEY_LAYOUT_UPDATE_METHOD_NEIGHBORS_ONLY.equals(selectedLUMethod)) {
+ tf_lu_method_neighborsDepth.setEnabled(true);
+ tf_lu_method_perimeterRadius.setEnabled(false);
+ tf_lu_method_perimeterRadiusInc.setEnabled(false);
+ } else if (KEY_LAYOUT_UPDATE_METHOD_PERIMETER.equals(selectedLUMethod)) {
+ tf_lu_method_neighborsDepth.setEnabled(true);
+ tf_lu_method_perimeterRadius.setEnabled(true);
+ tf_lu_method_perimeterRadiusInc.setEnabled(true);
+ }
+ }
+
+ /******************************************************************************/
+ protected boolean assertDouble(String text, String name, ArrayList errList) {
+ String errMsg = name + " is NOT a double value!";
+
+ try {
+ Double.parseDouble(text);
+ } catch (NumberFormatException e) {
+ // JOptionPane.showMessageDialog(this, errMsg, "Error", JOptionPane.INFORMATION_MESSAGE);
+ errList.add(errMsg);
+
+ return false;
+ }
+
+ return true;
+ }
+
+ /******************************************************************************/
+ protected boolean assertInteger(String text, String name, ArrayList errList) {
+ String errMsg = name + " is NOT a integer value!";
+
+ try {
+ Integer.parseInt(text);
+ } catch (NumberFormatException e) {
+ // JOptionPane.showMessageDialog(this, errMsg, "Error", JOptionPane.INFORMATION_MESSAGE);
+ errList.add(errMsg);
+
+ return false;
+ }
+
+ return true;
+ }
+
+ /******************************************************************************/
+ protected boolean assertRange(String value, double minValue, double maxValue,
+ boolean includeMinVal, boolean includeMaxVal, String name,
+ ArrayList errList) {
+ double val = Double.parseDouble(value);
+ boolean isOK = true;
+
+ if (includeMinVal) {
+ isOK &= (val >= minValue);
+ } else {
+ isOK &= (val > minValue);
+ }
+
+ if (isOK) {
+ if (includeMaxVal) {
+ isOK &= (val <= maxValue);
+ } else {
+ isOK &= (val < maxValue);
+ }
+ }
+
+ if (isOK) {
+ return true;
+ } else {
+ String errMsg = name + " is out the interval ";
+ errMsg += (includeMinVal ? "[" : "]");
+ errMsg += (minValue + ";" + maxValue);
+ errMsg += (includeMaxVal ? "]" : "[");
+ // JOptionPane.showMessageDialog(this, errMsg, "Error", JOptionPane.INFORMATION_MESSAGE);
+ errList.add(errMsg);
+
+ return false;
+ }
+ }
+
+ /******************************************************************************/
+ protected boolean assertRange(String value, int minValue, int maxValue, boolean includeMinVal,
+ boolean includeMaxVal, String name, ArrayList errList) {
+ double val = Integer.parseInt(value);
+ boolean isOK = true;
+
+ if (includeMinVal) {
+ isOK &= (val >= minValue);
+ } else {
+ isOK &= (val > minValue);
+ }
+
+ if (isOK) {
+ if (includeMaxVal) {
+ isOK &= (val <= maxValue);
+ } else {
+ isOK &= (val < maxValue);
+ }
+ }
+
+ if (isOK) {
+ return true;
+ } else {
+ String errMsg = name + " is out the interval ";
+ errMsg += (includeMinVal ? "[" : "]");
+ errMsg += (minValue + ";" + maxValue);
+ errMsg += (includeMaxVal ? "]" : "[");
+ // JOptionPane.showMessageDialog(this, errMsg, "Error", JOptionPane.INFORMATION_MESSAGE);
+ errList.add(errMsg);
+
+ return false;
+ }
+ }
+
+ /******************************************************************************/
+ protected boolean assertDoublePositiveSign(String value, boolean includeZero, String name,
+ ArrayList errList) {
+ double val = Double.parseDouble(value);
+ boolean isOK = true;
+
+ if (includeZero) {
+ isOK = val >= 0.0;
+ } else {
+ isOK = val > 0.0;
+ }
+
+ if (!isOK) {
+ String errMsg = name;
+
+ if (includeZero) {
+ errMsg += " has to be equal or bigger than 0.0";
+ } else {
+ errMsg += " has to be bigger than 0.0";
+ }
+
+ // JOptionPane.showMessageDialog(this, errMsg, "Error", JOptionPane.INFORMATION_MESSAGE);
+ errList.add(errMsg);
+
+ return false;
+ }
+
+ return isOK;
+ }
+
+ /******************************************************************************/
+ protected boolean assertIntegerPositiveSign(String value, boolean includeZero, String name,
+ ArrayList errList) {
+ int val = Integer.parseInt(value);
+ boolean isOK = true;
+
+ if (includeZero) {
+ isOK = val >= 0;
+ } else {
+ isOK = val > 0;
+ }
+
+ if (!isOK) {
+ String errMsg = name;
+
+ if (includeZero) {
+ errMsg += " has to be equal or bigger than 0";
+ } else {
+ errMsg += " has to be bigger than 0";
+ }
+
+ // JOptionPane.showMessageDialog(this, errMsg, "Error", JOptionPane.INFORMATION_MESSAGE);
+ errList.add(errList);
+
+ return false;
+ }
+
+ return isOK;
+ }
+
+ /******************************************************************************/
+ public double getInitTemperature() {
+ return Double.parseDouble(tf_initTemperature.getText());
+ }
+
+ /******************************************************************************/
+ public void setInitTemperature(double temperature) {
+ tf_initTemperature.setText(String.valueOf(temperature));
+ }
+
+ /******************************************************************************/
+ public double getMinTemperature() {
+ return Double.parseDouble(tf_minTemperature.getText());
+ }
+
+ /******************************************************************************/
+ public void setMinTemperature(double temperature) {
+ tf_minTemperature.setText(String.valueOf(temperature));
+ }
+
+ /******************************************************************************/
+ public double getMinDistance() {
+ return Double.parseDouble(tf_minDistance.getText());
+ }
+
+ /******************************************************************************/
+ public void setMinDistance(double distance) {
+ tf_minDistance.setText(String.valueOf(distance));
+ }
+
+ /******************************************************************************/
+ public double getTemperatureScaleFactor() {
+ return Double.parseDouble(tf_tempScaleFactor.getText());
+ }
+
+ /******************************************************************************/
+ public void setTemperatureScaleFactor(double factor) {
+ tf_tempScaleFactor.setText(String.valueOf(factor));
+ }
+
+ /******************************************************************************/
+ public int getMaxRounds() {
+ return Integer.parseInt(tf_maxRounds.getText());
+ }
+
+ /******************************************************************************/
+ public void setMaxRounds(int n) {
+ tf_maxRounds.setText(String.valueOf(n));
+ }
+
+ /******************************************************************************/
+ public int getTriesPerCell() {
+ return Integer.parseInt(tf_triesPerCell.getText());
+ }
+
+ /******************************************************************************/
+ public void setTriesPerCell(int tries) {
+ tf_triesPerCell.setText(String.valueOf(tries));
+ }
+
+ /******************************************************************************/
+ public int getCostFunctionConfiguration() {
+ int config = 0;
+
+ if (cb_useNodeDistance.isSelected()) {
+ config |= 32;
+ }
+
+ if (cb_useNodeDistribution.isSelected()) {
+ config |= 16;
+ }
+
+ if (cb_useBorderline.isSelected()) {
+ config |= 8;
+ }
+
+ if (cb_useEdgeLength.isSelected()) {
+ config |= 4;
+ }
+
+ if (cb_useEdgeCrossing.isSelected()) {
+ config |= 2;
+ }
+
+ if (cb_useEdgeDistribution.isSelected()) {
+ config |= 1;
+ }
+
+ config |= getAdditionalCostFunctionConfiguration();
+
+ return config;
+ }
+
+ /******************************************************************************/
+ protected int getAdditionalCostFunctionConfiguration() {
+ return 0;
+ }
+
+ /******************************************************************************/
+ public void setCostFunctionConfiguration(int config) {
+ cb_useNodeDistance.setSelected((config & 32) != 0);
+ cb_useNodeDistribution.setSelected((config & 16) != 0);
+ cb_useBorderline.setSelected((config & 8) != 0);
+ cb_useEdgeLength.setSelected((config & 4) != 0);
+ cb_useEdgeCrossing.setSelected((config & 2) != 0);
+ cb_useEdgeDistribution.setSelected((config & 1) != 0);
+ }
+
+ /******************************************************************************/
+ public ArrayList getLambda() {
+ ArrayList lambda = new ArrayList();
+ lambda.add(new Double(tf_lambdaNodeDistribution.getText()));
+ lambda.add(new Double(tf_lambdaBorderline.getText()));
+ lambda.add(new Double(tf_lambdaEdgeLength.getText()));
+ lambda.add(new Double(tf_lambdaEdgeCrossing.getText()));
+ lambda.add(new Double(tf_lambdaEdgeDistribution.getText()));
+ lambda.add(new Double(tf_lambdaNodeDistance.getText()));
+ lambda = getAdditionalLambda(lambda);
+
+ return lambda;
+ }
+
+ /******************************************************************************/
+ protected ArrayList getAdditionalLambda(ArrayList lambda) {
+ return lambda;
+ }
+
+ /******************************************************************************/
+ public void setLambda(ArrayList lambda) {
+ tf_lambdaNodeDistribution.setText(String.valueOf(((Double) lambda.get(0)).doubleValue()));
+ tf_lambdaBorderline.setText(String.valueOf(((Double) lambda.get(1)).doubleValue()));
+ tf_lambdaEdgeLength.setText(String.valueOf(((Double) lambda.get(2)).doubleValue()));
+ tf_lambdaEdgeCrossing.setText(String.valueOf(((Double) lambda.get(3)).doubleValue()));
+ tf_lambdaEdgeDistribution.setText(String.valueOf(((Double) lambda.get(4)).doubleValue()));
+ tf_lambdaNodeDistance.setText(String.valueOf(((Double) lambda.get(5)).doubleValue()));
+ }
+
+ /******************************************************************************/
+ public boolean getUphillMovesAllowed() {
+ return cb_uphillMovesAllowed.isSelected();
+ }
+
+ /******************************************************************************/
+ public void setUphillMovesAllowed(boolean allow) {
+ cb_uphillMovesAllowed.setSelected(allow);
+ }
+
+ /******************************************************************************/
+ public boolean getComputePermutation() {
+ return cb_computePermutation.isSelected();
+ }
+
+ /******************************************************************************/
+ public void setComputePermutation(boolean isSelected) {
+ cb_computePermutation.setSelected(isSelected);
+ }
+
+ /******************************************************************************/
+ public Rectangle getResultBounds() {
+ int x = 0;
+ int y = 0;
+ int w = Integer.parseInt(tf_boundsWidth.getText());
+ int h = Integer.parseInt(tf_boundsHeight.getText());
+
+ return new Rectangle(x, y, w, h);
+ }
+
+ /******************************************************************************/
+ public void setResultBounds(Rectangle r) {
+ tf_boundsWidth.setText(String.valueOf((int) r.getWidth()));
+ tf_boundsHeight.setText(String.valueOf((int) r.getHeight()));
+ }
+
+ /******************************************************************************/
+ public double getLayoutUpdateInitTemperature() {
+ return Double.parseDouble(tf_lu_initTemperature.getText());
+ }
+
+ /******************************************************************************/
+ public void setLayoutUpdateInitTemperature(double temperature) {
+ tf_lu_initTemperature.setText(String.valueOf(temperature));
+ }
+
+ /******************************************************************************/
+ public double getLayoutUpdateMinTemperature() {
+ return Double.parseDouble(tf_lu_minTemperature.getText());
+ }
+
+ /******************************************************************************/
+ public void setLayoutUpdateMinTemperature(double temperature) {
+ tf_lu_minTemperature.setText(String.valueOf(temperature));
+ }
+
+ /******************************************************************************/
+ public double getLayoutUpdateMinDistance() {
+ return Double.parseDouble(tf_lu_minDistance.getText());
+ }
+
+ /******************************************************************************/
+ public void setLayoutUpdateMinDistance(double distance) {
+ tf_lu_minDistance.setText(String.valueOf(distance));
+ }
+
+ /******************************************************************************/
+ public double getLayoutUpdateTemperatureScaleFactor() {
+ return Double.parseDouble(tf_lu_tempScaleFactor.getText());
+ }
+
+ /******************************************************************************/
+ public void setLayoutUpdateTemperatureScaleFactor(double factor) {
+ tf_lu_tempScaleFactor.setText(String.valueOf(factor));
+ }
+
+ /******************************************************************************/
+ public int getLayoutUpdateMaxRounds() {
+ return Integer.parseInt(tf_lu_maxRounds.getText());
+ }
+
+ /******************************************************************************/
+ public void setLayoutUpdateMaxRounds(int n) {
+ tf_lu_maxRounds.setText(String.valueOf(n));
+ }
+
+ /******************************************************************************/
+ public void setLayoutUpdateTriesPerCell(int tries) {
+ tf_lu_triesPerCell.setText(String.valueOf(tries));
+ }
+
+ /******************************************************************************/
+ public int getLayoutUpdateTriesPerCell() {
+ return Integer.parseInt(tf_lu_triesPerCell.getText());
+ }
+
+ /******************************************************************************/
+ public int getLayoutUpdateCostFunctionConfiguration() {
+ int config = 0;
+
+ if (cb_lu_useNodeDistance.isSelected()) {
+ config |= 32;
+ }
+
+ if (cb_lu_useNodeDistribution.isSelected()) {
+ config |= 16;
+ }
+
+ if (cb_lu_useBorderline.isSelected()) {
+ config |= 8;
+ }
+
+ if (cb_lu_useEdgeLength.isSelected()) {
+ config |= 4;
+ }
+
+ if (cb_lu_useEdgeCrossing.isSelected()) {
+ config |= 2;
+ }
+
+ if (cb_lu_useEdgeDistribution.isSelected()) {
+ config |= 1;
+ }
+
+ config |= getLayoutUpdateAdditionalCostFunctionConfiguration();
+
+ return config;
+ }
+
+ /******************************************************************************/
+ protected int getLayoutUpdateAdditionalCostFunctionConfiguration() {
+ return 0;
+ }
+
+ /******************************************************************************/
+ public void setLayoutUpdateCostFunctionConfiguration(int config) {
+ cb_lu_useNodeDistance.setSelected((config & 32) != 0);
+ cb_lu_useNodeDistribution.setSelected((config & 16) != 0);
+ cb_lu_useBorderline.setSelected((config & 8) != 0);
+ cb_lu_useEdgeLength.setSelected((config & 4) != 0);
+ cb_lu_useEdgeCrossing.setSelected((config & 2) != 0);
+ cb_lu_useEdgeDistribution.setSelected((config & 1) != 0);
+ }
+
+ /******************************************************************************/
+ public ArrayList getLayoutUpdateLambda() {
+ ArrayList lambda = new ArrayList();
+ lambda.add(new Double(tf_lu_lambdaNodeDistribution.getText()));
+ lambda.add(new Double(tf_lu_lambdaBorderline.getText()));
+ lambda.add(new Double(tf_lu_lambdaEdgeLength.getText()));
+ lambda.add(new Double(tf_lu_lambdaEdgeCrossing.getText()));
+ lambda.add(new Double(tf_lu_lambdaEdgeDistribution.getText()));
+ lambda.add(new Double(tf_lu_lambdaNodeDistance.getText()));
+ lambda = getLayoutUpdateAdditionalLambda(lambda);
+
+ return lambda;
+ }
+
+ /******************************************************************************/
+ protected ArrayList getLayoutUpdateAdditionalLambda(ArrayList lambda) {
+ return lambda;
+ }
+
+ /******************************************************************************/
+ public void setLayoutUpdateLambda(ArrayList lambda) {
+ tf_lu_lambdaNodeDistribution.setText(String.valueOf(((Double) lambda.get(0)).doubleValue()));
+ tf_lu_lambdaBorderline.setText(String.valueOf(((Double) lambda.get(1)).doubleValue()));
+ tf_lu_lambdaEdgeLength.setText(String.valueOf(((Double) lambda.get(2)).doubleValue()));
+ tf_lu_lambdaEdgeCrossing.setText(String.valueOf(((Double) lambda.get(3)).doubleValue()));
+ tf_lu_lambdaEdgeDistribution.setText(String.valueOf(((Double) lambda.get(4)).doubleValue()));
+ tf_lu_lambdaNodeDistance.setText(String.valueOf(((Double) lambda.get(5)).doubleValue()));
+ }
+
+ /******************************************************************************/
+ public boolean getLayoutUpdateUphillMovesAllowed() {
+ return cb_lu_uphillMovesAllowed.isSelected();
+ }
+
+ /******************************************************************************/
+ public void setLayoutUpdateUphillMovesAllowed(boolean allow) {
+ cb_lu_uphillMovesAllowed.setSelected(allow);
+ }
+
+ /******************************************************************************/
+ public boolean getLayoutUpdateComputePermutation() {
+ return cb_lu_computePermutation.isSelected();
+ }
+
+ /******************************************************************************/
+ public void setLayoutUpdateComputePermutation(boolean isSelected) {
+ cb_lu_computePermutation.setSelected(isSelected);
+ }
+
+ /******************************************************************************/
+ public Rectangle getLayoutUpdateResultBounds() {
+ int x = 0;
+ int y = 0;
+ int w = Integer.parseInt(tf_lu_boundsWidth.getText());
+ int h = Integer.parseInt(tf_lu_boundsHeight.getText());
+
+ return new Rectangle(x, y, w, h);
+ }
+
+ /******************************************************************************/
+ public void setLayoutUpdateResultBounds(Rectangle r) {
+ tf_lu_boundsWidth.setText(String.valueOf((int) r.getWidth()));
+ tf_lu_boundsHeight.setText(String.valueOf((int) r.getHeight()));
+ }
+
+ /******************************************************************************/
+ public void setLayoutUpdateEnabled(boolean enable) {
+ cb_enableLayoutUpdate.setSelected(enable);
+ switchLayoutUpdatePanel();
+ }
+
+ /******************************************************************************/
+ public boolean getLayoutUpdateEnabled() {
+ return cb_enableLayoutUpdate.isSelected();
+ }
+
+ /******************************************************************************/
+ public void setLayoutUpdateMethod(String method) {
+ comb_lu_Method.setSelectedItem(method);
+ }
+
+ /******************************************************************************/
+ public String getLayoutUpdateMethod() {
+ return (String) comb_lu_Method.getSelectedItem();
+ }
+
+ /******************************************************************************/
+ public void setLayoutUpdateMethodNeighborsDepth(int depth) {
+ tf_lu_method_neighborsDepth.setText(String.valueOf(depth));
+ }
+
+ /******************************************************************************/
+ public int getLayoutUpdateMethodNeighborsDepth() {
+ return Integer.parseInt(tf_lu_method_neighborsDepth.getText());
+ }
+
+ /******************************************************************************/
+ public void setLayoutUpdateMethodPerimeterRadius(double radius) {
+ tf_lu_method_perimeterRadius.setText(String.valueOf(radius));
+ }
+
+ /******************************************************************************/
+ public double getLayoutUpdateMethodPerimeterRadius() {
+ return Double.parseDouble(tf_lu_method_perimeterRadius.getText());
+ }
+
+ /******************************************************************************/
+ public void setLayoutUpdateMethodPerimeterRadiusIncrease(double radiusInc) {
+ tf_lu_method_perimeterRadiusInc.setText(String.valueOf(radiusInc));
+ }
+
+ /******************************************************************************/
+ public double getLayoutUpdateMethodPerimeterRadiusIncrease() {
+ return Double.parseDouble(tf_lu_method_perimeterRadiusInc.getText());
+ }
+
+ /******************************************************************************/
+ public void setLayoutUpdateClusteringEnabled(boolean enable) {
+ cb_lu_clustering_enable.setSelected(enable);
+ }
+
+ /******************************************************************************/
+ public boolean getLayoutUpdateClusteringEnabled() {
+ return cb_lu_clustering_enable.isSelected();
+ }
+
+ /******************************************************************************/
+ public void setLayoutUpdateClusteringFactor(double factor) {
+ tf_lu_clustering_factor.setText(String.valueOf(factor));
+ }
+
+ /******************************************************************************/
+ public double getLayoutUpdateClusteringFactor() {
+ return Double.parseDouble(tf_lu_clustering_factor.getText());
+ }
+
+ /******************************************************************************/
+ public void setLayoutUpdateClusteringMoveScaleFactor(double factor) {
+ tf_lu_clustering_moveScale.setText(String.valueOf(factor));
+ }
+
+ /******************************************************************************/
+ public double getLayoutUpdateClusteringMoveScaleFactor() {
+ return Double.parseDouble(tf_lu_clustering_moveScale.getText());
+ }
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/layout/CircleGraphLayout.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/layout/CircleGraphLayout.java
new file mode 100644
index 0000000..5b1716a
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/layout/CircleGraphLayout.java
@@ -0,0 +1,103 @@
+/*
+ * @(#)CircleLayoutAlgorithm.java 1.0 18-MAY-2004
+ *
+ * Copyright (c) 2004-2005, Gaudenz Alder
+ * All rights reserved.
+ *
+ * This library is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation; either
+ * version 2.1 of the License, or (at your option) any later version.
+ *
+ * This library is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this library; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+ */
+package org.jgraph.layout;
+
+import org.jgraph.JGraph;
+
+import org.jgraph.graph.CellView;
+import org.jgraph.graph.VertexView;
+
+import java.awt.geom.Rectangle2D;
+
+import java.util.ArrayList;
+import java.util.List;
+
+
+/**
+ * @author Gaudenz Alder
+ *
+ * TODO To change the template for this generated type comment go to
+ * Window - Preferences - Java - Code Generation - Code and Comments
+ */
+public class CircleGraphLayout extends JGraphLayoutAlgorithm {
+ /**
+ * Returns the name of this algorithm in human
+ * readable form.
+ */
+ public String toString() {
+ return "Simple Circle";
+ }
+
+ /* (non-Javadoc)
+ * @see java.lang.Runnable#run()
+ * @param graph JGraph instance
+ * @param dynamic_cells List of all nodes the layout should move
+ * @param static_cells List of node the layout should not move but allow for
+ */
+ /**
+ * DOCUMENT ME!
+ *
+ * @param graph DOCUMENT ME!
+ * @param dynamic_cells DOCUMENT ME!
+ * @param static_cells DOCUMENT ME!
+ */
+ public void run(JGraph graph, Object[] dynamic_cells, Object[] static_cells) {
+ // Fetch All Views
+ CellView[] views = graph.getGraphLayoutCache().getMapping(dynamic_cells);
+
+ // Create list to hold vertices
+ List vertices = new ArrayList();
+
+ // Maximum width or height
+ int max = 0;
+
+ // Loop through all views
+ for (int i = 0; i < views.length; i++) {
+ // Add vertex to list
+ if (views[i] instanceof VertexView) {
+ vertices.add(views[i]);
+
+ // Fetch Bounds
+ Rectangle2D bounds = views[i].getBounds();
+
+ // Update Maximum
+ if (bounds != null)
+ max = (int) Math.max(max, Math.max(bounds.getWidth(), bounds.getHeight()));
+ }
+ }
+
+ // Compute Radius
+ int r = (int) Math.max((vertices.size() * max) / Math.PI, 100);
+
+ // Compute angle step
+ double phi = (2 * Math.PI) / vertices.size();
+
+ // Arrange vertices in a circle
+ for (int i = 0; i < vertices.size(); i++) {
+ Rectangle2D bounds = ((CellView) vertices.get(i)).getBounds();
+
+ // Update Location
+ if (bounds != null)
+ bounds.setFrame(r + (r * Math.sin(i * phi)), r + (r * Math.cos(i * phi)),
+ bounds.getWidth(), bounds.getHeight());
+ }
+ }
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/layout/GEMLayoutAlgorithm.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/layout/GEMLayoutAlgorithm.java
new file mode 100644
index 0000000..757f075
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/layout/GEMLayoutAlgorithm.java
@@ -0,0 +1,2053 @@
+/*
+ * @(#)GEMLayoutAlgorithm.java 1.0 18-MAY-2004
+ *
+ * Copyright (c) 2004, Winkler
+ * All rights reserved.
+ *
+ * This library is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation; either
+ * version 2.1 of the License, or (at your option) any later version.
+ *
+ * This library is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this library; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+ */
+package org.jgraph.layout;
+
+import org.jgraph.JGraph;
+
+import org.jgraph.event.GraphModelEvent;
+import org.jgraph.event.GraphModelListener;
+
+import org.jgraph.graph.AttributeMap;
+import org.jgraph.graph.CellMapper;
+import org.jgraph.graph.CellView;
+import org.jgraph.graph.EdgeView;
+import org.jgraph.graph.GraphConstants;
+import org.jgraph.graph.GraphModel;
+import org.jgraph.graph.VertexView;
+
+import org.jgraph.layout.AnnealingLayoutAlgorithm.MathExtensions;
+
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Rectangle;
+import java.awt.geom.Point2D;
+import java.awt.geom.Rectangle2D;
+
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.Map;
+import java.util.Properties;
+
+
+/**
+ * <h1>GEM Layout Algorithm</h1>
+ * <p>
+ * Based on the work of Arne Frick, Andreas Ludwig, Heiko Mehldau:
+ * "A Fast Adaptive Layout Algorithm for Undirected Graphs";
+ * Extended Abstract and System Demonstration; Faculty of Informatik of
+ * the University Karlsruhe; 1994
+ * <p>
+ * This Algorithm works by giving every cell a position and a temperature.
+ * Then for every cell forces are computed. Every other cell repulses the
+ * actual calculated cell away. On the other hand, cells, connected by edges
+ * are attracted, until a minimum distance is reached. The result of this
+ * forces is a move of the position of the actual cell in the direction of
+ * the force and with the length of the temperature. Then the temperature
+ * will be decreased, if the last impulse and the current impulse looks like a
+ * rotation or a oscillation. this is done for every cell until the temperature
+ * of all cells or the average of the temperature of every cell is until a
+ * given minimum value or a maximum of rounds is reached.
+ * @author winkler
+ */
+public class GEMLayoutAlgorithm extends JGraphLayoutAlgorithm implements GraphModelListener {
+ /**
+ * Key used on every cell. This key indicates that in the cell are
+ * attributes stored by this algorithm. The algorithm itself never asks for
+ * this key. This is for others developers only, using this algorithm, to
+ * find out, where sometimes approaching attributes come from.
+ */
+ public final static String KEY_CAPTION = "GEM-TEMPORARY-DATA";
+
+ /**
+ * Key used on every cell. Under this key every cell stores temporary the
+ * temperature of itself. Temperature is a indicator how far a cell can move
+ * and all temperatures together indicating how long the algorithm will run.
+ */
+ public final static String KEY_TEMPERATURE = "Temperature";
+
+ /**
+ * Key used on every cell. Under this key every cell stores temporary the
+ * current force impulse affecting the cell.
+ */
+ public final static String KEY_CURRENT_IMPULSE = "Current_Impulse";
+
+ /**
+ * Key used on every cell. Under this key every cell stores temporary the
+ * last impulse. This is the value of the previous
+ * {@link #KEY_CURRENT_IMPULSE}.
+ */
+ public final static String KEY_LAST_IMPULSE = "Last_Impulse";
+
+ /**
+ * Key used on every cell. Under this key every cell stores the temporary
+ * position on the display, while the calculation is running. This makes
+ * the algorithm faster, than asking the Cell everytime for its position.
+ * So the algorithm can anytime be canceled, whithout changing something.
+ */
+ public final static String KEY_POSITION = "Position";
+
+ /**
+ * Key used on every cell. Under this key every cell stores the temporary
+ * skew gauge. This value is for punish rotations of the cells.
+ */
+ public final static String KEY_SKEWGAUGE = "Skew_Gauge";
+
+ /**
+ * Key used on every Cell. Under this key every cell stores the cells,
+ * that are only one edge away from it. The relatives are stored, after the
+ * first time, they are desired and calculated by
+ * {@link #getRelatives(CellView)}.
+ */
+ public final static String KEY_RELATIVES = "Relatives";
+
+ /**
+ * Key used on every Cell. This indicates a weight for the number of edges
+ * received by {@link #getNodeWeight(CellView)}
+ */
+ public final static String KEY_MASSINDEX = "Mass_Index";
+
+ /**
+ * Key used only with clusters. Under this key a cluster has an ArrayList.
+ * This list is filled with the clustered vertices.
+ * @see #clusterGraph()
+ */
+ public final static String KEY_CLUSTERED_VERTICES = "Clustered Vertices";
+
+ /**
+ * Key used only with clusters. Under this key vertices have the cluster
+ * they belong to.
+ * @see #clusterGraph()
+ */
+ public final static String KEY_CLUSTER = "Cluster";
+
+ /**
+ * Key used only with clusters. Under this key a cluster has a boolean value
+ * indicating that this vertice is a cluster (clusters are
+ * VertexView-instances like every other cell).
+ * @see #clusterGraph()
+ */
+ public final static String KEY_IS_CLUSTER = "is Cluster";
+
+ /**
+ * Key used only with clusters. Under this key every cluster has a position,
+ * which represents the position of the cluster, right after the clustering
+ * process. After the layout update process is finished, the move, resulting
+ * of subtracting the position under {@link #KEY_POSITION} from the
+ * position under this value, will be performed to all vertices in the
+ * cluster. By holding the initial position here clustering becomes
+ * possible.
+ *
+ * @see #clusterGraph()
+ * @see #declusterGraph()
+ */
+ public final static String KEY_CLUSTER_INIT_POSITION = "initial Position of the Cluster";
+
+ /**
+ * List of all nodes in the graph.
+ */
+ private ArrayList cellList;
+
+ /**
+ * List of all nodes the algorithm should be done for.
+ */
+ private ArrayList applyCellList;
+
+ /**
+ * List of all edges in the graph. This is only needed for the optimization
+ * Algorithm.
+ */
+ private ArrayList edgeList;
+
+ /**
+ * needed for comperation with other double values if they are 0.0.
+ */
+ private double equalsNull = 0.00000000000000001;
+
+ /**
+ * starting value for the temperatures of the cells
+ */
+ protected double initTemperature = 10;
+
+ /**
+ * if the temperature of all cells or the average of the temperatures of
+ * all cells is below this value, the algorithm stops
+ */
+ protected double minTemperature = 3;
+
+ /**
+ * temperature will never be over this value
+ */
+ protected double maxTemperature = 256;
+
+ /**
+ * the length of the Edges in Pixel, the algorithm tries to keep
+ */
+ protected double prefEdgeLength = 100;
+
+ /**
+ * the strength of the gravitation force, directed to the barycenter of the
+ * graph, added to all cells.
+ */
+ protected double gravitation = 0.0625;
+
+ /**
+ * length of a force vector with a random direction, added to all cells.
+ */
+ protected double randomImpulseRange = 32;
+
+ /**
+ * opening angle in radiant, that detects oscillations
+ */
+ protected double alphaOsc = Math.toRadians(90);
+
+ /**
+ * opening angle in radiant, that detects rotations
+ */
+ protected double alphaRot = Math.toRadians(60);
+
+ /**
+ * penalty value for a detected oscillation
+ */
+ protected double sigmaOsc = 1.0 / 3.0;
+
+ /**
+ * penalty value for a detected rotation
+ */
+ protected double sigmaRot = 1.0 / 2.0;
+
+ /**
+ * number of rounds until the algorithm will break. This value is
+ * precalculated to a aproximativ value of 4 times the count of Cells in
+ * {@link #applyCellList}
+ */
+ private int maxRounds;
+
+ /**
+ * counts the rounds
+ */
+ private int countRounds;
+
+ /**
+ * If the pathlength between an inserted cell and an allready layouted cell
+ * is below this value, the allready layouted cell will be layouted again.
+ */
+ private int recursionDepth;
+
+ /**
+ * Describes the distance around a cell, that will be whatched for other
+ * cells, intersecting this area. If another cell intersects, a force will
+ * be added to the cell, that pushes it away.
+ */
+ private double overlapDetectWidth;
+
+ /**
+ * Describes a distance the algorithm tries to keep, when he detects a
+ * overlapping cell.
+ */
+ private double overlapPrefDistance;
+
+ /**
+ * switches the feature to whatch for overlapping on/off
+ */
+ private boolean avoidOverlapping;
+
+ /**
+ * describes, what method will be taken, when cells are inserted. Posible
+ * values are
+ */
+ private String layoutUpdateMethod;
+
+ /**
+ * condition for method isFrozen(). decides whether the method returns true
+ * when the average of all temperatures or all temperatures are below
+ * {@link #minTemperature}.
+ */
+ private boolean shouldEndPerAverage;
+
+ /**
+ * condition for the method calculate(). decides whether the algorithm
+ * is computed for the cellViews every time in the same sequence
+ * or if the cellViews are computed every time in a random sequence.
+ */
+ private boolean shouldComputePermutation;
+
+ /**
+ * Switches the skill of the algorithm to perform the layout update process
+ */
+ private boolean isActive = true;
+
+ /**
+ * Checks if the algorithm is currently running. If this is the case, no
+ * GraphModelEvent will be computed and no new run can be initiated.
+ */
+ private boolean isRunning = false;
+
+ /**
+ * a reference to the instance of jgraph
+ */
+ private JGraph jgraph;
+
+ /**
+ * the configuration of this algorithm
+ */
+ protected Properties config;
+
+ /**
+ * to identify for the method {@link #loadRuntimeValues(int)}, that the
+ * algorithm wants to perform a new run
+ */
+ protected final static int VALUES_PUR = 0;
+
+ /**
+ * to identify for the method {@link #loadRuntimeValues(int)}, that the
+ * algorithm wants to perform a layout update
+ */
+ protected final static int VALUES_INC = 1;
+
+ /**
+ * algorithm used for optimizing the result of this algorithm
+ */
+ private AnnealingLayoutAlgorithm optimizationAlgorithm;
+
+ /**
+ * switches the usage of the optimizing algorithm
+ */
+ private boolean useOptimizeAlgorithm;
+
+ /**
+ * configuration of the optimizing algorithm
+ */
+ private Properties optimizationAlgorithmConfig;
+
+ /**
+ * Switches clustering for the layout update process on/off
+ */
+ private boolean isClusteringEnabled;
+
+ /**
+ * The initial temperature for clusters. It is recommended, that this value
+ * is lower than {@link #initTemperature} to get a good looking layout
+ */
+ private double clusterInitTemperature;
+
+ /**
+ * Scales forces, that are effecting clusters. It is recommendet to take
+ * a value between 1.0 and 0.0. This garanties, that clusters move slower
+ * than other cells. That rises the chance of getting a good looking layout
+ * after the calculation.
+ */
+ private double clusterForceScalingFactor;
+
+ /**
+ * Effects, how many clusters are created, when the layout update process
+ * starts. This affects the initial number of clusters, which is the number
+ * of cells available minus the number of cells to layout. The result of
+ * that term is divided by this factor, to get the maximum number of
+ * clusters. After this calculation, the clustering algorithm tries to
+ * minimize the number of clusters, so there might be less clusters than
+ * the maximum number.
+ */
+ private double clusteringFactor;
+
+ /**
+ * The initial size for the layout update method perimeter. This describes
+ * a radius around an inserted cell. Every other inserted cell in this
+ * radius increases the radius by {@link #perimeterSizeInc}. After finishing
+ * increasing the radius, every cell, from the cells, that are already
+ * layouted, in the radius is added to the list of cells, that'll gain a
+ * new position during the layout update process. This should bring up
+ * the behaviour, that the previous layouted cells make space for the layout
+ * of the inserted cells.
+ */
+ private double perimeterInitSize;
+
+ /**
+ * Inserted cells whithin a radius of {@link #perimeterInitSize} around
+ * a inserted cell are counted. After counting the inserted cells around
+ * a inserted cell, the initial radius is increased by this increase value
+ * times the number of inserted cells around the inserted cell. Every
+ * previous layouted cell in the resulting radius around the inserted cell
+ * is going to be layouted again.
+ */
+ private double perimeterSizeInc;
+
+ // private boolean isDebugging = false;
+
+ /******************************************************************************/
+ /**
+ * Constructs a new GEM Layout Algorithm.
+ */
+ public GEMLayoutAlgorithm(AnnealingLayoutAlgorithm optimizer) {
+ cellList = new ArrayList();
+ applyCellList = new ArrayList();
+ edgeList = new ArrayList();
+ optimizationAlgorithm = optimizer;
+ }
+
+ /**
+ * Returns the name of this algorithm in human
+ * readable form.
+ */
+ public String toString() {
+ return "GEM";
+ }
+
+ /**
+ * Get a human readable hint for using this layout.
+ */
+ public String getHint() {
+ return "Ignores selection";
+ }
+
+ /**
+ * Returns an new instance of SugiyamaLayoutSettings
+ */
+ public JGraphLayoutSettings createSettings() {
+ return new GEMLayoutSettings(this);
+ }
+
+ /******************************************************************************/
+ /**
+ * Starts the Calculation of a new layout with the GEM-Algorithm
+ * @param graph JGraph instance
+ * @param dynamic_cells List of all nodes the layout should move
+ * @param static_cells List of node the layout should not move but allow for
+ * @see #initialize()
+ * @see #calculate()
+ */
+ public void run(JGraph graph, Object[] dynamic_cells, Object[] static_cells) {
+ isRunning = true;
+
+ jgraph = graph;
+
+ jgraph.getModel().addGraphModelListener(this);
+
+ cellList = new ArrayList();
+ applyCellList = new ArrayList();
+
+ //extracting the nodes from jgraph, the algorithm should be performed on
+ getNodes(jgraph, dynamic_cells);
+
+ // long starttime = System.currentTimeMillis();
+ //ALGORITHM START
+ canceled = initialize(); // initializes algorithm
+ // sets the startvalues in cells
+
+ if (!canceled)
+ canceled = calculate(); //performs the algorithm on the cells
+ //ALGORITHM END
+
+ if (!canceled && useOptimizeAlgorithm)
+ optimizationAlgorithm.performOptimization(applyCellList, cellList, edgeList,
+ optimizationAlgorithmConfig);
+
+ if (!canceled)
+ correctCoordinates();
+
+ //sets the calculated data into cellView's bounds if not canceled
+ if (!canceled)
+ canceled = setNewCoordinates(jgraph);
+
+ //removes the temporary data, stored by the algorithm, from the nodes
+ removeTemporaryLayoutDataFromCells();
+
+ isRunning = false;
+ }
+
+ /******************************************************************************/
+ /**
+ * Loads the actual desired values from the {@link #config configuration} to
+ * the fields, where they are used later.
+ *
+ * @param valueID {@link #VALUES_PUR} for a normal run or {@link #VALUES_INC}
+ * for a layout update process.
+ */
+ protected void loadRuntimeValues(int valueID) {
+ maxRounds = applyCellList.size() * 4; //estimated value; reached rarely
+
+ countRounds = 0; //start value; counts the rounds in calculate()
+
+ isActive = isTrue((String) config.get(GEMLayoutSettings.KEY_LAYOUT_UPDATE_ENABLED));
+
+ recursionDepth = Integer.parseInt((String) config.get(GEMLayoutSettings.KEY_LAYOUT_UPDATE_DEPTH));
+
+ layoutUpdateMethod = (String) config.get(GEMLayoutSettings.KEY_LAYOUT_UPDATE_METHOD);
+
+ if (valueID == VALUES_PUR) {
+ initTemperature = Double.parseDouble((String) config.get(GEMLayoutSettings.KEY_INIT_TEMPERATURE));
+ minTemperature = Double.parseDouble((String) config.get(GEMLayoutSettings.KEY_MIN_TEMPERATURE));
+ maxTemperature = Double.parseDouble((String) config.get(GEMLayoutSettings.KEY_MAX_TEMPERATURE));
+ prefEdgeLength = Double.parseDouble((String) config.get(GEMLayoutSettings.KEY_PREF_EDGE_LENGTH));
+ gravitation = Double.parseDouble((String) config.get(GEMLayoutSettings.KEY_GRAVITATION));
+ randomImpulseRange = Double.parseDouble((String) config.get(GEMLayoutSettings.KEY_RANDOM_IMPULSE_RANGE));
+ overlapDetectWidth = Double.parseDouble((String) config.get(GEMLayoutSettings.KEY_OVERLAPPING_DETECTION_WIDTH));
+ overlapPrefDistance = Double.parseDouble((String) config.get(GEMLayoutSettings.KEY_OVERLAPPING_PREF_DISTANCE));
+ shouldEndPerAverage = isTrue((String) config.get(GEMLayoutSettings.KEY_COMPUTE_PERMUTATION));
+ shouldComputePermutation = isTrue((String) config.get(GEMLayoutSettings.KEY_END_CONDITION_AVERAGE));
+ avoidOverlapping = isTrue((String) config.get(GEMLayoutSettings.KEY_AVOID_OVERLAPPING));
+ alphaOsc = Double.parseDouble((String) config.get(GEMLayoutSettings.KEY_ALPHA_OSC));
+ alphaRot = Double.parseDouble((String) config.get(GEMLayoutSettings.KEY_ALPHA_ROT));
+ sigmaOsc = Double.parseDouble((String) config.get(GEMLayoutSettings.KEY_SIGMA_OSC));
+ sigmaRot = Double.parseDouble((String) config.get( //gets 1/x
+ GEMLayoutSettings.KEY_SIGMA_ROT));
+ useOptimizeAlgorithm = isTrue((String) config.get(GEMLayoutSettings.KEY_OPTIMIZE_ALGORITHM_ENABLED));
+ optimizationAlgorithmConfig = (Properties) config.get(GEMLayoutSettings.KEY_OPTIMIZE_ALGORITHM_CONFIG);
+ } else if (valueID == VALUES_INC) {
+ initTemperature = Double.parseDouble((String) config.get(GEMLayoutSettings.KEY_LAYOUT_UPDATE_INIT_TEMPERATURE));
+ minTemperature = Double.parseDouble((String) config.get(GEMLayoutSettings.KEY_LAYOUT_UPDATE_MIN_TEMPERATURE));
+ maxTemperature = Double.parseDouble((String) config.get(GEMLayoutSettings.KEY_LAYOUT_UPDATE_MAX_TEMPERATURE));
+ prefEdgeLength = Double.parseDouble((String) config.get(GEMLayoutSettings.KEY_LAYOUT_UPDATE_PREF_EDGE_LENGTH));
+ gravitation = Double.parseDouble((String) config.get(GEMLayoutSettings.KEY_LAYOUT_UPDATE_GRAVITATION));
+ randomImpulseRange = Double.parseDouble((String) config.get(GEMLayoutSettings.KEY_LAYOUT_UPDATE_RANDOM_IMPULSE_RANGE));
+ overlapDetectWidth = Double.parseDouble((String) config.get(GEMLayoutSettings.KEY_LAYOUT_UPDATE_OVERLAPPING_DETECTION_WIDTH));
+ overlapPrefDistance = Double.parseDouble((String) config.get(GEMLayoutSettings.KEY_LAYOUT_UPDATE_OVERLAPPING_PREF_DISTANCE));
+ shouldEndPerAverage = isTrue((String) config.get(GEMLayoutSettings.KEY_LAYOUT_UPDATE_COMPUTE_PERMUTATION));
+ shouldComputePermutation = isTrue((String) config.get(GEMLayoutSettings.KEY_LAYOUT_UPDATE_END_CONDITION_AVERAGE));
+ avoidOverlapping = isTrue((String) config.get(GEMLayoutSettings.KEY_LAYOUT_UPDATE_AVOID_OVERLAPPING));
+
+ alphaOsc = Double.parseDouble((String) config.get(GEMLayoutSettings.KEY_LAYOUT_UPDATE_ALPHA_OSC));
+ alphaRot = Double.parseDouble((String) config.get(GEMLayoutSettings.KEY_LAYOUT_UPDATE_ALPHA_ROT));
+ sigmaOsc = Double.parseDouble((String) config.get(GEMLayoutSettings.KEY_LAYOUT_UPDATE_SIGMA_OSC));
+ sigmaRot = Double.parseDouble((String) config.get( //gets 1/x
+ GEMLayoutSettings.KEY_LAYOUT_UPDATE_SIGMA_ROT));
+ useOptimizeAlgorithm = isTrue((String) config.get(GEMLayoutSettings.KEY_LAYOUT_UPDATE_OPTIMIZE_ALGORITHM_ENABLED));
+ optimizationAlgorithmConfig = (Properties) config.get(GEMLayoutSettings.KEY_LAYOUT_UPDATE_OPTIMIZE_ALGORITHM_CONFIG);
+ perimeterInitSize = Double.parseDouble((String) config.get(GEMLayoutSettings.KEY_LAYOUT_UPDATE_METHOD_PERIMETER_INIT_SIZE));
+ perimeterSizeInc = Double.parseDouble((String) config.get(GEMLayoutSettings.KEY_LAYOUT_UPDATE_METHOD_PERIMETER_SIZE_INC));
+ isClusteringEnabled = isTrue((String) config.get(GEMLayoutSettings.KEY_LAYOUT_UPDATE_CLUSTERING_ENABLED));
+ clusterInitTemperature = Double.parseDouble((String) config.get(GEMLayoutSettings.KEY_LAYOUT_UPDATE_CLUSTERING_INIT_TEMPERATURE));
+ clusterForceScalingFactor = Double.parseDouble((String) config.get(GEMLayoutSettings.KEY_LAYOUT_UPDATE_CLUSTERING_FORCE_SCALING_FACTOR));
+ clusteringFactor = Double.parseDouble((String) config.get(GEMLayoutSettings.KEY_LAYOUT_UPDATE_CLUSTERING_FACTOR));
+ }
+
+ //with that line sigmaRot will be 1/(x*cellCount) with x is configurable
+ sigmaRot *= (1.0 / (double) ((applyCellList.size() == 0) ? 1 : applyCellList.size()));
+ }
+
+ /******************************************************************************/
+ /**
+ * Helping method. Transforms a String, containing only the characters "true" or
+ * "false", regardless if upper or lower case, into a boolean value.
+ *
+ * @param boolValue String containing a boolean value
+ * @return boolean value represented by the given string
+ */
+ protected boolean isTrue(String boolValue) {
+ if (boolValue != null) {
+ if ("TRUE".equals(boolValue.toUpperCase())) {
+ return true;
+ } else if ("FALSE".equals(boolValue.toUpperCase())) {
+ return false;
+ }
+ }
+
+ return false;
+ }
+
+ /******************************************************************************/
+ /**
+ * Extracts the Cells from JGraph and fills {@link #applyCellList},
+ * {@link #cellList} and {@link #edgeList}. If applyToAll is
+ * <b><code>false</code></b> only in jgraph selected cells are added to
+ * {@link #applyCellList} else all cells are added.
+ *
+ * @param jgraph actual instance of jgraph
+ * cells or only on the selected.
+ */
+ private void getNodes(JGraph jgraph, Object[] cells) {
+ Object[] all = jgraph.getRoots();
+
+ CellView[] view = jgraph.getGraphLayoutCache().getMapping(all, false);
+ CellView[] selectedView = jgraph.getGraphLayoutCache().getMapping(cells, false);
+
+ for (int i = 0; i < view.length; i++)
+ if (view[i] instanceof VertexView) {
+ cellList.add(view[i]);
+ applyCellList.add(view[i]);
+ } else if (view[i] instanceof EdgeView) {
+ edgeList.add(view[i]);
+ }
+
+ for (int i = 0; i < selectedView.length; i++)
+ if (selectedView[i] instanceof VertexView)
+ applyCellList.add(selectedView[i]);
+ }
+
+ /******************************************************************************/
+ /**
+ * Sets the initial Values, gained from the {@link #config configuration}
+ * into the Cells.
+ *
+ * @return Because the progress dialog is allready visible during the
+ * initialisation, <b><code>true</code><b> is returned when cancel is pressed
+ * on it.
+ */
+ private boolean initialize() {
+ int length = cellList.size();
+
+ for (int i = 0; i < length; i++) {
+ CellView view = (CellView) cellList.get(i);
+
+ initializeVertice(view);
+ }
+
+ for (int i = 0; i < applyCellList.size(); i++)
+ computeLastImpulse((CellView) applyCellList.get(i));
+
+ return false; //not canceled
+ }
+
+ /******************************************************************************/
+ /**
+ * Sets the initial values for one Cell.
+ *
+ * @param view Cell, the initial values should be set for.
+ */
+ private void initializeVertice(CellView view) {
+ Map attributes = view.getAttributes();
+
+ if (attributes == null)
+ attributes = new Hashtable();
+
+ attributes.put(KEY_CAPTION, KEY_CAPTION);
+
+ initPosition(view);
+
+ if (isCluster(view)) {
+ attributes.put(KEY_TEMPERATURE, new Double(clusterInitTemperature));
+ } else
+ attributes.put(KEY_TEMPERATURE, new Double(initTemperature));
+
+ attributes.put(KEY_SKEWGAUGE, new Double(0.0));
+ attributes.put(KEY_CURRENT_IMPULSE, new Point2D.Double());
+ attributes.put(KEY_LAST_IMPULSE, new Point2D.Double());
+ }
+
+ /******************************************************************************/
+ /**
+ * Runs the algorithm. First a running sequence is initialised. If
+ * shouldComputePermuation is <b><code>true</code><b> then a new
+ * permutation is computed for every round, else a single determined sequence is
+ * established. After this for every Cell a current impulse is calculated,
+ * position and temperature is updated. This is done, until the graph is frozen,
+ * a maximum on rounds is reached or cancel on the progress dialog is pressed.
+ *
+ * @return <b><code>true</code></b> when cancel on the progress dialog is
+ * pressed
+ * @see #computeCurrentImpulse(CellView)
+ * @see #createPermutation(int)
+ * @see #isFrozen()
+ * @see #updatePosAndTemp(CellView)
+ */
+ private boolean calculate() {
+ int length = applyCellList.size();
+ int[] sequence = new int[length];
+ canceled = false;
+
+ //case no permutation is desired, the series is computed one time only
+ if (!shouldComputePermutation) //else is in the loop below
+ for (int i = 0; i < length; i++)
+ sequence[i] = i;
+
+ while (!isFrozen() && (countRounds <= maxRounds) && (!canceled)) {
+ //case permutation is desired, it's calculated every round
+ if (shouldComputePermutation)
+ sequence = createPermutation(length);
+
+ //loop over all nodes (order is in sequence)
+ for (int i = 0; i < sequence.length; i++) {
+ CellView view = (CellView) applyCellList.get(sequence[i]);
+
+ computeCurrentImpulse(view); //computes direction of impulse
+ updatePosAndTemp(view); //computes new position and temperature
+ }
+
+ countRounds++;
+ }
+
+ return canceled;
+ }
+
+ /******************************************************************************/
+ /**
+ * Calculates the current impulse for the given cell.
+ *
+ * @param view Cell, the current impulse should be calculated
+ * @see #computeImpulse(CellView)
+ */
+ private void computeCurrentImpulse(CellView view) {
+ //gets the impulse for view
+ Point2D.Double impulse = computeImpulse(view);
+
+ //set result into node
+ view.getAttributes().put(KEY_CURRENT_IMPULSE, impulse);
+ }
+
+ /******************************************************************************/
+ /**
+ * Calculates the last impulse for the given cell. This is only nesessary while
+ * initializing the cells.
+ *
+ * @param view Cell, the last impulse should be calculated
+ * @see #computeImpulse(CellView)
+ */
+ private void computeLastImpulse(CellView view) {
+ //gets the impulse for view
+ Point2D.Double impulse = computeImpulse(view);
+
+ //set result into node
+ view.getAttributes().put(KEY_LAST_IMPULSE, impulse);
+ }
+
+ /******************************************************************************/
+ /**
+ * Computes an Impulse representing a Force affecting the position of the given
+ * Cell. This impulse consists of a attracting force, pulling the cell to the
+ * barycenter of all cells, a pulse with user defined length and random
+ * direction, a force repulsing cells from each other, a force attracting
+ * connected cells together, and, as a additional feature, a force, repulsing
+ * the current cell from overlapping cells.
+ *
+ * @param view Cell, the impulse should be computed
+ * @return impulse, transformed in a Point2D.Double-Instance.
+ */
+ private Point2D.Double computeImpulse(CellView view) {
+ Point2D.Double impulse = new Point2D.Double();
+ Point2D.Double pos = getPosition(view);
+
+ // boolean isCellACluster = isCluster(view);
+
+ //the more edges a cell have, the heavier the cell is
+ double massIndex = getNodeWeight(view);
+
+ //gets the barycenter of all cells
+ Point2D.Double barycenter = computeBarycenter(cellList);
+
+ //attracting force from the barycenter to every cell
+ Point2D.Double gravitationForce = new Point2D.Double((barycenter.getX() - pos.getX()) * gravitation * massIndex,
+ (barycenter.getY() - pos.getY()) * gravitation * massIndex);
+
+ //random glitch is added to force
+ Point2D.Double randomImpulse = getRandomVector(randomImpulseRange);
+
+ //repulsive Forces
+ //from all nodes
+ ArrayList repulsiveForce = new ArrayList();
+
+ for (int i = 0; i < cellList.size(); i++)
+ if (cellList.get(i) != view) { //all cells except the actual view
+ // CellView uView = (CellView) cellList.get(i);
+ // if( !isCluster(uView)){
+
+ Point2D.Double uPos = getPosition(i, cellList);
+
+ double deltaX = (double) (pos.getX() - uPos.getX());
+ double deltaY = (double) (pos.getY() - uPos.getY());
+
+ /*
+ double sgnX = MathExtensions.sgn(deltaX);
+ double sgnY = MathExtensions.sgn(deltaY);
+
+ if( isCellACluster && isCluster(uView) ){
+ deltaX -= uView.getBounds().getWidth() / 2.0;
+ deltaY -= uView.getBounds().getHeight()/ 2.0;
+ }
+ if( isCellACluster ){
+ deltaX -= view.getBounds().getWidth() / 2.0;
+ deltaY -= view.getBounds().getHeight()/ 2.0;
+ }
+
+ if( sgnX != MathExtensions.sgn(deltaX) ){
+ deltaX *= sgnX;
+ }
+ if( sgnY != MathExtensions.sgn(deltaY) ){
+ deltaY *= sgnY;
+ }
+ */
+ double absDelta = MathExtensions.abs(deltaX, deltaY);
+
+ if (absDelta > equalsNull) {
+ repulsiveForce.add(new Point2D.Double(deltaX * ((prefEdgeLength * prefEdgeLength) / (absDelta * absDelta)),
+ deltaY * ((prefEdgeLength * prefEdgeLength) / (absDelta * absDelta))));
+ }
+
+ // }
+ }
+
+ //attractive Forces:
+ //from all nodes that have an edge with view
+ ArrayList relatives = getRelativesFrom(cellList, view);
+ ArrayList attractiveForce = new ArrayList(relatives.size());
+
+ for (int i = 0; i < relatives.size(); i++) {
+ // CellView child = (CellView) relatives.get(i);
+ Point2D.Double cPos = getPosition(i, relatives);
+
+ double deltaX = (double) (pos.getX() - cPos.getX());
+ double deltaY = (double) (pos.getY() - cPos.getY());
+
+ /*
+ double sgnX = MathExtensions.sgn(deltaX);
+ double sgnY = MathExtensions.sgn(deltaY);
+
+ if( isCellACluster && isCluster( child )){
+ deltaX -= child.getBounds().getWidth() / 2.0;
+ deltaY -= child.getBounds().getHeight()/ 2.0;
+ }
+ if( isCellACluster ){
+ deltaX -= view.getBounds().getWidth() / 2.0;
+ deltaY -= view.getBounds().getHeight()/ 2.0;
+ }
+
+ if( sgnX != MathExtensions.sgn(deltaX) )
+ deltaX *= sgnX;
+ if( sgnY != MathExtensions.sgn(deltaY) )
+ deltaY *= sgnY;
+ */
+ double absDelta = MathExtensions.abs(deltaX, deltaY);
+
+ attractiveForce.add(new Point2D.Double(deltaX * ((absDelta * absDelta) / (prefEdgeLength * prefEdgeLength * massIndex)),
+ deltaY * ((absDelta * absDelta) / (prefEdgeLength * prefEdgeLength * massIndex))));
+ }
+
+ /* the next part is NOT part of the original algorithm */
+ /* it adds a force if the actual cell overlapps another cell */
+ ArrayList forcesByOverlapping = new ArrayList();
+
+ if (avoidOverlapping) {
+ Rectangle viewBounds = new Rectangle((int) pos.x, (int) pos.y,
+ (int) view.getBounds().getWidth(),
+ (int) view.getBounds().getHeight());
+ Rectangle viewBorder = new Rectangle((int) (viewBounds.getX() - overlapDetectWidth),
+ (int) (viewBounds.getY() - overlapDetectWidth),
+ (int) (viewBounds.getWidth()
+ + (2.0 * overlapDetectWidth)),
+ (int) (viewBounds.getHeight()
+ + (2.0 * overlapDetectWidth)));
+
+ for (int i = 0; i < cellList.size(); i++) {
+ Point2D.Double uPos = getPosition(i, cellList);
+ Rectangle uBounds = new Rectangle((int) uPos.x, (int) uPos.y,
+ (int) ((CellView) cellList.get(i)).getBounds()
+ .getWidth(),
+ (int) ((CellView) cellList.get(i)).getBounds()
+ .getHeight());
+
+ if ((view != cellList.get(i)) && viewBorder.intersects(uBounds)) {
+ Dimension viewSize = viewBounds.getSize();
+ Dimension uSize = uBounds.getSize();
+
+ double minDistance = (Math.max(viewSize.getWidth(), viewSize.getHeight()) / 2.0)
+ + (Math.max(uSize.getWidth(), uSize.getHeight()) / 2.0)
+ + overlapPrefDistance;
+
+ double deltaX = (double) (pos.x - uPos.x);
+ double deltaY = (double) (pos.y - uPos.y);
+
+ /*
+ if( isCellACluster ){
+ deltaX -= view.getBounds().getWidth() / 2.0;
+ deltaY -= view.getBounds().getHeight()/ 2.0;
+ }
+ if( isCluster((CellView)cellList.get(i))){
+ deltaX -= ((CellView)cellList.get(i)).getBounds().getWidth() / 2.0;
+ deltaY -= ((CellView)cellList.get(i)).getBounds().getHeight()/ 2.0;
+ }*/
+ if ((deltaX < equalsNull) && (deltaX >= 0.0)) {
+ deltaX = equalsNull;
+ } else if ((deltaX > -equalsNull) && (deltaX <= 0.0)) {
+ deltaX = -equalsNull;
+ }
+
+ if ((deltaY < equalsNull) && (deltaY >= 0.0)) {
+ deltaY = equalsNull;
+ } else if ((deltaY > -equalsNull) && (deltaY <= 0.0)) {
+ deltaY = -equalsNull;
+ }
+
+ double absDelta = MathExtensions.abs(deltaX, deltaY);
+
+ Point2D.Double force = new Point2D.Double((deltaX * (minDistance * minDistance)) / (absDelta * absDelta),
+ (deltaY * (minDistance * minDistance)) / (absDelta * absDelta));
+ // System.out.println("Overlapping Nodes: ("+pos.x+"|"+pos.y+") and ("+uPos.x+"|"+uPos.y+") -> Distance = "+absDelta+" -> Force = "+force);
+ forcesByOverlapping.add(force);
+ }
+ }
+ }
+
+ ArrayList additionalForce = new ArrayList();
+
+ //adding the forces
+ impulse = add(impulse, gravitationForce);
+ impulse = add(impulse, randomImpulse);
+
+ for (int i = 0; i < repulsiveForce.size(); i++)
+ impulse = add(impulse, (Point2D.Double) repulsiveForce.get(i));
+
+ for (int i = 0; i < attractiveForce.size(); i++)
+ impulse = sub(impulse, (Point2D.Double) attractiveForce.get(i));
+
+ for (int i = 0; i < forcesByOverlapping.size(); i++)
+ impulse = add(impulse, (Point2D.Double) forcesByOverlapping.get(i));
+
+ for (int i = 0; i < additionalForce.size(); i++)
+ impulse = add(impulse, (Point2D.Double) additionalForce.get(i));
+
+ return impulse;
+ }
+
+ /******************************************************************************/
+ /**
+ * Updating the position of the given cell, by taking the direction of the
+ * current impulse and the length of the temperature of the cell. After this
+ * temperature will fall, when the last impulse and the current impulse are
+ * part of a rotation or a oscillation, temperature of the cell will be
+ * decreased.
+ *
+ * @param view Cell that should be updated
+ */
+ private void updatePosAndTemp(CellView view) {
+ Point2D.Double impulse = (Point2D.Double) view.getAttributes().get(KEY_CURRENT_IMPULSE);
+ Point2D.Double lastImpulse = (Point2D.Double) view.getAttributes().get(KEY_LAST_IMPULSE);
+ Point2D.Double position = getPosition(view);
+ double localTemperature = ((Double) view.getAttributes().get(KEY_TEMPERATURE)).doubleValue();
+ double skewGauge = ((Double) view.getAttributes().get(KEY_SKEWGAUGE)).doubleValue();
+ double absImpulse = MathExtensions.abs(impulse);
+ double absLastImpulse = MathExtensions.abs(lastImpulse);
+
+ if (absImpulse > equalsNull) { //if impulse != 0
+ //scaling with temperature
+
+ if (isCluster(view)) {
+ impulse.setLocation((impulse.getX() * localTemperature * clusterForceScalingFactor) / absImpulse,
+ (impulse.getY() * localTemperature * clusterForceScalingFactor) / absImpulse);
+ } else {
+ impulse.setLocation((impulse.getX() * localTemperature) / absImpulse,
+ (impulse.getY() * localTemperature) / absImpulse);
+ }
+
+ view.getAttributes().put(KEY_CURRENT_IMPULSE, impulse);
+ position.setLocation(position.getX() + impulse.getX(), position.getY() + impulse.getY());
+ view.getAttributes().put(KEY_POSITION, position);
+
+ /* if( isDebugging ){
+ check(impulse,"impulse12");
+ check(position,"position12");
+ }*/
+ }
+
+ if (absLastImpulse > equalsNull) {
+ //beta = angle between new and last impulse
+ double beta = MathExtensions.angleBetween(impulse, lastImpulse);
+
+ double sinBeta = Math.sin(beta);
+ double cosBeta = Math.cos(beta);
+
+ //detection for rotations
+ if (Math.abs(sinBeta) >= Math.sin((Math.PI / 2.0) + (alphaRot / 2.0)))
+ skewGauge += (sigmaRot * MathExtensions.sgn(sinBeta));
+
+ //detection for oscillation
+ if (cosBeta < Math.cos(Math.PI + (alphaOsc / 2.0)))
+ localTemperature *= (sigmaOsc * Math.abs(cosBeta));
+
+ localTemperature *= (1.0 - Math.abs(skewGauge));
+ localTemperature = Math.min(localTemperature, maxTemperature);
+ }
+
+ //applying changes
+ view.getAttributes().put(KEY_TEMPERATURE, new Double(localTemperature));
+ view.getAttributes().put(KEY_POSITION, position);
+ view.getAttributes().put(KEY_SKEWGAUGE, new Double(skewGauge));
+ view.getAttributes()
+ .put(KEY_LAST_IMPULSE, new Point2D.Double(impulse.getX(), impulse.getY()));
+
+ /* if( isDebugging )
+ checkCellList();*/
+ }
+
+ /******************************************************************************/
+ /**
+ * Adding two forces.
+ * @param v1 Force that should be added with v2
+ * @param v2 Force that should be added with v1
+ * @return Sum of both forces.
+ */
+ private Point2D.Double add(Point2D.Double v1, Point2D.Double v2) {
+ return new Point2D.Double(v1.getX() + v2.getX(), v1.getY() + v2.getY());
+ }
+
+ /******************************************************************************/
+ /**
+ * Subtracing two forces.
+ * @param v1 Force, v2 should be subtracted from
+ * @param v2 Force, that should be subtracted from v1.
+ */
+ private Point2D.Double sub(Point2D.Double v1, Point2D.Double v2) {
+ return new Point2D.Double(v1.getX() - v2.getX(), v1.getY() - v2.getY());
+ }
+
+ /******************************************************************************/
+ /**
+ * Returns all Cells, that have a direct connection with the given cell and are
+ * a member of the given list.
+ *
+ * @param list List of some cells, that should contain some relatives from view
+ * @param view Cell, the relatives are requested from
+ * @return List of all relatives that are in list.
+ * @see #getRelatives(CellView)
+ */
+ private ArrayList getRelativesFrom(ArrayList list, CellView view) {
+ ArrayList relatives = getRelatives(view);
+ ArrayList result = new ArrayList();
+
+ for (int i = 0; i < relatives.size(); i++)
+ if (list.contains(relatives.get(i)))
+ result.add(relatives.get(i));
+
+ return result;
+ }
+
+ /******************************************************************************/
+ /**
+ * Returns a list of all cells, that have a direct connection with the given
+ * cell via a edge. At the end of this method, the result is stored in the given
+ * cell, so it will be available the next time, the method runs. This temporary
+ * stored data will stay there, until the algorithm finishes
+ * (successfull or not).
+ *
+ * @param view Cell, the relatives requested from.
+ * @return List of all cells, that have a direct connection with a edge to
+ * the given cell.
+ */
+ private ArrayList getRelatives(CellView view) {
+ if (!(view instanceof VertexView)) {
+ new Exception("getRelatives 1").printStackTrace();
+
+ return null;
+ }
+
+ if (view.getAttributes().containsKey(KEY_RELATIVES))
+ return (ArrayList) view.getAttributes().get(KEY_RELATIVES);
+
+ ArrayList relatives = new ArrayList();
+
+ //if view is a cluster, then all clustered cells are extracted and
+ //getRelatives is called for every cell again. the resulting relatives
+ //are checked, if they are in the same cluster or another cluster.
+ //if the last condition is the case, the cluster is added, else the
+ //vertex is added to the list of relatives, iff he isn't already in the
+ //list
+ if (isCluster(view)) {
+ ArrayList clusteredVertices = (ArrayList) view.getAttributes()
+ .get(KEY_CLUSTERED_VERTICES);
+
+ for (int i = 0; i < clusteredVertices.size(); i++) {
+ ArrayList vertexRelatives = getRelatives((CellView) clusteredVertices.get(i));
+
+ for (int j = 0; j < vertexRelatives.size(); j++) {
+ CellView relative = (CellView) vertexRelatives.get(j);
+
+ if (!clusteredVertices.contains(relative)) {
+ /* if( relative.getAttributes().containsKey(KEY_CLUSTER) ){
+ relative = (CellView) relative.getAttributes().get(KEY_CLUSTER);
+ }*/
+ if (!relatives.contains(relative))
+ relatives.add(relative);
+ }
+ }
+ }
+ } else {
+ //runs only for vertices. finds all ports of the vertex. every
+ //edge in every port is checked on their source and target.
+ //the one, that isn't the vertex, we are searching the relatives of,
+ //is added to the list of relatives.
+ ArrayList portsCells = new ArrayList();
+
+ VertexView vertexView = (VertexView) view;
+ GraphModel model = jgraph.getModel();
+ CellMapper mapper = jgraph.getGraphLayoutCache();
+ Object vertexCell = vertexView.getCell();
+
+ for (int i = 0; i < model.getChildCount(vertexCell); i++) {
+ Object portCell = model.getChild(vertexCell, i);
+ portsCells.add(portCell);
+ }
+
+ for (int i = 0; i < portsCells.size(); i++) {
+ Object portCell = portsCells.get(i);
+
+ Iterator edges = model.edges(portCell);
+
+ while (edges.hasNext()) {
+ Object edge = edges.next();
+ Object nextPort = null;
+
+ if (model.getSource(edge) != portCell) {
+ nextPort = model.getSource(edge);
+ } else {
+ nextPort = model.getTarget(edge);
+ }
+
+ CellView nextVertex = mapper.getMapping(model.getParent(nextPort), true);
+ relatives.add(nextVertex);
+ }
+ }
+ }
+
+ view.getAttributes().put(KEY_RELATIVES, relatives);
+
+ return relatives;
+ }
+
+ /******************************************************************************/
+ /**
+ * This is a rating method for the cells. It is used during
+ * {@link #computeImpulse(CellView)} scale some forces.
+ *
+ * @param view Cell, the weight is of interest.
+ */
+
+ //TODO: method doesn't work right for clusters
+ private double getNodeWeight(CellView view) {
+ if (view.getAttributes().containsKey(KEY_MASSINDEX))
+ return ((Double) view.getAttributes().get(KEY_MASSINDEX)).doubleValue();
+
+ int childCount = getRelatives(view).size();
+ double massIndex = (double) (childCount + 1) / 2.0;
+
+ view.getAttributes().put(KEY_MASSINDEX, new Double(massIndex));
+
+ return massIndex;
+ }
+
+ /******************************************************************************/
+ /**
+ * Applies the changes to the Cells. This means, that all temporary stored
+ * positions are applied to all cells in {@link #applyCellList}
+ */
+ private boolean setNewCoordinates(JGraph jgraph) {
+ Map viewMap = new Hashtable();
+
+ for (int i = 0; i < cellList.size(); i++) {
+ Point2D.Double pos = getPosition(i, cellList);
+ Rectangle2D r = ((CellView) cellList.get(i)).getBounds();
+
+ r.setFrame(pos.getX() - ((double) r.getWidth() / 2.0),
+ pos.getY() - ((double) r.getHeight() / 2.0), r.getWidth(), r.getHeight());
+
+ Object cell = ((CellView) cellList.get(i)).getCell();
+
+ Map map = new Hashtable();
+ GraphConstants.setBounds(map, r);
+
+ viewMap.put(cell, map);
+ }
+
+ jgraph.getGraphLayoutCache().edit(viewMap, null, null, null);
+
+ return false;
+ }
+
+ /******************************************************************************/
+ /**
+ * Clears the temporary data from the cells in {@link #cellList} (all cells).
+ */
+ private void removeTemporaryLayoutDataFromCells() {
+ for (int i = 0; i < cellList.size(); i++)
+ ((CellView) cellList.get(i)).getAttributes().clear();
+ }
+
+ /******************************************************************************/
+ /**
+ * Checks, if the algorithm could break it's calculation earlier, than
+ * performing until {@link #countRounds} is {@link #maxRounds}. This depends on
+ * {@link #shouldEndPerAverage}.
+ *
+ */
+ private boolean isFrozen() {
+ double sumOfTemp = 0.0; //sum of temperatures to get the average value
+ double globalTemp = 0.0; //average value of all temperatures
+ boolean isFrozen = true; //true while all temperatures <= minTemperature
+
+ for (int i = 0; i < applyCellList.size(); i++) {
+ double temperature = getTemperature(i, applyCellList);
+ sumOfTemp += temperature;
+ isFrozen = isFrozen && (temperature <= minTemperature);
+
+ if (!isFrozen && !shouldEndPerAverage) //speeds up a little
+ break;
+ }
+
+ if (shouldEndPerAverage) {
+ globalTemp = sumOfTemp / (double) applyCellList.size();
+
+ return globalTemp < minTemperature;
+ } else
+
+ return isFrozen;
+ }
+
+ /******************************************************************************/
+ /**
+ * Erzeugt eine Permutation der Zahlen von 0 bis length
+ *
+ * @param length Count and highest value of the generated sequence.
+ * @return sequence of numbers, contains every number a single time. The
+ * sequence consists of numbers between 0 and length.
+ */
+ private int[] createPermutation(int length) {
+ int[] permutation = new int[length];
+
+ for (int i = 0; i < permutation.length; i++) {
+ int newValue = (int) (Math.random() * (double) length);
+
+ for (int j = 0; j < i; j++)
+ if (newValue == permutation[j]) {
+ newValue = (int) (Math.random() * (double) length);
+ j = -1; // wird auf 0 zur�ckgesetzt
+ }
+
+ permutation[i] = newValue;
+ }
+
+ return permutation;
+ }
+
+ /******************************************************************************/
+ /**
+ * Creates a random Vector, with a given length and a random direction.
+ *
+ * @param length Length of the Vector created by this method
+ * @return Vector represented by a Point2D.Double
+ */
+ private Point2D.Double getRandomVector(double length) {
+ double alpha = Math.random() * Math.PI * 2;
+
+ // double length = Math.random()*maxLength;
+ return new Point2D.Double(length * Math.cos(alpha), length * Math.sin(alpha));
+ }
+
+ /******************************************************************************/
+ /**
+ * Calculates the barycenter of a graph, given by a list. This calculation is
+ * done by summing the coordinates and dividing them with the number of
+ * coordinates.
+ *
+ * @param list List of CellView's
+ * @return Position of the barycenter
+ */
+ private Point2D.Double computeBarycenter(ArrayList list) {
+ double sumX = 0.0;
+ double sumY = 0.0;
+
+ for (int i = 0; i < list.size(); i++) {
+ CellView view = (CellView) list.get(i);
+
+ initPosition(view);
+
+ Point2D.Double pos = getPosition(view);
+ sumX += pos.x;
+ sumY += pos.y;
+ }
+
+ return new Point2D.Double(sumX / ((double) list.size()), sumY / ((double) list.size()));
+ }
+
+ /******************************************************************************/
+ /**
+ * Initialilzes the position of a CellView to the center point of the bounds
+ * of the cell. This initialization is only be done, when the cell isn't
+ * initialised before.
+ *
+ * @param view Cell, the position should be initialized.
+ */
+ private void initPosition(CellView view) {
+ if (!view.getAttributes().containsKey(KEY_POSITION))
+ view.getAttributes()
+ .put(KEY_POSITION,
+ new Point2D.Double(view.getBounds().getCenterX(), view.getBounds().getCenterY()));
+ }
+
+ /******************************************************************************/
+ /**
+ * Moves the graph to the upper left corner of the drawing space. This is done,
+ * after a successfull run of the algorithm, to correct it's output.
+ */
+ private void correctCoordinates() {
+ Rectangle boundingBox = getBoundingBox();
+
+ if (boundingBox != null) {
+ for (int i = 0; i < cellList.size(); i++) {
+ CellView view = (CellView) cellList.get(i);
+ Point2D.Double pos = getPosition(view);
+ Point2D.Double topLeftCorner = new Point2D.Double(pos.x
+ + ((view.getBounds().getWidth()) / 2),
+ pos.y
+ + ((view.getBounds().getHeight()) / 2));
+
+ Point2D.Double newPos = new Point2D.Double(topLeftCorner.x - boundingBox.getX(),
+ topLeftCorner.y - boundingBox.getY());
+ view.getAttributes().put(KEY_POSITION, newPos);
+ }
+ }
+ }
+
+ /******************************************************************************/
+ /**
+ * Computes the bounding box of the whole graph. The result is a Rectangle,
+ * parallel to the X- and Y-axises of the drawing system, closing about the
+ * whole graph.
+ * @return Rectangle, that contains the whole graph.
+ * @see #getBoundingBox(ArrayList)
+ */
+ private Rectangle getBoundingBox() {
+ return getBoundingBox(cellList);
+ }
+
+ /******************************************************************************/
+ /**
+ * Computes the bounding box of the graph in the given list of CellViews.
+ * The result is a Rectangle, parallel to the X- and Y-axises of the drawing
+ * system, closing about the graph in the given list.
+ *
+ * @param verticeList List containing the CellViews, the bounding box is of
+ * interest.
+ * @return Rectangle, that contains the whole graph, linked in the given list.
+ */
+ private Rectangle getBoundingBox(ArrayList verticeList) {
+ if (verticeList.size() > 0) {
+ Point2D.Double vertexPos = getPosition(0, verticeList);
+ Rectangle2D vertexSize = ((CellView) verticeList.get(0)).getBounds();
+
+ double minX = vertexPos.getX();
+ double minY = vertexPos.getY();
+ double maxX = vertexPos.getX() + vertexSize.getWidth();
+ double maxY = vertexPos.getY() + vertexSize.getHeight();
+
+ for (int i = 1; i < verticeList.size(); i++) {
+ vertexPos = getPosition(i, verticeList);
+ vertexSize = ((CellView) verticeList.get(i)).getBounds();
+
+ if (minX > vertexPos.getX())
+ minX = vertexPos.getX();
+
+ if (minY > vertexPos.getY())
+ minY = vertexPos.getY();
+
+ if (maxX < (vertexPos.getX() + vertexSize.getWidth()))
+ maxX = vertexPos.getX() + vertexSize.getWidth();
+
+ if (maxY < (vertexPos.getY() + vertexSize.getHeight()))
+ maxY = vertexPos.getY() + vertexSize.getHeight();
+ }
+
+ Rectangle boundingBox = new Rectangle((int) minX, (int) minY, (int) (maxX - minX),
+ (int) (maxY - minY));
+
+ return boundingBox;
+ }
+
+ return null;
+ }
+
+ /******************************************************************************/
+ /**
+ * Returns the Position of a Cell contained in {@link #applyCellList}.
+ *
+ * @param index Identifies the cell. This is the index of the cell in
+ * the given list of CellViews
+ * @param list List containing only CellViews
+ * @see #getAttribute(int,String,ArrayList)
+ */
+ private Point2D.Double getPosition(int index, ArrayList list) {
+ return (Point2D.Double) getAttribute(index, KEY_POSITION, list);
+ }
+
+ /******************************************************************************/
+ /**
+ * Returns the temperature of a cell contained in a given list.
+ *
+ * @param index Identifies the cell. This is the index of the cell in
+ * a given list of CellViews
+ * @param list List containing only CellViews
+ * @see #getAttribute(int,String,ArrayList)
+ */
+ private double getTemperature(int index, ArrayList list) {
+ Double temperature = (Double) getAttribute(index, KEY_TEMPERATURE, list);
+
+ return temperature.doubleValue();
+ }
+
+ /******************************************************************************/
+ /**
+ * Returns the Position of a Cell.
+ *
+ * @param cell The cell, that holds the position of interest.
+ */
+ private Point2D.Double getPosition(CellView cell) {
+ return (Point2D.Double) cell.getAttributes().get(KEY_POSITION);
+ }
+
+ /******************************************************************************/
+ /**
+ * Returns an attribute from a cell contained in a given list of CellViews.
+ *
+ * @param index Identifies the cell. This is the index of the cell in
+ * the given list of CellViews
+ * @param key Identifies the Attribute, that should be retrieved.
+ * @param list List containing only CellViews
+ */
+ private Object getAttribute(int index, String key, ArrayList list) {
+ CellView view = (CellView) list.get(index);
+
+ return view.getAttributes().get(key);
+ }
+
+ /******************************************************************************/
+ /**
+ * Arranges the initial cositions for the inserted cells. This is done, by
+ * placing the inserted cells in the barycenter of their relatives.
+ * (possible with errors ... might be fixed soon)
+ */
+ private void arrangePlacement(CellView[] views) {
+ for (int i = 0; i < cellList.size(); i++)
+ initPosition((CellView) cellList.get(i));
+
+ if (views != null) {
+ if (views.length > 0) {
+ ArrayList cellLevelList = new ArrayList();
+
+ for (int i = 0; i < views.length; i++) {
+ if (views[i] instanceof VertexView) {
+ ArrayList relatives = getRelativesFrom(cellList, views[i]);
+
+ if (relatives.size() > 0) {
+ if (views[i].getAttributes() == null)
+ views[i].changeAttributes(new AttributeMap());
+
+ views[i].getAttributes().put(KEY_POSITION, computeBarycenter(relatives));
+
+ cellLevelList.add(views[i]);
+ }
+ }
+ }
+
+ for (int i = 0; i < cellLevelList.size(); i++)
+ cellList.add(cellLevelList.get(i));
+
+ int childViewCount = 0;
+ CellView[] possibleChildViews = new CellView[views.length - cellLevelList.size()];
+
+ for (int i = 0; i < views.length; i++)
+ if (!cellLevelList.contains(views[i]))
+ possibleChildViews[childViewCount++] = views[i];
+
+ arrangePlacement(possibleChildViews);
+ }
+ }
+ }
+
+ /******************************************************************************/
+ /**
+ * Method for the process of layout update. Adds inserted cells to
+ * {@link #applyCellList} and some of their neighbors. Adding of neighbors is
+ * deceided by {@link #layoutUpdateMethod}. If a method is choosen with
+ * perimeter, than the inserted cells are counted, that have a position whithin
+ * the basic radius around inserted cells. then a new radius is calculated by
+ * multiplying the increasial radius with the number of inserted cells found and
+ * adding it to the basic radius. Then all cells, previously layouted whithin
+ * this radius are also added to {@link #applyCellList}. After this, cells
+ * within a given pathlength smaller than {@link #recursionDepth} are added
+ * to {@link #applyCellList} too.
+ *
+ * @param vertexList List of all inserted Vertices.
+ */
+ public void addApplyableVertices(VertexView[] vertexList) {
+ for (int i = 0; i < vertexList.length; i++) {
+ if (!applyCellList.contains(vertexList[i]))
+ applyCellList.add(vertexList[i]);
+
+ if (!cellList.contains(vertexList[i]))
+ cellList.add(vertexList[i]);
+ }
+
+ if (GEMLayoutSettings.KEY_LAYOUT_UPDATE_METHOD_PERIMETERS.equals(layoutUpdateMethod)) {
+ for (int i = 0; i < vertexList.length; i++) {
+ double perimeterSize = perimeterInitSize;
+ Point2D.Double pos = getPosition(vertexList[i]);
+
+ for (int j = 0; j < vertexList.length; j++) {
+ if (i != j) {
+ Point2D.Double oPos = getPosition(vertexList[j]);
+
+ if (Math.abs(pos.distance(oPos)) < (perimeterInitSize / 2.0))
+ perimeterSize += perimeterSizeInc;
+ }
+ }
+
+ for (int j = 0; j < cellList.size(); j++) {
+ Point2D.Double uPos = getPosition(j, cellList);
+
+ if ((Math.abs(pos.distance(uPos)) < (perimeterSize / 2.0))
+ && !applyCellList.contains(cellList.get(j)))
+ applyCellList.add(cellList.get(j));
+ }
+ }
+
+ vertexList = new VertexView[applyCellList.size()];
+
+ for (int i = 0; i < applyCellList.size(); i++)
+ vertexList[i] = (VertexView) applyCellList.get(i);
+ }
+
+ if (recursionDepth > 0)
+ addRelativesToList(vertexList, recursionDepth);
+ }
+
+ /******************************************************************************/
+ /**
+ * Recursiv method for adding all relatives whithin a given pathlength away
+ * from the given array of Vertices to {@link #applyCellList}.
+ *
+ * @param vertexList List of Vertices, which relatives might be added.
+ * @param depth pathlength, the vertices adding to {@link #applyCellList} could
+ * be away from the given array's vertices.
+ */
+ private void addRelativesToList(VertexView[] vertexList, int depth) {
+ if (vertexList == null)
+ return;
+
+ if (vertexList.length == 0)
+ return;
+
+ if (depth == 0)
+ return;
+
+ for (int i = 0; i < vertexList.length; i++) {
+ ArrayList relatives = getRelatives(vertexList[i]);
+ VertexView[] relativeList = new VertexView[relatives.size()];
+
+ for (int j = 0; j < relatives.size(); j++) {
+ if (!applyCellList.contains(relatives.get(j)))
+ applyCellList.add(relatives.get(j));
+
+ if (!cellList.contains(relatives.get(j)))
+ cellList.add(relatives.get(j));
+
+ relativeList[j] = (VertexView) relatives.get(j);
+ }
+
+ addRelativesToList(relativeList, depth - 1);
+ }
+ }
+
+ /******************************************************************************/
+ /**
+ * Will be called, when cells are inserted or removed. When cells are removed,
+ * they are also removed from {@link #cellList}, {@link #applyCellList} and
+ * {@link #edgeList}. If cells are inserted a new layout update process starts.
+ */
+ public void graphChanged(GraphModelEvent e) {
+ if (!isRunning && isActive) {
+ isRunning = true;
+
+ GraphModelEvent.GraphModelChange change = e.getChange();
+
+ Object[] objRem = change.getRemoved();
+ Object[] objIns = change.getInserted();
+
+ if ((objRem == null) && (objIns != null)) { // nodes inserted
+
+ for (int i = 0; i < cellList.size(); i++)
+ initPosition((CellView) cellList.get(i));
+
+ CellView[] viewInserted = jgraph.getGraphLayoutCache().getMapping(objIns, false);
+
+ applyCellList = new ArrayList();
+
+ /*extracting vertices into []*/
+ int vertexViewCount = 0;
+
+ for (int i = 0; i < viewInserted.length; i++)
+ if (viewInserted[i] instanceof VertexView)
+ vertexViewCount++;
+
+ VertexView[] vertexList = new VertexView[vertexViewCount];
+ vertexViewCount = 0;
+
+ for (int i = 0; i < viewInserted.length; i++)
+ if (viewInserted[i] instanceof VertexView)
+ vertexList[vertexViewCount++] = (VertexView) viewInserted[i];
+
+ /*extracting vertices into [] done*/
+
+ //stops inserting process, if no vertex was inserted
+ if (vertexList.length == 0) {
+ isRunning = false;
+
+ return;
+ }
+
+ //initialising runtime values from config
+ loadRuntimeValues(VALUES_INC);
+
+ //the number of cells in applyCellList will probably change
+ sigmaRot /= (1.0 / (double) applyCellList.size());
+
+ //positioning the new nodes in the barycenter of old relatives
+ arrangePlacement(vertexList);
+
+ //add new vertices and some relatives to applyCellList
+ addApplyableVertices(vertexList);
+
+ if (applyCellList.size() == 0) {
+ isRunning = false;
+
+ return;
+ }
+
+ // showCellList(applyCellList,Color.GREEN);
+ if (isClusteringEnabled) {
+ clusterGraph();
+ }
+
+ //the number of cells in applyCellList has changed probably
+ sigmaRot *= (1.0 / (double) applyCellList.size());
+ maxRounds = applyCellList.size() * 4;
+
+ // performing algorithm on all nodes in applyCellList
+ initialize();
+ calculate();
+
+ // algorithm done
+ if (isClusteringEnabled)
+ declusterGraph();
+
+ if (useOptimizeAlgorithm)
+ optimizationAlgorithm.run(jgraph, jgraph.getRoots(), null);
+
+ //moves graph to the upper left corner
+ correctCoordinates();
+
+ //taking changes
+ setNewCoordinates(jgraph);
+
+ //removing algorithms attributes from nodes
+ removeTemporaryLayoutDataFromCells();
+ } else if ((objRem != null) && (objIns == null)) { // nodes removed
+
+ CellView[] viewRemoved = jgraph.getGraphLayoutCache().getMapping(objRem, false);
+
+ for (int i = 0; i < viewRemoved.length; i++) {
+ if (viewRemoved[i] instanceof VertexView && cellList.contains(viewRemoved[i])) {
+ applyCellList.remove(viewRemoved[i]);
+ cellList.remove(viewRemoved[i]);
+ }
+ }
+ }
+
+ isRunning = false;
+ }
+ }
+
+ /******************************************************************************/
+ /******************** CLUSTERING METHODS **************************************/
+ /******************************************************************************/
+
+ /**
+ * Clusters a graph. Cells, contained in {@link #cellList} and not contained
+ * in {@link #applyCellList} are clustered by this short algorithm. The
+ * algorithm first tries to identify how many cells it should cluster. This
+ * is calculated by subtracting the size of {@link #applyCellList} from
+ * the size of {@link #cellList} and dividing the result by the
+ * {@link #clusteringFactor}. In the next step, the identified number of
+ * clusters are created, and their position is initialised by random. Then
+ * every clusterable cell is added to the cluster where the distance of the
+ * vertex and the cluster is minimal. After adding a cell, the clusters position
+ * is recalculated. Finishing this step, the algorithm tries to minimize the
+ * number of clusters, by sorting the clustered vertices, if there is another
+ * cluster, that distance is shorter than the distance to the cluster, the
+ * vertice is actually in. This can happen, because by moving vertices into the
+ * clusters, the position of the clusters are changed. The minimization runs
+ * until no vertice can be moved anymore. empty clusters are removed and finaly
+ * the clusters are added to {@link #applyCellList}, because they should move
+ * while the upcoming next calculations. That move can later be retrieved by
+ * subtracting the attributes {@link #KEY_POSITION} and
+ * {@link #KEY_CLUSTER_INIT_POSITION}.
+ *
+ * @see #declusterGraph()
+ */
+ protected void clusterGraph() {
+ //initialisation
+ int maxClusters = (int) ((double) (cellList.size() - applyCellList.size()) / clusteringFactor);
+
+ if (maxClusters == 0) {
+ // System.out.println("maxClusters = 0");
+
+ return;
+ }
+
+ if (cellList.size() <= 1) {
+ // System.out.println("cellList.size() <= 1");
+
+ return;
+ }
+
+ ArrayList clusterList = new ArrayList();
+ ArrayList cellsToCluster = new ArrayList();
+
+ //identifying all cells, that are clusterable
+ for (int i = 0; i < cellList.size(); i++)
+ if (!applyCellList.contains(cellList.get(i)))
+ cellsToCluster.add(cellList.get(i));
+
+ //initialize clusters
+ VertexView[] clusters = new VertexView[maxClusters];
+ Rectangle boundingBox = getBoundingBox();
+
+ for (int i = 0; i < clusters.length; i++) {
+ clusters[i] = new VertexView(null);
+
+ Map attributes = clusters[i].getAttributes();
+ attributes.put(KEY_IS_CLUSTER, "true");
+ attributes.put(KEY_POSITION,
+ new Point2D.Double(Math.random() * boundingBox.width,
+ Math.random() * boundingBox.height));
+ clusterList.add(clusters[i]);
+ }
+
+ //cluster all available cells
+ for (int i = 0; i < cellsToCluster.size(); i++) {
+ VertexView cell = (VertexView) cellsToCluster.get(i);
+ Point2D.Double cellPos = getPosition(cell);
+ int clusterID = 0;
+ Point2D.Double clusterPos = getPosition((CellView) clusterList.get(0));
+ double minDistance = MathExtensions.getEuclideanDistance(cellPos, clusterPos);
+
+ //search for nearest cluster
+ for (int j = 1; j < clusterList.size(); j++) {
+ clusterPos = getPosition(j, clusterList);
+
+ double distance = MathExtensions.getEuclideanDistance(cellPos, clusterPos);
+
+ if (minDistance > distance) {
+ minDistance = distance;
+ clusterID = j;
+ }
+ }
+
+ VertexView cluster = (VertexView) clusterList.get(clusterID);
+ moveVerticeToCluster(cell, cluster);
+ }
+
+ //initialization done
+
+ //sorting the clustered vertices. if a vertice is nearer to a clusters
+ //barycenter then to it's own clusters barycenter the vertice is moved
+ //to that cluster. The coordinates of both clusters are recalculated.
+ //this is done, until nothing could be done better.
+ boolean couldMakeItBetter = false;
+
+ do {
+ couldMakeItBetter = false;
+
+ for (int i = 0; i < cellsToCluster.size(); i++) {
+ VertexView cell = (VertexView) cellsToCluster.get(i);
+ VertexView oldCluster = (VertexView) cell.getAttributes().get(KEY_CLUSTER);
+ Point2D.Double cellPos = getPosition(cell);
+ Point2D.Double clusterPos = getPosition(oldCluster);
+ double distance = MathExtensions.getEuclideanDistance(cellPos, clusterPos);
+
+ for (int j = 0; j < clusterList.size(); j++) {
+ VertexView cluster = (VertexView) clusterList.get(j);
+
+ if (cluster != oldCluster) {
+ clusterPos = getPosition(cluster);
+
+ double newDistance = MathExtensions.getEuclideanDistance(cellPos, clusterPos);
+
+ if (newDistance < distance) {
+ moveVerticeToCluster(cell, cluster);
+ couldMakeItBetter = true;
+
+ break;
+ }
+ }
+ }
+ }
+ } while (couldMakeItBetter);
+
+ //empty clusters are removed
+ for (int i = 0; i < clusterList.size(); i++) {
+ if (!((VertexView) clusterList.get(i)).getAttributes()
+ .containsKey(KEY_CLUSTERED_VERTICES)) {
+ clusterList.remove(i--);
+ } else if (((ArrayList) ((VertexView) clusterList.get(i)).getAttributes()
+ .get(KEY_CLUSTERED_VERTICES)).size() == 0) {
+ clusterList.remove(i--);
+ }
+ }
+
+ //remove clustered vertices from cellList
+ for (int i = 0; i < cellsToCluster.size(); i++)
+ cellList.remove(cellsToCluster.get(i));
+
+ //adding clusters to applyCellList and cellList
+ for (int i = 0; i < clusterList.size(); i++) {
+ applyCellList.add(clusterList.get(i));
+ cellList.add(clusterList.get(i));
+ }
+
+ //storing a copy of position, to move vertices while declustering
+ for (int i = 0; i < clusterList.size(); i++) {
+ VertexView cluster = (VertexView) clusterList.get(i);
+ Map attribs = cluster.getAttributes();
+ Point2D.Double clusterPos = (Point2D.Double) attribs.get(KEY_POSITION);
+ attribs.put(KEY_CLUSTER_INIT_POSITION, new Point2D.Double(clusterPos.x, clusterPos.y));
+ }
+
+ for (int i = 0; i < clusterList.size(); i++) {
+ VertexView cluster = (VertexView) clusterList.get(i);
+ cluster.setCachedBounds(getBoundingBox((ArrayList) cluster.getAttributes()
+ .get(KEY_CLUSTERED_VERTICES)));
+ }
+
+ colorizeClusters(clusterList);
+ stop(20);
+ }
+
+ /******************************************************************************/
+ /**
+ * Moves a vertice from the cluster, it is holded, to another cluster. This
+ * implies that the vertice is removed from the old cluster and added to the
+ * new. After this, the positions of the old and the new cluster are
+ * recalculated.
+ *
+ * @param vertice Vertex that should be moved
+ * @param cluster Cluster the vertex should be moved
+ */
+ protected void moveVerticeToCluster(VertexView vertice, VertexView cluster) {
+ //adding vertice to new cluster
+ if (!cluster.getAttributes().containsKey(KEY_CLUSTERED_VERTICES))
+ cluster.getAttributes().put(KEY_CLUSTERED_VERTICES, new ArrayList());
+
+ ArrayList clusteredVertices = (ArrayList) cluster.getAttributes().get(KEY_CLUSTERED_VERTICES);
+ clusteredVertices.add(vertice);
+
+ //removing vertice from old cluster
+ if (vertice.getAttributes().containsKey(KEY_CLUSTER)) {
+ VertexView oldCluster = (VertexView) vertice.getAttributes().get(KEY_CLUSTER);
+ ArrayList list = (ArrayList) oldCluster.getAttributes().get(KEY_CLUSTERED_VERTICES);
+ list.remove(vertice);
+ computeClusterPosition(oldCluster);
+ }
+
+ //register cluster in vertice
+ vertice.getAttributes().put(KEY_CLUSTER, cluster);
+ //reposition cluster
+ computeClusterPosition(cluster);
+ }
+
+ /******************************************************************************/
+ /**
+ * Recalculates the position of a cluster. The position of a cluster is defined
+ * by the barycenter of the clustered vertices.
+ *
+ * @param cluster Cell, that has to be a cluster, should be repositioned.
+ */
+ protected void computeClusterPosition(VertexView cluster) {
+ ArrayList clusteredVertices = (ArrayList) cluster.getAttributes().get(KEY_CLUSTERED_VERTICES);
+ Point2D.Double clusterPos = computeBarycenter(clusteredVertices);
+ cluster.getAttributes().put(KEY_POSITION, clusterPos);
+ }
+
+ /******************************************************************************/
+ /**
+ * Moves all clusters from {@link #cellList} and {@link #applyCellList},
+ * extracts their clustered vertices and adds them to {@link #cellList}. While
+ * doing this, it repositions the clustered vertices with the move, the cluster
+ * has made during the calculation.
+ *
+ * @see #clusterGraph()
+ */
+ protected void declusterGraph() {
+ if (cellList.size() <= 1)
+ return;
+
+ //first collecting all clusters from applyCellList
+ ArrayList clusterList = new ArrayList();
+
+ for (int i = 0; i < cellList.size(); i++) {
+ VertexView cell = ((VertexView) cellList.get(i));
+
+ if (isCluster(cell))
+ clusterList.add(cell);
+ }
+
+ if (clusterList.size() == 0)
+ return;
+
+ //cleaning up the cell lists
+ for (int i = 0; i < clusterList.size(); i++) {
+ cellList.remove(clusterList.get(i));
+ applyCellList.remove(clusterList.get(i));
+ }
+
+ //repositioning and extracting vertices to cellList
+ for (int i = 0; i < clusterList.size(); i++) {
+ VertexView cluster = (VertexView) clusterList.get(i);
+ Map attribs = cluster.getAttributes();
+ Point2D.Double newClusterPos = getPosition(cluster);
+ Point2D.Double oldClusterPos = (Point2D.Double) attribs.get(KEY_CLUSTER_INIT_POSITION);
+
+ //calculating move, cluster has made during his existance
+ Point2D.Double move = new Point2D.Double(newClusterPos.x - oldClusterPos.x,
+ newClusterPos.y - oldClusterPos.y);
+ ArrayList vertexList = (ArrayList) attribs.get(KEY_CLUSTERED_VERTICES);
+
+ //applying move to clustered vertices
+ for (int j = 0; j < vertexList.size(); j++) {
+ VertexView cell = (VertexView) vertexList.get(j);
+ Point2D.Double cellPos = getPosition(cell);
+ Point2D.Double newCellPos = new Point2D.Double(cellPos.x + move.x,
+ cellPos.y + move.y);
+ cell.getAttributes().put(KEY_POSITION, newCellPos);
+ //refilling clustered vertices in cellList
+ cellList.add(cell);
+ }
+ }
+ }
+
+ /******************************************************************************/
+ /**
+ * Returns <code><b>true</b></code> when a cell is a cluster, else
+ * <code<b>false</b></code>. A cell is a cluster when it has under it's
+ * attributes a attribute with the boolean value <code><b>true</b></code> under
+ * the key {@link #KEY_IS_CLUSTER}.
+ *
+ * @param cell cell, that should be researched wheather it is a cluster or not.
+ * @return <code><b>true</b></code> if cell is a cluster, else
+ * <code><b>false</b></code>.
+ */
+ protected boolean isCluster(CellView cell) {
+ if (cell.getAttributes().containsKey(KEY_IS_CLUSTER)) {
+ if (isTrue((String) cell.getAttributes().get(KEY_IS_CLUSTER))) {
+ return true;
+ } else {
+ System.err.println("FATAL ERROR: CELL CANNOT CLEARLY BE IDENTIFIED AS A CLUSTER!!!");
+
+ return false;
+ }
+ } else
+
+ return false;
+ }
+
+ /******************************************************************************/
+ private void colorizeClusters(ArrayList clusterList) {
+ Color[] colorList = new Color[] {
+ Color.black, Color.magenta, Color.yellow, Color.blue, Color.green,
+ Color.gray, Color.cyan, Color.red, Color.darkGray, Color.lightGray,
+ Color.orange, Color.pink
+ };
+
+ for (int i = 0; i < clusterList.size(); i++)
+ if (i < colorList.length) {
+ ArrayList clusteredVertices = (ArrayList) ((CellView) clusterList.get(i)).getAttributes()
+ .get(KEY_CLUSTERED_VERTICES);
+ showCellList(clusteredVertices, colorList[i]);
+ }
+ }
+
+ /******************************************************************************/
+ private void showCellList(ArrayList list, Color color) {
+ Map viewMap = new Hashtable();
+
+ for (int i = 0; i < list.size(); i++) {
+ CellView view = (CellView) list.get(i);
+ Point2D.Double pos = getPosition(i, list);
+ Rectangle2D r = view.getBounds();
+
+ r.setFrame(pos.getX() - ((double) r.getWidth() / 2.0),
+ pos.getY() - ((double) r.getHeight() / 2.0), r.getWidth(), r.getHeight());
+
+ Object cell = view.getCell();
+
+ Map attributes = new Hashtable();
+
+ GraphConstants.setBackground(attributes, color);
+ GraphConstants.setBounds(attributes, r);
+
+ viewMap.put(cell, attributes);
+ }
+
+ jgraph.getGraphLayoutCache().edit(viewMap, null, null, null);
+ }
+
+ /******************************************************************************/
+ private synchronized void stop(double sec) {
+ try {
+ wait((long) (sec * 1000.0));
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+ }
+
+ /******************************************************************************/
+ private void stop(int sec) {
+ stop((double) sec);
+ }
+
+ /**
+ * @author winkler
+ *
+ * To change this generated comment edit the template variable "typecomment":
+ * Window>Preferences>Java>Templates.
+ * To enable and disable the creation of type comments go to
+ * Window>Preferences>Java>Code Generation.
+ */
+
+ /**
+ * @return Returns the optimizationAlgorithm.
+ */
+ public AnnealingLayoutAlgorithm getOptimizationAlgorithm() {
+ return optimizationAlgorithm;
+ }
+
+ /**
+ * @return Returns the config.
+ */
+ public Properties getConfig() {
+ return config;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param configuration DOCUMENT ME!
+ */
+ public void setConfig(Properties configuration) {
+ this.config = configuration;
+ loadRuntimeValues(VALUES_PUR);
+ }
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/layout/GEMLayoutSettings.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/layout/GEMLayoutSettings.java
new file mode 100644
index 0000000..fbbce89
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/layout/GEMLayoutSettings.java
@@ -0,0 +1,2036 @@
+/*
+ * @(#)GEMLayoutConfigurationDialog.java 1.0 12.08.2003
+ *
+ * Copyright (C) 2004-2005 Gaudenz Alder
+ * All rights reserved.
+ *
+ * This library is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation; either
+ * version 2.1 of the License, or (at your option) any later version.
+ *
+ * This library is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this library; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+ */
+package org.jgraph.layout;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.GridLayout;
+import java.awt.Insets;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import java.util.ArrayList;
+import java.util.Properties;
+
+import javax.swing.BorderFactory;
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JComboBox;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTabbedPane;
+import javax.swing.JTextField;
+import javax.swing.border.TitledBorder;
+
+
+/**
+ * @author winkler
+ * @author Sven Luzar
+ *
+ */
+public class GEMLayoutSettings extends JPanel implements JGraphLayoutSettings {
+ /**
+ *
+ */
+ public final static String KEY_TITLE = "GEM";
+
+ /**
+ *
+ */
+ public final static String KEY_CONFIG_NAME = "CONFIG_NAME";
+
+ /**
+ *
+ */
+ public final static String KEY_INIT_TEMPERATURE = "init temperature";
+
+ /**
+ *
+ */
+ public final static String KEY_MIN_TEMPERATURE = "min temperature";
+
+ /**
+ *
+ */
+ public final static String KEY_MAX_TEMPERATURE = "max temperature";
+
+ /**
+ *
+ */
+ public final static String KEY_PREF_EDGE_LENGTH = "preferred Edge length";
+
+ /**
+ *
+ */
+ public final static String KEY_GRAVITATION = "gravitation to barycenter";
+
+ /**
+ *
+ */
+ public final static String KEY_RANDOM_IMPULSE_RANGE = "random impulse range";
+
+ /**
+ *
+ */
+ public final static String KEY_COMPUTE_PERMUTATION = "compute permutation";
+
+ /**
+ *
+ */
+ public final static String KEY_END_CONDITION_AVERAGE = "end condition average";
+
+ /**
+ *
+ */
+ public final static String KEY_AVOID_OVERLAPPING = "avoid overlapping";
+
+ /**
+ *
+ */
+ public final static String KEY_OVERLAPPING_DETECTION_WIDTH = "overlapping detection width";
+
+ /**
+ *
+ */
+ public final static String KEY_OVERLAPPING_PREF_DISTANCE = "overlapping preferred distance";
+
+ /**
+ *
+ */
+ public final static String KEY_ALPHA_OSC = "alpha oscillation";
+
+ /**
+ *
+ */
+ public final static String KEY_ALPHA_ROT = "alpha rotation";
+
+ /**
+ *
+ */
+ public final static String KEY_SIGMA_OSC = "sigma oscillation";
+
+ /**
+ *
+ */
+ public final static String KEY_SIGMA_ROT = "sigma rotation";
+
+ /**
+ *
+ */
+ public final static String KEY_OPTIMIZE_ALGORITHM_ENABLED = "optimization algorithm enabled";
+
+ /**
+ *
+ */
+ public final static String KEY_OPTIMIZE_ALGORITHM_CONFIG = "optimization algorithm configuration";
+
+ /**
+ *
+ */
+ public final static String KEY_LAYOUT_UPDATE_INIT_TEMPERATURE = "Layout Update init temperature";
+
+ /**
+ *
+ */
+ public final static String KEY_LAYOUT_UPDATE_MIN_TEMPERATURE = "Layout Update min temperature";
+
+ /**
+ *
+ */
+ public final static String KEY_LAYOUT_UPDATE_MAX_TEMPERATURE = "Layout Update max temperature";
+
+ /**
+ *
+ */
+ public final static String KEY_LAYOUT_UPDATE_PREF_EDGE_LENGTH = "Layout Update preferred Edge length";
+
+ /**
+ *
+ */
+ public final static String KEY_LAYOUT_UPDATE_GRAVITATION = "Layout Update gravitation to barycenter";
+
+ /**
+ *
+ */
+ public final static String KEY_LAYOUT_UPDATE_RANDOM_IMPULSE_RANGE = "Layout Update random impulse range";
+
+ /**
+ *
+ */
+ public final static String KEY_LAYOUT_UPDATE_COMPUTE_PERMUTATION = "Layout Update compute permutation";
+
+ /**
+ *
+ */
+ public final static String KEY_LAYOUT_UPDATE_END_CONDITION_AVERAGE = "Layout Update end condition average";
+
+ /**
+ *
+ */
+ public final static String KEY_LAYOUT_UPDATE_AVOID_OVERLAPPING = "Layout Update avoid overlapping";
+
+ /**
+ *
+ */
+ public final static String KEY_LAYOUT_UPDATE_OVERLAPPING_DETECTION_WIDTH = "Layout Update overlapping detection width";
+
+ /**
+ *
+ */
+ public final static String KEY_LAYOUT_UPDATE_OVERLAPPING_PREF_DISTANCE = "Layout Update overlapping preferred distance";
+
+ /**
+ *
+ */
+ public final static String KEY_LAYOUT_UPDATE_ALPHA_ROT = "Layout Update alpha oscillation";
+
+ /**
+ *
+ */
+ public final static String KEY_LAYOUT_UPDATE_ALPHA_OSC = "Layout Update alpha rotation";
+
+ /**
+ *
+ */
+ public final static String KEY_LAYOUT_UPDATE_SIGMA_ROT = "Layout Update sigma oscillation";
+
+ /**
+ *
+ */
+ public final static String KEY_LAYOUT_UPDATE_SIGMA_OSC = "Layout Update sigma rotation";
+
+ /**
+ *
+ */
+ public final static String KEY_LAYOUT_UPDATE_ENABLED = "Layout Update enabled";
+
+ /**
+ *
+ */
+ public final static String KEY_LAYOUT_UPDATE_METHOD = "Layout Update method";
+
+ /**
+ *
+ */
+ public final static String KEY_LAYOUT_UPDATE_OPTIMIZE_ALGORITHM_ENABLED = "Layout Update optimization algorithm enabled";
+
+ /**
+ *
+ */
+ public final static String KEY_LAYOUT_UPDATE_OPTIMIZE_ALGORITHM_CONFIG = "Layout Update optimization algorithm configuration";
+
+ /**
+ *
+ */
+ public final static String KEY_LAYOUT_UPDATE_METHOD_NEIGHBORS_ONLY = "Neighbors only";
+
+ /**
+ *
+ */
+ public final static String KEY_LAYOUT_UPDATE_METHOD_PERIMETERS = "Perimeter";
+
+ /**
+ *
+ */
+ public final static String KEY_LAYOUT_UPDATE_DEPTH = "Layout Update depth";
+
+ /**
+ *
+ */
+ public final static String KEY_LAYOUT_UPDATE_METHOD_PERIMETER_INIT_SIZE = "Layout Update method perimeter initial size";
+
+ /**
+ *
+ */
+ public final static String KEY_LAYOUT_UPDATE_METHOD_PERIMETER_SIZE_INC = "Layout Update method perimeter size increase value";
+
+ /**
+ *
+ */
+ public final static String KEY_LAYOUT_UPDATE_CLUSTERING_ENABLED = "clustering enabled";
+
+ /**
+ *
+ */
+ public final static String KEY_LAYOUT_UPDATE_CLUSTERING_INIT_TEMPERATURE = "cluster init temperature";
+
+ /**
+ *
+ */
+ public final static String KEY_LAYOUT_UPDATE_CLUSTERING_FORCE_SCALING_FACTOR = "clustering force scaling factor";
+
+ /**
+ *
+ */
+ public final static String KEY_LAYOUT_UPDATE_CLUSTERING_FACTOR = "cluster size factor";
+ protected GEMLayoutAlgorithm layout;
+ private JTextField tf_initTemperature;
+ private JTextField tf_minTemperature;
+ private JTextField tf_maxTemperature;
+ private JTextField tf_prefEdgeLength;
+ private JTextField tf_gravitation;
+ private JTextField tf_randomImpulseRange;
+ private JTextField tf_overlapDetectWidth;
+ private JTextField tf_overlapPrefDistance;
+ private JTextField tf_alphaOsc;
+ private JTextField tf_alphaRot;
+ private JTextField tf_sigmaOsc;
+ private JTextField tf_sigmaRot;
+ private JTextField tf_lu_initTemperature;
+ private JTextField tf_lu_minTemperature;
+ private JTextField tf_lu_maxTemperature;
+ private JTextField tf_lu_prefEdgeLength;
+ private JTextField tf_lu_gravitation;
+ private JTextField tf_lu_randomImpulseRange;
+ private JTextField tf_lu_overlapDetectWidth;
+ private JTextField tf_lu_overlapPrefDistance;
+ private JTextField tf_lu_alphaOsc;
+ private JTextField tf_lu_alphaRot;
+ private JTextField tf_lu_sigmaOsc;
+ private JTextField tf_lu_sigmaRot;
+ private JTextField tf_lu_depth;
+ private JTextField tf_lu_cluster_initTemperature;
+ private JTextField tf_lu_cluster_forceScalingFactor;
+ private JTextField tf_lu_cluster_factor;
+ private JTextField tf_lu_perimeter_initSize;
+ private JTextField tf_lu_perimeter_sizeInc;
+ private JCheckBox cb_computePermutation;
+ private JCheckBox cb_endPerAverage;
+ private JCheckBox cb_avoidOverlapping;
+ private JCheckBox cb_useOptimizationAlg;
+ private JCheckBox cb_lu_enableLayoutUpdate;
+ private JCheckBox cb_lu_computePermutation;
+ private JCheckBox cb_lu_endPerAverage;
+ private JCheckBox cb_lu_avoidOverlapping;
+ private JCheckBox cb_lu_useOptimizationAlg;
+ private JCheckBox cb_lu_cluster_enable;
+ private JComboBox comb_lu_method;
+ private JComboBox comb_loadPreSets;
+ private JButton button_ConfigOptimizeAlg;
+ private JButton button_lu_ConfigOptimizeAlg;
+ private JPanel panelLayoutUpdate;
+ private JScrollPane panelLayoutRunWrapper;
+ private JScrollPane panelLayoutUpdateWrapper;
+
+ //private JPanel panelLUClusterWrapper;
+ private Properties[] presetConfigs;
+ private AnnealingLayoutSettings optimizeAlgController;
+ private AnnealingLayoutSettings lu_optimizeAlgController;
+ private JTabbedPane tp_main;
+
+ /******************************************************************************/
+ /**
+ * Creates new form GEMLayoutConfigurationDialog
+ */
+ public GEMLayoutSettings(GEMLayoutAlgorithm layout) {
+ this.layout = layout;
+
+ optimizeAlgController = new AnnealingLayoutSettings(new AnnealingLayoutAlgorithm(true), true);
+ lu_optimizeAlgController = new AnnealingLayoutSettings(new AnnealingLayoutAlgorithm(true),
+ true);
+
+ // Create Presets
+ Properties[] configs = new Properties[2];
+
+ for (int i = 0; i < configs.length; i++)
+ configs[i] = new Properties();
+
+ Properties optimizeConfig = optimizeAlgController.getConfiguration();
+ optimizeConfig.put(KEY_CONFIG_NAME, KEY_TITLE + " optimization values");
+ optimizeConfig.put(AnnealingLayoutSettings.KEY_COST_FUNCTION_CONFIG, "110111");
+ optimizeConfig.put(AnnealingLayoutSettings.KEY_INIT_TEMPERATURE, "40.0");
+ optimizeConfig.put(AnnealingLayoutSettings.KEY_MIN_DISTANCE, "100.0");
+ optimizeConfig.put(AnnealingLayoutSettings.KEY_TEMP_SCALE_FACTOR, "0.85");
+ optimizeAlgController.setConfiguration(optimizeConfig);
+
+ Properties lu_optimizeConfig = lu_optimizeAlgController.getConfiguration();
+ lu_optimizeConfig.put(KEY_CONFIG_NAME, KEY_TITLE + " optimization values");
+ lu_optimizeConfig.put(AnnealingLayoutSettings.KEY_COST_FUNCTION_CONFIG, "110111");
+ lu_optimizeConfig.put(KEY_INIT_TEMPERATURE, "40.0");
+ lu_optimizeConfig.put(AnnealingLayoutSettings.KEY_MIN_DISTANCE, "100.0");
+ lu_optimizeConfig.put(AnnealingLayoutSettings.KEY_TEMP_SCALE_FACTOR, "0.85");
+ lu_optimizeAlgController.setConfiguration(lu_optimizeConfig);
+
+ configs[0].put(KEY_CONFIG_NAME, "Default Values");
+ configs[0].put(KEY_INIT_TEMPERATURE, "50.0");
+ configs[0].put(KEY_MIN_TEMPERATURE, "3.0");
+ configs[0].put(KEY_MAX_TEMPERATURE, "256.0");
+ configs[0].put(KEY_PREF_EDGE_LENGTH, "100.0");
+ configs[0].put(KEY_GRAVITATION, "0.0625");
+ configs[0].put(KEY_RANDOM_IMPULSE_RANGE, "32.0");
+ configs[0].put(KEY_COMPUTE_PERMUTATION, "true");
+ configs[0].put(KEY_END_CONDITION_AVERAGE, "true");
+ configs[0].put(KEY_AVOID_OVERLAPPING, "false");
+ configs[0].put(KEY_OVERLAPPING_DETECTION_WIDTH, "40.0");
+ configs[0].put(KEY_OVERLAPPING_PREF_DISTANCE, "40.0");
+ configs[0].put(KEY_ALPHA_OSC, String.valueOf(Math.PI / 2.0));
+ configs[0].put(KEY_ALPHA_ROT, String.valueOf(Math.PI / 3.0));
+ configs[0].put(KEY_SIGMA_OSC, String.valueOf(1.0 / 3.0)); //a higher value leads to a faster falling temperature
+ configs[0].put(KEY_SIGMA_ROT, String.valueOf(1.0 / 2.0)); //as smaller this value is, the smaller the temperature alteration
+ configs[0].put(KEY_OPTIMIZE_ALGORITHM_ENABLED, "false");
+ configs[0].put(KEY_OPTIMIZE_ALGORITHM_CONFIG, optimizeConfig.clone());
+
+ configs[0].put(KEY_LAYOUT_UPDATE_INIT_TEMPERATURE, "10.0");
+ configs[0].put(KEY_LAYOUT_UPDATE_MIN_TEMPERATURE, "3.0");
+ configs[0].put(KEY_LAYOUT_UPDATE_MAX_TEMPERATURE, "256.0");
+ configs[0].put(KEY_LAYOUT_UPDATE_PREF_EDGE_LENGTH, "100.0");
+ configs[0].put(KEY_LAYOUT_UPDATE_GRAVITATION, "0.0625");
+ configs[0].put(KEY_LAYOUT_UPDATE_RANDOM_IMPULSE_RANGE, "32.0");
+ configs[0].put(KEY_LAYOUT_UPDATE_COMPUTE_PERMUTATION, "true");
+ configs[0].put(KEY_LAYOUT_UPDATE_END_CONDITION_AVERAGE, "true");
+ configs[0].put(KEY_LAYOUT_UPDATE_AVOID_OVERLAPPING, "false");
+ configs[0].put(KEY_LAYOUT_UPDATE_OVERLAPPING_DETECTION_WIDTH, "40.0");
+ configs[0].put(KEY_LAYOUT_UPDATE_OVERLAPPING_PREF_DISTANCE, "40.0");
+ configs[0].put(KEY_LAYOUT_UPDATE_ALPHA_OSC, String.valueOf(Math.toRadians(90.0)));
+ configs[0].put(KEY_LAYOUT_UPDATE_ALPHA_ROT, String.valueOf(Math.toRadians(60.0)));
+ configs[0].put(KEY_LAYOUT_UPDATE_SIGMA_OSC, String.valueOf(1.0 / 3.0));
+ configs[0].put(KEY_LAYOUT_UPDATE_SIGMA_ROT, String.valueOf(1.0 / 2.0));
+ configs[0].put(KEY_LAYOUT_UPDATE_ENABLED, "false");
+ configs[0].put(KEY_LAYOUT_UPDATE_DEPTH, "1");
+ configs[0].put(KEY_LAYOUT_UPDATE_METHOD, KEY_LAYOUT_UPDATE_METHOD_NEIGHBORS_ONLY);
+ configs[0].put(KEY_LAYOUT_UPDATE_OPTIMIZE_ALGORITHM_ENABLED, "false");
+ configs[0].put(KEY_LAYOUT_UPDATE_OPTIMIZE_ALGORITHM_CONFIG, lu_optimizeConfig.clone());
+ configs[0].put(KEY_LAYOUT_UPDATE_CLUSTERING_ENABLED, "false");
+ configs[0].put(KEY_LAYOUT_UPDATE_CLUSTERING_INIT_TEMPERATURE, "15.0");
+ configs[0].put(KEY_LAYOUT_UPDATE_CLUSTERING_FORCE_SCALING_FACTOR, "0.1");
+ configs[0].put(KEY_LAYOUT_UPDATE_CLUSTERING_FACTOR, "8.0");
+ configs[0].put(KEY_LAYOUT_UPDATE_METHOD_PERIMETER_INIT_SIZE, "100.0");
+ configs[0].put(KEY_LAYOUT_UPDATE_METHOD_PERIMETER_SIZE_INC, "20.0");
+
+ configs[1].put(KEY_CONFIG_NAME, "Long running Values");
+ configs[1].put(KEY_INIT_TEMPERATURE, "250.0");
+ configs[1].put(KEY_MIN_TEMPERATURE, "0.5");
+ configs[1].put(KEY_MAX_TEMPERATURE, "256.0");
+ configs[1].put(KEY_PREF_EDGE_LENGTH, "100.0");
+ configs[1].put(KEY_GRAVITATION, "0.0625");
+ configs[1].put(KEY_RANDOM_IMPULSE_RANGE, "32.0");
+ configs[1].put(KEY_COMPUTE_PERMUTATION, "true");
+ configs[1].put(KEY_END_CONDITION_AVERAGE, "false");
+ configs[1].put(KEY_AVOID_OVERLAPPING, "false");
+ configs[1].put(KEY_OVERLAPPING_DETECTION_WIDTH, "40.0");
+ configs[1].put(KEY_OVERLAPPING_PREF_DISTANCE, "40.0");
+ configs[1].put(KEY_ALPHA_OSC, String.valueOf(Math.toRadians(90.0)));
+ configs[1].put(KEY_ALPHA_ROT, String.valueOf(Math.toRadians(60.0)));
+ configs[1].put(KEY_SIGMA_OSC, String.valueOf(7.0 / 8.0));
+ configs[1].put(KEY_SIGMA_ROT, String.valueOf(1.0 / 5.0));
+ configs[1].put(KEY_OPTIMIZE_ALGORITHM_ENABLED, "false");
+ configs[1].put(KEY_OPTIMIZE_ALGORITHM_CONFIG, optimizeConfig.clone());
+
+ configs[1].put(KEY_LAYOUT_UPDATE_INIT_TEMPERATURE, "100.0");
+ configs[1].put(KEY_LAYOUT_UPDATE_MIN_TEMPERATURE, "2.0");
+ configs[1].put(KEY_LAYOUT_UPDATE_MAX_TEMPERATURE, "256.0");
+ configs[1].put(KEY_LAYOUT_UPDATE_PREF_EDGE_LENGTH, "100.0");
+ configs[1].put(KEY_LAYOUT_UPDATE_GRAVITATION, "0.0625");
+ configs[1].put(KEY_LAYOUT_UPDATE_RANDOM_IMPULSE_RANGE, "32.0");
+ configs[1].put(KEY_LAYOUT_UPDATE_COMPUTE_PERMUTATION, "true");
+ configs[1].put(KEY_LAYOUT_UPDATE_END_CONDITION_AVERAGE, "false");
+ configs[1].put(KEY_LAYOUT_UPDATE_AVOID_OVERLAPPING, "false");
+ configs[1].put(KEY_LAYOUT_UPDATE_OVERLAPPING_DETECTION_WIDTH, "40.0");
+ configs[1].put(KEY_LAYOUT_UPDATE_OVERLAPPING_PREF_DISTANCE, "40.0");
+ configs[1].put(KEY_LAYOUT_UPDATE_ALPHA_OSC, String.valueOf(Math.toRadians(90.0)));
+ configs[1].put(KEY_LAYOUT_UPDATE_ALPHA_ROT, String.valueOf(Math.toRadians(60.0)));
+ configs[1].put(KEY_LAYOUT_UPDATE_SIGMA_OSC, String.valueOf(7.0 / 8.0));
+ configs[1].put(KEY_LAYOUT_UPDATE_SIGMA_ROT, String.valueOf(1.0 / 5.0));
+ configs[1].put(KEY_LAYOUT_UPDATE_ENABLED, "false");
+ configs[1].put(KEY_LAYOUT_UPDATE_DEPTH, "1");
+ configs[1].put(KEY_LAYOUT_UPDATE_METHOD, KEY_LAYOUT_UPDATE_METHOD_PERIMETERS);
+ configs[1].put(KEY_LAYOUT_UPDATE_OPTIMIZE_ALGORITHM_ENABLED, "false");
+ configs[1].put(KEY_LAYOUT_UPDATE_OPTIMIZE_ALGORITHM_CONFIG, lu_optimizeConfig.clone());
+ configs[1].put(KEY_LAYOUT_UPDATE_CLUSTERING_ENABLED, "true");
+ configs[1].put(KEY_LAYOUT_UPDATE_CLUSTERING_INIT_TEMPERATURE, "20.0");
+ configs[1].put(KEY_LAYOUT_UPDATE_CLUSTERING_FORCE_SCALING_FACTOR, "0.1");
+ configs[1].put(KEY_LAYOUT_UPDATE_CLUSTERING_FACTOR, "12.0");
+ configs[1].put(KEY_LAYOUT_UPDATE_METHOD_PERIMETER_INIT_SIZE, "150.0");
+ configs[1].put(KEY_LAYOUT_UPDATE_METHOD_PERIMETER_SIZE_INC, "30.0");
+
+ presetConfigs = configs;
+
+ initComponents();
+ // TODO: Replace with revert if implemented
+ setConfiguration(presetConfigs[0]);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void revert() {
+ // TODO: Read config from algorithm
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void apply() {
+ layout.setConfig(getConfiguration());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param configuration DOCUMENT ME!
+ */
+ public void setConfiguration(Properties configuration) {
+ // Read config
+ double initTemperature = Double.parseDouble((String) configuration.get(KEY_INIT_TEMPERATURE));
+ double minTemperature = Double.parseDouble((String) configuration.get(KEY_MIN_TEMPERATURE));
+ double maxTemperature = Double.parseDouble((String) configuration.get(KEY_MAX_TEMPERATURE));
+ double prefEdgeLength = Double.parseDouble((String) configuration.get(KEY_PREF_EDGE_LENGTH));
+ double gravitation = Double.parseDouble((String) configuration.get(KEY_GRAVITATION));
+ double randomImpulseRange = Double.parseDouble((String) configuration.get(KEY_RANDOM_IMPULSE_RANGE));
+ double overlapDetectWidth = Double.parseDouble((String) configuration.get(KEY_OVERLAPPING_DETECTION_WIDTH));
+ double overlapPrefDist = Double.parseDouble((String) configuration.get(KEY_OVERLAPPING_PREF_DISTANCE));
+ double alphaOsc = Double.parseDouble((String) configuration.get(KEY_ALPHA_OSC));
+ double alphaRot = Double.parseDouble((String) configuration.get(KEY_ALPHA_ROT));
+ double sigmaOsc = Double.parseDouble((String) configuration.get(KEY_SIGMA_OSC));
+ double sigmaRot = Double.parseDouble((String) configuration.get(KEY_SIGMA_ROT));
+
+ boolean computePermut = isTrue((String) configuration.get(KEY_COMPUTE_PERMUTATION));
+ boolean endPerAverage = isTrue((String) configuration.get(KEY_END_CONDITION_AVERAGE));
+ boolean avoidOverlapping = isTrue((String) configuration.get(KEY_AVOID_OVERLAPPING));
+ boolean useOptimizeAlgorithm = isTrue((String) configuration.get(KEY_OPTIMIZE_ALGORITHM_ENABLED));
+
+ Properties optimizationConfig = (Properties) configuration.get(KEY_OPTIMIZE_ALGORITHM_CONFIG);
+
+ double lu_initTemperature = Double.parseDouble((String) configuration.get(KEY_LAYOUT_UPDATE_INIT_TEMPERATURE));
+ double lu_minTemperature = Double.parseDouble((String) configuration.get(KEY_LAYOUT_UPDATE_MIN_TEMPERATURE));
+ double lu_maxTemperature = Double.parseDouble((String) configuration.get(KEY_LAYOUT_UPDATE_MAX_TEMPERATURE));
+ double lu_prefEdgeLength = Double.parseDouble((String) configuration.get(KEY_LAYOUT_UPDATE_PREF_EDGE_LENGTH));
+ double lu_gravitation = Double.parseDouble((String) configuration.get(KEY_LAYOUT_UPDATE_GRAVITATION));
+ double lu_randomImpulseRange = Double.parseDouble((String) configuration.get(KEY_LAYOUT_UPDATE_RANDOM_IMPULSE_RANGE));
+ double lu_overlapDetectWidth = Double.parseDouble((String) configuration.get(KEY_LAYOUT_UPDATE_OVERLAPPING_DETECTION_WIDTH));
+ double lu_overlapPrefDist = Double.parseDouble((String) configuration.get(KEY_LAYOUT_UPDATE_OVERLAPPING_PREF_DISTANCE));
+ double lu_alphaOsc = Double.parseDouble((String) configuration.get(KEY_LAYOUT_UPDATE_ALPHA_OSC));
+ double lu_alphaRot = Double.parseDouble((String) configuration.get(KEY_LAYOUT_UPDATE_ALPHA_ROT));
+ double lu_sigmaOsc = Double.parseDouble((String) configuration.get(KEY_LAYOUT_UPDATE_SIGMA_OSC));
+ double lu_sigmaRot = Double.parseDouble((String) configuration.get(KEY_LAYOUT_UPDATE_SIGMA_ROT));
+ double lu_cluster_initTemp = Double.parseDouble((String) configuration.get(KEY_LAYOUT_UPDATE_CLUSTERING_INIT_TEMPERATURE));
+ double lu_cluster_forceScale = Double.parseDouble((String) configuration.get(KEY_LAYOUT_UPDATE_CLUSTERING_FORCE_SCALING_FACTOR));
+ double lu_cluster_factor = Double.parseDouble((String) configuration.get(KEY_LAYOUT_UPDATE_CLUSTERING_FACTOR));
+
+ int lu_depth = Integer.parseInt((String) configuration.get(KEY_LAYOUT_UPDATE_DEPTH));
+ double lu_perimeter_initSize = Double.parseDouble((String) configuration.get(KEY_LAYOUT_UPDATE_METHOD_PERIMETER_INIT_SIZE));
+ double lu_perimeter_sizeInc = Double.parseDouble((String) configuration.get(KEY_LAYOUT_UPDATE_METHOD_PERIMETER_SIZE_INC));
+
+ boolean lu_enabled = isTrue((String) configuration.get(KEY_LAYOUT_UPDATE_ENABLED));
+ boolean lu_cluster_enabled = isTrue((String) configuration.get(KEY_LAYOUT_UPDATE_CLUSTERING_ENABLED));
+
+ boolean lu_computePermut = isTrue((String) configuration.get(KEY_LAYOUT_UPDATE_COMPUTE_PERMUTATION));
+ boolean lu_endPerAverage = isTrue((String) configuration.get(KEY_LAYOUT_UPDATE_END_CONDITION_AVERAGE));
+ boolean lu_avoidOverlapping = isTrue((String) configuration.get(KEY_LAYOUT_UPDATE_AVOID_OVERLAPPING));
+ boolean lu_useOptimizeAlgorithm = isTrue((String) configuration.get(KEY_LAYOUT_UPDATE_OPTIMIZE_ALGORITHM_ENABLED));
+
+ Properties lu_optimizationConfig = (Properties) configuration.get(KEY_LAYOUT_UPDATE_OPTIMIZE_ALGORITHM_CONFIG);
+
+ String lu_method = (String) configuration.get(KEY_LAYOUT_UPDATE_METHOD);
+
+ setInitTemperature(initTemperature);
+ setMinTemperature(minTemperature);
+ setMaxTemperature(maxTemperature);
+ setPreferredEdgeLength(prefEdgeLength);
+ setGravitation(gravitation);
+ setRandomImpulseRange(randomImpulseRange);
+ setOverlapDetectionWidth(overlapDetectWidth);
+ setOverlapPreferredDistance(overlapPrefDist);
+ setAlphaOsc(alphaOsc);
+ setAlphaRot(alphaRot);
+ setSigmaOsc(sigmaOsc);
+ setSigmaRot(sigmaRot);
+ setComputePermutation(computePermut);
+ setEndPerAverage(endPerAverage);
+ setAvoidOverlapping(avoidOverlapping);
+ setOptimizationAlgorithmEnabled(useOptimizeAlgorithm);
+ setOptimizationConfiguration(optimizationConfig);
+
+ setLayoutUpdateInitTemperature(lu_initTemperature);
+ setLayoutUpdateMinTemperature(lu_minTemperature);
+ setLayoutUpdateMaxTemperature(lu_maxTemperature);
+ setLayoutUpdatePreferredEdgeLength(lu_prefEdgeLength);
+ setLayoutUpdateGravitation(lu_gravitation);
+ setLayoutUpdateRandomImpulseRange(lu_randomImpulseRange);
+ setLayoutUpdateOverlapDetectionWidth(lu_overlapDetectWidth);
+ setLayoutUpdateOverlapPreferredDistance(lu_overlapPrefDist);
+ setLayoutUpdateAlphaOsc(lu_alphaOsc);
+ setLayoutUpdateAlphaRot(lu_alphaRot);
+ setLayoutUpdateSigmaOsc(lu_sigmaOsc);
+ setLayoutUpdateSigmaRot(lu_sigmaRot);
+ setLayoutUpdateComputePermutation(lu_computePermut);
+ setLayoutUpdateEndPerAverage(lu_endPerAverage);
+ setLayoutUpdateAvoidOverlapping(lu_avoidOverlapping);
+ setLayoutUpdateOptimizationAlgorithmEnabled(lu_useOptimizeAlgorithm);
+ setLayoutUpdateOptimizationConfiguration(lu_optimizationConfig);
+
+ setLayoutUpdateEnabled(lu_enabled);
+ setLayoutUpdateDepth(lu_depth);
+ setLayoutUpdateMethodPerimeterInitSize(lu_perimeter_initSize);
+ setLayoutUpdateMethodPerimeterSizeInc(lu_perimeter_sizeInc);
+ setLayoutUpdateClusteringEnabled(lu_cluster_enabled);
+ setLayoutUpdateClusteringInitTemperature(lu_cluster_initTemp);
+ setLayoutUpdateClusteringForceScalingFactor(lu_cluster_forceScale);
+ setLayoutUpdateClusteringFactor(lu_cluster_factor);
+
+ setLayoutUpdateMethod(lu_method);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Properties getConfiguration() {
+ Properties configuration = new Properties();
+ double initTemperature = getInitTemperature();
+ double minTemperature = getMinTemperature();
+ double maxTemperature = getMaxTemperature();
+ double prefEdgeLength = getPreferredEdgeLength();
+ double gravitation = getGravitation();
+ double randomImpulseRange = getRandomImpulseRange();
+ double overlapDetectWidth = getOverlapDetectionWidth();
+ double overlapPrefDist = getOverlapPreferredDistance();
+ double alphaOsc = getAlphaOsc();
+ double alphaRot = getAlphaRot();
+ double sigmaOsc = getSigmaOsc();
+ double sigmaRot = getSigmaRot();
+ boolean computePermut = getComputePermutation();
+ boolean endPerAverage = getEndPerAverage();
+ boolean avoidOverlapping = getAvoidOverlapping();
+ boolean useOptimizationAlg = getOptimizationAlgorithmEnabled();
+ Properties optimizeConfig = getOptimizationConfiguration();
+
+ double lu_initTemperature = getLayoutUpdateInitTemperature();
+ double lu_minTemperature = getLayoutUpdateMinTemperature();
+ double lu_maxTemperature = getLayoutUpdateMaxTemperature();
+ double lu_prefEdgeLength = getLayoutUpdatePreferredEdgeLength();
+ double lu_gravitation = getLayoutUpdateGravitation();
+ double lu_randomImpulseRange = getLayoutUpdateRandomImpulseRange();
+ double lu_overlapDetectWidth = getLayoutUpdateOverlapDetectionWidth();
+ double lu_overlapPrefDist = getLayoutUpdateOverlapPreferredDistance();
+ double lu_alphaOsc = getLayoutUpdateAlphaOsc();
+ double lu_alphaRot = getLayoutUpdateAlphaRot();
+ double lu_sigmaOsc = getLayoutUpdateSigmaOsc();
+ double lu_sigmaRot = getLayoutUpdateSigmaRot();
+ boolean lu_computePermut = getLayoutUpdateComputePermutation();
+ boolean lu_endPerAverage = getLayoutUpdateEndPerAverage();
+ boolean lu_avoidOverlapping = getLayoutUpdateAvoidOverlapping();
+ boolean lu_useOptimizationAlg = getLayoutUpdateOptimizationAlgorithmEnabled();
+ boolean lu_enabled = getLayoutUpdateEnabled();
+ String lu_method = getLayoutUpdateMethod();
+ int lu_depth = getLayoutUpdateDepth();
+ double lu_perimeter_initSize = getLayoutUpdateMethodPerimeterInitSize();
+ double lu_perimeter_sizeInc = getLayoutUpdateMethodPerimeterSizeInc();
+ boolean lu_cluster_enabled = getLayoutUpdateClusteringEnabled();
+ double lu_cluster_initTemp = getLayoutUpdateClusteringInitTemperature();
+ double lu_cluster_forceScale = getLayoutUpdateClusteringForceScalingFactor();
+ double lu_cluster_factor = getLayoutUpdateClusteringFactor();
+ Properties lu_optimizeConfig = getLayoutUpdateOptimizationConfiguration();
+
+ configuration.put(KEY_INIT_TEMPERATURE, String.valueOf(initTemperature));
+ configuration.put(KEY_MIN_TEMPERATURE, String.valueOf(minTemperature));
+ configuration.put(KEY_MAX_TEMPERATURE, String.valueOf(maxTemperature));
+ configuration.put(KEY_PREF_EDGE_LENGTH, String.valueOf(prefEdgeLength));
+ configuration.put(KEY_GRAVITATION, String.valueOf(gravitation));
+ configuration.put(KEY_RANDOM_IMPULSE_RANGE, String.valueOf(randomImpulseRange));
+ configuration.put(KEY_OVERLAPPING_DETECTION_WIDTH, String.valueOf(overlapDetectWidth));
+ configuration.put(KEY_OVERLAPPING_PREF_DISTANCE, String.valueOf(overlapPrefDist));
+ configuration.put(KEY_COMPUTE_PERMUTATION, String.valueOf(computePermut));
+ configuration.put(KEY_END_CONDITION_AVERAGE, String.valueOf(endPerAverage));
+ configuration.put(KEY_AVOID_OVERLAPPING, String.valueOf(avoidOverlapping));
+ configuration.put(KEY_ALPHA_OSC, String.valueOf(alphaOsc));
+ configuration.put(KEY_ALPHA_ROT, String.valueOf(alphaRot));
+ configuration.put(KEY_SIGMA_OSC, String.valueOf(sigmaOsc));
+ configuration.put(KEY_SIGMA_ROT, String.valueOf(sigmaRot));
+ configuration.put(KEY_OPTIMIZE_ALGORITHM_ENABLED, String.valueOf(useOptimizationAlg));
+ configuration.put(KEY_OPTIMIZE_ALGORITHM_CONFIG, optimizeConfig);
+
+ configuration.put(KEY_LAYOUT_UPDATE_INIT_TEMPERATURE, String.valueOf(lu_initTemperature));
+ configuration.put(KEY_LAYOUT_UPDATE_MIN_TEMPERATURE, String.valueOf(lu_minTemperature));
+ configuration.put(KEY_LAYOUT_UPDATE_MAX_TEMPERATURE, String.valueOf(lu_maxTemperature));
+ configuration.put(KEY_LAYOUT_UPDATE_PREF_EDGE_LENGTH, String.valueOf(lu_prefEdgeLength));
+ configuration.put(KEY_LAYOUT_UPDATE_GRAVITATION, String.valueOf(lu_gravitation));
+ configuration.put(KEY_LAYOUT_UPDATE_RANDOM_IMPULSE_RANGE,
+ String.valueOf(lu_randomImpulseRange));
+ configuration.put(KEY_LAYOUT_UPDATE_OVERLAPPING_DETECTION_WIDTH,
+ String.valueOf(lu_overlapDetectWidth));
+ configuration.put(KEY_LAYOUT_UPDATE_OVERLAPPING_PREF_DISTANCE,
+ String.valueOf(lu_overlapPrefDist));
+ configuration.put(KEY_LAYOUT_UPDATE_COMPUTE_PERMUTATION, String.valueOf(lu_computePermut));
+ configuration.put(KEY_LAYOUT_UPDATE_END_CONDITION_AVERAGE, String.valueOf(lu_endPerAverage));
+ configuration.put(KEY_LAYOUT_UPDATE_AVOID_OVERLAPPING, String.valueOf(lu_avoidOverlapping));
+ configuration.put(KEY_LAYOUT_UPDATE_ALPHA_OSC, String.valueOf(lu_alphaOsc));
+ configuration.put(KEY_LAYOUT_UPDATE_ALPHA_ROT, String.valueOf(lu_alphaRot));
+ configuration.put(KEY_LAYOUT_UPDATE_SIGMA_OSC, String.valueOf(lu_sigmaOsc));
+ configuration.put(KEY_LAYOUT_UPDATE_SIGMA_ROT, String.valueOf(lu_sigmaRot));
+ configuration.put(KEY_LAYOUT_UPDATE_OPTIMIZE_ALGORITHM_ENABLED,
+ String.valueOf(lu_useOptimizationAlg));
+ configuration.put(KEY_LAYOUT_UPDATE_OPTIMIZE_ALGORITHM_CONFIG, lu_optimizeConfig);
+
+ configuration.put(KEY_LAYOUT_UPDATE_ENABLED, String.valueOf(lu_enabled));
+ configuration.put(KEY_LAYOUT_UPDATE_METHOD, lu_method);
+ configuration.put(KEY_LAYOUT_UPDATE_DEPTH, String.valueOf(lu_depth));
+ configuration.put(KEY_LAYOUT_UPDATE_METHOD_PERIMETER_INIT_SIZE,
+ String.valueOf(lu_perimeter_initSize));
+ configuration.put(KEY_LAYOUT_UPDATE_METHOD_PERIMETER_SIZE_INC,
+ String.valueOf(lu_perimeter_sizeInc));
+ configuration.put(KEY_LAYOUT_UPDATE_CLUSTERING_ENABLED, String.valueOf(lu_cluster_enabled));
+ configuration.put(KEY_LAYOUT_UPDATE_CLUSTERING_INIT_TEMPERATURE,
+ String.valueOf(lu_cluster_initTemp));
+ configuration.put(KEY_LAYOUT_UPDATE_CLUSTERING_FORCE_SCALING_FACTOR,
+ String.valueOf(lu_cluster_forceScale));
+ configuration.put(KEY_LAYOUT_UPDATE_CLUSTERING_FACTOR, String.valueOf(lu_cluster_factor));
+
+ return configuration;
+ }
+
+ /******************************************************************************/
+ protected Properties[] getPresetConfigs() {
+ return presetConfigs;
+ }
+
+ /******************************************************************************/
+ protected Properties getPresetConfig(int index) {
+ return presetConfigs[index];
+ }
+
+ /******************************************************************************/
+ protected void setPresetConfigs(Properties[] preSets) {
+ presetConfigs = preSets;
+ }
+
+ /******************************************************************************/
+ /**
+ * Changes the configuration of the This is one, of the array of
+ * configurations, gained in the constructor or with
+ * {@link #setPresetConfigs(Properties[])}. Therfore the index has to be
+ * whithin the bounds of this array.
+ *
+ * @param index Index of the configuration set
+ */
+ protected void switchPreferences(int index) {
+ Properties config = presetConfigs[index];
+
+ double alphaOsc = Math.toDegrees(Double.parseDouble((String) config.get(KEY_ALPHA_OSC)));
+ double alphaRot = Math.toDegrees(Double.parseDouble((String) config.get(KEY_ALPHA_ROT)));
+
+ double lu_alphaOsc = Math.toDegrees(Double.parseDouble((String) config.get(KEY_LAYOUT_UPDATE_ALPHA_OSC)));
+ double lu_alphaRot = Math.toDegrees(Double.parseDouble((String) config.get(KEY_LAYOUT_UPDATE_ALPHA_ROT)));
+
+ tf_initTemperature.setText((String) config.get(KEY_INIT_TEMPERATURE));
+ tf_minTemperature.setText((String) config.get(KEY_MIN_TEMPERATURE));
+ tf_maxTemperature.setText((String) config.get(KEY_MAX_TEMPERATURE));
+ tf_prefEdgeLength.setText((String) config.get(KEY_PREF_EDGE_LENGTH));
+ tf_gravitation.setText((String) config.get(KEY_GRAVITATION));
+ tf_randomImpulseRange.setText((String) config.get(KEY_RANDOM_IMPULSE_RANGE));
+ tf_overlapDetectWidth.setText((String) config.get(KEY_OVERLAPPING_DETECTION_WIDTH));
+ tf_overlapPrefDistance.setText((String) config.get(KEY_OVERLAPPING_PREF_DISTANCE));
+
+ tf_lu_initTemperature.setText((String) config.get(KEY_LAYOUT_UPDATE_INIT_TEMPERATURE));
+ tf_lu_minTemperature.setText((String) config.get(KEY_LAYOUT_UPDATE_MIN_TEMPERATURE));
+ tf_lu_maxTemperature.setText((String) config.get(KEY_LAYOUT_UPDATE_MAX_TEMPERATURE));
+ tf_lu_prefEdgeLength.setText((String) config.get(KEY_LAYOUT_UPDATE_PREF_EDGE_LENGTH));
+ tf_lu_gravitation.setText((String) config.get(KEY_LAYOUT_UPDATE_GRAVITATION));
+ tf_lu_randomImpulseRange.setText((String) config.get(KEY_LAYOUT_UPDATE_RANDOM_IMPULSE_RANGE));
+ tf_lu_overlapDetectWidth.setText((String) config.get(KEY_LAYOUT_UPDATE_OVERLAPPING_DETECTION_WIDTH));
+ tf_lu_overlapPrefDistance.setText((String) config.get(KEY_LAYOUT_UPDATE_OVERLAPPING_PREF_DISTANCE));
+ tf_lu_cluster_initTemperature.setText((String) config.get(KEY_LAYOUT_UPDATE_CLUSTERING_INIT_TEMPERATURE));
+ tf_lu_cluster_forceScalingFactor.setText((String) config.get(KEY_LAYOUT_UPDATE_CLUSTERING_FORCE_SCALING_FACTOR));
+ tf_lu_cluster_factor.setText((String) config.get(KEY_LAYOUT_UPDATE_CLUSTERING_FACTOR));
+
+ tf_alphaOsc.setText(String.valueOf(alphaOsc));
+ tf_alphaRot.setText(String.valueOf(alphaRot));
+ tf_sigmaOsc.setText((String) config.get(KEY_SIGMA_OSC));
+ tf_sigmaRot.setText((String) config.get(KEY_SIGMA_ROT));
+
+ tf_lu_alphaOsc.setText(String.valueOf(lu_alphaOsc));
+ tf_lu_alphaRot.setText(String.valueOf(lu_alphaRot));
+ tf_lu_sigmaOsc.setText((String) config.get(KEY_LAYOUT_UPDATE_SIGMA_OSC));
+ tf_lu_sigmaRot.setText((String) config.get(KEY_LAYOUT_UPDATE_SIGMA_ROT));
+
+ tf_lu_depth.setText((String) config.get(KEY_LAYOUT_UPDATE_DEPTH));
+ tf_lu_perimeter_initSize.setText((String) config.get(KEY_LAYOUT_UPDATE_METHOD_PERIMETER_INIT_SIZE));
+ tf_lu_perimeter_sizeInc.setText((String) config.get(KEY_LAYOUT_UPDATE_METHOD_PERIMETER_SIZE_INC));
+
+ cb_computePermutation.setSelected(isTrue((String) config.get(KEY_COMPUTE_PERMUTATION)));
+ cb_endPerAverage.setSelected(isTrue((String) config.get(KEY_END_CONDITION_AVERAGE)));
+ cb_avoidOverlapping.setSelected(isTrue((String) config.get(KEY_AVOID_OVERLAPPING)));
+ cb_useOptimizationAlg.setSelected(isTrue((String) config.get(KEY_OPTIMIZE_ALGORITHM_ENABLED)));
+
+ cb_lu_enableLayoutUpdate.setSelected(isTrue((String) config.get(KEY_LAYOUT_UPDATE_ENABLED)));
+ cb_lu_computePermutation.setSelected(isTrue((String) config.get(KEY_LAYOUT_UPDATE_COMPUTE_PERMUTATION)));
+ cb_lu_endPerAverage.setSelected(isTrue((String) config.get(KEY_LAYOUT_UPDATE_END_CONDITION_AVERAGE)));
+ cb_lu_avoidOverlapping.setSelected(isTrue((String) config.get(KEY_LAYOUT_UPDATE_AVOID_OVERLAPPING)));
+ cb_lu_useOptimizationAlg.setSelected(isTrue((String) config.get(KEY_LAYOUT_UPDATE_OPTIMIZE_ALGORITHM_ENABLED)));
+ cb_lu_cluster_enable.setSelected(isTrue((String) config.get(KEY_LAYOUT_UPDATE_CLUSTERING_ENABLED)));
+
+ comb_lu_method.setSelectedItem((String) config.get(KEY_LAYOUT_UPDATE_METHOD));
+ }
+
+ /******************************************************************************/
+ /**
+ * Transforms a string value in a boolean value. The string has be "true" or
+ * "false". Lower or upper case doesn't matter.
+ *
+ * @param boolValue A String, consisting of the word "true" or "false".
+ * @return The boolean expression of the string.
+ */
+ protected boolean isTrue(String boolValue) {
+ if (boolValue != null) {
+ if ("TRUE".equals(boolValue.toUpperCase())) {
+ return true;
+ } else if ("FALSE".equals(boolValue.toUpperCase())) {
+ return false;
+ }
+ }
+
+ return false;
+ }
+
+ /******************************************************************************/
+ /**
+ * Called by pressing the ok button. Checks all Textfields for their value
+ * and produce a list of errors, while checking. If an error has appeared,
+ * an error dialog is displayed, else the configuration dialog disappears.
+ */
+ protected void check(ArrayList errList) {
+ boolean isOK = true;
+
+ isOK &= assertDouble(tf_initTemperature.getText(), KEY_INIT_TEMPERATURE, errList);
+ isOK &= assertDouble(tf_minTemperature.getText(), KEY_MIN_TEMPERATURE, errList);
+ isOK &= assertDouble(tf_maxTemperature.getText(), KEY_MIN_TEMPERATURE, errList);
+ isOK &= assertDouble(tf_prefEdgeLength.getText(), KEY_PREF_EDGE_LENGTH, errList);
+ isOK &= assertDouble(tf_gravitation.getText(), KEY_GRAVITATION, errList);
+ isOK &= assertDouble(tf_randomImpulseRange.getText(), KEY_RANDOM_IMPULSE_RANGE, errList);
+ isOK &= assertDouble(tf_overlapDetectWidth.getText(), KEY_OVERLAPPING_DETECTION_WIDTH,
+ errList);
+ isOK &= assertDouble(tf_overlapPrefDistance.getText(), KEY_OVERLAPPING_PREF_DISTANCE,
+ errList);
+ isOK &= assertDouble(tf_alphaOsc.getText(), KEY_ALPHA_OSC, errList);
+ isOK &= assertDouble(tf_alphaRot.getText(), KEY_ALPHA_ROT, errList);
+ isOK &= assertDouble(tf_sigmaOsc.getText(), KEY_SIGMA_OSC, errList);
+ isOK &= assertDouble(tf_sigmaRot.getText(), KEY_SIGMA_ROT, errList);
+
+ isOK &= assertDouble(tf_lu_initTemperature.getText(), KEY_LAYOUT_UPDATE_INIT_TEMPERATURE,
+ errList);
+ isOK &= assertDouble(tf_lu_minTemperature.getText(), KEY_LAYOUT_UPDATE_MIN_TEMPERATURE,
+ errList);
+ isOK &= assertDouble(tf_lu_maxTemperature.getText(), KEY_LAYOUT_UPDATE_MAX_TEMPERATURE,
+ errList);
+ isOK &= assertDouble(tf_lu_prefEdgeLength.getText(), KEY_LAYOUT_UPDATE_PREF_EDGE_LENGTH,
+ errList);
+ isOK &= assertDouble(tf_lu_gravitation.getText(), KEY_LAYOUT_UPDATE_GRAVITATION, errList);
+ isOK &= assertDouble(tf_lu_randomImpulseRange.getText(),
+ KEY_LAYOUT_UPDATE_RANDOM_IMPULSE_RANGE, errList);
+ isOK &= assertDouble(tf_lu_overlapDetectWidth.getText(),
+ KEY_LAYOUT_UPDATE_OVERLAPPING_DETECTION_WIDTH, errList);
+ isOK &= assertDouble(tf_lu_overlapPrefDistance.getText(),
+ KEY_LAYOUT_UPDATE_OVERLAPPING_PREF_DISTANCE, errList);
+ isOK &= assertDouble(tf_lu_alphaOsc.getText(), KEY_LAYOUT_UPDATE_ALPHA_OSC, errList);
+ isOK &= assertDouble(tf_lu_alphaRot.getText(), KEY_LAYOUT_UPDATE_ALPHA_ROT, errList);
+ isOK &= assertDouble(tf_lu_sigmaOsc.getText(), KEY_LAYOUT_UPDATE_SIGMA_OSC, errList);
+ isOK &= assertDouble(tf_lu_sigmaRot.getText(), KEY_LAYOUT_UPDATE_SIGMA_ROT, errList);
+
+ isOK &= assertInteger(tf_lu_depth.getText(), KEY_LAYOUT_UPDATE_DEPTH, errList);
+ isOK &= assertDouble(tf_lu_perimeter_initSize.getText(),
+ KEY_LAYOUT_UPDATE_METHOD_PERIMETER_INIT_SIZE, errList);
+ isOK &= assertDouble(tf_lu_perimeter_sizeInc.getText(),
+ KEY_LAYOUT_UPDATE_METHOD_PERIMETER_SIZE_INC, errList);
+ isOK &= assertDouble(tf_lu_cluster_initTemperature.getText(),
+ KEY_LAYOUT_UPDATE_CLUSTERING_INIT_TEMPERATURE, errList);
+ isOK &= assertDouble(tf_lu_cluster_forceScalingFactor.getText(),
+ KEY_LAYOUT_UPDATE_CLUSTERING_FORCE_SCALING_FACTOR, errList);
+ isOK &= assertDouble(tf_lu_cluster_factor.getText(), KEY_LAYOUT_UPDATE_CLUSTERING_FACTOR,
+ errList);
+
+ if (isOK) {
+ isOK &= assertMinimum(tf_initTemperature.getText(), 0.0, false, KEY_INIT_TEMPERATURE,
+ errList);
+ isOK &= assertMinimum(tf_minTemperature.getText(), 0.0, false, KEY_MIN_TEMPERATURE,
+ errList);
+ isOK &= assertMinimum(tf_maxTemperature.getText(), 0.0, false, KEY_MAX_TEMPERATURE,
+ errList);
+ isOK &= assertMinimum(tf_prefEdgeLength.getText(), 0.0, false, KEY_PREF_EDGE_LENGTH,
+ errList);
+ isOK &= assertRange(tf_gravitation.getText(), 0.0, 1.0, true, true, KEY_GRAVITATION,
+ errList);
+ isOK &= assertMinimum(tf_randomImpulseRange.getText(), 0.0, false,
+ KEY_RANDOM_IMPULSE_RANGE, errList);
+ isOK &= assertMinimum(tf_overlapDetectWidth.getText(), 0.0, false,
+ KEY_OVERLAPPING_DETECTION_WIDTH, errList);
+ isOK &= assertMinimum(tf_overlapPrefDistance.getText(), 0.0, false,
+ KEY_OVERLAPPING_PREF_DISTANCE, errList);
+ isOK &= assertRange(tf_alphaOsc.getText(), 0.0, 360.0, true, false, KEY_ALPHA_OSC,
+ errList);
+ isOK &= assertRange(tf_alphaRot.getText(), 0.0, 360.0, true, false, KEY_ALPHA_ROT,
+ errList);
+ isOK &= assertRange(tf_sigmaOsc.getText(), 0.0, 360.0, true, false, KEY_SIGMA_OSC,
+ errList);
+ isOK &= assertRange(tf_sigmaRot.getText(), 0.0, 360.0, true, false, KEY_SIGMA_ROT,
+ errList);
+
+ isOK &= assertMinimum(tf_lu_initTemperature.getText(), 0.0, false,
+ KEY_LAYOUT_UPDATE_INIT_TEMPERATURE, errList);
+ isOK &= assertMinimum(tf_lu_minTemperature.getText(), 0.0, false,
+ KEY_LAYOUT_UPDATE_MIN_TEMPERATURE, errList);
+ isOK &= assertMinimum(tf_lu_maxTemperature.getText(), 0.0, false,
+ KEY_LAYOUT_UPDATE_MAX_TEMPERATURE, errList);
+ isOK &= assertMinimum(tf_lu_prefEdgeLength.getText(), 0.0, false,
+ KEY_LAYOUT_UPDATE_PREF_EDGE_LENGTH, errList);
+ isOK &= assertRange(tf_lu_gravitation.getText(), 0.0, 1.0, true, true,
+ KEY_LAYOUT_UPDATE_GRAVITATION, errList);
+ isOK &= assertMinimum(tf_lu_randomImpulseRange.getText(), 0.0, false,
+ KEY_LAYOUT_UPDATE_RANDOM_IMPULSE_RANGE, errList);
+ isOK &= assertMinimum(tf_lu_overlapDetectWidth.getText(), 0.0, false,
+ KEY_LAYOUT_UPDATE_OVERLAPPING_DETECTION_WIDTH, errList);
+ isOK &= assertMinimum(tf_lu_overlapPrefDistance.getText(), 0.0, false,
+ KEY_LAYOUT_UPDATE_OVERLAPPING_PREF_DISTANCE, errList);
+ isOK &= assertRange(tf_lu_alphaOsc.getText(), 0.0, 360.0, true, false,
+ KEY_LAYOUT_UPDATE_ALPHA_OSC, errList);
+ isOK &= assertRange(tf_lu_alphaRot.getText(), 0.0, 360.0, true, false,
+ KEY_LAYOUT_UPDATE_ALPHA_ROT, errList);
+ isOK &= assertRange(tf_lu_sigmaOsc.getText(), 0.0, 360.0, true, false,
+ KEY_LAYOUT_UPDATE_SIGMA_OSC, errList);
+ isOK &= assertRange(tf_lu_sigmaRot.getText(), 0.0, 360.0, true, false,
+ KEY_LAYOUT_UPDATE_SIGMA_ROT, errList);
+
+ isOK &= assertMinimum(tf_lu_depth.getText(), 0, true, KEY_LAYOUT_UPDATE_DEPTH, errList);
+ isOK &= assertMinimum(tf_lu_perimeter_initSize.getText(), 0.0, false,
+ KEY_LAYOUT_UPDATE_METHOD_PERIMETER_INIT_SIZE, errList);
+ isOK &= assertMinimum(tf_lu_perimeter_sizeInc.getText(), 0.0, false,
+ KEY_LAYOUT_UPDATE_METHOD_PERIMETER_SIZE_INC, errList);
+ isOK &= assertMinimum(tf_lu_cluster_initTemperature.getText(), 0.0, false,
+ KEY_LAYOUT_UPDATE_CLUSTERING_INIT_TEMPERATURE, errList);
+ isOK &= assertRange(tf_lu_cluster_forceScalingFactor.getText(), 0.0, 1.0, false, true,
+ KEY_LAYOUT_UPDATE_CLUSTERING_FORCE_SCALING_FACTOR, errList);
+ isOK &= assertMinimum(tf_lu_cluster_factor.getText(), 1.0, true,
+ KEY_LAYOUT_UPDATE_CLUSTERING_FACTOR, errList);
+ }
+
+ if (!isOK) {
+ String errorMsg = new String();
+
+ for (int i = 0; i < errList.size(); i++) {
+ errorMsg += (String) errList.get(i);
+
+ if (i != (errList.size() - 1))
+ errorMsg += "\n";
+ }
+
+ throw new IllegalArgumentException(errorMsg);
+ }
+ }
+
+ /******************************************************************************/
+ protected void action_LoadPreSets(int index) {
+ switchPreferences(index);
+ switchLayoutUpdatePanel();
+ switchVisibility();
+ }
+
+ /******************************************************************************/
+ /**
+ * Enables/Disables Textfields and other components, depending on the state of
+ * checkboxes and comboboxes on the
+ */
+ private void switchVisibility() {
+ tf_overlapDetectWidth.setEnabled(cb_avoidOverlapping.isSelected());
+ tf_overlapPrefDistance.setEnabled(cb_avoidOverlapping.isSelected());
+ tf_lu_overlapDetectWidth.setEnabled(cb_lu_avoidOverlapping.isSelected());
+ tf_lu_overlapPrefDistance.setEnabled(cb_lu_avoidOverlapping.isSelected());
+ button_ConfigOptimizeAlg.setEnabled(cb_useOptimizationAlg.isSelected());
+ button_lu_ConfigOptimizeAlg.setEnabled(cb_lu_useOptimizationAlg.isSelected());
+ tf_lu_cluster_initTemperature.setEnabled(cb_lu_cluster_enable.isSelected());
+ tf_lu_cluster_forceScalingFactor.setEnabled(cb_lu_cluster_enable.isSelected());
+ tf_lu_cluster_factor.setEnabled(cb_lu_cluster_enable.isSelected());
+
+ if (comb_lu_method.getSelectedItem() == KEY_LAYOUT_UPDATE_METHOD_NEIGHBORS_ONLY) {
+ tf_lu_perimeter_initSize.setEnabled(false);
+ tf_lu_perimeter_sizeInc.setEnabled(false);
+ } else if (comb_lu_method.getSelectedItem() == KEY_LAYOUT_UPDATE_METHOD_PERIMETERS) {
+ tf_lu_perimeter_initSize.setEnabled(true);
+ tf_lu_perimeter_sizeInc.setEnabled(true);
+ }
+ }
+
+ /******************************************************************************/
+ private void switchLayoutUpdatePanel() {
+ if (cb_lu_enableLayoutUpdate.isSelected()) {
+ tp_main.addTab("Update Values", panelLayoutUpdateWrapper);
+ } else {
+ tp_main.remove(panelLayoutUpdateWrapper);
+ }
+ }
+
+ /******************************************************************************/
+ /** Initialize the Swing Components
+ */
+ private void initComponents() {
+ JPanel panelGlobalValues = new JPanel(new GridBagLayout());
+ JPanel panelLabels = new JPanel(new GridLayout(12, 1, 0, 5));
+ JPanel panelFields = new JPanel(new GridLayout(12, 1, 0, 5));
+ JPanel panelLayoutRun = new JPanel(new BorderLayout(5, 10));
+ JPanel panelButtons = new JPanel(new GridLayout(1, 3, 10, 0));
+ JPanel panelDefaults = new JPanel(new GridLayout(1, 2, 10, 4));
+ JPanel panelOverlap = new JPanel(new GridLayout(3, 2, 10, 4));
+ JPanel panelOptimize = new JPanel(new BorderLayout());
+ JPanel panelOptiAlg = new JPanel(new GridLayout(2, 2));
+ tp_main = new JTabbedPane();
+
+ panelLayoutUpdate = new JPanel(new BorderLayout(5, 10));
+ panelLayoutUpdate.setBackground(new Color(205, 215, 215));
+ //panelLayoutUpdate.setBorder(BorderFactory.createTitledBorder(BorderFactory.createEtchedBorder(),"Update Values"));
+ panelDefaults.add(panelLabels);
+ panelDefaults.add(panelFields);
+
+ //panelLayoutRun.setBorder(BorderFactory.createTitledBorder(BorderFactory.createEtchedBorder(),"Apply Values"));
+ panelLayoutRun.add(panelDefaults, BorderLayout.NORTH);
+ panelLayoutRun.add(panelOptimize, BorderLayout.CENTER);
+ panelLayoutRun.add(getAdditionalForceConfig(), BorderLayout.SOUTH);
+ panelLayoutRun.setBackground(new Color(215, 215, 205));
+
+ panelOptimize.add(panelOptiAlg, BorderLayout.NORTH);
+ panelOptimize.add(panelOverlap, BorderLayout.CENTER);
+ panelOptimize.setOpaque(false);
+
+ panelDefaults.setOpaque(false);
+ panelOverlap.setOpaque(false);
+ panelLabels.setOpaque(false);
+ panelFields.setOpaque(false);
+
+ setLayout(new BorderLayout(5, 10));
+ add(panelGlobalValues, BorderLayout.NORTH);
+ add(tp_main, BorderLayout.CENTER);
+ add(panelButtons, BorderLayout.SOUTH);
+
+ panelGlobalValues.setBorder(BorderFactory.createTitledBorder(BorderFactory
+ [...]
+ "Global Settings"));
+
+ panelGlobalValues.add(new JLabel("run permanent :"),
+ new GridBagConstraints(0, 0, 1, 1, 0.0, 0.0, GridBagConstraints.WEST,
+ GridBagConstraints.NONE,
+ new Insets(0, 5, 0, 30), 0, 0));
+
+ cb_lu_enableLayoutUpdate = new JCheckBox();
+ panelGlobalValues.add(cb_lu_enableLayoutUpdate,
+ new GridBagConstraints(1, 0, 1, 1, 1.0, 1.0, GridBagConstraints.WEST,
+ GridBagConstraints.HORIZONTAL,
+ new Insets(0, 0, 0, 0), 0, 0));
+
+ panelLabels.add(new JLabel("start temperature :"));
+ panelLabels.add(new JLabel("min. temperature :"));
+ panelLabels.add(new JLabel("max. temperature :"));
+ panelLabels.add(new JLabel("preferred Edge length :"));
+ panelLabels.add(new JLabel("gravitation :"));
+ panelLabels.add(new JLabel("range of random impulse :"));
+ panelLabels.add(new JLabel("compute permutations :"));
+ panelLabels.add(new JLabel("end condition is average :"));
+ panelLabels.add(new JLabel("alpha oscillation :"));
+ panelLabels.add(new JLabel("alpha rotation :"));
+ panelLabels.add(new JLabel("sigma oscillation :"));
+ panelLabels.add(new JLabel("sigma rotation :"));
+
+ tf_initTemperature = new JTextField();
+ tf_minTemperature = new JTextField();
+ tf_maxTemperature = new JTextField();
+ tf_prefEdgeLength = new JTextField();
+ tf_gravitation = new JTextField();
+ tf_randomImpulseRange = new JTextField();
+
+ cb_computePermutation = new JCheckBox();
+ cb_endPerAverage = new JCheckBox();
+
+ cb_computePermutation.setOpaque(false);
+ cb_endPerAverage.setOpaque(false);
+
+ tf_alphaOsc = new JTextField();
+ tf_alphaRot = new JTextField();
+
+ tf_sigmaOsc = new JTextField();
+ tf_sigmaRot = new JTextField();
+
+ panelFields.add(tf_initTemperature);
+ panelFields.add(tf_minTemperature);
+ panelFields.add(tf_maxTemperature);
+ panelFields.add(tf_prefEdgeLength);
+ panelFields.add(tf_gravitation);
+ panelFields.add(tf_randomImpulseRange);
+ panelFields.add(cb_computePermutation);
+ panelFields.add(cb_endPerAverage);
+ panelFields.add(tf_alphaOsc);
+ panelFields.add(tf_alphaRot);
+ panelFields.add(tf_sigmaOsc);
+ panelFields.add(tf_sigmaRot);
+
+ cb_avoidOverlapping = new JCheckBox();
+ cb_avoidOverlapping.setOpaque(false);
+ tf_overlapDetectWidth = new JTextField();
+ tf_overlapPrefDistance = new JTextField();
+
+ JPanel panelOverlapSwitch = new JPanel(new GridLayout(1, 2, 10, 4));
+ panelOverlapSwitch.setOpaque(false);
+ panelOverlapSwitch.add(new JLabel("on/off"));
+ panelOverlapSwitch.add(cb_avoidOverlapping);
+
+ JPanel panelEmpty = new JPanel();
+ panelEmpty.setOpaque(false);
+
+ panelOverlap.setBorder(BorderFactory.createTitledBorder(BorderFactory
+ [...]
+ "Force for overlapping Cells",
+ TitledBorder.LEADING,
+ TitledBorder.ABOVE_TOP));
+ panelOverlap.add(panelOverlapSwitch);
+ panelOverlap.add(panelEmpty);
+ panelOverlap.add(new JLabel("detection width :"));
+ panelOverlap.add(tf_overlapDetectWidth);
+ panelOverlap.add(new JLabel("pref. distance :"));
+ panelOverlap.add(tf_overlapPrefDistance);
+
+ cb_useOptimizationAlg = new JCheckBox();
+ cb_useOptimizationAlg.setOpaque(false);
+ cb_useOptimizationAlg.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ switchVisibility();
+ }
+ });
+
+ button_ConfigOptimizeAlg = new JButton("Configure");
+ button_ConfigOptimizeAlg.setBackground(panelLayoutRun.getBackground());
+
+ JPanel panelEmpty2 = new JPanel();
+ panelEmpty2.setOpaque(false);
+
+ panelOptiAlg.add(new JLabel("Use optimization Algorithm:"));
+ panelOptiAlg.add(cb_useOptimizationAlg);
+ panelOptiAlg.add(panelEmpty2);
+ panelOptiAlg.add(button_ConfigOptimizeAlg);
+ panelOptiAlg.setOpaque(false);
+
+ button_ConfigOptimizeAlg.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ //optimizeAlgController.configure();
+ }
+ });
+
+ cb_avoidOverlapping.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ switchVisibility();
+ }
+ });
+
+ cb_lu_enableLayoutUpdate.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ switchLayoutUpdatePanel();
+ }
+ });
+
+ comb_loadPreSets = new JComboBox();
+
+ for (int i = 0; i < presetConfigs.length; i++)
+ comb_loadPreSets.addItem(presetConfigs[i].get(KEY_CONFIG_NAME));
+
+ panelButtons.add(comb_loadPreSets);
+
+ comb_loadPreSets.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ action_LoadPreSets(((JComboBox) e.getSource()).getSelectedIndex());
+ }
+ });
+
+ /*-----------------LAYOUT-UPDATE-------------------------*/
+ JPanel panelLULabels = new JPanel(new GridLayout(16, 1, 0, 5));
+ JPanel panelLUFields = new JPanel(new GridLayout(16, 1, 0, 5));
+ JPanel panelLUDefaults = new JPanel(new BorderLayout(10, 5));
+ JPanel panelLUOverlap = new JPanel(new GridLayout(3, 2, 10, 4));
+ JPanel panelLUOptimize = new JPanel(new BorderLayout());
+ JPanel panelLUOptiAlg = new JPanel(new GridLayout(2, 2, 10, 4));
+ JPanel panelLUCluster = new JPanel(new GridLayout(4, 2, 10, 4));
+
+ panelLUDefaults.setOpaque(false);
+ panelLULabels.setOpaque(false);
+ panelLUFields.setOpaque(false);
+ panelLUOverlap.setOpaque(false);
+ panelLUOptimize.setOpaque(false);
+ panelLUOptiAlg.setOpaque(false);
+ panelLUCluster.setOpaque(false);
+
+ panelLUDefaults.add(panelLULabels, BorderLayout.WEST);
+ panelLUDefaults.add(panelLUFields, BorderLayout.EAST);
+ panelLUDefaults.add(panelLUCluster, BorderLayout.SOUTH);
+
+ panelLUOptimize.add(panelLUOptiAlg, BorderLayout.NORTH);
+ panelLUOptimize.add(panelLUOverlap, BorderLayout.CENTER);
+
+ panelLayoutUpdate.add(panelLUDefaults, BorderLayout.NORTH);
+ panelLayoutUpdate.add(panelLUOptimize, BorderLayout.CENTER);
+ panelLayoutUpdate.add(getAdditionalForceLUConfig(), BorderLayout.SOUTH);
+
+ panelLULabels.add(new JLabel("start temperature :"));
+ panelLULabels.add(new JLabel("min. temperature :"));
+ panelLULabels.add(new JLabel("max. temperature :"));
+ panelLULabels.add(new JLabel("preferred Edge length :"));
+ panelLULabels.add(new JLabel("gravitation :"));
+ panelLULabels.add(new JLabel("range of random impulse :"));
+ panelLULabels.add(new JLabel("compute permutations :"));
+ panelLULabels.add(new JLabel("end condition is average :"));
+ panelLULabels.add(new JLabel("alpha oscillation :"));
+ panelLULabels.add(new JLabel("alpha rotation :"));
+ panelLULabels.add(new JLabel("sigma oscillation :"));
+ panelLULabels.add(new JLabel("sigma rotation :"));
+ panelLULabels.add(new JLabel("layout update method :"));
+ panelLULabels.add(new JLabel("layout update depth :"));
+ panelLULabels.add(new JLabel("layout update perimeter init size :"));
+ panelLULabels.add(new JLabel("layout update perimeter increase value :"));
+
+ tf_lu_initTemperature = new JTextField();
+ tf_lu_minTemperature = new JTextField();
+ tf_lu_maxTemperature = new JTextField();
+ tf_lu_prefEdgeLength = new JTextField();
+ tf_lu_gravitation = new JTextField();
+ tf_lu_randomImpulseRange = new JTextField();
+
+ cb_lu_computePermutation = new JCheckBox();
+ cb_lu_endPerAverage = new JCheckBox();
+
+ cb_lu_computePermutation.setOpaque(false);
+ cb_lu_endPerAverage.setOpaque(false);
+
+ tf_lu_alphaOsc = new JTextField();
+ tf_lu_alphaRot = new JTextField();
+
+ tf_lu_sigmaOsc = new JTextField();
+ tf_lu_sigmaRot = new JTextField();
+
+ tf_lu_depth = new JTextField();
+
+ comb_lu_method = new JComboBox();
+ comb_lu_method.addItem(KEY_LAYOUT_UPDATE_METHOD_NEIGHBORS_ONLY);
+ comb_lu_method.addItem(KEY_LAYOUT_UPDATE_METHOD_PERIMETERS);
+ comb_lu_method.setBackground(panelLayoutUpdate.getBackground());
+
+ tf_lu_perimeter_initSize = new JTextField();
+ tf_lu_perimeter_sizeInc = new JTextField();
+
+ panelLUFields.add(tf_lu_initTemperature);
+ panelLUFields.add(tf_lu_minTemperature);
+ panelLUFields.add(tf_lu_maxTemperature);
+ panelLUFields.add(tf_lu_prefEdgeLength);
+ panelLUFields.add(tf_lu_gravitation);
+ panelLUFields.add(tf_lu_randomImpulseRange);
+ panelLUFields.add(cb_lu_computePermutation);
+ panelLUFields.add(cb_lu_endPerAverage);
+ panelLUFields.add(tf_lu_alphaOsc);
+ panelLUFields.add(tf_lu_alphaRot);
+ panelLUFields.add(tf_lu_sigmaOsc);
+ panelLUFields.add(tf_lu_sigmaRot);
+ panelLUFields.add(comb_lu_method);
+ panelLUFields.add(tf_lu_depth);
+ panelLUFields.add(tf_lu_perimeter_initSize);
+ panelLUFields.add(tf_lu_perimeter_sizeInc);
+
+ tf_lu_cluster_initTemperature = new JTextField();
+ tf_lu_cluster_forceScalingFactor = new JTextField();
+ tf_lu_cluster_factor = new JTextField();
+ cb_lu_cluster_enable = new JCheckBox();
+ cb_lu_cluster_enable.setOpaque(false);
+ cb_lu_cluster_enable.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ switchVisibility();
+ }
+ });
+
+ JPanel panelLUClusteringSwitch = new JPanel(new GridLayout(1, 2, 10, 4));
+ panelLUClusteringSwitch.setOpaque(false);
+ panelLUClusteringSwitch.add(new JLabel("on/off"));
+ panelLUClusteringSwitch.add(cb_lu_cluster_enable);
+
+ JPanel panelLUClusterEmpty = new JPanel();
+ panelLUClusterEmpty.setOpaque(false);
+
+ panelLUCluster.setBorder(BorderFactory.createTitledBorder(BorderFactory
+ [...]
+ "Clustering",
+ TitledBorder.LEADING,
+ TitledBorder.ABOVE_TOP));
+
+ panelLUCluster.add(panelLUClusteringSwitch);
+ panelLUCluster.add(panelLUClusterEmpty);
+ panelLUCluster.add(new JLabel("clustering factor :"));
+ panelLUCluster.add(tf_lu_cluster_factor);
+ panelLUCluster.add(new JLabel("init temperature :"));
+ panelLUCluster.add(tf_lu_cluster_initTemperature);
+ panelLUCluster.add(new JLabel("force scaling factor :"));
+ panelLUCluster.add(tf_lu_cluster_forceScalingFactor);
+
+ cb_lu_avoidOverlapping = new JCheckBox();
+ cb_lu_avoidOverlapping.setOpaque(false);
+ tf_lu_overlapDetectWidth = new JTextField();
+ tf_lu_overlapPrefDistance = new JTextField();
+
+ JPanel panelLUOverlapSwitch = new JPanel(new GridLayout(1, 2, 10, 4));
+ panelLUOverlapSwitch.setOpaque(false);
+ panelLUOverlapSwitch.add(new JLabel("on/off"));
+ panelLUOverlapSwitch.add(cb_lu_avoidOverlapping);
+
+ JPanel panelLUEmpty = new JPanel();
+ panelLUEmpty.setOpaque(false);
+
+ panelLUOverlap.setBorder(BorderFactory.createTitledBorder(BorderFactory
+ [...]
+ "Force for overlapping Cells",
+ TitledBorder.LEADING,
+ TitledBorder.ABOVE_TOP));
+ panelLUOverlap.add(panelLUOverlapSwitch);
+ panelLUOverlap.add(panelLUEmpty);
+ panelLUOverlap.add(new JLabel("detection width :"));
+ panelLUOverlap.add(tf_lu_overlapDetectWidth);
+ panelLUOverlap.add(new JLabel("pref. distance :"));
+ panelLUOverlap.add(tf_lu_overlapPrefDistance);
+
+ cb_lu_avoidOverlapping.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ switchVisibility();
+ }
+ });
+
+ cb_lu_useOptimizationAlg = new JCheckBox();
+ cb_lu_useOptimizationAlg.setOpaque(false);
+ cb_lu_useOptimizationAlg.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ switchVisibility();
+ }
+ });
+
+ button_lu_ConfigOptimizeAlg = new JButton(button_ConfigOptimizeAlg.getText());
+ button_lu_ConfigOptimizeAlg.setBackground(panelLayoutUpdate.getBackground());
+ button_lu_ConfigOptimizeAlg.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ //lu_optimizeAlgController.configure();
+ }
+ });
+
+ JPanel emptyPanel3 = new JPanel();
+ emptyPanel3.setOpaque(false);
+
+ panelLUOptiAlg.add(new JLabel("Use optimization Algorithm:"));
+ panelLUOptiAlg.add(cb_lu_useOptimizationAlg);
+ panelLUOptiAlg.add(emptyPanel3);
+ panelLUOptiAlg.add(button_lu_ConfigOptimizeAlg);
+
+ panelLayoutRunWrapper = new JScrollPane(panelLayoutRun);
+
+ Dimension innerSize = new Dimension(500, 350);
+ panelLayoutRunWrapper.setPreferredSize(innerSize);
+ panelLayoutUpdateWrapper = new JScrollPane(panelLayoutUpdate);
+ panelLayoutUpdateWrapper.setPreferredSize(innerSize);
+
+ tp_main.addTab("Apply Values", panelLayoutRunWrapper);
+
+ setToolTipText();
+ }
+
+ /******************************************************************************/
+ protected JPanel getAdditionalForceConfig() {
+ return new JPanel();
+ }
+
+ /******************************************************************************/
+ protected JPanel getAdditionalForceLUConfig() {
+ return new JPanel();
+ }
+
+ /******************************************************************************/
+ protected void setToolTipText() {
+ tf_initTemperature.setToolTipText("Temperature Cells will be initialised with");
+ tf_minTemperature.setToolTipText("Algorithm stops when all Temperatures/the average of all Temperatures is below this value");
+ tf_maxTemperature.setToolTipText("Value, no temperature will surmount");
+ tf_prefEdgeLength.setToolTipText("preferred Length of Edges");
+ tf_gravitation.setToolTipText("attracting Force to the Barycenter of the Graph");
+ tf_randomImpulseRange.setToolTipText("Power of disturbing Forces");
+ tf_overlapDetectWidth.setToolTipText("Distance around a cell that will be searched for overlapping of other cells");
+ tf_overlapPrefDistance.setToolTipText("Distance the Algorithm try's to keep as mimimum between overlapped cells");
+ tf_alphaOsc.setToolTipText("Angle in witch Oscillations are detected");
+ tf_alphaRot.setToolTipText("Angle in witch Rotations are detected");
+ tf_sigmaOsc.setToolTipText("Penaltyvalue for Oscillations (with a higher Value Temperature decreases more slowly)");
+ tf_sigmaRot.setToolTipText("Penaltyvalue for Rotations (with a small Value Temperature decreases more slowly)");
+
+ tf_lu_initTemperature.setToolTipText(tf_initTemperature.getToolTipText());
+ tf_lu_minTemperature.setToolTipText(tf_minTemperature.getToolTipText());
+ tf_lu_maxTemperature.setToolTipText(tf_maxTemperature.getToolTipText());
+ tf_lu_prefEdgeLength.setToolTipText(tf_prefEdgeLength.getToolTipText());
+ tf_lu_gravitation.setToolTipText(tf_gravitation.getToolTipText());
+ tf_lu_randomImpulseRange.setToolTipText(tf_randomImpulseRange.getToolTipText());
+ tf_lu_overlapDetectWidth.setToolTipText(tf_overlapDetectWidth.getToolTipText());
+ tf_lu_overlapPrefDistance.setToolTipText(tf_overlapPrefDistance.getToolTipText());
+ tf_lu_alphaOsc.setToolTipText(tf_alphaOsc.getToolTipText());
+ tf_lu_alphaRot.setToolTipText(tf_alphaRot.getToolTipText());
+ tf_lu_sigmaOsc.setToolTipText(tf_sigmaOsc.getToolTipText());
+ tf_lu_sigmaRot.setToolTipText(tf_sigmaRot.getToolTipText());
+ tf_lu_depth.setToolTipText("Cells depth Edges away from the inserted Cells will also be updated");
+ tf_lu_cluster_initTemperature.setToolTipText("Initial temperature for clusters. It is recommended, that this value is below the initial temperature for normal vertices.");
+ tf_lu_cluster_forceScalingFactor.setToolTipText("Scales the forces, affecting clusters. Possible values are between 0.0 and 1.0. A small value ensures, that clusters move slow and over short distances.");
+ tf_lu_cluster_factor.setToolTipText("Factor the creation of clusters. A lower value leads to more clusters, with smaller size, a higher value to fewer, bigger clusters");
+
+ cb_computePermutation.setToolTipText("Algorithms will be calculated with the same/permutating order of Cells");
+ cb_endPerAverage.setToolTipText("Should the Algorithm stop when all Temperatures/the average of all Temperatures is below the min. Temperature");
+ cb_avoidOverlapping.setToolTipText("Switches the calculation of a Force, that appears when two Cells are overlapping");
+ cb_useOptimizationAlg.setToolTipText("Enables finetuning after the "
+ + GEMLayoutAlgorithm.KEY_CAPTION
+ + "-Algorithm with a short run of the " + KEY_TITLE
+ + "-Algorithm");
+
+ cb_lu_enableLayoutUpdate.setToolTipText("Should the Algorithm be performed, when Cells collapses/expand");
+ cb_lu_computePermutation.setToolTipText(cb_computePermutation.getToolTipText());
+ cb_lu_endPerAverage.setToolTipText(cb_endPerAverage.getToolTipText());
+ cb_lu_avoidOverlapping.setToolTipText(cb_avoidOverlapping.getToolTipText());
+ cb_lu_useOptimizationAlg.setToolTipText(cb_useOptimizationAlg.getToolTipText());
+ cb_lu_cluster_enable.setToolTipText("Switches clustering for the layout update process on/off");
+
+ comb_lu_method.setToolTipText("Method of organizing place for inserted Cells");
+
+ button_ConfigOptimizeAlg.setToolTipText("Configures the " + KEY_TITLE
+ + "-Algorithm for finetuning purpose");
+ button_lu_ConfigOptimizeAlg.setToolTipText(button_ConfigOptimizeAlg.getToolTipText());
+ }
+
+ /******************************************************************************/
+ protected boolean assertDouble(String text, String name, ArrayList errList) {
+ try {
+ Double.parseDouble(text);
+ } catch (NumberFormatException e) {
+ String errMsg = name + " is NOT a double value";
+ errList.add(errMsg);
+
+ return false;
+ }
+
+ return true;
+ }
+
+ /******************************************************************************/
+ protected boolean assertInteger(String text, String name, ArrayList errList) {
+ try {
+ Integer.parseInt(text);
+ } catch (NumberFormatException e) {
+ String errMsg = name + " is NOT a integer value";
+ errList.add(errMsg);
+
+ return false;
+ }
+
+ return true;
+ }
+
+ /******************************************************************************/
+ protected boolean assertRange(String value, double minValue, double maxValue,
+ boolean includeMinimum, boolean includeMaximum, String name,
+ ArrayList errList) {
+ double val = Double.parseDouble(value);
+ boolean isOK = true;
+
+ if (includeMinimum) {
+ isOK = minValue <= val;
+ } else {
+ isOK = minValue < val;
+ }
+
+ if (isOK) {
+ if (includeMaximum) {
+ isOK = maxValue >= val;
+ } else {
+ isOK = maxValue > val;
+ }
+
+ if (isOK)
+ return true;
+ }
+
+ //if isOK == false
+ String errMsg = name + " is out of the interval ";
+
+ if (includeMinimum) {
+ errMsg += "[";
+ } else {
+ errMsg += "]";
+ }
+
+ errMsg += (minValue + ";" + maxValue);
+
+ if (includeMaximum) {
+ errMsg += "]";
+ } else {
+ errMsg += "[";
+ }
+
+ errList.add(errMsg);
+
+ return false;
+ }
+
+ /******************************************************************************/
+ protected boolean assertRange(String value, int minValue, int maxValue, boolean includeMinimum,
+ boolean includeMaximum, String name, ArrayList errList) {
+ int val = Integer.parseInt(value);
+ boolean isOK = true;
+
+ if (includeMinimum) {
+ isOK = minValue <= val;
+ } else {
+ isOK = minValue < val;
+ }
+
+ if (isOK) {
+ if (includeMaximum) {
+ isOK = maxValue >= val;
+ } else {
+ isOK = maxValue > val;
+ }
+
+ if (isOK)
+ return true;
+ }
+
+ //if isOK == false
+ String errMsg = name + " is out of the interval ";
+
+ if (includeMinimum) {
+ errMsg += "[";
+ } else {
+ errMsg += "]";
+ }
+
+ errMsg += (minValue + ";" + maxValue);
+
+ if (includeMaximum) {
+ errMsg += "]";
+ } else {
+ errMsg += "[";
+ }
+
+ errList.add(errMsg);
+
+ return false;
+ }
+
+ /******************************************************************************/
+ protected boolean assertMinimum(String value, double minValue, boolean include, String name,
+ ArrayList errList) {
+ double val = Double.parseDouble(value);
+ boolean isOK = true;
+
+ if (include) {
+ isOK = minValue <= val;
+ } else {
+ isOK = minValue < val;
+ }
+
+ if (isOK)
+ return true;
+
+ String errMsg = name + " has to be bigger";
+
+ if (include) {
+ errMsg += " or equal to ";
+ } else {
+ errMsg += " then ";
+ }
+
+ errMsg += String.valueOf(minValue);
+ errList.add(errMsg);
+
+ return false;
+ }
+
+ /******************************************************************************/
+ protected boolean assertMinimum(String value, int minValue, boolean include, String name,
+ ArrayList errList) {
+ int val = Integer.parseInt(value);
+ boolean isOK = true;
+
+ if (include) {
+ isOK = minValue <= val;
+ } else {
+ isOK = minValue < val;
+ }
+
+ if (isOK)
+ return true;
+
+ String errMsg = name + " has to be bigger";
+
+ if (include) {
+ errMsg += " or equal to ";
+ } else {
+ errMsg += " then ";
+ }
+
+ errMsg += String.valueOf(minValue);
+ errList.add(errMsg);
+
+ return false;
+ }
+
+ /******************************************************************************/
+ public double getInitTemperature() {
+ return Double.parseDouble(tf_initTemperature.getText());
+ }
+
+ /******************************************************************************/
+ public void setInitTemperature(double temperature) {
+ tf_initTemperature.setText(String.valueOf(temperature));
+ }
+
+ /******************************************************************************/
+ public double getMinTemperature() {
+ return Double.parseDouble(tf_minTemperature.getText());
+ }
+
+ /******************************************************************************/
+ public void setMinTemperature(double temperature) {
+ tf_minTemperature.setText(String.valueOf(temperature));
+ }
+
+ /******************************************************************************/
+ public double getMaxTemperature() {
+ return Double.parseDouble(tf_maxTemperature.getText());
+ }
+
+ /******************************************************************************/
+ public void setMaxTemperature(double temperature) {
+ tf_maxTemperature.setText(String.valueOf(temperature));
+ }
+
+ /******************************************************************************/
+ public double getPreferredEdgeLength() {
+ return Double.parseDouble(tf_prefEdgeLength.getText());
+ }
+
+ /******************************************************************************/
+ public void setPreferredEdgeLength(double length) {
+ tf_prefEdgeLength.setText(String.valueOf(length));
+ }
+
+ /******************************************************************************/
+ public double getGravitation() {
+ return Double.parseDouble(tf_gravitation.getText());
+ }
+
+ /******************************************************************************/
+ public void setGravitation(double grav) {
+ tf_gravitation.setText(String.valueOf(grav));
+ }
+
+ /******************************************************************************/
+ public double getRandomImpulseRange() {
+ return Double.parseDouble(tf_randomImpulseRange.getText());
+ }
+
+ /******************************************************************************/
+ public void setRandomImpulseRange(double range) {
+ tf_randomImpulseRange.setText(String.valueOf(range));
+ }
+
+ /******************************************************************************/
+ public double getOverlapDetectionWidth() {
+ return Double.parseDouble(tf_overlapDetectWidth.getText());
+ }
+
+ /******************************************************************************/
+ public void setOverlapDetectionWidth(double width) {
+ tf_overlapDetectWidth.setText(String.valueOf(width));
+ }
+
+ /******************************************************************************/
+ public double getOverlapPreferredDistance() {
+ return Double.parseDouble(tf_overlapPrefDistance.getText());
+ }
+
+ /******************************************************************************/
+ public void setOverlapPreferredDistance(double distance) {
+ tf_overlapPrefDistance.setText(String.valueOf(distance));
+ }
+
+ /******************************************************************************/
+ public void setAvoidOverlapping(boolean avoid) {
+ cb_avoidOverlapping.setSelected(avoid);
+ switchVisibility();
+ }
+
+ /******************************************************************************/
+ public boolean getAvoidOverlapping() {
+ return cb_avoidOverlapping.isSelected();
+ }
+
+ /******************************************************************************/
+ public double getAlphaOsc() {
+ return Math.toRadians(Double.parseDouble(tf_alphaOsc.getText()));
+ }
+
+ /******************************************************************************/
+ public void setAlphaOsc(double alpha) {
+ tf_alphaOsc.setText(String.valueOf(Math.toDegrees(alpha)));
+ }
+
+ /******************************************************************************/
+ public double getAlphaRot() {
+ return Math.toRadians(Double.parseDouble(tf_alphaRot.getText()));
+ }
+
+ /******************************************************************************/
+ public void setAlphaRot(double alpha) {
+ tf_alphaRot.setText(String.valueOf(Math.toDegrees(alpha)));
+ }
+
+ /******************************************************************************/
+ public double getSigmaOsc() {
+ return Double.parseDouble(tf_sigmaOsc.getText());
+ }
+
+ /******************************************************************************/
+ public void setSigmaOsc(double sigma) {
+ tf_sigmaOsc.setText(String.valueOf(sigma));
+ }
+
+ /******************************************************************************/
+ public double getSigmaRot() {
+ return Double.parseDouble(tf_sigmaRot.getText());
+ }
+
+ /******************************************************************************/
+ public void setSigmaRot(double sigma) {
+ tf_sigmaRot.setText(String.valueOf(sigma));
+ }
+
+ /******************************************************************************/
+ public boolean getComputePermutation() {
+ return cb_computePermutation.isSelected();
+ }
+
+ /******************************************************************************/
+ public void setComputePermutation(boolean isSelected) {
+ cb_computePermutation.setSelected(isSelected);
+ }
+
+ /******************************************************************************/
+ public boolean getEndPerAverage() {
+ return cb_endPerAverage.isSelected();
+ }
+
+ /******************************************************************************/
+ public void setEndPerAverage(boolean isSelected) {
+ cb_computePermutation.setSelected(isSelected);
+ }
+
+ /******************************************************************************/
+ public double getLayoutUpdateInitTemperature() {
+ return Double.parseDouble(tf_lu_initTemperature.getText());
+ }
+
+ /******************************************************************************/
+ public void setLayoutUpdateInitTemperature(double temperature) {
+ tf_lu_initTemperature.setText(String.valueOf(temperature));
+ }
+
+ /******************************************************************************/
+ public double getLayoutUpdateMinTemperature() {
+ return Double.parseDouble(tf_lu_minTemperature.getText());
+ }
+
+ /******************************************************************************/
+ public void setLayoutUpdateMinTemperature(double temperature) {
+ tf_lu_minTemperature.setText(String.valueOf(temperature));
+ }
+
+ /******************************************************************************/
+ public double getLayoutUpdateMaxTemperature() {
+ return Double.parseDouble(tf_lu_maxTemperature.getText());
+ }
+
+ /******************************************************************************/
+ public void setLayoutUpdateMaxTemperature(double temperature) {
+ tf_lu_maxTemperature.setText(String.valueOf(temperature));
+ }
+
+ /******************************************************************************/
+ public double getLayoutUpdatePreferredEdgeLength() {
+ return Double.parseDouble(tf_lu_prefEdgeLength.getText());
+ }
+
+ /******************************************************************************/
+ public void setLayoutUpdatePreferredEdgeLength(double length) {
+ tf_lu_prefEdgeLength.setText(String.valueOf(length));
+ }
+
+ /******************************************************************************/
+ public double getLayoutUpdateGravitation() {
+ return Double.parseDouble(tf_lu_gravitation.getText());
+ }
+
+ /******************************************************************************/
+ public void setLayoutUpdateGravitation(double grav) {
+ tf_lu_gravitation.setText(String.valueOf(grav));
+ }
+
+ /******************************************************************************/
+ public double getLayoutUpdateRandomImpulseRange() {
+ return Double.parseDouble(tf_lu_randomImpulseRange.getText());
+ }
+
+ /******************************************************************************/
+ public void setLayoutUpdateRandomImpulseRange(double range) {
+ tf_lu_randomImpulseRange.setText(String.valueOf(range));
+ }
+
+ /******************************************************************************/
+ public double getLayoutUpdateOverlapDetectionWidth() {
+ return Double.parseDouble(tf_lu_overlapDetectWidth.getText());
+ }
+
+ /******************************************************************************/
+ public void setLayoutUpdateOverlapDetectionWidth(double width) {
+ tf_lu_overlapDetectWidth.setText(String.valueOf(width));
+ }
+
+ /******************************************************************************/
+ public double getLayoutUpdateOverlapPreferredDistance() {
+ return Double.parseDouble(tf_lu_overlapPrefDistance.getText());
+ }
+
+ /******************************************************************************/
+ public void setLayoutUpdateOverlapPreferredDistance(double distance) {
+ tf_lu_overlapPrefDistance.setText(String.valueOf(distance));
+ }
+
+ /******************************************************************************/
+ public void setLayoutUpdateAvoidOverlapping(boolean avoid) {
+ cb_lu_avoidOverlapping.setSelected(avoid);
+ switchVisibility();
+ }
+
+ /******************************************************************************/
+ public boolean getLayoutUpdateAvoidOverlapping() {
+ return cb_lu_avoidOverlapping.isSelected();
+ }
+
+ /******************************************************************************/
+ public double getLayoutUpdateAlphaOsc() {
+ return Math.toRadians(Double.parseDouble(tf_lu_alphaOsc.getText()));
+ }
+
+ /******************************************************************************/
+ public void setLayoutUpdateAlphaOsc(double alpha) {
+ tf_lu_alphaOsc.setText(String.valueOf(Math.toDegrees(alpha)));
+ }
+
+ /******************************************************************************/
+ public double getLayoutUpdateAlphaRot() {
+ return Math.toRadians(Double.parseDouble(tf_lu_alphaRot.getText()));
+ }
+
+ /******************************************************************************/
+ public void setLayoutUpdateAlphaRot(double alpha) {
+ tf_lu_alphaRot.setText(String.valueOf(Math.toDegrees(alpha)));
+ }
+
+ /******************************************************************************/
+ public double getLayoutUpdateSigmaOsc() {
+ return Double.parseDouble(tf_lu_sigmaOsc.getText());
+ }
+
+ /******************************************************************************/
+ public void setLayoutUpdateSigmaOsc(double sigma) {
+ tf_lu_sigmaOsc.setText(String.valueOf(sigma));
+ }
+
+ /******************************************************************************/
+ public double getLayoutUpdateSigmaRot() {
+ return Double.parseDouble(tf_lu_sigmaRot.getText());
+ }
+
+ /******************************************************************************/
+ public void setLayoutUpdateSigmaRot(double sigma) {
+ tf_lu_sigmaRot.setText(String.valueOf(sigma));
+ }
+
+ /******************************************************************************/
+ public boolean getLayoutUpdateComputePermutation() {
+ return cb_lu_computePermutation.isSelected();
+ }
+
+ /******************************************************************************/
+ public void setLayoutUpdateComputePermutation(boolean isSelected) {
+ cb_lu_computePermutation.setSelected(isSelected);
+ }
+
+ /******************************************************************************/
+ public void setLayoutUpdateEndPerAverage(boolean computeAverage) {
+ cb_lu_endPerAverage.setSelected(computeAverage);
+ }
+
+ /******************************************************************************/
+ public boolean getLayoutUpdateEndPerAverage() {
+ return cb_lu_endPerAverage.isSelected();
+ }
+
+ /******************************************************************************/
+ public void setLayoutUpdateEnabled(boolean isEnabled) {
+ cb_lu_enableLayoutUpdate.setSelected(isEnabled);
+ switchLayoutUpdatePanel();
+ }
+
+ /******************************************************************************/
+ public boolean getLayoutUpdateEnabled() {
+ return cb_lu_enableLayoutUpdate.isSelected();
+ }
+
+ /******************************************************************************/
+ public void setLayoutUpdateMethod(String key) {
+ comb_lu_method.setSelectedItem(key);
+ switchVisibility();
+ }
+
+ /******************************************************************************/
+ public String getLayoutUpdateMethod() {
+ return (String) comb_lu_method.getSelectedItem();
+ }
+
+ /******************************************************************************/
+ public void setLayoutUpdateDepth(int depth) {
+ tf_lu_depth.setText(String.valueOf(depth));
+ }
+
+ /******************************************************************************/
+ public int getLayoutUpdateDepth() {
+ return Integer.parseInt(tf_lu_depth.getText());
+ }
+
+ /******************************************************************************/
+ public void setOptimizationAlgorithmEnabled(boolean enable) {
+ cb_useOptimizationAlg.setSelected(enable);
+ switchVisibility();
+ }
+
+ /******************************************************************************/
+ public boolean getOptimizationAlgorithmEnabled() {
+ return cb_useOptimizationAlg.isSelected();
+ }
+
+ /******************************************************************************/
+ public Properties getOptimizationConfiguration() {
+ return optimizeAlgController.getConfiguration();
+ }
+
+ /******************************************************************************/
+ public void setOptimizationConfiguration(Properties config) {
+ optimizeAlgController.setConfiguration(config);
+ }
+
+ /******************************************************************************/
+ public void setLayoutUpdateOptimizationAlgorithmEnabled(boolean enable) {
+ cb_lu_useOptimizationAlg.setSelected(enable);
+ switchVisibility();
+ }
+
+ /******************************************************************************/
+ public boolean getLayoutUpdateOptimizationAlgorithmEnabled() {
+ return cb_lu_useOptimizationAlg.isSelected();
+ }
+
+ /******************************************************************************/
+ public void setLayoutUpdateOptimizationConfiguration(Properties config) {
+ lu_optimizeAlgController.setConfiguration(config);
+ }
+
+ /******************************************************************************/
+ public Properties getLayoutUpdateOptimizationConfiguration() {
+ return lu_optimizeAlgController.getConfiguration();
+ }
+
+ /******************************************************************************/
+ public void setLayoutUpdateMethodPerimeterInitSize(double size) {
+ tf_lu_perimeter_initSize.setText(String.valueOf(size));
+ }
+
+ /******************************************************************************/
+ public double getLayoutUpdateMethodPerimeterInitSize() {
+ return Double.parseDouble(tf_lu_perimeter_initSize.getText());
+ }
+
+ /******************************************************************************/
+ public void setLayoutUpdateMethodPerimeterSizeInc(double incValue) {
+ tf_lu_perimeter_sizeInc.setText(String.valueOf(incValue));
+ }
+
+ /******************************************************************************/
+ public double getLayoutUpdateMethodPerimeterSizeInc() {
+ return Double.parseDouble(tf_lu_perimeter_sizeInc.getText());
+ }
+
+ /******************************************************************************/
+ public void setLayoutUpdateClusteringEnabled(boolean isEnabled) {
+ cb_lu_cluster_enable.setSelected(isEnabled);
+ switchVisibility();
+ }
+
+ /******************************************************************************/
+ public boolean getLayoutUpdateClusteringEnabled() {
+ return cb_lu_cluster_enable.isSelected();
+ }
+
+ /******************************************************************************/
+ public void setLayoutUpdateClusteringInitTemperature(double temp) {
+ tf_lu_cluster_initTemperature.setText(String.valueOf(temp));
+ }
+
+ /******************************************************************************/
+ public double getLayoutUpdateClusteringInitTemperature() {
+ return Double.parseDouble(tf_lu_cluster_initTemperature.getText());
+ }
+
+ /******************************************************************************/
+ public void setLayoutUpdateClusteringForceScalingFactor(double factor) {
+ tf_lu_cluster_forceScalingFactor.setText(String.valueOf(factor));
+ }
+
+ /******************************************************************************/
+ public double getLayoutUpdateClusteringForceScalingFactor() {
+ return Double.parseDouble(tf_lu_cluster_forceScalingFactor.getText());
+ }
+
+ /******************************************************************************/
+ public void setLayoutUpdateClusteringFactor(double factor) {
+ tf_lu_cluster_factor.setText(String.valueOf(factor));
+ }
+
+ /******************************************************************************/
+ public double getLayoutUpdateClusteringFactor() {
+ return Double.parseDouble(tf_lu_cluster_factor.getText());
+ }
+
+ /******************************************************************************/
+ /*############################################################################*/
+ /*############################################################################*/
+ /*############################################################################*/
+ /*############################################################################*/
+ /******************************************************************************/
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/layout/JGraphLayoutAlgorithm.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/layout/JGraphLayoutAlgorithm.java
new file mode 100644
index 0000000..aeb89df
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/layout/JGraphLayoutAlgorithm.java
@@ -0,0 +1,319 @@
+/*
+ * @(#)JGraphLayoutAlgorithm.java 1.0 18-MAY-2004
+ *
+ * Copyright (c) 2001-2005, Gaudenz Alder
+ * All rights reserved.
+ *
+ * This library is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation; either
+ * version 2.1 of the License, or (at your option) any later version.
+ *
+ * This library is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this library; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+ */
+package org.jgraph.layout;
+
+import cytoscape.task.TaskMonitor;
+
+import org.jgraph.JGraph;
+
+import org.jgraph.graph.CellView;
+import org.jgraph.graph.GraphConstants;
+import org.jgraph.graph.GraphLayoutCache;
+import org.jgraph.graph.VertexView;
+
+import java.awt.BorderLayout;
+import java.awt.Component;
+import java.awt.FlowLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.geom.Rectangle2D;
+
+import java.util.HashSet;
+import java.util.Hashtable;
+import java.util.Map;
+import java.util.Set;
+
+import javax.swing.JButton;
+import javax.swing.JDialog;
+import javax.swing.JFrame;
+import javax.swing.JPanel;
+
+
+/**
+ *
+ */
+public abstract class JGraphLayoutAlgorithm {
+ protected static Set LAYOUT_ATTRIBUTES = new HashSet();
+
+ static {
+ LAYOUT_ATTRIBUTES.add(GraphConstants.BOUNDS);
+ LAYOUT_ATTRIBUTES.add(GraphConstants.POINTS);
+ LAYOUT_ATTRIBUTES.add(GraphConstants.LABELPOSITION);
+ LAYOUT_ATTRIBUTES.add(GraphConstants.ROUTING);
+ }
+
+ /**
+ * Set to false if the algorithm should terminate immediately
+ */
+ boolean isAllowedToRun = true;
+
+ /**
+ * Set to non zero if you want to indicate progress
+ */
+ int progress = 0;
+
+ /**
+ * Set to non zero if you want to indicate progress
+ */
+ int maximumProgress = 0;
+
+ /**
+ * Added for Cytoscape support
+ */
+ public TaskMonitor taskMonitor = null;
+
+ /**
+ *
+ */
+ public boolean canceled = false;
+
+ /**
+ * Subclassers may return a new JComponent that
+ * allows to configure the layout. The default
+ * implementation returns <code>null</code>.<br>
+ * Note: Settings creation may be expensive so
+ * the UI should cache the values returned by
+ * this method.
+ */
+ public JGraphLayoutSettings createSettings() {
+ return null;
+ }
+
+ /**
+ * Get a human readable hint for using this layout.
+ */
+ public String getHint() {
+ return "";
+ }
+
+ /**
+ * Executes the layout algorithm with the given cells to be moved
+ * @param graph JGraph to be altered by layout
+ * @param cells Array of cells to be moved by the layout
+ */
+ public void run(JGraph graph, Object[] cells) {
+ run(graph, cells, null);
+ }
+
+ /**
+ * Executes the layout algorithm specifying which cells are to remain
+ * in place after the layout is applied.
+ * @param jgraph JGraph to be altered by layout
+ * @param dynamic_cells Cells that are to be moved by the layout
+ * @param static_cells Cells that are not to be moved, but allowed for by the layout
+ */
+ public abstract void run(JGraph jgraph, Object[] dynamic_cells, Object[] static_cells);
+
+ /**
+ * @return Returns the isAllowedToRun.
+ */
+ public boolean isAllowedToRun() {
+ return isAllowedToRun;
+ }
+
+ /**
+ * @param isAllowedToRun The isAllowedToRun to set.
+ */
+ public void setAllowedToRun(boolean isAllowedToRun) {
+ this.isAllowedToRun = isAllowedToRun;
+ }
+
+ /**
+ * Returns the maximum progress
+ */
+ public int getMaximumProgress() {
+ return maximumProgress;
+ }
+
+ /**
+ * Sets the maximum progress.
+ */
+ public void setMaximumProgress(int maximumProgress) {
+ this.maximumProgress = maximumProgress;
+ }
+
+ /**
+ * Returns the current progress
+ */
+ public int getProgress() {
+ return progress;
+ }
+
+ /**
+ * @param progress The progress complete amount
+ */
+ public void setProgress(int progress) {
+ this.progress = progress;
+
+ if (taskMonitor != null) {
+ if (progress > 100)
+ progress = 100;
+ else if (progress < 1)
+ progress = 1;
+
+ taskMonitor.setPercentCompleted((int) progress);
+ Thread.yield();
+ }
+ }
+
+ /**
+ * A utility method to create a simple dialog with
+ * close and apply button.
+ * @param settings Layout settings instance
+ * @param parent Parent JFrame
+ * @param title Title of dialog box
+ * @param close Text for cancel button
+ * @param apply Text for apply button
+ * @return JDialog dialog to be displayed
+ */
+ public static JDialog createDialog(final JGraphLayoutSettings settings, JFrame parent,
+ String title, String close, String apply) {
+ if (settings instanceof Component)
+ return populateDialog(settings, new JDialog(parent, title, true), close, apply);
+
+ return null;
+ }
+
+ /**
+ * A utility method to create a simple dialog with
+ * close and apply button.
+ * @param settings Layout settings instance
+ * @param parent Parent JDialog
+ * @param title Title of dialog box
+ * @param close Text for cancel button
+ * @param apply Text for apply button
+ * @return JDialog dialog to be displayed
+ */
+ public static JDialog createDialog(final JGraphLayoutSettings settings, JDialog parent,
+ String title, String close, String apply) {
+ if (settings instanceof Component)
+ return populateDialog(settings, new JDialog(parent, title, true), close, apply);
+
+ return null;
+ }
+
+ /**
+ * A utility method to create a simple dialog with
+ * close and apply button.
+ * @param settings Layout settings instance
+ * @param dialog JDialog to be used
+ * @param close Text for cancel button
+ * @param apply Text for apply button
+ * @return JDialog showing the settings for the layout
+ */
+ public static JDialog populateDialog(final JGraphLayoutSettings settings, final JDialog dialog,
+ String close, String apply) {
+ if ((dialog != null) && settings instanceof Component) {
+ dialog.getContentPane().setLayout(new BorderLayout());
+ dialog.getContentPane().add((Component) settings, BorderLayout.CENTER);
+
+ JButton cancelButton = new JButton(close);
+ cancelButton.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ dialog.dispose();
+ }
+ });
+
+ JButton applyButton = new JButton(apply);
+ applyButton.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ settings.apply();
+ dialog.dispose();
+ }
+ });
+
+ JPanel buttonPanel = new JPanel(new FlowLayout(FlowLayout.RIGHT));
+ buttonPanel.add(applyButton);
+ buttonPanel.add(cancelButton);
+ dialog.getContentPane().add(buttonPanel, BorderLayout.SOUTH);
+ dialog.getRootPane().setDefaultButton(applyButton);
+
+ return dialog;
+ }
+
+ return dialog;
+ }
+
+ /**
+ * Calls applyLayout() with null static_cells
+ * @param sourceGraph The JGraph to have the layout applied
+ * @param layout The layout algorithm to be applied
+ * @param cells Cells that are to be moved by the layout
+ */
+ public static void applyLayout(JGraph sourceGraph, JGraphLayoutAlgorithm layout, Object[] cells) {
+ JGraphLayoutAlgorithm.applyLayout(sourceGraph, layout, cells, null);
+ }
+
+ /**
+ * Takes a local clone of the JGraph and calls the run() method on the
+ * specified layout algorithm on the local JGraph. After the layout has
+ * been applied, the changed attributes on the local JGraph are extracted
+ * and applied to the JGraph instance passed in, creating one undoable edit.
+ * @param sourceGraph The JGraph to have the layout applied
+ * @param layout The layout algorithm to be applied
+ * @param dynamic_cells Cells that are to be moved by the layout
+ * @param static_cells Cells that are not to be moved, but allowed for by the layout
+ */
+ public static void applyLayout(JGraph sourceGraph, JGraphLayoutAlgorithm layout,
+ Object[] dynamic_cells, Object[] static_cells) {
+ JGraph localGraph = new JGraph(sourceGraph.getModel());
+ localGraph.setBounds(sourceGraph.getBounds());
+
+ GraphLayoutCache cache = localGraph.getGraphLayoutCache();
+ cache.setLocalAttributes(LAYOUT_ATTRIBUTES);
+ layout.run(localGraph, dynamic_cells, static_cells);
+
+ if (layout.isAllowedToRun()) {
+ // fetch attributes from cellview and write to source Graph
+ Map nested = new Hashtable();
+ CellView[] cellViews = cache.getAllDescendants(cache.getRoots());
+
+ for (int i = 0; i < cellViews.length; i++) {
+ Map attrs = cellViews[i].getAttributes();
+ Rectangle2D bounds = GraphConstants.getBounds(attrs);
+
+ if (cellViews[i] instanceof VertexView && (bounds == null)) {
+ GraphConstants.setBounds(attrs, cellViews[i].getBounds());
+ }
+
+ if (!attrs.isEmpty())
+ nested.put(cellViews[i].getCell(), attrs);
+ }
+
+ if (!nested.isEmpty())
+ sourceGraph.getGraphLayoutCache().edit(nested, null, null, null);
+ }
+ }
+
+ /**
+ * Added for Cytoscape support
+ */
+ public void setTaskMonitor(TaskMonitor taskMonitor) {
+ this.taskMonitor = taskMonitor;
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void setCanceled() {
+ this.canceled = true;
+ }
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/layout/JGraphLayoutRegistry.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/layout/JGraphLayoutRegistry.java
new file mode 100644
index 0000000..d10bdcd
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/layout/JGraphLayoutRegistry.java
@@ -0,0 +1,76 @@
+/*
+ * @(#)JGraphLayoutRegistry.java 1.0 18-MAY-2004
+ *
+ * Copyright (c) 2001-2005, Gaudenz Alder
+ * All rights reserved.
+ *
+ * This library is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation; either
+ * version 2.1 of the License, or (at your option) any later version.
+ *
+ * This library is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this library; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+ */
+package org.jgraph.layout;
+
+import java.util.ArrayList;
+
+
+/**
+ * @author Gaudenz Alder
+ *
+ * Allows to maintain a list of layout algorithms. Contains all default
+ * algorithms that ship with this package. This is a singleton class.
+ */
+public class JGraphLayoutRegistry {
+ /**
+ * Contains the shared registry instance
+ */
+ protected static JGraphLayoutRegistry sharedJGraphLayoutRegistry = new JGraphLayoutRegistry();
+
+ static {
+ // Register Local Layouts
+ sharedJGraphLayoutRegistry.add(new AnnealingLayoutAlgorithm());
+ sharedJGraphLayoutRegistry.add(new CircleGraphLayout());
+ sharedJGraphLayoutRegistry.add(new GEMLayoutAlgorithm(new AnnealingLayoutAlgorithm(true)));
+ sharedJGraphLayoutRegistry.add(new MoenLayoutAlgorithm());
+ sharedJGraphLayoutRegistry.add(new RadialTreeLayoutAlgorithm());
+ sharedJGraphLayoutRegistry.add(new SpringEmbeddedLayoutAlgorithm());
+ sharedJGraphLayoutRegistry.add(new SugiyamaLayoutAlgorithm());
+ sharedJGraphLayoutRegistry.add(new TreeLayoutAlgorithm());
+ sharedJGraphLayoutRegistry.add(new OrderedTreeLayoutAlgorithm());
+ }
+
+ /**
+ * Returns the current registry (singleton)
+ */
+ public static JGraphLayoutRegistry getSharedJGraphLayoutRegistry() {
+ return sharedJGraphLayoutRegistry;
+ }
+
+ /**
+ * Contains the registered layouts
+ */
+ protected ArrayList layouts = new ArrayList();
+
+ /**
+ * Register a new Layout
+ */
+ public void add(JGraphLayoutAlgorithm layout) {
+ layouts.add(layout);
+ }
+
+ /**
+ * @return Returns the layouts.
+ */
+ public ArrayList getLayouts() {
+ return layouts;
+ }
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/layout/JGraphLayoutSettings.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/layout/JGraphLayoutSettings.java
new file mode 100644
index 0000000..a76287a
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/layout/JGraphLayoutSettings.java
@@ -0,0 +1,39 @@
+/*
+ * @(#)JGraphLayoutSettings.java 1.0 12-JUL-2004
+ *
+ * Copyright (c) 2001-2004, Gaudenz Alder
+ * All rights reserved.
+ *
+ * This library is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation; either
+ * version 2.1 of the License, or (at your option) any later version.
+ *
+ * This library is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this library; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+ */
+package org.jgraph.layout;
+
+
+/**
+ * Allows the algorithm to create an object that
+ * may be applied back to the algorithm.
+ */
+public interface JGraphLayoutSettings {
+ /**
+ * (Re)read settings from layout algorithm.
+ */
+ public void revert();
+
+ /**
+ * Apply the current settings to the layout that
+ * created this object.
+ */
+ public void apply();
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/layout/MoenLayoutAlgorithm.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/layout/MoenLayoutAlgorithm.java
new file mode 100644
index 0000000..b7155cd
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/layout/MoenLayoutAlgorithm.java
@@ -0,0 +1,658 @@
+/*
+ * @(#)MoenLayoutAlgorithm.java 1.0 18-MAY-2004
+ *
+ * Copyright (c) 2004-2005, Gaudenz Alder and others
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright notice,
+ * this list of conditions and the following disclaimer.
+ * - Redistributions in binary form must reproduce the above copyright notice,
+ * this list of conditions and the following disclaimer in the documentation
+ * and/or other materials provided with the distribution.
+ * - Neither the name of JGraph nor the names of its contributors may be used
+ * to endorse or promote products derived from this software without specific
+ * prior written permission.
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ */
+package org.jgraph.layout;
+
+import cytoscape.Cytoscape;
+
+import org.jgraph.JGraph;
+
+import org.jgraph.graph.CellView;
+import org.jgraph.graph.EdgeView;
+import org.jgraph.graph.GraphModel;
+import org.jgraph.graph.PortView;
+import org.jgraph.graph.VertexView;
+
+import java.awt.Point;
+import java.awt.geom.Rectangle2D;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.List;
+
+import javax.swing.JOptionPane;
+
+
+/**
+ *
+ */
+public class MoenLayoutAlgorithm extends JGraphLayoutAlgorithm {
+ /**
+ * layout,attachParent,layoutLeaf,join,merge,offset and bridge
+ * methods below were taken line by line from Moen's algorithm.
+ *
+ * Attempts to understand the above methods without reading the paper
+ * first are strongly discouraged.
+ *
+ * http://www.computer.org/software/so1990/s4021abs.htm
+ *
+ * */
+ public static final Object CELL_WRAPPER = new Object();
+
+ /**
+ *
+ */
+ public static final int LEFT_TO_RIGHT = 0;
+
+ /**
+ *
+ */
+ public static final int UP_TO_DOWN = 1;
+
+ /**
+ *
+ */
+ public static final int DEFAULT_ORIENTATION = LEFT_TO_RIGHT;
+ JGraph jgraph;
+ protected int orientation;
+ protected int childParentDistance;
+ private HashMap nodesSeen;
+
+ /**
+ * Creates a new MoenLayoutAlgorithm object.
+ */
+ public MoenLayoutAlgorithm() {
+ setChildParentDistance(30);
+ setLayoutOrientation(DEFAULT_ORIENTATION);
+ nodesSeen = new HashMap();
+ }
+
+ /**
+ * Returns the name of this algorithm in human
+ * readable form.
+ */
+ public String toString() {
+ return "Moen's Tree";
+ }
+
+ /**
+ * Get a human readable hint for using this layout.
+ */
+ public String getHint() {
+ return "Select a root node";
+ }
+
+ /**
+ * Returns an new instance of SugiyamaLayoutSettings
+ */
+ public JGraphLayoutSettings createSettings() {
+ return new MoenLayoutSettings(this);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param orientation DOCUMENT ME!
+ */
+ public void setLayoutOrientation(int orientation) {
+ if ((orientation < 0) && (orientation > 1)) {
+ orientation = DEFAULT_ORIENTATION;
+ } else {
+ this.orientation = orientation;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param distance DOCUMENT ME!
+ */
+ public void setChildParentDistance(int distance) {
+ if (distance <= 0)
+ throw new IllegalArgumentException("Distance has to be positive integer " + distance);
+
+ childParentDistance = distance;
+ }
+
+ protected void layout(TreeLayoutNode t) {
+ TreeLayoutNode c;
+
+ if (t == null) {
+ return;
+ }
+
+ c = t.child;
+
+ while (c != null) {
+ if (c.sibling != t.child) {
+ // Avoid loops
+ // throw new Exception("Found a loop in the network!");
+ layout(c);
+ }
+
+ c = c.sibling;
+ }
+
+ if (t.child != null) {
+ attachParent(t, join(t));
+ } else {
+ layoutLeaf(t);
+ }
+ }
+
+ protected void attachParent(TreeLayoutNode t, int h) {
+ final int x;
+ int y1;
+ final int y2;
+
+ x = t.border + childParentDistance;
+ y2 = ((h - t.height) / 2) - t.border;
+ y1 = (y2 + t.height + (2 * t.border)) - h;
+ t.child.offset.x = x + t.width;
+ t.child.offset.y = y1;
+ t.contour.upper_head = new PolyLine(t.width, 0, new PolyLine(x, y1, t.contour.upper_head));
+ t.contour.lower_head = new PolyLine(t.width, 0, new PolyLine(x, y2, t.contour.lower_head));
+ }
+
+ protected void layoutLeaf(TreeLayoutNode t) {
+ t.contour.upper_tail = new PolyLine(t.width + (2 * t.border), 0, null);
+ t.contour.upper_head = t.contour.upper_tail;
+ t.contour.lower_tail = new PolyLine(0, -t.height - (2 * t.border), null);
+ t.contour.lower_head = new PolyLine(t.width + (2 * t.border), 0, t.contour.lower_tail);
+ }
+
+ protected int join(TreeLayoutNode t) {
+ TreeLayoutNode c;
+ int d;
+ int h;
+ int sum;
+
+ c = t.child;
+ t.contour = c.contour;
+ sum = h = c.height + (2 * c.border);
+ c = c.sibling;
+
+ while (c != null) {
+ d = merge(t.contour, c.contour);
+ c.offset.y = d + h;
+ c.offset.x = 0;
+ h = c.height + (2 * c.border);
+ sum += (d + h);
+ c = c.sibling;
+ }
+
+ return sum;
+ }
+
+ protected int merge(Polygon c1, Polygon c2) {
+ int x;
+ int y;
+ int total;
+ int d;
+ PolyLine lower;
+ PolyLine upper;
+ PolyLine b;
+
+ x = y = total = 0;
+ upper = c1.lower_head;
+ lower = c2.upper_head;
+
+ while ((lower != null) && (upper != null)) {
+ d = offset(x, y, lower.dx, lower.dy, upper.dx, upper.dy);
+ y += d;
+ total += d;
+
+ if ((x + lower.dx) <= upper.dx) {
+ y += lower.dy;
+ x += lower.dx;
+ lower = lower.link;
+ } else {
+ y -= upper.dy;
+ x -= upper.dx;
+ upper = upper.link;
+ }
+ }
+
+ if (lower != null) {
+ b = bridge(c1.upper_tail, 0, 0, lower, x, y);
+ c1.upper_tail = (b.link != null) ? c2.upper_tail : b;
+ c1.lower_tail = c2.lower_tail;
+ } else {
+ b = bridge(c2.lower_tail, x, y, upper, 0, 0);
+
+ if (b.link == null) {
+ c1.lower_tail = b;
+ }
+ }
+
+ c1.lower_head = c2.lower_head;
+
+ return total;
+ }
+
+ protected int offset(int p1, int p2, int a1, int a2, int b1, int b2) {
+ int d;
+ int s;
+ int t;
+
+ if ((b1 <= p1) || ((p1 + a1) <= 0)) {
+ return 0;
+ }
+
+ t = (b1 * a2) - (a1 * b2);
+
+ if (t > 0) {
+ if (p1 < 0) {
+ s = p1 * a2;
+ d = (s / a1) - p2;
+ } else if (p1 > 0) {
+ s = p1 * b2;
+ d = (s / b1) - p2;
+ } else {
+ d = -p2;
+ }
+ } else if (b1 < (p1 + a1)) {
+ s = (b1 - p1) * a2;
+ d = b2 - (p2 + (s / a1));
+ } else if (b1 > (p1 + a1)) {
+ s = (a1 + p1) * b2;
+ d = (s / b1) - (p2 + a2);
+ } else {
+ d = b2 - (p2 + a2);
+ }
+
+ if (d > 0) {
+ return d;
+ } else {
+ return 0;
+ }
+ }
+
+ protected PolyLine bridge(PolyLine line1, int x1, int y1, PolyLine line2, int x2, int y2) {
+ int dy;
+ int dx;
+ int s;
+ PolyLine r;
+
+ dx = (x2 + line2.dx) - x1;
+
+ if (line2.dx == 0) {
+ dy = line2.dy;
+ } else {
+ s = dx * line2.dy;
+ dy = s / line2.dx;
+ }
+
+ r = new PolyLine(dx, dy, line2.link);
+ line1.link = new PolyLine(0, (y2 + line2.dy) - dy - y1, r);
+
+ return r;
+ }
+
+ protected void leftRightNodeLayout(TreeLayoutNode node, int off_x, int off_y) {
+ TreeLayoutNode child;
+ TreeLayoutNode s;
+ int siblingOffest;
+
+ node.pos.translate(off_x + node.offset.x, off_y + node.offset.y);
+ child = node.child; //topmost child
+
+ if (child != null) {
+ leftRightNodeLayout(child, node.pos.x, node.pos.y);
+ s = child.sibling;
+ siblingOffest = node.pos.y + child.offset.y;
+
+ while (s != null) {
+ leftRightNodeLayout(s, node.pos.x + child.offset.x, siblingOffest);
+ siblingOffest += s.offset.y;
+ s = s.sibling;
+ }
+ }
+ }
+
+ protected void upDownNodeLayout(TreeLayoutNode node, int off_x, int off_y) {
+ TreeLayoutNode child;
+ TreeLayoutNode s;
+ int siblingOffset;
+
+ node.pos.translate(off_x + (-1 * node.offset.y), off_y + node.offset.x);
+ child = node.child; //rightmost child
+
+ if (child != null) {
+ upDownNodeLayout(child, node.pos.x, node.pos.y);
+ s = child.sibling;
+ siblingOffset = node.pos.x - child.offset.y;
+
+ while (s != null) {
+ upDownNodeLayout(s, siblingOffset, node.pos.y + child.offset.x);
+ siblingOffset -= s.offset.y;
+ s = s.sibling;
+ }
+ }
+ }
+
+ /**
+ * This method assumes the graph describes a tree structure. It does not
+ * test to see if the graph is a network.
+ *
+ * Use extreme caution if applyToAll parameter is set to false and
+ * only the selected cells are to be used. In the set of selected cells,
+ * any vertex with no source edge in the set will be considered to be a tree
+ * root. This will work fine as long as all tree vertices in the set that
+ * are a child of a tree vertex in the set are connected by a path of edges
+ * to that parent tree vertex (I think).
+ *
+ * @param graph JGraph instance
+ * @param dynamic_cells List of all nodes the layout should move
+ * @param static_cells List of node the layout should not move but allow for
+ */
+ public void run(JGraph graph, Object[] dynamic_cells, Object[] static_cells) {
+ this.jgraph = graph;
+
+ try {
+ if (canceled)
+ return;
+
+ List roots = getRootVertices(dynamic_cells);
+
+ if (canceled)
+ return;
+
+ buildLayoutHelperTree(roots);
+
+ if (canceled)
+ return;
+
+ layoutTrees(roots);
+
+ if (canceled)
+ return;
+
+ display(roots);
+ } catch (Exception e) {
+ JOptionPane.showMessageDialog(Cytoscape.getDesktop(), e, "Error",
+ JOptionPane.INFORMATION_MESSAGE);
+ }
+ }
+
+ /**
+ * If it is a Vertex and it has no source, it must be a root vertex.
+ *
+ * !!!todo I will need to enforce that there is always at least one vertex,
+ * and that is the acq portal.
+ *
+ * @return all the tree root vertices
+ */
+ protected ArrayList getRootVertices(Object[] selectedCells) {
+ HashSet potentialRoot = new HashSet();
+ HashSet notARoot = new HashSet();
+ CellView viewTargetPort;
+ CellView viewTarget;
+
+ /*
+ * Loop through all the vertex and edge cells
+ */
+ for (int i = 0; i < selectedCells.length; i++) {
+ if (canceled)
+ return null;
+
+ Object view = jgraph.getGraphLayoutCache().getMapping(selectedCells[i], false);
+
+ /*
+ * If the vertex is not in the notARoot bucket, it is a potential
+ * root.
+ */
+ if (view instanceof VertexView) {
+ if (!(notARoot.contains(view))) {
+ potentialRoot.add(view);
+ }
+ }
+ /*
+ * The target of an edge is not a root.
+ */
+ else if (view instanceof EdgeView) {
+ viewTargetPort = ((EdgeView) view).getTarget();
+ viewTarget = viewTargetPort.getParentView();
+ potentialRoot.remove(viewTarget);
+ notARoot.add(viewTarget);
+ }
+ else if (view instanceof PortView) {
+ // Ignore ports
+ }
+ /*
+ * It should be impossible to get to the next statement
+ */
+ else {
+ throw new RuntimeException("Cell is other than Vertex or Edge.");
+ }
+ }
+
+ /*
+ * When the loop ends, only tree roots are left
+ */
+ return new ArrayList(potentialRoot);
+ }
+
+ protected List getChildren(VertexView node) {
+ ArrayList children = new ArrayList();
+ Object vertex = node.getCell();
+ GraphModel model = jgraph.getModel();
+ int portCount = model.getChildCount(vertex);
+
+ // iterate any NodePort
+ for (int i = 0; i < portCount; i++) {
+ Object port = model.getChild(vertex, i);
+
+ // iterate any Edge in the port
+ Iterator itrEdges = model.edges(port);
+
+ while (itrEdges.hasNext()) {
+ Object edge = itrEdges.next();
+
+ // if the Edge is a forward edge we should follow this edge
+ if (port == model.getSource(edge)) {
+ Object targetPort = model.getTarget(edge);
+ Object targetVertex = model.getParent(targetPort);
+ VertexView targetVertexView = (VertexView) jgraph.getGraphLayoutCache()
+ .getMapping(targetVertex, false);
+ children.add(targetVertexView);
+ }
+ }
+ }
+
+ return children;
+ }
+
+ protected void layoutTrees(Collection roots) throws Exception {
+ for (Iterator iterator = roots.iterator(); iterator.hasNext();) {
+ if (canceled)
+ return;
+
+ VertexView view = (VertexView) iterator.next();
+ TreeLayoutNode root = getTreeLayoutNode(view);
+
+ // kick off Moen's algorithm
+ layout(root);
+
+ Rectangle2D rect = view.getBounds();
+ Point rootPos = new Point((int) rect.getX(), (int) rect.getY()); //view.getBounds().getLocation();
+
+ switch (orientation) {
+ case LEFT_TO_RIGHT:
+ leftRightNodeLayout(root, rootPos.x, rootPos.y);
+
+ break;
+
+ case UP_TO_DOWN:
+ upDownNodeLayout(root, rootPos.x, rootPos.y);
+
+ break;
+
+ default:
+ leftRightNodeLayout(root, rootPos.x, rootPos.y);
+ }
+ }
+ }
+
+ protected void buildLayoutHelperTree(Collection roots) {
+ for (Iterator iterator = roots.iterator(); iterator.hasNext();) {
+ if (canceled)
+ return;
+
+ VertexView vv = (VertexView) iterator.next();
+ decorateNode(vv);
+ }
+ }
+
+ protected void decorateNode(VertexView node) {
+ List cl = getChildren(node);
+ TreeLayoutNode parent = getTreeLayoutNode(node);
+
+ // See if we're already traversed this node -- might have a loop
+ if (nodesSeen.containsKey(node)) {
+ throw new RuntimeException("Detected loop in graph!");
+ } else {
+ nodesSeen.put(node, node);
+ }
+
+ if (cl.size() > 0) {
+ //Decorate children with Moen's nodes, parent has a reference
+ //to a first child only. Each child has a reference to a parent
+ //and possible next sibling
+ for (int i = 0; i < cl.size(); i++) {
+ VertexView currentChild = (VertexView) cl.get(i);
+ TreeLayoutNode cln = getTreeLayoutNode(currentChild);
+
+ if (i == 0) {
+ parent.child = cln;
+ } else {
+ VertexView previousChild = (VertexView) cl.get(i - 1);
+ TreeLayoutNode pln = getTreeLayoutNode(previousChild);
+ pln.sibling = cln;
+ }
+
+ cln.parent = parent;
+ decorateNode(currentChild);
+ }
+ }
+ }
+
+ protected TreeLayoutNode getTreeLayoutNode(VertexView view) {
+ return getTreeLayoutNode(view, true);
+ }
+
+ protected TreeLayoutNode getTreeLayoutNode(VertexView view, boolean createIfNotPresent) {
+ TreeLayoutNode decor = (TreeLayoutNode) view.getAttributes().get(CELL_WRAPPER);
+
+ if ((decor == null) && createIfNotPresent) {
+ TreeLayoutNode n = new TreeLayoutNode(view);
+ view.getAttributes().put(CELL_WRAPPER, n);
+
+ return n;
+ } else {
+ return decor;
+ }
+ }
+
+ protected void display(Collection roots) {
+ for (Iterator iterator = roots.iterator(); iterator.hasNext();) {
+ VertexView vertexView = (VertexView) iterator.next();
+ displayHelper(vertexView);
+ }
+ }
+
+ protected void displayHelper(VertexView view) {
+ TreeLayoutNode node = getTreeLayoutNode(view);
+
+ /*
+ Object cell = view.getCell();
+ Map attributes =
+ GraphConstants.createAttributes(
+ cell,
+ GraphConstants.BOUNDS,
+ new Rectangle(node.pos, new Dimension(node.width, node.height)));
+
+ jgraph.getGraphLayoutCache().edit(attributes, null, null, null);
+ */
+ Rectangle2D rect = view.getBounds();
+ rect.setFrame(node.pos.x, node.pos.y, node.width, node.height);
+
+ List c = getChildren(view);
+
+ for (Iterator iterator = c.iterator(); iterator.hasNext();) {
+ VertexView vertexView = (VertexView) iterator.next();
+ displayHelper(vertexView);
+ }
+
+ view.getAttributes().remove(CELL_WRAPPER);
+ }
+
+ private class TreeLayoutNode {
+ TreeLayoutNode parent;
+ TreeLayoutNode child;
+ TreeLayoutNode sibling;
+ final int width;
+ final int height;
+ final int border;
+ final Point pos;
+ final Point offset;
+ Polygon contour;
+
+ public TreeLayoutNode(VertexView node) {
+ width = (int) node.getBounds().getWidth();
+ height = (int) node.getBounds().getHeight();
+ border = 5;
+ pos = new Point();
+ offset = new Point();
+ contour = new Polygon();
+ }
+ }
+
+ private static class Polygon {
+ PolyLine lower_head;
+ PolyLine lower_tail;
+ PolyLine upper_head;
+ PolyLine upper_tail;
+ }
+
+ private static class PolyLine {
+ final int dx;
+ final int dy;
+ PolyLine link;
+
+ PolyLine(int dx, int dy, PolyLine link) {
+ this.dx = dx;
+ this.dy = dy;
+ this.link = link;
+ }
+ }
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/layout/MoenLayoutSettings.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/layout/MoenLayoutSettings.java
new file mode 100644
index 0000000..853fb59
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/layout/MoenLayoutSettings.java
@@ -0,0 +1,112 @@
+/*
+ * @(#)TreeLayoutSettings.java 1.0 12-JUL-2004
+ *
+ * Copyright (c) 2004-2005, Gaudenz Alder
+ * All rights reserved.
+ *
+ * This library is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation; either
+ * version 2.1 of the License, or (at your option) any later version.
+ *
+ * This library is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this library; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+ */
+package org.jgraph.layout;
+
+import java.awt.BorderLayout;
+import java.awt.GridLayout;
+
+import javax.swing.JComboBox;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JTextField;
+
+
+/**
+ * A Dialog for configuring a TreeLayoutAlgorithm.
+ * You can use horizontal and vertical spacing.<br>
+ *<br>
+ *<br>
+ * @author Gaudenz Alder<br>
+ * @version 1.0 init
+ */
+public class MoenLayoutSettings extends JPanel implements JGraphLayoutSettings {
+ protected MoenLayoutAlgorithm layout;
+ private JComboBox orientationCombo = new JComboBox(new Object[] { "West-East", "North-South" });
+ private JTextField nodeDistanceTextField = new JTextField();
+
+ /**
+ * Creates new form SugiyamaLayoutConfigurationDialog
+ */
+ public MoenLayoutSettings(MoenLayoutAlgorithm layout) {
+ this.layout = layout;
+
+ JPanel jPanel1 = new javax.swing.JPanel(new GridLayout(2, 2, 4, 4));
+ jPanel1.add(new JLabel("Orientation"));
+ jPanel1.add(orientationCombo);
+ jPanel1.add(new JLabel("Node Distance"));
+ jPanel1.add(nodeDistanceTextField);
+ add(jPanel1, BorderLayout.CENTER);
+ revert();
+ }
+
+ /**
+ * Implementation.
+ */
+ public void revert() {
+ setOrientation(layout.orientation);
+ nodeDistanceTextField.setText(String.valueOf(layout.childParentDistance));
+ }
+
+ private void check() {
+ try {
+ Integer.parseInt(nodeDistanceTextField.getText());
+ } catch (Exception e) {
+ throw new IllegalArgumentException(e.getMessage());
+ }
+ }
+
+ /**
+ * Implementation.
+ */
+ public void apply() {
+ check();
+ layout.orientation = getOrientation();
+ layout.childParentDistance = Integer.parseInt(nodeDistanceTextField.getText());
+ }
+
+ /**
+ * Returns the value of the "Vertical spacing" as text.
+ */
+ public int getOrientation() {
+ int result = MoenLayoutAlgorithm.LEFT_TO_RIGHT;
+
+ switch (orientationCombo.getSelectedIndex()) {
+ case 1:
+ result = MoenLayoutAlgorithm.UP_TO_DOWN;
+ }
+
+ return result;
+ }
+
+ /**
+ * Set the value of the "Vertical Spacing" text field.
+ */
+ public void setOrientation(int orientation) {
+ int index = 0;
+
+ switch (orientation) {
+ case MoenLayoutAlgorithm.UP_TO_DOWN:
+ index = 1;
+ }
+
+ orientationCombo.setSelectedIndex(index);
+ }
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/layout/OrderedTreeLayoutAlgorithm.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/layout/OrderedTreeLayoutAlgorithm.java
new file mode 100644
index 0000000..42ea373
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/layout/OrderedTreeLayoutAlgorithm.java
@@ -0,0 +1,126 @@
+/*
+ * Copyright (c) 2004, Alain Michaud
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright notice,
+ * this list of conditions and the following disclaimer.
+ * - Redistributions in binary form must reproduce the above copyright notice,
+ * this list of conditions and the following disclaimer in the documentation
+ * and/or other materials provided with the distribution.
+ * - Neither the name of JGraph nor the names of its contributors may be used
+ * to endorse or promote products derived from this software without specific
+ * prior written permission.
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ */
+package org.jgraph.layout;
+
+import org.jgraph.graph.CellView;
+import org.jgraph.graph.GraphModel;
+
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.List;
+
+
+/**
+ * This class is similar to the TreeLayoutAlgorithm but it will sort
+ * the different levels of the graph using the default comparator
+ * or a custom comparator that you supply.
+ *
+ * @author Alain Michaud
+ */
+public class OrderedTreeLayoutAlgorithm extends TreeLayoutAlgorithm {
+ private Comparator comparator = null;
+
+ /**
+ * Constructor
+ * @param comparator use to sort the cells
+ */
+ public OrderedTreeLayoutAlgorithm(Comparator comparator) {
+ super();
+ setComparator(comparator);
+ }
+
+ /**
+ * Constructor (will use the default comparator)
+ */
+ public OrderedTreeLayoutAlgorithm() {
+ super();
+ setComparator(new DefaultComparator());
+ }
+
+ /**
+ * Returns the name of this algorithm in human
+ * readable form.
+ */
+ public String toString() {
+ return "Ordered Tree Layout";
+ }
+
+ /**
+ * @param comparator The cell's comparator
+ */
+ public void setComparator(Comparator comparator) {
+ this.comparator = comparator;
+ }
+
+ /**
+ * @return the cell comparator
+ */
+ public Comparator getComparator() {
+ return this.comparator;
+ }
+
+ /**
+ * Gets the children of the given cell view and sorts
+ * it using a supplied comparator or the default comparator if
+ * none is specified
+ */
+ public List getChildren(CellView view) {
+ //call in the getChildren methode of the TreeLayoutAlgorithm
+ List children = super.getChildren(view);
+
+ //Sort the list using the provided comparator
+ if (null == comparator) {
+ Collections.sort(children);
+ } else {
+ Collections.sort(children, comparator);
+ }
+
+ return children;
+ }
+
+ public class DefaultComparator implements Comparator {
+ /* (non-Javadoc)
+ * @see java.util.Comparator#compare(java.lang.Object, java.lang.Object)
+ */
+ public int compare(Object o1, Object o2) {
+ if (o1 instanceof CellView && o2 instanceof CellView) {
+ GraphModel m = graph.getModel();
+ Object c1 = ((CellView) o1).getCell();
+ Object c2 = ((CellView) o2).getCell();
+ Object p1 = m.getParent(c1);
+ Object p2 = m.getParent(c2);
+ int index1 = (p1 == null) ? m.getIndexOfRoot(c1) : m.getIndexOfChild(p1, c1);
+ int index2 = (p2 == null) ? m.getIndexOfRoot(c2) : m.getIndexOfChild(p2, c2);
+
+ return new Integer(index1).compareTo(new Integer(index2));
+ }
+
+ return -1;
+ }
+ }
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/layout/RadialTreeLayoutAlgorithm.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/layout/RadialTreeLayoutAlgorithm.java
new file mode 100644
index 0000000..810ac3e
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/layout/RadialTreeLayoutAlgorithm.java
@@ -0,0 +1,580 @@
+/*
+ * @(#)RadialTreeLayoutAlgorithm.java 1.0 18-MAY-2004
+ *
+ * Copyright (c) 2004, Michael J. Lawley
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright notice,
+ * this list of conditions and the following disclaimer.
+ * - Redistributions in binary form must reproduce the above copyright notice,
+ * this list of conditions and the following disclaimer in the documentation
+ * and/or other materials provided with the distribution.
+ * - Neither the name of JGraph nor the names of its contributors may be used
+ * to endorse or promote products derived from this software without specific
+ * prior written permission.
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ */
+package org.jgraph.layout;
+
+import org.jgraph.JGraph;
+
+import org.jgraph.graph.CellView;
+import org.jgraph.graph.GraphConstants;
+import org.jgraph.graph.GraphModel;
+import org.jgraph.graph.VertexView;
+
+import java.awt.Rectangle;
+import java.awt.geom.Rectangle2D;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Properties;
+
+
+/**
+ * Lays out the nodes in a graph as a radial tree (root at the centre, children in concentric ovals).
+ * <p>
+ * The layout algorithm is similar to that described in the paper
+ * <em>"Radial Tree Graph Drawing Algorithm for Representing Large Hierarchies"</em>
+ * by Greg Book and Neeta Keshary.
+ * <p>
+ * The algorithm is modified from that in the above paper since it
+ * contains bugs and the sample code contains major inefficiencies.
+ * <p>
+ * Since this algorithm needs to be applied to a tree but we have
+ * a directed graph, a spanning tree is first constructed then the
+ * algorithm is applied to it.
+ *
+ * @author <a href="mailto:lawley at dstc.edu.au">michael j lawley</a>
+ * @since 3.1
+ * @version 1.0 init
+ */
+public class RadialTreeLayoutAlgorithm extends JGraphLayoutAlgorithm {
+ /**
+ * Property key for specifying maximum width of layout area.
+ *
+ * If WIDTH is specified, then CENTRE_X and RADIUS_X are
+ * calculated from it based on the maximum depth of the
+ * spanning tree.
+ */
+ public static final String KEY_WIDTH = "Width";
+
+ /**
+ * Property key for specifying maximum height of layout area.
+ *
+ * If HEIGHT is specified, then CENTRE_Y and RADIUS_Y are
+ * calculated from it based on the maximum depth of the
+ * spanning tree.
+ */
+ public static final String KEY_HEIGHT = "Height";
+
+ /**
+ * Property key for specifying the X-axis coordinate of the centre of the layout.
+ *
+ * If WIDTH is specified, then the supplied value is ignored and
+ * CENTRE_X is calculated from it based on the maximum depth of the
+ * spanning tree.
+ */
+ public static final String KEY_CENTRE_X = "CentreX";
+
+ /**
+ * Property key for specifying the Y-axis coordinate of the centre of the layout.
+ *
+ * If HEIGHT is specified, then the supplied value is ignored and
+ * CENTRE_Y is calculated from it based on the maximum depth of the
+ * spanning tree.
+ */
+ public static final String KEY_CENTRE_Y = "CentreY";
+
+ /**
+ * Property key for specifying the maximum horizontal distance between a parent and child node.
+ *
+ * If WIDTH is specified, then the supplied value is ignored and
+ * RADIUS_X is calculated from it based on the maximum depth of the
+ * spanning tree.
+ */
+ public static final String KEY_RADIUS_X = "RadiusX";
+
+ /**
+ * Property key for specifying the maximum vertical distance between a parent and child node.
+ *
+ * If WIDTH is specified, then the supplied value is ignored and
+ * RADIUS_X is calculated from it based on the maximum depth of the
+ * spanning tree.
+ */
+ public static final String KEY_RADIUS_Y = "RadiusY";
+
+ // public static final String KEY_CONTINUOUS = "Continuous";
+ private static final String RADIAL_TREE_VISITED = "RadialTreeVisited";
+ private static final double TWO_PI = Math.PI * 2.0;
+ protected double RADIUSX;
+ protected double RADIUSY;
+ protected double ROOTX;
+ protected double ROOTY;
+ protected double WIDTH;
+ protected double HEIGHT;
+ private JGraph jgraph;
+
+ /**
+ * Creates a new RadialTreeLayoutAlgorithm object.
+ */
+ public RadialTreeLayoutAlgorithm() {
+ }
+
+ /**
+ * Returns the name of this algorithm in human
+ * readable form.
+ */
+ public String toString() {
+ return "Radial Tree";
+ }
+
+ /**
+ * Get a human readable hint for using this layout.
+ */
+ public String getHint() {
+ return "Select a tree";
+ }
+
+ /**
+ * Returns an new instance of SugiyamaLayoutSettings
+ */
+ public JGraphLayoutSettings createSettings() {
+ return new RadialTreeLayoutSettings(this);
+ }
+
+ /**
+ * Applies a radial tree layout to nodes in the jgraph with respect to the supplied configuration.
+ *
+ * @param graph JGraph instance
+ * @param dynamic_cells List of all nodes the layout should move
+ * @param static_cells List of node the layout should not move but allow for
+ */
+ public void run(JGraph graph, Object[] dynamic_cells, Object[] static_cells) {
+ this.jgraph = graph;
+
+ if ((dynamic_cells == null) || (dynamic_cells.length == 0))
+ return;
+
+ CellView[] selectedCellViews = graph.getGraphLayoutCache().getMapping(dynamic_cells);
+
+ // search all roots
+ List roots = getRoots(jgraph, selectedCellViews);
+
+ if (roots == null)
+ return;
+
+ TreeNode tree = getSpanningTree(selectedCellViews, roots);
+
+ if (null == tree) {
+ return;
+ }
+
+ double depth = tree.getDepth();
+
+ Rectangle2D bounds = jgraph.getCellBounds(dynamic_cells);
+
+ double autoW = WIDTH;
+
+ if ((WIDTH == ROOTX) && (ROOTX == RADIUSX) && (ROOTX == 0)) {
+ autoW = bounds.getWidth();
+ }
+
+ if (autoW != 0) {
+ ROOTX = autoW / 2.0;
+ RADIUSX = ROOTX / depth;
+ }
+
+ double autoH = HEIGHT;
+
+ if ((HEIGHT == ROOTY) && (ROOTY == RADIUSY) && (ROOTY == 0)) {
+ autoH = bounds.getHeight();
+ }
+
+ if (autoH != 0) {
+ ROOTY = autoH / 2.0;
+ RADIUSY = ROOTY / depth;
+ }
+
+ Map viewMap = new HashMap();
+ layoutTree0(viewMap, tree);
+ jgraph.getGraphLayoutCache().edit(viewMap, null, null, null);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param configuration DOCUMENT ME!
+ */
+ public void setConfiguration(Properties configuration) {
+ if (configuration.containsKey(KEY_WIDTH)) {
+ WIDTH = Double.parseDouble(configuration.getProperty(KEY_WIDTH));
+ } else {
+ if (configuration.containsKey(KEY_CENTRE_X)) {
+ ROOTX = Double.parseDouble(configuration.getProperty(KEY_CENTRE_X));
+ } else {
+ throw new IllegalArgumentException("Must specify one of KEY_WIDTH or KEY_CENTRE_X");
+ }
+
+ if (configuration.containsKey(KEY_RADIUS_X)) {
+ RADIUSX = Double.parseDouble(configuration.getProperty(KEY_RADIUS_X));
+ } else {
+ throw new IllegalArgumentException("Must specify one of KEY_WIDTH or KEY_RADIUS_X");
+ }
+ }
+
+ if (configuration.containsKey(KEY_HEIGHT)) {
+ HEIGHT = Double.parseDouble(configuration.getProperty(KEY_HEIGHT));
+ } else {
+ if (configuration.containsKey(KEY_CENTRE_Y)) {
+ ROOTY = Double.parseDouble(configuration.getProperty(KEY_CENTRE_Y));
+ } else {
+ throw new IllegalArgumentException("Must specify one of KEY_HEIGHT or KEY_CENTRE_Y");
+ }
+
+ if (configuration.containsKey(KEY_RADIUS_Y)) {
+ RADIUSY = Double.parseDouble(configuration.getProperty(KEY_RADIUS_Y));
+ } else {
+ throw new IllegalArgumentException("Must specify one of KEY_WIDTH or KEY_RADIUS_X");
+ }
+ }
+ }
+
+ private void layoutTree0(Map viewMap, TreeNode node) {
+ node.angle = 0;
+ node.x = ROOTX;
+ node.y = ROOTY;
+ node.rightBisector = 0;
+ node.rightTangent = 0;
+ node.leftBisector = TWO_PI;
+ node.leftTangent = TWO_PI;
+
+ VertexView view = (VertexView) node.getView();
+
+ if (null != view) {
+ placeView(viewMap, view, ROOTX, ROOTY);
+ }
+
+ List parent = new ArrayList(1);
+ parent.add(node);
+ layoutTreeN(viewMap, 1, parent);
+ }
+
+ private void layoutTreeN(Map viewMap, int level, List nodes) {
+ double i;
+ double prevAngle = 0.0;
+ TreeNode parent;
+ TreeNode node;
+ TreeNode firstParent = null;
+ TreeNode prevParent = null;
+ List parentNodes = new ArrayList();
+
+ Iterator nitr = nodes.iterator();
+
+ while (nitr.hasNext() && !canceled) {
+ parent = (TreeNode) nitr.next();
+
+ List children = parent.getChildren();
+ double rightLimit = parent.rightLimit();
+ double angleSpace = (parent.leftLimit() - rightLimit) / children.size();
+
+ Iterator itr = children.iterator();
+
+ for (i = 0.5; itr.hasNext(); i++) {
+ node = (TreeNode) itr.next();
+
+ VertexView view = node.getView();
+
+ node.angle = rightLimit + (i * angleSpace);
+ node.x = ROOTX + ((level * RADIUSX) * Math.cos(node.angle));
+ node.y = ROOTY + ((level * RADIUSY) * Math.sin(node.angle));
+
+ placeView(viewMap, view, node.x, node.y);
+
+ // Is it a parent node?
+ if (node.hasChildren()) {
+ parentNodes.add(node);
+
+ if (null == firstParent) {
+ firstParent = node;
+ }
+
+ // right bisector limit
+ double prevGap = node.angle - prevAngle;
+ node.rightBisector = node.angle - (prevGap / 2.0);
+
+ if (null != prevParent) {
+ prevParent.leftBisector = node.rightBisector;
+ }
+
+ double arcAngle = level / (level + 1.0);
+ double arc = 2.0 * Math.asin(arcAngle);
+
+ node.leftTangent = node.angle + arc;
+ node.rightTangent = node.angle - arc;
+
+ prevAngle = node.angle;
+ prevParent = node;
+ }
+ }
+ }
+
+ if (canceled)
+ return;
+
+ if (null != firstParent) {
+ double remaningAngle = TWO_PI - prevParent.angle;
+ firstParent.rightBisector = (firstParent.angle - remaningAngle) / 2.0;
+
+ if (firstParent.rightBisector < 0) {
+ prevParent.leftBisector = firstParent.rightBisector + TWO_PI + TWO_PI;
+ } else {
+ prevParent.leftBisector = firstParent.rightBisector + TWO_PI;
+ }
+ }
+
+ if ((parentNodes.size() > 0) && !canceled) {
+ layoutTreeN(viewMap, level + 1, parentNodes);
+ }
+ }
+
+ private void placeView(Map viewMap, VertexView view, double x, double y) {
+ Rectangle2D rect = view.getBounds();
+ Rectangle bounds = new Rectangle((int) rect.getX(), (int) rect.getY(),
+ (int) rect.getWidth(), (int) rect.getHeight());
+ //(Rectangle) view.getBounds().clone();
+ bounds.x = (int) Math.round(x);
+ bounds.y = (int) Math.round(y);
+
+ Object cell = view.getCell();
+ Map map = new Hashtable();
+ GraphConstants.setBounds(map, bounds);
+ viewMap.put(cell, map);
+ }
+
+ private List getChildren(VertexView view, List level) {
+ ArrayList children = new ArrayList();
+ Object vertex = view.getCell();
+ GraphModel model = jgraph.getModel();
+ int portCount = model.getChildCount(vertex);
+
+ // iterate any NodePort
+ for (int i = 0; i < portCount; i++) {
+ Object port = model.getChild(vertex, i);
+
+ // iterate any Edge in the port
+ Iterator itrEdges = model.edges(port);
+
+ while (itrEdges.hasNext()) {
+ Object edge = itrEdges.next();
+
+ // if the Edge is a forward edge we should follow this edge
+ if (port == model.getSource(edge)) {
+ Object targetPort = model.getTarget(edge);
+ Object targetVertex = model.getParent(targetPort);
+ VertexView targetVertexView = (VertexView) jgraph.getGraphLayoutCache()
+ .getMapping(targetVertex, false);
+
+ if (level.contains(targetVertexView)) {
+ children.add(targetVertexView);
+ }
+ }
+ }
+ }
+
+ return children;
+ }
+
+ private List getRoots(JGraph jgraph, CellView[] cellViews) {
+ List roots = new ArrayList();
+
+ GraphModel model = jgraph.getModel();
+
+ for (int i = 0; i < cellViews.length; i++) {
+ if (canceled)
+ return null;
+
+ if (cellViews[i] instanceof VertexView) {
+ VertexView vertexView = (VertexView) cellViews[i];
+ boolean isRoot = true;
+ Object vertex = vertexView.getCell();
+ int portCount = model.getChildCount(vertex);
+
+ for (int j = 0; isRoot && (j < portCount); j++) {
+ Object port = model.getChild(vertex, j);
+
+ Iterator itrEdges = model.edges(port);
+
+ while (isRoot && itrEdges.hasNext()) {
+ Object edge = itrEdges.next();
+
+ if (model.getTarget(edge) == port) {
+ isRoot = false;
+ }
+ }
+ }
+
+ if (isRoot) {
+ roots.add(vertexView);
+ }
+ }
+ }
+
+ return roots;
+ }
+
+ /**
+ * Algorithm assumes a single root node so if there are multiple roots
+ * (nodes with no incoming edges), then we construct the spanning tree
+ * with an invisible root node that is the parent of the real roots.
+ */
+ private TreeNode getSpanningTree(CellView[] cellViews, List roots) {
+ List vertexViews = new ArrayList(cellViews.length);
+
+ // first: mark all as not visited
+ for (int i = 0; i < cellViews.length; i++) {
+ if (canceled)
+ return null;
+
+ if (cellViews[i] instanceof VertexView) {
+ VertexView vertexView = (VertexView) cellViews[i];
+ vertexView.getAttributes().remove(RADIAL_TREE_VISITED);
+ vertexViews.add(vertexView);
+ }
+ }
+
+ TreeNode node;
+
+ if (roots.size() == 0) {
+ if (vertexViews.size() == 0) {
+ return null;
+ }
+
+ // else, pick an arbitrary node
+ roots.add(vertexViews.get(0));
+ }
+
+ if (roots.size() > 1) {
+ node = new TreeNode(null);
+ buildSpanningTree(vertexViews, node, roots);
+ } else {
+ VertexView vertexView = (VertexView) roots.get(0);
+ node = new TreeNode(vertexView);
+ vertexView.getAttributes().put(RADIAL_TREE_VISITED, Boolean.TRUE);
+ buildSpanningTree(vertexViews, node, getChildren(vertexView, vertexViews));
+ }
+
+ return node;
+ }
+
+ /**
+ * Breadth-first traversal of the graph.
+ */
+ private void buildSpanningTree(List vertexViews, TreeNode node, List children) {
+ Iterator itr = children.iterator();
+
+ while (itr.hasNext() && !canceled) {
+ VertexView vertexView = (VertexView) itr.next();
+
+ if (null == vertexView.getAttributes().get(RADIAL_TREE_VISITED)) {
+ vertexView.getAttributes().put(RADIAL_TREE_VISITED, Boolean.TRUE);
+
+ TreeNode childNode = new TreeNode(vertexView);
+ node.addChild(childNode);
+ }
+ }
+
+ itr = node.getChildren().iterator();
+
+ while (itr.hasNext() && !canceled) {
+ TreeNode childNode = (TreeNode) itr.next();
+ VertexView vertexView = childNode.getView();
+ buildSpanningTree(vertexViews, childNode, getChildren(vertexView, vertexViews));
+ }
+ }
+
+ private static class TreeNode {
+ private VertexView view;
+ private List children = new ArrayList();
+ public double angle;
+ public double x;
+ public double y;
+ public double rightBisector;
+ public double leftBisector;
+ public double rightTangent;
+ public double leftTangent;
+
+ TreeNode(VertexView view) {
+ this.view = view;
+ }
+
+ public int getDepth() {
+ int depth = 1;
+ Iterator itr = children.iterator();
+
+ while (itr.hasNext()) {
+ TreeNode node = (TreeNode) itr.next();
+ int childDepth = node.getDepth();
+
+ if (childDepth >= depth) {
+ depth = childDepth + 1;
+ }
+ }
+
+ return depth;
+ }
+
+ public VertexView getView() {
+ return view;
+ }
+
+ public void addChild(TreeNode node) {
+ children.add(node);
+ }
+
+ public List getChildren() {
+ return children;
+ }
+
+ public boolean hasChildren() {
+ return children.size() > 0;
+ }
+
+ public double leftLimit() {
+ return Math.min(normalize(leftBisector), (leftTangent));
+ }
+
+ public double rightLimit() {
+ return Math.max(normalize(rightBisector), (rightTangent));
+ }
+
+ private double normalize(double angle) {
+ /*
+ while (angle > TWO_PI) {
+ angle -= TWO_PI;
+ }
+ while (angle < -TWO_PI) {
+ angle += TWO_PI;
+ }
+ */
+ return angle;
+ }
+ }
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/layout/RadialTreeLayoutSettings.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/layout/RadialTreeLayoutSettings.java
new file mode 100644
index 0000000..d1f4b12
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/layout/RadialTreeLayoutSettings.java
@@ -0,0 +1,126 @@
+/*
+ * @(#)TreeLayoutSettings.java 1.0 12-JUL-2004
+ *
+ * Copyright (c) 2004-2005, Gaudenz Alder
+ * All rights reserved.
+ *
+ * This library is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation; either
+ * version 2.1 of the License, or (at your option) any later version.
+ *
+ * This library is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this library; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+ */
+package org.jgraph.layout;
+
+import java.awt.BorderLayout;
+import java.awt.GridLayout;
+
+import java.util.Properties;
+
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JTextField;
+
+
+/**
+ * A Dialog for configuring a TreeLayoutAlgorithm.
+ * You can use horizontal and vertical spacing.<br>
+ *<br>
+ *<br>
+ * @author Gaudenz Alder<br>
+ * @version 1.0 init
+ */
+public class RadialTreeLayoutSettings extends JPanel implements JGraphLayoutSettings {
+ protected RadialTreeLayoutAlgorithm layout;
+ private JTextField widthTextField = new JTextField();
+ private JTextField heightTextField = new JTextField();
+ private JTextField radiusXTextField = new JTextField();
+ private JTextField radiusYTextField = new JTextField();
+ private JTextField centerXTextField = new JTextField();
+ private JTextField centerYTextField = new JTextField();
+
+ /**
+ * Creates new form SugiyamaLayoutConfigurationDialog
+ */
+ public RadialTreeLayoutSettings(RadialTreeLayoutAlgorithm layout) {
+ this.layout = layout;
+
+ JPanel jPanel1 = new javax.swing.JPanel(new GridLayout(6, 2, 4, 4));
+ jPanel1.add(new JLabel("Width"));
+ jPanel1.add(widthTextField);
+ jPanel1.add(new JLabel("Height"));
+ jPanel1.add(heightTextField);
+ // XOr
+ jPanel1.add(new JLabel("Radius X"));
+ jPanel1.add(radiusXTextField);
+ jPanel1.add(new JLabel("Radius Y"));
+ jPanel1.add(radiusYTextField);
+ jPanel1.add(new JLabel("Center X"));
+ jPanel1.add(centerXTextField);
+ jPanel1.add(new JLabel("Center Y"));
+ jPanel1.add(centerYTextField);
+ add(jPanel1, BorderLayout.CENTER);
+ revert();
+ }
+
+ /**
+ * Implementation.
+ */
+ public void revert() {
+ widthTextField.setText(String.valueOf(layout.WIDTH));
+ heightTextField.setText(String.valueOf(layout.HEIGHT));
+
+ if (layout.WIDTH == 0) {
+ centerXTextField.setText(String.valueOf(layout.ROOTX));
+ radiusXTextField.setText(String.valueOf(layout.RADIUSX));
+ } else {
+ centerXTextField.setText("0");
+ radiusXTextField.setText("0");
+ }
+
+ if (layout.HEIGHT == 0) {
+ centerYTextField.setText(String.valueOf(layout.ROOTY));
+ radiusYTextField.setText(String.valueOf(layout.RADIUSY));
+ } else {
+ centerYTextField.setText("0");
+ radiusYTextField.setText("0");
+ }
+ }
+
+ private void check() {
+ try {
+ Double.parseDouble(widthTextField.getText());
+ Double.parseDouble(heightTextField.getText());
+ Double.parseDouble(centerXTextField.getText());
+ Double.parseDouble(centerYTextField.getText());
+ Double.parseDouble(radiusXTextField.getText());
+ Double.parseDouble(radiusYTextField.getText());
+ } catch (Exception e) {
+ throw new IllegalArgumentException(e.getMessage());
+ }
+ }
+
+ /**
+ * Implementation.
+ */
+ public void apply() {
+ check();
+
+ Properties props = new Properties();
+ props.put(RadialTreeLayoutAlgorithm.KEY_WIDTH, widthTextField.getText());
+ props.put(RadialTreeLayoutAlgorithm.KEY_HEIGHT, heightTextField.getText());
+ props.put(RadialTreeLayoutAlgorithm.KEY_CENTRE_X, centerXTextField.getText());
+ props.put(RadialTreeLayoutAlgorithm.KEY_CENTRE_Y, centerYTextField.getText());
+ props.put(RadialTreeLayoutAlgorithm.KEY_RADIUS_X, radiusXTextField.getText());
+ props.put(RadialTreeLayoutAlgorithm.KEY_RADIUS_Y, radiusYTextField.getText());
+ layout.setConfiguration(props);
+ }
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/layout/SpringEmbeddedLayoutAlgorithm.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/layout/SpringEmbeddedLayoutAlgorithm.java
new file mode 100644
index 0000000..6bd5cf6
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/layout/SpringEmbeddedLayoutAlgorithm.java
@@ -0,0 +1,775 @@
+/*
+ * Copyright (c) 2004, Jeremy Jedynak, NetCentric Technology Inc All rights reserved.
+ *
+ * Copyright (c) 2004, Sven Luzar All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ * - Redistributions of source code must retain the above copyright notice,
+ * this list of conditions and the following disclaimer. - Redistributions in
+ * binary form must reproduce the above copyright notice, this list of
+ * conditions and the following disclaimer in the documentation and/or other
+ * materials provided with the distribution. - Neither the name of JGraph nor
+ * the names of its contributors may be used to endorse or promote products
+ * derived from this software without specific prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ *
+ */
+package org.jgraph.layout;
+
+import org.jgraph.JGraph;
+
+import org.jgraph.graph.AttributeMap;
+import org.jgraph.graph.CellView;
+import org.jgraph.graph.EdgeView;
+import org.jgraph.graph.GraphConstants;
+import org.jgraph.graph.GraphLayoutCache;
+import org.jgraph.graph.PortView;
+import org.jgraph.graph.VertexView;
+
+import java.awt.Rectangle;
+import java.awt.geom.Rectangle2D;
+
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+import java.util.Random;
+
+
+/**
+ * Arranges the nodes with the Spring Embedded Layout Algorithm. <br>
+ *
+ * The algorithm takes O(|V|^2 * |E|) time.
+ *
+ * Jeremy Jedynak NetCentric Technology Inc www.NetCentricInc.com
+ *
+ * <br>
+ *
+ * This layout algorithm is derived from the one written by Sven Luzar. It fixes
+ * a bug in how the "u" and "v" vectors were stored and retrieved, which
+ * frequently caused IllegalArgumentExceptions and NullPointerExceptions,
+ * depending upon your luck.
+ *
+ * <br>
+ *
+ * Also, the original run method has been broken into several methods. Two new
+ * constructors and methods were added to support two constraints: the graph
+ * rendering frame and maxIterations. Most variable names have been modified for
+ * readability.
+ *
+ * <br>
+ *
+ * It now properly lays out the graph according to the algorithm. Work still
+ * needs to be done to better space vertices so that they do not overlap and so
+ * that edges do not pass through vertices. The new "step" parameter of the run
+ * method is currently not used. All that being said, this is a good starting
+ * point to understand the algorithm and make those changes.
+ *
+ * <br>
+ * <br>
+ *
+ * @author <a href="mailto:Jeremy.Jedynak at NetCentricInc.com">Jeremy Jedynak </a>
+ * @author <a href="mailto:Sven.Luzar at web.de">Sven Luzar </a>
+ * @author <a href="mailto:rmc at telemidia.puc-rio.br">Rogerio Coelho </a>
+ * @since 1.2.2
+ * @version 1.1 init
+ *
+ * Last Modification : 11/05/2005
+ * By : Rogerio Coelho <rmc at telemidia.puc-rio.br>
+ * Description: Now the SpringEmbeddedLayoutAlgorithm is working for group or
+ * Nested Graph. The other change was in method calculateAttractiveForces
+ * because have vertices without edges and your power in attractive doesn't
+ * count.
+ *
+ */
+public class SpringEmbeddedLayoutAlgorithm extends JGraphLayoutAlgorithm {
+ /**
+ * Key for an attribute. The value for this key is a Rectangle object and
+ * specifies the disposement.
+ */
+ public static final String SPRING_EMBEDDED_DISP = "SpringEmbeddedDisp";
+
+ /**
+ * Key for an attribute. The value for this key is a Rectangle object and
+ * specifies the calculated position.
+ */
+ public static final String SPRING_EMBEDDED_POS = "SpringEmbeddedPos";
+ private Rectangle myFrame = null;
+ private int myMaxIterations = -1;
+
+ /**
+ * Creates a new SpringEmbeddedLayoutAlgorithm object.
+ */
+ public SpringEmbeddedLayoutAlgorithm() {
+ myFrame = new Rectangle(0, 0, 500, 500); //It's ok 500,500
+ myMaxIterations = 30; //It's ok 30
+ }
+
+ /**
+ * Creates a new SpringEmbeddedLayoutAlgorithm object.
+ *
+ * @param frame DOCUMENT ME!
+ * @param maxIterations DOCUMENT ME!
+ */
+ public SpringEmbeddedLayoutAlgorithm(Rectangle frame, int maxIterations) {
+ if (frame == null) {
+ throw new IllegalArgumentException("frame may not be null");
+ }
+
+ if (frame.width <= 0) {
+ throw new IllegalArgumentException("frame width must be positive");
+ }
+
+ if (frame.height <= 0) {
+ throw new IllegalArgumentException("frame height must be positive");
+ } else {
+ myFrame = frame;
+ }
+
+ if (maxIterations < 0) {
+ throw new IllegalArgumentException("maxIterations must be a positive integer");
+ } else {
+ myMaxIterations = maxIterations;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param frame DOCUMENT ME!
+ */
+ public void setFrame(Rectangle frame) {
+ if (frame == null) {
+ throw new IllegalArgumentException("Frame may not be null");
+ } else if (frame.width <= 0) {
+ throw new IllegalArgumentException("frame width must be positive");
+ } else if (frame.height <= 0) {
+ throw new IllegalArgumentException("frame height must be positive");
+ }
+
+ myFrame = frame;
+ }
+
+ /**
+ * Returns the name of this algorithm in human readable form.
+ */
+ public String toString() {
+ return "Spring Embedded";
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param maxIterations DOCUMENT ME!
+ */
+ public void setMaxIterations(int maxIterations) {
+ if (maxIterations < 0) {
+ throw new IllegalArgumentException("maxIterations must be a positive integer");
+ }
+
+ myMaxIterations = maxIterations;
+ }
+
+ /**
+ * Replace all cells inside the frame because have cells with valeu negative
+ * for x and y
+ *
+ * @param vertices :
+ * list all vertices
+ * @param frameRectangle :
+ * Rectangle where x and y have the minX and minY the all cells
+ * in the graph.
+ */
+ private void replaceInsideFrame(List vertices, Rectangle2D frameRectangle) {
+ for (int i = 0; i < vertices.size(); i++) {
+ VertexView vertex = (VertexView) vertices.get(i);
+ Rectangle2D vPos = getVertexPosition(vertex, SPRING_EMBEDDED_POS);
+ Rectangle2D newRandomPosition = new Rectangle2D.Double(vPos.getX()
+ - frameRectangle.getX(),
+ vPos.getY()
+ - frameRectangle.getY(),
+ vPos.getWidth(), vPos.getHeight());
+ updateVertexPosition(vertex, SPRING_EMBEDDED_POS, newRandomPosition);
+ }
+ }
+
+ /**
+ * The implementation of the layout algorithm.
+ *
+ * @param graph :
+ * JGraph instance
+ * @param dynamic_cells :
+ * List of all nodes the layout should move
+ * @param static_cells :
+ * List of node the layout should not move but allow for
+ */
+ public void run(JGraph graph, Object[] dynamic_cells, Object[] static_cells) {
+ // ---------------------------------------------------------------------------
+ // initial work
+ // ---------------------------------------------------------------------------
+ GraphLayoutCache layoutCache = graph.getGraphLayoutCache();
+ List vertices = new ArrayList(); // vertices
+ List edges = new ArrayList(); // Edges
+ List verticesWithOutEdges = new ArrayList();
+
+ //Take all cells
+ CellView[] cellviews = layoutCache.getMapping(dynamic_cells, false);
+
+ //System.out.println("Number of Cells = " + cellviews.length);
+ partitionCells(cellviews, vertices, edges);
+
+ //System.out.println("Number of vertices = " + vertices.size());
+ //System.out.println("Number of Edges = " + edges.size());
+ double FrameWidth = myFrame.getWidth(); //Width of the selectionFrame
+ double FrameHeight = myFrame.getHeight(); //Height of the
+ //selectionFrame
+
+ double FrameArea = FrameWidth * FrameHeight; //area of the
+ //selectionFrame
+ /*
+ * System.out.println( " W = " + FrameWidth ) ; System.out.println( " H = " +
+ * FrameHeight ) ; System.out.println( " Area = " + FrameArea ) ;
+ */
+
+ randomizeVertexPositions(vertices);
+
+ // ---------------------------------------------------------------------------
+ // start the iterations
+ // ---------------------------------------------------------------------------
+
+ // calculate the field length for the area
+ double AreaFieldLength = Math.sqrt((FrameArea) / (vertices.size()));
+
+ verticesWithOutEdges = findVertexWithoutEdges(edges, vertices);
+
+ for (int loop = 0; loop < myMaxIterations; loop++) {
+ if (canceled)
+ return;
+
+ calculateRepulsiveForces(vertices, AreaFieldLength);
+
+ calculateAttractiveForces(edges, verticesWithOutEdges, AreaFieldLength);
+
+ calculateNewPositions(vertices, loop);
+ }
+
+ //calculate the stretch factor and the movement factor
+ //to fit the calculated frame to the selected Frame
+ Rectangle2D calculateFrame = calculateNewFrame(vertices);
+ replaceInsideFrame(vertices, calculateFrame);
+
+ calculateFrame.setFrame(0, 0, 900, 900); //this is necessary because
+ // the frame have w=500 and h=500
+
+ double stretchX = (myFrame.width) / (calculateFrame.getWidth());
+
+ double stretchY = (myFrame.height) / (calculateFrame.getHeight());
+
+ int movementX = (int) (myFrame.x - calculateFrame.getX());
+
+ int movementY = (int) (myFrame.y - calculateFrame.getY());
+
+ Map viewMap = drawGraph(layoutCache.getMapping(dynamic_cells, false), movementX, stretchX,
+ movementY, stretchY);
+
+ layoutCache.edit(viewMap, null, null, null);
+ }
+
+ private void partitionCells(CellView[] cells, List vertices, List edges) {
+ // Partition the list of cells into list of vertices and list of edges
+ for (int loop = 0; loop < cells.length; loop++) {
+ CellView cell = cells[loop];
+
+ if (cell == null) {
+ // Skip over null cells
+ continue;
+ } else if (cell instanceof EdgeView) {
+ EdgeView edge = (EdgeView) cell;
+ edges.add(edge);
+ } else if (cell instanceof VertexView) {
+ VertexView vertex = (VertexView) cell;
+ vertices.add(vertex);
+ }
+ }
+ }
+
+ private void randomizeVertexPositions(List vertices) {
+ int vertW;
+ int vertH;
+ int frameW;
+ int frameH;
+ int newX;
+ int newY = 0;
+ Rectangle newRandomPosition = null;
+
+ // Fill the initial positions with random positions
+ Random random = new Random();
+
+ for (int loop = 0; loop < vertices.size(); loop++) {
+ VertexView vertex = (VertexView) vertices.get(loop);
+ vertW = (int) vertex.getBounds().getWidth();
+ vertH = (int) vertex.getBounds().getHeight();
+
+ frameW = myFrame.width;
+ frameH = myFrame.height;
+
+ //newX = random.nextInt(frameW);
+ //Verify if newX is out of MyFrame
+ //while (newX < 0) {
+ //newX = random.nextInt(frameW);
+ //}
+ int rangeX = myFrame.width - myFrame.x;
+
+ do {
+ newX = random.nextInt(rangeX);
+ } while (!((myFrame.x < newX) && (newX < myFrame.width)));
+
+ newX += myFrame.x;
+
+ //newY = random.nextInt(frameH);
+ //Verify if newY is out of MyFrame
+ //while (newY < 0) {
+ //newY = random.nextInt(frameH);
+ //}
+ int rangeY = myFrame.height - myFrame.y;
+
+ do {
+ newY = random.nextInt(rangeY);
+ } while (!((myFrame.y < newY) && (newY < myFrame.height)));
+
+ newX += myFrame.y;
+
+ //System.out.println("Vertex = " + vertex.getCell().toString() + "
+ // x = " + newX + " y = " + newY + " w = " + vertW + " h = "
+ // +vertH);
+ newRandomPosition = new Rectangle(newX, newY, vertW, vertH);
+ updateVertexPosition(vertex, SPRING_EMBEDDED_POS, newRandomPosition);
+ }
+ }
+
+ private void calculateRepulsiveForces(List vertices, double AreaFieldLength) {
+ // ---------------------------------------------------------------------------
+ // calculate the repulsive forces
+ // ---------------------------------------------------------------------------
+
+ // calculate the repulsive forces
+ for (int vCount = 0; vCount < vertices.size(); vCount++) {
+ if (canceled)
+ return;
+
+ VertexView v = (VertexView) vertices.get(vCount);
+
+ Rectangle2D vPos = getVertexPosition(v, SPRING_EMBEDDED_POS);
+
+ //System.out.println( "vertex " + loop + " get: vPos = " + vPos ) ;
+
+ //Each vertex has two vectors: pos and disp
+ Rectangle vDisp = new Rectangle(0, 0);
+
+ for (int uCount = 0; uCount < vertices.size(); uCount++) {
+ VertexView u = (VertexView) vertices.get(uCount);
+
+ if (u != v) {
+ // delta is short hand for the difference
+ // vector between the positions of the two vertices
+ Rectangle2D uPos = getVertexPosition(u, SPRING_EMBEDDED_POS);
+
+ // System.out.println( "vertex " + uCount + " get: uPos = "
+ // + uPos ) ;
+ Rectangle delta = new Rectangle();
+ delta.x = (int) (vPos.getX() - uPos.getX());
+ delta.y = (int) (vPos.getY() - uPos.getY());
+
+ double fr = fr(norm(delta), AreaFieldLength);
+
+ //System.out.println("FR = " + fr);
+
+ //fr = fr - fr*0.20;
+ //System.out.println("FR = " + fr);
+ double deltaNormX = delta.x / norm(delta);
+ double dispX = deltaNormX * fr;
+ double deltaNormY = delta.y / norm(delta);
+ double dispY = deltaNormY * fr;
+
+ vDisp.x = vDisp.x + (int) dispX;
+ vDisp.y = vDisp.y + (int) dispY;
+ }
+ }
+
+ updateVertexPosition(v, SPRING_EMBEDDED_DISP, vDisp);
+ }
+ }
+
+ private void calculateAttractiveForces(List edges, List verticesWithoutEdges,
+ double AreaFieldLength) {
+ // ---------------------------------------------------------------------------
+ // calculate the attractive forces
+ // ---------------------------------------------------------------------------
+ double dispX = 0;
+
+ // ---------------------------------------------------------------------------
+ // calculate the attractive forces
+ // ---------------------------------------------------------------------------
+ double dispY = 0;
+ EdgeView e = null;
+
+ //Verify if have edges
+ if (edges.size() == 0) {
+ return;
+ }
+
+ for (int cellCount = 0; cellCount < edges.size(); cellCount++) {
+ if (canceled)
+ return;
+
+ e = (EdgeView) edges.get(cellCount);
+
+ if ((e.getSource() != null) && (e.getTarget() != null)
+ && (e.getSource() != e.getTarget())) {
+ // extract the used fields
+ CellView v = ((PortView) e.getSource()).getParentView();
+ CellView u = ((PortView) e.getTarget()).getParentView();
+
+ //Source and Target equal
+ if (v == u) {
+ continue;
+ }
+
+ Rectangle2D vPos = getVertexPosition(v, SPRING_EMBEDDED_POS);
+ Rectangle2D uPos = getVertexPosition(u, SPRING_EMBEDDED_POS);
+
+ // System.out.println( "vertex get: vPos = " + rtos(vPos) ) ;
+ // System.out.println( "vertex get: uPos = " + rtos(uPos) ) ;
+ if ((vPos == null) || (uPos == null)) {
+ continue;
+ }
+
+ Rectangle2D vDisp = getVertexPosition(v, SPRING_EMBEDDED_DISP);
+ Rectangle2D uDisp = getVertexPosition(u, SPRING_EMBEDDED_DISP);
+
+ // System.out.println( "vertex get: vDisp = " + vDisp ) ;
+ // System.out.println( "vertex get: uDisp = " + uDisp ) ;
+ if ((vDisp == null) || (uDisp == null)) {
+ continue;
+ }
+
+ // calculate the delta
+ Rectangle delta = new Rectangle();
+ delta.x = (int) (vPos.getX() - uPos.getX());
+ delta.y = (int) (vPos.getY() - uPos.getY());
+
+ if (delta.x == 0)
+ delta.x = 1;
+
+ if (delta.y == 0)
+ delta.y = 1;
+
+ // calculate the attractive forces
+ double fa = fa(norm(delta), AreaFieldLength);
+
+ //System.out.println("FA = " + fa);
+ double deltaNormX = delta.x / norm(delta);
+ double deltaNormY = delta.y / norm(delta);
+ dispX = deltaNormX * fa;
+ dispY = deltaNormY * fa;
+
+ vDisp.setFrame(vDisp.getX() - dispX, vDisp.getY() - dispY, vDisp.getWidth(),
+ vDisp.getHeight());
+
+ uDisp.setFrame(uDisp.getX() + dispX, uDisp.getY() + dispY, uDisp.getWidth(),
+ uDisp.getHeight());
+
+ //System.out.println( "Cell update: vDisp = " +
+ // v.getCell().toString() + " rec = " + vDisp ) ;
+ //System.out.println( "Cell update: uDisp = " +
+ // u.getCell().toString() + " rec = " + uDisp ) ;
+
+ // store the new values
+ updateVertexPosition(v, SPRING_EMBEDDED_DISP, vDisp);
+ updateVertexPosition(u, SPRING_EMBEDDED_DISP, uDisp);
+ }
+ }
+
+ //vertices without edges
+ for (int cellCount = 0; cellCount < verticesWithoutEdges.size(); cellCount++) {
+ if (canceled)
+ return;
+
+ VertexView vertex = (VertexView) verticesWithoutEdges.get(cellCount);
+
+ int vertW = (int) vertex.getBounds().getWidth();
+ int vertH = (int) vertex.getBounds().getHeight();
+ Rectangle newRandomPosition = null;
+
+ // Fill the initial positions with random positions
+ Random random = new Random();
+
+ //Take the new position inside the Frame
+ int newX = random.nextInt(500);
+
+ //Verify if newX is outSide of MyFrame
+ while (newX < 0) {
+ newX = random.nextInt((int) vertex.getBounds().getCenterX());
+ }
+
+ //Take the new position inside the Frame
+ int newY = random.nextInt(500);
+
+ //Verify if newY is outSide of MyFrame
+ while (newY < 0) {
+ newY = random.nextInt((int) vertex.getBounds().getCenterY());
+ }
+
+ //System.out.println("Vertex = " + vertex.getCell().toString() + "
+ // x = " + newX + " y = " + newY + " w = " + vertW + " h = "
+ // +vertH);
+ newRandomPosition = new Rectangle(newX, newY, vertW, vertH);
+ updateVertexPosition(vertex, SPRING_EMBEDDED_POS, newRandomPosition);
+ }
+ }
+
+ /**
+ * Take all vertices without edges and put in List vertexWithoutEdges.
+ * @param edges : List the all edges
+ * @param vertices : List the all vertices
+ * @return vertexWithoutEdges : List of vertices without edge
+ */
+ private List findVertexWithoutEdges(List edges, List vertices) {
+ List vertexWithoutEdges = new ArrayList();
+
+ //Load all vertices
+ for (int i = 0; i < vertices.size(); i++) {
+ vertexWithoutEdges.add(vertices.get(i));
+ }
+
+ //Remove all vertices of edges
+ for (int i = 0; i < edges.size(); i++) {
+ EdgeView e = (EdgeView) edges.get(i);
+ CellView source = e.getSource().getParentView();
+ CellView target = e.getTarget().getParentView();
+
+ vertexWithoutEdges.remove(source);
+ vertexWithoutEdges.remove(target);
+ }
+
+ return vertexWithoutEdges;
+ }
+
+ private void calculateNewPositions(List vertices, int curIteration) {
+ // ---------------------------------------------------------------------------
+ // calculate the new positions
+ // ---------------------------------------------------------------------------
+
+ // limit the maximum displacement to the temperature buttonText
+ // and then prevent from being displacement outside frame
+ double Temperature = Math.sqrt(Math.pow(myFrame.width, 2) + Math.pow(myFrame.height, 2)) * ((((double) myMaxIterations) / (curIteration
+ + 1)) / (myMaxIterations));
+
+ for (int vCount = 0; vCount < vertices.size(); vCount++) {
+ if (canceled)
+ return;
+
+ VertexView v = (VertexView) vertices.get(vCount);
+ Rectangle2D vDisp = getVertexPosition(v, SPRING_EMBEDDED_DISP);
+ Rectangle2D vPos = getVertexPosition(v, SPRING_EMBEDDED_POS);
+
+ //System.out.println( "vertex " + v.toString() + "get: vDisp = " +
+ // vDisp ) ;
+ //System.out.println( "vertex " + v.toString() + "get: vDisp = " +
+ // vPos ) ;
+ double dispNormX = vDisp.getX() / norm(vDisp);
+ double minX = Math.min(Math.abs(vDisp.getX()), Temperature);
+
+ double dispNormY = vDisp.getY() / norm(vDisp);
+ double minY = Math.min(Math.abs(vDisp.getY()), Temperature);
+
+ vPos.setFrame(vPos.getX() + (dispNormX * minX), vPos.getY() + (dispNormY * minY),
+ vPos.getWidth(), vPos.getHeight());
+
+ /*
+ * double maxX = Math.max(-W / 2, vPos.x); double maxY = Math.max(-L /
+ * 2, vPos.y); double minX2 = Math.min(W / 2, maxX); double minY2 =
+ * Math.min(L / 2, maxY); vPos.x = (int)minX2; vPos.y = (int)minY2;
+ */
+
+ // System.out.println( "cell update: vPos = " + vPos ) ;
+ updateVertexPosition(v, SPRING_EMBEDDED_POS, vPos);
+ }
+ }
+
+ private Rectangle2D calculateNewFrame(List vertices) {
+ double x = 0;
+ double y = 0;
+ double w = 0;
+ double h = 0;
+
+ // find the new positions for the
+ // calculated frame
+ Rectangle2D calculatedFrame = new Rectangle2D.Double();
+
+ for (int vCount = 0; vCount < vertices.size(); vCount++) {
+ VertexView v = (VertexView) vertices.get(vCount);
+ Rectangle2D vPos = getVertexPosition(v, SPRING_EMBEDDED_POS);
+
+ //System.out.println( "vertex get: vPos = " + vPos ) ;
+ x = calculatedFrame.getX();
+ y = calculatedFrame.getY();
+ w = calculatedFrame.getWidth();
+ h = calculatedFrame.getHeight();
+
+ if (vPos.getX() < calculatedFrame.getX()) {
+ x = vPos.getX();
+ }
+
+ if (vPos.getY() < calculatedFrame.getY()) {
+ y = vPos.getY();
+ }
+
+ double width = vPos.getX() - calculatedFrame.getX();
+
+ if (width > calculatedFrame.getWidth()) {
+ w = width;
+ }
+
+ double height = vPos.getY() - calculatedFrame.getY();
+
+ if (height > calculatedFrame.getHeight()) {
+ h = height;
+ }
+
+ //System.out.println( "vertex =" + v.getCell());
+ //System.out.println("x = " + x + " y = " + y + " w = " + w + " h =
+ // " + h);
+ calculatedFrame.setFrame(x, y, w, h);
+ }
+
+ return (calculatedFrame);
+ }
+
+ private Map drawGraph(CellView[] cells, int movementX, double stretchX, int movementY,
+ double stretchY) {
+ // ---------------------------------------------------------------------------
+ // draw the graph
+ // ---------------------------------------------------------------------------
+ Map viewMap = new Hashtable();
+
+ for (int loop = 0; loop < cells.length; loop++) {
+ CellView cell = cells[loop];
+
+ if (cell == null) {
+ continue;
+ } else if (cell instanceof EdgeView) {
+ cell.update();
+ } else if (cell instanceof VertexView) {
+ // get the current view object
+ VertexView vertex = (VertexView) cell;
+
+ // remove the temp objects
+ Rectangle2D newPosition = removeVertexPosition(vertex, SPRING_EMBEDDED_POS);
+
+ removeVertexPosition(vertex, SPRING_EMBEDDED_DISP);
+
+ //System.out.println( "vertex" + vertex.getCell() + "children =
+ // " + vertex.getChildViews().length+ " newPosition = " +
+ // newPosition);
+
+ // update the location to get the correct
+ newPosition.setFrame((newPosition.getX() + movementX) * stretchX,
+ (newPosition.getY() + movementY) * stretchY,
+ newPosition.getWidth(), newPosition.getHeight());
+
+ // update the view
+ AttributeMap vertAttrib = new AttributeMap();
+ GraphConstants.setBounds(vertAttrib, newPosition);
+ vertex.changeAttributes(vertAttrib);
+ // The statement above fixes a bug in the original code
+ viewMap.put(cells[loop], vertAttrib);
+ }
+ }
+
+ return (viewMap);
+ }
+
+ private void updateVertexPosition(CellView vert, String PosField, Rectangle2D Position) {
+ AttributeMap vertAttrib = vert.getAllAttributes();
+
+ vertAttrib.put(PosField, Position);
+
+ /*
+ * There is no contractual guarantee that the Attribute Map returned by
+ * CellView.getAllAttributes() or (especially) CellView.getAttributes()
+ * is the same Attribute Map stored within the VertexView, so a
+ * seemingly redundant call to CellView.setAttributes msut be made
+
+ * below. This fixes a bug in the original code.
+ */
+ vert.changeAttributes(vertAttrib);
+ }
+
+ private Rectangle2D getVertexPosition(CellView vert, String PosField) {
+ AttributeMap vertAttrib = vert.getAllAttributes();
+
+ Rectangle2D result = (Rectangle2D) vertAttrib.get(PosField);
+
+ return (result);
+ }
+
+ private Rectangle2D removeVertexPosition(CellView vert, String PosField) {
+ AttributeMap vertAttrib = vert.getAllAttributes();
+
+ Rectangle2D result = (Rectangle2D) vertAttrib.remove(PosField);
+
+ /*
+ * There is no contractual guarantee that the Attribute Map returned by
+ * CellView.getAllAttributes() or (especially) CellView.getAttributes()
+ * is the same Attribute Map stored within the VertexView, so a
+ * seemingly redundant call to CellView.setAttributes msut be made
+ * below. This fixes a bug in the original code.
+ */
+ vert.changeAttributes(vertAttrib);
+
+ return (result);
+ }
+
+ /**
+ * calculates the attractive forces
+ */
+ protected double fa(double x, double k) {
+ double force = ((x * x) / k);
+
+ return force;
+ }
+
+ /**
+ * calculates the repulsive forces
+ */
+ protected double fr(double x, double k) {
+ double force = (k * k) / x;
+
+ return force;
+ }
+
+ /**
+ * Calculates the euklidische Norm for the point p.
+ *
+ */
+ protected double norm(Rectangle2D p) {
+ double x = p.getX();
+ double y = p.getY();
+ double norm = Math.sqrt((x * x) + (y * y));
+
+ return norm;
+ }
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/layout/SugiyamaLayoutAlgorithm.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/layout/SugiyamaLayoutAlgorithm.java
new file mode 100644
index 0000000..b6d2345
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/layout/SugiyamaLayoutAlgorithm.java
@@ -0,0 +1,1168 @@
+/*
+ * @(#)SugiyamaLayoutAlgorithm.java 1.0 18-MAY-2004
+ *
+ * Copyright (c) 2004, Sven Luzar
+ * Copyright (c) 2004, Nicholas Sushkin
+ * Copyright (c) 2004-2005, Gaudenz Alder
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright notice,
+ * this list of conditions and the following disclaimer.
+ * - Redistributions in binary form must reproduce the above copyright notice,
+ * this list of conditions and the following disclaimer in the documentation
+ * and/or other materials provided with the distribution.
+ * - Neither the name of JGraph nor the names of its contributors may be used
+ * to endorse or promote products derived from this software without specific
+ * prior written permission.
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ */
+package org.jgraph.layout;
+
+import org.jgraph.JGraph;
+
+import org.jgraph.graph.CellView;
+import org.jgraph.graph.GraphConstants;
+import org.jgraph.graph.GraphLayoutCache;
+import org.jgraph.graph.GraphModel;
+import org.jgraph.graph.VertexView;
+
+import java.awt.Point;
+import java.awt.Rectangle;
+import java.awt.geom.Rectangle2D;
+
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Vector;
+
+
+/**
+ * Arranges the nodes with the Sugiyama Layout Algorithm.<br>
+ *
+ * <a href="http://plg.uwaterloo.ca/~itbowman/CS746G/Notes/Sugiyama1981_MVU/">
+ * Link to the algorithm</a>
+ *
+ *<br>
+ *<br>
+ * @author Sven Luzar<br>
+ * modified by Gaudenz Alder and Nicholas Sushkin
+ */
+public class SugiyamaLayoutAlgorithm extends JGraphLayoutAlgorithm {
+ /** Const to add Attributes at the Nodes
+ *
+ */
+ public static final String SUGIYAMA_VISITED = "SugiyamaVisited" /*#Frozen*/;
+
+ /** Const to add the Cell Wrapper to the Nodes
+ */
+ public static final String SUGIYAMA_CELL_WRAPPER = "SugiyamaCellWrapper" /*#Frozen*/;
+
+ /**
+ * Const to add Attributes at the Nodes indicating that the cell was explicitly specified to the layout.
+ *
+ * @see #run(org.jgraph.JGraph,Object[],Object[])
+ */
+ public static final String SUGIYAMA_SELECTED = "SugiyamaSelected" /*#Frozen*/;
+
+ /** represents the size of the grid in horizontal grid elements
+ *
+ */
+ protected int gridAreaSize = Integer.MIN_VALUE;
+
+ /** A list with Integer Objects. The list contains the
+ * history of movements per loop
+ * It was needed for the progress dialog
+ */
+ List movements = null;
+
+ /** Represents the movements in the current loop.
+ * It was needed for the progress dialog
+ */
+ int movementsCurrentLoop = -1;
+
+ /** Represents the maximum of movements in the current loop.
+ * It was needed for the progress dialog
+ */
+ int movementsMax = Integer.MIN_VALUE;
+
+ /** Represents the current loop number
+ * It was needed for the progress dialog
+ */
+ int iteration = 0;
+
+ /**
+ * The default layout direction is vertical (top-down)
+ */
+ protected boolean vertical = true;
+
+ /**
+ * The default grid spacing is (250, 150).
+ */
+ protected Point spacing = new Point(250, 150);
+
+ /**
+ * Controls whether the graph should be placed as close to the origin as possible.
+ */
+ protected boolean flushToOrigin = false;
+
+ /**
+ * Returns an new instance of SugiyamaLayoutSettings
+ */
+ public JGraphLayoutSettings createSettings() {
+ return new SugiyamaLayoutSettings(this);
+ }
+
+ /**
+ * Returns the name of this algorithm in human
+ * readable form.
+ */
+ public String toString() {
+ return "Sugiyama";
+ }
+
+ /**
+ * Get a human readable hint for using this layout.
+ */
+ public String getHint() {
+ return "Ignores selection";
+ }
+
+ /**
+ * Implementation.
+ *
+ * First of all the Algorithm searches the roots from the
+ * Graph. Starting from this roots the Algorithm creates
+ * levels and stores them in the member <code>levels</code>.
+ * The Member levels contains Vector Objects and the Vector per level
+ * contains Cell Wrapper Objects. After that the Algorithm
+ * tries to solve the edge crosses from level to level and
+ * goes top down and bottom up. After minimization of the
+ * edge crosses the algorithm moves each node to its
+ * bary center. Last but not Least the method draws the Graph.
+ *
+ * @param graph JGraph instance
+ * @param dynamic_cells List of all nodes the layout should move
+ * @param static_cells List of node the layout should not move but allow for
+ */
+ public void run(JGraph graph, Object[] dynamic_cells, Object[] static_cells) {
+ CellView[] selectedCellViews = graph.getGraphLayoutCache().getMapping(dynamic_cells);
+
+ // gridAreaSize should really belong to the run state.
+ gridAreaSize = Integer.MIN_VALUE;
+
+ /* The Algorithm distributes the nodes on a grid.
+ * For this grid you can configure the horizontal spacing.
+ * This field specifies the configured value
+ *
+ */
+ Rectangle2D maxBounds = new Rectangle2D.Double();
+
+ for (int i = 0; i < selectedCellViews.length; i++) {
+ if (canceled)
+ return;
+
+ // Add vertex to list
+ if (selectedCellViews[i] instanceof VertexView) {
+ // Fetch Bounds
+ Rectangle2D bounds = selectedCellViews[i].getBounds();
+
+ // Update Maximum
+ if (bounds != null)
+ maxBounds.setFrame(0, 0, Math.max(bounds.getWidth(), maxBounds.getWidth()),
+ Math.max(bounds.getHeight(), maxBounds.getHeight()));
+ }
+ }
+
+ if (spacing.x == 0)
+ spacing.x = (int) (2 * maxBounds.getWidth());
+
+ if (spacing.y == 0)
+ spacing.y = (int) (2 * maxBounds.getHeight()); // (jgraph.getGridSize()*6);
+
+ // mark selected cell views in the graph
+ markSelected(selectedCellViews, true);
+
+ // search all roots
+ List roots = searchRoots(graph, selectedCellViews);
+
+ // return if no root found
+ if (roots.size() == 0)
+ return;
+
+ // create levels
+ List levels = fillLevels(graph, selectedCellViews, roots);
+
+ // solves the edge crosses
+ solveEdgeCrosses(graph, levels);
+
+ // move all nodes into the barycenter
+ moveToBarycenter(graph, selectedCellViews, levels);
+
+ Point min = flushToOrigin ? new Point(0, 0) : findMinimumAndSpacing(selectedCellViews);
+
+ // draw the graph in the window
+ drawGraph(graph, levels, min, spacing);
+
+ // remove marks from the selected cell views in the graph
+ markSelected(selectedCellViews, false);
+ }
+
+ /**
+ * Adds an attribute {@link #SUGIYAMA_SELECTED SUGIYAMA_SELECTED} to the specified selected cell views.
+ *
+ * @param selectedCellViews the specified cell views
+ * @param addMark true to add the mark, false to remove the mark
+ */
+ protected void markSelected(CellView[] selectedCellViews, boolean addMark) {
+ if (addMark) {
+ for (int i = 0; i < selectedCellViews.length; i++) {
+ if (selectedCellViews[i] != null) {
+ selectedCellViews[i].getAttributes().put(SUGIYAMA_SELECTED, Boolean.TRUE);
+ }
+ }
+ } else {
+ for (int i = 0; i < selectedCellViews.length; i++) {
+ if (selectedCellViews[i] != null) {
+ selectedCellViews[i].getAttributes().remove(SUGIYAMA_SELECTED);
+ }
+ }
+ }
+ }
+
+ /**
+ * Detects whether the specified cell has been marked selected.
+ *
+ * @see #markSelected(CellView[], boolean)
+ *
+ * @param cell the cell to inspect
+ * @return true if the view has been marked selected and false otherwise.
+ */
+ protected boolean isSelected(final GraphLayoutCache cache, final Object cell) {
+ final CellView view = cache.getMapping(cell, false);
+
+ return (view != null) && (view.getAttributes().get(SUGIYAMA_SELECTED) != null);
+ }
+
+ /** Searches all Roots for the current Graph
+ * First the method marks any Node as not visited.
+ * Than calls searchRoots(MyGraphCell) for each
+ * not visited Cell.
+ * The Roots are stored in the Vector named roots
+ *
+ * @return returns a Vector with the roots
+ * @see #searchRoots(JGraph, CellView[])
+ */
+ protected List searchRoots(JGraph jgraph, CellView[] selectedCellViews) {
+ // get all cells and relations
+ List vertexViews = new ArrayList(selectedCellViews.length);
+ List roots = new ArrayList();
+
+ // first: mark all as not visited
+ // O(allCells&Edges)
+ for (int i = 0; i < selectedCellViews.length; i++) {
+ if (selectedCellViews[i] instanceof VertexView) {
+ VertexView vertexView = (VertexView) selectedCellViews[i];
+ vertexView.getAttributes().remove(SUGIYAMA_VISITED);
+ vertexViews.add(selectedCellViews[i]);
+ }
+ }
+
+ // O(graphCells)
+ for (int i = 0; i < vertexViews.size(); i++) {
+ VertexView vertexView = (VertexView) vertexViews.get(i);
+
+ if (vertexView.getAttributes().get(SUGIYAMA_VISITED) == null) {
+ searchRoots(jgraph, vertexView, roots);
+ }
+ }
+
+ // Error Msg if the graph has no roots
+ if (roots.size() == 0) {
+ throw new IllegalArgumentException("The Graph is not a DAG. Can't use Sugiyama Algorithm!");
+ }
+
+ return roots;
+ }
+
+ /** Searches Roots for the current Cell.
+ *
+ * Therefore he looks at all Ports from the Cell.
+ * At the Ports he looks for Edges.
+ * At the Edges he looks for the Target.
+ * If the Ports of the current Cell contains the target ReViewNodePort
+ * he follows the edge to the source and looks at the
+ * Cell for this source.
+ *
+ */
+ protected void searchRoots(JGraph jgraph, VertexView vertexViewToInspect, List roots) {
+ // the node already visited
+ if (vertexViewToInspect.getAttributes().get(SUGIYAMA_VISITED) != null) {
+ return;
+ }
+
+ // mark as visited for cycle tests
+ vertexViewToInspect.getAttributes().put(SUGIYAMA_VISITED, Boolean.TRUE);
+
+ GraphModel model = jgraph.getModel();
+ GraphLayoutCache cache = jgraph.getGraphLayoutCache();
+
+ // get all Ports and search the relations at the ports
+ //List vertexPortViewList = new ArrayList() ;
+ Object vertex = vertexViewToInspect.getCell();
+
+ int portCount = model.getChildCount(vertex);
+
+ for (int j = 0; j < portCount; j++) {
+ Object port = model.getChild(vertex, j);
+
+ // Test all relations for where
+ // the current node is a target node
+ // for roots
+ boolean isRoot = true;
+ Iterator itrEdges = model.edges(port);
+
+ while (itrEdges.hasNext()) {
+ Object edge = itrEdges.next();
+
+ // if not selected do not follow
+ if (!isSelected(cache, edge)) {
+ continue;
+ }
+
+ // if the current node is a target node
+ // get the source node and test
+ // the source node for roots
+ if (model.getTarget(edge) == port) {
+ Object sourcePort = model.getSource(edge);
+
+ Object sourceVertex = model.getParent(sourcePort);
+
+ CellView sourceVertexView = jgraph.getGraphLayoutCache()
+ .getMapping(sourceVertex, false);
+
+ if (sourceVertexView instanceof VertexView) {
+ searchRoots(jgraph, (VertexView) sourceVertexView, roots);
+ isRoot = false;
+ }
+ }
+ }
+
+ // The current node is never a Target Node
+ // -> The current node is a root node
+ if (isRoot) {
+ roots.add(vertexViewToInspect);
+ }
+ }
+ }
+
+ /** Method fills the levels and stores them in the member levels.
+
+ * Each level was represended by a Vector with Cell Wrapper objects.
+ * These Vectors are the elements in the <code>levels</code> Vector.
+ *
+ */
+ protected List fillLevels(JGraph jgraph, CellView[] selectedCellViews, List rootVertexViews) {
+ List levels = new Vector();
+
+ // mark as not visited
+ // O(allCells)
+ for (int i = 0; i < selectedCellViews.length; i++) {
+ CellView cellView = selectedCellViews[i];
+
+ // more stabile
+ if (cellView == null)
+ continue;
+
+ cellView.getAttributes().remove(SUGIYAMA_VISITED);
+ }
+
+ Iterator rootIter = rootVertexViews.iterator();
+
+ while (rootIter.hasNext()) {
+ VertexView vertexView = (VertexView) rootIter.next();
+ fillLevels(jgraph, levels, 0, vertexView);
+ }
+
+ return levels;
+ }
+
+ /** Fills the Vector for the specified level with a wrapper
+ * for the MyGraphCell. After that the method called for
+ * each neighbor graph cell.
+ *
+ * @param level The level for the graphCell
+ */
+ protected void fillLevels(JGraph jgraph, List levels, int level, VertexView vertexView) {
+ // precondition control
+ if (vertexView == null)
+ return;
+
+ // be sure that the list container exists for the current level
+ if (levels.size() == level)
+ levels.add(level, new ArrayList());
+
+ // if the cell already visited return
+ if (vertexView.getAttributes().get(SUGIYAMA_VISITED) != null) {
+ return;
+ }
+
+ // mark as visited for cycle tests
+ vertexView.getAttributes().put(SUGIYAMA_VISITED, Boolean.TRUE);
+
+ // put the current node into the current level
+ // get the Level list
+ List listForTheCurrentLevel = (ArrayList) levels.get(level);
+
+ // Create a wrapper for the node
+ int numberForTheEntry = listForTheCurrentLevel.size();
+
+ CellWrapper wrapper = new CellWrapper(level, numberForTheEntry, vertexView);
+
+ // put the Wrapper in the LevelVector
+ listForTheCurrentLevel.add(wrapper);
+
+ // concat the wrapper to the cell for an easy access
+ vertexView.getAttributes().put(SUGIYAMA_CELL_WRAPPER, wrapper);
+
+ // if the Cell has no Ports we can return, there are no relations
+ Object vertex = vertexView.getCell();
+ GraphModel model = jgraph.getModel();
+ GraphLayoutCache cache = jgraph.getGraphLayoutCache();
+ int portCount = model.getChildCount(vertex);
+
+ // iterate any NodePort
+ for (int i = 0; i < portCount; i++) {
+ Object port = model.getChild(vertex, i);
+
+ // iterate any Edge in the port
+ Iterator itrEdges = model.edges(port);
+
+ while (itrEdges.hasNext()) {
+ Object edge = itrEdges.next();
+
+ // if not selected, do not follow
+ if (!isSelected(cache, edge)) {
+ continue;
+ }
+
+ // if the Edge is a forward edge we should follow this edge
+ if (port == model.getSource(edge)) {
+ Object targetPort = model.getTarget(edge);
+ Object targetVertex = model.getParent(targetPort);
+
+ // if not selected, do not follow the vertex
+ if (!isSelected(cache, targetVertex)) {
+ continue;
+ }
+
+ VertexView targetVertexView = (VertexView) jgraph.getGraphLayoutCache()
+ .getMapping(targetVertex, false);
+ fillLevels(jgraph, levels, (level + 1), targetVertexView);
+ }
+ }
+ }
+
+ if (listForTheCurrentLevel.size() > gridAreaSize) {
+ gridAreaSize = listForTheCurrentLevel.size();
+ }
+ }
+
+ /** calculates the minimum for the paint area.
+ *
+ */
+ protected Point findMinimumAndSpacing(CellView[] graphCellViews) {
+ try {
+ // variables
+ /* represents the minimum x value for the paint area
+ */
+ int min_x = 1000000;
+
+ /* represents the minimum y value for the paint area
+ */
+ int min_y = 1000000;
+
+ // find the maximum & minimum coordinates
+ for (int i = 0; i < graphCellViews.length; i++) {
+ // the cellView and their bounds
+ CellView cellView = graphCellViews[i];
+
+ if (cellView == null)
+ continue;
+
+ Rectangle2D rect = cellView.getBounds();
+ Rectangle cellViewBounds = new Rectangle((int) rect.getX(), (int) rect.getY(),
+ (int) rect.getWidth(),
+ (int) rect.getHeight());
+
+ // checking min area
+ try {
+ if (cellViewBounds.x < min_x)
+ min_x = cellViewBounds.x;
+
+ if (cellViewBounds.y < min_y)
+ min_y = cellViewBounds.y;
+
+ /*
+ if (cellViewBounds.width > spacing.x)
+ spacing.x = cellViewBounds.width;
+ if (cellViewBounds.height > spacing.y)
+ spacing.y = cellViewBounds.height;
+ */
+ } catch (Exception e) {
+ System.err.println("---------> ERROR in calculateValues."/*#Frozen*/
+ );
+ e.printStackTrace();
+ }
+ }
+
+ // if the cell sice is bigger than the userspacing
+ // dublicate the spacingfactor
+ return new Point(min_x, min_y);
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ return null;
+ }
+
+ /** Updates the progress based on the movements count
+ *
+ */
+ protected void updateProgress4Movements() {
+ // adds the current loop count
+ movements.add(new Integer(movementsCurrentLoop));
+ iteration++;
+
+ // if the current loop count is higher than the max movements count
+ // memorize the new max
+ if (movementsCurrentLoop > movementsMax) {
+ movementsMax = movementsCurrentLoop;
+ }
+ }
+
+ protected void solveEdgeCrosses(JGraph jgraph, List levels) {
+ movements = new ArrayList(100);
+ movementsCurrentLoop = -1;
+ movementsMax = Integer.MIN_VALUE;
+ iteration = 0;
+
+ while (movementsCurrentLoop != 0) {
+ // reset the movements per loop count
+ movementsCurrentLoop = 0;
+
+ // top down
+ for (int i = 0; i < (levels.size() - 1); i++) {
+ movementsCurrentLoop += solveEdgeCrosses(jgraph, true, levels, i);
+ }
+
+ // bottom up
+ for (int i = levels.size() - 1; i >= 1; i--) {
+ movementsCurrentLoop += solveEdgeCrosses(jgraph, false, levels, i);
+ }
+
+ updateProgress4Movements();
+ }
+ }
+
+ /**
+ * @return movements
+ */
+ protected int solveEdgeCrosses(JGraph jgraph, boolean down, List levels, int levelIndex) {
+ // Get the current level
+ List currentLevel = (List) levels.get(levelIndex);
+ int movements = 0;
+
+ // restore the old sort
+ Object[] levelSortBefore = currentLevel.toArray();
+
+ // new sort
+ Collections.sort(currentLevel);
+
+ // test for movements
+ for (int j = 0; j < levelSortBefore.length; j++) {
+ if (((CellWrapper) levelSortBefore[j]).getEdgeCrossesIndicator() != ((CellWrapper) currentLevel
+ .get(j))
+ [...]
+ movements++;
+ }
+ }
+
+ GraphModel model = jgraph.getModel();
+ GraphLayoutCache cache = jgraph.getGraphLayoutCache();
+
+ // Colections Sort sorts the highest value to the first value
+ for (int j = currentLevel.size() - 1; j >= 0; j--) {
+ CellWrapper sourceWrapper = (CellWrapper) currentLevel.get(j);
+
+ VertexView sourceView = sourceWrapper.getVertexView();
+
+ Object sourceVertex = sourceView.getCell();
+ int sourcePortCount = model.getChildCount(sourceVertex);
+
+ for (int k = 0; k < sourcePortCount; k++) {
+ Object sourcePort = model.getChild(sourceVertex, k);
+
+ Iterator sourceEdges = model.edges(sourcePort);
+
+ while (sourceEdges.hasNext()) {
+ Object edge = sourceEdges.next();
+
+ // if not selected, do not follow
+ if (!isSelected(cache, edge)) {
+ continue;
+ }
+
+ // if it is a forward edge follow it
+ Object targetPort = null;
+
+ if (down && (sourcePort == model.getSource(edge))) {
+ targetPort = model.getTarget(edge);
+ }
+
+ if (!down && (sourcePort == model.getTarget(edge))) {
+ targetPort = model.getSource(edge);
+ }
+
+ if (targetPort == null)
+ continue;
+
+ Object targetCell = model.getParent(targetPort);
+
+ // if the target cell not selected, do not follow
+ if (!isSelected(cache, targetCell))
+ continue;
+
+ VertexView targetVertexView = (VertexView) jgraph.getGraphLayoutCache()
+ .getMapping(targetCell, false);
+
+ if (targetVertexView == null)
+ continue;
+
+ CellWrapper targetWrapper = (CellWrapper) targetVertexView.getAttributes()
+ .get(SUGIYAMA_CELL_WRAPPER);
+
+ // do it only if the edge is a forward edge to a deeper level
+ if (down && (targetWrapper != null) && (targetWrapper.getLevel() > levelIndex)) {
+ targetWrapper.addToEdgeCrossesIndicator(sourceWrapper
+ [...]
+ }
+
+ if (!down && (targetWrapper != null) && (targetWrapper.getLevel() < levelIndex)) {
+ targetWrapper.addToEdgeCrossesIndicator(sourceWrapper
+ [...]
+ }
+ }
+ }
+ }
+
+ return movements;
+ }
+
+ protected void moveToBarycenter(JGraph jgraph, CellView[] allSelectedViews, List levels) {
+ //================================================================
+ // iterate any ReViewNodePort
+ GraphModel model = jgraph.getModel();
+ GraphLayoutCache cache = jgraph.getGraphLayoutCache();
+
+ for (int i = 0; i < allSelectedViews.length; i++) {
+ if (!(allSelectedViews[i] instanceof VertexView))
+ continue;
+
+ VertexView vertexView = (VertexView) allSelectedViews[i];
+
+ CellWrapper currentwrapper = (CellWrapper) vertexView.getAttributes()
+ .get(SUGIYAMA_CELL_WRAPPER);
+
+ Object vertex = vertexView.getCell();
+ int portCount = model.getChildCount(vertex);
+
+ for (int k = 0; k < portCount; k++) {
+ Object port = model.getChild(vertex, k);
+
+ // iterate any Edge in the port
+ Iterator edges = model.edges(port);
+
+ while (edges.hasNext()) {
+ Object edge = edges.next();
+
+ // if edge not selected, do not follow
+ if (!isSelected(cache, edge))
+ continue;
+
+ Object neighborPort = null;
+
+ // if the Edge is a forward edge we should follow this edge
+ if (port == model.getSource(edge)) {
+ neighborPort = model.getTarget(edge);
+ } else {
+ if (port == model.getTarget(edge)) {
+ neighborPort = model.getSource(edge);
+ } else {
+ continue;
+ }
+ }
+
+ Object neighborVertex = model.getParent(neighborPort);
+
+ // if vertex not selected, do not follow
+ if (!isSelected(cache, neighborVertex))
+ continue;
+
+ VertexView neighborVertexView = (VertexView) jgraph.getGraphLayoutCache()
+ .getMapping(neighborVertex,
+ false);
+
+ if ((neighborVertexView == null) || (neighborVertexView == vertexView))
+ continue;
+
+ CellWrapper neighborWrapper = (CellWrapper) neighborVertexView.getAttributes()
+ .get(SUGIYAMA_CELL_WRAPPER);
+
+ if ((currentwrapper == null) || (neighborWrapper == null)
+ || (currentwrapper.level == neighborWrapper.level))
+ continue;
+
+ currentwrapper.priority++;
+ }
+ }
+ }
+
+ //================================================================
+ for (Iterator levelsIter = levels.iterator(); levelsIter.hasNext();) {
+ List level = (List) levelsIter.next();
+ int i = 0;
+
+ for (Iterator levelIter = level.iterator(); levelIter.hasNext(); i++) {
+ // calculate the initial Grid Positions 1, 2, 3, .... per Level
+ CellWrapper wrapper = (CellWrapper) levelIter.next();
+ wrapper.setGridPosition(i);
+ }
+ }
+
+ movements.clear();
+ movementsCurrentLoop = -1;
+ movementsMax = Integer.MIN_VALUE;
+ iteration = 0;
+
+ //int movements = 1;
+ while (movementsCurrentLoop != 0) {
+ // reset movements
+ movementsCurrentLoop = 0;
+
+ // top down
+ for (int i = 1; i < levels.size(); i++) {
+ movementsCurrentLoop += moveToBarycenter(jgraph, levels, i);
+ }
+
+ // bottom up
+ for (int i = levels.size() - 1; i >= 0; i--) {
+ movementsCurrentLoop += moveToBarycenter(jgraph, levels, i);
+ }
+
+ this.updateProgress4Movements();
+ }
+ }
+
+ protected int moveToBarycenter(JGraph jgraph, List levels, int levelIndex) {
+ // Counter for the movements
+ int movements = 0;
+
+ // Get the current level
+ List currentLevel = (List) levels.get(levelIndex);
+ GraphModel model = jgraph.getModel();
+ GraphLayoutCache cache = jgraph.getGraphLayoutCache();
+
+ for (int currentIndexInTheLevel = 0; currentIndexInTheLevel < currentLevel.size();
+ currentIndexInTheLevel++) {
+ CellWrapper sourceWrapper = (CellWrapper) currentLevel.get(currentIndexInTheLevel);
+
+ float gridPositionsSum = 0;
+ float countNodes = 0;
+
+ VertexView vertexView = sourceWrapper.getVertexView();
+ Object vertex = vertexView.getCell();
+ int portCount = model.getChildCount(vertex);
+
+ for (int i = 0; i < portCount; i++) {
+ Object port = model.getChild(vertex, i);
+
+ Iterator edges = model.edges(port);
+
+ while (edges.hasNext()) {
+ Object edge = edges.next();
+
+ // if edge not selected, do not follow
+ if (!isSelected(cache, edge))
+ continue;
+
+ // if it is a forward edge follow it
+ Object neighborPort = null;
+
+ if (port == model.getSource(edge)) {
+ neighborPort = model.getTarget(edge);
+ } else {
+ if (port == model.getTarget(edge)) {
+ neighborPort = model.getSource(edge);
+ } else {
+ continue;
+ }
+ }
+
+ Object neighborVertex = model.getParent(neighborPort);
+
+ // if vertex not selected, do not follow
+ if (!isSelected(cache, neighborVertex))
+ continue;
+
+ VertexView neighborVertexView = (VertexView) jgraph.getGraphLayoutCache()
+ .getMapping(neighborVertex,
+ false);
+
+ if (neighborVertexView == null)
+ continue;
+
+ CellWrapper targetWrapper = (CellWrapper) neighborVertexView.getAttributes()
+ .get(SUGIYAMA_CELL_WRAPPER);
+
+ if (targetWrapper == sourceWrapper)
+ continue;
+
+ if ((targetWrapper == null) || (targetWrapper.getLevel() == levelIndex))
+ continue;
+
+ gridPositionsSum += targetWrapper.getGridPosition();
+ countNodes++;
+ }
+ }
+
+ //----------------------------------------------------------
+ // move node to new x coord
+ //----------------------------------------------------------
+ if (countNodes > 0) {
+ float tmp = (gridPositionsSum / countNodes);
+ int newGridPosition = Math.round(tmp);
+ boolean toRight = (newGridPosition > sourceWrapper.getGridPosition());
+
+ boolean moved = true;
+
+ while ((newGridPosition != sourceWrapper.getGridPosition()) && moved) {
+ moved = move(toRight, currentLevel, currentIndexInTheLevel,
+ sourceWrapper.getPriority());
+
+ if (moved)
+ movements++;
+ }
+ }
+ }
+
+ return movements;
+ }
+
+ /**@param toRight <tt>true</tt> = try to move the currentWrapper to right; <tt>false</tt> = try to move the currentWrapper to left;
+ * @param currentLevel List which contains the CellWrappers for the current level
+ * @param currentIndexInTheLevel
+ * @param currentPriority
+ *
+ * @return The free GridPosition or -1 is position is not free.
+ */
+ protected boolean move(boolean toRight, List currentLevel, int currentIndexInTheLevel,
+ int currentPriority) {
+ CellWrapper currentWrapper = (CellWrapper) currentLevel.get(currentIndexInTheLevel);
+
+ boolean moved = false;
+ int neighborIndexInTheLevel = currentIndexInTheLevel + (toRight ? 1 : (-1));
+ int newGridPosition = currentWrapper.getGridPosition() + (toRight ? 1 : (-1));
+
+ // is the grid position possible?
+ if ((0 > newGridPosition) || (newGridPosition >= gridAreaSize)) {
+ return false;
+ }
+
+ // if the node is the first or the last we can move
+ if ((toRight && (currentIndexInTheLevel == (currentLevel.size() - 1)))
+ || (!toRight && (currentIndexInTheLevel == 0))) {
+ moved = true;
+ } else {
+ // else get the neighbor and ask his gridposition
+ // if he has the requested new grid position
+ // check the priority
+ CellWrapper neighborWrapper = (CellWrapper) currentLevel.get(neighborIndexInTheLevel);
+
+ int neighborPriority = neighborWrapper.getPriority();
+
+ if (neighborWrapper.getGridPosition() == newGridPosition) {
+ if (neighborPriority >= currentPriority) {
+ return false;
+ } else {
+ moved = move(toRight, currentLevel, neighborIndexInTheLevel, currentPriority);
+ }
+ } else {
+ moved = true;
+ }
+ }
+
+ if (moved) {
+ currentWrapper.setGridPosition(newGridPosition);
+ }
+
+ return moved;
+ }
+
+ /** This Method draws the graph. For the horizontal position
+ * we are using the grid position from each graphcell.
+ * For the vertical position we are using the level position.
+ *
+ */
+ protected void drawGraph(JGraph jgraph, List levels, Point min, Point spacing) {
+ // paint the graph
+ Map viewMap = new Hashtable();
+
+ for (int rowCellCount = 0; rowCellCount < levels.size(); rowCellCount++) {
+ List level = (List) levels.get(rowCellCount);
+
+ for (int colCellCount = 0; colCellCount < level.size(); colCellCount++) {
+ CellWrapper wrapper = (CellWrapper) level.get(colCellCount);
+ VertexView view = wrapper.vertexView;
+
+ // remove the temp objects
+ /* While the Algorithm is running we are putting some
+ * attributeNames to the MyGraphCells. This method
+ * cleans this objects from the MyGraphCells.
+ *
+ */
+ view.getAttributes().remove(SUGIYAMA_CELL_WRAPPER);
+ view.getAttributes().remove(SUGIYAMA_VISITED);
+ wrapper.vertexView = null;
+
+ // get the bounds from the cellView
+ if (view == null)
+ continue;
+
+ Rectangle2D rect = (Rectangle2D) view.getBounds().clone();
+ Rectangle bounds = new Rectangle((int) rect.getX(), (int) rect.getY(),
+ (int) rect.getWidth(), (int) rect.getHeight());
+ //(Rectangle) view.getBounds().clone();
+
+ // adjust
+ bounds.x = min.x
+ + (spacing.x * ((vertical) ? wrapper.getGridPosition() : rowCellCount));
+ bounds.y = min.y
+ + (spacing.y * ((vertical) ? rowCellCount : wrapper.getGridPosition()));
+
+ Object cell = view.getCell();
+ Map map = new Hashtable();
+ GraphConstants.setBounds(map, (Rectangle2D) bounds.clone());
+
+ viewMap.put(cell, map);
+ }
+ }
+
+ jgraph.getGraphLayoutCache().edit(viewMap, null, null, null);
+ }
+
+ /** cell wrapper contains all values
+ * for one node
+ */
+ class CellWrapper implements Comparable {
+ /** sum value for edge Crosses
+ */
+ private double edgeCrossesIndicator = 0;
+
+ /** counter for additions to the edgeCrossesIndicator
+ */
+ private int additions = 0;
+
+ /** the vertical level where the cell wrapper is inserted
+ */
+ int level = 0;
+
+ /** current position in the grid
+ */
+ int gridPosition = 0;
+
+ /** priority for movements to the barycenter
+ */
+ int priority = 0;
+
+ /** reference to the wrapped cell
+ */
+ VertexView vertexView = null;
+
+ /** creates an instance and memorizes the parameters
+ *
+ */
+ CellWrapper(int level, double edgeCrossesIndicator, VertexView vertexView) {
+ this.level = level;
+ this.edgeCrossesIndicator = edgeCrossesIndicator;
+ this.vertexView = vertexView;
+ additions++;
+ }
+
+ /** returns the wrapped cell
+ */
+ VertexView getVertexView() {
+ return vertexView;
+ }
+
+ /** resets the indicator for edge crosses to 0
+ */
+ void resetEdgeCrossesIndicator() {
+ edgeCrossesIndicator = 0;
+ additions = 0;
+ }
+
+ /** retruns the average value for the edge crosses indicator
+ *
+ * for the wrapped cell
+ *
+ */
+ double getEdgeCrossesIndicator() {
+ if (additions == 0)
+ return 0;
+
+ return edgeCrossesIndicator / additions;
+ }
+
+ /** Addes a value to the edge crosses indicator
+ * for the wrapped cell
+ *
+ */
+ void addToEdgeCrossesIndicator(double addValue) {
+ edgeCrossesIndicator += addValue;
+ additions++;
+ }
+
+ /** gets the level of the wrapped cell
+ */
+ int getLevel() {
+ return level;
+ }
+
+ /** gets the grid position for the wrapped cell
+ */
+ int getGridPosition() {
+ return gridPosition;
+ }
+
+ /** Sets the grid position for the wrapped cell
+ */
+ void setGridPosition(int pos) {
+ this.gridPosition = pos;
+ }
+
+ /** increments the the priority of this cell wrapper.
+ *
+ * The priority was used by moving the cell to its
+ * barycenter.
+ *
+ */
+ void incrementPriority() {
+ priority++;
+ }
+
+ /** returns the priority of this cell wrapper.
+ *
+ * The priority was used by moving the cell to its
+ * barycenter.
+ */
+ int getPriority() {
+ return priority;
+ }
+
+ /**
+ * @see java.lang.Comparable#compareTo(Object)
+ */
+ public int compareTo(Object compare) {
+ if (((CellWrapper) compare).getEdgeCrossesIndicator() == this.getEdgeCrossesIndicator())
+ return 0;
+
+ double compareValue = (((CellWrapper) compare).getEdgeCrossesIndicator()
+ - this.getEdgeCrossesIndicator());
+
+ return (int) (compareValue * 1000);
+ }
+ }
+
+ /**
+ * Returns the spacing.
+ *
+ * @see #setSpacing
+ */
+ public Point getSpacing() {
+ return spacing;
+ }
+
+ /**
+ * Sets grid spacing.
+ *
+ * The Algorithm distributes the nodes on a grid. For this
+ * grid you can configure the vertical and horizontal spacing.
+ *
+ */
+ public void setSpacing(Point spacing) {
+ this.spacing = spacing;
+ }
+
+ /**
+ * Returns the current layout direction
+ * @return boolean whether or not direction is vertical
+ * @see #setVertical(boolean)
+ */
+ public boolean isVertical() {
+ return vertical;
+ }
+
+ /**
+ * Sets the layout direction.
+ *
+ * @param vertical true for vertical and false for horizontal direction
+ */
+ public void setVertical(boolean vertical) {
+ this.vertical = vertical;
+ }
+
+ /**
+ * Get the <code>FlushToOrigin</code> value.
+ *
+ * @see #setFlushToOrigin(boolean)
+ *
+ * @return a <code>boolean</code> value
+ */
+ public final boolean getFlushToOrigin() {
+ return flushToOrigin;
+ }
+
+ /**
+ * After layout, moves the graph as close to origin as possible.
+ *
+ * <p>After the layout has complete, this algorithm calculates the
+ * minimum X and Y coordinates over all selected cells. If
+ * flushToOrigin parameter is set to false, the algorithm will place
+ * cells starting at coordinates corresponding to those minimum
+ * values.
+ *
+ * <p>If set to true, the layout will place cells starting at the
+ * origin, possibly shrinking the overall graph canvas size
+ *
+ * @param newFlushToOrigin The new FlushToOrigin value.
+ */
+ public final void setFlushToOrigin(final boolean newFlushToOrigin) {
+ this.flushToOrigin = newFlushToOrigin;
+ }
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/layout/SugiyamaLayoutSettings.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/layout/SugiyamaLayoutSettings.java
new file mode 100644
index 0000000..3a94c66
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/layout/SugiyamaLayoutSettings.java
@@ -0,0 +1,187 @@
+/*
+ * @(#)SugiyamaLayoutSettings.java 1.0 12-JUL-2004
+ *
+ * Copyright (c) 2004, Gaudenz Alder
+ * Copyright (c) 2004, Nicholas Sushkin
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright notice,
+ * this list of conditions and the following disclaimer.
+ * - Redistributions in binary form must reproduce the above copyright notice,
+ * this list of conditions and the following disclaimer in the documentation
+ * and/or other materials provided with the distribution.
+ * - Neither the name of JGraph nor the names of its contributors may be used
+ * to endorse or promote products derived from this software without specific
+ * prior written permission.
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ */
+package org.jgraph.layout;
+
+import java.awt.GridLayout;
+
+import javax.swing.JCheckBox;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JTextField;
+
+
+/**
+ * A Dialog for configuring a SugiyamaLayoutAlgorithm.
+ * You can use horizontal and vertical spacing.<br>
+ * <br>
+ * Will be shown by the SugiyamaLayoutController.<br>
+ *<br>
+ *<br>
+ * @author Gaudenz Alder<br>
+ * @version 1.0 init
+ */
+public class SugiyamaLayoutSettings extends JPanel implements JGraphLayoutSettings {
+ protected SugiyamaLayoutAlgorithm layout;
+ private JTextField verticalSpacingTextField = new JTextField();
+ private JTextField horizontalSpacingTextField = new JTextField();
+ private JCheckBox verticalDirectionCheckBox = new JCheckBox();
+ private JCheckBox flushToOriginCheckBox = new JCheckBox();
+
+ /**
+ * Creates new form SugiyamaLayoutConfigurationDialog
+ */
+ public SugiyamaLayoutSettings(SugiyamaLayoutAlgorithm layout) {
+ this.layout = layout;
+
+ JPanel jPanel1 = new javax.swing.JPanel(new GridLayout(4, 2, 5, 0));
+
+ JLabel label = new JLabel("Horizontal Spacing");
+ label.setToolTipText("Sets horizontal spacing of the layout grid");
+ label.setLabelFor(horizontalSpacingTextField);
+ label.setDisplayedMnemonic('h');
+ jPanel1.add(label);
+ jPanel1.add(horizontalSpacingTextField);
+
+ label = new JLabel("Vertical Spacing");
+ label.setToolTipText("Sets vertical spacing of the layout grid");
+ label.setLabelFor(verticalSpacingTextField);
+ label.setDisplayedMnemonic('v');
+ jPanel1.add(label);
+ jPanel1.add(verticalSpacingTextField);
+
+ label = new JLabel("Vertical Orientation");
+ label.setToolTipText("Check to set vertical (top-down) orientation of the layout. Uncheck for horizontal (left-right)");
+ label.setLabelFor(verticalDirectionCheckBox);
+ label.setDisplayedMnemonic('o');
+ jPanel1.add(label);
+ jPanel1.add(verticalDirectionCheckBox);
+
+ label = new JLabel("Flush to Origin");
+ label.setToolTipText("Check to flush the graph to the canvas origin");
+ label.setLabelFor(flushToOriginCheckBox);
+ label.setDisplayedMnemonic('f');
+ jPanel1.add(label);
+ jPanel1.add(flushToOriginCheckBox);
+
+ add(jPanel1, java.awt.BorderLayout.CENTER);
+ revert();
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void revert() {
+ horizontalSpacingTextField.setText(String.valueOf(layout.getSpacing().x));
+ verticalSpacingTextField.setText(String.valueOf(layout.getSpacing().y));
+ verticalDirectionCheckBox.setSelected(layout.isVertical());
+ flushToOriginCheckBox.setSelected(layout.getFlushToOrigin());
+ }
+
+ /**
+ * Implementation.
+ */
+ public void apply() {
+ check();
+ layout.setSpacing(new java.awt.Point(Integer.parseInt(getIndention()),
+ Integer.parseInt(getVerticalSpacing())));
+ layout.setVertical(getVerticalDirection());
+ layout.setFlushToOrigin(getFlushToOrigin());
+ }
+
+ private void check() {
+ try {
+ Integer.parseInt(horizontalSpacingTextField.getText());
+ Integer.parseInt(verticalSpacingTextField.getText());
+ } catch (Exception e) {
+ throw new IllegalArgumentException(e.getMessage());
+ }
+ }
+
+ /**
+ * Returns the value of the "Horizontal spacing" as text.
+ */
+ public String getIndention() {
+ return horizontalSpacingTextField.getText().trim();
+ }
+
+ /**
+ * Set the value of the "Horizontal spacing" text field.
+ */
+ public void setIndention(String text) {
+ horizontalSpacingTextField.setText(text);
+ }
+
+ /**
+ * Returns the value of the "Vertical spacing" as text.
+ */
+ public String getVerticalSpacing() {
+ return verticalSpacingTextField.getText().trim();
+ }
+
+ /**
+ * Set the value of the "Vertical Spacing" text field.
+ */
+ public void setVerticalSpacing(String text) {
+ verticalSpacingTextField.setText(text);
+ }
+
+ /**
+ * Returns the value of the "Vertical Direction" check box
+ */
+ public boolean getVerticalDirection() {
+ return verticalDirectionCheckBox.isSelected();
+ }
+
+ /**
+ * Sets the value of the "Vertical Direction" check box
+ */
+ public void setVerticalDirection(boolean vertical) {
+ verticalDirectionCheckBox.setSelected(vertical);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean getFlushToOrigin() {
+ return flushToOriginCheckBox.isSelected();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param flushToOrigin DOCUMENT ME!
+ */
+ public void setFlushToOrigin(boolean flushToOrigin) {
+ flushToOriginCheckBox.setSelected(flushToOrigin);
+ }
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/layout/TreeLayoutAlgorithm.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/layout/TreeLayoutAlgorithm.java
new file mode 100644
index 0000000..2283032
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/layout/TreeLayoutAlgorithm.java
@@ -0,0 +1,851 @@
+/*
+ * @(#)TreeLayoutAlgorithm.java 1.0 12-MAY-2004
+ *
+ * Copyright (c) 2004, Martin Krueger
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright notice,
+ * this list of conditions and the following disclaimer.
+ * - Redistributions in binary form must reproduce the above copyright notice,
+ * this list of conditions and the following disclaimer in the documentation
+ * and/or other materials provided with the distribution.
+ * - Neither the name of JGraph nor the names of its contributors may be used
+ * to endorse or promote products derived from this software without specific
+ * prior written permission.
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ */
+package org.jgraph.layout;
+
+import cytoscape.Cytoscape;
+
+import org.jgraph.JGraph;
+
+import org.jgraph.graph.CellView;
+import org.jgraph.graph.EdgeView;
+import org.jgraph.graph.GraphConstants;
+import org.jgraph.graph.GraphModel;
+import org.jgraph.graph.PortView;
+import org.jgraph.graph.VertexView;
+
+import java.awt.Dimension;
+import java.awt.Insets;
+import java.awt.Point;
+import java.awt.Rectangle;
+import java.awt.geom.Rectangle2D;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+
+import javax.swing.JOptionPane;
+import javax.swing.SwingConstants;
+
+
+/**
+ * TODO:COMMENT ME!
+ *
+ * @author krueger
+ */
+public class TreeLayoutAlgorithm extends JGraphLayoutAlgorithm {
+ protected int alignment = SwingConstants.TOP;
+ protected int orientation = SwingConstants.NORTH;
+ protected int levelDistance = 30;
+ protected int nodeDistance = 20;
+ protected boolean centerRoot = false;
+ protected boolean combineLevelNodes = true;
+ private HashMap nodesSeen = new HashMap();
+ protected JGraph graph;
+ protected Map cell2node = new HashMap(); //CellView -> TreeNode
+
+ /**
+ * Returns the name of this algorithm in human
+ * readable form.
+ */
+ public String toString() {
+ return "Tree Layout";
+ }
+
+ /**
+ * Get a human readable hint for using this layout.
+ */
+ public String getHint() {
+ return "Select a root node";
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public JGraphLayoutSettings createSettings() {
+ return new TreeLayoutSettings(this);
+ }
+
+ /**
+ * SwingConstants.TOP
+ * SwingConstants.CENTER
+ * SwingConstants.BOTTOM
+ * @param alignment
+ */
+ public void setAlignment(int alignment) {
+ if ((alignment != SwingConstants.TOP) && (alignment != SwingConstants.CENTER)
+ && (alignment != SwingConstants.BOTTOM)) {
+ throw new IllegalArgumentException("Alignment must be one of TOP, CENTER or BOTTOM"); //$NON-NLS-1$
+ }
+
+ this.alignment = alignment;
+ }
+
+ /**
+ * SwingConstants.NORTH
+ * SwingConstants.EAST
+ * SwingConstants.SOUTH
+ * SwingConstants.WEST
+ * @param orientation
+ */
+ public void setOrientation(int orientation) {
+ if ((orientation != SwingConstants.NORTH) && (orientation != SwingConstants.EAST)
+ && (orientation != SwingConstants.SOUTH) && (orientation != SwingConstants.WEST)) {
+ throw new IllegalArgumentException("Orientation must be one of NORTH, EAST, SOUTH or WEST");
+ }
+
+ this.orientation = orientation;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param distance DOCUMENT ME!
+ */
+ public void setLevelDistance(int distance) {
+ levelDistance = distance;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param distance DOCUMENT ME!
+ */
+ public void setNodeDistance(int distance) {
+ nodeDistance = distance;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param b DOCUMENT ME!
+ */
+ public void setCenterRoot(boolean b) {
+ centerRoot = b;
+ }
+
+ /*
+ * @param graph JGraph instance
+ * @param dynamic_cells List of all nodes the layout should move
+ * @param static_cells List of node the layout should not move but allow for
+ */
+ /**
+ * DOCUMENT ME!
+ *
+ * @param graph DOCUMENT ME!
+ * @param dynamic_cells DOCUMENT ME!
+ * @param static_cells DOCUMENT ME!
+ */
+ public void run(JGraph graph, Object[] dynamic_cells, Object[] static_cells) {
+ this.graph = graph;
+
+ try {
+ List roots = getRootVertices(dynamic_cells);
+
+ if (roots == null)
+ return;
+
+ roots = buildTrees(roots);
+
+ if (roots == null)
+ return;
+
+ layoutTrees(roots);
+
+ if (canceled)
+ return;
+
+ if (combineLevelNodes) {
+ setLevelHeights(roots);
+ }
+
+ setPosition(roots);
+ } catch (Exception e) {
+ JOptionPane.showMessageDialog(Cytoscape.getDesktop(), e, "Error",
+ JOptionPane.INFORMATION_MESSAGE);
+ }
+ }
+
+ /**
+ * If it is a Vertex and it has no source, it must be a root vertex.
+ *
+ * !!!todo I will need to enforce that there is always at least one vertex,
+ * and that is the acq portal.
+ *
+ * @return all the tree root vertices
+ */
+ protected ArrayList getRootVertices(Object[] selectedCells) {
+ HashSet potentialRoot = new HashSet();
+ HashSet notARoot = new HashSet();
+ CellView viewTargetPort;
+ CellView viewTarget;
+
+ /*
+ * Loop through all the vertex and edge cells
+ */
+ for (int i = 0; i < selectedCells.length; i++) {
+ if (canceled)
+ return null;
+
+ Object view = graph.getGraphLayoutCache().getMapping(selectedCells[i], false);
+
+ /*
+ * If the vertex is not in the notARoot bucket, it is a potential
+ * root.
+ */
+ if (view instanceof VertexView) {
+ if (!(notARoot.contains(view))) {
+ potentialRoot.add(view);
+ }
+ }
+ /*
+ * The target of an edge is not a root.
+ */
+ else if (view instanceof EdgeView) {
+ viewTargetPort = ((EdgeView) view).getTarget();
+ viewTarget = viewTargetPort.getParentView();
+ potentialRoot.remove(viewTarget);
+ notARoot.add(viewTarget);
+ }
+ else if (view instanceof PortView) {
+ // Ignore ports
+ }
+ /*
+ * It should be impossible to get to the next statement
+ */
+ else {
+ throw new RuntimeException("Cell is other than Vertex or Edge.");
+ }
+ }
+
+ /*
+ * When the loop ends, only tree roots are left
+ */
+ return new ArrayList(potentialRoot);
+ }
+
+ /* Building Tree */
+ protected List buildTrees(List roots) throws Exception {
+ List l = new ArrayList();
+
+ for (Iterator it = roots.iterator(); it.hasNext();) {
+ if (canceled)
+ return null;
+
+ TreeNode tn = buildTree((CellView) it.next());
+
+ if (tn != null) {
+ l.add(tn);
+ }
+ }
+
+ return l;
+ }
+
+ protected TreeNode buildTree(CellView view) {
+ if (nodesSeen.containsKey(view))
+
+ // throw new RuntimeException("Detected loop in graph!");
+ return null;
+ else
+ nodesSeen.put(view, view);
+
+ List children = getChildren(view);
+ TreeNode node = getTreeNode(view);
+
+ for (Iterator it = children.iterator(); it.hasNext();) {
+ if (canceled)
+ return null;
+
+ CellView c = (CellView) it.next();
+
+ if (c == node)
+ return null;
+
+ TreeNode n = buildTree(c);
+
+ if (n == null)
+ return null;
+
+ node.children.add(n);
+ }
+
+ return node;
+ }
+
+ protected List getChildren(CellView view) {
+ ArrayList children = new ArrayList();
+ GraphModel model = graph.getModel();
+ Object cell = view.getCell();
+
+ for (int i = 0; i < model.getChildCount(cell); i++) {
+ if (canceled)
+ return null;
+
+ Object port = model.getChild(cell, i);
+
+ for (Iterator edges = model.edges(port); edges.hasNext();) {
+ Object edge = edges.next();
+
+ if (port == model.getSource(edge)) {
+ Object targetPort = model.getTarget(edge);
+ Object targetVertex = model.getParent(targetPort);
+ children.add(graph.getGraphLayoutCache().getMapping(targetVertex, false));
+ }
+ }
+ }
+
+ return children;
+ }
+
+ protected TreeNode getTreeNode(CellView view) {
+ Object o = cell2node.get(view);
+
+ if (o != null) {
+ return (TreeNode) o;
+ }
+
+ TreeNode node = new TreeNode(view);
+ cell2node.put(view, node);
+
+ return node;
+ }
+
+ /* Layout trees */
+ protected void layoutTrees(List roots) throws Exception {
+ for (Iterator it = roots.iterator(); it.hasNext();) {
+ if (canceled)
+ return;
+
+ layout((TreeNode) it.next());
+ }
+ }
+
+ protected void layout(TreeNode node) throws Exception {
+ if (node.isDone())
+ return;
+
+ node.setDone();
+
+ if (node.children.size() == 0) {
+ //do nothing
+ } else if (node.children.size() == 1) {
+ TreeNode sub = (TreeNode) node.children.get(0);
+ sub.depth = node.depth + 1;
+
+ if (sub.isDone()) {
+ throw new Exception("Loop detected in graph!");
+ }
+
+ layout(sub);
+
+ sub.leftContour.dx = (sub.width - node.width) / 2;
+ sub.rightContour.dx = (sub.width - node.width) / 2;
+
+ node.leftContour.next = sub.leftContour;
+ node.rightContour.next = sub.rightContour;
+ } else {
+ for (Iterator it = node.children.iterator(); it.hasNext();) {
+ TreeNode n = (TreeNode) it.next();
+ n.depth = node.depth + 1;
+
+ if (n.isDone()) {
+ throw new Exception("Loop detected in graph!");
+ }
+
+ layout(n);
+ }
+
+ join(node);
+ }
+ }
+
+ /* Joining trees */
+ protected void join(TreeNode node) {
+ int distance = 0;
+
+ for (int i = 0; i < node.children.size(); i++) {
+ TreeNode n1 = (TreeNode) node.children.get(i);
+
+ for (int j = i + 1; j < node.children.size(); j++) {
+ TreeNode n2 = (TreeNode) node.children.get(j);
+ int dist = distance(n1.rightContour, n2.leftContour) / (j - i);
+ distance = Math.max(distance, dist);
+ }
+ }
+
+ distance += nodeDistance;
+
+ //set relative position
+ int left;
+
+ if ((node.children.size() % 2) == 0) {
+ left = (((node.children.size() / 2) - 1) * distance) + (distance / 2);
+ } else {
+ left = node.children.size() / 2 * distance;
+ }
+
+ Iterator it = node.children.iterator();
+
+ for (int i = 0; it.hasNext(); i++) {
+ ((TreeNode) it.next()).x = -left + (i * distance);
+ }
+
+ //new contour
+ TreeNode first = getLeftMostX(node);
+ TreeNode last = getRightMostX(node);
+
+ node.leftContour.next = first.leftContour;
+ node.rightContour.next = last.rightContour;
+
+ for (int i = 1; i < node.children.size(); i++) {
+ TreeNode n = (TreeNode) node.children.get(i);
+ merge(node.leftContour.next, n.leftContour, (i * distance) + node.width);
+ }
+
+ for (int i = node.children.size() - 2; i >= 0; i--) {
+ TreeNode n = (TreeNode) node.children.get(i);
+ merge(node.rightContour.next, n.rightContour, (i * distance) + node.width);
+ }
+
+ distance = ((node.children.size() - 1) * distance) / 2;
+
+ node.leftContour.next.dx += (distance - (node.width / 2));
+ node.rightContour.next.dx += (distance - (node.width / 2));
+ }
+
+ protected TreeNode getLeftMostX(TreeNode node) {
+ int tmp = Integer.MAX_VALUE;
+ TreeNode mostLeft = null;
+ Iterator iter = node.getChildren();
+
+ while (iter.hasNext()) {
+ TreeNode child = (TreeNode) iter.next();
+
+ int leftPos = child.x - child.getLeftWidth();
+
+ if (leftPos < tmp) {
+ mostLeft = child;
+ tmp = leftPos;
+ }
+ }
+
+ return (mostLeft != null) ? mostLeft : (TreeNode) node.children.get(0);
+ }
+
+ protected TreeNode getRightMostX(TreeNode node) {
+ int tmp = Integer.MIN_VALUE;
+
+ TreeNode mostRight = null;
+ Iterator iter = node.getChildren();
+
+ while (iter.hasNext()) {
+ TreeNode child = (TreeNode) iter.next();
+
+ int rightPos = child.x + child.getRightWidth();
+
+ if (rightPos > tmp) {
+ mostRight = child;
+ tmp = rightPos;
+ }
+ }
+
+ return (mostRight != null) ? mostRight : (TreeNode) node.children.get(0);
+ }
+
+ protected void merge(PolyLine main, PolyLine left, int distance) {
+ while (main != null) {
+ if (left.next == null) {
+ return;
+ }
+
+ if (main.next == null) {
+ left = left.next;
+
+ break;
+ }
+
+ distance += (main.dx - left.dx);
+ main = main.next;
+ left = left.next;
+ }
+
+ left.dx += -distance;
+ main.next = left;
+ }
+
+ protected int distance(PolyLine right, PolyLine left) {
+ int distance = 0;
+
+ for (int i = 0; (right != null) && (left != null);) {
+ i += (right.dx + left.dx);
+
+ if (i > 0) {
+ distance += i;
+ i = 0;
+ }
+
+ right = right.next;
+ left = left.next;
+ }
+
+ return distance;
+ }
+
+ /* Positioning */
+ protected void setPosition(List roots) {
+ for (Iterator it = roots.iterator(); it.hasNext();) {
+ ((TreeNode) it.next()).setPosition(null, 0);
+ }
+ }
+
+ protected void setLevelHeights(List roots) {
+ for (Iterator it = roots.iterator(); it.hasNext();) {
+ List level = ((TreeNode) it.next()).getNodesByLevel();
+
+ int max = 0;
+
+ for (int i = 0; i < level.size(); i++) {
+ List l = (List) level.get(i);
+
+ for (int j = 0; j < l.size(); j++) {
+ max = Math.max(max, ((TreeNode) l.get(j)).height);
+ }
+
+ for (int j = 0; j < l.size(); j++) {
+ ((TreeNode) l.get(j)).levelheight = max;
+ }
+
+ max = 0;
+ }
+ }
+ }
+
+ protected class TreeNode {
+ List children;
+ int width;
+ int height;
+ int x;
+ int y;
+ int levelheight;
+ PolyLine leftContour;
+ PolyLine rightContour;
+ int depth;
+ boolean done;
+ CellView view;
+
+ public TreeNode(CellView view) {
+ this.view = view;
+
+ if ((orientation == SwingConstants.NORTH) || (orientation == SwingConstants.SOUTH)) {
+ width = (int) view.getBounds().getWidth();
+ height = (int) view.getBounds().getHeight();
+ } else {
+ width = (int) view.getBounds().getHeight();
+ height = (int) view.getBounds().getWidth();
+ }
+
+ this.children = new ArrayList();
+ this.leftContour = new PolyLine(width / 2);
+ this.rightContour = new PolyLine(width / 2);
+ this.depth = 0;
+ this.done = false;
+ }
+
+ public Iterator getChildren() {
+ return children.iterator();
+ }
+
+ public int getLeftWidth() {
+ int width = 0;
+
+ PolyLine poly = leftContour;
+ int tmp = 0;
+
+ while (poly != null) {
+ tmp += poly.dx;
+
+ if (tmp > 0) {
+ width += tmp;
+ tmp = 0;
+ }
+
+ poly = poly.next;
+ }
+
+ return width;
+ }
+
+ public boolean isDone() {
+ return this.done;
+ }
+
+ public void setDone() {
+ this.done = true;
+ }
+
+ public int getRightWidth() {
+ int width = 0;
+
+ PolyLine poly = rightContour;
+ int tmp = 0;
+
+ while (poly != null) {
+ tmp += poly.dx;
+
+ if (tmp > 0) {
+ width += tmp;
+ tmp = 0;
+ }
+
+ poly = poly.next;
+ }
+
+ return width;
+ }
+
+ public int getHeight() {
+ if (children.isEmpty()) {
+ return levelheight;
+ }
+
+ int height = 0;
+
+ for (Iterator it = children.iterator(); it.hasNext();) {
+ height = Math.max(height, ((TreeNode) it.next()).getHeight());
+ }
+
+ return height + levelDistance + levelheight;
+ }
+
+ public void setPosition(Point parent, int levelHeight) {
+ int nextLevelHeight = 0;
+
+ for (Iterator it = children.iterator(); it.hasNext();) {
+ nextLevelHeight = Math.max(nextLevelHeight, ((TreeNode) it.next()).height);
+ }
+
+ if (parent == null) {
+ Rectangle2D b = view.getBounds();
+ Rectangle bounds = new Rectangle((int) b.getX(), (int) b.getY(),
+ (int) b.getWidth(), (int) b.getHeight());
+ Point p = bounds.getLocation();
+
+ if (centerRoot) {
+ int lw = getLeftWidth();
+ int rw = getRightWidth();
+ int h = getHeight();
+
+ Insets i = graph.getInsets();
+
+ if (orientation == SwingConstants.NORTH) {
+ bounds.x = lw - (width / 2);
+ bounds.y = i.top;
+ } else if (orientation == SwingConstants.EAST) {
+ bounds.x = (i.left + h) - width;
+ bounds.y = lw - (height / 2);
+ } else if (orientation == SwingConstants.SOUTH) {
+ bounds.x = lw - (width / 2);
+ bounds.y = i.top + h;
+ } else if (orientation == SwingConstants.WEST) {
+ bounds.x = i.right;
+ bounds.y = lw - (width / 2);
+ }
+
+ Object cell = view.getCell();
+ Map attributes = GraphConstants.createAttributes(cell, GraphConstants.BOUNDS,
+ bounds);
+ graph.getGraphLayoutCache().edit(attributes, null, null, null);
+
+ if ((orientation == SwingConstants.WEST)
+ || (orientation == SwingConstants.EAST)) {
+ graph.setPreferredSize(new Dimension(h + i.left + i.right,
+ lw + rw + i.top + i.bottom));
+ } else {
+ graph.setPreferredSize(new Dimension(lw + rw + i.left + i.right,
+ h + i.top + i.bottom));
+ }
+
+ p = bounds.getLocation();
+ }
+
+ if ((orientation == SwingConstants.WEST) || (orientation == SwingConstants.EAST)) {
+ int tmp = p.x;
+ p.x = p.y;
+ p.y = tmp;
+ }
+
+ if ((orientation == SwingConstants.NORTH) || (orientation == SwingConstants.WEST)) {
+ parent = new Point(p.x + (width / 2), p.y + height);
+ } else if ((orientation == SwingConstants.SOUTH)
+ || (orientation == SwingConstants.EAST)) {
+ parent = new Point(p.x + (width / 2), p.y);
+ }
+
+ for (Iterator it = children.iterator(); it.hasNext();) {
+ ((TreeNode) it.next()).setPosition(parent, nextLevelHeight);
+ }
+
+ return;
+ }
+
+ if (combineLevelNodes) {
+ levelHeight = this.levelheight;
+ }
+
+ Rectangle cellBounds = new Rectangle(width, height);
+
+ if ((orientation == SwingConstants.NORTH) || (orientation == SwingConstants.WEST)) {
+ cellBounds.x = (x + parent.x) - (width / 2);
+ cellBounds.y = parent.y + levelDistance;
+ } else {
+ cellBounds.x = (x + parent.x) - (width / 2);
+ cellBounds.y = parent.y - levelDistance - levelheight;
+ }
+
+ if (alignment == SwingConstants.CENTER) {
+ cellBounds.y += ((levelHeight - height) / 2);
+ } else if (alignment == SwingConstants.BOTTOM) {
+ cellBounds.y += (levelHeight - height);
+ }
+
+ if ((orientation == SwingConstants.WEST) || (orientation == SwingConstants.EAST)) {
+ int tmp = cellBounds.x;
+ cellBounds.x = cellBounds.y;
+ cellBounds.y = tmp;
+
+ tmp = cellBounds.width;
+ cellBounds.width = cellBounds.height;
+ cellBounds.height = tmp;
+ }
+
+ Object cell = view.getCell();
+ Map attributes = GraphConstants.createAttributes(cell, GraphConstants.BOUNDS, cellBounds);
+ graph.getGraphLayoutCache().edit(attributes, null, null, null);
+
+ if ((orientation == SwingConstants.NORTH) || (orientation == SwingConstants.WEST)) {
+ y = parent.y + levelDistance + levelHeight;
+ } else {
+ y = parent.y - levelDistance - levelHeight;
+ }
+
+ for (Iterator it = children.iterator(); it.hasNext();) {
+ ((TreeNode) it.next()).setPosition(new Point(x + parent.x, y), nextLevelHeight);
+ }
+ }
+
+ public List getNodesByLevel() {
+ List level = new ArrayList();
+
+ for (Iterator it = children.iterator(); it.hasNext();) {
+ List l2 = ((TreeNode) it.next()).getNodesByLevel();
+
+ if (level.size() < l2.size()) {
+ List tmp = level;
+ level = l2;
+ l2 = tmp;
+ }
+
+ for (int i = 0; i < l2.size(); i++) {
+ ((List) level.get(i)).addAll((List) l2.get(i));
+ }
+ }
+
+ ArrayList node = new ArrayList();
+ node.add(this);
+ level.add(0, node);
+
+ return level;
+ }
+ }
+
+ protected class PolyLine {
+ int dx;
+ PolyLine next;
+
+ public PolyLine(int dx) {
+ this.dx = dx;
+ }
+ }
+
+ /**
+ * @return Returns the combineLevelNodes.
+ */
+ public boolean isCombineLevelNodes() {
+ return combineLevelNodes;
+ }
+
+ /**
+ * @param combineLevelNodes The combineLevelNodes to set.
+ */
+ public void setCombineLevelNodes(boolean combineLevelNodes) {
+ this.combineLevelNodes = combineLevelNodes;
+ }
+
+ /**
+ * @return Returns the alignment.
+ */
+ public int getAlignment() {
+ return alignment;
+ }
+
+ /**
+ * @return Returns the centerRoot.
+ */
+ public boolean isCenterRoot() {
+ return centerRoot;
+ }
+
+ /**
+ * @return Returns the levelDistance.
+ */
+ public int getLevelDistance() {
+ return levelDistance;
+ }
+
+ /**
+ * @return Returns the nodeDistance.
+ */
+ public int getNodeDistance() {
+ return nodeDistance;
+ }
+
+ /**
+ * @return Returns the orientation.
+ */
+ public int getOrientation() {
+ return orientation;
+ }
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/layout/TreeLayoutSettings.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/layout/TreeLayoutSettings.java
new file mode 100644
index 0000000..19e7127
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/layout/TreeLayoutSettings.java
@@ -0,0 +1,182 @@
+/*
+ * @(#)TreeLayoutSettings.java 1.0 12-JUL-2004
+ *
+ * Copyright (c) 2004-2005, Gaudenz Alder
+ * All rights reserved.
+ *
+ * This library is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation; either
+ * version 2.1 of the License, or (at your option) any later version.
+ *
+ * This library is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this library; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+ */
+package org.jgraph.layout;
+
+import java.awt.BorderLayout;
+import java.awt.GridLayout;
+
+import javax.swing.JComboBox;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JTextField;
+import javax.swing.SwingConstants;
+
+
+/**
+ * A Dialog for configuring a TreeLayoutAlgorithm.
+ * You can use horizontal and vertical spacing.<br>
+ *<br>
+ *<br>
+ * @author Gaudenz Alder<br>
+ * @version 1.0 init
+ */
+public class TreeLayoutSettings extends JPanel implements JGraphLayoutSettings {
+ protected TreeLayoutAlgorithm layout;
+ private JComboBox alignmentCombo = new JComboBox(new Object[] { "Top", "Center", "Bottom" });
+ private JComboBox orientationCombo = new JComboBox(new Object[] { "North", "East", "South", "West" });
+ private JTextField nodeDistanceTextField = new JTextField();
+ private JTextField levelDistanceTextField = new JTextField();
+
+ /**
+ * Creates new form SugiyamaLayoutConfigurationDialog
+ */
+ public TreeLayoutSettings(TreeLayoutAlgorithm layout) {
+ this.layout = layout;
+
+ JPanel jPanel1 = new javax.swing.JPanel(new GridLayout(4, 2, 4, 4));
+ jPanel1.add(new JLabel("Alignment"));
+ jPanel1.add(alignmentCombo);
+ jPanel1.add(new JLabel("Orientation"));
+ jPanel1.add(orientationCombo);
+ jPanel1.add(new JLabel("Node Distance"));
+ jPanel1.add(nodeDistanceTextField);
+ jPanel1.add(new JLabel("Level Distance"));
+ jPanel1.add(levelDistanceTextField);
+ add(jPanel1, BorderLayout.CENTER);
+ revert();
+ }
+
+ /**
+ * Implementation.
+ */
+ public void revert() {
+ setAlignment(layout.getAlignment());
+ setOrientation(layout.getOrientation());
+ nodeDistanceTextField.setText(String.valueOf(layout.getNodeDistance()));
+ levelDistanceTextField.setText(String.valueOf(layout.getLevelDistance()));
+ }
+
+ private void check() {
+ try {
+ Integer.parseInt(nodeDistanceTextField.getText());
+ Integer.parseInt(levelDistanceTextField.getText());
+ } catch (Exception e) {
+ throw new IllegalArgumentException(e.getMessage());
+ }
+ }
+
+ /**
+ * Implementation.
+ */
+ public void apply() {
+ check();
+ layout.setAlignment(getAlignment());
+ layout.setOrientation(getOrientation());
+ layout.setNodeDistance(Integer.parseInt(nodeDistanceTextField.getText()));
+ layout.setLevelDistance(Integer.parseInt(levelDistanceTextField.getText()));
+ }
+
+ /**
+ * Returns the value of the "Horizontal spacing" as text.
+ */
+ public int getAlignment() {
+ int result = SwingConstants.TOP;
+
+ switch (alignmentCombo.getSelectedIndex()) {
+ case 1:
+ result = SwingConstants.CENTER;
+
+ break;
+
+ case 2:
+ result = SwingConstants.BOTTOM;
+ }
+
+ return result;
+ }
+
+ /**
+ * Set the value of the "Horizontal spacing" text field.
+ */
+ public void setAlignment(int alignment) {
+ int index = 0;
+
+ switch (alignment) {
+ case SwingConstants.CENTER:
+ index = 1;
+
+ break;
+
+ case SwingConstants.BOTTOM:
+ index = 2;
+ }
+
+ alignmentCombo.setSelectedIndex(index);
+ }
+
+ /**
+ * Returns the value of the "Vertical spacing" as text.
+ */
+ public int getOrientation() {
+ int result = SwingConstants.NORTH;
+
+ switch (orientationCombo.getSelectedIndex()) {
+ case 1:
+ result = SwingConstants.EAST;
+
+ break;
+
+ case 2:
+ result = SwingConstants.SOUTH;
+
+ break;
+
+ case 3:
+ result = SwingConstants.WEST;
+ }
+
+ return result;
+ }
+
+ /**
+ * Set the value of the "Vertical Spacing" text field.
+ */
+ public void setOrientation(int orientation) {
+ int index = 0;
+
+ switch (orientation) {
+ case SwingConstants.EAST:
+ index = 1;
+
+ break;
+
+ case SwingConstants.SOUTH:
+ index = 2;
+
+ break;
+
+ case SwingConstants.WEST:
+ index = 3;
+ }
+
+ orientationCombo.setSelectedIndex(index);
+ }
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/plaf/GraphUI.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/plaf/GraphUI.java
new file mode 100644
index 0000000..8aee3e1
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/plaf/GraphUI.java
@@ -0,0 +1,110 @@
+/*
+ * @(#)GraphUI.java 1.0 03-JUL-04
+ *
+ * Copyright (c) 2001-2004 Gaudenz Alder
+ *
+ */
+package org.jgraph.plaf;
+
+import org.jgraph.JGraph;
+
+import org.jgraph.graph.CellHandle;
+import org.jgraph.graph.CellView;
+
+import java.awt.Graphics;
+import java.awt.Point;
+import java.awt.event.MouseEvent;
+import java.awt.geom.Dimension2D;
+import java.awt.geom.Rectangle2D;
+
+import javax.swing.plaf.ComponentUI;
+
+
+/**
+ * Pluggable look and feel interface for JGraph.
+ *
+ * @version 1.0 1/1/02
+ * @author Gaudenz Alder
+ */
+public abstract class GraphUI extends ComponentUI {
+ /**
+ * Paints the renderer of <code>view</code> to <code>g</code>
+ * at <code>bounds</code>.
+ */
+ public abstract void paintCell(Graphics g, CellView view, Rectangle2D bounds, boolean preview);
+
+ /**
+ * Paints the renderers of <code>portViews</code> to <code>g</code>.
+ */
+ public abstract void paintPorts(Graphics g, CellView[] portViews);
+
+ /**
+ * Messaged to update the selection based on a MouseEvent for a group of
+ * cells. If the event is a toggle selection event, the cells are either
+ * selected, or deselected. Otherwise the cells are selected.
+ */
+ public abstract void selectCellsForEvent(JGraph graph, Object[] cells, MouseEvent event);
+
+ /**
+ * Returns the preferred size for <code>view</code>.
+ */
+ public abstract Dimension2D getPreferredSize(JGraph graph, CellView view);
+
+ /**
+ * Returns the <code>CellHandle</code> that is currently active,
+ * or <code>null</code> if no handle is active.
+ */
+ public abstract CellHandle getHandle();
+
+ /**
+ * Returns true if the graph is being edited. The item that is being
+ * edited can be returned by getEditingCell().
+ */
+ public abstract boolean isEditing(JGraph graph);
+
+ /**
+ * Stops the current editing session. This has no effect if the
+ * graph isn't being edited. Returns true if the editor allows the
+ * editing session to stop.
+ */
+ public abstract boolean stopEditing(JGraph graph);
+
+ /**
+ * Cancels the current editing session. This has no effect if the
+ * graph isn't being edited. Returns true if the editor allows the
+ * editing session to stop.
+ */
+ public abstract void cancelEditing(JGraph graph);
+
+ /**
+ * Selects the cell and tries to edit it. Editing will
+ * fail if the CellEditor won't allow it for the selected item.
+ */
+ public abstract void startEditingAtCell(JGraph graph, Object cell);
+
+ /**
+ * Returns the cell that is being edited.
+ */
+ public abstract Object getEditingCell(JGraph graph);
+
+ /**
+ * Sets the current location for Drag-and-Drop activity. Should be set to
+ * null after a drop.
+ */
+ public abstract void setInsertionLocation(Point p);
+
+ /**
+ * Returns the insertion location for DnD operations.
+ */
+ public abstract Point getInsertionLocation();
+
+ /**
+ * Updates the handle.
+ */
+ public abstract void updateHandle();
+
+ /**
+ * Returns the current drop action.
+ */
+ public abstract int getDropAction();
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/plaf/basic/BasicGraphDropTargetListener.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/plaf/basic/BasicGraphDropTargetListener.java
new file mode 100644
index 0000000..38c95e0
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/plaf/basic/BasicGraphDropTargetListener.java
@@ -0,0 +1,280 @@
+/*
+ * @(#)BasicGraphDropTargetListener 1.0 03-JUL-04
+ *
+ * Copyright (c) 2001-2004 Gaudenz Alder
+ *
+ */
+package org.jgraph.plaf.basic;
+
+import java.awt.Insets;
+import java.awt.Point;
+import java.awt.Rectangle;
+import java.awt.Toolkit;
+import java.awt.dnd.DropTargetContext;
+import java.awt.dnd.DropTargetDragEvent;
+import java.awt.dnd.DropTargetDropEvent;
+import java.awt.dnd.DropTargetEvent;
+import java.awt.dnd.DropTargetListener;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import javax.swing.JComponent;
+import javax.swing.Scrollable;
+import javax.swing.SwingConstants;
+import javax.swing.Timer;
+import javax.swing.plaf.UIResource;
+
+
+/**
+ *
+ */
+public class BasicGraphDropTargetListener implements DropTargetListener, UIResource, ActionListener {
+ /**
+ * construct a DropTargetAutoScroller
+ */
+ public BasicGraphDropTargetListener() {
+ }
+
+ /**
+ * called to save the state of a component in case it needs to
+ * be restored because a drop is not performed.
+ */
+ protected void saveComponentState(JComponent c) {
+ }
+
+ /**
+ * called to restore the state of a component in case a drop
+ * is not performed.
+ */
+ protected void restoreComponentState(JComponent c) {
+ }
+
+ /**
+ * called to restore the state of a component in case a drop
+ * is performed.
+ */
+ protected void restoreComponentStateForDrop(JComponent c) {
+ }
+
+ /**
+ * called to set the insertion location to match the current
+ * mouse pointer coordinates.
+ */
+ protected void updateInsertionLocation(JComponent c, Point p) {
+ }
+
+ /**
+ * Update the geometry of the autoscroll region. The geometry is
+ * maintained as a pair of rectangles. The region can cause
+ * a scroll if the pointer sits inside it for the duration of the
+ * timer. The region that causes the timer countdown is the area
+ * between the two rectangles.
+ * <p>
+ * This is implemented to use the visible area of the component
+ * as the outer rectangle and the insets are based upon the
+ * Scrollable information (if any). If the Scrollable is
+ * scrollable along an axis, the step increment is used as
+ * the autoscroll inset. If the component is not scrollable,
+ * the insets will be zero (i.e. autoscroll will not happen).
+ */
+ void updateAutoscrollRegion(JComponent c) {
+ // compute the outer
+ Rectangle visible = c.getVisibleRect();
+ outer.setBounds(visible.x, visible.y, visible.width, visible.height);
+
+ // compute the insets
+ // TBD - the thing with the scrollable
+ Insets i = new Insets(0, 0, 0, 0);
+
+ if (c instanceof Scrollable) {
+ Scrollable s = (Scrollable) c;
+ i.left = s.getScrollableUnitIncrement(visible, SwingConstants.HORIZONTAL, 1);
+ i.top = s.getScrollableUnitIncrement(visible, SwingConstants.VERTICAL, 1);
+ i.right = s.getScrollableUnitIncrement(visible, SwingConstants.HORIZONTAL, -1);
+ i.bottom = s.getScrollableUnitIncrement(visible, SwingConstants.VERTICAL, -1);
+ }
+
+ // set the inner from the insets
+ inner.setBounds(visible.x + i.left, visible.y + i.top, visible.width - (i.left + i.right),
+ visible.height - (i.top + i.bottom));
+ }
+
+ /**
+ * Perform an autoscroll operation. This is implemented to scroll by the
+ * unit increment of the Scrollable using scrollRectToVisible. If the
+ * cursor is in a corner of the autoscroll region, more than one axis will
+ * scroll.
+ */
+ void autoscroll(JComponent c, Point pos) {
+ if (c instanceof org.jgraph.JGraph)
+ BasicGraphUI.autoscroll((org.jgraph.JGraph) c, pos);
+ }
+
+ /**
+ * Initializes the internal properties if they haven't been already
+ * inited. This is done lazily to avoid loading of desktop properties.
+ */
+ private void initPropertiesIfNecessary() {
+ if (timer == null) {
+ Toolkit t = Toolkit.getDefaultToolkit();
+ Integer initial = new Integer(100);
+ Integer interval = new Integer(100);
+
+ try {
+ initial = (Integer) t.getDesktopProperty("DnD.Autoscroll.initialDelay");
+ } catch (Exception e) {
+ // ignore
+ }
+
+ try {
+ interval = (Integer) t.getDesktopProperty("DnD.Autoscroll.interval");
+ } catch (Exception e) {
+ // ignore
+ }
+
+ timer = new Timer(interval.intValue(), this);
+
+ timer.setCoalesce(true);
+ timer.setInitialDelay(initial.intValue());
+
+ try {
+ hysteresis = ((Integer) t.getDesktopProperty("DnD.Autoscroll.cursorHysteresis"))
+ .intValue();
+ } catch (Exception e) {
+ // ignore
+ }
+ }
+ }
+
+ static JComponent getComponent(DropTargetEvent e) {
+ DropTargetContext context = e.getDropTargetContext();
+
+ return (JComponent) context.getComponent();
+ }
+
+ // --- ActionListener methods --------------------------------------
+
+ /**
+ * The timer fired, perform autoscroll if the pointer is within the
+ * autoscroll region.
+ * <P>
+ * @param e the <code>ActionEvent</code>
+ */
+ public synchronized void actionPerformed(ActionEvent e) {
+ updateAutoscrollRegion(component);
+
+ if (outer.contains(lastPosition) && !inner.contains(lastPosition)) {
+ autoscroll(component, lastPosition);
+ }
+ }
+
+ // --- DropTargetListener methods -----------------------------------
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void dragEnter(DropTargetDragEvent e) {
+ component = getComponent(e);
+
+ // DO NOT REMOVE OR MODIFY THIS LINE!
+ javax.swing.TransferHandler // JAVA13: org.jgraph.plaf.basic.TransferHandler
+ th = ((JComponent) component).getTransferHandler();
+ canImport = th.canImport(component, e.getCurrentDataFlavors());
+
+ if (canImport) {
+ saveComponentState(component);
+ lastPosition = e.getLocation();
+ updateAutoscrollRegion(component);
+ initPropertiesIfNecessary();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void dragOver(DropTargetDragEvent e) {
+ if (canImport) {
+ Point p = e.getLocation();
+ updateInsertionLocation(component, p);
+
+ // check autoscroll
+ synchronized (this) {
+ if ((Math.abs(p.x - lastPosition.x) > hysteresis)
+ || (Math.abs(p.y - lastPosition.y) > hysteresis)) {
+ // no autoscroll
+ if (timer.isRunning())
+ timer.stop();
+ } else {
+ if (!timer.isRunning())
+ timer.start();
+ }
+
+ lastPosition = p;
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void dragExit(DropTargetEvent e) {
+ if (canImport) {
+ restoreComponentState(component);
+ }
+
+ cleanup();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void drop(DropTargetDropEvent e) {
+ if (canImport) {
+ restoreComponentStateForDrop(component);
+ }
+
+ cleanup();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void dropActionChanged(DropTargetDragEvent e) {
+ }
+
+ /**
+ * Cleans up internal state after the drop has finished (either succeeded
+ * or failed).
+ */
+ private void cleanup() {
+ if (timer != null) {
+ timer.stop();
+ }
+
+ component = null;
+ lastPosition = null;
+ }
+
+ // --- fields --------------------------------------------------
+ private Timer timer;
+ private Point lastPosition;
+ private Rectangle outer = new Rectangle();
+ private Rectangle inner = new Rectangle();
+ private int hysteresis = 10;
+ private boolean canImport;
+
+ /**
+ * The current component. The value is cached from the drop events and used
+ * by the timer. When a drag exits or a drop occurs, this value is cleared.
+ */
+ private JComponent component;
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/plaf/basic/BasicGraphTransferable.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/plaf/basic/BasicGraphTransferable.java
new file mode 100644
index 0000000..d29a22d
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/plaf/basic/BasicGraphTransferable.java
@@ -0,0 +1,277 @@
+/*
+ * @(#)BasicGraphTransferable 1.0 03-JUL-04
+ *
+ * Copyright (c) 2001-2004 Gaudenz Alder
+ *
+ */
+package org.jgraph.plaf.basic;
+
+import java.awt.datatransfer.DataFlavor;
+import java.awt.datatransfer.Transferable;
+import java.awt.datatransfer.UnsupportedFlavorException;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.StringBufferInputStream;
+import java.io.StringReader;
+
+import javax.swing.plaf.UIResource;
+
+
+/**
+ *
+ */
+public class BasicGraphTransferable implements Transferable, UIResource, Serializable {
+ private static DataFlavor[] htmlFlavors;
+ private static DataFlavor[] stringFlavors;
+ private static DataFlavor[] plainFlavors;
+
+ static {
+ try {
+ htmlFlavors = new DataFlavor[3];
+ htmlFlavors[0] = new DataFlavor("text/html;class=java.lang.String");
+ htmlFlavors[1] = new DataFlavor("text/html;class=java.io.Reader");
+ htmlFlavors[2] = new DataFlavor("text/html;charset=unicode;class=java.io.InputStream");
+
+ plainFlavors = new DataFlavor[3];
+ plainFlavors[0] = new DataFlavor("text/plain;class=java.lang.String");
+ plainFlavors[1] = new DataFlavor("text/plain;class=java.io.Reader");
+ plainFlavors[2] = new DataFlavor("text/plain;charset=unicode;class=java.io.InputStream");
+
+ stringFlavors = new DataFlavor[2];
+ stringFlavors[0] = new DataFlavor(DataFlavor.javaJVMLocalObjectMimeType
+ + ";class=java.lang.String");
+ stringFlavors[1] = DataFlavor.stringFlavor;
+ } catch (ClassNotFoundException cle) {
+ System.err.println("error initializing javax.swing.plaf.basic.BasicTranserable");
+ }
+ }
+
+ /**
+ * Returns an array of DataFlavor objects indicating the flavors the data
+ * can be provided in. The array should be ordered according to preference
+ * for providing the data (from most richly descriptive to least descriptive).
+ * @return an array of data flavors in which this data can be transferred
+ */
+ public DataFlavor[] getTransferDataFlavors() {
+ DataFlavor[] richerFlavors = getRicherFlavors();
+ int nRicher = (richerFlavors != null) ? richerFlavors.length : 0;
+ int nHTML = (isHTMLSupported()) ? htmlFlavors.length : 0;
+ int nPlain = (isPlainSupported()) ? plainFlavors.length : 0;
+ int nString = (isPlainSupported()) ? stringFlavors.length : 0;
+ int nFlavors = nRicher + nHTML + nPlain + nString;
+ DataFlavor[] flavors = new DataFlavor[nFlavors];
+
+ // fill in the array
+ int nDone = 0;
+
+ if (nRicher > 0) {
+ System.arraycopy(richerFlavors, 0, flavors, nDone, nRicher);
+ nDone += nRicher;
+ }
+
+ if (nHTML > 0) {
+ System.arraycopy(htmlFlavors, 0, flavors, nDone, nHTML);
+ nDone += nHTML;
+ }
+
+ if (nPlain > 0) {
+ System.arraycopy(plainFlavors, 0, flavors, nDone, nPlain);
+ nDone += nPlain;
+ }
+
+ if (nString > 0) {
+ System.arraycopy(stringFlavors, 0, flavors, nDone, nString);
+ nDone += nString;
+ }
+
+ return flavors;
+ }
+
+ /**
+ * Returns whether or not the specified data flavor is supported for
+ * this object.
+ * @param flavor the requested flavor for the data
+ * @return boolean indicating whether or not the data flavor is supported
+ */
+ public boolean isDataFlavorSupported(DataFlavor flavor) {
+ DataFlavor[] flavors = getTransferDataFlavors();
+
+ for (int i = 0; i < flavors.length; i++) {
+ if (flavors[i].equals(flavor)) {
+ return true;
+ }
+ }
+
+ return false;
+ }
+
+ /**
+ * Returns an object which represents the data to be transferred. The class
+ * of the object returned is defined by the representation class of the flavor.
+ *
+ * @param flavor the requested flavor for the data
+ * @see DataFlavor#getRepresentationClass
+ * @exception IOException if the data is no longer available
+ * in the requested flavor.
+ * @exception UnsupportedFlavorException if the requested data flavor is
+ * not supported.
+ */
+ public Object getTransferData(DataFlavor flavor) throws UnsupportedFlavorException, IOException {
+ if (isRicherFlavor(flavor)) {
+ return getRicherData(flavor);
+ } else if (isHTMLFlavor(flavor)) {
+ String data = getHTMLData();
+ data = (data == null) ? "" : data;
+
+ if (String.class.equals(flavor.getRepresentationClass())) {
+ return data;
+ } else if (Reader.class.equals(flavor.getRepresentationClass())) {
+ return new StringReader(data);
+ } else if (InputStream.class.equals(flavor.getRepresentationClass())) {
+ return new StringBufferInputStream(data);
+ }
+
+ // fall through to unsupported
+ } else if (isPlainFlavor(flavor)) {
+ String data = getPlainData();
+ data = (data == null) ? "" : data;
+
+ if (String.class.equals(flavor.getRepresentationClass())) {
+ return data;
+ } else if (Reader.class.equals(flavor.getRepresentationClass())) {
+ return new StringReader(data);
+ } else if (InputStream.class.equals(flavor.getRepresentationClass())) {
+ return new StringBufferInputStream(data);
+ }
+
+ // fall through to unsupported
+ } else if (isStringFlavor(flavor)) {
+ String data = getPlainData();
+ data = (data == null) ? "" : data;
+
+ return data;
+ }
+
+ throw new UnsupportedFlavorException(flavor);
+ }
+
+ // --- richer subclass flavors ----------------------------------------------
+ protected boolean isRicherFlavor(DataFlavor flavor) {
+ DataFlavor[] richerFlavors = getRicherFlavors();
+ int nFlavors = (richerFlavors != null) ? richerFlavors.length : 0;
+
+ for (int i = 0; i < nFlavors; i++) {
+ if (richerFlavors[i].equals(flavor)) {
+ return true;
+ }
+ }
+
+ return false;
+ }
+
+ /**
+ * Some subclasses will have flavors that are more descriptive than HTML
+ * or plain text. If this method returns a non-null value, it will be
+ * placed at the start of the array of supported flavors.
+ */
+ protected DataFlavor[] getRicherFlavors() {
+ return null;
+ }
+
+ protected Object getRicherData(DataFlavor flavor) throws UnsupportedFlavorException {
+ return null;
+ }
+
+ // --- html flavors ----------------------------------------------------------
+
+ /**
+ * Returns whether or not the specified data flavor is an HTML flavor that
+ * is supported.
+ * @param flavor the requested flavor for the data
+ * @return boolean indicating whether or not the data flavor is supported
+ */
+ protected boolean isHTMLFlavor(DataFlavor flavor) {
+ DataFlavor[] flavors = htmlFlavors;
+
+ for (int i = 0; i < flavors.length; i++) {
+ if (flavors[i].equals(flavor)) {
+ return true;
+ }
+ }
+
+ return false;
+ }
+
+ /**
+ * Whether the HTML flavors are offered. If so, the method
+ * getHTMLData should be implemented to provide something reasonable.
+ */
+ protected boolean isHTMLSupported() {
+ return false;
+ }
+
+ /**
+ * Fetch the data in a text/html format
+ */
+ protected String getHTMLData() {
+ return null;
+ }
+
+ // --- plain text flavors ----------------------------------------------------
+
+ /**
+ * Returns whether or not the specified data flavor is an plain flavor that
+ * is supported.
+ * @param flavor the requested flavor for the data
+ * @return boolean indicating whether or not the data flavor is supported
+ */
+ protected boolean isPlainFlavor(DataFlavor flavor) {
+ DataFlavor[] flavors = plainFlavors;
+
+ for (int i = 0; i < flavors.length; i++) {
+ if (flavors[i].equals(flavor)) {
+ return true;
+ }
+ }
+
+ return false;
+ }
+
+ /**
+ * Whether the plain text flavors are offered. If so, the method
+ * getPlainData should be implemented to provide something reasonable.
+ */
+ protected boolean isPlainSupported() {
+ return false;
+ }
+
+ /**
+ * Fetch the data in a text/plain format.
+ */
+ protected String getPlainData() {
+ return null;
+ }
+
+ // --- string flavorss --------------------------------------------------------
+
+ /**
+ * Returns whether or not the specified data flavor is a String flavor that
+ * is supported.
+ * @param flavor the requested flavor for the data
+ * @return boolean indicating whether or not the data flavor is supported
+ */
+ protected boolean isStringFlavor(DataFlavor flavor) {
+ DataFlavor[] flavors = stringFlavors;
+
+ for (int i = 0; i < flavors.length; i++) {
+ if (flavors[i].equals(flavor)) {
+ return true;
+ }
+ }
+
+ return false;
+ }
+}
diff --git a/coreplugins/AutomaticLayout/src/main/java/org/jgraph/plaf/basic/BasicGraphUI.java b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/plaf/basic/BasicGraphUI.java
new file mode 100644
index 0000000..adf84e8
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/org/jgraph/plaf/basic/BasicGraphUI.java
@@ -0,0 +1,3066 @@
+/*
+ * @(#)BasicGraphUI.java 1.0 03-JUL-04
+ *
+ * Copyright (c) 2001-2004 Gaudenz Alder
+ *
+ */
+package org.jgraph.plaf.basic;
+
+import org.jgraph.JGraph;
+
+import org.jgraph.event.GraphLayoutCacheEvent;
+import org.jgraph.event.GraphLayoutCacheListener;
+import org.jgraph.event.GraphModelEvent;
+import org.jgraph.event.GraphModelListener;
+import org.jgraph.event.GraphSelectionEvent;
+import org.jgraph.event.GraphSelectionListener;
+
+import org.jgraph.graph.AbstractCellView;
+import org.jgraph.graph.AttributeMap;
+import org.jgraph.graph.BasicMarqueeHandler;
+import org.jgraph.graph.CellHandle;
+import org.jgraph.graph.CellView;
+import org.jgraph.graph.CellViewRenderer;
+import org.jgraph.graph.ConnectionSet;
+import org.jgraph.graph.DefaultGraphModel;
+import org.jgraph.graph.EdgeRenderer;
+import org.jgraph.graph.EdgeView;
+import org.jgraph.graph.GraphCell;
+import org.jgraph.graph.GraphCellEditor;
+import org.jgraph.graph.GraphConstants;
+import org.jgraph.graph.GraphContext;
+import org.jgraph.graph.GraphLayoutCache;
+import org.jgraph.graph.GraphModel;
+import org.jgraph.graph.GraphSelectionModel;
+import org.jgraph.graph.GraphTransferHandler;
+import org.jgraph.graph.ParentMap;
+import org.jgraph.graph.PortView;
+
+import org.jgraph.plaf.GraphUI;
+
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Cursor;
+import java.awt.Dimension;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.Image;
+import java.awt.Insets;
+import java.awt.Point;
+import java.awt.Rectangle;
+import java.awt.RenderingHints;
+import java.awt.Toolkit;
+import java.awt.dnd.DropTarget;
+import java.awt.dnd.DropTargetDragEvent;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ComponentAdapter;
+import java.awt.event.ComponentEvent;
+import java.awt.event.ComponentListener;
+import java.awt.event.InputEvent;
+import java.awt.event.KeyAdapter;
+import java.awt.event.KeyEvent;
+import java.awt.event.KeyListener;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.awt.geom.AffineTransform;
+import java.awt.geom.Dimension2D;
+import java.awt.geom.Point2D;
+import java.awt.geom.Rectangle2D;
+import java.awt.image.BufferedImage;
+
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+
+import java.io.Serializable;
+
+import java.util.Map;
+import java.util.TooManyListenersException;
+
+import javax.swing.AbstractAction;
+import javax.swing.Action;
+import javax.swing.ActionMap;
+import javax.swing.CellRendererPane;
+import javax.swing.InputMap;
+import javax.swing.JComponent;
+import javax.swing.JScrollBar;
+import javax.swing.JScrollPane;
+import javax.swing.JViewport;
+import javax.swing.KeyStroke;
+import javax.swing.SwingUtilities;
+import javax.swing.Timer;
+import javax.swing.TransferHandler;
+import javax.swing.UIManager;
+import javax.swing.event.CellEditorListener;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.MouseInputListener;
+import javax.swing.plaf.ActionMapUIResource;
+import javax.swing.plaf.ComponentUI;
+import javax.swing.plaf.UIResource;
+
+
+/**
+ * The basic L&F for a graph data structure.
+ *
+ * @version 1.0 1/1/02
+ * @author Gaudenz Alder
+ */
+public class BasicGraphUI extends GraphUI implements Serializable {
+ /**
+ * Controls live-preview in dragEnabled mode. This is used to disable
+ * live-preview in dragEnabled mode on Java 1.4.0 to workaround a bug that
+ * cause the VM to hang during concurrent DnD and repaints. Is this still
+ * required?
+ */
+ public static final boolean DNDPREVIEW = (System.getProperty("java.version").compareTo("1.4.0") < 0)
+ || (System.getProperty("java.version")
+ .compareTo("1.4.0") > 0);
+
+ /** Border in pixels to scroll if marquee or dragging are active. */
+ public static int SCROLLBORDER = 18;
+
+ /** Multiplicator for width and height when autoscrolling (=stepsize). */
+ public static float SCROLLSTEP = 0.05f;
+
+ /** The maximum number of cells to paint when dragging. */
+ public static int MAXCELLS = 20;
+
+ /** The maximum number of handles to paint individually. */
+ public static int MAXHANDLES = 20;
+
+ /** Maximum number of cells to compute clipping bounds for. */
+ public static int MAXCLIPCELLS = 20;
+
+ /** Minimum preferred size. */
+ protected Dimension preferredMinSize;
+
+ /** Component that we're going to be drawing into. */
+ protected JGraph graph;
+
+ /** Reference to the graph's view (geometric pattern). */
+ protected GraphLayoutCache graphLayoutCache;
+
+ /** Current editor for the graph. */
+ protected GraphCellEditor cellEditor;
+
+ /**
+ * Set to false when editing and shouldSelectCell() returns true meaning the
+ * node should be selected before editing, used in completeEditing.
+ */
+ protected boolean stopEditingInCompleteEditing;
+
+ /** Used to paint the CellRenderer. */
+ protected CellRendererPane rendererPane;
+
+ /** Size needed to completely display all the cells. */
+ protected Dimension preferredSize;
+
+ /** Is the preferredSize valid? */
+ protected boolean validCachedPreferredSize;
+
+ /** Used to determine what to display. */
+ protected GraphModel graphModel;
+
+ /** Model maintaining the selection. */
+ protected GraphSelectionModel graphSelectionModel;
+
+ /** Handle that we are going to use. */
+ protected CellHandle handle;
+
+ /** Marquee that we are going to use. */
+ protected BasicMarqueeHandler marquee;
+
+ // Following 4 ivars are only valid when editing.
+ /**
+ * When editing, this will be the Component that is doing the actual
+ * editing.
+ */
+ protected Component editingComponent;
+
+ /** The focused cell under the mousepointer and the last focused cell. */
+ protected CellView focus;
+
+ /** The focused cell under the mousepointer and the last focused cell. */
+ protected CellView lastFocus;
+
+ /** Path that is being edited. */
+ protected Object editingCell;
+
+ /** Set to true if the editor has a different size than the renderer. */
+ protected boolean editorHasDifferentSize;
+
+ /** Needed to exchange information between Transfer- and MouseListener. */
+ protected Point insertionLocation;
+
+ /**
+ * Needed to exchange information between DropTargetHandler and
+ * TransferHandler.
+ */
+ protected int dropAction = TransferHandler.NONE;
+
+ /**
+ * If ture, a the view under mousepointer will be snapped to the grid lines
+ * during a drag operation. If snap-to-grid mode is disabled, views are
+ * moved by a snap increment.
+ */
+ protected boolean snapSelectedView = false;
+
+ // Cached listeners
+ /** Listens for JGraph property changes and updates display. */
+ protected PropertyChangeListener propertyChangeListener;
+
+ /** Listens for Mouse events. */
+ protected MouseListener mouseListener;
+
+ /** Listens for KeyListener events. */
+ protected KeyListener keyListener;
+
+ /** Listens for Component events. */
+ protected ComponentListener componentListener;
+
+ /** Listens for CellEditor events. */
+ protected CellEditorListener cellEditorListener = createCellEditorListener();
+
+ /** Updates the display when the selection changes. */
+ protected GraphSelectionListener graphSelectionListener;
+
+ /** Is responsible for updating the view based on model events. */
+ protected GraphModelListener graphModelListener;
+
+ /** Updates the display when the view has changed. */
+ protected GraphLayoutCacheListener graphLayoutCacheListener;
+
+ /** The default TransferHandler. */
+ protected TransferHandler defaultTransferHandler;
+
+ /** The default DropTargetListener. */
+ protected GraphDropTargetListener defaultDropTargetListener;
+
+ /** The drop target where the default listener was last installed. */
+ protected DropTarget dropTarget = null;
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param x DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static ComponentUI createUI(JComponent x) {
+ return new BasicGraphUI();
+ }
+
+ /**
+ * Creates a new BasicGraphUI object.
+ */
+ public BasicGraphUI() {
+ super();
+ }
+
+ //
+ // Methods for configuring the behavior of the graph. None of them
+ // push the value to the JGraph instance. You should really only
+ // call these methods on the JGraph instance.
+ //
+
+ /**
+ * Sets the GraphModel. This invokes <code>updateSize</code>.
+ */
+ protected void setModel(GraphModel model) {
+ cancelEditing(graph);
+
+ if ((graphModel != null) && (graphModelListener != null))
+ graphModel.removeGraphModelListener(graphModelListener);
+
+ graphModel = model;
+
+ if ((graphModel != null) && (graphModelListener != null))
+ graphModel.addGraphModelListener(graphModelListener);
+
+ if (graphModel != null) // jmv : to avoid NullPointerException
+ updateSize();
+ }
+
+ /**
+ * Sets the GraphLayoutCache (geometric pattern). This invokes
+ * <code>updateSize</code>.
+ */
+ protected void setGraphLayoutCache(GraphLayoutCache cache) {
+ cancelEditing(graph);
+
+ if ((graphLayoutCache != null) && (graphLayoutCacheListener != null))
+ graphLayoutCache.removeGraphLayoutCacheListener(graphLayoutCacheListener);
+
+ graphLayoutCache = cache;
+
+ if ((graphLayoutCache != null) && (graphLayoutCacheListener != null))
+ graphLayoutCache.addGraphLayoutCacheListener(graphLayoutCacheListener);
+
+ updateSize();
+ }
+
+ /**
+ * Sets the marquee handler.
+ */
+ protected void setMarquee(BasicMarqueeHandler marqueeHandler) {
+ marquee = marqueeHandler;
+ }
+
+ /**
+ * Resets the selection model. The appropriate listeners are installed on
+ * the model.
+ */
+ protected void setSelectionModel(GraphSelectionModel newLSM) {
+ cancelEditing(graph);
+
+ if ((graphSelectionListener != null) && (graphSelectionModel != null))
+ graphSelectionModel.removeGraphSelectionListener(graphSelectionListener);
+
+ graphSelectionModel = newLSM;
+
+ if ((graphSelectionModel != null) && (graphSelectionListener != null))
+ graphSelectionModel.addGraphSelectionListener(graphSelectionListener);
+
+ if (graph != null)
+ graph.repaint();
+ }
+
+ //
+ // GraphUI methods
+ //
+
+ /**
+ *
+ */
+
+ /**
+ * Returns the handle that is currently active, or null, if no handle is
+ * currently active. Typically, the returned objects are instances of the
+ * RootHandle inner class.
+ */
+ public CellHandle getHandle() {
+ return handle;
+ }
+
+ /**
+ * Returns the current drop action.
+ */
+ public int getDropAction() {
+ return dropAction;
+ }
+
+ /**
+ * Returns the cell that has the focus.
+ */
+ protected Object getFocusedCell() {
+ if (focus != null)
+ return focus.getCell();
+
+ return null;
+ }
+
+ /** Get the preferred Size for a cell view. */
+ public Dimension2D getPreferredSize(JGraph graph, CellView view) {
+ // Either label or icon
+ if (view != null) {
+ Object cell = view.getCell();
+ String valueStr = graph.convertValueToString(cell);
+ boolean label = ((valueStr != null) && (valueStr.length() > 0));
+ boolean icon = GraphConstants.getIcon(view.getAllAttributes()) != null;
+
+ if (label || icon) {
+ boolean focus = (getFocusedCell() == cell) && graph.hasFocus();
+
+ // Only ever removed when UI changes, this is OK!
+ Component component = view.getRendererComponent(graph, focus, false, false);
+
+ if (component != null) {
+ graph.add(component);
+ component.validate();
+
+ Dimension d = component.getPreferredSize();
+ int inset = 2 * GraphConstants.getInset(view.getAllAttributes());
+ d.width += inset;
+ d.height += inset;
+
+ return d;
+ }
+ }
+
+ if (view.getBounds() == null)
+ view.update();
+
+ Rectangle2D bounds = view.getBounds();
+
+ return new Dimension((int) bounds.getWidth(), (int) bounds.getHeight());
+ }
+
+ return null;
+ }
+
+ //
+ // Insertion Location
+ //
+ // Used to track the location of the mousepointer during Drag-and-Drop.
+ //
+
+ /**
+ * Returns the current location of the Drag-and-Drop activity.
+ */
+ public Point getInsertionLocation() {
+ return insertionLocation;
+ }
+
+ /**
+ * Sets the current location for Drag-and-Drop activity. Should be set to
+ * null after a drop. Used from within DropTargetListener.
+ */
+ public void setInsertionLocation(Point p) {
+ insertionLocation = p;
+ }
+
+ //
+ // Selection
+ //
+
+ /**
+ * From GraphUI interface.
+ */
+ public void selectCellsForEvent(JGraph graph, Object[] cells, MouseEvent event) {
+ selectCellsForEvent(cells, event);
+ }
+
+ /**
+ * Messaged to update the selection based on a MouseEvent for a group of
+ * cells. If the event is a toggle selection event, the cells are either
+ * selected, or deselected. Otherwise the cells are selected.
+ */
+ public void selectCellsForEvent(Object[] cells, MouseEvent event) {
+ if ((cells == null) || !graph.isSelectionEnabled())
+ return;
+
+ // Toggle selection
+ if (isToggleSelectionEvent(event)) {
+ for (int i = 0; i < cells.length; i++)
+ toggleSelectionCellForEvent(cells[i], event);
+
+ // Select cells
+ } else if (isAddToSelectionEvent(event))
+ graph.addSelectionCells(cells);
+ else
+ graph.setSelectionCells(cells);
+ }
+
+ /**
+ * Messaged to update the selection based on a MouseEvent over a particular
+ * cell. If the event is a toggle selection event, the cell is either
+ * selected, or deselected. Otherwise the cell is selected.
+ */
+ public void selectCellForEvent(Object cell, MouseEvent event) {
+ if (graph.isSelectionEnabled()) {
+ // Toggle selection
+ if (isToggleSelectionEvent(event))
+ toggleSelectionCellForEvent(cell, event);
+
+ // Select cell
+ else if (isAddToSelectionEvent(event))
+ graph.addSelectionCell(cell);
+ else
+ graph.setSelectionCell(cell);
+ }
+ }
+
+ /**
+ * Messaged to update the selection based on a toggle selection event, which
+ * means the cell's selection state is inverted.
+ */
+ protected void toggleSelectionCellForEvent(Object cell, MouseEvent event) {
+ if (graph.isCellSelected(cell))
+ graph.removeSelectionCell(cell);
+ else
+ graph.addSelectionCell(cell);
+ }
+
+ /**
+ * Returning true signifies that cells are added to the selection.
+ */
+ public boolean isAddToSelectionEvent(MouseEvent e) {
+ return e.isShiftDown();
+ }
+
+ /**
+ * Returning true signifies a mouse event on the cell should toggle the
+ * selection of only the cell under mouse.
+ */
+ public boolean isToggleSelectionEvent(MouseEvent e) {
+ switch (Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()) {
+ case InputEvent.CTRL_MASK:
+ return e.isControlDown();
+
+ case InputEvent.ALT_MASK:
+ return e.isAltDown();
+
+ case InputEvent.META_MASK:
+ return e.isMetaDown();
+
+ default:
+ return false;
+ }
+ }
+
+ /**
+ * Returning true signifies the marquee handler has precedence over other
+ * handlers, and is receiving subsequent mouse events.
+ */
+ public boolean isForceMarqueeEvent(MouseEvent event) {
+ if (marquee != null)
+ return marquee.isForceMarqueeEvent(event);
+
+ return false;
+ }
+
+ /**
+ * Returning true signifies a move should only be applied to one direction.
+ */
+ public boolean isConstrainedMoveEvent(MouseEvent event) {
+ if (event != null)
+ return event.isShiftDown();
+
+ return false;
+ }
+
+ //
+ // Editing
+ //
+
+ /**
+ * Returns true if the graph is being edited. The item that is being edited
+ * can be returned by getEditingPath().
+ */
+ public boolean isEditing(JGraph graph) {
+ return (editingComponent != null);
+ }
+
+ /**
+ * Stops the current editing session. This has no effect if the graph isn't
+ * being edited. Returns true if the editor allows the editing session to
+ * stop.
+ */
+ public boolean stopEditing(JGraph graph) {
+ if ((editingComponent != null) && cellEditor.stopCellEditing()) {
+ completeEditing(false, false, true);
+
+ return true;
+ }
+
+ return false;
+ }
+
+ /**
+ * Cancels all current editing sessions.
+ */
+ public void cancelEditing(JGraph graph) {
+ if (editingComponent != null)
+ completeEditing(false, true, false);
+
+ // Escape key is handled by the KeyHandler.keyPressed inner class method
+ }
+
+ /**
+ * Selects the cell and tries to edit it. Editing will fail if the
+ * CellEditor won't allow it for the selected item.
+ */
+ public void startEditingAtCell(JGraph graph, Object cell) {
+ graph.scrollCellToVisible(cell);
+
+ if (cell != null)
+ startEditing(cell, null);
+ }
+
+ /**
+ * Returns the element that is being edited.
+ */
+ public Object getEditingCell(JGraph graph) {
+ return editingCell;
+ }
+
+ //
+ /**
+ * DOCUMENT ME!
+ *
+ * @param c DOCUMENT ME!
+ */
+ public void installUI(JComponent c) {
+ if (c == null)
+ throw new NullPointerException("null component passed to BasicGraphUI.installUI()");
+
+ graph = (JGraph) c;
+ marquee = graph.getMarqueeHandler();
+ prepareForUIInstall();
+
+ // Boilerplate install block
+ installDefaults();
+ installListeners();
+ installKeyboardActions();
+ installComponents();
+
+ completeUIInstall();
+ }
+
+ /**
+ * Invoked after the <code>graph</code> instance variable has been set,
+ * but before any defaults/listeners have been installed.
+ */
+ protected void prepareForUIInstall() {
+ // Data member initializations
+ stopEditingInCompleteEditing = true;
+ preferredSize = new Dimension();
+ setGraphLayoutCache(graph.getGraphLayoutCache());
+ setModel(graph.getModel());
+ }
+
+ /**
+ * Invoked from installUI after all the defaults/listeners have been
+ * installed.
+ */
+ protected void completeUIInstall() {
+ // Custom install code
+ setSelectionModel(graph.getSelectionModel());
+ updateSize();
+ }
+
+ /**
+ * Invoked as part from the boilerplate install block. This sets the look
+ * and feel specific variables in JGraph.
+ */
+ protected void installDefaults() {
+ if ((graph.getBackground() == null) || graph.getBackground() instanceof UIResource) {
+ graph.setBackground(UIManager.getColor("Tree.background"));
+ }
+
+ if ((graph.getFont() == null) || graph.getFont() instanceof UIResource) {
+ // UIManager.getFont not supported in headless environment
+ try {
+ graph.setFont(UIManager.getFont("Tree.font"));
+ } catch (Error e) {
+ // No default font
+ }
+ }
+
+ // Set JGraph's laf-specific colors
+ graph.setMarqueeColor(UIManager.getColor("Table.gridColor"));
+ graph.setHandleColor(UIManager.getColor("MenuItem.selectionBackground"));
+ graph.setLockedHandleColor(UIManager.getColor("MenuItem.background"));
+ graph.setGridColor(UIManager.getColor("Tree.selectionBackground"));
+ graph.setOpaque(true);
+ }
+
+ /**
+ * Invoked as part from the boilerplate install block. This installs the
+ * listeners from BasicGraphUI in the graph.
+ */
+ protected void installListeners() {
+ // Install Local Handlers
+ TransferHandler th = graph.getTransferHandler();
+
+ if ((th == null) || th instanceof UIResource) {
+ defaultTransferHandler = createTransferHandler();
+
+ // Not supported in headless environment
+ try {
+ graph.setTransferHandler(defaultTransferHandler);
+ } catch (Error e) {
+ // No default font
+ }
+ }
+
+ if (graphLayoutCache != null) {
+ graphLayoutCacheListener = createGraphLayoutCacheListener();
+ graphLayoutCache.addGraphLayoutCacheListener(graphLayoutCacheListener);
+ }
+
+ dropTarget = graph.getDropTarget();
+
+ try {
+ if (dropTarget != null) {
+ defaultDropTargetListener = new GraphDropTargetListener();
+ dropTarget.addDropTargetListener(defaultDropTargetListener);
+ }
+ } catch (TooManyListenersException tmle) {
+ // should not happen... swing drop target is multicast
+ }
+
+ // Install Listeners
+ if ((propertyChangeListener = createPropertyChangeListener()) != null)
+ graph.addPropertyChangeListener(propertyChangeListener);
+
+ if ((mouseListener = createMouseListener()) != null) {
+ graph.addMouseListener(mouseListener);
+
+ if (mouseListener instanceof MouseMotionListener) {
+ graph.addMouseMotionListener((MouseMotionListener) mouseListener);
+ }
+ }
+
+ if ((keyListener = createKeyListener()) != null) {
+ graph.addKeyListener(keyListener);
+ }
+
+ if (((graphModelListener = createGraphModelListener()) != null) && (graphModel != null))
+ graphModel.addGraphModelListener(graphModelListener);
+
+ if (((graphSelectionListener = createGraphSelectionListener()) != null)
+ && (graphSelectionModel != null))
+ graphSelectionModel.addGraphSelectionListener(graphSelectionListener);
+ }
+
+ /**
+ * Invoked as part from the boilerplate install block.
+ */
+ protected void installKeyboardActions() {
+ InputMap km = getInputMap(JComponent.WHEN_ANCESTOR_OF_FOCUSED_COMPONENT);
+ SwingUtilities.replaceUIInputMap(graph, JComponent.WHEN_ANCESTOR_OF_FOCUSED_COMPONENT, km);
+ km = getInputMap(JComponent.WHEN_FOCUSED);
+ SwingUtilities.replaceUIInputMap(graph, JComponent.WHEN_FOCUSED, km);
+ SwingUtilities.replaceUIActionMap(graph, createActionMap());
+ }
+
+ /**
+ * Return JTree's input map.
+ */
+ InputMap getInputMap(int condition) {
+ if (condition == JComponent.WHEN_ANCESTOR_OF_FOCUSED_COMPONENT)
+ return (InputMap) UIManager.get("Tree.ancestorInputMap");
+ else if (condition == JComponent.WHEN_FOCUSED)
+ return (InputMap) UIManager.get("Tree.focusInputMap");
+
+ return null;
+ }
+
+ /**
+ * Return the mapping between JTree's input map and JGraph's actions.
+ */
+ ActionMap createActionMap() {
+ // 1: Up, 2: Right, 3: Down, 4: Left
+ ActionMap map = new ActionMapUIResource();
+
+ map.put("selectPrevious", new GraphIncrementAction(1, "selectPrevious"));
+ map.put("selectPreviousChangeLead", new GraphIncrementAction(1, "selectPreviousLead"));
+ map.put("selectPreviousExtendSelection",
+ new GraphIncrementAction(1, "selectPreviousExtendSelection"));
+
+ map.put("selectParent", new GraphIncrementAction(4, "selectParent"));
+ map.put("selectParentChangeLead", new GraphIncrementAction(4, "selectParentChangeLead"));
+
+ map.put("selectNext", new GraphIncrementAction(3, "selectNext"));
+ map.put("selectNextChangeLead", new GraphIncrementAction(3, "selectNextLead"));
+ map.put("selectNextExtendSelection",
+ new GraphIncrementAction(3, "selectNextExtendSelection"));
+
+ map.put("selectChild", new GraphIncrementAction(2, "selectChild"));
+ map.put("selectChildChangeLead", new GraphIncrementAction(2, "selectChildChangeLead"));
+
+ map.put("cancel", new GraphCancelEditingAction("cancel"));
+ map.put("startEditing", new GraphEditAction("startEditing"));
+ map.put("selectAll", new GraphSelectAllAction("selectAll", true));
+ map.put("clearSelection", new GraphSelectAllAction("clearSelection", false));
+
+ return map;
+ }
+
+ /**
+ * Intalls the subcomponents of the graph, which is the renderer pane.
+ */
+ protected void installComponents() {
+ if ((rendererPane = createCellRendererPane()) != null)
+ graph.add(rendererPane);
+ }
+
+ //
+ // Create methods.
+ //
+
+ /**
+ * Creates an instance of TransferHandler. Used for subclassers to provide
+ * different TransferHandler.
+ */
+ protected TransferHandler createTransferHandler() {
+ return new GraphTransferHandler();
+ }
+
+ /**
+ * Creates a listener that is responsible to update the UI based on how the
+ * graph's bounds properties change.
+ */
+ protected PropertyChangeListener createPropertyChangeListener() {
+ return new PropertyChangeHandler();
+ }
+
+ /**
+ * Creates the listener responsible for calling the correct handlers based
+ * on mouse events, and to select invidual cells.
+ */
+ protected MouseListener createMouseListener() {
+ return new MouseHandler();
+ }
+
+ /**
+ * Creates the listener reponsible for getting key events from the graph.
+ */
+ protected KeyListener createKeyListener() {
+ return new KeyHandler();
+ }
+
+ /**
+ * Creates the listener that updates the display based on selection change
+ * methods.
+ */
+ protected GraphSelectionListener createGraphSelectionListener() {
+ return new GraphSelectionHandler();
+ }
+
+ /**
+ * Creates a listener to handle events from the current editor.
+ */
+ protected CellEditorListener createCellEditorListener() {
+ return new CellEditorHandler();
+ }
+
+ /**
+ * Creates and returns a new ComponentHandler.
+ */
+ protected ComponentListener createComponentListener() {
+ return new ComponentHandler();
+ }
+
+ /**
+ * Returns the renderer pane that renderer components are placed in.
+ */
+ protected CellRendererPane createCellRendererPane() {
+ return new CellRendererPane();
+ }
+
+ /**
+ * Returns a listener that can update the graph when the view changes.
+ */
+ protected GraphLayoutCacheListener createGraphLayoutCacheListener() {
+ return new GraphLayoutCacheHandler();
+ }
+
+ /**
+ * Returns a listener that can update the graph when the model changes.
+ */
+ protected GraphModelListener createGraphModelListener() {
+ return new GraphModelHandler();
+ }
+
+ //
+ /**
+ * DOCUMENT ME!
+ *
+ * @param c DOCUMENT ME!
+ */
+ public void uninstallUI(JComponent c) {
+ cancelEditing(graph);
+ uninstallListeners();
+ uninstallKeyboardActions();
+ uninstallComponents();
+
+ completeUIUninstall();
+ }
+
+ protected void completeUIUninstall() {
+ graphLayoutCache = null;
+ rendererPane = null;
+ componentListener = null;
+ propertyChangeListener = null;
+ keyListener = null;
+ setSelectionModel(null);
+ graph = null;
+ graphModel = null;
+ graphSelectionModel = null;
+ graphSelectionListener = null;
+ }
+
+ protected void uninstallListeners() {
+ // Uninstall Handlers
+ TransferHandler th = graph.getTransferHandler();
+
+ if (th == defaultTransferHandler)
+ graph.setTransferHandler(null);
+
+ if (graphLayoutCacheListener != null)
+ graphLayoutCache.removeGraphLayoutCacheListener(graphLayoutCacheListener);
+
+ if ((dropTarget != null) && (defaultDropTargetListener != null))
+ dropTarget.removeDropTargetListener(defaultDropTargetListener);
+
+ if (componentListener != null)
+ graph.removeComponentListener(componentListener);
+
+ if (propertyChangeListener != null)
+ graph.removePropertyChangeListener(propertyChangeListener);
+
+ if (mouseListener != null) {
+ graph.removeMouseListener(mouseListener);
+
+ if (mouseListener instanceof MouseMotionListener)
+ graph.removeMouseMotionListener((MouseMotionListener) mouseListener);
+ }
+
+ if (keyListener != null)
+ graph.removeKeyListener(keyListener);
+
+ if ((graphModel != null) && (graphModelListener != null))
+ graphModel.removeGraphModelListener(graphModelListener);
+
+ if ((graphSelectionListener != null) && (graphSelectionModel != null))
+ graphSelectionModel.removeGraphSelectionListener(graphSelectionListener);
+ }
+
+ protected void uninstallKeyboardActions() {
+ SwingUtilities.replaceUIActionMap(graph, null);
+ SwingUtilities.replaceUIInputMap(graph, JComponent.WHEN_ANCESTOR_OF_FOCUSED_COMPONENT, null);
+ SwingUtilities.replaceUIInputMap(graph, JComponent.WHEN_FOCUSED, null);
+ }
+
+ /**
+ * Uninstalls the renderer pane.
+ */
+ protected void uninstallComponents() {
+ if (rendererPane != null)
+ graph.remove(rendererPane);
+ }
+
+ //
+ // Painting routines.
+ //
+
+ /**
+ * Main painting routine.
+ */
+ public void paint(Graphics g, JComponent c) {
+ if (graph != c)
+ throw new InternalError("BasicGraphUI cannot paint " + c.toString() + "; " + graph
+ + " was expected.");
+
+ Graphics2D g2 = (Graphics2D) g;
+ Rectangle2D tmp = g.getClipBounds();
+ Rectangle2D paintBounds = new Rectangle2D.Double(tmp.getX(), tmp.getY(), tmp.getWidth(),
+ tmp.getHeight());
+ Rectangle2D real = graph.fromScreen(new Rectangle2D.Double(paintBounds.getX(),
+ paintBounds.getY(),
+ paintBounds.getWidth(),
+ paintBounds.getHeight()));
+
+ // Paint Background (Typically Grid)
+ paintBackground(g);
+
+ // Remember current affine transform
+ AffineTransform at = g2.getTransform();
+
+ // Use anti aliasing
+ if (graph.isAntiAliased())
+ g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
+
+ // Use Swing's scaling
+ double scale = graph.getScale();
+ g2.scale(scale, scale);
+
+ // Paint cells
+ CellView[] views = graphLayoutCache.getRoots();
+
+ for (int i = 0; i < views.length; i++) {
+ Rectangle2D bounds = views[i].getBounds();
+
+ if ((bounds != null) && (real != null) && bounds.intersects(real))
+ paintCell(g, views[i], bounds, false);
+ }
+
+ // Reset affine transform and antialias
+ g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF);
+
+ // Paint Foreground (Typically Ports)
+ if (!graph.isPortsScaled())
+ g2.setTransform(at);
+
+ paintForeground(g);
+ g2.setTransform(at);
+
+ // Paint Handle
+ if (handle != null)
+ handle.paint(g);
+
+ // Paint Marquee
+ if (marquee != null)
+ marquee.paint(graph, g);
+
+ // Empty out the renderer pane, allowing renderers to be gc'ed.
+ if (rendererPane != null)
+ rendererPane.removeAll();
+ }
+
+ /**
+ * Paints the renderer of <code>view</code> to <code>g</code> at
+ * <code>bounds</code>. Recursive implementation that paints the children
+ * first.
+ * <p>
+ * The reciever should NOT modify <code>clipBounds</code>, or
+ * <code>insets</code>. The <code>preview</code> flag is passed to the
+ * renderer, and is not used here.
+ */
+ public void paintCell(Graphics g, CellView view, Rectangle2D bounds, boolean preview) {
+ // First Paint View
+ if ((view != null) && (bounds != null)) {
+ boolean bfocus = (view == this.focus);
+ boolean sel = graph.isCellSelected(view.getCell());
+ Component component = view.getRendererComponent(graph, sel, bfocus, preview);
+ rendererPane.paintComponent(g, component, graph, (int) bounds.getX(),
+ (int) bounds.getY(), (int) bounds.getWidth(),
+ (int) bounds.getHeight(), true);
+ }
+
+ // Then Paint Children
+ if (!view.isLeaf()) {
+ CellView[] children = view.getChildViews();
+
+ for (int i = 0; i < children.length; i++)
+ paintCell(g, children[i], children[i].getBounds(), preview);
+ }
+ }
+
+ //
+ // Background
+ //
+
+ /**
+ * Paint the background of this graph. Calls paintGrid.
+ */
+ protected void paintBackground(Graphics g) {
+ if (graph.isGridVisible())
+ paintGrid(graph.getGridSize(), g, g.getClipBounds());
+ }
+
+ /**
+ * Paint the grid.
+ */
+ protected void paintGrid(double gs, Graphics g, Rectangle2D r) {
+ // Parameter "r" is never used: remove it.
+ Rectangle rr = (Rectangle) g.getClipBounds();
+ double xl = rr.x;
+ double yt = rr.y;
+ double xr = xl + rr.width;
+ double yb = yt + rr.height;
+ double sgs = Math.max(2, gs * graph.getScale());
+
+ int xs = (int) (Math.floor(xl / sgs) * sgs);
+ int xe = (int) (Math.ceil(xr / sgs) * sgs);
+ int ys = (int) (Math.floor(yt / sgs) * sgs);
+ int ye = (int) (Math.ceil(yb / sgs) * sgs);
+
+ g.setColor(graph.getGridColor());
+
+ switch (graph.getGridMode()) {
+ case JGraph.CROSS_GRID_MODE: {
+ int cs = (sgs > 16.0) ? 2 : ((sgs < 8.0) ? 0 : 1);
+
+ for (double x = xs; x <= xe; x += sgs) {
+ for (double y = ys; y <= ye; y += sgs) {
+ int ix = (int) Math.round(x);
+ int iy = (int) Math.round(y);
+
+ g.drawLine(ix - cs, iy, ix + cs, iy);
+ g.drawLine(ix, iy - cs, ix, iy + cs);
+ }
+ }
+ }
+
+ break;
+
+ case JGraph.LINE_GRID_MODE: {
+ xe += (int) Math.ceil(sgs);
+ ye += (int) Math.ceil(sgs);
+
+ for (double x = xs; x <= xe; x += sgs) {
+ int ix = (int) Math.round(x);
+
+ g.drawLine(ix, ys, ix, ye);
+ }
+
+ for (double y = ys; y <= ye; y += sgs) {
+ int iy = (int) Math.round(y);
+
+ g.drawLine(xs, iy, xe, iy);
+ }
+ }
+
+ break;
+
+ case JGraph.DOT_GRID_MODE:default:
+
+ for (double x = xs; x <= xe; x += sgs) {
+ for (double y = ys; y <= ye; y += sgs) {
+ int ix = (int) Math.round(x);
+ int iy = (int) Math.round(y);
+
+ g.drawLine(ix, iy, ix, iy);
+ }
+ }
+
+ break;
+ }
+ }
+
+ //
+ // Foreground
+ //
+
+ /**
+ * Paint the foreground of this graph. Calls paintPorts.
+ */
+ protected void paintForeground(Graphics g) {
+ if (graph.isPortsVisible())
+ paintPorts(g, graphLayoutCache.getPorts());
+ }
+
+ /**
+ * Paint <code>ports</code>.
+ */
+ public void paintPorts(Graphics g, CellView[] ports) {
+ if (ports != null) {
+ Rectangle r = g.getClipBounds();
+
+ for (int i = 0; i < ports.length; i++) {
+ if (ports[i] != null) {
+ Rectangle2D tmp = ports[i].getBounds();
+ Rectangle2D bounds = new Rectangle2D.Double(tmp.getX(), tmp.getY(),
+ tmp.getWidth(), tmp.getHeight());
+ Point2D center = new Point2D.Double(bounds.getCenterX(), bounds.getCenterY());
+
+ if (!graph.isPortsScaled())
+ center = graph.toScreen(center);
+
+ bounds.setFrame(center.getX() - (bounds.getWidth() / 2),
+ center.getY() - (bounds.getHeight() / 2), bounds.getWidth(),
+ bounds.getHeight());
+
+ if ((r == null) || bounds.intersects(r))
+ paintCell(g, ports[i], bounds, false);
+ }
+ }
+ }
+ }
+
+ //
+ // Various local methods
+ //
+
+ /**
+ * Update the handle using createHandle.
+ */
+ public void updateHandle() {
+ if (graphLayoutCache != null) {
+ Object[] cells = graphLayoutCache.getVisibleCells(graph.getSelectionCells());
+
+ if ((cells != null) && (cells.length > 0))
+ handle = createHandle(createContext(graph, cells));
+ else
+ handle = null;
+ }
+ }
+
+ protected GraphContext createContext(JGraph graph, Object[] cells) {
+ return new GraphContext(graph, cells);
+ }
+
+ /**
+ * Constructs the "root handle" for <code>context</code>.
+ *
+ * @param context
+ * reference to the context of the current selection.
+ */
+ public CellHandle createHandle(GraphContext context) {
+ if ((context != null) && !context.isEmpty() && graph.isEnabled()) {
+ try {
+ return new RootHandle(context);
+ } catch (NullPointerException e) {
+ // ignore for now...
+ }
+ }
+
+ return null;
+ }
+
+ /**
+ * Messages the Graph with <code>graphDidChange</code>.
+ */
+ public void updateSize() {
+ validCachedPreferredSize = false;
+ graph.graphDidChange();
+ updateHandle();
+ }
+
+ /**
+ * Updates the <code>preferredSize</code> instance variable, which is
+ * returned from <code>getPreferredSize()</code>.
+ */
+ protected void updateCachedPreferredSize() {
+ Rectangle2D size = AbstractCellView.getBounds(graphLayoutCache.getRoots());
+
+ if (size == null)
+ size = new Rectangle2D.Double();
+
+ Point2D psize = new Point2D.Double(size.getX() + size.getWidth(),
+ size.getY() + size.getHeight());
+ Dimension d = graph.getMinimumSize();
+ Point2D min = (d != null) ? graph.toScreen(new Point(d.width, d.height)) : new Point(0, 0);
+ Point2D scaled = graph.toScreen(psize);
+ preferredSize = new Dimension((int) Math.max(min.getX(), scaled.getX()),
+ (int) Math.max(min.getY(), scaled.getY()));
+
+ Insets in = graph.getInsets();
+
+ if (in != null) {
+ preferredSize.setSize(preferredSize.getWidth() + in.left + in.right,
+ preferredSize.getHeight() + in.top + in.bottom);
+ }
+
+ validCachedPreferredSize = true;
+ }
+
+ /**
+ * Sets the preferred minimum size.
+ */
+ public void setPreferredMinSize(Dimension newSize) {
+ preferredMinSize = newSize;
+ }
+
+ /**
+ * Returns the minimum preferred size.
+ */
+ public Dimension getPreferredMinSize() {
+ if (preferredMinSize == null)
+ return null;
+
+ return new Dimension(preferredMinSize);
+ }
+
+ /**
+ * Returns the preferred size to properly display the graph.
+ */
+ public Dimension getPreferredSize(JComponent c) {
+ Dimension pSize = this.getPreferredMinSize();
+
+ if (!validCachedPreferredSize)
+ updateCachedPreferredSize();
+
+ if (graph != null) {
+ if (pSize != null)
+ return new Dimension(Math.max(pSize.width, preferredSize.width),
+ Math.max(pSize.height, preferredSize.height));
+
+ return new Dimension(preferredSize.width, preferredSize.height);
+ } else if (pSize != null)
+ return pSize;
+ else
+
+ return new Dimension(0, 0);
+ }
+
+ /**
+ * Returns the minimum size for this component. Which will be the min
+ * preferred size or 0, 0.
+ */
+ public Dimension getMinimumSize(JComponent c) {
+ if (this.getPreferredMinSize() != null)
+ return this.getPreferredMinSize();
+
+ return new Dimension(0, 0);
+ }
+
+ /**
+ * Returns the maximum size for this component, which will be the preferred
+ * size if the instance is currently in a JGraph, or 0, 0.
+ */
+ public Dimension getMaximumSize(JComponent c) {
+ if (graph != null)
+ return getPreferredSize(graph);
+
+ if (this.getPreferredMinSize() != null)
+ return this.getPreferredMinSize();
+
+ return new Dimension(0, 0);
+ }
+
+ /**
+ * Messages to stop the editing session. If the UI the receiver is providing
+ * the look and feel for returns true from
+ * <code>getInvokesStopCellEditing</code>, stopCellEditing will invoked
+ * on the current editor. Then completeEditing will be messaged with false,
+ * true, false to cancel any lingering editing.
+ */
+ protected void completeEditing() {
+ /* If should invoke stopCellEditing, try that */
+ if (graph.getInvokesStopCellEditing() && stopEditingInCompleteEditing
+ && (editingComponent != null)) {
+ cellEditor.stopCellEditing();
+ }
+
+ /*
+ * Invoke cancelCellEditing, this will do nothing if stopCellEditing was
+ * succesful.
+ */
+ completeEditing(false, true, false);
+ }
+
+ /**
+ * Stops the editing session. If messageStop is true the editor is messaged
+ * with stopEditing, if messageCancel is true the editor is messaged with
+ * cancelEditing. If messageGraph is true the graphModel is messaged with
+ * valueForCellChanged.
+ */
+ protected void completeEditing(boolean messageStop, boolean messageCancel, boolean messageGraph) {
+ if (stopEditingInCompleteEditing && (editingComponent != null)) {
+ Component oldComponent = editingComponent;
+ Object oldCell = editingCell;
+ GraphCellEditor oldEditor = cellEditor;
+ boolean requestFocus = ((graph != null)
+ && (graph.hasFocus()
+ || (SwingUtilities.findFocusOwner(editingComponent) != null)));
+ editingCell = null;
+ editingComponent = null;
+
+ if (messageStop)
+ oldEditor.stopCellEditing();
+ else if (messageCancel)
+ oldEditor.cancelCellEditing();
+
+ graph.remove(oldComponent);
+
+ if (requestFocus)
+ graph.requestFocus();
+
+ if (messageGraph) {
+ Object newValue = oldEditor.getCellEditorValue();
+ graphLayoutCache.valueForCellChanged(oldCell, newValue);
+ }
+
+ updateSize();
+
+ // Remove Editor Listener
+ if ((oldEditor != null) && (cellEditorListener != null))
+ oldEditor.removeCellEditorListener(cellEditorListener);
+
+ cellEditor = null;
+ }
+ }
+
+ /**
+ * Will start editing for cell if there is a cellEditor and shouldSelectCell
+ * returns true.
+ * <p>
+ * This assumes that cell is valid and visible.
+ */
+ protected boolean startEditing(Object cell, MouseEvent event) {
+ completeEditing();
+
+ if (graph.isCellEditable(cell)) {
+ CellView tmp = graphLayoutCache.getMapping(cell, false);
+ cellEditor = tmp.getEditor();
+ editingComponent = cellEditor.getGraphCellEditorComponent(graph, cell,
+ graph.isCellSelected(cell));
+
+ if (cellEditor.isCellEditable(event)) {
+ Rectangle2D cellBounds = graph.getCellBounds(cell);
+
+ editingCell = cell;
+
+ Dimension2D editorSize = editingComponent.getPreferredSize();
+
+ graph.add(editingComponent);
+
+ Point2D p = getEditorLocation(cell, editorSize,
+ graph.toScreen(new Point2D.Double(cellBounds.getX(),
+ cellBounds.getY())));
+
+ editingComponent.setBounds((int) p.getX(), (int) p.getY(),
+ (int) editorSize.getWidth(), (int) editorSize.getHeight());
+ editingCell = cell;
+ editingComponent.validate();
+
+ // Add Editor Listener
+ if (cellEditorListener == null)
+ cellEditorListener = createCellEditorListener();
+
+ if ((cellEditor != null) && (cellEditorListener != null))
+ cellEditor.addCellEditorListener(cellEditorListener);
+
+ Rectangle2D visRect = graph.getVisibleRect();
+ graph.paintImmediately((int) p.getX(), (int) p.getY(),
+ (int) ((visRect.getWidth() + visRect.getX())
+ - cellBounds.getX()), (int) editorSize.getHeight());
+
+ if (cellEditor.shouldSelectCell(event) && graph.isSelectionEnabled()) {
+ stopEditingInCompleteEditing = false;
+
+ try {
+ graph.setSelectionCell(cell);
+ } catch (Exception e) {
+ System.err.println("Editing exception: " + e);
+ }
+
+ stopEditingInCompleteEditing = true;
+ }
+
+ if (event instanceof MouseEvent) {
+ /*
+ * Find the component that will get forwarded all the mouse
+ * events until mouseReleased.
+ */
+ Point componentPoint = SwingUtilities.convertPoint(graph,
+ new Point(event.getX(),
+ event.getY()),
+ editingComponent);
+
+ /*
+ * Create an instance of BasicTreeMouseListener to handle
+ * passing the mouse/motion events to the necessary
+ * component.
+ */
+
+ // We really want similiar behavior to getMouseEventTarget,
+ // but it is package private.
+ Component activeComponent = SwingUtilities.getDeepestComponentAt(editingComponent,
+ componentPoint.x,
+ componentPoint.y);
+
+ if (activeComponent != null) {
+ new MouseInputHandler(graph, activeComponent, event);
+ }
+ }
+
+ return true;
+ } else
+ editingComponent = null;
+ }
+
+ return false;
+ }
+
+ /**
+ * Subclassers may override this to provide a better location for the
+ * in-place editing of edges (if you do not inherit from the EdgeRenderer
+ * class).
+ */
+ protected Point2D getEditorLocation(Object cell, Dimension2D editorSize, Point2D pt) {
+ // Edges have different editor position and size
+ CellView view = graphLayoutCache.getMapping(cell, false);
+
+ if (view instanceof EdgeView) {
+ EdgeView edgeView = (EdgeView) view;
+ CellViewRenderer renderer = edgeView.getRenderer();
+
+ if (renderer instanceof EdgeRenderer) {
+ Point2D tmp = ((EdgeRenderer) renderer).getLabelPosition(edgeView);
+
+ if (tmp != null)
+ pt = tmp;
+ else
+ pt = AbstractCellView.getCenterPoint(edgeView);
+
+ pt.setLocation(Math.max(0, pt.getX() - (editorSize.getWidth() / 2)),
+ Math.max(0, pt.getY() - (editorSize.getHeight() / 2)));
+ }
+
+ graph.toScreen(pt);
+ }
+
+ return pt;
+ }
+
+ /**
+ * Scroll the graph for an event at <code>p</code>.
+ */
+ public static void autoscroll(JGraph graph, Point p) {
+ Rectangle view = graph.getBounds();
+
+ if (graph.getParent() instanceof JViewport)
+ view = ((JViewport) graph.getParent()).getViewRect();
+
+ if (view.contains(p)) {
+ Point target = new Point(p);
+ int dx = (int) (graph.getWidth() * SCROLLSTEP);
+ int dy = (int) (graph.getHeight() * SCROLLSTEP);
+
+ if ((target.x - view.x) < SCROLLBORDER)
+ target.x -= dx;
+
+ if ((target.y - view.y) < SCROLLBORDER)
+ target.y -= dy;
+
+ if (((view.x + view.width) - target.x) < SCROLLBORDER)
+ target.x += dx;
+
+ if (((view.y + view.height) - target.y) < SCROLLBORDER)
+ target.y += dy;
+
+ graph.scrollPointToVisible(target);
+ }
+ }
+
+ /**
+ * Updates the preferred size when scrolling (if necessary).
+ */
+ public class ComponentHandler extends ComponentAdapter implements ActionListener {
+ /**
+ * Timer used when inside a scrollpane and the scrollbar is adjusting.
+ */
+ protected Timer timer;
+
+ /** ScrollBar that is being adjusted. */
+ protected JScrollBar scrollBar;
+
+ public void componentMoved(ComponentEvent e) {
+ if (timer == null) {
+ JScrollPane scrollPane = getScrollPane();
+
+ if (scrollPane == null)
+ updateSize();
+ else {
+ scrollBar = scrollPane.getVerticalScrollBar();
+
+ if ((scrollBar == null) || !scrollBar.getValueIsAdjusting()) {
+ // Try the horizontal scrollbar.
+ if (((scrollBar = scrollPane.getHorizontalScrollBar()) != null)
+ && scrollBar.getValueIsAdjusting())
+ startTimer();
+ else
+ updateSize();
+ } else
+ startTimer();
+ }
+ }
+ }
+
+ /**
+ * Creates, if necessary, and starts a Timer to check if need to resize
+ * the bounds.
+ */
+ protected void startTimer() {
+ if (timer == null) {
+ timer = new Timer(200, this);
+ timer.setRepeats(true);
+ }
+
+ timer.start();
+ }
+
+ /**
+ * Returns the JScrollPane housing the JGraph, or null if one isn't
+ * found.
+ */
+ protected JScrollPane getScrollPane() {
+ Component c = graph.getParent();
+
+ while ((c != null) && !(c instanceof JScrollPane))
+ c = c.getParent();
+
+ if (c instanceof JScrollPane)
+ return (JScrollPane) c;
+
+ return null;
+ }
+
+ /**
+ * Public as a result of Timer. If the scrollBar is null, or not
+ * adjusting, this stops the timer and updates the sizing.
+ */
+ public void actionPerformed(ActionEvent ae) {
+ if ((scrollBar == null) || !scrollBar.getValueIsAdjusting()) {
+ if (timer != null)
+ timer.stop();
+
+ updateSize();
+ timer = null;
+ scrollBar = null;
+ }
+ }
+ } // End of BasicGraphUI.ComponentHandler
+
+ /**
+ * Listens for changes in the graph model and updates the view accordingly.
+ */
+ public class GraphModelHandler implements GraphModelListener, Serializable {
+ public void graphChanged(GraphModelEvent e) {
+ Object[] removed = e.getChange().getRemoved();
+
+ // Remove from selection & focus
+ if ((removed != null) && (removed.length > 0)) {
+ // Update Focus If Necessary
+ if (focus != null) {
+ Object focusedCell = focus.getCell();
+
+ for (int i = 0; i < removed.length; i++) {
+ if (removed[i] == focusedCell) {
+ lastFocus = focus;
+ focus = null;
+
+ break;
+ }
+ }
+ }
+
+ // Remove from selection
+ graph.getSelectionModel().removeSelectionCells(removed);
+ }
+
+ if (graphLayoutCache != null)
+ graphLayoutCache.graphChanged(e.getChange());
+
+ // Get arrays
+ Object[] inserted = e.getChange().getInserted();
+ Object[] changed = e.getChange().getChanged();
+
+ // Insert
+ if ((inserted != null) && (inserted.length > 0)) {
+ // Update focus to first inserted cell
+ for (int i = 0; i < inserted.length; i++)
+ graph.updateAutoSize(graphLayoutCache.getMapping(inserted[i], false));
+ }
+
+ // Change (update size)
+ if ((changed != null) && (changed.length > 0)) {
+ for (int i = 0; i < changed.length; i++)
+ graph.updateAutoSize(graphLayoutCache.getMapping(changed[i], false));
+ }
+
+ // Select if not partial
+ if (!graphLayoutCache.isPartial() && graphLayoutCache.isSelectsAllInsertedCells()
+ && graph.isEnabled()) {
+ Object[] roots = DefaultGraphModel.getRoots(graphModel, inserted);
+
+ if ((roots != null) && (roots.length > 0)) {
+ lastFocus = focus;
+ focus = graphLayoutCache.getMapping(roots[0], false);
+ graph.setSelectionCells(roots);
+ }
+ }
+
+ updateSize();
+ }
+ } // End of BasicGraphUI.GraphModelHandler
+
+ /**
+ * Listens for changes in the graph view and updates the size accordingly.
+ */
+ public class GraphLayoutCacheHandler implements GraphLayoutCacheListener, Serializable {
+ /*
+ * (non-Javadoc)
+ *
+ * @see org.jgraph.event.GraphLayoutCacheListener#graphLayoutCacheChanged(org.jgraph.event.GraphLayoutCacheEvent)
+ */
+ public void graphLayoutCacheChanged(GraphLayoutCacheEvent e) {
+ Object[] changed = e.getChange().getChanged();
+
+ if ((changed != null) && (changed.length > 0)) {
+ for (int i = 0; i < changed.length; i++) {
+ graph.updateAutoSize(graphLayoutCache.getMapping(changed[i], false));
+ }
+ }
+
+ Object[] inserted = e.getChange().getInserted();
+
+ if ((inserted != null) && (inserted.length > 0)
+ && graphLayoutCache.isSelectsLocalInsertedCells()
+ && !(graphLayoutCache.isSelectsAllInsertedCells() && !graphLayoutCache.isPartial())
+ && graph.isEnabled()) {
+ Object[] roots = DefaultGraphModel.getRoots(graphModel, inserted);
+
+ if ((roots != null) && (roots.length > 0)) {
+ lastFocus = focus;
+ focus = graphLayoutCache.getMapping(roots[0], false);
+ graph.setSelectionCells(roots);
+ }
+ }
+
+ updateSize();
+ }
+ } // End of BasicGraphUI.GraphLayoutCacheHandler
+
+ /**
+ * Listens for changes in the selection model and updates the display
+ * accordingly.
+ */
+ public class GraphSelectionHandler implements GraphSelectionListener, Serializable {
+ /**
+ * Messaged when the selection changes in the graph we're displaying
+ * for. Stops editing, updates handles and displays the changed cells.
+ */
+ public void valueChanged(GraphSelectionEvent event) {
+ // cancelEditing(graph);
+ updateHandle();
+
+ Object[] cells = event.getCells();
+
+ if ((cells != null) && (cells.length <= MAXCLIPCELLS)) {
+ Rectangle2D r = graph.toScreen(graph.getCellBounds(cells));
+
+ // Includes dirty region of focused cell
+ if (focus != null) {
+ if (r != null)
+ Rectangle2D.union(r, focus.getBounds(), r);
+ else
+ r = focus.getBounds();
+ }
+
+ // And last focused cell
+ if (lastFocus != null) {
+ if (r != null)
+ Rectangle2D.union(r, lastFocus.getBounds(), r);
+ else
+ r = lastFocus.getBounds();
+ }
+
+ if (r != null) {
+ int hsize = (int) (graph.getHandleSize() * graph.getScale()) + 1;
+ updateHandle();
+ graph.repaint((int) r.getX() - hsize, (int) r.getY() - hsize,
+ (int) r.getWidth() + (2 * hsize),
+ (int) r.getHeight() + (2 * hsize));
+ }
+ } else
+ graph.repaint();
+ }
+ }
+
+ /**
+ * Listener responsible for getting cell editing events and updating the
+ * graph accordingly.
+ */
+ public class CellEditorHandler implements CellEditorListener, Serializable {
+ /** Messaged when editing has stopped in the graph. */
+ public void editingStopped(ChangeEvent e) {
+ completeEditing(false, false, true);
+ }
+
+ /** Messaged when editing has been canceled in the graph. */
+ public void editingCanceled(ChangeEvent e) {
+ completeEditing(false, false, false);
+ }
+ } // BasicGraphUI.CellEditorHandler
+
+ /**
+ * This is used to get mutliple key down events to appropriately generate
+ * events.
+ */
+ public class KeyHandler extends KeyAdapter implements Serializable {
+ /** Key code that is being generated for. */
+ protected Action repeatKeyAction;
+
+ /** Set to true while keyPressed is active. */
+ protected boolean isKeyDown;
+
+ public void keyPressed(KeyEvent e) {
+ if ((graph != null) && graph.hasFocus() && graph.isEnabled()) {
+ KeyStroke keyStroke = KeyStroke.getKeyStroke(e.getKeyCode(), e.getModifiers());
+
+ if (graph.getConditionForKeyStroke(keyStroke) == JComponent.WHEN_FOCUSED) {
+ ActionListener listener = graph.getActionForKeyStroke(keyStroke);
+
+ if (listener instanceof Action)
+ repeatKeyAction = (Action) listener;
+ else
+ repeatKeyAction = null;
+ } else {
+ repeatKeyAction = null;
+
+ if (keyStroke.getKeyCode() == KeyEvent.VK_ESCAPE) {
+ // System.out.println("Calling release on " + marquee);
+ if (marquee != null)
+ marquee.mouseReleased(null);
+
+ if (mouseListener != null)
+ mouseListener.mouseReleased(null);
+
+ updateHandle();
+ graph.repaint();
+ }
+ }
+
+ if (isKeyDown && (repeatKeyAction != null)) {
+ repeatKeyAction.actionPerformed(new ActionEvent(graph,
+ ActionEvent.ACTION_PERFORMED, ""));
+ e.consume();
+ } else
+ isKeyDown = true;
+ }
+ }
+
+ public void keyReleased(KeyEvent e) {
+ isKeyDown = false;
+ }
+ } // End of BasicGraphUI.KeyHandler
+
+ /**
+ * TreeMouseListener is responsible for updating the selection based on
+ * mouse events.
+ */
+ public class MouseHandler extends MouseAdapter implements MouseMotionListener, Serializable {
+ /* The cell under the mousepointer. */
+ protected CellView cell;
+
+ /* The object that handles mouse operations. */
+ protected Object handler;
+ protected transient Cursor previousCursor = null;
+
+ /**
+ * Invoked when a mouse button has been pressed on a component.
+ */
+ public void mousePressed(MouseEvent e) {
+ handler = null;
+
+ if (!e.isConsumed() && graph.isEnabled()) {
+ graph.requestFocus();
+
+ int s = graph.getTolerance();
+ Rectangle2D r = graph.fromScreen(new Rectangle2D.Double(e.getX() - s, e.getY() - s,
+ 2 * s, 2 * s));
+ lastFocus = focus;
+ focus = ((focus != null) && focus.intersects(graph, r)) ? focus : null;
+ cell = graph.getNextSelectableViewAt(focus, e.getX(), e.getY());
+
+ if (focus == null)
+ focus = cell;
+
+ completeEditing();
+
+ if (!isForceMarqueeEvent(e)) {
+ if ((e.getClickCount() == graph.getEditClickCount()) && (focus != null)
+ && focus.isLeaf() && (focus.getParentView() == null)
+ && graph.isCellEditable(focus.getCell())
+ && handleEditTrigger(cell.getCell(), e)) {
+ e.consume();
+ cell = null;
+ } else if (!isToggleSelectionEvent(e)) {
+ if (handle != null) {
+ handle.mousePressed(e);
+ handler = handle;
+ }
+
+ // Immediate Selection
+ if (!e.isConsumed() && (cell != null)
+ && !graph.isCellSelected(cell.getCell())) {
+ selectCellForEvent(cell.getCell(), e);
+ focus = cell;
+
+ if (handle != null) {
+ handle.mousePressed(e);
+ handler = handle;
+ }
+
+ e.consume();
+ cell = null;
+ }
+ }
+ }
+
+ // Marquee Selection
+ if (!e.isConsumed() && (marquee != null)
+ && (!isToggleSelectionEvent(e) || (focus == null))) {
+ marquee.mousePressed(e);
+ handler = marquee;
+ }
+ }
+ }
+
+ /**
+ * Handles edit trigger by starting the edit and return true if the
+ * editing has already started.
+ *
+ * @param cell
+ * the cell being edited
+ * @param e
+ * the mouse event triggering the edit
+ * @return <code>true</code> if the editing has already started
+ */
+ protected boolean handleEditTrigger(Object cell, MouseEvent e) {
+ graph.scrollCellToVisible(cell);
+
+ if (cell != null)
+ startEditing(cell, e);
+
+ return graph.isEditing();
+ }
+
+ public void mouseDragged(MouseEvent e) {
+ autoscroll(graph, e.getPoint());
+
+ if (graph.isEnabled()) {
+ if ((handler != null) && (handler == marquee))
+ marquee.mouseDragged(e);
+ else if ((handler == null) && !isEditing(graph) && (focus != null)) {
+ if (!graph.isCellSelected(focus.getCell())) {
+ selectCellForEvent(focus.getCell(), e);
+ cell = null;
+ }
+
+ if (handle != null)
+ handle.mousePressed(e);
+
+ handler = handle;
+ }
+
+ if ((handle != null) && (handler == handle))
+ handle.mouseDragged(e);
+ }
+ }
+
+ /**
+ * Invoked when the mouse pointer has been moved on a component (with no
+ * buttons down).
+ */
+ public void mouseMoved(MouseEvent e) {
+ if (previousCursor == null) {
+ previousCursor = graph.getCursor();
+ }
+
+ if ((graph != null) && graph.isEnabled()) {
+ if (marquee != null)
+ marquee.mouseMoved(e);
+
+ if (handle != null)
+ handle.mouseMoved(e);
+
+ if (!e.isConsumed() && (previousCursor != null)) {
+ Cursor currentCursor = graph.getCursor();
+
+ if (currentCursor != previousCursor) {
+ graph.setCursor(previousCursor);
+ }
+
+ previousCursor = null;
+ }
+ }
+ }
+
+ // Event may be null when called to cancel the current operation.
+ public void mouseReleased(MouseEvent e) {
+ try {
+ if ((e != null) && !e.isConsumed() && (graph != null) && graph.isEnabled()) {
+ if ((handler == marquee) && (marquee != null))
+ marquee.mouseReleased(e);
+ else if ((handler == handle) && (handle != null))
+ handle.mouseReleased(e);
+
+ if (isDescendant(cell, focus) && (e.getModifiers() != 0)) {
+ // Do not switch to parent if Special Selection
+ cell = focus;
+ }
+
+ if (!e.isConsumed() && (cell != null)) {
+ Object tmp = cell.getCell();
+ boolean wasSelected = graph.isCellSelected(tmp);
+ // if (!wasSelected || e.getModifiers() != 0)
+ selectCellForEvent(tmp, e);
+ focus = cell;
+ postProcessSelection(e, tmp, wasSelected);
+ }
+ }
+ } finally {
+ handler = null;
+ cell = null;
+ }
+ }
+
+ /**
+ * Invoked after a cell has been selected in the mouseReleased method.
+ * This can be used to do something interesting if the cell was already
+ * selected, in which case this implementation selects the parent.
+ * Override if you want different behaviour, such as start editing.
+ */
+ protected void postProcessSelection(MouseEvent e, Object cell, boolean wasSelected) {
+ if (wasSelected && graph.isCellSelected(cell) && (e.getModifiers() != 0)) {
+ Object parent = cell;
+ Object nextParent = null;
+
+ while (((nextParent = graphModel.getParent(parent)) != null)
+ && graphLayoutCache.isVisible(nextParent))
+ parent = nextParent;
+
+ selectCellForEvent(parent, e);
+ lastFocus = focus;
+ focus = graphLayoutCache.getMapping(parent, false);
+ }
+ }
+
+ protected boolean isDescendant(CellView parentView, CellView childView) {
+ if ((parentView == null) || (childView == null)) {
+ return false;
+ }
+
+ Object parent = parentView.getCell();
+ Object child = childView.getCell();
+ Object ancestor = child;
+
+ do {
+ if (ancestor == parent)
+ return true;
+ } while ((ancestor = graphModel.getParent(ancestor)) != null);
+
+ return false;
+ }
+ } // End of BasicGraphUI.MouseHandler
+
+ public class RootHandle implements CellHandle, Serializable {
+ // x and y offset from the mouse press event to the left/top corner of a
+ // view that is returned by a findViewForPoint().
+ // These are used only when the isSnapSelectedView mode is enabled.
+ protected transient double _mouseToViewDelta_x = 0;
+ protected transient double _mouseToViewDelta_y = 0;
+
+ // Double Buffered
+ protected transient Image offscreen;
+ protected transient Graphics offgraphics;
+ protected transient boolean firstDrag = true;
+
+ /* Temporary views for the cells. */
+ protected transient CellView[] views;
+ protected transient CellView[] contextViews;
+ protected transient CellView[] portViews;
+ protected transient CellView targetGroup;
+ protected transient CellView ignoreTargetGroup;
+
+ /* Bounds of the cells. Non-null if too many cells. */
+ protected transient Rectangle2D cachedBounds;
+
+ /* Initial top left corner of the selection */
+ protected transient Point2D initialLocation;
+
+ /* Child handles. Null if too many handles. */
+ protected transient CellHandle[] handles;
+
+ /* The point where the mouse was pressed. */
+ protected transient Point2D start = null;
+
+ /* The point where the mouse was pressed. */
+ protected transient Point2D last;
+
+ /* The point where the mouse was pressed. */
+ protected transient Point2D snapStart;
+
+ /* The point where the mouse was pressed. */
+ protected transient Point2D snapLast;
+
+ /**
+ * Indicates whether this handle is currently moving cells. Start may be
+ * non-null and isMoving false while the minimum movement has not been
+ * reached.
+ */
+ protected boolean isMoving = false;
+
+ /**
+ * Indicates whether this handle has started drag and drop. Note:
+ * isDragging => isMoving.
+ */
+ protected boolean isDragging = false;
+
+ /** The handle that consumed the last mousePressedEvent. Initially null. */
+ protected transient CellHandle activeHandle = null;
+
+ /* The current selection context, responsible for cloning the cells. */
+ protected transient GraphContext context;
+
+ /*
+ * True after the graph was repainted to block xor-ed painting of
+ * background.
+ */
+ protected boolean isContextVisible = true;
+ protected boolean blockPaint = false;
+
+ /* Defines the Disconnection if DisconnectOnMove is True */
+ protected transient ConnectionSet disconnect = null;
+
+ /**
+ * Creates a root handle which contains handles for the given cells. The
+ * root handle and all its childs point to the specified JGraph
+ * instance. The root handle is responsible for dragging the selection.
+ */
+ public RootHandle(GraphContext ctx) {
+ this.context = ctx;
+
+ if (!ctx.isEmpty()) {
+ // Temporary cells
+ views = ctx.createTemporaryCellViews();
+
+ Rectangle2D tmpBounds = graph.toScreen(graph.getCellBounds(ctx.getCells()));
+
+ if (ctx.getDescendantCount() < MAXCELLS) {
+ contextViews = ctx.createTemporaryContextViews();
+ initialLocation = graph.toScreen(getInitialLocation(ctx.getCells()));
+ } else
+ cachedBounds = tmpBounds;
+
+ if (initialLocation == null)
+ initialLocation = new Point2D.Double(tmpBounds.getX(), tmpBounds.getY());
+
+ // Sub-Handles
+ Object[] cells = ctx.getCells();
+
+ if (cells.length < MAXHANDLES) {
+ handles = new CellHandle[views.length];
+
+ for (int i = 0; i < views.length; i++)
+ handles[i] = views[i].getHandle(ctx);
+
+ // PortView Preview
+ portViews = ctx.createTemporaryPortViews();
+ }
+ }
+ }
+
+ /**
+ * Returns the initial location, which is the top left corner of the
+ * selection, ignoring all connected endpoints of edges.
+ */
+ protected Point2D getInitialLocation(Object[] cells) {
+ if ((cells != null) && (cells.length > 0)) {
+ Rectangle2D ret = null;
+
+ for (int i = 0; i < cells.length; i++) {
+ if (graphModel.isEdge(cells[i])) {
+ CellView cellView = graphLayoutCache.getMapping(cells[i], false);
+
+ if (cellView instanceof EdgeView) {
+ EdgeView edgeView = (EdgeView) cellView;
+
+ if (edgeView.getSource() == null) {
+ Point2D pt = edgeView.getPoint(0);
+
+ if (pt != null) {
+ if (ret == null)
+ ret = new Rectangle2D.Double(pt.getX(), pt.getY(), 0, 0);
+ else
+ Rectangle2D.union(ret,
+ new Rectangle2D.Double(pt.getX(),
+ pt.getY(), 0, 0),
+ ret);
+ }
+ }
+
+ if (edgeView.getTarget() == null) {
+ Point2D pt = edgeView.getPoint(edgeView.getPointCount() - 1);
+
+ if (pt != null) {
+ if (ret == null)
+ ret = new Rectangle2D.Double(pt.getX(), pt.getY(), 0, 0);
+ else
+ Rectangle2D.union(ret,
+ new Rectangle2D.Double(pt.getX(),
+ pt.getY(), 0, 0),
+ ret);
+ }
+ }
+ }
+ } else {
+ Rectangle2D r = graph.getCellBounds(cells[i]);
+
+ if (r != null) {
+ if (ret == null)
+ ret = (Rectangle2D) r.clone();
+
+ Rectangle2D.union(ret, r, ret);
+ }
+ }
+ }
+
+ if (ret != null)
+ return new Point2D.Double(ret.getX(), ret.getY());
+ }
+
+ return null;
+ }
+
+ /* Returns the context of this root handle. */
+ public GraphContext getContext() {
+ return context;
+ }
+
+ /* Paint the handles. Use overlay to paint the current state. */
+ public void paint(Graphics g) {
+ if ((handles != null) && (handles.length < MAXHANDLES))
+ for (int i = 0; i < handles.length; i++)
+ if (handles[i] != null)
+ handles[i].paint(g);
+
+ blockPaint = true;
+ }
+
+ public void overlay(Graphics g) {
+ if (isDragging && !DNDPREVIEW) // BUG IN 1.4.0 (FREEZE)
+ return;
+
+ if (cachedBounds != null) { // Paint Cached Bounds
+ g.setColor(Color.black);
+ g.drawRect((int) cachedBounds.getX(), (int) cachedBounds.getY(),
+ (int) cachedBounds.getWidth() - 2, (int) cachedBounds.getHeight() - 2);
+ } else {
+ Graphics2D g2 = (Graphics2D) g;
+ AffineTransform oldTransform = g2.getTransform();
+ g2.scale(graph.getScale(), graph.getScale());
+
+ if (views != null) { // Paint Temporary Views
+
+ for (int i = 0; i < views.length; i++)
+ paintCell(g, views[i], views[i].getBounds(), true);
+ }
+
+ // Paint temporary context
+ if ((contextViews != null) && isContextVisible) {
+ for (int i = 0; i < contextViews.length; i++)
+ paintCell(g, contextViews[i], contextViews[i].getBounds(), true);
+ }
+
+ if (!graph.isPortsScaled())
+ g2.setTransform(oldTransform);
+
+ if ((portViews != null) && graph.isPortsVisible())
+ paintPorts(g, portViews);
+
+ g2.setTransform(oldTransform);
+ }
+
+ // Paints the target group to move into
+ if (targetGroup != null) {
+ Rectangle2D b = graph.toScreen((Rectangle2D) targetGroup.getBounds().clone());
+ g.setColor(graph.getHandleColor());
+ g.fillRect((int) b.getX() - 1, (int) b.getY() - 1, (int) b.getWidth() + 2,
+ (int) b.getHeight() + 2);
+ g.setColor(graph.getMarqueeColor());
+ g.draw3DRect((int) b.getX() - 2, (int) b.getY() - 2, (int) b.getWidth() + 3,
+ (int) b.getHeight() + 3, true);
+ }
+ }
+
+ /**
+ * Invoked when the mouse pointer has been moved on a component (with no
+ * buttons down).
+ */
+ public void mouseMoved(MouseEvent event) {
+ if (!event.isConsumed() && (handles != null)) {
+ for (int i = handles.length - 1; (i >= 0) && !event.isConsumed(); i--)
+ if (handles[i] != null)
+ handles[i].mouseMoved(event);
+ }
+ }
+
+ public void mousePressed(MouseEvent event) {
+ if (!event.isConsumed() && graph.isMoveable()) {
+ if (handles != null) { // Find Handle
+
+ for (int i = handles.length - 1; i >= 0; i--) {
+ if (handles[i] != null) {
+ handles[i].mousePressed(event);
+
+ if (event.isConsumed()) {
+ activeHandle = handles[i];
+
+ return;
+ }
+ }
+ }
+ }
+
+ if (views != null) { // Start Move if over cell
+
+ Point2D screenPoint = event.getPoint();
+ Point2D pt = graph.fromScreen((Point2D) screenPoint.clone());
+ CellView view = findViewForPoint(pt);
+
+ if (view != null) {
+ if (snapSelectedView) {
+ Rectangle2D bounds = view.getBounds();
+ start = graph.toScreen(new Point2D.Double(bounds.getX(), bounds.getY()));
+ snapStart = graph.snap((Point2D) start.clone());
+ _mouseToViewDelta_x = screenPoint.getX() - start.getX();
+ _mouseToViewDelta_y = screenPoint.getY() - start.getY();
+ } else { // this is the original RootHandle's mode.
+ snapStart = graph.snap((Point2D) screenPoint.clone());
+ _mouseToViewDelta_x = snapStart.getX() - screenPoint.getX();
+ _mouseToViewDelta_y = snapStart.getY() - screenPoint.getY();
+ start = (Point2D) snapStart.clone();
+ }
+
+ last = (Point2D) start.clone();
+ snapLast = (Point2D) snapStart.clone();
+ isContextVisible = (contextViews != null)
+ && (contextViews.length < MAXCELLS)
+ && (!event.isControlDown() || !graph.isCloneable());
+ event.consume();
+ }
+ }
+
+ // Analyze for common parent
+ if (graph.isMoveIntoGroups() || graph.isMoveOutOfGroups()) {
+ Object[] cells = context.getCells();
+ Object ignoreGroup = graph.getModel().getParent(cells[0]);
+
+ for (int i = 1; i < cells.length; i++) {
+ Object tmp = graph.getModel().getParent(cells[i]);
+
+ if (ignoreGroup != tmp) {
+ ignoreGroup = null;
+
+ break;
+ }
+ }
+
+ if (ignoreGroup != null)
+ ignoreTargetGroup = graph.getGraphLayoutCache()
+ .getMapping(ignoreGroup, false);
+ }
+ }
+ }
+
+ /**
+ * Hook for subclassers to return a different view for a mouse click at
+ * <code>pt</code>. For example, this can be used to return a leaf
+ * cell instead of a group.
+ */
+ protected CellView findViewForPoint(Point2D pt) {
+ double snap = graph.getTolerance();
+ Rectangle2D r = new Rectangle2D.Double(pt.getX() - snap, pt.getY() - snap, 2 * snap,
+ 2 * snap);
+
+ for (int i = 0; i < views.length; i++)
+ if (views[i].intersects(graph, r))
+ return views[i];
+
+ return null;
+ }
+
+ /**
+ * Used for move into group to find the target group.
+ */
+ protected CellView findUnselectedInnermostGroup(double x, double y) {
+ Object[] cells = graph.getDescendants(graph.getRoots());
+
+ for (int i = cells.length - 1; i >= 0; i--) {
+ CellView view = graph.getGraphLayoutCache().getMapping(cells[i], false);
+
+ if ((view != null) && !view.isLeaf() && !context.contains(view.getCell())
+ && view.getBounds().contains(x, y))
+ return view;
+ }
+
+ return null;
+ }
+
+ protected void startDragging(MouseEvent event) {
+ isDragging = true;
+
+ if (graph.isDragEnabled()) {
+ int action = (event.isControlDown() && graph.isCloneable()) ? TransferHandler.COPY
+ : TransferHandler.MOVE;
+ TransferHandler th = graph.getTransferHandler();
+ setInsertionLocation(event.getPoint());
+
+ try {
+ th.exportAsDrag(graph, event, action);
+ } catch (Exception ex) {
+ // Ignore
+ }
+ }
+ }
+
+ /**
+ * @return Returns the parent graph scrollpane for the specified graph.
+ */
+ public Component getFirstOpaqueParent(Component component) {
+ if (component != null) {
+ Component parent = component;
+
+ while (parent != null) {
+ if (parent.isOpaque() && !(parent instanceof JViewport))
+ return parent;
+
+ parent = parent.getParent();
+ }
+ }
+
+ return component;
+ }
+
+ // Double Buffers by David Larsson
+ protected void initOffscreen() {
+ try {
+ Rectangle rect = graph.getBounds();
+ /*
+ * RepaintManager repMan = RepaintManager.currentManager(graph);
+ * offscreen = repMan.getVolatileOffscreenBuffer(graph, (int)
+ * rect.getWidth(), (int) rect.getHeight());
+ */
+ offscreen = new BufferedImage(rect.width, rect.height, BufferedImage.TYPE_INT_RGB);
+ offgraphics = offscreen.getGraphics();
+ offgraphics.setClip(0, 0, rect.width, rect.height);
+ /*
+ * Component comp = getFirstOpaqueParent(graph);
+ * offgraphics.translate(-rect.x, -rect.y);
+ * comp.paint(offgraphics); offgraphics.translate(rect.x,
+ * rect.y);
+ */
+ offgraphics.setColor(graph.getBackground());
+ offgraphics.fillRect(0, 0, rect.width, rect.height);
+ graph.getUI().paint(offgraphics, graph);
+ } catch (Exception e) {
+ offscreen = null;
+ offgraphics = null;
+ } catch (Error e) {
+ offscreen = null;
+ offgraphics = null;
+ }
+ }
+
+ /** Process mouse dragged event. */
+ public void mouseDragged(MouseEvent event) {
+ boolean constrained = isConstrainedMoveEvent(event);
+ boolean spread = false;
+ Rectangle2D dirty = null;
+
+ if (firstDrag && graph.isDoubleBuffered() && (cachedBounds == null)) {
+ initOffscreen();
+ firstDrag = false;
+ }
+
+ if ((event != null) && !event.isConsumed()) {
+ if (activeHandle != null) // Paint Active Handle
+ activeHandle.mouseDragged(event);
+
+ // Invoke Mouse Dragged
+ else if (start != null) { // Move Cells
+
+ Graphics g = (offgraphics != null) ? offgraphics : graph.getGraphics();
+ Point ep = event.getPoint();
+ Point2D point = new Point2D.Double(ep.getX() - _mouseToViewDelta_x,
+ ep.getY() - _mouseToViewDelta_y);
+ Point2D snapCurrent = graph.snap(point);
+ Point2D current = snapCurrent;
+ int thresh = graph.getMinimumMove();
+ double dx = current.getX() - start.getX();
+ double dy = current.getY() - start.getY();
+
+ if (isMoving || (Math.abs(dx) > thresh) || (Math.abs(dy) > thresh)) {
+ boolean overlayed = false;
+ isMoving = true;
+
+ if ((disconnect == null) && graph.isDisconnectOnMove())
+ disconnect = context.disconnect(graphLayoutCache.getAllDescendants(views));
+
+ // Constrained movement
+ double totDx = current.getX() - start.getX();
+ double totDy = current.getY() - start.getY();
+ dx = current.getX() - last.getX();
+ dy = current.getY() - last.getY();
+
+ if (constrained && (cachedBounds == null)) {
+ if (Math.abs(totDx) < Math.abs(totDy)) {
+ dx = 0;
+ dy = totDy;
+ } else {
+ dx = totDx;
+ dy = 0;
+ }
+ } else if (!graph.isMoveBelowZero() && (last != null)
+ && (initialLocation != null) && (start != null)) {
+ // TODO: remove?
+ if ((initialLocation.getX() + totDx) < 0)
+ dx = start.getX() - last.getX() - initialLocation.getX();
+
+ if ((initialLocation.getY() + totDy) < 0)
+ dy = start.getY() - last.getY() - initialLocation.getY();
+ }
+
+ double scale = graph.getScale();
+ dx = (int) (dx / scale);
+ // we don't want to round. The best thing is to get just
+ // the integer part.
+ // That way, the view won't "run away" from the mouse.
+ // It may lag behind
+ // a mouse pointer occasionally, but will be catching
+ // up.
+ dy = (int) (dy / scale);
+
+ g.setColor(graph.getForeground());
+
+ // use 'darker' to force XOR to distinguish between
+ // existing background elements during drag
+ // http://sourceforge.net/tracker/index.php?func=detail&aid=677743&group_id=43118&atid=435210
+ g.setXORMode(graph.getBackground().darker());
+
+ // Start Drag and Drop
+ if (graph.isDragEnabled() && !isDragging)
+ startDragging(event);
+
+ if ((dx != 0) || (dy != 0)) {
+ if (!snapLast.equals(snapStart) && ((offscreen != null) || !blockPaint)) {
+ overlay(g);
+ overlayed = true;
+ }
+
+ isContextVisible = (!event.isControlDown() || !graph.isCloneable())
+ && (contextViews != null)
+ && (contextViews.length < MAXCELLS);
+ blockPaint = false;
+
+ if (offscreen != null) {
+ dirty = graph.toScreen(AbstractCellView.getBounds(views));
+
+ Rectangle2D t = graph.toScreen(AbstractCellView.getBounds(contextViews));
+
+ if (t != null)
+ dirty.add(t);
+ }
+
+ if (constrained && (cachedBounds == null)) {
+ // Reset Initial Positions
+ CellView[] all = graphLayoutCache.getAllDescendants(views);
+
+ for (int i = 0; i < all.length; i++) {
+ CellView orig = graphLayoutCache.getMapping(all[i].getCell(),
+ false);
+ AttributeMap attr = orig.getAllAttributes();
+ all[i].changeAttributes((AttributeMap) attr.clone());
+ all[i].refresh(graph.getModel(), context, false);
+ }
+ }
+
+ if (cachedBounds != null)
+ cachedBounds.setFrame(cachedBounds.getX() + (dx * scale),
+ cachedBounds.getY() + (dy * scale),
+ cachedBounds.getWidth(),
+ cachedBounds.getHeight());
+ else {
+ // Translate
+ GraphLayoutCache.translateViews(views, dx, dy);
+
+ if (views != null)
+ graphLayoutCache.update(views);
+
+ if (contextViews != null)
+ graphLayoutCache.update(contextViews);
+ }
+
+ // Change preferred size of graph
+ if (graph.isAutoResizeGraph()
+ && ((event.getX() > (graph.getWidth() - SCROLLBORDER))
+ || (event.getY() > (graph.getHeight() - SCROLLBORDER)))) {
+ int SPREADSTEP = 25;
+ Rectangle view = null;
+
+ if (graph.getParent() instanceof JViewport)
+ view = ((JViewport) graph.getParent()).getViewRect();
+
+ if (view != null) {
+ if (view.contains(event.getPoint())) {
+ if (((view.x + view.width) - event.getPoint().x) < SCROLLBORDER) {
+ preferredSize.width = Math.max(preferredSize.width,
+ (int) view.getWidth())
+ + SPREADSTEP;
+ spread = true;
+ }
+
+ if (((view.y + view.height) - event.getPoint().y) < SCROLLBORDER) {
+ preferredSize.height = Math.max(preferredSize.height,
+ (int) view.getHeight())
+ + SPREADSTEP;
+ spread = true;
+ }
+
+ if (spread) {
+ graph.revalidate();
+ autoscroll(graph, event.getPoint());
+
+ if (graph.isDoubleBuffered())
+ initOffscreen();
+ }
+ }
+ }
+ }
+
+ // Move into groups
+ Rectangle2D ignoredRegion = (ignoreTargetGroup != null)
+ ? (Rectangle2D) ignoreTargetGroup.getBounds()
+ .clone()
+ : null;
+
+ if (targetGroup != null) {
+ Rectangle2D tmp = graph.toScreen((Rectangle2D) targetGroup.getBounds()
+ .clone());
+
+ if (dirty != null)
+ dirty.add(tmp);
+ else
+ dirty = tmp;
+ }
+
+ targetGroup = null;
+
+ if (graph.isMoveIntoGroups()
+ && ((ignoredRegion == null)
+ || !ignoredRegion.intersects(AbstractCellView.getBounds(views)))) {
+ targetGroup = (event.isControlDown()) ? null
+ : findUnselectedInnermostGroup(snapCurrent
+ .getX() / scale,
+ snapCurrent
+ .getY() / scale);
+
+ if (targetGroup == ignoreTargetGroup)
+ targetGroup = null;
+ }
+
+ if (!snapCurrent.equals(snapStart)
+ && ((offscreen != null) || !blockPaint) && !spread) {
+ overlay(g);
+ overlayed = true;
+ }
+
+ if (constrained)
+ last = (Point2D) start.clone();
+
+ last.setLocation(last.getX() + (dx * scale), last.getY() + (dy * scale));
+ // It is better to translate <code>last<code> by a
+ // scaled dx/dy
+ // instead of making it to be the
+ // <code>current<code> (as in prev version),
+ // so that the view would be catching up with a
+ // mouse pointer
+ snapLast = snapCurrent;
+
+ if (overlayed && (offscreen != null)) {
+ dirty.add(graph.toScreen(AbstractCellView.getBounds(views)));
+
+ Rectangle2D t = graph.toScreen(AbstractCellView.getBounds(contextViews));
+
+ if (t != null)
+ dirty.add(t);
+
+ // TODO: Should use real ports if portsVisible
+ // and check if ports are scaled
+ int border = PortView.SIZE + 4;
+
+ if (graph.isPortsScaled())
+ border = (int) (graph.getScale() * border);
+
+ int border2 = border / 2;
+ dirty.setFrame(dirty.getX() - border2, dirty.getY() - border2,
+ dirty.getWidth() + border, dirty.getHeight()
+ + border);
+
+ double sx1 = Math.max(0, dirty.getX());
+ double sy1 = Math.max(0, dirty.getY());
+ double sx2 = sx1 + dirty.getWidth();
+ double sy2 = sy1 + dirty.getHeight();
+
+ if (isDragging && !DNDPREVIEW) // BUG IN 1.4.0
+ // (FREEZE)
+
+ return;
+
+ graph.getGraphics()
+ .drawImage(offscreen, (int) sx1, (int) sy1, (int) sx2,
+ (int) sy2, (int) sx1, (int) sy1, (int) sx2,
+ (int) sy2, graph);
+ }
+ }
+ } // end if (isMoving or ...)
+ } // end if (start != null)
+ } else if (event == null)
+ graph.repaint();
+ }
+
+ public void mouseReleased(MouseEvent event) {
+ try {
+ if ((event != null) && !event.isConsumed()) {
+ if (activeHandle != null) {
+ activeHandle.mouseReleased(event);
+ activeHandle = null;
+ } else if (isMoving && !event.getPoint().equals(start)) {
+ if (cachedBounds != null) {
+ double dx = event.getX() - start.getX();
+ double dy = event.getY() - start.getY();
+ Point2D tmp = graph.fromScreen(new Point2D.Double(dx, dy));
+ GraphLayoutCache.translateViews(views, tmp.getX(), tmp.getY());
+ }
+
+ CellView[] all = graphLayoutCache.getAllDescendants(views);
+ Map attributes = GraphConstants.createAttributes(all, null);
+
+ if (event.isControlDown() && graph.isCloneable()) { // Clone
+ // Cells
+
+ Object[] cells = graph.getDescendants(graph.order(context.getCells()));
+
+ // Include properties from hidden cells
+ Map hiddenMapping = graphLayoutCache.getHiddenMapping();
+
+ for (int i = 0; i < cells.length; i++) {
+ Object witness = attributes.get(cells[i]);
+
+ if (witness == null) {
+ CellView view = (CellView) hiddenMapping.get(cells[i]);
+
+ if ((view != null) && !graphModel.isPort(view.getCell())) {
+ // TODO: Clone required? Same in
+ // GraphConstants.
+ AttributeMap attrs = (AttributeMap) view.getAllAttributes()
+ .clone();
+ // Maybe translate?
+ // attrs.translate(dx, dy);
+ attributes.put(cells[i], attrs.clone());
+ }
+ }
+ }
+
+ ConnectionSet cs = ConnectionSet.create(graphModel, cells, false);
+ ParentMap pm = ParentMap.create(graphModel, cells, false, true);
+ cells = graphLayoutCache.insertClones(cells, graph.cloneCells(cells),
+ attributes, cs, pm, 0, 0);
+ } else if (graph.isMoveable()) { // Move Cells
+
+ ParentMap pm = null;
+
+ // Moves into group
+ if (targetGroup != null) {
+ pm = new ParentMap(context.getCells(), targetGroup.getCell());
+ } else if (graph.isMoveOutOfGroups()
+ && ((ignoreTargetGroup != null)
+ && !ignoreTargetGroup.getBounds()
+ .intersects(AbstractCellView
+ [...]
+ pm = new ParentMap(context.getCells(), null);
+ }
+
+ graph.getGraphLayoutCache().edit(attributes, disconnect, pm, null);
+ }
+
+ event.consume();
+ }
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ } finally {
+ ignoreTargetGroup = null;
+ targetGroup = null;
+ initialLocation = null;
+ isDragging = false;
+ disconnect = null;
+ offscreen = null;
+ firstDrag = true;
+ start = null;
+ }
+ }
+ }
+
+ /**
+ * PropertyChangeListener for the graph. Updates the appropriate variable
+ * and takes the appropriate actions, based on what changes.
+ */
+ public class PropertyChangeHandler implements PropertyChangeListener, Serializable {
+ public void propertyChange(PropertyChangeEvent event) {
+ if (event.getSource() == graph) {
+ String changeName = event.getPropertyName();
+
+ if (changeName.equals("minimumSize"))
+ updateCachedPreferredSize();
+ else if (changeName.equals(JGraph.GRAPH_MODEL_PROPERTY))
+ setModel((GraphModel) event.getNewValue());
+ else if (changeName.equals(JGraph.GRAPH_LAYOUT_CACHE_PROPERTY)) {
+ setGraphLayoutCache((GraphLayoutCache) event.getNewValue());
+ graph.repaint();
+ } else if (changeName.equals(JGraph.MARQUEE_HANDLER_PROPERTY))
+ setMarquee((BasicMarqueeHandler) event.getNewValue());
+ else if (changeName.equals("transferHandler")) {
+ if (dropTarget != null)
+ dropTarget.removeDropTargetListener(defaultDropTargetListener);
+
+ dropTarget = graph.getDropTarget();
+
+ try {
+ if (dropTarget != null)
+ dropTarget.addDropTargetListener(defaultDropTargetListener);
+ } catch (TooManyListenersException tmle) {
+ // should not happen... swing drop target is multicast
+ }
+ } else if (changeName.equals(JGraph.EDITABLE_PROPERTY)) {
+ boolean editable = ((Boolean) event.getNewValue()).booleanValue();
+
+ if (!editable && isEditing(graph))
+ cancelEditing(graph);
+ } else if (changeName.equals(JGraph.SELECTION_MODEL_PROPERTY))
+ setSelectionModel(graph.getSelectionModel());
+ else if (changeName.equals(JGraph.GRID_VISIBLE_PROPERTY)
+ || changeName.equals(JGraph.GRID_SIZE_PROPERTY)
+ || changeName.equals(JGraph.GRID_COLOR_PROPERTY)
+ || changeName.equals(JGraph.HANDLE_COLOR_PROPERTY)
+ || changeName.equals(JGraph.LOCKED_HANDLE_COLOR_PROPERTY)
+ || changeName.equals(JGraph.HANDLE_SIZE_PROPERTY)
+ || changeName.equals(JGraph.PORTS_VISIBLE_PROPERTY)
+ || changeName.equals(JGraph.ANTIALIASED_PROPERTY))
+ graph.repaint();
+ else if (changeName.equals(JGraph.SCALE_PROPERTY))
+ updateSize();
+ else if (changeName.equals("font")) {
+ completeEditing();
+ updateSize();
+ } else if (changeName.equals("componentOrientation")) {
+ if (graph != null)
+ graph.graphDidChange();
+ }
+ }
+ }
+ } // End of BasicGraphUI.PropertyChangeHandler
+
+ /**
+ * GraphIncrementAction is used to handle up/down actions.
+ */
+ public class GraphIncrementAction extends AbstractAction {
+ /** Specifies the direction to adjust the selection by. */
+ protected int direction;
+
+ private GraphIncrementAction(int direction, String name) {
+ this.direction = direction;
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ if (graph != null) {
+ int step = 70;
+ Rectangle rect = graph.getVisibleRect();
+
+ if (direction == 1)
+ rect.translate(0, -step); // up
+ else if (direction == 2)
+ rect.translate(step, 0); // right
+ else if (direction == 3)
+ rect.translate(0, step); // down
+ else if (direction == 4)
+ rect.translate(-step, 0); // left
+
+ graph.scrollRectToVisible(rect);
+ }
+ }
+
+ public boolean isEnabled() {
+ return ((graph != null) && graph.isEnabled());
+ }
+ } // End of class BasicGraphUI.GraphIncrementAction
+
+ /**
+ * ActionListener that invokes cancelEditing when action performed.
+ */
+ private class GraphCancelEditingAction extends AbstractAction {
+ public GraphCancelEditingAction(String name) {
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ if (graph != null)
+ cancelEditing(graph);
+ }
+
+ public boolean isEnabled() {
+ return ((graph != null) && graph.isEnabled());
+ }
+ } // End of class BasicGraphUI.GraphCancelEditingAction
+
+ /**
+ * ActionListener invoked to start editing on the focused cell.
+ */
+ private class GraphEditAction extends AbstractAction {
+ public GraphEditAction(String name) {
+ }
+
+ public void actionPerformed(ActionEvent ae) {
+ if (isEnabled()) {
+ if (getFocusedCell() instanceof GraphCell) {
+ graph.startEditingAtCell(getFocusedCell());
+ }
+ }
+ }
+
+ public boolean isEnabled() {
+ return ((graph != null) && graph.isEnabled());
+ }
+ } // End of BasicGraphUI.GraphEditAction
+
+ /**
+ * Action to select everything in the graph.
+ */
+ private class GraphSelectAllAction extends AbstractAction {
+ private boolean selectAll;
+
+ public GraphSelectAllAction(String name, boolean selectAll) {
+ this.selectAll = selectAll;
+ }
+
+ public void actionPerformed(ActionEvent ae) {
+ if (graph != null) {
+ if (selectAll) {
+ graph.setSelectionCells(graph.getGraphLayoutCache()
+ .getVisibleCells(graph.getRoots()));
+ } else
+ graph.clearSelection();
+ }
+ }
+
+ public boolean isEnabled() {
+ return ((graph != null) && graph.isEnabled());
+ }
+ } // End of BasicGraphUI.GraphSelectAllAction
+
+ /**
+ * MouseInputHandler handles passing all mouse events, including mouse
+ * motion events, until the mouse is released to the destination it is
+ * constructed with. It is assumed all the events are currently target at
+ * source.
+ */
+ public class MouseInputHandler extends Object implements MouseInputListener {
+ /** Source that events are coming from. */
+ protected Component source;
+
+ /** Destination that receives all events. */
+ protected Component destination;
+
+ public MouseInputHandler(Component source, Component destination, MouseEvent event) {
+ this.source = source;
+ this.destination = destination;
+ this.source.addMouseListener(this);
+ this.source.addMouseMotionListener(this);
+ /* Dispatch the editing event */
+ destination.dispatchEvent(SwingUtilities.convertMouseEvent(source, event, destination));
+ }
+
+ public void mouseClicked(MouseEvent e) {
+ if (destination != null)
+ destination.dispatchEvent(SwingUtilities.convertMouseEvent(source, e, destination));
+ }
+
+ public void mousePressed(MouseEvent e) {
+ }
+
+ public void mouseReleased(MouseEvent e) {
+ if (destination != null)
+ destination.dispatchEvent(SwingUtilities.convertMouseEvent(source, e, destination));
+
+ removeFromSource();
+ }
+
+ public void mouseEntered(MouseEvent e) {
+ if (!SwingUtilities.isLeftMouseButton(e)) {
+ removeFromSource();
+ }
+ }
+
+ public void mouseExited(MouseEvent e) {
+ if (!SwingUtilities.isLeftMouseButton(e)) {
+ removeFromSource();
+ }
+
+ // insertionLocation = null;
+ }
+
+ public void mouseDragged(MouseEvent e) {
+ if (destination != null)
+ destination.dispatchEvent(SwingUtilities.convertMouseEvent(source, e, destination));
+ }
+
+ public void mouseMoved(MouseEvent e) {
+ removeFromSource();
+ }
+
+ protected void removeFromSource() {
+ if (source != null) {
+ source.removeMouseListener(this);
+ source.removeMouseMotionListener(this);
+ }
+
+ source = destination = null;
+ }
+ } // End of class BasicGraphUI.MouseInputHandler
+
+ /**
+ * Graph Drop Target Listener
+ */
+ public class GraphDropTargetListener extends BasicGraphDropTargetListener
+ implements Serializable {
+ /**
+ * called to save the state of a component in case it needs to be
+ * restored because a drop is not performed.
+ */
+ protected void saveComponentState(JComponent comp) {
+ }
+
+ /**
+ * called to restore the state of a component because a drop was not
+ * performed.
+ */
+ protected void restoreComponentState(JComponent comp) {
+ if (handle != null)
+ handle.mouseDragged(null);
+ }
+
+ /**
+ * called to set the insertion location to match the current mouse
+ * pointer coordinates.
+ */
+ protected void updateInsertionLocation(JComponent comp, Point p) {
+ setInsertionLocation(p);
+
+ if (handle != null) {
+ // How to fetch the shift state?
+ int mod = (dropAction == TransferHandler.COPY) ? InputEvent.CTRL_MASK : 0;
+ handle.mouseDragged(new MouseEvent(comp, 0, 0, mod, p.x, p.y, 1, false));
+ }
+ }
+
+ public void dragEnter(DropTargetDragEvent e) {
+ dropAction = e.getDropAction();
+ super.dragEnter(e);
+ }
+
+ public void dropActionChanged(DropTargetDragEvent e) {
+ dropAction = e.getDropAction();
+ super.dropActionChanged(e);
+ }
+ } // End of BasicGraphUI.GraphDropTargetListener
+
+ /**
+ * @return true if snapSelectedView mode is enabled during the drag
+ * operation. If it is enabled, the view, that is returned by the
+ * findViewForPoint(Point pt), will be snapped to the grid lines.
+ * <br>
+ * By default, findViewForPoint() returns the first view from the
+ * GraphContext whose bounds intersect with snap proximity of a
+ * mouse pointer. If snap-to-grid mode is disabled, views are moved
+ * by a snap increment.
+ */
+ public boolean isSnapSelectedView() {
+ return snapSelectedView;
+ }
+
+ /**
+ * Sets the mode of the snapSelectedView drag operation.
+ *
+ * @param snapSelectedView
+ * specifies if the snap-to-grid mode should be applied during a
+ * drag operation. If it is enabled, the view, that is returned
+ * by the findViewForPoint(Point pt), will be snapped to the grid
+ * lines. <br>
+ * By default, findViewForPoint() returns the first view from the
+ * GraphContext whose bounds intersect with snap proximity of a
+ * mouse pointer. If snap-to-grid mode is disabled, views are
+ * moved by a snap increment.
+ */
+ public void setSnapSelectedView(boolean snapSelectedView) {
+ this.snapSelectedView = snapSelectedView;
+ }
+} // End of class BasicGraphUI
diff --git a/coreplugins/AutomaticLayout/src/main/java/prefuse/util/force/AbstractForce.java b/coreplugins/AutomaticLayout/src/main/java/prefuse/util/force/AbstractForce.java
new file mode 100644
index 0000000..67d3b2c
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/prefuse/util/force/AbstractForce.java
@@ -0,0 +1,147 @@
+package prefuse.util.force;
+
+/**
+ * Abstract base class for force functions in a force simulation. This
+ * skeletal version provides support for storing and retrieving float-valued
+ * parameters of the force function. Subclasses should use the protected
+ * field <code>params</code> to store parameter values.
+ *
+ * @author <a href="http://jheer.org">jeffrey heer</a>
+ */
+public abstract class AbstractForce implements Force {
+
+ protected float[] params;
+ protected float[] minValues;
+ protected float[] maxValues;
+
+ /**
+ * Initialize this force function. This default implementation does nothing.
+ * Subclasses should override this method with any needed initialization.
+ * @param fsim the encompassing ForceSimulator
+ */
+ public void init(ForceSimulator fsim) {
+ // do nothing.
+ }
+
+ /**
+ * @see prefuse.util.force.Force#getParameterCount()
+ */
+ public int getParameterCount() {
+ return ( params == null ? 0 : params.length );
+ }
+
+ /**
+ * @see prefuse.util.force.Force#getParameter(int)
+ */
+ public float getParameter(int i) {
+ if ( i < 0 || params == null || i >= params.length ) {
+ throw new IndexOutOfBoundsException();
+ } else {
+ return params[i];
+ }
+ }
+
+ /**
+ * @see prefuse.util.force.Force#getMinValue(int)
+ */
+ public float getMinValue(int i) {
+ if ( i < 0 || params == null || i >= params.length ) {
+ throw new IndexOutOfBoundsException();
+ } else {
+ return minValues[i];
+ }
+ }
+
+ /**
+ * @see prefuse.util.force.Force#getMaxValue(int)
+ */
+ public float getMaxValue(int i) {
+ if ( i < 0 || params == null || i >= params.length ) {
+ throw new IndexOutOfBoundsException();
+ } else {
+ return maxValues[i];
+ }
+ }
+
+ /**
+ * @see prefuse.util.force.Force#getParameterName(int)
+ */
+ public String getParameterName(int i) {
+ String[] pnames = getParameterNames();
+ if ( i < 0 || pnames == null || i >= pnames.length ) {
+ throw new IndexOutOfBoundsException();
+ } else {
+ return pnames[i];
+ }
+ }
+
+ /**
+ * @see prefuse.util.force.Force#setParameter(int, float)
+ */
+ public void setParameter(int i, float val) {
+ if ( i < 0 || params == null || i >= params.length ) {
+ throw new IndexOutOfBoundsException();
+ } else {
+ params[i] = val;
+ }
+ }
+
+ /**
+ * @see prefuse.util.force.Force#setMinValue(int, float)
+ */
+ public void setMinValue(int i, float val) {
+ if ( i < 0 || params == null || i >= params.length ) {
+ throw new IndexOutOfBoundsException();
+ } else {
+ minValues[i] = val;
+ }
+ }
+
+ /**
+ * @see prefuse.util.force.Force#setMaxValue(int, float)
+ */
+ public void setMaxValue(int i, float val) {
+ if ( i < 0 || params == null || i >= params.length ) {
+ throw new IndexOutOfBoundsException();
+ } else {
+ maxValues[i] = val;
+ }
+ }
+
+ protected abstract String[] getParameterNames();
+
+ /**
+ * Returns false.
+ * @see prefuse.util.force.Force#isItemForce()
+ */
+ public boolean isItemForce() {
+ return false;
+ }
+
+ /**
+ * Returns false.
+ * @see prefuse.util.force.Force#isSpringForce()
+ */
+ public boolean isSpringForce() {
+ return false;
+ }
+
+ /**
+ * Throws an UnsupportedOperationException.
+ * @see prefuse.util.force.Force#getForce(prefuse.util.force.ForceItem)
+ */
+ public void getForce(ForceItem item) {
+ throw new UnsupportedOperationException(
+ "This class does not support this operation");
+ }
+
+ /**
+ * Throws an UnsupportedOperationException.
+ * @see prefuse.util.force.Force#getForce(prefuse.util.force.Spring)
+ */
+ public void getForce(Spring spring) {
+ throw new UnsupportedOperationException(
+ "This class does not support this operation");
+ }
+
+} // end of abstract class AbstractForce
diff --git a/coreplugins/AutomaticLayout/src/main/java/prefuse/util/force/BackwardEulerIntegrator.java b/coreplugins/AutomaticLayout/src/main/java/prefuse/util/force/BackwardEulerIntegrator.java
new file mode 100644
index 0000000..ed4f9f1
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/prefuse/util/force/BackwardEulerIntegrator.java
@@ -0,0 +1,46 @@
+/**
+ * @author ruschein
+ */
+package prefuse.util.force;
+
+import java.util.Iterator;
+
+//
+// **************************************************** WARNING: B R O K E N !!!
+//
+
+/**
+ * Updates velocity and position data using the Backward Euler Method. This is the
+ * simple and fast method, but is somewhat inaccurate and less smooth
+ * than more costly approaches.
+ *
+ * @author Johannes Ruscheinski
+ * @see RungeKuttaIntegrator
+ * @see EulerIntegrator
+ */
+public class BackwardEulerIntegrator implements Integrator {
+
+ /**
+ * @see prefuse.util.force.Integrator#integrate(prefuse.util.force.ForceSimulator, long)
+ */
+ public void integrate(final ForceSimulator sim, final long timestep) {
+ float speedLimit = sim.getSpeedLimit();
+ Iterator iter = sim.getItems();
+ while ( iter.hasNext() ) {
+ ForceItem item = (ForceItem)iter.next();
+ float coeff = timestep / item.mass;
+ item.velocity[0] += coeff * item.force[0];
+ item.velocity[1] += coeff * item.force[1];
+ item.location[0] += timestep * item.velocity[0];
+ item.location[1] += timestep * item.velocity[1];
+ float vx = item.velocity[0];
+ float vy = item.velocity[1];
+ float v = (float)Math.sqrt(vx*vx + vy*vy);
+ if ( v > speedLimit ) {
+ item.velocity[0] = speedLimit * vx / v;
+ item.velocity[1] = speedLimit * vy / v;
+ }
+ }
+ }
+
+} // end of class BackwardEulerIntegrator
diff --git a/coreplugins/AutomaticLayout/src/main/java/prefuse/util/force/CircularWallForce.java b/coreplugins/AutomaticLayout/src/main/java/prefuse/util/force/CircularWallForce.java
new file mode 100644
index 0000000..cfbabbe
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/prefuse/util/force/CircularWallForce.java
@@ -0,0 +1,83 @@
+package prefuse.util.force;
+
+/**
+ * Uses a gravitational force model to act as a circular "wall". Can be used to
+ * construct circles which either attract or repel items.
+ *
+ * @author <a href="http://jheer.org">jeffrey heer</a>
+ */
+public class CircularWallForce extends AbstractForce {
+
+ private static String[] pnames = new String[] { "GravitationalConstant" };
+
+ public static final float DEFAULT_GRAV_CONSTANT = -0.1f;
+ public static final float DEFAULT_MIN_GRAV_CONSTANT = -1.0f;
+ public static final float DEFAULT_MAX_GRAV_CONSTANT = 1.0f;
+ public static final int GRAVITATIONAL_CONST = 0;
+
+ private float x, y, r;
+
+ /**
+ * Create a new CircularWallForce.
+ * @param gravConst the gravitational constant to use
+ * @param x the center x-coordinate of the circle
+ * @param y the center y-coordinate of the circle
+ * @param r the radius of the circle
+ */
+ public CircularWallForce(float gravConst,
+ float x, float y, float r)
+ {
+ params = new float[] { gravConst };
+ minValues = new float[] { DEFAULT_MIN_GRAV_CONSTANT };
+ maxValues = new float[] { DEFAULT_MAX_GRAV_CONSTANT };
+ this.x = x; this.y = y;
+ this.r = r;
+ }
+
+ /**
+ * Create a new CircularWallForce with default gravitational constant.
+ * @param x the center x-coordinate of the circle
+ * @param y the center y-coordinate of the circle
+ * @param r the radius of the circle
+ */
+ public CircularWallForce(float x, float y, float r) {
+ this(DEFAULT_GRAV_CONSTANT,x,y,r);
+ }
+
+ /**
+ * Returns true.
+ * @see prefuse.util.force.Force#isItemForce()
+ */
+ public boolean isItemForce() {
+ return true;
+ }
+
+ /**
+ * @see prefuse.util.force.AbstractForce#getParameterNames()
+ */
+ protected String[] getParameterNames() {
+ return pnames;
+ }
+
+ /**
+ * @see prefuse.util.force.Force#getForce(prefuse.util.force.ForceItem)
+ */
+ public void getForce(ForceItem item) {
+ float[] n = item.location;
+ float dx = x-n[0];
+ float dy = y-n[1];
+ float d = (float)Math.sqrt(dx*dx+dy*dy);
+ float dr = r-d;
+ float c = dr > 0 ? -1 : 1;
+ float v = c*params[GRAVITATIONAL_CONST]*item.mass / (dr*dr);
+ if ( d == 0.0 ) {
+ dx = ((float)Math.random()-0.5f) / 50.0f;
+ dy = ((float)Math.random()-0.5f) / 50.0f;
+ d = (float)Math.sqrt(dx*dx+dy*dy);
+ }
+ item.force[0] += v*dx/d;
+ item.force[1] += v*dy/d;
+ //System.out.println(dx/d+","+dy/d+","+dr+","+v);
+ }
+
+} // end of class CircularWallForce
diff --git a/coreplugins/AutomaticLayout/src/main/java/prefuse/util/force/DragForce.java b/coreplugins/AutomaticLayout/src/main/java/prefuse/util/force/DragForce.java
new file mode 100644
index 0000000..8864e3c
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/prefuse/util/force/DragForce.java
@@ -0,0 +1,57 @@
+package prefuse.util.force;
+
+/**
+ * Implements a viscosity/drag force to help stabilize items.
+ *
+ * @author <a href="http://jheer.org">jeffrey heer</a>
+ */
+public class DragForce extends AbstractForce {
+
+ private static String[] pnames = new String[] { "DragCoefficient" };
+
+ public static final float DEFAULT_DRAG_COEFF = 0.01f;
+ public static final float DEFAULT_MIN_DRAG_COEFF = 0.0f;
+ public static final float DEFAULT_MAX_DRAG_COEFF = 0.1f;
+ public static final int DRAG_COEFF = 0;
+
+ /**
+ * Create a new DragForce.
+ * @param dragCoeff the drag co-efficient
+ */
+ public DragForce(float dragCoeff) {
+ params = new float[] { dragCoeff };
+ minValues = new float[] { DEFAULT_MIN_DRAG_COEFF };
+ maxValues = new float[] { DEFAULT_MAX_DRAG_COEFF };
+ }
+
+ /**
+ * Create a new DragForce with default drag co-efficient.
+ */
+ public DragForce() {
+ this(DEFAULT_DRAG_COEFF);
+ }
+
+ /**
+ * Returns true.
+ * @see prefuse.util.force.Force#isItemForce()
+ */
+ public boolean isItemForce() {
+ return true;
+ }
+
+ /**
+ * @see prefuse.util.force.AbstractForce#getParameterNames()
+ */
+ protected String[] getParameterNames() {
+ return pnames;
+ }
+
+ /**
+ * @see prefuse.util.force.Force#getForce(prefuse.util.force.ForceItem)
+ */
+ public void getForce(ForceItem item) {
+ item.force[0] -= params[DRAG_COEFF]*item.velocity[0];
+ item.force[1] -= params[DRAG_COEFF]*item.velocity[1];
+ }
+
+} // end of class DragForce
diff --git a/coreplugins/AutomaticLayout/src/main/java/prefuse/util/force/EulerIntegrator.java b/coreplugins/AutomaticLayout/src/main/java/prefuse/util/force/EulerIntegrator.java
new file mode 100644
index 0000000..c4ca98e
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/prefuse/util/force/EulerIntegrator.java
@@ -0,0 +1,38 @@
+package prefuse.util.force;
+
+import java.util.Iterator;
+
+/**
+ * Updates velocity and position data using Euler's Method. This is the
+ * simplest and fastest method, but is somewhat inaccurate and less smooth
+ * than more costly approaches.
+ *
+ * @author <a href="http://jheer.org">jeffrey heer</a>
+ * @see RungeKuttaIntegrator
+ */
+public class EulerIntegrator implements Integrator {
+
+ /**
+ * @see prefuse.util.force.Integrator#integrate(prefuse.util.force.ForceSimulator, long)
+ */
+ public void integrate(ForceSimulator sim, long timestep) {
+ float speedLimit = sim.getSpeedLimit();
+ Iterator iter = sim.getItems();
+ while ( iter.hasNext() ) {
+ ForceItem item = (ForceItem)iter.next();
+ item.location[0] += timestep * item.velocity[0];
+ item.location[1] += timestep * item.velocity[1];
+ float coeff = timestep / item.mass;
+ item.velocity[0] += coeff * item.force[0];
+ item.velocity[1] += coeff * item.force[1];
+ float vx = item.velocity[0];
+ float vy = item.velocity[1];
+ float v = (float)Math.sqrt(vx*vx+vy*vy);
+ if ( v > speedLimit ) {
+ item.velocity[0] = speedLimit * vx / v;
+ item.velocity[1] = speedLimit * vy / v;
+ }
+ }
+ }
+
+} // end of class EulerIntegrator
diff --git a/coreplugins/AutomaticLayout/src/main/java/prefuse/util/force/Force.java b/coreplugins/AutomaticLayout/src/main/java/prefuse/util/force/Force.java
new file mode 100644
index 0000000..08de763
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/prefuse/util/force/Force.java
@@ -0,0 +1,107 @@
+package prefuse.util.force;
+
+/**
+ * Interface for force functions in a force simulation.
+ *
+ * @author <a href="http://jheer.org">jeffrey heer</a>
+ */
+public interface Force {
+
+ /**
+ * Initialize this force function.
+ * @param fsim the encompassing ForceSimulator
+ */
+ public void init(ForceSimulator fsim);
+
+ /**
+ * Returns the number of parameters (e.g., gravitational constant or
+ * spring force coefficient) affecting this force function.
+ * @return the number of parameters
+ */
+ public int getParameterCount();
+
+ /**
+ * Returns the specified, numbered parameter.
+ * @param i the index of the parameter to return
+ * @return the parameter value
+ */
+ public float getParameter(int i);
+
+ /**
+ * Get the suggested minimum value for a parameter. This value is not
+ * strictly enforced, but is used by interface components that allow force
+ * parameters to be varied.
+ * @param param the parameter index
+ * @return the suggested minimum value.
+ */
+ public float getMinValue(int param);
+
+ /**
+ * Get the suggested maximum value for a parameter. This value is not
+ * strictly enforced, but is used by interface components that allow force
+ * parameters to be varied.
+ * @param param the parameter index
+ * @return the suggested maximum value.
+ */
+ public float getMaxValue(int param);
+
+ /**
+ * Gets the text name of the requested parameter.
+ * @param i the index of the parameter
+ * @return a String containing the name of this parameter
+ */
+ public String getParameterName(int i);
+
+ /**
+ * Sets the specified parameter value.
+ * @param i the index of the parameter
+ * @param val the new value of the parameter
+ */
+ public void setParameter(int i, float val);
+
+ /**
+ * Set the suggested minimum value for a parameter. This value is not
+ * strictly enforced, but is used by interface components that allow force
+ * parameters to be varied.
+ * @param i the parameter index
+ * @param val the suggested minimum value to use
+ */
+ public void setMinValue(int i, float val);
+
+ /**
+ * Set the suggested maximum value for a parameter. This value is not
+ * strictly enforced, but is used by interface components that allow force
+ * parameters to be varied.
+ * @param i the parameter index
+ * @return the suggested maximum value to use
+ */
+ public void setMaxValue(int i, float val);
+
+ /**
+ * Indicates if this force function will compute forces
+ * on Spring instances.
+ * @return true if this force function processes Spring instances
+ */
+ public boolean isSpringForce();
+
+ /**
+ * Indicates if this force function will compute forces
+ * on ForceItem instances
+ * @return true if this force function processes Force instances
+ */
+ public boolean isItemForce();
+
+ /**
+ * Updates the force calculation on the given ForceItem
+ * @param item the ForceItem on which to compute updated forces
+ */
+ public void getForce(ForceItem item);
+
+ /**
+ * Updates the force calculation on the given Spring. The ForceItems
+ * attached to Spring will have their force values updated appropriately.
+ * @param spring the Spring on which to compute updated forces
+ */
+ public void getForce(Spring spring);
+
+} // end of interface Force
diff --git a/coreplugins/AutomaticLayout/src/main/java/prefuse/util/force/ForceItem.java b/coreplugins/AutomaticLayout/src/main/java/prefuse/util/force/ForceItem.java
new file mode 100644
index 0000000..c00419b
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/prefuse/util/force/ForceItem.java
@@ -0,0 +1,71 @@
+package prefuse.util.force;
+
+/**
+ * Represents a point particle in a force simulation, maintaining values for
+ * mass, forces, velocity, and position.
+ *
+ * @author <a href="http://jheer.org">jeffrey heer</a>
+ */
+public class ForceItem implements Cloneable {
+
+ /**
+ * Create a new ForceItem.
+ */
+ public ForceItem() {
+ mass = 1.0f;
+ force = new float[] { 0.f, 0.f };
+ velocity = new float[] { 0.f, 0.f };
+ location = new float[] { 0.f, 0.f };
+ plocation = new float[] { 0.f, 0.f };
+ k = new float[4][2];
+ l = new float[4][2];
+ }
+
+ /**
+ * Clone a ForceItem.
+ * @see java.lang.Object#clone()
+ */
+ public Object clone() {
+ ForceItem item = new ForceItem();
+ item.mass = this.mass;
+ System.arraycopy(force,0,item.force,0,2);
+ System.arraycopy(velocity,0,item.velocity,0,2);
+ System.arraycopy(location,0,item.location,0,2);
+ System.arraycopy(plocation,0,item.plocation,0,2);
+ for ( int i=0; i<k.length; ++i ) {
+ System.arraycopy(k[i],0,item.k[i],0,2);
+ System.arraycopy(l[i],0,item.l[i],0,2);
+ }
+ return item;
+ }
+
+ /** The mass value of this ForceItem. */
+ public float mass;
+ /** The values of the forces acting on this ForceItem. */
+ public float[] force;
+ /** The velocity values of this ForceItem. */
+ public float[] velocity;
+ /** The location values of this ForceItem. */
+ public float[] location;
+ /** The previous location values of this ForceItem. */
+ public float[] plocation;
+ /** Temporary variables for Runge-Kutta integration */
+ public float[][] k;
+ /** Temporary variables for Runge-Kutta integration */
+ public float[][] l;
+
+ /**
+ * Checks a ForceItem to make sure its values are all valid numbers
+ * (i.e., not NaNs).
+ * @param item the item to check
+ * @return true if all the values are valid, false otherwise
+ */
+ public static final boolean isValid(ForceItem item) {
+ return
+ !( Float.isNaN(item.location[0]) || Float.isNaN(item.location[1]) ||
+ Float.isNaN(item.plocation[0]) || Float.isNaN(item.plocation[1]) ||
+ Float.isNaN(item.velocity[0]) || Float.isNaN(item.velocity[1]) ||
+ Float.isNaN(item.force[0]) || Float.isNaN(item.force[1]) );
+ }
+
+} // end of class ForceItem
diff --git a/coreplugins/AutomaticLayout/src/main/java/prefuse/util/force/ForceSimulator.java b/coreplugins/AutomaticLayout/src/main/java/prefuse/util/force/ForceSimulator.java
new file mode 100644
index 0000000..347aaf8
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/prefuse/util/force/ForceSimulator.java
@@ -0,0 +1,230 @@
+package prefuse.util.force;
+
+import java.util.ArrayList;
+import java.util.Iterator;
+
+/**
+ * Manages a simulation of physical forces acting on bodies. To create a
+ * custom ForceSimulator, add the desired {@link Force} functions and choose an
+ * appropriate {@link Integrator}.
+ *
+ * @author <a href="http://jheer.org">jeffrey heer</a>
+ */
+public class ForceSimulator {
+
+ private ArrayList items;
+ private ArrayList springs;
+ private Force[] iforces;
+ private Force[] sforces;
+ private int iflen, sflen;
+ private Integrator integrator;
+ private float speedLimit = 1.0f;
+
+ /**
+ * Create a new, empty ForceSimulator. A RungeKuttaIntegrator is used
+ * by default.
+ */
+ public ForceSimulator() {
+ this(new RungeKuttaIntegrator());
+ }
+
+ /**
+ * Create a new, empty ForceSimulator.
+ * @param integr the Integrator to use
+ */
+ public ForceSimulator(Integrator integr) {
+ integrator = integr;
+ iforces = new Force[5];
+ sforces = new Force[5];
+ iflen = 0;
+ sflen = 0;
+ items = new ArrayList();
+ springs = new ArrayList();
+ }
+
+ /**
+ * Get the speed limit, or maximum velocity value allowed by this
+ * simulator.
+ * @return the "speed limit" maximum velocity value
+ */
+ public float getSpeedLimit() {
+ return speedLimit;
+ }
+
+ /**
+ * Set the speed limit, or maximum velocity value allowed by this
+ * simulator.
+ * @param limit the "speed limit" maximum velocity value to use
+ */
+ public void setSpeedLimit(float limit) {
+ speedLimit = limit;
+ }
+
+ /**
+ * Get the Integrator used by this simulator.
+ * @return the Integrator
+ */
+ public Integrator getIntegrator() {
+ return integrator;
+ }
+
+ /**
+ * Set the Integrator used by this simulator.
+ * @param intgr the Integrator to use
+ */
+ public void setIntegrator(Integrator intgr) {
+ integrator = intgr;
+ }
+
+ /**
+ * Clear this simulator, removing all ForceItem and Spring instances
+ * for the simulator.
+ */
+ public void clear() {
+ items.clear();
+ Iterator siter = springs.iterator();
+ Spring.SpringFactory f = Spring.getFactory();
+ while ( siter.hasNext() )
+ f.reclaim((Spring)siter.next());
+ springs.clear();
+ }
+
+ /**
+ * Add a new Force function to the simulator.
+ * @param f the Force function to add
+ */
+ public void addForce(Force f) {
+ if ( f.isItemForce() ) {
+ if ( iforces.length == iflen ) {
+ // resize necessary
+ Force[] newf = new Force[iflen+10];
+ System.arraycopy(iforces, 0, newf, 0, iforces.length);
+ iforces = newf;
+ }
+ iforces[iflen++] = f;
+ }
+ if ( f.isSpringForce() ) {
+ if ( sforces.length == sflen ) {
+ // resize necessary
+ Force[] newf = new Force[sflen+10];
+ System.arraycopy(sforces, 0, newf, 0, sforces.length);
+ sforces = newf;
+ }
+ sforces[sflen++] = f;
+ }
+ }
+
+ /**
+ * Get an array of all the Force functions used in this simulator.
+ * @return an array of Force functions
+ */
+ public Force[] getForces() {
+ Force[] rv = new Force[iflen+sflen];
+ System.arraycopy(iforces, 0, rv, 0, iflen);
+ System.arraycopy(sforces, 0, rv, iflen, sflen);
+ return rv;
+ }
+
+ /**
+ * Add a ForceItem to the simulation.
+ * @param item the ForceItem to add
+ */
+ public void addItem(ForceItem item) {
+ items.add(item);
+ }
+
+ /**
+ * Remove a ForceItem to the simulation.
+ * @param item the ForceItem to remove
+ */
+ public boolean removeItem(ForceItem item) {
+ return items.remove(item);
+ }
+
+ /**
+ * Get an iterator over all registered ForceItems.
+ * @return an iterator over the ForceItems.
+ */
+ public Iterator getItems() {
+ return items.iterator();
+ }
+
+ /**
+ * Add a Spring to the simulation.
+ * @param item1 the first endpoint of the spring
+ * @param item2 the second endpoint of the spring
+ * @return the Spring added to the simulation
+ */
+ public Spring addSpring(ForceItem item1, ForceItem item2) {
+ return addSpring(item1, item2, -1.f, -1.f);
+ }
+
+ /**
+ * Add a Spring to the simulation.
+ * @param item1 the first endpoint of the spring
+ * @param item2 the second endpoint of the spring
+ * @param length the spring length
+ * @return the Spring added to the simulation
+ */
+ public Spring addSpring(ForceItem item1, ForceItem item2, float length) {
+ return addSpring(item1, item2, -1.f, length);
+ }
+
+ /**
+ * Add a Spring to the simulation.
+ * @param item1 the first endpoint of the spring
+ * @param item2 the second endpoint of the spring
+ * @param coeff the spring coefficient
+ * @param length the spring length
+ * @return the Spring added to the simulation
+ */
+ public Spring addSpring(ForceItem item1, ForceItem item2, float coeff, float length) {
+ if ( item1 == null || item2 == null )
+ throw new IllegalArgumentException("ForceItems must be non-null");
+ Spring s = Spring.getFactory().getSpring(item1, item2, coeff, length);
+ springs.add(s);
+ return s;
+ }
+
+ /**
+ * Get an iterator over all registered Springs.
+ * @return an iterator over the Springs.
+ */
+ public Iterator getSprings() {
+ return springs.iterator();
+ }
+
+ /**
+ * Run the simulator for one timestep.
+ * @param timestep the span of the timestep for which to run the simulator
+ */
+ public void runSimulator(long timestep) {
+ accumulate();
+ integrator.integrate(this, timestep);
+ }
+
+ /**
+ * Accumulate all forces acting on the items in this simulation
+ */
+ public void accumulate() {
+ for ( int i = 0; i < iflen; i++ )
+ iforces[i].init(this);
+ for ( int i = 0; i < sflen; i++ )
+ sforces[i].init(this);
+ Iterator itemIter = items.iterator();
+ while ( itemIter.hasNext() ) {
+ ForceItem item = (ForceItem)itemIter.next();
+ item.force[0] = 0.0f; item.force[1] = 0.0f;
+ for ( int i = 0; i < iflen; i++ )
+ iforces[i].getForce(item);
+ }
+ Iterator springIter = springs.iterator();
+ while ( springIter.hasNext() ) {
+ Spring s = (Spring)springIter.next();
+ for ( int i = 0; i < sflen; i++ ) {
+ sforces[i].getForce(s);
+ }
+ }
+ }
+
+} // end of class ForceSimulator
diff --git a/coreplugins/AutomaticLayout/src/main/java/prefuse/util/force/GravitationalForce.java b/coreplugins/AutomaticLayout/src/main/java/prefuse/util/force/GravitationalForce.java
new file mode 100644
index 0000000..c9f93a0
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/prefuse/util/force/GravitationalForce.java
@@ -0,0 +1,75 @@
+package prefuse.util.force;
+
+/**
+ * Represents a constant gravitational force, like the pull of gravity
+ * for an object on the Earth (F = mg). The force experienced by a
+ * given item is calculated as the product of a GravitationalConstant
+ * parameter and the mass of the item.
+ *
+ * @author <a href="http://jheer.org">jeffrey heer</a>
+ */
+public class GravitationalForce extends AbstractForce {
+
+ private static final String[] pnames
+ = { "GravitationalConstant", "Direction" };
+
+ public static final int GRAVITATIONAL_CONST = 0;
+ public static final int DIRECTION = 1;
+
+ public static final float DEFAULT_FORCE_CONSTANT = 1E-4f;
+ public static final float DEFAULT_MIN_FORCE_CONSTANT = 1E-5f;
+ public static final float DEFAULT_MAX_FORCE_CONSTANT = 1E-3f;
+
+ public static final float DEFAULT_DIRECTION = (float)-Math.PI/2;
+ public static final float DEFAULT_MIN_DIRECTION = (float)-Math.PI;
+ public static final float DEFAULT_MAX_DIRECTION = (float)Math.PI;
+
+ /**
+ * Create a new GravitationForce.
+ * @param forceConstant the gravitational constant to use
+ * @param direction the direction in which gravity should act,
+ * in radians.
+ */
+ public GravitationalForce(float forceConstant, float direction) {
+ params = new float[] { forceConstant, direction };
+ minValues = new float[]
+ { DEFAULT_MIN_FORCE_CONSTANT, DEFAULT_MIN_DIRECTION };
+ maxValues = new float[]
+ { DEFAULT_MAX_FORCE_CONSTANT, DEFAULT_MAX_DIRECTION };
+ }
+
+ /**
+ * Create a new GravitationalForce with default gravitational
+ * constant and direction.
+ */
+ public GravitationalForce() {
+ this(DEFAULT_FORCE_CONSTANT, DEFAULT_DIRECTION);
+ }
+
+ /**
+ * Returns true.
+ * @see prefuse.util.force.Force#isItemForce()
+ */
+ public boolean isItemForce() {
+ return true;
+ }
+
+ /**
+ * @see prefuse.util.force.AbstractForce#getParameterNames()
+ */
+ protected String[] getParameterNames() {
+ return pnames;
+ }
+
+ /**
+ * @see prefuse.util.force.Force#getForce(prefuse.util.force.ForceItem)
+ */
+ public void getForce(ForceItem item) {
+ float theta = params[DIRECTION];
+ float coeff = params[GRAVITATIONAL_CONST]*item.mass;
+
+ item.force[0] += Math.cos(theta)*coeff;
+ item.force[1] += Math.sin(theta)*coeff;
+ }
+
+} // end of class GravitationalForce
diff --git a/coreplugins/AutomaticLayout/src/main/java/prefuse/util/force/Integrator.java b/coreplugins/AutomaticLayout/src/main/java/prefuse/util/force/Integrator.java
new file mode 100644
index 0000000..518047f
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/prefuse/util/force/Integrator.java
@@ -0,0 +1,14 @@
+package prefuse.util.force;
+
+/**
+ * Interface for numerical integration routines. These routines are used
+ * to update the position and velocity of items in response to forces
+ * over a given time step.
+ *
+ * @author <a href="http://jheer.org">jeffrey heer</a>
+ */
+public interface Integrator {
+
+ public void integrate(ForceSimulator sim, long timestep);
+
+} // end of interface Integrator
diff --git a/coreplugins/AutomaticLayout/src/main/java/prefuse/util/force/NBodyForce.java b/coreplugins/AutomaticLayout/src/main/java/prefuse/util/force/NBodyForce.java
new file mode 100644
index 0000000..fab855c
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/prefuse/util/force/NBodyForce.java
@@ -0,0 +1,351 @@
+package prefuse.util.force;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Iterator;
+import java.util.Random;
+
+/**
+ * <p>Force function which computes an n-body force such as gravity,
+ * anti-gravity, or the results of electric charges. This function implements
+ * the the Barnes-Hut algorithm for efficient n-body force simulations,
+ * using a quad-tree with aggregated mass values to compute the n-body
+ * force in O(N log N) time, where N is the number of ForceItems.</p>
+ *
+ * <p>The algorithm used is that of J. Barnes and P. Hut, in their research
+ * paper <i>A Hierarchical O(n log n) force calculation algorithm</i>, Nature,
+ * v.324, December 1986. For more details on the algorithm, see one of
+ * the following links --
+ * <ul>
+ * <li><a href="http://www.cs.berkeley.edu/~demmel/cs267/lecture26/lecture26.html">James Demmel's UC Berkeley lecture notes</a>
+ * <li><a href="http://www.physics.gmu.edu/~large/lr_forces/desc/bh/bhdesc.html">Description of the Barnes-Hut algorithm</a>
+ * <li><a href="http://www.ifa.hawaii.edu/~barnes/treecode/treeguide.html">Joshua Barnes' recent implementation</a>
+ * </ul></p>
+ *
+ * @author <a href="http://jheer.org">jeffrey heer</a>
+ */
+public class NBodyForce extends AbstractForce {
+
+ /*
+ * The indexing scheme for quadtree child nodes goes row by row.
+ * 0 | 1 0 -> top left, 1 -> top right
+ * -------
+ * 2 | 3 2 -> bottom left, 3 -> bottom right
+ */
+
+ private static String[] pnames = new String[] { "GravitationalConstant",
+ "Distance", "BarnesHutTheta" };
+
+ public static final float DEFAULT_GRAV_CONSTANT = -1.0f;
+ public static final float DEFAULT_MIN_GRAV_CONSTANT = -10f;
+ public static final float DEFAULT_MAX_GRAV_CONSTANT = 10f;
+
+ public static final float DEFAULT_DISTANCE = -1f;
+ public static final float DEFAULT_MIN_DISTANCE = -1f;
+ public static final float DEFAULT_MAX_DISTANCE = 500f;
+
+ public static final float DEFAULT_THETA = 0.9f;
+ public static final float DEFAULT_MIN_THETA = 0.0f;
+ public static final float DEFAULT_MAX_THETA = 1.0f;
+
+ public static final int GRAVITATIONAL_CONST = 0;
+ public static final int MIN_DISTANCE = 1;
+ public static final int BARNES_HUT_THETA = 2;
+
+ private float xMin, xMax, yMin, yMax;
+ private QuadTreeNodeFactory factory = new QuadTreeNodeFactory();
+ private QuadTreeNode root;
+
+ private Random rand = null; // deterministic randomness
+
+ /**
+ * Create a new NBodyForce with default parameters.
+ */
+ public NBodyForce() {
+ this(DEFAULT_GRAV_CONSTANT, DEFAULT_DISTANCE, DEFAULT_THETA);
+ }
+
+ /**
+ * Create a new NBodyForce.
+ * @param gravConstant the gravitational constant to use. Nodes will
+ * attract each other if this value is positive, and will repel each
+ * other if it is negative.
+ * @param minDistance the distance within which two particles will
+ * interact. If -1, the value is treated as infinite.
+ * @param theta the Barnes-Hut parameter theta, which controls when
+ * an aggregated mass is used rather than drilling down to individual
+ * item mass values.
+ */
+ public NBodyForce(float gravConstant, float minDistance, float theta) {
+ params = new float[] { gravConstant, minDistance, theta };
+ minValues = new float[] { DEFAULT_MIN_GRAV_CONSTANT,
+ DEFAULT_MIN_DISTANCE, DEFAULT_MIN_THETA };
+ maxValues = new float[] { DEFAULT_MAX_GRAV_CONSTANT,
+ DEFAULT_MAX_DISTANCE, DEFAULT_MAX_THETA };
+ root = factory.getQuadTreeNode();
+ rand = new Random(12345678L); // deterministic randomness
+ }
+
+ /**
+ * Returns true.
+ * @see prefuse.util.force.Force#isItemForce()
+ */
+ public boolean isItemForce() {
+ return true;
+ }
+
+ /**
+ * @see prefuse.util.force.AbstractForce#getParameterNames()
+ */
+ protected String[] getParameterNames() {
+ return pnames;
+ }
+
+ /**
+ * Set the bounds of the region for which to compute the n-body simulation
+ * @param xMin the minimum x-coordinate
+ * @param yMin the minimum y-coordinate
+ * @param xMax the maximum x-coordinate
+ * @param yMax the maximum y-coordinate
+ */
+ private void setBounds(float xMin, float yMin, float xMax, float yMax) {
+ this.xMin = xMin;
+ this.yMin = yMin;
+ this.xMax = xMax;
+ this.yMax = yMax;
+ }
+
+ /**
+ * Clears the quadtree of all entries.
+ */
+ public void clear() {
+ clearHelper(root);
+ root = factory.getQuadTreeNode();
+ }
+
+ private void clearHelper(QuadTreeNode n) {
+ for ( int i = 0; i < n.children.length; i++ ) {
+ if ( n.children[i] != null )
+ clearHelper(n.children[i]);
+ }
+ factory.reclaim(n);
+ }
+
+ /**
+ * Initialize the simulation with the provided enclosing simulation. After
+ * this call has been made, the simulation can be queried for the
+ * n-body force acting on a given item.
+ * @param fsim the enclosing ForceSimulator
+ */
+ public void init(ForceSimulator fsim) {
+ clear(); // clear internal state
+
+ // compute and squarify bounds of quadtree
+ float x1 = Float.MAX_VALUE, y1 = Float.MAX_VALUE;
+ float x2 = Float.MIN_VALUE, y2 = Float.MIN_VALUE;
+ Iterator itemIter = fsim.getItems();
+ while ( itemIter.hasNext() ) {
+ ForceItem item = (ForceItem)itemIter.next();
+ float x = item.location[0];
+ float y = item.location[1];
+ if ( x < x1 ) x1 = x;
+ if ( y < y1 ) y1 = y;
+ if ( x > x2 ) x2 = x;
+ if ( y > y2 ) y2 = y;
+ }
+ float dx = x2-x1, dy = y2-y1;
+ if ( dx > dy ) { y2 = y1 + dx; } else { x2 = x1 + dy; }
+ setBounds(x1,y1,x2,y2);
+
+ // insert items into quadtree
+ itemIter = fsim.getItems();
+ while ( itemIter.hasNext() ) {
+ ForceItem item = (ForceItem)itemIter.next();
+ insert(item);
+ }
+
+ // calculate magnitudes and centers of mass
+ calcMass(root);
+ }
+
+ /**
+ * Inserts an item into the quadtree.
+ * @param item the ForceItem to add.
+ * @throws IllegalStateException if the current location of the item is
+ * outside the bounds of the quadtree
+ */
+ public void insert(ForceItem item) {
+ // insert item into the quadtrees
+ insert(item, root, xMin, yMin, xMax, yMax);
+ }
+
+ private void insert(ForceItem p, QuadTreeNode n,
+ float x1, float y1, float x2, float y2)
+ {
+ // try to insert particle p at node n in the quadtree
+ // by construction, each leaf will contain either 1 or 0 particles
+ if ( n.hasChildren ) {
+ // n contains more than 1 particle
+ insertHelper(p,n,x1,y1,x2,y2);
+ } else if ( n.value != null ) {
+ // n contains 1 particle
+ if ( isSameLocation(n.value, p) ) {
+ insertHelper(p,n,x1,y1,x2,y2);
+ } else {
+ ForceItem v = n.value; n.value = null;
+ insertHelper(v,n,x1,y1,x2,y2);
+ insertHelper(p,n,x1,y1,x2,y2);
+ }
+ } else {
+ // n is empty, so is a leaf
+ n.value = p;
+ }
+ }
+
+ private static boolean isSameLocation(ForceItem f1, ForceItem f2) {
+ float dx = Math.abs(f1.location[0]-f2.location[0]);
+ float dy = Math.abs(f1.location[1]-f2.location[1]);
+ return ( dx < 0.01 && dy < 0.01 );
+ }
+
+ private void insertHelper(ForceItem p, QuadTreeNode n,
+ float x1, float y1, float x2, float y2)
+ {
+ float x = p.location[0], y = p.location[1];
+ float splitx = (x1+x2)/2;
+ float splity = (y1+y2)/2;
+ int i = (x>=splitx ? 1 : 0) + (y>=splity ? 2 : 0);
+ // create new child node, if necessary
+ if ( n.children[i] == null ) {
+ n.children[i] = factory.getQuadTreeNode();
+ n.hasChildren = true;
+ }
+ // update bounds
+ if ( i==1 || i==3 ) x1 = splitx; else x2 = splitx;
+ if ( i > 1 ) y1 = splity; else y2 = splity;
+ // recurse
+ insert(p,n.children[i],x1,y1,x2,y2);
+ }
+
+ private void calcMass(QuadTreeNode n) {
+ float xcom = 0, ycom = 0;
+ n.mass = 0;
+ if ( n.hasChildren ) {
+ for ( int i=0; i < n.children.length; i++ ) {
+ if ( n.children[i] != null ) {
+ calcMass(n.children[i]);
+ n.mass += n.children[i].mass;
+ xcom += n.children[i].mass * n.children[i].com[0];
+ ycom += n.children[i].mass * n.children[i].com[1];
+ }
+ }
+ }
+ if ( n.value != null ) {
+ n.mass += n.value.mass;
+ xcom += n.value.mass * n.value.location[0];
+ ycom += n.value.mass * n.value.location[1];
+ }
+ n.com[0] = xcom / n.mass;
+ n.com[1] = ycom / n.mass;
+ }
+
+ /**
+ * Calculates the force vector acting on the given item.
+ * @param item the ForceItem for which to compute the force
+ */
+ public void getForce(ForceItem item) {
+ forceHelper(item,root,xMin,yMin,xMax,yMax);
+ }
+
+ private void forceHelper(ForceItem item, QuadTreeNode n,
+ float x1, float y1, float x2, float y2)
+ {
+ float dx = n.com[0] - item.location[0];
+ float dy = n.com[1] - item.location[1];
+ float r = (float)Math.sqrt(dx*dx+dy*dy);
+ boolean same = false;
+ if ( r == 0.0f ) {
+ // if items are in the exact same place, add some noise
+ dx = (rand.nextFloat()-0.5f) / 50.0f;
+ dy = (rand.nextFloat()-0.5f) / 50.0f;
+ r = (float)Math.sqrt(dx*dx+dy*dy);
+ same = true;
+ }
+ boolean minDist = params[MIN_DISTANCE]>0f && r>params[MIN_DISTANCE];
+
+ // the Barnes-Hut approximation criteria is if the ratio of the
+ // size of the quadtree box to the distance between the point and
+ // the box's center of mass is beneath some threshold theta.
+ if ( (!n.hasChildren && n.value != item) ||
+ (!same && (x2-x1)/r < params[BARNES_HUT_THETA]) )
+ {
+ if ( minDist ) return;
+ // either only 1 particle or we meet criteria
+ // for Barnes-Hut approximation, so calc force
+ float v = params[GRAVITATIONAL_CONST]*item.mass*n.mass
+ / (r*r*r);
+ item.force[0] += v*dx;
+ item.force[1] += v*dy;
+ } else if ( n.hasChildren ) {
+ // recurse for more accurate calculation
+ float splitx = (x1+x2)/2;
+ float splity = (y1+y2)/2;
+ for ( int i=0; i<n.children.length; i++ ) {
+ if ( n.children[i] != null ) {
+ forceHelper(item, n.children[i],
+ (i==1||i==3?splitx:x1), (i>1?splity:y1),
+ (i==1||i==3?x2:splitx), (i>1?y2:splity));
+ }
+ }
+ if ( minDist ) return;
+ if ( n.value != null && n.value != item ) {
+ float v = params[GRAVITATIONAL_CONST]*item.mass*n.value.mass
+ / (r*r*r);
+ item.force[0] += v*dx;
+ item.force[1] += v*dy;
+ }
+ }
+ }
+
+ /**
+ * Represents a node in the quadtree.
+ */
+ public static final class QuadTreeNode {
+ public QuadTreeNode() {
+ com = new float[] {0.0f, 0.0f};
+ children = new QuadTreeNode[4];
+ } //
+ boolean hasChildren = false;
+ float mass; // total mass held by this node
+ float[] com; // center of mass of this node
+ ForceItem value; // ForceItem in this node, null if node has children
+ QuadTreeNode[] children; // children nodes
+ } // end of inner class QuadTreeNode
+
+ /**
+ * Helper class to minimize number of object creations across multiple
+ * uses of the quadtree.
+ */
+ public static final class QuadTreeNodeFactory {
+ private int maxNodes = 50000;
+ private ArrayList nodes = new ArrayList();
+
+ public QuadTreeNode getQuadTreeNode() {
+ if ( nodes.size() > 0 ) {
+ return (QuadTreeNode)nodes.remove(nodes.size()-1);
+ } else {
+ return new QuadTreeNode();
+ }
+ }
+ public void reclaim(QuadTreeNode n) {
+ n.mass = 0;
+ n.com[0] = 0.0f; n.com[1] = 0.0f;
+ n.value = null;
+ n.hasChildren = false;
+ Arrays.fill(n.children, null);
+ if ( nodes.size() < maxNodes )
+ nodes.add(n);
+ }
+ } // end of inner class QuadTreeNodeFactory
+
+} // end of class NBodyForce
diff --git a/coreplugins/AutomaticLayout/src/main/java/prefuse/util/force/RungeKuttaIntegrator.java b/coreplugins/AutomaticLayout/src/main/java/prefuse/util/force/RungeKuttaIntegrator.java
new file mode 100644
index 0000000..95fd198
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/prefuse/util/force/RungeKuttaIntegrator.java
@@ -0,0 +1,128 @@
+package prefuse.util.force;
+
+import java.util.Iterator;
+
+/**
+ * Updates velocity and position data using the 4th-Order Runge-Kutta method.
+ * It is slower but more accurate than other techniques such as Euler's Method.
+ * The technique requires re-evaluating forces 4 times for a given timestep.
+ *
+ * @author <a href="http://jheer.org">jeffrey heer</a>
+ */
+public class RungeKuttaIntegrator implements Integrator {
+
+ /**
+ * @see prefuse.util.force.Integrator#integrate(prefuse.util.force.ForceSimulator, long)
+ */
+ public void integrate(ForceSimulator sim, long timestep) {
+ float speedLimit = sim.getSpeedLimit();
+ float vx, vy, v, coeff;
+ float[][] k, l;
+
+ Iterator iter = sim.getItems();
+ while ( iter.hasNext() ) {
+ ForceItem item = (ForceItem)iter.next();
+ coeff = timestep / item.mass;
+ k = item.k;
+ l = item.l;
+ item.plocation[0] = item.location[0];
+ item.plocation[1] = item.location[1];
+ k[0][0] = timestep*item.velocity[0];
+ k[0][1] = timestep*item.velocity[1];
+ l[0][0] = coeff*item.force[0];
+ l[0][1] = coeff*item.force[1];
+
+ // Set the position to the new predicted position
+ item.location[0] += 0.5f*k[0][0];
+ item.location[1] += 0.5f*k[0][1];
+ }
+
+ // recalculate forces
+ sim.accumulate();
+
+ iter = sim.getItems();
+ while ( iter.hasNext() ) {
+ ForceItem item = (ForceItem)iter.next();
+ coeff = timestep / item.mass;
+ k = item.k;
+ l = item.l;
+ vx = item.velocity[0] + .5f*l[0][0];
+ vy = item.velocity[1] + .5f*l[0][1];
+ v = (float)Math.sqrt(vx*vx+vy*vy);
+ if ( v > speedLimit ) {
+ vx = speedLimit * vx / v;
+ vy = speedLimit * vy / v;
+ }
+ k[1][0] = timestep*vx;
+ k[1][1] = timestep*vy;
+ l[1][0] = coeff*item.force[0];
+ l[1][1] = coeff*item.force[1];
+
+ // Set the position to the new predicted position
+ item.location[0] = item.plocation[0] + 0.5f*k[1][0];
+ item.location[1] = item.plocation[1] + 0.5f*k[1][1];
+ }
+
+ // recalculate forces
+ sim.accumulate();
+
+ iter = sim.getItems();
+ while ( iter.hasNext() ) {
+ ForceItem item = (ForceItem)iter.next();
+ coeff = timestep / item.mass;
+ k = item.k;
+ l = item.l;
+ vx = item.velocity[0] + .5f*l[1][0];
+ vy = item.velocity[1] + .5f*l[1][1];
+ v = (float)Math.sqrt(vx*vx+vy*vy);
+ if ( v > speedLimit ) {
+ vx = speedLimit * vx / v;
+ vy = speedLimit * vy / v;
+ }
+ k[2][0] = timestep*vx;
+ k[2][1] = timestep*vy;
+ l[2][0] = coeff*item.force[0];
+ l[2][1] = coeff*item.force[1];
+
+ // Set the position to the new predicted position
+ item.location[0] = item.plocation[0] + 0.5f*k[2][0];
+ item.location[1] = item.plocation[1] + 0.5f*k[2][1];
+ }
+
+ // recalculate forces
+ sim.accumulate();
+
+ iter = sim.getItems();
+ while ( iter.hasNext() ) {
+ ForceItem item = (ForceItem)iter.next();
+ coeff = timestep / item.mass;
+ k = item.k;
+ l = item.l;
+ float[] p = item.plocation;
+ vx = item.velocity[0] + l[2][0];
+ vy = item.velocity[1] + l[2][1];
+ v = (float)Math.sqrt(vx*vx+vy*vy);
+ if ( v > speedLimit ) {
+ vx = speedLimit * vx / v;
+ vy = speedLimit * vy / v;
+ }
+ k[3][0] = timestep*vx;
+ k[3][1] = timestep*vy;
+ l[3][0] = coeff*item.force[0];
+ l[3][1] = coeff*item.force[1];
+ item.location[0] = p[0] + (k[0][0]+k[3][0])/6.0f + (k[1][0]+k[2][0])/3.0f;
+ item.location[1] = p[1] + (k[0][1]+k[3][1])/6.0f + (k[1][1]+k[2][1])/3.0f;
+
+ vx = (l[0][0]+l[3][0])/6.0f + (l[1][0]+l[2][0])/3.0f;
+ vy = (l[0][1]+l[3][1])/6.0f + (l[1][1]+l[2][1])/3.0f;
+ v = (float)Math.sqrt(vx*vx+vy*vy);
+ if ( v > speedLimit ) {
+ vx = speedLimit * vx / v;
+ vy = speedLimit * vy / v;
+ }
+ item.velocity[0] += vx;
+ item.velocity[1] += vy;
+ }
+ }
+
+} // end of class RungeKuttaIntegrator
diff --git a/coreplugins/AutomaticLayout/src/main/java/prefuse/util/force/Spring.java b/coreplugins/AutomaticLayout/src/main/java/prefuse/util/force/Spring.java
new file mode 100644
index 0000000..ca39cc8
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/prefuse/util/force/Spring.java
@@ -0,0 +1,80 @@
+package prefuse.util.force;
+
+import java.util.ArrayList;
+
+/**
+ * Represents a spring in a force simulation.
+ *
+ * @author <a href="http://jheer.org">jeffrey heer</a>
+ */
+public class Spring {
+ private static SpringFactory s_factory = new SpringFactory();
+
+ /**
+ * Retrieve the SpringFactory instance, which serves as an object pool
+ * for Spring instances.
+ * @return the Spring Factory
+ */
+ public static SpringFactory getFactory() {
+ return s_factory;
+ }
+
+ /**
+ * Create a new Spring instance
+ * @param fi1 the first ForceItem endpoint
+ * @param fi2 the second ForceItem endpoint
+ * @param k the spring tension co-efficient
+ * @param len the spring's resting length
+ */
+ public Spring(ForceItem fi1, ForceItem fi2, float k, float len) {
+ item1 = fi1;
+ item2 = fi2;
+ coeff = k;
+ length = len;
+ }
+
+ /** The first ForceItem endpoint */
+ public ForceItem item1;
+ /** The second ForceItem endpoint */
+ public ForceItem item2;
+ /** The spring's resting length */
+ public float length;
+ /** The spring tension co-efficient */
+ public float coeff;
+
+ /**
+ * The SpringFactory is responsible for generating Spring instances
+ * and maintaining an object pool of Springs to reduce garbage collection
+ * overheads while force simulations are running.
+ */
+ public static final class SpringFactory {
+ private int maxSprings = 10000;
+ private ArrayList springs = new ArrayList();
+
+ /**
+ * Get a Spring instance and set it to the given parameters.
+ */
+ public Spring getSpring(ForceItem f1, ForceItem f2, float k, float length) {
+ if ( springs.size() > 0 ) {
+ Spring s = (Spring)springs.remove(springs.size()-1);
+ s.item1 = f1;
+ s.item2 = f2;
+ s.coeff = k;
+ s.length = length;
+ return s;
+ } else {
+ return new Spring(f1,f2,k,length);
+ }
+ }
+ /**
+ * Reclaim a Spring into the object pool.
+ */
+ public void reclaim(Spring s) {
+ s.item1 = null;
+ s.item2 = null;
+ if ( springs.size() < maxSprings )
+ springs.add(s);
+ }
+ } // end of inner class SpringFactory
+
+} // end of class Spring
diff --git a/coreplugins/AutomaticLayout/src/main/java/prefuse/util/force/SpringForce.java b/coreplugins/AutomaticLayout/src/main/java/prefuse/util/force/SpringForce.java
new file mode 100644
index 0000000..c796a15
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/prefuse/util/force/SpringForce.java
@@ -0,0 +1,90 @@
+package prefuse.util.force;
+import java.util.Random;
+
+/**
+ * Force function that computes the force acting on ForceItems due to a
+ * given Spring.
+ *
+ * @author <a href="http://jheer.org">jeffrey heer</a>
+ */
+public class SpringForce extends AbstractForce {
+
+ private static String[] pnames
+ = new String[] { "SpringCoefficient", "DefaultSpringLength" };
+
+ private Random rand = null; // deterministic randomness
+
+ public static final float DEFAULT_SPRING_COEFF = 1E-4f;
+ public static final float DEFAULT_MAX_SPRING_COEFF = 1E-3f;
+ public static final float DEFAULT_MIN_SPRING_COEFF = 1E-5f;
+ public static final float DEFAULT_SPRING_LENGTH = 50;
+ public static final float DEFAULT_MIN_SPRING_LENGTH = 0;
+ public static final float DEFAULT_MAX_SPRING_LENGTH = 200;
+ public static final int SPRING_COEFF = 0;
+ public static final int SPRING_LENGTH = 1;
+
+ /**
+ * Create a new SpringForce.
+ * @param springCoeff the default spring co-efficient to use. This will
+ * be used if the spring's own co-efficient is less than zero.
+ * @param defaultLength the default spring length to use. This will
+ * be used if the spring's own length is less than zero.
+ */
+ public SpringForce(float springCoeff, float defaultLength) {
+ params = new float[] { springCoeff, defaultLength };
+ minValues = new float[]
+ { DEFAULT_MIN_SPRING_COEFF, DEFAULT_MIN_SPRING_LENGTH };
+ maxValues = new float[]
+ { DEFAULT_MAX_SPRING_COEFF, DEFAULT_MAX_SPRING_LENGTH };
+ rand = new Random(12345678L); // deterministic randomness
+ }
+
+ /**
+ * Constructs a new SpringForce instance with default parameters.
+ */
+ public SpringForce() {
+ this(DEFAULT_SPRING_COEFF, DEFAULT_SPRING_LENGTH);
+ }
+
+ /**
+ * Returns true.
+ * @see prefuse.util.force.Force#isSpringForce()
+ */
+ public boolean isSpringForce() {
+ return true;
+ }
+
+ /**
+ * @see prefuse.util.force.AbstractForce#getParameterNames()
+ */
+ protected String[] getParameterNames() {
+ return pnames;
+ }
+
+ /**
+ * Calculates the force vector acting on the items due to the given spring.
+ * @param s the Spring for which to compute the force
+ * @see prefuse.util.force.Force#getForce(prefuse.util.force.Spring)
+ */
+ public void getForce(Spring s) {
+ ForceItem item1 = s.item1;
+ ForceItem item2 = s.item2;
+ float length = (s.length < 0 ? params[SPRING_LENGTH] : s.length);
+ float x1 = item1.location[0], y1 = item1.location[1];
+ float x2 = item2.location[0], y2 = item2.location[1];
+ float dx = x2-x1, dy = y2-y1;
+ float r = (float)Math.sqrt(dx*dx+dy*dy);
+ if ( r == 0.0 ) {
+ dx = (rand.nextFloat()-0.5f) / 50.0f;
+ dy = (rand.nextFloat()-0.5f) / 50.0f;
+ r = (float)Math.sqrt(dx*dx+dy*dy);
+ }
+ float d = r-length;
+ float coeff = (s.coeff < 0 ? params[SPRING_COEFF] : s.coeff)*d/r;
+ item1.force[0] += coeff*dx;
+ item1.force[1] += coeff*dy;
+ item2.force[0] += -coeff*dx;
+ item2.force[1] += -coeff*dy;
+ }
+
+} // end of class SpringForce
diff --git a/coreplugins/AutomaticLayout/src/main/java/prefuse/util/force/WallForce.java b/coreplugins/AutomaticLayout/src/main/java/prefuse/util/force/WallForce.java
new file mode 100644
index 0000000..68d8e70
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/java/prefuse/util/force/WallForce.java
@@ -0,0 +1,88 @@
+package prefuse.util.force;
+
+import java.awt.geom.Line2D;
+
+/**
+ * Uses a gravitational force model to act as a "wall". Can be used to
+ * construct line segments which either attract or repel items.
+ *
+ * @author <a href="http://jheer.org">jeffrey heer</a>
+ */
+public class WallForce extends AbstractForce {
+
+ private static String[] pnames = new String[] { "GravitationalConstant" };
+
+ public static final float DEFAULT_GRAV_CONSTANT = -0.1f;
+ public static final float DEFAULT_MIN_GRAV_CONSTANT = -1.0f;
+ public static final float DEFAULT_MAX_GRAV_CONSTANT = 1.0f;
+ public static final int GRAVITATIONAL_CONST = 0;
+
+ private float x1, y1, x2, y2;
+ private float dx, dy;
+
+ /**
+ * Create a new WallForce.
+ * @param gravConst the gravitational constant of the wall
+ * @param x1 the first x-coordinate of the wall
+ * @param y1 the first y-coordinate of the wall
+ * @param x2 the second x-coordinate of the wall
+ * @param y2 the second y-coordinate of the wall
+ */
+ public WallForce(float gravConst,
+ float x1, float y1, float x2, float y2)
+ {
+ params = new float[] { gravConst };
+ minValues = new float[] { DEFAULT_MIN_GRAV_CONSTANT };
+ maxValues = new float[] { DEFAULT_MAX_GRAV_CONSTANT };
+
+ this.x1 = x1; this.y1 = y1;
+ this.x2 = x2; this.y2 = y2;
+ dx = x2-x1;
+ dy = y2-y1;
+ float r = (float)Math.sqrt(dx*dx+dy*dy);
+ if ( dx != 0.0 ) dx /= r;
+ if ( dy != 0.0 ) dy /= r;
+ }
+
+ /**
+ * Create a new WallForce with default gravitational constant.
+ * @param x1 the first x-coordinate of the wall
+ * @param y1 the first y-coordinate of the wall
+ * @param x2 the second x-coordinate of the wall
+ * @param y2 the second y-coordinate of the wall
+ */
+ public WallForce(float x1, float y1, float x2, float y2) {
+ this(DEFAULT_GRAV_CONSTANT,x1,y1,x2,y2);
+ }
+
+ /**
+ * Returns true.
+ * @see prefuse.util.force.Force#isItemForce()
+ */
+ public boolean isItemForce() {
+ return true;
+ }
+
+ /**
+ * @see prefuse.util.force.AbstractForce#getParameterNames()
+ */
+ protected String[] getParameterNames() {
+ return pnames;
+ }
+
+ /**
+ * @see prefuse.util.force.Force#getForce(prefuse.util.force.ForceItem)
+ */
+ public void getForce(ForceItem item) {
+ float[] n = item.location;
+ int ccw = Line2D.relativeCCW(x1,y1,x2,y2,n[0],n[1]);
+ float r = (float)Line2D.ptSegDist(x1,y1,x2,y2,n[0],n[1]);
+ if ( r == 0.0 ) r = (float)Math.random() / 100.0f;
+ float v = params[GRAVITATIONAL_CONST]*item.mass / (r*r*r);
+ if ( n[0] >= Math.min(x1,x2) && n[0] <= Math.max(x1,x2) )
+ item.force[1] += ccw*v*dx;
+ if ( n[1] >= Math.min(y1,y2) && n[1] <= Math.max(y1,y2) )
+ item.force[0] += -1*ccw*v*dy;
+ }
+
+} // end of class WallForce
diff --git a/coreplugins/AutomaticLayout/src/main/resources/csplugins/layout/plugin.props b/coreplugins/AutomaticLayout/src/main/resources/csplugins/layout/plugin.props
new file mode 100644
index 0000000..2894eba
--- /dev/null
+++ b/coreplugins/AutomaticLayout/src/main/resources/csplugins/layout/plugin.props
@@ -0,0 +1,30 @@
+# This props file would be filled out and included in the plugin jar file. This props file will be used
+# to put information into the Plugin Manager about the plugin
+
+
+# -- The following properties are REQUIRED -- #
+
+# The plugin name that will be displayed to users
+pluginName=AutomaticLayout
+
+# Description used to give users information about the plugin such as what it does.
+# Html tags are encouraged for formatting purposes.
+pluginDescription=Algorithms for automatic layout of networks.
+
+# Plugin version number, this must be two numbers separated by a decimlal. Ex. 0.2, 14.03
+pluginVersion=1.0
+
+# Compatible Cytoscape version
+cytoscapeVersion=2.5,2.6,2.7,2.8
+
+# Category, use one of the categories listed on the website or create your own
+pluginCategory=Core
+
+
+# List of authors. Note each author and institution pair are separated by a : (colon)
+# each additional author institution pair must be separated from other pairs bye a ; (semicolon)
+pluginAuthorsIntsitutions=Mike Smoot,Samad Lotia:UCSD;Scooter Morris:UCSF;Rowan Christmas:Institute for Systems Biology;Rob Sheridan:Memorial Sloan-Kettering Cancer Center;Jeffery Heer:Prefuse Library;jGraph:jGraph Library
+
+# -- The following properties should be set ONLY BY CORE PLUGINS -- #
+downloadURL=http://cytoscape.org/plugins/plugins.xml
+uniqueID=1
diff --git a/coreplugins/BioMartClient/pom.xml b/coreplugins/BioMartClient/pom.xml
new file mode 100644
index 0000000..7020c56
--- /dev/null
+++ b/coreplugins/BioMartClient/pom.xml
@@ -0,0 +1,56 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>parent</artifactId>
+ <version>2.8.4-SNAPSHOT</version>
+ </parent>
+
+ <artifactId>biomart-client</artifactId>
+ <packaging>jar</packaging>
+
+ <name>BioMart Client</name>
+
+ <!-- bootstrap for cytoscape dependencies, namely the parent POM snapshots -->
+ <repositories>
+ <repository>
+ <id>cytoscape_snapshots</id>
+ <snapshots>
+ <enabled>true</enabled>
+ </snapshots>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <name>Cytoscape Snapshots</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/</url>
+ </repository>
+ <repository>
+ <id>cytoscape_releases</id>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ <name>Cytoscape Releases</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/releases/</url>
+ </repository>
+ </repositories>
+
+ <build>
+ <plugins>
+ <plugin>
+ <artifactId>maven-assembly-plugin</artifactId>
+ <configuration>
+ <archive>
+ <manifestEntries>
+ <Cytoscape-Plugin>edu.ucsd.bioeng.idekerlab.biomartclient.BiomartClientPlugin</Cytoscape-Plugin>
+ </manifestEntries>
+ </archive>
+ </configuration>
+ </plugin>
+ </plugins>
+ </build>
+
+</project>
+
diff --git a/coreplugins/BioMartClient/src/main/java/edu/ucsd/bioeng/idekerlab/biomartclient/BiomartClient.java b/coreplugins/BioMartClient/src/main/java/edu/ucsd/bioeng/idekerlab/biomartclient/BiomartClient.java
new file mode 100644
index 0000000..b3e9382
--- /dev/null
+++ b/coreplugins/BioMartClient/src/main/java/edu/ucsd/bioeng/idekerlab/biomartclient/BiomartClient.java
@@ -0,0 +1,357 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package edu.ucsd.bioeng.idekerlab.biomartclient;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.naming.ConfigurationException;
+
+import cytoscape.Cytoscape;
+import cytoscape.data.CyAttributes;
+import cytoscape.data.webservice.AttributeImportQuery;
+import cytoscape.data.webservice.CyWebServiceEvent;
+import cytoscape.data.webservice.CyWebServiceException;
+import cytoscape.data.webservice.WebServiceClient;
+import cytoscape.data.webservice.WebServiceClientImpl;
+import cytoscape.data.webservice.CyWebServiceEvent.WSEventType;
+import cytoscape.data.webservice.WebServiceClientManager.ClientType;
+import cytoscape.layout.Tunable;
+import cytoscape.util.ModulePropertiesImpl;
+import giny.model.Node;
+
+
+/**
+ * Biomart Web Service Client.
+ *
+ * @author kono
+ * @version 0.8
+ * @since Cytoscape 2.6
+ *
+ */
+public class BiomartClient extends WebServiceClientImpl<BiomartStub> {
+ // Client name
+ private static final String DISPLAY_NAME = "Biomart Web Service Client";
+
+ // Client ID
+ private static final String CLIENT_ID = "biomart";
+
+ // Actual biomart client.
+ private static WebServiceClient<BiomartStub> client;
+
+ // Biomart base URL
+ private static final String BASE_URL = "http://www.biomart.org/biomart/martservice";
+
+ private boolean cancelImport = false;
+
+ private String lastStatus;
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ * @throws Exception
+ */
+ public static WebServiceClient<BiomartStub> getClient() throws Exception {
+ if (client == null) {
+ client = new BiomartClient();
+ }
+
+ return client;
+ }
+
+
+
+ /**
+ * Creates a new Biomart Client object.
+ *
+ * @throws ServiceException
+ * @throws ConfigurationException
+ */
+ public BiomartClient() throws Exception {
+ super(CLIENT_ID, DISPLAY_NAME, new ClientType[] { ClientType.ATTRIBUTE });
+ clientStub = new BiomartStub(BASE_URL);
+
+ // Set properties
+ props = new ModulePropertiesImpl(clientID, "wsc");
+
+ // props.add(new Tunable("max_interactions", "Maximum number of records", Tunable.INTEGER,
+ // new Integer(1000)));
+
+ props.add(new Tunable("selected_only", "Map selected nodes only", Tunable.BOOLEAN, new Boolean(false)));
+ props.add(new Tunable("import_all", "Import all available entries", Tunable.BOOLEAN,
+ new Boolean(false)));
+
+ props.add(new Tunable("show_all_filter", "Show all available filters", Tunable.BOOLEAN,
+ new Boolean(false)));
+ props.add(new Tunable("base_url", "Biomart Base URL", Tunable.STRING, BASE_URL));
+ }
+
+ /**
+ * Execute service based on events.
+ * @throws
+ * @throws CyWebServiceException
+ */
+ @Override
+ public void executeService(CyWebServiceEvent e) throws CyWebServiceException {
+ if (e.getSource().equals(CLIENT_ID)) {
+ if (e.getEventType().equals(WSEventType.IMPORT_ATTRIBUTE)) {
+ importAttributes((AttributeImportQuery) e.getParameter());
+ } else if(e.getEventType().equals(WSEventType.CANCEL)) {
+ //System.out.println("========Cancelling...");
+ cancelImport = true;
+ }
+ }
+ }
+
+ /**
+ * Based on the query given, execute the data fetching.
+ *
+ * @param query
+ * @throws CyWebServiceException
+ * @throws IOException
+ * @throws Exception
+ */
+ private void importAttributes(AttributeImportQuery query) throws CyWebServiceException {
+ BufferedReader result = null;
+ List<String> report;
+ try {
+ result = clientStub.sendQuery(query.getParameter().toString());
+ if (result.ready() == false)
+ throw new CyWebServiceException(CyWebServiceException.WSErrorCode.REMOTE_EXEC_FAILED);
+ report = mapping(result, query.getKeyCyAttrName(), query.getKeyNameInWebService());
+ } catch (IOException e) {
+ throw new CyWebServiceException(CyWebServiceException.WSErrorCode.REMOTE_EXEC_FAILED);
+ }
+
+ lastStatus = reportBuilder(report);
+
+ Cytoscape.firePropertyChange(Cytoscape.ATTRIBUTES_CHANGED, null, null);
+ }
+
+ private String reportBuilder(List<String> report) {
+ StringBuilder builder = new StringBuilder();
+ builder.append("Import Finished:\n\n");
+ for(String s: report)
+ builder.append(s+"\n");
+
+
+ return builder.toString();
+ }
+
+ public String getLastStatus() {
+ return lastStatus;
+ }
+
+
+
+ private List<String> mapping(BufferedReader reader, String key, String keyAttrName) throws IOException, CyWebServiceException {
+ String line = reader.readLine();
+ System.out.println("Table Header: " + line);
+ final String[] columnNames = line.split("\\t");
+
+ if (columnNames[0].contains("Query ERROR"))
+ throw new CyWebServiceException(CyWebServiceException.WSErrorCode.REMOTE_EXEC_FAILED);
+
+
+ // For status report
+ int recordCount = 0;
+ List<String> report = new ArrayList<String>();
+
+
+ //final int rowCount = result.size();
+ final int colSize = columnNames.length;
+ int keyIdx = 0;
+
+ // Search column index of the key
+ for (int i = 0; i < colSize; i++) {
+ if (columnNames[i].equals(key))
+ keyIdx = i;
+ }
+
+ byte attrDataType = Cytoscape.getNodeAttributes().getType(keyAttrName);
+ final List<String> nodeIdList = new ArrayList<String>();
+
+ // Prepare list of node IDs.
+ // This is necessary for reverse-mapping.
+ if (keyAttrName.equals("ID") == false) {
+ final List<Node> nodes = Cytoscape.getRootGraph().nodesList();
+
+ for (Node node : nodes)
+ nodeIdList.add(node.getIdentifier());
+ }
+
+ final CyAttributes attr = Cytoscape.getNodeAttributes();
+
+ String[] row;
+ String val;
+
+ List<List<Object>> listOfValList;
+ List<String> ids = null;
+
+ List<Object> testList;
+ String keyVal = null;
+ int rowLength = 0;
+
+
+ int hitCount = 0;
+
+ long start = System.currentTimeMillis();
+ while ((line = reader.readLine()) != null) {
+ // Cancel the job.
+ if(cancelImport) {
+ cancelImport = false;
+ return null;
+ }
+
+ row = line.split("\\t");
+
+ // Ignore invalid length entry.
+ if ((row.length <= keyIdx) || (row.length == 0))
+ continue;
+
+
+ recordCount++;
+ keyVal = row[keyIdx];
+
+ // System.out.println("Key ====>" + keyVal + "<==");
+ // for(String s: entry)
+ // System.out.println("ENT ======>" + s + "<===");
+ rowLength = row.length;
+
+ for (int j = 0; j < rowLength; j++) {
+ val = row[j];
+
+ if ((val != null) && (val.length() != 0) && (j != keyIdx)) {
+ listOfValList = new ArrayList<List<Object>>();
+
+ if (keyAttrName.equals("ID")) {
+ testList = attr.getListAttribute(keyVal, columnNames[j]);
+
+ if (testList != null)
+ listOfValList.add(testList);
+ } else {
+ ids = getIdFromAttrValue(attrDataType, keyAttrName, keyVal, nodeIdList, attr);
+
+ if (ids.size() == 0)
+ continue;
+
+ for (String id : ids)
+ listOfValList.add(attr.getListAttribute(id, columnNames[j]));
+ }
+
+ if (listOfValList.size() == 0) {
+ List<Object> valList = new ArrayList<Object>();
+ listOfValList.add(valList);
+ }
+
+ int index = 0;
+ for (List<Object> valList : listOfValList) {
+ if (valList == null)
+ valList = new ArrayList<Object>();
+
+ if (valList.contains(row[j]) == false)
+ valList.add(row[j]);
+
+ if (keyAttrName.equals("ID")) {
+ attr.setListAttribute(keyVal, columnNames[j], valList);
+ attr.setAttribute(keyVal, columnNames[j] + "-TOP",
+ valList.get(0).toString());
+ } else {
+ attr.setListAttribute(ids.get(index), columnNames[j], valList);
+ attr.setAttribute(ids.get(index), columnNames[j] + "-TOP",
+ valList.get(0).toString());
+
+ }
+ hitCount++;
+ index++;
+ }
+ }
+ }
+ }
+
+ //System.out.println("Time =====> " + (System.currentTimeMillis()-start));
+
+ reader.close();
+ reader = null;
+
+ report.add("Number of Records (Rows) from BioMart = " + recordCount + "\n");
+ report.add("Number of Terms Mapped = " + hitCount + "\n");
+ report.add("The following node attributes are created:" + "\n");
+ for(String s: columnNames) {
+ report.add(s + ", " + s+"-TOP");
+ }
+ report.add("\nAttributes name ends with \'TOP\' contains first entry of the list");
+ return report;
+ }
+
+ private List<String> getIdFromAttrValue(final byte attrDataType, final String attrName,
+ Object attrValue, List<String> nodeIdList,
+ CyAttributes attr) {
+ final List<String> idList = new ArrayList<String>();
+
+ String value;
+
+ List<Object> l = null;
+
+ if (attrDataType == CyAttributes.TYPE_SIMPLE_LIST) {
+ for (String id : nodeIdList) {
+ l = attr.getListAttribute(id, attrName);
+
+ if ((l != null) && (l.size() > 0)) {
+ for (Object obj : l) {
+ if ((obj != null) && obj.equals(attrValue)) {
+ idList.add(id);
+
+ break;
+ }
+ }
+ }
+ }
+ } else if (attrDataType == CyAttributes.TYPE_STRING) {
+ for (String id : nodeIdList) {
+ // Extract attribute value from ID
+ value = attr.getStringAttribute(id, attrName);
+
+ if ((value != null) && value.equals(attrValue))
+ idList.add(id);
+ }
+ }
+
+ return idList;
+ }
+}
diff --git a/coreplugins/BioMartClient/src/main/java/edu/ucsd/bioeng/idekerlab/biomartclient/BiomartClientPlugin.java b/coreplugins/BioMartClient/src/main/java/edu/ucsd/bioeng/idekerlab/biomartclient/BiomartClientPlugin.java
new file mode 100644
index 0000000..6f8f77f
--- /dev/null
+++ b/coreplugins/BioMartClient/src/main/java/edu/ucsd/bioeng/idekerlab/biomartclient/BiomartClientPlugin.java
@@ -0,0 +1,76 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package edu.ucsd.bioeng.idekerlab.biomartclient;
+
+import java.awt.event.ActionEvent;
+
+import javax.swing.AbstractAction;
+import javax.swing.JMenu;
+
+import cytoscape.Cytoscape;
+import cytoscape.data.webservice.WebServiceClientManager;
+import cytoscape.plugin.CytoscapePlugin;
+import edu.ucsd.bioeng.idekerlab.biomartclient.ui.BiomartMainDialog;
+
+/**
+ * Biomart web service client plugin main class.
+ */
+public class BiomartClientPlugin extends CytoscapePlugin {
+ /**
+ * Creates a new BiomartClientPlugin object.
+ *
+ * @throws Exception
+ */
+ public BiomartClientPlugin() throws Exception {
+ // Register this client to the manager.
+ WebServiceClientManager.registerClient(BiomartClient.getClient());
+
+ final JMenu menu = Cytoscape.getDesktop().getCyMenus().getMenuBar()
+ .getMenu("File.Import");
+
+ if (menu != null) {
+ menu.add(new AbstractAction("Import attributes from Biomart...") {
+ private static final long serialVersionUID = -1303677510967797368L;
+
+ public void actionPerformed(ActionEvent e) {
+ BiomartMainDialog.showUI();
+ }
+ });
+ } else {
+ throw new IllegalStateException(
+ "Could not register BioMart Client to Cytoscape menu.");
+ }
+ }
+}
diff --git a/coreplugins/BioMartClient/src/main/java/edu/ucsd/bioeng/idekerlab/biomartclient/BiomartStub.java b/coreplugins/BioMartClient/src/main/java/edu/ucsd/bioeng/idekerlab/biomartclient/BiomartStub.java
new file mode 100644
index 0000000..7124251
--- /dev/null
+++ b/coreplugins/BioMartClient/src/main/java/edu/ucsd/bioeng/idekerlab/biomartclient/BiomartStub.java
@@ -0,0 +1,552 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package edu.ucsd.bioeng.idekerlab.biomartclient;
+
+import org.w3c.dom.Document;
+import org.w3c.dom.NamedNodeMap;
+import org.w3c.dom.NodeList;
+
+import org.xml.sax.SAXException;
+
+import cytoscape.util.URLUtil;
+
+import edu.ucsd.bioeng.idekerlab.biomartclient.utils.Attribute;
+import edu.ucsd.bioeng.idekerlab.biomartclient.utils.Dataset;
+import edu.ucsd.bioeng.idekerlab.biomartclient.utils.Filter;
+import edu.ucsd.bioeng.idekerlab.biomartclient.utils.XMLQueryBuilder;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.OutputStream;
+import java.io.PrintStream;
+
+import java.net.URL;
+import java.net.URLConnection;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
+import javax.xml.parsers.ParserConfigurationException;
+
+
+/**
+ *
+ */
+public class BiomartStub {
+
+ private static final int CONNECTION_TIMEOUT = 3000;
+ private static final int READ_TIMEOUT = 5000;
+
+ private String baseURL = "http://www.biomart.org/biomart/martservice?";
+ private static final String RESOURCE = "/resource/filterconversion.txt";
+ private static final String TAXONOMY_TABLE = "/resource/tax_report.txt";
+// private URL url;
+// private URLConnection uc;
+ private Map<String, Map<String, String>> databases = null;
+
+ // Key is datasource, value is database name.
+ private Map<String, String> datasourceMap = new HashMap<String, String>();
+ private Map<String, Map<String, String>> filterConversionMap;
+ private Map<String, String> taxonomyTable;
+
+
+ private static final int BUFFER_SIZE = 81920;
+
+ /**
+ * Creates a new BiomartStub object.
+ * @throws IOException
+ */
+ public BiomartStub() throws IOException {
+ this(null);
+ }
+
+ /**
+ * Creates a new BiomartStub object from given URL.
+ *
+ * @param baseURL DOCUMENT ME!
+ * @throws IOException
+ */
+ public BiomartStub(String baseURL) throws IOException {
+ if (baseURL != null) {
+ this.baseURL = baseURL + "?";
+ }
+
+ loadConversionFile();
+ }
+
+ private void loadConversionFile() throws IOException {
+ filterConversionMap = new HashMap<String, Map<String, String>>();
+
+ InputStreamReader inFile;
+
+ inFile = new InputStreamReader(this.getClass().getResource(RESOURCE).openStream());
+
+ BufferedReader inBuffer = new BufferedReader(inFile);
+
+ String line;
+ String trimed;
+ String oldName = null;
+ Map<String, String> oneEntry = new HashMap<String, String>();
+
+ String[] dbparts;
+
+ while ((line = inBuffer.readLine()) != null) {
+ trimed = line.trim();
+ dbparts = trimed.split("\\t");
+
+ if (dbparts[0].equals(oldName) == false) {
+ oneEntry = new HashMap<String, String>();
+ oldName = dbparts[0];
+ filterConversionMap.put(oldName, oneEntry);
+ }
+
+ oneEntry.put(dbparts[1], dbparts[2]);
+ }
+
+ inFile.close();
+ inBuffer.close();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param dbName DOCUMENT ME!
+ * @param filterID DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String toAttributeName(String dbName, String filterID) {
+ if (filterConversionMap.get(dbName) == null) {
+ return null;
+ } else {
+ return filterConversionMap.get(dbName).get(filterID);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param baseURL DOCUMENT ME!
+ */
+ public void setBaseURL(String baseURL) {
+ this.baseURL = baseURL + "?";
+ }
+
+ /**
+ * Get the registry information from the base URL.
+ *
+ * @return Map of registry information. Key value is "name" field.
+ * @throws ParserConfigurationException
+ * @throws SAXException
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public Map<String, Map<String, String>> getRegistry()
+ throws IOException, ParserConfigurationException, SAXException {
+ // If already loaded, just return it.
+ if (databases != null)
+ return databases;
+
+ // Initialize database map.
+ databases = new HashMap<String, Map<String, String>>();
+
+ // Prepare URL for the registry status
+ final String reg = "type=registry";
+ final URL targetURL = new URL(baseURL + reg);
+
+ // Get the result as XML document.
+ final DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
+ final DocumentBuilder builder = factory.newDocumentBuilder();
+
+ InputStream is = URLUtil.getBasicInputStream(targetURL);
+
+ final Document registry = builder.parse(is);
+
+ // Extract each datasource
+ NodeList locations = registry.getElementsByTagName("MartURLLocation");
+ int locSize = locations.getLength();
+ NamedNodeMap attrList;
+ int attrLen;
+ String dbID;
+
+ for (int i = 0; i < locSize; i++) {
+
+ attrList = locations.item(i).getAttributes();
+ attrLen = attrList.getLength();
+
+ // First, get the key value
+ dbID = attrList.getNamedItem("name").getNodeValue();
+ Map<String, String> entry = new HashMap<String, String>();
+
+ for (int j = 0; j < attrLen; j++) {
+ entry.put(attrList.item(j).getNodeName(), attrList.item(j).getNodeValue());
+ }
+
+ databases.put(dbID, entry);
+ }
+
+ is.close();
+ is = null;
+
+ return databases;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param martName DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public Map<String, String> getAvailableDatasets(final String martName)
+ throws IOException {
+ try {
+ getRegistry();
+ } catch (ParserConfigurationException e) {
+ e.printStackTrace();
+ } catch (SAXException e) {
+ e.printStackTrace();
+ }
+
+ final Map<String, String> datasources = new HashMap<String, String>();
+
+ Map<String, String> detail = databases.get(martName);
+
+ String urlStr = "http://" + detail.get("host") + ":" + detail.get("port")
+ + detail.get("path") + "?type=datasets&mart=" + detail.get("name");
+
+ //System.out.println("Connection start: DB name = " + martName + ", Target URL = " + urlStr + "\n");
+
+ URL url = new URL(urlStr);
+
+ final URLConnection connection = URLUtil.getURLConnection(url);
+ connection.setReadTimeout(READ_TIMEOUT);
+ connection.setConnectTimeout(CONNECTION_TIMEOUT);
+
+ InputStream is = null;
+ try {
+ is = connection.getInputStream();
+ } catch (Exception e) {
+ // Could not create connection.
+ throw new IOException("Could not create connection.");
+ }
+
+ BufferedReader reader = new BufferedReader(new InputStreamReader(is));
+ String s;
+
+ String[] parts;
+
+ while ((s = reader.readLine()) != null) {
+ parts = s.split("\\t");
+
+ if ((parts.length > 4) && parts[3].equals("1")) {
+ datasources.put(parts[1], parts[2]);
+ datasourceMap.put(parts[1], martName);
+ }
+ }
+
+ is.close();
+ reader.close();
+ reader = null;
+ is = null;
+
+ return datasources;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param datasetName DOCUMENT ME!
+ * @param getAll DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @throws IOException DOCUMENT ME!
+ */
+ public Map<String, String> getFilters(String datasetName, boolean getAll)
+ throws IOException {
+ Map<String, String> filters = new HashMap<String, String>();
+
+ String martName = datasourceMap.get(datasetName);
+ Map<String, String> detail = databases.get(martName);
+
+ String urlStr = "http://" + detail.get("host") + ":" + detail.get("port")
+ + detail.get("path") + "?virtualschema="
+ + detail.get("serverVirtualSchema") + "&type=filters&dataset="
+ + datasetName;
+
+ //System.out.println("Dataset name = " + datasetName + ", Target URL = " + urlStr + "\n");
+ URL url = new URL(urlStr);
+ InputStream is = URLUtil.getBasicInputStream(url);
+
+ BufferedReader reader = new BufferedReader(new InputStreamReader(is));
+ String s;
+
+ String[] parts;
+
+ while ((s = reader.readLine()) != null) {
+ parts = s.split("\\t");
+
+ if ((parts.length > 1)) {
+ if ((parts[1].contains("ID(s)") || parts[1].contains("Accession(s)")
+ || parts[1].contains("IDs")) && (parts[0].startsWith("with_") == false)
+ && (parts[0].endsWith("-2") == false) || parts.length>6 && parts[5].equals("id_list")) {
+ filters.put(parts[1], parts[0]);
+// System.out.println("### Filter Entry = " + parts[1] + " = " + parts[0]);
+ }
+ }
+ }
+
+ is.close();
+ reader.close();
+ reader = null;
+ is = null;
+
+ return filters;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param datasetName DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ * @throws IOException
+ *
+ * @throws IOException DOCUMENT ME!
+ */
+ public Map<String, String[]> getAttributes(String datasetName) throws IOException {
+ Map<String, String[]> attributes = new HashMap<String, String[]>();
+
+ String martName = datasourceMap.get(datasetName);
+ Map<String, String> detail = databases.get(martName);
+
+ String urlStr = "http://" + detail.get("host") + ":" + detail.get("port")
+ + detail.get("path") + "?virtualschema="
+ + detail.get("serverVirtualSchema") + "&type=attributes&dataset="
+ + datasetName;
+
+ //System.out.println("Dataset name = " + datasetName + ", Target URL = " + urlStr + "\n");
+ URL url = new URL(urlStr);
+ InputStream is = URLUtil.getBasicInputStream(url);
+
+ BufferedReader reader = new BufferedReader(new InputStreamReader(is));
+ String s;
+
+ String[] attrInfo;
+
+ String[] parts;
+
+ while ((s = reader.readLine()) != null) {
+ parts = s.split("\\t");
+ attrInfo = new String[3];
+
+ if (parts.length == 0)
+ continue;
+
+ if (parts.length == 4) {
+ // Display name of this attribute.
+ attrInfo[0] = parts[1];
+ attrInfo[1] = parts[2];
+ attrInfo[2] = parts[3];
+ } else if (parts.length > 1) {
+ attrInfo[0] = parts[1];
+ }
+
+ attributes.put(parts[0], attrInfo);
+ }
+
+ is.close();
+ reader.close();
+ reader = null;
+ is = null;
+
+ return attributes;
+ }
+
+ /**
+ * Send the XML query to Biomart, and get the result as table.
+ *
+ * @param xmlQuery DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public BufferedReader sendQuery(String xmlQuery) throws IOException {
+
+ System.out.println("Generated Query:\n\n" + xmlQuery);
+
+ URL url = new URL(baseURL);
+ URLConnection uc = URLUtil.getURLConnection(url);
+ uc.setDoOutput(true);
+ uc.setRequestProperty("User-Agent", "Java URLConnection");
+
+ OutputStream os = uc.getOutputStream();
+
+ final String postStr = "query=" + xmlQuery;
+ PrintStream ps = new PrintStream(os);
+
+ // Post the data
+ ps.print(postStr);
+ os.close();
+ ps.close();
+ ps = null;
+ os = null;
+
+ return new BufferedReader(new InputStreamReader(uc.getInputStream()), BUFFER_SIZE);
+// String line;
+// line = reader.readLine();
+//
+// String[] parts = line.split("\\t");
+// final List<String[]> result = new ArrayList<String[]>();
+// result.add(parts);
+
+// while ((line = reader.readLine()) != null) {
+//
+// System.out.println("Result ==> " + line);
+//
+// parts = line.split("\\t");
+// result.add(parts);
+// }
+//
+// is.close();
+// reader.close();
+// reader = null;
+
+// return result;
+ }
+
+ private String taxID2datasource(String ncbiTaxID) throws IOException {
+ if (taxonomyTable == null) {
+ final InputStreamReader inFile;
+ inFile = new InputStreamReader(this.getClass().getResource(TAXONOMY_TABLE).openStream());
+
+ BufferedReader inBuffer = new BufferedReader(inFile);
+
+ String line;
+ String trimed;
+ taxonomyTable = new HashMap<String, String>();
+
+ String[] dbparts;
+
+ String name1 = null;
+ String name2 = null;
+ String[] spName;
+ while ((line = inBuffer.readLine()) != null) {
+ trimed = line.trim();
+ dbparts = trimed.split("\\t");
+ spName = dbparts[0].split(" ");
+ name1 = spName[0].substring(0, 1);
+ name2 = spName[1];
+ taxonomyTable.put(dbparts[1], (name1 + name2).toLowerCase());
+ }
+
+ inFile.close();
+ inBuffer.close();
+ }
+
+ if(taxonomyTable.get(ncbiTaxID) == null)
+ return null;
+ else
+ return taxonomyTable.get(ncbiTaxID) + "_gene_ensembl";
+ }
+
+ /**
+ * Method to return all GO annotations for the given NCBI taxonomy ID.
+ *
+ * @param ncbiTaxID
+ * @return Annotation as a text table.
+ * @throws IOException
+ */
+ public List<String[]> getAllGOAnnotations(final String ncbiTaxID) throws IOException {
+ List<String[]> res = new ArrayList<String[]>();
+
+ final String dbName = taxID2datasource(ncbiTaxID);
+
+ if(dbName == null)
+ return res;
+
+ Dataset dataset;
+ Attribute[] attrs;
+ Filter[] filters;
+
+ dataset = new Dataset(dbName);
+ attrs = new Attribute[3];
+ attrs[0] = new Attribute("ensembl_gene_id");
+ attrs[1] = new Attribute("go");
+ attrs[2] = new Attribute("evidence_code");
+
+ filters = new Filter[1];
+ filters[0] = new Filter("with_go", null);
+
+ String query2 = XMLQueryBuilder.getQueryString(dataset, attrs, filters);
+
+ BufferedReader reader = sendQuery(query2);
+
+ String line;
+ line = reader.readLine();
+
+ String[] parts = line.split("\\t");
+
+ res.add(parts);
+
+ while ((line = reader.readLine()) != null) {
+ parts = line.split("\\t");
+ res.add(parts);
+ }
+
+ reader.close();
+ reader = null;
+
+ return res;
+ }
+
+ public List<String[]> getAllAliases(final String ncbiTaxID) throws IOException {
+ List<String[]> res = new ArrayList<String[]>();
+
+ final String dbName = taxID2datasource(ncbiTaxID);
+
+ return res;
+ }
+}
diff --git a/coreplugins/BioMartClient/src/main/java/edu/ucsd/bioeng/idekerlab/biomartclient/ui/BiomartAttrMappingPanel.java b/coreplugins/BioMartClient/src/main/java/edu/ucsd/bioeng/idekerlab/biomartclient/ui/BiomartAttrMappingPanel.java
new file mode 100644
index 0000000..c87aa7d
--- /dev/null
+++ b/coreplugins/BioMartClient/src/main/java/edu/ucsd/bioeng/idekerlab/biomartclient/ui/BiomartAttrMappingPanel.java
@@ -0,0 +1,564 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package edu.ucsd.bioeng.idekerlab.biomartclient.ui;
+
+import java.awt.event.ActionEvent;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.TreeSet;
+
+import javax.swing.DefaultListModel;
+import javax.swing.Icon;
+import javax.swing.ImageIcon;
+import javax.xml.parsers.ParserConfigurationException;
+
+import org.xml.sax.SAXException;
+
+import cytoscape.Cytoscape;
+import cytoscape.data.CyAttributes;
+import cytoscape.data.CyAttributesUtils;
+import cytoscape.data.webservice.AttributeImportQuery;
+import cytoscape.data.webservice.CyWebServiceEvent;
+import cytoscape.data.webservice.WebServiceClientManager;
+import cytoscape.data.webservice.CyWebServiceEvent.WSEventType;
+import cytoscape.layout.Tunable;
+import cytoscape.task.Task;
+import cytoscape.task.TaskMonitor;
+import cytoscape.task.ui.JTaskConfig;
+import cytoscape.task.util.TaskManager;
+import cytoscape.util.swing.AttributeImportPanel;
+import edu.ucsd.bioeng.idekerlab.biomartclient.BiomartClient;
+import edu.ucsd.bioeng.idekerlab.biomartclient.BiomartStub;
+import edu.ucsd.bioeng.idekerlab.biomartclient.utils.Attribute;
+import edu.ucsd.bioeng.idekerlab.biomartclient.utils.Dataset;
+import edu.ucsd.bioeng.idekerlab.biomartclient.utils.Filter;
+import edu.ucsd.bioeng.idekerlab.biomartclient.utils.XMLQueryBuilder;
+import giny.model.Node;
+
+
+/**
+ *
+ */
+public class BiomartAttrMappingPanel extends AttributeImportPanel implements PropertyChangeListener {
+
+ private static final long serialVersionUID = 3574198525811249639L;
+
+ private static final Icon LOGO = new ImageIcon(BiomartAttrMappingPanel.class.getResource("/images/logo_biomart2.png"));
+
+ private Map<String, String> datasourceMap;
+ private Map<String, Map<String, String[]>> attributeMap;
+ private Map<String, List<String>> attributeListOrder;
+ private Map<String, Map<String, String>> attrNameMap;
+ private Map<String, Map<String, String>> filterMap;
+
+ private final TaskMonitor monitor;
+
+ private enum SourceType {
+ DATABASE,
+ ATTRIBUTE,
+ FILTER;
+ }
+
+ private boolean cancelFlag = false;
+ private boolean initialized = false;
+
+ private final BiomartStub stub = (BiomartStub) WebServiceClientManager.getClient("biomart")
+ .getClientStub();
+
+ // These databases are not compatible with this UI.
+ private static final List<String> databaseFilter = new ArrayList<String>();
+
+ static {
+ // Database on this list will not appear on the list.
+ databaseFilter.add("compara_mart_pairwise_ga_47");
+ databaseFilter.add("compara_mart_multiple_ga_47");
+ databaseFilter.add("dicty");
+ databaseFilter.add("Pancreatic_Expression");
+ }
+
+ public BiomartAttrMappingPanel(final TaskMonitor monitor) throws Exception {
+ this(LOGO, "", "Available attributes", monitor);
+ }
+
+ /**
+ * Creates a new BiomartNameMappingPanel object.
+ *
+ * @param logo DOCUMENT ME!
+ * @param title DOCUMENT ME!
+ * @throws Exception
+ */
+ public BiomartAttrMappingPanel(Icon logo, String title, String attrPanelLabel, final TaskMonitor monitor)
+ throws Exception {
+ super(logo, title, attrPanelLabel);
+ this.monitor = monitor;
+
+ Cytoscape.getPropertyChangeSupport().addPropertyChangeListener(this);
+ BiomartMainDialog.getPropertyChangeSupport().addPropertyChangeListener(this);
+ initDataSources();
+ }
+
+
+ /**
+ * Access data sources and build GUI.
+ *
+ * @throws Exception
+ */
+ private void initDataSources() throws Exception {
+ datasourceMap = new HashMap<String, String>();
+ attributeMap = new HashMap<String, Map<String, String[]>>();
+ attributeListOrder = new HashMap<String, List<String>>();
+ filterMap = new HashMap<String, Map<String, String>>();
+ attrNameMap = new HashMap<String, Map<String, String>>();
+
+ monitor.setPercentCompleted(0);
+ loadMartServiceList();
+ loadFilter();
+ }
+
+ protected boolean isInitialized() {
+ return initialized;
+ }
+
+ private void loadMartServiceList() {
+ Map<String, Map<String, String>> reg = null;
+ monitor.setStatus("Accessing Mart service registry...");
+ try {
+ reg = stub.getRegistry();
+ } catch (IOException e1) {
+ monitor.setException(e1, "Could not retreve list of Mart Services from registry.");
+ } catch (ParserConfigurationException e1) {
+ monitor.setException(e1, "Could not parse list of Mart Services.");
+ } catch (SAXException e1) {
+ monitor.setException(e1, "Could not parse list of Mart Services.");
+ }
+ monitor.setPercentCompleted(10);
+
+ final int registryCount = reg.size();
+ int increment = 90/registryCount;
+ int percentCompleted = 10;
+
+ Map<String, String> datasources;
+ List<String> dsList = new ArrayList<String>();
+ for (String databaseName : reg.keySet()) {
+
+ Map<String, String> detail = reg.get(databaseName);
+
+ // Add the datasource if its visible
+ if (detail.get("visible").equals("1")
+ && (databaseFilter.contains(databaseName) == false) && (cancelFlag == false)) {
+ String dispName = detail.get("displayName");
+ monitor.setStatus("Connecting to " + dispName);
+ try {
+ datasources = stub.getAvailableDatasets(databaseName);
+ } catch (IOException e) {
+ // If timeout/connection error is found, skip the source.
+ percentCompleted += increment;
+ monitor.setPercentCompleted(percentCompleted);
+ continue;
+ }
+
+ for (String key : datasources.keySet()) {
+ dsList.add(dispName + " - " + datasources.get(key));
+ datasourceMap.put(dispName + " - " + datasources.get(key), key);
+ }
+ } else if (cancelFlag) {
+ cancelFlag = false;
+
+ return;
+ }
+
+ percentCompleted += increment;
+ monitor.setPercentCompleted(percentCompleted);
+ }
+
+ Collections.sort(dsList);
+
+ for (String ds : dsList) {
+ this.databaseComboBox.addItem(ds);
+ }
+
+ initialized = true;
+ }
+
+ private void loadFilter() throws Exception {
+ attributeTypeComboBox.removeAllItems();
+
+ final String selectedDB = databaseComboBox.getSelectedItem().toString();
+ final String selectedDBName = datasourceMap.get(selectedDB);
+
+ fetchData(selectedDBName, SourceType.FILTER);
+ }
+
+ protected void resetButtonActionPerformed(ActionEvent e) {
+ try {
+ updateAttributeList();
+ } catch (Exception e1) {
+ // TODO Auto-generated catch block
+ e1.printStackTrace();
+ }
+ }
+
+ protected void databaseComboBoxActionPerformed(java.awt.event.ActionEvent evt) {
+ try {
+ updateAttributeList();
+ loadFilter();
+ } catch (Exception e1) {
+ // TODO Auto-generated catch block
+ e1.printStackTrace();
+ }
+ }
+
+ private void updateAttributeList() throws Exception {
+ final String selectedDB = databaseComboBox.getSelectedItem().toString();
+ final String selectedDBName = datasourceMap.get(selectedDB);
+
+ List<String> order = attributeListOrder.get(selectedDBName);
+ model = new DefaultListModel();
+ attrList.setModel(model);
+
+ if (order != null) {
+ // List<String> sortedList = new ArrayList<String>(singleAttrMap.keySet());
+ // Collections.sort(sortedList);
+ for (String dispAttrName : order) {
+ model.addElement(dispAttrName);
+ }
+ } else {
+ fetchData(selectedDBName, SourceType.ATTRIBUTE);
+ }
+ }
+
+ private void fetchData(final String datasourceName, SourceType type) throws IOException {
+ Map<String, String> returnValMap = new HashMap<String, String>();
+ final List<String> order = new ArrayList<String>();
+ final String selectedDB = databaseComboBox.getSelectedItem().toString();
+ final String selectedDBName = datasourceMap.get(selectedDB);
+
+ if (type.equals(SourceType.ATTRIBUTE)) {
+ Map<String, String[]> attributeVals = stub.getAttributes(datasourceName);
+ Map<String, String> names = new HashMap<String, String>();
+ attributeMap.put(selectedDBName, attributeVals);
+ model.removeAllElements();
+
+ String[] entry;
+ String dispNameWithCategory;
+
+ for (String attr : attributeVals.keySet()) {
+ entry = attributeVals.get(attr);
+
+ if ((entry != null) && (entry[0] != null)) {
+ if ((entry.length > 2) && (entry[2] != null))
+ dispNameWithCategory = entry[2] + ": \t" + entry[0] + "\t (" + attr + ")";
+ else
+ dispNameWithCategory = " \t" + entry[0] + "\t (" + attr + ")";
+
+ names.put(dispNameWithCategory, attr);
+ order.add(dispNameWithCategory);
+ }
+ }
+
+ this.attrNameMap.put(selectedDBName, names);
+ Collections.sort(order);
+
+ for (String attrName : order) {
+ model.addElement(attrName);
+ }
+
+ attributeListOrder.put(selectedDBName, order);
+ attrList.repaint();
+ } else if (type.equals(SourceType.FILTER)) {
+ returnValMap = stub.getFilters(datasourceName, false);
+ filterMap.put(selectedDBName, returnValMap);
+
+ List<String> filterNames = new ArrayList<String>(returnValMap.keySet());
+ Collections.sort(filterNames);
+
+ for (String filter : filterNames)
+ attributeTypeComboBox.addItem(filter);
+ }
+ }
+
+ protected void importButtonActionPerformed(ActionEvent evt) {
+ final String datasource = datasourceMap.get(databaseComboBox.getSelectedItem());
+ final Map<String, String> attrMap = this.attrNameMap.get(datasource);
+ final Map<String, String> fMap = filterMap.get(datasource);
+
+ final String keyAttrName = attributeComboBox.getSelectedItem().toString();
+
+ System.out.println("Target attr name found: " + keyAttrName);
+
+ Dataset dataset;
+ Attribute[] attrs;
+ Filter[] filters;
+
+ // Name of the datasource
+ dataset = new Dataset(datasource);
+ //System.out.println("Target Dataset = " + dataset.getName());
+
+ final Object[] selectedAttr = attrList.getSelectedValues();
+ attrs = new Attribute[selectedAttr.length + 1];
+
+ // This is the mapping key
+ String filterName = fMap.get(attributeTypeComboBox.getSelectedItem());
+ String dbName = this.databaseComboBox.getSelectedItem().toString();
+ //System.out.println("Filter Name = " + filterName);
+
+ // Database-specific modification.
+ // This is not the best way, but cannot provide universal solution.
+ if (dbName.contains("REACTOME")) {
+ attrs[0] = new Attribute(stub.toAttributeName("REACTOME", filterName));
+ } else if (dbName.contains("VARIATION")) {
+// String newName = filterName.replace("_id", "_stable_id");
+// newName = newName.replace("_ensembl", "");
+ attrs[0] = new Attribute(filterName + "_stable_id");
+ } else {
+ attrs[0] = new Attribute(filterName);
+ }
+
+ for (int i = 1; i <= selectedAttr.length; i++) {
+ attrs[i] = new Attribute(attrMap.get(selectedAttr[i - 1]));
+ }
+
+ // For name mapping, just use ID list filter for query.
+ filters = new Filter[1];
+
+ filters[0] = new Filter(filterName, getIDFilterString(keyAttrName));
+
+ String keyInHeader = null;
+
+ for (String key : attrMap.keySet()) {
+ if (attrMap.get(key).equals(filterName)) {
+ keyInHeader = key.split("\\t")[1];
+ //System.out.println("Key Attr = " + keyInHeader);
+ }
+ }
+
+ // Create Task
+ final ImportAttributeTask task = new ImportAttributeTask(dataset, attrs, filters,
+ keyInHeader, keyAttrName);
+
+ // Configure JTask Dialog Pop-Up Box
+ final JTaskConfig jTaskConfig = new JTaskConfig();
+ jTaskConfig.setOwner(Cytoscape.getDesktop());
+ jTaskConfig.displayCloseButton(true);
+ jTaskConfig.displayCancelButton(true);
+ jTaskConfig.displayStatus(true);
+ jTaskConfig.setAutoDispose(false);
+
+ // Execute Task in New Thread; pop open JTask Dialog Box.
+ TaskManager.executeTask(task, jTaskConfig);
+
+ //firePropertyChange(CLOSE_EVENT, null, null);
+ }
+
+ private static String getIDFilterString(String keyAttrName) {
+
+ final Tunable tunable = WebServiceClientManager.getClient("biomart").getProps().get("selected_only");
+ tunable.updateValue();
+ final Object value = tunable.getValue();
+
+ final List<Node> nodes;
+ if (value != null && Boolean.parseBoolean(value.toString())) {
+ // Selected nodes only
+ nodes = new ArrayList<Node>(Cytoscape.getCurrentNetwork().getSelectedNodes());
+ } else {
+ // Send all nodes in current network
+ nodes = Cytoscape.getCurrentNetwork().nodesList();
+ }
+
+ final StringBuilder builder = new StringBuilder();
+
+ // If attribute name is ID, then use node id as the key.
+ if (keyAttrName.equals("ID")) {
+ for (Node n : nodes) {
+ builder.append(n.getIdentifier());
+ builder.append(",");
+ }
+ } else {
+ // Use Attributes for mapping
+ final CyAttributes attrs = Cytoscape.getNodeAttributes();
+ Map mapAttrs = CyAttributesUtils.getAttribute(keyAttrName, attrs);
+
+ if ((mapAttrs == null) || (mapAttrs.size() == 0))
+ return null;
+
+ // List acceptedClasses = Arrays.asList(mapping.getAcceptedDataClasses());
+ // Class mapAttrClass = CyAttributesUtils.getClass(attrName, attrs);
+ //
+ // if ((mapAttrClass == null) || !(acceptedClasses.contains(mapAttrClass)))
+ // return null;
+ for (String key : loadKeySet(mapAttrs)) {
+ builder.append(key);
+ builder.append(",");
+ }
+ }
+
+ String filterStr = builder.toString();
+ filterStr = filterStr.substring(0, filterStr.length() - 1);
+
+ return filterStr;
+ }
+
+ private static Set<String> loadKeySet(final Map mapAttrs) {
+ final Set<String> mappedKeys = new TreeSet<String>();
+
+ final Iterator keyIter = mapAttrs.values().iterator();
+
+ Object o = null;
+
+ while (keyIter.hasNext()) {
+ o = keyIter.next();
+
+ if (o instanceof List) {
+ List list = (List) o;
+
+ for (int i = 0; i < list.size(); i++) {
+ Object vo = list.get(i);
+
+ if (!mappedKeys.contains(vo))
+ mappedKeys.add(vo.toString());
+ }
+ } else {
+ if (!mappedKeys.contains(o))
+ mappedKeys.add(o.toString());
+ }
+ }
+
+ return mappedKeys;
+ }
+
+ @Override
+ protected void importAttributes() {
+ // Build Query
+ }
+
+ private class ImportAttributeTask implements Task {
+ private Dataset dataset;
+ private Attribute[] attrs;
+ private Filter[] filters;
+ private String key;
+ private String keyAttrName;
+ private TaskMonitor taskMonitor;
+
+ public ImportAttributeTask(Dataset dataset, Attribute[] attrs, Filter[] filters,
+ String key, String keyAttrName) {
+ this.dataset = dataset;
+ this.attrs = attrs;
+ this.filters = filters;
+ this.key = key;
+ this.keyAttrName = keyAttrName;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getTitle() {
+ return "Loading Attributes from Web Service";
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void halt() {
+ try {
+ WebServiceClientManager.getCyWebServiceEventSupport()
+ .fireCyWebServiceEvent(new CyWebServiceEvent("biomart",
+ WSEventType.CANCEL,
+ null));
+ } catch (Exception e) {
+ taskMonitor.setException(e, "Exception occured while canceling import task.");
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void run() {
+ taskMonitor.setStatus("Accessing Biomart Web Service.\n\nIt may take a while.\nPlease wait...");
+ taskMonitor.setPercentCompleted(-1);
+
+ String query2 = XMLQueryBuilder.getQueryString(dataset, attrs, filters);
+
+ AttributeImportQuery qObj = new AttributeImportQuery(query2, key, keyAttrName);
+
+ try {
+ WebServiceClientManager.getCyWebServiceEventSupport()
+ .fireCyWebServiceEvent(new CyWebServiceEvent("biomart",
+ WSEventType.IMPORT_ATTRIBUTE,
+ qObj));
+ } catch (Exception e) {
+ taskMonitor.setException(e, "Could not initialize connection to Biomart.");
+ }
+
+ taskMonitor.setPercentCompleted(100);
+ taskMonitor.setStatus( ((BiomartClient)WebServiceClientManager.getClient("biomart")).getLastStatus() );
+
+// JOptionPane.showMessageDialog(Cytoscape.getDesktop(), statusMessage, "Import Complete",
+// JOptionPane.INFORMATION_MESSAGE);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param arg0 DOCUMENT ME!
+ *
+ * @throws IllegalThreadStateException DOCUMENT ME!
+ */
+ public void setTaskMonitor(TaskMonitor taskMonitor) throws IllegalThreadStateException {
+ this.taskMonitor = taskMonitor;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void propertyChange(PropertyChangeEvent e) {
+ if (e.getPropertyName().equals("CANCEL")) {
+ this.cancelFlag = true;
+ //System.out.println("Cancelling Biomart client initialization...");
+ }
+ }
+}
diff --git a/coreplugins/BioMartClient/src/main/java/edu/ucsd/bioeng/idekerlab/biomartclient/ui/BiomartMainDialog.java b/coreplugins/BioMartClient/src/main/java/edu/ucsd/bioeng/idekerlab/biomartclient/ui/BiomartMainDialog.java
new file mode 100644
index 0000000..5f57305
--- /dev/null
+++ b/coreplugins/BioMartClient/src/main/java/edu/ucsd/bioeng/idekerlab/biomartclient/ui/BiomartMainDialog.java
@@ -0,0 +1,223 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package edu.ucsd.bioeng.idekerlab.biomartclient.ui;
+
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.GridLayout;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.beans.PropertyChangeSupport;
+import java.util.List;
+
+import javax.swing.JDialog;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JTabbedPane;
+import javax.swing.event.SwingPropertyChangeSupport;
+
+import cytoscape.Cytoscape;
+import cytoscape.data.webservice.WebServiceClientManager;
+import cytoscape.layout.Tunable;
+import cytoscape.task.Task;
+import cytoscape.task.TaskMonitor;
+import cytoscape.task.ui.JTaskConfig;
+import cytoscape.task.util.TaskManager;
+
+
+/**
+ * BioMart client main GUI.
+ */
+public class BiomartMainDialog extends JDialog implements PropertyChangeListener {
+
+ private static final long serialVersionUID = 8693726765795163080L;
+
+ // Actual dialog. This is a singleton.
+ private static BiomartMainDialog mainDialog = null;
+ protected static Object pcsO = new Object();
+ protected static PropertyChangeSupport pcs = new SwingPropertyChangeSupport(pcsO);
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static PropertyChangeSupport getPropertyChangeSupport() {
+ return pcs;
+ }
+
+ private static boolean initialized = true;
+ private static BiomartAttrMappingPanel panel;
+
+ /**
+ * Build and display Dialog
+ */
+ public static void showUI() {
+ if ((mainDialog == null) || (initialized == false)) {
+ // Create Task
+ final SetupUITask task = new SetupUITask();
+
+ // Configure JTask Dialog Pop-Up Box
+ final JTaskConfig jTaskConfig = new JTaskConfig();
+ jTaskConfig.setOwner(Cytoscape.getDesktop());
+ jTaskConfig.displayCloseButton(false);
+ jTaskConfig.displayCancelButton(true);
+ jTaskConfig.displayStatus(true);
+ jTaskConfig.setAutoDispose(true);
+
+ // Execute Task in New Thread; pop open JTask Dialog Box.
+ TaskManager.executeTask(task, jTaskConfig);
+ } else
+ mainDialog.setVisible(true);
+ }
+
+ private BiomartMainDialog(final TaskMonitor monitor) throws Exception {
+ super(Cytoscape.getDesktop(), false);
+ setTitle("BioMart Web Service Client");
+
+ // Create a tabbed pane
+ final JTabbedPane tabs = new JTabbedPane();
+ final List<Tunable> tunables = WebServiceClientManager.getClient("biomart").getProps()
+ .getTunables();
+
+ final JPanel tunablePanel = new JPanel();
+ tunablePanel.setBackground(Color.white);
+ final JPanel tPanel = new JPanel();
+ final Dimension panelSize = new Dimension(220, 250);
+ tPanel.setMinimumSize(panelSize);
+ tPanel.setMaximumSize(panelSize);
+ tPanel.setSize(panelSize);
+
+
+ tPanel.setBackground(Color.white);
+ tPanel.setLayout(new GridLayout(0,1));
+
+ for (Tunable t : tunables) {
+ final JPanel propPanel = t.getPanel();
+ propPanel.setBackground(Color.white);
+ tPanel.add(propPanel);
+ }
+
+ tunablePanel.add(tPanel);
+
+
+ panel = new BiomartAttrMappingPanel(monitor);
+ panel.addPropertyChangeListener(this);
+ tabs.addTab("Query", panel);
+ tabs.addTab("Options", tunablePanel);
+
+ add(tabs);
+
+ pack();
+ }
+
+ static class SetupUITask implements Task {
+ private TaskMonitor taskMonitor;
+
+ public SetupUITask() {
+ super();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getTitle() {
+ return "Checking accessible BioMart Services...";
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void halt() {
+ pcs.firePropertyChange("CANCEL", null, null);
+ initialized = false;
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void run() {
+ taskMonitor.setStatus("Checking available Mart services.\n\nThis process may take a while.\nPlease wait...");
+ taskMonitor.setPercentCompleted(-1);
+
+ try {
+ mainDialog = new BiomartMainDialog(taskMonitor);
+ } catch (InterruptedException ie) {
+ //System.out.println("============== GOT interaption");
+ } catch (Exception e) {
+ taskMonitor.setException(e, "Failed to initialize the Biomart dialog.");
+ }
+
+ taskMonitor.setPercentCompleted(100);
+
+ if ((panel != null) && panel.isInitialized()) {
+ mainDialog.setLocationRelativeTo(Cytoscape.getDesktop());
+ mainDialog.setVisible(true);
+ initialized = true;
+ } else {
+ //System.out.println("Biomart initialization process canceled by user.");
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param arg0 DOCUMENT ME!
+ *
+ * @throws IllegalThreadStateException DOCUMENT ME!
+ */
+ public void setTaskMonitor(TaskMonitor taskMonitor) throws IllegalThreadStateException {
+ this.taskMonitor = taskMonitor;
+ }
+ }
+
+ private void showStatusReport() {
+ JOptionPane.showInternalMessageDialog(Cytoscape.getDesktop(), "Biomart", "information",
+ JOptionPane.INFORMATION_MESSAGE);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt DOCUMENT ME!
+ */
+ public void propertyChange(PropertyChangeEvent evt) {
+ if (evt.getPropertyName().equals("CLOSE")) {
+ dispose();
+ }
+ }
+}
diff --git a/coreplugins/BioMartClient/src/main/java/edu/ucsd/bioeng/idekerlab/biomartclient/ui/DatabaseSpecificUtils.java b/coreplugins/BioMartClient/src/main/java/edu/ucsd/bioeng/idekerlab/biomartclient/ui/DatabaseSpecificUtils.java
new file mode 100644
index 0000000..a027535
--- /dev/null
+++ b/coreplugins/BioMartClient/src/main/java/edu/ucsd/bioeng/idekerlab/biomartclient/ui/DatabaseSpecificUtils.java
@@ -0,0 +1,56 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package edu.ucsd.bioeng.idekerlab.biomartclient.ui;
+
+import java.util.HashMap;
+import java.util.Map;
+
+/**
+ *
+ */
+public class DatabaseSpecificUtils {
+ static {
+ }
+
+
+ private static final Map<String, Map<String, String>> conversionMap = new HashMap<String, Map<String, String>>();
+
+ // Will be used to convert filter name to attribute name.
+ protected static String filter2attribute(String dbName, String filterName) {
+ return null;
+ }
+}
diff --git a/coreplugins/BioMartClient/src/main/java/edu/ucsd/bioeng/idekerlab/biomartclient/utils/Attribute.java b/coreplugins/BioMartClient/src/main/java/edu/ucsd/bioeng/idekerlab/biomartclient/utils/Attribute.java
new file mode 100644
index 0000000..6e2658f
--- /dev/null
+++ b/coreplugins/BioMartClient/src/main/java/edu/ucsd/bioeng/idekerlab/biomartclient/utils/Attribute.java
@@ -0,0 +1,14 @@
+package edu.ucsd.bioeng.idekerlab.biomartclient.utils;
+
+public class Attribute {
+ private String name;
+
+ public Attribute(String name) {
+ this.name = name;
+ }
+
+ public String getName() {
+ return name;
+ }
+
+}
diff --git a/coreplugins/BioMartClient/src/main/java/edu/ucsd/bioeng/idekerlab/biomartclient/utils/Dataset.java b/coreplugins/BioMartClient/src/main/java/edu/ucsd/bioeng/idekerlab/biomartclient/utils/Dataset.java
new file mode 100644
index 0000000..b9233ae
--- /dev/null
+++ b/coreplugins/BioMartClient/src/main/java/edu/ucsd/bioeng/idekerlab/biomartclient/utils/Dataset.java
@@ -0,0 +1,14 @@
+package edu.ucsd.bioeng.idekerlab.biomartclient.utils;
+
+public class Dataset {
+ private String name;
+
+ public Dataset(String name) {
+ this.name = name;
+ }
+
+ public String getName() {
+ return name;
+ }
+
+}
diff --git a/coreplugins/BioMartClient/src/main/java/edu/ucsd/bioeng/idekerlab/biomartclient/utils/Filter.java b/coreplugins/BioMartClient/src/main/java/edu/ucsd/bioeng/idekerlab/biomartclient/utils/Filter.java
new file mode 100644
index 0000000..9cedbc7
--- /dev/null
+++ b/coreplugins/BioMartClient/src/main/java/edu/ucsd/bioeng/idekerlab/biomartclient/utils/Filter.java
@@ -0,0 +1,25 @@
+package edu.ucsd.bioeng.idekerlab.biomartclient.utils;
+
+public class Filter {
+ private String name;
+ private String value;
+
+
+ public Filter(String name, String value) {
+ this.name = name;
+ this.value = value;
+ }
+
+ public String getName() {
+ return name;
+ }
+
+ public String getValue() {
+ return value;
+ }
+
+ public void setValue(String value) {
+ this.value = value;
+ }
+
+}
diff --git a/coreplugins/BioMartClient/src/main/java/edu/ucsd/bioeng/idekerlab/biomartclient/utils/QueryBuilderUtil.java b/coreplugins/BioMartClient/src/main/java/edu/ucsd/bioeng/idekerlab/biomartclient/utils/QueryBuilderUtil.java
new file mode 100644
index 0000000..47c9cd7
--- /dev/null
+++ b/coreplugins/BioMartClient/src/main/java/edu/ucsd/bioeng/idekerlab/biomartclient/utils/QueryBuilderUtil.java
@@ -0,0 +1,61 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package edu.ucsd.bioeng.idekerlab.biomartclient.utils;
+
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ *
+ */
+public class QueryBuilderUtil {
+ private enum IDType {
+ ENSEMBL,
+ ENTREZ_GENE;
+ }
+
+ private final List<String> dataset = new ArrayList<String>();
+
+ private void getDataset() {
+
+ }
+ public static String getAllAliases(String ncbiTaxonID) {
+
+ final String query = XMLQueryBuilder.getQueryString(new Dataset("hsapiens_gene_ensembl"), new Attribute[] {new Attribute("ensembl_gene_id")}, null);
+ return query;
+ }
+}
diff --git a/coreplugins/BioMartClient/src/main/java/edu/ucsd/bioeng/idekerlab/biomartclient/utils/XMLQueryBuilder.java b/coreplugins/BioMartClient/src/main/java/edu/ucsd/bioeng/idekerlab/biomartclient/utils/XMLQueryBuilder.java
new file mode 100644
index 0000000..79b8d48
--- /dev/null
+++ b/coreplugins/BioMartClient/src/main/java/edu/ucsd/bioeng/idekerlab/biomartclient/utils/XMLQueryBuilder.java
@@ -0,0 +1,141 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package edu.ucsd.bioeng.idekerlab.biomartclient.utils;
+
+import org.w3c.dom.Document;
+import org.w3c.dom.Element;
+
+import java.io.StringWriter;
+
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
+import javax.xml.parsers.ParserConfigurationException;
+import javax.xml.transform.OutputKeys;
+import javax.xml.transform.Transformer;
+import javax.xml.transform.TransformerConfigurationException;
+import javax.xml.transform.TransformerException;
+import javax.xml.transform.TransformerFactory;
+import javax.xml.transform.dom.DOMSource;
+import javax.xml.transform.stream.StreamResult;
+
+
+/**
+ *
+ */
+public class XMLQueryBuilder {
+ private static DocumentBuilderFactory factory;
+ private static DocumentBuilder builder;
+
+ static {
+ factory = DocumentBuilderFactory.newInstance();
+
+ try {
+ builder = factory.newDocumentBuilder();
+ } catch (ParserConfigurationException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param dataset DOCUMENT ME!
+ * @param attrs DOCUMENT ME!
+ * @param filters DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static String getQueryString(Dataset dataset, Attribute[] attrs, Filter[] filters) {
+ final Document doc = builder.newDocument();
+ Element query = doc.createElement("Query");
+ query.setAttribute("virtualSchemaName", "default");
+ query.setAttribute("header", "1");
+ query.setAttribute("uniqueRows", "1");
+ query.setAttribute("count", "");
+ query.setAttribute("datasetConfigVersion", "0.6");
+ query.setAttribute("formatter", "TSV");
+
+ doc.appendChild(query);
+
+ Element ds = doc.createElement("Dataset");
+ ds.setAttribute("name", dataset.getName());
+ query.appendChild(ds);
+
+ for (Attribute attr : attrs) {
+ Element at = doc.createElement("Attribute");
+ at.setAttribute("name", attr.getName());
+ ds.appendChild(at);
+ }
+
+ if ((filters != null) && (filters.length != 0)) {
+ for (Filter filter : filters) {
+ Element ft = doc.createElement("Filter");
+ ft.setAttribute("name", filter.getName());
+ if(filter.getValue() == null) {
+ ft.setAttribute("excluded", "0");
+ } else
+ ft.setAttribute("value", filter.getValue());
+ ds.appendChild(ft);
+ }
+ }
+
+ TransformerFactory tff = TransformerFactory.newInstance();
+ Transformer tf;
+ String result = null;
+
+ try {
+ tf = tff.newTransformer();
+ tf.setOutputProperty(OutputKeys.ENCODING, "UTF-8");
+
+ StringWriter strWtr = new StringWriter();
+ StreamResult strResult = new StreamResult(strWtr);
+
+ tf.transform(new DOMSource(doc.getDocumentElement()), strResult);
+
+ result = strResult.getWriter().toString();
+ } catch (TransformerConfigurationException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ } catch (TransformerException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+
+ return result;
+ }
+}
diff --git a/coreplugins/BioMartClient/src/main/resources/edu/ucsd/bioeng/idekerlab/biomartclient/plugin.props b/coreplugins/BioMartClient/src/main/resources/edu/ucsd/bioeng/idekerlab/biomartclient/plugin.props
new file mode 100644
index 0000000..240201d
--- /dev/null
+++ b/coreplugins/BioMartClient/src/main/resources/edu/ucsd/bioeng/idekerlab/biomartclient/plugin.props
@@ -0,0 +1,21 @@
+# -- The following properties are REQUIRED -- #
+
+# The plugin name that will be displayed to users
+pluginName=BiomartClient
+
+# Description used to give users information about the plugin such as what it does.
+# Html tags are encouraged for formatting purposes.
+pluginDescription=<p>Web Service client module for Biomart (<a href="http://www.biomart.org/">http://www.biomart.org/</a>).</p><p><strong><font color="red">Now GUI is integrated and you do not have to install UI plugin for this version.</font></strong>
+
+# Plugin version number, this must be two numbers separated by a decimlal. Ex. 0.2, 14.03
+pluginVersion=0.90
+
+# Compatible Cytoscape version
+cytoscapeVersion=2.6,2.7,2.8
+
+# Category, use one of the categories listed on the website or create your own
+pluginCategory=Core
+
+# List of authors. Note each author and institution pair are separated by a : (colon)
+# each additional author institution pair must be separated from other pairs bye a ; (semicolon)
+pluginAuthorsIntsitutions=Keiichiro Ono:UCSD Dept. of Medicine
diff --git a/coreplugins/BioMartClient/src/main/resources/images/logo_biomart2.png b/coreplugins/BioMartClient/src/main/resources/images/logo_biomart2.png
new file mode 100644
index 0000000..b718560
Binary files /dev/null and b/coreplugins/BioMartClient/src/main/resources/images/logo_biomart2.png differ
diff --git a/coreplugins/BioMartClient/src/main/resources/resource/databaselist.txt b/coreplugins/BioMartClient/src/main/resources/resource/databaselist.txt
new file mode 100644
index 0000000..c8b0ed3
--- /dev/null
+++ b/coreplugins/BioMartClient/src/main/resources/resource/databaselist.txt
@@ -0,0 +1,9 @@
+ENSEMBL 46 GENES (SANGER) http://www.biomart.org/biomart/martservice?type=datasets&mart=ensembl
+VEGA 21 (SANGER) http://www.biomart.org/biomart/martservice?type=datasets&mart=vega
+UNIPROT PROTOTYPE (EBI) http://www.biomart.org/biomart/martservice?type=datasets&mart=uniprot
+MSD PROTOTYPE (EBI) http://www.biomart.org/biomart/martservice?type=datasets&mart=msd
+GRAMENE (CSHL) http://www.biomart.org/biomart/martservice?type=datasets&mart=ENSEMBL_MART_ENSEMBL
+RGD GENES (MCW) http://rote.hmgc.mcw.edu:9999/biomart/martservice?type=datasets&mart=rgd__mart
+PANCREATIC EXPRESSION DATABASE (INSTITUTE OF CANCER) http://www.biomart.org/biomart/martservice?type=datasets&mart=Pancreatic_Expression
+WORMBASE (CSHL) http://www.wormbase.org/biomart/martservice?type=datasets&mart=wormbase176
+REACTOME http://banon.cshl.edu:5555/biomart/martservice?type=datasets&mart=REACTOME
\ No newline at end of file
diff --git a/coreplugins/BioMartClient/src/main/resources/resource/filterconversion.txt b/coreplugins/BioMartClient/src/main/resources/resource/filterconversion.txt
new file mode 100644
index 0000000..bcd1e26
--- /dev/null
+++ b/coreplugins/BioMartClient/src/main/resources/resource/filterconversion.txt
@@ -0,0 +1,19 @@
+REACTOME referencemolecule_chebi_id_list referencedatabase_chebi
+REACTOME referencednasequence_kegg_id_list referencedatabase_kegg_gene
+REACTOME referencednasequence_entrez_id_list referencedatabase_entrez_gene
+REACTOME referencepeptidesequence_uniprot_id_list referencedatabase_uniprot
+REACTOME referencepeptidesequence_tigr_id_list referencedatabase_tigr
+REACTOME referencepeptidesequence_wormbase_id_list referencedatabase_wormbase
+REACTOME referencednasequence_ensembl_id_list referencedatabase_ensembl
+REACTOME pathway_id_list stableidentifier_identifier
+REACTOME pathway_db_id_list pathway_db_id
+REACTOME reaction_id_list reaction__dm_stableidentifier_identifier
+REACTOME reaction_db_id_list Reaction reaction__dm_db_id
+REACTOME complex_id_list complex__dm_stableidentifier_identifier
+REACTOME complex_db_id_list db_id
+UNIPROT pidn_id pidn
+UNIPROT hssp_id hssp_id
+UNIPROT interpro_id ipro_id
+UNIPROT pdb_id pdb_id
+UNIPROT ec_id ec_id
+UNIPROT gene_name gene_name
\ No newline at end of file
diff --git a/coreplugins/BioMartClient/src/main/resources/resource/tax_report.txt b/coreplugins/BioMartClient/src/main/resources/resource/tax_report.txt
new file mode 100755
index 0000000..d3d9f94
--- /dev/null
+++ b/coreplugins/BioMartClient/src/main/resources/resource/tax_report.txt
@@ -0,0 +1,39 @@
+Canis familiaris 9615
+Danio rerio 7955
+Tupaia belangeri 37347
+Takifugu rubripes 31033
+Caenorhabditis elegans 6239
+Loxodonta africana 9785
+Gallus gallus 9031
+Saccharomyces cerevisiae 4932
+Rattus norvegicus 10116
+Aedes aegypti 7159
+Pongo pygmaeus 9600
+Tetraodon nigroviridis 99883
+Ochotona princeps 9978
+Felis catus 9685
+Gasterosteus aculeatus 69293
+Equus caballus 9796
+Echinops telfairi 9371
+Myotis lucifugus 59463
+Erinaceus europaeus 9365
+Dasypus novemcinctus 9361
+Mus musculus 10090
+Anopheles gambiae 7165
+Ciona savignyi 51511
+Oryctolagus cuniculus 9986
+Otolemur garnettii 30611
+Monodelphis domestica 13616
+Spermophilus tridecemlineatus 43179
+Oryzias latipes 8090
+Ciona intestinalis 7719
+Ornithorhynchus anatinus 9258
+Microcebus murinus 30608
+Macaca mulatta 9544
+Sorex araneus 42254
+Bos taurus 9913
+Homo sapiens 9606
+Drosophila melanogaster 7227
+Pan troglodytes 9598
+Cavia porcellus 10141
+Xenopus tropicalis 8364
diff --git a/coreplugins/BioMartClient/src/test/java/edu/ucsd/bioeng/idekerlab/biomartclient/tests/BiomartStubTest.java b/coreplugins/BioMartClient/src/test/java/edu/ucsd/bioeng/idekerlab/biomartclient/tests/BiomartStubTest.java
new file mode 100644
index 0000000..d3384ee
--- /dev/null
+++ b/coreplugins/BioMartClient/src/test/java/edu/ucsd/bioeng/idekerlab/biomartclient/tests/BiomartStubTest.java
@@ -0,0 +1,103 @@
+package edu.ucsd.bioeng.idekerlab.biomartclient.tests;
+
+import java.io.File;
+import java.util.Map;
+
+import junit.framework.TestCase;
+import edu.ucsd.bioeng.idekerlab.biomartclient.BiomartStub;
+
+public class BiomartStubTest extends TestCase {
+
+ BiomartStub stub;
+
+ protected void setUp() throws Exception {
+ super.setUp();
+ File f = new File("src/test/resources/mart.registry.xml");
+ stub = new BiomartStub(f.toURI().toURL().toString());
+ stub.getRegistry();
+ }
+
+ protected void tearDown() throws Exception {
+ super.tearDown();
+ }
+
+ public void testGetRegistry() throws Exception {
+ Map<String, Map<String, String>> reg = stub.getRegistry();
+
+ // FIXME: repository number may change...
+ //assertEquals(54, reg.keySet().size());
+ }
+
+ public void testGetAvailableDatasets() throws Exception {
+ Map<String, String> result = stub.getAvailableDatasets("ensembl");
+
+ assertTrue(result.keySet().contains("oprinceps_gene_ensembl"));
+ assertTrue(result.keySet().contains("etelfairi_gene_ensembl"));
+ assertTrue(result.keySet().contains("drerio_gene_ensembl"));
+ assertTrue(result.keySet().contains("cjacchus_gene_ensembl"));
+ assertTrue(result.keySet().contains("ocuniculus_gene_ensembl"));
+
+ //assertEquals(51, result.keySet().size());
+ }
+
+
+/* getAllGOAnnotations requires and actual web service to work
+ public void testGetAllGOAnnotations() throws Exception {
+ // Get Human annotation.
+ List<String[]> res = stub.getAllGOAnnotations("10090");
+ Set<String> uniqueID = new HashSet<String>();
+
+ for(String[] line: res) {
+ uniqueID.add(line[0]);
+ for(String entry: line) {
+
+ System.out.print(entry + "\t");
+ }
+ System.out.println("");
+ }
+ System.out.println("======== Total " + uniqueID.size() + " annotated genes ==========");
+ res.clear();
+ uniqueID.clear();
+ uniqueID = null;
+ res = null;
+ }
+*/
+
+/* sendQuery requires an actual webservice to work
+ public void testSendQuery() throws Exception {
+
+ Dataset dataset;
+ Attribute[] attrs;
+ Filter[] filters;
+
+ dataset = new Dataset("hsapiens_gene_ensembl");
+ attrs = new Attribute[3];
+ attrs[0] = new Attribute("ensembl_gene_id");
+ attrs[1] = new Attribute("go");
+ attrs[2] = new Attribute("evidence_code");
+
+ filters = new Filter[1];
+ filters[0] = new Filter("with_go", null);
+
+ String query2 = XMLQueryBuilder.getQueryString(dataset, attrs, filters);
+
+ List<String[]> res = stub.sendQuery(query2);
+
+
+ Set<String> uniqueID = new HashSet<String>();
+
+ for(String[] line: res) {
+ uniqueID.add(line[0]);
+ for(String entry: line) {
+
+ System.out.print(entry + "\t");
+ }
+ System.out.println("");
+ }
+
+ System.out.println("======== Total " + uniqueID.size() + " annotated genes ==========");
+
+ }
+ */
+
+}
diff --git a/coreplugins/BioMartClient/src/test/java/edu/ucsd/bioeng/idekerlab/biomartclient/tests/QueryBuilderUtilTest.java b/coreplugins/BioMartClient/src/test/java/edu/ucsd/bioeng/idekerlab/biomartclient/tests/QueryBuilderUtilTest.java
new file mode 100644
index 0000000..8fb5888
--- /dev/null
+++ b/coreplugins/BioMartClient/src/test/java/edu/ucsd/bioeng/idekerlab/biomartclient/tests/QueryBuilderUtilTest.java
@@ -0,0 +1,29 @@
+package edu.ucsd.bioeng.idekerlab.biomartclient.tests;
+
+import java.io.File;
+
+import junit.framework.TestCase;
+import edu.ucsd.bioeng.idekerlab.biomartclient.BiomartStub;
+import edu.ucsd.bioeng.idekerlab.biomartclient.utils.QueryBuilderUtil;
+
+public class QueryBuilderUtilTest extends TestCase {
+
+ BiomartStub stub;
+ private final String queryString = "<?xml version=\"1.0\" encoding=\"UTF-8\"?><Query count=\"\" datasetConfigVersion=\"0.6\" formatter=\"TSV\" header=\"1\" uniqueRows=\"1\" virtualSchemaName=\"default\"><Dataset name=\"hsapiens_gene_ensembl\"><Attribute name=\"ensembl_gene_id\"/></Dataset></Query>";
+
+ protected void setUp() throws Exception {
+ super.setUp();
+ File f = new File("src/test/resources/mart.registry.xml");
+ stub = new BiomartStub(f.toURI().toURL().toString());
+ }
+
+ protected void tearDown() throws Exception {
+ super.tearDown();
+ }
+
+
+ public void testGetAllAliases() throws Exception {
+ String query= QueryBuilderUtil.getAllAliases(null);
+ assertEquals( queryString, query );
+ }
+}
diff --git a/coreplugins/BioMartClient/src/test/java/edu/ucsd/bioeng/idekerlab/biomartclient/tests/XMLQueryBuilderTest.java b/coreplugins/BioMartClient/src/test/java/edu/ucsd/bioeng/idekerlab/biomartclient/tests/XMLQueryBuilderTest.java
new file mode 100644
index 0000000..1332ea3
--- /dev/null
+++ b/coreplugins/BioMartClient/src/test/java/edu/ucsd/bioeng/idekerlab/biomartclient/tests/XMLQueryBuilderTest.java
@@ -0,0 +1,37 @@
+package edu.ucsd.bioeng.idekerlab.biomartclient.tests;
+
+import edu.ucsd.bioeng.idekerlab.biomartclient.utils.Attribute;
+import edu.ucsd.bioeng.idekerlab.biomartclient.utils.Dataset;
+import edu.ucsd.bioeng.idekerlab.biomartclient.utils.Filter;
+import edu.ucsd.bioeng.idekerlab.biomartclient.utils.XMLQueryBuilder;
+import junit.framework.TestCase;
+
+public class XMLQueryBuilderTest extends TestCase {
+
+ private Dataset dataset;
+ private Attribute[] attrs;
+ private Filter[] filters;
+
+ protected void setUp() throws Exception {
+
+ dataset = new Dataset("hsapiens_gene_ensembl");
+ attrs = new Attribute[3];
+ attrs[0] = new Attribute("hgnc_symbol");
+ attrs[1] = new Attribute("entrezgene");
+ attrs[2] = new Attribute("uniprot_swissprot");
+
+ filters = new Filter[1];
+ filters[0] = new Filter("entrezgene", "6736,100,662");
+
+ }
+
+ protected void tearDown() throws Exception {
+ }
+
+ public void testGetQueryString() {
+ System.out.println("=================");
+
+ assertNotNull(XMLQueryBuilder.getQueryString(dataset, attrs, filters));
+ }
+
+}
diff --git a/coreplugins/BioMartClient/src/test/resources/mart.registry.xml b/coreplugins/BioMartClient/src/test/resources/mart.registry.xml
new file mode 100644
index 0000000..25d3e1b
--- /dev/null
+++ b/coreplugins/BioMartClient/src/test/resources/mart.registry.xml
@@ -0,0 +1,57 @@
+
+<MartRegistry>
+ <MartURLLocation database="ensembl_mart_59" default="1" displayName="ENSEMBL GENES 59 (SANGER UK)" host="www.biomart.org" includeDatasets="" martUser="" name="ensembl" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="snp_mart_59" default="0" displayName="ENSEMBL VARIATION 59 (SANGER UK)" host="www.biomart.org" includeDatasets="" martUser="" name="snp" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="functional_genomics_mart_59" default="0" displayName="ENSEMBL FUNCTIONAL GENOMICS 59 (SANGER UK)" host="www.biomart.org" includeDatasets="" martUser="" name="functional_genomics" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="vega_mart_59" default="0" displayName="VEGA 38 (SANGER UK)" host="www.biomart.org" includeDatasets="" martUser="" name="vega" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="genomic_features_mart_59" default="0" displayName="ENSEMBL GENOMIC FEATURES 59 (SANGER UK)" host="www.biomart.org" includeDatasets="" martUser="" name="genomic_features" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="0" />
+ <MartURLLocation database="ontology_mart_59" default="0" displayName="ENSEMBL ONTOLOGY 59 (SANGER UK)" host="www.biomart.org" includeDatasets="" martUser="" name="ontology" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="0" />
+ <MartURLLocation database="sequence_mart_59" default="0" displayName="ENSEMBL SEQUENCE 59 (SANGER UK)" host="www.biomart.org" includeDatasets="" martUser="" name="sequence" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="0" />
+ <MartURLLocation database="bacterial_mart_6" default="0" displayName="ENSEMBL BACTERIA 6 (EBI UK)" host="www.biomart.org" includeDatasets="" martUser="" name="bacterial_mart_6" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="bacterial_sequence_mart_6" default="0" displayName="" host="www.biomart.org" includeDatasets="" martUser="" name="bacterial_sequence_mart_6" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="0" />
+ <MartURLLocation database="fungal_mart_6" default="0" displayName="ENSEMBL FUNGAL 6 (EBI UK)" host="www.biomart.org" includeDatasets="" martUser="" name="fungal_mart_6" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="fungal_sequence_mart_6" default="0" displayName="" host="www.biomart.org" includeDatasets="" martUser="" name="fungal_sequence_mart_6" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="0" />
+ <MartURLLocation database="metazoa_genomic_features_mart_6" default="0" displayName="" host="www.biomart.org" includeDatasets="" martUser="" name="metazoa_genomic_features_mart_6" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="0" />
+ <MartURLLocation database="metazoa_mart_6" default="1" displayName="ENSEMBL METAZOA 6 (EBI UK)" host="www.biomart.org" includeDatasets="" martUser="" name="metazoa_mart_6" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="metazoa_sequence_mart_6" default="0" displayName="" host="www.biomart.org" includeDatasets="" martUser="" name="metazoa_sequence_mart_6" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="0" />
+ <MartURLLocation database="plant_mart_6" default="0" displayName="ENSEMBL PLANT 6 (EBI UK)" host="www.biomart.org" includeDatasets="" martUser="" name="plant_mart_6" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="plant_sequence_mart_6" default="0" displayName="" host="www.biomart.org" includeDatasets="" martUser="" name="plant_sequence_mart_6" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="0" />
+ <MartURLLocation database="protist_mart_6" default="1" displayName="ENSEMBL PROTISTS 6 (EBI UK)" host="www.biomart.org" includeDatasets="" martUser="" name="protist_mart_6" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="protist_sequence_mart_6" default="0" displayName="" host="www.biomart.org" includeDatasets="" martUser="" name="protist_sequence_mart_6" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="0" />
+ <MartURLLocation database="msd_mart_4" default="0" displayName="MSD PROTOTYPE (EBI UK)" host="www.biomart.org" includeDatasets="" martUser="" name="msd" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="utlp" default="" displayName="HIGH THROUGHPUT GENE TARGETING AND TRAPPING (SANGER UK)" host="www.sanger.ac.uk" includeDatasets="" martUser="" name="htgt" path="/htgt/biomart/martservice" port="80" redirect="1" serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="test_reactome_mart" default="1" displayName="REACTOME (CSHL US)" host="banon.cshl.edu" includeDatasets="complex,pathway,reaction,interaction" martUser="" name="REACTOME" path="/biomart/martservice" port="5555" redirect="1" serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="wormmart_215" default="1" displayName="WORMBASE 215 (CSHL US)" host="www.wormbase.org" includeDatasets="" martUser="" name="wormbase215" path="/biomart/martservice" port="80" redirect="1" serverVirtualSchema="WS215 --latest" visible="1" />
+ <MartURLLocation default="0" displayName="DICTYBASE (NORTHWESTERN US)" host="www.dictybase.org" includeDatasets="" martUser="" name="dicty" path="/biomart/martservice" port="80" redirect="1" serverVirtualSchema="dictyMart" visible="1" />
+ <MartURLLocation database="biomart" default="1" displayName="MGI (JACKSON LABORATORY US)" host="biomart.informatics.jax.org" includeDatasets="markers" name="biomart" path="/biomart/martservice" port="80" redirect="1" serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="rgd__mart" default="" displayName="RGD GENES (MCW US)" host="rote.hmgc.mcw.edu" includeDatasets="" martUser="" name="rgd__mart" path="/biomart/martservice" port="9999" redirect="1" serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="ipi_rat__mart" default="" displayName="RGD IPI MART (MCW US)" host="rote.hmgc.mcw.edu" includeDatasets="" martUser="" name="ipi_rat__mart" path="/biomart/martservice" port="9999" redirect="1" serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="SSLP__mart" default="" displayName="RGD MICROSATELLITE MARKERS (MCW US)" host="rote.hmgc.mcw.edu" includeDatasets="" martUser="" name="SSLP__mart" path="/biomart/martservice" port="9999" redirect="1" serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="g4public" default="" displayName="HGNC (EBI UK)" host="www.genenames.org" includeDatasets="" name="g4public" path="/biomart/martservice" port="80" redirect="1" serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="pride_mart_1" default="1" displayName="PRIDE (EBI UK)" host="www.ebi.ac.uk" includeDatasets="" martUser="" name="pride" path="/pride/biomart/martservice" port="80" redirect="1" serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="SPMART" default="" displayName="UNIPROT (EBI UK)" host="www.ebi.ac.uk" includeDatasets="" martUser="" name="uniprot_mart" path="/uniprot/biomart/martservice" port="80" redirect="1" serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="ensembl_expressionmart_48" default="1" displayName="EURATMART (EBI UK)" host="www.ebi.ac.uk" includeDatasets="" martUser="" name="ensembl_expressionmart_48" path="/euratools/biomart/martservice" port="80" redirect="1" serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="biomartDB" default="" displayName="PARAMECIUM GENOME (CNRS FRANCE)" host="paramecium.cgm.cnrs-gif.fr" includeDatasets="macronuclear" martUser="" name="biomartDB" path="/biomart/martservice" port="80" redirect="1" serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="tdb_biomart_new" default="" displayName="EUREXPRESS (MRC EDINBURGH UK)" host="biomart.eurexpress.org" includeDatasets="template" martUser="" name="Eurexpress Biomart" path="/biomart/martservice" port="80" redirect="1" serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="pepseekerGOLD_mart06" default="0" displayName="PEPSEEKER (UNIVERSITY OF MANCHESTER UK)" host="www.ispider.manchester.ac.uk" includeDatasets="peptide" martUser="" name="pepseekerGOLD_mart06" path="/pepseeker/biomart/martservice" port="80" redirect="1" serverVirtualSchema="pepseekerGOLD" visible="1" />
+ <MartURLLocation database="datacippotato_martpot_001" default="" displayName="DB_POTATO (INTERNATIONAL POTATO CENTER-CIP)" host="germplasmdb.cip.cgiar.org" includeDatasets="" martUser="" name="Potato_01" path="/biomart/martservice" port="80" redirect="1" serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="datacipsweet_martsweet_001" default="" displayName="DB_SWEETPOTATO (INTERNATIONAL POTATO CENTER-CIP)" host="germplasmdb.cip.cgiar.org" includeDatasets="" martUser="" name="Sweetpotato_01" path="/biomart/martservice" port="80" redirect="1" serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="phytozome_mart_v5" default="" displayName="PHYTOZOME (JGI/CIG US)" host="www.phytozome.net" includeDatasets="" martUser="" name="phytozome_mart" path="/biomart/martservice" port="80" redirect="1" serverVirtualSchema="zome_mart" visible="1" />
+ <MartURLLocation database="sequence_mart_v5" default="" displayName="Sequences" host="www.phytozome.net" includeDatasets="sequence_phytozome" martUser="" name="sequence_mart" path="/biomart/martservice" port="80" redirect="1" serverVirtualSchema="zome_mart" visible="0" />
+ <MartURLLocation database="mart_cyanobase_1" default="1" displayName="CYANOBASE 1 (KAZUSA JAPAN)" host="mart.kazusa.or.jp" includeDatasets="" martUser="default" name="cyanobase_1" path="/biomart/martservice" port="80" redirect="1" serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="hapmart_27_36" default="1" displayName="HAPMAP 27 (NCBI US)" host="hapmap.ncbi.nlm.nih.gov" includeDatasets="" name="HapMap_rel27" path="/biomart/martservice" port="80" redirect="1" serverVirtualSchema="rel27_NCBI_Build36" visible="1" />
+ <MartURLLocation database="cosp" default="1" displayName="COSMIC (SANGER UK)" host="www.sanger.ac.uk" includeDatasets="" martUser="" name="CosmicMart" path="/genetics/CGP/cosmic/biomart/martservice" port="80" redirect="1" serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="cildb_all_v2" default="" displayName="CILDB INPARANOID AND FILTERED BEST HIT (CNRS FRANCE)" host="cildb.cgm.cnrs-gif.fr" includeDatasets="" name="cildb_all_v2" path="/biomart/martservice" port="80" redirect="1" serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="cildb_inp_v2" default="" displayName="CILDB INPARANOID (CNRS FRANCE)" host="cildb.cgm.cnrs-gif.fr" includeDatasets="" name="cildb_inp_v2" path="/biomart/martservice" port="80" redirect="1" serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="marker_mart_30_55" default="" displayName="GRAMENE 30 MARKERS (CSHL/CORNELL US)" host="www.gramene.org" includeDatasets="" martUser="" name="GRAMENE_MARKER_30" path="/biomart/martservice" port="80" redirect="1" serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="map_mart_30_55" default="" displayName="GRAMENE 30 MAPPINGS (CSHL/CORNELL US)" host="www.gramene.org" includeDatasets="" martUser="" name="GRAMENE_MAP_30" path="/biomart/martservice" port="80" redirect="1" serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="qtl_mart_30_55" default="" displayName="GRAMENE 30 QTL DB (CSHL/CORNELL US)" host="www.gramene.org" includeDatasets="" martUser="" name="QTL_MART" path="/biomart/martservice" port="80" redirect="1" serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="genes" default="" displayName="INTOGEN GENES" host="biomart.intogen.org" includeDatasets="" martUser="" name="genes" path="/biomart/martservice" port="80" redirect="1" serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="oncomodules" default="" displayName="INTOGEN ONCOMODULES" host="biomart.intogen.org" includeDatasets="" martUser="" name="oncomodules" path="/biomart/martservice" port="80" redirect="1" serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="gmap_japonica" default="1" displayName="RICE-MAP JAPONICA (PEKING UNIVESITY CHINA)" host="ricemart.cbi.edu.cn" includeDatasets="" martUser="" name="gmap_japonica" path="/biomart/martservice" port="80" redirect="1" serverVirtualSchema="gmap_japonica" visible="1" />
+ <MartURLLocation database="europhenome_annotation_1_3_3_20100414" default="" displayName="EUROPHENOME" host="www.i-dcc.org" includeDatasets="europhenome" martUser="" name="europhenomeannotations" path="/biomart/martservice" port="80" redirect="1" serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="emma_biomart" default="" displayName="THE EUROPEAN MOUSE MUTANT ARCHIVE (EMMA)" host="www.i-dcc.org" includeDatasets="" martUser="" name="emma_biomart" path="/biomart/martservice" port="80" redirect="1" serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="ikmc_mart_alt" default="" displayName="IKMC GENES AND PRODUCTS (I-DCC)" host="www.i-dcc.org" includeDatasets="" martUser="" name="ikmc" path="/biomart/martservice" port="80" redirect="1" serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="gmap_indica" default="1" displayName="RICE-MAP INDICA (PEKING UNIVERSITY CHINA)" host="ricemart.cbi.edu.cn" includeDatasets="" martUser="" name="gmap_indica" path="/biomart/martservice" port="80" redirect="1" serverVirtualSchema="gmap_indica" visible="1" />
+ <MartURLLocation database="ensembl_latest" default="" displayName="PANCREATIC EXPRESSION DATABASE (INSTITUTE OF CANCER UK)" host="www.pancreasexpression.org" includeDatasets="" martUser="" name="Ensembl56" path="/biomart/martservice" port="80" redirect="1" serverVirtualSchema="default" visible="1" />
+</MartRegistry>
diff --git a/coreplugins/BioPAX/pom.xml b/coreplugins/BioPAX/pom.xml
new file mode 100644
index 0000000..7b4e0f4
--- /dev/null
+++ b/coreplugins/BioPAX/pom.xml
@@ -0,0 +1,121 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>parent</artifactId>
+ <version>2.8.4-SNAPSHOT</version>
+ </parent>
+
+ <artifactId>biopax</artifactId>
+ <packaging>jar</packaging>
+
+ <name>BioPAX</name>
+
+ <!-- bootstrap for cytoscape dependencies, namely the parent POM snapshots -->
+ <repositories>
+ <repository>
+ <id>cytoscape_snapshots</id>
+ <snapshots>
+ <enabled>true</enabled>
+ </snapshots>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <name>Cytoscape Snapshots</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/</url>
+ </repository>
+ <repository>
+ <id>cytoscape_releases</id>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ <name>Cytoscape Releases</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/releases/</url>
+ </repository>
+ <repository>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <id>cytoscape_thirdparty</id>
+ <name>Cytoscape Third Party</name>
+ <url>http://code.cytoscape.org/nexus/content/repositories/thirdparty/</url>
+ </repository>
+ <repository>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <id>cytoscape_biopax_release</id>
+ <name>Cytoscape BioPAX Release Mirror</name>
+ <url>http://code.cytoscape.org/nexus/content/repositories/biopax-release/</url>
+ </repository>
+ </repositories>
+
+ <build>
+ <plugins>
+ <plugin>
+ <artifactId>maven-assembly-plugin</artifactId>
+ <configuration>
+ <archive>
+ <manifestEntries>
+ <Cytoscape-Plugin>cytoscape.coreplugins.biopax.BiopaxPlugin</Cytoscape-Plugin>
+ </manifestEntries>
+ </archive>
+ </configuration>
+ </plugin>
+ </plugins>
+ </build>
+
+ <dependencies>
+ <dependency>
+ <groupId>commons-lang</groupId>
+ <artifactId>commons-lang</artifactId>
+ <version>2.4</version>
+ <scope>provided</scope> <!-- also in corelibs/commons-cli -->
+ </dependency>
+ <dependency>
+ <groupId>net.sourceforge.collections</groupId>
+ <artifactId>collections-generic</artifactId>
+ <version>4.01</version>
+ </dependency>
+ <dependency>
+ <groupId>org.biopax.paxtools</groupId>
+ <artifactId>paxtools-core</artifactId>
+ <version>${paxtools.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>commons-logging</groupId>
+ <artifactId>commons-logging</artifactId>
+ <version>1.1.1</version>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape-temp</groupId>
+ <artifactId>stax2-api</artifactId>
+ <version>3.0.1</version>
+ </dependency>
+<!-- <dependency> -->
+<!-- <groupId>cytoscape-temp</groupId> -->
+<!-- <artifactId>staxmate</artifactId> -->
+<!-- <version>2.0.0</version> -->
+<!-- </dependency> -->
+ <dependency>
+ <groupId>cytoscape-temp</groupId>
+ <artifactId>woodstox-core-lgpl</artifactId>
+ <version>4.0.5</version>
+ </dependency>
+ </dependencies>
+
+ <properties>
+ <paxtools.version>4.1.6</paxtools.version>
+ </properties>
+</project>
+
diff --git a/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/BioPaxFilter.java b/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/BioPaxFilter.java
new file mode 100644
index 0000000..d76ef5d
--- /dev/null
+++ b/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/BioPaxFilter.java
@@ -0,0 +1,128 @@
+// $Id: TestExternalLinkUtil.java,v 1.11 2006/06/15 22:07:49 grossb Exp $
+//------------------------------------------------------------------------------
+/** Copyright (c) 2006 Memorial Sloan-Kettering Cancer Center.
+ **
+ ** Code written by: Ethan Cerami, Benjamin Gross.
+ ** Authors: Ethan Cerami, Gary Bader, Chris Sander
+ **
+ ** This library is free software; you can redistribute it and/or modify it
+ ** under the terms of the GNU Lesser General Public License as published
+ ** by the Free Software Foundation; either version 2.1 of the License, or
+ ** any later version.
+ **
+ ** This library is distributed in the hope that it will be useful, but
+ ** WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ ** MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ ** documentation provided hereunder is on an "as is" basis, and
+ ** Memorial Sloan-Kettering Cancer Center
+ ** has no obligations to provide maintenance, support,
+ ** updates, enhancements or modifications. In no event shall
+ ** Memorial Sloan-Kettering Cancer Center
+ ** be liable to any party for direct, indirect, special,
+ ** incidental or consequential damages, including lost profits, arising
+ ** out of the use of this software and its documentation, even if
+ ** Memorial Sloan-Kettering Cancer Center
+ ** has been advised of the possibility of such damage. See
+ ** the GNU Lesser General Public License for more details.
+ **
+ ** You should have received a copy of the GNU Lesser General Public License
+ ** along with this library; if not, write to the Free Software Foundation,
+ ** Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ **/
+package cytoscape.coreplugins.biopax;
+
+import cytoscape.data.ImportHandler;
+
+import cytoscape.data.readers.GraphReader;
+
+import cytoscape.util.CyFileFilter;
+
+import java.io.File;
+import java.io.IOException;
+
+
+/**
+ * BioPax Filer class. Extends CyFileFilter for integration into the Cytoscape ImportHandler
+ * framework.
+ *
+ * @author Ethan Cerami.
+ */
+public class BioPaxFilter extends CyFileFilter {
+ /**
+ * XGMML Files are Graphs.
+ */
+ private static String fileNature = ImportHandler.GRAPH_NATURE;
+
+ /**
+ * File Extensions.
+ */
+ private static String[] fileExtensions = { "xml", "owl", "rdf" };
+
+ /**
+ * Content types
+ **/
+ private static String[] biopaxContentTypes = { "text/xml", "application/rdf+xml" };
+
+ /**
+ * Filter Description.
+ */
+ private static String description = "BioPAX files";
+
+ /**
+ * Constructor.
+ */
+ public BioPaxFilter() {
+ super(fileExtensions, description, fileNature);
+ // Add our content types
+ for (int i = 0; i < biopaxContentTypes.length; i++)
+ addContentType(biopaxContentTypes[i]);
+ }
+
+ /**
+ * Indicates which files the BioPaxFilter accepts.
+ * <p/>
+ * This method will return true only if:
+ * <UL>
+ * <LI>File ends in .xml or .owl; and
+ * <LI>File headers includes the www.biopax.org namespace declaration.
+ * </UL>
+ *
+ * @param file File
+ * @return true or false.
+ */
+ public boolean accept(File file) {
+ String fileName = file.getName();
+ boolean firstPass = false;
+
+ // First test: file must end with one of the registered file extensions.
+ for (int i = 0; i < fileExtensions.length; i++) {
+ if (fileName.endsWith(fileExtensions[i])) {
+ firstPass = true;
+ }
+ }
+
+ if (firstPass) {
+ // Second test: file header must contain the biopax declaration
+ try {
+ String header = getHeader(file);
+
+ if (header.indexOf("www.biopax.org") > 0) {
+ return true;
+ }
+ } catch (IOException e) {
+ }
+ }
+
+ return false;
+ }
+
+ /**
+ * Gets the appropirate GraphReader object.
+ *
+ * @param fileName File Name.
+ * @return GraphReader Object.
+ */
+ public GraphReader getReader(String fileName) {
+ return new BioPaxGraphReader(fileName);
+ }
+}
diff --git a/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/BioPaxGraphReader.java b/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/BioPaxGraphReader.java
new file mode 100644
index 0000000..649d656
--- /dev/null
+++ b/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/BioPaxGraphReader.java
@@ -0,0 +1,348 @@
+package cytoscape.coreplugins.biopax;
+
+import giny.model.RootGraph;
+import giny.view.GraphView;
+
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+import cytoscape.layout.CyLayouts;
+import cytoscape.util.CyNetworkNaming;
+import cytoscape.coreplugins.biopax.action.BiopaxNodeCtxMenuListener;
+import cytoscape.coreplugins.biopax.action.NetworkListener;
+import cytoscape.coreplugins.biopax.util.BioPaxUtil;
+import cytoscape.coreplugins.biopax.util.BioPaxVisualStyleUtil;
+import cytoscape.coreplugins.biopax.util.CytoscapeWrapper;
+import cytoscape.coreplugins.biopax.view.BioPaxContainer;
+import cytoscape.data.CyAttributes;
+import cytoscape.data.Semantics;
+import cytoscape.data.readers.GraphReader;
+import cytoscape.view.CyNetworkView;
+import cytoscape.visual.VisualMappingManager;
+import cytoscape.visual.VisualStyle;
+import cytoscape.layout.CyLayoutAlgorithm;
+import cytoscape.logger.CyLogger;
+
+import org.biopax.paxtools.converter.OneTwoThree;
+import org.biopax.paxtools.model.BioPAXLevel;
+import org.biopax.paxtools.model.Model;
+
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.io.UnsupportedEncodingException;
+import java.net.URLDecoder;
+import java.util.Iterator;
+
+import javax.swing.SwingUtilities;
+
+/**
+ * GraphReader Implementation for BioPAX Files.
+ *
+ * @author Ethan Cerami.
+ * @author Igor Rodchenkov (re-factoring, using PaxTools API)
+ */
+public class BioPaxGraphReader implements GraphReader {
+ public static final CyLogger log = CyLogger.getLogger(BioPaxGraphReader.class);
+
+ private int[] nodeIndices;
+ private int[] edgeIndices;
+ private String fileName;
+ private Model model;
+ private String networkName;
+ private CyLayoutAlgorithm layout;
+ private String networkId;
+ private static CyLayoutAlgorithm defaultLayout = CyLayouts.getLayout("force-directed");
+
+
+ /**
+ * Constructor
+ *
+ * @param fileName File Name.
+ */
+ public BioPaxGraphReader(String fileName) {
+ this.fileName = fileName;
+ this.model = null;
+ layout = getDefaultLayoutAlgorithm();
+ }
+
+ /**
+ * Constructor
+ *
+ * @param model PaxTools BioPAX Model
+ */
+ public BioPaxGraphReader(Model model) {
+ this.model= model;
+ this.fileName=null;
+ layout = getDefaultLayoutAlgorithm();
+ }
+
+ public String getNetworkId() {
+ return networkId;
+ }
+
+ public static void setDefaultLayoutAlgorithm(CyLayoutAlgorithm algo) {
+ defaultLayout = algo;
+ }
+
+ public static CyLayoutAlgorithm getDefaultLayoutAlgorithm() {
+ return defaultLayout;
+ }
+
+
+ /**
+ * Read file.
+ *
+ * @throws IOException IO Error.
+ */
+ public void read() throws IOException {
+
+ if(model == null && fileName != null) { // import new data
+ model = BioPaxUtil.read(new FileInputStream(fileName));
+ }
+
+ if(model == null) {
+ log.error("Failed to read BioPAX model");
+ return;
+ }
+
+ // immediately convert to BioPAX Level3 model
+ if(model != null && BioPAXLevel.L2.equals(model.getLevel())) {
+ log.info("Converting to BioPAX Level3 model internally... ");
+ model = new OneTwoThree().filter(model);
+ }
+
+ log.info("Model contains " + model.getObjects().size()
+ + " BioPAX elements");
+
+ networkName = getNetworkName(model);
+
+ // Map BioPAX Data to Cytoscape Nodes/Edges (run as task)
+ MapBioPaxToCytoscape mapper = new MapBioPaxToCytoscape();
+ mapper.doMapping(model);
+
+ nodeIndices = mapper.getNodeIndices();
+ if (nodeIndices.length == 0) {
+ log.error("Pathway is empty! " +
+ "Please check the BioPAX source file.");
+ return;
+ }
+ edgeIndices = mapper.getEdgeIndices();
+
+ }
+
+ private String getNetworkName(Model model) {
+ // make a network name from pathway name(s) or the file name
+ String candidateName;
+ String networkViewTitle = System.getProperty("biopax.network_view_title");
+ if (networkViewTitle != null && networkViewTitle.length() > 0) {
+ System.setProperty("biopax.network_view_title", "");
+ try {
+ networkViewTitle = URLDecoder.decode(networkViewTitle, "UTF-8");
+ }
+ catch (UnsupportedEncodingException e) {
+ // if exception occurs leave encoded string, but cmon, utf-8 not supported ??
+ }
+ candidateName = networkViewTitle;
+ } else {
+ candidateName = BioPaxUtil.getName(model);
+ }
+
+ if(candidateName == null || "".equalsIgnoreCase(candidateName)) {
+ candidateName = fileName;
+ if(log.isDebugging())
+ log.debug("Network name will be the file name: " + candidateName);
+ } else if(candidateName.length() > 100) {
+ if(log.isDebugging())
+ candidateName = fileName + " - " + candidateName.substring(0, 100);
+ log.debug("Based on multiple pathways network name is too long; " +
+ "it will be truncated: " + candidateName);
+ }
+
+ // Take appropriate adjustments, if name already exists
+ String name = CyNetworkNaming.getSuggestedNetworkTitle(candidateName);
+ if(log.isDebugging())
+ log.debug("Network name is: " + name);
+
+ return name;
+ }
+
+ /**
+ * Our implementation of GraphReader.getLayoutAlgorithm().
+ */
+ public CyLayoutAlgorithm getLayoutAlgorithm() {
+ return layout;
+ }
+
+ /**
+ * If yFiles available, perform organic layout,
+ * else matrix layout; same as that provided by the SIF reader.
+ * Keep this for pre-2.5 support
+ *
+ * @param view CyNetworkView Object.
+ */
+ public void layout(GraphView view) {
+ layout.doLayout((CyNetworkView)view);
+ }
+
+ /**
+ * Get Node Indices.
+ *
+ * @return array of root graph node indices.
+ */
+ public int[] getNodeIndicesArray() {
+ return nodeIndices;
+ }
+
+ /**
+ * Get Edge Indices.
+ *
+ * @return array of root graph edge indices.
+ */
+ public int[] getEdgeIndicesArray() {
+ return edgeIndices;
+ }
+
+ /**
+ * Gets network name.
+ *
+ * @return network name.
+ */
+ public String getNetworkName() {
+ return networkName;
+ }
+
+ /**
+ * Executes Post-Processing on newly created network.
+ *
+ * @param cyNetwork CyNetwork object.
+ */
+ public void doPostProcessing(final CyNetwork cyNetwork) {
+ // get cyNetwork id
+ this.networkId = cyNetwork.getIdentifier();
+
+ CyAttributes networkAttributes = Cytoscape.getNetworkAttributes();
+
+ // Sets a network attribute which indicates this network is a biopax network
+ networkAttributes.setAttribute(networkId, MapBioPaxToCytoscape.BIOPAX_NETWORK, Boolean.TRUE);
+
+ // Repair Canonical Name
+ repairNodesCanonicalName(cyNetwork);
+
+ // repair network name
+ //repairNetworkName(cyNetwork);
+ // Update UI. Must be done via SwingUtilities...
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ Cytoscape.getDesktop().getNetworkPanel().updateTitle(cyNetwork);
+ }
+ });
+
+ // Set default Quick Find Index
+ networkAttributes.setAttribute(cyNetwork.getIdentifier(), "quickfind.default_index", Semantics.CANONICAL_NAME);
+
+ // set url to pathway commons -
+ // used for pathway commons context menus
+ String urlToBioPAXWebServices = System.getProperty("biopax.web_services_url");
+ if (urlToBioPAXWebServices != null && urlToBioPAXWebServices.length() > 0) {
+ networkAttributes.setAttribute(cyNetwork.getIdentifier(),
+ "biopax.web_services_url",
+ urlToBioPAXWebServices);
+ System.setProperty("biopax.web_services_url", "");
+ }
+
+ // set data source attribute
+ // used for pathway commons context menus
+ String dataSources = System.getProperty("biopax.data_sources");
+ if (dataSources != null && dataSources.length() > 0) {
+ networkAttributes.setAttribute(cyNetwork.getIdentifier(),
+ "biopax.data_sources", dataSources);
+ System.setProperty("biopax.data_sources", "");
+ }
+
+ // associate the new network with its model
+ String modelString = (fileName!=null) ? fileName : "";
+ Cytoscape.getNetworkAttributes().setAttribute(networkId, BioPaxUtil.BIOPAX_DATA, modelString);
+
+ // Set-up the BioPax Visual Style
+ VisualStyle bioPaxVisualStyle = BioPaxVisualStyleUtil.getBioPaxVisualStyle();
+ VisualMappingManager manager = Cytoscape.getVisualMappingManager();
+ CyNetworkView view = Cytoscape.getNetworkView(cyNetwork.getIdentifier());
+ // set tooltips
+ BioPaxVisualStyleUtil.setNodeToolTips(view);
+ // set style
+ view.setVisualStyle(bioPaxVisualStyle.getName());
+ manager.setVisualStyle(bioPaxVisualStyle);
+ view.applyVizmapper(bioPaxVisualStyle);
+
+ // Set up BP UI
+ CytoscapeWrapper.initBioPaxPlugInUI();
+ BioPaxContainer bpContainer = BioPaxContainer.getInstance();
+ bpContainer.showLegend();
+
+ // add network listener
+ NetworkListener networkListener = bpContainer.getNetworkListener();
+ networkListener.registerNetwork(cyNetwork);
+
+ // add node's context menu
+ BiopaxNodeCtxMenuListener nodeCtxMenuListener = new BiopaxNodeCtxMenuListener();
+ view.addNodeContextMenuListener(nodeCtxMenuListener);
+
+ }
+
+ /**
+ * Read in graph; canonicalize all names.
+ * @deprecated Use read() instead. Will be removed Dec 2006.
+ * @param canonicalizeNodeNames flag for canonicalization.
+ * @throws IOException IO Error.
+ */
+ public void read(boolean canonicalizeNodeNames) throws IOException {
+ }
+
+ /**
+ * Get root graph.
+ * @deprecated Use Cytoscape.getRootGraph() instead. Will be removed Dec 2006.
+ * @return RootGraph Object.
+ */
+ public RootGraph getRootGraph() {
+ return null;
+ }
+
+ /**
+ * Get node attributes.
+ * @deprecated Use Cytoscape.getNodeAttributes() instead. Will be removed Dec 2006.
+ * @return CyAttributes object.
+ */
+ public CyAttributes getNodeAttributes() {
+ return null;
+ }
+
+ /**
+ * Get edge attributes.
+ * @deprecated Use Cytoscape.getEdgeAttributes() instead. Will be removed Dec 2006.
+ * @return CyAttributes object.
+ */
+ public CyAttributes getEdgeAttributes() {
+ return null;
+ }
+
+
+ /**
+ * Repairs Canonical Name; temporary fix for bug: 1001.
+ * By setting Canonical name to BIOPAX_NODE_LABEL, users can search for
+ * nodes via the Select Nodes --> By Name feature.
+ *
+ * @param cyNetwork CyNetwork Object.
+ */
+ private static void repairNodesCanonicalName(CyNetwork cyNetwork) {
+ CyAttributes nodeAttributes = Cytoscape.getNodeAttributes();
+ Iterator<CyNode> iter = cyNetwork.nodesIterator();
+ while (iter.hasNext()) {
+ CyNode node = iter.next();
+ String label = nodeAttributes.getStringAttribute(node.getIdentifier(),
+ BioPaxVisualStyleUtil.BIOPAX_NODE_LABEL);
+ if (label != null) {
+ nodeAttributes.setAttribute(node.getIdentifier(), Semantics.CANONICAL_NAME, label);
+ }
+ }
+ }
+}
diff --git a/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/BiopaxPlugin.java b/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/BiopaxPlugin.java
new file mode 100644
index 0000000..37dc5c9
--- /dev/null
+++ b/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/BiopaxPlugin.java
@@ -0,0 +1,99 @@
+/** BioPAX Plugin for Cytoscape
+ **
+ ** Copyright (c) 2010 University of Toronto (UofT)
+ ** and Memorial Sloan-Kettering Cancer Center (MSKCC).
+ **
+ ** This is free software; you can redistribute it and/or modify it
+ ** under the terms of the GNU Lesser General Public License as published
+ ** by the Free Software Foundation; either version 2.1 of the License, or
+ ** any later version.
+ **
+ ** This library is distributed in the hope that it will be useful, but
+ ** WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ ** MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ ** documentation provided hereunder is on an "as is" basis, and
+ ** both UofT and MSKCC have no obligations to provide maintenance,
+ ** support, updates, enhancements or modifications. In no event shall
+ ** UofT or MSKCC be liable to any party for direct, indirect, special,
+ ** incidental or consequential damages, including lost profits, arising
+ ** out of the use of this software and its documentation, even if
+ ** UofT or MSKCC have been advised of the possibility of such damage.
+ ** See the GNU Lesser General Public License for more details.
+ **
+ ** You should have received a copy of the GNU Lesser General Public License
+ ** along with this software; if not, write to the Free Software Foundation,
+ ** Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA;
+ ** or find it at http://www.fsf.org/ or http://www.gnu.org.
+ **/
+package cytoscape.coreplugins.biopax;
+
+
+import cytoscape.Cytoscape;
+import cytoscape.CytoscapeInit;
+import cytoscape.coreplugins.biopax.action.ExportAsBioPAXAction;
+import cytoscape.coreplugins.biopax.view.BioPaxContainer;
+import cytoscape.data.ImportHandler;
+import cytoscape.logger.CyLogger;
+import cytoscape.plugin.CytoscapePlugin;
+import cytoscape.view.CyMenus;
+
+import java.util.Properties;
+
+/**
+ * BioPAX Import PlugIn.
+ *
+ * @author Ethan Cerami, B. Arman Aksoy, Rex Dwyer, Igor Rodchenkov
+ */
+public class BiopaxPlugin extends CytoscapePlugin {
+
+ protected static final CyLogger log = CyLogger.getLogger(BiopaxPlugin.class);
+
+ /**
+ * Name of Plugin.
+ */
+ public static final String PLUGIN_NAME = "BioPAX Plugin";
+
+ /**
+ * Attribute Name for BioPAX Utility Class.
+ */
+ public static final String BP_UTIL = "BIO_PAX_UTIL";
+
+ /**
+ * Proxy Host Property Name
+ */
+ public static final String PROXY_HOST_PROPERTY = "dataservice.proxy_host";
+
+ /**
+ * Proxy Port Property Name
+ */
+ public static final String PROXY_PORT_PROPERTY = "dataservice.proxy_port";
+
+ /**
+ * Constructor.
+ * This method is called by the main Cytoscape Application upon startup.
+ */
+ public BiopaxPlugin() {
+ ImportHandler importHandler = new ImportHandler();
+ importHandler.addFilter(new BioPaxFilter());
+
+ // Optionally set up HTTP Proxy
+ Properties cytoProps = CytoscapeInit.getProperties();
+ String proxyHost = (String) cytoProps.get(PROXY_HOST_PROPERTY);
+ String proxyPort = (String) cytoProps.get(PROXY_PORT_PROPERTY);
+
+ if ((proxyHost != null) && (proxyPort != null)) {
+ System.getProperties().put("proxySet", "true");
+ System.getProperties().put("proxyHost", proxyHost);
+ System.getProperties().put("proxyPort", proxyPort);
+ }
+
+ // add export to BioPAX menu
+ CyMenus cyMenus = Cytoscape.getDesktop().getCyMenus();
+ cyMenus.addAction(new ExportAsBioPAXAction());
+
+ // to start listening to network events, like a load of a network from a session,
+ // we create an instance of a BioPaxContainerClass this contains the network listener
+ BioPaxContainer.getInstance();
+ }
+
+}
diff --git a/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/MapBioPaxToCytoscape.java b/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/MapBioPaxToCytoscape.java
new file mode 100644
index 0000000..bca700a
--- /dev/null
+++ b/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/MapBioPaxToCytoscape.java
@@ -0,0 +1,1157 @@
+package cytoscape.coreplugins.biopax;
+
+import cytoscape.CyEdge;
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+
+import cytoscape.coreplugins.biopax.util.BioPaxUtil;
+import cytoscape.coreplugins.biopax.util.BioPaxVisualStyleUtil;
+import cytoscape.coreplugins.biopax.util.ExternalLink;
+import cytoscape.coreplugins.biopax.util.ExternalLinkUtil;
+import cytoscape.coreplugins.biopax.util.NodeAttributesWrapper;
+import cytoscape.data.CyAttributes;
+import cytoscape.data.Semantics;
+
+import cytoscape.data.attr.CountedIterator;
+import cytoscape.data.attr.MultiHashMap;
+import cytoscape.data.attr.MultiHashMapDefinition;
+import cytoscape.logger.CyLogger;
+
+import cytoscape.task.TaskMonitor;
+import cytoscape.view.CyNetworkView;
+
+import cytoscape.render.stateful.NodeDetails;
+import cytoscape.render.stateful.CustomGraphic;
+
+import giny.model.Edge;
+import giny.view.NodeView;
+
+import org.apache.commons.lang.StringUtils;
+import org.biopax.paxtools.controller.AbstractTraverser;
+import org.biopax.paxtools.controller.ObjectPropertyEditor;
+import org.biopax.paxtools.controller.PropertyEditor;
+import org.biopax.paxtools.controller.SimpleEditorMap;
+import org.biopax.paxtools.model.BioPAXElement;
+import org.biopax.paxtools.model.Model;
+import org.biopax.paxtools.model.level3.Catalysis;
+import org.biopax.paxtools.model.level3.CellularLocationVocabulary;
+import org.biopax.paxtools.model.level3.Complex;
+import org.biopax.paxtools.model.level3.Control;
+import org.biopax.paxtools.model.level3.ControlType;
+import org.biopax.paxtools.model.level3.ControlledVocabulary;
+import org.biopax.paxtools.model.level3.Controller;
+import org.biopax.paxtools.model.level3.Conversion;
+import org.biopax.paxtools.model.level3.Entity;
+import org.biopax.paxtools.model.level3.Interaction;
+import org.biopax.paxtools.model.level3.Pathway;
+import org.biopax.paxtools.model.level3.PhysicalEntity;
+import org.biopax.paxtools.model.level3.Process;
+import org.biopax.paxtools.model.level3.PublicationXref;
+import org.biopax.paxtools.model.level3.RelationshipTypeVocabulary;
+import org.biopax.paxtools.model.level3.RelationshipXref;
+import org.biopax.paxtools.model.level3.SimplePhysicalEntity;
+import org.biopax.paxtools.model.level3.Stoichiometry;
+import org.biopax.paxtools.model.level3.UnificationXref;
+import org.biopax.paxtools.model.level3.XReferrable;
+import org.biopax.paxtools.model.level3.Xref;
+import org.biopax.paxtools.util.ClassFilterSet;
+import org.biopax.paxtools.util.Filter;
+
+import ding.view.DNodeView;
+
+import java.awt.Paint;
+import java.awt.geom.Rectangle2D;
+import java.awt.image.BufferedImage;
+import java.util.*;
+
+
+/**
+ * Maps a BioPAX Model to Cytoscape Nodes/Edges.
+ *
+ * @author Ethan Cerami, Igor Rodchenkov (re-factoring using PaxTools API)
+ */
+public class MapBioPaxToCytoscape {
+
+ public static final CyLogger log = CyLogger.getLogger(MapBioPaxToCytoscape.class);
+
+ /**
+ * Cytoscape Attribute: BioPAX Network.
+ * Stores boolean indicating this CyNetwork
+ * is a BioPAX network.
+ */
+ public static final String BIOPAX_NETWORK = "BIOPAX_NETWORK";
+
+
+ public final static String BINARY_NETWORK = "BINARY_NETWORK";
+
+ /**
+ * Cytoscape Attribute: BioPAX Edge Type.
+ */
+ public static final String BIOPAX_EDGE_TYPE = "BIOPAX_EDGE_TYPE";
+
+
+ /**
+ * Cytoscape Attribute: BioPAX RDF ID.
+ */
+ public static final String BIOPAX_RDF_ID = "URI";
+
+ /**
+ * BioPax Node Attribute: Entity TYPE
+ */
+ public static final String BIOPAX_ENTITY_TYPE = "BIOPAX_TYPE";
+
+
+ /**
+ * BioPax Node Attribute: CHEMICAL_MODIFICATIONS_MAP
+ */
+ public static final String BIOPAX_CHEMICAL_MODIFICATIONS_MAP = "CHEMICAL_MODIFICATIONS_MAP";
+
+ /**
+ * BioPax Node Attribute: CHEMICAL_MODIFICATIONS_LIST
+ */
+ public static final String BIOPAX_CHEMICAL_MODIFICATIONS_LIST = "CHEMICAL_MODIFICATIONS";
+
+ /**
+ * BioPax Node Attribute: UNIFICATION_REFERENCES
+ */
+ public static final String BIOPAX_UNIFICATION_REFERENCES = "UNIFICATION_REFERENCES";
+
+ /**
+ * BioPax Node Attribute: RELATIONSHIP_REFERENCES
+ */
+ public static final String BIOPAX_RELATIONSHIP_REFERENCES = "RELATIONSHIP_REFERENCES";
+
+ /**
+ * BioPax Node Attribute: PUBLICATION_REFERENCES
+ */
+ public static final String BIOPAX_PUBLICATION_REFERENCES = "PUBLICATION_REFERENCES";
+
+ /**
+ * BioPAX Node Attribute: XREF_IDs.
+ */
+ public static final String BIOPAX_XREF_IDS = "IDENTIFIERS";
+
+
+ /**
+ * BioPax Node Attribute: CELLULAR_LOCATION
+ */
+ public static final String BIOPAX_CELLULAR_LOCATIONS = "CELLULAR_LOCATIONS";
+
+
+ /**
+ * BioPax Node Attribute: IHOP_LINKS
+ */
+ public static final String BIOPAX_IHOP_LINKS = "IHOP_LINKS";
+
+ /**
+ * BioPax Node Attribute: AFFYMETRIX_REFERENCES
+ */
+ public static final String BIOPAX_AFFYMETRIX_REFERENCES_LIST = "AFFYMETRIX_REFERENCES";
+
+ // custom node images (phosphorylation)
+ private static final String PHOSPHORYLATION_GRAPHICS = "PHOSPHORYLATION_GRAPHICS";
+
+ // strange, cannot get this to work with final keyword
+ private static BufferedImage phosNode = null;
+ private static BufferedImage phosNodeSelectedTop = null;
+ private static BufferedImage phosNodeSelectedRight = null;
+ private static BufferedImage phosNodeSelectedBottom = null;
+ private static BufferedImage phosNodeSelectedLeft = null;
+
+ static {
+ try {
+ phosNode = javax.imageio.ImageIO.read
+ (MapBioPaxToCytoscape.class.getResource("phos-node.jpg"));
+ phosNodeSelectedTop = javax.imageio.ImageIO.read
+ (MapBioPaxToCytoscape.class.getResource("phos-node-selected-top.jpg"));
+ phosNodeSelectedRight = javax.imageio.ImageIO.read
+ (MapBioPaxToCytoscape.class.getResource("phos-node-selected-right.jpg"));
+ phosNodeSelectedBottom = javax.imageio.ImageIO.read
+ (MapBioPaxToCytoscape.class.getResource("phos-node-selected-bottom.jpg"));
+ phosNodeSelectedLeft = javax.imageio.ImageIO.read
+ (MapBioPaxToCytoscape.class.getResource("phos-node-selected-left.jpg"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+ }
+
+ private static BufferedImage[] customPhosGraphics = {
+ phosNodeSelectedTop,
+ phosNodeSelectedRight,
+ phosNodeSelectedBottom,
+ phosNodeSelectedLeft
+ };
+
+
+ private List<CyNode> nodeList = new ArrayList<CyNode>();
+
+ private List<Edge> edgeList = new ArrayList<Edge>();
+
+ private TaskMonitor taskMonitor;
+
+ //BioPAX element to CyNode map
+ private final Map<BioPAXElement, CyNode> bpeToCyNodeMap;
+
+ /**
+ * Constructor.
+ *
+ * @param bpUtil BioPAX Utility Class.
+ * @param taskMonitor TaskMonitor Object.
+ */
+ public MapBioPaxToCytoscape(TaskMonitor taskMonitor) {
+ this();
+ this.taskMonitor = taskMonitor;
+ }
+
+ /**
+ * Constructor.
+ *
+ * @param bpUtil BioPAX Utility Class.
+ */
+ public MapBioPaxToCytoscape() {
+ this.bpeToCyNodeMap = new HashMap<BioPAXElement, CyNode>();
+ }
+
+ /**
+ * Execute the Mapping.
+ */
+ public void doMapping(Model model) {
+ initAttributes(Cytoscape.getNodeAttributes());
+
+ createEntityNodes(model);
+
+ createInteractionEdges(model);
+
+ createComplexEdges(model);
+
+ createMemberEdges(model);
+
+ }
+
+
+ private void createEntityNodes(Model model) {
+
+ if (taskMonitor != null) {
+ taskMonitor.setStatus("Creating CyNodes (the first pass)...");
+ taskMonitor.setPercentCompleted(0);
+ }
+
+ int i = 0; //progress counter
+ Set<Entity> entities = model.getObjects(Entity.class);
+ for(Entity bpe: entities) {
+ // do not make nodes for top/main pathways
+ if(bpe instanceof Pathway) {
+ if(bpe.getParticipantOf().isEmpty()
+ && ((Process)bpe).getPathwayComponentOf().isEmpty())
+ continue;
+ }
+
+ // generate node id form the BioPAX URI
+ String id = BioPaxUtil.generateId(bpe);
+ if(log.isDebugging())
+ log.debug("Mapping " + BioPaxUtil.type(bpe) + " node : " + id);
+
+ // Create node symbolizing the interaction
+ CyNode cyNode = Cytoscape.getCyNode(id, true);
+ nodeList.add(cyNode);
+ bpeToCyNodeMap.put(bpe, cyNode);
+
+ // traverse the model, making attributes from BioPAX properties
+ mapNodeAttribute(bpe, model, id);
+
+ // update progress bar
+ if (taskMonitor != null) {
+ double perc = (double) i++ / entities.size();
+ taskMonitor.setPercentCompleted((int) (100.0 * perc));
+ }
+ }
+
+ if(log.isDebugging())
+ log.debug(nodeList.size() + " nodes created.");
+ }
+
+
+ private void createInteractionEdges(Model model) {
+ // Extract the List of all Interactions
+ Collection<Interaction> interactionList = model.getObjects(Interaction.class);
+
+ if (taskMonitor != null) {
+ taskMonitor.setStatus("Creating edges...");
+ taskMonitor.setPercentCompleted(0);
+ }
+
+ int i = 0;
+ for (Interaction itr : interactionList) {
+ if(log.isDebugging()) {
+ log.debug("Mapping " + itr.getModelInterface().getSimpleName()
+ + " edges : " + itr.getRDFId());
+ }
+
+ if (itr instanceof Conversion) {
+ addConversionInteraction((Conversion)itr);
+ } else if (itr instanceof Control) {
+ addControlInteraction((Control) itr);
+ } else {
+ addPhysicalInteraction(itr);
+ }
+
+ if (taskMonitor != null) {
+ double perc = (double) i++ / interactionList.size();
+ taskMonitor.setPercentCompleted((int) (100.0 * perc));
+ }
+ }
+ }
+
+
+ /**
+ * Adds a Conversion Interaction.
+ */
+ private void addConversionInteraction(Conversion interactionElement) {
+ // Add Left Side of Reaction
+ Collection<PhysicalEntity> leftSideElements = interactionElement.getLeft();
+ for (PhysicalEntity leftElement: leftSideElements) {
+ linkNodes(interactionElement, leftElement, "left");
+ }
+
+ // Add Right Side of Reaction
+ Collection<PhysicalEntity> rightSideElements = interactionElement.getRight();
+ for (PhysicalEntity rightElement : rightSideElements) {
+ linkNodes(interactionElement, rightElement, "right");
+ }
+ }
+
+ /**
+ * Gets all node indices.
+ *
+ * @return array of root graph indices.
+ */
+ public int[] getNodeIndices() {
+ int[] nodeIndices = new int[nodeList.size()];
+
+ for (int i = 0; i < nodeList.size(); i++) {
+ CyNode node = (CyNode) nodeList.get(i);
+ nodeIndices[i] = node.getRootGraphIndex();
+ }
+
+ return nodeIndices;
+ }
+
+ /**
+ * Gets all edge indices.
+ *
+ * @return array of root graph indices.
+ */
+ public int[] getEdgeIndices() {
+ int[] edgeIndices = new int[edgeList.size()];
+
+ for (int i = 0; i < edgeList.size(); i++) {
+ CyEdge edge = (CyEdge) edgeList.get(i);
+ edgeIndices[i] = edge.getRootGraphIndex();
+ }
+
+ return edgeIndices;
+ }
+
+
+ private void createMemberEdges(Model model) {
+ // for each PE,
+ for (PhysicalEntity par : model.getObjects(PhysicalEntity.class)) {
+ Set<PhysicalEntity> members = par.getMemberPhysicalEntity();
+ if(members.isEmpty())
+ continue;
+
+ CyNode cyParentNode = bpeToCyNodeMap.get(par);
+ assert cyParentNode != null : "cyParentNode is NULL.";
+ // for each its member PE, add the directed edge
+ for (PhysicalEntity member : members)
+ {
+ CyNode cyMemberNode = bpeToCyNodeMap.get(member);
+ CyEdge edge = Cytoscape.getCyEdge(cyParentNode, cyMemberNode, Semantics.INTERACTION, "contains", true);
+ Cytoscape.getEdgeAttributes().setAttribute(edge.getIdentifier(), BIOPAX_EDGE_TYPE, "member");
+ }
+ }
+ }
+
+
+ /*
+ * Iterates over complexElementList and connects members. This routine will
+ * modify and then return the complexElementList argument. It removes complexes
+ * that get processed during this call, and adds members which are complexes themselves.
+ */
+ private void createComplexEdges(Model model) {
+ // interate through all pe's
+ for (Complex complexElement : model.getObjects(Complex.class)) {
+ Set<PhysicalEntity> members = complexElement.getComponent();
+ if(members.isEmpty())
+ continue;
+
+ // get node
+ CyNode complexCyNode = bpeToCyNodeMap.get(complexElement);
+
+ // get all components. There can be 0 or more
+ for (PhysicalEntity member : members)
+ {
+ CyNode complexMemberCyNode = bpeToCyNodeMap.get(member);
+ // create edge, set attributes
+ Edge edge = Cytoscape.getCyEdge(complexCyNode, complexMemberCyNode,
+ Semantics.INTERACTION, "contains", true);
+ Cytoscape.getEdgeAttributes().setAttribute(edge.getIdentifier(), BIOPAX_EDGE_TYPE, "contains");
+ edgeList.add(edge);
+ }
+ }
+ }
+
+ /*
+ * Adds a Physical Interaction, such as a binding interaction between
+ * two proteins.
+ */
+ private void addPhysicalInteraction(Interaction interactionElement) {
+ // Add all Participants
+ Collection<Entity> participantElements = interactionElement.getParticipant();
+ for (Entity participantElement : participantElements) {
+ linkNodes(interactionElement, (BioPAXElement) participantElement, "participant");
+ }
+ }
+
+
+ /**
+ * Add Edges Between Interaction/Complex Node and Physical Entity Node.
+ *
+ */
+ private void linkNodes(BioPAXElement bpeA, BioPAXElement bpeB, String type)
+ {
+ // Note: getCyNode also assigns cellular location attribute...
+ CyNode nodeA = bpeToCyNodeMap.get(bpeA);
+ if(nodeA == null) {
+ log.debug("linkNodes: no node was created for "
+ + bpeA.getModelInterface() + " " + bpeA.getRDFId());
+ return; //e.g., we do not create any pathway nodes currently...
+ }
+
+ CyNode nodeB = bpeToCyNodeMap.get(bpeB);
+ if(nodeB == null) {
+ log.debug("linkNodes: no node was created for "
+ + bpeB.getModelInterface() + " " + bpeB.getRDFId());
+ return; //e.g., we do not create any pathway nodes currently...
+ }
+
+ CyEdge edge = null;
+ if (type.equals("right") || type.equals("cofactor")
+ || type.equals("participant")) {
+ edge = Cytoscape.getCyEdge(nodeA, nodeB, Semantics.INTERACTION,
+ type, true);
+ } else {
+ edge = Cytoscape.getCyEdge(nodeB, nodeA, Semantics.INTERACTION,
+ type, true);
+ }
+
+ Cytoscape.getEdgeAttributes().setAttribute(edge.getIdentifier(), BIOPAX_EDGE_TYPE, type);
+ edgeList.add(edge);
+ }
+
+ /*
+ * Adds a BioPAX Control Interaction.
+ */
+ private void addControlInteraction(Control control) {
+ Collection<Process> controlledList = control.getControlled();
+ for (Process process : controlledList) {
+ // Determine the BioPAX Edge Type
+ String typeStr = "controlled"; //default
+ ControlType cType = control.getControlType();
+ typeStr = (cType == null) ? typeStr : cType.toString();
+ //edge direction (trick) - from control to process (like for 'right', 'cofactor', 'participant')
+ linkNodes(process, control, typeStr);
+ }
+
+ Collection<Controller> controllerList = control.getController();
+ for (Controller controller : controllerList) {
+ // directed edge - from Controller to Control (like 'left')
+ linkNodes(control, controller, "controller");
+ }
+
+ // cofactor relationships
+ if(control instanceof Catalysis) {
+ Collection<PhysicalEntity> coFactorList = ((Catalysis) control).getCofactor();
+ for(PhysicalEntity cofactor : coFactorList) {
+ // direction - from control to cofactor (like 'right', 'participant', 'controlled')
+ linkNodes(control, cofactor, "cofactor");
+ }
+ }
+ }
+
+
+ /*
+ * A helper function to set chemical modification attributes
+ */
+ private static void setChemicalModificationAttributes(String cyNodeId, NodeAttributesWrapper chemicalModificationsWrapper) {
+
+ Map<String, Object> modificationsMap = (chemicalModificationsWrapper != null)
+ ? chemicalModificationsWrapper.getMap() : null;
+
+ if (modificationsMap != null) {
+
+ CyAttributes nodeAttributes = Cytoscape.getNodeAttributes();
+
+ // As discussed with Ben on August 29, 2006:
+ // We will now store chemical modifications in two places:
+ // 1. a regular list of strings (to be used by the view details panel,
+ // node attribute browser, and Quick Find.
+ // 2. a multihashmap, of the following form:
+ // chemical_modification --> modification(s) --> # of modifications.
+ // this cannot be represented as a SimpleMap, and must be represented as
+ // a multi-hashmap. This second form is used primarily by the custom
+ // rendering engine for, e.g. drawing number of phosphorylation sies.
+
+ // Store List of Chemical Modifications Only
+ List<String> list = new ArrayList<String>(modificationsMap.keySet());
+ nodeAttributes.setListAttribute(cyNodeId, BIOPAX_CHEMICAL_MODIFICATIONS_LIST, list);
+
+ // Store Complete Map of Chemical Modifications --> # of Modifications
+ setMultiHashMap(cyNodeId, nodeAttributes, BIOPAX_CHEMICAL_MODIFICATIONS_MAP, modificationsMap);
+
+ if (modificationsMap.containsKey(BioPaxUtil.PHOSPHORYLATION_SITE)) {
+ nodeAttributes.setAttribute(cyNodeId, BIOPAX_ENTITY_TYPE,
+ BioPaxUtil.PROTEIN_PHOSPHORYLATED);
+ }
+ }
+ }
+
+ /*
+ * A helper function to set a multihashmap consisting of name - value pairs.
+ */
+ private static void setMultiHashMap(String cyNodeId, CyAttributes attributes, String attributeName,
+ Map map) {
+ // our key format
+ final byte[] mhmKeyFormat = new byte[] { MultiHashMapDefinition.TYPE_STRING };
+
+ // define multihashmap if necessary
+ MultiHashMapDefinition mmapDefinition = attributes.getMultiHashMapDefinition();
+
+ try {
+ byte[] vals = mmapDefinition.getAttributeKeyspaceDimensionTypes(attributeName);
+ } catch (IllegalStateException e) {
+ // define the multihashmap attribute
+ mmapDefinition.defineAttribute(attributeName, MultiHashMapDefinition.TYPE_STRING,
+ mhmKeyFormat);
+ }
+
+ // add the map attributes
+ MultiHashMap mhmap = attributes.getMultiHashMap();
+ Set entrySet = map.entrySet();
+
+ for (Iterator i = entrySet.iterator(); i.hasNext();) {
+ Map.Entry me = (Map.Entry) i.next();
+ Object[] key = { (String) me.getKey() };
+ Integer value = (Integer) me.getValue();
+ mhmap.setAttributeValue(cyNodeId, attributeName, value.toString(), key);
+ }
+ }
+
+
+ /**
+ * Maps Attributes for a Single Node.
+ *
+ * @param element BioPAX Object.
+ * @param model BioPAX Model
+ * @param nodeId {@link CyNode} identifier
+ */
+ public static void mapNodeAttribute(BioPAXElement element, Model model, final String nodeID) {
+
+ final CyAttributes nodeAttributes = Cytoscape.getNodeAttributes();
+
+ if (element != null) {
+ Filter<PropertyEditor> filter = new Filter<PropertyEditor>() {
+ @Override
+ // skips for entity-range properties (which map to edges rather than attributes - not here though),
+ // and several utility classes ranges (for which we do not want generate attributes or do another way)
+ public boolean filter(PropertyEditor editor) {
+ if(editor instanceof ObjectPropertyEditor) {
+ Class c = editor.getRange();
+ String prop = editor.getProperty();
+ if( Entity.class.isAssignableFrom(c)
+ || Stoichiometry.class.isAssignableFrom(c)
+ || "nextStep".equals(prop)
+ ) {
+ return false;
+ }
+ }
+ return true;
+ }
+ };
+
+ String stringRef = "";
+ @SuppressWarnings("unchecked")
+ AbstractTraverser bpeAutoMapper = new AbstractTraverser(SimpleEditorMap.L3, filter)
+ {
+ final CyLogger log = CyLogger.getLogger(AbstractTraverser.class);
+
+ @SuppressWarnings("rawtypes")
+ @Override
+ protected void visit(final Object obj, final BioPAXElement bpe, final Model model, final PropertyEditor editor)
+ {
+ String attrName = getAttrName(getProps());
+
+ // skip those that are either nodes/edges themselves or mapped separately
+ if (obj != null
+ && !(
+ obj instanceof Entity
+ || obj instanceof Xref
+ || obj instanceof ControlledVocabulary
+ || obj instanceof Stoichiometry
+ )
+ ) {
+
+ // bug fix: biopax.SequenceSite.SequencePosition = -2147483648 ('unknown value') if the site is empty; 2010.03.14
+ String value = (editor.isUnknown(obj))? "" : obj.toString();
+
+ if(log.isDebugging()) {
+ log.debug("set attribute '" + attrName
+ + "' for " + bpe + " = "
+ + value);
+ }
+
+ if(editor.isMultipleCardinality()) {
+ final List<String> vals = new ArrayList<String>();
+ if(nodeAttributes.getAttributeNames().toString().contains(attrName)) {
+ final List oldVals = nodeAttributes.getListAttribute(nodeID, attrName);
+ if(oldVals != null) {
+ for(final Object o : oldVals) {
+ vals.add(o.toString());
+ }
+ }
+ }
+
+ if(value!= null && !"".equalsIgnoreCase(value.toString().replaceAll("\\]|\\[", "")))
+ {
+ vals.add(value);
+ }
+
+ if(!vals.isEmpty()) {
+ nodeAttributes.setListAttribute(nodeID, attrName, vals);
+ }
+
+ } else {
+ //this strange thing may never happen...
+ if(nodeAttributes.getAttributeNames().toString().contains(attrName)) {
+ value += ", " + nodeAttributes.getStringAttribute(nodeID, attrName);
+ }
+ nodeAttributes.setAttribute(nodeID, attrName, value);
+ }
+
+ if(obj instanceof BioPAXElement) {
+ traverse((BioPAXElement)obj, null);
+ }
+ }
+ }
+
+ private String getAttrName(Stack<String> props) {
+ return StringUtils.join(props, "/");
+ }
+
+ };
+
+ // set additional attributes
+
+ // this one is important
+ nodeAttributes.setAttribute(nodeID, BIOPAX_RDF_ID, element.getRDFId());
+
+ String name = BioPaxUtil.truncateLongStr(BioPaxUtil.getNodeName(element) + "");
+
+ nodeAttributes.setAttribute(nodeID, Semantics.CANONICAL_NAME, name);
+
+ nodeAttributes.setAttribute(nodeID, BIOPAX_ENTITY_TYPE, BioPaxUtil.type(element));
+
+ // type
+ stringRef = biopaxType(element, nodeAttributes);
+ if (stringRef != null) {
+ nodeAttributes.setAttribute(nodeID, BIOPAX_ENTITY_TYPE, stringRef);
+ }
+
+
+ if (!(element instanceof Interaction)) {
+ // get chemical modification & cellular location attributes
+ NodeAttributesWrapper chemicalModificationsWrapper = getInteractionChemicalModifications(element);
+ // add modifications to the label/name
+ String modificationsString = getModificationsString(chemicalModificationsWrapper);
+ name += modificationsString;
+ // add cellular location to the label/name
+ if(element instanceof PhysicalEntity) {
+ CellularLocationVocabulary cl = ((PhysicalEntity) element).getCellularLocation();
+ if(cl != null) {
+ String clAbbr = BioPaxUtil.getAbbrCellLocation(cl.toString())
+ .replaceAll("\\[|\\]", "");
+ name += (clAbbr.length() > 0) ? ("\n" + clAbbr) : "";
+ }
+ }
+ // set node attributes
+ setChemicalModificationAttributes(nodeID, chemicalModificationsWrapper);
+ }
+ // update the name (also used for node's label and quick find)
+
+ nodeAttributes.setAttribute(nodeID, BioPaxVisualStyleUtil.BIOPAX_NODE_LABEL, name);
+
+ bpeAutoMapper.traverse(element, null);
+
+ // create custom (convenience?) attributes, mainly - from xrefs
+ createExtraXrefAttributes(element, nodeID);
+
+ } else {
+ nodeAttributes.setAttribute(nodeID, Semantics.CANONICAL_NAME, "null");
+ nodeAttributes.setAttribute(nodeID, BIOPAX_ENTITY_TYPE, BioPaxUtil.NULL_ELEMENT_TYPE);
+ }
+ }
+
+ private static void createExtraXrefAttributes(BioPAXElement element, String nodeID) {
+
+ CyNode node = Cytoscape.getCyNode(nodeID);
+ CyAttributes nodeAttributes = Cytoscape.getNodeAttributes();
+
+ // the following code should replace the old way to set
+ // relationship references
+ List<String> xrefList = getXRefList(element, BIOPAX_AFFYMETRIX_REFERENCES_LIST);
+ if ((xrefList != null) && !xrefList.isEmpty()) {
+ nodeAttributes.setListAttribute(nodeID, BIOPAX_AFFYMETRIX_REFERENCES_LIST,
+ xrefList);
+ }
+
+ // ihop links
+ String stringRef = ihopLinks(element);
+ if (stringRef != null) {
+ nodeAttributes.setAttribute(nodeID, BIOPAX_IHOP_LINKS, stringRef);
+ }
+
+ List<String> allxList = new ArrayList<String>();
+ List<String> unifxfList = new ArrayList<String>();
+ List<String> relxList = new ArrayList<String>();
+ List<String> pubxList = new ArrayList<String>();
+ // add xref ids per database and per xref class
+ List<Xref> xList = BioPaxUtil.getXRefs(element, Xref.class);
+ for (Xref link : xList) {
+ if(link.getDb() == null)
+ continue; // too bad (data issue...); skip it
+
+ // per db -
+ String key = "ID_" + link.getDb().toUpperCase();
+ // Set individual XRefs; Max of 1 per database.
+ String existingId = nodeAttributes.getStringAttribute(nodeID, key);
+ if (existingId == null) {
+ nodeAttributes.setAttribute(nodeID, key, link.getId());
+ }
+
+ StringBuffer temp = new StringBuffer();
+
+ if(!"CPATH".equalsIgnoreCase(link.getDb()))
+ temp.append(ExternalLinkUtil.createLink(link.getDb(), link.getId()));
+ else
+ temp.append(link.toString());
+
+ if(link instanceof UnificationXref) {
+ unifxfList.add(temp.toString());
+ }
+ else if(link instanceof PublicationXref) {
+ PublicationXref xl = (PublicationXref) link;
+ temp.append(" ");
+ if (!xl.getAuthor().isEmpty()) {
+ temp.append(xl.getAuthor().toString() + " et al., ");
+ }
+ if (xl.getTitle() != null) {
+ temp.append(xl.getTitle());
+ }
+ if (!xl.getSource().isEmpty()) {
+ temp.append(" (" + xl.getSource().toString());
+ if (xl.getYear() > 0) {
+ temp.append(", " + xl.getYear());
+ }
+ temp.append(")");
+ }
+ pubxList.add(temp.toString());
+ }
+ else if(link instanceof RelationshipXref) {
+ relxList.add(temp.toString());
+ }
+
+ allxList.add(link.toString());
+ }
+
+ nodeAttributes.setListAttribute(nodeID, BIOPAX_XREF_IDS, allxList);
+ nodeAttributes.setListAttribute(nodeID, BIOPAX_UNIFICATION_REFERENCES, unifxfList);
+ nodeAttributes.setListAttribute(nodeID, BIOPAX_RELATIONSHIP_REFERENCES, relxList);
+ nodeAttributes.setListAttribute(nodeID, BIOPAX_PUBLICATION_REFERENCES, pubxList);
+
+ }
+
+
+
+ /**
+ * Adds custom node shapes to BioPAX nodes.
+ *
+ * @param networkView CyNetworkView
+ */
+ public static void customNodes(CyNetworkView networkView) {
+ // grab node attributes
+ CyNetwork cyNetwork = networkView.getNetwork();
+ CyAttributes nodeAttributes = Cytoscape.getNodeAttributes();
+
+ // iterate through the nodes
+ @SuppressWarnings("unchecked")
+ Iterator<CyNode> nodesIt = cyNetwork.nodesIterator();
+ if (nodesIt.hasNext()) {
+ // grab the node
+ CyNode node = nodesIt.next();
+
+ // get chemical modifications
+ int count = 0;
+ boolean isPhosphorylated = false;
+ MultiHashMapDefinition mhmdef = nodeAttributes.getMultiHashMapDefinition();
+
+ if (mhmdef.getAttributeValueType(BIOPAX_CHEMICAL_MODIFICATIONS_MAP) != -1) {
+ MultiHashMap mhmap = nodeAttributes.getMultiHashMap();
+ CountedIterator modsIt = mhmap.getAttributeKeyspan(node.getIdentifier(),
+ BIOPAX_CHEMICAL_MODIFICATIONS_MAP, null);
+
+ // do we have phosphorylation ?
+ while (modsIt.hasNext()) {
+ String modification = (String) modsIt.next();
+
+ if (modification.equalsIgnoreCase(BioPaxUtil.PHOSPHORYLATION_SITE)) {
+ isPhosphorylated = true;
+
+ Object[] key = { BioPaxUtil.PHOSPHORYLATION_SITE };
+ String countStr = (String) mhmap.getAttributeValue(node.getIdentifier(),
+ BIOPAX_CHEMICAL_MODIFICATIONS_MAP, key);
+ count = ((Integer) Integer.valueOf(countStr)).intValue();
+
+ break;
+ }
+ }
+ }
+
+ // if phosphorylated, add custom node
+ if (isPhosphorylated) {
+ addCustomShapes(networkView, node, PHOSPHORYLATION_GRAPHICS, count);
+ }
+ }
+ }
+
+ /**
+ * Initializes attribute descriptions and user interaction flags.
+ */
+ public static void initAttributes(CyAttributes nodeAttributes) {
+ nodeAttributes.setAttributeDescription(BIOPAX_RDF_ID,
+ "The Resource Description Framework (RDF) Identifier.");
+ nodeAttributes.setAttributeDescription(BIOPAX_ENTITY_TYPE,
+ "The BioPAX entity type. "
+ + "For example, interactions could be of type: "
+ + "physical interaction, control, conversion, etc. "
+ + "Likewise, "
+ + "physical entities could be of type: complex, DNA, "
+ + "RNA, protein or small molecule.");
+ nodeAttributes.setAttributeDescription(BIOPAX_CELLULAR_LOCATIONS,
+ "A list of one or more cellular locations, e.g. 'cytoplasm'. "
+ + "This attribute should reference a term in the "
+ + "Gene Ontology " + "Cellular Component ontology.");
+ nodeAttributes.setAttributeDescription(BIOPAX_AFFYMETRIX_REFERENCES_LIST,
+ "A list of one or more Affymetrix probeset identifers "
+ + "associated with the entity.");
+ nodeAttributes.setAttributeDescription(BIOPAX_CHEMICAL_MODIFICATIONS_LIST,
+ "A list of one or more chemical modifications "
+ + "associated with the entity. For example: "
+ + "phoshorylation, acetylation, etc.");
+ nodeAttributes.setAttributeDescription(BIOPAX_XREF_IDS,
+ "External reference IDs associated with this entity. For example, "
+ + "a protein record may be annotated with UNIPROT or "
+ + "REFSeq accession numbers.");
+
+ nodeAttributes.setUserVisible(BioPaxVisualStyleUtil.BIOPAX_NODE_LABEL, true);
+ nodeAttributes.setAttributeDescription(BioPaxVisualStyleUtil.BIOPAX_NODE_LABEL,
+ "BioPax Node Label. Short label used to identify each node in the network.");
+
+ // Hide these attributes from the user, as they currently
+ // contain HTML, and don't make much sense within the default
+ // attribute browser.
+ nodeAttributes.setUserVisible(BIOPAX_IHOP_LINKS, false);
+ nodeAttributes.setUserVisible(BIOPAX_PUBLICATION_REFERENCES, false);
+ nodeAttributes.setUserVisible(BIOPAX_RELATIONSHIP_REFERENCES, false);
+ nodeAttributes.setUserVisible(BIOPAX_UNIFICATION_REFERENCES, false);
+ nodeAttributes.setUserVisible(BIOPAX_CHEMICAL_MODIFICATIONS_MAP, false);
+ nodeAttributes.setUserVisible(BIOPAX_CELLULAR_LOCATIONS, false);
+
+ // Make these attributes non-editable
+ nodeAttributes.setUserEditable(BIOPAX_RDF_ID, false);
+ }
+
+ /**
+ * Based on given arguments, adds proper custom node shape to node.
+ */
+ private static void addCustomShapes(CyNetworkView networkView, CyNode node, String shapeType,
+ int modificationCount) {
+ // create refs to help views
+ CyNetwork cyNetwork = networkView.getNetwork();
+ NodeView nodeView = networkView.getNodeView(node);
+ DNodeView dingNodeView = (DNodeView) nodeView;
+
+ // remove existing custom nodes
+ Iterator<CustomGraphic> it = dingNodeView.customGraphicIterator();
+ while ( it.hasNext() ) {
+ dingNodeView.removeCustomGraphic( it.next() );
+ }
+
+ for (int lc = 0; lc < modificationCount; lc++) {
+ // set image
+ BufferedImage image = null;
+
+ if (shapeType.equalsIgnoreCase(PHOSPHORYLATION_GRAPHICS)) {
+ image = (cyNetwork.isSelected(node)) ? customPhosGraphics[lc] : phosNode;
+ }
+
+ // set rect
+ Rectangle2D rect = getCustomShapeRect(image, lc);
+
+ // create our texture paint
+ Paint paint = null;
+
+ try {
+ paint = new java.awt.TexturePaint(image, rect);
+ } catch (Exception exc) {
+ paint = java.awt.Color.black;
+ }
+
+ // add the graphic
+ dingNodeView.addCustomGraphic(rect, paint, NodeDetails.ANCHOR_CENTER);
+ }
+ }
+
+ /**
+ * Based on given arguments, determines proper rectangle coordinates
+ * used to render custom node shape.
+ */
+ private static Rectangle2D getCustomShapeRect(BufferedImage image, int modificationCount) {
+ // our scale factor
+ double scale = .1;
+ final double[] startX = {
+ 0,
+
+ (BioPaxVisualStyleUtil.BIO_PAX_VISUAL_STYLE_PHYSICAL_ENTITY_NODE_WIDTH * BioPaxVisualStyleUtil.BIO_PAX_VISUAL_STYLE_PHYSICAL_ENTITY_NODE_SIZE_SCALE) / 2,
+ 0,
+
+ (-1 * BioPaxVisualStyleUtil.BIO_PAX_VISUAL_STYLE_PHYSICAL_ENTITY_NODE_WIDTH * BioPaxVisualStyleUtil.BIO_PAX_VISUAL_STYLE_PHYSICAL_ENTITY_NODE_SIZE_SCALE) / 2
+ };
+
+ final double[] startY = {
+ (-1 * BioPaxVisualStyleUtil.BIO_PAX_VISUAL_STYLE_PHYSICAL_ENTITY_NODE_HEIGHT * BioPaxVisualStyleUtil.BIO_PAX_VISUAL_STYLE_PHYSICAL_ENTITY_NODE_SIZE_SCALE) / 2,
+ 0,
+
+ (BioPaxVisualStyleUtil.BIO_PAX_VISUAL_STYLE_PHYSICAL_ENTITY_NODE_HEIGHT * BioPaxVisualStyleUtil.BIO_PAX_VISUAL_STYLE_PHYSICAL_ENTITY_NODE_SIZE_SCALE) / 2,
+ 0
+ };
+
+ // create and return rect
+ return new java.awt.geom.Rectangle2D.Double(startX[modificationCount]
+ + ((-1 * (image.getWidth() / 2)) * scale),
+ startY[modificationCount]
+ + ((-1 * (image.getHeight() / 2)) * scale),
+ (double) image.getWidth() * scale,
+ (double) image.getHeight() * scale);
+ }
+
+
+ private static String biopaxType(BioPAXElement bpe, CyAttributes nodeAttributes) {
+ MultiHashMapDefinition mhmdef = nodeAttributes.getMultiHashMapDefinition();
+ // first check if attribute exists
+ if (mhmdef.getAttributeValueType(BIOPAX_CHEMICAL_MODIFICATIONS_MAP) != -1) {
+ MultiHashMap mhmap = nodeAttributes.getMultiHashMap();
+ CountedIterator modsIt = mhmap.getAttributeKeyspan(BioPaxUtil.generateId(bpe),
+ BIOPAX_CHEMICAL_MODIFICATIONS_MAP,
+ null);
+ while (modsIt.hasNext()) {
+ String modification = (String) modsIt.next();
+ if (modification.equalsIgnoreCase(BioPaxUtil.PHOSPHORYLATION_SITE)) {
+ return BioPaxUtil.PROTEIN_PHOSPHORYLATED;
+ }
+ }
+ }
+
+ return BioPaxUtil.type(bpe);
+ }
+
+ private static List<String> getXRefList(BioPAXElement bpe, String xrefType) {
+ List<String> listToReturn = new ArrayList<String>();
+
+ // get the xref list
+ List<ExternalLink> list = xrefToExternalLinks(bpe, RelationshipXref.class);
+ // what type of xref are we interested in ?
+ String type = null;
+ if (xrefType.equalsIgnoreCase(BIOPAX_AFFYMETRIX_REFERENCES_LIST)) {
+ type = "AFFYMETRIX";
+ }
+
+ if (!list.isEmpty()) {
+ for (ExternalLink link : list) {
+ if (link.getDbName().toUpperCase().startsWith(type)) {
+ listToReturn.add(link.getId());
+ }
+ }
+ }
+
+ return listToReturn;
+ }
+
+ private static String ihopLinks(BioPAXElement bpe) {
+ List<String> synList = new ArrayList<String>(BioPaxUtil.getSynonyms(bpe));
+ List<ExternalLink> dbList = xrefToExternalLinks(bpe, Xref.class);
+ String htmlLink = null;
+
+ if (!synList.isEmpty() || !dbList.isEmpty()) {
+ htmlLink = ExternalLinkUtil.createIHOPLink(bpe.getModelInterface().getSimpleName(),
+ synList, dbList, BioPaxUtil.getOrganismTaxonomyId(bpe));
+ }
+
+ return htmlLink;
+ }
+
+
+ private static <T extends Xref> List<ExternalLink> xrefToExternalLinks(BioPAXElement bpe, Class<T> xrefClass) {
+
+ if(bpe instanceof XReferrable) {
+ List<ExternalLink> erefs = new ArrayList<ExternalLink>();
+ erefs.addAll(extractXrefs(new ClassFilterSet<Xref,T>(
+ ((XReferrable)bpe).getXref(), xrefClass) ));
+ if(bpe instanceof SimplePhysicalEntity &&
+ ((SimplePhysicalEntity)bpe).getEntityReference() != null)
+ {
+ erefs.addAll(extractXrefs(new ClassFilterSet<Xref,T>(
+ ((SimplePhysicalEntity)bpe).getEntityReference().getXref(), xrefClass) ));
+ }
+ return erefs;
+ }
+ return new ArrayList<ExternalLink>();
+ }
+
+
+ private static List<ExternalLink> extractXrefs(Collection<? extends Xref> xrefs) {
+ List<ExternalLink> dbList = new ArrayList<ExternalLink>();
+
+ for (Xref x: xrefs) {
+ String db = null;
+ String id = null;
+ String relType = null;
+ String title = null;
+ String year = null;
+ String author = null;
+ String url = null;
+ String source = null;
+
+ db = x.getDb();
+ String ver = x.getIdVersion();
+ id = x.getId(); // + ((ver!=null) ? "_" + ver : "");
+ if(x instanceof RelationshipXref) {
+ RelationshipTypeVocabulary v = ((RelationshipXref)x).getRelationshipType();
+ if(v != null) relType = v.getTerm().toString();
+ }
+ if(x instanceof PublicationXref) {
+ PublicationXref px = (PublicationXref)x;
+ author = px.getAuthor().toString();
+ title = px.getTitle();
+ source = px.getSource().toString();
+ url =px.getUrl().toString();
+ year = px.getYear() + "";
+ }
+
+ if ((db != null) && (id != null)) {
+ ExternalLink link = new ExternalLink(db, id);
+ link.setAuthor(author);
+ link.setRelType(relType);
+ link.setTitle(title);
+ link.setYear(year);
+ link.setSource(source);
+ link.setUrl(url);
+ dbList.add(link);
+ }
+ }
+
+ return dbList;
+ }
+
+
+ /*
+ * Given a binding element (complex or interaction)
+ * and type (like left or right),
+ * returns chemical modification (abbreviated form).
+ *
+ */
+ private static NodeAttributesWrapper getInteractionChemicalModifications(BioPAXElement participantElement)
+ {
+
+ if(participantElement == null) {
+ return null;
+ }
+
+ // both of these objects will be used to contruct
+ // the NodeAttributesWrapper which gets returned
+ Map<String,Object> chemicalModificationsMap = null;
+ String chemicalModifications = null;
+
+ // if we are dealing with participant processes (interactions
+ // or complexes), we have to go through the participants to get the
+ // proper chemical modifications
+ Collection<?> modificationFeatures =
+ BioPaxUtil.getValues(participantElement, "feature", "notFeature");
+ // short ciruit routine if empty list
+ if (modificationFeatures == null) {
+ return null;
+ }
+
+ // interate through the list returned from the query
+ for (Object modification : modificationFeatures) {
+ if (modification != null) {
+ // initialize chemicalModifications string if necessary
+ chemicalModifications = (chemicalModifications == null || chemicalModifications.length()==0)
+ ? "-" : chemicalModifications;
+ // initialize chemicalModifications hashmap if necessary
+ chemicalModificationsMap = (chemicalModificationsMap == null)
+ ? new HashMap<String, Object>() : chemicalModificationsMap;
+
+ Object value = BioPaxUtil.getValue((BioPAXElement)modification, "modificationType");
+ String mod = (value == null) ? "" : value.toString();
+
+ // is this a new type of modification ?
+ if (!chemicalModificationsMap.containsKey(mod)) {
+ // determine abbreviation
+ String abbr = BioPaxUtil.getAbbrChemModification(mod);
+
+ // add abreviation to modifications string
+ // (the string "-P...")
+ chemicalModifications += abbr;
+
+ // update our map - modification, count
+ chemicalModificationsMap.put(mod, new Integer(1));
+ } else {
+ // we've seen this modification before, just update the count
+ Integer count = (Integer) chemicalModificationsMap.get(mod);
+ chemicalModificationsMap.put(mod, ++count);
+ }
+ }
+ }
+
+ return new NodeAttributesWrapper(chemicalModificationsMap, chemicalModifications);
+ }
+
+ /*
+ * A helper function to get post-translational modifications string.
+ */
+ private static String getModificationsString(NodeAttributesWrapper chemicalModificationsWrapper)
+ {
+
+ // check args
+ if (chemicalModificationsWrapper == null) return "";
+
+ // get chemical modifications
+ String chemicalModification = (chemicalModificationsWrapper != null)
+ ? chemicalModificationsWrapper.getAbbreviationString()
+ : null;
+
+ return (((chemicalModification != null) && (chemicalModification.length() > 0))
+ ? chemicalModification : "");
+ }
+}
diff --git a/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/action/BiopaxNodeCtxMenuListener.java b/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/action/BiopaxNodeCtxMenuListener.java
new file mode 100644
index 0000000..0dbca7c
--- /dev/null
+++ b/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/action/BiopaxNodeCtxMenuListener.java
@@ -0,0 +1,60 @@
+package cytoscape.coreplugins.biopax.action;
+
+import java.awt.Component;
+import java.awt.event.ActionEvent;
+
+import giny.view.NodeView;
+
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JPopupMenu;
+
+import cytoscape.Cytoscape;
+import cytoscape.coreplugins.biopax.util.BioPaxUtil;
+import cytoscape.coreplugins.biopax.util.BioPaxVisualStyleUtil;
+import cytoscape.logger.CyLogger;
+import cytoscape.util.CytoscapeAction;
+
+import ding.view.NodeContextMenuListener;
+
+public class BiopaxNodeCtxMenuListener implements NodeContextMenuListener {
+
+ public void addNodeContextMenuItems(NodeView nodeView, JPopupMenu menu) {
+// JMenuItem myMenuItem = new JMenuItem("Show OWL");
+// myMenuItem.addActionListener(new DisplayBiopaxXmlAction(nodeView));
+// if (menu == null) {
+// menu = new JPopupMenu();
+// }
+// menu.add(myMenuItem);
+
+ }
+
+
+
+ class DisplayBiopaxXmlAction extends CytoscapeAction {
+ private NodeView nodeView;
+
+ public DisplayBiopaxXmlAction(NodeView nodeView) {
+ this.nodeView = nodeView;
+ }
+
+ @Override
+ public void actionPerformed(ActionEvent event) {
+ String nodeId = nodeView.getNode().getIdentifier();
+
+ String owl = Cytoscape.getNodeAttributes()
+ .getStringAttribute(nodeId, BioPaxUtil.BIOPAX_DATA);
+
+ String label = Cytoscape.getNodeAttributes()
+ .getStringAttribute(nodeId, BioPaxVisualStyleUtil.BIOPAX_NODE_LABEL);
+
+ Component component = Cytoscape.getDesktop()
+ .findComponentAt((int)nodeView.getXPosition(), (int)nodeView.getYPosition());
+
+ JOptionPane.showMessageDialog(component, owl, label, JOptionPane.PLAIN_MESSAGE);
+ }
+
+ }
+
+
+}
diff --git a/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/action/DisplayBioPaxDetails.java b/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/action/DisplayBioPaxDetails.java
new file mode 100644
index 0000000..b648eb9
--- /dev/null
+++ b/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/action/DisplayBioPaxDetails.java
@@ -0,0 +1,160 @@
+// $Id: DisplayBioPaxDetails.java,v 1.10 2006/07/21 17:05:50 grossb Exp $
+//------------------------------------------------------------------------------
+/** Copyright (c) 2006 Memorial Sloan-Kettering Cancer Center.
+ **
+ ** Code written by: Ethan Cerami
+ ** Authors: Ethan Cerami, Gary Bader, Chris Sander
+ **
+ ** This library is free software; you can redistribute it and/or modify it
+ ** under the terms of the GNU Lesser General Public License as published
+ ** by the Free Software Foundation; either version 2.1 of the License, or
+ ** any later version.
+ **
+ ** This library is distributed in the hope that it will be useful, but
+ ** WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ ** MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ ** documentation provided hereunder is on an "as is" basis, and
+ ** Memorial Sloan-Kettering Cancer Center
+ ** has no obligations to provide maintenance, support,
+ ** updates, enhancements or modifications. In no event shall
+ ** Memorial Sloan-Kettering Cancer Center
+ ** be liable to any party for direct, indirect, special,
+ ** incidental or consequential damages, including lost profits, arising
+ ** out of the use of this software and its documentation, even if
+ ** Memorial Sloan-Kettering Cancer Center
+ ** has been advised of the possibility of such damage. See
+ ** the GNU Lesser General Public License for more details.
+ **
+ ** You should have received a copy of the GNU Lesser General Public License
+ ** along with this library; if not, write to the Free Software Foundation,
+ ** Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ **/
+package cytoscape.coreplugins.biopax.action;
+
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+
+import cytoscape.coreplugins.biopax.MapBioPaxToCytoscape;
+import cytoscape.coreplugins.biopax.util.CySessionUtil;
+import cytoscape.coreplugins.biopax.util.CytoscapeWrapper;
+import cytoscape.coreplugins.biopax.view.BioPaxContainer;
+import cytoscape.coreplugins.biopax.view.BioPaxDetailsPanel;
+import cytoscape.data.SelectEvent;
+import cytoscape.data.SelectEventListener;
+
+
+import java.awt.*;
+
+import java.util.HashSet;
+import java.util.Iterator;
+
+import javax.swing.*;
+
+
+/**
+ * Displays BioPAX Details when user clicks on a Node.
+ * <p/>
+ * When a user selects a node, the specified BioPaxDetailsPanel Object
+ * will display the node details. Additionally, if the BioPaxDetailsPanel
+ * Object is embedded inside a CytoPanel, its tab is automatically
+ * made active.
+ *
+ * @author Ethan Cerami
+ */
+public class DisplayBioPaxDetails implements SelectEventListener {
+ private int totalNumNodesSelected = 0;
+ private BioPaxDetailsPanel bpPanel;
+
+ /**
+ * Constructor.
+ *
+ * @param bpPanel BioPaxDetailsPanel Object that will actually display
+ * the BioPax details.
+ */
+ public DisplayBioPaxDetails(BioPaxDetailsPanel bpPanel) {
+ this.bpPanel = bpPanel;
+ }
+
+ /**
+ * User has selected/unselected one or more nodes.
+ *
+ * @param event Select Event.
+ */
+ @SuppressWarnings("unchecked")
+ public void onSelectEvent(SelectEvent event) {
+ int targetType = event.getTargetType();
+
+ // Only show details when exactly one node/edge is selected.
+ // This is done by keeping a running total of number of nodes/edges
+ // currently selected.
+
+ // A simpler option would be to obtain a SelectFilter object from
+ // the current network, and simply query it for a list of selected
+ // nodes/edges. However, we want the listener to work on multiple
+ // networks. For example, we want to display node/edge details
+ // for a parent network and any of its subnetworks.
+ if (targetType == SelectEvent.NODE_SET) {
+ HashSet set = (HashSet) event.getTarget();
+ trackTotalNumberNodesSelected(event, set);
+
+ if (event.getEventType() && (totalNumNodesSelected == 1)) {
+ Iterator iterator = set.iterator();
+ CyNode node = (CyNode) iterator.next();
+
+ // Get the BioPAX Util Object from the current network
+ CyNetwork cyNetwork = Cytoscape.getCurrentNetwork();
+ String id = node.getIdentifier();
+
+ if (id != null && !CySessionUtil.isSessionReadingInProgress()) {
+ // Conditionally, set up BP UI
+ // If we are reading a session file, ignore the node selection event.
+ CytoscapeWrapper.initBioPaxPlugInUI();
+ // Show the details
+ bpPanel.showDetails(id);
+ // If legend is showing, show details
+ BioPaxContainer bpContainer = BioPaxContainer.getInstance();
+ bpContainer.showDetails();
+ }
+ }
+ }
+
+ // update custom nodes
+ MapBioPaxToCytoscape.customNodes(Cytoscape.getCurrentNetworkView());
+ }
+
+ /**
+ * Recursive Method for Walking up a Containment Tree, looking for
+ * a CytoPanel
+ *
+ * @param c Container Object.
+ */
+ private void activateTabs(Container c) {
+ Container parent = c.getParent();
+
+ if (parent != null) {
+ if (parent instanceof JTabbedPane) {
+ JTabbedPane parentTabbedPane = (JTabbedPane) parent;
+ int index = parentTabbedPane.indexOfComponent(c);
+ parentTabbedPane.setSelectedIndex(index);
+ }
+
+ activateTabs(parent);
+ }
+ }
+
+ /**
+ * Keeps track of total number of Nodes currently selected by the user.
+ */
+ private void trackTotalNumberNodesSelected(SelectEvent event, HashSet set) {
+ if (event.getEventType()) {
+ totalNumNodesSelected += set.size();
+ } else {
+ totalNumNodesSelected -= set.size();
+
+ if (totalNumNodesSelected < 0) {
+ totalNumNodesSelected = 0;
+ }
+ }
+ }
+}
diff --git a/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/action/ExportAsBioPAXAction.java b/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/action/ExportAsBioPAXAction.java
new file mode 100644
index 0000000..d126019
--- /dev/null
+++ b/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/action/ExportAsBioPAXAction.java
@@ -0,0 +1,157 @@
+/* Copyright 2008 - The Cytoscape Consortium (www.cytoscape.org)
+ *
+ * The Cytoscape Consortium is:
+ * - Institute for Systems Biology
+ * - University of California San Diego
+ * - Memorial Sloan-Kettering Cancer Center
+ * - Institut Pasteur
+ * - Agilent Technologies
+ *
+ * Authors: B. Arman Aksoy, Thomas Kelder, Emek Demir
+ *
+ * This file is part of PaxtoolsPlugin.
+ *
+ * PaxtoolsPlugin is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * PaxtoolsPlugin is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this project. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package cytoscape.coreplugins.biopax.action;
+
+import cytoscape.util.CytoscapeAction;
+import cytoscape.util.FileUtil;
+import cytoscape.util.CyFileFilter;
+import cytoscape.Cytoscape;
+import cytoscape.CyNetwork;
+import cytoscape.task.Task;
+import cytoscape.task.TaskMonitor;
+import cytoscape.task.util.TaskManager;
+import cytoscape.task.ui.JTaskConfig;
+import cytoscape.coreplugins.biopax.util.BioPaxUtil;
+import cytoscape.data.CyAttributes;
+
+import javax.swing.event.MenuEvent;
+import java.awt.event.ActionEvent;
+import java.io.*;
+
+
+/**
+ * This is currently an experimental feature.
+ * Networks that were previously imported
+ * from a BioPAX file or web services may be saved.
+ * All the modifications to this network made
+ * within Cytoscape will be lost.
+ *
+ * @author rodche
+ *
+ */
+public class ExportAsBioPAXAction extends CytoscapeAction {
+ public ExportAsBioPAXAction() {
+ super("BioPAX Network to File...");
+ setPreferredMenu("File.Export");
+ }
+
+ /**
+ * User-initiated action to save the current BioPAX network
+ * to a user-specified file. If successfully saved, fires a
+ * PropertyChange event with property=Cytoscape.NETWORK_SAVED,
+ * old_value=null, and new_value=a three element Object array containing:
+ * <OL>
+ * <LI>first element = CyNetwork saved
+ * <LI>second element = URI of the location where saved
+ * <LI>third element = an Integer representing the format in which the
+ * Network was saved (e.g., Cytoscape.FILE_SIF).
+ * </OL>
+ * @param e ActionEvent Object.
+ */
+ public void actionPerformed(ActionEvent e) {
+ File file = FileUtil.getFile(
+ "Save BioPAX Network (experimental feature)",
+ FileUtil.SAVE,
+ new CyFileFilter[] { });
+ if (file != null) {
+ String fileName = file.getAbsolutePath();
+
+ if (!fileName.endsWith(".xml"))
+ fileName = fileName + ".xml";
+
+ ExportAsBioPAXTask task = new ExportAsBioPAXTask(fileName);
+
+ JTaskConfig jTaskConfig = new JTaskConfig();
+ jTaskConfig.setOwner(Cytoscape.getDesktop());
+ jTaskConfig.displayCloseButton(true);
+ jTaskConfig.displayStatus(true);
+ jTaskConfig.setAutoDispose(false);
+
+ TaskManager.executeTask(task, jTaskConfig);
+ }
+ }
+
+ public void menuSelected(MenuEvent e) {
+ CyNetwork cyNetwork = Cytoscape.getCurrentNetwork();
+
+ if( BioPaxUtil.isBioPaxNetwork(cyNetwork) )
+ enableForNetwork();
+ else
+ setEnabled(false);
+ }
+}
+
+class ExportAsBioPAXTask implements Task {
+ private String fileName;
+ private TaskMonitor taskMonitor;
+
+ ExportAsBioPAXTask(String fileName) {
+ this.fileName = fileName;
+ }
+
+ public void run() {
+ taskMonitor.setStatus("Exporting BioPAX...");
+ CyNetwork currentNetwork = Cytoscape.getCurrentNetwork();
+ CyAttributes networkAttributes = Cytoscape.getNetworkAttributes();
+ String bpModelStr = (String) networkAttributes
+ .getAttribute(currentNetwork.getIdentifier(), BioPaxUtil.BIOPAX_DATA);
+ try {
+ if(bpModelStr == null )
+ throw new IllegalArgumentException("Invalid/empty BioPAX data.");
+
+ Writer w = new OutputStreamWriter(new FileOutputStream(fileName));
+ w.write(bpModelStr);
+ w.close();
+
+ Object[] ret_val = new Object[3];
+ ret_val[0] = currentNetwork;
+ ret_val[1] = new File(fileName).toURI();
+ ret_val[2] = Cytoscape.FILE_BIOPAX;
+ Cytoscape.firePropertyChange(Cytoscape.NETWORK_SAVED, null, ret_val);
+
+ taskMonitor.setPercentCompleted(100);
+ taskMonitor.setStatus("Network successfully saved to: " + fileName + ".");
+ } catch (IllegalArgumentException e) {
+ taskMonitor.setException(e, "Network is invalid. Cannot be saved.");
+ } catch (IOException e) {
+ taskMonitor.setException(e, "Unable to save network.");
+ }
+ }
+
+ public void halt() {
+ // No halt support
+ }
+
+ public void setTaskMonitor(TaskMonitor taskMonitor) throws IllegalThreadStateException {
+ this.taskMonitor = taskMonitor;
+ }
+
+ public String getTitle() {
+ return "Saving BioPAX data (not modified)";
+ }
+}
diff --git a/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/action/LaunchExternalBrowser.java b/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/action/LaunchExternalBrowser.java
new file mode 100644
index 0000000..0bd060f
--- /dev/null
+++ b/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/action/LaunchExternalBrowser.java
@@ -0,0 +1,68 @@
+// $Id: LaunchExternalBrowser.java,v 1.8 2006/06/15 22:06:02 grossb Exp $
+//------------------------------------------------------------------------------
+/** Copyright (c) 2006 Memorial Sloan-Kettering Cancer Center.
+ **
+ ** Code written by: Ethan Cerami
+ ** Authors: Ethan Cerami, Gary Bader, Chris Sander
+ **
+ ** This library is free software; you can redistribute it and/or modify it
+ ** under the terms of the GNU Lesser General Public License as published
+ ** by the Free Software Foundation; either version 2.1 of the License, or
+ ** any later version.
+ **
+ ** This library is distributed in the hope that it will be useful, but
+ ** WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ ** MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ ** documentation provided hereunder is on an "as is" basis, and
+ ** Memorial Sloan-Kettering Cancer Center
+ ** has no obligations to provide maintenance, support,
+ ** updates, enhancements or modifications. In no event shall
+ ** Memorial Sloan-Kettering Cancer Center
+ ** be liable to any party for direct, indirect, special,
+ ** incidental or consequential damages, including lost profits, arising
+ ** out of the use of this software and its documentation, even if
+ ** Memorial Sloan-Kettering Cancer Center
+ ** has been advised of the possibility of such damage. See
+ ** the GNU Lesser General Public License for more details.
+ **
+ ** You should have received a copy of the GNU Lesser General Public License
+ ** along with this library; if not, write to the Free Software Foundation,
+ ** Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ **/
+package cytoscape.coreplugins.biopax.action;
+
+import cytoscape.coreplugins.biopax.util.CytoscapeWrapper;
+import cytoscape.util.OpenBrowser;
+
+import java.net.URL;
+
+import javax.swing.event.HyperlinkEvent;
+import javax.swing.event.HyperlinkListener;
+
+
+/**
+ * Launches the User's External Web Browser.
+ *
+ * @author Ethan Cerami.
+ */
+public class LaunchExternalBrowser implements HyperlinkListener {
+
+ /**
+ * User has clicked on a HyperLink.
+ *
+ * @param evt HyperLink Event Object.
+ */
+ public void hyperlinkUpdate(HyperlinkEvent evt) {
+ URL url = evt.getURL();
+
+ if (url != null) {
+ if (evt.getEventType() == HyperlinkEvent.EventType.ENTERED) {
+ CytoscapeWrapper.setStatusBarMsg(url.toString());
+ } else if (evt.getEventType() == HyperlinkEvent.EventType.EXITED) {
+ CytoscapeWrapper.clearStatusBar();
+ } else if (evt.getEventType() == HyperlinkEvent.EventType.ACTIVATED) {
+ OpenBrowser.openURL(url.toString());
+ }
+ }
+ }
+}
diff --git a/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/action/NetworkListener.java b/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/action/NetworkListener.java
new file mode 100644
index 0000000..80afeaf
--- /dev/null
+++ b/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/action/NetworkListener.java
@@ -0,0 +1,192 @@
+// $Id: NetworkListener.java,v 1.13 2006/06/15 22:02:52 grossb Exp $
+//------------------------------------------------------------------------------
+/** Copyright (c) 2006 Memorial Sloan-Kettering Cancer Center.
+ **
+ ** Code written by: Ethan Cerami
+ ** Authors: Ethan Cerami, Gary Bader, Chris Sander
+ **
+ ** This library is free software; you can redistribute it and/or modify it
+ ** under the terms of the GNU Lesser General Public License as published
+ ** by the Free Software Foundation; either version 2.1 of the License, or
+ ** any later version.
+ **
+ ** This library is distributed in the hope that it will be useful, but
+ ** WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ ** MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ ** documentation provided hereunder is on an "as is" basis, and
+ ** Memorial Sloan-Kettering Cancer Center
+ ** has no obligations to provide maintenance, support,
+ ** updates, enhancements or modifications. In no event shall
+ ** Memorial Sloan-Kettering Cancer Center
+ ** be liable to any party for direct, indirect, special,
+ ** incidental or consequential damages, including lost profits, arising
+ ** out of the use of this software and its documentation, even if
+ ** Memorial Sloan-Kettering Cancer Center
+ ** has been advised of the possibility of such damage. See
+ ** the GNU Lesser General Public License for more details.
+ **
+ ** You should have received a copy of the GNU Lesser General Public License
+ ** along with this library; if not, write to the Free Software Foundation,
+ ** Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ **/
+package cytoscape.coreplugins.biopax.action;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+
+import cytoscape.coreplugins.biopax.util.BioPaxUtil;
+import cytoscape.coreplugins.biopax.util.CySessionUtil;
+import cytoscape.coreplugins.biopax.view.BioPaxDetailsPanel;
+import cytoscape.data.SelectFilter;
+
+import cytoscape.view.CyNetworkView;
+import cytoscape.view.CytoscapeDesktop;
+
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+
+
+/**
+ * Listens for Network Events, and takes appropriate Actions.
+ * May be subclassed.
+ *
+ * @author Ethan Cerami / Benjamin Gross / Igor Rodchenkov.
+ */
+public class NetworkListener implements PropertyChangeListener {
+ private BioPaxDetailsPanel bpPanel;
+
+ /**
+ * Constructor.
+ *
+ * @param bpPanel BioPaxDetails Panel Object.
+ */
+ public NetworkListener(BioPaxDetailsPanel bpPanel) {
+ this.bpPanel = bpPanel;
+
+ // to catch network creation / destruction events
+ Cytoscape.getSwingPropertyChangeSupport().addPropertyChangeListener(this);
+
+ // to catch network selection / focus events
+ Cytoscape.getDesktop().getNetworkViewManager().getSwingPropertyChangeSupport()
+ .addPropertyChangeListener(this);
+ }
+
+ /**
+ * Registers a newly created Network.
+ *
+ * @param cyNetwork Object.
+ */
+ public void registerNetwork(CyNetwork cyNetwork) {
+ registerNodeSelectionEvents(cyNetwork);
+ }
+
+ /**
+ * Register to Listen for Node Selection Events
+ *
+ * @param cyNetwork CyNetwork Object.
+ */
+ private void registerNodeSelectionEvents(CyNetwork cyNetwork) {
+ SelectFilter flagFilter = cyNetwork.getSelectFilter();
+ flagFilter.addSelectEventListener(new DisplayBioPaxDetails(bpPanel));
+ bpPanel.resetText();
+ }
+
+ /**
+ * Property change listener - to get network/network view destroy events.
+ *
+ * @param event PropertyChangeEvent
+ */
+ public void propertyChange(PropertyChangeEvent event) {
+ boolean relevantEventFlag = false;
+
+ // network destroyed, we may have to remove it from our list
+ if (event.getPropertyName() == Cytoscape.NETWORK_CREATED) {
+ networkCreatedEvent(event);
+ } else if (event.getPropertyName() == Cytoscape.NETWORK_DESTROYED) {
+ relevantEventFlag = true;
+ } else if (event.getPropertyName() == CytoscapeDesktop.NETWORK_VIEW_DESTROYED) {
+ relevantEventFlag = true;
+ } else if (event.getPropertyName() == CytoscapeDesktop.NETWORK_VIEW_CREATED) {
+ networkFocusEvent(event, false);
+ } else if (event.getPropertyName() == CytoscapeDesktop.NETWORK_VIEW_FOCUSED) {
+ networkFocusEvent(event, false);
+ } else if (event.getPropertyName() == Cytoscape.SESSION_LOADED) {
+ CySessionUtil.setSessionReadingInProgress(false);
+ networkCreatedEvent(event);
+ networkFocusEvent(event, true);
+ } else if (event.getPropertyName().equals(Integer.toString(Cytoscape.SESSION_OPENED))) {
+ CySessionUtil.setSessionReadingInProgress(true);
+ }
+
+ if (relevantEventFlag) {
+ onZeroNetworkViewsRemain();
+ }
+ }
+
+ /**
+ * Network Created Event
+ */
+ private void networkCreatedEvent(PropertyChangeEvent event) {
+ // get the network
+ CyNetwork cyNetwork = null;
+ Object newValue = event.getNewValue();
+
+ if (event.getPropertyName() == Cytoscape.SESSION_LOADED) {
+ cyNetwork = Cytoscape.getCurrentNetwork();
+ } else if (newValue instanceof CyNetwork) {
+ cyNetwork = (CyNetwork) newValue;
+ } else if (newValue instanceof String) {
+ String networkID = (String) newValue;
+ cyNetwork = Cytoscape.getNetwork(networkID);
+ }
+
+ if(cyNetwork != null && BioPaxUtil.isBioPaxNetwork(cyNetwork)) {
+ Cytoscape.firePropertyChange(Cytoscape.NETWORK_CREATED, null, cyNetwork);
+ }
+
+ bpPanel.resetText();
+
+ }
+
+ /**
+ * Network Focus Event.
+ */
+ private void networkFocusEvent(PropertyChangeEvent event, boolean sessionLoaded) {
+ // get network id
+ String networkId = null;
+ CyNetwork cyNetwork = null;
+ Object newValue = event.getNewValue();
+
+ if (event.getPropertyName() == Cytoscape.SESSION_LOADED) {
+ cyNetwork = Cytoscape.getCurrentNetwork();
+ networkId = cyNetwork.getIdentifier();
+ } else if (newValue instanceof CyNetwork) {
+ cyNetwork = (CyNetwork) newValue;
+ networkId = cyNetwork.getIdentifier();
+ } else if (newValue instanceof String) {
+ networkId = (String) newValue;
+ cyNetwork = Cytoscape.getNetwork(networkId);
+ }
+
+ if (networkId != null) {
+ // update bpPanel accordingly
+ if (!sessionLoaded) {
+ bpPanel.resetText();
+ }
+
+ // due to quirky-ness in event model, we could get here without registering network
+ // check if this is a biopax network
+ registerNetwork(cyNetwork);
+ }
+ }
+
+ /**
+ * Event: No Registered Network Views Remain.
+ * May be subclassed.
+ */
+ protected void onZeroNetworkViewsRemain() {
+ bpPanel.resetText("BioPAX Details not available. Please load"
+ + " a BioPAX file to proceed.");
+ }
+
+}
diff --git a/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/util/BioPaxUtil.java b/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/util/BioPaxUtil.java
new file mode 100644
index 0000000..251ed0d
--- /dev/null
+++ b/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/util/BioPaxUtil.java
@@ -0,0 +1,515 @@
+/** Copyright (c) 2010 University of Toronto (UofT)
+ ** and Memorial Sloan-Kettering Cancer Center (MSKCC).
+ **
+ ** This is free software; you can redistribute it and/or modify it
+ ** under the terms of the GNU Lesser General Public License as published
+ ** by the Free Software Foundation; either version 2.1 of the License, or
+ ** any later version.
+ **
+ ** This library is distributed in the hope that it will be useful, but
+ ** WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ ** MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ ** documentation provided hereunder is on an "as is" basis, and
+ ** both UofT and MSKCC have no obligations to provide maintenance,
+ ** support, updates, enhancements or modifications. In no event shall
+ ** UofT or MSKCC be liable to any party for direct, indirect, special,
+ ** incidental or consequential damages, including lost profits, arising
+ ** out of the use of this software and its documentation, even if
+ ** UofT or MSKCC have been advised of the possibility of such damage.
+ ** See the GNU Lesser General Public License for more details.
+ **
+ ** You should have received a copy of the GNU Lesser General Public License
+ ** along with this software; if not, write to the Free Software Foundation,
+ ** Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA;
+ ** or find it at http://www.fsf.org/ or http://www.gnu.org.
+ **/
+package cytoscape.coreplugins.biopax.util;
+
+import java.io.FileNotFoundException;
+import java.io.InputStream;
+import java.io.StringWriter;
+import java.lang.reflect.Method;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import org.apache.commons.lang.StringEscapeUtils;
+import org.biopax.paxtools.controller.ModelUtils;
+import org.biopax.paxtools.controller.SimpleEditorMap;
+import org.biopax.paxtools.converter.OneTwoThree;
+import org.biopax.paxtools.io.SimpleIOHandler;
+import org.biopax.paxtools.model.BioPAXElement;
+import org.biopax.paxtools.model.BioPAXLevel;
+import org.biopax.paxtools.model.Model;
+import org.biopax.paxtools.model.level3.BioSource;
+import org.biopax.paxtools.model.level3.Interaction;
+import org.biopax.paxtools.model.level3.Named;
+import org.biopax.paxtools.model.level3.Pathway;
+import org.biopax.paxtools.model.level3.SimplePhysicalEntity;
+import org.biopax.paxtools.model.level3.XReferrable;
+import org.biopax.paxtools.model.level3.Xref;
+import org.biopax.paxtools.util.ClassFilterSet;
+
+import com.ctc.wstx.stax.WstxInputFactory;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import cytoscape.coreplugins.biopax.MapBioPaxToCytoscape;
+import cytoscape.data.CyAttributes;
+import cytoscape.logger.CyLogger;
+
+/**
+ * BioPax Utility Class - is a BioPAX Model Adapter
+ * that also defines additional constants.
+ */
+public final class BioPaxUtil {
+
+ public static final CyLogger log = CyLogger.getLogger(BioPaxUtil.class);
+
+ private static final Map<String,String> cellLocationMap;
+ private static final Map<String,String> chemModificationsMap;
+
+ public static final String BIOPAX_DATA = "biopax_data";
+ public static final String DEFAULT_CHARSET = "UTF-8";
+ public static final int MAX_DISPLAY_STRING_LEN = 25;
+ public static final String NULL_ELEMENT_TYPE = "BioPAX Element";
+
+ /**
+ * BioPAX Class: phosphorylation site
+ */
+ public static final String PHOSPHORYLATION_SITE = "phosphorylation site";
+
+ /**
+ * BioPAX Class: protein phosphorylated
+ */
+ public static final String PROTEIN_PHOSPHORYLATED = "Protein-phosphorylated";
+
+ public static class StaxHack {
+ public static final void runWithHack(Runnable runnable) {
+ Thread thread = Thread.currentThread();
+ ClassLoader loader = thread.getContextClassLoader();
+ try {
+ thread.setContextClassLoader(WstxInputFactory.class.getClassLoader());
+ runnable.run();
+ } finally {
+ thread.setContextClassLoader(loader);
+ }
+ }
+ }
+
+ // private Constructor
+ private BioPaxUtil() {}
+
+ static {
+ // the following is for node labels
+ cellLocationMap = new HashMap<String, String>();
+ cellLocationMap.put("cellular component unknown", "");
+ cellLocationMap.put("centrosome", "CE");
+ cellLocationMap.put("cytoplasm", "CY");
+ cellLocationMap.put("endoplasmic reticulum", "ER");
+ cellLocationMap.put("endosome", "EN");
+ cellLocationMap.put("extracellular", "EM");
+ cellLocationMap.put("golgi apparatus", "GA");
+ cellLocationMap.put("mitochondrion", "MI");
+ cellLocationMap.put("nucleoplasm", "NP");
+ cellLocationMap.put("nucleus", "NU");
+ cellLocationMap.put("plasma membrane", "PM");
+ cellLocationMap.put("ribosome", "RI");
+ cellLocationMap.put("transmembrane", "TM");
+
+ chemModificationsMap = new HashMap<String, String>();
+ chemModificationsMap.put("acetylation site", "A");
+ chemModificationsMap.put("glycosylation site", "G");
+ chemModificationsMap.put("phosphorylation site", "P");
+ chemModificationsMap.put("proteolytic cleavage site", "PCS");
+ chemModificationsMap.put("sumoylation site", "S");
+ chemModificationsMap.put("ubiquitination site", "U");
+ }
+
+
+ /**
+ * Constructor.
+ *
+ * @param in BioPAX data file name.
+ * @return BioPaxUtil new instance (containing the imported BioPAX data)
+ * @throws FileNotFoundException
+ */
+ public static Model read(final InputStream in) throws FileNotFoundException {
+ Model model = convertFromOwl(in);
+ // immediately convert to BioPAX Level3 model
+ if(model != null && BioPAXLevel.L2.equals(model.getLevel())) {
+ model = new OneTwoThree().filter(model);
+ }
+ return model;
+ }
+
+
+ private static Model convertFromOwl(final InputStream stream) {
+ final Model[] model = new Model[1];
+ final SimpleIOHandler handler = new SimpleIOHandler();
+ handler.mergeDuplicates(true); // a workaround (illegal) BioPAX data having duplicated rdf:ID...
+ StaxHack.runWithHack(new Runnable() {
+ @Override
+ public void run() {
+ try {
+ model[0] = handler.convertFromOWL(stream);
+ } catch (Throwable e) {
+ log.warn("Import failed: " + e);
+ }
+ }
+ });
+ return model[0];
+ }
+
+
+ /**
+ * Gets or infers the name of the node.
+ *
+ * @param bpe BioPAX Element
+ * @return
+ */
+ public static String getNodeName(BioPAXElement bpe) {
+
+ if(bpe == null) {
+ return "";
+ }
+
+ String nodeName = getShortName(bpe);
+ if (nodeName == null || nodeName.length()== 0) {
+ nodeName = getStandardName(bpe);
+ if (nodeName == null || nodeName.length() == 0) {
+ Collection<String> names = getSynonyms(bpe);
+ if (!names.isEmpty())
+ nodeName = getTheShortestString(names);
+ }
+ }
+
+ return (nodeName == null || nodeName.length() == 0)
+ ? bpe.getRDFId() : StringEscapeUtils.unescapeHtml(nodeName);
+ }
+
+
+ // get the shortest string
+ private static String getTheShortestString(Collection<String> nameList) {
+ String shortest = null;
+ if (nameList != null && !nameList.isEmpty()) {
+ int minLength = -1;
+ for (String name: nameList) {
+ if ( name.length() < minLength || minLength == -1) {
+ minLength = name.length();
+ shortest = name;
+ }
+ }
+ }
+ return shortest;
+ }
+
+
+ /**
+ * Attempts to get the value of any of the BioPAX properties
+ * in the list.
+ * @param bpe BioPAX Element
+ * @param properties BioPAX property names
+ *
+ * @return the value or null
+ */
+ public static Object getValue(BioPAXElement bpe, String... properties) {
+ for (String property : properties) {
+ try {
+ Method method = bpe.getModelInterface().getMethod(
+ "get" + property.substring(0, 1).toUpperCase()
+ + property.substring(1).replace('-', '_'));
+ Object invoke = method.invoke(bpe);
+ if (invoke != null) {
+ return invoke;
+ }
+// PropertyEditor editor = SimpleEditorMap.L3
+// .getEditorForProperty(property, bpe.getModelInterface());
+// return editor.getValueFromBean(bpe); // is always a Set!
+ } catch (Exception e) {
+ if(log.isDebugging()) {
+ // this is often OK, as we guess L2 or L3 properties...
+ log.debug("Ignore property " + property + " for "
+ + bpe.getRDFId() + ": " + e);
+ }
+ }
+ }
+ return null;
+ }
+
+
+ /**
+ * Attempts to get the values of specified BioPAX properties.
+ * @param bpe BioPAX Element
+ * @param properties BioPAX property names
+ *
+ * @return the set of property values or null
+ */
+ public static Collection<?> getValues(BioPAXElement bpe, String... properties) {
+ Collection<Object> col = new HashSet<Object>();
+
+ for (String property : properties) {
+ try {
+ Method method = bpe.getModelInterface().getMethod(
+ "get" + property.substring(0, 1).toUpperCase()
+ + property.substring(1).replace('-', '_'));
+
+ Object invoke = method.invoke(bpe);
+ if (invoke != null) {
+ // return value can be collection or Object
+ if (invoke instanceof Collection) {
+ col.addAll((Collection) invoke);
+ } else {
+ col.add(invoke);
+ }
+ }
+ } catch (Exception e) {
+ if(log.isDebugging()) {
+ log.debug("Cannot get value of '" + property + "' for "
+ + bpe.getRDFId() + ": " + e);
+ }
+ }
+ }
+
+ return col;
+ }
+
+
+ /**
+ * Gets the Short Name (or Display Name).
+ *
+ * @param bpe BioPAX element
+ * @return short name field, or null if not available.
+ */
+ private static String getShortName(BioPAXElement bpe) {
+ String shortName = null;
+
+ if(bpe instanceof Named) {
+ shortName = ((Named)bpe).getDisplayName();
+ }
+
+ return shortName;
+ }
+
+ /**
+ * Gets the Name Field.
+ *
+ * @param bpe BioPAX element
+ * @return name field, or null if not available.
+ */
+ private static String getStandardName(BioPAXElement bpe) {
+ if(bpe instanceof Named) {
+ return ((Named)bpe).getStandardName();
+ } else
+ return null;
+ }
+
+ /**
+ * Gets all names, if any.
+ *
+ * @param bpe BioPAX element
+ * @return Collection of names.
+ */
+ public static Collection<String> getSynonyms(BioPAXElement bpe) {
+ Collection<String> names = new HashSet<String>();
+ if(bpe instanceof Named) {
+ names = ((Named)bpe).getName();
+ }
+ return names;
+ }
+
+
+ /**
+ * Gets the NCBI Taxonomy ID.
+ *
+ * @param bpe BioPAX element
+ * @return taxonomyId, or -1, if not available.
+ */
+ public static int getOrganismTaxonomyId(BioPAXElement bpe) {
+ int taxonomyId = -1;
+
+ try {
+ Object bs = getValue(bpe, "organism");
+ if (bs instanceof BioSource) {
+ Set<Xref> xrefs = ((BioSource)bs).getXref();
+ if(!xrefs.isEmpty()) {
+ Xref tx = xrefs.iterator().next();
+ taxonomyId = Integer.parseInt(tx.getId());
+ }
+ }
+ } catch (Exception e) {
+ taxonomyId = -1;
+ }
+
+ return taxonomyId;
+ }
+
+
+ /**
+ * Gets the joint set of all known subclasses of the specified BioPAX types.
+ *
+ * @param classes BioPAX (PaxTools Model Interfaces) Classes
+ * @return
+ */
+ public static Collection<Class> getSubclassNames(Class<? extends BioPAXElement>... classes) {
+ Collection<Class> subclasses = new HashSet<Class>();
+
+ for (Class<? extends BioPAXElement> c : classes) {
+ subclasses.addAll(SimpleEditorMap.L3.getKnownSubClassesOf(c));
+ }
+
+ return subclasses;
+ }
+
+
+ /**
+ * Creates a name for to the BioPAX model
+ * using its top-level process name(s).
+ *
+ * @param model
+ * @return
+ */
+ public static String getName(Model model) {
+ StringBuffer modelName = new StringBuffer();
+
+ Collection<Pathway> pws = ModelUtils.getRootElements(model, Pathway.class);
+ for(Pathway pw: pws) {
+ modelName.append(" ").append(getNodeName(pw));
+ }
+
+ if(modelName.length()==0) {
+ Collection<Interaction> itrs = ModelUtils.getRootElements(model, Interaction.class);
+ for(Interaction it: itrs) {
+ modelName.append(" ").append(getNodeName(it));
+ }
+ }
+
+ if(modelName.length()==0) {
+ modelName.append(model.getXmlBase());
+ }
+
+ String name = modelName.toString().trim();
+
+ return name;
+ }
+
+
+ /**
+ * Gets abbreviated cellular location term.
+ *
+ * @param value
+ * @return
+ */
+ public static String getAbbrCellLocation(String value) {
+ for(String abr: cellLocationMap.keySet()) {
+ if(value.toLowerCase().contains(abr)) {
+ return cellLocationMap.get(abr);
+ }
+ }
+ return value;
+ }
+
+ /**
+ * Gets abbreviated chemical modification term.
+ *
+ * @param value
+ * @return
+ */
+ public static String getAbbrChemModification(String value) {
+ for(String abr: chemModificationsMap.keySet()) {
+ if(value.toLowerCase().contains(abr)) {
+ return chemModificationsMap.get(abr);
+ }
+ }
+ return value;
+ }
+
+
+ public static String truncateLongStr(String str) {
+ if(str != null) {
+ str = str.replaceAll("[\n\r \t]+", " ");
+ if (str.length() > MAX_DISPLAY_STRING_LEN) {
+ str = str.substring(0, MAX_DISPLAY_STRING_LEN/2-1) + "..." + str.substring(str.length()-MAX_DISPLAY_STRING_LEN/2);
+ }
+ }
+ return str;
+ }
+
+
+ public static String toOwl(final BioPAXElement bpe) {
+ final StringWriter writer = new StringWriter();
+ final SimpleIOHandler simpleExporter = new SimpleIOHandler(BioPAXLevel.L3);
+ StaxHack.runWithHack(new Runnable() {
+ @Override
+ public void run() {
+ try {
+ simpleExporter.writeObject(writer, bpe);
+ } catch (Exception e) {
+ log.error("Failed printing '" + bpe.getRDFId() + "' to OWL", e);
+ }
+ }
+ });
+ return writer.toString();
+ }
+
+
+ /*
+ * Method determines if given network is a biopax network.
+ *
+ * @param cyNetwork CyNetwork
+ * @return boolean if any network views that we have created remain.
+ */
+ public static boolean isBioPaxNetwork(CyNetwork cyNetwork) {
+
+ // get the network attributes
+ CyAttributes networkAttributes = Cytoscape.getNetworkAttributes();
+
+ // get cyNetwork id
+ String networkID = cyNetwork.getIdentifier();
+
+ // is the biopax network attribute true ?
+ Boolean b = networkAttributes.getBooleanAttribute(networkID,
+ MapBioPaxToCytoscape.BIOPAX_NETWORK);
+
+ // outta here
+ if (b == null) {
+ return false;
+ }
+ return b;
+ }
+
+ /**
+ * Generates a unique CyNode identifier
+ */
+ public static String generateId(BioPAXElement bpe) {
+ return ModelUtils.md5hex(Cytoscape.getCurrentNetwork().getIdentifier() + bpe.getRDFId());
+ }
+
+
+ public static String type(BioPAXElement bpe) {
+ if(bpe == null)
+ throw new IllegalArgumentException();
+ else
+ return bpe.getModelInterface().getSimpleName();
+ }
+
+
+ public static <T extends Xref> List<T> getXRefs(BioPAXElement bpe, Class<T> xrefClass) {
+ if(bpe instanceof XReferrable) {
+ List<T> erefs = new ArrayList<T>();
+ erefs.addAll(new ClassFilterSet<Xref,T>( ((XReferrable)bpe).getXref(), xrefClass) );
+ if(bpe instanceof SimplePhysicalEntity &&
+ ((SimplePhysicalEntity)bpe).getEntityReference() != null)
+ {
+ erefs.addAll(new ClassFilterSet<Xref,T>(
+ ((SimplePhysicalEntity)bpe).getEntityReference().getXref(), xrefClass) );
+ }
+ return erefs;
+ }
+ return new ArrayList<T>();
+ }
+}
diff --git a/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/util/BioPaxVisualStyleUtil.java b/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/util/BioPaxVisualStyleUtil.java
new file mode 100644
index 0000000..9b7f7aa
--- /dev/null
+++ b/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/util/BioPaxVisualStyleUtil.java
@@ -0,0 +1,368 @@
+// $Id: BioPaxVisualStyleUtil.java,v 1.17 2006/08/23 15:21:07 cerami Exp $
+//------------------------------------------------------------------------------
+/** Copyright (c) 2006 Memorial Sloan-Kettering Cancer Center.
+ **
+ ** Code written by: Ethan Cerami
+ ** Authors: Ethan Cerami, Gary Bader, Chris Sander
+ **
+ ** This library is free software; you can redistribute it and/or modify it
+ ** under the terms of the GNU Lesser General Public License as published
+ ** by the Free Software Foundation; either version 2.1 of the License, or
+ ** any later version.
+ **
+ ** This library is distributed in the hope that it will be useful, but
+ ** WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ ** MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ ** documentation provided hereunder is on an "as is" basis, and
+ ** Memorial Sloan-Kettering Cancer Center
+ ** has no obligations to provide maintenance, support,
+ ** updates, enhancements or modifications. In no event shall
+ ** Memorial Sloan-Kettering Cancer Center
+ ** be liable to any party for direct, indirect, special,
+ ** incidental or consequential damages, including lost profits, arising
+ ** out of the use of this software and its documentation, even if
+ ** Memorial Sloan-Kettering Cancer Center
+ ** has been advised of the possibility of such damage. See
+ ** the GNU Lesser General Public License for more details.
+ **
+ ** You should have received a copy of the GNU Lesser General Public License
+ ** along with this library; if not, write to the Free Software Foundation,
+ ** Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ **/
+package cytoscape.coreplugins.biopax.util;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.coreplugins.biopax.MapBioPaxToCytoscape;
+import cytoscape.data.CyAttributes;
+import cytoscape.logger.CyLogger;
+import cytoscape.view.CyNetworkView;
+import cytoscape.visual.*;
+
+import cytoscape.visual.calculators.*;
+
+import cytoscape.visual.mappings.DiscreteMapping;
+import cytoscape.visual.mappings.ObjectMapping;
+import cytoscape.visual.mappings.PassThroughMapping;
+
+import org.biopax.paxtools.model.BioPAXElement;
+import org.biopax.paxtools.model.level3.Complex;
+import org.biopax.paxtools.model.level3.Control;
+import org.biopax.paxtools.model.level3.ControlType;
+import org.biopax.paxtools.model.level3.Interaction;
+import org.biopax.paxtools.model.level3.PhysicalEntity;
+
+import giny.view.NodeView;
+
+import java.awt.*;
+import java.util.Iterator;
+
+
+/**
+ * Creates an "out-of-the-box" default Visual Mapper for rendering BioPAX
+ * networks.
+ *
+ * @author Ethan Cerami
+ * @author Igor Rodchenkov (re-factoring using PaxTools API)
+ */
+public class BioPaxVisualStyleUtil {
+ public static final CyLogger log = CyLogger.getLogger(BioPaxVisualStyleUtil.class);
+
+ /**
+ * Name of BioPax Visual Style.
+ */
+ public static final String BIO_PAX_VISUAL_STYLE = "BioPAX";
+
+ /**
+ * Node Label Attribute.
+ */
+ public static final String BIOPAX_NODE_LABEL = "LABEL";
+
+ /**
+ * size of physical entity node (default node size width)
+ */
+ public static final double BIO_PAX_VISUAL_STYLE_PHYSICAL_ENTITY_NODE_WIDTH = 20;
+
+ // taken from DNodeView
+
+ /**
+ * size of physical entity node (default node size height)
+ */
+ public static final double BIO_PAX_VISUAL_STYLE_PHYSICAL_ENTITY_NODE_HEIGHT = 20;
+
+ // taken from DNodeView
+
+ /**
+ * size of physical entity node scale - (used to scale post tranlational modification nodes)
+ */
+ public static final double BIO_PAX_VISUAL_STYLE_PHYSICAL_ENTITY_NODE_SIZE_SCALE = 3;
+
+ /**
+ * Size of interaction node
+ */
+ private static final double BIO_PAX_VISUAL_STYLE_INTERACTION_NODE_SIZE_SCALE = 0.33;
+
+ /**
+ * Size of complex node
+ */
+ private static final double BIO_PAX_VISUAL_STYLE_COMPLEX_NODE_SIZE_SCALE = 0.33;
+
+ /**
+ * Default color of nodes
+ */
+ private static final Color DEFAULT_NODE_COLOR = new Color(255, 255, 255);
+
+ /**
+ * Node border color
+ */
+ private static final Color DEFAULT_NODE_BORDER_COLOR = new Color(0, 102, 102);
+
+ /**
+ * Complex node color
+ */
+ private static final Color COMPLEX_NODE_COLOR = new Color(0, 0, 0);
+
+ /**
+ * Complex node color
+ */
+ private static final Color COMPLEX_NODE_BORDER_COLOR = COMPLEX_NODE_COLOR;
+
+ /**
+ * Constructor.
+ * If an existing BioPAX Viz Mapper already exists, we use it.
+ * Otherwise, we create a new one.
+ *
+ * @return VisualStyle Object.
+ */
+ public static VisualStyle getBioPaxVisualStyle() {
+ VisualMappingManager manager = Cytoscape.getVisualMappingManager();
+ CalculatorCatalog catalog = manager.getCalculatorCatalog();
+
+ VisualStyle bioPaxVisualStyle = catalog.getVisualStyle(BIO_PAX_VISUAL_STYLE);
+
+ // If the BioPAX Visual Style already exists, use this one instead.
+ // The user may have tweaked the out-of-the box mapping, and we don't
+ // want to over-ride these tweaks.
+ if (bioPaxVisualStyle == null) {
+ bioPaxVisualStyle = new VisualStyle(BIO_PAX_VISUAL_STYLE);
+
+ NodeAppearanceCalculator nac = bioPaxVisualStyle.getNodeAppearanceCalculator();
+ bioPaxVisualStyle.getDependency().set(VisualPropertyDependency.Definition.NODE_SIZE_LOCKED,false);
+
+ EdgeAppearanceCalculator eac = bioPaxVisualStyle.getEdgeAppearanceCalculator();
+
+ createNodeShape(nac);
+ createNodeSize(nac);
+ createNodeLabel(nac);
+ createNodeColor(nac);
+ createNodeBorderColor(nac);
+ createTargetArrows(eac);
+
+ bioPaxVisualStyle.setNodeAppearanceCalculator(nac);
+ bioPaxVisualStyle.setEdgeAppearanceCalculator(eac);
+
+ // The visual style must be added to the Global Catalog
+ // in order for it to be written out to vizmap.props upon user exit
+ catalog.addVisualStyle(bioPaxVisualStyle);
+ }
+
+ return bioPaxVisualStyle;
+ }
+
+ private static void createNodeShape(NodeAppearanceCalculator nac) {
+ // create a discrete mapper, for mapping a biopax type to a shape
+ DiscreteMapping discreteMapping = new DiscreteMapping(NodeShape.RECT,
+ MapBioPaxToCytoscape.BIOPAX_ENTITY_TYPE, ObjectMapping.NODE_MAPPING);
+
+ // map all physical entities to circles
+ for (Class<? extends BioPAXElement> claz : BioPaxUtil.getSubclassNames(PhysicalEntity.class)) {
+ String name = claz.getSimpleName();
+ discreteMapping.putMapValue(name, NodeShape.ELLIPSE);
+ }
+
+ // use a different shape for Complex nodes
+ discreteMapping.putMapValue("Complex", NodeShape.DIAMOND);
+
+ // hack for phosphorylated proteins
+ discreteMapping.putMapValue(BioPaxUtil.PROTEIN_PHOSPHORYLATED, NodeShape.ELLIPSE);
+
+ // map all interactions
+ // - control to triangles
+ // - others to square
+ for (Class<?> c : BioPaxUtil.getSubclassNames(Interaction.class)) {
+ String entityName = c.getSimpleName();
+ if (Control.class.isAssignableFrom(c)) {
+ discreteMapping.putMapValue(entityName, NodeShape.TRIANGLE);
+ } else {
+ discreteMapping.putMapValue(entityName, NodeShape.RECT);
+ }
+ }
+
+ // create and set node shape calculator in node appearance calculator
+ Calculator nodeShapeCalculator = new BasicCalculator("BioPAX Node Shape",
+ discreteMapping,
+ VisualPropertyType.NODE_SHAPE);
+ nac.setCalculator(nodeShapeCalculator);
+ }
+
+ private static void createNodeSize(NodeAppearanceCalculator nac) {
+ // create a discrete mapper, for mapping biopax node type
+ // to a particular node size.
+ DiscreteMapping discreteMappingWidth = new DiscreteMapping(new Double(BIO_PAX_VISUAL_STYLE_PHYSICAL_ENTITY_NODE_WIDTH),
+ MapBioPaxToCytoscape.BIOPAX_ENTITY_TYPE, ObjectMapping.NODE_MAPPING);
+ DiscreteMapping discreteMappingHeight = new DiscreteMapping(new Double(BIO_PAX_VISUAL_STYLE_PHYSICAL_ENTITY_NODE_HEIGHT),
+ MapBioPaxToCytoscape.BIOPAX_ENTITY_TYPE, ObjectMapping.NODE_MAPPING);
+
+ // map all interactions to required size
+ for (Class c : BioPaxUtil.getSubclassNames(Interaction.class)) {
+ String entityName = c.getSimpleName();
+ discreteMappingWidth.putMapValue(entityName,
+ new Double(BIO_PAX_VISUAL_STYLE_PHYSICAL_ENTITY_NODE_WIDTH * BIO_PAX_VISUAL_STYLE_INTERACTION_NODE_SIZE_SCALE));
+ discreteMappingHeight.putMapValue(entityName,
+ new Double(BIO_PAX_VISUAL_STYLE_PHYSICAL_ENTITY_NODE_HEIGHT * BIO_PAX_VISUAL_STYLE_INTERACTION_NODE_SIZE_SCALE));
+ }
+
+
+ // map all complex to required size
+ for (Class c: BioPaxUtil.getSubclassNames(Complex.class)) {
+ String entityName = c.getSimpleName();
+ discreteMappingWidth.putMapValue(entityName,
+ new Double(BIO_PAX_VISUAL_STYLE_PHYSICAL_ENTITY_NODE_WIDTH * BIO_PAX_VISUAL_STYLE_COMPLEX_NODE_SIZE_SCALE));
+ discreteMappingHeight.putMapValue(entityName,
+ new Double(BIO_PAX_VISUAL_STYLE_PHYSICAL_ENTITY_NODE_HEIGHT * BIO_PAX_VISUAL_STYLE_COMPLEX_NODE_SIZE_SCALE));
+ }
+
+ /*
+ // hack for phosphorylated proteins - make them large so label fits within node
+ // commented out by Ethan Cerami, November 15, 2006
+ discreteMappingWidth.putMapValue(BioPaxUtil.PROTEIN_PHOSPHORYLATED,
+ new Double(BIO_PAX_VISUAL_STYLE_PHYSICAL_ENTITY_NODE_WIDTH
+ * BIO_PAX_VISUAL_STYLE_PHYSICAL_ENTITY_NODE_SIZE_SCALE));
+ discreteMappingHeight.putMapValue(BioPaxUtil.PROTEIN_PHOSPHORYLATED,
+ new Double(BIO_PAX_VISUAL_STYLE_PHYSICAL_ENTITY_NODE_HEIGHT
+ * BIO_PAX_VISUAL_STYLE_PHYSICAL_ENTITY_NODE_SIZE_SCALE));
+ */
+
+ // create and set node height calculator in node appearance calculator
+ Calculator nodeWidthCalculator = new BasicCalculator("BioPAX Node Width",
+ discreteMappingWidth,
+ VisualPropertyType.NODE_WIDTH);
+ nac.setCalculator(nodeWidthCalculator);
+ nac.getDefaultAppearance().set(cytoscape.visual.VisualPropertyType.NODE_WIDTH,
+ new Double(BIO_PAX_VISUAL_STYLE_PHYSICAL_ENTITY_NODE_WIDTH));
+
+ Calculator nodeHeightCalculator = new BasicCalculator("BioPAX Node Height",
+ discreteMappingHeight,
+ VisualPropertyType.NODE_HEIGHT);
+ nac.setCalculator(nodeHeightCalculator);
+ nac.getDefaultAppearance().set(cytoscape.visual.VisualPropertyType.NODE_HEIGHT,
+ new Double(BIO_PAX_VISUAL_STYLE_PHYSICAL_ENTITY_NODE_HEIGHT));
+ }
+
+ private static void createNodeLabel(NodeAppearanceCalculator nac) {
+ // create pass through mapper for node labels
+ PassThroughMapping passThroughMapping = new PassThroughMapping("",
+ ObjectMapping.NODE_MAPPING);
+ passThroughMapping.setControllingAttributeName(BIOPAX_NODE_LABEL, null, false);
+
+ // create and set node label calculator in node appearance calculator
+ Calculator nodeLabelCalculator = new BasicCalculator("BioPAX Node Label",
+ passThroughMapping,
+ VisualPropertyType.NODE_LABEL);
+ nac.setCalculator(nodeLabelCalculator);
+ }
+
+ private static void createNodeColor(NodeAppearanceCalculator nac) {
+ // create a discrete mapper, for mapping biopax node type
+ // to a particular node color
+ DiscreteMapping discreteMapping = new DiscreteMapping(DEFAULT_NODE_COLOR,
+ MapBioPaxToCytoscape.BIOPAX_ENTITY_TYPE, ObjectMapping.NODE_MAPPING);
+
+ // map all complex to black
+ discreteMapping.putMapValue("Complex", COMPLEX_NODE_COLOR);
+
+ // create and set node label calculator in node appearance calculator
+ Calculator nodeColorCalculator = new BasicCalculator("BioPAX Node Color",
+ discreteMapping,
+ VisualPropertyType.NODE_FILL_COLOR);
+ nac.setCalculator(nodeColorCalculator);
+
+ // set default color
+ nac.getDefaultAppearance().set(cytoscape.visual.VisualPropertyType.NODE_FILL_COLOR,
+ DEFAULT_NODE_COLOR);
+ }
+
+ private static void createNodeBorderColor(NodeAppearanceCalculator nac) {
+ // create a discrete mapper, for mapping biopax node type
+ // to a particular node color
+ DiscreteMapping discreteMapping = new DiscreteMapping(DEFAULT_NODE_BORDER_COLOR,
+ MapBioPaxToCytoscape.BIOPAX_ENTITY_TYPE, ObjectMapping.NODE_MAPPING);
+
+ // map all complex to black
+ discreteMapping.putMapValue("Complex", COMPLEX_NODE_BORDER_COLOR);
+
+ // create and set node label calculator in node appearance calculator
+ Calculator nodeBorderColorCalculator = new BasicCalculator("BioPAX Node Border Color",
+ discreteMapping,
+ VisualPropertyType.NODE_BORDER_COLOR);
+ nac.setCalculator(nodeBorderColorCalculator);
+
+ // set default color
+ nac.getDefaultAppearance().set(cytoscape.visual.VisualPropertyType.NODE_BORDER_COLOR,
+ DEFAULT_NODE_BORDER_COLOR);
+ }
+
+ private static void createTargetArrows(EdgeAppearanceCalculator eac) {
+ DiscreteMapping discreteMapping = new DiscreteMapping(ArrowShape.NONE,
+ MapBioPaxToCytoscape.BIOPAX_EDGE_TYPE,
+ ObjectMapping.EDGE_MAPPING);
+
+ discreteMapping.putMapValue("right", ArrowShape.DELTA);
+ discreteMapping.putMapValue("controlled", ArrowShape.DELTA);
+ discreteMapping.putMapValue("cofactor", ArrowShape.DELTA);
+ discreteMapping.putMapValue("contains", ArrowShape.CIRCLE);
+
+ // Inhibition Edges
+ for (ControlType controlType : ControlType.values()) {
+ if(controlType.toString().startsWith("I")) {
+ discreteMapping.putMapValue(controlType.toString(), ArrowShape.T);
+ }
+ }
+
+ // Activation Edges
+ for (ControlType controlType : ControlType.values()) {
+ if(controlType.toString().startsWith("A")) {
+ discreteMapping.putMapValue(controlType.toString(), ArrowShape.DELTA);
+ }
+ }
+
+ Calculator edgeTargetArrowCalculator = new BasicCalculator("BioPAX Target Arrows",
+ discreteMapping,
+ VisualPropertyType.EDGE_TGTARROW_SHAPE);
+ eac.setCalculator(edgeTargetArrowCalculator);
+ }
+
+
+ @SuppressWarnings("unchecked")
+ public static void setNodeToolTips(CyNetworkView networkView) {
+ // grab node attributes
+ CyAttributes nodeAttributes = Cytoscape.getNodeAttributes();
+
+ // iterate through the nodes
+ Iterator<NodeView> nodesIt = networkView.getNodeViewsIterator();
+ while (nodesIt.hasNext()) {
+ NodeView nodeView = nodesIt.next();
+ String id = nodeView.getNode().getIdentifier();
+ String tip =
+ nodeAttributes.getStringAttribute(id, MapBioPaxToCytoscape.BIOPAX_ENTITY_TYPE)
+ + "\n" +
+ nodeAttributes.getListAttribute(id, MapBioPaxToCytoscape.BIOPAX_CELLULAR_LOCATIONS);
+
+ nodeView.setToolTip(tip);
+
+ if(log.isDebugging())
+ log.debug("tooltip set "+ tip + " for node " + id);
+ }
+ networkView.updateView();
+ }
+}
diff --git a/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/util/CyNetworkUtil.java b/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/util/CyNetworkUtil.java
new file mode 100644
index 0000000..d92e1cb
--- /dev/null
+++ b/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/util/CyNetworkUtil.java
@@ -0,0 +1,76 @@
+// $Id: CyNetworkUtil.java,v 1.4 2006/06/15 22:06:02 grossb Exp $
+//------------------------------------------------------------------------------
+/** Copyright (c) 2006 Memorial Sloan-Kettering Cancer Center.
+ **
+ ** Code written by: Ethan Cerami
+ ** Authors: Ethan Cerami, Gary Bader, Chris Sander
+ **
+ ** This library is free software; you can redistribute it and/or modify it
+ ** under the terms of the GNU Lesser General Public License as published
+ ** by the Free Software Foundation; either version 2.1 of the License, or
+ ** any later version.
+ **
+ ** This library is distributed in the hope that it will be useful, but
+ ** WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ ** MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ ** documentation provided hereunder is on an "as is" basis, and
+ ** Memorial Sloan-Kettering Cancer Center
+ ** has no obligations to provide maintenance, support,
+ ** updates, enhancements or modifications. In no event shall
+ ** Memorial Sloan-Kettering Cancer Center
+ ** be liable to any party for direct, indirect, special,
+ ** incidental or consequential damages, including lost profits, arising
+ ** out of the use of this software and its documentation, even if
+ ** Memorial Sloan-Kettering Cancer Center
+ ** has been advised of the possibility of such damage. See
+ ** the GNU Lesser General Public License for more details.
+ **
+ ** You should have received a copy of the GNU Lesser General Public License
+ ** along with this library; if not, write to the Free Software Foundation,
+ ** Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ **/
+package cytoscape.coreplugins.biopax.util;
+
+import cytoscape.CyNetwork;
+import cytoscape.CytoscapeInit;
+
+import java.text.DecimalFormat;
+import java.text.NumberFormat;
+
+
+
+/**
+ * Utility for Creating CyNetwork Objects.
+ *
+ * @author Ethan Cerami
+ */
+public class CyNetworkUtil {
+ /**
+ * Gets Network Stats, for presentation to end-user.
+ *
+ * @param network CyNetwork Object.
+ * @return Human Readable String.
+ */
+ public static String getNetworkStats(CyNetwork network) {
+ NumberFormat formatter = new DecimalFormat("#,###,###");
+ StringBuffer sb = new StringBuffer();
+
+ sb.append("Successfully loaded pathway.\n\n");
+ sb.append("Network contains " + formatter.format(network.getNodeCount()));
+ sb.append(" nodes and " + formatter.format(network.getEdgeCount()));
+ sb.append(" edges. ");
+
+ int thresh = Integer.parseInt(CytoscapeInit.getProperties().getProperty("viewThreshold"));
+
+ if (network.getNodeCount() > thresh) {
+ sb.append("Network is over " + thresh + " nodes. A view has not been created."
+ + " If you wish to view this network, use "
+ + "\"Create View\" from the \"Edit\" menu.");
+ }
+
+ sb.append("\n\nWhile importing data, warning messages might have been "
+ + "generated (check Cytoscape logs)\n\n");
+
+ return sb.toString();
+ }
+}
diff --git a/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/util/CySessionUtil.java b/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/util/CySessionUtil.java
new file mode 100644
index 0000000..e207b2b
--- /dev/null
+++ b/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/util/CySessionUtil.java
@@ -0,0 +1,24 @@
+package cytoscape.coreplugins.biopax.util;
+
+/**
+ * Indicates if Cytoscape Session is in Progress.
+ */
+public class CySessionUtil {
+ private static boolean sessionReadingInProgress;
+
+ /**
+ * Is Session Reading in Progress?
+ * @return true or false.
+ */
+ public static boolean isSessionReadingInProgress() {
+ return sessionReadingInProgress;
+ }
+
+ /**
+ * Sets if Session Reading is in Progress.
+ * @param inProgress true or false.
+ */
+ public static void setSessionReadingInProgress(boolean inProgress) {
+ sessionReadingInProgress = inProgress;
+ }
+}
\ No newline at end of file
diff --git a/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/util/CytoscapeWrapper.java b/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/util/CytoscapeWrapper.java
new file mode 100644
index 0000000..98128e5
--- /dev/null
+++ b/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/util/CytoscapeWrapper.java
@@ -0,0 +1,125 @@
+// $Id: CytoscapeWrapper.java,v 1.7 2006/06/15 22:06:02 grossb Exp $
+//------------------------------------------------------------------------------
+/** Copyright (c) 2006 Memorial Sloan-Kettering Cancer Center.
+ **
+ ** Code written by: Ethan Cerami
+ ** Authors: Ethan Cerami, Gary Bader, Chris Sander
+ **
+ ** This library is free software; you can redistribute it and/or modify it
+ ** under the terms of the GNU Lesser General Public License as published
+ ** by the Free Software Foundation; either version 2.1 of the License, or
+ ** any later version.
+ **
+ ** This library is distributed in the hope that it will be useful, but
+ ** WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ ** MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ ** documentation provided hereunder is on an "as is" basis, and
+ ** Memorial Sloan-Kettering Cancer Center
+ ** has no obligations to provide maintenance, support,
+ ** updates, enhancements or modifications. In no event shall
+ ** Memorial Sloan-Kettering Cancer Center
+ ** be liable to any party for direct, indirect, special,
+ ** incidental or consequential damages, including lost profits, arising
+ ** out of the use of this software and its documentation, even if
+ ** Memorial Sloan-Kettering Cancer Center
+ ** has been advised of the possibility of such damage. See
+ ** the GNU Lesser General Public License for more details.
+ **
+ ** You should have received a copy of the GNU Lesser General Public License
+ ** along with this library; if not, write to the Free Software Foundation,
+ ** Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ **/
+package cytoscape.coreplugins.biopax.util;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.coreplugins.biopax.view.BioPaxContainer;
+import cytoscape.coreplugins.biopax.view.BioPaxDetailsPanel;
+import cytoscape.view.CytoscapeDesktop;
+
+import cytoscape.view.cytopanels.CytoPanel;
+import cytoscape.view.cytopanels.CytoPanelState;
+
+
+import java.net.URL;
+
+import javax.swing.*;
+
+
+/**
+ * Wrapper Class for Cytoscape 2.1 and 2.2 Specific Code.
+ *
+ * @author Ethan Cerami.
+ */
+public class CytoscapeWrapper {
+ private static boolean bioPaxUIInitialized = false;
+
+ /**
+ * Sets the Status Bar Message.
+ * Feature only available in Cytoscape 2.2.
+ *
+ * @param msg User msg.
+ */
+ public static void setStatusBarMsg(String msg) {
+ //cytoscape 2.1 code
+ // BioPaxDetailsPanel bpPanel = BioPaxDetailsPanel.getInstance();
+ // bpPanel.setStatusBarMsg(msg);
+
+ // cytoscape 2.2 code
+ CytoscapeDesktop desktop = Cytoscape.getDesktop();
+ desktop.setStatusBarMsg(msg);
+ }
+
+ /**
+ * Clears the Status Bar Message.
+ * Feature only available in Cytoscape 2.2.
+ */
+ public static void clearStatusBar() {
+ // cytoscape 2.1 code
+ // BioPaxDetailsPanel bpPanel = BioPaxDetailsPanel.getInstance();
+ // bpPanel.clearStatusBarMsg();
+
+ // cytoscape 2.2 code
+ CytoscapeDesktop desktop = Cytoscape.getDesktop();
+ desktop.clearStatusBar();
+ }
+
+ /**
+ * Activates the BioPaxPlugIn Tab in a Cytopanel.
+ * Feature only available in Cytoscape 2.2.
+ *
+ * @param bpContainer BioPaxContainer Object.
+ */
+ public static void activateBioPaxPlugInTab(BioPaxContainer bpContainer) {
+ // cytoscape 2.2 code
+ CytoscapeDesktop desktop = Cytoscape.getDesktop();
+ CytoPanel cytoPanel = desktop.getCytoPanel(BioPaxContainer.CYTO_PANEL_LOCATION);
+ int index = cytoPanel.indexOfComponent(bpContainer);
+ cytoPanel.setSelectedIndex(index);
+ }
+
+ /**
+ * Initializes the BioPax PlugIn UI.
+ */
+ public static void initBioPaxPlugInUI() {
+ if (!bioPaxUIInitialized) {
+ // cytoscape 2.1 code
+ // BioPaxDetailsWindow bpWindow =
+ // BioPaxDetailsWindow.getInstance();
+
+ // cytoscape 2.2 code
+ final BioPaxContainer bpContainer = BioPaxContainer.getInstance();
+ final CytoscapeDesktop desktop = Cytoscape.getDesktop();
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ CytoPanel cytoPanel = desktop.getCytoPanel(BioPaxContainer.CYTO_PANEL_LOCATION);
+ URL url = BioPaxDetailsPanel.class.getResource("read_obj.gif");
+ Icon icon = new ImageIcon(url);
+ cytoPanel.add("Node Details", icon, bpContainer, "Node Details");
+ cytoPanel.setState(CytoPanelState.DOCK);
+ bioPaxUIInitialized = true;
+ }
+ });
+ }
+ }
+}
diff --git a/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/util/ExternalLink.java b/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/util/ExternalLink.java
new file mode 100644
index 0000000..98e80fc
--- /dev/null
+++ b/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/util/ExternalLink.java
@@ -0,0 +1,146 @@
+// $Id: ExternalLink.java,v 1.4 2006/06/15 22:06:02 grossb Exp $
+//------------------------------------------------------------------------------
+/** Copyright (c) 2006 Memorial Sloan-Kettering Cancer Center.
+ **
+ ** Code written by: Ethan Cerami
+ ** Authors: Ethan Cerami, Gary Bader, Chris Sander
+ **
+ ** This library is free software; you can redistribute it and/or modify it
+ ** under the terms of the GNU Lesser General Public License as published
+ ** by the Free Software Foundation; either version 2.1 of the License, or
+ ** any later version.
+ **
+ ** This library is distributed in the hope that it will be useful, but
+ ** WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ ** MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ ** documentation provided hereunder is on an "as is" basis, and
+ ** Memorial Sloan-Kettering Cancer Center
+ ** has no obligations to provide maintenance, support,
+ ** updates, enhancements or modifications. In no event shall
+ ** Memorial Sloan-Kettering Cancer Center
+ ** be liable to any party for direct, indirect, special,
+ ** incidental or consequential damages, including lost profits, arising
+ ** out of the use of this software and its documentation, even if
+ ** Memorial Sloan-Kettering Cancer Center
+ ** has been advised of the possibility of such damage. See
+ ** the GNU Lesser General Public License for more details.
+ **
+ ** You should have received a copy of the GNU Lesser General Public License
+ ** along with this library; if not, write to the Free Software Foundation,
+ ** Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ **/
+package cytoscape.coreplugins.biopax.util;
+
+
+/**
+ * Model Object for Encapsulating an External Link.
+ *
+ * @author Ethan Cerami
+ */
+public class ExternalLink {
+ private String dbName;
+ private String id;
+ private String relType;
+ private String title;
+ private String year;
+ private String author;
+ private String url;
+ private String source;
+
+ /**
+ * Constructor.
+ *
+ * @param dbName Database name.
+ * @param id Unique ID.
+ */
+ public ExternalLink(String dbName, String id) {
+ this.dbName = dbName;
+ this.id = id;
+ }
+
+ /**
+ * Gets the Database Name.
+ *
+ * @return Database Name.
+ */
+ public String getDbName() {
+ return dbName;
+ }
+
+ /**
+ * Sets the Database Name.
+ *
+ * @param dbName Database Name.
+ */
+ public void setDbName(String dbName) {
+ this.dbName = dbName;
+ }
+
+ /**
+ * Gets the Unique ID.
+ *
+ * @return Unique ID.
+ */
+ public String getId() {
+ return id;
+ }
+
+ /**
+ * Sets the Unique ID.
+ *
+ * @param id Unique ID.
+ */
+ public void setId(String id) {
+ this.id = id;
+ }
+
+ public String getRelType() {
+ return relType;
+ }
+
+ public void setRelType(String relType) {
+ this.relType = relType;
+ }
+
+ public String getTitle() {
+ return title;
+ }
+
+ public void setTitle(String title) {
+ this.title = title;
+ }
+
+ public String getYear() {
+ return year;
+ }
+
+ public void setYear(String year) {
+ this.year = year;
+ }
+
+ public String getAuthor() {
+ return author;
+ }
+
+ public void setAuthor(String author) {
+ this.author = author;
+ }
+
+ public String getUrl() {
+ return url;
+ }
+
+ public void setUrl(String url) {
+ this.url = url;
+ }
+
+ public String getSource() {
+ return source;
+ }
+
+ public void setSource(String source) {
+ this.source = source;
+ }
+
+
+}
diff --git a/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/util/ExternalLinkUtil.java b/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/util/ExternalLinkUtil.java
new file mode 100644
index 0000000..041095a
--- /dev/null
+++ b/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/util/ExternalLinkUtil.java
@@ -0,0 +1,347 @@
+// $Id: ExternalLinkUtil.java,v 1.10 2006/06/15 22:06:02 grossb Exp $
+//------------------------------------------------------------------------------
+/** Copyright (c) 2006 Memorial Sloan-Kettering Cancer Center.
+ **
+ ** Code written by: Ethan Cerami
+ ** Authors: Ethan Cerami, Gary Bader, Chris Sander
+ **
+ ** This library is free software; you can redistribute it and/or modify it
+ ** under the terms of the GNU Lesser General Public License as published
+ ** by the Free Software Foundation; either version 2.1 of the License, or
+ ** any later version.
+ **
+ ** This library is distributed in the hope that it will be useful, but
+ ** WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ ** MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ ** documentation provided hereunder is on an "as is" basis, and
+ ** Memorial Sloan-Kettering Cancer Center
+ ** has no obligations to provide maintenance, support,
+ ** updates, enhancements or modifications. In no event shall
+ ** Memorial Sloan-Kettering Cancer Center
+ ** be liable to any party for direct, indirect, special,
+ ** incidental or consequential damages, including lost profits, arising
+ ** out of the use of this software and its documentation, even if
+ ** Memorial Sloan-Kettering Cancer Center
+ ** has been advised of the possibility of such damage. See
+ ** the GNU Lesser General Public License for more details.
+ **
+ ** You should have received a copy of the GNU Lesser General Public License
+ ** along with this library; if not, write to the Free Software Foundation,
+ ** Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ **/
+package cytoscape.coreplugins.biopax.util;
+
+import java.util.*;
+
+
+
+
+/**
+ * Utility Class for Creating Links to External Databases.
+ *
+ * @author Ethan Cerami
+ *
+ * TODO replace with Miriam (MiriamLink) or identifiers.org API
+ */
+public class ExternalLinkUtil {
+ private static Map dbMap;
+ private static Map ihopMap;
+ private static final String SPACE = "%20";
+ private static final String PIPE_CHAR = "%7C";
+ private static final String AMPERSAND = "&";
+ private static final String COMMA = ",";
+ private static final String UNIPROT_AC = "UNIPROT__AC";
+ private static String pipeChar = PIPE_CHAR;
+
+ /**
+ * Gets a URL to the specified dbName/id Pair.
+ *
+ * @param dbName External Database.
+ * @param id External ID.
+ * @return a URL String, or null, if dbName is not found.
+ */
+ public static String getUrl(String dbName, String id) {
+ dbName = dbName.toUpperCase();
+
+ String url = (String) dbMap.get(dbName);
+
+ if (url != null) {
+ return url + id;
+ } else {
+ return null;
+ }
+ }
+
+ /**
+ * Enables URL Encoding.
+ * URL Encoding is on by default.
+ * The only reason to turn this off is to easily view URLs within a unit
+ * test. Note that URL Encoding must be done in order to properly
+ * launch an External Web Browser.
+ *
+ * @param flag boolean flag.
+ */
+ public static void useUrlEncoding(boolean flag) {
+ if (flag) {
+ pipeChar = "%7C";
+ } else {
+ pipeChar = "|";
+ }
+ }
+
+ /**
+ * Creates an HTML Link to the specified Database.
+ *
+ * @param dbName External Database.
+ * @param id External ID.
+ * @return HTML String.
+ */
+ public static String createLink(String dbName, String id) {
+ dbName = dbName.toUpperCase();
+ String url = getUrl(dbName, id);
+ StringBuffer buf = new StringBuffer();
+
+ if (url != null) {
+ buf.append("<A class=\"link\" HREF=\"" + url + "\">" + dbName + ": " + id + "</A>");
+ } else {
+ buf.append(dbName + ": " + id);
+ }
+
+ return buf.toString();
+ }
+
+ /**
+ * Gets a Link for Searching IHOP.
+ * <p/>
+ * The following rules apply for creating links to IHOP:
+ * <UL>
+ * <LI>Only create links for elements of type: protein, DNA and RNA.
+ * IHOP does not capture information about other BioPAX types.
+ * <LI>If synonyms exist, use them.
+ * <LI>If XRefs for UniProt, Entrez Gene or RefSeq exist, use them.
+ * <LI>If we have at least one synonym or xref, append a taxonomy ID.
+ * <LI>In the special case where we have just one UNIPROT ID, and
+ * no synonyms, we don't have enough information in IHOP to create a
+ * meaningful search result page. In this case, no link is created.
+ * </UL>
+ * For details on how to construct IHOP links, see:
+ * http://www.pdg.cnb.uam.es/UniPub/iHOP/info/dev/in.html
+ *
+ * @param type BioPAX Type, e.g. protein
+ * @param synList ArrayList of Synonym Strings.
+ * @param dbList ArrayList of ExternalLink Objects.
+ * @param taxonomyId NCBI TaxonomyID or -1 if unknown.
+ * @return URL String, or null if a URL cannot be constructed.
+ */
+ public static String getIHOPUrl(String type, List synList, List dbList, int taxonomyId)
+ {
+ if (type.equalsIgnoreCase("protein")
+ || type.equalsIgnoreCase("dna")
+ || type.equalsIgnoreCase("rna"))
+ {
+ StringBuffer url = new StringBuffer();
+
+ // Use the URL Below for local testing within cbio
+ // StringBuffer url = new StringBuffer
+ // ("http://cbio.mskcc.org/UniPub/iHOP/in?");
+ String synonymParameter = createSynonymParameter(synList);
+ String dbParameter = createDbParameter(dbList, synList);
+
+ url.append(synonymParameter);
+ if (dbParameter != null && dbParameter.length() > 0) {
+ appendAmpersand(synonymParameter, url);
+ url.append(dbParameter);
+ }
+
+ // Taxonomy ID appears like this:
+ // ncbi_tax_id_1=9609
+ if (url.length() > 0) {
+ // removed NCBI Taxonomy ID; results in nearly always getting a hit w/i iHOP.
+ // url.append("ncbi_tax_id_1=" + taxonomyId);
+ url.insert(0, "http://www.ihop-net.org/UniPub/iHOP/in?");
+
+ // return string - but encode spaces first
+ return url.toString().replaceAll("\\s", SPACE);
+ }
+ }
+
+ return null;
+ }
+
+ private static void appendAmpersand(String param, StringBuffer url) {
+ if (param.length() > 0) {
+ url.append(AMPERSAND);
+ }
+ }
+
+ /**
+ * DBRefs appear like this:
+ * dbrefs_1=UNIPROT__AC|P0214,NCBI_GENE__ID=327..
+ */
+ private static String createDbParameter(List dbList, List synList) {
+ int dbHits = 0;
+ int uniProtHits = 0;
+ StringBuffer temp = new StringBuffer();
+
+ if ((dbList != null) && (dbList.size() > 0)) {
+ for (int i = 0; i < dbList.size(); i++) {
+ ExternalLink link = (ExternalLink) dbList.get(i);
+ if(link != null && link.getDbName() != null) {
+ String code = (String) ihopMap.get(link.getDbName().toUpperCase());
+ if (code != null) {
+ if (code.equals(UNIPROT_AC)) {
+ uniProtHits++;
+ }
+
+ dbHits++;
+ temp.append(code + pipeChar + link.getId() + COMMA);
+ }
+ }
+ }
+
+ if (temp.length() > 0) {
+ // This is a special case.
+ if ((uniProtHits == dbHits) && (synList.size() == 0)) {
+ return new String();
+ } else {
+ // Insert parameter name; remove last comma
+ temp.insert(0, "dbrefs_1=");
+
+ return temp.substring(0, temp.length() - 1);
+ }
+ }
+ }
+
+ return new String();
+ }
+
+ /**
+ * Synonyms appear like this:
+ * syns_1=SYN1|SYN2|SYN3...
+ */
+ private static String createSynonymParameter(List synList) {
+ StringBuffer temp = new StringBuffer();
+
+ if ((synList != null) && (synList.size() > 0)) {
+ temp.append("syns_1=");
+
+ for (int i = 0; i < synList.size(); i++) {
+ temp.append((String) synList.get(i));
+
+ if (i < (synList.size() - 1)) {
+ temp.append(pipeChar);
+ }
+ }
+ }
+
+ return temp.toString();
+ }
+
+ /**
+ * Creates HTML for a Link to IHOP.
+ *
+ * @param type BioPAX Type, e.g. protein
+ * @param synList ArrayList of Synonym Strings.
+ * @param linkList ArrayList of ExternalLink Objects.
+ * @param taxonomyId NCBI TaxonomyID or -1 if unknown.
+ * @return HTML Link.
+ */
+ public static String createIHOPLink(String type,
+ List synList, List linkList, int taxonomyId)
+ {
+ String url = getIHOPUrl(type, synList, linkList, taxonomyId);
+
+ if (url != null) {
+ StringBuffer buf = new StringBuffer();
+ buf.append("<A class=\"link\" HREF=\"" + url + "\">" + "Search iHOP</A>");
+ return buf.toString();
+ } else {
+ return null;
+ }
+ }
+
+ static {
+ dbMap = new HashMap();
+ ihopMap = new HashMap();
+
+ // Pub Med
+ String url = "http://www.ncbi.nlm.nih.gov/entrez/"
+ + "query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract" + "&list_uids=";
+ dbMap.put("PUBMED", url);
+ dbMap.put("PMID", url);
+
+ // HPRD
+ url = "http://hprd.org/protein/";
+ dbMap.put ("HPRD", url);
+
+ // UniProt
+ url = "http://www.pir.uniprot.org/cgi-bin/upEntry?id=";
+
+ HashMap temp = new HashMap();
+ temp.put("UNIPROT", url);
+ temp.put("SWISSPROT", url);
+ temp.put("SWP", url);
+ temp.put("SWISS-PROT", url);
+ dbMap.putAll(temp);
+ addIHOPEntries(temp, UNIPROT_AC);
+
+ // Gene Ontology
+ url = "http://www.godatabase.org/cgi-bin/amigo/go.cgi?open_1=";
+ dbMap.put("GO", url);
+
+ // Reactome
+ url = "http://reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=";
+// dbMap.put("REACTOME", url);
+ dbMap.put("REACTOME DATABASE ID", url);
+ url = "http://www.reactome.org/cgi-bin/eventbrowser_st_id?FROM_REACTOME=1&ST_ID=";
+ dbMap.put("REACTOME", url);
+ dbMap.put("REACTOME STABLE ID", url);
+
+ // PDB
+ url = "http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=";
+ dbMap.put("PDB", url);
+
+ // Ref Seq
+ url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&" + "cmd=search&term=";
+ temp = new HashMap();
+ temp.put("REFSEQ", url);
+ temp.put("REF-SEQ", url);
+ temp.put("REF_SEQ", url);
+ dbMap.putAll(temp);
+ addIHOPEntries(temp, "NCBI_REFSEQ__NP");
+
+ // OMIM
+ url = "http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=";
+ dbMap.put("OMIM", url);
+
+ // Entrez Gene
+ url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&" + "cmd=search&term=";
+ temp = new HashMap();
+ temp.put("ENTREZGENE", url);
+ temp.put("ENTREZ_GENE", url);
+ temp.put("LOCUS_LINK", url);
+ temp.put("LOCUSLINK", url);
+ temp.put("LOCUS-LINK", url);
+ dbMap.putAll(temp);
+ addIHOPEntries(temp, "NCBI_GENE__ID");
+
+ // Unigene
+ url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?" + "db=unigene&cmd=search&term=";
+ dbMap.put("UNIGENE", url);
+
+ // NCBI GenBank
+ url = "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein" + "&val=";
+ dbMap.put("GENBANK", url);
+ dbMap.put("ENTREZ_GI", url);
+ dbMap.put("GI", url);
+ }
+
+ private static void addIHOPEntries(HashMap map, String iHopCode) {
+ Iterator iterator = map.keySet().iterator();
+
+ while (iterator.hasNext()) {
+ String key = (String) iterator.next();
+ ihopMap.put(key, iHopCode);
+ }
+ }
+}
diff --git a/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/util/NodeAttributesWrapper.java b/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/util/NodeAttributesWrapper.java
new file mode 100644
index 0000000..69fa5f7
--- /dev/null
+++ b/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/util/NodeAttributesWrapper.java
@@ -0,0 +1,40 @@
+package cytoscape.coreplugins.biopax.util;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+
+/**
+ * A class to store a given nodes's
+ * chemical modification(s), etc.,
+ * along with a string of abbreviations for the respective attribute
+ * (which is used in the construction of the node label).
+ */
+public class NodeAttributesWrapper {
+ // map of cellular location
+ // or chemical modifications
+ private Map<String, Object> attributesMap;
+ // abbreviations string
+ private String abbreviationString;
+
+ // contructor
+ public NodeAttributesWrapper(Map<String,Object> attributesMap, String abbreviationString) {
+ this.attributesMap = attributesMap;
+ this.abbreviationString = abbreviationString;
+ }
+
+ // gets the attributes map
+ public Map<String,Object> getMap() {
+ return attributesMap;
+ }
+
+ // gets the attributes map as list
+ public List<String> getList() {
+ return (attributesMap != null) ? new ArrayList<String>(attributesMap.keySet()) : null;
+ }
+
+ // gets the abbrevation string (used in node label)
+ public String getAbbreviationString() {
+ return abbreviationString;
+ }
+}
diff --git a/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/util/ParentFinder.java b/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/util/ParentFinder.java
new file mode 100644
index 0000000..079efdc
--- /dev/null
+++ b/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/util/ParentFinder.java
@@ -0,0 +1,57 @@
+package cytoscape.coreplugins.biopax.util;
+
+import org.biopax.paxtools.controller.AbstractTraverser;
+import org.biopax.paxtools.controller.EditorMap;
+import org.biopax.paxtools.controller.PropertyEditor;
+import org.biopax.paxtools.model.BioPAXElement;
+import org.biopax.paxtools.model.Model;
+import org.biopax.paxtools.util.Filter;
+
+/**
+ *
+ *
+ * @author rodch
+ *
+ */
+public final class ParentFinder extends AbstractTraverser {
+ private BioPAXElement query;
+ private boolean found;
+
+ public ParentFinder(EditorMap editorMap) {
+ super(editorMap, new Filter<PropertyEditor>() {
+ @Override
+ public boolean filter(PropertyEditor editor) {
+ return !editor.getProperty().equals("NEXT-STEP");
+ }
+ });
+ }
+
+ @Override
+ protected void visit(Object value, BioPAXElement parent, Model model,
+ PropertyEditor editor) {
+ // skip if already found or it's not a object property
+ if(!found && value instanceof BioPAXElement) {
+ if(getVisited().contains(query)) { // it is added there right before the visit method call
+ found = true;
+ } else {
+ // continue into the value's values:
+ traverse((BioPAXElement)value, model);
+ }
+ }
+ }
+
+ /**
+ * True if the 'parent' element is in fact contains 'child'
+ * (recursively)
+ *
+ * @param parent
+ * @return
+ */
+ public boolean isParentChild(BioPAXElement parent, BioPAXElement child) {
+ query = child;
+ found = false;
+ traverse(parent, null);
+ return found;
+ }
+
+}
\ No newline at end of file
diff --git a/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/util/WebFileConnect.java b/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/util/WebFileConnect.java
new file mode 100644
index 0000000..56ab33b
--- /dev/null
+++ b/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/util/WebFileConnect.java
@@ -0,0 +1,90 @@
+// $Id: WebFileConnect.java,v 1.2 2006/06/15 22:06:02 grossb Exp $
+//------------------------------------------------------------------------------
+/** Copyright (c) 2006 Memorial Sloan-Kettering Cancer Center.
+ **
+ ** Code written by: Ethan Cerami
+ ** Authors: Ethan Cerami, Gary Bader, Chris Sander
+ **
+ ** This library is free software; you can redistribute it and/or modify it
+ ** under the terms of the GNU Lesser General Public License as published
+ ** by the Free Software Foundation; either version 2.1 of the License, or
+ ** any later version.
+ **
+ ** This library is distributed in the hope that it will be useful, but
+ ** WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ ** MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ ** documentation provided hereunder is on an "as is" basis, and
+ ** Memorial Sloan-Kettering Cancer Center
+ ** has no obligations to provide maintenance, support,
+ ** updates, enhancements or modifications. In no event shall
+ ** Memorial Sloan-Kettering Cancer Center
+ ** be liable to any party for direct, indirect, special,
+ ** incidental or consequential damages, including lost profits, arising
+ ** out of the use of this software and its documentation, even if
+ ** Memorial Sloan-Kettering Cancer Center
+ ** has been advised of the possibility of such damage. See
+ ** the GNU Lesser General Public License for more details.
+ **
+ ** You should have received a copy of the GNU Lesser General Public License
+ ** along with this library; if not, write to the Free Software Foundation,
+ ** Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ **/
+package cytoscape.coreplugins.biopax.util;
+
+import java.io.*;
+
+import java.net.MalformedURLException;
+import java.net.URL;
+
+
+/**
+ * Web/File Connect Utility Class.
+ *
+ * @author Ethan Cerami.
+ */
+public class WebFileConnect {
+ /**
+ * Retrieves the Document from the Specified URL.
+ *
+ * @param urlStr URL String.
+ * @return String Object containing the full Document Content.
+ * @throws MalformedURLException URL is Malformed.
+ * @throws IOException Network Error.
+ */
+ public static String retrieveDocument(String urlStr) throws MalformedURLException, IOException {
+ URL url = new URL(urlStr);
+ BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream()));
+
+ return readFile(in);
+ }
+
+ /**
+ * Retrieves the Document from the Specified File.
+ *
+ * @param file File Object.
+ * @return String Object containing the full Document Content.
+ * @throws FileNotFoundException File Not Found.
+ * @throws IOException Read Error.
+ */
+ public static String retrieveDocument(File file) throws FileNotFoundException, IOException {
+ BufferedReader in = new BufferedReader(new FileReader(file));
+
+ return readFile(in);
+ }
+
+ /**
+ * Reads a Document from a Buffered Reader.
+ */
+ private static String readFile(BufferedReader in) throws IOException {
+ StringBuffer buf = new StringBuffer();
+ String str;
+
+ while ((str = in.readLine()) != null) {
+ buf.append(str + "\n");
+ }
+
+ in.close();
+
+ return buf.toString();
+ }
+}
diff --git a/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/view/AboutPanel.java b/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/view/AboutPanel.java
new file mode 100644
index 0000000..1d387e0
--- /dev/null
+++ b/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/view/AboutPanel.java
@@ -0,0 +1,109 @@
+// $Id: AboutPanel.java,v 1.7 2006/06/15 22:06:02 grossb Exp $
+//------------------------------------------------------------------------------
+/** Copyright (c) 2006 Memorial Sloan-Kettering Cancer Center.
+ **
+ ** Code written by: Ethan Cerami
+ ** Authors: Ethan Cerami, Gary Bader, Chris Sander
+ **
+ ** This library is free software; you can redistribute it and/or modify it
+ ** under the terms of the GNU Lesser General Public License as published
+ ** by the Free Software Foundation; either version 2.1 of the License, or
+ ** any later version.
+ **
+ ** This library is distributed in the hope that it will be useful, but
+ ** WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ ** MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ ** documentation provided hereunder is on an "as is" basis, and
+ ** Memorial Sloan-Kettering Cancer Center
+ ** has no obligations to provide maintenance, support,
+ ** updates, enhancements or modifications. In no event shall
+ ** Memorial Sloan-Kettering Cancer Center
+ ** be liable to any party for direct, indirect, special,
+ ** incidental or consequential damages, including lost profits, arising
+ ** out of the use of this software and its documentation, even if
+ ** Memorial Sloan-Kettering Cancer Center
+ ** has been advised of the possibility of such damage. See
+ ** the GNU Lesser General Public License for more details.
+ **
+ ** You should have received a copy of the GNU Lesser General Public License
+ ** along with this library; if not, write to the Free Software Foundation,
+ ** Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ **/
+package cytoscape.coreplugins.biopax.view;
+
+import cytoscape.CytoscapeInit;
+import cytoscape.coreplugins.biopax.BiopaxPlugin;
+import cytoscape.coreplugins.biopax.action.LaunchExternalBrowser;
+
+
+import java.awt.*;
+
+import java.util.Properties;
+
+import javax.swing.*;
+import javax.swing.border.EmptyBorder;
+
+
+/**
+ * Displays information "About this PlugIn...".
+ *
+ * @author Ethan Cerami
+ */
+public class AboutPanel extends JPanel {
+ /**
+ * Constructor.
+ *
+ * @param title PlugIn Title.
+ * @param majorVersion PlugIn Major Version.
+ * @param minorVersion PlugIn Minor Version.
+ */
+ public AboutPanel(String title, int majorVersion, int minorVersion) {
+ this.setLayout(new BorderLayout());
+
+ JTextPane textPane = new JTextPane();
+ textPane.setBorder(new EmptyBorder(5,5,5,5));
+ textPane.setEditable(false);
+ textPane.setContentType("text/html");
+ textPane.addHyperlinkListener(new LaunchExternalBrowser());
+
+ StringBuffer temp = new StringBuffer();
+ temp.append("<HTML><BODY>");
+ temp.append("<h2>");
+ temp.append(title + ", Version: " + majorVersion + ". " + minorVersion);
+ temp.append("</h2>");
+ temp.append("<P>");
+
+ Properties cytoProps = CytoscapeInit.getProperties();
+
+ if (cytoProps != null) {
+ String proxyHost = (String) cytoProps.get(BiopaxPlugin.PROXY_HOST_PROPERTY);
+ String proxyPort = (String) cytoProps.get(BiopaxPlugin.PROXY_PORT_PROPERTY);
+
+ if ((proxyHost != null) && (proxyPort != null)) {
+ temp.append("HTTP Proxy Support Enabled: ");
+ temp.append(proxyHost + " [Port: " + proxyPort + "]");
+ } else {
+ temp.append("HTTP Proxy Support: Not Enabled.");
+ }
+ }
+
+ temp.append("<BR><BR>Plugin released by: Sander Group, "
+ + "<A class=\"link\" HREF=\"http://www.cbio.mskcc.org/\">"
+ + "Computational Biology Center</A>, "
+ + "<A class=\"link\" HREF=\"http://www.mskcc.org\">Memorial Sloan-Kettering "
+ + "Cancer Center</A>.");
+ temp.append("<BR><BR>For any questions concerning this plugin, please "
+ + "contact:<BR><BR><UL><LI> - Gary Bader: baderg AT mskcc.org"
+ + "<LI> - Ethan Cerami: cerami AT cbio.mskcc.org"
+ + "<LI> - Benjamin Gross: grossb AT cbio.mskcc.org"
+ + "<BR><BR>This software is made available under the "
+ + "<A class=\"link\" HREF=\"http://www.gnu.org/licenses/lgpl.html\">LGPL "
+ + "(Lesser General Public License)</A>.");
+ temp.append("</BODY></HTML>");
+ textPane.setText(temp.toString());
+ textPane.setText(temp.toString());
+
+ JScrollPane scrollPane = new JScrollPane(textPane);
+ this.add(scrollPane, BorderLayout.CENTER);
+ }
+}
diff --git a/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/view/BioPaxContainer.java b/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/view/BioPaxContainer.java
new file mode 100644
index 0000000..2192aed
--- /dev/null
+++ b/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/view/BioPaxContainer.java
@@ -0,0 +1,174 @@
+// $Id: BioPaxContainer.java,v 1.7 2006/06/15 22:06:02 grossb Exp $
+//------------------------------------------------------------------------------
+/** Copyright (c) 2006 Memorial Sloan-Kettering Cancer Center.
+ **
+ ** Code written by: Ethan Cerami
+ ** Authors: Ethan Cerami, Gary Bader, Chris Sander
+ **
+ ** This library is free software; you can redistribute it and/or modify it
+ ** under the terms of the GNU Lesser General Public License as published
+ ** by the Free Software Foundation; either version 2.1 of the License, or
+ ** any later version.
+ **
+ ** This library is distributed in the hope that it will be useful, but
+ ** WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ ** MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ ** documentation provided hereunder is on an "as is" basis, and
+ ** Memorial Sloan-Kettering Cancer Center
+ ** has no obligations to provide maintenance, support,
+ ** updates, enhancements or modifications. In no event shall
+ ** Memorial Sloan-Kettering Cancer Center
+ ** be liable to any party for direct, indirect, special,
+ ** incidental or consequential damages, including lost profits, arising
+ ** out of the use of this software and its documentation, even if
+ ** Memorial Sloan-Kettering Cancer Center
+ ** has been advised of the possibility of such damage. See
+ ** the GNU Lesser General Public License for more details.
+ **
+ ** You should have received a copy of the GNU Lesser General Public License
+ ** along with this library; if not, write to the Free Software Foundation,
+ ** Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ **/
+package cytoscape.coreplugins.biopax.view;
+
+
+import java.awt.*;
+
+import javax.swing.*;
+import javax.swing.border.EmptyBorder;
+import javax.swing.event.HyperlinkListener;
+import javax.swing.event.HyperlinkEvent;
+
+import cytoscape.Cytoscape;
+import cytoscape.CyNetwork;
+import cytoscape.coreplugins.biopax.MapBioPaxToCytoscape;
+import cytoscape.coreplugins.biopax.action.NetworkListener;
+import cytoscape.data.CyAttributes;
+
+
+/**
+ * Container for all BioPax UI Components.
+ * <p/>
+ * Currently includes:
+ * <UL>
+ * <LI>BioPaxDetailsPanel
+ * <LI>BioPaxLegendPanel
+ * <LI>AboutPanel
+ * </UL>
+ *
+ * @author Ethan Cerami
+ */
+public class BioPaxContainer extends JPanel {
+ private static final long serialVersionUID = 1L;
+ /**
+ * CytoPanel Location of this Panel
+ */
+ public static final int CYTO_PANEL_LOCATION = SwingConstants.EAST;
+ private BioPaxDetailsPanel bpDetailsPanel;
+ private NetworkListener networkListener;
+ private static BioPaxContainer bioPaxContainer;
+ private JEditorPane label;
+ private JPanel cards;
+
+ private final static String DETAILS_CARD = "DETAILS";
+ private final static String LEGEND_BIOPAX_CARD = "LEGEND_BIOPAX";
+ private final static String LEGEND_BINARY_CARD = "LEGEND_BINARY";
+
+ /**
+ * Private Constructor.
+ */
+ private BioPaxContainer() {
+ cards = new JPanel(new CardLayout());
+ bpDetailsPanel = new BioPaxDetailsPanel();
+ LegendPanel bioPaxLegendPanel = new LegendPanel(LegendPanel.BIOPAX_LEGEND);
+ LegendPanel binaryLegendPanel = new LegendPanel(LegendPanel.BINARY_LEGEND);
+
+ cards.add (bpDetailsPanel, DETAILS_CARD);
+ cards.add (bioPaxLegendPanel, LEGEND_BIOPAX_CARD);
+ cards.add (binaryLegendPanel, LEGEND_BINARY_CARD);
+
+ this.setLayout(new BorderLayout());
+ this.add(cards, BorderLayout.CENTER);
+
+ label = new JEditorPane ("text/html", "<a href='LEGEND'>Visual Legend</a>");
+ label.setEditable(false);
+ label.setOpaque(false);
+ label.putClientProperty(JEditorPane.HONOR_DISPLAY_PROPERTIES, Boolean.TRUE);
+ label.addHyperlinkListener(new HyperlinkListener() {
+ public void hyperlinkUpdate(HyperlinkEvent hyperlinkEvent) {
+ if (hyperlinkEvent.getEventType() == HyperlinkEvent.EventType.ACTIVATED) {
+ String name = hyperlinkEvent.getDescription();
+ if (name.equalsIgnoreCase("LEGEND")) {
+ showLegend();
+ } else {
+ showDetails();
+ }
+ }
+ }
+ });
+
+ label.setAlignmentX(Component.LEFT_ALIGNMENT);
+ Font font = label.getFont();
+ Font newFont = new Font (font.getFamily(), font.getStyle(), font.getSize()-2);
+ label.setFont(newFont);
+ label.setBorder(new EmptyBorder(5,3,3,3));
+ this.add(label, BorderLayout.SOUTH);
+ this.networkListener = new NetworkListener(bpDetailsPanel);
+ }
+
+ /**
+ * Show Details Panel.
+ */
+ public void showDetails() {
+ CardLayout cl = (CardLayout)(cards.getLayout());
+ cl.show(cards, DETAILS_CARD);
+ label.setText("<a href='LEGEND'>Visual Legend</a>");
+ }
+
+ /**
+ * Show Legend Panel.
+ */
+ public void showLegend() {
+ CardLayout cl = (CardLayout)(cards.getLayout());
+ CyNetwork network = Cytoscape.getCurrentNetwork();
+ CyAttributes networkAttributes = Cytoscape.getNetworkAttributes();
+ Boolean isBioPaxNetwork = networkAttributes.getBooleanAttribute(network.getIdentifier(),
+ MapBioPaxToCytoscape.BIOPAX_NETWORK);
+ if (isBioPaxNetwork != null) {
+ cl.show(cards, LEGEND_BIOPAX_CARD);
+ } else {
+ cl.show(cards, LEGEND_BINARY_CARD);
+ }
+ label.setText("<a href='DETAILS'>View Details</a>");
+ }
+
+ /**
+ * Gets Instance of Singleton.
+ *
+ * @return BioPaxContainer Object.
+ */
+ public static BioPaxContainer getInstance() {
+ if (bioPaxContainer == null) {
+ bioPaxContainer = new BioPaxContainer();
+ }
+ return bioPaxContainer;
+ }
+
+ /**
+ * Gets the Embedded BioPax Details Panel.
+ *
+ * @return BioPaxDetailsPanel Object.
+ */
+ public BioPaxDetailsPanel getBioPaxDetailsPanel() {
+ return bpDetailsPanel;
+ }
+
+ /**
+ * Gets the Network Listener Object.
+ *
+ * @return Network Listener Object.
+ */
+ public NetworkListener getNetworkListener() {
+ return networkListener;
+ }
+}
diff --git a/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/view/BioPaxDetailsPanel.java b/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/view/BioPaxDetailsPanel.java
new file mode 100644
index 0000000..f9b8ae7
--- /dev/null
+++ b/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/view/BioPaxDetailsPanel.java
@@ -0,0 +1,367 @@
+// $Id: BioPaxDetailsPanel.java,v 1.24 2006/10/09 20:48:04 cerami Exp $
+//------------------------------------------------------------------------------
+/** Copyright (c) 2006 Memorial Sloan-Kettering Cancer Center.
+ **
+ ** Code written by: Ethan Cerami
+ ** Authors: Ethan Cerami, Gary Bader, Chris Sander
+ **
+ ** This library is free software; you can redistribute it and/or modify it
+ ** under the terms of the GNU Lesser General Public License as published
+ ** by the Free Software Foundation; either version 2.1 of the License, or
+ ** any later version.
+ **
+ ** This library is distributed in the hope that it will be useful, but
+ ** WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ ** MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ ** documentation provided hereunder is on an "as is" basis, and
+ ** Memorial Sloan-Kettering Cancer Center
+ ** has no obligations to provide maintenance, support,
+ ** updates, enhancements or modifications. In no event shall
+ ** Memorial Sloan-Kettering Cancer Center
+ ** be liable to any party for direct, indirect, special,
+ ** incidental or consequential damages, including lost profits, arising
+ ** out of the use of this software and its documentation, even if
+ ** Memorial Sloan-Kettering Cancer Center
+ ** has been advised of the possibility of such damage. See
+ ** the GNU Lesser General Public License for more details.
+ **
+ ** You should have received a copy of the GNU Lesser General Public License
+ ** along with this library; if not, write to the Free Software Foundation,
+ ** Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ **/
+package cytoscape.coreplugins.biopax.view;
+
+import cytoscape.Cytoscape;
+import cytoscape.CyNetwork;
+
+import cytoscape.coreplugins.biopax.MapBioPaxToCytoscape;
+import cytoscape.coreplugins.biopax.action.LaunchExternalBrowser;
+import cytoscape.coreplugins.biopax.util.BioPaxUtil;
+import cytoscape.data.CyAttributes;
+import cytoscape.data.Semantics;
+import cytoscape.logger.CyLogger;
+
+import org.biopax.paxtools.model.level3.PhysicalEntity;
+
+import java.awt.*;
+
+import java.util.List;
+import java.util.Set;
+import java.util.TreeSet;
+
+import javax.swing.*;
+import javax.swing.border.EmptyBorder;
+import javax.swing.text.AttributeSet;
+import javax.swing.text.StyleConstants;
+import javax.swing.text.View;
+import javax.swing.text.ViewFactory;
+import javax.swing.text.html.*;
+
+
+/**
+ * BioPAX Details Panel.
+ *
+ * @author Ethan Cerami.
+ */
+public class BioPaxDetailsPanel extends JPanel {
+ public static final CyLogger log = CyLogger.getLogger(BioPaxDetailsPanel.class);
+
+ /**
+ * Foreground Color.
+ */
+ public static final Color FG_COLOR = new Color(75, 75, 75);
+ private JScrollPane scrollPane;
+ private JTextPane textPane;
+ private CyAttributes nodeAttributes;
+
+ /**
+ * Constructor.
+ */
+ public BioPaxDetailsPanel() {
+ textPane = new JTextPane();
+
+ // Set Editor Kit that is capable of handling long words
+ MyEditorKit kit = new MyEditorKit();
+ textPane.setEditorKit(kit);
+ modifyStyleSheetForSingleDocument(textPane);
+
+ textPane.putClientProperty(JEditorPane.HONOR_DISPLAY_PROPERTIES, Boolean.TRUE);
+ textPane.setBorder(new EmptyBorder (5,5,5,5));
+ textPane.setContentType("text/html");
+ textPane.setEditable(false);
+ textPane.addHyperlinkListener(new LaunchExternalBrowser());
+ resetText();
+
+ scrollPane = new JScrollPane(textPane);
+ scrollPane.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED);
+ scrollPane.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED);
+ scrollPane.setBorder(new EmptyBorder(0, 0, 0, 0));
+ this.setLayout(new BorderLayout());
+ this.add(scrollPane, BorderLayout.CENTER);
+ this.setPreferredSize(new Dimension(300, 300));
+ this.setMaximumSize(new Dimension(300, 300));
+
+ // get a ref to node attributes
+ nodeAttributes = Cytoscape.getNodeAttributes();
+
+ }
+
+ public static void modifyStyleSheetForSingleDocument(JTextPane textPane) {
+ HTMLDocument htmlDoc = (HTMLDocument) textPane.getDocument();
+ StyleSheet styleSheet = htmlDoc.getStyleSheet();
+ styleSheet.addRule("h2 {color: #663333; font-size: 120%; font-weight: bold; "
+ + "margin-bottom:3px}");
+ styleSheet.addRule("h3 {color: #663333; font-size: 105%; font-weight: bold;"
+ + "margin-bottom:7px}");
+ styleSheet.addRule("ul { list-style-type: none; margin-left: 5px; "
+ + "padding-left: 1em; text-indent: -1em;}");
+ styleSheet.addRule("h4 {color: #66333; font-weight: bold; margin-bottom:3px;}");
+ styleSheet.addRule(".link {color:blue; text-decoration: underline;}");
+ styleSheet.addRule(".description {font-size: 85%;}");
+ styleSheet.addRule(".rule {font-size: 90%; font-weight:bold}");
+ styleSheet.addRule(".excerpt {font-size: 90%;}");
+ }
+
+ /**
+ * Resets the Text to "Select a node to view details...";
+ */
+ public void resetText() {
+ StringBuffer temp = new StringBuffer();
+ temp.append("<html><body>");
+ temp.append("Select a node to view details...");
+ temp.append("</body></html>");
+ textPane.setText(temp.toString());
+ }
+
+ /**
+ * Resets the Text to the specified Text String.
+ *
+ * @param text Text String.
+ */
+ public void resetText(String text) {
+ StringBuffer temp = new StringBuffer();
+ temp.append("<html><body>");
+ temp.append(text);
+ temp.append("</body></html>");
+ textPane.setText(temp.toString());
+ }
+
+ /**
+ * Shows details about the BioPAX Entity with the specified RDF ID.
+ *
+ * @param nodeID RDF ID String.
+ */
+ public void showDetails(String nodeID) {
+ String stringRef;
+
+ StringBuffer buf = new StringBuffer("<html><body>");
+
+ // name, shortname
+ stringRef = nodeAttributes.getStringAttribute(nodeID, Semantics.CANONICAL_NAME);
+
+ String shortName = nodeAttributes.getStringAttribute(nodeID, "displayName");
+ if ((shortName != null) && (shortName.length() > 0)) {
+ buf.append("<h2>").append(shortName).append("</h2>");
+ } else if (stringRef != null && stringRef.length() > 0) {
+ buf.append("<h2>").append(stringRef).append("</h2>");
+ }
+
+ String type = nodeAttributes.getStringAttribute(nodeID, MapBioPaxToCytoscape.BIOPAX_ENTITY_TYPE);
+ buf.append("<h3>").append(type).append("</h3>");
+
+ // organism
+ stringRef = null;
+ stringRef = nodeAttributes.getStringAttribute(nodeID, "entityReference/organism/displayName");
+ if(stringRef == null)
+ stringRef = nodeAttributes.getStringAttribute(nodeID, "entityReference/organism/standardName");
+ if(stringRef == null)
+ stringRef = nodeAttributes.getStringAttribute(nodeID, "organism/displayName");
+ if(stringRef == null)
+ stringRef = nodeAttributes.getStringAttribute(nodeID, "organism/standardName");
+ if (stringRef != null) {
+ buf.append("<h4>").append(stringRef).append("</h4>");
+ }
+
+ // Add (optional) cPath Link
+ addCPathLink(nodeID, buf);
+
+ // synonyms
+ addAttributeList(nodeID, "name;entityReference/name;memberPhysicalEntity/name;memberEntityReference/name", buf, "Synonyms:");
+
+ // cellular location
+ stringRef = null;
+ stringRef = nodeAttributes.getStringAttribute(nodeID, "cellularLocation");
+ if (stringRef != null) {
+ buf.append("<h4>").append("Cellular Location: ").append(stringRef).append("</h4>");
+ }
+// addAttributeList(nodeID, MapBioPaxToCytoscape.BIOPAX_CELLULAR_LOCATIONS, buf, "Cellular Location: ");
+
+ // chemical modification
+ addAttributeList(nodeID, MapBioPaxToCytoscape.BIOPAX_CHEMICAL_MODIFICATIONS_LIST, buf, "Chemical Modifications:");
+
+ // links
+ addLinks(nodeID, buf);
+
+ buf.append("</body></html>");
+ textPane.setText(buf.toString());
+ textPane.setCaretPosition(0);
+ }
+
+ private void addCPathLink(String nodeID, StringBuffer buf) {
+ CyNetwork cyNetwork = Cytoscape.getCurrentNetwork();
+ CyAttributes networkAttributes = Cytoscape.getNetworkAttributes();
+ String serverName = networkAttributes.getStringAttribute(cyNetwork.getIdentifier(),
+ "CPATH_SERVER_NAME");
+ String serverDetailsUrl = networkAttributes.getStringAttribute(cyNetwork.getIdentifier(),
+ "CPATH_SERVER_DETAILS_URL");
+ if (serverName != null && serverDetailsUrl != null) {
+ String type = nodeAttributes.getStringAttribute(nodeID,
+ MapBioPaxToCytoscape.BIOPAX_ENTITY_TYPE);
+ if (BioPaxUtil.getSubclassNames(PhysicalEntity.class).contains(type)) {
+ String url = serverDetailsUrl + nodeID;
+ buf.append ("<h3><A href='" + url + "'>" + serverName + ": " + nodeID + "</A>");
+ }
+ }
+ }
+
+
+ private void addLinks(String nodeID, StringBuffer buf) {
+ addAttributeList(nodeID, MapBioPaxToCytoscape.BIOPAX_UNIFICATION_REFERENCES
+ + ";" + MapBioPaxToCytoscape.BIOPAX_RELATIONSHIP_REFERENCES, buf, "Links:");
+ addAttributeList(nodeID, MapBioPaxToCytoscape.BIOPAX_PUBLICATION_REFERENCES, buf, "Publications:");
+
+ addIHOPLinks(nodeID, buf);
+ }
+
+ private void addAttributeList(String nodeID, String attributes, StringBuffer buf, String label)
+ {
+ StringBuilder displayString = new StringBuilder();
+
+ Set<String> set = new TreeSet<String>();
+ for (String attribute : attributes.split(";")) {
+ @SuppressWarnings("unchecked")
+ List<String> list = nodeAttributes.getListAttribute(nodeID,
+ attribute);
+ if (list != null)
+ set.addAll(list);
+ }
+
+ for (String listItem : set) {
+ if (listItem != null && listItem.length() > 0) {
+ displayString.append("<li> - " + listItem);
+ displayString.append("</li>");
+ }
+ }
+
+ // do we have a string to display ?
+ if (displayString.length() > 0) {
+ if(label != null)
+ appendHeader(label, buf);
+ buf.append("<ul>");
+ appendData(displayString.toString(), buf, false);
+ buf.append("</ul>");
+ }
+ }
+
+ private void appendHeader(String header, StringBuffer buf) {
+ buf.append("<h4>");
+ buf.append(header);
+ buf.append("</h4>");
+ }
+
+ private void appendData(String data, StringBuffer buf, boolean appendBr) {
+ buf.append(data);
+ if (appendBr) {
+ buf.append("<br/>");
+ }
+ }
+
+ private void addIHOPLinks(String nodeID, StringBuffer buf) {
+ String ihopLinks = nodeAttributes.getStringAttribute(nodeID,
+ MapBioPaxToCytoscape.BIOPAX_IHOP_LINKS);
+
+ if (ihopLinks != null) {
+ appendData(ihopLinks, buf, false);
+ }
+ }
+}
+
+
+/**
+ * Editor Kit which is capable of handling long words.
+ * <p/>
+ * Here is a description of the problem:
+ * By default, JTextPane uses an InlineView. It was designed to avoid
+ * wrapping. Text can't be broken if it doesn't contain spaces.
+ * <p/>
+ * This is a real problem with the BioPaxDetailsPanel, as BioPax Unique
+ * Identifiers can get really long, and this prevents the user from
+ * resizing the CytoPanel to any arbitrary size.
+ * <p/>
+ * The solution below comes from:
+ * http://joust.kano.net/weblog/archives/000074.html
+ * <p/>
+ * (The following code is released in the public domain.)
+ *
+ * @author Joust Team.
+ */
+class MyEditorKit extends HTMLEditorKit {
+
+ /**
+ * Gets the ViewFactor Object.
+ *
+ * @return View Factor Object.
+ */
+ public ViewFactory getViewFactory() {
+ return new MyViewFactory(super.getViewFactory());
+ }
+
+ /**
+ * Word Splitting Paragraph View.
+ */
+ private static class WordSplittingParagraphView extends ParagraphView {
+ public WordSplittingParagraphView(javax.swing.text.Element elem) {
+ super(elem);
+ }
+
+ protected SizeRequirements calculateMinorAxisRequirements(int axis, SizeRequirements r) {
+ SizeRequirements sup = super.calculateMinorAxisRequirements(axis, r);
+ sup.minimum = 1;
+
+ return sup;
+ }
+ }
+
+ /**
+ * View Factory.
+ */
+ private static class MyViewFactory implements ViewFactory {
+ private final ViewFactory parent;
+
+ /**
+ * Constructor.
+ *
+ * @param parent ViewFactory Object.
+ */
+ public MyViewFactory(ViewFactory parent) {
+ this.parent = parent;
+ }
+
+ /**
+ * Creates a Text Element View.
+ *
+ * @param elem Element Object.
+ * @return View Object.
+ */
+ public View create(javax.swing.text.Element elem) {
+ AttributeSet attr = elem.getAttributes();
+ Object name = attr.getAttribute(StyleConstants.NameAttribute);
+
+ if ((name == HTML.Tag.P) || (name == HTML.Tag.IMPLIED)) {
+ return new WordSplittingParagraphView(elem);
+ }
+
+ return parent.create(elem);
+ }
+ }
+}
diff --git a/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/view/EdgeFilterUi.java b/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/view/EdgeFilterUi.java
new file mode 100644
index 0000000..039b4c0
--- /dev/null
+++ b/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/view/EdgeFilterUi.java
@@ -0,0 +1,166 @@
+package cytoscape.coreplugins.biopax.view;
+
+import cytoscape.CyNetwork;
+import cytoscape.CyEdge;
+import cytoscape.Cytoscape;
+import cytoscape.view.CyNetworkView;
+import cytoscape.actions.GinyUtils;
+import cytoscape.data.CyAttributes;
+import cytoscape.data.Semantics;
+
+import javax.swing.*;
+import javax.swing.border.TitledBorder;
+import javax.swing.border.EmptyBorder;
+import javax.swing.border.Border;
+import javax.swing.border.CompoundBorder;
+import java.util.*;
+import java.awt.*;
+import java.awt.event.ActionListener;
+import java.awt.event.ActionEvent;
+
+import giny.view.EdgeView;
+
+/**
+ * Edge Filter Dialog.
+ */
+public class EdgeFilterUi extends JDialog {
+ private CyNetwork cyNetwork;
+ private HashSet checkBoxSet;
+
+ /**
+ * Constructor.
+ * @param cyNetwork CyNetwork Object.
+ */
+ public EdgeFilterUi(CyNetwork cyNetwork) {
+ this.cyNetwork = cyNetwork;
+ initGui();
+ }
+
+ /**
+ * Initializes GUI.
+ */
+ private void initGui() {
+ this.setModal(true);
+ this.setTitle("Edge Filter");
+ checkBoxSet = new HashSet();
+ Set interactionSet = new TreeSet();
+ CyAttributes edgeAttributes = Cytoscape.getEdgeAttributes();
+ Iterator edgeIterator = cyNetwork.edgesIterator();
+ while (edgeIterator.hasNext()) {
+ CyEdge edge = (CyEdge) edgeIterator.next();
+ String interactionType = edgeAttributes.getStringAttribute(edge.getIdentifier(),
+ Semantics.INTERACTION);
+ interactionSet.add(interactionType);
+ }
+ Iterator interactionIterator = interactionSet.iterator();
+
+ JPanel edgeSetPanel = new JPanel();
+
+ Border emptyBorder = new EmptyBorder (10,10,10,100);
+ Border titledBorder = new TitledBorder ("Edge Filter");
+ CompoundBorder compoundBorder = new CompoundBorder (titledBorder, emptyBorder);
+ edgeSetPanel.setBorder(compoundBorder);
+ edgeSetPanel.setLayout(new BoxLayout(edgeSetPanel, BoxLayout.Y_AXIS));
+ while (interactionIterator.hasNext()) {
+ String interactionType = (String) interactionIterator.next();
+ JCheckBox checkBox = new JCheckBox (interactionType);
+ checkBox.setActionCommand(interactionType);
+ checkBox.addActionListener(new ApplyEdgeFilter(cyNetwork, checkBoxSet));
+ checkBox.setSelected(true);
+ edgeSetPanel.add(checkBox);
+ checkBoxSet.add(checkBox);
+ }
+
+ // Select all edges
+ ApplyEdgeFilter apply = new ApplyEdgeFilter (cyNetwork, checkBoxSet);
+ apply.executeFilter();
+
+ Container contentPane = this.getContentPane();
+ contentPane.setLayout (new BorderLayout());
+ contentPane.add(edgeSetPanel, BorderLayout.CENTER);
+
+ JPanel panel = new JPanel();
+ JButton closeButton = new JButton ("Close");
+ closeButton.addActionListener(new ActionListener() {
+
+ public void actionPerformed(ActionEvent actionEvent) {
+ EdgeFilterUi.this.dispose();
+
+ }
+ });
+ panel.setLayout(new FlowLayout(FlowLayout.RIGHT));
+ panel.add(closeButton);
+ contentPane.add(panel, BorderLayout.SOUTH);
+
+ this.setLocationRelativeTo(Cytoscape.getDesktop());
+ this.pack();
+ this.setVisible(true);
+ }
+
+}
+
+/**
+ * Apply Edge Filter.
+ */
+class ApplyEdgeFilter implements ActionListener {
+ private CyNetwork cyNetwork;
+ private HashSet checkBoxSet;
+
+ /**
+ * Constructor.
+ * @param cyNetwork CyNetwork Object.
+ * @param checkBoxSet Set of JCheckBox Objects.
+ */
+ public ApplyEdgeFilter (CyNetwork cyNetwork, HashSet checkBoxSet) {
+ this.cyNetwork = cyNetwork;
+ this.checkBoxSet = checkBoxSet;
+ }
+
+ /**
+ * Check Box selected or unselected.
+ * @param actionEvent Action Event.
+ */
+ public void actionPerformed(ActionEvent actionEvent) {
+ executeFilter();
+ }
+
+ /**
+ * Executes the Edge Filter.
+ */
+ public void executeFilter() {
+ HashSet selectedInteractionSet = new HashSet();
+ Iterator checkBoxIterator = checkBoxSet.iterator();
+ while (checkBoxIterator.hasNext()) {
+ JCheckBox checkBox = (JCheckBox) checkBoxIterator.next();
+ String action = checkBox.getActionCommand();
+ if (checkBox.isSelected()) {
+ selectedInteractionSet.add(action);
+ }
+ }
+ ArrayList edgeSet = new ArrayList();
+ CyAttributes edgeAttributes = Cytoscape.getEdgeAttributes();
+ java.util.List edgeList = cyNetwork.edgesList();
+
+ int allEdgeIds[] = new int[edgeList.size()];
+ for (int i=0; i< edgeList.size(); i++) {
+ CyEdge edge = (CyEdge) edgeList.get(i);
+ String interactionType = edgeAttributes.getStringAttribute(edge.getIdentifier(),
+ Semantics.INTERACTION);
+ if (!selectedInteractionSet.contains(interactionType)) {
+ edgeSet.add(edge);
+ }
+ allEdgeIds[i] = edge.getRootGraphIndex();
+ }
+
+ CyNetworkView networkView = Cytoscape.getCurrentNetworkView();
+ GinyUtils.unHideAll(networkView);
+ ArrayList edgeViewList = new ArrayList();
+ for (int i=0; i<edgeSet.size(); i++) {
+ CyEdge edge = (CyEdge) edgeSet.get(i);
+ EdgeView edgeView = networkView.getEdgeView(edge);
+ edgeViewList.add(edgeView);
+
+ }
+ networkView.hideGraphObjects(edgeViewList);
+ }
+}
diff --git a/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/view/LegendPanel.java b/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/view/LegendPanel.java
new file mode 100644
index 0000000..ba2c52a
--- /dev/null
+++ b/coreplugins/BioPAX/src/main/java/cytoscape/coreplugins/biopax/view/LegendPanel.java
@@ -0,0 +1,82 @@
+package cytoscape.coreplugins.biopax.view;
+
+
+import javax.swing.*;
+import javax.swing.event.HyperlinkListener;
+import javax.swing.event.HyperlinkEvent;
+import java.awt.*;
+import java.net.URL;
+
+import cytoscape.Cytoscape;
+import cytoscape.coreplugins.biopax.util.WebFileConnect;
+
+/**
+ * Displays the Default Visual Style Legend for the BioPAX Mapper.
+ *
+ * @author Ethan Cerami
+ */
+public class LegendPanel extends JPanel {
+
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * BioPAX Legend.
+ */
+ public static int BIOPAX_LEGEND = 0;
+
+ /**
+ * Binary Legend.
+ */
+ public static int BINARY_LEGEND = 1;
+
+ /**
+ * Constructor.
+ *
+ */
+ public LegendPanel(int mode) {
+ this.setLayout(new BorderLayout());
+
+ JTextPane textPane = new JTextPane();
+ textPane.setEditable(false);
+ textPane.setContentType("text/html");
+ textPane.putClientProperty(JEditorPane.HONOR_DISPLAY_PROPERTIES, Boolean.TRUE);
+
+ URL legendUrl;
+ if (mode == BIOPAX_LEGEND) {
+ legendUrl = LegendPanel.class.getResource("legend.html");
+ } else {
+ legendUrl = LegendPanel.class.getResource("binary_legend.html");
+ }
+ StringBuffer temp = new StringBuffer();
+ temp.append("<HTML><BODY>");
+
+ try {
+ String legendHtml = WebFileConnect.retrieveDocument(legendUrl.toString());
+ temp.append(legendHtml);
+ } catch (Exception e) {
+ temp.append("Could not load legend... " + e.toString());
+ }
+
+ temp.append("</BODY></HTML>");
+ textPane.setText(temp.toString());
+
+ /*
+ textPane.addHyperlinkListener(new HyperlinkListener() {
+ public void hyperlinkUpdate(HyperlinkEvent hyperlinkEvent) {
+ if (hyperlinkEvent.getEventType() == HyperlinkEvent.EventType.ACTIVATED) {
+ String name = hyperlinkEvent.getDescription();
+ if (name.equalsIgnoreCase("filter")) {
+ EdgeFilterUi ui = new EdgeFilterUi(Cytoscape.getCurrentNetwork());
+ //TODO No action or logic was here; is something missing?..
+ }
+ }
+ }
+ });
+ */
+
+ BioPaxDetailsPanel.modifyStyleSheetForSingleDocument(textPane);
+
+ JScrollPane scrollPane = new JScrollPane(textPane);
+ this.add(scrollPane, BorderLayout.CENTER);
+ }
+}
diff --git a/coreplugins/BioPAX/src/main/resources/COPYING b/coreplugins/BioPAX/src/main/resources/COPYING
new file mode 100644
index 0000000..94a9ed0
--- /dev/null
+++ b/coreplugins/BioPAX/src/main/resources/COPYING
@@ -0,0 +1,674 @@
+ GNU GENERAL PUBLIC LICENSE
+ Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+ Preamble
+
+ The GNU General Public License is a free, copyleft license for
+software and other kinds of works.
+
+ The licenses for most software and other practical works are designed
+to take away your freedom to share and change the works. By contrast,
+the GNU General Public License is intended to guarantee your freedom to
+share and change all versions of a program--to make sure it remains free
+software for all its users. We, the Free Software Foundation, use the
+GNU General Public License for most of our software; it applies also to
+any other work released this way by its authors. You can apply it to
+your programs, too.
+
+ When we speak of free software, we are referring to freedom, not
+price. Our General Public Licenses are designed to make sure that you
+have the freedom to distribute copies of free software (and charge for
+them if you wish), that you receive source code or can get it if you
+want it, that you can change the software or use pieces of it in new
+free programs, and that you know you can do these things.
+
+ To protect your rights, we need to prevent others from denying you
+these rights or asking you to surrender the rights. Therefore, you have
+certain responsibilities if you distribute copies of the software, or if
+you modify it: responsibilities to respect the freedom of others.
+
+ For example, if you distribute copies of such a program, whether
+gratis or for a fee, you must pass on to the recipients the same
+freedoms that you received. You must make sure that they, too, receive
+or can get the source code. And you must show them these terms so they
+know their rights.
+
+ Developers that use the GNU GPL protect your rights with two steps:
+(1) assert copyright on the software, and (2) offer you this License
+giving you legal permission to copy, distribute and/or modify it.
+
+ For the developers' and authors' protection, the GPL clearly explains
+that there is no warranty for this free software. For both users' and
+authors' sake, the GPL requires that modified versions be marked as
+changed, so that their problems will not be attributed erroneously to
+authors of previous versions.
+
+ Some devices are designed to deny users access to install or run
+modified versions of the software inside them, although the manufacturer
+can do so. This is fundamentally incompatible with the aim of
+protecting users' freedom to change the software. The systematic
+pattern of such abuse occurs in the area of products for individuals to
+use, which is precisely where it is most unacceptable. Therefore, we
+have designed this version of the GPL to prohibit the practice for those
+products. If such problems arise substantially in other domains, we
+stand ready to extend this provision to those domains in future versions
+of the GPL, as needed to protect the freedom of users.
+
+ Finally, every program is threatened constantly by software patents.
+States should not allow patents to restrict development and use of
+software on general-purpose computers, but in those that do, we wish to
+avoid the special danger that patents applied to a free program could
+make it effectively proprietary. To prevent this, the GPL assures that
+patents cannot be used to render the program non-free.
+
+ The precise terms and conditions for copying, distribution and
+modification follow.
+
+ TERMS AND CONDITIONS
+
+ 0. Definitions.
+
+ "This License" refers to version 3 of the GNU General Public License.
+
+ "Copyright" also means copyright-like laws that apply to other kinds of
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+
+ "The Program" refers to any copyrightable work licensed under this
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+ This is free software, and you are welcome to redistribute it
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+The hypothetical commands `show w' and `show c' should show the appropriate
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diff --git a/coreplugins/BioPAX/src/main/resources/COPYING.LESSER b/coreplugins/BioPAX/src/main/resources/COPYING.LESSER
new file mode 100644
index 0000000..22db839
--- /dev/null
+++ b/coreplugins/BioPAX/src/main/resources/COPYING.LESSER
@@ -0,0 +1,193 @@
+/** BioPAX Plugin for Cytoscape
+ **
+ ** Copyright (c) 2010 University of Toronto (UofT)
+ ** and Memorial Sloan-Kettering Cancer Center (MSKCC).
+ **
+ ** This is free software; you can redistribute it and/or modify it
+ ** under the terms of the GNU Lesser General Public License as published
+ ** by the Free Software Foundation; either version 2.1 of the License, or
+ ** any later version.
+ **
+ ** This library is distributed in the hope that it will be useful, but
+ ** WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ ** MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ ** documentation provided hereunder is on an "as is" basis, and
+ ** both UofT and MSKCC have no obligations to provide maintenance,
+ ** support, updates, enhancements or modifications. In no event shall
+ ** UofT or MSKCC be liable to any party for direct, indirect, special,
+ ** incidental or consequential damages, including lost profits, arising
+ ** out of the use of this software and its documentation, even if
+ ** UofT or MSKCC have been advised of the possibility of such damage.
+ ** See the GNU Lesser General Public License for more details.
+ **
+ ** You should have received a copy of the GNU Lesser General Public License
+ ** along with this software; if not, write to the Free Software Foundation,
+ ** Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA;
+ ** or find it at http://www.fsf.org/ or http://www.gnu.org.
+ **/
+
+ GNU LESSER GENERAL PUBLIC LICENSE
+ Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+
+ This version of the GNU Lesser General Public License incorporates
+the terms and conditions of version 3 of the GNU General Public
+License, supplemented by the additional permissions listed below.
+
+ 0. Additional Definitions.
+
+ As used herein, "this License" refers to version 3 of the GNU Lesser
+General Public License, and the "GNU GPL" refers to version 3 of the GNU
+General Public License.
+
+ "The Library" refers to a covered work governed by this License,
+other than an Application or a Combined Work as defined below.
+
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+
+ You may convey a covered work under sections 3 and 4 of this License
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+
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+ a) Accompany the combined library with a copy of the same work based
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+
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+versions will be similar in spirit to the present version, but may
+differ in detail to address new problems or concerns.
+
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+Library as you received it specifies that a certain numbered version
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+received it does not specify a version number of the GNU Lesser
+General Public License, you may choose any version of the GNU Lesser
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+
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diff --git a/coreplugins/BioPAX/src/main/resources/cytoscape/coreplugins/biopax/phos-node.jpg b/coreplugins/BioPAX/src/main/resources/cytoscape/coreplugins/biopax/phos-node.jpg
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diff --git a/coreplugins/BioPAX/src/main/resources/cytoscape/coreplugins/biopax/plugin.props b/coreplugins/BioPAX/src/main/resources/cytoscape/coreplugins/biopax/plugin.props
new file mode 100644
index 0000000..2fa8c69
--- /dev/null
+++ b/coreplugins/BioPAX/src/main/resources/cytoscape/coreplugins/biopax/plugin.props
@@ -0,0 +1,31 @@
+# This props file would be filled out and included in the plugin jar file. This props file will be used
+# to put information into the Plugin Manager about the plugin
+
+# -- The following properties are REQUIRED -- #
+
+# The plugin name that will be displayed to users
+pluginName=BioPAX
+
+# Description used to give users information about the plugin such as what it does.
+# Html tags are encouraged for formatting purposes.
+pluginDescription=Enables import of BioPAX formatted files.
+
+# Plugin version number, this must be two numbers separated by a decimlal. Ex. 0.2, 14.03
+pluginVersion=1.1
+
+# Compatible Cytoscape version
+cytoscapeVersion=2.8
+
+# Category, use one of the categories listed on the website or create your own
+pluginCategory=Core
+
+# List of authors. Note each author and institution pair are separated by a : (colon)
+# each additional author institution pair must be separated from other pairs by a ; (semicolon)
+pluginAuthorsIntsitutions=Ethan Cerami, Benjamin Gross and Chris Sander:Memorial Sloan-Kettering Cancer Center;B. Arman Aksoy:Gerstner Sloan-Kettering Graduate School;Rex Dwyer:Singenta;Gary Bader and Igor Rodchenkov:University of Toronto
+# Date this plugin/plugin version was released
+releaseDate=October 16, 2012
+
+# -- The following properties should be set ONLY BY CORE PLUGINS -- #
+downloadURL=http://cytoscape.org/plugins/plugins.xml
+uniqueID=2
+
diff --git a/coreplugins/BioPAX/src/main/resources/cytoscape/coreplugins/biopax/view/binary_legend.html b/coreplugins/BioPAX/src/main/resources/cytoscape/coreplugins/biopax/view/binary_legend.html
new file mode 100644
index 0000000..18ad884
--- /dev/null
+++ b/coreplugins/BioPAX/src/main/resources/cytoscape/coreplugins/biopax/view/binary_legend.html
@@ -0,0 +1,224 @@
+<table cellpadding="3" cellspacing="3" width="100%">
+<tr>
+ <td><h2>Visual Legend</h2></td>
+ <td align='RIGHT'><a href="filter">Filter Edges</a></td>
+ </tr>
+</table>
+
+<table cellpadding="3" cellspacing="3">
+<tr bgcolor="#DDDDDD">
+ <td VALIGN=CENTER>
+ <h3>Edge Type</h3>
+ </td>
+ <td VALIGN=CENTER>
+ <h3>Color</h3>
+ </td>
+</tr>
+
+<tr>
+ <td VALIGN=CENTER>
+ <span class="rule">IN_SAME_COMPONENT</span>
+ </td>
+ <td BGCOLOR="#ffff00" VALIGN=CENTER>
+
+ </td>
+</tr>
+<tr>
+ <td>
+ <span class='description'>
+ Edge is drawn if the first entity is a component of the second entity, which is a complex.
+ This interaction is transient in the sense that A COMPONENT_OF B and B COMPONENT_OF
+ C implies A COMPONENT_OF C. This interaction is undirected.
+ </span>
+ </td>
+ </tr>
+
+<tr>
+ <td VALIGN=CENTER>
+ <span class="rule">COMPONENT_OF</span>
+ </td>
+ <td BGCOLOR="#ffc000" VALIGN=CENTER>
+
+ </td>
+</tr>
+<tr>
+ <td>
+ <span class='description'>
+ Edge is drawn if two entities belong to at least one molecular complex.
+ This does not necessarily mean they interact directly. In a complex with n molecules, this rule
+ will create a clique composed of n(n-1)/2 interactions. This
+ interaction is directed.
+ </span>
+ </td>
+ </tr>
+
+<tr>
+ <td VALIGN=CENTER>
+ <span class="rule">CO_CONTROL_DEPENDENT_ANTI</span>
+ </td>
+ <td BGCOLOR="#ff0000" VALIGN=CENTER>
+
+ </td>
+</tr>
+<tr>
+ <td>
+ <span class='description'>
+ Edge is drawn if the first and second entities have control over
+ the same process, their control is dependent, i.e. one of them have effect over control
+ of the other one, and their effect is in different directions (one of them activates,
+ the other inhibits. This interaction is undirected."
+ </span>
+ </td>
+ </tr>
+
+<tr>
+ <td VALIGN=CENTER>
+ <span class="rule">CO_CONTROL_DEPENDENT_SIMILAR</span>
+ </td>
+ <td BGCOLOR="#00b050" VALIGN=CENTER>
+
+ </td>
+</tr>
+<tr>
+ <td>
+ <span class='description'>
+ Edge is drawn if the first and second entities have control over the
+ same process, their control is dependent, i.e. one of them have effect over control of
+ the other one, and their effect is in the same direction (both activates or both inhibits).
+ This interaction is undirected.
+ </span>
+ </td>
+ </tr>
+
+<tr>
+ <td VALIGN=CENTER>
+ <span class="rule">CO_CONTROL_INDEPENDENT_ANTI</span>
+ </td>
+ <td BGCOLOR="#fd95a6" VALIGN=CENTER>
+
+ </td>
+</tr>
+<tr>
+ <td>
+ <span class='description'>
+ Edge is drawn if the first and second entities have control over the
+ same process, their control is independent, i.e. they act without affecting each
+ other's activity, and their effect is in different directions (one of them activates,
+ the other inhibits. This interaction is undirected.
+ </span>
+ </td>
+ </tr>
+
+<tr>
+ <td VALIGN=CENTER>
+ <span class="rule">CO_CONTROL_INDEPENDENT_SIMILAR</span>
+ </td>
+ <td BGCOLOR="#92d050" VALIGN=CENTER>
+
+ </td>
+</tr>
+<tr>
+ <td>
+ <span class='description'>
+ Edge is drawn if the first and second entities have control over
+ the same process, their control is independent, i.e. they act without affecting each
+ other's activity, and their effect is in the same direction (both activates or both inhibits).
+ This interaction is undirected.
+ </span>
+ </td>
+ </tr>
+
+<tr>
+ <td VALIGN=CENTER>
+ <span class="rule">METABOLIC_CATALYSIS</span>
+ </td>
+ <td BGCOLOR="#00b0f0" VALIGN=CENTER>
+
+ </td>
+</tr>
+<tr>
+ <td>
+ <span class='description'>
+ Edge is drawn if the first entity catalyses a reaction that either
+ consumes or produces the second entity. More specifically, this rule
+ will find an interaction between two entities A and B if and only
+ if A controls a conversion which B participates and appears only on
+ the left or right side of the conversion but not both. This interaction is directed.
+ </span>
+ </td>
+ </tr>
+
+<tr>
+ <td VALIGN=CENTER>
+ <span class="rule">STATE_CHANGE</span>
+ </td>
+ <td BGCOLOR="#0070c0" VALIGN=CENTER>
+
+ </td>
+</tr>
+<tr>
+ <td>
+ <span class='description'>
+ Edge is drawn if the first entity catalyses a reaction that either
+ consumes or produces the second entity. More specifically, this rule
+ will find an interaction between two entities A and B if and only
+ if A controls a conversion which B participates and appears both on
+ the left or right side of the conversion. This interaction is directed.
+ </span>
+ </td>
+ </tr>
+
+<tr>
+ <td VALIGN=CENTER>
+ <span class="rule">REACTS_WITH</span>
+ </td>
+ <td BGCOLOR="#ccc1da" VALIGN=CENTER>
+
+ </td>
+</tr>
+<tr>
+ <td>
+ <span class='description'>
+ Edge is drawn if both A and B participates in a conversion as
+ substrates or products. Controllers are not included. This interaction is
+ undirected.
+ </span>
+ </td>
+ </tr>
+
+<tr>
+ <td VALIGN=CENTER>
+ <span class="rule">INTERACTS_WITH</span>
+ </td>
+ <td BGCOLOR="#7030a0" VALIGN=CENTER>
+
+ </td>
+</tr>
+<tr>
+ <td>
+ <span class='description'>
+ Edge is drawn if both A and B participates in an interaction as
+ participants. Controllers are not included. This interaction is undirected.
+ </span>
+ </td>
+ </tr>
+
+<tr>
+ <td VALIGN=CENTER>
+ <span class="rule">SEQUENTIAL_CATALYSIS</span>
+ </td>
+ <td BGCOLOR="#7f7f7f" VALIGN=CENTER>
+
+ </td>
+</tr>
+<tr>
+ <td>
+ <span class='description'>
+ Edge is drawn if A and B catalyzes two conversions that are connected
+ via a common molecule, and where potentially that common substrate
+ is produced by the former and consumed by the latter.
+ This interaction is directed.
+ </span>
+ </td>
+ </tr>
+</table>
\ No newline at end of file
diff --git a/coreplugins/BioPAX/src/main/resources/cytoscape/coreplugins/biopax/view/glasses.gif b/coreplugins/BioPAX/src/main/resources/cytoscape/coreplugins/biopax/view/glasses.gif
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diff --git a/coreplugins/BioPAX/src/main/resources/cytoscape/coreplugins/biopax/view/info.gif b/coreplugins/BioPAX/src/main/resources/cytoscape/coreplugins/biopax/view/info.gif
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diff --git a/coreplugins/BioPAX/src/main/resources/cytoscape/coreplugins/biopax/view/legend.gif b/coreplugins/BioPAX/src/main/resources/cytoscape/coreplugins/biopax/view/legend.gif
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diff --git a/coreplugins/BioPAX/src/main/resources/cytoscape/coreplugins/biopax/view/legend.html b/coreplugins/BioPAX/src/main/resources/cytoscape/coreplugins/biopax/view/legend.html
new file mode 100644
index 0000000..02fcbf8
--- /dev/null
+++ b/coreplugins/BioPAX/src/main/resources/cytoscape/coreplugins/biopax/view/legend.html
@@ -0,0 +1,286 @@
+<h2>Visual Legend</h2>
+
+<table cellpadding="3" cellspacing="3">
+<tr bgcolor="#DDDDDD">
+ <td VALIGN=CENTER>
+ <h3>Entity</h3>
+ </td>
+ <td VALIGN=CENTER>
+ <h3>Visual Shape</h3>
+ </td>
+</tr>
+<tr>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">Physical Entities, such as proteins and
+ small molecules, except for complexes.</FONT>
+ </td>
+ <td VALIGN=TOP>Ellipse</td>
+</tr>
+<tr>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">Complexes.</FONT>
+ </td>
+ <td VALIGN=TOP>Diamond</td>
+</tr>
+<tr>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">Interaction Entities, except controls, such as
+ biochemical reactions, etc.</FONT>
+ </td>
+ <td VALIGN=TOP>Square</td>
+</tr>
+<tr>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">Control Interactions (catalyses, modulations, etc.)</FONT>
+ </td>
+ <td VALIGN=TOP>Triangle</td>
+</tr>
+<tr bgcolor="#DDDDDD">
+ <td VALIGN=CENTER>
+ <h3>Edge Type</h3>
+ </td>
+ <td VALIGN=CENTER>
+ <h3>Arrow Shape</h3>
+ </td>
+</tr>
+<tr>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">Inhibition</FONT>
+ </td>
+ <td VALIGN=TOP>Black T-shape arrow</td>
+</tr>
+<tr>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">Containment, e.g. a complex can
+ contain one or more proteins.</FONT>
+ </td>
+ <td VALIGN=TOP>Black circle arrow</td>
+</tr>
+<tr>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">All other edge types, e.g. activation,
+ left, right, etc.</FONT>
+ </td>
+ <td VALIGN=TOP>Black arrow</td>
+</tr>
+<tr bgcolor="#DDDDDD">
+ <td VALIGN=CENTER COLSPAN=2>
+ <h3>Labels for Physical Entities</h3>
+ </td>
+</tr>
+<tr>
+ <td VALIGN=TOP colspan=2>
+ <FONT FACE="ARIAL">All physical entities will be labeled as follows:</FONT>
+ </td>
+</tr>
+<tr>
+ <td VALIGN=TOP colspan=2>
+ <FONT FACE="ARIAL">[NAME] [-CHEMICAL MODIFICATION ABBR] [(CELLULAR LOCATION ABBR)]</FONT>
+ </td>
+</tr>
+<tr>
+ <td VALIGN=TOP colspan=2>
+ <FONT FACE="ARIAL">where [CHEMICAL MODIFICATION ABBR] and [CELLULAR LOCATION ABBR]
+ are one of the abbreviations described below.</FONT>
+ </td>
+</tr>
+<tr bgcolor="#DDDDDD">
+ <td VALIGN=CENTER colspan=2>
+ <h3>Examples</h3>
+ </td>
+</tr>
+<tr>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">MITF</FONT>
+ </td>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">MITF</FONT>
+ </td>
+</tr>
+<tr>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">MITF Phosphorylated</FONT>
+ </td>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">MITF-P</FONT>
+ </td>
+</tr>
+<tr>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">MITF Phosphorylated, in the cytoplasm</FONT>
+ </td>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">MITF-P (CP)</FONT>
+ </td>
+</tr>
+<tr bgcolor="#DDDDDD">
+ <td VALIGN=CENTER colspan=2>
+ <h3>Abbreviations for Chemical Modifications</h3>
+ </td>
+</tr>
+<tr>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">acetylated</FONT>
+ </td>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">A</FONT>
+ </td>
+</tr>
+<tr>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">glycosylated</FONT>
+ </td>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">G</FONT>
+ </td>
+</tr>
+<tr>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">phosphorylated</FONT>
+ </td>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">P</FONT>
+ </td>
+</tr>
+<tr>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">proteolytic cleavage</FONT>
+ </td>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">PCS</FONT>
+ </td>
+</tr>
+<tr>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">sumoylated</FONT>
+ </td>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">S</FONT>
+ </td>
+</tr>
+<tr>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">ubiquitinated</FONT>
+ </td>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">U</FONT>
+ </td>
+</tr>
+<tr>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">[All others]</FONT>
+ </td>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">No Abbreviation provided</FONT>
+ </td>
+</tr>
+<tr bgcolor="#DDDDDD">
+ <td VALIGN=CENTER COLSPAN=2>
+ <h3>Abbreviations for Cellular Locations</h3>
+ </td>
+</tr>
+<tr>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">centrosome</FONT>
+ </td>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">CE</FONT>
+ </td>
+</tr>
+<tr>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">cytoplasm</FONT>
+ </td>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">CY</FONT>
+ </td>
+</tr>
+<tr>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">endoplasmic reticulum</FONT>
+ </td>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">ER</FONT>
+ </td>
+</tr>
+<tr>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">endosome</FONT>
+ </td>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">EN</FONT>
+ </td>
+</tr>
+<tr>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">extracellular matrix</FONT>
+ </td>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">EM</FONT>
+ </td>
+</tr>
+<tr>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">golgi apparatus</FONT>
+ </td>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">GA</FONT>
+ </td>
+</tr>
+<tr>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">mitochondrion</FONT>
+ </td>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">MI</FONT>
+ </td>
+</tr>
+<tr>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">nucleoplasm</FONT>
+ </td>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">NP</FONT>
+ </td>
+</tr>
+<tr>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">nucleus</FONT>
+ </td>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">NU</FONT>
+ </td>
+</tr>
+<tr>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">plasma membrane</FONT>
+ </td>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">PM</FONT>
+ </td>
+</tr>
+<tr>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">ribosome</FONT>
+ </td>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">RI</FONT>
+ </td>
+</tr>
+<tr>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">transmembrane</FONT>
+ </td>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">TM</FONT>
+ </td>
+</tr>
+<tr>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">[All others]</FONT>
+ </td>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">No Abbreviation provided</FONT>
+ </td>
+</tr>
+</table>
\ No newline at end of file
diff --git a/coreplugins/BioPAX/src/main/resources/cytoscape/coreplugins/biopax/view/legend.png b/coreplugins/BioPAX/src/main/resources/cytoscape/coreplugins/biopax/view/legend.png
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diff --git a/coreplugins/BioPAX/src/main/resources/cytoscape/coreplugins/biopax/view/read_obj.gif b/coreplugins/BioPAX/src/main/resources/cytoscape/coreplugins/biopax/view/read_obj.gif
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diff --git a/coreplugins/BioPAX/src/main/resources/log4j.properties b/coreplugins/BioPAX/src/main/resources/log4j.properties
new file mode 100644
index 0000000..73ac4b4
--- /dev/null
+++ b/coreplugins/BioPAX/src/main/resources/log4j.properties
@@ -0,0 +1,11 @@
+# Set root logger level to DEBUG and its only appender to A1.
+log4j.rootLogger=WARN, A1
+
+# A1 is set to be a ConsoleAppender.
+log4j.appender.A1=org.apache.log4j.ConsoleAppender
+
+# A1 uses PatternLayout.
+log4j.appender.A1.layout=org.apache.log4j.PatternLayout
+log4j.appender.A1.layout.ConversionPattern=%-4r [%t] %-5p %c %x - %m%n
+
+#log4j.logger.org.biopax.paxtools = FATAL
\ No newline at end of file
diff --git a/coreplugins/BioPAX/src/site/resources/README.html b/coreplugins/BioPAX/src/site/resources/README.html
new file mode 100644
index 0000000..7279eea
--- /dev/null
+++ b/coreplugins/BioPAX/src/site/resources/README.html
@@ -0,0 +1,466 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html>
+<head>
+ <title>Cytoscape BioPAX Import PlugIn: READ ME</title>
+</head>
+<body style="font-family:Arial, Helvetica, sans-serif;
+ font-size: 11pt;">
+<h2>Cytoscape BioPAX Import PlugIn</h2>
+<h3>1. Introduction</h3> The BioPAX plugin enables Cytoscape to import BioPAX formatted documents. BioPAX is a collaborative effort to create a data exchange format for biological pathway data. Information is available at: <a href="http://biopax.org">http://biopax.org</a>.
+<p>
+ Updates regarding this plugin will be posted to the Cytoscape-announce mailing list. You can easily <a href="http://groups.google.com/group/cytoscape-announce/subscribe">subscribe</a> to the mailing list or <a href="http://groups.google.com/group/cytoscape-announce">browse the archives</a>.
+</p>
+<h3>2. PlugIn Installation Instructions [See The Latest Release Notes!]</h3> This release contains the following directory structure: <pre>
++
+|---biopax_XXX.jar JAR Files containing the BioPAX PlugIn
+|
++---docs/README.html This README File.
+|
++---test-resources A directory of sample BioPAX documents,
+| including sample files from <a href="http://www.reactome.org">Reactome</a>,
+| and <a href="http://ecocyc.org/">Ecocyc</a>.
+|
++---src Complete Source Code
+</pre>
+<p>
+ To use the BioPAX Plugin, you must first obtain a copy of <a href="http://www.cytoscape.org">Cytoscape</a>.
+</p>
+<p>
+ Once you have downloaded Cytoscape and verified that it works, install the BioPAX PlugIn as follows:
+</p>
+<ul>
+ <li>
+ Delete any previous biopax_XXX_YYY.jar files from your [Cytoscape_Home]/plugins directory.
+ </li>
+ <li>
+ Copy all the biopax_XXX_YYY.jar files to your [Cytoscape_Home]/plugins directory.
+ </li>
+</ul>
+<h3>3. Using the BioPAX PlugIn</h3>
+<ul>
+ <li>
+ Start Cytoscape. For example, run: ./cytoscape.sh or cytoscape.bat.
+ </li>
+ <li>
+ Select "PlugIns" from the Main Menu. Then, select "Import BioPAX Document from file..."
+ </li>
+ <li>
+ Choose one of the sample BioPAX files in the test-resources directory. For example, load the Reactome Apoptosis.owl file. The PlugIn will load and render the specified file.
+ </li>
+ <li>
+ Click on any individual node to view BioPAX details.
+ </li>
+</ul>
+Below is a sample screenshot of the apoptosis pathway:
+<p>
+ <a href="images/apoptosis.png"><img alt="Sample Screenshot of the BioPAX PlugIn" src="images/apoptosis_thumb.png" border="0"></a>
+ <br>
+ <font size="-1">[<a href="images/apoptosis.png">Click to enlarge</a>]</font>
+</p>
+
+<h3>4. Understanding Visual Rendering Clues</h3>By default, the Expression Viewer PlugIn renders nodes and edges as follows:
+<p>
+</p>
+<table cellpadding="3" cellspacing="3">
+ <tbody><tr bgcolor="#dddddd">
+ <td>
+ Entity
+ </td>
+ <td>
+ Visual Shape
+ </td>
+ </tr>
+ <tr>
+ <td>
+ Proteins, small molecules, complexes and other physical entities (as defined in the <a href="http://biopax.org">BioPAX pathway format</a>).
+ </td>
+ <td>
+ <img alt="Ellipse Shape" src="images/ellipse.jpg">
+ </td>
+ </tr>
+ <tr>
+ <td>
+ Conversions, biochemical reactions, modulations and other interaction entities (as defined in the <a href="http://biopax.org">BioPAX pathway format</a>).
+ </td>
+ <td>
+ <img alt="Square Shape" src="images/square.jpg">
+ </td>
+ </tr>
+ <tr bgcolor="#dddddd">
+ <td>
+ Interaction Type
+ </td>
+ <td>
+ Arrow Shape
+ </td>
+ </tr>
+ <tr>
+ <td>
+ Inhibition
+ </td>
+ <td>
+ <img alt="Black inhibition arrow type" src="images/BLACK_T.jpg">
+ </td>
+ </tr>
+ <tr>
+ <td>
+ Containment, e.g. a complex can contain one or more proteins.
+ </td>
+ <td>
+ <img alt="Black circle arrow type" src="images/BLACK_CIRCLE.jpg">
+ </td>
+ </tr>
+ <tr>
+ <td>
+ All other interaction types, e.g. activation, left, right, etc.
+ </td>
+ <td>
+ <img alt="Black arrow type" src="images/BLACK_DELTA.jpg">
+ </td>
+ </tr>
+ <tr bgcolor="#DDDDDD">
+ <td colspan=2 VALIGN=TOP COLSPAN="2">
+ <FONT FACE="ARIAL">Labels for Physical Entities</FONT>
+ </td>
+ </tr>
+ <tr>
+ <td colspan=2 VALIGN=TOP>
+ <FONT FACE="ARIAL">All physical entities will be labeled as follows:</FONT>
+ </td>
+ </tr>
+ <tr>
+ <td colspan=2 VALIGN=TOP NOWRAP>
+ <FONT FACE="ARIAL" SIZE="2">[NAME] [-CHEMICAL_MODIFICATION_ABBR] [(CELULAR_LOCATION_ABBR)]</FONT>
+ </td>
+ </tr>
+ <tr>
+ <td colspan=2 VALIGN=TOP>
+ <FONT FACE="ARIAL">where [NAME] is determined by the following order of precedence: NAME, SHORT NAME, or Shortest Synonym,</FONT>
+ </td>
+ </tr>
+ <tr>
+ <td colspan=2 VALIGN=TOP>
+ <FONT FACE="ARIAL">and [CHEMICAL_MODIFICATION_ABBR] and [CELLULAR_LOCATION_ABBR] are one of the abbreviations described below.</FONT>
+ </td>
+ </tr>
+ <tr bgcolor="#DDDDDD">
+ <td colspan=2 VALIGN=TOP COLSPAN="2">
+ <FONT FACE="ARIAL">Example:</FONT>
+ </td>
+ </tr>
+ <tr>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">MITF:</FONT>
+ </td>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">MITF</FONT>
+ </td>
+ </tr>
+ <tr>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">MITF Phosphorylated:</FONT>
+ </td>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">MITF-P</FONT>
+ </td>
+ </tr>
+ <tr>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">MITF Phosphorylated, in the cytoplasm:</FONT>
+ </td>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">MITF-P (CP)</FONT>
+ </td>
+ </tr>
+ <tr bgcolor="#DDDDDD">
+ <td VALIGN=TOP colspan=2>
+ <FONT FACE="ARIAL"><b>Abbreviations for Chemical Modifications</b></FONT>
+ </td>
+ </tr>
+ <tr>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">acetylated</FONT>
+ </td>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">A</FONT>
+ </td>
+ </tr>
+ <tr>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">glycosylated</FONT>
+ </td>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">G</FONT>
+ </td>
+ </tr>
+ <tr>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">phosphorylated</FONT>
+ </td>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">P</FONT>
+ </td>
+ </tr>
+ <tr>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">proteolytic cleavage</FONT>
+ </td>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">PCS</FONT>
+ </td>
+ </tr>
+ <tr>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">sumoylated</FONT>
+ </td>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">S</FONT>
+ </td>
+ </tr>
+ <tr>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">ubiquitinated</FONT>
+ </td>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">U</FONT>
+ </td>
+ </tr>
+ <tr>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">[All others]</FONT>
+ </td>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">No Abbreviation provided</FONT>
+ </td>
+ </tr>
+ <tr bgcolor="#DDDDDD">
+ <td VALIGN=TOP COLSPAN="2">
+ <FONT FACE="ARIAL">Abbreviations for Cellular Locations</FONT>
+ </td>
+ </tr>
+ <tr>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">cellular component unknown</FONT>
+ </td>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">No Abbreviation will be provided.</FONT>
+ </td>
+ </tr>
+ <tr>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">centrosome</FONT>
+ </td>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">CE</FONT>
+ </td>
+ </tr>
+ <tr>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">cytoplasm</FONT>
+ </td>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">CY</FONT>
+ </td>
+ </tr>
+ <tr>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">endoplasmic reticulum</FONT>
+ </td>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">ER</FONT>
+ </td>
+ </tr>
+ <tr>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">endosome</FONT>
+ </td>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">EN</FONT>
+ </td>
+ </tr>
+ <tr>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">extracellular</FONT>
+ </td>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">EM</FONT>
+ </td>
+ </tr>
+ <tr>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">golgi apparatus</FONT>
+ </td>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">GA</FONT>
+ </td>
+ </tr>
+ <tr>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">mitochondrion</FONT>
+ </td>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">MI</FONT>
+ </td>
+ </tr>
+ <tr>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">nucleus</FONT>
+ </td>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">NU</FONT>
+ </td>
+ </tr>
+ <tr>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">plasma membrane</FONT>
+ </td>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">PM</FONT>
+ </td>
+ </tr>
+ <tr>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">ribosome</FONT>
+ </td>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">RI</FONT>
+ </td>
+ </tr>
+ <tr>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">[All others]</FONT>
+ </td>
+ <td VALIGN=TOP>
+ <FONT FACE="ARIAL">No Abbreviation will be provided.</FONT>
+ </td>
+ </tr>
+</tbody></table>
+
+<h3>5. Bugs / Feature Requests</h3> If you encounter a bug with this plugin,
+email Ethan Cerami or Benjamin Gross at the address(es) below, or log a bug directly to
+the <a href="http://www.cbio.mskcc.org/cytoscape/bugs/">Cytoscape Bug Tracker</a>.
+
+<h3>6. Contacts</h3>
+<p>
+ Sander Group, <a href="http://www.cbio.mskcc.org/">Computational Biology Center</a>
+ <br>
+ <a href="http://www.mskcc.org">Memorial Sloan-Kettering Cancer Center</a>, New York City
+ <br>
+</p>
+<p>
+ For any questions concerning this plugin, please contact:
+</p>
+<p>
+ Ethan Cerami: cerami AT cbio.mskcc.org
+ <br>
+ Benjamin Gross: grossb AT cbio.mskcc.org
+</p>
+<p>
+ This software is made available under the <a href="http://www.gnu.org/licenses/lgpl.html">LGPL (Lesser General Public License)</a>.
+</p>
+<h3>7. Release Notes / Current Limitations</h3>
+<p>
+ Version: 0.1
+</p>
+<ul>
+ <li>
+ Date: June 24, 2005
+ </li>
+ <li>
+ Features:
+ <ul>
+ <li>
+ Enables Cytoscape users to load and visually render BioPAX Files from the Web or a local file system.
+ </li>
+ <li>
+ Supports BioPAX Levels 1 and 2.
+ </li>
+ <li>
+ Includes a sample visual style file for visually rendering different BioPAX entities. For example, proteins are rendered as square green nodes, and biochemical reactions are rendered as red, round rectangle nodes, etc. The style can be further modified by the end user.
+ </li>
+ <li>
+ Works with Cytoscape 2.1.
+ </li>
+ <li>
+ Distribution includes sample BioPAX files for quick demos, and complete source code.
+ </li>
+ <li>
+ Verified to work with moderate size BioPAX files. For example, the PlugIn will parse a 504KB BioPAX document with 340 nodes and 470 edges in 700 ms. The PlugIn has not yet been tested with larger files.
+ </li>
+ <li>
+ Small download (~100KB). Easy to install.
+ </li>
+ </ul>
+ </li>
+</ul>
+<p>
+ Version: 0.2 (requires Cytoscape v2.2)
+</p>
+<ul>
+ <li>
+ Date: August 10, 2005
+ </li>
+ <li>
+ Features:
+ <ul>
+ <li>
+ User can now click on any node and view BioPAX details in a separate pop-up window.
+ </li>
+ <li>
+ Easy 1-step installation. (No need to install the BioPAX visual style file separately).
+ </li>
+ <li>
+ External Links are now viewable in an external web browser.
+ </li>
+ <li>
+ Simplified visual rendering clues for nodes and edges.
+ </li>
+ <li>
+ Numerous bug fixes.
+ </li>
+ <li>
+ Now supports BioPAX Complexes.
+ </li>
+ </ul>
+ </li>
+</ul>
+<p>
+ Version: 0.3 (requires Cytoscape v2.3 or greater)
+</p>
+<ul>
+ <li>
+ Date: June 16, 2006
+ </li>
+ <li>
+ Features:
+ <ul>
+ <li>
+ Includes Simplified Visual Language to describe Biological Pathways.
+ </li>
+ </ul>
+ </li>
+</ul>
+<p>
+ Version: 0.7 (requires Cytoscape v2.7 or greater)
+</p>
+<ul>
+ <li>
+ Date: January 29, 2010
+ </li>
+ <li>
+ Features:
+ <ul>
+ <li>
+ Since version 0.5, it is core plugin (included in Cytoscape distributions). Supports BioPAX Level 3, uses PaxTools v2.0 library.
+ </li>
+ </ul>
+ </li>
+</ul>
+Known Limitations / Known Bugs:
+<ul>
+ <li>
+ Single COFACTORs are supported, but multiple COFACTORS are not supported. In the case of multiple COFACTORS, an explicit warning will be generated.
+ </li>
+</ul>
+</body>
+</html>
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--- /dev/null
+++ b/coreplugins/BioPAX/src/site/resources/index.html
@@ -0,0 +1,254 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html>
+<head>
+ <meta name="keywords" content="BioPAX pathway biopathway biopax open openbiopathways source database biological biology collaboration OBP group information resource KEGG BIND ECOCYC BIOCYC METACYC WIT WIT2 MIPS BIOCARTA BBID BIOBASE BMPH CSNDB CST DIP EMP MINT PATHDB PUBGENE SPAD PARIS OPENPARIS bioinformatics computational">
+ <meta name="copyright" content="copyright 2003-2009 BioPAX.org">
+ <meta http-equiv="content-type" content="text/html; charset=ISO-8859-1">
+ <title>BioPAX Cytoscape PlugIn</title>
+ <link rel="stylesheet" href="http://www.biopax.org/css/biopax.css" type="text/css">
+<script>
+ function openpopup(){
+ var popurl="SiteHistory.html"
+ winpops=window.open(popurl,"","width=500,height=200,scrollbars")
+ }
+ </script>
+</head>
+<body bgcolor="#ccccff" marginwidth="0" marginheight="0" leftmargin="0" topmargin="0" text="#ffffff">
+<div id="TitleBar">
+ <br>
+ <br>
+ <table cellpadding="2" cellspacing="2" border="0" width="100%">
+ <tr>
+ <td valign="Top" align="Right" bgcolor="#9999cc" nowrap>
+ <big><big><font face="Helvetica, Arial, sans-serif"><b><font color="#ffffff"> BioPAX : <font color="#333366">Biological Pathways Exchange</font> </font></b></font></big></big>
+ <br>
+ </td>
+ </tr>
+ <tr>
+ <td valign="Top" align="Right" bgcolor="#333366">
+ <table>
+ <tbody>
+ <tr>
+ <td valign="Top" bgcolor="#333366" nowrap>
+ <div align="Right">
+ <a href="http://www.biopax.org/index.html" class="HereSideBarLinks"> Home </a>
+ </div>
+ </td>
+ <td>
+
+ </td>
+ <td valign="Top" bgcolor="#333366" nowrap>
+ <div align="Right">
+ <a href="http://www.biopax.org/About.html" class="ThereSideBarLinks"> About </a>
+ </div>
+ </td>
+ <td>
+
+ </td>
+ <td valign="Top" bgcolor="#333366" nowrap>
+ <div align="Right">
+ <a href="http://www.biopax.org/Download.html" class="ThereSideBarLinks"> Download </a>
+ </div>
+ </td>
+ <td>
+
+ </td>
+ <td valign="Top" bgcolor="#333366" nowrap>
+ <div align="Right">
+ <a href="http://www.biopax.org/Documents.html" class="ThereSideBarLinks"> Documents </a>
+ </div>
+ </td>
+ <td>
+
+ </td>
+ <td valign="Top" bgcolor="#333366" nowrap>
+ <div align="Right">
+ <a href="http://www.biopax.org/Community.html" class="ThereSideBarLinks"> Community </a>
+ </div>
+ </td>
+ <td>
+
+ </td>
+ <td valign="Top" bgcolor="#333366" nowrap>
+ <div align="Right">
+ <a href="http://www.biopax.org/Development.html" class="ThereSideBarLinks"> Development </a>
+ </div>
+ </td>
+ <td>
+
+ </td>
+ </tr>
+ </tbody>
+ </table>
+ </td>
+ </tr>
+ </table>
+</div>
+<div id="ContentTop">
+ <table width="100%" cellpadding="0" cellspacing="2">
+ <tr>
+ <td bgcolor="#ffcc00" width="1%">
+ <table width="1%" cellpadding="10" cellspacing="0">
+ <tr>
+ <td width="1%">
+ <br>
+ </td>
+ </tr>
+ </table>
+ </td>
+ <td bgcolor="#666699">
+ <table width="100%" cellpadding="10" cellspacing="0">
+ <tr>
+ <td bgcolor="#666699">
+
+ <br>
+ <br>
+ <br>
+ <br>
+ <br>
+ <br>
+ <br>
+ </td>
+ </tr>
+ </table>
+ </td>
+ </tr>
+ </table>
+</div>
+<div id="ContentPane">
+ <table width="100%" cellpadding="0" cellspacing="2">
+ <tr>
+ <td bgcolor="#ffcc00" width="1%">
+ <table width="1%" cellpadding="10" cellspacing="0">
+ <tr>
+ <td width="1%">
+ <br>
+ </td>
+ </tr>
+ </table>
+ </td>
+ <td bgcolor="#666699">
+ <table width="100%" cellpadding="10" cellspacing="0">
+ <tr>
+ <td bgcolor="#666699">
+ <u><font face="Helvetica, Arial, sans-serif"><b><font color="#ffffff"><big>BioPAX Cytoscape PlugIn</big></font></b></font></u>
+ <p>
+ <b>Version 0.7 of the <a href="http://www.cytoscape.org">Cytoscape</a> BioPAX PlugIn is now available. </b>
+ <br>
+ <b>(requires Cytoscape v2.6 or greater)</b>
+ <br>
+ <br>
+ </p>
+ <table width="100%" cellspacing="0" bordercolor="#ffcc00" border="1" cellpadding="5">
+ <tr bgcolor="#333366">
+ <th>
+ BioPAX PlugIn Features
+ </th>
+ </tr>
+ <tr bgcolor="#666699">
+ <td>
+ <ul>
+ <li>
+ Enables Cytoscape users to load and visually render BioPAX files from the web or a local file system.
+ </li>
+ <li>
+ Supports All BioPAX Levels.
+ </li>
+ <li>
+ User can click on any node and immediately view BioPAX details about that node. When possible, links are provided to external resources, such as <a href="http://www.pir.uniprot.org/">UniProt</a>, <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi">PubMed</a>, <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene">Entrez Gene</a>, <a href="http://www.godatabase.org/cgi-bin/amigo/go.cgi">AmiGo</a> (Gene Ontology), and <a href="http://www.pdg.cnb.uam.es/UniPub/iHOP/ [...]
+ </li>
+ <li>
+ Default visual style automatically maps BioPAX entity types to specific shapes. For example, physical entities, such as proteins are represented as circles, whereas interaction entities are represented as diamonds, etc.
+ </li>
+ <li>
+ Distribution includes sample BioPAX documents, including sample files from <a href="http://www.reactome.org">Reactome</a>, and <a href="http://ecocyc.org/">Ecocyc</a>.
+ </li>
+ <li>
+ Verified to work with moderate size BioPAX files. For example, the PlugIn will parse a 504KB BioPAX document with 340 nodes and 470 edges in 700 ms.
+ </li>
+ <li>
+ Includes new Simplified Visual Language support.
+ </li>
+ <li>
+ Small download. Easy 1-step installation.
+ </li>
+ </ul>
+ </td>
+ </tr>
+ </table>
+ <br>
+ <br>
+ <table width="100%" cellspacing="0" bordercolor="#ffcc00" border="1" cellpadding="5">
+ <tr bgcolor="#333366">
+ <th>
+ Sample Screenshot
+ </th>
+ </tr>
+ <tr>
+ <td>
+ <table width="100%">
+ <tr>
+ <td>
+ <center>
+ <a href="images/apoptosis.png"><img border="0" title="Click for Larger Image" src="images/apoptosis_thumb.png" alt="Sample Screenshot of the BioPAX PlugIn"></a>
+ <br>
+ <font size="-1">[Click Image to Enlarge]</font>
+ </center>
+ </td>
+ </tr>
+ </table>
+ </td>
+ </tr>
+ </table>
+ <br>
+ <br>
+ <table width="100%" cellspacing="0" bordercolor="#ffcc00" border="1" cellpadding="5">
+ <tr bgcolor="#333366">
+ <th>
+ Download
+ </th>
+ </tr>
+ <tr bgcolor="#666699">
+ <td>
+ Version 0.7 (requires Cytoscape v2.6 or greater) <font color="black">*</font>
+ <ul>
+ <li>
+ Mac OS X / Linux Users: Download <a href="zip_release/biopax_0_7.tar.gz">biopax_0_7.tar.gz</a>
+ </li>
+ <li>
+ Windows Users: Download <a href="zip_release/biopax_0_7.zip">biopax_0_7.zip</a>
+ </li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td><font color="black"></font></td>
+ </tr>
+ </table>
+ <br>
+ <br>
+ <table width="100%" cellspacing="0" bordercolor="#ffcc00" border="1" cellpadding="5">
+ <tr bgcolor="#333366">
+ <th>
+ README File / Installation Instructions
+ </th>
+ </tr>
+ <tr bgcolor="#666699">
+ <td>
+ View the <a href="README.html">README.html</a> included in the download distribution.
+ </td>
+ </tr>
+ </table>
+ <br>
+ <center>
+ <big><i>The BioPAX project is funded in part by U.S. Department of Energy Workshop Grant #DE-FG02-04ER63931</i></big>
+ </center>
+ </td>
+ </tr>
+ </table>
+ </td>
+ </tr>
+ </table>
+</div>
+</body>
+</html>
diff --git a/coreplugins/BioPAX/src/test/java/cytoscape/coreplugins/biopax/TestBioPaxFilter.java b/coreplugins/BioPAX/src/test/java/cytoscape/coreplugins/biopax/TestBioPaxFilter.java
new file mode 100644
index 0000000..876fe14
--- /dev/null
+++ b/coreplugins/BioPAX/src/test/java/cytoscape/coreplugins/biopax/TestBioPaxFilter.java
@@ -0,0 +1,59 @@
+// $Id: TestExternalLinkUtil.java,v 1.11 2006/06/15 22:07:49 grossb Exp $
+//------------------------------------------------------------------------------
+/** Copyright (c) 2006 Memorial Sloan-Kettering Cancer Center.
+ **
+ ** Code written by: Ethan Cerami, Benjamin Gross.
+ ** Authors: Ethan Cerami, Gary Bader, Chris Sander
+ **
+ ** This library is free software; you can redistribute it and/or modify it
+ ** under the terms of the GNU Lesser General Public License as published
+ ** by the Free Software Foundation; either version 2.1 of the License, or
+ ** any later version.
+ **
+ ** This library is distributed in the hope that it will be useful, but
+ ** WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ ** MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ ** documentation provided hereunder is on an "as is" basis, and
+ ** Memorial Sloan-Kettering Cancer Center
+ ** has no obligations to provide maintenance, support,
+ ** updates, enhancements or modifications. In no event shall
+ ** Memorial Sloan-Kettering Cancer Center
+ ** be liable to any party for direct, indirect, special,
+ ** incidental or consequential damages, including lost profits, arising
+ ** out of the use of this software and its documentation, even if
+ ** Memorial Sloan-Kettering Cancer Center
+ ** has been advised of the possibility of such damage. See
+ ** the GNU Lesser General Public License for more details.
+ **
+ ** You should have received a copy of the GNU Lesser General Public License
+ ** along with this library; if not, write to the Free Software Foundation,
+ ** Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ **/
+package cytoscape.coreplugins.biopax;
+
+import junit.framework.TestCase;
+
+import cytoscape.coreplugins.biopax.BioPaxFilter;
+
+
+/**
+ * Tests the BioPax Import Wrapper, which integrates BioPax with the Cytoscape ImportHandler.
+ *
+ * @author Ethan Cerami.
+ */
+public class TestBioPaxFilter extends TestCase {
+ /**
+ * Tests the BioPaxFilter class.
+ */
+ public void testBioPaxFilter() {
+ BioPaxFilter filter = new BioPaxFilter();
+
+ // This should be accepted
+ boolean acceptFlag = filter.accept(getClass().getResource("/biopax_sample1.owl").getFile());
+ assertEquals(true, acceptFlag);
+
+ // This should be rejected
+ acceptFlag = filter.accept(getClass().getResource("/psi_sample1.xml").getFile());
+ assertEquals(false, acceptFlag);
+ }
+}
diff --git a/coreplugins/BioPAX/src/test/java/cytoscape/coreplugins/biopax/TestBioPaxUtil.java b/coreplugins/BioPAX/src/test/java/cytoscape/coreplugins/biopax/TestBioPaxUtil.java
new file mode 100644
index 0000000..bdbb0a6
--- /dev/null
+++ b/coreplugins/BioPAX/src/test/java/cytoscape/coreplugins/biopax/TestBioPaxUtil.java
@@ -0,0 +1,103 @@
+// $Id: TestBioPaxUtil.java,v 1.8 2006/06/15 22:06:02 grossb Exp $
+//------------------------------------------------------------------------------
+/** Copyright (c) 2006 Memorial Sloan-Kettering Cancer Center.
+ **
+ ** Code written by: Ethan Cerami
+ ** Authors: Ethan Cerami, Gary Bader, Chris Sander
+ **
+ ** This library is free software; you can redistribute it and/or modify it
+ ** under the terms of the GNU Lesser General Public License as published
+ ** by the Free Software Foundation; either version 2.1 of the License, or
+ ** any later version.
+ **
+ ** This library is distributed in the hope that it will be useful, but
+ ** WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ ** MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ ** documentation provided hereunder is on an "as is" basis, and
+ ** Memorial Sloan-Kettering Cancer Center
+ ** has no obligations to provide maintenance, support,
+ ** updates, enhancements or modifications. In no event shall
+ ** Memorial Sloan-Kettering Cancer Center
+ ** be liable to any party for direct, indirect, special,
+ ** incidental or consequential damages, including lost profits, arising
+ ** out of the use of this software and its documentation, even if
+ ** Memorial Sloan-Kettering Cancer Center
+ ** has been advised of the possibility of such damage. See
+ ** the GNU Lesser General Public License for more details.
+ **
+ ** You should have received a copy of the GNU Lesser General Public License
+ ** along with this library; if not, write to the Free Software Foundation,
+ ** Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ **/
+package cytoscape.coreplugins.biopax;
+
+import java.io.FileInputStream;
+
+import junit.framework.TestCase;
+
+import org.biopax.paxtools.model.Model;
+import org.biopax.paxtools.model.level3.Interaction;
+import org.biopax.paxtools.model.level3.Pathway;
+import org.biopax.paxtools.model.level3.PhysicalEntity;
+
+import cytoscape.coreplugins.biopax.util.BioPaxUtil;
+
+
+/**
+ * Tests the BioPaxUtil Class.
+ *
+ * @author Ethan Cerami; updated by Igor Rodchenkov
+ */
+public class TestBioPaxUtil extends TestCase {
+ /**
+ * Tests the BioPAX Utility Class.
+ *
+ * @throws Exception All Exceptions.
+ */
+ public void testUtil() throws Exception {
+ Model model = BioPaxUtil.read(new FileInputStream(getClass().getResource("/biopax_sample1.owl").getFile()));
+ // Validate Number of Entities
+ assertNotNull(model);
+ assertEquals(8, model.getObjects(PhysicalEntity.class).size());
+ assertEquals(4, model.getObjects(Interaction.class).size());
+ assertEquals(1, model.getObjects(Pathway.class).size());
+ }
+
+ /**
+ * Tests the BioPAX Utility Class on a second sample data file.
+ *
+ * @throws Exception All Exceptions.
+ */
+ /* TODO re-factor because BioPaxUtil.getParentPathwayName is removed
+ public void testUtil2() throws Exception {
+ Model model = BioPaxUtil.readFile("src/test/resources/biopax_complex.owl");
+ Set<String> pathways = BioPaxUtil.getParentPathwayName(
+ model.getByID("http://cbio.mskcc.org/cpath#CPATH-124"), model);
+ System.out.println("PARENT PROCESSes NAMES: " + pathways);
+ assertTrue(pathways.size()==0);
+ }
+ /
+
+ /**
+ * Tests the BioPAX Utility Class on a third sample data file.
+ * <p/>
+ * This tests a specially modified version of the Apoptosis pathway
+ * that contains one real pathway, and one "dummy" duplicate pathway.
+ * <p/>
+ * It provides a test case for entities, which can be members of multiple
+ * pathways at once.
+ *
+ * @throws Exception All Exceptions.
+ */
+ /* TODO re-factor because BioPaxUtil.getParentPathwayName is removed
+ public void testUtil3() throws Exception {
+ Model model = BioPaxUtil.readFile("src/test/resources/Apoptosis.owl");
+ String pathways = BioPaxUtil.getParentPathwayName(
+ model.getByID("http://www.biopax.org/examples/apoptosis#Pubmed_7530336"), model)
+ .toString();
+ System.out.println("PARENT PW NAMES: " + pathways);
+ assertTrue(pathways.contains("FasL/ CD95L signaling"));
+ }
+ */
+
+}
diff --git a/coreplugins/BioPAX/src/test/java/cytoscape/coreplugins/biopax/TestMapBioPaxToCytoscape.java b/coreplugins/BioPAX/src/test/java/cytoscape/coreplugins/biopax/TestMapBioPaxToCytoscape.java
new file mode 100644
index 0000000..9939b15
--- /dev/null
+++ b/coreplugins/BioPAX/src/test/java/cytoscape/coreplugins/biopax/TestMapBioPaxToCytoscape.java
@@ -0,0 +1,281 @@
+// $Id: TestMapBioPaxToCytoscape.java,v 1.15 2006/06/20 20:31:41 grossb Exp $
+//------------------------------------------------------------------------------
+/** Copyright (c) 2006 Memorial Sloan-Kettering Cancer Center.
+ **
+ ** Code written by: Ethan Cerami
+ ** Authors: Ethan Cerami, Gary Bader, Chris Sander
+ **
+ ** This library is free software; you can redistribute it and/or modify it
+ ** under the terms of the GNU Lesser General Public License as published
+ ** by the Free Software Foundation; either version 2.1 of the License, or
+ ** any later version.
+ **
+ ** This library is distributed in the hope that it will be useful, but
+ ** WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ ** MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ ** documentation provided hereunder is on an "as is" basis, and
+ ** Memorial Sloan-Kettering Cancer Center
+ ** has no obligations to provide maintenance, support,
+ ** updates, enhancements or modifications. In no event shall
+ ** Memorial Sloan-Kettering Cancer Center
+ ** be liable to any party for direct, indirect, special,
+ ** incidental or consequential damages, including lost profits, arising
+ ** out of the use of this software and its documentation, even if
+ ** Memorial Sloan-Kettering Cancer Center
+ ** has been advised of the possibility of such damage. See
+ ** the GNU Lesser General Public License for more details.
+ **
+ ** You should have received a copy of the GNU Lesser General Public License
+ ** along with this library; if not, write to the Free Software Foundation,
+ ** Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ **/
+package cytoscape.coreplugins.biopax;
+
+import java.io.FileInputStream;
+import java.util.*;
+
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+import cytoscape.coreplugins.biopax.MapBioPaxToCytoscape;
+import cytoscape.coreplugins.biopax.util.BioPaxUtil;
+import cytoscape.coreplugins.biopax.util.BioPaxVisualStyleUtil;
+
+import giny.model.RootGraph;
+
+import junit.framework.TestCase;
+
+import org.biopax.paxtools.model.Model;
+
+public class TestMapBioPaxToCytoscape extends TestCase {
+
+ /**
+ * Tests the Mapper on a Valid BioPAX File.
+ *
+ * @throws Exception All Exceptions.
+ */
+ public void testMapper1() throws Exception {
+ Model model = BioPaxUtil.read(new FileInputStream(getClass().getResource("/biopax_sample1.owl").getFile()));
+ MapBioPaxToCytoscape mapper = new MapBioPaxToCytoscape();
+ mapper.doMapping(model);
+
+ CyNetwork cyNetwork = createNetwork("network1", mapper);
+
+ verifyNodeList(cyNetwork);
+ verifyControlConversion(cyNetwork);
+ //verifyCoFactors(cyNetwork);
+
+ Cytoscape.destroyNetwork(cyNetwork);
+ }
+
+ /**
+ * Tests that we can map BioPAX Complexes Correctly.
+ *
+ * TODO re-factor this test as IT DEPENDS ON ORDER OF THE ELEMENTS, which is different when run from Ant or Eclipse...
+ *
+ * @throws Exception All Exceptions.
+ */
+ public void testComplexMapping() throws Exception {
+ Model model = BioPaxUtil.read(new FileInputStream(getClass().getResource("/biopax_complex.owl").getFile()));
+ MapBioPaxToCytoscape mapper = new MapBioPaxToCytoscape();
+ mapper.doMapping(model);
+
+ CyNetwork cyNetwork = createNetwork("network1", mapper);
+ int nodeCount = cyNetwork.getNodeCount();
+ assertEquals(3, nodeCount);
+
+ // First, find the Target Complex: CPATH-126.
+ int targetNodeIndex = 0;
+ RootGraph rootGraph = cyNetwork.getRootGraph();
+ Iterator nodeIterator = cyNetwork.nodesIterator();
+
+ while (nodeIterator.hasNext()) {
+ CyNode node = (CyNode) nodeIterator.next();
+ String uri = Cytoscape.getNodeAttributes()
+ .getStringAttribute(node.getIdentifier(), MapBioPaxToCytoscape.BIOPAX_RDF_ID);
+ if (uri.contains("CPATH-126")) {
+ targetNodeIndex = node.getRootGraphIndex();
+ }
+ }
+
+ // Get All Edges Adjacent to this Node
+ int[] edgeIndices = rootGraph.getAdjacentEdgeIndicesArray(targetNodeIndex, true, true, true);
+
+ // There should be two edges; one for each member protein
+ assertEquals(2, edgeIndices.length);
+
+ Cytoscape.destroyNetwork(cyNetwork);
+ }
+
+ private CyNetwork createNetwork(String name, MapBioPaxToCytoscape mapper) {
+ CyNetwork cyNetwork = Cytoscape.createNetwork(name,false);
+ int[] nodeIndices = mapper.getNodeIndices();
+ int[] edgeIndices = mapper.getEdgeIndices();
+
+ for (int i = 0; i < nodeIndices.length; i++) {
+ cyNetwork.addNode(nodeIndices[i]);
+ }
+
+ for (int i = 0; i < edgeIndices.length; i++) {
+ cyNetwork.addEdge(edgeIndices[i]);
+ }
+
+ return cyNetwork;
+ }
+
+ /**
+ * Tests that we can map BioPAX Physical Interactions Correctly.
+ *
+ * @throws Exception All Exceptions.
+ *
+ * TODO re-factor this test as IT DEPENDS ON ORDER OF THE ELEMENTS, which is different when run from Ant or Eclipse...
+ */
+ public void testPhysicalInteractions() throws Exception {
+ Model model = BioPaxUtil.read(new FileInputStream(getClass().getResource("/DIP_ppi.owl").getFile()));
+ MapBioPaxToCytoscape mapper = new MapBioPaxToCytoscape();
+ mapper.doMapping(model);
+
+ CyNetwork cyNetwork = createNetwork("network2", mapper);
+ int nodeCount = cyNetwork.getNodeCount();
+ assertEquals(3, nodeCount);
+
+ // First, find the Target Interaction: physicalInteraction1.
+ int targetNodeIndex = 0;
+ RootGraph rootGraph = cyNetwork.getRootGraph();
+ Iterator nodeIterator = cyNetwork.nodesIterator();
+
+ while (nodeIterator.hasNext()) {
+ CyNode node = (CyNode) nodeIterator.next();
+ String uri = Cytoscape.getNodeAttributes()
+ .getStringAttribute(node.getIdentifier(), MapBioPaxToCytoscape.BIOPAX_RDF_ID);
+ if (uri.endsWith("physicalInteraction1")) {
+ targetNodeIndex = node.getRootGraphIndex();
+ }
+ }
+
+ // Get All Edges Adjacent to this Node
+ int[] edgeIndices = rootGraph.getAdjacentEdgeIndicesArray(targetNodeIndex, true, true, true);
+
+ // There should be two edges; one for each participant
+ assertEquals(2, edgeIndices.length);
+ }
+
+ /**
+ * Verifies the List of Newly Added Nodes.
+ *
+ * @param cyNetwork CyNetwork Object.
+ */
+ private void verifyNodeList(CyNetwork cyNetwork) {
+ int nodeCount = cyNetwork.getNodeCount();
+ assertEquals(12, nodeCount);
+
+ // This HashMap contains all expected nodes.
+ // But node identifier is now a auto-generated md5hex digest;
+ // so it's easier to test here by using biopax.rdfid values instead)
+ Map<String, String> nodeMap = new HashMap<String, String>();
+ nodeMap.put("physicalEntityParticipant44", "");
+ nodeMap.put("physicalEntityParticipant31", "");
+ nodeMap.put("physicalEntityParticipant9", "");
+ nodeMap.put("physicalEntityParticipant17", "");
+ nodeMap.put("physicalEntityParticipant22", "");
+ nodeMap.put("physicalEntityParticipant26", "");
+ nodeMap.put("physicalEntityParticipant38", "");
+ nodeMap.put("physicalEntityParticipant99", "");
+
+ // These represent interaction nodes
+ nodeMap.put("catalysis43", "");
+ nodeMap.put("biochemicalReaction6", "");
+ nodeMap.put("biochemicalReaction37", "");
+ nodeMap.put("catalysis5", "");
+
+ // We don't know the order of nodes; so use nodeMap for look up.
+ Iterator nodeIterator = cyNetwork.nodesIterator();
+
+ while (nodeIterator.hasNext()) {
+ CyNode node = (CyNode) nodeIterator.next();
+ String id = node.getIdentifier();
+ String uri = Cytoscape.getNodeAttributes()
+ .getStringAttribute(id, MapBioPaxToCytoscape.BIOPAX_RDF_ID);
+ // Test a specific node label
+ if (uri.endsWith("physicalEntityParticipant99")) {
+ String label = Cytoscape.getNodeAttributes()
+ .getStringAttribute(id, BioPaxVisualStyleUtil.BIOPAX_NODE_LABEL);
+ assertEquals("Mg2+", label);
+ }
+
+ for(String key : new HashSet<String>(nodeMap.keySet())) {
+ if(uri.contains(key)) {
+ nodeMap.put(key, "found!");
+ break;
+ }
+ }
+ }
+
+ // Verify that we found all expected node identifiers.
+ StringBuilder sb = new StringBuilder();
+ for (String key : nodeMap.keySet()) {
+ if (nodeMap.get(key).isEmpty())
+ sb.append(key).append(",");
+ }
+ if(sb.length() > 0)
+ fail("Network does not contain: " + sb.toString());
+ }
+
+ /**
+ * Verifies that Control Interactions and Conversion Interactions
+ * were mapped over sucessfully.
+ *
+ * TODO re-factor this test as IT DEPENDS ON ORDER OF THE ELEMENTS, which is different when run from Ant or Eclipse...
+ */
+ private void verifyControlConversion(CyNetwork cyNetwork) {
+ // First, find the Target Interaction: biochemicalReaction37.
+ int targetNodeIndex = 0;
+ RootGraph rootGraph = cyNetwork.getRootGraph();
+ Iterator nodeIterator = cyNetwork.nodesIterator();
+
+ while (nodeIterator.hasNext()) {
+ CyNode node = (CyNode) nodeIterator.next();
+ String uri = Cytoscape.getNodeAttributes()
+ .getStringAttribute(node.getIdentifier(), MapBioPaxToCytoscape.BIOPAX_RDF_ID);
+ if (uri.endsWith("biochemicalReaction37")) {
+ targetNodeIndex = node.getRootGraphIndex();
+ break;
+ }
+ }
+
+ // Get All Edges Adjacent to this Node
+ int[] edgeIndices = rootGraph.getAdjacentEdgeIndicesArray(targetNodeIndex, true, true, true);
+
+ // There should only be three edges; one for left; one for right;
+ // and one for control
+ assertEquals(3, edgeIndices.length);
+ }
+
+ /**
+ * Verifies that CoFactors were mapped over successfully
+ *
+ * TODO re-factor this test as IT DEPENDS ON ORDER OF THE ELEMENTS, which is different when run from Ant or Eclipse...
+ */
+ private void verifyCoFactors(CyNetwork cyNetwork) {
+ // First, find the Target Interaction: protein45.
+ int targetNodeIndex = 0;
+ RootGraph rootGraph = cyNetwork.getRootGraph();
+ Iterator nodeIterator = cyNetwork.nodesIterator();
+
+ while (nodeIterator.hasNext()) {
+ CyNode node = (CyNode) nodeIterator.next();
+ String uri = Cytoscape.getNodeAttributes()
+ .getStringAttribute(node.getIdentifier(), MapBioPaxToCytoscape.BIOPAX_RDF_ID);
+ if (uri.equals("smallMolecule99-Mg2+")) {
+ targetNodeIndex = node.getRootGraphIndex();
+ }
+ }
+
+ // Get All Edges Adjacent to this Node
+ int[] edgeIndices = rootGraph.getAdjacentEdgeIndicesArray(targetNodeIndex, true, true, true);
+
+ // There should only be two edges; one for controller, and
+ // one for cofactor.
+ assertEquals(2, edgeIndices.length);
+ }
+}
diff --git a/coreplugins/BioPAX/src/test/java/cytoscape/coreplugins/biopax/util/TestExternalLinkUtil.java b/coreplugins/BioPAX/src/test/java/cytoscape/coreplugins/biopax/util/TestExternalLinkUtil.java
new file mode 100644
index 0000000..f544eac
--- /dev/null
+++ b/coreplugins/BioPAX/src/test/java/cytoscape/coreplugins/biopax/util/TestExternalLinkUtil.java
@@ -0,0 +1,128 @@
+// $Id: TestExternalLinkUtil.java,v 1.11 2006/06/15 22:07:49 grossb Exp $
+//------------------------------------------------------------------------------
+/** Copyright (c) 2006 Memorial Sloan-Kettering Cancer Center.
+ **
+ ** Code written by: Ethan Cerami, Benjamin Gross.
+ ** Authors: Ethan Cerami, Gary Bader, Chris Sander
+ **
+ ** This library is free software; you can redistribute it and/or modify it
+ ** under the terms of the GNU Lesser General Public License as published
+ ** by the Free Software Foundation; either version 2.1 of the License, or
+ ** any later version.
+ **
+ ** This library is distributed in the hope that it will be useful, but
+ ** WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ ** MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ ** documentation provided hereunder is on an "as is" basis, and
+ ** Memorial Sloan-Kettering Cancer Center
+ ** has no obligations to provide maintenance, support,
+ ** updates, enhancements or modifications. In no event shall
+ ** Memorial Sloan-Kettering Cancer Center
+ ** be liable to any party for direct, indirect, special,
+ ** incidental or consequential damages, including lost profits, arising
+ ** out of the use of this software and its documentation, even if
+ ** Memorial Sloan-Kettering Cancer Center
+ ** has been advised of the possibility of such damage. See
+ ** the GNU Lesser General Public License for more details.
+ **
+ ** You should have received a copy of the GNU Lesser General Public License
+ ** along with this library; if not, write to the Free Software Foundation,
+ ** Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ **/
+package cytoscape.coreplugins.biopax.util;
+
+import junit.framework.TestCase;
+
+
+import java.util.ArrayList;
+
+
+/**
+ * Tests the ExternalLink Utility Class.
+ *
+ * @author Ethan Cerami.
+ */
+public class TestExternalLinkUtil extends TestCase {
+
+ /**
+ * Tests External Database Links.
+ */
+ public void testExternalLinks() {
+ String url = ExternalLinkUtil.createLink("SWP", "ABC123");
+ assertEquals("<A class=\"link\" HREF=\"http://www.pir.uniprot.org/cgi-bin/upEntry?"
+ + "id=ABC123\">SWP: ABC123</A>", url);
+ }
+
+ /**
+ * Tests Links to IHOP.
+ */
+ public void testIHOPLinks() {
+ ArrayList dbList = new ArrayList();
+ dbList.add(new ExternalLink("UniProt", "P10275"));
+ dbList.add(new ExternalLink("GO", "4321"));
+ dbList.add(new ExternalLink("ENTREZ_GENE", "367"));
+ dbList.add(new ExternalLink("Reactome", "XYZ"));
+
+ ArrayList synList = new ArrayList();
+ synList.add("KD");
+ synList.add("AIS");
+ synList.add("TFM");
+
+ // Temporarily disable URL Encoding so we can more easily
+ // see the actual URL for connecting to IHOP
+ ExternalLinkUtil.useUrlEncoding(false);
+
+ // Verify a Sample URL to IHOP
+ String url = ExternalLinkUtil.getIHOPUrl("protein", synList, dbList, 9606);
+ assertEquals("http://www.ihop-net.org/UniPub/iHOP/in?syns_1=KD|"
+ + "AIS|TFM&dbrefs_1=UNIPROT__AC|P10275,NCBI_GENE__ID|367",
+ url);
+
+ // Verify that no link is generated for small molecules
+ url = ExternalLinkUtil.getIHOPUrl("smallMolecule", synList, dbList, 9606);
+ assertEquals(null, url);
+
+ // Very a Sample HREF Link to IHOP
+ String html = ExternalLinkUtil.createIHOPLink("protein", synList, dbList, 9606);
+ assertTrue(html.startsWith("<A class=\"link\" HREF=\"http://www.ihop-net.org/UniPub/iHOP/in?syns_1"));
+
+ // Try using Synonyms + XRefs not supported by IHOP
+ // Should result in link with synonyms only.
+ dbList = new ArrayList();
+ dbList.add(new ExternalLink("GO", "4321"));
+ dbList.add(new ExternalLink("Reactome", "XYZ"));
+ url = ExternalLinkUtil.getIHOPUrl("protein", synList, dbList, 9606);
+ assertEquals("http://www.ihop-net.org/UniPub/iHOP/in?syns_1=KD|AIS|TFM",
+ url);
+
+ // Try using no Synonyms + XRefs not supported by IHOP
+ // Should result in null.
+ url = ExternalLinkUtil.getIHOPUrl("protein", null, dbList, -1);
+ assertEquals(null, url);
+
+ // Try using null arguments.
+ // Should result in null.
+ url = ExternalLinkUtil.getIHOPUrl("protein", null, null, -1);
+ assertEquals(null, url);
+
+ // Now, turn URL Encoding back on, and verify a link
+ ExternalLinkUtil.useUrlEncoding(true);
+ url = ExternalLinkUtil.getIHOPUrl("protein", synList, dbList, 9606);
+ assertEquals("http://www.ihop-net.org/UniPub/iHOP/in?syns_1=KD%7"
+ + "CAIS%7CTFM", url);
+
+ // Test Special Case where we have exactly dbRef of type UniProt,
+ // and no synonyms
+ dbList = new ArrayList();
+ dbList.add(new ExternalLink("UniProt", "P10275"));
+ synList = new ArrayList();
+ url = ExternalLinkUtil.getIHOPUrl("protein", synList, dbList, 9606);
+ assertEquals(null, url);
+
+ // Now, add one synonym, and verify new link
+ synList.add("TNF");
+ url = ExternalLinkUtil.getIHOPUrl("protein", synList, dbList, 9606);
+ assertEquals("http://www.ihop-net.org/UniPub/iHOP/in?syns_1=TNF&dbrefs_1="
+ + "UNIPROT__AC%7CP10275", url);
+ }
+}
diff --git a/coreplugins/BioPAX/src/test/java/cytoscape/coreplugins/biopax/util/TestWebFileConnect.java b/coreplugins/BioPAX/src/test/java/cytoscape/coreplugins/biopax/util/TestWebFileConnect.java
new file mode 100644
index 0000000..ee157aa
--- /dev/null
+++ b/coreplugins/BioPAX/src/test/java/cytoscape/coreplugins/biopax/util/TestWebFileConnect.java
@@ -0,0 +1,67 @@
+// $Id: TestWebFileConnect.java,v 1.3 2006/06/15 22:06:02 grossb Exp $
+//------------------------------------------------------------------------------
+/** Copyright (c) 2006 Memorial Sloan-Kettering Cancer Center.
+ **
+ ** Code written by: Ethan Cerami
+ ** Authors: Ethan Cerami, Gary Bader, Chris Sander
+ **
+ ** This library is free software; you can redistribute it and/or modify it
+ ** under the terms of the GNU Lesser General Public License as published
+ ** by the Free Software Foundation; either version 2.1 of the License, or
+ ** any later version.
+ **
+ ** This library is distributed in the hope that it will be useful, but
+ ** WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ ** MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ ** documentation provided hereunder is on an "as is" basis, and
+ ** Memorial Sloan-Kettering Cancer Center
+ ** has no obligations to provide maintenance, support,
+ ** updates, enhancements or modifications. In no event shall
+ ** Memorial Sloan-Kettering Cancer Center
+ ** be liable to any party for direct, indirect, special,
+ ** incidental or consequential damages, including lost profits, arising
+ ** out of the use of this software and its documentation, even if
+ ** Memorial Sloan-Kettering Cancer Center
+ ** has been advised of the possibility of such damage. See
+ ** the GNU Lesser General Public License for more details.
+ **
+ ** You should have received a copy of the GNU Lesser General Public License
+ ** along with this library; if not, write to the Free Software Foundation,
+ ** Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ **/
+package cytoscape.coreplugins.biopax.util;
+
+import java.io.File;
+
+import junit.framework.TestCase;
+
+
+
+/**
+ * Tests the WebFileConnect Utility Class.
+ *
+ * @author Ethan Cerami.
+ */
+public class TestWebFileConnect extends TestCase {
+ /**
+ * Tests the File Connect.
+ *
+ * @throws Exception All Exceptions.
+ */
+ public void testFileConnect() throws Exception {
+ String str = WebFileConnect.retrieveDocument(new File(getClass().getResource("/biopax_sample1.owl").getFile()));
+ assertTrue(str.startsWith("<?xml version=\"1.0\""));
+ }
+
+ /**
+ * Tests the Web Connect.
+ *
+ * @throws Exception All Exceptions.
+ */
+ public void testWebConnect() throws Exception {
+ String str = WebFileConnect.retrieveDocument("http://www.google.com");
+ // This page may not actually start with <html>, so just look for the string.
+ // It should, however be present.
+ assertTrue(str.indexOf("<html") >= 0 );
+ }
+}
diff --git a/coreplugins/BioPAX/src/test/resources/Apoptosis.owl b/coreplugins/BioPAX/src/test/resources/Apoptosis.owl
new file mode 100644
index 0000000..d2310e2
--- /dev/null
+++ b/coreplugins/BioPAX/src/test/resources/Apoptosis.owl
@@ -0,0 +1,4919 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<rdf:RDF xmlns="http://www.biopax.org/examples/apoptosis#"
+ xmlns:bp="http://www.biopax.org/release/biopax-level2.owl#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+ xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
+ xmlns:owl="http://www.w3.org/2002/07/owl#" xml:base="http://www.biopax.org/examples/apoptosis">
+ <owl:Ontology rdf:about="">
+ <owl:imports rdf:resource="http://www.biopax.org/release/biopax-level2.owl" />
+ <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BioPAX pathway converted from "Apoptosis" in the Reactome database.</rdfs:comment>
+ </owl:Ontology>
+ <bp:pathway rdf:ID="Apoptosis">
+ <bp:PATHWAY-COMPONENTS rdf:resource="#Extrinsic_Pathway_for_ApoptosisStep" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#Activation_of__Effector_CaspasesStep" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#Apoptotic_execution__phaseStep" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#Intrinsic_Pathway_for_ApoptosisStep" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#Activation__myristolyation_of_BID_and_translocation_to_mitochondriaStep" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Apoptosis</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Apoptosis</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome109581" />
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Apoptosis is a distinct form of cell death that is functionally and morphologically different from necrosis. Nuclear chromatin condensation, cytoplasmic shrinking, dilated endoplasmic reticulum, and membrane blebbing characterize apoptosis in general. Mitochondria remain morphologically unchanged. In 1972 Kerr et al introduced the concept of apoptosis as a distinct form of "cell-death", and the mechanisms of various a [...]
+ <bp:EVIDENCE rdf:resource="#Summation_109577" />
+ <bp:XREF rdf:resource="#apoptosis" />
+ </bp:pathway>
+ <bp:pathway rdf:ID="Extrinsic_Pathway_for_Apoptosis">
+ <bp:PATHWAY-COMPONENTS rdf:resource="#Caspase_8_is_formed_from_procaspase_8Step" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#Death_Receptor__SignallingStep" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Extrinsic Pathway for Apoptosis</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Extrinsic Pathway for Apoptosis</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome109607" />
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Known as the "death receptor pathway" the extrinsic or caspase 8/10 dependent pathway is activated by ligand binding. The "death receptors" are specialized cell-surface receptors including Fas/CD95, tumor necrosis factor-alpha (TNF-alpha) receptor 1, and two receptors, DR4 and DR5, that bind to the TNF-alpha related apoptosis-inducing ligand (TRAIL). The extrinsic and intrinsic pathways unite in the activation of Casp [...]
+ <bp:EVIDENCE rdf:resource="#Summation_139959" />
+ <bp:XREF rdf:resource="#induction_of_apoptosis_by_extracellular_signals" />
+ </bp:pathway>
+ <bp:pathway rdf:ID="Death_Receptor__Signalling">
+ <bp:PATHWAY-COMPONENTS rdf:resource="#FasL__CD95L_signalingStep" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#TRAIL__signalingStep" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#TNF_signalingStep" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Death Receptor Signalling</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Death Receptor Signalling</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome73887" />
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The death receptors, all cell-surface receptors, begin the process of caspase activation. The common feature of these type 1 transmembrane proteins is the "death-domain" a conserved cytoplasmic motif found on all of the three receptors (FAS/CD95, TNF-receptor, and TRAIL-receptor) that binds the Fas-associated protein with death domain (FADD)</bp:COMMENT>
+ <bp:EVIDENCE rdf:resource="#Summation_139958" />
+ <bp:XREF rdf:resource="#induction_of_apoptosis_by_extracellular_signals" />
+ </bp:pathway>
+ <bp:pathway rdf:ID="FasL__CD95L_signaling">
+ <bp:PATHWAY-COMPONENTS rdf:resource="#FasL_Fas_binds_FADDStep" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#FASL_binds_FAS_ReceptorStep" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#FASL_FAS_Receptor_Trimer_FADD_complex_binds_pro_Caspase_10Step" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#FASL_FAS_Receptor_Trimer_FADD_complex_binds_pro_Caspase_8Step" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#Trimerization_of_the_FASL_FAS_receptor_complexStep" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FasL/ CD95L signaling</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FasL/ CD95L signaling</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome75157" />
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The Fas family of cell surface receptors initiate the apototic pathway through interaction with the external ligand, FasL. The cytoplasmic domain of Fas interacts with a number of molecules in the transduction of the external signal to the cytoplasmic side of the cell membrane. The most notable cytoplasmic domain is the Death Domain (DD) that is involved in recruiting the FAS-associating death domain-containing prote [...]
+ <bp:EVIDENCE rdf:resource="#Summation_140481" />
+ <bp:XREF rdf:resource="#Pubmed_11048727" />
+ <bp:XREF rdf:resource="#induction_of_apoptosis_by_extracellular_signals" />
+ </bp:pathway>
+ <bp:biochemicalReaction rdf:ID="FASL_binds_FAS_Receptor">
+ <bp:LEFT rdf:resource="#FASL__extracellular_region_" />
+ <bp:LEFT rdf:resource="#FAS_Receptor__plasma_membrane_" />
+ <bp:RIGHT rdf:resource="#FASL_FAS_Receptor_monomer__plasma_membrane_" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FASL binds FAS Receptor</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FASL binds FAS Receptor</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome75244" />
+ <bp:XREF rdf:resource="#Pubmed_7530336" />
+ <bp:XREF rdf:resource="#induction_of_apoptosis_by_extracellular_signals" />
+ </bp:biochemicalReaction>
+ <bp:sequenceParticipant rdf:ID="FASL__extracellular_region_">
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_P48023_1_Tumor_necrosis_factor_ligand_superfamily_member_6__FAS_antigen_ligand___Apoptosis_antigen_ligand___APTL___CD178_antigen_" />
+ </bp:sequenceParticipant>
+ <bp:openControlledVocabulary rdf:ID="extracellular_region">
+ <bp:TERM rdf:datatype="http://www.w3.org/2001/XMLSchema#string">extracellular region</bp:TERM>
+ <bp:XREF rdf:resource="#GO_0005576" />
+ </bp:openControlledVocabulary>
+ <bp:unificationXref rdf:ID="GO_0005576">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GO</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0005576</bp:ID>
+ </bp:unificationXref>
+ <bp:protein rdf:ID="UniProt_P48023_1_Tumor_necrosis_factor_ligand_superfamily_member_6__FAS_antigen_ligand___Apoptosis_antigen_ligand___APTL___CD178_antigen_">
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P48023-1 Tumor necrosis factor ligand superfamily member 6 (FAS antigen ligand) (Apoptosis antigen ligand) (APTL) (CD178 antigen)</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FASL</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TNFSF6</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">APT1LG1</bp:SYNONYMS>
+ <bp:XREF rdf:resource="#UniProt_P48023" />
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Cytokine that binds to TNFRSF6/FAS, a receptor that transduces the apoptotic signal into cells. May be involved in cytotoxic T cell mediated apoptosis and in T cell development. TNFRSF6/FAS-mediated apoptosis may have a role in the induction of peripheral tolerance, in the antigen-stimulated suicide of mature T cells, or both. Binding to the decoy receptor TNFRSF6B/DcR3 modulates its effects. SUBUNIT: Homotr [...]
+ </bp:protein>
+ <bp:bioSource rdf:ID="Homo_sapiens">
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Homo sapiens</bp:NAME>
+ <bp:TAXON-XREF rdf:resource="#NCBI_taxonomy_9606" />
+ </bp:bioSource>
+ <bp:unificationXref rdf:ID="NCBI_taxonomy_9606">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">NCBI_taxonomy</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">9606</bp:ID>
+ </bp:unificationXref>
+ <bp:unificationXref rdf:ID="UniProt_P48023">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P48023</bp:ID>
+ </bp:unificationXref>
+ <bp:sequenceParticipant rdf:ID="FAS_Receptor__plasma_membrane_">
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_P25445_1_Tumor_necrosis_factor_receptor_superfamily_member_6_precursor__FASL_receptor___Apoptosis_mediating_surface_antigen_FAS___Apo_1_antigen___CD95_antigen_" />
+ </bp:sequenceParticipant>
+ <bp:openControlledVocabulary rdf:ID="plasma_membrane">
+ <bp:TERM rdf:datatype="http://www.w3.org/2001/XMLSchema#string">plasma membrane</bp:TERM>
+ <bp:XREF rdf:resource="#GO_0005886" />
+ </bp:openControlledVocabulary>
+ <bp:unificationXref rdf:ID="GO_0005886">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GO</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0005886</bp:ID>
+ </bp:unificationXref>
+ <bp:protein rdf:ID="UniProt_P25445_1_Tumor_necrosis_factor_receptor_superfamily_member_6_precursor__FASL_receptor___Apoptosis_mediating_surface_antigen_FAS___Apo_1_antigen___CD95_antigen_">
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P25445-1 Tumor necrosis factor receptor superfamily member 6 precursor (FASL receptor) (Apoptosis-mediating surface antigen FAS) (Apo-1 antigen) (CD95 antigen)</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FAS</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TNFRSF6</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">APT1</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FAS1</bp:SYNONYMS>
+ <bp:XREF rdf:resource="#UniProt_P25445" />
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Receptor for TNFSF6/FASL. The adapter molecule FADD recruits caspase-8 to the activated receptor. The resulting death- inducing signaling complex (DISC) performs caspase-8 proteolytic activation which initiates the subsequent cascade of caspases (aspartate-specific cysteine proteases) mediating apoptosis. FAS- mediated apoptosis may have a role in the induction of peripheral tolerance, in the antigen-stimula [...]
+ </bp:protein>
+ <bp:unificationXref rdf:ID="UniProt_P25445">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P25445</bp:ID>
+ </bp:unificationXref>
+ <bp:sequenceParticipant rdf:ID="FASL_FAS_Receptor_monomer__plasma_membrane_">
+ <bp:CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#FASL_FAS_Receptor_monomer__plasma_membrane_1" />
+ </bp:sequenceParticipant>
+ <bp:complex rdf:ID="FASL_FAS_Receptor_monomer__plasma_membrane_1">
+ <bp:COMPONENTS rdf:resource="#FASL__extracellular_region_1" />
+ <bp:COMPONENTS rdf:resource="#FAS_Receptor__plasma_membrane_1" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FASL:FAS Receptor monomer [plasma membrane]</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FASL:FAS Receptor monomer</bp:SHORT-NAME>
+ </bp:complex>
+ <bp:sequenceParticipant rdf:ID="FASL__extracellular_region_1">
+ <bp:CELLULAR-LOCATION rdf:resource="#extracellular_region" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_P48023_1_Tumor_necrosis_factor_ligand_superfamily_member_6__FAS_antigen_ligand___Apoptosis_antigen_ligand___APTL___CD178_antigen_" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="FAS_Receptor__plasma_membrane_1">
+ <bp:CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_P25445_1_Tumor_necrosis_factor_receptor_superfamily_member_6_precursor__FASL_receptor___Apoptosis_mediating_surface_antigen_FAS___Apo_1_antigen___CD95_antigen_" />
+ </bp:sequenceParticipant>
+ <bp:unificationXref rdf:ID="Reactome75244">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">75244</bp:ID>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</bp:COMMENT>
+ </bp:unificationXref>
+ <bp:publicationXref rdf:ID="Pubmed_7530336">
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">7530336</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</bp:DB>
+ <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1995</bp:YEAR>
+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cell-autonomous Fas (CD95)/Fas-ligand interaction mediates activation-induced apoptosis in T-cell hybridomas</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Brunner, T</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mogil, RJ</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">LaFace, D</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Yoo, NJ</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mahboubi, A</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Echeverri, F</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Martin, SJ</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Force, WR</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Lynch, DH</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Ware, CF</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Nature 373:441-4</bp:SOURCE>
+ </bp:publicationXref>
+ <bp:relationshipXref rdf:ID="induction_of_apoptosis_by_extracellular_signals">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GO</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0008624</bp:ID>
+ </bp:relationshipXref>
+ <bp:openControlledVocabulary rdf:ID="cell">
+ <bp:TERM rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cell</bp:TERM>
+ <bp:XREF rdf:resource="#GO_0005623" />
+ </bp:openControlledVocabulary>
+ <bp:unificationXref rdf:ID="GO_0005623">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GO</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0005623</bp:ID>
+ </bp:unificationXref>
+ <bp:pathwayStep rdf:ID="FASL_binds_FAS_ReceptorStep">
+ <bp:STEP-INTERACTIONS rdf:resource="#FASL_binds_FAS_Receptor" />
+ <bp:NEXT-STEP rdf:resource="#Trimerization_of_the_FASL_FAS_receptor_complexStep" />
+ </bp:pathwayStep>
+ <bp:biochemicalReaction rdf:ID="Trimerization_of_the_FASL_FAS_receptor_complex">
+ <bp:LEFT rdf:resource="#FASL_FAS_Receptor_monomer__plasma_membrane_2" />
+ <bp:RIGHT rdf:resource="#FASL_FAS_Receptor_Trimer__plasma_membrane_" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Trimerization of the FASL:FAS receptor complex</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Trimerization of the FASL:FAS receptor complex</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome71050" />
+ <bp:XREF rdf:resource="#Pubmed_8521815" />
+ </bp:biochemicalReaction>
+ <bp:sequenceParticipant rdf:ID="FASL_FAS_Receptor_monomer__plasma_membrane_2">
+ <bp:CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#FASL_FAS_Receptor_monomer__plasma_membrane_1" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="FASL_FAS_Receptor_Trimer__plasma_membrane_">
+ <bp:CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#FASL_FAS_Receptor_Trimer__plasma_membrane_1" />
+ </bp:sequenceParticipant>
+ <bp:complex rdf:ID="FASL_FAS_Receptor_Trimer__plasma_membrane_1">
+ <bp:COMPONENTS rdf:resource="#FASL_FAS_Receptor_monomer__plasma_membrane_3" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FASL:FAS Receptor Trimer [plasma membrane]</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FASL:FAS Receptor Trimer</bp:SHORT-NAME>
+ </bp:complex>
+ <bp:sequenceParticipant rdf:ID="FASL_FAS_Receptor_monomer__plasma_membrane_3">
+ <bp:CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#FASL_FAS_Receptor_monomer__plasma_membrane_1" />
+ <bp:STOICHIOMETRIC-COEFFICIENT rdf:datatype="http://www.w3.org/2001/XMLSchema#int">3</bp:STOICHIOMETRIC-COEFFICIENT>
+ </bp:sequenceParticipant>
+ <bp:unificationXref rdf:ID="Reactome71050">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</bp:DB>
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+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cytotoxicity-dependent APO-1 (Fas/CD95)-associated proteins form a death-inducing signaling complex (DISC) with the receptor</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Kischkel, FC</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Hellbardt, S</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Behrmann, I</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Germer, M</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pawlita, M</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Krammer, PH</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Peter, ME</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">EMBO J 14:5579-88</bp:SOURCE>
+ </bp:publicationXref>
+ <bp:pathwayStep rdf:ID="Trimerization_of_the_FASL_FAS_receptor_complexStep">
+ <bp:STEP-INTERACTIONS rdf:resource="#Trimerization_of_the_FASL_FAS_receptor_complex" />
+ <bp:NEXT-STEP rdf:resource="#FasL_Fas_binds_FADDStep" />
+ </bp:pathwayStep>
+ <bp:biochemicalReaction rdf:ID="FasL_Fas_binds_FADD">
+ <bp:LEFT rdf:resource="#FASL_FAS_Receptor_Trimer__plasma_membrane_2" />
+ <bp:LEFT rdf:resource="#FADD__cytosol_" />
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+ </bp:biochemicalReaction>
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+ <bp:sequenceParticipant rdf:ID="FADD__cytosol_">
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+ </bp:sequenceParticipant>
+ <bp:openControlledVocabulary rdf:ID="cytosol">
+ <bp:TERM rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cytosol</bp:TERM>
+ <bp:XREF rdf:resource="#GO_0005829" />
+ </bp:openControlledVocabulary>
+ <bp:unificationXref rdf:ID="GO_0005829">
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+ </bp:unificationXref>
+ <bp:protein rdf:ID="UniProt_Q13158_FADD_protein__FAS_associating_death_domain_containing_protein___Mediator_of_receptor_induced_toxicity_">
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:Q13158 FADD protein (FAS-associating death domain-containing protein) (Mediator of receptor induced toxicity)</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">MORT1</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FADD</bp:SYNONYMS>
+ <bp:XREF rdf:resource="#UniProt_Q13158" />
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Apoptotic adaptor molecule that recruits caspase-8 or caspase-10 to the activated Fas (CD95) or TNFR-1 receptors. The resulting aggregate called the death-inducing signaling complex (DISC) performs caspase-8 proteolytic activation. Active caspase-8 initiates the subsequent cascade of caspases (aspartate-specific cysteine proteases) mediating apoptosis. SUBUNIT: Interacts with CFLAR, PEA15 and MBD4. TISSUE SP [...]
+ </bp:protein>
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+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Q13158</bp:ID>
+ </bp:unificationXref>
+ <bp:sequenceParticipant rdf:ID="FASL_FAS_Receptor_Trimer_FADD_complex__plasma_membrane_">
+ <bp:CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#FASL_FAS_Receptor_Trimer_FADD_complex__plasma_membrane_1" />
+ </bp:sequenceParticipant>
+ <bp:complex rdf:ID="FASL_FAS_Receptor_Trimer_FADD_complex__plasma_membrane_1">
+ <bp:COMPONENTS rdf:resource="#FASL_FAS_Receptor_Trimer__plasma_membrane_3" />
+ <bp:COMPONENTS rdf:resource="#FADD__cytosol_1" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FASL:FAS Receptor Trimer:FADD complex [plasma membrane]</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FASL:FAS Receptor Trimer:FADD complex</bp:SHORT-NAME>
+ </bp:complex>
+ <bp:sequenceParticipant rdf:ID="FASL_FAS_Receptor_Trimer__plasma_membrane_3">
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+ <bp:PHYSICAL-ENTITY rdf:resource="#FASL_FAS_Receptor_Trimer__plasma_membrane_1" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="FADD__cytosol_1">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q13158_FADD_protein__FAS_associating_death_domain_containing_protein___Mediator_of_receptor_induced_toxicity_" />
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+ <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1995</bp:YEAR>
+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A novel protein that interacts with the death domain of Fas/APO1 contains a sequence motif related to the death domain</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Boldin, MP</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Varfolomeev, EE</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pancer, Z</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mett, IL</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Camonis, JH</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Wallach, D</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Biol Chem 270:7795-8</bp:SOURCE>
+ </bp:publicationXref>
+ <bp:pathwayStep rdf:ID="FasL_Fas_binds_FADDStep">
+ <bp:STEP-INTERACTIONS rdf:resource="#FasL_Fas_binds_FADD" />
+ <bp:NEXT-STEP rdf:resource="#FASL_FAS_Receptor_Trimer_FADD_complex_binds_pro_Caspase_8Step" />
+ <bp:NEXT-STEP rdf:resource="#FASL_FAS_Receptor_Trimer_FADD_complex_binds_pro_Caspase_10Step" />
+ </bp:pathwayStep>
+ <bp:biochemicalReaction rdf:ID="FASL_FAS_Receptor_Trimer_FADD_complex_binds_pro_Caspase_8">
+ <bp:LEFT rdf:resource="#FASL_FAS_Receptor_Trimer_FADD_complex__plasma_membrane_2" />
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+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FASL:FAS Receptor Trimer:FADD complex binds pro-Caspase-8</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FASL:FAS Receptor Trimer:FADD complex binds pro-Caspase-8</bp:SHORT-NAME>
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+ <bp:XREF rdf:resource="#Pubmed_8681376" />
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+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="Caspase_8_precursor___cytosol_">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q14790_1_Caspase_8_precursor__EC_3_4_22_____CASP_8___ICE_like_apoptotic_protease_5___MORT1_associated_CED_3_homolog___MACH___FADD_homologous_ICE_CED_3_like_protease___FADD_like_ICE___FLICE___Apoptotic_cysteine_protease___Apoptotic_protease_Mch_5___CAP4_" />
+ </bp:sequenceParticipant>
+ <bp:protein rdf:ID="UniProt_Q14790_1_Caspase_8_precursor__EC_3_4_22_____CASP_8___ICE_like_apoptotic_protease_5___MORT1_associated_CED_3_homolog___MACH___FADD_homologous_ICE_CED_3_like_protease___FADD_like_ICE___FLICE___Apoptotic_cysteine_protease___Apoptotic_protease_Mch_5___CAP4_">
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:Q14790-1 Caspase-8 precursor (EC 3.4.22.-) (CASP-8) (ICE-like apoptotic protease 5) (MORT1-associated CED-3 homolog) (MACH) (FADD-homologous ICE/CED-3-like protease) (FADD-like ICE) (FLICE) (Apoptotic cysteine protease) (Apoptotic protease Mch-5) (CAP4)</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CASP8</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">MCH5</bp:SYNONYMS>
+ <bp:XREF rdf:resource="#UniProt_Q14790" />
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Most upstream protease of the activation cascade of caspases responsible for the TNFRSF6/FAS mediated and TNFRSF1A induced cell death. Binding to the adapter molecule FADD recruits it to either receptor. The resulting aggregate called death- inducing signaling complex (DISC) performs CASP8 proteolytic activation. The active dimeric enzyme is then liberated from the DISC and free to activate downstream apopto [...]
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+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Q14790</bp:ID>
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+ <bp:sequenceParticipant rdf:ID="FASL_FAS_Receptor_Trimer_FADD_pro_Caspase_8_DISC__plasma_membrane_">
+ <bp:CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#FASL_FAS_Receptor_Trimer_FADD_pro_Caspase_8_DISC__plasma_membrane_1" />
+ </bp:sequenceParticipant>
+ <bp:complex rdf:ID="FASL_FAS_Receptor_Trimer_FADD_pro_Caspase_8_DISC__plasma_membrane_1">
+ <bp:COMPONENTS rdf:resource="#FASL_FAS_Receptor_Trimer_FADD_complex__plasma_membrane_3" />
+ <bp:COMPONENTS rdf:resource="#Caspase_8_precursor___cytosol_1" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FASL:FAS Receptor Trimer:FADD:pro-Caspase-8 DISC [plasma membrane]</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FASL:FAS Receptor Trimer:FADD:pro-Caspase-8 DISC</bp:SHORT-NAME>
+ </bp:complex>
+ <bp:sequenceParticipant rdf:ID="FASL_FAS_Receptor_Trimer_FADD_complex__plasma_membrane_3">
+ <bp:CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
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+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="Caspase_8_precursor___cytosol_1">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q14790_1_Caspase_8_precursor__EC_3_4_22_____CASP_8___ICE_like_apoptotic_protease_5___MORT1_associated_CED_3_homolog___MACH___FADD_homologous_ICE_CED_3_like_protease___FADD_like_ICE___FLICE___Apoptotic_cysteine_protease___Apoptotic_protease_Mch_5___CAP4_" />
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+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</bp:DB>
+ <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1996</bp:YEAR>
+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Involvement of MACH, a novel MORT1/FADD-interacting protease, in Fas/APO-1- and TNF receptor-induced cell death</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Boldin, MP</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Goncharov, TM</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Goltsev, YV</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Wallach, D</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cell 85:803-15</bp:SOURCE>
+ </bp:publicationXref>
+ <bp:pathwayStep rdf:ID="FASL_FAS_Receptor_Trimer_FADD_complex_binds_pro_Caspase_8Step">
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+ <bp:sequenceParticipant rdf:ID="Caspase_10_precursor___plasma_membrane_">
+ <bp:CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q92851_1_Caspase_10_precursor__EC_3_4_22_____CASP_10___ICE_like_apoptotic_protease_4___Apoptotic_protease_Mch_4___FAS_associated_death_domain_protein_interleukin_1B_converting_enzyme_2___FLICE2_" />
+ </bp:sequenceParticipant>
+ <bp:protein rdf:ID="UniProt_Q92851_1_Caspase_10_precursor__EC_3_4_22_____CASP_10___ICE_like_apoptotic_protease_4___Apoptotic_protease_Mch_4___FAS_associated_death_domain_protein_interleukin_1B_converting_enzyme_2___FLICE2_">
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:Q92851-1 Caspase-10 precursor (EC 3.4.22.-) (CASP-10) (ICE-like apoptotic protease 4) (Apoptotic protease Mch-4) (FAS-associated death domain protein interleukin-1B-converting enzyme 2) (FLICE2)</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">MCH4</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CASP10</bp:SYNONYMS>
+ <bp:XREF rdf:resource="#UniProt_Q92851" />
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Involved in the activation cascade of caspases responsible for apoptosis execution. Recruited to both Fas- and TNFR-1 receptors in a FADD dependent manner. May participate in the granzyme B apoptotic pathways. Cleaves and activates caspase- 3, -4, -6, -7, -8, and -9. Hydrolyzes the small- molecule substrates, Tyr-Val-Ala-Asp-|-AMC and Asp-Glu-Val-Asp-|-AMC. FUNCTION: Isoform C is proteolytically inactive. SU [...]
+ </bp:protein>
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+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Q92851</bp:ID>
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+ <bp:sequenceParticipant rdf:ID="FASL_FAS_Receptor_Trimer_FADD_pro_Caspase_10__plasma_membrane_">
+ <bp:CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#FASL_FAS_Receptor_Trimer_FADD_pro_Caspase_10__plasma_membrane_1" />
+ </bp:sequenceParticipant>
+ <bp:complex rdf:ID="FASL_FAS_Receptor_Trimer_FADD_pro_Caspase_10__plasma_membrane_1">
+ <bp:COMPONENTS rdf:resource="#FASL_FAS_Receptor_Trimer_FADD_complex__plasma_membrane_5" />
+ <bp:COMPONENTS rdf:resource="#Caspase_10_precursor___plasma_membrane_1" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FASL:FAS Receptor Trimer:FADD:pro-Caspase-10 [plasma membrane]</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FASL:FAS Receptor Trimer:FADD:pro-Caspase-10</bp:SHORT-NAME>
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+ <bp:sequenceParticipant rdf:ID="FASL_FAS_Receptor_Trimer_FADD_complex__plasma_membrane_5">
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+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Caspase-10 is an initiator caspase in death receptor signaling</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Wang, J</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Chun, HJ</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Wong, W</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Spencer, DM</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Lenardo, MJ</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Proc Natl Acad Sci U S A 98:13884-8</bp:SOURCE>
+ </bp:publicationXref>
+ <bp:publicationXref rdf:ID="Pubmed_12198154">
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">12198154</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</bp:DB>
+ <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2002</bp:YEAR>
+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Caspase-10 is recruited to and activated at the native TRAIL and CD95 death-inducing signalling complexes in a FADD-dependent manner but can not functionally substitute caspase-8</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Sprick, MR</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Rieser, E</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Stahl, H</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Grosse-Wilde, A</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Weigand, MA</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Walczak, H</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">EMBO J 21:4520-30</bp:SOURCE>
+ </bp:publicationXref>
+ <bp:pathwayStep rdf:ID="FASL_FAS_Receptor_Trimer_FADD_complex_binds_pro_Caspase_10Step">
+ <bp:STEP-INTERACTIONS rdf:resource="#FASL_FAS_Receptor_Trimer_FADD_complex_binds_pro_Caspase_10" />
+ </bp:pathwayStep>
+ <bp:unificationXref rdf:ID="Reactome75157">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">75157</bp:ID>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</bp:COMMENT>
+ </bp:unificationXref>
+ <bp:evidence rdf:ID="Summation_140481">
+ <bp:XREF rdf:resource="#Pubmed_1713127" />
+ <bp:XREF rdf:resource="#Pubmed_2469768" />
+ <bp:XREF rdf:resource="#Pubmed_7538907" />
+ </bp:evidence>
+ <bp:publicationXref rdf:ID="Pubmed_1713127">
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">1713127</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</bp:DB>
+ <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1991</bp:YEAR>
+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The polypeptide encoded by the cDNA for human cell surface antigen Fas can mediate apoptosis</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Itoh, N</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Yonehara, S</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Ishii, A</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Yonehara, M</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mizushima, S</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Sameshima, M</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Hase, A</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Seto, Y</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Nagata, S</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cell 66:233-43</bp:SOURCE>
+ </bp:publicationXref>
+ <bp:publicationXref rdf:ID="Pubmed_2469768">
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2469768</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</bp:DB>
+ <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1989</bp:YEAR>
+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A cell-killing monoclonal antibody (anti-Fas) to a cell surface antigen co-downregulated with the receptor of tumor necrosis factor</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Yonehara, S</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Ishii, A</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Yonehara, M</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Exp Med 169:1747-56</bp:SOURCE>
+ </bp:publicationXref>
+ <bp:publicationXref rdf:ID="Pubmed_7538907">
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">7538907</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</bp:DB>
+ <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1995</bp:YEAR>
+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FADD, a novel death domain-containing protein, interacts with the death domain of Fas and initiates apoptosis</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Chinnaiyan, AM</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">O'Rourke, K</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Tewari, M</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Dixit, VM</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cell 81:505-12</bp:SOURCE>
+ </bp:publicationXref>
+ <bp:publicationXref rdf:ID="Pubmed_11048727">
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">11048727</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</bp:DB>
+ <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2000</bp:YEAR>
+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The biochemistry of apoptosis.</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Hengartner, MO</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Nature 407:770-6</bp:SOURCE>
+ </bp:publicationXref>
+ <bp:pathwayStep rdf:ID="FasL__CD95L_signalingStep">
+ <bp:STEP-INTERACTIONS rdf:resource="#FasL__CD95L_signaling" />
+ </bp:pathwayStep>
+ <bp:pathway rdf:ID="TNF_signaling">
+ <bp:PATHWAY-COMPONENTS rdf:resource="#TRADD_TRAF2_RIP1_complex_binds_FADDStep" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#TRADD_TRAF2_RIP1_complex_dissociates_from_the_TNF_alpha_TNF_R1_complex_Step" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#TNF_Binds_TNF_R1Step" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#TRADD_TRAF2_RIP1_FADD_complex_binds_Pro_Caspase_8__Step" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#TNF_TNF_R1_binds_TRADD__TRAF2_and_RIP_ComplexStep" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TNF signaling</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TNF signaling</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome75893" />
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The Tumor Necrosis Factor alpha (TNF-alpha) mediated apoptosis pathway has been implicated in the pathogenesis of a number of diseases including sepsis, diabetes, cancer, osteoporosis, multiple sclerosis, rheumatoid arthritis, and inflammatory bowel diseases. The TNF signaling network provides extensive cross talk between the apoptotic pathway, and the other NF-B, and JNK pathways that also emanate from TNF-R.</bp:COMMENT>
+ <bp:EVIDENCE rdf:resource="#Summation_140942" />
+ </bp:pathway>
+ <bp:biochemicalReaction rdf:ID="TNF_Binds_TNF_R1">
+ <bp:LEFT rdf:resource="#TNF_alpha__plasma_membrane_" />
+ <bp:LEFT rdf:resource="#TNF_RI__plasma_membrane_" />
+ <bp:RIGHT rdf:resource="#TNF_alpha_TNF_R1_complex__plasma_membrane_" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TNF Binds TNF-R1</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TNF Binds TNF-R1</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome83660" />
+ <bp:XREF rdf:resource="#Pubmed_2848815" />
+ </bp:biochemicalReaction>
+ <bp:sequenceParticipant rdf:ID="TNF_alpha__plasma_membrane_">
+ <bp:CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_P01375_Tumor_necrosis_factor_precursor__TNF_alpha___Tumor_necrosis_factor_ligand_superfamily_member_2___TNF_a___Cachectin_" />
+ </bp:sequenceParticipant>
+ <bp:protein rdf:ID="UniProt_P01375_Tumor_necrosis_factor_precursor__TNF_alpha___Tumor_necrosis_factor_ligand_superfamily_member_2___TNF_a___Cachectin_">
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P01375 Tumor necrosis factor precursor (TNF-alpha) (Tumor necrosis factor ligand superfamily member 2) (TNF-a) (Cachectin)</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TNF</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TNFA</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TNFSF2</bp:SYNONYMS>
+ <bp:XREF rdf:resource="#UniProt_P01375" />
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Cytokine that binds to TNFRSF1A/TNFR1 and TNFRSF1B/TNFBR. It is mainly secreted by macrophages and can induce cell death of certain tumor cell lines. It is potent pyrogen causing fever by direct action or by stimulation of interleukin 1 secretion and is implicated in the induction of cachexia, Under certain conditions it can stimulate cell proliferation and induce cell differentiation. SUBUNIT: Homotrimer. S [...]
+ </bp:protein>
+ <bp:unificationXref rdf:ID="UniProt_P01375">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P01375</bp:ID>
+ </bp:unificationXref>
+ <bp:sequenceParticipant rdf:ID="TNF_RI__plasma_membrane_">
+ <bp:CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_P19438_Tumor_necrosis_factor_receptor_superfamily_member_1A_precursor__p60___TNF_R1___TNF_RI___p55___CD120a___Contains__Tumor_necrosis_factor_binding_protein_1__TBPI__" />
+ </bp:sequenceParticipant>
+ <bp:protein rdf:ID="UniProt_P19438_Tumor_necrosis_factor_receptor_superfamily_member_1A_precursor__p60___TNF_R1___TNF_RI___p55___CD120a___Contains__Tumor_necrosis_factor_binding_protein_1__TBPI__">
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P19438 Tumor necrosis factor receptor superfamily member 1A precursor (p60) (TNF-R1) (TNF-RI) (p55) (CD120a) [Contains: Tumor necrosis factor binding protein 1 (TBPI)]</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TNFRSF1A</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TNFR1</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TNFAR</bp:SYNONYMS>
+ <bp:XREF rdf:resource="#UniProt_P19438" />
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Receptor for TNFSF2/TNF-alpha and homotrimeric TNFSF1/lymphotoxin-alpha. The adaptor molecule FADD recruits caspase-8 to the activated receptor. The resulting death-inducing signaling complex (DISC) performs caspase-8 proteolytic activation which initiates the subsequent cascade of caspases (aspartate- specific cysteine proteases) mediating apoptosis. Contributes to the induction of noncytocidal TNF effects [...]
+ </bp:protein>
+ <bp:unificationXref rdf:ID="UniProt_P19438">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P19438</bp:ID>
+ </bp:unificationXref>
+ <bp:sequenceParticipant rdf:ID="TNF_alpha_TNF_R1_complex__plasma_membrane_">
+ <bp:CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#TNF_alpha_TNF_R1_complex__plasma_membrane_1" />
+ </bp:sequenceParticipant>
+ <bp:complex rdf:ID="TNF_alpha_TNF_R1_complex__plasma_membrane_1">
+ <bp:COMPONENTS rdf:resource="#TNF_alpha__plasma_membrane_1" />
+ <bp:COMPONENTS rdf:resource="#TNF_RI__plasma_membrane_1" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TNF-alpha:TNF-R1 complex [plasma membrane]</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TNF-alpha:TNF-R1 complex</bp:SHORT-NAME>
+ </bp:complex>
+ <bp:sequenceParticipant rdf:ID="TNF_alpha__plasma_membrane_1">
+ <bp:CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_P01375_Tumor_necrosis_factor_precursor__TNF_alpha___Tumor_necrosis_factor_ligand_superfamily_member_2___TNF_a___Cachectin_" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="TNF_RI__plasma_membrane_1">
+ <bp:CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_P19438_Tumor_necrosis_factor_receptor_superfamily_member_1A_precursor__p60___TNF_R1___TNF_RI___p55___CD120a___Contains__Tumor_necrosis_factor_binding_protein_1__TBPI__" />
+ </bp:sequenceParticipant>
+ <bp:unificationXref rdf:ID="Reactome83660">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">83660</bp:ID>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</bp:COMMENT>
+ </bp:unificationXref>
+ <bp:publicationXref rdf:ID="Pubmed_2848815">
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2848815</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</bp:DB>
+ <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1988</bp:YEAR>
+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Human tumor necrosis factor-alpha receptor. Purification by immunoaffinity chromatography and initial characterization.</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Stauber, GB</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Aiyer, RA</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Aggarwal, BB</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Biol Chem 263:19098-104</bp:SOURCE>
+ </bp:publicationXref>
+ <bp:pathwayStep rdf:ID="TNF_Binds_TNF_R1Step">
+ <bp:STEP-INTERACTIONS rdf:resource="#TNF_Binds_TNF_R1" />
+ <bp:NEXT-STEP rdf:resource="#TNF_TNF_R1_binds_TRADD__TRAF2_and_RIP_ComplexStep" />
+ </bp:pathwayStep>
+ <bp:biochemicalReaction rdf:ID="TNF_TNF_R1_binds_TRADD__TRAF2_and_RIP_Complex">
+ <bp:LEFT rdf:resource="#TNF_receptor_associated_factor_2__cytosol_" />
+ <bp:LEFT rdf:resource="#RIP__cytosol_" />
+ <bp:LEFT rdf:resource="#TNF_alpha_TNF_R1_complex__plasma_membrane_2" />
+ <bp:LEFT rdf:resource="#Tumor_necrosis_factor_receptor_type_1_associated_DEATH_domain_protein__cytosol_" />
+ <bp:RIGHT rdf:resource="#TNF_alpha_TNF_R1_TRAPP_RIP1_TRAF2_Complex__plasma_membrane_" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TNF:TNF-R1 binds TRADD, TRAF2 and RIP Complex</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TNF:TNF-R1 binds TRADD, TRAF2 and RIP Complex</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome83656" />
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Once the TNF-aplha:TNF-R1:TRADD complex is formed the two TNF-alpha mediated pathways are possible. The variable is the recruitment of FADD to the larger complex formed by the TNF-aplha:TNF-R1 platform via the interaction of the Death Domains. The steps leading to the Jun, NF kappaB, or apoptotic pathways are rife with modulation.</bp:COMMENT>
+ <bp:EVIDENCE rdf:resource="#Summation_74302" />
+ <bp:XREF rdf:resource="#Pubmed_7758105" />
+ </bp:biochemicalReaction>
+ <bp:sequenceParticipant rdf:ID="TNF_receptor_associated_factor_2__cytosol_">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q12933_1_TNF_receptor_associated_factor_2__Tumor_necrosis_factor_type_2_receptor_associated_protein_3_" />
+ </bp:sequenceParticipant>
+ <bp:protein rdf:ID="UniProt_Q12933_1_TNF_receptor_associated_factor_2__Tumor_necrosis_factor_type_2_receptor_associated_protein_3_">
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:Q12933-1 TNF receptor associated factor 2 (Tumor necrosis factor type 2 receptor associated protein 3)</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRAP3</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRAF2</bp:SYNONYMS>
+ <bp:XREF rdf:resource="#UniProt_Q12933" />
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Adapter protein and signal transducer that links members of the tumor necrosis factor receptor family to different signaling pathways by association with the receptor cytoplasmic domain and kinases. Association to the receptor is also mediated by the interaction with TRADD. Mediates activation of NF-kappa-B and JNK and is involved in apoptosis. The TRAF1/TRAF2 complex recruits the apoptotic suppressors BIRC2 [...]
+ </bp:protein>
+ <bp:unificationXref rdf:ID="UniProt_Q12933">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Q12933</bp:ID>
+ </bp:unificationXref>
+ <bp:sequenceParticipant rdf:ID="RIP__cytosol_">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q13546_Receptor_interacting_serine_threonine_protein_kinase_2__EC_2_7_1_37___Serine_threonine_protein_kinase_RIP___Cell_death_protein_RIP___Receptor_interacting_protein_" />
+ </bp:sequenceParticipant>
+ <bp:protein rdf:ID="UniProt_Q13546_Receptor_interacting_serine_threonine_protein_kinase_2__EC_2_7_1_37___Serine_threonine_protein_kinase_RIP___Cell_death_protein_RIP___Receptor_interacting_protein_">
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:Q13546 Receptor-interacting serine/threonine-protein kinase 2 (EC 2.7.1.37) (Serine/threonine-protein kinase RIP) (Cell death protein RIP) (Receptor interacting protein)</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RIP</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RIPK1</bp:SYNONYMS>
+ <bp:XREF rdf:resource="#UniProt_Q13546" />
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Promotes apoptosis and activation of NF-kappa-B. Required for TNFRSF1A mediated activation of NF-kappa-B. CATALYTIC ACTIVITY: ATP + a protein = ADP + a phosphoprotein. SUBUNIT: Binds to the death domain of TNFRSF6 and TRADD. Is recruited by TRADD to TNFRSF1A in a TNF-dependent process. Binds RIPK3, UBCE7IP1, EGFR, IKBKG, TRAF1, TRAF2 and TRAF3. Interacts with BNLF1. SUBCELLULAR LOCATION: Cytoplasmic. PTM: Pr [...]
+ </bp:protein>
+ <bp:unificationXref rdf:ID="UniProt_Q13546">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Q13546</bp:ID>
+ </bp:unificationXref>
+ <bp:sequenceParticipant rdf:ID="TNF_alpha_TNF_R1_complex__plasma_membrane_2">
+ <bp:CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#TNF_alpha_TNF_R1_complex__plasma_membrane_1" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="Tumor_necrosis_factor_receptor_type_1_associated_DEATH_domain_protein__cytosol_">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q15628_Tumor_necrosis_factor_receptor_type_1_associated_DEATH_domain_protein__TNFR1_associated_DEATH_domain_protein___TNFRSF1A_associated_via_death_domain_" />
+ </bp:sequenceParticipant>
+ <bp:protein rdf:ID="UniProt_Q15628_Tumor_necrosis_factor_receptor_type_1_associated_DEATH_domain_protein__TNFR1_associated_DEATH_domain_protein___TNFRSF1A_associated_via_death_domain_">
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:Q15628 Tumor necrosis factor receptor type 1 associated DEATH domain protein (TNFR1-associated DEATH domain protein) (TNFRSF1A-associated via death domain)</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRADD</bp:SYNONYMS>
+ <bp:XREF rdf:resource="#UniProt_Q15628" />
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Adapter molecule for TNFRSF1A/TNFR1 that specifically associates with the cytoplasmic domain of activated TNFRSF1A/TNFR1 mediating its interaction with FADD. Overexpression of TRADD leads to two major TNF-induced responses, apoptosis and activation of NF-kappa-B. SUBUNIT: Heterodimer with TNFRSF1A/TNFR1. Binds to TRAF2. Interacts with TRAF1, FADD, RIPK1 and TRPC4AP (By similarity). TISSUE SPECIFICITY: Found [...]
+ </bp:protein>
+ <bp:unificationXref rdf:ID="UniProt_Q15628">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Q15628</bp:ID>
+ </bp:unificationXref>
+ <bp:sequenceParticipant rdf:ID="TNF_alpha_TNF_R1_TRAPP_RIP1_TRAF2_Complex__plasma_membrane_">
+ <bp:CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#TNF_alpha_TNF_R1_TRAPP_RIP1_TRAF2_Complex__plasma_membrane_1" />
+ </bp:sequenceParticipant>
+ <bp:complex rdf:ID="TNF_alpha_TNF_R1_TRAPP_RIP1_TRAF2_Complex__plasma_membrane_1">
+ <bp:COMPONENTS rdf:resource="#TNF_receptor_associated_factor_2__cytosol_1" />
+ <bp:COMPONENTS rdf:resource="#RIP__cytosol_1" />
+ <bp:COMPONENTS rdf:resource="#TNF_alpha_TNF_R1_complex__plasma_membrane_3" />
+ <bp:COMPONENTS rdf:resource="#Tumor_necrosis_factor_receptor_type_1_associated_DEATH_domain_protein__cytosol_1" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TNF-alpha:TNF-R1:TRAPP:RIP1:TRAF2 Complex [plasma membrane]</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TNF-alpha:TNF-R1:TRAPP:RIP1:TRAF2 Complex</bp:SHORT-NAME>
+ </bp:complex>
+ <bp:sequenceParticipant rdf:ID="TNF_receptor_associated_factor_2__cytosol_1">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q12933_1_TNF_receptor_associated_factor_2__Tumor_necrosis_factor_type_2_receptor_associated_protein_3_" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="RIP__cytosol_1">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q13546_Receptor_interacting_serine_threonine_protein_kinase_2__EC_2_7_1_37___Serine_threonine_protein_kinase_RIP___Cell_death_protein_RIP___Receptor_interacting_protein_" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="TNF_alpha_TNF_R1_complex__plasma_membrane_3">
+ <bp:CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#TNF_alpha_TNF_R1_complex__plasma_membrane_1" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="Tumor_necrosis_factor_receptor_type_1_associated_DEATH_domain_protein__cytosol_1">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q15628_Tumor_necrosis_factor_receptor_type_1_associated_DEATH_domain_protein__TNFR1_associated_DEATH_domain_protein___TNFRSF1A_associated_via_death_domain_" />
+ </bp:sequenceParticipant>
+ <bp:unificationXref rdf:ID="Reactome83656">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">83656</bp:ID>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</bp:COMMENT>
+ </bp:unificationXref>
+ <bp:evidence rdf:ID="Summation_74302" />
+ <bp:publicationXref rdf:ID="Pubmed_7758105">
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">7758105</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</bp:DB>
+ <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1995</bp:YEAR>
+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The TNF receptor 1-associated protein TRADD signals cell death and NF-kappa B activation</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Hsu, H</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Xiong, J</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Goeddel, DV</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cell 81:495-504</bp:SOURCE>
+ </bp:publicationXref>
+ <bp:pathwayStep rdf:ID="TNF_TNF_R1_binds_TRADD__TRAF2_and_RIP_ComplexStep">
+ <bp:STEP-INTERACTIONS rdf:resource="#TNF_TNF_R1_binds_TRADD__TRAF2_and_RIP_Complex" />
+ <bp:NEXT-STEP rdf:resource="#TRADD_TRAF2_RIP1_complex_dissociates_from_the_TNF_alpha_TNF_R1_complex_Step" />
+ </bp:pathwayStep>
+ <bp:biochemicalReaction rdf:ID="TRADD_TRAF2_RIP1_complex_dissociates_from_the_TNF_alpha_TNF_R1_complex_">
+ <bp:LEFT rdf:resource="#TNF_alpha_TNF_R1_TRAPP_RIP1_TRAF2_Complex__plasma_membrane_2" />
+ <bp:RIGHT rdf:resource="#TRAF2_TRADD_RIP1_Complex__cytosol_" />
+ <bp:RIGHT rdf:resource="#TNF_alpha_TNF_R1_complex__plasma_membrane_4" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRADD:TRAF2:RIP1 complex dissociates from the TNF-alpha:TNF-R1 complex.</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRADD:TRAF2:RIP1 complex dissociates from the TNF-alpha:TNF-R1 complex.</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome83582" />
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Once formed the TRADD:TRAF2:RIP1 complex may dissociate from the TNF:TNF-R1 platform and become cytosolic. If this complex recruits FADD then the cell will be pushed along the apoptotic pathway.</bp:COMMENT>
+ <bp:EVIDENCE rdf:resource="#Summation_74353" />
+ <bp:XREF rdf:resource="#Pubmed_12887920" />
+ </bp:biochemicalReaction>
+ <bp:sequenceParticipant rdf:ID="TNF_alpha_TNF_R1_TRAPP_RIP1_TRAF2_Complex__plasma_membrane_2">
+ <bp:CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#TNF_alpha_TNF_R1_TRAPP_RIP1_TRAF2_Complex__plasma_membrane_1" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="TRAF2_TRADD_RIP1_Complex__cytosol_">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#TRAF2_TRADD_RIP1_Complex__cytosol_1" />
+ </bp:sequenceParticipant>
+ <bp:complex rdf:ID="TRAF2_TRADD_RIP1_Complex__cytosol_1">
+ <bp:COMPONENTS rdf:resource="#TNF_receptor_associated_factor_2__cytosol_2" />
+ <bp:COMPONENTS rdf:resource="#RIP__cytosol_2" />
+ <bp:COMPONENTS rdf:resource="#Tumor_necrosis_factor_receptor_type_1_associated_DEATH_domain_protein__cytosol_2" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRAF2:TRADD:RIP1 Complex [cytosol]</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRAF2:TRADD:RIP1 Complex</bp:SHORT-NAME>
+ </bp:complex>
+ <bp:sequenceParticipant rdf:ID="TNF_receptor_associated_factor_2__cytosol_2">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q12933_1_TNF_receptor_associated_factor_2__Tumor_necrosis_factor_type_2_receptor_associated_protein_3_" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="RIP__cytosol_2">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q13546_Receptor_interacting_serine_threonine_protein_kinase_2__EC_2_7_1_37___Serine_threonine_protein_kinase_RIP___Cell_death_protein_RIP___Receptor_interacting_protein_" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="Tumor_necrosis_factor_receptor_type_1_associated_DEATH_domain_protein__cytosol_2">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q15628_Tumor_necrosis_factor_receptor_type_1_associated_DEATH_domain_protein__TNFR1_associated_DEATH_domain_protein___TNFRSF1A_associated_via_death_domain_" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="TNF_alpha_TNF_R1_complex__plasma_membrane_4">
+ <bp:CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#TNF_alpha_TNF_R1_complex__plasma_membrane_1" />
+ </bp:sequenceParticipant>
+ <bp:unificationXref rdf:ID="Reactome83582">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">83582</bp:ID>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</bp:COMMENT>
+ </bp:unificationXref>
+ <bp:evidence rdf:ID="Summation_74353" />
+ <bp:publicationXref rdf:ID="Pubmed_12887920">
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">12887920</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</bp:DB>
+ <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2003</bp:YEAR>
+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Induction of TNF receptor I-mediated apoptosis via two sequential signaling complexes</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Micheau, O</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Tschopp, J</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cell 114:181-90</bp:SOURCE>
+ </bp:publicationXref>
+ <bp:pathwayStep rdf:ID="TRADD_TRAF2_RIP1_complex_dissociates_from_the_TNF_alpha_TNF_R1_complex_Step">
+ <bp:STEP-INTERACTIONS rdf:resource="#TRADD_TRAF2_RIP1_complex_dissociates_from_the_TNF_alpha_TNF_R1_complex_" />
+ <bp:NEXT-STEP rdf:resource="#TRADD_TRAF2_RIP1_complex_binds_FADDStep" />
+ </bp:pathwayStep>
+ <bp:biochemicalReaction rdf:ID="TRADD_TRAF2_RIP1_complex_binds_FADD">
+ <bp:LEFT rdf:resource="#TRAF2_TRADD_RIP1_Complex__cytosol_2" />
+ <bp:LEFT rdf:resource="#FADD__cytosol_2" />
+ <bp:RIGHT rdf:resource="#TRAF2_TRADD_RIP1_FADD__cytosol_" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRADD:TRAF2:RIP1 complex binds FADD</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRADD:TRAF2:RIP1 complex binds FADD</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome140978" />
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Once formed the TRADD:TRAF2:RIP1 complex may dissociate from the TNF:TNF-R1 platform and become cytosolic. If this complex recruits FADD then the cell will be pushed along the apoptotic pathway.</bp:COMMENT>
+ <bp:EVIDENCE rdf:resource="#Summation_74353" />
+ <bp:XREF rdf:resource="#Pubmed_12887920" />
+ </bp:biochemicalReaction>
+ <bp:sequenceParticipant rdf:ID="TRAF2_TRADD_RIP1_Complex__cytosol_2">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#TRAF2_TRADD_RIP1_Complex__cytosol_1" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="FADD__cytosol_2">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q13158_FADD_protein__FAS_associating_death_domain_containing_protein___Mediator_of_receptor_induced_toxicity_" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="TRAF2_TRADD_RIP1_FADD__cytosol_">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#TRAF2_TRADD_RIP1_FADD__cytosol_1" />
+ </bp:sequenceParticipant>
+ <bp:complex rdf:ID="TRAF2_TRADD_RIP1_FADD__cytosol_1">
+ <bp:COMPONENTS rdf:resource="#TRAF2_TRADD_RIP1_Complex__cytosol_3" />
+ <bp:COMPONENTS rdf:resource="#FADD__cytosol_3" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRAF2:TRADD:RIP1:FADD [cytosol]</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRAF2:TRADD:RIP1:FADD</bp:SHORT-NAME>
+ </bp:complex>
+ <bp:sequenceParticipant rdf:ID="TRAF2_TRADD_RIP1_Complex__cytosol_3">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#TRAF2_TRADD_RIP1_Complex__cytosol_1" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="FADD__cytosol_3">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q13158_FADD_protein__FAS_associating_death_domain_containing_protein___Mediator_of_receptor_induced_toxicity_" />
+ </bp:sequenceParticipant>
+ <bp:unificationXref rdf:ID="Reactome140978">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">140978</bp:ID>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</bp:COMMENT>
+ </bp:unificationXref>
+ <bp:pathwayStep rdf:ID="TRADD_TRAF2_RIP1_complex_binds_FADDStep">
+ <bp:STEP-INTERACTIONS rdf:resource="#TRADD_TRAF2_RIP1_complex_binds_FADD" />
+ <bp:NEXT-STEP rdf:resource="#TRADD_TRAF2_RIP1_FADD_complex_binds_Pro_Caspase_8__Step" />
+ </bp:pathwayStep>
+ <bp:biochemicalReaction rdf:ID="TRADD_TRAF2_RIP1_FADD_complex_binds_Pro_Caspase_8__">
+ <bp:LEFT rdf:resource="#TRAF2_TRADD_RIP1_FADD__cytosol_2" />
+ <bp:LEFT rdf:resource="#Caspase_8_precursor___cytosol_2" />
+ <bp:RIGHT rdf:resource="#TRADD_TRAF2_RIP1_FADD_Capase_8_Complex__cytosol_" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRADD:TRAF2:RIP1:FADD complex binds Pro-Caspase 8</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRADD:TRAF2:RIP1:FADD complex binds Pro-Caspase 8</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome75240" />
+ <bp:XREF rdf:resource="#Pubmed_12887920" />
+ </bp:biochemicalReaction>
+ <bp:sequenceParticipant rdf:ID="TRAF2_TRADD_RIP1_FADD__cytosol_2">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#TRAF2_TRADD_RIP1_FADD__cytosol_1" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="Caspase_8_precursor___cytosol_2">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q14790_1_Caspase_8_precursor__EC_3_4_22_____CASP_8___ICE_like_apoptotic_protease_5___MORT1_associated_CED_3_homolog___MACH___FADD_homologous_ICE_CED_3_like_protease___FADD_like_ICE___FLICE___Apoptotic_cysteine_protease___Apoptotic_protease_Mch_5___CAP4_" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="TRADD_TRAF2_RIP1_FADD_Capase_8_Complex__cytosol_">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#TRADD_TRAF2_RIP1_FADD_Capase_8_Complex__cytosol_1" />
+ </bp:sequenceParticipant>
+ <bp:complex rdf:ID="TRADD_TRAF2_RIP1_FADD_Capase_8_Complex__cytosol_1">
+ <bp:COMPONENTS rdf:resource="#TRAF2_TRADD_RIP1_FADD__cytosol_3" />
+ <bp:COMPONENTS rdf:resource="#Caspase_8_precursor___cytosol_3" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRADD:TRAF2:RIP1:FADD:Capase-8 Complex [cytosol]</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRADD:TRAF2:RIP1:FADD:Capase-8 Complex</bp:SHORT-NAME>
+ </bp:complex>
+ <bp:sequenceParticipant rdf:ID="TRAF2_TRADD_RIP1_FADD__cytosol_3">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#TRAF2_TRADD_RIP1_FADD__cytosol_1" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="Caspase_8_precursor___cytosol_3">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q14790_1_Caspase_8_precursor__EC_3_4_22_____CASP_8___ICE_like_apoptotic_protease_5___MORT1_associated_CED_3_homolog___MACH___FADD_homologous_ICE_CED_3_like_protease___FADD_like_ICE___FLICE___Apoptotic_cysteine_protease___Apoptotic_protease_Mch_5___CAP4_" />
+ </bp:sequenceParticipant>
+ <bp:unificationXref rdf:ID="Reactome75240">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">75240</bp:ID>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</bp:COMMENT>
+ </bp:unificationXref>
+ <bp:pathwayStep rdf:ID="TRADD_TRAF2_RIP1_FADD_complex_binds_Pro_Caspase_8__Step">
+ <bp:STEP-INTERACTIONS rdf:resource="#TRADD_TRAF2_RIP1_FADD_complex_binds_Pro_Caspase_8__" />
+ <bp:NEXT-STEP rdf:resource="#TNF_Mediated_Activation_of_Pro_caspase_8Step" />
+ </bp:pathwayStep>
+ <bp:unificationXref rdf:ID="Reactome75893">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">75893</bp:ID>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</bp:COMMENT>
+ </bp:unificationXref>
+ <bp:evidence rdf:ID="Summation_140942">
+ <bp:XREF rdf:resource="#Pubmed_12040173" />
+ </bp:evidence>
+ <bp:publicationXref rdf:ID="Pubmed_12040173">
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">12040173</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</bp:DB>
+ <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2002</bp:YEAR>
+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TNF-R1 signaling: a beautiful pathway</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Chen, G</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Goeddel, DV</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Science 296:1634-5</bp:SOURCE>
+ </bp:publicationXref>
+ <bp:pathwayStep rdf:ID="TNF_signalingStep">
+ <bp:STEP-INTERACTIONS rdf:resource="#TNF_signaling" />
+ </bp:pathwayStep>
+ <bp:pathway rdf:ID="TRAIL__signaling">
+ <bp:PATHWAY-COMPONENTS rdf:resource="#TRAIL_TRAIL_Receptor2_Trimer_FADD_complex_binds_Caspase_10Step" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#TRAIL_TRAIL_Receptor2_Trimer_FADD_complex_binds_Caspase_8Step" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#TRAIL_TRAIL_receptor_2_Trimer_Binds_FADDStep" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#Trimerization_of_TRAIL__TRAIL_receptor_2_complexStep" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#TRAIL_Binds_TRAIL_Receptor2Step" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRAIL signaling</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRAIL signaling</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome75158" />
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Tumor necrosis factor-related apoptosis-inducing ligand or Apo 2 ligand (TRAIL/Apo2L) is a member of the tumor necrosis factor (TNF) family. This group of apoptosis induction pathways all work through protein interactions mediated by the intracellular death domain (DD), encoded within the cytoplasmic domain of the receptor. TRAIL selectively induces apoptosis through its interaction with the Fas-associated death domai [...]
+ <bp:EVIDENCE rdf:resource="#Summation_141083" />
+ <bp:XREF rdf:resource="#Pubmed_14634624" />
+ </bp:pathway>
+ <bp:biochemicalReaction rdf:ID="TRAIL_Binds_TRAIL_Receptor2">
+ <bp:LEFT rdf:resource="#TRAIL_receptor_2__plasma_membrane_" />
+ <bp:LEFT rdf:resource="#TRAIL__extracellular_region_" />
+ <bp:RIGHT rdf:resource="#TRAIL_receptor_2_TRAIL_complex__plasma_membrane_" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRAIL Binds TRAIL-Receptor2</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRAIL Binds TRAIL-Receptor2</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome75238" />
+ <bp:XREF rdf:resource="#Pubmed_8777713" />
+ </bp:biochemicalReaction>
+ <bp:sequenceParticipant rdf:ID="TRAIL_receptor_2__plasma_membrane_">
+ <bp:CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_O14763_1_Tumor_necrosis_factor_receptor_superfamily_member_10B_precursor__Death_receptor_5___TNF_related_apoptosis_inducing_ligand_receptor_2___TRAIL_receptor_2___TRAIL_R2_" />
+ </bp:sequenceParticipant>
+ <bp:protein rdf:ID="UniProt_O14763_1_Tumor_necrosis_factor_receptor_superfamily_member_10B_precursor__Death_receptor_5___TNF_related_apoptosis_inducing_ligand_receptor_2___TRAIL_receptor_2___TRAIL_R2_">
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:O14763-1 Tumor necrosis factor receptor superfamily member 10B precursor (Death receptor 5) (TNF-related apoptosis-inducing ligand receptor 2) (TRAIL receptor-2) (TRAIL-R2)</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">KILLER</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ZTNFR9</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRICK2</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DR5</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRAILR2</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TNFRSF10B</bp:SYNONYMS>
+ <bp:XREF rdf:resource="#UniProt_O14763" />
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Receptor for the cytotoxic ligand TNFSF10/TRAIL. The adaptor molecule FADD recruits caspase-8 to the activated receptor. The resulting death-inducing signaling complex (DISC) performs caspase-8 proteolytic activation which initiates the subsequent cascade of caspases (aspartate-specific cysteine proteases) mediating apoptosis. Promotes the activation of NF- kappa-B. SUBUNIT: Homotrimer. Can interact with TRA [...]
+ </bp:protein>
+ <bp:unificationXref rdf:ID="UniProt_O14763">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">O14763</bp:ID>
+ </bp:unificationXref>
+ <bp:sequenceParticipant rdf:ID="TRAIL__extracellular_region_">
+ <bp:CELLULAR-LOCATION rdf:resource="#extracellular_region" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_P50591_Tumor_necrosis_factor_ligand_superfamily_member_10__TNF_related_apoptosis_inducing_ligand___TRAIL_protein___Apo_2_ligand___Apo_2L_" />
+ </bp:sequenceParticipant>
+ <bp:protein rdf:ID="UniProt_P50591_Tumor_necrosis_factor_ligand_superfamily_member_10__TNF_related_apoptosis_inducing_ligand___TRAIL_protein___Apo_2_ligand___Apo_2L_">
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P50591 Tumor necrosis factor ligand superfamily member 10 (TNF-related apoptosis inducing ligand) (TRAIL protein) (Apo-2 ligand) (Apo-2L)</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">APO2L</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TNFSF10</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRAIL</bp:SYNONYMS>
+ <bp:XREF rdf:resource="#UniProt_P50591" />
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Cytokine that binds to TNFRSF10A/TRAILR1, TNFRSF10B/TRAILR2, TNFRSF10C/TRAILR3, TNFRSF10D/TRAILR4 and possibly also to TNFRSF11B/OPG. Induces apoptosis. Its activity may be modulated by binding to the decoy receptors TNFRSF10C/TRAILR3, TNFRSF10D/TRAILR4 and TNFRSF11B/OPG that cannot induce apoptosis. COFACTOR: Binds 1 zinc ion and one anionic solvent molecule per trimer. SUBUNIT: Homotrimer. SUBCELLULAR LOCA [...]
+ </bp:protein>
+ <bp:unificationXref rdf:ID="UniProt_P50591">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P50591</bp:ID>
+ </bp:unificationXref>
+ <bp:sequenceParticipant rdf:ID="TRAIL_receptor_2_TRAIL_complex__plasma_membrane_">
+ <bp:CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#TRAIL_receptor_2_TRAIL_complex__plasma_membrane_1" />
+ </bp:sequenceParticipant>
+ <bp:complex rdf:ID="TRAIL_receptor_2_TRAIL_complex__plasma_membrane_1">
+ <bp:COMPONENTS rdf:resource="#TRAIL_receptor_2__plasma_membrane_1" />
+ <bp:COMPONENTS rdf:resource="#TRAIL__extracellular_region_1" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRAIL receptor-2:TRAIL complex [plasma membrane]</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRAIL receptor-2:TRAIL complex</bp:SHORT-NAME>
+ </bp:complex>
+ <bp:sequenceParticipant rdf:ID="TRAIL_receptor_2__plasma_membrane_1">
+ <bp:CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_O14763_1_Tumor_necrosis_factor_receptor_superfamily_member_10B_precursor__Death_receptor_5___TNF_related_apoptosis_inducing_ligand_receptor_2___TRAIL_receptor_2___TRAIL_R2_" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="TRAIL__extracellular_region_1">
+ <bp:CELLULAR-LOCATION rdf:resource="#extracellular_region" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_P50591_Tumor_necrosis_factor_ligand_superfamily_member_10__TNF_related_apoptosis_inducing_ligand___TRAIL_protein___Apo_2_ligand___Apo_2L_" />
+ </bp:sequenceParticipant>
+ <bp:unificationXref rdf:ID="Reactome75238">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">75238</bp:ID>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</bp:COMMENT>
+ </bp:unificationXref>
+ <bp:publicationXref rdf:ID="Pubmed_8777713">
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">8777713</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</bp:DB>
+ <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1995</bp:YEAR>
+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Identification and characterization of a new member of the TNF family that induces apoptosis</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Wiley, SR</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Schooley, K</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Smolak, PJ</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Din, WS</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Huang, CP</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Nicholl, JK</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Sutherland, GR</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Smith, TD</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Rauch, C</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Smith, CA</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Immunity 3:673-82</bp:SOURCE>
+ </bp:publicationXref>
+ <bp:pathwayStep rdf:ID="TRAIL_Binds_TRAIL_Receptor2Step">
+ <bp:STEP-INTERACTIONS rdf:resource="#TRAIL_Binds_TRAIL_Receptor2" />
+ <bp:NEXT-STEP rdf:resource="#Trimerization_of_TRAIL__TRAIL_receptor_2_complexStep" />
+ <bp:NEXT-STEP rdf:resource="#TRAIL_TRAIL_receptor_2_Trimer_Binds_FADDStep" />
+ </bp:pathwayStep>
+ <bp:biochemicalReaction rdf:ID="Trimerization_of_TRAIL__TRAIL_receptor_2_complex">
+ <bp:LEFT rdf:resource="#TRAIL_receptor_2_TRAIL_complex__plasma_membrane_2" />
+ <bp:RIGHT rdf:resource="#TRAIL_receptor_2_TRAIL_Trimer__plasma_membrane_" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Trimerization of TRAIL: TRAIL receptor-2 complex</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Trimerization of TRAIL: TRAIL receptor-2 complex</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome141139" />
+ <bp:XREF rdf:resource="#Pubmed_10894160" />
+ </bp:biochemicalReaction>
+ <bp:sequenceParticipant rdf:ID="TRAIL_receptor_2_TRAIL_complex__plasma_membrane_2">
+ <bp:CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#TRAIL_receptor_2_TRAIL_complex__plasma_membrane_1" />
+ <bp:STOICHIOMETRIC-COEFFICIENT rdf:datatype="http://www.w3.org/2001/XMLSchema#int">3</bp:STOICHIOMETRIC-COEFFICIENT>
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="TRAIL_receptor_2_TRAIL_Trimer__plasma_membrane_">
+ <bp:CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#TRAIL_receptor_2_TRAIL_Trimer__plasma_membrane_1" />
+ </bp:sequenceParticipant>
+ <bp:complex rdf:ID="TRAIL_receptor_2_TRAIL_Trimer__plasma_membrane_1">
+ <bp:COMPONENTS rdf:resource="#TRAIL_receptor_2_TRAIL_complex__plasma_membrane_3" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRAIL receptor-2:TRAIL Trimer [plasma membrane]</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRAIL receptor-2:TRAIL Trimer</bp:SHORT-NAME>
+ </bp:complex>
+ <bp:sequenceParticipant rdf:ID="TRAIL_receptor_2_TRAIL_complex__plasma_membrane_3">
+ <bp:CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#TRAIL_receptor_2_TRAIL_complex__plasma_membrane_1" />
+ <bp:STOICHIOMETRIC-COEFFICIENT rdf:datatype="http://www.w3.org/2001/XMLSchema#int">3</bp:STOICHIOMETRIC-COEFFICIENT>
+ </bp:sequenceParticipant>
+ <bp:unificationXref rdf:ID="Reactome141139">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">141139</bp:ID>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</bp:COMMENT>
+ </bp:unificationXref>
+ <bp:publicationXref rdf:ID="Pubmed_10894160">
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">10894160</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</bp:DB>
+ <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2000</bp:YEAR>
+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FADD/MORT1 and caspase-8 are recruited to TRAIL receptors 1 and 2 and are essential for apoptosis mediated by TRAIL receptor 2</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Sprick, MR</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Weigand, MA</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Rieser, E</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Rauch, CT</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Juo, P</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Blenis, J</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Krammer, PH</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Walczak, H</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Immunity 12:599-609</bp:SOURCE>
+ </bp:publicationXref>
+ <bp:pathwayStep rdf:ID="Trimerization_of_TRAIL__TRAIL_receptor_2_complexStep">
+ <bp:STEP-INTERACTIONS rdf:resource="#Trimerization_of_TRAIL__TRAIL_receptor_2_complex" />
+ </bp:pathwayStep>
+ <bp:biochemicalReaction rdf:ID="TRAIL_TRAIL_receptor_2_Trimer_Binds_FADD">
+ <bp:LEFT rdf:resource="#FADD__cytosol_4" />
+ <bp:LEFT rdf:resource="#TRAIL_receptor_2_TRAIL_Trimer__plasma_membrane_2" />
+ <bp:RIGHT rdf:resource="#TRAIL_TRAIL_receptor_2_FADD_complex__plasma_membrane_" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRAIL:TRAIL receptor-2 Trimer Binds FADD</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRAIL:TRAIL receptor-2 Trimer Binds FADD</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome75187" />
+ <bp:XREF rdf:resource="#Pubmed_10894160" />
+ </bp:biochemicalReaction>
+ <bp:sequenceParticipant rdf:ID="FADD__cytosol_4">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q13158_FADD_protein__FAS_associating_death_domain_containing_protein___Mediator_of_receptor_induced_toxicity_" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="TRAIL_receptor_2_TRAIL_Trimer__plasma_membrane_2">
+ <bp:CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#TRAIL_receptor_2_TRAIL_Trimer__plasma_membrane_1" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="TRAIL_TRAIL_receptor_2_FADD_complex__plasma_membrane_">
+ <bp:CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#TRAIL_TRAIL_receptor_2_FADD_complex__plasma_membrane_1" />
+ </bp:sequenceParticipant>
+ <bp:complex rdf:ID="TRAIL_TRAIL_receptor_2_FADD_complex__plasma_membrane_1">
+ <bp:COMPONENTS rdf:resource="#FADD__cytosol_5" />
+ <bp:COMPONENTS rdf:resource="#TRAIL_receptor_2_TRAIL_Trimer__plasma_membrane_3" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRAIL:TRAIL receptor-2:FADD complex [plasma membrane]</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRAIL:TRAIL receptor-2:FADD complex</bp:SHORT-NAME>
+ </bp:complex>
+ <bp:sequenceParticipant rdf:ID="FADD__cytosol_5">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q13158_FADD_protein__FAS_associating_death_domain_containing_protein___Mediator_of_receptor_induced_toxicity_" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="TRAIL_receptor_2_TRAIL_Trimer__plasma_membrane_3">
+ <bp:CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#TRAIL_receptor_2_TRAIL_Trimer__plasma_membrane_1" />
+ </bp:sequenceParticipant>
+ <bp:unificationXref rdf:ID="Reactome75187">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">75187</bp:ID>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</bp:COMMENT>
+ </bp:unificationXref>
+ <bp:modulation rdf:ID="_CASP8_and_FADD_like_apoptosis_regulator_precursor__negatively_regulates__TRAIL_TRAIL_receptor_2_Trimer_Binds_FADD_">
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">'CASP8 and FADD-like apoptosis regulator precursor' negatively regulates 'TRAIL:TRAIL receptor-2 Trimer Binds FADD'</bp:NAME>
+ <bp:CONTROL-TYPE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">INHIBITION</bp:CONTROL-TYPE>
+ <bp:CONTROLLER rdf:resource="#CASP8_and_FADD_like_apoptosis_regulator_precursor__cytosol_" />
+ <bp:CONTROLLED rdf:resource="#TRAIL_TRAIL_receptor_2_Trimer_Binds_FADD" />
+ </bp:modulation>
+ <bp:sequenceParticipant rdf:ID="CASP8_and_FADD_like_apoptosis_regulator_precursor__cytosol_">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_O15519_1_CASP8_and_FADD_like_apoptosis_regulator_precursor__Cellular_FLICE_like_inhibitory_protein___c_FLIP___Caspase_eight_related_protein___Casper___Caspase_like_apoptosis_regulatory_protein___CLARP___MACH_related_inducer_of_toxicity___MRIT___Caspase_homolog___CASH___Inhibitor_of_FLICE___I_FLICE___FADD_like_antiapoptotic_molecule_1___Flame_1___Usurpin_" />
+ </bp:sequenceParticipant>
+ <bp:protein rdf:ID="UniProt_O15519_1_CASP8_and_FADD_like_apoptosis_regulator_precursor__Cellular_FLICE_like_inhibitory_protein___c_FLIP___Caspase_eight_related_protein___Casper___Caspase_like_apoptosis_regulatory_protein___CLARP___MACH_related_inducer_of_toxicity___MRIT___Caspase_homolog___CASH___Inhibitor_of_FLICE___I_FLICE___FADD_like_antiapoptotic_molecule_1___Flame_1___Usurpin_">
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:O15519-1 CASP8 and FADD-like apoptosis regulator precursor (Cellular FLICE-like inhibitory protein) (c-FLIP) (Caspase-eight-related protein) (Casper) (Caspase-like apoptosis regulatory protein) (CLARP) (MACH-related inducer of toxicity) (MRIT) (Caspase homolog) (CASH) (Inhibitor of FLICE) (I-FLICE) (FADD-like antiapoptotic molecule 1) (Flame-1) (Usurpin)</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CASH</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CFLAR</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">MRIT</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CLARP</bp:SYNONYMS>
+ <bp:XREF rdf:resource="#UniProt_O15519" />
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Apoptosis regulator protein which may function as a crucial link between cell survival and cell death pathways in mammalian cells. Acts as an inhibitor of TNFRSF6 mediated apoptosis. A proteolytic fragment (p43) is likely retained in the death-inducing signaling complex (DISC) thereby blocking further recruitment and processing of caspase-8 at the complex. Full length and shorter isoforms have been shown eit [...]
+ </bp:protein>
+ <bp:unificationXref rdf:ID="UniProt_O15519">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">O15519</bp:ID>
+ </bp:unificationXref>
+ <bp:pathwayStep rdf:ID="TRAIL_TRAIL_receptor_2_Trimer_Binds_FADDStep">
+ <bp:STEP-INTERACTIONS rdf:resource="#TRAIL_TRAIL_receptor_2_Trimer_Binds_FADD" />
+ <bp:NEXT-STEP rdf:resource="#TRAIL_TRAIL_Receptor2_Trimer_FADD_complex_binds_Caspase_8Step" />
+ <bp:NEXT-STEP rdf:resource="#TRAIL_TRAIL_Receptor2_Trimer_FADD_complex_binds_Caspase_10Step" />
+ <bp:STEP-INTERACTIONS rdf:resource="#_CASP8_and_FADD_like_apoptosis_regulator_precursor__negatively_regulates__TRAIL_TRAIL_receptor_2_Trimer_Binds_FADD_" />
+ </bp:pathwayStep>
+ <bp:biochemicalReaction rdf:ID="TRAIL_TRAIL_Receptor2_Trimer_FADD_complex_binds_Caspase_8">
+ <bp:LEFT rdf:resource="#TRAIL_TRAIL_receptor_2_FADD_complex__plasma_membrane_2" />
+ <bp:LEFT rdf:resource="#Caspase_8_precursor___cytosol_4" />
+ <bp:RIGHT rdf:resource="#TRAIL_TRAIL_receptor_2_Trimer_FADD_Caspase_8_precursor_complex__plasma_membrane_" />
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+ </bp:sequenceParticipant>
+ <bp:complex rdf:ID="Caspase_8_dimer__cytosol_1">
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+ <bp:COMPONENTS rdf:resource="#p18_subunit_of_Caspase_8__cytosol_4" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Caspase-8 dimer [cytosol]</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Caspase-8 dimer</bp:SHORT-NAME>
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+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="p18_subunit_of_Caspase_8__cytosol_4">
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+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</bp:DB>
+ <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2003</bp:YEAR>
+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mechanisms of caspase activation</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Boatright, KM</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Salvesen, GS</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Curr Opin Cell Biol 15:725-31</bp:SOURCE>
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+ <bp:XREF rdf:resource="#Pubmed_11048727" />
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+ <bp:STEP-INTERACTIONS rdf:resource="#Extrinsic_Pathway_for_Apoptosis" />
+ </bp:pathwayStep>
+ <bp:pathway rdf:ID="Activation__myristolyation_of_BID_and_translocation_to_mitochondria">
+ <bp:PATHWAY-COMPONENTS rdf:resource="#Translocation_of_tBID_to_mitochondriaStep" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#Caspase_8_activates_BID_by_cleavageStep" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#Myristoylation_of_tBID_by_NMT1Step" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#Granzyme_B_activates_BID_by_cleavageStep" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Activation, myristolyation of BID and translocation to mitochondria</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Activation, myristolyation of BID and translocation to mitochondria</bp:SHORT-NAME>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Activation of BID and translocation to mitochondria</bp:SYNONYMS>
+ <bp:XREF rdf:resource="#Reactome75108" />
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BID may promote cell death by activating BAX and BAK while inactivating anti-apoptotic proteins. The engagement of cell surface receptors activates the caspase-8, a heterodimer, that cleaves BID in its amino terminal region. This particular event may act as a link between Extrinsic (caspase 8/10 dependent) and Intrinsic (Bcl-2 inhibitable) pathways although some evidences from mouse genetic experiments suggest the con [...]
+ <bp:EVIDENCE rdf:resource="#Summation_140549" />
+ <bp:XREF rdf:resource="#activation_of_pro_apoptotic_gene_products" />
+ </bp:pathway>
+ <bp:biochemicalReaction rdf:ID="Caspase_8_activates_BID_by_cleavage">
+ <bp:LEFT rdf:resource="#BID__cytosol_" />
+ <bp:RIGHT rdf:resource="#tBID_p15__cytosol_" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Caspase-8 activates BID by cleavage</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Caspase-8 activates BID by cleavage</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome139898" />
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The caspase 8 -mediated cleavage of cytosolic, inactive p22 BID at internal Asp sites yields a major p15 and minor p13 and p11 fragments. After myristoylation, tBID translocates to mitochondria as an integral membrane protein.</bp:COMMENT>
+ <bp:EVIDENCE rdf:resource="#Summation_163355" />
+ <bp:XREF rdf:resource="#Pubmed_12804595" />
+ <bp:XREF rdf:resource="#activation_of_pro_apoptotic_gene_products" />
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+ <bp:sequenceParticipant rdf:ID="BID__cytosol_">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_P55957_BH3_interacting_domain_death_agonist__BID_" />
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+ <bp:protein rdf:ID="UniProt_P55957_BH3_interacting_domain_death_agonist__BID_">
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P55957 BH3 interacting domain death agonist (BID)</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BID</bp:SYNONYMS>
+ <bp:XREF rdf:resource="#UniProt_P55957" />
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Induces ICE-like proteases and apoptosis. Counters the protective effect of Bcl-2 (By similarity). SUBUNIT: Forms heterodimers either with the pro-apoptotic protein BAX or the anti-apoptotic protein Bcl-2 (By similarity). SUBCELLULAR LOCATION: Predominantly cytoplasmic (By similarity). DOMAIN: Intact BH3 domain is required by BIK, BID, BAK, BAD and BAX for their pro-apoptotic activity and for their interacti [...]
+ </bp:protein>
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+ <bp:catalysis rdf:ID="caspase_activity_of_Caspase_8_dimer__cytosol_">
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+ <bp:DIRECTION rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PHYSIOL-LEFT-TO-RIGHT</bp:DIRECTION>
+ <bp:XREF rdf:resource="#caspase_activity" />
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+ <bp:XREF rdf:resource="#Pubmed_9873064" />
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+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</bp:DB>
+ <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1999</bp:YEAR>
+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Caspase cleaved BID targets mitochondria and is required for cytochrome c release, while BCL-XL prevents this release but not tumor necrosis factor-R1/Fas death</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Gross, A</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Yin, XM</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Wang, K</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Wei, MC</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Jockel, J</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Milliman, C</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Erdjument-Bromage, H</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Tempst, P</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Korsmeyer, SJ</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Biol Chem 274:1156-63</bp:SOURCE>
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+ <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2003</bp:YEAR>
+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Caspase 8-mediated cleavage of the pro-apoptotic BCL-2 family member BID in p53-dependent apoptosis</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Fischer, B</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Coelho, D</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Dufour, P</bp:AUTHORS>
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+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Denis, JM</bp:AUTHORS>
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+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bischoff, P</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Biochem Biophys Res Commun 306:516-22</bp:SOURCE>
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+ <bp:NEXT-STEP rdf:resource="#tBID_activates_BAX_proteinStep" />
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+ <bp:biochemicalReaction rdf:ID="Granzyme_B_activates_BID_by_cleavage">
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+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Granzyme-B activates BID by cleavage</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Granzyme-B activates BID by cleavage</bp:SHORT-NAME>
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+ <bp:XREF rdf:resource="#Pubmed_11114298" />
+ <bp:XREF rdf:resource="#activation_of_pro_apoptotic_gene_products" />
+ </bp:biochemicalReaction>
+ <bp:sequenceParticipant rdf:ID="BID__cytosol_1">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_P55957_BH3_interacting_domain_death_agonist__BID_" />
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+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
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+ <bp:catalysis rdf:ID="granzyme_B_activity_of_Granzyme_B__cytosol_">
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+ <bp:XREF rdf:resource="#granzyme_B_activity" />
+ </bp:catalysis>
+ <bp:sequenceParticipant rdf:ID="Granzyme_B__cytosol_">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_P10144_Granzyme_B_precursor__EC_3_4_21_79___T_cell_serine_protease_1_3E___Cytotoxic_T_lymphocyte_proteinase_2___Lymphocyte_protease___SECT___Granzyme_2___Cathepsin_G_like_1___CTSGL1___CTLA_1___Fragmentin_2___Human_lymphocyte_protein___HLP___C11_" />
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+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P10144 Granzyme B precursor (EC 3.4.21.79) (T-cell serine protease 1-3E) (Cytotoxic T-lymphocyte proteinase 2) (Lymphocyte protease) (SECT) (Granzyme 2) (Cathepsin G-like 1) (CTSGL1) (CTLA-1) (Fragmentin 2) (Human lymphocyte protein) (HLP) (C11)</bp:NAME>
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+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CTLA1</bp:SYNONYMS>
+ <bp:XREF rdf:resource="#UniProt_P10144" />
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: This enzyme is necessary for target cell lysis in cell- mediated immune responses. It cleaves after Asp. Seems to be linked to an activation cascade of caspases (aspartate-specific cysteine proteases) responsible for apoptosis execution. Cleaves caspase-3, -7, -9 and 10 to give rise to active enzymes mediating apoptosis. CATALYTIC ACTIVITY: Preferential cleavage: Asp-|-Xaa >> Asn-|-Xaa > Met-|-Xaa, [...]
+ </bp:protein>
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+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P10144</bp:ID>
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+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</bp:COMMENT>
+ </bp:unificationXref>
+ <bp:publicationXref rdf:ID="Pubmed_11114298">
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">11114298</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</bp:DB>
+ <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2001</bp:YEAR>
+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Granzyme B induces BID-mediated cytochrome c release and mitochondrial permeability transition</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Alimonti, JB</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Shi, L</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Baijal, PK</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Greenberg, AH</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Biol Chem 276:6974-82</bp:SOURCE>
+ </bp:publicationXref>
+ <bp:pathwayStep rdf:ID="Granzyme_B_activates_BID_by_cleavageStep">
+ <bp:STEP-INTERACTIONS rdf:resource="#Granzyme_B_activates_BID_by_cleavage" />
+ <bp:NEXT-STEP rdf:resource="#tBID_activates_BAX_proteinStep" />
+ <bp:NEXT-STEP rdf:resource="#Myristoylation_of_tBID_by_NMT1Step" />
+ <bp:STEP-INTERACTIONS rdf:resource="#granzyme_B_activity_of_Granzyme_B__cytosol_" />
+ </bp:pathwayStep>
+ <bp:biochemicalReaction rdf:ID="Myristoylation_of_tBID_by_NMT1">
+ <bp:LEFT rdf:resource="#tBID_p15__cytosol_2" />
+ <bp:RIGHT rdf:resource="#tBID__cytosol_" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Myristoylation of tBID by NMT1</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Myristoylation of tBID by NMT1</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome141367" />
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">After proteolytic activation, tBID is myristoylated by NMT-1 at an exposed glycine. N-myristoylation may enable the activated tBID to associate with the lipid components of the mitochondrial membrane.</bp:COMMENT>
+ <bp:EVIDENCE rdf:resource="#Summation_142108" />
+ <bp:XREF rdf:resource="#Pubmed_11099414" />
+ </bp:biochemicalReaction>
+ <bp:sequenceParticipant rdf:ID="tBID_p15__cytosol_2">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_P55957_BH3_interacting_domain_death_agonist__BID_" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="tBID__cytosol_">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_P55957_BH3_interacting_domain_death_agonist__BID_" />
+ </bp:sequenceParticipant>
+ <bp:catalysis rdf:ID="myristoyltransferase_activity_of_NMT_1__cytosol_">
+ <bp:CONTROLLER rdf:resource="#NMT_1__cytosol_" />
+ <bp:CONTROLLED rdf:resource="#Myristoylation_of_tBID_by_NMT1" />
+ <bp:DIRECTION rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PHYSIOL-LEFT-TO-RIGHT</bp:DIRECTION>
+ <bp:XREF rdf:resource="#myristoyltransferase_activity" />
+ </bp:catalysis>
+ <bp:sequenceParticipant rdf:ID="NMT_1__cytosol_">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_P30419_1_Glycylpeptide_N_tetradecanoyltransferase_1__EC_2_3_1_97___Peptide_N__myristoyltransferase_1___Myristoyl_CoA_protein_N_myristoyltransferase_1___NMT_1___Type_I_N_myristoyltransferase_" />
+ </bp:sequenceParticipant>
+ <bp:protein rdf:ID="UniProt_P30419_1_Glycylpeptide_N_tetradecanoyltransferase_1__EC_2_3_1_97___Peptide_N__myristoyltransferase_1___Myristoyl_CoA_protein_N_myristoyltransferase_1___NMT_1___Type_I_N_myristoyltransferase_">
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P30419-1 Glycylpeptide N-tetradecanoyltransferase 1 (EC 2.3.1.97) (Peptide N- myristoyltransferase 1) (Myristoyl-CoA:protein N-myristoyltransferase 1) (NMT 1) (Type I N-myristoyltransferase)</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">NMT</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">NMT1</bp:SYNONYMS>
+ <bp:XREF rdf:resource="#UniProt_P30419" />
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Adds a myristoyl group to the N-terminal glycine residue of certain cellular and viral proteins. CATALYTIC ACTIVITY: Tetradecanoyl-CoA + glycyl-peptide = CoA + N- tetradecanoylglycyl-peptide. SUBCELLULAR LOCATION: Cytoplasmic. ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=Long; IsoId=P30419-1; Sequence=Displayed; Name=Short; IsoId=P30419-2; Sequence=VSP_003570; TISSUE SPECIFICITY: [...]
+ </bp:protein>
+ <bp:unificationXref rdf:ID="UniProt_P30419">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P30419</bp:ID>
+ </bp:unificationXref>
+ <bp:relationshipXref rdf:ID="myristoyltransferase_activity">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GO</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0019107</bp:ID>
+ </bp:relationshipXref>
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+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">141367</bp:ID>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</bp:COMMENT>
+ </bp:unificationXref>
+ <bp:evidence rdf:ID="Summation_142108" />
+ <bp:publicationXref rdf:ID="Pubmed_11099414">
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">11099414</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</bp:DB>
+ <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2000</bp:YEAR>
+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Posttranslational N-myristoylation of BID as a molecular switch for targeting mitochondria and apoptosis</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Zha, J</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Weiler, S</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Oh, KJ</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Wei, MC</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Korsmeyer, SJ</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Science 290:1761-5</bp:SOURCE>
+ </bp:publicationXref>
+ <bp:pathwayStep rdf:ID="Myristoylation_of_tBID_by_NMT1Step">
+ <bp:STEP-INTERACTIONS rdf:resource="#Myristoylation_of_tBID_by_NMT1" />
+ <bp:NEXT-STEP rdf:resource="#Translocation_of_tBID_to_mitochondriaStep" />
+ <bp:NEXT-STEP rdf:resource="#tBID_activates_BAK_proteinStep" />
+ <bp:STEP-INTERACTIONS rdf:resource="#myristoyltransferase_activity_of_NMT_1__cytosol_" />
+ </bp:pathwayStep>
+ <bp:biochemicalReaction rdf:ID="Translocation_of_tBID_to_mitochondria">
+ <bp:LEFT rdf:resource="#tBID__cytosol_1" />
+ <bp:RIGHT rdf:resource="#tBID__mitochondrial_outer_membrane_" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Translocation of tBID to mitochondria</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Translocation of tBID to mitochondria</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome139920" />
+ </bp:biochemicalReaction>
+ <bp:sequenceParticipant rdf:ID="tBID__cytosol_1">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_P55957_BH3_interacting_domain_death_agonist__BID_" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="tBID__mitochondrial_outer_membrane_">
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_P55957_BH3_interacting_domain_death_agonist__BID_" />
+ </bp:sequenceParticipant>
+ <bp:openControlledVocabulary rdf:ID="mitochondrial_outer_membrane">
+ <bp:TERM rdf:datatype="http://www.w3.org/2001/XMLSchema#string">mitochondrial outer membrane</bp:TERM>
+ <bp:XREF rdf:resource="#GO_0005741" />
+ </bp:openControlledVocabulary>
+ <bp:unificationXref rdf:ID="GO_0005741">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GO</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0005741</bp:ID>
+ </bp:unificationXref>
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+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</bp:COMMENT>
+ </bp:unificationXref>
+ <bp:pathwayStep rdf:ID="Translocation_of_tBID_to_mitochondriaStep">
+ <bp:STEP-INTERACTIONS rdf:resource="#Translocation_of_tBID_to_mitochondria" />
+ <bp:NEXT-STEP rdf:resource="#Sequestration_of_tBID_by_BCL_2Step" />
+ <bp:NEXT-STEP rdf:resource="#Permeabilization_of_mitochondriaStep" />
+ <bp:NEXT-STEP rdf:resource="#Interaction_of_tBID_with_BCL_xlStep" />
+ <bp:NEXT-STEP rdf:resource="#Release_of_Cytochrome_c_from_mitochondriaStep" />
+ </bp:pathwayStep>
+ <bp:unificationXref rdf:ID="Reactome75108">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">75108</bp:ID>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</bp:COMMENT>
+ </bp:unificationXref>
+ <bp:evidence rdf:ID="Summation_140549">
+ <bp:XREF rdf:resource="#Pubmed_14634621" />
+ <bp:XREF rdf:resource="#Pubmed_9727492" />
+ </bp:evidence>
+ <bp:publicationXref rdf:ID="Pubmed_14634621">
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">14634621</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</bp:DB>
+ <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2003</bp:YEAR>
+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The Bcl-2 family: roles in cell survival and oncogenesis.</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cory, S</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Huang, DC</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Adams, JM</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Oncogene 22:8590-607</bp:SOURCE>
+ </bp:publicationXref>
+ <bp:publicationXref rdf:ID="Pubmed_9727492">
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">9727492</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</bp:DB>
+ <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1998</bp:YEAR>
+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cleavage of BID by caspase 8 mediates the mitochondrial damage in the Fas pathway of apoptosis</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Li, H</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Zhu, H</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Xu, CJ</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Yuan, J</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cell 94:491-501</bp:SOURCE>
+ </bp:publicationXref>
+ <bp:pathwayStep rdf:ID="Activation__myristolyation_of_BID_and_translocation_to_mitochondriaStep">
+ <bp:STEP-INTERACTIONS rdf:resource="#Activation__myristolyation_of_BID_and_translocation_to_mitochondria" />
+ <bp:NEXT-STEP rdf:resource="#Intrinsic_Pathway_for_ApoptosisStep" />
+ </bp:pathwayStep>
+ <bp:pathway rdf:ID="Intrinsic_Pathway_for_Apoptosis">
+ <bp:PATHWAY-COMPONENTS rdf:resource="#Activation__translocation_and_oligomerization_of_BAXStep" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#BH3_only_proteins_associate_with_and_inactivate_anti_apoptotic_BCL_2_membersStep" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#Apoptotic_factor_mediated_responseStep" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#Activation_and_oligomerization_of_BAK_proteinStep" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#Release_of_apoptotic_factors_from_the_mitochondriaStep" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#Permeabilization_of_mitochondriaStep" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#Activation_of_BH3_only_proteinsStep" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Intrinsic Pathway for Apoptosis</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Intrinsic Pathway for Apoptosis</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome109606" />
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The intrinsic (Bcl-2 inhibitable or mitochondrial) pathway of apoptosis functions in response to various types of intracellular stress including growth factor withdrawal, DNA damage, unfolding stresses in the endoplasmic reticulum and death receptor stimulation. Following the reception of stress signals, proapoptotic BCL-2 family proteins are activated and subsequently interact with and inactivate antiapoptotic BCL-2 [...]
+ <bp:EVIDENCE rdf:resource="#Summation_140375" />
+ <bp:XREF rdf:resource="#Pubmed_15077149" />
+ <bp:XREF rdf:resource="#Pubmed_11711427" />
+ <bp:XREF rdf:resource="#Pubmed_12042762" />
+ <bp:XREF rdf:resource="#induction_of_apoptosis_by_intracellular_signals" />
+ </bp:pathway>
+ <bp:pathway rdf:ID="Activation_of_BH3_only_proteins">
+ <bp:PATHWAY-COMPONENTS rdf:resource="#Activation_of_NOXA_and_translocation_to_mitochondriaStep" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#Activation_of_PUMA_and_translocation_to_mitochondriaStep" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#Activation_of_BAD_and_translocation_to_mitochondria_Step" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#Activation_of_BIM_and_translocation_to_mitochondria_Step" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#Activation_of_BMF_and_translocation_to_mitochondriaStep" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Activation of BH3-only proteins</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Activation of BH3-only proteins</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome114452" />
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The BH3-only members act as sentinels that selectively trigger apoptosis in response to developmental cues or stress-signals like DNA damages. Widely expressed mammalian BH3-only proteins are thought to act by binding to and neutralizing their pro-survival counterparts. Activation of BH3-only proteins directly or indirectly results in the activation of proapoptotic BAX and BAK to trigger cell death. Anti-apoptotic BCL [...]
+ <bp:EVIDENCE rdf:resource="#Summation_140552" />
+ <bp:XREF rdf:resource="#activation_of_pro_apoptotic_gene_products" />
+ </bp:pathway>
+ <bp:pathway rdf:ID="Activation_of_BAD_and_translocation_to_mitochondria_">
+ <bp:PATHWAY-COMPONENTS rdf:resource="#BAD_displaces_tBID_from_BCL_2_sequestrationStep" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#Akt1_phosphorylates_BAD_proteinStep" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#Sequesteration_of_BAD_protein_by_14_3_3Step" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#Translocation_of_activated_BAD_protein_to_mitochondriaStep" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#Activation_of_BAD_by_calcineurinStep" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Activation of BAD and translocation to mitochondria</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Activation of BAD and translocation to mitochondria</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome111447" />
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The switching on/off of its phosphorylation by growth/survival factors regulates BAD activity. BAD remains sequestered by 14-3-3 scaffold proteins after phosphorylation by Akt1. Calcineurin activates BAD by dephosphorylation.</bp:COMMENT>
+ <bp:EVIDENCE rdf:resource="#Summation_140545" />
+ <bp:XREF rdf:resource="#Pubmed_15231831" />
+ <bp:XREF rdf:resource="#activation_of_pro_apoptotic_gene_products" />
+ </bp:pathway>
+ <bp:biochemicalReaction rdf:ID="Akt1_phosphorylates_BAD_protein">
+ <bp:LEFT rdf:resource="#BAD_protein__cytosol_" />
+ <bp:RIGHT rdf:resource="#Phospho_BAD__cytosol_" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Akt1 phosphorylates BAD protein</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Akt1 phosphorylates BAD protein</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome139903" />
+ <bp:XREF rdf:resource="#Pubmed_15183529" />
+ </bp:biochemicalReaction>
+ <bp:sequenceParticipant rdf:ID="BAD_protein__cytosol_">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q92934_Bcl2_antagonist_of_cell_death__BAD___Bcl_2_binding_component_6___Bcl__XL_Bcl_2_associated_death_promoter___Bcl_2_like_8_protein_" />
+ </bp:sequenceParticipant>
+ <bp:protein rdf:ID="UniProt_Q92934_Bcl2_antagonist_of_cell_death__BAD___Bcl_2_binding_component_6___Bcl__XL_Bcl_2_associated_death_promoter___Bcl_2_like_8_protein_">
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:Q92934 Bcl2-antagonist of cell death (BAD) (Bcl-2 binding component 6) (Bcl- XL/Bcl-2 associated death promoter) (Bcl-2-like 8 protein)</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BCL2L8</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BAD</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BBC6</bp:SYNONYMS>
+ <bp:XREF rdf:resource="#UniProt_Q92934" />
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Promotes cell death. Successfully competes for the binding to Bcl-X(L), Bcl-2 and Bcl-W, thereby affecting the level of heterodimerization of these proteins with BAX. Can reverse the death repressor activity of Bcl-X(L), but not that of Bcl-2 (By similarity). Appears to act as a link between growth factor receptor signaling and the apoptotic pathways. SUBUNIT: Forms heterodimers with the anti-apoptotic prote [...]
+ </bp:protein>
+ <bp:unificationXref rdf:ID="UniProt_Q92934">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Q92934</bp:ID>
+ </bp:unificationXref>
+ <bp:sequenceParticipant rdf:ID="Phospho_BAD__cytosol_">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q92934_Bcl2_antagonist_of_cell_death__BAD___Bcl_2_binding_component_6___Bcl__XL_Bcl_2_associated_death_promoter___Bcl_2_like_8_protein_" />
+ </bp:sequenceParticipant>
+ <bp:catalysis rdf:ID="kinase_activity_of_AKT1__cytosol_">
+ <bp:CONTROLLER rdf:resource="#AKT1__cytosol_" />
+ <bp:CONTROLLED rdf:resource="#Akt1_phosphorylates_BAD_protein" />
+ <bp:DIRECTION rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PHYSIOL-LEFT-TO-RIGHT</bp:DIRECTION>
+ <bp:XREF rdf:resource="#kinase_activity" />
+ </bp:catalysis>
+ <bp:sequenceParticipant rdf:ID="AKT1__cytosol_">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_P31749_RAC_alpha_serine_threonine_protein_kinase__EC_2_7_1_37___RAC_PK_alpha___Protein_kinase_B___PKB___C_AKT_" />
+ </bp:sequenceParticipant>
+ <bp:protein rdf:ID="UniProt_P31749_RAC_alpha_serine_threonine_protein_kinase__EC_2_7_1_37___RAC_PK_alpha___Protein_kinase_B___PKB___C_AKT_">
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P31749 RAC-alpha serine/threonine-protein kinase (EC 2.7.1.37) (RAC-PK-alpha) (Protein kinase B) (PKB) (C-AKT)</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PKB</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RAC</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">AKT1</bp:SYNONYMS>
+ <bp:XREF rdf:resource="#UniProt_P31749" />
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: General protein kinase capable of phosphorylating several known proteins. CATALYTIC ACTIVITY: ATP + a protein = ADP + a phosphoprotein. SUBCELLULAR LOCATION: Cytoplasmic and nuclear after activation by integrin-linked protein kinase 1 (ILK1). TISSUE SPECIFICITY: In all human cell types so far analyzed. DOMAIN: Binding of the PH domain to the phosphatidylinositol 3- kinase alpha (PI(3)K) results in its target [...]
+ </bp:protein>
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+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P31749</bp:ID>
+ </bp:unificationXref>
+ <bp:relationshipXref rdf:ID="kinase_activity">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GO</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0016301</bp:ID>
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+ </bp:unificationXref>
+ <bp:publicationXref rdf:ID="Pubmed_15183529">
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">15183529</bp:ID>
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+ <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2004</bp:YEAR>
+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Positive correlation between overexpression of phospho-BAD with phosphorylated Akt at serine 15183529</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Khor, TO</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Gul, YA</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Ithnin, H</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Seow, HF</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cancer Lett 210:139-50</bp:SOURCE>
+ </bp:publicationXref>
+ <bp:pathwayStep rdf:ID="Akt1_phosphorylates_BAD_proteinStep">
+ <bp:STEP-INTERACTIONS rdf:resource="#Akt1_phosphorylates_BAD_protein" />
+ <bp:NEXT-STEP rdf:resource="#Sequesteration_of_BAD_protein_by_14_3_3Step" />
+ <bp:STEP-INTERACTIONS rdf:resource="#kinase_activity_of_AKT1__cytosol_" />
+ </bp:pathwayStep>
+ <bp:biochemicalReaction rdf:ID="Sequesteration_of_BAD_protein_by_14_3_3">
+ <bp:LEFT rdf:resource="#_143B_protein__cytosol_" />
+ <bp:LEFT rdf:resource="#Phospho_BAD__cytosol_1" />
+ <bp:RIGHT rdf:resource="#_143B_phospo_BAD_complex__cytosol_" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Sequesteration of BAD protein by 14-3-3</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Sequesteration of BAD protein by 14-3-3</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome139899" />
+ <bp:XREF rdf:resource="#Pubmed_12657644" />
+ </bp:biochemicalReaction>
+ <bp:sequenceParticipant rdf:ID="_143B_protein__cytosol_">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_P31946_14_3_3_protein_beta_alpha__Protein_kinase_C_inhibitor_protein_1___KCIP_1___Protein_1054_" />
+ </bp:sequenceParticipant>
+ <bp:protein rdf:ID="UniProt_P31946_14_3_3_protein_beta_alpha__Protein_kinase_C_inhibitor_protein_1___KCIP_1___Protein_1054_">
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P31946 14-3-3 protein beta/alpha (Protein kinase C inhibitor protein-1) (KCIP-1) (Protein 1054)</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">YWHAB</bp:SYNONYMS>
+ <bp:XREF rdf:resource="#UniProt_P31946" />
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Activates tyrosine and tryptophan hydroxylases in the presence of Ca(2+)/calmodulin-dependent protein kinase II, and strongly activates protein kinase C. Is probably a multifunctional regulator of the cell signaling processes mediated by both kinases. SUBUNIT: Homodimer. SUBCELLULAR LOCATION: Cytoplasmic. ALTERNATIVE PRODUCTS: Event=Alternative initiation; Comment=2 isoforms, Long (shown here) and Short, are [...]
+ </bp:protein>
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+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P31946</bp:ID>
+ </bp:unificationXref>
+ <bp:sequenceParticipant rdf:ID="Phospho_BAD__cytosol_1">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q92934_Bcl2_antagonist_of_cell_death__BAD___Bcl_2_binding_component_6___Bcl__XL_Bcl_2_associated_death_promoter___Bcl_2_like_8_protein_" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="_143B_phospo_BAD_complex__cytosol_">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#_143B_phospo_BAD_complex__cytosol_1" />
+ </bp:sequenceParticipant>
+ <bp:complex rdf:ID="_143B_phospo_BAD_complex__cytosol_1">
+ <bp:COMPONENTS rdf:resource="#_143B_protein__cytosol_1" />
+ <bp:COMPONENTS rdf:resource="#Phospho_BAD__cytosol_2" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">143B:phospo-BAD complex [cytosol]</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">143B:phospo-BAD complex</bp:SHORT-NAME>
+ </bp:complex>
+ <bp:sequenceParticipant rdf:ID="_143B_protein__cytosol_1">
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+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_P31946_14_3_3_protein_beta_alpha__Protein_kinase_C_inhibitor_protein_1___KCIP_1___Protein_1054_" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="Phospho_BAD__cytosol_2">
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+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q92934_Bcl2_antagonist_of_cell_death__BAD___Bcl_2_binding_component_6___Bcl__XL_Bcl_2_associated_death_promoter___Bcl_2_like_8_protein_" />
+ </bp:sequenceParticipant>
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+ </bp:unificationXref>
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+ <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2003</bp:YEAR>
+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cleavage of 14-3-3 protein by caspase-3 facilitates bad interaction with Bcl-x(L) during apoptosis</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Won, J</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Kim, DY</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">La, M</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Kim, D</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Meadows, GG</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Joe, CO</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Biol Chem 278:19347-51</bp:SOURCE>
+ </bp:publicationXref>
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+ <bp:NEXT-STEP rdf:resource="#Activation_of_BAD_by_calcineurinStep" />
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+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Activation of BAD by calcineurin</bp:NAME>
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+ <bp:sequenceParticipant rdf:ID="BAD_protein__cytosol_1">
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+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="_143B_protein__cytosol_2">
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+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_P31946_14_3_3_protein_beta_alpha__Protein_kinase_C_inhibitor_protein_1___KCIP_1___Protein_1054_" />
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+ <bp:catalysis rdf:ID="calcium_dependent_protein_serine_threonine_phosphatase_regulator_activity_of_Calcineurin_B_complex__cytosol_">
+ <bp:CONTROLLER rdf:resource="#Calcineurin_B_complex__cytosol_" />
+ <bp:CONTROLLED rdf:resource="#Activation_of_BAD_by_calcineurin" />
+ <bp:DIRECTION rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PHYSIOL-LEFT-TO-RIGHT</bp:DIRECTION>
+ <bp:XREF rdf:resource="#calcium_dependent_protein_serine_threonine_phosphatase_regulator_activity" />
+ </bp:catalysis>
+ <bp:sequenceParticipant rdf:ID="Calcineurin_B_complex__cytosol_">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#Calcineurin_B_complex__cytosol_1" />
+ </bp:sequenceParticipant>
+ <bp:complex rdf:ID="Calcineurin_B_complex__cytosol_1">
+ <bp:COMPONENTS rdf:resource="#Calcineurin_B_gamma__catalytic__cytosol_" />
+ <bp:COMPONENTS rdf:resource="#Calcineurin_B__alpha_regulatory__cytosol_" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Calcineurin B complex [cytosol]</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Calcineurin B complex</bp:SHORT-NAME>
+ </bp:complex>
+ <bp:sequenceParticipant rdf:ID="Calcineurin_B_gamma__catalytic__cytosol_">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_P48454_Serine_threonine_protein_phosphatase_2B_catalytic_subunit__gamma_isoform__EC_3_1_3_16___Calmodulin_dependent_calcineurin_A_subunit__gamma_isoform___Calcineurin__testis_specific_catalytic_subunit___CAM__PRP_catalytic_subunit_" />
+ </bp:sequenceParticipant>
+ <bp:protein rdf:ID="UniProt_P48454_Serine_threonine_protein_phosphatase_2B_catalytic_subunit__gamma_isoform__EC_3_1_3_16___Calmodulin_dependent_calcineurin_A_subunit__gamma_isoform___Calcineurin__testis_specific_catalytic_subunit___CAM__PRP_catalytic_subunit_">
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P48454 Serine/threonine protein phosphatase 2B catalytic subunit, gamma isoform (EC 3.1.3.16) (Calmodulin-dependent calcineurin A subunit, gamma isoform) (Calcineurin, testis-specific catalytic subunit) (CAM- PRP catalytic subunit)</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CALNA3</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PPP3CC</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CNA3</bp:SYNONYMS>
+ <bp:XREF rdf:resource="#UniProt_P48454" />
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Calcium-dependent, calmodulin-stimulated protein phosphatase. This subunit may have a role in the calmodulin activation of calcineurin. CATALYTIC ACTIVITY: A phosphoprotein + H(2)O = a protein + phosphate. COFACTOR: Binds 1 iron(III) ion and 1 zinc ion per subunit (By similarity). SUBUNIT: Composed of two components (A and B), the A component is the catalytic subunit and the B component confers calcium sensi [...]
+ </bp:protein>
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+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P48454</bp:ID>
+ </bp:unificationXref>
+ <bp:sequenceParticipant rdf:ID="Calcineurin_B__alpha_regulatory__cytosol_">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_P63098_Calcineurin_B_subunit_isoform_1__Protein_phosphatase_2B_regulatory_subunit_1___Protein_phosphatase_3_regulatory_subunit_B_alpha_isoform_1_" />
+ </bp:sequenceParticipant>
+ <bp:protein rdf:ID="UniProt_P63098_Calcineurin_B_subunit_isoform_1__Protein_phosphatase_2B_regulatory_subunit_1___Protein_phosphatase_3_regulatory_subunit_B_alpha_isoform_1_">
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P63098 Calcineurin B subunit isoform 1 (Protein phosphatase 2B regulatory subunit 1) (Protein phosphatase 3 regulatory subunit B alpha isoform 1)</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CNA2</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CNB</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PPP3R1</bp:SYNONYMS>
+ <bp:XREF rdf:resource="#UniProt_P63098" />
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Regulatory subunit of calcineurin, a calcium-dependent, calmodulin stimulated protein phosphatase. Confers calcium sensitivity. SUBUNIT: Composed of a catalytic subunit (A) and a regulatory subunit (B). MISCELLANEOUS: This protein has four functional calcium-binding sites. SIMILARITY: Contains 4 EF-hand calcium-binding domains.</bp:COMMENT>
+ </bp:protein>
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+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P63098</bp:ID>
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+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0008597</bp:ID>
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+ <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1999</bp:YEAR>
+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Ca2+-induced apoptosis through calcineurin dephosphorylation of BAD.</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Wang, HG</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pathan, N</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Ethell, IM</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Krajewski, S</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Yamaguchi, Y</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Shibasaki, F</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">McKeon, F</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bobo, T</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Franke, TF</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reed, JC</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Science 284:339-43</bp:SOURCE>
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+ </bp:pathwayStep>
+ <bp:biochemicalReaction rdf:ID="Translocation_of_activated_BAD_protein_to_mitochondria">
+ <bp:LEFT rdf:resource="#BAD_protein__cytosol_2" />
+ <bp:RIGHT rdf:resource="#BAD_protein__mitochondrial_outer_membrane_" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Translocation of activated BAD protein to mitochondria</bp:NAME>
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+ </bp:biochemicalReaction>
+ <bp:sequenceParticipant rdf:ID="BAD_protein__cytosol_2">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
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+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="BAD_protein__mitochondrial_outer_membrane_">
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+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q92934_Bcl2_antagonist_of_cell_death__BAD___Bcl_2_binding_component_6___Bcl__XL_Bcl_2_associated_death_promoter___Bcl_2_like_8_protein_" />
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+ </bp:relationshipXref>
+ <bp:pathwayStep rdf:ID="Translocation_of_activated_BAD_protein_to_mitochondriaStep">
+ <bp:STEP-INTERACTIONS rdf:resource="#Translocation_of_activated_BAD_protein_to_mitochondria" />
+ <bp:NEXT-STEP rdf:resource="#BAD_displaces_tBID_from_BCL_2_sequestrationStep" />
+ </bp:pathwayStep>
+ <bp:biochemicalReaction rdf:ID="BAD_displaces_tBID_from_BCL_2_sequestration">
+ <bp:LEFT rdf:resource="#BAD_protein__mitochondrial_outer_membrane_1" />
+ <bp:LEFT rdf:resource="#tBID_BCL_2__mitochondrial_outer_membrane_" />
+ <bp:RIGHT rdf:resource="#tBID__mitochondrial_outer_membrane_2" />
+ <bp:RIGHT rdf:resource="#BAD_BCL_2__mitochondrial_outer_membrane_" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BAD displaces tBID from BCL-2 sequestration</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BAD displaces tBID from BCL-2 sequestration</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome139897" />
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Short peptides representing BAD and BIX were found to bind BCL-2 displacing BID-like BH3 domains that initiate mitochondrial dysfunction.</bp:COMMENT>
+ <bp:EVIDENCE rdf:resource="#Summation_140378" />
+ </bp:biochemicalReaction>
+ <bp:sequenceParticipant rdf:ID="BAD_protein__mitochondrial_outer_membrane_1">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q92934_Bcl2_antagonist_of_cell_death__BAD___Bcl_2_binding_component_6___Bcl__XL_Bcl_2_associated_death_promoter___Bcl_2_like_8_protein_" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="tBID_BCL_2__mitochondrial_outer_membrane_">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#tBID_BCL_2__mitochondrial_outer_membrane_1" />
+ </bp:sequenceParticipant>
+ <bp:complex rdf:ID="tBID_BCL_2__mitochondrial_outer_membrane_1">
+ <bp:COMPONENTS rdf:resource="#tBID__mitochondrial_outer_membrane_1" />
+ <bp:COMPONENTS rdf:resource="#Bcl_2_protein__mitochondrial_outer_membrane_" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">tBID:BCL-2 [mitochondrial outer membrane]</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">tBID:BCL-2</bp:SHORT-NAME>
+ </bp:complex>
+ <bp:sequenceParticipant rdf:ID="tBID__mitochondrial_outer_membrane_1">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_P55957_BH3_interacting_domain_death_agonist__BID_" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="Bcl_2_protein__mitochondrial_outer_membrane_">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_P10415_1_Apoptosis_regulator_Bcl_2" />
+ </bp:sequenceParticipant>
+ <bp:protein rdf:ID="UniProt_P10415_1_Apoptosis_regulator_Bcl_2">
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P10415-1 Apoptosis regulator Bcl-2</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BCL2</bp:SYNONYMS>
+ <bp:XREF rdf:resource="#UniProt_P10415" />
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Suppresses apoptosis in a variety of cell systems including factor-dependent lymphohematopoietic and neural cells. Regulates cell death by controlling the mitochondrial membrane permeability. Appears to function in a feedback loop system with caspases. Inhibits caspase activity either by preventing the release of cytochrome c from the mitochondria and/or by binding to the apoptosis-activating factor (APAF-1) [...]
+ </bp:protein>
+ <bp:unificationXref rdf:ID="UniProt_P10415">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P10415</bp:ID>
+ </bp:unificationXref>
+ <bp:sequenceParticipant rdf:ID="tBID__mitochondrial_outer_membrane_2">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_P55957_BH3_interacting_domain_death_agonist__BID_" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="BAD_BCL_2__mitochondrial_outer_membrane_">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#BAD_BCL_2__mitochondrial_outer_membrane_1" />
+ </bp:sequenceParticipant>
+ <bp:complex rdf:ID="BAD_BCL_2__mitochondrial_outer_membrane_1">
+ <bp:COMPONENTS rdf:resource="#BAD_protein__mitochondrial_outer_membrane_2" />
+ <bp:COMPONENTS rdf:resource="#Bcl_2_protein__mitochondrial_outer_membrane_1" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BAD:BCL-2 [mitochondrial outer membrane]</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BAD:BCL-2</bp:SHORT-NAME>
+ </bp:complex>
+ <bp:sequenceParticipant rdf:ID="BAD_protein__mitochondrial_outer_membrane_2">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q92934_Bcl2_antagonist_of_cell_death__BAD___Bcl_2_binding_component_6___Bcl__XL_Bcl_2_associated_death_promoter___Bcl_2_like_8_protein_" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="Bcl_2_protein__mitochondrial_outer_membrane_1">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_P10415_1_Apoptosis_regulator_Bcl_2" />
+ </bp:sequenceParticipant>
+ <bp:unificationXref rdf:ID="Reactome139897">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">139897</bp:ID>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</bp:COMMENT>
+ </bp:unificationXref>
+ <bp:evidence rdf:ID="Summation_140378">
+ <bp:XREF rdf:resource="#Pubmed_12242151" />
+ </bp:evidence>
+ <bp:publicationXref rdf:ID="Pubmed_12242151">
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">12242151</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</bp:DB>
+ <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2002</bp:YEAR>
+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Distinct BH3 domains either sensitize or activate mitochondrial apoptosis, serving as prototype cancer therapeutics</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Letai, A</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bassik, MC</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Walensky, LD</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Sorcinelli, MD</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Weiler, S</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Korsmeyer, SJ</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cancer Cell 2:183-92</bp:SOURCE>
+ </bp:publicationXref>
+ <bp:openControlledVocabulary rdf:ID="mitochondrial_membrane">
+ <bp:TERM rdf:datatype="http://www.w3.org/2001/XMLSchema#string">mitochondrial membrane</bp:TERM>
+ <bp:XREF rdf:resource="#GO_0005740" />
+ </bp:openControlledVocabulary>
+ <bp:unificationXref rdf:ID="GO_0005740">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GO</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0005740</bp:ID>
+ </bp:unificationXref>
+ <bp:pathwayStep rdf:ID="BAD_displaces_tBID_from_BCL_2_sequestrationStep">
+ <bp:STEP-INTERACTIONS rdf:resource="#BAD_displaces_tBID_from_BCL_2_sequestration" />
+ </bp:pathwayStep>
+ <bp:unificationXref rdf:ID="Reactome111447">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">111447</bp:ID>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</bp:COMMENT>
+ </bp:unificationXref>
+ <bp:evidence rdf:ID="Summation_140545">
+ <bp:XREF rdf:resource="#Pubmed_12209154" />
+ </bp:evidence>
+ <bp:publicationXref rdf:ID="Pubmed_12209154">
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">12209154</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</bp:DB>
+ <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2002</bp:YEAR>
+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The Bcl2 family: regulators of the cellular life-or-death switch</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cory, S</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Adams, JM</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Nat Rev Cancer 2:647-56</bp:SOURCE>
+ </bp:publicationXref>
+ <bp:publicationXref rdf:ID="Pubmed_15231831">
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">15231831</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</bp:DB>
+ <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2004</bp:YEAR>
+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BAD Is a Pro-survival Factor Prior to Activation of Its Pro-apoptotic Function.</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Seo, SY</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Chen, YB</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Ivanovska, I</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Ranger, AM</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Hong, SJ</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Dawson, VL</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Korsmeyer, SJ</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bellows, DS</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Fannjiang, Y</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Hardwick, JM</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Biol Chem 279:42240-9</bp:SOURCE>
+ </bp:publicationXref>
+ <bp:pathwayStep rdf:ID="Activation_of_BAD_and_translocation_to_mitochondria_Step">
+ <bp:STEP-INTERACTIONS rdf:resource="#Activation_of_BAD_and_translocation_to_mitochondria_" />
+ </bp:pathwayStep>
+ <bp:pathway rdf:ID="Activation_of_NOXA_and_translocation_to_mitochondria">
+ <bp:PATHWAY-COMPONENTS rdf:resource="#Transactivation_of_NOXA_by_E2F1Step" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#Translocation_of_NOXA_to_mitochondriaStep" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#Transactivation_of_NOXA_by_p53Step" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Activation of NOXA and translocation to mitochondria</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Activation of NOXA and translocation to mitochondria</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome111448" />
+ <bp:XREF rdf:resource="#activation_of_pro_apoptotic_gene_products" />
+ </bp:pathway>
+ <bp:biochemicalReaction rdf:ID="Transactivation_of_NOXA_by_p53">
+ <bp:RIGHT rdf:resource="#NOXA_protein__cytosol_" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Transactivation of NOXA by p53</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Transactivation of NOXA by p53</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome140214" />
+ <bp:XREF rdf:resource="#Pubmed_15126337" />
+ </bp:biochemicalReaction>
+ <bp:sequenceParticipant rdf:ID="NOXA_protein__cytosol_">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q13794_Phorbol_12_myristate_13_acetate_induced_protein_1__PMA_induced_protein_1___Immediate_early_response_protein_APR_" />
+ </bp:sequenceParticipant>
+ <bp:protein rdf:ID="UniProt_Q13794_Phorbol_12_myristate_13_acetate_induced_protein_1__PMA_induced_protein_1___Immediate_early_response_protein_APR_">
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:Q13794 Phorbol-12-myristate-13-acetate-induced protein 1 (PMA-induced protein 1) (Immediate-early-response protein APR)</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PMAIP1</bp:SYNONYMS>
+ <bp:XREF rdf:resource="#UniProt_Q13794" />
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TISSUE SPECIFICITY: Highly expressed in adult T-cell leukemia cell line.</bp:COMMENT>
+ </bp:protein>
+ <bp:unificationXref rdf:ID="UniProt_Q13794">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Q13794</bp:ID>
+ </bp:unificationXref>
+ <bp:unificationXref rdf:ID="Reactome140214">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">140214</bp:ID>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</bp:COMMENT>
+ </bp:unificationXref>
+ <bp:publicationXref rdf:ID="Pubmed_15126337">
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">15126337</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</bp:DB>
+ <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2004</bp:YEAR>
+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Apoptotic signaling pathways induced by nitric oxide in human lymphoblastoid cells expressing wild-type or mutant p53</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Li, CQ</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Robles, AI</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Hanigan, CL</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Hofseth, LJ</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Trudel, LJ</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Harris, CC</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Wogan, GN</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cancer Res 64:3022-9</bp:SOURCE>
+ </bp:publicationXref>
+ <bp:modulation rdf:ID="_transcriptional_activator_activity_of_p53_ser_15_phosphorylated__positively_regulates__Transactivation_of_NOXA_by_p53_">
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">'transcriptional activator activity of p53 ser-15 phosphorylated' positively regulates 'Transactivation of NOXA by p53'</bp:NAME>
+ <bp:CONTROL-TYPE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ACTIVATION</bp:CONTROL-TYPE>
+ <bp:CONTROLLED rdf:resource="#Transactivation_of_NOXA_by_p53" />
+ </bp:modulation>
+ <bp:pathwayStep rdf:ID="Transactivation_of_NOXA_by_p53Step">
+ <bp:STEP-INTERACTIONS rdf:resource="#Transactivation_of_NOXA_by_p53" />
+ <bp:NEXT-STEP rdf:resource="#Translocation_of_NOXA_to_mitochondriaStep" />
+ <bp:STEP-INTERACTIONS rdf:resource="#_transcriptional_activator_activity_of_p53_ser_15_phosphorylated__positively_regulates__Transactivation_of_NOXA_by_p53_" />
+ </bp:pathwayStep>
+ <bp:biochemicalReaction rdf:ID="Transactivation_of_NOXA_by_E2F1">
+ <bp:RIGHT rdf:resource="#NOXA_protein__cytosol_1" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Transactivation of NOXA by E2F1</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Transactivation of NOXA by E2F1</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome140217" />
+ <bp:XREF rdf:resource="#Pubmed_14684737" />
+ </bp:biochemicalReaction>
+ <bp:sequenceParticipant rdf:ID="NOXA_protein__cytosol_1">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q13794_Phorbol_12_myristate_13_acetate_induced_protein_1__PMA_induced_protein_1___Immediate_early_response_protein_APR_" />
+ </bp:sequenceParticipant>
+ <bp:unificationXref rdf:ID="Reactome140217">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">140217</bp:ID>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</bp:COMMENT>
+ </bp:unificationXref>
+ <bp:publicationXref rdf:ID="Pubmed_14684737">
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">14684737</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</bp:DB>
+ <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2004</bp:YEAR>
+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Up-regulation of Bcl-2 homology 3 (BH3)-only proteins by E2F1 mediates apoptosis</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Hershko, T</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Ginsberg, D</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Biol Chem 279:8627-34</bp:SOURCE>
+ </bp:publicationXref>
+ <bp:modulation rdf:ID="_transcriptional_activator_activity_of_E2F1__nucleoplasm___positively_regulates__Transactivation_of_NOXA_by_E2F1_">
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">'transcriptional activator activity of E2F1 [nucleoplasm]' positively regulates 'Transactivation of NOXA by E2F1'</bp:NAME>
+ <bp:CONTROL-TYPE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ACTIVATION</bp:CONTROL-TYPE>
+ <bp:CONTROLLED rdf:resource="#Transactivation_of_NOXA_by_E2F1" />
+ </bp:modulation>
+ <bp:pathwayStep rdf:ID="Transactivation_of_NOXA_by_E2F1Step">
+ <bp:STEP-INTERACTIONS rdf:resource="#Transactivation_of_NOXA_by_E2F1" />
+ <bp:NEXT-STEP rdf:resource="#Translocation_of_NOXA_to_mitochondriaStep" />
+ <bp:STEP-INTERACTIONS rdf:resource="#_transcriptional_activator_activity_of_E2F1__nucleoplasm___positively_regulates__Transactivation_of_NOXA_by_E2F1_" />
+ </bp:pathwayStep>
+ <bp:biochemicalReaction rdf:ID="Translocation_of_NOXA_to_mitochondria">
+ <bp:LEFT rdf:resource="#NOXA_protein__cytosol_2" />
+ <bp:RIGHT rdf:resource="#NOXA_protein__mitochondrial_outer_membrane_" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Translocation of NOXA to mitochondria</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Translocation of NOXA to mitochondria</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome140216" />
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">It was observed that cytosolic Noxa underwent BH3 motif-dependent localization to mitochondria and interacted with anti-apoptotic Bcl-2 family members, resulting in the activation of caspase-9.</bp:COMMENT>
+ <bp:EVIDENCE rdf:resource="#Summation_140386" />
+ <bp:XREF rdf:resource="#protein_insertion_into_mitochondrial_membrane_during_induction_of_apoptosis" />
+ </bp:biochemicalReaction>
+ <bp:sequenceParticipant rdf:ID="NOXA_protein__cytosol_2">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q13794_Phorbol_12_myristate_13_acetate_induced_protein_1__PMA_induced_protein_1___Immediate_early_response_protein_APR_" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="NOXA_protein__mitochondrial_outer_membrane_">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q13794_Phorbol_12_myristate_13_acetate_induced_protein_1__PMA_induced_protein_1___Immediate_early_response_protein_APR_" />
+ </bp:sequenceParticipant>
+ <bp:unificationXref rdf:ID="Reactome140216">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">140216</bp:ID>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</bp:COMMENT>
+ </bp:unificationXref>
+ <bp:evidence rdf:ID="Summation_140386">
+ <bp:XREF rdf:resource="#Pubmed_10807576" />
+ </bp:evidence>
+ <bp:publicationXref rdf:ID="Pubmed_10807576">
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">10807576</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</bp:DB>
+ <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2000</bp:YEAR>
+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Noxa, a BH3-only member of the Bcl-2 family and candidate mediator of p53-induced apoptosis</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Oda, E</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Ohki, R</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Murasawa, H</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Nemoto, J</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Shibue, T</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Yamashita, T</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Tokino, T</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Taniguchi, T</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Tanaka, N</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Science 288:1053-8</bp:SOURCE>
+ </bp:publicationXref>
+ <bp:pathwayStep rdf:ID="Translocation_of_NOXA_to_mitochondriaStep">
+ <bp:STEP-INTERACTIONS rdf:resource="#Translocation_of_NOXA_to_mitochondria" />
+ <bp:NEXT-STEP rdf:resource="#Interaction_of_NOXA_with_BCL2Step" />
+ <bp:NEXT-STEP rdf:resource="#Interaction_of_NOXA_with_BCL_xlStep" />
+ </bp:pathwayStep>
+ <bp:unificationXref rdf:ID="Reactome111448">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">111448</bp:ID>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</bp:COMMENT>
+ </bp:unificationXref>
+ <bp:pathwayStep rdf:ID="Activation_of_NOXA_and_translocation_to_mitochondriaStep">
+ <bp:STEP-INTERACTIONS rdf:resource="#Activation_of_NOXA_and_translocation_to_mitochondria" />
+ </bp:pathwayStep>
+ <bp:pathway rdf:ID="Activation_of_PUMA_and_translocation_to_mitochondria">
+ <bp:PATHWAY-COMPONENTS rdf:resource="#Transactivation_of_PUMA_by_p53Step" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#Transactivation_of_PUMA_by_E2F1Step" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#Translocation_of_PUMA_protein_to_mitochondriaStep" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Activation of PUMA and translocation to mitochondria</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Activation of PUMA and translocation to mitochondria</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome139915" />
+ <bp:XREF rdf:resource="#activation_of_pro_apoptotic_gene_products" />
+ </bp:pathway>
+ <bp:biochemicalReaction rdf:ID="Transactivation_of_PUMA_by_p53">
+ <bp:RIGHT rdf:resource="#PUMA_protein__cytosol_" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Transactivation of PUMA by p53</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Transactivation of PUMA by p53</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome139913" />
+ <bp:XREF rdf:resource="#Pubmed_11463392" />
+ </bp:biochemicalReaction>
+ <bp:sequenceParticipant rdf:ID="PUMA_protein__cytosol_">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q9BXH1_PUMA_protein" />
+ </bp:sequenceParticipant>
+ <bp:protein rdf:ID="UniProt_Q9BXH1_PUMA_protein">
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:Q9BXH1 PUMA protein</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PUMA protein</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#UniProt_Q9BXH1" />
+ </bp:protein>
+ <bp:unificationXref rdf:ID="UniProt_Q9BXH1">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Q9BXH1</bp:ID>
+ </bp:unificationXref>
+ <bp:unificationXref rdf:ID="Reactome139913">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">139913</bp:ID>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</bp:COMMENT>
+ </bp:unificationXref>
+ <bp:publicationXref rdf:ID="Pubmed_11463392">
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">11463392</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</bp:DB>
+ <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2001</bp:YEAR>
+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PUMA, a novel proapoptotic gene, is induced by p53</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Nakano, K</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Vousden, KH</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mol Cell 7:683-94</bp:SOURCE>
+ </bp:publicationXref>
+ <bp:modulation rdf:ID="_transcriptional_activator_activity_of_p53_ser_15_phosphorylated__positively_regulates__Transactivation_of_PUMA_by_p53_">
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">'transcriptional activator activity of p53 ser-15 phosphorylated' positively regulates 'Transactivation of PUMA by p53'</bp:NAME>
+ <bp:CONTROL-TYPE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ACTIVATION</bp:CONTROL-TYPE>
+ <bp:CONTROLLED rdf:resource="#Transactivation_of_PUMA_by_p53" />
+ </bp:modulation>
+ <bp:pathwayStep rdf:ID="Transactivation_of_PUMA_by_p53Step">
+ <bp:STEP-INTERACTIONS rdf:resource="#Transactivation_of_PUMA_by_p53" />
+ <bp:NEXT-STEP rdf:resource="#Translocation_of_PUMA_protein_to_mitochondriaStep" />
+ <bp:STEP-INTERACTIONS rdf:resource="#_transcriptional_activator_activity_of_p53_ser_15_phosphorylated__positively_regulates__Transactivation_of_PUMA_by_p53_" />
+ </bp:pathwayStep>
+ <bp:biochemicalReaction rdf:ID="Transactivation_of_PUMA_by_E2F1">
+ <bp:RIGHT rdf:resource="#PUMA_protein__cytosol_1" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Transactivation of PUMA by E2F1</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Transactivation of PUMA by E2F1</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome140221" />
+ <bp:XREF rdf:resource="#Pubmed_14684737" />
+ </bp:biochemicalReaction>
+ <bp:sequenceParticipant rdf:ID="PUMA_protein__cytosol_1">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q9BXH1_PUMA_protein" />
+ </bp:sequenceParticipant>
+ <bp:unificationXref rdf:ID="Reactome140221">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">140221</bp:ID>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</bp:COMMENT>
+ </bp:unificationXref>
+ <bp:modulation rdf:ID="_transcriptional_activator_activity_of_E2F1__nucleoplasm___positively_regulates__Transactivation_of_PUMA_by_E2F1_">
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">'transcriptional activator activity of E2F1 [nucleoplasm]' positively regulates 'Transactivation of PUMA by E2F1'</bp:NAME>
+ <bp:CONTROL-TYPE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ACTIVATION</bp:CONTROL-TYPE>
+ <bp:CONTROLLED rdf:resource="#Transactivation_of_PUMA_by_E2F1" />
+ </bp:modulation>
+ <bp:pathwayStep rdf:ID="Transactivation_of_PUMA_by_E2F1Step">
+ <bp:STEP-INTERACTIONS rdf:resource="#Transactivation_of_PUMA_by_E2F1" />
+ <bp:NEXT-STEP rdf:resource="#Translocation_of_PUMA_protein_to_mitochondriaStep" />
+ <bp:STEP-INTERACTIONS rdf:resource="#_transcriptional_activator_activity_of_E2F1__nucleoplasm___positively_regulates__Transactivation_of_PUMA_by_E2F1_" />
+ </bp:pathwayStep>
+ <bp:biochemicalReaction rdf:ID="Translocation_of_PUMA_protein_to_mitochondria">
+ <bp:LEFT rdf:resource="#PUMA_protein__cytosol_2" />
+ <bp:RIGHT rdf:resource="#PUMA_protein__mitochondrial_outer_membrane_" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Translocation of PUMA protein to mitochondria</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Translocation of PUMA protein to mitochondria</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome139914" />
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">It is thought that due to its p53 dependence for expression, PUMA could function as a mediator of p53-induced apoptosis. Newly synthesized PUMA protein translocates to mitochondria and binds to BCL-2 and Bcl-X(L) through a BH3 domain.</bp:COMMENT>
+ <bp:EVIDENCE rdf:resource="#Summation_140403" />
+ <bp:XREF rdf:resource="#protein_insertion_into_mitochondrial_membrane_during_induction_of_apoptosis" />
+ </bp:biochemicalReaction>
+ <bp:sequenceParticipant rdf:ID="PUMA_protein__cytosol_2">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q9BXH1_PUMA_protein" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="PUMA_protein__mitochondrial_outer_membrane_">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q9BXH1_PUMA_protein" />
+ </bp:sequenceParticipant>
+ <bp:unificationXref rdf:ID="Reactome139914">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">139914</bp:ID>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</bp:COMMENT>
+ </bp:unificationXref>
+ <bp:evidence rdf:ID="Summation_140403">
+ <bp:XREF rdf:resource="#Pubmed_11463391" />
+ </bp:evidence>
+ <bp:publicationXref rdf:ID="Pubmed_11463391">
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">11463391</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</bp:DB>
+ <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2001</bp:YEAR>
+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PUMA induces the rapid apoptosis of colorectal cancer cells</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Yu, J</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Zhang, L</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Hwang, PM</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Kinzler, KW</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Vogelstein, B</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mol Cell 7:673-82</bp:SOURCE>
+ </bp:publicationXref>
+ <bp:pathwayStep rdf:ID="Translocation_of_PUMA_protein_to_mitochondriaStep">
+ <bp:STEP-INTERACTIONS rdf:resource="#Translocation_of_PUMA_protein_to_mitochondria" />
+ <bp:NEXT-STEP rdf:resource="#Interaction_of_PUMA_and_Bcl_2Step" />
+ <bp:NEXT-STEP rdf:resource="#Interaction_of_PUMA_and_Bcl_XLStep" />
+ </bp:pathwayStep>
+ <bp:unificationXref rdf:ID="Reactome139915">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">139915</bp:ID>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</bp:COMMENT>
+ </bp:unificationXref>
+ <bp:pathwayStep rdf:ID="Activation_of_PUMA_and_translocation_to_mitochondriaStep">
+ <bp:STEP-INTERACTIONS rdf:resource="#Activation_of_PUMA_and_translocation_to_mitochondria" />
+ </bp:pathwayStep>
+ <bp:pathway rdf:ID="Activation_of_BIM_and_translocation_to_mitochondria_">
+ <bp:PATHWAY-COMPONENTS rdf:resource="#Phosphorylation_of_DLC1_by_MAPK_8Step" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#Translocation_of_BIM_to_mitochondriaStep" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Activation of BIM and translocation to mitochondria</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Activation of BIM and translocation to mitochondria</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome111446" />
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BIM acts as a sentinel to check the integrity of the cytoskeleton. It exists as two variant proteins: BIM-EL and BIM-L. In healthy cells, these two isoforms are sequestered to the dynein motor complex on microtubules via the dynein light chain DLC1. JNK or MAPK8 releases BIM in response to UV irradiation by phosphorylation.</bp:COMMENT>
+ <bp:EVIDENCE rdf:resource="#Summation_140550" />
+ <bp:XREF rdf:resource="#Pubmed_14764673" />
+ <bp:XREF rdf:resource="#activation_of_pro_apoptotic_gene_products" />
+ </bp:pathway>
+ <bp:biochemicalReaction rdf:ID="Phosphorylation_of_DLC1_by_MAPK_8">
+ <bp:LEFT rdf:resource="#BIM_sequestered_to_dynein__DLC1___plasma_membrane_" />
+ <bp:RIGHT rdf:resource="#BIM__cytosol_" />
+ <bp:RIGHT rdf:resource="#phospho_dynein_DLC1__on_microtubules__plasma_membrane_" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Phosphorylation of DLC1 by MAPK 8</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Phosphorylation of DLC1 by MAPK 8</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome139918" />
+ <bp:XREF rdf:resource="#Pubmed_12591950" />
+ </bp:biochemicalReaction>
+ <bp:sequenceParticipant rdf:ID="BIM_sequestered_to_dynein__DLC1___plasma_membrane_">
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</bp:COMMENT>
+ <bp:CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#BIM_sequestered_to_dynein__DLC1___plasma_membrane_1" />
+ </bp:sequenceParticipant>
+ <bp:complex rdf:ID="BIM_sequestered_to_dynein__DLC1___plasma_membrane_1">
+ <bp:COMPONENTS rdf:resource="#BIM_protein__plasma_membrane_" />
+ <bp:COMPONENTS rdf:resource="#DLC1__plasma_membrane_" />
+ <bp:COMPONENTS rdf:resource="#microtubules__plasma_membrane_" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BIM sequestered to dynein (DLC1) [plasma membrane]</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BIM sequestered to dynein (DLC1)</bp:SHORT-NAME>
+ </bp:complex>
+ <bp:sequenceParticipant rdf:ID="BIM_protein__plasma_membrane_">
+ <bp:CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_O43521_1_Bcl_2_like_protein_11__Bcl2_interacting_mediator_of_cell_death_" />
+ </bp:sequenceParticipant>
+ <bp:protein rdf:ID="UniProt_O43521_1_Bcl_2_like_protein_11__Bcl2_interacting_mediator_of_cell_death_">
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:O43521-1 Bcl-2-like protein 11 (Bcl2 interacting mediator of cell death)</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BCL2L11</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BIM</bp:SYNONYMS>
+ <bp:XREF rdf:resource="#UniProt_O43521" />
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Induces apoptosis. Isoform BimL is more potent than isoform BimEL. SUBUNIT: Forms heterodimers with a number of antiapoptotic Bcl-2 proteins including Mcl-1, Bcl-2, Bcl-X(L), BFL-1, and BHRF1. Does not heterodimerize with proapoptotic proteins such as BAD, BOK, BAX or BAK (By similarity). SUBCELLULAR LOCATION: Associated with intracytoplasmic membranes (By similarity). ALTERNATIVE PRODUCTS: Event=Alternative [...]
+ </bp:protein>
+ <bp:unificationXref rdf:ID="UniProt_O43521">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">O43521</bp:ID>
+ </bp:unificationXref>
+ <bp:sequenceParticipant rdf:ID="DLC1__plasma_membrane_">
+ <bp:CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_P63167_Dynein_light_chain_1__cytoplasmic__8_kDa_dynein_light_chain___DLC8___Protein_inhibitor_of_neuronal_nitric_oxide_synthase___PIN_" />
+ </bp:sequenceParticipant>
+ <bp:protein rdf:ID="UniProt_P63167_Dynein_light_chain_1__cytoplasmic__8_kDa_dynein_light_chain___DLC8___Protein_inhibitor_of_neuronal_nitric_oxide_synthase___PIN_">
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P63167 Dynein light chain 1, cytoplasmic (8 kDa dynein light chain) (DLC8) (Protein inhibitor of neuronal nitric oxide synthase) (PIN)</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DNCL1</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DNCLC1</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DLC1</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">HDLC1</bp:SYNONYMS>
+ <bp:XREF rdf:resource="#UniProt_P63167" />
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: May be involved in some aspects of dynein-related intracellular transport and motility. May play a role in changing or maintaining the spatial distribution of cytoskeletal structures. FUNCTION: Binds and inhibits the catalytic activity of neuronal nitric oxide synthase. SUBUNIT: Consists of at least two heavy chains and a number of intermediate and light chains. SUBCELLULAR LOCATION: Cytoplasmic. TISSUE SPEC [...]
+ </bp:protein>
+ <bp:unificationXref rdf:ID="UniProt_P63167">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P63167</bp:ID>
+ </bp:unificationXref>
+ <bp:physicalEntityParticipant rdf:ID="microtubules__plasma_membrane_">
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</bp:COMMENT>
+ <bp:CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#microtubules__plasma_membrane_1" />
+ </bp:physicalEntityParticipant>
+ <bp:physicalEntity rdf:ID="microtubules__plasma_membrane_1">
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">microtubules [plasma membrane]</bp:NAME>
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome. Each synonym is a name of a ConcreteEntity, and each XREF points to one ConcreteEntity</bp:COMMENT>
+ </bp:physicalEntity>
+ <bp:sequenceParticipant rdf:ID="BIM__cytosol_">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_O43521_1_Bcl_2_like_protein_11__Bcl2_interacting_mediator_of_cell_death_" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="phospho_dynein_DLC1__on_microtubules__plasma_membrane_">
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</bp:COMMENT>
+ <bp:CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#phospho_dynein_DLC1__on_microtubules__plasma_membrane_1" />
+ </bp:sequenceParticipant>
+ <bp:complex rdf:ID="phospho_dynein_DLC1__on_microtubules__plasma_membrane_1">
+ <bp:COMPONENTS rdf:resource="#Phospho_DLC1__cytosol_" />
+ <bp:COMPONENTS rdf:resource="#microtubules__plasma_membrane_2" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">phospho-dynein(DLC1) on microtubules [plasma membrane]</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">phospho-dynein(DLC1) on microtubules</bp:SHORT-NAME>
+ </bp:complex>
+ <bp:sequenceParticipant rdf:ID="Phospho_DLC1__cytosol_">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_P63167_Dynein_light_chain_1__cytoplasmic__8_kDa_dynein_light_chain___DLC8___Protein_inhibitor_of_neuronal_nitric_oxide_synthase___PIN_" />
+ </bp:sequenceParticipant>
+ <bp:physicalEntityParticipant rdf:ID="microtubules__plasma_membrane_2">
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</bp:COMMENT>
+ <bp:CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#microtubules__plasma_membrane_1" />
+ </bp:physicalEntityParticipant>
+ <bp:catalysis rdf:ID="kinase_activity_of_Mitogen_activated_protein_kinase_8___cytosol_">
+ <bp:CONTROLLER rdf:resource="#Mitogen_activated_protein_kinase_8___cytosol_" />
+ <bp:CONTROLLED rdf:resource="#Phosphorylation_of_DLC1_by_MAPK_8" />
+ <bp:DIRECTION rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PHYSIOL-LEFT-TO-RIGHT</bp:DIRECTION>
+ <bp:XREF rdf:resource="#kinase_activity" />
+ </bp:catalysis>
+ <bp:sequenceParticipant rdf:ID="Mitogen_activated_protein_kinase_8___cytosol_">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_P45983_1_Mitogen_activated_protein_kinase_8__EC_2_7_1_37___Stress_activated_protein_kinase_JNK1___c_Jun_N_terminal_kinase_1___JNK_46_" />
+ </bp:sequenceParticipant>
+ <bp:protein rdf:ID="UniProt_P45983_1_Mitogen_activated_protein_kinase_8__EC_2_7_1_37___Stress_activated_protein_kinase_JNK1___c_Jun_N_terminal_kinase_1___JNK_46_">
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P45983-1 Mitogen-activated protein kinase 8 (EC 2.7.1.37) (Stress-activated protein kinase JNK1) (c-Jun N-terminal kinase 1) (JNK-46)</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PRKM8</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">JNK1</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">MAPK8</bp:SYNONYMS>
+ <bp:XREF rdf:resource="#UniProt_P45983" />
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Responds to activation by environmental stress and pro- inflammatory cytokines by phosphorylating a number of transcription factors, primarily components of AP-1 such as c-Jun and ATF2 and thus regulates AP-1 transcriptional activity. In T- cells, JNK1 and JNK2 are required for polarized differentiation of T-helper cells into Th1 cells (By similarity). FUNCTION: JNK1 isoforms display different binding patter [...]
+ </bp:protein>
+ <bp:unificationXref rdf:ID="UniProt_P45983">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P45983</bp:ID>
+ </bp:unificationXref>
+ <bp:unificationXref rdf:ID="Reactome139918">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">139918</bp:ID>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</bp:COMMENT>
+ </bp:unificationXref>
+ <bp:publicationXref rdf:ID="Pubmed_12591950">
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">12591950</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</bp:DB>
+ <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2003</bp:YEAR>
+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">JNK phosphorylation of Bim-related members of the Bcl2 family induces Bax-dependent apoptosis</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Lei, K</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Davis, RJ</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Proc Natl Acad Sci U S A 100:2432-7</bp:SOURCE>
+ </bp:publicationXref>
+ <bp:pathwayStep rdf:ID="Phosphorylation_of_DLC1_by_MAPK_8Step">
+ <bp:STEP-INTERACTIONS rdf:resource="#Phosphorylation_of_DLC1_by_MAPK_8" />
+ <bp:STEP-INTERACTIONS rdf:resource="#kinase_activity_of_Mitogen_activated_protein_kinase_8___cytosol_" />
+ </bp:pathwayStep>
+ <bp:biochemicalReaction rdf:ID="Translocation_of_BIM_to_mitochondria">
+ <bp:LEFT rdf:resource="#BIM__cytosol_1" />
+ <bp:RIGHT rdf:resource="#BIM__mitochondrial_outer_membrane_" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Translocation of BIM to mitochondria</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Translocation of BIM to mitochondria</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome139919" />
+ <bp:XREF rdf:resource="#protein_insertion_into_mitochondrial_membrane_during_induction_of_apoptosis" />
+ </bp:biochemicalReaction>
+ <bp:sequenceParticipant rdf:ID="BIM__cytosol_1">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_O43521_1_Bcl_2_like_protein_11__Bcl2_interacting_mediator_of_cell_death_" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="BIM__mitochondrial_outer_membrane_">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_O43521_1_Bcl_2_like_protein_11__Bcl2_interacting_mediator_of_cell_death_" />
+ </bp:sequenceParticipant>
+ <bp:unificationXref rdf:ID="Reactome139919">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">139919</bp:ID>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</bp:COMMENT>
+ </bp:unificationXref>
+ <bp:pathwayStep rdf:ID="Translocation_of_BIM_to_mitochondriaStep">
+ <bp:STEP-INTERACTIONS rdf:resource="#Translocation_of_BIM_to_mitochondria" />
+ <bp:NEXT-STEP rdf:resource="#Interaction_of_BIM_with_BCL2_Step" />
+ </bp:pathwayStep>
+ <bp:unificationXref rdf:ID="Reactome111446">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">111446</bp:ID>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</bp:COMMENT>
+ </bp:unificationXref>
+ <bp:evidence rdf:ID="Summation_140550">
+ <bp:XREF rdf:resource="#Pubmed_14634621" />
+ </bp:evidence>
+ <bp:publicationXref rdf:ID="Pubmed_14764673">
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">14764673</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</bp:DB>
+ <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2004</bp:YEAR>
+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">B cell receptor-mediated apoptosis of human lymphocytes is associated with a new regulatory pathway of Bim isoform expression.</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mouhamad, S</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Besnault, L</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Auffredou, MT</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Leprince, C</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bourgeade, MF</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Leca, G</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Vazquez, A</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Immunol 172:2084-91</bp:SOURCE>
+ </bp:publicationXref>
+ <bp:pathwayStep rdf:ID="Activation_of_BIM_and_translocation_to_mitochondria_Step">
+ <bp:STEP-INTERACTIONS rdf:resource="#Activation_of_BIM_and_translocation_to_mitochondria_" />
+ </bp:pathwayStep>
+ <bp:pathway rdf:ID="Activation_of_BMF_and_translocation_to_mitochondria">
+ <bp:PATHWAY-COMPONENTS rdf:resource="#Translocation_of_BMF_to_mitochondriaStep" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#Phosphorylation_of_DLC2_by_MAPK_8Step" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Activation of BMF and translocation to mitochondria</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Activation of BMF and translocation to mitochondria</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome139910" />
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">In healthy cells, BMF is bound to the myosin V motor complex through its interaction with DLC2. UV irradiation or anoikis induces MAPK8 (JNK) to phosphorylate Dynein Light Chain 2 (DLC2) to release BMF.</bp:COMMENT>
+ <bp:EVIDENCE rdf:resource="#Summation_140551" />
+ <bp:XREF rdf:resource="#activation_of_pro_apoptotic_gene_products" />
+ </bp:pathway>
+ <bp:biochemicalReaction rdf:ID="Phosphorylation_of_DLC2_by_MAPK_8">
+ <bp:LEFT rdf:resource="#BMF_sequestered_to_dynein__DLC2___plasma_membrane_" />
+ <bp:RIGHT rdf:resource="#BMF__cytosol_" />
+ <bp:RIGHT rdf:resource="#phospho_dynein_DLC2__on_microtubules__plasma_membrane_" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Phosphorylation of DLC2 by MAPK-8</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Phosphorylation of DLC2 by MAPK-8</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome139908" />
+ <bp:XREF rdf:resource="#Pubmed_12591950" />
+ </bp:biochemicalReaction>
+ <bp:sequenceParticipant rdf:ID="BMF_sequestered_to_dynein__DLC2___plasma_membrane_">
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</bp:COMMENT>
+ <bp:CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#BMF_sequestered_to_dynein__DLC2___plasma_membrane_1" />
+ </bp:sequenceParticipant>
+ <bp:complex rdf:ID="BMF_sequestered_to_dynein__DLC2___plasma_membrane_1">
+ <bp:COMPONENTS rdf:resource="#DLC2__plasma_membrane_" />
+ <bp:COMPONENTS rdf:resource="#BMF_protein__plasma_membrane_" />
+ <bp:COMPONENTS rdf:resource="#microtubules__plasma_membrane_3" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BMF sequestered to dynein (DLC2) [plasma membrane]</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BMF sequestered to dynein (DLC2)</bp:SHORT-NAME>
+ </bp:complex>
+ <bp:sequenceParticipant rdf:ID="DLC2__plasma_membrane_">
+ <bp:CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q96FJ2" />
+ </bp:sequenceParticipant>
+ <bp:protein rdf:ID="UniProt_Q96FJ2">
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:Q96FJ2</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DLC1</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#UniProt_Q96FJ21" />
+ </bp:protein>
+ <bp:unificationXref rdf:ID="UniProt_Q96FJ21">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Q96FJ2</bp:ID>
+ </bp:unificationXref>
+ <bp:sequenceParticipant rdf:ID="BMF_protein__plasma_membrane_">
+ <bp:CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q96LC9_BMF_protein" />
+ </bp:sequenceParticipant>
+ <bp:protein rdf:ID="UniProt_Q96LC9_BMF_protein">
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:Q96LC9 BMF protein</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BMF protein</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#UniProt_Q96LC9" />
+ </bp:protein>
+ <bp:unificationXref rdf:ID="UniProt_Q96LC9">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Q96LC9</bp:ID>
+ </bp:unificationXref>
+ <bp:physicalEntityParticipant rdf:ID="microtubules__plasma_membrane_3">
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</bp:COMMENT>
+ <bp:CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#microtubules__plasma_membrane_1" />
+ </bp:physicalEntityParticipant>
+ <bp:sequenceParticipant rdf:ID="BMF__cytosol_">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q96LC9_BMF_protein" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="phospho_dynein_DLC2__on_microtubules__plasma_membrane_">
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</bp:COMMENT>
+ <bp:CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#phospho_dynein_DLC2__on_microtubules__plasma_membrane_1" />
+ </bp:sequenceParticipant>
+ <bp:complex rdf:ID="phospho_dynein_DLC2__on_microtubules__plasma_membrane_1">
+ <bp:COMPONENTS rdf:resource="#Phospho_DLC2__cytosol_" />
+ <bp:COMPONENTS rdf:resource="#microtubules__plasma_membrane_4" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">phospho-dynein(DLC2) on microtubules [plasma membrane]</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">phospho-dynein(DLC2) on microtubules</bp:SHORT-NAME>
+ </bp:complex>
+ <bp:sequenceParticipant rdf:ID="Phospho_DLC2__cytosol_">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q96FJ2" />
+ </bp:sequenceParticipant>
+ <bp:physicalEntityParticipant rdf:ID="microtubules__plasma_membrane_4">
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</bp:COMMENT>
+ <bp:CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#microtubules__plasma_membrane_1" />
+ </bp:physicalEntityParticipant>
+ <bp:catalysis rdf:ID="kinase_activity_of_Mitogen_activated_protein_kinase_8___cytosol_1">
+ <bp:CONTROLLER rdf:resource="#Mitogen_activated_protein_kinase_8___cytosol_1" />
+ <bp:CONTROLLED rdf:resource="#Phosphorylation_of_DLC2_by_MAPK_8" />
+ <bp:DIRECTION rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PHYSIOL-LEFT-TO-RIGHT</bp:DIRECTION>
+ <bp:XREF rdf:resource="#kinase_activity" />
+ </bp:catalysis>
+ <bp:sequenceParticipant rdf:ID="Mitogen_activated_protein_kinase_8___cytosol_1">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_P45983_1_Mitogen_activated_protein_kinase_8__EC_2_7_1_37___Stress_activated_protein_kinase_JNK1___c_Jun_N_terminal_kinase_1___JNK_46_" />
+ </bp:sequenceParticipant>
+ <bp:unificationXref rdf:ID="Reactome139908">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">139908</bp:ID>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</bp:COMMENT>
+ </bp:unificationXref>
+ <bp:pathwayStep rdf:ID="Phosphorylation_of_DLC2_by_MAPK_8Step">
+ <bp:STEP-INTERACTIONS rdf:resource="#Phosphorylation_of_DLC2_by_MAPK_8" />
+ <bp:STEP-INTERACTIONS rdf:resource="#kinase_activity_of_Mitogen_activated_protein_kinase_8___cytosol_1" />
+ </bp:pathwayStep>
+ <bp:biochemicalReaction rdf:ID="Translocation_of_BMF_to_mitochondria">
+ <bp:LEFT rdf:resource="#BMF__cytosol_1" />
+ <bp:RIGHT rdf:resource="#BMF__mitochondrial_outer_membrane_" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Translocation of BMF to mitochondria</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Translocation of BMF to mitochondria</bp:SHORT-NAME>
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+ <bp:XREF rdf:resource="#protein_insertion_into_mitochondrial_membrane_during_induction_of_apoptosis" />
+ </bp:biochemicalReaction>
+ <bp:sequenceParticipant rdf:ID="BMF__cytosol_1">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q96LC9_BMF_protein" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="BMF__mitochondrial_outer_membrane_">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q96LC9_BMF_protein" />
+ </bp:sequenceParticipant>
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+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">139909</bp:ID>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</bp:COMMENT>
+ </bp:unificationXref>
+ <bp:pathwayStep rdf:ID="Translocation_of_BMF_to_mitochondriaStep">
+ <bp:STEP-INTERACTIONS rdf:resource="#Translocation_of_BMF_to_mitochondria" />
+ </bp:pathwayStep>
+ <bp:unificationXref rdf:ID="Reactome139910">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">139910</bp:ID>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</bp:COMMENT>
+ </bp:unificationXref>
+ <bp:evidence rdf:ID="Summation_140551">
+ <bp:XREF rdf:resource="#Pubmed_14634621" />
+ </bp:evidence>
+ <bp:pathwayStep rdf:ID="Activation_of_BMF_and_translocation_to_mitochondriaStep">
+ <bp:STEP-INTERACTIONS rdf:resource="#Activation_of_BMF_and_translocation_to_mitochondria" />
+ </bp:pathwayStep>
+ <bp:unificationXref rdf:ID="Reactome114452">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">114452</bp:ID>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</bp:COMMENT>
+ </bp:unificationXref>
+ <bp:evidence rdf:ID="Summation_140552">
+ <bp:XREF rdf:resource="#Pubmed_12209154" />
+ <bp:XREF rdf:resource="#Pubmed_14634621" />
+ </bp:evidence>
+ <bp:pathwayStep rdf:ID="Activation_of_BH3_only_proteinsStep">
+ <bp:STEP-INTERACTIONS rdf:resource="#Activation_of_BH3_only_proteins" />
+ </bp:pathwayStep>
+ <bp:pathway rdf:ID="BH3_only_proteins_associate_with_and_inactivate_anti_apoptotic_BCL_2_members">
+ <bp:PATHWAY-COMPONENTS rdf:resource="#Interaction_of_PUMA_and_Bcl_XLStep" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#Interaction_of_NOXA_with_BCL2Step" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#Interaction_of_BIM_with_BCL2_Step" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#Sequestration_of_tBID_by_BCL_2Step" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#Interaction__of_BAD_with_BCL_xl___Step" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#Interaction_of_BAD_with_BCL2__Step" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#Interaction_of_BIM_with_BCL_xlStep" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#Interaction_of_NOXA_with_BCL_xlStep" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#Interaction_of_PUMA_and_Bcl_2Step" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#Interaction_of_tBID_with_BCL_xlStep" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome111453" />
+ </bp:pathway>
+ <bp:biochemicalReaction rdf:ID="Interaction_of_BAD_with_BCL2__">
+ <bp:LEFT rdf:resource="#Bcl_2_protein__mitochondrial_outer_membrane_2" />
+ <bp:LEFT rdf:resource="#BAD_protein__cytosol_3" />
+ <bp:RIGHT rdf:resource="#BAD_BCL_2__mitochondrial_outer_membrane_2" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Interaction of BAD with BCL2</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Interaction of BAD with BCL2</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome114277" />
+ <bp:EVIDENCE rdf:resource="#InferredFrom_Interaction_of_BAD_with_Bcl_2" />
+ </bp:biochemicalReaction>
+ <bp:sequenceParticipant rdf:ID="Bcl_2_protein__mitochondrial_outer_membrane_2">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_P10415_1_Apoptosis_regulator_Bcl_2" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="BAD_protein__cytosol_3">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q92934_Bcl2_antagonist_of_cell_death__BAD___Bcl_2_binding_component_6___Bcl__XL_Bcl_2_associated_death_promoter___Bcl_2_like_8_protein_" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="BAD_BCL_2__mitochondrial_outer_membrane_2">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#BAD_BCL_2__mitochondrial_outer_membrane_1" />
+ </bp:sequenceParticipant>
+ <bp:unificationXref rdf:ID="Reactome114277">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">114277</bp:ID>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</bp:COMMENT>
+ </bp:unificationXref>
+ <bp:evidence rdf:ID="InferredFrom_Interaction_of_BAD_with_Bcl_2">
+ <bp:XREF rdf:resource="#Pubmed_7834748" />
+ </bp:evidence>
+ <bp:publicationXref rdf:ID="Pubmed_7834748">
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">7834748</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</bp:DB>
+ <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1995</bp:YEAR>
+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bad, a heterodimeric partner for Bcl-XL and Bcl-2, displaces Bax and promotes cell death</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Yang, E</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Zha, J</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Jockel, J</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Boise, LH</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Thompson, CB</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Korsmeyer, SJ</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cell 80:285-91</bp:SOURCE>
+ </bp:publicationXref>
+ <bp:pathwayStep rdf:ID="Interaction_of_BAD_with_BCL2__Step">
+ <bp:STEP-INTERACTIONS rdf:resource="#Interaction_of_BAD_with_BCL2__" />
+ </bp:pathwayStep>
+ <bp:biochemicalReaction rdf:ID="Interaction__of_BAD_with_BCL_xl___">
+ <bp:LEFT rdf:resource="#Apoptosis_regulator_Bcl_X__mitochondrial_outer_membrane_" />
+ <bp:LEFT rdf:resource="#BAD_protein__cytosol_4" />
+ <bp:RIGHT rdf:resource="#BAD_BCL_xl__mitochondrial_outer_membrane_" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Interaction of BAD with BCL-xl</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Interaction of BAD with BCL-xl</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome114276" />
+ <bp:XREF rdf:resource="#Pubmed_10195903" />
+ </bp:biochemicalReaction>
+ <bp:sequenceParticipant rdf:ID="Apoptosis_regulator_Bcl_X__mitochondrial_outer_membrane_">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q07817_1_Apoptosis_regulator_Bcl_X__Bcl_2_like_1_protein_" />
+ </bp:sequenceParticipant>
+ <bp:protein rdf:ID="UniProt_Q07817_1_Apoptosis_regulator_Bcl_X__Bcl_2_like_1_protein_">
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:Q07817-1 Apoptosis regulator Bcl-X (Bcl-2-like 1 protein)</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BCL2L</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BCLX</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BCL2L1</bp:SYNONYMS>
+ <bp:XREF rdf:resource="#UniProt_Q07817" />
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Potent inhibitor of cell death. Isoform Bcl-X(L) anti- apoptotic activity is inhibited by association with SIVA isoform 1. Inhibits activation of caspases (By similarity). Appears to regulate cell death by blocking the voltage-dependent anion channnel (VDAC) by binding to it and preventing the release of the caspase activator, cytochrome c, from the mitochondrial membrane. The Bcl-X(S) isoform promotes apopt [...]
+ </bp:protein>
+ <bp:unificationXref rdf:ID="UniProt_Q07817">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Q07817</bp:ID>
+ </bp:unificationXref>
+ <bp:sequenceParticipant rdf:ID="BAD_protein__cytosol_4">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q92934_Bcl2_antagonist_of_cell_death__BAD___Bcl_2_binding_component_6___Bcl__XL_Bcl_2_associated_death_promoter___Bcl_2_like_8_protein_" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="BAD_BCL_xl__mitochondrial_outer_membrane_">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#BAD_BCL_xl__mitochondrial_outer_membrane_1" />
+ </bp:sequenceParticipant>
+ <bp:complex rdf:ID="BAD_BCL_xl__mitochondrial_outer_membrane_1">
+ <bp:COMPONENTS rdf:resource="#Apoptosis_regulator_Bcl_X__mitochondrial_outer_membrane_1" />
+ <bp:COMPONENTS rdf:resource="#BAD_protein__mitochondrial_outer_membrane_3" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BAD:BCL-xl [mitochondrial outer membrane]</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BAD:BCL-xl</bp:SHORT-NAME>
+ </bp:complex>
+ <bp:sequenceParticipant rdf:ID="Apoptosis_regulator_Bcl_X__mitochondrial_outer_membrane_1">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q07817_1_Apoptosis_regulator_Bcl_X__Bcl_2_like_1_protein_" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="BAD_protein__mitochondrial_outer_membrane_3">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q92934_Bcl2_antagonist_of_cell_death__BAD___Bcl_2_binding_component_6___Bcl__XL_Bcl_2_associated_death_promoter___Bcl_2_like_8_protein_" />
+ </bp:sequenceParticipant>
+ <bp:unificationXref rdf:ID="Reactome114276">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">114276</bp:ID>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</bp:COMMENT>
+ </bp:unificationXref>
+ <bp:pathwayStep rdf:ID="Interaction__of_BAD_with_BCL_xl___Step">
+ <bp:STEP-INTERACTIONS rdf:resource="#Interaction__of_BAD_with_BCL_xl___" />
+ </bp:pathwayStep>
+ <bp:biochemicalReaction rdf:ID="Sequestration_of_tBID_by_BCL_2">
+ <bp:LEFT rdf:resource="#tBID__mitochondrial_outer_membrane_3" />
+ <bp:LEFT rdf:resource="#Bcl_2_protein__mitochondrial_outer_membrane_3" />
+ <bp:RIGHT rdf:resource="#tBID_BCL_2__mitochondrial_outer_membrane_2" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Sequestration of tBID by BCL-2</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Sequestration of tBID by BCL-2</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome114352" />
+ <bp:XREF rdf:resource="#Pubmed_12624108" />
+ </bp:biochemicalReaction>
+ <bp:sequenceParticipant rdf:ID="tBID__mitochondrial_outer_membrane_3">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_P55957_BH3_interacting_domain_death_agonist__BID_" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="Bcl_2_protein__mitochondrial_outer_membrane_3">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_P10415_1_Apoptosis_regulator_Bcl_2" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="tBID_BCL_2__mitochondrial_outer_membrane_2">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#tBID_BCL_2__mitochondrial_outer_membrane_1" />
+ </bp:sequenceParticipant>
+ <bp:unificationXref rdf:ID="Reactome114352">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">114352</bp:ID>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</bp:COMMENT>
+ </bp:unificationXref>
+ <bp:publicationXref rdf:ID="Pubmed_12624108">
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">12624108</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</bp:DB>
+ <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2003</bp:YEAR>
+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Inhibition of Bid-induced apoptosis by Bcl-2. tBid insertion, Bax translocation, and Bax/Bak oligomerization suppressed.</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Yi, X</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Yin, XM</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Dong, Z</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Biol Chem 278:16992-9</bp:SOURCE>
+ </bp:publicationXref>
+ <bp:pathwayStep rdf:ID="Sequestration_of_tBID_by_BCL_2Step">
+ <bp:STEP-INTERACTIONS rdf:resource="#Sequestration_of_tBID_by_BCL_2" />
+ <bp:NEXT-STEP rdf:resource="#BAD_displaces_tBID_from_BCL_2_sequestrationStep" />
+ </bp:pathwayStep>
+ <bp:biochemicalReaction rdf:ID="Interaction_of_tBID_with_BCL_xl">
+ <bp:LEFT rdf:resource="#Apoptosis_regulator_Bcl_X__mitochondrial_outer_membrane_2" />
+ <bp:LEFT rdf:resource="#tBID__mitochondrial_outer_membrane_4" />
+ <bp:RIGHT rdf:resource="#tBID_BCL_xl__mitochondrial_outer_membrane_" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Interaction of tBID with BCL-xl</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Interaction of tBID with BCL-xl</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome114365" />
+ <bp:XREF rdf:resource="#Pubmed_9727492" />
+ </bp:biochemicalReaction>
+ <bp:sequenceParticipant rdf:ID="Apoptosis_regulator_Bcl_X__mitochondrial_outer_membrane_2">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q07817_1_Apoptosis_regulator_Bcl_X__Bcl_2_like_1_protein_" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="tBID__mitochondrial_outer_membrane_4">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_P55957_BH3_interacting_domain_death_agonist__BID_" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="tBID_BCL_xl__mitochondrial_outer_membrane_">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#tBID_BCL_xl__mitochondrial_outer_membrane_1" />
+ </bp:sequenceParticipant>
+ <bp:complex rdf:ID="tBID_BCL_xl__mitochondrial_outer_membrane_1">
+ <bp:COMPONENTS rdf:resource="#tBID__mitochondrial_outer_membrane_5" />
+ <bp:COMPONENTS rdf:resource="#Apoptosis_regulator_Bcl_X__mitochondrial_outer_membrane_3" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">tBID:BCL-xl [mitochondrial outer membrane]</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">tBID:BCL-xl</bp:SHORT-NAME>
+ </bp:complex>
+ <bp:sequenceParticipant rdf:ID="tBID__mitochondrial_outer_membrane_5">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_P55957_BH3_interacting_domain_death_agonist__BID_" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="Apoptosis_regulator_Bcl_X__mitochondrial_outer_membrane_3">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q07817_1_Apoptosis_regulator_Bcl_X__Bcl_2_like_1_protein_" />
+ </bp:sequenceParticipant>
+ <bp:unificationXref rdf:ID="Reactome114365">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">114365</bp:ID>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</bp:COMMENT>
+ </bp:unificationXref>
+ <bp:pathwayStep rdf:ID="Interaction_of_tBID_with_BCL_xlStep">
+ <bp:STEP-INTERACTIONS rdf:resource="#Interaction_of_tBID_with_BCL_xl" />
+ </bp:pathwayStep>
+ <bp:biochemicalReaction rdf:ID="Interaction_of_BIM_with_BCL2_">
+ <bp:LEFT rdf:resource="#BIM__mitochondrial_outer_membrane_1" />
+ <bp:LEFT rdf:resource="#Bcl_2_protein__mitochondrial_outer_membrane_4" />
+ <bp:RIGHT rdf:resource="#BIM_BCL2__mitochondrial_outer_membrane_" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Interaction of BIM with BCL2</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Interaction of BIM with BCL2</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome114279" />
+ <bp:XREF rdf:resource="#Pubmed_10198631" />
+ </bp:biochemicalReaction>
+ <bp:sequenceParticipant rdf:ID="BIM__mitochondrial_outer_membrane_1">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_O43521_1_Bcl_2_like_protein_11__Bcl2_interacting_mediator_of_cell_death_" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="Bcl_2_protein__mitochondrial_outer_membrane_4">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_P10415_1_Apoptosis_regulator_Bcl_2" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="BIM_BCL2__mitochondrial_outer_membrane_">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#BIM_BCL2__mitochondrial_outer_membrane_1" />
+ </bp:sequenceParticipant>
+ <bp:complex rdf:ID="BIM_BCL2__mitochondrial_outer_membrane_1">
+ <bp:COMPONENTS rdf:resource="#BIM__mitochondrial_outer_membrane_2" />
+ <bp:COMPONENTS rdf:resource="#Bcl_2_protein__mitochondrial_outer_membrane_5" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BIM:BCL2 [mitochondrial outer membrane]</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BIM:BCL2</bp:SHORT-NAME>
+ </bp:complex>
+ <bp:sequenceParticipant rdf:ID="BIM__mitochondrial_outer_membrane_2">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_O43521_1_Bcl_2_like_protein_11__Bcl2_interacting_mediator_of_cell_death_" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="Bcl_2_protein__mitochondrial_outer_membrane_5">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_P10415_1_Apoptosis_regulator_Bcl_2" />
+ </bp:sequenceParticipant>
+ <bp:unificationXref rdf:ID="Reactome114279">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">114279</bp:ID>
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+ </bp:unificationXref>
+ <bp:publicationXref rdf:ID="Pubmed_10198631">
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">10198631</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</bp:DB>
+ <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1999</bp:YEAR>
+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The proapoptotic activity of the Bcl-2 family member Bim is regulated by interaction with the dynein motor complex</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Puthalakath, H</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Huang, DC</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">O'Reilly, LA</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">King, SM</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Strasser, A</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mol Cell 3:287-96</bp:SOURCE>
+ </bp:publicationXref>
+ <bp:pathwayStep rdf:ID="Interaction_of_BIM_with_BCL2_Step">
+ <bp:STEP-INTERACTIONS rdf:resource="#Interaction_of_BIM_with_BCL2_" />
+ </bp:pathwayStep>
+ <bp:biochemicalReaction rdf:ID="Interaction_of_BIM_with_BCL_xl">
+ <bp:LEFT rdf:resource="#Apoptosis_regulator_Bcl_X__mitochondrial_outer_membrane_4" />
+ <bp:LEFT rdf:resource="#BIM__mitochondrial_outer_membrane_3" />
+ <bp:RIGHT rdf:resource="#BIM_BCL_xl__mitochondrial_outer_membrane_" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Interaction of BIM with BCL-xl</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Interaction of BIM with BCL-xl</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome114278" />
+ <bp:XREF rdf:resource="#Pubmed_10198631" />
+ </bp:biochemicalReaction>
+ <bp:sequenceParticipant rdf:ID="Apoptosis_regulator_Bcl_X__mitochondrial_outer_membrane_4">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q07817_1_Apoptosis_regulator_Bcl_X__Bcl_2_like_1_protein_" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="BIM__mitochondrial_outer_membrane_3">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_O43521_1_Bcl_2_like_protein_11__Bcl2_interacting_mediator_of_cell_death_" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="BIM_BCL_xl__mitochondrial_outer_membrane_">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#BIM_BCL_xl__mitochondrial_outer_membrane_1" />
+ </bp:sequenceParticipant>
+ <bp:complex rdf:ID="BIM_BCL_xl__mitochondrial_outer_membrane_1">
+ <bp:COMPONENTS rdf:resource="#Apoptosis_regulator_Bcl_X__mitochondrial_outer_membrane_5" />
+ <bp:COMPONENTS rdf:resource="#BIM__mitochondrial_outer_membrane_4" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BIM:BCL-xl [mitochondrial outer membrane]</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BIM:BCL-xl</bp:SHORT-NAME>
+ </bp:complex>
+ <bp:sequenceParticipant rdf:ID="Apoptosis_regulator_Bcl_X__mitochondrial_outer_membrane_5">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q07817_1_Apoptosis_regulator_Bcl_X__Bcl_2_like_1_protein_" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="BIM__mitochondrial_outer_membrane_4">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_O43521_1_Bcl_2_like_protein_11__Bcl2_interacting_mediator_of_cell_death_" />
+ </bp:sequenceParticipant>
+ <bp:unificationXref rdf:ID="Reactome114278">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">114278</bp:ID>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</bp:COMMENT>
+ </bp:unificationXref>
+ <bp:pathwayStep rdf:ID="Interaction_of_BIM_with_BCL_xlStep">
+ <bp:STEP-INTERACTIONS rdf:resource="#Interaction_of_BIM_with_BCL_xl" />
+ </bp:pathwayStep>
+ <bp:biochemicalReaction rdf:ID="Interaction_of_NOXA_with_BCL2">
+ <bp:LEFT rdf:resource="#Bcl_2_protein__mitochondrial_outer_membrane_6" />
+ <bp:LEFT rdf:resource="#NOXA_protein__mitochondrial_outer_membrane_1" />
+ <bp:RIGHT rdf:resource="#NOXA_BCL2__mitochondrial_outer_membrane_" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Interaction of NOXA with BCL2</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Interaction of NOXA with BCL2</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome114241" />
+ <bp:EVIDENCE rdf:resource="#InferredFrom_Interaction_of_NOXA_and_Bcl_2" />
+ </bp:biochemicalReaction>
+ <bp:sequenceParticipant rdf:ID="Bcl_2_protein__mitochondrial_outer_membrane_6">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_P10415_1_Apoptosis_regulator_Bcl_2" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="NOXA_protein__mitochondrial_outer_membrane_1">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q13794_Phorbol_12_myristate_13_acetate_induced_protein_1__PMA_induced_protein_1___Immediate_early_response_protein_APR_" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="NOXA_BCL2__mitochondrial_outer_membrane_">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#NOXA_BCL2__mitochondrial_outer_membrane_1" />
+ </bp:sequenceParticipant>
+ <bp:complex rdf:ID="NOXA_BCL2__mitochondrial_outer_membrane_1">
+ <bp:COMPONENTS rdf:resource="#Bcl_2_protein__mitochondrial_outer_membrane_7" />
+ <bp:COMPONENTS rdf:resource="#NOXA_protein__mitochondrial_outer_membrane_2" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">NOXA:BCL2 [mitochondrial outer membrane]</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">NOXA:BCL2</bp:SHORT-NAME>
+ </bp:complex>
+ <bp:sequenceParticipant rdf:ID="Bcl_2_protein__mitochondrial_outer_membrane_7">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_P10415_1_Apoptosis_regulator_Bcl_2" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="NOXA_protein__mitochondrial_outer_membrane_2">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q13794_Phorbol_12_myristate_13_acetate_induced_protein_1__PMA_induced_protein_1___Immediate_early_response_protein_APR_" />
+ </bp:sequenceParticipant>
+ <bp:unificationXref rdf:ID="Reactome114241">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">114241</bp:ID>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</bp:COMMENT>
+ </bp:unificationXref>
+ <bp:evidence rdf:ID="InferredFrom_Interaction_of_NOXA_and_Bcl_2">
+ <bp:XREF rdf:resource="#Pubmed_10807576" />
+ </bp:evidence>
+ <bp:pathwayStep rdf:ID="Interaction_of_NOXA_with_BCL2Step">
+ <bp:STEP-INTERACTIONS rdf:resource="#Interaction_of_NOXA_with_BCL2" />
+ </bp:pathwayStep>
+ <bp:biochemicalReaction rdf:ID="Interaction_of_PUMA_and_Bcl_2">
+ <bp:LEFT rdf:resource="#Bcl_2_protein__mitochondrial_outer_membrane_8" />
+ <bp:LEFT rdf:resource="#PUMA_protein__mitochondrial_outer_membrane_1" />
+ <bp:RIGHT rdf:resource="#PUMA_Bcl_2_complex__mitochondrial_outer_membrane_" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Interaction of PUMA and Bcl-2</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Interaction of PUMA and Bcl-2</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome140230" />
+ <bp:XREF rdf:resource="#Pubmed_11463392" />
+ </bp:biochemicalReaction>
+ <bp:sequenceParticipant rdf:ID="Bcl_2_protein__mitochondrial_outer_membrane_8">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_P10415_1_Apoptosis_regulator_Bcl_2" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="PUMA_protein__mitochondrial_outer_membrane_1">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q9BXH1_PUMA_protein" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="PUMA_Bcl_2_complex__mitochondrial_outer_membrane_">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#PUMA_Bcl_2_complex__mitochondrial_outer_membrane_1" />
+ </bp:sequenceParticipant>
+ <bp:complex rdf:ID="PUMA_Bcl_2_complex__mitochondrial_outer_membrane_1">
+ <bp:COMPONENTS rdf:resource="#Bcl_2_protein__mitochondrial_outer_membrane_9" />
+ <bp:COMPONENTS rdf:resource="#PUMA_protein__mitochondrial_outer_membrane_2" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PUMA:Bcl-2 complex [mitochondrial outer membrane]</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PUMA:Bcl-2 complex</bp:SHORT-NAME>
+ </bp:complex>
+ <bp:sequenceParticipant rdf:ID="Bcl_2_protein__mitochondrial_outer_membrane_9">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_P10415_1_Apoptosis_regulator_Bcl_2" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="PUMA_protein__mitochondrial_outer_membrane_2">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q9BXH1_PUMA_protein" />
+ </bp:sequenceParticipant>
+ <bp:unificationXref rdf:ID="Reactome140230">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">140230</bp:ID>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</bp:COMMENT>
+ </bp:unificationXref>
+ <bp:pathwayStep rdf:ID="Interaction_of_PUMA_and_Bcl_2Step">
+ <bp:STEP-INTERACTIONS rdf:resource="#Interaction_of_PUMA_and_Bcl_2" />
+ </bp:pathwayStep>
+ <bp:biochemicalReaction rdf:ID="Interaction_of_PUMA_and_Bcl_XL">
+ <bp:LEFT rdf:resource="#Apoptosis_regulator_Bcl_X__mitochondrial_outer_membrane_6" />
+ <bp:LEFT rdf:resource="#PUMA_protein__mitochondrial_outer_membrane_3" />
+ <bp:RIGHT rdf:resource="#PUMA_Bcl_XL_complex__mitochondrial_outer_membrane_" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Interaction of PUMA and Bcl-XL</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Interaction of PUMA and Bcl-XL</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome140232" />
+ <bp:XREF rdf:resource="#Pubmed_11463392" />
+ </bp:biochemicalReaction>
+ <bp:sequenceParticipant rdf:ID="Apoptosis_regulator_Bcl_X__mitochondrial_outer_membrane_6">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q07817_1_Apoptosis_regulator_Bcl_X__Bcl_2_like_1_protein_" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="PUMA_protein__mitochondrial_outer_membrane_3">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q9BXH1_PUMA_protein" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="PUMA_Bcl_XL_complex__mitochondrial_outer_membrane_">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#PUMA_Bcl_XL_complex__mitochondrial_outer_membrane_1" />
+ </bp:sequenceParticipant>
+ <bp:complex rdf:ID="PUMA_Bcl_XL_complex__mitochondrial_outer_membrane_1">
+ <bp:COMPONENTS rdf:resource="#Apoptosis_regulator_Bcl_X__mitochondrial_outer_membrane_7" />
+ <bp:COMPONENTS rdf:resource="#PUMA_protein__mitochondrial_outer_membrane_4" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PUMA:Bcl-XL complex [mitochondrial outer membrane]</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PUMA:Bcl-XL complex</bp:SHORT-NAME>
+ </bp:complex>
+ <bp:sequenceParticipant rdf:ID="Apoptosis_regulator_Bcl_X__mitochondrial_outer_membrane_7">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q07817_1_Apoptosis_regulator_Bcl_X__Bcl_2_like_1_protein_" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="PUMA_protein__mitochondrial_outer_membrane_4">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q9BXH1_PUMA_protein" />
+ </bp:sequenceParticipant>
+ <bp:unificationXref rdf:ID="Reactome140232">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">140232</bp:ID>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</bp:COMMENT>
+ </bp:unificationXref>
+ <bp:pathwayStep rdf:ID="Interaction_of_PUMA_and_Bcl_XLStep">
+ <bp:STEP-INTERACTIONS rdf:resource="#Interaction_of_PUMA_and_Bcl_XL" />
+ </bp:pathwayStep>
+ <bp:biochemicalReaction rdf:ID="Interaction_of_NOXA_with_BCL_xl">
+ <bp:LEFT rdf:resource="#Apoptosis_regulator_Bcl_X__mitochondrial_outer_membrane_8" />
+ <bp:LEFT rdf:resource="#NOXA_protein__mitochondrial_outer_membrane_3" />
+ <bp:RIGHT rdf:resource="#NOXA_BCL_xl__mitochondrial_outer_membrane_" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Interaction of NOXA with BCL-xl</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Interaction of NOXA with BCL-xl</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome114281" />
+ <bp:EVIDENCE rdf:resource="#InferredFrom_Interaction_of_NOXA_and_Bcl_XL" />
+ </bp:biochemicalReaction>
+ <bp:sequenceParticipant rdf:ID="Apoptosis_regulator_Bcl_X__mitochondrial_outer_membrane_8">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q07817_1_Apoptosis_regulator_Bcl_X__Bcl_2_like_1_protein_" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="NOXA_protein__mitochondrial_outer_membrane_3">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q13794_Phorbol_12_myristate_13_acetate_induced_protein_1__PMA_induced_protein_1___Immediate_early_response_protein_APR_" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="NOXA_BCL_xl__mitochondrial_outer_membrane_">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#NOXA_BCL_xl__mitochondrial_outer_membrane_1" />
+ </bp:sequenceParticipant>
+ <bp:complex rdf:ID="NOXA_BCL_xl__mitochondrial_outer_membrane_1">
+ <bp:COMPONENTS rdf:resource="#Apoptosis_regulator_Bcl_X__mitochondrial_outer_membrane_9" />
+ <bp:COMPONENTS rdf:resource="#NOXA_protein__mitochondrial_outer_membrane_4" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">NOXA:BCL-xl [mitochondrial outer membrane]</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">NOXA:BCL-xl</bp:SHORT-NAME>
+ </bp:complex>
+ <bp:sequenceParticipant rdf:ID="Apoptosis_regulator_Bcl_X__mitochondrial_outer_membrane_9">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q07817_1_Apoptosis_regulator_Bcl_X__Bcl_2_like_1_protein_" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="NOXA_protein__mitochondrial_outer_membrane_4">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q13794_Phorbol_12_myristate_13_acetate_induced_protein_1__PMA_induced_protein_1___Immediate_early_response_protein_APR_" />
+ </bp:sequenceParticipant>
+ <bp:unificationXref rdf:ID="Reactome114281">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">114281</bp:ID>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</bp:COMMENT>
+ </bp:unificationXref>
+ <bp:evidence rdf:ID="InferredFrom_Interaction_of_NOXA_and_Bcl_XL">
+ <bp:XREF rdf:resource="#Pubmed_10807576" />
+ </bp:evidence>
+ <bp:pathwayStep rdf:ID="Interaction_of_NOXA_with_BCL_xlStep">
+ <bp:STEP-INTERACTIONS rdf:resource="#Interaction_of_NOXA_with_BCL_xl" />
+ </bp:pathwayStep>
+ <bp:unificationXref rdf:ID="Reactome111453">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">111453</bp:ID>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</bp:COMMENT>
+ </bp:unificationXref>
+ <bp:pathwayStep rdf:ID="BH3_only_proteins_associate_with_and_inactivate_anti_apoptotic_BCL_2_membersStep">
+ <bp:STEP-INTERACTIONS rdf:resource="#BH3_only_proteins_associate_with_and_inactivate_anti_apoptotic_BCL_2_members" />
+ </bp:pathwayStep>
+ <bp:pathway rdf:ID="Activation__translocation_and_oligomerization_of_BAX">
+ <bp:PATHWAY-COMPONENTS rdf:resource="#tBID_activates_BAX_proteinStep" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#Oligomerization_of_BAX_at_the_mitochondrial_membraneStep" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#Translocation_of_activated_BAX_to_the_mitochondriaStep" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Activation, translocation and oligomerization of BAX</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Activation, translocation and oligomerization of BAX</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome114294" />
+ <bp:XREF rdf:resource="#Pubmed_11136736" />
+ <bp:XREF rdf:resource="#activation_of_pro_apoptotic_gene_products" />
+ </bp:pathway>
+ <bp:biochemicalReaction rdf:ID="tBID_activates_BAX_protein">
+ <bp:LEFT rdf:resource="#tBID_p15__cytosol_3" />
+ <bp:LEFT rdf:resource="#Bax_alpha_protein__cytosol_" />
+ <bp:RIGHT rdf:resource="#tBID_p15__cytosol_4" />
+ <bp:RIGHT rdf:resource="#Activated_BAX__cytosol_" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">tBID activates BAX protein</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">tBID activates BAX protein</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome139917" />
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">During certain types of apoptosis, activated tBID (p15) induces a change in conformation of Bax which leads to the unmasking of its NH2-terminal domain. This change in confirmation usually results in the release of cytochrome c from mitochondria.</bp:COMMENT>
+ <bp:EVIDENCE rdf:resource="#Summation_163347" />
+ <bp:XREF rdf:resource="#Pubmed_10629050" />
+ </bp:biochemicalReaction>
+ <bp:sequenceParticipant rdf:ID="tBID_p15__cytosol_3">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_P55957_BH3_interacting_domain_death_agonist__BID_" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="Bax_alpha_protein__cytosol_">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q07812_1_Apoptosis_regulator_BAX__membrane_isoform_alpha" />
+ </bp:sequenceParticipant>
+ <bp:protein rdf:ID="UniProt_Q07812_1_Apoptosis_regulator_BAX__membrane_isoform_alpha">
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:Q07812-1 Apoptosis regulator BAX, membrane isoform alpha</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BAX</bp:SYNONYMS>
+ <bp:XREF rdf:resource="#UniProt_Q07812" />
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Accelerates programmed cell death by binding to, and antagonizing the apoptosis repressor BCL2 or its adenovirus homolog E1B 19k protein. Induces the release of cytochrome c, activation of CASP3, and thereby apoptosis. SUBUNIT: Homodimers and heterodimers with BCL2, E1B 19K protein, BCL2L1 isoform Bcl-X(L), MCL1 and A1. Interacts with SH3GLB1 and HN. SUBCELLULAR LOCATION: Membrane-bound. ALTERNATIVE PRODUCTS [...]
+ </bp:protein>
+ <bp:unificationXref rdf:ID="UniProt_Q07812">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Q07812</bp:ID>
+ </bp:unificationXref>
+ <bp:sequenceParticipant rdf:ID="tBID_p15__cytosol_4">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_P55957_BH3_interacting_domain_death_agonist__BID_" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="Activated_BAX__cytosol_">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
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+ </bp:unificationXref>
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+ </bp:evidence>
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+ <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1999</bp:YEAR>
+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bid-induced conformational change of Bax is responsible for mitochondrial cytochrome c release during apoptosis</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Desagher, S</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Osen-Sand, A</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Nichols, A</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Eskes, R</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Montessuit, S</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Lauper, S</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Maundrell, K</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Antonsson, B</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Martinou, JC</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Cell Biol 144:891-901</bp:SOURCE>
+ </bp:publicationXref>
+ <bp:publicationXref rdf:ID="Pubmed_10629050">
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+ <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2000</bp:YEAR>
+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bid induces the oligomerization and insertion of Bax into the outer mitochondrial membrane</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Eskes, R</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Desagher, S</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Antonsson, B</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Martinou, JC</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mol Cell Biol 20:929-35</bp:SOURCE>
+ </bp:publicationXref>
+ <bp:pathwayStep rdf:ID="tBID_activates_BAX_proteinStep">
+ <bp:STEP-INTERACTIONS rdf:resource="#tBID_activates_BAX_protein" />
+ <bp:NEXT-STEP rdf:resource="#Translocation_of_activated_BAX_to_the_mitochondriaStep" />
+ </bp:pathwayStep>
+ <bp:biochemicalReaction rdf:ID="Translocation_of_activated_BAX_to_the_mitochondria">
+ <bp:LEFT rdf:resource="#Activated_BAX__cytosol_1" />
+ <bp:RIGHT rdf:resource="#Activated_BAX_inserted_into_mitochondrial_membrane__mitochondrial_outer_membrane_" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Translocation of activated BAX to the mitochondria</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Translocation of activated BAX to the mitochondria</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome114264" />
+ <bp:XREF rdf:resource="#Pubmed_11136736" />
+ <bp:XREF rdf:resource="#Pubmed_12176904" />
+ <bp:XREF rdf:resource="#Pubmed_12624108" />
+ <bp:XREF rdf:resource="#protein_insertion_into_mitochondrial_membrane_during_induction_of_apoptosis" />
+ </bp:biochemicalReaction>
+ <bp:sequenceParticipant rdf:ID="Activated_BAX__cytosol_1">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q07812_1_Apoptosis_regulator_BAX__membrane_isoform_alpha" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="Activated_BAX_inserted_into_mitochondrial_membrane__mitochondrial_outer_membrane_">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q07812_1_Apoptosis_regulator_BAX__membrane_isoform_alpha" />
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+ <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2001</bp:YEAR>
+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bax is present as a high molecular weight oligomer/complex in the mitochondrial membrane of apoptotic cells.</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Antonsson, B</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Montessuit, S</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Sanchez, B</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Martinou, JC</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Biol Chem 276:11615-23</bp:SOURCE>
+ </bp:publicationXref>
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+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Spontaneous and drug-induced apoptosis is mediated by conformational changes of Bax and Bak in B-cell chronic lymphocytic leukemia.</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bellosillo, B</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Villamor, N</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">López-Guillermo, A</bp:AUTHORS>
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+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bosch, F</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Campo, E</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Montserrat, E</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Colomer, D</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Blood 100:1810-6</bp:SOURCE>
+ </bp:publicationXref>
+ <bp:pathwayStep rdf:ID="Translocation_of_activated_BAX_to_the_mitochondriaStep">
+ <bp:STEP-INTERACTIONS rdf:resource="#Translocation_of_activated_BAX_to_the_mitochondria" />
+ <bp:NEXT-STEP rdf:resource="#Oligomerization_of_BAX_at_the_mitochondrial_membraneStep" />
+ </bp:pathwayStep>
+ <bp:biochemicalReaction rdf:ID="Oligomerization_of_BAX_at_the_mitochondrial_membrane">
+ <bp:LEFT rdf:resource="#Activated_BAX_inserted_into_mitochondrial_membrane__mitochondrial_outer_membrane_1" />
+ <bp:RIGHT rdf:resource="#Activated_BAX__mitochondrial_outer_membrane_" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Oligomerization of BAX at the mitochondrial membrane</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Oligomerization of BAX at the mitochondrial membrane</bp:SHORT-NAME>
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+ <bp:XREF rdf:resource="#Pubmed_11136736" />
+ </bp:biochemicalReaction>
+ <bp:sequenceParticipant rdf:ID="Activated_BAX_inserted_into_mitochondrial_membrane__mitochondrial_outer_membrane_1">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q07812_1_Apoptosis_regulator_BAX__membrane_isoform_alpha" />
+ <bp:STOICHIOMETRIC-COEFFICIENT rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2</bp:STOICHIOMETRIC-COEFFICIENT>
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="Activated_BAX__mitochondrial_outer_membrane_">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#Activated_BAX__mitochondrial_outer_membrane_1" />
+ </bp:sequenceParticipant>
+ <bp:complex rdf:ID="Activated_BAX__mitochondrial_outer_membrane_1">
+ <bp:COMPONENTS rdf:resource="#BAX_alpha_protein__mitochondrial_outer_membrane_" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Activated BAX [mitochondrial outer membrane]</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Activated BAX</bp:SHORT-NAME>
+ </bp:complex>
+ <bp:sequenceParticipant rdf:ID="BAX_alpha_protein__mitochondrial_outer_membrane_">
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+ <bp:NEXT-STEP rdf:resource="#Permeabilization_of_mitochondriaStep" />
+ </bp:pathwayStep>
+ <bp:pathway rdf:ID="Activation_and_oligomerization_of_BAK_protein">
+ <bp:PATHWAY-COMPONENTS rdf:resource="#Oligomerization__of_BAK_at_the_mitochondrial_membraneStep" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#tBID_activates_BAK_proteinStep" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Activation and oligomerization of BAK protein</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Activation and oligomerization of BAK protein</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome111452" />
+ <bp:XREF rdf:resource="#activation_of_pro_apoptotic_gene_products" />
+ </bp:pathway>
+ <bp:biochemicalReaction rdf:ID="tBID_activates_BAK_protein">
+ <bp:LEFT rdf:resource="#tBID__mitochondrial_outer_membrane_6" />
+ <bp:LEFT rdf:resource="#Inactive_BAK_protein__mitochondrial_outer_membrane_" />
+ <bp:RIGHT rdf:resource="#tBID__mitochondrial_outer_membrane_7" />
+ <bp:RIGHT rdf:resource="#Activated_BAK_protein__mitochondrial_outer_membrane_" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">tBID activates BAK protein</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">tBID activates BAK protein</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome139895" />
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">tBID binds to its mitochondrial partner BAK to release cytochrome c. It has been observed in mouse systems that the activated tBID results in an allosteric activation of BAK. That induces intramembranous oligomerization that may lead to a pore for cytochrome c efflux.</bp:COMMENT>
+ <bp:EVIDENCE rdf:resource="#Summation_140394" />
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+ </bp:biochemicalReaction>
+ <bp:sequenceParticipant rdf:ID="tBID__mitochondrial_outer_membrane_6">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_P55957_BH3_interacting_domain_death_agonist__BID_" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="Inactive_BAK_protein__mitochondrial_outer_membrane_">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q16611_Bcl_2_homologous_antagonist_killer__Apoptosis_regulator_BAK___BCL2__like_7_protein_" />
+ </bp:sequenceParticipant>
+ <bp:protein rdf:ID="UniProt_Q16611_Bcl_2_homologous_antagonist_killer__Apoptosis_regulator_BAK___BCL2__like_7_protein_">
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:Q16611 Bcl-2 homologous antagonist/killer (Apoptosis regulator BAK) (BCL2- like 7 protein)</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BCL2L7</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BAK</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BAK1</bp:SYNONYMS>
+ <bp:XREF rdf:resource="#UniProt_Q16611" />
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: In the presence of an appropriate stimulus, accelerates programmed cell death by binding to, and antagonizing the a repressor Bcl-2 or its adenovirus homolog E1B 19k protein. SUBUNIT: Forms heterodimers with Bcl-2, E1B 19k protein, and Bcl- X(L). SUBCELLULAR LOCATION: Membrane-bound (Potential). TISSUE SPECIFICITY: Expressed in a wide variety of tissues, with highest levels in the heart and skeletal muscle. [...]
+ </bp:protein>
+ <bp:unificationXref rdf:ID="UniProt_Q16611">
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+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Q16611</bp:ID>
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+ <bp:sequenceParticipant rdf:ID="tBID__mitochondrial_outer_membrane_7">
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+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_P55957_BH3_interacting_domain_death_agonist__BID_" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="Activated_BAK_protein__mitochondrial_outer_membrane_">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q16611_Bcl_2_homologous_antagonist_killer__Apoptosis_regulator_BAK___BCL2__like_7_protein_" />
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+ </bp:evidence>
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+ <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2000</bp:YEAR>
+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">tBID, a membrane-targeted death ligand, oligomerizes BAK to release cytochrome c</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Wei, MC</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Lindsten, T</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mootha, VK</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Weiler, S</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Gross, A</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Ashiya, M</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Thompson, CB</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Korsmeyer, SJ</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Genes Dev 14:2060-71</bp:SOURCE>
+ </bp:publicationXref>
+ <bp:pathwayStep rdf:ID="tBID_activates_BAK_proteinStep">
+ <bp:STEP-INTERACTIONS rdf:resource="#tBID_activates_BAK_protein" />
+ <bp:NEXT-STEP rdf:resource="#Oligomerization__of_BAK_at_the_mitochondrial_membraneStep" />
+ </bp:pathwayStep>
+ <bp:biochemicalReaction rdf:ID="Oligomerization__of_BAK_at_the_mitochondrial_membrane">
+ <bp:LEFT rdf:resource="#Activated_BAK_protein__mitochondrial_outer_membrane_1" />
+ <bp:RIGHT rdf:resource="#Active_BAK__mitochondrial_outer_membrane_" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Oligomerization of BAK at the mitochondrial membrane</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Oligomerization of BAK at the mitochondrial membrane</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome114263" />
+ <bp:XREF rdf:resource="#Pubmed_12721291" />
+ </bp:biochemicalReaction>
+ <bp:sequenceParticipant rdf:ID="Activated_BAK_protein__mitochondrial_outer_membrane_1">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q16611_Bcl_2_homologous_antagonist_killer__Apoptosis_regulator_BAK___BCL2__like_7_protein_" />
+ <bp:STOICHIOMETRIC-COEFFICIENT rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2</bp:STOICHIOMETRIC-COEFFICIENT>
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="Active_BAK__mitochondrial_outer_membrane_">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#Active_BAK__mitochondrial_outer_membrane_1" />
+ </bp:sequenceParticipant>
+ <bp:complex rdf:ID="Active_BAK__mitochondrial_outer_membrane_1">
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+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Active BAK [mitochondrial outer membrane]</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Active BAK</bp:SHORT-NAME>
+ </bp:complex>
+ <bp:sequenceParticipant rdf:ID="Activated_BAK_protein__mitochondrial_outer_membrane_2">
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+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</bp:COMMENT>
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+ <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2003</bp:YEAR>
+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BCL-2 selectively interacts with the BID-induced open conformer of BAK, inhibiting BAK auto-oligomerization.</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Ruffolo, SC</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Shore, GC</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Biol Chem 278:25039-45</bp:SOURCE>
+ </bp:publicationXref>
+ <bp:pathwayStep rdf:ID="Oligomerization__of_BAK_at_the_mitochondrial_membraneStep">
+ <bp:STEP-INTERACTIONS rdf:resource="#Oligomerization__of_BAK_at_the_mitochondrial_membrane" />
+ <bp:NEXT-STEP rdf:resource="#Release_of_Cytochrome_c_from_mitochondriaStep" />
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+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</bp:DB>
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+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</bp:COMMENT>
+ </bp:unificationXref>
+ <bp:pathwayStep rdf:ID="Activation_and_oligomerization_of_BAK_proteinStep">
+ <bp:STEP-INTERACTIONS rdf:resource="#Activation_and_oligomerization_of_BAK_protein" />
+ <bp:NEXT-STEP rdf:resource="#Permeabilization_of_mitochondriaStep" />
+ </bp:pathwayStep>
+ <bp:pathway rdf:ID="Permeabilization_of_mitochondria">
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Permeabilization of mitochondria</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Permeabilization of mitochondria</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome111455" />
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Activation and oligomerization of Bax and Bak result in the destabilization of the outer mitochondrial membrane. This results in the release of the apoptotic factors Cytochrome c and SMAC from the intermembrane space.</bp:COMMENT>
+ <bp:EVIDENCE rdf:resource="#Summation_140367" />
+ <bp:XREF rdf:resource="#Pubmed_12941691" />
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+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</bp:COMMENT>
+ </bp:unificationXref>
+ <bp:evidence rdf:ID="Summation_140367">
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+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</bp:DB>
+ <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2001</bp:YEAR>
+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The expanding role of mitochondria in apoptosis.</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Wang, X</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Genes Dev 15:2922-33</bp:SOURCE>
+ </bp:publicationXref>
+ <bp:publicationXref rdf:ID="Pubmed_12941691">
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+ <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2003</bp:YEAR>
+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mitochondrial release of AIF and EndoG requires caspase activation downstream of Bax/Bak-mediated permeabilization.</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Arnoult, D</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Gaume, B</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Karbowski, M</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Sharpe, JC</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cecconi, F</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Youle, RJ</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">EMBO J 22:4385-99</bp:SOURCE>
+ </bp:publicationXref>
+ <bp:pathwayStep rdf:ID="Permeabilization_of_mitochondriaStep">
+ <bp:STEP-INTERACTIONS rdf:resource="#Permeabilization_of_mitochondria" />
+ <bp:NEXT-STEP rdf:resource="#Release_of_apoptotic_factors_from_the_mitochondriaStep" />
+ </bp:pathwayStep>
+ <bp:pathway rdf:ID="Release_of_apoptotic_factors_from_the_mitochondria">
+ <bp:PATHWAY-COMPONENTS rdf:resource="#Release_of_Cytochrome_c_from_mitochondriaStep" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#Release_of_SMAC_from_mitochondriaStep" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Release of apoptotic factors from the mitochondria</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Release of apoptotic factors from the mitochondria</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome111457" />
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Apoptotic factors released from the mitochondria promote apoptosis through several different mechanisms. Cytochrome C participates in Apoptosome driven effector caspase activation while SMAC relieves IAP mediated caspase inhibition.</bp:COMMENT>
+ <bp:EVIDENCE rdf:resource="#Summation_140366" />
+ <bp:XREF rdf:resource="#Pubmed_10913597" />
+ <bp:XREF rdf:resource="#Pubmed_12941691" />
+ <bp:XREF rdf:resource="#Pubmed_12660240" />
+ </bp:pathway>
+ <bp:biochemicalReaction rdf:ID="Release_of_Cytochrome_c_from_mitochondria">
+ <bp:LEFT rdf:resource="#Cytochrome_c__mitochondrial_intermembrane_space_" />
+ <bp:RIGHT rdf:resource="#Cytochrome_c__cytosol_" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Release of Cytochrome c from mitochondria</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Release of Cytochrome c from mitochondria</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome114284" />
+ <bp:XREF rdf:resource="#Pubmed_12941691" />
+ <bp:XREF rdf:resource="#Pubmed_12660240" />
+ </bp:biochemicalReaction>
+ <bp:sequenceParticipant rdf:ID="Cytochrome_c__mitochondrial_intermembrane_space_">
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_P99999_Cytochrome_c" />
+ </bp:sequenceParticipant>
+ <bp:openControlledVocabulary rdf:ID="mitochondrial_intermembrane_space">
+ <bp:TERM rdf:datatype="http://www.w3.org/2001/XMLSchema#string">mitochondrial intermembrane space</bp:TERM>
+ <bp:XREF rdf:resource="#GO_0005758" />
+ </bp:openControlledVocabulary>
+ <bp:unificationXref rdf:ID="GO_0005758">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GO</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0005758</bp:ID>
+ </bp:unificationXref>
+ <bp:protein rdf:ID="UniProt_P99999_Cytochrome_c">
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P99999 Cytochrome c</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CYCS</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CYC</bp:SYNONYMS>
+ <bp:XREF rdf:resource="#UniProt_P99999" />
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Electron carrier protein. The oxidized form of the cytochrome c heme group can accept an electron from the heme group of the cytochrome c1 subunit of cytochrome reductase. Cytochrome c then transfers this electron to the cytochrome oxidase complex, the final protein carrier in the mitochondrial electron-transport chain. FUNCTION: Plays a role in apoptosis. Suppression of the anti- apoptotic members or activa [...]
+ </bp:protein>
+ <bp:unificationXref rdf:ID="UniProt_P99999">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P99999</bp:ID>
+ </bp:unificationXref>
+ <bp:sequenceParticipant rdf:ID="Cytochrome_c__cytosol_">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_P99999_Cytochrome_c" />
+ </bp:sequenceParticipant>
+ <bp:unificationXref rdf:ID="Reactome114284">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">114284</bp:ID>
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+ <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2003</bp:YEAR>
+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Direct interaction between survivin and Smac/DIABLO is essential for the anti-apoptotic activity of survivin during taxol-induced apoptosis.</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Song, Z</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Yao, X</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Wu, M</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Biol Chem 278:23130-40</bp:SOURCE>
+ </bp:publicationXref>
+ <bp:pathwayStep rdf:ID="Release_of_Cytochrome_c_from_mitochondriaStep">
+ <bp:STEP-INTERACTIONS rdf:resource="#Release_of_Cytochrome_c_from_mitochondria" />
+ <bp:NEXT-STEP rdf:resource="#Formation_of_apoptosomeStep" />
+ <bp:NEXT-STEP rdf:resource="#Cytochrome_c_mediated_apoptotic_responseStep" />
+ </bp:pathwayStep>
+ <bp:biochemicalReaction rdf:ID="Release_of_SMAC_from_mitochondria">
+ <bp:LEFT rdf:resource="#Smac_protein__mitochondrial_precursor__mitochondrial_intermembrane_space_" />
+ <bp:RIGHT rdf:resource="#SMAC__cytosol_" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Release of SMAC from mitochondria</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Release of SMAC from mitochondria</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome114307" />
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+ <bp:XREF rdf:resource="#Pubmed_12660240" />
+ </bp:biochemicalReaction>
+ <bp:sequenceParticipant rdf:ID="Smac_protein__mitochondrial_precursor__mitochondrial_intermembrane_space_">
+ <bp:CELLULAR-LOCATION rdf:resource="#mitochondrial_intermembrane_space" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q9NR28_1_Diablo_homolog__mitochondrial_precursor__Second_mitochondria_derived_activator_of_caspase___Smac_protein___Direct_IAP_binding_protein_with_low_pI_" />
+ </bp:sequenceParticipant>
+ <bp:protein rdf:ID="UniProt_Q9NR28_1_Diablo_homolog__mitochondrial_precursor__Second_mitochondria_derived_activator_of_caspase___Smac_protein___Direct_IAP_binding_protein_with_low_pI_">
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:Q9NR28-1 Diablo homolog, mitochondrial precursor (Second mitochondria-derived activator of caspase) (Smac protein) (Direct IAP binding protein with low pI)</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SMAC</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DIABLO</bp:SYNONYMS>
+ <bp:XREF rdf:resource="#UniProt_Q9NR28" />
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Promotes apoptosis by activating caspases in the cytochrome c/Apaf-1/caspase-9 pathway. Acts by opposing the inhibitory activity of inhibitor of apoptosis proteins (IAP). SUBUNIT: Homodimer. Interacts with BIRC2, BIRC3, BIRC4/XIAP and BIRC7. SUBCELLULAR LOCATION: Mitochondrial but released into the cytosol when cells undergo apoptosis. ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name= [...]
+ </bp:protein>
+ <bp:unificationXref rdf:ID="UniProt_Q9NR28">
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+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Q9NR28</bp:ID>
+ </bp:unificationXref>
+ <bp:sequenceParticipant rdf:ID="SMAC__cytosol_">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q9NR28_1_Diablo_homolog__mitochondrial_precursor__Second_mitochondria_derived_activator_of_caspase___Smac_protein___Direct_IAP_binding_protein_with_low_pI_" />
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+ <bp:pathwayStep rdf:ID="Release_of_SMAC_from_mitochondriaStep">
+ <bp:STEP-INTERACTIONS rdf:resource="#Release_of_SMAC_from_mitochondria" />
+ <bp:NEXT-STEP rdf:resource="#SMAC_binds_XIAP_Caspase_3Step" />
+ <bp:NEXT-STEP rdf:resource="#SMAC_binds_XIAP_Caspase_7Step" />
+ <bp:NEXT-STEP rdf:resource="#SMAC_binds_XIAP_Caspase_9Step" />
+ <bp:NEXT-STEP rdf:resource="#SMAC_mediated_apoptotic_responseStep" />
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+ </bp:unificationXref>
+ <bp:evidence rdf:ID="Summation_140366">
+ <bp:XREF rdf:resource="#Pubmed_15077149" />
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+ <bp:publicationXref rdf:ID="Pubmed_15077149">
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">15077149</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</bp:DB>
+ <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2004</bp:YEAR>
+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Toxic proteins released from mitochondria in cell death.</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Saelens, X</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Festjens, N</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Vande Walle, L</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">van Gurp, M</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">van Loo, G</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Vandenabeele, P</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Oncogene 23:2861-74</bp:SOURCE>
+ </bp:publicationXref>
+ <bp:publicationXref rdf:ID="Pubmed_10913597">
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">10913597</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</bp:DB>
+ <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2000</bp:YEAR>
+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Apoptosis-inducing factor (AIF): a ubiquitous mitochondrial oxidoreductase involved in apoptosis.</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Daugas, E</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Nochy, D</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Ravagnan, L</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Loeffler, M</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Susin, SA</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Zamzami, N</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Kroemer, G</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FEBS Lett 476:118-23</bp:SOURCE>
+ </bp:publicationXref>
+ <bp:pathwayStep rdf:ID="Release_of_apoptotic_factors_from_the_mitochondriaStep">
+ <bp:STEP-INTERACTIONS rdf:resource="#Release_of_apoptotic_factors_from_the_mitochondria" />
+ <bp:NEXT-STEP rdf:resource="#Apoptotic_factor_mediated_responseStep" />
+ </bp:pathwayStep>
+ <bp:pathway rdf:ID="Apoptotic_factor_mediated_response">
+ <bp:PATHWAY-COMPONENTS rdf:resource="#SMAC_mediated_apoptotic_responseStep" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#Cytochrome_c_mediated_apoptotic_responseStep" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Apoptotic factor-mediated response</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Apoptotic factor-mediated response</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome111471" />
+ <bp:XREF rdf:resource="#Pubmed_15077149" />
+ <bp:XREF rdf:resource="#Pubmed_12042762" />
+ </bp:pathway>
+ <bp:pathway rdf:ID="Cytochrome_c_mediated_apoptotic_response">
+ <bp:PATHWAY-COMPONENTS rdf:resource="#Activation_of_caspases_through_apoptosome_mediated_cleavageStep" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#Formation_of_apoptosomeStep" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cytochrome c-mediated apoptotic response</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cytochrome c-mediated apoptotic response</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome111461" />
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Upon its release from the mitochondrial intermembrane space, Cytochrome c binds to and causes a conformational change in the cytoplasmic protein Apaf1. This conformational change allows the Cytochrome c:Apaf1 complex to associate with ATP triggering oligomerization of the Apaf1:Cytochrome c:ATP complex. The apoptosome then associates with Procaspase-9 resulting in the formation of the active caspase-9 holoenzyme whic [...]
+ <bp:EVIDENCE rdf:resource="#Summation_140362" />
+ <bp:XREF rdf:resource="#Pubmed_15184073" />
+ </bp:pathway>
+ <bp:pathway rdf:ID="Formation_of_apoptosome">
+ <bp:PATHWAY-COMPONENTS rdf:resource="#Cleavage_of_Procaspase_9_to_Caspase_9Step" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#Cytochrome_C_Apaf_1_binds_Procaspase_9Step" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#Cytochrome_C_Binds_to_Apaf_1Step" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Formation of apoptosome</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Formation of apoptosome</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome111458" />
+ <bp:XREF rdf:resource="#Pubmed_15184073" />
+ </bp:pathway>
+ <bp:biochemicalReaction rdf:ID="Cytochrome_C_Binds_to_Apaf_1">
+ <bp:LEFT rdf:resource="#Cytochrome_c__cytosol_1" />
+ <bp:LEFT rdf:resource="#Apaf_1__cytosol_" />
+ <bp:RIGHT rdf:resource="#Apaf_1_Cytochrome_C__cytosol_" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cytochrome C Binds to Apaf-1</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cytochrome C Binds to Apaf-1</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome114254" />
+ <bp:XREF rdf:resource="#Pubmed_9267021" />
+ </bp:biochemicalReaction>
+ <bp:sequenceParticipant rdf:ID="Cytochrome_c__cytosol_1">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_P99999_Cytochrome_c" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="Apaf_1__cytosol_">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_O14727_1_Apoptotic_protease_activating_factor_1__Apaf_1_" />
+ </bp:sequenceParticipant>
+ <bp:protein rdf:ID="UniProt_O14727_1_Apoptotic_protease_activating_factor_1__Apaf_1_">
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:O14727-1 Apoptotic protease activating factor 1 (Apaf-1)</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">KIAA0413</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">APAF1</bp:SYNONYMS>
+ <bp:XREF rdf:resource="#UniProt_O14727" />
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Oligomeric Apaf-1 mediates the cytochrome c-dependent autocatalytic activation of pro-caspase-9 (Apaf-3), leading to the activation of caspase-3 and apoptosis. This activation requires ATP. Isoform 6 is less effective in inducing apoptosis. SUBUNIT: Monomer. Oligomerizes upon binding of cytochrome c and dATP. Oligomeric Apaf-1 and pro-caspase-9 bind to each other via their respective NH2-terminal CARD domain [...]
+ </bp:protein>
+ <bp:unificationXref rdf:ID="UniProt_O14727">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">O14727</bp:ID>
+ </bp:unificationXref>
+ <bp:sequenceParticipant rdf:ID="Apaf_1_Cytochrome_C__cytosol_">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#Apaf_1_Cytochrome_C__cytosol_1" />
+ </bp:sequenceParticipant>
+ <bp:complex rdf:ID="Apaf_1_Cytochrome_C__cytosol_1">
+ <bp:COMPONENTS rdf:resource="#Cytochrome_c__cytosol_2" />
+ <bp:COMPONENTS rdf:resource="#Apaf_1__cytosol_1" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Apaf-1:Cytochrome C [cytosol]</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Apaf-1:Cytochrome C</bp:SHORT-NAME>
+ </bp:complex>
+ <bp:sequenceParticipant rdf:ID="Cytochrome_c__cytosol_2">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_P99999_Cytochrome_c" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="Apaf_1__cytosol_1">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_O14727_1_Apoptotic_protease_activating_factor_1__Apaf_1_" />
+ </bp:sequenceParticipant>
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+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">114254</bp:ID>
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+ </bp:unificationXref>
+ <bp:publicationXref rdf:ID="Pubmed_9267021">
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">9267021</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</bp:DB>
+ <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1997</bp:YEAR>
+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Apaf-1, a human protein homologous to C. elegans CED-4, participates in cytochrome c-dependent activation of caspase-3.</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Zou, H</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Henzel, WJ</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Liu, X</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Lutschg, A</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Wang, X</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cell 90:405-13</bp:SOURCE>
+ </bp:publicationXref>
+ <bp:pathwayStep rdf:ID="Cytochrome_C_Binds_to_Apaf_1Step">
+ <bp:STEP-INTERACTIONS rdf:resource="#Cytochrome_C_Binds_to_Apaf_1" />
+ </bp:pathwayStep>
+ <bp:biochemicalReaction rdf:ID="Cytochrome_C_Apaf_1_binds_Procaspase_9">
+ <bp:LEFT rdf:resource="#Caspase_9_precursor___cytosol_" />
+ <bp:LEFT rdf:resource="#Apaf_1_Cytochrome_C__cytosol_2" />
+ <bp:RIGHT rdf:resource="#Cytochrome_C_Apaf_1_Procaspase_9__cytosol_" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cytochrome C:Apaf-1 binds Procaspase-9</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cytochrome C:Apaf-1 binds Procaspase-9</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome114256" />
+ <bp:XREF rdf:resource="#Pubmed_9390557" />
+ </bp:biochemicalReaction>
+ <bp:sequenceParticipant rdf:ID="Caspase_9_precursor___cytosol_">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_P55211_1_Caspase_9_precursor__EC_3_4_22_____CASP_9___ICE_like_apoptotic_protease_6___ICE_LAP6___Apoptotic_protease_Mch_6___Apoptotic_protease_activating_factor_3___APAF_3_" />
+ </bp:sequenceParticipant>
+ <bp:protein rdf:ID="UniProt_P55211_1_Caspase_9_precursor__EC_3_4_22_____CASP_9___ICE_like_apoptotic_protease_6___ICE_LAP6___Apoptotic_protease_Mch_6___Apoptotic_protease_activating_factor_3___APAF_3_">
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P55211-1 Caspase-9 precursor (EC 3.4.22.-) (CASP-9) (ICE-like apoptotic protease 6) (ICE-LAP6) (Apoptotic protease Mch-6) (Apoptotic protease activating factor 3) (APAF-3)</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CASP9</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">MCH6</bp:SYNONYMS>
+ <bp:XREF rdf:resource="#UniProt_P55211" />
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Involved in the activation cascade of caspases responsible for apoptosis execution. Binding of caspase-9 to Apaf- 1 leads to activation of the protease which then cleaves and activates caspase-3. Proteolytically cleaves poly(ADP-ribose) polymerase (PARP). FUNCTION: Isoform 2 lacks activity is an dominant-negative inhibitor of caspase-9. SUBUNIT: Heterodimer of a 35 kDa (P35) and a 10 kDa (P10) subunit. Caspa [...]
+ </bp:protein>
+ <bp:unificationXref rdf:ID="UniProt_P55211">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P55211</bp:ID>
+ </bp:unificationXref>
+ <bp:sequenceParticipant rdf:ID="Apaf_1_Cytochrome_C__cytosol_2">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#Apaf_1_Cytochrome_C__cytosol_1" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="Cytochrome_C_Apaf_1_Procaspase_9__cytosol_">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#Cytochrome_C_Apaf_1_Procaspase_9__cytosol_1" />
+ </bp:sequenceParticipant>
+ <bp:complex rdf:ID="Cytochrome_C_Apaf_1_Procaspase_9__cytosol_1">
+ <bp:COMPONENTS rdf:resource="#Caspase_9_precursor___cytosol_1" />
+ <bp:COMPONENTS rdf:resource="#Apaf_1_Cytochrome_C__cytosol_3" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cytochrome C:Apaf-1:Procaspase-9 [cytosol]</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cytochrome C:Apaf-1:Procaspase-9</bp:SHORT-NAME>
+ </bp:complex>
+ <bp:sequenceParticipant rdf:ID="Caspase_9_precursor___cytosol_1">
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+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="Apaf_1_Cytochrome_C__cytosol_3">
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+ <bp:PHYSICAL-ENTITY rdf:resource="#Apaf_1_Cytochrome_C__cytosol_1" />
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+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">9390557</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</bp:DB>
+ <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1997</bp:YEAR>
+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cytochrome c and dATP-dependent formation of Apaf-1/caspase-9 complex initiates an apoptotic protease cascade.</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Li, P</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Nijhawan, D</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Budihardjo, I</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Srinivasula, SM</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Ahmad, M</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Alnemri, ES</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Wang, X</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cell 91:479-89</bp:SOURCE>
+ </bp:publicationXref>
+ <bp:pathwayStep rdf:ID="Cytochrome_C_Apaf_1_binds_Procaspase_9Step">
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+ <bp:NEXT-STEP rdf:resource="#Cleavage_of_Procaspase_9_to_Caspase_9Step" />
+ </bp:pathwayStep>
+ <bp:biochemicalReaction rdf:ID="Cleavage_of_Procaspase_9_to_Caspase_9">
+ <bp:LEFT rdf:resource="#Cytochrome_C_Apaf_1_Procaspase_9__cytosol_2" />
+ <bp:RIGHT rdf:resource="#Apoptosome__cytosol_" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cleavage of Procaspase-9 to Caspase-9</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cleavage of Procaspase-9 to Caspase-9</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome114259" />
+ <bp:XREF rdf:resource="#Pubmed_9390557" />
+ </bp:biochemicalReaction>
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+ <bp:PHYSICAL-ENTITY rdf:resource="#Cytochrome_C_Apaf_1_Procaspase_9__cytosol_1" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="Apoptosome__cytosol_">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#Apoptosome__cytosol_1" />
+ </bp:sequenceParticipant>
+ <bp:complex rdf:ID="Apoptosome__cytosol_1">
+ <bp:COMPONENTS rdf:resource="#Apaf_1_Cytochrome_C__cytosol_4" />
+ <bp:COMPONENTS rdf:resource="#Cleaved_Caspase_9__cytosol_" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Apoptosome [cytosol]</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Apoptosome</bp:SHORT-NAME>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cytochrome C:Apaf-1:Caspase-9</bp:SYNONYMS>
+ </bp:complex>
+ <bp:sequenceParticipant rdf:ID="Apaf_1_Cytochrome_C__cytosol_4">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#Apaf_1_Cytochrome_C__cytosol_1" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="Cleaved_Caspase_9__cytosol_">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#Cleaved_Caspase_9__cytosol_1" />
+ </bp:sequenceParticipant>
+ <bp:complex rdf:ID="Cleaved_Caspase_9__cytosol_1">
+ <bp:COMPONENTS rdf:resource="#Caspase_9__large_subunit___cytosol_" />
+ <bp:COMPONENTS rdf:resource="#Caspase_9__small_subunit___cytosol_" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cleaved Caspase-9 [cytosol]</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cleaved Caspase-9</bp:SHORT-NAME>
+ </bp:complex>
+ <bp:sequenceParticipant rdf:ID="Caspase_9__large_subunit___cytosol_">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
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+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="Caspase_9__small_subunit___cytosol_">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
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+ </bp:sequenceParticipant>
+ <bp:catalysis rdf:ID="caspase_activity_of_Apoptosome__cytosol_">
+ <bp:CONTROLLER rdf:resource="#Apoptosome__cytosol_2" />
+ <bp:CONTROLLED rdf:resource="#Cleavage_of_Procaspase_9_to_Caspase_9" />
+ <bp:DIRECTION rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PHYSIOL-LEFT-TO-RIGHT</bp:DIRECTION>
+ <bp:XREF rdf:resource="#caspase_activity" />
+ </bp:catalysis>
+ <bp:sequenceParticipant rdf:ID="Apoptosome__cytosol_2">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
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+ </bp:sequenceParticipant>
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+ <bp:pathwayStep rdf:ID="Cleavage_of_Procaspase_9_to_Caspase_9Step">
+ <bp:STEP-INTERACTIONS rdf:resource="#Cleavage_of_Procaspase_9_to_Caspase_9" />
+ <bp:STEP-INTERACTIONS rdf:resource="#caspase_activity_of_Apoptosome__cytosol_" />
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+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</bp:DB>
+ <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2004</bp:YEAR>
+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Apo cytochrome c inhibits caspases by preventing apoptosome formation.</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Martin, AG</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Nguyen, J</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Wells, JA</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Fearnhead, HO</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Biochem Biophys Res Commun 319:944-50</bp:SOURCE>
+ </bp:publicationXref>
+ <bp:pathwayStep rdf:ID="Formation_of_apoptosomeStep">
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+ <bp:NEXT-STEP rdf:resource="#Cleavage_of_Procaspase_7_by_the_apoptosomeStep" />
+ </bp:pathwayStep>
+ <bp:pathway rdf:ID="Activation_of_caspases_through_apoptosome_mediated_cleavage">
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+ <bp:PATHWAY-COMPONENTS rdf:resource="#Cleavage_of__Procaspase_3_by_the_apoptosomeStep" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Activation of caspases through apoptosome-mediated cleavage</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Activation of caspases through apoptosome-mediated cleavage</bp:SHORT-NAME>
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+ <bp:XREF rdf:resource="#Pubmed_10206961" />
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+ </bp:sequenceParticipant>
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+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P42574 Caspase-3 precursor (EC 3.4.22.-) (CASP-3) (Apopain) (Cysteine protease CPP32) (Yama protein) (CPP-32) (SREBP cleavage activity 1) (SCA-1)</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CASP3</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CPP32</bp:SYNONYMS>
+ <bp:XREF rdf:resource="#UniProt_P42574" />
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Involved in the activation cascade of caspases responsible for apoptosis execution. At the onset of apoptosis it proteolytically cleaves poly(ADP-ribose) polymerase (PARP) at a 216-Asp-|-Gly-217 bond. Cleaves and activates sterol regulatory element binding proteins (SREBPs) between the basic helix-loop- helix leucine zipper domain and the membrane attachment domain. Cleaves and activates caspase-6, -7 and -9 [...]
+ </bp:protein>
+ <bp:unificationXref rdf:ID="UniProt_P42574">
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+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P42574</bp:ID>
+ </bp:unificationXref>
+ <bp:sequenceParticipant rdf:ID="Active_caspase_3__cytosol_">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#Active_caspase_3__cytosol_1" />
+ </bp:sequenceParticipant>
+ <bp:complex rdf:ID="Active_caspase_3__cytosol_1">
+ <bp:COMPONENTS rdf:resource="#Caspase_3__small_subunit___cytosol_" />
+ <bp:COMPONENTS rdf:resource="#Caspase_3__large_subunit___cytosol_" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Active caspase-3 [cytosol]</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Active caspase-3</bp:SHORT-NAME>
+ </bp:complex>
+ <bp:sequenceParticipant rdf:ID="Caspase_3__small_subunit___cytosol_">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_P42574_Caspase_3_precursor__EC_3_4_22_____CASP_3___Apopain___Cysteine_protease_CPP32___Yama_protein___CPP_32___SREBP_cleavage_activity_1___SCA_1_" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="Caspase_3__large_subunit___cytosol_">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_P42574_Caspase_3_precursor__EC_3_4_22_____CASP_3___Apopain___Cysteine_protease_CPP32___Yama_protein___CPP_32___SREBP_cleavage_activity_1___SCA_1_" />
+ </bp:sequenceParticipant>
+ <bp:catalysis rdf:ID="caspase_activity_of_Apoptosome__cytosol_1">
+ <bp:CONTROLLER rdf:resource="#Apoptosome__cytosol_3" />
+ <bp:CONTROLLED rdf:resource="#Cleavage_of__Procaspase_3_by_the_apoptosome" />
+ <bp:DIRECTION rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PHYSIOL-LEFT-TO-RIGHT</bp:DIRECTION>
+ <bp:XREF rdf:resource="#caspase_activity" />
+ </bp:catalysis>
+ <bp:sequenceParticipant rdf:ID="Apoptosome__cytosol_3">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#Apoptosome__cytosol_1" />
+ </bp:sequenceParticipant>
+ <bp:unificationXref rdf:ID="Reactome114252">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">114252</bp:ID>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</bp:COMMENT>
+ </bp:unificationXref>
+ <bp:publicationXref rdf:ID="Pubmed_10206961">
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">10206961</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</bp:DB>
+ <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1999</bp:YEAR>
+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An APAF-1.cytochrome c multimeric complex is a functional apoptosome that activates procaspase-9.</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Zou, H</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Li, Y</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Liu, X</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Wang, X</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Biol Chem 274:11549-56</bp:SOURCE>
+ </bp:publicationXref>
+ <bp:pathwayStep rdf:ID="Cleavage_of__Procaspase_3_by_the_apoptosomeStep">
+ <bp:STEP-INTERACTIONS rdf:resource="#Cleavage_of__Procaspase_3_by_the_apoptosome" />
+ <bp:NEXT-STEP rdf:resource="#Cleavage_of_cellular_proteins_by_active_caspasesStep" />
+ <bp:NEXT-STEP rdf:resource="#Activation_of__Effector_CaspasesStep" />
+ <bp:STEP-INTERACTIONS rdf:resource="#caspase_activity_of_Apoptosome__cytosol_1" />
+ </bp:pathwayStep>
+ <bp:biochemicalReaction rdf:ID="Cleavage_of_Procaspase_7_by_the_apoptosome">
+ <bp:LEFT rdf:resource="#Caspase_7_precursor___cytosol_" />
+ <bp:RIGHT rdf:resource="#Active_Caspase_7__cytosol_" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cleavage of Procaspase-7 by the apoptosome</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cleavage of Procaspase-7 by the apoptosome</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome114261" />
+ <bp:XREF rdf:resource="#Pubmed_9922454" />
+ </bp:biochemicalReaction>
+ <bp:sequenceParticipant rdf:ID="Caspase_7_precursor___cytosol_">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_P55210_1_Caspase_7_precursor__EC_3_4_22_____CASP_7___ICE_like_apoptotic_protease_3___ICE_LAP3___Apoptotic_protease_Mch_3___CMH_1_" />
+ </bp:sequenceParticipant>
+ <bp:protein rdf:ID="UniProt_P55210_1_Caspase_7_precursor__EC_3_4_22_____CASP_7___ICE_like_apoptotic_protease_3___ICE_LAP3___Apoptotic_protease_Mch_3___CMH_1_">
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P55210-1 Caspase-7 precursor (EC 3.4.22.-) (CASP-7) (ICE-like apoptotic protease 3) (ICE-LAP3) (Apoptotic protease Mch-3) (CMH-1)</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">MCH3</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CASP7</bp:SYNONYMS>
+ <bp:XREF rdf:resource="#UniProt_P55210" />
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Involved in the activation cascade of caspases responsible for apoptosis execution. Cleaves and activates sterol regulatory element binding proteins (SREBPs). Proteolytically cleaves poly(ADP-ribose) polymerase (PARP) at a 216-Asp-|-Gly-217 bond. Overexpression promotes programmed cell death. ENZYME REGULATION: Inhibited by isatin sulfonamides. SUBUNIT: Heterodimer of a 20 kDa (p20) and a 11 kDa (p11) subuni [...]
+ </bp:protein>
+ <bp:unificationXref rdf:ID="UniProt_P55210">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P55210</bp:ID>
+ </bp:unificationXref>
+ <bp:sequenceParticipant rdf:ID="Active_Caspase_7__cytosol_">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#Active_Caspase_7__cytosol_1" />
+ </bp:sequenceParticipant>
+ <bp:complex rdf:ID="Active_Caspase_7__cytosol_1">
+ <bp:COMPONENTS rdf:resource="#Caspase_7__large_subunit___cytosol_" />
+ <bp:COMPONENTS rdf:resource="#Caspase_7__small_subunit___cytosol_" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Active Caspase-7 [cytosol]</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Active Caspase-7</bp:SHORT-NAME>
+ </bp:complex>
+ <bp:sequenceParticipant rdf:ID="Caspase_7__large_subunit___cytosol_">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_P55210_1_Caspase_7_precursor__EC_3_4_22_____CASP_7___ICE_like_apoptotic_protease_3___ICE_LAP3___Apoptotic_protease_Mch_3___CMH_1_" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="Caspase_7__small_subunit___cytosol_">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_P55210_1_Caspase_7_precursor__EC_3_4_22_____CASP_7___ICE_like_apoptotic_protease_3___ICE_LAP3___Apoptotic_protease_Mch_3___CMH_1_" />
+ </bp:sequenceParticipant>
+ <bp:catalysis rdf:ID="caspase_activity_of_Apoptosome__cytosol_2">
+ <bp:CONTROLLER rdf:resource="#Apoptosome__cytosol_4" />
+ <bp:CONTROLLED rdf:resource="#Cleavage_of_Procaspase_7_by_the_apoptosome" />
+ <bp:DIRECTION rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PHYSIOL-LEFT-TO-RIGHT</bp:DIRECTION>
+ <bp:XREF rdf:resource="#caspase_activity" />
+ </bp:catalysis>
+ <bp:sequenceParticipant rdf:ID="Apoptosome__cytosol_4">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#Apoptosome__cytosol_1" />
+ </bp:sequenceParticipant>
+ <bp:unificationXref rdf:ID="Reactome114261">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">114261</bp:ID>
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+ </bp:unificationXref>
+ <bp:publicationXref rdf:ID="Pubmed_9922454">
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">9922454</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</bp:DB>
+ <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1999</bp:YEAR>
+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Ordering the cytochrome c-initiated caspase cascade: hierarchical activation of caspases-2, -3, -6, -7, -8, and -10 in a caspase-9-dependent manner.</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Slee, EA</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Harte, MT</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Kluck, RM</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Wolf, BB</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Casiano, CA</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Newmeyer, DD</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Wang, HG</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reed, JC</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Nicholson, DW</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Alnemri, ES</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Green, DR</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Martin, SJ</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Cell Biol 144:281-92</bp:SOURCE>
+ </bp:publicationXref>
+ <bp:pathwayStep rdf:ID="Cleavage_of_Procaspase_7_by_the_apoptosomeStep">
+ <bp:STEP-INTERACTIONS rdf:resource="#Cleavage_of_Procaspase_7_by_the_apoptosome" />
+ <bp:NEXT-STEP rdf:resource="#Cleavage_of_cellular_proteins_by_active_caspasesStep" />
+ <bp:NEXT-STEP rdf:resource="#Activation_of__Effector_CaspasesStep" />
+ <bp:STEP-INTERACTIONS rdf:resource="#caspase_activity_of_Apoptosome__cytosol_2" />
+ </bp:pathwayStep>
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+ </bp:unificationXref>
+ <bp:relationshipXref rdf:ID="caspase_activation_via_cytochrome_c">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GO</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0008635</bp:ID>
+ </bp:relationshipXref>
+ <bp:pathwayStep rdf:ID="Activation_of_caspases_through_apoptosome_mediated_cleavageStep">
+ <bp:STEP-INTERACTIONS rdf:resource="#Activation_of_caspases_through_apoptosome_mediated_cleavage" />
+ </bp:pathwayStep>
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+ </bp:unificationXref>
+ <bp:evidence rdf:ID="Summation_140362">
+ <bp:XREF rdf:resource="#Pubmed_11711427" />
+ </bp:evidence>
+ <bp:pathwayStep rdf:ID="Cytochrome_c_mediated_apoptotic_responseStep">
+ <bp:STEP-INTERACTIONS rdf:resource="#Cytochrome_c_mediated_apoptotic_response" />
+ </bp:pathwayStep>
+ <bp:pathway rdf:ID="SMAC_mediated_apoptotic_response">
+ <bp:PATHWAY-COMPONENTS rdf:resource="#SMAC_mediated_dissociation_of_IAP_caspase_complexes_Step" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#SMAC_binds_to_IAPs_Step" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SMAC-mediated apoptotic response</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SMAC-mediated apoptotic response</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome111469" />
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Once released from the mitochondria, SMAC binds to IAP family proteins displacing them from Caspase:IAP complexes liberating the active caspases.</bp:COMMENT>
+ <bp:EVIDENCE rdf:resource="#Summation_140376" />
+ <bp:XREF rdf:resource="#Pubmed_15077149" />
+ </bp:pathway>
+ <bp:pathway rdf:ID="SMAC_binds_to_IAPs_">
+ <bp:PATHWAY-COMPONENTS rdf:resource="#SMAC_binds_XIAP_Caspase_3Step" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#SMAC_binds_XIAP_Caspase_7Step" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#SMAC_binds_XIAP_Caspase_9Step" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SMAC binds to IAPs</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SMAC binds to IAPs</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome111463" />
+ </bp:pathway>
+ <bp:biochemicalReaction rdf:ID="SMAC_binds_XIAP_Caspase_3">
+ <bp:LEFT rdf:resource="#SMAC__cytosol_1" />
+ <bp:LEFT rdf:resource="#XIAP_Caspase_3__cytosol_" />
+ <bp:RIGHT rdf:resource="#SMAC_XIAP_Caspase_3__cytosol_" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SMAC binds XIAP:Caspase-3</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SMAC binds XIAP:Caspase-3</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome114306" />
+ <bp:XREF rdf:resource="#Pubmed_11257231" />
+ <bp:XREF rdf:resource="#Pubmed_9230442" />
+ <bp:XREF rdf:resource="#Pubmed_14960576" />
+ <bp:EVIDENCE rdf:resource="#InferredFrom_SMAC_binds_XIAP_Caspase_7" />
+ </bp:biochemicalReaction>
+ <bp:sequenceParticipant rdf:ID="SMAC__cytosol_1">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q9NR28_1_Diablo_homolog__mitochondrial_precursor__Second_mitochondria_derived_activator_of_caspase___Smac_protein___Direct_IAP_binding_protein_with_low_pI_" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="XIAP_Caspase_3__cytosol_">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#XIAP_Caspase_3__cytosol_1" />
+ </bp:sequenceParticipant>
+ <bp:complex rdf:ID="XIAP_Caspase_3__cytosol_1">
+ <bp:COMPONENTS rdf:resource="#XIAP__cytosol_" />
+ <bp:COMPONENTS rdf:resource="#Active_caspase_3__cytosol_2" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">XIAP:Caspase-3 [cytosol]</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">XIAP:Caspase-3</bp:SHORT-NAME>
+ </bp:complex>
+ <bp:sequenceParticipant rdf:ID="XIAP__cytosol_">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_P98170_Baculoviral_IAP_repeat_containing_protein_4__Inhibitor_of_apoptosis_protein_3___X_linked_inhibitor_of_apoptosis_protein___X_linked_IAP___IAP_like_protein___HILP_" />
+ </bp:sequenceParticipant>
+ <bp:protein rdf:ID="UniProt_P98170_Baculoviral_IAP_repeat_containing_protein_4__Inhibitor_of_apoptosis_protein_3___X_linked_inhibitor_of_apoptosis_protein___X_linked_IAP___IAP_like_protein___HILP_">
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P98170 Baculoviral IAP repeat-containing protein 4 (Inhibitor of apoptosis protein 3) (X-linked inhibitor of apoptosis protein) (X-linked IAP) (IAP-like protein) (HILP)</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">XIAP</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BIRC4</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">IAP3</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">API3</bp:SYNONYMS>
+ <bp:XREF rdf:resource="#UniProt_P98170" />
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Apoptotic suppressor. Inhibitor of caspase-3, -7 and -9. SUBUNIT: Interacts with SMAC and with PRSS25; these interactions inhibit apoptotic suppressor activity. SUBCELLULAR LOCATION: Cytoplasmic. TISSUE SPECIFICITY: Ubiquitous, except peripheral blood leukocytes. DOMAIN: The second BIR domain is sufficient to inhibit caspase-3 and -7, while the third BIR is involved in caspase-9 inhibition. The interactions [...]
+ </bp:protein>
+ <bp:unificationXref rdf:ID="UniProt_P98170">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P98170</bp:ID>
+ </bp:unificationXref>
+ <bp:sequenceParticipant rdf:ID="Active_caspase_3__cytosol_2">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#Active_caspase_3__cytosol_1" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="SMAC_XIAP_Caspase_3__cytosol_">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#SMAC_XIAP_Caspase_3__cytosol_1" />
+ </bp:sequenceParticipant>
+ <bp:complex rdf:ID="SMAC_XIAP_Caspase_3__cytosol_1">
+ <bp:COMPONENTS rdf:resource="#SMAC__cytosol_2" />
+ <bp:COMPONENTS rdf:resource="#XIAP_Caspase_3__cytosol_2" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SMAC:XIAP:Caspase-3 [cytosol]</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SMAC:XIAP:Caspase-3</bp:SHORT-NAME>
+ </bp:complex>
+ <bp:sequenceParticipant rdf:ID="SMAC__cytosol_2">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q9NR28_1_Diablo_homolog__mitochondrial_precursor__Second_mitochondria_derived_activator_of_caspase___Smac_protein___Direct_IAP_binding_protein_with_low_pI_" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="XIAP_Caspase_3__cytosol_2">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#XIAP_Caspase_3__cytosol_1" />
+ </bp:sequenceParticipant>
+ <bp:unificationXref rdf:ID="Reactome114306">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">114306</bp:ID>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</bp:COMMENT>
+ </bp:unificationXref>
+ <bp:publicationXref rdf:ID="Pubmed_11257231">
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">11257231</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</bp:DB>
+ <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2001</bp:YEAR>
+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Structural basis of caspase inhibition by XIAP: differential roles of the linker versus the BIR domain.</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Huang, Y</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Park, YC</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Rich, RL</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Segal, D</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Myszka, DG</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Wu, H</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cell 104:781-90</bp:SOURCE>
+ </bp:publicationXref>
+ <bp:publicationXref rdf:ID="Pubmed_9230442">
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">9230442</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</bp:DB>
+ <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1997</bp:YEAR>
+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">X-linked IAP is a direct inhibitor of cell-death proteases.</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Deveraux, QL</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Takahashi, R</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Salvesen, GS</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reed, JC</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Nature 388:300-4</bp:SOURCE>
+ </bp:publicationXref>
+ <bp:publicationXref rdf:ID="Pubmed_14960576">
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">14960576</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</bp:DB>
+ <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2004</bp:YEAR>
+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Smac/DIABLO selectively reduces the levels of c-IAP1 and c-IAP2 but not that of XIAP and livin in HeLa cells.</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Yang, QH</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Du, C</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Biol Chem 279:16963-70</bp:SOURCE>
+ </bp:publicationXref>
+ <bp:evidence rdf:ID="InferredFrom_SMAC_binds_XIAP_Caspase_7">
+ <bp:XREF rdf:resource="#Pubmed_9230442" />
+ <bp:XREF rdf:resource="#Pubmed_14960576" />
+ <bp:XREF rdf:resource="#Pubmed_11257231" />
+ </bp:evidence>
+ <bp:pathwayStep rdf:ID="SMAC_binds_XIAP_Caspase_3Step">
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+ <bp:NEXT-STEP rdf:resource="#Dissociation_of_Caspase_3_from_SMAC_XIAP_Caspase_3Step" />
+ </bp:pathwayStep>
+ <bp:biochemicalReaction rdf:ID="SMAC_binds_XIAP_Caspase_7">
+ <bp:LEFT rdf:resource="#SMAC__cytosol_3" />
+ <bp:LEFT rdf:resource="#XIAP_Caspase_7__cytosol_" />
+ <bp:RIGHT rdf:resource="#SMAC_XIAP_Caspase_7__cytosol_" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SMAC binds XIAP:Caspase-7</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SMAC binds XIAP:Caspase-7</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome114354" />
+ <bp:XREF rdf:resource="#Pubmed_11257231" />
+ <bp:XREF rdf:resource="#Pubmed_9230442" />
+ <bp:XREF rdf:resource="#Pubmed_14960576" />
+ </bp:biochemicalReaction>
+ <bp:sequenceParticipant rdf:ID="SMAC__cytosol_3">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q9NR28_1_Diablo_homolog__mitochondrial_precursor__Second_mitochondria_derived_activator_of_caspase___Smac_protein___Direct_IAP_binding_protein_with_low_pI_" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="XIAP_Caspase_7__cytosol_">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#XIAP_Caspase_7__cytosol_1" />
+ </bp:sequenceParticipant>
+ <bp:complex rdf:ID="XIAP_Caspase_7__cytosol_1">
+ <bp:COMPONENTS rdf:resource="#XIAP__cytosol_1" />
+ <bp:COMPONENTS rdf:resource="#Active_Caspase_7__cytosol_2" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">XIAP:Caspase-7 [cytosol]</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">XIAP:Caspase-7</bp:SHORT-NAME>
+ </bp:complex>
+ <bp:sequenceParticipant rdf:ID="XIAP__cytosol_1">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_P98170_Baculoviral_IAP_repeat_containing_protein_4__Inhibitor_of_apoptosis_protein_3___X_linked_inhibitor_of_apoptosis_protein___X_linked_IAP___IAP_like_protein___HILP_" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="Active_Caspase_7__cytosol_2">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#Active_Caspase_7__cytosol_1" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="SMAC_XIAP_Caspase_7__cytosol_">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#SMAC_XIAP_Caspase_7__cytosol_1" />
+ </bp:sequenceParticipant>
+ <bp:complex rdf:ID="SMAC_XIAP_Caspase_7__cytosol_1">
+ <bp:COMPONENTS rdf:resource="#SMAC__cytosol_4" />
+ <bp:COMPONENTS rdf:resource="#XIAP_Caspase_7__cytosol_2" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SMAC:XIAP:Caspase-7 [cytosol]</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SMAC:XIAP:Caspase-7</bp:SHORT-NAME>
+ </bp:complex>
+ <bp:sequenceParticipant rdf:ID="SMAC__cytosol_4">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q9NR28_1_Diablo_homolog__mitochondrial_precursor__Second_mitochondria_derived_activator_of_caspase___Smac_protein___Direct_IAP_binding_protein_with_low_pI_" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="XIAP_Caspase_7__cytosol_2">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#XIAP_Caspase_7__cytosol_1" />
+ </bp:sequenceParticipant>
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+ </bp:unificationXref>
+ <bp:pathwayStep rdf:ID="SMAC_binds_XIAP_Caspase_7Step">
+ <bp:STEP-INTERACTIONS rdf:resource="#SMAC_binds_XIAP_Caspase_7" />
+ <bp:NEXT-STEP rdf:resource="#Dissociation_of_Caspase_7_from_SMAC_XIAP_Caspase_7Step" />
+ </bp:pathwayStep>
+ <bp:biochemicalReaction rdf:ID="SMAC_binds_XIAP_Caspase_9">
+ <bp:LEFT rdf:resource="#SMAC__cytosol_5" />
+ <bp:LEFT rdf:resource="#XIAP_Caspase_9__cytosol_" />
+ <bp:RIGHT rdf:resource="#SMAC_XIAP_Caspase_9__cytosol_" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SMAC binds XIAP:Caspase-9</bp:NAME>
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+ <bp:XREF rdf:resource="#Pubmed_11084335" />
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+ <bp:EVIDENCE rdf:resource="#InferredFrom_SMAC_binds_XIAP_Caspase_7" />
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+ <bp:sequenceParticipant rdf:ID="SMAC__cytosol_5">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q9NR28_1_Diablo_homolog__mitochondrial_precursor__Second_mitochondria_derived_activator_of_caspase___Smac_protein___Direct_IAP_binding_protein_with_low_pI_" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="XIAP_Caspase_9__cytosol_">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#XIAP_Caspase_9__cytosol_1" />
+ </bp:sequenceParticipant>
+ <bp:complex rdf:ID="XIAP_Caspase_9__cytosol_1">
+ <bp:COMPONENTS rdf:resource="#XIAP__cytosol_2" />
+ <bp:COMPONENTS rdf:resource="#Cleaved_Caspase_9__cytosol_2" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">XIAP:Caspase-9 [cytosol]</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">XIAP:Caspase-9</bp:SHORT-NAME>
+ </bp:complex>
+ <bp:sequenceParticipant rdf:ID="XIAP__cytosol_2">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_P98170_Baculoviral_IAP_repeat_containing_protein_4__Inhibitor_of_apoptosis_protein_3___X_linked_inhibitor_of_apoptosis_protein___X_linked_IAP___IAP_like_protein___HILP_" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="Cleaved_Caspase_9__cytosol_2">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#Cleaved_Caspase_9__cytosol_1" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="SMAC_XIAP_Caspase_9__cytosol_">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#SMAC_XIAP_Caspase_9__cytosol_1" />
+ </bp:sequenceParticipant>
+ <bp:complex rdf:ID="SMAC_XIAP_Caspase_9__cytosol_1">
+ <bp:COMPONENTS rdf:resource="#SMAC__cytosol_6" />
+ <bp:COMPONENTS rdf:resource="#XIAP_Caspase_9__cytosol_2" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SMAC:XIAP:Caspase-9 [cytosol]</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SMAC:XIAP:Caspase-9</bp:SHORT-NAME>
+ </bp:complex>
+ <bp:sequenceParticipant rdf:ID="SMAC__cytosol_6">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#UniProt_Q9NR28_1_Diablo_homolog__mitochondrial_precursor__Second_mitochondria_derived_activator_of_caspase___Smac_protein___Direct_IAP_binding_protein_with_low_pI_" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="XIAP_Caspase_9__cytosol_2">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#XIAP_Caspase_9__cytosol_1" />
+ </bp:sequenceParticipant>
+ <bp:unificationXref rdf:ID="Reactome114361">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">114361</bp:ID>
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+ </bp:unificationXref>
+ <bp:publicationXref rdf:ID="Pubmed_11084335">
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">11084335</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</bp:DB>
+ <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2000</bp:YEAR>
+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ML-IAP, a novel inhibitor of apoptosis that is preferentially expressed in human melanomas.</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Vucic, D</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Stennicke, HR</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pisabarro, MT</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Salvesen, GS</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Dixit, VM</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Curr Biol 10:1359-66</bp:SOURCE>
+ </bp:publicationXref>
+ <bp:pathwayStep rdf:ID="SMAC_binds_XIAP_Caspase_9Step">
+ <bp:STEP-INTERACTIONS rdf:resource="#SMAC_binds_XIAP_Caspase_9" />
+ <bp:NEXT-STEP rdf:resource="#Dissociation_of_Caspase_9_from_SMAC_XIAP_Caspase_9Step" />
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+ </bp:unificationXref>
+ <bp:pathwayStep rdf:ID="SMAC_binds_to_IAPs_Step">
+ <bp:STEP-INTERACTIONS rdf:resource="#SMAC_binds_to_IAPs_" />
+ <bp:NEXT-STEP rdf:resource="#SMAC_mediated_dissociation_of_IAP_caspase_complexes_Step" />
+ </bp:pathwayStep>
+ <bp:pathway rdf:ID="SMAC_mediated_dissociation_of_IAP_caspase_complexes_">
+ <bp:PATHWAY-COMPONENTS rdf:resource="#Dissociation_of_Caspase_3_from_SMAC_XIAP_Caspase_3Step" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#Dissociation_of_Caspase_9_from_SMAC_XIAP_Caspase_9Step" />
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+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SMAC-mediated dissociation of IAP:caspase complexes</bp:NAME>
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+ </bp:pathway>
+ <bp:biochemicalReaction rdf:ID="Dissociation_of_Caspase_3_from_SMAC_XIAP_Caspase_3">
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+ <bp:EVIDENCE rdf:resource="#InferredFrom_Dissociation_of_Caspase_7_from_SMAC_XIAP_Caspase_7" />
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+ <bp:sequenceParticipant rdf:ID="SMAC_XIAP_Caspase_3__cytosol_2">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#SMAC_XIAP_Caspase_3__cytosol_1" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="Active_caspase_3__cytosol_3">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#Active_caspase_3__cytosol_1" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="SMAC_XIAP__cytosol_">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#SMAC_XIAP__cytosol_1" />
+ </bp:sequenceParticipant>
+ <bp:complex rdf:ID="SMAC_XIAP__cytosol_1">
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+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SMAC:XIAP [cytosol]</bp:NAME>
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+ </bp:sequenceParticipant>
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+ </bp:evidence>
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+ <bp:RIGHT rdf:resource="#SMAC_XIAP__cytosol_3" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Dissociation of Caspase-9 from SMAC:XIAP:Caspase-9</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Dissociation of Caspase-9 from SMAC:XIAP:Caspase-9</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome114440" />
+ <bp:EVIDENCE rdf:resource="#InferredFrom_Dissociation_of_Caspase_7_from_SMAC_XIAP_Caspase_7" />
+ </bp:biochemicalReaction>
+ <bp:sequenceParticipant rdf:ID="SMAC_XIAP_Caspase_9__cytosol_2">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#SMAC_XIAP_Caspase_9__cytosol_1" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="Cleaved_Caspase_9__cytosol_3">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#Cleaved_Caspase_9__cytosol_1" />
+ </bp:sequenceParticipant>
+ <bp:sequenceParticipant rdf:ID="SMAC_XIAP__cytosol_3">
+ <bp:CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#SMAC_XIAP__cytosol_1" />
+ </bp:sequenceParticipant>
+ <bp:unificationXref rdf:ID="Reactome114440">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">114440</bp:ID>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</bp:COMMENT>
+ </bp:unificationXref>
+ <bp:pathwayStep rdf:ID="Dissociation_of_Caspase_9_from_SMAC_XIAP_Caspase_9Step">
+ <bp:STEP-INTERACTIONS rdf:resource="#Dissociation_of_Caspase_9_from_SMAC_XIAP_Caspase_9" />
+ </bp:pathwayStep>
+ <bp:unificationXref rdf:ID="Reactome111464">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">111464</bp:ID>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</bp:COMMENT>
+ </bp:unificationXref>
+ <bp:pathwayStep rdf:ID="SMAC_mediated_dissociation_of_IAP_caspase_complexes_Step">
+ <bp:STEP-INTERACTIONS rdf:resource="#SMAC_mediated_dissociation_of_IAP_caspase_complexes_" />
+ <bp:NEXT-STEP rdf:resource="#Cleavage_of_cellular_proteins_by_active_caspasesStep" />
+ <bp:NEXT-STEP rdf:resource="#Activation_of__Effector_CaspasesStep" />
+ </bp:pathwayStep>
+ <bp:unificationXref rdf:ID="Reactome111469">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">111469</bp:ID>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</bp:COMMENT>
+ </bp:unificationXref>
+ <bp:evidence rdf:ID="Summation_140376">
+ <bp:XREF rdf:resource="#Pubmed_12042762" />
+ </bp:evidence>
+ <bp:publicationXref rdf:ID="Pubmed_12042762">
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">12042762</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</bp:DB>
+ <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2002</bp:YEAR>
+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">IAP proteins: blocking the road to death's door.</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Salvesen, GS</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Duckett, CS</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Nat Rev Mol Cell Biol 3:401-10</bp:SOURCE>
+ </bp:publicationXref>
+ <bp:pathwayStep rdf:ID="SMAC_mediated_apoptotic_responseStep">
+ <bp:STEP-INTERACTIONS rdf:resource="#SMAC_mediated_apoptotic_response" />
+ </bp:pathwayStep>
+ <bp:unificationXref rdf:ID="Reactome111471">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">111471</bp:ID>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</bp:COMMENT>
+ </bp:unificationXref>
+ <bp:pathwayStep rdf:ID="Apoptotic_factor_mediated_responseStep">
+ <bp:STEP-INTERACTIONS rdf:resource="#Apoptotic_factor_mediated_response" />
+ </bp:pathwayStep>
+ <bp:unificationXref rdf:ID="Reactome109606">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">109606</bp:ID>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</bp:COMMENT>
+ </bp:unificationXref>
+ <bp:evidence rdf:ID="Summation_140375">
+ <bp:XREF rdf:resource="#Pubmed_11711427" />
+ <bp:XREF rdf:resource="#Pubmed_14561771" />
+ <bp:XREF rdf:resource="#Pubmed_14634621" />
+ </bp:evidence>
+ <bp:publicationXref rdf:ID="Pubmed_14561771">
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">14561771</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</bp:DB>
+ <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2003</bp:YEAR>
+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Ways of dying: multiple pathways to apoptosis.</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Adams, JM</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Genes Dev 17:2481-95</bp:SOURCE>
+ </bp:publicationXref>
+ <bp:relationshipXref rdf:ID="induction_of_apoptosis_by_intracellular_signals">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GO</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0008629</bp:ID>
+ </bp:relationshipXref>
+ <bp:pathwayStep rdf:ID="Intrinsic_Pathway_for_ApoptosisStep">
+ <bp:STEP-INTERACTIONS rdf:resource="#Intrinsic_Pathway_for_Apoptosis" />
+ </bp:pathwayStep>
+ <bp:pathway rdf:ID="Activation_of__Effector_Caspases">
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Activation of Effector Caspases</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Activation of Effector Caspases</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome75142" />
+ </bp:pathway>
+ <bp:unificationXref rdf:ID="Reactome75142">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">75142</bp:ID>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</bp:COMMENT>
+ </bp:unificationXref>
+ <bp:pathwayStep rdf:ID="Activation_of__Effector_CaspasesStep">
+ <bp:STEP-INTERACTIONS rdf:resource="#Activation_of__Effector_Caspases" />
+ <bp:NEXT-STEP rdf:resource="#Apoptotic_execution__phaseStep" />
+ </bp:pathwayStep>
+ <bp:pathway rdf:ID="Apoptotic_execution__phase">
+ <bp:PATHWAY-COMPONENTS rdf:resource="#Cleavage_of_cellular_proteins_by_active_caspasesStep" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#Apoptosis_induced_DNA_fragmentationStep" />
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Apoptotic execution phase</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Apoptotic execution phase</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome75153" />
+ </bp:pathway>
+ <bp:pathway rdf:ID="Cleavage_of_cellular_proteins_by_active_caspases">
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cleavage of cellular proteins by active caspases</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cleavage of cellular proteins by active caspases</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome111465" />
+ </bp:pathway>
+ <bp:unificationXref rdf:ID="Reactome111465">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">111465</bp:ID>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</bp:COMMENT>
+ </bp:unificationXref>
+ <bp:pathwayStep rdf:ID="Cleavage_of_cellular_proteins_by_active_caspasesStep">
+ <bp:STEP-INTERACTIONS rdf:resource="#Cleavage_of_cellular_proteins_by_active_caspases" />
+ </bp:pathwayStep>
+ <bp:pathway rdf:ID="Apoptosis_induced_DNA_fragmentation">
+ <bp:ORGANISM rdf:resource="#Homo_sapiens" />
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Apoptosis induced DNA fragmentation</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Apoptosis induced DNA fragmentation</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#Reactome140342" />
+ <bp:XREF rdf:resource="#DNA_fragmentation_during_apoptosis" />
+ </bp:pathway>
+ <bp:unificationXref rdf:ID="Reactome140342">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">140342</bp:ID>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</bp:COMMENT>
+ </bp:unificationXref>
+ <bp:relationshipXref rdf:ID="DNA_fragmentation_during_apoptosis">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GO</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0006309</bp:ID>
+ </bp:relationshipXref>
+ <bp:openControlledVocabulary rdf:ID="nucleus">
+ <bp:TERM rdf:datatype="http://www.w3.org/2001/XMLSchema#string">nucleus</bp:TERM>
+ <bp:XREF rdf:resource="#GO_0005634" />
+ </bp:openControlledVocabulary>
+ <bp:unificationXref rdf:ID="GO_0005634">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GO</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0005634</bp:ID>
+ </bp:unificationXref>
+ <bp:pathwayStep rdf:ID="Apoptosis_induced_DNA_fragmentationStep">
+ <bp:STEP-INTERACTIONS rdf:resource="#Apoptosis_induced_DNA_fragmentation" />
+ </bp:pathwayStep>
+ <bp:unificationXref rdf:ID="Reactome75153">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">75153</bp:ID>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</bp:COMMENT>
+ </bp:unificationXref>
+ <bp:pathwayStep rdf:ID="Apoptotic_execution__phaseStep">
+ <bp:STEP-INTERACTIONS rdf:resource="#Apoptotic_execution__phase" />
+ </bp:pathwayStep>
+ <bp:unificationXref rdf:ID="Reactome109581">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">109581</bp:ID>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</bp:COMMENT>
+ </bp:unificationXref>
+ <bp:evidence rdf:ID="Summation_109577">
+ <bp:XREF rdf:resource="#Pubmed_12505355" />
+ <bp:XREF rdf:resource="#Pubmed_4561027" />
+ <bp:XREF rdf:resource="#Pubmed_15218528" />
+ <bp:XREF rdf:resource="#Pubmed_14634621" />
+ <bp:XREF rdf:resource="#Pubmed_14561771" />
+ <bp:XREF rdf:resource="#Pubmed_12189384" />
+ <bp:XREF rdf:resource="#Pubmed_12209154" />
+ </bp:evidence>
+ <bp:publicationXref rdf:ID="Pubmed_12505355">
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">12505355</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</bp:DB>
+ <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2002</bp:YEAR>
+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">History of the events leading to the formulation of the apoptosis concept</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Kerr, JF</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Toxicology 181:471-4</bp:SOURCE>
+ </bp:publicationXref>
+ <bp:publicationXref rdf:ID="Pubmed_4561027">
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">4561027</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</bp:DB>
+ <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1972</bp:YEAR>
+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Apoptosis: a basic biological phenomenon with wide-ranging implications in tissue kinetics</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Kerr, JF</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Wyllie, AH</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Currie, AR</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Br J Cancer 26:239-57</bp:SOURCE>
+ </bp:publicationXref>
+ <bp:publicationXref rdf:ID="Pubmed_15218528">
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">15218528</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</bp:DB>
+ <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2004</bp:YEAR>
+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Apoptosis and disease: a life or death decision</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">MacFarlane, M</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Williams, AC</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">EMBO Rep 5:674-8</bp:SOURCE>
+ </bp:publicationXref>
+ <bp:publicationXref rdf:ID="Pubmed_12189384">
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">12189384</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</bp:DB>
+ <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2002</bp:YEAR>
+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Targeting death and decoy receptors of the tumour-necrosis factor superfamily</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Ashkenazi, A</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Nat Rev Cancer 2:420-30</bp:SOURCE>
+ </bp:publicationXref>
+ <bp:relationshipXref rdf:ID="apoptosis">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GO</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0006915</bp:ID>
+ </bp:relationshipXref>
+ <bp:pathway rdf:ID="Apoptosis2">
+ <bp:PATHWAY-COMPONENTS rdf:resource="#Extrinsic_Pathway_for_ApoptosisStep" />
+ </bp:pathway>
+</rdf:RDF>
+
diff --git a/coreplugins/BioPAX/src/test/resources/DIP_ppi.owl b/coreplugins/BioPAX/src/test/resources/DIP_ppi.owl
new file mode 100644
index 0000000..3abfe52
--- /dev/null
+++ b/coreplugins/BioPAX/src/test/resources/DIP_ppi.owl
@@ -0,0 +1,115 @@
+<?xml version="1.0"?>
+<rdf:RDF
+ xmlns:bp="http://www.biopax.org/release/biopax-level2.owl#"
+ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+ xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
+ xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
+ xmlns:owl="http://www.w3.org/2002/07/owl#"
+ xmlns:daml="http://www.daml.org/2001/03/daml+oil#"
+ xmlns="http://www.owl-ontologies.com/unnamed.owl#"
+ xmlns:dc="http://purl.org/dc/elements/1.1/"
+ xml:base="http://www.owl-ontologies.com/unnamed.owl">
+ <owl:Ontology rdf:about="">
+ <owl:imports rdf:resource="http://www.biopax.org/release/biopax-level2.owl"/>
+ </owl:Ontology>
+ <bp:experimentalForm rdf:ID="Immunoprecipitation"/>
+ <bp:sequenceParticipant rdf:ID="sequenceParticipant2">
+ <bp:STOICHIOMETRIC-COEFFICIENT rdf:datatype="http://www.w3.org/2001/XMLSchema#double"
+ >1</bp:STOICHIOMETRIC-COEFFICIENT>
+ <bp:PHYSICAL-ENTITY>
+ <bp:protein rdf:ID="protein2">
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >Serine-protein kinase ATM</bp:NAME>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref_9">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >swiss-prot</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >Q13315</bp:ID>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref3">
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >24193N</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >dip</bp:DB>
+ </bp:unificationXref>
+ </bp:XREF>
+ </bp:protein>
+ </bp:PHYSICAL-ENTITY>
+ </bp:sequenceParticipant>
+ <bp:unificationXref rdf:ID="unificationXref2">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >dip</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >24187N</bp:ID>
+ </bp:unificationXref>
+ <bp:evidence rdf:ID="evidence1">
+ <bp:XREF>
+ <bp:publicationXref rdf:ID="publicationXref1">
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >9725899</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >pubmed</bp:DB>
+ </bp:publicationXref>
+ </bp:XREF>
+ <bp:EVIDENCE-CODE>
+ <bp:openControlledVocabulary rdf:ID="openControlledVocabulary1">
+ <bp:TERM rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >Immunoprecipitation</bp:TERM>
+ </bp:openControlledVocabulary>
+ </bp:EVIDENCE-CODE>
+ </bp:evidence>
+ <bp:openControlledVocabulary rdf:ID="openControlledVocabulary2">
+ <bp:TERM rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >In vitro binding</bp:TERM>
+ </bp:openControlledVocabulary>
+ <bp:experimentalForm rdf:ID="experimentalForm_4"/>
+ <bp:dataSource rdf:ID="dataSource1">
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >dip</bp:NAME>
+ </bp:dataSource>
+ <bp:unificationXref rdf:ID="unificationXref1">
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >40070E</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >dip</bp:DB>
+ </bp:unificationXref>
+ <bp:evidence rdf:ID="evidence2">
+ <bp:XREF rdf:resource="#publicationXref1"/>
+ <bp:EVIDENCE-CODE rdf:resource="#openControlledVocabulary2"/>
+ </bp:evidence>
+ <bp:unificationXref rdf:ID="unificationXref4">
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >P15927</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >swiss-prot</bp:DB>
+ </bp:unificationXref>
+ <bp:sequenceParticipant rdf:ID="sequenceParticipant1">
+ <bp:STOICHIOMETRIC-COEFFICIENT rdf:datatype="http://www.w3.org/2001/XMLSchema#double"
+ >1</bp:STOICHIOMETRIC-COEFFICIENT>
+ <bp:PHYSICAL-ENTITY>
+ <bp:protein rdf:ID="protein1">
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >replication protein repA 32K chain</bp:NAME>
+ <bp:XREF rdf:resource="#unificationXref4"/>
+ <bp:XREF rdf:resource="#unificationXref2"/>
+ </bp:protein>
+ </bp:PHYSICAL-ENTITY>
+ </bp:sequenceParticipant>
+ <bp:physicalInteraction rdf:ID="physicalInteraction1">
+ <bp:EVIDENCE rdf:resource="#evidence1"/>
+ <bp:PARTICIPANTS rdf:resource="#sequenceParticipant1"/>
+ <bp:EVIDENCE rdf:resource="#evidence2"/>
+ <bp:PARTICIPANTS rdf:resource="#sequenceParticipant2"/>
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >ATM phosphorylates p53 at serine 15</bp:NAME>
+ <bp:XREF rdf:resource="#unificationXref1"/>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >Division: BIND Metazoa</bp:COMMENT>
+ <bp:DATA-SOURCE rdf:resource="#dataSource1"/>
+ </bp:physicalInteraction>
+</rdf:RDF>
+
+<!-- Created with Protege (with OWL Plugin 2.1, Build 284) http://protege.stanford.edu -->
diff --git a/coreplugins/BioPAX/src/test/resources/DNA_Replication.owl b/coreplugins/BioPAX/src/test/resources/DNA_Replication.owl
new file mode 100644
index 0000000..1ae9e07
--- /dev/null
+++ b/coreplugins/BioPAX/src/test/resources/DNA_Replication.owl
@@ -0,0 +1,6596 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns="http://www.biopax.org/release/biopax-level2.owl#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:owl="http://www.w3.org/2002/07/owl#" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xml:base="http://www.biopax.org/release/biopax-level2.owl#">
+ <owl:Ontology rdf:about="">
+ <owl:imports rdf:resource="http://www.biopax.org/Downloads/Level2v0.9/biopax-level2.owl" />
+ <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BioPAX pathway converted from "DNA Replication" in the Reactome database.</rdfs:comment>
+ </owl:Ontology>
+ <pathway rdf:ID="DNA_Replication">
+ <PATHWAY-COMPONENTS rdf:resource="#Switching_of_origins_to_a_post_replicative_stateStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#DNA_Replication_Pre_InitiationStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#Regulation_of_DNA_replicationStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#DNA_replication_initiationStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#DNA_strand_elongationStep" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DNA Replication</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DNA Replication</SHORT-NAME>
+ <XREF rdf:resource="#Reactome69306" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Studies in the past decade have suggested that the basic mechanism of DNA replication initiation is conserved in all kingdoms of life. Initiation in unicellular eukaryotes, in particular Saccharomyces cerevisiae (budding yeast), is well understood, and has served as a model for studies of DNA replication initiation in multicellular eukaryotes, including humans. In general terms, the first step of initiation is the bindin [...]
+ <EVIDENCE rdf:resource="#Summation_69307" />
+ <CELLULAR-LOCATION rdf:resource="#nucleus" />
+ </pathway>
+ <pathway rdf:ID="DNA_Replication_Pre_Initiation">
+ <PATHWAY-COMPONENTS rdf:resource="#Assembly_of_the_pre_replicative_complexStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#Activation_of_the_pre_replicative_complexStep" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DNA Replication Pre-Initiation</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DNA Replication Pre-Initiation</SHORT-NAME>
+ <XREF rdf:resource="#Reactome69002" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Although, DNA replication occurs in the S phase of the cell cycle, the formation of the DNA replication pre-initiation complex begins during late G1/M transition.</COMMENT>
+ <EVIDENCE rdf:resource="#Summation_69003" />
+ </pathway>
+ <pathway rdf:ID="Assembly_of_the_pre_replicative_complex">
+ <PATHWAY-COMPONENTS rdf:resource="#Cdc6_association_with_the_ORC_origin_complexStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#Mcm2_7_associates_with_the_Cdt1_Cdc6_ORC_origin_complex__forming_the_pre_replicative_complex__preRC_Step" />
+ <PATHWAY-COMPONENTS rdf:resource="#Cdt1_association_with_the_Cdc6_ORC_origin_complexStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#Assembly_of_the_ORC_complex_at_the_origin_of_replicationStep" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Assembly of the pre-replicative complex</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Assembly of the pre-replicative complex</SHORT-NAME>
+ <XREF rdf:resource="#Reactome68867" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DNA replication pre-initiation in eukaryotic cells begins with the formation of the pre-replicative complex (pre-RC) during the late M phase and continues in the G1 phase of the mitotic cell cycle, a process also called DNA replication origin licensing. The association of initiation proteins (ORC, Cdc6, Cdt1, Mcm2-7) with the origin of replication in both <i>S. cerevisiae</i> and humans has been demonstrated [...]
+ <EVIDENCE rdf:resource="#Summation_69392" />
+ <CELLULAR-LOCATION rdf:resource="#nucleus" />
+ </pathway>
+ <pathway rdf:ID="Assembly_of_the_ORC_complex_at_the_origin_of_replication">
+ <PATHWAY-COMPONENTS rdf:resource="#Orc6_associates_with_Orc1_Orc4_Orc5_Orc3_Orc2_origin_complexes__forming_ORC_origin_complexesStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#Orc1_associates_with_Orc4_Orc5_Orc3_Orc2_origin_complexesStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#Orc5_associates_with_Orc3_Orc2_origin_complexesStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#Orc3_associates_with_Orc2_constitutively_bound_at_origins_of_replicationStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#Orc4_associates_with_Orc5_Orc3_Orc2_origin_complexesStep" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Assembly of the ORC complex at the origin of replication</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Assembly of the ORC complex at the origin of replication</SHORT-NAME>
+ <XREF rdf:resource="#Reactome68616" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">In Saccharomyces cerevisiae, the entire ORC complex is constitutively bound to the origin of replication. However, in mammalian cells, Orc1, and possibly other Orc subunits, dissociate from origins of replication, while Orc2 remains stably associated with chromatin across the cell cycle. The first step in formation of the pre-RC is assembly of the hexameric Origin Recognition Complex (ORC) at the origin of replication. R [...]
+ <EVIDENCE rdf:resource="#Summation_68618" />
+ <CELLULAR-LOCATION rdf:resource="#nucleus" />
+ </pathway>
+ <biochemicalReaction rdf:ID="Orc3_associates_with_Orc2_constitutively_bound_at_origins_of_replication">
+ <LEFT rdf:resource="#Orc3__nucleoplasm_" />
+ <LEFT rdf:resource="#Orc2_origin__nucleoplasm_" />
+ <RIGHT rdf:resource="#Orc3_Orc2_origin__nucleoplasm_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Orc3 associates with Orc2 constitutively bound at origins of replication</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Orc3 associates with Orc2 constitutively bound at origins of replication</SHORT-NAME>
+ <XREF rdf:resource="#Reactome68595" />
+ <XREF rdf:resource="#Pubmed_11395502" />
+ <XREF rdf:resource="#Pubmed_11323433" />
+ <XREF rdf:resource="#Pubmed_11046155" />
+ <XREF rdf:resource="#Pubmed_9733749" />
+ </biochemicalReaction>
+ <proteinParticipant rdf:ID="Orc3__nucleoplasm_">
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q9UBD5_Origin_recognition_complex_subunit_3__Origin_recognition_complex_subunit_Latheo_" />
+ </proteinParticipant>
+ <openControlledVocabulary rdf:ID="nucleoplasm">
+ <TERM rdf:datatype="http://www.w3.org/2001/XMLSchema#string">nucleoplasm</TERM>
+ <XREF rdf:resource="#GO_0005654" />
+ </openControlledVocabulary>
+ <xref rdf:ID="GO_0005654">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GO</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0005654</ID>
+ </xref>
+ <protein rdf:ID="UniProt_Q9UBD5_Origin_recognition_complex_subunit_3__Origin_recognition_complex_subunit_Latheo_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:Q9UBD5 Origin recognition complex subunit 3 (Origin recognition complex subunit Latheo)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">LATHEO</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ORC3L</SYNONYMS>
+ <XREF rdf:resource="#UniProt_Q9UBD5" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Component of the origin recognition complex (ORC) that binds origins of replication. It has a role in both chromosomal replication and mating type transcriptional silencing. Binds to the ARS consensus sequence (ACS) of origins of replication in an ATP-dependent manner. SUBUNIT: ORC is composed of six subunits (By similarity). SUBCELLULAR LOCATION: Nuclear. SIMILARITY: Belongs to the ORC3 family.</COMMENT>
+ </protein>
+ <bioSource rdf:ID="Homo_sapiens">
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Homo sapiens</NAME>
+ <TAXON-XREF rdf:resource="#NCBI_taxonomy_9606" />
+ </bioSource>
+ <xref rdf:ID="NCBI_taxonomy_9606">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">NCBI_taxonomy</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">9606</ID>
+ </xref>
+ <unificationXref rdf:ID="UniProt_Q9UBD5">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Q9UBD5</ID>
+ </unificationXref>
+ <complexParticipant rdf:ID="Orc2_origin__nucleoplasm_">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Orc2_origin__nucleoplasm_1" />
+ </complexParticipant>
+ <complex rdf:ID="Orc2_origin__nucleoplasm_1">
+ <COMPONENTS rdf:resource="#origin_of_replication__nucleoplasm_" />
+ <COMPONENTS rdf:resource="#Orc2__nucleoplasm_" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Orc2:origin [nucleoplasm]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Orc2:origin</SHORT-NAME>
+ </complex>
+ <physicalEntityParticipant rdf:ID="origin_of_replication__nucleoplasm_">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#origin_of_replication__nucleoplasm_1" />
+ </physicalEntityParticipant>
+ <physicalEntity rdf:ID="origin_of_replication__nucleoplasm_1">
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">origin of replication [nucleoplasm]</NAME>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome. Each synonym is a name of a ConcreteEntity, and each XREF points to one ConcreteEntity</COMMENT>
+ </physicalEntity>
+ <proteinParticipant rdf:ID="Orc2__nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q13416_Origin_recognition_complex_subunit_2" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_Q13416_Origin_recognition_complex_subunit_2">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:Q13416 Origin recognition complex subunit 2</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ORC2L</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ORC2</SYNONYMS>
+ <XREF rdf:resource="#UniProt_Q13416" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Component of the origin recognition complex (ORC) that binds origins of replication. It has a role in both chromosomal replication and mating type transcriptional silencing. Binds to the ARS consensus sequence (ACS) of origins of replication in an ATP-dependent manner. SUBUNIT: ORC is composed of six subunits (By similarity). SUBCELLULAR LOCATION: Nuclear. SIMILARITY: Belongs to the ORC2 family.</COMMENT>
+ </protein>
+ <unificationXref rdf:ID="UniProt_Q13416">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Q13416</ID>
+ </unificationXref>
+ <complexParticipant rdf:ID="Orc3_Orc2_origin__nucleoplasm_">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Orc3_Orc2_origin__nucleoplasm_1" />
+ </complexParticipant>
+ <complex rdf:ID="Orc3_Orc2_origin__nucleoplasm_1">
+ <COMPONENTS rdf:resource="#Orc3__nucleoplasm_1" />
+ <COMPONENTS rdf:resource="#Orc2_origin__nucleoplasm_2" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Orc3:Orc2:origin [nucleoplasm]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Orc3:Orc2:origin</SHORT-NAME>
+ </complex>
+ <proteinParticipant rdf:ID="Orc3__nucleoplasm_1">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q9UBD5_Origin_recognition_complex_subunit_3__Origin_recognition_complex_subunit_Latheo_" />
+ </proteinParticipant>
+ <complexParticipant rdf:ID="Orc2_origin__nucleoplasm_2">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Orc2_origin__nucleoplasm_1" />
+ </complexParticipant>
+ <unificationXref rdf:ID="Reactome68595">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">68595</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <publicationXref rdf:ID="Pubmed_11395502">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">11395502</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2001</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Architecture of the human origin recognition complex.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Dhar, SK</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Delmolino, L</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Dutta, A</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Biol Chem 276:29067-71</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_11323433">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">11323433</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2001</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Assembly of the human origin recognition complex.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Vashee, S</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Simancek, P</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Challberg, MD</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Kelly, TJ</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Biol Chem 276:26666-73</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_11046155">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">11046155</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2000</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Chromatin association of human origin recognition complex, cdc6, and minichromosome maintenance proteins during the cell cycle: assembly of prereplication complexes in late mitosis.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Méndez, J</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Stillman, B</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mol Cell Biol 20:8602-12</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_9733749">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">9733749</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1998</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Human minichromosome maintenance proteins and human origin recognition complex 2 protein on chromatin.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Ritzi, M</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Baack, M</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Musahl, C</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Romanowski, P</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Laskey, RA</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Knippers, R</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Biol Chem 273:24543-9</SOURCE>
+ </publicationXref>
+ <openControlledVocabulary rdf:ID="nucleus">
+ <TERM rdf:datatype="http://www.w3.org/2001/XMLSchema#string">nucleus</TERM>
+ <XREF rdf:resource="#GO_0005634" />
+ </openControlledVocabulary>
+ <xref rdf:ID="GO_0005634">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GO</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0005634</ID>
+ </xref>
+ <pathwayStep rdf:ID="Orc3_associates_with_Orc2_constitutively_bound_at_origins_of_replicationStep">
+ <STEP-INTERACTIONS rdf:resource="#Orc3_associates_with_Orc2_constitutively_bound_at_origins_of_replication" />
+ <NEXT-STEP rdf:resource="#Orc5_associates_with_Orc3_Orc2_origin_complexesStep" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="Orc5_associates_with_Orc3_Orc2_origin_complexes">
+ <LEFT rdf:resource="#Orc5__nucleoplasm_" />
+ <LEFT rdf:resource="#Orc3_Orc2_origin__nucleoplasm_2" />
+ <RIGHT rdf:resource="#Orc5_Orc3_Orc2_origin__nucleoplasm_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Orc5 associates with Orc3:Orc2:origin complexes</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Orc5 associates with Orc3:Orc2:origin complexes</SHORT-NAME>
+ <XREF rdf:resource="#Reactome68603" />
+ <XREF rdf:resource="#Pubmed_11395502" />
+ <XREF rdf:resource="#Pubmed_11323433" />
+ <XREF rdf:resource="#Pubmed_9765232" />
+ <CELLULAR-LOCATION rdf:resource="#nucleus" />
+ </biochemicalReaction>
+ <proteinParticipant rdf:ID="Orc5__nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_O43913_Origin_recognition_complex_subunit_5" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_O43913_Origin_recognition_complex_subunit_5">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:O43913 Origin recognition complex subunit 5</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ORC5L</SYNONYMS>
+ <XREF rdf:resource="#UniProt_O43913" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Component of the origin recognition complex (ORC) that binds origins of replication. It has a role in both chromosomal replication and mating type transcriptional silencing. Binds to the ARS consensus sequence (ACS) of origins of replication in an ATP-dependent manner. SUBUNIT: ORC is composed of six subunits. SUBCELLULAR LOCATION: Nuclear. SIMILARITY: Belongs to the ORC5 family.</COMMENT>
+ </protein>
+ <unificationXref rdf:ID="UniProt_O43913">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">O43913</ID>
+ </unificationXref>
+ <complexParticipant rdf:ID="Orc3_Orc2_origin__nucleoplasm_2">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Orc3_Orc2_origin__nucleoplasm_1" />
+ </complexParticipant>
+ <complexParticipant rdf:ID="Orc5_Orc3_Orc2_origin__nucleoplasm_">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Orc5_Orc3_Orc2_origin__nucleoplasm_1" />
+ </complexParticipant>
+ <complex rdf:ID="Orc5_Orc3_Orc2_origin__nucleoplasm_1">
+ <COMPONENTS rdf:resource="#Orc5__nucleoplasm_1" />
+ <COMPONENTS rdf:resource="#Orc3_Orc2_origin__nucleoplasm_3" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Orc5:Orc3:Orc2:origin [nucleoplasm]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Orc5:Orc3:Orc2:origin</SHORT-NAME>
+ </complex>
+ <proteinParticipant rdf:ID="Orc5__nucleoplasm_1">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_O43913_Origin_recognition_complex_subunit_5" />
+ </proteinParticipant>
+ <complexParticipant rdf:ID="Orc3_Orc2_origin__nucleoplasm_3">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Orc3_Orc2_origin__nucleoplasm_1" />
+ </complexParticipant>
+ <unificationXref rdf:ID="Reactome68603">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">68603</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <publicationXref rdf:ID="Pubmed_9765232">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">9765232</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1998</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ORC5L, a new member of the human origin recognition complex, is deleted in uterine leiomyomas and malignant myeloid diseases.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Quintana, DG</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Thome, KC</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Hou, ZH</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Ligon, AH</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Morton, CC</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Dutta, A</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Biol Chem 273:27137-45</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="Orc5_associates_with_Orc3_Orc2_origin_complexesStep">
+ <STEP-INTERACTIONS rdf:resource="#Orc5_associates_with_Orc3_Orc2_origin_complexes" />
+ <NEXT-STEP rdf:resource="#Orc4_associates_with_Orc5_Orc3_Orc2_origin_complexesStep" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="Orc4_associates_with_Orc5_Orc3_Orc2_origin_complexes">
+ <LEFT rdf:resource="#Orc4__nucleoplasm_" />
+ <LEFT rdf:resource="#Orc5_Orc3_Orc2_origin__nucleoplasm_2" />
+ <RIGHT rdf:resource="#Orc4_Orc5_Orc3_Orc2_origin__nucleoplasm_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Orc4 associates with Orc5:Orc3:Orc2:origin complexes</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Orc4 associates with Orc5:Orc3:Orc2:origin complexes</SHORT-NAME>
+ <XREF rdf:resource="#Reactome68610" />
+ <XREF rdf:resource="#Pubmed_11395502" />
+ <XREF rdf:resource="#Pubmed_11323433" />
+ <CELLULAR-LOCATION rdf:resource="#nucleus" />
+ </biochemicalReaction>
+ <proteinParticipant rdf:ID="Orc4__nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_O43929_Origin_recognition_complex_subunit_4" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_O43929_Origin_recognition_complex_subunit_4">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:O43929 Origin recognition complex subunit 4</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ORC4L</SYNONYMS>
+ <XREF rdf:resource="#UniProt_O43929" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Component of the origin recognition complex (ORC) that binds origins of replication. It has a role in both chromosomal replication and mating type transcriptional silencing. Binds to the ARS consensus sequence (ACS) of origins of replication in an ATP-dependent manner. SUBUNIT: ORC is composed of six subunits (By similarity). SUBCELLULAR LOCATION: Nuclear. SIMILARITY: Belongs to the ORC4 family.</COMMENT>
+ </protein>
+ <unificationXref rdf:ID="UniProt_O43929">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">O43929</ID>
+ </unificationXref>
+ <complexParticipant rdf:ID="Orc5_Orc3_Orc2_origin__nucleoplasm_2">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Orc5_Orc3_Orc2_origin__nucleoplasm_1" />
+ </complexParticipant>
+ <complexParticipant rdf:ID="Orc4_Orc5_Orc3_Orc2_origin__nucleoplasm_">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Orc4_Orc5_Orc3_Orc2_origin__nucleoplasm_1" />
+ </complexParticipant>
+ <complex rdf:ID="Orc4_Orc5_Orc3_Orc2_origin__nucleoplasm_1">
+ <COMPONENTS rdf:resource="#Orc4__nucleoplasm_1" />
+ <COMPONENTS rdf:resource="#Orc5_Orc3_Orc2_origin__nucleoplasm_3" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Orc4:Orc5:Orc3:Orc2:origin [nucleoplasm]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Orc4:Orc5:Orc3:Orc2:origin</SHORT-NAME>
+ </complex>
+ <proteinParticipant rdf:ID="Orc4__nucleoplasm_1">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_O43929_Origin_recognition_complex_subunit_4" />
+ </proteinParticipant>
+ <complexParticipant rdf:ID="Orc5_Orc3_Orc2_origin__nucleoplasm_3">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Orc5_Orc3_Orc2_origin__nucleoplasm_1" />
+ </complexParticipant>
+ <unificationXref rdf:ID="Reactome68610">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">68610</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <pathwayStep rdf:ID="Orc4_associates_with_Orc5_Orc3_Orc2_origin_complexesStep">
+ <STEP-INTERACTIONS rdf:resource="#Orc4_associates_with_Orc5_Orc3_Orc2_origin_complexes" />
+ <NEXT-STEP rdf:resource="#Orc1_associates_with_Orc4_Orc5_Orc3_Orc2_origin_complexesStep" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="Orc1_associates_with_Orc4_Orc5_Orc3_Orc2_origin_complexes">
+ <LEFT rdf:resource="#Orc1__nucleoplasm_" />
+ <LEFT rdf:resource="#Orc4_Orc5_Orc3_Orc2_origin__nucleoplasm_2" />
+ <RIGHT rdf:resource="#Orc1_Orc4_Orc5_Orc3_Orc2_origin__nucleoplasm_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Orc1 associates with Orc4:Orc5:Orc3:Orc2:origin complexes</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Orc1 associates with Orc4:Orc5:Orc3:Orc2:origin complexes</SHORT-NAME>
+ <XREF rdf:resource="#Reactome68611" />
+ <XREF rdf:resource="#Pubmed_11395502" />
+ <XREF rdf:resource="#Pubmed_11323433" />
+ <XREF rdf:resource="#Pubmed_11046155" />
+ <XREF rdf:resource="#Pubmed_11739726" />
+ <CELLULAR-LOCATION rdf:resource="#nucleus" />
+ </biochemicalReaction>
+ <proteinParticipant rdf:ID="Orc1__nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q13415_Origin_recognition_complex_subunit_1__Replication_control_protein_1_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_Q13415_Origin_recognition_complex_subunit_1__Replication_control_protein_1_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:Q13415 Origin recognition complex subunit 1 (Replication control protein 1)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PARC1</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ORC1</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ORC1L</SYNONYMS>
+ <XREF rdf:resource="#UniProt_Q13415" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Component of the origin recognition complex (ORC) that binds origins of replication. It has a role in both chromosomal replication and mating type transcriptional silencing. Binds to the ARS consensus sequence (ACS) of origins of replication in an ATP-dependent manner. SUBUNIT: ORC is composed of six subunits. Interacts with CDC6. SUBCELLULAR LOCATION: Nuclear. SIMILARITY: Belongs to the ORC1 family.</COMMENT>
+ </protein>
+ <unificationXref rdf:ID="UniProt_Q13415">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Q13415</ID>
+ </unificationXref>
+ <complexParticipant rdf:ID="Orc4_Orc5_Orc3_Orc2_origin__nucleoplasm_2">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Orc4_Orc5_Orc3_Orc2_origin__nucleoplasm_1" />
+ </complexParticipant>
+ <complexParticipant rdf:ID="Orc1_Orc4_Orc5_Orc3_Orc2_origin__nucleoplasm_">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Orc1_Orc4_Orc5_Orc3_Orc2_origin__nucleoplasm_1" />
+ </complexParticipant>
+ <complex rdf:ID="Orc1_Orc4_Orc5_Orc3_Orc2_origin__nucleoplasm_1">
+ <COMPONENTS rdf:resource="#Orc1__nucleoplasm_1" />
+ <COMPONENTS rdf:resource="#Orc4_Orc5_Orc3_Orc2_origin__nucleoplasm_3" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Orc1:Orc4:Orc5:Orc3:Orc2:origin [nucleoplasm]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Orc1:Orc4:Orc5:Orc3:Orc2:origin</SHORT-NAME>
+ </complex>
+ <proteinParticipant rdf:ID="Orc1__nucleoplasm_1">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q13415_Origin_recognition_complex_subunit_1__Replication_control_protein_1_" />
+ </proteinParticipant>
+ <complexParticipant rdf:ID="Orc4_Orc5_Orc3_Orc2_origin__nucleoplasm_3">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Orc4_Orc5_Orc3_Orc2_origin__nucleoplasm_1" />
+ </complexParticipant>
+ <unificationXref rdf:ID="Reactome68611">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">68611</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <publicationXref rdf:ID="Pubmed_11739726">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">11739726</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2001</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mammalian Orc1 protein is selectively released from chromatin and ubiquitinated during the S-to-M transition in the cell division cycle.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Li, CJ</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DePamphilis, ML</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mol Cell Biol 22:105-16</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="Orc1_associates_with_Orc4_Orc5_Orc3_Orc2_origin_complexesStep">
+ <STEP-INTERACTIONS rdf:resource="#Orc1_associates_with_Orc4_Orc5_Orc3_Orc2_origin_complexes" />
+ <NEXT-STEP rdf:resource="#Orc6_associates_with_Orc1_Orc4_Orc5_Orc3_Orc2_origin_complexes__forming_ORC_origin_complexesStep" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="Orc6_associates_with_Orc1_Orc4_Orc5_Orc3_Orc2_origin_complexes__forming_ORC_origin_complexes">
+ <LEFT rdf:resource="#Orc1_Orc4_Orc5_Orc3_Orc2_origin__nucleoplasm_2" />
+ <LEFT rdf:resource="#Orc6__nucleoplasm_" />
+ <RIGHT rdf:resource="#ORC_origin__nucleoplasm_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Orc6 associates with Orc1:Orc4:Orc5:Orc3:Orc2:origin complexes, forming ORC:origin complexes</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Orc6 associates with Orc1:Orc4:Orc5:Orc3:Orc2:origin complexes, forming ORC:origin complexes</SHORT-NAME>
+ <XREF rdf:resource="#Reactome68615" />
+ <XREF rdf:resource="#Pubmed_11395502" />
+ <XREF rdf:resource="#Pubmed_11323433" />
+ <CELLULAR-LOCATION rdf:resource="#nucleus" />
+ </biochemicalReaction>
+ <complexParticipant rdf:ID="Orc1_Orc4_Orc5_Orc3_Orc2_origin__nucleoplasm_2">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Orc1_Orc4_Orc5_Orc3_Orc2_origin__nucleoplasm_1" />
+ </complexParticipant>
+ <proteinParticipant rdf:ID="Orc6__nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q9Y5N6_Origin_recognition_complex_subunit_6" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_Q9Y5N6_Origin_recognition_complex_subunit_6">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:Q9Y5N6 Origin recognition complex subunit 6</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ORC6L</SYNONYMS>
+ <XREF rdf:resource="#UniProt_Q9Y5N6" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Component of the origin recognition complex (ORC) that binds origins of replication. It has a role in both chromosomal replication and mating type transcriptional silencing. Binds to the ARS consensus sequence (ACS) of origins of replication in an ATP-dependent manner. SUBUNIT: ORC is composed of six subunits. SUBCELLULAR LOCATION: Nuclear. SIMILARITY: Belongs to the ORC6 family.</COMMENT>
+ </protein>
+ <unificationXref rdf:ID="UniProt_Q9Y5N6">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Q9Y5N6</ID>
+ </unificationXref>
+ <complexParticipant rdf:ID="ORC_origin__nucleoplasm_">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#ORC_origin__nucleoplasm_1" />
+ </complexParticipant>
+ <complex rdf:ID="ORC_origin__nucleoplasm_1">
+ <COMPONENTS rdf:resource="#origin_of_replication__nucleoplasm_2" />
+ <COMPONENTS rdf:resource="#Orc3__nucleoplasm_2" />
+ <COMPONENTS rdf:resource="#Orc4__nucleoplasm_2" />
+ <COMPONENTS rdf:resource="#Orc1__nucleoplasm_2" />
+ <COMPONENTS rdf:resource="#Orc5__nucleoplasm_2" />
+ <COMPONENTS rdf:resource="#Orc2__nucleoplasm_1" />
+ <COMPONENTS rdf:resource="#Orc6__nucleoplasm_1" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ORC:origin [nucleoplasm]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ORC:origin</SHORT-NAME>
+ </complex>
+ <physicalEntityParticipant rdf:ID="origin_of_replication__nucleoplasm_2">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#origin_of_replication__nucleoplasm_1" />
+ </physicalEntityParticipant>
+ <proteinParticipant rdf:ID="Orc3__nucleoplasm_2">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q9UBD5_Origin_recognition_complex_subunit_3__Origin_recognition_complex_subunit_Latheo_" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="Orc4__nucleoplasm_2">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_O43929_Origin_recognition_complex_subunit_4" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="Orc1__nucleoplasm_2">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q13415_Origin_recognition_complex_subunit_1__Replication_control_protein_1_" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="Orc5__nucleoplasm_2">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_O43913_Origin_recognition_complex_subunit_5" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="Orc2__nucleoplasm_1">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q13416_Origin_recognition_complex_subunit_2" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="Orc6__nucleoplasm_1">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q9Y5N6_Origin_recognition_complex_subunit_6" />
+ </proteinParticipant>
+ <unificationXref rdf:ID="Reactome68615">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">68615</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <pathwayStep rdf:ID="Orc6_associates_with_Orc1_Orc4_Orc5_Orc3_Orc2_origin_complexes__forming_ORC_origin_complexesStep">
+ <STEP-INTERACTIONS rdf:resource="#Orc6_associates_with_Orc1_Orc4_Orc5_Orc3_Orc2_origin_complexes__forming_ORC_origin_complexes" />
+ <NEXT-STEP rdf:resource="#Cdc6_protein_associates_with_ORC_origin_complexesStep" />
+ </pathwayStep>
+ <unificationXref rdf:ID="Reactome68616">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">68616</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <evidence rdf:ID="Summation_68618">
+ <XREF rdf:resource="#Pubmed_1579162" />
+ <XREF rdf:resource="#Pubmed_8044842" />
+ <XREF rdf:resource="#Pubmed_9372948" />
+ <XREF rdf:resource="#Pubmed_1110244" />
+ <XREF rdf:resource="#Pubmed_11739726" />
+ <XREF rdf:resource="#Pubmed_11395502" />
+ <XREF rdf:resource="#Pubmed_11323433" />
+ <XREF rdf:resource="#Pubmed_10438470" />
+ <XREF rdf:resource="#Pubmed_11278932" />
+ </evidence>
+ <publicationXref rdf:ID="Pubmed_1579162">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">1579162</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1992</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ATP-dependent recognition of eukaryotic origins of DNA replication by a multiprotein complex.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bell, SP</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Stillman, B</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Nature 357:128-34</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_8044842">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">8044842</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1994</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Two steps in the assembly of complexes at yeast replication origins in vivo.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Diffley, JF</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cocker, JH</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Dowell, SJ</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Rowley, A</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cell 78:303-16</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_9372948">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">9372948</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1997</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Architecture of the yeast origin recognition complex bound to origins of DNA replication.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Lee, DG</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bell, SP</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mol Cell Biol 17:7159-68</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_1110244">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">1110244</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1975</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Forearm blood flow during body temperature transients produced by leg exercise.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Wenger, CB</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Roberts, MF</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Stolwijk, JA</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Nadel, ER</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Appl Physiol 38:58-63</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_10438470">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">10438470</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1999</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Histone acetyltransferase HBO1 interacts with the ORC1 subunit of the human initiator protein.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Iizuka, M</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Stillman, B</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Biol Chem 274:23027-34</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_11278932">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">11278932</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2001</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Replication factors MCM2 and ORC1 interact with the histone acetyltransferase HBO1.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Burke, TW</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cook, JG</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Asano, M</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Nevins, JR</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Biol Chem 276:15397-408</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="Assembly_of_the_ORC_complex_at_the_origin_of_replicationStep">
+ <STEP-INTERACTIONS rdf:resource="#Assembly_of_the_ORC_complex_at_the_origin_of_replication" />
+ <NEXT-STEP rdf:resource="#Cdc6_association_with_the_ORC_origin_complexStep" />
+ </pathwayStep>
+ <pathway rdf:ID="Cdc6_association_with_the_ORC_origin_complex">
+ <PATHWAY-COMPONENTS rdf:resource="#Cdc6_protein_associates_with_ORC_origin_complexesStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#Cdc6_protein_is_synthesized_under_the_control_of_E2F_transcription_factorsStep" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cdc6 association with the ORC:origin complex</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cdc6 association with the ORC:origin complex</SHORT-NAME>
+ <XREF rdf:resource="#Reactome68689" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cdc6 is a regulator of DNA replication initiation in both yeasts and human cells, but its mechanism of action differs between the two systems. Genetic studies in budding yeast (S. cerevisiae) and fission yeast (S. pombe) indicate that the normal function of Cdc6 protein is required to restrict DNA replication to once per cell cycle. Specifically, Cdc6 may function as an ATPase switch linked to Mcm2-7 association with the [...]
+ <EVIDENCE rdf:resource="#Summation_68691" />
+ <CELLULAR-LOCATION rdf:resource="#nucleus" />
+ </pathway>
+ <biochemicalReaction rdf:ID="Cdc6_protein_is_synthesized_under_the_control_of_E2F_transcription_factors">
+ <RIGHT rdf:resource="#Cdc6__cytosol_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cdc6 protein is synthesized under the control of E2F transcription factors</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cdc6 protein is synthesized under the control of E2F transcription factors</SHORT-NAME>
+ <XREF rdf:resource="#Reactome68637" />
+ <XREF rdf:resource="#Pubmed_9520412" />
+ </biochemicalReaction>
+ <proteinParticipant rdf:ID="Cdc6__cytosol_">
+ <SEQUENCE-FEATURE-LIST rdf:resource="#nucleotide_binding_site" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q99741_Cell_division_control_protein_6_homolog__CDC6_related_protein___p62_cdc6____HsCDC6___HsCDC18_" />
+ </proteinParticipant>
+ <openControlledVocabulary rdf:ID="cytosol">
+ <TERM rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cytosol</TERM>
+ <XREF rdf:resource="#GO_0005829" />
+ </openControlledVocabulary>
+ <xref rdf:ID="GO_0005829">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GO</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0005829</ID>
+ </xref>
+ <sequenceFeature rdf:ID="nucleotide_binding_site">
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">nucleotide binding site</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">nucleotide binding site</SHORT-NAME>
+ <FEATURE-LOCATION rdf:resource="#SequenceInternalnull_null_" />
+ </sequenceFeature>
+ <sequenceInterval rdf:ID="SequenceInternalnull_null_" />
+ <protein rdf:ID="UniProt_Q99741_Cell_division_control_protein_6_homolog__CDC6_related_protein___p62_cdc6____HsCDC6___HsCDC18_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:Q99741 Cell division control protein 6 homolog (CDC6-related protein) (p62(cdc6)) (HsCDC6) (HsCDC18)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CDC6</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CDC18L</SYNONYMS>
+ <XREF rdf:resource="#UniProt_Q99741" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Involved in the initiation of DNA replication. Also participates in checkpoint controls that ensure DNA replication is completed before mitosis is initiated. SUBUNIT: Interacts with PCNA, ORC1L and cyclin-CDK. SUBCELLULAR LOCATION: Nuclear and cytoplasmic. The protein is nuclear in G1 and cytoplasmic in S-phase cells. SIMILARITY: Belongs to the CDC6/cdc18 family.</COMMENT>
+ </protein>
+ <unificationXref rdf:ID="UniProt_Q99741">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Q99741</ID>
+ </unificationXref>
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+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <publicationXref rdf:ID="Pubmed_9520412">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">9520412</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1998</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cdc6 is regulated by E2F and is essential for DNA replication in mammalian cells.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Yan, Z</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DeGregori, J</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Shohet, R</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Leone, G</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Stillman, B</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Nevins, JR</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Williams, RS</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Proc Natl Acad Sci U S A 95:3603-8</SOURCE>
+ </publicationXref>
+ <modulation rdf:ID="_E2F2__positively_regulates__Cdc6_protein_is_synthesized_under_the_control_of_E2F_transcription_factors_">
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">'E2F2' positively regulates 'Cdc6 protein is synthesized under the control of E2F transcription factors'</NAME>
+ <CONTROL-TYPE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ACTIVATION</CONTROL-TYPE>
+ <CONTROLLER rdf:resource="#E2F2__nucleoplasm_" />
+ <CONTROLLED rdf:resource="#Cdc6_protein_is_synthesized_under_the_control_of_E2F_transcription_factors" />
+ </modulation>
+ <proteinParticipant rdf:ID="E2F2__nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q14209_Transcription_factor_E2F2__E2F_2_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_Q14209_Transcription_factor_E2F2__E2F_2_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:Q14209 Transcription factor E2F2 (E2F-2)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">E2F2</SYNONYMS>
+ <XREF rdf:resource="#UniProt_Q14209" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Transcription activator that binds DNA cooperatively with DP proteins through the E2 recognition site, 5'-TTTC[CG]CGC- 3' found in the promoter region of a number of genes whose products are involved in cell cycle regulation or in DNA replication. The DRTF1/E2F complex functions in the control of cell-cycle progression from g1 to s phase. E2F-2 binds specifically to RB1 protein, in a cell-cycle dependent manner [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_Q14209">
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+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Q14209</ID>
+ </unificationXref>
+ <modulation rdf:ID="_E2F1__positively_regulates__Cdc6_protein_is_synthesized_under_the_control_of_E2F_transcription_factors_">
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">'E2F1' positively regulates 'Cdc6 protein is synthesized under the control of E2F transcription factors'</NAME>
+ <CONTROL-TYPE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ACTIVATION</CONTROL-TYPE>
+ <CONTROLLER rdf:resource="#E2F1__nucleoplasm_" />
+ <CONTROLLED rdf:resource="#Cdc6_protein_is_synthesized_under_the_control_of_E2F_transcription_factors" />
+ </modulation>
+ <proteinParticipant rdf:ID="E2F1__nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q01094_Transcription_factor_E2F1__E2F_1___Retinoblastoma_binding_protein_3___RBBP_3___PRB_binding_protein_E2F_1___PBR3___Retinoblastoma_associated_protein_1___RBAP_1_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_Q01094_Transcription_factor_E2F1__E2F_1___Retinoblastoma_binding_protein_3___RBBP_3___PRB_binding_protein_E2F_1___PBR3___Retinoblastoma_associated_protein_1___RBAP_1_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:Q01094 Transcription factor E2F1 (E2F-1) (Retinoblastoma binding protein 3) (RBBP-3) (PRB-binding protein E2F-1) (PBR3) (Retinoblastoma-associated protein 1) (RBAP-1)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">E2F1</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RBBP3</SYNONYMS>
+ <XREF rdf:resource="#UniProt_Q01094" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Transcription activator that binds DNA cooperatively with dp proteins through the E2 recognition site, 5'-TTTC[CG]CGC- 3' found in the promoter region of a number of genes whose products are involved in cell cycle regulation or in DNA replication. The DRTF1/E2F complex functions in the control of cell-cycle progression from G1 to S phase. E2F-1 binds preferentially RB1 protein, in a cell-cycle dependent manner. [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_Q01094">
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+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Q01094</ID>
+ </unificationXref>
+ <modulation rdf:ID="_E2F3__positively_regulates__Cdc6_protein_is_synthesized_under_the_control_of_E2F_transcription_factors_">
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">'E2F3' positively regulates 'Cdc6 protein is synthesized under the control of E2F transcription factors'</NAME>
+ <CONTROL-TYPE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ACTIVATION</CONTROL-TYPE>
+ <CONTROLLER rdf:resource="#E2F3__nucleoplasm_" />
+ <CONTROLLED rdf:resource="#Cdc6_protein_is_synthesized_under_the_control_of_E2F_transcription_factors" />
+ </modulation>
+ <proteinParticipant rdf:ID="E2F3__nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_O00716_Transcription_factor_E2F3__E2F_3_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_O00716_Transcription_factor_E2F3__E2F_3_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:O00716 Transcription factor E2F3 (E2F-3)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">E2F3</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">KIAA0075</SYNONYMS>
+ <XREF rdf:resource="#UniProt_O00716" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Transcription activator that binds DNA cooperatively with DP proteins through the E2 recognition site, 5'-TTTC[CG]CGC- 3' found in the promoter region of a number of genes whose products are involved in cell cycle regulation or in DNA replication. The DRTF1/E2F complex functions in the control of cell-cycle progression from G1 to S phase. E2F-3 binds specifically to RB1 protein, in a cell-cycle dependent manner [...]
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+ <STEP-INTERACTIONS rdf:resource="#_E2F3__positively_regulates__Cdc6_protein_is_synthesized_under_the_control_of_E2F_transcription_factors_1" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="Cdc6_protein_associates_with_ORC_origin_complexes">
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+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cdc6 protein associates with ORC:origin complexes</NAME>
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+ <complexParticipant rdf:ID="ORC_origin__nucleoplasm_2">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#ORC_origin__nucleoplasm_1" />
+ </complexParticipant>
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+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
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+ </proteinParticipant>
+ <complexParticipant rdf:ID="Cdc6_ORC_origin_complex__nucleoplasm_">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Cdc6_ORC_origin_complex__nucleoplasm_1" />
+ </complexParticipant>
+ <complex rdf:ID="Cdc6_ORC_origin_complex__nucleoplasm_1">
+ <COMPONENTS rdf:resource="#ORC_origin__nucleoplasm_3" />
+ <COMPONENTS rdf:resource="#Cdc6__nucleoplasm_1" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cdc6:ORC:origin complex [nucleoplasm]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cdc6:ORC:origin complex</SHORT-NAME>
+ </complex>
+ <complexParticipant rdf:ID="ORC_origin__nucleoplasm_3">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#ORC_origin__nucleoplasm_1" />
+ </complexParticipant>
+ <proteinParticipant rdf:ID="Cdc6__nucleoplasm_1">
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+ <SEQUENCE-FEATURE-LIST rdf:resource="#nucleotide_binding_site" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q99741_Cell_division_control_protein_6_homolog__CDC6_related_protein___p62_cdc6____HsCDC6___HsCDC18_" />
+ </proteinParticipant>
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+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <pathwayStep rdf:ID="Cdc6_protein_associates_with_ORC_origin_complexesStep">
+ <STEP-INTERACTIONS rdf:resource="#Cdc6_protein_associates_with_ORC_origin_complexes" />
+ <NEXT-STEP rdf:resource="#Free_Cdt1_associates_with_Cdc6_ORC_origin_complexesStep" />
+ </pathwayStep>
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+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
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+ <evidence rdf:ID="Summation_68691">
+ <XREF rdf:resource="#Pubmed_10801458" />
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+ <XREF rdf:resource="#Pubmed_9889196" />
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+ </evidence>
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+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2000</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ATPase switches controlling DNA replication initiation.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Lee, DG</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bell, SP</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Curr Opin Cell Biol 12:280-5</SOURCE>
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+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1995</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cdc6 is an unstable protein whose de novo synthesis in G1 is important for the onset of S phase and for preventing a 'reductional' anaphase in the budding yeast Saccharomyces cerevisiae.</TITLE>
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+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Lengauer, C</AUTHORS>
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+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">EMBO J 14:3788-99</SOURCE>
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+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The Cdc4/34/53 pathway targets Cdc6p for proteolysis in budding yeast.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Drury, LS</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Perkins, G</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Diffley, JF</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">EMBO J 16:5966-76</SOURCE>
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+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Diffley, JF</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Curr Biol 10:231-40</SOURCE>
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+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Separate SCF(CDC4) recognition elements target Cdc6 for proteolysis in S phase and mitosis.</TITLE>
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+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Diffley, JF</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">EMBO J 20:4836-45</SOURCE>
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+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cell cycle- and cell growth-regulated proteolysis of mammalian CDC6 is dependent on APC-CDH1.</TITLE>
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+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Melixetian, M</AUTHORS>
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+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Helin, K</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Genes Dev 14:2330-43</SOURCE>
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+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mol Cell Biol 18:2758-67</SOURCE>
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+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Multistep regulation of DNA replication by Cdk phosphorylation of HsCdc6.</TITLE>
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+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Hunter, T</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Proc Natl Acad Sci U S A 96:6193-8</SOURCE>
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+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Phosphorylation of mammalian CDC6 by cyclin A/CDK2 regulates its subcellular localization.</TITLE>
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+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Helin, K</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">EMBO J 18:396-410</SOURCE>
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+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Initiation protein Cdt1 was first identified in X. laevis, where it has been shown to be the second component of licensing factor (RLF-B) and in S. pombe. Cdt1 homologs have been identified in D. melanogaster, humans, and S. cerevisiae. Genetic studies in S. pombe have shown that binding of Cdc6 to chromatin requires the prior binding of Cdc18, the S. pombe homolog of Cdc6. In humans, the function of Cdt1 is regulated du [...]
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+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The geminin component of geminin:Cdt1 complexes is ubiquitinated, releasing Cdt1</SHORT-NAME>
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+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#_26S_proteasome__cytosol_1" />
+ </complexParticipant>
+ <complex rdf:ID="_26S_proteasome__cytosol_1">
+ <COMPONENTS rdf:resource="#Proteasome_subunit_beta_type_8__cytosol_" />
+ <COMPONENTS rdf:resource="#Proteasome_subunit_beta_type_9__cytosol_" />
+ <COMPONENTS rdf:resource="#Proteasome_activator_complex_subunit_2__cytosol_" />
+ <COMPONENTS rdf:resource="#_26S_proteasome_non_ATPase_regulatory_subunit_6__cytosol_" />
+ <COMPONENTS rdf:resource="#_26S_proteasome_non_ATPase_regulatory_subunit_10__cytosol_" />
+ <COMPONENTS rdf:resource="#_26S_protease_regulatory_subunit_7__cytosol_" />
+ <COMPONENTS rdf:resource="#Probable_26S_protease_regulatory_subunit_8__cytosol_" />
+ <COMPONENTS rdf:resource="#_26S_proteasome_non_ATPase_regulatory_subunit_12__cytosol_" />
+ <COMPONENTS rdf:resource="#Proteasome_subunit_alpha_type_4___cytosol_" />
+ <COMPONENTS rdf:resource="#Proteasome_subunit_alpha_type_3___cytosol_" />
+ <COMPONENTS rdf:resource="#_26S_proteasome_non_ATPase_regulatory_subunit_1__cytosol_" />
+ <COMPONENTS rdf:resource="#_26S_proteasome_non_ATPase_regulatory_subunit_4__cytosol_" />
+ <COMPONENTS rdf:resource="#_26S_protease_regulatory_subunit_6A__cytosol_" />
+ <COMPONENTS rdf:resource="#Proteasome_activator_complex_subunit_3__cytosol_" />
+ <COMPONENTS rdf:resource="#_26S_proteasome_non_ATPase_regulatory_subunit_8__cytosol_" />
+ <COMPONENTS rdf:resource="#Proteasome_subunit_beta_type_4__cytosol_" />
+ <COMPONENTS rdf:resource="#Proteasome_subunit_alpha_type_7___cytosol_" />
+ <COMPONENTS rdf:resource="#_26S_proteasome_non_ATPase_regulatory_subunit_7__cytosol_" />
+ <COMPONENTS rdf:resource="#Proteasome_subunit_beta_type_3___cytosol_" />
+ <COMPONENTS rdf:resource="#_26S_proteasome_associated_pad1_homolog__cytosol_" />
+ <COMPONENTS rdf:resource="#_26S_protease_regulatory_subunit_4__cytosol_" />
+ <COMPONENTS rdf:resource="#_26S_protease_regulatory_subunit_6B__cytosol_" />
+ <COMPONENTS rdf:resource="#Proteasome_subunit_alpha_type_5___cytosol_" />
+ <COMPONENTS rdf:resource="#Proteasome_subunit_beta_type_7__cytosol_" />
+ <COMPONENTS rdf:resource="#Proteasome_subunit_beta_type_5__cytosol_" />
+ <COMPONENTS rdf:resource="#_26S_proteasome_non_ATPase_regulatory_subunit_13__cytosol_" />
+ <COMPONENTS rdf:resource="#Proteasome_subunit_beta_type_2___cytosol_" />
+ <COMPONENTS rdf:resource="#_26S_proteasome_non_ATPase_regulatory_subunit_5__cytosol_" />
+ <COMPONENTS rdf:resource="#_26S_proteasome_non_ATPase_regulatory_subunit_2__cytosol_" />
+ <COMPONENTS rdf:resource="#Proteasome_subunit_alpha_type_6___cytosol_" />
+ <COMPONENTS rdf:resource="#_26S_proteasome_non_ATPase_regulatory_subunit_9__cytosol_" />
+ <COMPONENTS rdf:resource="#Proteasome_subunit_beta_type_10__cytosol_" />
+ <COMPONENTS rdf:resource="#Proteasome_subunit_beta_type_6__cytosol_" />
+ <COMPONENTS rdf:resource="#_26S_protease_regulatory_subunit_S10B__cytosol_" />
+ <COMPONENTS rdf:resource="#Proteasome_subunit_beta_type_1___cytosol_" />
+ <COMPONENTS rdf:resource="#_26S_proteasome_non_ATPase_regulatory_subunit_11__cytosol_" />
+ <COMPONENTS rdf:resource="#Proteasome_subunit_alpha_type_2___cytosol_" />
+ <COMPONENTS rdf:resource="#Proteasome_inhibitor_PI31_subunit__cytosol_" />
+ <COMPONENTS rdf:resource="#Proteasome_subunit_alpha_type_1___cytosol_" />
+ <COMPONENTS rdf:resource="#_26S_proteasome_non_ATPase_regulatory_subunit_3__cytosol_" />
+ <COMPONENTS rdf:resource="#Proteasome_activator_complex_subunit_1__cytosol_" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">26S proteasome [cytosol]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">26S proteasome</SHORT-NAME>
+ </complex>
+ <proteinParticipant rdf:ID="Proteasome_subunit_beta_type_8__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P28062_1_Proteasome_subunit_beta_type_8_precursor__EC_3_4_25_1___Proteasome_component_C13___Macropain_subunit_C13___Multicatalytic_endopeptidase_complex_subunit_C13_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_P28062_1_Proteasome_subunit_beta_type_8_precursor__EC_3_4_25_1___Proteasome_component_C13___Macropain_subunit_C13___Multicatalytic_endopeptidase_complex_subunit_C13_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P28062-1 Proteasome subunit beta type 8 precursor (EC 3.4.25.1) (Proteasome component C13) (Macropain subunit C13) (Multicatalytic endopeptidase complex subunit C13)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PSMB8</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RING10</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">LMP7</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Y2</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P28062" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: The proteasome is a multicatalytic proteinase complex which is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. The proteasome has an ATP-dependent proteolytic activity. This subunit is involved in antigen processing to generate class I binding peptides. CATALYTIC ACTIVITY: Cleavage of peptide bonds with very broad sp [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_P28062">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P28062</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="Proteasome_subunit_beta_type_9__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P28065_1_Proteasome_subunit_beta_type_9_precursor__EC_3_4_25_1___Proteasome_chain_7___Macropain_chain_7___Multicatalytic_endopeptidase_complex_chain_7___RING12_protein___Low_molecular_mass_protein_2_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_P28065_1_Proteasome_subunit_beta_type_9_precursor__EC_3_4_25_1___Proteasome_chain_7___Macropain_chain_7___Multicatalytic_endopeptidase_complex_chain_7___RING12_protein___Low_molecular_mass_protein_2_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P28065-1 Proteasome subunit beta type 9 precursor (EC 3.4.25.1) (Proteasome chain 7) (Macropain chain 7) (Multicatalytic endopeptidase complex chain 7) (RING12 protein) (Low molecular mass protein 2)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PSMB9</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RING12</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">LMP2</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P28065" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: The proteasome is a multicatalytic proteinase complex which is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. The proteasome has an ATP-dependent proteolytic activity. This subunit is involved in antigen processing to generate class I binding peptides. CATALYTIC ACTIVITY: Cleavage of peptide bonds with very broad sp [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_P28065">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P28065</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="Proteasome_activator_complex_subunit_2__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q9UL46_Proteasome_activator_complex_subunit_2__Proteasome_activator_28_beta_subunit___PA28beta___PA28b___Activator_of_multicatalytic_protease_subunit_2___11S_regulator_complex_beta_subunit___REG_beta_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_Q9UL46_Proteasome_activator_complex_subunit_2__Proteasome_activator_28_beta_subunit___PA28beta___PA28b___Activator_of_multicatalytic_protease_subunit_2___11S_regulator_complex_beta_subunit___REG_beta_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:Q9UL46 Proteasome activator complex subunit 2 (Proteasome activator 28-beta subunit) (PA28beta) (PA28b) (Activator of multicatalytic protease subunit 2) (11S regulator complex beta subunit) (REG-beta)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PSME2</SYNONYMS>
+ <XREF rdf:resource="#UniProt_Q9UL46" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Implicated in immunoproteasome assembly and required for efficient antigen processing. The PA28 activator complex enhances the generation of class I binding peptides by altering the cleavage pattern of the proteasome. SUBUNIT: Heterodimer of PSME1 and PSME2, which forms a hexadimeric ring. INDUCTION: By interferon gamma. SIMILARITY: Belongs to the PA28 family.</COMMENT>
+ </protein>
+ <unificationXref rdf:ID="UniProt_Q9UL46">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Q9UL46</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="_26S_proteasome_non_ATPase_regulatory_subunit_6__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q15008_26S_proteasome_non_ATPase_regulatory_subunit_6__26S_proteasome_regulatory_subunit_S10___p42A___Proteasome_regulatory_particle_subunit_p44S10___Phosphonoformate_immuno_associated_protein_4___Breast_cancer_associated_protein_SGA_113M_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_Q15008_26S_proteasome_non_ATPase_regulatory_subunit_6__26S_proteasome_regulatory_subunit_S10___p42A___Proteasome_regulatory_particle_subunit_p44S10___Phosphonoformate_immuno_associated_protein_4___Breast_cancer_associated_protein_SGA_113M_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:Q15008 26S proteasome non-ATPase regulatory subunit 6 (26S proteasome regulatory subunit S10) (p42A) (Proteasome regulatory particle subunit p44S10) (Phosphonoformate immuno-associated protein 4) (Breast cancer associated protein SGA-113M)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PFAAP4</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PSMD6</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">KIAA0107</SYNONYMS>
+ <XREF rdf:resource="#UniProt_Q15008" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Acts as a regulatory subunit of the 26S proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins. SUBUNIT: Component of the PA700 complex. SIMILARITY: Contains 1 PCI domain.</COMMENT>
+ </protein>
+ <unificationXref rdf:ID="UniProt_Q15008">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Q15008</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="_26S_proteasome_non_ATPase_regulatory_subunit_10__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_O75832_26S_proteasome_non_ATPase_regulatory_subunit_10__26S_proteasome_regulatory_subunit_p28___Gankyrin_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_O75832_26S_proteasome_non_ATPase_regulatory_subunit_10__26S_proteasome_regulatory_subunit_p28___Gankyrin_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:O75832 26S proteasome non-ATPase regulatory subunit 10 (26S proteasome regulatory subunit p28) (Gankyrin)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PSMD10</SYNONYMS>
+ <XREF rdf:resource="#UniProt_O75832" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Acts as a regulatory subunit of the 26S proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins. SUBUNIT: Component of the PA700 complex. SIMILARITY: Contains 5 ANK repeats.</COMMENT>
+ </protein>
+ <unificationXref rdf:ID="UniProt_O75832">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">O75832</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="_26S_protease_regulatory_subunit_7__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P35998_26S_protease_regulatory_subunit_7__MSS1_protein_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_P35998_26S_protease_regulatory_subunit_7__MSS1_protein_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P35998 26S protease regulatory subunit 7 (MSS1 protein)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PSMC2</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">MSS1</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P35998" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: The 26S protease is involved in the ATP-dependent degradation of ubiquitinated proteins. The regulatory (or ATPase) complex confers ATP dependency and substrate specificity to the 26S complex. Positive modulator of Tat-mediated transactivation. SUBUNIT: Interacts with the HIV-1 Tat transactivator. SUBCELLULAR LOCATION: Cytoplasmic and nuclear. SIMILARITY: Belongs to the AAA ATPase family.</COMMENT>
+ </protein>
+ <unificationXref rdf:ID="UniProt_P35998">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P35998</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="Probable_26S_protease_regulatory_subunit_8__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_O43208" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_O43208">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:O43208</NAME>
+ <XREF rdf:resource="#UniProt_O432081" />
+ </protein>
+ <unificationXref rdf:ID="UniProt_O432081">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">O43208</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="_26S_proteasome_non_ATPase_regulatory_subunit_12__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_O00232_26S_proteasome_non_ATPase_regulatory_subunit_12__26S_proteasome_regulatory_subunit_p55_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_O00232_26S_proteasome_non_ATPase_regulatory_subunit_12__26S_proteasome_regulatory_subunit_p55_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:O00232 26S proteasome non-ATPase regulatory subunit 12 (26S proteasome regulatory subunit p55)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PSMD12</SYNONYMS>
+ <XREF rdf:resource="#UniProt_O00232" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Acts as a regulatory subunit of the 26S proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins. SUBUNIT: Component of the PA700 complex. SIMILARITY: Contains 1 PCI domain.</COMMENT>
+ </protein>
+ <unificationXref rdf:ID="UniProt_O00232">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">O00232</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="Proteasome_subunit_alpha_type_4___cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P25789_Proteasome_subunit_alpha_type_4__EC_3_4_25_1___Proteasome_component_C9___Macropain_subunit_C9___Multicatalytic_endopeptidase_complex_subunit_C9___Proteasome_subunit_L_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_P25789_Proteasome_subunit_alpha_type_4__EC_3_4_25_1___Proteasome_component_C9___Macropain_subunit_C9___Multicatalytic_endopeptidase_complex_subunit_C9___Proteasome_subunit_L_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P25789 Proteasome subunit alpha type 4 (EC 3.4.25.1) (Proteasome component C9) (Macropain subunit C9) (Multicatalytic endopeptidase complex subunit C9) (Proteasome subunit L)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PSC9</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PSMA4</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P25789" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: The proteasome is a multicatalytic proteinase complex which is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. The proteasome has an ATP-dependent proteolytic activity. CATALYTIC ACTIVITY: Cleavage of peptide bonds with very broad specificity. PATHWAY: Involved in an ATP/ubiquitin-dependent non-lysosomal proteolytic [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_P25789">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P25789</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="Proteasome_subunit_alpha_type_3___cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P25788_1_Proteasome_subunit_alpha_type_3__EC_3_4_25_1___Proteasome_component_C8___Macropain_subunit_C8___Multicatalytic_endopeptidase_complex_subunit_C8_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_P25788_1_Proteasome_subunit_alpha_type_3__EC_3_4_25_1___Proteasome_component_C8___Macropain_subunit_C8___Multicatalytic_endopeptidase_complex_subunit_C8_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P25788-1 Proteasome subunit alpha type 3 (EC 3.4.25.1) (Proteasome component C8) (Macropain subunit C8) (Multicatalytic endopeptidase complex subunit C8)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PSC8</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PSMA3</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P25788" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: The proteasome is a multicatalytic proteinase complex which is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. The proteasome has an ATP-dependent proteolytic activity. CATALYTIC ACTIVITY: Cleavage of peptide bonds with very broad specificity. PATHWAY: Involved in an ATP/ubiquitin-dependent non-lysosomal proteolytic [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_P25788">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P25788</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="_26S_proteasome_non_ATPase_regulatory_subunit_1__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q99460_1_26S_proteasome_non_ATPase_regulatory_subunit_1__26S_proteasome_regulatory_subunit_RPN2___26S_proteasome_regulatory_subunit_S1___26S_proteasome_subunit_p112_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_Q99460_1_26S_proteasome_non_ATPase_regulatory_subunit_1__26S_proteasome_regulatory_subunit_RPN2___26S_proteasome_regulatory_subunit_S1___26S_proteasome_subunit_p112_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:Q99460-1 26S proteasome non-ATPase regulatory subunit 1 (26S proteasome regulatory subunit RPN2) (26S proteasome regulatory subunit S1) (26S proteasome subunit p112)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PSMD1</SYNONYMS>
+ <XREF rdf:resource="#UniProt_Q99460" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Acts as a regulatory subunit of the 26 proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins. ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=Q99460-1; Sequence=Displayed; Name=2; IsoId=Q99460-2; Sequence=VSP_011475; Note=No experimental confirmation available; SIMILARITY: Belongs to the proteasome subunit S1 family. SIMILARITY: Contains 10 PC [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_Q99460">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Q99460</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="_26S_proteasome_non_ATPase_regulatory_subunit_4__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P55036_1_26S_proteasome_non_ATPase_regulatory_subunit_4__26S_proteasome_regulatory_subunit_S5A___Rpn10___Multiubiquitin_chain_binding_protein___Antisecretory_factor_1___AF___ASF_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_P55036_1_26S_proteasome_non_ATPase_regulatory_subunit_4__26S_proteasome_regulatory_subunit_S5A___Rpn10___Multiubiquitin_chain_binding_protein___Antisecretory_factor_1___AF___ASF_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P55036-1 26S proteasome non-ATPase regulatory subunit 4 (26S proteasome regulatory subunit S5A) (Rpn10) (Multiubiquitin chain binding protein) (Antisecretory factor-1) (AF) (ASF)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">MCB1</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PSMD4</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P55036" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Binds and presumably selects ubiquitin-conjugates for destruction. Modulates intestinal fluid secretion. SUBUNIT: The 26S proteasome is composed of a core protease, known as the 20S proteasome, capped at one or both ends by the 19S regulatory complex (RC). The RC is composed of at least 18 different subunits in two subcomplexes, the base and the lid, which form the portions proximal and distal to the 20S proteo [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_P55036">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P55036</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="_26S_protease_regulatory_subunit_6A__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P17980_26S_protease_regulatory_subunit_6A__TAT_binding_protein_1___TBP_1___Proteasome_subunit_P50_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_P17980_26S_protease_regulatory_subunit_6A__TAT_binding_protein_1___TBP_1___Proteasome_subunit_P50_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P17980 26S protease regulatory subunit 6A (TAT-binding protein 1) (TBP-1) (Proteasome subunit P50)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PSMC3</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TBP1</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P17980" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: The 26S protease is involved in the ATP-dependent degradation of ubiquitinated proteins. The regulatory (or ATPase) complex confers ATP dependency and substrate specificity to the 26S complex (By similarity). FUNCTION: Interacts with the human immunodeficiency virus tat transactivator. Specifically suppresses tat-mediated transactivation. Probably involved in ATP hydrolysis. It is possible that proteins MSS1 an [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_P17980">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P17980</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="Proteasome_activator_complex_subunit_3__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P61289_1_Proteasome_activator_complex_subunit_3__Proteasome_activator_28_gamma_subunit___PA28gamma___PA28g___Activator_of_multicatalytic_protease_subunit_3___11S_regulator_complex_gamma_subunit___REG_gamma___Ki_nuclear_autoantigen_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_P61289_1_Proteasome_activator_complex_subunit_3__Proteasome_activator_28_gamma_subunit___PA28gamma___PA28g___Activator_of_multicatalytic_protease_subunit_3___11S_regulator_complex_gamma_subunit___REG_gamma___Ki_nuclear_autoantigen_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P61289-1 Proteasome activator complex subunit 3 (Proteasome activator 28-gamma subunit) (PA28gamma) (PA28g) (Activator of multicatalytic protease subunit 3) (11S regulator complex gamma subunit) (REG-gamma) (Ki nuclear autoantigen)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PSME3</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P61289" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Implicated in immunoproteasome assembly and required for efficient antigen processing. The PA28 activator complex enhances the generation of class I binding peptides by altering the cleavage pattern of the proteasome. SUBUNIT: Homohexamer. ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=P61289-1, Q12920-1; Sequence=Displayed; Name=2; IsoId=P61289-2, Q12920-2; Sequence=VSP_00451 [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_P61289">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P61289</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="_26S_proteasome_non_ATPase_regulatory_subunit_8__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P48556_26S_proteasome_non_ATPase_regulatory_subunit_8__26S_proteasome_regulatory_subunit_S14___p31_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_P48556_26S_proteasome_non_ATPase_regulatory_subunit_8__26S_proteasome_regulatory_subunit_S14___p31_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P48556 26S proteasome non-ATPase regulatory subunit 8 (26S proteasome regulatory subunit S14) (p31)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PSMD8</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P48556" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Acts as a regulatory subunit of the 26S proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins. Necessary for activation of the CDC28 kinase. SIMILARITY: Belongs to the proteasome subunit S14 family.</COMMENT>
+ </protein>
+ <unificationXref rdf:ID="UniProt_P48556">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P48556</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="Proteasome_subunit_beta_type_4__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P28070_Proteasome_subunit_beta_type_4_precursor__EC_3_4_25_1___Proteasome_beta_chain___Macropain_beta_chain___Multicatalytic_endopeptidase_complex_beta_chain___Proteasome_chain_3___HSN3___HsBPROS26_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_P28070_Proteasome_subunit_beta_type_4_precursor__EC_3_4_25_1___Proteasome_beta_chain___Macropain_beta_chain___Multicatalytic_endopeptidase_complex_beta_chain___Proteasome_chain_3___HSN3___HsBPROS26_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P28070 Proteasome subunit beta type 4 precursor (EC 3.4.25.1) (Proteasome beta chain) (Macropain beta chain) (Multicatalytic endopeptidase complex beta chain) (Proteasome chain 3) (HSN3) (HsBPROS26)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PSMB4</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P28070" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: The proteasome is a multicatalytic proteinase complex which is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. The proteasome has an ATP-dependent proteolytic activity. CATALYTIC ACTIVITY: Cleavage of peptide bonds with very broad specificity. PATHWAY: Involved in an ATP/ubiquitin-dependent non-lysosomal proteolytic [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_P28070">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P28070</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="Proteasome_subunit_alpha_type_7___cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_O14818_1_Proteasome_subunit_alpha_type_7__EC_3_4_25_1___Proteasome_subunit_RC6__1___Proteasome_subunit_XAPC7_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_O14818_1_Proteasome_subunit_alpha_type_7__EC_3_4_25_1___Proteasome_subunit_RC6__1___Proteasome_subunit_XAPC7_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:O14818-1 Proteasome subunit alpha type 7 (EC 3.4.25.1) (Proteasome subunit RC6- 1) (Proteasome subunit XAPC7)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PSMA7</SYNONYMS>
+ <XREF rdf:resource="#UniProt_O14818" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: The proteasome is a multicatalytic proteinase complex which is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. The proteasome has an ATP-dependent proteolytic activity. CATALYTIC ACTIVITY: Cleavage of peptide bonds with very broad specificity. PATHWAY: Involved in an ATP/ubiquitin-dependent non-lysosomal proteolytic [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_O14818">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">O14818</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="_26S_proteasome_non_ATPase_regulatory_subunit_7__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P51665_26S_proteasome_non_ATPase_regulatory_subunit_7__26S_proteasome_regulatory_subunit_rpn8___26S_proteasome_regulatory_subunit_S12___Proteasome_subunit_p40___Mov34_protein_homolog_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_P51665_26S_proteasome_non_ATPase_regulatory_subunit_7__26S_proteasome_regulatory_subunit_rpn8___26S_proteasome_regulatory_subunit_S12___Proteasome_subunit_p40___Mov34_protein_homolog_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P51665 26S proteasome non-ATPase regulatory subunit 7 (26S proteasome regulatory subunit rpn8) (26S proteasome regulatory subunit S12) (Proteasome subunit p40) (Mov34 protein homolog)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PSMD7</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">MOV34L</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P51665" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Acts as a regulatory subunit of the 26S proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins. SIMILARITY: Contains 1 MPN (JAB/Mov34) domain.</COMMENT>
+ </protein>
+ <unificationXref rdf:ID="UniProt_P51665">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P51665</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="Proteasome_subunit_beta_type_3___cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P49720_Proteasome_subunit_beta_type_3__EC_3_4_25_1___Proteasome_theta_chain___Proteasome_chain_13___Proteasome_component_C10_II_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_P49720_Proteasome_subunit_beta_type_3__EC_3_4_25_1___Proteasome_theta_chain___Proteasome_chain_13___Proteasome_component_C10_II_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P49720 Proteasome subunit beta type 3 (EC 3.4.25.1) (Proteasome theta chain) (Proteasome chain 13) (Proteasome component C10-II)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PSMB3</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P49720" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: The proteasome is a multicatalytic proteinase complex which is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. The proteasome has an ATP-dependent proteolytic activity. CATALYTIC ACTIVITY: Cleavage of peptide bonds with very broad specificity. PATHWAY: Involved in an ATP/ubiquitin-dependent non-lysosomal proteolytic [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_P49720">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P49720</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="_26S_proteasome_associated_pad1_homolog__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_O00487_26S_proteasome_non_ATPase_regulatory_subunit_14__26S_proteasome_regulatory_subunit_rpn11___26S_proteasome_associated_PAD1_homolog_1_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_O00487_26S_proteasome_non_ATPase_regulatory_subunit_14__26S_proteasome_regulatory_subunit_rpn11___26S_proteasome_associated_PAD1_homolog_1_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:O00487 26S proteasome non-ATPase regulatory subunit 14 (26S proteasome regulatory subunit rpn11) (26S proteasome-associated PAD1 homolog 1)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">POH1</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PSMD14</SYNONYMS>
+ <XREF rdf:resource="#UniProt_O00487" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Acts as a regulatory subunit of the 26S proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins. SUBUNIT: Component of the 19S regulatory cap of the 26S proteasome. TISSUE SPECIFICITY: Widely expressed. Highest levels in heart and skeletal muscle. SIMILARITY: Contains 1 MPN (JAB/Mov34) domain.</COMMENT>
+ </protein>
+ <unificationXref rdf:ID="UniProt_O00487">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">O00487</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="_26S_protease_regulatory_subunit_4__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P62191_26S_protease_regulatory_subunit_4__P26s4___Proteasome_26S_subunit_ATPase_1_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_P62191_26S_protease_regulatory_subunit_4__P26s4___Proteasome_26S_subunit_ATPase_1_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P62191 26S protease regulatory subunit 4 (P26s4) (Proteasome 26S subunit ATPase 1)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PSMC1</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P62191" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: The 26S protease is involved in the ATP-dependent degradation of ubiquitinated proteins. The regulatory (or ATPase) complex confers ATP dependency and substrate specificity to the 26S complex. SUBUNIT: Interacts with SCA7. SUBCELLULAR LOCATION: Cytoplasmic and nuclear. SIMILARITY: Belongs to the AAA ATPase family.</COMMENT>
+ </protein>
+ <unificationXref rdf:ID="UniProt_P62191">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P62191</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="_26S_protease_regulatory_subunit_6B__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P43686_1_26S_protease_regulatory_subunit_6B__MIP224___MB67_interacting_protein___TAT_binding_protein_7___TBP_7_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_P43686_1_26S_protease_regulatory_subunit_6B__MIP224___MB67_interacting_protein___TAT_binding_protein_7___TBP_7_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P43686-1 26S protease regulatory subunit 6B (MIP224) (MB67 interacting protein) (TAT-binding protein-7) (TBP-7)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PSMC4</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TBP7</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P43686" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: The 26S protease is involved in the ATP-dependent degradation of ubiquitinated proteins. The regulatory (or ATPase) complex confers ATP dependency and substrate specificity to the 26S complex. SUBCELLULAR LOCATION: Cytoplasmic and nuclear. ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=P43686-1; Sequence=Displayed; Name=2; IsoId=P43686-2; Sequence=VSP_000022; Note=No experimen [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_P43686">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P43686</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="Proteasome_subunit_alpha_type_5___cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P28066_Proteasome_subunit_alpha_type_5__EC_3_4_25_1___Proteasome_zeta_chain___Macropain_zeta_chain___Multicatalytic_endopeptidase_complex_zeta_chain_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_P28066_Proteasome_subunit_alpha_type_5__EC_3_4_25_1___Proteasome_zeta_chain___Macropain_zeta_chain___Multicatalytic_endopeptidase_complex_zeta_chain_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P28066 Proteasome subunit alpha type 5 (EC 3.4.25.1) (Proteasome zeta chain) (Macropain zeta chain) (Multicatalytic endopeptidase complex zeta chain)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PSMA5</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P28066" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: The proteasome is a multicatalytic proteinase complex which is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. The proteasome has an ATP-dependent proteolytic activity. CATALYTIC ACTIVITY: Cleavage of peptide bonds with very broad specificity. PATHWAY: Involved in an ATP/ubiquitin-dependent non-lysosomal proteolytic [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_P28066">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P28066</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="Proteasome_subunit_beta_type_7__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q99436_Proteasome_subunit_beta_type_7_precursor__EC_3_4_25_1___Proteasome_subunit_Z___Macropain_chain_Z___Multicatalytic_endopeptidase_complex_chain_Z_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_Q99436_Proteasome_subunit_beta_type_7_precursor__EC_3_4_25_1___Proteasome_subunit_Z___Macropain_chain_Z___Multicatalytic_endopeptidase_complex_chain_Z_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:Q99436 Proteasome subunit beta type 7 precursor (EC 3.4.25.1) (Proteasome subunit Z) (Macropain chain Z) (Multicatalytic endopeptidase complex chain Z)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PSMB7</SYNONYMS>
+ <XREF rdf:resource="#UniProt_Q99436" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: The proteasome is a multicatalytic proteinase complex which is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. The proteasome has an ATP-dependent proteolytic activity. CATALYTIC ACTIVITY: Cleavage of peptide bonds with very broad specificity. PATHWAY: Involved in an ATP/ubiquitin-dependent non-lysosomal proteolytic [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_Q99436">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Q99436</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="Proteasome_subunit_beta_type_5__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P28074_Proteasome_subunit_beta_type_5_precursor__EC_3_4_25_1___Proteasome_epsilon_chain___Macropain_epsilon_chain___Multicatalytic_endopeptidase_complex_epsilon_chain___Proteasome_subunit_X___Proteasome_chain_6___Proteasome_subunit_MB1_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_P28074_Proteasome_subunit_beta_type_5_precursor__EC_3_4_25_1___Proteasome_epsilon_chain___Macropain_epsilon_chain___Multicatalytic_endopeptidase_complex_epsilon_chain___Proteasome_subunit_X___Proteasome_chain_6___Proteasome_subunit_MB1_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P28074 Proteasome subunit beta type 5 precursor (EC 3.4.25.1) (Proteasome epsilon chain) (Macropain epsilon chain) (Multicatalytic endopeptidase complex epsilon chain) (Proteasome subunit X) (Proteasome chain 6) (Proteasome subunit MB1)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">LMPX</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PSMB5</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P28074" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: The proteasome is a multicatalytic proteinase complex which is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. The proteasome has an ATP-dependent proteolytic activity. May catalyze basal processing of intracellular antigens. CATALYTIC ACTIVITY: Cleavage of peptide bonds with very broad specificity. PATHWAY: Involved [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_P28074">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P28074</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="_26S_proteasome_non_ATPase_regulatory_subunit_13__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q9UNM6_26S_proteasome_non_ATPase_regulatory_subunit_13__26S_proteasome_regulatory_subunit_S11___26S_proteasome_regulatory_subunit_p40_5_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_Q9UNM6_26S_proteasome_non_ATPase_regulatory_subunit_13__26S_proteasome_regulatory_subunit_S11___26S_proteasome_regulatory_subunit_p40_5_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:Q9UNM6 26S proteasome non-ATPase regulatory subunit 13 (26S proteasome regulatory subunit S11) (26S proteasome regulatory subunit p40.5)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PSMD13</SYNONYMS>
+ <XREF rdf:resource="#UniProt_Q9UNM6" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Acts as a regulatory subunit of the 26S proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins. SUBUNIT: Component of the PA700 complex. SIMILARITY: Contains 1 PCI domain.</COMMENT>
+ </protein>
+ <unificationXref rdf:ID="UniProt_Q9UNM6">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Q9UNM6</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="Proteasome_subunit_beta_type_2___cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P49721_Proteasome_subunit_beta_type_2__EC_3_4_25_1___Proteasome_component_C7__I___Macropain_subunit_C7_I___Multicatalytic_endopeptidase_complex_subunit_C7_I_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_P49721_Proteasome_subunit_beta_type_2__EC_3_4_25_1___Proteasome_component_C7__I___Macropain_subunit_C7_I___Multicatalytic_endopeptidase_complex_subunit_C7_I_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P49721 Proteasome subunit beta type 2 (EC 3.4.25.1) (Proteasome component C7- I) (Macropain subunit C7-I) (Multicatalytic endopeptidase complex subunit C7-I)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PSMB2</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P49721" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: The proteasome is a multicatalytic proteinase complex which is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. The proteasome has an ATP-dependent proteolytic activity. This subunit has a chymotrypsin-like activity. CATALYTIC ACTIVITY: Cleavage of peptide bonds with very broad specificity. PATHWAY: Involved in an ATP [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_P49721">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P49721</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="_26S_proteasome_non_ATPase_regulatory_subunit_5__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q16401_26S_proteasome_non_ATPase_regulatory_subunit_5__26S_proteasome_subunit_S5B___26S_protease_subunit_S5_basic_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_Q16401_26S_proteasome_non_ATPase_regulatory_subunit_5__26S_proteasome_subunit_S5B___26S_protease_subunit_S5_basic_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:Q16401 26S proteasome non-ATPase regulatory subunit 5 (26S proteasome subunit S5B) (26S protease subunit S5 basic)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PSMD5</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">KIAA0072</SYNONYMS>
+ <XREF rdf:resource="#UniProt_Q16401" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Belongs to the 26S multisubunit protease, which is required for ubiquitin-dependent proteolysis. Does not bind ubiquitin polymers. SUBUNIT: 26S protease is composed of a multicatalytic protease (proteasome) and a regulatory ATPase complex. Both are multisubunit structures that associate in the presence of ATP to form the protease. Subunit S5B is part of the regulatory complex. DOMAIN: Rich in dileucine repeats, [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_Q16401">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Q16401</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="_26S_proteasome_non_ATPase_regulatory_subunit_2__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q13200_26S_proteasome_non_ATPase_regulatory_subunit_2__26S_proteasome_regulatory_subunit_RPN1___26S_proteasome_regulatory_subunit_S2___26S_proteasome_subunit_p97___Tumor_necrosis_factor_type_1_receptor_associated_protein_2___55_11_protein_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_Q13200_26S_proteasome_non_ATPase_regulatory_subunit_2__26S_proteasome_regulatory_subunit_RPN1___26S_proteasome_regulatory_subunit_S2___26S_proteasome_subunit_p97___Tumor_necrosis_factor_type_1_receptor_associated_protein_2___55_11_protein_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:Q13200 26S proteasome non-ATPase regulatory subunit 2 (26S proteasome regulatory subunit RPN1) (26S proteasome regulatory subunit S2) (26S proteasome subunit p97) (Tumor necrosis factor type 1 receptor associated protein 2) (55.11 protein)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PSMD2</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRAP2</SYNONYMS>
+ <XREF rdf:resource="#UniProt_Q13200" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Acts as a regulatory subunit of the 26 proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins. FUNCTION: Binds to the intracellular domain of tumor necrosis factor type 1 receptor. The binding domain of TRAP1 and TRAP2 resides outside the death domain of TNFR1. TISSUE SPECIFICITY: Found in skeletal muscle, liver, heart, brain, kidney, pancreas, lung and placenta. SIMILARITY: Bel [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_Q13200">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Q13200</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="Proteasome_subunit_alpha_type_6___cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P60900_Proteasome_subunit_alpha_type_6__EC_3_4_25_1___Proteasome_iota_chain___Macropain_iota_chain___Multicatalytic_endopeptidase_complex_iota_chain___27_kDa_prosomal_protein___PROS_27___p27K_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_P60900_Proteasome_subunit_alpha_type_6__EC_3_4_25_1___Proteasome_iota_chain___Macropain_iota_chain___Multicatalytic_endopeptidase_complex_iota_chain___27_kDa_prosomal_protein___PROS_27___p27K_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P60900 Proteasome subunit alpha type 6 (EC 3.4.25.1) (Proteasome iota chain) (Macropain iota chain) (Multicatalytic endopeptidase complex iota chain) (27 kDa prosomal protein) (PROS-27) (p27K)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PROS27</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PSMA6</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P60900" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: The proteasome is a multicatalytic proteinase complex which is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. The proteasome has an ATP-dependent proteolytic activity. CATALYTIC ACTIVITY: Cleavage of peptide bonds with very broad specificity. PATHWAY: Involved in an ATP/ubiquitin-dependent non-lysosomal proteolytic [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_P60900">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P60900</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="_26S_proteasome_non_ATPase_regulatory_subunit_9__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_O00233_1_26S_proteasome_non_ATPase_regulatory_subunit_9__26S_proteasome_regulatory_subunit_p27_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_O00233_1_26S_proteasome_non_ATPase_regulatory_subunit_9__26S_proteasome_regulatory_subunit_p27_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:O00233-1 26S proteasome non-ATPase regulatory subunit 9 (26S proteasome regulatory subunit p27)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PSMD9</SYNONYMS>
+ <XREF rdf:resource="#UniProt_O00233" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Acts as a regulatory subunit of the 26S proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins. SUBUNIT: Subunit of the modulator trimer complex that stimulates the association of the PA700 regulator with the catalytic 20S proteasome to form the ATP-dependent active 26S proteasome. P27 is associated not only with the modulator complex but also significantly with the 26S proteaso [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_O00233">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">O00233</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="Proteasome_subunit_beta_type_10__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P40306_Proteasome_subunit_beta_type_10_precursor__EC_3_4_25_1___Proteasome_MECl_1___Macropain_subunit_MECl_1___Multicatalytic_endopeptidase_complex_subunit_MECl_1_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_P40306_Proteasome_subunit_beta_type_10_precursor__EC_3_4_25_1___Proteasome_MECl_1___Macropain_subunit_MECl_1___Multicatalytic_endopeptidase_complex_subunit_MECl_1_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P40306 Proteasome subunit beta type 10 precursor (EC 3.4.25.1) (Proteasome MECl-1) (Macropain subunit MECl-1) (Multicatalytic endopeptidase complex subunit MECl-1)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">MECL1</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PSMB10</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P40306" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: The proteasome is a multicatalytic proteinase complex which is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. The proteasome has an ATP-dependent proteolytic activity. This subunit is involved in antigen processing to generate class I binding peptides. CATALYTIC ACTIVITY: Cleavage of peptide bonds with very broad sp [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_P40306">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P40306</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="Proteasome_subunit_beta_type_6__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P28072_Proteasome_subunit_beta_type_6_precursor__EC_3_4_25_1___Proteasome_delta_chain___Macropain_delta_chain___Multicatalytic_endopeptidase_complex_delta_chain___Proteasome_subunit_Y_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_P28072_Proteasome_subunit_beta_type_6_precursor__EC_3_4_25_1___Proteasome_delta_chain___Macropain_delta_chain___Multicatalytic_endopeptidase_complex_delta_chain___Proteasome_subunit_Y_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P28072 Proteasome subunit beta type 6 precursor (EC 3.4.25.1) (Proteasome delta chain) (Macropain delta chain) (Multicatalytic endopeptidase complex delta chain) (Proteasome subunit Y)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">LMPY</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PSMB6</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P28072" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: The proteasome is a multicatalytic proteinase complex which is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. The proteasome has an ATP-dependent proteolytic activity. May catalyze basal processing of intracellular antigens. CATALYTIC ACTIVITY: Cleavage of peptide bonds with very broad specificity. PATHWAY: Involved [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_P28072">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P28072</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="_26S_protease_regulatory_subunit_S10B__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P62333_26S_protease_regulatory_subunit_S10B__Proteasome_subunit_p42___Proteasome_26S_subunit_ATPase_6_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_P62333_26S_protease_regulatory_subunit_S10B__Proteasome_subunit_p42___Proteasome_26S_subunit_ATPase_6_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P62333 26S protease regulatory subunit S10B (Proteasome subunit p42) (Proteasome 26S subunit ATPase 6)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PSMC6</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SUG2</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P62333" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: The 26S protease is involved in the ATP-dependent degradation of ubiquitinated proteins. The regulatory (or ATPase) complex confers ATP dependency and substrate specificity to the 26S complex. SUBUNIT: Found in the multi-protein complexes: the 26S proteasome (formed from the 20S proteasome and PA700), and the modulator. PA700 consists of 28 subunits arranged to form a cylinder-shaped complex by four stacked rin [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_P62333">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P62333</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="Proteasome_subunit_beta_type_1___cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P20618_Proteasome_subunit_beta_type_1__EC_3_4_25_1___Proteasome_component_C5___Macropain_subunit_C5___Multicatalytic_endopeptidase_complex_subunit_C5___Proteasome_gamma_chain_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_P20618_Proteasome_subunit_beta_type_1__EC_3_4_25_1___Proteasome_component_C5___Macropain_subunit_C5___Multicatalytic_endopeptidase_complex_subunit_C5___Proteasome_gamma_chain_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P20618 Proteasome subunit beta type 1 (EC 3.4.25.1) (Proteasome component C5) (Macropain subunit C5) (Multicatalytic endopeptidase complex subunit C5) (Proteasome gamma chain)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PSMB1</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PSC5</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P20618" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: The proteasome is a multicatalytic proteinase complex which is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. The proteasome has an ATP-dependent proteolytic activity. CATALYTIC ACTIVITY: Cleavage of peptide bonds with very broad specificity. PATHWAY: Involved in an ATP/ubiquitin-dependent non-lysosomal proteolytic [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_P20618">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P20618</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="_26S_proteasome_non_ATPase_regulatory_subunit_11__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_O00231_26S_proteasome_non_ATPase_regulatory_subunit_11__26S_proteasome_regulatory_subunit_S9___26S_proteasome_regulatory_subunit_p44_5_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_O00231_26S_proteasome_non_ATPase_regulatory_subunit_11__26S_proteasome_regulatory_subunit_S9___26S_proteasome_regulatory_subunit_p44_5_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:O00231 26S proteasome non-ATPase regulatory subunit 11 (26S proteasome regulatory subunit S9) (26S proteasome regulatory subunit p44.5)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PSMD11</SYNONYMS>
+ <XREF rdf:resource="#UniProt_O00231" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Acts as a regulatory subunit of the 26S proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins. SUBUNIT: Component of the PA700 complex. SIMILARITY: Contains 1 PCI domain.</COMMENT>
+ </protein>
+ <unificationXref rdf:ID="UniProt_O00231">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">O00231</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="Proteasome_subunit_alpha_type_2___cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P25787_Proteasome_subunit_alpha_type_2__EC_3_4_25_1___Proteasome_component_C3___Macropain_subunit_C3___Multicatalytic_endopeptidase_complex_subunit_C3_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_P25787_Proteasome_subunit_alpha_type_2__EC_3_4_25_1___Proteasome_component_C3___Macropain_subunit_C3___Multicatalytic_endopeptidase_complex_subunit_C3_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P25787 Proteasome subunit alpha type 2 (EC 3.4.25.1) (Proteasome component C3) (Macropain subunit C3) (Multicatalytic endopeptidase complex subunit C3)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PSMA2</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PSC3</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P25787" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: The proteasome is a multicatalytic proteinase complex which is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. The proteasome has an ATP-dependent proteolytic activity. The component C3 may have a potential regulatory effect on another component(s) of the proteasome complex through tyrosine phosphorylation. CATALYTIC [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_P25787">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P25787</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="Proteasome_inhibitor_PI31_subunit__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q92530_Proteasome_inhibitor_PI31_subunit__hPI31_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_Q92530_Proteasome_inhibitor_PI31_subunit__hPI31_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:Q92530 Proteasome inhibitor PI31 subunit (hPI31)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PSMF1</SYNONYMS>
+ <XREF rdf:resource="#UniProt_Q92530" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Plays an important role in control of proteasome function. Inhibits the hydrolysis of protein and peptide substrates by the 20S proteasome. Also inhibits the activation of the proteasome by the proteasome regulatory proteins PA700 and PA28. SUBUNIT: Monomer (Probable). SIMILARITY: Belongs to the proteasome inhibitor PI31 family.</COMMENT>
+ </protein>
+ <unificationXref rdf:ID="UniProt_Q92530">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Q92530</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="Proteasome_subunit_alpha_type_1___cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P25786_1_Proteasome_subunit_alpha_type_1__EC_3_4_25_1___Proteasome_component_C2___Macropain_subunit_C2___Multicatalytic_endopeptidase_complex_subunit_C2___Proteasome_nu_chain___30_kDa_prosomal_protein___PROS_30_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_P25786_1_Proteasome_subunit_alpha_type_1__EC_3_4_25_1___Proteasome_component_C2___Macropain_subunit_C2___Multicatalytic_endopeptidase_complex_subunit_C2___Proteasome_nu_chain___30_kDa_prosomal_protein___PROS_30_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P25786-1 Proteasome subunit alpha type 1 (EC 3.4.25.1) (Proteasome component C2) (Macropain subunit C2) (Multicatalytic endopeptidase complex subunit C2) (Proteasome nu chain) (30 kDa prosomal protein) (PROS-30)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PROS30</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PSC2</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PSMA1</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P25786" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: The proteasome is a multicatalytic proteinase complex which is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. The proteasome has an ATP-dependent proteolytic activity. CATALYTIC ACTIVITY: Cleavage of peptide bonds with very broad specificity. PATHWAY: Involved in an ATP/ubiquitin-dependent non-lysosomal proteolytic [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_P25786">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P25786</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="_26S_proteasome_non_ATPase_regulatory_subunit_3__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_O43242_26S_proteasome_non_ATPase_regulatory_subunit_3__26S_proteasome_regulatory_subunit_S3___Proteasome_subunit_p58_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_O43242_26S_proteasome_non_ATPase_regulatory_subunit_3__26S_proteasome_regulatory_subunit_S3___Proteasome_subunit_p58_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:O43242 26S proteasome non-ATPase regulatory subunit 3 (26S proteasome regulatory subunit S3) (Proteasome subunit p58)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PSMD3</SYNONYMS>
+ <XREF rdf:resource="#UniProt_O43242" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Acts as a regulatory subunit of the 26 proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins. SUBUNIT: The 26S proteasome is composed of a core protease, known as the 20S proteasome, capped at one or both ends by the 19S regulatory complex (RC). The RC is composed of at least 18 different subunits in two subcomplexes, the base and the lid, which form the portions proximal and d [...]
+ </protein>
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+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">O43242</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="Proteasome_activator_complex_subunit_1__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q06323_Proteasome_activator_complex_subunit_1__Proteasome_activator_28_alpha_subunit___PA28alpha___PA28a___Activator_of_multicatalytic_protease_subunit_1___11S_regulator_complex_alpha_subunit___REG_alpha___Interferon_gamma_up_regulated_I_5111_protein___IGUP_I_5111_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_Q06323_Proteasome_activator_complex_subunit_1__Proteasome_activator_28_alpha_subunit___PA28alpha___PA28a___Activator_of_multicatalytic_protease_subunit_1___11S_regulator_complex_alpha_subunit___REG_alpha___Interferon_gamma_up_regulated_I_5111_protein___IGUP_I_5111_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:Q06323 Proteasome activator complex subunit 1 (Proteasome activator 28-alpha subunit) (PA28alpha) (PA28a) (Activator of multicatalytic protease subunit 1) (11S regulator complex alpha subunit) (REG-alpha) (Interferon gamma up-regulated I-5111 protein) (IGUP I-5111)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PSME1</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">IFI5111</SYNONYMS>
+ <XREF rdf:resource="#UniProt_Q06323" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Implicated in immunoproteasome assembly and required for efficient antigen processing. The PA28 activator complex enhances the generation of class I binding peptides by altering the cleavage pattern of the proteasome. SUBUNIT: Heterodimer of PSME1 and PSME2, which forms a hexadimeric ring. PSME1 can form homoheptamers. INDUCTION: By interferon gamma. SIMILARITY: Belongs to the PA28 family.</COMMENT>
+ </protein>
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+ </unificationXref>
+ <relationshipXref rdf:ID="endopeptidase_activity">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GO</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0004175</ID>
+ </relationshipXref>
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+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <pathwayStep rdf:ID="Ubiquitinated_geminin_is_degraded_by_the_proteasomeStep">
+ <STEP-INTERACTIONS rdf:resource="#Ubiquitinated_geminin_is_degraded_by_the_proteasome" />
+ <STEP-INTERACTIONS rdf:resource="#endopeptidase_activity_of_26S_proteasome__cytosol_" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="Free_Cdt1_associates_with_Cdc6_ORC_origin_complexes">
+ <LEFT rdf:resource="#Cdt1__nucleoplasm_" />
+ <LEFT rdf:resource="#Cdc6_ORC_origin_complex__nucleoplasm_2" />
+ <RIGHT rdf:resource="#Cdt1_Cdc6_ORC_origin_complex__nucleoplasm_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Free Cdt1 associates with Cdc6:ORC:origin complexes</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Free Cdt1 associates with Cdc6:ORC:origin complexes</SHORT-NAME>
+ <XREF rdf:resource="#Reactome68826" />
+ <XREF rdf:resource="#Pubmed_11125146" />
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+ </biochemicalReaction>
+ <proteinParticipant rdf:ID="Cdt1__nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q9H211" />
+ </proteinParticipant>
+ <complexParticipant rdf:ID="Cdc6_ORC_origin_complex__nucleoplasm_2">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Cdc6_ORC_origin_complex__nucleoplasm_1" />
+ </complexParticipant>
+ <complexParticipant rdf:ID="Cdt1_Cdc6_ORC_origin_complex__nucleoplasm_">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Cdt1_Cdc6_ORC_origin_complex__nucleoplasm_1" />
+ </complexParticipant>
+ <complex rdf:ID="Cdt1_Cdc6_ORC_origin_complex__nucleoplasm_1">
+ <COMPONENTS rdf:resource="#Cdt1__nucleoplasm_1" />
+ <COMPONENTS rdf:resource="#Cdc6_ORC_origin_complex__nucleoplasm_3" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cdt1:Cdc6:ORC:origin complex [nucleoplasm]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cdt1:Cdc6:ORC:origin complex</SHORT-NAME>
+ </complex>
+ <proteinParticipant rdf:ID="Cdt1__nucleoplasm_1">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q9H211" />
+ </proteinParticipant>
+ <complexParticipant rdf:ID="Cdc6_ORC_origin_complex__nucleoplasm_3">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Cdc6_ORC_origin_complex__nucleoplasm_1" />
+ </complexParticipant>
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+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <pathwayStep rdf:ID="Free_Cdt1_associates_with_Cdc6_ORC_origin_complexesStep">
+ <STEP-INTERACTIONS rdf:resource="#Free_Cdt1_associates_with_Cdc6_ORC_origin_complexes" />
+ </pathwayStep>
+ <unificationXref rdf:ID="Reactome68827">
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+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">68827</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <evidence rdf:ID="Summation_68829">
+ <XREF rdf:resource="#Pubmed_10766247" />
+ <XREF rdf:resource="#Pubmed_11175741" />
+ <XREF rdf:resource="#Pubmed_10766248" />
+ <XREF rdf:resource="#Pubmed_10898791" />
+ <XREF rdf:resource="#Pubmed_9442876" />
+ <XREF rdf:resource="#Pubmed_11836525" />
+ <XREF rdf:resource="#Pubmed_9635433" />
+ <XREF rdf:resource="#Pubmed_11125146" />
+ </evidence>
+ <publicationXref rdf:ID="Pubmed_10766247">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">10766247</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2000</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">XCDT1 is required for the assembly of pre-replicative complexes in Xenopus laevis.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Maiorano, D</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Moreau, J</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Méchali, M</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Nature 404:622-5</SOURCE>
+ </publicationXref>
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+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2001</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Repression of origin assembly in metaphase depends on inhibition of RLF-B/Cdt1 by geminin.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Tada, S</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Li, A</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Maiorano, D</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Méchali, M</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Blow, JJ</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Nat Cell Biol 3:107-13</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_10766248">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">10766248</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2000</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The Cdt1 protein is required to license DNA for replication in fission yeast.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Nishitani, H</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Lygerou, Z</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Nishimoto, T</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Nurse, P</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Nature 404:625-8</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_10898791">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">10898791</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2000</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Drosophila double parked: a conserved, essential replication protein that colocalizes with the origin recognition complex and links DNA replication with mitosis and the down-regulation of S phase transcripts.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Whittaker, AJ</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Royzman, I</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Orr-Weaver, TL</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Genes Dev 14:1765-76</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_9442876">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">9442876</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1998</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Initiation of DNA replication in eukaryotic cells.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Dutta, A</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bell, SP</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Annu Rev Cell Dev Biol 13:293-332</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_11836525">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">11836525</ID>
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+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2002</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Interdependent nuclear accumulation of budding yeast Cdt1 and Mcm2-7 during G1 phase.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Tanaka, S</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Diffley, JF</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Nat Cell Biol 4:198-207</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="Cdt1_association_with_the_Cdc6_ORC_origin_complexStep">
+ <STEP-INTERACTIONS rdf:resource="#Cdt1_association_with_the_Cdc6_ORC_origin_complex" />
+ <NEXT-STEP rdf:resource="#Mcm2_7_associates_with_the_Cdt1_Cdc6_ORC_origin_complex__forming_the_pre_replicative_complex__preRC_Step" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="Mcm2_7_associates_with_the_Cdt1_Cdc6_ORC_origin_complex__forming_the_pre_replicative_complex__preRC_">
+ <LEFT rdf:resource="#Cdt1_Cdc6_ORC_origin_complex__nucleoplasm_2" />
+ <LEFT rdf:resource="#Mcm2_7_complex__nucleoplasm_" />
+ <RIGHT rdf:resource="#pre_replicative_complex__nucleoplasm_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mcm2-7 associates with the Cdt1:Cdc6:ORC:origin complex, forming the pre-replicative complex (preRC)</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mcm2-7 associates with the Cdt1:Cdc6:ORC:origin complex, forming the pre-replicative complex (preRC)</SHORT-NAME>
+ <XREF rdf:resource="#Reactome68849" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Genetic studies in S. cerevisiae indicate that wild-type Cdc6 function is required for correctly timed loading of Mcm2-7 onto ORC. Biochemical studies indicate that the human and Xenopus Cdc6 proteins likewise are required for Mcm2-7 loading, and that they are ATPase switches. Specifically, Cdc6 may function as a clamp loader, assembling Mcm2-7 onto DNA in an ATP-dependent reaction. All known Cdc6 proteins have the Walke [...]
+ <EVIDENCE rdf:resource="#Summation_68851" />
+ <CELLULAR-LOCATION rdf:resource="#nucleus" />
+ </biochemicalReaction>
+ <complexParticipant rdf:ID="Cdt1_Cdc6_ORC_origin_complex__nucleoplasm_2">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Cdt1_Cdc6_ORC_origin_complex__nucleoplasm_1" />
+ </complexParticipant>
+ <complexParticipant rdf:ID="Mcm2_7_complex__nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Mcm2_7_complex__nucleoplasm_1" />
+ </complexParticipant>
+ <complex rdf:ID="Mcm2_7_complex__nucleoplasm_1">
+ <COMPONENTS rdf:resource="#Mcm4__nucleoplasm_" />
+ <COMPONENTS rdf:resource="#Mcm5__nucleoplasm_" />
+ <COMPONENTS rdf:resource="#Mcm6__nucleoplasm_" />
+ <COMPONENTS rdf:resource="#Mcm7__nucleoplasm_" />
+ <COMPONENTS rdf:resource="#Mcm2__nucleoplasm_" />
+ <COMPONENTS rdf:resource="#Mcm3__nucleoplasm_" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mcm2-7 complex [nucleoplasm]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mcm2-7 complex</SHORT-NAME>
+ </complex>
+ <proteinParticipant rdf:ID="Mcm4__nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P33991_DNA_replication_licensing_factor_MCM4__CDC21_homolog___P1_CDC21_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_P33991_DNA_replication_licensing_factor_MCM4__CDC21_homolog___P1_CDC21_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P33991 DNA replication licensing factor MCM4 (CDC21 homolog) (P1-CDC21)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">MCM4</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CDC21</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P33991" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Involved in the control of DNA replication. SUBCELLULAR LOCATION: Nuclear (By similarity). SIMILARITY: Belongs to the MCM family.</COMMENT>
+ </protein>
+ <unificationXref rdf:ID="UniProt_P33991">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
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+ </unificationXref>
+ <proteinParticipant rdf:ID="Mcm5__nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P33992_DNA_replication_licensing_factor_MCM5__CDC46_homolog___P1_CDC46_" />
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+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P33992 DNA replication licensing factor MCM5 (CDC46 homolog) (P1-CDC46)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">MCM5</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CDC46</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P33992" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SUBCELLULAR LOCATION: Nuclear. SIMILARITY: Belongs to the MCM family.</COMMENT>
+ </protein>
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+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P33992</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="Mcm6__nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q14566_DNA_replication_licensing_factor_MCM6__P105MCM_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_Q14566_DNA_replication_licensing_factor_MCM6__P105MCM_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:Q14566 DNA replication licensing factor MCM6 (P105MCM)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">MCM6</SYNONYMS>
+ <XREF rdf:resource="#UniProt_Q14566" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: May be involved in the control of a single round of DNA replication during S phase. Binds to chromatin during G1 and detach from it during S phase as if it licenses the chromatin to replicate. SUBCELLULAR LOCATION: Nuclear (By similarity). SIMILARITY: Belongs to the MCM family.</COMMENT>
+ </protein>
+ <unificationXref rdf:ID="UniProt_Q14566">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Q14566</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="Mcm7__nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P33993_1_DNA_replication_licensing_factor_MCM7__CDC47_homolog___P1_1_MCM3_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_P33993_1_DNA_replication_licensing_factor_MCM7__CDC47_homolog___P1_1_MCM3_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P33993-1 DNA replication licensing factor MCM7 (CDC47 homolog) (P1.1-MCM3)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">MCM7</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CDC47</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">MCM2</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P33993" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Acts as a factor that allows the DNA to undergo a single round of replication per cell cycle. Required for DNA replication and cell proliferation. SUBCELLULAR LOCATION: Nuclear (By similarity). ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=P33993-1; Sequence=Displayed; Name=2; IsoId=P33993-2; Sequence=VSP_003205; Note=No experimental confirmation available; SIMILARITY: Belong [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_P33993">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P33993</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="Mcm2__nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P49736_DNA_replication_licensing_factor_MCM2__Minichromosome_maintenance_protein_2_homolog___Nuclear_protein_BM28_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_P49736_DNA_replication_licensing_factor_MCM2__Minichromosome_maintenance_protein_2_homolog___Nuclear_protein_BM28_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P49736 DNA replication licensing factor MCM2 (Minichromosome maintenance protein 2 homolog) (Nuclear protein BM28)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CDCL1</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BM28</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">MCM2</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">KIAA0030</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P49736" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Acts as a factor that allows the DNA to undergo a single round of replication per cell cycle. Required for the entry in S phase and for cell division. SUBCELLULAR LOCATION: Nuclear (Probable). SIMILARITY: Belongs to the MCM family. SIMILARITY: Contains 1 C4-type zinc finger.</COMMENT>
+ </protein>
+ <unificationXref rdf:ID="UniProt_P49736">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P49736</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="Mcm3__nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P25205_DNA_replication_licensing_factor_MCM3__DNA_polymerase_alpha_holoenzyme_associated_protein_P1___RLF_beta_subunit___P102_protein___P1_MCM3_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_P25205_DNA_replication_licensing_factor_MCM3__DNA_polymerase_alpha_holoenzyme_associated_protein_P1___RLF_beta_subunit___P102_protein___P1_MCM3_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P25205 DNA replication licensing factor MCM3 (DNA polymerase alpha holoenzyme-associated protein P1) (RLF beta subunit) (P102 protein) (P1-MCM3)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">MCM3</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P25205" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Acts as a factor that allows the DNA to undergo a single round of replication per cell cycle. Required for DNA replication and cell proliferation. SUBCELLULAR LOCATION: Nuclear. MISCELLANEOUS: Associated with the replication-specific DNA polymerase alpha. SIMILARITY: Belongs to the MCM family.</COMMENT>
+ </protein>
+ <unificationXref rdf:ID="UniProt_P25205">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P25205</ID>
+ </unificationXref>
+ <complexParticipant rdf:ID="pre_replicative_complex__nucleoplasm_">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#pre_replicative_complex__nucleoplasm_1" />
+ </complexParticipant>
+ <complex rdf:ID="pre_replicative_complex__nucleoplasm_1">
+ <COMPONENTS rdf:resource="#Cdt1_Cdc6_ORC_origin_complex__nucleoplasm_3" />
+ <COMPONENTS rdf:resource="#Mcm2_7_complex__nucleoplasm_2" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">pre-replicative complex [nucleoplasm]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">pre-replicative complex</SHORT-NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">preRC</SYNONYMS>
+ </complex>
+ <complexParticipant rdf:ID="Cdt1_Cdc6_ORC_origin_complex__nucleoplasm_3">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Cdt1_Cdc6_ORC_origin_complex__nucleoplasm_1" />
+ </complexParticipant>
+ <complexParticipant rdf:ID="Mcm2_7_complex__nucleoplasm_2">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Mcm2_7_complex__nucleoplasm_1" />
+ </complexParticipant>
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+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <evidence rdf:ID="Summation_68851">
+ <XREF rdf:resource="#Pubmed_9407030" />
+ <XREF rdf:resource="#Pubmed_10801458" />
+ <XREF rdf:resource="#Pubmed_10436018" />
+ <XREF rdf:resource="#Pubmed_11950940" />
+ <XREF rdf:resource="#Pubmed_11006548" />
+ </evidence>
+ <publicationXref rdf:ID="Pubmed_9407030">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">9407030</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1998</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Persistent initiation of DNA replication and chromatin-bound MCM proteins during the cell cycle in cdc6 mutants.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Liang, C</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Stillman, B</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Genes Dev 11:3375-86</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_10436018">
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+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1999</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The Cdc6 nucleotide-binding site regulates its activity in DNA replication in human cells.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Herbig, U</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Marlar, CA</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Fanning, E</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mol Biol Cell 10:2631-45</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_11950940">
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+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2002</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Xenopus Cdc6 performs separate functions in initiating DNA replication.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Frolova, NS</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Schek, N</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Tikhmyanova, N</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Coleman, TR</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mol Biol Cell 13:1298-312</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_11006548">
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+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2000</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mechanisms of DNA replication.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Davey, MJ</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">O'Donnell, M</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Curr Opin Chem Biol 4:581-6</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="Mcm2_7_associates_with_the_Cdt1_Cdc6_ORC_origin_complex__forming_the_pre_replicative_complex__preRC_Step">
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+ <NEXT-STEP rdf:resource="#Mcm10_associates_with_the_pre_replicative_complex__stabilizing_Mcm2_7Step" />
+ </pathwayStep>
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+ </unificationXref>
+ <evidence rdf:ID="Summation_69392">
+ <XREF rdf:resource="#Pubmed_9335335" />
+ <XREF rdf:resource="#Pubmed_9407030" />
+ <XREF rdf:resource="#Pubmed_9288745" />
+ <XREF rdf:resource="#Pubmed_11046155" />
+ <XREF rdf:resource="#Pubmed_11801723" />
+ <XREF rdf:resource="#Pubmed_9829972" />
+ <XREF rdf:resource="#Pubmed_9927482" />
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+ <publicationXref rdf:ID="Pubmed_9335335">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">9335335</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1997</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Components and dynamics of DNA replication complexes in S. cerevisiae: redistribution of MCM proteins and Cdc45p during S phase.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Aparicio, OM</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Weinstein, DM</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bell, SP</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cell 91:59-69</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_9288745">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">9288745</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1997</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Loading of an Mcm protein onto DNA replication origins is regulated by Cdc6p and CDKs.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Tanaka, T</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Knapp, D</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Nasmyth, K</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cell 90:649-60</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_11801723">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">11801723</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2002</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mammalian nuclei become licensed for DNA replication during late telophase.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Dimitrova, DS</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Prokhorova, TA</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Blow, JJ</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Todorov, IT</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Gilbert, DM</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Cell Sci 115:51-9</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_9829972">
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+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1999</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The Orc4p and Orc5p subunits of the Xenopus and human origin recognition complex are related to Orc1p and Cdc6p.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Tugal, T</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Zou-Yang, XH</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Gavin, K</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pappin, D</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Canas, B</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Kobayashi, R</AUTHORS>
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+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Stillman, B</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Biol Chem 273:32421-9</SOURCE>
+ </publicationXref>
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+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1999</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">AAA+: A class of chaperone-like ATPases associated with the assembly, operation, and disassembly of protein complexes.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Neuwald, AF</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Aravind, L</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Spouge, JL</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Koonin, EV</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Genome Res 9:27-43</SOURCE>
+ </publicationXref>
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+ </pathwayStep>
+ <pathway rdf:ID="Activation_of_the_pre_replicative_complex">
+ <PATHWAY-COMPONENTS rdf:resource="#Mcm10_associates_with_the_pre_replicative_complex__stabilizing_Mcm2_7Step" />
+ <PATHWAY-COMPONENTS rdf:resource="#DNA_polymerase_epsilon_binds_at_the_originStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#DNA_Replication_Factor_A__RPA__associates_with_the_pre_replicative_complex_at_the_originStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#Cdc45_associates_with_the_pre_replicative_complex_at_the_originStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#DNA_polymerase_alpha_primase_binds_at_the_originStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#Cdt1_is_displaced_from_the_pre_replicative_complex_Step" />
+ <PATHWAY-COMPONENTS rdf:resource="#Mcm2_7_is_phosphorylated_by_DDKStep" />
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+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Activation of the pre-replicative complex</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Activation of the pre-replicative complex</SHORT-NAME>
+ <XREF rdf:resource="#Reactome68962" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">In S. cerevisiae, two ORC subunits, Orc1 and Orc5, both bind ATP, and Orc1 in addition has ATPase activity. Both ATP binding and ATP hydrolysis appear to be essential functions in vivo. ATP binding by Orc1 is unaffected by the association of ORC with origin DNA (ARS) sequences, but ATP hydrolysis is ARS-dependent, being suppressed by associated double-stranded DNA and stimulated by associated single-stranded DNA. These d [...]
+ <EVIDENCE rdf:resource="#Summation_68963" />
+ <CELLULAR-LOCATION rdf:resource="#nucleus" />
+ </pathway>
+ <biochemicalReaction rdf:ID="Mcm10_associates_with_the_pre_replicative_complex__stabilizing_Mcm2_7">
+ <LEFT rdf:resource="#Mcm10__nucleoplasm_" />
+ <LEFT rdf:resource="#pre_replicative_complex__nucleoplasm_2" />
+ <RIGHT rdf:resource="#Mcm10_pre_replicative_complex__nucleoplasm_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mcm10 associates with the pre-replicative complex, stabilizing Mcm2-7</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mcm10 associates with the pre-replicative complex, stabilizing Mcm2-7</SHORT-NAME>
+ <XREF rdf:resource="#Reactome68919" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mcm10 is required for human DNA replication. In S. cerevisiae, Mcm10, like Mcm2-7, is required for minichromosome maintenance, but Mcm10 has no sequence homology with these other proteins. Genetic studies have demonstrated that Mcm10 is required for DNA replication in S. pombe and S. cerevisiae cells and immunodepletion of XlMcm10 interferes with DNA replication in Xenopus egg extracts. Human Mcm10 interacts with chromat [...]
+ <EVIDENCE rdf:resource="#Summation_68930" />
+ <XREF rdf:resource="#Pubmed_11095689" />
+ <CELLULAR-LOCATION rdf:resource="#nucleus" />
+ </biochemicalReaction>
+ <proteinParticipant rdf:ID="Mcm10__nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q9H3P9" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_Q9H3P9">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:Q9H3P9</NAME>
+ <XREF rdf:resource="#UniProt_Q9H3P91" />
+ </protein>
+ <unificationXref rdf:ID="UniProt_Q9H3P91">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Q9H3P9</ID>
+ </unificationXref>
+ <complexParticipant rdf:ID="pre_replicative_complex__nucleoplasm_2">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#pre_replicative_complex__nucleoplasm_1" />
+ </complexParticipant>
+ <complexParticipant rdf:ID="Mcm10_pre_replicative_complex__nucleoplasm_">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Mcm10_pre_replicative_complex__nucleoplasm_1" />
+ </complexParticipant>
+ <complex rdf:ID="Mcm10_pre_replicative_complex__nucleoplasm_1">
+ <COMPONENTS rdf:resource="#Mcm10__nucleoplasm_1" />
+ <COMPONENTS rdf:resource="#pre_replicative_complex__nucleoplasm_3" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mcm10:pre-replicative complex [nucleoplasm]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mcm10:pre-replicative complex</SHORT-NAME>
+ </complex>
+ <proteinParticipant rdf:ID="Mcm10__nucleoplasm_1">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q9H3P9" />
+ </proteinParticipant>
+ <complexParticipant rdf:ID="pre_replicative_complex__nucleoplasm_3">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#pre_replicative_complex__nucleoplasm_1" />
+ </complexParticipant>
+ <unificationXref rdf:ID="Reactome68919">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">68919</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <evidence rdf:ID="Summation_68930">
+ <XREF rdf:resource="#Pubmed_10783164" />
+ <XREF rdf:resource="#Pubmed_11864598" />
+ <XREF rdf:resource="#Pubmed_11095689" />
+ <XREF rdf:resource="#Pubmed_11282021" />
+ </evidence>
+ <publicationXref rdf:ID="Pubmed_10783164">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">10783164</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2000</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mcm10 and the MCM2-7 complex interact to initiate DNA synthesis and to release replication factors from origins.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Homesley, L</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Lei, M</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Kawasaki, Y</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Sawyer, S</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Christensen, T</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Tye, BK</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Genes Dev 14:913-26</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_11864598">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">11864598</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2002</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Xenopus Mcm10 binds to origins of DNA replication after Mcm2-7 and stimulates origin binding of Cdc45.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Wohlschlegel, JA</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Dhar, SK</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Prokhorova, TA</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Dutta, A</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Walter, JC</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mol Cell 9:233-40</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_11095689">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">11095689</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2000</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The human homolog of Saccharomyces cerevisiae Mcm10 interacts with replication factors and dissociates from nuclease-resistant nuclear structures in G(2) phase.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Izumi, M</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Yanagi, K</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mizuno, T</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Yokoi, M</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Kawasaki, Y</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Moon, KY</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Hurwitz, J</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Yatagai, F</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Hanaoka, F</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Nucleic Acids Res 28:4769-77</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_11282021">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">11282021</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2001</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Initiating DNA synthesis: from recruiting to activating the MCM complex.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Lei, M</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Tye, BK</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Cell Sci 114:1447-54</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="Mcm10_associates_with_the_pre_replicative_complex__stabilizing_Mcm2_7Step">
+ <STEP-INTERACTIONS rdf:resource="#Mcm10_associates_with_the_pre_replicative_complex__stabilizing_Mcm2_7" />
+ <NEXT-STEP rdf:resource="#Cdt1_is_displaced_from_the_pre_replicative_complex_Step" />
+ <NEXT-STEP rdf:resource="#CDK_and_DDK_associate_with_the_Mcm10_pre_replicative_complexStep" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="Cdt1_is_displaced_from_the_pre_replicative_complex_">
+ <LEFT rdf:resource="#Mcm10_pre_replicative_complex__nucleoplasm_2" />
+ <RIGHT rdf:resource="#Cdt1__nucleoplasm_2" />
+ <RIGHT rdf:resource="#Mcm10_active_pre_replicative_complex__nucleoplasm_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cdt1 is displaced from the pre-replicative complex.</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cdt1 is displaced from the pre-replicative complex.</SHORT-NAME>
+ <XREF rdf:resource="#Reactome68940" />
+ <XREF rdf:resource="#Pubmed_12045100" />
+ <CELLULAR-LOCATION rdf:resource="#nucleus" />
+ </biochemicalReaction>
+ <complexParticipant rdf:ID="Mcm10_pre_replicative_complex__nucleoplasm_2">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Mcm10_pre_replicative_complex__nucleoplasm_1" />
+ </complexParticipant>
+ <proteinParticipant rdf:ID="Cdt1__nucleoplasm_2">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q9H211" />
+ </proteinParticipant>
+ <complexParticipant rdf:ID="Mcm10_active_pre_replicative_complex__nucleoplasm_">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Mcm10_active_pre_replicative_complex__nucleoplasm_1" />
+ </complexParticipant>
+ <complex rdf:ID="Mcm10_active_pre_replicative_complex__nucleoplasm_1">
+ <COMPONENTS rdf:resource="#active_pre_replicative_complex__nucleoplasm_" />
+ <COMPONENTS rdf:resource="#Mcm10__nucleoplasm_2" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mcm10:active pre-replicative complex [nucleoplasm]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mcm10:active pre-replicative complex</SHORT-NAME>
+ </complex>
+ <complexParticipant rdf:ID="active_pre_replicative_complex__nucleoplasm_">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#active_pre_replicative_complex__nucleoplasm_1" />
+ </complexParticipant>
+ <complex rdf:ID="active_pre_replicative_complex__nucleoplasm_1">
+ <COMPONENTS rdf:resource="#Mcm2_7_complex__nucleoplasm_3" />
+ <COMPONENTS rdf:resource="#Cdc6_ORC_origin_complex__nucleoplasm_4" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">active pre-replicative complex [nucleoplasm]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">active pre-replicative complex</SHORT-NAME>
+ </complex>
+ <complexParticipant rdf:ID="Mcm2_7_complex__nucleoplasm_3">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Mcm2_7_complex__nucleoplasm_1" />
+ </complexParticipant>
+ <complexParticipant rdf:ID="Cdc6_ORC_origin_complex__nucleoplasm_4">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Cdc6_ORC_origin_complex__nucleoplasm_1" />
+ </complexParticipant>
+ <proteinParticipant rdf:ID="Mcm10__nucleoplasm_2">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q9H3P9" />
+ </proteinParticipant>
+ <unificationXref rdf:ID="Reactome68940">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">68940</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <publicationXref rdf:ID="Pubmed_12045100">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">12045100</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2002</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DNA replication in eukaryotic cells.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bell, SP</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Dutta, A</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Annu Rev Biochem 71:333-74</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="Cdt1_is_displaced_from_the_pre_replicative_complex_Step">
+ <STEP-INTERACTIONS rdf:resource="#Cdt1_is_displaced_from_the_pre_replicative_complex_" />
+ <NEXT-STEP rdf:resource="#Cdt1_associates_with_gemininStep" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="CDK_and_DDK_associate_with_the_Mcm10_pre_replicative_complex">
+ <LEFT rdf:resource="#CDK__nucleoplasm_" />
+ <LEFT rdf:resource="#Mcm10_active_pre_replicative_complex__nucleoplasm_2" />
+ <LEFT rdf:resource="#DDK__nucleoplasm_" />
+ <RIGHT rdf:resource="#CDK_DDK_Mcm10_pre_replicative_complex__nucleoplasm_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CDK and DDK associate with the Mcm10:pre-replicative complex</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CDK and DDK associate with the Mcm10:pre-replicative complex</SHORT-NAME>
+ <XREF rdf:resource="#Reactome68918" />
+ <CELLULAR-LOCATION rdf:resource="#nucleus" />
+ </biochemicalReaction>
+ <complexParticipant rdf:ID="CDK__nucleoplasm_">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#CDK__nucleoplasm_1" />
+ </complexParticipant>
+ <complex rdf:ID="CDK__nucleoplasm_1">
+ <COMPONENTS rdf:resource="#cyclin__nucleoplasm_" />
+ <COMPONENTS rdf:resource="#Cdk2__nucleoplasm_" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CDK [nucleoplasm]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CDK</SHORT-NAME>
+ </complex>
+ <physicalEntityParticipant rdf:ID="cyclin__nucleoplasm_">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#cyclin__nucleoplasm_1" />
+ </physicalEntityParticipant>
+ <physicalEntity rdf:ID="cyclin__nucleoplasm_1">
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cyclin [nucleoplasm]</NAME>
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome. Each synonym is a name of a ConcreteEntity, and each XREF points to one ConcreteEntity</COMMENT>
+ </physicalEntity>
+ <proteinParticipant rdf:ID="Cdk2__nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P24941_Cell_division_protein_kinase_2__EC_2_7_1_37___p33_protein_kinase_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_P24941_Cell_division_protein_kinase_2__EC_2_7_1_37___p33_protein_kinase_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P24941 Cell division protein kinase 2 (EC 2.7.1.37) (p33 protein kinase)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CDK2</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P24941" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Probably involved in the control of the cell cycle. Interacts with cyclins A, B3, D, or E. Activity of CDK2 is maximal during S phase and G2. CATALYTIC ACTIVITY: ATP + a protein = ADP + a phosphoprotein. ENZYME REGULATION: Phosphorylation at Thr-14 or Tyr-15 inactivates the enzyme, while phosphorylation at Thr-160 activates it. SIMILARITY: Belongs to the Ser/Thr protein kinase family. CDC2/CDKX subfamily.</COMMENT>
+ </protein>
+ <unificationXref rdf:ID="UniProt_P24941">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P24941</ID>
+ </unificationXref>
+ <complexParticipant rdf:ID="Mcm10_active_pre_replicative_complex__nucleoplasm_2">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Mcm10_active_pre_replicative_complex__nucleoplasm_1" />
+ </complexParticipant>
+ <complexParticipant rdf:ID="DDK__nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#DDK__nucleoplasm_1" />
+ </complexParticipant>
+ <complex rdf:ID="DDK__nucleoplasm_1">
+ <COMPONENTS rdf:resource="#Dbf4__nucleoplasm_" />
+ <COMPONENTS rdf:resource="#Cdc7__nucleoplasm_" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DDK [nucleoplasm]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DDK</SHORT-NAME>
+ </complex>
+ <proteinParticipant rdf:ID="Dbf4__nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q9UBU7" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_Q9UBU7">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:Q9UBU7</NAME>
+ <XREF rdf:resource="#UniProt_Q9UBU71" />
+ </protein>
+ <unificationXref rdf:ID="UniProt_Q9UBU71">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Q9UBU7</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="Cdc7__nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_O00311_1_Cell_division_cycle_7_related_protein_kinase__EC_2_7_1_____CDC7__related_kinase___HsCdc7___huCdc7_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_O00311_1_Cell_division_cycle_7_related_protein_kinase__EC_2_7_1_____CDC7__related_kinase___HsCdc7___huCdc7_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:O00311-1 Cell division cycle 7-related protein kinase (EC 2.7.1.-) (CDC7- related kinase) (HsCdc7) (huCdc7)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CDC7</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CDC7L1</SYNONYMS>
+ <XREF rdf:resource="#UniProt_O00311" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Seems to phosphorylate critical substrates that regulate the G1/S phase transition and/or DNA replication. Can phosphorylates MCM2 and MCM3. SUBCELLULAR LOCATION: Nuclear. ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=1; Comment=A number of isoforms may be produced; Name=1; IsoId=O00311-1; Sequence=Displayed; SIMILARITY: Belongs to the Ser/Thr protein kinase family. CDC7 subfamily.</COMMENT>
+ </protein>
+ <unificationXref rdf:ID="UniProt_O00311">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">O00311</ID>
+ </unificationXref>
+ <complexParticipant rdf:ID="CDK_DDK_Mcm10_pre_replicative_complex__nucleoplasm_">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#CDK_DDK_Mcm10_pre_replicative_complex__nucleoplasm_1" />
+ </complexParticipant>
+ <complex rdf:ID="CDK_DDK_Mcm10_pre_replicative_complex__nucleoplasm_1">
+ <COMPONENTS rdf:resource="#CDK__nucleoplasm_2" />
+ <COMPONENTS rdf:resource="#Mcm10_active_pre_replicative_complex__nucleoplasm_3" />
+ <COMPONENTS rdf:resource="#DDK__nucleoplasm_2" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CDK:DDK:Mcm10:pre-replicative complex [nucleoplasm]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CDK:DDK:Mcm10:pre-replicative complex</SHORT-NAME>
+ </complex>
+ <complexParticipant rdf:ID="CDK__nucleoplasm_2">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#CDK__nucleoplasm_1" />
+ </complexParticipant>
+ <complexParticipant rdf:ID="Mcm10_active_pre_replicative_complex__nucleoplasm_3">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Mcm10_active_pre_replicative_complex__nucleoplasm_1" />
+ </complexParticipant>
+ <complexParticipant rdf:ID="DDK__nucleoplasm_2">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#DDK__nucleoplasm_1" />
+ </complexParticipant>
+ <unificationXref rdf:ID="Reactome68918">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">68918</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
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+ <NEXT-STEP rdf:resource="#Cdc45_associates_with_the_pre_replicative_complex_at_the_originStep" />
+ <NEXT-STEP rdf:resource="#Mcm2_7_is_phosphorylated_by_DDKStep" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="Mcm2_7_is_phosphorylated_by_DDK">
+ <LEFT rdf:resource="#ATP__nucleoplasm_" />
+ <LEFT rdf:resource="#Mcm2_7_complex__nucleoplasm_4" />
+ <RIGHT rdf:resource="#ADP__nucleoplasm_" />
+ <RIGHT rdf:resource="#phosphorylated_Mcm2_7_complex__nucleoplasm_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mcm2-7 is phosphorylated by DDK</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mcm2-7 is phosphorylated by DDK</SHORT-NAME>
+ <XREF rdf:resource="#Reactome68954" />
+ <XREF rdf:resource="#Pubmed_10846177" />
+ <CELLULAR-LOCATION rdf:resource="#nucleus" />
+ </biochemicalReaction>
+ <smallMoleculeParticipant rdf:ID="ATP__nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#ATP__ChEBI_2359_" />
+ </smallMoleculeParticipant>
+ <smallMolecule rdf:ID="ATP__ChEBI_2359_">
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ATP [ChEBI:2359]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ATP</SHORT-NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Adenosine 5'-triphosphate</SYNONYMS>
+ </smallMolecule>
+ <complexParticipant rdf:ID="Mcm2_7_complex__nucleoplasm_4">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Mcm2_7_complex__nucleoplasm_1" />
+ </complexParticipant>
+ <smallMoleculeParticipant rdf:ID="ADP__nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#ADP__ChEBI_2342_" />
+ </smallMoleculeParticipant>
+ <smallMolecule rdf:ID="ADP__ChEBI_2342_">
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ADP [ChEBI:2342]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ADP</SHORT-NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Adenosine 5'-diphosphate</SYNONYMS>
+ </smallMolecule>
+ <complexParticipant rdf:ID="phosphorylated_Mcm2_7_complex__nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#phosphorylated_Mcm2_7_complex__nucleoplasm_1" />
+ </complexParticipant>
+ <complex rdf:ID="phosphorylated_Mcm2_7_complex__nucleoplasm_1">
+ <COMPONENTS rdf:resource="#Mcm2_7_complex__nucleoplasm_5" />
+ <COMPONENTS rdf:resource="#Orthophosphate__nucleoplasm_" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">phosphorylated Mcm2-7 complex [nucleoplasm]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">phosphorylated Mcm2-7 complex</SHORT-NAME>
+ </complex>
+ <complexParticipant rdf:ID="Mcm2_7_complex__nucleoplasm_5">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Mcm2_7_complex__nucleoplasm_1" />
+ </complexParticipant>
+ <smallMoleculeParticipant rdf:ID="Orthophosphate__nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Orthophosphate__ChEBI_7793_" />
+ </smallMoleculeParticipant>
+ <smallMolecule rdf:ID="Orthophosphate__ChEBI_7793_">
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Orthophosphate [ChEBI:7793]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Orthophosphate</SHORT-NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Phosphate</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Inorganic Phosphate</SYNONYMS>
+ </smallMolecule>
+ <catalysis rdf:ID="kinase_activity_of_DDK__nucleoplasm_">
+ <CONTROLLER rdf:resource="#DDK__nucleoplasm_3" />
+ <CONTROLLED rdf:resource="#Mcm2_7_is_phosphorylated_by_DDK" />
+ <DIRECTION rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PHYSIOL-LEFT-TO-RIGHT</DIRECTION>
+ <XREF rdf:resource="#kinase_activity" />
+ </catalysis>
+ <complexParticipant rdf:ID="DDK__nucleoplasm_3">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#DDK__nucleoplasm_1" />
+ </complexParticipant>
+ <relationshipXref rdf:ID="kinase_activity">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GO</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0016301</ID>
+ </relationshipXref>
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+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <publicationXref rdf:ID="Pubmed_10846177">
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+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2000</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Human Cdc7-related kinase complex. In vitro phosphorylation of MCM by concerted actions of Cdks and Cdc7 and that of a criticial threonine residue of Cdc7 bY Cdks.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Masai, H</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Matsui, E</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">You, Z</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Ishimi, Y</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Tamai, K</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Arai, K</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Biol Chem 275:29042-52</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="Mcm2_7_is_phosphorylated_by_DDKStep">
+ <STEP-INTERACTIONS rdf:resource="#Mcm2_7_is_phosphorylated_by_DDK" />
+ <STEP-INTERACTIONS rdf:resource="#kinase_activity_of_DDK__nucleoplasm_" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="Cdc45_associates_with_the_pre_replicative_complex_at_the_origin">
+ <LEFT rdf:resource="#CDK_DDK_Mcm10_pre_replicative_complex__nucleoplasm_2" />
+ <LEFT rdf:resource="#Cdc45__nucleoplasm_" />
+ <RIGHT rdf:resource="#Cdc45_CDK_DDK_Mcm10_pre_replicative_complex__nucleoplasm_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cdc45 associates with the pre-replicative complex at the origin</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cdc45 associates with the pre-replicative complex at the origin</SHORT-NAME>
+ <XREF rdf:resource="#Reactome68917" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Once the Mcm2-7 complex has been assembled onto the origin of replication, the next step is the assembly of Cdc45, an essential replication protein, in late G1. The assembly of Cdc45 onto origins of replication forms a complex distinct from the pre-replicative complex, sometimes called the pre-initiation complex. The assembly of Cdc45 onto origins correlates with the time of initiation. Like the Mcm2-7 proteins, Cdc45 bi [...]
+ <EVIDENCE rdf:resource="#Summation_69342" />
+ <XREF rdf:resource="#Pubmed_10518787" />
+ <XREF rdf:resource="#Pubmed_9660782" />
+ <CELLULAR-LOCATION rdf:resource="#nucleus" />
+ </biochemicalReaction>
+ <complexParticipant rdf:ID="CDK_DDK_Mcm10_pre_replicative_complex__nucleoplasm_2">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#CDK_DDK_Mcm10_pre_replicative_complex__nucleoplasm_1" />
+ </complexParticipant>
+ <proteinParticipant rdf:ID="Cdc45__nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_O75419_CDC45_related_protein__PORC_PI_1_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_O75419_CDC45_related_protein__PORC_PI_1_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:O75419 CDC45-related protein (PORC-PI-1)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CDC45L2</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CDC45L</SYNONYMS>
+ <XREF rdf:resource="#UniProt_O75419" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Required for initiation of chromosomal DNA replication. SUBUNIT: Associated with ORC2L. SUBCELLULAR LOCATION: Cytoplasmic and nuclear. TISSUE SPECIFICITY: Widely expressed, highest levels are found in adult testis and tyhmus and in fetal liver. DEVELOPMENTAL STAGE: Transcript peaks at G1-S transition, but total protein remains constant throughout the cell cycle. Expressed in multiple tissues during embryogenesi [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_O75419">
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+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">O75419</ID>
+ </unificationXref>
+ <complexParticipant rdf:ID="Cdc45_CDK_DDK_Mcm10_pre_replicative_complex__nucleoplasm_">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Cdc45_CDK_DDK_Mcm10_pre_replicative_complex__nucleoplasm_1" />
+ </complexParticipant>
+ <complex rdf:ID="Cdc45_CDK_DDK_Mcm10_pre_replicative_complex__nucleoplasm_1">
+ <COMPONENTS rdf:resource="#CDK_DDK_Mcm10_pre_replicative_complex__nucleoplasm_3" />
+ <COMPONENTS rdf:resource="#Cdc45__nucleoplasm_1" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cdc45:CDK:DDK:Mcm10:pre-replicative complex [nucleoplasm]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cdc45:CDK:DDK:Mcm10:pre-replicative complex</SHORT-NAME>
+ </complex>
+ <complexParticipant rdf:ID="CDK_DDK_Mcm10_pre_replicative_complex__nucleoplasm_3">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#CDK_DDK_Mcm10_pre_replicative_complex__nucleoplasm_1" />
+ </complexParticipant>
+ <proteinParticipant rdf:ID="Cdc45__nucleoplasm_1">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_O75419_CDC45_related_protein__PORC_PI_1_" />
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+ <evidence rdf:ID="Summation_69342">
+ <XREF rdf:resource="#Pubmed_9554851" />
+ <XREF rdf:resource="#Pubmed_10430907" />
+ <XREF rdf:resource="#Pubmed_10757793" />
+ <XREF rdf:resource="#Pubmed_9335335" />
+ <XREF rdf:resource="#Pubmed_10790374" />
+ <XREF rdf:resource="#Pubmed_7708676" />
+ <XREF rdf:resource="#Pubmed_12438414" />
+ <XREF rdf:resource="#Pubmed_11756551" />
+ <XREF rdf:resource="#Pubmed_11296242" />
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+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1998</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Formation of a preinitiation complex by S-phase cyclin CDK-dependent loading of Cdc45p onto chromatin.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Zou, L</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Stillman, B</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Science 280:593-6</SOURCE>
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+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1999</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Differential assembly of Cdc45p and DNA polymerases at early and late origins of DNA replication.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Aparicio, OM</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Stout, AM</AUTHORS>
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+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Proc Natl Acad Sci U S A 96:9130-5</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_10757793">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">10757793</ID>
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+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2000</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Assembly of a complex containing Cdc45p, replication protein A, and Mcm2p at replication origins controlled by S-phase cyclin-dependent kinases and Cdc7p-Dbf4p kinase.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Zou, L</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Stillman, B</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mol Cell Biol 20:3086-96</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_10790374">
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+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
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+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DNA synthesis at individual replication forks requires the essential initiation factor Cdc45p.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Tercero, JA</AUTHORS>
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+ </publicationXref>
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+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1995</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cell cycle-regulated nuclear import and export of Cdc47, a protein essential for initiation of DNA replication in budding yeast.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Dalton, S</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Whitbread, L</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Proc Natl Acad Sci U S A 92:2514-8</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_12438414">
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+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The Xenopus Xmus101 protein is required for the recruitment of Cdc45 to origins of DNA replication.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Van Hatten, RA</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Tutter, AV</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Holway, AH</AUTHORS>
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+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Cell Biol 159:541-7</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_11756551">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">11756551</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2001</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A DNA damage-regulated BRCT-containing protein, TopBP1, is required for cell survival.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Yamane, K</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Wu, X</AUTHORS>
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+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mol Cell Biol 22:555-66</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_11296242">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">11296242</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2001</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Sld3, which interacts with Cdc45 (Sld4), functions for chromosomal DNA replication in Saccharomyces cerevisiae.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Kamimura, Y</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Tak, YS</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Sugino, A</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Araki, H</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">EMBO J 20:2097-107</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_10518787">
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+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1999</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Human CDC45 protein binds to minichromosome maintenance 7 protein and the p70 subunit of DNA polymerase alpha.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Kukimoto, I</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Igaki, H</AUTHORS>
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+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Eur J Biochem 265:936-43</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_9660782">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">9660782</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1998</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The human homolog of Saccharomyces cerevisiae CDC45.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Saha, P</AUTHORS>
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+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Yamaguchi, R</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Hou, Z</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Weremowicz, S</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Dutta, A</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Biol Chem 273:18205-9</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="Cdc45_associates_with_the_pre_replicative_complex_at_the_originStep">
+ <STEP-INTERACTIONS rdf:resource="#Cdc45_associates_with_the_pre_replicative_complex_at_the_origin" />
+ <NEXT-STEP rdf:resource="#DNA_Replication_Factor_A__RPA__associates_with_the_pre_replicative_complex_at_the_originStep" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="DNA_Replication_Factor_A__RPA__associates_with_the_pre_replicative_complex_at_the_origin">
+ <LEFT rdf:resource="#DNA_Replication_Factor_A__nucleoplasm_" />
+ <LEFT rdf:resource="#Cdc45_CDK_DDK_Mcm10_pre_replicative_complex__nucleoplasm_2" />
+ <RIGHT rdf:resource="#RPA_Cdc45_CDK_DDK_Mcm10_pre_replicative_complex__nucleoplasm_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DNA Replication Factor A (RPA) associates with the pre-replicative complex at the origin</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DNA Replication Factor A (RPA) associates with the pre-replicative complex at the origin</SHORT-NAME>
+ <XREF rdf:resource="#Reactome68916" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">After pre-RC assembly and Cdc45 association with the origin of replication, Replication Protein A (RPA) also associates with chromatin. RPA is a heterotrimeric complex containing p70, p34, and p11 subunits, and also is required for DNA recombination and DNA repair. The p70 subunit of RPA binds to the primase subunits of Pol alpha:primase. The p70 and p34 subunits of RPA are phosphorylated in a cell cycle-dependent manner [...]
+ <EVIDENCE rdf:resource="#Summation_69369" />
+ <XREF rdf:resource="#Pubmed_10757793" />
+ <XREF rdf:resource="#Pubmed_10882098" />
+ <CELLULAR-LOCATION rdf:resource="#nucleus" />
+ </biochemicalReaction>
+ <complexParticipant rdf:ID="DNA_Replication_Factor_A__nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#DNA_Replication_Factor_A__nucleoplasm_1" />
+ </complexParticipant>
+ <complex rdf:ID="DNA_Replication_Factor_A__nucleoplasm_1">
+ <COMPONENTS rdf:resource="#DNA_Replication_factor_A_protein_A1__70kD___nucleoplasm_" />
+ <COMPONENTS rdf:resource="#DNA_Replication_factor_A_protein_3__14kD___nucleoplasm_" />
+ <COMPONENTS rdf:resource="#DNA_Replication_factor_A_protein_4__30kD___nucleoplasm_" />
+ <COMPONENTS rdf:resource="#DNA_Replication_factor_A_protein_2__32kD___nucleoplasm_" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DNA Replication Factor A [nucleoplasm]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DNA Replication Factor A</SHORT-NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RFA</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RPA</SYNONYMS>
+ </complex>
+ <proteinParticipant rdf:ID="DNA_Replication_factor_A_protein_A1__70kD___nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P27694_Replication_protein_A_70_kDa_DNA_binding_subunit__RP_A___RF_A___Replication_factor_A_protein_1___Single_stranded_DNA_binding_protein_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_P27694_Replication_protein_A_70_kDa_DNA_binding_subunit__RP_A___RF_A___Replication_factor_A_protein_1___Single_stranded_DNA_binding_protein_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P27694 Replication protein A 70 kDa DNA-binding subunit (RP-A) (RF-A) (Replication factor-A protein 1) (Single-stranded DNA-binding protein)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">REPA1</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RPA70</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RPA1</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P27694" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Absolutely required for simian virus 40 DNA replication in vitro. It participates in a very early step in initiation. RP-A is a single-stranded DNA-binding protein. SUBUNIT: Heterotrimer of 70, 32/30, and 14 kDa chains. The DNA- binding activity may reside exclusively on the 70 kDa subunit. SUBCELLULAR LOCATION: Nuclear. SIMILARITY: Belongs to the replication factor-A protein 1 family.</COMMENT>
+ </protein>
+ <unificationXref rdf:ID="UniProt_P27694">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P27694</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="DNA_Replication_factor_A_protein_3__14kD___nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P35244_Replication_protein_A_14_kDa_subunit__RP_A___RF_A___Replication_factor_A_protein_3_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_P35244_Replication_protein_A_14_kDa_subunit__RP_A___RF_A___Replication_factor_A_protein_3_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P35244 Replication protein A 14 kDa subunit (RP-A) (RF-A) (Replication factor-A protein 3)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RPA14</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">REPA3</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RPA3</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P35244" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Absolutely required for simian virus 40 DNA replication in vitro. It participates in a very early step in initiation. RP-A is a single-stranded DNA-binding protein. SUBUNIT: Heterotrimer of 70, 32/30, and 14 kDa chains. The DNA- binding activity may reside exclusively on the 70 kDa subunit. SUBCELLULAR LOCATION: Nuclear.</COMMENT>
+ </protein>
+ <unificationXref rdf:ID="UniProt_P35244">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P35244</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="DNA_Replication_factor_A_protein_4__30kD___nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q13156_Replication_protein_A_30_kDa_subunit__RP_A___RF_A___Replication_factor_A_protein_4_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_Q13156_Replication_protein_A_30_kDa_subunit__RP_A___RF_A___Replication_factor_A_protein_4_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:Q13156 Replication protein A 30 kDa subunit (RP-A) (RF-A) (Replication factor-A protein 4)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RPA4</SYNONYMS>
+ <XREF rdf:resource="#UniProt_Q13156" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Absolutely required for simian virus 40 DNA replication in vitro. It participates in a very early step in initiation. RP-A is a single-stranded DNA-binding protein (By similarity). SUBUNIT: Heterotrimer of 70, 32/30, and 14 kDa chains. The DNA- binding activity may reside exclusively on the 70 kDa subunit. SUBCELLULAR LOCATION: Nuclear. TISSUE SPECIFICITY: Preferentially expressed in placental and colon mucosa. [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_Q13156">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Q13156</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="DNA_Replication_factor_A_protein_2__32kD___nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P15927_Replication_protein_A_32_kDa_subunit__RP_A___RF_A___Replication_factor_A_protein_2_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_P15927_Replication_protein_A_32_kDa_subunit__RP_A___RF_A___Replication_factor_A_protein_2_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P15927 Replication protein A 32 kDa subunit (RP-A) (RF-A) (Replication factor-A protein 2)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RPA32</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">REPA2</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RPA2</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P15927" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Absolutely required for simian virus 40 DNA replication in vitro. It participates in a very early step in initiation. RP-A is a single-stranded DNA-binding protein. SUBUNIT: Heterotrimer of 70, 32/30, and 14 kDa chains. The DNA- binding activity may reside exclusively on the 70 kDa subunit. SUBCELLULAR LOCATION: Nuclear. PTM: Phosphorylated in a cell-cycle-dependent manner (from the S phase until mitosis).</COMMENT>
+ </protein>
+ <unificationXref rdf:ID="UniProt_P15927">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P15927</ID>
+ </unificationXref>
+ <complexParticipant rdf:ID="Cdc45_CDK_DDK_Mcm10_pre_replicative_complex__nucleoplasm_2">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Cdc45_CDK_DDK_Mcm10_pre_replicative_complex__nucleoplasm_1" />
+ </complexParticipant>
+ <complexParticipant rdf:ID="RPA_Cdc45_CDK_DDK_Mcm10_pre_replicative_complex__nucleoplasm_">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#RPA_Cdc45_CDK_DDK_Mcm10_pre_replicative_complex__nucleoplasm_1" />
+ </complexParticipant>
+ <complex rdf:ID="RPA_Cdc45_CDK_DDK_Mcm10_pre_replicative_complex__nucleoplasm_1">
+ <COMPONENTS rdf:resource="#DNA_Replication_Factor_A__nucleoplasm_2" />
+ <COMPONENTS rdf:resource="#Cdc45_CDK_DDK_Mcm10_pre_replicative_complex__nucleoplasm_3" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RPA:Cdc45:CDK:DDK:Mcm10:pre-replicative complex [nucleoplasm]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RPA:Cdc45:CDK:DDK:Mcm10:pre-replicative complex</SHORT-NAME>
+ </complex>
+ <complexParticipant rdf:ID="DNA_Replication_Factor_A__nucleoplasm_2">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#DNA_Replication_Factor_A__nucleoplasm_1" />
+ </complexParticipant>
+ <complexParticipant rdf:ID="Cdc45_CDK_DDK_Mcm10_pre_replicative_complex__nucleoplasm_3">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Cdc45_CDK_DDK_Mcm10_pre_replicative_complex__nucleoplasm_1" />
+ </complexParticipant>
+ <unificationXref rdf:ID="Reactome68916">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">68916</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <evidence rdf:ID="Summation_69369">
+ <XREF rdf:resource="#Pubmed_9242902" />
+ <XREF rdf:resource="#Pubmed_10473346" />
+ <XREF rdf:resource="#Pubmed_1311258" />
+ <XREF rdf:resource="#Pubmed_2200738" />
+ </evidence>
+ <publicationXref rdf:ID="Pubmed_9242902">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">9242902</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1997</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Replication protein A: a heterotrimeric, single-stranded DNA-binding protein required for eukaryotic DNA metabolism.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Wold, MS</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Annu Rev Biochem 66:61-92</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_10473346">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">10473346</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1999</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Replication protein A (RPA): the eukaryotic SSB.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Iftode, C</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Daniely, Y</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Borowiec, JA</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Crit Rev Biochem Mol Biol 34:141-80</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_1311258">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">1311258</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1992</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Interaction of DNA polymerase alpha-primase with cellular replication protein A and SV40 T antigen.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Dornreiter, I</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Erdile, LF</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Gilbert, IU</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">von Winkler, D</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Kelly, TJ</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Fanning, E</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">EMBO J 11:769-76</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_2200738">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2200738</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1990</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cell-cycle-regulated phosphorylation of DNA replication factor A from human and yeast cells.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Din, S</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Brill, SJ</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Fairman, MP</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Stillman, B</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Genes Dev 4:968-77</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_10882098">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">10882098</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2000</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Initiation of eukaryotic DNA replication: origin unwinding and sequential chromatin association of Cdc45, RPA, and DNA polymerase alpha.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Walter, J</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Newport, J</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mol Cell 5:617-27</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="DNA_Replication_Factor_A__RPA__associates_with_the_pre_replicative_complex_at_the_originStep">
+ <STEP-INTERACTIONS rdf:resource="#DNA_Replication_Factor_A__RPA__associates_with_the_pre_replicative_complex_at_the_origin" />
+ <NEXT-STEP rdf:resource="#DNA_polymerase_alpha_primase_binds_at_the_originStep" />
+ <NEXT-STEP rdf:resource="#DNA_polymerase_epsilon_binds_at_the_originStep" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="DNA_polymerase_alpha_primase_binds_at_the_origin">
+ <LEFT rdf:resource="#DNA_polymerase_alpha_primase__nucleoplasm_" />
+ <LEFT rdf:resource="#DNA_polymerase_epsilon_origin_complex__nucleoplasm_" />
+ <RIGHT rdf:resource="#DNA_polymerase_alpha_primase_DNA_polymerase_alpha_origin_complex__nucleoplasm_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DNA polymerase alpha:primase binds at the origin</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DNA polymerase alpha:primase binds at the origin</SHORT-NAME>
+ <XREF rdf:resource="#Reactome68914" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DNA polymerase alpha:primase is comprised of four subunits, p180, p70, p58, and p49. The two primase subunits, p58 and p49, form a tight complex. The p49 subunit contains the DNA primase activity and one role of p58 appears to be tethering p49 to p180, the DNA polymerase catalytic subunit. The fourth subunit, p70, binds p180 and may tether the DNA polymerase alpha:primase complex to Cdc45.</COMMENT>
+ <EVIDENCE rdf:resource="#Summation_69386" />
+ <XREF rdf:resource="#Pubmed_10757793" />
+ <XREF rdf:resource="#Pubmed_10882098" />
+ <XREF rdf:resource="#Pubmed_12045100" />
+ <CELLULAR-LOCATION rdf:resource="#nucleus" />
+ </biochemicalReaction>
+ <complexParticipant rdf:ID="DNA_polymerase_alpha_primase__nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#DNA_polymerase_alpha_primase__nucleoplasm_1" />
+ </complexParticipant>
+ <complex rdf:ID="DNA_polymerase_alpha_primase__nucleoplasm_1">
+ <COMPONENTS rdf:resource="#p49__nucleoplasm_" />
+ <COMPONENTS rdf:resource="#p180__nucleoplasm_" />
+ <COMPONENTS rdf:resource="#p70__nucleoplasm_" />
+ <COMPONENTS rdf:resource="#p58__nucleoplasm_" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DNA polymerase alpha:primase [nucleoplasm]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DNA polymerase alpha:primase</SHORT-NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">primosome</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DNA Pol alpha:primase</SYNONYMS>
+ </complex>
+ <proteinParticipant rdf:ID="p49__nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P49642_DNA_primase_small_subunit__EC_2_7_7_____DNA_primase_49_kDa_subunit___p49_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_P49642_DNA_primase_small_subunit__EC_2_7_7_____DNA_primase_49_kDa_subunit___p49_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P49642 DNA primase small subunit (EC 2.7.7.-) (DNA primase 49 kDa subunit) (p49)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PRIM1</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P49642" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: DNA primase is the polymerase that synthesizes small RNA primers for the Okazaki fragments made during discontinuous DNA replication. SUBUNIT: Heterodimer of a small subunit and a large subunit. MISCELLANEOUS: The bound zinc ion is not a cofactor. It is bound to a zinc knuckle motif that may be involved in sequence recognition and the binding of ssDNA (By similarity). SIMILARITY: Belongs to the eukaryotic-type [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_P49642">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P49642</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="p180__nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P09884_DNA_polymerase_alpha_catalytic_subunit__EC_2_7_7_7_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_P09884_DNA_polymerase_alpha_catalytic_subunit__EC_2_7_7_7_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P09884 DNA polymerase alpha catalytic subunit (EC 2.7.7.7)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">POLA</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P09884" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Polymerase alpha in a complex with DNA primase is a replicative polymerase. CATALYTIC ACTIVITY: N deoxynucleoside triphosphate = N diphosphate + {DNA}(N). SUBCELLULAR LOCATION: Nuclear. MISCELLANEOUS: In eukaryotes there are five DNA polymerases: alpha, beta, gamma, delta, and epsilon which are responsible for different reactions of DNA synthesis. SIMILARITY: Belongs to the DNA polymerase type-B family.</COMMENT>
+ </protein>
+ <unificationXref rdf:ID="UniProt_P09884">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P09884</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="p70__nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q14181_DNA_polymerase_alpha_70_kDa_subunit__DNA_polymerase_subunit_B_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_Q14181_DNA_polymerase_alpha_70_kDa_subunit__DNA_polymerase_subunit_B_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:Q14181 DNA polymerase alpha 70 kDa subunit (DNA polymerase subunit B)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">POLA2</SYNONYMS>
+ <XREF rdf:resource="#UniProt_Q14181" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: May play an essential role at the early stage of chromosomal DNA replication by coupling the polymerase alpha/primase complex to the cellular replication machinery (By similarity). SUBUNIT: DNA polymerase alpha-primase is a four subunit enzyme (subunits A, B, C and D), which is assembled throughout the cell cycle. The largest subunit (subunit A) has DNA polymerase activity, the two smallest subunits (subunits C [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_Q14181">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Q14181</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="p58__nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P49643_DNA_primase_large_subunit__EC_2_7_7_____DNA_primase_58_kDa_subunit___p58_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_P49643_DNA_primase_large_subunit__EC_2_7_7_____DNA_primase_58_kDa_subunit___p58_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P49643 DNA primase large subunit (EC 2.7.7.-) (DNA primase 58 kDa subunit) (p58)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PRIM2A</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PRIM2</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P49643" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: DNA primase is the polymerase that synthesizes small RNA primers for the Okazaki fragments made during discontinuous DNA replication. SUBUNIT: Heterodimer of a small subunit and a large subunit. SIMILARITY: Belongs to the eukaryotic-type primase large subunit family.</COMMENT>
+ </protein>
+ <unificationXref rdf:ID="UniProt_P49643">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P49643</ID>
+ </unificationXref>
+ <complexParticipant rdf:ID="DNA_polymerase_epsilon_origin_complex__nucleoplasm_">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#DNA_polymerase_epsilon_origin_complex__nucleoplasm_1" />
+ </complexParticipant>
+ <complex rdf:ID="DNA_polymerase_epsilon_origin_complex__nucleoplasm_1">
+ <COMPONENTS rdf:resource="#origin_of_replication__nucleoplasm_3" />
+ <COMPONENTS rdf:resource="#DNA_polymerase_epsilon__nucleoplasm_" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DNA polymerase epsilon:origin complex [nucleoplasm]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DNA polymerase epsilon:origin complex</SHORT-NAME>
+ </complex>
+ <physicalEntityParticipant rdf:ID="origin_of_replication__nucleoplasm_3">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#origin_of_replication__nucleoplasm_1" />
+ </physicalEntityParticipant>
+ <complexParticipant rdf:ID="DNA_polymerase_epsilon__nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#DNA_polymerase_epsilon__nucleoplasm_1" />
+ </complexParticipant>
+ <complex rdf:ID="DNA_polymerase_epsilon__nucleoplasm_1">
+ <COMPONENTS rdf:resource="#DNA_polymerase_epsilon_subunit_B___nucleoplasm_" />
+ <COMPONENTS rdf:resource="#DNA_polymerase_epsilon__catalytic_subunit_A___nucleoplasm_" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DNA polymerase epsilon [nucleoplasm]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DNA polymerase epsilon</SHORT-NAME>
+ </complex>
+ <proteinParticipant rdf:ID="DNA_polymerase_epsilon_subunit_B___nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P56282_DNA_polymerase_epsilon_subunit_B__EC_2_7_7_7___DNA_polymerase_II_subunit_B_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_P56282_DNA_polymerase_epsilon_subunit_B__EC_2_7_7_7___DNA_polymerase_II_subunit_B_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P56282 DNA polymerase epsilon subunit B (EC 2.7.7.7) (DNA polymerase II subunit B)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DPE2</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">POLE2</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P56282" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Participates in DNA repair and in chromosomal DNA replication. CATALYTIC ACTIVITY: N deoxynucleoside triphosphate = N diphosphate + {DNA}(N). SUBUNIT: Consists of two subunits (258 kDa and 55 kDa). SUBCELLULAR LOCATION: Nuclear. MISCELLANEOUS: In eukaryotes there are five DNA polymerases: alpha, beta, gamma, delta, and epsilon which are responsible for different reactions of DNA synthesis. SIMILARITY: Belongs t [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_P56282">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P56282</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="DNA_polymerase_epsilon__catalytic_subunit_A___nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q07864_DNA_polymerase_epsilon__catalytic_subunit_A__EC_2_7_7_7___DNA_polymerase_II_subunit_A_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_Q07864_DNA_polymerase_epsilon__catalytic_subunit_A__EC_2_7_7_7___DNA_polymerase_II_subunit_A_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:Q07864 DNA polymerase epsilon, catalytic subunit A (EC 2.7.7.7) (DNA polymerase II subunit A)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">POLE</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">POLE1</SYNONYMS>
+ <XREF rdf:resource="#UniProt_Q07864" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Participates in DNA repair and in chromosomal DNA replication. CATALYTIC ACTIVITY: N deoxynucleoside triphosphate = N diphosphate + {DNA}(N). SUBUNIT: Consists of two subunits (258 kDa and 55 kDa). SUBCELLULAR LOCATION: Nuclear. DOMAIN: The DNA polymerase activity domain resides in the N- terminal half of the protein, while the C-terminus is necessary for complexing subunits B and C. The C-terminus may also reg [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_Q07864">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Q07864</ID>
+ </unificationXref>
+ <complexParticipant rdf:ID="DNA_polymerase_alpha_primase_DNA_polymerase_alpha_origin_complex__nucleoplasm_">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#DNA_polymerase_alpha_primase_DNA_polymerase_alpha_origin_complex__nucleoplasm_1" />
+ </complexParticipant>
+ <complex rdf:ID="DNA_polymerase_alpha_primase_DNA_polymerase_alpha_origin_complex__nucleoplasm_1">
+ <COMPONENTS rdf:resource="#DNA_polymerase_alpha_primase__nucleoplasm_2" />
+ <COMPONENTS rdf:resource="#DNA_polymerase_epsilon_origin_complex__nucleoplasm_2" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DNA polymerase alpha:primase:DNA polymerase alpha:origin complex [nucleoplasm]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DNA polymerase alpha:primase:DNA polymerase alpha:origin complex</SHORT-NAME>
+ </complex>
+ <complexParticipant rdf:ID="DNA_polymerase_alpha_primase__nucleoplasm_2">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#DNA_polymerase_alpha_primase__nucleoplasm_1" />
+ </complexParticipant>
+ <complexParticipant rdf:ID="DNA_polymerase_epsilon_origin_complex__nucleoplasm_2">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#DNA_polymerase_epsilon_origin_complex__nucleoplasm_1" />
+ </complexParticipant>
+ <unificationXref rdf:ID="Reactome68914">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">68914</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <evidence rdf:ID="Summation_69386">
+ <XREF rdf:resource="#Pubmed_11395402" />
+ <XREF rdf:resource="#Pubmed_8253737" />
+ </evidence>
+ <publicationXref rdf:ID="Pubmed_11395402">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">11395402</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2002</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DNA primases.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Frick, DN</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Richardson, CC</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Annu Rev Biochem 70:39-80</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_8253737">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">8253737</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1994</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Enzymatic characterization of the individual mammalian primase subunits reveals a biphasic mechanism for initiation of DNA replication.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Copeland, WC</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Wang, TS</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Biol Chem 268:26179-89</SOURCE>
+ </publicationXref>
+ <modulation rdf:ID="_RPA_Cdc45_CDK_DDK_Mcm10_pre_replicative_complex__positively_regulates__DNA_polymerase_alpha_primase_binds_at_the_origin_">
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">'RPA:Cdc45:CDK:DDK:Mcm10:pre-replicative complex' positively regulates 'DNA polymerase alpha:primase binds at the origin'</NAME>
+ <CONTROL-TYPE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ACTIVATION</CONTROL-TYPE>
+ <CONTROLLER rdf:resource="#RPA_Cdc45_CDK_DDK_Mcm10_pre_replicative_complex__nucleoplasm_2" />
+ <CONTROLLED rdf:resource="#DNA_polymerase_alpha_primase_binds_at_the_origin" />
+ </modulation>
+ <complexParticipant rdf:ID="RPA_Cdc45_CDK_DDK_Mcm10_pre_replicative_complex__nucleoplasm_2">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#RPA_Cdc45_CDK_DDK_Mcm10_pre_replicative_complex__nucleoplasm_1" />
+ </complexParticipant>
+ <pathwayStep rdf:ID="DNA_polymerase_alpha_primase_binds_at_the_originStep">
+ <STEP-INTERACTIONS rdf:resource="#DNA_polymerase_alpha_primase_binds_at_the_origin" />
+ <NEXT-STEP rdf:resource="#The_primase_component_of_DNA_polymerase_primase_synthesizes_a_6_10_nucleotide_RNA_primer_at_the_originStep" />
+ <STEP-INTERACTIONS rdf:resource="#_RPA_Cdc45_CDK_DDK_Mcm10_pre_replicative_complex__positively_regulates__DNA_polymerase_alpha_primase_binds_at_the_origin_" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="DNA_polymerase_epsilon_binds_at_the_origin">
+ <LEFT rdf:resource="#origin_of_replication__nucleoplasm_4" />
+ <LEFT rdf:resource="#DNA_polymerase_epsilon__nucleoplasm_2" />
+ <RIGHT rdf:resource="#DNA_polymerase_epsilon_origin_complex__nucleoplasm_3" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DNA polymerase epsilon binds at the origin</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DNA polymerase epsilon binds at the origin</SHORT-NAME>
+ <XREF rdf:resource="#Reactome68960" />
+ <XREF rdf:resource="#Pubmed_12045100" />
+ </biochemicalReaction>
+ <physicalEntityParticipant rdf:ID="origin_of_replication__nucleoplasm_4">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#origin_of_replication__nucleoplasm_1" />
+ </physicalEntityParticipant>
+ <complexParticipant rdf:ID="DNA_polymerase_epsilon__nucleoplasm_2">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#DNA_polymerase_epsilon__nucleoplasm_1" />
+ </complexParticipant>
+ <complexParticipant rdf:ID="DNA_polymerase_epsilon_origin_complex__nucleoplasm_3">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#DNA_polymerase_epsilon_origin_complex__nucleoplasm_1" />
+ </complexParticipant>
+ <unificationXref rdf:ID="Reactome68960">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">68960</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <modulation rdf:ID="_RPA_Cdc45_CDK_DDK_Mcm10_pre_replicative_complex__positively_regulates__DNA_polymerase_epsilon_binds_at_the_origin_">
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">'RPA:Cdc45:CDK:DDK:Mcm10:pre-replicative complex' positively regulates 'DNA polymerase epsilon binds at the origin'</NAME>
+ <CONTROL-TYPE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ACTIVATION</CONTROL-TYPE>
+ <CONTROLLER rdf:resource="#RPA_Cdc45_CDK_DDK_Mcm10_pre_replicative_complex__nucleoplasm_3" />
+ <CONTROLLED rdf:resource="#DNA_polymerase_epsilon_binds_at_the_origin" />
+ </modulation>
+ <complexParticipant rdf:ID="RPA_Cdc45_CDK_DDK_Mcm10_pre_replicative_complex__nucleoplasm_3">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#RPA_Cdc45_CDK_DDK_Mcm10_pre_replicative_complex__nucleoplasm_1" />
+ </complexParticipant>
+ <pathwayStep rdf:ID="DNA_polymerase_epsilon_binds_at_the_originStep">
+ <STEP-INTERACTIONS rdf:resource="#DNA_polymerase_epsilon_binds_at_the_origin" />
+ <STEP-INTERACTIONS rdf:resource="#_RPA_Cdc45_CDK_DDK_Mcm10_pre_replicative_complex__positively_regulates__DNA_polymerase_epsilon_binds_at_the_origin_" />
+ </pathwayStep>
+ <unificationXref rdf:ID="Reactome68962">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">68962</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <evidence rdf:ID="Summation_68963">
+ <XREF rdf:resource="#Pubmed_9038340" />
+ <XREF rdf:resource="#Pubmed_11459976" />
+ <XREF rdf:resource="#Pubmed_10970868" />
+ <XREF rdf:resource="#Pubmed_10801458" />
+ <XREF rdf:resource="#Pubmed_7502077" />
+ <XREF rdf:resource="#Pubmed_11779870" />
+ <XREF rdf:resource="#Pubmed_10402192" />
+ <XREF rdf:resource="#Pubmed_9829972" />
+ <XREF rdf:resource="#Pubmed_9353276" />
+ <XREF rdf:resource="#Pubmed_9765232" />
+ <XREF rdf:resource="#Pubmed_12169736" />
+ <XREF rdf:resource="#Pubmed_11395502" />
+ <XREF rdf:resource="#Pubmed_11323433" />
+ </evidence>
+ <publicationXref rdf:ID="Pubmed_9038340">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">9038340</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1997</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Coordinate binding of ATP and origin DNA regulates the ATPase activity of the origin recognition complex.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Klemm, RD</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Austin, RJ</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bell, SP</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cell 88:493-502</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_11459976">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">11459976</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2001</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ATP bound to the origin recognition complex is important for preRC formation.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Klemm, RD</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bell, SP</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Proc Natl Acad Sci U S A 98:8361-7</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_10970868">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">10970868</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2000</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Regulation of origin recognition complex conformation and ATPase activity: differential effects of single-stranded and double-stranded DNA binding.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Lee, DG</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Makhov, AM</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Klemm, RD</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Griffith, JD</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bell, SP</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">EMBO J 19:4774-82</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_7502077">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">7502077</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1996</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Conserved initiator proteins in eukaryotes.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Gavin, KA</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Hidaka, M</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Stillman, B</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Science 270:1667-71</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_11779870">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">11779870</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2002</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Nuclear organization of DNA replication initiation proteins in mammalian cells.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Fujita, M</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Ishimi, Y</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Nakamura, H</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Kiyono, T</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Tsurumi, T</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Biol Chem 277:10354-61</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_10402192">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">10402192</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1999</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">latheo encodes a subunit of the origin recognition complex and disrupts neuronal proliferation and adult olfactory memory when mutant.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pinto, S</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Quintana, DG</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Smith, P</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mihalek, RM</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Hou, ZH</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Boynton, S</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Jones, CJ</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Hendricks, M</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Velinzon, K</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Wohlschlegel, JA</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Austin, RJ</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Lane, WS</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Tully, T</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Dutta, A</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Neuron 23:45-54</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_9353276">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">9353276</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1997</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Identification of HsORC4, a member of the human origin of replication recognition complex.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Quintana, DG</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Hou, Zh</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Thome, KC</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Hendricks, M</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Saha, P</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Dutta, A</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Biol Chem 272:28247-51</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_12169736">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">12169736</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2002</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Orc6 involved in DNA replication, chromosome segregation, and cytokinesis.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Prasanth, SG</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Prasanth, KV</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Stillman, B</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Science 297:1026-31</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="Activation_of_the_pre_replicative_complexStep">
+ <STEP-INTERACTIONS rdf:resource="#Activation_of_the_pre_replicative_complex" />
+ <NEXT-STEP rdf:resource="#DNA_replication_initiationStep" />
+ <NEXT-STEP rdf:resource="#The_primase_component_of_DNA_polymerase_primase_synthesizes_a_6_10_nucleotide_RNA_primer_at_the_originStep" />
+ </pathwayStep>
+ <unificationXref rdf:ID="Reactome69002">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">69002</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <evidence rdf:ID="Summation_69003" />
+ <pathwayStep rdf:ID="DNA_Replication_Pre_InitiationStep">
+ <STEP-INTERACTIONS rdf:resource="#DNA_Replication_Pre_Initiation" />
+ </pathwayStep>
+ <pathway rdf:ID="DNA_replication_initiation">
+ <PATHWAY-COMPONENTS rdf:resource="#The_primase_component_of_DNA_polymerase_primase_synthesizes_a_6_10_nucleotide_RNA_primer_at_the_originStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#The_polymerase_component_of_DNA_polymerase_alpha_primase_synthesizes_a_20_nucleotide_primer_at_the_originStep" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DNA replication initiation</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DNA replication initiation</SHORT-NAME>
+ <XREF rdf:resource="#Reactome68952" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DNA polymerases are not capable of de novo DNA synthesis and require synthesis of a primer, usually by a DNA-dependent RNA polymerase (primase) to begin DNA synthesis. In eukaryotic cells, the primer is synthesized by DNA polymerase alpha:primase. First, the DNA primase portion of this complex synthesizes approximately 6-10 nucleotides of RNA primer and then the DNA polymerase portion synthesizes an additional 20 nucleot [...]
+ <EVIDENCE rdf:resource="#Summation_69326" />
+ <CELLULAR-LOCATION rdf:resource="#nucleus" />
+ </pathway>
+ <biochemicalReaction rdf:ID="The_primase_component_of_DNA_polymerase_primase_synthesizes_a_6_10_nucleotide_RNA_primer_at_the_origin">
+ <LEFT rdf:resource="#DNA_polymerase_alpha_primase_DNA_polymerase_alpha_origin_complex__nucleoplasm_2" />
+ <LEFT rdf:resource="#NTP__nucleoplasm_" />
+ <RIGHT rdf:resource="#RNA_primer_origin_duplex_DNA_polymerase_alpha_primase_complex__nucleoplasm_" />
+ <RIGHT rdf:resource="#DNA_polymerase_epsilon__nucleoplasm_3" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The primase component of DNA polymerase:primase synthesizes a 6-10 nucleotide RNA primer at the origin</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The primase component of DNA polymerase:primase synthesizes a 6-10 nucleotide RNA primer at the origin</SHORT-NAME>
+ <XREF rdf:resource="#Reactome68913" />
+ <XREF rdf:resource="#Pubmed_6693436" />
+ <CELLULAR-LOCATION rdf:resource="#nucleus" />
+ </biochemicalReaction>
+ <complexParticipant rdf:ID="DNA_polymerase_alpha_primase_DNA_polymerase_alpha_origin_complex__nucleoplasm_2">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#DNA_polymerase_alpha_primase_DNA_polymerase_alpha_origin_complex__nucleoplasm_1" />
+ </complexParticipant>
+ <smallMoleculeParticipant rdf:ID="NTP__nucleoplasm_">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#NTP" />
+ </smallMoleculeParticipant>
+ <smallMolecule rdf:ID="NTP">
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">NTP</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">NTP</SHORT-NAME>
+ <XREF rdf:resource="#ChEBI_7442" />
+ </smallMolecule>
+ <unificationXref rdf:ID="ChEBI_7442">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ChEBI</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">7442</ID>
+ </unificationXref>
+ <complexParticipant rdf:ID="RNA_primer_origin_duplex_DNA_polymerase_alpha_primase_complex__nucleoplasm_">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#RNA_primer_origin_duplex_DNA_polymerase_alpha_primase_complex__nucleoplasm_1" />
+ </complexParticipant>
+ <complex rdf:ID="RNA_primer_origin_duplex_DNA_polymerase_alpha_primase_complex__nucleoplasm_1">
+ <COMPONENTS rdf:resource="#origin_of_replication__nucleoplasm_5" />
+ <COMPONENTS rdf:resource="#RNA_primer__nucleoplasm_" />
+ <COMPONENTS rdf:resource="#DNA_polymerase_alpha_primase__nucleoplasm_3" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RNA primer:origin duplex:DNA polymerase alpha:primase complex [nucleoplasm]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RNA primer:origin duplex:DNA polymerase alpha:primase complex</SHORT-NAME>
+ </complex>
+ <physicalEntityParticipant rdf:ID="origin_of_replication__nucleoplasm_5">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#origin_of_replication__nucleoplasm_1" />
+ </physicalEntityParticipant>
+ <physicalEntityParticipant rdf:ID="RNA_primer__nucleoplasm_">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#RNA_primer__nucleoplasm_1" />
+ </physicalEntityParticipant>
+ <physicalEntity rdf:ID="RNA_primer__nucleoplasm_1">
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RNA primer [nucleoplasm]</NAME>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome. Each synonym is a name of a ConcreteEntity, and each XREF points to one ConcreteEntity</COMMENT>
+ </physicalEntity>
+ <complexParticipant rdf:ID="DNA_polymerase_alpha_primase__nucleoplasm_3">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#DNA_polymerase_alpha_primase__nucleoplasm_1" />
+ </complexParticipant>
+ <complexParticipant rdf:ID="DNA_polymerase_epsilon__nucleoplasm_3">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#DNA_polymerase_epsilon__nucleoplasm_1" />
+ </complexParticipant>
+ <catalysis rdf:ID="DNA_directed_RNA_polymerase_activity_of_DNA_polymerase_alpha_primase__nucleoplasm_">
+ <CONTROLLER rdf:resource="#DNA_polymerase_alpha_primase__nucleoplasm_4" />
+ <CONTROLLED rdf:resource="#The_primase_component_of_DNA_polymerase_primase_synthesizes_a_6_10_nucleotide_RNA_primer_at_the_origin" />
+ <DIRECTION rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PHYSIOL-LEFT-TO-RIGHT</DIRECTION>
+ <XREF rdf:resource="#DNA_directed_RNA_polymerase_activity" />
+ </catalysis>
+ <complexParticipant rdf:ID="DNA_polymerase_alpha_primase__nucleoplasm_4">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#DNA_polymerase_alpha_primase__nucleoplasm_1" />
+ </complexParticipant>
+ <relationshipXref rdf:ID="DNA_directed_RNA_polymerase_activity">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GO</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0003899</ID>
+ </relationshipXref>
+ <unificationXref rdf:ID="Reactome68913">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">68913</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <publicationXref rdf:ID="Pubmed_6693436">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">6693436</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1984</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DNA primase from KB cells. Characterization of a primase activity tightly associated with immunoaffinity-purified DNA polymerase-alpha.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Wang, TS</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Hu, SZ</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Korn, D</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Biol Chem 259:1854-65</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="The_primase_component_of_DNA_polymerase_primase_synthesizes_a_6_10_nucleotide_RNA_primer_at_the_originStep">
+ <STEP-INTERACTIONS rdf:resource="#The_primase_component_of_DNA_polymerase_primase_synthesizes_a_6_10_nucleotide_RNA_primer_at_the_origin" />
+ <NEXT-STEP rdf:resource="#The_polymerase_component_of_DNA_polymerase_alpha_primase_synthesizes_a_20_nucleotide_primer_at_the_originStep" />
+ <STEP-INTERACTIONS rdf:resource="#DNA_directed_RNA_polymerase_activity_of_DNA_polymerase_alpha_primase__nucleoplasm_" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="The_polymerase_component_of_DNA_polymerase_alpha_primase_synthesizes_a_20_nucleotide_primer_at_the_origin">
+ <LEFT rdf:resource="#dGTP__nucleoplasm_" />
+ <LEFT rdf:resource="#dTTP__nucleoplasm_" />
+ <LEFT rdf:resource="#RNA_primer_origin_duplex_DNA_polymerase_alpha_primase_complex__nucleoplasm_2" />
+ <LEFT rdf:resource="#dATP__nucleoplasm_" />
+ <LEFT rdf:resource="#dCTP__nucleoplasm_" />
+ <RIGHT rdf:resource="#RNA_primer_DNA_primer_origin_duplex__nucleoplasm_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The polymerase component of DNA polymerase alpha:primase synthesizes a 20-nucleotide primer at the origin</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The polymerase component of DNA polymerase alpha:primase synthesizes a 20-nucleotide primer at the origin</SHORT-NAME>
+ <XREF rdf:resource="#Reactome68950" />
+ <CELLULAR-LOCATION rdf:resource="#nucleus" />
+ </biochemicalReaction>
+ <smallMoleculeParticipant rdf:ID="dGTP__nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#dGTP__ChEBI_10497_" />
+ </smallMoleculeParticipant>
+ <smallMolecule rdf:ID="dGTP__ChEBI_10497_">
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">dGTP [ChEBI:10497]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">dGTP</SHORT-NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Deoxyguanosine triphosphate</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Deoxyguanosine 5'-triphosphate</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2'-deoxyguanosine 5'-triphosphate</SYNONYMS>
+ <XREF rdf:resource="#ChEBI_10497" />
+ </smallMolecule>
+ <unificationXref rdf:ID="ChEBI_10497">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ChEBI</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">10497</ID>
+ </unificationXref>
+ <smallMoleculeParticipant rdf:ID="dTTP__nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#dTTP__ChEBI_10530_" />
+ </smallMoleculeParticipant>
+ <smallMolecule rdf:ID="dTTP__ChEBI_10530_">
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">dTTP [ChEBI:10530]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">dTTP</SHORT-NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Deoxythymidine triphosphate</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TTP</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Deoxythymidine 5'-triphosphate</SYNONYMS>
+ <XREF rdf:resource="#ChEBI_10530" />
+ </smallMolecule>
+ <unificationXref rdf:ID="ChEBI_10530">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ChEBI</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">10530</ID>
+ </unificationXref>
+ <complexParticipant rdf:ID="RNA_primer_origin_duplex_DNA_polymerase_alpha_primase_complex__nucleoplasm_2">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#RNA_primer_origin_duplex_DNA_polymerase_alpha_primase_complex__nucleoplasm_1" />
+ </complexParticipant>
+ <smallMoleculeParticipant rdf:ID="dATP__nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#dATP__ChEBI_10491_" />
+ </smallMoleculeParticipant>
+ <smallMolecule rdf:ID="dATP__ChEBI_10491_">
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">dATP [ChEBI:10491]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">dATP</SHORT-NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Deoxyadenosine 5'-triphosphate</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2'-deoxyadenosine 5'-triphosphate</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Deoxyadenosine triphosphate</SYNONYMS>
+ <XREF rdf:resource="#ChEBI_10491" />
+ </smallMolecule>
+ <unificationXref rdf:ID="ChEBI_10491">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ChEBI</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">10491</ID>
+ </unificationXref>
+ <smallMoleculeParticipant rdf:ID="dCTP__nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#dCTP__ChEBI_10494_" />
+ </smallMoleculeParticipant>
+ <smallMolecule rdf:ID="dCTP__ChEBI_10494_">
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">dCTP [ChEBI:10494]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">dCTP</SHORT-NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2'-Deoxycytidine 5'-triphosphate</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">deoxycytidine 5'-triphosphate</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Deoxycytidine triphosphate</SYNONYMS>
+ <XREF rdf:resource="#ChEBI_10494" />
+ </smallMolecule>
+ <unificationXref rdf:ID="ChEBI_10494">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ChEBI</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">10494</ID>
+ </unificationXref>
+ <complexParticipant rdf:ID="RNA_primer_DNA_primer_origin_duplex__nucleoplasm_">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#RNA_primer_DNA_primer_origin_duplex__nucleoplasm_1" />
+ </complexParticipant>
+ <complex rdf:ID="RNA_primer_DNA_primer_origin_duplex__nucleoplasm_1">
+ <COMPONENTS rdf:resource="#RNA_primer_origin_duplex_DNA_polymerase_alpha_primase_complex__nucleoplasm_3" />
+ <COMPONENTS rdf:resource="#DNA_primer__nucleoplasm_" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RNA primer-DNA primer:origin duplex [nucleoplasm]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RNA primer-DNA primer:origin duplex</SHORT-NAME>
+ </complex>
+ <complexParticipant rdf:ID="RNA_primer_origin_duplex_DNA_polymerase_alpha_primase_complex__nucleoplasm_3">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#RNA_primer_origin_duplex_DNA_polymerase_alpha_primase_complex__nucleoplasm_1" />
+ </complexParticipant>
+ <physicalEntityParticipant rdf:ID="DNA_primer__nucleoplasm_">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#DNA_primer__nucleoplasm_1" />
+ </physicalEntityParticipant>
+ <physicalEntity rdf:ID="DNA_primer__nucleoplasm_1">
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DNA primer [nucleoplasm]</NAME>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome. Each synonym is a name of a ConcreteEntity, and each XREF points to one ConcreteEntity</COMMENT>
+ </physicalEntity>
+ <catalysis rdf:ID="DNA_directed_DNA_polymerase_activity_of_DNA_polymerase_alpha_primase__nucleoplasm_">
+ <CONTROLLER rdf:resource="#DNA_polymerase_alpha_primase__nucleoplasm_5" />
+ <CONTROLLED rdf:resource="#The_polymerase_component_of_DNA_polymerase_alpha_primase_synthesizes_a_20_nucleotide_primer_at_the_origin" />
+ <DIRECTION rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PHYSIOL-LEFT-TO-RIGHT</DIRECTION>
+ <XREF rdf:resource="#DNA_directed_DNA_polymerase_activity" />
+ </catalysis>
+ <complexParticipant rdf:ID="DNA_polymerase_alpha_primase__nucleoplasm_5">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#DNA_polymerase_alpha_primase__nucleoplasm_1" />
+ </complexParticipant>
+ <relationshipXref rdf:ID="DNA_directed_DNA_polymerase_activity">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GO</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0003887</ID>
+ </relationshipXref>
+ <unificationXref rdf:ID="Reactome68950">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">68950</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <pathwayStep rdf:ID="The_polymerase_component_of_DNA_polymerase_alpha_primase_synthesizes_a_20_nucleotide_primer_at_the_originStep">
+ <STEP-INTERACTIONS rdf:resource="#The_polymerase_component_of_DNA_polymerase_alpha_primase_synthesizes_a_20_nucleotide_primer_at_the_origin" />
+ <NEXT-STEP rdf:resource="#RFC_binding_displaces_Pol_AlphaStep" />
+ <STEP-INTERACTIONS rdf:resource="#DNA_directed_DNA_polymerase_activity_of_DNA_polymerase_alpha_primase__nucleoplasm_" />
+ </pathwayStep>
+ <unificationXref rdf:ID="Reactome68952">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">68952</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <evidence rdf:ID="Summation_69326">
+ <XREF rdf:resource="#Pubmed_11395402" />
+ <XREF rdf:resource="#Pubmed_6693436" />
+ </evidence>
+ <pathwayStep rdf:ID="DNA_replication_initiationStep">
+ <STEP-INTERACTIONS rdf:resource="#DNA_replication_initiation" />
+ <NEXT-STEP rdf:resource="#Switching_of_origins_to_a_post_replicative_stateStep" />
+ <NEXT-STEP rdf:resource="#Cdc6_protein_is_phosphorylated_by_CDKStep" />
+ <NEXT-STEP rdf:resource="#Mcm4_6_7_trimer_forms_and_associates_with_the_replication_forkStep" />
+ <NEXT-STEP rdf:resource="#CDK_mediated_phosphorylation_and_removal_of_Cdc6Step" />
+ <NEXT-STEP rdf:resource="#Orc1_removal_from_chromatinStep" />
+ </pathwayStep>
+ <pathway rdf:ID="Switching_of_origins_to_a_post_replicative_state">
+ <PATHWAY-COMPONENTS rdf:resource="#CDK_mediated_phosphorylation_and_removal_of_Cdc6Step" />
+ <PATHWAY-COMPONENTS rdf:resource="#Orc1_removal_from_chromatinStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#Mcm4_6_7_trimer_forms_and_associates_with_the_replication_forkStep" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Switching of origins to a post-replicative state</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Switching of origins to a post-replicative state</SHORT-NAME>
+ <XREF rdf:resource="#Reactome69052" />
+ <CELLULAR-LOCATION rdf:resource="#nucleus" />
+ </pathway>
+ <pathway rdf:ID="Orc1_removal_from_chromatin">
+ <PATHWAY-COMPONENTS rdf:resource="#Phosphorylated_Orc1_is_ubiquitinated_while_still_associated_with_chromatinStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#Orc1_is_phosphorylated_by_cyclin_A_CDK2Step" />
+ <PATHWAY-COMPONENTS rdf:resource="#Ubiquitinated_Orc1_is_degraded_by_the_proteasomeStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#Ubiquitinated_Orc1_enters_the_cytosolStep" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Orc1 removal from chromatin</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Orc1 removal from chromatin</SHORT-NAME>
+ <XREF rdf:resource="#Reactome68949" />
+ <XREF rdf:resource="#Pubmed_11931757" />
+ <XREF rdf:resource="#Pubmed_11739726" />
+ <XREF rdf:resource="#Pubmed_1110244" />
+ <XREF rdf:resource="#Pubmed_11809796" />
+ <CELLULAR-LOCATION rdf:resource="#nucleus" />
+ </pathway>
+ <biochemicalReaction rdf:ID="Orc1_is_phosphorylated_by_cyclin_A_CDK2">
+ <LEFT rdf:resource="#ATP__nucleoplasm_1" />
+ <LEFT rdf:resource="#pre_replicative_complex__nucleoplasm_4" />
+ <RIGHT rdf:resource="#pre_replicative_complex__Orc1_minus___nucleoplasm_" />
+ <RIGHT rdf:resource="#ADP__nucleoplasm_1" />
+ <RIGHT rdf:resource="#phosphorylated_Orc1__nucleoplasm_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Orc1 is phosphorylated by cyclin A/CDK2</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Orc1 is phosphorylated by cyclin A/CDK2</SHORT-NAME>
+ <XREF rdf:resource="#Reactome68944" />
+ <XREF rdf:resource="#Pubmed_11931757" />
+ <CELLULAR-LOCATION rdf:resource="#nucleus" />
+ </biochemicalReaction>
+ <smallMoleculeParticipant rdf:ID="ATP__nucleoplasm_1">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#ATP__ChEBI_2359_" />
+ </smallMoleculeParticipant>
+ <complexParticipant rdf:ID="pre_replicative_complex__nucleoplasm_4">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#pre_replicative_complex__nucleoplasm_1" />
+ </complexParticipant>
+ <complexParticipant rdf:ID="pre_replicative_complex__Orc1_minus___nucleoplasm_">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#pre_replicative_complex__Orc1_minus___nucleoplasm_1" />
+ </complexParticipant>
+ <complex rdf:ID="pre_replicative_complex__Orc1_minus___nucleoplasm_1">
+ <COMPONENTS rdf:resource="#origin_of_replication__nucleoplasm_6" />
+ <COMPONENTS rdf:resource="#Orc3__nucleoplasm_3" />
+ <COMPONENTS rdf:resource="#Orc4__nucleoplasm_3" />
+ <COMPONENTS rdf:resource="#Cdt1__nucleoplasm_3" />
+ <COMPONENTS rdf:resource="#Cdc6__nucleoplasm_2" />
+ <COMPONENTS rdf:resource="#Mcm2_7_complex__nucleoplasm_6" />
+ <COMPONENTS rdf:resource="#Orc5__nucleoplasm_3" />
+ <COMPONENTS rdf:resource="#Orc2__nucleoplasm_2" />
+ <COMPONENTS rdf:resource="#Orc6__nucleoplasm_2" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">pre-replicative complex (Orc1-minus) [nucleoplasm]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">pre-replicative complex (Orc1-minus)</SHORT-NAME>
+ </complex>
+ <physicalEntityParticipant rdf:ID="origin_of_replication__nucleoplasm_6">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#origin_of_replication__nucleoplasm_1" />
+ </physicalEntityParticipant>
+ <proteinParticipant rdf:ID="Orc3__nucleoplasm_3">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q9UBD5_Origin_recognition_complex_subunit_3__Origin_recognition_complex_subunit_Latheo_" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="Orc4__nucleoplasm_3">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_O43929_Origin_recognition_complex_subunit_4" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="Cdt1__nucleoplasm_3">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q9H211" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="Cdc6__nucleoplasm_2">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <SEQUENCE-FEATURE-LIST rdf:resource="#nucleotide_binding_site" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q99741_Cell_division_control_protein_6_homolog__CDC6_related_protein___p62_cdc6____HsCDC6___HsCDC18_" />
+ </proteinParticipant>
+ <complexParticipant rdf:ID="Mcm2_7_complex__nucleoplasm_6">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Mcm2_7_complex__nucleoplasm_1" />
+ </complexParticipant>
+ <proteinParticipant rdf:ID="Orc5__nucleoplasm_3">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_O43913_Origin_recognition_complex_subunit_5" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="Orc2__nucleoplasm_2">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q13416_Origin_recognition_complex_subunit_2" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="Orc6__nucleoplasm_2">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q9Y5N6_Origin_recognition_complex_subunit_6" />
+ </proteinParticipant>
+ <smallMoleculeParticipant rdf:ID="ADP__nucleoplasm_1">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#ADP__ChEBI_2342_" />
+ </smallMoleculeParticipant>
+ <proteinParticipant rdf:ID="phosphorylated_Orc1__nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q13415_Origin_recognition_complex_subunit_1__Replication_control_protein_1_" />
+ </proteinParticipant>
+ <catalysis rdf:ID="kinase_activity_of_Cyclin_A_CDK2_complex__nucleoplasm_">
+ <CONTROLLER rdf:resource="#Cyclin_A_CDK2_complex__nucleoplasm_" />
+ <CONTROLLED rdf:resource="#Orc1_is_phosphorylated_by_cyclin_A_CDK2" />
+ <DIRECTION rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PHYSIOL-LEFT-TO-RIGHT</DIRECTION>
+ <XREF rdf:resource="#kinase_activity" />
+ </catalysis>
+ <complexParticipant rdf:ID="Cyclin_A_CDK2_complex__nucleoplasm_">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Cyclin_A_CDK2_complex__nucleoplasm_1" />
+ </complexParticipant>
+ <complex rdf:ID="Cyclin_A_CDK2_complex__nucleoplasm_1">
+ <COMPONENTS rdf:resource="#Cyclin_A__nucleoplasm_" />
+ <COMPONENTS rdf:resource="#Cdk2__nucleoplasm_1" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cyclin A:CDK2 complex [nucleoplasm]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cyclin A:CDK2 complex</SHORT-NAME>
+ </complex>
+ <proteinParticipant rdf:ID="Cyclin_A__nucleoplasm_">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Cyclin_A__nucleoplasm_1" />
+ </proteinParticipant>
+ <protein rdf:ID="Cyclin_A__nucleoplasm_1">
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cyclin A [nucleoplasm]</NAME>
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome. Each synonym is a name of a ConcreteEntity, and each XREF points to one ConcreteEntity</COMMENT>
+ <XREF rdf:resource="#UniProt_P20248" />
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cyclin A2 [nucleoplasm]</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P78396" />
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cyclin A1 [nucleoplasm]</SYNONYMS>
+ </protein>
+ <unificationXref rdf:ID="UniProt_P20248">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P20248</ID>
+ </unificationXref>
+ <unificationXref rdf:ID="UniProt_P78396">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P78396</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="Cdk2__nucleoplasm_1">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P24941_Cell_division_protein_kinase_2__EC_2_7_1_37___p33_protein_kinase_" />
+ </proteinParticipant>
+ <unificationXref rdf:ID="Reactome68944">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">68944</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <publicationXref rdf:ID="Pubmed_11931757">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">11931757</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2002</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Human origin recognition complex large subunit is degraded by ubiquitin-mediated proteolysis after initiation of DNA replication.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Méndez, J</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Zou-Yang, XH</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Kim, SY</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Hidaka, M</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Tansey, WP</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Stillman, B</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mol Cell 9:481-91</SOURCE>
+ </publicationXref>
+ <modulation rdf:ID="_cyclin__positively_regulates__Orc1_is_phosphorylated_by_cyclin_A_CDK2_">
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">'cyclin' positively regulates 'Orc1 is phosphorylated by cyclin A/CDK2'</NAME>
+ <CONTROL-TYPE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ACTIVATION</CONTROL-TYPE>
+ <CONTROLLER rdf:resource="#cyclin__nucleoplasm_2" />
+ <CONTROLLED rdf:resource="#Orc1_is_phosphorylated_by_cyclin_A_CDK2" />
+ </modulation>
+ <physicalEntityParticipant rdf:ID="cyclin__nucleoplasm_2">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#cyclin__nucleoplasm_1" />
+ </physicalEntityParticipant>
+ <pathwayStep rdf:ID="Orc1_is_phosphorylated_by_cyclin_A_CDK2Step">
+ <STEP-INTERACTIONS rdf:resource="#Orc1_is_phosphorylated_by_cyclin_A_CDK2" />
+ <NEXT-STEP rdf:resource="#Phosphorylated_Orc1_is_ubiquitinated_while_still_associated_with_chromatinStep" />
+ <STEP-INTERACTIONS rdf:resource="#kinase_activity_of_Cyclin_A_CDK2_complex__nucleoplasm_1" />
+ <STEP-INTERACTIONS rdf:resource="#_cyclin__positively_regulates__Orc1_is_phosphorylated_by_cyclin_A_CDK2_1" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="Phosphorylated_Orc1_is_ubiquitinated_while_still_associated_with_chromatin">
+ <LEFT rdf:resource="#ubiquitin__nucleoplasm_" />
+ <LEFT rdf:resource="#phosphorylated_Orc1__nucleoplasm_1" />
+ <RIGHT rdf:resource="#ubiquitinated_Orc1__nucleoplasm_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Phosphorylated Orc1 is ubiquitinated while still associated with chromatin</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Phosphorylated Orc1 is ubiquitinated while still associated with chromatin</SHORT-NAME>
+ <XREF rdf:resource="#Reactome68946" />
+ <XREF rdf:resource="#Pubmed_11931757" />
+ <CELLULAR-LOCATION rdf:resource="#nucleus" />
+ </biochemicalReaction>
+ <proteinParticipant rdf:ID="ubiquitin__nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P62988_Ubiquitin" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="phosphorylated_Orc1__nucleoplasm_1">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q13415_Origin_recognition_complex_subunit_1__Replication_control_protein_1_" />
+ </proteinParticipant>
+ <complexParticipant rdf:ID="ubiquitinated_Orc1__nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#ubiquitinated_Orc1__nucleoplasm_1" />
+ </complexParticipant>
+ <complex rdf:ID="ubiquitinated_Orc1__nucleoplasm_1">
+ <COMPONENTS rdf:resource="#ubiquitin__nucleoplasm_1" />
+ <COMPONENTS rdf:resource="#Orc1__nucleoplasm_3" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ubiquitinated Orc1 [nucleoplasm]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ubiquitinated Orc1</SHORT-NAME>
+ </complex>
+ <proteinParticipant rdf:ID="ubiquitin__nucleoplasm_1">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P62988_Ubiquitin" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="Orc1__nucleoplasm_3">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q13415_Origin_recognition_complex_subunit_1__Replication_control_protein_1_" />
+ </proteinParticipant>
+ <unificationXref rdf:ID="Reactome68946">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">68946</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <pathwayStep rdf:ID="Phosphorylated_Orc1_is_ubiquitinated_while_still_associated_with_chromatinStep">
+ <STEP-INTERACTIONS rdf:resource="#Phosphorylated_Orc1_is_ubiquitinated_while_still_associated_with_chromatin" />
+ <NEXT-STEP rdf:resource="#Ubiquitinated_Orc1_enters_the_cytosolStep" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="Ubiquitinated_Orc1_enters_the_cytosol">
+ <LEFT rdf:resource="#ubiquitinated_Orc1__nucleoplasm_2" />
+ <RIGHT rdf:resource="#ubiquitinated_Orc1__cytosol_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Ubiquitinated Orc1 enters the cytosol</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Ubiquitinated Orc1 enters the cytosol</SHORT-NAME>
+ <XREF rdf:resource="#Reactome68947" />
+ <XREF rdf:resource="#Pubmed_11931757" />
+ </biochemicalReaction>
+ <complexParticipant rdf:ID="ubiquitinated_Orc1__nucleoplasm_2">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#ubiquitinated_Orc1__nucleoplasm_1" />
+ </complexParticipant>
+ <complexParticipant rdf:ID="ubiquitinated_Orc1__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#ubiquitinated_Orc1__cytosol_1" />
+ </complexParticipant>
+ <complex rdf:ID="ubiquitinated_Orc1__cytosol_1">
+ <COMPONENTS rdf:resource="#ubiquitin__cytosol_3" />
+ <COMPONENTS rdf:resource="#Orc1__cytosol_" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ubiquitinated Orc1 [cytosol]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ubiquitinated Orc1</SHORT-NAME>
+ </complex>
+ <proteinParticipant rdf:ID="ubiquitin__cytosol_3">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P62988_Ubiquitin" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="Orc1__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q13415_Origin_recognition_complex_subunit_1__Replication_control_protein_1_" />
+ </proteinParticipant>
+ <unificationXref rdf:ID="Reactome68947">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">68947</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <openControlledVocabulary rdf:ID="nuclear_pore">
+ <TERM rdf:datatype="http://www.w3.org/2001/XMLSchema#string">nuclear pore</TERM>
+ <XREF rdf:resource="#GO_0005643" />
+ </openControlledVocabulary>
+ <xref rdf:ID="GO_0005643">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GO</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0005643</ID>
+ </xref>
+ <pathwayStep rdf:ID="Ubiquitinated_Orc1_enters_the_cytosolStep">
+ <STEP-INTERACTIONS rdf:resource="#Ubiquitinated_Orc1_enters_the_cytosol" />
+ <NEXT-STEP rdf:resource="#Ubiquitinated_Orc1_is_degraded_by_the_proteasomeStep" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="Ubiquitinated_Orc1_is_degraded_by_the_proteasome">
+ <LEFT rdf:resource="#ubiquitinated_Orc1__cytosol_2" />
+ <RIGHT rdf:resource="#ubiquitin__cytosol_4" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Ubiquitinated Orc1 is degraded by the proteasome</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Ubiquitinated Orc1 is degraded by the proteasome</SHORT-NAME>
+ <XREF rdf:resource="#Reactome68948" />
+ <XREF rdf:resource="#Pubmed_11931757" />
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ </biochemicalReaction>
+ <complexParticipant rdf:ID="ubiquitinated_Orc1__cytosol_2">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#ubiquitinated_Orc1__cytosol_1" />
+ </complexParticipant>
+ <proteinParticipant rdf:ID="ubiquitin__cytosol_4">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P62988_Ubiquitin" />
+ </proteinParticipant>
+ <catalysis rdf:ID="endopeptidase_activity_of_26S_proteasome__cytosol_1">
+ <CONTROLLER rdf:resource="#_26S_proteasome__cytosol_2" />
+ <CONTROLLED rdf:resource="#Ubiquitinated_Orc1_is_degraded_by_the_proteasome" />
+ <DIRECTION rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PHYSIOL-LEFT-TO-RIGHT</DIRECTION>
+ <XREF rdf:resource="#endopeptidase_activity" />
+ </catalysis>
+ <complexParticipant rdf:ID="_26S_proteasome__cytosol_2">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#_26S_proteasome__cytosol_1" />
+ </complexParticipant>
+ <unificationXref rdf:ID="Reactome68948">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">68948</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <pathwayStep rdf:ID="Ubiquitinated_Orc1_is_degraded_by_the_proteasomeStep">
+ <STEP-INTERACTIONS rdf:resource="#Ubiquitinated_Orc1_is_degraded_by_the_proteasome" />
+ <STEP-INTERACTIONS rdf:resource="#endopeptidase_activity_of_26S_proteasome__cytosol_3" />
+ </pathwayStep>
+ <unificationXref rdf:ID="Reactome68949">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">68949</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <publicationXref rdf:ID="Pubmed_11809796">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">11809796</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2002</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Identification of a binding region for human origin recognition complex proteins 1 and 2 that coincides with an origin of DNA replication.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Ladenburger, EM</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Keller, C</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Knippers, R</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mol Cell Biol 22:1036-48</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="Orc1_removal_from_chromatinStep">
+ <STEP-INTERACTIONS rdf:resource="#Orc1_removal_from_chromatin" />
+ </pathwayStep>
+ <pathway rdf:ID="CDK_mediated_phosphorylation_and_removal_of_Cdc6">
+ <PATHWAY-COMPONENTS rdf:resource="#Cdc6_protein_is_phosphorylated_by_CDKStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#Ubiquitinated_Cdc6_is_degraded_by_the_proteasomeStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#Phosphorylated_Cdc6_is_exported_from_the_nucleusStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#Cytoplasmic_phosphorylated_Cdc6_is_ubiquitinated_by_the_anaphase_promoting_complexStep" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CDK-mediated phosphorylation and removal of Cdc6</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CDK-mediated phosphorylation and removal of Cdc6</SHORT-NAME>
+ <XREF rdf:resource="#Reactome69017" />
+ <XREF rdf:resource="#Pubmed_12045100" />
+ <XREF rdf:resource="#Pubmed_11046155" />
+ <CELLULAR-LOCATION rdf:resource="#nucleus" />
+ </pathway>
+ <biochemicalReaction rdf:ID="Cdc6_protein_is_phosphorylated_by_CDK">
+ <LEFT rdf:resource="#ATP__nucleoplasm_2" />
+ <LEFT rdf:resource="#Cdc6__nucleoplasm_3" />
+ <RIGHT rdf:resource="#ADP__nucleoplasm_2" />
+ <RIGHT rdf:resource="#phosphorylated_Cdc6__nucleoplasm_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cdc6 protein is phosphorylated by CDK</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cdc6 protein is phosphorylated by CDK</SHORT-NAME>
+ <XREF rdf:resource="#Reactome69005" />
+ <XREF rdf:resource="#Pubmed_10339564" />
+ <CELLULAR-LOCATION rdf:resource="#nucleus" />
+ </biochemicalReaction>
+ <smallMoleculeParticipant rdf:ID="ATP__nucleoplasm_2">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#ATP__ChEBI_2359_" />
+ </smallMoleculeParticipant>
+ <proteinParticipant rdf:ID="Cdc6__nucleoplasm_3">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <SEQUENCE-FEATURE-LIST rdf:resource="#nucleotide_binding_site" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q99741_Cell_division_control_protein_6_homolog__CDC6_related_protein___p62_cdc6____HsCDC6___HsCDC18_" />
+ </proteinParticipant>
+ <smallMoleculeParticipant rdf:ID="ADP__nucleoplasm_2">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#ADP__ChEBI_2342_" />
+ </smallMoleculeParticipant>
+ <proteinParticipant rdf:ID="phosphorylated_Cdc6__nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q99741_Cell_division_control_protein_6_homolog__CDC6_related_protein___p62_cdc6____HsCDC6___HsCDC18_" />
+ </proteinParticipant>
+ <catalysis rdf:ID="kinase_activity_of_CDK__nucleoplasm_">
+ <CONTROLLER rdf:resource="#CDK__nucleoplasm_3" />
+ <CONTROLLED rdf:resource="#Cdc6_protein_is_phosphorylated_by_CDK" />
+ <DIRECTION rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PHYSIOL-LEFT-TO-RIGHT</DIRECTION>
+ <XREF rdf:resource="#kinase_activity" />
+ </catalysis>
+ <complexParticipant rdf:ID="CDK__nucleoplasm_3">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#CDK__nucleoplasm_1" />
+ </complexParticipant>
+ <unificationXref rdf:ID="Reactome69005">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">69005</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <pathwayStep rdf:ID="Cdc6_protein_is_phosphorylated_by_CDKStep">
+ <STEP-INTERACTIONS rdf:resource="#Cdc6_protein_is_phosphorylated_by_CDK" />
+ <NEXT-STEP rdf:resource="#Phosphorylated_Cdc6_is_exported_from_the_nucleusStep" />
+ <STEP-INTERACTIONS rdf:resource="#kinase_activity_of_CDK__nucleoplasm_1" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="Phosphorylated_Cdc6_is_exported_from_the_nucleus">
+ <LEFT rdf:resource="#phosphorylated_Cdc6__nucleoplasm_1" />
+ <RIGHT rdf:resource="#phosphorylated_Cdc6__cytosol_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Phosphorylated Cdc6 is exported from the nucleus</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Phosphorylated Cdc6 is exported from the nucleus</SHORT-NAME>
+ <XREF rdf:resource="#Reactome69006" />
+ <XREF rdf:resource="#Pubmed_10339564" />
+ <CELLULAR-LOCATION rdf:resource="#nuclear_pore" />
+ </biochemicalReaction>
+ <proteinParticipant rdf:ID="phosphorylated_Cdc6__nucleoplasm_1">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q99741_Cell_division_control_protein_6_homolog__CDC6_related_protein___p62_cdc6____HsCDC6___HsCDC18_" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="phosphorylated_Cdc6__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q99741_Cell_division_control_protein_6_homolog__CDC6_related_protein___p62_cdc6____HsCDC6___HsCDC18_" />
+ </proteinParticipant>
+ <unificationXref rdf:ID="Reactome69006">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">69006</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <pathwayStep rdf:ID="Phosphorylated_Cdc6_is_exported_from_the_nucleusStep">
+ <STEP-INTERACTIONS rdf:resource="#Phosphorylated_Cdc6_is_exported_from_the_nucleus" />
+ <NEXT-STEP rdf:resource="#Cytoplasmic_phosphorylated_Cdc6_is_ubiquitinated_by_the_anaphase_promoting_complexStep" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="Cytoplasmic_phosphorylated_Cdc6_is_ubiquitinated_by_the_anaphase_promoting_complex">
+ <LEFT rdf:resource="#ubiquitin__cytosol_5" />
+ <LEFT rdf:resource="#ATP__cytosol_" />
+ <LEFT rdf:resource="#phosphorylated_Cdc6__cytosol_1" />
+ <RIGHT rdf:resource="#ubiquitinated_Cdc6__cytosol_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cytoplasmic phosphorylated Cdc6 is ubiquitinated by the anaphase-promoting complex</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cytoplasmic phosphorylated Cdc6 is ubiquitinated by the anaphase-promoting complex</SHORT-NAME>
+ <XREF rdf:resource="#Reactome69015" />
+ <XREF rdf:resource="#Pubmed_10995389" />
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ </biochemicalReaction>
+ <proteinParticipant rdf:ID="ubiquitin__cytosol_5">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P62988_Ubiquitin" />
+ </proteinParticipant>
+ <smallMoleculeParticipant rdf:ID="ATP__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#ATP__ChEBI_2359_" />
+ </smallMoleculeParticipant>
+ <proteinParticipant rdf:ID="phosphorylated_Cdc6__cytosol_1">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q99741_Cell_division_control_protein_6_homolog__CDC6_related_protein___p62_cdc6____HsCDC6___HsCDC18_" />
+ </proteinParticipant>
+ <complexParticipant rdf:ID="ubiquitinated_Cdc6__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#ubiquitinated_Cdc6__cytosol_1" />
+ </complexParticipant>
+ <complex rdf:ID="ubiquitinated_Cdc6__cytosol_1">
+ <COMPONENTS rdf:resource="#ubiquitin__cytosol_6" />
+ <COMPONENTS rdf:resource="#Cdc6__cytosol_1" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ubiquitinated Cdc6 [cytosol]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ubiquitinated Cdc6</SHORT-NAME>
+ </complex>
+ <proteinParticipant rdf:ID="ubiquitin__cytosol_6">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P62988_Ubiquitin" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="Cdc6__cytosol_1">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <SEQUENCE-FEATURE-LIST rdf:resource="#nucleotide_binding_site" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q99741_Cell_division_control_protein_6_homolog__CDC6_related_protein___p62_cdc6____HsCDC6___HsCDC18_" />
+ </proteinParticipant>
+ <catalysis rdf:ID="endopeptidase_activity_of_anaphase_promoting_complex__APC___cytosol_">
+ <CONTROLLER rdf:resource="#anaphase_promoting_complex__APC___cytosol_" />
+ <CONTROLLED rdf:resource="#Cytoplasmic_phosphorylated_Cdc6_is_ubiquitinated_by_the_anaphase_promoting_complex" />
+ <DIRECTION rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PHYSIOL-LEFT-TO-RIGHT</DIRECTION>
+ <XREF rdf:resource="#endopeptidase_activity" />
+ </catalysis>
+ <physicalEntityParticipant rdf:ID="anaphase_promoting_complex__APC___cytosol_">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#anaphase_promoting_complex__APC___cytosol_1" />
+ </physicalEntityParticipant>
+ <physicalEntity rdf:ID="anaphase_promoting_complex__APC___cytosol_1">
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">anaphase-promoting complex (APC) [cytosol]</NAME>
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome. Each synonym is a name of a ConcreteEntity, and each XREF points to one ConcreteEntity</COMMENT>
+ </physicalEntity>
+ <unificationXref rdf:ID="Reactome69015">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">69015</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <pathwayStep rdf:ID="Cytoplasmic_phosphorylated_Cdc6_is_ubiquitinated_by_the_anaphase_promoting_complexStep">
+ <STEP-INTERACTIONS rdf:resource="#Cytoplasmic_phosphorylated_Cdc6_is_ubiquitinated_by_the_anaphase_promoting_complex" />
+ <NEXT-STEP rdf:resource="#Ubiquitinated_Cdc6_is_degraded_by_the_proteasomeStep" />
+ <STEP-INTERACTIONS rdf:resource="#endopeptidase_activity_of_anaphase_promoting_complex__APC___cytosol_1" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="Ubiquitinated_Cdc6_is_degraded_by_the_proteasome">
+ <LEFT rdf:resource="#ubiquitinated_Cdc6__cytosol_2" />
+ <RIGHT rdf:resource="#ubiquitin__cytosol_7" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Ubiquitinated Cdc6 is degraded by the proteasome</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Ubiquitinated Cdc6 is degraded by the proteasome</SHORT-NAME>
+ <XREF rdf:resource="#Reactome69016" />
+ <XREF rdf:resource="#Pubmed_11046155" />
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ </biochemicalReaction>
+ <complexParticipant rdf:ID="ubiquitinated_Cdc6__cytosol_2">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#ubiquitinated_Cdc6__cytosol_1" />
+ </complexParticipant>
+ <proteinParticipant rdf:ID="ubiquitin__cytosol_7">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P62988_Ubiquitin" />
+ </proteinParticipant>
+ <catalysis rdf:ID="endopeptidase_activity_of_26S_proteasome__cytosol_2">
+ <CONTROLLER rdf:resource="#_26S_proteasome__cytosol_3" />
+ <CONTROLLED rdf:resource="#Ubiquitinated_Cdc6_is_degraded_by_the_proteasome" />
+ <DIRECTION rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PHYSIOL-LEFT-TO-RIGHT</DIRECTION>
+ <XREF rdf:resource="#endopeptidase_activity" />
+ </catalysis>
+ <complexParticipant rdf:ID="_26S_proteasome__cytosol_3">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#_26S_proteasome__cytosol_1" />
+ </complexParticipant>
+ <unificationXref rdf:ID="Reactome69016">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">69016</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <pathwayStep rdf:ID="Ubiquitinated_Cdc6_is_degraded_by_the_proteasomeStep">
+ <STEP-INTERACTIONS rdf:resource="#Ubiquitinated_Cdc6_is_degraded_by_the_proteasome" />
+ <STEP-INTERACTIONS rdf:resource="#endopeptidase_activity_of_26S_proteasome__cytosol_4" />
+ </pathwayStep>
+ <unificationXref rdf:ID="Reactome69017">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">69017</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <pathwayStep rdf:ID="CDK_mediated_phosphorylation_and_removal_of_Cdc6Step">
+ <STEP-INTERACTIONS rdf:resource="#CDK_mediated_phosphorylation_and_removal_of_Cdc6" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="Mcm4_6_7_trimer_forms_and_associates_with_the_replication_fork">
+ <LEFT rdf:resource="#Mcm2_7_complex__nucleoplasm_7" />
+ <RIGHT rdf:resource="#Mcm5__nucleoplasm_1" />
+ <RIGHT rdf:resource="#Mcm4_6_7_complex__nucleoplasm_" />
+ <RIGHT rdf:resource="#Mcm3__nucleoplasm_1" />
+ <RIGHT rdf:resource="#Mcm2__nucleoplasm_1" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mcm4,6,7 trimer forms and associates with the replication fork</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mcm4,6,7 trimer forms and associates with the replication fork</SHORT-NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Rearrangement and mobilization of Mcm2-7</SYNONYMS>
+ <XREF rdf:resource="#Reactome69019" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">At the start of the elongation phase of DNA replication, the Mcm2-7 complex may re-arrange to function as the replicative helicase associated with the replication fork. In general, a replicative helicase is associated with the replication fork and unwinds DNA ahead of the polymerase. In yeast, the Mcm proteins associate with origin DNA in G1 phase and then exit the origin upon replication initiation, consistent with movi [...]
+ <EVIDENCE rdf:resource="#Summation_69033" />
+ <XREF rdf:resource="#Pubmed_10884341" />
+ <XREF rdf:resource="#Pubmed_12364596" />
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ </biochemicalReaction>
+ <complexParticipant rdf:ID="Mcm2_7_complex__nucleoplasm_7">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Mcm2_7_complex__nucleoplasm_1" />
+ </complexParticipant>
+ <proteinParticipant rdf:ID="Mcm5__nucleoplasm_1">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P33992_DNA_replication_licensing_factor_MCM5__CDC46_homolog___P1_CDC46_" />
+ </proteinParticipant>
+ <complexParticipant rdf:ID="Mcm4_6_7_complex__nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Mcm4_6_7_complex__nucleoplasm_1" />
+ </complexParticipant>
+ <complex rdf:ID="Mcm4_6_7_complex__nucleoplasm_1">
+ <COMPONENTS rdf:resource="#Mcm4__nucleoplasm_1" />
+ <COMPONENTS rdf:resource="#Mcm6__nucleoplasm_1" />
+ <COMPONENTS rdf:resource="#Mcm7__nucleoplasm_1" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mcm4,6,7 complex [nucleoplasm]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mcm4,6,7 complex</SHORT-NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">replicative helicase</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mcm4:Mcm6:Mcm7</SYNONYMS>
+ </complex>
+ <proteinParticipant rdf:ID="Mcm4__nucleoplasm_1">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P33991_DNA_replication_licensing_factor_MCM4__CDC21_homolog___P1_CDC21_" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="Mcm6__nucleoplasm_1">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q14566_DNA_replication_licensing_factor_MCM6__P105MCM_" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="Mcm7__nucleoplasm_1">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P33993_1_DNA_replication_licensing_factor_MCM7__CDC47_homolog___P1_1_MCM3_" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="Mcm3__nucleoplasm_1">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P25205_DNA_replication_licensing_factor_MCM3__DNA_polymerase_alpha_holoenzyme_associated_protein_P1___RLF_beta_subunit___P102_protein___P1_MCM3_" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="Mcm2__nucleoplasm_1">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P49736_DNA_replication_licensing_factor_MCM2__Minichromosome_maintenance_protein_2_homolog___Nuclear_protein_BM28_" />
+ </proteinParticipant>
+ <unificationXref rdf:ID="Reactome69019">
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+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">69019</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <evidence rdf:ID="Summation_69033">
+ <XREF rdf:resource="#Pubmed_11282021" />
+ <XREF rdf:resource="#Pubmed_10872463" />
+ <XREF rdf:resource="#Pubmed_9335335" />
+ <XREF rdf:resource="#Pubmed_10567526" />
+ <XREF rdf:resource="#Pubmed_9305914" />
+ <XREF rdf:resource="#Pubmed_10611290" />
+ <XREF rdf:resource="#Pubmed_10677495" />
+ <XREF rdf:resource="#Pubmed_10834843" />
+ <XREF rdf:resource="#Pubmed_11454864" />
+ <XREF rdf:resource="#Pubmed_10748114" />
+ </evidence>
+ <publicationXref rdf:ID="Pubmed_10872463">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">10872463</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2000</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">MCM proteins in DNA replication.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Tye, BK</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Annu Rev Biochem 68:649-86</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_10567526">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">10567526</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2000</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Biochemical analysis of the intrinsic Mcm4-Mcm6-mcm7 DNA helicase activity.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">You, Z</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Komamura, Y</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Ishimi, Y</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mol Cell Biol 19:8003-15</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_9305914">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">9305914</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1997</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A DNA helicase activity is associated with an MCM4, -6, and -7 protein complex.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Ishimi, Y</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Biol Chem 272:24508-13</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_10611290">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">10611290</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2000</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The single minichromosome maintenance protein of Methanobacterium thermoautotrophicum DeltaH contains DNA helicase activity.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Kelman, Z</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Lee, JK</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Hurwitz, J</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Proc Natl Acad Sci U S A 96:14783-8</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_10677495">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">10677495</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2000</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A double-hexamer archaeal minichromosome maintenance protein is an ATP-dependent DNA helicase.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Chong, JP</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Hayashi, MK</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Simon, MN</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Xu, RM</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Stillman, B</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Proc Natl Acad Sci U S A 97:1530-5</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_10834843">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">10834843</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2000</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Uninterrupted MCM2-7 function required for DNA replication fork progression.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Labib, K</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Tercero, JA</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Diffley, JF</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Science 288:1643-7</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_11454864">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">11454864</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2001</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Phosphorylation of Mcm4 at specific sites by cyclin-dependent kinase leads to loss of Mcm4,6,7 helicase activity.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Ishimi, Y</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Komamura-Kohno, Y</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Biol Chem 276:34428-33</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_10748114">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">10748114</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2000</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Inhibition of Mcm4,6,7 helicase activity by phosphorylation with cyclin A/Cdk2.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Ishimi, Y</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Komamura-Kohno, Y</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">You, Z</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Omori, A</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Kitagawa, M</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Biol Chem 275:16235-41</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_10884341">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">10884341</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2000</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Electron microscopic observation and single-stranded DNA binding activity of the Mcm4,6,7 complex.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Sato, M</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Gotow, T</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">You, Z</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Komamura-Kohno, Y</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Uchiyama, Y</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Yabuta, N</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Nojima, H</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Ishimi, Y</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Mol Biol 300:421-31</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_12364596">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">12364596</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2002</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Human Mcm proteins at a replication origin during the G1 to S phase transition.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Schaarschmidt, D</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Ladenburger, EM</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Keller, C</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Knippers, R</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Nucleic Acids Res 30:4176-85</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="Mcm4_6_7_trimer_forms_and_associates_with_the_replication_forkStep">
+ <STEP-INTERACTIONS rdf:resource="#Mcm4_6_7_trimer_forms_and_associates_with_the_replication_fork" />
+ </pathwayStep>
+ <unificationXref rdf:ID="Reactome69052">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">69052</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <pathwayStep rdf:ID="Switching_of_origins_to_a_post_replicative_stateStep">
+ <STEP-INTERACTIONS rdf:resource="#Switching_of_origins_to_a_post_replicative_state" />
+ <NEXT-STEP rdf:resource="#DNA_strand_elongationStep" />
+ </pathwayStep>
+ <pathway rdf:ID="DNA_strand_elongation">
+ <PATHWAY-COMPONENTS rdf:resource="#Leading_Strand_SynthesisStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#Lagging_Strand_SynthesisStep" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DNA strand elongation</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DNA strand elongation</SHORT-NAME>
+ <XREF rdf:resource="#Reactome69190" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Accurate and efficient genome duplication requires coordinated processes to replicate two template strands at eucaryotic replication forks. Knowledge of the fundamental reactions involved in replication fork progression is derived largely from biochemical studies of the replication of simian virus and from yeast genetic studies. Since duplex DNA forms an anti-parallel structure, and DNA polymerases are unidirectional, on [...]
+ <EVIDENCE rdf:resource="#Summation_69287" />
+ <CELLULAR-LOCATION rdf:resource="#nucleus" />
+ </pathway>
+ <pathway rdf:ID="Leading_Strand_Synthesis">
+ <PATHWAY-COMPONENTS rdf:resource="#Processive_synthesis_on_the_leading_strandStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#Polymerase_switchingStep" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Leading Strand Synthesis</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Leading Strand Synthesis</SHORT-NAME>
+ <XREF rdf:resource="#Reactome69109" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The processive complex is responsible for synthesizing at least 5-10 kb of DNA in a continuous manner during leading strand synthesis. The incorporation of nucleotides by pol delta is quite accurate. However, incorporation of an incorrect nucleotide does occur occasionally. Misincorporated nucleotides are removed by the 3' to 5' exonucleolytic proofreading capability of pol delta.</COMMENT>
+ <EVIDENCE rdf:resource="#Summation_69110" />
+ <CELLULAR-LOCATION rdf:resource="#nucleus" />
+ </pathway>
+ <pathway rdf:ID="Polymerase_switching">
+ <PATHWAY-COMPONENTS rdf:resource="#Loading_of_PCNA___Sliding_Clamp_FormationStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#RFC_dissociates_after_sliding_clamp_formationStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#Formation_of_Processive_ComplexStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#RFC_binding_displaces_Pol_AlphaStep" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Polymerase switching</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Polymerase switching</SHORT-NAME>
+ <XREF rdf:resource="#Reactome69091" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">After the primers are synthesized, Replication Factor C binds to the 3'-end of the initiator DNA to trigger polymerase switching. The non-processive nature of pol alpha catalytic activity and the tight binding of Replication Factor C to the primer-template junction presumably lead to the turnover of the pol alpha:primase complex. After the Pol alpha-primase primase complex is displaced from the primer, the proliferating [...]
+ <EVIDENCE rdf:resource="#Summation_69093" />
+ <CELLULAR-LOCATION rdf:resource="#nucleus" />
+ </pathway>
+ <biochemicalReaction rdf:ID="RFC_binding_displaces_Pol_Alpha">
+ <LEFT rdf:resource="#RFC_Heteropentamer__nucleoplasm_" />
+ <LEFT rdf:resource="#RNA_primer_DNA_primer_origin_duplex__nucleoplasm_2" />
+ <RIGHT rdf:resource="#RFC_Heteropentamer_RNA_primer_DNA_primer_origin_duplex__nucleoplasm_" />
+ <RIGHT rdf:resource="#DNA_polymerase_alpha_primase__nucleoplasm_6" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RFC binding displaces Pol Alpha</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RFC binding displaces Pol Alpha</SHORT-NAME>
+ <XREF rdf:resource="#Reactome69053" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Once the RNA-DNA primer is synthesized, replication factor C (RFC) initiates a reaction called "polymerase switching"; pol delta, the processive enzyme replaces pol alpha, the priming enzyme. RFC binds to the 3'-end of the RNA-DNA primer on the Primosome, to displace the pol alpha primase complex. The binding of RFC triggers the binding of the primer recognition complex.</COMMENT>
+ <EVIDENCE rdf:resource="#Summation_69054" />
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ </biochemicalReaction>
+ <complexParticipant rdf:ID="RFC_Heteropentamer__nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#RFC_Heteropentamer__nucleoplasm_1" />
+ </complexParticipant>
+ <complex rdf:ID="RFC_Heteropentamer__nucleoplasm_1">
+ <COMPONENTS rdf:resource="#RFC40__nucleoplasm_" />
+ <COMPONENTS rdf:resource="#RFC140__nucleoplasm_" />
+ <COMPONENTS rdf:resource="#RFC37__nucleoplasm_" />
+ <COMPONENTS rdf:resource="#RFC38__nucleoplasm_" />
+ <COMPONENTS rdf:resource="#RFC36__nucleoplasm_" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RFC Heteropentamer [nucleoplasm]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RFC Heteropentamer</SHORT-NAME>
+ </complex>
+ <proteinParticipant rdf:ID="RFC40__nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P35250_1_Activator_1_40_kDa_subunit__Replication_factor_C_40_kDa_subunit___A1_40_kDa_subunit___RF_C_40_kDa_subunit___RFC40_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_P35250_1_Activator_1_40_kDa_subunit__Replication_factor_C_40_kDa_subunit___A1_40_kDa_subunit___RF_C_40_kDa_subunit___RFC40_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P35250-1 Activator 1 40 kDa subunit (Replication factor C 40 kDa subunit) (A1 40 kDa subunit) (RF-C 40 kDa subunit) (RFC40)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RFC2</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P35250" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: The elongation of primed DNA templates by DNA polymerase delta and epsilon requires the action of the accessory proteins proliferating cell nuclear antigen (PCNA) and activator 1. The 40 kDa subunit binds ATP. SUBUNIT: Heteropentamer of subunits of 140/145, 40, 38, 37, and 36.5 kDa that forms a complex with PCNA in the presence of ATP. SUBCELLULAR LOCATION: Nuclear (Probable). ALTERNATIVE PRODUCTS: Event=Altern [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_P35250">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P35250</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="RFC140__nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P35251_1_Activator_1_140_kDa_subunit__Replication_factor_C_large_subunit___A1_140_kDa_subunit___RF_C_140_kDa_subunit___Activator_1_large_subunit___DNA_binding_protein_PO_GA_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_P35251_1_Activator_1_140_kDa_subunit__Replication_factor_C_large_subunit___A1_140_kDa_subunit___RF_C_140_kDa_subunit___Activator_1_large_subunit___DNA_binding_protein_PO_GA_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P35251-1 Activator 1 140 kDa subunit (Replication factor C large subunit) (A1 140 kDa subunit) (RF-C 140 kDa subunit) (Activator 1 large subunit) (DNA-binding protein PO-GA)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RFC140</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RFC1</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P35251" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: The elongation of primed DNA templates by DNA polymerase delta and epsilon requires the action of the accessory proteins PCNA and activator 1. The RFC1 subunit binds to the primer- template junction. Binds the PO-B transcription element as well as other GA rich DNA sequences. Could play a role in DNA transcription regulation as well as DNA replication and/or repair. Can bind single- or double-stranded DNA. FUNC [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_P35251">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P35251</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="RFC37__nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P35249_Activator_1_37_kDa_subunit__Replication_factor_C_37_kDa_subunit___A1_37_kDa_subunit___RF_C_37_kDa_subunit___RFC37_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_P35249_Activator_1_37_kDa_subunit__Replication_factor_C_37_kDa_subunit___A1_37_kDa_subunit___RF_C_37_kDa_subunit___RFC37_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P35249 Activator 1 37 kDa subunit (Replication factor C 37 kDa subunit) (A1 37 kDa subunit) (RF-C 37 kDa subunit) (RFC37)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RFC4</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P35249" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: The elongation of primed DNA templates by DNA polymerase delta and epsilon requires the action of the accessory proteins proliferating cell nuclear antigen (PCNA) and activator 1. The 37 kDa subunit may be involved in the elongation of the multiprimed DNA template. SUBUNIT: Heteropentamer of subunits of 140/145, 40, 38, 37, and 36.5 kDa that forms a complex with PCNA in the presence of ATP. SUBCELLULAR LOCATION [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_P35249">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P35249</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="RFC38__nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P40938_Activator_1_38_kDa_subunit__Replication_factor_C_38_kDa_subunit___A1_38_kDa_subunit___RF_C_38_kDa_subunit___RFC38___Replication_factor_C_subunit_3_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_P40938_Activator_1_38_kDa_subunit__Replication_factor_C_38_kDa_subunit___A1_38_kDa_subunit___RF_C_38_kDa_subunit___RFC38___Replication_factor_C_subunit_3_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P40938 Activator 1 38 kDa subunit (Replication factor C 38 kDa subunit) (A1 38 kDa subunit) (RF-C 38 kDa subunit) (RFC38) (Replication factor C subunit 3)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RFC3</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P40938" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: The elongation of primed DNA templates by DNA polymerase delta and epsilon requires the action of the accessory proteins proliferating cell nuclear antigen (PCNA) and activator 1. SUBUNIT: Heteropentamer of subunits of 140/145, 40, 38, 37, and 36.5 kDa that forms a complex with PCNA in the presence of ATP. SUBCELLULAR LOCATION: Nuclear (Probable). SIMILARITY: Belongs to the activator 1 small subunits family.</C [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_P40938">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P40938</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="RFC36__nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P40937_Activator_1_36_kDa_subunit__Replication_factor_C_36_kDa_subunit___A1_36_kDa_subunit___RF_C_36_kDa_subunit___RFC36___Replication_factor_C_subunit_5_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_P40937_Activator_1_36_kDa_subunit__Replication_factor_C_36_kDa_subunit___A1_36_kDa_subunit___RF_C_36_kDa_subunit___RFC36___Replication_factor_C_subunit_5_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P40937 Activator 1 36 kDa subunit (Replication factor C 36 kDa subunit) (A1 36 kDa subunit) (RF-C 36 kDa subunit) (RFC36) (Replication factor C subunit 5)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RFC5</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P40937" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: The elongation of primed DNA templates by DNA polymerase delta and epsilon requires the action of the accessory proteins proliferating cell nuclear antigen (PCNA) and activator 1. SUBUNIT: Heteropentamer of subunits of 140/145, 40, 38, 37, and 36.5 kDa that forms a complex with PCNA in the presence of ATP. Interacts with the C-terminus of PCNA. SUBCELLULAR LOCATION: Nuclear (Probable). SIMILARITY: Belongs to th [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_P40937">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P40937</ID>
+ </unificationXref>
+ <complexParticipant rdf:ID="RNA_primer_DNA_primer_origin_duplex__nucleoplasm_2">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#RNA_primer_DNA_primer_origin_duplex__nucleoplasm_1" />
+ </complexParticipant>
+ <complexParticipant rdf:ID="RFC_Heteropentamer_RNA_primer_DNA_primer_origin_duplex__nucleoplasm_">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#RFC_Heteropentamer_RNA_primer_DNA_primer_origin_duplex__nucleoplasm_1" />
+ </complexParticipant>
+ <complex rdf:ID="RFC_Heteropentamer_RNA_primer_DNA_primer_origin_duplex__nucleoplasm_1">
+ <COMPONENTS rdf:resource="#RFC_Heteropentamer__nucleoplasm_2" />
+ <COMPONENTS rdf:resource="#RNA_primer_DNA_primer_origin_duplex__nucleoplasm_3" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RFC Heteropentamer:RNA primer-DNA primer:origin duplex [nucleoplasm]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RFC Heteropentamer:RNA primer-DNA primer:origin duplex</SHORT-NAME>
+ </complex>
+ <complexParticipant rdf:ID="RFC_Heteropentamer__nucleoplasm_2">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#RFC_Heteropentamer__nucleoplasm_1" />
+ </complexParticipant>
+ <complexParticipant rdf:ID="RNA_primer_DNA_primer_origin_duplex__nucleoplasm_3">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#RNA_primer_DNA_primer_origin_duplex__nucleoplasm_1" />
+ </complexParticipant>
+ <complexParticipant rdf:ID="DNA_polymerase_alpha_primase__nucleoplasm_6">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#DNA_polymerase_alpha_primase__nucleoplasm_1" />
+ </complexParticipant>
+ <unificationXref rdf:ID="Reactome69053">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">69053</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <evidence rdf:ID="Summation_69054">
+ <XREF rdf:resource="#Pubmed_10656791" />
+ <XREF rdf:resource="#Pubmed_1671046" />
+ <XREF rdf:resource="#Pubmed_10656792" />
+ </evidence>
+ <publicationXref rdf:ID="Pubmed_10656791">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">10656791</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2000</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DNA polymerase switching: I. Replication factor C displaces DNA polymerase alpha prior to PCNA loading.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Maga, G</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Stucki, M</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Spadari, S</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Hübscher, U</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Mol Biol 295:791-801</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_1671046">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">1671046</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1991</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Replication factors required for SV40 DNA replication in vitro. II. Switching of DNA polymerase alpha and delta during initiation of leading and lagging strand synthesis.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Tsurimoto, T</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Stillman, B</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Biol Chem 266:1961-8</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_10656792">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">10656792</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2000</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DNA polymerase switching: II. Replication factor C abrogates primer synthesis by DNA polymerase alpha at a critical length.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mossi, R</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Keller, RC</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Ferrari, E</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Hübscher, U</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Mol Biol 295:803-14</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="RFC_binding_displaces_Pol_AlphaStep">
+ <STEP-INTERACTIONS rdf:resource="#RFC_binding_displaces_Pol_Alpha" />
+ <NEXT-STEP rdf:resource="#Loading_of_PCNA___Sliding_Clamp_FormationStep" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="Loading_of_PCNA___Sliding_Clamp_Formation">
+ <LEFT rdf:resource="#RFC_Heteropentamer_RNA_primer_DNA_primer_origin_duplex__nucleoplasm_2" />
+ <LEFT rdf:resource="#ATP__nucleoplasm_3" />
+ <LEFT rdf:resource="#PCNA_homotrimer__nucleoplasm_" />
+ <RIGHT rdf:resource="#ADP__nucleoplasm_3" />
+ <RIGHT rdf:resource="#RFC_Heteropentamer_RNA_primer_DNA_primer_origin_duplex_PCNA_homotrimer__nucleoplasm_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Loading of PCNA - Sliding Clamp Formation</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Loading of PCNA - Sliding Clamp Formation</SHORT-NAME>
+ <XREF rdf:resource="#Reactome69063" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The binding of the primer recognition complex involves the loading of proliferating cell nuclear antigen (PCNA). Replication Factor C transiently opens the PCNA toroid in an ATP-dependent reaction, and then allows PCNA to re-close around the double helix adjacent to the primer terminus. This leads to the formation of the "sliding clamp".</COMMENT>
+ <EVIDENCE rdf:resource="#Summation_69064" />
+ <CELLULAR-LOCATION rdf:resource="#nucleus" />
+ </biochemicalReaction>
+ <complexParticipant rdf:ID="RFC_Heteropentamer_RNA_primer_DNA_primer_origin_duplex__nucleoplasm_2">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#RFC_Heteropentamer_RNA_primer_DNA_primer_origin_duplex__nucleoplasm_1" />
+ </complexParticipant>
+ <smallMoleculeParticipant rdf:ID="ATP__nucleoplasm_3">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#ATP__ChEBI_2359_" />
+ </smallMoleculeParticipant>
+ <complexParticipant rdf:ID="PCNA_homotrimer__nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#PCNA_homotrimer__nucleoplasm_1" />
+ </complexParticipant>
+ <complex rdf:ID="PCNA_homotrimer__nucleoplasm_1">
+ <COMPONENTS rdf:resource="#PCNA__nucleoplasm_" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PCNA homotrimer [nucleoplasm]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PCNA homotrimer</SHORT-NAME>
+ </complex>
+ <proteinParticipant rdf:ID="PCNA__nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P12004_Proliferating_cell_nuclear_antigen__PCNA___Cyclin_" />
+ <STOICHIOMETRIC-COEFFICIENT rdf:datatype="http://www.w3.org/2001/XMLSchema#int">3</STOICHIOMETRIC-COEFFICIENT>
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_P12004_Proliferating_cell_nuclear_antigen__PCNA___Cyclin_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P12004 Proliferating cell nuclear antigen (PCNA) (Cyclin)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PCNA</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P12004" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: This protein is an auxiliary protein of DNA polymerase delta and is involved in the control of eukaryotic DNA replication by increasing the polymerase's processibility during elongation of the leading strand. SUBUNIT: Homotrimer. Forms a complex with activator 1 heteropentamer in the presence of ATP. Interacts with DNMT1, ERCC5/XPG, FEN1, CDC6 and POLDIP2. SUBCELLULAR LOCATION: Nuclear. DISEASE: Sera from patie [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_P12004">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P12004</ID>
+ </unificationXref>
+ <smallMoleculeParticipant rdf:ID="ADP__nucleoplasm_3">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#ADP__ChEBI_2342_" />
+ </smallMoleculeParticipant>
+ <complexParticipant rdf:ID="RFC_Heteropentamer_RNA_primer_DNA_primer_origin_duplex_PCNA_homotrimer__nucleoplasm_">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#RFC_Heteropentamer_RNA_primer_DNA_primer_origin_duplex_PCNA_homotrimer__nucleoplasm_1" />
+ </complexParticipant>
+ <complex rdf:ID="RFC_Heteropentamer_RNA_primer_DNA_primer_origin_duplex_PCNA_homotrimer__nucleoplasm_1">
+ <COMPONENTS rdf:resource="#RFC_Heteropentamer_RNA_primer_DNA_primer_origin_duplex__nucleoplasm_3" />
+ <COMPONENTS rdf:resource="#PCNA_homotrimer__nucleoplasm_2" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RFC Heteropentamer:RNA primer-DNA primer:origin duplex:PCNA homotrimer [nucleoplasm]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RFC Heteropentamer:RNA primer-DNA primer:origin duplex:PCNA homotrimer</SHORT-NAME>
+ </complex>
+ <complexParticipant rdf:ID="RFC_Heteropentamer_RNA_primer_DNA_primer_origin_duplex__nucleoplasm_3">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#RFC_Heteropentamer_RNA_primer_DNA_primer_origin_duplex__nucleoplasm_1" />
+ </complexParticipant>
+ <complexParticipant rdf:ID="PCNA_homotrimer__nucleoplasm_2">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#PCNA_homotrimer__nucleoplasm_1" />
+ </complexParticipant>
+ <unificationXref rdf:ID="Reactome69063">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">69063</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <evidence rdf:ID="Summation_69064">
+ <XREF rdf:resource="#Pubmed_2165567" />
+ <XREF rdf:resource="#Pubmed_9660172" />
+ </evidence>
+ <publicationXref rdf:ID="Pubmed_2165567">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2165567</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1990</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Sequential initiation of lagging and leading strand synthesis by two different polymerase complexes at the SV40 DNA replication origin.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Tsurimoto, T</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Melendy, T</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Stillman, B</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Nature 346:534-9</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_9660172">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">9660172</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1998</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Clamping down on clamps and clamp loaders--the eukaryotic replication factor C.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mossi, R</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Hübscher, U</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Eur J Biochem 254:209-16</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="Loading_of_PCNA___Sliding_Clamp_FormationStep">
+ <STEP-INTERACTIONS rdf:resource="#Loading_of_PCNA___Sliding_Clamp_Formation" />
+ <NEXT-STEP rdf:resource="#RFC_dissociates_after_sliding_clamp_formationStep" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="RFC_dissociates_after_sliding_clamp_formation">
+ <LEFT rdf:resource="#RFC_Heteropentamer_RNA_primer_DNA_primer_origin_duplex_PCNA_homotrimer__nucleoplasm_2" />
+ <RIGHT rdf:resource="#RFC_Heteropentamer__nucleoplasm_3" />
+ <RIGHT rdf:resource="#RNA_primer_DNA_primer_origin_duplex_PCNA___nucleoplasm_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RFC dissociates after sliding clamp formation</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RFC dissociates after sliding clamp formation</SHORT-NAME>
+ <XREF rdf:resource="#Reactome69068" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Replication factor C is proposed to dissociate from PCNA following sliding clamp formation, and the DNA toroid alone tethers pol delta to the DNA.</COMMENT>
+ <EVIDENCE rdf:resource="#Summation_69069" />
+ <CELLULAR-LOCATION rdf:resource="#nucleus" />
+ </biochemicalReaction>
+ <complexParticipant rdf:ID="RFC_Heteropentamer_RNA_primer_DNA_primer_origin_duplex_PCNA_homotrimer__nucleoplasm_2">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#RFC_Heteropentamer_RNA_primer_DNA_primer_origin_duplex_PCNA_homotrimer__nucleoplasm_1" />
+ </complexParticipant>
+ <complexParticipant rdf:ID="RFC_Heteropentamer__nucleoplasm_3">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#RFC_Heteropentamer__nucleoplasm_1" />
+ </complexParticipant>
+ <complexParticipant rdf:ID="RNA_primer_DNA_primer_origin_duplex_PCNA___nucleoplasm_">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#RNA_primer_DNA_primer_origin_duplex_PCNA___nucleoplasm_1" />
+ </complexParticipant>
+ <complex rdf:ID="RNA_primer_DNA_primer_origin_duplex_PCNA___nucleoplasm_1">
+ <COMPONENTS rdf:resource="#PCNA_homotrimer__nucleoplasm_3" />
+ <COMPONENTS rdf:resource="#RNA_primer_DNA_primer_origin_duplex__nucleoplasm_4" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RNA primer-DNA primer:origin duplex:PCNA [nucleoplasm]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RNA primer-DNA primer:origin duplex:PCNA</SHORT-NAME>
+ </complex>
+ <complexParticipant rdf:ID="PCNA_homotrimer__nucleoplasm_3">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#PCNA_homotrimer__nucleoplasm_1" />
+ </complexParticipant>
+ <complexParticipant rdf:ID="RNA_primer_DNA_primer_origin_duplex__nucleoplasm_4">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#RNA_primer_DNA_primer_origin_duplex__nucleoplasm_1" />
+ </complexParticipant>
+ <unificationXref rdf:ID="Reactome69068">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">69068</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <evidence rdf:ID="Summation_69069">
+ <XREF rdf:resource="#Pubmed_9822671" />
+ </evidence>
+ <publicationXref rdf:ID="Pubmed_9822671">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">9822671</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1998</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Replication factor C disengages from proliferating cell nuclear antigen (PCNA) upon sliding clamp formation, and PCNA itself tethers DNA polymerase delta to DNA.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Podust, VN</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Tiwari, N</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Stephan, S</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Fanning, E</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Biol Chem 273:31992-9</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="RFC_dissociates_after_sliding_clamp_formationStep">
+ <STEP-INTERACTIONS rdf:resource="#RFC_dissociates_after_sliding_clamp_formation" />
+ <NEXT-STEP rdf:resource="#Formation_of_Processive_ComplexStep" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="Formation_of_Processive_Complex">
+ <LEFT rdf:resource="#DNA_Polymerase_delta_tetramer__nucleoplasm_" />
+ <LEFT rdf:resource="#RNA_primer_DNA_primer_origin_duplex_PCNA___nucleoplasm_2" />
+ <RIGHT rdf:resource="#Processive_complex__nucleoplasm_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Formation of Processive Complex</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Formation of Processive Complex</SHORT-NAME>
+ <XREF rdf:resource="#Reactome69074" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The loading of proliferating cell nuclear antigen (PCNA) leads to recruitment of pol delta. Human PCNA is a homotrimer of 36 kDa subunits that form a toroidal structure. The loading of PCNA by RFC is a key event in the transition from the priming mode to the extension mode of DNA synthesis. The processive complex is composed of the pol delta holoenzyme and PCNA.</COMMENT>
+ <EVIDENCE rdf:resource="#Summation_69075" />
+ <CELLULAR-LOCATION rdf:resource="#nucleus" />
+ </biochemicalReaction>
+ <complexParticipant rdf:ID="DNA_Polymerase_delta_tetramer__nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#DNA_Polymerase_delta_tetramer__nucleoplasm_1" />
+ </complexParticipant>
+ <complex rdf:ID="DNA_Polymerase_delta_tetramer__nucleoplasm_1">
+ <COMPONENTS rdf:resource="#DNA_pol_delta_subunit_4__nucleoplasm_" />
+ <COMPONENTS rdf:resource="#DNA_pol_delta_catalytic_subunit__nucleoplasm_" />
+ <COMPONENTS rdf:resource="#DNA_pol_delta_subunit_2__nucleoplasm_" />
+ <COMPONENTS rdf:resource="#DNA_pol_delta_subunit_3__nucleoplasm_" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DNA Polymerase delta tetramer [nucleoplasm]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DNA Polymerase delta tetramer</SHORT-NAME>
+ </complex>
+ <proteinParticipant rdf:ID="DNA_pol_delta_subunit_4__nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q9HCU8_DNA_polymerase_delta_subunit_4__DNA_polymerase_delta_subunit_p12_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_Q9HCU8_DNA_polymerase_delta_subunit_4__DNA_polymerase_delta_subunit_p12_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:Q9HCU8 DNA polymerase delta subunit 4 (DNA polymerase delta subunit p12)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">POLDS</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">POLD4</SYNONYMS>
+ <XREF rdf:resource="#UniProt_Q9HCU8" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: The function of subunit 4 is not yet known. SUBUNIT: Heterotetramer composed of subunits of 125 kDa, 50 kDa, 66 kDa and 12 kDa. SUBCELLULAR LOCATION: Nuclear. SIMILARITY: Belongs to the DNA polymerase delta subunit 4 family.</COMMENT>
+ </protein>
+ <unificationXref rdf:ID="UniProt_Q9HCU8">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Q9HCU8</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="DNA_pol_delta_catalytic_subunit__nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P28340_DNA_polymerase_delta_catalytic_subunit__EC_2_7_7_7___DNA_polymerase_delta_subunit_p125_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_P28340_DNA_polymerase_delta_catalytic_subunit__EC_2_7_7_7___DNA_polymerase_delta_subunit_p125_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P28340 DNA polymerase delta catalytic subunit (EC 2.7.7.7) (DNA polymerase delta subunit p125)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">POLD</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">POLD1</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P28340" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Possesses two enzymatic activities: DNA synthesis (polymerase) and an exonucleolytic activity that degrades single stranded DNA in the 3' to 5' direction. Required with its accessory proteins (proliferating cell nuclear antigen (PCNA) and replication factor C (RFC) or activator 1) for leading strand synthesis. Also involved in completing Okazaki fragments initiated by the DNA polymerase alpha/primase complex. C [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_P28340">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P28340</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="DNA_pol_delta_subunit_2__nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P49005_DNA_polymerase_delta_subunit_2__EC_2_7_7_7___DNA_polymerase_delta_subunit_p50_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_P49005_DNA_polymerase_delta_subunit_2__EC_2_7_7_7___DNA_polymerase_delta_subunit_p50_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P49005 DNA polymerase delta subunit 2 (EC 2.7.7.7) (DNA polymerase delta subunit p50)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">POLD2</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P49005" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: The function of the small subunit is not yet clear. CATALYTIC ACTIVITY: N deoxynucleoside triphosphate = N diphosphate + {DNA}(N). SUBUNIT: Heterotetramer composed of subunits of 125 kDa, 50 kDa, 66 kDa and 12 kDa. Interacts with KCTD13/POLDIP1, POLDIP2 and POLDIP3. SUBCELLULAR LOCATION: Nuclear. SIMILARITY: Belongs to the DNA polymerase delta/II small subunit family.</COMMENT>
+ </protein>
+ <unificationXref rdf:ID="UniProt_P49005">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P49005</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="DNA_pol_delta_subunit_3__nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q15054_DNA_polymerase_delta_subunit_3__DNA_polymerase_delta_subunit_p66_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_Q15054_DNA_polymerase_delta_subunit_3__DNA_polymerase_delta_subunit_p66_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:Q15054 DNA polymerase delta subunit 3 (DNA polymerase delta subunit p66)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">POLD3</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">KIAA0039</SYNONYMS>
+ <XREF rdf:resource="#UniProt_Q15054" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: The function of subunit 3 is not clear. SUBUNIT: Heterotetramer composed of subunits of 125 kDa, 50 kDa, 66 kDa and 12 kDa. Interacts with subunit 2 and with PCNA. SUBCELLULAR LOCATION: Nuclear.</COMMENT>
+ </protein>
+ <unificationXref rdf:ID="UniProt_Q15054">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Q15054</ID>
+ </unificationXref>
+ <complexParticipant rdf:ID="RNA_primer_DNA_primer_origin_duplex_PCNA___nucleoplasm_2">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#RNA_primer_DNA_primer_origin_duplex_PCNA___nucleoplasm_1" />
+ </complexParticipant>
+ <complexParticipant rdf:ID="Processive_complex__nucleoplasm_">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Processive_complex__nucleoplasm_1" />
+ </complexParticipant>
+ <complex rdf:ID="Processive_complex__nucleoplasm_1">
+ <COMPONENTS rdf:resource="#DNA_Polymerase_delta_tetramer__nucleoplasm_2" />
+ <COMPONENTS rdf:resource="#RNA_primer_DNA_primer_origin_duplex_PCNA___nucleoplasm_3" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Processive complex [nucleoplasm]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Processive complex</SHORT-NAME>
+ </complex>
+ <complexParticipant rdf:ID="DNA_Polymerase_delta_tetramer__nucleoplasm_2">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#DNA_Polymerase_delta_tetramer__nucleoplasm_1" />
+ </complexParticipant>
+ <complexParticipant rdf:ID="RNA_primer_DNA_primer_origin_duplex_PCNA___nucleoplasm_3">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#RNA_primer_DNA_primer_origin_duplex_PCNA___nucleoplasm_1" />
+ </complexParticipant>
+ <unificationXref rdf:ID="Reactome69074">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">69074</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <evidence rdf:ID="Summation_69075">
+ <XREF rdf:resource="#Pubmed_1974050" />
+ <XREF rdf:resource="#Pubmed_1682322" />
+ <XREF rdf:resource="#Pubmed_8104944" />
+ <XREF rdf:resource="#Pubmed_7713898" />
+ </evidence>
+ <publicationXref rdf:ID="Pubmed_1974050">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">1974050</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1990</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mechanism of elongation of primed DNA by DNA polymerase delta, proliferating cell nuclear antigen, and activator 1.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Lee, SH</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Hurwitz, J</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Proc Natl Acad Sci U S A 87:5672-6</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_1682322">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">1682322</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1991</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Saccharomyces cerevisiae replication factor C. II. Formation and activity of complexes with the proliferating cell nuclear antigen and with DNA polymerases delta and epsilon.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Burgers, PM</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Biol Chem 266:22698-706</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_8104944">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">8104944</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1993</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Interaction of proliferating cell nuclear antigen with yeast DNA polymerase delta.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Brown, WC</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Campbell, JL</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Biol Chem 268:21706-10</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_7713898">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">7713898</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1995</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A conserved region in the amino terminus of DNA polymerase delta is involved in proliferating cell nuclear antigen binding.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Zhang, SJ</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Zeng, XR</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Zhang, P</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Toomey, NL</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Chuang, RY</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Chang, LS</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Lee, MY</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Biol Chem 270:7988-92</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="Formation_of_Processive_ComplexStep">
+ <STEP-INTERACTIONS rdf:resource="#Formation_of_Processive_Complex" />
+ </pathwayStep>
+ <unificationXref rdf:ID="Reactome69091">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">69091</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <evidence rdf:ID="Summation_69093">
+ <XREF rdf:resource="#Pubmed_1671046" />
+ <XREF rdf:resource="#Pubmed_1967833" />
+ <XREF rdf:resource="#Pubmed_1670772" />
+ </evidence>
+ <publicationXref rdf:ID="Pubmed_1967833">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">1967833</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1990</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Functions of replication factor C and proliferating-cell nuclear antigen: functional similarity of DNA polymerase accessory proteins from human cells and bacteriophage T4.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Tsurimoto, T</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Stillman, B</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Proc Natl Acad Sci U S A 87:1023-7</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_1670772">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">1670772</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1991</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Studies on the activator 1 protein complex, an accessory factor for proliferating cell nuclear antigen-dependent DNA polymerase delta.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Lee, SH</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Kwong, AD</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pan, ZQ</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Hurwitz, J</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Biol Chem 266:594-602</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="Polymerase_switchingStep">
+ <STEP-INTERACTIONS rdf:resource="#Polymerase_switching" />
+ <NEXT-STEP rdf:resource="#Processive_synthesis_on_the_lagging_strandStep" />
+ <NEXT-STEP rdf:resource="#Processive_synthesis_on_the_leading_strandStep" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="Processive_synthesis_on_the_leading_strand">
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Processive synthesis on the leading strand</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Processive synthesis on the leading strand</SHORT-NAME>
+ <XREF rdf:resource="#Reactome69098" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Polymerase switching is a key event that allows the processive synthesis of DNA by the pol delta and PCNA complex. Polymerase delta possesses polymerization and proofreading activities, which increases the overall fidelity of DNA replication. The pol delta holoenzyme is a heterotetrameric complex that contains p125, p66, p50, and p12 subunits, in human cells.</COMMENT>
+ <EVIDENCE rdf:resource="#Summation_69099" />
+ <CELLULAR-LOCATION rdf:resource="#nucleus" />
+ </biochemicalReaction>
+ <unificationXref rdf:ID="Reactome69098">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">69098</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <evidence rdf:ID="Summation_69099">
+ <XREF rdf:resource="#Pubmed_1671046" />
+ <XREF rdf:resource="#Pubmed_7378348" />
+ <XREF rdf:resource="#Pubmed_9191022" />
+ <XREF rdf:resource="#Pubmed_10751307" />
+ </evidence>
+ <publicationXref rdf:ID="Pubmed_7378348">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">7378348</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1980</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Purification of deoxyribonucleic acid polymerase delta from calf thymus: partial characterization of physical properties.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Lee, MY</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Tan, CK</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">So, AG</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Downey, KM</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Biochemistry 19:2096-101</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_9191022">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">9191022</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1997</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DNA polymerase delta, an essential enzyme for DNA transactions.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Hindges, R</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Hübscher, U</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Biol Chem 378:345-62</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_10751307">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">10751307</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2000</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Identification of a fourth subunit of mammalian DNA polymerase delta.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Liu, L</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mo, J</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Rodriguez-Belmonte, EM</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Lee, MY</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Biol Chem 275:18739-44</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="Processive_synthesis_on_the_leading_strandStep">
+ <STEP-INTERACTIONS rdf:resource="#Processive_synthesis_on_the_leading_strand" />
+ </pathwayStep>
+ <unificationXref rdf:ID="Reactome69109">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">69109</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <evidence rdf:ID="Summation_69110">
+ <XREF rdf:resource="#Pubmed_2175912" />
+ <XREF rdf:resource="#Pubmed_7378348" />
+ <XREF rdf:resource="#Pubmed_9191022" />
+ </evidence>
+ <publicationXref rdf:ID="Pubmed_2175912">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2175912</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1991</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Studies on the initiation and elongation reactions in the simian virus 40 DNA replication system.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Matsumoto, T</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Eki, T</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Hurwitz, J</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Proc Natl Acad Sci U S A 87:9712-6</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="Leading_Strand_SynthesisStep">
+ <STEP-INTERACTIONS rdf:resource="#Leading_Strand_Synthesis" />
+ </pathwayStep>
+ <pathway rdf:ID="Lagging_Strand_Synthesis">
+ <PATHWAY-COMPONENTS rdf:resource="#Processive_synthesis_on_the_lagging_strandStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#Polymerase_switchingStep" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Lagging Strand Synthesis</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Lagging Strand Synthesis</SHORT-NAME>
+ <XREF rdf:resource="#Reactome69186" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Due to the antiparallel nature of DNA, DNA polymerization is unidirectional, and one strand is synthesized discontinuously. This strand is called the lagging strand. Although the polymerase switching on the lagging strand is very similar to that on the leading strand, the processive synthesis on the two strands proceeds quite differently. Short DNA fragments, about 100 bases long, called Okazaki fragments are synthesized [...]
+ <EVIDENCE rdf:resource="#Summation_69187" />
+ <CELLULAR-LOCATION rdf:resource="#nucleus" />
+ </pathway>
+ <pathway rdf:ID="Polymerase_switching1">
+ <PATHWAY-COMPONENTS rdf:resource="#Loading_of_PCNA___Sliding_Clamp_FormationStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#RFC_dissociates_after_sliding_clamp_formationStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#Formation_of_Processive_ComplexStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#RFC_binding_displaces_Pol_AlphaStep" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Polymerase switching</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Polymerase switching</SHORT-NAME>
+ <XREF rdf:resource="#Reactome69091" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">After the primers are synthesized, Replication Factor C binds to the 3'-end of the initiator DNA to trigger polymerase switching. The non-processive nature of pol alpha catalytic activity and the tight binding of Replication Factor C to the primer-template junction presumably lead to the turnover of the pol alpha:primase complex. After the Pol alpha-primase primase complex is displaced from the primer, the proliferating [...]
+ <EVIDENCE rdf:resource="#Summation_69093" />
+ <CELLULAR-LOCATION rdf:resource="#nucleus" />
+ </pathway>
+ <biochemicalReaction rdf:ID="RFC_binding_displaces_Pol_Alpha1">
+ <LEFT rdf:resource="#RFC_Heteropentamer__nucleoplasm_4" />
+ <LEFT rdf:resource="#RNA_primer_DNA_primer_origin_duplex__nucleoplasm_5" />
+ <RIGHT rdf:resource="#RFC_Heteropentamer_RNA_primer_DNA_primer_origin_duplex__nucleoplasm_4" />
+ <RIGHT rdf:resource="#DNA_polymerase_alpha_primase__nucleoplasm_7" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RFC binding displaces Pol Alpha</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RFC binding displaces Pol Alpha</SHORT-NAME>
+ <XREF rdf:resource="#Reactome69053" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Once the RNA-DNA primer is synthesized, replication factor C (RFC) initiates a reaction called "polymerase switching"; pol delta, the processive enzyme replaces pol alpha, the priming enzyme. RFC binds to the 3'-end of the RNA-DNA primer on the Primosome, to displace the pol alpha primase complex. The binding of RFC triggers the binding of the primer recognition complex.</COMMENT>
+ <EVIDENCE rdf:resource="#Summation_69054" />
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ </biochemicalReaction>
+ <complexParticipant rdf:ID="RFC_Heteropentamer__nucleoplasm_4">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#RFC_Heteropentamer__nucleoplasm_1" />
+ </complexParticipant>
+ <complexParticipant rdf:ID="RNA_primer_DNA_primer_origin_duplex__nucleoplasm_5">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#RNA_primer_DNA_primer_origin_duplex__nucleoplasm_1" />
+ </complexParticipant>
+ <complexParticipant rdf:ID="RFC_Heteropentamer_RNA_primer_DNA_primer_origin_duplex__nucleoplasm_4">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#RFC_Heteropentamer_RNA_primer_DNA_primer_origin_duplex__nucleoplasm_1" />
+ </complexParticipant>
+ <complexParticipant rdf:ID="DNA_polymerase_alpha_primase__nucleoplasm_7">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#DNA_polymerase_alpha_primase__nucleoplasm_1" />
+ </complexParticipant>
+ <biochemicalReaction rdf:ID="Loading_of_PCNA___Sliding_Clamp_Formation1">
+ <LEFT rdf:resource="#RFC_Heteropentamer_RNA_primer_DNA_primer_origin_duplex__nucleoplasm_5" />
+ <LEFT rdf:resource="#ATP__nucleoplasm_4" />
+ <LEFT rdf:resource="#PCNA_homotrimer__nucleoplasm_4" />
+ <RIGHT rdf:resource="#ADP__nucleoplasm_4" />
+ <RIGHT rdf:resource="#RFC_Heteropentamer_RNA_primer_DNA_primer_origin_duplex_PCNA_homotrimer__nucleoplasm_3" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Loading of PCNA - Sliding Clamp Formation</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Loading of PCNA - Sliding Clamp Formation</SHORT-NAME>
+ <XREF rdf:resource="#Reactome69063" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The binding of the primer recognition complex involves the loading of proliferating cell nuclear antigen (PCNA). Replication Factor C transiently opens the PCNA toroid in an ATP-dependent reaction, and then allows PCNA to re-close around the double helix adjacent to the primer terminus. This leads to the formation of the "sliding clamp".</COMMENT>
+ <EVIDENCE rdf:resource="#Summation_69064" />
+ <CELLULAR-LOCATION rdf:resource="#nucleus" />
+ </biochemicalReaction>
+ <complexParticipant rdf:ID="RFC_Heteropentamer_RNA_primer_DNA_primer_origin_duplex__nucleoplasm_5">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#RFC_Heteropentamer_RNA_primer_DNA_primer_origin_duplex__nucleoplasm_1" />
+ </complexParticipant>
+ <smallMoleculeParticipant rdf:ID="ATP__nucleoplasm_4">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#ATP__ChEBI_2359_" />
+ </smallMoleculeParticipant>
+ <complexParticipant rdf:ID="PCNA_homotrimer__nucleoplasm_4">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#PCNA_homotrimer__nucleoplasm_1" />
+ </complexParticipant>
+ <smallMoleculeParticipant rdf:ID="ADP__nucleoplasm_4">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#ADP__ChEBI_2342_" />
+ </smallMoleculeParticipant>
+ <complexParticipant rdf:ID="RFC_Heteropentamer_RNA_primer_DNA_primer_origin_duplex_PCNA_homotrimer__nucleoplasm_3">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#RFC_Heteropentamer_RNA_primer_DNA_primer_origin_duplex_PCNA_homotrimer__nucleoplasm_1" />
+ </complexParticipant>
+ <biochemicalReaction rdf:ID="RFC_dissociates_after_sliding_clamp_formation1">
+ <LEFT rdf:resource="#RFC_Heteropentamer_RNA_primer_DNA_primer_origin_duplex_PCNA_homotrimer__nucleoplasm_4" />
+ <RIGHT rdf:resource="#RFC_Heteropentamer__nucleoplasm_5" />
+ <RIGHT rdf:resource="#RNA_primer_DNA_primer_origin_duplex_PCNA___nucleoplasm_4" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RFC dissociates after sliding clamp formation</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RFC dissociates after sliding clamp formation</SHORT-NAME>
+ <XREF rdf:resource="#Reactome69068" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Replication factor C is proposed to dissociate from PCNA following sliding clamp formation, and the DNA toroid alone tethers pol delta to the DNA.</COMMENT>
+ <EVIDENCE rdf:resource="#Summation_69069" />
+ <CELLULAR-LOCATION rdf:resource="#nucleus" />
+ </biochemicalReaction>
+ <complexParticipant rdf:ID="RFC_Heteropentamer_RNA_primer_DNA_primer_origin_duplex_PCNA_homotrimer__nucleoplasm_4">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#RFC_Heteropentamer_RNA_primer_DNA_primer_origin_duplex_PCNA_homotrimer__nucleoplasm_1" />
+ </complexParticipant>
+ <complexParticipant rdf:ID="RFC_Heteropentamer__nucleoplasm_5">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#RFC_Heteropentamer__nucleoplasm_1" />
+ </complexParticipant>
+ <complexParticipant rdf:ID="RNA_primer_DNA_primer_origin_duplex_PCNA___nucleoplasm_4">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#RNA_primer_DNA_primer_origin_duplex_PCNA___nucleoplasm_1" />
+ </complexParticipant>
+ <biochemicalReaction rdf:ID="Formation_of_Processive_Complex1">
+ <LEFT rdf:resource="#DNA_Polymerase_delta_tetramer__nucleoplasm_3" />
+ <LEFT rdf:resource="#RNA_primer_DNA_primer_origin_duplex_PCNA___nucleoplasm_5" />
+ <RIGHT rdf:resource="#Processive_complex__nucleoplasm_2" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Formation of Processive Complex</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Formation of Processive Complex</SHORT-NAME>
+ <XREF rdf:resource="#Reactome69074" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The loading of proliferating cell nuclear antigen (PCNA) leads to recruitment of pol delta. Human PCNA is a homotrimer of 36 kDa subunits that form a toroidal structure. The loading of PCNA by RFC is a key event in the transition from the priming mode to the extension mode of DNA synthesis. The processive complex is composed of the pol delta holoenzyme and PCNA.</COMMENT>
+ <EVIDENCE rdf:resource="#Summation_69075" />
+ <CELLULAR-LOCATION rdf:resource="#nucleus" />
+ </biochemicalReaction>
+ <complexParticipant rdf:ID="DNA_Polymerase_delta_tetramer__nucleoplasm_3">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#DNA_Polymerase_delta_tetramer__nucleoplasm_1" />
+ </complexParticipant>
+ <complexParticipant rdf:ID="RNA_primer_DNA_primer_origin_duplex_PCNA___nucleoplasm_5">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#RNA_primer_DNA_primer_origin_duplex_PCNA___nucleoplasm_1" />
+ </complexParticipant>
+ <complexParticipant rdf:ID="Processive_complex__nucleoplasm_2">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Processive_complex__nucleoplasm_1" />
+ </complexParticipant>
+ <pathway rdf:ID="Processive_synthesis_on_the_lagging_strand">
+ <PATHWAY-COMPONENTS rdf:resource="#Removal_of_the_Flap_IntermediateStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#Formation_of_the_Flap_IntermediateStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#Formation_of_Okazaki_fragmentsStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#Joining_of_adjacent_Okazaki_fragmentsStep" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Processive synthesis on the lagging strand</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Processive synthesis on the lagging strand</SHORT-NAME>
+ <XREF rdf:resource="#Reactome69183" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The key event that allows the processive synthesis on the lagging strand, is polymerase switching from pol alpha to pol delta, as on the leading strand. However, the processive synthesis on the lagging strand proceeds very differently. DNA synthesis is discontinuous, and involves the formation of short fragments called the Okazaki fragments. During the synthesis of Okazaki fragments, the RNA primer is folded into a singl [...]
+ <EVIDENCE rdf:resource="#Summation_69185" />
+ <CELLULAR-LOCATION rdf:resource="#nucleus" />
+ </pathway>
+ <biochemicalReaction rdf:ID="Formation_of_Okazaki_fragments">
+ <LEFT rdf:resource="#Processive_complex__nucleoplasm_3" />
+ <RIGHT rdf:resource="#Processive_complex_Okazaki_fragment_complex__nucleoplasm_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Formation of Okazaki fragments</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Formation of Okazaki fragments</SHORT-NAME>
+ <XREF rdf:resource="#Reactome69116" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">After RFC initiates the assembly of the primer recognition complex, the complex of pol delta and PCNA is responsible for incorporating the additional nucleotides prior to the position of the next downstream initiator RNA primer. On the lagging strand, short discontinuous segments of DNA, called Okazaki fragments, are synthesized on RNA primers. The average length of the Okazaki fragments is 100 nucleotides. Polymerase sw [...]
+ <EVIDENCE rdf:resource="#Summation_69117" />
+ <CELLULAR-LOCATION rdf:resource="#nucleus" />
+ </biochemicalReaction>
+ <complexParticipant rdf:ID="Processive_complex__nucleoplasm_3">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Processive_complex__nucleoplasm_1" />
+ </complexParticipant>
+ <complexParticipant rdf:ID="Processive_complex_Okazaki_fragment_complex__nucleoplasm_">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Processive_complex_Okazaki_fragment_complex__nucleoplasm_1" />
+ </complexParticipant>
+ <complex rdf:ID="Processive_complex_Okazaki_fragment_complex__nucleoplasm_1">
+ <COMPONENTS rdf:resource="#Processive_complex__nucleoplasm_4" />
+ <COMPONENTS rdf:resource="#Okazaki_fragment__nucleoplasm_" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Processive complex:Okazaki fragment complex [nucleoplasm]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Processive complex:Okazaki fragment complex</SHORT-NAME>
+ </complex>
+ <complexParticipant rdf:ID="Processive_complex__nucleoplasm_4">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Processive_complex__nucleoplasm_1" />
+ </complexParticipant>
+ <physicalEntityParticipant rdf:ID="Okazaki_fragment__nucleoplasm_">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Okazaki_fragment__nucleoplasm_1" />
+ </physicalEntityParticipant>
+ <physicalEntity rdf:ID="Okazaki_fragment__nucleoplasm_1">
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Okazaki fragment [nucleoplasm]</NAME>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome. Each synonym is a name of a ConcreteEntity, and each XREF points to one ConcreteEntity</COMMENT>
+ </physicalEntity>
+ <catalysis rdf:ID="delta_DNA_polymerase_activity_of_DNA_Polymerase_delta_tetramer__nucleoplasm_">
+ <CONTROLLER rdf:resource="#DNA_Polymerase_delta_tetramer__nucleoplasm_4" />
+ <CONTROLLED rdf:resource="#Formation_of_Okazaki_fragments" />
+ <DIRECTION rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PHYSIOL-LEFT-TO-RIGHT</DIRECTION>
+ <XREF rdf:resource="#delta_DNA_polymerase_activity" />
+ </catalysis>
+ <complexParticipant rdf:ID="DNA_Polymerase_delta_tetramer__nucleoplasm_4">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#DNA_Polymerase_delta_tetramer__nucleoplasm_1" />
+ </complexParticipant>
+ <relationshipXref rdf:ID="delta_DNA_polymerase_activity">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GO</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0003891</ID>
+ </relationshipXref>
+ <unificationXref rdf:ID="Reactome69116">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">69116</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <evidence rdf:ID="Summation_69117">
+ <XREF rdf:resource="#Pubmed_8144677" />
+ <XREF rdf:resource="#Pubmed_1974050" />
+ <XREF rdf:resource="#Pubmed_8104944" />
+ <XREF rdf:resource="#Pubmed_9081985" />
+ <XREF rdf:resource="#Pubmed_1328683" />
+ <XREF rdf:resource="#Pubmed_1671046" />
+ </evidence>
+ <publicationXref rdf:ID="Pubmed_8144677">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">8144677</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1994</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reconstitution of complete SV40 DNA replication with purified replication factors.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Waga, S</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bauer, G</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Stillman, B</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Biol Chem 269:10923-34</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_9081985">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">9081985</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1997</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Enzymes and reactions at the eukaryotic DNA replication fork.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bambara, RA</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Murante, RS</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Henricksen, LA</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Biol Chem 272:4647-50</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_1328683">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">1328683</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1992</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Assembly of simian virus 40 Okazaki pieces from DNA primers is reversibly arrested by ATP depletion.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Nethanel, T</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Zlotkin, T</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Kaufmann, G</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Virol 66:6634-40</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="Formation_of_Okazaki_fragmentsStep">
+ <STEP-INTERACTIONS rdf:resource="#Formation_of_Okazaki_fragments" />
+ <NEXT-STEP rdf:resource="#Formation_of_the_Flap_IntermediateStep" />
+ <STEP-INTERACTIONS rdf:resource="#delta_DNA_polymerase_activity_of_DNA_Polymerase_delta_tetramer__nucleoplasm_" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="Formation_of_the_Flap_Intermediate">
+ <LEFT rdf:resource="#Processive_complex_Okazaki_fragment_complex__nucleoplasm_2" />
+ <RIGHT rdf:resource="#Processive_complex_Okazaki_fragment_Flap__nucleoplasm_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Formation of the Flap Intermediate</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Formation of the Flap Intermediate</SHORT-NAME>
+ <XREF rdf:resource="#Reactome69127" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">When the polymerase delta:PCNA complex reaches a downstream Okazaki fragment, strand displacement synthesis occurs. The primer containing 5'-terminus of the downstream Okazaki fragment is folded into a single-stranded flap.</COMMENT>
+ <EVIDENCE rdf:resource="#Summation_69128" />
+ <CELLULAR-LOCATION rdf:resource="#nucleus" />
+ </biochemicalReaction>
+ <complexParticipant rdf:ID="Processive_complex_Okazaki_fragment_complex__nucleoplasm_2">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Processive_complex_Okazaki_fragment_complex__nucleoplasm_1" />
+ </complexParticipant>
+ <complexParticipant rdf:ID="Processive_complex_Okazaki_fragment_Flap__nucleoplasm_">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Processive_complex_Okazaki_fragment_Flap__nucleoplasm_1" />
+ </complexParticipant>
+ <complex rdf:ID="Processive_complex_Okazaki_fragment_Flap__nucleoplasm_1">
+ <COMPONENTS rdf:resource="#Processive_complex_Okazaki_fragment_complex__nucleoplasm_3" />
+ <COMPONENTS rdf:resource="#Flap__nucleoplasm_" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Processive complex:Okazaki fragment:Flap [nucleoplasm]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Processive complex:Okazaki fragment:Flap</SHORT-NAME>
+ </complex>
+ <complexParticipant rdf:ID="Processive_complex_Okazaki_fragment_complex__nucleoplasm_3">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Processive_complex_Okazaki_fragment_complex__nucleoplasm_1" />
+ </complexParticipant>
+ <physicalEntityParticipant rdf:ID="Flap__nucleoplasm_">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Flap__nucleoplasm_1" />
+ </physicalEntityParticipant>
+ <physicalEntity rdf:ID="Flap__nucleoplasm_1">
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Flap [nucleoplasm]</NAME>
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome. Each synonym is a name of a ConcreteEntity, and each XREF points to one ConcreteEntity</COMMENT>
+ </physicalEntity>
+ <unificationXref rdf:ID="Reactome69127">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">69127</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <evidence rdf:ID="Summation_69128">
+ <XREF rdf:resource="#Pubmed_7711022" />
+ <XREF rdf:resource="#Pubmed_11473323" />
+ <XREF rdf:resource="#Pubmed_11724925" />
+ </evidence>
+ <publicationXref rdf:ID="Pubmed_7711022">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">7711022</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1995</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DNA polymerase delta holoenzyme: action on single-stranded DNA and on double-stranded DNA in the presence of replicative DNA helicases.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Podust, VN</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Podust, LM</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Müller, F</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Hübscher, U</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Biochemistry 34:5003-10</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_11473323">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">11473323</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2001</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RPA governs endonuclease switching during processing of Okazaki fragments in eukaryotes.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bae, SH</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bae, KH</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Kim, JA</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Seo, YS</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Nature 412:456-61</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_11724925">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">11724925</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2001</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Okazaki fragment processing: modulation of the strand displacement activity of DNA polymerase delta by the concerted action of replication protein A, proliferating cell nuclear antigen, and flap endonuclease-1.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Maga, G</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Villani, G</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Tillement, V</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Stucki, M</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Locatelli, GA</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Frouin, I</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Spadari, S</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Hübscher, U</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Proc Natl Acad Sci U S A 98:14298-303</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="Formation_of_the_Flap_IntermediateStep">
+ <STEP-INTERACTIONS rdf:resource="#Formation_of_the_Flap_Intermediate" />
+ <NEXT-STEP rdf:resource="#Removal_of_the_Flap_IntermediateStep" />
+ <NEXT-STEP rdf:resource="#RPA_binds_to_the_FlapStep" />
+ </pathwayStep>
+ <pathway rdf:ID="Removal_of_the_Flap_Intermediate">
+ <PATHWAY-COMPONENTS rdf:resource="#Recruitment_of_Dna2_endonucleaseStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#RPA_binds_to_the_FlapStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#Removal_of_RNA_primer_and_dissociation_of_RPA_and_Dna2Step" />
+ <PATHWAY-COMPONENTS rdf:resource="#Removal_of_remaining_FlapStep" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Removal of the Flap Intermediate</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Removal of the Flap Intermediate</SHORT-NAME>
+ <XREF rdf:resource="#Reactome69166" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Two endonucleases, Dna2 and flap endonuclease 1 (FEN-1), are responsible for resolving the nascent flap structure. The Dna2 endonuclease/helicase in yeast is a monomer of approximately 172 kDa. Human FEN-1 is a single polypeptide of approximately 42 kDa. Replication Protein A regulates the switching of endonucleases during the removal of the displaced flap.</COMMENT>
+ <EVIDENCE rdf:resource="#Summation_69167" />
+ <CELLULAR-LOCATION rdf:resource="#nucleus" />
+ </pathway>
+ <biochemicalReaction rdf:ID="RPA_binds_to_the_Flap">
+ <LEFT rdf:resource="#RPA_heterotrimer__nucleoplasm_" />
+ <LEFT rdf:resource="#Processive_complex_Okazaki_fragment_Flap__nucleoplasm_2" />
+ <RIGHT rdf:resource="#Processive_complex_Okazaki_fragment_Flap_RPA_heterotrimer__nucleoplasm_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RPA binds to the Flap</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RPA binds to the Flap</SHORT-NAME>
+ <XREF rdf:resource="#Reactome69140" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The first step in the removal of the Flap intermediate is the binding of Replication Protein A (RPA) to the long flap structure. RPA is a eucaryotic single-stranded DNA binding protein.</COMMENT>
+ <EVIDENCE rdf:resource="#Summation_69141" />
+ <CELLULAR-LOCATION rdf:resource="#nucleus" />
+ </biochemicalReaction>
+ <complexParticipant rdf:ID="RPA_heterotrimer__nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#RPA_heterotrimer__nucleoplasm_1" />
+ </complexParticipant>
+ <complex rdf:ID="RPA_heterotrimer__nucleoplasm_1">
+ <COMPONENTS rdf:resource="#DNA_Replication_factor_A_protein_A1__70kD___nucleoplasm_1" />
+ <COMPONENTS rdf:resource="#DNA_Replication_factor_A_protein_3__14kD___nucleoplasm_1" />
+ <COMPONENTS rdf:resource="#DNA_Replication_factor_A_protein_2__32kD___nucleoplasm_1" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RPA heterotrimer [nucleoplasm]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RPA heterotrimer</SHORT-NAME>
+ </complex>
+ <proteinParticipant rdf:ID="DNA_Replication_factor_A_protein_A1__70kD___nucleoplasm_1">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P27694_Replication_protein_A_70_kDa_DNA_binding_subunit__RP_A___RF_A___Replication_factor_A_protein_1___Single_stranded_DNA_binding_protein_" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="DNA_Replication_factor_A_protein_3__14kD___nucleoplasm_1">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P35244_Replication_protein_A_14_kDa_subunit__RP_A___RF_A___Replication_factor_A_protein_3_" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="DNA_Replication_factor_A_protein_2__32kD___nucleoplasm_1">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P15927_Replication_protein_A_32_kDa_subunit__RP_A___RF_A___Replication_factor_A_protein_2_" />
+ </proteinParticipant>
+ <complexParticipant rdf:ID="Processive_complex_Okazaki_fragment_Flap__nucleoplasm_2">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Processive_complex_Okazaki_fragment_Flap__nucleoplasm_1" />
+ </complexParticipant>
+ <complexParticipant rdf:ID="Processive_complex_Okazaki_fragment_Flap_RPA_heterotrimer__nucleoplasm_">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Processive_complex_Okazaki_fragment_Flap_RPA_heterotrimer__nucleoplasm_1" />
+ </complexParticipant>
+ <complex rdf:ID="Processive_complex_Okazaki_fragment_Flap_RPA_heterotrimer__nucleoplasm_1">
+ <COMPONENTS rdf:resource="#RPA_heterotrimer__nucleoplasm_2" />
+ <COMPONENTS rdf:resource="#Processive_complex_Okazaki_fragment_Flap__nucleoplasm_3" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Processive complex:Okazaki fragment:Flap:RPA heterotrimer [nucleoplasm]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Processive complex:Okazaki fragment:Flap:RPA heterotrimer</SHORT-NAME>
+ </complex>
+ <complexParticipant rdf:ID="RPA_heterotrimer__nucleoplasm_2">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#RPA_heterotrimer__nucleoplasm_1" />
+ </complexParticipant>
+ <complexParticipant rdf:ID="Processive_complex_Okazaki_fragment_Flap__nucleoplasm_3">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Processive_complex_Okazaki_fragment_Flap__nucleoplasm_1" />
+ </complexParticipant>
+ <unificationXref rdf:ID="Reactome69140">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">69140</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <evidence rdf:ID="Summation_69141">
+ <XREF rdf:resource="#Pubmed_11473323" />
+ </evidence>
+ <pathwayStep rdf:ID="RPA_binds_to_the_FlapStep">
+ <STEP-INTERACTIONS rdf:resource="#RPA_binds_to_the_Flap" />
+ <NEXT-STEP rdf:resource="#Recruitment_of_Dna2_endonucleaseStep" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="Recruitment_of_Dna2_endonuclease">
+ <LEFT rdf:resource="#dna2_endonuclease__nucleoplasm_" />
+ <LEFT rdf:resource="#Processive_complex_Okazaki_fragment_Flap_RPA_heterotrimer__nucleoplasm_2" />
+ <RIGHT rdf:resource="#Processive_complex_Okazaki_fragment_Flap_RPA_heterotrimer_dna2__nucleoplasm_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Recruitment of Dna2 endonuclease</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Recruitment of Dna2 endonuclease</SHORT-NAME>
+ <XREF rdf:resource="#Reactome69142" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">After RPA binds the long flap, it recruits the Dna2 endonuclease. Dna2 endonuclease removes most of the Flap, but the job of complete removal of the flap is then completed by FEN-1.</COMMENT>
+ <EVIDENCE rdf:resource="#Summation_69143" />
+ <CELLULAR-LOCATION rdf:resource="#nucleus" />
+ </biochemicalReaction>
+ <proteinParticipant rdf:ID="dna2_endonuclease__nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P51530_DNA2_like_homolog__DNA_replication_helicase_like_homolog___Fragment_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_P51530_DNA2_like_homolog__DNA_replication_helicase_like_homolog___Fragment_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P51530 DNA2-like homolog (DNA replication helicase-like homolog) (Fragment)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DNA2L</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">KIAA0083</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P51530" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SIMILARITY: Belongs to the DNA2/NAM7 helicase family.</COMMENT>
+ </protein>
+ <unificationXref rdf:ID="UniProt_P51530">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P51530</ID>
+ </unificationXref>
+ <complexParticipant rdf:ID="Processive_complex_Okazaki_fragment_Flap_RPA_heterotrimer__nucleoplasm_2">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Processive_complex_Okazaki_fragment_Flap_RPA_heterotrimer__nucleoplasm_1" />
+ </complexParticipant>
+ <complexParticipant rdf:ID="Processive_complex_Okazaki_fragment_Flap_RPA_heterotrimer_dna2__nucleoplasm_">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Processive_complex_Okazaki_fragment_Flap_RPA_heterotrimer_dna2__nucleoplasm_1" />
+ </complexParticipant>
+ <complex rdf:ID="Processive_complex_Okazaki_fragment_Flap_RPA_heterotrimer_dna2__nucleoplasm_1">
+ <COMPONENTS rdf:resource="#dna2_endonuclease__nucleoplasm_1" />
+ <COMPONENTS rdf:resource="#Processive_complex_Okazaki_fragment_Flap_RPA_heterotrimer__nucleoplasm_3" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Processive complex:Okazaki fragment:Flap:RPA heterotrimer:dna2 [nucleoplasm]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Processive complex:Okazaki fragment:Flap:RPA heterotrimer:dna2</SHORT-NAME>
+ </complex>
+ <proteinParticipant rdf:ID="dna2_endonuclease__nucleoplasm_1">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P51530_DNA2_like_homolog__DNA_replication_helicase_like_homolog___Fragment_" />
+ </proteinParticipant>
+ <complexParticipant rdf:ID="Processive_complex_Okazaki_fragment_Flap_RPA_heterotrimer__nucleoplasm_3">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Processive_complex_Okazaki_fragment_Flap_RPA_heterotrimer__nucleoplasm_1" />
+ </complexParticipant>
+ <unificationXref rdf:ID="Reactome69142">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">69142</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <evidence rdf:ID="Summation_69143">
+ <XREF rdf:resource="#Pubmed_11473323" />
+ </evidence>
+ <pathwayStep rdf:ID="Recruitment_of_Dna2_endonucleaseStep">
+ <STEP-INTERACTIONS rdf:resource="#Recruitment_of_Dna2_endonuclease" />
+ <NEXT-STEP rdf:resource="#Removal_of_RNA_primer_and_dissociation_of_RPA_and_Dna2Step" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="Removal_of_RNA_primer_and_dissociation_of_RPA_and_Dna2">
+ <LEFT rdf:resource="#Processive_complex_Okazaki_fragment_Flap_RPA_heterotrimer_dna2__nucleoplasm_2" />
+ <RIGHT rdf:resource="#RPA_heterotrimer__nucleoplasm_3" />
+ <RIGHT rdf:resource="#UTP__nucleoplasm_" />
+ <RIGHT rdf:resource="#dna2_endonuclease__nucleoplasm_2" />
+ <RIGHT rdf:resource="#CTP__nucleoplasm_" />
+ <RIGHT rdf:resource="#ATP__nucleoplasm_5" />
+ <RIGHT rdf:resource="#GTP__nucleoplasm_" />
+ <RIGHT rdf:resource="#Processive_complex_Okazaki_fragments_Remaining_Flap__nucleoplasm_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Removal of RNA primer and dissociation of RPA and Dna2</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Removal of RNA primer and dissociation of RPA and Dna2</SHORT-NAME>
+ <XREF rdf:resource="#Reactome69144" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The Dna2 endonuclease removes the initiator RNA along with several downstream deoxyribonucleotides. The cleavage of the single-stranded RNA substrate results in the disassembly of RPA and Dna2. The current data for the role of the Dna2 endonuclease has been derived from studies with yeast and Xenopus Dna2.</COMMENT>
+ <EVIDENCE rdf:resource="#Summation_69145" />
+ <CELLULAR-LOCATION rdf:resource="#nucleus" />
+ </biochemicalReaction>
+ <complexParticipant rdf:ID="Processive_complex_Okazaki_fragment_Flap_RPA_heterotrimer_dna2__nucleoplasm_2">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Processive_complex_Okazaki_fragment_Flap_RPA_heterotrimer_dna2__nucleoplasm_1" />
+ </complexParticipant>
+ <complexParticipant rdf:ID="RPA_heterotrimer__nucleoplasm_3">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#RPA_heterotrimer__nucleoplasm_1" />
+ </complexParticipant>
+ <smallMoleculeParticipant rdf:ID="UTP__nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UTP__ChEBI_9850_" />
+ </smallMoleculeParticipant>
+ <smallMolecule rdf:ID="UTP__ChEBI_9850_">
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UTP [ChEBI:9850]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UTP</SHORT-NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Uridine triphosphate</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">uridine 5'-triphosphate</SYNONYMS>
+ <XREF rdf:resource="#ChEBI_9850" />
+ </smallMolecule>
+ <unificationXref rdf:ID="ChEBI_9850">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ChEBI</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">9850</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="dna2_endonuclease__nucleoplasm_2">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P51530_DNA2_like_homolog__DNA_replication_helicase_like_homolog___Fragment_" />
+ </proteinParticipant>
+ <smallMoleculeParticipant rdf:ID="CTP__nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#CTP__ChEBI_3285_" />
+ </smallMoleculeParticipant>
+ <smallMolecule rdf:ID="CTP__ChEBI_3285_">
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CTP [ChEBI:3285]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CTP</SHORT-NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cytidine 5'-triphosphate</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cytidine triphosphate</SYNONYMS>
+ <XREF rdf:resource="#ChEBI_3285" />
+ </smallMolecule>
+ <unificationXref rdf:ID="ChEBI_3285">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ChEBI</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">3285</ID>
+ </unificationXref>
+ <smallMoleculeParticipant rdf:ID="ATP__nucleoplasm_5">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#ATP__ChEBI_2359_" />
+ </smallMoleculeParticipant>
+ <smallMoleculeParticipant rdf:ID="GTP__nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#GTP__ChEBI_5234_" />
+ </smallMoleculeParticipant>
+ <smallMolecule rdf:ID="GTP__ChEBI_5234_">
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GTP [ChEBI:5234]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GTP</SHORT-NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Guanosine 5'-triphosphate</SYNONYMS>
+ <XREF rdf:resource="#ChEBI_5234" />
+ </smallMolecule>
+ <unificationXref rdf:ID="ChEBI_5234">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ChEBI</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">5234</ID>
+ </unificationXref>
+ <complexParticipant rdf:ID="Processive_complex_Okazaki_fragments_Remaining_Flap__nucleoplasm_">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Processive_complex_Okazaki_fragments_Remaining_Flap__nucleoplasm_1" />
+ </complexParticipant>
+ <complex rdf:ID="Processive_complex_Okazaki_fragments_Remaining_Flap__nucleoplasm_1">
+ <COMPONENTS rdf:resource="#Processive_complex__nucleoplasm_5" />
+ <COMPONENTS rdf:resource="#Remaining_Flap__nucleoplasm_" />
+ <COMPONENTS rdf:resource="#Okazaki_fragment__nucleoplasm_2" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Processive complex:Okazaki fragments:Remaining Flap [nucleoplasm]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Processive complex:Okazaki fragments:Remaining Flap</SHORT-NAME>
+ </complex>
+ <complexParticipant rdf:ID="Processive_complex__nucleoplasm_5">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Processive_complex__nucleoplasm_1" />
+ </complexParticipant>
+ <physicalEntityParticipant rdf:ID="Remaining_Flap__nucleoplasm_">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Remaining_Flap__nucleoplasm_1" />
+ </physicalEntityParticipant>
+ <physicalEntity rdf:ID="Remaining_Flap__nucleoplasm_1">
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Remaining Flap [nucleoplasm]</NAME>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome. Each synonym is a name of a ConcreteEntity, and each XREF points to one ConcreteEntity</COMMENT>
+ </physicalEntity>
+ <physicalEntityParticipant rdf:ID="Okazaki_fragment__nucleoplasm_2">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Okazaki_fragment__nucleoplasm_1" />
+ </physicalEntityParticipant>
+ <unificationXref rdf:ID="Reactome69144">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">69144</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <evidence rdf:ID="Summation_69145">
+ <XREF rdf:resource="#Pubmed_10748138" />
+ <XREF rdf:resource="#Pubmed_11473323" />
+ </evidence>
+ <publicationXref rdf:ID="Pubmed_10748138">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">10748138</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2000</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The nuclease activity of the yeast DNA2 protein, which is related to the RecB-like nucleases, is essential in vivo.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Budd, ME</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Choe, W</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Campbell, JL</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Biol Chem 275:16518-29</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="Removal_of_RNA_primer_and_dissociation_of_RPA_and_Dna2Step">
+ <STEP-INTERACTIONS rdf:resource="#Removal_of_RNA_primer_and_dissociation_of_RPA_and_Dna2" />
+ <NEXT-STEP rdf:resource="#Removal_of_remaining_FlapStep" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="Removal_of_remaining_Flap">
+ <LEFT rdf:resource="#Processive_complex_Okazaki_fragments_Remaining_Flap__nucleoplasm_2" />
+ <RIGHT rdf:resource="#Processive_complex_nicked_DNA_from_adjacent_Okazaki_fragments__nucleoplasm_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Removal of remaining Flap</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Removal of remaining Flap</SHORT-NAME>
+ <XREF rdf:resource="#Reactome69152" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The remaining Flap, that is too short to support RPA binding is then processed by FEN-1. There is evidence that binding of RPA to the displaced end of the RNA-containing Okazaki fragment prevents FEN-1 from accessing the substrate. FEN-1 is a structure-specific endonuclease that cleaves near the base of the flap at a position one nucleotide into the annealed region Biochemical studies have shown that the preferred subst [...]
+ <EVIDENCE rdf:resource="#Summation_69153" />
+ <CELLULAR-LOCATION rdf:resource="#nucleus" />
+ </biochemicalReaction>
+ <complexParticipant rdf:ID="Processive_complex_Okazaki_fragments_Remaining_Flap__nucleoplasm_2">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Processive_complex_Okazaki_fragments_Remaining_Flap__nucleoplasm_1" />
+ </complexParticipant>
+ <complexParticipant rdf:ID="Processive_complex_nicked_DNA_from_adjacent_Okazaki_fragments__nucleoplasm_">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Processive_complex_nicked_DNA_from_adjacent_Okazaki_fragments__nucleoplasm_1" />
+ </complexParticipant>
+ <complex rdf:ID="Processive_complex_nicked_DNA_from_adjacent_Okazaki_fragments__nucleoplasm_1">
+ <COMPONENTS rdf:resource="#Processive_complex__nucleoplasm_6" />
+ <COMPONENTS rdf:resource="#Okazaki_fragment_minus_Flap__nucleoplasm_" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Processive complex:nicked DNA from adjacent Okazaki fragments [nucleoplasm]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Processive complex:nicked DNA from adjacent Okazaki fragments</SHORT-NAME>
+ </complex>
+ <complexParticipant rdf:ID="Processive_complex__nucleoplasm_6">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Processive_complex__nucleoplasm_1" />
+ </complexParticipant>
+ <physicalEntityParticipant rdf:ID="Okazaki_fragment_minus_Flap__nucleoplasm_">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Okazaki_fragment_minus_Flap__nucleoplasm_1" />
+ </physicalEntityParticipant>
+ <physicalEntity rdf:ID="Okazaki_fragment_minus_Flap__nucleoplasm_1">
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Okazaki fragment minus Flap [nucleoplasm]</NAME>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome. Each synonym is a name of a ConcreteEntity, and each XREF points to one ConcreteEntity</COMMENT>
+ </physicalEntity>
+ <catalysis rdf:ID="_5__flap_endonuclease_activity_of_Flap_endonuclease_1___nucleoplasm_">
+ <CONTROLLER rdf:resource="#Flap_endonuclease_1___nucleoplasm_" />
+ <CONTROLLED rdf:resource="#Removal_of_remaining_Flap" />
+ <DIRECTION rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PHYSIOL-LEFT-TO-RIGHT</DIRECTION>
+ <XREF rdf:resource="#_5__flap_endonuclease_activity" />
+ </catalysis>
+ <proteinParticipant rdf:ID="Flap_endonuclease_1___nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P39748_Flap_endonuclease_1__EC_3_________Maturation_factor_1___MF1_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_P39748_Flap_endonuclease_1__EC_3_________Maturation_factor_1___MF1_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P39748 Flap endonuclease-1 (EC 3.-.-.-) (Maturation factor 1) (MF1)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FEN1</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P39748" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Endonuclease that cleave the 5'overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'end of a downstream Okazaki fragment. It fails to cleave other DNA structures, including 3'flaps and single stranded DNA (By similarity). SUBUNIT: Interacts with PCNA. SUBCELLULAR LOCATION: Nuclear. PTM: Acetylated by p300. SIMILARITY: Belongs to the XPG/RAD2 endonuclease fa [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_P39748">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P39748</ID>
+ </unificationXref>
+ <relationshipXref rdf:ID="_5__flap_endonuclease_activity">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GO</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0017108</ID>
+ </relationshipXref>
+ <unificationXref rdf:ID="Reactome69152">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">69152</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <evidence rdf:ID="Summation_69153">
+ <XREF rdf:resource="#Pubmed_8824221" />
+ <XREF rdf:resource="#Pubmed_9080773" />
+ <XREF rdf:resource="#Pubmed_7876218" />
+ <XREF rdf:resource="#Pubmed_8131753" />
+ <XREF rdf:resource="#Pubmed_10409700" />
+ <XREF rdf:resource="#Pubmed_11825897" />
+ <XREF rdf:resource="#Pubmed_10806216" />
+ </evidence>
+ <publicationXref rdf:ID="Pubmed_8824221">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">8824221</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1996</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Calf RTH-1 nuclease can remove the initiator RNAs of Okazaki fragments by endonuclease activity.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Murante, RS</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Rumbaugh, JA</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Barnes, CJ</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Norton, JR</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bambara, RA</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Biol Chem 271:25888-97</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_9080773">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">9080773</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1997</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The FEN-1 family of structure-specific nucleases in eukaryotic DNA replication, recombination and repair.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Lieber, MR</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bioessays 19:233-40</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_7876218">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">7876218</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1995</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DNA structural elements required for FEN-1 binding.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Harrington, JJ</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Lieber, MR</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Biol Chem 270:4503-8</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_8131753">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">8131753</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1994</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The characterization of a mammalian DNA structure-specific endonuclease.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Harrington, JJ</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Lieber, MR</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">EMBO J 13:1235-46</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_10409700">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">10409700</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1999</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A comparison of eubacterial and archaeal structure-specific 5'-exonucleases.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Kaiser, MW</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Lyamicheva, N</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Ma, W</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Miller, C</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Neri, B</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Fors, L</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Lyamichev, VI</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Biol Chem 274:21387-94</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_11825897">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">11825897</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2002</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cleavage specificity of Saccharomyces cerevisiae flap endonuclease 1 suggests a double-flap structure as the cellular substrate.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Kao, HI</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Henricksen, LA</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Liu, Y</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bambara, RA</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Biol Chem 277:14379-89</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_10806216">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">10806216</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2000</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Coordination between the polymerase and 5'-nuclease components of DNA polymerase I of Escherichia coli.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Xu, Y</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Grindley, ND</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Joyce, CM</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Biol Chem 275:20949-55</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="Removal_of_remaining_FlapStep">
+ <STEP-INTERACTIONS rdf:resource="#Removal_of_remaining_Flap" />
+ <STEP-INTERACTIONS rdf:resource="#_5__flap_endonuclease_activity_of_Flap_endonuclease_1___nucleoplasm_" />
+ </pathwayStep>
+ <unificationXref rdf:ID="Reactome69166">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">69166</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <evidence rdf:ID="Summation_69167">
+ <XREF rdf:resource="#Pubmed_7644470" />
+ <XREF rdf:resource="#Pubmed_7926735" />
+ <XREF rdf:resource="#Pubmed_8131753" />
+ </evidence>
+ <publicationXref rdf:ID="Pubmed_7644470">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">7644470</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1995</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A yeast gene required for DNA replication encodes a protein with homology to DNA helicases.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Budd, ME</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Campbell, JL</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Proc Natl Acad Sci U S A 92:7642-6</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_7926735">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">7926735</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1994</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Functional domains within FEN-1 and RAD2 define a family of structure-specific endonucleases: implications for nucleotide excision repair.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Harrington, JJ</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Lieber, MR</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Genes Dev 8:1344-55</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="Removal_of_the_Flap_IntermediateStep">
+ <STEP-INTERACTIONS rdf:resource="#Removal_of_the_Flap_Intermediate" />
+ <NEXT-STEP rdf:resource="#Joining_of_adjacent_Okazaki_fragmentsStep" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="Joining_of_adjacent_Okazaki_fragments">
+ <LEFT rdf:resource="#Okazaki_fragment__nucleoplasm_3" />
+ <RIGHT rdf:resource="#ligated_okazaki_fragment__nucleoplasm_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Joining of adjacent Okazaki fragments</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Joining of adjacent Okazaki fragments</SHORT-NAME>
+ <XREF rdf:resource="#Reactome69173" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Removal of the flap by FEN-1 leads to the generation of a nick between the 3'-end of the upstream Okazaki fragment and the 5'-end of the downstream Okazaki fragment. DNA ligase I then seals the nicks between adjacent processed Okazaki fragments to generate intact double-stranded DNA.</COMMENT>
+ <EVIDENCE rdf:resource="#Summation_69174" />
+ <CELLULAR-LOCATION rdf:resource="#nucleus" />
+ </biochemicalReaction>
+ <physicalEntityParticipant rdf:ID="Okazaki_fragment__nucleoplasm_3">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Okazaki_fragment__nucleoplasm_1" />
+ </physicalEntityParticipant>
+ <physicalEntityParticipant rdf:ID="ligated_okazaki_fragment__nucleoplasm_">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#ligated_okazaki_fragment__nucleoplasm_1" />
+ </physicalEntityParticipant>
+ <physicalEntity rdf:ID="ligated_okazaki_fragment__nucleoplasm_1">
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ligated okazaki fragment [nucleoplasm]</NAME>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome. Each synonym is a name of a ConcreteEntity, and each XREF points to one ConcreteEntity</COMMENT>
+ </physicalEntity>
+ <catalysis rdf:ID="DNA_ligase_activity_of_DNA_ligase__nucleoplasm_">
+ <CONTROLLER rdf:resource="#DNA_ligase__nucleoplasm_" />
+ <CONTROLLED rdf:resource="#Joining_of_adjacent_Okazaki_fragments" />
+ <DIRECTION rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PHYSIOL-LEFT-TO-RIGHT</DIRECTION>
+ <XREF rdf:resource="#DNA_ligase_activity" />
+ </catalysis>
+ <physicalEntityParticipant rdf:ID="DNA_ligase__nucleoplasm_">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#DNA_ligase__nucleoplasm_1" />
+ </physicalEntityParticipant>
+ <physicalEntity rdf:ID="DNA_ligase__nucleoplasm_1">
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DNA ligase [nucleoplasm]</NAME>
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome. Each synonym is a name of a ConcreteEntity, and each XREF points to one ConcreteEntity</COMMENT>
+ </physicalEntity>
+ <relationshipXref rdf:ID="DNA_ligase_activity">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GO</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0003909</ID>
+ </relationshipXref>
+ <unificationXref rdf:ID="Reactome69173">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">69173</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <evidence rdf:ID="Summation_69174">
+ <XREF rdf:resource="#Pubmed_8392066" />
+ <XREF rdf:resource="#Pubmed_9081985" />
+ <XREF rdf:resource="#Pubmed_9759502" />
+ <XREF rdf:resource="#Pubmed_10959839" />
+ </evidence>
+ <publicationXref rdf:ID="Pubmed_8392066">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">8392066</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1993</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Completion of mammalian lagging strand DNA replication using purified proteins.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Turchi, JJ</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bambara, RA</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Biol Chem 268:15136-41</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_9759502">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">9759502</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1998</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The DNA replication fork in eukaryotic cells.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Waga, S</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Stillman, B</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Annu Rev Biochem 67:721-51</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_10959839">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">10959839</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2000</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Interaction between PCNA and DNA ligase I is critical for joining of Okazaki fragments and long-patch base-excision repair.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Levin, DS</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">McKenna, AE</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Motycka, TA</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Matsumoto, Y</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Tomkinson, AE</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Curr Biol 10:919-22</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="Joining_of_adjacent_Okazaki_fragmentsStep">
+ <STEP-INTERACTIONS rdf:resource="#Joining_of_adjacent_Okazaki_fragments" />
+ <STEP-INTERACTIONS rdf:resource="#DNA_ligase_activity_of_DNA_ligase__nucleoplasm_" />
+ </pathwayStep>
+ <unificationXref rdf:ID="Reactome69183">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">69183</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <evidence rdf:ID="Summation_69185">
+ <XREF rdf:resource="#Pubmed_1671046" />
+ </evidence>
+ <pathwayStep rdf:ID="Processive_synthesis_on_the_lagging_strandStep">
+ <STEP-INTERACTIONS rdf:resource="#Processive_synthesis_on_the_lagging_strand" />
+ </pathwayStep>
+ <unificationXref rdf:ID="Reactome69186">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">69186</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <evidence rdf:ID="Summation_69187">
+ <XREF rdf:resource="#Pubmed_9081985" />
+ </evidence>
+ <pathwayStep rdf:ID="Lagging_Strand_SynthesisStep">
+ <STEP-INTERACTIONS rdf:resource="#Lagging_Strand_Synthesis" />
+ </pathwayStep>
+ <unificationXref rdf:ID="Reactome69190">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">69190</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <evidence rdf:ID="Summation_69287">
+ <XREF rdf:resource="#Pubmed_1976634" />
+ <XREF rdf:resource="#Pubmed_8594377" />
+ <XREF rdf:resource="#Pubmed_7623835" />
+ <XREF rdf:resource="#Pubmed_9121462" />
+ <XREF rdf:resource="#Pubmed_9081985" />
+ </evidence>
+ <publicationXref rdf:ID="Pubmed_1976634">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">1976634</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1990</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The in vitro replication of DNA containing the SV40 origin.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Hurwitz, J</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Dean, FB</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Kwong, AD</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Lee, SH</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Biol Chem 265:18043-6</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_8594377">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">8594377</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1996</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Identification of eukaryotic DNA replication proteins using simian virus 40 in vitro replication system.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Brush, GS</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Kelly, TJ</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Stillman, B</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Methods Enzymol 262:522-48</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_7623835">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">7623835</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1995</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A mutational analysis of the yeast proliferating cell nuclear antigen indicates distinct roles in DNA replication and DNA repair.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Ayyagari, R</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Impellizzeri, KJ</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Yoder, BL</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Gary, SL</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Burgers, PM</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mol Cell Biol 15:4420-9</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_9121462">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">9121462</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1997</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A yeast replicative helicase, Dna2 helicase, interacts with yeast FEN-1 nuclease in carrying out its essential function.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Budd, ME</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Campbell, JL</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mol Cell Biol 17:2136-42</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="DNA_strand_elongationStep">
+ <STEP-INTERACTIONS rdf:resource="#DNA_strand_elongation" />
+ </pathwayStep>
+ <pathway rdf:ID="Regulation_of_DNA_replication">
+ <PATHWAY-COMPONENTS rdf:resource="#Removal_of_licensing_factors_from_originsStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#Association_of_licensing_factors_with_the_pre_replicative_complexStep" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Regulation of DNA replication</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Regulation of DNA replication</SHORT-NAME>
+ <XREF rdf:resource="#Reactome69304" />
+ </pathway>
+ <pathway rdf:ID="Association_of_licensing_factors_with_the_pre_replicative_complex">
+ <PATHWAY-COMPONENTS rdf:resource="#Cdc6_protein_is_synthesized_under_the_control_of_E2F_transcription_factorsStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#Orc1_associates_with_Orc4_Orc5_Orc3_Orc2_origin_complexesStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#The_geminin_component_of_geminin_Cdt1_complexes_is_ubiquitinated__releasing_Cdt1Step" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Association of licensing factors with the pre-replicative complex</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Association of licensing factors with the pre-replicative complex</SHORT-NAME>
+ <XREF rdf:resource="#Reactome69298" />
+ </pathway>
+ <biochemicalReaction rdf:ID="Orc1_associates_with_Orc4_Orc5_Orc3_Orc2_origin_complexes1">
+ <LEFT rdf:resource="#Orc1__nucleoplasm_4" />
+ <LEFT rdf:resource="#Orc4_Orc5_Orc3_Orc2_origin__nucleoplasm_4" />
+ <RIGHT rdf:resource="#Orc1_Orc4_Orc5_Orc3_Orc2_origin__nucleoplasm_3" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Orc1 associates with Orc4:Orc5:Orc3:Orc2:origin complexes</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Orc1 associates with Orc4:Orc5:Orc3:Orc2:origin complexes</SHORT-NAME>
+ <XREF rdf:resource="#Reactome68611" />
+ <XREF rdf:resource="#Pubmed_11395502" />
+ <XREF rdf:resource="#Pubmed_11323433" />
+ <XREF rdf:resource="#Pubmed_11046155" />
+ <XREF rdf:resource="#Pubmed_11739726" />
+ <CELLULAR-LOCATION rdf:resource="#nucleus" />
+ </biochemicalReaction>
+ <proteinParticipant rdf:ID="Orc1__nucleoplasm_4">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q13415_Origin_recognition_complex_subunit_1__Replication_control_protein_1_" />
+ </proteinParticipant>
+ <complexParticipant rdf:ID="Orc4_Orc5_Orc3_Orc2_origin__nucleoplasm_4">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Orc4_Orc5_Orc3_Orc2_origin__nucleoplasm_1" />
+ </complexParticipant>
+ <complexParticipant rdf:ID="Orc1_Orc4_Orc5_Orc3_Orc2_origin__nucleoplasm_3">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Orc1_Orc4_Orc5_Orc3_Orc2_origin__nucleoplasm_1" />
+ </complexParticipant>
+ <biochemicalReaction rdf:ID="Cdc6_protein_is_synthesized_under_the_control_of_E2F_transcription_factors1">
+ <RIGHT rdf:resource="#Cdc6__cytosol_2" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cdc6 protein is synthesized under the control of E2F transcription factors</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cdc6 protein is synthesized under the control of E2F transcription factors</SHORT-NAME>
+ <XREF rdf:resource="#Reactome68637" />
+ <XREF rdf:resource="#Pubmed_9520412" />
+ </biochemicalReaction>
+ <proteinParticipant rdf:ID="Cdc6__cytosol_2">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <SEQUENCE-FEATURE-LIST rdf:resource="#nucleotide_binding_site" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q99741_Cell_division_control_protein_6_homolog__CDC6_related_protein___p62_cdc6____HsCDC6___HsCDC18_" />
+ </proteinParticipant>
+ <modulation rdf:ID="_E2F2__positively_regulates__Cdc6_protein_is_synthesized_under_the_control_of_E2F_transcription_factors_1">
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">'E2F2' positively regulates 'Cdc6 protein is synthesized under the control of E2F transcription factors'</NAME>
+ <CONTROL-TYPE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ACTIVATION</CONTROL-TYPE>
+ <CONTROLLER rdf:resource="#E2F2__nucleoplasm_1" />
+ <CONTROLLED rdf:resource="#Cdc6_protein_is_synthesized_under_the_control_of_E2F_transcription_factors1" />
+ </modulation>
+ <proteinParticipant rdf:ID="E2F2__nucleoplasm_1">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q14209_Transcription_factor_E2F2__E2F_2_" />
+ </proteinParticipant>
+ <modulation rdf:ID="_E2F1__positively_regulates__Cdc6_protein_is_synthesized_under_the_control_of_E2F_transcription_factors_1">
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">'E2F1' positively regulates 'Cdc6 protein is synthesized under the control of E2F transcription factors'</NAME>
+ <CONTROL-TYPE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ACTIVATION</CONTROL-TYPE>
+ <CONTROLLER rdf:resource="#E2F1__nucleoplasm_1" />
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+ </modulation>
+ <proteinParticipant rdf:ID="E2F1__nucleoplasm_1">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q01094_Transcription_factor_E2F1__E2F_1___Retinoblastoma_binding_protein_3___RBBP_3___PRB_binding_protein_E2F_1___PBR3___Retinoblastoma_associated_protein_1___RBAP_1_" />
+ </proteinParticipant>
+ <modulation rdf:ID="_E2F3__positively_regulates__Cdc6_protein_is_synthesized_under_the_control_of_E2F_transcription_factors_1">
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">'E2F3' positively regulates 'Cdc6 protein is synthesized under the control of E2F transcription factors'</NAME>
+ <CONTROL-TYPE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ACTIVATION</CONTROL-TYPE>
+ <CONTROLLER rdf:resource="#E2F3__nucleoplasm_1" />
+ <CONTROLLED rdf:resource="#Cdc6_protein_is_synthesized_under_the_control_of_E2F_transcription_factors1" />
+ </modulation>
+ <proteinParticipant rdf:ID="E2F3__nucleoplasm_1">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_O00716_Transcription_factor_E2F3__E2F_3_" />
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+ <biochemicalReaction rdf:ID="The_geminin_component_of_geminin_Cdt1_complexes_is_ubiquitinated__releasing_Cdt11">
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+ <RIGHT rdf:resource="#geminin_ubiquitin_complex__cytosol_3" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The geminin component of geminin:Cdt1 complexes is ubiquitinated, releasing Cdt1</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The geminin component of geminin:Cdt1 complexes is ubiquitinated, releasing Cdt1</SHORT-NAME>
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+ <XREF rdf:resource="#Pubmed_9635433" />
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+ <proteinParticipant rdf:ID="ubiquitin__cytosol_8">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P62988_Ubiquitin" />
+ </proteinParticipant>
+ <complexParticipant rdf:ID="Cdt1_geminin__cytosol_2">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#Cdt1_geminin__cytosol_1" />
+ </complexParticipant>
+ <proteinParticipant rdf:ID="Cdt1__cytosol_2">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q9H211" />
+ </proteinParticipant>
+ <complexParticipant rdf:ID="geminin_ubiquitin_complex__cytosol_3">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#geminin_ubiquitin_complex__cytosol_1" />
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+ <pathwayStep rdf:ID="Association_of_licensing_factors_with_the_pre_replicative_complexStep">
+ <STEP-INTERACTIONS rdf:resource="#Association_of_licensing_factors_with_the_pre_replicative_complex" />
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+ <pathway rdf:ID="Removal_of_licensing_factors_from_origins">
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+ <pathway rdf:ID="Orc1_removal_from_chromatin1">
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+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Orc1 removal from chromatin</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Orc1 removal from chromatin</SHORT-NAME>
+ <XREF rdf:resource="#Reactome68949" />
+ <XREF rdf:resource="#Pubmed_11931757" />
+ <XREF rdf:resource="#Pubmed_11739726" />
+ <XREF rdf:resource="#Pubmed_1110244" />
+ <XREF rdf:resource="#Pubmed_11809796" />
+ <CELLULAR-LOCATION rdf:resource="#nucleus" />
+ </pathway>
+ <biochemicalReaction rdf:ID="Orc1_is_phosphorylated_by_cyclin_A_CDK21">
+ <LEFT rdf:resource="#ATP__nucleoplasm_6" />
+ <LEFT rdf:resource="#pre_replicative_complex__nucleoplasm_5" />
+ <RIGHT rdf:resource="#pre_replicative_complex__Orc1_minus___nucleoplasm_2" />
+ <RIGHT rdf:resource="#ADP__nucleoplasm_5" />
+ <RIGHT rdf:resource="#phosphorylated_Orc1__nucleoplasm_2" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Orc1 is phosphorylated by cyclin A/CDK2</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Orc1 is phosphorylated by cyclin A/CDK2</SHORT-NAME>
+ <XREF rdf:resource="#Reactome68944" />
+ <XREF rdf:resource="#Pubmed_11931757" />
+ <CELLULAR-LOCATION rdf:resource="#nucleus" />
+ </biochemicalReaction>
+ <smallMoleculeParticipant rdf:ID="ATP__nucleoplasm_6">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#ATP__ChEBI_2359_" />
+ </smallMoleculeParticipant>
+ <complexParticipant rdf:ID="pre_replicative_complex__nucleoplasm_5">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#pre_replicative_complex__nucleoplasm_1" />
+ </complexParticipant>
+ <complexParticipant rdf:ID="pre_replicative_complex__Orc1_minus___nucleoplasm_2">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#pre_replicative_complex__Orc1_minus___nucleoplasm_1" />
+ </complexParticipant>
+ <smallMoleculeParticipant rdf:ID="ADP__nucleoplasm_5">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#ADP__ChEBI_2342_" />
+ </smallMoleculeParticipant>
+ <proteinParticipant rdf:ID="phosphorylated_Orc1__nucleoplasm_2">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q13415_Origin_recognition_complex_subunit_1__Replication_control_protein_1_" />
+ </proteinParticipant>
+ <catalysis rdf:ID="kinase_activity_of_Cyclin_A_CDK2_complex__nucleoplasm_1">
+ <CONTROLLER rdf:resource="#Cyclin_A_CDK2_complex__nucleoplasm_2" />
+ <CONTROLLED rdf:resource="#Orc1_is_phosphorylated_by_cyclin_A_CDK21" />
+ <DIRECTION rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PHYSIOL-LEFT-TO-RIGHT</DIRECTION>
+ <XREF rdf:resource="#kinase_activity" />
+ </catalysis>
+ <complexParticipant rdf:ID="Cyclin_A_CDK2_complex__nucleoplasm_2">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Cyclin_A_CDK2_complex__nucleoplasm_1" />
+ </complexParticipant>
+ <modulation rdf:ID="_cyclin__positively_regulates__Orc1_is_phosphorylated_by_cyclin_A_CDK2_1">
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">'cyclin' positively regulates 'Orc1 is phosphorylated by cyclin A/CDK2'</NAME>
+ <CONTROL-TYPE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ACTIVATION</CONTROL-TYPE>
+ <CONTROLLER rdf:resource="#cyclin__nucleoplasm_3" />
+ <CONTROLLED rdf:resource="#Orc1_is_phosphorylated_by_cyclin_A_CDK21" />
+ </modulation>
+ <physicalEntityParticipant rdf:ID="cyclin__nucleoplasm_3">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#cyclin__nucleoplasm_1" />
+ </physicalEntityParticipant>
+ <biochemicalReaction rdf:ID="Phosphorylated_Orc1_is_ubiquitinated_while_still_associated_with_chromatin1">
+ <LEFT rdf:resource="#ubiquitin__nucleoplasm_2" />
+ <LEFT rdf:resource="#phosphorylated_Orc1__nucleoplasm_3" />
+ <RIGHT rdf:resource="#ubiquitinated_Orc1__nucleoplasm_3" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Phosphorylated Orc1 is ubiquitinated while still associated with chromatin</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Phosphorylated Orc1 is ubiquitinated while still associated with chromatin</SHORT-NAME>
+ <XREF rdf:resource="#Reactome68946" />
+ <XREF rdf:resource="#Pubmed_11931757" />
+ <CELLULAR-LOCATION rdf:resource="#nucleus" />
+ </biochemicalReaction>
+ <proteinParticipant rdf:ID="ubiquitin__nucleoplasm_2">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P62988_Ubiquitin" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="phosphorylated_Orc1__nucleoplasm_3">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q13415_Origin_recognition_complex_subunit_1__Replication_control_protein_1_" />
+ </proteinParticipant>
+ <complexParticipant rdf:ID="ubiquitinated_Orc1__nucleoplasm_3">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#ubiquitinated_Orc1__nucleoplasm_1" />
+ </complexParticipant>
+ <biochemicalReaction rdf:ID="Ubiquitinated_Orc1_enters_the_cytosol1">
+ <LEFT rdf:resource="#ubiquitinated_Orc1__nucleoplasm_4" />
+ <RIGHT rdf:resource="#ubiquitinated_Orc1__cytosol_3" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Ubiquitinated Orc1 enters the cytosol</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Ubiquitinated Orc1 enters the cytosol</SHORT-NAME>
+ <XREF rdf:resource="#Reactome68947" />
+ <XREF rdf:resource="#Pubmed_11931757" />
+ <CELLULAR-LOCATION rdf:resource="#nuclear_pore" />
+ </biochemicalReaction>
+ <complexParticipant rdf:ID="ubiquitinated_Orc1__nucleoplasm_4">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#ubiquitinated_Orc1__nucleoplasm_1" />
+ </complexParticipant>
+ <complexParticipant rdf:ID="ubiquitinated_Orc1__cytosol_3">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#ubiquitinated_Orc1__cytosol_1" />
+ </complexParticipant>
+ <biochemicalReaction rdf:ID="Ubiquitinated_Orc1_is_degraded_by_the_proteasome1">
+ <LEFT rdf:resource="#ubiquitinated_Orc1__cytosol_4" />
+ <RIGHT rdf:resource="#ubiquitin__cytosol_9" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Ubiquitinated Orc1 is degraded by the proteasome</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Ubiquitinated Orc1 is degraded by the proteasome</SHORT-NAME>
+ <XREF rdf:resource="#Reactome68948" />
+ <XREF rdf:resource="#Pubmed_11931757" />
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ </biochemicalReaction>
+ <complexParticipant rdf:ID="ubiquitinated_Orc1__cytosol_4">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#ubiquitinated_Orc1__cytosol_1" />
+ </complexParticipant>
+ <proteinParticipant rdf:ID="ubiquitin__cytosol_9">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P62988_Ubiquitin" />
+ </proteinParticipant>
+ <catalysis rdf:ID="endopeptidase_activity_of_26S_proteasome__cytosol_3">
+ <CONTROLLER rdf:resource="#_26S_proteasome__cytosol_4" />
+ <CONTROLLED rdf:resource="#Ubiquitinated_Orc1_is_degraded_by_the_proteasome1" />
+ <DIRECTION rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PHYSIOL-LEFT-TO-RIGHT</DIRECTION>
+ <XREF rdf:resource="#endopeptidase_activity" />
+ </catalysis>
+ <complexParticipant rdf:ID="_26S_proteasome__cytosol_4">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#_26S_proteasome__cytosol_1" />
+ </complexParticipant>
+ <biochemicalReaction rdf:ID="Cdt1_is_displaced_from_the_pre_replicative_complex_1">
+ <LEFT rdf:resource="#Mcm10_pre_replicative_complex__nucleoplasm_3" />
+ <RIGHT rdf:resource="#Cdt1__nucleoplasm_4" />
+ <RIGHT rdf:resource="#Mcm10_active_pre_replicative_complex__nucleoplasm_4" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cdt1 is displaced from the pre-replicative complex.</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cdt1 is displaced from the pre-replicative complex.</SHORT-NAME>
+ <XREF rdf:resource="#Reactome68940" />
+ <XREF rdf:resource="#Pubmed_12045100" />
+ <CELLULAR-LOCATION rdf:resource="#nucleus" />
+ </biochemicalReaction>
+ <complexParticipant rdf:ID="Mcm10_pre_replicative_complex__nucleoplasm_3">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Mcm10_pre_replicative_complex__nucleoplasm_1" />
+ </complexParticipant>
+ <proteinParticipant rdf:ID="Cdt1__nucleoplasm_4">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q9H211" />
+ </proteinParticipant>
+ <complexParticipant rdf:ID="Mcm10_active_pre_replicative_complex__nucleoplasm_4">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Mcm10_active_pre_replicative_complex__nucleoplasm_1" />
+ </complexParticipant>
+ <biochemicalReaction rdf:ID="Cdt1_associates_with_geminin">
+ <LEFT rdf:resource="#geminin__nucleoplasm_" />
+ <LEFT rdf:resource="#Cdt1__nucleoplasm_5" />
+ <RIGHT rdf:resource="#Cdt1_geminin__nucleoplasm_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cdt1 associates with geminin</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cdt1 associates with geminin</SHORT-NAME>
+ <XREF rdf:resource="#Reactome69299" />
+ <XREF rdf:resource="#Pubmed_11125146" />
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ </biochemicalReaction>
+ <proteinParticipant rdf:ID="geminin__nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_O75496_Geminin" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="Cdt1__nucleoplasm_5">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q9H211" />
+ </proteinParticipant>
+ <complexParticipant rdf:ID="Cdt1_geminin__nucleoplasm_">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Cdt1_geminin__nucleoplasm_1" />
+ </complexParticipant>
+ <complex rdf:ID="Cdt1_geminin__nucleoplasm_1">
+ <COMPONENTS rdf:resource="#Cdt1__nucleoplasm_6" />
+ <COMPONENTS rdf:resource="#geminin__nucleoplasm_1" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cdt1:geminin [nucleoplasm]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cdt1:geminin</SHORT-NAME>
+ </complex>
+ <proteinParticipant rdf:ID="Cdt1__nucleoplasm_6">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q9H211" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="geminin__nucleoplasm_1">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_O75496_Geminin" />
+ </proteinParticipant>
+ <unificationXref rdf:ID="Reactome69299">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">69299</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <pathwayStep rdf:ID="Cdt1_associates_with_gemininStep">
+ <STEP-INTERACTIONS rdf:resource="#Cdt1_associates_with_geminin" />
+ </pathwayStep>
+ <pathway rdf:ID="CDK_mediated_phosphorylation_and_removal_of_Cdc61">
+ <PATHWAY-COMPONENTS rdf:resource="#Cdc6_protein_is_phosphorylated_by_CDKStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#Ubiquitinated_Cdc6_is_degraded_by_the_proteasomeStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#Phosphorylated_Cdc6_is_exported_from_the_nucleusStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#Cytoplasmic_phosphorylated_Cdc6_is_ubiquitinated_by_the_anaphase_promoting_complexStep" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CDK-mediated phosphorylation and removal of Cdc6</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CDK-mediated phosphorylation and removal of Cdc6</SHORT-NAME>
+ <XREF rdf:resource="#Reactome69017" />
+ <XREF rdf:resource="#Pubmed_12045100" />
+ <XREF rdf:resource="#Pubmed_11046155" />
+ <CELLULAR-LOCATION rdf:resource="#nucleus" />
+ </pathway>
+ <biochemicalReaction rdf:ID="Cdc6_protein_is_phosphorylated_by_CDK1">
+ <LEFT rdf:resource="#ATP__nucleoplasm_7" />
+ <LEFT rdf:resource="#Cdc6__nucleoplasm_4" />
+ <RIGHT rdf:resource="#ADP__nucleoplasm_6" />
+ <RIGHT rdf:resource="#phosphorylated_Cdc6__nucleoplasm_2" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cdc6 protein is phosphorylated by CDK</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cdc6 protein is phosphorylated by CDK</SHORT-NAME>
+ <XREF rdf:resource="#Reactome69005" />
+ <XREF rdf:resource="#Pubmed_10339564" />
+ <CELLULAR-LOCATION rdf:resource="#nucleus" />
+ </biochemicalReaction>
+ <smallMoleculeParticipant rdf:ID="ATP__nucleoplasm_7">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#ATP__ChEBI_2359_" />
+ </smallMoleculeParticipant>
+ <proteinParticipant rdf:ID="Cdc6__nucleoplasm_4">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <SEQUENCE-FEATURE-LIST rdf:resource="#nucleotide_binding_site" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q99741_Cell_division_control_protein_6_homolog__CDC6_related_protein___p62_cdc6____HsCDC6___HsCDC18_" />
+ </proteinParticipant>
+ <smallMoleculeParticipant rdf:ID="ADP__nucleoplasm_6">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#ADP__ChEBI_2342_" />
+ </smallMoleculeParticipant>
+ <proteinParticipant rdf:ID="phosphorylated_Cdc6__nucleoplasm_2">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q99741_Cell_division_control_protein_6_homolog__CDC6_related_protein___p62_cdc6____HsCDC6___HsCDC18_" />
+ </proteinParticipant>
+ <catalysis rdf:ID="kinase_activity_of_CDK__nucleoplasm_1">
+ <CONTROLLER rdf:resource="#CDK__nucleoplasm_4" />
+ <CONTROLLED rdf:resource="#Cdc6_protein_is_phosphorylated_by_CDK1" />
+ <DIRECTION rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PHYSIOL-LEFT-TO-RIGHT</DIRECTION>
+ <XREF rdf:resource="#kinase_activity" />
+ </catalysis>
+ <complexParticipant rdf:ID="CDK__nucleoplasm_4">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#CDK__nucleoplasm_1" />
+ </complexParticipant>
+ <biochemicalReaction rdf:ID="Phosphorylated_Cdc6_is_exported_from_the_nucleus1">
+ <LEFT rdf:resource="#phosphorylated_Cdc6__nucleoplasm_3" />
+ <RIGHT rdf:resource="#phosphorylated_Cdc6__cytosol_2" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Phosphorylated Cdc6 is exported from the nucleus</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Phosphorylated Cdc6 is exported from the nucleus</SHORT-NAME>
+ <XREF rdf:resource="#Reactome69006" />
+ <XREF rdf:resource="#Pubmed_10339564" />
+ <CELLULAR-LOCATION rdf:resource="#nuclear_pore" />
+ </biochemicalReaction>
+ <proteinParticipant rdf:ID="phosphorylated_Cdc6__nucleoplasm_3">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q99741_Cell_division_control_protein_6_homolog__CDC6_related_protein___p62_cdc6____HsCDC6___HsCDC18_" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="phosphorylated_Cdc6__cytosol_2">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q99741_Cell_division_control_protein_6_homolog__CDC6_related_protein___p62_cdc6____HsCDC6___HsCDC18_" />
+ </proteinParticipant>
+ <biochemicalReaction rdf:ID="Cytoplasmic_phosphorylated_Cdc6_is_ubiquitinated_by_the_anaphase_promoting_complex1">
+ <LEFT rdf:resource="#ubiquitin__cytosol_10" />
+ <LEFT rdf:resource="#ATP__cytosol_1" />
+ <LEFT rdf:resource="#phosphorylated_Cdc6__cytosol_3" />
+ <RIGHT rdf:resource="#ubiquitinated_Cdc6__cytosol_3" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cytoplasmic phosphorylated Cdc6 is ubiquitinated by the anaphase-promoting complex</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cytoplasmic phosphorylated Cdc6 is ubiquitinated by the anaphase-promoting complex</SHORT-NAME>
+ <XREF rdf:resource="#Reactome69015" />
+ <XREF rdf:resource="#Pubmed_10995389" />
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ </biochemicalReaction>
+ <proteinParticipant rdf:ID="ubiquitin__cytosol_10">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P62988_Ubiquitin" />
+ </proteinParticipant>
+ <smallMoleculeParticipant rdf:ID="ATP__cytosol_1">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#ATP__ChEBI_2359_" />
+ </smallMoleculeParticipant>
+ <proteinParticipant rdf:ID="phosphorylated_Cdc6__cytosol_3">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q99741_Cell_division_control_protein_6_homolog__CDC6_related_protein___p62_cdc6____HsCDC6___HsCDC18_" />
+ </proteinParticipant>
+ <complexParticipant rdf:ID="ubiquitinated_Cdc6__cytosol_3">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#ubiquitinated_Cdc6__cytosol_1" />
+ </complexParticipant>
+ <catalysis rdf:ID="endopeptidase_activity_of_anaphase_promoting_complex__APC___cytosol_1">
+ <CONTROLLER rdf:resource="#anaphase_promoting_complex__APC___cytosol_2" />
+ <CONTROLLED rdf:resource="#Cytoplasmic_phosphorylated_Cdc6_is_ubiquitinated_by_the_anaphase_promoting_complex1" />
+ <DIRECTION rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PHYSIOL-LEFT-TO-RIGHT</DIRECTION>
+ <XREF rdf:resource="#endopeptidase_activity" />
+ </catalysis>
+ <physicalEntityParticipant rdf:ID="anaphase_promoting_complex__APC___cytosol_2">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#anaphase_promoting_complex__APC___cytosol_1" />
+ </physicalEntityParticipant>
+ <biochemicalReaction rdf:ID="Ubiquitinated_Cdc6_is_degraded_by_the_proteasome1">
+ <LEFT rdf:resource="#ubiquitinated_Cdc6__cytosol_4" />
+ <RIGHT rdf:resource="#ubiquitin__cytosol_11" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Ubiquitinated Cdc6 is degraded by the proteasome</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Ubiquitinated Cdc6 is degraded by the proteasome</SHORT-NAME>
+ <XREF rdf:resource="#Reactome69016" />
+ <XREF rdf:resource="#Pubmed_11046155" />
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ </biochemicalReaction>
+ <complexParticipant rdf:ID="ubiquitinated_Cdc6__cytosol_4">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#ubiquitinated_Cdc6__cytosol_1" />
+ </complexParticipant>
+ <proteinParticipant rdf:ID="ubiquitin__cytosol_11">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P62988_Ubiquitin" />
+ </proteinParticipant>
+ <catalysis rdf:ID="endopeptidase_activity_of_26S_proteasome__cytosol_4">
+ <CONTROLLER rdf:resource="#_26S_proteasome__cytosol_5" />
+ <CONTROLLED rdf:resource="#Ubiquitinated_Cdc6_is_degraded_by_the_proteasome1" />
+ <DIRECTION rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PHYSIOL-LEFT-TO-RIGHT</DIRECTION>
+ <XREF rdf:resource="#endopeptidase_activity" />
+ </catalysis>
+ <complexParticipant rdf:ID="_26S_proteasome__cytosol_5">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#_26S_proteasome__cytosol_1" />
+ </complexParticipant>
+ <biochemicalReaction rdf:ID="Mcm4_6_7_trimer_forms_and_associates_with_the_replication_fork1">
+ <LEFT rdf:resource="#Mcm2_7_complex__nucleoplasm_8" />
+ <RIGHT rdf:resource="#Mcm5__nucleoplasm_2" />
+ <RIGHT rdf:resource="#Mcm4_6_7_complex__nucleoplasm_2" />
+ <RIGHT rdf:resource="#Mcm3__nucleoplasm_2" />
+ <RIGHT rdf:resource="#Mcm2__nucleoplasm_2" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mcm4,6,7 trimer forms and associates with the replication fork</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mcm4,6,7 trimer forms and associates with the replication fork</SHORT-NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Rearrangement and mobilization of Mcm2-7</SYNONYMS>
+ <XREF rdf:resource="#Reactome69019" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">At the start of the elongation phase of DNA replication, the Mcm2-7 complex may re-arrange to function as the replicative helicase associated with the replication fork. In general, a replicative helicase is associated with the replication fork and unwinds DNA ahead of the polymerase. In yeast, the Mcm proteins associate with origin DNA in G1 phase and then exit the origin upon replication initiation, consistent with movi [...]
+ <EVIDENCE rdf:resource="#Summation_69033" />
+ <XREF rdf:resource="#Pubmed_10884341" />
+ <XREF rdf:resource="#Pubmed_12364596" />
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ </biochemicalReaction>
+ <complexParticipant rdf:ID="Mcm2_7_complex__nucleoplasm_8">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Mcm2_7_complex__nucleoplasm_1" />
+ </complexParticipant>
+ <proteinParticipant rdf:ID="Mcm5__nucleoplasm_2">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P33992_DNA_replication_licensing_factor_MCM5__CDC46_homolog___P1_CDC46_" />
+ </proteinParticipant>
+ <complexParticipant rdf:ID="Mcm4_6_7_complex__nucleoplasm_2">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#Mcm4_6_7_complex__nucleoplasm_1" />
+ </complexParticipant>
+ <proteinParticipant rdf:ID="Mcm3__nucleoplasm_2">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P25205_DNA_replication_licensing_factor_MCM3__DNA_polymerase_alpha_holoenzyme_associated_protein_P1___RLF_beta_subunit___P102_protein___P1_MCM3_" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="Mcm2__nucleoplasm_2">
+ <CELLULAR-LOCATION rdf:resource="#nucleoplasm" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P49736_DNA_replication_licensing_factor_MCM2__Minichromosome_maintenance_protein_2_homolog___Nuclear_protein_BM28_" />
+ </proteinParticipant>
+ <unificationXref rdf:ID="Reactome69300">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">69300</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <pathwayStep rdf:ID="Removal_of_licensing_factors_from_originsStep">
+ <STEP-INTERACTIONS rdf:resource="#Removal_of_licensing_factors_from_origins" />
+ </pathwayStep>
+ <unificationXref rdf:ID="Reactome69304">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">69304</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <pathwayStep rdf:ID="Regulation_of_DNA_replicationStep">
+ <STEP-INTERACTIONS rdf:resource="#Regulation_of_DNA_replication" />
+ </pathwayStep>
+ <unificationXref rdf:ID="Reactome69306">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">69306</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <evidence rdf:ID="Summation_69307">
+ <XREF rdf:resource="#Pubmed_10966477" />
+ <XREF rdf:resource="#Pubmed_12045100" />
+ <XREF rdf:resource="#Pubmed_1536007" />
+ <XREF rdf:resource="#Pubmed_11257218" />
+ <XREF rdf:resource="#Pubmed_1579437" />
+ <XREF rdf:resource="#Pubmed_8223461" />
+ </evidence>
+ <publicationXref rdf:ID="Pubmed_10966477">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">10966477</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2000</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Regulation of chromosome replication.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Kelly, TJ</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Brown, GW</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Annu Rev Biochem 69:829-80</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_1536007">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">1536007</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1992</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A yeast chromosomal origin of DNA replication defined by multiple functional elements.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Marahrens, Y</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Stillman, B</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Science 255:817-23</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_11257218">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">11257218</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2001</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The control of mammalian DNA replication: a brief history of space and timing.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cimbora, DM</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Groudine, M</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cell 104:643-6</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_1579437">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">1579437</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1992</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DNA replication initiates at multiple sites on plasmid DNA in Xenopus egg extracts.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mahbubani, HM</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Paull, T</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Elder, JK</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Blow, JJ</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Nucleic Acids Res 20:1457-62</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_8223461">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">8223461</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1993</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Chromosomal replication initiates and terminates at random sequences but at regular intervals in the ribosomal DNA of Xenopus early embryos.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Hyrien, O</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Méchali, M</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">EMBO J 12:4511-20</SOURCE>
+ </publicationXref>
+</rdf:RDF>
+
diff --git a/coreplugins/BioPAX/src/test/resources/README.txt b/coreplugins/BioPAX/src/test/resources/README.txt
new file mode 100644
index 0000000..f6ed954
--- /dev/null
+++ b/coreplugins/BioPAX/src/test/resources/README.txt
@@ -0,0 +1,6 @@
+About these files:
+
+Apoptosis.owl: Apoptosis Pathway, from Reactome (http://reactome.org)
+DNA_Replication.owl: DNA Replicaton Pathway, from Reactome (http://reactome.org)
+biopax-example-ecocyc-glycolysis.owl: Glyolysis pathway from Ecocyc (http://ecocyc.org/).
+biopax_sample1.owl: Sample biopax file from biopax.org
diff --git a/coreplugins/BioPAX/src/test/resources/biopax-example-ecocyc-glycolysis.owl b/coreplugins/BioPAX/src/test/resources/biopax-example-ecocyc-glycolysis.owl
new file mode 100755
index 0000000..2f7bcc5
--- /dev/null
+++ b/coreplugins/BioPAX/src/test/resources/biopax-example-ecocyc-glycolysis.owl
@@ -0,0 +1,4676 @@
+<?xml version="1.0"?>
+<rdf:RDF xmlns="http://www.biopax.org/examples/myExample#"
+ xmlns:bp="http://www.biopax.org/release/biopax-level2.owl#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+ xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
+ xmlns:owl="http://www.w3.org/2002/07/owl#" xml:base="http://www.biopax.org/examples/myExample">
+ <owl:Ontology rdf:about="">
+ <owl:imports rdf:resource="http://www.biopax.org/release/biopax-level2.owl" />
+ </owl:Ontology>
+ <bp:modulation rdf:ID="modulation1">
+ <bp:CONTROLLED>
+ <bp:catalysis rdf:ID="catalysis2">
+ <bp:COMMENT rdf:datatype="xs:string">90% of the activity present in
+ the wild type strain is pfk-1. |CITS: [83294514]| The enzyme shows
+ cooperative kinetics with the substrate fructose-6-phosphate but
+ not with the other substrate ATP. |CITS: [85203917]| The reverse
+ reaction does not participate in gluconeogenesis: fdp phosphatase
+ mutants are deficient in gluconeogenesis.|CITS: [78194149]| Studies
+ on phosphfructokinase-1 include subunit structure
+ |CITS:[91255189]|, ligand binding |CITS: [91355204]| and pH
+ dependence |CITS: [91255189]|. The allosteric properties of
+ phosphofructokinase-1 are due in part to ligand binding and in part
+ to the kinetics of the reaction. |CITS: [92144584]|</bp:COMMENT>
+ <bp:SYNONYMS rdf:datatype="xs:string">PFK I</bp:SYNONYMS>
+ <bp:XREF>
+ <bp:publicationXref rdf:ID="publicationXref3">
+ <bp:SOURCE rdf:datatype="xs:string">Biochemistry 1989;28(17);6836-41
+ </bp:SOURCE>
+ <bp:AUTHORS rdf:datatype="xs:string">Bras GL</bp:AUTHORS>
+ <bp:DB rdf:datatype="xs:string">PubMed</bp:DB>
+ <bp:AUTHORS rdf:datatype="xs:string">Teschner W</bp:AUTHORS>
+ <bp:TITLE rdf:datatype="xs:string">Urea-induced inactivation,
+ dissociation, and unfolding of the allosteric phosphofructokinase
+ from Escherichia coli.</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="xs:string">Deville-Bonne D</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="xs:string">Garel JR</bp:AUTHORS>
+ <bp:ID rdf:datatype="xs:string">2531001</bp:ID>
+ <bp:YEAR>1989</bp:YEAR>
+ </bp:publicationXref>
+ </bp:XREF>
+ <bp:XREF>
+ <bp:publicationXref rdf:ID="publicationXref4">
+ <bp:ID rdf:datatype="xs:string">1828369</bp:ID>
+ <bp:TITLE rdf:datatype="xs:string">pH dependence of the kinetic
+ properties of allosteric phosphofructokinase from Escherichia
+ coli.</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="xs:string">Deville-Bonne D</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="xs:string">Bourgain F</bp:AUTHORS>
+ <bp:DB rdf:datatype="xs:string">PubMed</bp:DB>
+ <bp:SOURCE rdf:datatype="xs:string">Biochemistry 1991;30(23);5750-4
+ </bp:SOURCE>
+ <bp:AUTHORS rdf:datatype="xs:string">Garel JR</bp:AUTHORS>
+ <bp:YEAR>1991</bp:YEAR>
+ </bp:publicationXref>
+ </bp:XREF>
+ <bp:COFACTOR>
+ <bp:physicalEntityParticipant rdf:ID="physicalEntityParticipant5">
+ <bp:STOICHIOMETRIC-COEFFICIENT>1.0</bp:STOICHIOMETRIC-COEFFICIENT>
+ <bp:PHYSICAL-ENTITY>
+ <bp:smallMolecule rdf:ID="smallMolecule6">
+ <bp:STRUCTURE>
+ <bp:chemicalStructure rdf:ID="chemicalStructure7">
+ <bp:STRUCTURE-DATA rdf:datatype="xs:string">
+ <cml> <molecule id="MG+2" title="Mg2+"
+ dictRef="dictMG+2"> <atomArray> <atom id="MG+2-atom1"
+ elementType="MG" x2="-1.0" y2="-1.0" formalCharge="2"/>
+ </atomArray> <bondArray> </bondArray> <formula
+ concise="MG 1" formalCharge="2"/> <float
+ title="molecularWeight" units="g/mol">24.305</float>
+ <string title="smiles">[Mg+2]</string> </molecule>
+ </cml></bp:STRUCTURE-DATA>
+ <bp:STRUCTURE-FORMAT rdf:datatype="xs:string">
+ CML</bp:STRUCTURE-FORMAT>
+ </bp:chemicalStructure>
+ </bp:STRUCTURE>
+ <bp:MOLECULAR-WEIGHT>24.30500030517578</bp:MOLECULAR-WEIGHT>
+ <bp:SYNONYMS rdf:datatype="xs:string">magnesium ion
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">Mg<SUP>++</SUP>
+ </bp:SYNONYMS>
+ <bp:NAME rdf:datatype="xs:string">Mg2+</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="xs:string">Mg<SUP>+2</SUP>
+ </bp:SYNONYMS>
+ </bp:smallMolecule>
+ </bp:PHYSICAL-ENTITY>
+ </bp:physicalEntityParticipant>
+ </bp:COFACTOR>
+ <bp:XREF>
+ <bp:publicationXref rdf:ID="publicationXref8">
+ <bp:AUTHORS rdf:datatype="xs:string">Evans PR</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="xs:string">Rypniewski WR</bp:AUTHORS>
+ <bp:TITLE rdf:datatype="xs:string">Crystal structure of unliganded
+ phosphofructokinase from Escherichia coli.</bp:TITLE>
+ <bp:YEAR>1989</bp:YEAR>
+ <bp:DB rdf:datatype="xs:string">PubMed</bp:DB>
+ <bp:SOURCE rdf:datatype="xs:string">J Mol Biol 1989;207(4);805-21
+ </bp:SOURCE>
+ <bp:ID rdf:datatype="xs:string">2527305</bp:ID>
+ </bp:publicationXref>
+ </bp:XREF>
+ <bp:XREF>
+ <bp:publicationXref rdf:ID="publicationXref9">
+ <bp:AUTHORS rdf:datatype="xs:string">Garel JR</bp:AUTHORS>
+ <bp:TITLE rdf:datatype="xs:string">A conformational transition
+ involved in antagonistic substrate binding to the allosteric
+ phosphofructokinase from Escherichia coli.</bp:TITLE>
+ <bp:YEAR>1992</bp:YEAR>
+ <bp:AUTHORS rdf:datatype="xs:string">Deville-Bonne D</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="xs:string">Biochemistry 1992;31(6);1695-700
+ </bp:SOURCE>
+ <bp:DB rdf:datatype="xs:string">PubMed</bp:DB>
+ <bp:ID rdf:datatype="xs:string">1531298</bp:ID>
+ </bp:publicationXref>
+ </bp:XREF>
+ <bp:XREF>
+ <bp:publicationXref rdf:ID="publicationXref10">
+ <bp:ID rdf:datatype="xs:string">2975709</bp:ID>
+ <bp:AUTHORS rdf:datatype="xs:string">Shirakihara Y</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="xs:string">J Mol Biol 1988;204(4);973-94
+ </bp:SOURCE>
+ <bp:AUTHORS rdf:datatype="xs:string">Evans PR</bp:AUTHORS>
+ <bp:YEAR>1988</bp:YEAR>
+ <bp:TITLE rdf:datatype="xs:string">Crystal structure of the complex
+ of phosphofructokinase from Escherichia coli with its reaction
+ products.</bp:TITLE>
+ <bp:DB rdf:datatype="xs:string">PubMed</bp:DB>
+ </bp:publicationXref>
+ </bp:XREF>
+ <bp:XREF>
+ <bp:publicationXref rdf:ID="publicationXref11">
+ <bp:ID rdf:datatype="xs:string">2140983</bp:ID>
+ <bp:TITLE rdf:datatype="xs:string">Role of the C-terminal region in
+ the allosteric properties of Escherichia coli
+ phosphofructokinase-1.</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="xs:string">Serre MC</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="xs:string">Eur J Biochem 1990;189(3);487-92
+ </bp:SOURCE>
+ <bp:DB rdf:datatype="xs:string">PubMed</bp:DB>
+ <bp:AUTHORS rdf:datatype="xs:string">Garel JR</bp:AUTHORS>
+ <bp:YEAR>1990</bp:YEAR>
+ </bp:publicationXref>
+ </bp:XREF>
+ <bp:NAME rdf:datatype="xs:string">6-phosphofructokinase-1</bp:NAME>
+ <bp:XREF>
+ <bp:publicationXref rdf:ID="publicationXref12">
+ <bp:YEAR>1991</bp:YEAR>
+ <bp:AUTHORS rdf:datatype="xs:string">Evans PR</bp:AUTHORS>
+ <bp:ID rdf:datatype="xs:string">1832014</bp:ID>
+ <bp:SOURCE rdf:datatype="xs:string">Biochemistry 1991;30(34);8477-80
+ </bp:SOURCE>
+ <bp:DB rdf:datatype="xs:string">PubMed</bp:DB>
+ <bp:TITLE rdf:datatype="xs:string">Steady-state fluorescence of
+ Escherichia coli phosphofructokinase reveals a regulatory role
+ for ATP.</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="xs:string">Berger SA</bp:AUTHORS>
+ </bp:publicationXref>
+ </bp:XREF>
+ <bp:CONTROLLED>
+ <bp:biochemicalReaction rdf:ID="biochemicalReaction13">
+ <bp:COMMENT rdf:datatype="xs:string">This is a key control step in
+ glycolysis |CITS: [79100775]|</bp:COMMENT>
+ <bp:XREF>
+ <bp:publicationXref rdf:ID="publicationXref14">
+ <bp:TITLE rdf:datatype="xs:string">Biochemistry</bp:TITLE>
+ <bp:SOURCE rdf:datatype="xs:string">WH Freeman and Co., 3rd
+ edition, New York, 1988</bp:SOURCE>
+ <bp:AUTHORS rdf:datatype="xs:string">Stryer L</bp:AUTHORS>
+ </bp:publicationXref>
+ </bp:XREF>
+ <bp:SYNONYMS rdf:datatype="xs:string">fructose-6-phosphate
+ phosphorylation</bp:SYNONYMS>
+ <bp:EC-NUMBER rdf:datatype="xs:string">2.7.1.11</bp:EC-NUMBER>
+ <bp:XREF>
+ <bp:publicationXref rdf:ID="publicationXref15">
+ <bp:DB rdf:datatype="xs:string">PubMed</bp:DB>
+ <bp:AUTHORS rdf:datatype="xs:string">Uyeda K</bp:AUTHORS>
+ <bp:ID rdf:datatype="xs:string">153704</bp:ID>
+ <bp:TITLE rdf:datatype="xs:string">Phosphofructokinase.</bp:TITLE>
+ <bp:YEAR>1979</bp:YEAR>
+ <bp:SOURCE rdf:datatype="xs:string">Adv Enzymol Relat Areas Mol
+ Biol 1979;48;193-244</bp:SOURCE>
+ </bp:publicationXref>
+ </bp:XREF>
+ <bp:RIGHT>
+ <bp:physicalEntityParticipant
+ rdf:ID="physicalEntityParticipant16">
+ <bp:CELLULAR-LOCATION>
+ <bp:openControlledVocabulary
+ rdf:ID="openControlledVocabulary17">
+ <bp:TERM>cytoplasm</bp:TERM>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref18">
+ <bp:DB>GO</bp:DB>
+ <bp:ID>GO:0005737</bp:ID>
+ </bp:unificationXref>
+ </bp:XREF>
+ </bp:openControlledVocabulary>
+ </bp:CELLULAR-LOCATION>
+ <bp:PHYSICAL-ENTITY>
+ <bp:smallMolecule rdf:ID="smallMolecule19">
+ <bp:STRUCTURE>
+ <bp:chemicalStructure rdf:ID="chemicalStructure20">
+ <bp:STRUCTURE-FORMAT rdf:datatype="xs:string">
+ CML</bp:STRUCTURE-FORMAT>
+ <bp:STRUCTURE-DATA rdf:datatype="xs:string">
+ <cml> <molecule id="ADP" title="ADP"
+ dictRef="dictADP"> <atomArray> <atom id="ADP-atom1"
+ elementType="C" x2="0.6623" y2="-0.17049"/> <atom
+ id="ADP-atom2" elementType="N" x2="0.28197" y2="0.02295"/>
+ <atom id="ADP-atom3" elementType="N" x2="0.46557"
+ y2="-0.26885"/> <atom id="ADP-atom4" elementType="O"
+ x2="-0.77705" y2="-0.78689"/> <atom id="ADP-atom5"
+ elementType="O" x2="-0.36721" y2="-0.34098"/> <atom
+ id="ADP-atom6" elementType="C" x2="0.46557" y2="-0.65902"/>
+ <atom id="ADP-atom7" elementType="C" x2="0.22951"
+ y2="-0.54426"/> <atom id="ADP-atom8" elementType="C"
+ x2="0.87541" y2="-0.61967"/> <atom id="ADP-atom9"
+ elementType="O" x2="-1.0" y2="-0.54426"/> <atom
+ id="ADP-atom10" elementType="O" x2="-0.77705"
+ y2="-0.34098"/> <atom id="ADP-atom11" elementType="O"
+ x2="0.88525" y2="-0.97705"/> <atom id="ADP-atom12"
+ elementType="P" x2="-0.36721" y2="-0.54426"/> <atom
+ id="ADP-atom13" elementType="N" x2="0.46557" y2="0.34426"/>
+ <atom id="ADP-atom14" elementType="N" x2="0.87541"
+ y2="-0.21639"/> <atom id="ADP-atom15" elementType="P"
+ x2="-0.77705" y2="-0.54426"/> <atom id="ADP-atom16"
+ elementType="C" x2="0.99672" y2="-0.04262"/> <atom
+ id="ADP-atom17" elementType="O" x2="0.53115" y2="-1.0"/>
+ <atom id="ADP-atom18" elementType="O" x2="-0.57049"
+ y2="-0.54426"/> <atom id="ADP-atom19" elementType="O"
+ x2="-0.1541" y2="-0.54426"/> <atom id="ADP-atom20"
+ elementType="C" x2="0.46557" y2="0.12131"/> <atom
+ id="ADP-atom21" elementType="O" x2="0.65574"
+ y2="-0.47541"/> <atom id="ADP-atom22" elementType="C"
+ x2="0.6623" y2="0.02295"/> <atom id="ADP-atom23"
+ elementType="C" x2="0.81311" y2="-0.86557"/> <atom
+ id="ADP-atom24" elementType="H" x2="0.39344"
+ y2="-0.77377"/> <atom id="ADP-atom25" elementType="N"
+ x2="0.85246" y2="0.10492"/> <atom id="ADP-atom26"
+ elementType="C" x2="0.28197" y2="-0.17049"/> <atom
+ id="ADP-atom27" elementType="O" x2="-0.36721"
+ y2="-0.78689"/> <atom id="ADP-atom28" elementType="C"
+ x2="0.53115" y2="-0.86557"/> <atom id="ADP-atom29"
+ elementType="H" x2="0.77377" y2="-0.7377"/> <atom
+ id="ADP-atom30" elementType="H" x2="0.92459"
+ y2="-0.74426"/> <atom id="ADP-atom31" elementType="H"
+ x2="0.60328" y2="-0.75082"/> </atomArray> <bondArray>
+ <bond id="ADP-bond1" atomRefs="ADP-atom31 ADP-atom28"
+ order="1"/> <bond id="ADP-bond2" atomRefs="ADP-atom30
+ ADP-atom8" order="1"/> <bond id="ADP-bond3"
+ atomRefs="ADP-atom29 ADP-atom23" order="1"/> <bond
+ id="ADP-bond4" atomRefs="ADP-atom28 ADP-atom23" order="1"/>
+ <bond id="ADP-bond5" atomRefs="ADP-atom27 ADP-atom12"
+ order="1"/> <bond id="ADP-bond6" atomRefs="ADP-atom26
+ ADP-atom3" order="A"/> <bond id="ADP-bond7"
+ atomRefs="ADP-atom25 ADP-atom16" order="A"/> <bond
+ id="ADP-bond8" atomRefs="ADP-atom24 ADP-atom6" order="1"/>
+ <bond id="ADP-bond9" atomRefs="ADP-atom1 ADP-atom22"
+ order="A"/> <bond id="ADP-bond10" atomRefs="ADP-atom22
+ ADP-atom25" order="A"/> <bond id="ADP-bond11"
+ atomRefs="ADP-atom21 ADP-atom8" order="1"/> <bond
+ id="ADP-bond12" atomRefs="ADP-atom22 ADP-atom20"
+ order="A"/> <bond id="ADP-bond13" atomRefs="ADP-atom19
+ ADP-atom7" order="1"/> <bond id="ADP-bond14"
+ atomRefs="ADP-atom18 ADP-atom12" order="1"/> <bond
+ id="ADP-bond15" atomRefs="ADP-atom17 ADP-atom28"
+ order="1"/> <bond id="ADP-bond16" atomRefs="ADP-atom16
+ ADP-atom14" order="A"/> <bond id="ADP-bond17"
+ atomRefs="ADP-atom15 ADP-atom18" order="1"/> <bond
+ id="ADP-bond18" atomRefs="ADP-atom13 ADP-atom20"
+ order="1"/> <bond id="ADP-bond19" atomRefs="ADP-atom12
+ ADP-atom19" order="1"/> <bond id="ADP-bond20"
+ atomRefs="ADP-atom11 ADP-atom23" order="1"/> <bond
+ id="ADP-bond21" atomRefs="ADP-atom10 ADP-atom15"
+ order="2"/> <bond id="ADP-bond22" atomRefs="ADP-atom9
+ ADP-atom15" order="1"/> <bond id="ADP-bond23"
+ atomRefs="ADP-atom8 ADP-atom14" order="1"/> <bond
+ id="ADP-bond24" atomRefs="ADP-atom8 ADP-atom23" order="1"/>
+ <bond id="ADP-bond25" atomRefs="ADP-atom7 ADP-atom6"
+ order="1"/> <bond id="ADP-bond26" atomRefs="ADP-atom6
+ ADP-atom21" order="1"/> <bond id="ADP-bond27"
+ atomRefs="ADP-atom6 ADP-atom28" order="1"/> <bond
+ id="ADP-bond28" atomRefs="ADP-atom5 ADP-atom12" order="2"/>
+ <bond id="ADP-bond29" atomRefs="ADP-atom4 ADP-atom15"
+ order="1"/> <bond id="ADP-bond30" atomRefs="ADP-atom3
+ ADP-atom1" order="A"/> <bond id="ADP-bond31"
+ atomRefs="ADP-atom2 ADP-atom26" order="A"/> <bond
+ id="ADP-bond32" atomRefs="ADP-atom20 ADP-atom2" order="A"/>
+ <bond id="ADP-bond33" atomRefs="ADP-atom14 ADP-atom1"
+ order="A"/> </bondArray> <formula concise="C 10 H 15
+ N 5 O 10 P 2" formalCharge="-3"/> <float
+ title="molecularWeight" units="g/mol">427.203</float>
+ <string
+ title="smiles">c12(n(cnc(c(N)ncn1)2)[CH]3(O[CH]([CH](O)[CH](O)3)COP(=O)(O)OP(O)(=O)O))</string>
+ </molecule> </cml></bp:STRUCTURE-DATA>
+ </bp:chemicalStructure>
+ </bp:STRUCTURE>
+ <bp:SYNONYMS rdf:datatype="xs:string">adenosine-diphosphate
+ </bp:SYNONYMS>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref21">
+ <bp:DB rdf:datatype="xs:string">CAS</bp:DB>
+ <bp:ID rdf:datatype="xs:string">58-64-0</bp:ID>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:SYNONYMS rdf:datatype="xs:string">adenosine
+ 5'-pyrophosphate</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">adenosine pyrophosphate
+ </bp:SYNONYMS>
+ <bp:NAME rdf:datatype="xs:string">ADP</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="xs:string">adenosine-5-diphosphate
+ </bp:SYNONYMS>
+ <bp:MOLECULAR-WEIGHT>427.2030029296875</bp:MOLECULAR-WEIGHT>
+ <bp:SYNONYMS rdf:datatype="xs:string">adenosine-5'-diphosphate
+ </bp:SYNONYMS>
+ </bp:smallMolecule>
+ </bp:PHYSICAL-ENTITY>
+ <bp:STOICHIOMETRIC-COEFFICIENT>1</bp:STOICHIOMETRIC-COEFFICIENT>
+ </bp:physicalEntityParticipant>
+ </bp:RIGHT>
+ <bp:LEFT>
+ <bp:physicalEntityParticipant
+ rdf:ID="physicalEntityParticipant22">
+ <bp:CELLULAR-LOCATION rdf:resource="#openControlledVocabulary17" />
+ <bp:STOICHIOMETRIC-COEFFICIENT>1</bp:STOICHIOMETRIC-COEFFICIENT>
+ <bp:PHYSICAL-ENTITY>
+ <bp:smallMolecule rdf:ID="smallMolecule23">
+ <bp:MOLECULAR-WEIGHT>260.1369934082031</bp:MOLECULAR-WEIGHT>
+ <bp:STRUCTURE>
+ <bp:chemicalStructure rdf:ID="chemicalStructure24">
+ <bp:STRUCTURE-DATA rdf:datatype="xs:string">
+ <cml> <molecule id="FRUCTOSE-6P"
+ title="fructose-6-phosphate" dictRef="dictFRUCTOSE-6P">
+ <atomArray> <atom id="FRUCTOSE-6P-atom1"
+ elementType="O" x2="-0.41525424" y2="-0.3079096"/> <atom
+ id="FRUCTOSE-6P-atom2" elementType="C" x2="-0.124293804"
+ y2="-0.3079096"/> <atom id="FRUCTOSE-6P-atom3"
+ elementType="H" x2="0.028248549" y2="-0.65254235"/>
+ <atom id="FRUCTOSE-6P-atom4" elementType="C"
+ x2="-0.124293804" y2="-0.519774"/> <atom
+ id="FRUCTOSE-6P-atom5" elementType="H" x2="-0.124293804"
+ y2="-0.6949153"/> <atom id="FRUCTOSE-6P-atom6"
+ elementType="O" x2="0.6751412" y2="-0.279661"/> <atom
+ id="FRUCTOSE-6P-atom7" elementType="O" x2="0.028248549"
+ y2="-1.0"/> <atom id="FRUCTOSE-6P-atom8" elementType="O"
+ x2="0.27966106" y2="-0.29378533"/> <atom
+ id="FRUCTOSE-6P-atom9" elementType="O" x2="0.9971751"
+ y2="-0.7485876"/> <atom id="FRUCTOSE-6P-atom10"
+ elementType="P" x2="-0.70903957" y2="-0.3079096"/> <atom
+ id="FRUCTOSE-6P-atom11" elementType="C" x2="0.67231643"
+ y2="-0.519774"/> <atom id="FRUCTOSE-6P-atom12"
+ elementType="H" x2="0.52259886" y2="-1.0"/> <atom
+ id="FRUCTOSE-6P-atom13" elementType="O" x2="-0.70903957"
+ y2="-0.60169494"/> <atom id="FRUCTOSE-6P-atom14"
+ elementType="C" x2="0.52259886" y2="-0.8248588"/> <atom
+ id="FRUCTOSE-6P-atom15" elementType="O" x2="-1.0"
+ y2="-0.3079096"/> <atom id="FRUCTOSE-6P-atom16"
+ elementType="O" x2="-0.70903957" y2="-0.005649686"/>
+ <atom id="FRUCTOSE-6P-atom17" elementType="C"
+ x2="0.67231643" y2="-0.7485876"/> <atom
+ id="FRUCTOSE-6P-atom18" elementType="C" x2="0.028248549"
+ y2="-0.8248588"/> <atom id="FRUCTOSE-6P-atom19"
+ elementType="O" x2="0.52259886" y2="-0.65254235"/>
+ </atomArray> <bondArray> <bond
+ id="FRUCTOSE-6P-bond1" atomRefs="FRUCTOSE-6P-atom19
+ FRUCTOSE-6P-atom14" order="1"/> <bond
+ id="FRUCTOSE-6P-bond2" atomRefs="FRUCTOSE-6P-atom18
+ FRUCTOSE-6P-atom14" order="1"/> <bond
+ id="FRUCTOSE-6P-bond3" atomRefs="FRUCTOSE-6P-atom17
+ FRUCTOSE-6P-atom11" order="1"/> <bond
+ id="FRUCTOSE-6P-bond4" atomRefs="FRUCTOSE-6P-atom15
+ FRUCTOSE-6P-atom10" order="1"/> <bond
+ id="FRUCTOSE-6P-bond5" atomRefs="FRUCTOSE-6P-atom13
+ FRUCTOSE-6P-atom10" order="1"/> <bond
+ id="FRUCTOSE-6P-bond6" atomRefs="FRUCTOSE-6P-atom12
+ FRUCTOSE-6P-atom14" order="1"/> <bond
+ id="FRUCTOSE-6P-bond7" atomRefs="FRUCTOSE-6P-atom11
+ FRUCTOSE-6P-atom14" order="1"/> <bond
+ id="FRUCTOSE-6P-bond8" atomRefs="FRUCTOSE-6P-atom10
+ FRUCTOSE-6P-atom16" order="2"/> <bond
+ id="FRUCTOSE-6P-bond9" atomRefs="FRUCTOSE-6P-atom10
+ FRUCTOSE-6P-atom1" order="1"/> <bond
+ id="FRUCTOSE-6P-bond10" atomRefs="FRUCTOSE-6P-atom9
+ FRUCTOSE-6P-atom17" order="1"/> <bond
+ id="FRUCTOSE-6P-bond11" atomRefs="FRUCTOSE-6P-atom8
+ FRUCTOSE-6P-atom11" order="1"/> <bond
+ id="FRUCTOSE-6P-bond12" atomRefs="FRUCTOSE-6P-atom7
+ FRUCTOSE-6P-atom18" order="1"/> <bond
+ id="FRUCTOSE-6P-bond13" atomRefs="FRUCTOSE-6P-atom6
+ FRUCTOSE-6P-atom11" order="1"/> <bond
+ id="FRUCTOSE-6P-bond14" atomRefs="FRUCTOSE-6P-atom5
+ FRUCTOSE-6P-atom4" order="1"/> <bond
+ id="FRUCTOSE-6P-bond15" atomRefs="FRUCTOSE-6P-atom4
+ FRUCTOSE-6P-atom18" order="1"/> <bond
+ id="FRUCTOSE-6P-bond16" atomRefs="FRUCTOSE-6P-atom4
+ FRUCTOSE-6P-atom8" order="1"/> <bond
+ id="FRUCTOSE-6P-bond17" atomRefs="FRUCTOSE-6P-atom3
+ FRUCTOSE-6P-atom18" order="1"/> <bond
+ id="FRUCTOSE-6P-bond18" atomRefs="FRUCTOSE-6P-atom2
+ FRUCTOSE-6P-atom4" order="1"/> <bond
+ id="FRUCTOSE-6P-bond19" atomRefs="FRUCTOSE-6P-atom1
+ FRUCTOSE-6P-atom2" order="1"/> </bondArray> <formula
+ concise="C 6 H 13 O 9 P 1" formalCharge="0"/> <float
+ title="molecularWeight" units="g/mol">260.137</float>
+ <string
+ title="smiles">C(OP(O)(O)=O)[CH]1([CH](O)[CH](O)C(O)(O1)CO)</string>
+ </molecule> </cml></bp:STRUCTURE-DATA>
+ <bp:STRUCTURE-FORMAT rdf:datatype="xs:string">
+ CML</bp:STRUCTURE-FORMAT>
+ </bp:chemicalStructure>
+ </bp:STRUCTURE>
+ <bp:SYNONYMS rdf:datatype="xs:string">D-fructose-6-P
+ </bp:SYNONYMS>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref25">
+ <bp:DB rdf:datatype="xs:string">CAS</bp:DB>
+ <bp:ID rdf:datatype="xs:string">643-13-0</bp:ID>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:SYNONYMS rdf:datatype="xs:string">D-fructose-6-phosphate
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">fructose-6-P
+ </bp:SYNONYMS>
+ <bp:NAME rdf:datatype="xs:string">fructose-6-phosphate</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="xs:string">fruc6p</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">fru-6-P</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">A-D-fructose-6-P
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">fructose-6P
+ </bp:SYNONYMS>
+ </bp:smallMolecule>
+ </bp:PHYSICAL-ENTITY>
+ </bp:physicalEntityParticipant>
+ </bp:LEFT>
+ <bp:RIGHT>
+ <bp:physicalEntityParticipant
+ rdf:ID="physicalEntityParticipant26">
+ <bp:PHYSICAL-ENTITY>
+ <bp:smallMolecule rdf:ID="smallMolecule27">
+ <bp:NAME rdf:datatype="xs:string">H+</bp:NAME>
+ <bp:MOLECULAR-WEIGHT>1.0080000162124634</bp:MOLECULAR-WEIGHT>
+ <bp:SYNONYMS rdf:datatype="xs:string">hydrogen ion
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">H</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">proton</bp:SYNONYMS>
+ <bp:STRUCTURE>
+ <bp:chemicalStructure rdf:ID="chemicalStructure28">
+ <bp:STRUCTURE-DATA rdf:datatype="xs:string">
+ <cml> <molecule id="PROTON" title="H+"
+ dictRef="dictPROTON"> <atomArray> <atom
+ id="PROTON-atom1" elementType="H" x2="-1.0" y2="-1.0"
+ formalCharge="1"/> </atomArray> <bondArray>
+ </bondArray> <formula concise="H 1"
+ formalCharge="1"/> <float title="molecularWeight"
+ units="g/mol">1.008</float> <string
+ title="smiles">[H+1]</string> </molecule> </cml>
+ </bp:STRUCTURE-DATA>
+ <bp:STRUCTURE-FORMAT rdf:datatype="xs:string">
+ CML</bp:STRUCTURE-FORMAT>
+ </bp:chemicalStructure>
+ </bp:STRUCTURE>
+ </bp:smallMolecule>
+ </bp:PHYSICAL-ENTITY>
+ <bp:STOICHIOMETRIC-COEFFICIENT>1</bp:STOICHIOMETRIC-COEFFICIENT>
+ <bp:CELLULAR-LOCATION rdf:resource="#openControlledVocabulary17" />
+ </bp:physicalEntityParticipant>
+ </bp:RIGHT>
+ <bp:RIGHT>
+ <bp:physicalEntityParticipant
+ rdf:ID="physicalEntityParticipant29">
+ <bp:PHYSICAL-ENTITY>
+ <bp:smallMolecule rdf:ID="smallMolecule30">
+ <bp:NAME rdf:datatype="xs:string">fructose-1,6-bisphosphate
+ </bp:NAME>
+ <bp:MOLECULAR-WEIGHT>340.11700439453125</bp:MOLECULAR-WEIGHT>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref31">
+ <bp:DB rdf:datatype="xs:string">CAS</bp:DB>
+ <bp:ID rdf:datatype="xs:string">488-69-7</bp:ID>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:SYNONYMS rdf:datatype="xs:string">D-fructose-1,6-bisphosphate
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">D-fructose-1,6-diphosphate
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">α-D-fructose-1,6-diphosphate
+ </bp:SYNONYMS>
+ <bp:STRUCTURE>
+ <bp:chemicalStructure rdf:ID="chemicalStructure32">
+ <bp:STRUCTURE-FORMAT rdf:datatype="xs:string">
+ CML</bp:STRUCTURE-FORMAT>
+ <bp:STRUCTURE-DATA rdf:datatype="xs:string">
+ <cml> <molecule id="FRUCTOSE-16-DIPHOSPHATE"
+ title="fructose-1,6-bisphosphate"
+ dictRef="dictFRUCTOSE-16-DIPHOSPHATE"> <atomArray>
+ <atom id="FRUCTOSE-16-DIPHOSPHATE-atom1" elementType="H"
+ x2="0.16364" y2="-0.97355"/> <atom
+ id="FRUCTOSE-16-DIPHOSPHATE-atom2" elementType="C"
+ x2="0.28595" y2="-0.7686"/> <atom
+ id="FRUCTOSE-16-DIPHOSPHATE-atom3" elementType="C"
+ x2="-0.34876" y2="-0.42149"/> <atom
+ id="FRUCTOSE-16-DIPHOSPHATE-atom4" elementType="H"
+ x2="-0.34876" y2="-0.72893"/> <atom
+ id="FRUCTOSE-16-DIPHOSPHATE-atom5" elementType="O"
+ x2="0.76529" y2="-0.53719"/> <atom
+ id="FRUCTOSE-16-DIPHOSPHATE-atom6" elementType="C"
+ x2="0.28595" y2="-0.59008"/> <atom
+ id="FRUCTOSE-16-DIPHOSPHATE-atom7" elementType="P"
+ x2="0.76529" y2="-0.7686"/> <atom
+ id="FRUCTOSE-16-DIPHOSPHATE-atom8" elementType="C"
+ x2="-0.34876" y2="-0.59008"/> <atom
+ id="FRUCTOSE-16-DIPHOSPHATE-atom9" elementType="C"
+ x2="0.16364" y2="-0.83471"/> <atom
+ id="FRUCTOSE-16-DIPHOSPHATE-atom10" elementType="O"
+ x2="0.5405" y2="-0.7686"/> <atom
+ id="FRUCTOSE-16-DIPHOSPHATE-atom11" elementType="O"
+ x2="0.28595" y2="-0.35868"/> <atom
+ id="FRUCTOSE-16-DIPHOSPHATE-atom12" elementType="O"
+ x2="0.99669" y2="-0.7686"/> <atom
+ id="FRUCTOSE-16-DIPHOSPHATE-atom13" elementType="P"
+ x2="-0.7686" y2="-0.42149"/> <atom
+ id="FRUCTOSE-16-DIPHOSPHATE-atom14" elementType="H"
+ x2="-0.22645" y2="-0.69587"/> <atom
+ id="FRUCTOSE-16-DIPHOSPHATE-atom15" elementType="O"
+ x2="-1.0" y2="-0.42149"/> <atom
+ id="FRUCTOSE-16-DIPHOSPHATE-atom16" elementType="O"
+ x2="-0.0281" y2="-0.41157"/> <atom
+ id="FRUCTOSE-16-DIPHOSPHATE-atom17" elementType="O"
+ x2="-0.7686" y2="-0.2"/> <atom
+ id="FRUCTOSE-16-DIPHOSPHATE-atom18" elementType="O"
+ x2="-0.53388" y2="-0.42149"/> <atom
+ id="FRUCTOSE-16-DIPHOSPHATE-atom19" elementType="C"
+ x2="-0.22645" y2="-0.83471"/> <atom
+ id="FRUCTOSE-16-DIPHOSPHATE-atom20" elementType="O"
+ x2="0.76529" y2="-1.0"/> <atom
+ id="FRUCTOSE-16-DIPHOSPHATE-atom21" elementType="O"
+ x2="-0.7686" y2="-0.66281"/> <atom
+ id="FRUCTOSE-16-DIPHOSPHATE-atom22" elementType="O"
+ x2="0.16364" y2="-0.69587"/> <atom
+ id="FRUCTOSE-16-DIPHOSPHATE-atom23" elementType="O"
+ x2="-0.22645" y2="-0.97355"/> </atomArray>
+ <bondArray> <bond id="FRUCTOSE-16-DIPHOSPHATE-bond1"
+ atomRefs="FRUCTOSE-16-DIPHOSPHATE-atom23
+ FRUCTOSE-16-DIPHOSPHATE-atom19" order="1"/> <bond
+ id="FRUCTOSE-16-DIPHOSPHATE-bond2"
+ atomRefs="FRUCTOSE-16-DIPHOSPHATE-atom22
+ FRUCTOSE-16-DIPHOSPHATE-atom9" order="1"/> <bond
+ id="FRUCTOSE-16-DIPHOSPHATE-bond3"
+ atomRefs="FRUCTOSE-16-DIPHOSPHATE-atom21
+ FRUCTOSE-16-DIPHOSPHATE-atom13" order="1"/> <bond
+ id="FRUCTOSE-16-DIPHOSPHATE-bond4"
+ atomRefs="FRUCTOSE-16-DIPHOSPHATE-atom20
+ FRUCTOSE-16-DIPHOSPHATE-atom7" order="1"/> <bond
+ id="FRUCTOSE-16-DIPHOSPHATE-bond5"
+ atomRefs="FRUCTOSE-16-DIPHOSPHATE-atom19
+ FRUCTOSE-16-DIPHOSPHATE-atom9" order="1"/> <bond
+ id="FRUCTOSE-16-DIPHOSPHATE-bond6"
+ atomRefs="FRUCTOSE-16-DIPHOSPHATE-atom18
+ FRUCTOSE-16-DIPHOSPHATE-atom3" order="1"/> <bond
+ id="FRUCTOSE-16-DIPHOSPHATE-bond7"
+ atomRefs="FRUCTOSE-16-DIPHOSPHATE-atom17
+ FRUCTOSE-16-DIPHOSPHATE-atom13" order="2"/> <bond
+ id="FRUCTOSE-16-DIPHOSPHATE-bond8"
+ atomRefs="FRUCTOSE-16-DIPHOSPHATE-atom16
+ FRUCTOSE-16-DIPHOSPHATE-atom6" order="1"/> <bond
+ id="FRUCTOSE-16-DIPHOSPHATE-bond9"
+ atomRefs="FRUCTOSE-16-DIPHOSPHATE-atom15
+ FRUCTOSE-16-DIPHOSPHATE-atom13" order="1"/> <bond
+ id="FRUCTOSE-16-DIPHOSPHATE-bond10"
+ atomRefs="FRUCTOSE-16-DIPHOSPHATE-atom14
+ FRUCTOSE-16-DIPHOSPHATE-atom19" order="1"/> <bond
+ id="FRUCTOSE-16-DIPHOSPHATE-bond11"
+ atomRefs="FRUCTOSE-16-DIPHOSPHATE-atom13
+ FRUCTOSE-16-DIPHOSPHATE-atom18" order="1"/> <bond
+ id="FRUCTOSE-16-DIPHOSPHATE-bond12"
+ atomRefs="FRUCTOSE-16-DIPHOSPHATE-atom12
+ FRUCTOSE-16-DIPHOSPHATE-atom7" order="1"/> <bond
+ id="FRUCTOSE-16-DIPHOSPHATE-bond13"
+ atomRefs="FRUCTOSE-16-DIPHOSPHATE-atom11
+ FRUCTOSE-16-DIPHOSPHATE-atom6" order="1"/> <bond
+ id="FRUCTOSE-16-DIPHOSPHATE-bond14"
+ atomRefs="FRUCTOSE-16-DIPHOSPHATE-atom10
+ FRUCTOSE-16-DIPHOSPHATE-atom2" order="1"/> <bond
+ id="FRUCTOSE-16-DIPHOSPHATE-bond15"
+ atomRefs="FRUCTOSE-16-DIPHOSPHATE-atom8
+ FRUCTOSE-16-DIPHOSPHATE-atom19" order="1"/> <bond
+ id="FRUCTOSE-16-DIPHOSPHATE-bond16"
+ atomRefs="FRUCTOSE-16-DIPHOSPHATE-atom8
+ FRUCTOSE-16-DIPHOSPHATE-atom16" order="1"/> <bond
+ id="FRUCTOSE-16-DIPHOSPHATE-bond17"
+ atomRefs="FRUCTOSE-16-DIPHOSPHATE-atom7
+ FRUCTOSE-16-DIPHOSPHATE-atom10" order="1"/> <bond
+ id="FRUCTOSE-16-DIPHOSPHATE-bond18"
+ atomRefs="FRUCTOSE-16-DIPHOSPHATE-atom6
+ FRUCTOSE-16-DIPHOSPHATE-atom9" order="1"/> <bond
+ id="FRUCTOSE-16-DIPHOSPHATE-bond19"
+ atomRefs="FRUCTOSE-16-DIPHOSPHATE-atom5
+ FRUCTOSE-16-DIPHOSPHATE-atom7" order="2"/> <bond
+ id="FRUCTOSE-16-DIPHOSPHATE-bond20"
+ atomRefs="FRUCTOSE-16-DIPHOSPHATE-atom4
+ FRUCTOSE-16-DIPHOSPHATE-atom8" order="1"/> <bond
+ id="FRUCTOSE-16-DIPHOSPHATE-bond21"
+ atomRefs="FRUCTOSE-16-DIPHOSPHATE-atom3
+ FRUCTOSE-16-DIPHOSPHATE-atom8" order="1"/> <bond
+ id="FRUCTOSE-16-DIPHOSPHATE-bond22"
+ atomRefs="FRUCTOSE-16-DIPHOSPHATE-atom2
+ FRUCTOSE-16-DIPHOSPHATE-atom6" order="1"/> <bond
+ id="FRUCTOSE-16-DIPHOSPHATE-bond23"
+ atomRefs="FRUCTOSE-16-DIPHOSPHATE-atom1
+ FRUCTOSE-16-DIPHOSPHATE-atom9" order="1"/> </bondArray>
+ <formula concise="C 6 H 14 O 12 P 2" formalCharge="0"/>
+ <float title="molecularWeight"
+ units="g/mol">340.117</float> <string
+ title="smiles">C(OP(O)(O)=O)C1(O)(O[CH]([CH](O)[CH](O)1)COP(=O)(O)O)</string>
+ <string title="systematicName">D-Fructose
+ 1,6-bis(dihydrogenphosphate)</string> </molecule>
+ </cml></bp:STRUCTURE-DATA>
+ </bp:chemicalStructure>
+ </bp:STRUCTURE>
+ <bp:SYNONYMS rdf:datatype="xs:string">fructose-1,6-diphosphate
+ </bp:SYNONYMS>
+ </bp:smallMolecule>
+ </bp:PHYSICAL-ENTITY>
+ <bp:CELLULAR-LOCATION rdf:resource="#openControlledVocabulary17" />
+ <bp:STOICHIOMETRIC-COEFFICIENT>1</bp:STOICHIOMETRIC-COEFFICIENT>
+ </bp:physicalEntityParticipant>
+ </bp:RIGHT>
+ <bp:LEFT>
+ <bp:physicalEntityParticipant
+ rdf:ID="physicalEntityParticipant33">
+ <bp:STOICHIOMETRIC-COEFFICIENT>1</bp:STOICHIOMETRIC-COEFFICIENT>
+ <bp:CELLULAR-LOCATION rdf:resource="#openControlledVocabulary17" />
+ <bp:PHYSICAL-ENTITY>
+ <bp:smallMolecule rdf:ID="smallMolecule34">
+ <bp:STRUCTURE>
+ <bp:chemicalStructure rdf:ID="chemicalStructure35">
+ <bp:STRUCTURE-DATA rdf:datatype="xs:string">
+ <cml> <molecule id="ATP" title="ATP"
+ dictRef="dictATP"> <atomArray> <atom id="ATP-atom1"
+ elementType="C" x2="0.9971347" y2="-0.16905439"/> <atom
+ id="ATP-atom2" elementType="P" x2="-0.4641834"
+ y2="-0.68767905"/> <atom id="ATP-atom3" elementType="O"
+ x2="-1.0" y2="-0.68767905"/> <atom id="ATP-atom4"
+ elementType="N" x2="0.8767909" y2="-0.022922575"/> <atom
+ id="ATP-atom5" elementType="O" x2="-0.12320912"
+ y2="-0.5071633"/> <atom id="ATP-atom6" elementType="H"
+ x2="0.5616046" y2="-0.8538682"/> <atom id="ATP-atom7"
+ elementType="H" x2="0.6418339" y2="-0.7851003"/> <atom
+ id="ATP-atom8" elementType="O" x2="-0.12320912"
+ y2="-0.8653295"/> <atom id="ATP-atom9" elementType="O"
+ x2="-0.4641834" y2="-0.8653295"/> <atom id="ATP-atom10"
+ elementType="C" x2="0.5616046" y2="-0.7449857"/> <atom
+ id="ATP-atom11" elementType="N" x2="0.8939829"
+ y2="-0.3409742"/> <atom id="ATP-atom12" elementType="C"
+ x2="0.6418339" y2="-0.89111745"/> <atom id="ATP-atom13"
+ elementType="O" x2="-0.4641834" y2="-0.5071633"/> <atom
+ id="ATP-atom14" elementType="C" x2="0.8939829"
+ y2="-0.739255"/> <atom id="ATP-atom15" elementType="C"
+ x2="0.82234967" y2="-0.89111745"/> <atom id="ATP-atom16"
+ elementType="N" x2="0.4068768" y2="-0.10315186"/> <atom
+ id="ATP-atom17" elementType="C" x2="0.4068768"
+ y2="-0.29226357"/> <atom id="ATP-atom18" elementType="N"
+ x2="0.5587393" y2="-0.3925501"/> <atom id="ATP-atom19"
+ elementType="N" x2="0.5587393" y2="0.17478514"/> <atom
+ id="ATP-atom20" elementType="O" x2="0.82234967" y2="-1.0"/>
+ <atom id="ATP-atom21" elementType="C" x2="0.72206306"
+ y2="-0.10315186"/> <atom id="ATP-atom22" elementType="C"
+ x2="0.72206306" y2="-0.29226357"/> <atom id="ATP-atom23"
+ elementType="C" x2="0.5587393" y2="-0.0028653145"/>
+ <atom id="ATP-atom24" elementType="O" x2="0.6418339"
+ y2="-1.0"/> <atom id="ATP-atom25" elementType="P"
+ x2="-0.12320912" y2="-0.68767905"/> <atom
+ id="ATP-atom26" elementType="H" x2="0.82234967"
+ y2="-0.7851003"/> <atom id="ATP-atom27" elementType="O"
+ x2="-0.81948423" y2="-0.8653295"/> <atom id="ATP-atom28"
+ elementType="H" x2="0.8939829" y2="-0.8481375"/> <atom
+ id="ATP-atom29" elementType="C" x2="0.36389685"
+ y2="-0.68767905"/> <atom id="ATP-atom30" elementType="O"
+ x2="0.7306591" y2="-0.66762173"/> <atom id="ATP-atom31"
+ elementType="O" x2="-0.29226357" y2="-0.68767905"/>
+ <atom id="ATP-atom32" elementType="O" x2="-0.81948423"
+ y2="-0.5071633"/> <atom id="ATP-atom33" elementType="O"
+ x2="0.05157602" y2="-0.68767905"/> <atom id="ATP-atom34"
+ elementType="P" x2="-0.81948423" y2="-0.68767905"/>
+ <atom id="ATP-atom35" elementType="O" x2="-0.63610315"
+ y2="-0.68767905"/> </atomArray> <bondArray> <bond
+ id="ATP-bond1" atomRefs="ATP-atom35 ATP-atom2" order="1"/>
+ <bond id="ATP-bond2" atomRefs="ATP-atom34 ATP-atom35"
+ order="1"/> <bond id="ATP-bond3" atomRefs="ATP-atom33
+ ATP-atom29" order="1"/> <bond id="ATP-bond4"
+ atomRefs="ATP-atom32 ATP-atom34" order="2"/> <bond
+ id="ATP-bond5" atomRefs="ATP-atom31 ATP-atom25" order="1"/>
+ <bond id="ATP-bond6" atomRefs="ATP-atom30 ATP-atom14"
+ order="1"/> <bond id="ATP-bond7" atomRefs="ATP-atom29
+ ATP-atom10" order="1"/> <bond id="ATP-bond8"
+ atomRefs="ATP-atom28 ATP-atom14" order="1"/> <bond
+ id="ATP-bond9" atomRefs="ATP-atom27 ATP-atom34" order="1"/>
+ <bond id="ATP-bond10" atomRefs="ATP-atom26 ATP-atom15"
+ order="1"/> <bond id="ATP-bond11" atomRefs="ATP-atom25
+ ATP-atom33" order="1"/> <bond id="ATP-bond12"
+ atomRefs="ATP-atom24 ATP-atom12" order="1"/> <bond
+ id="ATP-bond13" atomRefs="ATP-atom23 ATP-atom16"
+ order="A"/> <bond id="ATP-bond14" atomRefs="ATP-atom22
+ ATP-atom21" order="A"/> <bond id="ATP-bond15"
+ atomRefs="ATP-atom21 ATP-atom4" order="A"/> <bond
+ id="ATP-bond16" atomRefs="ATP-atom21 ATP-atom23"
+ order="A"/> <bond id="ATP-bond17" atomRefs="ATP-atom20
+ ATP-atom15" order="1"/> <bond id="ATP-bond18"
+ atomRefs="ATP-atom19 ATP-atom23" order="1"/> <bond
+ id="ATP-bond19" atomRefs="ATP-atom18 ATP-atom22"
+ order="A"/> <bond id="ATP-bond20" atomRefs="ATP-atom17
+ ATP-atom18" order="A"/> <bond id="ATP-bond21"
+ atomRefs="ATP-atom16 ATP-atom17" order="A"/> <bond
+ id="ATP-bond22" atomRefs="ATP-atom14 ATP-atom15"
+ order="1"/> <bond id="ATP-bond23" atomRefs="ATP-atom14
+ ATP-atom11" order="1"/> <bond id="ATP-bond24"
+ atomRefs="ATP-atom13 ATP-atom2" order="2"/> <bond
+ id="ATP-bond25" atomRefs="ATP-atom12 ATP-atom15"
+ order="1"/> <bond id="ATP-bond26" atomRefs="ATP-atom11
+ ATP-atom22" order="A"/> <bond id="ATP-bond27"
+ atomRefs="ATP-atom10 ATP-atom12" order="1"/> <bond
+ id="ATP-bond28" atomRefs="ATP-atom10 ATP-atom30"
+ order="1"/> <bond id="ATP-bond29" atomRefs="ATP-atom9
+ ATP-atom2" order="1"/> <bond id="ATP-bond30"
+ atomRefs="ATP-atom8 ATP-atom25" order="1"/> <bond
+ id="ATP-bond31" atomRefs="ATP-atom7 ATP-atom12" order="1"/>
+ <bond id="ATP-bond32" atomRefs="ATP-atom6 ATP-atom10"
+ order="1"/> <bond id="ATP-bond33" atomRefs="ATP-atom5
+ ATP-atom25" order="2"/> <bond id="ATP-bond34"
+ atomRefs="ATP-atom4 ATP-atom1" order="A"/> <bond
+ id="ATP-bond35" atomRefs="ATP-atom3 ATP-atom34" order="1"/>
+ <bond id="ATP-bond36" atomRefs="ATP-atom2 ATP-atom31"
+ order="1"/> <bond id="ATP-bond37" atomRefs="ATP-atom1
+ ATP-atom11" order="A"/> </bondArray> <formula
+ concise="C 10 H 16 N 5 O 13 P 3" formalCharge="-4"/>
+ <float title="molecularWeight"
+ units="g/mol">507.183</float> <string
+ title="smiles">[CH]3(n1(c2(c(nc1)c(N)ncn2)))(O[CH]([CH](O)[CH](O)3)COP(=O)(O)OP(O)(=O)OP(O)(=O)O)</string>
+ </molecule> </cml></bp:STRUCTURE-DATA>
+ <bp:STRUCTURE-FORMAT rdf:datatype="xs:string">
+ CML</bp:STRUCTURE-FORMAT>
+ </bp:chemicalStructure>
+ </bp:STRUCTURE>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref36">
+ <bp:ID rdf:datatype="xs:string">56-65-5</bp:ID>
+ <bp:DB rdf:datatype="xs:string">CAS</bp:DB>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:SYNONYMS rdf:datatype="xs:string">adenosine-5'-triphosphate
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">adenylpyrophosphate
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">adenosine-triphosphate
+ </bp:SYNONYMS>
+ <bp:NAME rdf:datatype="xs:string">ATP</bp:NAME>
+ <bp:MOLECULAR-WEIGHT>507.1830139160156</bp:MOLECULAR-WEIGHT>
+ </bp:smallMolecule>
+ </bp:PHYSICAL-ENTITY>
+ </bp:physicalEntityParticipant>
+ </bp:LEFT>
+ <bp:NAME rdf:datatype="xs:string">6PFRUCTPHOS-RXN</bp:NAME>
+ <bp:DELTA-G><bp:deltaGprimeO rdf:ID="deltaG-minus-3.4"><bp:DELTA-G-PRIME-O>-3.4</bp:DELTA-G-PRIME-O></bp:deltaGprimeO></bp:DELTA-G>
+ </bp:biochemicalReaction>
+ </bp:CONTROLLED>
+ <bp:CONTROLLER>
+ <bp:physicalEntityParticipant rdf:ID="physicalEntityParticipant37">
+ <bp:PHYSICAL-ENTITY>
+ <bp:complex rdf:ID="complex38">
+ <bp:XREF rdf:resource="#publicationXref8" />
+ <bp:COMMENT rdf:datatype="xs:string">This enzyme is an isozyme
+ with phosphofructokinase-2. The nucleotide sequences of the
+ genes are not similar |CITS: [85203917]|. The tetrameric
+ species is the only one which can bind both substrates and
+ effectors, and thus have both catalytic and regulatory
+ properties. The C terminal end of the peptide is required for
+ allosteric properties.|CITS: [90276415]| Crystal structures
+ have been solved with and without activators and inhibitors.
+ |CITS: [89342465], [89125622]|</bp:COMMENT>
+ <bp:XREF rdf:resource="#publicationXref10" />
+ <bp:XREF rdf:resource="#publicationXref4" />
+ <bp:COMPONENTS>
+ <bp:physicalEntityParticipant
+ rdf:ID="physicalEntityParticipant39">
+ <bp:CELLULAR-LOCATION>
+ <bp:openControlledVocabulary
+ rdf:ID="openControlledVocabulary40">
+ <bp:TERM>cellular_component unknown</bp:TERM>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref41">
+ <bp:DB>GO</bp:DB>
+ <bp:ID>GO:0008372</bp:ID>
+ </bp:unificationXref>
+ </bp:XREF>
+ </bp:openControlledVocabulary>
+ </bp:CELLULAR-LOCATION>
+ <bp:PHYSICAL-ENTITY>
+ <bp:protein rdf:ID="protein42">
+ <bp:SEQUENCE rdf:datatype="xs:string">MIKKIGVLTSGGDAPGMNAAIRGVVRSALTEGLEVMGIYDGYLGLYEDRMVQLDRYSVSDMINRGGTFLGSARFPEFRDENIRAVAIENLKKRGIDALVVIGGDGSYMGAMRLTEMGFPCIGLPGTIDNDIKGTDYTIGFFTALSTVVEAIDRLRDTSSSHQRISVVEVMGRYCGDLTLAAAIAGGCEFVVVPEVEFSREDLVNEIKAGIAKGKKHAIVAITEHMCDVDELAHFIEKETGRETRATVLGHIQRGGSPVPYDRILASRMGAYAIDLLLAGYGGRCVGIQNEQLVHHDIIDAIENMKRPFKGDWLDCAKKLY
+ </bp:SEQUENCE>
+ <bp:ORGANISM>
+ <bp:bioSource rdf:ID="bioSource43">
+ <bp:NAME rdf:datatype="xs:string">Escherichia coli
+ K-12</bp:NAME>
+ <bp:TAXON-XREF>
+ <bp:unificationXref rdf:ID="unificationXref44">
+ <bp:ID>83333</bp:ID>
+ <bp:DB>taxon</bp:DB>
+ <bp:COMMENT>Escherichia coli K-12</bp:COMMENT>
+ </bp:unificationXref>
+ </bp:TAXON-XREF>
+ </bp:bioSource>
+ </bp:ORGANISM>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref45">
+ <bp:ID rdf:datatype="xs:string">P06998</bp:ID>
+ <bp:DB rdf:datatype="xs:string">SWISS-PROT</bp:DB>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:XREF>
+ <bp:relationshipXref rdf:ID="relationshipXref46">
+ <bp:RELATIONSHIP-TYPE rdf:datatype="xs:string">Ortholog
+ </bp:RELATIONSHIP-TYPE>
+ <bp:DB rdf:datatype="xs:string">EcoO157Cyc</bp:DB>
+ <bp:ID rdf:datatype="xs:string">PFKA-MONOMER</bp:ID>
+ </bp:relationshipXref>
+ </bp:XREF>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref47">
+ <bp:DB rdf:datatype="xs:string">PDB</bp:DB>
+ <bp:ID rdf:datatype="xs:string">2PFK</bp:ID>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref48">
+ <bp:ID rdf:datatype="xs:string">NP_418351</bp:ID>
+ <bp:DB rdf:datatype="xs:string">RefSeq</bp:DB>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:NAME rdf:datatype="xs:string">6-phosphofructokinase-1
+ monomer</bp:NAME>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref49">
+ <bp:ID rdf:datatype="xs:string">b3916</bp:ID>
+ <bp:DB rdf:datatype="xs:string">PIR</bp:DB>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:SYNONYMS rdf:datatype="xs:string">PfkA
+ </bp:SYNONYMS>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref50">
+ <bp:DB rdf:datatype="xs:string">SWISS-MODEL</bp:DB>
+ <bp:ID rdf:datatype="xs:string">P06998</bp:ID>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:SYNONYMS rdf:datatype="xs:string">B3916
+ </bp:SYNONYMS>
+ </bp:protein>
+ </bp:PHYSICAL-ENTITY>
+ <bp:STOICHIOMETRIC-COEFFICIENT>4
+ </bp:STOICHIOMETRIC-COEFFICIENT>
+ </bp:physicalEntityParticipant>
+ </bp:COMPONENTS>
+ <bp:XREF rdf:resource="#publicationXref11" />
+ <bp:NAME rdf:datatype="xs:string">6PFK-1-CPX</bp:NAME>
+ <bp:ORGANISM rdf:resource="#bioSource43" />
+ </bp:complex>
+ </bp:PHYSICAL-ENTITY>
+ </bp:physicalEntityParticipant>
+ </bp:CONTROLLER>
+ <bp:SYNONYMS rdf:datatype="xs:string">fructose-6-p-1-kinase
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">fructose-6-phosphate-1-phosphotransferase
+ </bp:SYNONYMS>
+ <bp:DIRECTION rdf:datatype="xs:string">REVERSIBLE</bp:DIRECTION>
+ </bp:catalysis>
+ </bp:CONTROLLED>
+ <bp:CONTROL-TYPE rdf:datatype="xs:string">ACTIVATION-NONALLOSTERIC
+ </bp:CONTROL-TYPE>
+ <bp:CONTROLLER rdf:resource="#physicalEntityParticipant22" />
+ </bp:modulation>
+ <bp:smallMolecule rdf:ID="smallMolecule51">
+ <bp:SYNONYMS rdf:datatype="xs:string">1,3-diphosphoglycerate
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">13-dpg</bp:SYNONYMS>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref52">
+ <bp:DB rdf:datatype="xs:string">CAS</bp:DB>
+ <bp:ID rdf:datatype="xs:string">1981-49-3</bp:ID>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:STRUCTURE>
+ <bp:chemicalStructure rdf:ID="chemicalStructure53">
+ <bp:STRUCTURE-FORMAT rdf:datatype="xs:string">CML
+ </bp:STRUCTURE-FORMAT>
+ <bp:STRUCTURE-DATA rdf:datatype="xs:string"> <cml>
+ <molecule id="DPG" title="3-phospho-D-glyceroyl-phosphate"
+ dictRef="dictDPG"> <atomArray> <atom id="DPG-atom1"
+ elementType="C" x2="-0.02174" y2="-0.73602"/> <atom
+ id="DPG-atom2" elementType="P" x2="0.73292" y2="-0.48137"/>
+ <atom id="DPG-atom3" elementType="O" x2="0.73292"
+ y2="-0.21739"/> <atom id="DPG-atom4" elementType="P"
+ x2="-0.73602" y2="-0.48137"/> <atom id="DPG-atom5"
+ elementType="O" x2="0.49379" y2="-0.48137"/> <atom
+ id="DPG-atom6" elementType="O" x2="-0.73602" y2="-0.21739"/>
+ <atom id="DPG-atom7" elementType="O" x2="-0.52484"
+ y2="-0.48137"/> <atom id="DPG-atom8" elementType="O"
+ x2="-0.02174" y2="-1.0"/> <atom id="DPG-atom9" elementType="C"
+ x2="-0.25776" y2="-0.48137"/> <atom id="DPG-atom10"
+ elementType="O" x2="0.99689" y2="-0.48137"/> <atom
+ id="DPG-atom11" elementType="O" x2="-0.25776" y2="-0.21739"/>
+ <atom id="DPG-atom12" elementType="O" x2="-0.73602"
+ y2="-0.74534"/> <atom id="DPG-atom13" elementType="O"
+ x2="0.73292" y2="-0.74534"/> <atom id="DPG-atom14"
+ elementType="O" x2="-1.0" y2="-0.48137"/> <atom id="DPG-atom15"
+ elementType="C" x2="0.21739" y2="-0.48137"/> </atomArray>
+ <bondArray> <bond id="DPG-bond1" atomRefs="DPG-atom15
+ DPG-atom5" order="1"/> <bond id="DPG-bond2" atomRefs="DPG-atom9
+ DPG-atom1" order="1"/> <bond id="DPG-bond3" atomRefs="DPG-atom9
+ DPG-atom11" order="2"/> <bond id="DPG-bond4" atomRefs="DPG-atom7
+ DPG-atom9" order="1"/> <bond id="DPG-bond5" atomRefs="DPG-atom5
+ DPG-atom2" order="1"/> <bond id="DPG-bond6" atomRefs="DPG-atom4
+ DPG-atom7" order="1"/> <bond id="DPG-bond7" atomRefs="DPG-atom4
+ DPG-atom6" order="1"/> <bond id="DPG-bond8" atomRefs="DPG-atom4
+ DPG-atom12" order="1"/> <bond id="DPG-bond9" atomRefs="DPG-atom4
+ DPG-atom14" order="2"/> <bond id="DPG-bond10"
+ atomRefs="DPG-atom2 DPG-atom3" order="1"/> <bond id="DPG-bond11"
+ atomRefs="DPG-atom2 DPG-atom13" order="1"/> <bond
+ id="DPG-bond12" atomRefs="DPG-atom2 DPG-atom10" order="2"/>
+ <bond id="DPG-bond13" atomRefs="DPG-atom1 DPG-atom15"
+ order="1"/> <bond id="DPG-bond14" atomRefs="DPG-atom1 DPG-atom8"
+ order="1"/> </bondArray> <formula concise="C 3 H 8 O 10 P 2"
+ formalCharge="0"/> <float title="molecularWeight"
+ units="g/mol">266.038</float> <string
+ title="smiles">C(OP(O)(O)=O)(=O)C(O)COP(O)(O)=O</string>
+ </molecule> </cml></bp:STRUCTURE-DATA>
+ </bp:chemicalStructure>
+ </bp:STRUCTURE>
+ <bp:MOLECULAR-WEIGHT>266.0379943847656</bp:MOLECULAR-WEIGHT>
+ <bp:SYNONYMS rdf:datatype="xs:string">1,3-bis-phosphoglycerate
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">3-phosphoglyceroyl-P
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">phosphoglyceroyl-P</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">3-phosphoglyceroyl-phosphate
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">dpg</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">1,3-biphosphoglycerate
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">3-P-glyceroyl-P</bp:SYNONYMS>
+ <bp:NAME rdf:datatype="xs:string">3-phospho-D-glyceroyl-phosphate
+ </bp:NAME>
+ <bp:SYNONYMS rdf:datatype="xs:string">1,3-diphosphateglycerate
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">glycerate 1,3-biphosphate
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">glycerate 1,3-diphosphate
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">P-glyceroyl-P</bp:SYNONYMS>
+ </bp:smallMolecule>
+ <bp:pathwayStep rdf:ID="pathwayStep54">
+ <bp:STEP-INTERACTIONS>
+ <bp:catalysis rdf:ID="catalysis55">
+ <bp:CONTROLLED>
+ <bp:biochemicalReaction rdf:ID="biochemicalReaction56">
+ <bp:LEFT>
+ <bp:physicalEntityParticipant
+ rdf:ID="physicalEntityParticipant57">
+ <bp:PHYSICAL-ENTITY>
+ <bp:smallMolecule rdf:ID="smallMolecule58">
+ <bp:MOLECULAR-WEIGHT>186.05799865722656</bp:MOLECULAR-WEIGHT>
+ <bp:SYNONYMS rdf:datatype="xs:string">g3p</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">3-phospho-glyceric acid
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">3-pg</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">3-phospho-(R)-glycerate
+ </bp:SYNONYMS>
+ <bp:NAME rdf:datatype="xs:string">3-phosphoglycerate</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="xs:string">glycerate 3-phosphate
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">glycerate-3-P
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">D-Glycerate 3-phosphate
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">3-P-D-glycerate
+ </bp:SYNONYMS>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref59">
+ <bp:ID rdf:datatype="xs:string">820-11-1</bp:ID>
+ <bp:DB rdf:datatype="xs:string">CAS</bp:DB>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:SYNONYMS rdf:datatype="xs:string">3-phospho-D-glycerate
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">3-P-glycerate
+ </bp:SYNONYMS>
+ <bp:STRUCTURE>
+ <bp:chemicalStructure rdf:ID="chemicalStructure60">
+ <bp:STRUCTURE-DATA rdf:datatype="xs:string">
+ <cml> <molecule id="G3P" title="3-phosphoglycerate"
+ dictRef="dictG3P"> <atomArray> <atom id="G3P-atom1"
+ elementType="C" x2="5.7" y2="-0.5"/> <atom
+ id="G3P-atom2" elementType="C" x2="5.7" y2="-1.25"/>
+ <atom id="G3P-atom3" elementType="C" x2="5.6995"
+ y2="0.25"/> <atom id="G3P-atom4" elementType="O"
+ x2="6.3499" y2="0.6232"/> <atom id="G3P-atom5"
+ elementType="O" x2="5.0484" y2="0.6225"/> <atom
+ id="G3P-atom6" elementType="O" x2="6.45" y2="-0.4998"/>
+ <atom id="G3P-atom7" elementType="P" x2="7.0977"
+ y2="-1.6376"/> <atom id="G3P-atom8" elementType="O"
+ x2="7.0887" y2="-2.3709"/> <atom id="G3P-atom9"
+ elementType="O" x2="7.8767" y2="-1.6513"/> <atom
+ id="G3P-atom10" elementType="O" x2="7.1108" y2="-0.9002"/>
+ <atom id="G3P-atom11" elementType="O" x2="6.3477"
+ y2="-1.6285"/> </atomArray> <bondArray> <bond
+ id="G3P-bond1" atomRefs="G3P-atom7 G3P-atom11" order="1"/>
+ <bond id="G3P-bond2" atomRefs="G3P-atom7 G3P-atom10"
+ order="1"/> <bond id="G3P-bond3" atomRefs="G3P-atom7
+ G3P-atom9" order="2"/> <bond id="G3P-bond4"
+ atomRefs="G3P-atom7 G3P-atom8" order="1"/> <bond
+ id="G3P-bond5" atomRefs="G3P-atom2 G3P-atom11" order="1"/>
+ <bond id="G3P-bond6" atomRefs="G3P-atom1 G3P-atom6"
+ order="1"/> <bond id="G3P-bond7" atomRefs="G3P-atom1
+ G3P-atom3" order="1"/> <bond id="G3P-bond8"
+ atomRefs="G3P-atom3 G3P-atom5" order="2"/> <bond
+ id="G3P-bond9" atomRefs="G3P-atom3 G3P-atom4" order="1"/>
+ <bond id="G3P-bond10" atomRefs="G3P-atom1 G3P-atom2"
+ order="1"/> </bondArray> <formula concise="C 3 H 7 O
+ 7 P 1" formalCharge="0"/> <float title="molecularWeight"
+ units="g/mol">186.058</float> <string
+ title="smiles">C(OP(=O)(O)O)C(O)C(=O)O</string>
+ </molecule> </cml></bp:STRUCTURE-DATA>
+ <bp:STRUCTURE-FORMAT rdf:datatype="xs:string">
+ CML</bp:STRUCTURE-FORMAT>
+ </bp:chemicalStructure>
+ </bp:STRUCTURE>
+ </bp:smallMolecule>
+ </bp:PHYSICAL-ENTITY>
+ <bp:CELLULAR-LOCATION rdf:resource="#openControlledVocabulary17" />
+ <bp:STOICHIOMETRIC-COEFFICIENT>1</bp:STOICHIOMETRIC-COEFFICIENT>
+ </bp:physicalEntityParticipant>
+ </bp:LEFT>
+ <bp:SYNONYMS rdf:datatype="xs:string">PGAM</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">PHOSPHOGLYCERATE
+ PHOSPHOMUTASE</bp:SYNONYMS>
+ <bp:EC-NUMBER rdf:datatype="xs:string">5.4.2.1</bp:EC-NUMBER>
+ <bp:DELTA-G><bp:deltaGprimeO rdf:ID="deltaG-1.1"><bp:DELTA-G-PRIME-O>1.1</bp:DELTA-G-PRIME-O></bp:deltaGprimeO></bp:DELTA-G>
+ <bp:SYNONYMS rdf:datatype="xs:string">PHOSPHOGLYCEROMUTASE
+ </bp:SYNONYMS>
+ <bp:NAME rdf:datatype="xs:string">3PGAREARR-RXN</bp:NAME>
+ <bp:RIGHT>
+ <bp:physicalEntityParticipant
+ rdf:ID="physicalEntityParticipant61">
+ <bp:STOICHIOMETRIC-COEFFICIENT>1</bp:STOICHIOMETRIC-COEFFICIENT>
+ <bp:CELLULAR-LOCATION rdf:resource="#openControlledVocabulary17" />
+ <bp:PHYSICAL-ENTITY>
+ <bp:smallMolecule rdf:ID="smallMolecule62">
+ <bp:STRUCTURE>
+ <bp:chemicalStructure rdf:ID="chemicalStructure63">
+ <bp:STRUCTURE-FORMAT rdf:datatype="xs:string">
+ CML</bp:STRUCTURE-FORMAT>
+ <bp:STRUCTURE-DATA rdf:datatype="xs:string">
+ <cml> <molecule id="2-PG" title="2-phosphoglycerate"
+ dictRef="dict2-PG"> <atomArray> <atom id="2-PG-atom1"
+ elementType="C" x2="2.8208" y2="-1.4"/> <atom
+ id="2-PG-atom2" elementType="C" x2="2.8208" y2="-0.65"/>
+ <atom id="2-PG-atom3" elementType="O" x2="2.1713"
+ y2="-1.775"/> <atom id="2-PG-atom4" elementType="O"
+ x2="3.4704" y2="-1.775"/> <atom id="2-PG-atom5"
+ elementType="C" x2="2.8208" y2="0.1"/> <atom
+ id="2-PG-atom6" elementType="O" x2="3.4704" y2="0.475"/>
+ <atom id="2-PG-atom7" elementType="P" x2="1.2603"
+ y2="-0.6662"/> <atom id="2-PG-atom8" elementType="O"
+ x2="1.2502" y2="0.0671"/> <atom id="2-PG-atom9"
+ elementType="O" x2="0.452" y2="-0.652"/> <atom
+ id="2-PG-atom10" elementType="O" x2="1.2663" y2="-1.4037"/>
+ <atom id="2-PG-atom11" elementType="O" x2="2.0727"
+ y2="-0.6505"/> </atomArray> <bondArray> <bond
+ id="2-PG-bond1" atomRefs="2-PG-atom7 2-PG-atom11"
+ order="1"/> <bond id="2-PG-bond2" atomRefs="2-PG-atom7
+ 2-PG-atom10" order="1"/> <bond id="2-PG-bond3"
+ atomRefs="2-PG-atom7 2-PG-atom9" order="2"/> <bond
+ id="2-PG-bond4" atomRefs="2-PG-atom7 2-PG-atom8"
+ order="1"/> <bond id="2-PG-bond5" atomRefs="2-PG-atom5
+ 2-PG-atom6" order="1"/> <bond id="2-PG-bond6"
+ atomRefs="2-PG-atom2 2-PG-atom5" order="1"/> <bond
+ id="2-PG-bond7" atomRefs="2-PG-atom2 2-PG-atom11"
+ order="1"/> <bond id="2-PG-bond8" atomRefs="2-PG-atom1
+ 2-PG-atom4" order="2"/> <bond id="2-PG-bond9"
+ atomRefs="2-PG-atom1 2-PG-atom3" order="1"/> <bond
+ id="2-PG-bond10" atomRefs="2-PG-atom1 2-PG-atom2"
+ order="1"/> </bondArray> <formula concise="C 3 H 7 O
+ 7 P 1" formalCharge="0"/> <float title="molecularWeight"
+ units="g/mol">186.058</float> <string
+ title="smiles">C(O)(=O)C(CO)OP(=O)(O)O</string>
+ </molecule> </cml></bp:STRUCTURE-DATA>
+ </bp:chemicalStructure>
+ </bp:STRUCTURE>
+ <bp:SYNONYMS rdf:datatype="xs:string">glycerate 2-phosphate
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">2-phospho-D-glycerate
+ </bp:SYNONYMS>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref64">
+ <bp:DB rdf:datatype="xs:string">CAS</bp:DB>
+ <bp:ID rdf:datatype="xs:string">2553-59-5</bp:ID>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:SYNONYMS rdf:datatype="xs:string">2-P-D-glycerate
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">2-phosphoglyceric acid
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">2-P-glycerate
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">D-Glycerate 2-phosphate
+ </bp:SYNONYMS>
+ <bp:MOLECULAR-WEIGHT>186.05799865722656</bp:MOLECULAR-WEIGHT>
+ <bp:SYNONYMS rdf:datatype="xs:string">2-pg</bp:SYNONYMS>
+ <bp:NAME rdf:datatype="xs:string">2-phosphoglycerate</bp:NAME>
+ </bp:smallMolecule>
+ </bp:PHYSICAL-ENTITY>
+ </bp:physicalEntityParticipant>
+ </bp:RIGHT>
+ </bp:biochemicalReaction>
+ </bp:CONTROLLED>
+ <bp:SYNONYMS rdf:datatype="xs:string">D-phosphoglycerate
+ 2,3-phosphomutase</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">PGAM, cofactor independent
+ </bp:SYNONYMS>
+ <bp:DIRECTION rdf:datatype="xs:string">REVERSIBLE</bp:DIRECTION>
+ <bp:SYNONYMS rdf:datatype="xs:string">phosphoglycerate mutase,
+ BPG-independent</bp:SYNONYMS>
+ <bp:CONTROLLER>
+ <bp:physicalEntityParticipant rdf:ID="physicalEntityParticipant65">
+ <bp:PHYSICAL-ENTITY>
+ <bp:protein rdf:ID="protein66">
+ <bp:XREF>
+ <bp:relationshipXref rdf:ID="relationshipXref67">
+ <bp:RELATIONSHIP-TYPE rdf:datatype="xs:string">
+ Ortholog</bp:RELATIONSHIP-TYPE>
+ <bp:DB rdf:datatype="xs:string">EcoO157Cyc</bp:DB>
+ <bp:ID rdf:datatype="xs:string">YIBO-MONOMER</bp:ID>
+ </bp:relationshipXref>
+ </bp:XREF>
+ <bp:SYNONYMS rdf:datatype="xs:string">PgmI</bp:SYNONYMS>
+ <bp:SEQUENCE rdf:datatype="xs:string">MLVSKKPMVLVILDGYGYREEQQDNAIFSAKTPVMDALWANRPHTLIDASGLEVGLPDRQMGNSEVGHVNLGAGRIVYQDLTRLDVEIKDRAFFANPVLTGAVDKAKNAGKAVHIMGLLSAGGVHSHEDHIMAMVELAAERGAEKIYLHAFLDGRDTPPRSAESSLKKFEEKFAALGKGRVASIIGRYYAMDRDNRWDRVEKAYDLLTLAQGEFQADTAVAGLQAAYARDENDEFVKATVIRAEGQPDAAMEDGDALIFMNFRADRAREITRAFVNADFDGFARKKVVNVDFVMLTEYAADIKTAVAYPPASLVNTFGEWMAKNDKTQLRISETEKYAHVTFFFNGGVEESFKGEDRILINSPKVATYDLQPEMSSAELTEKLVAAIKSGKYDTIICNYPNGDMVGHTGVMEAAVKAVEALDHCVEEVAKAVESVGGQLLITADHG [...]
+ </bp:SEQUENCE>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref68">
+ <bp:ID rdf:datatype="xs:string">P37689</bp:ID>
+ <bp:DB rdf:datatype="xs:string">SWISS-PROT</bp:DB>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:SYNONYMS rdf:datatype="xs:string">B3612</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">GpmC</bp:SYNONYMS>
+ <bp:ORGANISM rdf:resource="#bioSource43" />
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref69">
+ <bp:DB rdf:datatype="xs:string">PIR</bp:DB>
+ <bp:ID rdf:datatype="xs:string">b3612</bp:ID>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:SYNONYMS rdf:datatype="xs:string">GpmM</bp:SYNONYMS>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref70">
+ <bp:ID rdf:datatype="xs:string">NP_418069</bp:ID>
+ <bp:DB rdf:datatype="xs:string">RefSeq</bp:DB>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:NAME rdf:datatype="xs:string">PGMI-MONOMER</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="xs:string">YibO</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">GpmI</bp:SYNONYMS>
+ </bp:protein>
+ </bp:PHYSICAL-ENTITY>
+ </bp:physicalEntityParticipant>
+ </bp:CONTROLLER>
+ <bp:NAME rdf:datatype="xs:string">phosphoglycerate mutase, cofactor
+ independent</bp:NAME>
+ <bp:COFACTOR>
+ <bp:physicalEntityParticipant rdf:ID="physicalEntityParticipant71">
+ <bp:PHYSICAL-ENTITY>
+ <bp:smallMolecule rdf:ID="smallMolecule72">
+ <bp:SYNONYMS rdf:datatype="xs:string">Mn<SUP>++</SUP>
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">Mn<SUP>+2</SUP>
+ </bp:SYNONYMS>
+ <bp:NAME rdf:datatype="xs:string">Mn2+</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="xs:string">manganese ion
+ </bp:SYNONYMS>
+ </bp:smallMolecule>
+ </bp:PHYSICAL-ENTITY>
+ <bp:STOICHIOMETRIC-COEFFICIENT>1.0</bp:STOICHIOMETRIC-COEFFICIENT>
+ </bp:physicalEntityParticipant>
+ </bp:COFACTOR>
+ <bp:SYNONYMS rdf:datatype="xs:string">iPGM</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">BPG-independent PGAM
+ </bp:SYNONYMS>
+ <bp:COMMENT rdf:datatype="xs:string">E. coli contains three
+ phosphoglycerate mutases. Two are 2,3-bisphosphoglycerate-dependent
+ enzymes, encoded by the gpmA and gpmB genes. The third is a
+ 2,3-bisphosphoglycerate-independent enzyme encoded by the pgmI
+ gene. The two cofactor-dependent enzymes are similar in sequence
+ while the cofactor-independent enzyme is unrelated. The
+ cofactor-dependent enzymes have ten times higher specific activity
+ compared to the cofactor-independent enzyme. |CITS: [99364512]|
+ </bp:COMMENT>
+ <bp:SYNONYMS rdf:datatype="xs:string">phosphoglyceromutase
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">phosphoglycerate mutase,
+ 2,3-bisphosphoglycerate-independent</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">phosphoglycerate phosphomutase
+ </bp:SYNONYMS>
+ </bp:catalysis>
+ </bp:STEP-INTERACTIONS>
+ <bp:STEP-INTERACTIONS>
+ <bp:catalysis rdf:ID="catalysis73">
+ <bp:SYNONYMS rdf:datatype="xs:string">D-phosphoglycerate
+ 2,3-phosphomutase 1</bp:SYNONYMS>
+ <bp:COMMENT rdf:datatype="xs:string">E. coli contains three
+ phosphoglycerate mutases. Two are 2,3-bisphosphoglyerate-dependent
+ enzymes, encoded by the gpmA and gpmB genes. The third is a
+ 2,3-bisphosphoglyerate-independent enzyme encoded by the pgmI gene.
+ |CITS: [99364512]|</bp:COMMENT>
+ <bp:CONTROLLER>
+ <bp:physicalEntityParticipant rdf:ID="physicalEntityParticipant74">
+ <bp:PHYSICAL-ENTITY>
+ <bp:complex rdf:ID="complex75">
+ <bp:NAME rdf:datatype="xs:string">PHOSGLYCMUTASE</bp:NAME>
+ <bp:ORGANISM rdf:resource="#bioSource43" />
+ <bp:COMPONENTS>
+ <bp:physicalEntityParticipant
+ rdf:ID="physicalEntityParticipant76">
+ <bp:STOICHIOMETRIC-COEFFICIENT>2
+ </bp:STOICHIOMETRIC-COEFFICIENT>
+ <bp:PHYSICAL-ENTITY>
+ <bp:protein rdf:ID="protein77">
+ <bp:SYNONYMS rdf:datatype="xs:string">GpmA
+ </bp:SYNONYMS>
+ <bp:NAME rdf:datatype="xs:string">GpmA</bp:NAME>
+ <bp:COMMENT rdf:datatype="xs:string">Regulation has been
+ described |CITS: [11101675]|. Transcription is regulated by
+ Fur |CITS: [11101675]|.</bp:COMMENT>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref78">
+ <bp:DB rdf:datatype="xs:string">SWISS-PROT</bp:DB>
+ <bp:ID rdf:datatype="xs:string">P31217</bp:ID>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:ORGANISM rdf:resource="#bioSource43" />
+ <bp:SYNONYMS rdf:datatype="xs:string">Pgm
+ </bp:SYNONYMS>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref79">
+ <bp:DB rdf:datatype="xs:string">SWISS-MODEL</bp:DB>
+ <bp:ID rdf:datatype="xs:string">P31217</bp:ID>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:SYNONYMS rdf:datatype="xs:string">PgmA
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">Gpm
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">B0755
+ </bp:SYNONYMS>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref80">
+ <bp:ID rdf:datatype="xs:string">b0755</bp:ID>
+ <bp:DB rdf:datatype="xs:string">PIR</bp:DB>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref81">
+ <bp:ID rdf:datatype="xs:string">NP_415276</bp:ID>
+ <bp:DB rdf:datatype="xs:string">RefSeq</bp:DB>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:SEQUENCE rdf:datatype="xs:string">MAVTKLVLVRHGESQWNKENRFTGWYDVDLSEKGVSEAKAAGKLLKEEGYSFDFAYTSVLKRAIHTLWNVLDELDQAWLPVEKSWKLNERHYGALQGLNKAETAEKYGDEQVKQWRRGFAVTPPELTKDDERYPGHDPRYAKLSEKELPLTESLALTIDRVIPYWNETILPRMKSGERVIIAAHGNSLRALVKYLDNMSEEEILELNIPTGVPLVYEFDENFKPLKRYYLGNADEIAAKAAAVANQGKAK
+ </bp:SEQUENCE>
+ </bp:protein>
+ </bp:PHYSICAL-ENTITY>
+ <bp:CELLULAR-LOCATION rdf:resource="#openControlledVocabulary40" />
+ </bp:physicalEntityParticipant>
+ </bp:COMPONENTS>
+ </bp:complex>
+ </bp:PHYSICAL-ENTITY>
+ </bp:physicalEntityParticipant>
+ </bp:CONTROLLER>
+ <bp:SYNONYMS rdf:datatype="xs:string">PGAM 1</bp:SYNONYMS>
+ <bp:NAME rdf:datatype="xs:string">phosphoglycerate mutase 1</bp:NAME>
+ <bp:CONTROLLED rdf:resource="#biochemicalReaction56" />
+ <bp:SYNONYMS rdf:datatype="xs:string">phosphoglyceromutase 1
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">BPG-dependent PGAM1
+ </bp:SYNONYMS>
+ <bp:DIRECTION rdf:datatype="xs:string">REVERSIBLE</bp:DIRECTION>
+ <bp:SYNONYMS rdf:datatype="xs:string">phosphoglycerate phosphomutase
+ 1</bp:SYNONYMS>
+ </bp:catalysis>
+ </bp:STEP-INTERACTIONS>
+ <bp:STEP-INTERACTIONS rdf:resource="#biochemicalReaction56" />
+ <bp:NEXT-STEP>
+ <bp:pathwayStep rdf:ID="pathwayStep82">
+ <bp:STEP-INTERACTIONS>
+ <bp:catalysis rdf:ID="catalysis83">
+ <bp:DIRECTION rdf:datatype="xs:string">REVERSIBLE</bp:DIRECTION>
+ <bp:SYNONYMS rdf:datatype="xs:string">2,3-diphospho-D-glycerate
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">2-phospho-D-glycerate
+ hydrolyase</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">phosphopyruvate hydratase
+ </bp:SYNONYMS>
+ <bp:NAME rdf:datatype="xs:string">enolase</bp:NAME>
+ <bp:CONTROLLED>
+ <bp:biochemicalReaction rdf:ID="biochemicalReaction84">
+ <bp:RIGHT>
+ <bp:physicalEntityParticipant
+ rdf:ID="physicalEntityParticipant85">
+ <bp:STOICHIOMETRIC-COEFFICIENT>1
+ </bp:STOICHIOMETRIC-COEFFICIENT>
+ <bp:PHYSICAL-ENTITY>
+ <bp:smallMolecule rdf:ID="smallMolecule86">
+ <bp:SYNONYMS rdf:datatype="xs:string">P-enol-pyr
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">P-enol-pyruvate
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">PEP
+ </bp:SYNONYMS>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref87">
+ <bp:ID rdf:datatype="xs:string">c00074</bp:ID>
+ <bp:DB rdf:datatype="xs:string">LIGAND</bp:DB>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:STRUCTURE>
+ <bp:chemicalStructure rdf:ID="chemicalStructure88">
+ <bp:STRUCTURE-DATA rdf:datatype="xs:string">
+ <cml> <molecule id="PHOSPHO-ENOL-PYRUVATE"
+ title="phosphoenolpyruvate"
+ dictRef="dictPHOSPHO-ENOL-PYRUVATE"> <atomArray>
+ <atom id="PHOSPHO-ENOL-PYRUVATE-atom1" elementType="O"
+ x2="-0.57576" y2="-0.15789"/> <atom
+ id="PHOSPHO-ENOL-PYRUVATE-atom2" elementType="O"
+ x2="0.24721" y2="0.33652"/> <atom
+ id="PHOSPHO-ENOL-PYRUVATE-atom3" elementType="O"
+ x2="-1.0" y2="-0.57576"/> <atom
+ id="PHOSPHO-ENOL-PYRUVATE-atom4" elementType="C"
+ x2="-0.57576" y2="0.26635"/> <atom
+ id="PHOSPHO-ENOL-PYRUVATE-atom5" elementType="C"
+ x2="-0.9075" y2="0.52791"/> <atom
+ id="PHOSPHO-ENOL-PYRUVATE-atom6" elementType="O"
+ x2="-0.15152" y2="-0.57576"/> <atom
+ id="PHOSPHO-ENOL-PYRUVATE-atom7" elementType="O"
+ x2="-0.57576" y2="-1.0"/> <atom
+ id="PHOSPHO-ENOL-PYRUVATE-atom8" elementType="O"
+ x2="-0.10686" y2="0.99681"/> <atom
+ id="PHOSPHO-ENOL-PYRUVATE-atom9" elementType="P"
+ x2="-0.57576" y2="-0.57576"/> <atom
+ id="PHOSPHO-ENOL-PYRUVATE-atom10" elementType="C"
+ x2="-0.10686" y2="0.57257"/> </atomArray>
+ <bondArray> <bond id="PHOSPHO-ENOL-PYRUVATE-bond1"
+ atomRefs="PHOSPHO-ENOL-PYRUVATE-atom10
+ PHOSPHO-ENOL-PYRUVATE-atom4" order="1"/> <bond
+ id="PHOSPHO-ENOL-PYRUVATE-bond2"
+ atomRefs="PHOSPHO-ENOL-PYRUVATE-atom8
+ PHOSPHO-ENOL-PYRUVATE-atom10" order="2"/> <bond
+ id="PHOSPHO-ENOL-PYRUVATE-bond3"
+ atomRefs="PHOSPHO-ENOL-PYRUVATE-atom7
+ PHOSPHO-ENOL-PYRUVATE-atom9" order="2"/> <bond
+ id="PHOSPHO-ENOL-PYRUVATE-bond4"
+ atomRefs="PHOSPHO-ENOL-PYRUVATE-atom6
+ PHOSPHO-ENOL-PYRUVATE-atom9" order="1"/> <bond
+ id="PHOSPHO-ENOL-PYRUVATE-bond5"
+ atomRefs="PHOSPHO-ENOL-PYRUVATE-atom5
+ PHOSPHO-ENOL-PYRUVATE-atom4" order="2"/> <bond
+ id="PHOSPHO-ENOL-PYRUVATE-bond6"
+ atomRefs="PHOSPHO-ENOL-PYRUVATE-atom4
+ PHOSPHO-ENOL-PYRUVATE-atom1" order="1"/> <bond
+ id="PHOSPHO-ENOL-PYRUVATE-bond7"
+ atomRefs="PHOSPHO-ENOL-PYRUVATE-atom3
+ PHOSPHO-ENOL-PYRUVATE-atom9" order="1"/> <bond
+ id="PHOSPHO-ENOL-PYRUVATE-bond8"
+ atomRefs="PHOSPHO-ENOL-PYRUVATE-atom2
+ PHOSPHO-ENOL-PYRUVATE-atom10" order="1"/> <bond
+ id="PHOSPHO-ENOL-PYRUVATE-bond9"
+ atomRefs="PHOSPHO-ENOL-PYRUVATE-atom1
+ PHOSPHO-ENOL-PYRUVATE-atom9" order="1"/> </bondArray>
+ <formula concise="C 3 H 5 O 6 P 1" formalCharge="0"/>
+ <float title="molecularWeight"
+ units="g/mol">168.043</float> <string
+ title="smiles">C=C(C(=O)O)OP(O)(=O)O</string>
+ </molecule> </cml></bp:STRUCTURE-DATA>
+ <bp:STRUCTURE-FORMAT rdf:datatype="xs:string">CML
+ </bp:STRUCTURE-FORMAT>
+ </bp:chemicalStructure>
+ </bp:STRUCTURE>
+ <bp:NAME rdf:datatype="xs:string">phosphoenolpyruvate</bp:NAME>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref89">
+ <bp:ID rdf:datatype="xs:string">73-89-2</bp:ID>
+ <bp:DB rdf:datatype="xs:string">CAS</bp:DB>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:MOLECULAR-WEIGHT>168.04299926757812
+ </bp:MOLECULAR-WEIGHT>
+ </bp:smallMolecule>
+ </bp:PHYSICAL-ENTITY>
+ <bp:CELLULAR-LOCATION rdf:resource="#openControlledVocabulary17" />
+ </bp:physicalEntityParticipant>
+ </bp:RIGHT>
+ <bp:SYNONYMS rdf:datatype="xs:string">ENOLASE</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">2-PHOSPHOGLYCERATE
+ DEHYDRATASE</bp:SYNONYMS>
+ <bp:RIGHT>
+ <bp:physicalEntityParticipant
+ rdf:ID="physicalEntityParticipant90">
+ <bp:CELLULAR-LOCATION rdf:resource="#openControlledVocabulary17" />
+ <bp:PHYSICAL-ENTITY>
+ <bp:smallMolecule rdf:ID="smallMolecule91">
+ <bp:SYNONYMS rdf:datatype="xs:string">hydrogen
+ oxide</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">water
+ </bp:SYNONYMS>
+ <bp:NAME rdf:datatype="xs:string">H2O</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="xs:string">H20
+ </bp:SYNONYMS>
+ <bp:MOLECULAR-WEIGHT>18.014999389648438
+ </bp:MOLECULAR-WEIGHT>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref92">
+ <bp:ID rdf:datatype="xs:string">7732-18-5</bp:ID>
+ <bp:DB rdf:datatype="xs:string">CAS</bp:DB>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:STRUCTURE>
+ <bp:chemicalStructure rdf:ID="chemicalStructure93">
+ <bp:STRUCTURE-FORMAT rdf:datatype="xs:string">CML
+ </bp:STRUCTURE-FORMAT>
+ <bp:STRUCTURE-DATA rdf:datatype="xs:string">
+ <cml> <molecule id="WATER" title="H2O"
+ dictRef="dictWATER"> <atomArray> <atom
+ id="WATER-atom1" elementType="O" x2="0.08287"
+ y2="-0.19337"/> <atom id="WATER-atom2" elementType="H"
+ x2="-1.0" y2="-0.74586"/> <atom id="WATER-atom3"
+ elementType="H" x2="0.99448" y2="-1.0"/> </atomArray>
+ <bondArray> <bond id="WATER-bond1"
+ atomRefs="WATER-atom3 WATER-atom1" order="1"/> <bond
+ id="WATER-bond2" atomRefs="WATER-atom2 WATER-atom1"
+ order="1"/> </bondArray> <formula concise="H 2 O 1"
+ formalCharge="0"/> <float title="molecularWeight"
+ units="g/mol">18.015</float> <string
+ title="smiles">[OH2]</string> </molecule> </cml>
+ </bp:STRUCTURE-DATA>
+ </bp:chemicalStructure>
+ </bp:STRUCTURE>
+ </bp:smallMolecule>
+ </bp:PHYSICAL-ENTITY>
+ <bp:STOICHIOMETRIC-COEFFICIENT>1
+ </bp:STOICHIOMETRIC-COEFFICIENT>
+ </bp:physicalEntityParticipant>
+ </bp:RIGHT>
+ <bp:LEFT rdf:resource="#physicalEntityParticipant61" />
+ <bp:NAME rdf:datatype="xs:string">2-phosphoglycerate dehydration
+ </bp:NAME>
+ <bp:DELTA-G><bp:deltaGprimeO rdf:ID="deltaG-0.4"><bp:DELTA-G-PRIME-O>0.4</bp:DELTA-G-PRIME-O></bp:deltaGprimeO></bp:DELTA-G>
+ <bp:EC-NUMBER rdf:datatype="xs:string">4.2.1.11</bp:EC-NUMBER>
+ </bp:biochemicalReaction>
+ </bp:CONTROLLED>
+ <bp:COMMENT rdf:datatype="xs:string">There are two active sites per
+ active dimer. Functionally there are many similarities between E.
+ coli enolase and other enolases studied. Thus the dependence on
+ Mg for activity and the inhibition by fluoride in the presence of
+ phosphate are quantitatively very similar for all enolases. Other
+ catalytic parameters are also similar but minor quantitative
+ distinctions indicate that E. coli enolase is more closely
+ related to yeast enolase than to enolases from vertebrate muscle.
+ The pH optimum of 8.1 is significantly higher than that for
+ vertebrate enolases and even somewhat above that of yeast and
+ plant enolases. |CITS:[72060411]|</bp:COMMENT>
+ <bp:XREF>
+ <bp:publicationXref rdf:ID="publicationXref94">
+ <bp:AUTHORS rdf:datatype="xs:string">Wold F</bp:AUTHORS>
+ <bp:YEAR>1971</bp:YEAR>
+ <bp:AUTHORS rdf:datatype="xs:string">Spring TG</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="xs:string">J Biol Chem
+ 1971;246(22);6797-802</bp:SOURCE>
+ <bp:ID rdf:datatype="xs:string">4942326</bp:ID>
+ <bp:DB rdf:datatype="xs:string">PubMed</bp:DB>
+ <bp:TITLE rdf:datatype="xs:string">The purification and
+ characterization of Escherichia coli enolase.</bp:TITLE>
+ </bp:publicationXref>
+ </bp:XREF>
+ <bp:SYNONYMS rdf:datatype="xs:string">2-phosphoglycerate
+ dehydratase</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">2-phospho-D glycerate
+ phosphotransferase</bp:SYNONYMS>
+ <bp:CONTROLLER>
+ <bp:physicalEntityParticipant
+ rdf:ID="physicalEntityParticipant95">
+ <bp:PHYSICAL-ENTITY>
+ <bp:complex rdf:ID="complex96">
+ <bp:COMMENT rdf:datatype="xs:string">The enzyme denatures in
+ the absence of Mg. When E. coli enolase was treated with EDTA
+ in attempts to remove all residual activity prior to the Mg
+ activation studies, it was found that the enzyme was unstable
+ in the absence of Mg and that substantial and irreversible
+ loss of activity was observed after very short exposure of
+ the enzyme to EDTA. |CITS:[72060411]|</bp:COMMENT>
+ <bp:COMPONENTS>
+ <bp:physicalEntityParticipant
+ rdf:ID="physicalEntityParticipant97">
+ <bp:STOICHIOMETRIC-COEFFICIENT>2
+ </bp:STOICHIOMETRIC-COEFFICIENT>
+ <bp:PHYSICAL-ENTITY>
+ <bp:protein rdf:ID="protein98">
+ <bp:SEQUENCE rdf:datatype="xs:string">MSKIVKIIGREIIDSRGNPTVEAEVHLEGGFVGMAAAPSGASTGSREALELRDGDKSRFLGKGVTKAVAAVNGPIAQALIGKDAKDQAGIDKIMIDLDGTENKSKFGANAILAVSLANAKAAAAAKGMPLYEHIAELNGTPGKYSMPVPMMNIINGGEHADNNVDIQEFMIQPVGAKTVKEAIRMGSEVFHHLAKVLKAKGMNTAVGDEGGYAPNLGSNAEALAVIAEAVKAAGYELGKDITLAMDCAASEFYKDGKYVLAGEGNKAFTSEEFTHFLEELTKQYPIVSIEDGLDESDWDGFAYQTKVLGDKIQLVGDDLFVTNTKILKEGIEKGIANSILIKFNQIGSLTETLAAIKMAKDAGYTAVISHRSGETEDATIADLAVGTAAGQIKTGSMSRSDRVAKYNQLIRIEEALGEKAPYNGRKEIKGQA
+ </bp:SEQUENCE>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref99">
+ <bp:DB rdf:datatype="xs:string">SWISS-PROT</bp:DB>
+ <bp:ID rdf:datatype="xs:string">P08324</bp:ID>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref100">
+ <bp:ID rdf:datatype="xs:string">P08324</bp:ID>
+ <bp:DB rdf:datatype="xs:string">SWISS-MODEL
+ </bp:DB>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:NAME rdf:datatype="xs:string">Eno</bp:NAME>
+ <bp:ORGANISM rdf:resource="#bioSource43" />
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref101">
+ <bp:DB rdf:datatype="xs:string">PIR</bp:DB>
+ <bp:ID rdf:datatype="xs:string">b2779</bp:ID>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:XREF>
+ <bp:relationshipXref rdf:ID="relationshipXref102">
+ <bp:ID rdf:datatype="xs:string">ENO-MONOMER
+ </bp:ID>
+ <bp:DB rdf:datatype="xs:string">EcoO157Cyc</bp:DB>
+ <bp:RELATIONSHIP-TYPE rdf:datatype="xs:string">
+ Ortholog</bp:RELATIONSHIP-TYPE>
+ </bp:relationshipXref>
+ </bp:XREF>
+ <bp:SYNONYMS rdf:datatype="xs:string">B2779
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">Eno
+ </bp:SYNONYMS>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref103">
+ <bp:ID rdf:datatype="xs:string">NP_417259</bp:ID>
+ <bp:DB rdf:datatype="xs:string">RefSeq</bp:DB>
+ </bp:unificationXref>
+ </bp:XREF>
+ </bp:protein>
+ </bp:PHYSICAL-ENTITY>
+ <bp:CELLULAR-LOCATION rdf:resource="#openControlledVocabulary17" />
+ </bp:physicalEntityParticipant>
+ </bp:COMPONENTS>
+ <bp:NAME rdf:datatype="xs:string">ENOLASE-CPLX</bp:NAME>
+ <bp:ORGANISM rdf:resource="#bioSource43" />
+ </bp:complex>
+ </bp:PHYSICAL-ENTITY>
+ </bp:physicalEntityParticipant>
+ </bp:CONTROLLER>
+ <bp:COFACTOR rdf:resource="#physicalEntityParticipant5" />
+ </bp:catalysis>
+ </bp:STEP-INTERACTIONS>
+ <bp:STEP-INTERACTIONS rdf:resource="#biochemicalReaction84" />
+ <bp:STEP-INTERACTIONS>
+ <bp:modulation rdf:ID="modulation104">
+ <bp:CONTROL-TYPE rdf:datatype="xs:string">INHIBITION-UNKMECH
+ </bp:CONTROL-TYPE>
+ <bp:CONTROLLER>
+ <bp:physicalEntityParticipant
+ rdf:ID="physicalEntityParticipant105">
+ <bp:PHYSICAL-ENTITY>
+ <bp:smallMolecule rdf:ID="smallMolecule106">
+ <bp:SYNONYMS rdf:datatype="xs:string">F</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">fluoride ion
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">fluoride</bp:SYNONYMS>
+ <bp:NAME rdf:datatype="xs:string">F-</bp:NAME>
+ </bp:smallMolecule>
+ </bp:PHYSICAL-ENTITY>
+ <bp:STOICHIOMETRIC-COEFFICIENT>1.0
+ </bp:STOICHIOMETRIC-COEFFICIENT>
+ </bp:physicalEntityParticipant>
+ </bp:CONTROLLER>
+ <bp:CONTROLLED rdf:resource="#catalysis83" />
+ </bp:modulation>
+ </bp:STEP-INTERACTIONS>
+ <bp:NEXT-STEP>
+ <bp:pathwayStep rdf:ID="pathwayStep107">
+ <bp:STEP-INTERACTIONS>
+ <bp:modulation rdf:ID="modulation108">
+ <bp:COMMENT rdf:datatype="xs:string">high concentrations of Mg+2
+ and ADP |CITS:[89228557]|</bp:COMMENT>
+ <bp:CONTROL-TYPE rdf:datatype="xs:string">INHIBITION-UNKMECH
+ </bp:CONTROL-TYPE>
+ <bp:CONTROLLER rdf:resource="#physicalEntityParticipant33" />
+ <bp:CONTROLLED>
+ <bp:catalysis rdf:ID="catalysis109">
+ <bp:COFACTOR>
+ <bp:physicalEntityParticipant
+ rdf:ID="physicalEntityParticipant110">
+ <bp:PHYSICAL-ENTITY>
+ <bp:smallMolecule rdf:ID="smallMolecule111">
+ <bp:MOLECULAR-WEIGHT>39.097999572753906
+ </bp:MOLECULAR-WEIGHT>
+ <bp:NAME rdf:datatype="xs:string">K+</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="xs:string">potassium
+ ion</bp:SYNONYMS>
+ <bp:STRUCTURE>
+ <bp:chemicalStructure rdf:ID="chemicalStructure112">
+ <bp:STRUCTURE-DATA rdf:datatype="xs:string">
+ <cml> <molecule id="K+" title="K+"
+ dictRef="dictK+"> <atomArray> <atom id="K+-atom1"
+ elementType="K" x2="-1.0" y2="-1.0" formalCharge="1"/>
+ </atomArray> <bondArray> </bondArray>
+ <formula concise="K 1" formalCharge="1"/> <float
+ title="molecularWeight" units="g/mol">39.098</float>
+ <string title="smiles">[K+1]</string>
+ </molecule> </cml></bp:STRUCTURE-DATA>
+ <bp:STRUCTURE-FORMAT rdf:datatype="xs:string">CML
+ </bp:STRUCTURE-FORMAT>
+ </bp:chemicalStructure>
+ </bp:STRUCTURE>
+ </bp:smallMolecule>
+ </bp:PHYSICAL-ENTITY>
+ <bp:STOICHIOMETRIC-COEFFICIENT>1.0
+ </bp:STOICHIOMETRIC-COEFFICIENT>
+ </bp:physicalEntityParticipant>
+ </bp:COFACTOR>
+ <bp:COFACTOR rdf:resource="#physicalEntityParticipant5" />
+ <bp:SYNONYMS rdf:datatype="xs:string">pyruvate kinase
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">phosphoenol
+ transphosphorylase</bp:SYNONYMS>
+ <bp:CONTROLLED>
+ <bp:biochemicalReaction rdf:ID="biochemicalReaction113">
+ <bp:RIGHT rdf:resource="#physicalEntityParticipant85" />
+ <bp:LEFT rdf:resource="#physicalEntityParticipant33" />
+ <bp:NAME rdf:datatype="xs:string">phosphoenolpyruvate
+ dephosphorylation</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="xs:string">pyruvate
+ phosphorylation</bp:SYNONYMS>
+ <bp:LEFT>
+ <bp:physicalEntityParticipant
+ rdf:ID="physicalEntityParticipant114">
+ <bp:CELLULAR-LOCATION rdf:resource="#openControlledVocabulary17" />
+ <bp:PHYSICAL-ENTITY>
+ <bp:smallMolecule rdf:ID="smallMolecule115">
+ <bp:SYNONYMS rdf:datatype="xs:string">pyroracemic
+ acid</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">2-oxo-propionic
+ acid</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">alpha-ketopropionic
+ acid</bp:SYNONYMS>
+ <bp:NAME rdf:datatype="xs:string">pyruvate
+ </bp:NAME>
+ <bp:SYNONYMS rdf:datatype="xs:string">2-oxopropanoate
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">2-oxopropanoic
+ acid</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">BTS
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">pyruvic
+ acid</bp:SYNONYMS>
+ <bp:STRUCTURE>
+ <bp:chemicalStructure rdf:ID="chemicalStructure116">
+ <bp:STRUCTURE-FORMAT rdf:datatype="xs:string">
+ CML</bp:STRUCTURE-FORMAT>
+ <bp:STRUCTURE-DATA rdf:datatype="xs:string">
+ <cml> <molecule id="PYRUVATE" title="pyruvate"
+ dictRef="dictPYRUVATE"> <atomArray> <atom
+ id="PYRUVATE-atom1" elementType="C" x2="0.36301"
+ y2="-0.2363"/> <atom id="PYRUVATE-atom2"
+ elementType="C" x2="-1.0" y2="-0.2774"/> <atom
+ id="PYRUVATE-atom3" elementType="O" x2="-0.34247"
+ y2="0.87329"/> <atom id="PYRUVATE-atom4"
+ elementType="C" x2="-0.34247" y2="0.10959"/> <atom
+ id="PYRUVATE-atom5" elementType="O" x2="0.36301"
+ y2="-1.0"/> <atom id="PYRUVATE-atom6"
+ elementType="O" x2="0.99658" y2="0.18836"/>
+ </atomArray> <bondArray> <bond
+ id="PYRUVATE-bond1" atomRefs="PYRUVATE-atom6
+ PYRUVATE-atom1" order="1"/> <bond
+ id="PYRUVATE-bond2" atomRefs="PYRUVATE-atom5
+ PYRUVATE-atom1" order="2"/> <bond
+ id="PYRUVATE-bond3" atomRefs="PYRUVATE-atom4
+ PYRUVATE-atom1" order="1"/> <bond
+ id="PYRUVATE-bond4" atomRefs="PYRUVATE-atom3
+ PYRUVATE-atom4" order="2"/> <bond
+ id="PYRUVATE-bond5" atomRefs="PYRUVATE-atom2
+ PYRUVATE-atom4" order="1"/> </bondArray>
+ <formula concise="C 3 H 4 O 3" formalCharge="0"/>
+ <float title="molecularWeight"
+ units="g/mol">88.063</float> <string
+ title="smiles">C(=O)(O)C(=O)C</string>
+ </molecule> </cml></bp:STRUCTURE-DATA>
+ </bp:chemicalStructure>
+ </bp:STRUCTURE>
+ <bp:SYNONYMS rdf:datatype="xs:string">acetylformic
+ acid</bp:SYNONYMS>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref117">
+ <bp:DB rdf:datatype="xs:string">UMBBD</bp:DB>
+ <bp:ID rdf:datatype="xs:string">c0159</bp:ID>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref118">
+ <bp:ID rdf:datatype="xs:string">127-17-3</bp:ID>
+ <bp:DB rdf:datatype="xs:string">CAS</bp:DB>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:MOLECULAR-WEIGHT>88.06300354003906
+ </bp:MOLECULAR-WEIGHT>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref119">
+ <bp:DB rdf:datatype="xs:string">LIGAND</bp:DB>
+ <bp:ID rdf:datatype="xs:string">c00022</bp:ID>
+ </bp:unificationXref>
+ </bp:XREF>
+ </bp:smallMolecule>
+ </bp:PHYSICAL-ENTITY>
+ <bp:STOICHIOMETRIC-COEFFICIENT>1
+ </bp:STOICHIOMETRIC-COEFFICIENT>
+ </bp:physicalEntityParticipant>
+ </bp:LEFT>
+ <bp:EC-NUMBER rdf:datatype="xs:string">2.7.1.40
+ </bp:EC-NUMBER>
+ <bp:RIGHT rdf:resource="#physicalEntityParticipant26" />
+ <bp:RIGHT rdf:resource="#physicalEntityParticipant16" />
+ </bp:biochemicalReaction>
+ </bp:CONTROLLED>
+ <bp:SYNONYMS rdf:datatype="xs:string">pyruvate
+ 2-0-phosphotransferase</bp:SYNONYMS>
+ <bp:DIRECTION rdf:datatype="xs:string">REVERSIBLE
+ </bp:DIRECTION>
+ <bp:SYNONYMS rdf:datatype="xs:string">type I pyruvate kinase
+ </bp:SYNONYMS>
+ <bp:COMMENT rdf:datatype="xs:string">Pyruvate kinase I is
+ strongly activated by fructose 1,6 bisphosphate and shows
+ sigmoid kinetics with respect to the substrate
+ phophoenolpyruvate. The dependences of the reaction rate on
+ the concentrations of phosphoenolpyruvate,
+ Mg<SUP>+2</SUP>, and Mn<SUP>+2</SUP> are sigmoid.
+ These dependences become hyperbolic on addition of fructose
+ 1,6 bisphosphate. The dependences of the reaction rate on the
+ concentration of ADP are always hyperbolic. The catalytic
+ active complex of E. coli pyruvate kinase is formed by only
+ one conformational state of the enzyme, state R1. This state
+ binds randomly the Mg<SUP>+2</SUP> free ligands ADP or
+ phosphoenolpyruvate. Thereafter, the active enzyme complex is
+ formed by binding Mg<SUP>+2</SUP>-PEP or
+ Mg<SUP>+2</SUP>ADP respectively. State R2 of coli
+ pyruvate kinase binds randomly ADP and Mg<SUP>+2</SUP>.
+ It is the only state in which Mg<SUP>+2</SUP> can bind
+ to the free enzyme. Mg<SUP>+2</SUP> is not necesary for
+ the binding of ADP, PEP an ATP. Mg<SUP>+2</SUP> can
+ inhibit either by binding to the state R2 or by lowering the
+ concentration of Mg<SUP>+2</SUP>, free ADP and PEP
+ through complex formation. ATP inhibits by virtue of three
+ effects: increase in ionic strength, complex-formation with
+ Mg<SUP>+2</SUP> when this metal ion acts as an
+ activator and binding to the state R3. However when
+ conditions are such that Mg<SUP>+2</SUP> is an
+ inhibitor, then ATP is expected to activate because of
+ complex formation with Mg<SUP>+2</SUP>. In general, one
+ can say that the ligands Mg<SUP>+2</SUP> and ATP cannot
+ be classified as inhibitors or activators because their
+ regulatory effect on the reaction rate depends on the
+ concentration of the other ligands.|CITS:[81159972]| By
+ addition of fructose-1,6-bisphosphate the sigmoid kinetics
+ with respect to phosphoenolpyruvate and Mg<SUP>+2</SUP>
+ is abolished and the activity of the enzyme is described by
+ classical saturation kinetics. This is explained by exclusive
+ binding of fructose 1,6 bisphosphate at an allosteric site of
+ the conformational state that forms the active complex.
+ Ca<SUP>+2</SUP> is an activator of the enzyme at low
+ Mg<SUP>+2</SUP> and Ca<SUP>+2</SUP>
+ concentrations; otherwise it is an inhibitor. These effects
+ can be understood by assuming that Ca<SUP>+2</SUP> has
+ the same binding properties as Mg<SUP>+2</SUP>,
+ although it does not allow a catalytic
+ turnover.|CITS:[83282602]| The enzyme requires both bivalent
+ and monovalent cations. |CITS: [90336973]| </bp:COMMENT>
+ <bp:NAME rdf:datatype="xs:string">pyruvate kinase I</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="xs:string">pyruvate kinase F
+ </bp:SYNONYMS>
+ <bp:CONTROLLER>
+ <bp:physicalEntityParticipant
+ rdf:ID="physicalEntityParticipant120">
+ <bp:PHYSICAL-ENTITY>
+ <bp:complex rdf:ID="complex121">
+ <bp:NAME rdf:datatype="xs:string">PKI-COMPLEX
+ </bp:NAME>
+ <bp:COMPONENTS>
+ <bp:physicalEntityParticipant
+ rdf:ID="physicalEntityParticipant122">
+ <bp:STOICHIOMETRIC-COEFFICIENT>4
+ </bp:STOICHIOMETRIC-COEFFICIENT>
+ <bp:PHYSICAL-ENTITY>
+ <bp:protein rdf:ID="protein123">
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref124">
+ <bp:DB rdf:datatype="xs:string">PIR</bp:DB>
+ <bp:ID rdf:datatype="xs:string">b1676</bp:ID>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref125">
+ <bp:DB rdf:datatype="xs:string">SWISS-PROT
+ </bp:DB>
+ <bp:ID rdf:datatype="xs:string">P14178</bp:ID>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref126">
+ <bp:ID rdf:datatype="xs:string">1E0T</bp:ID>
+ <bp:DB rdf:datatype="xs:string">PDB</bp:DB>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:SYNONYMS rdf:datatype="xs:string">B1676
+ </bp:SYNONYMS>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref127">
+ <bp:ID rdf:datatype="xs:string">NP_416191
+ </bp:ID>
+ <bp:DB rdf:datatype="xs:string">RefSeq</bp:DB>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:SEQUENCE rdf:datatype="xs:string">MKKTKIVCTIGPKTESEEMLAKMLDAGMNVMRLNFSHGDYAEHGQRIQNLRNVMSKTGKTAAILLDTKGPEIRTMKLEGGNDVSLKAGQTFTFTTDKSVIGNSEMVAVTYEGFTTDLSVGNTVLVDDGLIGMEVTAIEGNKVICKVLNNGDLGENKGVNLPGVSIALPALAEKDKQDLIFGCEQGVDFVAASFIRKRSDVIEIREHLKAHGGENIHIISKIENQEGLNNFDEILEASDGIMVARGDLGVEIPVEEVIFAQKMMIEKCIRARKVVITATQMLDSMIKNPRPTRAEAGDVANAILDGTDAVMLSGESAKGKYPLEAVSIMATICERTDRVMNSRLEFNNDNRKLRITEAVCRGAVETAEKLDAPLIVVATQGGKSARAVRKYFPDATILALTTNEKTAHQLVLSKGVVPQLVKEITSTDDFYRLGKEL [...]
+ </bp:SEQUENCE>
+ <bp:COMMENT rdf:datatype="xs:string">Type I pyruvate
+ kinase is made up of 522 amino acids. Neither type I
+ nor II contains tryptophan. The two forms of the
+ enzyme, I and II are different
+ proteins.|CITS:[83114522]| Pyruvate kinase F was
+ previously referred to as pyruvate kinase B, now as I
+ |CITS:[84029179]| A free N-terminal amino acid can be
+ detected in both forms of pyruvate kinase it
+ corresponds to methionine for type I and serine for
+ type II.|CITS:[83114522]| Comparison with the known
+ primary structures shows that bacterial enzymes lack
+ a substantial portion of the N-terminal sequence with
+ respect to pyruvate kinases from vertebrates.
+ |CITS:[91315755]|</bp:COMMENT>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref128">
+ <bp:ID rdf:datatype="xs:string">P14178</bp:ID>
+ <bp:DB rdf:datatype="xs:string">SWISS-MODEL
+ </bp:DB>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:NAME rdf:datatype="xs:string">pyruvate
+ kinase I monomer</bp:NAME>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref129">
+ <bp:ID rdf:datatype="xs:string">1E0U</bp:ID>
+ <bp:DB rdf:datatype="xs:string">PDB</bp:DB>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:SYNONYMS rdf:datatype="xs:string">PykF
+ </bp:SYNONYMS>
+ <bp:ORGANISM rdf:resource="#bioSource43" />
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref130">
+ <bp:ID rdf:datatype="xs:string">1PKY</bp:ID>
+ <bp:DB rdf:datatype="xs:string">PDB</bp:DB>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:XREF>
+ <bp:relationshipXref rdf:ID="relationshipXref131">
+ <bp:DB rdf:datatype="xs:string">EcoO157Cyc
+ </bp:DB>
+ <bp:RELATIONSHIP-TYPE
+ rdf:datatype="xs:string">Ortholog
+ </bp:RELATIONSHIP-TYPE>
+ <bp:ID rdf:datatype="xs:string">PYKF-MONOMER
+ </bp:ID>
+ </bp:relationshipXref>
+ </bp:XREF>
+ </bp:protein>
+ </bp:PHYSICAL-ENTITY>
+ <bp:CELLULAR-LOCATION rdf:resource="#openControlledVocabulary40" />
+ </bp:physicalEntityParticipant>
+ </bp:COMPONENTS>
+ <bp:ORGANISM rdf:resource="#bioSource43" />
+ <bp:COMMENT rdf:datatype="xs:string">Pyruvate
+ kinase I and pyruvate kinase II differ in physical and
+ chemical properties as well as in their kinetic behavior.
+ Although the two forms are under independent genetic
+ control they do coexist in a wide range of nutritional
+ and metabolic states. The two forms are not
+ interconvertible. Both show positive cooperative effects
+ with respect to the substrate
+ phosphoenolpyruvate.|CITS:[83114522]| The enzyme has a
+ low nucleotide specificity and the 5'-diphosphates of
+ guanosine, inosine, uridine and cytidine can all serve as
+ phospho acceptors.|CITS: [90336973]| Form I from E coli
+ unlike form II is remarkably stable. |CITS:[91315755]|
+ </bp:COMMENT>
+ </bp:complex>
+ </bp:PHYSICAL-ENTITY>
+ </bp:physicalEntityParticipant>
+ </bp:CONTROLLER>
+ <bp:SYNONYMS rdf:datatype="xs:string">phosphoenolpyruvate
+ kinase</bp:SYNONYMS>
+ <bp:COFACTOR rdf:resource="#physicalEntityParticipant71" />
+ </bp:catalysis>
+ </bp:CONTROLLED>
+ </bp:modulation>
+ </bp:STEP-INTERACTIONS>
+ <bp:STEP-INTERACTIONS>
+ <bp:modulation rdf:ID="modulation132">
+ <bp:CONTROL-TYPE rdf:datatype="xs:string">ACTIVATION-UNKMECH
+ </bp:CONTROL-TYPE>
+ <bp:CONTROLLER>
+ <bp:physicalEntityParticipant
+ rdf:ID="physicalEntityParticipant133">
+ <bp:STOICHIOMETRIC-COEFFICIENT>1.0
+ </bp:STOICHIOMETRIC-COEFFICIENT>
+ <bp:PHYSICAL-ENTITY>
+ <bp:smallMolecule rdf:ID="smallMolecule134">
+ <bp:MOLECULAR-WEIGHT>40.08000183105469</bp:MOLECULAR-WEIGHT>
+ <bp:STRUCTURE>
+ <bp:chemicalStructure rdf:ID="chemicalStructure135">
+ <bp:STRUCTURE-DATA rdf:datatype="xs:string">
+ <cml> <molecule id="CA+2" title="Ca2+"
+ dictRef="dictCA+2"> <atomArray> <atom
+ id="CA+2-atom1" elementType="CA" x2="-1.0" y2="-1.0"
+ formalCharge="2"/> </atomArray> <bondArray>
+ </bondArray> <formula concise="CA 1"
+ formalCharge="2"/> <float title="molecularWeight"
+ units="g/mol">40.08</float> <string
+ title="smiles">[Ca+2]</string> </molecule>
+ </cml></bp:STRUCTURE-DATA>
+ <bp:STRUCTURE-FORMAT rdf:datatype="xs:string">CML
+ </bp:STRUCTURE-FORMAT>
+ </bp:chemicalStructure>
+ </bp:STRUCTURE>
+ <bp:SYNONYMS rdf:datatype="xs:string">calcium
+ ion</bp:SYNONYMS>
+ <bp:NAME rdf:datatype="xs:string">Ca2+</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="xs:string">Ca<SUP>++</SUP>
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">Ca<SUP>+2</SUP>
+ </bp:SYNONYMS>
+ </bp:smallMolecule>
+ </bp:PHYSICAL-ENTITY>
+ </bp:physicalEntityParticipant>
+ </bp:CONTROLLER>
+ <bp:COMMENT rdf:datatype="xs:string">An activator only at low
+ Mg<SUP>+2</SUP> and Ca<SUP>+2</SUP> concentrations,
+ otherwise it is an inhibitor. |CITS: [83282602]| </bp:COMMENT>
+ <bp:CONTROLLED rdf:resource="#catalysis109" />
+ </bp:modulation>
+ </bp:STEP-INTERACTIONS>
+ <bp:STEP-INTERACTIONS rdf:resource="#biochemicalReaction113" />
+ <bp:STEP-INTERACTIONS>
+ <bp:modulation rdf:ID="modulation136">
+ <bp:CONTROL-TYPE rdf:datatype="xs:string">INHIBITION-UNKMECH
+ </bp:CONTROL-TYPE>
+ <bp:CONTROLLER rdf:resource="#physicalEntityParticipant133" />
+ <bp:COMMENT rdf:datatype="xs:string">high concentrations of Mg+2
+ and ADP |CITS:[89228557]|</bp:COMMENT>
+ <bp:CONTROLLED rdf:resource="#catalysis109" />
+ </bp:modulation>
+ </bp:STEP-INTERACTIONS>
+ <bp:STEP-INTERACTIONS>
+ <bp:catalysis rdf:ID="catalysis137">
+ <bp:COFACTOR rdf:resource="#physicalEntityParticipant71" />
+ <bp:COMMENT rdf:datatype="xs:string">Pyruvate kinase II displays
+ only limited cooperativity amoung phosphoenolpyruvate binding
+ sites and is allosterically activated by AMP and several sugar
+ phosphates |CITS:[91315755]| The enzyme requires both bivalent
+ and monovalent cations. |CITS: [90336973]|</bp:COMMENT>
+ <bp:SYNONYMS rdf:datatype="xs:string">type II pyruvate kinase
+ </bp:SYNONYMS>
+ <bp:CONTROLLED rdf:resource="#biochemicalReaction113" />
+ <bp:NAME rdf:datatype="xs:string">pyruvate kinase II</bp:NAME>
+ <bp:CONTROLLER>
+ <bp:physicalEntityParticipant
+ rdf:ID="physicalEntityParticipant138">
+ <bp:PHYSICAL-ENTITY>
+ <bp:complex rdf:ID="complex139">
+ <bp:COMPONENTS>
+ <bp:physicalEntityParticipant
+ rdf:ID="physicalEntityParticipant140">
+ <bp:PHYSICAL-ENTITY>
+ <bp:protein rdf:ID="protein141">
+ <bp:XREF>
+ <bp:relationshipXref rdf:ID="relationshipXref142">
+ <bp:ID rdf:datatype="xs:string">PYKA-MONOMER
+ </bp:ID>
+ <bp:RELATIONSHIP-TYPE
+ rdf:datatype="xs:string">Ortholog</bp:RELATIONSHIP-TYPE>
+ <bp:DB rdf:datatype="xs:string">EcoO157Cyc
+ </bp:DB>
+ </bp:relationshipXref>
+ </bp:XREF>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref143">
+ <bp:DB rdf:datatype="xs:string">RefSeq</bp:DB>
+ <bp:ID rdf:datatype="xs:string">NP_416368
+ </bp:ID>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:NAME rdf:datatype="xs:string">pyruvate
+ kinase II monomer</bp:NAME>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref144">
+ <bp:ID rdf:datatype="xs:string">P21599</bp:ID>
+ <bp:DB rdf:datatype="xs:string">SWISS-PROT
+ </bp:DB>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:SEQUENCE rdf:datatype="xs:string">MSRRLRRTKIVTTLGPATDRDNNLEKVIAAGANVVRMNFSHGSPEDHKMRADKVREIAAKLGRHVAILGDLQGPKIRVSTFKEGKVFLNIGDKFLLDANLGKGEGDKEKVGIDYKGLPADVVPGDILLLDDGRVQLKVLEVQGMKVFTEVTVGGPLSNNKGINKLGGGLSAEALTEKDKADIKTAALIGVDYLAVSFPRCGEDLNYARRLARDAGCDAKIVAKVERAEAVCSQDAMDDIILASDVVMVARGDLGVEIGDPELVGIQKALIRRARQLNRAVITATQMMESMITNPMPTRAEVMDVANAVLDGTDAVMLSAETAAGQYPSETVAAMARVCLGAEKIPSINVSKHRLDVQFDNVEEAIAMSAMYAANHLKGVTAIITMTESGRTALMTSRISSGLPIFAMSRHERTLNLTALYRGVTPVHFDSANDGVAAA [...]
+ </bp:SEQUENCE>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref145">
+ <bp:ID rdf:datatype="xs:string">b1854</bp:ID>
+ <bp:DB rdf:datatype="xs:string">PIR</bp:DB>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:SYNONYMS rdf:datatype="xs:string">PykA
+ </bp:SYNONYMS>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref146">
+ <bp:ID rdf:datatype="xs:string">P21599</bp:ID>
+ <bp:DB rdf:datatype="xs:string">SWISS-MODEL
+ </bp:DB>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:SYNONYMS rdf:datatype="xs:string">B1854
+ </bp:SYNONYMS>
+ <bp:ORGANISM rdf:resource="#bioSource43" />
+ <bp:COMMENT rdf:datatype="xs:string">There
+ are 2 genes, pykA and pykF, for 2 isozymes</bp:COMMENT>
+ </bp:protein>
+ </bp:PHYSICAL-ENTITY>
+ <bp:STOICHIOMETRIC-COEFFICIENT>4
+ </bp:STOICHIOMETRIC-COEFFICIENT>
+ <bp:CELLULAR-LOCATION rdf:resource="#openControlledVocabulary40" />
+ </bp:physicalEntityParticipant>
+ </bp:COMPONENTS>
+ <bp:NAME rdf:datatype="xs:string">PKII-CPLX</bp:NAME>
+ <bp:ORGANISM rdf:resource="#bioSource43" />
+ </bp:complex>
+ </bp:PHYSICAL-ENTITY>
+ </bp:physicalEntityParticipant>
+ </bp:CONTROLLER>
+ <bp:DIRECTION rdf:datatype="xs:string">REVERSIBLE
+ </bp:DIRECTION>
+ <bp:SYNONYMS rdf:datatype="xs:string">pyruvate kinase A
+ </bp:SYNONYMS>
+ <bp:COFACTOR rdf:resource="#physicalEntityParticipant5" />
+ <bp:COFACTOR rdf:resource="#physicalEntityParticipant110" />
+ </bp:catalysis>
+ </bp:STEP-INTERACTIONS>
+ <bp:STEP-INTERACTIONS>
+ <bp:modulation rdf:ID="modulation147">
+ <bp:CONTROL-TYPE rdf:datatype="xs:string">INHIBITION-UNKMECH
+ </bp:CONTROL-TYPE>
+ <bp:COMMENT rdf:datatype="xs:string">high concentrations of Mg+2
+ and ADP |CITS:[89228557]|</bp:COMMENT>
+ <bp:CONTROLLER>
+ <bp:physicalEntityParticipant
+ rdf:ID="physicalEntityParticipant148">
+ <bp:STOICHIOMETRIC-COEFFICIENT>1.0
+ </bp:STOICHIOMETRIC-COEFFICIENT>
+ <bp:PHYSICAL-ENTITY>
+ <bp:smallMolecule rdf:ID="smallMolecule149">
+ <bp:SYNONYMS rdf:datatype="xs:string">succinyl-S-coenzyme-A
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">succ-S-coenzyme-A
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">suc-coa
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">succ-CoA
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">succ-coenzyme-A
+ </bp:SYNONYMS>
+ <bp:STRUCTURE>
+ <bp:chemicalStructure rdf:ID="chemicalStructure150">
+ <bp:STRUCTURE-FORMAT rdf:datatype="xs:string">CML
+ </bp:STRUCTURE-FORMAT>
+ <bp:STRUCTURE-DATA rdf:datatype="xs:string">
+ <cml> <molecule id="SUC-COA" title="succinyl-CoA"
+ dictRef="dictSUC-COA"> <atomArray> <atom
+ id="SUC-COA-atom1" elementType="C" x2="0.88294"
+ y2="-0.23077"/> <atom id="SUC-COA-atom2"
+ elementType="N" x2="-1.0" y2="-0.14381"/> <atom
+ id="SUC-COA-atom3" elementType="C" x2="0.8194"
+ y2="-0.35452"/> <atom id="SUC-COA-atom4"
+ elementType="C" x2="-0.60535" y2="0.11371"/> <atom
+ id="SUC-COA-atom5" elementType="N" x2="0.60535"
+ y2="0.05017"/> <atom id="SUC-COA-atom6"
+ elementType="O" x2="-0.86622" y2="0.11371"/> <atom
+ id="SUC-COA-atom7" elementType="P" x2="0.8194"
+ y2="-0.82274"/> <atom id="SUC-COA-atom8"
+ elementType="C" x2="-0.86622" y2="-0.06355"/> <atom
+ id="SUC-COA-atom9" elementType="O" x2="0.8194"
+ y2="-0.46154"/> <atom id="SUC-COA-atom10"
+ elementType="C" x2="0.98662" y2="0.21405"/> <atom
+ id="SUC-COA-atom11" elementType="O" x2="0.8194"
+ y2="-1.0"/> <atom id="SUC-COA-atom12" elementType="N"
+ x2="0.45151" y2="0.29097"/> <atom id="SUC-COA-atom13"
+ elementType="C" x2="0.22408" y2="-0.57525"/> <atom
+ id="SUC-COA-atom14" elementType="O" x2="0.71572"
+ y2="-0.14047"/> <atom id="SUC-COA-atom15"
+ elementType="O" x2="-0.66221" y2="-0.41472"/> <atom
+ id="SUC-COA-atom16" elementType="N" x2="-0.52843"
+ y2="-0.6689"/> <atom id="SUC-COA-atom17"
+ elementType="O" x2="-0.31773" y2="-0.04013"/> <atom
+ id="SUC-COA-atom18" elementType="C" x2="0.08696"
+ y2="-0.67559"/> <atom id="SUC-COA-atom19"
+ elementType="O" x2="0.48829" y2="-0.39799"/> <atom
+ id="SUC-COA-atom20" elementType="C" x2="0.48829"
+ y2="-0.57525"/> <atom id="SUC-COA-atom21"
+ elementType="O" x2="0.21405" y2="0.13712"/> <atom
+ id="SUC-COA-atom22" elementType="C" x2="-0.66221"
+ y2="-0.59197"/> <atom id="SUC-COA-atom23"
+ elementType="H" x2="0.8194" y2="-0.24749"/> <atom
+ id="SUC-COA-atom24" elementType="C" x2="0.58863"
+ y2="0.37793"/> <atom id="SUC-COA-atom25"
+ elementType="O" x2="0.21405" y2="-0.21739"/> <atom
+ id="SUC-COA-atom26" elementType="C" x2="-0.60535"
+ y2="-0.06355"/> <atom id="SUC-COA-atom27"
+ elementType="N" x2="0.88294" y2="0.05686"/> <atom
+ id="SUC-COA-atom28" elementType="C" x2="-0.60535"
+ y2="-0.2408"/> <atom id="SUC-COA-atom29"
+ elementType="O" x2="0.8194" y2="-0.62542"/> <atom
+ id="SUC-COA-atom30" elementType="O" x2="-0.11371"
+ y2="0.13712"/> <atom id="SUC-COA-atom31"
+ elementType="H" x2="0.61873" y2="-0.24749"/> <atom
+ id="SUC-COA-atom32" elementType="C" x2="-0.47492"
+ y2="-0.14381"/> <atom id="SUC-COA-atom33"
+ elementType="O" x2="0.04013" y2="-0.04013"/> <atom
+ id="SUC-COA-atom34" elementType="O" x2="-0.11371"
+ y2="-0.21739"/> <atom id="SUC-COA-atom35"
+ elementType="O" x2="0.99666" y2="-0.82274"/> <atom
+ id="SUC-COA-atom36" elementType="S" x2="-0.06355"
+ y2="-0.56522"/> <atom id="SUC-COA-atom37"
+ elementType="C" x2="-0.20401" y2="-0.6689"/> <atom
+ id="SUC-COA-atom38" elementType="O" x2="0.64548"
+ y2="-0.65552"/> <atom id="SUC-COA-atom39"
+ elementType="C" x2="0.7291" y2="0.29766"/> <atom
+ id="SUC-COA-atom40" elementType="C" x2="-0.35452"
+ y2="-0.57525"/> <atom id="SUC-COA-atom41"
+ elementType="O" x2="0.08696" y2="-0.85284"/> <atom
+ id="SUC-COA-atom42" elementType="C" x2="0.35786"
+ y2="-0.66555"/> <atom id="SUC-COA-atom43"
+ elementType="O" x2="0.38462" y2="-0.04013"/> <atom
+ id="SUC-COA-atom44" elementType="C" x2="-0.86957"
+ y2="-0.67559"/> <atom id="SUC-COA-atom45"
+ elementType="N" x2="0.87291" y2="0.3612"/> <atom
+ id="SUC-COA-atom46" elementType="H" x2="0.55184"
+ y2="-0.33779"/> <atom id="SUC-COA-atom47"
+ elementType="P" x2="0.21405" y2="-0.04013"/> <atom
+ id="SUC-COA-atom48" elementType="C" x2="0.7291"
+ y2="0.14047"/> <atom id="SUC-COA-atom49"
+ elementType="O" x2="-0.74916" y2="-0.32107"/> <atom
+ id="SUC-COA-atom50" elementType="P" x2="-0.11371"
+ y2="-0.04013"/> <atom id="SUC-COA-atom51"
+ elementType="C" x2="0.45151" y2="0.13378"/> <atom
+ id="SUC-COA-atom52" elementType="C" x2="-1.0"
+ y2="-0.59197"/> <atom id="SUC-COA-atom53"
+ elementType="C" x2="-0.74916" y2="-0.14381"/> <atom
+ id="SUC-COA-atom54" elementType="C" x2="0.55184"
+ y2="-0.04013"/> <atom id="SUC-COA-atom55"
+ elementType="C" x2="0.55184" y2="-0.23077"/> <atom
+ id="SUC-COA-atom56" elementType="O" x2="0.64214"
+ y2="-0.82274"/> <atom id="SUC-COA-atom57"
+ elementType="C" x2="0.61873" y2="-0.35452"/> <atom
+ id="SUC-COA-atom58" elementType="N" x2="0.58863"
+ y2="0.55518"/> <atom id="SUC-COA-atom59"
+ elementType="H" x2="0.88294" y2="-0.33779"/>
+ </atomArray> <bondArray> <bond
+ id="SUC-COA-bond1" atomRefs="SUC-COA-atom59
+ SUC-COA-atom1" order="1"/> <bond id="SUC-COA-bond2"
+ atomRefs="SUC-COA-atom58 SUC-COA-atom24" order="1"/>
+ <bond id="SUC-COA-bond3" atomRefs="SUC-COA-atom57
+ SUC-COA-atom29" order="1"/> <bond id="SUC-COA-bond4"
+ atomRefs="SUC-COA-atom57 SUC-COA-atom3" order="1"/>
+ <bond id="SUC-COA-bond5" atomRefs="SUC-COA-atom56
+ SUC-COA-atom7" order="2"/> <bond id="SUC-COA-bond6"
+ atomRefs="SUC-COA-atom55 SUC-COA-atom14" order="1"/>
+ <bond id="SUC-COA-bond7" atomRefs="SUC-COA-atom55
+ SUC-COA-atom57" order="1"/> <bond id="SUC-COA-bond8"
+ atomRefs="SUC-COA-atom54 SUC-COA-atom55" order="1"/>
+ <bond id="SUC-COA-bond9" atomRefs="SUC-COA-atom53
+ SUC-COA-atom26" order="1"/> <bond id="SUC-COA-bond10"
+ atomRefs="SUC-COA-atom52 SUC-COA-atom2" order="1"/>
+ <bond id="SUC-COA-bond11" atomRefs="SUC-COA-atom51
+ SUC-COA-atom5" order="A"/> <bond id="SUC-COA-bond12"
+ atomRefs="SUC-COA-atom50 SUC-COA-atom33" order="1"/>
+ <bond id="SUC-COA-bond13" atomRefs="SUC-COA-atom49
+ SUC-COA-atom53" order="1"/> <bond id="SUC-COA-bond14"
+ atomRefs="SUC-COA-atom27 SUC-COA-atom48" order="A"/>
+ <bond id="SUC-COA-bond15" atomRefs="SUC-COA-atom47
+ SUC-COA-atom43" order="1"/> <bond id="SUC-COA-bond16"
+ atomRefs="SUC-COA-atom46 SUC-COA-atom55" order="1"/>
+ <bond id="SUC-COA-bond17" atomRefs="SUC-COA-atom45
+ SUC-COA-atom10" order="A"/> <bond id="SUC-COA-bond18"
+ atomRefs="SUC-COA-atom39 SUC-COA-atom45" order="A"/>
+ <bond id="SUC-COA-bond19" atomRefs="SUC-COA-atom44
+ SUC-COA-atom52" order="1"/> <bond id="SUC-COA-bond20"
+ atomRefs="SUC-COA-atom43 SUC-COA-atom54" order="1"/>
+ <bond id="SUC-COA-bond21" atomRefs="SUC-COA-atom42
+ SUC-COA-atom13" order="1"/> <bond id="SUC-COA-bond22"
+ atomRefs="SUC-COA-atom41 SUC-COA-atom18" order="2"/>
+ <bond id="SUC-COA-bond23" atomRefs="SUC-COA-atom40
+ SUC-COA-atom16" order="1"/> <bond id="SUC-COA-bond24"
+ atomRefs="SUC-COA-atom48 SUC-COA-atom39" order="A"/>
+ <bond id="SUC-COA-bond25" atomRefs="SUC-COA-atom38
+ SUC-COA-atom20" order="1"/> <bond id="SUC-COA-bond26"
+ atomRefs="SUC-COA-atom37 SUC-COA-atom40" order="1"/>
+ <bond id="SUC-COA-bond27" atomRefs="SUC-COA-atom36
+ SUC-COA-atom37" order="1"/> <bond id="SUC-COA-bond28"
+ atomRefs="SUC-COA-atom35 SUC-COA-atom7" order="1"/>
+ <bond id="SUC-COA-bond29" atomRefs="SUC-COA-atom34
+ SUC-COA-atom50" order="1"/> <bond id="SUC-COA-bond30"
+ atomRefs="SUC-COA-atom33 SUC-COA-atom47" order="1"/>
+ <bond id="SUC-COA-bond31" atomRefs="SUC-COA-atom32
+ SUC-COA-atom17" order="1"/> <bond id="SUC-COA-bond32"
+ atomRefs="SUC-COA-atom31 SUC-COA-atom57" order="1"/>
+ <bond id="SUC-COA-bond33" atomRefs="SUC-COA-atom30
+ SUC-COA-atom50" order="2"/> <bond id="SUC-COA-bond34"
+ atomRefs="SUC-COA-atom28 SUC-COA-atom26" order="1"/>
+ <bond id="SUC-COA-bond35" atomRefs="SUC-COA-atom26
+ SUC-COA-atom32" order="1"/> <bond id="SUC-COA-bond36"
+ atomRefs="SUC-COA-atom25 SUC-COA-atom47" order="1"/>
+ <bond id="SUC-COA-bond37" atomRefs="SUC-COA-atom39
+ SUC-COA-atom24" order="A"/> <bond id="SUC-COA-bond38"
+ atomRefs="SUC-COA-atom24 SUC-COA-atom12" order="A"/>
+ <bond id="SUC-COA-bond39" atomRefs="SUC-COA-atom23
+ SUC-COA-atom3" order="1"/> <bond id="SUC-COA-bond40"
+ atomRefs="SUC-COA-atom22 SUC-COA-atom44" order="1"/>
+ <bond id="SUC-COA-bond41" atomRefs="SUC-COA-atom21
+ SUC-COA-atom47" order="2"/> <bond id="SUC-COA-bond42"
+ atomRefs="SUC-COA-atom20 SUC-COA-atom42" order="1"/>
+ <bond id="SUC-COA-bond43" atomRefs="SUC-COA-atom19
+ SUC-COA-atom20" order="2"/> <bond id="SUC-COA-bond44"
+ atomRefs="SUC-COA-atom18 SUC-COA-atom36" order="1"/>
+ <bond id="SUC-COA-bond45" atomRefs="SUC-COA-atom17
+ SUC-COA-atom50" order="1"/> <bond id="SUC-COA-bond46"
+ atomRefs="SUC-COA-atom16 SUC-COA-atom22" order="1"/>
+ <bond id="SUC-COA-bond47" atomRefs="SUC-COA-atom15
+ SUC-COA-atom22" order="2"/> <bond id="SUC-COA-bond48"
+ atomRefs="SUC-COA-atom14 SUC-COA-atom1" order="1"/>
+ <bond id="SUC-COA-bond49" atomRefs="SUC-COA-atom13
+ SUC-COA-atom18" order="1"/> <bond id="SUC-COA-bond50"
+ atomRefs="SUC-COA-atom12 SUC-COA-atom51" order="A"/>
+ <bond id="SUC-COA-bond51" atomRefs="SUC-COA-atom11
+ SUC-COA-atom7" order="1"/> <bond id="SUC-COA-bond52"
+ atomRefs="SUC-COA-atom10 SUC-COA-atom27" order="A"/>
+ <bond id="SUC-COA-bond53" atomRefs="SUC-COA-atom9
+ SUC-COA-atom3" order="1"/> <bond id="SUC-COA-bond54"
+ atomRefs="SUC-COA-atom8 SUC-COA-atom53" order="1"/>
+ <bond id="SUC-COA-bond55" atomRefs="SUC-COA-atom7
+ SUC-COA-atom29" order="1"/> <bond id="SUC-COA-bond56"
+ atomRefs="SUC-COA-atom6 SUC-COA-atom8" order="2"/>
+ <bond id="SUC-COA-bond57" atomRefs="SUC-COA-atom5
+ SUC-COA-atom48" order="A"/> <bond id="SUC-COA-bond58"
+ atomRefs="SUC-COA-atom4 SUC-COA-atom26" order="1"/>
+ <bond id="SUC-COA-bond59" atomRefs="SUC-COA-atom2
+ SUC-COA-atom8" order="1"/> <bond id="SUC-COA-bond60"
+ atomRefs="SUC-COA-atom1 SUC-COA-atom27" order="1"/>
+ <bond id="SUC-COA-bond61" atomRefs="SUC-COA-atom1
+ SUC-COA-atom3" order="1"/> </bondArray> <formula
+ concise="C 25 H 40 N 7 O 19 P 3 S 1" formalCharge="0"/>
+ <float title="molecularWeight"
+ units="g/mol">867.608</float> <string
+ title="smiles">[CH]3(n1(c2(c(nc1)c(N)ncn2)))(O[CH]([CH]([CH](O)3)OP(O)(=O)O)COP(=O)(O)OP(=O)(O)OCC(C)(C)C(O)C(=O)NCCC(=O)NCCSC(=O)CCC(O)=O)</string>
+ <string title="systematicName">Coenzyme A, S-(hydrogen
+ butanedioate)</string> </molecule> </cml>
+ </bp:STRUCTURE-DATA>
+ </bp:chemicalStructure>
+ </bp:STRUCTURE>
+ <bp:NAME rdf:datatype="xs:string">succinyl-CoA</bp:NAME>
+ <bp:MOLECULAR-WEIGHT>867.6079711914062</bp:MOLECULAR-WEIGHT>
+ <bp:SYNONYMS rdf:datatype="xs:string">suc-co-A
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">succ-S-CoA
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">succinylcoenzyme-A
+ </bp:SYNONYMS>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref151">
+ <bp:DB rdf:datatype="xs:string">CAS</bp:DB>
+ <bp:ID rdf:datatype="xs:string">604-98-8</bp:ID>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:SYNONYMS rdf:datatype="xs:string">succinyl-S-CoA
+ </bp:SYNONYMS>
+ </bp:smallMolecule>
+ </bp:PHYSICAL-ENTITY>
+ </bp:physicalEntityParticipant>
+ </bp:CONTROLLER>
+ <bp:CONTROLLED rdf:resource="#catalysis109" />
+ </bp:modulation>
+ </bp:STEP-INTERACTIONS>
+ <bp:STEP-INTERACTIONS>
+ <bp:modulation rdf:ID="modulation152">
+ <bp:CONTROLLER rdf:resource="#physicalEntityParticipant29" />
+ <bp:CONTROL-TYPE rdf:datatype="xs:string">ACTIVATION-ALLOSTERIC
+ </bp:CONTROL-TYPE>
+ <bp:CONTROLLED rdf:resource="#catalysis109" />
+ </bp:modulation>
+ </bp:STEP-INTERACTIONS>
+ <bp:STEP-INTERACTIONS rdf:resource="#catalysis109" />
+ <bp:STEP-INTERACTIONS>
+ <bp:modulation rdf:ID="modulation153">
+ <bp:CONTROLLER>
+ <bp:physicalEntityParticipant
+ rdf:ID="physicalEntityParticipant154">
+ <bp:PHYSICAL-ENTITY>
+ <bp:smallMolecule rdf:ID="smallMolecule155">
+ <bp:SYNONYMS rdf:datatype="xs:string">adenylate
+ </bp:SYNONYMS>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref156">
+ <bp:DB rdf:datatype="xs:string">CAS</bp:DB>
+ <bp:ID rdf:datatype="xs:string">61-19-8</bp:ID>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:SYNONYMS rdf:datatype="xs:string">adenylic
+ acid</bp:SYNONYMS>
+ <bp:STRUCTURE>
+ <bp:chemicalStructure rdf:ID="chemicalStructure157">
+ <bp:STRUCTURE-FORMAT rdf:datatype="xs:string">CML
+ </bp:STRUCTURE-FORMAT>
+ <bp:STRUCTURE-DATA rdf:datatype="xs:string">
+ <cml> <molecule id="AMP" title="AMP"
+ dictRef="dictAMP"> <atomArray> <atom id="AMP-atom1"
+ elementType="O" x2="0.45706" y2="-1.0"/> <atom
+ id="AMP-atom2" elementType="O" x2="0.25153"
+ y2="0.00307"/> <atom id="AMP-atom3" elementType="C"
+ x2="0.41718" y2="-0.2362"/> <atom id="AMP-atom4"
+ elementType="N" x2="-1.0" y2="-0.25767"/> <atom
+ id="AMP-atom5" elementType="N" x2="-0.15951"
+ y2="-0.25767"/> <atom id="AMP-atom6" elementType="H"
+ x2="0.56442" y2="-0.32822"/> <atom id="AMP-atom7"
+ elementType="N" x2="-0.16258" y2="0.2454"/> <atom
+ id="AMP-atom8" elementType="C" x2="0.70859"
+ y2="0.15031"/> <atom id="AMP-atom9" elementType="C"
+ x2="-0.57055" y2="-0.0184"/> <atom id="AMP-atom10"
+ elementType="C" x2="0.42025" y2="0.2454"/> <atom
+ id="AMP-atom11" elementType="C" x2="0.70859"
+ y2="-0.14417"/> <atom id="AMP-atom12" elementType="N"
+ x2="-0.57669" y2="-0.49693"/> <atom id="AMP-atom13"
+ elementType="O" x2="0.09509" y2="-0.58282"/> <atom
+ id="AMP-atom14" elementType="C" x2="-0.41718"
+ y2="0.41104"/> <atom id="AMP-atom15" elementType="O"
+ x2="0.99693" y2="-0.14417"/> <atom id="AMP-atom16"
+ elementType="O" x2="0.98466" y2="0.23006"/> <atom
+ id="AMP-atom17" elementType="C" x2="-0.30061"
+ y2="-0.0184"/> <atom id="AMP-atom18" elementType="C"
+ x2="-0.71166" y2="-0.25767"/> <atom id="AMP-atom19"
+ elementType="P" x2="0.26994" y2="-0.78221"/> <atom
+ id="AMP-atom20" elementType="N" x2="-0.67485"
+ y2="0.22086"/> <atom id="AMP-atom21" elementType="H"
+ x2="0.42025" y2="0.41718"/> <atom id="AMP-atom22"
+ elementType="C" x2="-0.29755" y2="-0.49693"/> <atom
+ id="AMP-atom23" elementType="O" x2="0.5" y2="-0.60736"/>
+ <atom id="AMP-atom24" elementType="C" x2="0.09509"
+ y2="-0.33742"/> <atom id="AMP-atom25" elementType="O"
+ x2="0.02761" y2="-0.93865"/> </atomArray>
+ <bondArray> <bond id="AMP-bond1"
+ atomRefs="AMP-atom25 AMP-atom19" order="1"/> <bond
+ id="AMP-bond2" atomRefs="AMP-atom23 AMP-atom19"
+ order="2"/> <bond id="AMP-bond3" atomRefs="AMP-atom22
+ AMP-atom5" order="A"/> <bond id="AMP-bond4"
+ atomRefs="AMP-atom9 AMP-atom20" order="A"/> <bond
+ id="AMP-bond5" atomRefs="AMP-atom20 AMP-atom14"
+ order="A"/> <bond id="AMP-bond6" atomRefs="AMP-atom19
+ AMP-atom13" order="1"/> <bond id="AMP-bond7"
+ atomRefs="AMP-atom18 AMP-atom12" order="A"/> <bond
+ id="AMP-bond8" atomRefs="AMP-atom9 AMP-atom18"
+ order="A"/> <bond id="AMP-bond9" atomRefs="AMP-atom7
+ AMP-atom17" order="A"/> <bond id="AMP-bond10"
+ atomRefs="AMP-atom14 AMP-atom7" order="A"/> <bond
+ id="AMP-bond11" atomRefs="AMP-atom13 AMP-atom24"
+ order="1"/> <bond id="AMP-bond12" atomRefs="AMP-atom12
+ AMP-atom22" order="A"/> <bond id="AMP-bond13"
+ atomRefs="AMP-atom11 AMP-atom15" order="1"/> <bond
+ id="AMP-bond14" atomRefs="AMP-atom11 AMP-atom8"
+ order="1"/> <bond id="AMP-bond15" atomRefs="AMP-atom10
+ AMP-atom21" order="1"/> <bond id="AMP-bond16"
+ atomRefs="AMP-atom10 AMP-atom7" order="1"/> <bond
+ id="AMP-bond17" atomRefs="AMP-atom17 AMP-atom9"
+ order="A"/> <bond id="AMP-bond18" atomRefs="AMP-atom8
+ AMP-atom16" order="1"/> <bond id="AMP-bond19"
+ atomRefs="AMP-atom8 AMP-atom10" order="1"/> <bond
+ id="AMP-bond20" atomRefs="AMP-atom5 AMP-atom17"
+ order="A"/> <bond id="AMP-bond21" atomRefs="AMP-atom4
+ AMP-atom18" order="1"/> <bond id="AMP-bond22"
+ atomRefs="AMP-atom3 AMP-atom11" order="1"/> <bond
+ id="AMP-bond23" atomRefs="AMP-atom3 AMP-atom6"
+ order="1"/> <bond id="AMP-bond24" atomRefs="AMP-atom3
+ AMP-atom24" order="1"/> <bond id="AMP-bond25"
+ atomRefs="AMP-atom3 AMP-atom2" order="1"/> <bond
+ id="AMP-bond26" atomRefs="AMP-atom2 AMP-atom10"
+ order="1"/> <bond id="AMP-bond27" atomRefs="AMP-atom1
+ AMP-atom19" order="1"/> </bondArray> <formula
+ concise="C 10 H 14 N 5 O 7 P 1" formalCharge="-2"/>
+ <float title="molecularWeight"
+ units="g/mol">347.224</float> <string
+ title="smiles">[CH]1(O[CH](C(O)C(O)1)COP(=O)(O)O)n2(c3(c(nc2)c(N)ncn3))</string>
+ </molecule> </cml></bp:STRUCTURE-DATA>
+ </bp:chemicalStructure>
+ </bp:STRUCTURE>
+ <bp:SYNONYMS rdf:datatype="xs:string">adenosine-5'-phosphate
+ </bp:SYNONYMS>
+ <bp:MOLECULAR-WEIGHT>347.2239990234375</bp:MOLECULAR-WEIGHT>
+ <bp:SYNONYMS rdf:datatype="xs:string">A
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">adenosine-phosphate
+ </bp:SYNONYMS>
+ <bp:NAME rdf:datatype="xs:string">AMP</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="xs:string">adenosine-monophosphate
+ </bp:SYNONYMS>
+ </bp:smallMolecule>
+ </bp:PHYSICAL-ENTITY>
+ <bp:CELLULAR-LOCATION rdf:resource="#openControlledVocabulary17" />
+ <bp:STOICHIOMETRIC-COEFFICIENT>1.0
+ </bp:STOICHIOMETRIC-COEFFICIENT>
+ </bp:physicalEntityParticipant>
+ </bp:CONTROLLER>
+ <bp:CONTROL-TYPE rdf:datatype="xs:string">ACTIVATION-ALLOSTERIC
+ </bp:CONTROL-TYPE>
+ <bp:CONTROLLED rdf:resource="#catalysis137" />
+ </bp:modulation>
+ </bp:STEP-INTERACTIONS>
+ </bp:pathwayStep>
+ </bp:NEXT-STEP>
+ </bp:pathwayStep>
+ </bp:NEXT-STEP>
+ <bp:STEP-INTERACTIONS>
+ <bp:modulation rdf:ID="modulation158">
+ <bp:CONTROLLER>
+ <bp:physicalEntityParticipant rdf:ID="physicalEntityParticipant159">
+ <bp:STOICHIOMETRIC-COEFFICIENT>1.0</bp:STOICHIOMETRIC-COEFFICIENT>
+ <bp:PHYSICAL-ENTITY>
+ <bp:smallMolecule rdf:ID="smallMolecule160">
+ <bp:NAME rdf:datatype="xs:string">vanadate</bp:NAME>
+ </bp:smallMolecule>
+ </bp:PHYSICAL-ENTITY>
+ </bp:physicalEntityParticipant>
+ </bp:CONTROLLER>
+ <bp:COMMENT rdf:datatype="xs:string">Vanadate strongly inhibits the
+ enzyme. |CITS: [99364512]|</bp:COMMENT>
+ <bp:CONTROLLED rdf:resource="#catalysis73" />
+ <bp:CONTROL-TYPE rdf:datatype="xs:string">INHIBITION-UNKMECH
+ </bp:CONTROL-TYPE>
+ </bp:modulation>
+ </bp:STEP-INTERACTIONS>
+ <bp:STEP-INTERACTIONS>
+ <bp:catalysis rdf:ID="catalysis161">
+ <bp:CONTROLLED rdf:resource="#biochemicalReaction56" />
+ <bp:SYNONYMS rdf:datatype="xs:string">D-phosphoglycerate
+ 2,3-phosphomutase 2</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">PGAM2</bp:SYNONYMS>
+ <bp:CONTROLLER>
+ <bp:physicalEntityParticipant rdf:ID="physicalEntityParticipant162">
+ <bp:PHYSICAL-ENTITY>
+ <bp:protein rdf:ID="protein163">
+ <bp:XREF>
+ <bp:relationshipXref rdf:ID="relationshipXref164">
+ <bp:ID rdf:datatype="xs:string">GPMB-MONOMER</bp:ID>
+ <bp:RELATIONSHIP-TYPE rdf:datatype="xs:string">
+ Ortholog</bp:RELATIONSHIP-TYPE>
+ <bp:DB rdf:datatype="xs:string">EcoO157Cyc</bp:DB>
+ </bp:relationshipXref>
+ </bp:XREF>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref165">
+ <bp:DB rdf:datatype="xs:string">PIR</bp:DB>
+ <bp:ID rdf:datatype="xs:string">b4395</bp:ID>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref166">
+ <bp:DB rdf:datatype="xs:string">SWISS-PROT</bp:DB>
+ <bp:ID rdf:datatype="xs:string">P36942</bp:ID>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:NAME rdf:datatype="xs:string">PGAM2-MONOMER</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="xs:string">B4395</bp:SYNONYMS>
+ <bp:ORGANISM rdf:resource="#bioSource43" />
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref167">
+ <bp:DB rdf:datatype="xs:string">RefSeq</bp:DB>
+ <bp:ID rdf:datatype="xs:string">NP_418812</bp:ID>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:COMMENT rdf:datatype="xs:string">The enzyme has not been
+ characterized and the subunit structure is unknown. However,
+ phosphoglycerate mutase 1 is a homodimer.</bp:COMMENT>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref168">
+ <bp:DB rdf:datatype="xs:string">SWISS-MODEL</bp:DB>
+ <bp:ID rdf:datatype="xs:string">P36942</bp:ID>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:SYNONYMS rdf:datatype="xs:string">GpmB</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">YtjC</bp:SYNONYMS>
+ <bp:SEQUENCE rdf:datatype="xs:string">MLQVYLVRHGETQWNAERRIQGQSDSPLTAKGEQQAMQVATRAKELGITHIISSDLGRTRRTAEIIAQACGCDIIFDSRLRELNMGVLEKRHIDSLTEEEENWRRQLVNGTVDGRIPEGESMQELSDRVNAALESCRDLPQGSRPLLVSHGIALGCLVSTILGLPAWAERRLRLRNCSISRVDYQESLWLASGWVVETAGDISHLDAPALDELQR
+ </bp:SEQUENCE>
+ </bp:protein>
+ </bp:PHYSICAL-ENTITY>
+ </bp:physicalEntityParticipant>
+ </bp:CONTROLLER>
+ <bp:DIRECTION rdf:datatype="xs:string">REVERSIBLE</bp:DIRECTION>
+ <bp:SYNONYMS rdf:datatype="xs:string">phosphoglyceromutase 2
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">BPG-dependent PGAM2
+ </bp:SYNONYMS>
+ <bp:COMMENT rdf:datatype="xs:string">E. coli contains three
+ phosphoglycerate mutases. Two are 2,3-bisphosphoglyerate-dependent
+ enzymes, encoded by the gpmA and gpmB genes. The third is a
+ 2,3-bisphosphoglyerate-independent enzyme encoded by the pgmI gene.
+ |CITS: [99364512]|</bp:COMMENT>
+ <bp:NAME rdf:datatype="xs:string">phosphoglycerate mutase 2</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="xs:string">phosphoglycerate phosphomutase
+ 2</bp:SYNONYMS>
+ </bp:catalysis>
+ </bp:STEP-INTERACTIONS>
+ </bp:pathwayStep>
+ <bp:relationshipXref rdf:ID="relationshipXref169">
+ <bp:DB rdf:datatype="xs:string">EcoO157Cyc</bp:DB>
+ <bp:RELATIONSHIP-TYPE rdf:datatype="xs:string">Ortholog
+ </bp:RELATIONSHIP-TYPE>
+ <bp:ID rdf:datatype="xs:string">GAPA-MONOMER</bp:ID>
+ </bp:relationshipXref>
+ <bp:publicationXref rdf:ID="publicationXref170">
+ <bp:AUTHORS rdf:datatype="xs:string">Vignais ML</bp:AUTHORS>
+ <bp:DB rdf:datatype="xs:string">PubMed</bp:DB>
+ <bp:AUTHORS rdf:datatype="xs:string">Seta FD</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="xs:string">J Bacteriol 1997;179(16);5218-21
+ </bp:SOURCE>
+ <bp:TITLE rdf:datatype="xs:string">Characterization of Escherichia coli
+ strains with gapA and gapB genes deleted.</bp:TITLE>
+ <bp:YEAR>1997</bp:YEAR>
+ <bp:AUTHORS rdf:datatype="xs:string">Boschi-Muller S</bp:AUTHORS>
+ <bp:ID rdf:datatype="xs:string">9260967</bp:ID>
+ <bp:AUTHORS rdf:datatype="xs:string">Branlant G</bp:AUTHORS>
+ </bp:publicationXref>
+ <bp:pathwayStep rdf:ID="pathwayStep171">
+ <bp:STEP-INTERACTIONS>
+ <bp:biochemicalReaction rdf:ID="biochemicalReaction172">
+ <bp:NAME rdf:datatype="xs:string">glyceraldehyde 3-phosphate oxidation
+ </bp:NAME>
+ <bp:SYNONYMS rdf:datatype="xs:string">TRIOSEPHOSPHATE DEHYDROGENASE
+ </bp:SYNONYMS>
+ <bp:LEFT>
+ <bp:physicalEntityParticipant rdf:ID="physicalEntityParticipant173">
+ <bp:CELLULAR-LOCATION rdf:resource="#openControlledVocabulary17" />
+ <bp:STOICHIOMETRIC-COEFFICIENT>1</bp:STOICHIOMETRIC-COEFFICIENT>
+ <bp:PHYSICAL-ENTITY>
+ <bp:smallMolecule rdf:ID="smallMolecule174">
+ <bp:SYNONYMS rdf:datatype="xs:string">PO<SUB>4</SUB><SUP>3-</SUP>
+ </bp:SYNONYMS>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref175">
+ <bp:DB rdf:datatype="xs:string">CAS</bp:DB>
+ <bp:ID rdf:datatype="xs:string">14265-44-2</bp:ID>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:SYNONYMS rdf:datatype="xs:string">phosphate-inorganic
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">inorganic phosphate
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">orthophosphate
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">Pi</bp:SYNONYMS>
+ <bp:NAME rdf:datatype="xs:string">phosphate</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="xs:string">HPO<SUB>4</SUB><SUP>2-</SUP>
+ </bp:SYNONYMS>
+ <bp:MOLECULAR-WEIGHT>94.97100067138672</bp:MOLECULAR-WEIGHT>
+ <bp:STRUCTURE>
+ <bp:chemicalStructure rdf:ID="chemicalStructure176">
+ <bp:STRUCTURE-DATA rdf:datatype="xs:string">
+ <cml> <molecule id="Pi" title="phosphate"
+ dictRef="dictPi"> <atomArray> <atom id="Pi-atom1"
+ elementType="P" x2="-0.00166" y2="-0.00166"/> <atom
+ id="Pi-atom2" elementType="O" x2="0.99667" y2="-0.00166"
+ formalCharge="-1"/> <atom id="Pi-atom3" elementType="O"
+ x2="-0.00166" y2="0.99667" formalCharge="-1"/> <atom
+ id="Pi-atom4" elementType="O" x2="-0.00166" y2="-1.0"
+ formalCharge="-1"/> <atom id="Pi-atom5" elementType="O"
+ x2="-1.0" y2="-0.00166"/> </atomArray> <bondArray>
+ <bond id="Pi-bond1" atomRefs="Pi-atom5 Pi-atom1"
+ order="2"/> <bond id="Pi-bond2" atomRefs="Pi-atom4
+ Pi-atom1" order="1"/> <bond id="Pi-bond3"
+ atomRefs="Pi-atom3 Pi-atom1" order="1"/> <bond
+ id="Pi-bond4" atomRefs="Pi-atom2 Pi-atom1" order="1"/>
+ </bondArray> <formula concise="O 4 P 1"
+ formalCharge="-3"/> <float title="molecularWeight"
+ units="g/mol">94.971</float> <string
+ title="smiles">P([O-1])([O-1])(=O)[O-1]</string>
+ </molecule> </cml></bp:STRUCTURE-DATA>
+ <bp:STRUCTURE-FORMAT rdf:datatype="xs:string">
+ CML</bp:STRUCTURE-FORMAT>
+ </bp:chemicalStructure>
+ </bp:STRUCTURE>
+ </bp:smallMolecule>
+ </bp:PHYSICAL-ENTITY>
+ </bp:physicalEntityParticipant>
+ </bp:LEFT>
+ <bp:RIGHT>
+ <bp:physicalEntityParticipant rdf:ID="physicalEntityParticipant177">
+ <bp:STOICHIOMETRIC-COEFFICIENT>1</bp:STOICHIOMETRIC-COEFFICIENT>
+ <bp:CELLULAR-LOCATION rdf:resource="#openControlledVocabulary17" />
+ <bp:PHYSICAL-ENTITY>
+ <bp:smallMolecule rdf:ID="smallMolecule178">
+ <bp:SYNONYMS rdf:datatype="xs:string">NAD-reduced</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">NADH2</bp:SYNONYMS>
+ <bp:NAME rdf:datatype="xs:string">NADH</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="xs:string">NADH+H+</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">NADH<sub>2</sub>
+ </bp:SYNONYMS>
+ <bp:STRUCTURE>
+ <bp:chemicalStructure rdf:ID="chemicalStructure179">
+ <bp:STRUCTURE-DATA rdf:datatype="xs:string">
+ <cml> <molecule id="NADH" title="NADH"
+ dictRef="dictNADH"> <atomArray> <atom id="NADH-atom1"
+ elementType="C" x2="0.34285715" y2="-0.7542857"/> <atom
+ id="NADH-atom2" elementType="C" x2="0.92" y2="-0.45142856"/>
+ <atom id="NADH-atom3" elementType="H" x2="0.37142858"
+ y2="-0.89428574"/> <atom id="NADH-atom4" elementType="O"
+ x2="0.08285714" y2="-0.64"/> <atom id="NADH-atom5"
+ elementType="O" x2="0.08285714" y2="-0.8657143"/> <atom
+ id="NADH-atom6" elementType="C" x2="0.42857143"
+ y2="-0.93142855"/> <atom id="NADH-atom7" elementType="C"
+ x2="-0.5914286" y2="-0.36"/> <atom id="NADH-atom8"
+ elementType="C" x2="-0.78571427" y2="-0.4342857"/> <atom
+ id="NADH-atom9" elementType="H" x2="-0.48857144"
+ y2="-0.70285714"/> <atom id="NADH-atom10" elementType="H"
+ x2="0.7" y2="-0.34285715"/> <atom id="NADH-atom11"
+ elementType="O" x2="0.42857143" y2="-1.0"/> <atom
+ id="NADH-atom12" elementType="C" x2="0.52" y2="-0.46285716"/>
+ <atom id="NADH-atom13" elementType="C" x2="-1.0"
+ y2="-0.4342857"/> <atom id="NADH-atom14" elementType="H"
+ x2="0.42857143" y2="-0.86285716"/> <atom id="NADH-atom15"
+ elementType="H" x2="-0.68" y2="-0.7542857"/> <atom
+ id="NADH-atom16" elementType="H" x2="0.6028572"
+ y2="-0.34571427"/> <atom id="NADH-atom17" elementType="C"
+ x2="-0.42285714" y2="-0.68285716"/> <atom id="NADH-atom18"
+ elementType="C" x2="0.7714286" y2="-0.45142856"/> <atom
+ id="NADH-atom19" elementType="H" x2="0.6457143"
+ y2="-0.89428574"/> <atom id="NADH-atom20" elementType="O"
+ x2="-0.5542857" y2="-0.61142856"/> <atom id="NADH-atom21"
+ elementType="C" x2="0.6457143" y2="-0.82857144"/> <atom
+ id="NADH-atom22" elementType="O" x2="-0.48857144"
+ y2="-0.8428571"/> <atom id="NADH-atom23" elementType="C"
+ x2="0.37142858" y2="-0.82857144"/> <atom id="NADH-atom24"
+ elementType="C" x2="0.52" y2="-0.6085714"/> <atom
+ id="NADH-atom25" elementType="C" x2="-0.48857144"
+ y2="-0.77428573"/> <atom id="NADH-atom26" elementType="C"
+ x2="-0.61714286" y2="-0.77428573"/> <atom id="NADH-atom27"
+ elementType="O" x2="0.5" y2="-0.7457143"/> <atom
+ id="NADH-atom28" elementType="N" x2="-0.8971428"
+ y2="-0.13142857"/> <atom id="NADH-atom29" elementType="O"
+ x2="0.21428572" y2="-0.7542857"/> <atom id="NADH-atom30"
+ elementType="O" x2="-0.17714286" y2="-0.64"/> <atom
+ id="NADH-atom31" elementType="N" x2="-1.0" y2="-0.31142858"/>
+ <atom id="NADH-atom32" elementType="N" x2="-0.68"
+ y2="-0.48285714"/> <atom id="NADH-atom33" elementType="N"
+ x2="0.9942857" y2="-0.5342857"/> <atom id="NADH-atom34"
+ elementType="C" x2="0.7714286" y2="-0.6085714"/> <atom
+ id="NADH-atom35" elementType="C" x2="-0.78571427"
+ y2="-0.31142858"/> <atom id="NADH-atom36" elementType="H"
+ x2="0.5714286" y2="-0.86285716"/> <atom id="NADH-atom37"
+ elementType="P" x2="0.08285714" y2="-0.7542857"/> <atom
+ id="NADH-atom38" elementType="O" x2="-0.61714286"
+ y2="-0.8428571"/> <atom id="NADH-atom39" elementType="N"
+ x2="-0.68" y2="-0.25714287"/> <atom id="NADH-atom40"
+ elementType="P" x2="-0.17714286" y2="-0.7542857"/> <atom
+ id="NADH-atom41" elementType="C" x2="-0.68"
+ y2="-0.68285716"/> <atom id="NADH-atom42" elementType="N"
+ x2="0.6457143" y2="-0.67714286"/> <atom id="NADH-atom43"
+ elementType="H" x2="-0.61714286" y2="-0.70285714"/> <atom
+ id="NADH-atom44" elementType="O" x2="0.99714285"
+ y2="-0.37142858"/> <atom id="NADH-atom45" elementType="N"
+ x2="-0.8971428" y2="-0.48857144"/> <atom id="NADH-atom46"
+ elementType="C" x2="-0.36857143" y2="-0.7657143"/> <atom
+ id="NADH-atom47" elementType="O" x2="0.5714286" y2="-1.0"/>
+ <atom id="NADH-atom48" elementType="O" x2="-0.17714286"
+ y2="-0.8657143"/> <atom id="NADH-atom49" elementType="C"
+ x2="-0.8971428" y2="-0.24857143"/> <atom id="NADH-atom50"
+ elementType="O" x2="-0.2742857" y2="-0.7542857"/> <atom
+ id="NADH-atom51" elementType="H" x2="-0.42285714"
+ y2="-0.61714286"/> <atom id="NADH-atom52" elementType="O"
+ x2="-0.042857144" y2="-0.7542857"/> <atom id="NADH-atom53"
+ elementType="C" x2="0.5714286" y2="-0.93142855"/> <atom
+ id="NADH-atom54" elementType="C" x2="0.6542857"
+ y2="-0.39142856"/> </atomArray> <bondArray> <bond
+ id="NADH-bond1" atomRefs="NADH-atom54 NADH-atom18"
+ order="1"/> <bond id="NADH-bond2" atomRefs="NADH-atom53
+ NADH-atom6" order="1"/> <bond id="NADH-bond3"
+ atomRefs="NADH-atom52 NADH-atom40" order="1"/> <bond
+ id="NADH-bond4" atomRefs="NADH-atom51 NADH-atom17"
+ order="1"/> <bond id="NADH-bond5" atomRefs="NADH-atom50
+ NADH-atom46" order="1"/> <bond id="NADH-bond6"
+ atomRefs="NADH-atom49 NADH-atom31" order="A"/> <bond
+ id="NADH-bond7" atomRefs="NADH-atom48 NADH-atom40"
+ order="1"/> <bond id="NADH-bond8" atomRefs="NADH-atom47
+ NADH-atom53" order="1"/> <bond id="NADH-bond9"
+ atomRefs="NADH-atom46 NADH-atom17" order="1"/> <bond
+ id="NADH-bond10" atomRefs="NADH-atom45 NADH-atom8"
+ order="A"/> <bond id="NADH-bond11" atomRefs="NADH-atom44
+ NADH-atom2" order="2"/> <bond id="NADH-bond12"
+ atomRefs="NADH-atom43 NADH-atom26" order="1"/> <bond
+ id="NADH-bond13" atomRefs="NADH-atom42 NADH-atom21"
+ order="1"/> <bond id="NADH-bond14" atomRefs="NADH-atom42
+ NADH-atom24" order="1"/> <bond id="NADH-bond15"
+ atomRefs="NADH-atom41 NADH-atom32" order="1"/> <bond
+ id="NADH-bond16" atomRefs="NADH-atom41 NADH-atom26"
+ order="1"/> <bond id="NADH-bond17" atomRefs="NADH-atom40
+ NADH-atom50" order="1"/> <bond id="NADH-bond18"
+ atomRefs="NADH-atom39 NADH-atom35" order="A"/> <bond
+ id="NADH-bond19" atomRefs="NADH-atom38 NADH-atom26"
+ order="1"/> <bond id="NADH-bond20" atomRefs="NADH-atom37
+ NADH-atom52" order="1"/> <bond id="NADH-bond21"
+ atomRefs="NADH-atom36 NADH-atom53" order="1"/> <bond
+ id="NADH-bond22" atomRefs="NADH-atom35 NADH-atom49"
+ order="A"/> <bond id="NADH-bond23" atomRefs="NADH-atom35
+ NADH-atom8" order="A"/> <bond id="NADH-bond24"
+ atomRefs="NADH-atom34 NADH-atom42" order="1"/> <bond
+ id="NADH-bond25" atomRefs="NADH-atom33 NADH-atom2"
+ order="1"/> <bond id="NADH-bond26" atomRefs="NADH-atom32
+ NADH-atom7" order="A"/> <bond id="NADH-bond27"
+ atomRefs="NADH-atom31 NADH-atom13" order="A"/> <bond
+ id="NADH-bond28" atomRefs="NADH-atom30 NADH-atom40"
+ order="2"/> <bond id="NADH-bond29" atomRefs="NADH-atom29
+ NADH-atom37" order="1"/> <bond id="NADH-bond30"
+ atomRefs="NADH-atom28 NADH-atom49" order="1"/> <bond
+ id="NADH-bond31" atomRefs="NADH-atom27 NADH-atom23"
+ order="1"/> <bond id="NADH-bond32" atomRefs="NADH-atom25
+ NADH-atom26" order="1"/> <bond id="NADH-bond33"
+ atomRefs="NADH-atom23 NADH-atom1" order="1"/> <bond
+ id="NADH-bond34" atomRefs="NADH-atom23 NADH-atom6"
+ order="1"/> <bond id="NADH-bond35" atomRefs="NADH-atom22
+ NADH-atom25" order="1"/> <bond id="NADH-bond36"
+ atomRefs="NADH-atom21 NADH-atom27" order="1"/> <bond
+ id="NADH-bond37" atomRefs="NADH-atom21 NADH-atom53"
+ order="1"/> <bond id="NADH-bond38" atomRefs="NADH-atom20
+ NADH-atom41" order="1"/> <bond id="NADH-bond39"
+ atomRefs="NADH-atom19 NADH-atom21" order="1"/> <bond
+ id="NADH-bond40" atomRefs="NADH-atom18 NADH-atom34"
+ order="2"/> <bond id="NADH-bond41" atomRefs="NADH-atom17
+ NADH-atom20" order="1"/> <bond id="NADH-bond42"
+ atomRefs="NADH-atom17 NADH-atom25" order="1"/> <bond
+ id="NADH-bond43" atomRefs="NADH-atom16 NADH-atom54"
+ order="1"/> <bond id="NADH-bond44" atomRefs="NADH-atom15
+ NADH-atom41" order="1"/> <bond id="NADH-bond45"
+ atomRefs="NADH-atom14 NADH-atom6" order="1"/> <bond
+ id="NADH-bond46" atomRefs="NADH-atom13 NADH-atom45"
+ order="A"/> <bond id="NADH-bond47" atomRefs="NADH-atom12
+ NADH-atom24" order="2"/> <bond id="NADH-bond48"
+ atomRefs="NADH-atom12 NADH-atom54" order="1"/> <bond
+ id="NADH-bond49" atomRefs="NADH-atom11 NADH-atom6"
+ order="1"/> <bond id="NADH-bond50" atomRefs="NADH-atom10
+ NADH-atom54" order="1"/> <bond id="NADH-bond51"
+ atomRefs="NADH-atom9 NADH-atom25" order="1"/> <bond
+ id="NADH-bond52" atomRefs="NADH-atom8 NADH-atom32"
+ order="A"/> <bond id="NADH-bond53" atomRefs="NADH-atom7
+ NADH-atom39" order="A"/> <bond id="NADH-bond54"
+ atomRefs="NADH-atom5 NADH-atom37" order="1"/> <bond
+ id="NADH-bond55" atomRefs="NADH-atom4 NADH-atom37"
+ order="2"/> <bond id="NADH-bond56" atomRefs="NADH-atom3
+ NADH-atom23" order="1"/> <bond id="NADH-bond57"
+ atomRefs="NADH-atom2 NADH-atom18" order="1"/> <bond
+ id="NADH-bond58" atomRefs="NADH-atom1 NADH-atom29"
+ order="1"/> </bondArray> <formula concise="C 21 H 29 N
+ 7 O 14 P 2" formalCharge="0"/> <float
+ title="molecularWeight" units="g/mol">665.446</float>
+ <string
+ title="smiles">C([CH]1(O[CH]([CH](O)[CH]1O)N2(C=C(C(=O)N)[CH2]C=C2)))OP(=O)(O)OP(=O)(O)OC[CH]3(O[CH]([CH](O)[CH](O)3)n4(c5(c(nc4)c(N)ncn5)))</string>
+ </molecule> </cml></bp:STRUCTURE-DATA>
+ <bp:STRUCTURE-FORMAT rdf:datatype="xs:string">
+ CML</bp:STRUCTURE-FORMAT>
+ </bp:chemicalStructure>
+ </bp:STRUCTURE>
+ <bp:SYNONYMS rdf:datatype="xs:string">DPNH</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">dihydrodiphosphopyridine
+ nucleotide</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">nicotinamide adenine
+ dinucleotide reduced</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">dihydronicotinamide
+ adenine dinucleotide</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">diphosphopyridine
+ nucleotide reduced</bp:SYNONYMS>
+ <bp:MOLECULAR-WEIGHT>665.4459838867188</bp:MOLECULAR-WEIGHT>
+ </bp:smallMolecule>
+ </bp:PHYSICAL-ENTITY>
+ </bp:physicalEntityParticipant>
+ </bp:RIGHT>
+ <bp:LEFT>
+ <bp:physicalEntityParticipant rdf:ID="physicalEntityParticipant180">
+ <bp:STOICHIOMETRIC-COEFFICIENT>1</bp:STOICHIOMETRIC-COEFFICIENT>
+ <bp:CELLULAR-LOCATION rdf:resource="#openControlledVocabulary17" />
+ <bp:PHYSICAL-ENTITY>
+ <bp:smallMolecule rdf:ID="smallMolecule181">
+ <bp:SYNONYMS rdf:datatype="xs:string">glyceraldehyde-phosphate
+ </bp:SYNONYMS>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref182">
+ <bp:ID rdf:datatype="xs:string">142-10-9</bp:ID>
+ <bp:DB rdf:datatype="xs:string">CAS</bp:DB>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:SYNONYMS rdf:datatype="xs:string">glyceraldehyde-3-P
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">3-phosphoglyceraldehyde
+ </bp:SYNONYMS>
+ <bp:NAME rdf:datatype="xs:string">glyceraldehyde-3-phosphate
+ </bp:NAME>
+ <bp:SYNONYMS rdf:datatype="xs:string">D-glyceraldehyde-3-phosphate
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">D-glyceraldehyde-3-P
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">gap</bp:SYNONYMS>
+ <bp:STRUCTURE>
+ <bp:chemicalStructure rdf:ID="chemicalStructure183">
+ <bp:STRUCTURE-FORMAT rdf:datatype="xs:string">
+ CML</bp:STRUCTURE-FORMAT>
+ <bp:STRUCTURE-DATA rdf:datatype="xs:string">
+ <cml> <molecule id="GAP"
+ title="glyceraldehyde-3-phosphate" dictRef="dictGAP">
+ <atomArray> <atom id="GAP-atom1" elementType="C"
+ x2="-1.0" y2="-0.54088"/> <atom id="GAP-atom2"
+ elementType="P" x2="-0.1478" y2="0.53774"/> <atom
+ id="GAP-atom3" elementType="O" x2="-0.13836" y2="-0.2044"/>
+ <atom id="GAP-atom4" elementType="O" x2="0.31132"
+ y2="0.53774"/> <atom id="GAP-atom5" elementType="O"
+ x2="-0.1478" y2="0.07862"/> <atom id="GAP-atom6"
+ elementType="O" x2="-1.0" y2="-1.0"/> <atom id="GAP-atom7"
+ elementType="O" x2="-0.1478" y2="0.99686"/> <atom
+ id="GAP-atom8" elementType="C" x2="-1.0" y2="0.1761"/>
+ <atom id="GAP-atom9" elementType="O" x2="-0.59748"
+ y2="0.53774"/> <atom id="GAP-atom10" elementType="C"
+ x2="-0.59748" y2="-0.2044"/> </atomArray> <bondArray>
+ <bond id="GAP-bond1" atomRefs="GAP-atom10 GAP-atom3"
+ order="1"/> <bond id="GAP-bond2" atomRefs="GAP-atom10
+ GAP-atom8" order="1"/> <bond id="GAP-bond3"
+ atomRefs="GAP-atom9 GAP-atom2" order="1"/> <bond
+ id="GAP-bond4" atomRefs="GAP-atom8 GAP-atom9" order="1"/>
+ <bond id="GAP-bond5" atomRefs="GAP-atom6 GAP-atom1"
+ order="2"/> <bond id="GAP-bond6" atomRefs="GAP-atom2
+ GAP-atom5" order="1"/> <bond id="GAP-bond7"
+ atomRefs="GAP-atom2 GAP-atom7" order="1"/> <bond
+ id="GAP-bond8" atomRefs="GAP-atom2 GAP-atom4" order="2"/>
+ <bond id="GAP-bond9" atomRefs="GAP-atom1 GAP-atom10"
+ order="1"/> </bondArray> <formula concise="C 3 H 7 O 6
+ P 1" formalCharge="0"/> <float title="molecularWeight"
+ units="g/mol">170.058</float> <string
+ title="smiles">C(=O)C(O)COP(O)(O)=O</string>
+ </molecule> </cml></bp:STRUCTURE-DATA>
+ </bp:chemicalStructure>
+ </bp:STRUCTURE>
+ <bp:SYNONYMS rdf:datatype="xs:string">glyceraldehyde-P
+ </bp:SYNONYMS>
+ <bp:MOLECULAR-WEIGHT>170.05799865722656</bp:MOLECULAR-WEIGHT>
+ </bp:smallMolecule>
+ </bp:PHYSICAL-ENTITY>
+ </bp:physicalEntityParticipant>
+ </bp:LEFT>
+ <bp:EC-NUMBER rdf:datatype="xs:string">1.2.1.12</bp:EC-NUMBER>
+ <bp:SYNONYMS rdf:datatype="xs:string">GAPDH</bp:SYNONYMS>
+ <bp:XREF rdf:resource="#publicationXref14" />
+ <bp:DELTA-G><bp:deltaGprimeO rdf:ID="deltaG-1.5"><bp:DELTA-G-PRIME-O>1.5</bp:DELTA-G-PRIME-O></bp:deltaGprimeO></bp:DELTA-G>
+ <bp:LEFT>
+ <bp:physicalEntityParticipant rdf:ID="physicalEntityParticipant184">
+ <bp:CELLULAR-LOCATION rdf:resource="#openControlledVocabulary17" />
+ <bp:STOICHIOMETRIC-COEFFICIENT>1</bp:STOICHIOMETRIC-COEFFICIENT>
+ <bp:PHYSICAL-ENTITY>
+ <bp:smallMolecule rdf:ID="smallMolecule185">
+ <bp:MOLECULAR-WEIGHT>663.4299926757812</bp:MOLECULAR-WEIGHT>
+ <bp:SYNONYMS rdf:datatype="xs:string">nicotinamide adenine
+ dinucleotide</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">nicotinamide adenine
+ dinucleotide oxidized</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">NAD+</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">diphosphopyridine
+ nucleotide</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">NAD-ox</bp:SYNONYMS>
+ <bp:STRUCTURE>
+ <bp:chemicalStructure rdf:ID="chemicalStructure186">
+ <bp:STRUCTURE-DATA rdf:datatype="xs:string">
+ <cml> <molecule id="NAD" title="NAD" dictRef="dictNAD">
+ <atomArray> <atom id="NAD-atom1" elementType="C"
+ x2="-0.35491604" y2="-0.73141485"/> <atom id="NAD-atom2"
+ elementType="N" x2="0.6834533" y2="-0.64028776"
+ formalCharge="1"/> <atom id="NAD-atom3" elementType="C"
+ x2="-0.7793765" y2="-0.2589928"/> <atom id="NAD-atom4"
+ elementType="N" x2="-0.67146283" y2="-0.41246998"/> <atom
+ id="NAD-atom5" elementType="H" x2="-0.6618705"
+ y2="-0.7050359"/> <atom id="NAD-atom6" elementType="C"
+ x2="0.45803356" y2="-0.9256595"/> <atom id="NAD-atom7"
+ elementType="O" x2="-0.016786575" y2="-0.71702635"/> <atom
+ id="NAD-atom8" elementType="O" x2="0.6139089" y2="-1.0"/>
+ <atom id="NAD-atom9" elementType="O" x2="-0.58752996"
+ y2="-0.7865707"/> <atom id="NAD-atom10" elementType="C"
+ x2="0.6906475" y2="-0.34532374"/> <atom id="NAD-atom11"
+ elementType="C" x2="-1.0" y2="-0.3860911"/> <atom
+ id="NAD-atom12" elementType="O" x2="-0.5467626"
+ y2="-0.5707434"/> <atom id="NAD-atom13" elementType="C"
+ x2="0.37649882" y2="-0.71702635"/> <atom id="NAD-atom14"
+ elementType="P" x2="-0.15347719" y2="-0.71702635"/> <atom
+ id="NAD-atom15" elementType="O" x2="0.24460435"
+ y2="-0.71702635"/> <atom id="NAD-atom16" elementType="C"
+ x2="-0.8920863" y2="-0.1966427"/> <atom id="NAD-atom17"
+ elementType="C" x2="-0.4028777" y2="-0.6522782"/> <atom
+ id="NAD-atom18" elementType="O" x2="-0.15347719"
+ y2="-0.5971223"/> <atom id="NAD-atom19" elementType="O"
+ x2="-0.47961628" y2="-0.7865707"/> <atom id="NAD-atom20"
+ elementType="C" x2="0.6139089" y2="-0.9256595"/> <atom
+ id="NAD-atom21" elementType="N" x2="-0.8920863"
+ y2="-0.076738596"/> <atom id="NAD-atom22" elementType="H"
+ x2="0.6139089" y2="-0.853717"/> <atom id="NAD-atom23"
+ elementType="H" x2="-0.58752996" y2="-0.64028776"/> <atom
+ id="NAD-atom24" elementType="C" x2="-0.5851319"
+ y2="-0.31414866"/> <atom id="NAD-atom25" elementType="H"
+ x2="0.45803356" y2="-0.853717"/> <atom id="NAD-atom26"
+ elementType="C" x2="0.96642685" y2="-0.40527576"/> <atom
+ id="NAD-atom27" elementType="C" x2="-0.67146283"
+ y2="-0.6354916"/> <atom id="NAD-atom28" elementType="C"
+ x2="0.556355" y2="-0.5683453"/> <atom id="NAD-atom29"
+ elementType="H" x2="-0.4028777" y2="-0.5779376"/> <atom
+ id="NAD-atom30" elementType="N" x2="-1.0" y2="-0.2589928"/>
+ <atom id="NAD-atom31" elementType="C" x2="0.6834533"
+ y2="-0.8057554"/> <atom id="NAD-atom32" elementType="C"
+ x2="0.37649882" y2="-0.8057554"/> <atom id="NAD-atom33"
+ elementType="H" x2="0.37649882" y2="-0.8800959"/> <atom
+ id="NAD-atom34" elementType="O" x2="-0.25659472"
+ y2="-0.71702635"/> <atom id="NAD-atom35" elementType="O"
+ x2="-0.15347719" y2="-0.83693045"/> <atom id="NAD-atom36"
+ elementType="O" x2="0.53237414" y2="-0.7505995"/> <atom
+ id="NAD-atom37" elementType="C" x2="-0.58752996"
+ y2="-0.7146283"/> <atom id="NAD-atom38" elementType="C"
+ x2="0.8153478" y2="-0.42206234"/> <atom id="NAD-atom39"
+ elementType="C" x2="0.8153478" y2="-0.5683453"/> <atom
+ id="NAD-atom40" elementType="O" x2="0.45803356" y2="-1.0"/>
+ <atom id="NAD-atom41" elementType="O" x2="0.10791373"
+ y2="-0.83693045" formalCharge="-1"/> <atom id="NAD-atom42"
+ elementType="O" x2="0.96642685" y2="-0.28537166"/> <atom
+ id="NAD-atom43" elementType="P" x2="0.10791373"
+ y2="-0.71702635"/> <atom id="NAD-atom44" elementType="N"
+ x2="-0.8920863" y2="-0.4484412"/> <atom id="NAD-atom45"
+ elementType="C" x2="-0.47961628" y2="-0.7146283"/> <atom
+ id="NAD-atom46" elementType="H" x2="-0.47961628"
+ y2="-0.64028776"/> <atom id="NAD-atom47" elementType="O"
+ x2="0.10791373" y2="-0.5971223"/> <atom id="NAD-atom48"
+ elementType="H" x2="0.6834533" y2="-0.8800959"/> <atom
+ id="NAD-atom49" elementType="C" x2="0.556355"
+ y2="-0.4172662"/> <atom id="NAD-atom50" elementType="N"
+ x2="-0.67146283" y2="-0.20383692"/> <atom id="NAD-atom51"
+ elementType="C" x2="-0.7793765" y2="-0.3860911"/> <atom
+ id="NAD-atom52" elementType="N" x2="0.997602"
+ y2="-0.5203837"/> </atomArray> <bondArray> <bond
+ id="NAD-bond1" atomRefs="NAD-atom52 NAD-atom26" order="1"/>
+ <bond id="NAD-bond2" atomRefs="NAD-atom51 NAD-atom3"
+ order="A"/> <bond id="NAD-bond3" atomRefs="NAD-atom50
+ NAD-atom24" order="A"/> <bond id="NAD-bond4"
+ atomRefs="NAD-atom49 NAD-atom10" order="A"/> <bond
+ id="NAD-bond5" atomRefs="NAD-atom48 NAD-atom31" order="1"/>
+ <bond id="NAD-bond6" atomRefs="NAD-atom47 NAD-atom43"
+ order="2"/> <bond id="NAD-bond7" atomRefs="NAD-atom46
+ NAD-atom45" order="1"/> <bond id="NAD-bond8"
+ atomRefs="NAD-atom45 NAD-atom37" order="1"/> <bond
+ id="NAD-bond9" atomRefs="NAD-atom44 NAD-atom51" order="A"/>
+ <bond id="NAD-bond10" atomRefs="NAD-atom43 NAD-atom7"
+ order="1"/> <bond id="NAD-bond11" atomRefs="NAD-atom42
+ NAD-atom26" order="2"/> <bond id="NAD-bond12"
+ atomRefs="NAD-atom41 NAD-atom43" order="1"/> <bond
+ id="NAD-bond13" atomRefs="NAD-atom40 NAD-atom6" order="1"/>
+ <bond id="NAD-bond14" atomRefs="NAD-atom39 NAD-atom2"
+ order="A"/> <bond id="NAD-bond15" atomRefs="NAD-atom38
+ NAD-atom39" order="A"/> <bond id="NAD-bond16"
+ atomRefs="NAD-atom36 NAD-atom32" order="1"/> <bond
+ id="NAD-bond17" atomRefs="NAD-atom35 NAD-atom14" order="1"/>
+ <bond id="NAD-bond18" atomRefs="NAD-atom34 NAD-atom1"
+ order="1"/> <bond id="NAD-bond19" atomRefs="NAD-atom33
+ NAD-atom32" order="1"/> <bond id="NAD-bond20"
+ atomRefs="NAD-atom32 NAD-atom6" order="1"/> <bond
+ id="NAD-bond21" atomRefs="NAD-atom32 NAD-atom13" order="1"/>
+ <bond id="NAD-bond22" atomRefs="NAD-atom31 NAD-atom20"
+ order="1"/> <bond id="NAD-bond23" atomRefs="NAD-atom31
+ NAD-atom36" order="1"/> <bond id="NAD-bond24"
+ atomRefs="NAD-atom30 NAD-atom11" order="A"/> <bond
+ id="NAD-bond25" atomRefs="NAD-atom29 NAD-atom17" order="1"/>
+ <bond id="NAD-bond26" atomRefs="NAD-atom28 NAD-atom49"
+ order="A"/> <bond id="NAD-bond27" atomRefs="NAD-atom27
+ NAD-atom37" order="1"/> <bond id="NAD-bond28"
+ atomRefs="NAD-atom27 NAD-atom4" order="1"/> <bond
+ id="NAD-bond29" atomRefs="NAD-atom26 NAD-atom38" order="1"/>
+ <bond id="NAD-bond30" atomRefs="NAD-atom25 NAD-atom6"
+ order="1"/> <bond id="NAD-bond31" atomRefs="NAD-atom24
+ NAD-atom4" order="A"/> <bond id="NAD-bond32"
+ atomRefs="NAD-atom23 NAD-atom37" order="1"/> <bond
+ id="NAD-bond33" atomRefs="NAD-atom22 NAD-atom20" order="1"/>
+ <bond id="NAD-bond34" atomRefs="NAD-atom21 NAD-atom16"
+ order="1"/> <bond id="NAD-bond35" atomRefs="NAD-atom20
+ NAD-atom6" order="1"/> <bond id="NAD-bond36"
+ atomRefs="NAD-atom19 NAD-atom45" order="1"/> <bond
+ id="NAD-bond37" atomRefs="NAD-atom18 NAD-atom14" order="2"/>
+ <bond id="NAD-bond38" atomRefs="NAD-atom17 NAD-atom45"
+ order="1"/> <bond id="NAD-bond39" atomRefs="NAD-atom17
+ NAD-atom12" order="1"/> <bond id="NAD-bond40"
+ atomRefs="NAD-atom16 NAD-atom30" order="A"/> <bond
+ id="NAD-bond41" atomRefs="NAD-atom15 NAD-atom43" order="1"/>
+ <bond id="NAD-bond42" atomRefs="NAD-atom14 NAD-atom34"
+ order="1"/> <bond id="NAD-bond43" atomRefs="NAD-atom13
+ NAD-atom15" order="1"/> <bond id="NAD-bond44"
+ atomRefs="NAD-atom12 NAD-atom27" order="1"/> <bond
+ id="NAD-bond45" atomRefs="NAD-atom11 NAD-atom44" order="A"/>
+ <bond id="NAD-bond46" atomRefs="NAD-atom10 NAD-atom38"
+ order="A"/> <bond id="NAD-bond47" atomRefs="NAD-atom9
+ NAD-atom37" order="1"/> <bond id="NAD-bond48"
+ atomRefs="NAD-atom8 NAD-atom20" order="1"/> <bond
+ id="NAD-bond49" atomRefs="NAD-atom7 NAD-atom14" order="1"/>
+ <bond id="NAD-bond50" atomRefs="NAD-atom5 NAD-atom27"
+ order="1"/> <bond id="NAD-bond51" atomRefs="NAD-atom4
+ NAD-atom51" order="A"/> <bond id="NAD-bond52"
+ atomRefs="NAD-atom3 NAD-atom50" order="A"/> <bond
+ id="NAD-bond53" atomRefs="NAD-atom3 NAD-atom16" order="A"/>
+ <bond id="NAD-bond54" atomRefs="NAD-atom2 NAD-atom31"
+ order="1"/> <bond id="NAD-bond55" atomRefs="NAD-atom2
+ NAD-atom28" order="A"/> <bond id="NAD-bond56"
+ atomRefs="NAD-atom1 NAD-atom17" order="1"/> </bondArray>
+ <formula concise="C 21 H 27 N 7 O 14 P 2"
+ formalCharge="0"/> <float title="molecularWeight"
+ units="g/mol">663.43</float> <string
+ title="smiles">C([CH]1(O[CH]([CH](O)[CH](O)1)n2(c3(c(nc2)c(N)ncn3))))OP(=O)(O)OP([O-1])(=O)OC[CH]4(O[CH]([CH](O)[CH](O)4)[n+1]5(cc(C(N)=O)ccc5))</string>
+ </molecule> </cml></bp:STRUCTURE-DATA>
+ <bp:STRUCTURE-FORMAT rdf:datatype="xs:string">
+ CML</bp:STRUCTURE-FORMAT>
+ </bp:chemicalStructure>
+ </bp:STRUCTURE>
+ <bp:NAME rdf:datatype="xs:string">NAD</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="xs:string">diphosphopyridine
+ nucleotide oxidized</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">DPN</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">DPN+</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">coenzyme I</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">NAD-oxidized</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">DPN-ox</bp:SYNONYMS>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref187">
+ <bp:ID rdf:datatype="xs:string">53-84-9</bp:ID>
+ <bp:DB rdf:datatype="xs:string">CAS</bp:DB>
+ </bp:unificationXref>
+ </bp:XREF>
+ </bp:smallMolecule>
+ </bp:PHYSICAL-ENTITY>
+ </bp:physicalEntityParticipant>
+ </bp:LEFT>
+ <bp:RIGHT>
+ <bp:physicalEntityParticipant rdf:ID="physicalEntityParticipant188">
+ <bp:STOICHIOMETRIC-COEFFICIENT>1</bp:STOICHIOMETRIC-COEFFICIENT>
+ <bp:CELLULAR-LOCATION rdf:resource="#openControlledVocabulary17" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#smallMolecule51" />
+ </bp:physicalEntityParticipant>
+ </bp:RIGHT>
+ </bp:biochemicalReaction>
+ </bp:STEP-INTERACTIONS>
+ <bp:STEP-INTERACTIONS>
+ <bp:catalysis rdf:ID="catalysis189">
+ <bp:COMMENT rdf:datatype="xs:string">The E.coli sequence contains a
+ certain number of amino acids which are conserved in all GAPDHs so
+ far sequenced and which are postulated to be directly implicated in
+ the NAD+ binding or in the catalysis mechanism. |CITS:[85257641]|
+ There appear to be only two active sites per
+ molecule.|CITS:[79255500]| NAD required for the phosphorylation as
+ well as the oxidation |CITS:[79255500]|</bp:COMMENT>
+ <bp:DIRECTION rdf:datatype="xs:string">REVERSIBLE</bp:DIRECTION>
+ <bp:XREF rdf:resource="#publicationXref170" />
+ <bp:CONTROLLED rdf:resource="#biochemicalReaction172" />
+ <bp:SYNONYMS rdf:datatype="xs:string">triosephosphate dehydrogenase
+ </bp:SYNONYMS>
+ <bp:NAME rdf:datatype="xs:string">glyceraldehyde 3-phosphate
+ dehydrogenase-A complex</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="xs:string">GAPDH-A</bp:SYNONYMS>
+ <bp:CONTROLLER>
+ <bp:physicalEntityParticipant rdf:ID="physicalEntityParticipant190">
+ <bp:PHYSICAL-ENTITY>
+ <bp:complex rdf:ID="complex191">
+ <bp:XREF>
+ <bp:publicationXref rdf:ID="publicationXref192">
+ <bp:ID rdf:datatype="xs:string">2990926</bp:ID>
+ <bp:DB rdf:datatype="xs:string">PubMed</bp:DB>
+ <bp:AUTHORS rdf:datatype="xs:string">Branlant C</bp:AUTHORS>
+ <bp:TITLE rdf:datatype="xs:string">Nucleotide sequence of the
+ Escherichia coli gap gene. Different evolutionary behavior of
+ the NAD+-binding domain and of the catalytic domain of
+ D-glyceraldehyde-3-phosphate dehydrogenase.</bp:TITLE>
+ <bp:YEAR>1985</bp:YEAR>
+ <bp:SOURCE rdf:datatype="xs:string">Eur J Biochem
+ 1985;150(1);61-6</bp:SOURCE>
+ <bp:AUTHORS rdf:datatype="xs:string">Branlant G</bp:AUTHORS>
+ </bp:publicationXref>
+ </bp:XREF>
+ <bp:NAME rdf:datatype="xs:string">GAPDH-A-CPLX</bp:NAME>
+ <bp:XREF>
+ <bp:publicationXref rdf:ID="publicationXref193">
+ <bp:TITLE rdf:datatype="xs:string">Involvement of the gapA- and
+ epd (gapB)-encoded dehydrogenases in pyridoxal 5'-phosphate
+ coenzyme biosynthesis in Escherichia coli K-12.</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="xs:string">Yang Y</bp:AUTHORS>
+ <bp:ID rdf:datatype="xs:string">9696782</bp:ID>
+ <bp:AUTHORS rdf:datatype="xs:string">Zhao G</bp:AUTHORS>
+ <bp:YEAR>1998</bp:YEAR>
+ <bp:AUTHORS rdf:datatype="xs:string">Winkler ME</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="xs:string">Man TK</bp:AUTHORS>
+ <bp:DB rdf:datatype="xs:string">PubMed</bp:DB>
+ <bp:SOURCE rdf:datatype="xs:string">J Bacteriol
+ 1998;180(16);4294-9</bp:SOURCE>
+ </bp:publicationXref>
+ </bp:XREF>
+ <bp:XREF rdf:resource="#publicationXref170" />
+ <bp:XREF>
+ <bp:publicationXref rdf:ID="publicationXref194">
+ <bp:ID rdf:datatype="xs:string">2124629</bp:ID>
+ <bp:DB rdf:datatype="xs:string">PubMed</bp:DB>
+ <bp:YEAR>1990</bp:YEAR>
+ <bp:SOURCE rdf:datatype="xs:string">J Mol Evol 1990;31(5);383-8
+ </bp:SOURCE>
+ <bp:AUTHORS rdf:datatype="xs:string">Alberro MR</bp:AUTHORS>
+ <bp:TITLE rdf:datatype="xs:string">A naturally occurring
+ horizontal gene transfer from a eukaryote to a prokaryote.
+ </bp:TITLE>
+ <bp:AUTHORS rdf:datatype="xs:string">Anderson KL</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="xs:string">Feng DF</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="xs:string">Doolittle RF</bp:AUTHORS>
+ </bp:publicationXref>
+ </bp:XREF>
+ <bp:COMPONENTS>
+ <bp:physicalEntityParticipant
+ rdf:ID="physicalEntityParticipant195">
+ <bp:CELLULAR-LOCATION rdf:resource="#openControlledVocabulary17" />
+ <bp:STOICHIOMETRIC-COEFFICIENT>4
+ </bp:STOICHIOMETRIC-COEFFICIENT>
+ <bp:PHYSICAL-ENTITY>
+ <bp:protein rdf:ID="protein196">
+ <bp:SEQUENCE rdf:datatype="xs:string">MTIKVGINGFGRIGRIVFRAAQKRSDIEIVAINDLLDADYMAYMLKYDSTHGRFDGTVEVKDGHLIVNGKKIRVTAERDPANLKWDEVGVDVVAEATGLFLTDETARKHITAGAKKVVMTGPSKDNTPMFVKGANFDKYAGQDIVSNASCTTNCLAPLAKVINDNFGIIEGLMTTVHATTATQKTVDGPSHKDWRGGRGASQNIIPSSTGAAKAVGKVLPELNGKLTGMAFRVPTPNVSVVDLTVRLEKAATYEQIKAAVKAAAEGEMKGVLGYTEDDVVSTDFNGEVCTSVFDAKAGIALNDNFVKLVSWYDNETGYSNKVLDLIAHISK
+ </bp:SEQUENCE>
+ <bp:XREF rdf:resource="#publicationXref192" />
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref197">
+ <bp:ID rdf:datatype="xs:string">NP_416293</bp:ID>
+ <bp:DB rdf:datatype="xs:string">RefSeq</bp:DB>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:SYNONYMS rdf:datatype="xs:string">B1779
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">Gap1
+ </bp:SYNONYMS>
+ <bp:XREF rdf:resource="#publicationXref170" />
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref198">
+ <bp:DB rdf:datatype="xs:string">SWISS-MODEL</bp:DB>
+ <bp:ID rdf:datatype="xs:string">P06977</bp:ID>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:NAME rdf:datatype="xs:string">glyceraldehyde 3-phosphate
+ dehydrogenase-A monomer</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="xs:string">GapA
+ </bp:SYNONYMS>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref199">
+ <bp:DB rdf:datatype="xs:string">PDB</bp:DB>
+ <bp:ID rdf:datatype="xs:string">1GAD</bp:ID>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:SYNONYMS rdf:datatype="xs:string">Gad
+ </bp:SYNONYMS>
+ <bp:ORGANISM rdf:resource="#bioSource43" />
+ <bp:COMMENT rdf:datatype="xs:string">A higher degree of
+ sequence homology exists between E.coli and eucaryotic
+ enzymes than betwen E. coli and the thermophilic bacterial
+ enzyme |CITS:[85257641]|. Mutant exhibits a growth defect
+ and also exhibits increased aggregation and lysis that are
+ rescued by high-salt media |CITS: [9260967]|. Regulation
+ has been described |CITS: [12672900]|. The regulation of
+ the fkpA, gapA, and hslT genes is affected by evolution
+ under conditions of chronic heat stress |CITS: [12672900]|.
+ </bp:COMMENT>
+ <bp:XREF rdf:resource="#relationshipXref169" />
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref200">
+ <bp:DB rdf:datatype="xs:string">PIR</bp:DB>
+ <bp:ID rdf:datatype="xs:string">b1779</bp:ID>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref201">
+ <bp:DB rdf:datatype="xs:string">PDB</bp:DB>
+ <bp:ID rdf:datatype="xs:string">1GAE</bp:ID>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref202">
+ <bp:DB rdf:datatype="xs:string">SWISS-PROT</bp:DB>
+ <bp:ID rdf:datatype="xs:string">P06977</bp:ID>
+ </bp:unificationXref>
+ </bp:XREF>
+ </bp:protein>
+ </bp:PHYSICAL-ENTITY>
+ </bp:physicalEntityParticipant>
+ </bp:COMPONENTS>
+ <bp:COMMENT rdf:datatype="xs:string">E.coli is unusual in having
+ two glyceraldehyde-3-phosphate dehydrogenases. The protein
+ GAPDH-A has a sequence that is more similar to eukaryotic
+ sequences than it is to prokaryotic types |CITS:[91087241]|.
+ GapA is required for glycolysis, while Epd (GapB) is not |CITS:
+ [9260967]|. GapA and Epd may be involved in production of
+ pyridoxal 5'-phosphate (PLP) |CITS: [9696782]|.</bp:COMMENT>
+ <bp:ORGANISM rdf:resource="#bioSource43" />
+ </bp:complex>
+ </bp:PHYSICAL-ENTITY>
+ </bp:physicalEntityParticipant>
+ </bp:CONTROLLER>
+ <bp:XREF>
+ <bp:publicationXref rdf:ID="publicationXref203">
+ <bp:SOURCE rdf:datatype="xs:string">The Enzymes, Vol.XIII Academic
+ Press, New York 1976;3rd Edition</bp:SOURCE>
+ <bp:TITLE rdf:datatype="xs:string">Oxidation-Reduction, Part C
+ </bp:TITLE>
+ </bp:publicationXref>
+ </bp:XREF>
+ </bp:catalysis>
+ </bp:STEP-INTERACTIONS>
+ <bp:NEXT-STEP>
+ <bp:pathwayStep rdf:ID="pathwayStep204">
+ <bp:STEP-INTERACTIONS>
+ <bp:biochemicalReaction rdf:ID="biochemicalReaction205">
+ <bp:RIGHT rdf:resource="#physicalEntityParticipant16" />
+ <bp:NAME rdf:datatype="xs:string">phosphoglycerate phosphorylation
+ </bp:NAME>
+ <bp:LEFT rdf:resource="#physicalEntityParticipant33" />
+ <bp:COMMENT rdf:datatype="xs:string">In this reaction a phosphoryl
+ group is transferred from the acyl phosphate of 1,3
+ diphosphoglycerate to ADP thereby forming ATP and
+ 3-phosphoglycerate.|CITS:[90336971]|</bp:COMMENT>
+ <bp:EC-NUMBER rdf:datatype="xs:string">2.7.2.3</bp:EC-NUMBER>
+ <bp:RIGHT rdf:resource="#physicalEntityParticipant188" />
+ <bp:LEFT rdf:resource="#physicalEntityParticipant57" />
+ </bp:biochemicalReaction>
+ </bp:STEP-INTERACTIONS>
+ <bp:NEXT-STEP rdf:resource="#pathwayStep54" />
+ <bp:STEP-INTERACTIONS>
+ <bp:modulation rdf:ID="modulation206">
+ <bp:CONTROLLER rdf:resource="#physicalEntityParticipant57" />
+ <bp:CONTROLLED>
+ <bp:catalysis rdf:ID="catalysis207">
+ <bp:SYNONYMS rdf:datatype="xs:string">2,3-diphospho-D-glycerate
+ </bp:SYNONYMS>
+ <bp:CONTROLLED rdf:resource="#biochemicalReaction205" />
+ <bp:CONTROLLER>
+ <bp:physicalEntityParticipant
+ rdf:ID="physicalEntityParticipant208">
+ <bp:PHYSICAL-ENTITY>
+ <bp:protein rdf:ID="protein209">
+ <bp:NAME rdf:datatype="xs:string">PGK</bp:NAME>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref210">
+ <bp:DB rdf:datatype="xs:string">SWISS-PROT</bp:DB>
+ <bp:ID rdf:datatype="xs:string">P11665</bp:ID>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:SEQUENCE rdf:datatype="xs:string">MSVIKMTDLDLAGKRVFIRADLNVPVKDGKVTSDARIRASLPTIELALKQGAKVMVTSHLGRPTEGEYNEEFSLLPVVNYLKDKLSNPVRLVKDYLDGVDVAEGELVVLENVRFNKGEKKDDETLSKKYAALCDVFVMDAFGTAHRAQASTHGIGKFADVACAGPLLAAELDALGKALKEPARPMVAIVGGSKVSTKLTVLDSLSKIADQLIVGGGIANTFIAAQGHDVGKSLYEADLVDEAKRLLTTCNIPVPSDVRVATEFSETAPATLKSVNDVKADEQILDIGDASAQELAEILKNAKTILWNGPVGVFEFPNFRKGTEIVANAIADSEAFSIAGGGDTLAAIDLFGIADKISYISTGGGAFLEFVEGKVLPAVAMLEERAKK
+ </bp:SEQUENCE>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref211">
+ <bp:ID rdf:datatype="xs:string">b2926</bp:ID>
+ <bp:DB rdf:datatype="xs:string">PIR</bp:DB>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:COMMENT rdf:datatype="xs:string">Phosphoglycerate kinase
+ is one of the proteins induced by anaerobiosis.
+ |CITS:[89306676]| The gene is transcribed from two
+ promoters, one immediately in front of an upstream gene
+ coding for a 38-kDa polypeptide of unknown function. The
+ pgk gene was also found to show growth phase regulation. A
+ structural determinant for glycerate 3-P kinase is located
+ near serA. The map order is
+ speB-pgk-serA-lysA-argA-eno-cysC.|CITS:[76195925]| Pgk has
+ similarity to an <i>Edwardsiella ictaluri</i> protein
+ |CITS: [12542086]|.</bp:COMMENT>
+ <bp:SYNONYMS rdf:datatype="xs:string">Pgk
+ </bp:SYNONYMS>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref212">
+ <bp:ID rdf:datatype="xs:string">NP_417401</bp:ID>
+ <bp:DB rdf:datatype="xs:string">RefSeq</bp:DB>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref213">
+ <bp:ID rdf:datatype="xs:string">P11665</bp:ID>
+ <bp:DB rdf:datatype="xs:string">SWISS-MODEL</bp:DB>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:SYNONYMS rdf:datatype="xs:string">B2926
+ </bp:SYNONYMS>
+ <bp:ORGANISM rdf:resource="#bioSource43" />
+ <bp:XREF>
+ <bp:relationshipXref rdf:ID="relationshipXref214">
+ <bp:DB rdf:datatype="xs:string">EcoO157Cyc</bp:DB>
+ <bp:RELATIONSHIP-TYPE rdf:datatype="xs:string">Ortholog
+ </bp:RELATIONSHIP-TYPE>
+ <bp:ID rdf:datatype="xs:string">G7E-3-MONOMER</bp:ID>
+ </bp:relationshipXref>
+ </bp:XREF>
+ </bp:protein>
+ </bp:PHYSICAL-ENTITY>
+ </bp:physicalEntityParticipant>
+ </bp:CONTROLLER>
+ <bp:COMMENT rdf:datatype="xs:string">The structure of Pgk
+ determined crystallographically is best described as an open
+ bi-lobal molecule. The active site of the enzyme lies deep in
+ the cleft formed between the two lobes.|CITS:[90336971]| When
+ purified enzymes were employed there was absolute dependence
+ upon the respective substrates of the glycolytic pathway. There
+ was no activity unless ATP and glycerate-3-P were both
+ included.|CITS:[71230170]|</bp:COMMENT>
+ <bp:SYNONYMS rdf:datatype="xs:string">2-phospho-D-glycerate
+ phosphotransferase</bp:SYNONYMS>
+ <bp:DIRECTION rdf:datatype="xs:string">REVERSIBLE
+ </bp:DIRECTION>
+ <bp:SYNONYMS rdf:datatype="xs:string">3-phosphoglycerate kinase
+ </bp:SYNONYMS>
+ <bp:NAME rdf:datatype="xs:string">phosphoglycerate kinase</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="xs:string">Glycerate 3-P kinase
+ </bp:SYNONYMS>
+ </bp:catalysis>
+ </bp:CONTROLLED>
+ <bp:CONTROL-TYPE rdf:datatype="xs:string">ACTIVATION-UNKMECH
+ </bp:CONTROL-TYPE>
+ </bp:modulation>
+ </bp:STEP-INTERACTIONS>
+ <bp:STEP-INTERACTIONS rdf:resource="#catalysis207" />
+ <bp:STEP-INTERACTIONS>
+ <bp:modulation rdf:ID="modulation215">
+ <bp:CONTROLLED rdf:resource="#catalysis207" />
+ <bp:CONTROLLER rdf:resource="#physicalEntityParticipant33" />
+ <bp:CONTROL-TYPE rdf:datatype="xs:string">ACTIVATION-UNKMECH
+ </bp:CONTROL-TYPE>
+ </bp:modulation>
+ </bp:STEP-INTERACTIONS>
+ </bp:pathwayStep>
+ </bp:NEXT-STEP>
+ <bp:STEP-INTERACTIONS>
+ <bp:modulation rdf:ID="modulation216">
+ <bp:CONTROLLER>
+ <bp:physicalEntityParticipant rdf:ID="physicalEntityParticipant217">
+ <bp:STOICHIOMETRIC-COEFFICIENT>1.0</bp:STOICHIOMETRIC-COEFFICIENT>
+ <bp:PHYSICAL-ENTITY>
+ <bp:smallMolecule rdf:ID="smallMolecule218">
+ <bp:SYNONYMS rdf:datatype="xs:string">AsO<SUB>4</SUB><SUP>3-</SUP>
+ </bp:SYNONYMS>
+ <bp:MOLECULAR-WEIGHT>138.91900634765625</bp:MOLECULAR-WEIGHT>
+ <bp:NAME rdf:datatype="xs:string">arsenate</bp:NAME>
+ <bp:STRUCTURE>
+ <bp:chemicalStructure rdf:ID="chemicalStructure219">
+ <bp:STRUCTURE-FORMAT rdf:datatype="xs:string">
+ CML</bp:STRUCTURE-FORMAT>
+ <bp:STRUCTURE-DATA rdf:datatype="xs:string">
+ <cml> <molecule id="ARSENATE" title="arsenate"
+ dictRef="dictARSENATE"> <atomArray> <atom
+ id="ARSENATE-atom1" elementType="AS" x2="0.0" y2="0.0"/>
+ <atom id="ARSENATE-atom2" elementType="O" x2="0.9961977"
+ y2="0.0" formalCharge="-1"/> <atom id="ARSENATE-atom3"
+ elementType="O" x2="0.0" y2="0.9961977" formalCharge="-1"/>
+ <atom id="ARSENATE-atom4" elementType="O" x2="0.0"
+ y2="-1.0" formalCharge="-1"/> <atom id="ARSENATE-atom5"
+ elementType="O" x2="-1.0" y2="0.0"/> </atomArray>
+ <bondArray> <bond id="ARSENATE-bond1"
+ atomRefs="ARSENATE-atom5 ARSENATE-atom1" order="2"/> <bond
+ id="ARSENATE-bond2" atomRefs="ARSENATE-atom4 ARSENATE-atom1"
+ order="1"/> <bond id="ARSENATE-bond3"
+ atomRefs="ARSENATE-atom3 ARSENATE-atom1" order="1"/> <bond
+ id="ARSENATE-bond4" atomRefs="ARSENATE-atom2 ARSENATE-atom1"
+ order="1"/> </bondArray> <formula concise="O 4 AS 1"
+ formalCharge="-3"/> <float title="molecularWeight"
+ units="g/mol">138.919</float> <string
+ title="smiles">[As]([O-1])([O-1])(=O)[O-1]</string>
+ </molecule> </cml></bp:STRUCTURE-DATA>
+ </bp:chemicalStructure>
+ </bp:STRUCTURE>
+ <bp:SYNONYMS rdf:datatype="xs:string">inorganic arsenate
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">orthoarsenate
+ </bp:SYNONYMS>
+ </bp:smallMolecule>
+ </bp:PHYSICAL-ENTITY>
+ </bp:physicalEntityParticipant>
+ </bp:CONTROLLER>
+ <bp:CONTROLLED rdf:resource="#catalysis189" />
+ <bp:CONTROL-TYPE rdf:datatype="xs:string">ACTIVATION-UNKMECH
+ </bp:CONTROL-TYPE>
+ <bp:XREF>
+ <bp:publicationXref rdf:ID="publicationXref220">
+ <bp:AUTHORS rdf:datatype="xs:string">Winkler ME</bp:AUTHORS>
+ <bp:DB rdf:datatype="xs:string">PubMed</bp:DB>
+ <bp:SOURCE rdf:datatype="xs:string">J Bacteriol 1995;177(10);2804-12
+ </bp:SOURCE>
+ <bp:YEAR>1995</bp:YEAR>
+ <bp:TITLE rdf:datatype="xs:string">Biochemical characterization of
+ gapB-encoded erythrose 4-phosphate dehydrogenase of Escherichia
+ coli K-12 and its possible role in pyridoxal 5'-phosphate
+ biosynthesis.</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="xs:string">Bharani N</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="xs:string">Pease AJ</bp:AUTHORS>
+ <bp:ID rdf:datatype="xs:string">7751290</bp:ID>
+ <bp:AUTHORS rdf:datatype="xs:string">Zhao G</bp:AUTHORS>
+ </bp:publicationXref>
+ </bp:XREF>
+ </bp:modulation>
+ </bp:STEP-INTERACTIONS>
+ </bp:pathwayStep>
+ <bp:protein rdf:ID="protein221">
+ <bp:ORGANISM rdf:resource="#bioSource43" />
+ <bp:XREF>
+ <bp:publicationXref rdf:ID="publicationXref222">
+ <bp:ID rdf:datatype="xs:string">6235149</bp:ID>
+ <bp:YEAR>1984</bp:YEAR>
+ <bp:SOURCE rdf:datatype="xs:string">Gene 1984;28(3);337-42</bp:SOURCE>
+ <bp:DB rdf:datatype="xs:string">PubMed</bp:DB>
+ <bp:TITLE rdf:datatype="xs:string">Nucleotide sequence of gene pfkB
+ encoding the minor phosphofructokinase of Escherichia coli K-12.
+ </bp:TITLE>
+ <bp:AUTHORS rdf:datatype="xs:string">Daldal F</bp:AUTHORS>
+ </bp:publicationXref>
+ </bp:XREF>
+ <bp:SYNONYMS rdf:datatype="xs:string">PfkB</bp:SYNONYMS>
+ <bp:NAME rdf:datatype="xs:string">6-phosphofructokinase-2 monomer
+ </bp:NAME>
+ <bp:XREF>
+ <bp:relationshipXref rdf:ID="relationshipXref223">
+ <bp:RELATIONSHIP-TYPE rdf:datatype="xs:string">Ortholog
+ </bp:RELATIONSHIP-TYPE>
+ <bp:ID rdf:datatype="xs:string">PFKB-MONOMER</bp:ID>
+ <bp:DB rdf:datatype="xs:string">EcoO157Cyc</bp:DB>
+ </bp:relationshipXref>
+ </bp:XREF>
+ <bp:SEQUENCE rdf:datatype="xs:string">MVRIYTLTLAPSLDSATITPQIYPEGKLRCTAPVFEPGGGGINVARAIAHLGGSATAIFPAGGATGEHLVSLLADENVPVATVEAKDWTRQNLHVHVEASGEQYRFVMPGAALNEDEFRQLEEQVLEIESGAILVISGSLPPGVKLEKLTQLISAAQKQGIRCIVDSSGEALSAALAIGNIELVKPNQKELSALVNRELTQPDDVRKAAQEIVNSGKAKRVVVSLGPQGALGVDSENCIQVVPPPVKSQSTVGAGDSMVGAMTLKLAENASLEEMVRFGVAAGSAATLNQGTRLCSHDDTQKIYAYLSR
+ </bp:SEQUENCE>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref224">
+ <bp:DB rdf:datatype="xs:string">RefSeq</bp:DB>
+ <bp:ID rdf:datatype="xs:string">NP_416237</bp:ID>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref225">
+ <bp:DB rdf:datatype="xs:string">SWISS-PROT</bp:DB>
+ <bp:ID rdf:datatype="xs:string">P06999</bp:ID>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:SYNONYMS rdf:datatype="xs:string">B1723</bp:SYNONYMS>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref226">
+ <bp:DB rdf:datatype="xs:string">PIR</bp:DB>
+ <bp:ID rdf:datatype="xs:string">b1723</bp:ID>
+ </bp:unificationXref>
+ </bp:XREF>
+ </bp:protein>
+ <bp:unificationXref rdf:ID="unificationXref227">
+ <bp:DB rdf:datatype="xs:string">CAS</bp:DB>
+ <bp:ID rdf:datatype="xs:string">56-73-5</bp:ID>
+ </bp:unificationXref>
+ <bp:physicalEntityParticipant rdf:ID="physicalEntityParticipant228">
+ <bp:STOICHIOMETRIC-COEFFICIENT>1</bp:STOICHIOMETRIC-COEFFICIENT>
+ <bp:CELLULAR-LOCATION rdf:resource="#openControlledVocabulary17" />
+ <bp:PHYSICAL-ENTITY>
+ <bp:smallMolecule rdf:ID="smallMolecule229">
+ <bp:STRUCTURE>
+ <bp:chemicalStructure rdf:ID="chemicalStructure230">
+ <bp:STRUCTURE-DATA rdf:datatype="xs:string"> <cml>
+ <molecule id="DIHYDROXY-ACETONE-PHOSPHATE"
+ title="dihydroxy-acetone-phosphate"
+ dictRef="dictDIHYDROXY-ACETONE-PHOSPHATE"> <atomArray>
+ <atom id="DIHYDROXY-ACETONE-PHOSPHATE-atom1" elementType="O"
+ x2="0.60784" y2="-1.0"/> <atom
+ id="DIHYDROXY-ACETONE-PHOSPHATE-atom2" elementType="O" x2="-1.0"
+ y2="-0.53922"/> <atom id="DIHYDROXY-ACETONE-PHOSPHATE-atom3"
+ elementType="P" x2="0.60784" y2="-0.61111"/> <atom
+ id="DIHYDROXY-ACETONE-PHOSPHATE-atom4" elementType="O"
+ x2="-0.38562" y2="-0.21242"/> <atom
+ id="DIHYDROXY-ACETONE-PHOSPHATE-atom5" elementType="C"
+ x2="-0.38562" y2="-0.60131"/> <atom
+ id="DIHYDROXY-ACETONE-PHOSPHATE-atom6" elementType="O"
+ x2="0.19608" y2="-0.61111"/> <atom
+ id="DIHYDROXY-ACETONE-PHOSPHATE-atom7" elementType="C"
+ x2="-0.68954" y2="-0.77451"/> <atom
+ id="DIHYDROXY-ACETONE-PHOSPHATE-atom8" elementType="O"
+ x2="0.99673" y2="-0.61111"/> <atom
+ id="DIHYDROXY-ACETONE-PHOSPHATE-atom9" elementType="O"
+ x2="0.60784" y2="-0.22222"/> <atom
+ id="DIHYDROXY-ACETONE-PHOSPHATE-atom10" elementType="C"
+ x2="-0.07843" y2="-0.77451"/> </atomArray> <bondArray>
+ <bond id="DIHYDROXY-ACETONE-PHOSPHATE-bond1"
+ atomRefs="DIHYDROXY-ACETONE-PHOSPHATE-atom10
+ DIHYDROXY-ACETONE-PHOSPHATE-atom6" order="1"/> <bond
+ id="DIHYDROXY-ACETONE-PHOSPHATE-bond2"
+ atomRefs="DIHYDROXY-ACETONE-PHOSPHATE-atom9
+ DIHYDROXY-ACETONE-PHOSPHATE-atom3" order="2"/> <bond
+ id="DIHYDROXY-ACETONE-PHOSPHATE-bond3"
+ atomRefs="DIHYDROXY-ACETONE-PHOSPHATE-atom8
+ DIHYDROXY-ACETONE-PHOSPHATE-atom3" order="1"/> <bond
+ id="DIHYDROXY-ACETONE-PHOSPHATE-bond4"
+ atomRefs="DIHYDROXY-ACETONE-PHOSPHATE-atom7
+ DIHYDROXY-ACETONE-PHOSPHATE-atom5" order="1"/> <bond
+ id="DIHYDROXY-ACETONE-PHOSPHATE-bond5"
+ atomRefs="DIHYDROXY-ACETONE-PHOSPHATE-atom6
+ DIHYDROXY-ACETONE-PHOSPHATE-atom3" order="1"/> <bond
+ id="DIHYDROXY-ACETONE-PHOSPHATE-bond6"
+ atomRefs="DIHYDROXY-ACETONE-PHOSPHATE-atom5
+ DIHYDROXY-ACETONE-PHOSPHATE-atom10" order="1"/> <bond
+ id="DIHYDROXY-ACETONE-PHOSPHATE-bond7"
+ atomRefs="DIHYDROXY-ACETONE-PHOSPHATE-atom4
+ DIHYDROXY-ACETONE-PHOSPHATE-atom5" order="2"/> <bond
+ id="DIHYDROXY-ACETONE-PHOSPHATE-bond8"
+ atomRefs="DIHYDROXY-ACETONE-PHOSPHATE-atom2
+ DIHYDROXY-ACETONE-PHOSPHATE-atom7" order="1"/> <bond
+ id="DIHYDROXY-ACETONE-PHOSPHATE-bond9"
+ atomRefs="DIHYDROXY-ACETONE-PHOSPHATE-atom1
+ DIHYDROXY-ACETONE-PHOSPHATE-atom3" order="1"/> </bondArray>
+ <formula concise="C 3 H 7 O 6 P 1" formalCharge="0"/>
+ <float title="molecularWeight"
+ units="g/mol">170.058</float> <string
+ title="smiles">C(O)C(=O)COP(O)(=O)O</string> </molecule>
+ </cml></bp:STRUCTURE-DATA>
+ <bp:STRUCTURE-FORMAT rdf:datatype="xs:string">CML
+ </bp:STRUCTURE-FORMAT>
+ </bp:chemicalStructure>
+ </bp:STRUCTURE>
+ <bp:NAME rdf:datatype="xs:string">dihydroxy-acetone-phosphate</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="xs:string">dihydroxyacetone-P
+ </bp:SYNONYMS>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref231">
+ <bp:ID rdf:datatype="xs:string">57-04-5</bp:ID>
+ <bp:DB rdf:datatype="xs:string">CAS</bp:DB>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:SYNONYMS rdf:datatype="xs:string">dihydroxyacetone 3-phosphate
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">DHAP</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">dihydroxyacetone-phosphate
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">glycerone-phosphate
+ </bp:SYNONYMS>
+ <bp:MOLECULAR-WEIGHT>170.05799865722656</bp:MOLECULAR-WEIGHT>
+ <bp:SYNONYMS rdf:datatype="xs:string">di-OH-acetone-P</bp:SYNONYMS>
+ </bp:smallMolecule>
+ </bp:PHYSICAL-ENTITY>
+ </bp:physicalEntityParticipant>
+ <bp:modulation rdf:ID="modulation232">
+ <bp:CONTROLLER>
+ <bp:physicalEntityParticipant rdf:ID="physicalEntityParticipant233">
+ <bp:PHYSICAL-ENTITY>
+ <bp:smallMolecule rdf:ID="smallMolecule234">
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref235">
+ <bp:ID rdf:datatype="xs:string">146-91-8</bp:ID>
+ <bp:DB rdf:datatype="xs:string">CAS</bp:DB>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:STRUCTURE>
+ <bp:chemicalStructure rdf:ID="chemicalStructure236">
+ <bp:STRUCTURE-DATA rdf:datatype="xs:string"> <cml>
+ <molecule id="GDP" title="GDP" dictRef="dictGDP">
+ <atomArray> <atom id="GDP-atom1" elementType="N"
+ x2="-0.05666667" y2="0.06666667"/> <atom id="GDP-atom2"
+ elementType="H" x2="0.99666667" y2="-0.7366667"/> <atom
+ id="GDP-atom3" elementType="N" x2="0.99666667" y2="0.2"/>
+ <atom id="GDP-atom4" elementType="N" x2="0.4"
+ y2="0.046666667"/> <atom id="GDP-atom5" elementType="N"
+ x2="0.18" y2="0.44"/> <atom id="GDP-atom6" elementType="C"
+ x2="0.26666668" y2="-0.39333335"/> <atom id="GDP-atom7"
+ elementType="C" x2="0.99666667" y2="0.42333335"/> <atom
+ id="GDP-atom8" elementType="O" x2="-0.7266667" y2="-0.12"/>
+ <atom id="GDP-atom9" elementType="N" x2="0.81666666"
+ y2="0.5466667"/> <atom id="GDP-atom10" elementType="O"
+ x2="0.41333333" y2="-1.0"/> <atom id="GDP-atom11"
+ elementType="C" x2="0.62" y2="0.44"/> <atom id="GDP-atom12"
+ elementType="H" x2="0.41333333" y2="-0.67333335"/> <atom
+ id="GDP-atom13" elementType="O" x2="-0.25333333"
+ y2="-0.6666667"/> <atom id="GDP-atom14" elementType="O"
+ x2="0.85333335" y2="-1.0"/> <atom id="GDP-atom15"
+ elementType="O" x2="-0.25333333" y2="-0.12"/> <atom
+ id="GDP-atom16" elementType="H" x2="0.0" y2="0.54333335"/>
+ <atom id="GDP-atom17" elementType="O" x2="0.4" y2="0.85"/>
+ <atom id="GDP-atom18" elementType="H" x2="0.85333335"
+ y2="-0.67333335"/> <atom id="GDP-atom19" elementType="C"
+ x2="0.26666668" y2="-0.5733333"/> <atom id="GDP-atom20"
+ elementType="C" x2="0.4" y2="0.57666665"/> <atom
+ id="GDP-atom21" elementType="O" x2="-0.7266667"
+ y2="-0.6666667"/> <atom id="GDP-atom22" elementType="H"
+ x2="0.26666668" y2="-0.7366667"/> <atom id="GDP-atom23"
+ elementType="P" x2="-0.25333333" y2="-0.39333335"/> <atom
+ id="GDP-atom24" elementType="C" x2="0.85333335"
+ y2="-0.83666664"/> <atom id="GDP-atom25" elementType="O"
+ x2="-1.0" y2="-0.39333335"/> <atom id="GDP-atom26"
+ elementType="O" x2="-0.45" y2="-0.39333335"/> <atom
+ id="GDP-atom27" elementType="C" x2="0.99666667"
+ y2="-0.5733333"/> <atom id="GDP-atom28" elementType="C"
+ x2="0.18" y2="0.2"/> <atom id="GDP-atom29" elementType="C"
+ x2="0.41333333" y2="-0.83666664"/> <atom id="GDP-atom30"
+ elementType="C" x2="0.62" y2="0.2"/> <atom id="GDP-atom31"
+ elementType="O" x2="0.62666667" y2="-0.35666665"/> <atom
+ id="GDP-atom32" elementType="P" x2="-0.7266667"
+ y2="-0.39333335"/> <atom id="GDP-atom33" elementType="O"
+ x2="0.02" y2="-0.39333335"/> </atomArray> <bondArray>
+ <bond id="GDP-bond1" atomRefs="GDP-atom33 GDP-atom6"
+ order="1"/> <bond id="GDP-bond2" atomRefs="GDP-atom32
+ GDP-atom26" order="1"/> <bond id="GDP-bond3"
+ atomRefs="GDP-atom31 GDP-atom27" order="1"/> <bond
+ id="GDP-bond4" atomRefs="GDP-atom30 GDP-atom4" order="A"/>
+ <bond id="GDP-bond5" atomRefs="GDP-atom30 GDP-atom3"
+ order="A"/> <bond id="GDP-bond6" atomRefs="GDP-atom29
+ GDP-atom24" order="1"/> <bond id="GDP-bond7"
+ atomRefs="GDP-atom28 GDP-atom5" order="A"/> <bond
+ id="GDP-bond8" atomRefs="GDP-atom27 GDP-atom24" order="1"/>
+ <bond id="GDP-bond9" atomRefs="GDP-atom27 GDP-atom3"
+ order="1"/> <bond id="GDP-bond10" atomRefs="GDP-atom26
+ GDP-atom23" order="1"/> <bond id="GDP-bond11"
+ atomRefs="GDP-atom25 GDP-atom32" order="2"/> <bond
+ id="GDP-bond12" atomRefs="GDP-atom23 GDP-atom33" order="1"/>
+ <bond id="GDP-bond13" atomRefs="GDP-atom22 GDP-atom19"
+ order="1"/> <bond id="GDP-bond14" atomRefs="GDP-atom21
+ GDP-atom32" order="1"/> <bond id="GDP-bond15"
+ atomRefs="GDP-atom20 GDP-atom11" order="A"/> <bond
+ id="GDP-bond16" atomRefs="GDP-atom19 GDP-atom29" order="1"/>
+ <bond id="GDP-bond17" atomRefs="GDP-atom19 GDP-atom31"
+ order="1"/> <bond id="GDP-bond18" atomRefs="GDP-atom18
+ GDP-atom24" order="1"/> <bond id="GDP-bond19"
+ atomRefs="GDP-atom17 GDP-atom20" order="2"/> <bond
+ id="GDP-bond20" atomRefs="GDP-atom16 GDP-atom5" order="1"/>
+ <bond id="GDP-bond21" atomRefs="GDP-atom15 GDP-atom23"
+ order="2"/> <bond id="GDP-bond22" atomRefs="GDP-atom14
+ GDP-atom24" order="1"/> <bond id="GDP-bond23"
+ atomRefs="GDP-atom13 GDP-atom23" order="1"/> <bond
+ id="GDP-bond24" atomRefs="GDP-atom12 GDP-atom29" order="1"/>
+ <bond id="GDP-bond25" atomRefs="GDP-atom11 GDP-atom30"
+ order="A"/> <bond id="GDP-bond26" atomRefs="GDP-atom10
+ GDP-atom29" order="1"/> <bond id="GDP-bond27"
+ atomRefs="GDP-atom9 GDP-atom11" order="A"/> <bond
+ id="GDP-bond28" atomRefs="GDP-atom8 GDP-atom32" order="1"/>
+ <bond id="GDP-bond29" atomRefs="GDP-atom7 GDP-atom9"
+ order="A"/> <bond id="GDP-bond30" atomRefs="GDP-atom6
+ GDP-atom19" order="1"/> <bond id="GDP-bond31"
+ atomRefs="GDP-atom5 GDP-atom20" order="A"/> <bond
+ id="GDP-bond32" atomRefs="GDP-atom4 GDP-atom28" order="A"/>
+ <bond id="GDP-bond33" atomRefs="GDP-atom3 GDP-atom7"
+ order="A"/> <bond id="GDP-bond34" atomRefs="GDP-atom2
+ GDP-atom27" order="1"/> <bond id="GDP-bond35"
+ atomRefs="GDP-atom1 GDP-atom28" order="1"/> </bondArray>
+ <formula concise="C 10 H 15 N 5 O 11 P 2"
+ formalCharge="-3"/> <float title="molecularWeight"
+ units="g/mol">443.203</float> <string
+ title="smiles">C(OP(O)(=O)OP(O)(=O)O)[CH]1(O[CH]([CH](O)[CH]1O)n2(c3(c(nc2)c(=O)[nH]c(n3)N)))</string>
+ </molecule> </cml></bp:STRUCTURE-DATA>
+ <bp:STRUCTURE-FORMAT rdf:datatype="xs:string">
+ CML</bp:STRUCTURE-FORMAT>
+ </bp:chemicalStructure>
+ </bp:STRUCTURE>
+ <bp:SYNONYMS rdf:datatype="xs:string">ppG</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">guanosine-5'-diphosphate
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">guanosine-diphosphate
+ </bp:SYNONYMS>
+ <bp:MOLECULAR-WEIGHT>443.2030029296875</bp:MOLECULAR-WEIGHT>
+ <bp:NAME rdf:datatype="xs:string">GDP</bp:NAME>
+ </bp:smallMolecule>
+ </bp:PHYSICAL-ENTITY>
+ <bp:CELLULAR-LOCATION rdf:resource="#openControlledVocabulary17" />
+ <bp:STOICHIOMETRIC-COEFFICIENT>1.0</bp:STOICHIOMETRIC-COEFFICIENT>
+ </bp:physicalEntityParticipant>
+ </bp:CONTROLLER>
+ <bp:CONTROLLED rdf:resource="#catalysis2" />
+ <bp:CONTROL-TYPE rdf:datatype="xs:string">ACTIVATION-ALLOSTERIC
+ </bp:CONTROL-TYPE>
+ </bp:modulation>
+ <bp:modulation rdf:ID="modulation237">
+ <bp:CONTROL-TYPE rdf:datatype="xs:string">INHIBITION-UNKMECH
+ </bp:CONTROL-TYPE>
+ <bp:CONTROLLER rdf:resource="#physicalEntityParticipant29" />
+ <bp:CONTROLLED>
+ <bp:catalysis rdf:ID="catalysis238">
+ <bp:DIRECTION rdf:datatype="xs:string">REVERSIBLE</bp:DIRECTION>
+ <bp:XREF>
+ <bp:publicationXref rdf:ID="publicationXref239">
+ <bp:YEAR>1981</bp:YEAR>
+ <bp:SOURCE rdf:datatype="xs:string">Eur J Biochem 1981;117(3);569-74
+ </bp:SOURCE>
+ <bp:DB rdf:datatype="xs:string">PubMed</bp:DB>
+ <bp:TITLE rdf:datatype="xs:string">Regulatory properties of
+ phosphofructokinase 2 from Escherichia coli.</bp:TITLE>
+ <bp:ID rdf:datatype="xs:string">6456900</bp:ID>
+ <bp:AUTHORS rdf:datatype="xs:string">Kotlarz D</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="xs:string">Buc H</bp:AUTHORS>
+ </bp:publicationXref>
+ </bp:XREF>
+ <bp:SYNONYMS rdf:datatype="xs:string">fructose-6-phosphate-1-phosphotransferase
+ </bp:SYNONYMS>
+ <bp:CONTROLLER>
+ <bp:physicalEntityParticipant rdf:ID="physicalEntityParticipant240">
+ <bp:PHYSICAL-ENTITY>
+ <bp:complex rdf:ID="complex241">
+ <bp:COMMENT rdf:datatype="xs:string">This enzyme is an isozyme
+ with phosphofructokinase-1. The nucleotide sequences of the
+ genes are not similar.|CITS: [85203917]|</bp:COMMENT>
+ <bp:COMPONENTS>
+ <bp:physicalEntityParticipant
+ rdf:ID="physicalEntityParticipant242">
+ <bp:STOICHIOMETRIC-COEFFICIENT>2
+ </bp:STOICHIOMETRIC-COEFFICIENT>
+ <bp:PHYSICAL-ENTITY rdf:resource="#protein221" />
+ <bp:CELLULAR-LOCATION rdf:resource="#openControlledVocabulary40" />
+ </bp:physicalEntityParticipant>
+ </bp:COMPONENTS>
+ <bp:ORGANISM rdf:resource="#bioSource43" />
+ <bp:XREF>
+ <bp:publicationXref rdf:ID="publicationXref243">
+ <bp:SOURCE rdf:datatype="xs:string">Eur J Biochem
+ 1985;149(2);363-73</bp:SOURCE>
+ <bp:ID rdf:datatype="xs:string">3158524</bp:ID>
+ <bp:AUTHORS rdf:datatype="xs:string">Hellinga HW</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="xs:string">Evans PR</bp:AUTHORS>
+ <bp:DB rdf:datatype="xs:string">PubMed</bp:DB>
+ <bp:TITLE rdf:datatype="xs:string">Nucleotide sequence and
+ high-level expression of the major Escherichia coli
+ phosphofructokinase.</bp:TITLE>
+ <bp:YEAR>1985</bp:YEAR>
+ </bp:publicationXref>
+ </bp:XREF>
+ <bp:XREF rdf:resource="#publicationXref239" />
+ <bp:NAME rdf:datatype="xs:string">6PFK-2-CPX</bp:NAME>
+ </bp:complex>
+ </bp:PHYSICAL-ENTITY>
+ </bp:physicalEntityParticipant>
+ </bp:CONTROLLER>
+ <bp:SYNONYMS rdf:datatype="xs:string">PFK II</bp:SYNONYMS>
+ <bp:NAME rdf:datatype="xs:string">6-phosphofructokinase-2</bp:NAME>
+ <bp:CONTROLLED rdf:resource="#biochemicalReaction13" />
+ <bp:XREF>
+ <bp:publicationXref rdf:ID="publicationXref244">
+ <bp:ID rdf:datatype="xs:string">149128</bp:ID>
+ <bp:SOURCE rdf:datatype="xs:string">J Biol Chem 1978;253(12);4350-5
+ </bp:SOURCE>
+ <bp:AUTHORS rdf:datatype="xs:string">Babul J</bp:AUTHORS>
+ <bp:DB rdf:datatype="xs:string">PubMed</bp:DB>
+ <bp:YEAR>1978</bp:YEAR>
+ <bp:TITLE rdf:datatype="xs:string">Phosphofructokinases from
+ Escherichia coli. Purification and characterization of the
+ nonallosteric isozyme.</bp:TITLE>
+ </bp:publicationXref>
+ </bp:XREF>
+ <bp:SYNONYMS rdf:datatype="xs:string">fructose-6-p-1-kinase
+ </bp:SYNONYMS>
+ <bp:COMMENT rdf:datatype="xs:string">Pfk-2 is somewhat sensitive to
+ inhibition by fructose-1,6-diphosphate and ATP. Pfk-2,unlike pfk-1,
+ does not show cooperative interaction with fructose-6-phosphate,
+ inhibition by PEP or activation by ADP. |CITS:[84262485]| MgATP is
+ an inhibitor of pfk-2 and it provokes the tetramerization of the
+ dimeric native enzyme.|CITS: [85289307],[88292964]| Its normal
+ function is not known and in strains with pfk-1, pfkB may be
+ deleted without apparent effect. |CITS: [83294514]| However in the
+ absence of pfk-1, slow growth on sugars depends on pfk-2. Its loss
+ causes complete inability to grow. |CITS: [84262485]| The
+ distribution of the two phosphofructokinases is variable among
+ enterobacteria and also among E.coli strains |CITS: [82027179]|
+ </bp:COMMENT>
+ </bp:catalysis>
+ </bp:CONTROLLED>
+ <bp:XREF rdf:resource="#publicationXref244" />
+ </bp:modulation>
+ <bp:unificationXref rdf:ID="unificationXref245">
+ <bp:ID rdf:datatype="xs:string">NP_417400</bp:ID>
+ <bp:DB rdf:datatype="xs:string">RefSeq</bp:DB>
+ </bp:unificationXref>
+ <bp:unificationXref rdf:ID="unificationXref246">
+ <bp:ID rdf:datatype="xs:string">1DOS</bp:ID>
+ <bp:DB rdf:datatype="xs:string">PDB</bp:DB>
+ </bp:unificationXref>
+ <bp:smallMolecule rdf:ID="smallMolecule247">
+ <bp:STRUCTURE>
+ <bp:chemicalStructure rdf:ID="chemicalStructure248">
+ <bp:STRUCTURE-DATA rdf:datatype="xs:string"> <cml>
+ <molecule id="CIT" title="citrate" dictRef="dictCIT">
+ <atomArray> <atom id="CIT-atom1" elementType="O"
+ x2="-0.62098" y2="0.17428"/> <atom id="CIT-atom2"
+ elementType="O" x2="0.6176" y2="0.20135"/> <atom id="CIT-atom3"
+ elementType="O" x2="-1.0" y2="-0.20474"/> <atom id="CIT-atom4"
+ elementType="C" x2="-0.022" y2="-0.45516"/> <atom id="CIT-atom5"
+ elementType="C" x2="-0.62098" y2="-0.20474"/> <atom
+ id="CIT-atom6" elementType="C" x2="-0.022" y2="-0.7665"/> <atom
+ id="CIT-atom7" elementType="C" x2="-0.47885" y2="-0.45516"/>
+ <atom id="CIT-atom8" elementType="O" x2="-0.022" y2="-0.07614"/>
+ <atom id="CIT-atom9" elementType="O" x2="0.27919" y2="-1.0"/>
+ <atom id="CIT-atom10" elementType="C" x2="0.36379"
+ y2="-0.45516"/> <atom id="CIT-atom11" elementType="O"
+ x2="0.99662" y2="-0.17766"/> <atom id="CIT-atom12"
+ elementType="O" x2="-0.3198" y2="-1.0"/> <atom id="CIT-atom13"
+ elementType="C" x2="0.6176" y2="-0.17766"/> </atomArray>
+ <bondArray> <bond id="CIT-bond1" atomRefs="CIT-atom13
+ CIT-atom10" order="1"/> <bond id="CIT-bond2"
+ atomRefs="CIT-atom12 CIT-atom6" order="1"/> <bond id="CIT-bond3"
+ atomRefs="CIT-atom11 CIT-atom13" order="1"/> <bond
+ id="CIT-bond4" atomRefs="CIT-atom10 CIT-atom4" order="1"/> <bond
+ id="CIT-bond5" atomRefs="CIT-atom9 CIT-atom6" order="2"/> <bond
+ id="CIT-bond6" atomRefs="CIT-atom8 CIT-atom4" order="1"/> <bond
+ id="CIT-bond7" atomRefs="CIT-atom7 CIT-atom4" order="1"/> <bond
+ id="CIT-bond8" atomRefs="CIT-atom6 CIT-atom4" order="1"/> <bond
+ id="CIT-bond9" atomRefs="CIT-atom5 CIT-atom7" order="1"/> <bond
+ id="CIT-bond10" atomRefs="CIT-atom3 CIT-atom5" order="1"/> <bond
+ id="CIT-bond11" atomRefs="CIT-atom2 CIT-atom13" order="2"/>
+ <bond id="CIT-bond12" atomRefs="CIT-atom1 CIT-atom5" order="2"/>
+ </bondArray> <formula concise="C 6 H 8 O 7"
+ formalCharge="0"/> <float title="molecularWeight"
+ units="g/mol">192.125</float> <string
+ title="smiles">C(=O)(O)CC(C(O)=O)(O)CC(O)=O</string>
+ </molecule> </cml></bp:STRUCTURE-DATA>
+ <bp:STRUCTURE-FORMAT rdf:datatype="xs:string">CML
+ </bp:STRUCTURE-FORMAT>
+ </bp:chemicalStructure>
+ </bp:STRUCTURE>
+ <bp:NAME rdf:datatype="xs:string">citrate</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="xs:string">citric acid</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">citr</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">cit</bp:SYNONYMS>
+ <bp:MOLECULAR-WEIGHT>192.125</bp:MOLECULAR-WEIGHT>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref249">
+ <bp:DB rdf:datatype="xs:string">CAS</bp:DB>
+ <bp:ID rdf:datatype="xs:string">77-92-9</bp:ID>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:SYNONYMS rdf:datatype="xs:string">2-hydroxy-1,2,3-propanetricarboxylic
+ acid</bp:SYNONYMS>
+ </bp:smallMolecule>
+ <bp:physicalEntityParticipant rdf:ID="physicalEntityParticipant250">
+ <bp:PHYSICAL-ENTITY>
+ <bp:protein rdf:ID="protein251">
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref252">
+ <bp:ID rdf:datatype="xs:string">1TMH</bp:ID>
+ <bp:DB rdf:datatype="xs:string">PDB</bp:DB>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:SYNONYMS rdf:datatype="xs:string">Tpi</bp:SYNONYMS>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref253">
+ <bp:ID rdf:datatype="xs:string">b3919</bp:ID>
+ <bp:DB rdf:datatype="xs:string">PIR</bp:DB>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:NAME rdf:datatype="xs:string">triose phosphate isomerase monomer
+ </bp:NAME>
+ <bp:ORGANISM rdf:resource="#bioSource43" />
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref254">
+ <bp:DB rdf:datatype="xs:string">PDB</bp:DB>
+ <bp:ID rdf:datatype="xs:string">1TRE</bp:ID>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:SEQUENCE rdf:datatype="xs:string">MRHPLVMGNWKLNGSRHMVHELVSNLRKELAGVAGCAVAIAPPEMYIDMAKREAEGSHIMLGAQNVDLNLSGAFTGETSAAMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKEQGLTPVLCIGETEAENEAGKTEEVCARQIDAVLKTQGAAAFEGAVIAYEPVWAIGTGKSATPAQAQAVHKFIRDHIAKVDANIAEQVIIQYGGSVNASNAAELFAQPDIDGALVGGASLKADAFAVIVKAAEAAKQA
+ </bp:SEQUENCE>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref255">
+ <bp:ID rdf:datatype="xs:string">P04790</bp:ID>
+ <bp:DB rdf:datatype="xs:string">SWISS-PROT</bp:DB>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref256">
+ <bp:ID rdf:datatype="xs:string">NP_418354</bp:ID>
+ <bp:DB rdf:datatype="xs:string">RefSeq</bp:DB>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref257">
+ <bp:ID rdf:datatype="xs:string">P04790</bp:ID>
+ <bp:DB rdf:datatype="xs:string">SWISS-MODEL</bp:DB>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:XREF>
+ <bp:relationshipXref rdf:ID="relationshipXref258">
+ <bp:ID rdf:datatype="xs:string">TPIA-MONOMER</bp:ID>
+ <bp:DB rdf:datatype="xs:string">EcoO157Cyc</bp:DB>
+ <bp:RELATIONSHIP-TYPE rdf:datatype="xs:string">Ortholog
+ </bp:RELATIONSHIP-TYPE>
+ </bp:relationshipXref>
+ </bp:XREF>
+ <bp:SYNONYMS rdf:datatype="xs:string">TpiA</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">B3919</bp:SYNONYMS>
+ </bp:protein>
+ </bp:PHYSICAL-ENTITY>
+ <bp:STOICHIOMETRIC-COEFFICIENT>2</bp:STOICHIOMETRIC-COEFFICIENT>
+ <bp:CELLULAR-LOCATION rdf:resource="#openControlledVocabulary40" />
+ </bp:physicalEntityParticipant>
+ <bp:publicationXref rdf:ID="publicationXref259">
+ <bp:TITLE rdf:datatype="xs:string">Purification and characterization of
+ two fructose diphosphate aldolases from Escherichia coli (Crookes'
+ strain).</bp:TITLE>
+ <bp:DB rdf:datatype="xs:string">PubMed</bp:DB>
+ <bp:ID rdf:datatype="xs:string">4198624</bp:ID>
+ <bp:AUTHORS rdf:datatype="xs:string">Perham RN</bp:AUTHORS>
+ <bp:YEAR>1973</bp:YEAR>
+ <bp:AUTHORS rdf:datatype="xs:string">Stribling D</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="xs:string">Biochem J 1973;131(4);833-41
+ </bp:SOURCE>
+ </bp:publicationXref>
+ <bp:biochemicalReaction rdf:ID="biochemicalReaction260">
+ <bp:LEFT>
+ <bp:physicalEntityParticipant rdf:ID="physicalEntityParticipant261">
+ <bp:PHYSICAL-ENTITY>
+ <bp:smallMolecule rdf:ID="smallMolecule262">
+ <bp:SYNONYMS rdf:datatype="xs:string">D-glucose-6-P</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">α-D-glucose-6-phosphate
+ </bp:SYNONYMS>
+ <bp:MOLECULAR-WEIGHT>260.1369934082031</bp:MOLECULAR-WEIGHT>
+ <bp:SYNONYMS rdf:datatype="xs:string">α-D-glucose-6-P
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">D-glucose-6-phosphate
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">glucose-6-P</bp:SYNONYMS>
+ <bp:XREF rdf:resource="#unificationXref227" />
+ <bp:STRUCTURE>
+ <bp:chemicalStructure rdf:ID="chemicalStructure263">
+ <bp:STRUCTURE-DATA rdf:datatype="xs:string"> <cml>
+ <molecule id="GLC-6-P" title="glucose-6-phosphate"
+ dictRef="dictGLC-6-P"> <atomArray> <atom
+ id="GLC-6-P-atom1" elementType="H" x2="-1.0" y2="-0.13312"/>
+ <atom id="GLC-6-P-atom2" elementType="C" x2="-0.68182"
+ y2="0.32792"/> <atom id="GLC-6-P-atom3" elementType="O"
+ x2="-0.37338" y2="0.62013"/> <atom id="GLC-6-P-atom4"
+ elementType="O" x2="0.00974" y2="0.24351"/> <atom
+ id="GLC-6-P-atom5" elementType="C" x2="-0.06494"
+ y2="-0.77273"/> <atom id="GLC-6-P-atom6" elementType="P"
+ x2="0.00974" y2="0.62013"/> <atom id="GLC-6-P-atom7"
+ elementType="C" x2="0.26299" y2="-0.36039"/> <atom
+ id="GLC-6-P-atom8" elementType="C" x2="-0.68182"
+ y2="-0.77273"/> <atom id="GLC-6-P-atom9" elementType="O"
+ x2="0.00974" y2="0.99675"/> <atom id="GLC-6-P-atom10"
+ elementType="O" x2="-0.68182" y2="-0.54545"/> <atom
+ id="GLC-6-P-atom11" elementType="H" x2="0.26299"
+ y2="-0.13312"/> <atom id="GLC-6-P-atom12" elementType="C"
+ x2="-1.0" y2="-0.36039"/> <atom id="GLC-6-P-atom13"
+ elementType="H" x2="-0.06494" y2="-0.54545"/> <atom
+ id="GLC-6-P-atom14" elementType="O" x2="-0.06494"
+ y2="0.06494"/> <atom id="GLC-6-P-atom15" elementType="O"
+ x2="0.38636" y2="0.62013"/> <atom id="GLC-6-P-atom16"
+ elementType="O" x2="-0.06494" y2="-1.0"/> <atom
+ id="GLC-6-P-atom17" elementType="C" x2="-0.68182"
+ y2="0.06494"/> <atom id="GLC-6-P-atom18" elementType="O"
+ x2="0.26299" y2="-0.58766"/> <atom id="GLC-6-P-atom19"
+ elementType="H" x2="-0.68182" y2="-1.0"/> <atom
+ id="GLC-6-P-atom20" elementType="O" x2="-1.0" y2="-0.58766"/>
+ <atom id="GLC-6-P-atom21" elementType="H" x2="-0.68182"
+ y2="-0.16234"/> </atomArray> <bondArray> <bond
+ id="GLC-6-P-bond1" atomRefs="GLC-6-P-atom21 GLC-6-P-atom17"
+ order="1"/> <bond id="GLC-6-P-bond2"
+ atomRefs="GLC-6-P-atom20 GLC-6-P-atom12" order="1"/> <bond
+ id="GLC-6-P-bond3" atomRefs="GLC-6-P-atom19 GLC-6-P-atom8"
+ order="1"/> <bond id="GLC-6-P-bond4"
+ atomRefs="GLC-6-P-atom18 GLC-6-P-atom7" order="1"/> <bond
+ id="GLC-6-P-bond5" atomRefs="GLC-6-P-atom17 GLC-6-P-atom12"
+ order="1"/> <bond id="GLC-6-P-bond6"
+ atomRefs="GLC-6-P-atom16 GLC-6-P-atom5" order="1"/> <bond
+ id="GLC-6-P-bond7" atomRefs="GLC-6-P-atom15 GLC-6-P-atom6"
+ order="1"/> <bond id="GLC-6-P-bond8"
+ atomRefs="GLC-6-P-atom14 GLC-6-P-atom17" order="1"/> <bond
+ id="GLC-6-P-bond9" atomRefs="GLC-6-P-atom14 GLC-6-P-atom7"
+ order="1"/> <bond id="GLC-6-P-bond10"
+ atomRefs="GLC-6-P-atom13 GLC-6-P-atom5" order="1"/> <bond
+ id="GLC-6-P-bond11" atomRefs="GLC-6-P-atom12 GLC-6-P-atom8"
+ order="1"/> <bond id="GLC-6-P-bond12"
+ atomRefs="GLC-6-P-atom11 GLC-6-P-atom7" order="1"/> <bond
+ id="GLC-6-P-bond13" atomRefs="GLC-6-P-atom10 GLC-6-P-atom8"
+ order="1"/> <bond id="GLC-6-P-bond14"
+ atomRefs="GLC-6-P-atom9 GLC-6-P-atom6" order="2"/> <bond
+ id="GLC-6-P-bond15" atomRefs="GLC-6-P-atom8 GLC-6-P-atom5"
+ order="1"/> <bond id="GLC-6-P-bond16"
+ atomRefs="GLC-6-P-atom7 GLC-6-P-atom5" order="1"/> <bond
+ id="GLC-6-P-bond17" atomRefs="GLC-6-P-atom6 GLC-6-P-atom3"
+ order="1"/> <bond id="GLC-6-P-bond18"
+ atomRefs="GLC-6-P-atom4 GLC-6-P-atom6" order="1"/> <bond
+ id="GLC-6-P-bond19" atomRefs="GLC-6-P-atom3 GLC-6-P-atom2"
+ order="1"/> <bond id="GLC-6-P-bond20"
+ atomRefs="GLC-6-P-atom2 GLC-6-P-atom17" order="1"/> <bond
+ id="GLC-6-P-bond21" atomRefs="GLC-6-P-atom1 GLC-6-P-atom12"
+ order="1"/> </bondArray> <formula concise="C 6 H 13 O 9 P
+ 1" formalCharge="0"/> <float title="molecularWeight"
+ units="g/mol">260.137</float> <string
+ title="smiles">C(OP(=O)(O)O)[CH]1([CH](O)[CH](O)[CH](O)[CH](O)O1)</string>
+ </molecule> </cml></bp:STRUCTURE-DATA>
+ <bp:STRUCTURE-FORMAT rdf:datatype="xs:string">
+ CML</bp:STRUCTURE-FORMAT>
+ </bp:chemicalStructure>
+ </bp:STRUCTURE>
+ <bp:NAME rdf:datatype="xs:string">glucose-6-phosphate</bp:NAME>
+ </bp:smallMolecule>
+ </bp:PHYSICAL-ENTITY>
+ <bp:STOICHIOMETRIC-COEFFICIENT>1</bp:STOICHIOMETRIC-COEFFICIENT>
+ <bp:CELLULAR-LOCATION rdf:resource="#openControlledVocabulary17" />
+ </bp:physicalEntityParticipant>
+ </bp:LEFT>
+ <bp:SYNONYMS rdf:datatype="xs:string">PHOSPHOGLUCOISOMERASE
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">OXOISOMERASE</bp:SYNONYMS>
+ <bp:EC-NUMBER rdf:datatype="xs:string">5.3.1.9</bp:EC-NUMBER>
+ <bp:SYNONYMS rdf:datatype="xs:string">PHOSPHOGLUCOSE ISOMERASE
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">PHOSPHOSACCHAROMUTASE
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">PHOSPHOHEXOMUTASE</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">PHOSPHOHEXOISOMERASE
+ </bp:SYNONYMS>
+ <bp:DELTA-G rdf:resource="#deltaG-0.4"></bp:DELTA-G>
+ <bp:RIGHT rdf:resource="#physicalEntityParticipant22" />
+ <bp:SYNONYMS rdf:datatype="xs:string">HEXOSEPHOSPHATE ISOMERASE
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">PHOSPHOHEXOSE ISOMERASE
+ </bp:SYNONYMS>
+ <bp:NAME rdf:datatype="xs:string">PGLUCISOM-RXN</bp:NAME>
+ </bp:biochemicalReaction>
+ <bp:physicalEntityParticipant rdf:ID="physicalEntityParticipant264">
+ <bp:PHYSICAL-ENTITY>
+ <bp:complex rdf:ID="complex265">
+ <bp:NAME rdf:datatype="xs:string">TPI</bp:NAME>
+ <bp:COMPONENTS rdf:resource="#physicalEntityParticipant250" />
+ <bp:ORGANISM rdf:resource="#bioSource43" />
+ </bp:complex>
+ </bp:PHYSICAL-ENTITY>
+ </bp:physicalEntityParticipant>
+ <bp:relationshipXref rdf:ID="relationshipXref266">
+ <bp:RELATIONSHIP-TYPE rdf:datatype="xs:string">Ortholog
+ </bp:RELATIONSHIP-TYPE>
+ <bp:DB rdf:datatype="xs:string">EcoO157Cyc</bp:DB>
+ <bp:ID rdf:datatype="xs:string">FBA-MONOMER</bp:ID>
+ </bp:relationshipXref>
+ <bp:unificationXref rdf:ID="unificationXref267">
+ <bp:DB rdf:datatype="xs:string">PDB</bp:DB>
+ <bp:ID rdf:datatype="xs:string">1ZEN</bp:ID>
+ </bp:unificationXref>
+ <bp:smallMolecule rdf:ID="smallMolecule268">
+ <bp:STRUCTURE>
+ <bp:chemicalStructure rdf:ID="chemicalStructure269">
+ <bp:STRUCTURE-FORMAT rdf:datatype="xs:string">CML
+ </bp:STRUCTURE-FORMAT>
+ <bp:STRUCTURE-DATA rdf:datatype="xs:string"> <cml>
+ <molecule id="GLYCEROL-3P" title="glycerol-3-phosphate"
+ dictRef="dictGLYCEROL-3P"> <atomArray> <atom
+ id="GLYCEROL-3P-atom1" elementType="O" x2="-0.06931" y2="0.43564"/>
+ <atom id="GLYCEROL-3P-atom2" elementType="O" x2="-1.0"
+ y2="-0.29703"/> <atom id="GLYCEROL-3P-atom3" elementType="P"
+ x2="0.63036" y2="-0.63036"/> <atom id="GLYCEROL-3P-atom4"
+ elementType="O" x2="0.25413" y2="-0.88779"/> <atom
+ id="GLYCEROL-3P-atom5" elementType="C" x2="-0.07261"
+ y2="-0.26073"/> <atom id="GLYCEROL-3P-atom6" elementType="O"
+ x2="0.36964" y2="-0.26073"/> <atom id="GLYCEROL-3P-atom7"
+ elementType="C" x2="-0.72277" y2="0.06271"/> <atom
+ id="GLYCEROL-3P-atom8" elementType="C" x2="-0.33003" y2="0.06271"/>
+ <atom id="GLYCEROL-3P-atom9" elementType="O" x2="0.9967"
+ y2="-0.35974"/> <atom id="GLYCEROL-3P-atom10" elementType="O"
+ x2="0.90099" y2="-1.0"/> </atomArray> <bondArray> <bond
+ id="GLYCEROL-3P-bond1" atomRefs="GLYCEROL-3P-atom10
+ GLYCEROL-3P-atom3" order="1"/> <bond id="GLYCEROL-3P-bond2"
+ atomRefs="GLYCEROL-3P-atom9 GLYCEROL-3P-atom3" order="2"/> <bond
+ id="GLYCEROL-3P-bond3" atomRefs="GLYCEROL-3P-atom8
+ GLYCEROL-3P-atom5" order="1"/> <bond id="GLYCEROL-3P-bond4"
+ atomRefs="GLYCEROL-3P-atom7 GLYCEROL-3P-atom8" order="1"/> <bond
+ id="GLYCEROL-3P-bond5" atomRefs="GLYCEROL-3P-atom6
+ GLYCEROL-3P-atom3" order="1"/> <bond id="GLYCEROL-3P-bond6"
+ atomRefs="GLYCEROL-3P-atom5 GLYCEROL-3P-atom6" order="1"/> <bond
+ id="GLYCEROL-3P-bond7" atomRefs="GLYCEROL-3P-atom4
+ GLYCEROL-3P-atom3" order="1"/> <bond id="GLYCEROL-3P-bond8"
+ atomRefs="GLYCEROL-3P-atom2 GLYCEROL-3P-atom7" order="1"/> <bond
+ id="GLYCEROL-3P-bond9" atomRefs="GLYCEROL-3P-atom1
+ GLYCEROL-3P-atom8" order="1"/> </bondArray> <formula
+ concise="C 3 H 9 O 6 P 1" formalCharge="0"/> <float
+ title="molecularWeight" units="g/mol">172.074</float> <string
+ title="smiles">C(C(O)CO)OP(=O)(O)O</string> </molecule>
+ </cml></bp:STRUCTURE-DATA>
+ </bp:chemicalStructure>
+ </bp:STRUCTURE>
+ <bp:SYNONYMS rdf:datatype="xs:string">α-glycerophosphate
+ </bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">glycerol-3-P</bp:SYNONYMS>
+ <bp:NAME rdf:datatype="xs:string">glycerol-3-phosphate</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="xs:string">D-glycerol-3-phosphate
+ </bp:SYNONYMS>
+ <bp:MOLECULAR-WEIGHT>172.07400512695312</bp:MOLECULAR-WEIGHT>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref270">
+ <bp:DB rdf:datatype="xs:string">CAS</bp:DB>
+ <bp:ID rdf:datatype="xs:string">57-03-4</bp:ID>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:SYNONYMS rdf:datatype="xs:string">sn-glycerol-3-phosphate
+ </bp:SYNONYMS>
+ </bp:smallMolecule>
+ <bp:unificationXref rdf:ID="unificationXref271">
+ <bp:ID rdf:datatype="xs:string">P11537</bp:ID>
+ <bp:DB rdf:datatype="xs:string">SWISS-PROT</bp:DB>
+ </bp:unificationXref>
+ <bp:unificationXref rdf:ID="unificationXref272">
+ <bp:DB rdf:datatype="xs:string">PIR</bp:DB>
+ <bp:ID rdf:datatype="xs:string">b4025</bp:ID>
+ </bp:unificationXref>
+ <bp:complex rdf:ID="complex273">
+ <bp:XREF>
+ <bp:publicationXref rdf:ID="publicationXref274">
+ <bp:AUTHORS rdf:datatype="xs:string">Baldwin SA</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="xs:string">Perham RN</bp:AUTHORS>
+ <bp:TITLE rdf:datatype="xs:string">Cloning, sequence analysis and
+ over-expression of the gene for the class II fructose
+ 1,6-bisphosphate aldolase of Escherichia coli.</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="xs:string">Alefounder PR</bp:AUTHORS>
+ <bp:DB rdf:datatype="xs:string">PubMed</bp:DB>
+ <bp:AUTHORS rdf:datatype="xs:string">Short NJ</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="xs:string">Biochem J 1989;257(2);529-34
+ </bp:SOURCE>
+ <bp:YEAR>1989</bp:YEAR>
+ <bp:ID rdf:datatype="xs:string">2649077</bp:ID>
+ </bp:publicationXref>
+ </bp:XREF>
+ <bp:COMMENT rdf:datatype="xs:string">In relation to the Class I enzymes
+ (primarily studied and found in eukaryotes) comparatively little is
+ known about the class II enzymes. The Class II aldolases of Sacc.
+ cer. and E. coli are the best characterized.|CITS: [89193446]| It
+ resembles the typical class II aldolase from yeast in size and amino
+ acid composition. This is a strong suggestion that they are related.
+ |CITS:[78165651]| These less well studied aldolases are found both in
+ the eukaryotic green algae and fungi, and in the prokaryotic
+ blue-green algae and bacteria. |CITS:[78165651]| The gene pgk,
+ encoding the enzyme phosphoglycerate kinase, was carried on plasmid
+ pLC33-5 of the collection of Clarke and Carbon. It was also noted
+ that E.coli cells tansformed with this plasmid exhibited raised
+ levels of Class II fructose 1,6 bisphosphate aldolase activity,
+ suggesting that the same plasmid might also carry the structural gene
+ (fba) for this enzyme. |CITS: [89193446]|</bp:COMMENT>
+ <bp:XREF>
+ <bp:publicationXref rdf:ID="publicationXref275">
+ <bp:SOURCE rdf:datatype="xs:string">Biochem J 1978;169(3);633-41
+ </bp:SOURCE>
+ <bp:YEAR>1978</bp:YEAR>
+ <bp:AUTHORS rdf:datatype="xs:string">Stribling D</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="xs:string">Baldwin SA</bp:AUTHORS>
+ <bp:DB rdf:datatype="xs:string">PubMed</bp:DB>
+ <bp:AUTHORS rdf:datatype="xs:string">Perham RN</bp:AUTHORS>
+ <bp:TITLE rdf:datatype="xs:string">Purification and characterization of
+ the class-II D-fructose 1,6-bisphosphate aldolase from Escherichia
+ coli (Crookes' strain).</bp:TITLE>
+ <bp:ID rdf:datatype="xs:string">417719</bp:ID>
+ </bp:publicationXref>
+ </bp:XREF>
+ <bp:COMPONENTS>
+ <bp:physicalEntityParticipant rdf:ID="physicalEntityParticipant276">
+ <bp:STOICHIOMETRIC-COEFFICIENT>2</bp:STOICHIOMETRIC-COEFFICIENT>
+ <bp:CELLULAR-LOCATION rdf:resource="#openControlledVocabulary40" />
+ <bp:PHYSICAL-ENTITY>
+ <bp:protein rdf:ID="protein277">
+ <bp:XREF rdf:resource="#relationshipXref266" />
+ <bp:SYNONYMS rdf:datatype="xs:string">Fda</bp:SYNONYMS>
+ <bp:XREF rdf:resource="#unificationXref267" />
+ <bp:COMMENT rdf:datatype="xs:string">The amino acid sequence of the
+ E.coli Class II fructose-1,6-bisphosphate aldolase inferred from
+ the DNA sequence of the fda gene is the first primary structure
+ of a Class II aldolase to be established. There is no immediately
+ apparent sequence homology with any of the Class I
+ fructose-1,6-bisphosphate aldolases which have been widely
+ studied. |CITS:[89193446]| An fda mutant exhibits a
+ heat-sensitive defect in rRNA transcription that is elicited via
+ altered abundance of ppGpp and of initiating NTPs |CITS:
+ [14526031]|. Fda has similarity to an <i>Edwardsiella
+ ictaluri</i> protein that provokes an immune response in
+ catfish |CITS: [12542086]|. </bp:COMMENT>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref278">
+ <bp:DB rdf:datatype="xs:string">SWISS-PROT</bp:DB>
+ <bp:ID rdf:datatype="xs:string">P11604</bp:ID>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:XREF rdf:resource="#unificationXref246" />
+ <bp:SEQUENCE rdf:datatype="xs:string">MSKIFDFVKPGVITGDDVQKVFQVAKENNFALPAVNCVGTDSINAVLETAAKVKAPVIVQFSNGGASFIAGKGVKSDVPQGAAILGAISGAHHVHQMAEHYGVPVILHTDHCAKKLLPWIDGLLDAGEKHFAATGKPLFSSHMIDLSEESLQENIEICSKYLERMSKIGMTLEIELGCTGGEEDGVDNSHMDASALYTQPEDVDYAYTELSKISPRFTIAASFGNVHGVYKPGNVVLTPTILRDSQEYVSKKHNLPHNSLNFVFHGGSGSTAQEIKDSVSYGVVKMNIDTDTQWATWEGVLNYYKANEAYLQGQLGNPKGEDQPNKKYYDPRVWLRAGQTSMIARLEKAFQELNAIDVL
+ </bp:SEQUENCE>
+ <bp:ORGANISM rdf:resource="#bioSource43" />
+ <bp:SYNONYMS rdf:datatype="xs:string">FbaA</bp:SYNONYMS>
+ <bp:XREF rdf:resource="#unificationXref245" />
+ <bp:NAME rdf:datatype="xs:string">fructose bisphosphate aldolase
+ monomer</bp:NAME>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref279">
+ <bp:ID rdf:datatype="xs:string">b2925</bp:ID>
+ <bp:DB rdf:datatype="xs:string">PIR</bp:DB>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:SYNONYMS rdf:datatype="xs:string">Ald</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">Fba</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">B2925</bp:SYNONYMS>
+ </bp:protein>
+ </bp:PHYSICAL-ENTITY>
+ </bp:physicalEntityParticipant>
+ </bp:COMPONENTS>
+ <bp:NAME rdf:datatype="xs:string">FRUCBISALD-CLASSII</bp:NAME>
+ <bp:ORGANISM rdf:resource="#bioSource43" />
+ </bp:complex>
+ <bp:publicationXref rdf:ID="publicationXref280">
+ <bp:DB rdf:datatype="xs:string">PubMed</bp:DB>
+ <bp:TITLE rdf:datatype="xs:string">Isolation and characterization of the
+ phosphoglucose isomerase gene from Escherichia coli.</bp:TITLE>
+ <bp:SOURCE rdf:datatype="xs:string">Mol Gen Genet 1989;217(1);126-31
+ </bp:SOURCE>
+ <bp:AUTHORS rdf:datatype="xs:string">Gottlieb LD</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="xs:string">Froman BE</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="xs:string">Tait RC</bp:AUTHORS>
+ <bp:ID rdf:datatype="xs:string">2549364</bp:ID>
+ <bp:YEAR>1989</bp:YEAR>
+ </bp:publicationXref>
+ <bp:physicalEntityParticipant rdf:ID="physicalEntityParticipant281">
+ <bp:PHYSICAL-ENTITY>
+ <bp:complex rdf:ID="complex282">
+ <bp:ORGANISM rdf:resource="#bioSource43" />
+ <bp:NAME rdf:datatype="xs:string">FRUCBISALD-CLASSI</bp:NAME>
+ <bp:COMPONENTS>
+ <bp:physicalEntityParticipant rdf:ID="physicalEntityParticipant283">
+ <bp:CELLULAR-LOCATION rdf:resource="#openControlledVocabulary40" />
+ <bp:STOICHIOMETRIC-COEFFICIENT>10</bp:STOICHIOMETRIC-COEFFICIENT>
+ <bp:PHYSICAL-ENTITY>
+ <bp:protein rdf:ID="protein284">
+ <bp:XREF>
+ <bp:relationshipXref rdf:ID="relationshipXref285">
+ <bp:ID rdf:datatype="xs:string">Z3260-MONOMER</bp:ID>
+ <bp:DB rdf:datatype="xs:string">EcoO157Cyc</bp:DB>
+ <bp:RELATIONSHIP-TYPE rdf:datatype="xs:string">
+ Ortholog</bp:RELATIONSHIP-TYPE>
+ </bp:relationshipXref>
+ </bp:XREF>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref286">
+ <bp:DB rdf:datatype="xs:string">RefSeq</bp:DB>
+ <bp:ID rdf:datatype="xs:string">NP_416600</bp:ID>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:NAME rdf:datatype="xs:string">fructose bisphosphate aldolase
+ monomer</bp:NAME>
+ <bp:ORGANISM rdf:resource="#bioSource43" />
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref287">
+ <bp:DB rdf:datatype="xs:string">SWISS-PROT</bp:DB>
+ <bp:ID rdf:datatype="xs:string">P71295</bp:ID>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref288">
+ <bp:DB rdf:datatype="xs:string">PIR</bp:DB>
+ <bp:ID rdf:datatype="xs:string">b2097</bp:ID>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:SEQUENCE rdf:datatype="xs:string">MIARKRRARTIHSRYPIGIYGSIVMTDIAQLLGKDADNLLQHRCMTIPSDQLYLPGHDYVDRVMIDNNRPPAVLRNMQTLYNTGRLAGTGYLSILPVDQGVEHSAGASFAANPLYFDPKNIVELAIEAGCNCVASTYGVLASVSRRYAHRIPFLVKLNHNETLSYPNTYDQTLYASVEQAFNMGAVAVGATIYFGSEESRRQIEEISAAFERAHELGMVTVLWAYLRNSAFKKDGVDYHVSADLTGQANHLAATIGADIVKQKMAENNGGYKAINYGYTDDRVYSKLTSENPIDLVRYQLANCYMGRAGLINSGGAAGGETDLSDAVRTAVINKRAGGMGLILGRKAFKKSMADGVKLINAVQDVYLDSKITIA
+ </bp:SEQUENCE>
+ <bp:SYNONYMS rdf:datatype="xs:string">DhnA</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">FbaB</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">B2097</bp:SYNONYMS>
+ </bp:protein>
+ </bp:PHYSICAL-ENTITY>
+ </bp:physicalEntityParticipant>
+ </bp:COMPONENTS>
+ <bp:COMMENT rdf:datatype="xs:string">The typical class I aldolases of
+ plants and animals have been throroughly studied |CITS: [78165651]|
+ Fructose-1,6-bisphosphate aldolases can be divided into two classes
+ on the basis of their catalytic and structural properties. |CITS:
+ [78165651]| Class I fructose 1,6 bisphosphate aldolases were once
+ thought to be confined to eukaryotic organisms but have since been
+ detected in several bacterial species. |CITS: [78165652]| The
+ occurence of such an aldolase in bacteria was unexpected in light
+ of the phylogenetic distribution of aldolases. |CITS: [73229139]|
+ The enzymes of eukaryotes generally fall into Class I and are
+ tetramers of identical polypeptide chains. |CITS: [89193446]| In
+ earlier studies |CITS: [73229139]| it was thought that the class I
+ E. coli aldolase was typical in that it was tetrameric with a mol.
+ wt. of approx. 140K. In 1978 new purification techniques were
+ used.The true aldolase 1 activity could be measured by using
+ Fru-1,6-P<SUB>2</SUB> that had been purified by
+ chromatography on DEAE-cellulose to remove the
+ fructose-6-phosphate. Using these methods the enzyme appeared to be
+ larger than was previously supposed and may be a decamer with a
+ mol. wt. of approx. 340,000. The size of aldolase 1 and the effect
+ of cross-linking reagents on it, indicate that its structure must
+ differ significantly from that of the typical tetrameric class-I
+ enzymes from eukaryotes. |CITS: [78165652] [73229139]|
+ </bp:COMMENT>
+ </bp:complex>
+ </bp:PHYSICAL-ENTITY>
+ </bp:physicalEntityParticipant>
+ <bp:physicalEntityParticipant rdf:ID="physicalEntityParticipant289">
+ <bp:PHYSICAL-ENTITY rdf:resource="#complex273" />
+ </bp:physicalEntityParticipant>
+ <bp:protein rdf:ID="protein290">
+ <bp:XREF rdf:resource="#unificationXref272" />
+ <bp:XREF>
+ <bp:relationshipXref rdf:ID="relationshipXref291">
+ <bp:ID rdf:datatype="xs:string">PGI-MONOMER</bp:ID>
+ <bp:RELATIONSHIP-TYPE rdf:datatype="xs:string">Ortholog
+ </bp:RELATIONSHIP-TYPE>
+ <bp:DB rdf:datatype="xs:string">EcoO157Cyc</bp:DB>
+ </bp:relationshipXref>
+ </bp:XREF>
+ <bp:XREF rdf:resource="#unificationXref271" />
+ <bp:SEQUENCE rdf:datatype="xs:string">MKNINPTQTAAWQALQKHFDEMKDVTIADLFAKDGDRFSKFSATFDDQMLVDYSKNRITEETLAKLQDLAKECDLAGAIKSMFSGEKINRTENRAVLHVALRNRSNTPILVDGKDVMPEVNAVLEKMKTFSEAIISGEWKGYTGKAITDVVNIGIGGSDLGPYMVTEALRPYKNHLNMHFVSNVDGTHIAEVLKKVNPETTLFLVASKTFTTQETMTNAHSARDWFLKAAGDEKHVAKHFAALSTNAKAVGEFGIDTANMFEFWDWVGGRYSLWSAIGLSIVLSIGFDNFVELLSGAHAMDKHFSTTPAEKNLPVLLALIGIWYNNFFGAETEAILPYDQYMHRFAAYFQQGNMESNGKYVDRNGNVVDYQTGPIIWGEPGTNGQHAFYQLIHQGTKMVPCDFIAPAITHNPLSDHHQKLLSNFFAQTEALAFGKSREVVEQEYRDQGKDPA [...]
+ </bp:SEQUENCE>
+ <bp:NAME rdf:datatype="xs:string">PGLUCISOM</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="xs:string">B4025</bp:SYNONYMS>
+ <bp:ORGANISM rdf:resource="#bioSource43" />
+ <bp:SYNONYMS rdf:datatype="xs:string">Pgi</bp:SYNONYMS>
+ <bp:COMMENT rdf:datatype="xs:string">phosphoglucose isomerase is found
+ primarily in the cytoplasm</bp:COMMENT>
+ <bp:XREF rdf:resource="#publicationXref280" />
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref292">
+ <bp:DB rdf:datatype="xs:string">RefSeq</bp:DB>
+ <bp:ID rdf:datatype="xs:string">NP_418449</bp:ID>
+ </bp:unificationXref>
+ </bp:XREF>
+ </bp:protein>
+ <bp:catalysis rdf:ID="catalysis293">
+ <bp:COMMENT rdf:datatype="xs:string">When E. coli K-12 is grown on C-3
+ carbon sources both classes of aldolase are present. However the
+ Class I enzyme is present only under these conditions. Therefore it
+ is likely that the Class I enzyme is involved in gluconeogenesis and
+ the class II enzyme in glycolysis. |CITS: [81000551]| The class I
+ enzymes function by imine formation between the substrate and a
+ catalytically essential lysine residue in the active site, which acts
+ to stabilize the intermediate carbanion. |CITS:[89193446]| They form
+ a Schiff base betwen the E-amino group of a specific lysine residue
+ in the active site and the carbonyl group of the substrate. This
+ imine may be reduced by borohydride which therefore irreversibly
+ inhibits class 1 aldolases in the presence of substrate.
+ |CITS:[73229139]| The enzyme's activity was unaffected by EDTA, but
+ it was inhibited by borohydride reduction in the presence of
+ Fru-1,6-P2 or dihydroxyacetone phosphate. Like mammalian aldolases,
+ it cleaved fructose 1-phosphate, albeit slowly and had a low Km for
+ Fru-1,6-P2. Its fructose 1,6 bisphosphate cleavage activity was
+ greatly enhanced by citrate, PEP, 2-oxoglutarate and sn-glycerol
+ 3-phosphate. Aldolase I is very efficient at Fru-1,6-P2 cleavage when
+ fully activated. Only a limited range of metabolites has been tested
+ as possible activators. In contrast, its fructose 1-phosphate
+ cleavage activity was unaffected by these compounds. The enhancement
+ exhibited a strong dependence on pH. These novel kinetic properties
+ do not seem to be shared by any other fructose 1,6 bisphosphate
+ aldolase. In view of its unusual properties, it is unlikely that
+ aldolase I from E.coli is closely related to the class-1 aldolases
+ that have been detected in several other prokaryotes, or to the
+ typical class I enzymes from eukaryote. |CITS: [78165652]|
+ </bp:COMMENT>
+ <bp:XREF>
+ <bp:publicationXref rdf:ID="publicationXref294">
+ <bp:AUTHORS rdf:datatype="xs:string">Howlett GJ</bp:AUTHORS>
+ <bp:ID rdf:datatype="xs:string">9531482</bp:ID>
+ <bp:YEAR>1998</bp:YEAR>
+ <bp:DB rdf:datatype="xs:string">PubMed</bp:DB>
+ <bp:SOURCE rdf:datatype="xs:string">Biochem J 1998;331 ( Pt 2);437-45
+ </bp:SOURCE>
+ <bp:AUTHORS rdf:datatype="xs:string">Berry A</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="xs:string">Thomson GJ</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="xs:string">Ashcroft AE</bp:AUTHORS>
+ <bp:TITLE rdf:datatype="xs:string">The dhnA gene of Escherichia coli
+ encodes a class I fructose bisphosphate aldolase.</bp:TITLE>
+ </bp:publicationXref>
+ </bp:XREF>
+ <bp:CONTROLLER rdf:resource="#physicalEntityParticipant281" />
+ <bp:NAME rdf:datatype="xs:string">fructose bisphosphate aldolase class I
+ </bp:NAME>
+ <bp:DIRECTION rdf:datatype="xs:string">REVERSIBLE</bp:DIRECTION>
+ <bp:CONTROLLED>
+ <bp:biochemicalReaction rdf:ID="biochemicalReaction295">
+ <bp:NAME rdf:datatype="xs:string">F16ALDOLASE-RXN</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="xs:string">FRUCTOSE-1,6-BISPHOSPHATE
+ TRIOSEPHOSPHATE-LYASE</bp:SYNONYMS>
+ <bp:RIGHT rdf:resource="#physicalEntityParticipant228" />
+ <bp:COMMENT rdf:datatype="xs:string">Dihydroxyacetone phosphate is
+ also called glycerone phosphate. Of the total aldolase activity in
+ cell-free extracts of E.coli grown on pyruvate and lactate, approx.
+ 60 % was accounted for by aldolase 1. On the other hand, E.coli
+ grown on glucose showed no aldolase 1 activity but had an increased
+ aldolase 2 activity. |CITS: [73229139]| During growth with CO2 as a
+ carbon source, only class I aldolase is produced but when acetate
+ replaces CO2 the class II aldolase is made. Similarly, in E.coli
+ the putative class I aldolase is only synthesized during growth on
+ C3 compounds and not on glucose, implying that a class I aldolase
+ is preferred for gluconeogenesis |CITS:[73229139]|</bp:COMMENT>
+ <bp:DELTA-G><bp:deltaGprimeO rdf:ID="deltaG-5.7"><bp:DELTA-G-PRIME-O>5.7</bp:DELTA-G-PRIME-O></bp:deltaGprimeO></bp:DELTA-G>
+ <bp:EC-NUMBER rdf:datatype="xs:string">4.1.2.13</bp:EC-NUMBER>
+ <bp:SYNONYMS rdf:datatype="xs:string">ALDOLASE</bp:SYNONYMS>
+ <bp:LEFT rdf:resource="#physicalEntityParticipant29" />
+ <bp:RIGHT rdf:resource="#physicalEntityParticipant180" />
+ </bp:biochemicalReaction>
+ </bp:CONTROLLED>
+ </bp:catalysis>
+ <bp:catalysis rdf:ID="catalysis296">
+ <bp:SYNONYMS rdf:datatype="xs:string">phosphotriose isomerase
+ </bp:SYNONYMS>
+ <bp:CONTROLLER rdf:resource="#physicalEntityParticipant264" />
+ <bp:SYNONYMS rdf:datatype="xs:string">triosephosphate isomerase
+ </bp:SYNONYMS>
+ <bp:COMMENT rdf:datatype="xs:string">The amino acid sequence around the
+ active site is perfectly conserved in all known triose phosphate
+ isomerases and can be used as a signature pattern for this type of
+ enzyme.|CITS: [Prosite]|</bp:COMMENT>
+ <bp:SYNONYMS rdf:datatype="xs:string">TIM</bp:SYNONYMS>
+ <bp:CONTROLLED>
+ <bp:biochemicalReaction rdf:ID="biochemicalReaction297">
+ <bp:SYNONYMS rdf:datatype="xs:string">PHOSPHOTRIOSE ISOMERASE
+ </bp:SYNONYMS>
+ <bp:EC-NUMBER rdf:datatype="xs:string">5.3.1.1</bp:EC-NUMBER>
+ <bp:SYNONYMS rdf:datatype="xs:string">TRIOSEPHOSPHATE MUTASE
+ </bp:SYNONYMS>
+ <bp:LEFT rdf:resource="#physicalEntityParticipant180" />
+ <bp:NAME rdf:datatype="xs:string">triose phosphate isomerization
+ </bp:NAME>
+ <bp:RIGHT rdf:resource="#physicalEntityParticipant228" />
+ </bp:biochemicalReaction>
+ </bp:CONTROLLED>
+ <bp:SYNONYMS rdf:datatype="xs:string">triosephosphate mutase
+ </bp:SYNONYMS>
+ <bp:NAME rdf:datatype="xs:string">triose phosphate isomerase</bp:NAME>
+ <bp:DIRECTION rdf:datatype="xs:string">REVERSIBLE</bp:DIRECTION>
+ </bp:catalysis>
+ <bp:modulation rdf:ID="modulation298">
+ <bp:CONTROLLED>
+ <bp:catalysis rdf:ID="catalysis299">
+ <bp:NAME rdf:datatype="xs:string">fructose bisphosphate aldolase class
+ II</bp:NAME>
+ <bp:CONTROLLED rdf:resource="#biochemicalReaction295" />
+ <bp:XREF rdf:resource="#publicationXref259" />
+ <bp:XREF rdf:resource="#publicationXref274" />
+ <bp:DIRECTION rdf:datatype="xs:string">REVERSIBLE</bp:DIRECTION>
+ <bp:COMMENT rdf:datatype="xs:string">Class II enzymes utilize a
+ divalent metal ion to act as the electron sink at the active site
+ in what appears to be an otherwise similar catalytic mechanism to
+ Class I. |CITS: [89193446]| The metal ion in the active site
+ varies, but several metals including zinc, cobalt, iron, nickel and
+ manganese can form an active metallo-protein complex |CITS:
+ [73229139]| In Crookes strain of E. coli it was found that the
+ kinetic behavior is not typical of a class-II aldolase; the enzyme
+ has no requirement for thiol compounds either for stability or
+ activity, added K+ ions have no effect, and the high pH optimum of
+ 9 is unusual for a class II enzyme. |CITS: [78165651]| Aldolase II
+ is relatively insensitive to compounds that react with thiol
+ groups.|CITS: [78165651]| It is strongly inhibited by
+ metal-chelating agents and is reactivated by bivalent metal
+ ions.|CITS: [73229139]| When E. coli K-12 is grown on C-3 carbon
+ sources both classes of aldolase are present. However the Class I
+ enzyme is present only under these conditions. Therefore the Class
+ I enzyme is most likely involved in gluconeogenesis and the Class
+ II enzyme with glycolysis. |CITS: [81000551]|</bp:COMMENT>
+ <bp:XREF rdf:resource="#publicationXref275" />
+ <bp:CONTROLLER rdf:resource="#physicalEntityParticipant289" />
+ <bp:SYNONYMS rdf:datatype="xs:string">fructose-1,6-bisphosphate
+ triosephosphate lyase</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">fructose-1,6-bisphosphate
+ aldolase</bp:SYNONYMS>
+ </bp:catalysis>
+ </bp:CONTROLLED>
+ <bp:CONTROL-TYPE rdf:datatype="xs:string">INHIBITION-UNKMECH
+ </bp:CONTROL-TYPE>
+ <bp:CONTROLLER>
+ <bp:physicalEntityParticipant rdf:ID="physicalEntityParticipant300">
+ <bp:STOICHIOMETRIC-COEFFICIENT>1.0</bp:STOICHIOMETRIC-COEFFICIENT>
+ <bp:PHYSICAL-ENTITY>
+ <bp:smallMolecule rdf:ID="smallMolecule301">
+ <bp:NAME rdf:datatype="xs:string">EDTA</bp:NAME>
+ </bp:smallMolecule>
+ </bp:PHYSICAL-ENTITY>
+ </bp:physicalEntityParticipant>
+ </bp:CONTROLLER>
+ </bp:modulation>
+ <bp:modulation rdf:ID="modulation302">
+ <bp:CONTROL-TYPE rdf:datatype="xs:string">INHIBITION-UNKMECH
+ </bp:CONTROL-TYPE>
+ <bp:CONTROLLER>
+ <bp:physicalEntityParticipant rdf:ID="physicalEntityParticipant303">
+ <bp:STOICHIOMETRIC-COEFFICIENT>1.0</bp:STOICHIOMETRIC-COEFFICIENT>
+ <bp:PHYSICAL-ENTITY>
+ <bp:smallMolecule rdf:ID="smallMolecule304">
+ <bp:NAME rdf:datatype="xs:string">BOROHYDRIDE</bp:NAME>
+ </bp:smallMolecule>
+ </bp:PHYSICAL-ENTITY>
+ </bp:physicalEntityParticipant>
+ </bp:CONTROLLER>
+ <bp:CONTROLLED rdf:resource="#catalysis293" />
+ </bp:modulation>
+ <bp:pathway rdf:ID="pathway305">
+ <bp:AVAILABILITY rdf:datatype="xs:string">This pathway is freely
+ available to all users and may be redistributed in whole or in part
+ provided proper source attribution is made. See
+ http://biocyc.org/open-reg.shtml for more information.
+ </bp:AVAILABILITY>
+ <bp:PATHWAY-COMPONENTS>
+ <bp:pathwayStep rdf:ID="pathwayStep306">
+ <bp:STEP-INTERACTIONS rdf:resource="#biochemicalReaction297" />
+ <bp:STEP-INTERACTIONS rdf:resource="#catalysis296" />
+ </bp:pathwayStep>
+ </bp:PATHWAY-COMPONENTS>
+ <bp:PATHWAY-COMPONENTS rdf:resource="#pathwayStep204" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#pathwayStep82" />
+ <bp:PATHWAY-COMPONENTS>
+ <bp:pathwayStep rdf:ID="pathwayStep307">
+ <bp:STEP-INTERACTIONS rdf:resource="#catalysis238" />
+ <bp:STEP-INTERACTIONS rdf:resource="#biochemicalReaction13" />
+ <bp:STEP-INTERACTIONS rdf:resource="#catalysis2" />
+ <bp:STEP-INTERACTIONS>
+ <bp:modulation rdf:ID="modulation308">
+ <bp:CONTROLLER rdf:resource="#physicalEntityParticipant16" />
+ <bp:CONTROL-TYPE rdf:datatype="xs:string">ACTIVATION-ALLOSTERIC
+ </bp:CONTROL-TYPE>
+ <bp:CONTROLLED rdf:resource="#catalysis2" />
+ </bp:modulation>
+ </bp:STEP-INTERACTIONS>
+ <bp:NEXT-STEP>
+ <bp:pathwayStep rdf:ID="pathwayStep309">
+ <bp:STEP-INTERACTIONS>
+ <bp:modulation rdf:ID="modulation310">
+ <bp:CONTROL-TYPE rdf:datatype="xs:string">ACTIVATION-UNKMECH
+ </bp:CONTROL-TYPE>
+ <bp:CONTROLLER rdf:resource="#physicalEntityParticipant85" />
+ <bp:CONTROLLED rdf:resource="#catalysis293" />
+ </bp:modulation>
+ </bp:STEP-INTERACTIONS>
+ <bp:STEP-INTERACTIONS rdf:resource="#catalysis293" />
+ <bp:STEP-INTERACTIONS rdf:resource="#modulation302" />
+ <bp:STEP-INTERACTIONS rdf:resource="#modulation298" />
+ <bp:NEXT-STEP rdf:resource="#pathwayStep171" />
+ <bp:NEXT-STEP rdf:resource="#pathwayStep306" />
+ <bp:STEP-INTERACTIONS rdf:resource="#biochemicalReaction295" />
+ <bp:STEP-INTERACTIONS rdf:resource="#catalysis299" />
+ <bp:STEP-INTERACTIONS>
+ <bp:modulation rdf:ID="modulation311">
+ <bp:CONTROLLED rdf:resource="#catalysis293" />
+ <bp:CONTROL-TYPE rdf:datatype="xs:string">ACTIVATION-UNKMECH
+ </bp:CONTROL-TYPE>
+ <bp:CONTROLLER>
+ <bp:physicalEntityParticipant
+ rdf:ID="physicalEntityParticipant312">
+ <bp:PHYSICAL-ENTITY rdf:resource="#smallMolecule247" />
+ <bp:STOICHIOMETRIC-COEFFICIENT>1.0
+ </bp:STOICHIOMETRIC-COEFFICIENT>
+ </bp:physicalEntityParticipant>
+ </bp:CONTROLLER>
+ </bp:modulation>
+ </bp:STEP-INTERACTIONS>
+ <bp:STEP-INTERACTIONS>
+ <bp:modulation rdf:ID="modulation313">
+ <bp:CONTROL-TYPE rdf:datatype="xs:string">INHIBITION-UNKMECH
+ </bp:CONTROL-TYPE>
+ <bp:CONTROLLED rdf:resource="#catalysis293" />
+ <bp:CONTROLLER rdf:resource="#physicalEntityParticipant228" />
+ </bp:modulation>
+ </bp:STEP-INTERACTIONS>
+ <bp:STEP-INTERACTIONS>
+ <bp:modulation rdf:ID="modulation314">
+ <bp:CONTROLLED rdf:resource="#catalysis293" />
+ <bp:CONTROL-TYPE rdf:datatype="xs:string">ACTIVATION-UNKMECH
+ </bp:CONTROL-TYPE>
+ <bp:CONTROLLER>
+ <bp:physicalEntityParticipant
+ rdf:ID="physicalEntityParticipant315">
+ <bp:PHYSICAL-ENTITY rdf:resource="#smallMolecule268" />
+ <bp:STOICHIOMETRIC-COEFFICIENT>1.0
+ </bp:STOICHIOMETRIC-COEFFICIENT>
+ </bp:physicalEntityParticipant>
+ </bp:CONTROLLER>
+ </bp:modulation>
+ </bp:STEP-INTERACTIONS>
+ </bp:pathwayStep>
+ </bp:NEXT-STEP>
+ <bp:STEP-INTERACTIONS>
+ <bp:modulation rdf:ID="modulation316">
+ <bp:CONTROL-TYPE rdf:datatype="xs:string">INHIBITION-ALLOSTERIC
+ </bp:CONTROL-TYPE>
+ <bp:CONTROLLER rdf:resource="#physicalEntityParticipant85" />
+ <bp:CONTROLLED rdf:resource="#catalysis2" />
+ </bp:modulation>
+ </bp:STEP-INTERACTIONS>
+ <bp:STEP-INTERACTIONS>
+ <bp:modulation rdf:ID="modulation317">
+ <bp:XREF rdf:resource="#publicationXref239" />
+ <bp:CONTROLLED rdf:resource="#catalysis238" />
+ <bp:CONTROLLER rdf:resource="#physicalEntityParticipant33" />
+ <bp:CONTROL-TYPE rdf:datatype="xs:string">INHIBITION-UNKMECH
+ </bp:CONTROL-TYPE>
+ </bp:modulation>
+ </bp:STEP-INTERACTIONS>
+ <bp:STEP-INTERACTIONS rdf:resource="#modulation232" />
+ <bp:STEP-INTERACTIONS rdf:resource="#modulation237" />
+ <bp:STEP-INTERACTIONS>
+ <bp:modulation rdf:ID="modulation318">
+ <bp:CONTROLLER rdf:resource="#physicalEntityParticipant154" />
+ <bp:CONTROLLED rdf:resource="#catalysis2" />
+ <bp:CONTROL-TYPE rdf:datatype="xs:string">ACTIVATION-UNKMECH
+ </bp:CONTROL-TYPE>
+ </bp:modulation>
+ </bp:STEP-INTERACTIONS>
+ <bp:STEP-INTERACTIONS rdf:resource="#modulation1" />
+ </bp:pathwayStep>
+ </bp:PATHWAY-COMPONENTS>
+ <bp:PATHWAY-COMPONENTS rdf:resource="#pathwayStep171" />
+ <bp:SYNONYMS rdf:datatype="xs:string">Embden-Meyerhof pathway
+ </bp:SYNONYMS>
+ <bp:NAME rdf:datatype="xs:string">glycolysis I</bp:NAME>
+ <bp:DATA-SOURCE>
+ <bp:dataSource rdf:ID="dataSource319">
+ <bp:NAME>EcoCyc Database (http://ecocyc.org)</bp:NAME>
+ </bp:dataSource>
+ </bp:DATA-SOURCE>
+ <bp:COMMENT rdf:datatype="xs:string">Pyruvate from glycolysis proceeds
+ to the pyruvate dehydrogenase multienzyme complex, and the acetyl CoA
+ produced then proceeds on to the superpathway of glyoxylate bypass
+ and TCA.</bp:COMMENT>
+ <bp:PATHWAY-COMPONENTS rdf:resource="#pathwayStep54" />
+ <bp:PATHWAY-COMPONENTS>
+ <bp:pathwayStep rdf:ID="pathwayStep320">
+ <bp:NEXT-STEP rdf:resource="#pathwayStep307" />
+ <bp:STEP-INTERACTIONS rdf:resource="#biochemicalReaction260" />
+ <bp:STEP-INTERACTIONS>
+ <bp:catalysis rdf:ID="catalysis321">
+ <bp:DIRECTION rdf:datatype="xs:string">REVERSIBLE</bp:DIRECTION>
+ <bp:CONTROLLED rdf:resource="#biochemicalReaction260" />
+ <bp:SYNONYMS rdf:datatype="xs:string">glucose-6-phosphate
+ isomerase</bp:SYNONYMS>
+ <bp:COMMENT rdf:datatype="xs:string">2-deoxyglucose-6-p is a known
+ inhibitor in mammalian systems. E.coli cells with mutated pgi
+ gene apparently utilize glucose primarily by the pentose
+ phosphate pathway and to a lesser extent by the Entner-Duodoroff
+ pathway. |CITS:[89364675]|</bp:COMMENT>
+ <bp:XREF rdf:resource="#publicationXref280" />
+ <bp:SYNONYMS rdf:datatype="xs:string">D-glucose-6-phosphate-ketol-isomerase
+ </bp:SYNONYMS>
+ <bp:NAME rdf:datatype="xs:string">phosphoglucose isomerase</bp:NAME>
+ <bp:XREF>
+ <bp:publicationXref rdf:ID="publicationXref322">
+ <bp:TITLE rdf:datatype="xs:string">Intracellular pH effect upon
+ phosphoglucose isomerase in Escherichia coli</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="xs:string">Klungsoyr L</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="xs:string">BBA 1964;92:378-387
+ </bp:SOURCE>
+ <bp:AUTHORS rdf:datatype="xs:string">Endresen A</bp:AUTHORS>
+ </bp:publicationXref>
+ </bp:XREF>
+ <bp:CONTROLLER>
+ <bp:physicalEntityParticipant
+ rdf:ID="physicalEntityParticipant323">
+ <bp:PHYSICAL-ENTITY rdf:resource="#protein290" />
+ </bp:physicalEntityParticipant>
+ </bp:CONTROLLER>
+ </bp:catalysis>
+ </bp:STEP-INTERACTIONS>
+ </bp:pathwayStep>
+ </bp:PATHWAY-COMPONENTS>
+ <bp:PATHWAY-COMPONENTS rdf:resource="#pathwayStep107" />
+ <bp:PATHWAY-COMPONENTS rdf:resource="#pathwayStep309" />
+ <bp:SYNONYMS rdf:datatype="xs:string">glucose degradation
+ </bp:SYNONYMS>
+ </bp:pathway>
+</rdf:RDF>
diff --git a/coreplugins/BioPAX/src/test/resources/biopax3-phosphorylation-reaction.owl b/coreplugins/BioPAX/src/test/resources/biopax3-phosphorylation-reaction.owl
new file mode 100644
index 0000000..4549e9a
--- /dev/null
+++ b/coreplugins/BioPAX/src/test/resources/biopax3-phosphorylation-reaction.owl
@@ -0,0 +1,370 @@
+<?xml version="1.0"?>
+<rdf:RDF
+ xmlns="http://www.biopax.org/examples/myExample#"
+ xmlns:bp="http://www.biopax.org/release/biopax-level3.owl#"
+ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+ xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
+ xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
+ xmlns:owl="http://www.w3.org/2002/07/owl#"
+ xml:base="http://www.biopax.org/examples/myExample">
+ <owl:Ontology rdf:about="">
+ <owl:imports rdf:resource="http://www.biopax.org/release/biopax-level3.owl"/>
+ </owl:Ontology>
+ <rdf:Property rdf:about="http://www.biopax.org/release/biopax-level3.owl#direction"/>
+ <bp:Protein rdf:ID="Protein_5">
+ <bp:dataSource>
+ <bp:Provenance rdf:ID="Provenance_3">
+ <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >Reactome (http://reactome.org)</bp:displayName>
+ <bp:xref>
+ <bp:PublicationXref rdf:ID="pubmed">
+ <bp:year rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
+ >2003</bp:year>
+ <bp:db rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >pubmed</bp:db>
+ <bp:title rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >The Genome Knowledgebase: a resource for biologists and bioinformaticists.</bp:title>
+ <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >15338623</bp:id>
+ </bp:PublicationXref>
+ </bp:xref>
+ </bp:Provenance>
+ </bp:dataSource>
+ <bp:cellularLocation>
+ <bp:CellularLocationVocabulary rdf:ID="CellularLocationVocabulary_6">
+ <bp:term rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >nucleoplasm</bp:term>
+ <bp:xref>
+ <bp:UnificationXref rdf:ID="UnificationXref_7">
+ <bp:db rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >GENE ONTOLOGY</bp:db>
+ <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >GO:0005654</bp:id>
+ </bp:UnificationXref>
+ </bp:xref>
+ </bp:CellularLocationVocabulary>
+ </bp:cellularLocation>
+ <bp:entityReference>
+ <bp:ProteinReference rdf:ID="CHK2">
+ <bp:organism>
+ <bp:BioSource rdf:ID="Homo_sapiens">
+ <bp:taxonXref>
+ <bp:UnificationXref rdf:ID="UnificationXref_10">
+ <bp:db rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >taxonomy</bp:db>
+ <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >9606</bp:id>
+ </bp:UnificationXref>
+ </bp:taxonXref>
+ <bp:standardName rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >Homo sapiens</bp:standardName>
+ <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >Human</bp:displayName>
+ </bp:BioSource>
+ </bp:organism>
+ <bp:standardName rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >Serine/threonine-protein kinase Chk2 (Cds1)</bp:standardName>
+ <bp:xref>
+ <bp:RelationshipXref rdf:ID="RelationshipXref_1">
+ <bp:relationshipType>
+ <bp:RelationshipTypeVocabulary rdf:ID="RelationshipTypeVocabulary_6">
+ <bp:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >EC Number</bp:comment>
+ <bp:term rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >see-also</bp:term>
+ </bp:RelationshipTypeVocabulary>
+ </bp:relationshipType>
+ <bp:db rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >IUBMB</bp:db>
+ <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >EC 2.7.1.37</bp:id>
+ </bp:RelationshipXref>
+ </bp:xref>
+ <bp:xref>
+ <bp:UnificationXref rdf:ID="UnificationXref_12">
+ <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >O96017</bp:id>
+ <bp:db rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >uniprot</bp:db>
+ </bp:UnificationXref>
+ </bp:xref>
+ <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >CHK2</bp:displayName>
+ <bp:name rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >CHEK2</bp:name>
+ </bp:ProteinReference>
+ </bp:entityReference>
+ <bp:standardName rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >Serine/threonine-protein kinase Chk2 (Cds1)</bp:standardName>
+ <bp:name rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >CHEK2</bp:name>
+ <bp:xref rdf:resource="#UnificationXref_12"/>
+ <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >CHK2</bp:displayName>
+ </bp:Protein>
+ <bp:PublicationXref rdf:ID="PublicationXref_24">
+ <bp:db rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >pubmed</bp:db>
+ <bp:source rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >EMBO J 22:2860-71 </bp:source>
+ <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >Foray, N </bp:author>
+ <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >Jeggo, P </bp:author>
+ <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >12773400</bp:id>
+ <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >Perricaudet, M </bp:author>
+ <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >Gabriel, A </bp:author>
+ <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >Ashworth, A </bp:author>
+ <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >Randrianarison, V </bp:author>
+ <bp:title rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >A subset of ATM- and ATR-dependent phosphorylation events requires the BRCA1 protein.</bp:title>
+ <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >Carr, AM </bp:author>
+ <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >Marot, D</bp:author>
+ <bp:year rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
+ >2003</bp:year>
+ </bp:PublicationXref>
+ <bp:SequenceSite rdf:ID="SequenceSite_20">
+ <bp:positionStatus rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >EQUAL</bp:positionStatus>
+ <bp:sequencePosition rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
+ >1981</bp:sequencePosition>
+ </bp:SequenceSite>
+ <bp:SmallMolecule rdf:ID="SmallMolecule_21">
+ <bp:standardName rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >Adenosine 5'-diphosphate</bp:standardName>
+ <bp:cellularLocation rdf:resource="#CellularLocationVocabulary_6"/>
+ <bp:dataSource rdf:resource="#Provenance_3"/>
+ <bp:xref>
+ <bp:UnificationXref rdf:ID="UnificationXref_22">
+ <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >CHEBI:2342</bp:id>
+ <bp:db rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >ChEBI</bp:db>
+ </bp:UnificationXref>
+ </bp:xref>
+ <bp:entityReference>
+ <bp:SmallMoleculeReference rdf:ID="SmallMoleculeReference_23">
+ <bp:xref rdf:resource="#UnificationXref_22"/>
+ <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >ADP</bp:displayName>
+ <bp:standardName rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >Adenosine 5'-diphosphate</bp:standardName>
+ </bp:SmallMoleculeReference>
+ </bp:entityReference>
+ <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >ADP</bp:displayName>
+ </bp:SmallMolecule>
+ <bp:ProteinReference rdf:ID="ATM">
+ <bp:name rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >Ataxia telangiectasia mutated) (A-T, mutated) </bp:name>
+ <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >ATM</bp:displayName>
+ <bp:standardName rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >Serine-protein kinase ATM (Ataxia telangiectasia mutated) (A-T, mutated)</bp:standardName>
+ <bp:xref rdf:resource="#RelationshipXref_1"/>
+ <bp:xref>
+ <bp:UnificationXref rdf:ID="UnificationXref_28">
+ <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >Q13315</bp:id>
+ <bp:db rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >uniprot</bp:db>
+ </bp:UnificationXref>
+ </bp:xref>
+ <bp:organism rdf:resource="#Homo_sapiens"/>
+ </bp:ProteinReference>
+ <bp:RelationshipXref rdf:ID="RelationshipXref_29">
+ <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >GO:0016301</bp:id>
+ <bp:db rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >GENE ONTOLOGY</bp:db>
+ <bp:relationshipType>
+ <bp:RelationshipTypeVocabulary rdf:ID="GO_molecular_function">
+ <bp:term rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >gene ontology term for cellular function</bp:term>
+ <bp:xref>
+ <bp:UnificationXref rdf:ID="UnificationXref_5">
+ <bp:db rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >PSI-MI</bp:db>
+ <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >MI:0355</bp:id>
+ </bp:UnificationXref>
+ </bp:xref>
+ </bp:RelationshipTypeVocabulary>
+ </bp:relationshipType>
+ </bp:RelationshipXref>
+ <bp:Catalysis rdf:ID="Catalysis_1">
+ <bp:dataSource rdf:resource="#Provenance_3"/>
+ <bp:controlled>
+ <bp:BiochemicalReaction rdf:ID="BiochemicalReaction_2">
+ <bp:right>
+ <bp:Protein rdf:ID="Protein_16">
+ <bp:entityReference rdf:resource="#CHK2"/>
+ <bp:name rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >CHEK2</bp:name>
+ <bp:xref rdf:resource="#UnificationXref_12"/>
+ <bp:feature>
+ <bp:ModificationFeature rdf:ID="ModificationFeature_17">
+ <bp:featureLocation rdf:resource="#SequenceSite_20"/>
+ <bp:modificationType>
+ <bp:SequenceModificationVocabulary rdf:ID="SequenceModificationVocabulary_18">
+ <bp:xref>
+ <bp:UnificationXref rdf:ID="UnificationXref_19">
+ <bp:db rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >PSI-MI</bp:db>
+ <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >MI:0176</bp:id>
+ </bp:UnificationXref>
+ </bp:xref>
+ <bp:term rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >o-phospho-serine</bp:term>
+ </bp:SequenceModificationVocabulary>
+ </bp:modificationType>
+ </bp:ModificationFeature>
+ </bp:feature>
+ <bp:standardName rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >Serine/threonine-protein kinase Chk2 (Cds1)</bp:standardName>
+ <bp:dataSource rdf:resource="#Provenance_3"/>
+ <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >CHK2</bp:displayName>
+ <bp:cellularLocation rdf:resource="#CellularLocationVocabulary_6"/>
+ </bp:Protein>
+ </bp:right>
+ <bp:xref rdf:resource="#PublicationXref_24"/>
+ <bp:right rdf:resource="#SmallMolecule_21"/>
+ <bp:participantStoichiometry>
+ <bp:Stoichiometry rdf:ID="Stoichiometry_2">
+ <bp:stoichiometricCoefficient rdf:datatype="http://www.w3.org/2001/XMLSchema#float"
+ >1.0</bp:stoichiometricCoefficient>
+ <bp:physicalEntity>
+ <bp:Protein rdf:ID="Protein_27">
+ <bp:dataSource rdf:resource="#Provenance_3"/>
+ <bp:entityReference rdf:resource="#ATM"/>
+ <bp:name rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >Ataxia telangiectasia mutated) (A-T, mutated) </bp:name>
+ <bp:standardName rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >Serine-protein kinase AT(Ataxia telangiectasia mutated) (A-T, mutated)</bp:standardName>
+ <bp:cellularLocation rdf:resource="#CellularLocationVocabulary_6"/>
+ <bp:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >"FUNCTION Involved in signal transduction, cell cycle control and DNA repair. May function as a tumor suppressor. Necessary for activation of ABL1 and SAPK"</bp:comment>
+ <bp:xref rdf:resource="#UnificationXref_28"/>
+ <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >ATM</bp:displayName>
+ </bp:Protein>
+ </bp:physicalEntity>
+ </bp:Stoichiometry>
+ </bp:participantStoichiometry>
+ <bp:left rdf:resource="#Protein_5"/>
+ <bp:left>
+ <bp:SmallMolecule rdf:ID="SmallMolecule_13">
+ <bp:entityReference>
+ <bp:SmallMoleculeReference rdf:ID="SmallMoleculeReference_15">
+ <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >ATP</bp:displayName>
+ <bp:xref>
+ <bp:UnificationXref rdf:ID="UnificationXref_14">
+ <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >CHEBI:2359</bp:id>
+ <bp:db rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >ChEBI</bp:db>
+ </bp:UnificationXref>
+ </bp:xref>
+ <bp:standardName rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >Adenosine 5'-triphosphate</bp:standardName>
+ </bp:SmallMoleculeReference>
+ </bp:entityReference>
+ <bp:xref rdf:resource="#UnificationXref_14"/>
+ <bp:cellularLocation rdf:resource="#CellularLocationVocabulary_6"/>
+ <bp:standardName rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >Adenosine 5'-triphosphate</bp:standardName>
+ <bp:dataSource rdf:resource="#Provenance_3"/>
+ <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >ATP</bp:displayName>
+ </bp:SmallMolecule>
+ </bp:left>
+ <bp:participantStoichiometry>
+ <bp:Stoichiometry rdf:ID="Stoichiometry_1">
+ <bp:physicalEntity rdf:resource="#Protein_5"/>
+ <bp:stoichiometricCoefficient rdf:datatype="http://www.w3.org/2001/XMLSchema#float"
+ >1.0</bp:stoichiometricCoefficient>
+ </bp:Stoichiometry>
+ </bp:participantStoichiometry>
+ <bp:xref>
+ <bp:UnificationXref rdf:ID="UnificationXref_26">
+ <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >REACT_69891</bp:id>
+ <bp:db rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >reactome</bp:db>
+ <bp:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >http://www.reactome.org </bp:comment>
+ </bp:UnificationXref>
+ </bp:xref>
+ <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >Phosphorylation and activation of CHK2 by ATM</bp:displayName>
+ <bp:conversionDirection rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >LEFT-TO-RIGHT</bp:conversionDirection>
+ <bp:dataSource rdf:resource="#Provenance_3"/>
+ <bp:participantStoichiometry>
+ <bp:Stoichiometry rdf:ID="Stoichiometry_4">
+ <bp:stoichiometricCoefficient rdf:datatype="http://www.w3.org/2001/XMLSchema#float"
+ >1.0</bp:stoichiometricCoefficient>
+ <bp:physicalEntity rdf:resource="#SmallMolecule_13"/>
+ </bp:Stoichiometry>
+ </bp:participantStoichiometry>
+ <bp:xref>
+ <bp:PublicationXref rdf:ID="PublicationXref_25">
+ <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >McGowan, CH </bp:author>
+ <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >Laus, MC </bp:author>
+ <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >Luyten, WH </bp:author>
+ <bp:title rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >A human homologue of the checkpoint kinase Cds1 directly inhibits Cdc25 phosphatase.</bp:title>
+ <bp:source rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >Curr Biol 9:1-10 </bp:source>
+ <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >Parker, AE </bp:author>
+ <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >de Weyer, IV </bp:author>
+ <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >Blasina, A </bp:author>
+ <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >9889122</bp:id>
+ <bp:db rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >pubmed</bp:db>
+ <bp:year rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
+ >1999</bp:year>
+ </bp:PublicationXref>
+ </bp:xref>
+ <bp:participantStoichiometry>
+ <bp:Stoichiometry rdf:ID="Stoichiometry_3">
+ <bp:physicalEntity rdf:resource="#SmallMolecule_21"/>
+ <bp:stoichiometricCoefficient rdf:datatype="http://www.w3.org/2001/XMLSchema#float"
+ >1.0</bp:stoichiometricCoefficient>
+ </bp:Stoichiometry>
+ </bp:participantStoichiometry>
+ <bp:spontaneous rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >NOT-SPONTANEOUS</bp:spontaneous>
+ </bp:BiochemicalReaction>
+ </bp:controlled>
+ <bp:controlType rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >ACTIVATION</bp:controlType>
+ <bp:controller rdf:resource="#Protein_27"/>
+ <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >ATM phosphorylates and activates CHK2</bp:displayName>
+ <bp:xref rdf:resource="#RelationshipXref_29"/>
+ <bp:availability rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >Reactome is a free on-line resource, and Reactome software is open-source. However, please take note of our disclaimer. (http://reactome.org/disclaimer.html) </bp:availability>
+ <bp:catalysisDirection rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >LEFT-TO-RIGHT</bp:catalysisDirection>
+ </bp:Catalysis>
+</rdf:RDF>
+
+<!-- Created with Protege (with OWL Plugin 3.3.1, Build 430) http://protege.stanford.edu -->
diff --git a/coreplugins/BioPAX/src/test/resources/biopax_complex.owl b/coreplugins/BioPAX/src/test/resources/biopax_complex.owl
new file mode 100644
index 0000000..bf582c1
--- /dev/null
+++ b/coreplugins/BioPAX/src/test/resources/biopax_complex.owl
@@ -0,0 +1,141 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<rdf:RDF
+xmlns="http://cbio.mskcc.org/cpath#"
+xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
+xmlns:xs="http://www.w3.org/2001/XMLSchema#"
+xmlns:bp="http://www.biopax.org/release/biopax-level2.owl#"
+xmlns:owl="http://www.w3.org/2002/07/owl#"
+xml:base="http://cbio.mskcc.org/cpath#">
+ <owl:Ontology rdf:about="">
+ <owl:imports rdf:resource="http://www.biopax.org/release/biopax-level2.owl" />
+ </owl:Ontology>
+
+ <bp:bioSource rdf:ID="CPATH-LOCAL-1154">
+ <bp:NAME rdf:datatype="xs:string">Homo sapiens</bp:NAME>
+ <bp:TAXON-XREF>
+ <bp:unificationXref rdf:ID="CPATH-LOCAL-1155">
+ <bp:DB rdf:datatype="xs:string">NCBI_taxonomy</bp:DB>
+ <bp:ID rdf:datatype="xs:string">9606</bp:ID>
+ </bp:unificationXref>
+ </bp:TAXON-XREF>
+ </bp:bioSource>
+ <bp:complex rdf:ID="CPATH-126">
+ <bp:COMPONENTS>
+ <bp:sequenceParticipant rdf:ID="CPATH-LOCAL-1160">
+ <bp:CELLULAR-LOCATION>
+ <bp:openControlledVocabulary rdf:ID="CPATH-LOCAL-1161">
+ <bp:TERM rdf:datatype="xs:string">plasma membrane</bp:TERM>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="CPATH-LOCAL-1162">
+ <bp:DB rdf:datatype="xs:string">GO</bp:DB>
+ <bp:ID rdf:datatype="xs:string">0005886</bp:ID>
+ </bp:unificationXref>
+ </bp:XREF>
+ </bp:openControlledVocabulary>
+ </bp:CELLULAR-LOCATION>
+ <bp:PHYSICAL-ENTITY rdf:resource="#CPATH-124" />
+ </bp:sequenceParticipant>
+ </bp:COMPONENTS>
+ <bp:COMPONENTS>
+ <bp:sequenceParticipant rdf:ID="CPATH-LOCAL-1163">
+ <bp:CELLULAR-LOCATION rdf:resource="#CPATH-LOCAL-1161" />
+ <bp:PHYSICAL-ENTITY rdf:resource="#CPATH-125" />
+ </bp:sequenceParticipant>
+ </bp:COMPONENTS>
+ <bp:ORGANISM rdf:resource="#CPATH-LOCAL-1154"/>
+ <bp:NAME rdf:datatype="xs:string">TNF-alpha:TNF-R1 complex [plasma membrane]</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="xs:string">TNF-alpha:TNF-R1 complex</bp:SHORT-NAME>
+ </bp:complex>
+ <bp:protein rdf:ID="CPATH-124">
+ <bp:ORGANISM rdf:resource="#CPATH-LOCAL-1154" />
+ <bp:NAME rdf:datatype="xs:string">UniProt:P01375 Tumor necrosis factor precursor (TNF-alpha) (Tumor necrosis factor ligand superfamily member 2) (TNF-a) (Cachectin)</bp:NAME>
+ <bp:SHORT-NAME rdf:datatype="xs:string">TNF</bp:SHORT-NAME>
+ <bp:SYNONYMS rdf:datatype="xs:string">TNF</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">TNFA</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">TNFSF2</bp:SYNONYMS>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="CPATH-LOCAL-1156">
+ <bp:DB rdf:datatype="xs:string">UniProt</bp:DB>
+ <bp:ID rdf:datatype="xs:string">P01375</bp:ID>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:XREF>
+ <bp:relationshipXref rdf:ID="induction_of_apoptosis_by_extracellular_signals">
+ <bp:DB rdf:datatype="xs:string">GO</bp:DB>
+ <bp:ID rdf:datatype="xs:string">0008624</bp:ID>
+ </bp:relationshipXref>
+ </bp:XREF>
+ <bp:XREF>
+ <bp:relationshipXref rdf:ID="caspase_activation">
+ <bp:DB rdf:datatype="xs:string">GO</bp:DB>
+ <bp:ID rdf:datatype="xs:string">0006919</bp:ID>
+ </bp:relationshipXref>
+ </bp:XREF>
+ <bp:XREF>
+ <bp:publicationXref rdf:ID="Pubmed_7530336">
+ <bp:ID rdf:datatype="xs:string">7530336</bp:ID>
+ <bp:DB rdf:datatype="xs:string">Pubmed</bp:DB>
+ <bp:YEAR rdf:datatype="xs:int">1995</bp:YEAR>
+ <bp:TITLE rdf:datatype="xs:string">Cell-autonomous Fas (CD95)/Fas-ligand interaction mediates activation-induced apoptosis in T-cell hybridomas</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="xs:string">Brunner, T</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="xs:string">Mogil, RJ</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="xs:string">LaFace, D</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="xs:string">Yoo, NJ</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="xs:string">Mahboubi, A</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="xs:string">Echeverri, F</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="xs:string">Martin, SJ</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="xs:string">Force, WR</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="xs:string">Lynch, DH</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="xs:string">Ware, CF</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="xs:string">Nature 373:441-4</bp:SOURCE>
+ </bp:publicationXref>
+ </bp:XREF>
+ <bp:XREF>
+ <bp:publicationXref rdf:ID="Pubmed_8521815">
+ <bp:ID rdf:datatype="xs:string">8521815</bp:ID>
+ <bp:DB rdf:datatype="xs:string">Pubmed</bp:DB>
+ <bp:YEAR rdf:datatype="xs:int">1995</bp:YEAR>
+ <bp:TITLE rdf:datatype="xs:string">Cytotoxicity-dependent APO-1 (Fas/CD95)-associated proteins form a death-inducing signaling complex (DISC) with the receptor</bp:TITLE>
+ <bp:AUTHORS rdf:datatype="xs:string">Kischkel, FC</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="xs:string">Hellbardt, S</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="xs:string">Behrmann, I</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="xs:string">Germer, M</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="xs:string">Pawlita, M</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="xs:string">Krammer, PH</bp:AUTHORS>
+ <bp:AUTHORS rdf:datatype="xs:string">Peter, ME</bp:AUTHORS>
+ <bp:SOURCE rdf:datatype="xs:string">EMBO J 14:5579-88</bp:SOURCE>
+ </bp:publicationXref>
+ </bp:XREF>
+ <bp:COMMENT rdf:datatype="xs:string">FUNCTION: Cytokine that binds to TNFRSF1A/TNFR1 and TNFRSF1B/TNFBR. It is mainly secreted by macrophages and can induce cell death of certain tumor cell lines. It is potent pyrogen causing fever by direct action or by stimulation of interleukin 1 secretion and is implicated in the induction of cachexia, Under certain conditions it can stimulate cell proliferation and induce cell differentiation. SUBUNIT: Homotrimer. SUBCELLULAR LOCATION: Type II m [...]
+ <bp:AVAILABILITY
+ rdf:datatype="xs:string">see http://www.amaze.ulb.ac.be/</bp:AVAILABILITY>
+ <bp:DATA-SOURCE>
+ <bp:dataSource rdf:ID="dataSource14">
+ <bp:NAME rdf:datatype="xs:string">aMAZE</bp:NAME>
+ <bp:COMMENT
+ rdf:datatype="xs:string">This
+ example is meant to provide an illustration of how
+ various BioPAX slots should be filled; it is not
+ intended to provide useful (or even accurate)
+ biological information</bp:COMMENT>
+ </bp:dataSource>
+ </bp:DATA-SOURCE>
+ </bp:protein>
+ <bp:protein rdf:ID="CPATH-125">
+ <bp:ORGANISM rdf:resource="#CPATH-LOCAL-1154"/>
+ <bp:NAME rdf:datatype="xs:string">UniProt:P19438 Tumor necrosis factor receptor superfamily member 1A precursor (p60) (TNF-R1) (TNF-RI) (p55) (CD120a) [Contains: Tumor necrosis factor binding protein 1 (TBPI)]</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="xs:string">TNFRSF1A</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">TNFR1</bp:SYNONYMS>
+ <bp:SYNONYMS rdf:datatype="xs:string">TNFAR</bp:SYNONYMS>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="CPATH-LOCAL-1159">
+ <bp:DB rdf:datatype="xs:string">UniProt</bp:DB>
+ <bp:ID rdf:datatype="xs:string">P19438</bp:ID>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:COMMENT rdf:datatype="xs:string">FUNCTION: Receptor for TNFSF2/TNF-alpha and homotrimeric TNFSF1/lymphotoxin-alpha. The adaptor molecule FADD recruits caspase-8 to the activated receptor. The resulting death-inducing signaling complex (DISC) performs caspase-8 proteolytic activation which initiates the subsequent cascade of caspases (aspartate- specific cysteine proteases) mediating apoptosis. Contributes to the induction of noncytocidal TNF effects including anti-viral state and [...]
+ </bp:protein>
+</rdf:RDF>
+
+
diff --git a/coreplugins/BioPAX/src/test/resources/biopax_sample1.owl b/coreplugins/BioPAX/src/test/resources/biopax_sample1.owl
new file mode 100644
index 0000000..3db58a4
--- /dev/null
+++ b/coreplugins/BioPAX/src/test/resources/biopax_sample1.owl
@@ -0,0 +1,737 @@
+<?xml version="1.0"?>
+<rdf:RDF
+ xml:base="http://www.biopax.org/examples/simple-demo-pathway#"
+ xmlns="http://www.biopax.org/examples/simple-demo-pathway#"
+ xmlns:bp="http://www.biopax.org/release/biopax-level2.owl#"
+ xmlns:owl="http://www.w3.org/2002/07/owl#"
+ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+ xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
+ xmlns:xs="http://www.w3.org/2001/XMLSchema#">
+ <owl:Ontology rdf:about="">
+ <owl:imports rdf:resource="http://www.biopax.org/release/biopax-level2.owl"/>
+ </owl:Ontology>
+ <bp:bioSource rdf:ID="bioSource33">
+ <bp:NAME
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Escherichia coli</bp:NAME>
+ <bp:TAXON-XREF>
+ <bp:unificationXref rdf:ID="unificationXref34">
+ <bp:ID>562</bp:ID>
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various
+ BioPAX slots should be filled; it is not intended to provide
+ useful (or even accurate) biological information</bp:COMMENT>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">taxon</bp:DB>
+ </bp:unificationXref>
+ </bp:TAXON-XREF>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various BioPAX
+ slots should be filled; it is not intended to provide useful (or
+ even accurate) biological information</bp:COMMENT>
+ </bp:bioSource>
+ <bp:unificationXref rdf:ID="unificationXref29">
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">aMAZESpecificCompound0000000638</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">aMAZE</bp:DB>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various BioPAX
+ slots should be filled; it is not intended to provide useful (or
+ even accurate) biological information</bp:COMMENT>
+ </bp:unificationXref>
+ <bp:unificationXref rdf:ID="unificationXref7">
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various BioPAX
+ slots should be filled; it is not intended to provide useful (or
+ even accurate) biological information</bp:COMMENT>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">R01786</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">KEGG</bp:DB>
+ </bp:unificationXref>
+ <bp:chemicalStructure rdf:ID="chemicalStructure12">
+ <bp:STRUCTURE-FORMAT>SMILES</bp:STRUCTURE-FORMAT>
+ <bp:STRUCTURE-DATA>C1(C(O)C(O)C(O)C(O1)CO)(O)</bp:STRUCTURE-DATA>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various BioPAX
+ slots should be filled; it is not intended to provide useful (or
+ even accurate) biological information</bp:COMMENT>
+ </bp:chemicalStructure>
+ <bp:unificationXref rdf:ID="unificationXref41">
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various BioPAX
+ slots should be filled; it is not intended to provide useful (or
+ even accurate) biological information</bp:COMMENT>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">C05345</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">KEGG</bp:DB>
+ </bp:unificationXref>
+ <bp:physicalEntityParticipant rdf:ID="physicalEntityParticipant9">
+ <bp:STOICHIOMETRIC-COEFFICIENT>1.0</bp:STOICHIOMETRIC-COEFFICIENT>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various BioPAX
+ slots should be filled; it is not intended to provide useful (or
+ even accurate) biological information</bp:COMMENT>
+ <bp:PHYSICAL-ENTITY>
+ <bp:smallMolecule rdf:ID="smallMolecule10">
+ <bp:SYNONYMS
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string"><FONT FACE="Symbol">a</FONT>-D-glucose</bp:SYNONYMS>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref11">
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">C00267</bp:ID>
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how
+ various BioPAX slots should be filled; it is not
+ intended to provide useful (or even accurate)
+ biological information</bp:COMMENT>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">KEGG</bp:DB>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">a-D-glu</bp:SHORT-NAME>
+ <bp:DATA-SOURCE>
+ <bp:dataSource rdf:ID="KB_439584_Individual_47">
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">KEGG</bp:NAME>
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how
+ various BioPAX slots should be filled; it is not
+ intended to provide useful (or even accurate)
+ biological information</bp:COMMENT>
+ </bp:dataSource>
+ </bp:DATA-SOURCE>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref13">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">aMAZE</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">aMAZESpecificCompound0000000263</bp:ID>
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how
+ various BioPAX slots should be filled; it is not
+ intended to provide useful (or even accurate)
+ biological information</bp:COMMENT>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various
+ BioPAX slots should be filled; it is not intended to provide
+ useful (or even accurate) biological information</bp:COMMENT>
+ <bp:AVAILABILITY
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">see http://www.amaze.ulb.ac.be/</bp:AVAILABILITY>
+ <bp:DATA-SOURCE>
+ <bp:dataSource rdf:ID="dataSource14">
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">aMAZE</bp:NAME>
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how
+ various BioPAX slots should be filled; it is not
+ intended to provide useful (or even accurate)
+ biological information</bp:COMMENT>
+ </bp:dataSource>
+ </bp:DATA-SOURCE>
+ <bp:STRUCTURE rdf:resource="#chemicalStructure12"/>
+ <bp:CHEMICAL-FORMULA rdf:datatype="http://www.w3.org/2001/XMLSchema#string">C6H12O6</bp:CHEMICAL-FORMULA>
+ <bp:MOLECULAR-WEIGHT>180.16</bp:MOLECULAR-WEIGHT>
+ <bp:NAME>alpha-D-glucose</bp:NAME>
+ </bp:smallMolecule>
+ </bp:PHYSICAL-ENTITY>
+ <bp:CELLULAR-LOCATION>
+ <bp:openControlledVocabulary rdf:ID="openControlledVocabulary15">
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref16">
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how
+ various BioPAX slots should be filled; it is not
+ intended to provide useful (or even accurate)
+ biological information</bp:COMMENT>
+ <bp:DB>Gene Ontology</bp:DB>
+ <bp:ID>GO:0005737</bp:ID>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various
+ BioPAX slots should be filled; it is not intended to provide
+ useful (or even accurate) biological information</bp:COMMENT>
+ <bp:TERM>cytoplasm</bp:TERM>
+ </bp:openControlledVocabulary>
+ </bp:CELLULAR-LOCATION>
+ </bp:physicalEntityParticipant>
+ <bp:unificationXref rdf:ID="unificationXref35">
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P46880</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Swiss-Prot/TrEMBL</bp:DB>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various BioPAX
+ slots should be filled; it is not intended to provide useful (or
+ even accurate) biological information</bp:COMMENT>
+ </bp:unificationXref>
+ <bp:smallMolecule rdf:ID="smallMolecule18">
+ <bp:NAME
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Adenosine 5'-diphosphate</bp:NAME>
+ <bp:SYNONYMS
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">adenosine diphosphate</bp:SYNONYMS>
+ <bp:DATA-SOURCE rdf:resource="#KB_439584_Individual_47"/>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various BioPAX
+ slots should be filled; it is not intended to provide useful (or
+ even accurate) biological information</bp:COMMENT>
+ <bp:DATA-SOURCE rdf:resource="#dataSource14"/>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref20">
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various
+ BioPAX slots should be filled; it is not intended to provide
+ useful (or even accurate) biological information</bp:COMMENT>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">aMAZE</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">aMAZESpecificCompound0000000008</bp:ID>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:MOLECULAR-WEIGHT>427.2</bp:MOLECULAR-WEIGHT>
+ <bp:SHORT-NAME>ADP</bp:SHORT-NAME>
+ <bp:STRUCTURE>
+ <bp:chemicalStructure rdf:ID="chemicalStructure21">
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various
+ BioPAX slots should be filled; it is not intended to provide
+ useful (or even accurate) biological information</bp:COMMENT>
+ <bp:STRUCTURE-DATA>c12(n(cnc(c(N)ncn1)2)[CH]3(O[CH]([CH](O)[CH](O)3)COP(=O)(O)OP(O)(=O)O))</bp:STRUCTURE-DATA>
+ <bp:STRUCTURE-FORMAT>SMILES</bp:STRUCTURE-FORMAT>
+ </bp:chemicalStructure>
+ </bp:STRUCTURE>
+ <bp:CHEMICAL-FORMULA rdf:datatype="http://www.w3.org/2001/XMLSchema#string">C10H15N5O10P2</bp:CHEMICAL-FORMULA>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref19">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">KEGG</bp:DB>
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various
+ BioPAX slots should be filled; it is not intended to provide
+ useful (or even accurate) biological information</bp:COMMENT>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">C00008</bp:ID>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:AVAILABILITY
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">see http://www.amaze.ulb.ac.be/</bp:AVAILABILITY>
+ </bp:smallMolecule>
+ <bp:unificationXref rdf:ID="unificationXref42">
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various BioPAX
+ slots should be filled; it is not intended to provide useful (or
+ even accurate) biological information</bp:COMMENT>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">aMAZESpecificCompound0000004507</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">aMAZE</bp:DB>
+ </bp:unificationXref>
+ <bp:biochemicalReaction rdf:ID="biochemicalReaction37">
+ <bp:DATA-SOURCE rdf:resource="#dataSource14"/>
+ <bp:LEFT>
+ <bp:physicalEntityParticipant rdf:ID="physicalEntityParticipant26">
+ <bp:STOICHIOMETRIC-COEFFICIENT>1.0</bp:STOICHIOMETRIC-COEFFICIENT>
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various
+ BioPAX slots should be filled; it is not intended to provide
+ useful (or even accurate) biological information</bp:COMMENT>
+ <bp:PHYSICAL-ENTITY>
+ <bp:smallMolecule rdf:ID="smallMolecule27">
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">a-D-glu-6-p</bp:SHORT-NAME>
+ <bp:CHEMICAL-FORMULA rdf:datatype="http://www.w3.org/2001/XMLSchema#string">C6H13O9P</bp:CHEMICAL-FORMULA>
+ <bp:SYNONYMS
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string"><FONT FACE="Symbol">a</FONT>-D-glucose-6-phoshate</bp:SYNONYMS>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref30">
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">C00668</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">KEGG</bp:DB>
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration
+ of how various BioPAX slots should be
+ filled; it is not intended to provide useful
+ (or even accurate) biological information</bp:COMMENT>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:XREF rdf:resource="#unificationXref29"/>
+ <bp:MOLECULAR-WEIGHT>260.14</bp:MOLECULAR-WEIGHT>
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how
+ various BioPAX slots should be filled; it is not
+ intended to provide useful (or even accurate)
+ biological information</bp:COMMENT>
+ <bp:AVAILABILITY
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">see http://www.amaze.ulb.ac.be/</bp:AVAILABILITY>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">glucose-6-P</bp:SYNONYMS>
+ <bp:DATA-SOURCE rdf:resource="#dataSource14"/>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">alpha-D-glucose-6-p</bp:SYNONYMS>
+ <bp:STRUCTURE>
+ <bp:chemicalStructure rdf:ID="chemicalStructure28">
+ <bp:STRUCTURE-FORMAT>SMILES</bp:STRUCTURE-FORMAT>
+ <bp:STRUCTURE-DATA>C(OP(=O)(O)O)[CH]1([CH](O)[CH](O)[CH](O)[CH](O)O1)</bp:STRUCTURE-DATA>
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration
+ of how various BioPAX slots should be
+ filled; it is not intended to provide useful
+ (or even accurate) biological information</bp:COMMENT>
+ </bp:chemicalStructure>
+ </bp:STRUCTURE>
+ <bp:NAME>alpha-D-glucose 6-phosphate</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">alpha-D-glucose-6-phosphate</bp:SYNONYMS>
+ <bp:SYNONYMS
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string"> D-glucose-6-P</bp:SYNONYMS>
+ <bp:DATA-SOURCE rdf:resource="#KB_439584_Individual_47"/>
+ </bp:smallMolecule>
+ </bp:PHYSICAL-ENTITY>
+ <bp:CELLULAR-LOCATION rdf:resource="#openControlledVocabulary15"/>
+ </bp:physicalEntityParticipant>
+ </bp:LEFT>
+ <bp:DELTA-G>
+ <bp:deltaGprimeO rdf:ID="biochemicalReaction37_deltaG">
+ <bp:DELTA-G-PRIME-O rdf:datatype="http://www.w3.org/2001/XMLSchema#float">0.4</bp:DELTA-G-PRIME-O>
+ </bp:deltaGprimeO>
+ </bp:DELTA-G>
+ <bp:SYNONYMS
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">alpha-D-Glucose
+ 6-phosphate <=> beta-D-Fructose 6-phosphate </bp:SYNONYMS>
+ <bp:RIGHT>
+ <bp:physicalEntityParticipant rdf:ID="physicalEntityParticipant38">
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various
+ BioPAX slots should be filled; it is not intended to provide
+ useful (or even accurate) biological information</bp:COMMENT>
+ <bp:CELLULAR-LOCATION rdf:resource="#openControlledVocabulary15"/>
+ <bp:PHYSICAL-ENTITY>
+ <bp:smallMolecule rdf:ID="smallMolecule39">
+ <bp:CHEMICAL-FORMULA rdf:datatype="http://www.w3.org/2001/XMLSchema#string">C6H13O9P</bp:CHEMICAL-FORMULA>
+ <bp:DATA-SOURCE rdf:resource="#dataSource14"/>
+ <bp:DATA-SOURCE rdf:resource="#KB_439584_Individual_47"/>
+ <bp:SYNONYMS
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string"><FONT FACE="Symbol">b</FONT>-D-fructose-6-phosphate</bp:SYNONYMS>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">b-D-fru-6-p</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#unificationXref42"/>
+ <bp:STRUCTURE>
+ <bp:chemicalStructure rdf:ID="chemicalStructure40">
+ <bp:STRUCTURE-DATA>C(OP(O)(O)=O)[CH]1([CH](O)[CH](O)C(O)(O1)CO)</bp:STRUCTURE-DATA>
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration
+ of how various BioPAX slots should be
+ filled; it is not intended to provide useful
+ (or even accurate) biological information</bp:COMMENT>
+ <bp:STRUCTURE-FORMAT>SMILES</bp:STRUCTURE-FORMAT>
+ </bp:chemicalStructure>
+ </bp:STRUCTURE>
+ <bp:MOLECULAR-WEIGHT>260.14</bp:MOLECULAR-WEIGHT>
+ <bp:NAME
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">beta-D-fructose 6-phosphate</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">beta-D-fructose-6-phosphate</bp:SYNONYMS>
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how
+ various BioPAX slots should be filled; it is not
+ intended to provide useful (or even accurate)
+ biological information</bp:COMMENT>
+ <bp:AVAILABILITY
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">see http://www.amaze.ulb.ac.be/</bp:AVAILABILITY>
+ <bp:XREF rdf:resource="#unificationXref41"/>
+ </bp:smallMolecule>
+ </bp:PHYSICAL-ENTITY>
+ <bp:STOICHIOMETRIC-COEFFICIENT>1.0</bp:STOICHIOMETRIC-COEFFICIENT>
+ </bp:physicalEntityParticipant>
+ </bp:RIGHT>
+ <bp:SHORT-NAME
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">a-D-glu-6-p
+ <=> b-D-fru-6-p</bp:SHORT-NAME>
+ <bp:DATA-SOURCE rdf:resource="#KB_439584_Individual_47"/>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Note:
+ If filled, the value of the PARTICIPANTS slot should be the union of
+ the LEFT and RIGHT slots.</bp:COMMENT>
+ <bp:AVAILABILITY
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">see http://www.amaze.ulb.ac.be/</bp:AVAILABILITY>
+ <bp:EC-NUMBER>5.3.1.9</bp:EC-NUMBER>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref1">
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">R02740</bp:ID>
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various
+ BioPAX slots should be filled; it is not intended to provide
+ useful (or even accurate) biological information</bp:COMMENT>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">KEGG</bp:DB>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:NAME
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">alpha-D-glu-6-p
+ <=> beta-D-fru-6-p</bp:NAME>
+ <bp:SYNONYMS
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">alpha-D-Glucose
+ 6-phosphate ketol-isomerase</bp:SYNONYMS>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref3">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">aMAZE</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">aMAZEReaction0000002504</bp:ID>
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various
+ BioPAX slots should be filled; it is not intended to provide
+ useful (or even accurate) biological information</bp:COMMENT>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various BioPAX
+ slots should be filled; it is not intended to provide useful (or
+ even accurate) biological information</bp:COMMENT>
+ </bp:biochemicalReaction>
+ <bp:physicalEntityParticipant rdf:ID="physicalEntityParticipant17">
+ <bp:CELLULAR-LOCATION rdf:resource="#openControlledVocabulary15"/>
+ <bp:STOICHIOMETRIC-COEFFICIENT>1.0</bp:STOICHIOMETRIC-COEFFICIENT>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various BioPAX
+ slots should be filled; it is not intended to provide useful (or
+ even accurate) biological information</bp:COMMENT>
+ <bp:PHYSICAL-ENTITY rdf:resource="#smallMolecule18"/>
+ </bp:physicalEntityParticipant>
+ <bp:smallMolecule rdf:ID="smallMolecule23">
+ <bp:DATA-SOURCE rdf:resource="#dataSource14"/>
+ <bp:AVAILABILITY
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">see http://www.amaze.ulb.ac.be/</bp:AVAILABILITY>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref24">
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various
+ BioPAX slots should be filled; it is not intended to provide
+ useful (or even accurate) biological information</bp:COMMENT>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">aMAZESpecificCompound0000000002</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">aMAZE</bp:DB>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:STRUCTURE>
+ <bp:chemicalStructure rdf:ID="chemicalStructure25">
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various
+ BioPAX slots should be filled; it is not intended to provide
+ useful (or even accurate) biological information</bp:COMMENT>
+ <bp:STRUCTURE-DATA>[CH]3(n1(c2(c(nc1)c(N)ncn2)))(O[CH]([CH](O)[CH](O)3)COP(=O)(O)OP(O)(=O)OP(O)(=O)O)</bp:STRUCTURE-DATA>
+ <bp:STRUCTURE-FORMAT>SMILES</bp:STRUCTURE-FORMAT>
+ </bp:chemicalStructure>
+ </bp:STRUCTURE>
+ <bp:MOLECULAR-WEIGHT>507.18</bp:MOLECULAR-WEIGHT>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various BioPAX
+ slots should be filled; it is not intended to provide useful (or
+ even accurate) biological information</bp:COMMENT>
+ <bp:CHEMICAL-FORMULA rdf:datatype="http://www.w3.org/2001/XMLSchema#string">C10H16N5O13P3</bp:CHEMICAL-FORMULA>
+ <bp:DATA-SOURCE rdf:resource="#KB_439584_Individual_47"/>
+ <bp:SYNONYMS
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">adenosine triphosphate</bp:SYNONYMS>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref2">
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various
+ BioPAX slots should be filled; it is not intended to provide
+ useful (or even accurate) biological information</bp:COMMENT>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">KEGG</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">C00002</bp:ID>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:SHORT-NAME>ATP</bp:SHORT-NAME>
+ <bp:NAME
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Adenosine 5'-triphosphate</bp:NAME>
+ </bp:smallMolecule>
+ <bp:unificationXref rdf:ID="unificationXref8">
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various BioPAX
+ slots should be filled; it is not intended to provide useful (or
+ even accurate) biological information</bp:COMMENT>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">aMAZEReaction0000001619</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">aMAZE</bp:DB>
+ </bp:unificationXref>
+ <bp:catalysis rdf:ID="catalysis5">
+ <bp:DATA-SOURCE rdf:resource="#dataSource14"/>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The
+ source of this data did not store catalyses of reactions as separate
+ objects, so there are no unification x-refs pointing to the source
+ of these BioPAX instances.</bp:COMMENT>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various BioPAX
+ slots should be filled; it is not intended to provide useful (or
+ even accurate) biological information</bp:COMMENT>
+ <bp:DIRECTION rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PHYSIOL-LEFT-TO-RIGHT</bp:DIRECTION>
+ <bp:DATA-SOURCE rdf:resource="#KB_439584_Individual_47"/>
+ <bp:AVAILABILITY
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">see http://www.amaze.ulb.ac.be/</bp:AVAILABILITY>
+ <bp:CONTROLLER>
+ <bp:physicalEntityParticipant rdf:ID="physicalEntityParticipant31">
+ <bp:PHYSICAL-ENTITY>
+ <bp:protein rdf:ID="protein32">
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GLK</bp:SHORT-NAME>
+ <bp:DATA-SOURCE>
+ <bp:dataSource rdf:ID="KB_439584_Individual_48">
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Swiss-Prot/TrEMBL</bp:NAME>
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration
+ of how various BioPAX slots should be
+ filled; it is not intended to provide useful
+ (or even accurate) biological information</bp:COMMENT>
+ </bp:dataSource>
+ </bp:DATA-SOURCE>
+ <bp:SEQUENCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">MTKYALVGDVGGTNARLALCDIASGEISQAKTYSGLDYPSLEAVIRVYLEEHKVEVKDGCIAIACPITGDWVAMTNHTWAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLKKEHLIQFGGAEPVEGKPIAVYGAGTGLGVAHLVHVDKRWVSLPGEGGHVDFAPNSEEEAIILEILRAEIGHVSAERVLSGPGLVNLYRAIVKADNRLPENLKPKDITERALADSCTDCRRALSLFCVIMGRFGGNLALNLGTFGGVFIAGGIVPRFLEFFKASGFRAAFEDKGRFKEYVHDIPVYLIVHDNPGLLGSGAHLRQTLGHIL</bp:SEQUENCE>
+ <bp:AVAILABILITY
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">see http://www.amaze.ulb.ac.be/</bp:AVAILABILITY>
+ <bp:XREF rdf:resource="#unificationXref35"/>
+ <bp:DATA-SOURCE rdf:resource="#dataSource14"/>
+ <bp:ORGANISM rdf:resource="#bioSource33"/>
+ <bp:SYNONYMS
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glucose kinase</bp:SYNONYMS>
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how
+ various BioPAX slots should be filled; it is not
+ intended to provide useful (or even accurate)
+ biological information</bp:COMMENT>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GLK_ECOLI</bp:SYNONYMS>
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">glucokinase</bp:NAME>
+ </bp:protein>
+ </bp:PHYSICAL-ENTITY>
+ <bp:CELLULAR-LOCATION rdf:resource="#openControlledVocabulary15"/>
+ <bp:STOICHIOMETRIC-COEFFICIENT rdf:datatype="http://www.w3.org/2001/XMLSchema#double">1.0</bp:STOICHIOMETRIC-COEFFICIENT>
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various
+ BioPAX slots should be filled; it is not intended to provide
+ useful (or even accurate) biological information</bp:COMMENT>
+ </bp:physicalEntityParticipant>
+ </bp:CONTROLLER>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Note:
+ The PARTICIPANTS slot may be left empty if both the CONTROLLED and
+ CONTROLLER slots are filled.</bp:COMMENT>
+ <bp:SHORT-NAME
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GLK ->
+ (a-D-glu <=> a-D-glu-6-p)</bp:SHORT-NAME>
+ <bp:NAME
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">catalysis of
+ (alpha-D-glu <=> alpha-D-glu-6-p)</bp:NAME>
+ <bp:CONTROLLED>
+ <bp:biochemicalReaction rdf:ID="biochemicalReaction6">
+ <bp:XREF rdf:resource="#unificationXref8"/>
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various
+ BioPAX slots should be filled; it is not intended to provide
+ useful (or even accurate) biological information</bp:COMMENT>
+ <bp:SYNONYMS
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ATP:D-glucose 6-phosphotransferase</bp:SYNONYMS>
+ <bp:NAME
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">alpha-D-glu
+ + ATP <=> alpha-D-glu-6-p + ADP</bp:NAME>
+ <bp:LEFT rdf:resource="#physicalEntityParticipant9"/>
+ <bp:EC-NUMBER rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2.7.1.2</bp:EC-NUMBER>
+ <bp:LEFT>
+ <bp:physicalEntityParticipant rdf:ID="physicalEntityParticipant22">
+ <bp:STOICHIOMETRIC-COEFFICIENT>1.0</bp:STOICHIOMETRIC-COEFFICIENT>
+ <bp:CELLULAR-LOCATION rdf:resource="#openControlledVocabulary15"/>
+ <bp:PHYSICAL-ENTITY rdf:resource="#smallMolecule23"/>
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how
+ various BioPAX slots should be filled; it is not
+ intended to provide useful (or even accurate)
+ biological information</bp:COMMENT>
+ </bp:physicalEntityParticipant>
+ </bp:LEFT>
+ <bp:RIGHT rdf:resource="#physicalEntityParticipant17"/>
+ <bp:AVAILABILITY
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">see http://www.amaze.ulb.ac.be/</bp:AVAILABILITY>
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Note:
+ The PARTICIPANTS slot may be left empty if both the LEFT and
+ RIGHT slots are filled.</bp:COMMENT>
+ <bp:SYNONYMS
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">glucose
+ ATP phosphotransferase</bp:SYNONYMS>
+ <bp:XREF rdf:resource="#unificationXref7"/>
+ <bp:RIGHT rdf:resource="#physicalEntityParticipant26"/>
+ <bp:DATA-SOURCE rdf:resource="#dataSource14"/>
+ <bp:DATA-SOURCE rdf:resource="#KB_439584_Individual_47"/>
+ <bp:SHORT-NAME
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">a-D-glu
+ <=> a-D-glu-6-p</bp:SHORT-NAME>
+ <bp:EC-NUMBER rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2.7.1.1</bp:EC-NUMBER>
+ </bp:biochemicalReaction>
+ </bp:CONTROLLED>
+ </bp:catalysis>
+ <bp:unificationXref rdf:ID="unificationXref48">
+ <bp:ID>aMAZEProcess0000000027</bp:ID>
+ <bp:DB>aMAZE</bp:DB>
+ <rdfs:comment>This is the source of this data.</rdfs:comment>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various BioPAX
+ slots should be filled; it is not intended to provide useful (or
+ even accurate) biological information</bp:COMMENT>
+ </bp:unificationXref>
+ <bp:pathway rdf:ID="pathway50">
+ <bp:PATHWAY-COMPONENTS>
+ <bp:pathwayStep rdf:ID="pathwayStep36">
+ <bp:STEP-INTERACTIONS>
+ <bp:catalysis rdf:ID="catalysis43">
+ <bp:COFACTOR>
+ <bp:physicalEntityParticipant rdf:ID="physicalEntityParticipant99">
+ <bp:STOICHIOMETRIC-COEFFICIENT>1.0</bp:STOICHIOMETRIC-COEFFICIENT>
+ <bp:PHYSICAL-ENTITY>
+ <bp:smallMolecule rdf:ID="smallMolecule99">
+ <bp:NAME rdf:datatype="xs:string">Mg2+</bp:NAME>
+ </bp:smallMolecule>
+ </bp:PHYSICAL-ENTITY>
+ </bp:physicalEntityParticipant>
+ </bp:COFACTOR>
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The
+ source of this data did not store catalyses of
+ reactions as separate objects, so there are no
+ unification x-refs pointing to the source of these
+ BioPAX instances.</bp:COMMENT>
+ <bp:DATA-SOURCE rdf:resource="#KB_439584_Individual_47"/>
+ <bp:DATA-SOURCE rdf:resource="#dataSource14"/>
+ <bp:DIRECTION>PHYSIOL-LEFT-TO-RIGHT</bp:DIRECTION>
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how
+ various BioPAX slots should be filled; it is not
+ intended to provide useful (or even accurate)
+ biological information</bp:COMMENT>
+ <bp:CONTROLLED rdf:resource="#biochemicalReaction37"/>
+ <bp:CONTROL-TYPE rdf:datatype="xs:string">ACTIVATION-NONALLOSTERIC</bp:CONTROL-TYPE>
+ <bp:CONTROLLER>
+ <bp:physicalEntityParticipant rdf:ID="physicalEntityParticipant44">
+ <bp:CELLULAR-LOCATION rdf:resource="#openControlledVocabulary15"/>
+ <bp:STOICHIOMETRIC-COEFFICIENT>1.0</bp:STOICHIOMETRIC-COEFFICIENT>
+ <bp:PHYSICAL-ENTITY>
+ <bp:protein rdf:ID="protein45">
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PHI</bp:SYNONYMS>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref47">
+ <bp:ID>Q9KH85</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Swiss-Prot/TrEMBL</bp:DB>
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide
+ an illustration of how
+ various BioPAX slots should
+ be filled; it is not
+ intended to provide useful
+ (or even accurate)
+ biological information</bp:COMMENT>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PGI</bp:SHORT-NAME>
+ <bp:DATA-SOURCE rdf:resource="#dataSource14"/>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GPI</bp:SYNONYMS>
+ <bp:AVAILABILITY
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">see http://www.amaze.ulb.ac.be/</bp:AVAILABILITY>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref46">
+ <bp:ID>aMAZEPolypeptide0000050740</bp:ID>
+ <bp:DB>aMAZE</bp:DB>
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide
+ an illustration of how
+ various BioPAX slots should
+ be filled; it is not
+ intended to provide useful
+ (or even accurate)
+ biological information</bp:COMMENT>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:SYNONYMS
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Phosphohexose isomerase</bp:SYNONYMS>
+ <bp:NAME>phosphoglucose isomerase</bp:NAME>
+ <bp:SEQUENCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">KTFSEAIISGEWKGYTGKAITDVVNIGIGGSDLGPYMVTEALRPYKNHLNMHFVSNVDGTHIAEVLKKVNPETTLFLVASKTFTTQETMTNAHSARDWFLKAAGDEKHVAKHFAALSTNAKAVGEFGIDTANMFEFWDWVGGRYSLWSAIGLSIVLSIGFDNFVELLSGAHAMDKHFSTTPAEKNLPVLLALIGIWYNNFFGAETEAILPYDQYMHRFAAYFQQGNMESNGKYVDRNGNVVDYQTGPIIWGEPGTNGQHAFYQLIHQGTKMVPCDFIAPAITHNPLFDHHQKLLSKFFAQTEALAFGKSREVVEQEYRDQGKDPAT</bp:SEQUENCE>
+ <bp:ORGANISM rdf:resource="#bioSource33"/>
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an
+ illustration of how various BioPAX
+ slots should be filled; it is not
+ intended to provide useful (or even
+ accurate) biological information</bp:COMMENT>
+ <bp:DATA-SOURCE rdf:resource="#KB_439584_Individual_48"/>
+ <bp:SYNONYMS
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glucose-6-phosphate isomerase</bp:SYNONYMS>
+ </bp:protein>
+ </bp:PHYSICAL-ENTITY>
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration
+ of how various BioPAX slots should be
+ filled; it is not intended to provide useful
+ (or even accurate) biological information</bp:COMMENT>
+ </bp:physicalEntityParticipant>
+ </bp:CONTROLLER>
+ <bp:SHORT-NAME
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PGI
+ -> (a-D-glu-6-p <=> b-D-fru-6-p)</bp:SHORT-NAME>
+ <bp:NAME
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">catalysis
+ of (alpha-D-glu-6-p <=> beta-D-fru-6-p)</bp:NAME>
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Note:
+ If filled, the value of the PARTICIPANTS slot should
+ be the union of the CONTROLLED and CONTROLLER slots.</bp:COMMENT>
+ <bp:AVAILABILITY
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">see http://www.amaze.ulb.ac.be/</bp:AVAILABILITY>
+ </bp:catalysis>
+ </bp:STEP-INTERACTIONS>
+ <bp:STEP-INTERACTIONS rdf:resource="#biochemicalReaction37"/>
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various
+ BioPAX slots should be filled; it is not intended to provide
+ useful (or even accurate) biological information</bp:COMMENT>
+ </bp:pathwayStep>
+ </bp:PATHWAY-COMPONENTS>
+ <bp:SYNONYMS
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">glucose degradation</bp:SYNONYMS>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various BioPAX
+ slots should be filled; it is not intended to provide useful (or
+ even accurate) biological information</bp:COMMENT>
+ <bp:XREF rdf:resource="#unificationXref48"/>
+ <bp:XREF>
+ <bp:publicationXref rdf:ID="publicationXref49">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PubMed</bp:DB>
+ <bp:ID>2549346</bp:ID>
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various
+ BioPAX slots should be filled; it is not intended to provide
+ useful (or even accurate) biological information</bp:COMMENT>
+ </bp:publicationXref>
+ </bp:XREF>
+ <bp:DATA-SOURCE rdf:resource="#KB_439584_Individual_47"/>
+ <bp:DATA-SOURCE rdf:resource="#dataSource14"/>
+ <bp:PATHWAY-COMPONENTS>
+ <bp:pathwayStep rdf:ID="pathwayStep4">
+ <bp:STEP-INTERACTIONS rdf:resource="#biochemicalReaction6"/>
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various
+ BioPAX slots should be filled; it is not intended to provide
+ useful (or even accurate) biological information</bp:COMMENT>
+ <bp:STEP-INTERACTIONS rdf:resource="#catalysis5"/>
+ <bp:NEXT-STEP rdf:resource="#pathwayStep36"/>
+ </bp:pathwayStep>
+ </bp:PATHWAY-COMPONENTS>
+ <bp:ORGANISM rdf:resource="#bioSource33"/>
+ <bp:SYNONYMS
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Embden-Meyerhof pathway</bp:SYNONYMS>
+ <bp:NAME>Glycolysis Pathway</bp:NAME>
+ <bp:SHORT-NAME>glycolysis</bp:SHORT-NAME>
+ <bp:AVAILABILITY
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">see http://www.amaze.ulb.ac.be/</bp:AVAILABILITY>
+ </bp:pathway>
+</rdf:RDF>
+<!-- Created with Protege (with OWL Plugin 1.1, Build 135) http://protege.stanford.edu -->
diff --git a/coreplugins/BioPAX/src/test/resources/biopax_with_rdf_error.owl b/coreplugins/BioPAX/src/test/resources/biopax_with_rdf_error.owl
new file mode 100644
index 0000000..38bebba
--- /dev/null
+++ b/coreplugins/BioPAX/src/test/resources/biopax_with_rdf_error.owl
@@ -0,0 +1,725 @@
+<?xml version="1.0" encoding="UTF-8" ?>
+<rdf:RDF xml:base="http://www.biopax.org/examples/simple-demo-pathway"
+ xmlns="http://www.biopax.org/examples/simple-demo-pathway#"
+ xmlns:bp="http://www.biopax.org/release/biopax-level1.owl#"
+ xmlns:owl="http://www.w3.org/2002/07/owl#"
+ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+ xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
+ xmlns:xs="http://www.w3.org/2001/XMLSchema#">
+ <owl:Ontology rdf:about="">
+ <owl:imports rdf:resource="http://www.biopax.org/release/biopax-level1.owl"/>
+ </owl:Ontology>
+ <bp:bioSource rdf:ID="bioSource33">
+ <bp:NAME
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Escherichia coli</bp:NAME>
+ <bp:TAXON-XREF>
+ <bp:unificationXref rdf:ID="unificationXref34">
+ <bp:ID>562</bp:ID>
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various
+ BioPAX slots should be filled; it is not intended to provide
+ useful (or even accurate) biological information</bp:COMMENT>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">taxon</bp:DB>
+ </bp:unificationXref>
+ </bp:TAXON-XREF>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various BioPAX
+ slots should be filled; it is not intended to provide useful (or
+ even accurate) biological information</bp:COMMENT>
+ </bp:bioSource>
+ <bp:unificationXref rdf:ID="unificationXref29">
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">aMAZESpecificCompound0000000638</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">aMAZE</bp:DB>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various BioPAX
+ slots should be filled; it is not intended to provide useful (or
+ even accurate) biological information</bp:COMMENT>
+ </bp:unificationXref>
+ <bp:unificationXref rdf:ID="unificationXref7">
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various BioPAX
+ slots should be filled; it is not intended to provide useful (or
+ even accurate) biological information</bp:COMMENT>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">R01786</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">KEGG</bp:DB>
+ </bp:unificationXref>
+ <bp:chemicalStructure rdf:ID="chemicalStructure12">
+ <bp:STRUCTURE-FORMAT>SMILES</bp:STRUCTURE-FORMAT>
+ <bp:STRUCTURE-DATA>C1(C(O)C(O)C(O)C(O1)CO)(O)</bp:STRUCTURE-DATA>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various BioPAX
+ slots should be filled; it is not intended to provide useful (or
+ even accurate) biological information</bp:COMMENT>
+ </bp:chemicalStructure>
+ <bp:unificationXref rdf:ID="unificationXref41">
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various BioPAX
+ slots should be filled; it is not intended to provide useful (or
+ even accurate) biological information</bp:COMMENT>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">C05345</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">KEGG</bp:DB>
+ </bp:unificationXref>
+ <bp:physicalEntityParticipant rdf:ID="physicalEntityParticipant9">
+ <bp:STOICHIOMETRIC-COEFFICIENT>1.0</bp:STOICHIOMETRIC-COEFFICIENT>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various BioPAX
+ slots should be filled; it is not intended to provide useful (or
+ even accurate) biological information</bp:COMMENT>
+ <bp:PHYSICAL-ENTITY>
+ <bp:smallMolecule rdf:ID="smallMolecule23">
+ <bp:SYNONYMS
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string"><FONT FACE="Symbol">a</FONT>-D-glucose</bp:SYNONYMS>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref11">
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">C00267</bp:ID>
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how
+ various BioPAX slots should be filled; it is not
+ intended to provide useful (or even accurate)
+ biological information</bp:COMMENT>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">KEGG</bp:DB>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">a-D-glu</bp:SHORT-NAME>
+ <bp:DATA-SOURCE>
+ <bp:dataSource rdf:ID="KB_439584_Individual_47">
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">KEGG</bp:NAME>
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how
+ various BioPAX slots should be filled; it is not
+ intended to provide useful (or even accurate)
+ biological information</bp:COMMENT>
+ </bp:dataSource>
+ </bp:DATA-SOURCE>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref13">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">aMAZE</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">aMAZESpecificCompound0000000263</bp:ID>
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how
+ various BioPAX slots should be filled; it is not
+ intended to provide useful (or even accurate)
+ biological information</bp:COMMENT>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various
+ BioPAX slots should be filled; it is not intended to provide
+ useful (or even accurate) biological information</bp:COMMENT>
+ <bp:AVAILABILITY
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">see http://www.amaze.ulb.ac.be/</bp:AVAILABILITY>
+ <bp:DATA-SOURCE>
+ <bp:dataSource rdf:ID="dataSource14">
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">aMAZE</bp:NAME>
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how
+ various BioPAX slots should be filled; it is not
+ intended to provide useful (or even accurate)
+ biological information</bp:COMMENT>
+ </bp:dataSource>
+ </bp:DATA-SOURCE>
+ <bp:STRUCTURE rdf:resource="#chemicalStructure12"/>
+ <bp:CHEMICAL-FORMULA rdf:datatype="http://www.w3.org/2001/XMLSchema#string">C6H12O6</bp:CHEMICAL-FORMULA>
+ <bp:MOLECULAR-WEIGHT>180.16</bp:MOLECULAR-WEIGHT>
+ <bp:NAME>alpha-D-glucose</bp:NAME>
+ </bp:smallMolecule>
+ </bp:PHYSICAL-ENTITY>
+ <bp:CELLULAR-LOCATION>
+ <bp:openControlledVocabulary rdf:ID="openControlledVocabulary15">
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref16">
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how
+ various BioPAX slots should be filled; it is not
+ intended to provide useful (or even accurate)
+ biological information</bp:COMMENT>
+ <bp:DB>Gene Ontology</bp:DB>
+ <bp:ID>GO:0005737</bp:ID>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various
+ BioPAX slots should be filled; it is not intended to provide
+ useful (or even accurate) biological information</bp:COMMENT>
+ <bp:TERM>cytoplasm</bp:TERM>
+ </bp:openControlledVocabulary>
+ </bp:CELLULAR-LOCATION>
+ </bp:physicalEntityParticipant>
+ <bp:unificationXref rdf:ID="unificationXref35">
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P46880</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Swiss-Prot/TrEMBL</bp:DB>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various BioPAX
+ slots should be filled; it is not intended to provide useful (or
+ even accurate) biological information</bp:COMMENT>
+ </bp:unificationXref>
+ <bp:smallMolecule rdf:ID="smallMolecule18">
+ <bp:NAME
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Adenosine 5'-diphosphate</bp:NAME>
+ <bp:SYNONYMS
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">adenosine diphosphate</bp:SYNONYMS>
+ <bp:DATA-SOURCE rdf:resource="#KB_439584_Individual_47"/>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various BioPAX
+ slots should be filled; it is not intended to provide useful (or
+ even accurate) biological information</bp:COMMENT>
+ <bp:DATA-SOURCE rdf:resource="#dataSource14"/>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref20">
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various
+ BioPAX slots should be filled; it is not intended to provide
+ useful (or even accurate) biological information</bp:COMMENT>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">aMAZE</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">aMAZESpecificCompound0000000008</bp:ID>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:MOLECULAR-WEIGHT>427.2</bp:MOLECULAR-WEIGHT>
+ <bp:SHORT-NAME>ADP</bp:SHORT-NAME>
+ <bp:STRUCTURE>
+ <bp:chemicalStructure rdf:ID="chemicalStructure21">
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various
+ BioPAX slots should be filled; it is not intended to provide
+ useful (or even accurate) biological information</bp:COMMENT>
+ <bp:STRUCTURE-DATA>c12(n(cnc(c(N)ncn1)2)[CH]3(O[CH]([CH](O)[CH](O)3)COP(=O)(O)OP(O)(=O)O))</bp:STRUCTURE-DATA>
+ <bp:STRUCTURE-FORMAT>SMILES</bp:STRUCTURE-FORMAT>
+ </bp:chemicalStructure>
+ </bp:STRUCTURE>
+ <bp:CHEMICAL-FORMULA rdf:datatype="http://www.w3.org/2001/XMLSchema#string">C10H15N5O10P2</bp:CHEMICAL-FORMULA>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref19">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">KEGG</bp:DB>
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various
+ BioPAX slots should be filled; it is not intended to provide
+ useful (or even accurate) biological information</bp:COMMENT>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">C00008</bp:ID>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:AVAILABILITY
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">see http://www.amaze.ulb.ac.be/</bp:AVAILABILITY>
+ </bp:smallMolecule>
+ <bp:unificationXref rdf:ID="unificationXref42">
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various BioPAX
+ slots should be filled; it is not intended to provide useful (or
+ even accurate) biological information</bp:COMMENT>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">aMAZESpecificCompound0000004507</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">aMAZE</bp:DB>
+ </bp:unificationXref>
+ <bp:biochemicalReaction rdf:ID="biochemicalReaction37">
+ <bp:DATA-SOURCE rdf:resource="#dataSource14"/>
+ <bp:LEFT>
+ <bp:physicalEntityParticipant rdf:ID="physicalEntityParticipant26">
+ <bp:STOICHIOMETRIC-COEFFICIENT>1.0</bp:STOICHIOMETRIC-COEFFICIENT>
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various
+ BioPAX slots should be filled; it is not intended to provide
+ useful (or even accurate) biological information</bp:COMMENT>
+ <bp:PHYSICAL-ENTITY>
+ <bp:smallMolecule rdf:ID="smallMolecule27">
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">a-D-glu-6-p</bp:SHORT-NAME>
+ <bp:CHEMICAL-FORMULA rdf:datatype="http://www.w3.org/2001/XMLSchema#string">C6H13O9P</bp:CHEMICAL-FORMULA>
+ <bp:SYNONYMS
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string"><FONT FACE="Symbol">a</FONT>-D-glucose-6-phoshate</bp:SYNONYMS>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref30">
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">C00668</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">KEGG</bp:DB>
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration
+ of how various BioPAX slots should be
+ filled; it is not intended to provide useful
+ (or even accurate) biological information</bp:COMMENT>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:XREF rdf:resource="#unificationXref29"/>
+ <bp:MOLECULAR-WEIGHT>260.14</bp:MOLECULAR-WEIGHT>
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how
+ various BioPAX slots should be filled; it is not
+ intended to provide useful (or even accurate)
+ biological information</bp:COMMENT>
+ <bp:AVAILABILITY
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">see http://www.amaze.ulb.ac.be/</bp:AVAILABILITY>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">glucose-6-P</bp:SYNONYMS>
+ <bp:DATA-SOURCE rdf:resource="#dataSource14"/>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">alpha-D-glucose-6-p</bp:SYNONYMS>
+ <bp:STRUCTURE>
+ <bp:chemicalStructure rdf:ID="chemicalStructure28">
+ <bp:STRUCTURE-FORMAT>SMILES</bp:STRUCTURE-FORMAT>
+ <bp:STRUCTURE-DATA>C(OP(=O)(O)O)[CH]1([CH](O)[CH](O)[CH](O)[CH](O)O1)</bp:STRUCTURE-DATA>
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration
+ of how various BioPAX slots should be
+ filled; it is not intended to provide useful
+ (or even accurate) biological information</bp:COMMENT>
+ </bp:chemicalStructure>
+ </bp:STRUCTURE>
+ <bp:NAME>alpha-D-glucose 6-phosphate</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">alpha-D-glucose-6-phosphate</bp:SYNONYMS>
+ <bp:SYNONYMS
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string"> D-glucose-6-P</bp:SYNONYMS>
+ <bp:DATA-SOURCE rdf:resource="#KB_439584_Individual_47"/>
+ </bp:smallMolecule>
+ </bp:PHYSICAL-ENTITY>
+ <bp:CELLULAR-LOCATION rdf:resource="#openControlledVocabulary15"/>
+ </bp:physicalEntityParticipant>
+ </bp:LEFT>
+ <bp:DELTA-G rdf:datatype="http://www.w3.org/2001/XMLSchema#double">0.4</bp:DELTA-G>
+ <bp:SYNONYMS
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">alpha-D-Glucose
+ 6-phosphate <=> beta-D-Fructose 6-phosphate </bp:SYNONYMS>
+ <bp:RIGHT>
+ <bp:physicalEntityParticipant rdf:ID="physicalEntityParticipant38">
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various
+ BioPAX slots should be filled; it is not intended to provide
+ useful (or even accurate) biological information</bp:COMMENT>
+ <bp:CELLULAR-LOCATION rdf:resource="#openControlledVocabulary15"/>
+ <bp:PHYSICAL-ENTITY>
+ <bp:smallMolecule rdf:ID="smallMolecule39">
+ <bp:CHEMICAL-FORMULA rdf:datatype="http://www.w3.org/2001/XMLSchema#string">C6H13O9P</bp:CHEMICAL-FORMULA>
+ <bp:DATA-SOURCE rdf:resource="#dataSource14"/>
+ <bp:DATA-SOURCE rdf:resource="#KB_439584_Individual_47"/>
+ <bp:SYNONYMS
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string"><FONT FACE="Symbol">b</FONT>-D-fructose-6-phosphate</bp:SYNONYMS>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">b-D-fru-6-p</bp:SHORT-NAME>
+ <bp:XREF rdf:resource="#unificationXref42"/>
+ <bp:STRUCTURE>
+ <bp:chemicalStructure rdf:ID="chemicalStructure40">
+ <bp:STRUCTURE-DATA>C(OP(O)(O)=O)[CH]1([CH](O)[CH](O)C(O)(O1)CO)</bp:STRUCTURE-DATA>
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration
+ of how various BioPAX slots should be
+ filled; it is not intended to provide useful
+ (or even accurate) biological information</bp:COMMENT>
+ <bp:STRUCTURE-FORMAT>SMILES</bp:STRUCTURE-FORMAT>
+ </bp:chemicalStructure>
+ </bp:STRUCTURE>
+ <bp:MOLECULAR-WEIGHT>260.14</bp:MOLECULAR-WEIGHT>
+ <bp:NAME
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">beta-D-fructose 6-phosphate</bp:NAME>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">beta-D-fructose-6-phosphate</bp:SYNONYMS>
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how
+ various BioPAX slots should be filled; it is not
+ intended to provide useful (or even accurate)
+ biological information</bp:COMMENT>
+ <bp:AVAILABILITY
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">see http://www.amaze.ulb.ac.be/</bp:AVAILABILITY>
+ <bp:XREF rdf:resource="#unificationXref41"/>
+ </bp:smallMolecule>
+ </bp:PHYSICAL-ENTITY>
+ <bp:STOICHIOMETRIC-COEFFICIENT>1.0</bp:STOICHIOMETRIC-COEFFICIENT>
+ </bp:physicalEntityParticipant>
+ </bp:RIGHT>
+ <bp:PARTICIPANTS rdf:resource="#physicalEntityParticipant38"/>
+ <bp:SHORT-NAME
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">a-D-glu-6-p
+ <=> b-D-fru-6-p</bp:SHORT-NAME>
+ <bp:DATA-SOURCE rdf:resource="#KB_439584_Individual_47"/>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Note:
+ If filled, the value of the PARTICIPANTS slot should be the union of
+ the LEFT and RIGHT slots.</bp:COMMENT>
+ <bp:AVAILABILITY
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">see http://www.amaze.ulb.ac.be/</bp:AVAILABILITY>
+ <bp:EC-NUMBER>5.3.1.9</bp:EC-NUMBER>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref1">
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">R02740</bp:ID>
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various
+ BioPAX slots should be filled; it is not intended to provide
+ useful (or even accurate) biological information</bp:COMMENT>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">KEGG</bp:DB>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:NAME
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">alpha-D-glu-6-p
+ <=> beta-D-fru-6-p</bp:NAME>
+ <bp:SYNONYMS
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">alpha-D-Glucose
+ 6-phosphate ketol-isomerase</bp:SYNONYMS>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref3">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">aMAZE</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">aMAZEReaction0000002504</bp:ID>
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various
+ BioPAX slots should be filled; it is not intended to provide
+ useful (or even accurate) biological information</bp:COMMENT>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:PARTICIPANTS rdf:resource="#physicalEntityParticipant26"/>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various BioPAX
+ slots should be filled; it is not intended to provide useful (or
+ even accurate) biological information</bp:COMMENT>
+ </bp:biochemicalReaction>
+ <bp:physicalEntityParticipant rdf:ID="physicalEntityParticipant17">
+ <bp:CELLULAR-LOCATION rdf:resource="#openControlledVocabulary15"/>
+ <bp:STOICHIOMETRIC-COEFFICIENT>1.0</bp:STOICHIOMETRIC-COEFFICIENT>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various BioPAX
+ slots should be filled; it is not intended to provide useful (or
+ even accurate) biological information</bp:COMMENT>
+ <bp:PHYSICAL-ENTITY rdf:resource="#smallMolecule18"/>
+ </bp:physicalEntityParticipant>
+ <bp:smallMolecule rdf:ID="smallMolecule23">
+ <bp:DATA-SOURCE rdf:resource="#dataSource14"/>
+ <bp:AVAILABILITY
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">see http://www.amaze.ulb.ac.be/</bp:AVAILABILITY>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref24">
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various
+ BioPAX slots should be filled; it is not intended to provide
+ useful (or even accurate) biological information</bp:COMMENT>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">aMAZESpecificCompound0000000002</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">aMAZE</bp:DB>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:STRUCTURE>
+ <bp:chemicalStructure rdf:ID="chemicalStructure25">
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various
+ BioPAX slots should be filled; it is not intended to provide
+ useful (or even accurate) biological information</bp:COMMENT>
+ <bp:STRUCTURE-DATA>[CH]3(n1(c2(c(nc1)c(N)ncn2)))(O[CH]([CH](O)[CH](O)3)COP(=O)(O)OP(O)(=O)OP(O)(=O)O)</bp:STRUCTURE-DATA>
+ <bp:STRUCTURE-FORMAT>SMILES</bp:STRUCTURE-FORMAT>
+ </bp:chemicalStructure>
+ </bp:STRUCTURE>
+ <bp:MOLECULAR-WEIGHT>507.18</bp:MOLECULAR-WEIGHT>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various BioPAX
+ slots should be filled; it is not intended to provide useful (or
+ even accurate) biological information</bp:COMMENT>
+ <bp:CHEMICAL-FORMULA rdf:datatype="http://www.w3.org/2001/XMLSchema#string">C10H16N5O13P3</bp:CHEMICAL-FORMULA>
+ <bp:DATA-SOURCE rdf:resource="#KB_439584_Individual_47"/>
+ <bp:SYNONYMS
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">adenosine triphosphate</bp:SYNONYMS>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref2">
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various
+ BioPAX slots should be filled; it is not intended to provide
+ useful (or even accurate) biological information</bp:COMMENT>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">KEGG</bp:DB>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">C00002</bp:ID>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:SHORT-NAME>ATP</bp:SHORT-NAME>
+ <bp:NAME
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Adenosine 5'-triphosphate</bp:NAME>
+ </bp:smallMolecule>
+ <bp:unificationXref rdf:ID="unificationXref8">
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various BioPAX
+ slots should be filled; it is not intended to provide useful (or
+ even accurate) biological information</bp:COMMENT>
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">aMAZEReaction0000001619</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">aMAZE</bp:DB>
+ </bp:unificationXref>
+ <bp:catalysis rdf:ID="catalysis5">
+ <bp:DATA-SOURCE rdf:resource="#dataSource14"/>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The
+ source of this data did not store catalyses of reactions as separate
+ objects, so there are no unification x-refs pointing to the source
+ of these BioPAX instances.</bp:COMMENT>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various BioPAX
+ slots should be filled; it is not intended to provide useful (or
+ even accurate) biological information</bp:COMMENT>
+ <bp:DIRECTION rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PHYSIOL-LEFT-TO-RIGHT</bp:DIRECTION>
+ <bp:DATA-SOURCE rdf:resource="#KB_439584_Individual_47"/>
+ <bp:AVAILABILITY
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">see http://www.amaze.ulb.ac.be/</bp:AVAILABILITY>
+ <bp:CONTROLLER>
+ <bp:physicalEntityParticipant rdf:ID="physicalEntityParticipant31">
+ <bp:PHYSICAL-ENTITY>
+ <bp:protein rdf:ID="protein32">
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GLK</bp:SHORT-NAME>
+ <bp:DATA-SOURCE>
+ <bp:dataSource rdf:ID="KB_439584_Individual_48">
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Swiss-Prot/TrEMBL</bp:NAME>
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration
+ of how various BioPAX slots should be
+ filled; it is not intended to provide useful
+ (or even accurate) biological information</bp:COMMENT>
+ </bp:dataSource>
+ </bp:DATA-SOURCE>
+ <bp:SEQUENCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">MTKYALVGDVGGTNARLALCDIASGEISQAKTYSGLDYPSLEAVIRVYLEEHKVEVKDGCIAIACPITGDWVAMTNHTWAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLKKEHLIQFGGAEPVEGKPIAVYGAGTGLGVAHLVHVDKRWVSLPGEGGHVDFAPNSEEEAIILEILRAEIGHVSAERVLSGPGLVNLYRAIVKADNRLPENLKPKDITERALADSCTDCRRALSLFCVIMGRFGGNLALNLGTFGGVFIAGGIVPRFLEFFKASGFRAAFEDKGRFKEYVHDIPVYLIVHDNPGLLGSGAHLRQTLGHIL</bp:SEQUENCE>
+ <bp:AVAILABILITY
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">see http://www.amaze.ulb.ac.be/</bp:AVAILABILITY>
+ <bp:XREF rdf:resource="#unificationXref35"/>
+ <bp:DATA-SOURCE rdf:resource="#dataSource14"/>
+ <bp:ORGANISM rdf:resource="#bioSource33"/>
+ <bp:SYNONYMS
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glucose kinase</bp:SYNONYMS>
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how
+ various BioPAX slots should be filled; it is not
+ intended to provide useful (or even accurate)
+ biological information</bp:COMMENT>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GLK_ECOLI</bp:SYNONYMS>
+ <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">glucokinase</bp:NAME>
+ </bp:protein>
+ </bp:PHYSICAL-ENTITY>
+ <bp:CELLULAR-LOCATION rdf:resource="#openControlledVocabulary15"/>
+ <bp:STOICHIOMETRIC-COEFFICIENT rdf:datatype="http://www.w3.org/2001/XMLSchema#double">1.0</bp:STOICHIOMETRIC-COEFFICIENT>
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various
+ BioPAX slots should be filled; it is not intended to provide
+ useful (or even accurate) biological information</bp:COMMENT>
+ </bp:physicalEntityParticipant>
+ </bp:CONTROLLER>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Note:
+ The PARTICIPANTS slot may be left empty if both the CONTROLLED and
+ CONTROLLER slots are filled.</bp:COMMENT>
+ <bp:SHORT-NAME
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GLK ->
+ (a-D-glu <=> a-D-glu-6-p)</bp:SHORT-NAME>
+ <bp:NAME
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">catalysis of
+ (alpha-D-glu <=> alpha-D-glu-6-p)</bp:NAME>
+ <bp:CONTROLLED>
+ <bp:biochemicalReaction rdf:ID="biochemicalReaction6">
+ <bp:XREF rdf:resource="#unificationXref8"/>
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various
+ BioPAX slots should be filled; it is not intended to provide
+ useful (or even accurate) biological information</bp:COMMENT>
+ <bp:SYNONYMS
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ATP:D-glucose 6-phosphotransferase</bp:SYNONYMS>
+ <bp:NAME
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">alpha-D-glu
+ + ATP <=> alpha-D-glu-6-p + ADP</bp:NAME>
+ <bp:LEFT rdf:resource="#physicalEntityParticipant9"/>
+ <bp:EC-NUMBER rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2.7.1.2</bp:EC-NUMBER>
+ <bp:LEFT>
+ <bp:physicalEntityParticipant rdf:ID="physicalEntityParticipant22">
+ <bp:STOICHIOMETRIC-COEFFICIENT>1.0</bp:STOICHIOMETRIC-COEFFICIENT>
+ <bp:CELLULAR-LOCATION rdf:resource="#openControlledVocabulary15"/>
+ <bp:PHYSICAL-ENTITY rdf:resource="#smallMolecule23"/>
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how
+ various BioPAX slots should be filled; it is not
+ intended to provide useful (or even accurate)
+ biological information</bp:COMMENT>
+ </bp:physicalEntityParticipant>
+ </bp:LEFT>
+ <bp:RIGHT rdf:resource="#physicalEntityParticipant17"/>
+ <bp:AVAILABILITY
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">see http://www.amaze.ulb.ac.be/</bp:AVAILABILITY>
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Note:
+ The PARTICIPANTS slot may be left empty if both the LEFT and
+ RIGHT slots are filled.</bp:COMMENT>
+ <bp:SYNONYMS
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">glucose
+ ATP phosphotransferase</bp:SYNONYMS>
+ <bp:XREF rdf:resource="#unificationXref7"/>
+ <bp:RIGHT rdf:resource="#physicalEntityParticipant26"/>
+ <bp:DATA-SOURCE rdf:resource="#dataSource14"/>
+ <bp:DATA-SOURCE rdf:resource="#KB_439584_Individual_47"/>
+ <bp:SHORT-NAME
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">a-D-glu
+ <=> a-D-glu-6-p</bp:SHORT-NAME>
+ <bp:EC-NUMBER rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2.7.1.1</bp:EC-NUMBER>
+ </bp:biochemicalReaction>
+ </bp:CONTROLLED>
+ </bp:catalysis>
+ <bp:unificationXref rdf:ID="unificationXref48">
+ <bp:ID>aMAZEProcess0000000027</bp:ID>
+ <bp:DB>aMAZE</bp:DB>
+ <rdfs:comment>This is the source of this data.</rdfs:comment>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various BioPAX
+ slots should be filled; it is not intended to provide useful (or
+ even accurate) biological information</bp:COMMENT>
+ </bp:unificationXref>
+ <bp:pathway rdf:ID="pathway50">
+ <bp:PATHWAY-COMPONENTS>
+ <bp:pathwayStep rdf:ID="pathwayStep36">
+ <bp:STEP-INTERACTIONS>
+ <bp:catalysis rdf:ID="catalysis43">
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The
+ source of this data did not store catalyses of
+ reactions as separate objects, so there are no
+ unification x-refs pointing to the source of these
+ BioPAX instances.</bp:COMMENT>
+ <bp:DATA-SOURCE rdf:resource="#KB_439584_Individual_47"/>
+ <bp:DATA-SOURCE rdf:resource="#dataSource14"/>
+ <bp:DIRECTION>PHYSIOL-LEFT-TO-RIGHT</bp:DIRECTION>
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how
+ various BioPAX slots should be filled; it is not
+ intended to provide useful (or even accurate)
+ biological information</bp:COMMENT>
+ <bp:CONTROLLED rdf:resource="#biochemicalReaction37"/>
+ <bp:CONTROLLER>
+ <bp:physicalEntityParticipant rdf:ID="physicalEntityParticipant44">
+ <bp:CELLULAR-LOCATION rdf:resource="#openControlledVocabulary15"/>
+ <bp:STOICHIOMETRIC-COEFFICIENT>1.0</bp:STOICHIOMETRIC-COEFFICIENT>
+ <bp:PHYSICAL-ENTITY>
+ <bp:protein rdf:ID="protein45">
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PHI</bp:SYNONYMS>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref47">
+ <bp:ID>Q9KH85</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Swiss-Prot/TrEMBL</bp:DB>
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide
+ an illustration of how
+ various BioPAX slots should
+ be filled; it is not
+ intended to provide useful
+ (or even accurate)
+ biological information</bp:COMMENT>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PGI</bp:SHORT-NAME>
+ <bp:DATA-SOURCE rdf:resource="#dataSource14"/>
+ <bp:SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GPI</bp:SYNONYMS>
+ <bp:AVAILABILITY
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">see http://www.amaze.ulb.ac.be/</bp:AVAILABILITY>
+ <bp:XREF>
+ <bp:unificationXref rdf:ID="unificationXref46">
+ <bp:ID>aMAZEPolypeptide0000050740</bp:ID>
+ <bp:DB>aMAZE</bp:DB>
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide
+ an illustration of how
+ various BioPAX slots should
+ be filled; it is not
+ intended to provide useful
+ (or even accurate)
+ biological information</bp:COMMENT>
+ </bp:unificationXref>
+ </bp:XREF>
+ <bp:SYNONYMS
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Phosphohexose isomerase</bp:SYNONYMS>
+ <bp:NAME>phosphoglucose isomerase</bp:NAME>
+ <bp:SEQUENCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">KTFSEAIISGEWKGYTGKAITDVVNIGIGGSDLGPYMVTEALRPYKNHLNMHFVSNVDGTHIAEVLKKVNPETTLFLVASKTFTTQETMTNAHSARDWFLKAAGDEKHVAKHFAALSTNAKAVGEFGIDTANMFEFWDWVGGRYSLWSAIGLSIVLSIGFDNFVELLSGAHAMDKHFSTTPAEKNLPVLLALIGIWYNNFFGAETEAILPYDQYMHRFAAYFQQGNMESNGKYVDRNGNVVDYQTGPIIWGEPGTNGQHAFYQLIHQGTKMVPCDFIAPAITHNPLFDHHQKLLSKFFAQTEALAFGKSREVVEQEYRDQGKDPAT</bp:SEQUENCE>
+ <bp:ORGANISM rdf:resource="#bioSource33"/>
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an
+ illustration of how various BioPAX
+ slots should be filled; it is not
+ intended to provide useful (or even
+ accurate) biological information</bp:COMMENT>
+ <bp:DATA-SOURCE rdf:resource="#KB_439584_Individual_48"/>
+ <bp:SYNONYMS
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glucose-6-phosphate isomerase</bp:SYNONYMS>
+ </bp:protein>
+ </bp:PHYSICAL-ENTITY>
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration
+ of how various BioPAX slots should be
+ filled; it is not intended to provide useful
+ (or even accurate) biological information</bp:COMMENT>
+ </bp:physicalEntityParticipant>
+ </bp:CONTROLLER>
+ <bp:PARTICIPANTS rdf:resource="#biochemicalReaction37"/>
+ <bp:SHORT-NAME
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PGI
+ -> (a-D-glu-6-p <=> b-D-fru-6-p)</bp:SHORT-NAME>
+ <bp:NAME
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">catalysis
+ of (alpha-D-glu-6-p <=> beta-D-fru-6-p)</bp:NAME>
+ <bp:PARTICIPANTS rdf:resource="#physicalEntityParticipant44"/>
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Note:
+ If filled, the value of the PARTICIPANTS slot should
+ be the union of the CONTROLLED and CONTROLLER slots.</bp:COMMENT>
+ <bp:AVAILABILITY
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">see http://www.amaze.ulb.ac.be/</bp:AVAILABILITY>
+ </bp:catalysis>
+ </bp:STEP-INTERACTIONS>
+ <bp:STEP-INTERACTIONS rdf:resource="#biochemicalReaction37"/>
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various
+ BioPAX slots should be filled; it is not intended to provide
+ useful (or even accurate) biological information</bp:COMMENT>
+ </bp:pathwayStep>
+ </bp:PATHWAY-COMPONENTS>
+ <bp:SYNONYMS
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">glucose degradation</bp:SYNONYMS>
+ <bp:COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various BioPAX
+ slots should be filled; it is not intended to provide useful (or
+ even accurate) biological information</bp:COMMENT>
+ <bp:XREF rdf:resource="#unificationXref48"/>
+ <bp:XREF>
+ <bp:publicationXref rdf:ID="publicationXref49">
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PubMed</bp:DB>
+ <bp:ID>2549346</bp:ID>
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various
+ BioPAX slots should be filled; it is not intended to provide
+ useful (or even accurate) biological information</bp:COMMENT>
+ </bp:publicationXref>
+ </bp:XREF>
+ <bp:DATA-SOURCE rdf:resource="#KB_439584_Individual_47"/>
+ <bp:DATA-SOURCE rdf:resource="#dataSource14"/>
+ <bp:PATHWAY-COMPONENTS>
+ <bp:pathwayStep rdf:ID="pathwayStep4">
+ <bp:STEP-INTERACTIONS rdf:resource="#biochemicalReaction6"/>
+ <bp:COMMENT
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This
+ example is meant to provide an illustration of how various
+ BioPAX slots should be filled; it is not intended to provide
+ useful (or even accurate) biological information</bp:COMMENT>
+ <bp:STEP-INTERACTIONS rdf:resource="#catalysis5"/>
+ <bp:NEXT-STEP rdf:resource="#pathwayStep36"/>
+ </bp:pathwayStep>
+ </bp:PATHWAY-COMPONENTS>
+ <bp:ORGANISM rdf:resource="#bioSource33"/>
+ <bp:SYNONYMS
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Embden-Meyerhof pathway</bp:SYNONYMS>
+ <bp:NAME>Glycolysis Pathway</bp:NAME>
+ <bp:SHORT-NAME>glycolysis</bp:SHORT-NAME>
+ <bp:AVAILABILITY
+ rdf:datatype="http://www.w3.org/2001/XMLSchema#string">see http://www.amaze.ulb.ac.be/</bp:AVAILABILITY>
+ </bp:pathway>
+</rdf:RDF>
+<!-- Created with Protege (with OWL Plugin 1.1, Build 135) http://protege.stanford.edu -->
diff --git a/coreplugins/BioPAX/src/test/resources/psi_sample1.xml b/coreplugins/BioPAX/src/test/resources/psi_sample1.xml
new file mode 100644
index 0000000..f158c1b
--- /dev/null
+++ b/coreplugins/BioPAX/src/test/resources/psi_sample1.xml
@@ -0,0 +1,358 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<entrySet level="1" version="1" xmlns="net:sf:psidev:mi"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="net:sf:psidev:mi /Users/cerami/dev/sander/cytoscape/xml/MIF.xsd">
+ <entry>
+ <interactorList>
+ <proteinInteractor id="YHR119W">
+ <names>
+ <shortLabel>YHR119W</shortLabel>
+ <fullName>Gene has a SET or TROMO domain at its carboxyterminus like the
+ trithorax gene family from human and Drosophila with postulated function in
+ chromatin-mediated gene regulation.</fullName>
+ </names>
+ <xref>
+ <primaryRef db="Entrez GI" id="529135"/>
+ <secondaryRef db="RefSeq GI" id="6321911"/>
+ <secondaryRef db="Entrez Protein_ID" id="AAB68867.1"/>
+ <secondaryRef db="CandidaDB" id="CA2985"/>
+ <secondaryRef db="InterPro" id="IPR001214"/>
+ <secondaryRef db="RefSeq Version" id="NP_011987.1"/>
+ <secondaryRef db="SwissProt" id="P38827"/>
+ <secondaryRef db="PIR" id="S48961"/>
+ <secondaryRef db="GenBank DNA Version" id="U00059.1"/>
+ <secondaryRef db="MIPS" id="YHR119W"/>
+ </xref>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>baker's yeast</shortLabel>
+ <fullName>Saccharomyces cerevisiae</fullName>
+ </names>
+ </organism>
+ <sequence>MNTYAQESKLRLKTKIGADGRCVIEDNFFTPPFKLMAPFYPKDDLAEIMLLAVSPGMMRGDAQDVQLNIGPNCKLRITSQSFEKIHNTEDGFASRDMHIVVGENAFLDFAPFPLIPFENAHFKGNTTISLRSSSQLLYSEIIVAGRVARNELFKFNRLHTKISILQDEKPIYYDNTILDPKTTDLNNMCMFDGYTHYLNLVLVNCPIELSGVRECIEESEGVDGAVSETASSHLCVKALAKGSEPLLHLREKIARLVTQTTTQKV</sequence>
+ </proteinInteractor>
+ <proteinInteractor id="YEL061C">
+ <names>
+ <shortLabel>YEL061C</shortLabel>
+ <fullName>Kinesin-related protein involved in establishment and maintenance of
+ mitotic spindle</fullName>
+ </names>
+ <xref>
+ <primaryRef db="Entrez GI" id="603257"/>
+ <secondaryRef db="RefSeq GI" id="6320774"/>
+ <secondaryRef db="Entrez Protein_ID" id="AAB65026.1"/>
+ <secondaryRef db="PIR" id="B42641"/>
+ <secondaryRef db="CandidaDB" id="CA4985"/>
+ <secondaryRef db="InterPro" id="IPR001752"/>
+ <secondaryRef db="GenBank DNA Version" id="M90522.1"/>
+ <secondaryRef db="RefSeq Version" id="NP_010853.1"/>
+ <secondaryRef db="SwissProt" id="P27895"/>
+ <secondaryRef db="GenBank DNA Version" id="U18795.1"/>
+ <secondaryRef db="MIPS" id="YEL061C"/>
+ <secondaryRef db="GenBank DNA Version" id="Z11859.1"/>
+ </xref>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>baker's yeast</shortLabel>
+ <fullName>Saccharomyces cerevisiae</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="YBR200W">
+ <names>
+ <shortLabel>YBR200W</shortLabel>
+ <fullName>SH3-domain protein that binds Cdc24p, Ste5p and Ste20p, and the
+ Rsr1p/Bud2p/Bup5p GTPase</fullName>
+ </names>
+ <xref>
+ <primaryRef db="Entrez GI" id="536573"/>
+ <secondaryRef db="RefSeq GI" id="6319677"/>
+ <secondaryRef db="CandidaDB" id="CA0514"/>
+ <secondaryRef db="Entrez Protein_ID" id="CAA85162.1"/>
+ <secondaryRef db="InterPro" id="IPR001452"/>
+ <secondaryRef db="InterPro" id="IPR001683"/>
+ <secondaryRef db="RefSeq Version" id="NP_009759.1"/>
+ <secondaryRef db="SwissProt" id="P29366"/>
+ <secondaryRef db="PIR" id="S23400"/>
+ <secondaryRef db="GenBank DNA Version" id="X63826.1"/>
+ <secondaryRef db="MIPS" id="YBR200W"/>
+ <secondaryRef db="GenBank DNA Version" id="Z21487.1"/>
+ <secondaryRef db="GenBank DNA Version" id="Z36069.1"/>
+ </xref>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>baker's yeast</shortLabel>
+ <fullName>Saccharomyces cerevisiae</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="YCR038C">
+ <names>
+ <shortLabel>YCR038C</shortLabel>
+ <fullName>GTP/GDP exchange factor for Rsr1 protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="RefSeq GI" id="10383799"/>
+ <secondaryRef db="Entrez GI" id="1907180"/>
+ <secondaryRef db="PIR" id="BWBYD5"/>
+ <secondaryRef db="CandidaDB" id="CA0382"/>
+ <secondaryRef db="Entrez Protein_ID" id="CAA42305.1"/>
+ <secondaryRef db="InterPro" id="IPR001895"/>
+ <secondaryRef db="GenBank DNA Version" id="M63552.1"/>
+ <secondaryRef db="GenBank DNA Version" id="M68938.1"/>
+ <secondaryRef db="RefSeq Version" id="NP_009967.2"/>
+ <secondaryRef db="SwissProt" id="P25300"/>
+ <secondaryRef db="SwissProt/TrEMBL" id="Q06729"/>
+ <secondaryRef db="GenBank DNA Version" id="X56909.1"/>
+ <secondaryRef db="GenBank DNA Version" id="X59720.2"/>
+ <secondaryRef db="GenBank DNA Version" id="X63853.1"/>
+ <secondaryRef db="MIPS" id="YCR038C"/>
+ </xref>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>baker's yeast</shortLabel>
+ <fullName>Saccharomyces cerevisiae</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="YAL036C">
+ <names>
+ <shortLabel>YAL036C</shortLabel>
+ <fullName>Function Unknown Now; similar to Xenopus GTP-binding protein DRG</fullName>
+ </names>
+ <xref>
+ <primaryRef db="Entrez GI" id="595548"/>
+ <secondaryRef db="RefSeq GI" id="6319281"/>
+ <secondaryRef db="Entrez Protein_ID" id="AAC04995.1"/>
+ <secondaryRef db="GenBank DNA Version" id="AQ876073.1"/>
+ <secondaryRef db="CandidaDB" id="CA3893"/>
+ <secondaryRef db="InterPro" id="IPR000765"/>
+ <secondaryRef db="RefSeq Version" id="NP_009364.1"/>
+ <secondaryRef db="SwissProt" id="P39729"/>
+ <secondaryRef db="PIR" id="S51983"/>
+ <secondaryRef db="GenBank DNA Version" id="U12980.1"/>
+ <secondaryRef db="MIPS" id="YAL036C"/>
+ </xref>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>baker's yeast</shortLabel>
+ <fullName>Saccharomyces cerevisiae</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="YDL065C">
+ <names>
+ <shortLabel>YDL065C</shortLabel>
+ <fullName>40 kDa farnesylated protein associated with peroxisomes</fullName>
+ </names>
+ <xref>
+ <primaryRef db="Entrez GI" id="1431072"/>
+ <secondaryRef db="RefSeq GI" id="6320138"/>
+ <secondaryRef db="CandidaDB" id="CA5105"/>
+ <secondaryRef db="Entrez Protein_ID" id="CAA98630.1"/>
+ <secondaryRef db="RefSeq Version" id="NP_010218.1"/>
+ <secondaryRef db="SwissProt" id="Q07418"/>
+ <secondaryRef db="PIR" id="S67600"/>
+ <secondaryRef db="MIPS" id="YDL065C"/>
+ <secondaryRef db="GenBank DNA Version" id="Z74113.1"/>
+ </xref>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>baker's yeast</shortLabel>
+ <fullName>Saccharomyces cerevisiae</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="YDR532C">
+ <names>
+ <shortLabel>YDR532C</shortLabel>
+ <fullName>Killer toxin REsistant</fullName>
+ </names>
+ <xref>
+ <primaryRef db="RefSeq GI" id="6320741"/>
+ <secondaryRef db="Entrez GI" id="927799"/>
+ <secondaryRef db="Entrez Protein_ID" id="AAB64971.1"/>
+ <secondaryRef db="CandidaDB" id="CA0383"/>
+ <secondaryRef db="RefSeq Version" id="NP_010821.1"/>
+ <secondaryRef db="SwissProt" id="Q04431"/>
+ <secondaryRef db="PIR" id="S69587"/>
+ <secondaryRef db="GenBank DNA Version" id="U33057.1"/>
+ <secondaryRef db="MIPS" id="YDR532C"/>
+ </xref>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>baker's yeast</shortLabel>
+ <fullName>Saccharomyces cerevisiae</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ </interactorList>
+ <interactionList>
+ <interaction>
+ <experimentList>
+ <experimentDescription id="no_id">
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="11283351"/>
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>classical two hybrid</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="PSI-MI" id="MI:0018"/>
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="YCR038C"/>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="YAL036C"/>
+ </proteinParticipant>
+ </participantList>
+ </interaction>
+ <interaction>
+ <experimentList>
+ <experimentDescription id="no_id">
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="11283351"/>
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>classical two hybrid</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="PSI-MI" id="MI:0018"/>
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="YCR038C"/>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="YDL065C"/>
+ </proteinParticipant>
+ </participantList>
+ </interaction>
+ <interaction>
+ <experimentList>
+ <experimentDescription id="no_id">
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="11283351"/>
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>classical two hybrid</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="PSI-MI" id="MI:0018"/>
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="YCR038C"/>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="YDR532C"/>
+ </proteinParticipant>
+ </participantList>
+ <xref>
+ <primaryRef db="DIP" id="61E"/>
+ <secondaryRef db="CPATH" id="12345"/>
+ </xref>
+ </interaction>
+ <interaction>
+ <experimentList>
+ <experimentDescription id="no_id">
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="11283351"/>
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>classical two hybrid</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="PSI-MI" id="MI:0018"/>
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="YCR038C"/>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="YEL061C"/>
+ </proteinParticipant>
+ </participantList>
+ </interaction>
+ <interaction>
+ <experimentList>
+ <experimentDescription id="no_id">
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="11283351"/>
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>classical two hybrid</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="PSI-MI" id="MI:0018"/>
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="YCR038C"/>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="YHR119W"/>
+ </proteinParticipant>
+ </participantList>
+ </interaction>
+ <interaction>
+ <experimentList>
+ <experimentDescription id="no_id">
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="91292524"/>
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>Synthetic Lethality</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="N/A" id="N/A"/>
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="YBR200W"/>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="YCR038C"/>
+ </proteinParticipant>
+ </participantList>
+ </interaction>
+ </interactionList>
+ </entry>
+</entrySet>
diff --git a/coreplugins/BioPAX/src/test/resources/soft1.txt b/coreplugins/BioPAX/src/test/resources/soft1.txt
new file mode 100644
index 0000000..19a7475
--- /dev/null
+++ b/coreplugins/BioPAX/src/test/resources/soft1.txt
@@ -0,0 +1,59 @@
+^database
+!database_name = Gene Expression Omnibus (GEO)
+!database_institute = NCBI NLM NIH
+!database_web_link = http://www.ncbi.nlm.nih.gov/geo
+!database_email = geo at ncbi.nlm.nih.gov
+!database_ref = Nucleic Acids Res. 2002 Jan 1;30(1):207-10
+^dataset = GDS362
+!dataset_completeness = all
+!dataset_description = Wild type and sgs1 null yeast grown with or without DNA damaging agent methyl methanesulfonate (MMS). sgs1 homologous genes linked with Bloom's and Werner's aging syndromes in humans. sgs1 mutants have high sensitivity to MMS.
+!dataset_experiment_type = single channel
+!dataset_maximum_probes = 9335
+!dataset_order = none
+!dataset_organism = Saccharomyces cerevisiae
+!dataset_platform = GPL90
+!dataset_probe_type = nucleotide
+!dataset_reference_series = GSE423
+!dataset_title = Aging in yeast
+!dataset_total_samples = 8
+!dataset_update_date = 07/01/2003
+!dataset_value_type = count
+^subset = GDS362_1
+!subset_dataset_id = GDS362
+!subset_description = sgs1 null mutant
+!subset_sample_id = GSM6219,GSM6220,GSM6221,GSM6222
+!subset_type = strain
+^subset = GDS362_2
+!subset_dataset_id = GDS362
+!subset_description = wild type
+!subset_sample_id = GSM6223,GSM6224,GSM6225,GSM6226
+!subset_type = strain
+^subset = GDS362_3
+!subset_dataset_id = GDS362
+!subset_description = methyl methanesulfonate
+!subset_sample_id = GSM6221,GSM6222,GSM6225,GSM6226
+!subset_type = agent
+^subset = GDS362_4
+!subset_dataset_id = GDS362
+!subset_description = no methyl methanesulfonate
+!subset_sample_id = GSM6219,GSM6220,GSM6223,GSM6224
+!subset_type = agent
+^DATASET = GDS362
+# ID_REF = Platform reference identifier
+# IDENTIFIER = probe identifier
+# GSM6219 = Value for GSM6219: sgs (6-C-20211); src: sgs (6-C-20211)
+# GSM6220 = Value for GSM6220: sgs rep (5) C-20229; src: sgs rep (5) C-20229
+# GSM6221 = Value for GSM6221: sgs + mms (6-C-20212); src: sgs + mms (6-C-20212)
+# GSM6222 = Value for GSM6222: sgs mms rep (7) C-20230; src: sgs mms rep (7) C-20230
+# GSM6223 = Value for GSM6223: wt (2-20156); src: wt (2-20156)
+# GSM6224 = Value for GSM6224: wt rep (1)C-20239; src: wt rep (1)C-20239
+# GSM6225 = Value for GSM6225: wt + mms (4-C-20157); src: wt + mms (4-C-20157)
+# GSM6226 = Value for GSM6226: wt mms rep (3) C-20228; src: wt mms rep (3) C-20228
+ID_REF IDENTIFIER GSM6219 GSM6220 GSM6221 GSM6222 GSM6223 GSM6224 GSM6225 GSM6226
+10000_at YHR119W 268.8 141.4 173.9 123.2 298.6 424.8 128.9 121.7
+10001_at YEL061C 5962.8 3892.9 4313.5 3604.4 4263.2 2786.8 5179.9 2634
+10003_f_at YBR200W 4282 4003 4189 4089.6 5236 4621.5 5944.6 5211.7
+10005_at YCR038C 48.5 45.3 98.2 64.9 20.7 47.1 17.6 56.3
+10006_at YAL036C 1024.8 1262.1 1125.3 1234.6 1021.9 1126.7 861 1380
+10007_at YDL065C 1325.6 1105.4 2058.8 2416.9 1199.7 1187.6 1894.5 2169.4
+10008_at YDR532C 17677.2 16258 16805.6 15458.1 20881.1 22167.5 18114.3 16265.3
diff --git a/coreplugins/CoreCommands/pom.xml b/coreplugins/CoreCommands/pom.xml
new file mode 100644
index 0000000..63e21f1
--- /dev/null
+++ b/coreplugins/CoreCommands/pom.xml
@@ -0,0 +1,56 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>parent</artifactId>
+ <version>2.8.4-SNAPSHOT</version>
+ </parent>
+
+ <artifactId>core-commands</artifactId>
+ <packaging>jar</packaging>
+
+ <name>Core Commands Plugin</name>
+
+ <!-- bootstrap for cytoscape dependencies, namely the parent POM snapshots -->
+ <repositories>
+ <repository>
+ <id>cytoscape_snapshots</id>
+ <snapshots>
+ <enabled>true</enabled>
+ </snapshots>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <name>Cytoscape Snapshots</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/</url>
+ </repository>
+ <repository>
+ <id>cytoscape_releases</id>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ <name>Cytoscape Releases</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/releases/</url>
+ </repository>
+ </repositories>
+
+ <build>
+ <plugins>
+ <plugin>
+ <artifactId>maven-assembly-plugin</artifactId>
+ <configuration>
+ <archive>
+ <manifestEntries>
+ <Cytoscape-Plugin>coreCommands.CoreCommands</Cytoscape-Plugin>
+ </manifestEntries>
+ </archive>
+ </configuration>
+ </plugin>
+ </plugins>
+ </build>
+
+</project>
+
diff --git a/coreplugins/CoreCommands/src/main/java/coreCommands/CoreCommands.java b/coreplugins/CoreCommands/src/main/java/coreCommands/CoreCommands.java
new file mode 100644
index 0000000..2dcb3fa
--- /dev/null
+++ b/coreplugins/CoreCommands/src/main/java/coreCommands/CoreCommands.java
@@ -0,0 +1,70 @@
+/* vim: set ts=2: */
+/**
+ * Copyright (c) 2009 The Regents of the University of California.
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ * notice, this list of conditions, and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above
+ * copyright notice, this list of conditions, and the following
+ * disclaimer in the documentation and/or other materials provided
+ * with the distribution.
+ * 3. Redistributions must acknowledge that this software was
+ * originally developed by the UCSF Computer Graphics Laboratory
+ * under support by the NIH National Center for Research Resources,
+ * grant P41-RR01081.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY
+ * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+ * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+ * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
+ * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ */
+package coreCommands;
+
+import cytoscape.Cytoscape;
+import cytoscape.command.CyCommandManager;
+import cytoscape.plugin.CytoscapePlugin;
+import cytoscape.CytoscapeInit;
+import cytoscape.logger.CyLogger;
+
+import coreCommands.namespaces.*;
+
+public class CoreCommands extends CytoscapePlugin {
+ private CyLogger logger = null;
+
+ /**
+ * We don't do much at initialization time
+ */
+ public CoreCommands() {
+ logger = CyLogger.getLogger(CoreCommands.class);
+
+ // Register our built-ins -- these should really be
+ // provided directly by the core...
+ try {
+ EdgeNamespace.register("edge");
+ QuitNamespace.register("exit");
+ LayoutNamespace.register("layout");
+ GroupNamespace.register("group");
+ NetworkNamespace.register("network");
+ NetworkViewNamespace.register("network view");
+ NodeNamespace.register("node");
+ PropertyNamespace.register("property");
+ SessionNamespace.register("session");
+ VizMapNamespace.register("vizmap");
+ QuitNamespace.register("quit");
+ } catch (Exception e) {
+ logger.error(e.getMessage());
+ }
+ }
+}
diff --git a/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/AbstractGraphObjectHandler.java b/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/AbstractGraphObjectHandler.java
new file mode 100644
index 0000000..2c09c8a
--- /dev/null
+++ b/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/AbstractGraphObjectHandler.java
@@ -0,0 +1,255 @@
+/* vim: set ts=2: */
+/**
+ * Copyright (c) 2009 The Regents of the University of California.
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ * notice, this list of conditions, and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above
+ * copyright notice, this list of conditions, and the following
+ * disclaimer in the documentation and/or other materials provided
+ * with the distribution.
+ * 3. Redistributions must acknowledge that this software was
+ * originally developed by the UCSF Computer Graphics Laboratory
+ * under support by the NIH National Center for Research Resources,
+ * grant P41-RR01081.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY
+ * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+ * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+ * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
+ * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ */
+package coreCommands.namespaces;
+
+import cytoscape.CyEdge;
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+
+import cytoscape.command.AbstractCommandHandler;
+import cytoscape.command.CyCommandException;
+import cytoscape.command.CyCommandNamespace;
+import cytoscape.command.CyCommandResult;
+
+import cytoscape.data.Semantics;
+
+import cytoscape.layout.Tunable;
+import cytoscape.logger.CyLogger;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+/**
+ * XXX FIXME XXX Description
+ */
+public abstract class AbstractGraphObjectHandler extends AbstractCommandHandler {
+ public static final String NODELIST = "nodelist";
+ public static final String NODE = "node";
+ public static final String SELECTED = "selected";
+ public static final String EDGELIST = "edgelist";
+ public static final String EDGE = "edge";
+
+ public AbstractGraphObjectHandler(CyCommandNamespace ns) {
+ super(ns);
+ }
+
+ protected CyNetwork getNetwork(String command, Map<String, Object> args) throws CyCommandException {
+ String netName = getArg(command, "network", args);
+ if (netName == null || netName.equalsIgnoreCase("current"))
+ return Cytoscape.getCurrentNetwork();
+ return getNetwork(command, netName);
+ }
+
+ protected CyNetwork getNetwork(String command, String title) throws CyCommandException {
+ Set<CyNetwork>networks = Cytoscape.getNetworkSet();
+ for (CyNetwork net: networks) {
+ if (net.getTitle().equalsIgnoreCase(title))
+ return net;
+ }
+ throw new CyCommandException(namespace.getNamespaceName()+" "+command+": no such network "+title);
+ }
+
+
+ protected String makeNodeList(Collection<CyNode>nodes) {
+ String nodeList = "";
+ if (nodes == null || nodes.size() == 0)
+ return nodeList;
+
+ for (CyNode node: nodes) {
+ nodeList += node.getIdentifier()+",";
+ }
+ return nodeList.substring(0, nodeList.length()-1);
+ }
+
+ /**
+ * This method is used to handle both <b>nodelist</b> and <b>node</b> parameters.
+ *
+ * @param net the network we are currently dealing with
+ * @param result the CyCommandResult to store our values in
+ * @param args the argument list we're use to look for <b>nodelist</b> and
+ * <b>node</b> arguments.
+ * @return the list of CyNode objects we found that matched the arguments
+ */
+ protected List<CyNode> getNodeList(CyNetwork net, CyCommandResult result,
+ Map<String, Object> args) {
+ return getNodeList(net, result, args, false);
+ }
+
+ /**
+ * This method is used to handle both <b>nodelist</b> and <b>node</b> parameters.
+ *
+ * @param net the network we are currently dealing with
+ * @param result the CyCommandResult to store our values in
+ * @param args the argument list we're use to look for <b>nodelist</b> and
+ * <b>node</b> arguments.
+ * @param create if true, create the node if it doesn't exist
+ * @return the list of CyNode objects we found that matched the arguments
+ */
+ protected List<CyNode> getNodeList(CyNetwork net, CyCommandResult result,
+ Map<String, Object> args, boolean create) {
+ if (args == null || args.size() == 0)
+ return null;
+
+ List<CyNode> retList = new ArrayList();
+ if (args.containsKey(NODELIST)) {
+ String[] nodes = args.get(NODELIST).toString().split(",");
+ // Handle special case for "selected" nodes
+ if (nodes[0].equals(SELECTED)) {
+ Set<CyNode> selectedNodes = net.getSelectedNodes();
+ for (CyNode node: selectedNodes) {
+ addNode(net, node.getIdentifier(), retList, result, create);
+ }
+ } else {
+ for (int nodeIndex = 0; nodeIndex < nodes.length; nodeIndex++) {
+ addNode(net, nodes[nodeIndex], retList, result, create);
+ }
+ }
+ } else if (args.containsKey(NODE)) {
+ String nodeName = args.get(NODE).toString();
+ addNode(net, nodeName, retList, result, create);
+ } else {
+ return null;
+ }
+ return retList;
+ }
+
+ protected String formatNodeList(List<CyNode> nodeList) {
+ if (nodeList == null || nodeList.size() == 0)
+ return "(none)";
+ String result = "";
+ for (CyNode node: nodeList)
+ result += node.getIdentifier()+", ";
+ result = result.substring(0, result.length()-2);
+ return result;
+ }
+
+ protected void addNode(CyNetwork net, String nodeName, List<CyNode> list,
+ CyCommandResult result, boolean create) {
+ CyNode node = Cytoscape.getCyNode(nodeName, create);
+ if (node == null)
+ result.addError(namespace.getNamespaceName()+": can't find node "+nodeName);
+ else
+ list.add(node);
+ return;
+ }
+
+
+ /**
+ * This method is used to handle both <b>edgelist</b> and <b>edge</b> parameters.
+ *
+ * @param net the network we are currently dealing with
+ * @param result the CyCommandResult to store our values in
+ * @param args the argument list we're use to look for <b>edgelist</b> and
+ * <b>edge</b> arguments.
+ * @return the list of CyEdge objects we found that matched the arguments
+ */
+ protected List<CyEdge> getEdgeList(CyNetwork net, CyCommandResult result,
+ Map<String, Object> args) {
+ return getEdgeList(net, result, args, false);
+ }
+
+ /**
+ * This method is used to handle both <b>edgelist</b> and <b>edge</b> parameters.
+ *
+ * @param net the network we are currently dealing with
+ * @param result the CyCommandResult to store our values in
+ * @param args the argument list we're use to look for <b>edgelist</b> and
+ * <b>edge</b> arguments.
+ * @param create if true, create the edge if it doesn't exist
+ * @return the list of CyEdge objects we found that matched the arguments
+ */
+ protected List<CyEdge> getEdgeList(CyNetwork net, CyCommandResult result,
+ Map<String, Object> args, boolean create) {
+ if (args == null || args.size() == 0)
+ return null;
+
+ List<CyEdge> retList = new ArrayList();
+ if (args.containsKey(EDGELIST)) {
+ String[] edges = args.get(EDGELIST).toString().split(",");
+ // Handle special case for "selected" edges
+ if (edges[0].equals(SELECTED)) {
+ Set<CyEdge> selectedEdges = net.getSelectedEdges();
+ for (CyEdge edge: selectedEdges) {
+ addEdge(net, edge.getIdentifier(), retList, result, create);
+ }
+ } else {
+ for (int edgeIndex = 0; edgeIndex < edges.length; edgeIndex++) {
+ addEdge(net, edges[edgeIndex], retList, result, create);
+ }
+ }
+ } else if (args.containsKey(EDGE)) {
+ String edgeName = args.get(EDGE).toString();
+ addEdge(net, edgeName, retList, result, create);
+ } else {
+ return null;
+ }
+ return retList;
+ }
+
+ protected void addEdge(CyNetwork net, String edgeName, List<CyEdge> list,
+ CyCommandResult result, boolean create) {
+ CyEdge edge = getCyEdge(edgeName, create);
+ if (edge == null)
+ result.addError(namespace.getNamespaceName()+": can't find edge "+edgeName);
+ else
+ list.add(edge);
+ return;
+ }
+
+ protected CyEdge getCyEdge(String edgeName, boolean create) {
+ // An edge name consists of "source (type) destination"
+ String comp[] = edgeName.split("[()]");
+ // comp[0] = source, comp[2] = destination, and comp[1] = interaction
+ CyNode source = Cytoscape.getCyNode(comp[0].trim(), create);
+ if (source == null) return null;
+ CyNode target = Cytoscape.getCyNode(comp[2].trim(), create);
+ if (target == null) return null;
+ CyEdge edge = Cytoscape.getCyEdge(source, target, Semantics.INTERACTION, comp[1].trim(), create);
+ return edge;
+ }
+
+ protected String makeEdgeList(Collection<CyEdge>edges) {
+ String edgeList = "";
+ if (edges == null || edges.size() == 0)
+ return edgeList;
+
+ for (CyEdge edge: edges) {
+ edgeList += edge.getIdentifier()+",";
+ }
+ return edgeList.substring(0, edgeList.length()-1);
+ }
+}
diff --git a/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/AttributeUtils.java b/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/AttributeUtils.java
new file mode 100644
index 0000000..a0d24e4
--- /dev/null
+++ b/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/AttributeUtils.java
@@ -0,0 +1,239 @@
+/* vim: set ts=2: */
+/**
+ * Copyright (c) 2009 The Regents of the University of California.
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ * notice, this list of conditions, and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above
+ * copyright notice, this list of conditions, and the following
+ * disclaimer in the documentation and/or other materials provided
+ * with the distribution.
+ * 3. Redistributions must acknowledge that this software was
+ * originally developed by the UCSF Computer Graphics Laboratory
+ * under support by the NIH National Center for Research Resources,
+ * grant P41-RR01081.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY
+ * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+ * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+ * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
+ * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ */
+package coreCommands.namespaces;
+
+import cytoscape.command.CyCommandResult;
+
+import cytoscape.data.CyAttributes;
+
+import giny.model.GraphObject;
+
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+/**
+ * XXX FIXME XXX Description
+ */
+public class AttributeUtils {
+
+ public static String attributeToString(Object attribute, byte attributeType) {
+ if (attributeType == CyAttributes.TYPE_SIMPLE_LIST) {
+ List attrList = (List)attribute;
+ String value = "[";
+ for (Object v: attrList) {
+ value+=v.toString()+",";
+ }
+ return value.substring(0, value.length()-1)+"]";
+ } else if (attributeType == CyAttributes.TYPE_SIMPLE_MAP) {
+ Map attrMap = (Map)attribute;
+ String value = "{";
+ for (Object key: attrMap.keySet()) {
+ Object v = attrMap.get(key);
+ value+=key.toString()+":"+v.toString()+",";
+ }
+ return value.substring(0, value.length()-1)+"}";
+ } else if (attributeType == CyAttributes.TYPE_COMPLEX)
+ return "{complex type}";
+ else if (attributeType == CyAttributes.TYPE_UNDEFINED)
+ return "{undefined type}";
+ else
+ return attribute.toString();
+ }
+
+ public static String attributeNamesToList(CyAttributes attrs, List<String>attrList) {
+ String value = "[";
+ for (String attr: attrList) {
+ byte type = attrs.getType(attr);
+ value += attr+"{"+attributeByteToString(type)+"},";
+ }
+ return value.substring(0, value.length()-1)+"]";
+ }
+
+ public static byte attributeStringToByte (String attributeType) {
+ if (attributeType.equalsIgnoreCase("float")) return CyAttributes.TYPE_FLOATING;
+ if (attributeType.equalsIgnoreCase("double")) return CyAttributes.TYPE_FLOATING;
+ if (attributeType.equalsIgnoreCase("int")) return CyAttributes.TYPE_INTEGER;
+ if (attributeType.equalsIgnoreCase("integer")) return CyAttributes.TYPE_INTEGER;
+ if (attributeType.equalsIgnoreCase("string")) return CyAttributes.TYPE_STRING;
+ if (attributeType.equalsIgnoreCase("boolean")) return CyAttributes.TYPE_BOOLEAN;
+ if (attributeType.equalsIgnoreCase("list")) return CyAttributes.TYPE_SIMPLE_LIST;
+ if (attributeType.equalsIgnoreCase("map")) return CyAttributes.TYPE_SIMPLE_MAP;
+ return CyAttributes.TYPE_UNDEFINED;
+ }
+
+ public static String attributeByteToString (byte type) {
+ if (type == CyAttributes.TYPE_FLOATING) return "float";
+ if (type == CyAttributes.TYPE_INTEGER) return "int";
+ if (type == CyAttributes.TYPE_STRING) return "string";
+ if (type == CyAttributes.TYPE_BOOLEAN) return "boolean";
+ if (type == CyAttributes.TYPE_SIMPLE_LIST) return "list";
+ if (type == CyAttributes.TYPE_SIMPLE_MAP) return "map";
+ return "undefined";
+ }
+
+ public static boolean setAttribute(CyCommandResult result, String command,
+ CyAttributes attributes, byte type,
+ String id, String attrName, String value) {
+ try {
+ if (type == CyAttributes.TYPE_STRING)
+ attributes.setAttribute(id, attrName, value);
+ else if (type == CyAttributes.TYPE_BOOLEAN)
+ attributes.setAttribute(id, attrName, new Boolean(value));
+ else if (type == CyAttributes.TYPE_FLOATING)
+ attributes.setAttribute(id, attrName, new Double(value));
+ else if (type == CyAttributes.TYPE_INTEGER)
+ attributes.setAttribute(id, attrName, new Integer(value));
+ else if (type == CyAttributes.TYPE_SIMPLE_LIST) {
+ List attrList = stringToList(value);
+ attributes.setListAttribute(id, attrName, attrList);
+ } else if (type == CyAttributes.TYPE_SIMPLE_MAP) {
+ Map attrMap = stringToMap(value);
+ attributes.setMapAttribute(id, attrName, attrMap);
+ }
+ } catch (Exception e) {
+ result.addError(command+": unable to convert '"+value+"' to type '"+attributeByteToString(type)+"'");
+ return false;
+ }
+ return true;
+ }
+
+ public static List stringToList(String value) throws Exception {
+ if (value == null || value.length() == 0)
+ throw new Exception();
+
+ if (value.startsWith("["))
+ value = value.substring(1);
+
+ if (value.endsWith("]"))
+ value = value.substring(0, value.length()-1);
+
+ String [] elements = value.split(",");
+ List<String> list = new ArrayList();
+ for (int index=0; index < elements.length; index++) {
+ list.add(elements[index]);
+ }
+ return list;
+ }
+
+ public static Map stringToMap(String value) throws Exception {
+ if (value == null || value.length() == 0)
+ throw new Exception();
+
+ if (value.startsWith("{") || value.startsWith("["))
+ value = value.substring(1);
+
+ if (value.endsWith("}") || value.endsWith("]"))
+ value = value.substring(0, value.length()-1);
+
+ String [] elements = value.split(",");
+ Map<String, String> map = new HashMap();
+ for (int index=0; index < elements.length; index++) {
+ String[] pair = elements[index].split(":");
+ map.put(pair[0], pair[1]);
+ }
+ return map;
+ }
+
+ /**
+ * Output a tab-delimited table of attributes
+ *
+ * @param outputFile the file to output our attributes to
+ * @param attrs the attributes we're going to use
+ * @param objects the list of CyNodes or CyEdges to output
+ * @param attrList the list of attributes we want to output
+ * @param delim the delimiter to use
+ */
+ public static int exportAttributes(File outputFile, CyAttributes attrs, List<GraphObject> objects,
+ List<String>attrList, String delim) throws IOException {
+
+ int lineCount = 0;
+ // Create our output file
+ BufferedWriter output = new BufferedWriter(new FileWriter(outputFile));
+
+ // Write out a header
+ for (String attr: attrList) {
+ if (attrs.getUserVisible(attr))
+ output.write(attr+delim);
+ }
+ output.newLine();
+
+ // For each object
+ for (GraphObject obj: objects) {
+ // Output a row
+ exportRow(output, obj.getIdentifier(), attrs, attrList, delim);
+ lineCount++;
+ }
+ output.close();
+ return lineCount;
+ }
+
+ private static void exportRow(BufferedWriter output, String name, CyAttributes attrs,
+ List<String>attrList, String delim) throws IOException {
+ for (String attr: attrList) {
+ if (attr.equals("ID")) {
+ output.write(name);
+ } else if (attrs.hasAttribute(name, attr) && attrs.getUserVisible(attr)) {
+ byte type = attrs.getType(attr);
+ // Special handling for Lists or Maps
+ if (type == CyAttributes.TYPE_SIMPLE_LIST) {
+ List l = attrs.getListAttribute(name, attr);
+ String lStr = "[";
+ for (Object o: l) {
+ lStr += o.toString()+",";
+ }
+ output.write(lStr.substring(0,lStr.length()-1)+"]");
+ } else if (type == CyAttributes.TYPE_SIMPLE_MAP) {
+ Map m = attrs.getMapAttribute(name, attr);
+ String mStr = "{";
+ for (Object k: m.keySet())
+ mStr += k.toString()+":"+m.get(k).toString()+",";
+ mStr = mStr.substring(0,mStr.length()-1)+"}";
+ output.write(mStr);
+ } else {
+ Object o = attrs.getAttribute(name, attr);
+ output.write(o.toString());
+ }
+ }
+ output.write(delim);
+ }
+ output.newLine();
+ }
+}
diff --git a/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/EdgeNamespace.java b/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/EdgeNamespace.java
new file mode 100644
index 0000000..238076e
--- /dev/null
+++ b/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/EdgeNamespace.java
@@ -0,0 +1,289 @@
+/* vim: set ts=2: */
+/**
+ * Copyright (c) 2009 The Regents of the University of California.
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ * notice, this list of conditions, and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above
+ * copyright notice, this list of conditions, and the following
+ * disclaimer in the documentation and/or other materials provided
+ * with the distribution.
+ * 3. Redistributions must acknowledge that this software was
+ * originally developed by the UCSF Computer Graphics Laboratory
+ * under support by the NIH National Center for Research Resources,
+ * grant P41-RR01081.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY
+ * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+ * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+ * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
+ * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ */
+package coreCommands.namespaces;
+
+import cytoscape.CyEdge;
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import cytoscape.command.AbstractCommandHandler;
+import cytoscape.command.CyCommandException;
+import cytoscape.command.CyCommandHandler;
+import cytoscape.command.CyCommandManager;
+import cytoscape.command.CyCommandNamespace;
+import cytoscape.command.CyCommandResult;
+import cytoscape.data.CyAttributes;
+import cytoscape.layout.Tunable;
+import cytoscape.logger.CyLogger;
+import cytoscape.view.CyNetworkView;
+
+import java.io.File;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import coreCommands.namespaces.edge.ExportEdgeAttributes;
+
+/**
+ * XXX FIXME XXX Description
+ */
+public class EdgeNamespace extends AbstractGraphObjectHandler {
+
+ // Commands
+ private static String DELETE = "delete";
+ private static String DESELECT = "deselect";
+ private static String EXPORT = "export attributes";
+ private static String FIND = "find";
+ private static String GETATTR = "get attribute";
+ private static String GETSEL = "get selected";
+ private static String IMPORTATTR = "import attributes";
+ private static String LISTATTR = "list attributes";
+ private static String SELECT = "select";
+ private static String SETATTR = "set attribute";
+
+ // Settings
+ private static String ATTRIBUTE = "attribute";
+ private static String EDGE = "edge";
+ private static String EDGELIST = "edgelist";
+ private static String EXPRESSION = "expression";
+ private static String FILE = "file";
+ private static String NAME = "name";
+ private static String NETWORK = "network";
+ private static String VALUE = "value";
+
+ protected EdgeNamespace(CyCommandNamespace ns) {
+ super(ns);
+
+ // Define our subcommands
+ addDescription(DELETE, "Delete an edge or group of edges.");
+ addArgument(DELETE, EDGE);
+ addArgument(DELETE, EDGELIST);
+
+ addDescription(DESELECT, "Deselect edges. If no edge(s) are provided, all edges are deselected");
+ addArgument(DESELECT, EDGE);
+ addArgument(DESELECT, EDGELIST);
+
+ //
+ // addArgument(FIND, EXPRESSION);
+
+ addDescription(GETATTR, "Returns edge attributes");
+ addArgument(GETATTR, EDGE);
+ addArgument(GETATTR, EDGELIST);
+ addArgument(GETATTR, NAME);
+
+ addDescription(GETSEL, "Lists the currently selected edges");
+ addArgument(GETSEL, NETWORK, "current");
+
+ addDescription(IMPORTATTR, "Import edge attributes from a file");
+ addArgument(IMPORTATTR, FILE);
+
+ addDescription(LISTATTR, "List edge attributes");
+ addArgument(LISTATTR);
+
+ addDescription(SELECT, "Select edges. If no edge(s) are provided, all edges are selected");
+ addArgument(SELECT, EDGE);
+ addArgument(SELECT, EDGELIST);
+
+ addDescription(SETATTR, "Set edge attributes to a new value");
+ addArgument(SETATTR, EDGE);
+ addArgument(SETATTR, EDGELIST);
+ addArgument(SETATTR, NAME);
+ addArgument(SETATTR, VALUE);
+
+ // Handle table import????
+ }
+
+ public CyCommandResult execute(String command, Collection<Tunable>args) throws CyCommandException {
+ return execute(command, createKVMap(args));
+ }
+
+ public CyCommandResult execute(String command, Map<String, Object>args) throws CyCommandException {
+ CyCommandResult result = new CyCommandResult();
+
+ // Import edge attributes from a file
+ if (IMPORTATTR.equals(command)) {
+ String fileName = getArg(IMPORTATTR, FILE, args);
+ if (fileName == null)
+ throw new CyCommandException("edge: filename is required to import attributes");
+
+ try {
+ File file = new File(fileName);
+ Cytoscape.loadAttributes(new String[] { },
+ new String[] { file.getAbsolutePath() });
+ result.addMessage("edge: attributes imported from "+file.getAbsolutePath());
+ } catch (Exception e) {
+ throw new CyCommandException("edge: unable to import attributes: "+e.getMessage());
+ }
+
+ // Select some edges
+ } else if (SELECT.equals(command)) {
+ CyNetwork net = getNetwork(SELECT, args);
+ List<CyEdge> edgeList = getEdgeList(net, result, args);
+ if (edgeList == null)
+ throw new CyCommandException("edge: nothing to select");
+ net.setSelectedEdgeState(edgeList, true);
+ result.addMessage("edge: selected "+edgeList.size()+" edges");
+ if (net == Cytoscape.getCurrentNetwork()) {
+ Cytoscape.getCurrentNetworkView().updateView();
+ }
+
+ // de-select some ndoes
+ } else if (DESELECT.equals(command)) {
+ CyNetwork net = getNetwork(DESELECT, args);
+ try {
+ List<CyEdge> edgeList = getEdgeList(net, result, args);
+ if (edgeList == null)
+ throw new CyCommandException("edge: nothing to deselect");
+ net.setSelectedNodeState(edgeList, false);
+ result.addMessage("edge: deselected "+edgeList.size()+" edges");
+ } catch (CyCommandException e) {
+ // deselect everything
+ net.unselectAllEdges();
+ result.addMessage("edge: deselected all edges");
+ }
+ if (net == Cytoscape.getCurrentNetwork()) {
+ Cytoscape.getCurrentNetworkView().updateView();
+ }
+
+ // delete some edges
+ } else if (DELETE.equals(command)) {
+ CyNetwork net = getNetwork(command, args);
+ List<CyEdge> edgeList = getEdgeList(net, result, args);
+ if (edgeList == null)
+ throw new CyCommandException("edge: nothing to delete");
+
+ for (CyEdge edge: edgeList) {
+ net.removeEdge(edge.getRootGraphIndex(), false);
+ }
+ result.addMessage("edge: deleted "+edgeList.size()+" nodes");
+ if (net == Cytoscape.getCurrentNetwork()) {
+ Cytoscape.getCurrentNetworkView().updateView();
+ }
+
+ // return the list of currently selected edges
+ } else if (GETSEL.equals(command)) {
+ CyNetwork net = getNetwork("get selected", args);
+ Set<CyEdge>edges = net.getSelectedEdges();
+ result.addMessage("edge: returned "+edges.size()+" selected edges");
+ result.addResult("edges", makeEdgeList(edges));
+
+ // Get attribute values
+ } else if (GETATTR.equals(command)) {
+ CyNetwork net = getNetwork(command, args);
+ CyAttributes edgeAttributes = Cytoscape.getEdgeAttributes();
+ String attrName = getArg(command, NAME, args);
+ if (attrName == null)
+ throw new CyCommandException("edge: attribute 'name' is required");
+ else if (edgeAttributes.getType(attrName) == CyAttributes.TYPE_UNDEFINED)
+ throw new CyCommandException("edge: attribute 'name' does not exist");
+
+ List<CyEdge> edgeList = getEdgeList(net, result, args);
+ if (edgeList == null)
+ edgeList = net.edgesList();
+
+ byte attributeType = edgeAttributes.getType(attrName);
+ result.addResult("attribute type", attributeType);
+ result.addMessage("edge: values for '"+attrName+"' attribute:");
+ for (CyEdge edge: edgeList) {
+ if (edgeAttributes.hasAttribute(edge.getIdentifier(), attrName)) {
+ Object attr = edgeAttributes.getAttribute(edge.getIdentifier(), attrName);
+ result.addResult(edge.getIdentifier(), attr);
+ result.addMessage(" "+edge.getIdentifier()+"='"+AttributeUtils.attributeToString(attr, attributeType)+"'");
+ }
+ }
+
+ // Set attribute values
+ } else if (SETATTR.equals(command)) {
+ CyNetwork net = getNetwork(command, args);
+ CyAttributes edgeAttributes = Cytoscape.getNodeAttributes();
+ String attrName = getArg(command, NAME, args);
+ String value = getArg(command, VALUE, args);
+ if (attrName == null || value == null)
+ throw new CyCommandException("edge: attribute 'name' and 'value' are required");
+
+ List<CyEdge> edgeList = getEdgeList(net, result, args);
+ if (edgeList == null)
+ edgeList = net.edgesList();
+
+ String typeName = getArg(command, "type", args);
+ byte attributeType = edgeAttributes.getType(attrName);
+ if (attributeType == CyAttributes.TYPE_UNDEFINED && typeName == null)
+ attributeType = CyAttributes.TYPE_STRING;
+ else if (attributeType == CyAttributes.TYPE_UNDEFINED && typeName != null) {
+ attributeType = AttributeUtils.attributeStringToByte(typeName);
+ }
+
+ int count = 0;
+ int edgeCount = edgeList.size();
+ for (CyEdge edge: edgeList) {
+ String id = edge.getIdentifier();
+ if (AttributeUtils.setAttribute(result, "edge", edgeAttributes, attributeType, id, attrName, value))
+ count++;
+ }
+ result.addMessage("edge: set "+count+" attributes (out of "+edgeCount+")");
+
+ // find edges based on an expression
+ } else if ("find".equals(command)) {
+
+ // list edge attributes
+ } else if (LISTATTR.equals(command)) {
+ CyNetwork net = getNetwork(command, args);
+ CyAttributes edgeAttributes = Cytoscape.getNodeAttributes();
+ String[] attrNames = edgeAttributes.getAttributeNames();
+ List<String>attrList = Arrays.asList(attrNames);
+ result.addResult(attrList);
+ result.addMessage("Edge attributes: "+AttributeUtils.attributeNamesToList(edgeAttributes, attrList));
+ } else {
+ throw new CyCommandException("edge: unknown command: "+command);
+ }
+ return result;
+ }
+
+ public static CyCommandHandler register(String namespace) throws RuntimeException {
+ // Get the namespace
+ CyCommandNamespace ns = CyCommandManager.reserveNamespace(namespace);
+
+ // Handle the simple commands ourselves
+ CyCommandHandler edgeNS = new EdgeNamespace(ns);
+
+ // More elaborate commands are in separate classes
+ new ExportEdgeAttributes(ns);
+
+ return edgeNS;
+ }
+
+}
diff --git a/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/GroupNamespace.java b/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/GroupNamespace.java
new file mode 100644
index 0000000..68932e8
--- /dev/null
+++ b/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/GroupNamespace.java
@@ -0,0 +1,312 @@
+/* vim: set ts=2: */
+/**
+ * Copyright (c) 2009 The Regents of the University of California.
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ * notice, this list of conditions, and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above
+ * copyright notice, this list of conditions, and the following
+ * disclaimer in the documentation and/or other materials provided
+ * with the distribution.
+ * 3. Redistributions must acknowledge that this software was
+ * originally developed by the UCSF Computer Graphics Laboratory
+ * under support by the NIH National Center for Research Resources,
+ * grant P41-RR01081.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY
+ * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+ * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+ * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
+ * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ */
+package coreCommands.namespaces;
+
+import cytoscape.CyEdge;
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+import cytoscape.CytoscapeInit;
+import cytoscape.command.AbstractCommandHandler;
+import cytoscape.command.CyCommandException;
+import cytoscape.command.CyCommandHandler;
+import cytoscape.command.CyCommandManager;
+import cytoscape.command.CyCommandNamespace;
+import cytoscape.command.CyCommandResult;
+import cytoscape.groups.CyGroup;
+import cytoscape.groups.CyGroupManager;
+import cytoscape.layout.Tunable;
+import cytoscape.logger.CyLogger;
+import cytoscape.logger.CyLogger;
+import cytoscape.view.CyNetworkView;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+/**
+ * XXX FIXME XXX Description
+ */
+public class GroupNamespace extends AbstractGraphObjectHandler {
+
+ // Group commands
+ static final String LIST = "list";
+ static final String CREATE = "create";
+ static final String DESTROY = "destroy";
+ static final String GETGROUP = "getGroup";
+ static final String ADD = "add";
+ static final String REMOVE = "remove";
+ static final String GETVIEWER = "getViewer";
+ static final String SETVIEWER = "setViewer";
+ static final String GETSTATE = "getState";
+ static final String SETSTATE = "setState";
+ static final String GETNODES = "getNodes";
+ static final String GETOUTEREDGES = "getOuterEdges";
+ static final String GETINNEREDGES = "getInnerEdges";
+
+ // Arguments
+ static final String NAME = "name";
+ static final String NETWORK = "network";
+ static final String NODE = "node";
+ static final String NODELIST = "nodelist";
+ static final String VIEWER = "viewer";
+ static final String STATE = "state";
+
+ public GroupNamespace(CyCommandNamespace ns) {
+ super(ns);
+
+ // Define our subcommands
+ addDescription(LIST, "List the current groups");
+ addArgument(LIST);
+
+ addDescription(CREATE, "Create a new group");
+ addArgument(CREATE, NAME);
+ addArgument(CREATE, NETWORK);
+ addArgument(CREATE, NODE);
+ addArgument(CREATE, NODELIST);
+ addArgument(CREATE, VIEWER);
+
+ addDescription(DESTROY, "Destroy (delete) a group");
+ addArgument(DESTROY, NAME);
+
+ addDescription(GETGROUP, "Get a group");
+ addArgument(GETGROUP, NAME);
+
+ addDescription(ADD, "Add a node (or nodes) to an existing group");
+ addArgument(ADD, NAME);
+ addArgument(ADD, NODE);
+ addArgument(ADD, NODELIST);
+
+ addDescription(REMOVE, "Remove a node (or nodes) from an existing group");
+ addArgument(REMOVE, NAME);
+ addArgument(REMOVE, NODE);
+ addArgument(REMOVE, NODELIST);
+
+ addDescription(GETVIEWER, "Get the current viewer for a group");
+ addArgument(GETVIEWER, NAME);
+
+ addDescription(SETVIEWER, "Set a viewer for a group");
+ addArgument(SETVIEWER, NAME);
+ addArgument(SETVIEWER, VIEWER);
+
+ addDescription(GETSTATE, "Get the current state for a group");
+ addArgument(GETSTATE, NAME);
+
+ addDescription(SETSTATE, "Set the current state for a group");
+ addArgument(SETSTATE, NAME);
+ addArgument(SETSTATE, STATE);
+
+ addDescription(GETNODES, "Get the current list of nodes for a group");
+ addArgument(GETNODES, NAME);
+ addDescription(GETOUTEREDGES, "Get the current list of outer edges for a group");
+ addArgument(GETOUTEREDGES, NAME);
+ addDescription(GETINNEREDGES, "Get the current list of inner edges for a group");
+ addArgument(GETINNEREDGES, NAME);
+ }
+
+ public CyCommandResult execute(String command, Collection<Tunable>args) throws CyCommandException {
+ return execute(command, createKVMap(args));
+ }
+
+ public CyCommandResult execute(String command, Map<String, Object>args) throws CyCommandException {
+ CyCommandResult result = new CyCommandResult();
+
+ // Get the list of groups
+ if (command.equals(LIST)) {
+ List<CyGroup> groupList = CyGroupManager.getGroupList();
+ result.addResult("groups",groupList);
+ result.addMessage("group: group list:");
+ for (CyGroup group: groupList) {
+ result.addMessage(" "+formatGroup(group));
+ }
+ return result;
+ }
+
+ // Handle required arguments up front
+ if (!args.containsKey(NAME))
+ throw new CyCommandException("group: need the name of the group for "+command);
+
+ String groupName = (String)args.get(NAME);
+ if ((command.equals(CREATE) || command.equals(ADD) || command.equals(REMOVE)) &&
+ (!args.containsKey(NODE) && !args.containsKey(NODELIST)))
+ throw new CyCommandException("group: need a node or list of nodes for "+command);
+
+ // OK, here are the commands
+
+ // Create a group
+ if (command.equals(CREATE)) {
+ CyGroup group = null;
+ List<CyNode> nodeList = getNodeList(Cytoscape.getCurrentNetwork(),result, args);
+ if (result.getErrors() != null && result.getErrors().size() > 0)
+ return result;
+
+ CyNetwork network = Cytoscape.getCurrentNetwork();
+ network = getNetwork(CREATE, args);
+
+ if (args.containsKey(VIEWER)) {
+ String viewer = (String)args.get(VIEWER);
+ group = CyGroupManager.createGroup(groupName, nodeList, viewer, network);
+ if (group != null)
+ CyGroupManager.notifyCreateGroup(group);
+ } else {
+ group = CyGroupManager.createGroup(groupName, nodeList, null, network);
+ }
+ if (group != null) {
+ result.addMessage("group: created group '"+groupName+"' with "+nodeList.size()+" nodes");
+ result.addResult("group",group);
+ } else
+ result.addError("group: creation of group '"+groupName+"' failed!");
+ return result;
+ }
+
+ // All of the other commands require a group -- get it now
+ CyGroup group = CyGroupManager.findGroup(groupName);
+ if (group == null) {
+ result.addError("group: cannot find a group named '"+groupName);
+ return result;
+ }
+
+ // Destroy a group
+ if (command.equals(DESTROY)) {
+ CyGroupManager.removeGroup(group);
+
+ // Get a group
+ } else if (command.equals(GETGROUP)) {
+ result.addResult("group", group);
+ result.addMessage("Group: "+formatGroup(group));
+
+ // Add a node (or nodes) to a group
+ } else if (command.equals(ADD)) {
+ List<CyNode> nodeList = getNodeList(Cytoscape.getCurrentNetwork(),result, args);
+ for (CyNode node: nodeList)
+ group.addNode(node);
+ result.addMessage("group: added "+nodeList.size()+" nodes to group: "+group);
+
+ // Remove a node (or nodes) from a group
+ } else if (command.equals(REMOVE)) {
+ List<CyNode> nodeList = getNodeList(Cytoscape.getCurrentNetwork(),result, args);
+ for (CyNode node: nodeList)
+ group.removeNode(node);
+ result.addMessage("group: removed "+nodeList.size()+" nodes from group: "+group);
+
+ // Get the current viewer for a group
+ } else if (command.equals(GETVIEWER)) {
+ if (group.getViewer() != null)
+ result.addMessage("group: viewer for group "+groupName+" is "+group.getViewer());
+ else
+ result.addMessage("group: no viewer for group "+groupName);
+ result.addResult("viewer", group.getViewer());
+
+ // Set the viewer for a group
+ } else if (command.equals(SETVIEWER)) {
+ if (!args.containsKey(VIEWER))
+ throw new CyCommandException("group: need a viewer for "+command);
+
+ String viewer = (String) args.get(VIEWER);
+ CyGroupManager.setGroupViewer(group, viewer, Cytoscape.getCurrentNetworkView(), true);
+ result.addMessage("group: set viewer for group '"+groupName+"' to '"+viewer+"'");
+
+ // Get the current state for a group
+ } else if (command.equals(GETSTATE)) {
+ int state = group.getState();
+ result.addResult("state", new Integer(state));
+ result.addMessage("group: state for group '"+groupName+"' = "+state);
+
+ // Set the current state for a group
+ } else if (command.equals(SETSTATE)) {
+ if (!args.containsKey(STATE))
+ throw new CyCommandException("group: need a state for "+command);
+
+ int state;
+ try {
+ state = Integer.parseInt((String)args.get(STATE));
+ } catch (NumberFormatException e) {
+ throw new CyCommandException("group: state nust be an integer for "+command);
+ }
+ group.setState(state);
+ result.addMessage("group: set the state for group '"+groupName+"' to "+state);
+
+ // Get the current list of nodes for a group
+ } else if (command.equals(GETNODES)) {
+ List<CyNode> nodeList = group.getNodes();
+ result.addResult("nodeList", nodeList);
+ result.addMessage("Nodes for group '"+groupName+"': ");
+ result.addMessage(" "+formatNodeList(nodeList));
+
+ // Get the current list of outer edges for a group
+ } else if (command.equals(GETOUTEREDGES)) {
+ List<CyEdge> edgeList = group.getOuterEdges();
+ result.addResult("edgeList", edgeList);
+ result.addMessage("Outer edges for group '"+groupName+"': ");
+ result.addMessage(" "+formatEdgeList(edgeList));
+
+ // Get the current list of inner edges for a group
+ } else if (command.equals(GETINNEREDGES)) {
+ List<CyEdge> edgeList = group.getInnerEdges();
+ result.addResult("edgeList", edgeList);
+ result.addMessage("Inner edges for group '"+groupName+"': ");
+ result.addMessage(" "+formatEdgeList(edgeList));
+ }
+
+ return result;
+
+ }
+
+ public static CyCommandHandler register(String namespace) throws RuntimeException {
+ // Get the namespace
+ return new GroupNamespace(CyCommandManager.reserveNamespace(namespace));
+ }
+
+ private String formatEdgeList(List<CyEdge> edgeList) {
+ if (edgeList == null || edgeList.size() == 0)
+ return "(none)";
+ String result = "";
+ for (CyEdge edge: edgeList)
+ result += edge.getIdentifier()+", ";
+ result = result.substring(0, result.length()-2);
+ return result;
+ }
+
+ private String formatGroup(CyGroup group) {
+ if (group == null) return "(none)";
+
+ List<CyNode> nodeList = group.getNodes();
+ List<CyEdge> innerEdges = group.getInnerEdges();
+ List<CyEdge> outerEdges = group.getOuterEdges();
+ return group.toString()+": "+nodeList.size()+" nodes, "+
+ innerEdges.size()+" inner edges, and "+outerEdges.size()+" outer edges";
+ }
+}
diff --git a/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/LayoutNamespace.java b/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/LayoutNamespace.java
new file mode 100644
index 0000000..9077e1c
--- /dev/null
+++ b/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/LayoutNamespace.java
@@ -0,0 +1,184 @@
+/* vim: set ts=2: */
+/**
+ * Copyright (c) 2009 The Regents of the University of California.
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ * notice, this list of conditions, and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above
+ * copyright notice, this list of conditions, and the following
+ * disclaimer in the documentation and/or other materials provided
+ * with the distribution.
+ * 3. Redistributions must acknowledge that this software was
+ * originally developed by the UCSF Computer Graphics Laboratory
+ * under support by the NIH National Center for Research Resources,
+ * grant P41-RR01081.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY
+ * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+ * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+ * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
+ * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ */
+package coreCommands.namespaces;
+
+import cytoscape.Cytoscape;
+import cytoscape.command.AbstractCommandHandler;
+import cytoscape.command.CyCommandException;
+import cytoscape.command.CyCommandHandler;
+import cytoscape.command.CyCommandManager;
+import cytoscape.command.CyCommandNamespace;
+import cytoscape.command.CyCommandResult;
+import cytoscape.data.CyAttributes;
+import cytoscape.layout.CyLayouts;
+import cytoscape.layout.CyLayoutAlgorithm;
+import cytoscape.layout.LayoutProperties;
+import cytoscape.layout.Tunable;
+import cytoscape.logger.CyLogger;
+import cytoscape.view.CyNetworkView;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+/**
+ * XXX FIXME XXX Description
+ */
+public class LayoutNamespace extends AbstractCommandHandler {
+ private static String LAYOUT = "layout";
+ private static String GETCURRENT = "get current";
+ private static String GETDEFAULT = "get default";
+ private static String DEFAULT = "default";
+
+ protected LayoutNamespace(CyCommandNamespace ns) {
+ super(ns);
+
+ // Define our subcommands
+ addDescription(GETCURRENT, "Return the name of the last layout performed on this network");
+ addArgument(GETCURRENT);
+
+ addDescription(GETCURRENT, "Return the name of the default layout");
+ addArgument(GETDEFAULT);
+
+ addDescription(DEFAULT, "Layout the current network with the default layout");
+ addArgument(DEFAULT);
+
+ updateLayouts();
+ }
+
+ public CyCommandResult execute(String command, Collection<Tunable>args) throws CyCommandException {
+ updateLayouts();
+ return execute(command, createKVMap(args));
+ }
+
+ public CyCommandResult execute(String command, Map<String, Object>args) throws CyCommandException {
+ CyCommandResult result = new CyCommandResult();
+ updateLayouts();
+
+ List<Tunable> tL = new ArrayList();
+ if (args == null || args.size() == 0) {
+ return execute(command, tL);
+ }
+
+ if (!getCommands().contains(command.toLowerCase()))
+ throw new CyCommandException("layout: unknown algorithm: "+command.toLowerCase());
+
+ if (command.equalsIgnoreCase(GETCURRENT) ||
+ command.equalsIgnoreCase(GETDEFAULT) ||
+ command.equalsIgnoreCase(DEFAULT)) {
+ throw new CyCommandException("layout: "+command+" doesn't take any arguments");
+ }
+
+ Map<String, Tunable> tMap = getTunables(command);
+
+ for (String key: args.keySet()) {
+ if (tMap.containsKey(key)) {
+ Tunable t = tMap.get(key);
+ t.setValue(args.get(key));
+ tL.add(t);
+ } else {
+ result.addError("layout: algorithm '"+command+"' doesn't have a '"+key+"' parameter");
+ }
+ }
+ if (result.successful())
+ return execute(command, tL);
+
+ return result;
+ }
+
+ public CyCommandResult execute(String command, List<Tunable> args) throws CyCommandException {
+ CyCommandResult result = new CyCommandResult();
+
+ if (command.equalsIgnoreCase(GETCURRENT)) {
+ CyAttributes networkAttributes = Cytoscape.getNetworkAttributes();
+ String networkID = Cytoscape.getCurrentNetwork().getIdentifier();
+
+ if (networkAttributes.hasAttribute(networkID, "__layoutAlgorithm")) {
+ String alg = (String)networkAttributes.getAttribute(networkID, "__layoutAlgorithm");
+ result.addMessage("layout: last layout of network '"+networkID+"' was with "+alg);
+ } else {
+ result.addMessage("layout: last layout information is unavailable for '"+networkID+"'");
+ }
+ } else if (command.equalsIgnoreCase("get default")) {
+ CyLayoutAlgorithm alg = CyLayouts.getDefaultLayout();
+ result.addMessage("layout: default algorithm is "+alg.getName());
+ result.addResult("algorithm", alg);
+ result.addResult("name", alg.getName());
+ } else if (command.equalsIgnoreCase("default")) {
+ CyLayoutAlgorithm alg = CyLayouts.getDefaultLayout();
+ alg.doLayout();
+ result.addMessage("layout: laid current network out using "+alg.getName()+"(default) algorithm");
+ } else {
+ CyLayoutAlgorithm alg = CyLayouts.getLayout(command);
+ LayoutProperties props = alg.getSettings();
+
+ for (Tunable t: args) {
+ Tunable layoutTunable = props.get(t.getName());
+ if (layoutTunable == null) {
+ result.addError("layout: algorithm '"+command+"' doesn't have a '"+t.getName()+"' parameter");
+ continue;
+ }
+ layoutTunable.setValue(t.getValue());
+ alg.updateSettings();
+ }
+ if (result.successful()) {
+ alg.doLayout();
+ result.addMessage("layout: laid current network out using "+alg.getName()+" algorithm");
+ }
+ }
+
+ return result;
+ }
+
+ public static CyCommandHandler register(String namespace) throws RuntimeException {
+ // Get the namespace
+ return new LayoutNamespace(CyCommandManager.reserveNamespace(namespace));
+ }
+
+ private void updateLayouts() {
+ // Get the list of layouts from the layout manager
+ for (CyLayoutAlgorithm alg: CyLayouts.getAllLayouts()) {
+ String layout = alg.getName();
+ addDescription(layout, alg.toString());
+ LayoutProperties props = alg.getSettings();
+ if (props == null) {
+ addArgument(layout);
+ continue;
+ }
+ for (Tunable t: props.getTunables())
+ addArgument(layout, t);
+ }
+ }
+}
diff --git a/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/NetworkNamespace.java b/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/NetworkNamespace.java
new file mode 100644
index 0000000..7d21b62
--- /dev/null
+++ b/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/NetworkNamespace.java
@@ -0,0 +1,167 @@
+/* vim: set ts=2: */
+/**
+ * Copyright (c) 2009 The Regents of the University of California.
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ * notice, this list of conditions, and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above
+ * copyright notice, this list of conditions, and the following
+ * disclaimer in the documentation and/or other materials provided
+ * with the distribution.
+ * 3. Redistributions must acknowledge that this software was
+ * originally developed by the UCSF Computer Graphics Laboratory
+ * under support by the NIH National Center for Research Resources,
+ * grant P41-RR01081.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY
+ * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+ * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+ * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
+ * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ */
+package coreCommands.namespaces;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+
+import cytoscape.command.AbstractCommandHandler;
+import cytoscape.command.CyCommandException;
+import cytoscape.command.CyCommandHandler;
+import cytoscape.command.CyCommandManager;
+import cytoscape.command.CyCommandNamespace;
+import cytoscape.command.CyCommandResult;
+
+import coreCommands.namespaces.network.CreateNetwork;
+import coreCommands.namespaces.network.ExportNetwork;
+import coreCommands.namespaces.network.ImportNetwork;
+import coreCommands.namespaces.network.AddNodeNetwork;
+import coreCommands.namespaces.network.AddEdgeNetwork;
+
+import cytoscape.layout.Tunable;
+import cytoscape.logger.CyLogger;
+import cytoscape.view.CyNetworkView;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+/**
+ * XXX FIXME XXX Description
+ */
+public class NetworkNamespace extends AbstractGraphObjectHandler {
+ static String NETWORK = "network";
+
+ // Commands
+ static String CREATE = "create";
+ static String DESTROY = "destroy";
+ static String EXPORT = "export";
+ static String GETCURRENT = "get current";
+ static String IMPORT = "import";
+ static String LIST = "list";
+ static String MAKECURRENT = "make current";
+
+ // Arguments
+ static String NAME = "name";
+ static String CREATEVIEW = "createview";
+ static String CURRENT = "current";
+ static String PARENT = "parent";
+ static String FILE = "file";
+ static String TYPE = "type";
+
+ protected NetworkNamespace(CyCommandNamespace ns) {
+ super(ns);
+
+ // Define our subcommands
+ addDescription(DESTROY, "Destroy (delete) a network");
+ addArgument(DESTROY, NAME);
+
+ addDescription(GETCURRENT, "Return the name of the current network");
+ addArgument(GETCURRENT);
+
+ addDescription(LIST, "Return a list of all of the networks currently loaded");
+ addArgument(LIST);
+
+ addDescription(MAKECURRENT, "Make the network with the provided name the 'current' network");
+ addArgument(MAKECURRENT, NAME);
+ }
+
+ public CyCommandResult execute(String command, Collection<Tunable>args) throws CyCommandException {
+ return execute(command, createKVMap(args));
+ }
+
+ public CyCommandResult execute(String command, Map<String, Object>args) throws CyCommandException {
+ CyCommandResult result = new CyCommandResult();
+
+ if (command.equals(DESTROY)) {
+ String netName = getArg(command, NAME, args);
+ if (netName == null)
+ throw new CyCommandException("network: need the name of the network to destroy");
+
+ CyNetwork net = getNetwork(DESTROY, args);
+ Cytoscape.destroyNetwork(net);
+
+ // Return the current network
+ } else if (command.equals(GETCURRENT)) {
+ CyNetwork current = Cytoscape.getCurrentNetwork();
+ result.addMessage("network: current network is "+current.getIdentifier()+": "+current.getTitle());
+ result.addResult("currentnetwork", current);
+
+ // Make the designated network current
+ } else if (command.equals(MAKECURRENT)) {
+ String netName = getArg(command, NAME, args);
+ if (netName == null)
+ throw new CyCommandException("network: need a network name to make current");
+
+ // Get the network
+ CyNetwork net = getNetwork(MAKECURRENT, netName);
+
+ Cytoscape.setCurrentNetwork(netName);
+ result.addMessage("network: set current network to "+netName);
+
+ // Return a list of all networks
+ } else if (command.equals(LIST)) {
+ Set<CyNetwork>networkList = Cytoscape.getNetworkSet();
+ result.addMessage("network: network list:");
+ result.addResult("networks",networkList);
+ for (CyNetwork net: networkList) {
+ result.addMessage(" "+net.getIdentifier()+": "+net.getTitle());
+ }
+
+ } else {
+ throw new CyCommandException("network: unknown command "+command);
+ }
+
+ return result;
+ }
+
+ public static CyCommandHandler register(String namespace) throws RuntimeException {
+ // Get the namespace
+ CyCommandNamespace ns = CyCommandManager.reserveNamespace(namespace);
+
+ // Handle the simple commands ourselves
+ CyCommandHandler net = new NetworkNamespace(ns);
+
+ // Now register the more complicated commands
+ new AddEdgeNetwork(ns);
+ new AddNodeNetwork(ns);
+ new CreateNetwork(ns);
+ new ExportNetwork(ns);
+ new ImportNetwork(ns);
+
+ return net;
+ }
+}
diff --git a/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/NetworkViewNamespace.java b/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/NetworkViewNamespace.java
new file mode 100644
index 0000000..1dc2536
--- /dev/null
+++ b/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/NetworkViewNamespace.java
@@ -0,0 +1,242 @@
+/* vim: set ts=2: */
+/**
+ * Copyright (c) 2009 The Regents of the University of California.
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ * notice, this list of conditions, and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above
+ * copyright notice, this list of conditions, and the following
+ * disclaimer in the documentation and/or other materials provided
+ * with the distribution.
+ * 3. Redistributions must acknowledge that this software was
+ * originally developed by the UCSF Computer Graphics Laboratory
+ * under support by the NIH National Center for Research Resources,
+ * grant P41-RR01081.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY
+ * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+ * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+ * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
+ * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ */
+package coreCommands.namespaces;
+
+import cytoscape.CyEdge;
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+import cytoscape.CytoscapeInit;
+import cytoscape.command.AbstractCommandHandler;
+import cytoscape.command.CyCommandException;
+import cytoscape.command.CyCommandHandler;
+import cytoscape.command.CyCommandManager;
+import cytoscape.command.CyCommandNamespace;
+import cytoscape.command.CyCommandResult;
+import cytoscape.ding.DingNetworkView;
+import cytoscape.layout.Tunable;
+import cytoscape.logger.CyLogger;
+import cytoscape.view.CyNetworkView;
+import cytoscape.view.InternalFrameComponent;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import coreCommands.namespaces.AbstractGraphObjectHandler;
+import coreCommands.namespaces.networkView.ExportNetworkView;
+
+/**
+ * XXX FIXME XXX Description
+ */
+public class NetworkViewNamespace extends AbstractGraphObjectHandler {
+ static String NETWORKVIEW = "networkview";
+
+ static String CREATE = "create";
+ static String FIT = "fit";
+ static String FOCUS = "focus";
+ static String GETCURRENT = "get current";
+ static String GETSIZE = "get size";
+ static String LIST = "list";
+ static String MAKECURRENT = "make current";
+ static String SETWINDOW = "set window";
+ static String UPDATE = "update";
+ static String ZOOM = "zoom";
+
+ static String NETWORK = "network";
+ static String CURRENT = "current";
+ static String NODELIST = "nodelist";
+ static String FACTOR = "factor";
+ static String SCALE = "scale";
+
+ public NetworkViewNamespace(CyCommandNamespace ns) {
+ super(ns);
+
+ // Define our subcommands
+ addDescription(CREATE,"Create a network view for the named network");
+ addArgument(CREATE, NETWORK, CURRENT);
+
+ addDescription(GETCURRENT,"Return the name of the current network view");
+ addArgument(GETCURRENT);
+
+ // addDescription(GETSIZE,"Return the size of the named network view");
+ // addArgument(GETSIZE, "network", "current");
+
+ addDescription(FIT,"Fit the named network view to the window");
+ addArgument(FIT, NETWORK, CURRENT);
+
+ addDescription(FOCUS,"Focus the network view (zoom+pan) to the list of nodes");
+ addArgument(FOCUS, NODELIST);
+ addArgument(FOCUS, NETWORK, CURRENT);
+
+ addDescription(LIST,"Return a list of all network views");
+ addArgument(LIST);
+
+ addDescription(MAKECURRENT,"Make the named network view the 'current' network view");
+ addArgument(MAKECURRENT, NETWORK);
+
+ // addDescription(SETWINDOW,"Sets the window size parameters");
+ // addArgument(SETWINDOW, "network", "current");
+ // addArgument(SETWINDOW, "x");
+ // addArgument(SETWINDOW, "y");
+ // addArgument(SETWINDOW, "height");
+ // addArgument(SETWINDOW, "width");
+
+ addDescription(UPDATE,"Update (redraw) the named network view");
+ addArgument(UPDATE, NETWORK, CURRENT);
+
+ addDescription(ZOOM,"Zoom the named network view");
+ addArgument(ZOOM, FACTOR, "2.0");
+ addArgument(ZOOM, SCALE);
+ addArgument(ZOOM, NETWORK, CURRENT);
+ }
+
+ public CyCommandResult execute(String command, Collection<Tunable>args) throws CyCommandException {
+ return execute(command, createKVMap(args));
+ }
+
+ public CyCommandResult execute(String command, Map<String, Object>args) throws CyCommandException {
+ CyCommandResult result = new CyCommandResult();
+ Map<String, CyNetworkView> viewMap = Cytoscape.getNetworkViewMap();
+ CyNetwork net = Cytoscape.getCurrentNetwork();
+
+ if (command.equals(GETCURRENT)) {
+ CyNetworkView current = Cytoscape.getCurrentNetworkView();
+ result.addMessage("networkview: current network view is "+current.getIdentifier());
+ result.addResult("currentview", current);
+ return result;
+ } else if (command.equals(LIST)) {
+ result.addResult("views",viewMap.keySet());
+
+ result.addMessage("networkview: current network views:");
+ for (String key: viewMap.keySet()) {
+ result.addMessage(" "+key);
+ }
+ return result;
+ }
+
+ net = getNetwork(command, args);
+ if (!viewMap.containsKey(net.getIdentifier()) && !command.equals("create"))
+ throw new CyCommandException("networkview: can't find view for network: "+net.getTitle());
+
+ if (command.equals(CREATE)) {
+ CyNetworkView view = Cytoscape.createNetworkView(net);
+ result.addResult("newview",view);
+ result.addMessage("networkview: created view for :"+view.getIdentifier());
+
+ } else if (command.equals(MAKECURRENT)) {
+ Cytoscape.setCurrentNetworkView(net.getIdentifier());
+ result.addMessage("networkview: set network view for "+net.getTitle()+" as current");
+ } else if (command.equals(FIT)) {
+ CyNetworkView view = viewMap.get(net.getIdentifier());
+ view.fitContent();
+ result.addMessage("networkview: fit view to content for "+net.getTitle());
+
+ } else if (command.equals(UPDATE)) {
+ CyNetworkView view = viewMap.get(net.getIdentifier());
+ view.updateView();
+ result.addMessage("networkview: view '"+net.getTitle()+"' updated");
+
+ } else if (command.equals(FOCUS)) {
+ CyNetworkView view = viewMap.get(net.getIdentifier());
+ String nodes = getArg(command, NODELIST, args);
+ if (nodes == null || nodes.length() == 0) {
+ ((DingNetworkView) view).fitSelected();
+ view.updateView();
+ result.addMessage("networkview: focused '"+net.getTitle()+"' on selected nodes/edges");
+ } else {
+ // get the list of nodes
+ List<CyNode> nodeList = getNodeList(net, result, args);
+
+ // Remember our currently selected nodes and edges
+ List<CyNode>selNodes = new ArrayList(net.getSelectedNodes());
+ List<CyEdge>selEdges = new ArrayList(net.getSelectedEdges());
+
+ // Select the desire nodes
+ net.unselectAllEdges();
+ net.unselectAllNodes();
+ net.setSelectedNodeState(nodeList, true);
+
+ // focus
+ ((DingNetworkView) view).fitSelected();
+
+ // Reselect the previously selected nodes and edges
+ net.setSelectedNodeState(nodeList, false);
+ net.setSelectedNodeState(selNodes, true);
+ net.setSelectedEdgeState(selEdges, true);
+
+ view.updateView();
+ result.addMessage("networkview: focused '"+net.getIdentifier()+"' on node(s)");
+ }
+ } else if (command.equals(ZOOM)) {
+ CyNetworkView view = viewMap.get(net.getIdentifier());
+ double factor = Double.parseDouble(getArg(command, FACTOR, args));
+ String scale = getArg(command, SCALE, args);
+ double zoom = view.getZoom();
+ // If we have a scale, use that -- otherwise, use the factor
+ if (scale != null) {
+ view.setZoom(Double.parseDouble(scale));
+ } else {
+ view.setZoom(zoom*factor);
+ }
+ result.addMessage("networkview: network '"+net.getIdentifier()+"' zoom set to "+view.getZoom());
+ result.addResult("scale", new Double(view.getZoom()));
+
+ // } else if (command.equals("get size")) {
+
+ // } else if (command.equals("set window")) {
+
+ } else {
+ throw new CyCommandException("networkview: unknown command "+command);
+ }
+
+ return result;
+ }
+
+ public static CyCommandHandler register(String namespace) throws RuntimeException {
+ // Get the namespace
+ CyCommandNamespace ns = CyCommandManager.reserveNamespace(namespace);
+
+ // We'll handle the simple stuff ourselves
+ CyCommandHandler h = new NetworkViewNamespace(ns);
+
+ // Now register the export stuff
+ new ExportNetworkView(ns);
+
+ return h;
+ }
+
+}
diff --git a/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/NodeNamespace.java b/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/NodeNamespace.java
new file mode 100644
index 0000000..94a9415
--- /dev/null
+++ b/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/NodeNamespace.java
@@ -0,0 +1,290 @@
+/* vim: set ts=2: */
+/**
+ * Copyright (c) 2009 The Regents of the University of California.
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ * notice, this list of conditions, and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above
+ * copyright notice, this list of conditions, and the following
+ * disclaimer in the documentation and/or other materials provided
+ * with the distribution.
+ * 3. Redistributions must acknowledge that this software was
+ * originally developed by the UCSF Computer Graphics Laboratory
+ * under support by the NIH National Center for Research Resources,
+ * grant P41-RR01081.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY
+ * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+ * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+ * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
+ * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ */
+package coreCommands.namespaces;
+
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+import cytoscape.command.AbstractCommandHandler;
+import cytoscape.command.CyCommandException;
+import cytoscape.command.CyCommandHandler;
+import cytoscape.command.CyCommandManager;
+import cytoscape.command.CyCommandNamespace;
+import cytoscape.command.CyCommandResult;
+import cytoscape.data.CyAttributes;
+import cytoscape.layout.Tunable;
+import cytoscape.logger.CyLogger;
+import cytoscape.view.CyNetworkView;
+
+import giny.model.GraphObject;
+
+import java.io.IOException;
+import java.io.File;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import coreCommands.namespaces.node.ExportNodeAttributes;
+
+/**
+ * XXX FIXME XXX Description
+ */
+public class NodeNamespace extends AbstractGraphObjectHandler {
+
+ // Commands
+ private static String DELETE = "delete";
+ private static String DESELECT = "deselect";
+ private static String FIND = "find";
+ private static String GETATTR = "get attribute";
+ private static String GETSEL = "get selected";
+ private static String IMPORTATTR = "import attributes";
+ private static String SELECT = "select";
+ private static String SETATTR = "set attribute";
+ private static String LISTATTR = "list attributes";
+
+ // Settings
+ private static String EXPRESSION = "expression";
+ private static String FILE = "file";
+ private static String NAME = "name";
+ private static String NETWORK = "network";
+ private static String NODE = "node";
+ private static String NODELIST = "nodelist";
+ private static String TYPE = "type";
+ private static String VALUE = "value";
+
+ public NodeNamespace(CyCommandNamespace ns) {
+ super(ns);
+
+ // Define our subcommands
+ addDescription(DELETE, "Delete a node or group of nodes.");
+ addArgument(DELETE, NODE);
+ addArgument(DELETE, NODELIST);
+
+ addDescription(DESELECT, "Deselect nodes. If no node(s) are provided, all nodes are deselected");
+ addArgument(DESELECT, NODE);
+ addArgument(DESELECT, NODELIST);
+
+ //
+ // addArgument(FIND, EXPRESSION);
+
+ addDescription(GETATTR, "Returns node attributes");
+ addArgument(GETATTR, NODE);
+ addArgument(GETATTR, NODELIST);
+ addArgument(GETATTR, NAME);
+
+ addDescription(GETSEL, "Lists the currently selected nodes");
+ addArgument(GETSEL, NETWORK, "current");
+
+ addDescription(IMPORTATTR, "Import node attributes from a file");
+ addArgument(IMPORTATTR, FILE);
+
+ addDescription(LISTATTR, "List node attributes");
+ addArgument(LISTATTR);
+
+ addDescription(SELECT, "Select nodes. If no node(s) are provided, all nodes are selected");
+ addArgument(SELECT, NODE);
+ addArgument(SELECT, NODELIST);
+
+ addDescription(SETATTR, "Set node attributes to a new value");
+ addArgument(SETATTR, NODE);
+ addArgument(SETATTR, NODELIST);
+ addArgument(SETATTR, NAME);
+ addArgument(SETATTR, VALUE);
+ addArgument(SETATTR, TYPE);
+ }
+
+ public CyCommandResult execute(String command, Collection<Tunable>args) throws CyCommandException {
+ return execute(command, createKVMap(args));
+ }
+
+ public CyCommandResult execute(String command, Map<String, Object>args) throws CyCommandException {
+ CyCommandResult result = new CyCommandResult();
+
+ // Import node attributes from a file
+ if (IMPORTATTR.equals(command)) {
+ String fileName = getArg(command, FILE, args);
+ if (fileName == null)
+ throw new CyCommandException("node: filename is required to import attributes");
+ try {
+ File file = new File(fileName);
+ Cytoscape.loadAttributes(new String[] { file.getAbsolutePath() },
+ new String[] {});
+ result.addMessage("node: attributes imported from "+file.getAbsolutePath());
+ } catch (Exception e) {
+ throw new CyCommandException("node: unable to import attributes: "+e.getMessage());
+ }
+
+ // Export node attributes to a file
+ // } else if ("export attributes".equals(command)) {
+
+ // Select some ndoes
+ } else if (SELECT.equals(command)) {
+ CyNetwork net = getNetwork(command, args);
+ List<CyNode> nodeList = getNodeList(net, result, args);
+ if (nodeList == null) {
+ net.selectAllNodes();
+ result.addMessage("node: selected all nodes");
+ } else {
+ net.setSelectedNodeState(nodeList, true);
+ result.addMessage("node: selected "+nodeList.size()+" nodes");
+ }
+ if (net == Cytoscape.getCurrentNetwork()) {
+ Cytoscape.getCurrentNetworkView().updateView();
+ }
+
+ // de-select some ndoes
+ } else if (DESELECT.equals(command)) {
+ CyNetwork net = getNetwork(command, args);
+ List<CyNode> nodeList = getNodeList(net, result, args);
+ if (nodeList == null) {
+ net.unselectAllNodes();
+ result.addMessage("node: deselected all nodes");
+ } else {
+ net.setSelectedNodeState(nodeList, false);
+ result.addMessage("node: deselected "+nodeList.size()+" nodes");
+ }
+
+ if (net == Cytoscape.getCurrentNetwork()) {
+ Cytoscape.getCurrentNetworkView().updateView();
+ }
+
+ // delete some ndoes
+ } else if (DELETE.equals(command)) {
+ CyNetwork net = getNetwork(command, args);
+ List<CyNode> nodeList = getNodeList(net, result, args);
+ if (nodeList == null)
+ throw new CyCommandException("node: nothing to delete");
+
+ for (CyNode node: nodeList) {
+ net.removeNode(node.getRootGraphIndex(), false);
+ }
+ result.addMessage("node: deleted "+nodeList.size()+" nodes");
+ if (net == Cytoscape.getCurrentNetwork()) {
+ Cytoscape.getCurrentNetworkView().updateView();
+ }
+
+ // return the list of currently selected nodes
+ } else if (GETSEL.equals(command)) {
+ CyNetwork net = getNetwork(command, args);
+ Set<CyNode>nodes = net.getSelectedNodes();
+ result.addMessage("node: returned "+nodes.size()+" selected nodes");
+ result.addResult("nodes", makeNodeList(nodes));
+
+ // Get attribute values
+ } else if (GETATTR.equals(command)) {
+ CyNetwork net = getNetwork(command, args);
+ CyAttributes nodeAttributes = Cytoscape.getNodeAttributes();
+ String attrName = getArg(command, NAME, args);
+ if (attrName == null)
+ throw new CyCommandException("node: attribute 'name' is required");
+ else if (nodeAttributes.getType(attrName) == CyAttributes.TYPE_UNDEFINED)
+ throw new CyCommandException("node: attribute 'name' does not exist");
+
+ List<CyNode> nodeList = getNodeList(net, result, args);
+ if (nodeList == null)
+ nodeList = net.nodesList();
+
+ byte attributeType = nodeAttributes.getType(attrName);
+ result.addResult("attribute type", attributeType);
+ result.addMessage("node: values for '"+attrName+"' attribute:");
+ for (CyNode node: nodeList) {
+ if (nodeAttributes.hasAttribute(node.getIdentifier(), attrName)) {
+ Object attr = nodeAttributes.getAttribute(node.getIdentifier(), attrName);
+ result.addResult(node.getIdentifier(), attr);
+ result.addMessage(" "+node.getIdentifier()+"='"+AttributeUtils.attributeToString(attr, attributeType)+"'");
+ }
+ }
+
+ // Set attribute values
+ } else if (SETATTR.equals(command)) {
+ CyNetwork net = getNetwork(command, args);
+ CyAttributes nodeAttributes = Cytoscape.getNodeAttributes();
+ String attrName = getArg(command, NAME, args);
+ String value = getArg(command, VALUE, args);
+ if (attrName == null || value == null)
+ throw new CyCommandException("node: attribute 'name' and 'value' are required");
+
+ List<CyNode> nodeList = getNodeList(net, result, args);
+ if (nodeList == null)
+ nodeList = net.nodesList();
+
+ String typeName = getArg(command, TYPE, args);
+ byte attributeType = nodeAttributes.getType(attrName);
+ if (attributeType == CyAttributes.TYPE_UNDEFINED && typeName == null)
+ attributeType = CyAttributes.TYPE_STRING;
+ else if (attributeType == CyAttributes.TYPE_UNDEFINED && typeName != null) {
+ attributeType = AttributeUtils.attributeStringToByte(typeName);
+ }
+
+ int count = 0;
+ int nodeCount = nodeList.size();
+ for (CyNode node: nodeList) {
+ String id = node.getIdentifier();
+ if (AttributeUtils.setAttribute(result, "node", nodeAttributes, attributeType, id, attrName, value))
+ count++;
+ }
+ result.addMessage("node: set "+count+" attributes (out of "+nodeCount+")");
+
+ // find nodes based on an expression
+ } else if ("find".equals(command)) {
+
+ // list node attributes
+ } else if (LISTATTR.equals(command)) {
+ CyNetwork net = getNetwork(command, args);
+ CyAttributes nodeAttributes = Cytoscape.getNodeAttributes();
+ String[] attrNames = nodeAttributes.getAttributeNames();
+ List<String>attrList = Arrays.asList(attrNames);
+ result.addResult(attrList);
+ result.addMessage("Node attributes: "+AttributeUtils.attributeNamesToList(nodeAttributes, attrList));
+ }
+
+ return result;
+ }
+
+ public static CyCommandHandler register(String namespace) throws RuntimeException {
+ // Get the namespace
+ CyCommandNamespace ns = CyCommandManager.reserveNamespace(namespace);
+
+ // Handle the simple commands ourselves
+ CyCommandHandler nodeNS = new NodeNamespace(ns);
+
+ // More elaborate commands are in separate classes
+ new ExportNodeAttributes(ns);
+
+ return nodeNS;
+ }
+}
diff --git a/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/PropertyNamespace.java b/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/PropertyNamespace.java
new file mode 100644
index 0000000..525fd4d
--- /dev/null
+++ b/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/PropertyNamespace.java
@@ -0,0 +1,116 @@
+/* vim: set ts=2: */
+/**
+ * Copyright (c) 2009 The Regents of the University of California.
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ * notice, this list of conditions, and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above
+ * copyright notice, this list of conditions, and the following
+ * disclaimer in the documentation and/or other materials provided
+ * with the distribution.
+ * 3. Redistributions must acknowledge that this software was
+ * originally developed by the UCSF Computer Graphics Laboratory
+ * under support by the NIH National Center for Research Resources,
+ * grant P41-RR01081.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY
+ * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+ * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+ * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
+ * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ */
+package coreCommands.namespaces;
+
+import cytoscape.Cytoscape;
+import cytoscape.CytoscapeInit;
+import cytoscape.command.AbstractCommandHandler;
+import cytoscape.command.CyCommandException;
+import cytoscape.command.CyCommandHandler;
+import cytoscape.command.CyCommandManager;
+import cytoscape.command.CyCommandNamespace;
+import cytoscape.command.CyCommandResult;
+import cytoscape.layout.Tunable;
+import cytoscape.logger.CyLogger;
+import cytoscape.view.CyNetworkView;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Properties;
+
+/**
+ * XXX FIXME XXX Description
+ */
+public class PropertyNamespace extends AbstractCommandHandler {
+ static String PROPERTY = "property";
+
+ static String SET = "set";
+ static String GET = "get";
+ static String CLEAR = "clear";
+
+ static String NAME = "name";
+ static String VALUE = "value";
+
+ public PropertyNamespace(CyCommandNamespace ns) {
+ super(ns);
+
+ // Define our subcommands
+ addDescription(SET, "Sets a Cytoscape property");
+ addArgument(SET, NAME);
+ addArgument(SET, VALUE);
+
+ addDescription(GET, "Gets the value of a Cytoscape property");
+ addArgument(GET, NAME);
+
+ addDescription(CLEAR, "Clears the value of a Cytoscape property");
+ addArgument(CLEAR, NAME);
+ }
+
+ public CyCommandResult execute(String command, Collection<Tunable>args) throws CyCommandException {
+ return execute(command, createKVMap(args));
+ }
+
+ public CyCommandResult execute(String command, Map<String, Object>args) throws CyCommandException {
+ CyCommandResult result = new CyCommandResult();
+ Properties props = CytoscapeInit.getProperties();
+
+ if (args == null || args.size() == 0 || !args.containsKey(NAME))
+ throw new CyCommandException("property: no property name to "+command);
+
+ String propertyName = args.get(NAME).toString();
+ if (SET.equals(command)) {
+ if (!args.containsKey(VALUE))
+ throw new CyCommandException("property: no 'value' to set "+propertyName+" to");
+ props.setProperty(propertyName, args.get(VALUE).toString());
+ result.addMessage("property: set "+propertyName+" to "+args.get(VALUE).toString());
+
+ } else if (GET.equals(command)) {
+ String value = props.getProperty(propertyName);
+ result.addMessage("property: "+propertyName+" = "+value);
+ result.addResult(propertyName, value);
+
+ } else if (CLEAR.equals(command)) {
+ props.remove(propertyName);
+ result.addMessage("property: cleared "+propertyName);
+ }
+ return result;
+ }
+
+ public static CyCommandHandler register(String namespace) throws RuntimeException {
+ // Get the namespace
+ return new PropertyNamespace(CyCommandManager.reserveNamespace(namespace));
+ }
+}
diff --git a/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/QuitNamespace.java b/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/QuitNamespace.java
new file mode 100644
index 0000000..d81380d
--- /dev/null
+++ b/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/QuitNamespace.java
@@ -0,0 +1,79 @@
+/* vim: set ts=2: */
+/**
+ * Copyright (c) 2009 The Regents of the University of California.
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ * notice, this list of conditions, and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above
+ * copyright notice, this list of conditions, and the following
+ * disclaimer in the documentation and/or other materials provided
+ * with the distribution.
+ * 3. Redistributions must acknowledge that this software was
+ * originally developed by the UCSF Computer Graphics Laboratory
+ * under support by the NIH National Center for Research Resources,
+ * grant P41-RR01081.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY
+ * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+ * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+ * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
+ * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ */
+package coreCommands.namespaces;
+
+import cytoscape.Cytoscape;
+import cytoscape.CytoscapeInit;
+import cytoscape.command.AbstractCommandHandler;
+import cytoscape.command.CyCommandException;
+import cytoscape.command.CyCommandHandler;
+import cytoscape.command.CyCommandManager;
+import cytoscape.command.CyCommandNamespace;
+import cytoscape.command.CyCommandResult;
+import cytoscape.layout.Tunable;
+import cytoscape.logger.CyLogger;
+import cytoscape.view.CyNetworkView;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Properties;
+
+/**
+ * XXX FIXME XXX Description
+ */
+public class QuitNamespace extends AbstractCommandHandler {
+
+ public QuitNamespace(CyCommandNamespace ns) {
+ super(ns);
+ addDescription("", "Exits Cytoscape");
+ addArgument("");
+ }
+
+ public CyCommandResult execute(String command, Collection<Tunable>args) throws CyCommandException {
+ System.exit(0);
+ return null;
+ }
+
+ public CyCommandResult execute(String command, Map<String, Object>args) throws CyCommandException {
+ System.exit(0);
+ return null;
+ }
+
+ public static CyCommandHandler register(String namespace) throws RuntimeException {
+ // Get the namespace
+ return new QuitNamespace(CyCommandManager.reserveNamespace(namespace));
+ }
+}
diff --git a/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/SessionNamespace.java b/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/SessionNamespace.java
new file mode 100644
index 0000000..84f1034
--- /dev/null
+++ b/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/SessionNamespace.java
@@ -0,0 +1,154 @@
+/* vim: set ts=2: */
+/**
+ * Copyright (c) 2009 The Regents of the University of California.
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ * notice, this list of conditions, and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above
+ * copyright notice, this list of conditions, and the following
+ * disclaimer in the documentation and/or other materials provided
+ * with the distribution.
+ * 3. Redistributions must acknowledge that this software was
+ * originally developed by the UCSF Computer Graphics Laboratory
+ * under support by the NIH National Center for Research Resources,
+ * grant P41-RR01081.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY
+ * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+ * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+ * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
+ * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ */
+package coreCommands.namespaces;
+
+import cytoscape.Cytoscape;
+import cytoscape.command.AbstractCommandHandler;
+import cytoscape.command.CyCommandException;
+import cytoscape.command.CyCommandHandler;
+import cytoscape.command.CyCommandManager;
+import cytoscape.command.CyCommandNamespace;
+import cytoscape.command.CyCommandResult;
+import cytoscape.data.readers.CytoscapeSessionReader;
+import cytoscape.data.writers.CytoscapeSessionWriter;
+import cytoscape.layout.Tunable;
+import cytoscape.logger.CyLogger;
+import cytoscape.view.CyNetworkView;
+
+import java.io.File;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+/**
+ * XXX FIXME XXX Description
+ */
+public class SessionNamespace extends AbstractCommandHandler {
+ static String SESSION = "session";
+
+ static String OPEN = "open";
+ static String NEW = "new";
+ static String SAVE = "save";
+
+ static String FILE = "file";
+
+ public SessionNamespace(CyCommandNamespace ns) {
+ super(ns);
+
+ // Define our subcommands
+ addDescription(OPEN, "Open an existing Cytoscape session");
+ addArgument(OPEN, FILE);
+
+ addDescription(NEW, "Create a new (empty) Cytoscape session");
+ addArgument(NEW);
+
+ addDescription(SAVE, "Save the current Cytoscape session into a file");
+ addArgument(SAVE, FILE);
+ }
+
+ public CyCommandResult execute(String command, Collection<Tunable>args) throws CyCommandException {
+ return execute(command, createKVMap(args));
+ }
+
+ public CyCommandResult execute(String command, Map<String, Object>args) throws CyCommandException {
+ CyCommandResult result = new CyCommandResult();
+
+ if (command.equals(OPEN)) {
+ // Load a session from a file
+ String fileName = null;
+ if (args.containsKey(FILE))
+ fileName = args.get(FILE).toString();
+ else
+ throw new CyCommandException("session: need file argument to open a session");
+
+ // Close all networks in the workspace.
+ Cytoscape.setSessionState(Cytoscape.SESSION_OPENED);
+ Cytoscape.createNewSession();
+ Cytoscape.setSessionState(Cytoscape.SESSION_NEW);
+
+ try {
+ CytoscapeSessionReader reader = new CytoscapeSessionReader(fileName);
+ reader.read();
+ } catch (Exception e) {
+ throw new CyCommandException("session: unable to open session file "+
+ fileName+": "+e.getMessage());
+ }
+
+ result.addMessage("session: opened session: "+fileName);
+
+ // TODO: figure some things out about the session
+ // TODO: Get the number of networks
+ // TODO: Get the current network
+
+ } else if (command.equals(NEW)) {
+ // Create a new session
+ Cytoscape.setSessionState(Cytoscape.SESSION_OPENED);
+ Cytoscape.createNewSession();
+ Cytoscape.getDesktop().setTitle("Cytoscape Desktop (New Session)");
+ Cytoscape.getDesktop().getNetworkPanel().repaint();
+ Cytoscape.getDesktop().repaint();
+ Cytoscape.setSessionState(Cytoscape.SESSION_NEW);
+ Cytoscape.getPropertyChangeSupport().firePropertyChange(Cytoscape.CYTOSCAPE_INITIALIZED, null, null);
+ result.addMessage("session: created new session");
+
+ } else if (command.equals(SAVE)) {
+ // Save a session. If no file argument is given, save the current session
+ String fileName = null;
+ if (args.containsKey(FILE))
+ fileName = args.get(FILE).toString();
+ else
+ fileName = Cytoscape.getCurrentSessionFileName();
+
+ if (!fileName.endsWith(".cys"))
+ fileName = fileName + ".cys";
+
+ try {
+ CytoscapeSessionWriter writer = new CytoscapeSessionWriter(fileName);
+ writer.writeSessionToDisk();
+ } catch (Exception e) {
+ throw new CyCommandException("session: unable to save session file "+
+ fileName+": "+e.getMessage());
+ }
+ result.addMessage("session: saved session to file "+fileName);
+ }
+ return result;
+ }
+
+ public static CyCommandHandler register(String namespace) throws RuntimeException {
+ // Get the namespace
+ return new SessionNamespace(CyCommandManager.reserveNamespace(namespace));
+ }
+}
diff --git a/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/VizMapNamespace.java b/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/VizMapNamespace.java
new file mode 100644
index 0000000..93b2460
--- /dev/null
+++ b/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/VizMapNamespace.java
@@ -0,0 +1,147 @@
+/* vim: set ts=2: */
+/**
+ * Copyright (c) 2009 The Regents of the University of California.
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ * notice, this list of conditions, and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above
+ * copyright notice, this list of conditions, and the following
+ * disclaimer in the documentation and/or other materials provided
+ * with the distribution.
+ * 3. Redistributions must acknowledge that this software was
+ * originally developed by the UCSF Computer Graphics Laboratory
+ * under support by the NIH National Center for Research Resources,
+ * grant P41-RR01081.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY
+ * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+ * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+ * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
+ * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ */
+package coreCommands.namespaces;
+
+import cytoscape.Cytoscape;
+import cytoscape.command.AbstractCommandHandler;
+import cytoscape.command.CyCommandException;
+import cytoscape.command.CyCommandHandler;
+import cytoscape.command.CyCommandManager;
+import cytoscape.command.CyCommandNamespace;
+import cytoscape.command.CyCommandResult;
+import cytoscape.layout.Tunable;
+import cytoscape.logger.CyLogger;
+import cytoscape.view.CyNetworkView;
+import cytoscape.visual.CalculatorCatalog;
+import cytoscape.visual.VisualMappingManager;
+import cytoscape.visual.VisualStyle;
+
+import java.io.File;
+
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+/**
+ * This Command provides a set of subcommands related to the management
+ * and setting of VizMaps
+ */
+public class VizMapNamespace extends AbstractCommandHandler {
+ String styleName = "default";
+ CyLogger logger = CyLogger.getLogger(VizMapNamespace.class);
+
+ static String VIZMAP = "vizmap";
+ static String APPLY = "apply";
+ static String IMPORT = "import";
+
+ static String STYLE = "style";
+ static String FILE = "file";
+ static String NETWORK = "network";
+ static String CURRENT = "current";
+
+ public VizMapNamespace(CyCommandNamespace ns) {
+ super(ns);
+
+ // Define our subcommands
+ addDescription(APPLY, "Apply the named visual style to the current (or named) network");
+ addArgument(APPLY);
+ addArgument(APPLY, STYLE, "default");
+ addArgument(APPLY, NETWORK, CURRENT);
+
+ addDescription(IMPORT, "Import a visual style from a file");
+ addArgument(IMPORT, FILE, null);
+ }
+
+ public CyCommandResult execute(String command, Collection<Tunable>args) throws CyCommandException {
+ return execute(command, createKVMap(args));
+ }
+
+ public CyCommandResult execute(String command, Map<String, Object>args) throws CyCommandException {
+ CyCommandResult result = new CyCommandResult();
+ if (command.equals(APPLY)) {
+ // We want to apply a vizmap to the current network
+ if (args.containsKey(STYLE))
+ styleName = args.get(STYLE).toString();
+
+ CyNetworkView networkView;
+
+ if (args.containsKey(NETWORK) && !args.get(NETWORK).equals(CURRENT)) {
+ networkView = Cytoscape.getNetworkView(args.get(NETWORK).toString());
+ if (networkView == null)
+ throw new CyCommandException("Can't find view for network "+args.get(NETWORK).toString());
+ } else
+ networkView = Cytoscape.getCurrentNetworkView();
+
+ // Make sure the style exists
+ VisualMappingManager vizMapper =
+ new VisualMappingManager(networkView);
+
+ // We need to get the visual style directly from the catalog because,
+ // unlike what the documentation says, setVisualStyle does /not/ return
+ // null if the style doesn't exist!
+ CalculatorCatalog catalog = vizMapper.getCalculatorCatalog();
+ VisualStyle vs = catalog.getVisualStyle(styleName);
+ if (vs == null)
+ throw new CyCommandException("Unknown style "+styleName);
+ vizMapper.setVisualStyle(vs);
+
+ vizMapper.applyAppearances();
+ networkView.updateView();
+ result.addMessage("vizmap: applied style "+styleName);
+ return result;
+ } else if (command.equals(IMPORT)) {
+ if (!args.containsKey(FILE) || args.get(FILE) == null)
+ throw new CyCommandException("vizmap: no filename specified for import");
+
+ File file = new File(args.get(FILE).toString());
+
+ // Do a little sanity checking....
+ if (!file.exists())
+ throw new CyCommandException("vizmap: no such file: "+file.getAbsolutePath());
+ if (!file.canRead())
+ throw new CyCommandException("vizmap: can't read the file: "+file.getAbsolutePath());
+
+ Cytoscape.firePropertyChange(Cytoscape.VIZMAP_LOADED, null, file.getAbsolutePath());
+ result.addMessage("vizmap: new style imported");
+ return result;
+ }
+ throw new CyCommandException("vizmap: unknown subcommand: "+command);
+ }
+
+ public static CyCommandHandler register(String namespace) throws RuntimeException {
+ // Get the namespace
+ return new VizMapNamespace(CyCommandManager.reserveNamespace(namespace));
+ }
+
+}
diff --git a/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/edge/ExportEdgeAttributes.java b/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/edge/ExportEdgeAttributes.java
new file mode 100644
index 0000000..8d9af4f
--- /dev/null
+++ b/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/edge/ExportEdgeAttributes.java
@@ -0,0 +1,144 @@
+/* vim: set ts=2: */
+/**
+ * Copyright (c) 2009 The Regents of the University of California.
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ * notice, this list of conditions, and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above
+ * copyright notice, this list of conditions, and the following
+ * disclaimer in the documentation and/or other materials provided
+ * with the distribution.
+ * 3. Redistributions must acknowledge that this software was
+ * originally developed by the UCSF Computer Graphics Laboratory
+ * under support by the NIH National Center for Research Resources,
+ * grant P41-RR01081.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY
+ * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+ * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+ * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
+ * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ */
+package coreCommands.namespaces.edge;
+
+import cytoscape.CyNetwork;
+import cytoscape.CyEdge;
+import cytoscape.Cytoscape;
+import cytoscape.command.CyCommandException;
+import cytoscape.command.CyCommandHandler;
+import cytoscape.command.CyCommandManager;
+import cytoscape.command.CyCommandNamespace;
+import cytoscape.command.CyCommandResult;
+import cytoscape.data.CyAttributes;
+import cytoscape.layout.Tunable;
+import cytoscape.logger.CyLogger;
+import cytoscape.view.CyNetworkView;
+
+import giny.model.GraphObject;
+
+import java.io.IOException;
+import java.io.File;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import coreCommands.namespaces.AbstractGraphObjectHandler;
+import coreCommands.namespaces.AttributeUtils;
+
+/**
+ * XXX FIXME XXX Description
+ */
+public class ExportEdgeAttributes extends AbstractGraphObjectHandler {
+
+ // Commands
+ private static String EXPORT = "export attributes";
+
+ // Settings
+ private static String ATTRIBUTE = "attributeList";
+ private static String DELIMITER = "delimiter";
+ private static String FILE = "file";
+ private static String NETWORK = "network";
+ private static String EDGELIST = "edgelist";
+
+ public ExportEdgeAttributes(CyCommandNamespace ns) {
+ super(ns);
+
+ // Define our subcommands
+ addDescription(EXPORT, "Export edge attributes as a table");
+ addArgument(EXPORT, FILE);
+ addArgument(EXPORT, ATTRIBUTE);
+ addArgument(EXPORT, DELIMITER);
+ addArgument(EXPORT, NETWORK, "current");
+ addArgument(EXPORT, EDGELIST);
+ }
+
+ public CyCommandResult execute(String command, Collection<Tunable>args) throws CyCommandException {
+ return execute(command, createKVMap(args));
+ }
+
+ public CyCommandResult execute(String command, Map<String, Object>args) throws CyCommandException {
+ CyCommandResult result = new CyCommandResult();
+
+ if (EXPORT.equals(command)) {
+ CyAttributes edgeAttributes = Cytoscape.getEdgeAttributes();
+ // Do we have a filename?
+ String fileName = getArg(command, FILE, args);
+ if (fileName == null)
+ throw new CyCommandException("edge: filename is required to export attributes");
+
+ // Get our delimiter
+ String delim = getArg(command, DELIMITER, args);
+ if (delim == null)
+ delim = "\t";
+
+ // Get the attribute list
+ String[] attrArray;
+ String attrStr = getArg(command, ATTRIBUTE, args);
+ if (attrStr == null) {
+ attrArray = edgeAttributes.getAttributeNames();
+ } else {
+ attrArray = attrStr.split(",");
+ }
+
+ List<String> attrList = Arrays.asList(attrArray);
+
+ // Get the edge list
+ CyNetwork net = getNetwork(command, args);
+ List edgeList = getEdgeList(net, result, args);
+ if (edgeList == null)
+ edgeList = net.edgesList();
+
+ int lineCount = 0;
+ try {
+ File outputFile = new File(fileName);
+ lineCount = AttributeUtils.exportAttributes(outputFile, edgeAttributes, edgeList, attrList, delim);
+ } catch (IOException e) {
+ throw new CyCommandException("edge: export failed: "+e.getMessage());
+ }
+ result.addMessage("edge: exported "+lineCount+" lines to "+fileName);
+ }
+
+ return result;
+ }
+
+ public static CyCommandHandler register(String namespace) throws RuntimeException {
+ // Get the namespace
+ return new ExportEdgeAttributes(CyCommandManager.reserveNamespace(namespace));
+ }
+
+}
diff --git a/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/network/AddEdgeNetwork.java b/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/network/AddEdgeNetwork.java
new file mode 100644
index 0000000..722087e
--- /dev/null
+++ b/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/network/AddEdgeNetwork.java
@@ -0,0 +1,97 @@
+/* vim: set ts=2: */
+/**
+ * Copyright (c) 2009 The Regents of the University of California.
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ * notice, this list of conditions, and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above
+ * copyright notice, this list of conditions, and the following
+ * disclaimer in the documentation and/or other materials provided
+ * with the distribution.
+ * 3. Redistributions must acknowledge that this software was
+ * originally developed by the UCSF Computer Graphics Laboratory
+ * under support by the NIH National Center for Research Resources,
+ * grant P41-RR01081.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY
+ * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+ * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+ * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
+ * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ */
+package coreCommands.namespaces.network;
+
+import cytoscape.CyEdge;
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+
+import cytoscape.command.CyCommandException;
+import cytoscape.command.CyCommandHandler;
+import cytoscape.command.CyCommandNamespace;
+import cytoscape.command.CyCommandResult;
+
+import coreCommands.namespaces.AbstractGraphObjectHandler;
+
+import cytoscape.layout.Tunable;
+import cytoscape.logger.CyLogger;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+/**
+ * XXX FIXME XXX Description
+ */
+public class AddEdgeNetwork extends AbstractGraphObjectHandler {
+
+ // Commands
+ static String ADDEDGE = "add edges";
+
+ // Arguments
+ static String NETWORK = "network";
+
+ public AddEdgeNetwork(CyCommandNamespace ns) {
+ super(ns);
+
+ // Define our subcommands
+ addDescription(ADDEDGE, "Add one or more new edges to a network");
+ addArgument(ADDEDGE, NETWORK);
+ addArgument(ADDEDGE, EDGE);
+ addArgument(ADDEDGE, EDGELIST);
+ }
+
+ public CyCommandResult execute(String command, Collection<Tunable>args) throws CyCommandException {
+ return execute(command, createKVMap(args));
+ }
+
+ public CyCommandResult execute(String command, Map<String, Object>args) throws CyCommandException {
+ CyCommandResult result = new CyCommandResult();
+
+ CyNetwork network = getNetwork(command, args);
+
+ List<CyEdge> edgeList = getEdgeList(network, result, args, true);
+ if (edgeList == null)
+ throw new CyCommandException("add edges requires an 'edge' or an 'edgelist' argument");
+ for (CyEdge edge: edgeList) {
+ network.addEdge(edge);
+ }
+ result.addMessage("Added "+edgeList.size()+" edge(s) to network "+network.getTitle());
+
+ return result;
+ }
+
+}
diff --git a/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/network/AddNodeNetwork.java b/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/network/AddNodeNetwork.java
new file mode 100644
index 0000000..3e9ab42
--- /dev/null
+++ b/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/network/AddNodeNetwork.java
@@ -0,0 +1,97 @@
+/* vim: set ts=2: */
+/**
+ * Copyright (c) 2009 The Regents of the University of California.
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ * notice, this list of conditions, and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above
+ * copyright notice, this list of conditions, and the following
+ * disclaimer in the documentation and/or other materials provided
+ * with the distribution.
+ * 3. Redistributions must acknowledge that this software was
+ * originally developed by the UCSF Computer Graphics Laboratory
+ * under support by the NIH National Center for Research Resources,
+ * grant P41-RR01081.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY
+ * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+ * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+ * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
+ * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ */
+package coreCommands.namespaces.network;
+
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+
+import cytoscape.command.CyCommandException;
+import cytoscape.command.CyCommandHandler;
+import cytoscape.command.CyCommandNamespace;
+import cytoscape.command.CyCommandResult;
+
+import coreCommands.namespaces.AbstractGraphObjectHandler;
+
+import cytoscape.layout.Tunable;
+import cytoscape.logger.CyLogger;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+/**
+ * XXX FIXME XXX Description
+ */
+public class AddNodeNetwork extends AbstractGraphObjectHandler {
+
+ // Commands
+ static String ADDNODE = "add nodes";
+
+ // Arguments
+ static String NETWORK = "network";
+
+ public AddNodeNetwork(CyCommandNamespace ns) {
+ super(ns);
+
+ // Define our subcommands
+ addDescription(ADDNODE, "Add one or more new nodes to a network");
+ addArgument(ADDNODE, NETWORK);
+ addArgument(ADDNODE, NODE, "New Node");
+ addArgument(ADDNODE, NODELIST);
+ }
+
+ public CyCommandResult execute(String command, Collection<Tunable>args) throws CyCommandException {
+ return execute(command, createKVMap(args));
+ }
+
+ public CyCommandResult execute(String command, Map<String, Object>args) throws CyCommandException {
+ CyCommandResult result = new CyCommandResult();
+
+ CyNetwork network = getNetwork(command, args);
+
+ List<CyNode> nodeList = getNodeList(network, result, args, true);
+ if (nodeList == null)
+ throw new CyCommandException("add nodes requires a 'node' or a 'nodelist' argument");
+ for (CyNode node: nodeList) {
+ network.addNode(node);
+ }
+
+ result.addMessage("Added "+nodeList.size()+" node(s) to network "+network.getTitle());
+
+ return result;
+ }
+
+}
diff --git a/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/network/CreateNetwork.java b/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/network/CreateNetwork.java
new file mode 100644
index 0000000..217603c
--- /dev/null
+++ b/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/network/CreateNetwork.java
@@ -0,0 +1,160 @@
+/* vim: set ts=2: */
+/**
+ * Copyright (c) 2009 The Regents of the University of California.
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ * notice, this list of conditions, and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above
+ * copyright notice, this list of conditions, and the following
+ * disclaimer in the documentation and/or other materials provided
+ * with the distribution.
+ * 3. Redistributions must acknowledge that this software was
+ * originally developed by the UCSF Computer Graphics Laboratory
+ * under support by the NIH National Center for Research Resources,
+ * grant P41-RR01081.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY
+ * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+ * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+ * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
+ * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ */
+package coreCommands.namespaces.network;
+
+import cytoscape.CyEdge;
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+
+import cytoscape.command.CyCommandException;
+import cytoscape.command.CyCommandHandler;
+import cytoscape.command.CyCommandNamespace;
+import cytoscape.command.CyCommandResult;
+
+import cytoscape.data.Semantics;
+import cytoscape.layout.Tunable;
+import cytoscape.logger.CyLogger;
+
+import coreCommands.namespaces.AbstractGraphObjectHandler;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+/**
+ * XXX FIXME XXX Description
+ */
+public class CreateNetwork extends AbstractGraphObjectHandler {
+ static String NETWORK = "network";
+
+ // Commands
+ static String CREATE = "create";
+
+ // Arguments
+ static String CREATEVIEW = "createview";
+ static String DIRECTED = "directed";
+ static String EDGETYPE = "edgetype";
+ static String NAME = "name";
+ static String PARENT = "parent";
+ static String SOURCELIST = "sourcelist";
+ static String TARGETLIST = "targetlist";
+
+ public CreateNetwork(CyCommandNamespace ns) {
+ super(ns);
+
+ // Define our subcommands
+ addDescription(CREATE, "Create a new network");
+ addArgument(CREATE, NAME, "NewNetwork");
+ addArgument(CREATE, CREATEVIEW, "true");
+ addArgument(CREATE, PARENT);
+ addArgument(CREATE, TARGETLIST);
+ addArgument(CREATE, SOURCELIST);
+ addArgument(CREATE, EDGETYPE, "pp");
+ addArgument(CREATE, DIRECTED, "true");
+ }
+
+ public CyCommandResult execute(String command, Collection<Tunable>args) throws CyCommandException {
+ return execute(command, createKVMap(args));
+ }
+
+ public CyCommandResult execute(String command, Map<String, Object>args) throws CyCommandException {
+ CyCommandResult result = new CyCommandResult();
+
+ String netName = getArg(command, NAME, args);
+ if (netName == null)
+ throw new CyCommandException("network: need a network name for the new network");
+
+ // Handle create view
+ boolean createView = true;
+ {
+ String cv = getArg(command, CREATEVIEW, args);
+ if (cv != null && (cv.equalsIgnoreCase("false") || cv.equalsIgnoreCase("no")))
+ createView = false;
+ }
+
+ // Handle parent network name
+ CyNetwork parent = null;
+ {
+ String pName = getArg(command, PARENT, args);
+ if (pName != null) {
+ parent = getNetwork(command, pName);
+ }
+ }
+
+ CyNetwork net = Cytoscape.createNetwork(netName, parent, createView);
+ if (net == null) {
+ result.addError("network: unable to create new network "+netName);
+ return result;
+ }
+
+ // See if we have source and target
+ String sourceList = getArg(command, SOURCELIST, args);
+ String targetList = getArg(command, TARGETLIST, args);
+ String edgeType = getArg(command, EDGETYPE, args);
+ boolean directed = Boolean.getBoolean(getArg(command, DIRECTED, args));
+ if (sourceList != null || targetList != null || edgeType != null) {
+ if (targetList != null && sourceList == null)
+ throw new CyCommandException("network: if 'targetlist' is specified, 'sourcelist' must be specified");
+
+ String[] sourceNodes = sourceList.split(",");
+ String[] targetNodes = null;
+
+ if (targetList != null)
+ targetNodes = targetList.split(",");
+
+ if (targetList != null && (sourceNodes.length != targetNodes.length))
+ throw new CyCommandException("network: 'targetlist' and 'sourcelist' must have the same number of nodes");
+
+ for (int nodeIndex = 0; nodeIndex < sourceNodes.length; nodeIndex++) {
+ CyNode source = Cytoscape.getCyNode(sourceNodes[nodeIndex], true);
+ net.addNode(source);
+
+ if (targetNodes != null) {
+ CyNode target = Cytoscape.getCyNode(targetNodes[nodeIndex], true);
+
+ CyEdge edge = Cytoscape.getCyEdge(source, target, Semantics.INTERACTION, edgeType, true, directed);
+ net.addNode(target);
+ net.addEdge(edge);
+ }
+ }
+
+ result.addMessage("Created network "+netName+" with "+sourceNodes.length+" edges");
+ }
+
+ return result;
+ }
+
+}
diff --git a/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/network/ExportNetwork.java b/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/network/ExportNetwork.java
new file mode 100644
index 0000000..ec22c8b
--- /dev/null
+++ b/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/network/ExportNetwork.java
@@ -0,0 +1,192 @@
+/* vim: set ts=2: */
+/**
+ * Copyright (c) 2009 The Regents of the University of California.
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ * notice, this list of conditions, and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above
+ * copyright notice, this list of conditions, and the following
+ * disclaimer in the documentation and/or other materials provided
+ * with the distribution.
+ * 3. Redistributions must acknowledge that this software was
+ * originally developed by the UCSF Computer Graphics Laboratory
+ * under support by the NIH National Center for Research Resources,
+ * grant P41-RR01081.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY
+ * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+ * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+ * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
+ * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ */
+package coreCommands.namespaces.network;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+
+import cytoscape.command.AbstractCommandHandler;
+import cytoscape.command.CyCommandException;
+import cytoscape.command.CyCommandHandler;
+import cytoscape.command.CyCommandNamespace;
+import cytoscape.command.CyCommandResult;
+
+import cytoscape.data.readers.GMLParser;
+import cytoscape.data.readers.GMLReader;
+import cytoscape.data.readers.GMLWriter;
+import cytoscape.data.readers.GraphReader;
+import cytoscape.data.writers.InteractionWriter;
+import cytoscape.data.writers.XGMMLWriter;
+
+import cytoscape.layout.Tunable;
+import cytoscape.logger.CyLogger;
+import cytoscape.view.CyNetworkView;
+
+import coreCommands.namespaces.AbstractGraphObjectHandler;
+
+import java.io.File;
+import java.io.FileWriter;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+/**
+ * XXX FIXME XXX Description
+ */
+public class ExportNetwork extends AbstractGraphObjectHandler {
+ static String NETWORK = "network";
+
+ // Commands
+ static String EXPORT = "export";
+
+ // Arguments
+ static String NAME = "name";
+ static String CURRENT = "current";
+ static String PARENT = "parent";
+ static String FILE = "file";
+ static String TYPE = "type";
+
+ // File types
+ static String XGMML = "xgmml";
+ static String GML = "gml";
+ static String SIF = "sif";
+
+ public ExportNetwork(CyCommandNamespace ns) {
+ super(ns);
+
+ // Define our subcommands
+ addDescription(EXPORT, "Export a network to a network format file");
+ addArgument(EXPORT, NAME , CURRENT);
+ addArgument(EXPORT, FILE);
+ addArgument(EXPORT, TYPE, XGMML);
+ }
+
+ public CyCommandResult execute(String command, Collection<Tunable>args) throws CyCommandException {
+ return execute(command, createKVMap(args));
+ }
+
+ public CyCommandResult execute(String command, Map<String, Object>args) throws CyCommandException {
+ CyCommandResult result = new CyCommandResult();
+
+ String netName = getArg(command, NAME, args);
+ String type = getArg(command, TYPE, args);
+ String fileName = getArg(command, FILE, args);
+ Object[] ret_val = new Object[3]; // For property change event
+
+ if (fileName == null)
+ throw new CyCommandException("network: 'file' must be specified for export");
+
+ CyNetwork net = Cytoscape.getCurrentNetwork();
+ CyNetworkView view = Cytoscape.getCurrentNetworkView();
+ if (!netName.equalsIgnoreCase(CURRENT)) {
+ net = getNetwork(command, netName);
+ view = Cytoscape.getNetworkView(net.getIdentifier());
+ }
+
+ ret_val[0] = net;
+
+ if (type.equalsIgnoreCase(XGMML)) {
+ if (!fileName.endsWith(".xgmml"))
+ fileName += fileName + ".xgmml";
+
+ try {
+ FileWriter fileWriter = new FileWriter(fileName);
+ XGMMLWriter xgmmlWriter = new XGMMLWriter(net, view);
+ xgmmlWriter.write(fileWriter);
+ result.addMessage("network: exported network '"+
+ net.getIdentifier()+"' to '"+fileName);
+ ret_val[2] = new Integer(Cytoscape.FILE_XGMML);
+ fileWriter.close();
+ } catch (Exception e) {
+ result.addError("network: unable to export network '"+
+ net.getIdentifier()+"' to '"+fileName+": "+e.getMessage());
+ }
+
+ } else if (type.equalsIgnoreCase(GML)) {
+ if (!fileName.endsWith(".gml"))
+ fileName = fileName + ".gml";
+
+ List list;
+ GMLReader reader = (GMLReader) net.getClientData("GML");
+ if (reader != null) {
+ list = reader.getList();
+ } else {
+ list = new ArrayList();
+ }
+
+ try {
+ FileWriter fileWriter = new FileWriter(fileName);
+ GMLWriter gmlWriter = new GMLWriter();
+ gmlWriter.writeGML(net, view, list);
+ GMLParser.printList(list, fileWriter);
+ fileWriter.close();
+ result.addMessage("network: exported network '"+
+ net.getIdentifier()+"' to '"+fileName);
+
+ ret_val[2] = new Integer(Cytoscape.FILE_GML);
+ } catch (Exception e) {
+ result.addError("network: unable to export network '"+
+ net.getIdentifier()+"' to '"+fileName+": "+e.getMessage());
+ }
+
+ } else if (type.equalsIgnoreCase(SIF)) {
+ if (!fileName.endsWith(".sif"))
+ fileName = fileName + ".sif";
+
+ try {
+ FileWriter fileWriter = new FileWriter(fileName);
+ InteractionWriter.writeInteractions(net, fileWriter, null);
+ fileWriter.close();
+ result.addMessage("network: exported network '"+
+ net.getIdentifier()+"' to '"+fileName);
+
+ ret_val[2] = new Integer(Cytoscape.FILE_SIF);
+ } catch (Exception e) {
+ result.addError("network: unable to export network '"+
+ net.getIdentifier()+"' to '"+fileName+": "+e.getMessage());
+ }
+
+ } else
+ throw new CyCommandException("network: export type "+type+" is not supported");
+
+ if (result.successful()) {
+ ret_val[1] = new File(fileName).toURI();
+ Cytoscape.firePropertyChange(Cytoscape.NETWORK_SAVED, null, ret_val);
+ }
+
+ return result;
+ }
+}
diff --git a/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/network/ImportNetwork.java b/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/network/ImportNetwork.java
new file mode 100644
index 0000000..353b71e
--- /dev/null
+++ b/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/network/ImportNetwork.java
@@ -0,0 +1,142 @@
+/* vim: set ts=2: */
+/**
+ * Copyright (c) 2009 The Regents of the University of California.
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ * notice, this list of conditions, and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above
+ * copyright notice, this list of conditions, and the following
+ * disclaimer in the documentation and/or other materials provided
+ * with the distribution.
+ * 3. Redistributions must acknowledge that this software was
+ * originally developed by the UCSF Computer Graphics Laboratory
+ * under support by the NIH National Center for Research Resources,
+ * grant P41-RR01081.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY
+ * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+ * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+ * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
+ * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ */
+package coreCommands.namespaces.network;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+
+import cytoscape.command.AbstractCommandHandler;
+import cytoscape.command.CyCommandException;
+import cytoscape.command.CyCommandHandler;
+import cytoscape.command.CyCommandNamespace;
+import cytoscape.command.CyCommandResult;
+
+import cytoscape.data.readers.GMLParser;
+import cytoscape.data.readers.GMLReader;
+import cytoscape.data.readers.GraphReader;
+
+import cytoscape.layout.Tunable;
+import cytoscape.logger.CyLogger;
+import cytoscape.view.CyNetworkView;
+
+import coreCommands.namespaces.AbstractGraphObjectHandler;
+
+import java.io.File;
+import java.io.FileWriter;
+
+import java.net.URI;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+/**
+ * XXX FIXME XXX Description
+ */
+public class ImportNetwork extends AbstractGraphObjectHandler {
+ static String NETWORK = "network";
+
+ // Commands
+ static String IMPORT = "import";
+
+ // Arguments
+ static String NAME = "name";
+ static String CREATEVIEW = "createview";
+ static String PARENT = "parent";
+ static String FILE = "file";
+ static String TYPE = "type";
+
+ // File types
+ static String XGMML = "xgmml";
+ static String GML = "gml";
+ static String SIF = "sif";
+
+ public ImportNetwork(CyCommandNamespace ns) {
+ super(ns);
+
+ // Define our subcommands
+ addDescription(IMPORT, "Import a network from a file");
+ addArgument(IMPORT, FILE);
+ addArgument(IMPORT, CREATEVIEW, "true");
+ addArgument(IMPORT, PARENT);
+ }
+
+ public CyCommandResult execute(String command, Collection<Tunable>args) throws CyCommandException {
+ return execute(command, createKVMap(args));
+ }
+
+ public CyCommandResult execute(String command, Map<String, Object>args) throws CyCommandException {
+ CyCommandResult result = new CyCommandResult();
+
+ String fileName = getArg(command, FILE, args);
+ if (fileName == null)
+ throw new CyCommandException("network: 'file' must be specified for import");
+
+ File file = new File(fileName);
+ GraphReader reader = Cytoscape.getImportHandler().getReader(file.getAbsolutePath());
+ URI uri = file.toURI();
+
+ // Handle create view
+ boolean createView = true;
+ {
+ String cv = getArg(command, CREATEVIEW, args);
+ if (cv != null && (cv.equalsIgnoreCase("false") || cv.equalsIgnoreCase("no")))
+ createView = false;
+ }
+
+ // Handle parent network name
+ CyNetwork parent = null;
+ {
+ String pName = getArg(command, PARENT, args);
+ if (pName != null) {
+ parent = getNetwork(command, pName);
+ }
+ }
+
+ try {
+ CyNetwork cyNetwork = Cytoscape.createNetwork(reader, createView, parent);
+ result.addMessage("network: import complete. Network has "+cyNetwork.getNodeCount()+
+ " nodes and "+cyNetwork.getEdgeCount()+" edges");
+ result.addResult("nodecount",""+cyNetwork.getNodeCount());
+ result.addResult("edgecount",""+cyNetwork.getEdgeCount());
+ } catch (Exception e) {
+ throw new CyCommandException("network: unable to import network from file '"+
+ file.getAbsolutePath()+"': "+e.getMessage());
+ }
+
+ return result;
+ }
+
+}
diff --git a/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/networkView/ExportNetworkView.java b/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/networkView/ExportNetworkView.java
new file mode 100644
index 0000000..27a71cf
--- /dev/null
+++ b/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/networkView/ExportNetworkView.java
@@ -0,0 +1,163 @@
+/* vim: set ts=2: */
+/**
+ * Copyright (c) 2009 The Regents of the University of California.
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ * notice, this list of conditions, and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above
+ * copyright notice, this list of conditions, and the following
+ * disclaimer in the documentation and/or other materials provided
+ * with the distribution.
+ * 3. Redistributions must acknowledge that this software was
+ * originally developed by the UCSF Computer Graphics Laboratory
+ * under support by the NIH National Center for Research Resources,
+ * grant P41-RR01081.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY
+ * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+ * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+ * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
+ * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ */
+package coreCommands.namespaces.networkView;
+
+import cytoscape.CyEdge;
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+import cytoscape.CytoscapeInit;
+
+import cytoscape.command.AbstractCommandHandler;
+import cytoscape.command.CyCommandException;
+import cytoscape.command.CyCommandHandler;
+import cytoscape.command.CyCommandManager;
+import cytoscape.command.CyCommandNamespace;
+import cytoscape.command.CyCommandResult;
+import cytoscape.ding.DingNetworkView;
+import cytoscape.layout.Tunable;
+import cytoscape.logger.CyLogger;
+import cytoscape.view.CyNetworkView;
+import cytoscape.view.InternalFrameComponent;
+
+// Cytoscape exporter imports
+import cytoscape.util.export.BitmapExporter;
+import cytoscape.util.export.PDFExporter;
+import cytoscape.util.export.SVGExporter;
+import cytoscape.util.export.Exporter;
+
+import ding.view.DGraphView;
+
+import coreCommands.namespaces.AbstractGraphObjectHandler;
+
+import java.io.File;
+import java.io.FileOutputStream;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+/**
+ * XXX FIXME XXX Description
+ */
+public class ExportNetworkView extends AbstractGraphObjectHandler {
+ private static String NETWORKVIEW = "networkview";
+
+ private static String EXPORT = "export";
+
+ private static String CURRENT = "current";
+ private static String NETWORK = "network";
+ private static String FILE = "file";
+ private static String TYPE = "type";
+ private static String ZOOM = "zoom";
+
+ // Export types
+ private static String PNG = "png";
+ private static String PDF = "pdf";
+ private static String SVG = "svg";
+ private static String JPG = "jpg";
+ private static String JPEG = "jpeg";
+ private static String BMP = "bmp";
+
+ public ExportNetworkView(CyCommandNamespace ns) {
+ super(ns);
+
+ // Define our subcommands
+ addDescription(EXPORT, "Export a network view as a graphic file");
+ addArgument(EXPORT, FILE);
+ addArgument(EXPORT, NETWORK, CURRENT);
+ addArgument(EXPORT, TYPE, PNG);
+ addArgument(EXPORT, ZOOM, "1.0");
+ }
+
+ public CyCommandResult execute(String command, Collection<Tunable>args) throws CyCommandException {
+ return execute(command, createKVMap(args));
+ }
+
+ public CyCommandResult execute(String command, Map<String, Object>args) throws CyCommandException {
+ CyCommandResult result = new CyCommandResult();
+ Map<String, CyNetworkView> viewMap = Cytoscape.getNetworkViewMap();
+ CyNetwork net = Cytoscape.getCurrentNetwork();
+
+ net = getNetwork(command, args);
+ if (!viewMap.containsKey(net.getIdentifier()) && !command.equals("create"))
+ throw new CyCommandException("networkview: can't find view for network: "+net.getTitle());
+
+ CyNetworkView view = viewMap.get(net.getIdentifier());
+ float zoom = Float.parseFloat(getArg(command, ZOOM, args));
+ String type = getArg(command, TYPE, args);
+ String fileName = getArg(command, FILE, args);
+ if (fileName == null)
+ throw new CyCommandException("networkview: no file name specified for export");
+
+ // Get the component to export
+ InternalFrameComponent ifc =
+ Cytoscape.getDesktop().getNetworkViewManager().getInternalFrameComponent(view);
+
+ // Handle the exportTextAsShape property
+ DGraphView theViewToPrint = (DingNetworkView) view;
+ boolean exportTextAsShape =
+ new Boolean(CytoscapeInit.getProperties().getProperty("exportTextAsShape")).booleanValue();
+ theViewToPrint.setPrintingTextAsShape(exportTextAsShape);
+
+ // Now get the right export handler & handle any options
+ Exporter exporter = null;
+ if (type.equalsIgnoreCase(PDF) ){
+ exporter = new PDFExporter();
+ } else if (type.equalsIgnoreCase(SVG)) {
+ exporter = new SVGExporter();
+ } else if (type.equalsIgnoreCase(PNG)) {
+ exporter = new BitmapExporter(PNG, zoom);
+ } else if (type.equalsIgnoreCase(JPG)) {
+ exporter = new BitmapExporter(JPG, zoom);
+ } else if (type.equalsIgnoreCase(JPEG)) {
+ exporter = new BitmapExporter(JPG, zoom);
+ } else if (type.equalsIgnoreCase(BMP)) {
+ exporter = new BitmapExporter(BMP, zoom);
+ } else
+ throw new CyCommandException("networkview: don't know how to export to type "+type);
+
+ // Handle filename changes
+ try {
+ FileOutputStream outputFile = new FileOutputStream(fileName);
+ exporter.export(view, outputFile);
+ } catch (Exception e) {
+ throw new CyCommandException("networkview: unable to export view: "+e.getMessage());
+ }
+ result.addMessage("networkview: exported view for "+net.getIdentifier()+" to "+fileName);
+ return result;
+ }
+}
diff --git a/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/node/ExportNodeAttributes.java b/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/node/ExportNodeAttributes.java
new file mode 100644
index 0000000..e2ed5af
--- /dev/null
+++ b/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/node/ExportNodeAttributes.java
@@ -0,0 +1,144 @@
+/* vim: set ts=2: */
+/**
+ * Copyright (c) 2009 The Regents of the University of California.
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ * notice, this list of conditions, and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above
+ * copyright notice, this list of conditions, and the following
+ * disclaimer in the documentation and/or other materials provided
+ * with the distribution.
+ * 3. Redistributions must acknowledge that this software was
+ * originally developed by the UCSF Computer Graphics Laboratory
+ * under support by the NIH National Center for Research Resources,
+ * grant P41-RR01081.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY
+ * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+ * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+ * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
+ * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ */
+package coreCommands.namespaces.node;
+
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+import cytoscape.command.CyCommandException;
+import cytoscape.command.CyCommandHandler;
+import cytoscape.command.CyCommandManager;
+import cytoscape.command.CyCommandNamespace;
+import cytoscape.command.CyCommandResult;
+import cytoscape.data.CyAttributes;
+import cytoscape.layout.Tunable;
+import cytoscape.logger.CyLogger;
+import cytoscape.view.CyNetworkView;
+
+import giny.model.GraphObject;
+
+import java.io.IOException;
+import java.io.File;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import coreCommands.namespaces.AbstractGraphObjectHandler;
+import coreCommands.namespaces.AttributeUtils;
+
+/**
+ * XXX FIXME XXX Description
+ */
+public class ExportNodeAttributes extends AbstractGraphObjectHandler {
+
+ // Commands
+ private static String EXPORT = "export attributes";
+
+ // Settings
+ private static String ATTRIBUTE = "attributeList";
+ private static String DELIMITER = "delimiter";
+ private static String FILE = "file";
+ private static String NETWORK = "network";
+ private static String NODELIST = "nodelist";
+
+ public ExportNodeAttributes(CyCommandNamespace ns) {
+ super(ns);
+
+ // Define our subcommands
+ addDescription(EXPORT, "Export node attributes as a table");
+ addArgument(EXPORT, FILE);
+ addArgument(EXPORT, ATTRIBUTE);
+ addArgument(EXPORT, DELIMITER);
+ addArgument(EXPORT, NETWORK, "current");
+ addArgument(EXPORT, NODELIST);
+ }
+
+ public CyCommandResult execute(String command, Collection<Tunable>args) throws CyCommandException {
+ return execute(command, createKVMap(args));
+ }
+
+ public CyCommandResult execute(String command, Map<String, Object>args) throws CyCommandException {
+ CyCommandResult result = new CyCommandResult();
+
+ if (EXPORT.equals(command)) {
+ CyAttributes nodeAttributes = Cytoscape.getNodeAttributes();
+ // Do we have a filename?
+ String fileName = getArg(command, FILE, args);
+ if (fileName == null)
+ throw new CyCommandException("node: filename is required to export attributes");
+
+ // Get our delimiter
+ String delim = getArg(command, DELIMITER, args);
+ if (delim == null)
+ delim = "\t";
+
+ // Get the attribute list
+ String[] attrArray;
+ String attrStr = getArg(command, ATTRIBUTE, args);
+ if (attrStr == null) {
+ attrArray = nodeAttributes.getAttributeNames();
+ } else {
+ attrArray = attrStr.split(",");
+ }
+
+ List<String> attrList = Arrays.asList(attrArray);
+
+ // Get the node list
+ CyNetwork net = getNetwork(command, args);
+ List nodeList = getNodeList(net, result, args);
+ if (nodeList == null)
+ nodeList = net.nodesList();
+
+ int lineCount = 0;
+ try {
+ File outputFile = new File(fileName);
+ lineCount = AttributeUtils.exportAttributes(outputFile, nodeAttributes, nodeList, attrList, delim);
+ } catch (IOException e) {
+ throw new CyCommandException("node: export failed: "+e.getMessage());
+ }
+ result.addMessage("node: exported "+lineCount+" lines to "+fileName);
+ }
+
+ return result;
+ }
+
+ public static CyCommandHandler register(String namespace) throws RuntimeException {
+ // Get the namespace
+ return new ExportNodeAttributes(CyCommandManager.reserveNamespace(namespace));
+ }
+
+}
diff --git a/coreplugins/CoreCommands/src/main/resources/coreCommands/plugin.props b/coreplugins/CoreCommands/src/main/resources/coreCommands/plugin.props
new file mode 100644
index 0000000..24efe7a
--- /dev/null
+++ b/coreplugins/CoreCommands/src/main/resources/coreCommands/plugin.props
@@ -0,0 +1,29 @@
+# This props file would be filled out and included in the plugin jar file. This props file will be used
+# to put information into the Plugin Manager about the plugin
+
+# -- The following properties are REQUIRED -- #
+
+# The plugin name that will be displayed to users
+pluginName=coreCommands
+
+# Description used to give users information about the plugin such as what it does.
+# Html tags are encouraged for formatting purposes.
+pluginDescription=Core Commands
+
+# Plugin version number, this must be two numbers separated by a decimlal. Ex. 0.2, 14.03
+pluginVersion=1.0
+
+# Compatible Cytoscape version
+cytoscapeVersion=2.8
+
+# Category, use one of the categories listed on the website or create your own
+pluginCategory=Core
+
+
+# List of authors. Note each author and institution pair are separated by a : (colon)
+# each additional author institution pair must be separated from other pairs bye a ; (semicolon)
+pluginAuthorsIntstiutions=John "Scooter" Morris:UCSF
+
+# -- The following properties should be set ONLY BY CORE PLUGINS -- #
+downloadURL=http://cytoscape.org/plugins/plugins.xml
+uniqueID=17
diff --git a/coreplugins/CytoscapeEditor2/pom.xml b/coreplugins/CytoscapeEditor2/pom.xml
new file mode 100644
index 0000000..ce87548
--- /dev/null
+++ b/coreplugins/CytoscapeEditor2/pom.xml
@@ -0,0 +1,56 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>parent</artifactId>
+ <version>2.8.4-SNAPSHOT</version>
+ </parent>
+
+ <artifactId>editor</artifactId>
+ <packaging>jar</packaging>
+
+ <name>Editor</name>
+
+ <!-- bootstrap for cytoscape dependencies, namely the parent POM snapshots -->
+ <repositories>
+ <repository>
+ <id>cytoscape_snapshots</id>
+ <snapshots>
+ <enabled>true</enabled>
+ </snapshots>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <name>Cytoscape Snapshots</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/</url>
+ </repository>
+ <repository>
+ <id>cytoscape_releases</id>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ <name>Cytoscape Releases</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/releases/</url>
+ </repository>
+ </repositories>
+
+ <build>
+ <plugins>
+ <plugin>
+ <artifactId>maven-assembly-plugin</artifactId>
+ <configuration>
+ <archive>
+ <manifestEntries>
+ <Cytoscape-Plugin>cytoscape.editor.CytoscapeEditorPlugin</Cytoscape-Plugin>
+ </manifestEntries>
+ </archive>
+ </configuration>
+ </plugin>
+ </plugins>
+ </build>
+
+</project>
+
diff --git a/coreplugins/CytoscapeEditor2/release-notes.html b/coreplugins/CytoscapeEditor2/release-notes.html
new file mode 100644
index 0000000..09da140
--- /dev/null
+++ b/coreplugins/CytoscapeEditor2/release-notes.html
@@ -0,0 +1,220 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+<meta http-equiv="content-type" content="text/html; charset=utf-8"/>
+<title>CytoscapeEditor Release Notes (version 2.62)</title>
+</head>
+
+<body>
+
+<h1>CytoscapeEditor Release Notes (version 2.62)</h1>
+Various bug fixes including (numbers are Mantis bug numbers):
+<ol>
+<li>Ctrl-click on a one-button Mac brings up both the bypass menu AND creates an edge (1738)</li>
+<li><p></p>Connect Selected Nodes not undoable as an atomic action. (1384)</li>
+<li><p></p>"Connect Selected Node" not always show up (1264)</li>
+<li><p></p>Creating new edges via CTRL-click opens interfering menu on Mac (1806)</li>
+<li><p></p>Creating new edge leaves streaks on canvas (still) (1730)</li>
+<li><p></p>CytoscapeEditor in 2.6 throws exception when adding (globally) existing node (1917)</li>
+<li><p></p>Fixed ClassCastException where using the VizMapper and changing ArrowShapes could lead to a ClassCastException.</li>
+<li><p></p>Multiple NeworkViews stopped editor's drag and drop from working (1977)</li>
+<li><p></p>Rubberband line continued to function after selecting another network (1978)</li>
+<li><p></p>NullPointerException when Drag&Drop of edge under certain conditions (1979)</li>
+</ol>
+
+<h1>Prior Notes</h1>
+
+<h2>CytoscapeEditor Release Notes (version 2.60)</h2>
+<ol>
+<li>Patched Editor so that mouse, key, and drop events are ignored
+when the Editor tab of the CytoPanel is not active.</li>
+<li><p></p>Fixed the "ESC" key to correctly stop drop of an edge.</li>
+</ol>
+
+<h2>CytoscapeEditor Release Notes (version 2.53)</h2>
+<ol>
+<li>Fixed bug where palette was being redrawn when the Editor tab wasn't
+ selected.</li>
+<li><p></p>Some code cleanup changes to CytoscapeEditorManagerSupport.</li>
+</ol>
+
+<h2>CytoscapeEditor Release Notes (version 2.52)</h2>
+<ol>
+
+<li>Changed File->New-Network->EmptyNetwork (NewNetworkAction) to not
+produce an extra (accidental) CyNetworkView and to set the visual
+style of the new network to be the VisualMappingManager's current
+visual style.</li>
+
+<li><p></p>Removed arrowhead on default "Directed Edge" edge palette entry in
+DefaultCytoscapeEditor.</li>
+
+<li><p></p>Fixed so that clicking on the Editor tab would correctly show the correct
+editor palette for a given visual style (for sublass editors).
+
+<p></p>This required stopping the creation of a CyNetworkView in
+CytoscapeEditorManagerSupport.onComponentSelected() that would be set
+to the default visual style thereby resetting the editor palette for
+subclasses (like the HyperEdgeEditor).</li>
+
+<li><p></p>Changed call to buildVisualStyle() in
+CytoscapeEditorManager.initializeEditor() to occur before
+VisualMappingManager.setVisualStyle() is called.</li>
+
+</ol>
+
+
+<h2>CytoscapeEditor Release Notes (version 2.51)</h2>
+<ol>
+<li>Simplified CytoscapeEditor initialization with assumption that
+the CytoscapeEditor is always loaded before any extension to
+this editor.</li>
+<li><p></p>Removed unneeded definitions of getPluginInfoObject() and describe().</li>
+<li><p></p>Removed manual setting of EdgeView tooltips, since tooltips should
+now be set using Visual Styles.</li>
+<li><p></p>Fixed NPE bug in CyotscapeEditorManger.register() where
+CytoscapeEditorManager.log() statements were being called without null
+pointer check.</li>
+<li><p></p>Updated missed deprecated code reference to use new Cytoscape 2.5
+ VizMap API.</li>
+</ol>
+
+<h2>CytoscapeEditor Release Notes (version 2.50)</h2>
+<ol>
+<li>Made CytoscapeEditor be a good citizen for the Cytoscape PluginManager.
+<p></p> Added CytoscapeEditorPlugin.getPluginInfoObject().</li>
+<li><p></p>Updated code to use new Cytoscape 2.5 VizMap API.</li>
+<li><p></p>Fixed various deprecations and warnings.</li>
+</ol>
+
+<h2>CytoscapeEditor Release Notes (version 2.4 alfa 4)</h2>
+<ol>
+<li>Added keyboard accelerator for "Delete Selected Nodes and Edges"
+menu item.</li>
+</ol>
+
+<h2>CytoscapeEditor Release Notes (version 2.4 alfa 3)</h2>
+<ol>
+
+<li>Various changes and cleanup to allow easier subclassing of
+CytoscapeEditor and access to the DeleteAction.
+<ol>
+
+<li><p></p>Some cleanup of DeleteAction an removed 2 parameter
+ DeleteAction constructor.</li>
+<li>Cleanup and changed
+ BasicCytoscapeEditor.addNodeContextMenuItems(),
+ addEdgeContextMenuItems(), and
+ removeExistingDeleteMenuItemIfNecessary() to handle changes to
+ DeleteAction.</li>
+<li>Added CytoscapeEditorManagerSupport.getDeleteAction() and
+ DeleteAction parameter to constructor.</li>
+<li>Changed CytoscapeEditorManager.initialize() to send
+CytoscapeEditorManagerSupport the DeleteAction created for use by
+subclasses.</li>
+</ol>
+</li>
+</ol>
+
+<h2>CytoscapeEditor Release Notes (version 2.4 alfa 2)</h2>
+<ol>
+<li>Changed the CytoscapeEditor to be intelligent about what drag
+cursor is shown when performing a drag-drop from a shape palette entry
+to a CyNetworkView of interest.
+
+<p></p>Built a flexible framework using DragSourceContextCursorSetters
+to determine cursor for each palette entry.</li>
+</ol>
+
+<h2>CytoscapeEditor Release Notes (version 2.4 alfa 1)</h2>
+<ol>
+
+<li>Refactored BasicNetworkEditEventHandler.finishEdge() into smaller
+pieces for subclass usage. Cleaned up
+BasicNetworkEditEventHandler.mousePressed() and a few protected
+instance variables that should be private.</li>
+
+<li><p></p>Cleaned up code and refactored
+PaletteNetworkEditEventHandler.itemDropped() and associated methods
+for easier use by subclasses and code cleanup.</li>
+<li><p></p>Removed BioPAXNetworkEditEventHandler.</li>
+</ol>
+
+<h2>CytoscapeEditor Release Notes (version 2.3.03)</h2>
+<ol>
+
+<li>Created a new way to easily produce ShapePalette entries for
+editors.
+
+<p></p>This involves the use of new interfaces ShapePaletteInfo and
+ShapePaletteInfoGenerator and their supporting classes. Refactored
+DefaultCytoscapeEditor to use this new ShapePaletteInfoGenerator.</li>
+
+
+<li><p></p>Added ability of ShapePalette entries to handle visual style
+size information.
+
+<p></p>Changed computation of BasicCytoShapeEntity size to allow for
+ larger CytoShapeIcons. Added CytoShapeIcon constructor for handling
+ size information. Changed getIconWidth/Height() to return real width
+ and height of icon. Changed the ShapePalette JList to no longer use
+ setFixedCellHeight() since BasicCytoShapeEntitys can now have
+ different sizes.</li>
+
+<li><p></p>Added CytoShapeIcon.DEFAULT_WIDTH and DEFAULT_HEIGHT and deprecated
+ CytoShapeIcon.WIDTH & HEIGHT.</li>
+<li><p></p>Removed SimpleBioPAX_Editor.</li>
+</ol>
+
+
+<h2>CytoscapeEditor Release Notes (version 2.3.02)</h2>
+<ol>
+<li>Fixed compilation problem caused by accidental release of changes
+to CytoscapeEditorManager.java.</li>
+</ol>
+
+<h2>CytoscapeEditor Release Notes (version 2.3.01)</h2>
+
+<ol>
+
+<li>CytoscapeEditorManagerSupport: Fixed updateEditorPalette() to not
+assume visualStyleName is the same as Editor name. Added some
+comments.</li>
+
+<li><p></p>BasicCytoscapeEditor: Removed setting of BIO_PAX attributes from
+addNode(). Fixed deprecated method usage in addNode().</li>
+
+<li><p></p>BasicCytoShapeEntity, ShapePalette, InvalidEditorException: Added
+generated serial version UUID for serializable classes.
+
+CytoscapeEditor: Updated to remove deprecated use of FlagEventListener
+(now is SelectEventListener)</li>
+
+<li><p></p>CytoscapeEditorManager:
+<ol>
+ <li> Fixed so visualStyleName can be different from the editor name.</li>
+ <li> Added getEditorNameForVisualStyleName() and changed
+ initializeEditor() to take a visualStyleName parameter.</li>
+ <li> Changed many instance variables to be private vs protected.</li>
+ <li> Added intialization of this manager if register() is called by
+ another plugin before this plugin is loaded.</li>
+</ol>
+</li>
+<li><p></p>CytoscapeEditorPlugin:
+<ol>
+ <li> Removed deprecated call to CytoscapeInit.getDefaultVisualStyle() in
+ initializeCytoscapeEditor().</li>
+ <li> Removed some misleading code--println that editor is loaded and
+ initialization code as though editor is initialized via a menu item,
+ when it is not.</li>
+</ol>
+</li>
+</ol>
+
+<hr />
+<p><em><small>This page was last updated: 02/04/09</small></em></p>
+
+</body>
+</html>
\ No newline at end of file
diff --git a/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/AddEdgeEdit.java b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/AddEdgeEdit.java
new file mode 100644
index 0000000..5f4cc74
--- /dev/null
+++ b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/AddEdgeEdit.java
@@ -0,0 +1,40 @@
+
+package cytoscape.editor;
+
+import cytoscape.CyEdge;
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import cytoscape.util.undo.CyAbstractEdit;
+
+/**
+ * An edit used by the Editor when adding new edges to a network.
+ */
+public class AddEdgeEdit extends CyAbstractEdit {
+
+ // MLC 05/09/07:
+ private static final long serialVersionUID = 2403924055921657412L;
+ protected CyNetwork net;
+ protected CyEdge edge;
+
+ public AddEdgeEdit(CyNetwork net, CyEdge edge) {
+ super("Add Edge");
+ if ( net == null || edge == null )
+ throw new IllegalArgumentException("network or edge is null");
+ this.net = net;
+ this.edge = edge;
+ }
+
+ public void undo() {
+ super.undo();
+ net.hideEdge( edge );
+ Cytoscape.firePropertyChange(Cytoscape.NETWORK_MODIFIED,
+ CytoscapeEditorManager.CYTOSCAPE_EDITOR, net);
+ }
+
+ public void redo() {
+ super.redo();
+ net.restoreEdge( edge );
+ Cytoscape.firePropertyChange(Cytoscape.NETWORK_MODIFIED,
+ CytoscapeEditorManager.CYTOSCAPE_EDITOR, net);
+ }
+}
diff --git a/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/AddNodeEdit.java b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/AddNodeEdit.java
new file mode 100644
index 0000000..a5147bd
--- /dev/null
+++ b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/AddNodeEdit.java
@@ -0,0 +1,59 @@
+
+package cytoscape.editor;
+
+import giny.view.NodeView;
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+import cytoscape.util.undo.CyAbstractEdit;
+import cytoscape.view.CyNetworkView;
+
+/**
+ * An edit used by the Editor when adding new nodes to a network.
+ */
+public class AddNodeEdit extends CyAbstractEdit {
+
+ // MLC 05/09/07:
+ private static final long serialVersionUID = 4869581496913388294L;
+ protected CyNetwork net;
+ protected CyNode node;
+ protected double xPos = 0.0;
+ protected double yPos = 0.0;
+
+ public AddNodeEdit(CyNetwork net, CyNode node) {
+ super("Add Node");
+ if ( net == null || node == null )
+ throw new IllegalArgumentException("network or node is null");
+ this.net = net;
+ this.node = node;
+
+ CyNetworkView view = Cytoscape.getNetworkView(net.getIdentifier());
+ if ( view != null || view != Cytoscape.getNullNetworkView() ) {
+ NodeView nv = view.getNodeView(node);
+ xPos = nv.getXPosition();
+ yPos = nv.getYPosition();
+ }
+ }
+
+ public void undo() {
+ super.undo();
+ net.hideNode( node );
+ Cytoscape.firePropertyChange(Cytoscape.NETWORK_MODIFIED,
+ CytoscapeEditorManager.CYTOSCAPE_EDITOR, net);
+ }
+
+ public void redo() {
+ super.redo();
+ net.restoreNode( node );
+
+ CyNetworkView view = Cytoscape.getNetworkView(net.getIdentifier());
+ if ( view != null || view != Cytoscape.getNullNetworkView() ) {
+ NodeView nv = view.getNodeView(node);
+ nv.setXPosition(xPos);
+ nv.setYPosition(yPos);
+ }
+
+ Cytoscape.firePropertyChange(Cytoscape.NETWORK_MODIFIED,
+ CytoscapeEditorManager.CYTOSCAPE_EDITOR, net);
+ }
+}
diff --git a/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/CytoscapeEditor.java b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/CytoscapeEditor.java
new file mode 100644
index 0000000..9048be8
--- /dev/null
+++ b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/CytoscapeEditor.java
@@ -0,0 +1,393 @@
+/* -*-Java-*-
+********************************************************************************
+*
+* File: CytoscapeEditor.java
+* RCS: $Header: $
+* Description:
+* Author: Allan Kuchinsky
+* Created: Fri Jul 29 13:24:47 2005
+* Modified: Fri Jul 28 13:27:56 2006 (Michael L. Creech) creech at w235krbza760
+* Language: Java
+* Package:
+/*
+
+ Copyright (c) 2006, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+
+//---------------------------------------------------------------------------
+* Revisions:
+*
+* Fri Jul 28 13:27:05 2006 (Michael L. Creech) creech at w235krbza760
+* Updated to remove deprecated use of FlagEventListener (now is
+* SelectEventListener)
+********************************************************************************
+*/
+package cytoscape.editor;
+
+import giny.model.Node;
+
+import java.awt.geom.Point2D;
+import java.util.List;
+
+import cytoscape.CyEdge;
+import cytoscape.CyNode;
+import cytoscape.data.SelectEventListener;
+import cytoscape.editor.event.NetworkEditEventAdapter;
+
+
+/**
+ *
+ * <b>CytoscapeEditor</b> provides a framework for developers to implement specialized, semantics
+ * driven graphical
+ * editors and incorporate them into Cytoscape. For example, a developer might build a <em>BioPAX</em>
+ * editor whose operations adhere to the semantics of the <em>BioPAX</em> specification.
+ * The basic idea of the framework is to provide, on the Cytotoscape side, a set of common operations that
+ * all editors would use to interact with the Cytoscape environment. Such common operations include drag/drop
+ * support, mouse event handling, management of CyNetworks and CyNetworkViews, and wrappers for Cytoscape core
+ * methods that add and delete Cytoscape nodes and edges.
+ * <p>
+ * <b>CytoscapeEditor</b> is an interface that specifies common methods which all editors must implement.
+ * These methods will be called by methods in the framework.
+ * <p>
+ * @author Allan Kuchinsky, Agilent Technologies
+ * @version 1.0
+ *
+ */
+
+// MLC 07/27/06:
+// public interface CytoscapeEditor extends FlagEventListener {
+// MLC 07/27/06:
+public interface CytoscapeEditor extends SelectEventListener {
+ /**
+ * build the visual style for this editor
+ * should be overidden by specialized editors
+ *
+ */
+ public void buildVisualStyle();
+
+ /**
+ * specialized initialization code for editor, called by CyNetworkEditorFactory, should be overridden
+ * @param args an arbitrary list of arguments to be used in initializing the editor
+ */
+ public void initializeControls(List args);
+
+ /**
+ * specialized code that disables and/or removes controls when a ntework view changes, should be
+ * overridden by the developer
+ * @param args arbitrary list of arguments
+ */
+ public void disableControls(List args);
+
+ /**
+ * specialized code that enables and/or adds controls when a network view changes. Currently not used;
+ * rather a combination of intializeControls() and disableControls() is used to manage the association of
+ * visual controls with Network views.
+ * @param args
+ */
+ public void enableControls(List args);
+
+ /**
+ * set the name of the editor. This name also serves as 'Editor Type' attribute.
+ * @param editorName
+ */
+ public void setEditorName(String editorName);
+
+ /**
+ * gets the name of the editor
+ * @return the name of the editor
+ */
+ public String getEditorName();
+
+ /**
+ * wrapper for adding a node in Cytoscape. This is intended to be called by
+ * the CytoscapeEditor in lieu of making direct modifications to the
+ * Cytoscape model. Thus, it provides an insulating level of abstraction
+ * between the CytoscapeEditor and the Cytoscape implementation, allowing
+ * for portability and extensibility of the editor.
+ *
+ * this method will ensure that the node added is unique. If it finds that
+ * there is an existing node for <em>nodeName</em>, it will attempt to
+ * generate a new, unique, <em>nodeName</em> by extending the <em>nodeName</em>
+ * argument with a randomly generated extension.
+ *
+ * @param nodeName
+ * the name of the node to be created. This will be used as a
+ * unique identifier for the node.
+ * @param attribute
+ * a defining property for the node, that can be used in
+ * conjunction with the Visual Mapper to assign visual
+ * characteristics to different types of nodes. Also can be used,
+ * by the canvas when handling a dropped item, to distinguish
+ * between nodes and edges, so should be set to something like
+ * "NodeType".
+ * @param value
+ * the value of the attribute for this node. This can be used in
+ * conjunction with the Visual Mapper to assign visual
+ * characteristics to different types of nodes, for example to
+ * assign a violet diamond shape to a 'smallMolecule' node type.
+ * @return the CyNode that has been either reused or created.
+ */
+ public CyNode addNode(String nodeName, String attribute, String value);
+
+ /**
+ * wrapper for adding a node in Cytoscape. This is intended to be called by
+ * the CytoscapeEditor in lieu of making direct modifications to the
+ * Cytoscape model. Thus, it provides an insulating level of abstraction
+ * between the CytoscapeEditor and the Cytoscape implementation, allowing
+ * for portability and extensibility of the editor.
+ *
+ * this method will ensure that the node added is unique. If it finds that
+ * there is an existing node for <em>nodeName</em>, it will attempt to
+ * generate a new, unique, <em>nodeName</em> by extending the <em>nodeName</em>
+ * argument with a randomly generated extension.
+ *
+ * @param nodeName
+ * the name of the node to be created. This will be used as a
+ * unique identifier for the node.
+ * @param attribute
+ * a defining property for the node, that can be used in
+ * conjunction with the Visual Mapper to assign visual
+ * characteristics to different types of nodes. Also can be used,
+ * by the canvas when handling a dropped item, to distinguish
+ * between nodes and edges, so should be set to something like
+ * "NodeType".
+ * @param value
+ * the value of the attribute for this node. This can be used in
+ * conjunction with the Visual Mapper to assign visual
+ * characteristics to different types of nodes, for example to
+ * assign a violet diamond shape to a 'smallMolecule' node type.
+ * @param location
+ * position at which to add the node
+ * @return the CyNode that has been either reused or created.
+ */
+ public CyNode addNode(String nodeName, String attribute, String value, Point2D location);
+
+ /**
+ * wrapper for adding a node in Cytoscape. This is intended to be called by
+ * the CytoscapeEditor in lieu of making direct modifications to the
+ * Cytoscape model. Thus, it provides an insulating level of abstraction
+ * between the CytoscapeEditor and the Cytoscape implementation, allowing
+ * for portability and extensibility of the editor.
+ *
+ * @param nodeName
+ * the name of the node to be created. This will be used as a
+ * unique identifier for the node.
+ * @param nodeType
+ * the value of the 'NodeType' attribute for this node. This can
+ * be used in conjunction with the Visual Mapper to assign visual
+ * characteristics to different types of nodes. Also can be used,
+ * by the canvas when handling, a dropped item, to distinguish
+ * between nodes and edges.
+ * @return the CyNode that has been either reused or created.
+ */
+ public CyNode addNode(String nodeName, String nodeType);
+
+ /**
+ * wrapper for adding a node in Cytoscape. This is intended to be called by
+ * the CytoscapeEditor in lieu of making direct modifications to the
+ * Cytoscape model. Thus, it provides an insulating level of abstraction
+ * between the CytoscapeEditor and the Cytoscape implementation, allowing
+ * for portability and extensibility of the editor. This form of addNode()
+ * will create a node in all cases, whether it previously exists or not.
+ *
+ * @param nodeName
+ * the name of the node to be created. This will be used as a
+ * unique identifier for the node.
+ * @return the CyNode that has been either reused or created.
+ */
+ public CyNode addNode(String nodeName);
+
+ /**
+ *
+ * wrapper for adding an edge in Cytoscape. This is intended to be called by
+ * the CytoscapeEditor in lieu of making direct modifications to the
+ * Cytoscape model. Thus, it provides an insulating level of abstraction
+ * between the CytoscapeEditor and the Cytoscape implementation, allowing
+ * for portability and extensibility of the editor.
+ *
+ * @param node_1
+ * Node at one end of the edge
+ * @param node_2
+ * Node at the other end of the edge
+ * @param attribute
+ * the attribute of the edge to be searched, a common one is
+ * Semantics.INTERACTION
+ * @param attribute_value
+ * a value for the attribute, like "pp" or "default"
+ * @param create
+ * if true, then create an edge if one does not already exist.
+ * Otherwise, return the edge if it already exists.
+ * @param edgeType
+ * a value for the "EdgeType" attribute assigned to the edge.
+ * This can be used in conjunction with the Visual Mapper.
+ * @return the CyEdge that has either been reused or created
+ *
+ */
+ public CyEdge addEdge(Node node_1, Node node_2, String attribute, Object attribute_value,
+ boolean create, String edgeType);
+
+ /**
+ *
+ * wrapper for adding an edge in Cytoscape. This is intended to be called by
+ * the CytoscapeEditor in lieu of making direct modifications to the
+ * Cytoscape model. Thus, it provides an insulating level of abstraction
+ * between the CytoscapeEditor and the Cytoscape implementation, allowing
+ * for portability and extensibility of the editor. This version always
+ * creates an edge, whether or not one already exists.
+ *
+ * @param node_1
+ * Node at one end of the edge
+ * @param node_2
+ * Node at the other end of the edge
+ * @param attribute
+ * the attribute of the edge to be searched, a common one is
+ * Semantics.INTERACTION
+ * @param attribute_value
+ * a value for the attribute, like "pp" or "default"
+ * @return the CyEdge that has been created
+ *
+ */
+ public CyEdge addEdge(Node node_1, Node node_2, String attribute, Object attribute_value);
+
+ /**
+ *
+ * wrapper for adding an edge in Cytoscape. This is intended to be called by
+ * the CytoscapeEditor in lieu of making direct modifications to the
+ * Cytoscape model. Thus, it provides an insulating level of abstraction
+ * between the CytoscapeEditor and the Cytoscape implementation, allowing
+ * for portability and extensibility of the editor. This version always
+ * creates an edge, whether or not one already exists.
+ *
+ * @param node_1
+ * Node at one end of the edge
+ * @param node_2
+ * Node at the other end of the edge
+ * @param attribute
+ * the attribute of the edge to be searched, a common one is
+ * Semantics.INTERACTION
+ * @param attribute_value
+ * a value for the attribute, like "pp" or "default"
+ * @param edgeType
+ * a value for the "EdgeType" attribute assigned to the edge.
+ * This can be used in conjunction with the Visual Mapper.
+ * @return the CyEdge that has been created
+ *
+ */
+ public CyEdge addEdge(Node node_1, Node node_2, String attribute, Object attribute_value,
+ String edgeType);
+
+ /**
+ *
+ * wrapper for adding an edge in Cytoscape. This is intended to be called by
+ * the CytoscapeEditor in lieu of making direct modifications to the
+ * Cytoscape model. Thus, it provides an insulating level of abstraction
+ * between the CytoscapeEditor and the Cytoscape implementation, allowing
+ * for portability and extensibility of the editor.
+ *
+ * @param node_1
+ * Node at one end of the edge
+ * @param node_2
+ * Node at the other end of the edge
+ * @param attribute
+ * the attribute of the edge to be searched, a common one is
+ * Semantics.INTERACTION
+ * @param attribute_value
+ * a value for the attribute, like "pp" or "default"
+ * @param create
+ * if true, then create an edge if one does not already exist.
+ * Otherwise, return the edge if it already exists.
+ * @return the CyEdge that has either been reused or created
+ *
+ */
+ public CyEdge addEdge(Node node_1, Node node_2, String attribute, Object attribute_value,
+ boolean create);
+
+ /**
+ * Deletes (hides) a node from the current network
+ *
+ * @param node
+ * the node to be deleted
+ */
+ public void deleteNode(Node node);
+
+ /**
+ * Deletes (hides) an edge from the current network
+ *
+ * @param edge
+ * the edge to be deleted
+ */
+ public void deleteEdge(CyEdge edge);
+
+ /**
+ *
+ * @return the name of the attribute used to determine edge shapes on palette
+ * this is the same as the controllingEdgeAttribute for mapping of visual style to edge line type, target arrow
+ */
+ public String getControllingEdgeAttribute();
+
+ /**
+ *
+ * @param controllingEdgeAttribute
+ * the name of the attribute used to determine edge shapes on palette
+ * this is the same as the controllingEdgeAttribute for mapping of visual style to edge line type, target arrow
+ *
+ */
+ public void setControllingEdgeAttribute(String controllingEdgeAttribute);
+
+ /**
+ *
+ * @return the name of the attribute used to determine Node shapes on palette
+ * this is the same as the controllingNodeAttribute for mapping of visual style to Node line type, target arrow
+ */
+ public String getControllingNodeAttribute();
+
+ /**
+ *
+ * @param controllingNodeAttribute
+ * the name of the attribute used to determine Node shapes on palette
+ * this is the same as the controllingNodeAttribute for mapping of visual style to Node line type, target arrow
+ *
+ */
+ public void setControllingNodeAttribute(String controllingNodeAttribute);
+
+
+ public String getControllingNetworkAttribute();
+
+ public void setControllingNetworkAttribute(String controllingNetworkAttribute);
+
+
+ /**
+ *
+ * @return the network event handler that is associated with this editor
+ */
+ public NetworkEditEventAdapter getNetworkEditEventAdapter();
+
+ /**
+ *
+ * @param adapter the network event handler that is associated with this editor
+ */
+ public void setNetworkEditEventAdapter(NetworkEditEventAdapter adapter);
+}
diff --git a/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/CytoscapeEditorFactory.java b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/CytoscapeEditorFactory.java
new file mode 100644
index 0000000..5aa3696
--- /dev/null
+++ b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/CytoscapeEditorFactory.java
@@ -0,0 +1,127 @@
+/* -*-Java-*-
+********************************************************************************
+*
+* File: CytoscapeEditorFactory.java
+* RCS: $Header: $
+* Description:
+* Author: Allan Kuchinsky
+* Created: Mon July 05 18:41:21 2005
+* Modified: Mon Dec 04 18:42:31 2006 (Michael L. Creech) creech at w235krbza760
+* Language: Java
+* Package:
+*
+/*
+
+ Copyright (c) 2006, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+
+********************************************************************************
+*
+* Revisions:
+*
+* Mon Dec 04 18:41:50 2006 (Michael L. Creech) creech at w235krbza760
+* Added createShapePaletteInfoGenerator() and createShapePaletteInfo().
+********************************************************************************
+*/
+package cytoscape.editor;
+
+import java.util.Collection;
+import java.util.Iterator;
+
+import cytoscape.editor.event.NetworkEditEventAdapter;
+import cytoscape.editor.impl.CytoscapeEditorFactoryImpl;
+
+
+/**
+ *
+ * Interface used for building new instances of editors. Before an editor can be built, it first needs to be
+ * registered with the CytoscapeEditorManager.
+ *
+ * @author Allan Kuchinsky, Agilent Technologies
+ * @version 1.0
+ * @see CytoscapeEditorManager
+ *
+ */
+public interface CytoscapeEditorFactory {
+ /**
+ *
+ */
+ public static CytoscapeEditorFactory INSTANCE = new CytoscapeEditorFactoryImpl();
+
+ /**
+ * Get the network editor, creating a new one if it doesn't already exist.
+ * @param editorType non null type of editor to get
+ * @return editor
+ * @throws InvalidEditorException if the editor cannot be created
+ */
+ public CytoscapeEditor getEditor(String editorType) throws InvalidEditorException;
+
+ /**
+ * Get the set of valid editor types
+ * @return non null collection of editor types (String)
+ */
+ public Collection getEditorTypes();
+
+ /**
+ * Returns a non-null, read-only Iterator (doesn't allow modification) over
+ * all the fully qualified names of Editors.
+ */
+ public Iterator<String> getEditorNames();
+
+ /**
+ * adds an editor type to the collection of editor types
+ * @param editorType a name that specifies the type of the editor
+ */
+ public void addEditorType(String editorType);
+
+ /**
+ * gets an instance of the NetworkEditEventAdaptor associated with the input editor
+ * The NetworkEditEventAdapter handles events that are associated with user input to the
+ * editor, such as mouse actions, drag/drop, keystrokes. Each NetworkEditEventAdapter is specialized
+ * for the editor that is is associated with. This is written by the developer and is at the heart of
+ * the specialized behaviour of the editor.
+ * @param editor
+ * @return the NetworkEditEventAdapter that is assigned to the editor
+ *
+ */
+ public NetworkEditEventAdapter getNetworkEditEventAdapter(CytoscapeEditor editor);
+
+ // MLC 12/04/06 BEGIN:
+ /**
+ * Create a ShapePaletteInfoGenerator for easily creating ShapePalette
+ * entries.
+ */
+ public ShapePaletteInfoGenerator createShapePaletteInfoGenerator();
+
+ /**
+ * Create a new ShapePaletteInfo object based on the given
+ * controlling Attribute name and controlling attribute value.
+ */
+ public ShapePaletteInfo createShapePaletteInfo(String controllingAttributeName,
+ String controllingAttributeValue);
+
+ // MLC 12/04/06 END.
+}
diff --git a/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/CytoscapeEditorManager.java b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/CytoscapeEditorManager.java
new file mode 100644
index 0000000..13ee05e
--- /dev/null
+++ b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/CytoscapeEditorManager.java
@@ -0,0 +1,1063 @@
+/* -*-Java-*-
+********************************************************************************
+*
+* File: CytoscapeEditorManager.java
+* RCS: $Header: $
+* Description:
+* Author: Allan Kuchinsky
+* Created: Tue Jul 05 11:44:41 2005
+* Modified: Wed Feb 04 08:29:29 2009 (Michael L. Creech) creech at w235krbza760
+* Language: Java
+* Package:
+/*
+
+ Copyright (c) 2006, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+
+* Revisions:
+*
+* Wed Feb 04 08:28:38 2009 (Michael L. Creech) creech at w235krbza760
+* Changed setEventHandlerForView() to no longer set and pass in the
+* view to the handler.
+* Tue Jul 29 14:54:22 2008 (Michael L. Creech) creech at w235krbza760
+* Added isEditorInOperation().
+* Thu Oct 25 05:40:57 2007 (Michael L. Creech) creech at w235krbza760
+* Changed call to buildVisualStyle() in
+* CytoscapeEditorManager.initializeEditor() to occur before
+* VisualMappingManager.setVisualStyle() is called. Removed old MLC
+* comments.
+* Mon Jul 23 19:24:02 2007 (Michael L. Creech) creech at w235krbza760
+* Fixed NPE bug in register() where CytoscapeEditorManager.log() statements
+* were being called without null pointer check.
+* Fri Jul 20 08:36:25 2007 (Michael L. Creech) creech at w235krbza760
+* Removed use of _initialized and simplified to assume CytoscapeEditor
+* is always loaded before any other editor. Added getDeleteAction().
+* Fri May 11 16:58:47 2007 (Michael L. Creech) creech at w235krbza760
+* Removed unneeded imports.
+* Wed Dec 27 09:03:24 2006 (Michael L. Creech) creech at w235krbza760
+* Changed initialize() to send CytoscapeEditorManagerSupport the
+* DeleteAction created for use by subclasses.
+* Thu Sep 14 08:57:24 2006 (Michael L. Creech) creech at w235krbza760
+* Removed all casting warnings for Java 1.5 & strongly types collections.
+* Sun Aug 06 05:50:30 2006 (Michael L. Creech) creech at w235krbza760
+* Fixed so visualStyleName can be different from the editor name.
+* Added getEditorNameForVisualStyleName() and changed initializeEditor()
+* to take a visualStyleName parameter.
+* Changed many instance variables to be private vs protected.
+* Fri Jul 28 04:46:31 2006 (Michael L. Creech) creech at w235krbza760
+* Added intialization of this manager if register is called by another
+* plugin before this plugin is loaded.
+********************************************************************************
+*/
+package cytoscape.editor;
+
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import javax.swing.SwingConstants;
+import javax.swing.undo.UndoableEdit;
+
+import cern.colt.list.IntArrayList;
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import cytoscape.data.CyAttributes;
+import cytoscape.data.Semantics;
+import cytoscape.editor.event.NetworkEditEventAdapter;
+import cytoscape.editor.impl.CytoscapeEditorManagerSupport;
+import cytoscape.editor.impl.ShapePalette;
+import cytoscape.logger.CyLogger;
+import cytoscape.util.undo.CyUndo;
+import cytoscape.view.CyNetworkView;
+import cytoscape.visual.CalculatorCatalog;
+import cytoscape.visual.VisualMappingManager;
+import cytoscape.visual.VisualStyle;
+import ding.view.DGraphView;
+import ding.view.InnerCanvas;
+import ding.view.DGraphView.Canvas;
+
+
+/**
+ * The <b>CytoscapeEditorManager </b> is the central class in the editor
+ * framework API. It maintains the state of the editing environment, maintains
+ * global state information, and implements static methods for editor
+ * registration, editor invocation (via CytoscapeEditorFactory), node/edge
+ * addition, undo/redo.
+ *
+ * @author Allan Kuchinsky, Agilent Technologies
+ * @version 1.0
+ * @see cytoscape.editor.CytoscapeEditorFactory
+ * @see cytoscape.editor.impl.CytoscapeEditorManagerSupport
+ *
+ */
+public abstract class CytoscapeEditorManager {
+ /**
+ * holding area for deleted nodes used when undo-ing deletes.
+ */
+
+ // AJK: 09/05/05: nodeClipBoard, edgeClipBoard, and networkClipBoard seem to
+ // be set but never referenced
+ // so I will not bother making one per NetworkView
+ private static IntArrayList nodeClipBoard;
+
+ /**
+ * holding area for deleted edges used when undo-ing deletes
+ */
+ private static IntArrayList edgeClipBoard;
+
+ /**
+ * default border width for a node. Used for highlighted the node upon
+ * mouseEnter, via thickening the node border.
+ */
+
+ private static float defaultBorderWidth = Float.NaN;
+
+ /**
+ * subsidiary class which implements methods that require non-static
+ * references, e.g. a Swing PropertyChangeListener
+ */
+
+ private static CytoscapeEditorManagerSupport manager;
+
+ /**
+ * pointer to currently active editor
+ */
+
+ private static CytoscapeEditor currentEditor = null;
+
+
+ /**
+ * flag that tells whether the full multi-editor framework is enabled for
+ * Cytoscape 2.2, only a simple editor will be deployed, and that simple
+ * editor will be invoked when Cytoscape is initialized future versions of
+ * Cytoscape will contain the full editor framework, with multiple available
+ * editors In Cytoscape 2.2, this flag can be set TRUE via a command line
+ * argument to Cytoscape (which is not advertised) when this flag is set,
+ * the full editor framewok will be loaded This functionality is for testing
+ * and prototyping purposes only please send an email to
+ * mailto:sysbio at labs.agilent.com if you are interested in experimenting
+ * with this multi-editorframework
+ */
+
+ private static boolean runningEditorFramework = false;
+
+ /**
+ * flag that tells whether an editor setup is in process used to consume
+ * stateChanged() events when visual style it set, so that we don't try to
+ * set editor twice
+ */
+ private static boolean settingUpEditor = false;
+
+ /**
+ * map that associates a network view with its editor
+ */
+
+ private static Map<CyNetworkView, CytoscapeEditor> editorViewMap = new HashMap<CyNetworkView, CytoscapeEditor>();
+
+
+ private static boolean editingEnabled = false;
+
+
+ /**
+ * palette from which shapes are dropped onto the canvas to form Nodes and Edges
+ */
+
+ private static ShapePalette currentShapePalette;
+
+
+ /**
+ * associates a view with its NetworkEditEventAdapter
+ */
+
+ private static Map<CyNetworkView, NetworkEditEventAdapter> viewNetworkEditEventAdapterMap = new HashMap<CyNetworkView, NetworkEditEventAdapter>();
+
+
+ /**
+ * associate a CyNetworkView with a ShapePalette
+ */
+
+ private static Map<CyNetworkView, ShapePalette> viewShapePaletteMap = new HashMap<CyNetworkView, ShapePalette>();
+
+
+ /**
+ * associates a network with all nodes hidden from it
+ */
+ private static Map<CyNetwork, List<Integer>> networkHiddenNodesMap = new HashMap<CyNetwork, List<Integer>>();
+
+
+ /**
+ * associates a network with all edges hidden from it
+ */
+ private static Map<CyNetwork, List<Integer>> networkHiddenEdgesMap = new HashMap<CyNetwork, List<Integer>>();
+
+
+ /**
+ * associates a network with the visual style used to edit it
+ */
+
+ // protected static HashMap networkVisualStyleMap = new HashMap();
+
+ /**
+ * associates a visual style with its set of EDGE_TYPEs
+ */
+ private static HashMap<VisualStyle, List<String>> visualStyleEdgeTypesMap = new HashMap<VisualStyle, List<String>>();
+
+ // protected static HashMap visualStyleEdgeTypesMap = new HashMap();
+
+ // map String names of visual styles to a list of the names of editors
+ // that use that style:
+ private static Map<String, String> visualStyleNameToEditorNameMap = new HashMap<String, String>();
+
+ /**
+ * CytoscapeAttribute: NODE_TYPE
+ */
+ public static final String NODE_TYPE = "NODE_TYPE";
+
+ public static final String NETWORK_TYPE = "NETWORK_TYPE";
+
+ // MLC 08/06/06 TODO: This should not be here!:
+ /**
+ * attribute used for BioPAX-like editor
+ */
+ public static final String BIOPAX_NODE_TYPE = "BIOPAX_NODE_TYPE";
+
+ /**
+ * CytoscapeAttribute: EDGE_TYPE
+ *
+ */
+// public static final String EDGE_TYPE = "EDGE_TYPE";
+ // AJK: 02/20/2010 should be usign Semantics.INTERACTION
+ public static final String EDGE_TYPE = Semantics.INTERACTION;
+
+
+ /**
+ *
+ */
+ public static final String ANY_VISUAL_STYLE = "ANY_VISUAL_STYLE";
+
+ /**
+ *
+ */
+ public static final String DEFAULT_EDITOR_TYPE = "cytoscape.editor.editors.DefaultCytoscapeEditor";
+
+ /**
+ * AJK: 06/19/06 CytoscapeEditor class descriptor -- for checking against NETWORK_MODIFIED events
+ */
+ public static final String CYTOSCAPE_EDITOR = "cytoscape.editor";
+
+
+
+
+ // AJK: 12/06/06: flag for "logging" diagnostic output
+ private static boolean loggingEnabled = true;
+
+ private static CyLogger logger = null;
+
+ /**
+ * initial setup of controls, menu items, undo/redo actions, and keyboard
+ * accelerators
+ *
+ */
+ protected static void initialize() {
+ CytoscapeEditorManager.setRunningEditorFramework(true);
+ CytoscapeEditorManager.setEditingEnabled(true);
+ manager = new CytoscapeEditorManagerSupport();
+ ShapePalette shapePalette = new ShapePalette();
+ Cytoscape.getDesktop().getCytoPanel(SwingConstants.WEST).add("Editor", shapePalette);
+ logger = CyLogger.getLogger(CytoscapeEditor.class);
+ }
+
+
+ /**
+ * initialize the editor as a side-effect of registering it.
+ * builds editor and its associated event handler
+ * builds visual style associated with editor
+ * @param editorName
+ * @param networkEditAdapterName
+ * @return the editor that is built
+ */
+
+ private static CytoscapeEditor initializeEditor(String editorName,
+ String networkEditAdapterName,
+ String visualStyleName) {
+ try {
+ CytoscapeEditorManager.setSettingUpEditor(true);
+
+ // setup a new editor
+
+ // AJK: 12/09/06
+ logger.debug("initializing Cytoscape editor: " + editorName);
+
+ CytoscapeEditor cyEditor = CytoscapeEditorFactory.INSTANCE.getEditor(editorName);
+ logger.debug("got CytoscapeEditor: " + cyEditor);
+
+ NetworkEditEventAdapter event = initializeEditEventAdapter(cyEditor,
+ networkEditAdapterName);
+ cyEditor.setNetworkEditEventAdapter(event);
+
+ cyEditor.buildVisualStyle();
+
+ if ((visualStyleName != null)
+ && (!(visualStyleName.equals(CytoscapeEditorManager.ANY_VISUAL_STYLE)))) {
+ VisualMappingManager manager = Cytoscape.getVisualMappingManager();
+ CalculatorCatalog catalog = manager.getCalculatorCatalog();
+ VisualStyle existingStyle = catalog.getVisualStyle(visualStyleName);
+
+ if (existingStyle != null) {
+ manager.setVisualStyle(existingStyle);
+ }
+ }
+
+ // AJK: 09/19/05 END
+ CytoscapeEditorManager.setCurrentEditor(cyEditor);
+
+ CytoscapeEditorManager.setSettingUpEditor(false);
+
+ // enable the "File.New" submenu
+ Cytoscape.getDesktop().getCyMenus().getMenuBar().getMenu("File.New").setEnabled(true);
+
+ return cyEditor;
+ } catch (InvalidEditorException ex) {
+ CytoscapeEditorManager.setSettingUpEditor(false);
+ logger.warn("Unable to set up Cytoscape editor", ex);
+
+ return null;
+ }
+ }
+
+ /**
+ * builds the named event handler and associates it with the input editor
+ * @param editor
+ * @param adapterName
+ * @return A NetworkEditEventAdapter object.
+ */
+ public static NetworkEditEventAdapter initializeEditEventAdapter(CytoscapeEditor editor,
+ String adapterName) {
+ NetworkEditEventAdapter event = editor.getNetworkEditEventAdapter();
+
+ if (event != null) {
+ return event;
+ }
+
+ try {
+ Class eventAdapterClass = Class.forName(adapterName);
+ event = (NetworkEditEventAdapter) eventAdapterClass.newInstance();
+ // AJK: 12/05/05 set caller for event class
+ event.set_caller(editor);
+ } catch (ClassNotFoundException ex) {
+ logger.warn("Can't find class for "+adapterName, ex);
+ } catch (InstantiationException ex) {
+ logger.warn("Can't instantiate "+adapterName, ex);
+ } catch (IllegalAccessException ex) {
+ logger.warn("Can't access "+adapterName, ex);
+ }
+
+ return event;
+ }
+
+ /**
+ * returns the network edit event adapter associated with the editor
+ * @param editor the CytoscapeEditor
+ */
+ public static NetworkEditEventAdapter getNetworkEditEventAdapter(CytoscapeEditor editor) {
+ return editor.getNetworkEditEventAdapter();
+ }
+
+ /**
+ * sets up menus for invoking the editor
+ *
+ * @param editorName
+ * text for editor name, to appear in menus
+ *
+ */
+ public static void register(String editorName) {
+ register(editorName, "BasicNetworkEventHandler", CytoscapeEditorManager.NODE_TYPE,
+ CytoscapeEditorManager.EDGE_TYPE, CytoscapeEditorManager.NETWORK_TYPE, CytoscapeEditorManager.ANY_VISUAL_STYLE);
+ }
+
+ /**
+ * makes the system aware of the editor. adds the editor's type to the list
+ * of editor types maintained by the CytoscapeEditorFactory.
+ *
+ * @param editorName
+ * specifies the 'type' of the editor
+ * @param networkEditAdapterName
+ * every editor has a NetworkEditEventHandler that handles user
+ * input in in a way that is specialized for that editor. This is
+ * the heart of the editors behaviour.
+ */
+ public static void register(String editorName, String networkEditAdapterName) {
+ register(editorName, networkEditAdapterName, CytoscapeEditorManager.NODE_TYPE,
+ CytoscapeEditorManager.EDGE_TYPE, CytoscapeEditorManager.NETWORK_TYPE, CytoscapeEditorManager.ANY_VISUAL_STYLE);
+ }
+
+ /**
+ *
+ * makes the system aware of the editor. adds the editor's type to the list
+ * of editor types maintained by the CytoscapeEditorFactory.
+ *
+ * @param editorName
+ * specifies the 'type' of the editor
+ * @param networkEditAdapterName
+ * every editor has a NetworkEditEventHandler that handles user
+ * input in in a way that is specialized for that editor. This is
+ * the heart of the editors behaviour.
+ * @param visualStyleName
+ * specifies the visual style that is to be associated with the editor
+ */
+ public static void register(String editorName, String networkEditAdapterName,
+ String visualStyleName) {
+ register(editorName, networkEditAdapterName, CytoscapeEditorManager.NODE_TYPE,
+ CytoscapeEditorManager.EDGE_TYPE, CytoscapeEditorManager.NETWORK_TYPE, visualStyleName);
+ }
+
+ /**
+ * makes the system aware of the editor. adds the editor's type to the list
+ * of editor types maintained by the CytoscapeEditorFactory.
+ *
+ * @param editorName
+ * specifies the 'type' of the editor
+ * @param networkEditAdapterName
+ * every editor has a NetworkEditEventHandler that handles user
+ * input in in a way that is specialized for that editor. This is
+ * the heart of the editors behaviour.
+ * @param controllingNodeAttribute
+ * attribute used by the visual style to map node attribute values into
+ * shapes, colors of nodes on palette
+ * @param controllingEdgeAttribute
+ * attribute used by the visual style to map edge attribute values into
+ * target arrows, line types of edges on palette
+ *
+ */
+ public static void register(String editorName, String networkEditAdapterName,
+ String controllingNodeAttribute, String controllingEdgeAttribute, String controllingNetworkAttribute) {
+ register(editorName, networkEditAdapterName, controllingNodeAttribute,
+ controllingEdgeAttribute, controllingNetworkAttribute, CytoscapeEditorManager.ANY_VISUAL_STYLE);
+ }
+
+ /**
+ *
+ * makes the system aware of the editor. adds the editor's type to the list
+ * of editor types maintained by the CytoscapeEditorFactory.
+ *
+ * @param editorName
+ * specifies the 'type' of the editor
+ * @param networkEditAdapterName
+ * every editor has a NetworkEditEventHandler that handles user
+ * input in in a way that is specialized for that editor. This is
+ * the heart of the editors behaviour.
+ * @param controllingNodeAttribute
+ * attribute used by the visual style to map node attribute values into
+ * shapes, colors of nodes on palette
+ * @param controllingEdgeAttribute
+ * attribute used by the visual style to map edge attribute values into
+ * target arrows, line types of edges on palette
+ * @param visualStyleName
+ * specifies the visual style that is to be associated with the editor
+ *
+ */
+ public static void register(String editorName, String networkEditAdapterName,
+ String controllingNodeAttribute, String controllingEdgeAttribute, String controllingNetworkAttribute,
+ String visualStyleName) {
+ // ASSUME: We have been initialized() before register() is ever called.
+ logger.debug ("BEGIN CEM.register()");
+ CytoscapeEditorManager.log("Putting " + visualStyleName + " --> " + editorName);
+ visualStyleNameToEditorNameMap.put(visualStyleName, editorName);
+
+ CytoscapeEditor cyEditor = CytoscapeEditorManager.initializeEditor(editorName,
+ networkEditAdapterName,
+ visualStyleName);
+
+ if (cyEditor != null) {
+ CytoscapeEditorManager.log("setting controlling attributes for editor " + cyEditor);
+ CytoscapeEditorManager.log("to " + controllingNodeAttribute + " and "
+ + controllingEdgeAttribute);
+ cyEditor.setControllingNodeAttribute(controllingNodeAttribute);
+ cyEditor.setControllingEdgeAttribute(controllingEdgeAttribute);
+ cyEditor.setControllingNetworkAttribute(controllingNetworkAttribute);
+ CytoscapeEditorManager.log("now controlling attributes for editor " + cyEditor);
+ CytoscapeEditorManager.log("are " + cyEditor.getControllingNodeAttribute() + " and "
+ + cyEditor.getControllingEdgeAttribute());
+ }
+ // CytoscapeEditorManager.log("now controlling attributes for editor " + cyEditor);
+ // CytoscapeEditorManager.log("are " + cyEditor.getControllingNodeAttribute() + " and "
+ // + cyEditor.getControllingEdgeAttribute());
+ }
+
+ /**
+ * Return the List of the names of editors associated with a given
+ * visual style. Usually this list has one element, however
+ * certain styles, such as ANY_VISUAL_STYLE, may have more than
+ * one.
+ */
+ public static String getEditorNameForVisualStyleName(String visualStyleName) {
+ // AJK: 12/09/06: bug fix. return editor for ANY_VISUAL_STYLE if no style is found
+ return (String) visualStyleNameToEditorNameMap.get(visualStyleName);
+ }
+
+ /**
+ * Handles the logistics of setting up a New Network view.
+ * <ul>
+ * <li>checks to see if context methods are already loadedfor the view. If
+ * not, then they are created.
+ * <li>sets dimensions, background, layers, camera, coloring for canvas
+ * <li>sets up a NetworkEditEventHandler for the view
+ * </ul>
+ *
+ * @param newView
+ * the NetworkView being created
+ */
+ public static void setupNewNetworkView(CyNetworkView newView) {
+ CytoscapeEditor cyEditor = CytoscapeEditorManager.getCurrentEditor();
+
+ if (cyEditor != null) {
+ CytoscapeEditorManager.setEditorForView(newView, cyEditor);
+ }
+
+ ding.view.DGraphView wiwx = (DGraphView) newView;
+ ding.view.InnerCanvas canvas = wiwx.getCanvas();
+
+ // AJK: 09/22/06 fix for opacity of foreground canvas
+ wiwx.getCanvas(Canvas.FOREGROUND_CANVAS).setOpaque(false);
+
+ NetworkEditEventAdapter event = CytoscapeEditorManager.getViewNetworkEditEventAdapter(newView);
+
+ if (event == null) {
+ event = CytoscapeEditorFactory.INSTANCE.getNetworkEditEventAdapter(cyEditor);
+ CytoscapeEditorManager.setViewNetworkEditEventAdapter(newView, event);
+ canvas.addPhoebeCanvasDropListener(event);
+ Cytoscape.getNodeAttributes().getMultiHashMap().addDataListener(event);
+ Cytoscape.getEdgeAttributes().getMultiHashMap().addDataListener(event);
+ }
+
+ canvas.setEnabled(true);
+ }
+
+ /**
+ * sets mapping of event handler to CyNetworkView. Typically done when a
+ * NETWORK_VIEW_FOCUSED event is received.
+ * removes various listeners on canvas from previous view and sets up
+ * the listeners for this view on the canvas.
+ *
+ * @param view
+ */
+ public static void setEventHandlerForView(CyNetworkView view) {
+ DGraphView thisView = (DGraphView) view;
+ InnerCanvas canvas = ((InnerCanvas) thisView.getCanvas());
+ NetworkEditEventAdapter oldEvent = CytoscapeEditorManager.getViewNetworkEditEventAdapter((CyNetworkView) thisView);
+
+ if (oldEvent != null) // remove event from this canvas
+ {
+ canvas.removeMouseListener(oldEvent);
+ canvas.removeMouseMotionListener(oldEvent);
+ canvas.removePhoebeCanvasDropListener(oldEvent);
+ }
+
+ CytoscapeEditor cyEditor = CytoscapeEditorManager.getCurrentEditor();
+ NetworkEditEventAdapter newEvent = CytoscapeEditorFactory.INSTANCE.getNetworkEditEventAdapter(cyEditor);
+ CytoscapeEditorManager.setViewNetworkEditEventAdapter((CyNetworkView) thisView, newEvent);
+ // MLC 02/03/09 BEGIN:
+ // Setting and passing the view is no longer needed since the current network view is used:
+ // newEvent.setView((DGraphView) view);
+ // newEvent.start((DGraphView) thisView);
+ newEvent.start();
+ // MLC 02/03/09 END.
+ canvas.addPhoebeCanvasDropListener(newEvent);
+ }
+
+ /**
+ * set the adapter that handles drags/drops, other mouse events on the
+ * canvas. Associate it with the input view.
+ *
+ * @param view
+ * the Network View
+ * @param event
+ * the NetworkEditEventHandler associated with the view.
+ */
+ public static void setViewNetworkEditEventAdapter(CyNetworkView view,
+ NetworkEditEventAdapter event) {
+ // MLC 02/03/09:
+ // log ("CEM: mapping view '" + view.getTitle() + "' to event handler '" + event + "'.");
+ viewNetworkEditEventAdapterMap.put(view, event);
+ }
+
+ /**
+ * retrieves the adapter that handles drags/drops, other mouse events on the
+ * canvas
+ *
+ * @return the NetworkEventAdapter
+ */
+ public static NetworkEditEventAdapter getViewNetworkEditEventAdapter(CyNetworkView view) {
+ Object obj = viewNetworkEditEventAdapterMap.get(view);
+
+ if (obj != null) {
+ if (obj instanceof NetworkEditEventAdapter) {
+ return (NetworkEditEventAdapter) obj;
+ }
+ }
+
+ return null;
+ }
+
+ /**
+ * get the editor that is assigned to this CyNetworkView
+ *
+ * @param view
+ * a CyNetworkView
+ * @return the editor assigned to this CyNetworkView
+ */
+ public static CytoscapeEditor getEditorForView(CyNetworkView view) {
+ Object obj = editorViewMap.get(view);
+
+ if (obj != null) {
+ if (obj instanceof CytoscapeEditor) {
+ return (CytoscapeEditor) obj;
+ }
+ }
+
+ return null;
+ }
+
+ /**
+ * get the ShapePalette that is associated with a CyNetworkView. needed when
+ * a view changes
+ *
+ * @param view The view we're getting the pallete for.
+ * @return The ShapePalette object for the view.
+ */
+ public static ShapePalette getShapePaletteForView(CyNetworkView view) {
+ return (ShapePalette) viewShapePaletteMap.get(view);
+ }
+
+ /**
+ * sets the ShapePalette that is associated with a CyNetworkView. needed when
+ * a view changes
+ * @param view
+ * @param shape
+ */
+ public static void setShapePaletteForView(CyNetworkView view, ShapePalette shape) {
+ viewShapePaletteMap.put(view, shape);
+ }
+
+ /**
+ * returns nodes hidden from network
+ *
+ * @param net The network to look for hidden nodes in.
+ * @return An array of hidden node indices.
+ */
+ public static int[] getHiddenNodesForNetwork(CyNetwork net) {
+ List hiddenNodesList = (List) networkHiddenNodesMap.get(net);
+
+ if (hiddenNodesList == null) {
+ return new int[0];
+ }
+
+ int[] nodeIndices = new int[hiddenNodesList.size()];
+
+ for (int i = 0; i < hiddenNodesList.size(); i++) {
+ nodeIndices[i] = ((Integer) hiddenNodesList.get(i)).intValue();
+ }
+
+ return nodeIndices;
+ }
+
+ /**
+ * returns edges hidden from network
+ *
+ * @param net The network we're looking for hidden edges in.
+ * @return An array of hidden edge indices in the network.
+ */
+ public static int[] getHiddenEdgesForNetwork(CyNetwork net) {
+ List hiddenEdgesList = (List) networkHiddenEdgesMap.get(net);
+
+ if (hiddenEdgesList == null) {
+ return new int[0];
+ }
+
+ int[] edgeIndices = new int[hiddenEdgesList.size()];
+
+ for (int i = 0; i < hiddenEdgesList.size(); i++) {
+ edgeIndices[i] = ((Integer) hiddenEdgesList.get(i)).intValue();
+ }
+
+ return edgeIndices;
+ }
+
+ /**
+ * adds a node to the list of nodes hidden from network
+ *
+ * @param net The network to add the node to.
+ * @param nodeIdx index of the node to be added
+ */
+ public static void addHiddenNodeForNetwork(CyNetwork net, int nodeIdx) {
+ List<Integer> hiddenNodesList = networkHiddenNodesMap.get(net);
+
+ if (hiddenNodesList == null) {
+ hiddenNodesList = new ArrayList<Integer>();
+ }
+
+ hiddenNodesList.add(new Integer(nodeIdx)); // don't worry about
+ // duplicates
+
+ networkHiddenNodesMap.put(net, hiddenNodesList);
+ }
+
+ /**
+ * adds an edge to the list of edges hidden from network
+ *
+ * @param net The network to add the node to.
+ * @param edgeIdx index of the edge to be added
+ */
+ public static void addHiddenEdgeForNetwork(CyNetwork net, int edgeIdx) {
+ List<Integer> hiddenEdgesList = networkHiddenEdgesMap.get(net);
+
+ if (hiddenEdgesList == null) {
+ hiddenEdgesList = new ArrayList<Integer>();
+ }
+
+ hiddenEdgesList.add(new Integer(edgeIdx)); // don't worry about
+ // duplicates
+
+ networkHiddenEdgesMap.put(net, hiddenEdgesList);
+ }
+
+ /**
+ * adds an edge type to the mappings kept between visual style and its EDGE_TYPE
+ * attribute values
+ * @param vizStyle
+ * @param edgeType
+ */
+ public static void addEdgeTypeForVisualStyle(VisualStyle vizStyle, String edgeType) {
+ List<String> edgeTypes = visualStyleEdgeTypesMap.get(vizStyle);
+
+ if (edgeTypes == null) {
+ edgeTypes = new ArrayList<String>();
+ }
+
+ if (!edgeTypes.contains(edgeType)) {
+ edgeTypes.add(edgeType);
+ }
+
+ visualStyleEdgeTypesMap.put(vizStyle, edgeTypes);
+ }
+
+ /**
+ *
+ * @param vizStyle
+ * @return a list of the EDGE_TYPEs associated with the visual style
+ */
+ public static List getEdgeTypesForVisualStyle(VisualStyle vizStyle) {
+ return (List) visualStyleEdgeTypesMap.get(vizStyle);
+ }
+
+ /**
+ * set the editor for a CyNetworkView
+ *
+ * @param view
+ * the CyNetworkView
+ * @param editor
+ * the editor to be assigned to the CyNetworkView
+ */
+ public static void setEditorForView(CyNetworkView view, CytoscapeEditor editor) {
+ editorViewMap.put(view, editor);
+ }
+
+ /**
+ * adds an undoable edit to the UndoManager. Currently the Cytoscape Editor
+ * framework supports undo/redo for deletion operations. This method is
+ * typically invoked from within the code for performing deletion.
+ *
+ *
+ *
+ * @param edit
+ * the edit method to be added to the UndoManager.
+ */
+ public static void addEdit(UndoableEdit edit) {
+ CyUndo.getUndoableEditSupport().postEdit(edit);
+ }
+
+ /**
+ * clipboard for storing deleted nodes. Used by undo/redo.
+ *
+ * @return clipboard for storing deleted nodes.
+ */
+ public static IntArrayList getNodeClipBoard() {
+ if (nodeClipBoard == null) {
+ nodeClipBoard = new IntArrayList();
+ }
+
+ return nodeClipBoard;
+ }
+
+ /**
+ * clipboard for storing deleted edges. Used by undo/redo.
+ *
+ * @return clipboard for storing deleted edges.
+ */
+ public static IntArrayList getEdgeClipBoard() {
+ if (edgeClipBoard == null) {
+ edgeClipBoard = new IntArrayList();
+ }
+
+ return edgeClipBoard;
+ }
+
+ /**
+ * Returns the editor being currently used in Cytoscape.
+ *
+ * @return the editor
+ */
+ public static CytoscapeEditor getCurrentEditor() {
+ return currentEditor;
+ }
+
+ /**
+ * @param currentEditor
+ * the editor being currently used
+ *
+ */
+ public static void setCurrentEditor(CytoscapeEditor currentEditor) {
+ CytoscapeEditorManager.currentEditor = currentEditor;
+ }
+
+ /**
+ * returns the default node border width. This is used in highlighting a
+ * node, by thickening its border, upon mouseEntry.
+ *
+ * @return the default border width
+ */
+ public static float getDefaultBorderWidth() {
+ return defaultBorderWidth;
+ }
+
+ /**
+ * sets the default node border width. This is used in highlighting a node,
+ * by thickening its border, upon mouseEntry.
+ *
+ * @param defaultBorderWidth defaultBorderWidth to set.
+ */
+ public static void setDefaultBorderWidth(float defaultBorderWidth) {
+ CytoscapeEditorManager.defaultBorderWidth = defaultBorderWidth;
+ }
+
+ /**
+ * flag that indicates whether or not the editor framework is running
+ *
+ * @return true if the editor framework is running, false otherwise
+ */
+ public static boolean isRunningEditorFramework() {
+ return runningEditorFramework;
+ }
+
+ /**
+ * set the flag that indicates whether or not the editor framework is
+ * running. Currently this is done via command line argument to Cytoscape
+ *
+ * @param runningEditorFramework true if the editor framework is running, false otherwise
+ */
+ public static void setRunningEditorFramework(boolean runningEditorFramework) {
+ CytoscapeEditorManager.runningEditorFramework = runningEditorFramework;
+ }
+
+ /**
+ * @return Returns the editingEnabled.
+ */
+ public static boolean isEditingEnabled() {
+ return editingEnabled;
+ }
+
+ /**
+ * @param editingEnabled
+ * The editingEnabled to set.
+ */
+ public static void setEditingEnabled(boolean editingEnabled) {
+ CytoscapeEditorManager.editingEnabled = editingEnabled;
+ }
+
+ public static boolean isEditorInOperation (int tabIdx) {
+ int idx = Cytoscape.getDesktop().getCytoPanel(SwingConstants.WEST).indexOfComponent("Editor");
+ return (idx == tabIdx);
+ }
+ /**
+ * Does the Editor possibly have focus because the Editor tab is selected?
+ */
+ public static boolean isEditorInOperation () {
+ return isEditorInOperation (Cytoscape.getDesktop().getCytoPanel(SwingConstants.WEST).getSelectedIndex());
+ }
+
+ /**
+ * @return Returns the currentShapePalette.
+ */
+ public static ShapePalette getCurrentShapePalette() {
+ return currentShapePalette;
+ }
+
+ /**
+ * @param currentShapePalette
+ * The currentShapePalette to set.
+ */
+ public static void setCurrentShapePalette(ShapePalette currentShapePalette) {
+ CytoscapeEditorManager.currentShapePalette = currentShapePalette;
+ }
+
+
+ /**
+ * @return Returns the settingUpEditor.
+ */
+ public static boolean isSettingUpEditor() {
+ return settingUpEditor;
+ }
+
+ /**
+ * @param settingUpEditor
+ * The settingUpEditor to set.
+ */
+ public static void setSettingUpEditor(boolean settingUpEditor) {
+ CytoscapeEditorManager.settingUpEditor = settingUpEditor;
+ }
+
+ /**
+ * generate a unique name (title) for the network under construction
+ * "Network 0", "Network 1","Network 2", ...
+ *
+ * @return A unique network name string.
+ */
+ public static String createUniqueNetworkName() {
+ int iteration_limit = 100;
+ String netNamePre = "Network ";
+ String netName = "";
+
+ //Get the set of network title
+ java.util.Set theNetworkSet = Cytoscape.getNetworkSet();
+ java.util.Set<String> networkTitleSet = new java.util.TreeSet<String>();
+
+ for (Object cn : theNetworkSet) {
+ networkTitleSet.add(((CyNetwork) cn).getTitle());
+ }
+
+ while (iteration_limit > 0) {
+ netName = netNamePre + newNetworkTitleSuffix++;
+
+ // Check if the created title already exists
+ if (networkTitleSet.contains(netName)) {
+ iteration_limit--;
+
+ continue;
+ } else {
+ return netName;
+ }
+ }
+
+ // in the unlikely condition where we couldn't generate a
+ // unique name after a number of tries,
+ // return a random string and hope for the best
+ return new String("Agilent:" + Math.random());
+ }
+
+ private static int newNetworkTitleSuffix = 0;
+
+ /**
+ * reset attributes for a CyNode whose identifier has been reset, basically
+ * by copying over attributes from old identifier to new identifier
+ *
+ * @param oldId
+ * old node identifier
+ * @param newId
+ * new node identifier
+ * @param attrs
+ * attributes
+ *
+ */
+ public static void resetAttributes(String oldId, String newId, CyAttributes attrs) {
+ final String[] attrNames = attrs.getAttributeNames();
+
+ for (int i = 0; i < attrNames.length; i++) {
+ final byte type = attrs.getType(attrNames[i]);
+
+ if (attrs.hasAttribute(oldId, attrNames[i])) {
+ if (type == CyAttributes.TYPE_SIMPLE_LIST) {
+ List l = attrs.getListAttribute(oldId, attrNames[i]);
+
+ if ((l != null) && (l.size() > 0)) {
+ attrs.setListAttribute(newId, attrNames[i], l);
+ }
+ } else if (type == CyAttributes.TYPE_SIMPLE_MAP) {
+ Map m = attrs.getMapAttribute(oldId, attrNames[i]);
+
+ if (m != null) {
+ attrs.setMapAttribute(newId, attrNames[i], m);
+ }
+ } else if (type == CyAttributes.TYPE_BOOLEAN) {
+ attrs.setAttribute(newId, attrNames[i],
+ attrs.getBooleanAttribute(oldId, attrNames[i]));
+ } else if (type == CyAttributes.TYPE_INTEGER) {
+ attrs.setAttribute(newId, attrNames[i],
+ attrs.getIntegerAttribute(oldId, attrNames[i]));
+ } else if (type == CyAttributes.TYPE_FLOATING) {
+ attrs.setAttribute(newId, attrNames[i],
+ attrs.getDoubleAttribute(oldId, attrNames[i]));
+ } else if (type == CyAttributes.TYPE_STRING) {
+ attrs.setAttribute(newId, attrNames[i],
+ attrs.getStringAttribute(oldId, attrNames[i]));
+ }
+ }
+ }
+ }
+
+ // AJK: 12/06/06: BEGIN
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static boolean isLoggingEnabled() {
+ return loggingEnabled;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param loggingEnabled DOCUMENT ME!
+ */
+ public static void setLoggingEnabled(boolean loggingEnabled) {
+ CytoscapeEditorManager.loggingEnabled = loggingEnabled;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param msg DOCUMENT ME!
+ */
+ public static void log(String msg) {
+ if (isLoggingEnabled()) {
+ logger.debug(msg);
+ }
+ }
+
+ // AJK: 12/06/06
+}
diff --git a/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/CytoscapeEditorPlugin.java b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/CytoscapeEditorPlugin.java
new file mode 100644
index 0000000..4b118bf
--- /dev/null
+++ b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/CytoscapeEditorPlugin.java
@@ -0,0 +1,261 @@
+/* -*-Java-*-
+********************************************************************************
+*
+* File: CytoscapeEditorPlugin.java
+* RCS: $Header: $
+* Description:
+* Author: Allan Kuchinsky
+* Created: Mon Aug 01 08:42:41 2005
+* Modified: Mon Aug 18 07:41:47 2008 (Michael L. Creech) creech at w235krbza760
+* Language: Java
+* Package:
+/*
+
+ Copyright (c) 2006, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*
+* Revisions:
+*
+* Wed Jul 09 10:21:03 2008 (Michael L. Creech) creech at w235krbza760
+* Updated to version 2.60.
+* Tue Oct 30 11:22:23 2007 (Michael L. Creech) creech at w235krbza760
+* Updated to version 2.53.
+* Thu Oct 25 13:30:25 2007 (Michael L. Creech) creech at w235krbza760
+* Updated to version 2.52.
+* Thu Jul 19 13:29:22 2007 (Michael L. Creech) creech at w235krbza760
+* Removed use of _initialized and simplified to assume CytoscapeEditor
+* is always loaded before any other editor. Removed
+* unneeded definitions of getPluginInfoObject() and describe().
+* Fri May 11 16:37:23 2007 (Michael L. Creech) creech at w235krbza760
+* Updated VERSION to 2.50 and added getPluginInfoObject() for Cytoscape 2.5.
+* Fri Dec 15 10:08:07 2006 (Michael L. Creech) creech at w235krbza760
+* Hacked a fix for not reinitializing the plugin if it is loaded
+* first by another plugin.
+* Sat Aug 05 08:14:51 2006 (Michael L. Creech) creech at w235krbza760
+* Removed deprecated call to CytoscapeInit.getDefaultVisualStyle() in
+* initializeCytoscapeEditor().
+* Mon Jul 24 08:43:51 2006 (Michael L. Creech) creech at w235krbza760
+* Removed some misleading code--println that editor is loaded and
+* initialization code as though editor is initialized via a menu item, when
+* it is not.
+********************************************************************************
+*/
+package cytoscape.editor;
+
+import cytoscape.Cytoscape;
+import cytoscape.CytoscapeInit;
+import cytoscape.plugin.CytoscapePlugin;
+
+/**
+ * core plugin for CytoscapeEditor.
+ *
+ * @author Allan Kuchinsky, Agilent Technologies
+ * @version 1.0
+ *
+ */
+public class CytoscapeEditorPlugin extends CytoscapePlugin {
+ // MLC 07/20/07:
+ // private static boolean _initialized = false;
+ // MLC 07/20/07:
+ private static final double VERSION = 2.60;
+
+ /**
+ * Creates a new CytoscapeEditorPlugin object.
+ */
+ public CytoscapeEditorPlugin() {
+ // MLC 07/24/06 BEGIN:
+ // CytoscapeEditorManager.log("CytoscapeEditor loaded ");
+ // MainPluginAction mpa = new MainPluginAction();
+ // CytoscapeEditorManager.setRunningEditorFramework(true);
+ // CytoscapeEditorManager.log("Setting up CytoscapeEditor");
+ // mpa.initializeCytoscapeEditor();
+ // MLC 07/23/07:
+ //CytoscapeEditorManager.setLoggingEnabled(true);
+ initializeCytoscapeEditor();
+
+ // MLC 07/24/06 END.
+ }
+
+ // MLC 07/20/07 BEGIN:
+ // // overrides CytoscapePlugin.getPluginInfoObject():
+ // public PluginInfo getPluginInfoObject() {
+ // PluginInfo info = new PluginInfo();
+ // info.setName("CytoscapeEditor");
+ // info.setDescription("Add nodes and edges to a Cytoscape Network.");
+ //// info.setCategory(PluginInfo.Category.CORE);
+ //// info.setPluginVersion("2.5.01");
+ // info.setCytoscapeVersion("2.5");
+ // // info.setProjectUrl("http://www.cytoscape.org/download_agilent_literature_search_v2.5.php?file=litsearch_v2.4");
+ // info.addAuthor("Allan Kuchinsky", "Agilent Labs");
+ // info.addAuthor("Michael Creech", "Blue Oak Software");
+ // return info;
+ // }
+ // MLC 07/20/07 END.
+
+ // MLC 07/20/07 BEGIN:
+
+ // /**
+ // * Overrides CytoscapePlugin.describe():
+ // */
+ // public String describe() {
+ // return "Add nodes and edges to a Cytoscape Network. ";
+ // }
+
+ /**
+ * sets various flags and registers various editors with the CytoscapeEditorManager
+ *
+ */
+
+ private void initializeCytoscapeEditor() {
+ // public static void initializeCytoscapeEditor() {
+ //if (_initialized) {
+ // return;
+ // }
+ // CytoscapeEditorManager.setRunningEditorFramework(true);
+ // CytoscapeEditorManager.setEditingEnabled(true);
+ // MLC 07/20/07 END.
+ CytoscapeEditorManager.initialize();
+
+ // add default palette-based editor
+ CytoscapeEditorManager.register(CytoscapeEditorManager.DEFAULT_EDITOR_TYPE,
+ "cytoscape.editor.event.PaletteNetworkEditEventHandler",
+ // AJK: 02/03/06 have Default editor use current visual
+ // style
+ CytoscapeEditorManager.NODE_TYPE, CytoscapeEditorManager.EDGE_TYPE, CytoscapeEditorManager.NETWORK_TYPE,
+ CytoscapeEditorManager.ANY_VISUAL_STYLE);
+
+ // AJK: 12/09/06 SimpleBioMoleculeEditor deleted
+ /*
+ CytoscapeEditorManager.register("SimpleBioMoleculeEditor",
+ "cytoscape.editor.event.PaletteNetworkEditEventHandler",
+ CytoscapeEditorManager.NODE_TYPE, CytoscapeEditorManager.EDGE_TYPE,
+ MapBioMoleculeEditorToVisualStyle.BIOMOLECULE_VISUAL_STYLE);
+
+ */
+
+ // AJK: 12/09/06 BEGIN
+ // register an editor to handle BioPAX visual style
+ // TODO: this is a short-term contingency, to be overhauled
+ // when vizmapper is overhauled for Cytoscape 2.5
+ // CytoscapeEditorManager.register("cytoscape.editor.editors.SimpleBioPAXEditor",
+ // "cytoscape.editor.event.PaletteNetworkEditEventHandler",
+ // "biopax.entity_type", // controlling node attribute
+ // "BIOPAX_EDGE_TYPE", // controlling edge type
+ // "BioPAX v 0_5");
+ //
+
+ // AJK: 12/09/06 END
+ String editorName = CytoscapeEditorManager.DEFAULT_EDITOR_TYPE;
+
+ try {
+ CytoscapeEditor cyEditor = CytoscapeEditorFactory.INSTANCE.getEditor(editorName);
+ CytoscapeEditorManager.setCurrentEditor(cyEditor);
+
+ // MLC 08/06/06:
+ // CytoscapeEditorManager.setDefaultEditor(cyEditor);
+ } catch (InvalidEditorException ex) {
+ CytoscapeEditorManager.log("Error: cannot set up Cytoscape Editor: " + editorName);
+ }
+
+ Cytoscape.getDesktop().setVisualStyle(Cytoscape.getVisualMappingManager()
+ .getCalculatorCatalog()
+ .getVisualStyle( // MLC 08/06/06:
+ // CytoscapeInit.getDefaultVisualStyle()));
+ // MLC 08/06/06:
+ CytoscapeInit.getProperties().getProperty("defaultVisualStyle")));
+ // MLC 07/20/07:
+ // _initialized = true;
+ }
+
+ // MLC 07/24/06 BEGIN:
+ // public class MainPluginAction extends AbstractAction {
+ // public MainPluginAction() {
+ // super("Cytoscape Editor");
+ // }
+ //
+ // /**
+ // * Gives a description of this plugin.
+ // */
+ // public String describe() {
+ // StringBuffer sb = new StringBuffer();
+ // sb.append("Add nodes and edges to a Cytoscape Network. ");
+ // return sb.toString();
+ // }
+ //
+ // /**
+ // * This method is called when the user selects the menu item.
+ // */
+ // public void actionPerformed(ActionEvent ae) {
+ // initializeCytoscapeEditor();
+ // }
+ //
+ // /**
+ // * sets various flags and registers various editors with the CytoscapeEditorManager
+ // *
+ // */
+ // public void initializeCytoscapeEditor() {
+ //
+ //
+ // CytoscapeEditorManager.setEditingEnabled(false);
+ //
+ // CytoscapeEditorManager.initialize();
+ //
+ // // add default palette-based editor
+ // CytoscapeEditorManager.register(
+ // CytoscapeEditorManager.DEFAULT_EDITOR_TYPE,
+ // "cytoscape.editor.event.PaletteNetworkEditEventHandler",
+ // // AJK: 02/03/06 have Default editor use current visual
+ // // style
+ // CytoscapeEditorManager.NODE_TYPE,
+ // CytoscapeEditorManager.EDGE_TYPE,
+ // CytoscapeEditorManager.ANY_VISUAL_STYLE);
+ //
+ // CytoscapeEditorManager.register("SimpleBioMoleculeEditor",
+ // "cytoscape.editor.event.PaletteNetworkEditEventHandler",
+ // CytoscapeEditorManager.NODE_TYPE,
+ // CytoscapeEditorManager.EDGE_TYPE,
+ // MapBioMoleculeEditorToVisualStyle.BIOMOLECULE_VISUAL_STYLE);
+ //
+ // String editorName = CytoscapeEditorManager.DEFAULT_EDITOR_TYPE;
+ // try {
+ // CytoscapeEditor cyEditor = CytoscapeEditorFactory.INSTANCE
+ // .getEditor(editorName);
+ // CytoscapeEditorManager.setCurrentEditor(cyEditor);
+ // CytoscapeEditorManager.setDefaultEditor(cyEditor);
+ // } catch (InvalidEditorException ex) {
+ // CytoscapeEditorManager.log("Error: cannot set up Cytoscape Editor: "
+ // + editorName);
+ // }
+ //
+ // Cytoscape.getDesktop().setVisualStyle(
+ // Cytoscape.getVisualMappingManager()
+ // .getCalculatorCatalog().getVisualStyle(
+ // CytoscapeInit.getDefaultVisualStyle()));
+ // }
+ //
+ // }
+ // MLC 07/24/06 END.
+}
diff --git a/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/DragSourceContextCursorSetter.java b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/DragSourceContextCursorSetter.java
new file mode 100644
index 0000000..9074272
--- /dev/null
+++ b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/DragSourceContextCursorSetter.java
@@ -0,0 +1,70 @@
+/* -*-Java-*-
+********************************************************************************
+*
+* File: DragSourceContextCurorSetter.java
+* RCS: $Header: $
+* Description:
+* Author: Michael L. Creech
+* Created: Sat Dec 16 14:54:45 2006
+* Modified: Sun Dec 17 05:41:06 2006 (Michael L. Creech) creech at w235krbza760
+* Language: Java
+* Package:
+/*
+
+ Copyright (c) 2006, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+********************************************************************************
+*/
+package cytoscape.editor;
+
+import java.awt.Cursor;
+import java.awt.Point;
+import java.awt.dnd.DragSourceDragEvent;
+
+import cytoscape.view.CyNetworkView;
+
+
+/**
+ * Interface used to allow a general computation to determine
+ * the cursor to show during a drag operation originating
+ * from a BasicCytoShapeEntity (palette entry) that is dragged over a
+ * CyNetworkView of interest.
+ * @author Michael L. Creech
+ */
+public interface DragSourceContextCursorSetter {
+ /**
+ * Used to determine the cursor to show during a drag operation originating
+ * from a BasicCytoShapeEntity (palette entry) that is dragged over a
+ * CyNetworkView of interest. For example, we might want to show that
+ * it is illegal to drop on certain objects, such as Edges.
+ * @param netView the CyNetworkView that is being dragged over.
+ * @param netViewLoc the location within netView of the cursor, in netView coordinates.
+ * @param dsde the DragSourceDragEvent that describes this particular
+ * drag operation.
+ * @return the Cursor to display during this drag (e.g, DragSource.DefaultCopyNoDrop).
+ */
+ public Cursor computeCursor(CyNetworkView netView, Point netViewLoc, DragSourceDragEvent dsde);
+}
diff --git a/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/GraphicalEntity.java b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/GraphicalEntity.java
new file mode 100644
index 0000000..4a180e2
--- /dev/null
+++ b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/GraphicalEntity.java
@@ -0,0 +1,105 @@
+/*
+ * Created on May 28, 2005
+ *
+ */
+package cytoscape.editor;
+
+import java.awt.Image;
+import java.awt.dnd.DragSource;
+
+import javax.swing.Icon;
+
+
+/**
+ *
+ * Interface for defining draggable/droppable visual components in the
+ * Cytoscape editor framework. The framework provides for dragging and dropping graphical
+ * entities from palette onto the canvas. Graphical entities are associated with
+ * semantic objects, i.e. nodes and edges, that are created when the graphical entities
+ * are dropped onto the canvas.
+ *
+ * @author Allan Kuchinsky, Agilent Technologies
+ *
+ */
+public interface GraphicalEntity {
+ /**
+ * get the Title of the graphical entity
+ * @return the Title
+ */
+ public String getTitle();
+
+ /**
+ * set the Title of the graphical entity
+ * @param title The title to set.
+ */
+ public void setTitle(String title);
+
+ /**
+ * retrieves the source of the drag operation, used when dragging a graphical entity from the palette onto
+ * the canvas
+ * @return the drag source
+ */
+ public DragSource getMyDragSource();
+
+ /**
+ * defines the source of the drag operation, used when dragging a graphical entity from the palette onto
+ * the canvas
+ * @param myDragSource the drag source
+ */
+ public void setMyDragSource(DragSource myDragSource);
+
+ /**
+ * get the image for the icon used on the palette to represent the graphical entity
+ * @return the image
+ */
+ public Image get_image();
+
+ /**
+ * set the image for the icon used on the palette to represent the graphical entity
+ * @param _image the icon to set
+ *
+ */
+ public void set_image(Image _image);
+
+ /**
+ * get the icon used on the palette to represent the graphical entity
+ * @return the icon used on the palette to represent the graphical entity
+ */
+ public Icon getIcon();
+
+ /**
+ * set the icon used on the palette to represent the graphical entity
+ * @param icon the icon to set
+ */
+ public void setIcon(Icon icon);
+
+ /**
+ * returns the name of the attribute associated with the Graphical Entity.
+ * This is used to determine whether a Node or an Edge has been dropped on the canvas.
+ * This attribute will also be set for the CyNode or CyEdge created as a result of the drop operation.
+ * @return the attribute name
+ */
+ public String getAttributeName();
+
+ /**
+ * sets the name of the attribute associated with the Graphical Entity.
+ * This is used to determine whether a Node or an Edge has been dropped on the canvas.
+ * This attribute will also be set for the CyNode or CyEdge created as a result of the drop operation.
+ * @param attributeName the attribute name to set
+ */
+ public void setAttributeName(String attributeName);
+
+ /**
+ * returns the value of the attribute associated with the Graphical Entity.
+ * This attribute will be set for the CyNode or CyEdge created as a result of the drop operation.
+ * @return the attribute value
+ */
+ public String getAttributeValue();
+
+ /**
+ * sets the value of the attribute associated with the Graphical Entity.
+ * This attribute will be set for the CyNode or CyEdge created as a result of the drop operation.
+ * @param attributeValue The attributeValue to set.
+ */
+ public void setAttributeValue(String attributeValue);
+}
diff --git a/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/InvalidEditorException.java b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/InvalidEditorException.java
new file mode 100644
index 0000000..ce5ebbd
--- /dev/null
+++ b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/InvalidEditorException.java
@@ -0,0 +1,31 @@
+/*
+ * Created on Jul 5, 2005
+ *
+ */
+package cytoscape.editor;
+
+
+/**
+ *
+ * Create a new exception when there is no registered editor corresponding
+ * to the editor type suppied to the CytoscapeEditorFactory.getEditor() method.
+ *
+ * @author Allan Kuchinsky, Agilent Technologies
+ * @version 1.0
+ *
+ */
+public class InvalidEditorException extends Exception {
+ // MLC 08/06/06:
+ private static final long serialVersionUID = 1850310863690996166L;
+
+ /**
+ * Create a new exception when there is no registered editor corresponding
+ * to the editor type suppied to the CytoscapeEditorFactory.getEditor() method.
+ * @param msg message, may be null
+ * @param cause cause, may be null
+ * @see CytoscapeEditorFactory
+ */
+ public InvalidEditorException(String msg, Throwable cause) {
+ super(msg, cause);
+ }
+}
diff --git a/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/ShapePaletteInfo.java b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/ShapePaletteInfo.java
new file mode 100644
index 0000000..0598efd
--- /dev/null
+++ b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/ShapePaletteInfo.java
@@ -0,0 +1,109 @@
+/* -*-Java-*-
+********************************************************************************
+*
+* File: ShapePaletteInfo.java
+* RCS: $Header: $
+* Description:
+* Author: Michael L. Creech
+* Created: Mon Dec 04 18:09:29 2006
+* Modified: Thu May 10 09:18:21 2007 (Michael L. Creech) creech at w235krbza760
+* Language: Java
+* Package:
+/*
+
+ Copyright (c) 2006, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+
+********************************************************************************
+*
+* Revisions:
+*
+* Thu May 10 09:17:30 2007 (Michael L. Creech) creech at w235krbza760
+* Changed use of 'calcType' from byte to VisualPropertyType for Cytoscape 2.5.
+********************************************************************************
+*/
+package cytoscape.editor;
+
+import cytoscape.visual.VisualPropertyType;
+
+
+/**
+ * Interface for obtaining information for creating and using
+ * ShapePalette entries.
+ */
+public interface ShapePaletteInfo {
+ /**
+ * Add a entry to this info object associating a given type of
+ * Calculator with a given value.
+ * @param calcType the VisualPropertyType repesentation of the
+ * Calculator (e.g., VisualPropertyType.NODE_FILL_COLOR). If
+ * calcType already exists in this object, it's information
+ * will be replaced.
+ * @param value the value associated with the key of this info
+ * object (see getKey() from the Calculator specified by calcType.
+ */
+ // MLC 05/09/07:
+ // void add(byte calcType, Object value);
+ // MLC 05/09/07:
+ void add(VisualPropertyType calcType, Object value);
+
+ /**
+ * Return the value that was obtained from the DiscreteMapping
+ * of the given Calculator for the controlling attribute value
+ * specified by the key of this ShapePaletteInfo. For
+ * example, if this ShapePaletteInfo has a key of "type1",
+ * then a call with
+ * calcType="VisualPropertyType.NODE_FILL_COLOR" would return
+ * the Color value that was associated with key "type1" from
+ * the DiscreteMapping in the Node Color Calculator.
+ * @param calcType the type of the Calculator for which we are
+ * to obtain the stored value.
+ * @return the Object value from the DiscreteMapping. If
+ * no such calculator exists for this object, null is
+ * returned. Note that a default value may be
+ * returned if calcType doesn't have a mapping for
+ * this Object's key.
+ */
+ // MLC 05/09/07:
+ // Object getValue(byte calcType);
+ // MLC 05/09/07:
+ Object getValue(VisualPropertyType calcType);
+
+ /**
+ * Return the key associated with this ShapePaletteInfo.
+ * This corresponds to a specific value from the
+ * controlling attribute name.
+ */
+ String getKey();
+
+ /**
+ * Return the name of the controlling attribute associated with
+ * this ShapePaletteInfo.
+ */
+ String getControllingAttributeName();
+
+ String toString();
+}
diff --git a/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/ShapePaletteInfoFilter.java b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/ShapePaletteInfoFilter.java
new file mode 100644
index 0000000..dfcbfc9
--- /dev/null
+++ b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/ShapePaletteInfoFilter.java
@@ -0,0 +1,56 @@
+/* -*-Java-*-
+********************************************************************************
+*
+* File: ShapePaletteInfoFilter.java
+* RCS: $Header: $
+* Description:
+* Author: Michael L. Creech
+* Created: Sun Dec 03 19:16:10 2006
+* Modified: Sun Dec 03 19:18:35 2006 (Michael L. Creech) creech at w235krbza760
+* Language: Java
+* Package:
+/*
+
+ Copyright (c) 2006, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+
+********************************************************************************
+*/
+package cytoscape.editor;
+
+
+/**
+ * Interface for defining filters to determing which ShapePaletteInfoImpl objects
+ * should be used.
+ */
+public interface ShapePaletteInfoFilter {
+ /**
+ * Should we use a given ShapePaletteInfoImpl entry?
+ * @param info the ShapePaletteInfoImpl under consideration.
+ * @return true if the info should be used. false otherwise.
+ */
+ public boolean useEntry(ShapePaletteInfo info);
+}
diff --git a/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/ShapePaletteInfoGenerator.java b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/ShapePaletteInfoGenerator.java
new file mode 100644
index 0000000..c9a3a7d
--- /dev/null
+++ b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/ShapePaletteInfoGenerator.java
@@ -0,0 +1,105 @@
+/* -*-Java-*-
+********************************************************************************
+*
+* File: ShapePaletteInfoGenerator.java
+* RCS: $Header: $
+* Description:
+* Author: Michael L. Creech
+* Created: Tue Dec 05 08:47:35 2006
+* Modified: Thu May 10 09:12:27 2007 (Michael L. Creech) creech at w235krbza760
+* Language: Java
+* Package:
+/*
+
+ Copyright (c) 2006, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+
+********************************************************************************
+*
+* Revisions:
+*
+* Thu May 10 09:08:25 2007 (Michael L. Creech) creech at w235krbza760
+* Changed buildShapePaletteInfo 'calcsToUse' from byte[] to
+* VisualPropertyType[] for Cytoscape 2.5.
+********************************************************************************
+*/
+package cytoscape.editor;
+
+import java.util.Iterator;
+
+import javax.swing.event.ChangeListener;
+
+import cytoscape.visual.VisualPropertyType;
+
+
+/**
+ * Generate information needed to easily build ShapePalette entries.
+ */
+public interface ShapePaletteInfoGenerator {
+ /**
+ * Return an Iterator over ShapePaletteInfo objects where each object
+ * represents the specific values from each Calculator of
+ * interest for a given mapping key. For example, if we had:
+ * <PRE>
+ * ENTITY_TYPE VisualPropertyType.NODE_FILL_COLOR VisualPropertyType.NODE_SHAPE
+ * "type1" Color.GREEN <default>
+ * "type2" <default> NodeShape.RECT
+ * </PRE>
+ * where ENTITY_TYPE is a controllingAttribute and <default>
+ * are missing values that should be filled in with the
+ * Appearance defaults for this Node/EdgeAppearanceCalculator,
+ * then this method would return 2 ShapePaletteInfoImpl entries:
+ * 1) key "type1" and map associations for
+ * VisualPropertyType.NODE_COLOR-->Color.GREEN and
+ * VisualPropertyType.NODE_SHAPE--> NodeShape.ELLIPSE (say is
+ * default).
+ * 2) key "type2" and map associations for
+ * VisualPropertyType.NODE_COLOR-->Color.WHITE (say is default) and
+ * VisualPropertyType.NODE_SHAPE-->NodeShape.RECT.
+ *
+ * @param appearanceCalc the Node/EdgeAppearanceCalculator
+ * from which to derive information.
+ * @param calcsToUse an Array of VisualPropertyType that represents what
+ * specific calculators of appearanceCalc to consider
+ * in computing shape palette information entries.
+ * @param controllingAttribute the attribute name for which we are
+ * gathering Calculator information.
+ * @param listener the ChangeListener to call when each given calculator
+ * specified by calcsToUse changes state. If null,
+ * no listening is performed.
+ * @param filter a ShapePaletteInfoFilter used to determine which
+ * ShapePaletteInfoImpl entries should be ignored. If filter=null,
+ * no filtering is performed--all entries are used.
+ */
+ Iterator<ShapePaletteInfo> buildShapePaletteInfo(Object appearanceCalc,
+ // 05/09/07:
+ // byte[] calcsToUse,
+ // 05/09/07:
+ VisualPropertyType[] calcsToUse,
+ String controllingAttribute,
+ ChangeListener listener,
+ ShapePaletteInfoFilter filter);
+}
diff --git a/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/editors/BasicCytoscapeEditor.java b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/editors/BasicCytoscapeEditor.java
new file mode 100644
index 0000000..8943171
--- /dev/null
+++ b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/editors/BasicCytoscapeEditor.java
@@ -0,0 +1,1034 @@
+/* -*-Java-*-
+ ********************************************************************************
+ *
+ * File: BasicCytoscapeEditor.java
+ * RCS: $Header: $
+ * Description:
+ * Author: Allan Kuchinsky
+ * Created: Thu Jul 27 14:27:11 2006
+ * Modified: Sun Aug 06 05:40:43 2006 (Michael L. Creech) creech at w235krbza760
+ * Language: Java
+ * Package:
+ /*
+
+ Copyright (c) 2006, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+
+ ********************************************************************************
+ *
+ * Revisions:
+ *
+ * Mon Jul 23 16:23:00 2007 (Michael L. Creech) creech at w235krbza760
+ * Removed adding of tooltips in addEdge() since this is now done
+ * using visual styles.
+ * Wed Dec 27 06:51:00 2006 (Michael L. Creech) creech at w235krbza760
+ * Cleanup and changed addNodeContextMenuItems(),
+ * addEdgeContextMenuItems(), and
+ * removeExistingDeleteMenuItemIfNecessary() to handle changes to
+ * DeleteAction.
+ * Thu Jul 27 14:27:55 2006 (Michael L. Creech) creech at w235krbza760
+ * Removed setting of BIO_PAX attributes from addNode().
+ * Fixed deprecated method usage in addNode().
+ ********************************************************************************
+ */
+package cytoscape.editor.editors;
+
+import giny.model.Node;
+import giny.view.EdgeView;
+import giny.view.NodeView;
+
+import java.awt.Cursor;
+import java.awt.Image;
+import java.awt.event.ActionEvent;
+import java.awt.geom.Point2D;
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JPopupMenu;
+import javax.swing.MenuElement;
+import javax.swing.event.MenuEvent;
+
+import cytoscape.CyEdge;
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+import cytoscape.CytoscapeModifiedNetworkManager;
+import cytoscape.actions.DeleteAction;
+import cytoscape.data.SelectEvent;
+import cytoscape.data.SelectEventListener;
+import cytoscape.data.Semantics;
+import cytoscape.editor.AddEdgeEdit;
+import cytoscape.editor.AddNodeEdit;
+import cytoscape.editor.CytoscapeEditor;
+import cytoscape.editor.CytoscapeEditorManager;
+import cytoscape.editor.event.BasicNetworkEditEventHandler;
+import cytoscape.editor.event.NetworkEditEventAdapter;
+import cytoscape.util.CytoscapeAction;
+import cytoscape.util.CytoscapeToolBar;
+import cytoscape.util.undo.CyAbstractEdit;
+import cytoscape.util.undo.CyUndo;
+import cytoscape.view.CyMenus;
+import cytoscape.view.CyNetworkView;
+import ding.view.DGraphView;
+import ding.view.EdgeContextMenuListener;
+import ding.view.NodeContextMenuListener;
+
+
+/**
+ * The <b>BasicCytoscapeEditor</b> provides base level graph editing
+ * functionality for Cytoscape, in particular the base level methods for adding
+ * nodes, edges, and context menu items.
+ * <p>
+ * Provides an "Edit => Connect Selected Nodes" menu item that, when chosen,
+ * creates a clique amongst the selected nodes.
+ * <p>
+ * Provides accelerators for modeless addition of nodes and edges.
+ * Control-clicking at a position on the canvas creates a node with default
+ * label in that position. The default label appears in an editable text field,
+ * so the user can edit its name immediately by just beginning to type. Hit
+ * ENTER or click (or control-click) anywhere outside the field, and the edited
+ * field is assigned as the label for the node. Control-clicking on a node on
+ * the canvas starts an edge with source at that node. Move the cursor and a
+ * rubber-banded line follows the cursor. As the cursor passes over another
+ * node, that node is highlighted and the rubber-banded line will snap to a
+ * connection point on that second node. Control-click the mouse again and the
+ * connection is established.
+ * <p>
+ * Provides functionality for deleting selected nodes and edges and an undo/redo
+ * framework for deletion of nodes and edges
+ *
+ * @author Allan Kuchinsky, Agilent Technologies
+ * @version 1.0
+ * @see BasicNetworkEditEventHandler
+ *
+ */
+
+public class BasicCytoscapeEditor implements CytoscapeEditor, SelectEventListener,
+ NodeContextMenuListener, EdgeContextMenuListener {
+ /**
+ * title of menu item for connecting selected Nodes
+ */
+ private static final String _connectedTitle = "Connect Selected Nodes";
+
+ /**
+ * name and type of the editor
+ */
+ protected String editorName;
+
+ /**
+ * pointer to Cytoscape menus
+ */
+ CyMenus _cyMenus;
+
+ /**
+ * pointer to Cytoscape toolbar
+ */
+ CytoscapeToolBar _toolBar;
+
+ boolean DEBUG = false;
+
+ /**
+ * 32x32 image for edge cursor
+ */
+ Image _connectionCursorImage;
+
+ /**
+ * default cursor used by Cytoscape
+ */
+ Cursor _originalCursor;
+
+ /**
+ *
+ * the name of the attribute used to determine Node shapes on palette this
+ * is the same as the controllingNodeAttribute for mapping of visual style
+ * to Node shape and color
+ */
+ private String _controllingNodeAttribute;
+
+ /**
+ * the name of the attribute used to determine edge shapes on palette this
+ * is the same as the controllingEdgeAttribute for mapping of visual style
+ * to edge line type, target arrow
+ */
+ private String _controllingEdgeAttribute;
+
+ private String _controllingNetworkAttribute;
+
+ /**
+ *
+ * the network event handler that is associated with this editor
+ */
+ NetworkEditEventAdapter _networkEditEventAdapter;
+
+ /**
+ *
+ */
+ public BasicCytoscapeEditor() {
+ super();
+ ConnectSelectedNodesAction connectAction = new ConnectSelectedNodesAction();
+ connectAction.setPreferredMenu("Edit");
+ Cytoscape.getDesktop().getCyMenus().addAction(connectAction);
+ }
+
+ /**
+ * wrapper for adding a node in Cytoscape. This is intended to be called by
+ * the CytoscapeEditor in lieu of making direct modifications to the
+ * Cytoscape model. Thus, it provides an insulating level of abstraction
+ * between the CytoscapeEditor and the Cytoscape implementation, allowing
+ * for portability and extensibility of the editor.
+ *
+ * this method will ensure that the node added is unique. If it finds that
+ * there is an existing node for <em>nodeName</em>, it will attempt to
+ * generate a new, unique, <em>nodeName</em> by extending the
+ * <em>nodeName</em> argument with a randomly generated extension.
+ *
+ * @param nodeName
+ * the name of the node to be created. This will be used as a
+ * unique identifier for the node.
+ * @param attribute
+ * a defining property for the node, that can be used in
+ * conjunction with the Visual Mapper to assign visual
+ * characteristics to different types of nodes. Also can be used,
+ * by the canvas when handling a dropped item, to distinguish
+ * between nodes and edges, so should be set to something like
+ * "NodeType".
+ * @param value
+ * the value of the attribute for this node. This can be used in
+ * conjunction with the Visual Mapper to assign visual
+ * characteristics to different types of nodes, for example to
+ * assign a violet diamond shape to a 'smallMolecule' node type.
+ * @param location
+ * the position at which to add the node
+ * @return the CyNode that has been either reused or created.
+ *
+ */
+ public CyNode addNode(String nodeName, String attribute, String value, Point2D location) {
+ CytoscapeEditorManager.log("Adding node " + nodeName + " at position " + location);
+
+ CyNode cn = Cytoscape.getCyNode(nodeName, false); // first see if
+ // there is an
+ // existing node
+
+ int iteration_limit = 100;
+
+ while ((cn != null) && (iteration_limit > 0)) {
+ java.util.Date d1 = new java.util.Date();
+ long t1 = d1.getTime();
+ String s1 = Long.toString(t1);
+ nodeName += ("_" + s1.substring(s1.length() - 3)); // append last 4
+ // digits of
+ // time stamp to node name
+
+ cn = Cytoscape.getCyNode(nodeName, false);
+ iteration_limit--;
+ }
+
+ // check for unlikely error condition where we couldn't generate a
+ // unique node after a number of tries
+ if (iteration_limit <= 0) {
+ String expDescript = "Cytoscape Editor cannot generate a unique node for this network. A serious internal error has occurred. Please file a bug report at http://www.cytoscape.org.";
+ String title = "Cannot generate a unique node";
+ JOptionPane.showMessageDialog(Cytoscape.getDesktop(), expDescript, title,
+ JOptionPane.PLAIN_MESSAGE);
+
+ return null;
+ }
+
+ // now create a unique node
+ cn = Cytoscape.getCyNode(nodeName, true);
+
+ CyNetwork net = Cytoscape.getCurrentNetwork();
+
+ if (attribute != null) {
+ Cytoscape.getNodeAttributes().setAttribute(cn.getIdentifier(), attribute, value);
+
+ if (attribute != CytoscapeEditorManager.NODE_TYPE) {
+ Cytoscape.getNodeAttributes()
+ .setAttribute(cn.getIdentifier(), CytoscapeEditorManager.NODE_TYPE, value);
+ }
+
+ net.restoreNode(cn);
+ }
+
+ net.unselectAllNodes();
+
+ List<CyNode> l = new ArrayList<CyNode>(1);
+ l.add(cn);
+ net.setSelectedNodeState(l, true);
+
+ NodeView nv = Cytoscape.getCurrentNetworkView().getNodeView(cn);
+ nv.setToolTip(cn.getIdentifier());
+
+ if (location != null) {
+ double[] nextLocn = new double[2];
+ nextLocn[0] = location.getX();
+ nextLocn[1] = location.getY();
+ ((DGraphView) Cytoscape.getCurrentNetworkView()).xformComponentToNodeCoords(nextLocn);
+ nv.setOffset(nextLocn[0], nextLocn[1]);
+ CytoscapeEditorManager.log("Offset for node " + cn + "set to " + nv.getOffset());
+ }
+
+ CyUndo.getUndoableEditSupport().postEdit( new AddNodeEdit(net,cn) );
+
+ // set tooltip on the node's view
+ Cytoscape.getCurrentNetworkView().addNodeContextMenuListener(this);
+ Cytoscape.firePropertyChange(Cytoscape.NETWORK_MODIFIED,
+ CytoscapeEditorManager.CYTOSCAPE_EDITOR, net);
+
+ return cn;
+ }
+
+ /**
+ * respond to selection of a Node. Does nothing right now. Implements
+ * SelectionEventListener interface:
+ */
+ public void onSelectEvent(SelectEvent e) {
+ }
+
+ // MLC 07/27/06 END.
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nodeView DOCUMENT ME!
+ * @param menu DOCUMENT ME!
+ */
+ public void addNodeContextMenuItems(NodeView nodeView, JPopupMenu menu) {
+ removeExistingDeleteMenuItemIfNecessary(menu);
+ menu.add(new DeleteAction(nodeView.getNode()));
+ }
+
+ protected void removeExistingDeleteMenuItemIfNecessary(JPopupMenu menu) {
+ MenuElement[] elements = menu.getSubElements();
+
+ for (int i = 0; i < elements.length; i++) {
+ MenuElement elem = elements[i];
+
+ if (elem instanceof JMenuItem) {
+ JMenuItem item = (JMenuItem) elem;
+
+ if (item.getText().equals(DeleteAction.ACTION_TITLE)) {
+ menu.remove(item);
+ }
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param menu DOCUMENT ME!
+ * @param label DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean menuItemExists(JPopupMenu menu, String label) {
+ boolean itemExists = false;
+
+ MenuElement[] elements = menu.getSubElements();
+
+ for (int i = 0; i < elements.length; i++) {
+ MenuElement elem = elements[i];
+
+ if (elem instanceof JMenuItem) {
+ JMenuItem item = (JMenuItem) elem;
+
+ if (item.getText().equals(label)) {
+ itemExists = true;
+
+ break;
+ }
+ }
+ }
+
+ return itemExists;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edgeView DOCUMENT ME!
+ * @param menu DOCUMENT ME!
+ */
+ public void addEdgeContextMenuItems(EdgeView edgeView, JPopupMenu menu) {
+ removeExistingDeleteMenuItemIfNecessary(menu);
+ menu.add(new DeleteAction(edgeView.getEdge()));
+ }
+
+ /**
+ * wrapper for adding a node in Cytoscape. This is intended to be called by
+ * the CytoscapeEditor in lieu of making direct modifications to the
+ * Cytoscape model. Thus, it provides an insulating level of abstraction
+ * between the CytoscapeEditor and the Cytoscape implementation, allowing
+ * for portability and extensibility of the editor.
+ *
+ * this method will ensure that the node added is unique. If it finds that
+ * there is an existing node for <em>nodeName</em>, it will attempt to
+ * generate a new, unique, <em>nodeName</em> by extending the
+ * <em>nodeName</em> argument with a randomly generated extension.
+ *
+ * @param nodeName
+ * the name of the node to be created. This will be used as a
+ * unique identifier for the node.
+ * @param attribute
+ * a defining property for the node, that can be used in
+ * conjunction with the Visual Mapper to assign visual
+ * characteristics to different types of nodes. Also can be used,
+ * by the canvas when handling a dropped item, to distinguish
+ * between nodes and edges, so should be set to something like
+ * "NodeType".
+ * @param value
+ * the value of the attribute for this node. This can be used in
+ * conjunction with the Visual Mapper to assign visual
+ * characteristics to different types of nodes, for example to
+ * assign a violet diamond shape to a 'smallMolecule' node type.
+ * @return the CyNode that has been either reused or created.
+ *
+ */
+ public CyNode addNode(String nodeName, String attribute, String value) {
+ return addNode(nodeName, attribute, value, null);
+ }
+
+ /**
+ * wrapper for adding a node in Cytoscape. This is intended to be called by
+ * the CytoscapeEditor in lieu of making direct modifications to the
+ * Cytoscape model. Thus, it provides an insulating level of abstraction
+ * between the CytoscapeEditor and the Cytoscape implementation, allowing
+ * for portability and extensibility of the editor.
+ *
+ * @param nodeName
+ * the name of the node to be created. This will be used as a
+ * unique identifier for the node.
+ * @param nodeType
+ * the value of the 'NodeType' attribute for this node. This can
+ * be used in conjunction with the Visual Mapper to assign visual
+ * characteristics to different types of nodes. Also can be used,
+ * by the canvas when handling, a dropped item, to distinguish
+ * between nodes and edges.
+ * @return the CyNode that has been either reused or created.
+ */
+ public CyNode addNode(String nodeName, String nodeType) {
+ return addNode(nodeName, CytoscapeEditorManager.NODE_TYPE, nodeType);
+ }
+
+ /**
+ * wrapper for adding a node in Cytoscape. This is intended to be called by
+ * the CytoscapeEditor in lieu of making direct modifications to the
+ * Cytoscape model. Thus, it provides an insulating level of abstraction
+ * between the CytoscapeEditor and the Cytoscape implementation, allowing
+ * for portability and extensibility of the editor. This form of addNode()
+ * will create a node in all cases, whether it previously exists or not.
+ *
+ * @param nodeName
+ * the name of the node to be created. This will be used as a
+ * unique identifier for the node.
+ * @return the CyNode that has been either reused or created.
+ */
+ public CyNode addNode(String nodeName) {
+ return addNode(nodeName, null);
+ }
+
+ /**
+ *
+ * wrapper for adding an edge in Cytoscape. This is intended to be called by
+ * the CytoscapeEditor in lieu of making direct modifications to the
+ * Cytoscape model. Thus, it provides an insulating level of abstraction
+ * between the CytoscapeEditor and the Cytoscape implementation, allowing
+ * for portability and extensibility of the editor.
+ *
+ * @param node_1
+ * Node at one end of the edge
+ * @param node_2
+ * Node at the other end of the edge
+ * @param attribute
+ * the attribute of the edge to be searched, a common one is
+ * Semantics.INTERACTION
+ * @param attribute_value
+ * a value for the attribute, like "pp" or "default"
+ * @param create
+ * if true, then create an edge if one does not already exist.
+ * Otherwise, return the edge if it already exists.
+ * @param edgeType
+ * a value for the "EdgeType" attribute assigned to the edge.
+ * This can be used in conjunction with the Visual Mapper.
+ * @return the CyEdge that has either been reused or created
+ *
+ */
+ public CyEdge addEdge(Node node_1, Node node_2, String attribute, Object attribute_value,
+ boolean create, String edgeType) {
+ // first see if edge already exists. If it does, then
+ // there is no need to set up undoable edit or fire event
+ CyEdge edge;
+ boolean uniqueEdge = true;
+ edge = Cytoscape.getCyEdge(node_1, node_2, attribute, attribute_value, false, true); // edge is directed
+
+ if (edge != null) {
+ uniqueEdge = false;
+ } else {
+ edge = Cytoscape.getCyEdge(node_1, node_2, attribute, attribute_value, create, true); // edge is directed
+ }
+
+ if (edge != null) {
+ CyNetwork net = Cytoscape.getCurrentNetwork();
+ net.restoreEdge(edge);
+
+ if (uniqueEdge) {
+ if (edgeType != null) {
+ Cytoscape.getEdgeAttributes()
+ .setAttribute(edge.getIdentifier(), CytoscapeEditorManager.EDGE_TYPE,
+ edgeType);
+ }
+
+ CyUndo.getUndoableEditSupport().postEdit( new AddEdgeEdit(net,edge) );
+
+ Cytoscape.firePropertyChange(Cytoscape.NETWORK_MODIFIED,
+ CytoscapeEditorManager.CYTOSCAPE_EDITOR, net);
+
+ Cytoscape.getCurrentNetworkView().addEdgeContextMenuListener(this);
+ }
+ }
+ // MLC 07/13/07 BEGIN:
+ // tooltips are now handles as vismap entries:
+ // set tooltip
+ // if (edge != null) {
+ // EdgeView ev = Cytoscape.getCurrentNetworkView().getEdgeView(edge);
+ // ev.setToolTip(edge.getIdentifier());
+ // }
+// MLC 07/13/07 END.
+ return edge;
+ }
+
+ /**
+ *
+ * wrapper for adding an edge in Cytoscape. This is intended to be called by
+ * the CytoscapeEditor in lieu of making direct modifications to the
+ * Cytoscape model. Thus, it provides an insulating level of abstraction
+ * between the CytoscapeEditor and the Cytoscape implementation, allowing
+ * for portability and extensibility of the editor.
+ *
+ * This particular method adds the edge without firing an event, such as
+ * would be done in a 'batch' operation such as 'ConnectSelectedNodes'
+ *
+ * @param node_1
+ * Node at one end of the edge
+ * @param node_2
+ * Node at the other end of the edge
+ * @param attribute
+ * the attribute of the edge to be searched, a common one is
+ * Semantics.INTERACTION
+ * @param attribute_value
+ * a value for the attribute, like "pp" or "default"
+ * @param create
+ * if true, then create an edge if one does not already exist.
+ * Otherwise, return the edge if it already exists.
+ * @param edgeType
+ * a value for the "EdgeType" attribute assigned to the edge.
+ * This can be used in conjunction with the Visual Mapper.
+ * @return the CyEdge that has either been reused or created
+ *
+ */
+ public CyEdge addEdgeWithoutFiringEvent (Node node_1, Node node_2, String attribute, Object attribute_value,
+ boolean create, String edgeType) {
+ // first see if edge already exists. If it does, then
+ // there is no need to set up undoable edit or fire event
+ CyEdge edge;
+ boolean uniqueEdge = true;
+ edge = Cytoscape.getCyEdge(node_1, node_2, attribute, attribute_value, false, true); // edge is directed
+
+ if (edge != null) {
+ uniqueEdge = false;
+ } else {
+ edge = Cytoscape.getCyEdge(node_1, node_2, attribute, attribute_value, create, true); // edge is directed
+ }
+
+ if (edge != null) {
+ CyNetwork net = Cytoscape.getCurrentNetwork();
+ net.restoreEdge(edge);
+
+ if (uniqueEdge) {
+ if (edgeType != null) {
+ Cytoscape.getEdgeAttributes()
+ .setAttribute(edge.getIdentifier(), CytoscapeEditorManager.EDGE_TYPE,
+ edgeType);
+ }
+
+// CyUndo.getUndoableEditSupport().postEdit( new AddEdgeEdit(net,edge) );
+//
+// Cytoscape.firePropertyChange(Cytoscape.NETWORK_MODIFIED,
+// CytoscapeEditorManager.CYTOSCAPE_EDITOR, net);
+
+ Cytoscape.getCurrentNetworkView().addEdgeContextMenuListener(this);
+ }
+ }
+ // MLC 07/13/07 BEGIN:
+ // tooltips are now handles as vismap entries:
+ // set tooltip
+ // if (edge != null) {
+ // EdgeView ev = Cytoscape.getCurrentNetworkView().getEdgeView(edge);
+ // ev.setToolTip(edge.getIdentifier());
+ // }
+//MLC 07/13/07 END.
+ return edge;
+ }
+
+
+ /**
+ *
+ * wrapper for adding an edge in Cytoscape. This is intended to be called by
+ * the CytoscapeEditor in lieu of making direct modifications to the
+ * Cytoscape model. Thus, it provides an insulating level of abstraction
+ * between the CytoscapeEditor and the Cytoscape implementation, allowing
+ * for portability and extensibility of the editor. This version always
+ * creates an edge, whether or not one already exists.
+ *
+ * @param node_1
+ * Node at one end of the edge
+ * @param node_2
+ * Node at the other end of the edge
+ * @param attribute
+ * the attribute of the edge to be searched, a common one is
+ * Semantics.INTERACTION
+ * @param attribute_value
+ * a value for the attribute, like "pp" or "default"
+ * @return the CyEdge that has been created
+ *
+ */
+ public CyEdge addEdge(Node node_1, Node node_2, String attribute, Object attribute_value) {
+ return addEdge(node_1, node_2, attribute, attribute_value, true, null);
+ }
+
+ /**
+ *
+ * wrapper for adding an edge in Cytoscape. This is intended to be called by
+ * the CytoscapeEditor in lieu of making direct modifications to the
+ * Cytoscape model. Thus, it provides an insulating level of abstraction
+ * between the CytoscapeEditor and the Cytoscape implementation, allowing
+ * for portability and extensibility of the editor. This version always
+ * creates an edge, whether or not one already exists.
+ *
+ * @param node_1
+ * Node at one end of the edge
+ * @param node_2
+ * Node at the other end of the edge
+ * @param attribute
+ * the attribute of the edge to be searched, a common one is
+ * Semantics.INTERACTION
+ * @param attribute_value
+ * a value for the attribute, like "pp" or "default"
+ * @param edgeType
+ * a value for the "EdgeType" attribute assigned to the edge.
+ * This can be used in conjunction with the Visual Mapper.
+ * @return the CyEdge that has been created
+ *
+ */
+ public CyEdge addEdge(Node node_1, Node node_2, String attribute, Object attribute_value,
+ String edgeType) {
+ return addEdge(node_1, node_2, attribute, attribute_value, true, edgeType);
+ }
+
+ /**
+ *
+ * wrapper for adding an edge in Cytoscape. This is intended to be called by
+ * the CytoscapeEditor in lieu of making direct modifications to the
+ * Cytoscape model. Thus, it provides an insulating level of abstraction
+ * between the CytoscapeEditor and the Cytoscape implementation, allowing
+ * for portability and extensibility of the editor.
+ *
+ * @param node_1
+ * Node at one end of the edge
+ * @param node_2
+ * Node at the other end of the edge
+ * @param attribute
+ * the attribute of the edge to be searched, a common one is
+ * Semantics.INTERACTION
+ * @param attribute_value
+ * a value for the attribute, like "pp" or "default"
+ * @param create
+ * if true, then create an edge if one does not already exist.
+ * Otherwise, return the edge if it already exists.
+ * @return the CyEdge that has either been reused or created
+ *
+ */
+ public CyEdge addEdge(Node node_1, Node node_2, String attribute, Object attribute_value,
+ boolean create) {
+ return addEdge(node_1, node_2, attribute, attribute_value, create, null);
+ }
+
+ /**
+ * Deletes (hides) a node from the current network
+ *
+ * @param node
+ * the node to be deleted
+ */
+ public void deleteNode(Node node) {
+ CyNetwork net = Cytoscape.getCurrentNetwork();
+ net.hideNode(node);
+ CytoscapeModifiedNetworkManager.setModified(net, CytoscapeModifiedNetworkManager.MODIFIED);
+ }
+
+ /**
+ * Deletes (hides) an edge from the current network
+ *
+ * @param edge
+ * the edge to be deleted
+ */
+ public void deleteEdge(CyEdge edge) {
+ CyNetwork net = Cytoscape.getCurrentNetwork();
+ net.hideEdge(edge);
+ CytoscapeModifiedNetworkManager.setModified(net, CytoscapeModifiedNetworkManager.MODIFIED);
+ }
+
+ /**
+ * build the visualStyle for this editor this code should be overidden by
+ * more specialized editors that programmatically create a visual style
+ *
+ */
+ public void buildVisualStyle() {
+ }
+
+ /**
+ * specialized initialization code for editor, called by
+ * CytoscapeEditorManager when a new editor is built, should be overridden
+ *
+ * @param args
+ * an arbitrary list of arguments passed to initialization
+ * routine. Not used in this editor
+ */
+ public void initializeControls(List args) {
+ // first, check to see if there already is a menu item to "Connect
+ // Selected Nodes"
+ // if not, then add an item
+ // TODO: look for routines to find a menu item given a string; there
+ // should be such a utility
+// JMenu editMenu = Cytoscape.getDesktop().getCyMenus().getEditMenu();
+// boolean foundConnectSelected = false;
+// CytoscapeEditorManager.log("item count = " + editMenu.getItemCount());
+//
+// for (int i = 0; i < editMenu.getItemCount(); i++) {
+// JMenuItem jIt = editMenu.getItem(i);
+//
+// if (jIt != null) {
+// String name = jIt.getText();
+//
+// if (name.equals(_connectedTitle)) {
+// foundConnectSelected = true;
+//
+// break;
+// }
+// }
+// }
+//
+// if (!foundConnectSelected) {
+// ConnectSelectedNodesAction connectAction = new ConnectSelectedNodesAction();
+// connectAction.setPreferredMenu("Edit");
+// Cytoscape.getDesktop().getCyMenus().addAction(connectAction);
+// }
+
+ _cyMenus = Cytoscape.getDesktop().getCyMenus();
+
+ _originalCursor = Cytoscape.getDesktop().getCursor();
+ }
+
+ /**
+ * sets controls invisible when editor type is switched
+ *
+ * @param args
+ * args an arbitrary list of arguments (not used in this editor)
+ */
+ public void disableControls(List args) {
+ }
+
+ /**
+ * sets controls visible when editor type is switched back to this editor
+ *
+ * @param args
+ * args an arbitrary list of arguments (not used in this editor) *
+ */
+ public void enableControls(List args) {
+ }
+
+ /**
+ * gets the name (type) of this editor
+ *
+ * @return the editorName.
+ */
+ public String getEditorName() {
+ return editorName;
+ }
+
+ /**
+ * sets the name (type) for this editor
+ *
+ * @param editorName
+ * the editorName to set.
+ */
+ public void setEditorName(String editorName) {
+ this.editorName = editorName;
+ }
+
+ /**
+ *
+ * @return the name of the attribute used to determine edge shapes on
+ * palette this is the same as the controllingEdgeAttribute for
+ * mapping of visual style to edge line type, target arrow
+ */
+ public String getControllingEdgeAttribute() {
+ return _controllingEdgeAttribute;
+ }
+
+ /**
+ *
+ * @param controllingEdgeAttribute
+ * the name of the attribute used to determine edge shapes on
+ * palette this is the same as the controllingEdgeAttribute for
+ * mapping of visual style to edge line type, target arrow
+ *
+ */
+ public void setControllingEdgeAttribute(String controllingEdgeAttribute) {
+ _controllingEdgeAttribute = controllingEdgeAttribute;
+ }
+
+ /**
+ *
+ * @return the name of the attribute used to determine Node shapes on
+ * palette this is the same as the controllingNodeAttribute for
+ * mapping of visual style to Node shape and color
+ */
+ public String getControllingNodeAttribute() {
+ return _controllingNodeAttribute;
+ }
+
+ /**
+ *
+ * @param controllingNodeAttribute
+ * the name of the attribute used to determine Node shapes on
+ * palette this is the same as the controllingNodeAttribute for
+ * mapping of visual style to Node shape and color
+ *
+ */
+ public void setControllingNodeAttribute(String controllingNodeAttribute) {
+ _controllingNodeAttribute = controllingNodeAttribute;
+ }
+
+
+ public String getControllingNetworkAttribute() {
+ return _controllingNetworkAttribute;
+ }
+
+ public void setControllingNetworkAttribute(String controllingNetworkAttribute) {
+ _controllingNetworkAttribute = controllingNetworkAttribute;
+ }
+
+ /**
+ *
+ * @return the network event handler that is associated with this editor
+ */
+ public NetworkEditEventAdapter getNetworkEditEventAdapter() {
+ return _networkEditEventAdapter;
+ }
+
+ /**
+ *
+ * @param adapter
+ * the network event handler that is associated with this editor
+ */
+ public void setNetworkEditEventAdapter(NetworkEditEventAdapter adapter) {
+ _networkEditEventAdapter = adapter;
+ }
+
+ /**
+ * action performed with the Edit->Connect Selected Nodes menu item is
+ * clicked on creates a clique from the set of selected nodes
+ *
+ * @author ajk
+ *
+ */
+ class ConnectSelectedNodesAction extends CytoscapeAction {
+ private static final long serialVersionUID = 3131183861434497429L;
+
+ public ConnectSelectedNodesAction() {
+ super(_connectedTitle);
+ setPreferredMenu("Edit");
+ setPreferredIndex(Cytoscape.getDesktop().getCyMenus().getEditMenu().getItemCount() - 2);
+ }
+
+ public ConnectSelectedNodesAction(boolean label) {
+ this();
+ }
+
+ public String getName() {
+ return _connectedTitle;
+ }
+
+ public void menuSelected(MenuEvent me) {
+ CyNetwork n = Cytoscape.getCurrentNetwork();
+ if ( n == null || n == Cytoscape.getNullNetwork() ) {
+ setEnabled(false);
+ return;
+ }
+
+ java.util.Set nodes = n.getSelectedNodes();
+ if ( nodes != null && nodes.size() > 0 )
+ {
+
+ setEnabled(true);
+ }
+
+ else
+ setEnabled(false);
+ }
+
+
+ public void actionPerformed(ActionEvent e) {
+ CyNetworkView view = Cytoscape.getCurrentNetworkView();
+ java.util.List nodes = view.getSelectedNodes();
+
+ String edgeTypeValue = "default";
+ String edgeTypeName = "DefaultEdge";
+ List edgeTypesList = CytoscapeEditorManager.getEdgeTypesForVisualStyle(view.getVisualStyle());
+
+ if (edgeTypesList != null) {
+ if (edgeTypesList.size() == 1) // just use only edge type
+ {
+ edgeTypeValue = edgeTypesList.get(0).toString();
+ edgeTypeName = edgeTypesList.get(0).toString();
+ } else {
+ String[] possibilities = new String[edgeTypesList.size()];
+
+ for (int i = 0; i < edgeTypesList.size(); i++) {
+ possibilities[i] = edgeTypesList.get(i).toString();
+ }
+
+ String s = (String) JOptionPane.showInputDialog(Cytoscape.getDesktop(),
+ "Please choose an EDGE_TYPE",
+ "Connect Selected Nodes",
+ JOptionPane.PLAIN_MESSAGE,
+ null, possibilities,
+ possibilities[0]);
+
+ // If a string was returned, say so.
+ if ((s != null) && (s.length() > 0)) {
+ edgeTypeValue = s;
+ edgeTypeName = s;
+ }
+ }
+ }
+
+ Set<Integer> edgeIndices = new HashSet<Integer>();
+
+ for (int i = 0; i < (nodes.size() - 1); i++) {
+ NodeView nv = (NodeView) nodes.get(i);
+ CyNode firstCyNode = (CyNode) nv.getNode();
+
+ for (int j = i + 1; j < nodes.size(); j++) {
+ NodeView nv2 = (NodeView) nodes.get(j);
+ CyNode secondCyNode = (CyNode) nv2.getNode();
+ CyEdge myedge = addEdgeWithoutFiringEvent (firstCyNode, secondCyNode, Semantics.INTERACTION, edgeTypeValue, true,
+ edgeTypeName);
+ edgeIndices.add(myedge.getRootGraphIndex());
+ }
+ }
+
+ // convert
+ int i = 0;
+ int[] edgeInd = new int[edgeIndices.size()];
+ for (Integer ei : edgeIndices)
+ edgeInd[i++] = ei.intValue();
+
+ CyNetwork net = Cytoscape.getCurrentNetwork();
+ CyUndo.getUndoableEditSupport().postEdit( new ConnectEdit(net,edgeInd, this) );
+
+ Cytoscape.firePropertyChange(Cytoscape.NETWORK_MODIFIED,
+ CytoscapeEditorManager.CYTOSCAPE_EDITOR, net);
+
+ }
+ }
+
+ /**
+ * An undoable edit that will undo and redo connection of nodes and edges.
+ */
+ class ConnectEdit extends CyAbstractEdit {
+
+// private static final long serialVersionUID = -1164181258019250610L;
+
+ int[] edges;
+
+ CyNetwork net;
+ // AJK: 03082008 ConnectSelectedNodesAction to be reenabled upon undo
+ ConnectSelectedNodesAction connectAction;
+
+
+ ConnectEdit(CyNetwork net, int[] edgeInd) {
+ super("Connect Selected Nodes");
+ if ( net == null )
+ throw new IllegalArgumentException("network is null");
+ this.net = net;
+
+ edges = new int[edgeInd.length];
+ for ( int i = 0; i < edgeInd.length; i++ )
+ edges[i] = edgeInd[i];
+
+ }
+
+ // AJK: 03082008 DeleteAction to be reenabled upon undo
+ ConnectEdit(CyNetwork net, int[] edgeInd, ConnectSelectedNodesAction connectAction) {
+ this (net, edgeInd);
+ this.connectAction = connectAction;
+ }
+
+
+
+
+
+
+ public void redo() {
+ super.redo();
+
+ net.restoreEdges(edges);
+ CyNetworkView netView = Cytoscape.getNetworkView(net.getIdentifier());
+ netView.redrawGraph(true, true);
+ Cytoscape.firePropertyChange(Cytoscape.NETWORK_MODIFIED, null , net);
+ // AJK: 03082008 disable ConnectSelectedNodesAction
+ connectAction.setEnabled(false);
+ }
+
+ public void undo() {
+ super.undo();
+
+ net.hideEdges(edges);
+ CyNetworkView netView = Cytoscape.getNetworkView(net.getIdentifier());
+
+ netView.redrawGraph(true, true);
+ Cytoscape.firePropertyChange(Cytoscape.NETWORK_MODIFIED, null, net);
+ // AJK: 03082008 re-enable ConnectSelectedNodesAction
+ connectAction.setEnabled(true);
+ }
+ }
+
+}
diff --git a/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/editors/DefaultCytoscapeEditor.java b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/editors/DefaultCytoscapeEditor.java
new file mode 100644
index 0000000..dfb99c6
--- /dev/null
+++ b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/editors/DefaultCytoscapeEditor.java
@@ -0,0 +1,352 @@
+/* -*-Java-*-
+********************************************************************************
+*
+* File: DefaultCytoscapeEditor.java
+* RCS: $Header: $
+* Description:
+* Author: Allan Kuchinsky
+* Created: Sun Oct 04 05:35:56 2005
+* Modified: Tue Dec 02 18:16:25 2008 (Michael L. Creech) creech at w235krbza760
+* Language: Java
+* Package:
+/*
+
+ Copyright (c) 2006, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+
+*
+********************************************************************************
+*
+* Revisions:
+*
+* Tue Dec 02 18:15:52 2008 (Michael L. Creech) creech at w235krbza760
+* Added arrowShapeToArrow() and fixed bug where an ArrowShape was
+* being given to CytoShapeIcon constructor.
+* Fri Jun 29 09:24:02 2007 (Michael L. Creech) creech at w235krbza760
+* Removed deprecated use in getNodeShape() and getFillColor() in
+* generateNodePaletteEntries().
+* Thu May 10 09:37:06 2007 (Michael L. Creech) creech at w235krbza760
+* Updated to use VisualPropertyType versus VizMapUI for Cytoscape 2.5.
+* Sun Dec 17 05:36:01 2006 (Michael L. Creech) creech at w235krbza760
+* Added creation of EdgePaletteItemDragCursorSetter and passing it into
+* ShapePalette.addShape() calls.
+********************************************************************************
+*/
+
+/*
+ * TODO To change the template for this generated file go to
+ * Window - Preferences - Java - Code Style - Code Templates
+ */
+package cytoscape.editor.editors;
+
+import giny.view.NodeView;
+
+import java.awt.Color;
+import java.awt.Cursor;
+import java.awt.Dimension;
+import java.awt.Point;
+import java.awt.dnd.DragSource;
+import java.awt.dnd.DragSourceDragEvent;
+import java.util.Iterator;
+import java.util.List;
+
+import javax.swing.ImageIcon;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+
+import cytoscape.Cytoscape;
+import cytoscape.editor.CytoscapeEditorFactory;
+import cytoscape.editor.CytoscapeEditorManager;
+import cytoscape.editor.DragSourceContextCursorSetter;
+import cytoscape.editor.ShapePaletteInfo;
+import cytoscape.editor.ShapePaletteInfoGenerator;
+import cytoscape.editor.event.PaletteNetworkEditEventHandler;
+import cytoscape.editor.impl.CytoShapeIcon;
+import cytoscape.editor.impl.ShapePalette;
+import cytoscape.view.CyNetworkView;
+import cytoscape.visual.Arrow;
+import cytoscape.visual.ArrowShape;
+import cytoscape.visual.EdgeAppearanceCalculator;
+import cytoscape.visual.NodeAppearanceCalculator;
+import cytoscape.visual.NodeShape;
+import cytoscape.visual.VisualPropertyType;
+import ding.view.DGraphView;
+
+
+/**
+ * /** An example editor that extends the basic Cytoscape editor and is based
+ * upon a drag-and-drop and palette framework into which developers plug in
+ * semantics. The framework consists of
+ * <ul>
+ * <li> a palette, from which the user drags and drops shapes onto the canvas
+ * <li> an extensible shape class for the palette,
+ * <li> a drawing canvas upon which shapes are dropped, and
+ * <li> event handlers which respond to drop events generated by the canvas.
+ * </ul>
+ * <p>
+ * The dropping of shapes onto the canvas results in the addition of nodes and
+ * edges to the current Cytoscape network, as defined by the behavior of the
+ * event handler that responds to the drop events.
+ * <p>
+ *
+ *
+ * @author Allan Kuchinsky
+ * @version 1.0
+ * @see PaletteNetworkEditEventHandler
+ *
+ */
+public class DefaultCytoscapeEditor extends BasicCytoscapeEditor implements ChangeListener {
+
+ /**
+ * main data structures for all node and edge attributes
+ */
+ public static cytoscape.data.CyAttributes nodeAttribs = Cytoscape.getNodeAttributes();
+
+ /**
+ *
+ */
+ public static cytoscape.data.CyAttributes edgeAttribs = Cytoscape.getEdgeAttributes();
+ private ShapePalette shapePalette;
+
+ // MLC 12/16/06 BEGIN:
+ // Determine how edge palette items show up during a drag op:
+ private DragSourceContextCursorSetter _edgeCursorSetter = new EdgePaletteItemDragCursorSetter();
+
+ // MLC 12/16/06 END.
+ /**
+ *
+ */
+ public DefaultCytoscapeEditor() {
+ super();
+ }
+
+ // MLC 12/02/06 BEGIN:
+ /**
+ * specialized initialization code for editor, called by
+ * CytoscapeEditorManager when a new editor is built.
+ * draws shapes on the palette, based upon the visual style
+ *
+ * @param args
+ * an arbitrary list of arguments passed to initialization
+ * routine. Not used in this editor
+ */
+ public void initializeControls(List args) {
+ shapePalette = CytoscapeEditorManager.getCurrentShapePalette();
+ shapePalette.clear();
+ generatePaletteEntries();
+ shapePalette.showPalette();
+ super.initializeControls(null);
+ }
+
+ protected void generatePaletteEntries() {
+ CytoscapeEditorManager.log("generating palette entries for controlling attributes "
+ + getControllingNodeAttribute() + " and "
+ + getControllingEdgeAttribute());
+ CytoscapeEditorManager.log("for editor " + this);
+ generateEdgePaletteEntries(getControllingEdgeAttribute());
+ generateNodePaletteEntries(getControllingNodeAttribute());
+ generateNetworkPaletteEntries(getControllingNetworkAttribute());
+ }
+
+ protected void generateEdgePaletteEntries(String controllingAttribute) {
+ EdgeAppearanceCalculator eac = Cytoscape.getVisualMappingManager().getVisualStyle()
+ .getEdgeAppearanceCalculator();
+
+ if (eac == null) {
+ return;
+ }
+
+ // CytoscapeEditorManager.log("Got edgeAppearanceCalculator: " + eac);
+ ShapePaletteInfoGenerator palGen = CytoscapeEditorFactory.INSTANCE
+ .createShapePaletteInfoGenerator();
+
+ VisualPropertyType[] calcsToUse = new VisualPropertyType [] { VisualPropertyType.EDGE_TGTARROW_SHAPE };
+
+ Iterator<ShapePaletteInfo> spEntries = palGen.buildShapePaletteInfo(eac, calcsToUse,
+ controllingAttribute,
+ this, null);
+
+ CytoscapeEditorManager.log("any edge types for shape palette? " + spEntries.hasNext());
+
+ if (!spEntries.hasNext()) {
+ shapePalette.addShape(controllingAttribute, "DirectedEdge",
+ // MLC 10/24/07:
+ // new CytoShapeIcon(Arrow.DELTA), "Directed Edge",
+ // MLC 10/24/07:
+ new CytoShapeIcon(Arrow.NONE), "Add an Edge",
+ _edgeCursorSetter);
+ } else {
+ while (spEntries.hasNext()) {
+ ShapePaletteInfo spi = spEntries.next();
+ shapePalette.addShape(spi.getControllingAttributeName(), spi.getKey(),
+ // MLC 05/09/07:
+ // new CytoShapeIcon((Arrow) spi.getValue(VizMapUI.EDGE_TGTARROW)),
+ // MLC 12/02/08 BEGIN:
+ // new CytoShapeIcon((Arrow) spi.getValue(VisualPropertyType.EDGE_TGTARROW_SHAPE)),
+ new CytoShapeIcon(arrowShapeToArrow((ArrowShape) spi.getValue(VisualPropertyType.EDGE_TGTARROW_SHAPE))),
+ // MLC 12/02/08 END.
+ spi.getKey(), // MLC 12/16/06:
+ _edgeCursorSetter);
+ }
+ }
+ }
+
+ // MLC 12/02/08 BEGIN:
+ protected Arrow arrowShapeToArrow(ArrowShape as) {
+ if (as == ArrowShape.ARROW) {
+ return Arrow.ARROW;
+ } else if (as == ArrowShape.CIRCLE) {
+ return Arrow.CIRCLE;
+ } else if (as == ArrowShape.DELTA) {
+ return Arrow.DELTA;
+ } else if (as == ArrowShape.DIAMOND) {
+ return Arrow.DIAMOND;
+ } else if (as == ArrowShape.NONE) {
+ return Arrow.NONE;
+ } else if (as == ArrowShape.T) {
+ return Arrow.T;
+ }
+
+ return null;
+ }
+ // MLC 12/02/08 END
+
+ protected void generateNodePaletteEntries(String controllingAttribute) {
+ NodeAppearanceCalculator nac = Cytoscape.getVisualMappingManager().getVisualStyle()
+ .getNodeAppearanceCalculator();
+
+ if (nac == null) {
+ return;
+ }
+
+ ShapePaletteInfoGenerator palGen = CytoscapeEditorFactory.INSTANCE
+ .createShapePaletteInfoGenerator();
+ VisualPropertyType[] calcsToUse = new VisualPropertyType[] { VisualPropertyType.NODE_FILL_COLOR, VisualPropertyType.NODE_SHAPE, VisualPropertyType.NODE_SIZE };
+ Iterator<ShapePaletteInfo> spEntries = palGen.buildShapePaletteInfo(nac, calcsToUse,
+ controllingAttribute,
+ this, null);
+
+ if (!spEntries.hasNext()) {
+ shapePalette.addShape(controllingAttribute, "DefaultNode",
+ // MLC 06/30/07 BEGIN:
+ // new CytoShapeIcon(nac.getDefaultAppearance().getNodeShape(),
+ // nac.getDefaultAppearance().getFillColor()),
+ new CytoShapeIcon((NodeShape)(nac.getDefaultAppearance().get (VisualPropertyType.NODE_SHAPE)),
+ (Color)(nac.getDefaultAppearance().get (VisualPropertyType.NODE_FILL_COLOR))),
+ // MLC 06/30/07 END.
+ "Add a Node", // MLC 12/16/06:
+ null);
+ } else {
+ while (spEntries.hasNext()) {
+ ShapePaletteInfo spi = spEntries.next();
+
+ Color nodeColor = (Color) spi.getValue(VisualPropertyType.NODE_FILL_COLOR);
+ NodeShape nodeShape = (NodeShape) spi.getValue(VisualPropertyType.NODE_SHAPE);
+ int nodeSize = (int) ((Double) spi.getValue(VisualPropertyType.NODE_SIZE)).longValue();
+ // MLC 05/09/07 END.
+ shapePalette.addShape(spi.getControllingAttributeName(), spi.getKey(),
+ new CytoShapeIcon(nodeShape, nodeColor,
+ new Dimension(nodeSize, nodeSize)),
+ spi.getKey(), // MLC 12/16/06:
+ null);
+ }
+ }
+ }
+
+
+ protected void generateNetworkPaletteEntries(String controllingAttribute) {
+
+ javax.swing.ImageIcon icon = new ImageIcon(getClass().getResource("/network.png"));
+
+ shapePalette.addShape(controllingAttribute, "DefaultNestedNetwork",
+ new CytoShapeIcon(icon.getImage()),
+ "Add a Nested Network",
+ null);
+ }
+
+
+
+ protected ShapePalette getShapePalette() {
+ return shapePalette;
+ }
+
+ /**
+ * sets controls invisible when editor type is switched
+ *
+ * @param args
+ * args an arbitrary list of arguments (not used in this editor)
+ */
+ public void disableControls(List args) {
+ // super.disableControls(args);
+ if (shapePalette != null) {
+ shapePalette.setVisible(false);
+ }
+ }
+
+ /**
+ * sets controls visible when editor type is switched back to this editor
+ *
+ * @param args
+ * args an arbitrary list of arguments (not used in this editor) *
+ */
+ public void enableControls(List args) {
+ // super.enableControls(args);
+ shapePalette.showPalette();
+ shapePalette.setVisible(true);
+ }
+
+ /**
+ * redraw palette when a shape, color, or arrow mapping changes
+ *
+ * @param e
+ */
+ public void stateChanged(ChangeEvent e) {
+ initializeControls(null);
+ }
+
+ // MLC 12/16/06 BEGIN:
+ // give sublcasses access to the default setter for edge palette entries:
+ protected DragSourceContextCursorSetter getDefaultEdgePaletteItemDragCursorSetter() {
+ return _edgeCursorSetter;
+ }
+
+ // A CursorSetter that says it's only ok to drop when we are on a Node:
+ private class EdgePaletteItemDragCursorSetter implements DragSourceContextCursorSetter {
+ public Cursor computeCursor(CyNetworkView netView, Point netViewLoc,
+ DragSourceDragEvent dsde) {
+ // Now check if we are on a NodeView?
+ NodeView nv = ((DGraphView) netView).getPickedNodeView(netViewLoc);
+
+ if (nv != null) {
+ return DragSource.DefaultCopyDrop;
+ }
+
+ return DragSource.DefaultCopyNoDrop;
+ }
+ }
+
+ // MLC 12/16/06 END.
+}
diff --git a/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/event/BasicCytoShapeTransferHandler.java b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/event/BasicCytoShapeTransferHandler.java
new file mode 100644
index 0000000..a463dfd
--- /dev/null
+++ b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/event/BasicCytoShapeTransferHandler.java
@@ -0,0 +1,213 @@
+/*
+ * Created on May 31, 2005
+ *
+ */
+package cytoscape.editor.event;
+
+import java.awt.datatransfer.DataFlavor;
+import java.awt.datatransfer.Transferable;
+import java.awt.datatransfer.UnsupportedFlavorException;
+import java.awt.dnd.DragGestureListener;
+
+import javax.swing.JComponent;
+import javax.swing.TransferHandler;
+
+import cytoscape.editor.CytoscapeEditorManager;
+import cytoscape.editor.impl.BasicCytoShapeEntity;
+import cytoscape.logger.CyLogger;
+
+
+/**
+ * transfer handler for shapes that are dragged from the palette onto the canvas.
+ * Creates appropriate data flavor and transferrable.
+ * part of drag/drop editor framework.
+ *
+ * @author Allan Kuchinsky
+ * @version 1.0
+ * @see cytoscape.editor.GraphicalEntity
+ * @see cytoscape.editor.impl.BasicCytoShapeEntity
+ *
+ */
+public class BasicCytoShapeTransferHandler extends TransferHandler {
+ // MLC 09/14/06:
+ private static final long serialVersionUID = 778042405547689517L;
+ DataFlavor basicCytoShapeFlavor;
+ DragGestureListener _cytoShape;
+
+ /**
+ * @return Returns the _attributeName.
+ */
+ public String get_attributeName() {
+ return _attributeName;
+ }
+
+ /**
+ * @return Returns the _attributeValue.
+ */
+ public String get_attributeValue() {
+ return _attributeValue;
+ }
+
+ String _attributeName;
+ String _attributeValue;
+ Object[] _args;
+
+ /**
+ * creates a DataFlavor for the BasicCytoShapeEntity class
+ *
+ */
+ public BasicCytoShapeTransferHandler() {
+ try {
+ basicCytoShapeFlavor = new DataFlavor(BasicCytoShapeEntity.class, "BasicCytoShapeEntity");
+ } catch (Exception e) {
+ CyLogger.getLogger(BasicCytoShapeTransferHandler.class).warn("Unable to create data flavor for BasicCytoShapeEntity",e);
+ }
+ }
+
+ /**
+ * creates a DataFlavor and sets instance variables for a BasicCytoShapeEntity that is
+ * added to the palette
+ * @param cytoShape shape that is added to the palette
+ * @param args arbitrary list of arguments that can be passed in
+ */
+ public BasicCytoShapeTransferHandler(BasicCytoShapeEntity cytoShape, Object[] args) {
+ try {
+ basicCytoShapeFlavor = new DataFlavor(BasicCytoShapeEntity.class, "BasicCytoShapeEntity");
+ } catch (Exception e) {
+ CyLogger.getLogger(BasicCytoShapeTransferHandler.class).warn("Unable to create data flavor for BasicCytoShapeEntity",e);
+ }
+
+ _cytoShape = cytoShape;
+ _args = args;
+ _attributeName = cytoShape.getAttributeName();
+ _attributeValue = cytoShape.getAttributeValue();
+ }
+
+ /**
+ * @return Returns the _args.
+ */
+ public Object[] get_args() {
+ return _args;
+ }
+
+ /**
+ * sets the _args instance variable
+ * @param _args The _args to set.
+ */
+ public void set_args(Object[] _args) {
+ this._args = _args;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param c DOCUMENT ME!
+ * @param t DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean importData(JComponent c, Transferable t) {
+ CytoscapeEditorManager.log("importing data from transferable " + t);
+
+ if (canImport(c, t.getTransferDataFlavors())) {
+ }
+
+ return false;
+ }
+
+ // AJK: 11/13/05 BEGIN
+ /**
+ * DOCUMENT ME!
+ *
+ * @param val DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String exportString(Object val) {
+ if (val instanceof BasicCytoShapeEntity) {
+ return ((BasicCytoShapeEntity) val).getTitle();
+ } else {
+ return null;
+ }
+ }
+
+ // AJK: 11/13/05 END
+ /**
+ * DOCUMENT ME!
+ *
+ * @param c DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Transferable createTransferable(JComponent c) {
+ return new BasicCytoShapeTransferable(c);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param c DOCUMENT ME!
+ * @param flavors DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean canImport(JComponent c, DataFlavor[] flavors) {
+ for (int i = 0; i < flavors.length; i++) {
+ if (basicCytoShapeFlavor.equals(flavors[i])) {
+ return true;
+ }
+ }
+
+ return false;
+ }
+
+ /**
+ * packages the BasicCytoShapeEntity for transfer upon a drag/drop operation
+ * @author Allan Kuchinsky
+ * @version 1.0
+ *
+ *
+ */
+ class BasicCytoShapeTransferable implements Transferable {
+ private BasicCytoShapeEntity _cytoShape;
+
+ BasicCytoShapeTransferable(JComponent obj) {
+ if (obj instanceof BasicCytoShapeEntity) {
+ _cytoShape = (BasicCytoShapeEntity) obj;
+ _attributeName = _cytoShape.getAttributeName();
+ _attributeValue = _cytoShape.getAttributeValue();
+ }
+ }
+
+ public Object getTransferData(DataFlavor flavor) throws UnsupportedFlavorException {
+ if (!isDataFlavorSupported(flavor)) {
+ throw new UnsupportedFlavorException(flavor);
+ }
+
+ return exportString(_cytoShape);
+ }
+
+ public DataFlavor[] getTransferDataFlavors() {
+ return new DataFlavor[] { basicCytoShapeFlavor };
+ }
+
+ public boolean isDataFlavorSupported(DataFlavor flavor) {
+ return basicCytoShapeFlavor.equals(flavor);
+ }
+ }
+
+ /**
+ * @return Returns the _cytoShape.
+ */
+ public DragGestureListener get_cytoShape() {
+ return _cytoShape;
+ }
+
+ /**
+ * sets the instance variable for a BasicCytoShapeEntity
+ * @param shape The _cytoShape to set.
+ */
+ public void set_cytoShape(DragGestureListener shape) {
+ _cytoShape = shape;
+ }
+}
diff --git a/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/event/BasicNetworkEditEventHandler.java b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/event/BasicNetworkEditEventHandler.java
new file mode 100644
index 0000000..79347b4
--- /dev/null
+++ b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/event/BasicNetworkEditEventHandler.java
@@ -0,0 +1,1083 @@
+/*
+ Copyright (c) 2006, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package cytoscape.editor.event;
+
+
+import ding.view.DGraphView;
+import ding.view.DingCanvas;
+import ding.view.InnerCanvas;
+
+import giny.model.Node;
+import giny.view.EdgeView;
+import giny.view.NodeView;
+
+import java.awt.Color;
+import java.awt.Graphics;
+import java.awt.event.ActionListener;
+import java.awt.event.KeyEvent;
+import java.awt.event.InputEvent;
+import java.awt.event.MouseEvent;
+import java.awt.geom.Point2D;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+
+import javax.swing.JOptionPane;
+
+import cytoscape.CyEdge;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+import cytoscape.data.Semantics;
+import cytoscape.editor.CytoscapeEditor;
+import cytoscape.editor.CytoscapeEditorManager;
+import cytoscape.editor.editors.BasicCytoscapeEditor;
+import cytoscape.editor.impl.SIF_Interpreter;
+import cytoscape.editor.impl.ShapePalette;
+import cytoscape.view.CyNetworkView;
+import cytoscape.view.CytoscapeDesktop;
+
+
+// TODO: No instance variables should be protected--only private and
+// all access by subclasses should be thru set/get methods.
+// Also, most of the methods only accessed thru sublasses should
+// be protected, not public.
+
+/**
+ *
+ * The <b>BasicNetworkEditEventHandler </b> class provides specialized methods
+ * defining the behavior of the basic Cytoscape editor provided in Cytoscape
+ * 2.2. The behavior is defined in terms of how the event handler responds to
+ * mouse events, drag/drop events, and button press events.
+ *
+ * @author Allan Kuchinsky
+ * @version 1.0
+ * @see BasicCytoscapeEditor
+ *
+ * revised: 04/15/2006 to integrate with Cytoscape 2.3 renderer Phase 1: switch
+ * underlying node identification and edge drawing code Phase 2: remove
+ * dependencies upon Piccolo
+ *
+ */
+//TODO: dont need MultiHashMapListener
+public class BasicNetworkEditEventHandler extends NetworkEditEventAdapter implements ActionListener, cytoscape.data.attr.MultiHashMapListener, PropertyChangeListener
+{
+ // PNodeLocator locator;
+
+ /**
+ * counter variable used in setting unique names for nodes
+ */
+ protected static int counter = 0;
+
+ /**
+ * CytoscapeAttribute: NODE_TYPE
+ */
+ public static final String NODE_TYPE = "NODE_TYPE";
+
+ /**
+ * CytoscapeAttribute: EDGE_TYPE
+ *
+ */
+ public static final String EDGE_TYPE = Semantics.INTERACTION;
+
+
+ public static final String NETWORK_TYPE = "NETWORK_TYPE";
+
+ /**
+ *
+ */
+ public static final String DEFAULT_NODE = "DefaultNode";
+
+ /**
+ *
+ */
+ public static final String DEFAULT_EDGE = "DefaultEdge";
+
+ /**
+ *
+ */
+ public static final String DEFAULT_NETWORK = "DefaultNetwork";
+
+
+ /**
+ * the node that will be dropped
+ */
+
+ // FIX: Should really change the name--this can easily be shadowed by other
+ // local variables:
+ // protected NodeView node;
+ private NodeView node;
+
+ /**
+ * the edge that will be dropped
+ */
+
+ /**
+ * flag that indicates whether there is an edge under construction
+ */
+
+ private boolean edgeStarted;
+
+ /**
+ * the mouse press location for the drop point
+ */
+
+ private Point2D startPoint;
+
+ /**
+ * point used in tracking mouse movement
+ */
+ protected Point2D nextPoint;
+
+ /**
+ * the canvas that this event handler is listening to
+ */
+
+ /**
+ * attribute used to set NODE_TYPE
+ */
+ protected String nodeAttributeName = NODE_TYPE;
+
+ /**
+ * value for attribute used in setting NODE_TYPE
+ */
+ protected String nodeAttributeValue = DEFAULT_NODE;
+
+ /**
+ * attribute used to set EDGE_TYPE
+ */
+ protected String edgeAttributeName = EDGE_TYPE;
+
+ /**
+ * attribute used to set NETWORK_TYPE
+ */
+ protected String networkAttributeName = NETWORK_TYPE;
+
+ /**
+ * value for attribute used in setting NETWORK_TYPE
+ */
+ protected String networkAttributeValue = DEFAULT_NETWORK;
+
+ /**
+ * value for attribute used in setting EDGE_TYPE
+ */
+ protected String edgeAttributeValue = DEFAULT_EDGE;
+
+ /*
+ * for drawing rubberbanded lines
+ */
+ double saveX1 = Double.MIN_VALUE;
+ double saveY1 = Double.MIN_VALUE;
+ double saveX2 = Double.MIN_VALUE;
+ double saveY2 = Double.MIN_VALUE;
+
+ /**
+ * flag that indicates whether we are currently in the process of handling a
+ * dropped edge TODO: handling dropped edges should probably be moved to the
+ * PaletteNetworkEditEventHandler
+ */
+ public boolean handlingEdgeDrop = false;
+
+ /**
+ * String used to compare against os.name System property -
+ * to determine if we are running on Windows platform.
+ */
+ static final String MAC_OS_ID = "mac";
+
+ /**
+ * node or edge which has been highlighted for drop or edge connection
+ * during mouseDrag
+ */
+
+ /**
+ * Creates a new BasicNetworkEditEventHandler object.
+ */
+ public BasicNetworkEditEventHandler() {
+ Cytoscape.getDesktop().getSwingPropertyChangeSupport()
+ .addPropertyChangeListener(CytoscapeDesktop.NETWORK_VIEW_FOCUSED, this);
+ }
+
+ /**
+ *
+ * @param caller
+ */
+ public BasicNetworkEditEventHandler(CytoscapeEditor caller) {
+ this();
+ _caller = caller;
+ Cytoscape.getDesktop().getSwingPropertyChangeSupport()
+ .addPropertyChangeListener(CytoscapeDesktop.NETWORK_VIEW_FOCUSED, this);
+ }
+
+ /**
+ * @deprecated Use the one argument constructor--second argument is no longer used.
+ * @param caller
+ * @param view
+ */
+ // TODO: Change all calls to this to use the one argument version of this method
+ public BasicNetworkEditEventHandler(CytoscapeEditor caller, CyNetworkView view) {
+ this();
+ _caller = caller;
+ Cytoscape.getDesktop().getSwingPropertyChangeSupport()
+ .addPropertyChangeListener(CytoscapeDesktop.NETWORK_VIEW_FOCUSED, this);
+ }
+
+ /**
+ * Routine which determines if we are running on mac platform
+ *
+ * @return boolean
+ */
+ private boolean isMacPlatform() {
+ String os = System.getProperty("os.name");
+
+ return os.regionMatches(true, 0, MAC_OS_ID, 0, MAC_OS_ID.length());
+ }
+
+ /**
+ * The <b>mousePressed() </b> method is at the heart of the basic Cytoscape
+ * editor.
+ * <p>
+ * Control-clicking at a position on the canvas creates a node with default
+ * label in that position.
+ * <p>
+ * Control-clicking on a node on the canvas starts an edge with source at
+ * that node. Move the cursor and a rubber-banded line follows the cursor.
+ * As the cursor passes over another node, that node is highlighted and the
+ * rubber-banded line will snap to a connection point on that second node.
+ * Control-click the mouse again and the connection is established.
+ *
+ * @param e
+ * inputEvent for mouse pressed
+ * @see BasicCytoscapeEditor
+ */
+ @Override public void mousePressed(MouseEvent e) {
+ // TODO: This check should really be avoided by having the editor remove all mouse and key
+ // listeners when the editor looses focus (another tab is clicked on).
+ // Since this is somewhat involved and so is left for when the editor is refactored.
+ if (!CytoscapeEditorManager.isEditorInOperation())
+ return;
+
+ CytoscapeEditorManager.log("CE: mousePressed!");
+
+ nextPoint = e.getPoint();
+
+ DGraphView cView = getCurrentDGraphView ();
+ NodeView nv = cView.getPickedNodeView(nextPoint);
+ boolean onNode = (nv != null);
+
+
+ // Bail out if we're on a node and it was a right-click event:
+ if (onNode && ((isMacPlatform() && e.isMetaDown())
+ || (!isMacPlatform() && ((e.getModifiers() & InputEvent.BUTTON3_MASK)
+ == InputEvent.BUTTON3_MASK))))
+ return;
+
+ // if we have control-clicked on an edge, then just return
+ // because the user is adding edge anchors for bending edges in
+ // Cytoscape:
+ if (e.isControlDown()){
+ // MLC 02/03/09 BEGIN:
+ // if (view.getPickedEdgeView(nextPoint) != null) {
+ if (cView.getPickedEdgeView(nextPoint) != null) {
+ // MLC 02/03/09 END.
+ return;
+ }
+ }
+
+ if ((onNode && !edgeStarted && (e.isControlDown()) && !(isMacPlatform())) ||
+ (onNode && !edgeStarted && (e.isMetaDown()) && isMacPlatform()))
+ {
+ // begin edge creation
+ beginEdge(nextPoint, nv);
+
+ } else if (onNode && edgeStarted) {
+ CytoscapeEditorManager.log("calling finishEdge for NodeView " + nv);
+ // Finish Edge Creation
+ finishEdge(nextPoint, nv);
+
+ } else if (!onNode && edgeStarted) // turn off rubberbanding if clicked
+ // on empty area of canvas
+ {
+ edgeStarted = false;
+ saveX1 = Double.MIN_VALUE;
+ saveX2 = Double.MIN_VALUE;
+ saveY1 = Double.MIN_VALUE;
+ saveY2 = Double.MIN_VALUE;
+ this.setHandlingEdgeDrop(false);
+ } else if ((!onNode && !edgeStarted && (e.isControlDown()) && !(isMacPlatform())) ||
+ (!onNode && !edgeStarted && (e.isMetaDown()) && isMacPlatform()))
+ {
+ // control-click on a empty place will make a new Node:
+ createNode(nextPoint);
+ }
+
+ // invoke SIF interpreter for user to enter nodes/edges via text input
+ else if ((e.getClickCount() == 2) && (!e.isAltDown()) && !onNode)
+ SIF_Interpreter.processInput(e.getPoint(), _caller);
+
+ // toggle diagnostic logging with alt_triple-click
+ else if ((e.getClickCount() > 2) && (e.isAltDown())) {
+ CytoscapeEditorManager.setLoggingEnabled(!CytoscapeEditorManager.isLoggingEnabled());
+ CytoscapeEditorManager.log("Cytoscape editor logging = "
+ + CytoscapeEditorManager.isLoggingEnabled());
+ }
+
+ else
+ {
+ // super.mousePressed(e);
+ }
+ }
+
+ /**
+ * processed keyTypedEvents, in particular use of ESC key to interupt edge drawing
+ */
+
+ @Override public void keyPressed(KeyEvent e) {
+ // TODO: This check should really be avoided by having the editor remove all mouse and key
+ // listeners when the editor looses focus (another tab is clicked on).
+ // Since this is somewhat involved and so is left for when the editor is refactored.
+ if (!CytoscapeEditorManager.isEditorInOperation()) {
+ return;
+ }
+ int keyVal = e.getKeyCode();
+ CytoscapeEditorManager.log("Key code for typed key = " + keyVal);
+ CytoscapeEditorManager.log("VK_ESCAPE = " + KeyEvent.VK_ESCAPE);
+ if (keyVal == KeyEvent.VK_ESCAPE) {
+ // MLC 02/03/09 BEGIN:
+ resetDragAndDrop();
+ // if (edgeStarted) // turn off rubberbanding if clicked
+ // // on empty area of canvas
+ // {
+ // edgeStarted = false;
+ // saveX1 = Double.MIN_VALUE;
+ // saveX2 = Double.MIN_VALUE;
+ // saveY1 = Double.MIN_VALUE;
+ // saveY2 = Double.MIN_VALUE;
+ // this.setHandlingEdgeDrop(false);
+ // // repaint so that the rubberband line is removed:
+ // this.getCanvas().repaint();
+ // }
+ }
+ }
+
+ // implements PropertyChangeListener interface:
+ // Whenever we switch to another network view, make sure we stop
+ // any drag and drop going on.
+ // TODO: THis is probably not the best place for this and we need to add a removal of
+ // the listener at the right place.
+ public void propertyChange(PropertyChangeEvent e) {
+ if (e.getPropertyName().equals(CytoscapeDesktop.NETWORK_VIEW_FOCUSED)) {
+ resetDragAndDrop ();
+ }
+ }
+
+ /**
+ * Reset the state associated with being in the middle of a drag and drop operation.
+ */
+ private void resetDragAndDrop () {
+ if (edgeStarted) // turn off rubberbanding if clicked
+ // on empty area of canvas
+ {
+ edgeStarted = false;
+ saveX1 = Double.MIN_VALUE;
+ saveX2 = Double.MIN_VALUE;
+ saveY1 = Double.MIN_VALUE;
+ saveY2 = Double.MIN_VALUE;
+ this.setHandlingEdgeDrop(false);
+ // repaint so that the rubberband line is removed:
+ this.getCanvas().repaint();
+ }
+ }
+
+ /**
+ * begin drawing an edge from the input point
+ *
+ *
+ * @param location works in Canvas coordinates
+ *
+ */
+ public void beginEdge(Point2D location, NodeView nv) {
+ edgeStarted = true;
+ // node = (NodeView) e.getPickedNode();
+ node = nv;
+ startPoint = location;
+ updateEdge();
+ setEdgeStarted(true);
+ setStartPoint(startPoint);
+ }
+
+ /**
+ * finish edge on node containing input pointf
+ *
+ * @param location works in Canvas coordinates
+ */
+ public CyEdge finishEdge(Point2D location, NodeView target) {
+ NodeView source = node;
+
+ Node source_node = source.getNode();
+ Node target_node = target.getNode();
+
+ CyEdge myEdge;
+ if (ShapePalette.specifyIdentifier){
+ String _edgeAttributeValue = getEdgeAttributeValueFromUser(source_node, target_node);
+ if (_edgeAttributeValue == null)
+ return null;
+ myEdge = _caller.addEdge(source_node, target_node,
+ cytoscape.data.Semantics.INTERACTION,
+ _edgeAttributeValue, true,
+ _edgeAttributeValue);
+ }
+ else {
+ myEdge = _caller.addEdge(source_node, target_node,
+ cytoscape.data.Semantics.INTERACTION,
+ (this.getEdgeAttributeValue() != null)
+ ? this.getEdgeAttributeValue()
+ : BasicNetworkEditEventHandler.DEFAULT_EDGE, true,
+ (this.getEdgeAttributeValue() != null)
+ ? this.getEdgeAttributeValue()
+ : BasicNetworkEditEventHandler.DEFAULT_EDGE);
+ }
+
+ completeFinishEdge();
+ return myEdge;
+ }
+
+
+ private String getEdgeAttributeValueFromUser(Node source_node, Node target_node) {
+ String _edgeAttributeValue = null;
+
+ while (true){
+ _edgeAttributeValue =
+ JOptionPane.showInputDialog(Cytoscape.getDesktop(),
+ "Please Specify Edge Interaction Type",
+ this.getEdgeAttributeValue());
+ if (_edgeAttributeValue == null){
+ return null;
+ }
+ // Check if the Edge ID already exists
+ CyEdge aEdge = Cytoscape.getCyEdge(source_node, target_node,
+ cytoscape.data.Semantics.INTERACTION,
+ _edgeAttributeValue, false, true);
+
+ if (aEdge == null)
+ break;
+
+ JOptionPane.showMessageDialog(Cytoscape.getDesktop(), _edgeAttributeValue + " already exists!", "Duplicated Edge Identifier",
+ JOptionPane.WARNING_MESSAGE);
+ }
+
+ return _edgeAttributeValue;
+ }
+
+
+ /**
+ * Perform all cleanup and refresh activities to complete
+ * finishEdge().
+ */
+ protected void completeFinishEdge() {
+ edgeStarted = false;
+ updateEdge();
+
+ saveX1 = Double.MIN_VALUE;
+ saveX2 = Double.MIN_VALUE;
+ saveY1 = Double.MIN_VALUE;
+ saveY2 = Double.MIN_VALUE;
+
+ node = null;
+
+ if (isHandlingEdgeDrop()) {
+ this.setHandlingEdgeDrop(false);
+ }
+
+ // AJK: 11/18/2005 invert selection of any nodes/edges that have been highlighted
+ // AJK: 12/09/06 comment out the toggling of selection, due to bug caused
+ // invertSelections(null);
+ this.getCanvas().repaint();
+
+ // redraw graph so that the correct arrow is shown (but only if network
+ // is small enough to see the edge...
+ // NOTE: this is not needed
+ if (Cytoscape.getCurrentNetwork().getNodeCount() <= 500) {
+ Cytoscape.getCurrentNetworkView().redrawGraph(true, true);
+ }
+ }
+
+ /**
+ * create a new node at the point where mouse was pressed
+ *
+ * @param location point of mouse press (in Canvas coordinates)
+ */
+ public CyNode createNode(Point2D location) {
+ CyNode cn = null;
+ cn = _caller.addNode("node" + counter, this.getNodeAttributeName(),
+ this.getNodeAttributeValue(), location);
+ counter++;
+
+ return cn;
+ }
+
+ /**
+ * updates rendering of edge if an edge is under construction
+ */
+ @Override public void mouseMoved(MouseEvent e) {
+ // TODO: This check should really be avoided by having the editor remove all mouse and key
+ // listeners when the editor looses focus (another tab is clicked on).
+ // Since this is somewhat involved and so is left for when the editor is refactored.
+ if (!CytoscapeEditorManager.isEditorInOperation()) {
+ return;
+ }
+ // CytoscapeEditorManager.log("CE: mouseMoved!");
+ nextPoint = e.getPoint();
+
+ if (edgeStarted) {
+ // we need to update the latest section of the edge
+ updateEdge();
+
+ // if over NodeView or EdgeView, then highlight
+ // AJK: 12/09/06 comment out the toggling of selection, due to bug caused
+ // MLC 02/03/09 BEGIN:
+ DGraphView cView = getCurrentDGraphView();
+ // NodeView nv = view.getPickedNodeView(nextPoint);
+ // EdgeView ev = view.getPickedEdgeView(nextPoint);
+ NodeView nv = cView.getPickedNodeView(nextPoint);
+ EdgeView ev = cView.getPickedEdgeView(nextPoint);
+ // MLC 02/03/09 END.
+ if ((nv != null) || (ev != null)) {
+ // invertSelections(nv);
+ // } else if (ev != null) {
+ // invertSelections(ev);
+ } else {
+ // invertSelections(null);
+ }
+ }
+ }
+
+ // MLC 02/03/09 BEGIN:
+ // Already defined in NetworkEditEventAdapter:
+ // /**
+ // * if hovering over a node, then highlight the node by temporarily
+ // * inverting its selection
+ // *
+ // *
+ // */
+ //
+ // // TODO: this doesn't work because we are entering Canvas, NOT nodeview
+ // public void mouseEntered(MouseEvent e) {
+ // // AJK: 12/09/06 comment out the toggling of selection, due to bug caused
+ // // Point2D location = e.getPoint();
+ // // NodeView nv = view.getPickedNodeView(location);
+ // //
+ // // if (nv != null) {
+ // // if (edgeStarted) {
+ // // nv.setSelected(!nv.isSelected());
+ // // }
+ // //
+ // // this.getCanvas().repaint();
+ // // }
+ // }
+ //
+ // /**
+ // * revert temporary node highlighting that was done upon MouseEnter
+ // */
+ // public void mouseExited(MouseEvent e) {
+ // // AJK: 12/09/06 comment out the toggling of selection, due to bug caused
+ // // Point2D location = e.getPoint();
+ // // NodeView nv = view.getPickedNodeView(location);
+ // //
+ // // if (nv != null) {
+ // // if (edgeStarted) {
+ // // nv.setSelected(!nv.isSelected());
+ // // }
+ // //
+ // // this.getCanvas().repaint();
+ // // }
+ // }
+ // MLC 02/03/09 END.
+
+ /**
+ * begin or continue drawing an edge as mouse is dragged
+ */
+ @Override public void mouseDragged(MouseEvent e) {
+ // TODO: This check should really be avoided by having the editor remove all mouse and key
+ // listeners when the editor looses focus (another tab is clicked on).
+ // Since this is somewhat involved and so is left for when the editor is refactored.
+ if (!CytoscapeEditorManager.isEditorInOperation()) {
+ return;
+ }
+ nextPoint = e.getPoint();
+
+ boolean onNode = false;
+ Point2D location = e.getPoint();
+ // MLC 02/03/09 BEGIN:
+ DGraphView cView = getCurrentDGraphView();
+ // NodeView nv = view.getPickedNodeView(location);
+ NodeView nv = cView.getPickedNodeView(location);
+ // MLC 02/03/09 END.
+ if (nv != null) {
+ onNode = true;
+ }
+
+ if (onNode && !edgeStarted && (e.isControlDown() && !(isMacPlatform()))) {
+ // begin edge creation
+ beginEdge(nextPoint, nv);
+ }
+
+ if (!edgeStarted) {
+ // super.mouseDragged(e);
+ }
+
+ if (edgeStarted) {
+ // we need to update the latest section of the edge
+ updateEdge();
+ }
+ }
+
+ // AJK: 12/09/06 comment out the toggling of selection, due to bug caused
+ /* private void invertSelections(Object nodeOrEdgeView) {
+ if (nodeOrEdgeView == null) // we have moved off a node or edge
+ {
+ if (_highlightedEdgeView != null) {
+ _highlightedEdgeView.setSelected(!_highlightedEdgeView.isSelected());
+ // if (_savedStrokeWidth != Float.NaN)
+ // {
+ // _highlightedEdgeView.setStrokeWidth(_savedStrokeWidth);
+ // }
+ _highlightedEdgeView = null;
+ }
+
+ if (_highlightedNodeView != null) {
+ _highlightedNodeView.setSelected(!_highlightedNodeView.isSelected());
+ _highlightedNodeView = null;
+ }
+
+ if (_savedCursor != null) {
+ Cytoscape.getDesktop().setCursor(_savedCursor);
+ }
+ } else if (nodeOrEdgeView instanceof NodeView) {
+ NodeView nv = (NodeView) nodeOrEdgeView;
+
+ if (_highlightedEdgeView != null) {
+ _highlightedEdgeView.setSelected(!_highlightedEdgeView.isSelected());
+ // if (_savedStrokeWidth != Float.NaN)
+ // {
+ // _highlightedEdgeView.setStrokeWidth(_savedStrokeWidth);
+ // Cytoscape.getCurrentNetworkView().redrawGraph(true, true);
+ // }
+ // _highlightedEdgeView = null;
+ }
+
+ if (_highlightedNodeView != null) {
+ _highlightedNodeView.setSelected(!_highlightedNodeView.isSelected());
+ }
+
+ _highlightedNodeView = nv;
+ nv.setSelected(!nv.isSelected());
+ CytoscapeEditorManager.log("Hovering near: " + nv +
+ " setting cursor to " +
+ Cursor.HAND_CURSOR);
+ _savedCursor = Cytoscape.getDesktop().getCursor();
+ Cytoscape.getDesktop()
+ .setCursor(Cursor.getPredefinedCursor(Cursor.HAND_CURSOR));
+ } else if (nodeOrEdgeView instanceof EdgeView) {
+ EdgeView ev = (EdgeView) nodeOrEdgeView;
+
+ if (_highlightedNodeView != null) {
+ _highlightedNodeView.setSelected(!_highlightedNodeView.isSelected());
+ _highlightedNodeView = null;
+ }
+
+ if (_highlightedEdgeView != null) {
+ _highlightedEdgeView.setSelected(!_highlightedEdgeView.isSelected());
+ // if (_savedStrokeWidth != Float.NaN)
+ // {
+ // _highlightedEdgeView.setStrokeWidth(_savedStrokeWidth);
+ // Cytoscape.getCurrentNetworkView().redrawGraph(true, true);
+ // }
+ }
+
+ _highlightedEdgeView = ev;
+ ev.setSelected(!ev.isSelected());
+ // _savedStrokeWidth = ev.getStrokeWidth();
+ // ev.setStrokeWidth(4.0f);
+ _savedCursor = Cytoscape.getDesktop().getCursor();
+ CytoscapeEditorManager.log("Hovering near: " + ev +
+ " setting cursor to " +
+ Cursor.HAND_CURSOR);
+ Cytoscape.getDesktop()
+ .setCursor(Cursor.getPredefinedCursor(Cursor.HAND_CURSOR));
+ }
+ }
+ */
+
+ /**
+ * updates the rubberbanded edge line as the mouse is moved, works in Canvas coordinates
+ */
+ @Override public void updateEdge() {
+ // This can happen under certain D&D conditions where no mouse events occur before the drop
+ // event that lead here. In this case, just start nextPoint at startPoint:
+ if (nextPoint == null) {
+ nextPoint = startPoint;
+ }
+ double x1 = startPoint.getX();
+ double y1 = startPoint.getY();
+ double x2 = nextPoint.getX();
+ double y2 = nextPoint.getY();
+ double lineLen = Math.sqrt(((x2 - x1) * (x2 - x1)) + ((y2 - y1) * (y2 - y1)));
+ double offset = 5;
+
+ if (lineLen == 0) {
+ lineLen = 1;
+ }
+
+ y2 = y2 + (((y1 - y2) / lineLen) * offset);
+ x2 = x2 + (((x1 - x2) / lineLen) * offset);
+
+ nextPoint.setLocation(x2, y2);
+
+ // MLC 02/03/09 BEGIN:
+ // Graphics g = canvas.getGraphics();
+ DGraphView dnv = getCurrentDGraphView();
+ InnerCanvas curCanvas = dnv.getCanvas();
+ // Graphics g = canvas.getGraphics();
+ Graphics g = curCanvas.getGraphics();
+ // MLC 02/03/09 END.
+
+ Color saveColor = g.getColor();
+
+ if (saveX1 != Double.MIN_VALUE) {
+ // AJK: 11/07/06 BEGIN
+ // fix for fanout bug
+ // canvas.getGraphics().setColor(canvas.getBackground());
+ // MLC 02/03/09:
+ // DGraphView dnv = (DGraphView) Cytoscape.getCurrentNetworkView();
+ DingCanvas backgroundCanvas = dnv.getCanvas(DGraphView.Canvas.BACKGROUND_CANVAS);
+ g.setColor(backgroundCanvas.getBackground());
+ // AJK: 11/04/06 END
+ g.drawLine(((int) saveX1) - 1, ((int) saveY1) - 1, ((int) saveX2) + 1,
+ ((int) saveY2) + 1);
+ }
+
+ // MLC 02/03/09 BEGIN:
+ // canvas.update(g);
+ curCanvas.update(g);
+ // MLC 02/03/09 END.
+ g.setColor(Color.BLACK);
+ g.drawLine(((int) x1) - 1, ((int) y1) - 1, ((int) x2) + 1, ((int) y2) + 1);
+ g.setColor(saveColor);
+
+ saveX1 = x1;
+ saveX2 = x2;
+ saveY1 = y1;
+ saveY2 = y2;
+ }
+
+ // MLC 02/03/09 BEGIN:
+ // Already defined in NetworkEditEventAdapter:
+ // /**
+ // *
+ // * MultiHashMapListener methods
+ // *
+ // */
+ // public void attributeValueAssigned(java.lang.String objectKey, java.lang.String attributeName,
+ // java.lang.Object[] keyIntoValue,
+ // java.lang.Object oldAttributeValue,
+ // java.lang.Object newAttributeValue) {
+ // }
+ //
+ // /**
+ // * DOCUMENT ME!
+ // *
+ // * @param objectKey DOCUMENT ME!
+ // * @param attributeName DOCUMENT ME!
+ // * @param keyIntoValue DOCUMENT ME!
+ // * @param attributeValue DOCUMENT ME!
+ // */
+ // public void attributeValueRemoved(java.lang.String objectKey, java.lang.String attributeName,
+ // java.lang.Object[] keyIntoValue,
+ // java.lang.Object attributeValue) {
+ // }
+ // MLC 02/03/09 END.
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param objectKey DOCUMENT ME!
+ * @param attributeName DOCUMENT ME!
+ */
+ public void allAttributeValuesRemoved(java.lang.String objectKey, java.lang.String attributeName) {
+ }
+
+ /**
+ * @return flag indicating whether an edge is under construction
+ */
+ public boolean isEdgeStarted() {
+ return edgeStarted;
+ }
+
+ /**
+ * set the flag that indicates whether an edge is under construction
+ *
+ * @param edgeStarted
+ *
+ */
+ public void setEdgeStarted(boolean edgeStarted) {
+ this.edgeStarted = edgeStarted;
+ }
+
+ /**
+ * @return Returns the nextPoint.
+ */
+ public Point2D getNextPoint() {
+ return nextPoint;
+ }
+
+ /**
+ * @param nextPoint
+ * The nextPoint to set
+ *
+ */
+ public void setNextPoint(Point2D nextPoint) {
+ this.nextPoint = nextPoint;
+ }
+
+ /**
+ * @return Returns the node.
+ */
+ public NodeView getNode() {
+ return node;
+ }
+
+ /**
+ * @param node
+ * The node to set.
+ *
+ */
+ public void setNode(NodeView node) {
+ this.node = node;
+ }
+
+ /**
+ * @return Returns the startPoint.
+ */
+ public Point2D getStartPoint() {
+ return startPoint;
+ }
+
+ /**
+ * @param startPoint
+ * The startPoint to set.
+ *
+ */
+ public void setStartPoint(Point2D startPoint) {
+ this.startPoint = startPoint;
+ }
+
+ // MLC 02/03/09 BEGIN:
+ // Already defined in NetworkEditEventAdapter:
+ // /**
+ // * @return Returns the view.
+ // */
+ // // AJK: 04/15/06 for Cytoscape 2.3 renderer
+ // // public PGraphView getView() {
+ // public DGraphView getView() {
+ // return view;
+ // }
+ //
+ // /**
+ // * @param view
+ // * The view to set.
+ // *
+ // */
+ //
+ // // AJK: 04/15/06 for Cytoscape 2.3 renderer
+ // // public void setView(PGraphView view) {
+ // public void setView(DGraphView view) {
+ // this.view = view;
+ // }
+ // MLC 02/03/09 END.
+
+ /**
+ * @return Returns the flag that indicates whether we are handling the drop
+ * of an edge onto the canvas TODO: move edge drop handling into
+ * PaletteNetworkEditEventHandler
+ */
+ public boolean isHandlingEdgeDrop() {
+ return handlingEdgeDrop;
+ }
+
+ /**
+ * @param handlingEdgeDrop
+ * sets the flag that indicates whether we are handling the drop
+ * of an edge onto the canvas
+ *
+ *
+ */
+ public void setHandlingEdgeDrop(boolean handlingEdgeDrop) {
+ this.handlingEdgeDrop = handlingEdgeDrop;
+ }
+
+ // MLC 02/03/09 BEGIN:
+ // Already defined in NetworkEditEventAdapter:
+ // /**
+ // * starts up the event handler on the input network view adds an input event
+ // * listener to the view's canvas
+ // *
+ // * @param view
+ // * a Cytoscape network view
+ // */
+ //
+ // // AJK: 04/15/06 for Cytoscape 2.3 renderer
+ // // public void start(PGraphView view) {
+ // public void start(DGraphView view) {
+ // this.view = view;
+ // this.canvas = view.getCanvas();
+ // // canvas.addInputEventListener(this);
+ // CytoscapeEditorManager.log("Started event listener: " + this);
+ // canvas.addMouseListener(this);
+ // canvas.addMouseMotionListener(this);
+ // canvas.addKeyListener(this);
+ // }
+ //
+ // /**
+ // * stops the event handler by removing the input event listener from the
+ // * canvas this is called when the user switches between editors
+ // *
+ // */
+ // public void stop() {
+ // if (canvas != null) {
+ // // AJK: 04/15/06 for Cytoscape 2.3 renderer
+ // // canvas.removeInputEventListener(this);
+ // // CytoscapeEditorManager.log("stopped event listener: " + this);
+ // canvas.removeMouseListener(this);
+ // canvas.removeMouseMotionListener(this);
+ // canvas.removeKeyListener(this);
+ // this.view = null;
+ // this.canvas = null;
+ // }
+ // }
+ // MLC 02/03/09 END.
+
+ /**
+ * @return Returns the edgeAttributeValue.
+ */
+ public String getEdgeAttributeValue() {
+ return edgeAttributeValue;
+ }
+
+ /**
+ * @param edgeAttributeValue
+ * The edgeAttributeValue to set.
+ */
+ public void setEdgeAttributeValue(String edgeAttributeValue) {
+ this.edgeAttributeValue = edgeAttributeValue;
+ }
+
+ /**
+ * @return Returns the nodeAttributeName.
+ */
+ public String getNodeAttributeName() {
+ return nodeAttributeName;
+ }
+
+ /**
+ * @param nodeAttributeName
+ * The nodeAttributeName to set.
+ */
+ public void setNodeAttributeName(String nodeAttributeName) {
+ this.nodeAttributeName = nodeAttributeName;
+ }
+
+ /**
+ * @return Returns the edgeAttributeName.
+ */
+ public String getEdgeAttributeName() {
+ return edgeAttributeName;
+ }
+
+ /**
+ * @param edgeAttributeName
+ * The edgeAttributeName to set.
+ */
+ public void setEdgeAttributeName(String edgeAttributeName) {
+ this.edgeAttributeName = edgeAttributeName;
+ }
+
+ /**
+ * @return Returns the networkAttributeName.
+ */
+ public String getNetworkAttributeName() {
+ return networkAttributeName;
+ }
+
+ /**
+ * @param networkAttributeName
+ * The networkAttributeName to set.
+ */
+ public void setNetworkAttributeName(String networkAttributeName) {
+ this.networkAttributeName = networkAttributeName;
+ }
+
+ /**
+ * @param networkAttributeValue
+ * The networkAttributeValue to set.
+ */
+ public void setNetworkAttributeValue(String networkAttributeValue) {
+ this.networkAttributeValue = networkAttributeValue;
+ }
+
+
+ /**
+ * @return Returns the nodeAttributeValue.
+ */
+ public String getNodeAttributeValue() {
+ return nodeAttributeValue;
+ }
+
+ /**
+ * @param nodeAttributeValue
+ * The nodeAttributeValue to set.
+ */
+ public void setNodeAttributeValue(String nodeAttributeValue) {
+ this.nodeAttributeValue = nodeAttributeValue;
+ }
+
+ // MLC 02/03/09 BEGIN:
+ // Already defined in NetworkEditEventAdapter:
+ // /**
+ // * @return Returns the _caller.
+ // */
+ // public CytoscapeEditor get_caller() {
+ // return _caller;
+ // }
+ //
+ // /**
+ // * @param _caller
+ // * The _caller to set.
+ // */
+ // public void set_caller(CytoscapeEditor _caller) {
+ // this._caller = _caller;
+ // }
+ // MLC 02/03/09 END.
+}
diff --git a/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/event/NetworkEditEventAdapter.java b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/event/NetworkEditEventAdapter.java
new file mode 100644
index 0000000..0c00101
--- /dev/null
+++ b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/event/NetworkEditEventAdapter.java
@@ -0,0 +1,344 @@
+/* -*-Java-*-
+********************************************************************************
+*
+* File: NetworkEditEventAdapter.java
+* RCS: $Header: $
+* Description:
+* Author: Allan Kuchinsky
+* Created: Tue May 17 11:17:49 2005
+* Modified: Wed Feb 04 08:44:13 2009 (Michael L. Creech) creech at w235krbza760
+* Language: Java
+* Package:
+* Status: Experimental (Do Not Distribute)
+*
+* (c) Copyright 2009, Agilent Technologies, all rights reserved.
+*
+********************************************************************************
+*
+* Revisions:
+*
+* Tue Feb 03 11:19:51 2009 (Michael L. Creech) creech at w235krbza760
+* Removed use of canvas and view in favor of deriving these from the
+* current network view. Added getCurrentDGraphView().
+********************************************************************************
+*/
+
+package cytoscape.editor.event;
+
+import cytoscape.Cytoscape;
+import cytoscape.editor.CytoscapeEditor;
+import cytoscape.view.CyNetworkView;
+
+import ding.view.DGraphView;
+import ding.view.InnerCanvas;
+
+import phoebe.PhoebeCanvasDropEvent;
+import phoebe.PhoebeCanvasDropListener;
+
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.KeyEvent;
+import java.awt.event.KeyListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+
+// TODO (02/03/09): All deprecated references to setView(), getView(),
+// and start(DGraphView) should be updated along with all higher-level
+// methods that pass unneeded variables DGrapViews to lower-level
+// methods. ALso, this class should probably be turned into an
+// interface or an abstract class and BasicNetworkEditEventHandler
+// become the first full implementation.
+
+/**
+ *
+ * The <b>NetworkEditEventAdapter</b> class provides stub methods for
+ * specialized network edit event handlers, as part of the graph editing
+ * framework. The specialized network edit event handler is the key class in the
+ * Cytoscape editor for defining the behavior of the editor. The behavior is
+ * defined in terms of how the event handler responds to mouse events, drag/drop
+ * events, and button press events. All editors must include a network edit
+ * event handler class that extends the <b>NetworkEditEventAdapter</b> class.
+ * * revised: 04/15/2006 to integrate with Cytoscape 2.3 renderer Phase 1:
+ * switch underlying node identification and edge drawing code Phase 2: remove
+ * dependencies upon Piccolo
+ *
+ * @author Allan Kuchinsky
+ * @version 1.0
+ *
+ */
+public class NetworkEditEventAdapter implements MouseListener, MouseMotionListener, ActionListener,
+ PhoebeCanvasDropListener, KeyListener,
+ cytoscape.data.attr.MultiHashMapListener {
+ // MLC 02/03/09 BEGIN:
+ // protected InnerCanvas canvas;
+ // protected DGraphView view;
+ // CytoscapeEditor _caller;
+ protected CytoscapeEditor _caller;
+ private boolean started;
+ // MLC 02/03/09 END.
+
+ /**
+ * Creates a new NetworkEditEventAdapter object.
+ */
+ public NetworkEditEventAdapter() {
+ }
+
+ /**
+ * starts up the event handler on the input network view adds an input event
+ * listener to the view's canvas
+ *
+ * @deprecated Use no argument start().
+ * @param view
+ * a Cytoscape network view
+ */
+
+ public void start(DGraphView view) {
+ // MLC 02/03/09 BEGIN:
+ start();
+ // this.view = view;
+ // this.canvas = view.getCanvas();
+ // // AJK: 04/15/06 for Cytoscape 2.3
+ // // canvas.addInputEventListener(this);
+ //
+ // canvas.addMouseListener(this);
+ // canvas.addMouseMotionListener(this);
+ // canvas.addKeyListener(this);
+ // // CytoscapeEditorManager.log("Mouse and MotionListeners added to " + canvas);
+ // // CytoscapeEditorManager.log("Canvas has total number of Listeners = " +
+ // // canvas.getMouseListeners().length);
+ // MLC 02/03/09 END.
+ }
+
+ // MLC 02/03/09 BEGIN:
+ public void start() {
+ InnerCanvas canvas = getCurrentDGraphView().getCanvas();
+ started = true;
+ canvas.addMouseListener(this);
+ canvas.addMouseMotionListener(this);
+ canvas.addKeyListener(this);
+ }
+
+ // MLC 02/03/09 END.
+ /**
+ * stops the event handler by removing the input event listener from the
+ * canvas this is called when the user switches between editors
+ *
+ */
+ public void stop() {
+ // MLC 02/03/09 BEGIN:
+ // if (canvas != null) {
+ if (started) {
+ InnerCanvas canvas = getCurrentDGraphView().getCanvas();
+ // MLC 02/03/09 END.
+ // AJKL: 04/15/06 for Cytoscape 2.3
+ // canvas.removeInputEventListener(this);
+ canvas.removeMouseListener(this);
+ canvas.removeMouseMotionListener(this);
+ canvas.removeKeyListener(this);
+ // MLC 02/03/09 BEGIN:
+ started = false;
+ // this.view = null;
+ // this.canvas = null;
+ // MLC 02/03/09 END.
+ }
+ }
+
+ /**
+ * Gets the current canvas based on Cytoscape.getCurrentNetworkView().
+ * @return the current canvas
+ */
+
+ // public PCanvas getCanvas() {
+ public InnerCanvas getCanvas() {
+ // MLC 02/03/09 BEGIN:
+ // return canvas;
+ return getCurrentDGraphView().getCanvas();
+ // MLC 02/03/09 END.
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void mouseExited(MouseEvent e) {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void mouseEntered(MouseEvent e) {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void mousePressed(MouseEvent e) {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void mouseMoved(MouseEvent e) {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void mouseDragged(MouseEvent e) {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void mouseClicked(MouseEvent e) {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void mouseReleased(MouseEvent e) {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param event DOCUMENT ME!
+ */
+ public void keyPressed(KeyEvent event) {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param event DOCUMENT ME!
+ */
+ public void keyReleased(KeyEvent event) {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param event DOCUMENT ME!
+ */
+ public void keyTyped(KeyEvent event) {
+ }
+
+ /**
+ * method for rendering an edge under construction as the user moves the
+ * mouse typically this may be done via a rubberband-line that udpates as
+ * the mouse position changes
+ *
+ */
+ public void updateEdge() {
+ }
+
+ /**
+ * actionPerformed() method should be overwritten by child classes
+ */
+ public void actionPerformed(ActionEvent evt) {
+ }
+
+ /**
+ * method for responding when an item is dropped onto the canvas. typically
+ * this would result in the addition of a node or an edge to the current
+ * Cytoscape network.
+ */
+ public void itemDropped(PhoebeCanvasDropEvent dte) {
+ }
+
+ /**
+ *
+ * MultiHashMapListener methods
+ */
+ public void attributeValueAssigned(java.lang.String objectKey, java.lang.String attributeName,
+ java.lang.Object[] keyIntoValue,
+ java.lang.Object oldAttributeValue,
+ java.lang.Object newAttributeValue) {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param objectKey DOCUMENT ME!
+ * @param attributeName DOCUMENT ME!
+ * @param keyIntoValue DOCUMENT ME!
+ * @param attributeValue DOCUMENT ME!
+ */
+ public void attributeValueRemoved(java.lang.String objectKey, java.lang.String attributeName,
+ java.lang.Object[] keyIntoValue,
+ java.lang.Object attributeValue) {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param objectKey DOCUMENT ME!
+ * @param attributeName DOCUMENT ME!
+ */
+ public void allAttributeValuesRemoved(java.lang.String objectKey, java.lang.String attributeName) {
+ }
+
+ /**
+ * @return Returns the _caller.
+ */
+ public CytoscapeEditor get_caller() {
+ return _caller;
+ }
+
+ /**
+ * @param _caller
+ * The _caller to set.
+ */
+ public void set_caller(CytoscapeEditor _caller) {
+ this._caller = _caller;
+ }
+
+ /**
+ * @deprecated Use getCurrentDGraphView().
+ * @return Returns the view.
+ */
+
+ // public PGraphView getView() {
+
+ public DGraphView getView() {
+ // MLC 02/03/09 BEGIN:
+ return getCurrentDGraphView ();
+ // return view;
+ // MLC 02/03/09 END.
+ }
+
+ /**
+ * @deprecated There is no longer any need to set the view.
+ * @param view
+ * The view to set.
+ */
+ // public void setView(PGraphView view) {
+ public void setView(DGraphView view) {
+
+ // this.view = view;
+ }
+
+ // MLC 02/03/09 BEGIN:
+ // Return the Cytoscape current network view as a DGraphView:
+ public DGraphView getCurrentDGraphView () {
+ CyNetworkView cnv = Cytoscape.getCurrentNetworkView();
+ // CytoscapeEditorManager.log ("current newtork view used: " + cnv.getTitle());
+ return (DGraphView)cnv;
+ }
+ // MLC 02/03/09 END.
+
+}
diff --git a/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/event/PaletteNetworkEditEventHandler.java b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/event/PaletteNetworkEditEventHandler.java
new file mode 100644
index 0000000..ab06ff9
--- /dev/null
+++ b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/event/PaletteNetworkEditEventHandler.java
@@ -0,0 +1,401 @@
+/* -*-Java-*-
+********************************************************************************
+*
+* File: PaletteNetworkEditEventHandler.java
+* RCS: $Header: $
+* Description:
+* Author: Allan Kuchinsky
+* Created: Fri Jul 31 05:14:41 2005
+* Modified: Wed Feb 04 09:01:03 2009 (Michael L. Creech) creech at w235krbza760
+* Language: Java
+* Package:
+/*
+
+ Copyright (c) 2006, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+
+********************************************************************************
+*
+* Revisions:
+*
+* Wed Feb 04 08:57:26 2009 (Michael L. Creech) creech at w235krbza760
+* Removed view in favor of deriving from the current network view.
+* Wed Jul 09 09:54:56 2008 (Michael L. Creech) creech at w235krbza760
+* Added check that Editor component is active to itemDropped()
+* to avoid handling events when the editor tab isn't the current tab.
+* Fri May 11 17:04:38 2007 (Michael L. Creech) creech at w235krbza760
+* Removed uneeded imports.
+* Fri Dec 08 05:15:16 2006 (Michael L. Creech) creech at w235krbza760
+* Refactored itemDropped() and handleDroppedEdge() and broke into
+* smaller methods. Removed findEdgeDropTarget().
+********************************************************************************
+*/
+package cytoscape.editor.event;
+
+import giny.view.NodeView;
+
+import java.awt.Point;
+import java.awt.datatransfer.DataFlavor;
+import java.awt.datatransfer.Transferable;
+import java.awt.datatransfer.UnsupportedFlavorException;
+import java.io.IOException;
+
+import phoebe.PhoebeCanvasDropEvent;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+import cytoscape.dialogs.SetNestedNetworkDialog;
+import cytoscape.editor.CytoscapeEditor;
+import cytoscape.editor.CytoscapeEditorManager;
+import cytoscape.editor.impl.BasicCytoShapeEntity;
+import cytoscape.editor.impl.ShapePalette;
+import cytoscape.logger.CyLogger;
+import cytoscape.view.CyNetworkView;
+import ding.view.DGraphView;
+import ding.view.InnerCanvas;
+import javax.swing.JOptionPane;
+import cytoscape.CyNetwork;
+
+/**
+ *
+ * The <b>PaletteNetworkEditEventHandler</b> extends the basic network edit event handler with the
+ * capability to drag and drop shapes from a palette onto
+ * the canvas, resulting in the addition of nodes and edges to the current
+ * Cytoscape network.
+ *
+ * @author Allan Kuchinsky, Agilent Technologies
+ * @version 1.0
+ *
+ */
+public class PaletteNetworkEditEventHandler extends BasicNetworkEditEventHandler {
+ CyLogger logger = CyLogger.getLogger(PaletteNetworkEditEventHandler.class);
+
+ /**
+ *
+ */
+ public PaletteNetworkEditEventHandler() {
+ super();
+ }
+
+ /**
+ * @param caller
+ */
+ public PaletteNetworkEditEventHandler(CytoscapeEditor caller) {
+ super(caller);
+ }
+
+ /**
+ * @deprecated call single argument constructor
+ * @param caller
+ * @param view
+ */
+ public PaletteNetworkEditEventHandler(CytoscapeEditor caller, CyNetworkView view) {
+ // MLC 02/03/09 BEGIN:
+ // super(caller, view);
+ super(caller);
+ // MLC 02/03/09 END.
+ }
+
+ protected BasicCytoShapeEntity getShapeEntityForLocation(Point location, Transferable t) {
+ Object shape = null;
+ BasicCytoShapeEntity myShape = null;
+ Class shapeClass = null;
+
+ try {
+ shapeClass = Class.forName("cytoscape.editor.impl.BasicCytoShapeEntity");
+ } catch (Exception except) {
+ logger.warn("Can't get class for BasicCytoShapeEntity", except);
+ return null;
+ }
+
+ DataFlavor[] dfl = t.getTransferDataFlavors();
+
+ for (DataFlavor d : dfl) {
+
+ CytoscapeEditorManager.log("Item dropped of Mime Type: " + d.getMimeType());
+ CytoscapeEditorManager.log("Mime subtype is: " + d.getSubType());
+ CytoscapeEditorManager.log("Mime class is: " + d.getRepresentationClass());
+
+ Class mimeClass = d.getRepresentationClass();
+
+ if (mimeClass == shapeClass) {
+ CytoscapeEditorManager.log("got shape: " + d.getRepresentationClass());
+
+ try {
+ shape = t.getTransferData(d);
+ } catch (UnsupportedFlavorException exc) {
+ logger.warn("Unsupported shape flavor", exc);
+ return null;
+ } catch (IOException exc) {
+ logger.warn("I/O exception getting shape", exc);
+
+ return null;
+ }
+
+ break;
+ } else if (d.isMimeTypeEqual("application/x-java-url")) {
+ handleDroppedURL(t, d, location);
+
+ break;
+ }
+ }
+
+ if (shape != null) {
+ myShape = ShapePalette.getBasicCytoShapeEntity(shape.toString());
+ }
+
+ return myShape;
+ }
+
+ /**
+ * The <b>itemDropped()</b> method is at the heart of the palette-based
+ * editor. The method can respond to a variety of DataFlavors that
+ * correspond to the shape being dragged and dropped from the palette. These
+ * include Cytoscape nodes and edges, as well as URLs that can be dragged
+ * and dropped from other applications onto the palette.
+ *
+ */
+
+ // implements PhoebeCanvasDropListener interface:
+ public void itemDropped(PhoebeCanvasDropEvent e) {
+ // TODO: This check should really be avoided by having the editor remove the PhoebeCanvasDropListener
+ // when the editor looses focus (another tab is clicked on).
+ // Since this is somewhat involved and so is left for when the editor is refactored.
+ if (!CytoscapeEditorManager.isEditorInOperation()) {
+ return;
+ }
+ Point location = e.getLocation();
+ CytoscapeEditorManager.log("Item dropped at: " + e.getLocation());
+ CytoscapeEditorManager.log("on object: " + e.getSource());
+
+ // AJK: 07/03/07 BEGIN
+ // do nothing if we are not dropping on canvas for current network view
+ InnerCanvas dropCanvas = (InnerCanvas) e.getSource();
+ // MLC 02/03/09 BEGIN:
+ // InnerCanvas currentCanvas = ((DGraphView) Cytoscape.getCurrentNetworkView()).getCanvas();
+ InnerCanvas currentCanvas = getCurrentDGraphView().getCanvas();
+ // MLC 02/03/09 END.
+
+ if (dropCanvas != currentCanvas)
+ {
+ return;
+ }
+ // AJK: 07/03/07 END
+
+ BasicCytoShapeEntity myShape = getShapeEntityForLocation(location, e.getTransferable());
+
+ if (myShape != null) {
+ // need to handle nodes and edges differently
+ String attributeName = myShape.getAttributeName();
+ String attributeValue = myShape.getAttributeValue();
+
+ // CytoscapeEditorManager.log("Item dropped of type: " +
+ // attributeName);
+ if (attributeName.equals(get_caller().getControllingNodeAttribute())) {
+ setNodeAttributeName(attributeName);
+ setNodeAttributeValue(attributeValue);
+ handleDroppedNode(attributeName, attributeValue, location);
+ } else if (attributeName.equals(get_caller().getControllingEdgeAttribute())) {
+ setEdgeAttributeName(attributeName);
+ setEdgeAttributeValue(attributeValue);
+ handleDroppedEdge(attributeName, attributeValue, location);
+ } else if (attributeName.equals(get_caller().getControllingNetworkAttribute())){
+ setNetworkAttributeName(attributeName);
+ setNetworkAttributeValue(attributeValue);
+ handleDroppedNetwork(getNodeAttributeName(), getNodeAttributeValue(), location); }
+ }
+ }
+
+ // overwridden by subclasses:
+ protected void handleDroppedNode(String attributeName, String attributeValue, Point location) {
+ String nodeID = "node" + counter;
+
+ if (ShapePalette.specifyIdentifier){
+ nodeID = getNodeID(nodeID);
+ if (nodeID == null){
+ return;
+ }
+ }
+
+ get_caller().addNode(nodeID, attributeName, attributeValue, location);
+ counter++;
+ }
+
+ private String getNodeID(String nodeID){
+ String newNodeID = null;
+
+ while (true){
+ newNodeID = JOptionPane.showInputDialog(Cytoscape.getDesktop(),"Please Specify Node identifier", nodeID);
+ if (newNodeID == null){
+ return null;
+ }
+
+ // Check if the nodeID already exists
+ CyNode aNode = Cytoscape.getCyNode(newNodeID);
+ if (aNode == null){
+ break;
+ }
+ JOptionPane.showMessageDialog(Cytoscape.getDesktop(), newNodeID + " already exists!", "Duplicated Identifier",
+ JOptionPane.WARNING_MESSAGE);
+ }
+
+ return newNodeID;
+ }
+
+ // overwridden by subclasses:
+ protected void handleDroppedEdge(String attributeName, String attributeValue, Point location) {
+ if (isEdgeStarted()) {
+ // if there is another edit in progress, then don't
+ // process a drag/drop
+ return;
+ }
+
+ // NB: targetNode is *drop* target
+ // MLC 02/03/09 BEGIN:
+ // NodeView targetNode = getView().getPickedNodeView(location);
+ // Things that add new network views, like HyperEdgeEditor sample networks, can cause the
+ // cached view to not be the correct view where we are clicking, so we use the current network view:
+ // CytoscapeEditorManager.log ("In handleDroppedEdge");
+ NodeView targetNode = getCurrentDGraphView().getPickedNodeView(location);
+ // MLC 02/03/09 END.
+ if (targetNode == null) {
+ return;
+ }
+
+ // if we reach this point, then the edge shape has been
+ // dropped onto a node Begin Edge creation
+ setHandlingEdgeDrop(true);
+ beginEdge(location, targetNode);
+ }
+
+ // Support Nested Network
+ protected void handleDroppedNetwork(String attributeName, String attributeValue, Point location) {
+ //get_caller().addNetwork("network" + counter, attributeName, attributeValue, location);
+ //counter++;
+
+ NodeView targetNode = getCurrentDGraphView().getPickedNodeView(location);
+ if (targetNode == null) {
+
+ // Select the nested network
+ SetNestedNetworkDialog dlg = new SetNestedNetworkDialog(Cytoscape.getDesktop(), true);
+ dlg.setLocationRelativeTo(Cytoscape.getDesktop());
+ dlg.setVisible(true);
+
+ CyNetwork selectedNetwork = dlg.getSelectedNetwork();
+
+ if (selectedNetwork == null){
+ return;
+ }
+
+ // Create a new Node
+ String nodeID = getSuggestedNodeID(selectedNetwork);//selectedNetwork.getIdentifier();//"node" + counter;
+
+ if (ShapePalette.specifyIdentifier){
+ nodeID = getNodeID(nodeID);
+ if (nodeID == null){
+ return;
+ }
+ }
+
+ CyNode newNode = get_caller().addNode(nodeID, attributeName, attributeValue, location);
+ counter++;
+
+ // Set a nested network for this newly created node
+ NodeView newNodeView = Cytoscape.getCurrentNetworkView().getNodeView(newNode);
+
+ if (newNodeView == null){
+ return;
+ }
+ newNode.setNestedNetwork(selectedNetwork);
+
+ }
+ else {
+ SetNestedNetworkDialog dlg = new SetNestedNetworkDialog(Cytoscape.getDesktop(), true, targetNode);
+ dlg.setLocationRelativeTo(Cytoscape.getDesktop());
+ dlg.setVisible(true);
+ }
+ }
+
+ private String getSuggestedNodeID(CyNetwork pSelectedNetwork){
+
+ if (pSelectedNetwork == null){
+ return null;
+ }
+
+ String suggestedNodeID = pSelectedNetwork.getIdentifier();
+
+ while (true){
+ CyNode aNode = Cytoscape.getCyNode(suggestedNodeID);
+ if (aNode == null){
+ // suggestedNodeID is still available, so we get one we need
+ break;
+ }
+
+ suggestedNodeID += suggestedNodeID + "_"+counter;
+ }
+
+ return suggestedNodeID;
+ }
+
+ /**
+ * A stub routine that currently just adds a node at the drop position. In
+ * theory, the URL can be traversed and the retrieved document parsed to
+ * extract information that can be added to the Cytoscape network. For
+ * example, the user could drag a URL an NCBI Unigene Web page and a node
+ * could be added to the network for that gene, with certain pieces of
+ * information on that Web extracted and assigned as attributes for that
+ * gene.
+ *
+ * @param t
+ * the Transferable that is dropped onto the canvas
+ * @param d
+ * the DataFlavor that represents the dropped URL.
+ * @param location
+ * the location of the drop event.
+ */
+ public void handleDroppedURL(Transferable t, DataFlavor d, Point location) {
+ Object URL;
+
+ try {
+ URL = t.getTransferData(d);
+
+ if (URL != null) {
+ // CytoscapeEditorManager.log ("Handling dropped URL = " +
+ // URLString);
+ CyNode cn = get_caller().addNode("node" + counter, "URL");
+ counter++;
+ Cytoscape.getCurrentNetwork().restoreNode(cn);
+ }
+ } catch (UnsupportedFlavorException exc) {
+ logger.warn("Unsupported shape flavor", exc);
+
+ return;
+ } catch (IOException exc) {
+ logger.warn("I/O exception getting shape", exc);
+
+ return;
+ }
+ }
+}
diff --git a/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/impl/BackgroundImage.java b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/impl/BackgroundImage.java
new file mode 100644
index 0000000..f033a58
--- /dev/null
+++ b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/impl/BackgroundImage.java
@@ -0,0 +1,92 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.editor.impl;
+
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.image.BufferedImage;
+
+import javax.swing.JLabel;
+
+
+/**
+ *
+ */
+public class BackgroundImage extends JLabel {
+
+ // MLC 05/10/07:
+ private static final long serialVersionUID = -8785860158854559085L;
+ private BufferedImage img;
+
+ /**
+ * Creates a new BackgroundImage object.
+ *
+ * @param img DOCUMENT ME!
+ */
+ public BackgroundImage(BufferedImage img) {
+ super();
+ this.img = img;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public BufferedImage getImg() {
+ return img;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param img DOCUMENT ME!
+ */
+ public void setImg(BufferedImage img) {
+ this.img = img;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g DOCUMENT ME!
+ */
+ public void paint(Graphics g) {
+ Graphics2D g2 = (Graphics2D) g;
+ g2.drawImage(img, null, 0, 0);
+ }
+}
diff --git a/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/impl/BasicCytoShapeEntity.java b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/impl/BasicCytoShapeEntity.java
new file mode 100644
index 0000000..e0b2561
--- /dev/null
+++ b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/impl/BasicCytoShapeEntity.java
@@ -0,0 +1,458 @@
+/* -*-Java-*-
+********************************************************************************
+*
+* File: BasicCytoShapeEntity.java
+* RCS: $Header: $
+* Description:
+* Author: Allan Kuchinsky
+* Created: Sun May 29 11:22:33 2005
+* Modified: Sun Dec 17 05:29:24 2006 (Michael L. Creech) creech at w235krbza760
+* Language: Java
+* Package:
+/*
+
+ Copyright (c) 2006, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+
+********************************************************************************
+*
+* Revisions:
+*
+* Sat Dec 16 14:50:40 2006 (Michael L. Creech) creech at w235krbza760
+* Completely rewrote TestDragSourceListener (now is EntityDragSourceListener) to
+* allow for intelligent setting of the drag cursor. Changed constructor to
+* take a DragSourceContextCursorSetter.
+* Changed all instance variables to be private.
+* Tue Dec 05 04:39:09 2006 (Michael L. Creech) creech at w235krbza760
+* Changed computation of BasicCytoShapeEntity size to allow for
+* larger CytoShapeIcons.
+* Sun Aug 06 11:22:50 2006 (Michael L. Creech) creech at w235krbza760
+* Added generated serial version UUID for serializable classes.
+********************************************************************************
+*/
+package cytoscape.editor.impl;
+
+import java.awt.Component;
+import java.awt.Cursor;
+import java.awt.Dimension;
+import java.awt.GridLayout;
+import java.awt.Image;
+import java.awt.Point;
+import java.awt.dnd.DnDConstants;
+import java.awt.dnd.DragGestureEvent;
+import java.awt.dnd.DragGestureListener;
+import java.awt.dnd.DragSource;
+import java.awt.dnd.DragSourceAdapter;
+import java.awt.dnd.DragSourceContext;
+import java.awt.dnd.DragSourceDragEvent;
+import java.awt.dnd.DragSourceEvent;
+
+import javax.swing.BorderFactory;
+import javax.swing.Icon;
+import javax.swing.ImageIcon;
+import javax.swing.JComponent;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.SwingConstants;
+import javax.swing.SwingUtilities;
+import javax.swing.border.TitledBorder;
+
+import cytoscape.Cytoscape;
+import cytoscape.editor.DragSourceContextCursorSetter;
+import cytoscape.editor.GraphicalEntity;
+import cytoscape.editor.event.BasicCytoShapeTransferHandler;
+import cytoscape.view.CyNetworkView;
+
+
+/**
+ *
+ * The <b>BasicCytoShapeEntity</b> class defines draggable/droppable visual components in the
+ * Cytoscape editor framework. The framework provides for dragging and dropping graphical
+ * entities from palette onto the canvas. BasicCytoShapeEntity objects are associated with
+ * semantic objects, i.e. nodes and edges, that are created when the graphical entities
+ * are dropped onto the canvas.
+ * @author Allan Kuchinsky
+ * @version 1.0
+ *
+ */
+public class BasicCytoShapeEntity extends JComponent implements DragGestureListener,
+ GraphicalEntity {
+ // MLC 07/27/06:
+ private static final long serialVersionUID = -5229827235046946347L;
+
+ // MLC 12/16/06 BEGIN:
+ private static DragSourceContextCursorSetter _defaultCursorSetter = new DragSourceContextCursorSetter() {
+ // The default shows that a drop is possible anywhere on the netView:
+ public Cursor computeCursor(CyNetworkView netView, Point netViewLoc,
+ DragSourceDragEvent dsde) {
+ return DragSource.DefaultCopyDrop;
+ }
+ };
+
+ /**
+ * used for setting tooltip text
+ */
+
+ // MLC 12/16/06:
+ // JLabel _cytoShape;
+ // MLC 12/16/06:
+ private JLabel _cytoShape;
+
+ /**
+ * the title of the shape
+ */
+
+ // MLC 12/16/06:
+ // String title;
+ // MLC 12/16/06:
+ private String title;
+
+ /**
+ * attribute name for the shape
+ * should be one of "NodeType" or "EdgeType"
+ */
+
+ // MLC 12/16/06:
+ // String attributeName;
+ // MLC 12/16/06:
+ private String attributeName;
+
+ /**
+ * value for the attribute assigned to the shape
+ * for example a "NodeType" of "protein"
+ */
+
+ // MLC 12/16/06:
+ // String attributeValue;
+ // MLC 12/16/06:
+ private String attributeValue;
+
+ /**
+ * the icon associated with the shape
+ */
+
+ // MLC 12/16/06:
+ // Icon _image;
+ // MLC 12/16/06:
+ private Icon _image;
+
+ /**
+ * the source of a drag event
+ */
+
+ // MLC 12/16/06 BEGIN:
+ // DragSource myDragSource;
+ private DragSource myDragSource;
+
+ // DragGestureRecognizer myDragGestureRecognizer;
+ // BasicCytoShapeTransferHandler handler;
+ private BasicCytoShapeTransferHandler handler;
+
+ // MLC 12/16/06 END.
+
+ /**
+ * the image associated with the Icon for the shape
+ */
+
+ // MLC 12/16/06:
+ // Image _img;
+ // MLC 12/16/06:
+ private Image _img;
+
+ // A possibly null method to determine the dragSourceContext cursor to show
+ // users what can and cannot be dropped on.
+ private DragSourceContextCursorSetter _cursorSetter = _defaultCursorSetter;
+
+ // MLC 12/16/06 END.
+ /**
+ *
+ * @param attributeName attribute name for the shape, should be one of "NodeType" or "EdgeType"
+ * @param attributeValue value for the attribute assigned to the shape, for example a "NodeType" of "protein"
+ * @param image the icon for the shape
+ * @param title the title of the shape
+ * @param cursorSetter a possibly null DragSourceContextCursorSetter used to specify
+ * the cursor so show when dragging over the current network view.
+ * If null, a default cursor setter is used shows its ok
+ * to drop anywhere on the network view.
+ */
+
+ // MLC 12/16/06 BEGIN:
+ // public BasicCytoShapeEntity(String attributeName, String attributeValue,
+ // Icon image, String title) {
+ public BasicCytoShapeEntity(String attributeName, String attributeValue, Icon image,
+ String title, DragSourceContextCursorSetter cursorSetter) {
+ // MLC 12/16/06 END.
+ super();
+ this.setTitle(title);
+ _image = image;
+
+ // MLC 12/16/06 BEGIN:
+ if (cursorSetter != null) {
+ // use the default:
+ _cursorSetter = cursorSetter;
+ }
+
+ // MLC 12/16/06 END.
+ this.attributeName = attributeName;
+ this.attributeValue = attributeValue;
+
+ if (image instanceof ImageIcon) {
+ _img = ((ImageIcon) image).getImage();
+ }
+
+ _cytoShape = new JLabel(image);
+
+ if (this.attributeName != null) {
+ if (this.attributeName.equals("NODE_TYPE")) {
+ _cytoShape.setToolTipText("<html>To add a node to a network,<br>"
+ + "drag and drop a shape<br>"
+ + "from the palette onto the canvas<br>"
+ + "OR<br>"
+ + "simply CTRL-click on the canvas.</html>");
+ } else if (this.attributeName.equals("EDGE_TYPE")) {
+ _cytoShape.setToolTipText("<html>To connect two nodes with an edge<br>"
+ + "drag and drop the arrow onto a node<br>"
+ + "on the canvas, then move the cursor<br>"
+ + "over a second node and click the mouse.<br>"
+ + "OR<br>"
+ + "CTRL-click on the first node and then<br>"
+ + "click on the second node. </html>");
+ } else if (this.attributeName.equals("NETWORK_TYPE")) {
+ _cytoShape.setToolTipText("<html>To create a nested network<br>"
+ + "drag and drop the network onto a node<br>"
+ + "to assign a nested network,<br>"
+ + "or on the canvas to create a new node and<br>"
+ + "assign a nested network. </html>");
+ }
+ }
+
+ this.setLayout(new GridLayout(1, 1));
+
+ TitledBorder t2 = BorderFactory.createTitledBorder(title);
+ this.add(_cytoShape);
+ this.setBorder(t2);
+
+ myDragSource = new DragSource();
+ // MLC 12/16/06 BEGIN:
+ // myDragSource.addDragSourceListener(new TestDragSourceListener());
+ myDragSource.addDragSourceListener(new EntityDragSourceListener());
+ // myDragGestureRecognizer = myDragSource.createDefaultDragGestureRecognizer(_cytoShape,
+ // DnDConstants.ACTION_COPY,
+ // this);
+ myDragSource.createDefaultDragGestureRecognizer(_cytoShape, DnDConstants.ACTION_COPY, this);
+ // MLC 12/16/06 END.
+ handler = (new BasicCytoShapeTransferHandler(this, null));
+ this.setTransferHandler(handler);
+
+ // MLC 12/04/06 BEGIN:
+ // force height to be at least
+ // CytoscapeShapeIcon.DEFAULT_HEIGHT but larger if needed:
+ /*
+ Dimension mySize = new Dimension(((JPanel) Cytoscape.getDesktop()
+ .getCytoPanel(SwingConstants.WEST))
+ .getSize().width
+ - 5,
+ Math.max(_image.getIconHeight(),
+ CytoShapeIcon.DEFAULT_HEIGHT)
+ + CytoShapeIcon.DEFAULT_HEIGHT);
+ */
+ Dimension mySize = new Dimension(32767,
+ Math.max(_image.getIconHeight(), CytoShapeIcon.DEFAULT_HEIGHT)
+ +(int)((double)CytoShapeIcon.DEFAULT_HEIGHT/.75));
+
+ this.setMaximumSize(mySize);
+
+ mySize = new Dimension(300,
+ Math.max(_image.getIconHeight(), CytoShapeIcon.DEFAULT_HEIGHT)
+ +(int)((double)CytoShapeIcon.DEFAULT_HEIGHT/.75));
+ this.setPreferredSize(mySize);
+
+
+ }
+
+ /**
+ * @return Returns the title.
+ */
+ public String getTitle() {
+ return title;
+ }
+
+ /**
+ * @param title The title to set.
+ *
+ */
+ public void setTitle(String title) {
+ this.title = title;
+ }
+
+ /**
+ * @return Returns the DragSource.
+ */
+ public DragSource getMyDragSource() {
+ return myDragSource;
+ }
+
+ /**
+ * @param myDragSource The DragSource to set.
+ */
+ public void setMyDragSource(DragSource myDragSource) {
+ this.myDragSource = myDragSource;
+ }
+
+ /**
+ * @return Returns the icon associated with the shape
+ */
+ public Icon getIcon() {
+ return _image;
+ }
+
+ /**
+ * @param _image the icon to set for the shape
+ *
+ */
+ public void setIcon(Icon _image) {
+ this._image = _image;
+ }
+
+ /**
+ * @return Returns the image associated with the shape's icon
+ */
+ public Image get_image() {
+ return _img;
+ }
+
+ /**
+ * @param _img The _img to set.
+ */
+ public void set_image(Image _img) {
+ this._img = _img;
+ }
+
+ /**
+ * @return Returns the attributeName.
+ */
+ public String getAttributeName() {
+ return attributeName;
+ }
+
+ /**
+ * @param attributeName The attributeName to set.
+ */
+ public void setAttributeName(String attributeName) {
+ this.attributeName = attributeName;
+ }
+
+ /**
+ * @return Returns the attributeValue.
+ */
+ public String getAttributeValue() {
+ return attributeValue;
+ }
+
+ /**
+ * @param attributeValue The attributeValue to set.
+ */
+ public void setAttributeValue(String attributeValue) {
+ this.attributeValue = attributeValue;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void dragGestureRecognized(DragGestureEvent e) {
+ e.startDrag(DragSource.DefaultCopyDrop, handler.createTransferable(this));
+ }
+
+ // MLC 12/16/06 BEGIN:
+ // private class TestDragSourceListener extends DragSourceAdapter {
+ private class EntityDragSourceListener extends DragSourceAdapter {
+ public void dragEnter(DragSourceDragEvent dsde) {
+ determineCursor(dsde);
+
+ // dsde.getDragSourceContext().setCursor(DragSource.DefaultCopyDrop);
+ }
+
+ public void dragOver(DragSourceDragEvent dsde) {
+ determineCursor(dsde);
+
+ // DragSourceContext dsc = (DragSourceContext) dsde.getSource();
+ // Component comp = dsc.getComponent();
+ // CytoscapeEditorManager.log("dragOver = " + comp);
+ }
+
+ private void determineCursor(DragSourceDragEvent dsde) {
+ DragSourceContext dsc = dsde.getDragSourceContext();
+ Point compLoc = getLocationInsideComponent(Cytoscape.getCurrentNetworkView()
+ .getComponent(), dsde.getLocation());
+
+ if (compLoc != null) {
+ Cursor newCursor = _cursorSetter.computeCursor(Cytoscape.getCurrentNetworkView(),
+ compLoc, dsde);
+
+ if (newCursor == null) {
+ newCursor = DragSource.DefaultCopyNoDrop;
+ }
+
+ dsc.setCursor(newCursor);
+ } else {
+ // check if on the drag source. We want to show ok cursor
+ // for it:
+
+ // sourceLoc now now in source component coordinates:
+ Point paletteLoc = getLocationInsideComponent(dsc.getComponent(), dsde.getLocation());
+
+ if (paletteLoc != null) {
+ dsc.setCursor(DragSource.DefaultCopyDrop);
+ } else {
+ dsc.setCursor(DragSource.DefaultCopyNoDrop);
+ }
+ }
+ }
+
+ // return the point in component coordinates of a given point
+ // in screen ccordinates only if the point is within the component.
+ // Otherwise return null;
+ private Point getLocationInsideComponent(Component desiredComp, Point screenLoc) {
+ // loc now component location
+ Point compLoc = new Point(screenLoc);
+ SwingUtilities.convertPointFromScreen(compLoc, desiredComp);
+
+ if (desiredComp.contains(compLoc)) {
+ // the point is in desiredComp:
+ return compLoc;
+ }
+
+ return null;
+ }
+
+ // MLC 12/16/06 END.
+ public void dragExit(DragSourceEvent dse) {
+ dse.getDragSourceContext().setCursor(DragSource.DefaultCopyNoDrop);
+ }
+ }
+}
diff --git a/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/impl/CytoShapeIcon.java b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/impl/CytoShapeIcon.java
new file mode 100644
index 0000000..ec138e9
--- /dev/null
+++ b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/impl/CytoShapeIcon.java
@@ -0,0 +1,236 @@
+/* -*-Java-*-
+********************************************************************************
+*
+* File: CytoShapeIcon.java
+* RCS: $Header: $
+* Description:
+* Author: Allan Kuchinksy
+* Created: Mon Sept 06 11:43:57 2005
+* Modified: Thu May 10 15:05:50 2007 (Michael L. Creech) creech at w235krbza760
+* Language: Java
+* Package:
+* Status: Experimental (Do Not Distribute)
+*
+* (c) Copyright 2006, Agilent Technologies, all rights reserved.
+*
+********************************************************************************
+*
+* Revisions:
+*
+* Wed May 09 17:14:25 2007 (Michael L. Creech) creech at w235krbza760
+* Updated to Cytoscape 2.5-the byte _shape --> NodeShape enum,
+* and changes to use of Arrows.
+* Mon Dec 04 11:44:33 2006 (Michael L. Creech) creech at w235krbza760
+* Added constructor for handling size information. Changed
+* getIconWidth/Height() to return real width and height of
+* icon. Added DEFAULT_WIDTH and DEFAULT_HEIGHT and deprecated
+* WIDTH & HEIGHT.
+********************************************************************************
+*/
+package cytoscape.editor.impl;
+
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Dimension;
+import java.awt.Graphics;
+import java.awt.Image;
+
+import javax.swing.Icon;
+
+import cytoscape.visual.Arrow;
+import cytoscape.visual.ArrowShape;
+import cytoscape.visual.NodeShape;
+
+
+/**
+ * Specialized Icon for Cytoscape editor palette entry. Renders icon
+ * based upon input shape, size, color.
+ *
+ * @author Allan Kuchinsky
+ * @version 2.0
+ */
+public class CytoShapeIcon implements Icon {
+ public static final int DEFAULT_WIDTH = 32;
+ public static final int DEFAULT_HEIGHT = 32;
+ public static final int YOFFSET = 7;
+
+ private Dimension _size = new Dimension(DEFAULT_WIDTH, DEFAULT_HEIGHT);
+ private Color _color;
+ private Image _image = null;
+ private NodeShape _shape;
+ private Arrow _arrowType = null;
+
+ public CytoShapeIcon(NodeShape shape, Color color, Dimension size) {
+ this(shape, color);
+ _size = size;
+ }
+
+ public CytoShapeIcon(NodeShape shape, Color color) {
+ _color = color;
+ _shape = shape;
+ _image = null;
+ _arrowType = null;
+ }
+
+ /**
+ * Creates a new CytoShapeIcon object.
+ *
+ * @param img DOCUMENT ME!
+ */
+ public CytoShapeIcon(Image img) {
+ _image = img;
+ _arrowType = null;
+ }
+
+ /**
+ * Creates a new CytoShapeIcon object.
+ *
+ * @param arrowType DOCUMENT ME!
+ */
+ public CytoShapeIcon(Arrow arrowType) {
+ _arrowType = arrowType;
+ }
+
+ /* (non-Javadoc)
+ * @see javax.swing.Icon#getIconHeight()
+ */
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getIconHeight() {
+ return _size.height + 2 * YOFFSET;
+ }
+
+ /* (non-Javadoc)
+ * @see javax.swing.Icon#getIconWidth()
+ */
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getIconWidth() {
+ return _size.width;
+ }
+
+ /**
+ * Implements specialized coordinate line drawing for palette shapes
+ *
+ * (non-Javadoc)
+ * @see javax.swing.Icon#paintIcon(java.awt.Component, java.awt.Graphics, int, int)
+ */
+ public void paintIcon(Component c, Graphics g, int x, int y) {
+ y += YOFFSET;
+
+ if (_image != null) {
+ g.drawImage(_image, x, y, c);
+ return;
+ }
+
+ int width = getIconWidth();
+ int height = getIconHeight() - 2 * YOFFSET;
+
+ if (_arrowType != null) {
+ g.setColor(_arrowType.getColor());
+
+ if (_arrowType.getShape() == ArrowShape.DELTA) {
+ g.fillPolygon(new int[] {
+ x, x + ((3 * width) / 4), x + ((3 * width) / 4), x + width,
+ x + ((3 * width) / 4), x + ((3 * width) / 4), x
+ },
+ new int[] {
+ y + ((7 * height) / 16), y + ((7 * height) / 16),
+ y + ((5 * height) / 16), y + (height / 2),
+ y + ((11 * height) / 16), y + ((9 * height) / 16),
+ y + ((9 * height) / 16)
+ }, 7);
+ } else if (_arrowType.getShape() == ArrowShape.CIRCLE) {
+ g.fillRect(x, y + ((7 * height) / 16), (13 * (width / 16)), height / 8);
+ g.fillOval(x + ((5 * width) / 8), y + ((5 * height) / 16), (6 * width) / 16,
+ (6 * height) / 16);
+ } else if (_arrowType.getShape() == ArrowShape.T) {
+ g.fillRect(x, y + ((7 * height) / 16), (15 * (width / 16)), height / 8);
+ g.fillRect(x + (15 * (width / 16)), y + ((5 * height) / 16), width / 16,
+ (height * 6) / 16);
+ } else if (_arrowType.getShape() == ArrowShape.NONE) {
+ g.fillRect(x, y + ((7 * height) / 16), (15 * (width / 16)), height / 8);
+ }
+
+ return;
+ }
+
+ g.setColor(_color);
+
+ if (_shape == NodeShape.TRIANGLE) {
+ g.fillPolygon(new int[] { x, x + (width / 2), x + width },
+ new int[] { y + height, y, y + height }, 3);
+ g.setColor(Color.BLACK);
+ g.drawPolygon(new int[] { x, x + (width / 2), x + width },
+ new int[] { y + height, y, y + height }, 3);
+ } else if (_shape == NodeShape.ROUND_RECT) {
+ g.fillRoundRect(x, y, width, height, width / 2, height / 2);
+ g.setColor(Color.BLACK);
+ g.drawRoundRect(x, y, width, height, width / 2, height / 2);
+ } else if (_shape == NodeShape.DIAMOND) {
+ g.fillPolygon(new int[] { x, x + (width / 2), x + width, x + (width / 2) },
+ new int[] { y + (height / 2), y, y + (height / 2), y + height }, 4);
+ g.setColor(Color.BLACK);
+ g.drawPolygon(new int[] { x, x + (width / 2), x + width, x + (width / 2) },
+ new int[] { y + (height / 2), y, y + (height / 2), y + height }, 4);
+ } else if (_shape == NodeShape.ELLIPSE) {
+ g.fillOval(x, y, width, height);
+ g.setColor(Color.BLACK);
+ g.drawOval(x, y, width, height);
+ } else if (_shape == NodeShape.HEXAGON) {
+ g.fillPolygon(new int[] {
+ x, x + (width / 4), x + ((3 * width) / 4), x + width,
+ x + ((3 * width) / 4), x + (width / 4)
+ },
+ new int[] { y + (height / 2), y, y, y + (height / 2), y + height, y
+ + height }, 6);
+ g.setColor(Color.BLACK);
+ g.drawPolygon(new int[] {
+ x, x + (width / 4), x + ((3 * width) / 4), x + width,
+ x + ((3 * width) / 4), x + (width / 4)
+ },
+ new int[] { y + (height / 2), y, y, y + (height / 2), y + height, y
+ + height }, 6);
+ } else if (_shape == NodeShape.OCTAGON) {
+ g.fillPolygon(new int[] {
+ x, x + (width / 4), x + ((3 * width) / 4), x + width, x + width,
+ x + ((3 * width) / 4), x + (width / 4), x
+ },
+ new int[] {
+ y + (height / 4), y, y, y + (height / 4), y + (3 * (height / 4)),
+ y + height, y + height, y + (3 * (height / 4))
+ }, 8);
+ g.setColor(Color.BLACK);
+ g.drawPolygon(new int[] {
+ x, x + (width / 4), x + ((3 * width) / 4), x + width, x + width,
+ x + ((3 * width) / 4), x + (width / 4), x
+ },
+ new int[] {
+ y + (height / 4), y, y, y + (height / 4), y + (3 * (height / 4)),
+ y + height, y + height, y + (3 * (height / 4))
+ }, 8);
+ // MLC 05/09/07:
+ // } else if (_shape == ShapeNodeRealizer.PARALLELOGRAM) {
+ // MLC 05/09/07:
+ } else if (_shape == NodeShape.PARALLELOGRAM) {
+ g.fillPolygon(new int[] { x, x + ((3 * width) / 4), x + width, x + (width / 4) },
+ new int[] { y, y, y + height, y + height }, 4);
+ g.setColor(Color.BLACK);
+ g.drawPolygon(new int[] { x, x + ((3 * width) / 4), x + width, x + (width / 4) },
+ new int[] { y, y, y + height, y + height }, 4);
+ // MLC 05/09/07:
+ // } else if (_shape == ShapeNodeRealizer.RECT) {
+ // MLC 05/09/07:
+ } else if (_shape == NodeShape.RECT) {
+ g.fillRect(x, y, width, height);
+ g.setColor(Color.BLACK);
+ g.drawRect(x, y, width, height);
+ }
+ }
+}
diff --git a/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/impl/CytoscapeEditorFactoryImpl.java b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/impl/CytoscapeEditorFactoryImpl.java
new file mode 100644
index 0000000..a17821a
--- /dev/null
+++ b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/impl/CytoscapeEditorFactoryImpl.java
@@ -0,0 +1,232 @@
+/* -*-Java-*-
+ ********************************************************************************
+ *
+ * File: CytoscapeEditorFactoryImpl.java
+ * RCS: $Header: $
+ * Description:
+ * Author: Allan Kuchinsky
+ * Created: Mon Jul 05 18:56:28 2006
+ * Modified: Mon Dec 04 18:58:34 2006 (Michael L. Creech) creech at w235krbza760
+ * Language: Java
+ * Package:
+ * Status: Experimental (Do Not Distribute)
+ *
+ * (c) Copyright 2006, Agilent Technologies, all rights reserved.
+ *
+ ********************************************************************************
+ *
+ * Revisions:
+ *
+ * Mon Dec 04 18:56:57 2006 (Michael L. Creech) creech at w235krbza760
+ * Added createShapePaletteInfoGenerator() and createShapePaletteInfo().
+ ********************************************************************************
+ */
+
+/*
+ * Created on Jul 5, 2005
+ *
+ */
+package cytoscape.editor.impl;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+
+import cytoscape.editor.CytoscapeEditor;
+import cytoscape.editor.CytoscapeEditorFactory;
+import cytoscape.editor.CytoscapeEditorManager;
+import cytoscape.editor.InvalidEditorException;
+import cytoscape.editor.ShapePaletteInfo;
+import cytoscape.editor.ShapePaletteInfoGenerator;
+import cytoscape.editor.event.NetworkEditEventAdapter;
+import cytoscape.logger.CyLogger;
+
+
+/**
+ *
+ * builds new instances of editors and network edit event adapters. Before an
+ * editor and its network edit event adapter can be built, the editor first
+ * needs to be registered with the CytoscapeEditorManager.
+ *
+ * @author Allan Kuchinsky, Agilent Technologies
+ * @version 1.0
+ *
+ * @see CytoscapeEditorManager
+ */
+public class CytoscapeEditorFactoryImpl implements CytoscapeEditorFactory {
+ private Collection<String> editorTypes = new ArrayList<String>();
+ private CyLogger logger = CyLogger.getLogger(CytoscapeEditorFactoryImpl.class);
+
+ /**
+ * mapping of editor types to editors
+ */
+ private Map<String, CytoscapeEditor> editors = new HashMap<String, CytoscapeEditor>();
+
+ /**
+ * get the Cytoscape editor for the specified type
+ *
+ * @param editorType
+ * the type of the editor
+ * @param args
+ * an arbitrary list of arguments
+ * @return the Cytoscape editor for the specified editor type
+ * @throws InvalidEditorException
+ */
+ public CytoscapeEditor getEditor(String editorType, List args) throws InvalidEditorException {
+ Class editorClass;
+ CytoscapeEditor cyEditor = null;
+
+ Object cyEditObj = editors.get(editorType);
+
+ if (cyEditObj != null) {
+ cyEditor = (CytoscapeEditor) cyEditObj;
+
+ return cyEditor;
+ }
+
+ if (editorType == null) {
+ editorType = CytoscapeEditorManager.DEFAULT_EDITOR_TYPE;
+ cyEditor = (CytoscapeEditor) editors.get(editorType);
+
+ if (cyEditor != null) {
+ return cyEditor;
+ }
+ }
+
+ // AJK: 12/10/06 END
+ try {
+ // AJK: 12/09/06 have the CytoscapeEditorFactory take a fully
+ // qualified path
+ // for editor
+ // editorClass = Class.forName("cytoscape.editor.editors." +
+ CytoscapeEditorManager.log("trying to instantiate editor type: " + editorType);
+ // AJK: we have to now correct for a null editorType, since we are
+ // no longer
+ // prepending a "cytoscape.editor.editors." to a string, so we
+ // can get a NullPointerException on Class.forName
+ editorClass = Class.forName(editorType);
+ editorTypes.add(editorType);
+ CytoscapeEditorManager.log("trying to instantiate editor class: " + editorClass);
+ cyEditor = (CytoscapeEditor) editorClass.newInstance();
+ CytoscapeEditorManager.log("got editor: " + cyEditor);
+ editors.put(editorType, cyEditor);
+ cyEditor.setEditorName(editorType);
+ } catch (ClassNotFoundException e) {
+ // AJK: 12/10/06 BEGIN
+ // for backward compatibility, try prepending
+ // "cytoscape.editor.editors" to editorType
+ try {
+ editorClass = Class.forName((new String("cytoscape.editor.editors." + editorType)));
+ editorTypes.add(editorType);
+ cyEditor = (CytoscapeEditor) editorClass.newInstance();
+ CytoscapeEditorManager.log("got editor: " + cyEditor);
+ editors.put(editorType, cyEditor);
+ cyEditor.setEditorName(editorType);
+ } catch (ClassNotFoundException e1) {
+ String msg = "Cannot create editor of type: " + editorType;
+ InvalidEditorException ex = new InvalidEditorException(msg, new Throwable("type not found"));
+
+ throw ex;
+ } catch (InstantiationException ex) {
+ logger.warn("Unable to instantiate editor!", ex);
+ } catch (IllegalAccessException ex) {
+ logger.warn("Unable to access editor!", ex);
+ }
+
+ // AJK: 12/10/06 END
+ } catch (InstantiationException ex) {
+ logger.warn("Unable to instantiate editor!", ex);
+ } catch (IllegalAccessException ex) {
+ logger.warn("Unable to access editor!", ex);
+ }
+
+ CytoscapeEditorManager.setCurrentEditor(cyEditor);
+
+ CytoscapeEditorManager.log("returning editor: " + cyEditor);
+
+ return cyEditor;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param editorType DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @throws InvalidEditorException DOCUMENT ME!
+ */
+ public CytoscapeEditor getEditor(String editorType) throws InvalidEditorException {
+ return getEditor(editorType, null);
+ }
+
+ /**
+ * Get the set of valid editor types
+ *
+ * @return non null collection of editor types (String)
+ */
+ public Collection getEditorTypes() {
+ return this.editorTypes;
+ }
+
+ // implements CytoscapeEditorFactory interface:
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Iterator<String> getEditorNames() {
+ return Collections.unmodifiableCollection(this.editorTypes).iterator();
+ }
+
+ /**
+ * adds a new editorType to the collection of editor types
+ *
+ * @param editorType
+ */
+ public void addEditorType(String editorType) {
+ editorTypes.add(editorType);
+ }
+
+ /**
+ * gets an instance of the NetworkEditEventAdaptor associated with the input
+ * editor The NetworkEditEventAdapter handles events that are associated
+ * with user input to the editor, such as mouse actions, drag/drop,
+ * keystrokes. Each NetworkEditEventAdapter is specialized for the editor
+ * that is is associated with. This is written by the developer and is at
+ * the heart of the specialized behaviour of the editor.
+ *
+ * @param editor
+ * @return the NetworkEditEventAdapter that is assigned to the editor
+ *
+ */
+ public NetworkEditEventAdapter getNetworkEditEventAdapter(CytoscapeEditor editor) {
+ return editor.getNetworkEditEventAdapter();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public ShapePaletteInfoGenerator createShapePaletteInfoGenerator() {
+ return new ShapePaletteInfoGeneratorImpl();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param controllingAttributeName DOCUMENT ME!
+ * @param controllingAttributeValue DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public ShapePaletteInfo createShapePaletteInfo(String controllingAttributeName,
+ String controllingAttributeValue) {
+ return new ShapePaletteInfoImpl(controllingAttributeName, controllingAttributeValue);
+ }
+}
diff --git a/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/impl/CytoscapeEditorManagerSupport.java b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/impl/CytoscapeEditorManagerSupport.java
new file mode 100644
index 0000000..3aea8aa
--- /dev/null
+++ b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/impl/CytoscapeEditorManagerSupport.java
@@ -0,0 +1,411 @@
+/* -*-Java-*-
+********************************************************************************
+*
+* File: CytoscapeEditorManagerSupport.java
+* RCS: $Header: $
+* Description:
+* Author: Allan Kuchinsky
+* Created: Sat Jul 30 17:00:27 2005
+* Modified: Wed Jul 09 08:35:21 2008 (Michael L. Creech) creech at w235krbza760
+* Language: Java
+* Package:
+* Status: Experimental (Do Not Distribute)
+*
+* (c) Copyright 2006, Agilent Technologies, all rights reserved.
+*
+********************************************************************************
+*
+* Revisions:
+*
+* Wed Jul 09 08:34:53 2008 (Michael L. Creech) creech at w235krbza760
+* Migrated isEditorInOperation() to CytoscapeEditorManager and changed
+* references.
+* Tue Oct 30 10:58:16 2007 (Michael L. Creech) creech at w235krbza760
+* Fixed bug in propertyChange() for NETWORK_VIEW_FOCUSED where
+* palette was being redrawn when the Editor tab wasn't
+* selected. Added isEditorInOperation(). Changed
+* updateEditorPalette() to be private.
+* Thu Oct 25 05:42:55 2007 (Michael L. Creech) creech at w235krbza760
+* Changed onComponentSelected() to not generate a bogus CyNetworkView
+* but the desired CyNetworkView.
+* Wed May 09 13:59:45 2007 (Michael L. Creech) creech at w235krbza760
+* Removed several unneeded imports.
+* Wed Dec 27 09:04:18 2006 (Michael L. Creech) creech at w235krbza760
+* Added getDeleteAction() and parameter to constructor.
+* Sun Aug 06 11:14:28 2006 (Michael L. Creech) creech at w235krbza760
+* Fixed updateEditorPalette() to not assume visualStyleName is the
+* same as Editor name.
+* Sat Aug 05 17:01:38 2006 (Michael L. Creech) creech at w235krbza760
+* Added some comments.
+********************************************************************************
+*/
+package cytoscape.editor.impl;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+
+import cytoscape.editor.CytoscapeEditor;
+import cytoscape.editor.CytoscapeEditorFactory;
+import cytoscape.editor.CytoscapeEditorManager;
+import cytoscape.editor.InvalidEditorException;
+
+import cytoscape.logger.CyLogger;
+
+import cytoscape.view.CyNetworkView;
+import cytoscape.view.CytoscapeDesktop;
+
+import cytoscape.view.cytopanels.CytoPanelListener;
+import cytoscape.view.cytopanels.CytoPanelState;
+
+import cytoscape.visual.VisualMappingManager;
+import cytoscape.visual.VisualStyle;
+
+import giny.model.GraphPerspectiveChangeEvent;
+import giny.model.GraphPerspectiveChangeListener;
+
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+
+import javax.swing.SwingConstants;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+
+
+/**
+ * provides non-static methods needed by the CytoscapeEditorManager, in
+ * particular those methods associated with the PropertyChangeListener class
+ *
+ * @author Allan Kuchinsky, Agilent Technologies
+ * @version 1.0
+ * @see CytoscapeEditorManager
+ *
+ */
+public class CytoscapeEditorManagerSupport implements PropertyChangeListener, ChangeListener,
+ GraphPerspectiveChangeListener,
+ CytoPanelListener {
+ private CyLogger logger = CyLogger.getLogger(CytoscapeEditorManagerSupport.class);
+ /**
+ * register interest in NETWORK_VIEW_FOCUSED and NETWORK_VIEW_CREATED events
+ *
+ */
+
+
+ /**
+ * Creates a new CytoscapeEditorManagerSupport object.
+ *
+ */
+ public CytoscapeEditorManagerSupport() {
+ super();
+ Cytoscape.getDesktop().getSwingPropertyChangeSupport()
+ .addPropertyChangeListener(CytoscapeDesktop.NETWORK_VIEW_FOCUSED, this);
+ Cytoscape.getDesktop().getSwingPropertyChangeSupport()
+ .addPropertyChangeListener(CytoscapeDesktop.NETWORK_VIEW_CREATED, this);
+ Cytoscape.getSwingPropertyChangeSupport().addPropertyChangeListener(this);
+
+ Cytoscape.getVisualMappingManager().addChangeListener(this);
+ Cytoscape.getDesktop().getCytoPanel(SwingConstants.WEST).addCytoPanelListener(this);
+
+ new NewEmptyNetworkListener();
+ }
+
+
+ /**
+ * respond to a ChangeEvent, typically this is caused by switching
+ * visual styles
+ */
+
+ // implements ChangeListener interface:
+ // TODO: Since this can be frequently called, this code should check
+ // if the current palette already reflects the current visual style before
+ // updateEditorPalette is called.
+ public void stateChanged(ChangeEvent e) {
+ CytoscapeEditorManager.log("Got State change: " +
+ e.toString());
+ if (!CytoscapeEditorManager.isEditingEnabled()) {
+ return;
+ }
+
+ // AJK: 06/10/06 BEGIN
+ // don't do any work building editor palette if editor tab is not
+ // selected in CytoPanel
+ // MLC 07/09/08:
+ // if (!isEditorInOperation ()) {
+ // MLC 07/09/08:
+ if (!CytoscapeEditorManager.isEditorInOperation ()) {
+ return;
+ }
+ VisualMappingManager VMM = (VisualMappingManager) e.getSource();
+
+ if (VMM != null) {
+ updateEditorPalette(VMM.getVisualStyle());
+ }
+ }
+
+
+ /**
+ * respond to selection of a CytoPanels component, in particular respond to
+ * selection of a tab on the WEST CytoPanel.
+ */
+
+ // implements CytoPanelListener interface:
+ public void onComponentSelected(int componentIndex) {
+ // MLC 07/09/08:
+ // if (isEditorInOperation (componentIndex)) {
+ // MLC 07/09/08:
+ if (CytoscapeEditorManager.isEditorInOperation (componentIndex)) {
+
+ updateEditorPalette(Cytoscape.getVisualMappingManager().getVisualStyle());
+
+ // If no networks exist, create an empty network.
+ if ( Cytoscape.getNetworkSet().size() == 0 ) {
+ // MLC 10/24/07 BEGIN:
+ // DON'T call the one argument createNetwork()--it will end up setting
+ // our current visual style to "default" thru CytoscapeDesktop
+ // event listener:
+ // CyNetwork newNet = Cytoscape.createNetwork(CytoscapeEditorManager.createUniqueNetworkName());
+ // DON'T create a CyNetworkView:
+ CyNetwork newNet = Cytoscape.createNetwork(new int[] { }, new int[] { },
+ CytoscapeEditorManager.createUniqueNetworkName(),
+ null,
+ false);
+ // CyNetworkView newView = Cytoscape.createNetworkView(newNet);
+ // Now build the right view:
+ CyNetworkView newView = Cytoscape.createNetworkView(newNet,
+ newNet.getTitle(),
+ null,
+ // use the existing visual style:
+ Cytoscape.getVisualMappingManager().getVisualStyle());
+ // MLC 10/24/07 END.
+ CytoscapeEditorManager.setEditorForView(newView, CytoscapeEditorManager.getCurrentEditor());
+ // AJK: 10/25/2007 if we have a new view then we need to set it up with event handler
+ CytoscapeEditorManager.setupNewNetworkView(newView);
+ }
+ }
+ }
+
+ /**
+ * Notifies the listener on a change in the CytoPanel state.
+ *
+ * @param newState
+ * The new CytoPanel state - see CytoPanelState class.
+ */
+ public void onStateChange(CytoPanelState newState) {
+ }
+
+ /**
+ * Notifies the listener when a component is added to the CytoPanel.
+ *
+ * @param count
+ * The number of components on the CytoPanel after the add.
+ */
+
+ // implements CytoPanelListener interface:
+ public void onComponentAdded(int count) {
+ }
+
+ /**
+ * Notifies the listener when a component is removed from the CytoPanel.
+ *
+ * @param count
+ * The number of components on the CytoPanel after the remove.
+ */
+
+ // implements CytoPanelListener interface:
+ public void onComponentRemoved(int count) {
+ }
+
+ /**
+ * sets up editor and visual style and builds the ShapePalette
+ * @param style
+ */
+ // public void updateEditorPalette(VisualStyle style) {
+ private void updateEditorPalette(VisualStyle style) {
+ // AJK: 06/16/06 only update palette after CYTOSCAPE_INITIALIZED
+ CytoscapeEditorManager.log("setting up editor for visual style: " + style);
+
+ if (!CytoscapeEditorManager.isEditingEnabled()) {
+ return;
+ }
+
+ // ASSUMES visual style name is the same as the editor!
+ // String editorType = style.getName();
+ String editorType = CytoscapeEditorManager.getEditorNameForVisualStyleName(style.getName());
+ CytoscapeEditorManager.log("got editor name for visual style: " + editorType);
+
+ CytoscapeEditor editorForStyle = null;
+
+ try {
+ editorForStyle = CytoscapeEditorFactory.INSTANCE.getEditor(editorType);
+ CytoscapeEditorManager.log("got editor for style: " + style.getName() + " = "
+ + editorForStyle);
+ } catch (InvalidEditorException ex) {
+ CytoscapeEditorManager.log("Could not find editor for editor type: " + editorType);
+ editorType = CytoscapeEditorManager.DEFAULT_EDITOR_TYPE;
+
+ try {
+ editorForStyle = CytoscapeEditorFactory.INSTANCE.getEditor(editorType);
+ } catch (InvalidEditorException exe) {
+ logger.warn("Error building editor for editor type = " + editorType, exe);
+ }
+ }
+
+ if (editorForStyle != null) {
+ CyNetworkView view = Cytoscape.getCurrentNetworkView();
+ CytoscapeEditor editorForView = CytoscapeEditorManager.getEditorForView(Cytoscape.getCurrentNetworkView());
+
+ CytoscapeEditorManager.log("Got editor for view: " + editorForView);
+
+ if ((editorForView != null) && (!CytoscapeEditorManager.isSettingUpEditor())) {
+ CytoscapeEditorManager.log("Disabling controls for editor: " + editorForView);
+ editorForView.disableControls(null);
+ }
+
+ CytoscapeEditorManager.log("Initializing controls for " + editorForStyle);
+ editorForStyle.initializeControls(null);
+ CytoscapeEditorManager.setEditorForView(view, editorForStyle);
+ CytoscapeEditorManager.setupNewNetworkView(view);
+ CytoscapeEditorManager.setCurrentEditor(editorForStyle);
+ CytoscapeEditorManager.setEventHandlerForView(view);
+ }
+ }
+
+ /**
+ * respond to a PropertyChangeEvent. This is typically the Creation or Modification
+ * of a Network or NetworkView.
+ * If networkView focus changes, then bring up the appropriate editor for the
+ * enw network view.
+ */
+
+ // implements PropertyChangeListener interface:
+ public void propertyChange(PropertyChangeEvent e) {
+ //CytoscapeEditorManager.log("Got property change: " + e.getPropertyName());
+ if (e.getPropertyName().equals(Cytoscape.NETWORK_CREATED)) {
+ String netId = e.getNewValue().toString();
+ CyNetwork net = Cytoscape.getNetwork(netId);
+ net.addGraphPerspectiveChangeListener(this);
+ }
+
+ // redraw graph if the network is modified, e.g. by an undoable edit
+ // else if (e.getPropertyName().equals(Cytoscape.NETWORK_MODIFIED)) {
+ if (e.getPropertyName().equals(Cytoscape.NETWORK_MODIFIED)) {
+ if (e.getOldValue() != null) {
+ // AJK: 06/19/06 hack that uses OldValue field to indicate that this
+ // event was fired from CytoscapeEditor, thus avoids any
+ // unnecessary redraws due to multiple event firings from an
+ // -- any non-null value will do
+ if ((e.getOldValue().equals(CytoscapeEditorManager.CYTOSCAPE_EDITOR))
+ || (e.getOldValue().equals("cytoscape.util.UndoManager"))) {
+ Cytoscape.getCurrentNetworkView().redrawGraph(true, true);
+ }
+ }
+ }
+ // AJK: 06/15/06: enable editing once Cytoscape has been initialized
+ else if (e.getPropertyName().equals(Cytoscape.CYTOSCAPE_INITIALIZED)) {
+ CytoscapeEditorManager.setEditingEnabled(true);
+ } else if (e.getPropertyName().equals(CytoscapeDesktop.NETWORK_VIEW_FOCUSED)) {
+ CytoscapeEditorManager.log("NETWORK_VIEW_FOCUSED: " + e.getNewValue());
+ CytoscapeEditorManager.log("From older network view: " + e.getOldValue());
+ CyNetworkView view = Cytoscape.getCurrentNetworkView();
+ CytoscapeEditorManager.log("Current network view = " + view);
+
+ view = Cytoscape.getNetworkView(e.getNewValue().toString());
+ CytoscapeEditorManager.log("Current network view = " + view);
+
+ // AJK: 12/09/06 BEGIN
+ // try to get editor for visual style
+ // VisualStyle vs = view.getVisualStyle();
+ CytoscapeEditor cyEditor = CytoscapeEditorManager.getEditorForView(view);
+ CytoscapeEditorManager.log("Editor for this view is: " + cyEditor);
+
+ if (cyEditor == null) {
+ try {
+ CytoscapeEditorManager.log("looking for default editor");
+ cyEditor = CytoscapeEditorFactory.INSTANCE.getEditor(CytoscapeEditorManager.DEFAULT_EDITOR_TYPE);
+ CytoscapeEditorManager.log("got default editor: " + cyEditor);
+ // AJK: 10/25/07 need to update editor palette because we have a new edito
+ // but this may cause two update palettes when we have first new network
+ // will that matter?
+ // only redraw the palette when we are on the Editor tab:
+ // MLC 07/09/08:
+ // if (isEditorInOperation ()) {
+ // MLC 07/09/08
+ if (CytoscapeEditorManager.isEditorInOperation ()) {
+ updateEditorPalette(Cytoscape.getVisualMappingManager().getVisualStyle());
+ }
+ } catch (InvalidEditorException ex) {
+ }
+ }
+
+ if (cyEditor == null) {
+ cyEditor = CytoscapeEditorManager.getCurrentEditor();
+
+ if (cyEditor == null) {
+ // this would be because no editor has been set yet. Just
+ // return
+ return;
+ } else {
+ // at this point there is an editor but it is not assigned
+ // to this view
+ // this is probably the case if we are loading a network,
+ // rather than creating a new one
+ // in this case, we need to setup the network view, which
+ // sets all the event handler, etc.
+ CytoscapeEditorManager.log("Building network view for: " + view
+ + " using editor " + cyEditor);
+ CytoscapeEditorManager.setupNewNetworkView(view);
+ }
+ }
+ }
+ }
+
+ /**
+ * Implementation of the GraphPerspectiveChangeListener interface. Responds
+ * to the removal of nodes and edges by saving them, so that they can be
+ * restored via RestoreDeleted action. Fires a NETWORK_MODIFIED event.
+ */
+ public void graphPerspectiveChanged(GraphPerspectiveChangeEvent event) {
+ // careful: this event can represent both hidden nodes and hidden edges
+ // if a hide node operation implicitly hid its incident edges
+ CyNetwork net = Cytoscape.getCurrentNetwork();
+
+ // CytoscapeEditorManager.log ("GraphPerspectiveChanged for network: " + net);
+ boolean nodeChanges = false; // only create the set if we need it
+
+ // CytoscapeEditorManager.log ("GraphPerspectiveChanged for network: " + net);
+ boolean edgeChanges = false; // only create the set if we need it
+
+ // at least one node was hidden
+ if (event.isNodesHiddenType()) {
+ int[] hiddenNodes = event.getHiddenNodeIndices();
+
+ for (int i = 0; i < hiddenNodes.length; i++) {
+ CytoscapeEditorManager.addHiddenNodeForNetwork(net, hiddenNodes[i]);
+ }
+
+ if (hiddenNodes != null) {
+ nodeChanges = true;
+ }
+ }
+
+ // at least one edge is hidden
+ if (event.isEdgesHiddenType()) {
+ int[] hiddenEdges = event.getHiddenEdgeIndices();
+
+ if (hiddenEdges != null) {
+ edgeChanges = true;
+ }
+
+ for (int i = 0; i < hiddenEdges.length; i++) {
+ CytoscapeEditorManager.addHiddenEdgeForNetwork(net, hiddenEdges[i]);
+ }
+ }
+
+ if (nodeChanges || edgeChanges) {
+ // AJK: 12/13/06 to fix NPE bug
+ // Cytoscape.firePropertyChange(Cytoscape.NETWORK_MODIFIED,
+ // for distinguishing from batch firing of event
+ // CytoscapeEditorManager.CYTOSCAPE_EDITOR,
+ // Cytoscape.getCurrentNetwork());
+ }
+ }
+}
diff --git a/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/impl/NewEmptyNetworkListener.java b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/impl/NewEmptyNetworkListener.java
new file mode 100644
index 0000000..97cd201
--- /dev/null
+++ b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/impl/NewEmptyNetworkListener.java
@@ -0,0 +1,87 @@
+/*
+ File: NewEmptyNetworkListener.java
+
+ Copyright (c) 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+package cytoscape.editor.impl;
+
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.swing.SwingConstants;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import cytoscape.view.CytoscapeDesktop;
+
+/**
+ * Used to switch to the Editor cytopanel when a new empty network is created.
+ */
+class NewEmptyNetworkListener implements PropertyChangeListener {
+
+ // AJK: 03/13/2008 need to check that network is NEW as well as empty
+ private List<CyNetwork> networksSeen = new ArrayList<CyNetwork>();
+
+ NewEmptyNetworkListener() {
+ Cytoscape.getDesktop().getSwingPropertyChangeSupport()
+ .addPropertyChangeListener(CytoscapeDesktop.NETWORK_VIEW_FOCUSED, this);
+ }
+
+ public void propertyChange(PropertyChangeEvent e) {
+
+ // listen for new views that get created
+ if ( e.getPropertyName().equals(CytoscapeDesktop.NETWORK_VIEW_FOCUSED)) {
+ CyNetwork net = Cytoscape.getCurrentNetwork();
+
+ // only if the network in question doesn't have any nodes (i.e. it's an
+ // empty network), do we automatically switch to the editor
+ // AJK: 02/28/08 but check against null network
+// if ( net.getNodeCount() <= 0 ) {
+ // AJK: 03/13/2008 need to check that network is NEW as well as empty
+// if (( net.getNodeCount() <= 0 ) && (net != Cytoscape.getNullNetwork())){
+ if (!networksSeen.contains (net))
+ {
+ networksSeen.add(net);
+ if (( net.getNodeCount() <= 0 ) && (net != Cytoscape.getNullNetwork())) {
+ int idx = Cytoscape.getDesktop().getCytoPanel(SwingConstants.WEST).indexOfComponent("Editor");
+ if (idx >= 0)
+ Cytoscape.getDesktop().getCytoPanel(SwingConstants.WEST).setSelectedIndex(idx);
+ }
+ }
+ }
+ }
+}
diff --git a/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/impl/SIF_Interpreter.java b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/impl/SIF_Interpreter.java
new file mode 100644
index 0000000..1e9ce54
--- /dev/null
+++ b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/impl/SIF_Interpreter.java
@@ -0,0 +1,160 @@
+package cytoscape.editor.impl;
+
+import giny.view.NodeView;
+
+import java.awt.Point;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.swing.JOptionPane;
+
+import cytoscape.CyEdge;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+import cytoscape.data.Semantics;
+import cytoscape.editor.CytoscapeEditor;
+import cytoscape.editor.CytoscapeEditorManager;
+import ding.view.DGraphView;
+
+/**
+ * add Nodes and Edges to the network based upon a line of SIF typed in by the
+ * user
+ *
+ * @author ajk
+ *
+ */
+public class SIF_Interpreter {
+
+ public static void interpret(String input, Point p, CytoscapeEditor editor) {
+ String[] terms = input.split(" ");
+ NodeView nv1, nv2;
+ if (terms != null) {
+ if (terms.length > 0) {
+ String name1 = terms[0].trim();
+ if (!name1.equals(null)) {
+ // first see if we already have a node
+ CyNode node1 = Cytoscape.getCyNode(terms[0], false);
+ if (node1 == null) {
+
+ node1 = Cytoscape.getCyNode(terms[0], true);
+ Cytoscape.getCurrentNetwork().restoreNode(node1);
+ nv1 = Cytoscape.getCurrentNetworkView().getNodeView(
+ node1);
+ CytoscapeEditorManager.log("Node 1 = " + node1);
+ CytoscapeEditorManager.log("NodeView 1 = " + nv1);
+ double[] nextLocn = new double[2];
+ nextLocn[0] = p.getX();
+ nextLocn[1] = p.getY();
+ ((DGraphView) Cytoscape.getCurrentNetworkView())
+ .xformComponentToNodeCoords(nextLocn);
+ nv1.setOffset(nextLocn[0], nextLocn[1]);
+ } else {
+ Cytoscape.getCurrentNetwork().restoreNode(node1);
+ nv1 = Cytoscape.getCurrentNetworkView().getNodeView(
+ node1);
+ }
+ double spacing = 3.0 * Cytoscape.getCurrentNetworkView()
+ .getNodeView(node1).getWidth();
+ if (terms.length == 3) // simple case of 'A interaction B'
+ {
+ CyNode node2 = Cytoscape.getCyNode(terms[2], false);
+ if (node2 == null) {
+ node2 = Cytoscape.getCyNode(terms[2], true);
+ Cytoscape.getCurrentNetwork().restoreNode(node2);
+ nv2 = Cytoscape.getCurrentNetworkView()
+ .getNodeView(node2);
+ nv2.setOffset(nv1.getXPosition() + spacing, nv1
+ .getYPosition());
+ }
+ // CytoscapeEditorManager.log("Node 2 = " + node2);
+ // CytoscapeEditorManager.log("NodeView 2 = " + nv2);
+ CyEdge edge = Cytoscape.getCyEdge(node1, node2,
+ Semantics.INTERACTION, terms[1], true, true);
+ Cytoscape.getCurrentNetwork().restoreEdge(edge);
+
+ } else if (terms.length > 3) {
+ // process multiple targets and one source
+ // MLC 07/03/07:
+ // List nodeViews = new ArrayList();
+// MLC 07/03/07:
+ List<NodeView> nodeViews = new ArrayList<NodeView>();
+ String interactionType = terms[1];
+ for (int i = 2; i < terms.length; i++)
+ {
+ CyNode node2 = Cytoscape.getCyNode(terms[i], false);
+ if (node2 == null) {
+ node2 = Cytoscape.getCyNode(terms[i], true);
+
+ Cytoscape.getCurrentNetwork().restoreNode(node2);
+ nv2 = Cytoscape.getCurrentNetworkView()
+ .getNodeView(node2);
+ nodeViews.add(nv2);
+ }
+ CyEdge edge = Cytoscape.getCyEdge(node1, node2,
+ Semantics.INTERACTION, interactionType, true, true);
+ Cytoscape.getCurrentNetwork().restoreEdge(edge);
+ }
+ doCircleLayout(nodeViews, nv1);
+ }
+ }
+ }
+ Cytoscape.getCurrentNetworkView().redrawGraph(true, true);
+ }
+
+ }
+
+ public static void processInput(Point p, CytoscapeEditor editor) {
+ String input = JOptionPane.showInputDialog(((DGraphView) Cytoscape
+ .getCurrentNetworkView()).getCanvas(),
+ "Type in a nodes/edges expression in SIF format"
+ + ", e.g. A inhibit B");
+ if (input != null) {
+ interpret(input, p, editor);
+ }
+ }
+
+ public static void doCircleLayout(List nodeViews, NodeView nv1) {
+ //
+ // Maximum width or height
+ // MLC 07/03/07:
+ // int max = 0;
+
+ NodeView nv;
+
+ // // Loop through all nodeViews
+ // for (int i = 0; i < nodeViews.size(); i++) {
+ // // Add vertex to list
+ //
+ // // Fetch Bounds
+ // // Rectangle bounds = nodeViews[i].getBounds ();
+ // Rectangle bounds = ((Rectangle) nodeViews.get(i)).getBounds();
+ //
+ // // Update Maximum
+ // if (bounds != null) {
+ // max = Math.max(Math.max(bounds.width, bounds.height), max);
+ // }
+ //
+ // //
+ // // int max = BaseHeight;
+ // // Compute Radius
+
+ int r = (int) Math.max((nodeViews.size() * nv1.getWidth()) / Math.PI,
+ 30);
+
+ // Compute angle step
+ double phi = (2 * Math.PI) / nodeViews.size();
+
+ // Arrange vertices in a circle
+ for (int i = 0; i < nodeViews.size(); i++) {
+
+ nv = (NodeView) nodeViews.get(i);
+ nv.setOffset(
+ nv1.getXPosition() + (int) (r * Math.sin(i * phi)),
+ nv1.getYPosition() + (int) (r * Math.cos(i * phi)));
+ }
+
+ Cytoscape.getCurrentNetworkView().redrawGraph(true, true);
+
+ }
+
+}
diff --git a/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/impl/ShapePalette.java b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/impl/ShapePalette.java
new file mode 100644
index 0000000..6c6dffd
--- /dev/null
+++ b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/impl/ShapePalette.java
@@ -0,0 +1,346 @@
+/* -*-Java-*-
+********************************************************************************
+*
+* File: ShapePalette.java
+* RCS: $Header: $
+* Description:
+* Author: Allan Kuchinsky
+* Created: Sun May 29 11:18:17 2005
+* Modified: Sun Dec 17 05:33:30 2006 (Michael L. Creech) creech at w235krbza760
+* Language: Java
+* Package:
+/*
+
+ Copyright (c) 2006, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+
+********************************************************************************
+*
+* Revisions:
+*
+* Sun Dec 17 05:30:11 2006 (Michael L. Creech) creech at w235krbza760
+* Added DragSourceContextCursorSetter parameter to addShape().
+* Mon Dec 04 11:57:11 2006 (Michael L. Creech) creech at w235krbza760
+* Changed the JList to no longer use
+* setFixedCellHeight() since BasicCytoShapeEntitys can now have
+* different sizes.
+* Sun Aug 06 11:19:38 2006 (Michael L. Creech) creech at w235krbza760
+* Added generated serial version UUID for serializable classes.
+********************************************************************************
+*/
+package cytoscape.editor.impl;
+
+import java.awt.BorderLayout;
+import java.awt.Component;
+import java.awt.Dimension;
+import java.awt.Color;
+import java.util.HashMap;
+import java.util.Map;
+
+import javax.swing.BorderFactory;
+import javax.swing.BoxLayout;
+import javax.swing.DefaultListModel;
+import javax.swing.Icon;
+import javax.swing.JComponent;
+import javax.swing.JLabel;
+import javax.swing.JList;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTextArea;
+import javax.swing.JEditorPane;
+import javax.swing.ListCellRenderer;
+import javax.swing.border.TitledBorder;
+
+import cytoscape.Cytoscape;
+import cytoscape.editor.CytoscapeEditorManager;
+import cytoscape.editor.DragSourceContextCursorSetter;
+import cytoscape.editor.event.BasicCytoShapeTransferHandler;
+import cytoscape.view.CyNetworkView;
+import ding.view.DGraphView;
+
+
+/**
+ *
+ * The <b>ShapePalette</b> class implements a palette from which the user drags and drops shapes onto the canvas
+ * The dropping of shapes onto the canvas results in the addition of nodes and edges to the current Cytoscape
+ * network, as defined by the behavior of the event handler that responds to the drop events. For example, in the
+ * simple "BioPAX-like" editor, there are node types for proteins, catalysis, small molecules, and biochemical
+ * reactions, as well as a directed edge type.
+ * <p>
+ * The user interface for the ShapePalette is built upon the JList class.
+ *
+ * @author Allan Kuchinsky
+ * @version 1.0
+ *
+ */
+public class ShapePalette extends JPanel {
+ // MLC 08/06/06:
+ private static final long serialVersionUID = -4018789452330887392L;
+
+ /**
+ * mapping of shapes to their titles
+ */
+ static Map<String, BasicCytoShapeEntity> _shapeMap = new HashMap<String, BasicCytoShapeEntity>();
+
+ /**
+ * the user interface for the ShapePalette
+ */
+ protected JList dataList;
+ protected DefaultListModel listModel;
+ private JPanel _controlPane;
+ protected JScrollPane scrollPane;
+ protected JPanel _shapePane;
+
+ /**
+ * Creates a new ShapePalette object.
+ */
+ public ShapePalette() {
+ super();
+
+ _controlPane = new JPanel();
+ _controlPane.setLayout(new BoxLayout(_controlPane, BoxLayout.Y_AXIS));
+ TitledBorder t2 = BorderFactory.createTitledBorder("Instructions:");
+ _controlPane.setBorder(t2);
+ String instructions = "<html><style type='text/css'>body{ font-family: sans-serif; font-size: 11pt; }</style><b>Drag and Drop:</b> <ul> <li>A node shape onto the network view. <li>An edge shape onto the source node, then click on the target node. </ul> <b>Double-click:</b> <ul> <li>To add nodes and edges specified in SIF format </ul>" + (System.getProperty("os.name").startsWith("Mac") ? "<b>CMD-click:</b>" : "<b>CTRL-click:</b>") + "<ul> <li>On empty space to create a node. <li>On a [...]
+
+ JEditorPane instructionsArea = new JEditorPane("text/html",instructions);
+ // 32767 ????
+ instructionsArea.setPreferredSize(new java.awt.Dimension(300, 300));
+ instructionsArea.setBackground(Cytoscape.getDesktop().getBackground());
+ _controlPane.add(instructionsArea);
+ _controlPane.setBackground(Cytoscape.getDesktop().getBackground());
+
+ JPanel pnlSpecifyIdentifier = new JPanel();
+ // 32767 ????
+ pnlSpecifyIdentifier.setMaximumSize(new java.awt.Dimension(32767, 100));
+ JLabel chkSpecifyLabel = new JLabel("Specify Identifier:");
+ chkSpecifyIdentifier = new javax.swing.JCheckBox();
+ chkSpecifyIdentifier.setToolTipText("Checking the box will allow you to choose the identifier for added nodes and edges.");
+ pnlSpecifyIdentifier.setLayout(new java.awt.GridBagLayout());
+ pnlSpecifyIdentifier.setBorder(BorderFactory.createTitledBorder(""));
+ chkSpecifyIdentifier.addChangeListener(new javax.swing.event.ChangeListener() {
+ public void stateChanged(javax.swing.event.ChangeEvent evt) {
+ CheckBoxSpecifyIdentifierStateChanged(evt);
+ }
+ });
+ pnlSpecifyIdentifier.add(chkSpecifyLabel);
+ pnlSpecifyIdentifier.add(chkSpecifyIdentifier);
+ chkSpecifyIdentifier.setBorder(javax.swing.BorderFactory.createEmptyBorder(0, 0, 0, 0));
+ chkSpecifyIdentifier.setHorizontalAlignment(javax.swing.SwingConstants.RIGHT);
+ chkSpecifyIdentifier.setHorizontalTextPosition(javax.swing.SwingConstants.LEFT);
+ chkSpecifyIdentifier.setMargin(new java.awt.Insets(0, 0, 0, 0));
+ java.awt.GridBagConstraints gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
+ gridBagConstraints.weightx = 1.0;
+ pnlSpecifyIdentifier.add(chkSpecifyIdentifier, gridBagConstraints);
+
+ listModel = new DefaultListModel();
+ dataList = new JList(listModel);
+ dataList.setCellRenderer(new MyCellRenderer());
+ dataList.setDragEnabled(true);
+
+ dataList.setTransferHandler(new PaletteListTransferHandler());
+ _shapePane = new JPanel();
+ _shapePane.setLayout(new BoxLayout(_shapePane, BoxLayout.Y_AXIS));
+
+ scrollPane = new JScrollPane(_shapePane);
+
+ scrollPane.setBorder(BorderFactory.createEtchedBorder());
+ dataList.setBackground(Cytoscape.getDesktop().getBackground());
+ scrollPane.setBackground(Cytoscape.getDesktop().getBackground());
+
+ scrollPane.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED);
+ scrollPane.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED);
+
+ this.setLayout(new java.awt.GridBagLayout());
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ add(_controlPane, gridBagConstraints);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = 1;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ add(pnlSpecifyIdentifier, gridBagConstraints);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = 2;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.BOTH;
+ gridBagConstraints.weightx = 1.0;
+ gridBagConstraints.weighty = 1.0;
+ this.add(scrollPane, gridBagConstraints);
+
+ CytoscapeEditorManager.setCurrentShapePalette(this);
+
+ CyNetworkView view = Cytoscape.getCurrentNetworkView();
+ CytoscapeEditorManager.setShapePaletteForView(view, this);
+
+ this.setBackground(Cytoscape.getDesktop().getBackground());
+ this.setVisible(true);
+ }
+
+ private javax.swing.JCheckBox chkSpecifyIdentifier;
+ public void CheckBoxSpecifyIdentifierStateChanged(javax.swing.event.ChangeEvent evt){
+ if (chkSpecifyIdentifier.isSelected()){
+ specifyIdentifier = true;
+ }
+ else {
+ specifyIdentifier = false;
+ }
+ }
+
+ public static boolean specifyIdentifier = false;
+
+ /**
+ * clear the ShapePalette by removing all its shape components
+ *
+ */
+ public void clear() {
+ _shapePane.removeAll();
+ }
+
+ /**
+ * add a shape to the palette
+ * @param attributeName attribute name for the shape, should be one of "NodeType" or "EdgeType"
+ * @param attributeValue value for the attribute assigned to the shape, for example a "NodeType" of "protein"
+ * @param img the icon for the shape
+ * @param name the title of the shape
+ * @param cursorSetter a possibly null DragSourceContextCursorSetter used to specify
+ * the cursor so show when dragging over the current network view.
+ */
+
+ // MLC 12/16/06 BEGIN:
+ public void addShape(String attributeName, String attributeValue, Icon img, String name,
+ DragSourceContextCursorSetter cursorSetter) {
+ BasicCytoShapeEntity cytoShape = new BasicCytoShapeEntity(attributeName, attributeValue,
+ img, name, cursorSetter);
+ cytoShape.setTransferHandler(new BasicCytoShapeTransferHandler(cytoShape, null));
+ _shapeMap.put(cytoShape.getTitle(), cytoShape);
+
+ if (attributeName.equals(CytoscapeEditorManager.EDGE_TYPE)) {
+ CytoscapeEditorManager.addEdgeTypeForVisualStyle(Cytoscape.getCurrentNetworkView()
+ .getVisualStyle(),
+ attributeValue);
+ }
+
+ _shapePane.add(cytoShape);
+ }
+
+ /**
+ * show the palette in the WEST cytopanel
+ *
+ */
+ public void showPalette() {
+ CyNetworkView view = Cytoscape.getCurrentNetworkView();
+ CytoscapeEditorManager.setShapePaletteForView(view, this);
+ this.setVisible(true);
+ }
+
+ /**
+ *
+ * @param key the name of the shape to be returned
+ * @return return the BasicCytoShapeEntity associated with the input shape name
+ */
+ public static BasicCytoShapeEntity getBasicCytoShapeEntity(String key) {
+ Object val = _shapeMap.get(key);
+
+ if (val instanceof BasicCytoShapeEntity) {
+ return ((BasicCytoShapeEntity) val);
+ } else {
+ return null;
+ }
+ }
+
+ /**
+ * renders each cell of the ShapePalette
+ * @author Allan Kuchinsky
+ * @version 1.0
+ *
+ */
+ class MyCellRenderer extends JLabel implements ListCellRenderer {
+ // This is the only method defined by ListCellRenderer.
+ // We just reconfigure the JLabel each time we're called.
+ // MLC 08/06/06:
+ private static final long serialVersionUID = -4704405703871398609L;
+
+ public Component getListCellRendererComponent(JList list, Object value, // value to display
+ int index, // cell index
+ boolean isSelected, // is the cell selected
+ boolean cellHasFocus) // the list and the cell have the focus
+ {
+ if (value instanceof BasicCytoShapeEntity) {
+ BasicCytoShapeEntity cytoShape = (BasicCytoShapeEntity) value;
+ setText(cytoShape.getTitle());
+ setIcon(cytoShape.getIcon());
+ setToolTipText(cytoShape.getToolTipText());
+ }
+
+ if (isSelected) {
+ setBackground(list.getSelectionBackground());
+ setForeground(list.getSelectionForeground());
+ } else {
+ setBackground(list.getBackground());
+ setForeground(list.getForeground());
+ }
+
+ setEnabled(list.isEnabled());
+ setFont(list.getFont());
+ setOpaque(true);
+
+ return this;
+ }
+ }
+
+ /**
+ * bundles up the name of the BasicCytoShapeEntity for export via drag/drop from the palette
+ * @author Allan Kuchinsky
+ * @version 1.0
+ *
+ */
+ class PaletteListTransferHandler extends StringTransferHandler {
+ // MLC 08/06/06:
+ private static final long serialVersionUID = -3858539899491771525L;
+
+ protected void cleanup(JComponent c, boolean remove) {
+ }
+
+ protected void importString(JComponent c, String str) {
+ }
+
+ //Bundle up the selected items in the list
+ //as a single string, for export.
+ protected String exportString(JComponent c) {
+ JList list = (JList) c;
+ Object val = list.getSelectedValue();
+
+ if (val instanceof BasicCytoShapeEntity) {
+ return ((BasicCytoShapeEntity) val).getTitle();
+ } else {
+ return null;
+ }
+ }
+ }
+}
diff --git a/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/impl/ShapePaletteInfoGeneratorImpl.java b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/impl/ShapePaletteInfoGeneratorImpl.java
new file mode 100644
index 0000000..fe08565
--- /dev/null
+++ b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/impl/ShapePaletteInfoGeneratorImpl.java
@@ -0,0 +1,214 @@
+/* -*-Java-*-
+********************************************************************************
+*
+* File: ShapePaletteInfoGeneratorImpl.java
+* RCS: $Header: $
+* Description:
+* Author: Michael L. Creech
+* Created: Sun Dec 03 19:19:49 2006
+* Modified: Fri May 11 16:56:57 2007 (Michael L. Creech) creech at w235krbza760
+* Language: Java
+* Package:
+/*
+
+ Copyright (c) 2006, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+
+*
+********************************************************************************
+*
+* Revisions:
+*
+* Fri May 11 16:56:45 2007 (Michael L. Creech) creech at w235krbza760
+* Updated to Cytoscape 2.5 VizMap API.
+********************************************************************************
+*/
+package cytoscape.editor.impl;
+
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.Vector;
+
+import javax.swing.event.ChangeListener;
+
+import cytoscape.editor.CytoscapeEditorFactory;
+import cytoscape.editor.ShapePaletteInfo;
+import cytoscape.editor.ShapePaletteInfoFilter;
+import cytoscape.editor.ShapePaletteInfoGenerator;
+import cytoscape.visual.EdgeAppearanceCalculator;
+import cytoscape.visual.NodeAppearanceCalculator;
+import cytoscape.visual.VisualPropertyType;
+import cytoscape.visual.calculators.Calculator;
+import cytoscape.visual.mappings.DiscreteMapping;
+import cytoscape.visual.mappings.ObjectMapping;
+
+
+/**
+ * Implementation of ShapePaletteInfoGenerator.
+ */
+public class ShapePaletteInfoGeneratorImpl implements ShapePaletteInfoGenerator {
+ protected ShapePaletteInfoGeneratorImpl() {
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ public Iterator<ShapePaletteInfo> buildShapePaletteInfo(Object appearanceCalc,
+ VisualPropertyType [] calcsToUse,
+ String controllingAttribute,
+ ChangeListener listener,
+ ShapePaletteInfoFilter filter) {
+ // setup listening for changes when needed:
+ if (listener != null) {
+ for (VisualPropertyType calcType : calcsToUse) {
+ DiscreteMapping dm = getDiscreteMapping(getCalculator(appearanceCalc, calcType),
+ controllingAttribute);
+ if (dm != null) {
+ dm.removeChangeListener(listener);
+ dm.addChangeListener(listener);
+ }
+ }
+ }
+
+ // get union of all DiscreteMapping keys:
+ List<ShapePaletteInfo> spInfos = new ArrayList<ShapePaletteInfo>();
+ Set<String> mappingKeys = computeAllMappingKeys(appearanceCalc, calcsToUse,
+ controllingAttribute);
+
+ for (String key : mappingKeys) {
+ ShapePaletteInfo pi = CytoscapeEditorFactory.INSTANCE.createShapePaletteInfo(controllingAttribute,
+ key);
+
+ for (VisualPropertyType calcType : calcsToUse) {
+ Object value = null;
+ DiscreteMapping dm = getDiscreteMapping(getCalculator(appearanceCalc, calcType),
+ controllingAttribute);
+
+ if (dm != null) {
+ value = dm.getMapValue(key);
+ }
+
+ if (value == null) {
+ value = getDefaultAppearanceValue(appearanceCalc, calcType);
+ }
+
+ pi.add(calcType, value);
+ }
+
+ if ((filter == null) || (filter.useEntry(pi))) {
+ spInfos.add(pi);
+ }
+ }
+
+ return spInfos.iterator();
+ }
+
+
+
+
+ /**
+ * Across a set of given calculators types, create the set
+ * of all the unique discrete mapping keys from
+ * calculators with the given type from the given Node or Edge
+ * AppearanceCalculator.
+ * @return a non-null Set of the String mapping keys
+ */
+ private Set<String> computeAllMappingKeys(Object appearanceCalc, VisualPropertyType[] calculatorTypes,
+ String controllingAttribute) {
+ Set<String> mappingKeys = new HashSet<String>();
+
+ for (VisualPropertyType calcType : calculatorTypes) {
+ mappingKeys.addAll(getMappingKeys(getCalculator(appearanceCalc, calcType),
+ controllingAttribute));
+ }
+
+ return mappingKeys;
+ }
+
+ private Calculator getCalculator(Object appearanceCalc, VisualPropertyType calcType) {
+ // The Cytoscape API should be changed to have an AppearanceCalculator that
+ // underlies NodeAppearanceCalculator and EdgeAppearanceCalculator. For now,
+ // check type:
+ if (appearanceCalc instanceof NodeAppearanceCalculator) {
+ return ((NodeAppearanceCalculator) appearanceCalc).getCalculator(calcType);
+ } else if (appearanceCalc instanceof EdgeAppearanceCalculator) {
+ return ((EdgeAppearanceCalculator) appearanceCalc).getCalculator(calcType);
+ }
+
+ return null;
+ }
+
+ private Object getDefaultAppearanceValue(Object appearanceCalc, VisualPropertyType calcType) {
+ // The Cytoscape API should be changed to have an AppearanceCalculator that
+ // underlies NodeAppearanceCalculator and EdgeAppearanceCalculator. For now,
+ // check type:
+ if (appearanceCalc instanceof NodeAppearanceCalculator) {
+ return ((NodeAppearanceCalculator) appearanceCalc).getDefaultAppearance().get(calcType);
+ } else if (appearanceCalc instanceof EdgeAppearanceCalculator) {
+ return ((EdgeAppearanceCalculator) appearanceCalc).getDefaultAppearance().get(calcType);
+ }
+
+ return null;
+ }
+ // MLC 05/09/07 END.
+
+ private Set<String> getMappingKeys(Calculator calc, String controllingAttribute) {
+ DiscreteMapping dm = getDiscreteMapping(calc, controllingAttribute);
+
+ if (dm == null) {
+ return new HashSet<String>(0);
+ }
+
+ Map<String, Object> keyValuePairs = (Map<String, Object>) dm.getAll();
+
+ // don't know if the map can ever be null, but check anyway:
+ if (keyValuePairs == null) {
+ return new HashSet<String>(0);
+ }
+
+ return keyValuePairs.keySet();
+ }
+
+ private DiscreteMapping getDiscreteMapping(Calculator calc, String controllingAttribute) {
+ if (calc != null) {
+ // Vector edgeMappings = calc.getMappings();
+ // for (int i = 0; i < edgeMappings.size(); i++) {
+ for (ObjectMapping possibleMatch : (Vector<ObjectMapping>) calc.getMappings()) {
+ if ((possibleMatch instanceof DiscreteMapping)
+ && controllingAttribute.equals(((DiscreteMapping) possibleMatch)
+ .getControllingAttributeName())) {
+ return (DiscreteMapping) possibleMatch;
+ }
+ }
+ }
+
+ return null;
+ }
+}
diff --git a/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/impl/ShapePaletteInfoImpl.java b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/impl/ShapePaletteInfoImpl.java
new file mode 100644
index 0000000..7ca5502
--- /dev/null
+++ b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/impl/ShapePaletteInfoImpl.java
@@ -0,0 +1,145 @@
+/* -*-Java-*-
+********************************************************************************
+*
+* File: ShapePaletteInfoImpl.java
+* RCS: $Header: $
+* Description:
+* Author: Michael L. Creech
+* Created: Sun Dec 03 19:18:11 2006
+* Modified: Thu May 10 09:24:52 2007 (Michael L. Creech) creech at w235krbza760
+* Language: Java
+* Package:
+/*
+
+ Copyright (c) 2006, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+
+********************************************************************************
+*
+* Revisions:
+*
+* Thu May 10 09:22:58 2007 (Michael L. Creech) creech at w235krbza760
+* Changed use of byte and Byte from byte calcType to
+* VisualPropertyType for Cytoscape 2.5.
+********************************************************************************
+*/
+package cytoscape.editor.impl;
+
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Set;
+
+import cytoscape.editor.ShapePaletteInfo;
+import cytoscape.visual.VisualPropertyType;
+
+
+/**
+ * Stores information about the values obtains from a certain set of Calculators
+ * based on a String key.
+ */
+public class ShapePaletteInfoImpl implements ShapePaletteInfo {
+ private String _key;
+ private String _attributeName;
+ // MLC 05/09/07:
+ // private Map<Byte, Object> _valueMap = new HashMap<Byte, Object>();
+ // MLC 05/09/07:
+ private Map<VisualPropertyType, Object> _valueMap = new HashMap<VisualPropertyType, Object>();
+
+ protected ShapePaletteInfoImpl(String controllingAttributeName, String controllingAttributeKey) {
+ _key = controllingAttributeKey;
+ _attributeName = controllingAttributeName;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param calcType DOCUMENT ME!
+ * @param value DOCUMENT ME!
+ */
+ // MLC 05/09/07:
+ // public void add(byte calcType, Object value) {
+ // MLC 05/09/07:
+ public void add(VisualPropertyType calcType, Object value) {
+ _valueMap.put(calcType, value);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param calcType DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ // MLC 05/09/07:
+ // public Object getValue(byte calcType) {
+ // MLC 05/09/07:
+ public Object getValue(VisualPropertyType calcType) {
+ return _valueMap.get(calcType);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getKey() {
+ return _key;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getControllingAttributeName() {
+ return _attributeName;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String toString() {
+ StringBuilder sb = new StringBuilder();
+ sb.append("controllingAttributeName: ");
+ sb.append(_attributeName);
+ sb.append("key: ");
+ sb.append(_key);
+
+ // MLC 05/09/07 BEGIN:
+ // Set<Byte> calcTypes = _valueMap.keySet();
+ // for (Byte calcType : calcTypes) {
+ Set<VisualPropertyType> calcTypes = _valueMap.keySet();
+ for (VisualPropertyType calcType : calcTypes) {
+ // MLC 05/09/07 END.
+ sb.append(" calcType: ");
+ sb.append(_valueMap.get(calcType));
+ }
+
+ return sb.toString();
+ }
+}
diff --git a/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/impl/StringTransferHandler.java b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/impl/StringTransferHandler.java
new file mode 100644
index 0000000..8f16e93
--- /dev/null
+++ b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/impl/StringTransferHandler.java
@@ -0,0 +1,87 @@
+/*
+ * Created on Jun 1, 2005
+ *
+ */
+package cytoscape.editor.impl;
+
+import java.awt.datatransfer.DataFlavor;
+import java.awt.datatransfer.StringSelection;
+import java.awt.datatransfer.Transferable;
+import java.awt.datatransfer.UnsupportedFlavorException;
+import java.io.IOException;
+
+import javax.swing.JComponent;
+import javax.swing.TransferHandler;
+
+
+/**
+ * base class for the PaletteListTransferHandler of the ShapePalette
+ * taken from Java drag and drop tutorial, see http://java.sun.com/docs/books/tutorial/uiswing/misc/dnd.html
+ */
+public abstract class StringTransferHandler extends TransferHandler {
+ protected abstract String exportString(JComponent c);
+
+ protected abstract void importString(JComponent c, String str);
+
+ protected abstract void cleanup(JComponent c, boolean remove);
+
+ protected Transferable createTransferable(JComponent c) {
+ return new StringSelection(exportString(c));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param c DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getSourceActions(JComponent c) {
+ return COPY_OR_MOVE;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param c DOCUMENT ME!
+ * @param t DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean importData(JComponent c, Transferable t) {
+ if (canImport(c, t.getTransferDataFlavors())) {
+ try {
+ String str = (String) t.getTransferData(DataFlavor.stringFlavor);
+ importString(c, str);
+
+ return true;
+ } catch (UnsupportedFlavorException ufe) {
+ } catch (IOException ioe) {
+ }
+ }
+
+ return false;
+ }
+
+ protected void exportDone(JComponent c, Transferable data, int action) {
+ cleanup(c, action == MOVE);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param c DOCUMENT ME!
+ * @param flavors DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean canImport(JComponent c, DataFlavor[] flavors) {
+ for (int i = 0; i < flavors.length; i++) {
+ if (DataFlavor.stringFlavor.equals(flavors[i])) {
+ return true;
+ }
+ }
+
+ return false;
+ }
+}
diff --git a/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/impl/TextAnnotation.java b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/impl/TextAnnotation.java
new file mode 100644
index 0000000..b8904c7
--- /dev/null
+++ b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/impl/TextAnnotation.java
@@ -0,0 +1,253 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.editor.impl;
+
+import java.awt.AlphaComposite;
+import java.awt.Color;
+import java.awt.Composite;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.image.BufferedImage;
+
+import javax.swing.JComponent;
+import javax.swing.JLabel;
+
+import cytoscape.editor.CytoscapeEditorManager;
+
+
+/**
+ *
+ */
+public class TextAnnotation extends JComponent {
+ // MLC 05/09/07:
+ private static final long serialVersionUID = -2388758275776657147L;
+ private BufferedImage img; // image for figure we are drawing
+ private int x1;
+ private int y1;
+ private int h1;
+ private int w1;
+ private BufferedImage image; // enclosing image for rendering on the
+ // canvas
+ private String text;
+
+ /**
+ * Creates a new TextAnnotation object.
+ *
+ * @param text DOCUMENT ME!
+ * @param x1 DOCUMENT ME!
+ * @param y1 DOCUMENT ME!
+ * @param w1 DOCUMENT ME!
+ * @param h1 DOCUMENT ME!
+ */
+ public TextAnnotation(String text, int x1, int y1, int w1, int h1) {
+ // super();
+ // this.img = new BufferedImage(44, 33, BufferedImage.TYPE_INT_ARGB);
+ // Graphics2D grafx = img.createGraphics();
+ this.text = text;
+ // MLC 05/09/07:
+ // this.img = img;
+ this.x1 = x1;
+ this.y1 = y1;
+ this.w1 = w1;
+ this.h1 = y1;
+
+ JLabel label = new JLabel(text);
+ this.add(label);
+ label.setVisible(true);
+ label.setOpaque(true);
+
+ setBounds(x1, y1, w1, h1);
+ label.repaint();
+ this.repaint();
+ }
+
+ // public void setBounds(int x, int y, int width, int height) {
+ /**
+ * DOCUMENT ME!
+ *
+ * @param x DOCUMENT ME!
+ * @param y DOCUMENT ME!
+ * @param width DOCUMENT ME!
+ * @param height DOCUMENT ME!
+ */
+ public void setBounds(int x, int y, int width, int height) {
+ super.setBounds(x, y, width, height);
+
+ // set member vars
+ this.x1 = x;
+ this.y1 = y;
+ this.w1 = width;
+ this.h1 = height;
+
+ // our bounds have changed, create a new image with new size
+ if ((width > 0) && (height > 0)) {
+ image = new BufferedImage(width, height, BufferedImage.TYPE_INT_ARGB);
+ }
+ }
+
+ // }
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g DOCUMENT ME!
+ */
+ public void paint(Graphics g) {
+ Graphics2D image2D = image.createGraphics();
+
+ // draw into the image
+ Composite origComposite = image2D.getComposite();
+ image2D.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC));
+ //// image2D.drawString(this.text, this.x1, this.y1);
+ CytoscapeEditorManager.log("drawing " + text + " to " + image);
+
+ image2D.setColor(Color.red);
+ // image2D.fillRect(0, 0, image.getWidth(null), image.getHeight(null));
+ image2D.setColor(Color.black);
+ image2D.drawString(text, 10, 10);
+ image2D.setComposite(origComposite);
+
+ ((Graphics2D) g).drawImage(image, null, 0, 0);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getH1() {
+ return h1;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param h1 DOCUMENT ME!
+ */
+ public void setH1(int h1) {
+ this.h1 = h1;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getW1() {
+ return w1;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param w1 DOCUMENT ME!
+ */
+ public void setW1(int w1) {
+ this.w1 = w1;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getX1() {
+ return x1;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param x1 DOCUMENT ME!
+ */
+ public void setX1(int x1) {
+ this.x1 = x1;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getY1() {
+ return y1;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param y1 DOCUMENT ME!
+ */
+ public void setY1(int y1) {
+ this.y1 = y1;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public BufferedImage getImg() {
+ return img;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param img DOCUMENT ME!
+ */
+ public void setImg(BufferedImage img) {
+ this.img = img;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getText() {
+ return text;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param text DOCUMENT ME!
+ */
+ public void setText(String text) {
+ this.text = text;
+ }
+}
diff --git a/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/impl/images/deleteIcon.gif b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/impl/images/deleteIcon.gif
new file mode 100644
index 0000000..b197043
Binary files /dev/null and b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/impl/images/deleteIcon.gif differ
diff --git a/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/impl/images/pspbrwse.jbf b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/impl/images/pspbrwse.jbf
new file mode 100644
index 0000000..0047f36
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diff --git a/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/impl/images/redo.gif b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/impl/images/redo.gif
new file mode 100644
index 0000000..5d93c9b
Binary files /dev/null and b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/impl/images/redo.gif differ
diff --git a/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/impl/images/undo.gif b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/impl/images/undo.gif
new file mode 100644
index 0000000..b8b4f2b
Binary files /dev/null and b/coreplugins/CytoscapeEditor2/src/main/java/cytoscape/editor/impl/images/undo.gif differ
diff --git a/coreplugins/CytoscapeEditor2/src/main/resources/cytoscape/editor/plugin.props b/coreplugins/CytoscapeEditor2/src/main/resources/cytoscape/editor/plugin.props
new file mode 100644
index 0000000..aeedbc3
--- /dev/null
+++ b/coreplugins/CytoscapeEditor2/src/main/resources/cytoscape/editor/plugin.props
@@ -0,0 +1,33 @@
+# This props file would be filled out and included in the plugin jar file. This props file will be used
+# to put information into the Plugin Manager about the plugin
+
+# -- The following properties are REQUIRED -- #
+
+# The plugin name that will be displayed to users
+pluginName=CytoscapeEditor
+
+# Description used to give users information about the plugin such as what it does.
+# Html tags are encouraged for formatting purposes.
+pluginDescription=Provides basic ability to edit nodes and edges in a network.
+
+# Plugin version number, this must be two numbers separated by a decimlal. Ex. 0.2, 14.03
+pluginVersion=2.62
+
+# Compatible Cytoscape version
+cytoscapeVersion=2.5,2.6,2.7,2.8
+
+# Category, use one of the categories listed on the website or create your own
+pluginCategory=Core
+
+
+# List of authors. Note each author and institution pair are separated by a : (colon)
+# each additional author institution pair must be separated from other pairs bye a ; (semicolon)
+pluginAuthorsIntsitutions=Allan Kuchinsky:Agilent Technologies;Michael Creech:Blue Oak Software
+
+# Date this plugin/plugin version was released
+releaseDate=February 04, 2009
+
+# -- The following properties should be set ONLY BY CORE PLUGINS -- #
+downloadURL=http://cytoscape.org/plugins/plugins.xml
+uniqueID=5
+
diff --git a/coreplugins/CytoscapeEditor2/src/main/resources/network.png b/coreplugins/CytoscapeEditor2/src/main/resources/network.png
new file mode 100644
index 0000000..7d2d92c
Binary files /dev/null and b/coreplugins/CytoscapeEditor2/src/main/resources/network.png differ
diff --git a/coreplugins/CytoscapeEditor2/version-history.html b/coreplugins/CytoscapeEditor2/version-history.html
new file mode 100644
index 0000000..6bdbafa
--- /dev/null
+++ b/coreplugins/CytoscapeEditor2/version-history.html
@@ -0,0 +1,192 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+<meta http-equiv="content-type" content="text/html; charset=utf-8"/>
+<title>CytoscapeEditor Version History</title>
+</head>
+<body>
+
+<h1>CytoscapeEditor Version History</h1>
+
+<ul>
+
+<li><strong>CytoscapeEditor, Version 2.62 (02/04/09)</strong>
+<ol>
+<li>Ctrl-click on a one-button Mac brings up both the bypass menu AND creates an edge (1738)</li>
+<li>Connect Selected Nodes not undoable as an atomic action. (1384)</li>
+<li>"Connect Selected Node" not always show up (1264)</li>
+<li>Creating new edges via CTRL-click opens interfering menu on Mac (1806)</li>
+<li>Creating new edge leaves streaks on canvas (still) (1730)</li>
+<li>CytoscapeEditor in 2.6 throws exception when adding (globally) existing node (1917)</li>
+<li>Fixed ClassCastException where using the VizMapper and changing ArrowShapes could lead to a ClassCastException.</li
+<li>Multiple NeworkViews stopped editor's drag and drop from working (1977)</li>
+<li>Rubberband line continued to function after selecting another network (1978)</li>
+<li>NullPointerException when Drag&Drop of edge under certain conditions (1979)</li>
+
+</ol>
+<li><strong>CytoscapeEditor, Version 2.60 (07/09/08)</strong>
+<ol>
+<li>Patched Editor so that mouse, key, and drop events are ignored
+when the Editor tab of the CytoPanel is not active.</li>
+<li>Fixed the "ESC" key to correctly stop drop of an edge.</li>
+</ol>
+</li>
+
+<li><strong>CytoscapeEditor, Version 2.53 (10/30/07)</strong>
+<ol>
+<li>Fixed bug where palette was being redrawn when the Editor tab wasn't
+ selected.</li>
+<li>Some code cleanup changes to CytoscapeEditorManagerSupport.</li>
+</ol>
+</li>
+
+<li><strong>CytoscapeEditor, Version 2.52 (10/25/07)</strong>
+<ol>
+
+<li>Changed File->New-Network->EmptyNetwork (NewNetworkAction) to not
+produce an extra (accidental) CyNetworkView and to set the visual
+style of the new network to be the VisualMappingManager's current
+visual style.</li>
+
+<li>Removed arrowhead on default "Directed Edge" edge palette entry in
+DefaultCytoscapeEditor.</li>
+
+<li>Fixed so that clicking on the Editor tab would correctly show the correct
+editor palette for a given visual style (for sublass editors).</li>
+
+<li>Changed call to buildVisualStyle() in
+CytoscapeEditorManager.initializeEditor() to occur before
+VisualMappingManager.setVisualStyle() is called.</li>
+
+</ol>
+</li>
+
+<li><strong>CytoscapeEditor, Version 2.51 (07/23/07)</strong>
+<ol>
+<li>Simplified CytoscapeEditor initialization with assumption that
+the CytoscapeEditor is always loaded before any extension to
+this editor.</li>
+<li>Removed unneeded definitions of getPluginInfoObject() and describe().</li>
+<li>Removed manual setting of EdgeView tooltips, since tooltips should
+now be set using Visual Styles.</li>
+<li>Fixed NPE bug in CyotscapeEditorManger.register() where
+CytoscapeEditorManager.log() statements were being called without null
+pointer check.</li>
+<li>Updated missed deprecated code reference to use new Cytoscape 2.5
+ VizMap API.</li>
+</ol>
+</li>
+
+<li><strong>CytoscapeEditor, Version 2.501 (06/30/07)</strong>
+<ol>
+<li>Updated missed deprecated code reference to use new Cytoscape 2.5
+ VizMap API.</li>
+</ol>
+</li>
+
+<li><strong>CytoscapeEditor, Version 2.50 (05/11/07)</strong>
+<ol>
+<li>Made CytoscapeEditor be a good citizen for the Cytoscape PluginManager.</li>
+<li>Updated code to use new Cytoscape 2.5 VizMap API.</li>
+<li>Fixed various deprecations and warnings.</li>
+</ol>
+</li>
+
+<li><strong>CytoscapeEditor, Version 2.4 alfa 4 (01/09/07)</strong>
+<ol>
+<li>Added keyboard accelerator for "Delete Selected Nodes and Edges"
+menu item.</li>
+</ol>
+</li>
+
+<li><strong>CytoscapeEditor, Version 2.4 alfa 3 (12/29/06)</strong>
+<ol>
+<li>Various changes and cleanup to allow easier subclassing of
+CytoscapeEditor and access to the DeleteAction.</li>
+</ol>
+</li>
+
+<li><strong>CytoscapeEditor, Version 2.4 alfa 2 (12/17/06)</strong>
+<ol>
+<li>Changed the CytoscapeEditor to be intelligent about what drag
+cursor is shown when performing a drag-drop from a shape palette entry
+to a CyNetworkView of interest.</li>
+</ol>
+
+</li>
+<li><strong>CytoscapeEditor, Version 2.4 alfa 1 (12/08/06)</strong>
+<ol>
+
+<li>Refactored BasicNetworkEditEventHandler.finishEdge() into smaller
+pieces for subclass usage. Cleaned up
+BasicNetworkEditEventHandler.mousePressed() and a few protected
+instance variables that should be private.</li>
+<li>Cleaned up code and refactored
+PaletteNetworkEditEventHandler.itemDropped() and associated methods
+for easier use by subclasses and code cleanup.</li>
+<li>Removed BioPAXNetworkEditEventHandler.</li>
+</ol>
+</li>
+
+<li><strong>CytoscapeEditor, Version 2.3.03 (12/05/06)</strong>
+<ol>
+<li>Created a new way to easily produce ShapePalette entries for
+editors.</li>
+<li>Added ability of ShapePalette entries to handle visual style
+size information.</li>
+<li>Added CytoShapeIcon.DEFAULT_WIDTH and DEFAULT_HEIGHT and deprecated
+ CytoShapeIcon.WIDTH & HEIGHT.</li>
+<li>Removed SimpleBioPAX_Editor.</li>
+</ol>
+</li>
+
+<li><strong>CytoscapeEditor, Version 2.3.02 (11/06/06)</strong>
+<ol>
+<li>Fixed compilation problem caused by accidental release of changes
+to CytoscapeEditorManager.java.</li>
+</ol>
+</li>
+
+<li><strong>CytoscapeEditor, Version 2.3.01 (09/13/06)</strong>
+<ol>
+<li>CytoscapeEditorManagerSupport: Fixed updateEditorPalette() to not
+assume visualStyleName is the same as Editor name. Added some
+comments.</li>
+
+<li>BasicCytoscapeEditor: Removed setting of BIO_PAX attributes from
+addNode(). Fixed deprecated method usage in addNode().</li>
+
+<li>BasicCytoShapeEntity, ShapePalette, InvalidEditorException: Added
+generated serial version UUID for serializable classes.
+
+CytoscapeEditor: Updated to remove deprecated use of FlagEventListener
+(now is SelectEventListener)</li>
+
+<li>CytoscapeEditorManager:
+<ol>
+ <li> Fixed so visualStyleName can be different from the editor name.</li>
+ <li> Added getEditorNameForVisualStyleName() and changed
+ initializeEditor() to take a visualStyleName parameter.</li>
+ <li> Changed many instance variables to be private vs protected.</li>
+ <li> Added intialization of this manager if register() is called by
+ another plugin before this plugin is loaded.</li>
+</ol>
+</li>
+<li>CytoscapeEditorPlugin:
+<ol>
+ <li> Removed deprecated call to CytoscapeInit.getDefaultVisualStyle() in
+ initializeCytoscapeEditor().</li>
+ <li> Removed some misleading code--println that editor is loaded and
+ initialization code as though editor is initialized via a menu item,
+ when it is not.</li>
+</ol>
+</li>
+</ol>
+</li>
+</ul>
+<hr />
+<p><small><em>This page was last updated: 02/04/09</em></small></p>
+</body>
+</html>
\ No newline at end of file
diff --git a/coreplugins/EquationFunctions/pom.xml b/coreplugins/EquationFunctions/pom.xml
new file mode 100644
index 0000000..ea173c7
--- /dev/null
+++ b/coreplugins/EquationFunctions/pom.xml
@@ -0,0 +1,65 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>parent</artifactId>
+ <version>2.8.4-SNAPSHOT</version>
+ </parent>
+
+ <artifactId>equation-functions</artifactId>
+ <packaging>jar</packaging>
+
+ <name>Equation Functions</name>
+
+ <!-- bootstrap for cytoscape dependencies, namely the parent POM snapshots -->
+ <repositories>
+ <repository>
+ <id>cytoscape_snapshots</id>
+ <snapshots>
+ <enabled>true</enabled>
+ </snapshots>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <name>Cytoscape Snapshots</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/</url>
+ </repository>
+ <repository>
+ <id>cytoscape_releases</id>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ <name>Cytoscape Releases</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/releases/</url>
+ </repository>
+ </repositories>
+
+ <build>
+ <plugins>
+ <plugin>
+ <artifactId>maven-assembly-plugin</artifactId>
+ <configuration>
+ <archive>
+ <manifestEntries>
+ <Cytoscape-Plugin>org.cytoscape.EquationFunctions.EquationFunctionsPlugin</Cytoscape-Plugin>
+ </manifestEntries>
+ </archive>
+ </configuration>
+ </plugin>
+ </plugins>
+ </build>
+
+ <dependencies>
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>equations</artifactId>
+ <version>${project.version}</version>
+ <scope>provided</scope>
+ </dependency>
+ </dependencies>
+
+</project>
+
diff --git a/coreplugins/EquationFunctions/src/main/java/org/cytoscape/EquationFunctions/EquationFunctionsPlugin.java b/coreplugins/EquationFunctions/src/main/java/org/cytoscape/EquationFunctions/EquationFunctionsPlugin.java
new file mode 100644
index 0000000..382eb35
--- /dev/null
+++ b/coreplugins/EquationFunctions/src/main/java/org/cytoscape/EquationFunctions/EquationFunctionsPlugin.java
@@ -0,0 +1,24 @@
+/*
+ * A plug-in to add Cytoscape-specific attribute functions.
+ */
+package org.cytoscape.EquationFunctions;
+
+
+import cytoscape.plugin.CytoscapePlugin;
+
+import org.cytoscape.equations.EqnParser;
+import org.cytoscape.equations.Parser;
+
+import org.cytoscape.EquationFunctions.functions.*;
+
+
+public class EquationFunctionsPlugin extends CytoscapePlugin {
+ public EquationFunctionsPlugin() {
+ final EqnParser theParser = Parser.getParser();
+ theParser.registerFunction(new Degree());
+ theParser.registerFunction(new InDegree());
+ theParser.registerFunction(new OutDegree());
+ theParser.registerFunction(new SourceID());
+ theParser.registerFunction(new TargetID());
+ }
+}
diff --git a/coreplugins/EquationFunctions/src/main/java/org/cytoscape/EquationFunctions/functions/Degree.java b/coreplugins/EquationFunctions/src/main/java/org/cytoscape/EquationFunctions/functions/Degree.java
new file mode 100644
index 0000000..ba39ab5
--- /dev/null
+++ b/coreplugins/EquationFunctions/src/main/java/org/cytoscape/EquationFunctions/functions/Degree.java
@@ -0,0 +1,109 @@
+/*
+ File: Degree.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.EquationFunctions.functions;
+
+
+import java.util.ArrayList;
+import java.util.List;
+
+import cytoscape.Cytoscape;
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+
+import org.cytoscape.equations.Function;
+
+
+public class Degree implements Function {
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "DEGREE"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Returns degree of a node."; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of how to use this function
+ */
+ public String getUsageDescription() { return "Call this with \"DEGREE(node_ID)\""; }
+
+ public Class getReturnType() { return Long.class; }
+
+ /**
+ * @return String.class or null if there is not exactly 1 arg or the arg is not of type String
+ */
+ public Class validateArgTypes(final Class[] argTypes) {
+ if (argTypes.length != 1 || (argTypes[0] != String.class))
+ return null;
+
+ return Long.class;
+ }
+
+ /**
+ * @param args the function arguments which must be either one object of type Double or Long
+ * @return the result of the function evaluation which is the natural logarithm of the first argument
+ */
+ public Object evaluateFunction(final Object[] args) {
+ final String nodeID = (String)args[0];
+
+ final CyNetwork currentNetwork = Cytoscape.getCurrentNetwork();
+ if (currentNetwork == null)
+ return (Long)(-1L);
+
+ final CyNode node = Cytoscape.getCyNode(nodeID);
+ if (node == null)
+ throw new IllegalArgumentException("\"" + nodeID + "\" is not a valid node identifier!");
+
+ return (Long)(long)currentNetwork.getDegree(node);
+ }
+
+ /**
+ * Used with the equation builder.
+ *
+ * @param leadingArgs the types of the arguments that have already been selected by the user.
+ * @return the set of arguments (must be a collection of String.class, Long.class, Double.class,
+ * Boolean.class and List.class) that are candidates for the next argument. An empty
+ * set indicates that no further arguments are valid.
+ */
+ public List<Class> getPossibleArgTypes(final Class[] leadingArgs) {
+ if (leadingArgs.length == 0) {
+ final List<Class> possibleNextArgs = new ArrayList<Class>();
+ possibleNextArgs.add(String.class);
+ return possibleNextArgs;
+ }
+
+ return null;
+ }
+}
diff --git a/coreplugins/EquationFunctions/src/main/java/org/cytoscape/EquationFunctions/functions/InDegree.java b/coreplugins/EquationFunctions/src/main/java/org/cytoscape/EquationFunctions/functions/InDegree.java
new file mode 100644
index 0000000..39acafb
--- /dev/null
+++ b/coreplugins/EquationFunctions/src/main/java/org/cytoscape/EquationFunctions/functions/InDegree.java
@@ -0,0 +1,78 @@
+/*
+ File: InDegree.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.EquationFunctions.functions;
+
+
+import cytoscape.Cytoscape;
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+import org.cytoscape.equations.AbstractFunction;
+
+
+public class InDegree extends AbstractFunction {
+ public InDegree() {
+ super(new ArgDescriptor[] { new ArgDescriptor(ArgType.STRICT_STRING, "edge_ID", "An ID identifying a node.") });
+ }
+
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "INDEGREE"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Returns indegree of a node."; }
+
+ public Class getReturnType() { return Long.class; }
+
+ /**
+ * @param args the function arguments which must be either one object of type Double or Long
+ * @return the result of the function evaluation which is the natural logarithm of the first argument
+ */
+ public Object evaluateFunction(final Object[] args) {
+ final String nodeID = (String)args[0];
+
+ final CyNetwork currentNetwork = Cytoscape.getCurrentNetwork();
+ if (currentNetwork == null)
+ return (Long)(-1L);
+
+ final CyNode node = Cytoscape.getCyNode(nodeID);
+ if (node == null)
+ throw new IllegalArgumentException("\"" + nodeID + "\" is not a valid node identifier!");
+
+ return (Long)(long)currentNetwork.getInDegree(node, /* count_undirected_edges = */ false);
+ }
+}
diff --git a/coreplugins/EquationFunctions/src/main/java/org/cytoscape/EquationFunctions/functions/OutDegree.java b/coreplugins/EquationFunctions/src/main/java/org/cytoscape/EquationFunctions/functions/OutDegree.java
new file mode 100644
index 0000000..e5da560
--- /dev/null
+++ b/coreplugins/EquationFunctions/src/main/java/org/cytoscape/EquationFunctions/functions/OutDegree.java
@@ -0,0 +1,78 @@
+/*
+ File: OutDegree.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.EquationFunctions.functions;
+
+
+import cytoscape.Cytoscape;
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+import org.cytoscape.equations.AbstractFunction;
+
+
+public class OutDegree extends AbstractFunction {
+ public OutDegree() {
+ super(new ArgDescriptor[] { new ArgDescriptor(ArgType.STRICT_STRING, "edge_ID", "An ID identifying a node.") });
+ }
+
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "OUTDEGREE"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Returns indegree of a node."; }
+
+ public Class getReturnType() { return Long.class; }
+
+ /**
+ * @param args the function arguments which must be either one object of type Double or Long
+ * @return the result of the function evaluation which is the natural logarithm of the first argument
+ */
+ public Object evaluateFunction(final Object[] args) {
+ final String nodeID = (String)args[0];
+
+ final CyNetwork currentNetwork = Cytoscape.getCurrentNetwork();
+ if (currentNetwork == null)
+ return (Long)(-1L);
+
+ final CyNode node = Cytoscape.getCyNode(nodeID);
+ if (node == null)
+ throw new IllegalArgumentException("\"" + nodeID + "\" is not a valid node identifier!");
+
+ return (Long)(long)currentNetwork.getOutDegree(node, /* count_undirected_edges = */ false);
+ }
+}
diff --git a/coreplugins/EquationFunctions/src/main/java/org/cytoscape/EquationFunctions/functions/SourceID.java b/coreplugins/EquationFunctions/src/main/java/org/cytoscape/EquationFunctions/functions/SourceID.java
new file mode 100644
index 0000000..489449f
--- /dev/null
+++ b/coreplugins/EquationFunctions/src/main/java/org/cytoscape/EquationFunctions/functions/SourceID.java
@@ -0,0 +1,73 @@
+/*
+ File: SourceID.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.EquationFunctions.functions;
+
+
+import cytoscape.CyEdge;
+import cytoscape.Cytoscape;
+import cytoscape.CyNetwork;
+
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+import org.cytoscape.equations.AbstractFunction;
+
+public class SourceID extends AbstractFunction {
+ public SourceID() {
+ super(new ArgDescriptor[] { new ArgDescriptor(ArgType.STRICT_STRING, "edge_ID", "An ID identifying an edge.") });
+ }
+
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "SOURCEID"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Returns source ID of an edge."; }
+
+ public Class getReturnType() { return Long.class; }
+
+ /**
+ * @param args the function arguments which must be either one object of type Double or Long
+ * @return the result of the function evaluation which is the natural logarithm of the first argument
+ */
+ public Object evaluateFunction(final Object[] args) {
+ final String edgeID = (String)args[0];
+
+ final CyEdge edge = Cytoscape.getRootGraph().getEdge(edgeID);
+ if (edge == null)
+ throw new IllegalArgumentException("\"" + edgeID + "\" is not a valid edge identifier!");
+
+ return edge.getSource().getIdentifier();
+ }
+}
diff --git a/coreplugins/EquationFunctions/src/main/java/org/cytoscape/EquationFunctions/functions/TargetID.java b/coreplugins/EquationFunctions/src/main/java/org/cytoscape/EquationFunctions/functions/TargetID.java
new file mode 100644
index 0000000..7956f24
--- /dev/null
+++ b/coreplugins/EquationFunctions/src/main/java/org/cytoscape/EquationFunctions/functions/TargetID.java
@@ -0,0 +1,74 @@
+/*
+ File: TargetID.java
+
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.EquationFunctions.functions;
+
+
+import cytoscape.CyEdge;
+import cytoscape.Cytoscape;
+import cytoscape.CyNetwork;
+
+import org.cytoscape.equations.ArgDescriptor;
+import org.cytoscape.equations.ArgType;
+import org.cytoscape.equations.AbstractFunction;
+
+
+public class TargetID extends AbstractFunction {
+ public TargetID() {
+ super(new ArgDescriptor[] { new ArgDescriptor(ArgType.STRICT_STRING, "edge_ID", "An ID identifying an edge.") });
+ }
+
+ /**
+ * Used to parse the function string. This name is treated in a case-insensitive manner!
+ * @return the name by which you must call the function when used in an attribute equation.
+ */
+ public String getName() { return "TARGETID"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Returns target ID of an edge."; }
+
+ public Class getReturnType() { return Long.class; }
+
+ /**
+ * @param args the function arguments which must be either one object of type Double or Long
+ * @return the result of the function evaluation which is the natural logarithm of the first argument
+ */
+ public Object evaluateFunction(final Object[] args) {
+ final String edgeID = (String)args[0];
+
+ final CyEdge edge = Cytoscape.getRootGraph().getEdge(edgeID);
+ if (edge == null)
+ throw new IllegalArgumentException("\"" + edgeID + "\" is not a valid edge identifier!");
+
+ return edge.getTarget().getIdentifier();
+ }
+}
diff --git a/coreplugins/EquationFunctions/src/main/resources/org/cytoscape/EquationFunctions/plugin.props b/coreplugins/EquationFunctions/src/main/resources/org/cytoscape/EquationFunctions/plugin.props
new file mode 100644
index 0000000..4048a6e
--- /dev/null
+++ b/coreplugins/EquationFunctions/src/main/resources/org/cytoscape/EquationFunctions/plugin.props
@@ -0,0 +1,32 @@
+# This props file would be filled out and included in the plugin jar file. This props file will be used
+# to put information into the Plugin Manager about the plugin
+
+# -- The following properties are REQUIRED -- #
+
+# The plugin name that will be displayed to users
+pluginName=EquationFunctions
+
+# Description used to give users information about the plugin such as what it does.
+# Html tags are encouraged for formatting purposes.
+pluginDescription=Provides various attribute equation functions.
+
+# Plugin version number, this must be two numbers separated by a decimlal. Ex. 0.2, 14.03
+pluginVersion=1.0
+
+# Compatible Cytoscape version
+cytoscapeVersion=2.8
+
+# Category, use one of the categories listed on the website or create your own
+pluginCategory=Core
+
+
+# List of authors. Note each author and institution pair are separated by a : (colon)
+# each additional author institution pair must be separated from other pairs bye a ; (semicolon)
+pluginAuthorsInstitutions=Dr. Johannes Ruscheinski:UCSD
+
+# -- The following properties should be set ONLY BY CORE PLUGINS -- #
+downloadURL=http://cytoscape.org/plugins/plugins.xml
+uniqueID=34341901274245
+
+
+
diff --git a/coreplugins/ManualLayout/pom.xml b/coreplugins/ManualLayout/pom.xml
new file mode 100644
index 0000000..afc4305
--- /dev/null
+++ b/coreplugins/ManualLayout/pom.xml
@@ -0,0 +1,64 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>parent</artifactId>
+ <version>2.8.4-SNAPSHOT</version>
+ </parent>
+
+ <artifactId>manual-layout</artifactId>
+ <packaging>jar</packaging>
+
+ <name>Manual Layout</name>
+
+ <!-- bootstrap for cytoscape dependencies, namely the parent POM snapshots -->
+ <repositories>
+ <repository>
+ <id>cytoscape_snapshots</id>
+ <snapshots>
+ <enabled>true</enabled>
+ </snapshots>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <name>Cytoscape Snapshots</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/</url>
+ </repository>
+ <repository>
+ <id>cytoscape_releases</id>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ <name>Cytoscape Releases</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/releases/</url>
+ </repository>
+ </repositories>
+
+ <build>
+ <plugins>
+ <plugin>
+ <artifactId>maven-assembly-plugin</artifactId>
+ <configuration>
+ <archive>
+ <manifestEntries>
+ <Cytoscape-Plugin>ManualLayout.ManualLayoutPlugin</Cytoscape-Plugin>
+ </manifestEntries>
+ </archive>
+ </configuration>
+ </plugin>
+ </plugins>
+ </build>
+
+ <dependencies>
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>nerius-math-xform</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ </dependencies>
+
+</project>
+
diff --git a/coreplugins/ManualLayout/src/main/java/ManualLayout/ManualLayoutPlugin.java b/coreplugins/ManualLayout/src/main/java/ManualLayout/ManualLayoutPlugin.java
new file mode 100644
index 0000000..23e78af
--- /dev/null
+++ b/coreplugins/ManualLayout/src/main/java/ManualLayout/ManualLayoutPlugin.java
@@ -0,0 +1,86 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package ManualLayout;
+
+import ManualLayout.control.ControlPanel;
+import ManualLayout.control.ControlPanelAction;
+
+import ManualLayout.rotate.RotatePanel;
+import ManualLayout.rotate.RotatePanelAction;
+
+import ManualLayout.scale.ScalePanel;
+import ManualLayout.scale.ScalePanelAction;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.plugin.CytoscapePlugin;
+
+import java.awt.Dimension;
+
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JMenu;
+import javax.swing.SwingConstants;
+
+
+/**
+ *
+ */
+public class ManualLayoutPlugin extends CytoscapePlugin {
+
+ /**
+ * Creates a new ManualLayoutPlugin object.
+ */
+ public ManualLayoutPlugin() {
+
+ // create the panels
+ RotatePanel rotatePanel = new RotatePanel();
+ ScalePanel scalePanel = new ScalePanel();
+ ControlPanel controlPanel = new ControlPanel();
+
+ // add them to the cytopanel
+ Cytoscape.getDesktop().getCytoPanel(SwingConstants.SOUTH_WEST)
+ .add("Align and Distribute", controlPanel);
+ Cytoscape.getDesktop().getCytoPanel(SwingConstants.SOUTH_WEST).add("Rotate", rotatePanel);
+ Cytoscape.getDesktop().getCytoPanel(SwingConstants.SOUTH_WEST).add("Scale", scalePanel);
+
+ // create the actions
+ Cytoscape.getDesktop().getCyMenus().addAction( new ControlPanelAction(), 0);
+ Cytoscape.getDesktop().getCyMenus().addAction( new RotatePanelAction(), 1);
+ Cytoscape.getDesktop().getCyMenus().addAction( new ScalePanelAction(), 2);
+
+ }
+}
diff --git a/coreplugins/ManualLayout/src/main/java/ManualLayout/common/AbstractManualLayoutAction.java b/coreplugins/ManualLayout/src/main/java/ManualLayout/common/AbstractManualLayoutAction.java
new file mode 100644
index 0000000..f159e6d
--- /dev/null
+++ b/coreplugins/ManualLayout/src/main/java/ManualLayout/common/AbstractManualLayoutAction.java
@@ -0,0 +1,158 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package ManualLayout.common;
+
+
+import cytoscape.Cytoscape;
+import cytoscape.data.SelectEvent;
+import cytoscape.data.SelectEventListener;
+import cytoscape.graph.layout.algorithm.MutablePolyEdgeGraphLayout;
+import cytoscape.util.CytoscapeAction;
+import cytoscape.view.CytoscapeDesktop;
+import cytoscape.view.cytopanels.CytoPanel;
+import cytoscape.view.cytopanels.CytoPanelListener;
+import cytoscape.view.cytopanels.CytoPanelState;
+import java.awt.Dimension;
+import java.awt.event.ActionEvent;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.util.HashMap;
+import javax.swing.Action;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JMenu;
+import javax.swing.JPanel;
+import javax.swing.JSplitPane;
+import javax.swing.SwingConstants;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+import javax.swing.event.MenuEvent;
+
+
+/**
+ * Base class for displaying cytopanel menu items. This class primarily
+ * manages the Layout Menu logic and tab selection of the tools cytopanel.
+ */
+public abstract class AbstractManualLayoutAction
+ extends CytoscapeAction
+ implements CytoPanelListener {
+
+ static protected CytoPanel manualLayoutPanel =
+ Cytoscape.getDesktop().getCytoPanel(SwingConstants.SOUTH_WEST);
+
+ private static int selectedIndex = -1;
+
+ int menuIndex;
+
+ /**
+ * Base class for displaying cytopanel menu items.
+ *
+ * @param title The title of the menu item.
+ * @param menuIndex The desired menu index for the action.
+ */
+ public AbstractManualLayoutAction(String title, int menuIndex) {
+ super(title);
+ this.menuIndex = menuIndex;
+ setPreferredMenu("Layout");
+ useCheckBoxMenuItem = true;
+ manualLayoutPanel.addCytoPanelListener(this);
+ }
+
+ /**
+ * Selects the component and hides/unhides the cytopanel as necessary.
+ *
+ * @param ev Triggering event - not used.
+ */
+ public void actionPerformed(ActionEvent ev) {
+
+ // Check the state of the manual layout Panel
+ CytoPanelState curState = manualLayoutPanel.getState();
+
+ // Case 1: Panel is disabled
+ if (curState == CytoPanelState.HIDE) {
+ manualLayoutPanel.setState(CytoPanelState.DOCK);
+ manualLayoutPanel.setSelectedIndex(menuIndex);
+ selectedIndex = menuIndex;
+
+ // Case 2: Panel is in the DOCK/FLOAT and a different panel is selected
+ } else if ( manualLayoutPanel.getSelectedIndex() != menuIndex ) {
+ manualLayoutPanel.setSelectedIndex(menuIndex);
+ selectedIndex = menuIndex;
+
+ // Case 3: The currently selected item is selected
+ } else {
+ manualLayoutPanel.setState(CytoPanelState.HIDE);
+ selectedIndex = -1;
+ }
+ }
+
+ /**
+ * Enables of disables the action based on system state.
+ *
+ * @param ev Triggering event - not used.
+ */
+ public void menuSelected(MenuEvent e) {
+ enableForNetworkAndView();
+ JCheckBoxMenuItem item = (JCheckBoxMenuItem)Cytoscape.getDesktop().getCyMenus().getLayoutMenu().getItem(menuIndex);
+ if ( manualLayoutPanel.getSelectedIndex() != menuIndex ||
+ manualLayoutPanel.getState() == CytoPanelState.HIDE )
+ item.setState(false);
+ else
+ item.setState(true);
+
+ CytoPanelState parentState = Cytoscape.getDesktop().getCytoPanel(SwingConstants.WEST).getState();
+ if ( parentState == CytoPanelState.HIDE ) {
+ setEnabled(false);
+ }
+ else {
+ setEnabled(true);
+ }
+
+ }
+
+ /**
+ * Makes sure the menu check stays in sync with the selections made in the cytopanel.
+ *
+ * @param componentIndex the index of the menu
+ */
+ public void onComponentSelected(int componentIndex) {
+ selectedIndex = componentIndex;
+ }
+
+ public void onStateChange(CytoPanelState newState) {}
+ public void onComponentAdded(int count) {}
+ public void onComponentRemoved(int count) {}
+}
diff --git a/coreplugins/ManualLayout/src/main/java/ManualLayout/common/CheckBoxTracker.java b/coreplugins/ManualLayout/src/main/java/ManualLayout/common/CheckBoxTracker.java
new file mode 100644
index 0000000..7c4ddf6
--- /dev/null
+++ b/coreplugins/ManualLayout/src/main/java/ManualLayout/common/CheckBoxTracker.java
@@ -0,0 +1,101 @@
+/*
+ Copyright (c) 2006, 2007, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package ManualLayout.common;
+
+
+import ManualLayout.rotate.RotatePanel;
+import ManualLayout.rotate.RotationLayouter;
+
+import ManualLayout.scale.ScaleLayouter;
+import ManualLayout.scale.ScalePanel;
+
+import cytoscape.Cytoscape;
+import cytoscape.CyNetwork;
+
+import cytoscape.data.SelectEvent;
+import cytoscape.data.SelectEventListener;
+
+import cytoscape.graph.layout.algorithm.MutablePolyEdgeGraphLayout;
+
+import cytoscape.util.CytoscapeAction;
+
+import cytoscape.view.CytoscapeDesktop;
+
+import cytoscape.view.cytopanels.BiModalJSplitPane;
+import cytoscape.view.cytopanels.CytoPanelImp;
+import cytoscape.view.cytopanels.CytoPanelListener;
+import cytoscape.view.cytopanels.CytoPanelState;
+
+import java.awt.Dimension;
+import java.awt.event.ActionEvent;
+
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+
+import java.util.HashSet;
+import java.util.Set;
+
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JCheckBox;
+import javax.swing.JMenu;
+import javax.swing.JPanel;
+import javax.swing.JSplitPane;
+import javax.swing.SwingConstants;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+
+
+public class CheckBoxTracker implements SelectEventListener, PropertyChangeListener {
+ private JCheckBox jCheckBox;
+ private Set<String> listeningNetworks;
+
+ public CheckBoxTracker(JCheckBox j) {
+ jCheckBox = j;
+ listeningNetworks = new HashSet<String>();
+ Cytoscape.getDesktop().getNetworkViewManager().getSwingPropertyChangeSupport()
+ .addPropertyChangeListener(CytoscapeDesktop.NETWORK_VIEW_FOCUSED,this);
+ }
+
+ public void onSelectEvent(SelectEvent event) {
+ jCheckBox.setSelected(Cytoscape.getCurrentNetworkView().getSelectedNodeIndices().length > 0);
+ }
+
+ public void propertyChange(PropertyChangeEvent e) {
+ if (e.getPropertyName() == CytoscapeDesktop.NETWORK_VIEW_FOCUSED) {
+ CyNetwork curr = Cytoscape.getCurrentNetwork();
+ String nid = curr.getIdentifier();
+
+ // only add this as a listener if it hasn't been done already
+ if ( !listeningNetworks.contains(nid) )
+ curr.addSelectEventListener(this);
+
+ // to make sure we're set intially
+ onSelectEvent(null);
+ }
+ }
+}
diff --git a/coreplugins/ManualLayout/src/main/java/ManualLayout/common/GraphConverter2.java b/coreplugins/ManualLayout/src/main/java/ManualLayout/common/GraphConverter2.java
new file mode 100644
index 0000000..ab6233b
--- /dev/null
+++ b/coreplugins/ManualLayout/src/main/java/ManualLayout/common/GraphConverter2.java
@@ -0,0 +1,302 @@
+/*
+ File: GraphConverter2.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Pasteur Institute
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package ManualLayout.common;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.graph.fixed.FixedGraph;
+
+import cytoscape.graph.layout.algorithm.MutablePolyEdgeGraphLayout;
+
+import cytoscape.util.intr.IntEnumerator;
+import cytoscape.util.intr.IntIterator;
+
+import cytoscape.view.CyNetworkView;
+
+import giny.view.EdgeView;
+import giny.view.NodeView;
+
+import java.awt.geom.Point2D;
+
+import java.util.Iterator;
+import java.util.List;
+
+
+/**
+ *
+ */
+public final class GraphConverter2 {
+ private GraphConverter2() {
+ }
+
+ /**
+ * Returns a representation of Cytoscape's current network view.
+ * Returns a MutablePolyEdgeGraphLayout, which, when mutated,
+ * has a direct effect on the underlying Cytoscape network view. You'd
+ * sure as heck better be using the returned object from the AWT event
+ * dispatch thread! Better yet, lock the Cytoscape desktop somehow
+ * (with a modal dialog for example) while using this returned object.
+ * Movable nodes are defined to be selected nodes in Cytoscape - if no
+ * nodes are selected then all nodes are movable. If selected node
+ * information changes while we have a reference to this return object,
+ * then the movability of corresponding node also changes. This is one
+ * reason why it's important to lock the Cytoscape desktop while operating
+ * on this return object.
+ **/
+ public static MutablePolyEdgeGraphLayout getGraphReference(double percentBorder,
+ boolean preserveEdgeAnchors,
+ boolean onlySelectedNodesMovable) {
+ if (percentBorder < 0.0d)
+ throw new IllegalArgumentException("percentBorder < 0.0");
+
+ double minX = Double.MAX_VALUE;
+ double maxX = Double.MIN_VALUE;
+ double minY = Double.MAX_VALUE;
+ double maxY = Double.MIN_VALUE;
+ final CyNetworkView graphView = Cytoscape.getCurrentNetworkView();
+ Iterator iter = graphView.getNodeViewsIterator();
+
+ while (iter.hasNext()) {
+ NodeView currentNodeView = (NodeView) iter.next();
+ minX = Math.min(minX, currentNodeView.getXPosition());
+ maxX = Math.max(maxX, currentNodeView.getXPosition());
+ minY = Math.min(minY, currentNodeView.getYPosition());
+ maxY = Math.max(maxY, currentNodeView.getYPosition());
+ }
+
+ iter = graphView.getEdgeViewsIterator();
+
+ final boolean noNodesSelected = (!onlySelectedNodesMovable)
+ || (graphView.getSelectedNodeIndices().length == 0);
+
+ while (iter.hasNext()) {
+ EdgeView currentEdgeView = (EdgeView) iter.next();
+
+ if ((!preserveEdgeAnchors)
+ && (noNodesSelected
+ || graphView.getNodeView(currentEdgeView.getEdge().getSource()).isSelected()
+ || graphView.getNodeView(currentEdgeView.getEdge().getTarget()).isSelected())) {
+ currentEdgeView.getBend().removeAllHandles();
+ } else {
+ List handles = currentEdgeView.getBend().getHandles();
+
+ for (int h = 0; h < handles.size(); h++) {
+ Point2D point = (Point2D) handles.get(h);
+ minX = Math.min(minX, point.getX());
+ maxX = Math.max(maxX, point.getX());
+ minY = Math.min(minY, point.getY());
+ maxY = Math.max(maxY, point.getY());
+ }
+ }
+ }
+
+ double border = Math.max(maxX - minX, maxY - minY) * percentBorder * 0.5d;
+ final double width = maxX - minX + border + border;
+ final double height = maxY - minY + border + border;
+ final double xOff = minX - border;
+ final double yOff = minY - border;
+
+ final FixedGraph fixedGraph = (FixedGraph) (graphView.getNetwork());
+
+ return new MutablePolyEdgeGraphLayout() {
+ // FixedGraph methods.
+ public IntEnumerator nodes() {
+ return fixedGraph.nodes();
+ }
+
+ public IntEnumerator edges() {
+ return fixedGraph.edges();
+ }
+
+ public boolean nodeExists(int node) {
+ return fixedGraph.nodeExists(node);
+ }
+
+ public byte edgeType(int edge) {
+ return fixedGraph.edgeType(edge);
+ }
+
+ public int edgeSource(int edge) {
+ return fixedGraph.edgeSource(edge);
+ }
+
+ public int edgeTarget(int edge) {
+ return fixedGraph.edgeTarget(edge);
+ }
+
+ public IntEnumerator edgesAdjacent(int node, boolean out, boolean in, boolean undir) {
+ return fixedGraph.edgesAdjacent(node, out, in, undir);
+ }
+
+ public IntIterator edgesConnecting(int node0, int node1, boolean out, boolean in,
+ boolean undir) {
+ return fixedGraph.edgesConnecting(node0, node1, out, in, undir);
+ }
+
+ // GraphLayout methods.
+ public double getMaxWidth() {
+ return width;
+ }
+
+ public double getMaxHeight() {
+ return height;
+ }
+
+ public double getNodePosition(int node, boolean xPosition) {
+ NodeView nodeView = getNodeView(node);
+
+ if (xPosition)
+ return nodeView.getXPosition() - xOff;
+
+ return nodeView.getYPosition() - yOff;
+ }
+
+ // MutableGraphLayout methods.
+ public boolean isMovableNode(int node) {
+ NodeView nodeView = getNodeView(node);
+
+ if (noNodesSelected)
+ return true;
+
+ return nodeView.isSelected();
+ }
+
+ public void setNodePosition(int node, double xPos, double yPos) {
+ NodeView nodeView = getNodeView(node);
+ checkPosition(xPos, yPos);
+
+ if (!isMovableNode(node))
+ throw new UnsupportedOperationException("node " + node + " is not movable");
+
+ nodeView.setXPosition(xPos + xOff);
+ nodeView.setYPosition(yPos + yOff);
+ }
+
+ // PolyEdgeGraphLayout methods.
+ public int getNumAnchors(int edge) {
+ return getEdgeView(edge).getBend().getHandles().size();
+ }
+
+ public double getAnchorPosition(int edge, int anchorIndex, boolean xPosition) {
+ Point2D point = (Point2D) getEdgeView(edge).getBend().getHandles()
+ .get(anchorIndex);
+
+ return (xPosition ? (point.getX() - xOff) : (point.getY() - yOff));
+ }
+
+ // MutablePolyEdgeGraphLayout methods.
+ public void deleteAnchor(int edge, int anchorIndex) {
+ checkAnchorIndexBounds(edge, anchorIndex, false);
+ checkMutableAnchor(edge);
+ getEdgeView(edge).getBend().removeHandle(anchorIndex);
+ }
+
+ public void createAnchor(int edge, int anchorIndex) {
+ checkAnchorIndexBounds(edge, anchorIndex, true);
+ checkMutableAnchor(edge);
+ getEdgeView(edge).getBend().addHandle(anchorIndex, new Point2D.Double());
+
+ Point2D src = ((anchorIndex == 0)
+ ? (new Point2D.Double(getNodePosition(edgeSource(edge), true),
+ getNodePosition(edgeSource(edge), false)))
+ : (new Point2D.Double(getAnchorPosition(edge, anchorIndex - 1,
+ true),
+ getAnchorPosition(edge, anchorIndex - 1,
+ false))));
+ Point2D trg = ((anchorIndex == (getNumAnchors(edge) - 1))
+ ? (new Point2D.Double(getNodePosition(edgeTarget(edge), true),
+ getNodePosition(edgeTarget(edge), false)))
+ : (new Point2D.Double(getAnchorPosition(edge, anchorIndex + 1,
+ true),
+ getAnchorPosition(edge, anchorIndex + 1,
+ false))));
+ setAnchorPosition(edge, anchorIndex, (src.getX() + trg.getX()) / 2.0d,
+ (src.getY() + trg.getY()) / 2.0d);
+ }
+
+ public void setAnchorPosition(int edge, int anchorIndex, double xPos, double yPos) {
+ checkAnchorIndexBounds(edge, anchorIndex, false);
+ checkMutableAnchor(edge);
+ checkPosition(xPos, yPos);
+ getEdgeView(edge).getBend()
+ .moveHandle(anchorIndex, new Point2D.Double(xPos + xOff, yPos + yOff));
+ }
+
+ // Helper methods.
+ private NodeView getNodeView(int node) {
+ NodeView nodeView = graphView.getNodeView(~node);
+
+ if (nodeView == null)
+ throw new IllegalArgumentException("node " + node + " not in this graph");
+
+ return nodeView;
+ }
+
+ private EdgeView getEdgeView(int edge) {
+ EdgeView edgeView = graphView.getEdgeView(~edge);
+
+ if (edgeView == null)
+ throw new IllegalArgumentException("edge " + edge + " not in this graph");
+
+ return edgeView;
+ }
+
+ private void checkPosition(double xPos, double yPos) {
+ if (Double.isNaN(xPos) || (xPos < 0.0d) || (xPos > getMaxWidth()))
+ throw new IllegalArgumentException("X position out of bounds");
+
+ if (Double.isNaN(yPos) || (yPos < 0.0d) || (yPos > getMaxHeight()))
+ throw new IllegalArgumentException("Y position out of bounds");
+ }
+
+ private void checkAnchorIndexBounds(int edge, int anchorIndex, boolean create) {
+ int numAnchors = getNumAnchors(edge) + (create ? 0 : (-1));
+
+ if ((anchorIndex < 0) || (anchorIndex > numAnchors))
+ throw new IndexOutOfBoundsException("anchor index out of bounds");
+ }
+
+ private void checkMutableAnchor(int edge) {
+ int srcNode = edgeSource(edge);
+ int trgNode = edgeTarget(edge);
+
+ if ((!isMovableNode(srcNode)) && (!isMovableNode(trgNode)))
+ throw new UnsupportedOperationException("anchors at specified edge cannot be changed");
+ }
+ };
+ }
+}
diff --git a/coreplugins/ManualLayout/src/main/java/ManualLayout/common/PolymorphicSlider.java b/coreplugins/ManualLayout/src/main/java/ManualLayout/common/PolymorphicSlider.java
new file mode 100644
index 0000000..09bf9ec
--- /dev/null
+++ b/coreplugins/ManualLayout/src/main/java/ManualLayout/common/PolymorphicSlider.java
@@ -0,0 +1,43 @@
+
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package ManualLayout.common;
+
+public interface PolymorphicSlider {
+ public void updateSlider(int x);
+ public int getSliderValue();
+}
diff --git a/coreplugins/ManualLayout/src/main/java/ManualLayout/common/SliderStateTracker.java b/coreplugins/ManualLayout/src/main/java/ManualLayout/common/SliderStateTracker.java
new file mode 100644
index 0000000..83c2370
--- /dev/null
+++ b/coreplugins/ManualLayout/src/main/java/ManualLayout/common/SliderStateTracker.java
@@ -0,0 +1,131 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package ManualLayout.common;
+
+import ManualLayout.rotate.RotatePanel;
+import ManualLayout.rotate.RotationLayouter;
+
+import ManualLayout.scale.ScaleLayouter;
+import ManualLayout.scale.ScalePanel;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.data.SelectEvent;
+import cytoscape.data.SelectEventListener;
+
+import cytoscape.graph.layout.algorithm.MutablePolyEdgeGraphLayout;
+
+import cytoscape.util.CytoscapeAction;
+
+import cytoscape.view.CytoscapeDesktop;
+import cytoscape.view.CyNetworkView;
+
+import cytoscape.view.cytopanels.BiModalJSplitPane;
+import cytoscape.view.cytopanels.CytoPanelImp;
+import cytoscape.view.cytopanels.CytoPanelListener;
+import cytoscape.view.cytopanels.CytoPanelState;
+
+import java.awt.Dimension;
+import java.awt.event.ActionEvent;
+
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+
+import java.util.HashMap;
+import java.util.Map;
+
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JCheckBox;
+import javax.swing.JSlider;
+import javax.swing.JMenu;
+import javax.swing.JPanel;
+import javax.swing.JSplitPane;
+import javax.swing.SwingConstants;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+
+
+/**
+ *
+ */
+public class SliderStateTracker implements PropertyChangeListener {
+
+ String preFocusedViewId;
+ Map<String,Integer> layoutStateMap;
+ PolymorphicSlider slider;
+
+ public SliderStateTracker(PolymorphicSlider s) {
+ Cytoscape.getDesktop().getNetworkViewManager().getSwingPropertyChangeSupport()
+ .addPropertyChangeListener(CytoscapeDesktop.NETWORK_VIEW_FOCUSED,this);
+ layoutStateMap = new HashMap<String,Integer>();
+ preFocusedViewId = "none";
+ slider = s;
+ }
+
+ /**
+ * Keep track of the state for each view focused.
+ */
+ public void propertyChange(PropertyChangeEvent e) {
+ if (e.getPropertyName() == CytoscapeDesktop.NETWORK_VIEW_FOCUSED) {
+ CyNetworkView curr = Cytoscape.getCurrentNetworkView();
+
+ if ( curr == null || curr == Cytoscape.getNullNetworkView() )
+ return;
+
+ String curFocusedViewId = curr.getIdentifier();
+
+ // detect duplicate NETWORK_VIEW_FOCUSED event
+ if (preFocusedViewId.equals(curFocusedViewId)) {
+ return;
+ }
+
+ //save layout state for the previous network view
+ layoutStateMap.put(preFocusedViewId, slider.getSliderValue());
+
+ //Restore layout state for the current network view, if any
+ Integer stateValue = layoutStateMap.get(curFocusedViewId);
+
+ if (stateValue == null) {
+ slider.updateSlider(0);
+ } else {
+ slider.updateSlider(stateValue.intValue());
+ }
+
+ preFocusedViewId = curFocusedViewId;
+ }
+ }
+}
diff --git a/coreplugins/ManualLayout/src/main/java/ManualLayout/common/SliderTracker.java b/coreplugins/ManualLayout/src/main/java/ManualLayout/common/SliderTracker.java
new file mode 100644
index 0000000..ecbcb61
--- /dev/null
+++ b/coreplugins/ManualLayout/src/main/java/ManualLayout/common/SliderTracker.java
@@ -0,0 +1,68 @@
+/*
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package ManualLayout.common;
+
+
+import cytoscape.Cytoscape;
+import cytoscape.CyNetwork;
+import cytoscape.data.SelectEvent;
+import cytoscape.data.SelectEventListener;
+import cytoscape.view.CytoscapeDesktop;
+
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+
+import javax.swing.JCheckBox;
+import javax.swing.JPanel;
+import javax.swing.JSlider;
+
+
+public class SliderTracker implements SelectEventListener, PropertyChangeListener {
+ private final JSlider slider;
+ private final JCheckBox controllingCheckBox;
+
+ public SliderTracker(final JSlider slider, final JCheckBox controllingCheckBox) {
+ this.slider = slider;
+ this.controllingCheckBox = controllingCheckBox;
+
+ Cytoscape.getDesktop().getNetworkViewManager().getSwingPropertyChangeSupport()
+ .addPropertyChangeListener(CytoscapeDesktop.NETWORK_VIEW_FOCUSED, this);
+ }
+
+ public void onSelectEvent(final SelectEvent event) {
+ final boolean currentNetworkHasSelectedNodes =
+ Cytoscape.getCurrentNetworkView().getSelectedNodeIndices().length > 0;
+
+ slider.setEnabled(!controllingCheckBox.isSelected() || currentNetworkHasSelectedNodes);
+ }
+
+ public void propertyChange(final PropertyChangeEvent e) {
+ if (e.getPropertyName() == CytoscapeDesktop.NETWORK_VIEW_FOCUSED)
+ Cytoscape.getCurrentNetwork().addSelectEventListener(this);
+ }
+}
diff --git a/coreplugins/ManualLayout/src/main/java/ManualLayout/control/ControlPanel.java b/coreplugins/ManualLayout/src/main/java/ManualLayout/control/ControlPanel.java
new file mode 100644
index 0000000..8447a94
--- /dev/null
+++ b/coreplugins/ManualLayout/src/main/java/ManualLayout/control/ControlPanel.java
@@ -0,0 +1,73 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package ManualLayout.control;
+
+import ManualLayout.control.view.AlignPanel;
+import ManualLayout.control.view.DistPanel;
+import ManualLayout.control.view.StackPanel;
+
+import cytoscape.Cytoscape;
+
+import java.awt.*;
+
+import javax.swing.JPanel;
+
+
+/**
+ *
+ * GUI for Align and Distribute of manualLayout
+ *
+ * Rewrite based on the class ControlAction 9/13/2006 Peng-Liang Wang
+ *
+ */
+public class ControlPanel extends JPanel {
+ /**
+ * Creates a new ControlPanel object.
+ */
+ public ControlPanel() {
+ setBorder(javax.swing.BorderFactory.createEmptyBorder(3, 3, 3, 3));
+
+ AlignPanel ap = new AlignPanel();
+ DistPanel dp = new DistPanel();
+ StackPanel sp = new StackPanel();
+
+ setLayout(new java.awt.GridLayout(3,1));
+ add(ap);
+ add(dp);
+ add(sp);
+ } // constructor
+} // End of class ControlPanel
diff --git a/coreplugins/ManualLayout/src/main/java/ManualLayout/control/ControlPanelAction.java b/coreplugins/ManualLayout/src/main/java/ManualLayout/control/ControlPanelAction.java
new file mode 100644
index 0000000..a200f97
--- /dev/null
+++ b/coreplugins/ManualLayout/src/main/java/ManualLayout/control/ControlPanelAction.java
@@ -0,0 +1,52 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package ManualLayout.control;
+
+import ManualLayout.common.AbstractManualLayoutAction;
+
+/**
+ * Action for the Align and Distribute functionality.
+ */
+public class ControlPanelAction extends AbstractManualLayoutAction {
+
+ /**
+ * Action for the Align and Distribute functionality. Should be in menu slot 2.
+ */
+ public ControlPanelAction() {
+ super("Align and Distribute",2);
+ }
+}
diff --git a/coreplugins/ManualLayout/src/main/java/ManualLayout/control/actions/AbstractControlAction.java b/coreplugins/ManualLayout/src/main/java/ManualLayout/control/actions/AbstractControlAction.java
new file mode 100644
index 0000000..ad4e79e
--- /dev/null
+++ b/coreplugins/ManualLayout/src/main/java/ManualLayout/control/actions/AbstractControlAction.java
@@ -0,0 +1,202 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package ManualLayout.control.actions;
+
+import cytoscape.*;
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+
+import cytoscape.data.*;
+
+import cytoscape.util.*;
+
+import cytoscape.view.*;
+import cytoscape.view.CyNetworkView;
+
+import giny.model.*;
+import giny.view.*;
+
+import ding.view.DGraphView;
+import ding.view.ViewChangeEdit;
+
+import java.awt.event.*;
+
+import java.util.*;
+
+import javax.swing.*;
+
+
+/**
+ *
+ */
+public abstract class AbstractControlAction extends CytoscapeAction {
+ protected double X_min;
+ protected double X_max;
+ protected double Y_min;
+ protected double Y_max;
+ protected NodeView node_view;
+ protected Iterator sel_nodes;
+ protected String title;
+
+ /**
+ * Creates a new AbstractControlAction object.
+ *
+ * @param icon DOCUMENT ME!
+ */
+ public AbstractControlAction(String title, ImageIcon icon) {
+ super("", icon);
+ this.title = title;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ GraphView view = Cytoscape.getCurrentNetworkView();
+ ViewChangeEdit vce = new ViewChangeEdit((DGraphView)view, title);
+ computeDimensions(view);
+ control(view.getSelectedNodes());
+ view.updateView();
+ vce.post();
+ }
+
+ protected abstract void control(List l);
+
+ /**
+ * This may look silly, but it is meant to be overridden
+ * with special cases.
+ */
+ protected double getX(NodeView n) {
+ return n.getXPosition();
+ }
+
+ /**
+ * This may look silly, but it is meant to be overridden
+ * with special cases.
+ */
+ protected double getY(NodeView n) {
+ return n.getYPosition();
+ }
+
+ protected void computeDimensions(GraphView view) {
+ X_min = Double.POSITIVE_INFINITY;
+ X_max = Double.NEGATIVE_INFINITY;
+ Y_min = Double.POSITIVE_INFINITY;
+ Y_max = Double.NEGATIVE_INFINITY;
+ sel_nodes = view.getSelectedNodes().iterator();
+
+ while (sel_nodes.hasNext()) {
+ node_view = (NodeView) sel_nodes.next();
+
+ double X = getX(node_view);
+
+ if (X > X_max)
+ X_max = X;
+
+ if (X < X_min)
+ X_min = X;
+
+ double Y = getY(node_view);
+
+ if (Y > Y_max)
+ Y_max = Y;
+
+ if (Y < Y_min)
+ Y_min = Y;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isInToolBar() {
+ return false;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isInMenuBar() {
+ return false;
+ }
+
+ public class XComparator implements Comparator<NodeView> {
+ public int compare(NodeView n1, NodeView n2) {
+ if (getX(n1) == getX(n2))
+ return 0;
+ else if (getX(n1) < getX(n2))
+ return -1;
+ else
+
+ return 1;
+ }
+
+ public boolean equals(NodeView n1, NodeView n2) {
+ if (getX(n1) == getX(n2))
+ return true;
+ else
+
+ return false;
+ }
+ }
+
+ public class YComparator implements Comparator<NodeView> {
+ public int compare(NodeView n1, NodeView n2) {
+ if (getY(n1) == getY(n2))
+ return 0;
+ else if (getY(n1) < getY(n2))
+ return -1;
+ else
+
+ return 1;
+ }
+
+ public boolean equals(NodeView n1, NodeView n2) {
+ if (getY(n1) == getY(n2))
+ return true;
+ else
+
+ return false;
+ }
+ }
+}
diff --git a/coreplugins/ManualLayout/src/main/java/ManualLayout/control/actions/align/HAlignCenter.java b/coreplugins/ManualLayout/src/main/java/ManualLayout/control/actions/align/HAlignCenter.java
new file mode 100644
index 0000000..9a0202f
--- /dev/null
+++ b/coreplugins/ManualLayout/src/main/java/ManualLayout/control/actions/align/HAlignCenter.java
@@ -0,0 +1,81 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package ManualLayout.control.actions.align;
+
+import ManualLayout.control.actions.AbstractControlAction;
+
+import cytoscape.*;
+
+import cytoscape.data.*;
+
+import cytoscape.util.*;
+
+import cytoscape.view.*;
+
+import giny.model.*;
+
+import giny.view.*;
+
+import java.awt.event.*;
+
+import java.util.*;
+
+import javax.swing.*;
+
+
+/**
+ *
+ */
+public class HAlignCenter extends AbstractControlAction {
+ /**
+ * Creates a new HAlignCenter object.
+ *
+ * @param i DOCUMENT ME!
+ */
+ public HAlignCenter(ImageIcon i) {
+ super("Horizontal Align Center",i);
+ }
+
+ protected void control(List nodes) {
+ Iterator sel_nodes = nodes.iterator();
+ double mid = (X_min + ((X_max - X_min) / 2));
+
+ while (sel_nodes.hasNext()) {
+ ((NodeView) sel_nodes.next()).setXPosition(mid);
+ }
+ }
+}
diff --git a/coreplugins/ManualLayout/src/main/java/ManualLayout/control/actions/align/HAlignLeft.java b/coreplugins/ManualLayout/src/main/java/ManualLayout/control/actions/align/HAlignLeft.java
new file mode 100644
index 0000000..73b2c8f
--- /dev/null
+++ b/coreplugins/ManualLayout/src/main/java/ManualLayout/control/actions/align/HAlignLeft.java
@@ -0,0 +1,92 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package ManualLayout.control.actions.align;
+
+import ManualLayout.control.actions.AbstractControlAction;
+
+import cytoscape.*;
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+
+import cytoscape.data.*;
+
+import cytoscape.util.*;
+
+import cytoscape.view.*;
+import cytoscape.view.CyNetworkView;
+
+import giny.model.*;
+
+import giny.view.*;
+
+import java.awt.event.*;
+
+import java.util.*;
+
+import javax.swing.*;
+
+
+/**
+ *
+ */
+public class HAlignLeft extends AbstractControlAction {
+ /**
+ * Creates a new HAlignLeft object.
+ *
+ * @param i DOCUMENT ME!
+ */
+ public HAlignLeft(ImageIcon i) {
+ super("Horizontal Align Left", i);
+ }
+
+ protected void control(List nodes) {
+ Iterator sel_nodes = nodes.iterator();
+
+ while (sel_nodes.hasNext()) {
+ NodeView n = (NodeView) sel_nodes.next();
+ double w = n.getWidth() / 2;
+ n.setXPosition(X_min + w);
+ }
+ }
+
+ protected double getX(NodeView n) {
+ double x = n.getXPosition();
+ double w = n.getWidth() / 2;
+
+ return x - w;
+ }
+}
diff --git a/coreplugins/ManualLayout/src/main/java/ManualLayout/control/actions/align/HAlignRight.java b/coreplugins/ManualLayout/src/main/java/ManualLayout/control/actions/align/HAlignRight.java
new file mode 100644
index 0000000..480abcd
--- /dev/null
+++ b/coreplugins/ManualLayout/src/main/java/ManualLayout/control/actions/align/HAlignRight.java
@@ -0,0 +1,89 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package ManualLayout.control.actions.align;
+
+import ManualLayout.control.actions.AbstractControlAction;
+
+import cytoscape.*;
+
+import cytoscape.data.*;
+
+import cytoscape.util.*;
+
+import cytoscape.view.*;
+
+import giny.model.*;
+
+import giny.view.*;
+
+import java.awt.event.*;
+
+import java.util.*;
+
+import javax.swing.*;
+
+
+/**
+ *
+ */
+public class HAlignRight extends AbstractControlAction {
+ /**
+ * Creates a new HAlignRight object.
+ *
+ * @param i DOCUMENT ME!
+ */
+ public HAlignRight(ImageIcon i) {
+ super("Horizontal Align Right", i);
+ }
+
+ protected void control(List nodes) {
+ Iterator sel_nodes = nodes.iterator();
+
+ while (sel_nodes.hasNext()) {
+ NodeView n = (NodeView) sel_nodes.next();
+ double w = n.getWidth() / 2;
+ n.setXPosition(X_max - w);
+ }
+ }
+
+ protected double getX(NodeView n) {
+ double x = n.getXPosition();
+ double w = n.getWidth() / 2;
+
+ return x + w;
+ }
+}
diff --git a/coreplugins/ManualLayout/src/main/java/ManualLayout/control/actions/align/VAlignBottom.java b/coreplugins/ManualLayout/src/main/java/ManualLayout/control/actions/align/VAlignBottom.java
new file mode 100644
index 0000000..c3a0197
--- /dev/null
+++ b/coreplugins/ManualLayout/src/main/java/ManualLayout/control/actions/align/VAlignBottom.java
@@ -0,0 +1,89 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package ManualLayout.control.actions.align;
+
+import ManualLayout.control.actions.AbstractControlAction;
+
+import cytoscape.*;
+
+import cytoscape.data.*;
+
+import cytoscape.util.*;
+
+import cytoscape.view.*;
+
+import giny.model.*;
+
+import giny.view.*;
+
+import java.awt.event.*;
+
+import java.util.*;
+
+import javax.swing.*;
+
+
+/**
+ *
+ */
+public class VAlignBottom extends AbstractControlAction {
+ /**
+ * Creates a new VAlignBottom object.
+ *
+ * @param i DOCUMENT ME!
+ */
+ public VAlignBottom(ImageIcon i) {
+ super("Vertical Align Bottom", i);
+ }
+
+ protected void control(List nodes) {
+ Iterator sel_nodes = nodes.iterator();
+
+ while (sel_nodes.hasNext()) {
+ NodeView n = (NodeView) sel_nodes.next();
+ double h = n.getHeight() / 2;
+ n.setYPosition(Y_max - h);
+ }
+ }
+
+ protected double getY(NodeView n) {
+ double y = n.getYPosition();
+ double h = n.getHeight() / 2;
+
+ return y + h;
+ }
+}
diff --git a/coreplugins/ManualLayout/src/main/java/ManualLayout/control/actions/align/VAlignCenter.java b/coreplugins/ManualLayout/src/main/java/ManualLayout/control/actions/align/VAlignCenter.java
new file mode 100644
index 0000000..784a612
--- /dev/null
+++ b/coreplugins/ManualLayout/src/main/java/ManualLayout/control/actions/align/VAlignCenter.java
@@ -0,0 +1,81 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package ManualLayout.control.actions.align;
+
+import ManualLayout.control.actions.AbstractControlAction;
+
+import cytoscape.*;
+
+import cytoscape.data.*;
+
+import cytoscape.util.*;
+
+import cytoscape.view.*;
+
+import giny.model.*;
+
+import giny.view.*;
+
+import java.awt.event.*;
+
+import java.util.*;
+
+import javax.swing.*;
+
+
+/**
+ *
+ */
+public class VAlignCenter extends AbstractControlAction {
+ /**
+ * Creates a new VAlignCenter object.
+ *
+ * @param i DOCUMENT ME!
+ */
+ public VAlignCenter(ImageIcon i) {
+ super("Vertical Align Center", i);
+ }
+
+ protected void control(List nodes) {
+ Iterator sel_nodes = nodes.iterator();
+ double mid = Y_min + ((Y_max - Y_min) / 2);
+
+ while (sel_nodes.hasNext()) {
+ ((NodeView) sel_nodes.next()).setYPosition(mid);
+ }
+ }
+}
diff --git a/coreplugins/ManualLayout/src/main/java/ManualLayout/control/actions/align/VAlignTop.java b/coreplugins/ManualLayout/src/main/java/ManualLayout/control/actions/align/VAlignTop.java
new file mode 100644
index 0000000..1ab23a2
--- /dev/null
+++ b/coreplugins/ManualLayout/src/main/java/ManualLayout/control/actions/align/VAlignTop.java
@@ -0,0 +1,89 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package ManualLayout.control.actions.align;
+
+import ManualLayout.control.actions.AbstractControlAction;
+
+import cytoscape.*;
+
+import cytoscape.data.*;
+
+import cytoscape.util.*;
+
+import cytoscape.view.*;
+
+import giny.model.*;
+
+import giny.view.*;
+
+import java.awt.event.*;
+
+import java.util.*;
+
+import javax.swing.*;
+
+
+/**
+ *
+ */
+public class VAlignTop extends AbstractControlAction {
+ /**
+ * Creates a new VAlignTop object.
+ *
+ * @param i DOCUMENT ME!
+ */
+ public VAlignTop(ImageIcon i) {
+ super("Vertical Align Top", i);
+ }
+
+ protected void control(List nodes) {
+ Iterator sel_nodes = nodes.iterator();
+
+ while (sel_nodes.hasNext()) {
+ NodeView n = (NodeView) sel_nodes.next();
+ double h = n.getHeight() / 2;
+ n.setYPosition(Y_min + h);
+ }
+ }
+
+ protected double getY(NodeView n) {
+ double y = n.getYPosition();
+ double h = n.getHeight() / 2;
+
+ return y - h;
+ }
+}
diff --git a/coreplugins/ManualLayout/src/main/java/ManualLayout/control/actions/dist/HDistCenter.java b/coreplugins/ManualLayout/src/main/java/ManualLayout/control/actions/dist/HDistCenter.java
new file mode 100644
index 0000000..7c1a280
--- /dev/null
+++ b/coreplugins/ManualLayout/src/main/java/ManualLayout/control/actions/dist/HDistCenter.java
@@ -0,0 +1,86 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package ManualLayout.control.actions.dist;
+
+import ManualLayout.control.actions.AbstractControlAction;
+
+import cytoscape.*;
+
+import cytoscape.data.*;
+
+import cytoscape.util.*;
+
+import cytoscape.view.*;
+
+import giny.model.*;
+
+import giny.view.*;
+
+import java.awt.event.*;
+
+import java.util.*;
+
+import javax.swing.*;
+
+
+/**
+ *
+ */
+public class HDistCenter extends AbstractControlAction {
+ /**
+ * Creates a new HDistCenter object.
+ *
+ * @param icon DOCUMENT ME!
+ */
+ public HDistCenter(ImageIcon icon) {
+ super("Horizontal Distritbute Center", icon);
+ }
+
+ protected void control(List nodes) {
+ if (nodes.size() <= 1)
+ return;
+
+ Collections.sort(nodes, new XComparator());
+
+ double d = X_max - X_min;
+ d = d / (nodes.size() - 1);
+
+ for (int i = 0; i < nodes.size(); i++) {
+ ((NodeView) nodes.get(i)).setXPosition(X_min + (i * d));
+ }
+ }
+}
diff --git a/coreplugins/ManualLayout/src/main/java/ManualLayout/control/actions/dist/HDistLeft.java b/coreplugins/ManualLayout/src/main/java/ManualLayout/control/actions/dist/HDistLeft.java
new file mode 100644
index 0000000..c3b6af4
--- /dev/null
+++ b/coreplugins/ManualLayout/src/main/java/ManualLayout/control/actions/dist/HDistLeft.java
@@ -0,0 +1,95 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package ManualLayout.control.actions.dist;
+
+import ManualLayout.control.actions.AbstractControlAction;
+
+import cytoscape.*;
+
+import cytoscape.data.*;
+
+import cytoscape.util.*;
+
+import cytoscape.view.*;
+
+import giny.model.*;
+
+import giny.view.*;
+
+import java.awt.event.*;
+
+import java.util.*;
+
+import javax.swing.*;
+
+
+/**
+ *
+ */
+public class HDistLeft extends AbstractControlAction {
+ /**
+ * Creates a new HDistLeft object.
+ *
+ * @param icon DOCUMENT ME!
+ */
+ public HDistLeft(ImageIcon icon) {
+ super("Horizontal Distribute Left", icon);
+ }
+
+ protected void control(List nodes) {
+ if (nodes.size() <= 1)
+ return;
+
+ Collections.sort(nodes, new XComparator());
+
+ double d = X_max - X_min;
+ d = d / (nodes.size() - 1);
+
+ for (int i = 0; i < nodes.size(); i++) {
+ NodeView n = (NodeView) nodes.get(i);
+ double w = n.getWidth() / 2;
+ n.setXPosition(X_min + (i * d) + w);
+ }
+ }
+
+ protected double getX(NodeView n) {
+ double x = n.getXPosition();
+ double w = n.getWidth() / 2;
+
+ return x - w;
+ }
+}
diff --git a/coreplugins/ManualLayout/src/main/java/ManualLayout/control/actions/dist/HDistRight.java b/coreplugins/ManualLayout/src/main/java/ManualLayout/control/actions/dist/HDistRight.java
new file mode 100644
index 0000000..8f2ca3a
--- /dev/null
+++ b/coreplugins/ManualLayout/src/main/java/ManualLayout/control/actions/dist/HDistRight.java
@@ -0,0 +1,95 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package ManualLayout.control.actions.dist;
+
+import ManualLayout.control.actions.AbstractControlAction;
+
+import cytoscape.*;
+
+import cytoscape.data.*;
+
+import cytoscape.util.*;
+
+import cytoscape.view.*;
+
+import giny.model.*;
+
+import giny.view.*;
+
+import java.awt.event.*;
+
+import java.util.*;
+
+import javax.swing.*;
+
+
+/**
+ *
+ */
+public class HDistRight extends AbstractControlAction {
+ /**
+ * Creates a new HDistRight object.
+ *
+ * @param icon DOCUMENT ME!
+ */
+ public HDistRight(ImageIcon icon) {
+ super("Horizontal Distribute Right", icon);
+ }
+
+ protected void control(List nodes) {
+ if (nodes.size() <= 1)
+ return;
+
+ Collections.sort(nodes, new XComparator());
+
+ double d = X_max - X_min;
+ d = d / (nodes.size() - 1);
+
+ for (int i = 0; i < nodes.size(); i++) {
+ NodeView n = (NodeView) nodes.get(i);
+ double w = n.getWidth() / 2;
+ n.setXPosition((X_min + (i * d)) - w);
+ }
+ }
+
+ protected double getX(NodeView n) {
+ double x = n.getXPosition();
+ double w = n.getWidth() / 2;
+
+ return x + w;
+ }
+}
diff --git a/coreplugins/ManualLayout/src/main/java/ManualLayout/control/actions/dist/VDistBottom.java b/coreplugins/ManualLayout/src/main/java/ManualLayout/control/actions/dist/VDistBottom.java
new file mode 100644
index 0000000..967fd3e
--- /dev/null
+++ b/coreplugins/ManualLayout/src/main/java/ManualLayout/control/actions/dist/VDistBottom.java
@@ -0,0 +1,95 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package ManualLayout.control.actions.dist;
+
+import ManualLayout.control.actions.AbstractControlAction;
+
+import cytoscape.*;
+
+import cytoscape.data.*;
+
+import cytoscape.util.*;
+
+import cytoscape.view.*;
+
+import giny.model.*;
+
+import giny.view.*;
+
+import java.awt.event.*;
+
+import java.util.*;
+
+import javax.swing.*;
+
+
+/**
+ *
+ */
+public class VDistBottom extends AbstractControlAction {
+ /**
+ * Creates a new VDistBottom object.
+ *
+ * @param icon DOCUMENT ME!
+ */
+ public VDistBottom(ImageIcon icon) {
+ super("Vertical Distribute Bottom", icon);
+ }
+
+ protected void control(List nodes) {
+ if (nodes.size() <= 1)
+ return;
+
+ Collections.sort(nodes, new YComparator());
+
+ double d = Y_max - Y_min;
+ d = d / (nodes.size() - 1);
+
+ for (int i = 0; i < nodes.size(); i++) {
+ NodeView n = (NodeView) nodes.get(i);
+ double h = n.getHeight() / 2;
+ n.setYPosition((Y_min + (i * d)) - h);
+ }
+ }
+
+ protected double getY(NodeView n) {
+ double y = n.getYPosition();
+ double h = n.getHeight() / 2;
+
+ return y + h;
+ }
+}
diff --git a/coreplugins/ManualLayout/src/main/java/ManualLayout/control/actions/dist/VDistCenter.java b/coreplugins/ManualLayout/src/main/java/ManualLayout/control/actions/dist/VDistCenter.java
new file mode 100644
index 0000000..e26c650
--- /dev/null
+++ b/coreplugins/ManualLayout/src/main/java/ManualLayout/control/actions/dist/VDistCenter.java
@@ -0,0 +1,86 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package ManualLayout.control.actions.dist;
+
+import ManualLayout.control.actions.AbstractControlAction;
+
+import cytoscape.*;
+
+import cytoscape.data.*;
+
+import cytoscape.util.*;
+
+import cytoscape.view.*;
+
+import giny.model.*;
+
+import giny.view.*;
+
+import java.awt.event.*;
+
+import java.util.*;
+
+import javax.swing.*;
+
+
+/**
+ *
+ */
+public class VDistCenter extends AbstractControlAction {
+ /**
+ * Creates a new VDistCenter object.
+ *
+ * @param icon DOCUMENT ME!
+ */
+ public VDistCenter(ImageIcon icon) {
+ super("Veritcal Distribute Center", icon);
+ }
+
+ protected void control(List nodes) {
+ if (nodes.size() <= 1)
+ return;
+
+ Collections.sort(nodes, new YComparator());
+
+ double d = Y_max - Y_min;
+ d = d / (nodes.size() - 1);
+
+ for (int i = 0; i < nodes.size(); i++) {
+ ((NodeView) nodes.get(i)).setYPosition(Y_min + (i * d));
+ }
+ }
+}
diff --git a/coreplugins/ManualLayout/src/main/java/ManualLayout/control/actions/dist/VDistTop.java b/coreplugins/ManualLayout/src/main/java/ManualLayout/control/actions/dist/VDistTop.java
new file mode 100644
index 0000000..126f8ca
--- /dev/null
+++ b/coreplugins/ManualLayout/src/main/java/ManualLayout/control/actions/dist/VDistTop.java
@@ -0,0 +1,95 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package ManualLayout.control.actions.dist;
+
+import ManualLayout.control.actions.AbstractControlAction;
+
+import cytoscape.*;
+
+import cytoscape.data.*;
+
+import cytoscape.util.*;
+
+import cytoscape.view.*;
+
+import giny.model.*;
+
+import giny.view.*;
+
+import java.awt.event.*;
+
+import java.util.*;
+
+import javax.swing.*;
+
+
+/**
+ *
+ */
+public class VDistTop extends AbstractControlAction {
+ /**
+ * Creates a new VDistTop object.
+ *
+ * @param icon DOCUMENT ME!
+ */
+ public VDistTop(ImageIcon icon) {
+ super("Vertical Districute Top", icon);
+ }
+
+ protected void control(List nodes) {
+ if (nodes.size() <= 1)
+ return;
+
+ Collections.sort(nodes, new YComparator());
+
+ double d = Y_max - Y_min;
+ d = d / (nodes.size() - 1);
+
+ for (int i = 0; i < nodes.size(); i++) {
+ NodeView n = (NodeView) nodes.get(i);
+ double h = n.getHeight() / 2;
+ n.setYPosition(Y_min + (i * d) + h);
+ }
+ }
+
+ protected double getY(NodeView n) {
+ double y = n.getYPosition();
+ double h = n.getHeight() / 2;
+
+ return y - h;
+ }
+}
diff --git a/coreplugins/ManualLayout/src/main/java/ManualLayout/control/actions/stack/HStackBottom.java b/coreplugins/ManualLayout/src/main/java/ManualLayout/control/actions/stack/HStackBottom.java
new file mode 100644
index 0000000..485f6e4
--- /dev/null
+++ b/coreplugins/ManualLayout/src/main/java/ManualLayout/control/actions/stack/HStackBottom.java
@@ -0,0 +1,95 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package ManualLayout.control.actions.stack;
+
+import ManualLayout.control.actions.AbstractControlAction;
+
+import cytoscape.*;
+
+import cytoscape.data.*;
+
+import cytoscape.util.*;
+
+import cytoscape.view.*;
+
+import giny.model.*;
+
+import giny.view.*;
+
+import java.awt.event.*;
+
+import java.util.*;
+
+import javax.swing.*;
+
+
+/**
+ *
+ */
+public class HStackBottom extends AbstractControlAction {
+ /**
+ * Creates a new VStack object.
+ *
+ * @param icon DOCUMENT ME!
+ */
+ public HStackBottom(ImageIcon icon) {
+ super("Horizontal Stack", icon);
+ }
+
+ protected void control(List nodes) {
+ if (nodes.size() <= 1)
+ return;
+
+ Collections.sort(nodes, new XComparator());
+
+
+ //Note: X, Y are at node centers
+ for (int i = 1; i < nodes.size(); i++) {
+ ((NodeView) nodes.get(i)).setXPosition(
+ ((NodeView) nodes.get(i-1)).getXPosition() +
+ ((NodeView) nodes.get(i-1)).getWidth() *0.5 +
+ ((NodeView) nodes.get(i)).getWidth() * 0.5
+ );
+ ((NodeView) nodes.get(i)).setYPosition(
+ ((NodeView) nodes.get(i-1)).getYPosition() +
+ ((NodeView) nodes.get(i-1)).getHeight() * 0.5 -
+ ((NodeView) nodes.get(i)).getHeight() * 0.5
+ );
+
+ }
+ }
+}
diff --git a/coreplugins/ManualLayout/src/main/java/ManualLayout/control/actions/stack/HStackCenter.java b/coreplugins/ManualLayout/src/main/java/ManualLayout/control/actions/stack/HStackCenter.java
new file mode 100644
index 0000000..082adfb
--- /dev/null
+++ b/coreplugins/ManualLayout/src/main/java/ManualLayout/control/actions/stack/HStackCenter.java
@@ -0,0 +1,93 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package ManualLayout.control.actions.stack;
+
+import ManualLayout.control.actions.AbstractControlAction;
+
+import cytoscape.*;
+
+import cytoscape.data.*;
+
+import cytoscape.util.*;
+
+import cytoscape.view.*;
+
+import giny.model.*;
+
+import giny.view.*;
+
+import java.awt.event.*;
+
+import java.util.*;
+
+import javax.swing.*;
+
+
+/**
+ *
+ */
+public class HStackCenter extends AbstractControlAction {
+ /**
+ * Creates a new VStack object.
+ *
+ * @param icon DOCUMENT ME!
+ */
+ public HStackCenter(ImageIcon icon) {
+ super("Horizontal Stack", icon);
+ }
+
+ protected void control(List nodes) {
+ if (nodes.size() <= 1)
+ return;
+
+ Collections.sort(nodes, new XComparator());
+
+
+ //Note: X, Y are at node centers
+ for (int i = 1; i < nodes.size(); i++) {
+ ((NodeView) nodes.get(i)).setXPosition(
+ ((NodeView) nodes.get(i-1)).getXPosition() +
+ ((NodeView) nodes.get(i-1)).getWidth() *0.5 +
+ ((NodeView) nodes.get(i)).getWidth() * 0.5
+ );
+ ((NodeView) nodes.get(i)).setYPosition(
+ ((NodeView) nodes.get(i-1)).getYPosition()
+ );
+
+ }
+ }
+}
diff --git a/coreplugins/ManualLayout/src/main/java/ManualLayout/control/actions/stack/HStackTop.java b/coreplugins/ManualLayout/src/main/java/ManualLayout/control/actions/stack/HStackTop.java
new file mode 100644
index 0000000..99dfd48
--- /dev/null
+++ b/coreplugins/ManualLayout/src/main/java/ManualLayout/control/actions/stack/HStackTop.java
@@ -0,0 +1,95 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package ManualLayout.control.actions.stack;
+
+import ManualLayout.control.actions.AbstractControlAction;
+
+import cytoscape.*;
+
+import cytoscape.data.*;
+
+import cytoscape.util.*;
+
+import cytoscape.view.*;
+
+import giny.model.*;
+
+import giny.view.*;
+
+import java.awt.event.*;
+
+import java.util.*;
+
+import javax.swing.*;
+
+
+/**
+ *
+ */
+public class HStackTop extends AbstractControlAction {
+ /**
+ * Creates a new VStack object.
+ *
+ * @param icon DOCUMENT ME!
+ */
+ public HStackTop(ImageIcon icon) {
+ super("Horizontal Stack", icon);
+ }
+
+ protected void control(List nodes) {
+ if (nodes.size() <= 1)
+ return;
+
+ Collections.sort(nodes, new XComparator());
+
+
+ //Note: X, Y are at node centers
+ for (int i = 1; i < nodes.size(); i++) {
+ ((NodeView) nodes.get(i)).setXPosition(
+ ((NodeView) nodes.get(i-1)).getXPosition() +
+ ((NodeView) nodes.get(i-1)).getWidth() *0.5 +
+ ((NodeView) nodes.get(i)).getWidth() * 0.5
+ );
+ ((NodeView) nodes.get(i)).setYPosition(
+ ((NodeView) nodes.get(i-1)).getYPosition() -
+ ((NodeView) nodes.get(i-1)).getHeight() * 0.5 +
+ ((NodeView) nodes.get(i)).getHeight() * 0.5
+ );
+
+ }
+ }
+}
diff --git a/coreplugins/ManualLayout/src/main/java/ManualLayout/control/actions/stack/VStackCenter.java b/coreplugins/ManualLayout/src/main/java/ManualLayout/control/actions/stack/VStackCenter.java
new file mode 100644
index 0000000..6d5e57a
--- /dev/null
+++ b/coreplugins/ManualLayout/src/main/java/ManualLayout/control/actions/stack/VStackCenter.java
@@ -0,0 +1,96 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package ManualLayout.control.actions.stack;
+
+import ManualLayout.control.actions.AbstractControlAction;
+
+import cytoscape.*;
+
+import cytoscape.data.*;
+
+import cytoscape.util.*;
+
+import cytoscape.view.*;
+
+import giny.model.*;
+
+import giny.view.*;
+
+import java.awt.event.*;
+
+import java.util.*;
+
+import javax.swing.*;
+
+
+/**
+ *
+ */
+public class VStackCenter extends AbstractControlAction {
+ /**
+ * Creates a new VStack object.
+ *
+ * @param icon DOCUMENT ME!
+ */
+ public VStackCenter(ImageIcon icon) {
+ super("Veritcal Stack", icon);
+ }
+
+ protected void control(List nodes) {
+ if (nodes.size() <= 1)
+ return;
+
+ Collections.sort(nodes, new YComparator());
+
+
+// double d = Y_max - Y_min;
+// d = d / (nodes.size() - 1);
+
+ //Note: X, Y are at node centers
+ for (int i = 1; i < nodes.size(); i++) {
+ ((NodeView) nodes.get(i)).setYPosition(
+ ((NodeView) nodes.get(i-1)).getYPosition() +
+ ((NodeView) nodes.get(i-1)).getHeight() *0.5 +
+ ((NodeView) nodes.get(i)).getHeight() * 0.5
+ );
+ ((NodeView) nodes.get(i)).setXPosition(
+ ((NodeView) nodes.get(i-1)).getXPosition()
+ );
+
+ }
+ }
+}
diff --git a/coreplugins/ManualLayout/src/main/java/ManualLayout/control/actions/stack/VStackLeft.java b/coreplugins/ManualLayout/src/main/java/ManualLayout/control/actions/stack/VStackLeft.java
new file mode 100644
index 0000000..fc6aeea
--- /dev/null
+++ b/coreplugins/ManualLayout/src/main/java/ManualLayout/control/actions/stack/VStackLeft.java
@@ -0,0 +1,98 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package ManualLayout.control.actions.stack;
+
+import ManualLayout.control.actions.AbstractControlAction;
+
+import cytoscape.*;
+
+import cytoscape.data.*;
+
+import cytoscape.util.*;
+
+import cytoscape.view.*;
+
+import giny.model.*;
+
+import giny.view.*;
+
+import java.awt.event.*;
+
+import java.util.*;
+
+import javax.swing.*;
+
+
+/**
+ *
+ */
+public class VStackLeft extends AbstractControlAction {
+ /**
+ * Creates a new VStack object.
+ *
+ * @param icon DOCUMENT ME!
+ */
+ public VStackLeft(ImageIcon icon) {
+ super("Veritcal Stack", icon);
+ }
+
+ protected void control(List nodes) {
+ if (nodes.size() <= 1)
+ return;
+
+ Collections.sort(nodes, new YComparator());
+
+
+// double d = Y_max - Y_min;
+// d = d / (nodes.size() - 1);
+
+ //Note: X, Y are at node centers
+ for (int i = 1; i < nodes.size(); i++) {
+ ((NodeView) nodes.get(i)).setYPosition(
+ ((NodeView) nodes.get(i-1)).getYPosition() +
+ ((NodeView) nodes.get(i-1)).getHeight() *0.5 +
+ ((NodeView) nodes.get(i)).getHeight() * 0.5
+ );
+ ((NodeView) nodes.get(i)).setXPosition(
+ ((NodeView) nodes.get(i-1)).getXPosition() -
+ ((NodeView) nodes.get(i-1)).getWidth() * 0.5 +
+ ((NodeView) nodes.get(i)).getWidth() * 0.5
+ );
+
+ }
+ }
+}
diff --git a/coreplugins/ManualLayout/src/main/java/ManualLayout/control/actions/stack/VStackRight.java b/coreplugins/ManualLayout/src/main/java/ManualLayout/control/actions/stack/VStackRight.java
new file mode 100644
index 0000000..91aa94e
--- /dev/null
+++ b/coreplugins/ManualLayout/src/main/java/ManualLayout/control/actions/stack/VStackRight.java
@@ -0,0 +1,98 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package ManualLayout.control.actions.stack;
+
+import ManualLayout.control.actions.AbstractControlAction;
+
+import cytoscape.*;
+
+import cytoscape.data.*;
+
+import cytoscape.util.*;
+
+import cytoscape.view.*;
+
+import giny.model.*;
+
+import giny.view.*;
+
+import java.awt.event.*;
+
+import java.util.*;
+
+import javax.swing.*;
+
+
+/**
+ *
+ */
+public class VStackRight extends AbstractControlAction {
+ /**
+ * Creates a new VStack object.
+ *
+ * @param icon DOCUMENT ME!
+ */
+ public VStackRight(ImageIcon icon) {
+ super("Veritcal Stack", icon);
+ }
+
+ protected void control(List nodes) {
+ if (nodes.size() <= 1)
+ return;
+
+ Collections.sort(nodes, new YComparator());
+
+
+// double d = Y_max - Y_min;
+// d = d / (nodes.size() - 1);
+
+ //Note: X, Y are at node centers
+ for (int i = 1; i < nodes.size(); i++) {
+ ((NodeView) nodes.get(i)).setYPosition(
+ ((NodeView) nodes.get(i-1)).getYPosition() +
+ ((NodeView) nodes.get(i-1)).getHeight() *0.5 +
+ ((NodeView) nodes.get(i)).getHeight() * 0.5
+ );
+ ((NodeView) nodes.get(i)).setXPosition(
+ ((NodeView) nodes.get(i-1)).getXPosition() +
+ ((NodeView) nodes.get(i-1)).getWidth() * 0.5 -
+ ((NodeView) nodes.get(i)).getWidth() * 0.5
+ );
+
+ }
+ }
+}
diff --git a/coreplugins/ManualLayout/src/main/java/ManualLayout/control/view/AlignPanel.java b/coreplugins/ManualLayout/src/main/java/ManualLayout/control/view/AlignPanel.java
new file mode 100644
index 0000000..ceaced0
--- /dev/null
+++ b/coreplugins/ManualLayout/src/main/java/ManualLayout/control/view/AlignPanel.java
@@ -0,0 +1,97 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package ManualLayout.control.view;
+
+import ManualLayout.control.actions.align.*;
+
+import cytoscape.view.*;
+
+import java.awt.*;
+
+import javax.swing.*;
+import javax.swing.border.*;
+
+
+/**
+ *
+ */
+public class AlignPanel extends JPanel {
+ /**
+ * Creates a new AlignPanel object.
+ */
+ public AlignPanel() {
+ ImageIcon hari = new ImageIcon(getClass().getResource("/H_ALIGN_RIGHT.gif"));
+ ImageIcon haci = new ImageIcon(getClass().getResource("/H_ALIGN_CENTER.gif"));
+ ImageIcon hali = new ImageIcon(getClass().getResource("/H_ALIGN_LEFT.gif"));
+ ImageIcon vati = new ImageIcon(getClass().getResource("/V_ALIGN_TOP.gif"));
+ ImageIcon vaci = new ImageIcon(getClass().getResource("/V_ALIGN_CENTER.gif"));
+ ImageIcon vabi = new ImageIcon(getClass().getResource("/V_ALIGN_BOTTOM.gif"));
+
+ HAlignRight har = new HAlignRight(hari);
+ HAlignCenter hac = new HAlignCenter(haci);
+ HAlignLeft hal = new HAlignLeft(hali);
+
+ VAlignTop vat = new VAlignTop(vati);
+ VAlignCenter vac = new VAlignCenter(vaci);
+ VAlignBottom vab = new VAlignBottom(vabi);
+
+ setLayout(new GridLayout(1,6));
+
+ add(createJButton(hal, "Horizontal Left"));
+ add(createJButton(hac, "Horizontal Center"));
+ add(createJButton(har, "Horizontal Right"));
+
+ add(createJButton(vat, "Vertical Top"));
+ add(createJButton(vac, "Vertical Center"));
+ add(createJButton(vab, "Vertical Bottom"));
+
+ setBorder(new TitledBorder("Align"));
+ }
+
+ protected JButton createJButton(Action a, String tt) {
+ JButton b = new JButton(a);
+ b.setToolTipText(tt);
+ b.setPreferredSize(new Dimension(27, 18));
+ b.setMaximumSize(new Dimension(27, 18));
+ b.setBorder(BorderFactory.createEmptyBorder());
+ b.setBorderPainted(false);
+ b.setOpaque(false);
+ b.setContentAreaFilled(false);
+
+ return b;
+ }
+}
diff --git a/coreplugins/ManualLayout/src/main/java/ManualLayout/control/view/DistPanel.java b/coreplugins/ManualLayout/src/main/java/ManualLayout/control/view/DistPanel.java
new file mode 100644
index 0000000..8fe0ad5
--- /dev/null
+++ b/coreplugins/ManualLayout/src/main/java/ManualLayout/control/view/DistPanel.java
@@ -0,0 +1,96 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package ManualLayout.control.view;
+
+import ManualLayout.control.actions.dist.*;
+
+import cytoscape.view.*;
+
+import java.awt.*;
+
+import javax.swing.*;
+import javax.swing.border.*;
+
+
+/**
+ *
+ */
+public class DistPanel extends JPanel {
+ /**
+ * Creates a new DistPanel object.
+ */
+ public DistPanel() {
+ ImageIcon hali = new ImageIcon(getClass().getResource("/H_DIST_LEFT.gif"));
+ ImageIcon haci = new ImageIcon(getClass().getResource("/H_DIST_CENTER.gif"));
+ ImageIcon hari = new ImageIcon(getClass().getResource("/H_DIST_RIGHT.gif"));
+ ImageIcon vati = new ImageIcon(getClass().getResource("/V_DIST_TOP.gif"));
+ ImageIcon vaci = new ImageIcon(getClass().getResource("/V_DIST_CENTER.gif"));
+ ImageIcon vabi = new ImageIcon(getClass().getResource("/V_DIST_BOTTOM.gif"));
+
+ HDistLeft hal = new HDistLeft(hali);
+ HDistCenter hac = new HDistCenter(haci);
+ HDistRight har = new HDistRight(hari);
+
+ VDistTop vat = new VDistTop(vati);
+ VDistCenter vac = new VDistCenter(vaci);
+ VDistBottom vab = new VDistBottom(vabi);
+
+ setLayout(new java.awt.GridLayout(1,6));
+
+ add(createJButton(hal, "Horizontal Left"));
+ add(createJButton(hac, "Horizontal Center"));
+ add(createJButton(har, "Horizontal Right"));
+ add(createJButton(vat, "Vertical Top"));
+ add(createJButton(vac, "Vertical Center"));
+ add(createJButton(vab, "Vertical Bottom"));
+
+ setBorder(new TitledBorder("Distribute"));
+ }
+
+ protected JButton createJButton(Action a, String tt) {
+ JButton b = new JButton(a);
+ b.setToolTipText(tt);
+ b.setPreferredSize(new Dimension(27, 18));
+ b.setMaximumSize(new Dimension(27, 18));
+ b.setBorder(BorderFactory.createEmptyBorder());
+ b.setBorderPainted(false);
+ b.setOpaque(false);
+ b.setContentAreaFilled(false);
+
+ return b;
+ }
+}
diff --git a/coreplugins/ManualLayout/src/main/java/ManualLayout/control/view/StackPanel.java b/coreplugins/ManualLayout/src/main/java/ManualLayout/control/view/StackPanel.java
new file mode 100644
index 0000000..b6fc7c5
--- /dev/null
+++ b/coreplugins/ManualLayout/src/main/java/ManualLayout/control/view/StackPanel.java
@@ -0,0 +1,97 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package ManualLayout.control.view;
+
+import ManualLayout.control.actions.stack.*;
+
+import cytoscape.view.*;
+
+import java.awt.*;
+
+import javax.swing.*;
+import javax.swing.border.*;
+
+
+/**
+ *
+ */
+public class StackPanel extends JPanel {
+ /**
+ * Creates a new StackPanel object.
+ */
+ public StackPanel() {
+
+ ImageIcon vali = new ImageIcon(getClass().getResource("/V_STACK_LEFT.gif"));
+ ImageIcon vaci = new ImageIcon(getClass().getResource("/V_STACK_CENTER.gif"));
+ ImageIcon vari = new ImageIcon(getClass().getResource("/V_STACK_RIGHT.gif"));
+ ImageIcon hati = new ImageIcon(getClass().getResource("/H_STACK_TOP.gif"));
+ ImageIcon haci = new ImageIcon(getClass().getResource("/H_STACK_CENTER.gif"));
+ ImageIcon habi = new ImageIcon(getClass().getResource("/H_STACK_BOTTOM.gif"));
+
+ VStackLeft val = new VStackLeft(vali);
+ VStackCenter vac = new VStackCenter(vaci);
+ VStackRight var = new VStackRight(vari);
+
+ HStackTop hat = new HStackTop(hati);
+ HStackCenter hac = new HStackCenter(haci);
+ HStackBottom hab = new HStackBottom(habi);
+
+ setLayout(new GridLayout(1,6,0,0));
+ add(createJButton(val, "Vertical Left"));
+ add(createJButton(vac, "Vertical Center"));
+ add(createJButton(var, "Vertical Right"));
+ add(createJButton(hat, "Horizontal Top"));
+ add(createJButton(hac, "Horizontal Center"));
+ add(createJButton(hab, "Horizontal Bottom"));
+
+ setBorder(new TitledBorder("Stack"));
+ }
+
+ protected JButton createJButton(Action a, String tt) {
+ JButton b = new JButton(a);
+ b.setToolTipText(tt);
+ b.setPreferredSize(new Dimension(27, 18));
+ b.setMaximumSize(new Dimension(27, 18));
+ b.setMinimumSize(new Dimension(27, 18));
+ b.setBorder(BorderFactory.createEmptyBorder());
+ b.setBorderPainted(false);
+ b.setOpaque(false);
+ b.setContentAreaFilled(false);
+
+ return b;
+ }
+}
diff --git a/coreplugins/ManualLayout/src/main/java/ManualLayout/rotate/RotatePanel.java b/coreplugins/ManualLayout/src/main/java/ManualLayout/rotate/RotatePanel.java
new file mode 100644
index 0000000..4af4ac0
--- /dev/null
+++ b/coreplugins/ManualLayout/src/main/java/ManualLayout/rotate/RotatePanel.java
@@ -0,0 +1,150 @@
+/*
+ Copyright (c) 2006, 2007, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package ManualLayout.rotate;
+
+import cytoscape.Cytoscape;
+
+import ding.view.ViewChangeEdit;
+import ding.view.DGraphView;
+
+import java.awt.Dimension;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.Insets;
+
+import javax.swing.JCheckBox;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JSlider;
+
+import ManualLayout.common.*;
+
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+
+import cytoscape.graph.layout.algorithm.MutablePolyEdgeGraphLayout;
+
+
+/**
+ * GUI for rotation of manualLayout
+ *
+ * Rewrite based on the class RotateAction 9/13/2006 Peng-Liang Wang
+ */
+public class RotatePanel extends JPanel implements ChangeListener, PolymorphicSlider {
+ private JCheckBox jCheckBox;
+ private JSlider jSlider;
+ private int prevValue;
+
+ private boolean startAdjusting = true;
+ private ViewChangeEdit currentEdit = null;
+
+ public RotatePanel() {
+ // set up the user interface
+ JLabel jLabel = new JLabel();
+ jLabel.setText("Rotate in Degrees:");
+ jLabel.setPreferredSize(new Dimension(120, 50));
+
+ jSlider = new JSlider();
+ jSlider.setMaximum(360);
+ jSlider.setMajorTickSpacing(90);
+ jSlider.setPaintLabels(true);
+ jSlider.setPaintTicks(true);
+ jSlider.setMinorTickSpacing(15);
+ jSlider.setValue(0);
+ jSlider.setPreferredSize(new Dimension(120, 50));
+ jSlider.addChangeListener(this);
+
+ prevValue = jSlider.getValue();
+
+ jCheckBox = new JCheckBox("Rotate Selected Nodes Only", /* selected = */true);
+
+ new CheckBoxTracker( jCheckBox );
+
+ GridBagConstraints gbc = new GridBagConstraints();
+
+ setLayout(new GridBagLayout());
+
+ gbc.gridy = 0;
+ gbc.anchor = GridBagConstraints.WEST;
+ gbc.weightx = 1.0;
+ gbc.insets = new Insets(0, 15, 0, 15);
+ add(jLabel, gbc);
+
+ gbc.gridy = 1;
+ gbc.fill = GridBagConstraints.HORIZONTAL;
+ add(jSlider, gbc);
+
+ gbc.gridy = 2;
+ gbc.anchor = GridBagConstraints.WEST;
+ gbc.fill = GridBagConstraints.NONE;
+ add(jCheckBox, gbc);
+
+ new SliderStateTracker(this);
+
+ setMinimumSize(new Dimension(100,1200));
+ setPreferredSize(new Dimension(100,1200));
+ setMaximumSize(new Dimension(100,1200));
+ }
+
+ public void updateSlider(int x) {
+ // this will prevent the state change from producing a change
+ prevValue = x;
+ jSlider.setValue(x);
+ }
+
+ public int getSliderValue() {
+ return jSlider.getValue();
+ }
+
+ public void stateChanged(ChangeEvent e) {
+ if (e.getSource() != jSlider)
+ return;
+
+ // only create the edit at the beginning of the adjustment
+ if ( startAdjusting ) {
+ currentEdit = new ViewChangeEdit((DGraphView)(Cytoscape.getCurrentNetworkView()), "Rotate");
+ startAdjusting = false;
+ }
+
+ MutablePolyEdgeGraphLayout nativeGraph = GraphConverter2.getGraphReference(128.0d, true,
+ jCheckBox.isSelected());
+ RotationLayouter rotation = new RotationLayouter(nativeGraph);
+
+ double radians = (((double) (jSlider.getValue() - prevValue)) * 2.0d * Math.PI) / 360.0d;
+ rotation.rotateGraph(radians);
+ Cytoscape.getCurrentNetworkView().updateView();
+
+ prevValue = jSlider.getValue();
+
+ // only post edit when adjustment is complete
+ if ( !jSlider.getValueIsAdjusting() ) {
+ currentEdit.post();
+ startAdjusting = true;
+ }
+ }
+}
diff --git a/coreplugins/ManualLayout/src/main/java/ManualLayout/rotate/RotatePanelAction.java b/coreplugins/ManualLayout/src/main/java/ManualLayout/rotate/RotatePanelAction.java
new file mode 100644
index 0000000..5a99dbc
--- /dev/null
+++ b/coreplugins/ManualLayout/src/main/java/ManualLayout/rotate/RotatePanelAction.java
@@ -0,0 +1,52 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package ManualLayout.rotate;
+
+import ManualLayout.common.AbstractManualLayoutAction;
+
+/**
+ * Rotate network action.
+ */
+public class RotatePanelAction extends AbstractManualLayoutAction {
+
+ /**
+ * Rotate network action. Should be in menu slot 0.
+ */
+ public RotatePanelAction() {
+ super("Rotate",0);
+ }
+}
diff --git a/coreplugins/ManualLayout/src/main/java/ManualLayout/rotate/RotationLayouter.java b/coreplugins/ManualLayout/src/main/java/ManualLayout/rotate/RotationLayouter.java
new file mode 100644
index 0000000..fceeeed
--- /dev/null
+++ b/coreplugins/ManualLayout/src/main/java/ManualLayout/rotate/RotationLayouter.java
@@ -0,0 +1,183 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package ManualLayout.rotate;
+
+import com.nerius.math.xform.AffineTransform3D;
+import com.nerius.math.xform.AxisRotation3D;
+import com.nerius.math.xform.Translation3D;
+
+import cytoscape.graph.layout.algorithm.MutablePolyEdgeGraphLayout;
+
+import cytoscape.util.intr.IntEnumerator;
+
+
+/**
+ *
+ */
+public final class RotationLayouter {
+ private final MutablePolyEdgeGraphLayout m_graph;
+ private final Translation3D m_translationToOrig;
+ private final Translation3D m_translationFromOrig;
+
+ /**
+ * This operation does not affect edge anchor points which belong to edges
+ * containing at least one non-movable node.
+ *
+ * @exception IllegalStateException
+ * if the minimum bounding rectangle containing all movable nodes and
+ * respective edge anchor points
+ * is not fully free to rotate around its center while staying within
+ * allowable area for specified mutable graph..
+ **/
+ public RotationLayouter(MutablePolyEdgeGraphLayout graph) {
+ m_graph = graph;
+
+ double xMin = Double.MAX_VALUE;
+ double xMax = Double.MIN_VALUE;
+ double yMin = Double.MAX_VALUE;
+ double yMax = Double.MIN_VALUE;
+ IntEnumerator edges = m_graph.edges();
+
+ while (edges.numRemaining() > 0) {
+ int edge = edges.nextInt();
+
+ if (!(m_graph.isMovableNode(m_graph.edgeSource(edge))
+ && m_graph.isMovableNode(m_graph.edgeTarget(edge))))
+ continue;
+
+ final int numAnchors = m_graph.getNumAnchors(edge);
+
+ for (int j = 0; j < numAnchors; j++) {
+ double anchXPosition = m_graph.getAnchorPosition(edge, j, true);
+ double anchYPosition = m_graph.getAnchorPosition(edge, j, false);
+ xMin = Math.min(xMin, anchXPosition);
+ xMax = Math.max(xMax, anchXPosition);
+ yMin = Math.min(yMin, anchYPosition);
+ yMax = Math.max(yMax, anchYPosition);
+ }
+ }
+
+ IntEnumerator nodes = m_graph.nodes();
+
+ while (nodes.numRemaining() > 0) {
+ int node = nodes.nextInt();
+
+ if (!m_graph.isMovableNode(node))
+ continue;
+
+ double nodeXPosition = m_graph.getNodePosition(node, true);
+ double nodeYPosition = m_graph.getNodePosition(node, false);
+ xMin = Math.min(xMin, nodeXPosition);
+ xMax = Math.max(xMax, nodeXPosition);
+ yMin = Math.min(yMin, nodeYPosition);
+ yMax = Math.max(yMax, nodeYPosition);
+ }
+
+ if (xMax < 0) // Nothing is movable.
+ {
+ m_translationToOrig = null;
+ m_translationFromOrig = null;
+ } else {
+ final double xRectCenter = (xMin + xMax) / 2.0d;
+ final double yRectCenter = (yMin + yMax) / 2.0d;
+ double rectWidth = xMax - xMin;
+ double rectHeight = yMax - yMin;
+ double hypotenuse = 0.5d * Math.sqrt((rectWidth * rectWidth)
+ + (rectHeight * rectHeight));
+
+ if (((xRectCenter - hypotenuse) < 0.0d)
+ || ((xRectCenter + hypotenuse) > m_graph.getMaxWidth())
+ || ((yRectCenter - hypotenuse) < 0.0d)
+ || ((yRectCenter + hypotenuse) > m_graph.getMaxHeight()))
+ throw new IllegalStateException("minimum bounding rectangle of movable nodes and edge anchors "
+ + "not free to rotate within MutableGraphLayout boundaries");
+
+ m_translationToOrig = new Translation3D(-xRectCenter, -yRectCenter, 0.0d);
+ m_translationFromOrig = new Translation3D(xRectCenter, yRectCenter, 0.0d);
+ }
+ }
+
+ private final double[] m_pointBuff = new double[3];
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param radians DOCUMENT ME!
+ */
+ public void rotateGraph(double radians) {
+ if (m_translationToOrig == null)
+ return;
+
+ final AffineTransform3D xform = m_translationToOrig.concatenatePost((new AxisRotation3D(AxisRotation3D.Z_AXIS,
+ radians))
+ .concatenatePost(m_translationFromOrig));
+ IntEnumerator nodes = m_graph.nodes();
+
+ while (nodes.numRemaining() > 0) {
+ int node = nodes.nextInt();
+
+ if (!m_graph.isMovableNode(node))
+ continue;
+
+ m_pointBuff[0] = m_graph.getNodePosition(node, true);
+ m_pointBuff[1] = m_graph.getNodePosition(node, false);
+ m_pointBuff[2] = 0.0d;
+ xform.transformArr(m_pointBuff);
+ m_graph.setNodePosition(node, m_pointBuff[0], m_pointBuff[1]);
+ }
+
+ IntEnumerator edges = m_graph.edges();
+
+ while (edges.numRemaining() > 0) {
+ int edge = edges.nextInt();
+
+ if (!(m_graph.isMovableNode(m_graph.edgeSource(edge))
+ && m_graph.isMovableNode(m_graph.edgeTarget(edge))))
+ continue;
+
+ final int numAnchors = m_graph.getNumAnchors(edge);
+
+ for (int j = 0; j < numAnchors; j++) {
+ m_pointBuff[0] = m_graph.getAnchorPosition(edge, j, true);
+ m_pointBuff[1] = m_graph.getAnchorPosition(edge, j, false);
+ m_pointBuff[2] = 0.0d;
+ xform.transformArr(m_pointBuff);
+ m_graph.setAnchorPosition(edge, j, m_pointBuff[0], m_pointBuff[1]);
+ }
+ }
+ }
+}
diff --git a/coreplugins/ManualLayout/src/main/java/ManualLayout/scale/ScaleLayouter.java b/coreplugins/ManualLayout/src/main/java/ManualLayout/scale/ScaleLayouter.java
new file mode 100644
index 0000000..61f8f04
--- /dev/null
+++ b/coreplugins/ManualLayout/src/main/java/ManualLayout/scale/ScaleLayouter.java
@@ -0,0 +1,175 @@
+/*
+ Copyright (c) 2006, 2007, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package ManualLayout.scale;
+
+
+import com.nerius.math.xform.AffineTransform3D;
+import com.nerius.math.xform.Scale3D;
+import com.nerius.math.xform.Translation3D;
+
+import cytoscape.graph.layout.algorithm.MutablePolyEdgeGraphLayout;
+
+import cytoscape.util.intr.IntEnumerator;
+
+
+public final class ScaleLayouter {
+ public enum Direction {
+ X_AXIS_ONLY,
+ Y_AXIS_ONLY,
+ BOTH_AXES
+ };
+
+ private final MutablePolyEdgeGraphLayout m_graph;
+ private final Translation3D m_translationToOrig;
+ private final Translation3D m_translationFromOrig;
+
+ /**
+ * This operation does not affect edge anchor points which belong to edges
+ * containing at least one non-movable node.
+ **/
+ public ScaleLayouter(MutablePolyEdgeGraphLayout graph) {
+ m_graph = graph;
+
+ double xMin = Double.MAX_VALUE;
+ double xMax = Double.MIN_VALUE;
+ double yMin = Double.MAX_VALUE;
+ double yMax = Double.MIN_VALUE;
+ IntEnumerator edges = m_graph.edges();
+
+ while (edges.numRemaining() > 0) {
+ int edge = edges.nextInt();
+
+ if (!(m_graph.isMovableNode(m_graph.edgeSource(edge))
+ && m_graph.isMovableNode(m_graph.edgeTarget(edge))))
+ continue;
+
+ final int numAnchors = m_graph.getNumAnchors(edge);
+
+ for (int j = 0; j < numAnchors; j++) {
+ double anchXPosition = m_graph.getAnchorPosition(edge, j, true);
+ double anchYPosition = m_graph.getAnchorPosition(edge, j, false);
+ xMin = Math.min(xMin, anchXPosition);
+ xMax = Math.max(xMax, anchXPosition);
+ yMin = Math.min(yMin, anchYPosition);
+ yMax = Math.max(yMax, anchYPosition);
+ }
+ }
+
+ IntEnumerator nodes = m_graph.nodes();
+
+ while (nodes.numRemaining() > 0) {
+ int node = nodes.nextInt();
+
+ if (!m_graph.isMovableNode(node))
+ continue;
+
+ double nodeXPosition = m_graph.getNodePosition(node, true);
+ double nodeYPosition = m_graph.getNodePosition(node, false);
+ xMin = Math.min(xMin, nodeXPosition);
+ xMax = Math.max(xMax, nodeXPosition);
+ yMin = Math.min(yMin, nodeYPosition);
+ yMax = Math.max(yMax, nodeYPosition);
+ }
+
+ if (xMax < 0) { // Nothing is movable.
+ m_translationToOrig = null;
+ m_translationFromOrig = null;
+ } else {
+ final double xRectCenter = (xMin + xMax) / 2.0d;
+ final double yRectCenter = (yMin + yMax) / 2.0d;
+ m_translationToOrig = new Translation3D(-xRectCenter, -yRectCenter, 0.0d);
+ m_translationFromOrig = new Translation3D(xRectCenter, yRectCenter, 0.0d);
+ }
+ }
+
+ private final double[] m_pointBuff = new double[3];
+
+ /**
+ * A scaleFactor of 1.0 does not move anything.
+ *
+ * @exception IllegalArgumentException if
+ * scaleFactor < 0.001 or if scaleFactor > 1000.0.
+ **/
+ public void scaleGraph(double scaleFactor, final Direction direction) {
+ if ((scaleFactor < 0.001d) || (scaleFactor > 1000.0d))
+ throw new IllegalArgumentException("scaleFactor is outside allowable range [0.001, 1000.0]");
+
+ if (m_translationToOrig == null)
+ return;
+
+ double xFactor = scaleFactor, yFactor = scaleFactor;
+ switch (direction) {
+ case X_AXIS_ONLY:
+ yFactor = 1.0;
+ break;
+ case Y_AXIS_ONLY:
+ xFactor = 1.0;
+ break;
+ case BOTH_AXES:
+ /* Intentionally empty! */
+ break;
+ }
+
+ final AffineTransform3D xform = m_translationToOrig.concatenatePost(
+ (new Scale3D(xFactor, yFactor, 1.0d)).concatenatePost(m_translationFromOrig));
+ IntEnumerator nodes = m_graph.nodes();
+
+ while (nodes.numRemaining() > 0) {
+ int node = nodes.nextInt();
+
+ if (!m_graph.isMovableNode(node))
+ continue;
+
+ m_pointBuff[0] = m_graph.getNodePosition(node, true);
+ m_pointBuff[1] = m_graph.getNodePosition(node, false);
+ m_pointBuff[2] = 0.0d;
+ xform.transformArr(m_pointBuff);
+ m_graph.setNodePosition(node, m_pointBuff[0], m_pointBuff[1]);
+ }
+
+ IntEnumerator edges = m_graph.edges();
+
+ while (edges.numRemaining() > 0) {
+ int edge = edges.nextInt();
+
+ if (!(m_graph.isMovableNode(m_graph.edgeSource(edge))
+ && m_graph.isMovableNode(m_graph.edgeTarget(edge))))
+ continue;
+
+ final int numAnchors = m_graph.getNumAnchors(edge);
+
+ for (int j = 0; j < numAnchors; j++) {
+ m_pointBuff[0] = m_graph.getAnchorPosition(edge, j, true);
+ m_pointBuff[1] = m_graph.getAnchorPosition(edge, j, false);
+ m_pointBuff[2] = 0.0d;
+ xform.transformArr(m_pointBuff);
+ m_graph.setAnchorPosition(edge, j, m_pointBuff[0], m_pointBuff[1]);
+ }
+ }
+ }
+}
diff --git a/coreplugins/ManualLayout/src/main/java/ManualLayout/scale/ScalePanel.java b/coreplugins/ManualLayout/src/main/java/ManualLayout/scale/ScalePanel.java
new file mode 100644
index 0000000..89cd889
--- /dev/null
+++ b/coreplugins/ManualLayout/src/main/java/ManualLayout/scale/ScalePanel.java
@@ -0,0 +1,227 @@
+/*
+ Copyright (c) 2006, 2007, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package ManualLayout.scale;
+
+
+import ManualLayout.common.*;
+
+import cytoscape.Cytoscape;
+import cytoscape.graph.layout.algorithm.MutablePolyEdgeGraphLayout;
+
+import ding.view.DGraphView;
+import ding.view.ViewChangeEdit;
+
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.GridLayout;
+import java.awt.Insets;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import java.util.Hashtable;
+
+import javax.swing.AbstractAction;
+import javax.swing.ButtonGroup;
+import javax.swing.JCheckBox;
+import javax.swing.JButton;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JRadioButton;
+import javax.swing.JSlider;
+import javax.swing.WindowConstants;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+
+
+/**
+ *
+ * GUI for scale of manualLayout
+ *
+ * Rewrite based on the class ScaleAction 9/13/2006 Peng-Liang Wang
+ *
+ */
+public class ScalePanel extends JPanel implements ChangeListener, PolymorphicSlider {
+ private JCheckBox jCheckBox;
+ private JSlider jSlider;
+ private JRadioButton alongXAxisOnlyRadioButton;
+ private JRadioButton alongYAxisOnlyRadioButton;
+ private JRadioButton alongBothAxesRadioButton;
+ private ButtonGroup radioButtonGroup;
+ private int prevValue;
+
+ private boolean startAdjusting = true;
+ private ViewChangeEdit currentEdit = null;
+
+ public ScalePanel() {
+ JLabel jLabel = new JLabel();
+ jLabel.setText("Scale:");
+
+ jSlider = new JSlider();
+
+ jSlider.setMajorTickSpacing(100);
+ jSlider.setPaintTicks(true);
+ jSlider.setPaintLabels(true);
+
+ jSlider.setMaximum(300);
+ jSlider.setValue(0);
+ jSlider.setMinimum(-300);
+
+ jSlider.addChangeListener(this);
+
+ prevValue = jSlider.getValue();
+
+ Hashtable<Integer,JLabel> labels = new Hashtable<Integer,JLabel>();
+ labels.put(new Integer(-300), new JLabel("1/8"));
+ labels.put(new Integer(-200), new JLabel("1/4"));
+ labels.put(new Integer(-100), new JLabel("1/2"));
+ labels.put(new Integer(0), new JLabel("1"));
+ labels.put(new Integer(100), new JLabel("2"));
+ labels.put(new Integer(200), new JLabel("4"));
+ labels.put(new Integer(300), new JLabel("8"));
+
+ jSlider.setLabelTable(labels);
+
+ jCheckBox = new JCheckBox("Scale Selected Nodes Only", /* selected = */true);
+ new CheckBoxTracker( jCheckBox );
+
+ alongXAxisOnlyRadioButton = new JRadioButton("along x-axis only");
+ alongYAxisOnlyRadioButton = new JRadioButton("along y-axis only");
+ alongBothAxesRadioButton = new JRadioButton("along both axes", /* selected = */true);
+ radioButtonGroup = new ButtonGroup();
+ radioButtonGroup.add(alongXAxisOnlyRadioButton);
+ radioButtonGroup.add(alongYAxisOnlyRadioButton);
+ radioButtonGroup.add(alongBothAxesRadioButton);
+
+ setLayout(new GridBagLayout());
+
+ GridBagConstraints gbc = new GridBagConstraints();
+
+ gbc.gridy = 0;
+ gbc.anchor = GridBagConstraints.WEST;
+ gbc.weightx = 1.0;
+ gbc.insets = new Insets(0, 15, 0, 15);
+ add(jLabel, gbc);
+
+ gbc.gridy = 1;
+ gbc.fill = GridBagConstraints.HORIZONTAL;
+ gbc.insets = new Insets(10, 15, 10, 15);
+ add(jSlider, gbc);
+
+ JButton clearButton = new JButton("Reset scale bar");
+ clearButton.addActionListener(new AbstractAction() {
+ public void actionPerformed(ActionEvent e) {
+ updateSlider(0);
+ }
+ });
+ gbc.gridy = 2;
+ gbc.fill = GridBagConstraints.NONE;
+ gbc.anchor = GridBagConstraints.WEST;
+ gbc.insets = new Insets(5, 15, 5, 15);
+ add(clearButton, gbc);
+
+ gbc.gridy = 3;
+ gbc.anchor = GridBagConstraints.WEST;
+ gbc.fill = GridBagConstraints.NONE;
+ gbc.insets = new Insets(0, 15, 0, 15);
+ add(jCheckBox, gbc);
+
+ new SliderStateTracker(this);
+
+ gbc.gridy = 4;
+ gbc.anchor = GridBagConstraints.WEST;
+ gbc.fill = GridBagConstraints.NONE;
+ gbc.insets = new Insets(20, 15, 0, 15);
+ add(alongXAxisOnlyRadioButton, gbc);
+
+ gbc.gridy = 5;
+ gbc.anchor = GridBagConstraints.WEST;
+ gbc.fill = GridBagConstraints.NONE;
+ gbc.insets = new Insets(0, 15, 0, 15);
+ add(alongYAxisOnlyRadioButton, gbc);
+
+ gbc.gridy = 6;
+ gbc.anchor = GridBagConstraints.WEST;
+ gbc.fill = GridBagConstraints.NONE;
+ gbc.insets = new Insets(0, 15, 0, 15);
+ add(alongBothAxesRadioButton, gbc);
+ /*
+ setMinimumSize(new java.awt.Dimension(100,2200));
+ setPreferredSize(new java.awt.Dimension(100,2200));
+ setMaximumSize(new java.awt.Dimension(100,2200));
+ */
+ }
+
+ public void updateSlider(int x) {
+ prevValue = x;
+ jSlider.setValue(x);
+ }
+
+ public int getSliderValue() {
+ return jSlider.getValue();
+ }
+
+ public void stateChanged(ChangeEvent e) {
+ if (e.getSource() != jSlider)
+ return;
+
+ // only create the edit when we're beginning to adjust
+ if ( startAdjusting ) {
+ currentEdit = new ViewChangeEdit((DGraphView)(Cytoscape.getCurrentNetworkView()), "Scale");
+ startAdjusting = false;
+ }
+
+ // do the scaling
+ MutablePolyEdgeGraphLayout nativeGraph = GraphConverter2.getGraphReference(128.0d, true,
+ jCheckBox.isSelected());
+ ScaleLayouter scale = new ScaleLayouter(nativeGraph);
+
+ double prevAbsoluteScaleFactor = Math.pow(2, ((double) prevValue) / 100.0d);
+
+ double currentAbsoluteScaleFactor = Math.pow(2, ((double) jSlider.getValue()) / 100.0d);
+
+ double neededIncrementalScaleFactor = currentAbsoluteScaleFactor / prevAbsoluteScaleFactor;
+
+ final ScaleLayouter.Direction direction;
+ if (alongXAxisOnlyRadioButton.isSelected())
+ direction = ScaleLayouter.Direction.X_AXIS_ONLY;
+ else if (alongYAxisOnlyRadioButton.isSelected())
+ direction = ScaleLayouter.Direction.Y_AXIS_ONLY;
+ else
+ direction = ScaleLayouter.Direction.BOTH_AXES;
+
+ scale.scaleGraph(neededIncrementalScaleFactor, direction);
+ Cytoscape.getCurrentNetworkView().updateView();
+ prevValue = jSlider.getValue();
+
+ // only post the edit when we're finished adjusting
+ if (!jSlider.getValueIsAdjusting()) {
+ currentEdit.post();
+ startAdjusting = true;
+ }
+ }
+}
diff --git a/coreplugins/ManualLayout/src/main/java/ManualLayout/scale/ScalePanelAction.java b/coreplugins/ManualLayout/src/main/java/ManualLayout/scale/ScalePanelAction.java
new file mode 100644
index 0000000..5a4d1a0
--- /dev/null
+++ b/coreplugins/ManualLayout/src/main/java/ManualLayout/scale/ScalePanelAction.java
@@ -0,0 +1,52 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package ManualLayout.scale;
+
+import ManualLayout.common.AbstractManualLayoutAction;
+
+/**
+ * Scale network action.
+ */
+public class ScalePanelAction extends AbstractManualLayoutAction {
+
+ /**
+ * Scale network action. Should be in menu slot 1.
+ */
+ public ScalePanelAction() {
+ super("Scale",1);
+ }
+}
diff --git a/coreplugins/ManualLayout/src/main/java/ManualLayout/scale/ScalingDirectionTracker.java b/coreplugins/ManualLayout/src/main/java/ManualLayout/scale/ScalingDirectionTracker.java
new file mode 100644
index 0000000..4b479ec
--- /dev/null
+++ b/coreplugins/ManualLayout/src/main/java/ManualLayout/scale/ScalingDirectionTracker.java
@@ -0,0 +1,95 @@
+/*
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package ManualLayout.scale;
+
+
+import cytoscape.Cytoscape;
+import cytoscape.CyNetwork;
+
+import cytoscape.data.SelectEvent;
+import cytoscape.data.SelectEventListener;
+
+import cytoscape.graph.layout.algorithm.MutablePolyEdgeGraphLayout;
+
+import cytoscape.util.CytoscapeAction;
+
+import cytoscape.view.CytoscapeDesktop;
+
+import cytoscape.view.cytopanels.BiModalJSplitPane;
+import cytoscape.view.cytopanels.CytoPanelImp;
+import cytoscape.view.cytopanels.CytoPanelListener;
+import cytoscape.view.cytopanels.CytoPanelState;
+
+import java.awt.Dimension;
+import java.awt.event.ActionEvent;
+
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+
+import java.util.HashSet;
+import java.util.Set;
+
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JCheckBox;
+import javax.swing.JMenu;
+import javax.swing.JPanel;
+import javax.swing.JSplitPane;
+import javax.swing.SwingConstants;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+
+
+public class ScalingDirectionTracker implements SelectEventListener, PropertyChangeListener {
+ private JCheckBox jCheckBox;
+ private Set<String> listeningNetworks;
+
+ public ScalingDirectionTracker(JCheckBox j) {
+ jCheckBox = j;
+ listeningNetworks = new HashSet<String>();
+ Cytoscape.getDesktop().getNetworkViewManager().getSwingPropertyChangeSupport()
+ .addPropertyChangeListener(CytoscapeDesktop.NETWORK_VIEW_FOCUSED,this);
+ }
+
+ public void onSelectEvent(SelectEvent event) {
+ jCheckBox.setSelected(Cytoscape.getCurrentNetworkView().getSelectedNodeIndices().length > 0);
+ }
+
+ public void propertyChange(PropertyChangeEvent e) {
+ if (e.getPropertyName() == CytoscapeDesktop.NETWORK_VIEW_FOCUSED) {
+ CyNetwork curr = Cytoscape.getCurrentNetwork();
+ String nid = curr.getIdentifier();
+
+ // only add this as a listener if it hasn't been done already
+ if ( !listeningNetworks.contains(nid) )
+ curr.addSelectEventListener(this);
+
+ // to make sure we're set intially
+ onSelectEvent(null);
+ }
+ }
+}
diff --git a/coreplugins/ManualLayout/src/main/java/cytoscape/graph/layout/GraphLayout.java b/coreplugins/ManualLayout/src/main/java/cytoscape/graph/layout/GraphLayout.java
new file mode 100644
index 0000000..f88046d
--- /dev/null
+++ b/coreplugins/ManualLayout/src/main/java/cytoscape/graph/layout/GraphLayout.java
@@ -0,0 +1,75 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.graph.layout;
+
+import cytoscape.graph.fixed.FixedGraph;
+
+
+/**
+ * This class represents not just a graph's topology but also a layout of its
+ * nodes in 2D space (a "straight-line graph drawing").
+ **/
+public interface GraphLayout extends FixedGraph {
+ /**
+ * Returns the maximum allowable value of X positions of nodes.
+ * All X positions of nodes in this graph will lie in the interval
+ * [0.0, getMaxWidth()].
+ *
+ * @see #getNodePosition(int, boolean)
+ **/
+ public double getMaxWidth();
+
+ /**
+ * Returns the maximum allowable value of Y positions of nodes.
+ * All Y positions of nodes in this graph will lie in the interval
+ * [0.0, getMaxHeight()].
+ *
+ * @see #getNodePosition(int, boolean)
+ **/
+ public double getMaxHeight();
+
+ /**
+ * Returns the X or Y position of a node.
+ *
+ * @param node the node whose position we're seeking.
+ * @param xPosition if true, return X position; if false, return Y position.
+ * @return the X or Y position of node.
+ * @exception IllegalArgumentException if specified node is not
+ * a node in this graph.
+ **/
+ public double getNodePosition(int node, boolean xPosition);
+}
diff --git a/coreplugins/ManualLayout/src/main/java/cytoscape/graph/layout/PolyEdgeGraphLayout.java b/coreplugins/ManualLayout/src/main/java/cytoscape/graph/layout/PolyEdgeGraphLayout.java
new file mode 100644
index 0000000..e3a411f
--- /dev/null
+++ b/coreplugins/ManualLayout/src/main/java/cytoscape/graph/layout/PolyEdgeGraphLayout.java
@@ -0,0 +1,91 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.graph.layout;
+
+
+/**
+ * This class extends <code>GraphLayout</code> to offer the possibility
+ * of defining poly-line edges (as opposed to just straight-line edges).<p>
+ * For a given edge E in this graph, the definition of a poly-line
+ * for E is as follows.
+ * If we define a sequence of points {P[0], P[1], ... P[N+1]} where<ul>
+ * <li>P[0] is the source node of edge E,</li>
+ * <li>P[N+1] is the target node of edge E, and</li>
+ * <li>for i not equal to 0 or N+1, P[i] is edge E's anchor
+ * point at index i-1,</li></ul>
+ * then the poly-line for edge E is defined to be the union of line segments
+ * {S[0], S[1], ... S[N]} where
+ * each S[i] is the straight-line segment starting
+ * at P[i] and ending at P[i+1].
+ **/
+public interface PolyEdgeGraphLayout extends GraphLayout {
+ /**
+ * Returns the number of anchor points belonging to an edge.
+ * In other methods of this
+ * interface an anchor point is referenced by the edge to which
+ * the anchor point belongs along with the anchor point's index within that
+ * edge. Indices of anchor points within an edge E
+ * start at 0 and end at getNumAnchors(E) - 1, inclusive.
+ *
+ * @return the number of edge anchor points belonging to specified ege.
+ * @exception IllegalArgumentException if specified edge is not
+ * an edge in this graph.
+ **/
+ public int getNumAnchors(int edge);
+
+ /**
+ * Returns the X or Y position of an edge anchor point.
+ *
+ * @param edge the edge to which the anchor point whose
+ * position we're seeking belongs.
+ * @param anchorIndex the index of anchor point, within specified edge,
+ * whose position we're seeking.
+ * @param xPosition if true, return X position of anchor point;
+ * if false, return Y position of anchor point.
+ * @return the X or Y position of anchor point with index
+ * anchorIndex within specified edge;
+ * X return values are within the interval
+ * [0.0, getMaxWidth()] and Y return values
+ * are within the interval [0.0, getMaxHeight()].
+ *
+ * @exception IllegalArgumentException if specified edge is not an
+ * edge in this graph.
+ * @exception IndexOutOfBoundsException if anchorIndex is not
+ * in the interval [0, getNumAnchors(edge) - 1].
+ **/
+ public double getAnchorPosition(int edge, int anchorIndex, boolean xPosition);
+}
diff --git a/coreplugins/ManualLayout/src/main/java/cytoscape/graph/layout/algorithm/MutableGraphLayout.java b/coreplugins/ManualLayout/src/main/java/cytoscape/graph/layout/algorithm/MutableGraphLayout.java
new file mode 100644
index 0000000..5c8a92b
--- /dev/null
+++ b/coreplugins/ManualLayout/src/main/java/cytoscape/graph/layout/algorithm/MutableGraphLayout.java
@@ -0,0 +1,94 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.graph.layout.algorithm;
+
+import cytoscape.graph.layout.GraphLayout;
+
+
+/**
+ * This class offers a hook for layout algorithms to operate on.
+ */
+public interface MutableGraphLayout extends GraphLayout {
+ /**
+ * Tells us whether or not the specified node
+ * can be moved by setNodePosition().
+ *
+ * @param node node whose mobility we are querying.
+ * @exception IllegalArgumentException if specified node is not a node
+ * in this graph.
+ * @see #setNodePosition(int, double, double)
+ */
+ public boolean isMovableNode(int node);
+
+ /**
+ * Sets the X,Y position of a node.
+ * This is a hook for layout algorithms to actually set locations of
+ * nodes. Layout algorithms should call this method.<p>
+ * X, Y values set by this method shall be reflected in the return values
+ * of getNodePosition() -- that is, if we call
+ * <blockquote><code>setNodePosition(node, x, y)</code></blockquote>
+ * then the subsequent expressions
+ * <blockquote>
+ * <nobr><code>x == getNodePosition(node, true)</code></nobr><br />
+ * <nobr><code>y == getNodePosition(node, false)</code></nobr>
+ * </blockquote>
+ * both evaluate to true.<p>
+ * Layout algorithms are encouraged to set node positions such that
+ * their X and Y values use the full range of allowable values, including
+ * the boundary values 0, getMaxWidth(), and
+ * getMaxHeight(). Any notion of node thickness, graph
+ * border on perimeter, etc. should be predetermined by the application
+ * using a layout algorithm; getMaxWidth() and
+ * getMaxHeight() should be defined accordingly by the
+ * application using a layout algorithm.
+ *
+ * @exception IllegalArgumentException if xPos or yPos are out of
+ * allowable range [0.0, getMaxWidth()] and [0.0, getMaxHeight()].
+ * respectively.
+ * <nobr><code>xPos < 0.0</code></nobr>, if
+ * @exception IllegalArgumentException if specified node is not
+ * a node in this graph.
+ * @exception UnsupportedOperationException if
+ * isMovableNode(node) returns false.
+ *
+ * @see #getMaxWidth()
+ * @see #getMaxHeight()
+ * @see #getNodePosition(int, boolean)
+ * @see #isMovableNode(int)
+ */
+ public void setNodePosition(int node, double xPos, double yPos);
+}
diff --git a/coreplugins/ManualLayout/src/main/java/cytoscape/graph/layout/algorithm/MutablePolyEdgeGraphLayout.java b/coreplugins/ManualLayout/src/main/java/cytoscape/graph/layout/algorithm/MutablePolyEdgeGraphLayout.java
new file mode 100644
index 0000000..4b7edb4
--- /dev/null
+++ b/coreplugins/ManualLayout/src/main/java/cytoscape/graph/layout/algorithm/MutablePolyEdgeGraphLayout.java
@@ -0,0 +1,123 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.graph.layout.algorithm;
+
+import cytoscape.graph.layout.PolyEdgeGraphLayout;
+
+
+/**
+ * This class extends MutableGraphLayout to offer the possibility
+ * of defining poly-line edges (as opposed to just straight-line edges).
+ **/
+public interface MutablePolyEdgeGraphLayout extends PolyEdgeGraphLayout, MutableGraphLayout {
+ /**
+ * Deletes an edge anchor point.<p>
+ * The deletion of an anchor point is accomplished such that the ordering of
+ * remaining anchor points stays the same. An anchor point [belonging
+ * to specified edge] with index greater than
+ * anchorIndex will be assigned a new index equal to its
+ * previous index minus one; an anchor point with index less than
+ * anchorIndex will keep its index.
+ *
+ * @param edge the edge to which the anchor point to be
+ * deleted belongs.
+ * @param anchorIndex the index of anchor point, within specified edge,
+ * which we're trying to delete.
+ * @exception IllegalArgumentException if specified edge is not
+ * an edge in this graph.
+ * @exception IndexOutOfBoundsException if anchorIndex is not
+ * in the interval [0, getNumAnchors(edge) - 1].
+ * @exception UnsupportedOperationException if specified edge
+ * has source and target nodes that are both
+ * non-movable.
+ **/
+ public void deleteAnchor(int edge, int anchorIndex);
+
+ /**
+ * Creates a new edge anchor point.<p>
+ * The creation of an anchor point is accomplished such that the ordering
+ * of existing anchor points stays the same. An existing anchor point
+ * [belonging to specified edge] with index greater
+ * than or equal to anchorIndex will be assigned a new index
+ * equal to its previous index plus one; an existing anchor point with index
+ * less than anchorIndex will keep its index.<p>
+ * A new anchor point P's X,Y position is the midpoint along the segment
+ * whose end points are P's neighbors in the edge poly-line definition;
+ * X,Y positions of existing anchor points and nodes are unchanged.
+ *
+ * @param edge new anchor point will be created on specified edge.
+ * @param anchorIndex new anchor point will have index
+ * anchorIndex within specified edge.
+ * @exception IllegalArgumentException if specified edge is not
+ * an edge in this graph.
+ * @exception IndexOutOfBoundsException if anchorIndex is not
+ * in the interval [0, getNumAnchors(edge)].
+ * @exception UnsupportedOperationException if specified edge
+ * source and target nodes that are both non-movable.
+ **/
+ public void createAnchor(int edge, int anchorIndex);
+
+ /**
+ * Sets the X,Y position of an edge anchor point.<p>
+ * X, Y values set by this method shall be reflected in the return values
+ * of getAnchorPosition() - that is, if we call
+ * <blockquote><code>setAnchorPosition(edge, aInx, x, y)</code></blockquote>
+ * then the subsequent expressions
+ * <blockquote>
+ * <nobr><code>x == getAnchorPosition(edge, aInx, true)</code></nobr><br />
+ * <nobr><code>y == getAnchorPosition(edge, aInx, false)</code></nobr>
+ * </blockquote>
+ * both evaluate to true.
+ *
+ * @param edge the edge to which the anchor point to be
+ * positioned belongs.
+ * @param anchorIndex the index of anchor point, within specified edge,
+ * which we're trying to position.
+ * @param xPosition the desired X position of specified edge anchor point.
+ * @param yPosition the desired Y position of specified edge anchor point.
+ * @exception IllegalArgumentException if specified edge is not
+ * an edge in this graph.
+ * @exception IndexOutOfBoundsException if anchorIndex is not
+ * in the interval [0, getNumAnchors(edge) - 1].
+ * @exception IllegalArgumentException if specified X position or
+ * specified Y position falls outside of [0.0, getMaxWidth()] and
+ * [0.0, getMaxHeight()], respectively.
+ * @exception UnsupportedOperationException if specified edge
+ * has source and target nodes that are both non-movable.
+ **/
+ public void setAnchorPosition(int edge, int anchorIndex, double xPosition, double yPosition);
+}
diff --git a/coreplugins/ManualLayout/src/main/java/cytoscape/graph/layout/algorithm/package.html b/coreplugins/ManualLayout/src/main/java/cytoscape/graph/layout/algorithm/package.html
new file mode 100644
index 0000000..2a237d3
--- /dev/null
+++ b/coreplugins/ManualLayout/src/main/java/cytoscape/graph/layout/algorithm/package.html
@@ -0,0 +1,12 @@
+<html>
+<head>
+ <!-- $Revision: 1251 $
+ $Date: 2005-01-21 11:58:02 -0800 (Fri, 21 Jan 2005) $
+ $Author: nlandys $
+ -->
+</head>
+
+<body>
+Provides a layout algorithm framework with minimal ties to external code.
+</body>
+</html>
diff --git a/coreplugins/ManualLayout/src/main/java/cytoscape/graph/layout/impl/RotationLayouter.java b/coreplugins/ManualLayout/src/main/java/cytoscape/graph/layout/impl/RotationLayouter.java
new file mode 100644
index 0000000..48fb0c0
--- /dev/null
+++ b/coreplugins/ManualLayout/src/main/java/cytoscape/graph/layout/impl/RotationLayouter.java
@@ -0,0 +1,183 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.graph.layout.impl;
+
+import com.nerius.math.xform.AffineTransform3D;
+import com.nerius.math.xform.AxisRotation3D;
+import com.nerius.math.xform.Translation3D;
+
+import cytoscape.graph.layout.algorithm.MutablePolyEdgeGraphLayout;
+
+import cytoscape.util.intr.IntEnumerator;
+
+
+/**
+ *
+ */
+public final class RotationLayouter {
+ private final MutablePolyEdgeGraphLayout m_graph;
+ private final Translation3D m_translationToOrig;
+ private final Translation3D m_translationFromOrig;
+
+ /**
+ * This operation does not affect edge anchor points which belong to edges
+ * containing at least one non-movable node.
+ *
+ * @exception IllegalStateException
+ * if the minimum bounding rectangle containing all movable nodes and
+ * respective edge anchor points
+ * is not fully free to rotate around its center while staying within
+ * allowable area for specified mutable graph..
+ **/
+ public RotationLayouter(MutablePolyEdgeGraphLayout graph) {
+ m_graph = graph;
+
+ double xMin = Double.MAX_VALUE;
+ double xMax = Double.MIN_VALUE;
+ double yMin = Double.MAX_VALUE;
+ double yMax = Double.MIN_VALUE;
+ IntEnumerator edges = m_graph.edges();
+
+ while (edges.numRemaining() > 0) {
+ int edge = edges.nextInt();
+
+ if (!(m_graph.isMovableNode(m_graph.edgeSource(edge))
+ && m_graph.isMovableNode(m_graph.edgeTarget(edge))))
+ continue;
+
+ final int numAnchors = m_graph.getNumAnchors(edge);
+
+ for (int j = 0; j < numAnchors; j++) {
+ double anchXPosition = m_graph.getAnchorPosition(edge, j, true);
+ double anchYPosition = m_graph.getAnchorPosition(edge, j, false);
+ xMin = Math.min(xMin, anchXPosition);
+ xMax = Math.max(xMax, anchXPosition);
+ yMin = Math.min(yMin, anchYPosition);
+ yMax = Math.max(yMax, anchYPosition);
+ }
+ }
+
+ IntEnumerator nodes = m_graph.nodes();
+
+ while (nodes.numRemaining() > 0) {
+ int node = nodes.nextInt();
+
+ if (!m_graph.isMovableNode(node))
+ continue;
+
+ double nodeXPosition = m_graph.getNodePosition(node, true);
+ double nodeYPosition = m_graph.getNodePosition(node, false);
+ xMin = Math.min(xMin, nodeXPosition);
+ xMax = Math.max(xMax, nodeXPosition);
+ yMin = Math.min(yMin, nodeYPosition);
+ yMax = Math.max(yMax, nodeYPosition);
+ }
+
+ if (xMax < 0) // Nothing is movable.
+ {
+ m_translationToOrig = null;
+ m_translationFromOrig = null;
+ } else {
+ final double xRectCenter = (xMin + xMax) / 2.0d;
+ final double yRectCenter = (yMin + yMax) / 2.0d;
+ double rectWidth = xMax - xMin;
+ double rectHeight = yMax - yMin;
+ double hypotenuse = 0.5d * Math.sqrt((rectWidth * rectWidth)
+ + (rectHeight * rectHeight));
+
+ if (((xRectCenter - hypotenuse) < 0.0d)
+ || ((xRectCenter + hypotenuse) > m_graph.getMaxWidth())
+ || ((yRectCenter - hypotenuse) < 0.0d)
+ || ((yRectCenter + hypotenuse) > m_graph.getMaxHeight()))
+ throw new IllegalStateException("minimum bounding rectangle of movable nodes and edge anchors "
+ + "not free to rotate within MutableGraphLayout boundaries");
+
+ m_translationToOrig = new Translation3D(-xRectCenter, -yRectCenter, 0.0d);
+ m_translationFromOrig = new Translation3D(xRectCenter, yRectCenter, 0.0d);
+ }
+ }
+
+ private final double[] m_pointBuff = new double[3];
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param radians DOCUMENT ME!
+ */
+ public void rotateGraph(double radians) {
+ if (m_translationToOrig == null)
+ return;
+
+ final AffineTransform3D xform = m_translationToOrig.concatenatePost((new AxisRotation3D(AxisRotation3D.Z_AXIS,
+ radians))
+ .concatenatePost(m_translationFromOrig));
+ IntEnumerator nodes = m_graph.nodes();
+
+ while (nodes.numRemaining() > 0) {
+ int node = nodes.nextInt();
+
+ if (!m_graph.isMovableNode(node))
+ continue;
+
+ m_pointBuff[0] = m_graph.getNodePosition(node, true);
+ m_pointBuff[1] = m_graph.getNodePosition(node, false);
+ m_pointBuff[2] = 0.0d;
+ xform.transformArr(m_pointBuff);
+ m_graph.setNodePosition(node, m_pointBuff[0], m_pointBuff[1]);
+ }
+
+ IntEnumerator edges = m_graph.edges();
+
+ while (edges.numRemaining() > 0) {
+ int edge = edges.nextInt();
+
+ if (!(m_graph.isMovableNode(m_graph.edgeSource(edge))
+ && m_graph.isMovableNode(m_graph.edgeTarget(edge))))
+ continue;
+
+ final int numAnchors = m_graph.getNumAnchors(edge);
+
+ for (int j = 0; j < numAnchors; j++) {
+ m_pointBuff[0] = m_graph.getAnchorPosition(edge, j, true);
+ m_pointBuff[1] = m_graph.getAnchorPosition(edge, j, false);
+ m_pointBuff[2] = 0.0d;
+ xform.transformArr(m_pointBuff);
+ m_graph.setAnchorPosition(edge, j, m_pointBuff[0], m_pointBuff[1]);
+ }
+ }
+ }
+}
diff --git a/coreplugins/ManualLayout/src/main/java/cytoscape/graph/layout/impl/ScaleLayouter.java b/coreplugins/ManualLayout/src/main/java/cytoscape/graph/layout/impl/ScaleLayouter.java
new file mode 100644
index 0000000..ec646d8
--- /dev/null
+++ b/coreplugins/ManualLayout/src/main/java/cytoscape/graph/layout/impl/ScaleLayouter.java
@@ -0,0 +1,170 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.graph.layout.impl;
+
+import com.nerius.math.xform.AffineTransform3D;
+import com.nerius.math.xform.Scale3D;
+import com.nerius.math.xform.Translation3D;
+
+import cytoscape.graph.layout.algorithm.MutablePolyEdgeGraphLayout;
+
+import cytoscape.util.intr.IntEnumerator;
+
+
+/**
+ *
+ */
+public final class ScaleLayouter {
+ private final MutablePolyEdgeGraphLayout m_graph;
+ private final Translation3D m_translationToOrig;
+ private final Translation3D m_translationFromOrig;
+
+ /**
+ * This operation does not affect edge anchor points which belong to edges
+ * containing at least one non-movable node.
+ **/
+ public ScaleLayouter(MutablePolyEdgeGraphLayout graph) {
+ m_graph = graph;
+
+ double xMin = Double.MAX_VALUE;
+ double xMax = Double.MIN_VALUE;
+ double yMin = Double.MAX_VALUE;
+ double yMax = Double.MIN_VALUE;
+ IntEnumerator edges = m_graph.edges();
+
+ while (edges.numRemaining() > 0) {
+ int edge = edges.nextInt();
+
+ if (!(m_graph.isMovableNode(m_graph.edgeSource(edge))
+ && m_graph.isMovableNode(m_graph.edgeTarget(edge))))
+ continue;
+
+ final int numAnchors = m_graph.getNumAnchors(edge);
+
+ for (int j = 0; j < numAnchors; j++) {
+ double anchXPosition = m_graph.getAnchorPosition(edge, j, true);
+ double anchYPosition = m_graph.getAnchorPosition(edge, j, false);
+ xMin = Math.min(xMin, anchXPosition);
+ xMax = Math.max(xMax, anchXPosition);
+ yMin = Math.min(yMin, anchYPosition);
+ yMax = Math.max(yMax, anchYPosition);
+ }
+ }
+
+ IntEnumerator nodes = m_graph.nodes();
+
+ while (nodes.numRemaining() > 0) {
+ int node = nodes.nextInt();
+
+ if (!m_graph.isMovableNode(node))
+ continue;
+
+ double nodeXPosition = m_graph.getNodePosition(node, true);
+ double nodeYPosition = m_graph.getNodePosition(node, false);
+ xMin = Math.min(xMin, nodeXPosition);
+ xMax = Math.max(xMax, nodeXPosition);
+ yMin = Math.min(yMin, nodeYPosition);
+ yMax = Math.max(yMax, nodeYPosition);
+ }
+
+ if (xMax < 0) // Nothing is movable.
+ {
+ m_translationToOrig = null;
+ m_translationFromOrig = null;
+ } else {
+ final double xRectCenter = (xMin + xMax) / 2.0d;
+ final double yRectCenter = (yMin + yMax) / 2.0d;
+ m_translationToOrig = new Translation3D(-xRectCenter, -yRectCenter, 0.0d);
+ m_translationFromOrig = new Translation3D(xRectCenter, yRectCenter, 0.0d);
+ }
+ }
+
+ private final double[] m_pointBuff = new double[3];
+
+ /**
+ * A scaleFactor of 1.0 does not move anything.
+ *
+ * @exception IllegalArgumentException if
+ * scaleFactor < 0.001 or if scaleFactor > 1000.0.
+ **/
+ public void scaleGraph(double scaleFactor) {
+ if ((scaleFactor < 0.001d) || (scaleFactor > 1000.0d))
+ throw new IllegalArgumentException("scaleFactor is outside allowable range [0.001, 1000.0]");
+
+ if (m_translationToOrig == null)
+ return;
+
+ final AffineTransform3D xform = m_translationToOrig.concatenatePost((new Scale3D(scaleFactor,
+ scaleFactor,
+ 1.0d))
+ .concatenatePost(m_translationFromOrig));
+ IntEnumerator nodes = m_graph.nodes();
+
+ while (nodes.numRemaining() > 0) {
+ int node = nodes.nextInt();
+
+ if (!m_graph.isMovableNode(node))
+ continue;
+
+ m_pointBuff[0] = m_graph.getNodePosition(node, true);
+ m_pointBuff[1] = m_graph.getNodePosition(node, false);
+ m_pointBuff[2] = 0.0d;
+ xform.transformArr(m_pointBuff);
+ m_graph.setNodePosition(node, m_pointBuff[0], m_pointBuff[1]);
+ }
+
+ IntEnumerator edges = m_graph.edges();
+
+ while (edges.numRemaining() > 0) {
+ int edge = edges.nextInt();
+
+ if (!(m_graph.isMovableNode(m_graph.edgeSource(edge))
+ && m_graph.isMovableNode(m_graph.edgeTarget(edge))))
+ continue;
+
+ final int numAnchors = m_graph.getNumAnchors(edge);
+
+ for (int j = 0; j < numAnchors; j++) {
+ m_pointBuff[0] = m_graph.getAnchorPosition(edge, j, true);
+ m_pointBuff[1] = m_graph.getAnchorPosition(edge, j, false);
+ m_pointBuff[2] = 0.0d;
+ xform.transformArr(m_pointBuff);
+ m_graph.setAnchorPosition(edge, j, m_pointBuff[0], m_pointBuff[1]);
+ }
+ }
+ }
+}
diff --git a/coreplugins/ManualLayout/src/main/java/cytoscape/graph/layout/impl/package.html b/coreplugins/ManualLayout/src/main/java/cytoscape/graph/layout/impl/package.html
new file mode 100644
index 0000000..522e71c
--- /dev/null
+++ b/coreplugins/ManualLayout/src/main/java/cytoscape/graph/layout/impl/package.html
@@ -0,0 +1,12 @@
+<html>
+<head>
+ <!-- $Revision: 1251 $
+ $Date: 2005-01-21 11:58:02 -0800 (Fri, 21 Jan 2005) $
+ $Author: nlandys $
+ -->
+</head>
+
+<body>
+Contains layout algorithm implementations.
+</body>
+</html>
diff --git a/coreplugins/ManualLayout/src/main/java/cytoscape/graph/layout/package.html b/coreplugins/ManualLayout/src/main/java/cytoscape/graph/layout/package.html
new file mode 100644
index 0000000..78efd91
--- /dev/null
+++ b/coreplugins/ManualLayout/src/main/java/cytoscape/graph/layout/package.html
@@ -0,0 +1,16 @@
+<html>
+<head>
+ <!-- $Revision: 1251 $
+ $Date: 2005-01-21 11:58:02 -0800 (Fri, 21 Jan 2005) $
+ $Author: nlandys $
+ -->
+</head>
+
+<body>
+Extends the minimalistic topological definition of a graph to include
+information about position of a graph's nodes in some space. Right now,
+"some space" means "2D real space", and I'm not sure
+how I'd structure additional code/packages if I were to support, say,
+layouts in 3D space.
+</body>
+</html>
diff --git a/coreplugins/ManualLayout/src/main/resources/H_ALIGN_CENTER.gif b/coreplugins/ManualLayout/src/main/resources/H_ALIGN_CENTER.gif
new file mode 100644
index 0000000..3ff4892
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diff --git a/coreplugins/ManualLayout/src/main/resources/H_ALIGN_LEFT.gif b/coreplugins/ManualLayout/src/main/resources/H_ALIGN_LEFT.gif
new file mode 100644
index 0000000..1e73a2d
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diff --git a/coreplugins/ManualLayout/src/main/resources/H_ALIGN_RIGHT.gif b/coreplugins/ManualLayout/src/main/resources/H_ALIGN_RIGHT.gif
new file mode 100644
index 0000000..f3f06fe
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diff --git a/coreplugins/ManualLayout/src/main/resources/H_DIST_CENTER.gif b/coreplugins/ManualLayout/src/main/resources/H_DIST_CENTER.gif
new file mode 100644
index 0000000..7485ce3
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diff --git a/coreplugins/ManualLayout/src/main/resources/H_DIST_LEFT.gif b/coreplugins/ManualLayout/src/main/resources/H_DIST_LEFT.gif
new file mode 100644
index 0000000..2d94543
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diff --git a/coreplugins/ManualLayout/src/main/resources/H_DIST_RIGHT.gif b/coreplugins/ManualLayout/src/main/resources/H_DIST_RIGHT.gif
new file mode 100644
index 0000000..8db20bd
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diff --git a/coreplugins/ManualLayout/src/main/resources/H_STACK_BOTTOM.gif b/coreplugins/ManualLayout/src/main/resources/H_STACK_BOTTOM.gif
new file mode 100644
index 0000000..771b13d
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diff --git a/coreplugins/ManualLayout/src/main/resources/H_STACK_CENTER.gif b/coreplugins/ManualLayout/src/main/resources/H_STACK_CENTER.gif
new file mode 100644
index 0000000..472dc22
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diff --git a/coreplugins/ManualLayout/src/main/resources/H_STACK_TOP.gif b/coreplugins/ManualLayout/src/main/resources/H_STACK_TOP.gif
new file mode 100644
index 0000000..6b20c05
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diff --git a/coreplugins/ManualLayout/src/main/resources/ManualLayout/plugin.props b/coreplugins/ManualLayout/src/main/resources/ManualLayout/plugin.props
new file mode 100644
index 0000000..20ac338
--- /dev/null
+++ b/coreplugins/ManualLayout/src/main/resources/ManualLayout/plugin.props
@@ -0,0 +1,30 @@
+# This props file would be filled out and included in the plugin jar file. This props file will be used
+# to put information into the Plugin Manager about the plugin
+
+# -- The following properties are REQUIRED -- #
+
+# The plugin name that will be displayed to users
+pluginName=ManualLayout
+
+# Description used to give users information about the plugin such as what it does.
+# Html tags are encouraged for formatting purposes.
+pluginDescription=User-defined positioning of layouts
+
+# Plugin version number, this must be two numbers separated by a decimlal. Ex. 0.2, 14.03
+pluginVersion=1.0
+
+# Compatible Cytoscape version
+cytoscapeVersion=2.5,2.6,2.7,2.8
+
+# Category, use one of the categories listed on the website or create your own
+pluginCategory=Core
+
+
+# List of authors. Note each author and institution pair are separated by a : (colon)
+# each additional author institution pair must be separated from other pairs bye a ; (semicolon)
+pluginAuthorsIntsitutions=Mike Smoot,Nerius Landys:UCSD;Alex Pico:UCSF;Allan Kuchinsky:Agilent Technologies
+
+# -- The following properties should be set ONLY BY CORE PLUGINS -- #
+downloadURL=http://cytoscape.org/plugins/plugins.xml
+uniqueID=12
+
diff --git a/coreplugins/ManualLayout/src/main/resources/V_ALIGN_BOTTOM.gif b/coreplugins/ManualLayout/src/main/resources/V_ALIGN_BOTTOM.gif
new file mode 100644
index 0000000..2e6caa0
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diff --git a/coreplugins/ManualLayout/src/main/resources/V_ALIGN_CENTER.gif b/coreplugins/ManualLayout/src/main/resources/V_ALIGN_CENTER.gif
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index 0000000..0ed1b61
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diff --git a/coreplugins/ManualLayout/src/main/resources/V_ALIGN_TOP.gif b/coreplugins/ManualLayout/src/main/resources/V_ALIGN_TOP.gif
new file mode 100644
index 0000000..7eeea77
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diff --git a/coreplugins/ManualLayout/src/main/resources/V_DIST_BOTTOM.gif b/coreplugins/ManualLayout/src/main/resources/V_DIST_BOTTOM.gif
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index 0000000..163bc52
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diff --git a/coreplugins/ManualLayout/src/main/resources/V_DIST_CENTER.gif b/coreplugins/ManualLayout/src/main/resources/V_DIST_CENTER.gif
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index 0000000..b36521e
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diff --git a/coreplugins/ManualLayout/src/main/resources/V_DIST_TOP.gif b/coreplugins/ManualLayout/src/main/resources/V_DIST_TOP.gif
new file mode 100644
index 0000000..cdf8e82
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diff --git a/coreplugins/ManualLayout/src/main/resources/V_STACK_CENTER.gif b/coreplugins/ManualLayout/src/main/resources/V_STACK_CENTER.gif
new file mode 100644
index 0000000..574cb6b
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diff --git a/coreplugins/ManualLayout/src/main/resources/V_STACK_LEFT.gif b/coreplugins/ManualLayout/src/main/resources/V_STACK_LEFT.gif
new file mode 100644
index 0000000..25092e3
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diff --git a/coreplugins/ManualLayout/src/main/resources/V_STACK_RIGHT.gif b/coreplugins/ManualLayout/src/main/resources/V_STACK_RIGHT.gif
new file mode 100644
index 0000000..79f38c6
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diff --git a/coreplugins/NCBIClient/pom.xml b/coreplugins/NCBIClient/pom.xml
new file mode 100644
index 0000000..13b18ab
--- /dev/null
+++ b/coreplugins/NCBIClient/pom.xml
@@ -0,0 +1,75 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>parent</artifactId>
+ <version>2.8.4-SNAPSHOT</version>
+ </parent>
+
+ <artifactId>ncbi-client</artifactId>
+ <packaging>jar</packaging>
+
+ <name>NCBI Client</name>
+
+ <!-- bootstrap for cytoscape dependencies, namely the parent POM snapshots -->
+ <repositories>
+ <repository>
+ <id>cytoscape_snapshots</id>
+ <snapshots>
+ <enabled>true</enabled>
+ </snapshots>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <name>Cytoscape Snapshots</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/</url>
+ </repository>
+ <repository>
+ <id>cytoscape_releases</id>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ <name>Cytoscape Releases</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/releases/</url>
+ </repository>
+ </repositories>
+
+ <build>
+ <plugins>
+ <plugin>
+ <artifactId>maven-assembly-plugin</artifactId>
+ <configuration>
+ <archive>
+ <manifestEntries>
+ <Cytoscape-Plugin>edu.ucsd.bioeng.idekerlab.ncbiclient.NCBIClientPlugin</Cytoscape-Plugin>
+ </manifestEntries>
+ </archive>
+ </configuration>
+ </plugin>
+ </plugins>
+ </build>
+
+ <dependencies>
+ <dependency>
+ <groupId>cytoscape-temp</groupId>
+ <artifactId>ncbi-eutil2-core</artifactId>
+ <version>1.0</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape-temp</groupId>
+ <artifactId>ncbi-eutil2-gene</artifactId>
+ <version>1.0</version>
+ </dependency>
+ <dependency>
+ <groupId>junit</groupId>
+ <artifactId>junit</artifactId>
+ <version>4.8.1</version>
+ <scope>test</scope>
+ </dependency>
+ </dependencies>
+
+</project>
+
diff --git a/coreplugins/NCBIClient/src/main/java/edu/ucsd/bioeng/idekerlab/ncbiclient/NCBIClient.java b/coreplugins/NCBIClient/src/main/java/edu/ucsd/bioeng/idekerlab/ncbiclient/NCBIClient.java
new file mode 100644
index 0000000..adf8256
--- /dev/null
+++ b/coreplugins/NCBIClient/src/main/java/edu/ucsd/bioeng/idekerlab/ncbiclient/NCBIClient.java
@@ -0,0 +1,1471 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package edu.ucsd.bioeng.idekerlab.ncbiclient;
+
+import edu.ucsd.bioeng.idekerlab.ncbiclient.util.BioGRIDUtil;
+import edu.ucsd.bioeng.idekerlab.ncbiclient.util.VisualStyleBuilder;
+import giny.model.Edge;
+import giny.model.Node;
+import giny.view.NodeView;
+import gov.nih.ncbi.soap.eutils.gene.Dbtag;
+import gov.nih.ncbi.soap.eutils.gene.EFetchGeneService;
+import gov.nih.ncbi.soap.eutils.gene.EFetchRequest;
+import gov.nih.ncbi.soap.eutils.gene.EFetchResult;
+import gov.nih.ncbi.soap.eutils.gene.Entrezgene;
+import gov.nih.ncbi.soap.eutils.gene.GeneCommentary;
+import gov.nih.ncbi.soap.eutils.gene.GeneRef;
+import gov.nih.ncbi.soap.eutils.gene.OtherSource;
+import gov.nih.ncbi.soap.eutils.gene.Pub;
+import gov.nih.ncbi.soap.eutils.gene.Entrezgene.EntrezgeneType;
+import gov.nih.ncbi.soap.eutils.gene.GeneRef.GeneRefDb;
+import gov.nih.ncbi.soap.eutils.gene.GeneRef.GeneRefSyn;
+import gov.nih.nlm.ncbi.soap.eutils.EUtilsService;
+import gov.nih.nlm.ncbi.soap.eutils.EUtilsServiceSoap;
+import gov.nih.nlm.ncbi.soap.eutils.esearch.ESearchRequest;
+import gov.nih.nlm.ncbi.soap.eutils.esearch.ESearchResult;
+import gov.nih.nlm.ncbi.soap.eutils.esearch.IdListType;
+
+import java.beans.PropertyChangeEvent;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.concurrent.Callable;
+import java.util.concurrent.ConcurrentHashMap;
+import java.util.concurrent.ConcurrentMap;
+import java.util.concurrent.CopyOnWriteArrayList;
+import java.util.concurrent.ExecutionException;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
+import java.util.concurrent.Future;
+import java.util.concurrent.FutureTask;
+import java.util.concurrent.TimeUnit;
+import java.util.concurrent.TimeoutException;
+
+import javax.swing.Icon;
+import javax.swing.ImageIcon;
+import javax.swing.JMenuItem;
+import javax.swing.JPanel;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import cytoscape.data.CyAttributes;
+import cytoscape.data.webservice.AttributeImportQuery;
+import cytoscape.data.webservice.CyWebServiceEvent;
+import cytoscape.data.webservice.CyWebServiceEventListener;
+import cytoscape.data.webservice.CyWebServiceException;
+import cytoscape.data.webservice.DatabaseSearchResult;
+import cytoscape.data.webservice.NetworkImportWebServiceClient;
+import cytoscape.data.webservice.WebServiceClient;
+import cytoscape.data.webservice.WebServiceClientImplWithGUI;
+import cytoscape.data.webservice.WebServiceClientManager;
+import cytoscape.data.webservice.CyWebServiceEvent.WSEventType;
+import cytoscape.data.webservice.CyWebServiceEvent.WSResponseType;
+import cytoscape.data.webservice.WebServiceClientManager.ClientType;
+import cytoscape.data.webservice.util.NetworkExpansionMenu;
+import cytoscape.layout.Tunable;
+import cytoscape.util.ModulePropertiesImpl;
+import cytoscape.visual.VisualStyle;
+
+/**
+ * NCBI Web Service Client Plugin main class.
+ * <p>This is part of the core since 2.7.</p>
+ *
+ *
+ * @author kono
+ * @since Cytoscape 2.7
+ */
+public class NCBIClient extends
+ WebServiceClientImplWithGUI<EUtilsServiceSoap, JPanel> implements
+ NetworkImportWebServiceClient {
+
+ private static final long serialVersionUID = -8920082175139743743L;
+
+ private static final Icon ABOUT_ICON = new ImageIcon(NCBIClient.class
+ .getResource("/images/entrez32.png"));
+
+ /**
+ * Annotation categories available in NCBI
+ *
+ * @author kono
+ *
+ */
+ public enum AnnotationCategory {
+ SUMMARY("Summary"), PUBLICATION("Publications"), PHENOTYPE("Phenotypes"), PATHWAY(
+ "Pathways"), GENERAL("General Protein Information"), LINK(
+ "Additional Links"),
+
+ // MARKERS("Markers"),
+ GO("Gene Ontology");
+ private String name;
+
+ private AnnotationCategory(String name) {
+ this.name = name;
+ }
+
+ public String getName() {
+ return name;
+ }
+
+ public static AnnotationCategory getValue(String dispName) {
+ for (AnnotationCategory ann : values()) {
+ if (ann.name.equals(dispName)) {
+ return ann;
+ }
+ }
+
+ return null;
+ }
+ }
+
+ private static final String GENE_ID_TAG = "GeneID";
+
+ // Display name for this Client
+ private static final String DISPLAY_NAME = "NCBI Entrez EUtilities Web Service Client";
+
+ // Client's ID
+ private static final String CLIENT_ID = "ncbi_entrez";
+ private static NCBIClient client;
+ private static final String DEF_ITR_TYPE = "pp";
+ private CopyOnWriteArrayList<Node> nodeList;
+ private CopyOnWriteArrayList<Edge> edgeList;
+ private ConcurrentMap<String, String> nodeAltName;
+ private ConcurrentMap<String, String> nodeTypes;
+
+ private Boolean canceled = null;
+ private ExecutorService executer;
+
+ private Map<String[], Object> attrMap = new ConcurrentHashMap<String[], Object>();
+ private List<AnnotationCategory> selectedAnn = new ArrayList<AnnotationCategory>();
+ private int threadNum;
+ private int buketNum;
+ private static final int DEF_BUCKET_SIZE = 10;
+ private static final int DEF_POOL_SIZE = Runtime.getRuntime()
+ .availableProcessors() * 2;
+ private Map<String, Set<String>> reverseMap;
+
+ // Visual Style name for the networks generated by this client.
+
+ static {
+ try {
+ client = new NCBIClient();
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static WebServiceClient<EUtilsServiceSoap> getClient() {
+ return client;
+ }
+
+ /**
+ * Creates a new NCBIClient object.
+ *
+ * @throws CyWebServiceException
+ *
+ * @throws Exception
+ * DOCUMENT ME!
+ */
+ public NCBIClient() throws CyWebServiceException {
+ super(CLIENT_ID, DISPLAY_NAME, new ClientType[] { ClientType.NETWORK,
+ ClientType.ATTRIBUTE }, null, null, null);
+
+ EUtilsService service = new EUtilsService();
+
+ clientStub = service.getEUtilsServiceSoap();
+
+ props = new ModulePropertiesImpl(clientID, "wsc");
+ props.add(new Tunable("timeout", "Timeout for search (sec.)",
+ Tunable.INTEGER, new Integer(6000)));
+ props.add(new Tunable("max_search_result",
+ "Maximum number of search result", Tunable.INTEGER,
+ new Integer(10000)));
+ props.add(new Tunable("thread_pool_size", "Thread pool size",
+ Tunable.INTEGER, new Integer(DEF_POOL_SIZE)));
+ props.add(new Tunable("buket_size", "Number of IDs send at once",
+ Tunable.INTEGER, new Integer(DEF_BUCKET_SIZE)));
+
+ prepareDescription();
+
+ executer = Executors.newFixedThreadPool(DEF_POOL_SIZE);
+ }
+
+ private void prepareDescription() {
+ description = "http://www.ncbi.nlm.nih.gov/entrez/query/static/esoap_help.html";
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ * @throws CyWebServiceException
+ */
+ @Override
+ public void executeService(CyWebServiceEvent e)
+ throws CyWebServiceException {
+ if (e.getSource().equals(CLIENT_ID)) {
+ if (e.getEventType().equals(WSEventType.IMPORT_NETWORK)) {
+ importNetwork(e.getParameter(), null);
+ } else if (e.getEventType().equals(WSEventType.EXPAND_NETWORK)) {
+ importNetwork(e.getParameter(), Cytoscape.getCurrentNetwork());
+ } else if (e.getEventType().equals(WSEventType.SEARCH_DATABASE)) {
+ search(e);
+ } else if (e.getEventType().equals(WSEventType.IMPORT_ATTRIBUTE)) {
+ importAnnotations(e.getParameter());
+ }
+ }
+ }
+
+ private void search(CyWebServiceEvent<String> e)
+ throws CyWebServiceException {
+ final ESearchRequest searchParam = new ESearchRequest();
+ final String keyword = e.getParameter();
+
+ searchParam.setDb("gene");
+ searchParam.setRetMax(props.getValue("max_search_result"));
+ // keyword = keyword.replace(" ", "+");
+ searchParam.setTerm(keyword);
+
+ ESearchResult result = null;
+
+ long startTime = System.currentTimeMillis();
+ executer = Executors.newSingleThreadExecutor();
+
+ Future<ESearchResult> res = executer.submit(new SearchDatabaseTask(
+ searchParam));
+
+ try {
+ result = res.get(Integer.parseInt(props.getValue("timeout")),
+ TimeUnit.SECONDS);
+
+ long endTime = System.currentTimeMillis();
+ double sec = (endTime - startTime) / (1000.0);
+ System.out.println("NCBI Search finished in " + sec + " msec.");
+ } catch (ExecutionException ee) {
+ // TODO Auto-generated catch block
+ ee.printStackTrace();
+ } catch (TimeoutException te) {
+ // TODO Auto-generated catch block
+ te.printStackTrace();
+ } catch (InterruptedException ie) {
+ // TODO Auto-generated catch block
+ ie.printStackTrace();
+ } finally {
+ res.cancel(true);
+ executer.shutdown();
+ }
+
+ if (result == null) {
+ return;
+ }
+
+ final String count = result.getCount();
+ final int resSize = (count == null) ? 0 : Integer.parseInt(count);
+
+ if (e.getNextMove() != null) {
+ Cytoscape.firePropertyChange(WSResponseType.SEARCH_FINISHED
+ .toString(), this.clientID,
+ new DatabaseSearchResult<ESearchResult>(resSize, result, e
+ .getNextMove()));
+ } else {
+ Cytoscape.firePropertyChange(WSResponseType.SEARCH_FINISHED
+ .toString(), this.clientID,
+ new DatabaseSearchResult<ESearchResult>(Integer
+ .getInteger(result.getCount()), result,
+ WSEventType.IMPORT_NETWORK));
+ }
+ }
+
+ private void importAnnotations(Object parameter)
+ throws CyWebServiceException {
+ /*
+ * Extract parameter from the message object
+ */
+ if (parameter instanceof AttributeImportQuery == false)
+ return;
+
+ final Object[] selectedAttr = (Object[]) ((AttributeImportQuery) parameter)
+ .getParameter();
+
+ AnnotationCategory ann;
+ selectedAnn = new ArrayList<AnnotationCategory>();
+
+ for (Object name : selectedAttr) {
+ System.out.println("Category Selected: " + name);
+ ann = AnnotationCategory.getValue(name.toString());
+
+ if (ann != null)
+ selectedAnn.add(ann);
+ }
+
+ final String keyAttrName = ((AttributeImportQuery) parameter)
+ .getKeyCyAttrName();
+ System.out.println("Mapping key attribute name: " + keyAttrName);
+
+ // nodeAttrMap = new ConcurrentHashMap<String[], Object>();
+ attrMap = new ConcurrentHashMap<String[], Object>();
+
+ long startTime = System.currentTimeMillis();
+ setPerformanceParameters();
+
+ final ExecutorService e = Executors.newFixedThreadPool(threadNum);
+
+ final List<Node> nodes = Cytoscape.getRootGraph().nodesList();
+
+ final Set<String> query = new HashSet<String>();
+
+ if (keyAttrName == "ID")
+ for (Node n : nodes) {
+ if (n.getIdentifier().contains(":") == false)
+ query.add(n.getIdentifier());
+ }
+ else {
+ reverseMap = new HashMap<String, Set<String>>();
+
+ Set<String> ids;
+ Object attrVal = null;
+ CyAttributes nodeAttr = Cytoscape.getNodeAttributes();
+
+ for (Node n : nodes) {
+ if (nodeAttr.getType(keyAttrName) == CyAttributes.TYPE_SIMPLE_LIST) {
+ attrVal = nodeAttr.getListAttribute(n.getIdentifier(),
+ keyAttrName);
+ } else {
+ attrVal = nodeAttr.getAttribute(n.getIdentifier(),
+ keyAttrName);
+ }
+
+ if (attrVal != null) {
+ if (attrVal.getClass() == String.class) {
+ if (attrVal.toString().contains(":") == false) {
+ query.add(attrVal.toString());
+ ids = reverseMap.get(attrVal.toString());
+
+ if (ids == null) {
+ ids = new HashSet<String>();
+ }
+
+ ids.add(n.getIdentifier());
+ reverseMap.put(attrVal.toString(), ids);
+ }
+ } else if (attrVal instanceof List) {
+ for (Object val : ((List) attrVal)) {
+ if (val.toString().contains(":") == false) {
+ query.add(val.toString());
+ ids = reverseMap.get(val.toString());
+
+ if (ids == null)
+ ids = new HashSet<String>();
+
+ ids.add(n.getIdentifier());
+ reverseMap.put(val.toString(), ids);
+ }
+ }
+ }
+ }
+ }
+ }
+
+ System.out.println("Number of EntrezGene ID to be sent: "
+ + query.size());
+
+ int group = 0;
+ String[] box = new String[buketNum];
+
+ for (String q : query) {
+ box[group] = q;
+ group++;
+
+ if (group == buketNum) {
+ e.submit(new ImportTask(new ImportAnnotationTask(box)));
+ group = 0;
+ box = new String[buketNum];
+ }
+ }
+
+ String[] newbox = new String[group];
+
+ for (int i = 0; i < group; i++) {
+ newbox[i] = box[i];
+ }
+
+ e.submit(new ImportTask(new ImportAnnotationTask(newbox)));
+
+ try {
+ e.shutdown();
+ e.awaitTermination(Integer.parseInt(props.getValue("timeout")),
+ TimeUnit.SECONDS);
+
+ long endTime = System.currentTimeMillis();
+ double msec = (endTime - startTime) / (1000.0);
+ System.out.println("NCBI Import finished in " + msec + " sec.");
+
+ if ((canceled != null) && canceled) {
+ canceled = null;
+
+ return;
+ }
+
+ // Copy to CyAttributes.
+ final CyAttributes nodeAttr = Cytoscape.getNodeAttributes();
+
+ Object attrVal;
+
+ if (keyAttrName.equals("ID")) {
+ for (String[] key : attrMap.keySet()) {
+ attrVal = attrMap.get(key);
+
+ if (attrVal instanceof List) {
+ nodeAttr.setListAttribute(key[0], key[1],
+ (List) attrVal);
+ } else {
+ nodeAttr.setAttribute(key[0], key[1], attrVal
+ .toString());
+ }
+ }
+ } else {
+ System.out.println("This is not ID. ATTR conv.");
+
+ // Need to convert attr to node ID
+ for (String[] key : attrMap.keySet()) {
+ attrVal = attrMap.get(key);
+
+ Set<String> nodeIDs = reverseMap.get(key[0]);
+
+ for (String id : nodeIDs) {
+ if (attrVal instanceof List) {
+ nodeAttr.setListAttribute(id, key[1],
+ (List) attrVal);
+ } else {
+ nodeAttr.setAttribute(id, key[1], attrVal
+ .toString());
+ }
+ }
+ }
+ }
+
+ Cytoscape.firePropertyChange(Cytoscape.ATTRIBUTES_CHANGED, null,
+ null);
+ } catch (InterruptedException e1) {
+ System.out.println("TIMEOUT!");
+ throw new CyWebServiceException(
+ CyWebServiceException.WSErrorCode.REMOTE_EXEC_FAILED);
+ }
+ }
+
+ public CyNetwork importNetwork(ESearchResult result)
+ throws CyWebServiceException {
+ return importNetwork(result, null);
+ }
+
+ private void setPerformanceParameters() {
+ final String threadPool = props.getValue("thread_pool_size");
+ threadNum = DEF_POOL_SIZE;
+
+ try {
+ threadNum = Integer.parseInt(threadPool);
+ } catch (NumberFormatException e) {
+ threadNum = DEF_POOL_SIZE;
+ }
+
+ final String buket = props.getValue("buket_size");
+
+ try {
+ buketNum = Integer.parseInt(buket);
+ } catch (NumberFormatException e) {
+ buketNum = DEF_BUCKET_SIZE;
+ }
+ }
+
+ private CyNetwork importNetwork(Object searchResult, CyNetwork net)
+ throws CyWebServiceException {
+ ESearchResult res = (ESearchResult) searchResult;
+ IdListType ids = res.getIdList();
+
+ nodeList = new CopyOnWriteArrayList<Node>();
+ edgeList = new CopyOnWriteArrayList<Edge>();
+
+ nodeAltName = new ConcurrentHashMap<String, String>();
+ nodeTypes = new ConcurrentHashMap<String, String>();
+
+ System.gc();
+
+ long startTime = System.currentTimeMillis();
+ setPerformanceParameters();
+
+ executer = Executors.newFixedThreadPool(threadNum);
+
+ System.out.println("Thread Pool Initialized.");
+
+ int group = 0;
+ String[] box = new String[buketNum];
+
+ for (String entrezID : ids.getId()) {
+ box[group] = entrezID;
+ group++;
+
+ if (group == buketNum) {
+ executer.submit(new ImportTask(new ImportNetworkTask(box)));
+ group = 0;
+ box = new String[buketNum];
+ }
+ }
+
+ String[] newbox = new String[group];
+
+ for (int i = 0; i < group; i++)
+ newbox[i] = box[i];
+
+ executer.submit(new ImportTask(new ImportNetworkTask(newbox)));
+
+ try {
+ executer.shutdown();
+ executer.awaitTermination(Integer.parseInt(props
+ .getValue("timeout")), TimeUnit.SECONDS);
+
+ long endTime = System.currentTimeMillis();
+ double sec = (endTime - startTime) / (1000.0);
+ System.out.println("Finished in " + sec + " sec.");
+
+ if ((canceled != null) && canceled) {
+ canceled = null;
+
+ return null;
+ }
+
+ // Set attributes
+ CyAttributes nodeAttr = Cytoscape.getNodeAttributes();
+ CyAttributes edgeAttr = Cytoscape.getEdgeAttributes();
+
+ Object attrVal;
+ for (String key : nodeAltName.keySet()) {
+ if (nodeAltName.get(key) != null)
+ nodeAttr.setAttribute(key, "Alt Name", nodeAltName.get(key));
+ if (nodeTypes.get(key) != null)
+ nodeAttr.setAttribute(key, "Interactor Type", nodeTypes.get(key));
+ }
+
+ for (String[] key : attrMap.keySet()) {
+ attrVal = attrMap.get(key);
+
+ if (attrVal instanceof List) {
+ edgeAttr.setListAttribute(key[0], key[1], (List) attrVal);
+ } else {
+ edgeAttr.setAttribute(key[0], key[1], attrVal.toString());
+ }
+ }
+
+ if (net == null) {
+
+ net = Cytoscape.createNetwork(nodeList, edgeList, "NCBI-Net",
+ null, true);
+ Cytoscape.getVisualMappingManager().setVisualStyle(getDefaultVisualStyle());
+
+ Cytoscape.firePropertyChange(
+ WSResponseType.DATA_IMPORT_FINISHED.toString(), null,
+ net);
+ } else {
+ for (Node node : nodeList) {
+ net.addNode(node);
+ }
+
+ for (Edge edge : edgeList) {
+ net.addEdge(edge);
+ }
+
+ net.setSelectedNodeState(nodeList, true);
+
+ final PropertyChangeEvent pce = new PropertyChangeEvent(this,
+ Cytoscape.NETWORK_MODIFIED, null, null);
+ Cytoscape.getPropertyChangeSupport().firePropertyChange(pce);
+ }
+
+ } catch (InterruptedException e1) {
+ System.out.println("TIMEOUT");
+ throw new CyWebServiceException(
+ CyWebServiceException.WSErrorCode.REMOTE_EXEC_FAILED);
+ } finally {
+ nodeList.clear();
+ edgeList.clear();
+ nodeAltName.clear();
+ nodeTypes.clear();
+
+ nodeList = null;
+ edgeList = null;
+ nodeAltName = null;
+ nodeTypes = null;
+
+ System.gc();
+ }
+
+ return net;
+ }
+
+ class ImportTask extends FutureTask implements CyWebServiceEventListener {
+ public ImportTask(Callable task) {
+ super(task);
+ WebServiceClientManager.getCyWebServiceEventSupport()
+ .addCyWebServiceEventListener(this);
+ }
+
+ public void executeService(CyWebServiceEvent event)
+ throws CyWebServiceException {
+ if (event.getEventType().equals(WSEventType.CANCEL)) {
+ cancel(true);
+
+ if (canceled == null)
+ canceled = true;
+ }
+ }
+ }
+
+ /**
+ * Thereads which will be executed
+ *
+ * @author kono
+ *
+ */
+ class ImportNetworkTask implements Callable {
+ private String[] entrezID;
+
+ public ImportNetworkTask(String[] id) {
+ this.entrezID = id;
+ }
+
+ public void run() {
+ final EFetchRequest parameters = new EFetchRequest();
+ final EFetchGeneService geneService = new EFetchGeneService();
+ final gov.nih.ncbi.soap.eutils.gene.EUtilsServiceSoap geneServiceStub = geneService
+ .getEUtilsServiceSoap();
+
+ final StringBuilder builder = new StringBuilder();
+
+ for (String id : entrezID)
+ builder.append(id + ",");
+
+ String query = builder.toString();
+ System.out.println("Current Query ====> " + query);
+ parameters.setId(query.substring(0, query.length() - 1));
+
+ EFetchResult res = null;
+
+ int retryCounter = 0;
+
+ while (res == null) {
+ try {
+ res = geneServiceStub.runEFetch(parameters);
+ } catch (Exception e) {
+ // TODO Auto-generated catch block
+ // e.printStackTrace();
+ res = null;
+
+ try {
+ System.out.println("Could not fetch data from NCBI: "
+ + query.substring(0, query.length()));
+ TimeUnit.SECONDS.sleep(1);
+ } catch (InterruptedException e2) {
+ System.out.println("Interrupted: "
+ + query.substring(0, query.length() - 1));
+ }
+ }
+
+ if ((res == null) && (retryCounter < 3))
+ System.out.println("Retry: "
+ + query.substring(0, query.length() - 1));
+ else if ((res == null) && (retryCounter >= 3))
+ return;
+
+ retryCounter++;
+ }
+
+ // Create network from Interactions section
+ final int entryLen = res.getEntrezgeneSet().getEntrezgene().size();
+ Node centerNode = null;
+ String interactionType = null;
+
+ // String sourceDB = null;
+ String otherGeneName = null;
+ String nodeid = null;
+ List<GeneCommentary> gc = null;
+ List<GeneCommentary> interactions = null;
+
+ Node n1;
+
+ // Edge e1;
+ String edgeID;
+
+ String nodeType = null;
+ String altName = null;
+
+ for (int i = 0; i < entryLen; i++) {
+ if ((canceled != null) && canceled)
+ return;
+
+ // Get commentary section.
+ gc = res.getEntrezgeneSet().getEntrezgene().get(i)
+ .getEntrezgeneComments().getGeneCommentary();
+
+ for (GeneCommentary g : gc) {
+ if ((g.getGeneCommentaryHeading() != null)
+ && g.getGeneCommentaryHeading().equals(
+ "Interactions")) {
+ // Interaction section found.
+ try {
+ centerNode = Cytoscape.getCyNode(res
+ .getEntrezgeneSet().getEntrezgene().get(i)
+ .getEntrezgeneTrackInfo().getGeneTrack()
+ .getGeneTrackGeneid().toString(), true);
+ // Add attributes
+ final String centerNodeAltName = res.getEntrezgeneSet().getEntrezgene().get(i).getEntrezgeneGene().getGeneRef().getGeneRefLocus();
+ if(centerNodeAltName != null)
+ nodeAltName.put(centerNode.getIdentifier(), centerNodeAltName);
+ // Center node is always a gene in Entrez Gene Database.
+ nodeTypes.put(centerNode.getIdentifier(), "GeneID");
+ System.out.println("Got Interactions for: "
+ + centerNode.getIdentifier());
+ } catch (Exception e) {
+ System.out.println("NPE!!!!!!!!!!!!!!!!");
+ }
+
+ nodeList.add(centerNode);
+
+ // Parse individual interactions.
+ interactions = g.getGeneCommentaryComment()
+ .getGeneCommentary();
+
+ for (GeneCommentary itr : interactions) {
+ interactionType = itr.getGeneCommentaryText();
+
+ if (interactionType == null) {
+ interactionType = DEF_ITR_TYPE;
+ }
+
+ if (itr.getGeneCommentaryComment()
+ .getGeneCommentary().size() > 1) {
+ // Find node ID. If available, use Entrez Gene
+ // ID.
+ // If not, use the database-specific ID instead.
+ try {
+ nodeid = itr.getGeneCommentaryComment()
+ .getGeneCommentary().get(1)
+ .getGeneCommentarySource()
+ .getOtherSource().get(0)
+ .getOtherSourceSrc().getDbtag()
+ .getDbtagTag().getObjectId()
+ .getObjectIdId().toString();
+ } catch (NullPointerException npe) {
+ // This gene is not in NCBI DB.
+ // Use original database ID
+ continue;
+ }
+
+ // Check source Type
+
+ nodeType = itr.getGeneCommentaryComment()
+ .getGeneCommentary().get(1)
+ .getGeneCommentarySource()
+ .getOtherSource().get(0)
+ .getOtherSourceSrc().getDbtag()
+ .getDbtagDb();
+
+// System.out.println("DB Tag for nodeID: "
+// + nodeid + " = " + nodeType);
+
+ // In case ID is not GeneID, put tag
+ if (nodeType.equals(GENE_ID_TAG) == false) {
+ nodeid = nodeType + ":" + nodeid;
+ }
+
+ n1 = Cytoscape.getCyNode(nodeid, true);
+ nodeList.add(n1);
+
+ // Add node attributes
+ nodeTypes.put(nodeid, nodeType);
+
+ altName = itr.getGeneCommentaryComment()
+ .getGeneCommentary().get(1)
+ .getGeneCommentarySource()
+ .getOtherSource().get(0)
+ .getOtherSourceAnchor();
+ if (altName != null && altName.length() != 0)
+ nodeAltName.put(nodeid, altName);
+
+ final String dataSource = itr
+ .getGeneCommentarySource()
+ .getOtherSource().get(0)
+ .getOtherSourceSrc().getDbtag()
+ .getDbtagDb();
+
+ List<Edge> eList2 = new ArrayList<Edge>();
+
+ if (dataSource.equals("BioGRID")) {
+ final String[] expTypes = interactionType
+ .split(";");
+
+ String etString = null;
+ Edge newEdge = null;
+
+ for (String eType : expTypes) {
+ etString = eType.trim();
+
+ eList2.add(newEdge = Cytoscape
+ .getCyEdge(centerNode, n1,
+ "interaction",
+ etString, true));
+
+ if (dataSource.equals("BioGRID")) {
+ attrMap
+ .put(
+ new String[] {
+ newEdge
+ .getIdentifier(),
+ "interaction type" },
+ BioGRIDUtil
+ .getInteractionType(etString));
+ }
+ }
+ } else {
+ eList2.add(Cytoscape.getCyEdge(centerNode,
+ n1, "interaction", interactionType,
+ true));
+ }
+
+ // e1 = Cytoscape.getCyEdge(centerNode, n1,
+ // "interaction", interactionType, true);
+ for (Edge e1 : eList2) {
+ edgeList.add(e1);
+ edgeID = e1.getIdentifier();
+
+ // Add edge attributes
+ attrMap.put(new String[] { edgeID,
+ "datasource" }, dataSource);
+
+ List<Pub> pubmed = itr
+ .getGeneCommentaryRefs().getPub();
+
+ if ((pubmed != null) && (pubmed.size() > 0)) {
+ String[] pmid = new String[] { edgeID,
+ "PubMed ID" };
+ List<String> pmids = new ArrayList<String>();
+
+ for (Pub pub : pubmed) {
+ pmids.add(pub.getPubPmid()
+ .getPubMedId().toString());
+ }
+
+ attrMap.put(pmid, pmids);
+ } // /
+ }
+ }
+ }
+
+ break;
+ }
+ }
+ }
+ }
+
+ public Object call() throws Exception {
+ run();
+
+ return null;
+ }
+ }
+
+ // Task for importing annotations
+ //
+ class SearchDatabaseTask implements Callable<ESearchResult> {
+ private final ESearchRequest query;
+
+ public SearchDatabaseTask(final ESearchRequest query) {
+ this.query = query;
+ }
+
+ public ESearchResult call() throws Exception {
+ ESearchResult result = null;
+ result = clientStub.runESearch(query);
+ return result;
+ }
+ }
+
+ // Task for importing annotations
+ //
+ class ImportAnnotationTask implements Callable {
+ private String[] ids;
+
+ public ImportAnnotationTask(String[] ids) {
+ this.ids = ids;
+ }
+
+
+ public Object call() {
+ StringBuilder builder = new StringBuilder();
+ final EFetchRequest parameters = new EFetchRequest();
+ final EFetchGeneService geneService = new EFetchGeneService();
+ final gov.nih.ncbi.soap.eutils.gene.EUtilsServiceSoap geneServiceStub = geneService
+ .getEUtilsServiceSoap();
+
+ int numIDs = 0;
+
+ for (String id : ids) {
+
+ try {
+ // Entrez ID should be an integer
+ Integer.parseInt(id);
+ builder.append(id + ",");
+ numIDs++;
+ } catch (NumberFormatException ne) {
+ continue;
+ }
+ }
+
+ String query = builder.toString();
+ query = query.substring(0, query.length() - 1);
+ System.out.println("Current Query String ====> " + query);
+ parameters.setId(query);
+
+ EFetchResult res = null;
+ int retry = 0;
+
+ while (res == null) {
+ try {
+ res = geneServiceStub.runEFetch(parameters);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+
+ res = null;
+
+ try {
+ retry++;
+ System.out.println("Data fetching failed for: "
+ + query.substring(0, query.length()));
+ TimeUnit.SECONDS.sleep(1);
+ } catch (InterruptedException e2) {
+ // TODO Auto-generated catch block
+ System.out.println("Time out!");
+ }
+ }
+
+ if ((res == null) && (retry < 3)) {
+ System.out.println("Retry: " + query);
+ } else if (retry >= 3) {
+ return null;
+ }
+ }
+
+ final List<Entrezgene> entries = res.getEntrezgeneSet()
+ .getEntrezgene();
+
+ for (Entrezgene entry : entries) {
+ if ((canceled != null) && canceled) {
+ System.out.println("Operation canceled by user.");
+
+ return null;
+ }
+
+ // Current target gene ID
+ String entrezID = entry.getEntrezgeneTrackInfo().getGeneTrack()
+ .getGeneTrackGeneid().toString();
+
+ System.out.println("Extracting annotation for: " + entrezID);
+
+ try {
+ // Extract summary
+ if (selectedAnn.contains(AnnotationCategory.SUMMARY)) {
+ // Species
+ String species = entry.getEntrezgeneSource()
+ .getBioSource().getBioSourceOrg().getOrgRef()
+ .getOrgRefTaxname();
+ String[] sp = new String[] { entrezID, "Speices" };
+ attrMap.put(sp, species);
+
+ // General info
+ final GeneRef geneRef = entry.getEntrezgeneGene()
+ .getGeneRef();
+
+ if (geneRef != null) {
+ // Extract Official Symbol
+ final String officialSymbol = geneRef
+ .getGeneRefLocus();
+
+ if (officialSymbol != null) {
+ String[] os = new String[] { entrezID,
+ "Official Symbol" };
+ attrMap.put(os, officialSymbol);
+ }
+
+ // Extract Locus Tag
+ final String locusTag = geneRef
+ .getGeneRefLocusTag();
+
+ if (locusTag != null) {
+ String[] lt = new String[] { entrezID,
+ "Locus Tag" };
+ attrMap.put(lt, locusTag);
+ }
+
+ // Extract Location
+ final String mapLoc = geneRef.getGeneRefMaploc();
+
+ if (mapLoc != null) {
+ String[] ds = new String[] { entrezID,
+ "Location" };
+ attrMap.put(ds, mapLoc);
+ }
+
+ // Extract source DB and its ID
+ final GeneRefDb db = geneRef.getGeneRefDb();
+
+ if ((db != null) && (db.getDbtag() != null)
+ && (db.getDbtag().size() != 0)) {
+ final List<String> dbNames = new ArrayList<String>();
+ final List<String> dbID = new ArrayList<String>();
+
+ String id;
+ String idStr;
+
+ for (Dbtag dbTag : db.getDbtag()) {
+ dbNames.add(dbTag.getDbtagDb());
+
+ id = dbTag.getDbtagTag().getObjectId()
+ .getObjectIdStr();
+ idStr = dbTag.getDbtagTag().getObjectId()
+ .getObjectIdStr();
+
+ String[] singleID = new String[] {
+ entrezID,
+
+ dbTag.getDbtagDb() + " ID" };
+
+ if (id != null) {
+ dbID.add(id);
+ attrMap.put(singleID, id);
+ } else if (idStr != null) {
+ dbID.add(idStr);
+ attrMap.put(singleID, idStr);
+ }
+ }
+
+ String[] dbn = new String[] { entrezID,
+ "Source Database" };
+ attrMap.put(dbn, dbNames);
+
+ String[] dbid = new String[] { entrezID,
+ "Source Database ID" };
+ attrMap.put(dbid, dbID);
+ }
+
+ final GeneRefSyn syn = geneRef.getGeneRefSyn();
+
+ if ((syn != null) && (syn.getGeneRefSynE() != null)
+ && (syn.getGeneRefSynE().size() != 0)) {
+ final List<String> synonyms = new ArrayList<String>();
+
+ for (String synonym : syn.getGeneRefSynE())
+ synonyms.add(synonym);
+
+ String[] sy = new String[] { entrezID,
+ "aliases" };
+ attrMap.put(sy, synonyms);
+ }
+
+ // Extract (official full name)
+ final String desc = geneRef.getGeneRefDesc();
+
+ if (desc != null) {
+ String[] ds = new String[] { entrezID,
+ "Description" };
+ attrMap.put(ds, desc);
+ }
+
+ final EntrezgeneType t = entry.getEntrezgeneType();
+
+ if ((t != null) && (t.getValue() != null)) {
+ String[] ds = new String[] { entrezID,
+ "Gene Type" };
+ attrMap.put(ds, t.getValue().toString());
+ }
+
+ // Extract summary
+ final String summary = entry.getEntrezgeneSummary();
+
+ if (summary != null) {
+ String[] sm = new String[] { entrezID,
+ "Summary" };
+ attrMap.put(sm, summary);
+ }
+ }
+ }
+
+ if (selectedAnn.contains(AnnotationCategory.GENERAL)) {
+ // Prot. info
+ List<String> proteinInfo = new ArrayList<String>();
+
+ if ((entry.getEntrezgeneProt() != null)
+ && (entry.getEntrezgeneProt().getProtRef() != null)
+ && (entry.getEntrezgeneProt().getProtRef()
+ .getProtRefName() != null)) {
+ List<String> pNames = entry.getEntrezgeneProt()
+ .getProtRef().getProtRefName()
+ .getProtRefNameE();
+
+ for (String name : pNames)
+ proteinInfo.add(name);
+
+ String[] pn = new String[] { entrezID,
+ "General protein information" };
+ attrMap.put(pn, proteinInfo);
+ }
+ }
+
+ // final GeneCommentaryType[] geneProps = entry
+ // .getEntrezgene_properties().getGeneCommentary();
+ if ((entry.getEntrezgeneProperties() != null)
+ && (entry.getEntrezgeneProperties()
+ .getGeneCommentary() != null)) {
+ final List<GeneCommentary> geneProps = entry
+ .getEntrezgeneProperties().getGeneCommentary();
+
+ for (GeneCommentary comment : geneProps) {
+ if (selectedAnn.contains(AnnotationCategory.GO)
+ && (comment.getGeneCommentaryHeading() != null)
+ && comment.getGeneCommentaryHeading()
+ .equals("GeneOntology")) {
+ // Extract GO section
+ final List<GeneCommentary> go = comment
+ .getGeneCommentaryComment()
+ .getGeneCommentary();
+
+ for (GeneCommentary goCategory : go) {
+ List<GeneCommentary> goTermsObject = goCategory
+ .getGeneCommentaryComment()
+ .getGeneCommentary();
+
+ List<String> goTerms = new ArrayList<String>();
+ List<String> evidenceCodes = new ArrayList<String>();
+ List<String> goTermIDs = new ArrayList<String>();
+
+ List<String> goTermsProcess = new ArrayList<String>();
+ List<String> evidenceCodesProcess = new ArrayList<String>();
+ List<String> goTermIDsProcess = new ArrayList<String>();
+
+ List<String> goTermsComponent = new ArrayList<String>();
+ List<String> evidenceCodesComponent = new ArrayList<String>();
+ List<String> goTermIDsComponent = new ArrayList<String>();
+
+ for (GeneCommentary gt : goTermsObject) {
+ List<OtherSource> oneTerm = gt
+ .getGeneCommentarySource()
+ .getOtherSource();
+
+ if ((oneTerm != null)
+ && (oneTerm.size() != 0)) {
+ String goTerm = oneTerm.get(0)
+ .getOtherSourceAnchor();
+ String goTermID = oneTerm.get(0)
+ .getOtherSourceSrc()
+ .getDbtag().getDbtagTag()
+ .getObjectId()
+ .getObjectIdId().toString();
+ String evidence = oneTerm.get(0)
+ .getOtherSourcePostText();
+
+ if (goCategory
+ .getGeneCommentaryLabel()
+ .equals("Function") && goTermIDs.contains(goTermID) == false) {
+ goTerms.add(goTerm);
+ goTermIDs.add(goTermID);
+ evidenceCodes.add(evidence
+ .split(": ")[1]);
+ } else if (goCategory
+ .getGeneCommentaryLabel()
+ .equals("Process") && goTermIDsProcess.contains(goTermID) == false) {
+ goTermsProcess.add(goTerm);
+ goTermIDsProcess.add(goTermID);
+ evidenceCodesProcess
+ .add(evidence
+ .split(": ")[1]);
+ } else if (goCategory
+ .getGeneCommentaryLabel()
+ .equals("Component") && goTermIDsComponent.contains(goTermID) == false) {
+ goTermsComponent.add(goTerm);
+ goTermIDsComponent
+ .add(goTermID);
+ evidenceCodesComponent
+ .add(evidence
+ .split(": ")[1]);
+ }
+ }
+ }
+
+ String[] got = new String[] { entrezID,
+ "GO Term: Molecular Function" };
+ attrMap.put(got, goTerms);
+
+ String[] gotid = new String[] { entrezID,
+ "GO ID: Molecular Function" };
+ attrMap.put(gotid, goTermIDs);
+
+ String[] ev = new String[] { entrezID,
+ "GO Evidence Code: Molecular Function" };
+ attrMap.put(ev, evidenceCodes);
+
+ got = new String[] { entrezID,
+ "GO Term: Biological Process" };
+ attrMap.put(got, goTermsProcess);
+ gotid = new String[] { entrezID,
+ "GO ID: Biological Process" };
+ attrMap.put(gotid, goTermIDsProcess);
+ ev = new String[] { entrezID,
+ "GO Evidence Code: Biological Process" };
+ attrMap.put(ev, evidenceCodesProcess);
+
+ got = new String[] { entrezID,
+ "GO Term: Cellular Component" };
+ attrMap.put(got, goTermsComponent);
+ gotid = new String[] { entrezID,
+ "GO ID: Cellular Component" };
+ attrMap.put(gotid, goTermIDsComponent);
+ ev = new String[] { entrezID,
+ "GO Evidence Code: Cellular Component" };
+ attrMap.put(ev, evidenceCodesComponent);
+ }
+ }
+ }
+ }
+
+ List<GeneCommentary> commentary = entry
+ .getEntrezgeneComments().getGeneCommentary();
+
+ final List<String> geneRIFs = new ArrayList<String>();
+ final List<String> geneRIFText = new ArrayList<String>();
+
+ for (GeneCommentary comment : commentary) {
+ // if (selectedAnn.contains(AnnotationCategory.MARKERS)
+ // && (comment.getGeneCommentary_heading() != null)
+ // &&
+ // comment.getGeneCommentary_heading().startsWith("Markers"))
+ // {
+ // // Extract Marker section
+ //
+ if (selectedAnn.contains(AnnotationCategory.PATHWAY)
+ && (comment.getGeneCommentaryHeading() != null)
+ && comment.getGeneCommentaryHeading().equals(
+ "Pathways")) {
+ final List<GeneCommentary> pathways = comment
+ .getGeneCommentaryComment()
+ .getGeneCommentary();
+
+ List<String> pathwayNames = new ArrayList<String>();
+ List<String> pathwayLinks = new ArrayList<String>();
+
+ for (GeneCommentary p : pathways) {
+ String pName = p.getGeneCommentaryText();
+ String pLink = p.getGeneCommentarySource()
+ .getOtherSource().get(0)
+ .getOtherSourceUrl();
+ pathwayNames.add(pName);
+ pathwayLinks.add(pLink);
+ }
+
+ String[] pwn = new String[] { entrezID, "Pathway" };
+ attrMap.put(pwn, pathwayNames);
+
+ String[] pwl = new String[] { entrezID,
+ "Pathway Link" };
+ attrMap.put(pwl, pathwayLinks);
+ } else if (selectedAnn
+ .contains(AnnotationCategory.PHENOTYPE)
+ && (comment.getGeneCommentaryHeading() != null)
+ && comment.getGeneCommentaryHeading().equals(
+ "Phenotypes")) {
+ final List<GeneCommentary> phenotypes = comment
+ .getGeneCommentaryComment()
+ .getGeneCommentary();
+
+ List<String> phenotypeNames = new ArrayList<String>();
+ List<String> phenotypeIDs = new ArrayList<String>();
+
+ for (GeneCommentary p : phenotypes) {
+ String pName = p.getGeneCommentaryText();
+ String pID = p.getGeneCommentarySource()
+ .getOtherSource().get(0)
+ .getOtherSourceAnchor();
+ phenotypeNames.add(pName);
+ phenotypeIDs.add(pID);
+ }
+
+ String[] pwn = new String[] { entrezID,
+ "Phenotypes" };
+ attrMap.put(pwn, phenotypeNames);
+
+ String[] pwl = new String[] { entrezID,
+ "Phenotype ID" };
+ attrMap.put(pwl, phenotypeIDs);
+ } else if (selectedAnn
+ .contains(AnnotationCategory.LINK)
+ && (comment.getGeneCommentaryHeading() != null)
+ && comment.getGeneCommentaryHeading().equals(
+ "Additional Links")) {
+ final List<GeneCommentary> links = comment
+ .getGeneCommentaryComment()
+ .getGeneCommentary();
+
+ List<String> sourceName = new ArrayList<String>();
+ List<String> externalLink = new ArrayList<String>();
+
+ for (GeneCommentary p : links) {
+ String link = p.getGeneCommentarySource()
+ .getOtherSource().get(0)
+ .getOtherSourceUrl();
+ String name = p.getGeneCommentarySource()
+ .getOtherSource().get(0)
+ .getOtherSourceAnchor();
+
+ if (link != null) {
+ externalLink.add(link);
+ }
+
+ if (name != null) {
+ sourceName.add(name);
+ }
+ }
+
+ String[] pwn = new String[] { entrezID,
+ "Additional Links Name" };
+ attrMap.put(pwn, sourceName);
+
+ String[] pwl = new String[] { entrezID,
+ "Additional Links" };
+ attrMap.put(pwl, externalLink);
+ } else if (selectedAnn
+ .contains(AnnotationCategory.PUBLICATION)
+ && (comment.getGeneCommentaryRefs() != null)
+ && (comment.getGeneCommentaryType() != null)
+ && (comment.getGeneCommentaryRefs() != null)) {
+ final String comType = comment
+ .getGeneCommentaryType().getValue()
+ .toString();
+ List<String> pubMedIDs = new ArrayList<String>();
+
+ if (comType.equals("generif")) {
+ geneRIFText
+ .add(comment.getGeneCommentaryText());
+ }
+
+ final List<Pub> refs = comment
+ .getGeneCommentaryRefs().getPub();
+ String pmid = null;
+
+ for (Pub ref : refs) {
+ pmid = ref.getPubPmid().getPubMedId()
+ .toString();
+
+ if ((pmid != null) && comType.equals("comment"))
+ pubMedIDs.add(pmid);
+ else
+ geneRIFs.add(pmid);
+ }
+
+ // Extract PubMed ID and GeneRif
+ if (comType.equals("comment")) {
+ String[] pmids = new String[] { entrezID,
+ "PubMed ID" };
+ attrMap.put(pmids, pubMedIDs);
+ }
+ }
+ }
+
+ // Add GeneRIF
+ String[] grid = new String[] { entrezID, "GeneRIF ID" };
+ attrMap.put(grid, geneRIFs);
+
+ String[] grtx = new String[] { entrezID, "GeneRIF" };
+ attrMap.put(grtx, geneRIFText);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+ }
+
+ return null;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nv
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public List<JMenuItem> getNodeContextMenuItems(NodeView nv) {
+ List<JMenuItem> menuList = new ArrayList<JMenuItem>();
+ menuList.add(NetworkExpansionMenu.getExpander(this));
+
+ return menuList;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param type
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Icon getIcon(IconSize type) {
+ return ABOUT_ICON;
+ }
+
+ /**
+ * Returns default visual style for networks build from this database
+ *
+ * @return DOCUMENT ME!
+ */
+ public VisualStyle getDefaultVisualStyle() {
+ return VisualStyleBuilder.getNewVisualStyle();
+ }
+}
diff --git a/coreplugins/NCBIClient/src/main/java/edu/ucsd/bioeng/idekerlab/ncbiclient/NCBIClientPlugin.java b/coreplugins/NCBIClient/src/main/java/edu/ucsd/bioeng/idekerlab/ncbiclient/NCBIClientPlugin.java
new file mode 100644
index 0000000..477fa07
--- /dev/null
+++ b/coreplugins/NCBIClient/src/main/java/edu/ucsd/bioeng/idekerlab/ncbiclient/NCBIClientPlugin.java
@@ -0,0 +1,78 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+package edu.ucsd.bioeng.idekerlab.ncbiclient;
+
+import java.awt.event.ActionEvent;
+
+import javax.swing.AbstractAction;
+import javax.swing.JDialog;
+import javax.swing.JMenuItem;
+
+import cytoscape.Cytoscape;
+import cytoscape.data.webservice.WebServiceClientManager;
+import cytoscape.plugin.CytoscapePlugin;
+import edu.ucsd.bioeng.idekerlab.ncbiclient.ui.NCBIGeneDialog;
+
+/**
+ * NCBI Entrez Web Service Client
+ */
+public class NCBIClientPlugin extends CytoscapePlugin {
+ private JDialog annotationDialog;
+
+ /**
+ * Register NCBIClientPlugin to the Web Service Client Manager.
+ */
+ public NCBIClientPlugin() throws Exception {
+ // Register this client to the manager.
+ WebServiceClientManager.registerClient(NCBIClient.getClient());
+
+ Cytoscape.getDesktop().getCyMenus().getMenuBar().getMenu("File.Import")
+ .add(
+ new JMenuItem(new AbstractAction(
+ "Import Attributes from NCBI Entrez Gene...") {
+
+ private static final long serialVersionUID = 3263699405477145319L;
+
+ public void actionPerformed(ActionEvent e) {
+ if (annotationDialog == null)
+ annotationDialog = new NCBIGeneDialog();
+
+ annotationDialog.setVisible(true);
+ }
+ }));
+
+ }
+}
diff --git a/coreplugins/NCBIClient/src/main/java/edu/ucsd/bioeng/idekerlab/ncbiclient/ui/NCBIGeneDialog.java b/coreplugins/NCBIClient/src/main/java/edu/ucsd/bioeng/idekerlab/ncbiclient/ui/NCBIGeneDialog.java
new file mode 100644
index 0000000..b8cd6a3
--- /dev/null
+++ b/coreplugins/NCBIClient/src/main/java/edu/ucsd/bioeng/idekerlab/ncbiclient/ui/NCBIGeneDialog.java
@@ -0,0 +1,37 @@
+package edu.ucsd.bioeng.idekerlab.ncbiclient.ui;
+
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+
+import javax.swing.JDialog;
+import javax.swing.JPanel;
+
+import cytoscape.Cytoscape;
+
+public class NCBIGeneDialog extends JDialog implements PropertyChangeListener {
+
+ private static final long serialVersionUID = -2609215983943863094L;
+
+ public NCBIGeneDialog() {
+ super(Cytoscape.getDesktop(), false);
+ setTitle("NCBI Entrez Gene");
+
+ try {
+ final JPanel panel = new NCBIGenePanel();
+ panel.addPropertyChangeListener(this);
+ add(panel);
+ pack();
+ setLocationRelativeTo(Cytoscape.getDesktop());
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+ }
+
+ public void propertyChange(PropertyChangeEvent evt) {
+ if(evt.getPropertyName().equals("CLOSE")) {
+ dispose();
+ }
+
+ }
+
+}
diff --git a/coreplugins/NCBIClient/src/main/java/edu/ucsd/bioeng/idekerlab/ncbiclient/ui/NCBIGenePanel.java b/coreplugins/NCBIClient/src/main/java/edu/ucsd/bioeng/idekerlab/ncbiclient/ui/NCBIGenePanel.java
new file mode 100644
index 0000000..b5e65ae
--- /dev/null
+++ b/coreplugins/NCBIClient/src/main/java/edu/ucsd/bioeng/idekerlab/ncbiclient/ui/NCBIGenePanel.java
@@ -0,0 +1,226 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package edu.ucsd.bioeng.idekerlab.ncbiclient.ui;
+
+import java.awt.Dimension;
+import java.awt.event.ActionEvent;
+import java.io.IOException;
+
+import javax.swing.DefaultListModel;
+import javax.swing.Icon;
+import javax.swing.ImageIcon;
+
+import cytoscape.Cytoscape;
+import cytoscape.data.webservice.AttributeImportQuery;
+import cytoscape.data.webservice.CyWebServiceEvent;
+import cytoscape.data.webservice.CyWebServiceException;
+import cytoscape.data.webservice.WebServiceClient;
+import cytoscape.data.webservice.WebServiceClientManager;
+import cytoscape.data.webservice.CyWebServiceEvent.WSEventType;
+import cytoscape.task.Task;
+import cytoscape.task.TaskMonitor;
+import cytoscape.task.ui.JTaskConfig;
+import cytoscape.task.util.TaskManager;
+import cytoscape.util.swing.AttributeImportPanel;
+import edu.ucsd.bioeng.idekerlab.ncbiclient.NCBIClient.AnnotationCategory;
+
+
+
+
+/**
+ * Simple attribute import GUI for Entrez Gene database
+ * This UI depends on
+ */
+public class NCBIGenePanel extends AttributeImportPanel {
+ protected static WebServiceClient ncbi = WebServiceClientManager.getClient("ncbi_entrez");
+ private static final Icon LOGO = new ImageIcon(NCBIGenePanel.class.getResource("/images/entrez_page_title.gif"));
+
+ /**
+ * Creates a new NCBIGenePanel object.
+ *
+ * @throws IOException DOCUMENT ME!
+ */
+ public NCBIGenePanel() throws IOException {
+ this(LOGO, "", "Available Annotation Category");
+ }
+
+ /**
+ * Creates a new NCBIGenePanel object.
+ *
+ * @param logo DOCUMENT ME!
+ * @param title DOCUMENT ME!
+ * @param attrPanelName DOCUMENT ME!
+ *
+ * @throws IOException DOCUMENT ME!
+ */
+ public NCBIGenePanel(Icon logo, String title, String attrPanelName) throws IOException {
+ super(logo, title, attrPanelName);
+ initDataSources();
+ this.setPreferredSize(new Dimension(550, 480));
+ }
+
+ private void initDataSources() {
+ this.databaseComboBox.addItem("NCBI Entrez Gene");
+ databaseComboBox.setEnabled(false);
+ setDataType();
+ }
+
+ private void setDataType() {
+ this.attributeTypeComboBox.addItem("Entrez Gene ID");
+ attributeTypeComboBox.setEnabled(false);
+
+ buildList();
+ }
+
+ protected void importButtonActionPerformed(ActionEvent e) {
+ importAttributes();
+ }
+
+ protected void resetButtonActionPerformed(ActionEvent e) {
+ buildList();
+ }
+
+ private void buildList() {
+ model = new DefaultListModel();
+ attrList.setModel(model);
+ for(AnnotationCategory dispAttrName : AnnotationCategory.values()) {
+ model.addElement(dispAttrName.getName());
+ }
+ }
+
+
+
+ @Override
+ protected void databaseComboBoxActionPerformed(ActionEvent arg0) {
+ // TODO Auto-generated method stub
+ }
+
+ @Override
+ protected void importAttributes() {
+ String keyInHeader = null;
+ // Create Task
+ final ImportAttributeTask task = new ImportAttributeTask(attributeComboBox.getSelectedItem().toString(), keyInHeader);
+
+ // Configure JTask Dialog Pop-Up Box
+ final JTaskConfig jTaskConfig = new JTaskConfig();
+ jTaskConfig.setOwner(Cytoscape.getDesktop());
+ jTaskConfig.displayCloseButton(true);
+ jTaskConfig.displayCancelButton(true);
+ jTaskConfig.displayStatus(true);
+ jTaskConfig.setAutoDispose(false);
+
+ // Execute Task in New Thread; pop open JTask Dialog Box.
+ TaskManager.executeTask(task, jTaskConfig);
+
+ this.firePropertyChange("CLOSE", null, null);
+ }
+
+ private class ImportAttributeTask implements Task {
+
+ private String key;
+ private String keyAttrName;
+ private TaskMonitor taskMonitor;
+
+ public ImportAttributeTask(String key, String keyAttrName) {
+ this.key = key;
+ this.keyAttrName = keyAttrName;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getTitle() {
+ // TODO Auto-generated method stub
+ return "Loading Attributes from Web Service";
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void halt() {
+ Thread.currentThread().interrupt();
+ taskMonitor.setPercentCompleted(100);
+
+ // Kill the import task.
+ CyWebServiceEvent<String> cancelEvent = new CyWebServiceEvent<String>(ncbi.getClientID(), WSEventType.CANCEL,
+ null,
+ null);
+ try {
+ WebServiceClientManager.getCyWebServiceEventSupport().fireCyWebServiceEvent(cancelEvent);
+ } catch (CyWebServiceException e) {
+ // TODO Auto-generated catch block
+ taskMonitor.setException(e, "Cancel Failed.");
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void run() {
+ taskMonitor.setStatus("Importing annotation from Entrez Gene.\n\nIt may take a while.\nPlease wait...");
+ taskMonitor.setPercentCompleted(-1);
+
+ final Object[] selectedAttr = attrList.getSelectedValues();
+
+ AttributeImportQuery qObj = new AttributeImportQuery(selectedAttr, key, keyAttrName);
+
+ try {
+ WebServiceClientManager.getCyWebServiceEventSupport().fireCyWebServiceEvent(new CyWebServiceEvent("ncbi_entrez", WSEventType.IMPORT_ATTRIBUTE, qObj));
+ } catch (Exception e) {
+ taskMonitor.setException(e, "Could not load attributes from NCBI.");
+ }
+
+ taskMonitor.setPercentCompleted(100);
+ taskMonitor.setStatus("Attributes successfully loaded.");
+
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param arg0 DOCUMENT ME!
+ *
+ * @throws IllegalThreadStateException DOCUMENT ME!
+ */
+ public void setTaskMonitor(TaskMonitor taskMonitor) throws IllegalThreadStateException {
+ this.taskMonitor = taskMonitor;
+ }
+ }
+
+
+
+}
diff --git a/coreplugins/NCBIClient/src/main/java/edu/ucsd/bioeng/idekerlab/ncbiclient/util/BioGRIDUtil.java b/coreplugins/NCBIClient/src/main/java/edu/ucsd/bioeng/idekerlab/ncbiclient/util/BioGRIDUtil.java
new file mode 100755
index 0000000..172055e
--- /dev/null
+++ b/coreplugins/NCBIClient/src/main/java/edu/ucsd/bioeng/idekerlab/ncbiclient/util/BioGRIDUtil.java
@@ -0,0 +1,57 @@
+package edu.ucsd.bioeng.idekerlab.ncbiclient.util;
+
+import java.util.Set;
+import java.util.TreeSet;
+
+public class BioGRIDUtil {
+
+ private static final String[] PHYSICAL = {
+ "Affinity Capture-Luminescence",
+ "Affinity Capture-MS",
+ "Affinity Capture-RNA",
+ "Affinity Capture-Western",
+ "Biochemical Activity",
+ "Co-crystal Structure",
+ "Co-fractionation",
+ "Co-localization",
+ "Co-purification",
+ "Far Western",
+ "FRET",
+ "PCA",
+ "Protein-peptide",
+ "Protein-RNA",
+ "Reconstituted Complex",
+ "Two-hybrid" };
+
+ private static final String[] GENETIC = {
+ "Dosage Growth Defect",
+ "Dosage Lethality",
+ "Dosage Rescue",
+ "Phenotypic Enhancement",
+ "Phenotypic Suppression",
+ "Synthetic Growth Defect",
+ "Synthetic Haploinsufficiency",
+ "Synthetic Lethality",
+ "Synthetic Rescue"
+ };
+
+ private static final Set<String> P_LIST = new TreeSet<String>();
+ private static final Set<String> G_LIST = new TreeSet<String>();
+
+ static {
+ for(String p:PHYSICAL)
+ P_LIST.add(p);
+ for(String g:GENETIC)
+ G_LIST.add(g);
+ }
+
+ public static String getInteractionType(String typeString) {
+ if(P_LIST.contains(typeString))
+ return "physical";
+ else if(G_LIST.contains(typeString))
+ return "genetic";
+ else
+ return "unknown";
+ }
+
+}
diff --git a/coreplugins/NCBIClient/src/main/java/edu/ucsd/bioeng/idekerlab/ncbiclient/util/VisualStyleBuilder.java b/coreplugins/NCBIClient/src/main/java/edu/ucsd/bioeng/idekerlab/ncbiclient/util/VisualStyleBuilder.java
new file mode 100644
index 0000000..6d4ac02
--- /dev/null
+++ b/coreplugins/NCBIClient/src/main/java/edu/ucsd/bioeng/idekerlab/ncbiclient/util/VisualStyleBuilder.java
@@ -0,0 +1,305 @@
+package edu.ucsd.bioeng.idekerlab.ncbiclient.util;
+
+import static cytoscape.visual.VisualPropertyType.EDGE_LABEL;
+import static cytoscape.visual.VisualPropertyType.NODE_LABEL;
+
+import java.awt.Color;
+
+import cytoscape.Cytoscape;
+import cytoscape.visual.EdgeAppearanceCalculator;
+import cytoscape.visual.GlobalAppearanceCalculator;
+import cytoscape.visual.LineStyle;
+import cytoscape.visual.NodeAppearanceCalculator;
+import cytoscape.visual.NodeShape;
+import cytoscape.visual.VisualPropertyType;
+import cytoscape.visual.VisualStyle;
+import cytoscape.visual.calculators.AbstractCalculator;
+import cytoscape.visual.calculators.BasicCalculator;
+import cytoscape.visual.calculators.Calculator;
+import cytoscape.visual.mappings.DiscreteMapping;
+import cytoscape.visual.mappings.ObjectMapping;
+import cytoscape.visual.mappings.PassThroughMapping;
+
+public class VisualStyleBuilder {
+
+ private static final String NUCLEOTIDE = "Nucleotide";
+ private static final String PROTEIN = "Protein";
+ private static final String GENE_ID = "GeneID";
+ private VisualStyle defaultVS = null;
+ private VisualStyle newVS = null;
+
+ private static final String DEF_VS_NAME = "Entrez Gene Style";
+ private static final String NEW_VS_NAME = "Entrez Gene Style 2";
+
+ // Tag definitions
+
+ private static VisualStyleBuilder builder = new VisualStyleBuilder();
+
+ public static VisualStyle getDefaultStyle() {
+ return builder.getDefStyle();
+ }
+
+ public static VisualStyle getNewVisualStyle() {
+ return builder.getNewStyle();
+ }
+
+ private VisualStyleBuilder() {
+ defaultVS = buidlDefaultStyle();
+ newVS = buildNewStyle();
+
+ if (Cytoscape.getVisualMappingManager().getCalculatorCatalog()
+ .getVisualStyle(newVS.getName()) == null) {
+ Cytoscape.getVisualMappingManager().getCalculatorCatalog()
+ .addVisualStyle(newVS);
+ }
+
+ }
+
+ public VisualStyle getDefStyle() {
+ return defaultVS;
+ }
+
+ public VisualStyle getNewStyle() {
+ return newVS;
+ }
+
+ /**
+ * Generate default visual style. The style is database-dependent.
+ *
+ * @return default visual style.
+ */
+ private VisualStyle buidlDefaultStyle() {
+ final Color NODE_COLOR = new Color(25, 25, 200);
+ final Color NODE_LABEL_COLOR = new Color(10, 10, 10);
+
+ final Color EDGE_COLOR = new Color(10, 10, 10);
+ final Color EDGE_LABEL_COLOR = new Color(50, 50, 255);
+
+ final VisualStyle defStyle = new VisualStyle(DEF_VS_NAME);
+
+ NodeAppearanceCalculator nac = defStyle.getNodeAppearanceCalculator();
+ EdgeAppearanceCalculator eac = defStyle.getEdgeAppearanceCalculator();
+ GlobalAppearanceCalculator gac = defStyle
+ .getGlobalAppearanceCalculator();
+
+ gac.setDefaultBackgroundColor(Color.white);
+
+ PassThroughMapping m = new PassThroughMapping("", AbstractCalculator.ID);
+
+ final Calculator calc = new BasicCalculator(DEF_VS_NAME + "-"
+ + "NodeLabelMapping", m, NODE_LABEL);
+ PassThroughMapping me = new PassThroughMapping("", "interaction");
+
+ final Calculator calce = new BasicCalculator(DEF_VS_NAME + "-"
+ + "EdgeLabelMapping", me, EDGE_LABEL);
+ nac.setCalculator(calc);
+
+ nac.getDefaultAppearance().set(VisualPropertyType.NODE_FILL_COLOR,
+ NODE_COLOR);
+ nac.getDefaultAppearance().set(VisualPropertyType.NODE_SHAPE,
+ NodeShape.ROUND_RECT);
+ nac.getDefaultAppearance().set(VisualPropertyType.NODE_OPACITY, 50);
+ nac.getDefaultAppearance().set(VisualPropertyType.NODE_LABEL_OPACITY,
+ 225);
+ nac.getDefaultAppearance().set(VisualPropertyType.NODE_LINE_WIDTH, 0);
+ nac.getDefaultAppearance().set(VisualPropertyType.NODE_WIDTH, 65);
+ nac.getDefaultAppearance().set(VisualPropertyType.NODE_HEIGHT, 34);
+ nac.getDefaultAppearance().set(VisualPropertyType.NODE_LABEL_COLOR,
+ NODE_LABEL_COLOR);
+ nac.setNodeSizeLocked(false);
+
+ eac.setCalculator(calce);
+ eac.getDefaultAppearance().set(VisualPropertyType.EDGE_COLOR,
+ EDGE_COLOR);
+ eac.getDefaultAppearance().set(VisualPropertyType.EDGE_LABEL_COLOR,
+ EDGE_LABEL_COLOR);
+ eac.getDefaultAppearance().set(VisualPropertyType.EDGE_FONT_SIZE, 5);
+ eac.getDefaultAppearance().set(VisualPropertyType.EDGE_OPACITY, 90);
+ eac.getDefaultAppearance().set(
+ VisualPropertyType.EDGE_SRCARROW_OPACITY, 120);
+ eac.getDefaultAppearance().set(
+ VisualPropertyType.EDGE_TGTARROW_OPACITY, 120);
+ eac.getDefaultAppearance().set(VisualPropertyType.EDGE_LABEL_OPACITY,
+ 70);
+ eac.getDefaultAppearance().set(VisualPropertyType.EDGE_LINE_WIDTH, 3);
+ eac.getDefaultAppearance().set(VisualPropertyType.EDGE_LABEL, "");
+
+ // Set edge color based on datasource name
+ DiscreteMapping edgeColor = new DiscreteMapping(EDGE_COLOR,
+ "datasource", ObjectMapping.EDGE_MAPPING);
+
+ edgeColor.putMapValue("BIND", new Color(Integer.decode("#b0c4de")));
+ edgeColor.putMapValue("BioGRID", new Color(Integer.decode("#3cb371")));
+ edgeColor.putMapValue("HPRD", new Color(Integer.decode("#800000")));
+
+ DiscreteMapping edgeLineStyle = new DiscreteMapping(LineStyle.SOLID,
+ "interaction type", ObjectMapping.EDGE_MAPPING);
+
+ edgeLineStyle.putMapValue("physical", LineStyle.SOLID);
+ edgeLineStyle.putMapValue("genetic", LineStyle.LONG_DASH);
+
+ Calculator edgeColorCalc = new BasicCalculator(DEF_VS_NAME + "-"
+ + "EdgeColorMapping", edgeColor, VisualPropertyType.EDGE_COLOR);
+
+ eac.setCalculator(edgeColorCalc);
+
+ Calculator edgeLineStyleCalc = new BasicCalculator(DEF_VS_NAME + "-"
+ + "EdgeLineStyleMapping", edgeLineStyle,
+ VisualPropertyType.EDGE_LINE_STYLE);
+
+ eac.setCalculator(edgeLineStyleCalc);
+
+ return defStyle;
+ }
+
+ private VisualStyle buildNewStyle() {
+ final Color NODE_COLOR = new Color(0x00, 0x8b, 0x8b);
+ final Color NODE_NUCLEOTIDE_COLOR = new Color(25, 25, 200);
+ final Color NODE_BORDER_COLOR = new Color(0x00, 0x64, 0x00);
+ final Color NODE_NUCLEOTIDE_BORDER_COLOR = new Color(25, 25, 200);
+ final Color NODE_LABEL_COLOR = new Color(0x69, 0x69, 0x69);
+
+ final Color EDGE_COLOR = new Color(0x80, 0x80, 0x80);
+ final Color EDGE_LABEL_COLOR = new Color(50, 50, 255);
+
+ final VisualStyle newStyle = new VisualStyle(NEW_VS_NAME);
+
+ NodeAppearanceCalculator nac = newStyle.getNodeAppearanceCalculator();
+ EdgeAppearanceCalculator eac = newStyle.getEdgeAppearanceCalculator();
+ GlobalAppearanceCalculator gac = newStyle
+ .getGlobalAppearanceCalculator();
+
+ gac.setDefaultBackgroundColor(Color.white);
+
+ PassThroughMapping m = new PassThroughMapping("", "Alt Name");
+
+ final Calculator calc = new BasicCalculator(NEW_VS_NAME + "-"
+ + "NodeLabelMapping", m, NODE_LABEL);
+ PassThroughMapping me = new PassThroughMapping("", "interaction");
+
+ final Calculator calce = new BasicCalculator(NEW_VS_NAME + "-"
+ + "EdgeLabelMapping", me, EDGE_LABEL);
+ nac.setCalculator(calc);
+
+ // Setup default view
+ nac.getDefaultAppearance().set(VisualPropertyType.NODE_FILL_COLOR,
+ NODE_COLOR);
+ nac.getDefaultAppearance().set(VisualPropertyType.NODE_BORDER_COLOR,
+ NODE_BORDER_COLOR);
+
+ nac.getDefaultAppearance().set(VisualPropertyType.NODE_SHAPE,
+ NodeShape.RECT);
+ nac.getDefaultAppearance().set(VisualPropertyType.NODE_OPACITY, 110);
+ nac.getDefaultAppearance().set(VisualPropertyType.NODE_BORDER_OPACITY,
+ 240);
+ nac.getDefaultAppearance().set(VisualPropertyType.NODE_LABEL_OPACITY,
+ 225);
+ nac.getDefaultAppearance().set(VisualPropertyType.NODE_LINE_WIDTH, 3);
+ nac.getDefaultAppearance().set(VisualPropertyType.NODE_WIDTH, 100);
+ nac.getDefaultAppearance().set(VisualPropertyType.NODE_HEIGHT, 38);
+ nac.getDefaultAppearance().set(VisualPropertyType.NODE_LABEL_COLOR,
+ NODE_LABEL_COLOR);
+ nac.setNodeSizeLocked(false);
+
+ eac.setCalculator(calce);
+ eac.getDefaultAppearance().set(VisualPropertyType.EDGE_COLOR,
+ EDGE_COLOR);
+ eac.getDefaultAppearance().set(VisualPropertyType.EDGE_LABEL_COLOR,
+ EDGE_LABEL_COLOR);
+ eac.getDefaultAppearance().set(VisualPropertyType.EDGE_FONT_SIZE, 5);
+ eac.getDefaultAppearance().set(VisualPropertyType.EDGE_OPACITY, 200);
+ eac.getDefaultAppearance().set(
+ VisualPropertyType.EDGE_SRCARROW_OPACITY, 120);
+ eac.getDefaultAppearance().set(
+ VisualPropertyType.EDGE_TGTARROW_OPACITY, 120);
+ eac.getDefaultAppearance().set(VisualPropertyType.EDGE_LABEL_OPACITY,
+ 70);
+ eac.getDefaultAppearance().set(VisualPropertyType.EDGE_LINE_WIDTH, 2);
+ eac.getDefaultAppearance().set(VisualPropertyType.EDGE_LABEL, "");
+
+ // Modify node apeearence based on type
+
+ // Color
+ DiscreteMapping nodeColor = new DiscreteMapping(NODE_COLOR,
+ "Interactor Type", ObjectMapping.NODE_MAPPING);
+
+ nodeColor.putMapValue(GENE_ID, NODE_COLOR);
+ nodeColor.putMapValue(PROTEIN, new Color(0x64, 0x95, 0xed));
+ nodeColor.putMapValue(NUCLEOTIDE, new Color(0xff, 0x7f, 0x50));
+
+ final Calculator nodeColorCalc = new BasicCalculator(NEW_VS_NAME + "-"
+ + "NodeColorMapping", nodeColor,
+ VisualPropertyType.NODE_FILL_COLOR);
+
+ nac.setCalculator(nodeColorCalc);
+
+ // Border Color
+ DiscreteMapping nodeBorderColor = new DiscreteMapping(
+ NODE_BORDER_COLOR, "Interactor Type",
+ ObjectMapping.NODE_MAPPING);
+
+ nodeBorderColor.putMapValue(GENE_ID, NODE_BORDER_COLOR);
+ nodeBorderColor.putMapValue(PROTEIN, new Color(0x0000cd));
+ nodeBorderColor.putMapValue(NUCLEOTIDE, new Color(0x800000));
+
+ final Calculator nodeBorderColorCalc = new BasicCalculator(NEW_VS_NAME
+ + "-" + "NodeBorderColorMapping", nodeBorderColor,
+ VisualPropertyType.NODE_BORDER_COLOR);
+
+ nac.setCalculator(nodeBorderColorCalc);
+
+ // Shape
+ DiscreteMapping nodeShape = new DiscreteMapping(NodeShape.RECT,
+ "Interactor Type", ObjectMapping.NODE_MAPPING);
+
+ nodeShape.putMapValue(GENE_ID, NodeShape.RECT);
+ nodeShape.putMapValue(PROTEIN, NodeShape.ELLIPSE);
+ nodeShape.putMapValue(NUCLEOTIDE, NodeShape.OCTAGON);
+
+ final Calculator nodeShapeCalc = new BasicCalculator(NEW_VS_NAME + "-"
+ + "NodeShapeMapping", nodeShape, VisualPropertyType.NODE_SHAPE);
+
+ nac.setCalculator(nodeShapeCalc);
+
+ // Set edge color based on datasource name
+ DiscreteMapping edgeColor = new DiscreteMapping(EDGE_COLOR,
+ "datasource", ObjectMapping.EDGE_MAPPING);
+
+ edgeColor.putMapValue("BIND", new Color(Integer.decode("#b0c4de")));
+ edgeColor.putMapValue("BioGRID", new Color(Integer.decode("#3cb371")));
+ edgeColor.putMapValue("HPRD", new Color(Integer.decode("#800000")));
+
+ DiscreteMapping edgeLineStyle = new DiscreteMapping(LineStyle.SOLID,
+ "interaction type", ObjectMapping.EDGE_MAPPING);
+
+ edgeLineStyle.putMapValue("physical", LineStyle.SOLID);
+ edgeLineStyle.putMapValue("genetic", LineStyle.LONG_DASH);
+
+ final Calculator edgeColorCalc = new BasicCalculator(NEW_VS_NAME + "-"
+ + "EdgeColorMapping", edgeColor, VisualPropertyType.EDGE_COLOR);
+
+ eac.setCalculator(edgeColorCalc);
+
+ final Calculator edgeLineStyleCalc = new BasicCalculator(NEW_VS_NAME
+ + "-" + "EdgeLineStyleMapping", edgeLineStyle,
+ VisualPropertyType.EDGE_LINE_STYLE);
+
+ eac.setCalculator(edgeLineStyleCalc);
+
+ // Edge line width mapping.
+ DiscreteMapping edgeWidth = new DiscreteMapping(2, "interaction type",
+ ObjectMapping.EDGE_MAPPING);
+
+ edgeWidth.putMapValue("physical", 3);
+ edgeWidth.putMapValue("genetic", 2);
+
+ final Calculator edgeWidthCalc = new BasicCalculator(NEW_VS_NAME + "-"
+ + "EdgeWidthMapping", edgeWidth,
+ VisualPropertyType.EDGE_LINE_WIDTH);
+
+ eac.setCalculator(edgeWidthCalc);
+
+ return newStyle;
+ }
+
+}
diff --git a/coreplugins/NCBIClient/src/main/resources/edu/ucsd/bioeng/idekerlab/ncbiclient/plugin.props b/coreplugins/NCBIClient/src/main/resources/edu/ucsd/bioeng/idekerlab/ncbiclient/plugin.props
new file mode 100644
index 0000000..1e2a514
--- /dev/null
+++ b/coreplugins/NCBIClient/src/main/resources/edu/ucsd/bioeng/idekerlab/ncbiclient/plugin.props
@@ -0,0 +1,22 @@
+# -- The following properties are REQUIRED -- #
+
+# The plugin name that will be displayed to users
+pluginName=NCBIClient
+
+# Description used to give users information about the plugin such as what it does.
+# Html tags are encouraged for formatting purposes.
+pluginDescription=<p>Web Service client module for <a href="http://www.ncbi.nlm.nih.gov/entrez/query/static/esoap_help.html">NCBI Entrez Utilities Web Service</a>.</p><p>For more information, please visit the following pages:</p><ul><li><a href="http://www.cytoscape.org/cgi-bin/moin.cgi/SampleWebServiceClients">Sample clients</a></li><li><a href="http://www.cytoscape.org/cgi-bin/moin.cgi/WebServiceWorkflow">Sample workflow</a></li></ul><p><strong><font color="red">To use this function fr [...]
+
+# Plugin version number, this must be two numbers separated by a decimlal. Ex. 0.2, 14.03
+pluginVersion=0.97
+
+# Compatible Cytoscape version
+cytoscapeVersion=2.7,2.8
+
+# Category, use one of the categories listed on the website or create your own
+pluginCategory=Core
+
+
+# List of authors. Note each author and institution pair are separated by a : (colon)
+# each additional author institution pair must be separated from other pairs bye a ; (semicolon)
+pluginAuthorsIntsitutions=Keiichiro Ono:UCSD Dept. of Medicine
diff --git a/coreplugins/NCBIClient/src/main/resources/images/entrez32.png b/coreplugins/NCBIClient/src/main/resources/images/entrez32.png
new file mode 100644
index 0000000..e7bb037
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diff --git a/coreplugins/NCBIClient/src/main/resources/images/entrez_page_title.gif b/coreplugins/NCBIClient/src/main/resources/images/entrez_page_title.gif
new file mode 100644
index 0000000..d048b6f
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diff --git a/coreplugins/NCBIClient/src/test/java/org/cytoscape/webservice/ncbi/test/Test2.java b/coreplugins/NCBIClient/src/test/java/org/cytoscape/webservice/ncbi/test/Test2.java
new file mode 100644
index 0000000..21daa56
--- /dev/null
+++ b/coreplugins/NCBIClient/src/test/java/org/cytoscape/webservice/ncbi/test/Test2.java
@@ -0,0 +1,59 @@
+package org.cytoscape.webservice.ncbi.test;
+
+
+
+import gov.nih.ncbi.soap.eutils.gene.EFetchGeneService;
+import gov.nih.ncbi.soap.eutils.gene.EFetchRequest;
+import gov.nih.ncbi.soap.eutils.gene.EFetchResult;
+import gov.nih.nlm.ncbi.soap.eutils.EUtilsService;
+import gov.nih.nlm.ncbi.soap.eutils.EUtilsServiceSoap;
+import gov.nih.nlm.ncbi.soap.eutils.esearch.ESearchRequest;
+import gov.nih.nlm.ncbi.soap.eutils.esearch.ESearchResult;
+
+import org.junit.Test;
+
+public class Test2 {
+
+
+
+ @Test
+ public void TestNCBIService() {
+ System.out.println("========= Testing NCBI 2 ==============");
+
+ try {
+ EUtilsService service = new EUtilsService();
+ EUtilsServiceSoap ss = service.getEUtilsServiceSoap();
+ ESearchRequest req = new ESearchRequest();
+ req.setDb("gene");
+ req.setTerm("2276311");
+ req.setRetMax("15");
+
+
+ ESearchResult res = ss.runESearch(req);
+
+
+ System.out.println("Found ids: " + res.getCount());
+ System.out.print("First " + res.getRetMax() + " ids: ");
+
+ for (int i = 0; i < res.getIdList().getId().size(); i++) {
+ System.out.print(res.getIdList().getId().get(i) + " ");
+ }
+ System.out.println();
+
+ EFetchRequest req2 = new EFetchRequest();
+ req2.setId("6599,6598,6597,3621,983,25898,8837,55339,4860");
+
+ EFetchGeneService geneService = new EFetchGeneService();
+ gov.nih.ncbi.soap.eutils.gene.EUtilsServiceSoap service2 = geneService.getEUtilsServiceSoap();
+
+ EFetchResult res2 = service2.runEFetch(req2);
+ System.out.println("========> res = " + res2.getEntrezgeneSet().getEntrezgene().get(0).getEntrezgeneSummary());
+
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ System.out.println(e.toString());
+ }
+ }
+
+}
diff --git a/coreplugins/NetworkAnalyzer/pom.xml b/coreplugins/NetworkAnalyzer/pom.xml
new file mode 100644
index 0000000..b119e31
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/pom.xml
@@ -0,0 +1,69 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>parent</artifactId>
+ <version>2.8.4-SNAPSHOT</version>
+ </parent>
+
+ <artifactId>network-analyzer</artifactId>
+ <packaging>jar</packaging>
+
+ <name>NetworkAnalyzer</name>
+
+ <!-- bootstrap for cytoscape dependencies, namely the parent POM snapshots -->
+ <repositories>
+ <repository>
+ <id>cytoscape_snapshots</id>
+ <snapshots>
+ <enabled>true</enabled>
+ </snapshots>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <name>Cytoscape Snapshots</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/</url>
+ </repository>
+ <repository>
+ <id>cytoscape_releases</id>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ <name>Cytoscape Releases</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/releases/</url>
+ </repository>
+ </repositories>
+
+ <build>
+ <plugins>
+ <plugin>
+ <artifactId>maven-assembly-plugin</artifactId>
+ <configuration>
+ <archive>
+ <manifestEntries>
+ <Cytoscape-Plugin>de.mpg.mpi_inf.bioinf.netanalyzer.Plugin</Cytoscape-Plugin>
+ </manifestEntries>
+ </archive>
+ </configuration>
+ </plugin>
+ </plugins>
+ </build>
+
+ <dependencies>
+ <dependency>
+ <groupId>jfree</groupId>
+ <artifactId>jfreechart</artifactId>
+ <version>1.0.13</version>
+ </dependency>
+ <dependency>
+ <groupId>jfree</groupId>
+ <artifactId>jcommon</artifactId>
+ <version>1.0.15</version>
+ </dependency>
+ </dependencies>
+
+</project>
+
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/AboutAction.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/AboutAction.java
new file mode 100644
index 0000000..ff4db07
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/AboutAction.java
@@ -0,0 +1,57 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer;
+
+import java.awt.event.ActionEvent;
+
+import cytoscape.Cytoscape;
+import cytoscape.util.CytoscapeAction;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Messages;
+import de.mpg.mpi_inf.bioinf.netanalyzer.ui.AboutDialog;
+
+/**
+ * Action handler for the menu item "About NetworkAnalyzer".
+ *
+ * @author Yassen Assenov
+ */
+public final class AboutAction extends CytoscapeAction {
+
+ /**
+ * Initializes a new instance of <code>AboutAction</code>.
+ */
+ public AboutAction() {
+ super(Messages.AC_ABOUT);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.event.ActionListener#actionPerformed(java.awt.event.ActionEvent)
+ */
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ AboutDialog d = new AboutDialog(Cytoscape.getDesktop());
+ d.setLocationRelativeTo(Cytoscape.getDesktop());
+ d.setVisible(true);
+ }
+
+ /**
+ * Unique ID for this version of this class. It is used in serialization.
+ */
+ private static final long serialVersionUID = -6208980061184138790L;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/AnalysisExecutor.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/AnalysisExecutor.java
new file mode 100644
index 0000000..7ea958a
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/AnalysisExecutor.java
@@ -0,0 +1,184 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer;
+
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.swing.JFrame;
+import javax.swing.ProgressMonitor;
+import javax.swing.Timer;
+
+import cytoscape.logger.CyLogger;
+import cytoscape.util.SwingWorker;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Messages;
+import de.mpg.mpi_inf.bioinf.netanalyzer.ui.AnalysisDialog;
+
+/**
+ * Initializer and starter of a separate thread dedicated to network analysis.
+ * <p>
+ * This class manages the UI binding to the analysis of a network, in particular it:
+ * <ul>
+ * <li>initializes a dialog that enables the user to keep track of the current progress;</li>
+ * <li>starts the network analyzer;</li>
+ * <li>stops the analyzer if the user presses the "Cancel" button of the dialog;</li>
+ * <li>(optionally) creates an {@link de.mpg.mpi_inf.bioinf.netanalyzer.ui.AnalysisDialog} to
+ * display results once the analysis completes successfully.</li>
+ * </ul>
+ * </p>
+ *
+ * @author Yassen Assenov
+ */
+public class AnalysisExecutor extends SwingWorker implements ActionListener {
+
+ /**
+ * Initializes a new instance of <code>AnalysisExecutor</code>.
+ * <p>
+ * The executor displays analysis results dialog once the analysis is completed.
+ * </p>
+ * <p>
+ * Note that the constructor does not start the process of network analysis - this is performed
+ * by the <code>start()</code> method. It is recommended that <code>start()</code> is called
+ * immediately after the initialization.
+ * </p>
+ *
+ * @param aDesktop
+ * Owner of the dialog(s) that will appear.
+ * @param aAnalyzer
+ * <code>NetworkAnalyzer</code> instance to be started.
+ */
+ public AnalysisExecutor(JFrame aDesktop, NetworkAnalyzer aAnalyzer) {
+ desktop = aDesktop;
+ analyzer = aAnalyzer;
+ listeners = new ArrayList<AnalysisListener>();
+ showDialog = true;
+ int maxProgress = analyzer.getMaxProgress();
+ monitor = new ProgressMonitor(aDesktop, Messages.DT_ANALYZING, null, 0, maxProgress);
+ monitor.setMillisToDecideToPopup(1500);
+ timer = new Timer(1000, this);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.event.ActionListener#actionPerformed(java.awt.event.ActionEvent)
+ */
+ public void actionPerformed(ActionEvent e) {
+ monitor.setProgress(analyzer.getCurrentProgress());
+ if (monitor.isCanceled()) {
+ // Analysis canceled by user
+ timer.stop();
+ timer = null;
+ monitor.close();
+ analyzer.cancel();
+ interrupt();
+ for (final AnalysisListener listener : listeners) {
+ listener.analysisCancelled();
+ }
+ } else if (getValue() != null) {
+ // Analysis finished successfully
+ timer.stop();
+ timer = null;
+ monitor.close();
+ if (showDialog) {
+ try {
+ AnalysisDialog d = new AnalysisDialog(desktop, analyzer.getStats(), analyzer);
+ d.setVisible(true);
+ } catch (InnerException ex) {
+ // NetworkAnalyzer internal error
+ CyLogger.getLogger().error(Messages.SM_LOGERROR, ex);
+ }
+ }
+ for (final AnalysisListener listener : listeners) {
+ listener.analysisCompleted(analyzer);
+ }
+ }
+ }
+
+ /**
+ * Adds an <code>AnalysisListener</code> to this executor.
+ *
+ * @param aListener
+ * Listener to be added. If this parameter is <code>null</code>, calling this method
+ * has no effect.
+ */
+ public void addAnalysisListener(AnalysisListener aListener) {
+ if (aListener != null && (!listeners.contains(aListener))) {
+ listeners.add(aListener);
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see cytoscape.util.SwingWorker#construct()
+ */
+ @Override
+ public Object construct() {
+ if (timer != null) {
+ timer.start();
+ analyzer.computeAll();
+ return analyzer;
+ }
+ return null;
+ }
+
+ /**
+ * Enables or disables the display of analysis results dialog.
+ *
+ * @param aShowDialog
+ * Flag indicating if an analysis results dialog must be displayed after the analysis
+ * is complete.
+ */
+ public void setShowDialog(boolean aShowDialog) {
+ showDialog = aShowDialog;
+ }
+
+ /**
+ * Network analyzer started by this instance.
+ */
+ private NetworkAnalyzer analyzer;
+
+ /**
+ * Currently registered listeners on this analysis.
+ */
+ private List<AnalysisListener> listeners;
+
+ /**
+ * Progress monitor to reflect current progress in the analysis process.
+ */
+ private ProgressMonitor monitor;
+
+ /**
+ * Timer responsible for regular updates of the progress monitor.
+ */
+ private Timer timer;
+
+ /**
+ * Parent (owner) of the dialog(s) displayed.
+ */
+ private JFrame desktop;
+
+ /**
+ * Flag indicating if an analysis results dialog must be displayed after the analysis is
+ * complete.
+ */
+ private boolean showDialog;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/AnalysisListener.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/AnalysisListener.java
new file mode 100644
index 0000000..e9f068d
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/AnalysisListener.java
@@ -0,0 +1,39 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer;
+
+/**
+ * Listener interface for analysis results listeners.
+ *
+ * @author Yassen Assenov
+ */
+public interface AnalysisListener {
+
+ /**
+ * Invoked when analysis is cancelled by the user.
+ */
+ public void analysisCancelled();
+
+ /**
+ * Invoked when analysis
+ *
+ * @param aAnalyzer
+ * Analyzer instance which has successfully completed the analysis of a network.
+ */
+ public void analysisCompleted(NetworkAnalyzer aAnalyzer);
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/AnalyzeNetworkAction.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/AnalyzeNetworkAction.java
new file mode 100644
index 0000000..4236436
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/AnalyzeNetworkAction.java
@@ -0,0 +1,134 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer;
+
+import giny.model.Node;
+
+import java.awt.event.ActionEvent;
+import java.util.Set;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import cytoscape.logger.CyLogger;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Messages;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.NetworkInspection;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.NetworkInterpretation;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.NetworkStatus;
+import de.mpg.mpi_inf.bioinf.netanalyzer.ui.InterpretationDialog;
+import de.mpg.mpi_inf.bioinf.netanalyzer.ui.Utils;
+
+/**
+ * Action handler for the menu item "Analyze Network".
+ *
+ * @author Yassen Assenov
+ */
+public class AnalyzeNetworkAction extends NetAnalyzerAction {
+
+ /**
+ * Initializes a new instance of <code>AnalyzeNetworkAction</code>.
+ */
+ public AnalyzeNetworkAction() {
+ super(Messages.AC_ANALYZE);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see cytoscape.util.CytoscapeAction#actionPerformed(java.awt.event.ActionEvent)
+ */
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ try {
+ if (selectNetwork()) {
+ final AnalysisExecutor exec = initAnalysisExecuter(network, null);
+ if (exec != null) {
+ exec.start();
+ }
+ }
+ } catch (InnerException ex) {
+ // NetworkAnalyzer internal error
+ CyLogger.getLogger().error(Messages.SM_LOGERROR, ex);
+ }
+ }
+
+ /**
+ * Asks the user for interpretation and initializes the analysis executor class to perform the requested
+ * topological analysis.
+ *
+ * @param aNetwork
+ * Network to be analyzed.
+ * @param aNodeSet
+ * Subset of nodes in <code>aNetwork</code>, for which topological parameters are to be
+ * calculated. Set this to <code>null</code> if parameters must be calculated for all nodes in
+ * the network.
+ * @return Newly initialized analysis executor; <code>null</code> if the user has decided to cancel the
+ * operation.
+ */
+ public static AnalysisExecutor initAnalysisExecuter(CyNetwork aNetwork, Set<Node> aNodeSet) {
+ // Ask the user for an interpretation of the network edges
+ try {
+ final NetworkInspection status = CyNetworkUtils.inspectNetwork(aNetwork);
+ NetworkInterpretation interpr = interpretNetwork(status);
+ if (interpr == null) {
+ return null;
+ }
+
+ NetworkAnalyzer analyzer = null;
+ if (interpr.isDirected()) {
+ analyzer = new DirNetworkAnalyzer(aNetwork, aNodeSet, interpr);
+ } else {
+ analyzer = new UndirNetworkAnalyzer(aNetwork, aNodeSet, interpr);
+ }
+ return new AnalysisExecutor(Cytoscape.getDesktop(), analyzer);
+ } catch (IllegalArgumentException ex) {
+ Utils.showInfoBox(Messages.DT_INFO, Messages.SM_NETWORKEMPTY);
+ return null;
+ }
+ }
+
+ /**
+ * Attempts to find an interpretation for network's edges.
+ * <p>
+ * This method displays a dialog to the user. If the network status leads to a unique interpretation, the
+ * dialog informs the user about it. In case multiple interpretations are possible, the dialog asks the
+ * user to choose one.
+ * </p>
+ *
+ * @param aInsp
+ * Results of inspection on the edges of a network.
+ * @return Interpretation instance containing the directions for interpretation of network's edges;
+ * <code>null</code> if the user has decided to cancel the operation.
+ *
+ * @see InterpretationDialog
+ */
+ private static NetworkInterpretation interpretNetwork(NetworkInspection aInsp) {
+ final NetworkStatus status = NetworkStatus.getStatus(aInsp);
+ final InterpretationDialog dialog = new InterpretationDialog(status);
+ dialog.setVisible(true);
+
+ if (dialog.pressedOK()) {
+ return status.getInterpretations()[dialog.getUserChoice()];
+ }
+ return null;
+ }
+
+ /**
+ * Unique ID for this version of this class. It is used in serialization.
+ */
+ private static final long serialVersionUID = 1079760835761343070L;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/AnalyzeSubsetAction.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/AnalyzeSubsetAction.java
new file mode 100644
index 0000000..4cac535
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/AnalyzeSubsetAction.java
@@ -0,0 +1,107 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer;
+
+import giny.model.Node;
+
+import java.awt.event.ActionEvent;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import cytoscape.Cytoscape;
+import cytoscape.logger.CyLogger;
+import cytoscape.view.CyNetworkView;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Messages;
+import de.mpg.mpi_inf.bioinf.netanalyzer.ui.Utils;
+import ding.view.DNodeView;
+
+/**
+ * Action handler for the menu item "Analyze Subset of Nodes".
+ *
+ * @author Yassen Assenov
+ * @author Nadezhda Doncheva
+ */
+public class AnalyzeSubsetAction extends NetAnalyzerAction {
+
+ /**
+ * Initializes a new instance of <code>NetSubsetAction</code>.
+ */
+ public AnalyzeSubsetAction() {
+ super(Messages.AC_ANALYZE_SUBSET);
+ selected = null;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see cytoscape.util.CytoscapeAction#actionPerformed(java.awt.event.ActionEvent)
+ */
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ try {
+ if (selectNetwork()) {
+ final AnalysisExecutor exec = AnalyzeNetworkAction.initAnalysisExecuter(network, selected);
+ if (exec != null) {
+ exec.start();
+ }
+ }
+ } catch (InnerException ex) {
+ // NetworkAnalyzer internal error
+ CyLogger.getLogger().error(Messages.SM_LOGERROR, ex);
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see de.mpg.mpi_inf.bioinf.netanalyzer.NetAnalyzerAction#selectNetwork()
+ */
+ @Override
+ protected boolean selectNetwork() {
+ if (super.selectNetwork()) {
+ final CyNetworkView view = Cytoscape.getNetworkView(network.getIdentifier());
+ if (view == null) {
+ Utils.showErrorBox(Messages.DT_WRONGDATA, Messages.SM_CREATEVIEW);
+ return false;
+ }
+ // TODO: [Cytoscape 2.8] Check if the returned list is parameterized
+ final List<?> nodes = view.getSelectedNodes();
+ if (nodes.isEmpty()) {
+ Utils.showErrorBox(Messages.DT_WRONGDATA, Messages.SM_SELECTNODES);
+ return false;
+ }
+ selected = new HashSet<Node>();
+ for (final Object node : nodes) {
+ selected.add(((DNodeView) node).getNode());
+ }
+ return true;
+ }
+ return false;
+ }
+
+ /**
+ * Set of nodes in the networks that were selected before the user clicked on the item.
+ */
+ protected Set<Node> selected;
+
+ /**
+ * Unique ID for this version of this class. It is used in serialization.
+ */
+ private static final long serialVersionUID = 4670655302334870699L;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/BatchAnalysisAction.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/BatchAnalysisAction.java
new file mode 100644
index 0000000..02a186e
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/BatchAnalysisAction.java
@@ -0,0 +1,126 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer;
+
+import java.awt.event.ActionEvent;
+import java.io.File;
+import java.io.FileFilter;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.List;
+
+import cytoscape.Cytoscape;
+import cytoscape.data.ImportHandler;
+import cytoscape.data.readers.GraphReader;
+import cytoscape.logger.CyLogger;
+import cytoscape.view.CytoscapeDesktop;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Interpretations;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Messages;
+import de.mpg.mpi_inf.bioinf.netanalyzer.ui.BatchAnalysisDialog;
+import de.mpg.mpi_inf.bioinf.netanalyzer.ui.BatchResultsDialog;
+import de.mpg.mpi_inf.bioinf.netanalyzer.ui.BatchSettingsDialog;
+import de.mpg.mpi_inf.bioinf.netanalyzer.ui.Utils;
+
+/**
+ * Action handler for the menu item "Batch Analysis".
+ *
+ * @author Yassen Assenov
+ * @author Nadezhda Doncheva
+ */
+public class BatchAnalysisAction extends NetAnalyzerAction {
+
+ /**
+ * Constructs a new batch analysis action.
+ */
+ protected BatchAnalysisAction() {
+ super(Messages.AC_BATCH_ANALYSIS);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see cytoscape.util.CytoscapeAction#actionPerformed(java.awt.event.ActionEvent)
+ */
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ try {
+ final CytoscapeDesktop desktop = Cytoscape.getDesktop();
+ // Step 1 - Adjust settings
+ BatchSettingsDialog d1 = new BatchSettingsDialog(desktop);
+ d1.setVisible(true);
+ final File[] inOutDirs = d1.getInOutDirs();
+
+ // Step 2 - Run the analysis
+ if (inOutDirs != null) {
+ final List<File> files = getInputFiles(inOutDirs[0]);
+ if (files.size() > 0) {
+ final Interpretations ins = d1.getInterpretations();
+ final BatchNetworkAnalyzer analyzer = new BatchNetworkAnalyzer(inOutDirs[1], files, ins);
+ final BatchAnalysisDialog d2 = new BatchAnalysisDialog(desktop, analyzer);
+ d2.setVisible(true);
+ if (d2.resultsPressed()) {
+ // Step 3 - Show results
+ BatchResultsDialog d3 = new BatchResultsDialog(analyzer.getReports());
+ d3.setVisible(true);
+ }
+ } else {
+ Utils.showInfoBox(Messages.DT_INFO, Messages.SM_NOINPUTFILES);
+ }
+ }
+ } catch (InnerException ex) {
+ // NetworkAnalyzer internal error
+ CyLogger.getLogger().error(Messages.SM_LOGERROR, ex);
+ }
+ }
+
+ /**
+ * Get all readable Network files from the input directory. These are all SIF, GML and XGMML files.
+ * <p>
+ * This method is called upon initialization only.
+ * </p>
+ *
+ * @param inputDir
+ * Input directory as selected by the user.
+ * @return All readable Network files in the input directory, as a list of <code>File</code> instances.
+ */
+ private List<File> getInputFiles(File inputDir) {
+ final FileFilter inputFileFilter = new FileFilter() {
+
+ public boolean accept(File aPathname) {
+ if (aPathname.isFile() && aPathname.canRead()) {
+ final String name = aPathname.getAbsolutePath();
+ ImportHandler handler = new ImportHandler();
+ GraphReader reader = handler.getReader(name);
+ if (reader != null) {
+ return true;
+ }
+ }
+ return false;
+ }
+ };
+
+ final List<File> inputFiles = Arrays.asList(inputDir.listFiles(inputFileFilter));
+ Collections.sort(inputFiles);
+ return inputFiles;
+ }
+
+ /**
+ * Unique ID for this version of this class. It is used in serialization.
+ */
+ private static final long serialVersionUID = -1228030064334629585L;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/BatchNetworkAnalyzer.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/BatchNetworkAnalyzer.java
new file mode 100644
index 0000000..93011e1
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/BatchNetworkAnalyzer.java
@@ -0,0 +1,521 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer;
+
+import giny.model.Node;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Set;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import cytoscape.data.CyAttributes;
+import cytoscape.util.SwingWorker;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.AnalysisError;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Interpretations;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Messages;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.NetworkAnalysisReport;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.NetworkInspection;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.NetworkInterpretation;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.NetworkStats;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.NetworkStatus;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.io.SettingsSerializer;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.io.StatsSerializer;
+import de.mpg.mpi_inf.bioinf.netanalyzer.ui.BatchAnalysisDialog;
+
+/**
+ * Class for batch analysis of networks.
+ *
+ * @author Yassen Assenov
+ * @author Nadezhda Doncheva
+ */
+public class BatchNetworkAnalyzer extends SwingWorker {
+
+ /**
+ * Initializes a new instance of <code>BatchNetworkAnalyzer</code>.
+ *
+ * @param aOutputDir
+ * Output directory as chosen by the user.
+ * @param aInputFiles
+ * List of all input files for the analysis.
+ * @param aInterpr
+ * Parameter specifying which interpretations to be applied to each network.
+ */
+ public BatchNetworkAnalyzer(File aOutputDir, List<File> aInputFiles, Interpretations aInterpr) {
+ analyzer = null;
+ cancelled = false;
+ dialog = null;
+ progress = 0;
+ outputDir = aOutputDir;
+ inputFiles = aInputFiles;
+ interpretations = aInterpr;
+ reports = new ArrayList<NetworkAnalysisReport>();
+ scale = 0.0;
+ analyzing = false;
+ subProgress = 0;
+ }
+
+ /**
+ * Cancels the process of network analysis.
+ * <p>
+ * Note that this method does not force the analyzer to cancel immediately; it takes an unspecified period of time
+ * until the analysis thread actually stops.
+ * </p>
+ */
+ public void cancel() {
+ cancelled = true;
+ synchronized (this) {
+ if (analyzer != null) {
+ analyzer.cancel();
+ }
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see cytoscape.util.SwingWorker#construct()
+ */
+ @Override
+ public Object construct() {
+ progress = 0;
+ for (final File inputFile : inputFiles) {
+
+ // Make a new network in cytoscape from a filename in
+ // the network-directory
+ CyNetwork network = null;
+ try {
+ write(Messages.SM_LOADING + inputFile.getName() + " ... ");
+ if (!inputFile.isFile()) {
+ throw new RuntimeException();
+ }
+ network = Cytoscape.createNetworkFromFile(inputFile.getPath(), false);
+ } catch (RuntimeException e) {
+ writeLine(Messages.SM_READERROR);
+ reports.add(new NetworkAnalysisReport(inputFile, null, AnalysisError.NETWORK_NOT_OPENED));
+ progress += PROGRESS_PER_NET;
+ continue;
+ }
+
+ // Get all possible interpretations for the network
+ NetworkInspection inspection = null;
+ try {
+ inspection = CyNetworkUtils.inspectNetwork(network);
+ } catch (IllegalArgumentException e) {
+ writeLine(Messages.SM_DONE);
+ reports.add(new NetworkAnalysisReport(inputFile, null, AnalysisError.NETWORK_EMPTY));
+ unloadNetwork(inputFile, network);
+ continue;
+ } catch (NullPointerException e) {
+ reports.add(new NetworkAnalysisReport(inputFile, null, AnalysisError.NETWORK_FILE_INVALID));
+ progress += PROGRESS_PER_NET;
+ continue;
+ }
+
+ final NetworkInterpretation[] interprs = filterInterpretations(getInterpretations(inspection));
+ final int intCount = interprs.length;
+ final int advance = PROGRESS_PER_NET / intCount;
+
+ // Run NetworkAnalyzer on all accepted interpretations
+ writeLine(Messages.SM_DONE);
+ for (int j = 0; j < intCount; progress += advance, ++j) {
+ if (cancelled) {
+ writeLine(Messages.SM_ANALYSISC);
+ return null;
+ }
+
+ // Run the analysis for an interpretation
+ final NetworkInterpretation interpretation = interprs[j];
+ try {
+ if (interpretation.isDirected()) {
+ analyzer = new DirNetworkAnalyzer(network, null, interpretation);
+ } else {
+ analyzer = new UndirNetworkAnalyzer(network, null, interpretation);
+ }
+ writeLine(Messages.DI_ANALYZINGINTERP1 + (j + 1) + Messages.DI_ANALYZINGINTERP2 + intCount);
+ final int maxProgress = analyzer.getMaxProgress();
+ scale = (double) advance / (double) maxProgress;
+ analyzing = true;
+ subProgress = 0;
+ analyzer.computeAll();
+ analyzing = false;
+ if (cancelled) {
+ writeLine(Messages.SM_ANALYSISC);
+ return null;
+ }
+ final NetworkStats stats = analyzer.getStats();
+ synchronized (this) {
+ analyzer = null;
+ }
+
+ final String networkName = network.getTitle();
+ stats.setTitle(networkName + interpretation.getInterpretSuffix());
+ final String extendedName = networkName + createID(interpretation);
+ try {
+ if (SettingsSerializer.getPluginSettings().getUseNodeAttributes()) {
+ if (!saveNodeAttributes(network, interpretation.isDirected(), outputDir,
+ extendedName)) {
+ writeLine(Messages.SM_ATTRIBUTESNOTSAVED);
+ }
+ }
+ File netstatFile = new File(outputDir, extendedName + ".netstats");
+ StatsSerializer.save(stats, netstatFile);
+ writeLine(Messages.SM_RESULTSSAVED);
+ reports.add(new NetworkAnalysisReport(inputFile, interpretation, netstatFile));
+ } catch (SecurityException ex) {
+ writeError(Messages.SM_SAVEERROR);
+ reports.add(new NetworkAnalysisReport(inputFile, interpretation,
+ AnalysisError.OUTPUT_NOT_CREATED));
+ } catch (FileNotFoundException ex) {
+ writeError(Messages.SM_SAVEERROR);
+ reports.add(new NetworkAnalysisReport(inputFile, interpretation,
+ AnalysisError.OUTPUT_NOT_CREATED));
+ } catch (IOException e) {
+ writeError(Messages.SM_SAVEERROR);
+ reports
+ .add(new NetworkAnalysisReport(inputFile, interpretation, AnalysisError.OUTPUT_IO_ERROR));
+ }
+
+ if (cancelled) {
+ writeLine(Messages.SM_ANALYSISC);
+ return null;
+ }
+ } catch (Exception e) {
+ reports.add(new NetworkAnalysisReport(inputFile, interpretation, AnalysisError.INTERNAL_ERROR));
+ }
+ }
+
+ unloadNetwork(inputFile, network);
+ }
+ return null;
+ }
+
+ /**
+ * Filters the set of network interpretations based on the setting selected by the user.
+ *
+ * @param interprs
+ * All possible interpretations of the current network.
+ * @return Array of all acceptable interpretations of the current network.
+ *
+ * @see #interpretations
+ */
+ private NetworkInterpretation[] filterInterpretations(NetworkInterpretation[] interprs) {
+ if (interpretations != Interpretations.ALL) {
+ ArrayList<NetworkInterpretation> accepted = null;
+ for (int i = 0; i < interprs.length; i++) {
+ if ((interpretations == Interpretations.DIRECTED) != interprs[i].isDirected()) {
+ if (accepted == null) {
+ accepted = new ArrayList<NetworkInterpretation>(interprs.length - 1);
+ for (int j = 0; j < i; j++) {
+ accepted.add(interprs[j]);
+ }
+ }
+ } else if (accepted != null) {
+ accepted.add(interprs[i]);
+ }
+ }
+ if (accepted != null) {
+ NetworkInterpretation[] result = new NetworkInterpretation[accepted.size()];
+ accepted.toArray(result);
+ return result;
+ }
+ }
+ return interprs;
+ }
+
+ /**
+ * Save node attributes computed by NetworkAnalyzer for this network into a tab-delimited file with extension
+ * "nattributes" (1st column corresponds to the node ids, each subsequent column contains the values of a node
+ * attribute).
+ *
+ * @param aNetwork
+ * Target network.
+ * @param aDir
+ * Flag indicating if the network interpretation is directed.
+ * @param aOutputDir
+ * Output directory for writing files as chosen by the user.
+ * @param aExtendedName
+ * Name of the analyzed network including the current interpretation.
+ * @return <code>true</code> if any node attributes where present and have been saved, and <code>false</code>
+ * otherwise.
+ */
+ private boolean saveNodeAttributes(CyNetwork aNetwork, boolean aDir, File aOutputDir,
+ String aExtendedName) {
+ // get node attributes computed in the last analysis run
+ Set<String> netAnayzerAttr = new HashSet<String>();
+ if (aDir) {
+ netAnayzerAttr = Messages.getDirNodeAttributes();
+ } else {
+ netAnayzerAttr = Messages.getUndirNodeAttributes();
+ }
+ if (netAnayzerAttr.size() == 0) {
+ return false;
+
+ }
+ // save chosen node attributes in a file, 1st column corresponds to the node ids, each subsequent column
+ // contains the values of a node attribute
+ final CyAttributes nodeAttr = Cytoscape.getNodeAttributes();
+ try {
+ final FileWriter writer = new FileWriter(new File(outputDir, aExtendedName + ".nattributes"));
+ writer.write("Node ID");
+ for (final String attr : netAnayzerAttr) {
+ writer.write("\t" + attr);
+ }
+ writer.write("\n");
+ final Iterator<?> it = aNetwork.nodesIterator();
+ while (it.hasNext()) {
+ final String id = ((Node) it.next()).getIdentifier();
+ writer.write(id);
+ for (final String attr : netAnayzerAttr) {
+ final Object attrValue = nodeAttr.getAttribute(id, attr);
+ if (attrValue != null) {
+ writer.write("\t" + attrValue.toString());
+ }
+ }
+ writer.write("\n");
+ }
+ writer.close();
+ } catch (IOException ex) {
+ // attributes file could not be written
+ return false;
+ }
+ return true;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see cytoscape.util.SwingWorker#finished()
+ */
+ @Override
+ public void finished() {
+ progress++;
+ if (dialog != null) {
+ dialog.analysisFinished();
+ }
+ interrupt();
+ }
+
+ /**
+ * Gets the current progress of the tester as a number of steps.
+ *
+ * @return Number of steps completed in the analysis process.
+ */
+ public int getCurrentProgress() {
+ if (analyzing) {
+ subProgress = +analyzer.getCurrentProgress();
+ return (progress + (int) (subProgress * scale));
+ }
+ return progress;
+ }
+
+ /**
+ * Gets the maximum progress of the tester as a number of steps.
+ *
+ * @return Total number of steps required for the tester to finish.
+ */
+ public int getMaxProgress() {
+ return inputFiles.size() * PROGRESS_PER_NET + 1;
+ }
+
+ /**
+ * Gets the number of input files, i.e. the number of networks to be analyzed.
+ *
+ * @return Number of input files, i.e. networks to be analyzed.
+ */
+ public int getInputFilesCount() {
+ return inputFiles.size();
+ }
+
+ /**
+ * Gets the list with reports after the analysis is finished.
+ *
+ * @return List of reports describing the success or failure of the analysis of each network.
+ */
+ public List<NetworkAnalysisReport> getReports() {
+ return reports;
+ }
+
+ /**
+ * Sets the corresponding batch analysis dialog.
+ *
+ * @param aDialog
+ * Dialog of the batch analysis.
+ */
+ public void setDialog(BatchAnalysisDialog aDialog) {
+ dialog = aDialog;
+ }
+
+ /**
+ * Creates an integer identifier of the network interpretation, where 1 means directed network and 0 - undirected.
+ *
+ * @param aInterp
+ * Network Interpretation.
+ * @return A String of the integer identifier of the network interpretation.
+ */
+ private static String createID(NetworkInterpretation aInterp) {
+ String newName = "";
+ final boolean flag1 = aInterp.isDirected();
+ final boolean flag2 = aInterp.isIgnoreUSL();
+ final boolean flag3 = aInterp.isPaired();
+ if (flag1) {
+ newName += "-d";
+ if (flag2) {
+ newName += "-isl";
+ }
+ } else {
+ newName += "-u";
+ if (flag3) {
+ newName += "-cpe";
+ }
+ }
+ return newName;
+ }
+
+ /**
+ * Gets the network interpretations from the network inspection.
+ *
+ * @param inspection
+ * Network inspection.
+ * @return Array with different network interpretations.
+ */
+ private static NetworkInterpretation[] getInterpretations(NetworkInspection inspection) {
+ return NetworkStatus.getStatus(inspection).getInterpretations();
+ }
+
+ /**
+ * Fixed integer estimating the analysis time of a single network.
+ */
+ private static final int PROGRESS_PER_NET = 12;
+
+ /**
+ * Unloads the network from Cytoscape and writes a message in the batch analysis dialog.
+ *
+ * @param inputFile
+ * File from which the network was loaded.
+ * @param network
+ * Network to be unloaded.
+ */
+ private void unloadNetwork(final File inputFile, CyNetwork network) {
+ // Unload the network
+ write(Messages.SM_UNLOADING + inputFile.getName() + " ... ");
+ try {
+ Cytoscape.destroyNetwork(network, true);
+ } catch (Exception ex) {
+ // Network already removed (by another plugin); ignore
+ }
+ writeLine(Messages.SM_DONE + "\n");
+ }
+
+ /**
+ * Writes a message to the user in the batch analysis dialog.
+ *
+ * @param aMessage
+ * Message to be written (showed) to the user.
+ */
+ private void write(String aMessage) {
+ if (dialog != null) {
+ dialog.write(aMessage);
+ }
+ }
+
+ /**
+ * Writes a message, followed by a new line, to the user in the batch analysis dialog.
+ *
+ * @param aMessage
+ * Message to be written to the user.
+ */
+ private void writeLine(String aMessage) {
+ write(aMessage + "\n");
+ }
+
+ /**
+ * Writes an error message, followed by a new line, to the user in the batch analysis dialog.
+ *
+ * @param aMessage
+ * An error message to be written to the user.
+ */
+ private void writeError(String aMessage) {
+ if (dialog != null) {
+ dialog.write(aMessage + "\n");
+ }
+ }
+
+ /**
+ * Instance of <code>UndirNetowkrAnalyzer</code> or <code>DirNetowkrAnalyzer</code> responsible for the network
+ * parameters computation.
+ */
+ private NetworkAnalyzer analyzer;
+
+ /**
+ * Flag indicating if the analysis has been canceled.
+ */
+ private boolean cancelled;
+
+ /**
+ * Dialog showing the progress of the batch analysis.
+ */
+ private BatchAnalysisDialog dialog;
+
+ /**
+ * Progress of the batch analysis.
+ */
+ private int progress;
+
+ /**
+ * Array with the names of the input (inOutDir[0]) and output directory (inOutDir[1]).
+ */
+ private File outputDir;
+
+ /**
+ * List of input files, that can be loaded in Cytoscape and analyzed by NetworkAnalyzer.
+ */
+ private List<File> inputFiles;
+
+ /**
+ * Interpretations to applied for every loaded network.
+ */
+ private Interpretations interpretations;
+
+ /**
+ * List of reports describing the success or failure of the analysis of each network.
+ */
+ private List<NetworkAnalysisReport> reports;
+
+ /**
+ * Scaling factor needed for showing the analysis progress.
+ */
+ private double scale;
+
+ /**
+ * Flag indicating if parameters are computed by <code>NetworkAnalyzer</code>.
+ */
+ private boolean analyzing;
+
+ /**
+ * Progress of <code>NetworkAnalyzer</code> analysis for a single network interpretation.
+ */
+ private double subProgress;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/CompareAction.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/CompareAction.java
new file mode 100644
index 0000000..009c02c
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/CompareAction.java
@@ -0,0 +1,62 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer;
+
+import java.awt.event.ActionEvent;
+
+import cytoscape.Cytoscape;
+import cytoscape.logger.CyLogger;
+import cytoscape.util.CytoscapeAction;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Messages;
+import de.mpg.mpi_inf.bioinf.netanalyzer.ui.CompareDialog;
+
+/**
+ * Action handler for the menu item "Compare Two Networks".
+ *
+ * @author Yassen Assenov
+ */
+public class CompareAction extends CytoscapeAction {
+
+ /**
+ * Initializes a new instance of <code>GOPTRunAlgorithm</code>.
+ */
+ public CompareAction() {
+ super(Messages.AC_COMPARE);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.event.ActionListener#actionPerformed(java.awt.event.ActionEvent)
+ */
+ @Override
+ public void actionPerformed(ActionEvent event) {
+ try {
+ CompareDialog d = new CompareDialog(Cytoscape.getDesktop());
+ d.setVisible(true);
+ } catch (InnerException ex) {
+ // NetworkAnalyzer internal error
+ CyLogger.getLogger().error(Messages.SM_LOGERROR, ex);
+ }
+ }
+
+ /**
+ * Unique ID for this version of this class. It is used in serialization.
+ */
+ private static final long serialVersionUID = -8249265620304925132L;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ConnComponentAction.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ConnComponentAction.java
new file mode 100644
index 0000000..f846873
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ConnComponentAction.java
@@ -0,0 +1,83 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer;
+
+import java.awt.event.ActionEvent;
+import java.util.Arrays;
+import java.util.Set;
+
+import cytoscape.Cytoscape;
+import cytoscape.logger.CyLogger;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.CCInfo;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.CCInfoInvComparator;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Messages;
+import de.mpg.mpi_inf.bioinf.netanalyzer.ui.ConnComponentsDialog;
+import de.mpg.mpi_inf.bioinf.netanalyzer.ui.Utils;
+
+/**
+ * Action handler for the menu item "Connected Components".
+ *
+ * @author Yassen Assenov
+ */
+public class ConnComponentAction extends NetAnalyzerAction {
+
+ /**
+ * Initializes a new instance of <code>ConnComponentAction</code>.
+ */
+ public ConnComponentAction() {
+ super(Messages.AC_CONNCOMP);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.event.ActionListener#actionPerformed(java.awt.event.ActionEvent)
+ */
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ try {
+ if (!selectNetwork()) {
+ return;
+ }
+
+ ConnComponentAnalyzer an = new ConnComponentAnalyzer(network);
+
+ Set<CCInfo> compsSet = an.findComponents();
+ final int compsCount = compsSet.size();
+ CCInfo[] comps = new CCInfo[compsCount];
+ compsSet.toArray(comps);
+
+ if (compsCount == 1) {
+ final String msg = "<html><b>" + network.getTitle() + "</b>" + Messages.SM_CONNECTED;
+ Utils.showInfoBox(Messages.DT_CONNCOMP, msg);
+ } else {
+ Arrays.sort(comps, new CCInfoInvComparator());
+ ConnComponentsDialog d = new ConnComponentsDialog(Cytoscape.getDesktop(), network, comps);
+ d.setVisible(true);
+ }
+ } catch (InnerException ex) {
+ // NetworkAnalyzer internal error
+ CyLogger.getLogger().error(Messages.SM_LOGERROR, ex);
+ }
+ }
+
+ /**
+ * Unique ID for this version of this class. It is used in serialization.
+ */
+ private static final long serialVersionUID = -7465036491341908005L;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ConnComponentAnalyzer.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ConnComponentAnalyzer.java
new file mode 100644
index 0000000..64d515b
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ConnComponentAnalyzer.java
@@ -0,0 +1,175 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer;
+
+import giny.model.Node;
+
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.LinkedList;
+import java.util.Set;
+
+import cytoscape.CyNetwork;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.CCInfo;
+
+/**
+ * Control class providing analysis of the connected components in a Cytoscape network.
+ *
+ * @author Yassen Assenov
+ */
+public class ConnComponentAnalyzer {
+
+ /**
+ * Gets all nodes in the given connected component.
+ *
+ * @param aNetwork Network in which the given connected components is contained.
+ * @param aCompInfo Information about the connected component of interest.
+ * @return Set of all nodes in <code>aCompInfo</code>; empty set if this component is not
+ * contained in <code>aNetwork</code>.
+ */
+ public static Set<Node> getNodesOf(CyNetwork aNetwork, CCInfo aCompInfo) {
+ Set<Node> nodes = new HashSet<Node>(aCompInfo.getSize());
+ nodes.add(aCompInfo.getNode());
+ LinkedList<Node> toTraverse = new LinkedList<Node>();
+ toTraverse.add(aCompInfo.getNode());
+
+ while (!toTraverse.isEmpty()) {
+ final Node node = toTraverse.removeFirst();
+ final Set<Node> neighbors = CyNetworkUtils.getNeighbors(aNetwork, node);
+ for (Node nb : neighbors) {
+ if (!nodes.contains(nb)) {
+ nodes.add(nb);
+ toTraverse.add(nb);
+ }
+ }
+ }
+ return nodes;
+ }
+
+ /**
+ * Initializes a new instance of <code>ConnComponentAnalyzer</code>.
+ *
+ * @param aNetwork Network to be analyzed.
+ */
+ public ConnComponentAnalyzer(CyNetwork aNetwork) {
+ network = aNetwork;
+ }
+
+ /**
+ * Finds all components in the analyzer network.
+ *
+ * @return Set of all components in the analyzed network ({@link #getNetwork()}); empty set if
+ * the analyzed network is empty.
+ */
+ public Set<CCInfo> findComponents() {
+ int untravCount = network.getNodeCount();
+
+ Set<Node> traversed = new HashSet<Node>(untravCount);
+ Set<CCInfo> components = new HashSet<CCInfo>();
+
+ // TODO: [Cytoscape 2.8] Check if the returned iterator is parameterized
+ Iterator<?> it = network.nodesIterator();
+ while (untravCount > 0 && it.hasNext()) {
+ final Node node = (Node) it.next();
+ if (!traversed.contains(node)) {
+ // Unmarked node reached - create new conn. component
+ final int ccSize = traverseReachable(node, traversed);
+ untravCount -= ccSize;
+ components.add(new CCInfo(ccSize, node));
+ }
+ }
+ return components;
+ }
+
+ /**
+ * Finds (the) largest connected component of the analyzed network. The largest component is the
+ * one that contains the most nodes.
+ * <p>
+ * If the network contains more than one largest connected components, one of them is returned.
+ * There is no guarantee that the one returned satisfies any requirements (apart from having
+ * largest size).
+ * </p>
+ *
+ * @return Connected component C in the analyzed network, such that no other connected component
+ * in the network contains more nodes than C.
+ */
+ public CCInfo findLargestComponent() {
+ CCInfo largest = new CCInfo(0, null);
+ final Set<CCInfo> comps = findComponents();
+ for (CCInfo current : comps) {
+ if (current.getSize() > largest.getSize()) {
+ largest = current;
+ }
+ }
+ return largest;
+ }
+
+ /**
+ * Gets the analyzed network.
+ *
+ * @return Network instance to be analyzed.
+ */
+ public CyNetwork getNetwork() {
+ return network;
+ }
+
+ /**
+ * Gets all nodes in the given connected component.
+ *
+ * @param aCompInfo Information about the connected component of interest.
+ * @return Set of all nodes in <code>aCompInfo</code>; empty set if this component is not
+ * contained in the analyzed network ({@link #getNetwork()}).
+ *
+ * @see #getNodesOf(CyNetwork, CCInfo)
+ */
+ public Set<Node> getNodesOf(CCInfo aCompInfo) {
+ return getNodesOf(network, aCompInfo);
+ }
+
+ /**
+ * Traverses all nodes that are reachable from the given node.
+ *
+ * @param aNode Node to start the traversal from.
+ * @param aTraversed Set of traversed nodes. This method add all visited nodes to this set.
+ * @return Number of nodes which were traversed. <code>aNode</code> itself is also counted as
+ * traversed.
+ */
+ private int traverseReachable(Node aNode, Set<Node> aTraversed) {
+ int size = 1;
+ LinkedList<Node> toTraverse = new LinkedList<Node>();
+ aTraversed.add(aNode);
+ toTraverse.add(aNode);
+ while (!toTraverse.isEmpty()) {
+ final Node currentNode = toTraverse.removeFirst();
+ final Set<Node> neighbors = CyNetworkUtils.getNeighbors(network, currentNode);
+ for (Node nb : neighbors) {
+ if (!aTraversed.contains(nb)) {
+ size++;
+ toTraverse.add(nb);
+ aTraversed.add(nb);
+ }
+ }
+ }
+ return size;
+ }
+
+ /**
+ * Analyzed network.
+ */
+ private CyNetwork network;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/CyNetworkUtils.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/CyNetworkUtils.java
new file mode 100644
index 0000000..416b755
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/CyNetworkUtils.java
@@ -0,0 +1,619 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer;
+
+import giny.model.Edge;
+import giny.model.Node;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import cytoscape.data.CyAttributes;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Messages;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.MutInteger;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.NetworkInspection;
+
+/**
+ * Utility class providing network functionality absent or deprecated in {@link cytoscape.CyNetwork} .
+ *
+ * @author Yassen Assenov
+ * @author Sven-Eric Schelhorn
+ */
+public abstract class CyNetworkUtils {
+
+ /**
+ * Keeps attributes that are computed by NetworkAnalyzer in this network and can be visualized.
+ *
+ * @param aNetwork
+ * The selected network.
+ * @param computedAttr
+ * Set of the names of all attributes computed in the network.
+ * @param cyAttr
+ * Set of node/edge attributes in Cytoscape.
+ * @param netAnalyzerAttr
+ * Set of all node/edge attributes computed by NetworkAnalyzer
+ *
+ * @return The computed attribute names in the form of two arrays. The names are placed in the returned
+ * array in alphabetical order.
+ */
+ private static String[][] keepAvailableAttributes(CyNetwork aNetwork, Set<String> computedAttr,
+ CyAttributes cyAttr, Set<String> netAnalyzerAttr) {
+ final List<String> visualizeAttr = new ArrayList<String>(computedAttr.size() + 1);
+ for (final String attr : computedAttr) {
+ if (cyAttr.getType(attr) == CyAttributes.TYPE_FLOATING
+ || cyAttr.getType(attr) == CyAttributes.TYPE_INTEGER) {
+ visualizeAttr.add(attr);
+ }
+ }
+ final List<String> resultNetAnalyzer = new ArrayList<String>(visualizeAttr);
+ final List<String> resultOther = new ArrayList<String>(visualizeAttr);
+ resultNetAnalyzer.retainAll(netAnalyzerAttr);
+ resultOther.removeAll(netAnalyzerAttr);
+ Collections.sort(resultNetAnalyzer);
+ Collections.sort(resultOther);
+ String[][] result = new String[2][];
+ result[0] = resultNetAnalyzer.toArray(new String[resultNetAnalyzer.size()]);
+ result[1] = resultOther.toArray(new String[resultOther.size()]);
+ return result;
+ }
+
+ /**
+ * Checks the specified network has values for the given edge attributes.
+ *
+ * @param aNetwork
+ * Network of interest.
+ * @return Array of all attributes for which all edges in <code>aNetwork</code> have values; an empty
+ * set if no such attributes are found.
+ */
+ public static String[][] getComputedEdgeAttributes(CyNetwork aNetwork) {
+ final CyAttributes edgeAttributes = Cytoscape.getEdgeAttributes();
+ final Collection<String> allAttrs = Arrays.asList(edgeAttributes.getAttributeNames());
+ final Set<String> computedAttr = new HashSet<String>(allAttrs);
+ // TODO: [Cytoscape 2.8] Check if the returned iterator is parameterized
+ final Iterator<?> itn = aNetwork.edgesIterator();
+ while (itn.hasNext()) {
+ final String id = ((Edge) itn.next()).getIdentifier();
+ for (final String attr : allAttrs) {
+ if (!hasAttr(id, edgeAttributes, attr)) {
+ computedAttr.remove(attr);
+ }
+ }
+ }
+ return keepAvailableAttributes(aNetwork, computedAttr, edgeAttributes, Messages.getEdgeAttributes());
+ }
+
+ /**
+ * Checks the specified network has values for the given node attributes.
+ *
+ * @param aNetwork
+ * Network of interest.
+ * @return Array of all attributes for which all nodes in <code>aNetwork</code> have values; an empty
+ * set if no such attributes are found.
+ */
+ public static String[][] getComputedNodeAttributes(CyNetwork aNetwork) {
+ final CyAttributes nodeAttributes = Cytoscape.getNodeAttributes();
+ final Collection<String> allAttrs = Arrays.asList(nodeAttributes.getAttributeNames());
+ final Set<String> computedAttr = new HashSet<String>(allAttrs);
+ // TODO: [Cytoscape 2.8] Check if the returned iterator is parameterized
+ final Iterator<?> itn = aNetwork.nodesIterator();
+ while (itn.hasNext()) {
+ final String id = ((Node) itn.next()).getIdentifier();
+ for (final String attr : allAttrs) {
+ if (!hasAttr(id, nodeAttributes, attr)) {
+ computedAttr.remove(attr);
+ }
+ }
+ }
+ return keepAvailableAttributes(aNetwork, computedAttr, nodeAttributes, Messages.getNodeAttributes());
+ }
+
+ /**
+ * Checks if the attribute of a node with current id has a computed value.
+ *
+ * @param id
+ * Id of a node of interest.
+ * @param cyAttr
+ * Set of node/edge attributes in Cytoscape.
+ * @param attr
+ * An attribute shown in Cytoscape.
+ * @return <code>true</code> when there are computed values for the given attribute; <code>false</code>
+ * otherwise.
+ */
+ private static boolean hasAttr(String id, CyAttributes cyAttr, String attr) {
+ final byte attrType = cyAttr.getType(attr);
+ if (attrType == CyAttributes.TYPE_FLOATING) {
+ if (cyAttr.getDoubleAttribute(id, attr) != null) {
+ return true;
+ }
+ }
+ if (attrType == CyAttributes.TYPE_INTEGER) {
+ if (cyAttr.getIntegerAttribute(id, attr) != null) {
+ return true;
+ }
+ }
+ return false;
+ }
+
+ /**
+ * Returns the edges connecting two nodes.
+ *
+ * @param aNode1
+ * Node that has an edge with aNode2
+ * @param aNode2
+ * Node that has an edge with aNode1
+ * @return Edges connecting aNode1 and aNode2
+ */
+ protected static List<Edge> getConnEdge(CyNetwork aNetwork, Node aNode1, Node aNode2) {
+ final List<Node> nodes = new ArrayList<Node>(2);
+ nodes.add(aNode1);
+ nodes.add(aNode2);
+ // TODO: [Cytoscape 2.8] Check if the returned iterator is parameterized
+ final List<?> allEdges = aNetwork.getConnectingEdges(nodes);
+ final List<Edge> connEdges = new ArrayList<Edge>();
+ for (int i = 0; i < allEdges.size(); i++) {
+ final Edge e = (Edge) allEdges.get(i);
+ if (!e.getSource().equals(e.getTarget())) {
+ connEdges.add(e);
+ }
+ }
+ return connEdges;
+ }
+
+ /**
+ * Gets the number of pair connections between the given set of nodes.
+ * <p>
+ * This method effectively counts the number of edges between nodes in the given set, ignoring self-loops
+ * and multiple edges.
+ * </p>
+ *
+ * @param aNetwork
+ * Network containing the nodes of interest.
+ * @param aNodeIndices
+ * Indices of the nodes to be examined.
+ * @param aIgnoreDir
+ * Flag indicating if connections are undirected.
+ * @return Number of pair connections between the nodes in the given node set. The returned value is
+ * always in the range <code>[0, n(n-1)/2]</code> for undirected networks (
+ * <code>aIgnoreDir == true</code>) and <code>[0, n(n-1)]</code> for directed networks (
+ * <code>aIgnoreDir == true</code>).
+ */
+ public static int getPairConnCount(CyNetwork aNetwork, int[] aNodeIndices, boolean aIgnoreDir) {
+ int[] connEdges = aNetwork.getConnectingEdgeIndicesArray(aNodeIndices);
+ int edgeCount = connEdges.length;
+
+ for (int i = 0; i < connEdges.length; ++i) {
+ int edgeIndex = connEdges[i];
+ int sourceNodeIndex = aNetwork.getEdgeSourceIndex(edgeIndex);
+ int targetNodeIndex = aNetwork.getEdgeTargetIndex(edgeIndex);
+ if (sourceNodeIndex == targetNodeIndex) {
+ // Ignore self-loops
+ edgeCount--;
+ } else {
+ for (int j = i + 1; j < connEdges.length; j++) {
+ if (edgeMatches(aNetwork, connEdges[j], sourceNodeIndex, targetNodeIndex, aIgnoreDir)) {
+ // Ignore multiple edges
+ edgeCount--;
+ break;
+ }
+ }
+ }
+ }
+
+ return edgeCount;
+ }
+
+ /**
+ * Gets all the neighbors of the given node. All types of edges incident on the node are considered -
+ * incoming, outgoing and undirected.
+ * <p>
+ * Note that the node itself is never returned as its neighbor.
+ * </p>
+ *
+ * @param aNetwork
+ * Network that contains the node of interest - <code>aNode</code>.
+ * @param aNode
+ * Node, whose neighbors are to be found.
+ * @return <code>Set</code> of <code>Node</code> instances, containing all the neighbors of
+ * <code>aNode</code>; empty set if the node specified is an isolated vertex.
+ * @see #getNeighbors(CyNetwork, Node, int[])
+ */
+ public static Set<Node> getNeighbors(CyNetwork aNetwork, Node aNode) {
+ return getNeighbors(aNetwork, aNode, aNetwork.getAdjacentEdgeIndicesArray(aNode.getRootGraphIndex(),
+ true, true, true));
+ }
+
+ /**
+ * Gets all the neighbors of the given node.
+ * <p>
+ * Note that the node itself is never returned as its neighbor.
+ * </p>
+ *
+ * @param aNetwork
+ * Network that contains the node of interest - <code>aNode</code>.
+ * @param aNode
+ * Node, whose neighbors are to be found.
+ * @param aIncEdges
+ * Array of all the edges incident on <code>aNode</code>.
+ * @return <code>Set</code> of <code>Node</code> instances, containing all the neighbors of
+ * <code>aNode</code>; empty set if the node specified is an isolated vertex.
+ */
+ public static Set<Node> getNeighbors(CyNetwork aNetwork, Node aNode, int[] aIncEdges) {
+ Set<Node> neighborsSet = new HashSet<Node>();
+ for (int i = 0; i < aIncEdges.length; ++i) {
+ Edge e = aNetwork.getEdge(aIncEdges[i]);
+ Node sourceNode = e.getSource();
+ if (sourceNode != aNode) {
+ neighborsSet.add(sourceNode);
+ } else {
+ Node targetNode = e.getTarget();
+ if (targetNode != aNode) {
+ neighborsSet.add(targetNode);
+ }
+ }
+ }
+ return neighborsSet;
+ }
+
+ /**
+ * Gets all the neighbors of the given node and their frequencies. All types of edges incident on the node
+ * are considered - incoming, outgoing and undirected.
+ * <p>
+ * Note that the node itself is never counted as its neighbor.
+ * </p>
+ *
+ * @param aNetwork
+ * Network that contains the node of interest - <code>aNode</code>.
+ * @param aNode
+ * Node, whose neighbors are to be found.
+ * @return <code>Map</code> of <code>Node</code> instances as keys, containing all the neighbors of
+ * <code>aNode</code> and the number of their occurrences as the values, encapsulated in
+ * <code>MutInteger</code> instances.
+ * @see #getNeighborMap(CyNetwork, Node, int[])
+ */
+ public static Map<Node, MutInteger> getNeighborMap(CyNetwork aNetwork, Node aNode) {
+ return getNeighborMap(aNetwork, aNode, aNetwork.getAdjacentEdgeIndicesArray(
+ aNode.getRootGraphIndex(), true, true, true));
+ }
+
+ /**
+ * Gets all the neighbors of the given node and their frequencies.
+ * <p>
+ * All types of edges incident on the node are considered - incoming, outgoing and undirected.
+ * </p>
+ * <p>
+ * Note that the node itself is never counted as its neighbor.
+ * </p>
+ *
+ * @param aNetwork
+ * Network that contains the node of interest - <code>aNode</code>.
+ * @param aNode
+ * Node, whose neighbors are to be found.
+ * @param aIncEdges
+ * Array of all the edges incident on <code>aNode</code>.
+ * @return <code>Map</code> of <code>Node</code> instances as keys, containing all the neighbors of
+ * <code>aNode</code> and the number of their occurrences as values, encapsulated in
+ * <code>MutInteger</code> instances.
+ */
+ public static Map<Node, MutInteger> getNeighborMap(CyNetwork aNetwork, Node aNode, int[] aIncEdges) {
+ Map<Node, MutInteger> m = new HashMap<Node, MutInteger>();
+ for (int i = 0; i < aIncEdges.length; i++) {
+ Edge e = aNetwork.getEdge(aIncEdges[i]);
+ Node n = (e.getSource() == aNode) ? e.getTarget() : e.getSource();
+ if (n != aNode) {
+ MutInteger count = m.get(n);
+ if (count == null)
+ m.put(n, new MutInteger(1));
+ else
+ count.value++;
+ }
+ }
+ return m;
+ }
+
+ /**
+ * Gets the indices of a given set of nodes.
+ * <p>
+ * Note that the method stores the indices found in an array. The order in which the indices are stored is
+ * unspecified.
+ * </p>
+ *
+ * @param aNodeSet
+ * Set of nodes, whose indices are to be found.
+ * @return Array of indices of the nodes contained in <code>aNodeSet</code>.
+ */
+ public static int[] getIndices(Set<Node> aNodeSet) {
+ int nodeCount = aNodeSet.size();
+ int[] indices = new int[nodeCount];
+ int i = 0;
+ for (final Node node : aNodeSet) {
+ indices[i++] = node.getRootGraphIndex();
+ }
+ return indices;
+ }
+
+ /**
+ * Checks if two edges match.
+ *
+ * @param aNetwork
+ * Network containing the edges.
+ * @param aEdgeIndex
+ * Index of the first edge.
+ * @param aSourceIndex
+ * Source node of the second edge.
+ * @param aTargetIndex
+ * Target node of the second edge.
+ * @param aIgnoreDir
+ * Flag indicating if the direction of the edges is to be ignored.
+ * @return <code>true</code> if the edges connect the same pair of nodes (and have same direction, when
+ * <code>aIgnoreDir</code> is <code>false</code>); <code>false</code> otherwise.
+ */
+ private static boolean edgeMatches(CyNetwork aNetwork, int aEdgeIndex, int aSourceIndex,
+ int aTargetIndex, boolean aIgnoreDir) {
+ int eSource = aNetwork.getEdgeSourceIndex(aEdgeIndex);
+ int eTarget = aNetwork.getEdgeTargetIndex(aEdgeIndex);
+ return (eSource == aSourceIndex && eTarget == aTargetIndex)
+ || (aIgnoreDir && eSource == aTargetIndex && eTarget == aSourceIndex);
+ }
+
+ /**
+ * Performs an inspection on what kind of edges the given network contains.
+ *
+ * @param aNetwork
+ * Network to be inspected.
+ * @return Results of the inspection, encapsulated in a <code>NetworkInspection</code> instance.
+ *
+ * @throws IllegalArgumentException
+ * If <code>aNetwork</code> is empty, that is, contains zero nodes.
+ * @throws NullPointerException
+ * If <code>aNetwork</code> is <code>null</code>.
+ */
+ public static NetworkInspection inspectNetwork(CyNetwork aNetwork) {
+ if (aNetwork.getNodeCount() == 0) {
+ throw new IllegalArgumentException();
+ }
+ final NetworkInspection insp = new NetworkInspection();
+
+ // TODO: [Cytoscape 2.8] Check if the returned iterator is parameterized
+ Iterator<?> edgesIter = aNetwork.edgesIterator();
+ while (edgesIter.hasNext()) {
+ final Edge edge = (Edge) edgesIter.next();
+ final int ei = edge.getRootGraphIndex();
+
+ // Get all the edges that connect the two ends of the given edge
+ final int[] nodeIndices = new int[2];
+ final int source = nodeIndices[0] = aNetwork.getEdgeSourceIndex(ei);
+ nodeIndices[1] = aNetwork.getEdgeTargetIndex(ei);
+ final int[] connecting = aNetwork.getConnectingEdgeIndicesArray(nodeIndices);
+
+ if (nodeIndices[1] == source) {
+ // Self-loop inspection
+ int d = 0;
+ int u = 0;
+ for (final int cei : connecting) {
+ if (aNetwork.isEdgeDirected(cei)) {
+ d++;
+ } else {
+ u++;
+ }
+ }
+ if (d > 0) {
+ insp.dirLoops = true;
+ if ((d & 1) != 0) {
+ insp.uniqueDir = true;
+ }
+ }
+ if (u > 0) {
+ insp.undirLoops = true;
+ }
+ } else {
+ int ssd = 0;
+ int ttd = 0;
+ int std = 0;
+ int tsd = 0;
+ int ssu = 0;
+ int ttu = 0;
+ int u = 0;
+
+ for (final int cei : connecting) {
+ final int ceiSource = aNetwork.getEdgeSourceIndex(cei);
+ final int ceiTarget = aNetwork.getEdgeTargetIndex(cei);
+ final boolean directed = aNetwork.isEdgeDirected(cei);
+ if (ceiSource == source) {
+ if (ceiTarget == source) {
+ if (directed) {
+ ssd++;
+ } else {
+ ssu++;
+ }
+ } else if (directed) {
+ std++;
+ } else {
+ u++;
+ }
+ } else if (ceiTarget == source) {
+ if (directed) {
+ tsd++;
+ } else {
+ u++;
+ }
+ } else if (directed) {
+ ttd++;
+ } else {
+ ttu++;
+ }
+ }
+
+ if (ssd != 0 || ttd != 0) {
+ insp.dirLoops = true;
+ }
+ if (std != 0 || tsd != 0) {
+ insp.dir = true;
+ }
+ if (ssu != 0 || ttu != 0) {
+ insp.undirLoops = true;
+ }
+ if (u != 0) {
+ insp.undir = true;
+ }
+ if (((ssd & 1) != 0) || ((ttd & 1) != 0) || std != tsd) {
+ insp.uniqueDir = true;
+ }
+ if (std > 1 || tsd > 1) {
+ insp.dupDirEdges = insp.dupEdges = true;
+ } else if (std + tsd + u > 1) {
+ insp.dupEdges = true;
+ }
+ }
+ }
+
+ insp.stopTimer();
+ return insp;
+ }
+
+ /**
+ * Removes all duplicated edges in the network, not including self-loops.
+ *
+ * @param aNetwork
+ * Network from which duplicated edges are to be removed.
+ * @param aIgnoreDir
+ * Flag indicating if edge direction should be ignored. Set this to <code>true</code> if all
+ * edges are to be treated as undirected.
+ * @param aCreateEdgeAttr
+ * Flag indicating if an edge attribute representing the number of duplicated edges should be
+ * created.
+ *
+ * @return Number of edges removed from the network.
+ */
+ public static int removeDuplEdges(CyNetwork aNetwork, boolean aIgnoreDir, boolean aCreateEdgeAttr) {
+ final Set<Node> visited = new HashSet<Node>(aNetwork.getNodeCount());
+ int removedCount = 0;
+
+ // TODO: [Cytoscape 2.8] Check if the returned iterator is parameterized
+ final Iterator<?> itn = aNetwork.nodesIterator();
+ while (itn.hasNext()) {
+ final Node n1 = (Node) itn.next();
+ final int ni = n1.getRootGraphIndex();
+ final int[] incEdges = aNetwork.getAdjacentEdgeIndicesArray(ni, true, true, true);
+ final Map<Node, MutInteger> neighborMap = CyNetworkUtils.getNeighborMap(aNetwork, n1, incEdges);
+ // Check all neighbors of the node for multiple edges
+ for (final Map.Entry<Node, MutInteger> nf : neighborMap.entrySet()) {
+ final Node n2 = nf.getKey();
+ if (!visited.contains(n2)) {
+ final List<Node> nodes = new ArrayList<Node>(2);
+ nodes.add(n1);
+ nodes.add(n2);
+ Edge undirEdge = null;
+ Edge dir12Edge = null;
+ Edge dir21Edge = null;
+ int numUndir = 0;
+ int numDir12 = 0;
+ int numDir21 = 0;
+
+ // Traverse all edges connecting n1 and n2
+ for (final Object obj : aNetwork.getConnectingEdges(nodes)) {
+ final Edge e = (Edge) obj;
+ final Node source = e.getSource();
+ final Node target = e.getTarget();
+ if (source != target) {
+ if (aIgnoreDir == false && e.isDirected()) {
+ if (source == n1) {
+ if (dir12Edge != null) {
+ aNetwork.removeEdge(e.getRootGraphIndex(), false);
+ removedCount++;
+ } else {
+ dir12Edge = e;
+ }
+ numDir12++;
+ } else if (dir21Edge != null) {
+ aNetwork.removeEdge(e.getRootGraphIndex(), false);
+ removedCount++;
+ numDir21++;
+ } else {
+ dir21Edge = e;
+ numDir21++;
+ }
+ } else if (undirEdge != null) {
+ aNetwork.removeEdge(e.getRootGraphIndex(), false);
+ removedCount++;
+ numUndir++;
+ } else {
+ undirEdge = e;
+ numUndir++;
+ }
+ }
+ }
+ // store the number of removed edges as edge attribute
+ if (aCreateEdgeAttr) {
+ saveNumDuplEdges(undirEdge, numUndir);
+ saveNumDuplEdges(dir12Edge, numDir12);
+ saveNumDuplEdges(dir21Edge, numDir21);
+ }
+ }
+ }
+ visited.add(n1);
+ }
+ return removedCount;
+ }
+
+ /**
+ * Saves the number of edges duplicated to aEdge as an edge attribute.
+ *
+ * @param aEdge
+ * Edge for which duplicated edges are saved.
+ * @param aNumEdges
+ * NUmber of edges duplicated to aEdge.
+ */
+ private static void saveNumDuplEdges(Edge aEdge, int aNumEdges) {
+ if (aEdge != null) {
+ Cytoscape.getEdgeAttributes().setAttribute(aEdge.getIdentifier(), Messages.getAttr("dpe"),
+ new Integer(aNumEdges));
+ }
+ }
+
+ /**
+ * Removes all self-loops in a network and returns the number of removed self-loops. All types of edges
+ * are considered - incoming, outgoing and undirected.
+ *
+ * @param aNetwork
+ * Network from which self-loops are to be removed.
+ * @return Number of removed self-loops.
+ */
+ public static int removeSelfLoops(CyNetwork aNetwork) {
+ // TODO: [Cytoscape 2.8] Check if the returned iterator is parameterized
+ Iterator<?> iter = aNetwork.edgesIterator();
+ int removedCount = 0;
+ while (iter.hasNext()) {
+ Edge e = (Edge) iter.next();
+ if (e.getSource() == e.getTarget()) {
+ aNetwork.removeEdge(e.getRootGraphIndex(), false);
+ removedCount++;
+ }
+ }
+ return removedCount;
+ }
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/DirNetworkAnalyzer.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/DirNetworkAnalyzer.java
new file mode 100644
index 0000000..0ff74d2
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/DirNetworkAnalyzer.java
@@ -0,0 +1,789 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer;
+
+import giny.model.Edge;
+import giny.model.Node;
+
+import java.awt.geom.Point2D;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.CCInfo;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.DegreeDistribution;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.LogBinDistribution;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.LongHistogram;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.MutInteger;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.NetworkInterpretation;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.NodeBetweenInfo;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.PathLengthData;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Points2D;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.SumCountPair;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Utils;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.io.SettingsSerializer;
+
+/**
+ * Network analyzer for networks that contain directed edges only.
+ *
+ * @author Yassen Assenov
+ * @author Sven-Eric Schelhorn
+ * @author Nadezhda Doncheva
+ */
+public class DirNetworkAnalyzer extends NetworkAnalyzer {
+
+ /**
+ * Initializes a new instance of <code>DirNetworkAnalyzer</code>.
+ *
+ * @param aNetwork
+ * Network to be analyzed.
+ * @param aNodeSet
+ * Subset of nodes in <code>aNetwork</code>, for which topological parameters are to
+ * be calculated. Set this to <code>null</code> if parameters must be calculated for
+ * all nodes in the network.
+ * @param aInterpr
+ * Interpretation of the network edges.
+ */
+ public DirNetworkAnalyzer(CyNetwork aNetwork, Set<Node> aNodeSet,
+ NetworkInterpretation aInterpr) {
+ super(aNetwork, aNodeSet, aInterpr);
+ if (nodeSet != null) {
+ stats.set("nodeCount", nodeSet.size());
+ }
+ nodeCount = stats.getInt("nodeCount");
+ this.sPathLengths = new long[nodeCount];
+ this.visited = new HashSet<Node>();
+ this.useNodeAttributes = SettingsSerializer.getPluginSettings().getUseNodeAttributes();
+ this.useEdgeAttributes = SettingsSerializer.getPluginSettings().getUseEdgeAttributes();
+ this.roundingDigits = 8;
+ this.numberOfIsolatedNodes = 0;
+ this.numberOfSelfLoops = 0;
+ this.multiEdgePartners = 0;
+ this.nodeBetweenness = new HashMap<Node, NodeBetweenInfo>();
+ this.edgeBetweenness = new HashMap<Edge, Double>();
+ this.stress = new HashMap<Node, Long>();
+ computeNB = true;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see de.mpg.mpi_inf.bioinf.netanalyzer.NetworkAnalyzer#computeAll()
+ */
+ @Override
+ public void computeAll() {
+ long time = System.currentTimeMillis();
+ analysisStarting();
+ DegreeDistribution inDegreeDist = new DegreeDistribution(nodeCount);
+ DegreeDistribution outDegreeDist = new DegreeDistribution(nodeCount);
+ SumCountPair neighborsAccum = null; // used to compute av. number of
+ // neighbors
+ // neighborhood connectivity - all edges
+ HashMap<Integer, SumCountPair> ioNCps = new HashMap<Integer, SumCountPair>();
+ // neighborhood connectivity - incoming edges
+ HashMap<Integer, SumCountPair> inNCps = new HashMap<Integer, SumCountPair>();
+ // neighborhood connectivity - outgoing edges
+ HashMap<Integer, SumCountPair> outNCps = new HashMap<Integer, SumCountPair>();
+ // clustering coefficients
+ HashMap<Integer, SumCountPair> CCps = new HashMap<Integer, SumCountPair>();
+ // closeness centrality
+ ArrayList<Point2D.Double> closenessCent = new ArrayList<Point2D.Double>(nodeCount);
+ // node betweenness
+ ArrayList<Point2D.Double> nodeBetweennessArray = new ArrayList<Point2D.Double>(nodeCount);
+ // average shortest path length
+ Map<Node, Double> aplMap = new HashMap<Node, Double>();
+ // stress
+ LogBinDistribution stressDist = new LogBinDistribution();
+ long outNeighbors = 0; // total number of out-neighbors
+ diameter = 0;
+ radius = Integer.MAX_VALUE;
+
+ // Compute number of connected components
+ final ConnComponentAnalyzer cca = new ConnComponentAnalyzer(network);
+ Set<CCInfo> components = cca.findComponents();
+ final int connectedComponentsCount = components.size();
+
+ // Compute node and edge betweenness
+ for (CCInfo aCompInfo : components) {
+
+ // Get nodes of connected component
+ Set<Node> connNodes = cca.getNodesOf(aCompInfo);
+ // Set<Node> connNodes = new HashSet<Node>(connNodes);
+ if (nodeSet != null) {
+ connNodes.retainAll(nodeSet);
+ }
+ if (nodeSet == null && computeNB){
+ // Initialize parameter for node and edge betweenness calculation
+ // Clear elements of last component analyzed
+ nodeBetweenness.clear();
+ edgeBetweenness.clear();
+ // initialize betweenness map
+ for (Node n : connNodes) {
+ nodeBetweenness.put(n, new NodeBetweenInfo(0, -1, 0.0));
+ stress.put(n, Long.valueOf(0));
+ }
+ }
+
+ for (final Node node : connNodes) {
+ ++progress;
+ final int[] inEdges = getInEdges(node);
+ final int[] outEdges = getOutEdges(node);
+ inDegreeDist.addObservation(inEdges.length);
+ outDegreeDist.addObservation(outEdges.length);
+ String nodeID = node.getIdentifier();
+
+ Set<Node> neighbors = getNeighbors(node, inEdges, outEdges);
+ int neighborCount = neighbors.size();
+ if (neighborsAccum == null) {
+ neighborsAccum = new SumCountPair(neighborCount);
+ } else {
+ neighborsAccum.add(neighborCount);
+ }
+
+ // Number of unconnected nodes calculation
+ if (neighborCount == 0) {
+ numberOfIsolatedNodes++;
+ }
+ // Number of self-loops calculation
+ int selfloops = 0;
+ for (int j = 0; j < inEdges.length; j++) {
+ Edge e = network.getEdge(inEdges[j]);
+ if (e.getSource() == node) {
+ selfloops++;
+ }
+ }
+ numberOfSelfLoops += selfloops;
+
+ // Multi-edge node pair computation. Currently edge direction is ignored.
+ int partnerOfMultiEdgeNodePairs = 0;
+ for (final MutInteger freq : CyNetworkUtils.getNeighborMap(network, node).values()) {
+ if (freq.value > 1) {
+ partnerOfMultiEdgeNodePairs++;
+ }
+ }
+ multiEdgePartners += partnerOfMultiEdgeNodePairs;
+
+ if (useNodeAttributes) {
+ setAttr(nodeID, "cco", 0.0);
+ setAttr(nodeID, "din", inEdges.length);
+ setAttr(nodeID, "dou", outEdges.length);
+ setAttr(nodeID, "dal", inEdges.length + outEdges.length);
+ setAttr(nodeID, "isn", (neighborCount == 0));
+ setAttr(nodeID, "slo", selfloops);
+ setAttr(nodeID, "pmn", partnerOfMultiEdgeNodePairs);
+ }
+
+ if (neighborCount > 1) {
+
+ // Clustering coefficients calculation
+ // -----------------------------------
+ int[] neighborInd = CyNetworkUtils.getIndices(neighbors);
+ final double nodeCCp = computeCC(neighborInd);
+ accumulate(CCps, neighborCount, nodeCCp);
+ if (useNodeAttributes) {
+ setAttr(nodeID, "cco", Utils.roundTo(nodeCCp, roundingDigits));
+ }
+ } else if (useNodeAttributes) {
+ setAttr(nodeID, "cco", 0.0);
+ }
+
+ // Neighborhood connectivity calculation
+ // -------------------------------------
+ final double nco = averageNeighbors(neighbors, true, true);
+ if (neighborCount > 0) {
+ accumulate(ioNCps, neighborCount, nco);
+ }
+ neighbors = getNeighbors(node, inEdges, new int[0]);
+ neighborCount = neighbors.size();
+ if (neighborCount > 0) {
+ double inNC = averageNeighbors(neighbors, false, true);
+ accumulate(inNCps, neighborCount, inNC);
+ }
+ neighbors = getNeighbors(node, new int[0], outEdges);
+ neighborCount = neighbors.size();
+ if (neighborCount > 0) {
+ outNeighbors += neighborCount;
+ double outNC = averageNeighbors(neighbors, true, false);
+ accumulate(outNCps, neighborCount, outNC);
+ }
+
+ if (useNodeAttributes) {
+ setAttr(nodeID, "nco", nco);
+ }
+
+ if (nodeSet == null) {
+ // Compute shortest path lengths
+ PathLengthData pathLengths = computeSP(node);
+ final int eccentricity = pathLengths.getMaxLength();
+ if (diameter < eccentricity) {
+ diameter = eccentricity;
+ }
+ if (0 < eccentricity && eccentricity < radius) {
+ radius = eccentricity;
+ }
+ final double apl = (pathLengths.getCount() > 0) ? pathLengths
+ .getAverageLength() : 0;
+ aplMap.put(node, Double.valueOf(apl));
+ final double closeness = (apl > 0.0) ? 1 / apl : 0.0;
+ closenessCent.add(new Point2D.Double(neighborCount, closeness));
+
+ if (useNodeAttributes) {
+ setAttr(nodeID, "spl", eccentricity);
+ setAttr(nodeID, "apl", Utils.roundTo(apl, roundingDigits));
+ setAttr(nodeID, "clc", Utils.roundTo(closeness, roundingDigits));
+ }
+
+ // Node and edge betweenness calculation
+ if (computeNB) {
+ computeNBandEB(node);
+ // reset everything except the betweenness value
+ for (Node n : connNodes) {
+ NodeBetweenInfo nodeInfo = nodeBetweenness.get(n);
+ nodeInfo.reset();
+ }
+ }
+ }
+
+ if (cancelled) {
+ analysisFinished();
+ return;
+ }
+ }
+
+ // Normalize and save betweenness and stress
+ if (nodeSet == null && computeNB) {
+ final double nNormFactor = computeNormFactor(nodeBetweenness.size());
+ for (final Node n : connNodes) {
+ String id = n.getIdentifier();
+ final NodeBetweenInfo nbi = nodeBetweenness.get(n);
+ double nb = nbi.getBetweenness() * nNormFactor;
+ final int connectivity = getNeighbors(n).size();
+ if (Double.isNaN(nb)) {
+ nb = 0.0;
+ }
+ nodeBetweennessArray.add(new Point2D.Double(connectivity, nb));
+ final long nodeStress = stress.get(n).longValue();
+ stressDist.addObservation(nodeStress);
+ if (useNodeAttributes) {
+ setAttr(n.getIdentifier(), "nbt", Utils.roundTo(nb, roundingDigits));
+ setAttr(id, "stress", nodeStress);
+ }
+ }
+
+ // Save edge betweenness
+ if (useEdgeAttributes) {
+ for (final Map.Entry<Edge, Double> betEntry : edgeBetweenness.entrySet()) {
+ double eb = betEntry.getValue().doubleValue();
+ if (Double.isNaN(eb)) {
+ eb = 0.0;
+ }
+ setEAttr(betEntry.getKey().getIdentifier(), "ebt",
+ Utils.roundTo(eb, roundingDigits));
+ }
+ }
+ }
+ }
+
+ // Save in and out degree distributions in the statistics instance
+ stats.set("inDegreeDist", inDegreeDist.createHistogram());
+ stats.set("outDegreeDist", outDegreeDist.createHistogram());
+
+ // Save C(k) in the statistics instance
+ if (CCps.size() > 0) {
+ Point2D.Double[] averages = new Point2D.Double[CCps.size()];
+ double cc = accumulateCCs(CCps, averages) / nodeCount;
+ stats.set("cc", cc);
+ if (averages.length > 1) {
+ stats.set("cksDist", new Points2D(averages));
+ }
+ }
+
+ if (nodeSet == null) {
+ long connPairs = 0; // total number of connected pairs of nodes
+ long totalPathLength = 0;
+ for (int i = 1; i <= diameter; ++i) {
+ connPairs += sPathLengths[i];
+ totalPathLength += i * sPathLengths[i];
+ }
+ stats.set("connPairs", connPairs);
+
+ if (diameter > 0) {
+ // Save the diameter and the shortest path lengths distribution
+ stats.set("diameter", diameter);
+ stats.set("radius", radius);
+ stats.set("avSpl", (double) totalPathLength / connPairs);
+ if (diameter > 1) {
+ stats.set("splDist", new LongHistogram(sPathLengths, 1, diameter));
+ }
+ }
+ }
+
+ if (neighborsAccum != null) {
+ stats.set("avNeighbors", neighborsAccum.getAverage());
+ }
+ stats.set("density", (double) (outNeighbors / (nodeCount * (nodeCount - 1))));
+ stats.set("ncc", connectedComponentsCount);
+ stats.set("usn", numberOfIsolatedNodes);
+ stats.set("nsl", numberOfSelfLoops);
+ stats.set("mnp", multiEdgePartners / 2);
+
+ // Save the neighborhood connectivities for incoming edges, outgoing edges and both
+ if (inNCps.size() > 1) {
+ stats.set("inNeighborConn", new Points2D(getAverages(inNCps)));
+ }
+ if (outNCps.size() > 1) {
+ stats.set("outNeighborConn", new Points2D(getAverages(outNCps)));
+ }
+ if (ioNCps.size() > 1) {
+ stats.set("allNeighborConn", new Points2D(getAverages(ioNCps)));
+ }
+
+ // Save closeness centrality in the statistics instance
+ if (closenessCent.size() > 1) {
+ stats.set("closenessCent", new Points2D(closenessCent));
+ }
+
+ // Save node betweenness
+ if (nodeBetweennessArray.size() > 0) {
+ stats.set("nodeBetween", new Points2D(nodeBetweennessArray));
+ }
+
+ // Save stress distribution in the statistics instance
+ if (nodeSet == null && computeNB) {
+ stats.set("stressDist", stressDist.createPoints2D());
+ }
+
+ analysisFinished();
+ time = System.currentTimeMillis() - time;
+ stats.set("time", time / 1000.0);
+ progress = nodeCount;
+ if (useNodeAttributes || useEdgeAttributes) {
+ Cytoscape.firePropertyChange(Cytoscape.ATTRIBUTES_CHANGED, null, null);
+ }
+ }
+
+ /**
+ * Gets all incoming edges of the given node.
+ *
+ * @param aNode
+ * Node, of which incoming edges are to be found.
+ * @return Array of edge indices, containing all the edges in the network that point to
+ * <code>aNode</code> .
+ */
+ private int[] getInEdges(Node aNode) {
+ return network.getAdjacentEdgeIndicesArray(aNode.getRootGraphIndex(), false, true, false);
+ }
+
+ /**
+ * Gets all outgoing edges of the given node.
+ *
+ * @param aNode
+ * Node, of which outgoing edges are to be found.
+ * @return Array of edge indices, containing all the edges in the network that start from
+ * <code>aNode</code>.
+ */
+ private int[] getOutEdges(Node aNode) {
+ return network.getAdjacentEdgeIndicesArray(aNode.getRootGraphIndex(), false, false, true);
+ }
+
+ /**
+ * Gets all the neighbors of the given node.
+ * <p>
+ * Note that the node is never returned as its neighbor.
+ * </p>
+ *
+ * @param aNode
+ * Node, whose neighbors are to be found.
+ * @param aInEdges
+ * Array of all incoming edges of <code>aNode</code>.
+ * @param aOutEdges
+ * Array of all outgoing edges of <code>aNode</code>.
+ * @return <code>Set</code> of <code>Node</code> instances, containing all the neighbors of
+ * <code>aNode</code>; empty set if the node specified is an isolatd vertex.
+ */
+ private Set<Node> getNeighbors(Node aNode, int[] aInEdges, int[] aOutEdges) {
+ Set<Node> neighborSet = new HashSet<Node>();
+ for (final int edgeIndex : aInEdges) {
+ final Node sourceNode = network.getEdge(edgeIndex).getSource();
+ if (sourceNode != aNode) {
+ neighborSet.add(sourceNode);
+ }
+ }
+ for (final int edgeIndex : aOutEdges) {
+ final Node targetNode = network.getEdge(edgeIndex).getTarget();
+ if (targetNode != aNode) {
+ neighborSet.add(targetNode);
+ }
+ }
+ return neighborSet;
+ }
+
+ /**
+ * Gets all neighbors of the given node.
+ *
+ * @param aNode
+ * Node, whose neighbors are to be found.
+ * @return <code>Set</code> of <code>Node</code> instances, containing all the neighbors of
+ * <code>aNode</code>; empty set if the node specified is an isolated vertex.
+ * @see CyNetworkUtils#getNeighbors(CyNetwork, Node, int[])
+ */
+ private Set<Node> getNeighbors(Node aNode) {
+ return getNeighbors(aNode, getInEdges(aNode), getOutEdges(aNode));
+ }
+
+ /**
+ * Gets all out-neighbors of the given node.
+ *
+ * @param aNode
+ * Node, whose out-neighbors are to be found.
+ * @return <code>Set</code> of <code>Node</code> instances, containing all the out-neighbors of
+ * <code>aNode</code>; empty set if the specified node does not have outgoing edges.
+ * @see CyNetworkUtils#getNeighbors(CyNetwork, Node, int[])
+ */
+ private Set<Node> getOutNeighbors(Node aNode) {
+ return CyNetworkUtils.getNeighbors(network, aNode, getOutEdges(aNode));
+ }
+
+ /**
+ * Computes the shortest path lengths from the given node to all other nodes in the network. As
+ * a side effect, this method accumulates values in the field {@link #sPathLengths}.
+ * <p>
+ * This method uses a breadth-first traversal through the network, starting from the specified
+ * node, in order to find all reachable nodes and accumulate their distances to
+ * <code>aNode</code> in {@link #sPathLengths}.
+ * </p>
+ *
+ * @param aNode
+ * Starting node of the shortest paths to be found.
+ * @return Data on the shortest path lengths from the current node to all other reachable nodes
+ * in the network.
+ */
+ private PathLengthData computeSP(Node aNode) {
+ visited.clear();
+ visited.add(aNode);
+ LinkedList<Node> reachedNodes = new LinkedList<Node>();
+ reachedNodes.add(aNode);
+ reachedNodes.add(null); // marks a new level of BFS
+
+ PathLengthData result = new PathLengthData();
+ int spl = 1;
+ for (Node currentNode = reachedNodes.removeFirst(); !reachedNodes.isEmpty(); currentNode = reachedNodes
+ .removeFirst()) {
+ if (currentNode == null) {
+ // Next level of the BFS tree
+ spl++;
+ reachedNodes.add(null);
+ } else {
+ // Traverse next reached node
+ final Set<Node> neighbors = getOutNeighbors(currentNode);
+ for (final Node neighbor : neighbors) {
+ if (visited.add(neighbor)) {
+ sPathLengths[spl]++;
+ result.addSPL(spl);
+ reachedNodes.add(neighbor);
+ }
+ }
+ }
+ }
+ sPathLengths[0]++;
+ return result;
+ }
+
+ /**
+ * Computes the average number of neighbors of the nodes in a given node set.
+ *
+ * @param aNodes
+ * Non-empty set of nodes. Specifying <code>null</code> or an empty set for this
+ * parameter results in throwing an exception.
+ * @param aInEdges
+ * Flag indicating if incoming edges must be considered.
+ * @param aOutEdges
+ * Flag indicating if outgoing edges must be considered.
+ * @return Average number of neighbors of the nodes in <code>aNodes</code>.
+ */
+ private double averageNeighbors(Set<Node> aNodes, boolean aInEdges, boolean aOutEdges) {
+ int neighbors = 0;
+ for (final Node nNode : aNodes) {
+ if (aInEdges) {
+ if (aOutEdges) {
+ neighbors += getNeighbors(nNode, getInEdges(nNode), getOutEdges(nNode)).size();
+ } else {
+ neighbors += getNeighbors(nNode, getInEdges(nNode), new int[0]).size();
+ }
+ } else {
+ neighbors += getNeighbors(nNode, new int[0], getOutEdges(nNode)).size();
+ }
+ }
+ return (double) neighbors / aNodes.size();
+ }
+
+ /**
+ * Computes the clustering coefficient of a node.
+ *
+ * @param aNeighborIndices
+ * Array of the indices of all the neighbors of the node of interest.
+ * @return Clustering coefficient of <code>aNode</code> as a value in the range
+ * <code>[0,1]</code>.
+ */
+ private double computeCC(int[] aNeighborIndices) {
+ int edgeCount = CyNetworkUtils.getPairConnCount(network, aNeighborIndices, false);
+ int neighborsCount = aNeighborIndices.length;
+ return (double) edgeCount / (neighborsCount * (neighborsCount - 1));
+ }
+
+ /**
+ * Accumulates the node and edge betweenness of all nodes in a connected component. The node
+ * betweenness is calculated using the algorithm of Brandes (U. Brandes: A Faster Algorithm for
+ * Betweenness Centrality. Journal of Mathematical Sociology 25(2):163-177, 2001). The edge
+ * betweenness is calculated as used by Newman and Girvan (M.E. Newman and M. Girvan: Finding
+ * and Evaluating Community Structure in Networks. Phys. Rev. E Stat. Nonlin. Soft. Matter
+ * Phys., 69, 026113.). In each run of this method a different source node is chosen and the
+ * betweenness of all nodes is replaced by the new one. For the final result this method has to
+ * be run for all nodes of the connected component.
+ *
+ * This method uses a breadth-first search through the network, starting from a specified source
+ * node, in order to find all paths to the other nodes in the network and to accumulate their
+ * betweenness.
+ *
+ * @param source
+ * Node where a run of breadth-first search is started, in order to accumulate the
+ * node and edge betweenness of all other nodes
+ */
+ private void computeNBandEB(Node source) {
+ LinkedList<Node> done = new LinkedList<Node>();
+ LinkedList<Node> reached = new LinkedList<Node>();
+ HashMap<Edge, Double> edgeDependency = new HashMap<Edge, Double>();
+ HashMap<Node, Long> stressDependency = new HashMap<Node, Long>();
+
+ final NodeBetweenInfo sourceNBInfo = nodeBetweenness.get(source);
+ sourceNBInfo.setSource();
+ reached.add(source);
+ stressDependency.put(source, Long.valueOf(0));
+
+ // Use BFS to find shortest paths from source to all nodes in the network
+ while (!reached.isEmpty()) {
+ final Node current = reached.removeFirst();
+ done.addFirst(current);
+ final NodeBetweenInfo currentNBInfo = nodeBetweenness.get(current);
+ final Set<Node> neighbors = getOutNeighbors(current);
+ for (Node neighbor : neighbors) {
+ final NodeBetweenInfo neighborNBInfo = nodeBetweenness.get(neighbor);
+ final List<Edge> edges = CyNetworkUtils.getConnEdge(network, current, neighbor);
+ final int expectSPLength = currentNBInfo.getSPLength() + 1;
+
+ if (neighborNBInfo.getSPLength() < 0) {
+ // Neighbor traversed for the first time
+ reached.add(neighbor);
+ neighborNBInfo.setSPLength(expectSPLength);
+ stressDependency.put(neighbor, Long.valueOf(0));
+ }
+ if (neighborNBInfo.getSPLength() == expectSPLength) {
+ // shortest path from current to neighbor found
+ neighborNBInfo.addSPCount(currentNBInfo.getSPCount());
+ neighborNBInfo.addPredecessor(current);
+ for (final Edge edge : edges) {
+ currentNBInfo.addOutedge(edge);
+ }
+ // check for long overflow
+ if (neighborNBInfo.getSPCount() < 0) {
+ computeNB = false;
+ }
+ }
+ for (final Edge edge : edges) {
+ if (!edgeDependency.containsKey(edge)) {
+ edgeDependency.put(edge, new Double(0.0));
+ }
+ }
+ }
+ }
+
+ // Return nodes in order of non-increasing distance from source
+ while (!done.isEmpty()) {
+ final Node current = done.removeFirst();
+ final NodeBetweenInfo currentNBInfo = nodeBetweenness.get(current);
+ if (currentNBInfo != null) {
+ final long currentStress = stressDependency.get(current).longValue();
+ while (!currentNBInfo.isEmptyPredecessors()) {
+ final Node predecessor = currentNBInfo.pullPredecessor();
+ final NodeBetweenInfo predecessorNBInfo = nodeBetweenness.get(predecessor);
+ predecessorNBInfo.addDependency((1.0 + currentNBInfo.getDependency())
+ * ((double) predecessorNBInfo.getSPCount() / (double) currentNBInfo
+ .getSPCount()));
+ // accumulate all sp count
+ final long oldStress = stressDependency.get(predecessor).longValue();
+ stressDependency.put(predecessor, new Long(oldStress + 1 + currentStress));
+ // accumulate edge betweenness
+ final List<Edge> edges = CyNetworkUtils.getConnEdge(network, predecessor, current);
+ if (edges.size() != 0) {
+ final Edge compEdge = edges.get(0);
+ final LinkedList<Edge> currentedges = currentNBInfo.getOutEdges();
+ double oldbetweenness = 0.0;
+ double newbetweenness = 0.0;
+ for (final Edge edge : edges) {
+ if (edgeBetweenness.containsKey(edge)) {
+ oldbetweenness = edgeBetweenness.get(edge).doubleValue();
+ break;
+ }
+ }
+ // if the node is a leaf node in this search tree
+ if (currentedges.size() == 0) {
+ newbetweenness = (double) predecessorNBInfo.getSPCount()
+ / (double) currentNBInfo.getSPCount();
+ } else {
+ double neighbourbetw = 0.0;
+ for (Edge neighbouredge : currentedges) {
+ if (!edges.contains(neighbouredge)) {
+ neighbourbetw += edgeDependency.get(neighbouredge)
+ .doubleValue();
+ }
+ }
+ newbetweenness = (1 + neighbourbetw)
+ * ((double) predecessorNBInfo.getSPCount() / (double) currentNBInfo
+ .getSPCount());
+ }
+ edgeDependency.put(compEdge, new Double(newbetweenness));
+ for (final Edge edge : edges) {
+ edgeBetweenness.put(edge, new Double(newbetweenness + oldbetweenness));
+ }
+ }
+ }
+ // accumulate betweenness in each run
+ if (!current.equals(source)) {
+ currentNBInfo.addBetweenness(currentNBInfo.getDependency());
+ // accumulate number of shortest paths
+ final long allSpPaths = stress.get(current).longValue();
+ stress.put(current, new Long(allSpPaths + currentNBInfo.getSPCount()
+ * currentStress));
+ }
+ }
+ }
+ }
+
+ /**
+ * Computes a normalization factor for node betweenness normalization.
+ *
+ * @param count
+ * Number of nodes for which betweenness has been computed.
+ * @return Normalization factor for node betweenness normalization.
+ */
+ protected double computeNormFactor(int count) {
+ return (count > 2) ? (1.0 / ((count - 1) * (count - 2))) : 1.0;
+ }
+
+ /**
+ * Stores the diameter of the network.
+ * <p>
+ * The greatest known diameter is constantly updated in {@link #computeAll()}.
+ * </p>
+ */
+ private int diameter;
+
+ /**
+ * Stores the radius of the network.
+ * <p>
+ * The value of the radius is computed in {@link #computeAll()}.
+ * </p>
+ */
+ private int radius;
+
+ /**
+ * Histogram of shortest path lengths.
+ * <p>
+ * <code>sPathLength[0]</code> stores the number of nodes processed so far.<br/>
+ * <code>sPathLength[i]</code> for <code>i > 0</code> stores the number of shortest paths of
+ * length <code>i</code> found so far.
+ * </p>
+ */
+ private long[] sPathLengths;
+
+ /**
+ * Set of visited nodes.
+ * <p>
+ * This set is used exclusively by the method {@link #computeSP(Node)}.
+ * </p>
+ */
+ private final Set<Node> visited;
+
+ /**
+ * Integer of how many nodes are in the network.
+ * <p>
+ * This is used by all histograms as range.
+ * </p>
+ */
+ private int nodeCount;
+
+ /**
+ * Flag, if we want to compute and store node attributes.
+ */
+ private boolean useNodeAttributes;
+
+ /**
+ * Flag, if we want to compute and store edge attributes.
+ */
+ private boolean useEdgeAttributes;
+
+ /**
+ * Round doubles in attributes to <code>roundingDigits</code> decimals after the point.
+ */
+ private int roundingDigits;
+
+ /**
+ * Number of nodes that are not connected to any other nodes.
+ */
+ private int numberOfIsolatedNodes;
+
+ /**
+ * Total number of self-loops in the network (edges that connect a node with itself).
+ */
+ private int numberOfSelfLoops;
+
+ /**
+ * Overall number of partners of multi-edged node pairs. A partner is one member of such a pair.
+ * <code>multiEdgePartners / 2</code> is the number of multi-edged node pairs.
+ */
+ private int multiEdgePartners;
+
+ /**
+ * Flag indicating if node(edge) betweenness and stress should be computed. It is set to false if the
+ * number of shortest paths exceeds the maximum long value.
+ */
+ private boolean computeNB;
+
+ /**
+ * Map of all nodes with their respective node betweenness information, which stores information
+ * needed for the node betweenness calculation
+ */
+ private Map<Node, NodeBetweenInfo> nodeBetweenness;
+
+ /**
+ * Map of all nodes with their respective edge betweenness
+ */
+ private Map<Edge, Double> edgeBetweenness;
+
+ /**
+ * Map of all nodes with their respective stress, i.e. number of shortest paths passing through
+ * a node.
+ */
+ private Map<Node, Long> stress;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/GOPTAlgorithm.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/GOPTAlgorithm.java
new file mode 100644
index 0000000..2bd2cdb
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/GOPTAlgorithm.java
@@ -0,0 +1,170 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer;
+
+import giny.model.Edge;
+import giny.model.Node;
+
+import java.util.Iterator;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+
+/**
+ * Controller class providing algorithms for intersection, union and difference of two networks.
+ *
+ * @author Caroline Becker
+ * @author Yassen Assenov
+ * @version 1.0
+ */
+public class GOPTAlgorithm {
+
+ /**
+ * Initializes a new instance of <code>GOPTAlgorithm</code>.
+ *
+ * @param aNetwork1 First network.
+ * @param aNetwork2 Second network.
+ * @throws NullPointerException If <code>aNetwork1</code> or <code>aNetwork2</code> is
+ * <code>null</code>.
+ */
+ public GOPTAlgorithm(CyNetwork aNetwork1, CyNetwork aNetwork2) {
+ if (aNetwork1 == null || aNetwork2 == null) {
+ throw new NullPointerException();
+ }
+ network1 = aNetwork1;
+ network2 = aNetwork2;
+ }
+
+ /**
+ * Computes the requested operations of the networks this instance was initialized with.
+ *
+ * @param aIntersection Flag indicating if the intersection of the two networks must be computed.
+ * @param aUnion Flag indicating if the union of the two networks must be computed.
+ * @param aDifference Flag indicating if the differences of the two networks must be computed.
+ */
+ public void computeNetworks(boolean aIntersection, boolean aUnion, boolean aDifference) {
+ if (aIntersection || aUnion || aDifference) {
+ // Create the required (empty) networks
+ final String title1 = network1.getTitle();
+ final String title2 = network2.getTitle();
+ if (aIntersection) {
+ intersectionNw = Cytoscape.createNetwork(title1 + " AND " + title2);
+ }
+ if (aUnion) {
+ unionNw = Cytoscape.createNetwork(title1 + " OR " + title2);
+ }
+ if (aDifference) {
+ diffNw1 = Cytoscape.createNetwork(title1 + " - " + title2);
+ diffNw2 = Cytoscape.createNetwork(title2 + " - " + title1);
+ }
+
+ // Iterate over the nodes of the two networks
+ // TODO: [Cytoscape 2.8] Check if the returned iterator is parameterized
+ Iterator<?> nodeIt = network1.nodesIterator();
+ Node actNode;
+ while (nodeIt.hasNext()) {
+ actNode = (Node) nodeIt.next();
+ if (network2.containsNode(actNode)) {
+ if (aIntersection) {
+ intersectionNw.addNode(actNode);
+ }
+ } else {
+ if (aUnion) {
+ unionNw.addNode(actNode);
+ }
+ if (aDifference) {
+ diffNw1.addNode(actNode);
+ }
+ }
+ }
+ nodeIt = network2.nodesIterator();
+ while (nodeIt.hasNext()) {
+ actNode = (Node) nodeIt.next();
+ if (aUnion) {
+ unionNw.addNode(actNode);
+ }
+ if (aDifference && (! network1.containsNode(actNode))) {
+ diffNw2.addNode(actNode);
+ }
+ }
+
+ // Iterate over the edges of the two networks
+ // TODO: [Cytoscape 2.8] Check if the returned iterator is parameterized
+ Iterator<?> edgeIt = network1.edgesIterator();
+ Edge actEdge;
+ while (edgeIt.hasNext()) {
+ actEdge = (Edge) edgeIt.next();
+ if (network2.containsEdge(actEdge)) {
+ if (aIntersection) {
+ intersectionNw.addEdge(actEdge);
+ }
+ } else {
+ if (aUnion) {
+ unionNw.addEdge(actEdge);
+ }
+ if (aDifference && diffNw1.containsNode(actEdge.getSource())
+ && diffNw1.containsNode(actEdge.getTarget())) {
+ diffNw1.addEdge(actEdge);
+ }
+ }
+ }
+ edgeIt = network2.edgesIterator();
+ while (edgeIt.hasNext()) {
+ actEdge = (Edge) edgeIt.next();
+ if (aUnion) {
+ unionNw.addEdge(actEdge);
+ }
+ if (aDifference && ( !network1.containsEdge(actEdge))
+ && diffNw2.containsNode(actEdge.getSource())
+ && diffNw2.containsNode(actEdge.getTarget())) {
+ diffNw2.addEdge(actEdge);
+ }
+ }
+ }
+ }
+
+ /**
+ * First of the two manipulated networks.
+ */
+ private CyNetwork network1;
+
+ /**
+ * Second manipulated network.
+ */
+ private CyNetwork network2;
+
+ /**
+ * Network obtained by intersecting {@link #network1} and {@link #network2}.
+ */
+ private CyNetwork intersectionNw;
+
+ /**
+ * Network obtained by the union of {@link #network1} and {@link #network2}.
+ */
+ private CyNetwork unionNw;
+
+ /**
+ * Network obtained the difference {@link #network1} <code>\</code> {@link #network2}.
+ */
+ private CyNetwork diffNw1;
+
+ /**
+ * Network obtained the difference {@link #network2} <code>\</code> {@link #network1}.
+ */
+ private CyNetwork diffNw2;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/InnerException.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/InnerException.java
new file mode 100644
index 0000000..7f355d0
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/InnerException.java
@@ -0,0 +1,40 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer;
+
+/**
+ * Exception raised to indicate plugin's internal error, i.e. a bug.
+ *
+ * @author Yassen Assenov
+ */
+public class InnerException extends RuntimeException {
+
+ /**
+ * Initializes a new instance of <code>InnerException</code>.
+ *
+ * @param cause Exception that was unexpectedly raised.
+ */
+ public InnerException(Throwable cause) {
+ super(cause);
+ }
+
+ /**
+ * Unique ID for this version of this class. It is used in serialization.
+ */
+ private static final long serialVersionUID = -2600004852243398033L;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/LoadNetstatsAction.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/LoadNetstatsAction.java
new file mode 100644
index 0000000..f817d17
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/LoadNetstatsAction.java
@@ -0,0 +1,102 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer;
+
+import java.awt.event.ActionEvent;
+import java.io.File;
+import java.io.IOException;
+
+import javax.swing.JFileChooser;
+
+import cytoscape.Cytoscape;
+import cytoscape.logger.CyLogger;
+import cytoscape.util.CytoscapeAction;
+import cytoscape.view.CytoscapeDesktop;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Messages;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.NetworkStats;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.io.StatsSerializer;
+import de.mpg.mpi_inf.bioinf.netanalyzer.ui.AnalysisDialog;
+import de.mpg.mpi_inf.bioinf.netanalyzer.ui.Utils;
+
+/**
+ * Action handler for the menu item "Load Network Statistics".
+ *
+ * @author Yassen Assenov
+ */
+public class LoadNetstatsAction extends CytoscapeAction {
+
+ /**
+ * Initializes a new instance of <code>LoadNetstatsAction</code>.
+ */
+ public LoadNetstatsAction() {
+ super(Messages.AC_LOAD);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.event.ActionListener#actionPerformed(java.awt.event.ActionEvent)
+ */
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ try {
+ final CytoscapeDesktop desktop = Cytoscape.getDesktop();
+ final JFileChooser dialog = AnalysisDialog.netstatsDialog;
+ final int openIt = dialog.showOpenDialog(desktop);
+ if (openIt == JFileChooser.APPROVE_OPTION) {
+ openNetstats(dialog.getSelectedFile());
+ Utils.removeSelectedFile(dialog);
+ }
+ if (openIt == JFileChooser.ERROR_OPTION) {
+ Utils.showErrorBox(desktop, Messages.DT_GUIERROR, Messages.SM_GUIERROR);
+ }
+ } catch (InnerException ex) {
+ // NetworkAnalyzer internal error
+ CyLogger.getLogger().error(Messages.SM_LOGERROR, ex);
+ }
+ }
+
+ /**
+ * Opens the given network statistics file and visualizes its contents in an analysis dialog.
+ * <p>
+ * In case the file could not be opened, or if it contains invalid data, an informative error box is
+ * displayed.
+ * </p>
+ *
+ * @param aFile
+ * Network statistics file to be open.
+ */
+ public static void openNetstats(File aFile) {
+ final CytoscapeDesktop desktop = Cytoscape.getDesktop();
+ try {
+ final NetworkStats stats = StatsSerializer.load(aFile);
+ final AnalysisDialog d = new AnalysisDialog(desktop, stats, null);
+ d.setVisible(true);
+ } catch (IOException ex) {
+ // FileNotFoundException, IOException
+ Utils.showErrorBox(desktop, Messages.DT_IOERROR, Messages.SM_IERROR);
+ } catch (NullPointerException ex) {
+ Utils.showErrorBox(desktop, Messages.DT_WRONGDATA, Messages.SM_WRONGDATAFILE);
+ }
+ }
+
+ /**
+ * Unique ID for this version of this class. It is used in serialization.
+ */
+ private static final long serialVersionUID = 5924903386374164549L;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/MapParameterAction.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/MapParameterAction.java
new file mode 100644
index 0000000..4aa903f
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/MapParameterAction.java
@@ -0,0 +1,145 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer;
+
+import java.awt.event.ActionEvent;
+
+import javax.swing.JOptionPane;
+
+import cytoscape.Cytoscape;
+import cytoscape.logger.CyLogger;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Messages;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.io.SettingsSerializer;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.settings.PluginSettings;
+import de.mpg.mpi_inf.bioinf.netanalyzer.ui.MapParameterDialog;
+
+/**
+ * Action handler for the menu item "Visualize Parameters".
+ *
+ * @author Nadezhda Doncheva
+ * @author Yassen Assenov
+ */
+public class MapParameterAction extends NetAnalyzerAction implements AnalysisListener {
+
+ /**
+ * Initializes a new instance of <code>MapParameterAction</code>.
+ */
+ public MapParameterAction() {
+ super(Messages.AC_MAPPARAM);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see cytoscape.util.CytoscapeAction#actionPerformed(java.awt.event.ActionEvent)
+ */
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ try {
+ // Verify there is a network loaded in Cytoscape and selected
+ if (!selectNetwork()) {
+ return;
+ }
+ // Display a dialog for mapping the computed attributes to the network
+ // only if NetworkAnalyzer has computed any parameters and
+ // and theses are stored in the node/edge attributes
+ nodeAttr = CyNetworkUtils.getComputedNodeAttributes(network);
+ edgeAttr = CyNetworkUtils.getComputedEdgeAttributes(network);
+ final PluginSettings settings = SettingsSerializer.getPluginSettings();
+ if ((nodeAttr[0].length > 0) || (nodeAttr[1].length > 0) || (edgeAttr[0].length > 0)
+ || (edgeAttr[1].length > 0)) {
+ openMapParameterDialog();
+ } else if (!settings.getUseNodeAttributes() && !settings.getUseEdgeAttributes()) {
+ // Network does not contain computed parameters stored as attributes
+ if (JOptionPane.showConfirmDialog(Cytoscape.getDesktop(), Messages.SM_LOADPARAMETERS,
+ Messages.DT_ANALYSISNEEDED, JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION) {
+ settings.setUseNodeAttributes(true);
+ settings.setUseEdgeAttributes(true);
+ runNetworkAnalyzer();
+ }
+ } else {
+ // Network does not contain computed parameters stored as attributes
+ if (JOptionPane.showConfirmDialog(Cytoscape.getDesktop(), Messages.SM_RUNNETWORKANALYZER,
+ Messages.DT_ANALYSISNEEDED, JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION) {
+ runNetworkAnalyzer();
+ }
+ }
+ } catch (InnerException ex) {
+ // NetworkAnalyzer internal error
+ CyLogger.getLogger().error(Messages.SM_LOGERROR, ex);
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see de.mpg.mpi_inf.bioinf.netanalyzer.AnalysisListener#analysisCancelled()
+ */
+ public void analysisCancelled() {
+ // No specific action is required
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see de.mpg.mpi_inf.bioinf.netanalyzer.AnalysisListener#analysisCompleted(de.mpg.mpi_inf.bioinf
+ * .netanalyzer.NetworkAnalyzer)
+ */
+ public void analysisCompleted(NetworkAnalyzer analyzer) {
+ openMapParameterDialog();
+ }
+
+ /**
+ * Runs the NetworkAnalyzer analysis on all nodes so that the network parameters are computed and can be
+ * mapped to visual styles afterwards.
+ */
+ private void runNetworkAnalyzer() {
+ final AnalysisExecutor exec = AnalyzeNetworkAction.initAnalysisExecuter(network, null);
+ if (exec != null) {
+ exec.setShowDialog(false);
+ exec.addAnalysisListener(this);
+ exec.start();
+ }
+ }
+
+ /**
+ * Opens the "Map Parameters" dialog.
+ */
+ private void openMapParameterDialog() {
+ nodeAttr = CyNetworkUtils.getComputedNodeAttributes(network);
+ edgeAttr = CyNetworkUtils.getComputedEdgeAttributes(network);
+ final MapParameterDialog d = new MapParameterDialog(Cytoscape.getDesktop(), network, nodeAttr,
+ edgeAttr);
+ d.setVisible(true);
+ }
+
+ /**
+ * Unique ID for this version of this class. It is used in serialization.
+ */
+ private static final long serialVersionUID = -1321805300911486774L;
+
+ /**
+ * Array with node attributes to be mapped to visual styles.
+ */
+ private String[][] nodeAttr;
+
+ /**
+ * Array with edge attributes to be mapped to visual styles.
+ */
+ private String[][] edgeAttr;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/NetAnalyzerAction.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/NetAnalyzerAction.java
new file mode 100644
index 0000000..31c5ed5
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/NetAnalyzerAction.java
@@ -0,0 +1,105 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer;
+
+import java.util.List;
+import java.util.Set;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import cytoscape.util.CytoscapeAction;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Messages;
+import de.mpg.mpi_inf.bioinf.netanalyzer.ui.Utils;
+
+/**
+ * Base class for all NetworkAnalyzer actions which operate on a single network.
+ *
+ * @author Yassen Assenov
+ */
+public abstract class NetAnalyzerAction extends CytoscapeAction {
+
+ /**
+ * Constructs an action with the given name.
+ *
+ * @param aName
+ * Name of the action as it will appear in a menu.
+ */
+ protected NetAnalyzerAction(String aName) {
+ super(aName);
+ network = null;
+ }
+
+ /**
+ * Finds the network of interest to the user.
+ * <p>
+ * In case a network has been identified, the value of the field {@link #network} is updated, otherwise
+ * the value of <code>network</code> is set to the empty network or <code>null</code>. There are
+ * three possible reasons for the inability to choose a network - (1) no network is loaded; (2) there are
+ * two or more networks loaded and none selected; and (3) there is more than one network selected. For
+ * each of the two cases above, the method displays an appropriate message dialog before exiting and
+ * returning <code>false</code>.
+ * </p>
+ *
+ * @return <code>true</code> if a network targeting analysis has been identified, <code>false</code>
+ * otherwise.
+ */
+ @SuppressWarnings("fallthrough")
+ protected boolean selectNetwork() {
+ network = null;
+ String error = null;
+ final Set<CyNetwork> networksSet = Cytoscape.getNetworkSet();
+ switch (networksSet.size()) {
+ case 0: // no network is loaded
+ error = Messages.SM_LOADNET;
+ break;
+ case 1: // single network is available
+ network = networksSet.iterator().next();
+ break;
+ default:
+ final List<CyNetwork> networks = Cytoscape.getSelectedNetworks();
+ switch (networks.size()) {
+ case 1:
+ network = networks.get(0);
+ if (network != null && network != Cytoscape.getNullNetwork()) {
+ // single network is selected
+ break;
+ }
+ case 0: // no network is selected
+ error = Messages.SM_SELECTNET;
+ break;
+ default: // multiple networks are selected
+ error = Messages.SM_SELECTONENET;
+ }
+ }
+ if (error != null) {
+ Utils.showErrorBox(Messages.DT_WRONGDATA, error);
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ * Target network for the action.
+ */
+ protected CyNetwork network;
+
+ /**
+ * Unique ID for this version of this class. It is used in serialization.
+ */
+ private static final long serialVersionUID = -6263068520728141892L;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/NetworkAnalyzer.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/NetworkAnalyzer.java
new file mode 100644
index 0000000..b3b65a6
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/NetworkAnalyzer.java
@@ -0,0 +1,452 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer;
+
+import giny.model.Edge;
+import giny.model.Node;
+
+import java.awt.geom.Point2D;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.Map;
+import java.util.Set;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import cytoscape.data.CyAttributes;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Messages;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.NetworkInterpretation;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.NetworkStats;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.SumCountPair;
+
+/**
+ * Base class for all control classes that perform analysis on a specific network type.
+ *
+ * @author Yassen Assenov
+ * @author Nadezhda Doncheva
+ */
+public abstract class NetworkAnalyzer {
+
+ /**
+ * Gets the title of the network being analyzed.
+ *
+ * @return Title of the network as a <code>String</code> instance; <code>null</code> if the network does
+ * not have a title.
+ */
+ public String getNetworkTitle() {
+ return stats.getTitle();
+ }
+
+ /**
+ * Gets the statistics of the analyzed network.
+ * <p>
+ * This method should be called only after the call to {@link #computeAll()}. Otherwise the
+ * <code>NetworkStats</code> instance returned will not be populated with data.
+ * </p>
+ *
+ * @return Computed statistics of the analyzed network, wrapped as a <code>NetworkStats</code> instance.
+ */
+ public NetworkStats getStats() {
+ return stats;
+ }
+
+ /**
+ * Gets the current progress of the analyzer as a number of steps.
+ *
+ * @return Number of steps completed in the analysis process.
+ */
+ public int getCurrentProgress() {
+ return progress;
+ }
+
+ /**
+ * Gets the maximum progress of the analyzer as a number of steps.
+ *
+ * @return Total number of steps required for the analyzer to finish.
+ */
+ public int getMaxProgress() {
+ return stats.getInt("nodeCount") + 1;
+ }
+
+ /**
+ * Computes all the network parameters.
+ */
+ public abstract void computeAll();
+
+ /**
+ * Cancels the process of network analysis.
+ * <p>
+ * Note that this method does not force the analyzer to cancel immediately; it takes an unspecified period
+ * of time until the analysis thread actually stops.
+ * </p>
+ */
+ public void cancel() {
+ cancelled = true;
+ }
+
+ /**
+ * Checks if this analyzer performs analysis on the whole network.
+ *
+ * @return <code>true</code> if this analyzed calculates topological parameters for all nodes in the
+ * targeted network; <code>false</code> if topological parameters are calculated for a subset of
+ * nodes only.
+ */
+ public boolean isGlobal() {
+ return nodeSet == null;
+ }
+
+ /**
+ * Initializes the fields of this class.
+ *
+ * @param aNetwork
+ * Network to be analyzed.
+ * @param aNodeSet
+ * Subset of nodes in <code>aNetwork</code>, for which topological parameters are to be
+ * calculated. Set this to <code>null</code> if parameters must be calculated for all nodes in
+ * the network.
+ * @param aInterpr
+ * Interpretation of network's edges.
+ * @see #network
+ * @see #interpr
+ * @see #stats
+ */
+ protected NetworkAnalyzer(CyNetwork aNetwork, Set<Node> aNodeSet, NetworkInterpretation aInterpr) {
+ network = aNetwork;
+ nodeSet = aNodeSet;
+ interpr = aInterpr;
+ stats = new NetworkStats(aNetwork, aInterpr.getInterpretSuffix());
+ nodeAttributes = Cytoscape.getNodeAttributes();
+ edgeAttributes = Cytoscape.getEdgeAttributes();
+ progress = 0;
+ }
+
+ /**
+ * Prepares the network, if necessary, before the analysis starts.
+ * <p>
+ * If stored in the interpretation, this method removes all undirected self-loops from the network.
+ * </p>
+ */
+ protected void analysisStarting() {
+ if (interpr.isIgnoreUSL()) {
+ removedEdges = new HashSet<Edge>();
+ // TODO: [Cytoscape 2.8] Check if the returned iterator is parameterized
+ Iterator<?> edgesIter = network.edgesIterator();
+ while (edgesIter.hasNext()) {
+ Edge edge = (Edge) edgesIter.next();
+ if (!edge.isDirected()) {
+ int ei = edge.getRootGraphIndex();
+ if (network.getEdgeSourceIndex(ei) == network.getEdgeTargetIndex(ei)) {
+ network.removeEdge(ei, false);
+ removedEdges.add(edge);
+ }
+ }
+ }
+ // Update edge count
+ stats.set("edgeCount", new Integer(network.getEdgeCount()));
+ }
+ }
+
+ /**
+ * Returns the network to initial state, if necessary, after the analysis has finished.
+ * <p>
+ * If previously removed, this method puts back all undirected self-loops in the network.
+ * </p>
+ */
+ protected void analysisFinished() {
+ if (interpr.isIgnoreUSL()) {
+ for (final Edge e : removedEdges) {
+ network.addEdge(e);
+ }
+ }
+ }
+
+ /**
+ * Adds a value in a mapping of integers and <code>SummCountPair</code>s.
+ * <p>
+ * This method accumulates the given value to the sequence statistics (<code>SummCountPair</code>
+ * instance) mapped to the specified key. If the mapping does not contain such a key, a new (key, value)
+ * pair is created, where the value is a new <code>SummCountPair</code> instance with the given value
+ * added.
+ * </p>
+ *
+ * @param aMapping
+ * Mapping between integers and sequence statistics.
+ * @param aKey
+ * Key to which the value is to ba added.
+ * @param aValue
+ * Value to be added.
+ */
+ protected void accumulate(Map<Integer, SumCountPair> aMapping, int aKey, double aValue) {
+ accumulate(aMapping, new Integer(aKey), aValue);
+ }
+
+ /**
+ * Adds a value in a mapping of integers and <code>SummCountPair</code>s.
+ * <p>
+ * This method accumulates the given value to the sequence statistics (<code>SummCountPair</code>
+ * instance) mapped to the specified key. If the mapping does not contain such a key, a new (key, value)
+ * pair is created, where the value is a new <code>SummCountPair</code> instance with the given value
+ * added.
+ * </p>
+ *
+ * @param aMapping
+ * Mapping between integers and sequence statistics.
+ * @param aKey
+ * Key to which the value is to ba added.
+ * @param aValue
+ * Value to be added.
+ */
+ protected void accumulate(Map<Integer, SumCountPair> aMapping, Integer aKey, double aValue) {
+ final SumCountPair sequenceStat = aMapping.get(aKey);
+ if (sequenceStat != null) {
+ sequenceStat.add(aValue);
+ } else {
+ aMapping.put(aKey, new SumCountPair(aValue));
+ }
+ }
+
+ /**
+ * Fills the values for the average clustering coefficients given their sums.
+ *
+ * @param aCCps
+ * Map of clustering coefficients. The keys of the map must be node connectivities, and the
+ * values - their sums, encapsulated in <code>SumCountPair</code> instances.
+ * @param aAverages
+ * Array of points to be filled with the average clustering coefficient for every connectivity.
+ * @return Sum of all clustering coefficients in the given hashmap.
+ *
+ * @throws ArrayIndexOutOfBoundsException
+ * If the size of the <code>aAverages</code> array is less than the number of entries in
+ * <code>aCCps</code>.
+ * @throws NullPointerException
+ * If <code>aCCps</code> is <code>null</code>; or if <code>aCCps</code> is non-empty and
+ * <code>aAverages</code> is <code>null</code>.
+ */
+ protected double accumulateCCs(Map<Integer, SumCountPair> aCCps, Point2D.Double[] aAverages) {
+ double total = 0;
+ Set<Integer> neighborCounts = aCCps.keySet();
+ int i = 0;
+ for (Integer nc : neighborCounts) {
+ SumCountPair coefs = aCCps.get(nc);
+ total += coefs.getSum();
+ aAverages[i++] = new Point2D.Double(nc.doubleValue(), coefs.getAverage());
+ }
+ return total;
+ }
+
+ /**
+ * Gets the averages of the accumulated values and stores them in a set.
+ * <p>
+ * This method is used for computing the average neighborhood connectivity. In this case, the keys of the
+ * map are node connectivities and the values - the accumulated connectivities of the neighbors of a node
+ * with k links.
+ * </p>
+ *
+ * @param pAccumulatedValues
+ * Mapping of integers and accumulated values.
+ * @return Set of points that stores the averages of the accumulated values in the mapping. The
+ * <code>x</code> coordinate of each point is a key in the mapping and the <code>y</code>
+ * coordinate - the average of the accumulated numbers in the corresponding value of the map.
+ */
+ protected static Set<Point2D.Double> getAverages(Map<Integer, SumCountPair> pAccumulatedValues) {
+ Set<Point2D.Double> averages = new HashSet<Point2D.Double>(pAccumulatedValues.size());
+ for (Integer x : pAccumulatedValues.keySet()) {
+ final double y = pAccumulatedValues.get(x).getAverage();
+ averages.add(new Point2D.Double(x.doubleValue(), y));
+ }
+ return averages;
+ }
+
+ /**
+ * Sets the boolean value of the given node attribute.
+ *
+ * @param aNodeID
+ * ID of node to have its attribute set.
+ * @param aAttributeID
+ * ID of attribute name. The attribute name itself is obtained by calling
+ * {@link Messages#getAttr(String)}.
+ * @param aValue
+ * Value of the attribute.
+ */
+ protected void setAttr(String aNodeID, String aAttributeID, boolean aValue) {
+ nodeAttributes.setAttribute(aNodeID, Messages.getAttr(aAttributeID), new Boolean(aValue));
+ }
+
+ /**
+ * Sets the floating-point value of the given node attribute.
+ *
+ * @param aNodeID
+ * ID of node to have its attribute set.
+ * @param aAttributeID
+ * ID of attribute name. The attribute name itself is obtained by calling
+ * {@link Messages#getAttr(String)}.
+ * @param aValue
+ * Value of the attribute.
+ */
+ protected void setAttr(String aNodeID, String aAttributeID, double aValue) {
+ nodeAttributes.setAttribute(aNodeID, Messages.getAttr(aAttributeID), new Double(aValue));
+ }
+
+ /**
+ * Sets the floating-point (<code>Double</code>) value of the given node attribute.
+ *
+ * @param aNodeID
+ * ID of node to have its attribute set.
+ * @param aAttributeID
+ * ID of attribute name. The attribute name itself is obtained by calling
+ * {@link Messages#getAttr(String)}.
+ * @param aValue
+ * Value of the attribute.
+ */
+ protected void setAttr(String aNodeID, String aAttributeID, Double aValue) {
+ nodeAttributes.setAttribute(aNodeID, Messages.getAttr(aAttributeID), aValue);
+ }
+
+ /**
+ * Sets the integer value of the given node attribute.
+ *
+ * @param aNodeID
+ * ID of node to have its attribute set.
+ * @param aAttributeID
+ * ID of attribute name. The attribute name itself is obtained by calling
+ * {@link Messages#getAttr(String)}.
+ * @param aValue
+ * Value of the attribute.
+ */
+ protected void setAttr(String aNodeID, String aAttributeID, int aValue) {
+ nodeAttributes.setAttribute(aNodeID, Messages.getAttr(aAttributeID), new Integer(aValue));
+ }
+
+ /**
+ * Sets the boolean value of the given edge attribute.
+ *
+ * @param anEdgeID
+ * ID of edge to have its attribute set.
+ * @param aAttributeID
+ * ID of attribute name. The attribute name itself is obtained by calling
+ * {@link Messages#getAttr(String)}.
+ * @param aValue
+ * Value of the attribute.
+ */
+ protected void setEAttr(String anEdgeID, String aAttributeID, boolean aValue) {
+ edgeAttributes.setAttribute(anEdgeID, Messages.getAttr(aAttributeID), new Boolean(aValue));
+ }
+
+ /**
+ * Sets the floating-point value of the given edge attribute.
+ *
+ * @param anEdgeID
+ * ID of edge to have its attribute set.
+ * @param aAttributeID
+ * ID of attribute name. The attribute name itself is obtained by calling
+ * {@link Messages#getAttr(String)}.
+ * @param aValue
+ * Value of the attribute.
+ */
+ protected void setEAttr(String anEdgeID, String aAttributeID, double aValue) {
+ edgeAttributes.setAttribute(anEdgeID, Messages.getAttr(aAttributeID), new Double(aValue));
+ }
+
+ /**
+ * Sets the floating-point (<code>Double</code>) value of the given edge attribute.
+ *
+ * @param anEdgeID
+ * ID of edge to have its attribute set.
+ * @param aAttributeID
+ * ID of attribute name. The attribute name itself is obtained by calling
+ * {@link Messages#getAttr(String)}.
+ * @param aValue
+ * Value of the attribute.
+ */
+ protected void setEAttr(String anEdgeID, String aAttributeID, Double aValue) {
+ edgeAttributes.setAttribute(anEdgeID, Messages.getAttr(aAttributeID), aValue);
+ }
+
+ /**
+ * Sets the integer value of the given edge attribute.
+ *
+ * @param anEdgeID
+ * ID of edge to have its attribute set.
+ * @param aAttributeID
+ * ID of attribute name. The attribute name itself is obtained by calling
+ * {@link Messages#getAttr(String)}.
+ * @param aValue
+ * Value of the attribute.
+ */
+ protected void setEAttr(String anEdgeID, String aAttributeID, int aValue) {
+ edgeAttributes.setAttribute(anEdgeID, Messages.getAttr(aAttributeID), new Integer(aValue));
+ }
+
+ /**
+ * Target network for analysis.
+ */
+ protected CyNetwork network;
+
+ /**
+ * Subset of nodes to be analyzed.
+ */
+ protected Set<Node> nodeSet;
+
+ /**
+ * Interpretation of edges in {@link #network}.
+ */
+ protected NetworkInterpretation interpr;
+
+ /**
+ * Statistics computed over the network.
+ */
+ protected NetworkStats stats;
+
+ /**
+ * Current progress of the analysis.
+ * <p>
+ * The progress of the analyzer is measured in number of steps. Extender classes are responsible for
+ * maintaining the value of this field up to date. The progress must be a natural number not greater than
+ * the maximal progress.
+ * </p>
+ *
+ * @see #getMaxProgress()
+ */
+ protected int progress;
+
+ /**
+ * Flag indicating if the process of analysis was cancelled by the user.
+ * <p>
+ * This flag should only be modified by calling {@link #cancel()}. Extender classes should terminate the
+ * analysis once this flag is set to <code>true</code>. Therefore, in the process of network analysis, the
+ * value of this flag should be checked at regular intervals.
+ * </p>
+ */
+ protected boolean cancelled;
+
+ /**
+ * Global <code>HashMap</code> for storing node attributes.
+ */
+ protected CyAttributes nodeAttributes;
+
+ /**
+ * Global <code>HashMap</code> for storing edge attributes.
+ */
+ protected CyAttributes edgeAttributes;
+
+ /**
+ * Set of all edges that are removed from {@link #network} before the analysis. These edges are added back
+ * to the network after the analysis completes or is cancelled.
+ */
+ private Set<Edge> removedEdges;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/PlotParameterAction.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/PlotParameterAction.java
new file mode 100644
index 0000000..706d69c
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/PlotParameterAction.java
@@ -0,0 +1,137 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer;
+
+import java.awt.event.ActionEvent;
+
+import javax.swing.JOptionPane;
+
+import cytoscape.Cytoscape;
+import cytoscape.logger.CyLogger;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Messages;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.io.SettingsSerializer;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.settings.PluginSettings;
+import de.mpg.mpi_inf.bioinf.netanalyzer.ui.PlotParameterDialog;
+
+/**
+ * Action handler for the menu item "Plot Parameters".
+ *
+ * @author Nadezhda Doncheva
+ */
+public class PlotParameterAction extends NetAnalyzerAction implements AnalysisListener {
+
+ /**
+ * Initializes a new instance of <code>PlotParameterAction</code>.
+ */
+ public PlotParameterAction() {
+ super(Messages.AC_PLOTPARAM);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see cytoscape.util.CytoscapeAction#actionPerformed(java.awt.event.ActionEvent)
+ */
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ try {
+ // Verify there is a network loaded in Cytoscape and selected
+ if (!selectNetwork()) {
+ return;
+ }
+ // Display a dialog for mapping the computed attributes to the network
+ // only if NetworkAnalyzer has computed any parameters and
+ // and theses are stored in the node/edge attributes
+ nodeAttr = CyNetworkUtils.getComputedNodeAttributes(network);
+ // edgeAttr = CyNetworkUtils.getComputedEdgeAttributes(network);
+ final PluginSettings settings = SettingsSerializer.getPluginSettings();
+ if ((nodeAttr[0].length > 1) || (nodeAttr[1].length > 0)) {
+ openDialog();
+ } else if (!settings.getUseNodeAttributes() && !settings.getUseEdgeAttributes()) {
+ // Network does not contain computed parameters stored as attributes
+ if (JOptionPane.showConfirmDialog(Cytoscape.getDesktop(), Messages.SM_LOADPARAMETERS,
+ Messages.DT_ANALYSISNEEDED, JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION) {
+ settings.setUseNodeAttributes(true);
+ settings.setUseEdgeAttributes(true);
+ runNetworkAnalyzer();
+ }
+ } else {
+ // Network does not contain computed parameters stored as attributes
+ if (JOptionPane.showConfirmDialog(Cytoscape.getDesktop(), Messages.SM_RUNNETWORKANALYZER,
+ Messages.DT_ANALYSISNEEDED, JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION) {
+ runNetworkAnalyzer();
+ }
+ }
+ } catch (InnerException ex) {
+ // NetworkAnalyzer internal error
+ CyLogger.getLogger().error(Messages.SM_LOGERROR, ex);
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see de.mpg.mpi_inf.bioinf.netanalyzer.AnalysisListener#analysisCancelled()
+ */
+ public void analysisCancelled() {
+ // No specific action is required
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see de.mpg.mpi_inf.bioinf.netanalyzer.AnalysisListener#analysisCompleted(de.mpg.mpi_inf.bioinf
+ * .netanalyzer.NetworkAnalyzer)
+ */
+ public void analysisCompleted(NetworkAnalyzer analyzer) {
+ openDialog();
+ }
+
+ /**
+ * Opens the "Plot Computed Parameters" dialog.
+ */
+ private void openDialog() {
+ nodeAttr = CyNetworkUtils.getComputedNodeAttributes(network);
+ final PlotParameterDialog d = new PlotParameterDialog(Cytoscape.getDesktop(), network, nodeAttr);
+ d.setVisible(true);
+ }
+
+ /**
+ * Runs the NetworkAnalyzer analysis on all nodes so that the network parameters are computed and can be
+ * visualized afterwards.
+ */
+ private void runNetworkAnalyzer() {
+ final AnalysisExecutor exec = AnalyzeNetworkAction.initAnalysisExecuter(network, null);
+ if (exec != null) {
+ exec.setShowDialog(false);
+ exec.addAnalysisListener(this);
+ exec.start();
+ }
+ }
+
+ /**
+ * Unique ID for this version of this class. It is used in serialization.
+ */
+ private static final long serialVersionUID = -7530206812954428688L;
+
+ /**
+ * Array with node attributes to be plotted.
+ */
+ private String[][] nodeAttr;
+
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/Plugin.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/Plugin.java
new file mode 100644
index 0000000..7e14761
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/Plugin.java
@@ -0,0 +1,268 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer;
+
+import java.awt.Component;
+import java.io.ByteArrayOutputStream;
+import java.io.File;
+import java.io.PrintStream;
+
+import javax.swing.JMenu;
+
+import cytoscape.Cytoscape;
+import cytoscape.logger.CyLogger;
+import cytoscape.plugin.CytoscapePlugin;
+import cytoscape.util.CytoscapeAction;
+import cytoscape.view.CyMenus;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Messages;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.io.SettingsSerializer;
+import de.mpg.mpi_inf.bioinf.netanalyzer.ui.Utils;
+
+/**
+ * Wrapper class for the NetworkAnalyzer plugin.
+ *
+ * @author Yassen Assenov
+ */
+public class Plugin extends CytoscapePlugin {
+
+ /**
+ * Name of directory that contains Cytoscape plugins as a path relative to Cytoscape's root directory.
+ */
+ public static final String cytoscapeDir = System.getProperty("user.home") + File.separator + ".cytoscape";
+
+ /**
+ * Name of XML settings file. Both the internal and external setting files have this name.
+ */
+ public static final String settingsFileName = "NetworkAnalyzer.xml";
+
+ /**
+ * Current version of the NetworkAnalyzer plugin.
+ */
+ public static final String version = "2.7";
+
+ /**
+ * Gets the decorator class given decorators name.
+ *
+ * @param aName
+ * Name of the decorator as defined in XML settings file.
+ * @return <code>Class</code> instance of the decorator.
+ * @throws ClassNotFoundException
+ * If the given decorator does not exist.
+ */
+ public static Class<?> getDecoratorClass(String aName) throws ClassNotFoundException {
+ return Class.forName("de.mpg.mpi_inf.bioinf.netanalyzer.dec." + aName);
+ }
+
+ /**
+ * Gets the filter class corresponding to the given complex parameter type.
+ *
+ * @param aParamType
+ * Complex parameter type.
+ * @return <code>Class</code> instance of the filter for the specified complex parameter type.
+ * @throws ClassNotFoundException
+ * If the given complex parameter type is invalid or it does not have a corresponding filter.
+ */
+ public static Class<?> getFilterClass(String aParamType) throws ClassNotFoundException {
+ return Class.forName("de.mpg.mpi_inf.bioinf.netanalyzer.data.filter." + aParamType + "Filter");
+ }
+
+ /**
+ * Gets the filter dialog class (extending
+ * {@link de.mpg.mpi_inf.bioinf.netanalyzer.ui.filter.ComplexParamFilterDialog}) corresponding to the
+ * given complex parameter type.
+ *
+ * @param aParamClass
+ * <code>Class</code> instance of a complex parameter type.
+ * @return <code>Class</code> instance of the filter dialog for the specified complex parameter.
+ * @throws ClassNotFoundException
+ * If the given complex parameter type is invalid or it does not have a corresponding filter.
+ */
+ public static Class<?> getFilterDialogClass(Class<?> aParamClass) throws ClassNotFoundException {
+ return getFilterDialogClass(aParamClass.getSimpleName());
+ }
+
+ /**
+ * Gets the filter dialog class (extending
+ * {@link de.mpg.mpi_inf.bioinf.netanalyzer.ui.filter.ComplexParamFilterDialog}) corresponding to the
+ * given complex parameter type.
+ *
+ * @param aParamType
+ * Complex parameter type.
+ * @return <code>Class</code> instance of the filter dialog for the specified complex parameter.
+ * @throws ClassNotFoundException
+ * If the given complex parameter type is invalid or it does not have a corresponding filter.
+ */
+ public static Class<?> getFilterDialogClass(String aParamType) throws ClassNotFoundException {
+ return Class.forName("de.mpg.mpi_inf.bioinf.netanalyzer.ui.filter." + aParamType + "FilterDialog");
+ }
+
+ /**
+ * Gets the settings group class corresponding to the given complex parameter type.
+ *
+ * @param aParamType
+ * Complex parameter type.
+ * @return <code>Class</code> instance of the settings group type that manages the visual settings for the
+ * specified complex parameter.
+ * @throws ClassNotFoundException
+ * If the given complex parameter type is invalid.
+ */
+ public static Class<?> getSettingsGroupClass(String aParamType) throws ClassNotFoundException {
+ return Class.forName("de.mpg.mpi_inf.bioinf.netanalyzer.data.settings." + aParamType + "Group");
+ }
+
+ /**
+ * Gets the name of the external XML settings file.
+ *
+ * @return Name of the external XML settings file as a path relative to Cytoscape's root directory.
+ */
+ public static String getSettingsFileName() {
+ return cytoscapeDir + File.separator + settingsFileName;
+ }
+
+ /**
+ * Gets the visualizer class for the given complex parameter type.
+ *
+ * @param aParamType
+ * Complex parameter type.
+ * @return <code>Class</code> instance of a visualizer that displays data stored in instances of the
+ * specified complex parameter.
+ * @throws ClassNotFoundException
+ * If the given complex parameter type is invalid.
+ */
+ public static Class<?> getVisualizerClass(String aParamType) throws ClassNotFoundException {
+ return Class.forName("de.mpg.mpi_inf.bioinf.netanalyzer.ui." + aParamType + "Visualizer");
+ }
+
+ /**
+ * Checks if the specified complex parameter type has a filter.
+ *
+ * @param aParamClass
+ * <code>Class</code> instance of a complex parameter type to be checked for filter.
+ * @return <code>true</code> if <code>aParamType</code> is class a representing valid complex parameter
+ * type and there is a filter class for this type; <code>false</code> otherwise.
+ */
+ public static boolean hasFilter(Class<?> aParamClass) {
+ return hasFilter(aParamClass.getSimpleName());
+ }
+
+ /**
+ * Checks if the specified complex parameter type has a filter.
+ *
+ * @param aParamType
+ * Complex parameter type to be checked for filter.
+ * @return <code>true</code> if <code>aParamType</code> is a valid complex parameter type and there is a
+ * filter class for this type; <code>false</code> otherwise.
+ */
+ public static boolean hasFilter(String aParamType) {
+ try {
+ getFilterClass(aParamType);
+ return true;
+ } catch (ClassNotFoundException ex) {
+ return false;
+ }
+ }
+
+ /**
+ * Initializes a new instance of <code>Plugin</code>.
+ */
+ public Plugin() {
+ // loadLibraries();
+ CyMenus menus = Cytoscape.getDesktop().getCyMenus();
+
+ new JMenu("Hello");
+ try {
+ // Initiate default visual settings
+ SettingsSerializer.initVisualSettings();
+ // If initialization fails, the following lines are not executed:
+
+ // Add "Analyze Network" action
+ addAction(menus, Messages.AC_MENU_ANALYSIS, new AnalyzeNetworkAction());
+ // Add "Analyze subset" action
+ addAction(menus, Messages.AC_MENU_ANALYSIS, new AnalyzeSubsetAction());
+ // Add "Batch Analysis" action
+ addAction(menus, Messages.AC_MENU_ANALYSIS, new BatchAnalysisAction());
+ // Add "Load Network Statistics" action
+ addAction(menus, Messages.AC_MENU_ANALYSIS, new LoadNetstatsAction());
+
+ // Add separators
+ JMenu analysis = null;
+ for (final Component cmp : menus.getOperationsMenu().getMenuComponents()) {
+ if (cmp instanceof JMenu && Messages.AC_MENU_ANALYSIS.equals(((JMenu) cmp).getText())) {
+ analysis = (JMenu) cmp;
+ break;
+ }
+ }
+ if (analysis != null) {
+ analysis.addSeparator();
+ }
+ // Add "Plot Parameters" action
+ addAction(menus, Messages.AC_MENU_ANALYSIS, new PlotParameterAction());
+ // Add "Map To Visual Style" action
+ addAction(menus, Messages.AC_MENU_ANALYSIS, new MapParameterAction());
+ if (analysis != null) {
+ analysis.addSeparator();
+ }
+ // Add "NetworkAnalyzer Settings" action
+ addAction(menus, Messages.AC_MENU_ANALYSIS, new SettingsAction());
+
+ // Add "Compare Two Networks" action
+ addAction(menus, Messages.AC_MENU_MODIFICATION, new CompareAction());
+ // Add "Connected Components" action
+ addAction(menus, Messages.AC_MENU_MODIFICATION, new ConnComponentAction());
+ // Add "Clear multiple edges" action
+ addAction(menus, Messages.AC_MENU_MODIFICATION, new RemDupEdgesAction());
+ // Add "Remove Self-Loops" action
+ addAction(menus, Messages.AC_MENU_MODIFICATION, new RemoveSelfLoopsAction());
+
+ // Add "About" action
+ addAction(menus, Messages.AC_MENU_ANALYSIS, new AboutAction());
+ addAction(menus, Messages.AC_MENU_MODIFICATION, new AboutAction());
+
+ } catch (SecurityException ex) {
+ Utils.showErrorBox(Messages.DT_SECERROR, Messages.SM_SECERROR1);
+ System.err.println(Messages.SM_SECERROR1);
+ } catch (InnerException ex) {
+ final ByteArrayOutputStream os = new ByteArrayOutputStream();
+ final PrintStream ps = new PrintStream(os);
+ ex.printStackTrace(ps);
+ ps.flush();
+ if (os.toString().contains("NoClassDefFoundError:")) {
+ // Library is missing
+ CyLogger.getLogger().error(Messages.SM_LOGERROR, ex);
+ } else {
+ // NetworkAnalyzer internal error
+ CyLogger.getLogger().error(Messages.SM_LOGERROR, ex);
+ }
+ }
+ }
+
+ /**
+ * Adds a new action to the given submenu.
+ *
+ * @param aMenus
+ * Cytoscape menus instance.
+ * @param aSubMenu
+ * Name of the submenu that will contain the action.
+ * @param aAction
+ * Action to be added.
+ */
+ private static void addAction(CyMenus aMenus, String aSubMenu, CytoscapeAction aAction) {
+ aAction.setPreferredMenu("Plugins." + aSubMenu);
+ aMenus.addCytoscapeAction(aAction);
+ }
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/RemDupEdgesAction.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/RemDupEdgesAction.java
new file mode 100644
index 0000000..29b9fb2
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/RemDupEdgesAction.java
@@ -0,0 +1,88 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer;
+
+import java.awt.Frame;
+import java.awt.event.ActionEvent;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import cytoscape.logger.CyLogger;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Messages;
+import de.mpg.mpi_inf.bioinf.netanalyzer.ui.ClearMultEdgesDialog;
+import de.mpg.mpi_inf.bioinf.netanalyzer.ui.Utils;
+
+/**
+ * Action handler for the menu item "Remove Duplicated Edges".
+ *
+ * @author Yassen Assenov
+ */
+public class RemDupEdgesAction extends NetAnalyzerAction {
+
+ /**
+ * Initializes a new instance of <code>ReDupEdgesAction</code>.
+ */
+ public RemDupEdgesAction() {
+ super(Messages.AC_REMDUPEDGES);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see cytoscape.util.CytoscapeAction#actionPerformed(java.awt.event.ActionEvent)
+ */
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ try {
+ if (!selectNetwork()) {
+ return;
+ }
+
+ final Frame desktop = Cytoscape.getDesktop();
+ final ClearMultEdgesDialog d = new ClearMultEdgesDialog(desktop);
+ d.setVisible(true);
+
+ // Clear duplicated edges from all networks selected by the user
+ final CyNetwork[] networks = d.getSelectedNetworks();
+ final boolean ignoreDir = d.getIgnoreDirection();
+ final boolean createEdgeAttr = d.getCreateEdgeAttr();
+ if (networks != null) {
+ final int size = networks.length;
+ int[] removedEdges = new int[size];
+ String[] networkNames = new String[size];
+ for (int i = 0; i < size; ++i) {
+ final CyNetwork currentNet = networks[i];
+ networkNames[i] = currentNet.getTitle();
+ removedEdges[i] = CyNetworkUtils.removeDuplEdges(currentNet, ignoreDir, createEdgeAttr);
+ }
+
+ final String r = Messages
+ .constructReport(removedEdges, Messages.SM_REMDUPEDGES, networkNames);
+ Utils.showInfoBox(desktop, Messages.DT_REMDUPEDGES, r);
+ }
+ } catch (InnerException ex) {
+ // NetworkAnalyzer internal error
+ CyLogger.getLogger().error(Messages.SM_LOGERROR, ex);
+ }
+ }
+
+ /**
+ * Unique ID for this version of this class. It is used in serialization.
+ */
+ private static final long serialVersionUID = 3389808503156586737L;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/RemoveSelfLoopsAction.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/RemoveSelfLoopsAction.java
new file mode 100644
index 0000000..115a4ce
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/RemoveSelfLoopsAction.java
@@ -0,0 +1,90 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer;
+
+import java.awt.Frame;
+import java.awt.event.ActionEvent;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import cytoscape.logger.CyLogger;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Messages;
+import de.mpg.mpi_inf.bioinf.netanalyzer.sconnect.HelpConnector;
+import de.mpg.mpi_inf.bioinf.netanalyzer.ui.NetModificationDialog;
+import de.mpg.mpi_inf.bioinf.netanalyzer.ui.Utils;
+
+/**
+ * Action handler for the menu item "Remove Self-loops".
+ *
+ * @author Yassen Assenov
+ * @author Sven-Eric Schelhorn
+ */
+public class RemoveSelfLoopsAction extends NetAnalyzerAction {
+
+ /**
+ * Initializes a new instance of <code>RemoveSelfLoopsAction</code>.
+ */
+ public RemoveSelfLoopsAction() {
+ super(Messages.AC_REMSELFLOOPS);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.event.ActionListener#actionPerformed(java.awt.event.ActionEvent)
+ */
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ try {
+ if (!selectNetwork()) {
+ return;
+ }
+
+ final Frame desktop = Cytoscape.getDesktop();
+ final String helpURL = HelpConnector.getRemSelfloopsURL();
+ final NetModificationDialog d = new NetModificationDialog(desktop, Messages.DT_REMSELFLOOPS,
+ Messages.DI_REMOVESL, helpURL);
+ d.setVisible(true);
+
+ // Remove the self-loops from all networks selected by the user
+ final CyNetwork[] networks = d.getSelectedNetworks();
+ if (networks != null) {
+ final int size = networks.length;
+ int[] removedLoops = new int[size];
+ String[] networkNames = new String[size];
+ for (int i = 0; i < size; ++i) {
+ final CyNetwork currentNet = networks[i];
+ networkNames[i] = currentNet.getTitle();
+ removedLoops[i] = CyNetworkUtils.removeSelfLoops(currentNet);
+ }
+
+ final String r = Messages.constructReport(removedLoops, Messages.SM_REMSELFLOOPS,
+ networkNames);
+ Utils.showInfoBox(desktop, Messages.DT_REMSELFLOOPS, r);
+ }
+ } catch (InnerException ex) {
+ // NetworkAnalyzer internal error
+ CyLogger.getLogger().error(Messages.SM_LOGERROR, ex);
+ }
+ }
+
+ /**
+ * Unique ID for this version of this class. It is used in serialization.
+ */
+ private static final long serialVersionUID = -7465036491341908005L;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/SettingsAction.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/SettingsAction.java
new file mode 100644
index 0000000..cddaf49
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/SettingsAction.java
@@ -0,0 +1,63 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer;
+
+import java.awt.event.ActionEvent;
+
+import cytoscape.Cytoscape;
+import cytoscape.logger.CyLogger;
+import cytoscape.util.CytoscapeAction;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Messages;
+import de.mpg.mpi_inf.bioinf.netanalyzer.ui.PluginSettingsDialog;
+
+/**
+ * Action handler for the menu item "NetworkAnalyzer Settings".
+ *
+ * @author Yassen Assenov
+ */
+public class SettingsAction extends CytoscapeAction {
+
+ /**
+ * Initializes a new instance of <code>SettingsAction</code>.
+ */
+ public SettingsAction() {
+ super(Messages.AC_SETTINGS);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.event.ActionListener#actionPerformed(java.awt.event.ActionEvent)
+ */
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ try {
+ // Display settings dialog
+ PluginSettingsDialog d = new PluginSettingsDialog(Cytoscape.getDesktop());
+ d.setVisible(true);
+ } catch (InnerException ex) {
+ // NetworkAnalyzer internal error
+ CyLogger.getLogger().error(Messages.SM_LOGERROR, ex);
+ }
+ }
+
+ /**
+ * Unique ID for this version of this class. It is used in serialization.
+ */
+ private static final long serialVersionUID = 7321507757114057304L;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/UndirNetworkAnalyzer.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/UndirNetworkAnalyzer.java
new file mode 100644
index 0000000..6da9245
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/UndirNetworkAnalyzer.java
@@ -0,0 +1,848 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer;
+
+import giny.model.Edge;
+import giny.model.Node;
+
+import java.awt.geom.Point2D;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.CCInfo;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.DegreeDistribution;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.LogBinDistribution;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.LongHistogram;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.MutInteger;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.NetworkInterpretation;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.NodeBetweenInfo;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.PathLengthData;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Points2D;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.SimpleUndirParams;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.SumCountPair;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Utils;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.io.SettingsSerializer;
+
+/**
+ * Network analyzer for networks that contain undirected edges only.
+ *
+ * @author Yassen Assenov
+ * @author Sven-Eric Schelhorn
+ * @author Nadezhda Doncheva
+ */
+public class UndirNetworkAnalyzer extends NetworkAnalyzer {
+
+ /**
+ * Initializes a new instance of <code>UndirNetworkAnalyzer</code>.
+ *
+ * @param aNetwork
+ * Network to be analyzed.
+ * @param aNodeSet
+ * Subset of nodes in <code>aNetwork</code>, for which topological parameters are to
+ * be calculated. Set this to <code>null</code> if parameters must be calculated for
+ * all nodes in the network.
+ * @param aInterpr
+ * Interpretation of the network edges.
+ */
+ public UndirNetworkAnalyzer(CyNetwork aNetwork, Set<Node> aNodeSet,
+ NetworkInterpretation aInterpr) {
+ super(aNetwork, aNodeSet, aInterpr);
+ if (nodeSet != null) {
+ stats.set("nodeCount", nodeSet.size());
+ }
+ nodeCount = stats.getInt("nodeCount");
+ sPathLengths = new long[nodeCount];
+ sharedNeighborsHist = new long[nodeCount];
+ visited = new HashSet<Node>(nodeCount);
+ useNodeAttributes = SettingsSerializer.getPluginSettings().getUseNodeAttributes();
+ useEdgeAttributes = SettingsSerializer.getPluginSettings().getUseEdgeAttributes();
+ nodeBetweenness = new HashMap<Node, NodeBetweenInfo>();
+ edgeBetweenness = new HashMap<Edge, Double>();
+ stress = new HashMap<Node, Long>();
+ roundingDigits = 8;
+ computeNB = true;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see de.mpg.mpi_inf.bioinf.netanalyzer.NetworkAnalyzer#computeAll()
+ */
+ @Override
+ public void computeAll() {
+
+ long time = System.currentTimeMillis();
+ analysisStarting();
+ int edgeCount = 0;
+ SimpleUndirParams params = new SimpleUndirParams();
+ int maxConnectivity = 0;
+ DegreeDistribution degreeDist = new DegreeDistribution(nodeCount);
+ // clustering coefficients
+ HashMap<Integer, SumCountPair> CCps = new HashMap<Integer, SumCountPair>();
+ // topological coefficients
+ ArrayList<Point2D.Double> topCoefs = new ArrayList<Point2D.Double>(nodeCount);
+ // closeness centrality
+ ArrayList<Point2D.Double> closenessCent = new ArrayList<Point2D.Double>(nodeCount);
+ // node betweenness
+ ArrayList<Point2D.Double> nodeBetweennessArray = new ArrayList<Point2D.Double>(nodeCount);
+ // neighborhood connectivity
+ HashMap<Integer, SumCountPair> NCps = new HashMap<Integer, SumCountPair>();
+ // average shortest path length
+ Map<Node, Double> aplMap = new HashMap<Node, Double>();
+ // stress
+ LogBinDistribution stressDist = new LogBinDistribution();
+ // Compute number of connected components
+ ConnComponentAnalyzer cca = new ConnComponentAnalyzer(network);
+ Set<CCInfo> components = cca.findComponents();
+ params.connectedComponentCount = components.size();
+
+ for (CCInfo aCompInfo : components) {
+ // Get nodes of connected component
+ Set<Node> connNodes = cca.getNodesOf(aCompInfo);
+ // Set<Node> connNodes = new HashSet<Node>(connNodes);
+ if (nodeSet != null) {
+ connNodes.retainAll(nodeSet);
+ }
+
+ // Initialize the parameters for node and edge betweenness calculation
+ if (nodeSet == null && computeNB) {
+ nodeBetweenness.clear();
+ edgeBetweenness.clear();
+ stress.clear();
+ aplMap.clear();
+ for (Node n : connNodes) {
+ nodeBetweenness.put(n, new NodeBetweenInfo(0, -1, 0.0));
+ stress.put(n, Long.valueOf(0));
+ }
+ }
+
+ int componentDiameter = 0;
+ for (final Node node : connNodes) {
+ ++progress;
+ final String nodeID = node.getIdentifier();
+ final int[] incEdges = getIncidentEdges(node);
+ final Map<Node, MutInteger> neighborMap = CyNetworkUtils.getNeighborMap(network,
+ node, incEdges);
+
+ // Degree distribution calculation
+ final int degree = getDegree(node, incEdges);
+ edgeCount += degree;
+ degreeDist.addObservation(degree);
+ if (useNodeAttributes) {
+ setAttr(nodeID, "deg", degree);
+ }
+ final int neighborCount = calcSimple(nodeID, incEdges, neighborMap, params);
+ if (maxConnectivity < neighborCount) {
+ maxConnectivity = neighborCount;
+ }
+
+ if (neighborCount > 0) {
+ final Set<Node> neighbors = neighborMap.keySet();
+
+ // Neighborhood connectivity computation
+ int[] neighborInd = CyNetworkUtils.getIndices(neighbors);
+ final double neighborConnect = averageNeighbors(neighbors);
+ accumulate(NCps, neighborCount, neighborConnect);
+
+ if (neighborCount > 1) {
+
+ // Topological coefficients computation
+ double topCoef = computeTC(node, neighbors);
+ if (!Double.isNaN(topCoef)) {
+ topCoefs.add(new Point2D.Double(neighborCount, topCoef));
+ } else {
+ topCoef = 0.0;
+ }
+
+ // Clustering coefficients computation
+ final double nodeCCp = computeCC(neighborInd);
+ accumulate(CCps, neighborCount, nodeCCp);
+ if (useNodeAttributes) {
+ setAttr(nodeID, "cco", Utils.roundTo(nodeCCp, roundingDigits));
+ setAttr(nodeID, "tco", Utils.roundTo(topCoef, roundingDigits));
+ }
+
+ } else if (useNodeAttributes) {
+ setAttr(nodeID, "cco", 0.0);
+ setAttr(nodeID, "tco", 0.0);
+ }
+ setAttr(nodeID, "nco", Utils.roundTo(neighborConnect, roundingDigits));
+ } else if (useNodeAttributes) {
+ setAttr(nodeID, "nco", 0.0);
+ setAttr(nodeID, "cco", 0.0);
+ setAttr(nodeID, "tco", 0.0);
+ }
+ if (cancelled) {
+ analysisFinished();
+ return;
+ }
+
+ // Shortest path lengths computation
+ if (nodeSet != null) {
+ continue;
+ }
+ PathLengthData pathLengths = computeSPandSN(node);
+ final int eccentricity = pathLengths.getMaxLength();
+ if (params.diameter < eccentricity) {
+ params.diameter = eccentricity;
+ }
+ if (0 < eccentricity && eccentricity < params.radius) {
+ params.radius = eccentricity;
+ }
+ if (componentDiameter < eccentricity) {
+ componentDiameter = eccentricity;
+ }
+ final double apl = (pathLengths.getCount() > 0) ? pathLengths.getAverageLength()
+ : 0;
+ aplMap.put(node, Double.valueOf(apl));
+ final double closeness = (apl > 0.0) ? 1 / apl : 0.0;
+ closenessCent.add(new Point2D.Double(neighborCount, closeness));
+
+ // Store max. and avg. shortest path lengths, and closeness in
+ // node attributes
+ if (useNodeAttributes) {
+ setAttr(nodeID, "spl", eccentricity);
+ setAttr(nodeID, "apl", Utils.roundTo(apl, roundingDigits));
+ setAttr(nodeID, "clc", Utils.roundTo(closeness, roundingDigits));
+ }
+
+ // Node and edge betweenness calculation
+ if (computeNB) {
+ computeNBandEB(node);
+ // Reset everything except the betweenness value
+ for (final Node n : connNodes) {
+ NodeBetweenInfo nodeInfo = nodeBetweenness.get(n);
+ nodeInfo.reset();
+ }
+ }
+
+ if (cancelled) {
+ analysisFinished();
+ return;
+ }
+ } // end node iteration
+
+ if (nodeSet == null) {
+ // Normalize and save node betweenness
+ final double nNormFactor = computeNormFactor(nodeBetweenness.size());
+ for (final Node n : connNodes) {
+ String id = n.getIdentifier();
+ // Compute node radiality
+ final double rad = (componentDiameter + 1.0 - aplMap.get(n).doubleValue())
+ / componentDiameter;
+ if (useNodeAttributes) {
+ setAttr(id, "rad", Utils.roundTo(rad, roundingDigits));
+ }
+ if (computeNB) {
+ final NodeBetweenInfo nbi = nodeBetweenness.get(n);
+ double nb = nbi.getBetweenness() * nNormFactor;
+ if (Double.isNaN(nb)) {
+ nb = 0.0;
+ }
+ final int degree = getDegree(n, getIncidentEdges(n));
+ nodeBetweennessArray.add(new Point2D.Double(degree, nb));
+ final long nodeStress = stress.get(n).longValue();
+ stressDist.addObservation(nodeStress);
+ if (useNodeAttributes) {
+ setAttr(id, "nbt", Utils.roundTo(nb, roundingDigits));
+ setAttr(id, "stress", nodeStress);
+ }
+ }
+ } // end iterate over nodes
+
+ // Save edge betweenness
+ if (useEdgeAttributes && computeNB) {
+ for (final Map.Entry<Edge, Double> betEntry : edgeBetweenness.entrySet()) {
+ double eb = betEntry.getValue().doubleValue();
+ if (Double.isNaN(eb)) {
+ eb = 0.0;
+ }
+ setEAttr(betEntry.getKey().getIdentifier(), "ebt",
+ Utils.roundTo(eb, roundingDigits));
+ }
+ }
+ }
+ } // end iteration over connected component
+
+ // save statistics
+ if (params.connectivityAccum != null) {
+ final double meanConnectivity = params.connectivityAccum.getAverage();
+ stats.set("avNeighbors", meanConnectivity);
+ final double density = meanConnectivity / (nodeCount - 1);
+ stats.set("density", meanConnectivity / (nodeCount - 1));
+ stats.set("centralization", (nodeCount / ((double) nodeCount - 2))
+ * (maxConnectivity / ((double) nodeCount - 1) - density));
+ final double nom = params.sqConnectivityAccum.getSum() * nodeCount;
+ final double denom = params.connectivityAccum.getSum()
+ * params.connectivityAccum.getSum();
+ stats.set("heterogeneity", Math.sqrt(nom / denom - 1));
+ }
+
+ // Save degree distribution in the statistics instance
+ stats.set("degreeDist", degreeDist.createHistogram());
+
+ // Save C(k) in the statistics instance
+ if (CCps.size() > 0) {
+ Point2D.Double[] averages = new Point2D.Double[CCps.size()];
+ double cc = accumulateCCs(CCps, averages) / nodeCount;
+ stats.set("cc", cc);
+ if (averages.length > 1) {
+ stats.set("cksDist", new Points2D(averages));
+ }
+ }
+
+ // Save topological coefficients in the statistics instance
+ if (topCoefs.size() > 1) {
+ stats.set("topCoefs", new Points2D(topCoefs));
+ }
+
+ stats.set("ncc", params.connectedComponentCount);
+ stats.set("usn", params.unconnectedNodeCount);
+ stats.set("nsl", params.selfLoopCount);
+ stats.set("mnp", params.multiEdgePartners / 2);
+ if (interpr.isPaired()) {
+ stats.set("edgeCount", edgeCount / 2);
+ }
+
+ if (nodeSet == null) {
+ long connPairs = 0; // total number of connected pairs of nodes
+ long totalPathLength = 0;
+ for (int i = 1; i <= params.diameter; ++i) {
+ connPairs += sPathLengths[i];
+ totalPathLength += i * sPathLengths[i];
+ }
+ stats.set("connPairs", connPairs);
+
+ // Save shortest path lengths distribution
+ if (params.diameter > 0) {
+ stats.set("diameter", params.diameter);
+ stats.set("radius", params.radius);
+ stats.set("avSpl", (double) totalPathLength / connPairs);
+ if (params.diameter > 1) {
+ stats.set("splDist", new LongHistogram(sPathLengths, 1, params.diameter));
+ }
+ int largestCommN = 0;
+ for (int i = 1; i < nodeCount; ++i) {
+ if (sharedNeighborsHist[i] != 0) {
+ sharedNeighborsHist[i] /= 2;
+ largestCommN = i;
+ }
+ }
+ // Save common neighbors distribution
+ if (largestCommN > 0) {
+ stats.set("commNeighbors", new LongHistogram(sharedNeighborsHist, 1,
+ largestCommN));
+ }
+ }
+ }
+
+ // Save closeness centrality in the statistics instance
+ if (closenessCent.size() > 1) {
+ stats.set("closenessCent", new Points2D(closenessCent));
+ }
+
+ // Save node betweenness in the statistics instance
+ if (nodeBetweennessArray.size() > 2) {
+ stats.set("nodeBetween", new Points2D(nodeBetweennessArray));
+ }
+
+ // Save neighborhood connectivity in the statistics instance
+ if (NCps.size() > 1) {
+ stats.set("neighborConn", new Points2D(getAverages(NCps)));
+ }
+
+ // Save stress distribution in the statistics instance
+ if (nodeSet == null && computeNB) {
+ stats.set("stressDist", stressDist.createPoints2D());
+ }
+
+ analysisFinished();
+ time = System.currentTimeMillis() - time;
+ stats.set("time", time / 1000.0);
+ progress = nodeCount;
+ if (useNodeAttributes || useEdgeAttributes) {
+ Cytoscape.firePropertyChange(Cytoscape.ATTRIBUTES_CHANGED, null, null);
+ }
+ }
+
+ /**
+ * Calculates a set of simple properties of the given node.
+ *
+ * @param aNodeID
+ * ID of the node of interest. This parameter is used for storing attribute values.
+ * @param aIncEdges
+ * Array of the indices of all the neighbors of the node of interest.
+ * @param aNeMap
+ * Map of neighbors of the node of interest and their frequency.
+ * @param aParams
+ * Instance to accumulate the computed values.
+ * @return Number of neighbors of the node of interest.
+ */
+ private int calcSimple(String aNodeID, int[] aIncEdges, Map<Node, MutInteger> aNeMap,
+ SimpleUndirParams aParams) {
+ final int neighborCount = aNeMap.size();
+
+ // Avg. number of neighbors, density & centralization calculation
+ if (aParams.connectivityAccum != null) {
+ aParams.connectivityAccum.add(neighborCount);
+ } else {
+ aParams.connectivityAccum = new SumCountPair(neighborCount);
+ }
+ // Heterogeneity calculation
+ if (aParams.sqConnectivityAccum != null) {
+ aParams.sqConnectivityAccum.add(neighborCount * neighborCount);
+ } else {
+ aParams.sqConnectivityAccum = new SumCountPair(neighborCount * neighborCount);
+ }
+
+ // Number of unconnected nodes calculation
+ if (neighborCount == 0) {
+ aParams.unconnectedNodeCount++;
+ }
+
+ // Number of self-loops and number of directed/undireceted edges
+ // calculation
+ int selfLoops = 0;
+ int dirEdges = 0;
+ for (int j = 0; j < aIncEdges.length; j++) {
+ Edge e = network.getEdge(aIncEdges[j]);
+ if (e.isDirected()) {
+ dirEdges++;
+ }
+ if (e.getSource() == e.getTarget()) {
+ selfLoops++;
+ }
+ }
+ aParams.selfLoopCount += selfLoops;
+ int undirEdges = aIncEdges.length - dirEdges;
+
+ // Number of multi-edge node partners calculation
+ int partnerOfMultiEdgeNodePairs = 0;
+ for (final MutInteger freq : aNeMap.values()) {
+ if (freq.value > 1) {
+ partnerOfMultiEdgeNodePairs++;
+ }
+ }
+ aParams.multiEdgePartners += partnerOfMultiEdgeNodePairs;
+
+ // Storing the values in attributes
+ if (useNodeAttributes) {
+ setAttr(aNodeID, "slo", selfLoops);
+ setAttr(aNodeID, "isn", (neighborCount == 0));
+ setAttr(aNodeID, "nue", undirEdges);
+ setAttr(aNodeID, "nde", dirEdges);
+ setAttr(aNodeID, "pmn", partnerOfMultiEdgeNodePairs);
+ }
+ return neighborCount;
+ }
+
+ /**
+ * Computes the clustering coefficient of a node.
+ *
+ * @param aNeighborIndices
+ * Array of the indices of all the neighbors of the node of interest.
+ * @return Clustering coefficient of <code>aNode</code> as a value in the range
+ * <code>[0,1]</code>.
+ */
+ private double computeCC(int[] aNeighborIndices) {
+ int edgeCount = CyNetworkUtils.getPairConnCount(network, aNeighborIndices, true);
+ int neighborsCount = aNeighborIndices.length;
+ return (double) 2 * edgeCount / (neighborsCount * (neighborsCount - 1));
+ }
+
+ /**
+ * Computes the shortest path lengths from the given node to all other nodes in the network. In
+ * addition, this method accumulates values in the {@link #sharedNeighborsHist} histogram.
+ * <p>
+ * This method stores the lengths found in the array {@link #sPathLengths}.<br/>
+ * <code>sPathLengths[i] == 0</code> when i is the index of <code>aNode</code>.<br/>
+ * <code>sPathLengths[i] == Integer.MAX_VALUE</code> when node i and <code>aNode</code> are
+ * disconnected.<br/>
+ * <code>sPathLengths[i] == d > 0</code> when every shortest path between node i and
+ * <code>aNode</code> contains <code>d</code> edges.
+ * </p>
+ * <p>
+ * This method uses a breadth-first traversal through the network, starting from the specified
+ * node, in order to find all reachable nodes and accumulate their distances to
+ * <code>aNode</code> in {@link #sPathLengths}.
+ * </p>
+ *
+ * @param aNode
+ * Starting node of the shortest paths to be found.
+ * @return Data on the shortest path lengths from the current node to all other reachable nodes
+ * in the network.
+ */
+ private PathLengthData computeSPandSN(Node aNode) {
+ visited.clear();
+ visited.add(aNode);
+ Set<Node> nbs = null;
+ LinkedList<Node> reachedNodes = new LinkedList<Node>();
+ reachedNodes.add(aNode);
+ reachedNodes.add(null);
+ int currentDist = 1;
+ PathLengthData result = new PathLengthData();
+
+ for (Node currentNode = reachedNodes.removeFirst(); !reachedNodes.isEmpty(); currentNode = reachedNodes
+ .removeFirst()) {
+ if (currentNode == null) {
+ // Next level of the BFS tree
+ currentDist++;
+ reachedNodes.add(null);
+ } else {
+ // Traverse next reached node
+ final Set<Node> neighbors = getNeighbors(currentNode);
+ if (nbs == null) {
+ nbs = neighbors;
+ }
+ for (final Node neighbor : neighbors) {
+ if (visited.add(neighbor)) {
+ final int snCount = (currentDist > 2) ? 0 : countNeighborsIn(nbs, neighbor);
+ sharedNeighborsHist[snCount]++;
+ sPathLengths[currentDist]++;
+ result.addSPL(currentDist);
+ reachedNodes.add(neighbor);
+ }
+ }
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Accumulates the node and edge betweenness of all nodes in a connected component. The node
+ * betweenness is calculate using the algorithm of Brandes (U. Brandes: A Faster Algorithm for
+ * Betweenness Centrality. Journal of Mathematical Sociology 25(2):163-177, 2001). The edge
+ * betweenness is calculated as used by Newman and Girvan (M.E. Newman and M. Girvan: Finding
+ * and Evaluating Community Structure in Networks. Phys. Rev. E Stat. Nonlin. Soft. Matter
+ * Phys., 69, 026113.). In each run of this method a different source node is chosen and the
+ * betweenness of all nodes is replaced by the new one. For the final result this method has to
+ * be run for all nodes of the connected component.
+ *
+ * This method uses a breadth-first search through the network, starting from a specified source
+ * node, in order to find all paths to the other nodes in the network and to accumulate their
+ * betweenness.
+ *
+ * @param source
+ * Node where a run of breadth-first search is started, in order to accumulate the
+ * node and edge betweenness of all other nodes
+ */
+ private void computeNBandEB(Node source) {
+ LinkedList<Node> done_nodes = new LinkedList<Node>();
+ LinkedList<Node> reached = new LinkedList<Node>();
+ HashMap<Edge, Double> edgeDependency = new HashMap<Edge, Double>();
+ HashMap<Node, Long> stressDependency = new HashMap<Node, Long>();
+
+ final NodeBetweenInfo sourceNBInfo = nodeBetweenness.get(source);
+ sourceNBInfo.setSource();
+ reached.add(source);
+ stressDependency.put(source, Long.valueOf(0));
+
+ // Use BFS to find shortest paths from source to all nodes in the
+ // network
+ while (!reached.isEmpty()) {
+ final Node current = reached.removeFirst();
+ done_nodes.addFirst(current);
+ final NodeBetweenInfo currentNBInfo = nodeBetweenness.get(current);
+ final Set<Node> neighbors = getNeighbors(current);
+ for (Node neighbor : neighbors) {
+ final NodeBetweenInfo neighborNBInfo = nodeBetweenness.get(neighbor);
+ final List<Edge> edges = CyNetworkUtils.getConnEdge(network, current, neighbor);
+ final int expectSPLength = currentNBInfo.getSPLength() + 1;
+ if (neighborNBInfo.getSPLength() < 0) {
+ // Neighbor traversed for the first time
+ reached.add(neighbor);
+ neighborNBInfo.setSPLength(expectSPLength);
+ stressDependency.put(neighbor, Long.valueOf(0));
+ }
+ // shortest path via current to neighbor found
+ if (neighborNBInfo.getSPLength() == expectSPLength) {
+ neighborNBInfo.addSPCount(currentNBInfo.getSPCount());
+ // check for long overflow
+ if (neighborNBInfo.getSPCount() < 0) {
+ computeNB = false;
+ }
+ // add predecessors and outgoing edges, needed for
+ // accumulation of betweenness scores
+ neighborNBInfo.addPredecessor(current);
+ for (final Edge edge : edges) {
+ currentNBInfo.addOutedge(edge);
+ }
+ }
+ // initialize edge dependency
+ for (final Edge edge : edges) {
+ if (!edgeDependency.containsKey(edge)) {
+ edgeDependency.put(edge, new Double(0.0));
+ }
+ }
+ }
+ }
+
+ // Return nodes in order of non-increasing distance from source
+ while (!done_nodes.isEmpty()) {
+ final Node current = done_nodes.removeFirst();
+ final NodeBetweenInfo currentNBInfo = nodeBetweenness.get(current);
+ if (currentNBInfo != null) {
+ final long currentStress = stressDependency.get(current).longValue();
+ while (!currentNBInfo.isEmptyPredecessors()) {
+ final Node predecessor = currentNBInfo.pullPredecessor();
+ final NodeBetweenInfo predecessorNBInfo = nodeBetweenness.get(predecessor);
+ predecessorNBInfo.addDependency((1.0 + currentNBInfo.getDependency())
+ * ((double) predecessorNBInfo.getSPCount() / (double) currentNBInfo
+ .getSPCount()));
+ // accumulate all sp count
+ final long oldStress = stressDependency.get(predecessor).longValue();
+ stressDependency.put(predecessor, new Long(oldStress + 1 + currentStress));
+ // accumulate edge betweenness
+ final List<Edge> edges = CyNetworkUtils.getConnEdge(network, predecessor,
+ current);
+ if (edges.size() != 0) {
+ final Edge compEdge = edges.get(0);
+ final LinkedList<Edge> currentedges = currentNBInfo.getOutEdges();
+ double oldbetweenness = 0.0;
+ double newbetweenness = 0.0;
+ for (final Edge edge : edges) {
+ if (edgeBetweenness.containsKey(edge)) {
+ oldbetweenness = edgeBetweenness.get(edge).doubleValue();
+ break;
+ }
+ }
+ // if the node is a leaf node in this search tree
+ if (currentedges.size() == 0) {
+ newbetweenness = (double) predecessorNBInfo.getSPCount()
+ / (double) currentNBInfo.getSPCount();
+ } else {
+ double neighbourbetw = 0.0;
+ for (Edge neighbouredge : currentedges) {
+ if (!edges.contains(neighbouredge)) {
+ neighbourbetw += edgeDependency.get(neighbouredge)
+ .doubleValue();
+ }
+ }
+ newbetweenness = (1 + neighbourbetw)
+ * ((double) predecessorNBInfo.getSPCount() / (double) currentNBInfo
+ .getSPCount());
+ }
+ edgeDependency.put(compEdge, new Double(newbetweenness));
+ for (final Edge edge : edges) {
+ edgeBetweenness.put(edge, new Double(newbetweenness + oldbetweenness));
+ }
+ }
+ }
+ // accumulate node betweenness in each run
+ if (!current.equals(source)) {
+ currentNBInfo.addBetweenness(currentNBInfo.getDependency());
+ // accumulate number of shortest paths
+ final long allSpPaths = stress.get(current).longValue();
+ stress.put(current, new Long(allSpPaths + currentNBInfo.getSPCount()
+ * currentStress));
+ }
+ }
+ }
+ }
+
+ /**
+ * Computes a normalization factor for node betweenness normalization.
+ *
+ * @param count
+ * Number of nodes for which betweenness has been computed.
+ * @return Normalization factor for node betweenness normalization.
+ */
+ protected double computeNormFactor(int count) {
+ return (count > 2) ? (1.0 / ((count - 1) * (count - 2))) : 1.0;
+ }
+
+ /**
+ * Computes the average number of neighbors of the nodes in a given node set.
+ *
+ * @param aNodes
+ * Non-empty set of nodes. Specifying <code>null</code> or an empty set for this
+ * parameter results in throwing an exception.
+ * @return Average number of neighbors of the nodes in <code>aNodes</code>.
+ */
+ private double averageNeighbors(Set<Node> aNodes) {
+ int neighbors = 0;
+ for (final Node node : aNodes) {
+ neighbors += getNeighbors(node).size();
+ }
+ return (double) neighbors / aNodes.size();
+ }
+
+ /**
+ * Counts the number of neighbors of the given node that occur in the given set of nodes.
+ *
+ * @param aSet
+ * Set of nodes to be searched in.
+ * @param aNode
+ * Node whose neighbors will be searched in <code>aSet</code>.
+ * @return Number of nodes in <code>aSet</code> that are neighbors of <code>aNode</code>.
+ */
+ private int countNeighborsIn(Set<Node> aSet, Node aNode) {
+ Set<Node> nbs = CyNetworkUtils.getNeighbors(network, aNode, getIncidentEdges(aNode));
+ nbs.retainAll(aSet);
+ return nbs.size();
+ }
+
+ /**
+ * Computes the topological coefficient of the given node.
+ *
+ * @param aNode
+ * Node to get the topological coefficient of.
+ * @param aNeighbors
+ * Set of all the neighbors of the given node.
+ * @return Topological coefficient of the <code>aNode</code> as a number in the range [0, 1];
+ * <code>NaN</code> if the topological coefficient function is not defined for the given
+ * node.
+ */
+ private double computeTC(Node aNode, Set<Node> aNeighbors) {
+ Set<Node> comNeNodes = new HashSet<Node>(); // nodes that share common
+ // neighbor with aNode
+ int tc = 0;
+ for (final Node nb : aNeighbors) {
+ Set<Node> currentComNeNodes = getNeighbors(nb);
+ for (final Node n : currentComNeNodes) {
+ if (n != aNode) {
+ tc++;
+ if (comNeNodes.add(n)) {
+ if (aNeighbors.contains(n)) {
+ tc++;
+ }
+ }
+ }
+ }
+ }
+ return (double) tc / (double) (comNeNodes.size() * aNeighbors.size());
+ }
+
+ /**
+ * Gets all the neighbors of the given node.
+ *
+ * @param aNode
+ * Node, whose neighbors are to be found.
+ * @return <code>Set</code> of <code>Node</code> instances, containing all the neighbors of
+ * <code>aNode</code>; empty set if the node specified is an isolated vertex.
+ * @see CyNetworkUtils#getNeighbors(CyNetwork, Node, int[])
+ */
+ private Set<Node> getNeighbors(Node aNode) {
+ return CyNetworkUtils.getNeighbors(network, aNode, getIncidentEdges(aNode));
+ }
+
+ /**
+ * Gets the degree of a given node.
+ *
+ * @param aNode
+ * Node to get the degree of.
+ * @param aIncEdges
+ * Array of the indices of all edges incident on the given node.
+ * @return Degree of the given node, as defined in the book &qout;Graph Theory&qout; by Reinhard
+ * Diestel.
+ */
+ private int getDegree(Node aNode, int[] aIncEdges) {
+ int degree = aIncEdges.length;
+ for (int i = 0; i < aIncEdges.length; ++i) {
+ Edge e = network.getEdge(aIncEdges[i]);
+ if (e.getSource() == e.getTarget() && (!(e.isDirected() && interpr.isPaired()))) {
+ degree++;
+ }
+ }
+ return degree;
+ }
+
+ /**
+ * Gets all edges incident on the given node.
+ *
+ * @param aNode
+ * Node, on which incident edges are to be found.
+ * @return Array of edge indices, containing all the edges in the network incident on
+ * <code>aNode</code>.
+ */
+ private int[] getIncidentEdges(Node aNode) {
+ int ni = aNode.getRootGraphIndex();
+ return network.getAdjacentEdgeIndicesArray(ni, true, !interpr.isPaired(), true);
+ }
+
+ /**
+ * Histogram of shortest path lengths.
+ * <p>
+ * <code>sPathLength[0]</code> stores the number of nodes processed so far.<br/>
+ * <code>sPathLength[i]</code> for <code>i > 0</code> stores the number of shortest paths of
+ * length <code>i</code> found so far.
+ * </p>
+ */
+ private long[] sPathLengths;
+
+ /**
+ * Flag, indicating if the computed parameters must be stored as node attributes.
+ */
+ private boolean useNodeAttributes;
+
+ /**
+ * Flag, indicating if the computed parameters must be stored as edge attributes.
+ */
+ private boolean useEdgeAttributes;
+
+ /**
+ * Histogram of pairs of nodes that share common neighbors. The i-th element of this array
+ * accumulates the number of node pairs that share i neighbors.
+ */
+ private long[] sharedNeighborsHist;
+
+ /**
+ * Round doubles in attributes to <code>roundingDigits</code> decimals after the point.
+ */
+ private int roundingDigits;
+
+ /**
+ * Set of visited nodes.
+ * <p>
+ * This set is used exclusively by the method {@link #computeSPandSN(Node)}.
+ * </p>
+ */
+ private final Set<Node> visited;
+
+ /**
+ * Flag indicating if node(edge) betweenness and stress should be computed. It is set to false if the
+ * number of shortest paths exceeds the maximum long value.
+ */
+ private boolean computeNB;
+
+ /**
+ * Map of all nodes with their respective node betweenness information, which stores information
+ * needed for the node betweenness calculation.
+ */
+ private Map<Node, NodeBetweenInfo> nodeBetweenness;
+
+ /**
+ * Map of all nodes with their respective edge betweenness.
+ */
+ private Map<Edge, Double> edgeBetweenness;
+
+ /**
+ * Map of all nodes with their respective stress, i.e. number of shortest paths passing through
+ * a node.
+ */
+ private Map<Node, Long> stress;
+
+ private int nodeCount;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/AnalysisError.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/AnalysisError.java
new file mode 100644
index 0000000..5c4add8
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/AnalysisError.java
@@ -0,0 +1,81 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.data;
+
+/**
+ * Enumeration on possible errors which can occur on a single network analysis during batch processing.
+ *
+ * @author Nadezhda Doncheva
+ */
+public enum AnalysisError {
+
+ /**
+ * Output (.netstats) file could not be created.
+ */
+ OUTPUT_NOT_CREATED,
+
+ /**
+ * I/O error has occurred while writing to the netstats file.
+ */
+ OUTPUT_IO_ERROR,
+
+ /**
+ * Exception has occurred during computation of topological parameters.
+ */
+ INTERNAL_ERROR,
+
+ /**
+ * Network with no nodes loaded.
+ */
+ NETWORK_EMPTY,
+
+ /**
+ * Network file is invalid.
+ */
+ NETWORK_FILE_INVALID,
+
+ /**
+ * Network file could not be opened.
+ */
+ NETWORK_NOT_OPENED;
+
+ /**
+ * Gets the message explaining the occurred <code>aError</code> to the user.
+ *
+ * @param aError Error occurred during batch analysis.
+ * @return Message for the user explaining the occurred error.
+ */
+ public static String getMessage(AnalysisError aError) {
+ switch (aError) {
+ case OUTPUT_NOT_CREATED:
+ return Messages.SM_OUTPUTNOTCREATED;
+ case OUTPUT_IO_ERROR:
+ return Messages.SM_OUTPUTIOERROR;
+ case INTERNAL_ERROR:
+ return Messages.SM_INTERNALERROR;
+ case NETWORK_EMPTY:
+ return Messages.SM_NETWORKEMPTY;
+ case NETWORK_FILE_INVALID:
+ return Messages.SM_NETWORKFILEINVALID;
+ case NETWORK_NOT_OPENED:
+ return Messages.SM_NETWORKNOTOPENED;
+ default:
+ return Messages.SM_UNKNOWNERROR;
+ }
+ }
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/ArrayUtils.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/ArrayUtils.java
new file mode 100644
index 0000000..92a74f9
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/ArrayUtils.java
@@ -0,0 +1,208 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.data;
+
+import java.awt.geom.Point2D;
+
+/**
+ * Utility class providing helper methods for manipulation of arrays.
+ *
+ * @author Yassen Assenov
+ */
+public abstract class ArrayUtils {
+
+ /**
+ * Stores the coordinates of the given points in separate arrays.
+ *
+ * @param aPoints Array of points from which coordinate values are to be read.
+ * @param aX Array to store the values of the <i>x</i> coordinates of the points. The length of
+ * this array must be at least the length of <code>aPoints</code>.
+ * @param aY Array to store the values of the <i>y</i> coordinates of the points. The length of
+ * this array must be at least the length of <code>aPoints</code>.
+ *
+ * @throws ArrayIndexOutOfBoundsException If the length of <code>aX</code> or of
+ * <code>aY</code> is smaller than the length of <code>aPoints</code>.
+ * @throws NullPointerException If any of the parameters is <code>null</code>.
+ */
+ public static void coordinateSplit(Point2D.Double[] aPoints, double[] aX, double[] aY) {
+ final int count = aPoints.length;
+ if (aX.length < count || aY.length < count) {
+ throw new ArrayIndexOutOfBoundsException(count);
+ }
+ for (int i = 0; i < count; ++i) {
+ final Point2D.Double point = aPoints[i];
+ aX[i] = point.x;
+ aY[i] = point.y;
+ }
+ }
+
+ /**
+ * Applies natural logarithm to the coordinate values of all numbers in the given array.
+ *
+ * @param aPoints Array of points to which logarithm is to be applied.
+ * @param aModifyOriginal Flag indicating if the original array (<code>aPoints</code>)
+ * should be modified. If this parameter is <code>true</code>, the coordinates of the
+ * points in <code>aPoints</code> are modified to contain the logarithms of the
+ * original coordinate values. If this parameter is <code>false</code>, the logarithms
+ * of the point coordinates are stored in a newly created array.
+ * @return If <code>aModifyOriginal</code> is <code>false</code>, newly created array in
+ * which the <code>i</code>-th element is a point having as coordinates the natural
+ * logarithm of the coordinates of <code>aPoints[i]</code>. If
+ * <code>aModifyOriginal</code> is <code>false</code>, the returned value is (the
+ * modified) <code>aPoints</code>.
+ *
+ * @throws NullPointerException If <code>aPoints</code> is <code>null</code>.
+ */
+ public static Point2D.Double[] log(Point2D.Double[] aPoints, boolean aModifyOriginal) {
+ final int pointCount = aPoints.length;
+ final Point2D.Double[] result = aModifyOriginal ? aPoints : new Point2D.Double[pointCount];
+ for (int i = 0; i < pointCount; ++i) {
+ final Point2D.Double p = aPoints[i];
+ if (aModifyOriginal) {
+ p.x = Math.log(p.x);
+ p.y = Math.log(p.y);
+ } else {
+ result[i] = new Point2D.Double(Math.log(p.x), Math.log(p.y));
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Applies natural logarithm to all numbers in the given array.
+ *
+ * @param aPoints Array of numbers to which logarithm is to be applied.
+ * @param aModifyOriginal Flag indicating if the original array (<code>aPoints</code>)
+ * should be modified. If this parameter is <code>true</code>, the values of
+ * <code>aPoints</code> are modified to contain the logarithms of the original values.
+ * If this parameter is <code>false</code>, the logarithms of the elements of
+ * <code>aPoints</code> are stored in a newly created array.
+ * @return If <code>aModifyOriginal</code> is <code>false</code>, newly created array in
+ * which the <code>i</code>-th element contains the natural logarithm of
+ * <code>aPoints[i]</code>. If <code>aModifyOriginal</code> is <code>false</code>,
+ * the returned value is (the modified) <code>aPoints</code>.
+ *
+ * @throws NullPointerException If <code>aPoints</code> is <code>null</code>.
+ */
+ public static double[] log(double[] aPoints, boolean aModifyOriginal) {
+ final int pointCount = aPoints.length;
+ final double[] result = aModifyOriginal ? aPoints : new double[pointCount];
+ for (int i = 0; i < pointCount; ++i) {
+ result[i] = Math.log(aPoints[i]);
+ }
+ return result;
+ }
+
+ /**
+ * Computes the sum of all values in the given array.
+ *
+ * @param aArray Array of numbers.
+ * @return Sum of all values in <code>aArray</code>; <code>0</code> if <code>aArray</code>
+ * is empty.
+ *
+ * @throws NullPointerException If <code>aArray</code> is <code>null</code>.
+ */
+ public static double sum(double[] aArray) {
+ double result = 0;
+ for (final double a : aArray) {
+ result += a;
+ }
+ return result;
+ }
+
+ /**
+ * Computes the arithmetic mean of the values in the given array.
+ *
+ * @param aArray Array of numbers.
+ * @return Mean of all values in <code>aArray</code>; <code>0</code> if <code>aArray</code>
+ * is empty.
+ *
+ * @throws NullPointerException If <code>aArray</code> is <code>null</code>.
+ */
+ public static double mean(double[] aArray) {
+ return sum(aArray) / aArray.length;
+ }
+
+ /**
+ * Computes the sum of the multiplications of the given arrays.
+ *
+ * @param aArray1 First array of numbers.
+ * @param aArray2 Second array of numbers.
+ *
+ * @return Sum of the multiplicated pairs of the elements of <code>aArray1</code> and
+ * <code>aArray2</code> :
+ * <code>aArray1[0] * aArray2[0] + aArray1[1] * aArray2[1] + ...</code>.
+ *
+ */
+ public static double sumMult(double[] aArray1, double[] aArray2) {
+ double result = 0;
+ for (int i = 0; i < aArray1.length; ++i) {
+ result += aArray1[i] * aArray2[i];
+ }
+ return result;
+ }
+
+ /**
+ * Computes the sum of the squares all elements in the given array.
+ *
+ * @param aArray Array of numbers.
+ * @return Sum of the squares of all elements of <code>aArray</code>.
+ */
+ public static double sumSquares(double[] aArray) {
+ double result = 0;
+ for (final double a : aArray) {
+ result += a * a;
+ }
+ return result;
+ }
+
+ /**
+ * Finds the minimum and maximum values for <i>x</i> and <i>y</i> coordinates in the given
+ * array of points.
+ *
+ * @param aPoints Array of two-dimensional points to be traversed.
+ * @param aMin Point to store the minimum values for <i>x</i> and <i>y</i> coordinates. If
+ * <code>aPoints</code> is an empty array, the value of this parameter remains
+ * unmodified.
+ * @param aMax Point to store the maximum values for <i>x</i> and <i>y</i> coordinates. If
+ * <code>aPoints</code> is an empty array, the value of this parameter remains
+ * unmodified.
+ *
+ * @throws NullPointerException If <code>aPoints</code> is <code>null</code>, or if
+ * <code>aPoints</code> is non-empty and any of the other parameters is
+ * <code>null</code>.
+ */
+ public static void minMax(Point2D.Double[] aPoints, Point2D.Double aMin, Point2D.Double aMax) {
+ if (aPoints.length > 0) {
+ aMin.x = aMax.x = aPoints[0].x;
+ aMin.y = aMax.y = aPoints[0].y;
+ for (final Point2D.Double point : aPoints) {
+ if (point.x < aMin.x) {
+ aMin.x = point.x;
+ } else if (point.x > aMax.x) {
+ aMax.x = point.x;
+ }
+ if (point.y < aMin.y) {
+ aMin.y = point.y;
+ } else if (point.y > aMax.y) {
+ aMax.y = point.y;
+ }
+ }
+ }
+ }
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/CCInfo.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/CCInfo.java
new file mode 100644
index 0000000..5a8b252
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/CCInfo.java
@@ -0,0 +1,67 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.data;
+
+import giny.model.Node;
+
+/**
+ * Immutable storage of information on a connected component.
+ *
+ * @author Yassen Assenov
+ */
+public class CCInfo {
+
+ /**
+ * Initializes a new instance of <code>CCInfo</code>.
+ *
+ * @param aSize Size of the connected component (number of nodes).
+ * @param aNode One of the nodes in the component.
+ */
+ public CCInfo(int aSize, Node aNode) {
+ size = aSize;
+ node = aNode;
+ }
+
+ /**
+ * Gets the size of the connected component.
+ *
+ * @return Number of nodes in the connected component.
+ */
+ public int getSize() {
+ return size;
+ }
+
+ /**
+ * Gets a node from the connected component.
+ *
+ * @return Node belonging to this connected component.
+ */
+ public Node getNode() {
+ return node;
+ }
+
+ /**
+ * Number of nodes in the connected component.
+ */
+ private int size;
+
+ /**
+ * One of the nodes in the connected component.
+ */
+ private Node node;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/CCInfoInvComparator.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/CCInfoInvComparator.java
new file mode 100644
index 0000000..8497a4d
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/CCInfoInvComparator.java
@@ -0,0 +1,54 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.data;
+
+import java.util.Comparator;
+
+/**
+ * Comparator of connected components ({@link de.mpg.mpi_inf.bioinf.netanalyzer.data.CCInfo} instances)
+ * based on their sizes.
+ * <p>
+ * Note that this is an inverted comparator - a component of size <code>A</code> is reported as
+ * larger than component of size <code>B</code> if and only if <code>A < B</code>.
+ * </p>
+ *
+ * @author Yassen Assenov
+ */
+public class CCInfoInvComparator implements Comparator<CCInfo> {
+
+ /**
+ * Initializes a new instance of <code>CCInfoComparator</code>.
+ */
+ public CCInfoInvComparator() {
+ // No specific initialization required
+ }
+
+ /**
+ * Compares the two given connected components.
+ *
+ * @param o1 First connected component.
+ * @param o2 Second connected component.
+ * @return An integer which reflects the difference in the sizes of the two connected components -
+ * positive integer if the first component is smaller than the second, negative if the
+ * first component is larger, and <code>0</code> if both components are of the same
+ * size.
+ */
+ public int compare(CCInfo o1, CCInfo o2) {
+ return o2.getSize() - o1.getSize();
+ }
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/ComplexParam.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/ComplexParam.java
new file mode 100644
index 0000000..d989466
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/ComplexParam.java
@@ -0,0 +1,79 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.data;
+
+import java.io.FileWriter;
+import java.io.IOException;
+
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.io.LineReader;
+
+/**
+ * Interface implemented by all types of complex parameters.
+ * <p>
+ * Complex network parameters are immutable collections of numbers. This interface specifies how the
+ * parameters are saved to and loaded from text files. Methods for accessing the underlying data are
+ * specific for every parameter and are not declared in this interface.
+ * </p>
+ *
+ * @author Yassen Assenov
+ */
+public interface ComplexParam {
+
+ /**
+ * String used to separate values on one row when saving complex parameter to a text stream.
+ */
+ public static final String SEP = "\t";
+
+ /**
+ * Regular expression that matches the string {@link #SEP}.
+ * <p>
+ * This regular expression is used when a complex parameter is loaded from a text stream.
+ * </p>
+ */
+ public static final String SEPREGEX = "\\t";
+
+ /**
+ * Parameter types of the {@link #load(String[], LineReader)} method of this interface.
+ */
+ public static final Class<?>[] loadParams = new Class[] { String[].class, LineReader.class };
+
+ /**
+ * Loads the data of the parameter from the given stream.
+ *
+ * @param aArgs Arguments passed to this complex parameter type. These arguments are specific
+ * for every complex parameter; for more information look at the documentation of this
+ * method in the implementing classes.
+ * @param aReader Reader from a text stream. The reader must be open and positioned in the
+ * stream such that the data for the complex parameter follows.
+ * @throws IOException If I/O error occurs.
+ * @throws NumberFormatException If the stream contains invalid data.
+ * @throws NullPointerException If at least one of the parameters is <code>null</code>.
+ */
+ public void load(String[] aArgs, LineReader aReader) throws IOException;
+
+ /**
+ * Saves the data of the parameter in the given file.
+ *
+ * @param aWriter Writer to a text stream. The writer must be open.
+ * @param aSaveArgs Flag indicating if type arguments must also be saved. Setting this parameter
+ * to <code>true</code> enables reconstruction of the complex parameter from the stream
+ * using the {@link #load(String[], LineReader)} method.
+ * @throws IOException If I/O error occurs.
+ */
+ public void save(FileWriter aWriter, boolean aSaveArgs) throws IOException;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/Decorators.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/Decorators.java
new file mode 100644
index 0000000..6bfb873
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/Decorators.java
@@ -0,0 +1,113 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.data;
+
+import java.lang.reflect.Constructor;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+
+import org.jdom.Element;
+
+import de.mpg.mpi_inf.bioinf.netanalyzer.InnerException;
+import de.mpg.mpi_inf.bioinf.netanalyzer.Plugin;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.settings.XMLSerializable;
+import de.mpg.mpi_inf.bioinf.netanalyzer.dec.Decorator;
+
+/**
+ * Storage class for all available chart decorators.
+ *
+ * @author Yassen Assenov
+ */
+public abstract class Decorators {
+
+ /**
+ * Tag name used in XML settings file to identify decorators definition.
+ */
+ public static final String tag = "decorators";
+
+ /**
+ * Gets the decorators for the specified complex parameter.
+ *
+ * @param aParamID ID of complex parameter to get the decorators for.
+ * @return Array of <code>Decorator</code> instances for the given complex parameter;
+ * <code>null</code> if no decorators were registered for it.
+ */
+ public static Decorator[] get(String aParamID) {
+ Decorator[] decs = decorators.get(aParamID);
+ if (decs != null) {
+ final int decCount = decs.length;
+ Decorator[] decsCopy = new Decorator[decCount];
+ for (int i = 0; i < decCount; ++i) {
+ decsCopy[i] = (Decorator) decs[i].clone();
+ }
+ return decsCopy;
+ }
+ return null;
+ }
+
+ /**
+ * Registers the decorators defined in XML file for the specified complex parameter.
+ * <p>
+ * The children of the given XML node define all decorators for the specified complex parameter.
+ * </p>
+ *
+ * @param aParamID ID of complex parameter to receive decorators.
+ * @param aElement Node in XML settings file defining the decorators.
+ */
+ public static void set(String aParamID, Element aElement) {
+ List<?> children = aElement.getChildren();
+ final int size = children.size();
+ Decorator[] decs = new Decorator[size];
+ Iterator<?> it = children.iterator();
+ for (int i = 0; i < size; ++i) {
+ try {
+ Element el = (Element) it.next();
+ Class<?> decClass = Plugin.getDecoratorClass(el.getName());
+ Constructor<?> constr = decClass.getConstructor(XMLSerializable.constructorParams);
+ decs[i] = (Decorator) constr.newInstance(new Object[] { el });
+ } catch (SecurityException ex) {
+ throw ex;
+ } catch (Exception ex) {
+ throw new InnerException(ex);
+ }
+ }
+ set(aParamID, decs);
+ }
+
+ /**
+ * Registers the given decorators for the specified complex parameter.
+ * <p>
+ * Registering an array of decorators overrides all decorators, if any, previously registered
+ * for this complex parameter.
+ * </p>
+ *
+ * @param aParamID ID of complex parameter to receive decorators.
+ * @param aDecs Array of decorators for the given complex parameter. Setting this parameter to
+ * <code>null</code> effectively erases all registered decorators.
+ */
+ private static void set(String aParamID, Decorator[] aDecs) {
+ decorators.put(aParamID, aDecs);
+ }
+
+ /**
+ * Map of all registered decorators.
+ */
+ private static Map<String, Decorator[]> decorators = new HashMap<String, Decorator[]>();
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/DegreeDistribution.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/DegreeDistribution.java
new file mode 100644
index 0000000..210fc1f
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/DegreeDistribution.java
@@ -0,0 +1,133 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.data;
+
+/**
+ * Histogram dataset for degree distribution histograms.
+ *
+ * @author Yassen Assenov
+ */
+public class DegreeDistribution {
+
+ /**
+ * Initializes a new instance of <code>DegreeDistribution</code>.
+ *
+ * @param aNodeCount Number of nodes in the graph. This number is used to predict the maximum degree of a
+ * node.
+ */
+ public DegreeDistribution(int aNodeCount) {
+ int initialSize = Math.max(aNodeCount / 4, MIN_INITIAL_SIZE);
+ distribution = new int[initialSize];
+ maxDegree = 0;
+ }
+
+ /**
+ * Gets the number of nodes of the given degree.
+ *
+ * @param aDegree Degree to find the nodes of.
+ * @return Number of nodes of <code>aDegree</code> added to this instance; <code>0</code> if the
+ * specified degree is a negative number or if no nodes of <code>aDegree</code> were added.
+ */
+ public int getCount(int aDegree) {
+ if (0 <= aDegree && aDegree <= maxDegree) {
+ return distribution[aDegree];
+ }
+ return 0;
+ }
+
+ /**
+ * Gets the maximum degree of a node found in the graph.
+ *
+ * @return Maximum degree of added observation.
+ * @see #addObservation(int)
+ */
+ public int getMaxDegree() {
+ return maxDegree;
+ }
+
+ /**
+ * Creates an <code>IntHistogram</code> complex param instance that contains the data of this
+ * distribution.
+ *
+ * @return Newly created instance of <code>IntHistogram</code> based on this distribution.
+ */
+ public IntHistogram createHistogram() {
+ return new IntHistogram(distribution, 0, maxDegree);
+ }
+
+ /**
+ * Adds a new observation (node degree) to this distribution.
+ *
+ * @param aDegree Degree of node observed.
+ * @throws ArrayIndexOutOfBoundsException If <code>aDegree</code> is a negative number.
+ */
+ public void addObservation(int aDegree) {
+ if (aDegree >= distribution.length) {
+ ensureCapacity(aDegree + 1);
+ }
+ if (maxDegree < aDegree) {
+ maxDegree = aDegree;
+ }
+ distribution[aDegree]++;
+ }
+
+ /**
+ * Enlarges the size of {@link #distribution}, if necessary, to be at least the specified capacity.
+ *
+ * @param aCapacity Desired minimum size of {@link #distribution}.
+ */
+ private void ensureCapacity(int aCapacity) {
+ int currentCap = distribution.length;
+ int newCap = currentCap;
+ while (newCap < aCapacity) {
+ newCap = (int) (GROWTH_FACTOR * newCap);
+ }
+ if (newCap != currentCap) {
+ int[] newDist = new int[newCap];
+ System.arraycopy(distribution, 0, newDist, 0, currentCap);
+ distribution = newDist;
+ }
+ }
+
+ /**
+ * Minimum initial size of {@link #distribution}.
+ */
+ private static final int MIN_INITIAL_SIZE = 256;
+
+ /**
+ * Growth factor of enlarging the size of {@link #distribution}.
+ * <p>
+ * Note that this number must be > 1. The initial size ({@link #MIN_INITIAL_SIZE}) and the growth
+ * factor must be chosen such that:<br/> - The method {@link #ensureCapacity(int)} is called as rarely as
+ * possible, since it is a costly operation.<br/> - The size of {@link #distribution} is not excessively
+ * larger than {@link #maxDegree} for this would result in waste of memory.
+ * </p>
+ */
+ private static final double GROWTH_FACTOR = 2;
+
+ /**
+ * Node degree distribution. The <code>i</code>-th element of this array contains the number of
+ * observations (nodes) with degree <code>i</code>.
+ */
+ private int[] distribution;
+
+ /**
+ * Maximum degree of a node observed.
+ */
+ private int maxDegree;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/IntHistogram.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/IntHistogram.java
new file mode 100644
index 0000000..0d03ea8
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/IntHistogram.java
@@ -0,0 +1,186 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.data;
+
+import java.io.FileWriter;
+import java.io.IOException;
+
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.io.LineReader;
+
+/**
+ * Complex parameter that stores histograms of integer values only.
+ * <p>
+ * An integer histogram shows the number of observations on integer values. Formally, this type of histogram
+ * is characterized by:<br/>
+ * <ul>
+ * <li>every bin is in the form <code>[i; j)</code> where <code>i</code> and <code>j</code> are
+ * integers and <code>i < j</code>.</li>
+ * <li>the value of every bin is an integer.</li>
+ * </ul>
+ * </p>
+ *
+ * @author Yassen Assenov
+ */
+public class IntHistogram implements ComplexParam {
+
+ /**
+ * Initializes a new instance of <code>IntHistogram</code> by loading it from the given stream.
+ *
+ * @param aArgs One-element array representing the argument passed to this type. This argument must be the
+ * <code>String</code> representation of an integer and it specifies the number of bins in this
+ * histogram.
+ * @param aReader Reader from a text stream. The reader must be open and positioned in the stream such
+ * that the data for the histogram follows.
+ *
+ * @throws IOException If I/O error occurs while reading from <code>aReader</code>.
+ *
+ * @see #load(String[], LineReader)
+ * @see ComplexParam#load(String[], LineReader)
+ */
+ public IntHistogram(String[] aArgs, LineReader aReader) throws IOException {
+ load(aArgs, aReader);
+ }
+
+ /**
+ * Initializes a new instance of <code>IntHistogram</code> as a subset of the given histogram.
+ *
+ * @param aBins Bins of the source histogram.
+ * @param aFromIndex Index of first bin to be included in the histogram.
+ * @param aToIndex Index of last bin to be included in the histogram.
+ * @throws ArrayIndexOutOfBoundsException If one of the following is <code>true</code>:
+ * <ul>
+ * <li><code>aBins.length</code> < <code>2</code></li>
+ * <li><code>aBins[0].length</code> ≠ <code>aBins[1].length</code></li>
+ * <li><code>aFromIndex</code> ∉ [<code>0</code>; <code>aBins[0].length</code>)</li>
+ * <li><code>aToIndex</code> ∉ [<code>0</code>; <code>aBins[0].length</code>)</li>
+ * <li><code>aFromIndex</code> > <code>aToIndex</code></li>
+ * </ul>
+ */
+ public IntHistogram(int[][] aBins, int aFromIndex, int aToIndex) {
+ if (aBins[0].length != aBins[1].length || aFromIndex > aToIndex) {
+ throw new ArrayIndexOutOfBoundsException();
+ }
+ final int binCount = aToIndex - aFromIndex + 1;
+ bins = new int[2][binCount];
+ for (int i = 0; i < binCount; ++i) {
+ bins[0][i] = aBins[0][i + aFromIndex];
+ bins[1][i] = aBins[1][i + aFromIndex];
+ }
+ }
+
+ /**
+ * Initializes a new instance of <code>IntHistogram</code> based on the given observations.
+ *
+ * @param aData Array of observations. The <code>i</code>-th element of this array contains the number
+ * of observations for <code>[i; i + 1)</code>.
+ * @param aFromIndex Index of the array to be considered a starting index.
+ * @param aToIndex Index of the array to be considered last index; the observation at
+ * <code>aToIndex</code> (the value of <code>aData[aToIndex]</code>) is also included in the
+ * histogram.
+ * @throws ArrayIndexOutOfBoundsException If one of the following is <code>true</code>:
+ * <ul>
+ * <li><code>aFromIndex</code> ∉ [<code>0</code>; <code>aData.length</code>)</li>
+ * <li><code>aToIndex</code> ∉ [<code>0</code>; <code>aData.length</code>)</li>
+ * <li><code>aFromIndex</code> > <code>aToIndex</code></li>
+ * </ul>
+ */
+ public IntHistogram(int[] aData, int aFromIndex, int aToIndex) {
+ if (aFromIndex > aToIndex) {
+ throw new ArrayIndexOutOfBoundsException();
+ }
+ final int binCount = aToIndex - aFromIndex + 1;
+ bins = new int[2][binCount];
+ for (int i = 0; i < binCount; ++i) {
+ bins[0][i] = i + aFromIndex;
+ bins[1][i] = aData[i + aFromIndex];
+ }
+ }
+
+ /**
+ * Gets the number of bins in this histogram.
+ *
+ * @return Number of bins in this histogram.
+ */
+ public int getBinCount() {
+ return bins[0].length;
+ }
+
+ /**
+ * Gets the range of observation values for this histogram.
+ *
+ * @return Array of two elements - the minimum and the maximum value of observations. This is the left end
+ * of the interval for the first bin and the right end of the interval for last bin, as described
+ * in the description of this class.
+ */
+ public int[] getObservedRange() {
+ return new int[] { bins[0][0], bins[0][bins[0].length - 1] };
+ }
+
+ /**
+ * Gets the bins of this histogram.
+ *
+ * @return Bins of this histogram in the form of a table of two rows.
+ */
+ public int[][] getBins() {
+ return bins;
+ }
+
+ /**
+ * Loads the data of the histogram from the given stream.
+ *
+ * @param aArgs One-element array representing the argument passed to this type. This argument must be the
+ * <code>String</code> representation of an integer and it specifies the number of bins in this
+ * histogram.
+ * @param aReader Reader from a text stream. The reader must be open and positioned in the stream such
+ * that the data for the histogram follows.
+ *
+ * @throws IOException If I/O error occurs.
+ * @throws NumberFormatException If the stream contains invalid data.
+ * @throws NullPointerException If at least one of the parameters is <code>null</code>.
+ * @throws ArrayIndexOutOfBoundsException If an empty array is specified for <code>aArgs</code>.
+ */
+ public void load(String[] aArgs, LineReader aReader) throws IOException {
+ final int binCount = Integer.parseInt(aArgs[0]);
+ bins = new int[2][binCount];
+ for (int i = 0; i < binCount; ++i) {
+ String[] values = aReader.readLine().split(SEPREGEX);
+ bins[0][i] = Integer.parseInt(values[0]);
+ bins[1][i] = Integer.parseInt(values[1]);
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see de.mpg.mpi_inf.bioinf.netanalyzer.data.ComplexParam#save(java.io.FileWriter)
+ */
+ public void save(FileWriter aWriter, boolean aSaveArgs) throws IOException {
+ final int binCount = bins[0].length;
+ if (aSaveArgs) {
+ aWriter.write(String.valueOf(binCount) + "\n");
+ }
+ for (int i = 0; i < binCount; ++i) {
+ aWriter.write(String.valueOf(bins[0][i]) + SEP + String.valueOf(bins[1][i]) + "\n");
+ }
+ }
+
+ /**
+ * Histogram values in the form of a table of 2 rows.
+ */
+ private int[][] bins;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/IntRange.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/IntRange.java
new file mode 100644
index 0000000..5df145f
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/IntRange.java
@@ -0,0 +1,112 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.data;
+
+/**
+ * Integer range.
+ *
+ * @author Yassen Assenov
+ */
+public final class IntRange {
+
+ /**
+ * Initializes a new instance of <code>IntRange</code>.
+ *
+ * @param aMin Minimum value in the integer range.
+ * @param aMax Maximum value in the integer range.
+ */
+ public IntRange(Integer aMin, Integer aMax) {
+ min = aMin;
+ max = aMax;
+ }
+
+ /**
+ * Gets the maximum value of this integer range.
+ *
+ * @return Maximum value of the range; <code>null</code> if no maximum value is present.
+ */
+ public Integer getMax() {
+ return max;
+ }
+
+ /**
+ * Gets the minimum value of this integer range.
+ *
+ * @return Minimum value of the range; <code>null</code> if no minimum value is present.
+ */
+ public Integer getMin() {
+ return min;
+ }
+
+ /**
+ * Checks if a maximum value for this range is defined.
+ * <p>
+ * This is a convenience method only. Calling this method is equivalent to calling:<br/>
+ * <code>getMax() != null</code>
+ * </p>
+ *
+ * @return <code>true</code> if this range has a maximum value; <code>false</code> otherwise.
+ */
+ public boolean hasMax() {
+ return max != null;
+ }
+
+ /**
+ * Checks if a minimum value for this range is defined.
+ * <p>
+ * This is a convenience method only. Calling this method is equivalent to calling:<br/>
+ * <code>getMin() != null</code>
+ * </p>
+ *
+ * @return <code>true</code> if this range has a minimum value; <code>false</code> otherwise.
+ */
+ public boolean hasMin() {
+ return min != null;
+ }
+
+ /**
+ * Checks if this range is fully defined, that is, if it minimum and maximum value are defined.
+ *
+ * @return <code>true</code> if this range has a minimum and a maximum value; <code>false</code>
+ * otherwise.
+ */
+ public boolean isFullyDefined() {
+ return max != null && min != null;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.lang.Object#toString()
+ */
+ @Override
+ public String toString() {
+ return "[" + (min != null ? String.valueOf(min) : "") + ", "
+ + (max != null ? String.valueOf(max) : "") + "]";
+ }
+
+ /**
+ * Maximum value of the range.
+ */
+ private Integer max;
+
+ /**
+ * Minimum value of the range.
+ */
+ private Integer min;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/Interpretations.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/Interpretations.java
new file mode 100644
index 0000000..1ebf4b5
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/Interpretations.java
@@ -0,0 +1,41 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.data;
+
+/**
+ * Enumeration on which interpretations to be applied for each network during batch processing.
+ *
+ * @author Yassen Assenov
+ */
+public enum Interpretations {
+
+ /**
+ * Apply all possible interpretations.
+ */
+ ALL,
+
+ /**
+ * Apply only interpretations that treat the networks as directed.
+ */
+ DIRECTED,
+
+ /**
+ * Apply only interpretations that treat the networks as undirected.
+ */
+ UNDIRECTED
+}
\ No newline at end of file
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/LogBinDistribution.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/LogBinDistribution.java
new file mode 100644
index 0000000..631f97c
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/LogBinDistribution.java
@@ -0,0 +1,151 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.data;
+
+import java.awt.geom.Point2D;
+
+import de.mpg.mpi_inf.bioinf.netanalyzer.ui.charts.MyLogarithmicAxis;
+
+/**
+ * Histogram dataset which puts the observations in log bins (bins of exponentially growing size).
+ *
+ * @author Yassen Assenov
+ * @author Nadezhda Doncheva
+ */
+public class LogBinDistribution {
+
+ /**
+ * Initializes a new instance of <code>LogBinDistribution</code>.
+ *
+ */
+ public LogBinDistribution() {
+ bins = new long[2][INITIAL_SIZE];
+ bins[0][0] = 0;
+ for (int i = 1, power = 1; i < INITIAL_SIZE; ++i, power *= LOGBASE) {
+ bins[0][i] = power;
+ }
+ maxObservation = 0;
+ }
+
+ /**
+ * Gets the maximum value for an observation added to the distribution.
+ *
+ * @return Maximum added observation.
+ * @see #addObservation(long)
+ */
+ public long getMaxObservation() {
+ return maxObservation;
+ }
+
+ /**
+ * Creates an <code>LongHistogram</code> complex parameter instance that contains the data of this
+ * distribution.
+ *
+ * @return Newly created instance of <code>LongHistogram</code> based on this distribution.
+ */
+ public LongHistogram createHistogram() {
+ return new LongHistogram(bins, 0, getBinIndex(maxObservation));
+ }
+
+ /**
+ * Creates an <code>Points2D</code> complex parameter instance that contains the data of this
+ * distribution.
+ *
+ * @return Newly created instance of <code>Points2D</code> based on this distribution.
+ */
+ public Points2D createPoints2D() {
+ final int size = getBinIndex(maxObservation) + 1;
+ final Point2D.Double[] points = new Point2D.Double[size];
+ for (int i = 0; i < size; ++i) {
+ points[i] = new Point2D.Double(bins[0][i], bins[1][i]);
+ }
+ return new Points2D(points);
+ }
+
+ /**
+ * Adds a new observation to this distribution.
+ *
+ * @param aObservation Observed value to be added.
+ */
+ public void addObservation(long aObservation) {
+ final int binIndex = getBinIndex(aObservation);
+ if (binIndex >= bins[0].length) {
+ ensureCapacity(binIndex + 1);
+ }
+ if (maxObservation < aObservation) {
+ maxObservation = aObservation;
+ }
+ bins[1][binIndex]++;
+ }
+
+ /**
+ * Enlarges the size of {@link #bins}, if necessary, to be at least the specified capacity.
+ *
+ * @param aCapacity Desired minimum size of {@link #bins}.
+ */
+ private void ensureCapacity(long aCapacity) {
+ int currentCap = bins[0].length;
+ int newCap = currentCap;
+ while (newCap < aCapacity) {
+ newCap += 2;
+ }
+ if (newCap != currentCap) {
+ long[][] newDist = new long[2][newCap];
+ System.arraycopy(bins[0], 0, newDist[0], 0, currentCap);
+ System.arraycopy(bins[1], 0, newDist[1], 0, currentCap);
+ bins = newDist;
+ for (int i = currentCap; i < newCap; ++i) {
+ bins[0][i] = bins[0][i - 1] * (int)LOGBASE;
+ }
+ }
+ }
+
+ /**
+ * Gets the bin to which the given value should be assigned.
+ *
+ * @param aObservation Value to be assigned to a bin.
+ * @return Zero-based index of the bin to which <code>aObservation</code> belongs.
+ */
+ private static int getBinIndex(long aObservation) {
+ return aObservation != 0 ? (int) (Math.log(aObservation) / Math.log(LOGBASE)) + 1 : 0;
+ }
+
+ /**
+ * Initial size of {@link #bins}.
+ */
+ private static final int INITIAL_SIZE = 8;
+
+ /**
+ * Base of the logarithmic function applied in binning.
+ */
+ private static final double LOGBASE = MyLogarithmicAxis.LOGBASE;
+
+ /**
+ * Bins in an long distribution in the form of two arrays. The <code>i</code>-th element of the
+ * first array contains the left end of the <code>i</code>-th bin: <code>0</code> for
+ * <code>i = 0</code> and <code>{@link #LOGBASE}<sup>i - 1</sup></code> for <code>i > 0</code>.
+ * The <code>i</code>-th element of the second array contains the number of observations (nodes) with
+ * values assigned to the <code>i</code>-th bin.
+ */
+ private long[][] bins;
+
+ /**
+ * Maximum observation of a node.
+ */
+ private long maxObservation;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/LongHistogram.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/LongHistogram.java
new file mode 100644
index 0000000..01928ba
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/LongHistogram.java
@@ -0,0 +1,191 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.data;
+
+import java.io.FileWriter;
+import java.io.IOException;
+
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.io.LineReader;
+
+/**
+ * Complex parameter that stores histograms of long values only.
+ * <p>
+ * A long histogram shows the number of observations on long values. Formally, this type of
+ * histogram is characterized by:<br/>
+ * <ul>
+ * <li>every bin is in the form <code>[i; j)</code> where <code>i</code> and <code>j</code>
+ * are longs and <code>i < j</code>.</li>
+ * <li>the value of every bin is a long.</li>
+ * </ul>
+ * </p>
+ *
+ * @author Yassen Assenov
+ * @author Sven-Eric Schelhorn
+ */
+public class LongHistogram
+ implements ComplexParam {
+
+ /**
+ * Initializes a new instance of <code>LongHistogram</code> by loading it from the given
+ * stream.
+ *
+ * @param aArgs One-element array representing the argument passed to this type. This argument
+ * must be the <code>String</code> representation of an integer and it specifies the
+ * number of bins in this histogram.
+ * @param aReader Reader from a text stream. The reader must be open and positioned in the
+ * stream such that the data for the histogram follows.
+ *
+ * @throws IOException If I/O error occurs while reading from <code>aReader</code>.
+ *
+ * @see #load(String[], LineReader)
+ * @see ComplexParam#load(String[], LineReader)
+ */
+ public LongHistogram(String[] aArgs, LineReader aReader)
+ throws IOException {
+ load(aArgs, aReader);
+ }
+
+ /**
+ * Initializes a new instance of <code>LongHistogram</code> as a subset of the given histogram.
+ *
+ * @param aBins Bins of the source histogram.
+ * @param aFromIndex Index of first bin to be included in the histogram.
+ * @param aToIndex Index of last bin to be included in the histogram.
+ * @throws ArrayIndexOutOfBoundsException If one of the following is <code>true</code>:
+ * <ul>
+ * <li><code>aBins.length</code> < <code>2</code></li>
+ * <li><code>aBins[0].length</code> ≠ <code>aBins[1].length</code></li>
+ * <li><code>aFromIndex</code> ∉ [<code>0</code>;
+ * <code>aBins[0].length</code>)</li>
+ * <li><code>aToIndex</code> ∉ [<code>0</code>;
+ * <code>aBins[0].length</code>)</li>
+ * <li><code>aFromIndex</code> > <code>aToIndex</code></li>
+ * </ul>
+ */
+ public LongHistogram(long[][] aBins, int aFromIndex, int aToIndex) {
+ if (aBins[0].length != aBins[1].length || aFromIndex > aToIndex) {
+ throw new ArrayIndexOutOfBoundsException();
+ }
+ final int binCount = aToIndex - aFromIndex + 1;
+ bins = new long[2][binCount];
+ for (int i = 0; i < binCount; ++i) {
+ bins[0][i] = aBins[0][i + aFromIndex];
+ bins[1][i] = aBins[1][i + aFromIndex];
+ }
+ }
+
+ /**
+ * Initializes a new instance of <code>LongHistogram</code> based on the given observations.
+ *
+ * @param aData Array of observations. The <code>i</code>-th element of this array contains
+ * the number of observations for <code>[i; i + 1)</code>.
+ * @param aFromIndex Index of the array to be considered a starting index.
+ * @param aToIndex Index of the array to be considered last index; the observation at
+ * <code>aToIndex</code> (the value of <code>aData[aToIndex]</code>) is also included
+ * in the histogram.
+ * @throws ArrayIndexOutOfBoundsException If one of the following is <code>true</code>:
+ * <ul>
+ * <li><code>aFromIndex</code> ∉ [<code>0</code>; <code>aData.length</code>)</li>
+ * <li><code>aToIndex</code> ∉ [<code>0</code>; <code>aData.length</code>)</li>
+ * <li><code>aFromIndex</code> > <code>aToIndex</code></li>
+ * </ul>
+ */
+ public LongHistogram(long[] aData, int aFromIndex, int aToIndex) {
+ if (aFromIndex > aToIndex) {
+ throw new ArrayIndexOutOfBoundsException();
+ }
+ final int binCount = aToIndex - aFromIndex + 1;
+ bins = new long[2][binCount];
+ for (int i = 0; i < binCount; ++i) {
+ bins[0][i] = i + aFromIndex;
+ bins[1][i] = aData[i + aFromIndex];
+ }
+ }
+
+ /**
+ * Gets the number of bins in this histogram.
+ *
+ * @return Number of bins in this histogram.
+ */
+ public int getBinCount() {
+ return bins[0].length;
+ }
+
+ /**
+ * Gets the range of observation values for this histogram.
+ *
+ * @return Array of two elements - the minimum and the maximum value of observations. This is the
+ * left end of the interval for the first bin and the right end of the interval for last
+ * bin, as described in the description of this class.
+ */
+ public long[] getObservedRange() {
+ return new long[] { bins[0][0], bins[0][bins[0].length - 1] };
+ }
+
+ /**
+ * Gets the bins of this histogram.
+ *
+ * @return Bins of this histogram in the form of a table of two rows.
+ */
+ public long[][] getBins() {
+ return bins;
+ }
+
+ /**
+ * Loads the data of the histogram from the given stream.
+ *
+ * @param aArgs One-element array representing the argument passed to this type. This argument
+ * must be the <code>String</code> representation of an integer and it specifies the
+ * number of bins in this histogram.
+ * @param aReader Reader from a text stream. The reader must be open and positioned in the
+ * stream such that the data for the histogram follows.
+ * @throws IOException If I/O error occurs.
+ * @throws NumberFormatException If the stream contains invalid data.
+ * @throws NullPointerException If at least one of the parameters is <code>null</code>.
+ * @throws ArrayIndexOutOfBoundsException If an empty array is specified for <code>aArgs</code>.
+ */
+ public void load(String[] aArgs, LineReader aReader) throws IOException {
+ final int binCount = Integer.parseInt(aArgs[0]);
+ bins = new long[2][binCount];
+ for (int i = 0; i < binCount; ++i) {
+ String[] values = aReader.readLine().split(SEPREGEX);
+ bins[0][i] = Integer.parseInt(values[0]);
+ bins[1][i] = Integer.parseInt(values[1]);
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see de.mpg.mpi_inf.bioinf.netanalyzer.data.ComplexParam#save(java.io.FileWriter)
+ */
+ public void save(FileWriter aWriter, boolean aSaveArgs) throws IOException {
+ final int binCount = bins[0].length;
+ if (aSaveArgs) {
+ aWriter.write(String.valueOf(binCount) + "\n");
+ }
+ for (int i = 0; i < binCount; ++i) {
+ aWriter.write(String.valueOf(bins[0][i]) + SEP + String.valueOf(bins[1][i]) + "\n");
+ }
+ }
+
+ /**
+ * Histogram values in the form of a table of 2 rows.
+ */
+ private long[][] bins;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/Messages.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/Messages.java
new file mode 100644
index 0000000..3486be5
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/Messages.java
@@ -0,0 +1,792 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.data;
+
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Map;
+import java.util.Set;
+
+/**
+ * Storage class for human-readable messages.
+ *
+ * @author Yassen Assenov
+ * @author Mario Albrecht
+ * @author Sven-Eric Schelhorn
+ * @author Nadezhda Doncheva
+ */
+public abstract class Messages {
+
+ /**
+ * Simple parameter names in the form of a hash map, the keys being the IDs and the values - the textual
+ * <code>String</code>s in human readable form.
+ */
+ private static final Map<String, String> simpleParams;
+
+ /**
+ * Node attributes names for parameters computed by NetworkAnalyzer for directed network interpretations.
+ */
+ private static final Set<String> dirNodeAttributes;
+
+ /**
+ * Node attributes names for parameters computed by NetworkAnalyzer for undirected network
+ * interpretations.
+ */
+ private static final Set<String> undirNodeAttributes;
+
+ /**
+ * Node attribute names in the form of a hash map, the keys being the IDs and the values - the textual
+ * <code>String</code>s in human readable form.
+ */
+ private static final Map<String, String> nodeAttributes;
+
+ /**
+ * Edge attribute names in the form of a hash map, the keys being the IDs and the values - the textual
+ * <code>String</code>s in human readable form.
+ */
+ private static final Map<String, String> edgeAttributes;
+
+ static {
+ simpleParams = new HashMap<String, String>(16);
+ simpleParams.put("time", "Analysis time (sec)");
+ simpleParams.put("nodeCount", "Number of nodes");
+ simpleParams.put("edgeCount", "Number of edges");
+ simpleParams.put("density", "Network density");
+ simpleParams.put("heterogeneity", "Network heterogeneity");
+ simpleParams.put("centralization", "Network centralization");
+ simpleParams.put("avNeighbors", "Avg. number of neighbors");
+ simpleParams.put("ncc", "Connected components");
+ simpleParams.put("connPairs", "Shortest paths");
+ simpleParams.put("diameter", "Network diameter");
+ simpleParams.put("radius", "Network radius");
+ simpleParams.put("avSpl", "Characteristic path length");
+ simpleParams.put("cc", "Clustering coefficient");
+ simpleParams.put("nsl", "Number of self-loops");
+ simpleParams.put("mnp", "Multi-edge node pairs");
+ simpleParams.put("usn", "Isolated nodes");
+
+ nodeAttributes = new HashMap<String, String>(32);
+ nodeAttributes.put("spl", "Eccentricity");
+ nodeAttributes.put("cco", "ClusteringCoefficient");
+ nodeAttributes.put("tco", "TopologicalCoefficient");
+ nodeAttributes.put("apl", "AverageShortestPathLength");
+ nodeAttributes.put("clc", "ClosenessCentrality");
+ nodeAttributes.put("isn", "IsSingleNode");
+ nodeAttributes.put("nco", "NeighborhoodConnectivity");
+ nodeAttributes.put("nde", "NumberOfDirectedEdges");
+ nodeAttributes.put("nue", "NumberOfUndirectedEdges");
+ nodeAttributes.put("slo", "SelfLoops");
+ nodeAttributes.put("deg", "Degree");
+ nodeAttributes.put("pmn", "PartnerOfMultiEdgedNodePairs");
+ nodeAttributes.put("din", "Indegree");
+ nodeAttributes.put("dou", "Outdegree");
+ nodeAttributes.put("dal", "EdgeCount");
+ nodeAttributes.put("nbt", "BetweennessCentrality");
+ nodeAttributes.put("rad", "Radiality");
+ nodeAttributes.put("stress", "Stress");
+
+ dirNodeAttributes = new HashSet<String>(16);
+ dirNodeAttributes.add("Eccentricity");
+ dirNodeAttributes.add("AverageShortestPathLength");
+ dirNodeAttributes.add("ClosenessCentrality");
+ dirNodeAttributes.add("ClusteringCoefficient");
+ dirNodeAttributes.add("Indegree");
+ dirNodeAttributes.add("Outdegree");
+ dirNodeAttributes.add("EdgeCount");
+ dirNodeAttributes.add("IsSingleNode");
+ dirNodeAttributes.add("SelfLoops");
+ dirNodeAttributes.add("PartnerOfMultiEdgedNodePairs");
+ dirNodeAttributes.add("NeighborhoodConnectivity");
+ dirNodeAttributes.add("BetweennessCentrality");
+ dirNodeAttributes.add("Stress");
+
+ undirNodeAttributes = new HashSet<String>(16);
+ undirNodeAttributes.add("Degree");
+ undirNodeAttributes.add("NeighborhoodConnectivity");
+ undirNodeAttributes.add("ClusteringCoefficient");
+ undirNodeAttributes.add("TopologicalCoefficient");
+ undirNodeAttributes.add("Eccentricity");
+ undirNodeAttributes.add("AverageShortestPathLength");
+ undirNodeAttributes.add("ClosenessCentrality");
+ undirNodeAttributes.add("BetweennessCentrality");
+ undirNodeAttributes.add("Stress");
+ undirNodeAttributes.add("Radiality");
+ undirNodeAttributes.add("SelfLoops");
+ undirNodeAttributes.add("IsSingleNode");
+ undirNodeAttributes.add("NumberOfUndirectedEdges");
+ undirNodeAttributes.add("NumberOfDirectedEdges");
+ undirNodeAttributes.add("PartnerOfMultiEdgedNodePairs");
+
+ edgeAttributes = new HashMap<String, String>(2);
+ edgeAttributes.put("ebt", "EdgeBetweenness");
+ edgeAttributes.put("dpe", "NumberOfUnderlyingEdges");
+ }
+
+ // Dialog titles
+
+ public static String DT_ABOUT = "About NetworkAnalyzer";
+
+ public static String DT_ANALYZING = "Analyzing network - please wait...";
+
+ public static String DT_ANALYSIS = "Network Analysis of ";
+
+ public static String DT_ANALYSISNEEDED = "NetworkAnalyzer - Analysis";
+
+ public static String DT_BATCHANALYSIS = "Batch Analysis";
+
+ public static String DT_BATCHRESULTS = "Batch Analysis - Results";
+
+ public static String DT_BATCHSETTINGS = "Batch Analysis - Select Directories";
+
+ public static String DT_CLOSEWARN = "Warning - Unsaved Data";
+
+ public static String DT_COMPNETWORKS = "Compare Networks";
+
+ public static String DT_CONNCOMP = "Connected Components";
+
+ public static String DT_DIRECTED = " (directed)";
+
+ public static String DT_FILEEXISTS = "Warning - File Exists";
+
+ public static String DT_FILTERDATA = "Filter Displayed Data";
+
+ public static String DT_FIT = "NetworkAnalyzer - Fitting Function";
+
+ public static String DT_FITTED = "NetworkAnalyzer - Fitted Function";
+
+ public static String DT_GUIERROR = "NetworkAnalyzer - Error";
+
+ public static String DT_INFO = "NetworkAnalyzer - Information";
+
+ public static String DT_IOERROR = "NetworkAnalyzer - Error";
+
+ public static String DT_INTERPRETATION = "NetworkAnalyzer - Network Interpretation";
+
+ public static String DT_MAPPARAM = "NetworkAnalyzer - Visualize Parameters";
+
+ public static String DT_PLOTPARAM = "NetworkAnalyzer - Plot Parameters";
+
+ public static String DT_REMDUPEDGES = "Remove Duplicated Edges";
+
+ public static String DT_REMOVEFILTER = "Restore Range";
+
+ public static String DT_REMSELFLOOPS = "Remove Self-Loops";
+
+ public static String DT_SAVECHART = "Save Chart to File";
+
+ public static String DT_SECERROR = "NetworkAnalyzer - Error";
+
+ public static String DT_SETTINGS = "NetworkAnalyzer Settings";
+
+ public static String DT_UNDIRECTED = " (undirected)";
+
+ public static String DT_WRONGDATA = "NetworkAnalyzer - Error";
+
+ // Short informative messages to the user
+
+ public static String SM_AMBIGUOUSFTYPE = constructLabel("File type not specified!",
+ "When giving file name, please also select one of the supported file types.");
+
+ public static String SM_ANALYSISC = "Analysis cancelled.";
+
+ public static String SM_ATTRIBUTESNOTSAVED = " ERROR: Could not save node attributes to a file!";
+
+ public static String SM_BADINPUT = constructLabel("Selected input directory is not acceptable.",
+ "Please make sure you have selected an existing non-empty directory.");
+
+ public static String SM_BADOUTPUT = constructLabel("Selected output directory is not acceptable.",
+ "Please make sure you have selected an existing empty directory<br>"
+ + "for which NetworkAnalyzer has write permissions.");
+
+ public static String SM_CHOOSEINTERPR = "Please choose an interpretation for the edges.";
+
+ public static String SM_CLOSEWARN = "<html>You have not saved the network statistics. They will be lost when you close this window.<br>Are you sure you want to close the window?";
+
+ public static String SM_CONNECTED = " is connected, i.e. has a single connected component.";
+
+ public static String SM_CREATEVIEW = constructLabel("No nodes are selected.",
+ "Please create a network view and select nodes.");
+
+ public static String SM_DEFFAILED = "An I/O error occurred while saving the settings as default.";
+
+ public static String SM_DONE = "done";
+
+ public static String SM_FILEEXISTS = "<html>The specified file already exists.<br>Overwrite?";
+
+ public static String SM_FITLINE = "<html>A line in the form y = a + b x was fitted.</html>";
+
+ public static String SM_FITLINEERROR = "Could not fit line to the points.";
+
+ public static String SM_FITLINENODATA = "There are not enough data points to fit a line!";
+
+ public static String SM_FITNONPOSITIVE = "<html>Some data points have non-positive coordinates.<br>Only points with positive coordinates are included in the fit.</html>";
+
+ public static String SM_FITPL = "<html>A power law of the form y = ax<sup>b</sup> was fitted.</html>";
+
+ public static String SM_FITPLERROR = "Could not fit power law to the points.";
+
+ public static String SM_FITPLNODATA = "There are not enough data points to fit a power law!";
+
+ public static String SM_GUIERROR = "An error occurred while initializing the window.";
+
+ public static String SM_IERROR = "An error occurred while opening or reading from the file.";
+
+ public static String SM_NOINPUTFILES = "No network files found in the specified input directory.";
+
+ public static String SM_INTERNALERROR = "Internal error occurred during computation.";
+
+ public static String SM_LOADING = "Loading ";
+
+ public static String SM_LOADNET = "Please load a network first.";
+
+ public static String SM_LOADPARAMETERS = constructLabel(
+ "Storing node and edge parameters as attributes is disabled.",
+ "You need to compute node or edge attributes.<br>"
+ + "Do you want to enable storing parameters and run NetworkAnalyzer on the selected network?");
+
+ public static String SM_LOADSETTINGSFAIL1 = "NetworkAnalyzer: Loading settings from ";
+
+ public static String SM_LOADSETTINGSFAIL2 = " failed.";
+
+ public static String SM_LOGERROR = "Network Analyzer - Internal Error";
+
+ public static String SM_NETWORKEMPTY = "Network contains no nodes.";
+
+ public static String SM_NETMODIFICATION = "<html>Please note that this option effectively modifies the selected network(s)<br>"
+ + "and the operations performed cannot be undone.</html>";
+
+ public static String SM_NETWORKFILEINVALID = "Network file is invalid.";
+
+ public static String SM_NETWORKNOTOPENED = "Could not load network from file.";
+
+ public static String SM_OERROR = "An error occurred while creating or writing to the file.";
+
+ public static String SM_OUTPUTIOERROR = "Could not save network statistics file.";
+
+ public static String SM_OUTPUTNOTCREATED = "Could not write to output directory.";
+
+ public static String SM_READERROR = "\n ERROR: Could not create network from network file!\n";
+
+ public static String SM_REMDUPEDGES = " duplicated edge(s) removed from ";
+
+ public static String SM_REMOVEFILTER = "Do you want to restore the whole range for this topological parameter?";
+
+ public static String SM_REMSELFLOOPS = " self-loop(s) removed from ";
+
+ public static String SM_RESULTSSAVED = " Results saved to network statistics file.";
+
+ public static String SM_RUNNETWORKANALYZER = constructLabel(
+ "No node or edge attributes are computed for this network.",
+ "You need to run NetworkAnalyzer to compute node or edge attributes.<br>"
+ + "Do you want to run NetworkAnalyzer on the selected network?");
+
+ public static String SM_SAVEERROR = " ERROR: Could not save results to network statistics file!";
+
+ public static String SM_SAVESETERROR = constructLabel(
+ "NetworkAnalyzer cannot save plugin's settings due to security restrictions.",
+ "Changes in the settings will be lost after closing Cytoscape.");
+
+ public static String SM_SECERROR1 = "NetworkAnalyzer could not be initialized due to security restrictions.";
+
+ public static String SM_SECERROR2 = "The operation was stopped due to security restrictions.";
+
+ public static String SM_SELECTNET = "Please select a network from the list of loaded networks.";
+
+ public static String SM_SELECTNODES = constructLabel("No nodes are selected.",
+ "Please select nodes from the network of interest.");
+
+ public static String SM_SELECTONENET = "Please select a single network from the list of loaded networks.";
+
+ public static String SM_VISUALIZEERROR = "Parameters cannot be visualized because the network was modified or deleted.";
+
+ public static String SM_UNKNOWNERROR = "Unknown error occurred.";
+
+ public static String SM_UNLOADING = "Unloading ";
+
+ public static final String SM_WRONGDATAFILE = "The file specified is not recognized as Network Statistics file.";
+
+ // Menu items added in Cytoscape
+
+ public static String AC_ABOUT = "About NetworkAnalyzer";
+
+ public static String AC_ANALYZE = "Analyze Network";
+
+ public static String AC_ANALYZE_SUBSET = "Analyze Subset of Nodes";
+
+ public static String AC_BATCH_ANALYSIS = "Batch Analysis";
+
+ public static String AC_COMPARE = "Compare Two Networks";
+
+ public static String AC_CONNCOMP = "Connected Components";
+
+ public static String AC_LOAD = "Load Network Statistics";
+
+ /**
+ * Name of Submenu in Cytoscape's menubar, where network analysis actions are added.
+ */
+ public static String AC_MENU_ANALYSIS = "Network Analysis";
+
+ /**
+ * Name of Submenu in Cytoscape's menubar, where network modification actions are added.
+ */
+ public static String AC_MENU_MODIFICATION = "Network Modifications";
+
+ public static String AC_PLOTPARAM = "Plot Parameters";
+
+ public static String AC_SETTINGS = "NetworkAnalyzer Settings";
+
+ public static String AC_REMDUPEDGES = "Remove Duplicated Edges";
+
+ public static String AC_REMSELFLOOPS = "Remove Self-Loops";
+
+ public static String AC_MAPPARAM = "Visualize Parameters";
+
+ // Labels of items in dialogs
+
+ public static String DI_ANALYZINGINTERP1 = " Analyzing interpretation ";
+
+ public static String DI_ANALYZINGINTERP2 = " of ";
+
+ public static String DI_APPLY = "Apply";
+
+ public static String DI_APPLYVS = "Apply visual styles to ";
+
+ public static String DI_ATTRIBUTE1 = "Attribute 1";
+
+ public static String DI_ATTRIBUTE2 = "Attribute 2";
+
+ public static String DI_AUTOANALYSIS1 = "Performing automatic analysis of ";
+
+ public static String DI_AUTOANALYSIS2 = " networks.";
+
+ public static String DI_AXES = "Axes";
+
+ public static String DI_BATCHREPORT = " networks were analyzed. The results are shown below.";
+
+ public static String DI_CANCEL = "Cancel";
+
+ public static String DI_CHARTSETTINGS = "Chart Settings";
+
+ public static String DI_CCOF = "Connected Components of ";
+
+ public static String DI_CDIFF = "Compute Differences";
+
+ public static String DI_CLOSE = "Close";
+
+ public static String DI_CNETWORKS = "Please select two networks from the list below:";
+
+ public static String DI_CINTERSECTION = "Compute Intersection";
+
+ public static String DI_CONNCOMP = "List of connected components";
+
+ public static String DI_COMP = "Component";
+
+ public static String DI_CORR = "Correlation = ";
+
+ public static String DI_CUNION = "Compute Union";
+
+ public static String DI_EXPORTCHART = "Export Chart";
+
+ public static String DI_EXPORTDATA = "Export Data";
+
+ public static String DI_EXTR = "Extract";
+
+ public static String DI_EXTRCOMP = "Extract Component";
+
+ public static String DI_EXTRCOMPLONG = "Extract the selected connected component into a new network named:";
+
+ public static String DI_FILTERDATA = "Change Range";
+
+ public static String DI_FITLINE = "Fit Line";
+
+ public static String DI_FITPL = "Fit Power Law";
+
+ public static String DI_GENERAL = "General";
+
+ public static String DI_GRID = "Gridlines";
+
+ public static String DI_HEIGHT = "Height:";
+
+ public static String DI_HELP = "Help";
+
+ public static String DI_HISTOGRAM = "Histogram";
+
+ public static String DI_IGNOREEDGEDIR = "Ignore edge direction";
+
+ public static String DI_IMAGESIZE = "Image Size";
+
+ public static String DI_INPUTDIR = "Input Directory";
+
+ public static String DI_INTERPR = "Interpretation";
+
+ public static String DI_INTERPRS = "Network Interpretations";
+
+ public static String DI_INTERPR_ALL = "Apply all possible interpretations.";
+
+ public static String DI_INTERPR_DIRECTED = "Consider networks as directed.";
+
+ public static String DI_INTERPR_UNDIRECTED = "Consider networks as undirected.";
+
+ public static String DI_LOWTOBRIGHT = "Low values to bright colors";
+
+ public static String DI_LOWTODARK = "Low values to dark colors";
+
+ public static String DI_LOWTOLARGE = "Low values to large sizes";
+
+ public static String DI_LOWTOSMALL = "Low values to small sizes";
+
+ public static String DI_MAPEDGECOLOR = "Map edge color to:";
+
+ public static String DI_MAPEDGESIZE = "Map edge size to:";
+
+ public static String DI_MAPNODECOLOR = "Map node color to:";
+
+ public static String DI_MAPNODESIZE = "Map node size to:";
+
+ public static String DI_MAPTYPE = "Mapping type:";
+
+ public static String DI_NETFILE = "Network";
+
+ public static String DI_NETSTATSFILE = "Network Statistics File";
+
+ public static String DI_NODEATTR_SAVE = "<html><i>Node parameters stored as node attributes will be written to tab-delimited files. You can disable<br />"
+ + "this option in the NetworkAnalyzer Settings dialog.</i></html>";
+
+ public static String DI_NODEATTR_SAVENOT = "<html><i>Node parameters are not stored as node attributes and will not be saved to files. You can enable<br />"
+ + "this option in the NetworkAnalyzer Settings dialog.</i></html>";
+
+ public static String DI_OK = "OK";
+
+ public static String DI_OUTPUTDIR = "Output Directory";
+
+ public static String DI_PIXELS = "pixels";
+
+ public static String DI_PLOT1 = "Plot node attributes of ";
+
+ public static String DI_PLOT2 = " against each other.";
+
+ public static String DI_REMDUPEDGES = "Remove duplicated edges from the following networks:";
+
+ public static String DI_REMOVE = "Remove";
+
+ public static String DI_REMOVEFILTER = "Restore Range";
+
+ public static String DI_REMOVELINE = "Remove Fitted Line";
+
+ public static String DI_REMOVEPL = "Remove Power Law";
+
+ public static String DI_REMOVESL = "Remove self-loops from the following networks:";
+
+ public static String DI_RESULTS = "Show Results";
+
+ public static String DI_RSQUARED = "R-squared = ";
+
+ public static String DI_SAVE = "Save";
+
+ public static String DI_SAVEDEFAULT = "Save as Default";
+
+ public static String DI_SAVENUMBEREDGES = "Create an edge attribute with number of duplicated edges";
+
+ public static String DI_SAVESTATISTICS = "Save Statistics";
+
+ public static String DI_SCATTER = "Scatter Plot";
+
+ public static String DI_SELECTCOLOR = "Select Color";
+
+ public static String DI_SELECTDIR = "Select Directory";
+
+ public static String DI_SENDREPORT = "Send Report";
+
+ public static String DI_SHOWHIST = "Display as Histogram";
+
+ public static String DI_SHOWSCAT = "Display as Scatter Plot";
+
+ public static String DI_SIMPLEPARAMS = "Simple Parameters";
+
+ public static String DI_STARTANALYSIS = "Start Analysis >";
+
+ public static String DI_UNDEF = "Undefined";
+
+ public static String DI_VIEWENLARGED = "Enlarge Chart";
+
+ public static String DI_VISUALIZEPARAMETER = "Visualize Parameters";
+
+ public static String DI_WIDTH = "Width:";
+
+ // Messages related to the network interpretation
+
+ public static String NI_COMBPAIRED = "Combine paired edges.";
+
+ public static String NI_DIRPAIRED = "The network contains only directed edges and they are paired.";
+
+ public static String NI_DIRUNPAIRED = "The network contains only directed edges and they are not paired.";
+
+ public static String NI_FORCETU = "It will be treated as undirected.";
+
+ public static String NI_IGNOREUSL = "Ignore undirected self-loops.";
+
+ public static String NI_LOOPSBOTH = "It also contains both directed and undirected self-loops.";
+
+ public static String NI_LOOPSDIR = "It also contains directed self-loops.";
+
+ public static String NI_LOOPSUNDIR = "It also contains undirected self-loops.";
+
+ public static String NI_MIXED = "The network contains both directed and undirected edges.";
+
+ public static String NI_NOTCOMB = "Do not combine paired edges.";
+
+ public static String NI_PAIRED = "The directed edges are paired.";
+
+ public static String NI_R_DIR = "Directed.";
+
+ public static String NI_R_DIRL = " Undirected self-loops were ignored.";
+
+ public static String NI_R_UNDIR = "Undirected.";
+
+ public static String NI_R_UNDIRC = " Paired edges were combined.";
+
+ public static String NI_TD = "Treat the network as directed.";
+
+ public static String NI_TU = "Treat the network as undirected.";
+
+ public static String NI_UNDIR = "The network contains only undirected edges.";
+
+ public static String NI_UNPAIRED = "The directed edges are not paired.";
+
+ // Labels to display in settings dialogs
+
+ public static final String SET_PREFIX = "SET_";
+
+ public static String SET_BARCOLOR = "Color of bars";
+
+ public static String SET_BACKGROUNDCOLOR = "Background color for parameter visualization";
+
+ public static String SET_BGCOLOR = "Background color";
+
+ public static String SET_BRIGHTCOLOR = "Bright color to map parameters";
+
+ public static String SET_COLORBUTTON = "Click to Change";
+
+ public static String SET_DARKCOLOR = "Dark color to map parameters";
+
+ public static String SET_DOMAINAXISLABEL = "Label of category axis";
+
+ public static String SET_EXPANDABLE = "Use expandable dialog interface for the display of network statistics";
+
+ public static String SET_GRIDLINESCOLOR = "Color of gridlines";
+
+ public static String SET_HELPURLSTRING = "Location of the help documents";
+
+ public static String SET_HORIZONTALGRIDLINES = "Show horizontal gridlines";
+
+ public static String SET_LOGARITHMICDOMAINAXIS = "Set domain (horizontal) axis to logarithmic";
+
+ public static String SET_LOGARITHMICRANGEAXIS = "Set range (vertical) axis to logarithmic";
+
+ public static String SET_MIDDLECOLOR = "Middle color to map parameters";
+
+ public static String SET_OUTLINE = "Show outline of bars";
+
+ public static String SET_POINTCOLOR = "Color of points";
+
+ public static String SET_POINTSHAPE = "Shape of points";
+
+ public static String SET_RANGEAXISLABEL = "Label of value axis";
+
+ public static String SET_SCIRCLE = "circle";
+
+ public static String SET_SCROSS = "cross";
+
+ public static String SET_SFILLCIRCLE = "filled circle";
+
+ public static String SET_SFILLSQUARE = "filled square";
+
+ public static String SET_SPOINT = "point";
+
+ public static String SET_SSQUARE = "square";
+
+ public static String SET_TITLE = "Chart title";
+
+ public static String SET_USEEDGEATTRIBUTES = "Store edge parameters in edge attributes";
+
+ public static String SET_USENODEATTRIBUTES = "Store node parameters in node attributes";
+
+ public static String SET_VERTICALGRIDLINES = "Show vertical gridlines";
+
+ // Tool tip texts
+
+ public static String TT_AXESSETTINGS = "Axes-related Settings";
+
+ public static String TT_CHARTSETTINGS = "Adjust labels, colors and other visual attributes of the chart";
+
+ public static String TT_CLICK2EXPAND = "Click to expand";
+
+ public static String TT_CLICK2HIDE = "Click to hide";
+
+ public static String TT_FILTERDATA = "Display part of the data in the chart";
+
+ public static String TT_FITLINE = "<html>Fit a line.</html>";
+
+ public static String TT_FITLOGLINE = "<html>Fit a line after computing logarithms of all positive values.</html>";
+
+ public static String TT_FITPL = "<html>Fit a law of the form y = ax<sup>b</sup>.</html>";
+
+ public static String TT_GENSETTINGS = "General Settings";
+
+ public static String TT_GRIDSETTINGS = "Gridlines-related Settings";
+
+ public static String TT_HISTSETTINGS = "Histogram Settings";
+
+ public static String TT_IGNOREEDGEDIR = "Treat all edges as undirected";
+
+ public static String TT_ONLHELP = "Visit the online help of NetworkAnalyzer";
+
+ public static String TT_REMOVEFILTER = "Display the whole data in the chart";
+
+ public static String TT_SAVECHART = "Save the chart as an image";
+
+ public static String TT_SAVEDATA = "Save chart data to a text file";
+
+ public static String TT_SAVENUMBEREDGES = "<html>Edge attribute represents the number of duplicated edges<br>"
+ + "between two nodes, i.e. 1 means no duplicated edges.</html>";
+
+ public static String TT_SCATSETTINGS = "Scatter Plot Settings";
+
+ public static String TT_VIEWENLARGED = "View the chart in a separate window";
+
+ /**
+ * Checks if a description for a given simple parameter is present.
+ *
+ * @param aParamID
+ * ID of the simple parameter to inspect.
+ * @return <code>true</code> if a human-readable description for the specified simple parameter exists;
+ * <code>false</code> otherwise.
+ */
+ public static boolean containsSimpleParam(String aParamID) {
+ return simpleParams.containsKey(aParamID);
+ }
+
+ /**
+ * Gets simple parameter description by the specified ID.
+ *
+ * @param aParamID
+ * ID of the simple parameter to get.
+ * @return Human-readable description mapped to the given <code>aParamID</code>; <code>null</code> if such
+ * a description does not exist.
+ */
+ public static String get(String aParamID) {
+ return simpleParams.get(aParamID);
+ }
+
+ /**
+ * Gets attribute name for the specified ID.
+ *
+ * @param aID
+ * ID of attribute name.
+ * @return Attribute name in human-readable form that is mapped to the given ID; <code>null</code> if such
+ * a name does not exist.
+ */
+ public static String getAttr(String aID) {
+ String attribute = nodeAttributes.get(aID);
+ if (attribute == null) {
+ attribute = edgeAttributes.get(aID);
+ }
+ return attribute;
+ }
+
+ /**
+ * Gets all possible computed edge attributes.
+ *
+ * @return Set of the names of all edge attributes which are computed by NetworkAnalyzer.
+ */
+ public static Set<String> getEdgeAttributes() {
+ return new HashSet<String>(edgeAttributes.values());
+ }
+
+ /**
+ * Gets all possible computed node attributes.
+ *
+ * @return Set of the names of all node attributes which are computed by NetworkAnalyzer.
+ */
+ public static Set<String> getNodeAttributes() {
+ return new HashSet<String>(nodeAttributes.values());
+ }
+
+ /**
+ * Gets node attributes computed for directed network interpretation.
+ *
+ * @return Set of the names of all node attributes which are computed by NetworkAnalyzer for a directed
+ * network interpretation.
+ */
+ public static Set<String> getDirNodeAttributes() {
+ return new HashSet<String>(dirNodeAttributes);
+ }
+
+ /**
+ * Gets node attributes computed for undirected network interpretation.
+ *
+ * @return Set of the names of all node attributes which are computed by NetworkAnalyzer for an undirected
+ * network interpretation.
+ */
+ public static Set<String> getUndirNodeAttributes() {
+ return new HashSet<String>(undirNodeAttributes);
+ }
+
+ /**
+ * Constructs a two-line message for an HTML label.
+ *
+ * @param aLine1
+ * First line of the text in the label. This text will be bold.
+ * @param aLine2
+ * Second line of the text in the label.
+ * @return String of newly constructed HTML message.
+ */
+ public static String constructLabel(String aLine1, String aLine2) {
+ return "<html><b>" + aLine1 + "</b><br><br>" + aLine2 + "</html>";
+ }
+
+ /**
+ * Constructs a multi-line report for an HTML label.
+ *
+ * @param aValues
+ * Values to be reported, one value per network.
+ * @param aAction
+ * Action performed on each network.
+ * @param aNetworks
+ * Networks on which the action was performed.
+ * @return String of newly constructed HTML report.
+ *
+ * @throws IllegalArgumentException
+ * If the length of <code>aValues</code> is different than the length of
+ * <code>aNetworks</code>.
+ * @throws NullPointerException
+ * If ant of the given parameters is <code>null</code>.
+ */
+ public static String constructReport(int[] aValues, String aAction, String[] aNetworks) {
+ if (aValues.length != aNetworks.length) {
+ throw new IllegalArgumentException();
+ }
+ final StringBuilder answer = new StringBuilder("<html>");
+ for (int i = 0; i < aValues.length; ++i) {
+ answer.append(String.valueOf(aValues[i]) + Messages.SM_REMDUPEDGES + aNetworks[i]);
+ answer.append("<br>");
+ }
+ answer.append("</html>");
+ return answer.toString();
+ }
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/MutInteger.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/MutInteger.java
new file mode 100644
index 0000000..99fd6a3
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/MutInteger.java
@@ -0,0 +1,47 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.data;
+
+/**
+ * Mutable integer.
+ *
+ * @author Yassen Assenov
+ */
+public class MutInteger {
+
+ /**
+ * Initializes a new instance of <code>MutInteger</code> and sets the value to <code>0</code>.
+ */
+ public MutInteger() {
+ value = 0;
+ }
+
+ /**
+ * Initializes a new instance of <code>MutInteger</code>.
+ *
+ * @param aValue Initial value of this integer.
+ */
+ public MutInteger(int aValue) {
+ value = aValue;
+ }
+
+ /**
+ * Value of this mutable integer.
+ */
+ public int value;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/NetworkAnalysisReport.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/NetworkAnalysisReport.java
new file mode 100644
index 0000000..d22deee
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/NetworkAnalysisReport.java
@@ -0,0 +1,121 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.data;
+
+import java.io.File;
+
+/**
+ * Storage class for the success or failure of the analysis of a single network.
+ *
+ * @author Yassen Assenov
+ */
+public class NetworkAnalysisReport {
+
+ /**
+ * Initializes a new instance of <code>NetworkAnalysisReport</code> for a successful analysis.
+ *
+ * @param aNetwork
+ * File from which the network was loaded.
+ * @param aInterpr
+ * Network interpretation applied.
+ * @param aResultFile
+ * File in which the analysis results were stored.
+ */
+ public NetworkAnalysisReport(File aNetwork, NetworkInterpretation aInterpr, File aResultFile) {
+ error = null;
+ network = aNetwork;
+ interpretation = aInterpr;
+ resultFile = aResultFile;
+ }
+
+ /**
+ * Initializes a new instance of <code>NetworkAnalysisReport</code> for failed analysis.
+ *
+ * @param aNetwork
+ * File from which the network was loaded (or attempted to be loaded).
+ * @param aInterpr
+ * Network interpretation applied. Set this to <code>null</code> if the network could not be
+ * loaded.
+ * @param aError
+ * Reason for the failure of the analysis.
+ */
+ public NetworkAnalysisReport(File aNetwork, NetworkInterpretation aInterpr, AnalysisError aError) {
+ error = aError;
+ network = aNetwork;
+ interpretation = aInterpr;
+ resultFile = null;
+ }
+
+ /**
+ * Gets the error that has occurred during the analysis.
+ *
+ * @return Reason for the failure of the analysis; <code>null</code> if the analysis has completed
+ * successfully.
+ */
+ public AnalysisError getError() {
+ return error;
+ }
+
+ /**
+ * Gets the network file.
+ *
+ * @return File from which the network was loaded (or attempted to be loaded).
+ */
+ public File getNetwork() {
+ return network;
+ }
+
+ /**
+ * Gets the network interpretation.
+ *
+ * @return Network interpretation applied; <code>null</code> if the network could not be loaded.
+ */
+ public NetworkInterpretation getInterpretation() {
+ return interpretation;
+ }
+
+ /**
+ * Gets the analysis results file.
+ *
+ * @return File in which the analysis results were stored; <code>null</code> if the analysis has not
+ * completed successfully.
+ */
+ public File getResultFile() {
+ return resultFile;
+ }
+
+ /**
+ * Reason for the failure of the analysis, if such exists.
+ */
+ private AnalysisError error;
+
+ /**
+ * File from which the network was loaded (or attempted to be loaded).
+ */
+ private File network;
+
+ /**
+ * Network interpretation applied, if any.
+ */
+ private NetworkInterpretation interpretation;
+
+ /**
+ * File in which the analysis results were stored, if such exists.
+ */
+ private File resultFile;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/NetworkInspection.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/NetworkInspection.java
new file mode 100644
index 0000000..506af58
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/NetworkInspection.java
@@ -0,0 +1,90 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.data;
+
+/**
+ * Storage class for results of inspection on the edges in a network.
+ *
+ * @author Yassen Assenov
+ */
+public class NetworkInspection {
+
+ /**
+ * Initializes a new instance of <code>NetworkInspection</code>.
+ */
+ public NetworkInspection() {
+ time = System.currentTimeMillis();
+ dir = false;
+ uniqueDir = false;
+ undir = false;
+ dirLoops = false;
+ undirLoops = false;
+ dupEdges = false;
+ dupDirEdges = false;
+ }
+
+ /**
+ * Stops the timer, indicating the inspection has ended.
+ * <p>
+ * This method must be called exactly once in the lifetime of this instance.
+ * </p>
+ */
+ public void stopTimer() {
+ time = System.currentTimeMillis() - time;
+ }
+
+ /**
+ * Time, in milliseconds, taken for the inspection.
+ */
+ public long time;
+
+ /**
+ * Flag indicating if the network contains directed edge(s).
+ */
+ public boolean dir;
+
+ /**
+ * Flag indicating if the network contains unpaired directed edge(s).
+ */
+ public boolean uniqueDir;
+
+ /**
+ * Flag indicating if the network contains undirected edge(s).
+ */
+ public boolean undir;
+
+ /**
+ * Flag indicating if the network contains directed self-loop(s).
+ */
+ public boolean dirLoops;
+
+ /**
+ * Flag indicating if the network contains undirected self-loop(s).
+ */
+ public boolean undirLoops;
+
+ /**
+ * Flag indicating if the network contains a pair of nodes connected by more than one edge.
+ */
+ public boolean dupEdges;
+
+ /**
+ * Flag indicating if the network contains two or more identical directed edges.
+ */
+ public boolean dupDirEdges;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/NetworkInterpretation.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/NetworkInterpretation.java
new file mode 100644
index 0000000..504c7b2
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/NetworkInterpretation.java
@@ -0,0 +1,194 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.data;
+
+import javax.swing.ImageIcon;
+
+/**
+ * Storage class for information on how to interpret a network.
+ *
+ * @author Yassen Assenov
+ */
+public class NetworkInterpretation {
+
+ /**
+ * Initializes a new instance of <code>NetworkInterpretation</code>.
+ *
+ * @param aIcon
+ * Image showing the state of the network resulting from the interpretation.
+ * @param aMessage
+ * Message describing the network interpretation.
+ * @param aDirected
+ * Flag indicating whether the network should be treated as directed.
+ */
+ public NetworkInterpretation(ImageIcon aIcon, String aMessage, boolean aDirected) {
+ directed = aDirected;
+ ignoreUSL = false;
+ paired = false;
+ icon = aIcon;
+ message = "<html>" + aMessage;
+ }
+
+ /**
+ * Initializes a new instance of <code>NetworkInterpretation</code>.
+ *
+ * @param aIcon
+ * Image showing the state of the network resulting from the interpretation.
+ * @param aDirected
+ * Flag indicating whether the network should be treated as directed.
+ */
+ public NetworkInterpretation(ImageIcon aIcon, boolean aDirected) {
+ icon = aIcon;
+ if (aDirected) {
+ message = "<html>" + Messages.NI_TD;
+ } else {
+ message = "<html>" + Messages.NI_TU;
+ }
+ directed = aDirected;
+ ignoreUSL = false;
+ paired = false;
+ }
+
+ /**
+ * Initializes a new instance of <code>NetworkInterpretation</code>.
+ *
+ * @param aIcon
+ * Image showing the state of the network resulting from the interpretation.
+ * @param aDirected
+ * Flag indicating whether the network should be treated as directed.
+ * @param aAdditional
+ * Flag giving additional information to this interpretation. If <code>aDirected</code> is
+ * <code>true</code>, this flag indicates whether undirected self-loops exist (and must be
+ * ignored). If <code>aDirected</code> is <code>false</code>, this flag indicates whether
+ * directed edges must be paired.
+ */
+ public NetworkInterpretation(ImageIcon aIcon, boolean aDirected, boolean aAdditional) {
+ icon = aIcon;
+ directed = aDirected;
+ if (aDirected) {
+ ignoreUSL = aAdditional;
+ paired = false;
+ if (aAdditional) {
+ message = "<html>" + Messages.NI_IGNOREUSL + "<br>" + Messages.NI_TD;
+ } else {
+ message = "<html>" + Messages.NI_TD;
+ }
+ } else {
+ ignoreUSL = false;
+ paired = aAdditional;
+ if (aAdditional) {
+ message = "<html>" + Messages.NI_COMBPAIRED + "<br>" + Messages.NI_TU;
+ } else {
+ message = "<html>" + Messages.NI_NOTCOMB + "<br>" + Messages.NI_TU;
+ }
+ }
+ }
+
+ /**
+ * Gets the icon of the interpretation results.
+ *
+ * @return Image showing the state of the network resulting from the interpretation.
+ */
+ public ImageIcon getIcon() {
+ return icon;
+ }
+
+ /**
+ * Gets the interpretation suffix.
+ *
+ * @return Interpretation suffix which states if the network is treated as directed or undirected.
+ */
+ public String getInterpretSuffix() {
+ return directed ? Messages.DT_DIRECTED : Messages.DT_UNDIRECTED;
+ }
+
+ /**
+ * Gets the message describing this network interpretation.
+ * <p>
+ * The message always starts with the <code><html></code> tag.
+ * </p>
+ *
+ * @return Message describing this network interpretation in human-readable form.
+ */
+ public String getMessage() {
+ return message;
+ }
+
+ /**
+ * Checks if the network must be considered directed.
+ *
+ * @return <code>true</code> if the network must by interpreted as directed; <code>false</code> if the
+ * network must be interpreted as undirected.
+ */
+ public boolean isDirected() {
+ return directed;
+ }
+
+ /**
+ * Checks if undirected self-loops must be ignored.
+ * <p>
+ * If the network is to be treated as undirected; this method always returns <code>false</code>.
+ * </p>
+ *
+ * @return <code>true</code> if undirected self-loops must be ignored in the analysis; <code>false</code>
+ * otherwise.
+ */
+ public boolean isIgnoreUSL() {
+ return ignoreUSL;
+ }
+
+ /**
+ * Checks if the directed edges are to be paired.
+ *
+ * @return <code>true</code> if every pair of opposite directed edges must be interpreted as a single
+ * undirected edge; <code>false</code> otherwise.
+ */
+ public boolean isPaired() {
+ return paired;
+ }
+
+ /**
+ * Flag indicating whether the network should be treated as directed.
+ */
+ private boolean directed;
+
+ /**
+ * Flag indicating whether undirected self-loops must be ignored in the analysis.
+ */
+ private boolean ignoreUSL;
+
+ /**
+ * Flag indicating whether directed edges should be paired.
+ * <p>
+ * Directed edges may be paired when a network containing directed edges must be treated as undirected. If
+ * this flag is <code>true</code>, every (directed) outgoing edge of a given node is combined with one
+ * opposite (incoming), and thus both edges are counted as one.
+ * </p>
+ */
+ private boolean paired;
+
+ /**
+ * Image showing the state of the network resulting from the interpretation.
+ */
+ private ImageIcon icon;
+
+ /**
+ * Message describing this network interpretation.
+ */
+ private String message;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/NetworkStats.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/NetworkStats.java
new file mode 100644
index 0000000..cd18fab
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/NetworkStats.java
@@ -0,0 +1,287 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.data;
+
+import java.util.HashMap;
+import java.util.Map;
+
+import cytoscape.CyNetwork;
+
+/**
+ * Storage class for network parameters.
+ *
+ * @author Yassen Assenov
+ * @author Sven-Eric Schelhorn
+ * @author Nadezhda Doncheva
+ */
+public class NetworkStats {
+
+ /**
+ * ID of parameter that stores the network title.
+ */
+ public static final String titleParam = "networkTitle";
+
+ /**
+ * List of IDs for parameters that are numbers or <code>String</code>s.
+ * <p>
+ * It is recommended that the parameters are displayed to the user in the order they appear in
+ * this list.
+ * </p>
+ */
+ public static final String[] simpleParams = new String[] {
+ "cc",
+ "ncc",
+ "diameter",
+ "radius",
+ "centralization",
+ "connPairs",
+ "avSpl",
+ "avNeighbors",
+ "nodeCount",
+ "edgeCount",
+ "density",
+ "heterogeneity",
+ "usn",
+ "nsl",
+ "mnp",
+ "time"
+ };
+
+ /**
+ * List of IDs and types for parameters that are datasets.
+ * <p>
+ * It is recommended that the parameters are displayed to the user in the order they appear in
+ * this list.
+ * </p>
+ */
+ public static final String[] complexParams = new String[] {
+ "degreeDist", // undirected
+ "inDegreeDist", // directed
+ "outDegreeDist", // directed
+ "cksDist", // undirected
+ "topCoefs", // undirected
+ "splDist", // undirected
+ "commNeighbors", // undirected
+ "neighborConn", // undirected
+ "allNeighborConn", // directed
+ "inNeighborConn", // directed
+ "outNeighborConn", // directed
+ "nodeBetween", // undirected
+ "closenessCent", // undirected
+ "stressDist" // undirected
+ };
+
+ /**
+ * Initializes a new instance of <code>NetworkStats</code>.
+ */
+ public NetworkStats() {
+ params = new HashMap<String, Object>();
+ networkID = null;
+ }
+
+ /**
+ * Initializes a new instance of <code>NetworkStats</code>.
+ *
+ * @param aNetwork Network, on which parameters will be stored.
+ */
+ public NetworkStats(CyNetwork aNetwork, String aInterpretName) {
+ params = new HashMap<String, Object>();
+ set("networkTitle", aNetwork.getTitle() + aInterpretName);
+ set("nodeCount", new Integer(aNetwork.getNodeCount()));
+ networkID = aNetwork.getIdentifier();
+ }
+
+ /**
+ * Checks if the specified parameter is computed.
+ *
+ * @param aParam ID of parameter.
+ * @return <code>true</code> if the parameter with the specified ID is stored in this instance;
+ * <code>false</code> otherwise.
+ */
+ public boolean contains(String aParam) {
+ return params.containsKey(aParam);
+ }
+
+ /**
+ * Gets the value of the specified parameter.
+ *
+ * @param aParam ID of the parameter to get.
+ * @return Instance of parameter's value; <code>null</code> if such a parameter is not stored.
+ */
+ public Object get(String aParam) {
+ return params.get(aParam);
+ }
+
+ /**
+ * Gets the value of the specified complex parameter.
+ *
+ * @param aParam ID of the complex parameter to get.
+ * @return Parameter's value as a <code>ComplexParam</code>.
+ * @throws ClassCastException If the specified parameter is simple.
+ * @throws NullPointerException If the specified parameter does not exist.
+ */
+ public ComplexParam getComplex(String aParam) {
+ return (ComplexParam) params.get(aParam);
+ }
+
+ /**
+ * Gets the IDs of the computed simple parameters.
+ *
+ * @return Array of IDs of all the simple parameters stored in this instance.
+ */
+ public String[] getComputedSimple() {
+ return getComputed(simpleParams);
+ }
+
+ /**
+ * Gets the IDs of the computed complex parameters.
+ *
+ * @return Array of IDs of all the complex parameters stored in this instance.
+ */
+ public String[] getComputedComplex() {
+ return getComputed(complexParams);
+ }
+
+ /**
+ * Gets the integer value of the specified simple parameter.
+ *
+ * @param aParam ID of the simple parameter to get.
+ * @return Parameter's value as an integer.
+ * @throws ClassCastException If the specified parameter is not an integer.
+ * @throws NullPointerException If the specified parameter does not exist.
+ */
+ public int getInt(String aParam) {
+ return ((Integer) params.get(aParam)).intValue();
+ }
+
+ /**
+ * Gets the integer value of the specified simple parameter.
+ *
+ * @param aParam ID of the simple parameter to get.
+ * @return Parameter's value as a long integer.
+ * @throws ClassCastException If the specified parameter is not a long integer.
+ * @throws NullPointerException If the specified parameter does not exist.
+ */
+ public long getLong(String aParam) {
+ return ((Long) params.get(aParam)).longValue();
+ }
+
+ /**
+ * Gets the title of the analyzed network.
+ *
+ * @return Network title; <code>null</code> if the title is not stored in this instance.
+ */
+ public String getTitle() {
+ return (String) get(NetworkStats.titleParam);
+ }
+
+ /**
+ * Gets the id of the analyzed network.
+ *
+ * @return Network id; <code>null</code> if the id is not stored in this instance.
+ */
+ public String getID() {
+ return networkID;
+ }
+
+ /**
+ * Sets the value of the specified simple parameter.
+ *
+ * @param aParam ID of the parameter to get.
+ * @param aValue Instance of parameter's value.
+ */
+ public void set(String aParam, Object aValue) {
+ params.put(aParam, aValue);
+ }
+
+ /**
+ * Sets the integer value of the specified simple parameter.
+ *
+ * @param aParam ID of the parameter to get.
+ * @param aValue Parameter's value as an integer number.
+ */
+ public void set(String aParam, int aValue) {
+ set(aParam, new Integer(aValue));
+ }
+
+ /**
+ * Sets the integer value of the specified simple parameter.
+ *
+ * @param aParam ID of the parameter to get.
+ * @param aValue Parameter's value as an integer number.
+ */
+ public void set(String aParam, long aValue) {
+ set(aParam, new Long(aValue));
+ }
+
+ /**
+ * Sets the real-number value of the specified simple parameter.
+ *
+ * @param aParam ID of the parameter to get.
+ * @param aValue Parameter's value as a real number.
+ */
+ public void set(String aParam, double aValue) {
+ set(aParam, new Double(aValue));
+ }
+
+ /**
+ * Sets the title of the analyzed network.
+ *
+ * @param aTitle Network title.
+ */
+ public void setTitle(String aTitle) {
+ set(NetworkStats.titleParam, aTitle);
+ }
+
+ /**
+ * Gets the computed parameters among the given IDs.
+ *
+ * @param aIDs Array of IDs of network parameters.
+ * @return Array of those IDs among <code>aIDs</code> that are contained as keys in
+ * {@link #params}.
+ */
+ private String[] getComputed(String[] aIDs) {
+ int size = 0;
+ for (int i = 0; i < aIDs.length; ++i) {
+ if (params.containsKey(aIDs[i])) {
+ size++;
+ }
+ }
+ if (size == aIDs.length) {
+ return aIDs;
+ }
+ String[] computed = new String[size];
+ size = 0;
+ for (int i = 0; i < aIDs.length; ++i) {
+ if (params.containsKey(aIDs[i])) {
+ computed[size++] = aIDs[i];
+ }
+ }
+ return computed;
+ }
+
+ /**
+ * Network parameters in the form of a (ID, value) map.
+ */
+ private Map<String, Object> params;
+
+ /**
+ * Unique network id. Needed for parameter visualization.
+ */
+ private String networkID;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/NetworkStatus.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/NetworkStatus.java
new file mode 100644
index 0000000..6eb8f39
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/NetworkStatus.java
@@ -0,0 +1,436 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.data;
+
+import javax.swing.ImageIcon;
+
+/**
+ * Enumeration on edge construction principles of networks, as well as options (in human readable
+ * form) for interpretations.
+ *
+ * @author Yassen Assenov
+ */
+public class NetworkStatus {
+
+ /**
+ * Images used to depict network statuses.
+ */
+ private static final ImageIcon[] allIcons = new ImageIcon[] { Utils.getImage("00.png", ""),
+ Utils.getImage("01.png", ""), Utils.getImage("02.png", ""), Utils.getImage("03.png", ""),
+ Utils.getImage("04.png", ""), Utils.getImage("05.png", ""), Utils.getImage("06.png", ""),
+ Utils.getImage("07.png", ""), Utils.getImage("08.png", ""), Utils.getImage("09.png", ""),
+ Utils.getImage("10.png", ""), Utils.getImage("11.png", ""), Utils.getImage("12.png", ""),
+ Utils.getImage("13.png", ""), Utils.getImage("14.png", ""), Utils.getImage("15.png", ""),
+ Utils.getImage("16.png", ""), Utils.getImage("17.png", ""), Utils.getImage("18.png", ""),
+ Utils.getImage("19.png", ""), Utils.getImage("20.png", ""), Utils.getImage("21.png", ""),
+ Utils.getImage("22.png", ""), Utils.getImage("23.png", ""), Utils.getImage("24.png", ""),
+ Utils.getImage("25.png", ""), Utils.getImage("26.png", ""), Utils.getImage("27.png", ""),
+ Utils.getImage("28.png", ""), Utils.getImage("29.png", "") };
+
+ /**
+ * HTML tag for line break. Used in generating interpretation descriptions.
+ */
+ private static final String BR = "<br>";
+
+ /**
+ * All possible network interpretations according to the different network statuses.
+ */
+ private static final NetworkInterpretation[] allTrs = new NetworkInterpretation[33];
+
+ static {
+ // dir_paired_n_n :
+ allTrs[0] = new NetworkInterpretation(allIcons[0], true);
+ allTrs[1] = new NetworkInterpretation(allIcons[26], false, true);
+ allTrs[2] = new NetworkInterpretation(allIcons[1], false, false);
+ // dir_paired_s_n :
+ allTrs[3] = new NetworkInterpretation(allIcons[2], true);
+ allTrs[4] = new NetworkInterpretation(allIcons[3], false, true);
+ allTrs[5] = new NetworkInterpretation(allIcons[4], false, false);
+ // dir_paired_n_s :
+ allTrs[6] = new NetworkInterpretation(allIcons[0], true, true);
+ allTrs[7] = new NetworkInterpretation(allIcons[28], false, true);
+ allTrs[8] = new NetworkInterpretation(allIcons[6], false, false);
+ // dir_paired_s_s :
+ allTrs[9] = new NetworkInterpretation(allIcons[2], true, true);
+ allTrs[10] = new NetworkInterpretation(allIcons[8], false, true);
+ allTrs[11] = new NetworkInterpretation(allIcons[9], false, false);
+ // dir_unpaired_n_n :
+ allTrs[12] = new NetworkInterpretation(allIcons[10], true);
+ allTrs[13] = new NetworkInterpretation(allIcons[26], false);
+ // dir_unpaired_s_n :
+ allTrs[14] = new NetworkInterpretation(allIcons[11], true);
+ allTrs[15] = new NetworkInterpretation(allIcons[3], false);
+ // dir_unpaired_n_s :
+ allTrs[16] = new NetworkInterpretation(allIcons[10], true, true);
+ allTrs[17] = new NetworkInterpretation(allIcons[28], false);
+ // dir_unpaired_s_s :
+ allTrs[18] = new NetworkInterpretation(allIcons[11], true, true);
+ allTrs[19] = new NetworkInterpretation(allIcons[8], false);
+ // mixed_paired_n_n :
+ allTrs[20] = new NetworkInterpretation(allIcons[26], false, true);
+ allTrs[21] = new NetworkInterpretation(allIcons[15], false, false);
+ // mixed_paired_s_n :
+ allTrs[22] = new NetworkInterpretation(allIcons[3], false, true);
+ allTrs[23] = new NetworkInterpretation(allIcons[17], false, false);
+ // mixed_paired_n_s :
+ allTrs[24] = new NetworkInterpretation(allIcons[28], false, true);
+ allTrs[25] = new NetworkInterpretation(allIcons[19], false, false);
+ // mixed_paired_s_s :
+ allTrs[26] = new NetworkInterpretation(allIcons[8], false, true);
+ allTrs[27] = new NetworkInterpretation(allIcons[21], false, false);
+ // mixed_unpaired_n_n :
+ allTrs[28] = new NetworkInterpretation(allIcons[26], Messages.NI_FORCETU, false);
+ // mixed_unpaired_s_n :
+ allTrs[29] = new NetworkInterpretation(allIcons[3], Messages.NI_FORCETU, false);
+ // mixed_unpaired_n_s :
+ allTrs[30] = new NetworkInterpretation(allIcons[28], Messages.NI_FORCETU, false);
+ // mixed_unpaired_s_s :
+ allTrs[31] = new NetworkInterpretation(allIcons[8], Messages.NI_FORCETU, false);
+ // undir_n_n :
+ allTrs[32] = new NetworkInterpretation(null, Messages.NI_FORCETU, false);
+ // undir_s_n : allTrs[29]
+ // undir_n_s : allTrs[32]
+ // undir_s_s : allTrs[31]
+ }
+
+ /**
+ * A network containing only directed edges which are paired, no self-loops.
+ */
+ public static final NetworkStatus DIR_PAIRED_N_N = new NetworkStatus(Messages.NI_DIRPAIRED,
+ allIcons[0], allTrs[0], allTrs[1], allTrs[2], 1);
+
+ /**
+ * A network containing only directed edges which are paired, plus directed (paired) self-loops.
+ */
+ public static final NetworkStatus DIR_PAIRED_S_N = new NetworkStatus(Messages.NI_DIRPAIRED + BR
+ + Messages.NI_LOOPSDIR, allIcons[2], allTrs[3], allTrs[4], allTrs[5], 1);
+
+ /**
+ * A network containing only directed edges which are paired, plus undirected self-loops.
+ */
+ public static final NetworkStatus DIR_PAIRED_N_S = new NetworkStatus(Messages.NI_DIRPAIRED + BR
+ + Messages.NI_LOOPSUNDIR, allIcons[5], allTrs[6], allTrs[7], allTrs[8], 1);
+
+ /**
+ * A network containing only directed edges which are paired, plus both directed and undirected
+ * self-loops.
+ */
+ public static final NetworkStatus DIR_PAIRED_S_S = new NetworkStatus(Messages.NI_DIRPAIRED + BR
+ + Messages.NI_LOOPSBOTH, allIcons[7], allTrs[9], allTrs[10], allTrs[11], 1);
+
+ /**
+ * A network containing only directed edges which are not paired, and no self-loops.
+ */
+ public static final NetworkStatus DIR_UNPAIRED_N_N = new NetworkStatus(Messages.NI_DIRUNPAIRED,
+ allIcons[10], allTrs[12], allTrs[13], 1);
+
+ /**
+ * A network containing only directed edges which are not paired, plus directed self-loops.
+ */
+ public static final NetworkStatus DIR_UNPAIRED_S_N = new NetworkStatus(Messages.NI_DIRUNPAIRED
+ + BR + Messages.NI_LOOPSDIR, allIcons[11], allTrs[14], allTrs[15], 1);
+
+ /**
+ * A network containing only directed edges which are not paired, plus undirected self-loops.
+ */
+ public static final NetworkStatus DIR_UNPAIRED_N_S = new NetworkStatus(Messages.NI_DIRUNPAIRED
+ + BR + Messages.NI_LOOPSUNDIR, allIcons[12], allTrs[16], allTrs[17], 1);
+
+ /**
+ * A network containing only directed edges which are not paired, plus both directed and
+ * undirected self-loops.
+ */
+ public static final NetworkStatus DIR_UNPAIRED_S_S = new NetworkStatus(Messages.NI_DIRUNPAIRED
+ + BR + Messages.NI_LOOPSBOTH, allIcons[13], allTrs[18], allTrs[19], 1);
+
+ /**
+ * A network containing both undirected and paired directed edges, no self-loops.
+ */
+ public static final NetworkStatus MIXED_PAIRED_N_N = new NetworkStatus(Messages.NI_MIXED + BR
+ + Messages.NI_PAIRED, allIcons[14], allTrs[20], allTrs[21], 0);
+
+ /**
+ * A network containing both undirected and paired directed edges, plus directed (paired)
+ * self-loops.
+ */
+ public static final NetworkStatus MIXED_PAIRED_S_N = new NetworkStatus(Messages.NI_MIXED + BR
+ + Messages.NI_PAIRED + BR + Messages.NI_LOOPSDIR, allIcons[16], allTrs[22], allTrs[23], 0);
+
+ /**
+ * A network containing both undirected and paired directed edges, plus undirected self-loops.
+ */
+ public static final NetworkStatus MIXED_PAIRED_N_S = new NetworkStatus(Messages.NI_MIXED + BR
+ + Messages.NI_PAIRED + BR + Messages.NI_LOOPSUNDIR, allIcons[18], allTrs[24], allTrs[25], 0);
+
+ /**
+ * A network containing both undirected and paired directed edges, plus both undirected and
+ * paired directed self-loops.
+ */
+ public static final NetworkStatus MIXED_PAIRED_S_S = new NetworkStatus(Messages.NI_MIXED + BR
+ + Messages.NI_UNPAIRED + BR + Messages.NI_LOOPSBOTH, allIcons[20], allTrs[26], allTrs[27],
+ 0);
+
+ /**
+ * A network containing both undirected and unpaired directed edges, no self-loops.
+ */
+ public static final NetworkStatus MIXED_UNPAIRED_N_N = new NetworkStatus(Messages.NI_MIXED + BR
+ + Messages.NI_UNPAIRED, allIcons[22], allTrs[28]);
+
+ /**
+ * A network containing both undirected and unpaired directed edges, plus directed self-loops.
+ */
+ public static final NetworkStatus MIXED_UNPAIRED_S_N = new NetworkStatus(Messages.NI_MIXED + BR
+ + Messages.NI_UNPAIRED + BR + Messages.NI_LOOPSDIR, allIcons[23], allTrs[29]);
+
+ /**
+ * A network containing both undirected and unpaired directed edges, plus undirected self-loops.
+ */
+ public static final NetworkStatus MIXED_UNPAIRED_N_S = new NetworkStatus(Messages.NI_MIXED + BR
+ + Messages.NI_UNPAIRED + BR + Messages.NI_LOOPSUNDIR, allIcons[24], allTrs[30]);
+
+ /**
+ * A network containing both undirected and unpaired directed edges, plus both undirected and
+ * directed self-loops.
+ */
+ public static final NetworkStatus MIXED_UNPAIRED_S_S = new NetworkStatus(Messages.NI_MIXED + BR
+ + Messages.NI_UNPAIRED + BR + Messages.NI_LOOPSBOTH, allIcons[25], allTrs[31]);
+
+ /**
+ * A network containing undirected edges only, and no self-loops.
+ */
+ public static final NetworkStatus UNDIR_N_N = new NetworkStatus(Messages.NI_UNDIR,
+ allIcons[26], allTrs[32]);
+
+ /**
+ * A network containing undirected edges only, plus directed self-loops.
+ */
+ public static final NetworkStatus UNDIR_S_N = new NetworkStatus(Messages.NI_UNDIR + BR
+ + Messages.NI_LOOPSDIR, allIcons[27], allTrs[29]);
+
+ /**
+ * A network containing undirected edges only, plus undirected self-loops.
+ */
+ public static final NetworkStatus UNDIR_N_S = new NetworkStatus(Messages.NI_UNDIR + BR
+ + Messages.NI_LOOPSUNDIR, allIcons[28], allTrs[32]);
+
+ /**
+ * A network containing undirected edges only, plus both undirected and directed self-loops.
+ */
+ public static final NetworkStatus UNDIR_S_S = new NetworkStatus(Messages.NI_UNDIR + BR
+ + Messages.NI_LOOPSBOTH, allIcons[29], allTrs[31]);
+
+ /**
+ * Gets the network status describing the given boolean network parameters.
+ * <p>
+ * Note that this method never returns <code>null</code>. In particular, networks that
+ * contain neither directed, nor undirected edges, are considered undirected.
+ * </p>
+ *
+ * @param aInsp Results of inspection on the edges of a network.
+ * @return The <code>NetworkStatus</code> instance that suits best the specified parameters.
+ */
+ public static NetworkStatus getStatus(NetworkInspection aInsp) {
+ int loops = (aInsp.dirLoops ? 1 : 0) + (aInsp.undirLoops ? 2 : 0);
+ if (aInsp.dir) {
+ if (aInsp.uniqueDir) {
+ if (aInsp.undir) {
+ // Status: mixed unpaired
+ switch (loops) {
+ case 0:
+ return NetworkStatus.MIXED_UNPAIRED_N_N;
+ case 1:
+ return NetworkStatus.MIXED_UNPAIRED_S_N;
+ case 2:
+ return NetworkStatus.MIXED_UNPAIRED_N_S;
+ default:
+ return NetworkStatus.MIXED_UNPAIRED_S_S;
+ }
+ }
+ // Status: directed unpaired
+ switch (loops) {
+ case 0:
+ return NetworkStatus.DIR_UNPAIRED_N_N;
+ case 1:
+ return NetworkStatus.DIR_UNPAIRED_S_N;
+ case 2:
+ return NetworkStatus.DIR_UNPAIRED_N_S;
+ default:
+ return NetworkStatus.DIR_UNPAIRED_S_S;
+ }
+
+ }
+ if (aInsp.undir) {
+ // Status: mixed paired
+ switch (loops) {
+ case 0:
+ return NetworkStatus.MIXED_PAIRED_N_N;
+ case 1:
+ return NetworkStatus.MIXED_PAIRED_S_N;
+ case 2:
+ return NetworkStatus.MIXED_PAIRED_N_S;
+ default:
+ return NetworkStatus.MIXED_PAIRED_S_S;
+ }
+ }
+ // Status: directed paired
+ switch (loops) {
+ case 0:
+ return NetworkStatus.DIR_PAIRED_N_N;
+ case 1:
+ return NetworkStatus.DIR_PAIRED_S_N;
+ case 2:
+ return NetworkStatus.DIR_PAIRED_N_S;
+ default:
+ return NetworkStatus.DIR_PAIRED_S_S;
+ }
+ }
+ // Status: undirected
+ switch (loops) {
+ case 0:
+ return NetworkStatus.UNDIR_N_N;
+ case 1:
+ return NetworkStatus.UNDIR_S_N;
+ case 2:
+ return NetworkStatus.UNDIR_N_S;
+ default:
+ return NetworkStatus.UNDIR_S_S;
+ }
+ }
+
+ /**
+ * Gets the description of this network status.
+ *
+ * @return Description of the network status in human-readable form.
+ */
+ public String getDescription() {
+ return description;
+ }
+
+ /**
+ * Gets the image icon of this network status.
+ *
+ * @return Icon identifying this network status.
+ */
+ public ImageIcon getIcon() {
+ return icon;
+ }
+
+ /**
+ * Gets the interpretations for this status.
+ *
+ * @return Array containing all possible interpretations of this network status.
+ */
+ public NetworkInterpretation[] getInterpretations() {
+ return interprs;
+ }
+
+ /**
+ * Gets the default interpretation index.
+ *
+ * @return Index of the default interpretation for this status.
+ * @see #getInterpretations()
+ */
+ public int getDefaultInterprIndex() {
+ return defaultInterprIndex;
+ }
+
+ /**
+ * Initializes a new instance of <code>NetworkStatus</code> with a unique interpretation.
+ *
+ * @param aDescription Status description in a human-readable format.
+ * @param aIcon Image that schematically represents the status. This should be one of the
+ * elements of {@link #allIcons}.
+ * @param aInterpr The only network interpretation for this status.
+ */
+ private NetworkStatus(String aDescription, ImageIcon aIcon, NetworkInterpretation aInterpr) {
+ this(aDescription, aIcon, new NetworkInterpretation[] { aInterpr }, 0);
+ }
+
+ /**
+ * Initializes a new instance of <code>NetworkStatus</code> with two interpretations.
+ *
+ * @param aDescription Status description in a human-readable format.
+ * @param aIcon Image that schematically represents the status. This should be one of the
+ * elements of {@link #allIcons}.
+ * @param aInterpr1 The first network interpretation for this status.
+ * @param aInterpr2 The second network interpretation for this status.
+ * @param aDefIndex Index of the default interpretation. This value must be <code>0</code> or
+ * <code>1</code>.
+ */
+ private NetworkStatus(String aDescription, ImageIcon aIcon, NetworkInterpretation aInterpr1,
+ NetworkInterpretation aInterpr2, int aDefIndex) {
+ this(aDescription, aIcon, new NetworkInterpretation[] { aInterpr1, aInterpr2 }, aDefIndex);
+ }
+
+ /**
+ * Initializes a new instance of <code>NetworkStatus</code> with three interpretations.
+ *
+ * @param aDescription Status description in a human-readable format.
+ * @param aIcon Image that schematically represents the status. This should be one of the
+ * elements of {@link #allIcons}.
+ * @param aInterpr1 The first network interpretation for this status.
+ * @param aInterpr2 The second network interpretation for this status.
+ * @param aInterpr3 The third network interpretation for this status.
+ * @param aDefIndex Index of the default interpretation. This value must be <code>0</code>,
+ * <code>1</code> or <code>2</code>.
+ */
+ private NetworkStatus(String aDescription, ImageIcon aIcon, NetworkInterpretation aInterpr1,
+ NetworkInterpretation aInterpr2, NetworkInterpretation aInterpr3, int aDefIndex) {
+ this(aDescription, aIcon, new NetworkInterpretation[] { aInterpr1, aInterpr2, aInterpr3 },
+ aDefIndex);
+ }
+
+ /**
+ * Initializes a new instance of <code>NetworkStatus</code>.
+ *
+ * @param aDescription Status description in a human-readable format.
+ * @param aIcon Image that schematically represents the status. This should be one of the
+ * elements of {@link #allIcons}.
+ * @param aInterprs Array of possible interpretations for this status.
+ * @param aDefIndex Index of the default interpretation. This value must point to an element in
+ * the array of possible interpretations.
+ */
+ private NetworkStatus(String aDescription, ImageIcon aIcon, NetworkInterpretation[] aInterprs,
+ int aDefIndex) {
+ description = "<html><b>" + aDescription + "</b>";
+ icon = aIcon;
+ interprs = aInterprs;
+ defaultInterprIndex = aDefIndex;
+ }
+
+ /**
+ * Description of the network status in a human-readable form.
+ */
+ private String description;
+
+ /**
+ * Image icon identifying this network status.
+ */
+ private ImageIcon icon;
+
+ /**
+ * Array of possible network interpretations.
+ */
+ private NetworkInterpretation[] interprs;
+
+ /**
+ * Index of the default interpretation. The default interpretation is obtained by:<br>
+ * <code>interprs[defaultInterprIndex]</code>
+ */
+ private int defaultInterprIndex;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/NodeBetweenInfo.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/NodeBetweenInfo.java
new file mode 100644
index 0000000..f472695
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/NodeBetweenInfo.java
@@ -0,0 +1,249 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.data;
+
+import giny.model.Edge;
+import giny.model.Node;
+
+import java.util.LinkedList;
+import java.util.NoSuchElementException;
+
+/**
+ * Storage class for information needed by node betweenness calculation.
+ * <p>
+ * An instance of this class is assigned to every node during the computation of
+ * node and edge betweenness.
+ * </p>
+ *
+ * @author Nadezhda Doncheva
+ */
+public class NodeBetweenInfo {
+
+ /**
+ * Initializes a new instance of <code>NodeBetweenInfo</code>.
+ *
+ * @param initCount
+ * Number of shortest paths to this node. Default value is
+ * usually <code>0</code>.
+ * @param initLength
+ * Length of a shortest path to this node Default value is
+ * usually <code>-1</code>.
+ * @param initBetweenness
+ * Node betweenness value of this node. Default value is usually
+ * <code>0</code>.
+ */
+ public NodeBetweenInfo(long initCount, int initLength, double initBetweenness) {
+ spCount = initCount;
+ spLength = initLength;
+ dependency = 0.0;
+ betweenness = initBetweenness;
+ predecessors = new LinkedList<Node>();
+ outedges = new LinkedList<Edge>();
+ }
+
+ /**
+ * Gets the length of the shortest path from a source node to this node
+ *
+ * @return spLength Shortest path length to this node
+ */
+ public int getSPLength() {
+ return spLength;
+ }
+
+ /**
+ * Gets the number of shortest paths to this node
+ *
+ * @return spCount Number of shortest paths to this node
+ */
+ public long getSPCount() {
+ return spCount;
+ }
+
+ /**
+ * Gets the dependency of this node to any other vertex
+ *
+ * @return dependency Dependency of this node to any other vertex
+ */
+ public double getDependency() {
+ return dependency;
+ }
+
+ /**
+ * Gets the betweenness value for this node
+ *
+ * @return betweenness Betweenness value of this node
+ */
+ public double getBetweenness() {
+ return betweenness;
+ }
+
+ /**
+ * Retrieves the next predecessor of this node.
+ *
+ * @return predecessor First one of the predecessors of this node. The
+ * returned element is removed from the list of precedecessors.
+ * @throws NoSuchElementException
+ * If this node does not have predecessors.
+ */
+ public Node pullPredecessor() {
+ return predecessors.removeFirst();
+ }
+
+ /**
+ * Gets the list of outgoing edges of this node visited by exploring the
+ * network
+ *
+ * @return outedges List of outgoing edges of this node visited by exploring
+ * the network
+ */
+
+ public LinkedList<Edge> getOutEdges() {
+ return outedges;
+ }
+
+ /**
+ * Checks if the predecessor list is empty
+ *
+ * @return true if the list is empty, false otherwise
+ */
+ public boolean isEmptyPredecessors() {
+ if (predecessors.isEmpty()) {
+ return true;
+ }
+ return false;
+ }
+
+ /**
+ * Sets the new length of the shortest path to this node from a source node
+ *
+ * @param newLength
+ * Length of the shortest path to this node
+ */
+ public void setSPLength(int newLength) {
+ spLength = newLength;
+ }
+
+ /**
+ * Accumulates the number of shortest paths leading to this node
+ *
+ * @param newSPCount
+ * Number of further shortest paths leading to this node
+ */
+ public void addSPCount(long newSPCount) {
+ spCount += newSPCount;
+ }
+
+ /**
+ * Accumulates the dependency of this node
+ *
+ * @param newDependency
+ * New dependency to be added
+ */
+ public void addDependency(double newDependency) {
+ dependency += newDependency;
+ }
+
+ /**
+ * Adds a predecessor to the predecessor list of this node
+ *
+ * @param pred
+ * Node to be added since it is a predecessor of this node
+ */
+ public void addPredecessor(Node pred) {
+ predecessors.add(pred);
+ }
+
+ /**
+ * Adds a further visited outgoing edge for this node
+ *
+ * @param outedge
+ * Visited outgoing edge of this node
+ */
+ public void addOutedge(Edge outedge) {
+ outedges.add(outedge);
+ }
+
+ /**
+ * Accumulates the betweenness value in each run by adding the new
+ * betweenness value to the old
+ *
+ * @param newBetweenness
+ * betweenness value from a run starting at certain source node
+ */
+ public void addBetweenness(double newBetweenness) {
+ betweenness += newBetweenness;
+ }
+
+ /**
+ * Resets all variables for the calculation of edge and node betweenness to
+ * their default values except the node betweenness.
+ */
+ public void reset() {
+ spCount = 0;
+ spLength = -1;
+ dependency = 0.0;
+ predecessors = new LinkedList<Node>();
+ outedges = new LinkedList<Edge>();
+ }
+
+ /**
+ * Changes the shortest path count and length for the source node of this
+ * run if BFS
+ */
+ public void setSource() {
+ spCount = 1;
+ spLength = 0;
+ dependency = 0.0;
+ predecessors = new LinkedList<Node>();
+ outedges = new LinkedList<Edge>();
+ }
+
+ /**
+ * List of the predecessors of this node, i.e. the nodes lying on the
+ * shortest path to this node
+ */
+ private LinkedList<Node> predecessors;
+
+ /**
+ * List of outgoing edges of this node visited by exploring the network
+ */
+ private LinkedList<Edge> outedges;
+
+ /**
+ * Number of shortest paths leading to this node starting from a certain
+ * source
+ */
+ private long spCount;
+
+ /**
+ * Length of shortest path starting from certain source and leading to this
+ * node
+ */
+ private int spLength;
+
+ /**
+ * Dependency of this node on any other vertex
+ */
+ private double dependency;
+
+ /**
+ * Betweenness value of this node
+ */
+ private double betweenness;
+
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/PathLengthData.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/PathLengthData.java
new file mode 100644
index 0000000..c5f209b
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/PathLengthData.java
@@ -0,0 +1,105 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.data;
+
+/**
+ * Data type storing information about the shortest path lengths from one node to other nodes in the
+ * networks.
+ *
+ * @author Yassen Assenov
+ */
+public class PathLengthData {
+
+ /**
+ * Number of shortest path lengths accumulated in this instance.
+ */
+ private int count;
+
+ /**
+ * Sum of all shortest path lengths accumulated in this instance.
+ */
+ private long totalLength;
+
+ /**
+ * Maximum length of a shortest path accumulated in this instance.
+ */
+ private int maxLength;
+
+ /**
+ * Initializes a new instance of <code>PathLengthData</code>.
+ */
+ public PathLengthData() {
+ count = 0;
+ totalLength = 0;
+ maxLength = 0;
+ }
+
+ /**
+ * Accumulates a new shortest path length to this data instance.
+ *
+ * @param aLength Length of shortest path to be accumulated.
+ */
+ public void addSPL(int aLength) {
+ count++;
+ totalLength += aLength;
+ if (maxLength < aLength) {
+ maxLength = aLength;
+ }
+ }
+
+ /**
+ * Gets the number of shortest path lengths.
+ *
+ * @return Number of shortest path lengths accumulated in this instance.
+ */
+ public int getCount() {
+ return count;
+ }
+
+ /**
+ * Gets the total length of shortest paths.
+ *
+ * @return Sum of all shortest path lengths accumulated in this instance.
+ */
+ public long getTotalLength() {
+ return totalLength;
+ }
+
+ /**
+ * Longest among the shortest path lengths added to this data instance.
+ *
+ * @return Maximum length of a shortest path accumulated in this instance.
+ */
+ public int getMaxLength() {
+ return maxLength;
+ }
+
+ /**
+ * Average shortest path length.
+ *
+ * @return Average length of a shortest path accumulated in this instance.
+ *
+ * @throws IllegalStateException If no SPLs were accumulated in this instance ({@link #getCount()}<code> == 0</code>).
+ */
+ public double getAverageLength() {
+ if (count == 0) {
+ throw new IllegalStateException();
+ }
+ return ((double) totalLength) / count;
+ }
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/Points2D.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/Points2D.java
new file mode 100644
index 0000000..eadb4a7
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/Points2D.java
@@ -0,0 +1,162 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.data;
+
+import java.awt.geom.Point2D;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.util.List;
+import java.util.Set;
+
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.io.LineReader;
+
+/**
+ * Complex parameter that stores a set of points in the 2D space. Every point is stored as a pair of its
+ * coordinates - two <code>Double</code> values.
+ *
+ * @author Yassen Assenov
+ */
+public class Points2D implements ComplexParam {
+
+ /**
+ * Initializes a new instance of <code>Points2D</code> by loading it from the given stream.
+ *
+ * @param aArgs View the documentation of {@link #load(String[], LineReader)} for a description of this
+ * parameter.
+ * @param aReader View the documentation of {@link #load(String[], LineReader)} for a description of this
+ * parameter.
+ * @throws IOException View the documentation of {@link #load(String[], LineReader)} for details.
+ * @see #load(String[], LineReader)
+ * @see ComplexParam#load(String[], LineReader)
+ */
+ public Points2D(String[] aArgs, LineReader aReader) throws IOException {
+ load(aArgs, aReader);
+ }
+
+ /**
+ * Initializes a new instance of <code>Points2D</code> based on the given list of points.
+ *
+ * @param aPoints List of 2D points. The order of the points in preserved.
+ * @throws NullPointerException If <code>aPoints</code> is <code>null</code>.
+ */
+ public Points2D(List<Point2D.Double> aPoints) {
+ points = new Point2D.Double[aPoints.size()];
+ aPoints.toArray(points);
+ }
+
+ /**
+ * Initializes a new instance of <code>Points2D</code> based on the given point set.
+ *
+ * @param aPoints Set of 2D points.
+ * @throws NullPointerException If <code>aPoints</code> is <code>null</code>.
+ */
+ public Points2D(Set<Point2D.Double> aPoints) {
+ points = new Point2D.Double[aPoints.size()];
+ aPoints.toArray(points);
+ }
+
+ /**
+ * Initializes a new instance of <code>Points2D</code> based on the given point set.
+ *
+ * @param aPoints Set of 2D points in the form of {@link java.awt.geom.Point2D.Double} array.
+ */
+ public Points2D(Point2D.Double[] aPoints) {
+ points = (aPoints != null) ? aPoints : new Point2D.Double[0];
+ }
+
+ /**
+ * Gets the points in this point set.
+ *
+ * @return All the points in this point set in the form of an array of
+ * {@link java.awt.geom.Point2D.Double} instances.
+ */
+ public Point2D.Double[] getPoints() {
+ return points;
+ }
+
+ /**
+ * Gets the range of <i>x</i> values for this histogram.
+ *
+ * @return Array of two elements - the minimum and the maximum value of the <i>x</i> coordinates in this
+ * point set.
+ *
+ * @throws IllegalStateException If this point set is empty, that is, if it contains no data points.
+ */
+ public double[] getRangeX() {
+ if (points.length == 0) {
+ throw new IllegalStateException();
+ }
+ double[] range = new double[] { Double.MAX_VALUE, Double.MIN_VALUE };
+ for (final Point2D.Double point : points) {
+ if (point.x < range[0]) {
+ range[0] = point.x;
+ }
+ if (point.x > range[1]) {
+ range[1] = point.x;
+ }
+ }
+ return range;
+ }
+
+ /**
+ * Loads the data of the point set from the given stream.
+ *
+ * @param aArgs One-element array representing the argument passed to this type. This argument must be the
+ * <code>String</code> representation of an integer and it specifies the cardinality of the point
+ * set (the number of points).
+ * @param aReader Reader from a text stream. The reader must be open and positioned in the stream such
+ * that the data for the points follows.
+ * @throws IOException If I/O error occurs.
+ * @throws NumberFormatException If the stream contains invalid data.
+ * @throws NullPointerException If at least one of the parameters is <code>null</code>.
+ */
+ public void load(String[] aArgs, LineReader aReader) throws IOException {
+ final int itemCount = Integer.parseInt(aArgs[0]);
+ points = new Point2D.Double[itemCount];
+ for (int i = 0; i < itemCount; ++i) {
+ String[] coords = aReader.readLine().split(SEPREGEX);
+ double x = Double.parseDouble(coords[0]);
+ double y = Double.parseDouble(coords[1]);
+ points[i] = new Point2D.Double(x, y);
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see de.mpg.mpi_inf.bioinf.netanalyzer.data.ComplexParam#save(java.io.FileWriter)
+ */
+ public void save(FileWriter aWriter, boolean aSaveArgs) throws IOException {
+ final int itemCount = points.length;
+ if (aSaveArgs) {
+ aWriter.write(String.valueOf(itemCount) + "\n");
+ }
+ for (int i = 0; i < itemCount; ++i) {
+ double x = points[i].x;
+ double y = points[i].y;
+ String xStr = x < Long.MAX_VALUE && Math.floor(x) != x ? String.valueOf(x) : String.valueOf((long) x);
+ String yStr = y < Long.MAX_VALUE && Math.floor(y) != y ? String.valueOf(y) : String.valueOf((long) y);
+ aWriter.write(xStr + SEP + yStr + "\n");
+ }
+ }
+
+ /**
+ * The set of 2D points.
+ */
+ private Point2D.Double[] points;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/RegInfo.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/RegInfo.java
new file mode 100644
index 0000000..211985d
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/RegInfo.java
@@ -0,0 +1,189 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.data;
+
+import de.mpg.mpi_inf.bioinf.netanalyzer.Plugin;
+
+/**
+ * Class storing and managing the NetworkAnalyzer registration information.
+ *
+ * @author Yassen Assenov
+ * @author Nadezhda Doncheva
+ */
+public class RegInfo {
+
+ /**
+ * Initialize a new instance of <code>RegInfo</code> with all user's data except registration code.
+ *
+ * @param aName
+ * User's name.
+ * @param aSurname
+ * User's surname.
+ * @param aInstitute
+ * User's institution.
+ * @param aEmail
+ * User's email.
+ */
+ public RegInfo(String aName, String aSurname, String aInstitute, String aEmail) {
+ name = aName;
+ surname = aSurname;
+ institute = aInstitute;
+ email = aEmail;
+ version = Plugin.version;
+ }
+
+ /**
+ * Get user's name.
+ *
+ * @return User's name.
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * Set new user's name.
+ *
+ * @param aName
+ * User's name.
+ */
+ public void setName(String aName) {
+ name = aName;
+ }
+
+ /**
+ * Get user's surname.
+ *
+ * @return User's surname.
+ */
+ public String getSurname() {
+ return surname;
+ }
+
+ /**
+ * Set new user's surname.
+ *
+ * @param aSurname
+ * User's surname.
+ */
+ public void setSurname(String aSurname) {
+ surname = aSurname;
+ }
+
+ /**
+ * Get user's institute.
+ *
+ * @return User's institute.
+ */
+ public String getInstitute() {
+ return institute;
+ }
+
+ /**
+ * Set new user's institute.
+ *
+ * @param aInstitute
+ * New user's institute.
+ */
+ public void setInstitute(String aInstitute) {
+ institute = aInstitute;
+ }
+
+ /**
+ * Get user's email address.
+ *
+ * @return User's email address.
+ */
+ public String getEmail() {
+ return email;
+ }
+
+ /**
+ * Set new user's email address.
+ *
+ * @param aEmail
+ * New user's email address.
+ */
+ public void setEmail(String aEmail) {
+ email = aEmail;
+ }
+
+ /**
+ * Get NetworkAnalyzer version number.
+ *
+ * @return NetworkAnalyzer version number.
+ */
+ public String getVersion() {
+ return version;
+ }
+
+ /**
+ * Set new NetworkAnalyzer version number.
+ *
+ * @param aVersion
+ * New NetworkAnalyzer version number.
+ */
+ public void setVersion(String aVersion) {
+ version = aVersion;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.lang.Object#toString()
+ */
+ @Override
+ public String toString() {
+ final StringBuilder buffer = new StringBuilder();
+ buffer.append(name);
+ buffer.append("\t");
+ buffer.append(surname);
+ buffer.append("\t");
+ buffer.append(institute);
+ buffer.append("\t");
+ buffer.append(email);
+ buffer.append("\t");
+ buffer.append(version);
+ return buffer.toString();
+ }
+
+ /**
+ * User's name.
+ */
+ private String name;
+
+ /**
+ * User's surname.
+ */
+ private String surname;
+
+ /**
+ * User's institute.
+ */
+ private String institute;
+
+ /**
+ * User's email address.
+ */
+ private String email;
+
+ /**
+ * Current NetworkAnalyzer version.
+ */
+ private String version;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/SimpleUndirParams.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/SimpleUndirParams.java
new file mode 100644
index 0000000..9c234b9
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/SimpleUndirParams.java
@@ -0,0 +1,80 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.data;
+
+/**
+ * Storage class for some of the simple network parameters of an undirected network.
+ *
+ * @author Yassen Assenov
+ * @author Sven-Eric Schelhorn
+ */
+public class SimpleUndirParams {
+
+ /**
+ * Initializes a new instance of <code>SimpleUndirParams</code>.
+ */
+ public SimpleUndirParams() {
+ connectedComponentCount = 0;
+ diameter = 0;
+ radius = Integer.MAX_VALUE;
+ unconnectedNodeCount = 0;
+ }
+
+ /**
+ * Accumulates the connectivities of all nodes. These values are used in the calculation of
+ * network density and centralization.
+ */
+ public SumCountPair connectivityAccum;
+
+ /**
+ * Accumulates the squared connectivities of all nodes. These values are used in the calculation
+ * of network heterogeneity.
+ */
+ public SumCountPair sqConnectivityAccum;
+
+ /**
+ * Number of connected components.
+ */
+ public int connectedComponentCount;
+
+ /**
+ * Length of diameter.
+ */
+ public int diameter;
+
+ /**
+ * Length of radius.
+ */
+ public int radius;
+
+ /**
+ * Number of nodes that are not connected to any other nodes.
+ */
+ public int unconnectedNodeCount;
+
+ /**
+ * Number of self-loops (edges that connect a node with itself).
+ */
+ public int selfLoopCount;
+
+ /**
+ * Overall number of partners of multi-edged node pairs. A partner is one member of such a pair.
+ * <code>multiEdgePartners / 2</code> is the number of multi-edged node pairs.
+ */
+ public int multiEdgePartners;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/SumCountPair.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/SumCountPair.java
new file mode 100644
index 0000000..ea3508d
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/SumCountPair.java
@@ -0,0 +1,86 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.data;
+
+/**
+ * Utility class for storing the sum and length of a non-empty sequence of numbers.
+ *
+ * @author Yassen Assenov
+ */
+public class SumCountPair {
+
+ /**
+ * Initializes a new instance of <code>SumCountPair</code>.
+ *
+ * @param aValue The first number of the sequence.
+ */
+ public SumCountPair(double aValue) {
+ mSum = aValue;
+ mCount = 1;
+ }
+
+ /**
+ * Adds a new number to the sequence.
+ *
+ * @param aValue New number to be added.
+ */
+ public void add(double aValue) {
+ mSum += aValue;
+ mCount++;
+ }
+
+ /**
+ * Gets the sum of the numbers in the sequence.
+ *
+ * @return Sum of the numbers added so far to the sequence.
+ */
+ public double getSum() {
+ return mSum;
+ }
+
+ /**
+ * Gets the average of the numbers in the sequence.
+ * <p>
+ * This method facilitates the calls <code>{@link #getSum()} / {@link #getCount()}</code>.
+ * </p>
+ *
+ * @return Average of the numbers added so far to the sequence.
+ */
+ public double getAverage() {
+ return mSum / mCount;
+ }
+
+ /**
+ * Gets the size of the sequence.
+ *
+ * @return Number of numbers added to the sequence so far.
+ */
+ public int getCount() {
+ return mCount;
+ }
+
+ /**
+ * Sum of numbers added to the sequence.
+ */
+ private double mSum;
+
+ /**
+ * Number of numbers added to the sequence.
+ */
+ private int mCount;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/Utils.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/Utils.java
new file mode 100644
index 0000000..5342914
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/Utils.java
@@ -0,0 +1,72 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.data;
+
+import java.net.URL;
+
+import javax.swing.ImageIcon;
+
+import de.mpg.mpi_inf.bioinf.netanalyzer.Plugin;
+
+/**
+ * Utility class providing helper methods for data manipulation.
+ *
+ * @author Yassen Assenov
+ */
+public abstract class Utils {
+
+ /**
+ * Loads an image stored in the given file.
+ *
+ * @param aFileName Name of file storing the image.
+ * @param aDescription Human-readable description of the image.
+ * @return The <code>ImageIcon</code> instance representing the loaded image, or an empty
+ * image if the file specified does not exist.
+ */
+ public static ImageIcon getImage(String aFileName, String aDescription) {
+ URL imageURL = Plugin.class.getResource("data/images/" + aFileName);
+ return new ImageIcon(imageURL, aDescription);
+ }
+
+ /**
+ * Computes a relaxed power function.
+ *
+ * @param a Base number.
+ * @param b Power number.
+ * @return <code>a<sup>b</sup></code> if <code>a</code> ≠ <code>0</code>; <code>0</code>
+ * otherwise.
+ */
+ public static double pow(double a, double b) {
+ if (a != 0) {
+ return Math.pow(a, b);
+ }
+ return 0;
+ }
+
+ /**
+ * Rounds a double <code>value</code> to <code>digit</code> digits after the point.
+ *
+ * @param aValue Value to be rounded.
+ * @param aDigits Digits the value should have after the point after the rounding.
+ * @return <code>Double</code> object that contains the rounded <code>value</code>.
+ */
+ public static Double roundTo(double aValue, int aDigits) {
+ double d = Math.pow(10, aDigits);
+ return new Double(Math.round(aValue*d)/d);
+ }
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/Version.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/Version.java
new file mode 100644
index 0000000..e07ee90
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/Version.java
@@ -0,0 +1,151 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.data;
+
+/**
+ * Storage class for plugin and Cytoscape version.
+ * <p>
+ * In the plugin definition files, a version is defined as the string
+ * <code><MAJOR> . >MINOR<</code>. This class supports a more flexible version format of unlimited
+ * granularity, for example <code>2.7.1.1</code>.
+ * </p>
+ *
+ * @author Yassen Assenov
+ */
+public class Version implements Comparable<Version> {
+
+ /**
+ * Initializes a new instance of <code>Version</code> based on the given version string.
+ * <p>
+ * The version string must be a non-empty sequence of integers separated by the dot character (
+ * <code>.</code>). At least one of this integers must be non-zero.
+ * </p>
+ *
+ * @param aVersionString
+ * Text representation of the version.
+ *
+ * @throws NullPointerException
+ * If <code>aVersionString</code> is <code>null</code>.
+ * @throws IllegalArgumentException
+ * If <code>aVersionString</code> is not in the expected format.
+ */
+ public Version(String aVersionString) {
+ try {
+ // Read the sequence of integers
+ if (aVersionString.endsWith(".")) {
+ throw new IllegalArgumentException();
+ }
+ String[] elements = aVersionString.split("\\.");
+ int elemCount = elements.length;
+ mVersion = new int[elemCount];
+ for (int i = 0; i < elemCount; ++i) {
+ mVersion[i] = Integer.parseInt(elements[i]);
+ }
+ // Remove trailing zeroes, if any
+ int nonTrailZeroCount = elemCount;
+ for (; nonTrailZeroCount > 0; --nonTrailZeroCount) {
+ if (mVersion[nonTrailZeroCount - 1] != 0) {
+ break;
+ }
+ }
+ if (nonTrailZeroCount == 0) {
+ throw new IllegalArgumentException();
+ }
+ if (nonTrailZeroCount != elemCount) {
+ // TODO: [Java 1.6] Use Arrays.copyOf( ... );
+ int[] copied = new int[nonTrailZeroCount];
+ for (int i = 0; i < nonTrailZeroCount; ++i) {
+ copied[i] = mVersion[i];
+ }
+ mVersion = copied;
+ }
+ } catch (NumberFormatException ex) {
+ throw new IllegalArgumentException(ex);
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.lang.Comparable#compareTo(java.lang.Object)
+ */
+ public int compareTo(Version aVersion) {
+ final int[] version2 = aVersion.mVersion;
+ final int length1 = mVersion.length;
+ final int length2 = version2.length;
+ for (int i = 0; i < length1 && i < length2; ++i) {
+ if (mVersion[i] < version2[i]) {
+ return -1;
+ }
+ if (mVersion[i] > version2[i]) {
+ return 1;
+ }
+ }
+ return length1 - length2;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.lang.Object#hashCode()
+ */
+ @Override
+ public int hashCode() {
+ int hashCode = 0;
+ int mult = 1;
+ for (int i = 0; i < mVersion.length; mult *= 10, ++i) {
+ hashCode += mVersion[i] * mult;
+ }
+ return hashCode;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.lang.Object#equals(java.lang.Object)
+ */
+ @Override
+ public boolean equals(Object o) {
+ try {
+ return this == o || compareTo((Version) o) == 0;
+ } catch (Exception ex) {
+ return false;
+ }
+ }
+
+ /**
+ * Checks if this version is newer than the given one.
+ *
+ * @param aVersion
+ * Version to be compared to.
+ * @return <code>true</code> if this instance represents a later version than <code>aVersion</code>;
+ * <code>false</code> otherwise.
+ */
+ public boolean isNewer(Version aVersion) {
+ return (compareTo(aVersion) > 0);
+ }
+
+ /**
+ * Internal representation of a version - list of the version numbers.
+ * <p>
+ * The elements in this array are ordered by priority. The element at index <code>0</code> is usually the
+ * major version number.
+ * </p>
+ */
+ private int[] mVersion;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/filter/ComplexParamFilter.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/filter/ComplexParamFilter.java
new file mode 100644
index 0000000..641920e
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/filter/ComplexParamFilter.java
@@ -0,0 +1,38 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.data.filter;
+
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.ComplexParam;
+
+/**
+ * Interface implemented by all filters for complex parameters.
+ *
+ * @author Yassen Assenov
+ */
+public interface ComplexParamFilter {
+
+ /**
+ * Performs filtering on the given complex parameter.
+ *
+ * @param aParam Complex parameter instance whose data is to be filtered.
+ * @return New instance of the same complex parameter type whose data is the result of applying
+ * filtering criteria on <code>aParam</code>'s data.
+ * @throws UnsupportedOperationException If the complex parameter is not of the expected type.
+ */
+ public ComplexParam filter(ComplexParam aParam);
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/filter/IntHistogramFilter.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/filter/IntHistogramFilter.java
new file mode 100644
index 0000000..898bdcc
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/filter/IntHistogramFilter.java
@@ -0,0 +1,147 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.data.filter;
+
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.ComplexParam;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.IntHistogram;
+
+/**
+ * Filter for complex parameters of type <code>IntHistogram</code>.
+ *
+ * @author Yassen Assenov
+ */
+public class IntHistogramFilter implements ComplexParamFilter {
+
+ /**
+ * Initializes a new instance of <code>IntHistogramFilter</code>.
+ */
+ public IntHistogramFilter() {
+ observationMin = Integer.MIN_VALUE;
+ observationMax = Integer.MAX_VALUE;
+ }
+
+ /**
+ * Initializes a new instance of <code>IntHistogramFilter</code> based on the given range.
+ *
+ * @param aObservationMin Minimal observed value to be considered.
+ * @param aObservationMax Maximal observer value to be considered.
+ * @see #getObservationMin()
+ * @see #getObservationMax()
+ */
+ public IntHistogramFilter(int aObservationMin, int aObservationMax) {
+ observationMin = aObservationMin;
+ observationMax = aObservationMax;
+ }
+
+ /**
+ * Performs filtering on the given histogram.
+ *
+ * @param aParam <code>IntHistogram</code> instance whose data is to be filtered.
+ * @return New instance of <code>IntHistogram</code> whose data is the result of applying
+ * filtering criteria on <code>aParam</code>'s data.
+ * @throws UnsupportedOperationException If the complex parameter is not of type
+ * {@link de.mpg.mpi_inf.bioinf.netanalyzer.data.IntHistogram}.
+ */
+ public ComplexParam filter(ComplexParam aParam) {
+ if (!(aParam instanceof IntHistogram)) {
+ throw new UnsupportedOperationException();
+ }
+ int[][] bins = ((IntHistogram) aParam).getBins();
+ int[] dataRange = bins[0];
+ int fromIndex = 0;
+ while (dataRange[fromIndex] < observationMin) {
+ fromIndex++;
+ }
+ int toIndex = fromIndex;
+ while (toIndex < dataRange.length && dataRange[toIndex] <= observationMax) {
+ toIndex++;
+ }
+ toIndex--;
+ return new IntHistogram(bins, fromIndex, toIndex);
+ }
+
+ /**
+ * Gets the minimal observed value to be considered.
+ * <p>
+ * When filtering of a histogram is performed, only bins defined over intervals
+ * "right" of the minimal observed value are retained; all other bins are dropped.
+ * Formally, a bin defined over the interval <code>[i, j)</code> is dropped ⇔
+ * <code>i < n</code>, where <code>n</code> is the value returned by this method.
+ * </p>
+ *
+ * @return Minimal observed value to be considered when filtering.
+ */
+ public int getObservationMin() {
+ return observationMin;
+ }
+
+ /**
+ * Gets the maximal observed value to be considered.
+ * <p>
+ * When filtering of a histogram is performed, only bins defined over intervals
+ * "left" of the maximal observed value are retained; all other bins are dropped.
+ * Formally, a bin defined over the interval <code>[i, j)</code> is dropped ⇔
+ * <code>j > n</code>, where <code>n</code> is the value returned by this method.
+ * </p>
+ *
+ * @return Maximal observed value to be considered when filtering.
+ */
+ public int getObservationMax() {
+ return observationMax;
+ }
+
+ /**
+ * Sets the minimal observed value to be considered.
+ * <p>
+ * Note that if you set the minimal observation value to be ≥ the maximal observation value
+ * ({@link #setObservationMax(int)}), the filter will effectively drop any data from a
+ * passed histogram.
+ * </p>
+ *
+ * @param aObservation Minimal observation value to be considered.
+ * @see #getObservationMin()
+ */
+ public void setObservationMin(int aObservation) {
+ observationMin = aObservation;
+ }
+
+ /**
+ * Sets the maximal observed value to be considered.
+ * <p>
+ * Note that if you set the maximal observation value to be ≤ the minimal observation value
+ * ({@link #setObservationMin(int)}), the filter will effectively drop any data from a
+ * passed histogram.
+ * </p>
+ *
+ * @param aObservation Maximal observation value to be considered.
+ * @see #getObservationMax()
+ */
+ public void setObservationMax(int aObservation) {
+ observationMax = aObservation;
+ }
+
+ /**
+ * Minimal observed value considered in filtering.
+ */
+ private int observationMin;
+
+ /**
+ * Maximal observed value considered in filtering.
+ */
+ private int observationMax;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/filter/LongHistogramFilter.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/filter/LongHistogramFilter.java
new file mode 100644
index 0000000..b12acdd
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/filter/LongHistogramFilter.java
@@ -0,0 +1,147 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.data.filter;
+
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.ComplexParam;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.LongHistogram;
+
+/**
+ * Filter for complex parameters of type <code>LongHistogram</code>.
+ *
+ * @author Yassen Assenov
+ */
+public class LongHistogramFilter implements ComplexParamFilter {
+
+ /**
+ * Initializes a new instance of <code>LongHistogramFilter</code>.
+ */
+ public LongHistogramFilter() {
+ observationMin = Long.MIN_VALUE;
+ observationMax = Long.MAX_VALUE;
+ }
+
+ /**
+ * Initializes a new instance of <code>LongHistogramFilter</code> based on the given range.
+ *
+ * @param aObservationMin Minimal observed value to be considered.
+ * @param aObservationMax Maximal observer value to be considered.
+ * @see #getObservationMin()
+ * @see #getObservationMax()
+ */
+ public LongHistogramFilter(long aObservationMin, long aObservationMax) {
+ observationMin = aObservationMin;
+ observationMax = aObservationMax;
+ }
+
+ /**
+ * Performs filtering on the given histogram.
+ *
+ * @param aParam <code>LongHistogram</code> instance whose data is to be filtered.
+ * @return New instance of <code>LongHistogram</code> whose data is the result of applying
+ * filtering criteria on <code>aParam</code>'s data.
+ * @throws UnsupportedOperationException If the complex parameter is not of type
+ * {@link de.mpg.mpi_inf.bioinf.netanalyzer.data.LongHistogram}.
+ */
+ public ComplexParam filter(ComplexParam aParam) {
+ if (!(aParam instanceof LongHistogram)) {
+ throw new UnsupportedOperationException();
+ }
+ long[][] bins = ((LongHistogram) aParam).getBins();
+ long[] dataRange = bins[0];
+ int fromIndex = 0;
+ while (dataRange[fromIndex] < observationMin) {
+ fromIndex++;
+ }
+ int toIndex = fromIndex;
+ while (toIndex < dataRange.length && dataRange[toIndex] <= observationMax) {
+ toIndex++;
+ }
+ toIndex--;
+ return new LongHistogram(bins, fromIndex, toIndex);
+ }
+
+ /**
+ * Gets the minimal observed value to be considered.
+ * <p>
+ * When filtering of a histogram is performed, only bins defined over intervals
+ * "right" of the minimal observed value are retained; all other bins are dropped.
+ * Formally, a bin defined over the interval <code>[i, j)</code> is dropped ⇔
+ * <code>i < n</code>, where <code>n</code> is the value returned by this method.
+ * </p>
+ *
+ * @return Minimal observed value to be considered when filtering.
+ */
+ public long getObservationMin() {
+ return observationMin;
+ }
+
+ /**
+ * Gets the maximal observed value to be considered.
+ * <p>
+ * When filtering of a histogram is performed, only bins defined over intervals
+ * "left" of the maximal observed value are retained; all other bins are dropped.
+ * Formally, a bin defined over the interval <code>[i, j)</code> is dropped ⇔
+ * <code>j > n</code>, where <code>n</code> is the value returned by this method.
+ * </p>
+ *
+ * @return Maximal observed value to be considered when filtering.
+ */
+ public long getObservationMax() {
+ return observationMax;
+ }
+
+ /**
+ * Sets the minimal observed value to be considered.
+ * <p>
+ * Note that if you set the minimal observation value to be ≥ the maximal observation value
+ * ({@link #setObservationMax(long)}), the filter will effectively drop any data from a
+ * passed histogram.
+ * </p>
+ *
+ * @param aObservation Minimal observation value to be considered.
+ * @see #getObservationMin()
+ */
+ public void setObservationMin(long aObservation) {
+ observationMin = aObservation;
+ }
+
+ /**
+ * Sets the maximal observed value to be considered.
+ * <p>
+ * Note that if you set the maximal observation value to be ≤ the minimal observation value
+ * ({@link #setObservationMin(long)}, the filter will effectively drop any data from a
+ * passed histogram.
+ * </p>
+ *
+ * @param aObservation Maximal observation value to be considered.
+ * @see #getObservationMax()
+ */
+ public void setObservationMax(long aObservation) {
+ observationMax = aObservation;
+ }
+
+ /**
+ * Minimal observed value considered in filtering.
+ */
+ private long observationMin;
+
+ /**
+ * Maximal observed value considered in filtering.
+ */
+ private long observationMax;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/filter/Points2DFilter.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/filter/Points2DFilter.java
new file mode 100644
index 0000000..51b5253
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/filter/Points2DFilter.java
@@ -0,0 +1,75 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.data.filter;
+
+import java.awt.geom.Point2D;
+import java.util.ArrayList;
+import java.util.List;
+
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.ComplexParam;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Points2D;
+
+/**
+ * Filter for complex parameters of type <code>Points2D</code>.
+ *
+ * @author Yassen Assenov
+ */
+public class Points2DFilter implements ComplexParamFilter {
+
+ /**
+ * Initializes a new instance of <code>Points2DFilter</code> based on the given range.
+ *
+ * @param aXMin Minimal value of the x coordinate to be considered.
+ * @param aXMax Maximal value of the x coordinate to be considered.
+ */
+ public Points2DFilter(double aXMin, double aXMax) {
+ xMin = aXMin;
+ xMax = aXMax;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see de.mpg.mpi_inf.bioinf.netanalyzer.data.filter.ComplexParamFilter#filter(de.mpg.mpi_inf.bioinf.netanalyzer.data.ComplexParam)
+ */
+ public ComplexParam filter(ComplexParam aParam) {
+ if (!(aParam instanceof Points2D)) {
+ throw new UnsupportedOperationException();
+ }
+ final Point2D.Double[] original = ((Points2D) aParam).getPoints();
+ final List<Point2D.Double> filtered = new ArrayList<Point2D.Double>(original.length);
+ for (final Point2D.Double point : original) {
+ if (xMin <= point.x && point.x <= xMax) {
+ filtered.add(point);
+ }
+ }
+
+ return new Points2D(filtered);
+ }
+
+ /**
+ * Minimal observed value considered in filtering.
+ */
+ private double xMin;
+
+ /**
+ * Maximal observed value considered in filtering.
+ */
+ private double xMax;
+
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/io/IOUtils.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/io/IOUtils.java
new file mode 100644
index 0000000..8b5bd3e
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/io/IOUtils.java
@@ -0,0 +1,81 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.data.io;
+
+import java.io.BufferedReader;
+import java.io.Closeable;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+
+/**
+ * Utility class providing helper methods for stream manipulation.
+ *
+ * @author Yassen Assenov
+ */
+public abstract class IOUtils {
+
+ /**
+ * Reads the contents of the given stream as a <code>String</code> and closes the stream.
+ *
+ * @param aStream
+ * Stream to be read.
+ * @return The text read from the stream.
+ *
+ * @throws IOException
+ * If an I/O error occurs while reading from or while closing the stream.
+ * @throws NullPointerException
+ * If <code>aStream</code> is <code>null</code>.
+ */
+ public static final String readFile(InputStream aStream) throws IOException {
+ final StringBuilder text = new StringBuilder();
+
+ BufferedReader reader = null;
+ try {
+ reader = new BufferedReader(new InputStreamReader(aStream));
+ for (String line = reader.readLine(); line != null; line = reader.readLine()) {
+ if (text.length() != 0) {
+ text.append("\n");
+ }
+ text.append(line);
+ }
+ } catch (IOException ex) {
+ closeStream(reader);
+ throw ex;
+ }
+ reader.close();
+ return text.toString();
+ }
+
+ /**
+ * Silently closes the given stream.
+ * <p>
+ * This method does not throw an exception in any circumstances.
+ * </p>
+ *
+ * @param aStream
+ * Stream to be closed.
+ */
+ public static void closeStream(Closeable aStream) {
+ try {
+ aStream.close();
+ } catch (Exception ex) {
+ // Unsuccessful attempt to close the stream; ignore
+ }
+ }
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/io/LineReader.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/io/LineReader.java
new file mode 100644
index 0000000..64ac804
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/io/LineReader.java
@@ -0,0 +1,57 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.data.io;
+
+import java.io.Closeable;
+import java.io.IOException;
+
+/**
+ * Interface for reading text streams one line at a time.
+ *
+ * @author Yassen Assenov
+ */
+public interface LineReader extends Closeable {
+
+ /**
+ * Closes the stream. Once the stream is closed, further invocations of {@link #readLine()}
+ * cause <code>IOException</code>. Closing a previously-closed stream, however, has no effect.
+ *
+ * @throws IOException If an I/O error occurs.
+ */
+ public void close() throws IOException;
+
+ /**
+ * Reads a line of text. A line is considered to be terminated by any one of a line feed ('\n'),
+ * a carriage return ('\r'), or a carriage return followed immediately by a line feed.
+ *
+ * @return A <code>String</code> containing the contents of the line, not including any
+ * line-termination characters; or <code>null</code> if the end of the stream has been reached.
+ * @throws IOException If an I/O error occurs.
+ */
+ public String readLine() throws IOException;
+
+ /**
+ * Checks whether this stream is ready to be read.
+ *
+ * @return <code>true</code> if the next invocation of {@link #readLine()} is guaranteed not to
+ * block for input, <code>false</code> otherwise. Note that returning <code>false</code> does
+ * not guarantee that the next read will block.
+ * @throws IOException If an I/O error occurs.
+ */
+ public boolean ready() throws IOException;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/io/Netstats1Reader.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/io/Netstats1Reader.java
new file mode 100644
index 0000000..0420feb
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/io/Netstats1Reader.java
@@ -0,0 +1,80 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.data.io;
+
+import java.io.IOException;
+
+/**
+ * Reader for ".netstats": version 1 files. It is a wrapper around a
+ * {@link Netstats2Reader} instance, providing conversion wherever necessary.
+ *
+ * @author Yassen Assenov
+ */
+class Netstats1Reader implements LineReader {
+
+ /**
+ * Initializes a new instance of <code>Netstats1Reader</code>.
+ *
+ * @param aReader Successfully initialized Netstats version 2 reader.
+ * @throws NullPointerException If <code>aReader</code> is <code>null</code>.
+ */
+ public Netstats1Reader(Netstats2Reader aReader) {
+ if (aReader == null) {
+ throw new NullPointerException();
+ }
+ reader = aReader;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see de.mpg.mpi_inf.bioinf.netanalyzer.data.io.LineReader#close()
+ */
+ public void close() throws IOException {
+ reader.close();
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see de.mpg.mpi_inf.bioinf.netanalyzer.data.io.LineReader#readLine()
+ */
+ public String readLine() throws IOException {
+ String line = reader.readLine();
+ if (line != null) {
+ if (line.startsWith("splDist IntHistogram")) {
+ line = "splDist LongHistogram" + line.substring(20);
+ }
+ }
+ return line;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see de.mpg.mpi_inf.bioinf.netanalyzer.data.io.LineReader#ready()
+ */
+ public boolean ready() throws IOException {
+ return reader.ready();
+ }
+
+ /**
+ * Underlying Netstats version 2 reader.
+ */
+ private Netstats2Reader reader;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/io/Netstats2Reader.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/io/Netstats2Reader.java
new file mode 100644
index 0000000..b73a091
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/io/Netstats2Reader.java
@@ -0,0 +1,72 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.data.io;
+
+import java.io.BufferedReader;
+import java.io.FileReader;
+import java.io.IOException;
+
+/**
+ * Reader for ".netstats": version 2 files. It uses <code>BufferedReader</code> for
+ * accessing the underlying stream.
+ *
+ * @author Yassen Assenov
+ */
+class Netstats2Reader implements LineReader {
+
+ /**
+ * Initializes a new instance of <code>Netstats2Reader</code>.
+ *
+ * @param aFileReader Reader of the underlying file stream.
+ */
+ public Netstats2Reader(FileReader aFileReader) {
+ reader = new BufferedReader(aFileReader);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see de.mpg.mpi_inf.bioinf.netanalyzer.data.io.LineReader#close()
+ */
+ public void close() throws IOException {
+ reader.close();
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see de.mpg.mpi_inf.bioinf.netanalyzer.data.io.LineReader#readLine()
+ */
+ public String readLine() throws IOException {
+ return reader.readLine();
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see de.mpg.mpi_inf.bioinf.netanalyzer.data.io.LineReader#ready()
+ */
+ public boolean ready() throws IOException {
+ return reader.ready();
+ }
+
+ /**
+ * Buffered reader of the underlying stream.
+ */
+ private BufferedReader reader;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/io/SettingsSerializer.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/io/SettingsSerializer.java
new file mode 100644
index 0000000..2f897bc
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/io/SettingsSerializer.java
@@ -0,0 +1,322 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.data.io;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.lang.reflect.Constructor;
+import java.net.URL;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import org.jdom.Document;
+import org.jdom.Element;
+import org.jdom.input.SAXBuilder;
+import org.jdom.output.Format;
+import org.jdom.output.XMLOutputter;
+import org.w3c.dom.DOMException;
+
+import cytoscape.logger.CyLogger;
+import de.mpg.mpi_inf.bioinf.netanalyzer.InnerException;
+import de.mpg.mpi_inf.bioinf.netanalyzer.Plugin;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Messages;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Version;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.settings.PluginSettings;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.settings.SettingsGroup;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.settings.XMLSerializable;
+import de.mpg.mpi_inf.bioinf.netanalyzer.ui.Utils;
+
+/**
+ * Controller class providing static methods for loading and saving settings.
+ * <p>
+ * This class also provides interface for getting and updating plugin's settings, as well as the default
+ * visual settings for a specified complex parameter.
+ * </p>
+ *
+ * @author Yassen Assenov
+ */
+public abstract class SettingsSerializer {
+
+ /**
+ * Gets the default visual settings group for the specified complex parameter.
+ *
+ * @param aParam
+ * ID of complex parameter.
+ * @return Instance of the default visual settings group for the specified parameter; <code>null</code> if
+ * the parameter ID is unknown.
+ */
+ public static SettingsGroup getDefault(String aParam) {
+ return visualSettings.get(aParam);
+ }
+
+ /**
+ * Gets the name of the expected type of the given complex parameter.
+ *
+ * @param aParam
+ * ID of complex parameter.
+ * @return <code>String</code> instance storing the simple name (not prefixed by package name) of the type
+ * of the given complex parameter; <code>null</code> if the parameter ID is unknown.
+ */
+ public static String getDefaultType(String aParam) {
+ SettingsGroup settings = visualSettings.get(aParam);
+ if (settings != null) {
+ String settingsType = settings.getClass().getSimpleName();
+ if (settingsType.endsWith("Group")) {
+ return settingsType.substring(0, settingsType.length() - 5);
+ }
+ }
+ return null;
+ }
+
+ /**
+ * Gets the current plugin's general settings.
+ *
+ * @return General settings of the NetworkAnalyzer plugin, encapsulated in a <code>PluginSettings</code>
+ * instance.
+ */
+ public static PluginSettings getPluginSettings() {
+ return pluginSettings;
+ }
+
+ /**
+ * Initializes the default visual settings by loading them from file(s). This method is called upon plugin
+ * initialization only.
+ * <p>
+ * If an external settings file exists, the settings are loaded from it. Otherwise, settings are loaded
+ * from the internal XML settings file (the file in the JAR archive).<br/>
+ * If the external settings file is from a previous version, it contains incomplete data. The missing data
+ * is taken from the internal file.
+ * </p>
+ *
+ * @throws InnerException
+ * If locating, opening or parsing the internal XML settings file has failed.
+ */
+ public static void initVisualSettings() {
+ visualSettings = new HashMap<String, SettingsGroup>();
+
+ // Try to load settings from external XML file
+ Document doc = getDocExternal();
+ if (doc != null) {
+ try {
+ loadSettings(doc);
+ return;
+ } catch (Exception ex) {
+ final String msg = Messages.SM_LOADSETTINGSFAIL1 + Plugin.getSettingsFileName()
+ + Messages.SM_LOADSETTINGSFAIL2;
+ CyLogger.getLogger().warning(msg);
+ }
+ }
+
+ // Loading from external XML file failed, load from internal XML file
+ doc = getDocInternal();
+ loadSettings(doc);
+
+ // We are starting the plugin for the first time; save the settings
+ try {
+ save();
+ } catch (Exception ex) {
+ // FileNotFoundException; IOException; SecurityException
+ Utils.showErrorBox(Messages.DT_IOERROR, Messages.SM_SAVESETERROR);
+ return;
+ }
+ }
+
+ /**
+ * Saves the settings to the XML settings file.
+ *
+ * @throws FileNotFoundException
+ * If the default XML settings file could not be created.
+ * @throws IOException
+ * If an I/O error occurred while writing to the XML settings file.
+ * @throws SecurityException
+ * If the program does not have write permission for the XML settings file.
+ * @see Plugin#getSettingsFileName()
+ */
+ public static void save() throws IOException {
+ Element settingsRoot = new Element(rootTag);
+ settingsRoot.setAttribute(versionAttribute, Plugin.version);
+ settingsRoot.addContent(pluginSettings.toXmlNode());
+
+ for (String id : visualSettings.keySet()) {
+ settingsRoot.addContent(visualSettings.get(id).toXmlNode());
+ }
+ Document settingsDoc = new Document(settingsRoot);
+ final Format format = Format.getCompactFormat();
+ format.setIndent("\t");
+ XMLOutputter saver = new XMLOutputter(format);
+ FileOutputStream stream = null;
+ try {
+ stream = new FileOutputStream(Plugin.getSettingsFileName());
+ saver.output(settingsDoc, stream);
+ stream.close();
+ stream = null;
+ } catch (IOException ex) {
+ if (stream != null) {
+ stream.close();
+ }
+ throw ex;
+ }
+ }
+
+ /**
+ * Sets the default visual settings group for the specified parameter.
+ * <p>
+ * This method also saves the parameters to the XML settings file.
+ * </p>
+ *
+ * @param aValue
+ * Instance of the default visual settings group for one of the complex parameter types.
+ * @throws FileNotFoundException
+ * If the default XML settings file could not be created.
+ * @throws IOException
+ * If an I/O error occurred while writing to the XML settings file.
+ * @throws SecurityException
+ * If the program does not have write permission for the XML settings file.
+ * @see #save()
+ */
+ public static void setDefault(SettingsGroup aValue) throws IOException {
+ visualSettings.put(aValue.getParamID(), aValue);
+ save();
+ }
+
+ /**
+ * Gets the XML document contained in the external XML settings file.
+ *
+ * @return <code>Document</code> instance loaded from the external XML settings file; <code>null</code> if
+ * one of the following is true:
+ * <ul>
+ * <li>the plugin does not have read access to the external file</li>
+ * <li>the external file does not exist</li>
+ * <li>the external file is not a regular file (e.g. it is a directory)</li>
+ * <li>the external file is not a valid XML file</li>
+ * <li>an I/O error has occurred while reading the contents of the external file.</li>
+ * </ul>
+ */
+ private static Document getDocExternal() {
+ File settingsFile = new File(Plugin.getSettingsFileName());
+ if (settingsFile.exists() && settingsFile.isFile()) {
+ try {
+ return new SAXBuilder().build(settingsFile);
+ } catch (Exception ex) {
+ // Opening XML settings file failed, fall through
+ }
+ }
+ return null;
+ }
+
+ /**
+ * Gets the XML document contained in the internal XML settings file.
+ *
+ * @return <code>Document</code> instance loaded from the internal XML settings file.
+ * @throws InnerException
+ * If locating, opening or parsing the internal XML settings file has failed.
+ */
+ private static Document getDocInternal() {
+ final URL settingsURL = Plugin.class.getResource(Plugin.settingsFileName);
+ try {
+ return new SAXBuilder().build(settingsURL);
+ } catch (Exception ex) {
+ // JDOMException
+ // IOException
+ // NullPointerException
+ throw new InnerException(ex);
+ }
+ }
+
+ /**
+ * Loads the settings from a given XML document.
+ *
+ * @param aDoc
+ * Document that contains the settings.
+ */
+ private static void loadSettings(Document aDoc) {
+ try {
+ Element root = aDoc.getRootElement();
+ verifyVersion(root.getAttributeValue("ver"));
+ pluginSettings = new PluginSettings(root.getChild(PluginSettings.tag));
+ // TODO: [Cytoscape 2.8] Check if a new version of JDom is used
+ final List<?> paramSettings = root.getChildren(SettingsGroup.tag);
+ for (final Object el : paramSettings) {
+ final Element complexParamEl = (Element) el;
+ final String type = complexParamEl.getAttributeValue("type");
+ final Class<?> sGroup = Plugin.getSettingsGroupClass(type);
+ final Constructor<?> constr = sGroup.getConstructor(XMLSerializable.constructorParams);
+ final Object[] params = new Object[] { complexParamEl };
+ final SettingsGroup value = (SettingsGroup) constr.newInstance(params);
+ visualSettings.put(value.getParamID(), value);
+ }
+ } catch (SecurityException ex) {
+ throw ex;
+ } catch (Exception ex) {
+ // ClassCastException
+ // ClassNotFoundException
+ // DOMException
+ // IllegalArgumentException
+ // IllegalAccessException
+ // InstantiationException
+ // InvocationTargetException
+ // NoSuchElementException
+ // NoSuchMethodException
+ // NullPointerException
+ throw new InnerException(ex);
+ }
+ }
+
+ /**
+ * Verifies the given version is compatible with the version of this plugin.
+ * <p>
+ * In case the versions are incompatible, this method throws an exception.
+ * </p>
+ *
+ * @param aVersion
+ * Version to be checked for compatibility.
+ *
+ * @throws DOMException
+ * If <code>aVersion</code> is incompatible with {@link Plugin#version}.
+ * @throws NullPointerException
+ * If <code>aVersion</code> is <code>null</code>.
+ */
+ private static void verifyVersion(String aVersion) {
+ if (!(new Version(Plugin.version).equals(new Version(aVersion)))) {
+ throw new DOMException((short) 9, "Version is not supported");
+ }
+ }
+
+ /**
+ * Tag name used in the XML settings file to identify NetworkAnalyzer settings.
+ */
+ private static final String rootTag = "networkanalyzersettings";
+
+ /**
+ * Name of {@link #rootTag}'s attribute that specifies version of the XML settings file.
+ */
+ private static final String versionAttribute = "ver";
+
+ /**
+ * Map of the visual settings for the all complex parameters.
+ */
+ private static Map<String, SettingsGroup> visualSettings;
+
+ /**
+ * General settings of the plugin.
+ */
+ private static PluginSettings pluginSettings;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/io/StatsSerializer.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/io/StatsSerializer.java
new file mode 100644
index 0000000..0a0c1af
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/io/StatsSerializer.java
@@ -0,0 +1,352 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.data.io;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.lang.reflect.Constructor;
+import java.lang.reflect.InvocationTargetException;
+
+import de.mpg.mpi_inf.bioinf.netanalyzer.InnerException;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.ComplexParam;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Messages;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.NetworkStats;
+
+/**
+ * Controller class providing methods for loading and saving <code>NetworkStats</code> instances.
+ *
+ * @author Yassen Assenov
+ */
+public class StatsSerializer {
+
+ /**
+ * Loads network parameters from file.
+ *
+ * @param aFile
+ * File containing network parameters.
+ * @return The loaded parameters encapsulated in a <code>NetworkStatistics</code> instance;
+ * <code>null</code> if the file is not a valid network parameters file.
+ * @throws IOException
+ * If I/O error occurs.
+ * @throws FileNotFoundException
+ * If the specified file does not exist, is a directory rather than a regular file, or for
+ * some other reason cannot be opened for reading.
+ */
+ @SuppressWarnings("fallthrough")
+ public static NetworkStats load(File aFile) throws IOException {
+ NetworkStats stats = null;
+ LineReader reader = null;
+ try {
+ reader = new Netstats2Reader(new FileReader(aFile));
+ switch (getVersion(reader.readLine())) {
+ case 1:
+ reader = new Netstats1Reader((Netstats2Reader) reader);
+ // Fall through to the next case:
+ case 2:
+ stats = new NetworkStats();
+ stats.setTitle(reader.readLine());
+ for (String line = reader.readLine(); line != null; line = reader.readLine()) {
+ if (SIMPLE_HEADER.equals(line)) {
+ loadSimple(stats, reader);
+ } else if (COMPLEX_HEADER.equals(line)) {
+ loadComplex(stats, reader);
+ }
+ }
+ }
+ } catch (NumberFormatException ex) {
+ stats = null;
+ } finally {
+ IOUtils.closeStream(reader);
+ }
+ return stats;
+ }
+
+ /**
+ * Saves the computed network parameters to file.
+ *
+ * @param aStats
+ * Network parameters encapsulated in a <code>NetworkStats</code> instance.
+ * @param aFileName
+ * Name of file to be saved to.
+ *
+ * @throws FileNotFoundException
+ * If <code>aFileName</code> denotes a directory rather than a regular file, does not exist
+ * but cannot be created, or cannot be opened for any other reason.
+ * @throws IOException
+ * If I/O error occurs.
+ */
+ public static void save(NetworkStats aStats, String aFileName) throws IOException {
+ save(aStats, new FileWriter(aFileName));
+ }
+
+ /**
+ * Saves the computed network parameters to file.
+ *
+ * @param aStats
+ * Network parameters encapsulated in a <code>NetworkStats</code> instance.
+ * @param aFile
+ * File to be saved to.
+ *
+ * @throws FileNotFoundException
+ * If <code>aFile</code> is a directory rather than a regular file, does not exist but cannot
+ * be created, or cannot be opened for any other reason.
+ * @throws IOException
+ * If I/O error occurs.
+ */
+ public static void save(NetworkStats aStats, File aFile) throws IOException {
+ save(aStats, new FileWriter(aFile));
+ }
+
+ /**
+ * Loads simple network parameters from file.
+ *
+ * @param aStats
+ * Network parameters encapsulated in a <code>NetworkStats</code> instance.
+ * @param aReader
+ * Stream (open for reading) to load data from.
+ *
+ * @throws IOException
+ * If I/O error occurs, for example, if <code>aReader</code> could not be closed.
+ * @throws NumberFormatException
+ * If the data read is invalid.
+ */
+ private static void loadSimple(NetworkStats aStats, LineReader aReader) throws IOException,
+ NumberFormatException {
+ String line = aReader.readLine();
+ int linesToRead = Integer.parseInt(line);
+ for (int i = 0; i < linesToRead; ++i) {
+ String[] data = aReader.readLine().split("\\s");
+ if (!Messages.containsSimpleParam(data[0])) {
+ throw new NumberFormatException();
+ }
+ String type = data[1];
+ Object param = null;
+ if ("Boolean".equals(type)) {
+ param = new Boolean(data[2].equalsIgnoreCase("true"));
+ } else if ("Double".equals(type)) {
+ param = new Double(data[2]);
+ } else if ("Integer".equals(type)) {
+ param = new Integer(data[2]);
+ } else if ("Long".equals(type)) {
+ param = new Long(data[2]);
+ } else if ("String".equals(type)) {
+ param = data[2];
+ } else {
+ throw new NumberFormatException();
+ }
+ aStats.set(data[0], param);
+ }
+ }
+
+ /**
+ * Loads complex network parameters from file.
+ *
+ * @param aStats
+ * Network parameters encapsulated in a <code>NetworkStats</code> instance.
+ * @param aReader
+ * Stream (open for reading) to load data from.
+ * @throws IOException
+ * If I/O error occurs, for example, if <code>aReader</code> is not open.
+ * @throws NumberFormatException
+ * If the data read is invalid.
+ */
+ private static void loadComplex(NetworkStats aStats, LineReader aReader) throws IOException {
+ String line = aReader.readLine();
+ final Object[] initParams = new Object[] { null, aReader };
+ try {
+ while (line != null) {
+ String[] headerData = line.split("\\s");
+ String paramID = headerData[0];
+ String paramType = headerData[1];
+ if (!paramType.equals(SettingsSerializer.getDefaultType(paramID))) {
+ throw new NumberFormatException();
+ }
+ Class<?> type = Class.forName(getTypeName(headerData[1]));
+ Constructor<?> con = type.getConstructor(ComplexParam.loadParams);
+ initParams[0] = extractParams(headerData);
+ aStats.set(paramID, con.newInstance(initParams));
+ line = aReader.readLine();
+ }
+ } catch (SecurityException ex) {
+ throw ex;
+ } catch (IOException ex) {
+ throw ex;
+ } catch (Exception ex) {
+ if (ex instanceof ArrayIndexOutOfBoundsException || ex instanceof ClassNotFoundException
+ || ex instanceof InvocationTargetException || ex instanceof NumberFormatException) {
+ // Corrupt data
+ throw new NumberFormatException();
+ }
+ // IllegalAccessException
+ // IllegalArgumentException
+ // InstantiationException
+ // NoSuchMethodException
+ throw new InnerException(ex);
+ }
+ }
+
+ /**
+ * Saves all the computed network parameters to file.
+ *
+ * @param aStats
+ * Network parameters encapsulated in a <code>NetworkStats</code> instance.
+ * @param aWriter
+ * Stream (open for writing) to save the parameters to.
+ * @throws IOException
+ * If I/O error occurs, for example, if <code>aWriter</code> is not open.
+ */
+ public static void save(NetworkStats aStats, FileWriter aWriter) throws IOException {
+ aWriter.write(FILE_HEADERS[FILE_HEADERS.length - 1] + "\n");
+ aWriter.write(aStats.getTitle() + "\n");
+ saveSimple(aStats, aWriter);
+ saveComplex(aStats, aWriter);
+ aWriter.close();
+ }
+
+ /**
+ * Saves the computed simple network parameters to file.
+ *
+ * @param aStats
+ * Network parameters encapsulated in a <code>NetworkStats</code> instance.
+ * @param aWriter
+ * Stream (open for writing) to save the parameters to.
+ * @throws IOException
+ * If I/O error occurs, for example, if <code>aWriter</code> is not open.
+ */
+ private static void saveSimple(NetworkStats aStats, FileWriter aWriter) throws IOException {
+ String[] statNames = aStats.getComputedSimple();
+ if (statNames.length == 0) {
+ return;
+ }
+ aWriter.write(SIMPLE_HEADER + "\n" + statNames.length + "\n");
+ for (int i = 0; i < statNames.length; ++i) {
+ aWriter.write(statNames[i] + " ");
+ Object value = aStats.get(statNames[i]);
+ aWriter.write(value.getClass().getSimpleName() + " ");
+ aWriter.write(value.toString() + "\n");
+ }
+ }
+
+ /**
+ * Saves the computed complex network parameters to file.
+ *
+ * @param aStats
+ * Network parameters encapsulated in a <code>NetworkStats</code> instance.
+ * @param aWriter
+ * Stream (open for writing) to save the parameters to.
+ * @throws IOException
+ * If I/O error occurs, for example, if <code>aWriter</code> is not open.
+ */
+ private static void saveComplex(NetworkStats aStats, FileWriter aWriter) throws IOException {
+ String[] statNames = aStats.getComputedComplex();
+ if (statNames.length == 0) {
+ return;
+ }
+ aWriter.write(COMPLEX_HEADER + "\n");
+ for (int i = 0; i < statNames.length; ++i) {
+ final String name = statNames[i];
+ final ComplexParam value = aStats.getComplex(name);
+ aWriter.write(name + " " + value.getClass().getSimpleName() + " ");
+ value.save(aWriter, true);
+ }
+ }
+
+ /**
+ * Creates an array of type parameters given an array items as saved in a file.
+ * <p>
+ * In a network statistics file, the first line of a complex parameter looks like:<br/>
+ * <code>name type [typeparam]*</code><br/>
+ * This method does constructs an array that contains only the <code>typeparam</code>s given.
+ * </p>
+ *
+ * @param aHeaderData
+ * Complex parameter header data in the form of <code>String</code> array.
+ * @return Array of type parameters; an empty array if no type parameters are specified.
+ */
+ private static String[] extractParams(String[] aHeaderData) {
+ String[] params = new String[aHeaderData.length - 2];
+ for (int i = 0; i < params.length; ++i) {
+ params[i] = aHeaderData[i + 2];
+ }
+ return params;
+ }
+
+ /**
+ * Gets the full name of a specified type (class).
+ *
+ * @param aShortName
+ * short name for the type to get.
+ * @return Full name of the type, obtained by prepending the data package to it.
+ */
+ private static String getTypeName(String aShortName) {
+ String[] packageName = StatsSerializer.class.getName().split("\\.");
+ StringBuffer type = new StringBuffer(64);
+ for (int i = 0; i < packageName.length - 2; ++i) {
+ type.append(packageName[i] + ".");
+ }
+ type.append(aShortName);
+ return type.toString();
+ }
+
+ /**
+ * Gets the version of the netstats file by its header line.
+ *
+ * @param aHeader
+ * First line of the Netstats file. This string given must be <b>without</b> an end-of-line
+ * delimiter.
+ * @return Version number of the Netstats file; <code>0</code> (zero) if the <code>String</code> passed is
+ * not recognized as a Netstats header.
+ */
+ private static int getVersion(String aHeader) {
+ for (int i = 0; i < FILE_HEADERS.length; ++i) {
+ if (FILE_HEADERS[i].equals(aHeader)) {
+ return i + 1;
+ }
+ }
+ return 0;
+ }
+
+ /**
+ * Array of acceptable header lines of a ".netstats" files.
+ * <p>
+ * Note that the elements of this array are strings that do <b>not</b> include the end-of-line delimiter.
+ * </p>
+ */
+ private static final String[] FILE_HEADERS = new String[] {
+ "#org.mpii.bio.networkanalyzer Network Analysis 1.0",
+ "#de.mpg.mpi_inf.bioinf.netanalyzer Network Analysis 2.0" };
+
+ /**
+ * Line in the file indicating simple parameters follow.
+ * <p>
+ * Note that this string does <b>not</b> include the end-of-line delimiter.
+ * </p>
+ */
+ private static final String SIMPLE_HEADER = "#simple";
+
+ /**
+ * Line in the file indicating complex parameters follow.
+ * <p>
+ * Note that this string does <b>not</b> include the end-of-line delimiter.
+ * </p>
+ */
+ private static final String COMPLEX_HEADER = "#complex";
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/settings/AxesSettings.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/settings/AxesSettings.java
new file mode 100644
index 0000000..fcec5e0
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/settings/AxesSettings.java
@@ -0,0 +1,250 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.data.settings;
+
+import org.jdom.Element;
+import org.w3c.dom.DOMException;
+
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.IntRange;
+
+/**
+ * Storage class for axis-related visual settings of a chart.
+ *
+ * @author Yassen Assenov
+ * @author Sven-Eric Schelhorn
+ */
+public final class AxesSettings extends Settings {
+
+ /**
+ * Tag name used in XML settings file to identify axis-related settings.
+ */
+ public static final String tag = "axes";
+
+ /**
+ * Initializes a new instance of <code>AxesSettings</code> based on the given XML node.
+ *
+ * @param aElement Node in XML settings file that identifies axis-related settings.
+ * @throws DOMException When the given element is not an element node with the expected name ({@link #tag})
+ * or when the subtree rooted at <code>aElement</code> does not have the expected
+ * structure.
+ */
+ public AxesSettings(Element aElement) {
+ super(aElement);
+ }
+
+ /**
+ * Gets the label of the domain axis (the "x"-axis).
+ *
+ * @return Label of the domain axis.
+ */
+ public String getDomainAxisLabel() {
+ return domainAxisLabel;
+ }
+
+ /**
+ * Sets the label of the domain axis (the "x"-axis).
+ *
+ * @param aDomainAxisLabel New label of the domain axis.
+ */
+ public void setDomainAxisLabel(String aDomainAxisLabel) {
+ domainAxisLabel = aDomainAxisLabel;
+ }
+
+ /**
+ * Gets the label of the range axis (the "y"-axis).
+ *
+ * @return Label of the range axis.
+ */
+ public String getRangeAxisLabel() {
+ return rangeAxisLabel;
+ }
+
+ /**
+ * Sets the label of the range axis (the "y"-axis).
+ *
+ * @param aRangeAxisLabel New label of the range axis.
+ */
+ public void setRangeAxisLabel(String aRangeAxisLabel) {
+ rangeAxisLabel = aRangeAxisLabel;
+ }
+
+ /**
+ * Gets the value restrictions to be imposed on the domain axis.
+ *
+ * @return Value restrictions for the domain axis.
+ */
+ public IntRange getDomainRange() {
+ return domainRange;
+ }
+
+ /**
+ * Gets the value restrictions to be imposed on the range axis.
+ *
+ * @return Value restrictions for the range axis.
+ */
+ public IntRange getRangeRange() {
+ return rangeRange;
+ }
+
+ /**
+ * Gets logarithmic range axis flag.
+ *
+ * @return aLogRangeAxis Logarithmic range axis flag.
+ */
+ public boolean getLogarithmicRangeAxis() {
+ return logarithmicRangeAxis;
+ }
+
+ /**
+ * Sets logarithmic range axis flag.
+ *
+ * @param aLogRangeAxis New logarithmic range axis flag.
+ */
+ public void setLogarithmicRangeAxis(boolean aLogRangeAxis) {
+ logarithmicRangeAxis = aLogRangeAxis;
+ }
+
+ /**
+ * Gets logarithmic domain axis flag.
+ *
+ * @return aLogDomainAxis Logarithmic domain axis flag.
+ */
+ public boolean getLogarithmicDomainAxis() {
+ return logarithmicDomainAxis;
+ }
+
+ /**
+ * Sets logarithmic domain axis flag.
+ *
+ * @param aLogDomainAxis New logarithmic domain axis flag.
+ */
+ public void setLogarithmicDomainAxis(boolean aLogDomainAxis) {
+ logarithmicDomainAxis = aLogDomainAxis;
+ }
+
+ /**
+ * Gets force integer ticks flag for domain axis.
+ *
+ * @return <code>true</code> if the domain axis should have integer ticks only;
+ * <code>false</code> otherwise.
+ */
+ public boolean getIntegerDomainAxisTick() {
+ return integerDomainAxisTick;
+ }
+
+ /**
+ * Gets force integer ticks flag for range axis.
+ *
+ * @return <code>true</code> if the domain axis should have integer ticks only;
+ * <code>false</code> otherwise.
+ */
+ public boolean getIntegerRangeAxisTick() {
+ return integerRangeAxisTick;
+ }
+
+ /**
+ * Name of the tag identifying the domain axis label.
+ */
+ static final String domainAxisLabelTag = "catlabel";
+
+ /**
+ * Name of the tag identifying the range axis label.
+ */
+ static final String rangeAxisLabelTag = "rangelabel";
+
+ /**
+ * Name of the tag identifying value restrictions for the domain axis.
+ */
+ static final String domainRangeTag = "domrange";
+
+ /**
+ * Name of the tag identifying value restrictions for the range axis.
+ */
+ static final String rangeRangeTag = "ranrange";
+
+ /**
+ * Name of the tag identifying the logarithmic range axis.
+ */
+ static final String logarithmicRangeAxisTag = "lograngeaxis";
+
+ /**
+ * Name of the tag identifying the logarithmic domain axis.
+ */
+ static final String logarithmicDomainAxisTag = "logdomainaxis";
+
+ /**
+ * Name of the tag identifying the forced integer domain axis ticks.
+ */
+ static final String integerDomainAxisTickTag = "intdomainaxis";
+
+ /**
+ * Name of the tag identifying the forced integer range axis ticks.
+ */
+ static final String integerRangeAxisTickTag = "intrangeaxis";
+
+ /**
+ * Initializes a new instance of <code>AxesSettings</code>.
+ * <p>
+ * The initialized instance contains no data and therefore this constructor is used only by the
+ * {@link Settings#clone()} method.
+ * </p>
+ */
+ AxesSettings() {
+ super();
+ }
+
+ /**
+ * Label of the domain axis.
+ */
+ String domainAxisLabel;
+
+ /**
+ * Label of the range axis.
+ */
+ String rangeAxisLabel;
+
+ /**
+ * Value restrictions for the domain axis.
+ */
+ IntRange domainRange;
+
+ /**
+ * Value restrictions for the range axis.
+ */
+ IntRange rangeRange;
+
+ /**
+ * Flag for displaying the range axis logarithmically.
+ */
+ boolean logarithmicRangeAxis;
+
+ /**
+ * Flag for displaying the domain axis logarithmically.
+ */
+ boolean logarithmicDomainAxis;
+
+ /**
+ * Flag for forcing domain axis ticks to be integers.
+ */
+ boolean integerDomainAxisTick;
+
+ /**
+ * Flag for forcing range axis ticks to be integers.
+ */
+ boolean integerRangeAxisTick;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/settings/BarsSettings.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/settings/BarsSettings.java
new file mode 100644
index 0000000..aa63810
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/settings/BarsSettings.java
@@ -0,0 +1,87 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.data.settings;
+
+import java.awt.Color;
+
+import org.jdom.Element;
+import org.w3c.dom.DOMException;
+
+/**
+ * Storage class for visual settings on bars in a bar chart.
+ *
+ * @author Yassen Assenov
+ */
+public final class BarsSettings extends Settings {
+
+ /**
+ * Initializes a new instance of <code>BarsSettings</code> based on the given XML node.
+ *
+ * @param aElement Node in XML settings file that identifies bar settings.
+ * @throws DOMException When the given element is not an element node with the expected name ({@link #tag})
+ * or when the subtree rooted at <code>aElement</code> does not have the expected
+ * structure.
+ */
+ public BarsSettings(Element aElement) {
+ super(aElement);
+ }
+
+ /**
+ * Gets the color of the bars.
+ *
+ * @return Color the bars are filled with.
+ */
+ public Color getBarColor() {
+ return barColor;
+ }
+
+ /**
+ * Sets the color of the bars.
+ *
+ * @param aBarColor New color to be used for filling bars.
+ */
+ public void setBarColor(Color aBarColor) {
+ barColor = aBarColor;
+ }
+
+ /**
+ * Tag name used in XML settings file to identify bar settings.
+ */
+ static final String tag = "bars";
+
+ /**
+ * Name of the tag identifying the color of bars.
+ */
+ static final String barColorTag = "barcolor";
+
+ /**
+ * Initializes a new instance of <code>BarsSettings</code>.
+ * <p>
+ * The initialized instance contains no data and therefore this constructor is used only by the
+ * {@link Settings#clone()} method.
+ * </p>
+ */
+ BarsSettings() {
+ super();
+ }
+
+ /**
+ * Color of the bars.
+ */
+ Color barColor;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/settings/BooleanSettings.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/settings/BooleanSettings.java
new file mode 100644
index 0000000..af21d3f
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/settings/BooleanSettings.java
@@ -0,0 +1,103 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.data.settings;
+
+import org.jdom.Element;
+
+/**
+ * Storage class for flag setting.
+ *
+ * @author Yassen Assenov
+ */
+public final class BooleanSettings extends Settings {
+
+ /**
+ * Initializes a new instance of <code>BooleanSettings</code>.
+ *
+ * @param aElement Node in the XML settings file that identifies general settings.
+ */
+ public BooleanSettings(Element aElement) {
+ super();
+ name = aElement.getName();
+ value = aElement.getText().equals("true");
+ }
+
+ /**
+ * Produces an exact copy of the settings instance.
+ *
+ * @return Copy of the settings instance.
+ * @see Object#clone()
+ */
+ @Override
+ public Object clone() {
+ return new BooleanSettings(name, value);
+ }
+
+ /**
+ * Gets the value of this flag.
+ *
+ * @return Current value of the flag in the form of a <code>boolean</code>.
+ */
+ public boolean getValue() {
+ return value;
+ }
+
+ /**
+ * Sets the value of this flag.
+ *
+ * @param aValue New value of the flag in the form of a <code>boolean</code>.
+ */
+ public void setValue(boolean aValue) {
+ value = aValue;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see de.mpg.mpi_inf.bioinf.netanalyzer.data.settings.XMLSerializable#toXmlNode()
+ */
+ @Override
+ public Element toXmlNode() {
+ return new Element(name).setText(value ? "true" : "false");
+ }
+
+ /**
+ * Initializes a new instance of <code>BooleanSettings</code>.
+ * <p>
+ * This constructor is used by the {@link #clone()} method only.
+ * </p>
+ *
+ * @param aName Name of the tag to be used for this flag.
+ * @param aValue Value of the flag.
+ */
+ private BooleanSettings(String aName, boolean aValue) {
+ super();
+ name = aName;
+ value = aValue;
+ }
+
+ /**
+ * Name of the tag for this flag.
+ */
+ private String name;
+
+ /**
+ * Value of the flag.
+ */
+ private boolean value;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/settings/GeneralVisSettings.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/settings/GeneralVisSettings.java
new file mode 100644
index 0000000..8093465
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/settings/GeneralVisSettings.java
@@ -0,0 +1,117 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.data.settings;
+
+import java.awt.Color;
+
+import org.jdom.Element;
+import org.w3c.dom.DOMException;
+
+/**
+ * Storage class for general visual settings of a chart.
+ *
+ * @author Yassen Assenov
+ * @author Sven-Eric Schelhorn
+ */
+public final class GeneralVisSettings extends Settings {
+
+ /**
+ * Initializes a new instance of <code>GeneralVisSettings</code>.
+ *
+ * @param aElement Node in the XML settings file that identifies general settings.
+ * @throws DOMException When the given element is not an element node with the expected name ({@link #tag})
+ * or when the subtree rooted at <code>aElement</code> does not have the expected
+ * structure.
+ */
+ public GeneralVisSettings(Element aElement) {
+ super(aElement);
+ }
+
+ /**
+ * Gets the chart title.
+ *
+ * @return Title of the chart.
+ */
+ public String getTitle() {
+ return title;
+ }
+
+ /**
+ * Sets the chart title.
+ *
+ * @param aTitle New title of the chart.
+ */
+ public void setTitle(String aTitle) {
+ title = aTitle;
+ }
+
+ /**
+ * Gets the color of the background.
+ *
+ * @return Color the background is filled with.
+ */
+ public Color getBgColor() {
+ return bgColor;
+ }
+
+ /**
+ * Sets the color of the background.
+ *
+ * @param aBgColor New color to be used for filling the background.
+ */
+ public void setBgColor(Color aBgColor) {
+ bgColor = aBgColor;
+ }
+
+
+ /**
+ * Tag name used in XML settings file to identify general settings.
+ */
+ public static final String tag = "general";
+
+ /**
+ * Initializes a new instance of <code>GeneralVisSettings</code>.
+ * <p>
+ * The initialized instance contains no data and therefore this constructor is used only by the
+ * {@link Settings#clone()} method.
+ * </p>
+ */
+ GeneralVisSettings() {
+ super();
+ }
+
+ /**
+ * Name of the tag identifying the title.
+ */
+ static final String titleTag = "title";
+
+ /**
+ * Name of the tag identifying the background color.
+ */
+ static final String bgColorTag = "background";
+
+ /**
+ * Title of the chart.
+ */
+ String title;
+
+ /**
+ * Color of the background.
+ */
+ Color bgColor;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/settings/GridSettings.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/settings/GridSettings.java
new file mode 100644
index 0000000..4986534
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/settings/GridSettings.java
@@ -0,0 +1,144 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.data.settings;
+
+import java.awt.Color;
+
+import org.jdom.Element;
+import org.w3c.dom.DOMException;
+
+/**
+ * Storage class for gridline-related visual settings of a chart.
+ *
+ * @author Yassen Assenov
+ * @author Sven-Eric Schelhorn
+ */
+public final class GridSettings extends Settings {
+
+ /**
+ * Tag name used in XML settings file to identify axis-related settings.
+ */
+ public static final String tag = "grid";
+
+ /**
+ * Initializes a new instance of <code>GridSettings</code> based on the given XML node.
+ *
+ * @param aElement Node in XML settings file that identifies gridline-related settings.
+ * @throws DOMException When the given element is not an element node with the expected name ({@link #tag})
+ * or when the subtree rooted at <code>aElement</code> does not have the expected
+ * structure.
+ */
+ public GridSettings(Element aElement) {
+ super(aElement);
+ }
+
+ /**
+ * Gets the boolean flag signifying if we want to display horizontal gridlines.
+ *
+ * @return Flag if we display gridlines.
+ */
+ public boolean getHorizontalGridLines() {
+ return horizontalGridLines;
+ }
+
+ /**
+ * Sets the boolean flag signifying if we want to display horizontal gridlines.
+ *
+ * @param aGridLine New gridline flag.
+ */
+ public void setHorizontalGridLines(boolean aGridLine) {
+ horizontalGridLines = aGridLine;
+ }
+
+ /**
+ * Gets the boolean flag signifying if we want to display vertical gridlines.
+ *
+ * @return Flag if we display gridlines.
+ */
+ public boolean getVerticalGridLines() {
+ return verticalGridLines;
+ }
+
+ /**
+ * Sets the boolean flag signifying if we want to display vertical gridlines.
+ *
+ * @param aGridLine New gridline flag.
+ */
+ public void setVerticalGridLines(boolean aGridLine) {
+ verticalGridLines = aGridLine;
+ }
+
+ /**
+ * Gets the color of the gridlines.
+ *
+ * @return Color the background is filled with.
+ */
+ public Color getGridLinesColor() {
+ return gridLinesColor;
+ }
+
+ /**
+ * Sets the color of the gridlines.
+ *
+ * @param aBgColor New color to be used for drawing the gridlines.
+ */
+ public void setGridLinesColor(Color aBgColor) {
+ gridLinesColor = aBgColor;
+ }
+
+ /**
+ * Name of the tag identifying the gridlines flag.
+ */
+ static final String horizontalGridLinesTag = "horizontal";
+
+ /**
+ * Name of the tag identifying the gridlines flag.
+ */
+ static final String verticalGridLinesTag = "vertical";
+
+ /**
+ * Name of the tag identifying the gridlines color.
+ */
+ static final String gridLinesColorTag = "cgridlines";
+
+ /**
+ * Initializes a new instance of <code>GridSettings</code>.
+ * <p>
+ * The initialized instance contains no data and therefore this constructor is used only by the
+ * {@link Settings#clone()} method.
+ * </p>
+ */
+ GridSettings() {
+ super();
+ }
+
+ /**
+ * Flag for displaying horizontal gridlines.
+ */
+ boolean horizontalGridLines;
+
+ /**
+ * Flag for displaying vertical gridlines.
+ */
+ boolean verticalGridLines;
+
+ /**
+ * Color of the gridlines.
+ */
+ Color gridLinesColor;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/settings/IntHistogramFilterSettings.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/settings/IntHistogramFilterSettings.java
new file mode 100644
index 0000000..1e44e1b
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/settings/IntHistogramFilterSettings.java
@@ -0,0 +1,98 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.data.settings;
+
+import org.jdom.Element;
+import org.w3c.dom.DOMException;
+
+/**
+ * Settings for filters on {@link de.mpg.mpi_inf.bioinf.netanalyzer.data.IntHistogram} instances.
+ *
+ * @see de.mpg.mpi_inf.bioinf.netanalyzer.data.filter.IntHistogramFilter
+ * @author Yassen Assenov
+ */
+public class IntHistogramFilterSettings extends Settings {
+
+ /**
+ * Initializes a new instance of <code>IntHistogramFilterSettings</code> based on the given
+ * XML node.
+ *
+ * @param aElement Node in the XML settings file that identifies integer histogram filter
+ * settings.
+ * @throws DOMException When the given element is not an element node with the expected name ({@link #tag})
+ * or when the subtree rooted at <code>aElement</code> does not have the expected
+ * structure.
+ */
+ public IntHistogramFilterSettings(Element aElement) {
+ super(aElement);
+ }
+
+ /**
+ * Gets the label to be displayed for entering a value for minimal observation.
+ *
+ * @return Human-readable message explaining the semantics of the minimal observation.
+ */
+ public String getMinObservationLabel() {
+ return minObservationLabel;
+ }
+
+ /**
+ * Gets the label to be displayed for entering a value for maximal observation.
+ *
+ * @return Human-readable message explaining the semantics of the maximal observation.
+ */
+ public String getMaxObservationLabel() {
+ return maxObservationLabel;
+ }
+
+ /**
+ * Tag name used in XML settings file to identify <code>IntHistogram</code> filter settings.
+ */
+ public static final String tag = "filter";
+
+ /**
+ * Name of the tag identifying the minimal observation label.
+ */
+ static final String minObservationLabelTag = "minobslabel";
+
+ /**
+ * Name of the tag identifying the maximal observation label.
+ */
+ static final String maxObservationLabelTag = "maxobslabel";
+
+ /**
+ * Initializes a new instance of <code>IntHistogramFilterSettings</code>.
+ * <p>
+ * The initialized instance contains no data and therefore this constructor is used only by the
+ * {@link Settings#clone()} method.
+ * </p>
+ */
+ IntHistogramFilterSettings() {
+ super();
+ }
+
+ /**
+ * Label for entering value for the minimal observation.
+ */
+ String minObservationLabel;
+
+ /**
+ * Label for entering value for the maximal observation.
+ */
+ String maxObservationLabel;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/settings/IntHistogramGroup.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/settings/IntHistogramGroup.java
new file mode 100644
index 0000000..b661922
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/settings/IntHistogramGroup.java
@@ -0,0 +1,156 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.data.settings;
+
+import org.jdom.Element;
+import org.w3c.dom.DOMException;
+
+/**
+ * Group of settings used by {@link de.mpg.mpi_inf.bioinf.netanalyzer.data.IntHistogram} complex
+ * parameter type.
+ *
+ * @author Yassen Assenov
+ */
+public class IntHistogramGroup extends SettingsGroup {
+
+ /**
+ * Initializes a new instance of <code>IntHistogramGroup</code>.
+ *
+ * @param aElement Node in XML settings file for this complex parameter settings group.
+ */
+ public IntHistogramGroup(Element aElement) {
+ super(aElement);
+ try {
+ useScatter = new BooleanSettings(aElement.getChild("usescatter"));
+ general = new GeneralVisSettings(aElement.getChild(GeneralVisSettings.tag));
+ axes = new AxesSettings(aElement.getChild(AxesSettings.tag));
+ grid = new GridSettings(aElement.getChild(GridSettings.tag));
+ bars = new BarsSettings(aElement.getChild(BarsSettings.tag));
+ scatter = new ScatterSettings(aElement.getChild(ScatterSettings.tag));
+ filter = new IntHistogramFilterSettings(aElement.getChild(IntHistogramFilterSettings.tag));
+ } catch (NullPointerException ex) {
+ throw new DOMException(DOMException.NOT_FOUND_ERR, "");
+ }
+ }
+
+ /**
+ * Produces an exact copy of this settings group instance.
+ *
+ * @return Copy of the settings group instance.
+ * @see Object#clone()
+ */
+ @Override
+ public Object clone() {
+ IntHistogramGroup cloned = new IntHistogramGroup(getParamID());
+ cloned.useScatter = (BooleanSettings) useScatter.clone();
+ cloned.general = (GeneralVisSettings) general.clone();
+ cloned.axes = (AxesSettings) axes.clone();
+ cloned.grid = (GridSettings) grid.clone();
+ cloned.bars = (BarsSettings) bars.clone();
+ cloned.scatter = (ScatterSettings) scatter.clone();
+ cloned.filter = (IntHistogramFilterSettings) filter.clone();
+ return cloned;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see de.mpg.mpi_inf.bioinf.netanalyzer.data.settings.XMLSerializable#toXmlNode()
+ */
+ public Element toXmlNode() {
+ Element el = new Element(SettingsGroup.tag);
+ el.setAttribute("name", getParamID());
+ el.setAttribute("type", "IntHistogram");
+ el.addContent(useScatter.toXmlNode());
+ el.addContent(general.toXmlNode());
+ el.addContent(axes.toXmlNode());
+ el.addContent(bars.toXmlNode());
+ el.addContent(scatter.toXmlNode());
+ // New elements must NOT be added above this line (for backward compatibility)
+ el.addContent(grid.toXmlNode());
+ el.addContent(filter.toXmlNode());
+ attachDecoratorsTo(el);
+ return el;
+ }
+
+ /**
+ * Gets the "scatter" property of this settings group.
+ * <p>
+ * If the value of this property is <code>true</code>, the
+ * {@link de.mpg.mpi_inf.bioinf.netanalyzer.data.IntHistogram} this settings group applies to must be
+ * visualizes by a scatter plot. If the value is <code>false</code>, a bar chart must be used
+ * </p>
+ *
+ * @return Value of the "scatter" boolean property.
+ */
+ public boolean useScatter() {
+ return useScatter.getValue();
+ }
+
+ /**
+ * "Scatter" boolean property - if the data must be visualized by a bar chart (<code>false</code>)
+ * or a scatter plot (<code>true</code>).
+ */
+ public BooleanSettings useScatter;
+
+ /**
+ * General visual settings for the chart.
+ */
+ public GeneralVisSettings general;
+
+ /**
+ * Axis-related settings for the chart.
+ */
+ public AxesSettings axes;
+
+ /**
+ * Gridline-related settings for the chart.
+ */
+ public GridSettings grid;
+
+ /**
+ * Visual settings specific for the bar chart, in case such is used ({@link #useScatter()}
+ * <code>== false</code>).
+ */
+ public BarsSettings bars;
+
+ /**
+ * Visual settings specific for the scatter plot, in case such is used ({@link #useScatter()}
+ * <code>== true</code>).
+ */
+ public ScatterSettings scatter;
+
+ /**
+ * Settings for the filter assigned to this complex parameter type, an
+ * {@link de.mpg.mpi_inf.bioinf.netanalyzer.data.filter.IntHistogramFilter} instance.
+ */
+ public IntHistogramFilterSettings filter;
+
+ /**
+ * Initializes a new instance of <code>IntHistogramGroup</code>.
+ * <p>
+ * The initialized instance contains no data and therefore this constructor is used only by the
+ * {@link #clone()} method.
+ * </p>
+ *
+ * @param aParamID ID of the complex parameter this settings group applies to.
+ */
+ private IntHistogramGroup(String aParamID) {
+ super(aParamID);
+ }
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/settings/LongHistogramFilterSettings.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/settings/LongHistogramFilterSettings.java
new file mode 100644
index 0000000..c07a9db
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/settings/LongHistogramFilterSettings.java
@@ -0,0 +1,99 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.data.settings;
+
+import org.jdom.Element;
+import org.w3c.dom.DOMException;
+
+/**
+ * Settings for filters on {@link de.mpg.mpi_inf.bioinf.netanalyzer.data.LongHistogram} instances.
+ *
+ * @see de.mpg.mpi_inf.bioinf.netanalyzer.data.filter.LongHistogramFilter
+ * @author Yassen Assenov
+ * @author Sven-Eric Schelhorn
+ */
+public class LongHistogramFilterSettings extends Settings {
+
+ /**
+ * Initializes a new instance of <code>LongHistogramFilterSettings</code> based on the given
+ * XML node.
+ *
+ * @param aElement Node in the XML settings file that identifies long histogram filter
+ * settings.
+ * @throws DOMException When the given element is not an element node with the expected name ({@link #tag})
+ * or when the subtree rooted at <code>aElement</code> does not have the expected
+ * structure.
+ */
+ public LongHistogramFilterSettings(Element aElement) {
+ super(aElement);
+ }
+
+ /**
+ * Gets the label to be displayed for entering a value for minimal observation.
+ *
+ * @return Human-readable message explaining the semantics of the minimal observation.
+ */
+ public String getMinObservationLabel() {
+ return minObservationLabel;
+ }
+
+ /**
+ * Gets the label to be displayed for entering a value for maximal observation.
+ *
+ * @return Human-readable message explaining the semantics of the maximal observation.
+ */
+ public String getMaxObservationLabel() {
+ return maxObservationLabel;
+ }
+
+ /**
+ * Tag name used in XML settings file to identify <code>LongHistogram</code> filter settings.
+ */
+ public static final String tag = "filter";
+
+ /**
+ * Name of the tag identifying the minimal observation label.
+ */
+ static final String minObservationLabelTag = "minobslabel";
+
+ /**
+ * Name of the tag identifying the maximal observation label.
+ */
+ static final String maxObservationLabelTag = "maxobslabel";
+
+ /**
+ * Initializes a new instance of <code>LongHistogramFilterSettings</code>.
+ * <p>
+ * The initialized instance contains no data and therefore this constructor is used only by the
+ * {@link Settings#clone()} method.
+ * </p>
+ */
+ LongHistogramFilterSettings() {
+ super();
+ }
+
+ /**
+ * Label for entering value for the minimal observation.
+ */
+ String minObservationLabel;
+
+ /**
+ * Label for entering value for the maximal observation.
+ */
+ String maxObservationLabel;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/settings/LongHistogramGroup.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/settings/LongHistogramGroup.java
new file mode 100644
index 0000000..dfbc696
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/settings/LongHistogramGroup.java
@@ -0,0 +1,157 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.data.settings;
+
+import org.jdom.Element;
+import org.w3c.dom.DOMException;
+
+/**
+ * Group of settings used by {@link de.mpg.mpi_inf.bioinf.netanalyzer.data.LongHistogram} complex
+ * parameter type.
+ *
+ * @author Yassen Assenov
+ * @author Sven-Eric Schelhorn
+ */
+public class LongHistogramGroup extends SettingsGroup {
+
+ /**
+ * Initializes a new instance of <code>LongHistogramGroup</code>.
+ *
+ * @param aElement Node in XML settings file for this complex parameter settings group.
+ */
+ public LongHistogramGroup(Element aElement) {
+ super(aElement);
+ try {
+ useScatter = new BooleanSettings(aElement.getChild("usescatter"));
+ general = new GeneralVisSettings(aElement.getChild(GeneralVisSettings.tag));
+ axes = new AxesSettings(aElement.getChild(AxesSettings.tag));
+ grid = new GridSettings(aElement.getChild(GridSettings.tag));
+ bars = new BarsSettings(aElement.getChild(BarsSettings.tag));
+ scatter = new ScatterSettings(aElement.getChild(ScatterSettings.tag));
+ filter = new LongHistogramFilterSettings(aElement.getChild(LongHistogramFilterSettings.tag));
+ } catch (NullPointerException ex) {
+ throw new DOMException(DOMException.NOT_FOUND_ERR, "");
+ }
+ }
+
+ /**
+ * Produces an exact copy of this settings group instance.
+ *
+ * @return Copy of the settings group instance.
+ * @see Object#clone()
+ */
+ @Override
+ public Object clone() {
+ LongHistogramGroup cloned = new LongHistogramGroup(getParamID());
+ cloned.useScatter = (BooleanSettings) useScatter.clone();
+ cloned.general = (GeneralVisSettings) general.clone();
+ cloned.axes = (AxesSettings) axes.clone();
+ cloned.grid = (GridSettings) grid.clone();
+ cloned.bars = (BarsSettings) bars.clone();
+ cloned.scatter = (ScatterSettings) scatter.clone();
+ cloned.filter = (LongHistogramFilterSettings) filter.clone();
+ return cloned;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see de.mpg.mpi_inf.bioinf.netanalyzer.data.settings.XMLSerializable#toXmlNode()
+ */
+ public Element toXmlNode() {
+ Element el = new Element(SettingsGroup.tag);
+ el.setAttribute("name", getParamID());
+ el.setAttribute("type", "LongHistogram");
+ el.addContent(useScatter.toXmlNode());
+ el.addContent(general.toXmlNode());
+ el.addContent(axes.toXmlNode());
+ el.addContent(bars.toXmlNode());
+ el.addContent(scatter.toXmlNode());
+ // New elements must NOT be added above this line (for backward compatibility)
+ el.addContent(grid.toXmlNode());
+ el.addContent(filter.toXmlNode());
+ attachDecoratorsTo(el);
+ return el;
+ }
+
+ /**
+ * Gets the "scatter" property of this settings group.
+ * <p>
+ * If the value of this property is <code>true</code>, the
+ * {@link de.mpg.mpi_inf.bioinf.netanalyzer.data.LongHistogram} this settings group applies to must be
+ * visualizes by a scatter plot. If the value is <code>false</code>, a bar chart must be used
+ * </p>
+ *
+ * @return Value of the "scatter" boolean property.
+ */
+ public boolean useScatter() {
+ return useScatter.getValue();
+ }
+
+ /**
+ * "Scatter" boolean property - if the data must be visualized by a bar chart (<code>false</code>)
+ * or a scatter plot (<code>true</code>).
+ */
+ public BooleanSettings useScatter;
+
+ /**
+ * General visual settings for the chart.
+ */
+ public GeneralVisSettings general;
+
+ /**
+ * Axis-related setting for the chart.
+ */
+ public AxesSettings axes;
+
+ /**
+ * Gridline-related settings for the chart.
+ */
+ public GridSettings grid;
+
+ /**
+ * Visual settings specific for the bar chart, in case such is used ({@link #useScatter()}
+ * <code>== false</code>).
+ */
+ public BarsSettings bars;
+
+ /**
+ * Visual settings specific for the scatter plot, in case such is used ({@link #useScatter()}
+ * <code>== true</code>).
+ */
+ public ScatterSettings scatter;
+
+ /**
+ * Settings for the filter assigned to this complex parameter type, an
+ * {@link de.mpg.mpi_inf.bioinf.netanalyzer.data.filter.LongHistogramFilter} instance.
+ */
+ public LongHistogramFilterSettings filter;
+
+ /**
+ * Initializes a new instance of <code>LongHistogramGroup</code>.
+ * <p>
+ * The initialized instance contains no data and therefore this constructor is used only by the
+ * {@link #clone()} method.
+ * </p>
+ *
+ * @param aParamID ID of the complex parameter this settings group applies to.
+ */
+ private LongHistogramGroup(String aParamID) {
+ super(aParamID);
+ }
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/settings/PluginSettings.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/settings/PluginSettings.java
new file mode 100644
index 0000000..9247f61
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/settings/PluginSettings.java
@@ -0,0 +1,429 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.data.settings;
+
+import java.awt.Color;
+
+import org.jdom.Element;
+import org.w3c.dom.DOMException;
+
+/**
+ * Plugin's general settings.
+ *
+ * @author Yassen Assenov
+ * @author Sven-Eric Schelhorn
+ * @author Nadezhda Doncheva
+ */
+public class PluginSettings extends Settings {
+
+ /**
+ * Initializes a new instance of <code>PluginSettings</code>.
+ *
+ * @param aElement
+ * Node in the XML settings file that identifies plugin general settings.
+ * @throws DOMException
+ * When the given element is not an element node with the expected name ({@link #tag}) or when
+ * the subtree rooted at <code>aElement</code> does not have the expected structure.
+ */
+ public PluginSettings(Element aElement) {
+ super(aElement);
+ }
+
+ /**
+ * Checks if expandable chart panels must be used.
+ *
+ * @return <code>true</code> if {@link de.mpg.mpi_inf.bioinf.netanalyzer.ui.ChartExpandablePanel} must be
+ * used as building blocks for {@link de.mpg.mpi_inf.bioinf.netanalyzer.ui.AnalysisDialog};
+ * <code>false</code> otherwise.
+ */
+ public boolean getExpandable() {
+ return expandable;
+ }
+
+ /**
+ * Gets the help section about function fitting in NetworkAnalyzer.
+ *
+ * @return Document name for the "Fitting a Function" help section. Currently this section is
+ * named "Fitting a Power Law" since this is the only function NetworkAnalyzer can fit
+ * on parameter data. Concatenating the returned <code>String</code> to the help base URL gives
+ * the URL of the help on function fitting.
+ */
+ public String getHelpFitting() {
+ return helpFitting;
+ }
+
+ /**
+ * Gets the help section about interpretation of network's status.
+ *
+ * @return Document name for the "Network Interpretation" help section. Concatenating this
+ * <code>String</code> to the help base URL gives the URL of the help on network interpretations.
+ */
+ public String getHelpInterpret() {
+ return helpInterpret;
+ }
+
+ /**
+ * Gets the help section about network parameters.
+ *
+ * @return Document name for the "Network Parameters" help section. Concatenating this
+ * <code>String</code> to the help base URL gives the URL of the help on network parameters.
+ */
+ public String getHelpParams() {
+ return helpParams;
+ }
+
+ /**
+ * Gets the help section about removing duplicated edges.
+ *
+ * @return Document name for the "Remove Duplicated Edges" help section. Concatenating this
+ * <code>String</code> to the help base URL gives the URL of the help on network parameters.
+ */
+ public String getHelpRemDuplicates() {
+ return helpRemDuplicates;
+ }
+
+ /**
+ * Gets the help section about removing self-loops.
+ *
+ * @return Document name for the "Remove Self-Loops" help section. Concatenating this
+ * <code>String</code> to the help base URL gives the URL of the help on network parameters.
+ */
+ public String getHelpRemSelfloops() {
+ return helpRemSelfloops;
+ }
+
+ /**
+ * Gets the help section about plugin's settings.
+ *
+ * @return Document name for the "NetworkAnalyzer Settings" help section. Concatenating this
+ * <code>String</code> to the help base URL gives the URL of the help on network parameters.
+ */
+ public String getHelpSettings() {
+ return helpSettings;
+ }
+
+ /**
+ * Gets the base URL for the help documents of this plugin.
+ * <p>
+ * The help documents are in HTML format and are open automatically in a browser's window.
+ * </p>
+ *
+ * @return <code>String</code> containing the URL for the help documents.
+ */
+ public String getHelpUrlString() {
+ return helpUrlString;
+ }
+
+ /**
+ * Checks if node attributes are computed and stored.
+ *
+ * @return <code>true</code> if node attributes must be computed by the analyzers and stored in the
+ * hashmap provided by <code>Cytoscape.data.CyAttributes</code> and <code>false</code> otherwise.
+ */
+ public boolean getUseNodeAttributes() {
+ return useNodeAttributes;
+ }
+
+ /**
+ * Checks if edge attributes are computed and stored.
+ *
+ * @return <code>true</code> if edge attributes must be computed by the analyzers and stored in the
+ * hashmap provided by <code>Cytoscape.data.CyAttributes</code> and <code>false</code> otherwise.
+ */
+ public boolean getUseEdgeAttributes() {
+ return useEdgeAttributes;
+ }
+
+ /**
+ * Gets the color of the background.
+ *
+ * @return Color the background is filled with for visualizing network parameters.
+ */
+ public Color getBackgroundColor() {
+ return backgroundColor;
+ }
+
+ /**
+ * Gets the bright color.
+ *
+ * @return Bright color to be used for visualizing network parameters.
+ */
+ public Color getBrightColor() {
+ return brightColor;
+ }
+
+ /**
+ * Gets the middle color.
+ *
+ * @return Middle color to be used for visualizing network parameters.
+ */
+ public Color getMiddleColor() {
+ return middleColor;
+ }
+
+ /**
+ * Gets the dark color.
+ *
+ * @return Dark color to be used for visualizing network parameters.
+ */
+ public Color getDarkColor() {
+ return darkColor;
+ }
+
+ /**
+ * Sets the value of the "expandable" flag.
+ * <p>
+ * This flag identifies if expandable chart panels must be used in the dialog presenting network analysis
+ * results.
+ *
+ * @param aExpandable
+ * New value of the "expandable" flag.
+ * @see #getExpandable()
+ */
+ public void setExpandable(boolean aExpandable) {
+ expandable = aExpandable;
+ }
+
+ /**
+ * Sets the base URL for the help documents.
+ *
+ * @param aHelpUrlString
+ * New URL of the help document.
+ * @see #getHelpUrlString()
+ */
+ public void setHelpUrlString(String aHelpUrlString) {
+ helpUrlString = aHelpUrlString;
+ }
+
+ /**
+ * Sets the value of the "useNodeAttributes" flag.
+ * <p>
+ * This flag identifies if node attributes are computed and used.
+ * </p>
+ *
+ * @param aNodeAttribute
+ * New value of the "useNodeAttributes" flag.
+ * @see #getUseNodeAttributes()
+ */
+ public void setUseNodeAttributes(boolean aNodeAttribute) {
+ useNodeAttributes = aNodeAttribute;
+ }
+
+ /**
+ * Sets the value of the "useEdgeAttributes" flag.
+ * <p>
+ * This flag identifies if edge attributes are computed and used.
+ * </p>
+ *
+ * @param anEdgeAttribute
+ * New value of the "useEdgeAttributes" flag.
+ * @see #getUseEdgeAttributes()
+ */
+ public void setUseEdgeAttributes(boolean anEdgeAttribute) {
+ useEdgeAttributes = anEdgeAttribute;
+ }
+
+ /**
+ * Sets the background color to be used for visualizing network parameters.
+ *
+ * @param aBackgroundColor
+ * New value of the background color.
+ * @see #getBackgroundColor()
+ */
+ public void setBackgroundColor(Color aBackgroundColor) {
+ backgroundColor = aBackgroundColor;
+ }
+
+ /**
+ * Sets the value of the bright color to be used for visualizing network parameters.
+ *
+ * @param aBrightColor
+ * New value of the bright color.
+ * @see #getBrightColor()
+ */
+ public void setBrightColor(Color aBrightColor) {
+ brightColor = aBrightColor;
+ }
+
+ /**
+ * Sets the value of the middle color to be used for visualizing network parameters.
+ *
+ * @param aMiddleColor
+ * New value of the middle color.
+ * @see #getMiddleColor()
+ */
+ public void setMiddleColor(Color aMiddleColor) {
+ middleColor = aMiddleColor;
+ }
+
+ /**
+ * Sets the value of the dark color to be used for visualizing network parameters.
+ *
+ * @param aDarkColor
+ * New value of the dark color.
+ * @see #getDarkColor()
+ */
+ public void setDarkColor(Color aDarkColor) {
+ darkColor = aDarkColor;
+ }
+
+ /**
+ * Tag name used in XML settings file to identify plugin's general settings.
+ */
+ public static final String tag = "plugin";
+
+ /**
+ * Name of the tag identifying the "expandable" flag.
+ */
+ static final String expandableTag = "expandable";
+
+ /**
+ * Name of the tag identifying the base URL for the online help.
+ */
+ static final String helpUrlStringTag = "helpurl";
+
+ /**
+ * Name of the tag identifying the "Fitting a Function" help section.
+ */
+ static final String helpFittingTag = "helpfitting";
+
+ /**
+ * Name of the tag identifying the "Network Interpretation" help section.
+ */
+ static final String helpInterpretTag = "helpinterpret";
+
+ /**
+ * Name of the tag identifying the "Network Parameters" help section.
+ */
+ static final String helpParamsTag = "helpparams";
+
+ /**
+ * Name of the tag identifying the "Remove Duplicated Edges" help section.
+ */
+ static final String helpRemDuplicatesTag = "helpremduplicates";
+
+ /**
+ * Name of the tag identifying the "Remove Self-Loops" help section.
+ */
+ static final String helpRemSelfloopsTag = "helpremselfloops";
+
+ /**
+ * Name of the tag identifying the "Network Settings" help section.
+ */
+ static final String helpSettingsTag = "helpsettings";
+
+ /**
+ * Name of the tag identifying the the "useNodeAttributes" flag.
+ */
+ static final String useNodeAttributesTag = "nodeattributes";
+
+ /**
+ * Name of the tag identifying the the "useEdgeAttributes" flag.
+ */
+ static final String useEdgeAttributesTag = "edgeattributes";
+
+ /**
+ * Name of the tag identifying the background color.
+ */
+ static final String backgroundColorTag = "background";
+
+ /**
+ * Name of the tag identifying the background color.
+ */
+ static final String brightColorTag = "brightcolor";
+
+ /**
+ * Name of the tag identifying the background color.
+ */
+ static final String middleColorTag = "middlecolor";
+
+ /**
+ * Name of the tag identifying the background color.
+ */
+ static final String darkColorTag = "darkcolor";
+
+ /**
+ * Flag indicating if expandable panels must be used.
+ */
+ boolean expandable;
+
+ /**
+ * Help section (document) about function fitting.
+ */
+ String helpFitting;
+
+ /**
+ * Help section (document) about interpretation of network's status.
+ */
+ String helpInterpret;
+
+ /**
+ * Help section (document) about network parameters.
+ */
+ String helpParams;
+
+ /**
+ * Help section (document) about removing duplicated edges.
+ */
+ String helpRemDuplicates;
+
+ /**
+ * Help section (document) about removing self-loops.
+ */
+ String helpRemSelfloops;
+
+ /**
+ * Help section (document) about NetworkAnalyzer's settings.
+ */
+ String helpSettings;
+
+ /**
+ * Base URL for online help.
+ */
+ String helpUrlString;
+
+ /**
+ * Flag indicating if node attributes are computed.
+ */
+ boolean useNodeAttributes;
+
+ /**
+ * Flag indicating if edge attributes are computed.
+ */
+ boolean useEdgeAttributes;
+
+ /**
+ * Color to be used for the background when visualizing network parameters.
+ */
+ Color backgroundColor;
+
+ /**
+ * Bright color to be used for visualizing of network parameters.
+ */
+ Color brightColor;
+
+ /**
+ * Middle color to be used for visualizing of network parameters.
+ */
+ Color middleColor;
+
+ /**
+ * Dark color to be used for visualizing of network parameters.
+ */
+ Color darkColor;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/settings/PointShape.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/settings/PointShape.java
new file mode 100644
index 0000000..8319c20
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/settings/PointShape.java
@@ -0,0 +1,143 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.data.settings;
+
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Messages;
+
+/**
+ * Enumeration on supported shapes for points in a scatter plot.
+ *
+ * @author Yassen Assenov
+ */
+public enum PointShape {
+
+ /**
+ * Single pixel.
+ */
+ POINT,
+
+ /**
+ * Circle.
+ */
+ CIRCLE,
+
+ /**
+ * Filled circle.
+ */
+ FILLED_CIRCLE,
+
+ /**
+ * Square.
+ */
+ SQUARE,
+
+ /**
+ * Filled square.
+ */
+ FILLED_SQUARE,
+
+ /**
+ * An x-like shape.
+ */
+ CROSS;
+
+ /**
+ * Text encodings of all shapes. These encodings are returned by the method {@link #toString()}
+ * of instances of this enumeration.
+ */
+ public static String[] Texts = new String[] { "point", "circle", "filled circle", "square",
+ "filled square", "cross" };
+
+ /**
+ * Loads the point shape as encoded in the given text.
+ *
+ * @param text
+ * Text that specifies a point shape.
+ * @return The shape specified in the text, in the form of a {@link PointShape} instance.
+ *
+ * @throws IllegalArgumentException
+ * If <code>text</code> is <code>null</code> or if it does not encode a supported
+ * shape.
+ */
+ public static PointShape parse(String text) {
+ if (Texts[0].equals(text)) {
+ return POINT;
+ }
+ if (Texts[1].equals(text)) {
+ return CIRCLE;
+ }
+ if (Texts[2].equals(text)) {
+ return FILLED_CIRCLE;
+ }
+ if (Texts[3].equals(text)) {
+ return SQUARE;
+ }
+ if (Texts[4].equals(text)) {
+ return FILLED_SQUARE;
+ }
+ if (Texts[5].equals(text)) {
+ return CROSS;
+ }
+ throw new IllegalArgumentException();
+ }
+
+ /**
+ * Gets the description of this shape.
+ *
+ * @return Description, in human-readable form, of this shape.
+ */
+ public String getDescription() {
+ switch (this) {
+ case POINT:
+ return Messages.SET_SPOINT;
+ case CIRCLE:
+ return Messages.SET_SCIRCLE;
+ case FILLED_CIRCLE:
+ return Messages.SET_SFILLCIRCLE;
+ case SQUARE:
+ return Messages.SET_SSQUARE;
+ case FILLED_SQUARE:
+ return Messages.SET_SFILLSQUARE;
+ default: // CROSS:
+ return Messages.SET_SCROSS;
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.lang.Enum#toString()
+ */
+ @Override
+ public String toString() {
+ switch (this) {
+ case POINT:
+ return Texts[0];
+ case CIRCLE:
+ return Texts[1];
+ case FILLED_CIRCLE:
+ return Texts[2];
+ case SQUARE:
+ return Texts[3];
+ case FILLED_SQUARE:
+ return Texts[4];
+ default: // CROSS:
+ return Texts[5];
+ }
+ }
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/settings/Points2DFilterSettings.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/settings/Points2DFilterSettings.java
new file mode 100644
index 0000000..07742d3
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/settings/Points2DFilterSettings.java
@@ -0,0 +1,97 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.data.settings;
+
+import org.jdom.Element;
+import org.w3c.dom.DOMException;
+
+/**
+ * Settings for filters on {@link de.mpg.mpi_inf.bioinf.netanalyzer.data.Points2D} instances.
+ *
+ * @see de.mpg.mpi_inf.bioinf.netanalyzer.data.filter.Points2DFilter
+ * @author Yassen Assenov
+ */
+public class Points2DFilterSettings extends Settings {
+
+ /**
+ * Initializes a new instance of <code>Points2DFilterSettings</code> based on the given XML node.
+ *
+ * @param aElement
+ * Node in the XML settings file that identifies data points filter settings.
+ * @throws DOMException
+ * When the given element is not an element node with the expected name ({@link #tag}) or
+ * when the subtree rooted at <code>aElement</code> does not have the expected structure.
+ */
+ public Points2DFilterSettings(Element aElement) {
+ super(aElement);
+ }
+
+ /**
+ * Gets the label to be displayed for entering a value for minimal value on the x axis.
+ *
+ * @return Human-readable message explaining the semantics of the minimal x.
+ */
+ public String getMinXLabel() {
+ return minXLabel;
+ }
+
+ /**
+ * Gets the label to be displayed for entering a value for maximal value on the x axis.
+ *
+ * @return Human-readable message explaining the semantics of the maximal x.
+ */
+ public String getMaxXLabel() {
+ return maxXLabel;
+ }
+
+ /**
+ * Tag name used in XML settings file to identify <code>Points2D</code> filter settings.
+ */
+ public static final String tag = "filter";
+
+ /**
+ * Name of the tag identifying the minimal x label.
+ */
+ static final String minXLabelTag = "minxlabel";
+
+ /**
+ * Name of the tag identifying the maximal x label.
+ */
+ static final String maxXLabelTag = "maxxlabel";
+
+ /**
+ * Initializes a new instance of <code>Points2DFilterSettings</code>.
+ * <p>
+ * The initialized instance contains no data and therefore this constructor is used only by the
+ * {@link Settings#clone()} method.
+ * </p>
+ */
+ Points2DFilterSettings() {
+ super();
+ }
+
+ /**
+ * Label for entering value for the minimal value on the x axis.
+ */
+ String minXLabel;
+
+ /**
+ * Label for entering value for the maximal value on the x axis.
+ */
+ String maxXLabel;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/settings/Points2DGroup.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/settings/Points2DGroup.java
new file mode 100644
index 0000000..b69472f
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/settings/Points2DGroup.java
@@ -0,0 +1,123 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.data.settings;
+
+import org.jdom.Element;
+import org.w3c.dom.DOMException;
+
+/**
+ * Group of settings used by {@link de.mpg.mpi_inf.bioinf.netanalyzer.data.Points2D} complex parameter type.
+ *
+ * @author Yassen Assenov
+ */
+public class Points2DGroup extends SettingsGroup {
+
+ /**
+ * Initializes a new instance of <code>Points2DGroup</code>.
+ *
+ * @param aElement Node in XML settings file for this complex parameter settings group.
+ */
+ public Points2DGroup(Element aElement) {
+ super(aElement);
+ try {
+ general = new GeneralVisSettings(aElement.getChild(GeneralVisSettings.tag));
+ axes = new AxesSettings(aElement.getChild(AxesSettings.tag));
+ grid = new GridSettings(aElement.getChild(GridSettings.tag));
+ scatter = new ScatterSettings(aElement.getChild(ScatterSettings.tag));
+ final Element fe = aElement.getChild(IntHistogramFilterSettings.tag);
+ filter = (fe != null) ? new Points2DFilterSettings(fe) : null;
+ } catch (NullPointerException ex) {
+ throw new DOMException(DOMException.NOT_FOUND_ERR, "");
+ }
+ }
+
+ /**
+ * Produces an exact copy of this settings group instance.
+ *
+ * @return Copy of the settings group instance.
+ * @see Object#clone()
+ */
+ @Override
+ public Object clone() {
+ Points2DGroup cloned = new Points2DGroup(getParamID());
+ cloned.general = (GeneralVisSettings) general.clone();
+ cloned.axes = (AxesSettings) axes.clone();
+ cloned.grid = (GridSettings) grid.clone();
+ cloned.scatter = (ScatterSettings) scatter.clone();
+ cloned.filter = (filter != null) ? (Points2DFilterSettings) filter.clone() : null;
+ return cloned;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see de.mpg.mpi_inf.bioinf.netanalyzer.data.settings.XMLSerializable#toXmlNode()
+ */
+ public Element toXmlNode() {
+ Element el = new Element(SettingsGroup.tag);
+ el.setAttribute("name", getParamID());
+ el.setAttribute("type", "Points2D");
+ el.addContent(general.toXmlNode());
+ el.addContent(axes.toXmlNode());
+ el.addContent(scatter.toXmlNode());
+ // New elements must NOT be added above this line (for backward compatibility)
+ el.addContent(filter.toXmlNode());
+ el.addContent(grid.toXmlNode());
+ attachDecoratorsTo(el);
+ return el;
+ }
+
+ /**
+ * General visual settings for the plot.
+ */
+ public GeneralVisSettings general;
+
+ /**
+ * Axis-related setting for the plot.
+ */
+ public AxesSettings axes;
+
+ /**
+ * Gridline-related settings for the chart.
+ */
+ public GridSettings grid;
+
+ /**
+ * Visual settings specific for the scatter plot used.
+ */
+ public ScatterSettings scatter;
+
+ /**
+ * Settings for the filter assigned to this complex parameter type, an
+ * {@link de.mpg.mpi_inf.bioinf.netanalyzer.data.filter.Points2DFilter} instance.
+ */
+ public Points2DFilterSettings filter;
+
+ /**
+ * Initializes a new instance of <code>Points2DGroup</code>.
+ * <p>
+ * The initialized instance contains no data and therefore this constructor is used only by the
+ * {@link #clone()} method.
+ * </p>
+ *
+ * @param aParamID ID of the complex parameter this settings group applies to.
+ */
+ private Points2DGroup(String aParamID) {
+ super(aParamID);
+ }
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/settings/ReturnTypeComparator.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/settings/ReturnTypeComparator.java
new file mode 100644
index 0000000..97ce888
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/settings/ReturnTypeComparator.java
@@ -0,0 +1,47 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.data.settings;
+
+import java.lang.reflect.Method;
+import java.util.Comparator;
+
+/**
+ * Comparator of methods based on the name of their return types.
+ *
+ * @author Yassen Assenov
+ */
+public class ReturnTypeComparator implements Comparator<Method> {
+
+ /**
+ * Initializes a new instance of <code>ReturnTypeComparator</code>.
+ */
+ public ReturnTypeComparator() {
+ // No specific initialization is required.
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.util.Comparator#compare(java.lang.Object, java.lang.Object)
+ */
+ public int compare(Method o1, Method o2) {
+ final String r1 = o1.getReturnType().getSimpleName().toLowerCase();
+ final String r2 = o2.getReturnType().getSimpleName().toLowerCase();
+ return r1.compareTo(r2);
+ }
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/settings/ScatterSettings.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/settings/ScatterSettings.java
new file mode 100644
index 0000000..d911ce6
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/settings/ScatterSettings.java
@@ -0,0 +1,115 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.data.settings;
+
+import java.awt.Color;
+
+import org.jdom.Element;
+import org.w3c.dom.DOMException;
+
+/**
+ * Storage class for visual settings of scatter plots.
+ *
+ * @author Yassen Assenov
+ */
+public final class ScatterSettings extends Settings {
+
+ /**
+ * Initializes a new instance of <code>ScatterSettings</code>.
+ *
+ * @param aElement Node in the XML settings file that identifies scatter plot related settings.
+ * @throws DOMException When the given element is not an element node with the expected name ({@link #tag})
+ * or when the subtree rooted at <code>aElement</code> does not have the expected
+ * structure.
+ */
+ public ScatterSettings(Element aElement) {
+ super(aElement);
+ }
+
+ /**
+ * Gets the color of points.
+ *
+ * @return Color of points in the scatter plot.
+ */
+ public Color getPointColor() {
+ return pointColor;
+ }
+
+ /**
+ * Gets the shape for points.
+ *
+ * @return Shape of each point in the scatter plot.
+ */
+ public PointShape getPointShape() {
+ return pointShape;
+ }
+
+ /**
+ * Sets the color of points.
+ *
+ * @param aPointColor Color of points in the scatter plot.
+ */
+ public void setPointColor(Color aPointColor) {
+ pointColor = aPointColor;
+ }
+
+ /**
+ * Sets the shape for points.
+ *
+ * @param aPointShape Shape of each point in the scatter plot.
+ */
+ public void setPointShape(PointShape aPointShape) {
+ pointShape = aPointShape;
+ }
+
+ /**
+ * Tag name used in XML settings file to identify scatter plot settings.
+ */
+ static final String tag = "scatter";
+
+ /**
+ * Tag name used in XML settings file to identify color of points in the scatter plot.
+ */
+ static final String pointColorTag = "pointcolor";
+
+ /**
+ * Tag name used in XML settings file to identify point shape in the scatter plot.
+ */
+ static final String pointShapeTag = "pointshape";
+
+ /**
+ * Initializes a new instance of <code>ScatterSettings</code>.
+ * <p>
+ * The initialized instance contains no data and therefore this constructor is used only by the
+ * {@link Settings#clone()} method.
+ * </p>
+ */
+ ScatterSettings() {
+ super();
+ }
+
+ /**
+ * Color of points in the scatter plot.
+ */
+ Color pointColor;
+
+ /**
+ * Shape of each point in the scatter plot.
+ */
+ PointShape pointShape;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/settings/Settings.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/settings/Settings.java
new file mode 100644
index 0000000..a9a46e0
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/settings/Settings.java
@@ -0,0 +1,402 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.data.settings;
+
+import java.awt.Color;
+import java.lang.reflect.Field;
+import java.lang.reflect.Method;
+import java.lang.reflect.Modifier;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+import org.jdom.Element;
+import org.w3c.dom.DOMException;
+
+import de.mpg.mpi_inf.bioinf.netanalyzer.InnerException;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.IntRange;
+
+/**
+ * Base class for all NetworkAnalyzer settings.
+ *
+ * @author Yassen Assenov
+ */
+public abstract class Settings implements Cloneable, XMLSerializable {
+
+ /**
+ * Extracts the get methods for all the read/write properties of the given settings instance.
+ *
+ * @param aSettings Settings instance to query for properties.
+ * @return Array of getter methods for all the read/write properties of the settings instance;
+ * an empty array if no such properties are found.
+ */
+ public static Method[] propertyGetters(Settings aSettings) {
+ List<Method> getters = new ArrayList<Method>();
+ final Method[] dataMethods = aSettings.getClass().getMethods();
+ for (final Method m : dataMethods) {
+ final String methodName = m.getName();
+ if (methodName.startsWith("get") && m.getParameterTypes().length == 0
+ && (!methodName.equals("getClass"))) {
+ getters.add(m);
+ }
+ }
+ final Method[] result = getters.toArray(new Method[getters.size()]);
+ Arrays.sort(result, new ReturnTypeComparator());
+ return result;
+ }
+
+ /**
+ * Extracts the name of a property given its getter or setter method.
+ *
+ * @param aGetter Getter (or setter) method for the property.
+ * @return Name of the property the given method targets.
+ * @throws InnerException If the method is not a getter or setter method.
+ */
+ public static String propertyName(Method aGetter) {
+ String methodName = aGetter.getName();
+ if (methodName.startsWith("get") || methodName.startsWith("set")) {
+ return methodName.substring(3);
+ }
+ throw new InnerException(null);
+ }
+
+ /**
+ * Searches for the setter method for a property given its getter method.
+ *
+ * @param aGetter Getter method for the property of interest.
+ * @return Setter method for the property of interest, <code>null</code> if none exists.
+ */
+ public static Method findSetter(Method aGetter) {
+ Class<?>[] sParam = new Class<?>[] { aGetter.getReturnType() };
+ try {
+ return aGetter.getDeclaringClass().getMethod("set" + propertyName(aGetter), sParam);
+ } catch (NoSuchMethodException ex) {
+ return null;
+ }
+ }
+
+ /**
+ * Produces an exact copy of the settings instance.
+ *
+ * @return Copy of the settings instance.
+ * @see Object#clone()
+ */
+ @Override
+ public Object clone() {
+ try {
+ Class<? extends Settings> thisType = getClass();
+ ArrayList<Field> fields = getSettingProperties(thisType);
+ Object cloned = thisType.newInstance();
+ for (final Field f : fields) {
+ Class<?> t = f.getType();
+ Object value = f.get(this);
+ if (t == Boolean.class || t == boolean.class) {
+ // Leave the value unchanged
+ } else if (t == Color.class) {
+ value = new Color(((Color) value).getRGB());
+ } else if (t == Double.class || t == double.class) {
+ // Leave the value unchanged
+ } else if (t == Float.class || t == float.class) {
+ // Leave the value unchanged
+ } else if (t == Integer.class || t == int.class) {
+ // Leave the value unchanged
+ } else if (t == IntRange.class) {
+ // Leave the value unchanged
+ } else if (t == Long.class || t == long.class) {
+ // Leave the value unchanged
+ } else if (t == PointShape.class) {
+ // Leave the value unchanged
+ } else if (t == String.class) {
+ // Leave the value unchaged
+ } else {
+ // Unsupported type
+ throw new UnsupportedOperationException();
+ }
+ f.set(cloned, value);
+ }
+ return cloned;
+ } catch (Exception ex) {
+ // IllegalAccessException
+ // InstantiationException
+ // UnsupportedOperationException
+ throw new InnerException(ex);
+ }
+ }
+
+ /**
+ * Saves the data of the visual settings to an XML node.
+ *
+ * @return The newly created XML node which contains the data of the settings.
+ */
+ public Element toXmlNode() {
+ try {
+ Element root = new Element(getTagName());
+ ArrayList<Field> props = getSettingProperties(getClass());
+ for (final Field f : props) {
+ String tagName = getPropertyTagName(f.getName());
+ Element el = new Element(tagName);
+ Class<?> t = f.getType();
+ Object value = f.get(this);
+
+ try {
+ if (t == Boolean.class || t == boolean.class) {
+ el.setText(value.toString());
+ } else if (t == Color.class) {
+ el.setText(String.valueOf(((Color) value).getRGB()));
+ } else if (t == Double.class || t == double.class) {
+ el.setText(value.toString());
+ } else if (t == Float.class || t == float.class) {
+ el.setText(value.toString());
+ } else if (t == Integer.class || t == int.class) {
+ el.setText(value.toString());
+ } else if (t == IntRange.class) {
+ IntRange range = (IntRange) value;
+ if (range.hasMax()) {
+ el.setAttribute(MAX_ATTR, range.getMax().toString());
+ }
+ if (range.hasMin()) {
+ el.setAttribute(MIN_ATTR, range.getMin().toString());
+ }
+ } else if (t == Long.class || t == long.class) {
+ el.setText(value.toString());
+ } else if (t == PointShape.class) {
+ el.setText(value.toString());
+ } else if (t == String.class) {
+ el.setText(value.toString());
+ } else {
+ // Unsupported type
+ throw new UnsupportedOperationException();
+ }
+ } catch (Exception ex) {
+ throw new DOMException(DOMException.SYNTAX_ERR, tagName);
+ }
+
+ root.addContent(el);
+ }
+ return root;
+
+ } catch (SecurityException ex) {
+ throw ex;
+ } catch (Exception ex) {
+ if (ex instanceof DOMException) {
+ throw (DOMException) ex;
+ }
+ // NoSuchFieldException
+ // IllegalAccessException
+ // IllegalArgumentException
+ // UnsupportedOperationException
+ throw new InnerException(ex);
+ }
+ }
+
+ /**
+ * Gets all the setting properties of the given settings class.
+ *
+ * @param aClass Settings class, should be extending this class.
+ * @return List of all the settings properties as {@link java.lang.reflect.Field} instances.
+ */
+ protected static ArrayList<Field> getSettingProperties(Class<? extends Settings> aClass) {
+ Field[] fields = aClass.getDeclaredFields();
+ ArrayList<Field> settingPrs = new ArrayList<Field>(fields.length / 2);
+ for (int i = 0; i < fields.length; ++i) {
+ if (isSettingProperty(fields[i])) {
+ settingPrs.add(fields[i]);
+ }
+ }
+ return settingPrs;
+ }
+
+ /**
+ * Constructor used in cloning an instance.
+ */
+ protected Settings() {
+ // This constructor is used only in cloning and does not initialize its fields
+ }
+
+ /**
+ * Initializes a new instance of <code>Settings</code>.
+ *
+ * @param aElement Node in the XML settings file that identifies settings.
+ * @throws DOMException When the given element is not an element node with the expected name or
+ * when the subtree rooted at <code>aElement</code> does not have the expected
+ * structure.
+ */
+ protected Settings(Element aElement) {
+ verifyTagName(aElement.getName());
+
+ ArrayList<Field> props = getSettingProperties(getClass());
+ for (final Field f : props) {
+ String tagName = getPropertyTagName(f.getName());
+ Element tag = aElement.getChild(tagName);
+ if (tag == null) {
+ throw new DOMException(DOMException.NOT_FOUND_ERR, tagName);
+ }
+ String text = aElement.getChildText(tagName);
+ Object value = null;
+
+ Class<?> t = f.getType();
+ try {
+ if (t == Boolean.class || t == boolean.class) {
+ value = Boolean.valueOf(text);
+ } else if (t == Color.class) {
+ value = new Color(Integer.parseInt(text));
+ } else if (t == Double.class || t == double.class) {
+ value = Double.valueOf(text);
+ } else if (t == Float.class || t == float.class) {
+ value = Float.valueOf(text);
+ } else if (t == Integer.class || t == int.class) {
+ value = Integer.valueOf(text);
+ } else if (t == IntRange.class) {
+ Integer min = null;
+ if (tag.getAttribute(MIN_ATTR) != null) {
+ min = Integer.valueOf(tag.getAttributeValue(MIN_ATTR));
+ }
+ Integer max = null;
+ if (tag.getAttribute(MAX_ATTR) != null) {
+ max = Integer.valueOf(tag.getAttributeValue(MAX_ATTR));
+ }
+ value = new IntRange(min, max);
+ } else if (t == Long.class || t == long.class) {
+ value = Long.valueOf(text);
+ } else if (t == PointShape.class) {
+ value = PointShape.parse(text);
+ } else if (t == String.class) {
+ value = text;
+ } else {
+ // Unsupported type
+ throw new UnsupportedOperationException();
+ }
+ } catch (Exception ex) {
+ throw new DOMException(DOMException.SYNTAX_ERR, tagName);
+ }
+
+ try {
+ f.set(this, value);
+ } catch (Exception ex) {
+ // IllegalAccessException
+ // IllegalArgumentException
+ // UnsupportedOperationException
+ throw new InnerException(ex);
+ }
+ }
+ }
+
+ /**
+ * Checks if the given field stores a setting property.
+ *
+ * @param aField Field to be checked.
+ * @return <code>true</code> if the field modifiers suggest this field is used for a property,
+ * <code>false</code> if the field is <code>private</code>, <code>protected</code>
+ * or <code>static</code>.
+ */
+ private static boolean isSettingProperty(Field aField) {
+ int mods = aField.getModifiers();
+ if (Modifier.isStatic(mods) || Modifier.isPrivate(mods) || Modifier.isProtected(mods)) {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ * Name of the attribute that designates the maximum value in an integer range.
+ *
+ * @see IntRange
+ */
+ private static final String MAX_ATTR = "max";
+
+ /**
+ * Name of the attribute that designates the maximum value in an integer range.
+ *
+ * @see IntRange
+ */
+ private static final String MIN_ATTR = "min";
+
+ /**
+ * Gets the name of XML tag identifying the given property.
+ *
+ * @param aPropName Name of property to find the XML tag for.
+ * @return Name of the XML tag identifying <code>aPropName</code>.
+ * @throws SecurityException If the security manager blocks the attempt to get the value of the
+ * corresponding field through reflection.
+ */
+ private String getPropertyTagName(String aPropName) {
+ try {
+ String name = getClass().getDeclaredField(aPropName + "Tag").get(null).toString();
+ if (name == null) {
+ throw new NullPointerException();
+ }
+ return name;
+ } catch (SecurityException ex) {
+ throw ex;
+ } catch (Exception ex) {
+ // IllegalAccessException
+ // IllegalArgumentException
+ // NoSuchFieldException
+ // NullPointerException
+ throw new InnerException(ex);
+ }
+ }
+
+ /**
+ * Gets the name of the XML tag identifying the settings class.
+ *
+ * @return Name of the XML tag expected by the calling settings type.
+ * @throws IllegalArgumentException If the class calling this method does not define the
+ * <code>tag</code> field as <code>static</code>.
+ * @throws SecurityException If the security manager blocks the attempt to get the value of the
+ * <code>tag</code> field.
+ * @throws IllegalAccessException If the <code>tag</code> field is inaccessible.
+ * @throws NoSuchFieldException If the class calling this method does not define a field named
+ * <code>tag</code>.
+ */
+ private String getTagName() throws IllegalArgumentException, SecurityException,
+ IllegalAccessException, NoSuchFieldException {
+ return getClass().getDeclaredField("tag").get(null).toString();
+ }
+
+ /**
+ * Verifies the given name of XML element matches the expected name for the settings class.
+ *
+ * @param aElementName Name of the XML element to be checked.
+ * @throws SecurityException If the security manager blocks the attempt to get the value of the
+ * <code>tag</code> field through reflection.
+ * @throws DOMException If the value of the field named <code>tag</code> is different than
+ * <code>aElementName</code>.
+ * @see #getTagName()
+ */
+ private void verifyTagName(String aElementName) {
+ String tagName = null;
+ try {
+ tagName = getTagName();
+ if (tagName == null) {
+ throw new NullPointerException();
+ }
+ } catch (SecurityException ex) {
+ throw ex;
+ } catch (Exception ex) {
+ // NoSuchFieldException
+ // IllegalAccessException
+ // IllegalArgumentException
+ // NullPonterException
+ throw new InnerException(ex);
+ }
+ if (!tagName.equals(aElementName)) {
+ throw new DOMException(DOMException.NOT_FOUND_ERR, tagName);
+ }
+ }
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/settings/SettingsGroup.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/settings/SettingsGroup.java
new file mode 100644
index 0000000..e29cb96
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/settings/SettingsGroup.java
@@ -0,0 +1,101 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.data.settings;
+
+import org.jdom.Element;
+import org.w3c.dom.DOMException;
+
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Decorators;
+import de.mpg.mpi_inf.bioinf.netanalyzer.dec.Decorator;
+
+/**
+ * Base class for the group of settings for a complex parameter.
+ *
+ * @author Yassen Assenov
+ */
+public abstract class SettingsGroup
+ implements XMLSerializable {
+
+ /**
+ * Tag name used in XML settings file to identify complex parameter settings group.
+ */
+ public static final String tag = "complexparam";
+
+ /**
+ * Gets the complex parameter ID for this settings group.
+ *
+ * @return ID of the complex parameter this settings group is applied to.
+ */
+ public String getParamID() {
+ return paramID;
+ }
+
+ /**
+ * Initializes the fields of a <code>SettingsGroup</code> instance.
+ *
+ * @param aElement Node in the XML settings file that identifies complex parameter settings
+ * group.
+ * @throws DOMException When the given element is not an element node with the expected
+ * attributes.
+ */
+ protected SettingsGroup(Element aElement) {
+ paramID = aElement.getAttributeValue("name");
+ if (paramID == null) {
+ throw new DOMException(DOMException.NOT_FOUND_ERR, "");
+ }
+ Element decorators = aElement.getChild("decorators");
+ if (decorators != null) {
+ Decorators.set(paramID, decorators);
+ }
+ }
+
+ /**
+ * Initializes the fields of a <code>SettingsGroup</code> instance.
+ *
+ * @param aParamID ID of the complex parameter this settings group is applied to.
+ */
+ protected SettingsGroup(String aParamID) {
+ paramID = aParamID;
+ }
+
+ /**
+ * Attaches nodes describing the decorators for the complex parameter this setting group is
+ * applied to.
+ * <p>
+ * If no decorators are defined for this complex parameter, calling this method has no effect.
+ * </p>
+ *
+ * @param aNode Root XML node for this setting group, to which the decorators are to be
+ * attached.
+ */
+ protected void attachDecoratorsTo(Element aNode) {
+ Decorator[] decs = Decorators.get(paramID);
+ if (decs != null) {
+ Element decsEl = new Element("decorators");
+ for (int i = 0; i < decs.length; ++i) {
+ decsEl.addContent(decs[i].toXmlNode());
+ }
+ aNode.addContent(decsEl);
+ }
+ }
+
+ /**
+ * ID of the complex parameter this settings group is applied to.
+ */
+ private String paramID;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/settings/XMLSerializable.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/settings/XMLSerializable.java
new file mode 100644
index 0000000..b87d976
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/settings/XMLSerializable.java
@@ -0,0 +1,54 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.data.settings;
+
+import org.jdom.Element;
+
+/**
+ * Interface identifying the ability of a class to store its state in an XML tree using the JDOM
+ * library.
+ * <p>
+ * A class implementing this interface is recommended to have a constructor with parameters
+ * {@link #constructorParams}.
+ * </p>
+ *
+ * @author Yassen Assenov
+ */
+public interface XMLSerializable {
+
+ /**
+ * Parameters of a constructor of class that implements this interface. This identifies a
+ * constructor with a single parameter of type <code>Element</code>.
+ * <p>
+ * Every class that implements this interface should by able to create instances given an XML
+ * tree as returned by the {@link #toXmlNode()} method. This field is used when classes that
+ * implement this interface are initialized through reflection.
+ * </p>
+ */
+ public static final Class<?>[] constructorParams = new Class<?>[] { Element.class };
+
+ /**
+ * Saves the state of the class instance to an XML tree.
+ * <p>
+ * The resulting tree can be used to create identical copies of this instance.
+ * </p>
+ *
+ * @return Root of the created XML tree.
+ */
+ public Element toXmlNode();
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/ui/Cross.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/ui/Cross.java
new file mode 100644
index 0000000..2686e2b
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/ui/Cross.java
@@ -0,0 +1,283 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.data.ui;
+
+import java.awt.Rectangle;
+import java.awt.Shape;
+import java.awt.geom.AffineTransform;
+import java.awt.geom.PathIterator;
+import java.awt.geom.Point2D;
+import java.awt.geom.Rectangle2D;
+
+/**
+ * Implementer of the {@link Shape} interface for an x-like shape.
+ * <p>
+ * Instances of this shape have no area and, therefore, must not be rendered filled.
+ * </p>
+ *
+ * @author Yassen Assenov
+ */
+public class Cross implements Shape {
+
+ /**
+ * Initializes new instance of the <code>Cross</code> shape.
+ *
+ * @param aX
+ * X coordinate of the beginning of the cross.
+ * @param aY
+ * Y coordinate of the beginning of the cross.
+ * @param aWidth
+ * Width of the cross.
+ * @param aHeight
+ * Height of the cross.
+ */
+ public Cross(double aX, double aY, double aWidth, double aHeight) {
+ x = aX;
+ y = aY;
+ width = aWidth;
+ height = aHeight;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.Shape#contains(java.awt.geom.Point2D)
+ */
+ public boolean contains(Point2D p) {
+ return false;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.Shape#contains(java.awt.geom.Rectangle2D)
+ */
+ public boolean contains(Rectangle2D r) {
+ return false;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.Shape#contains(double, double)
+ */
+ public boolean contains(double x, double y) {
+ return false;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.Shape#contains(double, double, double, double)
+ */
+ public boolean contains(double x, double y, double w, double h) {
+ return false;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.Shape#getBounds()
+ */
+ public Rectangle getBounds() {
+ return new Rectangle((int) x, (int) y, (int) Math.round(width), (int) Math.round(height));
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.Shape#getBounds2D()
+ */
+ public Rectangle2D getBounds2D() {
+ return new Rectangle2D.Double(x, y, width, height);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.Shape#getPathIterator(java.awt.geom.AffineTransform)
+ */
+ public PathIterator getPathIterator(AffineTransform at) {
+ final double[] points = new double[] { x, y, x + width, y + height };
+ if (at != null) {
+ at.transform(points, 0, points, 0, 2);
+ }
+ return new Iterator(points);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.Shape#getPathIterator(java.awt.geom.AffineTransform, double)
+ */
+ public PathIterator getPathIterator(AffineTransform at, double flatness) {
+ return getPathIterator(at);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.Shape#intersects(java.awt.geom.Rectangle2D)
+ */
+ public boolean intersects(Rectangle2D r) {
+ return r.contains(x, y);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.Shape#intersects(double, double, double, double)
+ */
+ public boolean intersects(double x, double y, double w, double h) {
+ return new Rectangle2D.Double(x, y, w, h).intersects(getBounds2D());
+ }
+
+ /**
+ * X coordinate of the beginning of the cross.
+ */
+ private double x;
+
+ /**
+ * Y coordinate of the beginning of the cross.
+ */
+ private double y;
+
+ /**
+ * Height of the cross.
+ */
+ private double height;
+
+ /**
+ * Width of the cross.
+ */
+ private double width;
+
+ /**
+ * Path iterator for a (transformed) cross.
+ */
+ private class Iterator implements PathIterator {
+
+ /**
+ * Initializes a new instance of <code>Iterator</code>.
+ *
+ * @param aPoints
+ * Four-element array containing two diagonal points of the cross shape to be
+ * iterated.
+ */
+ public Iterator(double[] aPoints) {
+ points = aPoints;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.geom.PathIterator#currentSegment(float[])
+ */
+ public int currentSegment(float[] aCoords) {
+ switch (segment) {
+ case 0:
+ case 4:
+ aCoords[0] = (float) points[0];
+ aCoords[1] = (float) points[1];
+ return PathIterator.SEG_MOVETO;
+ case 1:
+ aCoords[0] = (float) points[2];
+ aCoords[1] = (float) points[3];
+ return PathIterator.SEG_LINETO;
+ case 2:
+ aCoords[0] = (float) points[0];
+ aCoords[1] = (float) points[3];
+ return PathIterator.SEG_MOVETO;
+ case 3:
+ aCoords[0] = (float) points[2];
+ aCoords[1] = (float) points[1];
+ return PathIterator.SEG_LINETO;
+ default:
+ return PathIterator.SEG_CLOSE;
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.geom.PathIterator#currentSegment(double[])
+ */
+ public int currentSegment(double[] aCoords) {
+ switch (segment) {
+ case 0:
+ case 4:
+ aCoords[0] = points[0];
+ aCoords[1] = points[1];
+ return PathIterator.SEG_MOVETO;
+ case 1:
+ aCoords[0] = points[2];
+ aCoords[1] = points[3];
+ return PathIterator.SEG_LINETO;
+ case 2:
+ aCoords[0] = points[0];
+ aCoords[1] = points[3];
+ return PathIterator.SEG_MOVETO;
+ case 3:
+ aCoords[0] = points[2];
+ aCoords[1] = points[1];
+ return PathIterator.SEG_LINETO;
+ default:
+ return PathIterator.SEG_CLOSE;
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.geom.PathIterator#getWindingRule()
+ */
+ public int getWindingRule() {
+ return WIND_EVEN_ODD;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.geom.PathIterator#isDone()
+ */
+ public boolean isDone() {
+ return (segment == 6);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.geom.PathIterator#next()
+ */
+ public void next() {
+ if (segment < 6) {
+ ++segment;
+ }
+ }
+
+ /**
+ * Four-element array containing two diagonal points of the cross shape being iterated.
+ */
+ private double[] points;
+
+ /**
+ * Current segment in the iteration.
+ */
+ private int segment = 0;
+ }
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/dec/Decorator.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/dec/Decorator.java
new file mode 100644
index 0000000..4681aa9
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/dec/Decorator.java
@@ -0,0 +1,92 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.dec;
+
+import javax.swing.JDialog;
+
+import org.jfree.chart.JFreeChart;
+
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.settings.XMLSerializable;
+import de.mpg.mpi_inf.bioinf.netanalyzer.ui.ComplexParamVisualizer;
+
+/**
+ * Base class for all decorators in NetworkAnalyzer.
+ *
+ * @author Yassen Assenov
+ */
+public abstract class Decorator implements Cloneable, XMLSerializable {
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.lang.Object#clone()
+ */
+ @Override
+ public abstract Object clone();
+
+ /**
+ * Adds a decoration to the specified chart, or updates the current one.
+ *
+ * @param aOwner Analysis dialog instance which uses this decorator.
+ * @param aChart Chart to be decorated.
+ * @param aVisualizer Visualizer that that created the chart.
+ * @param aVerbose Flag indicating if the decorator must be run in verbose mode - asking the
+ * user user to specify parameters and/or informing the user about the results.
+ */
+ public abstract void decorate(JDialog aOwner, JFreeChart aChart, ComplexParamVisualizer aVisualizer, boolean aVerbose);
+
+ /**
+ * Removes the decoration added to the specified chart.
+ * <p>
+ * If the chart was not decorated by this decorator, calling this method has no effect.
+ * </p>
+ *
+ * @param aChart Chart to be cleared of the decoration previously added.
+ */
+ public abstract void undecorate(JFreeChart aChart);
+
+ /**
+ * Gets the label of the decorator's button.
+ * <p>
+ * The return value of this method typically depends on the state of the decorator, as returned
+ * by the {@link #isActive()} method.
+ * </p>
+ *
+ * @return Label for the button in the form of a <code>String</code> instance.
+ */
+ public abstract String getButtonLabel();
+
+ /**
+ * Gets the tooltip for the decorator's button.
+ * <p>
+ * The return value of this method typically depends on the state of the decorator, as returned
+ * by the {@link #isActive()} method.
+ * </p>
+ *
+ * @return Tooltip for the button in the form of a <code>String</code> instance;
+ * <code>null</code> if no tooltip is to be displayed.
+ */
+ public abstract String getButtonToolTip();
+
+ /**
+ * Checks if the decorator is currently active.
+ *
+ * @return <code>true</code> if the decorator is active; <code>false</code> otherwise.
+ */
+ public abstract boolean isActive();
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/dec/Fitter.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/dec/Fitter.java
new file mode 100644
index 0000000..67f65fc
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/dec/Fitter.java
@@ -0,0 +1,160 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.dec;
+
+import java.awt.geom.Point2D;
+
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.ArrayUtils;
+
+/**
+ * Utility class providing methods for fitting functions and working with numerical sequences.
+ *
+ * @author Yassen Assenov
+ */
+public abstract class Fitter {
+
+ /**
+ * Fits a power to a set of data points using the least squares method.
+ *
+ * @param aPoints Set of data points to fit a power law to. All data points must have positive
+ * coordinates.
+ * @return Coefficients of the fitted power law (<i>y</i> = <i>αx<sup>β</sup></i>)
+ * encapsulated in a <code>Point2D.Double</code> instance.
+ *
+ * @throws NullPointerException If <code>aPoints</code> is <code>null</code>.
+ */
+ public static Point2D.Double leastSquaresPowerLawFit(Point2D.Double[] aPoints) {
+ final int n = aPoints.length;
+ double[] lnX = new double[n];
+ double[] lnY = new double[n];
+ for (int i = 0; i < n; ++i) {
+ lnX[i] = Math.log(aPoints[i].x);
+ lnY[i] = Math.log(aPoints[i].y);
+ }
+ final Point2D.Double coefs = computeLeastSquares(lnX, lnY);
+ coefs.x = Math.exp(coefs.x);
+ return coefs;
+ }
+
+ /**
+ * Fits a line to a set of data points using the least squares method.
+ *
+ * @param aPoints Set of data points to fit a line to.
+ * @return Coefficients of the fitted line (<i>y</i> = <i>α</i> + <i>x β</i>)
+ * encapsulated in a <code>Point2D.Double</code> instance.
+ */
+ public static Point2D.Double leastSquaresLineFit(Point2D.Double[] aPoints) {
+ final int count = aPoints.length;
+ final double[] x = new double[count];
+ final double[] y = new double[count];
+ ArrayUtils.coordinateSplit(aPoints, x, y);
+ return computeLeastSquares(x, y);
+ }
+
+ /**
+ * Computes the Pearson correlation coefficient between the two data series.
+ *
+ * @param aSeries1 First series of values.
+ * @param aSeries2 Second series of values.
+ * @return Correlation between <code>aSeries1</code> and <code>aSeries2</code>.
+ *
+ * @throws ArithmeticException If the correlation between the two series cannot be computed.
+ * @throws IllegalArgumentException If the length of <code>aSeries1</code> is different than
+ * the length of <code>aSeries2</code>, or if the series are empty.
+ * @throws NullPointerException If <code>aSeries1</code> or <code>aSeries2</code> is
+ * <code>null</code>.
+ */
+ public static double computeCorr(double[] aSeries1, double[] aSeries2) {
+ final int count = aSeries1.length;
+ if (count == 0 || aSeries2.length != count) {
+ throw new IllegalArgumentException();
+ }
+ final double mean1 = ArrayUtils.sum(aSeries1) / count;
+ final double mean2 = ArrayUtils.sum(aSeries2) / count;
+ double nom = 0;
+ double denom1 = 0;
+ double denom2 = 0;
+ for (int i = 0; i < count; ++i) {
+ final double diff1 = aSeries1[i] - mean1;
+ final double diff2 = aSeries2[i] - mean2;
+ nom += diff1 * diff2;
+ denom1 += diff1 * diff1;
+ denom2 += diff2 * diff2;
+ }
+ if (denom1 == 0 || denom2 == 0) {
+ throw new ArithmeticException();
+ }
+ return nom / Math.sqrt(denom1 * denom2);
+ }
+
+ /**
+ * Computes the coefficient of determination for the given data series and prediction outcomes.
+ *
+ * @param aValues True data values.
+ * @param aPredicted Predicted values.
+ * @return R-Squared coefficient for the given true and predicted data series.
+ *
+ * @throws ArithmeticException If the R-Squared value cannot be computed.
+ * @throws IllegalArgumentException If the length of <code>aValues</code> is different than
+ * the length of <code>aPredicted</code>, or if the series are empty.
+ * @throws NullPointerException If <code>aValues</code> or <code>aPredicted</code> is
+ * <code>null</code>.
+ */
+ public static double computeRSquared(double[] aValues, double[] aPredicted) {
+ final int count = aValues.length;
+ if (count == 0 || aPredicted.length != count) {
+ throw new IllegalArgumentException();
+ }
+ final double mean = ArrayUtils.mean(aValues);
+ double nom = 0;
+ double denom = 0;
+ for (int i = 0; i < count; ++i) {
+ final double diff1 = aPredicted[i] - mean;
+ final double diff2 = aValues[i] - mean;
+ nom += diff1 * diff1;
+ denom += diff2 * diff2;
+ }
+ if (denom == 0) {
+ throw new ArithmeticException();
+ }
+ return nom / denom;
+ }
+
+ /**
+ * Fits a line to a set of data points using the least squares method.
+ *
+ * @param aX Array storing the <i>x</i> values of the data points.
+ * @param aY Array storing the <i>y</i> values of the data points.
+ * @return Coefficients of the fitted line (<i>y</i> = <i>α + β x</i>)
+ * encapsulated in a <code>Point2D.Double</code> instance; <code>null</code> if a
+ * line could not be fitted.
+ */
+ private static Point2D.Double computeLeastSquares(double[] aX, double[] aY) {
+ final double sumX = ArrayUtils.sum(aX);
+ final double sumY = ArrayUtils.sum(aY);
+ final double n = aX.length;
+
+ final double b = (n * ArrayUtils.sumMult(aX, aY) - sumX * sumY)
+ / (n * ArrayUtils.sumSquares(aX) - sumX * sumX);
+ final double a = (sumY - b * sumX) / n;
+ if (Double.isNaN(a) || Double.isNaN(b)) {
+ return null;
+ }
+ return new Point2D.Double(a, b);
+ }
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/dec/LeastSquaresLineDecorator.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/dec/LeastSquaresLineDecorator.java
new file mode 100644
index 0000000..edb567f
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/dec/LeastSquaresLineDecorator.java
@@ -0,0 +1,280 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.dec;
+
+import java.awt.geom.Point2D;
+
+import javax.swing.JDialog;
+
+import org.jdom.Element;
+import org.jfree.chart.ChartPanel;
+import org.jfree.chart.JFreeChart;
+import org.jfree.chart.plot.XYPlot;
+import org.jfree.data.xy.XYSeries;
+import org.jfree.data.xy.XYSeriesCollection;
+
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.ArrayUtils;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Messages;
+import de.mpg.mpi_inf.bioinf.netanalyzer.sconnect.HelpConnector;
+import de.mpg.mpi_inf.bioinf.netanalyzer.ui.ComplexParamVisualizer;
+import de.mpg.mpi_inf.bioinf.netanalyzer.ui.Utils;
+import de.mpg.mpi_inf.bioinf.netanalyzer.ui.charts.JFreeChartConn;
+import de.mpg.mpi_inf.bioinf.netanalyzer.ui.dec.FitData;
+import de.mpg.mpi_inf.bioinf.netanalyzer.ui.dec.FittingReportDialog;
+
+/**
+ * Decorator for fitting a line with the least squares methods.
+ * <p>
+ * The power law has the form f(x) = α + β x. The coefficients are stored in a
+ * <code>Point2D.Double</code> instance as a couple (α, β).
+ * </p>
+ *
+ * @author Yassen Assenov
+ */
+public class LeastSquaresLineDecorator extends TwoCoefsDecorator {
+
+ /**
+ * Initializes a new instance of <code>LeastSquaresLineDecorator</code>.
+ *
+ * @param aElement Node in XML settings file that defines a least squares linear fitter.
+ */
+ public LeastSquaresLineDecorator(Element aElement) {
+ super(null);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see de.mpg.mpi_inf.bioinf.netanalyzer.dec.Decorator#clone()
+ */
+ @Override
+ public Object clone() {
+ return new LeastSquaresLineDecorator(coefs);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see de.mpg.mpi_inf.bioinf.netanalyzer.dec.Decorator#decorate(javax.swing.JDialog,
+ * org.jfree.chart.JFreeChart, de.mpg.mpi_inf.bioinf.netanalyzer.ui.ComplexParamVisualizer,
+ * boolean)
+ */
+ @Override
+ public void decorate(JDialog aOwner, JFreeChart aChart, ComplexParamVisualizer aVisualizer,
+ boolean aVerbose) {
+ clearDataset(aChart, LeastSquaresLineDecorator.seriesName);
+
+ final Point2D.Double[] dataPoints = JFreeChartConn.extractData(aChart);
+ if (dataPoints.length < 2) {
+ // Error - not enough data points
+ if (aVerbose) {
+ Utils.showErrorBox(aOwner, Messages.DT_FIT, Messages.SM_FITLINENODATA);
+ }
+ return;
+ }
+ coefs = Fitter.leastSquaresLineFit(dataPoints);
+
+ if (coefs != null) {
+ final XYSeries newData = createFittingData(dataPoints, isLinear(aVisualizer.getSettings()));
+ final XYPlot plot = aChart.getXYPlot();
+ int i = getDatasetIndex(plot, LeastSquaresLineDecorator.seriesName);
+ if (i == -1) {
+ i = createDataset(plot);
+ }
+ plot.setDataset(i, new XYSeriesCollection(newData));
+
+ if (aVerbose) {
+ // Compute correlation
+ final int count = dataPoints.length;
+ final double[] s1 = new double[count];
+ final double[] s2 = new double[count];
+ for (int j = 0; j < count; ++j) {
+ s1[j] = dataPoints[j].y;
+ s2[j] = valueAt(dataPoints[j].x);
+ }
+ Double corr = null;
+ Double rsquared = null;
+ try {
+ corr = new Double(Fitter.computeCorr(s1, s2));
+ } catch (ArithmeticException ex) {
+ // Correlation could not be computed; ignore
+ }
+ try {
+ rsquared = new Double(Fitter.computeRSquared(s1, s2));
+ } catch (ArithmeticException ex) {
+ // R-Squared could not be computed; ignore
+ }
+
+ // Inform the user what the coefficients are
+ showReport(aOwner, corr, rsquared);
+ }
+ } else {
+ // Could not fit a line
+ if (aVerbose) {
+ Utils.showErrorBox(aOwner, Messages.DT_FIT, Messages.SM_FITLINEERROR);
+ }
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see de.mpg.mpi_inf.bioinf.netanalyzer.dec.Decorator#getButtonLabel()
+ */
+ @Override
+ public String getButtonLabel() {
+ return isActive() ? Messages.DI_REMOVELINE : Messages.DI_FITLINE;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see de.mpg.mpi_inf.bioinf.netanalyzer.dec.Decorator#getButtonToolTip()
+ */
+ @Override
+ public String getButtonToolTip() {
+ return isActive() ? null : Messages.TT_FITLINE;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see de.mpg.mpi_inf.bioinf.netanalyzer.dec.Decorator#undecorate(org.jfree.chart.JFreeChart)
+ */
+ @Override
+ public void undecorate(JFreeChart aChart) {
+ clearDataset(aChart, LeastSquaresLineDecorator.seriesName);
+ coefs = null;
+ }
+
+ /**
+ * Initializes a new instance of <code>LeastSquaresLineaDecorator</code>.
+ * <p>
+ * This constructor is used only by the {@link #clone()} method.
+ * </p>
+ *
+ * @param aCoefs Coefficients of the fitted line. Set this parameter to <code>null</code> if
+ * coefficients are not computed.
+ */
+ protected LeastSquaresLineDecorator(Point2D.Double aCoefs) {
+ super(aCoefs);
+ }
+
+ /**
+ * Name of the data series this decorator adds to the chart.
+ */
+ private static final String seriesName = "LS Linear";
+
+ /**
+ * Creates a collection of points lying on the line determined by the computed coefficients.
+ *
+ * @param aPoints Data points to which the line was fitted. They are used to determine the range
+ * in which the newly created data series will lie.
+ * @param aIsLinear Flag indicating if the points will be drawn on a plot with linear axes only.
+ * If this parameter is <code>true</code>, this method creates only two points.
+ * @return Newly created collection of points that lie on the line determined by the
+ * coefficients in {@link #coefs}.
+ */
+ private XYSeries createFittingData(Point2D.Double[] aPoints, boolean aIsLinear) {
+ XYSeries series = new XYSeries(LeastSquaresLineDecorator.seriesName, false, false);
+
+ final Point2D.Double min = new Point2D.Double();
+ final Point2D.Double max = new Point2D.Double();
+ ArrayUtils.minMax(aPoints, min, max);
+ final double xmin = min.x;
+ final double xmax = max.x;
+ final double ymin = min.y;
+ final double ymax = max.y;
+ final int resolution = ChartPanel.DEFAULT_WIDTH;
+ final double step = (xmax - xmin) / resolution;
+
+ if (aIsLinear) {
+ double x = xmin;
+ double y = valueAt(x);
+ if (y < ymin) {
+ y = valueAt(x = pointAt(ymin));
+ } else if (ymax < y) {
+ y = valueAt(x = pointAt(ymax));
+ }
+ series.add(x, y);
+
+ x = xmax;
+ y = valueAt(x);
+ if (y < ymin) {
+ y = valueAt(x = pointAt(ymin));
+ } else if (ymax < y) {
+ y = valueAt(x = pointAt(ymax));
+ }
+ series.add(x, y);
+ } else {
+ double x = xmin;
+ for (int i = 0; i < resolution; ++i) {
+ final double y = valueAt(x);
+ if (ymin <= y && y <= ymax) {
+ series.add(x, y);
+ }
+ x += step;
+ }
+ final double y = valueAt(xmax);
+ if (ymin <= y && y <= ymax) {
+ series.add(xmax, y);
+ }
+ }
+ return series;
+ }
+
+ /**
+ * Displays a dialog to report the result of fitting a line.
+ *
+ * @param aOwner Dialog from which the report dialog is to be displayed.
+ * @param aCorr Correlation between the original and the fitted data points.
+ * @param aRSquared R-Squared value for goodness of the fit.
+ */
+ private void showReport(JDialog aOwner, Double aCorr, Double aRSquared) {
+ final String linearSection = "#linear";
+ final String helpURL = HelpConnector.getFittingURL() + linearSection;
+ final FitData data = new FitData(Messages.SM_FITLINE, coefs, aCorr, aRSquared, helpURL);
+ FittingReportDialog d = new FittingReportDialog(aOwner, Messages.DT_FITTED, data);
+ d.setVisible(true);
+ }
+
+ /**
+ * Computes the fitted value at a given point.
+ *
+ * @param aPoint Point to compute the fitted value at.
+ * @return Fitted value at <code>aPoint</code>, computed according to the formula <i>f</i>(<i>x</i>) =
+ * <i>α</i> + <i>x β</i>.
+ */
+ private double valueAt(double aPoint) {
+ return coefs.x + aPoint * coefs.y;
+ }
+
+ /**
+ * Computes the inverted function of the fitted line.
+ *
+ * @param aValue Value of the fitted line.
+ * @return Point <code>x</code> such that the value of the line at <code>x</code>
+ * (approximately) equals <code>aValue</code>.
+ */
+ private double pointAt(double aValue) {
+ if (-EPSILON <= coefs.y && coefs.y <= EPSILON) {
+ return 0;
+ }
+ return (aValue - coefs.x) / coefs.y;
+ }
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/dec/LeastSquaresPowerLawDecorator.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/dec/LeastSquaresPowerLawDecorator.java
new file mode 100644
index 0000000..0e0acc3
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/dec/LeastSquaresPowerLawDecorator.java
@@ -0,0 +1,293 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.dec;
+
+import java.awt.geom.Point2D;
+
+import javax.swing.JDialog;
+import javax.swing.JOptionPane;
+
+import org.jdom.Element;
+import org.jfree.chart.ChartPanel;
+import org.jfree.chart.JFreeChart;
+import org.jfree.chart.plot.XYPlot;
+import org.jfree.data.xy.XYSeries;
+import org.jfree.data.xy.XYSeriesCollection;
+
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.ArrayUtils;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Messages;
+import de.mpg.mpi_inf.bioinf.netanalyzer.sconnect.HelpConnector;
+import de.mpg.mpi_inf.bioinf.netanalyzer.ui.ComplexParamVisualizer;
+import de.mpg.mpi_inf.bioinf.netanalyzer.ui.Utils;
+import de.mpg.mpi_inf.bioinf.netanalyzer.ui.charts.JFreeChartConn;
+import de.mpg.mpi_inf.bioinf.netanalyzer.ui.dec.FitData;
+import de.mpg.mpi_inf.bioinf.netanalyzer.ui.dec.FittingReportDialog;
+
+/**
+ * Decorator for fitting a power law with the least squares methods.
+ * <p>
+ * The power law has the form f(x) = α x<sup>β</sup>. The coefficients are stored in a
+ * <code>Point2D.Double</code> instance as a couple (α, β).
+ * </p>
+ *
+ * @author Yassen Assenov
+ */
+public class LeastSquaresPowerLawDecorator extends TwoCoefsDecorator {
+
+ /**
+ * Initializes a new instance of <code>LeastSquaresPowerLawDecorator</code>.
+ *
+ * @param aElement Node in XML settings file that defines a least squares power law fitter.
+ */
+ public LeastSquaresPowerLawDecorator(Element aElement) {
+ super(null);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.lang.Object#clone()
+ */
+ @Override
+ public Object clone() {
+ return new LeastSquaresPowerLawDecorator(coefs);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see de.mpg.mpi_inf.bioinf.netanalyzer.dec.Decorator#decorate(javax.swing.JDialog,
+ * org.jfree.chart.JFreeChart, de.mpg.mpi_inf.bioinf.netanalyzer.ui.ComplexParamVisualizer,
+ * boolean)
+ */
+ @Override
+ public void decorate(JDialog aOwner, JFreeChart aChart, ComplexParamVisualizer aVisualizer, boolean aVerbose) {
+ clearDataset(aChart, seriesName);
+ final Point2D.Double[] dataPoints = JFreeChartConn.extractData(aChart);
+ final Point2D.Double[] posPoints = keepPositive(dataPoints);
+ if (posPoints != dataPoints && aVerbose) {
+ // Display a warning that not all points will be included in the fit
+ if (aVerbose) {
+ JOptionPane.showMessageDialog(aOwner, Messages.SM_FITNONPOSITIVE, Messages.DT_FIT,
+ JOptionPane.WARNING_MESSAGE);
+ }
+ }
+ if (posPoints.length < 2) {
+ // Error - not enough data points
+ if (aVerbose) {
+ Utils.showErrorBox(aOwner, Messages.DT_FIT, Messages.SM_FITPLNODATA);
+ }
+ return;
+ }
+ coefs = Fitter.leastSquaresPowerLawFit(posPoints);
+
+ if (coefs != null) {
+ final XYSeries newData = createFittingData(posPoints, isLogLog(aVisualizer.getSettings()));
+ final XYPlot plot = aChart.getXYPlot();
+ int i = getDatasetIndex(plot, seriesName);
+ if (i == -1) {
+ i = createDataset(plot);
+ }
+ plot.setDataset(i, new XYSeriesCollection(newData));
+
+ if (aVerbose) {
+ // Compute correlation
+ final int count = posPoints.length;
+ final double[] s1 = new double[count];
+ final double[] s2 = new double[count];
+ for (int j = 0; j < count; ++j) {
+ s1[j] = posPoints[j].y;
+ s2[j] = valueAt(posPoints[j].x);
+ }
+ Double corr = null;
+ Double rsquared = null;
+ try {
+ corr = new Double(Fitter.computeCorr(s1, s2));
+ } catch (ArithmeticException ex) {
+ // Correlation could not be computed; ignore
+ }
+ try {
+ ArrayUtils.log(s1, true);
+ ArrayUtils.log(s2, true);
+ rsquared = new Double(Fitter.computeRSquared(s1, s2));
+ } catch (ArithmeticException ex) {
+ // R-Squared could not be computed; ignore
+ }
+
+ // Inform the user what the coefficients are
+ showReport(aOwner, corr, rsquared);
+ }
+ } else {
+ // Could not fit power law
+ if (aVerbose) {
+ Utils.showErrorBox(aOwner, Messages.DT_FIT, Messages.SM_FITPLERROR);
+ }
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see de.mpg.mpi_inf.bioinf.netanalyzer.dec.Decorator#undecorate(org.jfree.chart.JFreeChart)
+ */
+ @Override
+ public void undecorate(JFreeChart aChart) {
+ clearDataset(aChart, seriesName);
+ coefs = null;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see de.mpg.mpi_inf.bioinf.netanalyzer.dec.Decorator#getButtonLabel()
+ */
+ @Override
+ public String getButtonLabel() {
+ return isActive() ? Messages.DI_REMOVEPL : Messages.DI_FITPL;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see de.mpg.mpi_inf.bioinf.netanalyzer.dec.Decorator#getButtonToolTip()
+ */
+ @Override
+ public String getButtonToolTip() {
+ return isActive() ? null : Messages.TT_FITPL;
+ }
+
+ /**
+ * Name of the data series this decorator adds to the chart.
+ */
+ private static final String seriesName = "LS Power Law";
+
+ /**
+ * Initializes a new instance of <code>LeastSquaresPowerLawDecorator</code>.
+ * <p>
+ * This constructor is used only by the {@link #clone()} method.
+ * </p>
+ *
+ * @param aCoefs Coefficients of the fitted power law. Set this parameter to <code>null</code>
+ * if coefficients are not computed.
+ */
+ protected LeastSquaresPowerLawDecorator(Point2D.Double aCoefs) {
+ super(aCoefs);
+ }
+
+ /**
+ * Creates a collection of points that adhere to the power law with the computed coefficients.
+ *
+ * @param aPoints Data points to which the power law was fitted. They are used to determine the
+ * range in which the newly created data series will lie.
+ * @param aIsLogLog Flag indicating if the points will be drawn on a log-log plot. If this
+ * parameter is <code>true</code>, this method creates only two points.
+ * @return Newly created collection of points that follow the power law with coefficients in
+ * {@link #coefs}.
+ */
+ protected XYSeries createFittingData(Point2D.Double[] aPoints, boolean aIsLogLog) {
+ XYSeries series = new XYSeries(seriesName, false, false);
+
+ final Point2D.Double min = new Point2D.Double();
+ final Point2D.Double max = new Point2D.Double();
+ ArrayUtils.minMax(aPoints, min, max);
+ final double xmin = min.x;
+ final double xmax = max.x;
+ final double ymin = min.y;
+ final double ymax = max.y;
+ if (xmin != 0) {
+ final int resolution = ChartPanel.DEFAULT_WIDTH;
+ final double step = (xmax - xmin) / resolution;
+
+ if (aIsLogLog) {
+ double x = xmin;
+ double y = valueAt(x);
+ if (y < ymin) {
+ y = valueAt(x = pointAt(ymin));
+ } else if (ymax < y) {
+ y = valueAt(x = pointAt(ymax));
+ }
+ series.add(x, y);
+
+ x = xmax;
+ y = valueAt(x);
+ if (y < ymin) {
+ y = valueAt(x = pointAt(ymin));
+ } else if (ymax < y) {
+ y = valueAt(x = pointAt(ymax));
+ }
+ series.add(x, y);
+ } else {
+ double x = xmin;
+ for (int i = 0; i < resolution; ++i) {
+ final double y = valueAt(x);
+ if (ymin <= y && y <= ymax) {
+ series.add(x, y);
+ }
+ x += step;
+ }
+ final double y = valueAt(xmax);
+ if (ymin <= y && y <= ymax) {
+ series.add(xmax, y);
+ }
+ }
+ }
+ return series;
+ }
+
+ /**
+ * Displays a dialog to report the result of fitting the power law.
+ *
+ * @param aOwner Dialog from which the report dialog is to be displayed.
+ * @param aCorr Correlation between the original and the fitted data points.
+ * @param aRSquared R-Squared value, as computed on a logarithmized data.
+ */
+ private void showReport(JDialog aOwner, Double aCorr, Double aRSquared) {
+ final String powerLawSection = "#powerlaw";
+ final String helpURL = HelpConnector.getFittingURL() + powerLawSection;
+ final String note = "R-squared is computed on logarithmized values.";
+ final FitData data = new FitData(Messages.SM_FITPL, coefs, aCorr, aRSquared, helpURL, note);
+ FittingReportDialog d = new FittingReportDialog(aOwner, Messages.DT_FITTED, data);
+ d.setVisible(true);
+ }
+
+ /**
+ * Computes the fitted value at a given point.
+ *
+ * @param aPoint Point to compute the fitted value at.
+ * @return Fitted value at <code>aPoint</code>, computed according to the power law f(x) =
+ * αx<sup>β</sup>.
+ */
+ private double valueAt(double aPoint) {
+ return coefs.x * de.mpg.mpi_inf.bioinf.netanalyzer.data.Utils.pow(aPoint, coefs.y);
+ }
+
+ /**
+ * Computes the inverted function of the fitted power law.
+ *
+ * @param aValue Value of the fitted power law.
+ * @return Point <code>x</code> such that the value of the power law at <code>x</code>
+ * (approximately) equals <code>aValue</code>.
+ */
+ private double pointAt(double aValue) {
+ if (-EPSILON <= coefs.x && coefs.x <= EPSILON) {
+ return 0;
+ }
+ final double power = coefs.y != 0 ? 1 / coefs.y : 1;
+ return de.mpg.mpi_inf.bioinf.netanalyzer.data.Utils.pow(aValue / coefs.x, power);
+ }
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/dec/TwoCoefsDecorator.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/dec/TwoCoefsDecorator.java
new file mode 100644
index 0000000..6c37010
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/dec/TwoCoefsDecorator.java
@@ -0,0 +1,211 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.dec;
+
+import java.awt.geom.Point2D;
+
+import org.jdom.Element;
+import org.jfree.chart.JFreeChart;
+import org.jfree.chart.plot.DatasetRenderingOrder;
+import org.jfree.chart.plot.XYPlot;
+import org.jfree.chart.renderer.xy.XYLineAndShapeRenderer;
+import org.jfree.data.xy.XYSeries;
+import org.jfree.data.xy.XYSeriesCollection;
+
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.settings.AxesSettings;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.settings.IntHistogramGroup;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.settings.LongHistogramGroup;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.settings.Points2DGroup;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.settings.SettingsGroup;
+
+/**
+ * Base class for all decorators which are uniquely identified by a pair of coefficients.
+ *
+ * @author Yassen Assenov
+ */
+public abstract class TwoCoefsDecorator extends Decorator {
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see de.mpg.mpi_inf.bioinf.netanalyzer.dec.Decorator#isActive()
+ */
+ @Override
+ public boolean isActive() {
+ return coefs != null;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see de.mpg.mpi_inf.bioinf.netanalyzer.data.settings.XMLSerializable#toXmlNode()
+ */
+ public Element toXmlNode() {
+ return new Element(this.getClass().getSimpleName());
+ }
+
+ /**
+ * Checks if the given settings group specifies a plot with two linear axes.
+ *
+ * @param aSettings Settings group to be checked.
+ * @return <code>false</code> if the settings group and contains a logarithm domain axis flag
+ * which is enabled or a logarithm range axis flags which is enabled; <code>true</code>
+ * otherwise.
+ */
+ protected static boolean isLinear(SettingsGroup aSettings) {
+ AxesSettings s = null;
+ if (aSettings instanceof IntHistogramGroup) {
+ s = ((IntHistogramGroup) aSettings).axes;
+ } else if (aSettings instanceof LongHistogramGroup) {
+ s = ((LongHistogramGroup) aSettings).axes;
+ } else if (aSettings instanceof Points2DGroup) {
+ s = ((Points2DGroup) aSettings).axes;
+ }
+ if (s != null) {
+ return !(s.getLogarithmicDomainAxis() || s.getLogarithmicRangeAxis());
+ }
+ return true;
+ }
+
+ /**
+ * Checks if the given settings group specifies a log-log plot.
+ *
+ * @param aSettings Settings group to be checked.
+ * @return <code>true</code> the settings group contains a logarithmin domain axis flag and a
+ * logarithmic range flags and they are both enabled; <code>false</code> otherwise.
+ */
+ protected static boolean isLogLog(SettingsGroup aSettings) {
+ AxesSettings s = null;
+ if (aSettings instanceof IntHistogramGroup) {
+ s = ((IntHistogramGroup) aSettings).axes;
+ } else if (aSettings instanceof LongHistogramGroup) {
+ s = ((LongHistogramGroup) aSettings).axes;
+ } else if (aSettings instanceof Points2DGroup) {
+ s = ((Points2DGroup) aSettings).axes;
+ }
+ if (s != null) {
+ return s.getLogarithmicDomainAxis() && s.getLogarithmicRangeAxis();
+ }
+ return false;
+ }
+
+ /**
+ * Keeps the points with positive coordinates in the given collection.
+ *
+ * @param aPoints Collection of points to be scanned.
+ * @return <code>aPoints</code> if all points in the collection are with positive coordinates.
+ * Otherwise, the returned value is a newly created array of points containing those
+ * elements in <code>aPoints</code> that have positive coordinates.
+ */
+ protected static Point2D.Double[] keepPositive(Point2D.Double[] aPoints) {
+ int nonZeroCount = 0;
+ for (Point2D.Double p : aPoints) {
+ if (p.x > 0 && p.y > 0) {
+ nonZeroCount++;
+ }
+ }
+ Point2D.Double[] result = aPoints;
+ if (nonZeroCount != aPoints.length) {
+ int i = 0;
+ result = new Point2D.Double[nonZeroCount];
+ for (Point2D.Double p : aPoints) {
+ if (p.x > 0 && p.y > 0) {
+ result[i++] = p;
+ }
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Clears the dataset containing the data used to visualizes the fitted function.
+ * <p>
+ * If the chart does not contain a decorating dataset, calling this method has no effect.
+ * </p>
+ *
+ * @param aChart Chart to be cleared from the decorating dataset.
+ * @param aSeriesName Name of data series to be used for locating the decorating dataset.
+ */
+ protected static void clearDataset(JFreeChart aChart, String aSeriesName) {
+ XYPlot plot = aChart.getXYPlot();
+ final int i = getDatasetIndex(plot, aSeriesName);
+ if (i != -1) {
+ plot.setDataset(i, new XYSeriesCollection(new XYSeries(aSeriesName)));
+ }
+ }
+
+ /**
+ * Creates a new dataset for visualizing the fitted function.
+ * <p>
+ * The new dataset is added to the end of the dataset list of the given plot.
+ * </p>
+ *
+ * @param aPlot Plot to which the new dataset must be added.
+ * @return Index of the newly created dataset in the dataset list of <code>aPlot</code>.
+ */
+ protected static int createDataset(XYPlot aPlot) {
+ int i = aPlot.getDatasetCount();
+ aPlot.setDatasetRenderingOrder(DatasetRenderingOrder.FORWARD);
+ XYLineAndShapeRenderer rend = new XYLineAndShapeRenderer();
+ rend.setSeriesLinesVisible(0, true);
+ rend.setSeriesShapesVisible(0, false);
+ aPlot.setRenderer(i, rend);
+ return i;
+ }
+
+ /**
+ * Gets the index of the first dataset containing the specified series.
+ *
+ * @param aPlot Plot to be searched for the dataset of the fitted function.
+ * @param aSeriesName Name of series the dataset should contain.
+ * @return Index of the dataset which contains series named <code>aSeriesName</code>,
+ * <code>-1</code> if such dataset does not exist.
+ */
+ protected static int getDatasetIndex(XYPlot aPlot, String aSeriesName) {
+ final int datasetCount = aPlot.getDatasetCount();
+ for (int i = 0; i < datasetCount; ++i) {
+ if (aSeriesName.equals(aPlot.getDataset(i).getSeriesKey(0))) {
+ return i;
+ }
+ }
+ return -1;
+ }
+
+ /**
+ * Smallest value to be considered different than 0.
+ */
+ protected static double EPSILON = 0.00001;
+
+ /**
+ * Initializes the fields of a new <code>TwoCoefsDecorator</code>.
+ *
+ * @param aCoefs Coefficients of the decorator. Set this parameter to <code>null</code> if
+ * coefficients are not computed.
+ */
+ protected TwoCoefsDecorator(Point2D.Double aCoefs) {
+ coefs = aCoefs != null ? new Point2D.Double(aCoefs.x, aCoefs.y) : null;
+ }
+
+ /**
+ * Coefficients of the decorator.
+ * <p>
+ * This field is <code>null</code> when the coefficients are not yet computed.
+ * </p>
+ */
+ protected Point2D.Double coefs;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/sconnect/HelpConnector.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/sconnect/HelpConnector.java
new file mode 100644
index 0000000..e6b5512
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/sconnect/HelpConnector.java
@@ -0,0 +1,130 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.sconnect;
+
+import java.net.HttpURLConnection;
+import java.net.URL;
+import java.net.URLConnection;
+
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.io.SettingsSerializer;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.settings.PluginSettings;
+
+/**
+ * Controller class providing static methods that construct URLs to specific online help sections.
+ *
+ * @author Yassen Assenov
+ */
+public final class HelpConnector {
+
+ /**
+ * Gets the full URL for network interpretation.
+ *
+ * @return URL for online help on network interpretation.
+ */
+ public static String getInterpretURL() {
+ final PluginSettings settings = SettingsSerializer.getPluginSettings();
+ return getBaseUrl(settings) + settings.getHelpInterpret();
+ }
+
+ /**
+ * Gets the full URL for complex parameter definition.
+ *
+ * @param aID ID of the complex parameter of interest.
+ * @return URL for online help on the given complex parameter.
+ */
+ public static String getParamURL(String aID) {
+ final PluginSettings settings = SettingsSerializer.getPluginSettings();
+ return getBaseUrl(settings) + settings.getHelpParams() + "#" + aID;
+ }
+
+ /**
+ * Gets the full URL for removing duplicated edges.
+ *
+ * @return URL for online help on removing duplicated edges.
+ */
+ public static String getRemDuplicatesURL() {
+ final PluginSettings settings = SettingsSerializer.getPluginSettings();
+ return getBaseUrl(settings) + settings.getHelpRemDuplicates();
+ }
+
+ /**
+ * Gets the full URL for removing self-loops.
+ *
+ * @return URL for online help on removing self-loops.
+ */
+ public static String getRemSelfloopsURL() {
+ final PluginSettings settings = SettingsSerializer.getPluginSettings();
+ return getBaseUrl(settings) + settings.getHelpRemSelfloops();
+ }
+
+ /**
+ * Gets the full URL for plugin's settings.
+ *
+ * @return URL for online help on NetworkAnalyzer's settings.
+ */
+ public static String getSettingsURL() {
+ final PluginSettings settings = SettingsSerializer.getPluginSettings();
+ return getBaseUrl(settings) + settings.getHelpSettings();
+ }
+
+ /**
+ * Gets the full URL for fitting functions.
+ *
+ * @return URL for online help on NetworkAnalyzer's fitting functions.
+ */
+ public static String getFittingURL() {
+ final PluginSettings settings = SettingsSerializer.getPluginSettings();
+ return getBaseUrl(settings) + settings.getHelpFitting();
+ }
+
+ /**
+ * Gets the help base URL.
+ *
+ * @param aSettings Plugin settings instance, storing help URL and section names.
+ * @return Base URL for help documents, ending with <code>/</code> (or <code>\</code>, if
+ * help is stored locally on a windows machine).
+ */
+ private static String getBaseUrl(PluginSettings aSettings) {
+ String baseURL = aSettings.getHelpUrlString();
+ HttpURLConnection.setFollowRedirects(false);
+ try {
+ URL url = new URL(baseURL);
+ URLConnection conn = url.openConnection();
+ if (conn instanceof HttpURLConnection) {
+ HttpURLConnection httpConn = (HttpURLConnection) conn;
+ httpConn.setRequestMethod("HEAD");
+ httpConn.connect();
+ String location = httpConn.getHeaderField("Location");
+ if (location != null && (!"".equals(location))) {
+ baseURL = location;
+ }
+ httpConn.disconnect();
+ }
+ } catch (Exception ex) {
+ // MalformedURLException, ...
+ // Fall through
+ } finally {
+ HttpURLConnection.setFollowRedirects(true);
+ }
+ final String endChar = baseURL.indexOf('\\') != -1 ? "\\" : "/";
+ if (!baseURL.endsWith(endChar)) {
+ baseURL += endChar;
+ }
+ return baseURL;
+ }
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/sconnect/ServerUtils.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/sconnect/ServerUtils.java
new file mode 100644
index 0000000..47aff5c
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/sconnect/ServerUtils.java
@@ -0,0 +1,40 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.sconnect;
+
+import java.io.UnsupportedEncodingException;
+import java.net.URLEncoder;
+
+/**
+ * Utility class containing helping methods related to communications with the MPII server over HTTP.
+ *
+ * @author Yassen Assenov
+ */
+public abstract class ServerUtils {
+
+ /**
+ * Translates the given string to UTF-8 encoding.
+ *
+ * @param aString String to be encoded.
+ * @return The string encoded in UTF-8.
+ * @throws UnsupportedEncodingException If the system does not support the UTF-8 encoding.
+ */
+ public static String encode(String aString) throws UnsupportedEncodingException {
+ return URLEncoder.encode(aString, "UTF-8");
+ }
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/AboutDialog.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/AboutDialog.java
new file mode 100644
index 0000000..71ed110
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/AboutDialog.java
@@ -0,0 +1,166 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.ui;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Cursor;
+import java.awt.Frame;
+import java.awt.Rectangle;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+
+import javax.swing.JDialog;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+
+import cytoscape.util.OpenBrowser;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Messages;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Utils;
+
+/**
+ * NetworkAnalyzer About box.
+ * <p>
+ * This dialog displays an image for its contents.
+ * </p>
+ *
+ * @author Yassen Assenov
+ */
+public class AboutDialog extends JDialog
+ implements MouseMotionListener, MouseListener {
+
+ /**
+ * URL of the official NetworkAnalyzer web site at the time this plugin is published.
+ */
+ public static final String WEB_SITE = "http://med.bioinf.mpi-inf.mpg.de/netanalyzer/";
+
+ /**
+ * Initializes a new instance of <code></code>.
+ *
+ * @param aOwner The <code>Frame</code> from which this dialog is displayed.
+ */
+ public AboutDialog(Frame aOwner) {
+ super(aOwner, Messages.DT_ABOUT, true);
+
+ initControls();
+ setResizable(false);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.event.MouseListener#mouseClicked(java.awt.event.MouseEvent)
+ */
+ public void mouseClicked(MouseEvent e) {
+ if (getCursor() == onURLCursor) {
+ // User clicked on the URL
+ OpenBrowser.openURL(WEB_SITE);
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.event.MouseMotionListener#mouseDragged(java.awt.event.MouseEvent)
+ */
+ public void mouseDragged(MouseEvent e) {
+ // Event is not processed
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.event.MouseListener#mouseEntered(java.awt.event.MouseEvent)
+ */
+ public void mouseEntered(MouseEvent e) {
+ // Event is not processed
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.event.MouseListener#mouseExited(java.awt.event.MouseEvent)
+ */
+ public void mouseExited(MouseEvent e) {
+ // Event is not processed
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.event.MouseMotionListener#mouseMoved(java.awt.event.MouseEvent)
+ */
+ public void mouseMoved(MouseEvent e) {
+ if (URL.contains(e.getX(), e.getY())) {
+ setCursor(onURLCursor);
+ } else {
+ setCursor(null);
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.event.MouseListener#mousePressed(java.awt.event.MouseEvent)
+ */
+ public void mousePressed(MouseEvent e) {
+ // Event is not processed
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.event.MouseListener#mouseReleased(java.awt.event.MouseEvent)
+ */
+ public void mouseReleased(MouseEvent e) {
+ // Event is not processed
+ }
+
+ /**
+ * Unique ID for this version of this class. It is used in serialization.
+ */
+ private static final long serialVersionUID = 7976825262362844385L;
+
+ /**
+ * Mouse cursor when over an URL address.
+ */
+ private static final Cursor onURLCursor = Cursor.getPredefinedCursor(Cursor.HAND_CURSOR);
+
+ /**
+ * Area on the about box that is treated as a URL.
+ */
+ private static final Rectangle URL = new Rectangle(196, 252, 412, 21);
+
+ /**
+ * Creates and lays out the controls inside this dialog.
+ * <p>
+ * This method is called upon initialization only.
+ * </p>
+ */
+ private void initControls() {
+ JPanel contentPane = new JPanel(new BorderLayout());
+ contentPane.setBackground(Color.WHITE);
+ JLabel labContents = new JLabel(Utils.getImage("AboutBox.png", ""));
+ contentPane.add(labContents, BorderLayout.CENTER);
+ labContents.addMouseListener(this);
+ labContents.addMouseMotionListener(this);
+ setContentPane(contentPane);
+ pack();
+ }
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/AnalysisDialog.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/AnalysisDialog.java
new file mode 100644
index 0000000..ed3296f
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/AnalysisDialog.java
@@ -0,0 +1,329 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.ui;
+
+import java.awt.Container;
+import java.awt.FlowLayout;
+import java.awt.Frame;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.WindowEvent;
+import java.awt.event.WindowListener;
+import java.io.File;
+import java.io.IOException;
+import java.lang.reflect.Constructor;
+
+import javax.swing.BorderFactory;
+import javax.swing.Box;
+import javax.swing.BoxLayout;
+import javax.swing.JButton;
+import javax.swing.JComponent;
+import javax.swing.JDialog;
+import javax.swing.JFileChooser;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JTabbedPane;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import de.mpg.mpi_inf.bioinf.netanalyzer.CyNetworkUtils;
+import de.mpg.mpi_inf.bioinf.netanalyzer.InnerException;
+import de.mpg.mpi_inf.bioinf.netanalyzer.NetworkAnalyzer;
+import de.mpg.mpi_inf.bioinf.netanalyzer.Plugin;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.ComplexParam;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Decorators;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Messages;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.NetworkStats;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.io.SettingsSerializer;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.io.StatsSerializer;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.settings.PluginSettings;
+import de.mpg.mpi_inf.bioinf.netanalyzer.dec.Decorator;
+
+/**
+ * Dialog presenting results of network analysis.
+ *
+ * @author Yassen Assenov
+ */
+public class AnalysisDialog extends JDialog implements ActionListener, WindowListener {
+
+ /**
+ * Dialog window for choosing a filename when saving and loading .netstats files.
+ */
+ public static JFileChooser netstatsDialog = new JFileChooser();
+
+ static {
+ netstatsDialog.addChoosableFileFilter(SupportedExtensions.netStatsFilter);
+ }
+
+ /**
+ * Initializes a new instance of <code>AnalysisDialog</code>.
+ * <p>
+ * The dialog created is non-modal and has a title "Network Analysis - [name]", where [name] is
+ * the name of the network, as saved in the <code>aStats</code> parameter. The constructor creates and
+ * lays out all the controls of the dialog. It also positions the window according to its parent, so no
+ * subsequent calls to <code>pack</code> or <code>setLocation(...)</code> are necessary.
+ * </p>
+ *
+ * @param aOwner
+ * The <code>Frame</code> from which this dialog is displayed.
+ * @param aStats
+ * Network statistics to be visualized.
+ * @param aAnalyzer
+ * Analyzer class that performed the topological analysis. Set this to <code>null</code> if the
+ * results were loaded from a file rather than just computed.
+ */
+ public AnalysisDialog(Frame aOwner, NetworkStats aStats, NetworkAnalyzer aAnalyzer) {
+ super(aOwner, Messages.DT_ANALYSIS + aStats.getTitle(), false);
+
+ stats = aStats;
+ boolean paramMapping = false;
+ if (aAnalyzer != null) {
+ final PluginSettings s = SettingsSerializer.getPluginSettings();
+ paramMapping = aAnalyzer.isGlobal() && (s.getUseNodeAttributes() || s.getUseEdgeAttributes());
+ saved = false;
+ } else {
+ saved = true;
+ }
+ initControls(paramMapping);
+ addWindowListener(this);
+
+ pack();
+ setDefaultCloseOperation(DO_NOTHING_ON_CLOSE);
+ setResizable(false);
+ setLocationRelativeTo(aOwner);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.event.ActionListener#actionPerformed(java.awt.event.ActionEvent)
+ */
+ public void actionPerformed(ActionEvent e) {
+ final Object src = e.getSource();
+ if (src == saveButton) {
+ saveNetstats();
+ } else if (src == visualizeButton) {
+ visualizeParameter();
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.event.WindowListener#windowActivated(java.awt.event.WindowEvent)
+ */
+ public void windowActivated(WindowEvent e) {
+ // Event is not processed
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.event.WindowListener#windowDeactivated(java.awt.event.WindowEvent)
+ */
+ public void windowDeactivated(WindowEvent e) {
+ // Event is not processed
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.event.WindowListener#windowOpened(java.awt.event.WindowEvent)
+ */
+ public void windowOpened(WindowEvent e) {
+ // Event is not processed
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.event.WindowListener#windowClosing(java.awt.event.WindowEvent)
+ */
+ public void windowClosing(WindowEvent e) {
+ if (!saved) {
+ int choice = JOptionPane.showConfirmDialog(this, Messages.SM_CLOSEWARN, Messages.DT_CLOSEWARN,
+ JOptionPane.YES_NO_OPTION, JOptionPane.WARNING_MESSAGE);
+ if (choice == JOptionPane.NO_OPTION) {
+ return;
+ }
+ }
+ setVisible(false);
+ dispose();
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.event.WindowListener#windowClosed(java.awt.event.WindowEvent)
+ */
+ public void windowClosed(WindowEvent e) {
+ // Event is not processed
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.event.WindowListener#windowIconified(java.awt.event.WindowEvent)
+ */
+ public void windowIconified(WindowEvent e) {
+ // Event is not processed
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.event.WindowListener#windowDeiconified(java.awt.event.WindowEvent)
+ */
+ public void windowDeiconified(WindowEvent e) {
+ // Event is not processed
+ }
+
+ /**
+ * Creates and lays out the controls inside this dialog.
+ * <p>
+ * This method is called upon initialization only.
+ * </p>
+ */
+ private void initControls(boolean enableParameterMapping) {
+ final boolean useExpandable = SettingsSerializer.getPluginSettings().getExpandable();
+ final Container contentPane = getContentPane();
+ contentPane.setLayout(new BoxLayout(contentPane, BoxLayout.Y_AXIS));
+ final JTabbedPane tabs = useExpandable ? null : new JTabbedPane();
+
+ final JComponent simpleStatsPanel = new SimpleStatsPanel(stats);
+ if (useExpandable) {
+ simpleStatsPanel.setBorder(BorderFactory.createTitledBorder(Messages.DI_SIMPLEPARAMS));
+ contentPane.add(simpleStatsPanel);
+ } else {
+ contentPane.add(tabs);
+ tabs.addTab(Messages.DI_SIMPLEPARAMS, simpleStatsPanel);
+ }
+
+ final String[] complexNames = stats.getComputedComplex();
+ for (int i = 0; i < complexNames.length; ++i) {
+ final String id = complexNames[i];
+ final ComplexParam cp = stats.getComplex(id);
+ final String typeName = cp.getClass().getSimpleName();
+ try {
+ final Class<?> visClass = Plugin.getVisualizerClass(typeName);
+ final Constructor<?> con = visClass.getConstructors()[0];
+ final Object[] conParams = new Object[] { cp, SettingsSerializer.getDefault(id) };
+ ComplexParamVisualizer v = (ComplexParamVisualizer) con.newInstance(conParams);
+ final Decorator[] decs = Decorators.get(id);
+ if (useExpandable) {
+ contentPane.add(new ChartExpandablePanel(this, id, v, (i == 0), decs));
+ } else {
+ tabs.addTab(v.getTitle(), new ChartDisplayPanel(this, id, v, decs));
+ }
+ } catch (Exception ex) {
+ throw new InnerException(ex);
+ }
+ }
+
+ contentPane.add(Box.createVerticalStrut(Utils.BORDER_SIZE));
+ saveButton = new JButton(Messages.DI_SAVESTATISTICS);
+ saveButton.addActionListener(this);
+ visualizeButton = new JButton(Messages.DI_VISUALIZEPARAMETER);
+ visualizeButton.setEnabled(false);
+ visualizeButton.addActionListener(this);
+ visualizeButton.setEnabled(enableParameterMapping);
+ JPanel buttonPane = new JPanel(new FlowLayout(FlowLayout.CENTER, Utils.BORDER_SIZE, 0));
+ Utils.equalizeSize(saveButton, visualizeButton);
+ buttonPane.add(saveButton);
+ buttonPane.add(Box.createHorizontalStrut(Utils.BORDER_SIZE * 2));
+ buttonPane.add(visualizeButton);
+ contentPane.add(buttonPane);
+ contentPane.add(Box.createVerticalStrut(Utils.BORDER_SIZE));
+ }
+
+ /**
+ * Displays a dialog prompting to save the network analysis in a <code>.netstats</code> file.
+ */
+ private void saveNetstats() {
+ int saveIt = netstatsDialog.showSaveDialog(this);
+ if (saveIt == JFileChooser.APPROVE_OPTION) {
+ try {
+ String fileName = netstatsDialog.getSelectedFile().getAbsolutePath();
+ Utils.removeSelectedFile(netstatsDialog);
+ if (!SupportedExtensions.netStatsFilter.hasExtension(fileName)) {
+ fileName = SupportedExtensions.netStatsFilter.appendExtension(fileName);
+ }
+ if (Utils.canSave(new File(fileName), this)) {
+ StatsSerializer.save(stats, fileName);
+ saved = true;
+ }
+ } catch (IOException ex) {
+ // Could not save file
+ Utils.showErrorBox(this, Messages.DT_IOERROR, Messages.SM_OERROR);
+ } catch (SecurityException ex) {
+ // Could not save file - security manager has denied access
+ Utils.showErrorBox(this, Messages.DT_SECERROR, Messages.SM_SECERROR2);
+ }
+ } else if (saveIt == JFileChooser.ERROR_OPTION) {
+ Utils.showErrorBox(this, Messages.DT_GUIERROR, Messages.SM_GUIERROR);
+ }
+ }
+
+ /**
+ * Opens the "Map Parameters to Visual Styles" dialog when the "Map Parameters to Visual
+ * Styles" button is activated.
+ */
+ private void visualizeParameter() {
+ CyNetwork network = Cytoscape.getNetwork(stats.getID());
+ if (network != null && network != Cytoscape.getNullNetwork()) {
+ final String[][] nodeAttr = CyNetworkUtils.getComputedNodeAttributes(network);
+ final String[][] edgeAttr = CyNetworkUtils.getComputedEdgeAttributes(network);
+ if ((nodeAttr[0].length > 0) || (nodeAttr[1].length > 0) || (edgeAttr[0].length > 0)
+ || (edgeAttr[1].length > 0)) {
+ final MapParameterDialog d = new MapParameterDialog(Cytoscape.getDesktop(), network,
+ nodeAttr, edgeAttr);
+ d.setVisible(true);
+ return;
+ }
+ }
+ // Could not locate network - display an error message to the user
+ Utils.showErrorBox(Messages.DT_WRONGDATA, Messages.SM_VISUALIZEERROR);
+ visualizeButton.setEnabled(false);
+ }
+
+ /**
+ * Unique ID for this version of this class. It is used in serialization.
+ */
+ private static final long serialVersionUID = 5759174742857183439L;
+
+ /**
+ * Flag indicating if the network analysis results were successfully saved to a file.
+ */
+ private boolean saved;
+
+ /**
+ * "Save Statistics" button.
+ */
+ private JButton saveButton;
+
+ /**
+ * "Visualize Parameters" button.
+ */
+ private JButton visualizeButton;
+
+ /**
+ * Network parameters instance displayed in this dialog.
+ */
+ private NetworkStats stats;
+
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/AnalysisTableModel.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/AnalysisTableModel.java
new file mode 100644
index 0000000..52f9c30
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/AnalysisTableModel.java
@@ -0,0 +1,277 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.ui;
+
+import java.awt.Dimension;
+import java.io.File;
+import java.util.List;
+
+import javax.swing.JTable;
+import javax.swing.table.AbstractTableModel;
+import javax.swing.table.TableCellRenderer;
+import javax.swing.table.TableColumn;
+import javax.swing.table.TableColumnModel;
+
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.AnalysisError;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Messages;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.NetworkAnalysisReport;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.NetworkInterpretation;
+
+/**
+ * Table model presenting a table of analysis reports.
+ * <p>
+ * This model contains three columns:
+ * <ol>
+ * <li><b>Network</b> The file from which the was loaded;</li>
+ * <li><b>Interpretation</b> Network interpretation applied;</li>
+ * <li><b>Network Statistics File</b> File in which the network statistics were saved.</li>
+ * </ol>
+ * </p>
+ *
+ * @author Yassen Assenov
+ */
+public class AnalysisTableModel extends AbstractTableModel {
+
+ /**
+ * Initializes a new instance of <code>AnalysisTableModel</code>.
+ *
+ * @param aReports
+ * List of reports that will fill the table.
+ */
+ public AnalysisTableModel(List<NetworkAnalysisReport> aReports) {
+ reports = aReports;
+ }
+
+ /**
+ * Sets preferred widths for columns in the table, as well as row height.
+ *
+ * @param aTable
+ * Table instance which uses <code>AnalysisTableModel</code> for managing its data.
+ * If the table does not use <code>AnalysisTableModel</code>, the result of this
+ * method is unspecified; in particular, the method might throw an instance of
+ * <code>ClassCastException</code>, <code>IndexOutOfBoundsException</code> or
+ * another exception type.
+ *
+ * @throws NullPointerException
+ * If <code>aTable</code> is <code>null</code>.
+ */
+ public void adjustDimensions(final JTable aTable) {
+ // Compute values for preferred width and height
+ final TableColumnModel model = aTable.getColumnModel();
+ final int cc = getColumnCount(); // = 3
+ final int rc = getRowCount();
+ final int[] widths = new int[cc];
+ int height = 0;
+ // Traverse the table header to set initial preferred widths
+ final TableCellRenderer hr = aTable.getTableHeader().getDefaultRenderer();
+ for (int i = 0; i < cc; ++i) {
+ final Object header = model.getColumn(i).getHeaderValue();
+ final Dimension size = getPreferredSize(hr, header);
+ widths[i] = size.width;
+ }
+ // Traverse all table records
+ for (int i = 0; i < cc; ++i) {
+ final TableCellRenderer rend = aTable.getDefaultRenderer(getColumnClass(i));
+ for (int r = 0; r < rc; ++r) {
+ final int h = updateDimensions(aTable, widths, i, rend, getValueAt(r, i));
+ if (height < h) {
+ height = h;
+ }
+ }
+ }
+ // Reduce widths if necessary
+ for (int i = 0; i < cc; ++i) {
+ widths[i] += 4;
+ widths[i] = Math.max(Math.min(widths[i], ColumnWidthsMax[i]), ColumnWidthsMin[i]);
+ }
+ // Set computed values for width and height
+ for (int i = 0; i < cc; ++i) {
+ final TableColumn c = model.getColumn(i);
+ c.setPreferredWidth(widths[i]);
+ }
+ height += 2 + aTable.getRowMargin();
+ aTable.setRowHeight(height);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see javax.swing.table.AbstractTableModel#getColumnClass(int)
+ */
+ @Override
+ public Class<?> getColumnClass(int columnIndex) {
+ switch (columnIndex) {
+ case 0:
+ return String.class;
+ case 1:
+ return NetworkInterpretation.class;
+ case 2:
+ return String.class;
+ }
+ throw new IndexOutOfBoundsException();
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see javax.swing.table.TableModel#getColumnCount()
+ */
+ public int getColumnCount() {
+ return columnNames.length;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see javax.swing.table.AbstractTableModel#getColumnName(int)
+ */
+ @Override
+ public String getColumnName(int column) {
+ return columnNames[column];
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see javax.swing.table.TableModel#getRowCount()
+ */
+ public int getRowCount() {
+ return reports.size();
+ }
+
+ /**
+ * Gets the network file of the report on the given line.
+ *
+ * @param index
+ * Zero-based index of a table row which contains the report of interest.
+ * @return Network file for the report on row <code>index</code>.
+ *
+ * @throws IndexOutOfBoundsException
+ * If <code>index</code> is negative or if it not less than {@link #getRowCount()}.
+ *
+ * @see NetworkAnalysisReport#getNetwork()
+ */
+ public File getNetwork(int index) {
+ return reports.get(index).getNetwork();
+ }
+
+ /**
+ * Gets the statistics file of the report on the given line.
+ *
+ * @param index
+ * Zero-based index of a table row which contains the report of interest.
+ * @return Network statistics file for the report on row <code>index</code>.
+ *
+ * @throws IndexOutOfBoundsException
+ * If <code>index</code> is negative or if it not less than {@link #getRowCount()}.
+ *
+ * @see NetworkAnalysisReport#getResultFile()
+ */
+ public File getNetstatsFile(int index) {
+ return reports.get(index).getResultFile();
+ }
+
+ /**
+ * Get a hyperlink representation of a string.
+ *
+ * @param aName
+ * String to be represented as hyperlink.
+ * @return String represented as a hyperlink.
+ */
+ private String getHrefName(String aName) {
+ return "<html><a href=\"" + aName + "\">" + aName + "</a></html>";
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see javax.swing.table.TableModel#getValueAt(int, int)
+ */
+ public Object getValueAt(int aRowIndex, int aColumnIndex) {
+ switch (aColumnIndex) {
+ case 0:
+ final File network = getNetwork(aRowIndex);
+ if (reports.get(aRowIndex).getError() == AnalysisError.NETWORK_NOT_OPENED) {
+ return network.getName();
+ }
+ return getHrefName(network.getName());
+ case 1:
+ return reports.get(aRowIndex).getInterpretation();
+ case 2:
+ final File f = getNetstatsFile(aRowIndex);
+ if (f != null) {
+ return getHrefName(f.getName());
+ }
+ final AnalysisError error = reports.get(aRowIndex).getError();
+ return AnalysisError.getMessage(error);
+ }
+ throw new IndexOutOfBoundsException();
+ }
+
+ /**
+ * Unique ID for this version of this class. It is used in serialization.
+ */
+ private static final long serialVersionUID = -9125782709654482796L;
+
+ /**
+ * Maximum widths, in pixels, of the table columns.
+ */
+ private static final int[] ColumnWidthsMax = new int[] { 300, 350, 450 };
+
+ /**
+ * Minimum widths, in pixels, of the table columns.
+ */
+ private static final int[] ColumnWidthsMin = new int[] { 100, 120, 140 };
+
+ /**
+ * Names of the columns in this table model.
+ */
+ private static String[] columnNames;
+
+ static {
+ columnNames = new String[3];
+ columnNames[0] = Messages.DI_NETFILE;
+ columnNames[1] = Messages.DI_INTERPR;
+ columnNames[2] = Messages.DI_NETSTATSFILE;
+ }
+
+ private static Dimension getPreferredSize(JTable aTable, TableCellRenderer aRend, Object aValue) {
+ return aRend.getTableCellRendererComponent(aTable, aValue, false, false, 0, 0)
+ .getPreferredSize();
+ }
+
+ private static Dimension getPreferredSize(TableCellRenderer aRend, Object aValue) {
+ return aRend.getTableCellRendererComponent(null, aValue, false, false, 0, 0)
+ .getPreferredSize();
+ }
+
+ private int updateDimensions(JTable aTable, int[] aWidths, int aIndex, TableCellRenderer aRend,
+ Object aValue) {
+ final Dimension size = getPreferredSize(aTable, aRend, aValue);
+ final int width = size.width;
+ if (aWidths[aIndex] < width) {
+ aWidths[aIndex] = width;
+ }
+ return size.height;
+ }
+
+ /**
+ * List of reports managed by this table model.
+ */
+ private List<NetworkAnalysisReport> reports;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/BatchAnalysisDialog.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/BatchAnalysisDialog.java
new file mode 100644
index 0000000..ab2a6a0
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/BatchAnalysisDialog.java
@@ -0,0 +1,246 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.ui;
+
+import java.awt.BorderLayout;
+import java.awt.FlowLayout;
+import java.awt.Frame;
+import java.awt.GridLayout;
+import java.awt.Insets;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import javax.swing.BorderFactory;
+import javax.swing.JButton;
+import javax.swing.JDialog;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JProgressBar;
+import javax.swing.JScrollPane;
+import javax.swing.JTextArea;
+import javax.swing.ScrollPaneConstants;
+import javax.swing.SwingConstants;
+import javax.swing.Timer;
+
+import de.mpg.mpi_inf.bioinf.netanalyzer.BatchNetworkAnalyzer;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Messages;
+
+/**
+ * Dialog showing the progress of the batch analysis of networks.
+ *
+ * @author Yassen Assenov
+ * @author Nadezhda Doncheva
+ */
+public class BatchAnalysisDialog extends JDialog implements ActionListener {
+
+ /**
+ * Initializes a new instance of <code>BatchAnalysisDialog</code>.
+ *
+ * @param aOwner
+ * The <code>Frame</code> from which this dialog is displayed.
+ * @param aBatchAnalyzer
+ */
+ public BatchAnalysisDialog(Frame aOwner, BatchNetworkAnalyzer aBatchAnalyzer) {
+ super(aOwner, Messages.DT_BATCHANALYSIS, true);
+ resultsPressed = false;
+ batchAnalyzer = aBatchAnalyzer;
+ analyzerStarted = false;
+ aBatchAnalyzer.setDialog(this);
+
+ initControls();
+ pack();
+ setDefaultCloseOperation(DO_NOTHING_ON_CLOSE);
+ setLocationRelativeTo(aOwner);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.event.ActionListener#actionPerformed(java.awt.event.ActionEvent)
+ */
+ public void actionPerformed(ActionEvent e) {
+ final Object src = e.getSource();
+ if (src == btnCancel) {
+ synchronized (this) {
+ if (timer == null) {
+ setVisible(false);
+ dispose();
+ } else {
+ btnCancel.setEnabled(false);
+ btnCancel.setText(Messages.DI_CLOSE);
+ timer.stop();
+ timer = null;
+ batchAnalyzer.cancel();
+ }
+ }
+ } else if (src == btnResults) {
+ resultsPressed = true;
+ setVisible(false);
+ dispose();
+ } else if (src == timer && timer != null) {
+ proAnalysis.setValue(batchAnalyzer.getCurrentProgress());
+ repaint();
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.Dialog#setVisible
+ */
+ @Override
+ public void setVisible(boolean b) {
+ if (!analyzerStarted) {
+ analyzerStarted = true;
+ timer = new Timer(1000, this);
+ timer.start();
+ batchAnalyzer.start();
+ }
+ super.setVisible(b);
+ }
+
+ /**
+ * Indicates that the batch analysis has finished and enables the "Show Results" button.
+ */
+ public void analysisFinished() {
+ synchronized (this) {
+ if (timer != null) {
+ timer.stop();
+ timer = null;
+ proAnalysis.setValue(proAnalysis.getMaximum());
+ btnCancel.setText(Messages.DI_CLOSE);
+ btnResults.setEnabled(true);
+ }
+ btnCancel.setEnabled(true);
+ }
+ }
+
+ /**
+ * Gets the status of the flag indicating if the "Show Results" button is pressed.
+ *
+ * @return <code>true</code> if the "Show Results" button is pressed, and <code>false</code>
+ * otherwise.
+ */
+ public boolean resultsPressed() {
+ return resultsPressed;
+ }
+
+ /**
+ * Appends a string to the other text in the dialog window.
+ *
+ * @param aString
+ * String to be appended.
+ */
+ public void write(String aString) {
+ texOutput.append(aString);
+ texOutput.setCaretPosition(texOutput.getDocument().getLength());
+ repaint();
+ }
+
+ /**
+ * Creates and lays out the controls inside this dialog.
+ * <p>
+ * This method is called upon initialization only.
+ * </p>
+ */
+ private void initControls() {
+ final int BS = Utils.BORDER_SIZE;
+ final JPanel contentPane = new JPanel(new BorderLayout(BS, BS));
+ Utils.setStandardBorder(contentPane);
+
+ // Add network number info and progress bar.
+ final JPanel panTop = new JPanel(new BorderLayout(BS, BS));
+ final JLabel labTitle = new JLabel(Messages.DI_AUTOANALYSIS1 + batchAnalyzer.getInputFilesCount()
+ + Messages.DI_AUTOANALYSIS2, SwingConstants.CENTER);
+ panTop.add(labTitle, BorderLayout.NORTH);
+ proAnalysis = new JProgressBar(0, batchAnalyzer.getMaxProgress());
+ proAnalysis.setValue(0);
+ proAnalysis.setStringPainted(true);
+ panTop.add(proAnalysis, BorderLayout.SOUTH);
+ contentPane.add(panTop, BorderLayout.NORTH);
+
+ // Add console
+ texOutput = new JTextArea(10, 40);
+ texOutput.setMargin(new Insets(5, 5, 5, 5));
+ texOutput.setEditable(false);
+ texOutput.setCursor(null);
+ texOutput.setFont(labTitle.getFont());
+ JPanel panConsole = new JPanel(new BorderLayout(0, 0));
+ panConsole.setBorder(BorderFactory.createEmptyBorder(BS, BS, BS, BS));
+ final int vsp = ScrollPaneConstants.VERTICAL_SCROLLBAR_ALWAYS;
+ final int hsp = ScrollPaneConstants.HORIZONTAL_SCROLLBAR_NEVER;
+ panConsole.add(new JScrollPane(texOutput, vsp, hsp), BorderLayout.CENTER);
+ contentPane.add(panConsole, BorderLayout.CENTER);
+
+ // Add Cancel and Results buttons
+ JPanel panBottom = new JPanel(new FlowLayout(FlowLayout.CENTER, 0, 0));
+ JPanel panButtons = new JPanel(new GridLayout(1, 2, BS, 0));
+ panButtons.add(btnCancel = Utils.createButton(Messages.DI_CANCEL, null, this));
+ panButtons.add(btnResults = Utils.createButton(Messages.DI_RESULTS, null, this));
+ btnResults.setEnabled(false);
+ panBottom.add(panButtons);
+ contentPane.add(panBottom, BorderLayout.SOUTH);
+ setContentPane(contentPane);
+ }
+
+ /**
+ * Unique ID for this version of this class. It is used in serialization.
+ */
+ private static final long serialVersionUID = 1074422259082449432L;
+
+ /**
+ * Flag indicating if the analysis has started yet.
+ */
+ private boolean analyzerStarted;
+
+ /**
+ * Instance of <code>BatchNetworkAnalyzer</code>.
+ */
+ private BatchNetworkAnalyzer batchAnalyzer;
+
+ /**
+ * "Cancel" button.
+ */
+ private JButton btnCancel;
+
+ /**
+ * "Show Results" button.
+ */
+ private JButton btnResults;
+
+ /**
+ * A progress bar in the dialog showing how many networks have been processed.
+ */
+ private JProgressBar proAnalysis;
+
+ /**
+ * Flag indicating if the user had pressed the "Show Results" button.
+ */
+ private boolean resultsPressed;
+
+ /**
+ * A text console that logs the progress of the analysis
+ */
+ private JTextArea texOutput;
+
+ /**
+ * Timer responsible for regular updates of the progress monitor.
+ */
+ private Timer timer;
+
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/BatchResultsDialog.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/BatchResultsDialog.java
new file mode 100644
index 0000000..187671d
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/BatchResultsDialog.java
@@ -0,0 +1,213 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.ui;
+
+import java.awt.BorderLayout;
+import java.awt.Dimension;
+import java.awt.FlowLayout;
+import java.awt.Frame;
+import java.awt.Point;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.io.File;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import javax.swing.JButton;
+import javax.swing.JDialog;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTable;
+import javax.swing.ListSelectionModel;
+import javax.swing.SwingConstants;
+import javax.swing.event.ListSelectionEvent;
+import javax.swing.event.ListSelectionListener;
+
+import cytoscape.Cytoscape;
+import de.mpg.mpi_inf.bioinf.netanalyzer.LoadNetstatsAction;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Messages;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.NetworkAnalysisReport;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.NetworkInterpretation;
+
+/**
+ * Dialog displaying the results of network batch analysis.
+ *
+ * @author Yassen Assenov
+ */
+public class BatchResultsDialog extends JDialog implements ActionListener, ListSelectionListener {
+
+ /**
+ * Initializes a new instance of <code>BatchResultsDialog</code>.
+ *
+ * @param aReports
+ * List of analysis reports to be visualized.
+ */
+ public BatchResultsDialog(List<NetworkAnalysisReport> aReports) {
+ this(Cytoscape.getDesktop(), aReports);
+ }
+
+ /**
+ * Initializes a new instance of <code>BatchResultsDialog</code>.
+ *
+ * @param aOwner
+ * <code>Frame</code> from which this dialog is displayed.
+ * @param aReports
+ * List of analysis reports to be visualized.
+ */
+ public BatchResultsDialog(Frame aOwner, List<NetworkAnalysisReport> aReports) {
+ super(aOwner, Messages.DT_BATCHRESULTS, false);
+ init(aReports);
+ setLocationRelativeTo(aOwner);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.event.ActionListener#actionPerformed(java.awt.event.ActionEvent)
+ */
+ public void actionPerformed(ActionEvent e) {
+ if (e.getSource() == btnClose) {
+ setVisible(false);
+ dispose();
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see javax.swing.event.ListSelectionListener#valueChanged(javax.swing.event.ListSelectionEvent)
+ */
+ public void valueChanged(ListSelectionEvent e) {
+ if (!e.getValueIsAdjusting()) {
+ try {
+ final AnalysisTableModel model = (AnalysisTableModel) tabResults.getModel();
+ final int r = tabResults.getSelectedRow();
+ final int c = tabResults.getSelectedColumn();
+ if (lastSelected.x == c && lastSelected.y == r) {
+ return;
+ }
+ lastSelected.x = c;
+ lastSelected.y = r;
+ if (c == 2) {
+ final File file = model.getNetstatsFile(r);
+ if (file != null) {
+ LoadNetstatsAction.openNetstats(file);
+ }
+ } else if (c == 0) {
+ final File file = model.getNetwork(r);
+ if (file != null && file.isFile()) {
+ Cytoscape.createNetworkFromFile(file.getAbsolutePath(), false);
+ }
+ }
+ } catch (ClassCastException ex) {
+ // Ignore
+ } catch (IndexOutOfBoundsException ex) {
+ // Ignore
+ }
+ }
+ }
+
+ /**
+ * Gets the number of networks discussed in the reports.
+ *
+ * @param aReports
+ * List of reports to be traversed.
+ * @return Number of unique instances for network files in the given reports.
+ *
+ * @throws NullPointerException
+ * If <code>aReports</code> is <code>null</code>.
+ */
+ private static int getNetworkCount(List<NetworkAnalysisReport> aReports) {
+ final Set<File> files = new HashSet<File>();
+ for (final NetworkAnalysisReport report : aReports) {
+ files.add(report.getNetwork());
+ }
+ return files.size();
+ }
+
+ /**
+ * Unique ID for this version of this class. It is used in serialization.
+ */
+ private static final long serialVersionUID = -4513989513140591013L;
+
+ /**
+ * Maximum height, in pixels, of the table control as initially displayed in this dialog.
+ */
+ private static final int TAB_HEIGHT_MAX = 400;
+
+ /**
+ * Initializes and lays out the controls in this dialog.
+ *
+ * @param aReports
+ * List of analysis reports to be listed in a table.
+ */
+ private void init(List<NetworkAnalysisReport> aReports) {
+ lastSelected = new Point(-1, -1);
+ final int BS = Utils.BORDER_SIZE;
+ final JPanel contentPane = new JPanel(new BorderLayout(BS, BS));
+ Utils.setStandardBorder(contentPane);
+
+ // Add title label
+ final String netCount = String.valueOf(getNetworkCount(aReports));
+ final JLabel label = new JLabel(netCount + Messages.DI_BATCHREPORT, SwingConstants.CENTER);
+ contentPane.add(label, BorderLayout.PAGE_START);
+
+ // Add results table
+ final AnalysisTableModel model = new AnalysisTableModel(aReports);
+ tabResults = new JTable(model);
+ tabResults.setDefaultRenderer(File.class, new FileCellRenderer());
+ tabResults.setDefaultRenderer(NetworkInterpretation.class, new InterpretationCellRenderer());
+ tabResults.getColumnModel().getSelectionModel().addListSelectionListener(this);
+ tabResults.getSelectionModel().addListSelectionListener(this);
+ tabResults.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
+ model.adjustDimensions(tabResults);
+ final Dimension size = tabResults.getPreferredSize();
+ if (size.height > TAB_HEIGHT_MAX) {
+ size.height = TAB_HEIGHT_MAX;
+ }
+ tabResults.setPreferredScrollableViewportSize(size);
+ contentPane.add(new JScrollPane(tabResults), BorderLayout.CENTER);
+
+ // Add Close button
+ btnClose = Utils.createButton(Messages.DI_CLOSE, null, this);
+ final JPanel panButton = new JPanel(new FlowLayout(FlowLayout.CENTER, 0, 0));
+ panButton.add(btnClose);
+ contentPane.add(panButton, BorderLayout.PAGE_END);
+
+ setContentPane(contentPane);
+ pack();
+ setResizable(true);
+ }
+
+ /**
+ * "Close" button for closing this dialog.
+ */
+ private JButton btnClose;
+
+ /**
+ * Last selected table cell.
+ */
+ private Point lastSelected;
+
+ /**
+ * Table listing the analysis reports.
+ */
+ private JTable tabResults;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/BatchSettingsDialog.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/BatchSettingsDialog.java
new file mode 100644
index 0000000..7889c5e
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/BatchSettingsDialog.java
@@ -0,0 +1,423 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.ui;
+
+import java.awt.BorderLayout;
+import java.awt.FlowLayout;
+import java.awt.Frame;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.GridLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.io.File;
+
+import javax.swing.Box;
+import javax.swing.ButtonGroup;
+import javax.swing.JButton;
+import javax.swing.JDialog;
+import javax.swing.JFileChooser;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JRadioButton;
+import javax.swing.JTextField;
+import javax.swing.border.TitledBorder;
+
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Interpretations;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Messages;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.io.SettingsSerializer;
+
+/**
+ * Dialog for adjusting the input and output directories for the batch analysis. This is the first step in the
+ * automatic batch analysis on networks.
+ *
+ * @author Yassen Assenov
+ * @author Nadezhda Doncheva
+ */
+public class BatchSettingsDialog extends JDialog implements ActionListener {
+
+ /**
+ * Initializes a new instance of <code>BatchSettingsDialog</code>.
+ *
+ * @param aOwner
+ * The <code>Frame</code> from which this dialog is displayed.
+ */
+ public BatchSettingsDialog(Frame aOwner) {
+ super(aOwner, Messages.DT_BATCHSETTINGS, true);
+
+ inOutDirs = null;
+ initControls();
+ pack();
+ setLocationRelativeTo(aOwner);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.event.ActionListener#actionPerformed(java.awt.event.ActionEvent)
+ */
+ public void actionPerformed(ActionEvent e) {
+ final Object src = e.getSource();
+ if (src == btnInputDir) {
+ final File file = updateSetting(choInputDir);
+ if (file != null) {
+ if (checkInputDir(file)) {
+ txfInputDir.setText(file.getAbsolutePath());
+ } else {
+ txfInputDir.setText("");
+ Utils.showErrorBox(Messages.DT_IOERROR, Messages.SM_BADINPUT);
+ }
+ updateStartButton();
+ }
+
+ } else if (src == btnOutputDir) {
+ final File file = updateSetting(choOutputDir);
+ if (file != null) {
+ if (checkOutputDir(file)) {
+ txfOutputDir.setText(file.getAbsolutePath());
+ } else {
+ txfOutputDir.setText("");
+ Utils.showErrorBox(Messages.DT_IOERROR, Messages.SM_BADOUTPUT);
+ }
+ updateStartButton();
+ }
+
+ } else if (src == btnStart) {
+ this.inOutDirs = new File[2];
+ inOutDirs[0] = choInputDir.getSelectedFile();
+ inOutDirs[1] = choOutputDir.getSelectedFile();
+ setVisible(false);
+ dispose();
+ } else if (src == btnCancel) {
+ setVisible(false);
+ dispose();
+ }
+ }
+
+ /**
+ * Gets the settings for input and output directory for batch analysis.
+ *
+ * @return Array of <code>File</code> instances, containing the input and output directory for batch
+ * analysis.
+ */
+ public File[] getInOutDirs() {
+ return inOutDirs;
+ }
+
+ /**
+ * Gets the selected option for acceptable interpretations.
+ *
+ * @return Interpretations to be applied for each network during batch processing, in the form of an
+ * <code>Interpretations</code> instance.
+ */
+ public Interpretations getInterpretations() {
+ if (btnInterpretAll.isSelected()) {
+ return Interpretations.ALL;
+ }
+ if (btnInterpretDir.isSelected()) {
+ return Interpretations.DIRECTED;
+ }
+ return Interpretations.UNDIRECTED;
+ }
+
+ /**
+ * Creates and lays out the controls inside this dialog.
+ * <p>
+ * This method is called upon initialization only.
+ * </p>
+ */
+ private void initControls() {
+
+ // Create the outer box and panel
+ Box contentPane = Box.createVerticalBox();
+ Utils.setStandardBorder(contentPane);
+
+ JPanel panTitle = new JPanel();
+ panTitle.add(new JLabel(Messages.DT_BATCHSETTINGS));
+ contentPane.add(panTitle);
+ final int BS = Utils.BORDER_SIZE / 2;
+ contentPane.add(Box.createVerticalStrut(BS));
+
+ // Create file choosers and pre-load with paths in settings
+ choInputDir = new JFileChooser();
+ choInputDir.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
+ // choInputDir.setSelectedFile(new File(inputDir));
+ choOutputDir = new JFileChooser();
+ choOutputDir.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
+ // choOutputDir.setSelectedFile(new File(outputDir));
+
+ // Initialize text fields for displaying currently selected paths
+ final int columnsCount = Utils.BORDER_SIZE * 6;
+ txfInputDir = new JTextField("", columnsCount);
+ txfOutputDir = new JTextField("", columnsCount);
+
+ // Create buttons for changing the settings
+ JButton[] buttons = new JButton[2];
+ buttons[0] = btnInputDir = Utils.createButton(Messages.DI_SELECTDIR, null, this);
+ buttons[1] = btnOutputDir = Utils.createButton(Messages.DI_SELECTDIR, null, this);
+ Utils.equalizeSize(buttons);
+
+ // Add buttons for selecting paths and files
+ JPanel panTop = new JPanel();
+ JPanel panSelects = new JPanel(new GridBagLayout());
+ GridBagConstraints constr = new GridBagConstraints();
+ constr.insets.left = BS;
+ constr.insets.right = BS;
+ constr.gridx = constr.gridy = 0;
+
+ // Layout the controls in tabular form
+ addPathSelector(Messages.DI_INPUTDIR, txfInputDir, btnInputDir, panSelects, constr);
+ addPathSelector(Messages.DI_OUTPUTDIR, txfOutputDir, btnOutputDir, panSelects, constr);
+
+ panTop.add(panSelects);
+ contentPane.add(panTop);
+ contentPane.add(Box.createVerticalStrut(Utils.BORDER_SIZE));
+
+ // Add radio buttons for network interpretations
+ final JPanel panCenter = new JPanel(new FlowLayout(FlowLayout.CENTER, 0, 0));
+ final JPanel panInterpr = new JPanel(new BorderLayout());
+ panInterpr.setBorder(new TitledBorder(Messages.DI_INTERPRS));
+ btnInterpretAll = new JRadioButton(Messages.DI_INTERPR_ALL, true);
+ btnInterpretDir = new JRadioButton(Messages.DI_INTERPR_DIRECTED);
+ btnInterpretUndir = new JRadioButton(Messages.DI_INTERPR_UNDIRECTED);
+ final ButtonGroup group = new ButtonGroup();
+ group.add(btnInterpretAll);
+ group.add(btnInterpretDir);
+ group.add(btnInterpretUndir);
+ panInterpr.add(btnInterpretAll, BorderLayout.PAGE_START);
+ panInterpr.add(btnInterpretDir, BorderLayout.CENTER);
+ panInterpr.add(btnInterpretUndir, BorderLayout.PAGE_END);
+ panCenter.add(panInterpr);
+ contentPane.add(panCenter);
+ contentPane.add(Box.createVerticalStrut(Utils.BORDER_SIZE));
+
+ // Add info about node attributes
+ final JPanel panAttr = new JPanel(new FlowLayout(FlowLayout.CENTER, BS, BS));
+ if (SettingsSerializer.getPluginSettings().getUseNodeAttributes()) {
+ panAttr.add(new JLabel(Messages.DI_NODEATTR_SAVE));
+ } else {
+ panAttr.add(new JLabel(Messages.DI_NODEATTR_SAVENOT));
+ }
+ contentPane.add(panAttr);
+ contentPane.add(Box.createVerticalStrut(Utils.BORDER_SIZE));
+
+ // Add Start Analysis and Cancel buttons
+ final JPanel panBottom = new JPanel(new FlowLayout(FlowLayout.CENTER, 0, 0));
+ final JPanel panButtons = new JPanel(new GridLayout(1, 2, Utils.BORDER_SIZE, 0));
+ panButtons.add(btnCancel = Utils.createButton(Messages.DI_CANCEL, null, this));
+ panButtons.add(btnStart = Utils.createButton(Messages.DI_STARTANALYSIS, null, this));
+ panBottom.add(panButtons);
+ updateStartButton();
+
+ contentPane.add(panBottom);
+ setContentPane(contentPane);
+ setResizable(false);
+ }
+
+ /**
+ * Adds a path selector to the dialog.
+ *
+ * @param aMessage
+ * Label of the path to be selected.
+ * @param aField
+ * Field for the selected path name.
+ * @param aButton
+ * Button to be pressed for choosing the path.
+ * @param aPanel
+ * Panel to add aMessage, aField and aButton.
+ * @param aConstr
+ * Constraints for visualization.
+ */
+ private void addPathSelector(String aMessage, JTextField aField, JButton aButton, JPanel aPanel,
+ GridBagConstraints aConstr) {
+ aConstr.gridx = 0;
+ aConstr.anchor = GridBagConstraints.LINE_END;
+ aPanel.add(new JLabel(aMessage), aConstr);
+
+ aConstr.gridx = 1;
+ aConstr.anchor = GridBagConstraints.CENTER;
+ aField.setEditable(false);
+ aPanel.add(aField, aConstr);
+
+ aConstr.gridx = 2;
+ aPanel.add(aButton, aConstr);
+ aConstr.gridy++;
+ }
+
+ /**
+ * Updates the status of the button for starting the batch processing.
+ */
+ private void updateStartButton() {
+ if ("".equals(txfInputDir.getText()) || "".equals(txfOutputDir.getText())) {
+ btnStart.setEnabled(false);
+ } else {
+ btnStart.setEnabled(true);
+ }
+ }
+
+ /**
+ * Updates the chosen (input/output) file.
+ *
+ * @param aChooser
+ * JFileChooser, from which a new file has to be chosen.
+ * @return Chosen file.
+ */
+ private File updateSetting(JFileChooser aChooser) {
+ if (aChooser.showOpenDialog(this) == JFileChooser.APPROVE_OPTION) {
+ return aChooser.getSelectedFile();
+ }
+ return null;
+ }
+
+ /**
+ * Checks the output directory, i.e. if aFile exists, is a directory, is empty and is writable.
+ *
+ * @param aFile
+ * File to be checked.
+ * @return <code>true</code> if the output directory fulfills the criterion, and <code>false</code>
+ * otherwise.
+ */
+ public static boolean checkOutputDir(File aFile) {
+ try {
+ if (aFile.exists() && aFile.isDirectory() && aFile.list().length == 0 && aFile.canWrite()) {
+ return true;
+ }
+ } catch (Exception ex) {
+ // Fall through
+ }
+ return false;
+ }
+
+ /**
+ * Checks the output directory given by aFileName, i.e. if the directory exists, is a directory, is empty
+ * and is writable.
+ *
+ * @param aFileName
+ * Name of the directory to check.
+ * @return <code>true</code> if the output directory fulfills the criterion, and <code>false</code>
+ * otherwise.
+ */
+ public static boolean checkOutputDir(String aFileName) {
+ try {
+ return checkOutputDir(new File(aFileName));
+ } catch (Exception ex) {
+ return false;
+ }
+ }
+
+ /**
+ * Checks the input directory, i.e. if aFile exists, is a directory, is not empty and is readable.
+ *
+ * @param aFile
+ * File to be checked.
+ * @return <code>true</code> if the input directory fulfills the criterion, and <code>false</code>
+ * otherwise.
+ */
+ public static boolean checkInputDir(File aFile) {
+ try {
+ if (aFile.exists() && aFile.isDirectory() && aFile.canRead() && aFile.listFiles().length > 0) {
+ return true;
+ }
+ } catch (Exception ex) {
+ // Fall through
+ }
+ return false;
+ }
+
+ /**
+ * Checks the input directory given by aFileName, i.e. if the directory exists, is a directory, is empty
+ * and is writable.
+ *
+ * @param aFileName
+ * Name of the directory to check.
+ * @return <code>true</code> if the input directory fulfills the criterion, and <code>false</code>
+ * otherwise.
+ */
+ public static boolean checkInputDir(String aFileName) {
+ try {
+ return checkInputDir(new File(aFileName));
+ } catch (Exception ex) {
+ return false;
+ }
+ }
+
+ /**
+ * Unique ID for this version of this class. It is used in serialization.
+ */
+ private static final long serialVersionUID = 7767545827871267966L;
+
+ /**
+ * "Cancel" button.
+ */
+ private JButton btnCancel;
+
+ /**
+ * Button to select input directory (.sif, .gml, .xgmml files)
+ */
+ private JButton btnInputDir;
+
+ /**
+ * Button to select output directory (.netstats files)
+ */
+ private JButton btnOutputDir;
+
+ /**
+ * Radio button for applying all possible interpretations.
+ */
+ private JRadioButton btnInterpretAll;
+
+ /**
+ * Radio button for applying only interpretations that treat the networks as directed.
+ */
+ private JRadioButton btnInterpretDir;
+
+ /**
+ * Radio button for applying only interpretations that treat the networks as undirected.
+ */
+ private JRadioButton btnInterpretUndir;
+
+ /**
+ * Start analysis button.
+ */
+ private JButton btnStart;
+
+ /**
+ * Directory chooser for the Networks.
+ */
+ private JFileChooser choInputDir;
+
+ /**
+ * Directory chooser for the ".netstat" files.
+ */
+ private JFileChooser choOutputDir;
+
+ /**
+ * Two-element array storing the input and output directory as selected by the user.
+ */
+ private File[] inOutDirs;
+
+ /**
+ * Text field showing the name of the selected input directory.
+ */
+ private JTextField txfInputDir;
+
+ /**
+ * Text field showing the name of the selected output directory.
+ */
+ private JTextField txfOutputDir;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/ChartDisplayPanel.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/ChartDisplayPanel.java
new file mode 100644
index 0000000..9de57fe
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/ChartDisplayPanel.java
@@ -0,0 +1,429 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.ui;
+
+import java.awt.Dimension;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.lang.reflect.Constructor;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.swing.Box;
+import javax.swing.BoxLayout;
+import javax.swing.JButton;
+import javax.swing.JDialog;
+import javax.swing.JFileChooser;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+
+import org.jfree.chart.JFreeChart;
+
+import cytoscape.logger.CyLogger;
+import cytoscape.util.OpenBrowser;
+import de.mpg.mpi_inf.bioinf.netanalyzer.InnerException;
+import de.mpg.mpi_inf.bioinf.netanalyzer.Plugin;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.ComplexParam;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Messages;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.filter.ComplexParamFilter;
+import de.mpg.mpi_inf.bioinf.netanalyzer.dec.Decorator;
+import de.mpg.mpi_inf.bioinf.netanalyzer.sconnect.HelpConnector;
+import de.mpg.mpi_inf.bioinf.netanalyzer.ui.charts.JFreeChartConn;
+import de.mpg.mpi_inf.bioinf.netanalyzer.ui.filter.ComplexParamFilterDialog;
+
+/**
+ * Panel used to display chart.
+ * <p>
+ * In addition to a chart control (<code>ChartPanel</code>), this panel also contains buttons for
+ * enlarged view, saving and viewing/editing visual settings, and others.
+ * </p>
+ *
+ * @author Yassen Assenov
+ */
+public class ChartDisplayPanel extends JPanel implements ActionListener {
+
+ /**
+ * Initializes a new instance of <code>ChartDisplayPanel</code>.
+ *
+ * @param aOwner
+ * Owner dialog.
+ * @param aID
+ * ID of complex parameter to be displayed.
+ * @param aVisualizer
+ * Visualizer of the complex parameter to be displayed.
+ */
+ public ChartDisplayPanel(JDialog aOwner, String aID, ComplexParamVisualizer aVisualizer) {
+ this(aOwner, aID, aVisualizer, null);
+ }
+
+ /**
+ * Initializes a new instance of <code>ChartDisplayPanel</code>.
+ *
+ * @param aOwner
+ * Owner dialog.
+ * @param aID
+ * ID of complex parameter to be displayed.
+ * @param aVisualizer
+ * Visualizer of the complex parameter to be displayed.
+ * @param aDecorators
+ * Decorator instances for the complex parameter visualized.
+ */
+ public ChartDisplayPanel(JDialog aOwner, String aID, ComplexParamVisualizer aVisualizer,
+ Decorator[] aDecorators) {
+ super();
+ visualizer = aVisualizer;
+ id = aID;
+ decorators = aDecorators;
+ originalParam = aVisualizer.getComplexParam();
+ chart = aVisualizer.createControl();
+ ownerDialog = aOwner;
+
+ initControls();
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.event.ActionListener#actionPerformed(java.awt.event.ActionEvent)
+ */
+ public void actionPerformed(ActionEvent e) {
+ Object source = e.getSource();
+
+ try {
+ if (source == btnEnlarged) {
+ displayEnlarged();
+ } else if (source == btnSaveChart) {
+ SaveChartDialog dialog = new SaveChartDialog(ownerDialog, chart);
+ dialog.setVisible(true);
+ } else if (source == btnSaveData) {
+ saveChartData();
+ } else if (source == btnFilter) {
+ performFilter();
+ } else if (source == btnChartSettings) {
+ if (changeVisSettings()) {
+ repaint();
+ }
+ } else if (source == btnHelp) {
+ OpenBrowser.openURL(HelpConnector.getParamURL(id));
+ } else if (btnsDec != null) {
+ for (int i = 0; i < btnsDec.length; ++i) {
+ if (source == btnsDec[i]) {
+ Decorator dec = decorators[i];
+ if (dec.isActive()) {
+ dec.undecorate(chart);
+ } else {
+ dec.decorate(ownerDialog, chart, visualizer, true);
+ }
+ btnsDec[i].setText(dec.getButtonLabel());
+ btnsDec[i].setToolTipText(dec.getButtonToolTip());
+ break;
+ }
+ }
+ }
+ } catch (InnerException ex) {
+ // NetworkAnalyzer internal error
+ CyLogger.getLogger().error(Messages.SM_LOGERROR, ex);
+ }
+ }
+
+ /**
+ * Displays a dialog for changing the visual settings and aplies the changes if necessary.
+ *
+ * @return <code>true</code> if the user has pressed one of "Set Default" or
+ * "OK" buttons and changes were applied; <code>false</code> otherwise.
+ */
+ protected boolean changeVisSettings() {
+ // Display dialog to view/edit the settings
+ if (visualizer.showSettingsDialog(ownerDialog) != SettingsDialog.STATUS_CANCEL) {
+ // User has pressed SET DEFAULT or OK
+ final JFreeChart newChart = visualizer.updateControl(chart);
+ if (decorators != null) {
+ for (int i = 0; i < decorators.length; ++i) {
+ if (decorators[i].isActive()) {
+ decorators[i].decorate(ownerDialog, newChart, visualizer, false);
+ }
+ }
+ }
+ JFreeChartConn.setChart(chartPanel, chart = newChart);
+ return true;
+ }
+ return false;
+ }
+
+ /**
+ * Visualizer instance for the displayed parameter chart. Used for viewing/editing of visual
+ * settings.
+ */
+ protected ComplexParamVisualizer visualizer;
+
+ /**
+ * Owner dialog of this panel.
+ */
+ protected JDialog ownerDialog;
+
+ /**
+ * "Chart Settings" button.
+ */
+ protected JButton btnChartSettings;
+
+ /**
+ * Unique ID for this version of this class. It is used in serialization.
+ */
+ private static final long serialVersionUID = 1662216221117859713L;
+
+ /**
+ * Creates and lays out the controls inside this panel.
+ * <p>
+ * This method is called upon initialization only.
+ * </p>
+ */
+ private void initControls() {
+ setLayout(new BoxLayout(this, BoxLayout.X_AXIS));
+
+ add(createChartPanel());
+
+ final Box buttonPanel = Box.createVerticalBox();
+ final List<JButton> buttons = new ArrayList<JButton>(8);
+ btnEnlarged = Utils.createButton(Messages.DI_VIEWENLARGED, Messages.TT_VIEWENLARGED, this);
+ if (Plugin.hasFilter(originalParam.getClass())) {
+ btnFilter = Utils.createButton(Messages.DI_FILTERDATA, Messages.TT_FILTERDATA, this);
+ } else {
+ btnFilter = null;
+ }
+ btnSaveChart = Utils.createButton(Messages.DI_EXPORTCHART, Messages.TT_SAVECHART, this);
+ btnSaveData = Utils.createButton(Messages.DI_EXPORTDATA, Messages.TT_SAVEDATA, this);
+ btnChartSettings = Utils.createButton(Messages.DI_CHARTSETTINGS, Messages.TT_CHARTSETTINGS,
+ this);
+ btnHelp = Utils.createButton(Messages.DI_HELP, Messages.TT_ONLHELP, this);
+
+ buttonPanel.add(btnChartSettings);
+ buttons.add(btnChartSettings);
+ buttonPanel.add(btnEnlarged);
+ buttons.add(btnEnlarged);
+ if (btnFilter != null) {
+ buttonPanel.add(btnFilter);
+ buttons.add(btnFilter);
+ }
+ buttonPanel.add(Box.createVerticalStrut(Utils.BORDER_SIZE * 2));
+ if (decorators != null) {
+ btnsDec = new JButton[decorators.length];
+ for (int i = 0; i < decorators.length; ++i) {
+ Decorator d = decorators[i];
+ btnsDec[i] = Utils.createButton(d.getButtonLabel(), d.getButtonToolTip(), this);
+ buttonPanel.add(btnsDec[i]);
+ buttons.add(btnsDec[i]);
+ }
+ buttonPanel.add(Box.createVerticalStrut(Utils.BORDER_SIZE * 2));
+ }
+ buttonPanel.add(btnSaveChart);
+ buttons.add(btnSaveChart);
+ buttonPanel.add(btnSaveData);
+ buttons.add(btnSaveData);
+ buttonPanel.add(Box.createVerticalStrut(Utils.BORDER_SIZE * 2));
+ buttonPanel.add(btnHelp);
+ buttons.add(btnHelp);
+ buttonPanel.add(Box.createVerticalGlue());
+ // Ensure buttons are large enough to fit all possible messages
+ final JButton[] btnsArray = new JButton[buttons.size()];
+ Utils.setSizes(buttons.toArray(btnsArray), preferred, preferred);
+ add(buttonPanel);
+ add(Box.createHorizontalGlue());
+ }
+
+ /**
+ * Creates a Swing control that displays this panel's chart.
+ * <p>
+ * The newly created panel is stored in the {@link #chartPanel} field.
+ * </p>
+ *
+ * @return The newly created panel instance that displays the chart.
+ */
+ private JPanel createChartPanel() {
+ chartPanel = JFreeChartConn.createPanel(chart);
+ Dimension size = chartPanel.getPreferredSize();
+ size.setSize(size.getWidth() / 3 * 2, size.getHeight() / 3 * 2);
+ chartPanel.setPreferredSize(size);
+ return chartPanel;
+ }
+
+ /**
+ * Creates a dialog window which contains the chart in its preferred size.
+ */
+ private void displayEnlarged() {
+ JDialog dialog = new JDialog(ownerDialog, visualizer.getTitle(), false);
+ dialog.getContentPane().add(JFreeChartConn.createPanel(chart));
+ dialog.pack();
+ dialog.setLocationRelativeTo(ownerDialog);
+ dialog.setVisible(true);
+ }
+
+ /**
+ * Handles the pressing of the {@link #btnFilter} button.
+ * <p>
+ * After asking the user for confirmation, this method adds or removes filter to the complex
+ * parameter displayed.
+ * </p>
+ */
+ private void performFilter() {
+ if (originalParam == visualizer.getComplexParam()) {
+ // Create filter
+ try {
+ final Class<?> paramClass = originalParam.getClass();
+ final Class<?> filterClass = Plugin.getFilterDialogClass(paramClass);
+ final Constructor<?> constr = filterClass.getConstructors()[0];
+ Object[] cParams = new Object[] { ownerDialog, Messages.DT_FILTERDATA,
+ originalParam, visualizer.getSettings() };
+ ComplexParamFilterDialog d = (ComplexParamFilterDialog) constr.newInstance(cParams);
+ ComplexParamFilter filter = d.showDialog();
+ if (filter != null) {
+ btnFilter.setText(Messages.DI_REMOVEFILTER);
+ btnFilter.setToolTipText(Messages.TT_REMOVEFILTER);
+ visualizer.setComplexParam(filter.filter(originalParam));
+ chart = visualizer.createControl();
+ JFreeChartConn.setChart(chartPanel, chart);
+ }
+ } catch (InnerException ex) {
+ // NetworkAnalyzer internal error
+ CyLogger.getLogger().error(Messages.SM_LOGERROR, ex);
+ } catch (SecurityException ex) {
+ Utils.showErrorBox(this, Messages.DT_SECERROR, Messages.SM_SECERROR2);
+ } catch (Exception ex) {
+ // ClassCastException, ClassNotFoundException, IllegalAccessException
+ // IllegalArgumentException, InstantiationException, InvocationTargetException
+ // NetworkAnalyzer internal error
+ CyLogger.getLogger().error(Messages.SM_LOGERROR, ex);
+ }
+
+ } else {
+ // Remove filter
+ int res = JOptionPane.showConfirmDialog(this, Messages.SM_REMOVEFILTER,
+ Messages.DT_REMOVEFILTER, JOptionPane.YES_NO_OPTION);
+ if (res == JOptionPane.YES_OPTION) {
+ btnFilter.setText(Messages.DI_FILTERDATA);
+ btnFilter.setToolTipText(Messages.TT_FILTERDATA);
+ visualizer.setComplexParam(originalParam);
+ chart = visualizer.createControl();
+ JFreeChartConn.setChart(chartPanel, chart);
+ }
+ }
+ }
+
+ /**
+ * Displays a dialog for saving the complex parameter data into a text file.
+ * <p>
+ * If the user presses the "Save" button of the shown dialog, the complex parameter is
+ * saved to the chosen file.
+ * </p>
+ */
+ private void saveChartData() {
+ JFileChooser saveFileDialog = new JFileChooser();
+ int saveIt = saveFileDialog.showSaveDialog(this);
+ if (saveIt == JFileChooser.APPROVE_OPTION) {
+ FileWriter writer = null;
+ try {
+ File file = saveFileDialog.getSelectedFile();
+ if (Utils.canSave(file, this)) {
+ writer = new FileWriter(file);
+ visualizer.getComplexParam().save(writer, false);
+ }
+ } catch (IOException ex) {
+ Utils.showErrorBox(this, Messages.DT_IOERROR, Messages.SM_OERROR);
+ } finally {
+ if (writer != null) {
+ try {
+ writer.close();
+ } catch (IOException ex) {
+ // Fall through
+ }
+ }
+ }
+ }
+ }
+
+ private static Dimension preferred = null;
+
+ static {
+ final JButton b = new JButton("");
+ preferred = b.getPreferredSize();
+ final String[] texts = new String[] { Messages.DI_VIEWENLARGED, Messages.DI_FILTERDATA,
+ Messages.DI_EXPORTCHART, Messages.DI_EXPORTDATA, Messages.DI_CHARTSETTINGS,
+ Messages.DI_HELP, Messages.DI_FITLINE, Messages.DI_REMOVELINE, Messages.DI_FITPL, Messages.DI_REMOVEPL };
+ for (final String text : texts) {
+ b.setText(text);
+ Utils.ensureSize(preferred, b.getPreferredSize());
+ }
+ }
+
+ /**
+ * Decorators registered for the complex parameter instance visualized.
+ */
+ private Decorator[] decorators;
+
+ /**
+ * Original (unfiltered) complex parameter displayed in this panel.
+ */
+ private ComplexParam originalParam;
+
+ /**
+ * Chart to be displayed.
+ */
+ private JFreeChart chart;
+
+ /**
+ * Swing control that displays the chart.
+ */
+ private JPanel chartPanel;
+
+ /**
+ * "View Enlarged" button.
+ */
+ private JButton btnEnlarged;
+
+ /**
+ * "Save Chart" button.
+ */
+ private JButton btnSaveChart;
+
+ /**
+ * "Save Data" button.
+ */
+ private JButton btnSaveData;
+
+ /**
+ * "Filter Data" / "Remove Filter" button.
+ */
+ private JButton btnFilter;
+
+ /**
+ * Buttons for the decorators.
+ */
+ private JButton[] btnsDec;
+
+ /**
+ * "Help" button.
+ */
+ private JButton btnHelp;
+
+ /**
+ * ID of the visualized complex parameter.
+ */
+ private String id;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/ChartExpandablePanel.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/ChartExpandablePanel.java
new file mode 100644
index 0000000..b156705
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/ChartExpandablePanel.java
@@ -0,0 +1,289 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.ui;
+
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Cursor;
+import java.awt.event.ActionEvent;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+
+import javax.swing.BorderFactory;
+import javax.swing.JDialog;
+import javax.swing.border.TitledBorder;
+
+
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Messages;
+import de.mpg.mpi_inf.bioinf.netanalyzer.dec.Decorator;
+
+/**
+ * Chart display panel with a title border.
+ * <p>
+ * Clicking on the title of the border expands/collapses the contents of panel.
+ * </p>
+ *
+ * @author Yassen Assenov
+ */
+public class ChartExpandablePanel extends ChartDisplayPanel
+ implements MouseListener, MouseMotionListener {
+
+ /**
+ * Initializes a new instance of <code>ChartExpandablePanel</code>.
+ * <p>
+ * The panel is initially expanded.
+ * </p>
+ *
+ * @param aOwner Owner dialog.
+ * @param aID ID of complex parameter to be displayed.
+ * @param aVisualizer Visualizer of the complex parameter to be displayed.
+ */
+ public ChartExpandablePanel(JDialog aOwner, String aID, ComplexParamVisualizer aVisualizer) {
+ this(aOwner, aID, aVisualizer, true, null);
+ }
+
+ /**
+ * Initializes a new instance of <code>ChartExpandablePanel</code>.
+ *
+ * @param aOwner Owner dialog.
+ * @param aID ID of complex parameter to be displayed.
+ * @param aVisualizer Visualizer of the complex parameter to be displayed.
+ * @param aExpanded Flag indicating if the panel must be initially expanded or hidden.
+ */
+ public ChartExpandablePanel(JDialog aOwner, String aID, ComplexParamVisualizer aVisualizer, boolean aExpanded) {
+ this(aOwner, aID, aVisualizer, aExpanded, null);
+ }
+
+ /**
+ * Initializes a new instance of <code>ChartBorderPanel</code>.
+ *
+ * @param aOwner Owner dialog.
+ * @param aID ID of complex parameter to be displayed.
+ * @param aVisualizer Visualizer of the complex parameter to be displayed.
+ * @param aExpanded Flag indicating if the panel must be initially expanded or hidden.
+ * @param aDecorators Decorator instances for the complex parameter visualized.
+ */
+ public ChartExpandablePanel(JDialog aOwner, String aID, ComplexParamVisualizer aVisualizer, boolean aExpanded,
+ Decorator[] aDecorators) {
+ super(aOwner, aID, aVisualizer, aDecorators);
+
+ initControls(aExpanded);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.event.ActionListener#actionPerformed(java.awt.event.ActionEvent)
+ */
+ @Override
+ public void actionPerformed(ActionEvent e) {
+
+ if (e.getSource() == btnChartSettings) {
+ if (changeVisSettings()) {
+ String titleText = visualizer.getTitle();
+ titleExpanded = "- " + titleText;
+ titleHidden = "+ " + titleText;
+ title.setTitle(titleExpanded);
+ repaint();
+ }
+ } else {
+ super.actionPerformed(e);
+ }
+ }
+
+ /**
+ * Checks if this panel is currently expanded.
+ * <p>
+ * The panel is expanded when the controls it contains are visible, otherwise the panel is
+ * referred to as hidden.
+ * </p>
+ *
+ * @return <code>true</code> when this control is expanded; <code>false</code> otherwise.
+ */
+ public boolean isExpanded() {
+ return getComponent(0).isVisible();
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.event.MouseListener#mouseClicked(java.awt.event.MouseEvent)
+ */
+ public void mouseClicked(MouseEvent e) {
+ if (e.getY() <= titleHeight) {
+ setExpanded(!isExpanded());
+ ownerDialog.pack();
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.event.MouseListener#mousePressed(java.awt.event.MouseEvent)
+ */
+ public void mousePressed(MouseEvent e) {
+ // Event is not processed
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.event.MouseListener#mouseReleased(java.awt.event.MouseEvent)
+ */
+ public void mouseReleased(MouseEvent e) {
+ // Event is not processed
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.event.MouseListener#mouseEntered(java.awt.event.MouseEvent)
+ */
+ public void mouseEntered(MouseEvent e) {
+ // Event is not processed
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.event.MouseListener#mouseExited(java.awt.event.MouseEvent)
+ */
+ public void mouseExited(MouseEvent e) {
+ if (getCursor() == onTitleCursor) {
+ setCursor(null);
+ title.setTitleColor(normalTitleColor);
+ setToolTipText(null);
+ repaint();
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.event.MouseMotionListener#mouseDragged(java.awt.event.MouseEvent)
+ */
+ public void mouseDragged(MouseEvent e) {
+ // Event is not processed
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.event.MouseMotionListener#mouseMoved(java.awt.event.MouseEvent)
+ */
+ public void mouseMoved(MouseEvent e) {
+ if (e.getY() <= titleHeight) {
+ if (getCursor() != onTitleCursor) {
+ setCursor(onTitleCursor);
+ title.setTitleColor(selTitleColor);
+ if (isExpanded()) {
+ setToolTipText(Messages.TT_CLICK2HIDE);
+ } else {
+ setToolTipText(Messages.TT_CLICK2EXPAND);
+ }
+ repaint();
+ }
+ } else {
+ if (getCursor() == onTitleCursor) {
+ setCursor(null);
+ title.setTitleColor(normalTitleColor);
+ setToolTipText(null);
+ repaint();
+ }
+ }
+ }
+
+ /**
+ * Unique ID for this version of this class. It is used in serialization.
+ */
+ private static final long serialVersionUID = 8700420732833264603L;
+
+ /**
+ * Mouse cursor when over the top border of this panel.
+ */
+ private static Cursor onTitleCursor = Cursor.getPredefinedCursor(Cursor.HAND_CURSOR);
+
+ /**
+ * Creates and lays out the controls inside this panel.
+ * <p>
+ * This method is called upon initialization only.
+ * </p>
+ *
+ * @param aExpanded Flag indicating if the panel must be initially expanded or hidden.
+ */
+ private void initControls(boolean aExpanded) {
+
+ String titleText = visualizer.getTitle();
+ titleExpanded = "- " + titleText;
+ titleHidden = "+ " + titleText;
+ title = BorderFactory.createTitledBorder(titleExpanded);
+ setBorder(title);
+ titleHeight = title.getMinimumSize(this).height / 2;
+ normalTitleColor = title.getTitleColor();
+ selTitleColor = Utils.invertOf(normalTitleColor);
+ addMouseListener(this);
+ addMouseMotionListener(this);
+ if (aExpanded == false) {
+ setExpanded(false);
+ }
+ }
+
+ /**
+ * Changes the "expanded" status of this control.
+ *
+ * @param aExpanded Flag indicating if this panel must become expanded or hidden.
+ */
+ private void setExpanded(boolean aExpanded) {
+ Component[] controls = getComponents();
+ for (int i = 0; i < controls.length - 1; ++i) {
+ controls[i].setVisible(aExpanded);
+ }
+ ((TitledBorder) getBorder()).setTitle(aExpanded ? titleExpanded : titleHidden);
+ }
+
+ /**
+ * Border of the panel.
+ */
+ private TitledBorder title;
+
+ /**
+ * Title text when this panel is expanded, that is, when the controls inside it are visible.
+ */
+ private String titleExpanded;
+
+ /**
+ * Title text when this panel is hidden, that is, when the controls inside it are invisible.
+ */
+ private String titleHidden;
+
+ /**
+ * Color of title text when mouse cursor is <b>not</b> over the top border of this panel.
+ */
+ private Color normalTitleColor;
+
+ /**
+ * Color of title text when mouse cursor is over the top border of this panel.
+ */
+ private Color selTitleColor;
+
+ /**
+ * Height, in pixels, of the top border of this panel.
+ */
+ private int titleHeight;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/ClearMultEdgesDialog.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/ClearMultEdgesDialog.java
new file mode 100644
index 0000000..fe96151
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/ClearMultEdgesDialog.java
@@ -0,0 +1,128 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.ui;
+
+import java.awt.Frame;
+import java.awt.GridLayout;
+import java.awt.event.ActionEvent;
+
+import javax.swing.JCheckBox;
+import javax.swing.JComponent;
+import javax.swing.JPanel;
+
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Messages;
+import de.mpg.mpi_inf.bioinf.netanalyzer.sconnect.HelpConnector;
+
+/**
+ * Dialog for selecting networks on which multiple edges are to be cleared.
+ *
+ * @author Yassen Assenov
+ */
+public class ClearMultEdgesDialog extends NetModificationDialog {
+
+ /**
+ * Initializes a new instance of <code>ClearMultEdgesDialog</code>.
+ *
+ * @param aOwner
+ * The <code>Frame</code> from which this dialog is displayed.
+ */
+ public ClearMultEdgesDialog(Frame aOwner) {
+ super(aOwner, Messages.DT_REMDUPEDGES, Messages.DI_REMDUPEDGES, HelpConnector.getRemDuplicatesURL());
+
+ ignoreDirection = false;
+ createEdgeAttr = false;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see de.mpg.mpi_inf.bioinf.netanalyzer.ui.NetModificationDialog#actionPerformed(java.awt.event.ActionEvent)
+ */
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ if (e.getSource() == cbxIgnoreDirection) {
+ ignoreDirection = cbxIgnoreDirection.isSelected();
+ } else if (e.getSource() == cbxCreateEdgeAttr) {
+ createEdgeAttr = cbxCreateEdgeAttr.isSelected();
+ } else {
+ super.actionPerformed(e);
+ }
+ }
+
+ /**
+ * Gets the value of the "Ignore edge direction" flag.
+ *
+ * @return <code>true</code> if the user has chosen to ignore edge direction; <code>false</code>
+ * otherwise.
+ */
+ public boolean getIgnoreDirection() {
+ return ignoreDirection;
+ }
+
+ /**
+ * Gets the value of the "Create edge attribute " flag.
+ *
+ * @return <code>true</code> if the user has chosen to create an edge attribute; <code>false</code>
+ * otherwise.
+ */
+ public boolean getCreateEdgeAttr() {
+ return createEdgeAttr;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see de.mpg.mpi_inf.bioinf.netanalyzer.ui.NetModificationDialog#initAdditionalControls()
+ */
+ @Override
+ protected JComponent initAdditionalControls() {
+ final JPanel panel = new JPanel(new GridLayout(2, 1));
+ cbxIgnoreDirection = Utils.createCheckBox(Messages.DI_IGNOREEDGEDIR, Messages.TT_IGNOREEDGEDIR, this);
+ panel.add(cbxIgnoreDirection);
+ cbxCreateEdgeAttr = Utils.createCheckBox(Messages.DI_SAVENUMBEREDGES, Messages.TT_SAVENUMBEREDGES, this);
+ panel.add(cbxCreateEdgeAttr);
+ return panel;
+ }
+
+ /**
+ * Unique ID for this version of this class. It is used in serialization.
+ */
+ private static final long serialVersionUID = -2207325147812076427L;
+
+ /**
+ * Check box control for selecting if edge direction should be ignored.
+ */
+ private JCheckBox cbxIgnoreDirection;
+
+ /**
+ * Flag indicating if edge direction should be ignored, that is, if all edges are to be treated as
+ * undirected.
+ */
+ private boolean ignoreDirection;
+
+ /**
+ * Check box control for selecting if an edge attribute representing the number of duplicated edges should
+ * be created.
+ */
+ private JCheckBox cbxCreateEdgeAttr;
+
+ /**
+ * Flag indicating if an edge attribute representing the number of duplicated edges should be created.
+ */
+ private boolean createEdgeAttr;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/ComboBoxRenderer.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/ComboBoxRenderer.java
new file mode 100644
index 0000000..1d83b35
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/ComboBoxRenderer.java
@@ -0,0 +1,93 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.ui;
+
+import java.awt.Component;
+import java.awt.Dimension;
+
+import javax.swing.JLabel;
+import javax.swing.JList;
+import javax.swing.JSeparator;
+import javax.swing.ListCellRenderer;
+import javax.swing.SwingConstants;
+import javax.swing.border.EmptyBorder;
+
+/**
+ * A class that extends the ListCellRenderer class to visualize a separator
+ * line at a certain position between the JComboBoxItems.
+ */
+class ComboBoxRenderer extends JLabel implements ListCellRenderer {
+
+ /**
+ * Default constructor for creation of a ComboBoxRenderer.
+ */
+ public ComboBoxRenderer() {
+ setOpaque(true);
+ setBorder(new EmptyBorder(1, 1, 1, 1));
+ separator = new JSeparator(SwingConstants.HORIZONTAL);
+ fixedHeight = new JLabel(
+ "0123456789ABCDEFGHIJKLMNOPQRSTUVWXYZ(){}[]'\",;/?!@#$%^&*()_+")
+ .getPreferredSize().height * 12 / 10;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see javax.swing.ListCellRenderer#getListCellRenderer
+ */
+ public Component getListCellRendererComponent(JList list, Object value, int index,
+ boolean isSelected, boolean cellHasFocus) {
+ String str = (value == null) ? null : value.toString();
+ if (Utils.SEPARATOR.equals(str)) {
+ return separator;
+ }
+ if (isSelected) {
+ setBackground(list.getSelectionBackground());
+ setForeground(list.getSelectionForeground());
+ } else {
+ setBackground(list.getBackground());
+ setForeground(list.getForeground());
+ }
+ setFont(list.getFont());
+ setText(str);
+ updateHeight();
+ return this;
+ }
+
+ /**
+ * Unique ID for this version of this class. It is used in serialization.
+ */
+ private static final long serialVersionUID = 1977983924324671280L;
+
+ private void updateHeight() {
+ setPreferredSize(null);
+ final Dimension size = getPreferredSize();
+ size.height = fixedHeight;
+ setPreferredSize(size);
+ }
+
+ /**
+ * A separator line in a JComboBox.
+ */
+ private JSeparator separator;
+
+ /**
+ * A fixed height of the separator line.
+ */
+ private int fixedHeight;
+}
\ No newline at end of file
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/CompareDialog.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/CompareDialog.java
new file mode 100644
index 0000000..98542fa
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/CompareDialog.java
@@ -0,0 +1,182 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.ui;
+
+import java.awt.Frame;
+import java.awt.GridLayout;
+import java.awt.HeadlessException;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import javax.swing.Box;
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.event.ListSelectionEvent;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import de.mpg.mpi_inf.bioinf.netanalyzer.GOPTAlgorithm;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Messages;
+
+/**
+ * Dialog for choosing networks to compare and operations to perform on the networks.
+ *
+ * @author Yassen Assenov
+ * @author Caroline Becker
+ */
+public class CompareDialog extends NetworkListDialog implements ActionListener {
+
+ /**
+ * Initializes a new instance of <code>CompareDialog</code>.
+ *
+ * @param aOwner The <code>Frame</code> from which this dialog is displayed.
+ *
+ * @throws HeadlessException If <code>GraphicsEnvironment.isHeadless()</code> returns
+ * <code>true</code>.
+ */
+ public CompareDialog(Frame aOwner) throws HeadlessException {
+ super(aOwner, Messages.DT_COMPNETWORKS);
+
+ initControls();
+ pack();
+ setLocationRelativeTo(Cytoscape.getDesktop());
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.event.ActionListener#actionPerformed(java.awt.event.ActionEvent)
+ */
+ public void actionPerformed(ActionEvent e) {
+ Object src = e.getSource();
+ if (union == src || intersect == src || diff == src) {
+ updateOKButton();
+ } else if (btnCancel == src) {
+ setVisible(false);
+ dispose();
+ } else if (btnOK == src) {
+ final int[] indices = listNetNames.getSelectedIndices();
+ final CyNetwork network1 = networks.get(indices[0]);
+ final CyNetwork network2 = networks.get(indices[1]);
+ GOPTAlgorithm algorithm = new GOPTAlgorithm(network1, network2);
+ algorithm.computeNetworks(intersect.isSelected(), union.isSelected(), diff.isSelected());
+ setVisible(false);
+ dispose();
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see javax.swing.event.ListSelectionListener#valueChanged(javax.swing.event.ListSelectionEvent)
+ */
+ public void valueChanged(ListSelectionEvent e) {
+ updateOKButton();
+ }
+
+ /**
+ * Unique ID for this version of this class. It is used in serialization.
+ */
+ private static final long serialVersionUID = 5093100205881455450L;
+
+ /**
+ * Creates and lays out the controls inside this dialog.
+ * <p>
+ * This method is called upon initialization only.
+ * </p>
+ */
+ private void initControls() {
+ Box contentPane = Box.createVerticalBox();
+ Utils.setStandardBorder(contentPane);
+
+ JLabel title = new JLabel(Messages.DI_CNETWORKS);
+ JPanel panTitle = new JPanel();
+ panTitle.add(title);
+ contentPane.add(panTitle);
+ contentPane.add(Box.createVerticalStrut(Utils.BORDER_SIZE / 2));
+
+ final JScrollPane scroller = new JScrollPane(listNetNames);
+ final JPanel panNetList = new JPanel();
+ panNetList.add(scroller);
+ contentPane.add(panNetList);
+
+ // Add checkboxes for the functions
+ JPanel panCheckBoxes = new JPanel(new GridLayout(0, 1));
+ union = Utils.createCheckBox(Messages.DI_CUNION, null, this);
+ panCheckBoxes.add(union);
+ intersect = Utils.createCheckBox(Messages.DI_CINTERSECTION, null, this);
+ panCheckBoxes.add(intersect);
+ diff = Utils.createCheckBox(Messages.DI_CDIFF, null, this);
+ panCheckBoxes.add(diff);
+ JPanel panChoices = new JPanel();
+ panChoices.add(panCheckBoxes);
+ contentPane.add(panChoices);
+
+ // Add OK and Cancel buttons
+ JPanel panBottom = new JPanel();
+ JPanel panButtons = new JPanel(new GridLayout(1, 2, Utils.BORDER_SIZE, 0));
+ btnOK = Utils.createButton(Messages.DI_OK, null, this);
+ btnOK.setEnabled(false);
+ panButtons.add(btnOK);
+ btnCancel = Utils.createButton(Messages.DI_CANCEL, null, this);
+ panButtons.add(btnCancel);
+ panBottom.add(panButtons);
+ contentPane.add(panBottom);
+ setContentPane(contentPane);
+ }
+
+ /**
+ * Updates the "enabled" status of the "OK" button.
+ */
+ private void updateOKButton() {
+ boolean enable = false;
+ if (union.isEnabled() || intersect.isEnabled() || diff.isEnabled()) {
+ int[] indices = listNetNames.getSelectedIndices();
+ enable = (indices.length == 2);
+ }
+ btnOK.setEnabled(enable);
+ }
+
+ /**
+ * "OK" button.
+ */
+ private JButton btnOK;
+
+ /**
+ * "Cancel" button.
+ */
+ private JButton btnCancel;
+
+ /**
+ * "Compute Intersection" check box.
+ */
+ private JCheckBox intersect;
+
+ /**
+ * "Compute Union" check box.
+ */
+ private JCheckBox union;
+
+ /**
+ * "Compute Difference" check box.
+ */
+ private JCheckBox diff;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/ComplexParamVisualizer.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/ComplexParamVisualizer.java
new file mode 100644
index 0000000..1b415ba
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/ComplexParamVisualizer.java
@@ -0,0 +1,209 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.ui;
+
+import java.awt.Component;
+import java.awt.Dialog;
+import java.io.IOException;
+import java.lang.reflect.InvocationTargetException;
+
+import javax.swing.JComponent;
+import javax.swing.JTabbedPane;
+
+import org.jfree.chart.JFreeChart;
+
+import de.mpg.mpi_inf.bioinf.netanalyzer.InnerException;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.ComplexParam;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Messages;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.settings.GeneralVisSettings;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.settings.SettingsGroup;
+
+/**
+ * Base class for all classes responsible for the visualization of a certain complex parameter type.
+ *
+ * @author Yassen Assenov
+ */
+public abstract class ComplexParamVisualizer {
+
+ /**
+ * Creates the chart control that displays the complex parameter.
+ *
+ * @return Chart control as a <code>JFreeChart</code> instance.
+ */
+ public abstract JFreeChart createControl();
+
+ /**
+ * Gets the complex parameter instance managed by this visualizer.
+ *
+ * @return Complex parameter instance managed by this visualizer.
+ */
+ public abstract ComplexParam getComplexParam();
+
+ /**
+ * Gets the settings for the visualized complex parameter instance.
+ *
+ * @return The <code>SettingsGroup</code> instance for the visualized complex parameter.
+ */
+ public abstract SettingsGroup getSettings();
+
+ /**
+ * Sets the complex parameter instance managed by this visualizer.
+ * <p>
+ * <b>Note:</b> It is the responsibility of the caller to recreate all the controls created by this
+ * visualizer by calling the {@link #createControl()} method for each of them.
+ * </p>
+ *
+ * @param aParam Complex parameter instance to be managed by this visualizer.
+ * @throws ClassCastException If the specified complex parameter is not of the expected type.
+ * @throws NullPointerException If <code>aParam</code> is <code>null</code>.
+ */
+ public abstract void setComplexParam(ComplexParam aParam);
+
+ /**
+ * Gets the title of the displayed complex parameter.
+ *
+ * @return Description of the complex parameter in a human readable form.
+ */
+ public String getTitle() {
+ if (general != null) {
+ return general.getTitle();
+ }
+ return null;
+ }
+
+ /**
+ * Pops up a dialog for viewing/editing complex parameter settings.
+ * <p>
+ * This method automatically updates the visual settings for the complex parameter if the user presses the
+ * "OK" or "Save as Default" button. It also attempts to save the settings if the user
+ * presses the "Save as Default" button and displays an error message in case the attempt was
+ * not successful.
+ * </p>
+ * <p>
+ * <b>Note:</b> It is the responsibility of the caller to update all the controls created by the
+ * visualizer by calling the {@link #updateControl(JFreeChart)} method for each of them.
+ * </p>
+ *
+ * @param aOwner The <code>Dialog</code> from which the settings dialog is displayed.
+ * @return The status as returned by the settings dialog.
+ * @see SettingsDialog#STATUS_CANCEL
+ * @see SettingsDialog#STATUS_DEFAULT
+ * @see SettingsDialog#STATUS_OK
+ */
+ public int showSettingsDialog(Dialog aOwner) {
+ SettingsDialog d = new SettingsDialog(aOwner, Messages.DI_CHARTSETTINGS);
+ JComponent dataComp = addSettingsPanels(d.getSettingsPane());
+
+ d.pack();
+ d.setLocationRelativeTo(aOwner);
+ d.setVisible(true);
+
+ int status = d.getStatus();
+ if (status != SettingsDialog.STATUS_CANCEL) {
+ try {
+ d.update();
+ updateSettings(dataComp);
+ if (status == SettingsDialog.STATUS_DEFAULT) {
+ try {
+ saveDefault();
+ } catch (SecurityException ex) {
+ Utils.showErrorBox(aOwner, Messages.DT_SECERROR, Messages.SM_SECERROR2);
+ } catch (Exception ex) {
+ // FileNotFoundException
+ // IOException
+ Utils.showErrorBox(aOwner, Messages.DT_IOERROR, Messages.SM_DEFFAILED);
+ }
+ }
+ } catch (InvocationTargetException ex) {
+ throw new InnerException(ex);
+ }
+ }
+ return status;
+ }
+
+ /**
+ * Updates the given chart control according to the visual settings for the complex parameter.
+ *
+ * @param aControl Control to be updated. This must be an instance of <code>JFreeChart</code>, as
+ * returned by {@link #createControl()}.
+ * @return The updated chart control, which may be the same instance as <code>aControl</code>, but it
+ * may also be a newly created instance.
+ */
+ public abstract JFreeChart updateControl(JFreeChart aControl);
+
+ /**
+ * Adds a new tab to the given tabbed pane.
+ *
+ * @param aPanel Tabbed pane to be used.
+ * @param aTitle Title of the new tab.
+ * @param aComp Component to be added.
+ * @param aToolTip Tool-tip of the new tab. Set this to <code>null</code> if the tab title does not a
+ * have a tool-tip.
+ */
+ protected static void addTab(JTabbedPane aPanel, String aTitle, Component aComp, String aToolTip) {
+ aPanel.addTab(aTitle, null, aComp, aToolTip);
+ }
+
+ /**
+ * Adds the tabs for the parameter-specific visual settings, e.g. axes-related settings, bar chart
+ * setting, and others.
+ *
+ * @param aPanel Tabbed control to adds tabs to.
+ * @return Component to be passed as an argument of {@link #updateSettings(JComponent)};
+ * <code>null</code> if the visualizer instance does not encode any visualization settings
+ * information into controls other than {@link SettingsPanel}.
+ */
+ protected abstract JComponent addSettingsPanels(JTabbedPane aPanel);
+
+ /**
+ * Sets the stored settings for this complex parameter as default.
+ * <p>
+ * This method calls
+ * {@link de.mpg.mpi_inf.bioinf.netanalyzer.data.io.SettingsSerializer#setDefault(SettingsGroup)} which
+ * results in saving the settings to the XML settings file of the plugin.
+ * </p>
+ *
+ * @throws IOException If saving the XML settings file failed due to an I/O error.
+ */
+ protected abstract void saveDefault() throws IOException;
+
+ /**
+ * Updates the visual settings instances based on the state of some component in the settings dialog.
+ * <p>
+ * This method is called only in the scenario when the settings dialog is displayed and the user presses
+ * the "OK" or "Save as Default" button. In such a case, this method is invoked
+ * <b>after</b> invoking {@link SettingsDialog#update()}.
+ * </p>
+ * <p>
+ * An inheriting class should override this method when some properties are not automatically updated by
+ * the {@link SettingsDialog#update()}, that is, when some visual properties were added outside a
+ * {@link SettingsPanel}.
+ * </p>
+ *
+ * @param aDataComp Component in the settings dialog that carries the information required to update the
+ * visual settings instance(s).
+ */
+ protected void updateSettings(JComponent aDataComp) {
+ // Default implementation is empty. See the Javadoc of the method for details.
+ }
+
+ /**
+ * General visual settings for the complex parameter.
+ */
+ protected GeneralVisSettings general;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/ConnComponentsDialog.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/ConnComponentsDialog.java
new file mode 100644
index 0000000..3d388ab
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/ConnComponentsDialog.java
@@ -0,0 +1,252 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.ui;
+
+import giny.model.Node;
+
+import java.awt.BorderLayout;
+import java.awt.Component;
+import java.awt.FlowLayout;
+import java.awt.Frame;
+import java.awt.HeadlessException;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.swing.BorderFactory;
+import javax.swing.Box;
+import javax.swing.BoxLayout;
+import javax.swing.JButton;
+import javax.swing.JDialog;
+import javax.swing.JLabel;
+import javax.swing.JList;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTextField;
+import javax.swing.ListSelectionModel;
+import javax.swing.event.DocumentEvent;
+import javax.swing.event.DocumentListener;
+import javax.swing.event.ListSelectionEvent;
+import javax.swing.event.ListSelectionListener;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import de.mpg.mpi_inf.bioinf.netanalyzer.ConnComponentAnalyzer;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.CCInfo;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Messages;
+
+/**
+ * Dialog listing the connected components of a network. This dialog also allows for a connected
+ * component to be saved as a new network.
+ *
+ * @author Yassen Assenov
+ */
+public class ConnComponentsDialog extends JDialog
+ implements ActionListener, DocumentListener, ListSelectionListener {
+
+ /**
+ * Initializes a new instance of <code>ConnComponentsDialog</code>.
+ *
+ * @param aOwner The <code>Frame</code> from which this dialog is displayed.
+ * @param aNetwork Target network, to which the connected components belong.
+ * @param aComponents Array of all the connected components of <code>aNetwork</code>.
+ * @throws HeadlessException if <code>GraphicsEnvironment.isHeadless()</code> returns
+ * <code>true</code>.
+ */
+ public ConnComponentsDialog(Frame aOwner, CyNetwork aNetwork, CCInfo[] aComponents)
+ throws HeadlessException {
+ super(aOwner, Messages.DT_CONNCOMP, true);
+ network = aNetwork;
+ components = aComponents;
+ initControls();
+ pack();
+ setResizable(false);
+ setLocationRelativeTo(aOwner);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.event.ActionListener#actionPerformed(java.awt.event.ActionEvent)
+ */
+ public void actionPerformed(ActionEvent e) {
+ Object src = e.getSource();
+ if (btnClose == src) {
+ setVisible(false);
+ dispose();
+ } else if (btnExtract == src) {
+ CCInfo comp = components[listComp.getSelectedIndex()];
+ ArrayList<Node> nodes = new ArrayList<Node>(ConnComponentAnalyzer.getNodesOf(network, comp));
+ // TODO: [Cytoscape 2.8] Check if the returned list is parameterized
+ List<?> edges = network.getConnectingEdges(nodes);
+ Cytoscape.createNetwork(nodes, edges, fieldNetName.getText());
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see javax.swing.event.ListSelectionListener#valueChanged(javax.swing.event.ListSelectionEvent)
+ */
+ public void valueChanged(ListSelectionEvent e) {
+ int i = listComp.getSelectedIndex() + 1;
+ boolean enabled = (i != 0);
+ btnExtract.setEnabled(enabled);
+ if (enabled) {
+ String title = network.getTitle();
+ if (title == null) {
+ title = "_" + i;
+ } else if (title.endsWith(".gml") || title.endsWith(".sif")) {
+ final int cut = title.length() - 4;
+ title = title.substring(0, cut) + "_" + i + title.substring(cut);
+ } else {
+ title = title + "_" + i;
+ }
+ fieldNetName.setText(title);
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see javax.swing.event.DocumentListener#insertUpdate(javax.swing.event.DocumentEvent)
+ */
+ public void insertUpdate(DocumentEvent e) {
+ updateBtnExtract();
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see javax.swing.event.DocumentListener#removeUpdate(javax.swing.event.DocumentEvent)
+ */
+ public void removeUpdate(DocumentEvent e) {
+ updateBtnExtract();
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see javax.swing.event.DocumentListener#changedUpdate(javax.swing.event.DocumentEvent)
+ */
+ public void changedUpdate(DocumentEvent e) {
+ // Event is not processed
+ }
+
+ /**
+ * Unique ID for this version of this class. It is used in serialization.
+ */
+ private static final long serialVersionUID = 6103679911736096166L;
+
+ /**
+ * Creates and lays out the controls inside this dialog.
+ * <p>
+ * This method is called upon initialization only.
+ * </p>
+ */
+ private void initControls() {
+ Box contentPane = new Box(BoxLayout.PAGE_AXIS);
+ Utils.setStandardBorder(contentPane);
+
+ String tt = "<html>" + Messages.DI_CCOF + "<b>" + network.getTitle() + "</b>";
+ JPanel panTitle = new JPanel();
+ panTitle.setAlignmentX(Component.CENTER_ALIGNMENT);
+ panTitle.add(new JLabel(tt));
+ contentPane.add(panTitle);
+
+ final int compCount = components.length;
+ String[] ccItems = new String[compCount];
+ for (int i = 0; i < compCount; ++i) {
+ ccItems[i] = Messages.DI_COMP + " " + (i + 1) + " (" + components[i].getSize() + ")";
+ }
+ listComp = new JList(ccItems);
+ listComp.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
+ listComp.addListSelectionListener(this);
+ if (compCount < 8) {
+ listComp.setVisibleRowCount(compCount);
+ }
+ JScrollPane scrollList = new JScrollPane(listComp);
+ scrollList.setAlignmentX(Component.CENTER_ALIGNMENT);
+ JPanel panList = new JPanel();
+ panList.setBorder(BorderFactory.createTitledBorder(Messages.DI_CONNCOMP));
+ panList.add(scrollList);
+ contentPane.add(panList);
+
+ JPanel panExtract = new JPanel(new BorderLayout());
+ panExtract.setBorder(BorderFactory.createTitledBorder(Messages.DI_EXTRCOMP));
+ panExtract.add(new JLabel(Messages.DI_EXTRCOMPLONG), BorderLayout.NORTH);
+ fieldNetName = new JTextField();
+ fieldNetName.getDocument().addDocumentListener(this);
+ panExtract.add(fieldNetName, BorderLayout.CENTER);
+ btnExtract = Utils.createButton(Messages.DI_EXTR, null, this);
+ btnExtract.setEnabled(false);
+ JPanel panExtr = new JPanel(new FlowLayout(FlowLayout.TRAILING));
+ panExtr.add(btnExtract);
+ panExtract.add(panExtr, BorderLayout.SOUTH);
+ contentPane.add(panExtract);
+
+ JPanel panButtons = new JPanel();
+ panButtons.setAlignmentX(Component.CENTER_ALIGNMENT);
+ btnClose = Utils.createButton(Messages.DI_CLOSE, null, this);
+ panButtons.add(btnClose);
+ contentPane.add(panButtons);
+ setContentPane(contentPane);
+ }
+
+ /**
+ * Updates the "enabled" status of the Extract button.
+ */
+ private void updateBtnExtract() {
+ if ("".equals(fieldNetName.getText()) || listComp.getSelectedIndex() == -1) {
+ btnExtract.setEnabled(false);
+ } else {
+ btnExtract.setEnabled(true);
+ }
+ }
+
+ /**
+ * Network that contains the connected components listed in this dialog.
+ */
+ private CyNetwork network;
+
+ /**
+ * List of all connected component contained in {@link #network}.
+ */
+ private CCInfo[] components;
+
+ /**
+ * "Close" button.
+ */
+ private JButton btnClose;
+
+ /**
+ * "Extract" button.
+ */
+ private JButton btnExtract;
+
+ /**
+ * List control that contains the connected components.
+ */
+ private JList listComp;
+
+ /**
+ * Text field for entering the name of a new network.
+ */
+ private JTextField fieldNetName;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/ExtensionFileFilter.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/ExtensionFileFilter.java
new file mode 100644
index 0000000..8384474
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/ExtensionFileFilter.java
@@ -0,0 +1,204 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.ui;
+
+import java.io.File;
+
+import javax.swing.filechooser.FileFilter;
+
+/**
+ * Fle filter based on file's extension. Instances of this class are used by Swing's class
+ * <code>JFileChooser</code>.
+ * <p>
+ * This class follows a different conception than the one in JCommon - it encodes a file type by its
+ * description and one or more acceptable extensions, whereas
+ * <code>org.jfree.ui.ExtensionFileFilter</code> supports only one extension per file type.
+ * </p>
+ * <p>
+ * The behavior of this class is similar to <code>cytoscape.util.CyFileFilter</code>. It is,
+ * however, more efficient when the number of acceptable extensions is low.
+ * </p>
+ *
+ * @author Yassen Assenov
+ */
+public class ExtensionFileFilter extends FileFilter {
+
+ /**
+ * Initializes a new instance of <code>ExtensionFileFilter</code>.
+ *
+ * @param aExtension Extension to be used in accepting filenames.
+ * @param aDescription Description of the file type, identified by the specified extension.
+ */
+ public ExtensionFileFilter(String aExtension, String aDescription) {
+ super();
+
+ extensions = new String[1];
+ setExtension(0, aExtension);
+ description = aDescription;
+ }
+
+ /**
+ * Initializes a new instance of <code>ExtensionFileFilter</code>.
+ *
+ * @param aExtension1 First extension to be used in accepting filenames.
+ * @param aExtension2 Second extension to be used in accepting filenames.
+ * @param aDescription Description of the file type, identified by the specified extension.
+ */
+ public ExtensionFileFilter(String aExtension1, String aExtension2, String aDescription) {
+ super();
+
+ extensions = new String[2];
+ setExtension(0, aExtension1);
+ setExtension(1, aExtension2);
+ description = aDescription;
+ }
+
+ /**
+ * Initializes a new instance of <code>ExtensionFileFilter</code>.
+ *
+ * @param aExtensions Extensions to be used in accepting filenames.
+ * @param aDescription Description of the file type, identified by the specified extensions.
+ */
+ public ExtensionFileFilter(String[] aExtensions, String aDescription) {
+ super();
+
+ extensions = new String[aExtensions.length];
+ for (int i = 0; i < aExtensions.length; ++i) {
+ setExtension(i, aExtensions[i]);
+ }
+
+ description = aDescription;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see javax.swing.filechooser.FileFilter#accept(java.io.File)
+ */
+ @Override
+ public boolean accept(File file) {
+ if (file.isDirectory() || hasExtension(file.getName())) {
+ return true;
+ }
+ return false;
+ }
+
+ /**
+ * Appends an extension to a specified file.
+ * <p>
+ * The extension appended is the typical extension of the filetypes identifed by this instance.
+ * </p>
+ *
+ * @param aFile File to get an extension.
+ * @return File with the same name as the specified one, but with appended extension.
+ */
+ public File appendExtension(File aFile) {
+ return new File(aFile.getAbsolutePath() + extensions[0]);
+ }
+
+ /**
+ * Appends an extension to a filename.
+ * <p>
+ * The extension appended is the typical extension of the filetypes identifed by this instance.
+ * </p>
+ *
+ * @param aFileName Name of file to get an extension.
+ * @return <code>String</code> containing the given filename with appended extension.
+ */
+ public String appendExtension(String aFileName) {
+ return aFileName + extensions[0];
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see javax.swing.filechooser.FileFilter#getDescription()
+ */
+ @Override
+ public String getDescription() {
+ return description;
+ }
+
+ /**
+ * Gets the typical extension.
+ *
+ * @return <code>String</code> encoding the typical extension of the filetypes identified by
+ * this instance.
+ */
+ public String getExtension() {
+ return extensions[0].substring(1);
+ }
+
+ /**
+ * Checks if a given filename ends with one of the accepted extensions.
+ *
+ * @param aFile File, whose name is to be checked.
+ * @return <code>true</code> if the name of <code>aFile</code> ends with one of the accepted
+ * extensions; <code>false</code> otherwise.
+ */
+ public boolean hasExtension(File aFile) {
+ return hasExtension(aFile.getName());
+ }
+
+ /**
+ * Checks if a given filename ends with one of the accepted extensions.
+ *
+ * @param aFilename Name of file to be checked.
+ * @return <code>true</code> if the name of <code>aFile</code> ends with one of the accepted
+ * extensions; <code>false</code> otherwise.
+ */
+ public boolean hasExtension(String aFilename) {
+ for (int i = 0; i < extensions.length; ++i) {
+ if (aFilename.toLowerCase().endsWith(extensions[i])) {
+ return true;
+ }
+ }
+ return false;
+ }
+
+ /**
+ * Sets one of the accepted extensions.
+ * <p>
+ * This method is called only from the constructor. It set the value of {@link #extensions}<code>[aIndex]</code>
+ * to <code>aExtension</code>, prefixing it by "." if necessary.
+ * </p>
+ *
+ * @param aIndex Index of the extension to set.
+ * @param aExtension Value to set.
+ */
+ private void setExtension(int aIndex, String aExtension) {
+ if (aExtension.startsWith(".")) {
+ extensions[aIndex] = aExtension.toLowerCase();
+ } else {
+ extensions[aIndex] = "." + aExtension.toLowerCase();
+ }
+ }
+
+ /**
+ * Array of extensions to be used in accepting filenames.
+ * <p>
+ * Every extension is a word in lower case letters, prefixed by the symbol ".".
+ * </p>
+ */
+ private String[] extensions;
+
+ /**
+ * Description of file type, identified by the extensions.
+ */
+ private String description;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/FileCellRenderer.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/FileCellRenderer.java
new file mode 100644
index 0000000..f1e83c7
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/FileCellRenderer.java
@@ -0,0 +1,63 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.ui;
+
+import java.io.File;
+
+import javax.swing.JTable;
+import javax.swing.table.DefaultTableCellRenderer;
+
+/**
+ * Cell renderer for instance of the {@link File} type.
+ * <p>
+ * This class is to be used for visualization of files (file names) in the {@link JTable} Swing control.
+ * </p>
+ *
+ * @author Yassen Assenov
+ */
+class FileCellRenderer extends DefaultTableCellRenderer {
+
+ /**
+ * Unique ID for this version of this class. It is used in serialization.
+ */
+ private static final long serialVersionUID = 6855862789588816843L;
+
+ /**
+ * Initializes a new instance of <code>FileCellRenderer</code>.
+ */
+ public FileCellRenderer() {
+ // No fields to initialize
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see javax.swing.table.DefaultTableCellRenderer#setValue(java.lang.Object)
+ */
+ @Override
+ public void setValue(Object value) {
+ String text = "";
+ if (value != null) {
+ final File f = (File) value;
+ final String name = f.getName();
+ text = "<html><a href=\"" + name + "\">" + name + "</a></html>";
+ setToolTipText(f.getAbsolutePath());
+ }
+ setText(text);
+ }
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/IntHistogramVisualizer.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/IntHistogramVisualizer.java
new file mode 100644
index 0000000..9a58bdc
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/IntHistogramVisualizer.java
@@ -0,0 +1,234 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.ui;
+
+import java.awt.CardLayout;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.io.IOException;
+
+import javax.swing.Box;
+import javax.swing.JComboBox;
+import javax.swing.JComponent;
+import javax.swing.JPanel;
+import javax.swing.JTabbedPane;
+
+import org.jfree.chart.JFreeChart;
+import org.jfree.chart.plot.XYPlot;
+import org.jfree.chart.renderer.xy.XYBarRenderer;
+
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.ComplexParam;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.IntHistogram;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Messages;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.io.SettingsSerializer;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.settings.IntHistogramGroup;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.settings.SettingsGroup;
+import de.mpg.mpi_inf.bioinf.netanalyzer.ui.charts.JFreeChartConn;
+
+/**
+ * Handles the visualization of the {@link de.mpg.mpi_inf.bioinf.netanalyzer.data.IntHistogram} complex
+ * parameter type instances.
+ *
+ * @author Yassen Assenov
+ * @author Sven-Eric Schelhorn
+ */
+public class IntHistogramVisualizer extends ComplexParamVisualizer {
+
+ /**
+ * Initializes a new instance of <code>IntHistogramVisualizer</code>.
+ *
+ * @param aParam Instance of the integer histogram complex parameter type.
+ * @param aSettings Visual settings for the complex parameter.
+ */
+ public IntHistogramVisualizer(IntHistogram aParam, IntHistogramGroup aSettings) {
+ param = aParam;
+ settings = (IntHistogramGroup) aSettings.clone();
+ general = settings.general;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see de.mpg.mpi_inf.bioinf.netanalyzer.ui.ComplexParamVisualizer#getComplexParam()
+ */
+ @Override
+ public ComplexParam getComplexParam() {
+ return param;
+ }
+
+ /**
+ * Gets the settings for the visualized <code>IntHistogram</code>.
+ *
+ * @return The <code>IntHistogramGroup</code> instance for the visualized complex parameter.
+ */
+ @Override
+ public SettingsGroup getSettings() {
+ return settings;
+ }
+
+ /**
+ * Sets the complex parameter instance managed by this visualizer.
+ * <p>
+ * <b>Note:</b> It is the responsibility of the caller to recreate all the controls created by this
+ * visualizer by calling the {@link #createControl()} method for each of them.
+ * </p>
+ *
+ * @param aParam Complex parameter instance to be managed by this visualizer.
+ * @throws ClassCastException If the specified complex parameter is not of type
+ * {@link de.mpg.mpi_inf.bioinf.netanalyzer.data.IntHistogram}.
+ * @throws NullPointerException If <code>aParam</code> is <code>null</code>.
+ */
+ @Override
+ public void setComplexParam(ComplexParam aParam) {
+ if (aParam == null) {
+ throw new NullPointerException();
+ }
+ param = (IntHistogram) aParam;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see de.mpg.mpi_inf.bioinf.netanalyzer.ui.ComplexParamVisualizer#createControl()
+ */
+ @Override
+ public JFreeChart createControl() {
+ return JFreeChartConn.createChart(param, settings);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see de.mpg.mpi_inf.bioinf.netanalyzer.ui.ComplexParamVisualizer#updateControl(org.jfree.chart.JFreeChart)
+ */
+ @Override
+ public JFreeChart updateControl(JFreeChart aControl) {
+ XYPlot plot = (XYPlot) aControl.getPlot();
+ if (plot.getRenderer() instanceof XYBarRenderer) {
+ // Current control is Histogram
+ if (settings.useScatter()) {
+ return JFreeChartConn.createScatter(param, settings);
+ }
+ JFreeChartConn.updateGeneral(aControl, general);
+ JFreeChartConn.updateAxes(aControl, settings.axes, settings.grid);
+ JFreeChartConn.updateBars(aControl, settings.bars);
+ return aControl;
+ }
+
+ // else: plot.getRenderer() instanceof StandardXYItemRenderer
+ // Current control is Scatter Plot
+ if (settings.useScatter()) {
+ JFreeChartConn.updateGeneral(aControl, general);
+ JFreeChartConn.updateAxes(aControl, settings.axes, settings.grid);
+ JFreeChartConn.updateScatter(aControl, settings.scatter);
+ return aControl;
+ }
+ return JFreeChartConn.createHistogram(param, settings);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see de.mpg.mpi_inf.bioinf.netanalyzer.ui.ComplexParamVisualizer#addSettingsPanels(javax.swing.JTabbedPane)
+ */
+ @Override
+ protected JComponent addSettingsPanels(JTabbedPane aPanel) {
+
+ addTab(aPanel, Messages.DI_GENERAL, new SettingsPanel(general), Messages.TT_GENSETTINGS);
+ addTab(aPanel, Messages.DI_AXES, new SettingsPanel(settings.axes), Messages.TT_AXESSETTINGS);
+ addTab(aPanel, Messages.DI_GRID, new SettingsPanel(settings.grid), Messages.TT_GRIDSETTINGS);
+
+ boolean useScatter = settings.useScatter();
+ final Box histPanel = Box.createVerticalBox();
+
+ final JComboBox choiceCombo = addChoice(histPanel, useScatter ? 1 : 0);
+
+ final CardLayout innerLayout = new CardLayout();
+ final JPanel innerPanel = new JPanel(innerLayout);
+ histPanel.add(innerPanel);
+ aPanel.addTab(Messages.DI_HISTOGRAM, null, histPanel, Messages.TT_HISTSETTINGS);
+
+ ItemListener listener = new ItemListener() {
+
+ public void itemStateChanged(ItemEvent e) {
+ if (e.getStateChange() == ItemEvent.SELECTED) {
+ innerLayout.next(innerPanel);
+ }
+ }
+ };
+ choiceCombo.addItemListener(listener);
+
+ innerPanel.add(new SettingsPanel(settings.bars), "0");
+ innerPanel.add(new SettingsPanel(settings.scatter), "1");
+ if (useScatter) {
+ innerLayout.next(innerPanel);
+ }
+
+ return choiceCombo;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see de.mpg.mpi_inf.bioinf.netanalyzer.ui.ComplexParamVisualizer#saveDefault()
+ */
+ @Override
+ protected void saveDefault() throws IOException {
+ SettingsSerializer.setDefault(settings);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see de.mpg.mpi_inf.bioinf.netanalyzer.ui.ComplexParamVisualizer#updateSettings(javax.swing.JComponent)
+ */
+ @Override
+ protected void updateSettings(JComponent aDataComp) {
+ settings.useScatter.setValue(((JComboBox) aDataComp).getSelectedIndex() == 1);
+ }
+
+ /**
+ * Creates the combo box (drop-down list) to choose between visualization of the histogram as bar chart or
+ * as a scatter plot.
+ *
+ * @param aContainer Container control, to which the combo box is to be added.
+ * @param aSelectedIndex Which choice is to be initially selected. This parameter must have one of the
+ * values <code>{1; 2}</code>.
+ * @return The newly created combo box control.
+ */
+ private static JComboBox addChoice(Box aContainer, int aSelectedIndex) {
+ final String[] choices = new String[] { Messages.DI_SHOWHIST, Messages.DI_SHOWSCAT };
+ JComboBox choiceCombo = new JComboBox(choices);
+ choiceCombo.setSelectedIndex(aSelectedIndex);
+ choiceCombo.setEditable(false);
+ JPanel choicePanel = new JPanel();
+ choicePanel.add(choiceCombo);
+ aContainer.add(choicePanel);
+ return choiceCombo;
+ }
+
+ /**
+ * Integer histogram instance to be visualized.
+ */
+ private IntHistogram param;
+
+ /**
+ * Visual settings for the integer histogram instance.
+ */
+ private IntHistogramGroup settings;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/InterpretationCellRenderer.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/InterpretationCellRenderer.java
new file mode 100644
index 0000000..931a042
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/InterpretationCellRenderer.java
@@ -0,0 +1,75 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.ui;
+
+import javax.swing.JTable;
+
+import com.l2fprod.common.swing.renderer.DefaultCellRenderer;
+
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Messages;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.NetworkInterpretation;
+
+/**
+ * Cell renderer for instance of the {@link NetworkInterpretation} type.
+ * <p>
+ * This class is to be used for visualization applied network interpretations in a {@link JTable} Swing
+ * control.
+ * </p>
+ *
+ * @author Yassen Assenov
+ */
+public class InterpretationCellRenderer extends DefaultCellRenderer {
+
+ /**
+ * Initializes a new instance of <code>InterpretationCellRenderer</code>.
+ */
+ public InterpretationCellRenderer() {
+ // No specific initialization is required.
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see javax.swing.table.DefaultTableCellRenderer#setValue(java.lang.Object)
+ */
+ @Override
+ public void setValue(Object value) {
+ final StringBuilder text = new StringBuilder();
+ text.append("<html>");
+ if (value != null) {
+ final NetworkInterpretation interpr = (NetworkInterpretation) value;
+ if (interpr.isDirected()) {
+ text.append(Messages.NI_R_DIR);
+ if (interpr.isIgnoreUSL()) {
+ text.append(Messages.NI_R_DIRL);
+ }
+ } else {
+ text.append(Messages.NI_R_UNDIR);
+ if (interpr.isPaired()) {
+ text.append(Messages.NI_R_UNDIRC);
+ }
+ }
+ }
+ setText(text.toString());
+ }
+
+ /**
+ * Unique ID for this version of this class. It is used in serialization.
+ */
+ private static final long serialVersionUID = -4847632212033029150L;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/InterpretationDialog.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/InterpretationDialog.java
new file mode 100644
index 0000000..f879db6
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/InterpretationDialog.java
@@ -0,0 +1,312 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.ui;
+
+import java.awt.BorderLayout;
+import java.awt.FlowLayout;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.HeadlessException;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import javax.swing.BorderFactory;
+import javax.swing.Box;
+import javax.swing.ButtonGroup;
+import javax.swing.ImageIcon;
+import javax.swing.JButton;
+import javax.swing.JDialog;
+import javax.swing.JFrame;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JRadioButton;
+import javax.swing.SwingConstants;
+import javax.swing.WindowConstants;
+
+import cytoscape.Cytoscape;
+import cytoscape.util.OpenBrowser;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Messages;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.NetworkInterpretation;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.NetworkStatus;
+import de.mpg.mpi_inf.bioinf.netanalyzer.sconnect.HelpConnector;
+
+/**
+ * Generic class for interpretation dialogs.
+ * <p>
+ * These are modal dialogs that either ask the user for an interpretation of the network edges, or
+ * inform the user of a non-trivial interpretation that will be performed.
+ * </p>
+ *
+ * @author Yassen Assenov
+ */
+public final class InterpretationDialog extends JDialog implements ActionListener {
+
+ /**
+ * Initializes a new instance of <code>InterpretationDialog</code>.
+ * <p>
+ * The dialog created is modal and has a title "NetworkAnalyzer - Network
+ * Interpretation". The constructor creates and lays out all the controls of the dialog. It
+ * also positions the window according to its parent, so no subsequent calls to
+ * <code>pack()</code> or <code>setLocation(...)</code> are necessary.
+ * </p>
+ * <p>
+ * The owner frame of this dialog is set to be Cytoscape's window.
+ * </p>
+ *
+ * @param aStatus
+ * Status of the network to be analyzed.
+ * @exception HeadlessException
+ * if <code>GraphicsEnvironment.isHeadless()</code> returns <code>true</code>.
+ */
+ public InterpretationDialog(NetworkStatus aStatus) throws HeadlessException {
+ this(Cytoscape.getDesktop(), aStatus);
+ }
+
+ /**
+ * Initializes a new instance of <code>InterpretationDialog</code>.
+ * <p>
+ * The dialog created is modal and has a title "NetworkAnalyzer - Network
+ * Interpretation". The constructor creates and lays out all the controls of the dialog. It
+ * also positions the window according to its parent, so no subsequent calls to
+ * <code>pack()</code> or <code>setLocation(...)</code> are necessary.
+ * </p>
+ *
+ * @param aOwner
+ * The <code>JFrame</code> from which this dialog is displayed.
+ * @param aStatus
+ * Status of the network to be analyzed.
+ * @throws HeadlessException
+ * if <code>GraphicsEnvironment.isHeadless()</code> returns <code>true</code>.
+ */
+ public InterpretationDialog(JFrame aOwner, NetworkStatus aStatus)
+ throws HeadlessException {
+ super(aOwner, Messages.DT_INTERPRETATION, true);
+
+ pressedOK = false;
+ userChoice = aStatus.getDefaultInterprIndex();
+ initControls(aStatus);
+ pack();
+ setLocationRelativeTo(aOwner);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.event.ActionListener#actionPerformed(java.awt.event.ActionEvent)
+ */
+ public void actionPerformed(ActionEvent e) {
+ Object source = e.getSource();
+ if (source == btnOK) {
+ pressedOK = true;
+ this.setVisible(false);
+ this.dispose();
+ } else if (source == btnCancel) {
+ userChoice = -1;
+ this.setVisible(false);
+ this.dispose();
+ } else if (source == btnHelp) {
+ OpenBrowser.openURL(HelpConnector.getInterpretURL());
+ } else if (radOptions != null) {
+ for (int i = 0; i < radOptions.length; ++i) {
+ if (source == radOptions[i]) {
+ userChoice = i;
+ break;
+ }
+ }
+ }
+ }
+
+ /**
+ * Checks if the user has chosen that the network analysis should proceed.
+ * <p>
+ * If (and only if) this method returns <code>true</code>, the
+ * {@link de.mpg.mpi_inf.bioinf.netanalyzer.data.NetworkInterpretation} instance passed to the
+ * constructor may be updated.
+ * </p>
+ *
+ * @return <code>true</code> if the user has pressed the OK button of this dialog;
+ * <code>false</code> otherwise.
+ */
+ public boolean pressedOK() {
+ return pressedOK;
+ }
+
+ /**
+ * Gets the user choice as a number.
+ *
+ * @return Natural number representing the option the user has chosen; <code>-1</code> if the
+ * user has pressed the "Cancel" button.
+ */
+ public int getUserChoice() {
+ return userChoice;
+ }
+
+ /**
+ * Unique ID for this version of this class. It is used in serialization.
+ */
+ private static final long serialVersionUID = -6915331490559980802L;
+
+ /**
+ * Image of a horizontal arrow pointing to the right.
+ */
+ private static ImageIcon arrowRight = de.mpg.mpi_inf.bioinf.netanalyzer.data.Utils.getImage(
+ "arrow-right.png", "->");
+
+ /**
+ * Creates and lays out the controls inside this dialog.
+ * <p>
+ * This method is called upon initialization only.
+ * </p>
+ *
+ * @param aStatus
+ * Status of the network to be analyzed.
+ */
+ private void initControls(NetworkStatus aStatus) {
+ JPanel contentPane = new JPanel(new BorderLayout(0, Utils.BORDER_SIZE));
+ Utils.setStandardBorder(contentPane);
+
+ JPanel interprPanel = new JPanel(new BorderLayout(0, Utils.BORDER_SIZE));
+ // Add the title (information) label
+ JLabel descrLabel = new JLabel(aStatus.getDescription(), SwingConstants.CENTER);
+ JPanel panTitle = new JPanel();
+ panTitle.add(descrLabel);
+ interprPanel.add(panTitle, BorderLayout.NORTH);
+ // Add the state of the network resulting from the interpretation
+ interprPanel.add(initInterprPanel(aStatus), BorderLayout.CENTER);
+ contentPane.add(interprPanel, BorderLayout.CENTER);
+
+ // Add OK, Cancel and Help buttons
+ JPanel panButtons = new JPanel(new FlowLayout(FlowLayout.CENTER, Utils.BORDER_SIZE, 0));
+ btnOK = Utils.createButton(Messages.DI_OK, null, this);
+ btnCancel = Utils.createButton(Messages.DI_CANCEL, null, this);
+ btnHelp = Utils.createButton(Messages.DI_HELP, null, this);
+ Utils.equalizeSize(btnOK, btnCancel, btnHelp);
+ panButtons.add(btnOK);
+ panButtons.add(btnCancel);
+ panButtons.add(Box.createHorizontalStrut(Utils.BORDER_SIZE * 2));
+ panButtons.add(btnHelp);
+ contentPane.add(panButtons, BorderLayout.SOUTH);
+
+ setDefaultCloseOperation(WindowConstants.DISPOSE_ON_CLOSE);
+ getContentPane().add(contentPane);
+ getRootPane().setDefaultButton(btnOK);
+ btnOK.requestFocusInWindow();
+ }
+
+ /**
+ * Creates and lays out the controls that visualize the possible network interpretations.
+ * <p>
+ * In case multiple interpretations are possible, this method creates and lays out radio boxes,
+ * stored in {@link #radOptions}.
+ * </p>
+ *
+ * @param aStatus
+ * Network status.
+ * @return Newly created panel containing the images visualizing network interpretations and the
+ * controls for choosing one (if multiple are possible).
+ */
+ @SuppressWarnings("null")
+ private JPanel initInterprPanel(NetworkStatus aStatus) {
+ final NetworkInterpretation[] trs = aStatus.getInterpretations();
+ JPanel panBody = new JPanel(new GridBagLayout());
+ ButtonGroup group = null;
+ if (trs.length > 1) {
+ group = new ButtonGroup();
+ radOptions = new JRadioButton[trs.length];
+ panBody.setBorder(BorderFactory.createTitledBorder(Messages.DI_INTERPR));
+ }
+ GridBagConstraints constr = new GridBagConstraints();
+ constr.insets.left = Utils.BORDER_SIZE / 2;
+ constr.insets.right = Utils.BORDER_SIZE / 2;
+ constr.gridy = 0;
+ constr.gridheight = trs.length;
+
+ JLabel labImage = new JLabel(aStatus.getIcon());
+ labImage.setBorder(BorderFactory.createEtchedBorder());
+ panBody.add(labImage, constr);
+ constr.gridheight = 1;
+
+ for (int i = 0; i < trs.length; ++i, ++constr.gridy) {
+ constr.gridx = 1;
+ if (trs.length > 1) {
+ radOptions[i] = new JRadioButton();
+ radOptions[i].addActionListener(this);
+ if (aStatus.getDefaultInterprIndex() == i) {
+ radOptions[i].setSelected(true);
+ }
+ group.add(radOptions[i]);
+ panBody.add(radOptions[i], constr);
+ constr.gridx++;
+ }
+ if (trs[i].getIcon() != null) {
+ panBody.add(new JLabel(arrowRight), constr);
+ constr.gridx++;
+ labImage = new JLabel(trs[i].getIcon());
+ labImage.setBorder(BorderFactory.createEtchedBorder());
+ panBody.add(labImage, constr);
+ constr.gridx++;
+ }
+
+ constr.fill = GridBagConstraints.BOTH;
+ JLabel labText = new JLabel(trs[i].getMessage());
+ panBody.add(labText, constr);
+ constr.fill = GridBagConstraints.NONE;
+ }
+
+ return panBody;
+ }
+
+ /**
+ * "Cancel" button.
+ */
+ private JButton btnCancel;
+
+ /**
+ * "Help" button.
+ */
+ private JButton btnHelp;
+
+ /**
+ * "OK" button.
+ */
+ private JButton btnOK;
+
+ /**
+ * Flag indicating if the user has pressed the OK button.
+ */
+ private boolean pressedOK;
+
+ /**
+ * Array of the radio buttons giving the interpretation options.
+ * <p>
+ * The number of options depends on the
+ * {@link de.mpg.mpi_inf.bioinf.netanalyzer.data.NetworkStatus} instance passed to the
+ * constructor.
+ * </p>
+ */
+ private JRadioButton[] radOptions;
+
+ /**
+ * User's choice as a positive natural number.
+ * <p>
+ * This field is initialed to <code>0</code> and is updated only when the user presses the
+ * "OK" button.
+ * </p>
+ */
+ private int userChoice;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/LongHistogramVisualizer.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/LongHistogramVisualizer.java
new file mode 100644
index 0000000..55cf123
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/LongHistogramVisualizer.java
@@ -0,0 +1,233 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.ui;
+
+import java.awt.CardLayout;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.io.IOException;
+
+import javax.swing.Box;
+import javax.swing.JComboBox;
+import javax.swing.JComponent;
+import javax.swing.JPanel;
+import javax.swing.JTabbedPane;
+
+import org.jfree.chart.JFreeChart;
+import org.jfree.chart.plot.XYPlot;
+import org.jfree.chart.renderer.xy.XYBarRenderer;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.ComplexParam;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.LongHistogram;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Messages;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.io.SettingsSerializer;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.settings.LongHistogramGroup;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.settings.SettingsGroup;
+import de.mpg.mpi_inf.bioinf.netanalyzer.ui.charts.JFreeChartConn;
+
+/**
+ * Handles the visualization of the {@link de.mpg.mpi_inf.bioinf.netanalyzer.data.IntHistogram} complex
+ * parameter type instances.
+ *
+ * @author Yassen Assenov
+ * @author Sven-Eric Schelhorn
+ */
+public class LongHistogramVisualizer extends ComplexParamVisualizer {
+
+ /**
+ * Initializes a new instance of <code>LongHistogramVisualizer</code>.
+ *
+ * @param aParam Instance of the integer histogram complex parameter type.
+ * @param aSettings Visual settings for the complex parameter.
+ */
+ public LongHistogramVisualizer(LongHistogram aParam, LongHistogramGroup aSettings) {
+ param = aParam;
+ settings = (LongHistogramGroup) aSettings.clone();
+ general = settings.general;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see de.mpg.mpi_inf.bioinf.netanalyzer.ui.ComplexParamVisualizer#getComplexParam()
+ */
+ @Override
+ public ComplexParam getComplexParam() {
+ return param;
+ }
+
+ /**
+ * Gets the settings for the visualized <code>LongHistogram</code>.
+ *
+ * @return The <code>LongHistogramGroup</code> instance for the visualized complex parameter.
+ */
+ @Override
+ public SettingsGroup getSettings() {
+ return settings;
+ }
+
+ /**
+ * Sets the complex parameter instance managed by this visualizer.
+ * <p>
+ * <b>Note:</b> It is the responsibility of the caller to recreate all the controls created by this
+ * visualizer by calling the {@link #createControl()} method for each of them.
+ * </p>
+ *
+ * @param aParam Complex parameter instance to be managed by this visualizer.
+ * @throws ClassCastException If the specified complex parameter is not of type
+ * {@link de.mpg.mpi_inf.bioinf.netanalyzer.data.LongHistogram}.
+ * @throws NullPointerException If <code>aParam</code> is <code>null</code>.
+ */
+ @Override
+ public void setComplexParam(ComplexParam aParam) {
+ if (aParam == null) {
+ throw new NullPointerException();
+ }
+ param = (LongHistogram) aParam;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see de.mpg.mpi_inf.bioinf.netanalyzer.ui.ComplexParamVisualizer#createControl()
+ */
+ @Override
+ public JFreeChart createControl() {
+ return JFreeChartConn.createChart(param, settings);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see de.mpg.mpi_inf.bioinf.netanalyzer.ui.ComplexParamVisualizer#updateControl(org.jfree.chart.JFreeChart)
+ */
+ @Override
+ public JFreeChart updateControl(JFreeChart aControl) {
+ XYPlot plot = (XYPlot) aControl.getPlot();
+ if (plot.getRenderer() instanceof XYBarRenderer) {
+ // Current control is Histogram
+ if (settings.useScatter()) {
+ return JFreeChartConn.createScatter(param, settings);
+ }
+ JFreeChartConn.updateGeneral(aControl, general);
+ JFreeChartConn.updateAxes(aControl, settings.axes, settings.grid);
+ JFreeChartConn.updateBars(aControl, settings.bars);
+ return aControl;
+ }
+
+ // else: plot.getRenderer() instanceof StandardXYItemRenderer
+ // Current control is Scatter Plot
+ if (settings.useScatter()) {
+ JFreeChartConn.updateGeneral(aControl, general);
+ JFreeChartConn.updateAxes(aControl, settings.axes, settings.grid);
+ JFreeChartConn.updateScatter(aControl, settings.scatter);
+ return aControl;
+ }
+ return JFreeChartConn.createHistogram(param, settings);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see de.mpg.mpi_inf.bioinf.netanalyzer.ui.ComplexParamVisualizer#addSettingsPanels(javax.swing.JTabbedPane)
+ */
+ @Override
+ protected JComponent addSettingsPanels(JTabbedPane aPanel) {
+
+ addTab(aPanel, Messages.DI_GENERAL, new SettingsPanel(general), Messages.TT_GENSETTINGS);
+ addTab(aPanel, Messages.DI_AXES, new SettingsPanel(settings.axes), Messages.TT_AXESSETTINGS);
+ addTab(aPanel, Messages.DI_GRID, new SettingsPanel(settings.grid), Messages.TT_GRIDSETTINGS);
+
+ boolean useScatter = settings.useScatter();
+ final Box histPanel = Box.createVerticalBox();
+
+ final JComboBox choiceCombo = addChoice(histPanel, useScatter ? 1 : 0);
+
+ final CardLayout innerLayout = new CardLayout();
+ final JPanel innerPanel = new JPanel(innerLayout);
+ histPanel.add(innerPanel);
+ aPanel.addTab(Messages.DI_HISTOGRAM, null, histPanel, Messages.TT_HISTSETTINGS);
+
+ ItemListener listener = new ItemListener() {
+
+ public void itemStateChanged(ItemEvent e) {
+ if (e.getStateChange() == ItemEvent.SELECTED) {
+ innerLayout.next(innerPanel);
+ }
+ }
+ };
+ choiceCombo.addItemListener(listener);
+
+ innerPanel.add(new SettingsPanel(settings.bars), "0");
+ innerPanel.add(new SettingsPanel(settings.scatter), "1");
+ if (useScatter) {
+ innerLayout.next(innerPanel);
+ }
+
+ return choiceCombo;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see de.mpg.mpi_inf.bioinf.netanalyzer.ui.ComplexParamVisualizer#saveDefault()
+ */
+ @Override
+ protected void saveDefault() throws IOException {
+ SettingsSerializer.setDefault(settings);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see de.mpg.mpi_inf.bioinf.netanalyzer.ui.ComplexParamVisualizer#updateSettings(javax.swing.JComponent)
+ */
+ @Override
+ protected void updateSettings(JComponent aDataComp) {
+ settings.useScatter.setValue(((JComboBox) aDataComp).getSelectedIndex() == 1);
+ }
+
+ /**
+ * Creates the combo box (drop-down list) to choose between visualization of the histogram as bar chart or
+ * as a scatter plot.
+ *
+ * @param aContainer Container control, to which the combo box is to be added.
+ * @param aSelectedIndex Which choice is to be initially selected. This parameter must have one of the
+ * values <code>{1; 2}</code>.
+ * @return The newly created combo box control.
+ */
+ private static JComboBox addChoice(Box aContainer, int aSelectedIndex) {
+ final String[] choices = new String[] { Messages.DI_SHOWHIST, Messages.DI_SHOWSCAT };
+ JComboBox choiceCombo = new JComboBox(choices);
+ choiceCombo.setSelectedIndex(aSelectedIndex);
+ choiceCombo.setEditable(false);
+ JPanel choicePanel = new JPanel();
+ choicePanel.add(choiceCombo);
+ aContainer.add(choicePanel);
+ return choiceCombo;
+ }
+
+ /**
+ * Integer histogram instance to be visualized.
+ */
+ private LongHistogram param;
+
+ /**
+ * Visual settings for the long histogram instance.
+ */
+ private LongHistogramGroup settings;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/MapParameterDialog.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/MapParameterDialog.java
new file mode 100644
index 0000000..c3f4006
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/MapParameterDialog.java
@@ -0,0 +1,775 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.ui;
+
+import giny.model.Edge;
+import giny.model.Node;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.FlowLayout;
+import java.awt.Frame;
+import java.awt.GridLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.Map;
+
+import javax.swing.ButtonGroup;
+import javax.swing.JButton;
+import javax.swing.JComboBox;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JRadioButton;
+import javax.swing.SwingConstants;
+import javax.swing.border.TitledBorder;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import cytoscape.data.CyAttributes;
+import cytoscape.view.CyNetworkView;
+import cytoscape.visual.CalculatorCatalog;
+import cytoscape.visual.EdgeAppearance;
+import cytoscape.visual.EdgeAppearanceCalculator;
+import cytoscape.visual.GlobalAppearanceCalculator;
+import cytoscape.visual.NodeAppearance;
+import cytoscape.visual.NodeAppearanceCalculator;
+import cytoscape.visual.NodeShape;
+import cytoscape.visual.VisualMappingManager;
+import cytoscape.visual.VisualPropertyDependency;
+import cytoscape.visual.VisualPropertyType;
+import cytoscape.visual.VisualStyle;
+import cytoscape.visual.calculators.BasicCalculator;
+import cytoscape.visual.calculators.Calculator;
+import cytoscape.visual.mappings.BoundaryRangeValues;
+import cytoscape.visual.mappings.ContinuousMapping;
+import cytoscape.visual.mappings.Interpolator;
+import cytoscape.visual.mappings.LinearNumberToColorInterpolator;
+import cytoscape.visual.mappings.LinearNumberToNumberInterpolator;
+import cytoscape.visual.mappings.ObjectMapping;
+import cytoscape.visual.mappings.PassThroughMapping;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Messages;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.io.SettingsSerializer;
+
+/**
+ * Dialog for applying computed attributes to visual properties of a network.
+ *
+ * @author Nadezhda Doncheva
+ * @author Yassen Assenov
+ */
+public class MapParameterDialog extends VisualizeParameterDialog implements ActionListener {
+
+ /**
+ * Initializes a new instance of <code>MapParameterDialog</code>.
+ *
+ * @param aOwner
+ * The <code>Frame</code> from which this dialog is displayed.
+ * @param aNetwork
+ * Network to which a visual style is to be applied.
+ * @param aNodeAttr
+ * Two-dimensional array with computed parameters stored as node attributes. The first column
+ * contains all networkAnalyzer attributes, and the second one other attributes.
+ * @param aEdgeAttr
+ * Two-dimensional array with computed parameters stored as edge attributes. The first column
+ * contains all networkAnalyzer attributes, and the second one other attributes.
+ * @throws IllegalArgumentException
+ * If no attributes computed by NetworkAnalyzer are found in <code>aNetwork</code>.
+ * @throws NullPointerException
+ * If <code>aNetwork</code> is <code>null</code>.
+ */
+ public MapParameterDialog(Frame aOwner, CyNetwork aNetwork, String[][] aNodeAttr, String[][] aEdgeAttr) {
+ super(aOwner, Messages.DT_MAPPARAM, true, aNetwork, aNodeAttr, aEdgeAttr);
+ getMinMaxMeanValues();
+ init();
+ setResizable(false);
+ setLocationRelativeTo(Cytoscape.getDesktop());
+
+ attrNodeColor = "";
+ attrNodeSize = "";
+ attrEdgeColor = "";
+ attrEdgeSize = "";
+
+ mapNodeSize = Messages.DI_LOWTOSMALL;
+ mapNodeColor = Messages.DI_LOWTOBRIGHT;
+ mapEdgeSize = Messages.DI_LOWTOSMALL;
+ mapEdgeColor = Messages.DI_LOWTOBRIGHT;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.event.ActionListener#actionPerformed(java.awt.event.ActionEvent)
+ */
+ public void actionPerformed(ActionEvent e) {
+ final Object src = e.getSource();
+ if (src == btnApply) {
+ if (cbxNodeSize != null && cbxNodeSize.getSelectedItem() != null) {
+ attrNodeSize = (String) cbxNodeSize.getSelectedItem();
+ }
+ if (cbxNodeColor != null && cbxNodeColor.getSelectedItem() != null) {
+ attrNodeColor = (String) cbxNodeColor.getSelectedItem();
+ }
+ if (cbxEdgeSize != null && cbxEdgeSize.getSelectedItem() != null) {
+ attrEdgeSize = (String) cbxEdgeSize.getSelectedItem();
+ }
+ if (cbxEdgeColor != null && cbxEdgeColor.getSelectedItem() != null) {
+ attrEdgeColor = (String) cbxEdgeColor.getSelectedItem();
+ }
+ // get the network view on which to apply the visual style based on
+ // this.network
+ CyNetworkView networkView = null;
+ Map<String, CyNetworkView> networkViewMap = Cytoscape.getNetworkViewMap();
+ if (networkViewMap.containsKey(network.getIdentifier())) {
+ networkView = networkViewMap.get(network.getIdentifier());
+ } else {
+ networkView = Cytoscape.createNetworkView(network);
+ }
+ // get the current visual style and modify it according to the user
+ // specified criteria
+ VisualMappingManager manager = Cytoscape.getVisualMappingManager();
+ CalculatorCatalog catalog = manager.getCalculatorCatalog();
+ VisualStyle newStyle = createVisualStyle();
+ String name = newStyle.getName();
+ if (catalog.getVisualStyle(name) != null) {
+ catalog.removeVisualStyle(name);
+ }
+ catalog.addVisualStyle(newStyle);
+ manager.setVisualStyle(newStyle);
+ networkView.redrawGraph(true, true);
+
+ setVisible(false);
+ dispose();
+ } else if (src == btnClose) {
+ setVisible(false);
+ dispose();
+ } else if (src == cbxEdgeColor) {
+ btnApply.setEnabled(isMappingSelected());
+ } else if (src == cbxEdgeSize) {
+ btnApply.setEnabled(isMappingSelected());
+ } else if (src == cbxNodeColor) {
+ btnApply.setEnabled(isMappingSelected());
+ } else if (src == cbxNodeSize) {
+ btnApply.setEnabled(isMappingSelected());
+ } else if (src == btnNodeSize1) {
+ mapNodeSize = btnNodeSize1.getText();
+ } else if (src == btnNodeSize2) {
+ mapNodeSize = btnNodeSize2.getText();
+ } else if (src == btnNodeColor1) {
+ mapNodeColor = btnNodeColor1.getText();
+ } else if (src == btnNodeColor2) {
+ mapNodeColor = btnNodeColor2.getText();
+ } else if (src == btnEdgeSize1) {
+ mapEdgeSize = btnEdgeSize1.getText();
+ } else if (src == btnEdgeSize2) {
+ mapEdgeSize = btnEdgeSize2.getText();
+ } else if (src == btnEdgeColor1) {
+ mapEdgeColor = btnEdgeColor1.getText();
+ } else if (src == btnEdgeColor2) {
+ mapEdgeColor = btnEdgeColor2.getText();
+ }
+ }
+
+ /**
+ * Creates and lays out the controls inside this dialog.
+ * <p>
+ * This method is called upon initialization only.
+ * </p>
+ *
+ * @throws IllegalArgumentException
+ * If no attributes computed by NetworkAnalyzer are found in {@link #network}.
+ * @throws NullPointerException
+ * If {@link #network} is <code>null</code>.
+ */
+ private void init() {
+ final int BS = Utils.BORDER_SIZE;
+ final JPanel contentPane = new JPanel(new BorderLayout(BS, BS));
+ Utils.setStandardBorder(contentPane);
+
+ // Add a title label
+ String tt = "<html>" + Messages.DI_APPLYVS + "<b>" + network.getTitle() + "</b>";
+ contentPane.add(new JLabel(tt, SwingConstants.CENTER), BorderLayout.PAGE_START);
+
+ boolean attrCalculated = false;
+
+ // Get colors from plugin settings
+ final Color c1 = SettingsSerializer.getPluginSettings().getBrightColor();
+ final Color c2 = SettingsSerializer.getPluginSettings().getMiddleColor();
+ final Color c3 = SettingsSerializer.getPluginSettings().getDarkColor();
+
+ // Add controls for mapping attributes to node size and node color
+ final JPanel panMapping = new JPanel(new BorderLayout(BS, BS));
+ final JPanel panNode = new JPanel(new GridLayout(1, 2, BS, BS));
+ final JPanel panEdge = new JPanel(new GridLayout(1, 2, BS, BS));
+
+ if (nodeAttr[0].length > 0 || nodeAttr[1].length > 0) {
+ attrCalculated = true;
+ // Panel for node size mapping
+ final JPanel panNodeSize = new JPanel(new BorderLayout(BS, BS));
+ panNodeSize.setBorder(new TitledBorder(null, Messages.DI_MAPNODESIZE, TitledBorder.CENTER,
+ TitledBorder.CENTER));
+
+ final JPanel panNodeSizeAttr = new JPanel(new FlowLayout(FlowLayout.CENTER));
+ cbxNodeSize = new JComboBox(combineAttrArray(nodeAttr, true));
+ cbxNodeSize.setLightWeightPopupEnabled(false);
+ cbxNodeSize.addActionListener(this);
+ cbxNodeSize.setRenderer(new ComboBoxRenderer());
+ panNodeSizeAttr.add(cbxNodeSize);
+ panNodeSize.add(panNodeSizeAttr, BorderLayout.NORTH);
+
+ final JPanel panNodeSizeMap = new JPanel(new GridLayout(2, 2, BS, BS));
+ btnNodeSize1 = new JRadioButton(Messages.DI_LOWTOSMALL, true);
+ btnNodeSize1.addActionListener(this);
+ btnNodeSize2 = new JRadioButton(Messages.DI_LOWTOLARGE, false);
+ btnNodeSize2.addActionListener(this);
+ final ButtonGroup btngNodeSize = new ButtonGroup();
+ btngNodeSize.add(btnNodeSize1);
+ btngNodeSize.add(btnNodeSize2);
+ panNodeSizeMap.add(btnNodeSize1);
+ panNodeSizeMap.add(new NodeEdgeCanvas(true, true));
+ panNodeSizeMap.add(btnNodeSize2);
+ panNodeSizeMap.add(new NodeEdgeCanvas(false, true));
+ panNodeSize.add(panNodeSizeMap, BorderLayout.SOUTH);
+ panNode.add(panNodeSize);
+
+ // Panel for node color mapping
+ final JPanel panNodeColor = new JPanel(new BorderLayout(BS, BS));
+ panNodeColor.setBorder(new TitledBorder(null, Messages.DI_MAPNODECOLOR, TitledBorder.CENTER,
+ TitledBorder.CENTER));
+
+ final JPanel panNodeColorAttr = new JPanel(new FlowLayout(FlowLayout.CENTER));
+ cbxNodeColor = new JComboBox(combineAttrArray(nodeAttr, true));
+ cbxNodeColor.setLightWeightPopupEnabled(false);
+ cbxNodeColor.addActionListener(this);
+ cbxNodeColor.setRenderer(new ComboBoxRenderer());
+ panNodeColorAttr.add(cbxNodeColor);
+ panNodeColor.add(panNodeColorAttr, BorderLayout.NORTH);
+
+ final JPanel panNodeColorMap = new JPanel(new GridLayout(2, 2, BS, BS));
+ btnNodeColor1 = new JRadioButton(Messages.DI_LOWTOBRIGHT, true);
+ btnNodeColor1.addActionListener(this);
+ btnNodeColor2 = new JRadioButton(Messages.DI_LOWTODARK, false);
+ btnNodeColor2.addActionListener(this);
+ final ButtonGroup btngNodeColor = new ButtonGroup();
+ btngNodeColor.add(btnNodeColor1);
+ btngNodeColor.add(btnNodeColor2);
+ panNodeColorMap.add(btnNodeColor1);
+ panNodeColorMap.add(new RainbowCanvas(new Color[] { c1, c2, c3 }));
+ panNodeColorMap.add(btnNodeColor2);
+ panNodeColorMap.add(new RainbowCanvas(new Color[] { c3, c2, c1 }));
+ panNodeColor.add(panNodeColorMap, BorderLayout.SOUTH);
+
+ panNode.add(panNodeColor);
+ }
+ if (edgeAttr[0].length > 0 || edgeAttr[1].length > 0) {
+ attrCalculated = true;
+ // Panel for edge size mapping
+ final JPanel panEdgeSize = new JPanel(new BorderLayout(BS, BS));
+ panEdgeSize.setBorder(new TitledBorder(null, Messages.DI_MAPEDGESIZE, TitledBorder.CENTER,
+ TitledBorder.CENTER));
+
+ final JPanel panEdgeSizeAttr = new JPanel(new FlowLayout(FlowLayout.CENTER));
+ cbxEdgeSize = new JComboBox(combineAttrArray(edgeAttr, true));
+ cbxEdgeSize.setLightWeightPopupEnabled(false);
+ cbxEdgeSize.addActionListener(this);
+ cbxEdgeSize.setRenderer(new ComboBoxRenderer());
+ panEdgeSizeAttr.add(cbxEdgeSize);
+ panEdgeSize.add(panEdgeSizeAttr, BorderLayout.NORTH);
+
+ final JPanel panEdgeSizeMap = new JPanel(new GridLayout(2, 2, BS, BS));
+ btnEdgeSize1 = new JRadioButton(Messages.DI_LOWTOSMALL, true);
+ btnEdgeSize1.addActionListener(this);
+ btnEdgeSize2 = new JRadioButton(Messages.DI_LOWTOLARGE, false);
+ btnEdgeSize2.addActionListener(this);
+ final ButtonGroup btngEdgeSize = new ButtonGroup();
+ btngEdgeSize.add(btnEdgeSize1);
+ btngEdgeSize.add(btnEdgeSize2);
+ panEdgeSizeMap.add(btnEdgeSize1);
+ panEdgeSizeMap.add(new NodeEdgeCanvas(true, false));
+ panEdgeSizeMap.add(btnEdgeSize2);
+ panEdgeSizeMap.add(new NodeEdgeCanvas(false, false));
+ panEdgeSize.add(panEdgeSizeMap, BorderLayout.SOUTH);
+ panEdge.add(panEdgeSize);
+
+ // Panel for edge color mapping
+ final JPanel panEdgeColor = new JPanel(new BorderLayout(BS, BS));
+ panEdgeColor.setBorder(new TitledBorder(null, Messages.DI_MAPEDGECOLOR, TitledBorder.CENTER,
+ TitledBorder.CENTER));
+
+ final JPanel panEdgeColorAttr = new JPanel(new FlowLayout(FlowLayout.CENTER));
+ cbxEdgeColor = new JComboBox(combineAttrArray(edgeAttr, true));
+ cbxEdgeColor.setLightWeightPopupEnabled(false);
+ cbxEdgeColor.addActionListener(this);
+ cbxEdgeColor.setRenderer(new ComboBoxRenderer());
+ panEdgeColorAttr.add(cbxEdgeColor);
+ panEdgeColor.add(panEdgeColorAttr, BorderLayout.NORTH);
+
+ final JPanel panEdgeColorMap = new JPanel(new GridLayout(2, 2, BS, BS));
+ btnEdgeColor1 = new JRadioButton(Messages.DI_LOWTOBRIGHT, true);
+ btnEdgeColor1.addActionListener(this);
+ btnEdgeColor2 = new JRadioButton(Messages.DI_LOWTODARK, false);
+ btnEdgeColor2.addActionListener(this);
+ final ButtonGroup btngEdgeColor = new ButtonGroup();
+ btngEdgeColor.add(btnEdgeColor1);
+ btngEdgeColor.add(btnEdgeColor2);
+ panEdgeColorMap.add(btnEdgeColor1);
+ panEdgeColorMap.add(new RainbowCanvas(new Color[] { c1, c2, c3 }));
+ panEdgeColorMap.add(btnEdgeColor2);
+ panEdgeColorMap.add(new RainbowCanvas(new Color[] { c3, c2, c1 }));
+
+ panEdgeColor.add(panEdgeColorMap, BorderLayout.SOUTH);
+
+ panEdge.add(panEdgeColor);
+ }
+ if (attrCalculated == false) {
+ throw new IllegalArgumentException();
+ }
+ panMapping.add(panNode, BorderLayout.PAGE_START);
+ panMapping.add(panEdge, BorderLayout.PAGE_END);
+ contentPane.add(panMapping, BorderLayout.CENTER);
+
+ // Add Apply and Cancel buttons
+ final JPanel panBottom = new JPanel(new FlowLayout(FlowLayout.CENTER, 0, 0));
+ final JPanel panButtons = new JPanel(new GridLayout(1, 2, BS, 0));
+ btnApply = Utils.createButton(Messages.DI_APPLY, null, this);
+ btnApply.setEnabled(false);
+ panButtons.add(btnApply);
+ btnClose = Utils.createButton(Messages.DI_CLOSE, null, this);
+ panButtons.add(btnClose);
+ panBottom.add(panButtons);
+
+ contentPane.add(panBottom, BorderLayout.PAGE_END);
+
+ setContentPane(contentPane);
+ pack();
+ }
+
+ /**
+ * Checks if the user has selected to apply a mapping from an attribute to a visual style.
+ *
+ * @return <code>true</code> if the user has selected to map at least one attribute to a visual style;
+ * <code>false</code> otherwise.
+ */
+ private boolean isMappingSelected() {
+ if (cbxEdgeColor != null && cbxEdgeColor.getSelectedIndex() != 0) {
+ return true;
+ }
+ if (cbxEdgeSize != null && cbxEdgeSize.getSelectedIndex() != 0) {
+ return true;
+ }
+ if (cbxNodeColor != null && cbxNodeColor.getSelectedIndex() != 0) {
+ return true;
+ }
+ if (cbxNodeSize != null && cbxNodeSize.getSelectedIndex() != 0) {
+ return true;
+ }
+ return false;
+ }
+
+ /**
+ * Creates a new visual style in Cytoscape's VizMapper depending on the by the user defined mappings of
+ * computed attributes.
+ *
+ * @return New visual style.
+ */
+ private VisualStyle createVisualStyle() {
+
+ // Create new visual style
+ String name = network.getTitle();
+ VisualStyle visualStyle = new VisualStyle(name); // , nodeAppCalc, edgeAppCalc, globalAppCalc);
+
+ NodeAppearanceCalculator nodeAppCalc = visualStyle.getNodeAppearanceCalculator();
+ EdgeAppearanceCalculator edgeAppCalc = visualStyle.getEdgeAppearanceCalculator();
+ GlobalAppearanceCalculator globalAppCalc = new GlobalAppearanceCalculator();
+ globalAppCalc.setDefaultBackgroundColor(SettingsSerializer.getPluginSettings().getBackgroundColor());
+ // Color.getHSBColor(0.6666667f, 0.2f, 1.0f)
+
+ // Create default appearance
+ Calculator nlc = Cytoscape.getVisualMappingManager().getCalculatorCatalog().getCalculator(
+ VisualPropertyType.NODE_LABEL, "label");
+ if (nlc == null) {
+ PassThroughMapping m = new PassThroughMapping("", "ID");
+ nlc = new BasicCalculator("label", m, VisualPropertyType.NODE_LABEL);
+ }
+ nodeAppCalc.setCalculator(nlc);
+
+ NodeAppearance na = nodeAppCalc.getDefaultAppearance();
+ na.set(VisualPropertyType.NODE_SHAPE, NodeShape.ELLIPSE);
+ na.set(VisualPropertyType.NODE_FILL_COLOR, Color.getHSBColor(0.0f, 0.4f, 1.0f));
+ nodeAppCalc.setDefaultAppearance(na);
+
+ EdgeAppearance ea = edgeAppCalc.getDefaultAppearance();
+ ea.set(VisualPropertyType.EDGE_COLOR, Color.BLUE);
+ edgeAppCalc.setDefaultAppearance(ea);
+
+ // Apply new visual settings
+ if (attrNodeColor.length() > 0) {
+ // Continuous Mapping - set node color
+ name += "_NodeColor_" + attrNodeColor;
+ ContinuousMapping conMapNodeColor = getColorMapping(attrNodeColor, ObjectMapping.NODE_MAPPING);
+ conMapNodeColor = addBoundaries(conMapNodeColor, attrNodeColor, mapNodeColor, SettingsSerializer
+ .getPluginSettings().getBrightColor(), SettingsSerializer.getPluginSettings()
+ .getMiddleColor(), SettingsSerializer.getPluginSettings().getDarkColor());
+ Calculator nodeColorCalculator = new BasicCalculator("NetworkAnalyzer Node Color Calc",
+ conMapNodeColor, VisualPropertyType.NODE_FILL_COLOR);
+ nodeAppCalc.setCalculator(nodeColorCalculator);
+ }
+ if (attrNodeSize.length() > 0) {
+ // Continuous Mapping - set node size
+ name += "_NodeSize_" + attrNodeSize;
+ visualStyle.getDependency().set(VisualPropertyDependency.Definition.NODE_SIZE_LOCKED, false);
+ ContinuousMapping conMapNodeSize = getSizeMapping(attrNodeSize, ObjectMapping.NODE_MAPPING);
+ conMapNodeSize = addBoundaries(conMapNodeSize, attrNodeSize, mapNodeSize, new Double(10.0),
+ new Double(50.0), new Double(100.0));
+ Calculator nodeHeightCalculator = new BasicCalculator("NetworkAnalyzer Node Height Calc",
+ conMapNodeSize, VisualPropertyType.NODE_HEIGHT);
+ Calculator nodeWidthCalculator = new BasicCalculator("NetworkAnalyzer Node Width Calc",
+ conMapNodeSize, VisualPropertyType.NODE_WIDTH);
+ nodeAppCalc.setCalculator(nodeHeightCalculator);
+ nodeAppCalc.setCalculator(nodeWidthCalculator);
+ }
+ if (attrEdgeColor.length() > 0) {
+ // Continuous Mapping - set edge color
+ name += "_EdgeColor_" + attrEdgeColor;
+ ContinuousMapping conMapEdgeColor = getColorMapping(attrEdgeColor, ObjectMapping.EDGE_MAPPING);
+ conMapEdgeColor = addBoundaries(conMapEdgeColor, attrEdgeColor, mapEdgeColor, SettingsSerializer
+ .getPluginSettings().getBrightColor(), SettingsSerializer.getPluginSettings()
+ .getMiddleColor(), SettingsSerializer.getPluginSettings().getDarkColor());
+ Calculator edgeColorCalculator = new BasicCalculator("NetworkAnalyzer Edge Color Calc",
+ conMapEdgeColor, VisualPropertyType.EDGE_COLOR);
+ edgeAppCalc.setCalculator(edgeColorCalculator);
+ }
+ if (attrEdgeSize.length() > 0) {
+ // Continuous Mapping - set line width
+ name += "_EdgeSize_" + attrEdgeSize;
+ ContinuousMapping conMapEdgeSize = getSizeMapping(attrEdgeSize, ObjectMapping.EDGE_MAPPING);
+ conMapEdgeSize = addBoundaries(conMapEdgeSize, attrEdgeSize, mapEdgeSize, new Double(1.0),
+ new Double(4.0), new Double(8.0));
+ Calculator edgeSizeCalculator = new BasicCalculator("NetworkAnalyzer Edge Size Calc",
+ conMapEdgeSize, VisualPropertyType.EDGE_LINE_WIDTH);
+ edgeAppCalc.setCalculator(edgeSizeCalculator);
+ }
+
+ visualStyle.setName(name);
+ return visualStyle;
+ }
+
+ /**
+ * Computes the minimal, maximal and mean value for each computed attribute by consequently processing
+ * each node.
+ *
+ * @param attrMap
+ * Map containing for each node and attribute the computed value of this attribute.
+ * @param attr
+ * Array with attributes' names, for which the minimal, maximal and mean value have to be
+ * retrieved.
+ * @param id
+ * A node id, whose computed attribute values are retrieved.
+ */
+ private void getBoundaryValues(CyAttributes attrMap, String[][] attr, String id) {
+ for (int i = 0; i < attr.length; i++) {
+ for (int j = 0; j < attr[i].length; j++) {
+ final byte attrType = attrMap.getType(attr[i][j]);
+ Double attrValue = new Double(0.0);
+ if (attrType == CyAttributes.TYPE_INTEGER) {
+ attrValue = new Double(attrMap.getIntegerAttribute(id, attr[i][j]).doubleValue());
+ } else if (attrType == CyAttributes.TYPE_FLOATING) {
+ attrValue = attrMap.getDoubleAttribute(id, attr[i][j]);
+ }
+ if (attrValue != null && !attrValue.isNaN()) {
+ final Double oldMinValue = minAttrValue.get(attr[i][j]);
+ final double value = attrValue.doubleValue();
+ if (oldMinValue == null || oldMinValue.doubleValue() > value) {
+ minAttrValue.put(attr[i][j], attrValue);
+ }
+ final Double oldMaxValue = maxAttrValue.get(attr[i][j]);
+ if (oldMaxValue == null || oldMaxValue.doubleValue() < value) {
+ maxAttrValue.put(attr[i][j], attrValue);
+ }
+ final Double meanValue = meanAttrValue.get(attr[i][j]);
+ if (meanValue == null) {
+ meanAttrValue.put(attr[i][j], attrValue);
+ } else {
+ meanAttrValue.put(attr[i][j], new Double(value + meanValue.doubleValue()));
+ }
+ }
+ }
+ }
+ }
+
+ /**
+ * Computes the minimum, maximum and mean values for each available attribute and saves them in a min, max
+ * and mean hash maps, respectively.
+ */
+ private void getMinMaxMeanValues() {
+ minAttrValue = new HashMap<String, Double>(32);
+ maxAttrValue = new HashMap<String, Double>(32);
+ meanAttrValue = new HashMap<String, Double>(32);
+
+ // Find min, max and mean for each node attribute
+ // TODO: [Cytoscape 2.8] Check if the returned iterator is parameterized
+ Iterator<?> itn = network.nodesIterator();
+ while (itn.hasNext()) {
+ final String id = ((Node) itn.next()).getIdentifier();
+ getBoundaryValues(Cytoscape.getNodeAttributes(), nodeAttr, id);
+ }
+ calculateMean(network.getNodeCount(), nodeAttr);
+ // Find min, max and mean for each node attribute
+ Iterator<?> ite = network.edgesIterator();
+ while (ite.hasNext()) {
+ final String id = ((Edge) ite.next()).getIdentifier();
+ getBoundaryValues(Cytoscape.getEdgeAttributes(), edgeAttr, id);
+ }
+ calculateMean(network.getEdgeCount(), edgeAttr);
+ }
+
+ /**
+ * Calculates the mean by dividing the sum of all values by the number of values.
+ *
+ * @param values
+ * Number of values for a computed attribute.
+ * @param attr
+ * Array of attributes, whose means are calculated.
+ */
+ private void calculateMean(int values, String[][] attr) {
+ for (int i = 0; i < attr.length; i++) {
+ for (int j = 0; j < attr[i].length; j++) {
+ final double meanValue = meanAttrValue.get(attr[i][j]).doubleValue();
+ meanAttrValue.put(attr[i][j], new Double(meanValue / values));
+ }
+ }
+ }
+
+ /**
+ * Creates a continuous mapping of a node or edge attribute to the color of the nodes/edges.
+ *
+ * @param attr
+ * Attribute to be mapped to the color of nodes/edges.
+ * @param objectMapping
+ * Contains the information whether a node or edge attribute is mapped.
+ * @return A continuous mapping ot an attribute to the color of nodes/edges.
+ */
+ private ContinuousMapping getColorMapping(String attr, byte objectMapping) {
+ ContinuousMapping conMapColor = new ContinuousMapping(Color.WHITE, objectMapping);
+ conMapColor.setControllingAttributeName(attr, network, false);
+
+ Interpolator numToColor = new LinearNumberToColorInterpolator();
+ conMapColor.setInterpolator(numToColor);
+
+ return conMapColor;
+ }
+
+ /**
+ * Creates a continuous mapping of a node or edge attribute to the size of the nodes (width &
+ * height)/edges(tickness).
+ *
+ * @param attr
+ * Attribute to be mapped to the size of nodes/edges.
+ * @param objectMapping
+ * Contains the information whether a node or edge attribute is mapped.
+ * @return A continuous mapping ot an attribute to the size of nodes/edges.
+ */
+ private ContinuousMapping getSizeMapping(String attr, byte objectMapping) {
+ ContinuousMapping conMapSize = new ContinuousMapping(new Double(1.0), objectMapping);
+ conMapSize.setControllingAttributeName(attr, network, false);
+
+ Interpolator numToNum = new LinearNumberToNumberInterpolator();
+ conMapSize.setInterpolator(numToNum);
+
+ return conMapSize;
+ }
+
+ /**
+ * Adds boundaries to the continuous mapping by defining minimal, maximal and middle values for both color
+ * and size mapping.
+ *
+ * @param conMap
+ * Continuous mapping for which boundaries are set.
+ * @param attr
+ * Node/Edge attribute that is mapped.
+ * @param mapType
+ * Type of the mapping, i.e. low values to small sizes or otherwise or low values to bright
+ * colors and otherwise respectively.
+ * @param min
+ * Minimal value of size/color for the mapping.
+ * @param mid
+ * Middle value of size/color for the mapping.
+ * @param max
+ * Maximal value of size/color for the mapping.
+ * @return The value of the <code>conMap</code> parameter.
+ */
+ private ContinuousMapping addBoundaries(ContinuousMapping conMap, String attr, String mapType,
+ Object min, Object mid, Object max) {
+ Object min_ = min;
+ Object mid_ = mid;
+ Object max_ = max;
+ if (min instanceof Color && mapType.equals(Messages.DI_LOWTODARK)) {
+ min_ = max;
+ max_ = min;
+ }
+ if (min instanceof Double && mapType.equals(Messages.DI_LOWTOLARGE)) {
+ min_ = max;
+ max_ = min;
+ }
+
+ // Create boundary conditions less than, equals, greater than
+ BoundaryRangeValues bv0 = new BoundaryRangeValues(min_, min_, min_);
+ BoundaryRangeValues bv1 = new BoundaryRangeValues(mid_, mid_, mid_);
+ BoundaryRangeValues bv2 = new BoundaryRangeValues(max_, max_, max_);
+
+ // Set the attribute point values associated with the boundary values
+ conMap.addPoint(minAttrValue.get(attr).doubleValue(), bv0);
+ conMap.addPoint(meanAttrValue.get(attr).doubleValue(), bv1);
+ conMap.addPoint(maxAttrValue.get(attr).doubleValue(), bv2);
+
+ return conMap;
+ }
+
+ /**
+ * Unique ID for this version of this class. It is used in serialization.
+ */
+ private static final long serialVersionUID = 1514650388927387666L;
+
+ /**
+ * Drop-down list for selecting an edge attribute to be mapped to edge color.
+ */
+ private JComboBox cbxEdgeColor;
+
+ /**
+ * JRadioButton specifying a <code>Small values to bright colors</code> attribute mapping of the node
+ * color.
+ */
+ private JRadioButton btnEdgeColor1;
+
+ /**
+ * JRadioButton specifying a <code>Small values to bright colors</code> attribute mapping of the node
+ * color.
+ */
+ private JRadioButton btnEdgeColor2;
+
+ /**
+ * Drop-down list for selecting an edge attribute to be mapped to edge size.
+ */
+ private JComboBox cbxEdgeSize;
+
+ /**
+ * JRadioButton specifying a <code>Small values to small sizes</code> attribute mapping of the edge size.
+ */
+ private JRadioButton btnEdgeSize1;
+
+ /**
+ * JRadioButton specifying a <code>Small values to big sizes</code> attribute mapping of the edge size.
+ */
+ private JRadioButton btnEdgeSize2;
+
+ /**
+ * Drop-down list for selecting a node attribute to be mapped to node color.
+ */
+ private JComboBox cbxNodeColor;
+
+ /**
+ * JRadioButton specifying a <code>Small values to bright colors</code> attribute mapping of the node
+ * color.
+ */
+ private JRadioButton btnNodeColor1;
+
+ /**
+ * JRadioButton specifying a <code>Small values to dark colors</code> attribute mapping of the node color.
+ */
+ private JRadioButton btnNodeColor2;
+
+ /**
+ * Drop-down list for selecting a node attribute to be mapped to node size.
+ */
+ private JComboBox cbxNodeSize;
+
+ /**
+ * JRadioButton specifying a <code>Small values to small sizes</code> attribute mapping of the node size.
+ */
+ private JRadioButton btnNodeSize1;
+
+ /**
+ * JRadioButton specifying a <code>Small values to big sizes</code> attribute mapping of the node size.
+ */
+ private JRadioButton btnNodeSize2;
+
+ /**
+ * Button for applying the selected attributes to node and/or edge size and/or color.
+ */
+ private JButton btnApply;
+
+ /**
+ * Button for closing this dialog.
+ */
+ private JButton btnClose;
+
+ /**
+ * Attribute that is mapped to node size.
+ */
+ private String attrNodeSize;
+
+ /**
+ * Type of mapping the node attributes, i.e. low values to small sizes or otherwise.
+ */
+ private String mapNodeSize;
+
+ /**
+ * Attribute that is mapped to node color.
+ */
+ private String attrNodeColor;
+
+ /**
+ * Type of mapping the node attributes, i.e. low values to bright colors or otherwise.
+ */
+ private String mapNodeColor;
+
+ /**
+ * Attribute that is mapped to edge size.
+ */
+ private String attrEdgeSize;
+
+ /**
+ * Type of mapping the edge attributes, i.e. low values to small sizes or otherwise.
+ */
+ private String mapEdgeSize;
+
+ /**
+ * Attribute that is mapped to edge color.
+ */
+ private String attrEdgeColor;
+
+ /**
+ * Type of mapping the edge attributes, i.e. low values to bright colors or otherwise.
+ */
+ private String mapEdgeColor;
+
+ /**
+ * Map with the minimal computed value for each attribute.
+ */
+ private HashMap<String, Double> minAttrValue;
+
+ /**
+ * Map with the maximal computed value for each attribute.
+ */
+ private HashMap<String, Double> maxAttrValue;
+
+ /**
+ * Map with the mean computed value for each attribute.
+ */
+ private HashMap<String, Double> meanAttrValue;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/NetModificationDialog.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/NetModificationDialog.java
new file mode 100644
index 0000000..1f79091
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/NetModificationDialog.java
@@ -0,0 +1,242 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.ui;
+
+import java.awt.FlowLayout;
+import java.awt.Frame;
+import java.awt.HeadlessException;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import javax.swing.Box;
+import javax.swing.JButton;
+import javax.swing.JComponent;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.SwingConstants;
+import javax.swing.event.ListSelectionEvent;
+
+import cytoscape.CyNetwork;
+import cytoscape.util.OpenBrowser;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Messages;
+
+/**
+ * Dialog for selecting networks on which to apply analysis or a basic modification.
+ *
+ * @author Yassen Assenov
+ */
+public class NetModificationDialog extends NetworkListDialog implements ActionListener {
+
+ /**
+ * Initializes a new instance of <code>NetworkModificationDialog</code> with a modification warning.
+ *
+ * @param aOwner
+ * The <code>Frame</code> from which this dialog is displayed.
+ * @param aTitle
+ * Window's title.
+ * @param aLabel
+ * Label to be displayed on top of the network list.
+ * @param aHelpURL
+ * URL of the page to be displayed when the user clicks on the "Help" button.
+ *
+ * @throws HeadlessException
+ * If <code>GraphicsEnvironment.isHeadless()</code> returns <code>true</code>.
+ */
+ public NetModificationDialog(Frame aOwner, String aTitle, String aLabel, String aHelpURL)
+ throws HeadlessException {
+ this(aOwner, aTitle, aLabel, aHelpURL, true);
+ }
+
+ /**
+ * Initializes a new instance of <code>NetworkModificationDialog</code>.
+ *
+ * @param aOwner
+ * The <code>Frame</code> from which this dialog is displayed.
+ * @param aTitle
+ * Window's title.
+ * @param aLabel
+ * Label to be displayed on top of the network list.
+ * @param aHelpURL
+ * URL of the page to be displayed when the user clicks on the "Help" button.
+ * @param aWarning
+ * Flag indicating if a modification warning must be displayed. The text of the modification
+ * warning is {@link Messages#SM_NETMODIFICATION}.
+ *
+ * @throws HeadlessException
+ * If <code>GraphicsEnvironment.isHeadless()</code> returns <code>true</code>.
+ */
+ public NetModificationDialog(Frame aOwner, String aTitle, String aLabel, String aHelpURL, boolean aWarning)
+ throws HeadlessException {
+ super(aOwner, aTitle);
+
+ helpURL = aHelpURL;
+ selectedNetworks = null;
+ initControls(aLabel, aWarning);
+ pack();
+ setLocationRelativeTo(aOwner);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.event.ActionListener#actionPerformed(java.awt.event.ActionEvent)
+ */
+ public void actionPerformed(ActionEvent e) {
+ final Object source = e.getSource();
+ if (source == btnCancel) {
+ setVisible(false);
+ dispose();
+ } else if (source == btnHelp) {
+ OpenBrowser.openURL(helpURL);
+ } else if (source == btnOK) {
+ // Store the list of networks selected by the user
+ final int[] indices = listNetNames.getSelectedIndices();
+ final int size = indices.length;
+ selectedNetworks = new CyNetwork[size];
+ for (int i = 0; i < size; ++i) {
+ selectedNetworks[i] = networks.get(indices[i]);
+ }
+
+ setVisible(false);
+ dispose();
+ }
+ }
+
+ /**
+ * Gets an array of all networks selected by the user.
+ *
+ * @return A non-empty array of all networks selected by the user; <code>null</code> if the user has not
+ * closed this dialog by clicking on the "OK" button.
+ */
+ public CyNetwork[] getSelectedNetworks() {
+ return selectedNetworks;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see javax.swing.event.ListSelectionListener#valueChanged(javax.swing.event.ListSelectionEvent)
+ */
+ public void valueChanged(ListSelectionEvent e) {
+ // Update the enabled status of the "OK" button.
+ btnOK.setEnabled(isNetNameSelected());
+ }
+
+ /**
+ * Initializes and lays out additional controls to be added to this dialog.
+ * <p>
+ * Extender classes can override this method to create control(s).
+ * </p>
+ *
+ * @return Newly initialized control or container with controls; <code>null</code> if no additional
+ * controls are to be placed on the content pane of this dialog.
+ */
+ protected JComponent initAdditionalControls() {
+ return null;
+ }
+
+ /**
+ * Creates and lays out the controls inside this dialog.
+ * <p>
+ * This method is called upon initialization only.
+ * </p>
+ *
+ * @param aLabel
+ * Label to be displayed on top of the network list.
+ * @param aWarning
+ * Flag indicating if a modification warning must be displayed. The text of the modification
+ * warning is {@link Messages#SM_NETMODIFICATION}.
+ */
+ protected void initControls(String aLabel, boolean aWarning) {
+ Box contentPane = Box.createVerticalBox();
+ Utils.setStandardBorder(contentPane);
+
+ // Add the main message
+ final JPanel panTitle = new JPanel(new FlowLayout(FlowLayout.CENTER, 0, 0));
+ panTitle.add(new JLabel(aLabel));
+ contentPane.add(panTitle);
+ contentPane.add(Box.createVerticalStrut(Utils.BORDER_SIZE));
+
+ // Add a list of loaded networks to select from
+ final JScrollPane scroller = new JScrollPane(listNetNames);
+ final JPanel panNetList = new JPanel(new FlowLayout(FlowLayout.CENTER, 0, 0));
+ panNetList.add(scroller);
+ contentPane.add(panNetList);
+ contentPane.add(Box.createVerticalStrut(Utils.BORDER_SIZE));
+
+ final JComponent additional = initAdditionalControls();
+ if (additional != null) {
+ additional.setAlignmentX(0.5f);
+ contentPane.add(additional);
+ contentPane.add(Box.createVerticalStrut(Utils.BORDER_SIZE));
+ }
+
+ // Add OK and Cancel buttons
+ JPanel panButtons = new JPanel(new FlowLayout(FlowLayout.CENTER, Utils.BORDER_SIZE, 0));
+ btnOK = Utils.createButton(Messages.DI_OK, null, this);
+ btnOK.setEnabled(false);
+ btnCancel = Utils.createButton(Messages.DI_CANCEL, null, this);
+ btnHelp = Utils.createButton(Messages.DI_HELP, null, this);
+ Utils.equalizeSize(btnOK, btnCancel, btnHelp);
+ panButtons.add(btnOK);
+ panButtons.add(btnCancel);
+ panButtons.add(Box.createHorizontalStrut(Utils.BORDER_SIZE * 2));
+ panButtons.add(btnHelp);
+ contentPane.add(panButtons);
+
+ // Add a warning message
+ if (aWarning) {
+ final JPanel panWarning = new JPanel(new FlowLayout(FlowLayout.CENTER, 0, 0));
+ panWarning.add(new JLabel(Messages.SM_NETMODIFICATION, SwingConstants.LEADING));
+ contentPane.add(Box.createVerticalStrut(Utils.BORDER_SIZE));
+ contentPane.add(panWarning);
+ }
+ setContentPane(contentPane);
+ }
+
+ /**
+ * Unique ID for this version of this class. It is used in serialization.
+ */
+ private static final long serialVersionUID = 1576652348409963833L;
+
+ /**
+ * "Cancel" button.
+ */
+ private JButton btnCancel;
+
+ /**
+ * "Help" button.
+ */
+ private JButton btnHelp;
+
+ /**
+ * "OK" button.
+ */
+ private JButton btnOK;
+
+ /**
+ * URL of the page to be displayed when the user clicks on the "Help" button.
+ */
+ private String helpURL;
+
+ /**
+ * Array of networks selected by the user.
+ */
+ private CyNetwork[] selectedNetworks;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/NetworkListDialog.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/NetworkListDialog.java
new file mode 100644
index 0000000..badc029
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/NetworkListDialog.java
@@ -0,0 +1,112 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.ui;
+
+import java.awt.Dialog;
+import java.awt.Frame;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Set;
+
+import javax.swing.JDialog;
+import javax.swing.JList;
+import javax.swing.event.ListSelectionListener;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+
+/**
+ * Base class for dialogs which display a list of all loaded networks in Cytoscape.
+ * <p>
+ * This type of dialog is always created modal in order to prevent network modification (e.g.
+ * deletion of network from Cytoscape) while the dialog is visible.
+ * </p>
+ *
+ * @author Yassen Assenov
+ */
+abstract class NetworkListDialog extends JDialog implements ListSelectionListener {
+
+ /**
+ * Initializes the fields of <code>NetworkListDialog</code>.
+ *
+ * @param aOwner The <code>Frame</code> from which this dialog is displayed.
+ * @param aTitle Title of the dialog.
+ */
+ protected NetworkListDialog(Frame aOwner, String aTitle) {
+ super(aOwner, aTitle, true);
+ initNetworkList();
+ }
+
+ /**
+ * Initializes the fields of <code>NetworkListDialog</code>.
+ *
+ * @param aOwner The <code>Dialog</code> from which this dialog is displayed.
+ * @param aTitle Title of the dialog.
+ */
+ protected NetworkListDialog(Dialog aOwner, String aTitle) {
+ super(aOwner, aTitle, true);
+ initNetworkList();
+ }
+
+ /**
+ * Checks if a network name in the list of networks is selected.
+ *
+ * @return <code>true</code> if at least one of the listed network names is selected; <code>false</code> otherwise.
+ */
+ protected boolean isNetNameSelected() {
+ int[] indices = listNetNames.getSelectedIndices();
+ return indices.length > 0;
+ }
+
+ /**
+ * List of all available networks.
+ */
+ protected List<CyNetwork> networks;
+
+ /**
+ * List control that contains the names of the available networks.
+ *
+ * @see #networks
+ */
+ protected JList listNetNames;
+
+ /**
+ * Unique ID for this version of this class. It is used in serialization.
+ */
+ private static final long serialVersionUID = 5706001778102104118L;
+
+ /**
+ * Initializes the network list and list control containing network names.
+ */
+ private void initNetworkList() {
+ final Set<CyNetwork> networkSet = Cytoscape.getNetworkSet();
+ final int netCount = networkSet.size();
+ networks = new ArrayList<CyNetwork>(netCount);
+ String[] netTitles = new String[netCount];
+ int i = 0;
+ for (final CyNetwork network : networkSet) {
+ networks.add(network);
+ netTitles[i++] = network.getTitle();
+ }
+ listNetNames = new JList(netTitles);
+ listNetNames.addListSelectionListener(this);
+ if (netCount < 8) {
+ listNetNames.setVisibleRowCount(netCount);
+ }
+ }
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/NodeEdgeCanvas.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/NodeEdgeCanvas.java
new file mode 100644
index 0000000..f52edd6
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/NodeEdgeCanvas.java
@@ -0,0 +1,132 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.ui;
+
+import java.awt.Canvas;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.RenderingHints;
+
+/**
+ * Class displaying two circles with different sizes and an arrow between them.
+ *
+ * @author Nadezhda Doncheva
+ */
+public class NodeEdgeCanvas extends Canvas {
+
+ /**
+ * Initializes a new instance of <code>NodeEdgeCanvas</code>
+ *
+ * @param aSmallToBig
+ * Flag indicating that the small circle is drawn before the big
+ * one it <code>true</code> and after it otherwise.
+ * @param aNodeCanvas
+ * Flag indicating that the node mapping is drawn if
+ * <code>true</code> or the edge size mapping otherwise.
+ */
+ public NodeEdgeCanvas(boolean aSmallToBig, boolean aNodeCanvas) {
+ smallToBig = aSmallToBig;
+ nodeCanvas = aNodeCanvas;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.Canvas#paint(java.awt.Graphics)
+ */
+ @Override
+ public void paint(Graphics g) {
+ ((Graphics2D)g).setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
+ final Dimension size = getSize();
+ // Size of the circles depends on the height of the panel.
+ final int h = size.height;
+ final int bigR = h - 1;
+ final int smallR = h / 2;
+ final int y = h / 2;
+ final int bigLeftAlign = h;
+ final int smallLeftAlign = bigLeftAlign + smallR/2;
+ final int bigRightAlign = size.width - 2 * h;
+ final int smallRightAlign = bigRightAlign + smallR/2;
+ final int edgeWidth1 = 2;
+ final int edgeWidth2 = 2*edgeWidth1;
+ if (nodeCanvas) {
+ if (smallToBig) {
+ // Draw a small and a big pink circle
+ drawNode(g, y, smallLeftAlign, bigRightAlign, smallR, bigR);
+ } else {
+ // Draw a big and a small pink circle
+ drawNode(g, y, smallRightAlign, bigLeftAlign, smallR, bigR);
+ }
+ } else {
+ if (smallToBig) {
+ // Draw a small and a big pink circle
+ drawEdge(g, smallLeftAlign, smallRightAlign, smallR, h, edgeWidth1, edgeWidth2);
+ } else {
+ // Draw a big and a small pink circle
+ drawEdge(g, smallLeftAlign, smallRightAlign, smallR, h, edgeWidth2, edgeWidth1);
+ }
+ }
+ // Draw line between the two circles (nodes)
+ drawArrow(g, y, smallR, size.width, bigLeftAlign);
+ }
+
+ private void drawNode(Graphics g, int y, int smallAlign, int bigAlign, int smallR, int bigR){
+ g.setColor(Color.PINK);
+ g.fillOval(smallAlign, y/2, smallR, smallR);
+ g.fillOval(bigAlign, 0, bigR, bigR);
+ g.setColor(Color.BLACK);
+ g.drawOval(smallAlign, y/2, smallR, smallR);
+ g.drawOval(bigAlign, 0, bigR, bigR);
+ }
+
+ private void drawEdge(Graphics g, int leftAlign, int rightAlign, int smallR, int h, int edgeWidth1, int edgeWidth2){
+ g.setColor(Color.BLACK);
+// g.drawLine(leftAlign, h, leftAlign+smallR, 0);
+ for (int i = 0; i< edgeWidth1; i++) {
+ g.drawLine(leftAlign + i, h, leftAlign+smallR + i, 0);
+ }
+ for (int i = 0; i< edgeWidth2; i++) {
+ g.drawLine(rightAlign + i, h, rightAlign+smallR + i, 0);
+ }
+ }
+
+ private void drawArrow(Graphics g, int y, int smallR, int width, int bigLeftAlign) {
+ g.setColor(Color.BLACK);
+ final int x1 = 3 * bigLeftAlign;
+ final int x2 = width - x1;
+ g.drawLine(x1, y, x2, y);
+ g.drawLine(x2 - smallR, y - smallR, x2, y);
+ g.drawLine(x2 - smallR, y + smallR, x2, y);
+ }
+
+ /**
+ * Unique ID for this version of this class. It is used in serialization.
+ */
+ private static final long serialVersionUID = -9126275712496557815L;
+
+ /**
+ * Flag indicating which circle should be drawn first. If <code>true</code>
+ * first the small and then the big one is drawn, and if <code>false</code>
+ * otherwise.
+ */
+ private boolean smallToBig;
+
+ private boolean nodeCanvas;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/PlotParameterDialog.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/PlotParameterDialog.java
new file mode 100644
index 0000000..9bc6ebd
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/PlotParameterDialog.java
@@ -0,0 +1,280 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.ui;
+
+import giny.model.Node;
+
+import java.awt.BorderLayout;
+import java.awt.FlowLayout;
+import java.awt.Frame;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.Insets;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.geom.Point2D;
+import java.lang.reflect.Constructor;
+import java.lang.reflect.Field;
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Random;
+
+import javax.swing.JButton;
+import javax.swing.JComboBox;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import cytoscape.data.CyAttributes;
+import de.mpg.mpi_inf.bioinf.netanalyzer.InnerException;
+import de.mpg.mpi_inf.bioinf.netanalyzer.Plugin;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.ComplexParam;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Decorators;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Messages;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Points2D;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.io.SettingsSerializer;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.settings.Points2DGroup;
+import de.mpg.mpi_inf.bioinf.netanalyzer.dec.Decorator;
+
+/**
+ * Dialog for plotting two computed attributes, i.e. plotting the correlation between two
+ * user-defined attributes.
+ *
+ * @author Nadezhda Doncheva
+ */
+public class PlotParameterDialog extends VisualizeParameterDialog implements ActionListener {
+
+ /**
+ * Initializes a new instance of <code>PlotParameterDialog</code>.
+ *
+ * @param aOwner
+ * The <code>Frame</code> from which this dialog is displayed.
+ * @param aNetwork
+ * Network whose attributes are to be plotted.
+ * @param aNodeAttr
+ * Two-dimensional array with computed parameters stored as node attributes. The
+ * first column contains all networkAnalyzer attributes, and the second one other
+ * attributes.
+ */
+ public PlotParameterDialog(Frame aOwner, CyNetwork aNetwork, String[][] aNodeAttr) {
+ super(aOwner, Messages.DT_PLOTPARAM, true, aNetwork, aNodeAttr, null);
+ cyAttr = Cytoscape.getNodeAttributes();
+ init();
+ setResizable(true);
+ setLocationRelativeTo(Cytoscape.getDesktop());
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.event.ActionListener#actionPerformed(java.awt.event.ActionEvent)
+ */
+ public void actionPerformed(ActionEvent e) {
+ Object src = e.getSource();
+ if (src == cbxAttr1 || src == cbxAttr2) {
+ update();
+ } else if (src == btnClose) {
+ setVisible(false);
+ dispose();
+ }
+ }
+
+ /**
+ * Returns the value of an attribute named "attr" for the node with a node identifier "id" as a
+ * Double.
+ *
+ * @param id
+ * Node identifier of the node whose attribute has to be returned.
+ * @param attr
+ * Name of the attribute whose value has to be returned.
+ * @param attrType
+ * Type of the attribute. Can only be float or integer.
+ * @return A Double value representation of the attribute value for the node with node
+ * identifier id.
+ */
+ private Double getAttrValue(String id, String attr, byte attrType) {
+ if (attrType == CyAttributes.TYPE_FLOATING) {
+ return cyAttr.getDoubleAttribute(id, attr);
+ }
+ if (attrType == CyAttributes.TYPE_INTEGER) {
+ return new Double(cyAttr.getIntegerAttribute(id, attr).doubleValue());
+ }
+ return null;
+ }
+
+ /**
+ * Creates and lays out the controls inside this dialog.
+ * <p>
+ * This method is called upon initialization only.
+ * </p>
+ */
+ private void init() {
+ final JPanel contentPane = new JPanel(
+ new BorderLayout(Utils.BORDER_SIZE, Utils.BORDER_SIZE));
+ Utils.setStandardBorder(contentPane);
+
+ // Add title
+ final JPanel panTop = new JPanel(new BorderLayout(0, 0));
+ final JPanel panTitle = new JPanel(new FlowLayout(FlowLayout.CENTER));
+ final JLabel title = new JLabel("<html>" + Messages.DI_PLOT1 + "<b>" + network.getTitle()
+ + "</b>" + Messages.DI_PLOT2);
+ panTitle.add(title);
+ panTop.add(panTitle, BorderLayout.PAGE_START);
+
+ // Add drop-down menus with node attributes to plot against each other
+ final JPanel panAttr = new JPanel();
+ GridBagLayout gbl = new GridBagLayout();
+ GridBagConstraints constraints = new GridBagConstraints();
+ constraints.fill = GridBagConstraints.BOTH;
+ constraints.gridx = 0;
+ constraints.gridy = 0;
+ constraints.insets = new Insets(Utils.BORDER_SIZE, Utils.BORDER_SIZE, Utils.BORDER_SIZE,
+ Utils.BORDER_SIZE);
+ panAttr.setLayout(gbl);
+ final String[] combined = combineAttrArray(nodeAttr, false);
+ JLabel label1 = new JLabel(Messages.DI_ATTRIBUTE1);
+ gbl.setConstraints(label1, constraints);
+ panAttr.add(label1);
+ constraints.gridx++;
+ cbxAttr1 = new JComboBox(combined);
+ cbxAttr1.addActionListener(this);
+ cbxAttr1.setRenderer(new ComboBoxRenderer());
+ gbl.setConstraints(cbxAttr1, constraints);
+ constraints.gridx++;
+ panAttr.add(cbxAttr1);
+ JLabel label2 = new JLabel(Messages.DI_ATTRIBUTE2);
+ gbl.setConstraints(label2, constraints);
+ panAttr.add(label2);
+ constraints.gridx++;
+ cbxAttr2 = new JComboBox(combined);
+ cbxAttr2.addActionListener(this);
+ cbxAttr2.setRenderer(new ComboBoxRenderer());
+ gbl.setConstraints(cbxAttr2, constraints);
+ panAttr.add(cbxAttr2);
+ panTop.add(panAttr, BorderLayout.PAGE_END);
+ contentPane.add(panTop, BorderLayout.PAGE_START);
+
+ panPlot = new JPanel(new FlowLayout(FlowLayout.CENTER, 0, 0));
+ contentPane.add(panPlot, BorderLayout.CENTER);
+
+ // Add Close button
+ final JPanel panBottom = new JPanel(new FlowLayout(FlowLayout.CENTER, 0, 0));
+ btnClose = new JButton(Messages.DI_CLOSE);
+ btnClose.addActionListener(this);
+ panBottom.add(btnClose);
+ contentPane.add(panBottom, BorderLayout.PAGE_END);
+
+ setContentPane(contentPane);
+
+ final Random r = new Random();
+ cbxAttr1.setSelectedIndex(r.nextInt(combined.length));
+ cbxAttr2.setSelectedIndex(r.nextInt(combined.length));
+ update();
+ }
+
+ /**
+ * Plots the attributes attr1 and attr2 against each other if they aren't null. This method is
+ * called every time a new node attribute is chosen. If only one of the attributes is chosen,
+ * then an empty chart is shown.
+ */
+ private void update() {
+ final String attrX = cbxAttr1.getSelectedItem().toString();
+ final String attrY = cbxAttr2.getSelectedItem().toString();
+ final byte attrType1 = cyAttr.getType(attrX);
+ final byte attrType2 = cyAttr.getType(attrY);
+ final List<Point2D.Double> plotValues = new ArrayList<Point2D.Double>(network
+ .getNodeCount());
+ Iterator<?> it = network.nodesIterator();
+ while (it.hasNext()) {
+ String id = ((Node) it.next()).getIdentifier();
+ Double value1 = getAttrValue(id, attrX, attrType1);
+ Double value2 = getAttrValue(id, attrY, attrType2);
+ if (value1 != null && value2 != null) {
+ plotValues.add(new Point2D.Double(value1.doubleValue(), value2.doubleValue()));
+ }
+ }
+ initChartPanel(plotValues, attrX, attrY);
+ pack();
+ ((JPanel) getContentPane()).updateUI();
+ setLocationRelativeTo(Cytoscape.getDesktop());
+ }
+
+ private void initChartPanel(List<Point2D.Double> plotValues, String attrX, String attrY) {
+ ComplexParam cp = new Points2D(plotValues);
+ String typeName = cp.getClass().getSimpleName();
+ try {
+ final Class<?> visClass = Plugin.getVisualizerClass(typeName);
+ final Constructor<?> con = visClass.getConstructors()[0];
+
+ final Points2DGroup settings = (Points2DGroup) SettingsSerializer.getDefault(paramID);
+ final Class<?> settingsClass = Plugin.getSettingsGroupClass(typeName);
+ final Field axesField = settingsClass.getField("axes");
+ final Object aSettings = axesField.get(settings);
+ final Class<?> axesFieldType = axesField.getType();
+ axesFieldType.getMethod("setDomainAxisLabel", new Class[] { String.class }).invoke(
+ aSettings, attrX);
+ axesFieldType.getMethod("setRangeAxisLabel", new Class[] { String.class }).invoke(
+ aSettings, attrY);
+ final Object[] conParams = new Object[] { cp, settings };
+ final ComplexParamVisualizer v = (ComplexParamVisualizer) con.newInstance(conParams);
+ final Decorator[] decs = Decorators.get(paramID);
+ final ChartDisplayPanel cPanel = new ChartDisplayPanel(this, paramID, v, decs);
+ panPlot.removeAll();
+ panPlot.add(cPanel, BorderLayout.CENTER);
+ } catch (Exception ex) {
+ throw new InnerException(ex);
+ }
+ }
+
+ /**
+ * Unique ID for this version of this class. It is used in serialization.
+ */
+ private static final long serialVersionUID = 9024129225256810465L;
+
+ /**
+ * Name of the ComplexParameter used as wrapper for the plot of two arbitrary parameters.
+ */
+ private static final String paramID = "userDefined";
+
+ /**
+ * Panel containing the Parameter Plot.
+ */
+ private JPanel panPlot;
+
+ /**
+ * Button for closing this dialog.
+ */
+ private JButton btnClose;
+
+ /**
+ * Drop-down list for selecting a node attribute to be plotted on the x-axis.
+ */
+ private JComboBox cbxAttr1;
+
+ /**
+ * Drop-down list for selecting a node attribute to be plotted on the y-axis.
+ */
+ private JComboBox cbxAttr2;
+
+ /**
+ * Cytoscape's node attributes.
+ */
+ private CyAttributes cyAttr;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/PluginSettingsDialog.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/PluginSettingsDialog.java
new file mode 100644
index 0000000..0164290
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/PluginSettingsDialog.java
@@ -0,0 +1,163 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.ui;
+
+import java.awt.BorderLayout;
+import java.awt.Dialog;
+import java.awt.FlowLayout;
+import java.awt.Frame;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.io.IOException;
+import java.lang.reflect.InvocationTargetException;
+
+import javax.swing.Box;
+import javax.swing.JButton;
+import javax.swing.JDialog;
+import javax.swing.JPanel;
+import javax.swing.WindowConstants;
+
+import cytoscape.logger.CyLogger;
+import cytoscape.util.OpenBrowser;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Messages;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.io.SettingsSerializer;
+import de.mpg.mpi_inf.bioinf.netanalyzer.sconnect.HelpConnector;
+
+/**
+ * Dialog for viewing and editing plugin's settings.
+ *
+ * @author Yassen Assenov
+ */
+public class PluginSettingsDialog extends JDialog implements ActionListener {
+
+ /**
+ * Initializes a new instance of <code>PluginSettingsDialog</code>.
+ * <p>
+ * The dialog created is modal and has a title "NetworkAnalyzer Settings". The
+ * constructor creates and lays out all the controls of the dialog. It also positions the window
+ * according to its parent, so no subsequent calls to <code>pack()</code> or
+ * <code>setLocation(...)</code> are necessary.
+ * </p>
+ *
+ * @param aOwner The <code>Dialog</code> from which this dialog is displayed.
+ *
+ */
+ public PluginSettingsDialog(Dialog aOwner) {
+ super(aOwner, Messages.DT_SETTINGS, true);
+ initControls();
+ pack();
+ setLocationRelativeTo(aOwner);
+ }
+
+ /**
+ * Initializes a new instance of <code>PluginSettingsDialog</code>.
+ *
+ * @param aOwner The <code>Dialog</code> from which this dialog is displayed.
+ *
+ */
+ public PluginSettingsDialog(Frame aOwner) {
+ super(aOwner, Messages.DT_SETTINGS, true);
+ initControls();
+ pack();
+ setLocationRelativeTo(aOwner);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.event.ActionListener#actionPerformed(java.awt.event.ActionEvent)
+ */
+ public void actionPerformed(ActionEvent e) {
+ Object source = e.getSource();
+ if (source == btnOK) {
+ try {
+ panSettings.updateData();
+ SettingsSerializer.save();
+ } catch (InvocationTargetException ex) {
+ // NetworkAnalyzer internal error
+ CyLogger.getLogger().error(Messages.SM_LOGERROR, ex);
+ } catch (IOException ex) {
+ Utils.showErrorBox(Messages.DT_IOERROR, Messages.SM_DEFFAILED);
+ } finally {
+ this.setVisible(false);
+ this.dispose();
+ }
+ } else if (source == btnCancel) {
+ this.setVisible(false);
+ this.dispose();
+ } else if (source == btnHelp) {
+ OpenBrowser.openURL(HelpConnector.getSettingsURL());
+ }
+ }
+
+ /**
+ * Unique ID for this version of this class. It is used in serialization.
+ */
+ private static final long serialVersionUID = 7118008694414543131L;
+
+ /**
+ * Creates and lays out the controls inside this dialog.
+ * <p>
+ * This method is called upon initialization only.
+ * </p>
+ */
+ private void initControls() {
+ JPanel contentPane = new JPanel(new BorderLayout(0, Utils.BORDER_SIZE));
+ Utils.setStandardBorder(contentPane);
+
+ panSettings = new SettingsPanel(SettingsSerializer.getPluginSettings());
+ contentPane.add(panSettings, BorderLayout.CENTER);
+
+ // Add OK, Cancel and Help buttons
+ JPanel panButtons = new JPanel(new FlowLayout(FlowLayout.CENTER, Utils.BORDER_SIZE, 0));
+ btnOK = Utils.createButton(Messages.DI_OK, null, this);
+ btnCancel = Utils.createButton(Messages.DI_CANCEL, null, this);
+ btnHelp = Utils.createButton(Messages.DI_HELP, null, this);
+ Utils.equalizeSize(btnOK, btnCancel, btnHelp);
+ panButtons.add(btnOK);
+ panButtons.add(btnCancel);
+ panButtons.add(Box.createHorizontalStrut(Utils.BORDER_SIZE * 2));
+ panButtons.add(btnHelp);
+ contentPane.add(panButtons, BorderLayout.SOUTH);
+
+ setDefaultCloseOperation(WindowConstants.DISPOSE_ON_CLOSE);
+ getContentPane().add(contentPane);
+ getRootPane().setDefaultButton(btnOK);
+ btnOK.requestFocusInWindow();
+ }
+
+ /**
+ * "Cancel" button.
+ */
+ private JButton btnCancel;
+
+ /**
+ * "Help" button.
+ */
+ private JButton btnHelp;
+
+ /**
+ * "OK" button.
+ */
+ private JButton btnOK;
+
+ /**
+ * Panel that contains the controls for adjusting the plugin's settings.
+ */
+ private SettingsPanel panSettings;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/Points2DVisualizer.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/Points2DVisualizer.java
new file mode 100644
index 0000000..df824f0
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/Points2DVisualizer.java
@@ -0,0 +1,153 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.ui;
+
+import java.io.IOException;
+
+import javax.swing.JComponent;
+import javax.swing.JTabbedPane;
+
+import org.jfree.chart.JFreeChart;
+
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.ComplexParam;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Messages;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Points2D;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.io.SettingsSerializer;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.settings.Points2DGroup;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.settings.SettingsGroup;
+import de.mpg.mpi_inf.bioinf.netanalyzer.ui.charts.JFreeChartConn;
+
+/**
+ * Handles the visualization of the {@link de.mpg.mpi_inf.bioinf.netanalyzer.data.Points2D} complex parameter
+ * type instances.
+ *
+ * @author Yassen Assenov
+ * @author Sven-Eric Schelhorn
+ */
+public class Points2DVisualizer extends ComplexParamVisualizer {
+
+ /**
+ * Initializes a new instance of <code>Points2DVisualizer</code>.
+ *
+ * @param aParam Instance of the point set complex parameter type.
+ * @param aSettings Visual settings for the complex parameter.
+ */
+ public Points2DVisualizer(Points2D aParam, Points2DGroup aSettings) {
+ param = aParam;
+ settings = (Points2DGroup) aSettings.clone();
+ general = settings.general;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see de.mpg.mpi_inf.bioinf.netanalyzer.ui.ComplexParamVisualizer#getComplexParam()
+ */
+ @Override
+ public ComplexParam getComplexParam() {
+ return param;
+ }
+
+ /**
+ * Gets the settings for the visualized <code>Points2D</code>.
+ *
+ * @return The <code>Points2DGroup</code> instance for the visualized complex parameter.
+ */
+ @Override
+ public SettingsGroup getSettings() {
+ return settings;
+ }
+
+ /**
+ * Sets the complex parameter instance managed by this visualizer.
+ * <p>
+ * <b>Note:</b> It is the responsibility of the caller to recreate all the controls created by this
+ * visualizer by calling the {@link #createControl()} method for each of them.
+ * </p>
+ *
+ * @param aParam Complex parameter instance to be managed by this visualizer.
+ * @throws ClassCastException If the specified complex parameter is not of type
+ * {@link de.mpg.mpi_inf.bioinf.netanalyzer.data.Points2D}.
+ * @throws NullPointerException If <code>aParam</code> is <code>null</code>.
+ */
+ @Override
+ public void setComplexParam(ComplexParam aParam) {
+ if (aParam == null) {
+ throw new NullPointerException();
+ }
+ param = (Points2D) aParam;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see de.mpg.mpi_inf.bioinf.netanalyzer.ui.ComplexParamVisualizer#createControl()
+ */
+ @Override
+ public JFreeChart createControl() {
+ JFreeChart chart = JFreeChartConn.createScatter(param, settings);
+ return chart;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see de.mpg.mpi_inf.bioinf.netanalyzer.ui.ComplexParamVisualizer#updateControl(org.jfree.chart.JFreeChart)
+ */
+ @Override
+ public JFreeChart updateControl(JFreeChart aControl) {
+ JFreeChartConn.updateGeneral(aControl, general);
+ JFreeChartConn.updateAxes(aControl, settings.axes, settings.grid);
+ JFreeChartConn.updateScatter(aControl, settings.scatter);
+ return aControl;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see de.mpg.mpi_inf.bioinf.netanalyzer.ui.ComplexParamVisualizer#addSettingsPanels(javax.swing.JTabbedPane)
+ */
+ @Override
+ protected JComponent addSettingsPanels(JTabbedPane aPanel) {
+ addTab(aPanel, Messages.DI_GENERAL, new SettingsPanel(general), Messages.TT_GENSETTINGS);
+ addTab(aPanel, Messages.DI_AXES, new SettingsPanel(settings.axes), Messages.TT_AXESSETTINGS);
+ addTab(aPanel, Messages.DI_GRID, new SettingsPanel(settings.grid), Messages.TT_GRIDSETTINGS);
+ addTab(aPanel, Messages.DI_SCATTER, new SettingsPanel(settings.scatter), Messages.TT_SCATSETTINGS);
+ return null;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see de.mpg.mpi_inf.bioinf.netanalyzer.ui.ComplexParamVisualizer#saveDefault()
+ */
+ @Override
+ protected void saveDefault() throws IOException {
+ SettingsSerializer.setDefault(settings);
+ }
+
+ /**
+ * Point set instance to be visualized.
+ */
+ private Points2D param;
+
+ /**
+ * Visual settings for the point set instance.
+ */
+ private Points2DGroup settings;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/RainbowCanvas.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/RainbowCanvas.java
new file mode 100644
index 0000000..77380bf
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/RainbowCanvas.java
@@ -0,0 +1,115 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.ui;
+
+import java.awt.Canvas;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Graphics;
+
+/**
+ * Rainbow control displaying the gradual pairwise transitions between three colors.
+ *
+ * @author Yassen Assenov
+ * @author Nadezhda Doncheva
+ */
+public class RainbowCanvas extends Canvas {
+
+ /**
+ * Initializes a new instance of <code>RainbowCanvas</code> with a breakpoint of <code>0.5</code>.
+ *
+ * @param aColors
+ * Three-dimensional array of colors to be used.
+ *
+ * @see #RainbowCanvas(Color[], double)
+ */
+ public RainbowCanvas(Color[] aColors) {
+ this(aColors, 0.5);
+ }
+
+ /**
+ * Initializes a new instance of <code>RainbowCanvas</code>.
+ *
+ * @param aColors
+ * Three-dimensional array of colors to be used.
+ * @param aBreakpoint
+ * A relative location of the second color in the rainbow. This must be a number between 0 and
+ * 1.
+ *
+ * @throws IllegalArgumentException
+ * If at least one of the following does <b>not</b> hold:
+ * <ul>
+ * <li><code>aBreakpoint</code> is a value in the range <code>[0, 1]</code>.</li>
+ * <li><code>aColors</code> contains exactly three non-<code>null</code> elements.</li>
+ * </ul>
+ * @throws NullPointerException
+ * If <code>aColors</code> is <code>null</code>.
+ */
+ public RainbowCanvas(Color[] aColors, double aBreakpoint) {
+ if (aColors.length != 3 || aBreakpoint < 0 || aBreakpoint > 1) {
+ throw new IllegalArgumentException();
+ }
+ if (aColors[0] == null || aColors[1] == null || aColors[2] == null) {
+ throw new IllegalArgumentException();
+ }
+ colors = aColors;
+ breakpoint = aBreakpoint;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.Canvas#paint(java.awt.Graphics)
+ */
+ @Override
+ public void paint(Graphics g) {
+ final Dimension size = getSize();
+
+ final int breakX = (int) Math.round(breakpoint * size.width);
+ final int rightX = size.width - breakX;
+ int rc, gc, bc;
+ for (int x = 0; x < size.width; ++x) {
+ if (x < breakX) {
+ rc = ((breakX - x) * colors[0].getRed() + x * colors[1].getRed()) / breakX;
+ gc = ((breakX - x) * colors[0].getGreen() + x * colors[1].getGreen()) / breakX;
+ bc = ((breakX - x) * colors[0].getBlue() + x * colors[1].getBlue()) / breakX;
+ } else {
+ rc = ((size.width - x) * colors[1].getRed() + (x - breakX) * colors[2].getRed()) / rightX;
+ gc = ((size.width - x) * colors[1].getGreen() + (x - breakX) * colors[2].getGreen()) / rightX;
+ bc = ((size.width - x) * colors[1].getBlue() + (x - breakX) * colors[2].getBlue()) / rightX;
+ }
+ g.setColor(new Color(rc, gc, bc));
+ g.drawLine(x, 0, x, size.height - 1);
+ }
+ }
+
+ /**
+ * Unique ID for this version of this class. It is used in serialization.
+ */
+ private static final long serialVersionUID = 1514313656921206969L;
+
+ /**
+ * Colors to be used in the rainbow.
+ */
+ private Color[] colors;
+
+ /**
+ * Relative position of the second color in the rainbow.
+ */
+ private double breakpoint;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/SaveChartDialog.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/SaveChartDialog.java
new file mode 100644
index 0000000..cf8926a
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/SaveChartDialog.java
@@ -0,0 +1,254 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.ui;
+
+import java.awt.BorderLayout;
+import java.awt.Container;
+import java.awt.Dialog;
+import java.awt.GridLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.io.File;
+import java.io.IOException;
+
+import javax.swing.BorderFactory;
+import javax.swing.Box;
+import javax.swing.JButton;
+import javax.swing.JDialog;
+import javax.swing.JFileChooser;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JSpinner;
+import javax.swing.SpinnerModel;
+import javax.swing.SpinnerNumberModel;
+import javax.swing.SwingConstants;
+import javax.swing.WindowConstants;
+import javax.swing.filechooser.FileFilter;
+
+import org.jfree.chart.ChartPanel;
+import org.jfree.chart.JFreeChart;
+
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Messages;
+import de.mpg.mpi_inf.bioinf.netanalyzer.ui.charts.JFreeChartConn;
+
+/**
+ * Dialog for saving a chart to a file.
+ * <p>
+ * This dialog prompts the user to specify chart dimensions and then a filename.
+ * </p>
+ *
+ * @author Yassen Assenov
+ */
+public class SaveChartDialog extends JDialog
+ implements ActionListener {
+
+ /**
+ * Initializes a new instance of <code>SaveChartDialog</code>. The constructor creates and
+ * lays out all the controls of the dialog. It also positions the window according to its
+ * parent, so no subsequent calls to <code>pack</code> or <code>setLocation(...)</code> are
+ * necessary.
+ *
+ * @param aOwner The <code>Dialog</code> from which this dialog is displayed.
+ * @param aChart Chart instance to be saved to a file.
+ */
+ public SaveChartDialog(Dialog aOwner, JFreeChart aChart) {
+ super(aOwner, Messages.DT_SAVECHART, false);
+
+ chart = aChart;
+
+ initControls();
+ pack();
+ setModal(true);
+ setResizable(false);
+ setLocationRelativeTo(aOwner);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.event.ActionListener#actionPerformed(java.awt.event.ActionEvent)
+ */
+ public void actionPerformed(ActionEvent e) {
+ Object source = e.getSource();
+ if (source == btnCancel) {
+ // Cancel button pressed -> close the window
+ this.setVisible(false);
+ this.dispose();
+ } else if (source == btnSave) {
+ // Save button pressed -> choose file name and save the chart
+ int saveIt = saveFileDialog.showSaveDialog(this);
+ if (saveIt == JFileChooser.APPROVE_OPTION) {
+
+ // Choose file name
+ File file = saveFileDialog.getSelectedFile();
+ int width = getChosenWidth();
+ int height = getChosenHeight();
+ ExtensionFileFilter filter = null;
+ try {
+ filter = (ExtensionFileFilter) saveFileDialog.getFileFilter();
+ if (!filter.hasExtension(file)) {
+ file = filter.appendExtension(file);
+ }
+ } catch (ClassCastException ex) {
+ // Try to infer the type of file by its extension
+ FileFilter[] filters = saveFileDialog.getChoosableFileFilters();
+ for (int i = 0; i < filters.length; ++i) {
+ if (filters[i] instanceof ExtensionFileFilter) {
+ filter = (ExtensionFileFilter) filters[i];
+ if (filter.hasExtension(file)) {
+ break;
+ }
+ filter = null;
+ }
+ }
+
+ if (filter == null) {
+ // Could not infer the type
+ Utils.showErrorBox(this, Messages.DT_IOERROR, Messages.SM_AMBIGUOUSFTYPE);
+ return;
+ }
+ }
+
+ // Save the chart to the specified file name
+ try {
+ if (Utils.canSave(file, this)) {
+ String ext = filter.getExtension();
+ if (ext.equals("jpeg")) {
+ JFreeChartConn.saveAsJpeg(file, chart, width, height);
+ } else if (ext.equals("png")) {
+ JFreeChartConn.saveAsPng(file, chart, width, height);
+ } else { // ext.equals("svg")
+ JFreeChartConn.saveAsSvg(file, chart, width, height);
+ }
+ }
+ } catch (IOException ex) {
+ Utils.showErrorBox(this, Messages.DT_IOERROR, Messages.SM_OERROR);
+ return;
+ }
+ this.setVisible(false);
+ this.dispose();
+ } else if (saveIt == JFileChooser.ERROR_OPTION) {
+ Utils.showErrorBox(this, Messages.DT_GUIERROR, Messages.SM_GUIERROR);
+ }
+ }
+ }
+
+ /**
+ * Unique ID for this version of this class. It is used in serialization.
+ */
+ private static final long serialVersionUID = -6256113953155955101L;
+
+ /**
+ * &qout;Save file&qout; dialog, reused by the instances of this class.
+ */
+ private static final JFileChooser saveFileDialog = new JFileChooser();
+
+ static {
+ saveFileDialog.addChoosableFileFilter(SupportedExtensions.jpegFilesFilter);
+ saveFileDialog.addChoosableFileFilter(SupportedExtensions.pngFilesFilter);
+ saveFileDialog.addChoosableFileFilter(SupportedExtensions.svgFilesFilter);
+ }
+
+ /**
+ * Gets the user choice for height of the image.
+ *
+ * @return Desired height, in pixels, of the image.
+ */
+ private int getChosenHeight() {
+ return Utils.getSpinnerInt(heightSpinner);
+ }
+
+ /**
+ * Gets the user choice for width of the image.
+ *
+ * @return Desired width, in pixels, of the image.
+ */
+ private int getChosenWidth() {
+ return Utils.getSpinnerInt(widthSpinner);
+ }
+
+ /**
+ * Creates and lays out the controls inside this dialog's content pane.
+ * <p>
+ * This method is called upon initialization only.
+ * </p>
+ */
+ private void initControls() {
+ JPanel sizePanel = new JPanel(new GridLayout(2, 3, 4, 4));
+ sizePanel.setBorder(BorderFactory.createTitledBorder(Messages.DI_IMAGESIZE));
+
+ // Add a spinner for choosing width
+ sizePanel.add(new JLabel(Messages.DI_WIDTH, SwingConstants.RIGHT));
+ int width = ChartPanel.DEFAULT_WIDTH;
+ int minWidth = ChartPanel.DEFAULT_MINIMUM_DRAW_WIDTH;
+ int maxWidth = ChartPanel.DEFAULT_MAXIMUM_DRAW_WIDTH;
+ SpinnerModel widthSettings = new SpinnerNumberModel(width, minWidth, maxWidth, 1);
+ sizePanel.add(widthSpinner = new JSpinner(widthSettings));
+ sizePanel.add(new JLabel(Messages.DI_PIXELS));
+
+ // Add a spinner for choosing height
+ sizePanel.add(new JLabel(Messages.DI_HEIGHT, SwingConstants.RIGHT));
+ int height = ChartPanel.DEFAULT_HEIGHT;
+ int minHeight = ChartPanel.DEFAULT_MINIMUM_DRAW_HEIGHT;
+ int maxHeight = ChartPanel.DEFAULT_MAXIMUM_DRAW_HEIGHT;
+ SpinnerModel heightSettings = new SpinnerNumberModel(height, minHeight, maxHeight, 1);
+ sizePanel.add(heightSpinner = new JSpinner(heightSettings));
+ sizePanel.add(new JLabel(Messages.DI_PIXELS));
+
+ // Add Save and Cancel buttons
+ JPanel buttons = new JPanel(new GridLayout(1, 2, 4, 0));
+ buttons.add(btnSave = Utils.createButton(Messages.DI_SAVE, null, this));
+ buttons.add(btnCancel = Utils.createButton(Messages.DI_CANCEL, null, this));
+ Box buttonsBox = Box.createHorizontalBox();
+ buttonsBox.add(Box.createHorizontalGlue());
+ buttonsBox.add(buttons);
+ buttonsBox.add(Box.createHorizontalGlue());
+
+ Container contentPane = getContentPane();
+ contentPane.add(sizePanel, BorderLayout.NORTH);
+ contentPane.add(Box.createVerticalStrut(Utils.BORDER_SIZE / 2));
+ contentPane.add(buttonsBox, BorderLayout.PAGE_END);
+ setDefaultCloseOperation(WindowConstants.DISPOSE_ON_CLOSE);
+ Utils.setStandardBorder(getRootPane());
+ }
+
+ /**
+ * Chart to be saved to a file.
+ */
+ private JFreeChart chart;
+
+ /**
+ * "Save" button.
+ */
+ private JButton btnSave;
+
+ /**
+ * "Cancel" button.
+ */
+ private JButton btnCancel;
+
+ /**
+ * Spinner control for choosing height of the image.
+ */
+ private JSpinner heightSpinner;
+
+ /**
+ * Spinner control for choosing width of the image.
+ */
+ private JSpinner widthSpinner;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/SettingsDialog.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/SettingsDialog.java
new file mode 100644
index 0000000..2344396
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/SettingsDialog.java
@@ -0,0 +1,205 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.ui;
+
+import java.awt.BorderLayout;
+import java.awt.Component;
+import java.awt.Container;
+import java.awt.Dialog;
+import java.awt.HeadlessException;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.lang.reflect.InvocationTargetException;
+import java.util.Stack;
+
+import javax.swing.Box;
+import javax.swing.JButton;
+import javax.swing.JDialog;
+import javax.swing.JPanel;
+import javax.swing.JTabbedPane;
+
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Messages;
+
+/**
+ * Dialog used to view and edit the visual settings assigned to a specific complex parameter.
+ *
+ * @author Yassen Assenov
+ */
+public class SettingsDialog extends JDialog implements ActionListener {
+
+ /**
+ * Constant identifying the user has pressed the "Cancel" button.
+ */
+ public static final int STATUS_CANCEL = 0;
+
+ /**
+ * Constant identifying the user has pressed the "Save as Default" button.
+ */
+ public static final int STATUS_DEFAULT = 1;
+
+ /**
+ * Constant identifying the user has pressed the "OK" button.
+ */
+ public static final int STATUS_OK = 2;
+
+ /**
+ * Initializes a new instance of <code>SettingsDialog</code>.
+ * <p>
+ * The created instance is a modal dialog.
+ * </p>
+ *
+ * @param aOwner The <code>Dialog</code> from which this dialog is displayed.
+ * @param aTitle Title of the dialog.
+ * @throws HeadlessException If GraphicsEnvironment.isHeadless()
+ */
+ public SettingsDialog(Dialog aOwner, String aTitle) throws HeadlessException {
+ this(aOwner, aTitle, true);
+ }
+
+ /**
+ * Initializes a new instance of <code>SettingsDialog</code>.
+ *
+ * @param aOwner The <code>Dialog</code> from which this dialog is displayed.
+ * @param aTitle Title of the dialog.
+ * @param aModal Flag indicating if the dialog must be modal or not.
+ * @throws HeadlessException If GraphicsEnvironment.isHeadless()
+ */
+ public SettingsDialog(Dialog aOwner, String aTitle, boolean aModal) throws HeadlessException {
+ super(aOwner, aTitle, aModal);
+
+ status = STATUS_CANCEL;
+ initControls();
+ setResizable(false);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.event.ActionListener#actionPerformed(java.awt.event.ActionEvent)
+ */
+ public void actionPerformed(ActionEvent e) {
+ Object source = e.getSource();
+ if (source == btnSaveDefault) {
+ status = STATUS_DEFAULT;
+ } else if (source == btnOK) {
+ status = STATUS_OK;
+ }
+ setVisible(false);
+ }
+
+ /**
+ * Gets the central panel, to which tabs are added for viewing and editing settings.
+ *
+ * @return Setting's panel container of this dialog.
+ */
+ public JTabbedPane getSettingsPane() {
+ return settingsPane;
+ }
+
+ /**
+ * Gets the status of this windows's closure.
+ * <p>
+ * The following constants are used to describe the way this window was closed:
+ * </p>
+ * <ul>
+ * <li>{@link #STATUS_CANCEL}</li>
+ * <li>{@link #STATUS_DEFAULT}</li>
+ * <li>{@link #STATUS_OK}</li>
+ * </ul>
+ *
+ * @return Status of this window's closure as one of the constants described above.
+ */
+ public int getStatus() {
+ return status;
+ }
+
+ /**
+ * Updates the underlying data of all the settings panels displayed in this dialog.
+ *
+ * @throws InvocationTargetException If an internal error occurs.
+ */
+ public void update() throws InvocationTargetException {
+ Stack<Container> containers = new Stack<Container>();
+ containers.push(settingsPane);
+ do {
+ Component[] comp = containers.pop().getComponents();
+ for (int i = 0; i < comp.length; ++i) {
+ if (comp[i] instanceof SettingsPanel) {
+ ((SettingsPanel) comp[i]).updateData();
+ } else if (comp[i] instanceof Container) {
+ containers.add((Container) comp[i]);
+ }
+ }
+ } while (!containers.isEmpty());
+ }
+
+ /**
+ * Unique ID for this version of this class. It is used in serialization.
+ */
+ private static final long serialVersionUID = -5462354078680551493L;
+
+ /**
+ * Creates and lays out the controls inside this dialog.
+ * <p>
+ * This method is called upon initialization only.
+ * </p>
+ */
+ private void initControls() {
+ Container contentPane = getContentPane();
+
+ settingsPane = new JTabbedPane();
+ contentPane.add(settingsPane);
+
+ // Add Save as Default, OK and Cancel buttons
+ JPanel buttonsPanel = new JPanel();
+ btnSaveDefault = Utils.createButton(Messages.DI_SAVEDEFAULT, null, this);
+ btnOK = Utils.createButton(Messages.DI_OK, null, this);
+ btnCancel = Utils.createButton(Messages.DI_CANCEL, null, this);
+ buttonsPanel.add(btnSaveDefault);
+ buttonsPanel.add(Box.createHorizontalStrut(10));
+ buttonsPanel.add(btnOK);
+ buttonsPanel.add(btnCancel);
+ Utils.equalizeSize(btnSaveDefault, btnOK, btnCancel);
+ contentPane.add(buttonsPanel, BorderLayout.SOUTH);
+ }
+
+ /**
+ * Status of this window's closure.
+ */
+ private int status;
+
+ /**
+ * Setting's panels container of this dialog.
+ */
+ private JTabbedPane settingsPane;
+
+ /**
+ * "Save as Default" button.
+ */
+ private JButton btnSaveDefault;
+
+ /**
+ * "OK" button.
+ */
+ private JButton btnOK;
+
+ /**
+ * "Cancel" button.
+ */
+ private JButton btnCancel;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/SettingsPanel.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/SettingsPanel.java
new file mode 100644
index 0000000..361c4da
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/SettingsPanel.java
@@ -0,0 +1,369 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.ui;
+
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.Insets;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.lang.reflect.InvocationTargetException;
+import java.lang.reflect.Method;
+
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JColorChooser;
+import javax.swing.JComboBox;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JTextField;
+import javax.swing.SwingConstants;
+
+import de.mpg.mpi_inf.bioinf.netanalyzer.InnerException;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Messages;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.settings.PointShape;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.settings.Settings;
+
+/**
+ * Panel to view and edit a visual settings group.
+ * <p>
+ * This panel presents all the editable properties of a given settings instance.
+ * </p>
+ *
+ * @author Yassen Assenov
+ */
+public class SettingsPanel extends JPanel implements ActionListener {
+
+ /**
+ * Initializes a new instance of <code>SettingsPanel</code>.
+ *
+ * @param aSettings Settings instance, whose editable properties are to be presented in the panel.
+ * @param aIsDoubleBuffered Flag indicating if double buffering for this panel must be enabled.
+ */
+ public SettingsPanel(Settings aSettings, boolean aIsDoubleBuffered) {
+ super(new GridBagLayout(), aIsDoubleBuffered);
+
+ initLayout();
+ data = aSettings;
+
+ populate();
+ }
+
+ /**
+ * Initializes a new instance of <code>SettingsPanel</code>.
+ * <p>
+ * The panel initialized has double buffering enabled.
+ * </p>
+ *
+ * @param aSettings Settings instance, whose editable properties are to be presented in the panel.
+ */
+ public SettingsPanel(Settings aSettings) {
+ this(aSettings, true);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.event.ActionListener#actionPerformed(java.awt.event.ActionEvent)
+ */
+ public void actionPerformed(ActionEvent e) {
+ if ("color".equals(e.getActionCommand())) {
+ JButton invoker = (JButton) e.getSource();
+ Color newColor = JColorChooser.showDialog(this, Messages.DI_SELECTCOLOR, invoker.getForeground());
+ if (newColor != null) {
+ invoker.setForeground(newColor);
+ }
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.Component#setEnabled(boolean)
+ */
+ @Override
+ public void setEnabled(boolean enabled) {
+ Component[] comps = getComponents();
+ for (int i = 0; i < comps.length; ++i) {
+ comps[i].setEnabled(enabled);
+ }
+ super.setEnabled(enabled);
+ }
+
+ /**
+ * Gets the value of the given editable property.
+ *
+ * @param aPropName Name of the property to get the value of.
+ * @return Value of the property as instance of <code>Boolean</code>, <code>Color</code>,
+ * <code>PointShape</code> or <code>String</code>; <code>null</code> if the property could
+ * not be found.
+ */
+ public Object getValueOf(String aPropName) {
+ Component[] comps = getComponents();
+ for (int i = 0; i < comps.length; ++i) {
+ Component c = comps[i];
+ if (aPropName.equals(c.getName())) {
+ if (c instanceof JButton) {
+ if ("color".equals(((JButton) c).getActionCommand())) {
+ return c.getForeground();
+ }
+ } else if (c instanceof JCheckBox) {
+ return new Boolean(((JCheckBox) c).isSelected());
+ } else if (c instanceof JTextField) {
+ return ((JTextField) c).getText();
+ } else if (c instanceof JComboBox) {
+ return PointShape.parse(((JComboBox) c).getSelectedItem().toString());
+ }
+ }
+ }
+ return null;
+ }
+
+ /**
+ * Updates the values of the properties in the settings instance passed to this panel.
+ * <p>
+ * This method uses reflection to update the values of the properties of the settings instance.
+ * </p>
+ *
+ * @throws InvocationTargetException If an internal error occurs.
+ */
+ public void updateData() throws InvocationTargetException {
+ Method[] getters = Settings.propertyGetters(data);
+ for (int i = 0; i < getters.length; ++i) {
+ Method setter = Settings.findSetter(getters[i]);
+ if (setter == null) {
+ continue;
+ }
+ String propName = Settings.propertyName(getters[i]);
+ Object[] value = new Object[] { getValueOf(propName) };
+ try {
+ setter.invoke(data, value);
+ } catch (InvocationTargetException ex) {
+ throw ex;
+ } catch (Exception ex) {
+ // IllegalAccessException
+ // IllegalArgumentException
+ throw new InvocationTargetException(ex);
+ }
+ }
+ }
+
+ /**
+ * Initializes the properties of the <code>GridBagLayout</code> used by this panel.
+ * <p>
+ * This method is called upon initialization only.
+ * </p>
+ */
+ private void initLayout() {
+ layout = (GridBagLayout) getLayout();
+ firstColumn = new GridBagConstraints();
+ firstColumn.anchor = GridBagConstraints.LINE_END;
+ firstColumn.weightx = firstColumn.weighty = 0.2;
+ firstColumn.fill = GridBagConstraints.NONE;
+ firstColumn.insets = new Insets(VER_INSETS, HOR_INSETS, VER_INSETS, HOR_INSETS);
+ lastColumn = new GridBagConstraints();
+ lastColumn.anchor = GridBagConstraints.LINE_START;
+ lastColumn.weightx = lastColumn.weighty = 1.0;
+ lastColumn.fill = GridBagConstraints.HORIZONTAL;
+ lastColumn.insets = new Insets(VER_INSETS, HOR_INSETS, VER_INSETS, HOR_INSETS);
+ lastColumn.gridwidth = GridBagConstraints.REMAINDER;
+ }
+
+ /**
+ * Populates the panel with all the controls for the editable properties.
+ * <p>
+ * This method is only called upon initialization.
+ * </p>
+ */
+ private void populate() {
+ final Method[] getters = Settings.propertyGetters(data);
+ for (int i = 0; i < getters.length; ++i) {
+ Method m = getters[i];
+ if (Settings.findSetter(m) == null) {
+ // Ignore read-only properties
+ continue;
+ }
+ try {
+ Object value = m.invoke(data, (Object[]) null);
+ String propName = Settings.propertyName(m);
+ Class<?> propType = m.getReturnType();
+ addControls(propName, propType, value);
+ } catch (InnerException ex) {
+ throw ex;
+ } catch (Exception ex) {
+ // InvocationTargetException
+ // IllegalArgumentException
+ // IllegalAccessException
+ throw new InnerException(ex);
+ }
+ }
+ }
+
+ /**
+ * Adds a control or a pair of controls for presenting the given property.
+ *
+ * @param aPropName Name of the property to be presented.
+ * @param aPropType Type of the property in the form of a <code>Class</code> instance.
+ * @param aValue Value of the property to be presented.
+ */
+ private void addControls(String aPropName, Class<?> aPropType, Object aValue) {
+ try {
+ String labelID = Messages.SET_PREFIX + aPropName.toUpperCase();
+ String labelText = (String) Messages.class.getField(labelID).get(null);
+ String typeName = aPropType.getName();
+ if (boolean.class.getName().equals(typeName)) {
+ addBooleanInput(aPropName, labelText, (Boolean) aValue);
+ } else {
+ JLabel label = new JLabel(labelText, SwingConstants.TRAILING);
+ add(label, firstColumn);
+ if (String.class.getName().equals(typeName)) {
+ addStringInput(aPropName, (String) aValue);
+ } else if (Color.class.getName().equals(typeName)) {
+ addColorInput(aPropName, (Color) aValue);
+ } else if (PointShape.class.getName().equals(typeName)) {
+ addPointShapeInput(aPropName, (PointShape) aValue);
+ }
+ }
+ } catch (Exception ex) {
+ throw new InnerException(ex);
+ }
+ }
+
+ /**
+ * Creates a checkbox to present a boolean property.
+ *
+ * @param aPropName Name of the property to be presented.
+ * @param aButtonLabel Label to be used for the checkbox.
+ * @param aValue Value of the property to be presented. Settings this parameter to <code>true</code>
+ * results in the checkbox being selected.
+ */
+ private void addBooleanInput(String aPropName, String aButtonLabel, Boolean aValue) {
+ JCheckBox checkBox = new JCheckBox(aButtonLabel);
+ checkBox.setName(aPropName);
+ checkBox.setSelected(aValue.booleanValue());
+ lastColumn.fill = GridBagConstraints.NONE;
+ lastColumn.insets.left += CHECKBOX_INDENT;
+ lastColumn.insets.right += CHECKBOX_INDENT;
+ add(checkBox, lastColumn);
+ lastColumn.insets.left -= CHECKBOX_INDENT;
+ lastColumn.insets.right -= CHECKBOX_INDENT;
+ lastColumn.fill = GridBagConstraints.HORIZONTAL;
+ }
+
+ /**
+ * Creates a label and a text field to present a string property.
+ *
+ * @param aPropName Name of the property to be presented.
+ * @param aValue Value of the property in the form of a <code>String</code> instance.
+ */
+ private void addStringInput(String aPropName, String aValue) {
+ JTextField inputField = new JTextField(aValue);
+ inputField.setName(aPropName);
+ Utils.adjustWidth(inputField, CONTROL_COLUMN_WIDTH);
+ layout.setConstraints(inputField, lastColumn);
+ add(inputField);
+ }
+
+ /**
+ * Creates a label and a button to present a <code>Color</code> property.
+ *
+ * @param aPropName Name of the property to be presented.
+ * @param aColor Value of the property in the form of a <code>Color</code> instance.
+ */
+ private void addColorInput(String aPropName, Color aColor) {
+ final JButton colorButton = new JButton(Messages.SET_COLORBUTTON);
+ colorButton.addActionListener(this);
+ colorButton.setActionCommand("color");
+ colorButton.setForeground(aColor);
+ colorButton.setName(aPropName);
+ lastColumn.fill = GridBagConstraints.NONE;
+ add(colorButton, lastColumn);
+ lastColumn.fill = GridBagConstraints.HORIZONTAL;
+ }
+
+ /**
+ * Creates a drop-down list to present the possible values of a <code>PointShape</code> property.
+ *
+ * @param aPropName Name of the property to be presented.
+ * @param aShape Value of the property in the form of a <code>PointShape</code> instance.
+ */
+ private void addPointShapeInput(String aPropName, PointShape aShape) {
+ final JComboBox comShapes = new JComboBox(PointShape.Texts);
+ comShapes.setSelectedItem(aShape.getDescription());
+ comShapes.setName(aPropName);
+ lastColumn.fill = GridBagConstraints.NONE;
+ add(comShapes, lastColumn);
+ lastColumn.fill = GridBagConstraints.HORIZONTAL;
+ }
+
+ /**
+ * Unique ID for this version of this class. It is used in serialization.
+ */
+ private static final long serialVersionUID = -610827874488404038L;
+
+ /**
+ * Preferred width, in pixels, for labels spanning a whole column.
+ */
+ private static final int CHECKBOX_INDENT = 15;
+
+ /**
+ * Preferred width, in pixels, for controls spanning a whole column.
+ */
+ private static final int CONTROL_COLUMN_WIDTH = 200;
+
+ /**
+ * Horizontal spacing for every control.
+ * <p>
+ * Settings this field to <i>k</i> results in effective horizontal spacing of <i>2k</i> pixels between
+ * controls.
+ * </p>
+ */
+ private static final int HOR_INSETS = 6;
+
+ /**
+ * Vertical spacing for every control.
+ * <p>
+ * Settings this field to <i>k</i> results in effective vertical spacing of <i>2k</i> pixels between
+ * controls.
+ * </p>
+ */
+ private static final int VER_INSETS = 4;
+
+ /**
+ * Layout manager for the controls in the panel.
+ */
+ private GridBagLayout layout;
+
+ /**
+ * Constraints for the first column of the grid. This column contains labels.
+ */
+ private GridBagConstraints firstColumn;
+
+ /**
+ * Constraints for the last (second) column of the grid. This column contains input controls, such as text
+ * boxes and buttons.
+ */
+ private GridBagConstraints lastColumn;
+
+ /**
+ * Settings instance, whose properties are presented in this panel.
+ */
+ private Settings data;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/SimpleStatsPanel.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/SimpleStatsPanel.java
new file mode 100644
index 0000000..1424fe5
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/SimpleStatsPanel.java
@@ -0,0 +1,162 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.ui;
+
+import java.awt.BorderLayout;
+import java.awt.FlowLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import javax.swing.Box;
+import javax.swing.BoxLayout;
+import javax.swing.JButton;
+import javax.swing.JComponent;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.SwingConstants;
+
+import cytoscape.util.OpenBrowser;
+
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Messages;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.NetworkStats;
+import de.mpg.mpi_inf.bioinf.netanalyzer.sconnect.HelpConnector;
+
+/**
+ * Panel (group box) displaying the simple network statistics.
+ *
+ * @author Yassen Assenov
+ */
+public class SimpleStatsPanel extends JPanel
+ implements ActionListener {
+
+ /**
+ * Initializes a new instance of <code>SimpleStatsPanel</code>.
+ *
+ * @param aStats Network statistics, whose simple parameters are to be visualized.
+ */
+ public SimpleStatsPanel(NetworkStats aStats) {
+ super(new BorderLayout(0, Utils.BORDER_SIZE));
+
+ String[] statNames = aStats.getComputedSimple();
+ int nameCount = statNames.length;
+
+ JPanel simpleStatsPanel = new JPanel();
+ Box descrCol = new Box(BoxLayout.Y_AXIS);
+ simpleStatsPanel.add(descrCol);
+ Box valueCol = new Box(BoxLayout.Y_AXIS);
+ simpleStatsPanel.add(valueCol);
+
+ if (nameCount > 3) {
+ // Order simple parameters in two columns
+ simpleStatsPanel.add(Box.createHorizontalStrut(12));
+ Box descrCol2 = new Box(BoxLayout.Y_AXIS);
+ simpleStatsPanel.add(descrCol2);
+ Box valueCol2 = new Box(BoxLayout.Y_AXIS);
+ simpleStatsPanel.add(valueCol2);
+ int half = nameCount / 2 + nameCount % 2;
+ addDescrValuePair(aStats, statNames, 0, half, descrCol, valueCol);
+ addDescrValuePair(aStats, statNames, half, nameCount, descrCol2, valueCol2);
+ } else {
+ // Order simlple parameters in one column
+ addDescrValuePair(aStats, statNames, 0, nameCount, descrCol, valueCol);
+ }
+ add(simpleStatsPanel, BorderLayout.CENTER);
+
+ // Add a help button
+ final int bs = Utils.BORDER_SIZE;
+ JPanel panHelp = new JPanel(new FlowLayout(FlowLayout.TRAILING, bs, bs));
+ panHelp.add(btnHelp = Utils.createButton(Messages.DI_HELP, Messages.TT_ONLHELP, this));
+ add(panHelp, BorderLayout.SOUTH);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.event.ActionListener#actionPerformed(java.awt.event.ActionEvent)
+ */
+ public void actionPerformed(ActionEvent e) {
+ if (e.getSource() == btnHelp) {
+ OpenBrowser.openURL(HelpConnector.getParamURL("simple"));
+ }
+ }
+
+ /**
+ * (Relative) maximum number of symbols used to display a real value.
+ */
+ private static final int NUMBER_LENGTH_MAX = 8;
+
+ /**
+ * Maximum precision of a real value to be displayed.
+ */
+ private static final int PRECISION_MAX = 3;
+
+ /**
+ * Unique ID for this version of this class. It is used in serialization.
+ */
+ private static final long serialVersionUID = 6346913948150828482L;
+
+ /**
+ * Adds pairs of labels to display the descriptions of simple network parameters along with
+ * their values.
+ *
+ * @param aNames Array of parameter IDs.
+ * @param aFromIndex Starting index of IDs for the parameters to add.
+ * @param aToIndex Ending index of IDs for the parameters to add. All parameters in the range [<code>aFromIndex</code>,
+ * <code>aToIndex - 1</code>] are added.
+ * @param aDescrCont Container component for the description labels.
+ * @param aValueCont Container component for the value labels.
+ */
+ private void addDescrValuePair(NetworkStats aStats, String[] aNames, int aFromIndex,
+ int aToIndex, JComponent aDescrCont, JComponent aValueCont) {
+ for (int i = aFromIndex; i < aToIndex; ++i) {
+ String stat = aNames[i];
+ JLabel messageLabel = new JLabel(Messages.get(stat) + " :", SwingConstants.RIGHT);
+ messageLabel.setAlignmentX(1.0f);
+ aDescrCont.add(messageLabel);
+ aValueCont.add(createValueLabel(aStats, stat));
+ }
+ }
+
+ /**
+ * Creates a label for the value of the given simple parameter.
+ *
+ * @param aName ID of simple parameter to get the value of.
+ * @return Label with HTML text showing the value of the simple parameter <code>aName</code>.
+ */
+ private JLabel createValueLabel(NetworkStats aStats, String aName) {
+ Object value = aStats.get(aName);
+ String labelText = value.toString();
+ String toolTipText = null;
+ if ("connPairs".equals(aName)) {
+ long connPairs = aStats.getLong("connPairs");
+ long totalPairs = aStats.getInt("nodeCount");
+ totalPairs = totalPairs * (totalPairs - 1);
+ long percentage = (connPairs * 100) / totalPairs;
+ labelText = labelText + " (" + percentage + "%)";
+ } else if (value instanceof Double) {
+ toolTipText = labelText;
+ labelText = Utils.doubleToString((Double) value, NUMBER_LENGTH_MAX, PRECISION_MAX);
+ }
+ return Utils.createLabel("<html><b>" + labelText + "</b></html>", toolTipText);
+ }
+
+ /**
+ * "Help" button.
+ */
+ private JButton btnHelp;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/SpringUtilities.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/SpringUtilities.java
new file mode 100644
index 0000000..5a00758
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/SpringUtilities.java
@@ -0,0 +1,162 @@
+package de.mpg.mpi_inf.bioinf.netanalyzer.ui;
+
+import java.awt.Component;
+import java.awt.Container;
+
+import javax.swing.Spring;
+import javax.swing.SpringLayout;
+
+/**
+ * A 1.4 file that provides utility methods for creating form- or grid-style layouts with
+ * SpringLayout. These utilities are used by several programs, such as SpringBox and
+ * SpringCompactGrid.
+ */
+public abstract class SpringUtilities {
+
+ /**
+ * Aligns the first <code>rows</code> * <code>cols</code> components of <code>parent</code>
+ * in a grid. Each component is as big as the maximum preferred width and height of the
+ * components. The parent is made just big enough to fit them all.
+ *
+ * @param parent container with a SpringLayout layout manager
+ * @param rows number of rows
+ * @param cols number of columns
+ * @param initialX x location to start the grid at
+ * @param initialY y location to start the grid at
+ * @param xPad x padding between cells
+ * @param yPad y padding between cells
+ */
+ @SuppressWarnings("null")
+ public static void makeGrid(Container parent, int rows, int cols, int initialX, int initialY,
+ int xPad, int yPad) {
+ SpringLayout layout;
+ try {
+ layout = (SpringLayout) parent.getLayout();
+ } catch (ClassCastException exc) {
+ System.err.println("The first argument to makeGrid must use SpringLayout.");
+ return;
+ }
+
+ Spring xPadSpring = Spring.constant(xPad);
+ Spring yPadSpring = Spring.constant(yPad);
+ Spring initialXSpring = Spring.constant(initialX);
+ Spring initialYSpring = Spring.constant(initialY);
+ int max = rows * cols;
+
+ // Calculate Springs that are the max of the width/height so that all
+ // cells have the same size.
+ Spring maxWidthSpring = layout.getConstraints(parent.getComponent(0)).getWidth();
+ Spring maxHeightSpring = layout.getConstraints(parent.getComponent(0)).getWidth();
+ for (int i = 1; i < max; i++) {
+ SpringLayout.Constraints cons = layout.getConstraints(parent.getComponent(i));
+
+ maxWidthSpring = Spring.max(maxWidthSpring, cons.getWidth());
+ maxHeightSpring = Spring.max(maxHeightSpring, cons.getHeight());
+ }
+
+ // Apply the new width/height Spring. This forces all the
+ // components to have the same size.
+ for (int i = 0; i < max; i++) {
+ SpringLayout.Constraints cons = layout.getConstraints(parent.getComponent(i));
+
+ cons.setWidth(maxWidthSpring);
+ cons.setHeight(maxHeightSpring);
+ }
+
+ // Then adjust the x/y constraints of all the cells so that they
+ // are aligned in a grid.
+ SpringLayout.Constraints lastCons = null;
+ SpringLayout.Constraints lastRowCons = null;
+ for (int i = 0; i < max; i++) {
+ SpringLayout.Constraints cons = layout.getConstraints(parent.getComponent(i));
+ if (i % cols == 0) { // start of new row
+ lastRowCons = lastCons;
+ cons.setX(initialXSpring);
+ } else { // x position depends on previous component
+ cons.setX(Spring.sum(lastCons.getConstraint(SpringLayout.EAST), xPadSpring));
+ }
+
+ if (i / cols == 0) { // first row
+ cons.setY(initialYSpring);
+ } else { // y position depends on previous row
+ cons.setY(Spring.sum(lastRowCons.getConstraint(SpringLayout.SOUTH), yPadSpring));
+ }
+ lastCons = cons;
+ }
+
+ // Set the parent's size.
+ SpringLayout.Constraints pCons = layout.getConstraints(parent);
+ pCons.setConstraint(SpringLayout.SOUTH, Spring.sum(Spring.constant(yPad), lastCons
+ .getConstraint(SpringLayout.SOUTH)));
+ pCons.setConstraint(SpringLayout.EAST, Spring.sum(Spring.constant(xPad), lastCons
+ .getConstraint(SpringLayout.EAST)));
+ }
+
+ /* Used by makeCompactGrid. */
+ private static SpringLayout.Constraints getConstraintsForCell(int row, int col,
+ Container parent, int cols) {
+ SpringLayout layout = (SpringLayout) parent.getLayout();
+ Component c = parent.getComponent(row * cols + col);
+ return layout.getConstraints(c);
+ }
+
+ /**
+ * Aligns the first <code>rows</code> * <code>cols</code> components of <code>parent</code>
+ * in a grid. Each component in a column is as wide as the maximum preferred width of the
+ * components in that column; height is similarly determined for each row. The parent is made
+ * just big enough to fit them all.
+ *
+ * @param parent container with a SpringLayout layout manager
+ * @param rows number of rows
+ * @param cols number of columns
+ * @param initialX x location to start the grid at
+ * @param initialY y location to start the grid at
+ * @param xPad x padding between cells
+ * @param yPad y padding between cells
+ */
+ public static void makeCompactGrid(Container parent, int rows, int cols, int initialX,
+ int initialY, int xPad, int yPad) {
+ SpringLayout layout;
+ try {
+ layout = (SpringLayout) parent.getLayout();
+ } catch (ClassCastException exc) {
+ System.err.println("The first argument to makeCompactGrid must use SpringLayout.");
+ return;
+ }
+
+ // Align all cells in each column and make them the same width.
+ Spring x = Spring.constant(initialX);
+ for (int c = 0; c < cols; c++) {
+ Spring width = Spring.constant(0);
+ for (int r = 0; r < rows; r++) {
+ width = Spring.max(width, getConstraintsForCell(r, c, parent, cols).getWidth());
+ }
+ for (int r = 0; r < rows; r++) {
+ SpringLayout.Constraints constraints = getConstraintsForCell(r, c, parent, cols);
+ constraints.setX(x);
+ constraints.setWidth(width);
+ }
+ x = Spring.sum(x, Spring.sum(width, Spring.constant(xPad)));
+ }
+
+ // Align all cells in each row and make them the same height.
+ Spring y = Spring.constant(initialY);
+ for (int r = 0; r < rows; r++) {
+ Spring height = Spring.constant(0);
+ for (int c = 0; c < cols; c++) {
+ height = Spring.max(height, getConstraintsForCell(r, c, parent, cols).getHeight());
+ }
+ for (int c = 0; c < cols; c++) {
+ SpringLayout.Constraints constraints = getConstraintsForCell(r, c, parent, cols);
+ constraints.setY(y);
+ constraints.setHeight(height);
+ }
+ y = Spring.sum(y, Spring.sum(height, Spring.constant(yPad)));
+ }
+
+ // Set the parent's size.
+ SpringLayout.Constraints pCons = layout.getConstraints(parent);
+ pCons.setConstraint(SpringLayout.SOUTH, y);
+ pCons.setConstraint(SpringLayout.EAST, x);
+ }
+}
\ No newline at end of file
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/SupportedExtensions.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/SupportedExtensions.java
new file mode 100644
index 0000000..a5cd367
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/SupportedExtensions.java
@@ -0,0 +1,54 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.ui;
+
+/**
+ * Storage class for file types that are supported by the plugin for reading and/or writing data.
+ * <p>
+ * This class contains all instances of
+ * {@link de.mpg.mpi_inf.bioinf.netanalyzer.ui.ExtensionFileFilter} created within this plugin.
+ * </p>
+ *
+ * @author Yassen Assenov
+ */
+public final class SupportedExtensions {
+
+ /**
+ * Extension filter for JPEG images.
+ */
+ public static ExtensionFileFilter jpegFilesFilter = new ExtensionFileFilter(".jpeg", ".jpg",
+ "Jpeg images (.jpeg, .jpg)");
+
+ /**
+ * Extension filter for PNG images.
+ */
+ public static ExtensionFileFilter pngFilesFilter = new ExtensionFileFilter(".png",
+ "Portable Network Graphic images (.png)");
+
+ /**
+ * Extension filter for SVG images.
+ */
+ public static ExtensionFileFilter svgFilesFilter = new ExtensionFileFilter(".svg",
+ "Scalable Vector Graphics (.svg)");
+
+ /**
+ * Extension filter for .netstats data files.
+ */
+ public static final ExtensionFileFilter netStatsFilter = new ExtensionFileFilter(".netstats",
+ "Network Statistics (.netstats)");
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/Utils.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/Utils.java
new file mode 100644
index 0000000..3d09bb7
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/Utils.java
@@ -0,0 +1,458 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.ui;
+
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Dimension;
+import java.awt.event.ActionListener;
+import java.io.File;
+
+import javax.swing.BorderFactory;
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JComponent;
+import javax.swing.JFileChooser;
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+import javax.swing.JSpinner;
+import javax.swing.SpinnerNumberModel;
+import javax.swing.event.HyperlinkEvent;
+import javax.swing.event.HyperlinkListener;
+
+import cytoscape.Cytoscape;
+import cytoscape.util.OpenBrowser;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Messages;
+
+/**
+ * Utility class containing helping methods for laying out and getting data from UI controls.
+ *
+ * @author Yassen Assenov
+ */
+public abstract class Utils {
+
+ /**
+ * Default border size (padding) of dialog windows.
+ */
+ public static final int BORDER_SIZE = 6;
+
+ /**
+ * Unique string used as separator for attribute names.
+ */
+ public static final String SEPARATOR = "SEPARATOR";
+
+ /**
+ * Adjust the size of a component such that it has the specified preferred width.
+ *
+ * @param aComponent
+ * Component to be adjusted.
+ * @param aWidth
+ * Value for the preferred width of the component.
+ */
+ public static void adjustWidth(JComponent aComponent, int aWidth) {
+ Dimension preferedSize = aComponent.getPreferredSize();
+ preferedSize.width = aWidth;
+ aComponent.setPreferredSize(preferedSize);
+ }
+
+ /**
+ * Verifies the given file does not exist and can therefore be created.
+ * <p>
+ * If the file exists, it will be overwritten. In such a case a confirmation dialog is displayed to the
+ * user.
+ * </p>
+ *
+ * @param aFile
+ * File to be checked.
+ * @param aParent
+ * Parent component of the confirmation dialog. This parameter is used only if a confirmation
+ * dialog is displayed.
+ * @return <code>true</code> if the specified file does not exist, or if it exists and the user has
+ * confirmed it can be overwritten; <code>false</code> otherwise.
+ */
+ public static boolean canSave(File aFile, Component aParent) {
+ if (aFile.exists()) {
+ return JOptionPane.showConfirmDialog(aParent, Messages.SM_FILEEXISTS, Messages.DT_FILEEXISTS,
+ JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION;
+ }
+ return true;
+ }
+
+ /**
+ * Creates a new button with manageable width.
+ *
+ * @param aText
+ * Text of the button.
+ * @param aTooltip
+ * Tooltip text for the button. Set this to <code>null</code> if no tooltip is to be displayed.
+ * @param aListener
+ * Button click's listener.
+ * @return Newly created instance of <code>JButton</code>.
+ */
+ public static JButton createButton(String aText, String aTooltip, ActionListener aListener) {
+ JButton button = new JButton(aText);
+ button.setToolTipText(aTooltip);
+ button.addActionListener(aListener);
+ button.setMaximumSize(new Dimension(Short.MAX_VALUE, button.getHeight()));
+ return button;
+ }
+
+ /**
+ * Creates a new checkbox with manageable width.
+ *
+ * @param aText
+ * Text of the checkbox.
+ * @param aToolTip
+ * Tooltip text for the checkbox. Set this to <code>null</code> if no tooltip is to be
+ * displayed.
+ * @param aListener
+ * Checkbox click's listener.
+ * @return Newly created instance of <code>JCheckBox</code>.
+ */
+ public static JCheckBox createCheckBox(String aText, String aToolTip, ActionListener aListener) {
+ JCheckBox button = new JCheckBox(aText);
+ button.setToolTipText(aToolTip);
+ button.addActionListener(aListener);
+ button.setMaximumSize(new Dimension(Short.MAX_VALUE, button.getHeight()));
+ return button;
+ }
+
+ /**
+ * Creates a new text label.
+ *
+ * @param aText
+ * Text of the label.
+ * @param aToolTip
+ * Tooltip text of the label. Set this to <code>null</code> if no tooltip is to be displayed.
+ * @return Newly created instance of <code>JLabel</code>.
+ */
+ public static JLabel createLabel(String aText, String aToolTip) {
+ JLabel l = new JLabel(aText);
+ l.setToolTipText(aToolTip);
+ return l;
+ }
+
+ /**
+ * Creates a <code>String</code> representation of a double based on the given maximum length and
+ * precision.
+ *
+ * @param aValue
+ * Value to find the <code>String</code> representation of.
+ * @param aMaxLength
+ * Maximum length, in number of characters, of the output string. Note that the length of the
+ * returned <code>String</code> may be greater than the number specified by this parameter.
+ * @param aMaxPrecision
+ * Maximum precision to use for the value.
+ * @return <code>String</code> representation of <code>aValue</code>.
+ */
+ public static String doubleToString(double aValue, int aMaxLength, int aMaxPrecision) {
+ return doubleToString(new Double(aValue), aMaxLength, aMaxPrecision);
+ }
+
+ /**
+ * Creates a <code>String</code> representation of a double based on the given maximum length and
+ * precision.
+ *
+ * @param aValue
+ * Value to find the <code>String</code> representation of.
+ * @param aMaxLength
+ * Maximum length, in number of characters, of the output string. Note that the length of the
+ * returned <code>String</code> may be greater than the number specified by this parameter.
+ * @param aMaxPrecision
+ * Maximum precision to use for the value.
+ * @return <code>String</code> representation of <code>aValue</code>.
+ */
+ public static String doubleToString(Double aValue, int aMaxLength, int aMaxPrecision) {
+ if (aValue.isNaN() || aValue.isInfinite()) {
+ return Messages.DI_UNDEF;
+ }
+ String text = aValue.toString();
+ int pointIndex = text.indexOf('.');
+ if (pointIndex >= 0 && text.length() > aMaxLength) {
+ if (pointIndex + 1 >= aMaxLength) {
+ text = text.substring(0, pointIndex);
+ } else {
+ int dap = Math.min(aMaxPrecision, aMaxLength - 1 - pointIndex);
+ double v = aValue.doubleValue();
+ long rounded = Math.round(v * Math.pow(10, dap));
+ text = String.valueOf(rounded);
+ String sign = rounded < 0 ? "-" : "";
+ text = text.substring(sign.length());
+ while (text.length() <= aMaxPrecision) {
+ text = "0" + text;
+ }
+ text = sign + text;
+ if (text.length() < aMaxLength) {
+ text = text.substring(0, pointIndex) + "." + text.substring(pointIndex);
+ } else {
+ text = text.substring(0, pointIndex + 1) + "."
+ + text.substring(pointIndex + 1, aMaxLength - 1);
+ }
+ }
+ }
+ return text;
+ }
+
+ /**
+ * Enlarges, if necessary, the given current size to cover the given other size.
+ * <p>
+ * If both the width and height of <code>aCurrentSize</code> are larger than the width and height of
+ * <code>aSize</code>, respectively, calling this method has no effect.
+ * </p>
+ *
+ * @param aCurrentSize
+ * Size to be enlarged if necessary.
+ * @param aSize
+ * Minimal required size of <code>aCurrentSize</code>.
+ *
+ * @throws NullPointerException
+ * If any of the given parameters is <code>null</code>.
+ */
+ public static void ensureSize(Dimension aCurrentSize, Dimension aSize) {
+ if (aCurrentSize.height < aSize.height) {
+ aCurrentSize.height = aSize.height;
+ }
+ if (aCurrentSize.width < aSize.width) {
+ aCurrentSize.width = aSize.width;
+ }
+ }
+
+ /**
+ * Resizes the given buttons making them equal in size.
+ * <p>
+ * The sizes of the buttons are equalized only by enlarging their widths and heights (when necessary).
+ * </p>
+ *
+ * @param aButtons
+ * Array of buttons to be made equal size.
+ *
+ * @throws NullPointerException
+ * If <code>aButtons</code> is <code>null</code>.
+ */
+ public static void equalizeSize(JButton[] aButtons) {
+ final Dimension preferredSize = aButtons[0].getPreferredSize();
+ final Dimension maximumSize = aButtons[0].getMaximumSize();
+ for (int i = 1; i < aButtons.length; ++i) {
+ ensureSize(preferredSize, aButtons[i].getPreferredSize());
+ ensureSize(maximumSize, aButtons[i].getMaximumSize());
+ }
+ setSizes(aButtons, preferredSize, maximumSize);
+ }
+
+ /**
+ * Resizes the given buttons making them equal in size.
+ * <p>
+ * This a convenience method only. Calling this method is equivalent to calling:<br/> <code>
+ * equalizeSize(new JButton[] { aButton1, aButton2 });
+ * </code>
+ * </p>
+ *
+ * @param aButton1
+ * First of the buttons to be made equal in size.
+ * @param aButton2
+ * Second of the buttons to be made equal in size.
+ * @see #equalizeSize(JButton[])
+ */
+ public static void equalizeSize(JButton aButton1, JButton aButton2) {
+ equalizeSize(new JButton[] { aButton1, aButton2 });
+ }
+
+ /**
+ * Resizes the given buttons making them equal in size.
+ * <p>
+ * This a convenience method only. Calling this method is equivalent to calling:<br/> <code>
+ * equalizeSize(new JButton[] { aButton1, aButton2, aButton3 });
+ * </code>
+ * </p>
+ *
+ * @param aButton1
+ * First of the buttons to be made equal in size.
+ * @param aButton2
+ * Second of the buttons to be made equal in size.
+ * @param aButton3
+ * Third of the buttons to be made equal in size.
+ * @see #equalizeSize(JButton[])
+ */
+ public static void equalizeSize(JButton aButton1, JButton aButton2, JButton aButton3) {
+ equalizeSize(new JButton[] { aButton1, aButton2, aButton3 });
+ }
+
+ /**
+ * Gets the currently selected integer value in a spinner control.
+ *
+ * @param aSpinner
+ * Spinner, whose chosen value is to be extracted.
+ * @return The selected value of the spinner rounded to integer.
+ * @throws ClassCastException
+ * If the spinner's model is not a {@link javax.swing.SpinnerNumberModel}.
+ */
+ public static int getSpinnerInt(JSpinner aSpinner) {
+ return ((SpinnerNumberModel) aSpinner.getModel()).getNumber().intValue();
+ }
+
+ /**
+ * Gets the invert of the given color.
+ *
+ * @param aColor
+ * Color to get the invert of.
+ * @return New <code>Color</code> instance which stores the invert of <code>aColor</code>.
+ */
+ public static Color invertOf(Color aColor) {
+ return new Color(255 - aColor.getRed(), 255 - aColor.getGreen(), 255 - aColor.getBlue());
+ }
+
+ /**
+ * Removes the selection from a file chooser in single selection mode.
+ *
+ * @param aDialog
+ * File selection dialog to be modified.
+ */
+ public static void removeSelectedFile(JFileChooser aDialog) {
+ File file = aDialog.getSelectedFile();
+ if (file != null) {
+ aDialog.setSelectedFile(null);
+ try {
+ ((javax.swing.plaf.basic.BasicFileChooserUI) aDialog.getUI()).setFileName(null);
+ } catch (Exception ex) {
+ // Could not remove file name from the text field, ignore
+ }
+ }
+ }
+
+ /**
+ * Sets the preferred and maximum sizes of the given buttons.
+ *
+ * @param aButtons
+ * Buttons to be modified.
+ * @param aPreferred
+ * Preferred size to be set to each of the buttons. If this is <code>null</code>, every
+ * button's preferred size is set to its default value.
+ * @param aMax
+ * Maximum size to be set to each of the buttons. If this is <code>null</code>, every button's
+ * maximum size is set to its default value.
+ *
+ * @throws NullPointerException
+ * If <code>aButtons</code> is <code>null</code>.
+ */
+ public static void setSizes(JButton[] aButtons, Dimension aPreferred, Dimension aMax) {
+ for (final JButton button : aButtons) {
+ button.setPreferredSize(aPreferred);
+ button.setMaximumSize(aMax);
+ }
+ }
+
+ /**
+ * Sets a standard border of the given component.
+ * <p>
+ * The standard border is an empty border of with {@link #BORDER_SIZE}.
+ * </p>
+ *
+ * @param aComponent
+ * Component to get a standard border. This component will lose its previous border, if any.
+ */
+ public static void setStandardBorder(JComponent aComponent) {
+ final int bs = BORDER_SIZE;
+ aComponent.setBorder(BorderFactory.createEmptyBorder(bs, bs, bs, bs));
+ }
+
+ /**
+ * Displays an error message dialog.
+ * <p>
+ * The owner of the dialog is set to be the Cytoscape desktop.
+ * </p>
+ *
+ * @param aTitle
+ * Title of the dialog.
+ * @param aMessage
+ * Message to be displayed in the dialog.
+ *
+ * @see #showErrorBox(Component, String, String)
+ */
+ public static void showErrorBox(String aTitle, String aMessage) {
+ showErrorBox(Cytoscape.getDesktop(), aTitle, aMessage);
+ }
+
+ /**
+ * Displays an error message dialog.
+ *
+ * @param aParent
+ * Owner of the dialog. Please note that the displayed dialog is modal.
+ * @param aTitle
+ * Title of the dialog.
+ * @param aMessage
+ * Message to be displayed in the dialog.
+ */
+ public static void showErrorBox(Component aParent, String aTitle, String aMessage) {
+ JOptionPane.showMessageDialog(aParent, aMessage, aTitle, JOptionPane.ERROR_MESSAGE);
+ }
+
+ /**
+ * Displays an information dialog.
+ * <p>
+ * The owner of the dialog is set to be the Cytoscape desktop.
+ * </p>
+ *
+ * @param aTitle
+ * Title of the dialog.
+ * @param aMessage
+ * Message to be displayed in the dialog.
+ *
+ * @see #showInfoBox(Component, String, String)
+ */
+ public static void showInfoBox(String aTitle, String aMessage) {
+ showInfoBox(Cytoscape.getDesktop(), aTitle, aMessage);
+ }
+
+ /**
+ * Displays an information dialog.
+ *
+ * @param aParent
+ * Owner of the dialog. Please note that the displayed dialog is modal.
+ * @param aTitle
+ * Title of the dialog.
+ * @param aMessage
+ * Message to be displayed in the dialog.
+ */
+ public static void showInfoBox(Component aParent, String aTitle, String aMessage) {
+ JOptionPane.showMessageDialog(aParent, aMessage, aTitle, JOptionPane.INFORMATION_MESSAGE);
+ }
+
+ /**
+ * Hyperlink listener for instances of <code>JEditorPane</code> with HTML contents.
+ * <p>
+ * Whenever a link is clicked, this listener opens the referenced URL with the default system's browser.
+ * </p>
+ *
+ * @author Mario Albrecht
+ * @author Yassen Assenov
+ * @author Carola Huthmacher
+ */
+ public static class MenuPaneHyperlinkListener implements HyperlinkListener {
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see javax.swing.event.HyperlinkListener#hyperlinkUpdate(javax.swing.event.HyperlinkEvent)
+ */
+ public void hyperlinkUpdate(HyperlinkEvent e) {
+ if (e.getEventType() == HyperlinkEvent.EventType.ACTIVATED) {
+ OpenBrowser.openURL(e.getURL().toString());
+ }
+ }
+ }
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/VisualizeParameterDialog.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/VisualizeParameterDialog.java
new file mode 100644
index 0000000..9c456b6
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/VisualizeParameterDialog.java
@@ -0,0 +1,120 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.ui;
+
+import java.awt.Frame;
+
+import javax.swing.JDialog;
+
+import cytoscape.CyNetwork;
+
+/**
+ * Basic class for a visualization dialog.
+ *
+ * @author Nadezhda Doncheva
+ */
+public abstract class VisualizeParameterDialog extends JDialog {
+
+ /**
+ * Initializes a new instance of <code>MapParameterDialog</code>.
+ *
+ * @param aOwner
+ * The <code>Frame</code> from which this dialog is displayed.
+ * @param aName
+ * Name of the dialog.
+ * @param modal
+ * Flag indicating if the dialog should be modal or not.
+ * @param aNetwork
+ * Target network for visualization of network parameters.
+ * @param aNodeAttr
+ * Two-dimensional array with computed parameters stored as node attributes. The
+ * first column contains all NetworkAnalyzer attributes, and the second one other
+ * attributes.
+ * @param aEdgeAttr
+ * Two-dimensional array with computed parameters stored as edge attributes. The
+ * first column contains all NetworkAnalyzer attributes, and the second one other
+ * attributes.
+ */
+ protected VisualizeParameterDialog(Frame aOwner, String aName, boolean modal,
+ CyNetwork aNetwork, String[][] aNodeAttr, String[][] aEdgeAttr) {
+ super(aOwner, aName, modal);
+ network = aNetwork;
+ nodeAttr = aNodeAttr;
+ edgeAttr = aEdgeAttr;
+ }
+
+ /**
+ * Combines two string arrays in one and adds the empty string at the beginning if
+ * <code>addEmpty</code> is <code>true</code>, and the string "SEPARATOR" between the two
+ * arrays.
+ *
+ * @param attr
+ * A 2d-String array with attributes. <code>attr[0]</code> are attributes computed
+ * by NetworkAnalyzer and <code>attr[1]</code> other attributes.
+ * @param addEmpty
+ * The method adds an empty string at the beginning of the new array, if this flag is
+ * <code>true</code>.
+ * @return One string array that combines both the arrays from attr and adds the string
+ * "SEPARATOR" between them. Depending on the flag <code>addEmpty</code> the first
+ * position of the array could be an empty string.
+ */
+ protected String[] combineAttrArray(String[][] attr, boolean addEmpty) {
+ final int length0 = attr[0].length;
+ final int length1 = attr[1].length;
+ int combinedLength = length0 + length1;
+ if (length0 > 0 && length1 != 0) {
+ combinedLength++;
+ }
+ final int emptyCount = addEmpty ? 1 : 0;
+ combinedLength = combinedLength + emptyCount;
+ final String[] combined = new String[combinedLength];
+ if (addEmpty) {
+ combined[0] = "";
+ }
+ System.arraycopy(attr[0], 0, combined, emptyCount, length0);
+ if (length1 > 0) {
+ if (length0 > 0) {
+ combined[length0 + emptyCount] = Utils.SEPARATOR;
+ }
+ System.arraycopy(attr[1], 0, combined, combinedLength - length1, length1);
+ }
+ return combined;
+ }
+
+ /**
+ * Two-dimensional array with computed parameters stored as node attributes. The first column
+ * contains all networkAnalyzer attributes, and the second one other attributes.
+ */
+ protected String[][] nodeAttr;
+
+ /**
+ * Two-dimensional array with computed parameters stored as edge attributes. The first column
+ * contains all networkAnalyzer attributes, and the second one other attributes.
+ */
+ protected String[][] edgeAttr;
+
+ /**
+ * Target network for visualization of network parameters.
+ */
+ protected CyNetwork network;
+
+ /**
+ * Unique ID for this version of this class. It is used in serialization.
+ */
+ private static final long serialVersionUID = 2349065850841032444L;
+}
\ No newline at end of file
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/charts/JFreeChartConn.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/charts/JFreeChartConn.java
new file mode 100644
index 0000000..35600f2
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/charts/JFreeChartConn.java
@@ -0,0 +1,657 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.ui.charts;
+
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Shape;
+import java.awt.geom.Ellipse2D;
+import java.awt.geom.Point2D;
+import java.awt.geom.Rectangle2D;
+import java.io.File;
+import java.io.IOException;
+
+import javax.swing.JPanel;
+
+import org.freehep.graphics2d.VectorGraphics;
+import org.freehep.graphicsio.svg.SVGGraphics2D;
+import org.jfree.chart.ChartFactory;
+import org.jfree.chart.ChartPanel;
+import org.jfree.chart.ChartUtilities;
+import org.jfree.chart.JFreeChart;
+import org.jfree.chart.axis.NumberAxis;
+import org.jfree.chart.plot.PlotOrientation;
+import org.jfree.chart.plot.XYPlot;
+import org.jfree.chart.renderer.AbstractRenderer;
+import org.jfree.chart.renderer.xy.XYBarRenderer;
+import org.jfree.chart.renderer.xy.XYLineAndShapeRenderer;
+import org.jfree.data.Range;
+import org.jfree.data.xy.XYDataset;
+import org.jfree.data.xy.XYSeries;
+import org.jfree.data.xy.XYSeriesCollection;
+
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.IntHistogram;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.IntRange;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.LongHistogram;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Points2D;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.settings.AxesSettings;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.settings.BarsSettings;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.settings.GeneralVisSettings;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.settings.GridSettings;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.settings.IntHistogramGroup;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.settings.LongHistogramGroup;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.settings.Points2DGroup;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.settings.ScatterSettings;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.ui.Cross;
+
+/**
+ * Connector to the JFreeChart chart drawing library.
+ * <p>
+ * Note to developers: In order to switch to or add support for another chart library, extract all
+ * public methods of this class to an interface and implement the interface.
+ * </p>
+ *
+ * @author Yassen Assenov
+ * @author Sven-Eric Schelhorn
+ */
+public abstract class JFreeChartConn {
+
+ /**
+ * Creates a chart that displays the given integer histogram data.
+ * <p>
+ * This is a convenience method, it calls
+ * {@link #createHistogram(IntHistogram, IntHistogramGroup)} or
+ * {@link #createScatter(IntHistogram, IntHistogramGroup)} based on the value of the given
+ * settings group.
+ * </p>
+ *
+ * @param aHistogram
+ * Complex parameter that stores the data to be visualized.
+ * @param aSettings
+ * Settings group for integer histogram.
+ * @return Newly created chart control.
+ * @see IntHistogramGroup#useScatter()
+ * @see #createHistogram(IntHistogram, IntHistogramGroup)
+ * @see #createScatter(IntHistogram, IntHistogramGroup)
+ */
+ public static JFreeChart createChart(IntHistogram aHistogram, IntHistogramGroup aSettings) {
+ if (aSettings.useScatter()) {
+ return createScatter(aHistogram, aSettings);
+ }
+ return createHistogram(aHistogram, aSettings);
+ }
+
+ /**
+ * Creates a chart that displays the given long histogram data.
+ * <p>
+ * This is a convenience method, it calls
+ * {@link #createHistogram(LongHistogram, LongHistogramGroup)} or
+ * {@link #createScatter(LongHistogram, LongHistogramGroup)} based on the value of the given
+ * settings group.
+ * </p>
+ *
+ * @param aHistogram
+ * Complex parameter that stores the data to be visualized.
+ * @param aSettings
+ * Settings group for integer histogram.
+ * @return Newly created chart control.
+ * @see LongHistogramGroup#useScatter()
+ * @see #createHistogram(LongHistogram, LongHistogramGroup)
+ * @see #createScatter(LongHistogram, LongHistogramGroup)
+ */
+ public static JFreeChart createChart(LongHistogram aHistogram, LongHistogramGroup aSettings) {
+ if (aSettings.useScatter()) {
+ return createScatter(aHistogram, aSettings);
+ }
+ return createHistogram(aHistogram, aSettings);
+ }
+
+ /**
+ * Creates a histogram chart that displays the given integer histogram data.
+ *
+ * @param aHistogram
+ * Complex parameter that stores the data to be visualized.
+ * @param aSettings
+ * Settings group for integer histogram.
+ * @return Newly created chart control.
+ */
+ public static JFreeChart createHistogram(IntHistogram aHistogram, IntHistogramGroup aSettings) {
+
+ XYSeriesCollection collection = fromIntHistogram(aHistogram);
+ JFreeChart chart = ChartFactory.createHistogram(null, // title
+ convertLabel(aSettings.axes.getDomainAxisLabel()), // label of X axis
+ convertLabel(aSettings.axes.getRangeAxisLabel()), // label of Y axis
+ collection, // dataset
+ PlotOrientation.VERTICAL, // orientation
+ false, // create legend
+ false, // display tooltips
+ false); // generate urls
+ XYPlot plot = chart.getXYPlot();
+ NumberAxis domainAxis = (NumberAxis) plot.getDomainAxis();
+ domainAxis.setStandardTickUnits(NumberAxis.createIntegerTickUnits());
+ NumberAxis rangeAxis = (NumberAxis) plot.getRangeAxis();
+ rangeAxis.setStandardTickUnits(NumberAxis.createIntegerTickUnits());
+ updateGeneral(plot, aSettings.general);
+ updateAxes(chart, aSettings.axes, aSettings.grid);
+ updateBars(plot, aSettings.bars);
+ chart.setBackgroundPaint(null);
+ return chart;
+ }
+
+ /**
+ * Creates a histogram chart that displays the given long histogram data.
+ *
+ * @param aHistogram
+ * Complex parameter that stores the data to be visualized.
+ * @param aSettings
+ * Settings group for long histogram.
+ * @return Newly created chart control.
+ */
+ public static JFreeChart createHistogram(LongHistogram aHistogram, LongHistogramGroup aSettings) {
+ XYSeriesCollection collection = fromLongHistogram(aHistogram);
+ JFreeChart chart = ChartFactory.createHistogram(null, // title
+ convertLabel(aSettings.axes.getDomainAxisLabel()), // label of X axis
+ convertLabel(aSettings.axes.getRangeAxisLabel()), // label of Y axis
+ collection, // dataset
+ PlotOrientation.VERTICAL, // orientation
+ false, // create legend
+ false, // display tooltips
+ false); // generate urls
+ XYPlot plot = chart.getXYPlot();
+ NumberAxis domainAxis = (NumberAxis) plot.getDomainAxis();
+ domainAxis.setStandardTickUnits(NumberAxis.createIntegerTickUnits());
+ NumberAxis rangeAxis = (NumberAxis) plot.getRangeAxis();
+ rangeAxis.setStandardTickUnits(NumberAxis.createIntegerTickUnits());
+ updateGeneral(plot, aSettings.general);
+ updateAxes(chart, aSettings.axes, aSettings.grid);
+ updateBars(plot, aSettings.bars);
+ chart.setBackgroundPaint(null);
+ return chart;
+ }
+
+ /**
+ * Encloses the given chart into a panel.
+ *
+ * @param aChart
+ * Chart to be enclosed in a panel.
+ * @return Panel that contains <code>aChart</code>.
+ */
+ public static JPanel createPanel(JFreeChart aChart) {
+ return new ChartPanel(aChart);
+ }
+
+ /**
+ * Creates a scatter plot that displays the given integer histogram data.
+ *
+ * @param aHistogram
+ * Complex parameter that stores the data to be visualized.
+ * @param aSettings
+ * Settings group for integer histogram.
+ * @return Newly created chart control.
+ */
+ public static JFreeChart createScatter(IntHistogram aHistogram, IntHistogramGroup aSettings) {
+ return createScatter(fromIntHistogram(aHistogram), aSettings.general, aSettings.axes,
+ aSettings.grid, aSettings.scatter);
+ }
+
+ /**
+ * Creates a scatter plot that displays the given long histogram data.
+ *
+ * @param aHistogram
+ * Complex parameter that stores the data to be visualized.
+ * @param aSettings
+ * Settings group for long histogram.
+ * @return Newly created chart control.
+ */
+ public static JFreeChart createScatter(LongHistogram aHistogram, LongHistogramGroup aSettings) {
+ return createScatter(fromLongHistogram(aHistogram), aSettings.general, aSettings.axes,
+ aSettings.grid, aSettings.scatter);
+ }
+
+ /**
+ * Creates a scatter plot that displays the given data points.
+ *
+ * @param aPoints
+ * Complex parameter that stores the data to be visualized.
+ * @param aSettings
+ * Settings group for data points.
+ * @return Newly created chart control.
+ */
+ public static JFreeChart createScatter(Points2D aPoints, Points2DGroup aSettings) {
+ return createScatter(fromPoints2D(aPoints), aSettings.general, aSettings.axes,
+ aSettings.grid, aSettings.scatter);
+ }
+
+ /**
+ * Extracts the visualized data from a given chart instance.
+ * <p>
+ * This methods extracts the default data series from the default dataset of the given chart.
+ * </p>
+ *
+ * @param aChart
+ * Chart to extract the data from.
+ * @return Visualized data in the form of an array of points.
+ */
+ public static Point2D.Double[] extractData(JFreeChart aChart) {
+ XYDataset dataColl = aChart.getXYPlot().getDataset();
+ final int n = dataColl.getItemCount(0);
+ Point2D.Double[] dataPoints = new Point2D.Double[n];
+ for (int i = 0; i < n; ++i) {
+ dataPoints[i] = new Point2D.Double(dataColl.getXValue(0, i), dataColl.getYValue(0, i));
+ }
+ return dataPoints;
+ }
+
+ /**
+ * Saves the given chart to a JPEG image file.
+ *
+ * @param aFile
+ * File to be saved to.
+ * @param aChart
+ * Chart to be saved.
+ * @param aWidth
+ * Desired width of the image.
+ * @param aHeight
+ * Desired height of the image.
+ * @throws IOException
+ * If I/O error occurs.
+ */
+ public static void saveAsJpeg(File aFile, JFreeChart aChart, int aWidth, int aHeight)
+ throws IOException {
+ // Force white background because JPEG does not support transparency
+ aChart.setBackgroundPaint(Color.WHITE);
+ ChartUtilities.saveChartAsJPEG(aFile, aChart, aWidth, aHeight);
+ aChart.setBackgroundPaint(null);
+ }
+
+ /**
+ * Saves the given chart to a PNG image file.
+ *
+ * @param aFile
+ * File to be saved to.
+ * @param aChart
+ * Chart to be saved.
+ * @param aWidth
+ * Desired width of the image.
+ * @param aHeight
+ * Desired height of the image.
+ * @throws IOException
+ * If I/O error occurs.
+ */
+ public static void saveAsPng(File aFile, JFreeChart aChart, int aWidth, int aHeight)
+ throws IOException {
+ ChartUtilities.saveChartAsPNG(aFile, aChart, aWidth, aHeight);
+ }
+
+ /**
+ * Saves the given chart to a SVG image file.
+ * <p>
+ * This method uses the FreeHEP VectorGraphics library.
+ * </p>
+ *
+ * @param aFile
+ * File to be saved to.
+ * @param aChart
+ * Chart to be saved.
+ * @param aWidth
+ * Desired width of the image.
+ * @param aHeight
+ * Desired height of the image.
+ * @throws IOException
+ * If I/O error occurs.
+ */
+ public static void saveAsSvg(File aFile, JFreeChart aChart, int aWidth, int aHeight)
+ throws IOException {
+ final VectorGraphics graphics = new SVGGraphics2D(aFile, new Dimension(aWidth, aHeight));
+ graphics.startExport();
+ aChart.draw(graphics, new Rectangle2D.Double(0, 0, aWidth, aHeight));
+ graphics.endExport();
+ }
+
+ /**
+ * Changes the chart displayed in the given panel.
+ *
+ * @param aPanel
+ * Panel to be used for storing the chart.
+ * @param aChart
+ * Chart to be set to <code>aPanel</code>.
+ */
+ public static void setChart(JPanel aPanel, JFreeChart aChart) {
+ ((ChartPanel) aPanel).setChart(aChart);
+ }
+
+ /**
+ * Updates the axis-related properties of a chart.
+ *
+ * @param aControl
+ * Chart control to be updated.
+ * @param aAxes
+ * Axis-related visual settings to be applied.
+ * @param aGrid
+ * Grid-related visual settings to be applied.
+ */
+ public static void updateAxes(JFreeChart aControl, AxesSettings aAxes, GridSettings aGrid) {
+ XYPlot plot = aControl.getXYPlot();
+ Range domainDataRange = aAxes.getLogarithmicDomainAxis() ? new Range(logLowerBound(plot
+ .getDataset(), true), plot.getDataRange(plot.getDomainAxis()).getUpperBound())
+ : plot.getDataRange(plot.getDomainAxis());
+ Range rangeDataRange = aAxes.getLogarithmicRangeAxis() ? new Range(logLowerBound(plot
+ .getDataset(), false), plot.getDataRange(plot.getRangeAxis()).getUpperBound())
+ : plot.getDataRange(plot.getRangeAxis());
+ updateAxes(plot, aAxes, aGrid, domainDataRange, rangeDataRange);
+ }
+
+ /**
+ * Updates the bar properties of a chart.
+ *
+ * @param aControl
+ * Chart control to be updated.
+ * @param aBars
+ * Bar visual settings to be applied.
+ */
+ public static void updateBars(JFreeChart aControl, BarsSettings aBars) {
+ updateBars(aControl.getXYPlot(), aBars);
+ }
+
+ /**
+ * Updates the general properties of a chart.
+ *
+ * @param aControl
+ * Chart control to be updated.
+ * @param aGeneral
+ * General visual settings to be applied.
+ */
+ public static void updateGeneral(JFreeChart aControl, GeneralVisSettings aGeneral) {
+ updateGeneral(aControl.getXYPlot(), aGeneral);
+ }
+
+ /**
+ * Updates the point-related properties of a scatter plot.
+ *
+ * @param aControl
+ * Chart control to be updated.
+ * @param aScatter
+ * Visual settings to be applied.
+ */
+ public static void updateScatter(JFreeChart aControl, ScatterSettings aScatter) {
+ updateScatter(aControl.getXYPlot(), aScatter);
+ }
+
+ /**
+ * Converts the <code>String</code> value to be used for label.
+ *
+ * @param aLabel
+ * Label text.
+ * @return <code>aLabel</code> if the parameter is not the empty string; <code>null</code>
+ * otherwise.
+ */
+ private static String convertLabel(String aLabel) {
+ if ("".equals(aLabel)) {
+ return null;
+ }
+ return aLabel;
+ }
+
+ private static double logLowerBound(XYDataset aDataset, boolean isDomainAxis) {
+ double lowerBound = 0.0;
+ for (int i = 0; i < aDataset.getItemCount(0); i++) {
+ double tmp = isDomainAxis ? aDataset.getXValue(0, i) : aDataset.getYValue(0, i);
+ if (lowerBound == 0.0 || tmp < lowerBound)
+ lowerBound = tmp;
+ }
+
+ return lowerBound;
+ }
+
+ /**
+ * Delegates the creation of either a domain- or a range-axis according to its
+ * <code>AxesSettings</code>
+ *
+ * @param aAxes
+ * AxesSettings according to which the axis is build
+ * @param domain
+ * Flag indicating if the axis to be created is a domain-axis or not. If this flag is
+ * set to <code>false</code>, a range-axis is created.
+ * @return NumberAxis
+ */
+ private static NumberAxis createAxis(AxesSettings aAxes, boolean domain, Range aDataRange) {
+ if (domain) {
+ return createAxis(convertLabel(aAxes.getDomainAxisLabel()), aAxes
+ .getIntegerDomainAxisTick(), aAxes.getLogarithmicDomainAxis(), aAxes
+ .getDomainRange(), aDataRange);
+ }
+ return createAxis(convertLabel(aAxes.getRangeAxisLabel()), aAxes.getIntegerRangeAxisTick(),
+ aAxes.getLogarithmicRangeAxis(), aAxes.getRangeRange(), aDataRange);
+ }
+
+ /**
+ * Creates either a domain- or a range-axis according to its <code>AxesSettings</code>
+ *
+ * @param aLabel
+ * Axis label.
+ * @param aTick
+ * Flag indicating if IntegerTicks are to be created.
+ * @param aLog
+ * Flag indicating if axis must be logarithmic.
+ * @param aRange
+ * Suggested data as specified in the settings. Currently ignored.
+ * @param aDataRange
+ * Range of the data, as computed from the point coordinates.
+ * @return Newly initialized <code>NumberAxis</code>.
+ */
+ private static NumberAxis createAxis(String aLabel, boolean aTick, boolean aLog,
+ IntRange aRange, Range aDataRange) {
+ NumberAxis axis = null;
+ if (aLog) {
+ MyLogarithmicAxis logAxis = new MyLogarithmicAxis(aLabel, aDataRange);
+ // LogarithmicAxis logAxis = new LogarithmicAxis(aLabel);
+ axis = logAxis;
+ logAxis.autoAdjustRange();
+ logAxis.setAllowNegativesFlag(true);
+ // logAxis.setAutoTickUnitSelection(false);
+ logAxis.setAutoRange(false);
+ } else {
+ axis = new NumberAxis(aLabel);
+ if (aTick)
+ axis.setStandardTickUnits(NumberAxis.createIntegerTickUnits());
+ }
+ return axis;
+ }
+
+ /**
+ * Creates a scatter plot that visualizes the given data collection.
+ *
+ * @param aCollection
+ * Data to be visualized.
+ * @param aGeneral
+ * General visual settings to be applied.
+ * @param aAxes
+ * Axis-related visual settings to be applied.
+ * @param aGrid
+ * Grid-related visual settings to be applied.
+ * @param aScatter
+ * Point-related visual settings to be applied.
+ * @return Newly created chart control.
+ */
+ private static JFreeChart createScatter(XYSeriesCollection aCollection,
+ GeneralVisSettings aGeneral, AxesSettings aAxes, GridSettings aGrid,
+ ScatterSettings aScatter) {
+
+ JFreeChart chart = ChartFactory.createScatterPlot(null, // title
+ convertLabel(aAxes.getDomainAxisLabel()), // label of X axis
+ convertLabel(aAxes.getRangeAxisLabel()), // label of Y axis
+ aCollection, // dataset
+ PlotOrientation.VERTICAL, // orientation
+ false, // create legend
+ true, // display tooltips
+ false); // generate urls
+ XYPlot plot = chart.getXYPlot();
+ Range domainDataRange = aAxes.getLogarithmicDomainAxis() ? new Range(logLowerBound(plot
+ .getDataset(), true), plot.getDataRange(plot.getDomainAxis()).getUpperBound())
+ : plot.getDataRange(plot.getDomainAxis());
+ Range rangeDataRange = aAxes.getLogarithmicRangeAxis() ? new Range(logLowerBound(plot
+ .getDataset(), false), plot.getDataRange(plot.getRangeAxis()).getUpperBound())
+ : plot.getDataRange(plot.getRangeAxis());
+ updateGeneral(plot, aGeneral);
+ updateAxes(plot, aAxes, aGrid, domainDataRange, rangeDataRange);
+ updateScatter(plot, aScatter);
+ chart.setBackgroundPaint(null);
+ return chart;
+ }
+
+ /**
+ * Converts the given integer histogram data to a data collection.
+ *
+ * @param aHistogram
+ * IntHistgogram data to be converted.
+ * @return Data collection to be used in the creation of a chart.
+ */
+ private static XYSeriesCollection fromIntHistogram(IntHistogram aHistogram) {
+ int[][] bars = aHistogram.getBins();
+ XYSeries dataSeries = new XYSeries("", true, true);
+ for (int i = 0; i < bars[0].length; ++i) {
+ dataSeries.add(bars[0][i], bars[1][i], false);
+ }
+ return new XYSeriesCollection(dataSeries);
+ }
+
+ /**
+ * Converts the given long histogram data to a data collection.
+ *
+ * @param aHistogram
+ * LongHistgogram data to be converted.
+ * @return Data collection to be used in the creation of a chart.
+ */
+ private static XYSeriesCollection fromLongHistogram(LongHistogram aHistogram) {
+ long[][] bars = aHistogram.getBins();
+ XYSeries dataSeries = new XYSeries("", true, true);
+ for (int i = 0; i < bars[0].length; ++i) {
+ dataSeries.add(bars[0][i], bars[1][i], false);
+ }
+ return new XYSeriesCollection(dataSeries);
+ }
+
+ /**
+ * Converts the given point set to a data collection.
+ *
+ * @param aPoints
+ * Set of points to be converted.
+ * @return Data collection to be used in the creation of a chart.
+ */
+ private static XYSeriesCollection fromPoints2D(Points2D aPoints) {
+ Point2D.Double[] points = aPoints.getPoints();
+ XYSeries dataSeries = new XYSeries("", true, true);
+ for (int i = 0; i < points.length; ++i) {
+ dataSeries.add(points[i].x, points[i].y, false);
+ }
+ return new XYSeriesCollection(dataSeries);
+ }
+
+ /**
+ * Updates the axis-related properties of a plot.
+ *
+ * @param aPlot
+ * Plot to be updated.
+ * @param aAxes
+ * Axis-related visual settings to be applied.
+ * @param aGrid
+ * Grid-related visual settings to be applied.
+ */
+ private static void updateAxes(XYPlot aPlot, AxesSettings aAxes, GridSettings aGrid,
+ Range aDomainDataRange, Range aRangeDataRange) {
+
+ aPlot.setDomainAxis(createAxis(aAxes, true, aDomainDataRange));
+ aPlot.setRangeAxis(createAxis(aAxes, false, aRangeDataRange));
+
+ aPlot.setDomainGridlinesVisible(aGrid.getVerticalGridLines()); // set gridlines for X axis
+ aPlot.setDomainGridlinePaint(aGrid.getGridLinesColor()); // set color of domain gridline
+
+ aPlot.setRangeGridlinesVisible(aGrid.getHorizontalGridLines()); // set gridlines for Y axis
+ aPlot.setRangeGridlinePaint(aGrid.getGridLinesColor()); // set color of range gridline
+ }
+
+ /**
+ * Updates the bar properties of a plot.
+ *
+ * @param aPlot
+ * Plot to be updated.
+ * @param aBars
+ * Bar visual settings to be applied.
+ */
+ private static void updateBars(XYPlot aPlot, BarsSettings aBars) {
+ XYBarRenderer renderer = (XYBarRenderer) aPlot.getRenderer();
+ renderer.setSeriesPaint(0, aBars.getBarColor());
+ }
+
+ /**
+ * Updates the general properties of a plot.
+ *
+ * @param aPlot
+ * Plot to be updated.
+ * @param aGeneral
+ * General visual settings to be applied.
+ */
+ private static void updateGeneral(XYPlot aPlot, GeneralVisSettings aGeneral) {
+ aPlot.setBackgroundPaint(aGeneral.getBgColor());
+ }
+
+ /**
+ * Updates the point-related properties of a plot.
+ *
+ * @param aPlot
+ * Plot to be updated.
+ * @param aScatter
+ * Visual settings to be applied.
+ */
+ private static void updateScatter(XYPlot aPlot, ScatterSettings aScatter) {
+ XYLineAndShapeRenderer renderer = (XYLineAndShapeRenderer) aPlot.getRenderer();
+ renderer.setSeriesPaint(0, aScatter.getPointColor());
+ final Rectangle2D ds = AbstractRenderer.DEFAULT_SHAPE.getBounds2D();
+ final double x = ds.getX();
+ final double y = ds.getY();
+ final double w = ds.getWidth();
+ final double h = ds.getHeight();
+ Shape shape = null;
+ switch (aScatter.getPointShape()) {
+ case POINT:
+ shape = new Rectangle2D.Double(x + w / 2, y + h / 2, 1, 1);
+ renderer.setBaseShapesFilled(true);
+ break;
+ case CIRCLE:
+ shape = new Ellipse2D.Double(x, y, w, h);
+ renderer.setBaseShapesFilled(false);
+ break;
+ case FILLED_CIRCLE:
+ shape = new Ellipse2D.Double(x, y, w, h);
+ renderer.setBaseShapesFilled(true);
+ break;
+ case SQUARE:
+ shape = new Rectangle2D.Double(x, y, w, h);
+ renderer.setBaseShapesFilled(false);
+ break;
+ case FILLED_SQUARE:
+ shape = new Rectangle2D.Double(x, y, w, h);
+ renderer.setBaseShapesFilled(true);
+ break;
+ case CROSS:
+ shape = new Cross(x, y, w, h);
+ renderer.setBaseShapesFilled(false);
+ }
+ renderer.setSeriesShape(0, shape);
+ }
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/charts/MyLogarithmicAxis.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/charts/MyLogarithmicAxis.java
new file mode 100644
index 0000000..a1479e6
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/charts/MyLogarithmicAxis.java
@@ -0,0 +1,402 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.ui.charts;
+
+import java.awt.Graphics2D;
+import java.awt.geom.Rectangle2D;
+import java.text.DecimalFormat;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.jfree.chart.axis.LogarithmicAxis;
+import org.jfree.chart.axis.NumberTick;
+import org.jfree.chart.axis.Tick;
+import org.jfree.data.Range;
+import org.jfree.ui.RectangleEdge;
+import org.jfree.ui.TextAnchor;
+
+/**
+ * This class is based on the original <code>com.jrefinery.chart.axlibrary</code> with additional functions.
+ * It supports correct logarithmic scaling and ticks for numbers < 1.
+ *
+ * @see <a
+ * href="http://www.jfree.org/jfreechart/javadoc/org/jfree/chart/axis/LogarithmicAxis.html">com.jrefinery.chart.axis.LogarithmicAxis</a>
+ *
+ * @author Sven-Eric Schelhorn
+ */
+public class MyLogarithmicAxis extends LogarithmicAxis {
+
+ public static final double LOGBASE = 10.0;
+
+ protected Range dataRange;
+
+ protected int offset = 0;
+
+ protected final double[] allticks = { 0.0, 0.0001, 0.001, 0.01, 0.1, 1.0, 10.0, 100.0, 1000.0, 10000.0,
+ 100000.0, 1000000.0, 10000000.0, 100000000.0, 1000000000.0, 10000000000.0, 100000000000.0,
+ 1000000000000.0, 10000000000000.0, 100000000000000.0, 1000000000000000.0, 10000000000000000.0,
+ 100000000000000000.0, 1000000000000000000.0, 10000000000000000000.0 };
+
+ /**
+ * Constructor. Constructs a VerticalLogarithmicAxis with default log base of 10 a default tick label
+ * factor of 1.
+ *
+ * @param label the axis label (null permitted).
+ */
+ public MyLogarithmicAxis(String label) {
+ super(label);
+ this.allowNegativesFlag = false;
+ }
+
+ /**
+ * Constructor.
+ *
+ * @param label Axis label or null.
+ * @param aDataRange range of the data.
+ */
+ public MyLogarithmicAxis(String label, Range aDataRange) {
+ this(label);
+ setDataRange(aDataRange);
+ this.offset = computeOffset(aDataRange);
+ }
+
+ /**
+ * Computes the offset for the method {@link #adjustedLog(double)} to display the logarithmic scale
+ * correctly.
+ *
+ * @param aDataRange Range of the data.
+ * @return Integer denoting the correct offset for the data.
+ */
+ protected int computeOffset(Range aDataRange) {
+ final double lowerBound = aDataRange.getLowerBound();
+ for (int i = 1; i < allticks.length; ++i) {
+ if (lowerBound <= allticks[i]) {
+ return 1 - i;
+ }
+ }
+ return 0;
+ }
+
+ /**
+ * Sets the data range of the data to be shown. A range value of zero has to be excluded before to avoid
+ * strange behavior of the log axis.
+ *
+ * @param aDataRange the range.
+ */
+ public void setDataRange(Range aDataRange) {
+ dataRange = aDataRange;
+ }
+
+ /**
+ * Overridden version that calls original and then sets up flag for log axis processing.
+ *
+ * @param range the range.
+ */
+ @Override
+ public void setRange(Range range) {
+ super.setRange(range, true, true);
+ setupSmallLogFlag(); // setup flag based on bounds values
+ }
+
+ /**
+ * Sets up flag for log axis processing.
+ */
+ @Override
+ protected void setupSmallLogFlag() {
+ // set flag true if negative values not allowed and the
+ // lower bound is between 0 and logBase:
+ final double lowerVal = getRange().getLowerBound();
+ smallLogFlag = (!allowNegativesFlag && lowerVal < LOGBASE && lowerVal > 0.0);
+ }
+
+ /**
+ * Re-scales the axis to ensure that all data is visible.
+ */
+ @Override
+ public void autoAdjustRange() {
+ setupSmallLogFlag(); // setup flag based on bounds values
+ double lower = computeLogFloor(dataRange.getLowerBound());
+ double upper = computeCeiling(dataRange.getUpperBound());
+ if (lower > upper) {
+ lower = upper;
+ }
+ setRange(new Range(lower, upper));
+ }
+
+ /**
+ * Zooms in on the current range (currently not implemented).
+ *
+ * @param lowerPercent the new lower bound.
+ * @param upperPercent the new upper bound.
+ */
+ @Override
+ public void zoomRange(double lowerPercent, double upperPercent) {
+ // Zoom into logarithmic axis is disabled.
+ }
+
+ /**
+ * Returns the smallest (closest to negative infinity) double value that is not less than the argument, is
+ * equal to a mathematical integer and satisfying the condition that log base of the value is an integer
+ * (i.e., the value returned will be a power of 10 for logBase=10: 1, 10, 100, 1000, etc.).
+ *
+ * @param upper a double value above which a ceiling will be calculated.
+ * @return logBase<sup>N</sup> with N .. { 1 ... }
+ */
+ @Override
+ protected double computeLogCeil(double upper) {
+ double logCeil = allticks[allticks.length - 1];
+
+ for (int i = allticks.length - 1; i >= 0; i--) {
+ if (allticks[i] >= upper)
+ logCeil = allticks[i];
+ }
+ return logCeil;
+ }
+
+ // TODO: Add Javadoc
+ private double computeCeiling(double aUpper) {
+ double ceiling = 1;
+ int i = allticks.length - 1;
+ while (i >= 0 && allticks[i] >= aUpper) {
+ ceiling = allticks[i];
+ i--;
+ }
+ if (i > 0 && ceiling > 1) {
+ double step = (allticks[i] != 0) ? allticks[i] : allticks[i + 1] / 10;
+ double c = 2 * step;
+ for (int j = 2; j < 10; ++j, c += step) {
+ if (c >= aUpper) {
+ ceiling = c;
+ break;
+ }
+ }
+ }
+ return ceiling;
+ }
+
+ /**
+ * Returns the largest (closest to positive infinity) double value that is not greater than the argument,
+ * is equal to a mathematical integer and satisfying the condition that log base of the value is an
+ * integer (i.e., the value returned will be a power of 10 for logBase=10: 1, 10, 100, 1000, etc.).
+ *
+ * @param lower a double value below which a floor will be calculated.
+ * @return logBase<sup>N</sup> with N .. { 1 ... }
+ */
+ @Override
+ protected double computeLogFloor(double lower) {
+ double logFloor = allticks[1];
+
+ for (int i = 1; i < allticks.length; i++) {
+ if (allticks[i] <= lower)
+ logFloor = allticks[i];
+ }
+ return logFloor;
+ }
+
+ /**
+ * Main change of Logarithmic class that overwrites super method. Calculates the values of the
+ * System.out.println("Upper = " + aUpper + "\tCeiling = " + ceiling); tick labels for the axis, storing
+ * the results in the tick label list (ready for drawing).
+ *
+ * @param g2 the graphics device.
+ * @param dataArea the area in which the plot should be drawn.
+ * @param edge Rectangle edge for axis location.
+ * @return A list of ticks.
+ */
+ @Override
+ public List<?> refreshTicksVertical(Graphics2D g2, Rectangle2D dataArea, RectangleEdge edge) {
+
+ // Ticklist that has to be filled with sensible values
+ List<Tick> ticks = new ArrayList<Tick>();
+
+ // Formatting of the tick labels
+ TextAnchor anchor = null;
+ TextAnchor rotationAnchor = null;
+ double angle = 0.0;
+ if (isVerticalTickLabels()) {
+ if (edge == RectangleEdge.LEFT) {
+ anchor = TextAnchor.BOTTOM_CENTER;
+ rotationAnchor = TextAnchor.BOTTOM_CENTER;
+ angle = -Math.PI / 2.0;
+ } else {
+ anchor = TextAnchor.BOTTOM_CENTER;
+ rotationAnchor = TextAnchor.BOTTOM_CENTER;
+ angle = Math.PI / 2.0;
+ }
+ } else {
+ if (edge == RectangleEdge.LEFT) {
+ anchor = TextAnchor.CENTER_RIGHT;
+ rotationAnchor = TextAnchor.CENTER_RIGHT;
+ } else {
+ anchor = TextAnchor.TOP_CENTER;
+ rotationAnchor = TextAnchor.TOP_CENTER;
+ }
+ }
+
+ List<Double> myticks = new ArrayList<Double>();
+
+ double lowerBound = dataRange.getLowerBound();
+ double upperBound = dataRange.getUpperBound();
+
+ // Select minimal tick set that fully contains the data range
+ for (int i = 0; i < allticks.length - 1; i++) {
+ if (allticks[i + 1] > lowerBound && allticks[i] <= upperBound) {
+ myticks.add(new Double(allticks[i]));
+ }
+ }
+
+ boolean isLastTickAdded = false;
+ final boolean sci = (myticks.size() > 4);
+
+ // Add all ticks that were selected before and their eight following unlabeled subticks
+ for (final Double tick : myticks) {
+ final double t = tick.doubleValue();
+ ticks.add(new NumberTick(tick, toString(t, sci), anchor, rotationAnchor, angle));
+ if (t < upperBound) {
+ for (int j = 2; j < 10; j++) {
+ double s = (t == 0.0 ? allticks[1] / 10.0 : t) * j; // to allows subticks from 0
+ String label = "";
+ if (s >= upperBound) {
+ isLastTickAdded = true;
+ label = toString(s, sci);
+ }
+ ticks.add(new NumberTick(new Double(s), label, anchor, rotationAnchor, angle));
+ if (isLastTickAdded) {
+ break;
+ }
+ }
+ }
+ }
+
+ // Add the very last tick value
+ if (!isLastTickAdded) {
+ Double t = new Double(computeLogCeil(upperBound));
+ ticks.add(new NumberTick(t, toString(t, sci), anchor, rotationAnchor, angle));
+ }
+
+ return ticks;
+ }
+
+ /**
+ * Main change of Logarithmic class that overwrites super method. Calculates the positions of the tick
+ * labels for the axis, storing the results in the tick label list (ready for drawing).
+ *
+ * @param g2 the graphics device.
+ * @param dataArea the area in which the plot should be drawn.
+ * @param edge Rectangle edge for axis location.
+ * @return A list of ticks.
+ */
+ @Override
+ public List<?> refreshTicksHorizontal(Graphics2D g2, Rectangle2D dataArea, RectangleEdge edge) {
+ return refreshTicksVertical(g2, dataArea, edge);
+ }
+
+ /**
+ * Returns the log value, depending on if values between 0 and 1 are being plotted.
+ *
+ * @param val the value.
+ *
+ * @return adjusted log value
+ */
+ protected double switchedLog(double val) {
+ return adjustedLog(val);
+ }
+
+ /**
+ * Returns the log value, depending on if values between 0 and 1 are being plotted.
+ *
+ * @param val the value.
+ *
+ * @return adjusted log value
+ */
+ @Override
+ protected double switchedLog10(double val) {
+ return adjustedLog(val);
+ }
+
+ /**
+ * Returns an adjusted log value for graphing purposes. The first adjustment is that negative values are
+ * changed to positive during the calculations, and then the answer is negated at the end. The second is
+ * that, for values less than the log base, an increasingly large (0 to 1) scaling factor is added such
+ * that at 0 the value is adjusted to 1, resulting in a returned result of 0.
+ *
+ * @param val the value.
+ * @return the adjusted value.
+ */
+ public double adjustedLog(double val) {
+ double value = 0.0;
+ if (val == 0.0)
+ value = 0.0;
+ else {
+ for (int i = 1; i < allticks.length; ++i) {
+ if (val <= allticks[i]) {
+ value = log(LOGBASE, ((val * 10) / allticks[i])) + offset + i - 1;
+ }
+ }
+ }
+ return value;
+ }
+
+ /**
+ * Compute logarithm of <i>power</i> with base <i>base</i>.
+ *
+ * @param base Base for logarithm.
+ * @param power Value to compute logarithm of.
+ * @return Exponent. The logarithm with base <i>base</i> of <i>power</i>.
+ * @see <a href="http://www.math.utah.edu/~alfeld/math/log.html">What on Earth is a Logarithm?</a>
+ */
+ protected double log(double base, double power) {
+ return Math.log(power) / Math.log(base);
+ }
+
+ /**
+ * Gives the <code>String</code> representation of the given number.
+ *
+ * @param aValue Number to be converted to <code>String</code>.
+ * @param aScientific Flag indicating if scientific notation is preferred.
+ * @return String representation of <code>aValue</code>.
+ */
+ private static String toString(Double aValue, boolean aScientific) {
+ return toString(aValue.doubleValue(), aScientific);
+ }
+
+ /**
+ * Gives the <code>String</code> representation of the given number.
+ *
+ * @param aValue Number to be converted to <code>String</code>.
+ * @param aScientific Flag indicating if scientific notation is preferred.
+ * @return String representation of <code>aValue</code>.
+ */
+ private static String toString(double aValue, boolean aScientific) {
+ final int intValue = (int) aValue;
+ if (intValue == aValue) {
+ if (intValue == 0 || intValue == 1 || aScientific == false) {
+ return String.valueOf(intValue);
+ }
+ }
+ if (aScientific) {
+ return new DecimalFormat("0.#####E0#").format(aValue);
+ }
+ return String.valueOf(aValue);
+ }
+
+ /**
+ * Unique ID for this version of this class. It is used in serialization.
+ */
+ private static final long serialVersionUID = -3172819531427016894L;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/dec/FitData.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/dec/FitData.java
new file mode 100644
index 0000000..7a538b4
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/dec/FitData.java
@@ -0,0 +1,152 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.ui.dec;
+
+import java.awt.geom.Point2D;
+
+/**
+ * Data on a fitted function which is presented to the user.
+ *
+ * @author Yassen Assenov
+ */
+public class FitData {
+
+ /**
+ * Initializes a new instance of <code>FitData</code> without additional note.
+ *
+ * @param aMessage Message indicating the fitting function that was used.
+ * @param aCoefs Coefficients of the fitted function.
+ * @param aCorrelation Correlation between the original and fitted data points. Set this
+ * parameter to <code>null</code> if correlation is not computed.
+ * @param aRSquared Coefficient of determination (R-squared value) of the fitted points. Set
+ * this parameter to <code>null</code> if r-squared is not computed.
+ * @param aHelpURL URL of the help page (or section) about the fitted function.
+ */
+ public FitData(String aMessage, Point2D.Double aCoefs, Double aCorrelation, Double aRSquared, String aHelpURL) {
+ this(aMessage, aCoefs, aCorrelation, aRSquared, aHelpURL, null);
+ }
+
+ /**
+ * Initializes a new instance of <code>FitData</code>.
+ *
+ * @param aMessage Message indicating the fitting function that was used.
+ * @param aCoefs Coefficients of the fitted function.
+ * @param aCorrelation Correlation between the original and fitted data points. Set this
+ * parameter to <code>null</code> if correlation is not computed.
+ * @param aRSquared Coefficient of determination (R-squared value) of the fitted points. Set
+ * this parameter to <code>null</code> if r-squared is not computed.
+ * @param aHelpURL URL of the help page (or section) about the fitted function.
+ * @param aNote Additional note to be displayed, if any.
+ */
+ public FitData(String aMessage, Point2D.Double aCoefs, Double aCorrelation, Double aRSquared, String aHelpURL, String aNote) {
+ message = aMessage;
+ coefs = aCoefs;
+ correlation = aCorrelation;
+ rSquared = aRSquared;
+ helpURL = aHelpURL;
+ note = aNote;
+ }
+
+ /**
+ * Gets a human-readable message about the fitted function.
+ *
+ * @return Message indicating the fitting function that was used.
+ */
+ public String getMessage() {
+ return message;
+ }
+
+ /**
+ * Gets the coefficients of the fitted function.
+ *
+ * @return Coefficients of the fitted function. Interpretation of these coefficients depends on
+ * the type of fitted function.
+ */
+ public Point2D.Double getCoefs() {
+ return coefs;
+ }
+
+ /**
+ * Get the value for the correlation.
+ *
+ * @return Correlation between the original and fitted data points; <code>null</code> if
+ * correlation is not computed.
+ */
+ public Double getCorrelation() {
+ return correlation;
+ }
+
+ /**
+ * Gets the r-squared value.
+ *
+ * @return Coefficient of determination (R-squared value) of the fitted points;
+ * <code>null</code> if r-squared is not computed.
+ */
+ public Double getRSquared() {
+ return rSquared;
+ }
+
+ /**
+ * Gets the help URL about the fitted function.
+ *
+ * @return URL of the help page (or section) about the fitted function.
+ */
+ public String getHelpURL() {
+ return helpURL;
+ }
+
+ /**
+ * Gets the note to displayed.
+ *
+ * @return Additional note to be displayed; <code>null</code> if no additional note should be
+ * displayed.
+ */
+ public String getNote() {
+ return note;
+ }
+
+ /**
+ * Message indicating the fitting function that was used.
+ */
+ private String message;
+
+ /**
+ * Coefficients of the fitted function.
+ */
+ private Point2D.Double coefs;
+
+ /**
+ * Correlation between the original and fitted data points.
+ */
+ private Double correlation;
+
+ /**
+ * Coefficient of determination.
+ */
+ private Double rSquared;
+
+ /**
+ * URL of the help page (or section) about the fitted function.
+ */
+ private String helpURL;
+
+ /**
+ * Notes to be given, if any.
+ */
+ private String note;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/dec/FittingReportDialog.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/dec/FittingReportDialog.java
new file mode 100644
index 0000000..45ae9cd
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/dec/FittingReportDialog.java
@@ -0,0 +1,194 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.ui.dec;
+
+import java.awt.BorderLayout;
+import java.awt.Component;
+import java.awt.Dialog;
+import java.awt.FlowLayout;
+import java.awt.Frame;
+import java.awt.GridLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.geom.Point2D;
+
+import javax.swing.Box;
+import javax.swing.BoxLayout;
+import javax.swing.JButton;
+import javax.swing.JDialog;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JTextField;
+import javax.swing.SwingConstants;
+
+import cytoscape.util.OpenBrowser;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Messages;
+import de.mpg.mpi_inf.bioinf.netanalyzer.ui.Utils;
+
+/**
+ * Dialog window which reports the results after fitting a function.
+ *
+ * @author Yassen Assenov
+ */
+public class FittingReportDialog extends JDialog implements ActionListener {
+
+ /**
+ * Initializes the common controls of <code>FittingReportDialog</code>.
+ *
+ * @param aOwner The <code>Frame</code> from which this dialog is displayed.
+ * @param aTitle Dialog's title.
+ * @param aData Fit data to be displayed, encapsulated in a <code>FitData</code> instance.
+ */
+ public FittingReportDialog(Frame aOwner, String aTitle, FitData aData) {
+ super(aOwner, aTitle, true);
+ initControls(aData);
+ setLocationRelativeTo(aOwner);
+ }
+
+ /**
+ * Initializes the common controls of <code>FittingReportDialog</code>.
+ *
+ * @param aOwner The <code>Dialog</code> from which this dialog is displayed.
+ * @param aTitle Dialog's title.
+ * @param aData Fit data to be displayed, encapsulated in a <code>FitData</code> instance.
+ */
+ public FittingReportDialog(Dialog aOwner, String aTitle, FitData aData) {
+ super(aOwner, aTitle, true);
+ initControls(aData);
+ setLocationRelativeTo(aOwner);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.event.ActionListener#actionPerformed(java.awt.event.ActionEvent)
+ */
+ public void actionPerformed(ActionEvent e) {
+ final Object src = e.getSource();
+ if (src == btnOK) {
+ setVisible(false);
+ dispose();
+ } else if (src == btnHelp) {
+ OpenBrowser.openURL(helpURL);
+ }
+ }
+
+ /**
+ * Unique ID for this version of this class. It is used in serialization.
+ */
+ private static final long serialVersionUID = 1519314486190160307L;
+
+ /**
+ * Creates and lays out the controls inside this dialog.
+ * <p>
+ * This method is called upon initialization only.
+ * </p>
+ *
+ * @param aData Fit data to be displayed.
+ */
+ private void initControls(FitData aData) {
+ final int bs = Utils.BORDER_SIZE;
+ final JPanel contentPane = new JPanel(new BorderLayout(0, bs));
+ Utils.setStandardBorder(contentPane);
+ final Box boxData = new Box(BoxLayout.PAGE_AXIS);
+ contentPane.add(boxData, BorderLayout.CENTER);
+
+ // Display informative message to the user
+ contentPane.add(new JLabel(aData.getMessage(), SwingConstants.CENTER), BorderLayout.NORTH);
+
+ // Display coefficients of the fitted function
+ final Point2D.Double coefs = aData.getCoefs();
+ final JTextField txfA = new JTextField(Utils.doubleToString(coefs.x, 6, 3));
+ txfA.setEditable(false);
+ txfA.setColumns(9);
+ final JTextField txfB = new JTextField(Utils.doubleToString(coefs.y, 6, 3));
+ txfB.setEditable(false);
+ txfB.setColumns(9);
+ final Box boxCoefs = new Box(BoxLayout.LINE_AXIS);
+ boxCoefs.add(new JLabel("a = "));
+ boxCoefs.add(txfA);
+ boxCoefs.add(Box.createHorizontalStrut(bs * 2));
+ boxCoefs.add(new JLabel("b = "));
+ boxCoefs.add(txfB);
+ boxCoefs.add(Box.createHorizontalGlue());
+ boxCoefs.setAlignmentX(Component.CENTER_ALIGNMENT);
+ boxData.add(boxCoefs);
+ boxData.add(Box.createVerticalStrut(bs * 2));
+
+ // Display goodness fit measures
+ final JPanel panMeasures = new JPanel(new GridLayout(0, 2, bs, bs));
+ final Double corr = aData.getCorrelation();
+ if (corr != null) {
+ createReport(panMeasures, Messages.DI_CORR, corr);
+ }
+ final Double rSquared = aData.getRSquared();
+ if (rSquared != null) {
+ createReport(panMeasures, Messages.DI_RSQUARED, rSquared);
+ }
+ if (corr != null || rSquared != null) {
+ panMeasures.setAlignmentX(Component.CENTER_ALIGNMENT);
+ boxData.add(panMeasures);
+ boxData.add(Box.createVerticalStrut(bs * 2));
+ }
+
+ // Display a note
+ final String note = aData.getNote();
+ if (note != null && note.length() > 0) {
+ final JLabel label = new JLabel("<html><b>Note:</b> " + note + "</html>");
+ label.setAlignmentX(Component.CENTER_ALIGNMENT);
+ boxData.add(label);
+ boxData.add(Box.createVerticalStrut(bs * 2));
+ }
+
+ // Add "OK" and "Help" buttons
+ JPanel bottomPanel = new JPanel(new FlowLayout(FlowLayout.CENTER, bs, 0));
+ btnOK = Utils.createButton(Messages.DI_OK, null, this);
+ btnHelp = Utils.createButton(Messages.DI_HELP, null, this);
+ helpURL = aData.getHelpURL();
+ Utils.equalizeSize(btnOK, btnHelp);
+ bottomPanel.add(btnOK);
+ bottomPanel.add(btnHelp);
+ contentPane.add(bottomPanel, BorderLayout.SOUTH);
+
+ setContentPane(contentPane);
+ pack();
+ }
+
+ private void createReport(JPanel aPanel, String aMessage, Double aValue) {
+ aPanel.add(new JLabel(aMessage, SwingConstants.TRAILING));
+ final JTextField txf = new JTextField(Utils.doubleToString(aValue, 6, 3));
+ txf.setEditable(false);
+ txf.setColumns(9);
+ aPanel.add(txf);
+ }
+
+ /**
+ * "OK" button.
+ */
+ private JButton btnOK;
+
+ /**
+ * "Help" button.
+ */
+ private JButton btnHelp;
+
+ /**
+ * URL to be visited when the user clicks on the "Help" button.
+ */
+ private String helpURL;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/filter/ComplexParamFilterDialog.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/filter/ComplexParamFilterDialog.java
new file mode 100644
index 0000000..483e723
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/filter/ComplexParamFilterDialog.java
@@ -0,0 +1,141 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.ui.filter;
+
+import java.awt.BorderLayout;
+import java.awt.Dialog;
+import java.awt.FlowLayout;
+import java.awt.GridLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import javax.swing.JButton;
+import javax.swing.JDialog;
+import javax.swing.JPanel;
+
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Messages;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.filter.ComplexParamFilter;
+import de.mpg.mpi_inf.bioinf.netanalyzer.ui.Utils;
+
+/**
+ * Base class for all dialogs for creating filters by the user.
+ *
+ * @author Yassen Assenov
+ */
+public abstract class ComplexParamFilterDialog extends JDialog
+ implements ActionListener {
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.awt.event.ActionListener#actionPerformed(java.awt.event.ActionEvent)
+ */
+ public void actionPerformed(ActionEvent e) {
+ Object source = e.getSource();
+ if (btnOK == source) {
+ btnOK = null;
+ setVisible(false);
+ } else if (btnCancel == source) {
+ setVisible(false);
+ }
+ }
+
+ /**
+ * Displays the dialog and initializes a filter based on user's input.
+ *
+ * @return Instance of a class extending <code>ComplexParamFilter</code> reflecting the user's
+ * filtering criteria; <code>null</code> if the user has pressed the
+ * "Cancel" button.
+ */
+ public ComplexParamFilter showDialog() {
+ setModal(true); // make sure this window is modal
+ setVisible(true);
+ if (btnOK == null) {
+ // User has pressed OK
+ return createFilter();
+ }
+ // User has pressed Cancel
+ return null;
+ }
+
+ /**
+ * Initializes the common controls of <code>ComplexParamFilterDialog</code>.
+ *
+ * @param aOwner The <code>Dialog</code> from which this dialog is displayed.
+ * @param aTitle Dialog's title.
+ */
+ protected ComplexParamFilterDialog(Dialog aOwner, String aTitle) {
+ super(aOwner, aTitle, true);
+ initControls();
+ }
+
+ /**
+ * Creates and initializes a filter instance based on user's input.
+ *
+ * @return Instance of a class extending <code>ComplexParamFilter</code> reflecting the user's
+ * filtering criteria.
+ */
+ protected abstract ComplexParamFilter createFilter();
+
+ /**
+ * "OK" button.
+ */
+ protected JButton btnOK;
+
+ /**
+ * "Cancel" button.
+ */
+ protected JButton btnCancel;
+
+ /**
+ * Panel in the dialog that contains filter-specific controls.
+ */
+ protected JPanel centralPane;
+
+ /**
+ * Unique ID for this version of this class. It is used in serialization.
+ */
+ private static final long serialVersionUID = -5390738966565631892L;
+
+ /**
+ * Creates and lays out the common controls for this dialog.
+ * <p>
+ * The common controls include a central panel for adding filter-specific controls and
+ * "OK" and "Cancel" buttons.
+ * </p>
+ */
+ private void initControls() {
+ final int BS = Utils.BORDER_SIZE;
+ final JPanel contentPane = new JPanel(new BorderLayout(BS, BS));
+ Utils.setStandardBorder(contentPane);
+
+ centralPane = new JPanel(new FlowLayout(FlowLayout.CENTER, 0, 0));
+ contentPane.add(centralPane, BorderLayout.CENTER);
+
+ // Add OK and Cancel Buttons
+ JPanel buttonsPanel = new JPanel(new GridLayout(1, 2, Utils.BORDER_SIZE, 0));
+ btnOK = Utils.createButton(Messages.DI_OK, null, this);
+ btnCancel = Utils.createButton(Messages.DI_CANCEL, null, this);
+ buttonsPanel.add(btnOK);
+ buttonsPanel.add(btnCancel);
+ JPanel bottomPanel = new JPanel(new FlowLayout(FlowLayout.CENTER, 0, 0));
+ bottomPanel.add(buttonsPanel);
+ contentPane.add(bottomPanel, BorderLayout.SOUTH);
+ setContentPane(contentPane);
+ }
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/filter/IntHistogramFilterDialog.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/filter/IntHistogramFilterDialog.java
new file mode 100644
index 0000000..22d49b3
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/filter/IntHistogramFilterDialog.java
@@ -0,0 +1,113 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.ui.filter;
+
+import java.awt.Dialog;
+
+import javax.swing.JLabel;
+import javax.swing.JSpinner;
+import javax.swing.SpinnerModel;
+import javax.swing.SpinnerNumberModel;
+import javax.swing.SpringLayout;
+import javax.swing.SwingConstants;
+
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.IntHistogram;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.filter.ComplexParamFilter;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.filter.IntHistogramFilter;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.settings.IntHistogramGroup;
+import de.mpg.mpi_inf.bioinf.netanalyzer.ui.SpringUtilities;
+import de.mpg.mpi_inf.bioinf.netanalyzer.ui.Utils;
+
+/**
+ * Dialog for creating {@link de.mpg.mpi_inf.bioinf.netanalyzer.data.filter.IntHistogramFilter} based on
+ * user's input.
+ *
+ * @author Yassen Assenov
+ */
+public class IntHistogramFilterDialog extends ComplexParamFilterDialog {
+
+ /**
+ * Initializes a new instance of <code>IntHistogramFilterDialog</code> based on the given IntHistgoram
+ * instance.
+ *
+ * @param aOwner The <code>Dialog</code> from which this dialog is displayed.
+ * @param aTitle Title of the dialog.
+ * @param aHistogram Histogram instance, based on which the ranges for the minimum and maximum degrees are
+ * to be chosen.
+ * @param aSettings Visual settings for <code>aHistogram</code>.
+ */
+ public IntHistogramFilterDialog(Dialog aOwner, String aTitle, IntHistogram aHistogram,
+ IntHistogramGroup aSettings) {
+ super(aOwner, aTitle);
+
+ populate(aHistogram, aSettings);
+ pack();
+ setResizable(false);
+ setLocationRelativeTo(aOwner);
+ }
+
+ /**
+ * Creates and initializes a filter instance based on user's choice for minimum and maximum degree.
+ *
+ * @return Instance of <code>IntHistogramFilter</code> reflecting the user's filtering criteria.
+ */
+ @Override
+ protected ComplexParamFilter createFilter() {
+ return new IntHistogramFilter(Utils.getSpinnerInt(spnMin), Utils.getSpinnerInt(spnMax));
+ }
+
+ /**
+ * Unique ID for this version of this class. It is used in serialization.
+ */
+ private static final long serialVersionUID = 1556691517305385646L;
+
+ /**
+ * Creates and lays out the two spinner controls for choosing minimum and maximum degree.
+ *
+ * @param aHistogram Histogram instance, based on which the ranges for the minimum and maximum degrees are
+ * to be chosen.
+ * @param aSettings Visual settings for <code>aHistogram</code>.
+ */
+ private void populate(IntHistogram aHistogram, IntHistogramGroup aSettings) {
+ centralPane.setLayout(new SpringLayout());
+ int[] range = aHistogram.getObservedRange();
+
+ // Add a spinner for minimum observation
+ centralPane.add(new JLabel(aSettings.filter.getMinObservationLabel() + ":", SwingConstants.RIGHT));
+ SpinnerModel minSettings = new SpinnerNumberModel(range[0], range[0], range[1], 1);
+ centralPane.add(spnMin = new JSpinner(minSettings));
+
+ // Add a spinner for maximum observation
+ centralPane.add(new JLabel(aSettings.filter.getMaxObservationLabel() + ":", SwingConstants.RIGHT));
+ SpinnerModel maxSettings = new SpinnerNumberModel(range[1], range[0], range[1], 1);
+ centralPane.add(spnMax = new JSpinner(maxSettings));
+
+ final int gap = Utils.BORDER_SIZE / 2;
+ SpringUtilities.makeCompactGrid(centralPane, 2, 2, 0, 0, gap, gap);
+ }
+
+ /**
+ * Spinner to choose the maximum observation value to display.
+ */
+ private JSpinner spnMin;
+
+ /**
+ * Spinner to choose the maximum observation value to display.
+ */
+ private JSpinner spnMax;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/filter/LongHistogramFilterDialog.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/filter/LongHistogramFilterDialog.java
new file mode 100644
index 0000000..03ac721
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/filter/LongHistogramFilterDialog.java
@@ -0,0 +1,117 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.ui.filter;
+
+import java.awt.Dialog;
+
+import javax.swing.JLabel;
+import javax.swing.JSpinner;
+import javax.swing.SpinnerModel;
+import javax.swing.SpinnerNumberModel;
+import javax.swing.SpringLayout;
+import javax.swing.SwingConstants;
+
+
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.LongHistogram;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.filter.ComplexParamFilter;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.filter.LongHistogramFilter;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.settings.LongHistogramGroup;
+import de.mpg.mpi_inf.bioinf.netanalyzer.ui.SpringUtilities;
+import de.mpg.mpi_inf.bioinf.netanalyzer.ui.Utils;
+
+/**
+ * Dialog for creating {@link de.mpg.mpi_inf.bioinf.netanalyzer.data.filter.LongHistogramFilter} based on
+ * user's input.
+ *
+ * @author Yassen Assenov
+ * @author Sven-Eric Schelhorn
+ */
+public class LongHistogramFilterDialog extends ComplexParamFilterDialog {
+
+ /**
+ * Initializes a new instance of <code>LongHistogramFilterDialog</code> based on the given
+ * IntHistgoram instance.
+ *
+ * @param aOwner The <code>Dialog</code> from which this dialog is displayed.
+ * @param aTitle Title of the dialog.
+ * @param aHistogram LongHistogram instance, based on which the ranges for the minimum and maximum
+ * degrees are to be chosen.
+ * @param aSettings Visual settings for <code>aHistogram</code>.
+ */
+ public LongHistogramFilterDialog(Dialog aOwner, String aTitle, LongHistogram aHistogram,
+ LongHistogramGroup aSettings) {
+ super(aOwner, aTitle);
+
+ populate(aHistogram, aSettings);
+ pack();
+ setResizable(false);
+ setLocationRelativeTo(aOwner);
+ }
+
+ /**
+ * Creates and initializes a filter instance based on user's choice for minimum and maximum
+ * degree.
+ *
+ * @return Instance of <code>LongHistogramFilter</code> reflecting the user's filtering
+ * criteria.
+ */
+ @Override
+ protected ComplexParamFilter createFilter() {
+ return new LongHistogramFilter(Utils.getSpinnerInt(spnMin), Utils.getSpinnerInt(spnMax));
+ }
+
+ /**
+ * Unique ID for this version of this class. It is used in serialization.
+ */
+ private static final long serialVersionUID = 1556691517305385646L;
+
+ /**
+ * Creates and lays out the two spinner controls for choosing minimum and maximum degree.
+ *
+ * @param aHistogram Histogram instance, based on which the ranges for the minimum and maximum
+ * degrees are to be chosen.
+ * @param aSettings Visual settings for <code>aHistogram</code>.
+ */
+ private void populate(LongHistogram aHistogram, LongHistogramGroup aSettings) {
+ centralPane.setLayout(new SpringLayout());
+ long[] range = aHistogram.getObservedRange();
+
+ // Add a spinner for minimum observation
+ centralPane.add(new JLabel(aSettings.filter.getMinObservationLabel() + ":", SwingConstants.RIGHT));
+ SpinnerModel minSettings = new SpinnerNumberModel(range[0], range[0], range[1], 1);
+ centralPane.add(spnMin = new JSpinner(minSettings));
+
+ // Add a spinner for maximum observation
+ centralPane.add(new JLabel(aSettings.filter.getMaxObservationLabel() + ":", SwingConstants.RIGHT));
+ SpinnerModel maxSettings = new SpinnerNumberModel(range[1], range[0], range[1], 1);
+ centralPane.add(spnMax = new JSpinner(maxSettings));
+
+ final int gap = Utils.BORDER_SIZE / 2;
+ SpringUtilities.makeCompactGrid(centralPane, 2, 2, 0, 0, gap, gap);
+ }
+
+ /**
+ * Spinner to choose the maximum observation value to display.
+ */
+ private JSpinner spnMin;
+
+ /**
+ * Spinner to choose the maximum observation value to display.
+ */
+ private JSpinner spnMax;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/filter/Points2DFilterDialog.java b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/filter/Points2DFilterDialog.java
new file mode 100644
index 0000000..8e57de0
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/filter/Points2DFilterDialog.java
@@ -0,0 +1,188 @@
+/*
+ * Copyright (c) 2006, 2007, 2008, 2010, Max Planck Institute for Informatics, Saarbruecken, Germany.
+ *
+ * This file is part of NetworkAnalyzer.
+ *
+ * NetworkAnalyzer is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * NetworkAnalyzer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
+ * implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with NetworkAnalyzer. If not, see
+ * <http://www.gnu.org/licenses/>.
+ */
+
+package de.mpg.mpi_inf.bioinf.netanalyzer.ui.filter;
+
+import java.awt.Dialog;
+import java.awt.Dimension;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.text.NumberFormat;
+import java.text.ParseException;
+import java.util.Locale;
+
+import javax.swing.JFormattedTextField;
+import javax.swing.JLabel;
+import javax.swing.SpringLayout;
+import javax.swing.SwingConstants;
+
+import de.mpg.mpi_inf.bioinf.netanalyzer.InnerException;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Points2D;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.filter.ComplexParamFilter;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.filter.Points2DFilter;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.settings.Points2DGroup;
+import de.mpg.mpi_inf.bioinf.netanalyzer.ui.SpringUtilities;
+import de.mpg.mpi_inf.bioinf.netanalyzer.ui.Utils;
+
+/**
+ * Dialog for creating {@link de.mpg.mpi_inf.bioinf.netanalyzer.data.filter.Points2DFilter} based on user's
+ * input.
+ *
+ * @author Yassen Assenov
+ */
+public class Points2DFilterDialog extends ComplexParamFilterDialog implements PropertyChangeListener {
+
+ /**
+ * Initializes a new instance of <code>Points2DFilterDialog</code> based on the given
+ * <code>Points2D</code> instance.
+ *
+ * @param aOwner The <code>Dialog</code> from which this dialog is displayed.
+ * @param aTitle Title of the dialog.
+ * @param aPoints Data points, based on which the ranges for the minimum and maximum coordinate values are
+ * to be chosen.
+ * @param aSettings Visual settings for <code>aPoints</code>.
+ */
+ public Points2DFilterDialog(Dialog aOwner, String aTitle, Points2D aPoints, Points2DGroup aSettings) {
+ super(aOwner, aTitle);
+
+ populate(aPoints, aSettings);
+ pack();
+ setResizable(false);
+ setLocationRelativeTo(aOwner);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.beans.PropertyChangeListener#propertyChange(java.beans.PropertyChangeEvent)
+ */
+ public void propertyChange(PropertyChangeEvent evt) {
+ updateStatus();
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see de.mpg.mpi_inf.bioinf.netanalyzer.ui.filter.ComplexParamFilterDialog#createFilter()
+ */
+ @Override
+ protected ComplexParamFilter createFilter() {
+ try {
+ final double xmin = formatter.parse(txfXMin.getText()).doubleValue();
+ final double xmax = formatter.parse(txfXMax.getText()).doubleValue();
+ return new Points2DFilter(xmin, xmax);
+ } catch (ParseException ex) {
+ throw new InnerException(ex);
+ }
+ }
+
+ /**
+ * Unique ID for this version of this class. It is used in serialization.
+ */
+ private static final long serialVersionUID = 4746985046081748678L;
+
+ /**
+ * Number formatting style used in the text fields.
+ */
+ private static final NumberFormat formatter = NumberFormat.getInstance(Locale.US);
+
+ /**
+ *
+ * @param aPoints Data points, based on which the ranges for the minimum and maximum coordinate values are
+ * to be chosen.
+ * @param aSettings Visual settings for <code>aPoints</code>.
+ */
+ private void populate(Points2D aPoints, Points2DGroup aSettings) {
+ centralPane.setLayout(new SpringLayout());
+ rangeX = aPoints.getRangeX();
+
+ formatter.setParseIntegerOnly(false);
+ formatter.setMaximumFractionDigits(12);
+
+ // Add a text field for minimum x
+ centralPane.add(new JLabel(aSettings.filter.getMinXLabel() + ":", SwingConstants.RIGHT));
+ centralPane.add(txfXMin = new JFormattedTextField(formatter));
+ final Dimension size = txfXMin.getPreferredSize();
+ size.width = 70;
+ txfXMin.setPreferredSize(size);
+ txfXMin.setValue(new Double(xMin = rangeX[0]));
+ txfXMin.addPropertyChangeListener("value", this);
+
+ // Add a text field for maximum x
+ centralPane.add(new JLabel(aSettings.filter.getMaxXLabel() + ":", SwingConstants.RIGHT));
+ centralPane.add(txfXMax = new JFormattedTextField(formatter));
+ txfXMax.setPreferredSize(size);
+ txfXMax.setValue(new Double(xMax = rangeX[1]));
+ txfXMax.addPropertyChangeListener("value", this);
+
+ final int gap = Utils.BORDER_SIZE / 2;
+ SpringUtilities.makeCompactGrid(centralPane, 2, 2, 0, 0, gap, gap);
+ }
+
+ /**
+ * Updates the status of the OK button based on the values entered in the text fields of this dialog.
+ */
+ private void updateStatus() {
+ try {
+ xMin = formatter.parse(txfXMin.getText()).doubleValue();
+ if (xMin < rangeX[0] || xMin > rangeX[1]) {
+ xMin = Math.min(Math.max(xMin, rangeX[0]), rangeX[1]);
+ txfXMin.setText(String.valueOf(xMin));
+ txfXMin.commitEdit();
+ }
+ } catch (Exception ex) {
+ xMin = Double.MAX_VALUE;
+ }
+ try {
+ xMax = formatter.parse(txfXMax.getText()).doubleValue();
+ if (xMax < rangeX[0] || xMax > rangeX[1]) {
+ xMax = Math.min(Math.max(xMax, rangeX[0]), rangeX[1]);
+ txfXMax.setText(String.valueOf(xMax));
+ txfXMax.commitEdit();
+ }
+ } catch (Exception ex) {
+ xMax = Double.MIN_VALUE;
+ }
+ btnOK.setEnabled(xMin <= xMax);
+ }
+
+ /**
+ * Text field for typing in the value for minimum x.
+ */
+ private JFormattedTextField txfXMin;
+
+ /**
+ * Text field for typing in the value for maximum x.
+ */
+ private JFormattedTextField txfXMax;
+
+ /**
+ * Range of allowed values to be typed for X. The element at index <code>0</code> in this array is the
+ * minimum, and the element at index <code>1</code> - the maximum.
+ */
+ private double[] rangeX;
+
+ /**
+ * New value to be used for minimum x, as typed by the user.
+ */
+ private double xMin;
+
+ /**
+ * New value to be used for maximum x, as typed by the user.
+ */
+ private double xMax;
+}
diff --git a/coreplugins/NetworkAnalyzer/src/main/javadoc/de/mpg/mpi_inf/bioinf/netanalyzer/data/filter/package.html b/coreplugins/NetworkAnalyzer/src/main/javadoc/de/mpg/mpi_inf/bioinf/netanalyzer/data/filter/package.html
new file mode 100644
index 0000000..3b4430e
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/javadoc/de/mpg/mpi_inf/bioinf/netanalyzer/data/filter/package.html
@@ -0,0 +1,10 @@
+<html>
+ <head>
+ </head>
+ <body>
+ <p>Filters of complex parameter types.</p>
+ @author Mario Albrecht
+ @author Yassen Assenov
+ <p>Developed at the Max Planck Institute for Informatics, Saarbrücken, Germany</p>
+ </body>
+</html>
\ No newline at end of file
diff --git a/coreplugins/NetworkAnalyzer/src/main/javadoc/de/mpg/mpi_inf/bioinf/netanalyzer/data/io/package.html b/coreplugins/NetworkAnalyzer/src/main/javadoc/de/mpg/mpi_inf/bioinf/netanalyzer/data/io/package.html
new file mode 100644
index 0000000..ba8fa18
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/javadoc/de/mpg/mpi_inf/bioinf/netanalyzer/data/io/package.html
@@ -0,0 +1,10 @@
+<html>
+ <head>
+ </head>
+ <body>
+ <p>Serialization of network parameters and plugin settings.</p>
+ @author Mario Albrecht
+ @author Yassen Assenov
+ <p>Developed at the Max Planck Institute for Informatics, Saarbrücken, Germany</p>
+ </body>
+</html>
\ No newline at end of file
diff --git a/coreplugins/NetworkAnalyzer/src/main/javadoc/de/mpg/mpi_inf/bioinf/netanalyzer/data/package.html b/coreplugins/NetworkAnalyzer/src/main/javadoc/de/mpg/mpi_inf/bioinf/netanalyzer/data/package.html
new file mode 100644
index 0000000..e385c59
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/javadoc/de/mpg/mpi_inf/bioinf/netanalyzer/data/package.html
@@ -0,0 +1,10 @@
+<html>
+ <head>
+ </head>
+ <body>
+ <p>Data storage classes.</p>
+ @author Mario Albrecht
+ @author Yassen Assenov
+ <p>Developed at the Max Planck Institute for Informatics, Saarbrücken, Germany</p>
+ </body>
+</html>
\ No newline at end of file
diff --git a/coreplugins/NetworkAnalyzer/src/main/javadoc/de/mpg/mpi_inf/bioinf/netanalyzer/data/settings/package.html b/coreplugins/NetworkAnalyzer/src/main/javadoc/de/mpg/mpi_inf/bioinf/netanalyzer/data/settings/package.html
new file mode 100644
index 0000000..1ae9ed7
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/javadoc/de/mpg/mpi_inf/bioinf/netanalyzer/data/settings/package.html
@@ -0,0 +1,10 @@
+<html>
+ <head>
+ </head>
+ <body>
+ <p>Storage classes for various plugin settings.</p>
+ @author Mario Albrecht
+ @author Yassen Assenov
+ <p>Developed at the Max Planck Institute for Informatics, Saarbrücken, Germany</p>
+ </body>
+</html>
\ No newline at end of file
diff --git a/coreplugins/NetworkAnalyzer/src/main/javadoc/de/mpg/mpi_inf/bioinf/netanalyzer/data/ui/package.html b/coreplugins/NetworkAnalyzer/src/main/javadoc/de/mpg/mpi_inf/bioinf/netanalyzer/data/ui/package.html
new file mode 100644
index 0000000..11df12f
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/javadoc/de/mpg/mpi_inf/bioinf/netanalyzer/data/ui/package.html
@@ -0,0 +1,10 @@
+<html>
+ <head>
+ </head>
+ <body>
+ <p>Data storage classes specifically designed to enhance user interface elements.</p>
+ @author Mario Albrecht
+ @author Yassen Assenov
+ <p>Developed at the Max Planck Institute for Informatics, Saarbrücken, Germany</p>
+ </body>
+</html>
\ No newline at end of file
diff --git a/coreplugins/NetworkAnalyzer/src/main/javadoc/de/mpg/mpi_inf/bioinf/netanalyzer/dec/package.html b/coreplugins/NetworkAnalyzer/src/main/javadoc/de/mpg/mpi_inf/bioinf/netanalyzer/dec/package.html
new file mode 100644
index 0000000..d8af682
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/javadoc/de/mpg/mpi_inf/bioinf/netanalyzer/dec/package.html
@@ -0,0 +1,17 @@
+<html>
+ <head>
+ </head>
+ <body>
+ <p>Definitions of chart decorators.</p>
+
+ <p>A decorator is a class that provides additional information on a chart. One decorator can
+ be applied to a chart of one or more complex parameter instances. In its definition in XML
+ settings file, every complex parameter includes information about which decorators can be
+ applied to it. A decorator is activated (applied) by the user by clicking on its button in
+ the chart panel.</p>
+
+ @author Mario Albrecht
+ @author Yassen Assenov
+ <p>Developed at the Max Planck Institute for Informatics, Saarbrücken, Germany</p>
+ </body>
+</html>
\ No newline at end of file
diff --git a/coreplugins/NetworkAnalyzer/src/main/javadoc/de/mpg/mpi_inf/bioinf/netanalyzer/package.html b/coreplugins/NetworkAnalyzer/src/main/javadoc/de/mpg/mpi_inf/bioinf/netanalyzer/package.html
new file mode 100644
index 0000000..7f34aec
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/javadoc/de/mpg/mpi_inf/bioinf/netanalyzer/package.html
@@ -0,0 +1,17 @@
+<html>
+ <head>
+ </head>
+ <body>
+ <p>Base package for the <b>NetworkAnalyzer</b> plugin.</p>
+
+ This package contains the following source elements:
+ <ul>
+ <li>The plugin wrapper class - <code>Plugin</code></li>
+ <li>All <code>CytoscapeAction</code>s the plugin adds to the Cytoscape platform</li>
+ <li>The main control classes - the classes that perform network analysis</li>
+ </ul>
+ @author Mario Albrecht
+ @author Yassen Assenov
+ <p>Developed at the Max Planck Institute for Informatics, Saarbrücken, Germany</p>
+ </body>
+</html>
\ No newline at end of file
diff --git a/coreplugins/NetworkAnalyzer/src/main/javadoc/de/mpg/mpi_inf/bioinf/netanalyzer/sconnect/package.html b/coreplugins/NetworkAnalyzer/src/main/javadoc/de/mpg/mpi_inf/bioinf/netanalyzer/sconnect/package.html
new file mode 100644
index 0000000..9900560
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/javadoc/de/mpg/mpi_inf/bioinf/netanalyzer/sconnect/package.html
@@ -0,0 +1,11 @@
+<html>
+ <head>
+ </head>
+ <body>
+ <p>Classes that manage connections to the MPII server with the purpose of information
+ exchange between the plugin and the server.</p>
+ @author Mario Albrecht
+ @author Yassen Assenov
+ <p>Developed at the Max Planck Institute for Informatics, Saarbrücken, Germany</p>
+ </body>
+</html>
\ No newline at end of file
diff --git a/coreplugins/NetworkAnalyzer/src/main/javadoc/de/mpg/mpi_inf/bioinf/netanalyzer/ui/charts/package.html b/coreplugins/NetworkAnalyzer/src/main/javadoc/de/mpg/mpi_inf/bioinf/netanalyzer/ui/charts/package.html
new file mode 100644
index 0000000..f38d9a2
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/javadoc/de/mpg/mpi_inf/bioinf/netanalyzer/ui/charts/package.html
@@ -0,0 +1,10 @@
+<html>
+ <head>
+ </head>
+ <body>
+ <p>Connectors to chart visualization libraries. Currently, the only supported library is <a href="http://www.jfree.org/jfreechart/">JFreeChart</a>.</p>
+ @author Mario Albrecht
+ @author Yassen Assenov
+ <p>Developed at the Max Planck Institute for Informatics, Saarbrücken, Germany</p>
+ </body>
+</html>
\ No newline at end of file
diff --git a/coreplugins/NetworkAnalyzer/src/main/javadoc/de/mpg/mpi_inf/bioinf/netanalyzer/ui/dec/package.html b/coreplugins/NetworkAnalyzer/src/main/javadoc/de/mpg/mpi_inf/bioinf/netanalyzer/ui/dec/package.html
new file mode 100644
index 0000000..acc806c
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/javadoc/de/mpg/mpi_inf/bioinf/netanalyzer/ui/dec/package.html
@@ -0,0 +1,10 @@
+<html>
+ <head>
+ </head>
+ <body>
+ <p>Set of dialogs related to chart decorators.</p>
+ @author Mario Albrecht
+ @author Yassen Assenov
+ <p>Developed at the Max Planck Institute for Informatics, Saarbrücken, Germany</p>
+ </body>
+</html>
\ No newline at end of file
diff --git a/coreplugins/NetworkAnalyzer/src/main/javadoc/de/mpg/mpi_inf/bioinf/netanalyzer/ui/filter/package.html b/coreplugins/NetworkAnalyzer/src/main/javadoc/de/mpg/mpi_inf/bioinf/netanalyzer/ui/filter/package.html
new file mode 100644
index 0000000..0074eec
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/javadoc/de/mpg/mpi_inf/bioinf/netanalyzer/ui/filter/package.html
@@ -0,0 +1,10 @@
+<html>
+ <head>
+ </head>
+ <body>
+ <p>Set of dialogs for creating complex parameter filters.</p>
+ @author Mario Albrecht
+ @author Yassen Assenov
+ <p>Developed at the Max Planck Institute for Informatics, Saarbrücken, Germany</p>
+ </body>
+</html>
\ No newline at end of file
diff --git a/coreplugins/NetworkAnalyzer/src/main/javadoc/de/mpg/mpi_inf/bioinf/netanalyzer/ui/package.html b/coreplugins/NetworkAnalyzer/src/main/javadoc/de/mpg/mpi_inf/bioinf/netanalyzer/ui/package.html
new file mode 100644
index 0000000..5fbaeab
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/javadoc/de/mpg/mpi_inf/bioinf/netanalyzer/ui/package.html
@@ -0,0 +1,10 @@
+<html>
+ <head>
+ </head>
+ <body>
+ <p>User-interface controls and dialogs displayed by the plugin.</p>
+ @author Mario Albrecht
+ @author Yassen Assenov
+ <p>Developed at the Max Planck Institute for Informatics, Saarbrücken, Germany</p>
+ </body>
+</html>
\ No newline at end of file
diff --git a/coreplugins/NetworkAnalyzer/src/main/resources/de/mpg/mpi_inf/bioinf/netanalyzer/NetworkAnalyzer.xml b/coreplugins/NetworkAnalyzer/src/main/resources/de/mpg/mpi_inf/bioinf/netanalyzer/NetworkAnalyzer.xml
new file mode 100644
index 0000000..2095b16
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/resources/de/mpg/mpi_inf/bioinf/netanalyzer/NetworkAnalyzer.xml
@@ -0,0 +1,524 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<networkanalyzersettings ver="2.7">
+ <plugin>
+ <agreed>false</agreed>
+ <expandable>false</expandable>
+ <nodeattributes>true</nodeattributes>
+ <edgeattributes>true</edgeattributes>
+ <background>-3355393</background>
+ <brightcolor>-16711936</brightcolor>
+ <middlecolor>-256</middlecolor>
+ <darkcolor>-65536</darkcolor>
+ <helpurl>http://med.bioinf.mpi-inf.mpg.de/netanalyzer/help/2.7/</helpurl>
+ <helpfitting>index.html</helpfitting>
+ <helpinterpret>index.html#interpret</helpinterpret>
+ <helpparams>index.html</helpparams>
+ <helpremduplicates>index.html#remduplicates</helpremduplicates>
+ <helpremselfloops>index.html#remselfloops</helpremselfloops>
+ <helpsettings>index.html#settings</helpsettings>
+ </plugin>
+ <complexparam name="degreeDist" type="IntHistogram">
+ <usescatter>true</usescatter>
+ <general>
+ <title>Node Degree Distribution</title>
+ <background>-1</background>
+ </general>
+ <axes>
+ <catlabel>Degree</catlabel>
+ <rangelabel>Number of nodes</rangelabel>
+ <domrange min="0"/>
+ <ranrange min="0"/>
+ <lograngeaxis>true</lograngeaxis>
+ <logdomainaxis>true</logdomainaxis>
+ <intrangeaxis>true</intrangeaxis>
+ <intdomainaxis>true</intdomainaxis>
+ </axes>
+ <bars>
+ <barcolor>0</barcolor>
+ </bars>
+ <scatter>
+ <pointcolor>0</pointcolor>
+ <pointshape>filled circle</pointshape>
+ </scatter>
+ <grid>
+ <horizontal>true</horizontal>
+ <vertical>false</vertical>
+ <cgridlines>-6710887</cgridlines>
+ </grid>
+ <filter>
+ <minobslabel>Minimum degree to display</minobslabel>
+ <maxobslabel>Maximum degree to display</maxobslabel>
+ </filter>
+ <decorators>
+ <LeastSquaresLineDecorator/>
+ <LeastSquaresPowerLawDecorator/>
+ </decorators>
+ </complexparam>
+ <complexparam name="cksDist" type="Points2D">
+ <general>
+ <title>Avg. Clustering Coefficient Distribution</title>
+ <background>-1</background>
+ </general>
+ <axes>
+ <catlabel>Number of neighbors</catlabel>
+ <rangelabel>Avg. clustering coefficient</rangelabel>
+ <domrange min="0"/>
+ <ranrange min="0" max="1"/>
+ <lograngeaxis>false</lograngeaxis>
+ <logdomainaxis>true</logdomainaxis>
+ <intrangeaxis>false</intrangeaxis>
+ <intdomainaxis>true</intdomainaxis>
+ </axes>
+ <scatter>
+ <pointcolor>0</pointcolor>
+ <pointshape>filled circle</pointshape>
+ </scatter>
+ <grid>
+ <horizontal>true</horizontal>
+ <vertical>false</vertical>
+ <cgridlines>-6710887</cgridlines>
+ </grid>
+ <filter>
+ <minxlabel>Minimum number of neighbors to display</minxlabel>
+ <maxxlabel>Maximum number of neighbors to display</maxxlabel>
+ </filter>
+ <decorators>
+ <LeastSquaresLineDecorator/>
+ <LeastSquaresPowerLawDecorator/>
+ </decorators>
+ </complexparam>
+ <complexparam name="topCoefs" type="Points2D">
+ <general>
+ <title>Topological Coefficients</title>
+ <background>-1</background>
+ </general>
+ <axes>
+ <catlabel>Number of neighbors</catlabel>
+ <rangelabel>Topol. coefficients</rangelabel>
+ <domrange min="0"/>
+ <ranrange min="0" max="1"/>
+ <lograngeaxis>false</lograngeaxis>
+ <logdomainaxis>true</logdomainaxis>
+ <intdomainaxis>true</intdomainaxis>
+ <intrangeaxis>false</intrangeaxis>
+ </axes>
+ <scatter>
+ <pointcolor>0</pointcolor>
+ <pointshape>circle</pointshape>
+ </scatter>
+ <grid>
+ <horizontal>true</horizontal>
+ <vertical>false</vertical>
+ <cgridlines>-6710887</cgridlines>
+ </grid>
+ <filter>
+ <minxlabel>Minimum number of neighbors to display</minxlabel>
+ <maxxlabel>Maximum number of neighbors to display</maxxlabel>
+ </filter>
+ <decorators>
+ <LeastSquaresLineDecorator/>
+ <LeastSquaresPowerLawDecorator/>
+ </decorators>
+ </complexparam>
+ <complexparam name="splDist" type="LongHistogram">
+ <usescatter>false</usescatter>
+ <general>
+ <title>Shortest Path Length Distribution</title>
+ <background>-1</background>
+ </general>
+ <axes>
+ <catlabel>Path length</catlabel>
+ <rangelabel>Frequency</rangelabel>
+ <domrange min="1"/>
+ <ranrange min="0"/>
+ <lograngeaxis>false</lograngeaxis>
+ <logdomainaxis>false</logdomainaxis>
+ <intrangeaxis>true</intrangeaxis>
+ <intdomainaxis>true</intdomainaxis>
+ </axes>
+ <bars>
+ <barcolor>0</barcolor>
+ </bars>
+ <scatter>
+ <pointcolor>0</pointcolor>
+ <pointshape>filled square</pointshape>
+ </scatter>
+ <grid>
+ <horizontal>true</horizontal>
+ <vertical>false</vertical>
+ <cgridlines>-6710887</cgridlines>
+ </grid>
+ <filter>
+ <minobslabel>Minimum path length to display</minobslabel>
+ <maxobslabel>Maximum path length to display</maxobslabel>
+ </filter>
+ </complexparam>
+ <complexparam name="commNeighbors" type="LongHistogram">
+ <usescatter>false</usescatter>
+ <general>
+ <title>Shared Neighbors Distribution</title>
+ <background>-1</background>
+ </general>
+ <axes>
+ <catlabel>Number of shared neighbors</catlabel>
+ <rangelabel>Frequency</rangelabel>
+ <domrange min="0"/>
+ <ranrange min="0"/>
+ <lograngeaxis>false</lograngeaxis>
+ <logdomainaxis>false</logdomainaxis>
+ <intrangeaxis>true</intrangeaxis>
+ <intdomainaxis>true</intdomainaxis>
+ </axes>
+ <bars>
+ <barcolor>0</barcolor>
+ </bars>
+ <scatter>
+ <pointcolor>0</pointcolor>
+ <pointshape>filled circle</pointshape>
+ </scatter>
+ <grid>
+ <horizontal>true</horizontal>
+ <vertical>false</vertical>
+ <cgridlines>-6710887</cgridlines>
+ </grid>
+ <filter>
+ <minobslabel>Minimum number of shared partners to display</minobslabel>
+ <maxobslabel>Maximum number of shared partners to display</maxobslabel>
+ </filter>
+ </complexparam>
+ <complexparam name="neighborConn" type="Points2D">
+ <general>
+ <title>Neighborhood Connectivity Distribution</title>
+ <background>-1</background>
+ </general>
+ <axes>
+ <catlabel>Number of neighbors</catlabel>
+ <rangelabel>Avg. neighborhood connectivity</rangelabel>
+ <domrange min="1"/>
+ <ranrange min="0"/>
+ <lograngeaxis>false</lograngeaxis>
+ <logdomainaxis>true</logdomainaxis>
+ <intrangeaxis>false</intrangeaxis>
+ <intdomainaxis>true</intdomainaxis>
+ </axes>
+ <scatter>
+ <pointcolor>0</pointcolor>
+ <pointshape>filled circle</pointshape>
+ </scatter>
+ <grid>
+ <horizontal>true</horizontal>
+ <vertical>false</vertical>
+ <cgridlines>-6710887</cgridlines>
+ </grid>
+ <filter>
+ <minxlabel>Minimum number of neighbors to display</minxlabel>
+ <maxxlabel>Maximum number of neighbors to display</maxxlabel>
+ </filter>
+ <decorators>
+ <LeastSquaresLineDecorator/>
+ <LeastSquaresPowerLawDecorator/>
+ </decorators>
+ </complexparam>
+ <complexparam name="nodeBetween" type="Points2D">
+ <general>
+ <title>Betweenness Centrality</title>
+ <background>-1</background>
+ </general>
+ <axes>
+ <catlabel>Number of neighbors</catlabel>
+ <rangelabel>Betweenness centrality</rangelabel>
+ <domrange min="0"/>
+ <ranrange min="0" max="1"/>
+ <lograngeaxis>false</lograngeaxis>
+ <logdomainaxis>false</logdomainaxis>
+ <intrangeaxis>false</intrangeaxis>
+ <intdomainaxis>true</intdomainaxis>
+ </axes>
+ <scatter>
+ <pointcolor>0</pointcolor>
+ <pointshape>filled circle</pointshape>
+ </scatter>
+ <grid>
+ <horizontal>true</horizontal>
+ <vertical>false</vertical>
+ <cgridlines>0</cgridlines>
+ </grid>
+ <filter>
+ <minxlabel>Minimum number of neighbors to display</minxlabel>
+ <maxxlabel>Maximum number of neighbors to display</maxxlabel>
+ </filter>
+ <decorators>
+ <LeastSquaresPowerLawDecorator/>
+ </decorators>
+ </complexparam>
+ <complexparam name="closenessCent" type="Points2D">
+ <general>
+ <title>Closeness Centrality</title>
+ <background>-1</background>
+ </general>
+ <axes>
+ <catlabel>Number of neighbors</catlabel>
+ <rangelabel>Closeness centrality</rangelabel>
+ <domrange min="0"/>
+ <ranrange min="0" max="1"/>
+ <lograngeaxis>false</lograngeaxis>
+ <logdomainaxis>true</logdomainaxis>
+ <intrangeaxis>false</intrangeaxis>
+ <intdomainaxis>true</intdomainaxis>
+ </axes>
+ <scatter>
+ <pointcolor>0</pointcolor>
+ <pointshape>filled circle</pointshape>
+ </scatter>
+ <grid>
+ <horizontal>true</horizontal>
+ <vertical>false</vertical>
+ <cgridlines>0</cgridlines>
+ </grid>
+ <filter>
+ <minxlabel>Minimum number of neighbors to display</minxlabel>
+ <maxxlabel>Maximum number of neighbors to display</maxxlabel>
+ </filter>
+ <decorators>
+ <LeastSquaresPowerLawDecorator/>
+ </decorators>
+ </complexparam>
+ <complexparam name="stressDist" type="Points2D">
+ <general>
+ <title>Stress Centrality Distribution</title>
+ <background>-1</background>
+ </general>
+ <axes>
+ <catlabel>Stress centrality</catlabel>
+ <rangelabel>Number of nodes</rangelabel>
+ <domrange min="0"/>
+ <ranrange min="0"/>
+ <lograngeaxis>true</lograngeaxis>
+ <logdomainaxis>true</logdomainaxis>
+ <intrangeaxis>true</intrangeaxis>
+ <intdomainaxis>true</intdomainaxis>
+ </axes>
+ <scatter>
+ <pointcolor>0</pointcolor>
+ <pointshape>filled circle</pointshape>
+ </scatter>
+ <grid>
+ <horizontal>true</horizontal>
+ <vertical>false</vertical>
+ <cgridlines>-6710887</cgridlines>
+ </grid>
+ <filter>
+ <minxlabel>Minimum stress to display</minxlabel>
+ <maxxlabel>Maximum stress to display</maxxlabel>
+ </filter>
+ <decorators>
+ <LeastSquaresLineDecorator/>
+ <LeastSquaresPowerLawDecorator/>
+ </decorators>
+ </complexparam>
+ <complexparam name="allNeighborConn" type="Points2D">
+ <general>
+ <title>Neighborhood Connectivity (in and out)</title>
+ <background>-1</background>
+ </general>
+ <axes>
+ <catlabel>Number of neighbors</catlabel>
+ <rangelabel>Avg. connectivity</rangelabel>
+ <domrange min="1"/>
+ <ranrange min="0"/>
+ <lograngeaxis>false</lograngeaxis>
+ <logdomainaxis>true</logdomainaxis>
+ <intrangeaxis>false</intrangeaxis>
+ <intdomainaxis>true</intdomainaxis>
+ </axes>
+ <scatter>
+ <pointcolor>0</pointcolor>
+ <pointshape>filled circle</pointshape>
+ </scatter>
+ <grid>
+ <horizontal>true</horizontal>
+ <vertical>false</vertical>
+ <cgridlines>-6710887</cgridlines>
+ </grid>
+ <filter>
+ <minxlabel>Minimum number of neighbors to display</minxlabel>
+ <maxxlabel>Maximum number of neighbors to display</maxxlabel>
+ </filter>
+ <decorators>
+ <LeastSquaresLineDecorator/>
+ <LeastSquaresPowerLawDecorator/>
+ </decorators>
+ </complexparam>
+ <complexparam name="inNeighborConn" type="Points2D">
+ <general>
+ <title>Neighborhood Connectivity (only in)</title>
+ <background>-1</background>
+ </general>
+ <axes>
+ <catlabel>Number of in-neighbors</catlabel>
+ <rangelabel>Avg. out-connectivity</rangelabel>
+ <domrange min="1"/>
+ <ranrange min="0"/>
+ <lograngeaxis>false</lograngeaxis>
+ <logdomainaxis>true</logdomainaxis>
+ <intrangeaxis>false</intrangeaxis>
+ <intdomainaxis>true</intdomainaxis>
+ </axes>
+ <scatter>
+ <pointcolor>0</pointcolor>
+ <pointshape>filled circle</pointshape>
+ </scatter>
+ <grid>
+ <horizontal>true</horizontal>
+ <vertical>false</vertical>
+ <cgridlines>-6710887</cgridlines>
+ </grid>
+ <filter>
+ <minxlabel>Minimum number of in-neighbors to display</minxlabel>
+ <maxxlabel>Maximum number of in-neighbors to display</maxxlabel>
+ </filter>
+ <decorators>
+ <LeastSquaresLineDecorator/>
+ <LeastSquaresPowerLawDecorator/>
+ </decorators>
+ </complexparam>
+ <complexparam name="outNeighborConn" type="Points2D">
+ <general>
+ <title>Neighborhood Connectivity (only out)</title>
+ <background>-1</background>
+ </general>
+ <axes>
+ <catlabel>Number of out-neighbors</catlabel>
+ <rangelabel>Avg. in-connectivity</rangelabel>
+ <domrange min="1"/>
+ <ranrange min="0"/>
+ <lograngeaxis>false</lograngeaxis>
+ <logdomainaxis>true</logdomainaxis>
+ <intrangeaxis>false</intrangeaxis>
+ <intdomainaxis>true</intdomainaxis>
+ </axes>
+ <scatter>
+ <pointcolor>0</pointcolor>
+ <pointshape>filled circle</pointshape>
+ </scatter>
+ <grid>
+ <horizontal>true</horizontal>
+ <vertical>false</vertical>
+ <cgridlines>-6710887</cgridlines>
+ </grid>
+ <filter>
+ <minxlabel>Minimum number of out-neighbors to display</minxlabel>
+ <maxxlabel>Maximum number of out-neighbors to display</maxxlabel>
+ </filter>
+ <decorators>
+ <LeastSquaresLineDecorator/>
+ <LeastSquaresPowerLawDecorator/>
+ </decorators>
+ </complexparam>
+ <complexparam name="inDegreeDist" type="IntHistogram">
+ <usescatter>false</usescatter>
+ <general>
+ <title>In-Degree Distribution</title>
+ <background>-1</background>
+ </general>
+ <axes>
+ <catlabel>In-degree</catlabel>
+ <rangelabel>Number of nodes</rangelabel>
+ <domrange min="0"/>
+ <ranrange min="0"/>
+ <lograngeaxis>false</lograngeaxis>
+ <logdomainaxis>false</logdomainaxis>
+ <intrangeaxis>true</intrangeaxis>
+ <intdomainaxis>true</intdomainaxis>
+ </axes>
+ <bars>
+ <barcolor>0</barcolor>
+ </bars>
+ <scatter>
+ <pointcolor>0</pointcolor>
+ <pointshape>filled circle</pointshape>
+ </scatter>
+ <grid>
+ <horizontal>true</horizontal>
+ <vertical>false</vertical>
+ <cgridlines>-6710887</cgridlines>
+ </grid>
+ <filter>
+ <minobslabel>Minimum in-degree to display</minobslabel>
+ <maxobslabel>Maximum in-degree to display</maxobslabel>
+ </filter>
+ <decorators>
+ <LeastSquaresLineDecorator/>
+ <LeastSquaresPowerLawDecorator/>
+ </decorators>
+ </complexparam>
+ <complexparam name="outDegreeDist" type="IntHistogram">
+ <usescatter>false</usescatter>
+ <general>
+ <title>Out-Degree Distribution</title>
+ <background>-1</background>
+ </general>
+ <axes>
+ <catlabel>Out-degree</catlabel>
+ <rangelabel>Number of nodes</rangelabel>
+ <domrange min="0"/>
+ <ranrange min="0"/>
+ <lograngeaxis>false</lograngeaxis>
+ <logdomainaxis>false</logdomainaxis>
+ <intrangeaxis>true</intrangeaxis>
+ <intdomainaxis>true</intdomainaxis>
+ </axes>
+ <bars>
+ <barcolor>0</barcolor>
+ </bars>
+ <scatter>
+ <pointcolor>0</pointcolor>
+ <pointshape>filled circle</pointshape>
+ </scatter>
+ <grid>
+ <horizontal>true</horizontal>
+ <vertical>false</vertical>
+ <cgridlines>-6710887</cgridlines>
+ </grid>
+ <filter>
+ <minobslabel>Minimum out-degree to display</minobslabel>
+ <maxobslabel>Maximum out-degree to display</maxobslabel>
+ </filter>
+ <decorators>
+ <LeastSquaresLineDecorator/>
+ <LeastSquaresPowerLawDecorator/>
+ </decorators>
+ </complexparam>
+ <complexparam name="userDefined" type="Points2D">
+ <general>
+ <title>User defined plot</title>
+ <background>-1</background>
+ </general>
+ <axes>
+ <catlabel>Attribute 1</catlabel>
+ <rangelabel>Attribute 2</rangelabel>
+ <domrange min="0"/>
+ <ranrange min="0"/>
+ <lograngeaxis>false</lograngeaxis>
+ <logdomainaxis>false</logdomainaxis>
+ <intrangeaxis>false</intrangeaxis>
+ <intdomainaxis>false</intdomainaxis>
+ </axes>
+ <scatter>
+ <pointcolor>0</pointcolor>
+ <pointshape>filled circle</pointshape>
+ </scatter>
+ <grid>
+ <horizontal>true</horizontal>
+ <vertical>false</vertical>
+ <cgridlines>-6710887</cgridlines>
+ </grid>
+ <filter>
+ <minxlabel>Minimum </minxlabel>
+ <maxxlabel>Maximum </maxxlabel>
+ </filter>
+ <decorators>
+ <LeastSquaresLineDecorator/>
+ </decorators>
+ </complexparam>
+</networkanalyzersettings>
\ No newline at end of file
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diff --git a/coreplugins/NetworkAnalyzer/src/main/resources/de/mpg/mpi_inf/bioinf/netanalyzer/data/images/AboutBox.png b/coreplugins/NetworkAnalyzer/src/main/resources/de/mpg/mpi_inf/bioinf/netanalyzer/data/images/AboutBox.png
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diff --git a/coreplugins/NetworkAnalyzer/src/main/resources/de/mpg/mpi_inf/bioinf/netanalyzer/plugin.props b/coreplugins/NetworkAnalyzer/src/main/resources/de/mpg/mpi_inf/bioinf/netanalyzer/plugin.props
new file mode 100644
index 0000000..06307db
--- /dev/null
+++ b/coreplugins/NetworkAnalyzer/src/main/resources/de/mpg/mpi_inf/bioinf/netanalyzer/plugin.props
@@ -0,0 +1,30 @@
+# This props file would be filled out and included in the plugin jar file. This props file will be used
+# to put information into the Plugin Manager about the plugin
+
+
+# -- The following properties are REQUIRED -- #
+
+# The plugin name that will be displayed to users
+pluginName=NetworkAnalyzer
+
+# Description used to give users information about the plugin such as what it does.
+# Html tags are encouraged for formatting purposes.
+pluginDescription=Analyze networks with various statistical measures.
+
+# Plugin version number, this must be two numbers separated by a decimlal. Ex. 0.2, 14.03
+pluginVersion=1.0
+
+# Compatible Cytoscape version
+cytoscapeVersion=2.7,2.8
+
+# Category, use one of the categories listed on the website or create your own
+pluginCategory=Core
+
+
+# List of authors. Note each author and institution pair are separated by a : (colon)
+# each additional author institution pair must be separated from other pairs bye a ; (semicolon)
+pluginAuthorsIntsitutions=Yassen Assenov:MPII;Nadezhda T. Doncheva:MPII;Sven-Eric Schelhorn:MPII;Thomas Lengauer:MPII;Mario Albrecht:Max Planck Institute for Informatics
+
+# -- The following properties should be set ONLY BY CORE PLUGINS -- #
+downloadURL=http://cytoscape.org/plugins/plugins.xml
+uniqueID=18
diff --git a/coreplugins/PSI-MI/pom.xml b/coreplugins/PSI-MI/pom.xml
new file mode 100644
index 0000000..ea38708
--- /dev/null
+++ b/coreplugins/PSI-MI/pom.xml
@@ -0,0 +1,105 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>parent</artifactId>
+ <version>2.8.4-SNAPSHOT</version>
+ </parent>
+
+ <artifactId>psi-mi</artifactId>
+ <packaging>jar</packaging>
+
+ <name>PSI-MI</name>
+
+ <!-- bootstrap for cytoscape dependencies, namely the parent POM snapshots -->
+ <repositories>
+ <repository>
+ <id>cytoscape_snapshots</id>
+ <snapshots>
+ <enabled>true</enabled>
+ </snapshots>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <name>Cytoscape Snapshots</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/</url>
+ </repository>
+ <repository>
+ <id>cytoscape_releases</id>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ <name>Cytoscape Releases</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/releases/</url>
+ </repository>
+ </repositories>
+
+
+ <build>
+ <plugins>
+ <plugin>
+ <artifactId>maven-assembly-plugin</artifactId>
+ <configuration>
+ <archive>
+ <manifestEntries>
+ <Cytoscape-Plugin>org.cytoscape.coreplugin.psi_mi.plugin.PsiMiPlugIn</Cytoscape-Plugin>
+ </manifestEntries>
+ </archive>
+ </configuration>
+ </plugin>
+ <plugin>
+ <groupId>org.jvnet.jaxb2.maven2</groupId>
+ <artifactId>maven-jaxb2-plugin</artifactId>
+ <version>0.7.4</version>
+ <executions>
+ <execution>
+ <id>mi1</id>
+ <goals>
+ <goal>generate</goal>
+ </goals>
+ <configuration>
+ <schemaDirectory>src/main/resources/xsd</schemaDirectory>
+ <schemaIncludes>
+ <include>MIF1.xsd</include>
+ </schemaIncludes>
+ <generatePackage>org.cytoscape.coreplugin.psi_mi.schema.mi1</generatePackage>
+ <verbose>true</verbose>
+ <removeOldOutput>false</removeOldOutput>
+ <forceRegenerate>true</forceRegenerate>
+ </configuration>
+ </execution>
+ <execution>
+ <id>mi25</id>
+ <goals>
+ <goal>generate</goal>
+ </goals>
+ <configuration>
+ <schemaDirectory>src/main/resources/xsd</schemaDirectory>
+ <schemaIncludes>
+ <include>MIF25.xsd</include>
+ </schemaIncludes>
+ <generatePackage>org.cytoscape.coreplugin.psi_mi.schema.mi25</generatePackage>
+ <verbose>true</verbose>
+ <removeOldOutput>false</removeOldOutput>
+ <forceRegenerate>true</forceRegenerate>
+ </configuration>
+ </execution>
+ </executions>
+ </plugin>
+ </plugins>
+ </build>
+
+ <pluginRepositories>
+ <pluginRepository>
+ <id>maven2-repository.dev.java.net</id>
+ <name>Java.net Maven 2 Repository</name>
+ <url>http://download.java.net/maven/2</url>
+ </pluginRepository>
+ </pluginRepositories>
+
+
+</project>
+
diff --git a/coreplugins/PSI-MI/sampleData/psi_sample_1.xml b/coreplugins/PSI-MI/sampleData/psi_sample_1.xml
new file mode 100755
index 0000000..831581f
--- /dev/null
+++ b/coreplugins/PSI-MI/sampleData/psi_sample_1.xml
@@ -0,0 +1,4920 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<entrySet xsi:schemaLocation="net:sf:psidev:mi http://psidev.sourceforge.net/mi/xml/src/MIF.xsd" level="1" version="1" xmlns="net:sf:psidev:mi" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+ <entry>
+ <interactorList>
+ <proteinInteractor id="CPATH-369">
+ <names>
+ <shortLabel/>
+ <fullName>helix-loop-helix protein m-beta</fullName>
+ </names>
+ <xref>
+ <primaryRef db="DIP" id="721N"/>
+ <secondaryRef db="SwissProt" id="Q01069"/>
+ <secondaryRef db="Entrez GI" id="24650224"/>
+ <secondaryRef db="RefSeq" id="NP_524505"/>
+ </xref>
+ <organism ncbiTaxId="7227">
+ <names>
+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-7140">
+ <names>
+ <shortLabel/>
+ <fullName>odd paired (CG1133-PA)</fullName>
+ </names>
+ <xref>
+ <primaryRef db="DIP" id="17067N"/>
+ <secondaryRef db="Entrez GI" id="24644093"/>
+ <secondaryRef db="RefSeq" id="NP_524228"/>
+ </xref>
+ <organism ncbiTaxId="7227">
+ <names>
+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-7121">
+ <names>
+ <shortLabel/>
+ <fullName>Probable phosphoserine aminotransferase (PSAT)</fullName>
+ </names>
+ <xref>
+ <primaryRef db="DIP" id="17047N"/>
+ <secondaryRef db="SwissProt" id="Q9VAN0"/>
+ <secondaryRef db="Entrez GI" id="21356589"/>
+ <secondaryRef db="RefSeq" id="NP_652046"/>
+ </xref>
+ <organism ncbiTaxId="7227">
+ <names>
+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-287">
+ <names>
+ <shortLabel/>
+ <fullName>trp protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="DIP" id="526N"/>
+ <secondaryRef db="PIR" id="JU0092"/>
+ <secondaryRef db="Entrez GI" id="17136554"/>
+ <secondaryRef db="RefSeq" id="NP_476768"/>
+ </xref>
+ <organism ncbiTaxId="7227">
+ <names>
+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-368">
+ <names>
+ <shortLabel/>
+ <fullName>helix-loop-helix protein m-delta</fullName>
+ </names>
+ <xref>
+ <primaryRef db="DIP" id="722N"/>
+ <secondaryRef db="SwissProt" id="Q01071"/>
+ <secondaryRef db="PIR" id="A46177"/>
+ <secondaryRef db="Entrez GI" id="24650220"/>
+ <secondaryRef db="RefSeq" id="NP_524503"/>
+ </xref>
+ <organism ncbiTaxId="7227">
+ <names>
+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-363">
+ <names>
+ <shortLabel/>
+ <fullName>achaete-scute complex protein T4</fullName>
+ </names>
+ <xref>
+ <primaryRef db="DIP" id="325N"/>
+ <secondaryRef db="SwissProt" id="P10084"/>
+ <secondaryRef db="PIR" id="B43731"/>
+ <secondaryRef db="Entrez GI" id="17136616"/>
+ <secondaryRef db="RefSeq" id="NP_476803"/>
+ </xref>
+ <organism ncbiTaxId="7227">
+ <names>
+ <shortLabel/>
+ <fullName>Drosophila melanogaster </fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-7131">
+ <names>
+ <shortLabel/>
+ <fullName>CG4959-PB open reading frame</fullName>
+ </names>
+ <xref>
+ <primaryRef db="DIP" id="17057N"/>
+ <secondaryRef db="Entrez GI" id="24584547"/>
+ <secondaryRef db="RefSeq" id="NP_652576"/>
+ </xref>
+ <organism ncbiTaxId="7227">
+ <names>
+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-7149">
+ <names>
+ <shortLabel/>
+ <fullName>Cyclin-dependent kinase 7 (CG3319-PA)</fullName>
+ </names>
+ <xref>
+ <primaryRef db="DIP" id="17075N"/>
+ <secondaryRef db="Entrez GI" id="17530793"/>
+ <secondaryRef db="RefSeq" id="NP_511044"/>
+ </xref>
+ <organism ncbiTaxId="7227">
+ <names>
+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-7159">
+ <names>
+ <shortLabel/>
+ <fullName>Merlin (CG14228-PA)</fullName>
+ </names>
+ <xref>
+ <primaryRef db="DIP" id="17087N"/>
+ <secondaryRef db="SwissProt" id="Q24564"/>
+ <secondaryRef db="Entrez GI" id="17647629"/>
+ <secondaryRef db="RefSeq" id="NP_523413"/>
+ </xref>
+ <organism ncbiTaxId="7227">
+ <names>
+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-7122">
+ <names>
+ <shortLabel/>
+ <fullName>Casein kinase II beta subunit (CG15224-PA)</fullName>
+ </names>
+ <xref>
+ <primaryRef db="DIP" id="17048N"/>
+ <secondaryRef db="SwissProt" id="P08182"/>
+ <secondaryRef db="Entrez GI" id="18104935"/>
+ <secondaryRef db="RefSeq" id="NP_511131"/>
+ </xref>
+ <organism ncbiTaxId="7227">
+ <names>
+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-7154">
+ <names>
+ <shortLabel/>
+ <fullName>Pox meso (CG9610-PA)</fullName>
+ </names>
+ <xref>
+ <primaryRef db="DIP" id="17081N"/>
+ <secondaryRef db="SwissProt" id="P23757"/>
+ <secondaryRef db="Entrez GI" id="17986167"/>
+ <secondaryRef db="RefSeq" id="NP_524276"/>
+ </xref>
+ <organism ncbiTaxId="7227">
+ <names>
+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-223">
+ <names>
+ <shortLabel/>
+ <fullName>white protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="DIP" id="388N"/>
+ <secondaryRef db="SwissProt" id="P10090"/>
+ <secondaryRef db="PIR" id="FYFFW"/>
+ <secondaryRef db="Entrez GI" id="17136592"/>
+ <secondaryRef db="RefSeq" id="NP_476787"/>
+ </xref>
+ <organism ncbiTaxId="7227">
+ <names>
+ <shortLabel/>
+ <fullName>Drosophila melanogaster </fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-286">
+ <names>
+ <shortLabel/>
+ <fullName>phospholipase C</fullName>
+ </names>
+ <xref>
+ <primaryRef db="DIP" id="45N"/>
+ <secondaryRef db="PIR" id="A31225"/>
+ <secondaryRef db="Entrez GI" id="24639671"/>
+ <secondaryRef db="RefSeq" id="NP_525069"/>
+ </xref>
+ <organism ncbiTaxId="7227">
+ <names>
+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-7165">
+ <names>
+ <shortLabel/>
+ <fullName>scully (CG7113-PA)</fullName>
+ </names>
+ <xref>
+ <primaryRef db="DIP" id="17092N"/>
+ <secondaryRef db="SwissProt" id="O18404"/>
+ <secondaryRef db="Entrez GI" id="17737361"/>
+ <secondaryRef db="RefSeq" id="NP_523396"/>
+ </xref>
+ <organism ncbiTaxId="7227">
+ <names>
+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-7155">
+ <names>
+ <shortLabel/>
+ <fullName>CG15436-PA open reading frame</fullName>
+ </names>
+ <xref>
+ <primaryRef db="DIP" id="17083N"/>
+ <secondaryRef db="Entrez GI" id="19920688"/>
+ <secondaryRef db="RefSeq" id="NP_608840"/>
+ </xref>
+ <organism ncbiTaxId="7227">
+ <names>
+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-7128">
+ <names>
+ <shortLabel/>
+ <fullName>mutagen-sensitive 205 (CG1925-PA)</fullName>
+ </names>
+ <xref>
+ <primaryRef db="DIP" id="17054N"/>
+ <secondaryRef db="Entrez GI" id="24586371"/>
+ <secondaryRef db="RefSeq" id="NP_524881"/>
+ </xref>
+ <organism ncbiTaxId="7227">
+ <names>
+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-7150">
+ <names>
+ <shortLabel/>
+ <fullName>CG6945-PA open reading frame</fullName>
+ </names>
+ <xref>
+ <primaryRef db="DIP" id="17076N"/>
+ <secondaryRef db="Entrez GI" id="24664458"/>
+ <secondaryRef db="RefSeq" id="NP_648745"/>
+ </xref>
+ <organism ncbiTaxId="7227">
+ <names>
+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-188">
+ <names>
+ <shortLabel/>
+ <fullName>transcription initiation factor IID</fullName>
+ </names>
+ <xref>
+ <primaryRef db="DIP" id="80N"/>
+ <secondaryRef db="SwissProt" id="P20227"/>
+ <secondaryRef db="PIR" id="A35615"/>
+ <secondaryRef db="Entrez GI" id="17647997"/>
+ <secondaryRef db="RefSeq" id="NP_523805"/>
+ </xref>
+ <organism ncbiTaxId="7227">
+ <names>
+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-285">
+ <names>
+ <shortLabel/>
+ <fullName>gene fused protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="DIP" id="492N"/>
+ <secondaryRef db="PIR" id="JC4234"/>
+ <secondaryRef db="Entrez GI" id="17137760"/>
+ <secondaryRef db="RefSeq" id="NP_477499"/>
+ </xref>
+ <organism ncbiTaxId="7227">
+ <names>
+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-7144">
+ <names>
+ <shortLabel/>
+ <fullName>CG14546-PA open reading frame</fullName>
+ </names>
+ <xref>
+ <primaryRef db="DIP" id="17070N"/>
+ <secondaryRef db="Entrez GI" id="24650202"/>
+ <secondaryRef db="RefSeq" id="NP_651448"/>
+ </xref>
+ <organism ncbiTaxId="7227">
+ <names>
+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-7139">
+ <names>
+ <shortLabel/>
+ <fullName>modifier of mdg4 CG32491-PT</fullName>
+ </names>
+ <xref>
+ <primaryRef db="DIP" id="17065N"/>
+ <secondaryRef db="Entrez GI" id="28572129"/>
+ <secondaryRef db="RefSeq" id="NP_788698"/>
+ </xref>
+ <organism ncbiTaxId="7227">
+ <names>
+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-189">
+ <names>
+ <shortLabel/>
+ <fullName>transcription initiation factor IID 230K chain</fullName>
+ </names>
+ <xref>
+ <primaryRef db="DIP" id="228N"/>
+ <secondaryRef db="SwissProt" id="P51123"/>
+ <secondaryRef db="PIR" id="A47371"/>
+ <secondaryRef db="Entrez GI" id="28571540"/>
+ <secondaryRef db="RefSeq" id="NP_476956"/>
+ </xref>
+ <organism ncbiTaxId="7227">
+ <names>
+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-288">
+ <names>
+ <shortLabel/>
+ <fullName>protein kinase C 53E(ey)</fullName>
+ </names>
+ <xref>
+ <primaryRef db="DIP" id="54N"/>
+ <secondaryRef db="SwissProt" id="P13677"/>
+ <secondaryRef db="PIR" id="A32392"/>
+ <secondaryRef db="Entrez GI" id="17136716"/>
+ <secondaryRef db="RefSeq" id="NP_476863"/>
+ </xref>
+ <organism ncbiTaxId="7227">
+ <names>
+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-7164">
+ <names>
+ <shortLabel/>
+ <fullName>CG4818-PA open reading frame</fullName>
+ </names>
+ <xref>
+ <primaryRef db="DIP" id="17091N"/>
+ <secondaryRef db="Entrez GI" id="21357211"/>
+ <secondaryRef db="RefSeq" id="NP_648882"/>
+ </xref>
+ <organism ncbiTaxId="7227">
+ <names>
+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-596">
+ <names>
+ <shortLabel/>
+ <fullName>DHR38 protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="DIP" id="929N"/>
+ <secondaryRef db="SwissProt" id="P49869"/>
+ <secondaryRef db="PIR" id="S58238"/>
+ <secondaryRef db="Entrez GI" id="2133651"/>
+ </xref>
+ <organism ncbiTaxId="7227">
+ <names>
+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-283">
+ <names>
+ <shortLabel/>
+ <fullName>DNA-binding protein ci (D)</fullName>
+ </names>
+ <xref>
+ <primaryRef db="DIP" id="121N"/>
+ <secondaryRef db="SwissProt" id="P19538"/>
+ <secondaryRef db="PIR" id="A38926"/>
+ <secondaryRef db="Entrez GI" id="24638496"/>
+ <secondaryRef db="RefSeq" id="NP_524617"/>
+ </xref>
+ <organism ncbiTaxId="7227">
+ <names>
+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-7153">
+ <names>
+ <shortLabel/>
+ <fullName>CG10014-PA open reading frame</fullName>
+ </names>
+ <xref>
+ <primaryRef db="DIP" id="17078N"/>
+ <secondaryRef db="Entrez GI" id="21357001"/>
+ <secondaryRef db="RefSeq" id="NP_650164"/>
+ </xref>
+ <organism ncbiTaxId="7227">
+ <names>
+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-373">
+ <names>
+ <shortLabel/>
+ <fullName>basic-helix-loop-helix protein ato</fullName>
+ </names>
+ <xref>
+ <primaryRef db="DIP" id="151N"/>
+ <secondaryRef db="SwissProt" id="P48987"/>
+ <secondaryRef db="PIR" id="A40708"/>
+ <secondaryRef db="Entrez GI" id="476802"/>
+ <secondaryRef db="RefSeq" id="NP_731223"/>
+ </xref>
+ <organism ncbiTaxId="7227">
+ <names>
+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-290">
+ <names>
+ <shortLabel/>
+ <fullName>calmodulin</fullName>
+ </names>
+ <xref>
+ <primaryRef db="DIP" id="537N"/>
+ <secondaryRef db="SwissProt" id="P07181"/>
+ <secondaryRef db="PIR" id="MCFF"/>
+ <secondaryRef db="Entrez GI" id="17647231"/>
+ <secondaryRef db="RefSeq" id="NP_523710"/>
+ </xref>
+ <organism ncbiTaxId="7227">
+ <names>
+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-7125">
+ <names>
+ <shortLabel/>
+ <fullName>CG17666-PA open reading frame</fullName>
+ </names>
+ <xref>
+ <primaryRef db="DIP" id="17051N"/>
+ <secondaryRef db="Entrez GI" id="24663462"/>
+ <secondaryRef db="RefSeq" id="NP_648599"/>
+ </xref>
+ <organism ncbiTaxId="7227">
+ <names>
+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-359">
+ <names>
+ <shortLabel/>
+ <fullName>Achaete-scute complex protein T5</fullName>
+ </names>
+ <xref>
+ <primaryRef db="DIP" id="187N"/>
+ <secondaryRef db="SwissProt" id="P10083"/>
+ <secondaryRef db="PIR" id="A43731"/>
+ <secondaryRef db="Entrez GI" id="17136654"/>
+ <secondaryRef db="RefSeq" id="NP_476824"/>
+ </xref>
+ <organism ncbiTaxId="7227">
+ <names>
+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-7127">
+ <names>
+ <shortLabel/>
+ <fullName>Male-specific RNA 84Da (CG17946-PA)</fullName>
+ </names>
+ <xref>
+ <primaryRef db="DIP" id="17053N"/>
+ <secondaryRef db="SwissProt" id="Q01642"/>
+ <secondaryRef db="PIR" id="S25772"/>
+ <secondaryRef db="Entrez GI" id="17737809"/>
+ <secondaryRef db="RefSeq" id="NP_524256"/>
+ </xref>
+ <organism ncbiTaxId="7227">
+ <names>
+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-7166">
+ <names>
+ <shortLabel/>
+ <fullName>lark (CG8597-PA)</fullName>
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+ <xref>
+ <primaryRef db="DIP" id="17093N"/>
+ <secondaryRef db="Entrez GI" id="17647581"/>
+ <secondaryRef db="RefSeq" id="NP_523957"/>
+ </xref>
+ <organism ncbiTaxId="7227">
+ <names>
+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-7151">
+ <names>
+ <shortLabel/>
+ <fullName>CG9778-PA open reading frame</fullName>
+ </names>
+ <xref>
+ <primaryRef db="DIP" id="17077N"/>
+ <secondaryRef db="Entrez GI" id="24643915"/>
+ <secondaryRef db="RefSeq" id="NP_649453"/>
+ </xref>
+ <organism ncbiTaxId="7227">
+ <names>
+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-7137">
+ <names>
+ <shortLabel/>
+ <fullName>CG10007-PA open reading frame</fullName>
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+ <xref>
+ <primaryRef db="DIP" id="17062N"/>
+ <secondaryRef db="Entrez GI" id="21356787"/>
+ <secondaryRef db="RefSeq" id="NP_650136"/>
+ </xref>
+ <organism ncbiTaxId="7227">
+ <names>
+ <shortLabel/>
+ <fullName>Drosophila melanogaster </fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-194">
+ <names>
+ <shortLabel/>
+ <fullName>transcription initiation factor IID 110K chain</fullName>
+ </names>
+ <xref>
+ <primaryRef db="DIP" id="237N"/>
+ <secondaryRef db="SwissProt" id="P47825"/>
+ <secondaryRef db="PIR" id="A48184"/>
+ <secondaryRef db="Entrez GI" id="477148"/>
+ <secondaryRef db="RefSeq" id="NP_524102"/>
+ </xref>
+ <organism ncbiTaxId="7227">
+ <names>
+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-594">
+ <names>
+ <shortLabel/>
+ <fullName>ecdysone receptor (CG1765-PB)</fullName>
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+ <secondaryRef db="PIR" id="A41055"/>
+ <secondaryRef db="Entrez GI" id="24585970"/>
+ <secondaryRef db="RefSeq" id="NP_724460"/>
+ </xref>
+ <organism ncbiTaxId="7227">
+ <names>
+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-616">
+ <names>
+ <shortLabel/>
+ <fullName>notch protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="DIP" id="5N"/>
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+ <secondaryRef db="PIR" id="A24420"/>
+ <secondaryRef db="Entrez GI" id="85085"/>
+ <secondaryRef db="RefSeq" id="NP_476859"/>
+ </xref>
+ <organism ncbiTaxId="7227">
+ <names>
+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-181">
+ <names>
+ <shortLabel/>
+ <fullName>transcription initiation factor IID chain p42</fullName>
+ </names>
+ <xref>
+ <primaryRef db="DIP" id="239N"/>
+ <secondaryRef db="SwissProt" id="Q27272"/>
+ <secondaryRef db="PIR" id="A49067"/>
+ <secondaryRef db="Entrez GI" id="1079142"/>
+ </xref>
+ <organism ncbiTaxId="7227">
+ <names>
+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-7134">
+ <names>
+ <shortLabel/>
+ <fullName>CG7081-PA open reading frame</fullName>
+ </names>
+ <xref>
+ <primaryRef db="DIP" id="17060N"/>
+ <secondaryRef db="Entrez GI" id="21355975"/>
+ <secondaryRef db="RefSeq" id="NP_648210"/>
+ </xref>
+ <organism ncbiTaxId="7227">
+ <names>
+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-7138">
+ <names>
+ <shortLabel/>
+ <fullName>DISCO Interacting Protein 1 (CG17686-PD)</fullName>
+ </names>
+ <xref>
+ <primaryRef db="DIP" id="17064N"/>
+ <secondaryRef db="Entrez GI" id="24643777"/>
+ <secondaryRef db="RefSeq" id="NP_728449"/>
+ </xref>
+ <organism ncbiTaxId="7227">
+ <names>
+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-7129">
+ <names>
+ <shortLabel/>
+ <fullName>CG31054-PA open reading frame</fullName>
+ </names>
+ <xref>
+ <primaryRef db="DIP" id="17055N"/>
+ <secondaryRef db="Entrez GI" id="24650771"/>
+ <secondaryRef db="RefSeq" id="NP_733242"/>
+ </xref>
+ <organism ncbiTaxId="7227">
+ <names>
+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-284">
+ <names>
+ <shortLabel/>
+ <fullName>calcium-binding protein 32</fullName>
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+ <xref>
+ <primaryRef db="DIP" id="754N"/>
+ <secondaryRef db="SwissProt" id="P41044"/>
+ <secondaryRef db="PIR" id="S37695"/>
+ <secondaryRef db="Entrez GI" id="17136674"/>
+ <secondaryRef db="RefSeq" id="NP_476838"/>
+ </xref>
+ <organism ncbiTaxId="7227">
+ <names>
+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-7168">
+ <names>
+ <shortLabel/>
+ <fullName>CG10019-PA open reading frame</fullName>
+ </names>
+ <xref>
+ <primaryRef db="DIP" id="17094N"/>
+ <secondaryRef db="Entrez GI" id="20129213"/>
+ <secondaryRef db="RefSeq" id="NP_608805"/>
+ </xref>
+ <organism ncbiTaxId="7227">
+ <names>
+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-7132">
+ <names>
+ <shortLabel/>
+ <fullName>slingshot (CG6238-PB)</fullName>
+ </names>
+ <xref>
+ <primaryRef db="DIP" id="17058N"/>
+ <secondaryRef db="Entrez GI" id="24649859"/>
+ <secondaryRef db="RefSeq" id="NP_733063"/>
+ </xref>
+ <organism ncbiTaxId="7227">
+ <names>
+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-222">
+ <names>
+ <shortLabel/>
+ <fullName>brown protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="DIP" id="387N"/>
+ <secondaryRef db="SwissProt" id="P12428"/>
+ <secondaryRef db="PIR" id="FYFFB"/>
+ <secondaryRef db="Entrez GI" id="72497"/>
+ <secondaryRef db="RefSeq" id="NP_523824"/>
+ </xref>
+ <organism ncbiTaxId="7227">
+ <names>
+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-7157">
+ <names>
+ <shortLabel/>
+ <fullName>CG2316-PA open reading frame</fullName>
+ </names>
+ <xref>
+ <primaryRef db="DIP" id="17084N"/>
+ <secondaryRef db="Entrez GI" id="24638546"/>
+ <secondaryRef db="RefSeq" id="NP_651906"/>
+ </xref>
+ <organism ncbiTaxId="7227">
+ <names>
+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-7152">
+ <names>
+ <shortLabel/>
+ <fullName>CG11327-PA open reading frame</fullName>
+ </names>
+ <xref>
+ <primaryRef db="DIP" id="17079N"/>
+ <secondaryRef db="Entrez GI" id="20129291"/>
+ <secondaryRef db="RefSeq" id="NP_609065"/>
+ </xref>
+ <organism ncbiTaxId="7227">
+ <names>
+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-7167">
+ <names>
+ <shortLabel/>
+ <fullName>CG3953-PA open reading frame</fullName>
+ </names>
+ <xref>
+ <primaryRef db="DIP" id="17095N"/>
+ <secondaryRef db="Entrez GI" id="21357023"/>
+ <secondaryRef db="RefSeq" id="NP_652072"/>
+ </xref>
+ <organism ncbiTaxId="7227">
+ <names>
+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-7120">
+ <names>
+ <shortLabel/>
+ <fullName>fork head (CG10002-PA) </fullName>
+ </names>
+ <xref>
+ <primaryRef db="DIP" id="17045N"/>
+ <secondaryRef db="SwissProt" id="P14734"/>
+ <secondaryRef db="PIR" id="A32380"/>
+ <secondaryRef db="Entrez GI" id="17738265"/>
+ <secondaryRef db="RefSeq" id="NP_524542"/>
+ </xref>
+ <organism ncbiTaxId="7227">
+ <names>
+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-617">
+ <names>
+ <shortLabel/>
+ <fullName>Suppressor of Hairless</fullName>
+ </names>
+ <xref>
+ <primaryRef db="DIP" id="177N"/>
+ <secondaryRef db="SwissProt" id="P28159"/>
+ <secondaryRef db="PIR" id="A42770"/>
+ <secondaryRef db="Entrez GI" id="17136726"/>
+ <secondaryRef db="RefSeq" id="NP_476868"/>
+ </xref>
+ <organism ncbiTaxId="7227">
+ <names>
+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-7141">
+ <names>
+ <shortLabel/>
+ <fullName>CG10009-PA open reading frame</fullName>
+ </names>
+ <xref>
+ <primaryRef db="DIP" id="17066N"/>
+ <secondaryRef db="Entrez GI" id="24650829"/>
+ <secondaryRef db="RefSeq" id="NP_651622"/>
+ </xref>
+ <organism ncbiTaxId="7227">
+ <names>
+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-7119">
+ <names>
+ <shortLabel/>
+ <fullName>CG10032-PA open reading frame</fullName>
+ </names>
+ <xref>
+ <primaryRef db="DIP" id="17046N"/>
+ <secondaryRef db="Entrez GI" id="24644797"/>
+ <secondaryRef db="RefSeq" id="NP_649714"/>
+ </xref>
+ <organism ncbiTaxId="7227">
+ <names>
+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-7130">
+ <names>
+ <shortLabel/>
+ <fullName>CG4849-PA open reading frame</fullName>
+ </names>
+ <xref>
+ <primaryRef db="DIP" id="17056N"/>
+ <secondaryRef db="Entrez GI" id="21357743"/>
+ <secondaryRef db="RefSeq" id="NP_651605"/>
+ </xref>
+ <organism ncbiTaxId="7227">
+ <names>
+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-7162">
+ <names>
+ <shortLabel/>
+ <fullName>lethal (2) 35Ea (CG4148-PA)</fullName>
+ </names>
+ <xref>
+ <primaryRef db="DIP" id="17089N"/>
+ <secondaryRef db="Entrez GI" id="17933736"/>
+ <secondaryRef db="RefSeq" id="NP_524930"/>
+ </xref>
+ <organism ncbiTaxId="7227">
+ <names>
+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-180">
+ <names>
+ <shortLabel/>
+ <fullName>transcription initiation factor IID chain p62</fullName>
+ </names>
+ <xref>
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+ <organism ncbiTaxId="7227">
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+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
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+ </proteinInteractor>
+ <proteinInteractor id="CPATH-7133">
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+ <shortLabel/>
+ <fullName>CG6459-PA open reading frame</fullName>
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+ <secondaryRef db="Entrez GI" id="20130085"/>
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+ <organism ncbiTaxId="7227">
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+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
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+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-360">
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+ <shortLabel/>
+ <fullName>extramacrochaetae protein</fullName>
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+ <secondaryRef db="RefSeq" id="NP_523876"/>
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+ <organism ncbiTaxId="7227">
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+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
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+ <proteinInteractor id="CPATH-371">
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+ <fullName>neurogenic gene complex E(spl) protein m7</fullName>
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+ <secondaryRef db="RefSeq" id="NP_536753"/>
+ </xref>
+ <organism ncbiTaxId="7227">
+ <names>
+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
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+ </organism>
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+ <proteinInteractor id="CPATH-7123">
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+ <fullName>CG15529-PA open reading frame</fullName>
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+ <secondaryRef db="RefSeq" id="NP_651773"/>
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+ <organism ncbiTaxId="7227">
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+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
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+ <proteinInteractor id="CPATH-7142">
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+ <fullName>CG11635-PA open reading frame</fullName>
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+ <organism ncbiTaxId="7227">
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+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
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+ <organism ncbiTaxId="7227">
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+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
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+ <proteinInteractor id="CPATH-1119">
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+ <shortLabel/>
+ <fullName>Presenilin (CG18803-PA)</fullName>
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+ <secondaryRef db="SwissProt" id="O02194"/>
+ <secondaryRef db="Entrez GI" id="17737687"/>
+ <secondaryRef db="RefSeq" id="NP_524184"/>
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+ <organism ncbiTaxId="7227">
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+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
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+ </proteinInteractor>
+ <proteinInteractor id="CPATH-7156">
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+ <shortLabel/>
+ <fullName>drumstick (CG10016-PB)</fullName>
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+ <primaryRef db="DIP" id="17082N"/>
+ <secondaryRef db="Entrez GI" id="24581481"/>
+ <secondaryRef db="RefSeq" id="NP_536788"/>
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+ <organism ncbiTaxId="7227">
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+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
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+ <proteinInteractor id="CPATH-196">
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+ <shortLabel/>
+ <fullName>TATA-binding protein-associated factor II</fullName>
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+ <secondaryRef db="SwissProt" id="Q24325"/>
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+ <organism ncbiTaxId="7227">
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+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
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+ <proteinInteractor id="CPATH-372">
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+ <shortLabel/>
+ <fullName>neurogenic gene complex E(spl) protein m5</fullName>
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+ <organism ncbiTaxId="7227">
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+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
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+ <proteinInteractor id="CPATH-7136">
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+ <shortLabel/>
+ <fullName>photorepair (CG11205-PA) </fullName>
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+ <secondaryRef db="Entrez GI" id="24586396"/>
+ <secondaryRef db="RefSeq" id="NP_523653"/>
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+ <organism ncbiTaxId="7227">
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+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
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+ <proteinInteractor id="CPATH-7147">
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+ <shortLabel/>
+ <fullName>CG31122-PA open reading frame</fullName>
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+ <secondaryRef db="RefSeq" id="NP_732342"/>
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+ <organism ncbiTaxId="7227">
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+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
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+ <proteinInteractor id="CPATH-364">
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+ <shortLabel/>
+ <fullName>enhancer of split locus protein m3</fullName>
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+ <organism ncbiTaxId="7227">
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+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
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+ <proteinInteractor id="CPATH-7126">
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+ <shortLabel/>
+ <fullName>Male-specific RNA 84Dc (CG17945-PA)</fullName>
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+ <organism ncbiTaxId="7227">
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+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
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+ <proteinInteractor id="CPATH-7135">
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+ <shortLabel/>
+ <fullName>CG9572-PA open reading frame</fullName>
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+ <organism ncbiTaxId="7227">
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+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
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+ <shortLabel/>
+ <fullName>CG3062-PA open reading frame</fullName>
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+ <organism ncbiTaxId="7227">
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+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
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+ <proteinInteractor id="CPATH-7163">
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+ <fullName>CG4621-PA open reading frame</fullName>
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+ <fullName>Drosophila melanogaster</fullName>
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+ <fullName>Drosophila melanogaster</fullName>
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+ <fullName>helix-loop-helix protein m-gamma </fullName>
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+ <fullName>Drosophila melanogaster</fullName>
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+ <fullName>CG7101-PA open reading frame</fullName>
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+ <shortLabel/>
+ <fullName>Drosophila melanogaster</fullName>
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+ <proteinInteractor id="CPATH-362">
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+ <shortLabel/>
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+ <fullName>Drosophila melanogaster</fullName>
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+ <fullName>CG1792-PA open reading frame</fullName>
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+ <fullName>Drosophila melanogaster</fullName>
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+ <fullName>CG10017-PA open reading frame</fullName>
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+ <fullName>Drosophila melanogaster</fullName>
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+ <fullName>Drosophila melanogaster</fullName>
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+ <fullName>CG2244-PA open reading frame</fullName>
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+ <fullName>Drosophila melanogaster</fullName>
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+ <fullName>CG32183-PB open reading frame</fullName>
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+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-7144"/>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-7141"/>
+ </proteinParticipant>
+ </participantList>
+ <xref>
+ <primaryRef db="DIP" id="18905E"/>
+ <secondaryRef db="CPATH" id="35403"/>
+ </xref>
+ </interaction>
+ <interaction>
+ <experimentList>
+ <experimentDescription id="DIP_24721X">
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="14605208"/>
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>Two hybrid test</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="DO" id="DO:00018"/>
+ <secondaryRef db="PSI" id="MI:0018"/>
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-7145"/>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-7141"/>
+ </proteinParticipant>
+ </participantList>
+ <xref>
+ <primaryRef db="DIP" id="18906E"/>
+ <secondaryRef db="CPATH" id="35404"/>
+ </xref>
+ </interaction>
+ <interaction>
+ <experimentList>
+ <experimentDescription id="DIP_24722X">
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="14605208"/>
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>Two hybrid test</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="DO" id="DO:00018"/>
+ <secondaryRef db="PSI" id="MI:0018"/>
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-7146"/>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-7141"/>
+ </proteinParticipant>
+ </participantList>
+ <xref>
+ <primaryRef db="DIP" id="18907E"/>
+ <secondaryRef db="CPATH" id="35405"/>
+ </xref>
+ </interaction>
+ <interaction>
+ <experimentList>
+ <experimentDescription id="DIP_24723X">
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="14605208"/>
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>Two hybrid test</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="DO" id="DO:00018"/>
+ <secondaryRef db="PSI" id="MI:0018"/>
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-7147"/>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-7141"/>
+ </proteinParticipant>
+ </participantList>
+ <xref>
+ <primaryRef db="DIP" id="18908E"/>
+ <secondaryRef db="CPATH" id="35406"/>
+ </xref>
+ </interaction>
+ <interaction>
+ <experimentList>
+ <experimentDescription id="DIP_37802X">
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="14605208"/>
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>Two hybrid test</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="DO" id="DO:00018"/>
+ <secondaryRef db="PSI" id="MI:0018"/>
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-7148"/>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-7141"/>
+ </proteinParticipant>
+ </participantList>
+ <xref>
+ <primaryRef db="DIP" id="18909E"/>
+ <secondaryRef db="CPATH" id="35407"/>
+ </xref>
+ </interaction>
+ <interaction>
+ <experimentList>
+ <experimentDescription id="DIP_24724X">
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="14605208"/>
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>Two hybrid test</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="DO" id="DO:00018"/>
+ <secondaryRef db="PSI" id="MI:0018"/>
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-7149"/>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-7141"/>
+ </proteinParticipant>
+ </participantList>
+ <xref>
+ <primaryRef db="DIP" id="18910E"/>
+ <secondaryRef db="CPATH" id="35408"/>
+ </xref>
+ </interaction>
+ <interaction>
+ <experimentList>
+ <experimentDescription id="DIP_24725X">
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="14605208"/>
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>Two hybrid test</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="DO" id="DO:00018"/>
+ <secondaryRef db="PSI" id="MI:0018"/>
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-7150"/>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-7141"/>
+ </proteinParticipant>
+ </participantList>
+ <xref>
+ <primaryRef db="DIP" id="18911E"/>
+ <secondaryRef db="CPATH" id="35409"/>
+ </xref>
+ </interaction>
+ <interaction>
+ <experimentList>
+ <experimentDescription id="DIP_24726X">
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="14605208"/>
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>Two hybrid test</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="DO" id="DO:00018"/>
+ <secondaryRef db="PSI" id="MI:0018"/>
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-7151"/>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-7141"/>
+ </proteinParticipant>
+ </participantList>
+ <xref>
+ <primaryRef db="DIP" id="18912E"/>
+ <secondaryRef db="CPATH" id="35410"/>
+ </xref>
+ </interaction>
+ <interaction>
+ <experimentList>
+ <experimentDescription id="DIP_24727X">
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="14605208"/>
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>Two hybrid test</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="DO" id="DO:00018"/>
+ <secondaryRef db="PSI" id="MI:0018"/>
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-7152"/>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-7153"/>
+ </proteinParticipant>
+ </participantList>
+ <xref>
+ <primaryRef db="DIP" id="18913E"/>
+ <secondaryRef db="CPATH" id="35411"/>
+ </xref>
+ </interaction>
+ <interaction>
+ <experimentList>
+ <experimentDescription id="DIP_24728X">
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="14605208"/>
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>Two hybrid test</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="DO" id="DO:00018"/>
+ <secondaryRef db="PSI" id="MI:0018"/>
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-290"/>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-7153"/>
+ </proteinParticipant>
+ </participantList>
+ <xref>
+ <primaryRef db="DIP" id="18914E"/>
+ <secondaryRef db="CPATH" id="35412"/>
+ </xref>
+ </interaction>
+ <interaction>
+ <experimentList>
+ <experimentDescription id="DIP_37803X">
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="14605208"/>
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>Two hybrid test</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="DO" id="DO:00018"/>
+ <secondaryRef db="PSI" id="MI:0018"/>
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-7154"/>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-7153"/>
+ </proteinParticipant>
+ </participantList>
+ <xref>
+ <primaryRef db="DIP" id="18915E"/>
+ <secondaryRef db="CPATH" id="35413"/>
+ </xref>
+ </interaction>
+ <interaction>
+ <experimentList>
+ <experimentDescription id="DIP_24729X">
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="14605208"/>
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>Two hybrid test</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="DO" id="DO:00018"/>
+ <secondaryRef db="PSI" id="MI:0018"/>
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-7155"/>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-7156"/>
+ </proteinParticipant>
+ </participantList>
+ <xref>
+ <primaryRef db="DIP" id="18916E"/>
+ <secondaryRef db="CPATH" id="35414"/>
+ </xref>
+ </interaction>
+ <interaction>
+ <experimentList>
+ <experimentDescription id="DIP_37804X">
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="14605208"/>
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>Two hybrid test</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="DO" id="DO:00018"/>
+ <secondaryRef db="PSI" id="MI:0018"/>
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-7157"/>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-7156"/>
+ </proteinParticipant>
+ </participantList>
+ <xref>
+ <primaryRef db="DIP" id="18917E"/>
+ <secondaryRef db="CPATH" id="35415"/>
+ </xref>
+ </interaction>
+ <interaction>
+ <experimentList>
+ <experimentDescription id="DIP_24730X">
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="14605208"/>
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>Two hybrid test</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="DO" id="DO:00018"/>
+ <secondaryRef db="PSI" id="MI:0018"/>
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-7158"/>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-7156"/>
+ </proteinParticipant>
+ </participantList>
+ <xref>
+ <primaryRef db="DIP" id="18918E"/>
+ <secondaryRef db="CPATH" id="35416"/>
+ </xref>
+ </interaction>
+ <interaction>
+ <experimentList>
+ <experimentDescription id="DIP_24731X">
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="14605208"/>
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>Two hybrid test</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="DO" id="DO:00018"/>
+ <secondaryRef db="PSI" id="MI:0018"/>
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-7159"/>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-7160"/>
+ </proteinParticipant>
+ </participantList>
+ <xref>
+ <primaryRef db="DIP" id="18919E"/>
+ <secondaryRef db="CPATH" id="35417"/>
+ </xref>
+ </interaction>
+ <interaction>
+ <experimentList>
+ <experimentDescription id="DIP_37805X">
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="14605208"/>
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>Two hybrid test</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="DO" id="DO:00018"/>
+ <secondaryRef db="PSI" id="MI:0018"/>
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-7161"/>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-7160"/>
+ </proteinParticipant>
+ </participantList>
+ <xref>
+ <primaryRef db="DIP" id="18920E"/>
+ <secondaryRef db="CPATH" id="35418"/>
+ </xref>
+ </interaction>
+ <interaction>
+ <experimentList>
+ <experimentDescription id="DIP_24732X">
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="14605208"/>
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>Two hybrid test</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="DO" id="DO:00018"/>
+ <secondaryRef db="PSI" id="MI:0018"/>
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-7162"/>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-7160"/>
+ </proteinParticipant>
+ </participantList>
+ <xref>
+ <primaryRef db="DIP" id="18921E"/>
+ <secondaryRef db="CPATH" id="35419"/>
+ </xref>
+ </interaction>
+ <interaction>
+ <experimentList>
+ <experimentDescription id="DIP_24733X">
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="14605208"/>
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>Two hybrid test</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="DO" id="DO:00018"/>
+ <secondaryRef db="PSI" id="MI:0018"/>
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-7163"/>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-7160"/>
+ </proteinParticipant>
+ </participantList>
+ <xref>
+ <primaryRef db="DIP" id="18922E"/>
+ <secondaryRef db="CPATH" id="35420"/>
+ </xref>
+ </interaction>
+ <interaction>
+ <experimentList>
+ <experimentDescription id="DIP_24734X">
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="14605208"/>
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>Two hybrid test</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="DO" id="DO:00018"/>
+ <secondaryRef db="PSI" id="MI:0018"/>
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-7164"/>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-7160"/>
+ </proteinParticipant>
+ </participantList>
+ <xref>
+ <primaryRef db="DIP" id="18923E"/>
+ <secondaryRef db="CPATH" id="35421"/>
+ </xref>
+ </interaction>
+ <interaction>
+ <experimentList>
+ <experimentDescription id="DIP_24735X">
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="14605208"/>
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>Two hybrid test</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="DO" id="DO:00018"/>
+ <secondaryRef db="PSI" id="MI:0018"/>
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-7165"/>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-7160"/>
+ </proteinParticipant>
+ </participantList>
+ <xref>
+ <primaryRef db="DIP" id="18924E"/>
+ <secondaryRef db="CPATH" id="35422"/>
+ </xref>
+ </interaction>
+ <interaction>
+ <experimentList>
+ <experimentDescription id="DIP_24736X">
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="14605208"/>
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>Two hybrid test</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="DO" id="DO:00018"/>
+ <secondaryRef db="PSI" id="MI:0018"/>
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-7166"/>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-7160"/>
+ </proteinParticipant>
+ </participantList>
+ <xref>
+ <primaryRef db="DIP" id="18925E"/>
+ <secondaryRef db="CPATH" id="35423"/>
+ </xref>
+ </interaction>
+ <interaction>
+ <experimentList>
+ <experimentDescription id="DIP_24737X">
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="14605208"/>
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>Two hybrid test</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="DO" id="DO:00018"/>
+ <secondaryRef db="PSI" id="MI:0018"/>
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-7167"/>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-7168"/>
+ </proteinParticipant>
+ </participantList>
+ <xref>
+ <primaryRef db="DIP" id="18926E"/>
+ <secondaryRef db="CPATH" id="35424"/>
+ </xref>
+ </interaction>
+ </interactionList>
+ </entry>
+</entrySet>
\ No newline at end of file
diff --git a/coreplugins/PSI-MI/sampleData/psi_sample_2_5.xml b/coreplugins/PSI-MI/sampleData/psi_sample_2_5.xml
new file mode 100755
index 0000000..e9f521a
--- /dev/null
+++ b/coreplugins/PSI-MI/sampleData/psi_sample_2_5.xml
@@ -0,0 +1,2624 @@
+<?xml version="1.0" encoding="UTF-8"?>
+ <entrySet level="2" version="5" xmlns="net:sf:psidev:mi" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="net:sf:psidev:mi http://psidev.sourceforge.net/mi/rel25/src/MIF25.xsd">
+ <entry>
+ <source releaseDate="2006-02-19">
+ <names>
+ <shortLabel>European Bioinformatics Institute</shortLabel>
+ </names>
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" dbAc="MI:0446" id="14681455" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </bibref>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0469" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ <attributeList>
+ <attribute name="postalAddress">Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom</attribute>
+ <attribute name="url">http://www.ebi.ac.uk</attribute>
+ </attributeList>
+ </source>
+ <experimentList>
+ <experimentDescription id="2">
+ <names>
+ <shortLabel>falsone-2005-1</shortLabel>
+ <fullName>A proteomic snapshot of the human heat shock protein 90 interactome.</fullName>
+ </names>
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" dbAc="MI:0446" id="16263121" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </bibref>
+ <xref>
+ <primaryRef db="intact" dbAc="MI:0469" id="EBI-709759" secondary="falsone-2005-1"/>
+ <secondaryRef db="newt" dbAc="MI:0247" id="9606" refType="target-species" secondary="human"/>
+ </xref>
+ <hostOrganismList>
+ <hostOrganism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human-293</shortLabel>
+ <fullName>Homo sapiens transformed primary embryonal kidney cells</fullName>
+ </names>
+ <cellType>
+ <names>
+ <shortLabel>293</shortLabel>
+ <fullName>Transformed human primary embryonal kidney cells.</fullName>
+ </names>
+ <xref>
+ <primaryRef db="cabri" dbAc="MI:0246" id="ACC 305" refType="identity" refTypeAc="MI:0356"/>
+ </xref>
+ </cellType>
+ </hostOrganism>
+ </hostOrganismList>
+ <interactionDetectionMethod>
+ <names>
+ <shortLabel>anti bait coip</shortLabel>
+ <fullName>anti bait coimmunoprecipitation</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0006" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="7708014" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactionDetectionMethod>
+ <participantIdentificationMethod>
+ <names>
+ <shortLabel>fingerprinting</shortLabel>
+ <fullName>peptide massfingerprinting</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0082" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="10967324" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="11752590" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="11805826" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </participantIdentificationMethod>
+ <attributeList>
+ <attribute name="exp-modification">Anti-Hsp90 antibody (clone AC68) was used to immunopreciptate endogenous Hsp90 in HEK293 cell line. Co-immunoprecipitated proteins were analyzed by SDS-PAGE folllowed by silver staining. The bands were cut, dried, subjected to tryptic digestion and peptides were gel-extracted. Nano-HPLC-MS/MS sequencing was then used for protein identification.</attribute>
+ <attribute name="contact-email">andreas.kungl at uni-graz.at</attribute>
+ <attribute name="figure-legend">Table 1</attribute>
+ <attribute name="author-list">Falsone SF., Gesslbauer B., Tirk F., Piccinini AM., Kungl AJ.</attribute>
+ </attributeList>
+ </experimentDescription>
+ </experimentList>
+ <interactorList>
+ <interactor id="4">
+ <names>
+ <shortLabel>hs90b_human</shortLabel>
+ <fullName>Heat shock protein HSP 90-beta</fullName>
+ <alias type="gene name" typeAc="MI:0301">HSPCB</alias>
+ <alias type="gene name synonym" typeAc="MI:0302">HSP90B</alias>
+ <alias type="gene name synonym" typeAc="MI:0302">HSPC2</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="P08238" refType="identity" refTypeAc="MI:0356" secondary="hs90b_human" version="SP_77"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005737" secondary="C:cytoplasm"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0030235" secondary="F:nitric-oxide synthase regula"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR003594" secondary="ATPbind_ATPase"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR001404" secondary="Hsp90"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q9NQW0" refType="secondary-ac" refTypeAc="MI:0360" secondary="hs90b_human" version="SP_77"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0030911" secondary="F:TPR domain binding"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0051082" secondary="F:unfolded protein binding"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0045429" secondary="P:positive regulation of nitri"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0006986" secondary="P:response to unfolded protein"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-352572" secondary="hs90b_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>PEEVHHGEEEVETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNASDALDKIRYESLTDPSKLDSGKELKIDIIPNPQERTLTLVDTGIGMTKADLINNLGTIAKSGTKAFMEALQAGADISMIGQFGVGFYSAYLVAEKVVVITKHNDDEQYAWESSAGGSFTVRADHGEPIGRGTKVILHLKEDQTEYLEERRVKEVVKKHSQFIGYPITLYLEKEREKEISDDEAEEEKGEKEEEDKDDEEKPKIEDVGSDEEDDSGKDKKKKTKKIKEKYIDQEELNKTKPIWTRNPDDITQEEYGEFYKSLTNDWEDHLAVKHFSVEGQLEFRALLFIPRRAPFDLFENKKKKNNIKLYVRRVFIMDSCDELIPEYLNFIRGVVDSEDLPLNISREMLQQSKILKVIRKNIVKKCLELFSELAEDKENYKKFYEAFSKNLKLGIHEDSTNRRRLSELLRYHTSQSGDEMTSLSEY [...]
+ </interactor>
+ <interactor id="6">
+ <names>
+ <shortLabel>hsp71_human</shortLabel>
+ <fullName>Heat shock 70 kDa protein 1</fullName>
+ <alias type="gene name" typeAc="MI:0301">HSPA1A</alias>
+ <alias type="gene name synonym" typeAc="MI:0302">HSPA1</alias>
+ <alias type="gene name" typeAc="MI:0301">HSPA1B</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="P08107" refType="identity" refTypeAc="MI:0356" secondary="hsp71_human" version="SP_71"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005737" secondary="C:cytoplasm"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005634" secondary="C:nucleus"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0006402" secondary="P:mRNA catabolism"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0006986" secondary="P:response to unfolded protein"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR001023" secondary="Hsp70"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="P19790" refType="secondary-ac" refTypeAc="MI:0360" secondary="hsp71_human" version="SP_71"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q9UQL9" refType="secondary-ac" refTypeAc="MI:0360" secondary="hsp71_human" version="SP_71"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q9UQM0" refType="secondary-ac" refTypeAc="MI:0360" secondary="hsp71_human" version="SP_71"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-629985" secondary="hsp71_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>MAKAAAIGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQVALNPQNTVFDAKRLIGRKFGDPVVQSDMKHWPFQVINDGDKPKVQVSYKGETKAFYPEEISSMVLTKMKEIAEAYLGYPVTNAVITVPAYFNDSQRQATKDAGVIAGLNVLRIINEPTAAAIAYGLDRTGKGERNVLIFDLGGGTFDVSILTIDDGIFEVKATAGDTHLGGEDFDNRLVNHFVEEFKRKHKKDISQNKRAVRRLRTACERAKRTLSSSTQASLEIDSLFEGIDFYTSITRARFEELCSDLFRSTLEPVEKALRDAKLDKAQIHDLVLVGGSTRIPKVQKLLQDFFNGRDLNKSINPDEAVAYGAAVQAAILMGDKSENVQDLLLLDVAPLSLGLETAGGVMTALIKRNSTIPTKQTQIFTTYSDNQPGVLIQVYEGERAMTKDNNLLGRFELSGIPPAPRGV [...]
+ </interactor>
+ <interactor id="8">
+ <names>
+ <shortLabel>tcpa_human</shortLabel>
+ <fullName>T-complex protein 1, alpha subunit</fullName>
+ <alias type="gene name" typeAc="MI:0301">CCT1</alias>
+ <alias type="gene name synonym" typeAc="MI:0302">CCTA</alias>
+ <alias type="gene name synonym" typeAc="MI:0302">TCP1</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="P17987" refType="identity" refTypeAc="MI:0356" secondary="tcpa_human" version="SP_48"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005829" secondary="C:cytosol"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0051082" secondary="F:unfolded protein binding"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0007021" secondary="P:tubulin folding"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR002194" secondary="Chaperonin_TCP-1"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR001844" secondary="Chaprnin_Cpn60"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR002423" secondary="Cpn60/TCP-1"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR012715" secondary="Chap_CCT_alpha"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q15556" refType="secondary-ac" refTypeAc="MI:0360" secondary="tcpa_human" version="SP_48"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q5TCM3" refType="secondary-ac" refTypeAc="MI:0360" secondary="tcpa_human" version="SP_48"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-356553" secondary="tcpa_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>MEGPLSVFGDRSTGETIRSQNVMAAASIANIVKSSLGPVGLDKMLVDDIGDVTITNDGATILKLLEVEHPAAKVLCELADLQDKEVGDGTTSVVIIAAELLKNADELVKQKIHPTSVISGYRLACKEAVRYINENLIVNTDELGRDCLINAAKTSMSSKIIGINGDFFANMVVDAVLAIKYTDIRGQPRYPVNSVNILKAHGRSQMESMLISGYALNCVVGSQGMPKRIVNAKIACLDFSLQKTKMKLGVQVVITDPEKLDQIRQRESDITKERIQKILATGANVILTTGGIDDMCLKYFVEAGAMAVRRVLKRDLKRIAKASGATILSTLANLEGEETFEAAMLGQAEEVVQERICDDELILIKNTKARTSASIILRGANDFMCDEMERSLHDALCVVKRVLESKSVVPGGGAVEAALSIYLENYATSMGSREQLAIAEFARSLLVIPNTLAVNAAQDSTDLVAKLRAFH [...]
+ </interactor>
+ <interactor id="10">
+ <names>
+ <shortLabel>hs105_human</shortLabel>
+ <fullName>Heat-shock protein 105 kDa</fullName>
+ <alias type="gene name" typeAc="MI:0301">HSPH1</alias>
+ <alias type="gene name synonym" typeAc="MI:0302">HSP105</alias>
+ <alias type="gene name synonym" typeAc="MI:0302">HSP110</alias>
+ <alias type="gene name synonym" typeAc="MI:0302">KIAA0201</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="Q92598" refType="identity" refTypeAc="MI:0356" secondary="hs105_human" version="SP_48"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005737" secondary="C:cytoplasm"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0006986" secondary="P:response to unfolded protein"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR001023" secondary="Hsp70"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="O95739" refType="secondary-ac" refTypeAc="MI:0360" secondary="hs105_human" version="SP_48"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q9UPC4" refType="secondary-ac" refTypeAc="MI:0360" secondary="hs105_human" version="SP_48"/>
+ <secondaryRef db="huge" dbAc="MI:0249" id="KIAA0201"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-356829" secondary="hs105_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>MSVVGLDVGSQSCYIAVARAGGIETIANEFSDRCTPSVISFGSKNRTIGVAAKNQQITHANNTVSNFKRFHGRAFNDPFIQKEKENLSYDLVPLKNGGVGIKVMYMGEEHLFSVEQITAMLLTKLKETAENSLKKPVTDCVISVPSFFTDAERRSVLDAAQIVGLNCLRLMNDMTAVALNYGIYKQDLPSLDEKPRIVVFVDMGHSAFQVSACAFNKGKLKVLGTAFDPFLGGKNFDEKLVEHFCAEFKTKYKLDAKSKIRALLRLYQECEKLKKLMSSNSTDLPLNIECFMNDKDVSGKMNRSQFEELCAELLQKIEVPLYSLLEQTHLKVEDVSAVEIVGGATRIPAVKERIAKFFGKDISTTLNADEAVARGCALQCAILSPAFKVREFSVTDAVPFPISLIWNHDSEDTEGVHEVFSRNHAAPFSKVLTFLRRGPFELEAFYSDPQGVPYPEAKIGRFVVQNVSAQK [...]
+ </interactor>
+ <interactor id="12">
+ <names>
+ <shortLabel>prkdc_human</shortLabel>
+ <fullName>DNA-dependent protein kinase catalytic subunit</fullName>
+ <alias type="gene name" typeAc="MI:0301">PRKDC</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="P78527" refType="identity" refTypeAc="MI:0356" secondary="prkdc_human" version="SP_48"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0004672" secondary="F:protein kinase activity"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0006464" secondary="P:protein modification"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR003151" secondary="FAT"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR003152" secondary="FATC"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR000403" secondary="PI3_PI4_kinase"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="P78528" refType="secondary-ac" refTypeAc="MI:0360" secondary="prkdc_human" version="SP_48"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q13327" refType="secondary-ac" refTypeAc="MI:0360" secondary="prkdc_human" version="SP_48"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q13337" refType="secondary-ac" refTypeAc="MI:0360" secondary="prkdc_human" version="SP_48"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q14175" refType="secondary-ac" refTypeAc="MI:0360" secondary="prkdc_human" version="SP_48"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q7Z611" refType="secondary-ac" refTypeAc="MI:0360" secondary="prkdc_human" version="SP_48"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q96SE6" refType="secondary-ac" refTypeAc="MI:0360" secondary="prkdc_human" version="SP_48"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q9UME3" refType="secondary-ac" refTypeAc="MI:0360" secondary="prkdc_human" version="SP_48"/>
+ <secondaryRef db="reactome protein" dbAc="MI:0245" id="P78527"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005515" secondary="F:protein binding"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR011989" secondary="ARM-like"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR000357" secondary="HEAT"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR012582" secondary="NUC194"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR002885" secondary="PPR"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR011990" secondary="TPR-like_helical"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-352053" secondary="prkdc_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>MAGSGAGVRCSLLRLQETLSAADRCGAALAGHQLIRGLGQECVLSSSPAVLALQTSLVFSRDFGLLVFVRKSLNSIEFRECREEILKFLCIFLEKMGQKIAPYSVEIKNTCTSVYTKDRAAKCKIPALDLLIKLLQTFRSSRLMDEFKIGELFSKFYGELALKKKIPDTVLEKVYELLGLLGEVHPSEMINNAENLFRAFLGELKTQMTSAVREPKLPVLAGCLKGLSSLLCNFTKSMEEDPQTSREIFNFVLKAIRPQIDLKRYAVPSAGLRLFALHASQFSTCLLDNYVSLFEVLLKWCAHTNVELKKAALSALESFLKQVSNMVAKNAEMHKNKLQYFMEQFYGIIRNVDSNNKELSIAIRGYGLFAGPCKVINAKDVDFMYVELIQRCKQMFLTQTDTGDDRVYQMPSFLQSVASVLLYLDTVPEVYTPVLEHLVVMQIDSFPQYSPKMQLVCCRAIVKVFLALAAK [...]
+ </interactor>
+ <interactor id="14">
+ <names>
+ <shortLabel>gnai2_human</shortLabel>
+ <fullName>Guanine nucleotide-binding protein G(i), alpha-2 subunit</fullName>
+ <alias type="gene name" typeAc="MI:0301">GNAI2</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="P04899" refType="identity" refTypeAc="MI:0356" secondary="gnai2_human" version="SP_48"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0003924" secondary="F:GTPase activity"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0007186" secondary="P:G-protein coupled receptor p"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0007194" secondary="P:negative regulation of adeny"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0007584" secondary="P:response to nutrients"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0007165" secondary="P:signal transduction"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR001019" secondary="Gprotein_alpha"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR001408" secondary="Gprotein_alphaI"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR011025" secondary="Transducn_insert"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-353997" secondary="gnai2_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>GCTVSAEDKAAAERSKMIDKNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEDGYSEEECRQYRAVVYSNTIQSIMAIVKAMGNLQIDFADPSRADDARQLFALSCTAEEQGVLPDDLSGVIRRLWADHGVQACFGRSREYQLNDSAAYYLNDLERIAQSDYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSAYDLVLAEDEEMNRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKITHSPLTICFPEYTGANKYDEAASYIQSKFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF</sequence>
+ </interactor>
+ <interactor id="16">
+ <names>
+ <shortLabel>xpo1_human</shortLabel>
+ <fullName>Exportin-1</fullName>
+ <alias type="gene name" typeAc="MI:0301">XPO1</alias>
+ <alias type="gene name synonym" typeAc="MI:0302">CRM1</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="O14980" refType="identity" refTypeAc="MI:0356" secondary="xpo1_human" version="SP_48"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005737" secondary="C:cytoplasm"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005635" secondary="C:nuclear membrane"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005654" secondary="C:nucleoplasm"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR001494" secondary="Importinb_N"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q63HP8" refType="secondary-ac" refTypeAc="MI:0360" secondary="xpo1_human" version="SP_48"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005515" secondary="F:protein binding"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR011989" secondary="ARM-like"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR000357" secondary="HEAT"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q68CP3" refType="secondary-ac" refTypeAc="MI:0360" secondary="xpo1_human" version="SP_48"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q99433" refType="secondary-ac" refTypeAc="MI:0360" secondary="xpo1_human" version="SP_48"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-355867" secondary="xpo1_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>MPAIMTMLADHAARQLLDFSQKLDINLLDNVVNCLYHGEGAQQRMAQEVLTHLKEHPDAWTRVDTILEFSQNMNTKYYGLQILENVIKTRWKILPRNQCEGIKKYVVGLIIKTSSDPTCVEKEKVYIGKLNMILVQILKQEWPKHWPTFISDIVGASRTSESLCQNNMVILKLLSEEVFDFSSGQITQVKSKHLKDSMCNEFSQIFQLCQFVMENSQNAPLVHATLETLLRFLNWIPLGYIFETKLISTLIYKFLNVPMFRNVSLKCLTEIAGVSVSQYEEQFVTLFTLTMMQLKQMLPLNTNIRLAYSNGKDDEQNFIQNLSLFLCTFLKEHDQLIEKRLNLRETLMEALHYMLLVSEVEETEIFKICLEYWNHLAAELYRESPFSTSASPLLSGSQHFDVPPRRQLYLPMLFKVRLLMVSRMAKPEEVLVVENDQGEVVREFMKDTDSINLYKNMRETLVYLTHLDYVD [...]
+ </interactor>
+ <interactor id="18">
+ <names>
+ <shortLabel>kpym_human</shortLabel>
+ <fullName>Pyruvate kinase, isozymes M1/M2</fullName>
+ <alias type="gene name" typeAc="MI:0301">PKM2</alias>
+ <alias type="gene name synonym" typeAc="MI:0302">PKM</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="P14618" refType="identity" refTypeAc="MI:0356" secondary="kpym_human" version="SP_48"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005829" secondary="C:cytosol"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0004743" secondary="F:pyruvate kinase activity"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0006096" secondary="P:glycolysis"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR001697" secondary="Pyruvate_kinase"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="P14786" refType="secondary-ac" refTypeAc="MI:0360" secondary="kpym_human" version="SP_48"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q96E76" refType="secondary-ac" refTypeAc="MI:0360" secondary="kpym_human" version="SP_48"/>
+ <secondaryRef db="reactome protein" dbAc="MI:0245" id="P14618"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q9BWB5" refType="secondary-ac" refTypeAc="MI:0360" secondary="kpym_human" version="SP_48"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q9UPF2" refType="secondary-ac" refTypeAc="MI:0360" secondary="kpym_human" version="SP_48"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005515" secondary="F:protein binding"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-353408" secondary="kpym_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>SKPHSEAGTAFIQTQQLHAAMADTFLEHMCRLDIDSPPITARNTGIICTIGPASRSVETLKEMIKSGMNVARLNFSHGTHEYHAETIKNVRTATESFASDPILYRPVAVALDTKGPEIRTGLIKGSGTAEVELKKGATLKITLDNAYMEKCDENILWLDYKNICKVVEVGSKIYVDDGLISLQVKQKGADFLVTEVENGGSLGSKKGVNLPGAAVDLPAVSEKDIQDLKFGVEQDVDMVFASFIRKASDVHEVRKVLGEKGKNIKIISKIENHEGVRRFDEILEASDGIMVARGDLGIEIPAEKVFLAQKMMIGRCNRAGKPVICATQMLESMIKKPRPTRAEGSDVANAVLDGADCIMLSGETAKGDYPLEAVRMQHLIAREAEAAIYHLQLFEELRRLAPITSDPTEATAVGAVEASFKCCSGAIIVLTKSGRSAHQVARYRPRAPIIAVTRNPQTARQAHLYRGIFPV [...]
+ </interactor>
+ <interactor id="20">
+ <names>
+ <shortLabel>g3p1_human</shortLabel>
+ <fullName>Glyceraldehyde-3-phosphate dehydrogenase, muscle</fullName>
+ <alias type="gene name" typeAc="MI:0301">GAPD</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="P00354" refType="identity" refTypeAc="MI:0356" secondary="g3p1_human" version="SP_47"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0004365" secondary="F:glyceraldehyde-3-phosphate d"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005737" secondary="C:cytoplasm"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0006096" secondary="P:glycolysis"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR000173" secondary="GAP_dhdrogenase"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR006424" secondary="GAPDH-I"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-709590" secondary="g3p1_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>GKVKVGVDGFGRIGRLVTRAAFNSGKVDIVAINDPFIDLHYMVYMFQYDSTHGKFHGTVKAEDGKLVIDGKAITIFQERDPENIKWGDAGTAYVVESTGVFTTMEKAGAHLKGGAKRIVISAPSADAPMFVMGVNHFKYANSLKIISNASCTTNCLAPLAKVIHDHFGIVEGLMTTVHAITATQKTVDSPSGKLWRGGRGAAQNLIPASTGAAKAVGKVIPELDGKLTGMAFRVPTANVSVLDLTCRLEKPAKYDDIKKVVKEASEGPLKGILGYTEDEVVSDDFNGSNHSSIFDAGAGIELNDTFVKLVSWYDNEFGYSERVVDLMAHMASKE</sequence>
+ </interactor>
+ <interactor id="22">
+ <names>
+ <shortLabel>pgk1_human</shortLabel>
+ <fullName>Phosphoglycerate kinase 1</fullName>
+ <alias type="gene name" typeAc="MI:0301">PGK1</alias>
+ <alias type="gene name synonym" typeAc="MI:0302">PGKA</alias>
+ <alias type="orf name" typeAc="MI:0306">OK/SW-cl.110</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="P00558" refType="identity" refTypeAc="MI:0356" secondary="pgk1_human" version="SP_48"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005524" secondary="F:ATP binding"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0004618" secondary="F:phosphoglycerate kinase acti"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0006096" secondary="P:glycolysis"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0016310" secondary="P:phosphorylation"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR001576" secondary="PGK"/>
+ <secondaryRef db="reactome protein" dbAc="MI:0245" id="P00558"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q6IBT6" refType="secondary-ac" refTypeAc="MI:0360" secondary="pgk1_human" version="SP_48"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q8NI87" refType="secondary-ac" refTypeAc="MI:0360" secondary="pgk1_human" version="SP_48"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-709599" secondary="pgk1_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>SLSNKLTLDKLDVKGKRVVMRVDFNVPMKNNQITNNQRIKAAVPSIKFCLDNGAKSVVLMSHLGRPDGVPMPDKYSLEPVAVELKSLLGKDVLFLKDCVGPEVEKACANPAAGSVILLENLRFHVEEEGKGKDASGNKVKAEPAKIEAFRASLSKLGDVYVNDAFGTAHRAHSSMVGVNLPQKAGGFLMKKELNYFAKALESPERPFLAILGGAKVADKIQLINNMLDKVNEMIIGGGMAFTFLKVLNNMEIGTSLFDEEGAKIVKDLMSKAEKNGVKITLPVDFVTADKFDENAKTGQATVASGIPAGWMGLDCGPESSKKYAEAVTRAKQIVWNGPVGVFEWEAFARGTKALMDEVVKATSRGCITIIGGGDTATCCAKWNTEDKVSHVSTGGGASLELLEGKVLPGVDALSNI</sequence>
+ </interactor>
+ <interactor id="24">
+ <names>
+ <shortLabel>ldha_human</shortLabel>
+ <fullName>L-lactate dehydrogenase A chain</fullName>
+ <alias type="gene name" typeAc="MI:0301">LDHA</alias>
+ <alias type="gene name synonym" typeAc="MI:0302">PIG19</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="P00338" refType="identity" refTypeAc="MI:0356" secondary="ldha_human" version="SP_48"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005829" secondary="C:cytosol"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0004459" secondary="F:L-lactate dehydrogenase acti"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR001236" secondary="ldh"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR001557" secondary="L_LDH_MDH"/>
+ <secondaryRef db="reactome protein" dbAc="MI:0245" id="P00338"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR011304" secondary="L-LDH-NAD"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005515" secondary="F:protein binding"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q53G53" refType="secondary-ac" refTypeAc="MI:0360" secondary="ldha_human" version="SP_48"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q6IBM7" refType="secondary-ac" refTypeAc="MI:0360" secondary="ldha_human" version="SP_48"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q6ZNV1" refType="secondary-ac" refTypeAc="MI:0360" secondary="ldha_human" version="SP_48"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-372327" secondary="ldha_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>ATLKDQLIYNLLKEEQTPQNKITVVGVGAVGMACAISILMKDLADELALVDVIEDKLKGEMMDLQHGSLFLRTPKIVSGKDYNVTANSKLVIITAGARQQEGESRLNLVQRNVNIFKFIIPNVVKYSPNCKLLIVSNPVDILTYVAWKISGFPKNRVIGSGCNLDSARFRYLMGERLGVHPLSCHGWVLGEHGDSSVPVWSGMNVAGVSLKTLHPDLGTDKDKEQWKEVHKQVVESAYEVIKLKGYTSWAIGLSVADLAESIMKNLRRVHPVSTMIKGLYGIKDDVFLSVPCILGQNGISDLVKVTLTSEEEARLKKSADTLWGIQKELQF</sequence>
+ </interactor>
+ <interactor id="26">
+ <names>
+ <shortLabel>aldoa_human</shortLabel>
+ <fullName>Fructose-bisphosphate aldolase A</fullName>
+ <alias type="gene name" typeAc="MI:0301">ALDOA</alias>
+ <alias type="gene name synonym" typeAc="MI:0302">ALDA</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="P04075" refType="identity" refTypeAc="MI:0356" secondary="aldoa_human" version="SP_49"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0004332" secondary="F:fructose-bisphosphate aldola"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0006000" secondary="P:fructose metabolism"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0006096" secondary="P:glycolysis"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0006941" secondary="P:striated muscle contraction"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR000741" secondary="Aldolase_I"/>
+ <secondaryRef db="reactome protein" dbAc="MI:0245" id="P04075"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q6FH76" refType="secondary-ac" refTypeAc="MI:0360" secondary="aldoa_human" version="SP_49"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-709613" secondary="aldoa_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>PYQYPALTPEQKKELSDIAHRIVAPGKGILAADESTGSIAKRLQSIGTENTEENRRFYRQLLLTADDRVNPCIGGVILFHETLYQKADDGRPFPQVIKSKGGVVGIKVDKGVVPLAGTNGETTTQGLDGLSERCAQYKKDGADFAKWRCVLKIGEHTPSALAIMENANVLARYASICQQNGIVPIVEPEILPDGDHDLKRCQYVTEKVLAAVYKALSDHHIYLEGTLLKPNMVTPGHACTQKFSHEEIAMATVTALRRTVPPAVTGITFLSGGQSEEEASINLNAINKCPLLKPWALTFSYGRALQASALKAWGGKKENLKAAQEEYVKRALANSLACQGKYTPSGQAGAAASESLFVSNHAY</sequence>
+ </interactor>
+ <interactor id="28">
+ <names>
+ <shortLabel>mdhc_human</shortLabel>
+ <fullName>Malate dehydrogenase, cytoplasmic</fullName>
+ <alias type="gene name" typeAc="MI:0301">MDH1</alias>
+ <alias type="gene name synonym" typeAc="MI:0302">MDHA</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="P40925" refType="identity" refTypeAc="MI:0356" secondary="mdhc_human" version="SP_49"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005829" secondary="C:cytosol"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0004470" secondary="F:malic enzyme activity"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR001557" secondary="L_LDH_MDH"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR001236" secondary="ldh"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR008267" secondary="Mal_dehydrog"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR010945" secondary="MalateDH_SF1"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR001252" secondary="Mdh_AS"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR011274" secondary="MDH_euk_cyt"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-709625" secondary="mdhc_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>SEPIRVLVTGAAGQIAYSLLYSIGNGSVFGKDQPIILVLLDITPMMGVLDGVLMELQDCALPLLKDVIATDKEDVAFKDLDVAILVGSMPRREGMERKDLLKANVKIFKSQGAALDKYAKKSVKVIVVGNPANTNCLTASKSAPSIPKENFSCLTRLDHNRAKAQIALKLGVTANDVKNVIIWGNHSSTQYPDVNHAKVKLQGKEVGVYEALKDDSWLKGEFVTTVQQRGAAVIKARKLSSAMSAAKAICDHVRDIWFGTPEGEFVSMGVISDGNSYGVPDDLLYSFPVVIKNKTWKFVEGLPINDFSREKMDLTAKELTEEKESAFEFLSSA</sequence>
+ </interactor>
+ <interactor id="30">
+ <names>
+ <shortLabel>fas_human</shortLabel>
+ <fullName>Fatty acid synthase</fullName>
+ <alias type="gene name" typeAc="MI:0301">FASN</alias>
+ <alias type="gene name synonym" typeAc="MI:0302">FAS</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="P49327" refType="identity" refTypeAc="MI:0356" secondary="fas_human" version="SP_48"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0006631" secondary="P:fatty acid metabolism"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR001227" secondary="Ac_trans"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR002085" secondary="Adh_zn_family"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR000794" secondary="Ketoacyl_synth"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR006162" secondary="Ppantne_S"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR006163" secondary="Pp_bind"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR000051" secondary="SAM_bind"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR001031" secondary="Thioesterase"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR002198" secondary="ADH_short"/>
+ <secondaryRef db="reactome protein" dbAc="MI:0245" id="P49327"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q13479" refType="secondary-ac" refTypeAc="MI:0360" secondary="fas_human" version="SP_48"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q16702" refType="secondary-ac" refTypeAc="MI:0360" secondary="fas_human" version="SP_48"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q6P4U5" refType="secondary-ac" refTypeAc="MI:0360" secondary="fas_human" version="SP_48"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q6SS02" refType="secondary-ac" refTypeAc="MI:0360" secondary="fas_human" version="SP_48"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q969R1" refType="secondary-ac" refTypeAc="MI:0360" secondary="fas_human" version="SP_48"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q96C68" refType="secondary-ac" refTypeAc="MI:0360" secondary="fas_human" version="SP_48"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q96IT0" refType="secondary-ac" refTypeAc="MI:0360" secondary="fas_human" version="SP_48"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR009081" secondary="ACP_like"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-356658" secondary="fas_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>MEEVVIAGMSGKLPESENLQEFWDNLIGGVDMVTDDDRRWKAGLYGLPRRSGKLKDLSRFDASFFGVHPKQAHTMDPQLRLLLEVTYEAIVDGGINPDSLRGTHTGVWVGVSGSETSEALSRDPETLVGYSMVGCQRAMMANRLSFFFDFRGPSIALDTACSSSLMALQNAYQAIHSGQCPAAIVGGINVLLKPNTSVQFLRLGMLSPEGTCKAFDTAGNGYCRSEGVVAVLLTKKSLARRVYATILNAGTNTDGFKEQGVTFPSGDIQEQLIRSLYQSAGVAPESFEYIEAHGTGTKVGDPQELNGITRALCATRQEPLLIGSTKSNMGHPEPASGLAALAKVLLSLEHGLWAPNLHFHSPNPEIPALLDGRLQVVDQPLPVRGGNVGINSFGFGGSNVHIILRPNTQPPPAPAPHATLPRLLRASGRTPEAVQKLLEQGLRHSQDLAFLSMLNDIAAVPATAMPFRGYA [...]
+ </interactor>
+ <interactor id="32">
+ <names>
+ <shortLabel>c1tc_human</shortLabel>
+ <fullName>C-1-tetrahydrofolate synthase, cytoplasmic</fullName>
+ <alias type="gene name" typeAc="MI:0301">MTHFD1</alias>
+ <alias type="gene name synonym" typeAc="MI:0302">MTHFC</alias>
+ <alias type="gene name synonym" typeAc="MI:0302">MTHFD</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="P11586" refType="identity" refTypeAc="MI:0356" secondary="c1tc_human" version="SP_49"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005739" secondary="C:mitochondrion"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0004329" secondary="F:formate-tetrahydrofolate lig"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0004477" secondary="F:methenyltetrahydrofolate cyc"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0004486" secondary="F:methylenetetrahydrofolate de"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR000559" secondary="Fmtethyd_synth"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR000672" secondary="THFDhg/Cyc_hydro"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q86VC9" refType="secondary-ac" refTypeAc="MI:0360" secondary="c1tc_human" version="SP_49"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q9BVP5" refType="secondary-ac" refTypeAc="MI:0360" secondary="c1tc_human" version="SP_49"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-709638" secondary="c1tc_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>APAEILNGKEISAQIRARLKNQVTQLKEQVPGFTPRLAILQVGNRDDSNLYINVKLKAAEEIGIKATHIKLPRTTTESEVMKYITSLNEDSTVHGFLVQLPLDSENSINTEEVINAIAPEKDVDGLTSINAGRLARGDLNDCFIPCTPKGCLELIKETGVPIAGRHAVVVGRSKIVGAPMHDLLLWNNATVTTCHSKTAHLDEEVNKGDILVVATGQPEMVKGEWIKPGAIVIDCGINYVPDDKKPNGRKVVGDVAYDEAKERASFITPVPGGVGPMTVAMLMQSTVESAKRFLEKFKPGKWMIQYNNLNLKTPVPSDIDISRSCKPKPIGKLAREIGLLSEEVELYGETKAKVLLSALERLKHRPDGKYVVVTGITPTPLGEGKSTTTIGLVQALGAHLYQNVFACVRQPSQGPTFGIKGGAAGGGYSQVIPMEEFNLHLTGDIHAITAANNLVAAAIDARIFHELTQTD [...]
+ </interactor>
+ <interactor id="34">
+ <names>
+ <shortLabel>serc_human</shortLabel>
+ <fullName>Phosphoserine aminotransferase</fullName>
+ <alias type="gene name" typeAc="MI:0301">PSAT1</alias>
+ <alias type="gene name synonym" typeAc="MI:0302">PSA</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="Q9Y617" refType="identity" refTypeAc="MI:0356" secondary="serc_human" version="SP_49"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0004648" secondary="F:phosphoserine transaminase a"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0006564" secondary="P:L-serine biosynthesis"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0008615" secondary="P:pyridoxine biosynthesis"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR000192" secondary="Aminotrans_V"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR003248" secondary="Pser_amintransf"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q96AW2" refType="secondary-ac" refTypeAc="MI:0360" secondary="serc_human" version="SP_49"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q9BQ12" refType="secondary-ac" refTypeAc="MI:0360" secondary="serc_human" version="SP_49"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-709652" secondary="serc_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>MDAPRQVVNFGPGPAKLPHSVLLEIQKELLDYKGVGISVLEMSHRSSDFAKIINNTENLVRELLAVPDNYKVIFLQGGGCGQFSAVPLNLIGLKAGRCADYVVTGAWSAKAAEEAKKFGTINIVHPKLGSYTKIPDPSTWNLNPDASYVYYCANETVHGVEFDFIPDVKGAVLVCDMSSNFLSKPVDVSKFGVIFAGAQKNVGSAGVTVVIVRDDLLGFALRECPSVLEYKVQAGNSSLYNTPPCFSIYVMGLVLEWIKNNGGAAAMEKLSSIKSQTIYEIIDNSQGFYVCPVEPQNRSKMNIPFRIGNAKGDDALEKRFLDKALELNMLSLKGHRSVGGIRASLYNAVTIEDVQKLAAFMKKFLEMHQL</sequence>
+ </interactor>
+ <interactor id="36">
+ <names>
+ <shortLabel>sias_human</shortLabel>
+ <fullName>Sialic acid synthase (N-acetylneuraminate synthase)</fullName>
+ <alias type="gene name" typeAc="MI:0301">NANS</alias>
+ <alias type="gene name synonym" typeAc="MI:0302">SAS</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="Q9NR45" refType="identity" refTypeAc="MI:0356" secondary="sias_human" version="SP_47"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005737" secondary="C:cytoplasm"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0008781" secondary="F:N-acylneuraminate cytidylylt"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0009103" secondary="P:lipopolysaccharide biosynthe"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR006190" secondary="Antifreeze_like"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR004144" secondary="NeuB"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q8WUV9" refType="secondary-ac" refTypeAc="MI:0360" secondary="sias_human" version="SP_47"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q9BWS6" refType="secondary-ac" refTypeAc="MI:0360" secondary="sias_human" version="SP_47"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q9NVD4" refType="secondary-ac" refTypeAc="MI:0360" secondary="sias_human" version="SP_47"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-709675" secondary="sias_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>MPLELELCPGRWVGGQHPCFIIAEIGQNHQGDLDVAKRMIRMAKECGADCAKFQKSELEFKFNRKALERPYTSKHSWGKTYGEHKRHLEFSHDQYRELQRYAEEVGIFFTASGMDEMAVEFLHELNVPFFKVGSGDTNNFPYLEKTAKKGRPMVISSGMQSMDTMKQVYQIVKPLNPNFCFLQCTSAYPLQPEDVNLRVISEYQKLFPDIPIGYSGHETGIAISVAAVALGAKVLERHITLDKTWKGSDHSASLEPGELAELVRSVRLVERALGSPTKQLLPCEMACNEKLGKSVVAKVKIPEGTILTMDMLTVKVGEPKGYPPEDIFNLVGKKVLVTVEEDDTIMEELVDNHGKKIKS</sequence>
+ </interactor>
+ <interactor id="38">
+ <names>
+ <shortLabel>actg_human</shortLabel>
+ <fullName>Actin, cytoplasmic 2</fullName>
+ <alias type="gene name" typeAc="MI:0301">ACTG1</alias>
+ <alias type="gene name synonym" typeAc="MI:0302">ACTG</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="P63261" refType="identity" refTypeAc="MI:0356" secondary="actg_human" version="SP_48"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR004001" secondary="Actin"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR004000" secondary="Actin_like"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="P02571" refType="secondary-ac" refTypeAc="MI:0360" secondary="actg_human" version="SP_48"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="P14104" refType="secondary-ac" refTypeAc="MI:0360" secondary="actg_human" version="SP_48"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="P99022" refType="secondary-ac" refTypeAc="MI:0360" secondary="actg_human" version="SP_48"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-351292" secondary="actg_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>MEEEIAALVIDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVLSLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFNSIMKCDVDIRKDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQEYDESGPSIVHRKCF</sequence>
+ </interactor>
+ <interactor id="40">
+ <names>
+ <shortLabel>tpm3_human</shortLabel>
+ <fullName>Tropomyosin alpha 3 chain</fullName>
+ <alias type="gene name" typeAc="MI:0301">TPM3</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="P06753" refType="identity" refTypeAc="MI:0356" secondary="tpm3_human" version="SP_48"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005856" secondary="C:cytoskeleton"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005862" secondary="C:muscle thin filament tropomy"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0006937" secondary="P:regulation of muscle contrac"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR002017" secondary="Spectrin"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR000533" secondary="Tropomyosin"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="P12324" refType="secondary-ac" refTypeAc="MI:0360" secondary="tpm3_human" version="SP_48"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q969Q2" refType="secondary-ac" refTypeAc="MI:0360" secondary="tpm3_human" version="SP_48"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q9NQH8" refType="secondary-ac" refTypeAc="MI:0360" secondary="tpm3_human" version="SP_48"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-355607" secondary="tpm3_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>MEAIKKKMQMLKLDKENALDRAEQAEAEQKQAEERSKQLEDELAAMQKKLKGTEDELDKYSEALKDAQEKLELAEKKAADAEAEVASLNRRIQLVEEELDRAQERLATALQKLEEAEKAADESERGMKVIENRALKDEEKMELQEIQLKEAKHIAEEADRKYEEVARKLVIIEGDLERTEERAELAESKCSELEEELKNVTNNLKSLEAQAEKYSQKEDKYEEEIKILTDKLKEAETRAEFAERSVAKLEKTIDDLEDELYAQKLKYKAISEELDHALNDMTSI</sequence>
+ </interactor>
+ <interactor id="42">
+ <names>
+ <shortLabel>flna_human</shortLabel>
+ <fullName>Filamin-A</fullName>
+ <alias type="gene name" typeAc="MI:0301">FLNA</alias>
+ <alias type="gene name synonym" typeAc="MI:0302">FLN</alias>
+ <alias type="gene name synonym" typeAc="MI:0302">FLN1</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="P21333" refType="identity" refTypeAc="MI:0356" secondary="flna_human" version="SP_68"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0015629" secondary="C:actin cytoskeleton"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0051015" secondary="F:actin filament binding"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0004871" secondary="F:signal transducer activity"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0030036" secondary="P:actin cytoskeleton organizat"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0007399" secondary="P:neurogenesis"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0043123" secondary="P:positive regulation of I-kap"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR001589" secondary="Actbind_actnin"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR001715" secondary="Calponin-like"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR001298" secondary="Filamin"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-350432" secondary="flna_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>SSSHSRAGQSAAGAAPGGGVDTRDAEMPATEKDLAEDAPWKKIQQNTFTRWCNEHLKCVSKRIANLQTDLSDGLRLIALLEVLSQKKMHRKHNQRPTFRQMQLENVSVALEFLDRESIKLVSIDSKAIVDGNLKLILGLIWTLILHYSISMPMWDEEEDEEAKKQTPKQRLLGWIQNKLPQLPITNFSRDWQSGRALGALVDSCAPGLCPDWDSWDASKPVTNAREAMQQADDWLGIPQVITPEEIVDPNVDEHSVMTYLSQFPKAKLKPGAPLRPKLNPKKARAYGPGIEPTGNMVKKRAEFTVETRSAGQGEVLVYVEDPAGHQEEAKVTANNDKNRTFSVWYVPEVTGTHKVTVLFAGQHIAKSPFEVYVDKSQGDASKVTAQGPGLEPSGNIANKTTYFEIFTAGAGTGEVEVVIQDPMGQKGTVEPQLEARGDSTYRCSYQPTMEGVHTVHVTFAGVPIPRSPYTV [...]
+ </interactor>
+ <interactor id="44">
+ <names>
+ <shortLabel>myh9_human</shortLabel>
+ <fullName>Myosin-9</fullName>
+ <alias type="gene name" typeAc="MI:0301">MYH9</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="P35579" refType="identity" refTypeAc="MI:0356" secondary="myh9_human" version="SP_48"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR000048" secondary="IQ_region"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR001609" secondary="myosin_head"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR004009" secondary="Myosin_N"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR002928" secondary="Myosin_tail"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR002017" secondary="Spectrin"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="O60805" refType="secondary-ac" refTypeAc="MI:0360" secondary="myh9_human" version="SP_48"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR000861" secondary="REM_rpt_rho_bd"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-350338" secondary="myh9_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>AQQAADKYLYVDKNFINNPLAQADWAAKKLVWVPSDKSGFEPASLKEEVGEEAIVELVENGKKVKVNKDDIQKMNPPKFSKVEDMAELTCLNEASVLHNLKERYYSGLIYTYSGLFCVVINPYKNLPIYSEEIVEMYKGKKRHEMPPHIYAITDTAYRSMMQDREDQSILCTGESGAGKTENTKKVIQYLAYVASSHKSKKDQGELERQLLQANPILEAFGNAKTVKNDNSSRFGKFIRINFDVNGYIVGANIETYLLEKSRAIRQAKEERTFHIFYYLLSGAGEHLKTDLLLEPYNKYRFLSNGHVTIPGQQDKDMFQETMEAMRIMGIPEEEQMGLLRVISGVLQLGNIVFKKERNTDQASMPDNTAAQKVSHLLGINVTDFTRGILTPRIKVGRDYVQKAQTKEQADFAIEALAKATYERMFRWLVLRINKALDKTKRQGASFIGILDIAGFEIFDLNSFEQLCINYT [...]
+ </interactor>
+ <interactor id="46">
+ <names>
+ <shortLabel>spta2_human</shortLabel>
+ <fullName>Spectrin alpha chain, brain</fullName>
+ <alias type="gene name" typeAc="MI:0301">SPTAN1</alias>
+ <alias type="gene name synonym" typeAc="MI:0302">SPTA2</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="Q13813" refType="identity" refTypeAc="MI:0356" secondary="spta2_human" version="SP_48"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005624" secondary="C:membrane fraction"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0008091" secondary="C:spectrin"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0003779" secondary="F:actin binding"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005200" secondary="F:structural constituent of cy"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR002048" secondary="EF-hand"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR001452" secondary="SH3"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR002017" secondary="Spectrin"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q13186" refType="secondary-ac" refTypeAc="MI:0360" secondary="spta2_human" version="SP_48"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q15324" refType="secondary-ac" refTypeAc="MI:0360" secondary="spta2_human" version="SP_48"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q16606" refType="secondary-ac" refTypeAc="MI:0360" secondary="spta2_human" version="SP_48"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR011992" secondary="EF-Hand_type"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q7Z6M5" refType="secondary-ac" refTypeAc="MI:0360" secondary="spta2_human" version="SP_48"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q9P0V0" refType="secondary-ac" refTypeAc="MI:0360" secondary="spta2_human" version="SP_48"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-351450" secondary="spta2_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>MDPSGVKVLETAEDIQERRQQVLDRYHRFKELSTLRRQKLEDSYRFQFFQRDAEELEKWIQEKLQIASDENYKDPTNLQGKLQKHQAFEAEVQANSGAIVKLDETGNLMISEGHFASETIRTRLMELHRQWELLLEKMREKGIKLLQAQKLVQYLRECEDVMDWINDKEAIVTSEELGQDLEHVEVLQKKFEEFQTDMAAHEERVNEVNQFAAKLIQEQHPEEELIKTKQDEVNAAWQRLKGLALQRQGKLFGAAEVQRFNRDVDETISWIKEKEQLMASDDFGRDLASVQALLRKHEGLERDLAALEDKVKALCAEADRLQQSHPLSATQIQVKREELITNWEQIRTLAAERHARLNDSYRLQRFLADFRDLTSWVTEMKALINADELASDVAGAEALLDRHQEHKGEIDAHEDSFKSADESGQALLAAGHYASDEVREKLTVLSEERAALLELWELRRQQYEQCMDLQL [...]
+ </interactor>
+ <interactor id="48">
+ <names>
+ <shortLabel>q14981</shortLabel>
+ <fullName>NuMA protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="Q14981" refType="identity" refTypeAc="MI:0356" secondary="q14981" version="25"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005634" secondary="C:nucleus"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005876" secondary="C:spindle microtubule"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005198" secondary="F:structural molecule activity"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0000090" secondary="P:mitotic anaphase"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0006997" secondary="P:nuclear organization and bio"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR002017" secondary="Spectrin"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-395496" secondary="q14981"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>MTLHATRGAALLSWVNSLHVADPVEAVLQLQDCSIFIKIIDRIHGTEEGQQILKQPVSERLDFVCSFLQKNRKHPSSPECLVSAQKVLEGSELELAKMTMLLLYHSTMSSKSPRDWEQFEYKIQAELAVILKFVLDHEDGLNLNEDLENFLQKAPVPSTCSSTFPEELSPPSHQAKREIRFLELQKVASSSSGNNFLSGSPASPMGDILQTPQFQMRRLKKQLADERSNRDELELELAENRKLLTEKDAQIAMMQQRIDRLALLNEKQAASPLEPKELEELRDKNESLTMRLHETLKQCQDLKTEKSQMDRKINQLSEENGDLSFKLREFASHLQQLQDALNELTEEHSKATQEWLEKQAQLEKELSAALQDKKCLEEKNEILQGKLSQLEEHLSQLQDNPPQEKGEVLGDVLQLETLKQEAATLAANNTQLQARVEMLETERGQQEAKLLAERGHFEEEKQQLSSLITDL [...]
+ </interactor>
+ <interactor id="50">
+ <names>
+ <shortLabel>actn1_human</shortLabel>
+ <fullName>Alpha-actinin 1</fullName>
+ <alias type="gene name" typeAc="MI:0301">ACTN1</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="P12814" refType="identity" refTypeAc="MI:0356" secondary="actn1_human" version="SP_48"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0015629" secondary="C:actin cytoskeleton"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005200" secondary="F:structural constituent of cy"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR001589" secondary="Actbind_actnin"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR001715" secondary="Calponin-like"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR002048" secondary="EF-hand"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR002017" secondary="Spectrin"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q9BTN1" refType="secondary-ac" refTypeAc="MI:0360" secondary="actn1_human" version="SP_48"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR011992" secondary="EF-Hand_type"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-351710" secondary="actn1_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>MDHYDSQQTNDYMQPEEDWDRDLLLDPAWEKQQRKTFTAWCNSHLRKAGTQIENIEEDFRDGLKLMLLLEVISGERLAKPERGKMRVHKISNVNKALDFIASKGVKLVSIGAEEIVDGNVKMTLGMIWTIILRFAIQDISVEETSAKEGLLLWCQRKTAPYKNVNIQNFHISWKDGLGFCALIHRHRPELIDYGKLRKDDPLTNLNTAFDVAEKYLDIPKMLDAEDIVGTARPDEKAIMTYVSSFYHAFSGAQKAETAANRICKVLAVNQENEQLMEDYEKLASDLLEWIRRTIPWLENRVPENTMHAMQQKLEDFRDYRRLHKPPKVQEKCQLEINFNTLQTKLRLSNRPAFMPSEGRMVSDINNAWGCLEQVEKGYEEWLLNEIRRLERLDHLAEKFRQKASIHEAWTDGKEAMLRQKDYETATLSEIKALLKKHEAFESDLAAHQDRVEQIAAIAQELNELDYYDSPS [...]
+ </interactor>
+ <interactor id="52">
+ <names>
+ <shortLabel>ube1_human</shortLabel>
+ <fullName>Ubiquitin-activating enzyme E1</fullName>
+ <alias type="gene name" typeAc="MI:0301">UBE1</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="P22314" refType="identity" refTypeAc="MI:0356" secondary="ube1_human" version="SP_49"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005524" secondary="F:ATP binding"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0046872" secondary="F:metal ion binding"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR000594" secondary="ThiF_NAD_FAD_bd"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR000127" secondary="UBact_repeat"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR000011" secondary="UBQ-activ_enz_E1"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q96E13" refType="secondary-ac" refTypeAc="MI:0360" secondary="ube1_human" version="SP_49"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-709688" secondary="ube1_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>MSSSPLSKKRRVSGPDPKPGSNCSPAQSVLSEVPSVPTNGMAKNGSEADIDEGLYSRQLYVLGHEAMKRLQTSSVLVSGLRGLGVEIAKNIILGGVKAVTLHDQGTAQWADLSSQFYLREEDIGKNRAEVSQPRLAELNSYVPVTAYTGPLVEDFLSGFQVVVLTNTPLEDQLRVGEFCHNRGIKLVVADTRGLFGQLFCDFGEEMILTDSNGEQPLSAMVSMVTKDNPGVVTCLDEARHGFESGDFVSFSEVQGMVELNGNQPMEIKVLGPYTFSICDTSNFSDYIRGGIVSQVKVPKKISFKSLVASLAEPDFVVTDFAKFSRPAQLHIGFQALHQFCAQHGRPPRPRNEEDAAELVALAQAVNARALPAVQQNNLDEDLIRKLAYVAAGDLAPINAFIGGLAAQEVMKACSGKFMPIMQWLYFDALECLPEDKEVLTEDKCLQRQNRYDGQVAVFGSDLQEKLGKQKY [...]
+ </interactor>
+ <interactor id="54">
+ <names>
+ <shortLabel>psd1_human</shortLabel>
+ <fullName>26S proteasome non-ATPase regulatory subunit 1</fullName>
+ <alias type="gene name" typeAc="MI:0301">PSMD1</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="Q99460" refType="identity" refTypeAc="MI:0356" secondary="psd1_human" version="SP_47"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005838" secondary="C:proteasome regulatory partic"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR002015" secondary="APC_proteasome"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR011989" secondary="ARM-like"/>
+ <secondaryRef db="reactome protein" dbAc="MI:0245" id="Q99460"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q6GMU5" refType="secondary-ac" refTypeAc="MI:0360" secondary="psd1_human" version="SP_47"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q6P2P4" refType="secondary-ac" refTypeAc="MI:0360" secondary="psd1_human" version="SP_47"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q6PJM7" refType="secondary-ac" refTypeAc="MI:0360" secondary="psd1_human" version="SP_47"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q6PKG9" refType="secondary-ac" refTypeAc="MI:0360" secondary="psd1_human" version="SP_47"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q86VU1" refType="secondary-ac" refTypeAc="MI:0360" secondary="psd1_human" version="SP_47"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q8IV79" refType="secondary-ac" refTypeAc="MI:0360" secondary="psd1_human" version="SP_47"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005515" secondary="F:protein binding"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-357874" secondary="psd1_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>MITSAAGIISLLDEDEPQLKEFALHKLNAVVNDFWAEISESVDKIEVLYEDEGFRSRQFAALVASKVFYHLGAFEESLNYALGAGDLFNVNDNSEYVETIIAKCIDHYTKQCVENADLPEGEKKPIDQRLEGIVNKMFQRCLDDHKYKQAIGIALETRRLDVFEKTILESNDVPGMLAYSLKLCMSLMQNKQFRNKVLRVLVKIYMNLEKPDFINVCQCLIFLDDPQAVSDILEKLVKEDNLLMAYQICFDLYESASQQFLSSVIQNLRTVGTPIASVPGSTNTGTVPGSEKDSDSMETEEKTSSAFVGKTPEASPEPKDQTLKMIKILSGEMAIELHLQFLIRNNNTDLMILKNTKDAVRNSVCHTATVIANSFMHCGTTSDQFLRDNLEWLARATNWAKFTATASLGVIHKGHEKEALQLMATYLPKDTSPGSAYQEGGGLYALGLIHANHGGDIIDYLLNQLKNASND [...]
+ </interactor>
+ <interactor id="56">
+ <names>
+ <shortLabel>q6pew2_human</shortLabel>
+ <fullName>Proteasome beta 5 subunit</fullName>
+ <alias type="gene name" typeAc="MI:0301">PSMB5</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="Q6PEW2" refType="identity" refTypeAc="MI:0356" secondary="q6pew2_human" version="TrEMBL_27"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0043234" secondary="C:protein complex"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0004298" secondary="F:threonine endopeptidase acti"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0006511" secondary="P:ubiquitin-dependent protein "/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR000243" secondary="Pept_T1A_subB"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR001353" secondary="Proteasome_A_B"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005829" secondary="C:cytosol"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005839" secondary="C:proteasome core complex (sen"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-709699" secondary="q6pew2_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>MALASVLERPLPVNQRGFFGLGGRADLLDLGPGSLSDGLSLAAPGWGVPEEPGIEMLHGTTTLAFKFRHGVIVAADSRATAGAYIASQTVKKVIEINPYLLGTMAGGAADCSFWERLLARQCRIYELRNKERISVAAASKLLANMVYQYKGMGLSMGTMICGWDKRGPGLYYVDSEGNRISGATFSVGSGSVYAYGVMDRGYSYDLEVEQAYDLARRAIYQATYRDAYSGGAVNLYHVREDGWIRVSSDNVADLHEKYSGSTP</sequence>
+ </interactor>
+ <interactor id="58">
+ <names>
+ <shortLabel>sya_human</shortLabel>
+ <fullName>Alanyl-tRNA synthetase</fullName>
+ <alias type="gene name" typeAc="MI:0301">AARS</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="P49588" refType="identity" refTypeAc="MI:0356" secondary="sya_human" version="SP_49"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005737" secondary="C:cytoplasm"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005625" secondary="C:soluble fraction"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0000049" secondary="F:tRNA binding"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0006419" secondary="P:alanyl-tRNA aminoacylation"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0008033" secondary="P:tRNA processing"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR003156" secondary="Pesterase_DHHA1"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR002318" secondary="tRNA-synt_2c"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR012947" secondary="tRNA_SAD"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q96FA0" refType="secondary-ac" refTypeAc="MI:0360" secondary="sya_human" version="SP_49"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-709710" secondary="sya_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>MDSTLTASEIRQRFIDFFKRNEHTYVHSSATIPLDDPTLLFANAGMNQFKPIFLNTIDPSHPMAKLSRAANTQKCIRAGGKQNDLDDVGKDVYHHTFFEMLGSWSFGDYFKELACKMALELLTQEFGIPIERLYVTYFGGDEAAGLEADLECKQIWQNLGLDDTKILPGNMKDNFWEMGDTGPCGPCSEIHYDRIGGRDAAHLVNQDDPNVLEIWNLVFIQYNREADGILKPLPKKSIDTGMGLERLVSVLQNKMSNYDTDLFVPYFEAIQKGTGARPYTGKVGAEDADGIDMAYRVLADHARTITVALADGGRPDNTGRGYVLRRILRRAVRYAHEKLNASRGFFATLVDVVVQSLGDAFPELKKDPDMVKDIINEEEVQFLKTLSRGRRILDRKIQSLGDSKTIPGDTAWLLYDTYGFPVDLTGLIAEEKGLVVDMDGFEEERKLAQLKSQGKGAGGEDLIMLDIYAIE [...]
+ </interactor>
+ <interactor id="60">
+ <names>
+ <shortLabel>q6pi85_human</shortLabel>
+ <fullName>IARS2 protein</fullName>
+ <alias type="gene name" typeAc="MI:0301">IARS2</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="Q6PI85" refType="identity" refTypeAc="MI:0356" secondary="q6pi85_human" version="TrEMBL_27"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005524" secondary="F:ATP binding"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0004822" secondary="F:isoleucine-tRNA ligase activ"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0008270" secondary="F:zinc ion binding"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0006428" secondary="P:isoleucyl-tRNA aminoacylatio"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR002300" secondary="tRNA-synt_1a"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR001412" secondary="tRNA-synt_I"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR002301" secondary="tRNA-synt_ile"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR010663" secondary="Znf_Fpg"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-709723" secondary="q6pi85_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>MKLLGRQQPDTELEIQQKCGFSELYSWQRERKVKTEFCLHDGPPYANGDPHVGHALNKILKDIANRFHMMNGSKIHFVPGWDCHGLPIEIKVLSELGREAQNLSAMEIRKKARSFAKAAIEKQKSAFIRWGIMADWNNCYYTFDGKYEAKQLRTFYQMYDKGLVYRSYKPVFWSPSSRTALAEAELEYNPEHVSRSIYVKFPLLKPSPKLASLIDGSSPVSILVWTTQPWTIPANEAVCYMPESKYAVVKCSKSGDLYVLAADKVASVASTLETTFETISTLSGVDLENGTCSHPLIPDKASPLLPANHVTMAKGTGLVHTAPAHGMEDYGVASQHNLPMDCLVDEDGVFTDVAGPELQNKAVLEEGTDVVIKMLQTAKNLLKEEKLVHSYPYDWRTKKPVVIRASKQWFINITDIKTAAKELLKKVKFIPGSALNGMVEMMDRRPYWCISRQRVWGVPIPVFHHKTKDEY [...]
+ </interactor>
+ <interactor id="62">
+ <names>
+ <shortLabel>ef2_human</shortLabel>
+ <fullName>Elongation factor 2</fullName>
+ <alias type="gene name" typeAc="MI:0301">EEF2</alias>
+ <alias type="gene name synonym" typeAc="MI:0302">EF2</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="P13639" refType="identity" refTypeAc="MI:0356" secondary="ef2_human" version="SP_48"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR000795" secondary="EF_GTPbind"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR000640" secondary="EFG_C"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR005517" secondary="EFG_IV"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR004161" secondary="EFTU_D2"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR005225" secondary="Small_GTP"/>
+ <secondaryRef db="reactome protein" dbAc="MI:0245" id="P13639"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-352560" secondary="ef2_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>VNFTVDQIRAIMDKKANIRNMSVIAHVDHGKSTLTDSLVCKAGIIASARAGETRFTDTRKDEQERCITIKSTAISLFYELSENDLNFIKQSKDGAGFLINLIDSPGHVDFSSEVTAALRVTDGALVVVDCVSGVCVQTETVLRQAIAERIKPVLMMNKMDRALLELQLEPEELYQTFQRIVENVNVIISTYGEGESGPMGNIMIDPVLGTVGFGSGLHGWAFTLKQFAEMYVAKFAAKGEGQLGPAERAKKVEDMMKKLWGDRYFDPANGKFSKSATSPEGKKLPRTFCQLILDPIFKVFDAIMNFKKEETAKLIEKLDIKLDSEDKDKEGKPLLKAVMRRWLPAGDALLQMITIHLPSPVTAQKYRCELLYEGPPDDEAAMGIKSCDPKGPLMMYISKMVPTSDKGRFYAFGRVFSGLVSTGLKVRIMGPNYTPGKKEDLYLKPIQRTILMMGRYVEPIEDVPCGNIVGL [...]
+ </interactor>
+ <interactor id="64">
+ <names>
+ <shortLabel>if33_human</shortLabel>
+ <fullName>Eukaryotic translation initiation factor 3 subunit 3</fullName>
+ <alias type="gene name" typeAc="MI:0301">EIF3S3</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="O15372" refType="identity" refTypeAc="MI:0356" secondary="if33_human" version="SP_47"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005852" secondary="C:eukaryotic translation initi"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0008135" secondary="F:translation factor activity,"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0006446" secondary="P:regulation of translational "/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR000555" secondary="Mov34_MPN_PAD1"/>
+ <secondaryRef db="reactome protein" dbAc="MI:0245" id="O15372"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-709735" secondary="if33_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>MASRKEGTGSTATSSSSTAGAAGKGKGKGGSGDSAVKQVQIDGLVVLKIIKHYQEEGQGTEVVQGVLLGLVVEDRLEITNCFPFPQHTEDDADFDEVQYQMEMMRSLRHVNIDHLHVGWYQSTYYGSFVTRALLDSQFSYQHAIEESVVLIYDPIKTAQGSLSLKAYRLTPKLMEVCKEKDFSPEALKKANITFEYMFEEVPIVIKNSHLINVLMWELEKKSAVADKHELLSLASSNHLGKNLQLLMDRVDEMSQDIVKYNTYMRNTSKQQQQKHQYQQRRQQENMQRQSRGEPPLPEEDLSKLFKPPQPPARMDSLLIAGQINTYCQNIKEFTAQNLGKLFMAQALQEYNN</sequence>
+ </interactor>
+ <interactor id="66">
+ <names>
+ <shortLabel>q6ipd1_human</shortLabel>
+ <fullName>Similar to Laminin receptor 1</fullName>
+ <alias type="gene name" typeAc="MI:0301">LOC388524</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="Q6IPD1" refType="identity" refTypeAc="MI:0356" secondary="q6ipd1_human" version="TrEMBL_27"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0015935" secondary="C:small ribosomal subunit"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0004872" secondary="F:receptor activity"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0003735" secondary="F:structural constituent of ri"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0006412" secondary="P:protein biosynthesis"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR001865" secondary="Ribosomal_S2"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR005707" secondary="Ribosomal_S2_e/a"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-709744" secondary="q6ipd1_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>MSGALDVLQMKEEDVLKFLAAGTHLGGTNLDFQMEQYIYKRKSDGIYIINLKRTWEKLLLAARAIVAIENPADVSVISSRNTGQRAVLKFAAATGATPIAGRFTPGTFTNQIQAAFWEPRLLVVTDPRADHQPLTEASYVNLPTIALCNTDSPLRYVDIAIPCNNKGAHSVGLMWWMLAREVLRMRGTISREHPWEVMPDLYFYRDPEEIEKEEQAAAEKAVTKEEFQGEWTAPAPEFTATQPEVADWSEGVQVPSVPIQQFPTEDWSAQPAMEDWSAAPTAQATEWVGATTDWS</sequence>
+ </interactor>
+ <interactor id="68">
+ <names>
+ <shortLabel>rla0_human</shortLabel>
+ <fullName>60S acidic ribosomal protein P0</fullName>
+ <alias type="gene name" typeAc="MI:0301">RPLP0</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="P05388" refType="identity" refTypeAc="MI:0356" secondary="rla0_human" version="SP_48"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005842" secondary="C:cytosolic large ribosomal su"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0003723" secondary="F:RNA binding"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0003735" secondary="F:structural constituent of ri"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0006412" secondary="P:protein biosynthesis"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR001813" secondary="Ribosomal_60S"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR001790" secondary="Ribosomal_L10"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q9BVK4" refType="secondary-ac" refTypeAc="MI:0360" secondary="rla0_human" version="SP_48"/>
+ <secondaryRef db="reactome protein" dbAc="MI:0245" id="P05388"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005515" secondary="F:protein binding"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-354101" secondary="rla0_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>MPREDRATWKSNYFLKIIQLLDDYPKCFIVGADNVGSKQMQQIRMSLRGKAVVLMGKNTMMRKAIRGHLENNPALEKLLPHIRGNVGFVFTKEDLTEIRDMLLANKVPAAARAGAIAPCEVTVPAQNTGLGPEKTSFFQALGITTKISRGTIEILSDVQLIKTGDKVGASEATLLNMLNISPFSFGLVIQQVFDNGSIYNPEVLDITEETLHSRFLEGVRNVASVCLQIGYPTVASVPHSIINGYKRVLALSVETDYTFPLAEKVKAFLADPSAFVAAAPVAAATTAAPAAAAAPAKVEAKEESEESDEDMGFGLFD</sequence>
+ </interactor>
+ <interactor id="70">
+ <names>
+ <shortLabel>rs6_human</shortLabel>
+ <fullName>40S ribosomal protein S6</fullName>
+ <alias type="orf name" typeAc="MI:0306">OK/SW-cl.2</alias>
+ <alias type="gene name" typeAc="MI:0301">RPS6</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="P62753" refType="identity" refTypeAc="MI:0356" secondary="rs6_human" version="SP_48"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR001377" secondary="Ribosomal_S6E"/>
+ <secondaryRef db="reactome protein" dbAc="MI:0245" id="P62753"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="P08227" refType="secondary-ac" refTypeAc="MI:0360" secondary="rs6_human" version="SP_48"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="P10660" refType="secondary-ac" refTypeAc="MI:0360" secondary="rs6_human" version="SP_48"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-356625" secondary="rs6_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>MKLNISFPATGCQKLIEVDDERKLRTFYEKRMATEVAADALGEEWKGYVVRISGGNDKQGFPMKQGVLTHGRVRLLLSKGHSCYRPRRTGERKRKSVRGCIVDANLSVLNLVIVKKGEKDIPGLTDTTVPRRLGPKRASRIRKLFNLSKEDDVRQYVVRKPLNKEGKKPRTKAPKIQRLVTPRVLQHKRRRIALKKQRTKKNKEEAAEYAKLLAKRMKEAKEKRQEQIAKRRRLSSLRASTSKSESSQK</sequence>
+ </interactor>
+ <interactor id="72">
+ <names>
+ <shortLabel>rs4x_human</shortLabel>
+ <fullName>40S ribosomal protein S4, X isoform</fullName>
+ <alias type="gene name" typeAc="MI:0301">RPS4X</alias>
+ <alias type="gene name synonym" typeAc="MI:0302">CCG2</alias>
+ <alias type="gene name synonym" typeAc="MI:0302">RPS4</alias>
+ <alias type="gene name synonym" typeAc="MI:0302">SCAR</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="P62701" refType="identity" refTypeAc="MI:0356" secondary="rs4x_human" version="SP_47"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR005824" secondary="KOW"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR000876" secondary="Ribosomal_S4E"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR002942" secondary="S4"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="P12631" refType="secondary-ac" refTypeAc="MI:0360" secondary="rs4x_human" version="SP_47"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="P12750" refType="secondary-ac" refTypeAc="MI:0360" secondary="rs4x_human" version="SP_47"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="P27576" refType="secondary-ac" refTypeAc="MI:0360" secondary="rs4x_human" version="SP_47"/>
+ <secondaryRef db="reactome protein" dbAc="MI:0245" id="P62701"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="P55831" refType="secondary-ac" refTypeAc="MI:0360" secondary="rs4x_human" version="SP_47"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q14727" refType="secondary-ac" refTypeAc="MI:0360" secondary="rs4x_human" version="SP_47"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-354303" secondary="rs4x_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>ARGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDEVKKICMQRFIKIDGKVRTDITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAKYKLCKVRKIFVGTKGIPHLVTHDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNLCMVTGGANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWISLPRGKGIRLTIAEERDKRLAAKQSSG</sequence>
+ </interactor>
+ <interactor id="74">
+ <names>
+ <shortLabel>rl7_human</shortLabel>
+ <fullName>60S ribosomal protein L7</fullName>
+ <alias type="gene name" typeAc="MI:0301">RPL7</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="P18124" refType="identity" refTypeAc="MI:0356" secondary="rl7_human" version="SP_47"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005842" secondary="C:cytosolic large ribosomal su"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0003723" secondary="F:RNA binding"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0003735" secondary="F:structural constituent of ri"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0006412" secondary="P:protein biosynthesis"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR000517" secondary="Ribosomal_L30"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR005998" secondary="Ribosomal_L7_euk"/>
+ <secondaryRef db="reactome protein" dbAc="MI:0245" id="P18124"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q6IBM9" refType="secondary-ac" refTypeAc="MI:0360" secondary="rl7_human" version="SP_47"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR012988" secondary="Ribosomal_L30_N"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-350806" secondary="rl7_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>MEGVEEKKKEVPAVPETLKKKRRNFAELKIKRLRKKFAQKMLRKARRKLIYEKAKHYHKEYRQMYRTEIRMARMARKAGNFYVPAEPKLAFVIRIRGINGVSPKVRKVLQLLRLRQIFNGTFVKLNKASINMLRIVEPYIAWGYPNLKSVNELIYKRGYGKINKKRIALTDNALIARSLGKYGIICMEDLIHEIYTVGKRFKEANNFLWPFKLSSPRGGMKKKTTHFVEGGDAGNREDQINRLIRRMN</sequence>
+ </interactor>
+ <interactor id="76">
+ <names>
+ <shortLabel>rs3a_human</shortLabel>
+ <fullName>40S ribosomal protein S3a</fullName>
+ <alias type="gene name" typeAc="MI:0301">RPS3A</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="P61247" refType="identity" refTypeAc="MI:0356" secondary="rs3a_human" version="SP_47"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR001593" secondary="Ribosomal_S3AE"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="P33443" refType="secondary-ac" refTypeAc="MI:0360" secondary="rs3a_human" version="SP_47"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="P49241" refType="secondary-ac" refTypeAc="MI:0360" secondary="rs3a_human" version="SP_47"/>
+ <secondaryRef db="reactome protein" dbAc="MI:0245" id="P61247"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-352378" secondary="rs3a_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>AVGKNKRLTKGGKKGAKKKVVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASDGLKGRVFEVSLADLQNDEVAFRKFKLITEDVQGKNCLTNFHGMDLTRDKMCSMVKKWQTMIEAHVDVKTTDGYLLRLFCVGFTKKRNNQIRKTSYAQHQQVRQIRKKMMEIMTREVQTNDLKEVVNKLIPDSIGKDIEKACQSIYPLHDVFVRKVKMLKKPKFELGKLMELHGEGSSSGKATGDETGAKVERADGYEPPVQESV</sequence>
+ </interactor>
+ <interactor id="78">
+ <names>
+ <shortLabel>rl5_human</shortLabel>
+ <fullName>60S ribosomal protein L5</fullName>
+ <alias type="gene name" typeAc="MI:0301">RPL5</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="P46777" refType="identity" refTypeAc="MI:0356" secondary="rl5_human" version="SP_47"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005842" secondary="C:cytosolic large ribosomal su"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0003723" secondary="F:RNA binding"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0003735" secondary="F:structural constituent of ri"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0006412" secondary="P:protein biosynthesis"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR005484" secondary="Ribosomal_L18p"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR005485" secondary="Ribosomal_L5euk"/>
+ <secondaryRef db="reactome protein" dbAc="MI:0245" id="P46777"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005515" secondary="F:protein binding"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-358018" secondary="rl5_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>GFVKVVKNKAYFKRYQVKFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVTNRDIICQIAYARIEGDMIVCARYAHELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYEGQVEVTGDEYNVESIDGQPGAFTCYLDAGLARTTTGNKVFGALKGAVDGGLSIPHSTKRFPGYDSESKEFNAEVHRKHIMGQNVADYMRYLMEEDEDAYKKQFSQYIKNSVTPDMMEEMYKKAHAAIRENPVYEKKPKKEVKKKRWNRPKMSLAQKKDRVAQKKASFLRAQERAAES</sequence>
+ </interactor>
+ <interactor id="80">
+ <names>
+ <shortLabel>myg1_human</shortLabel>
+ <fullName>MYG1 protein</fullName>
+ <alias type="gene name" typeAc="MI:0301">C12orf10</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="Q9HB07" refType="identity" refTypeAc="MI:0356" secondary="myg1_human" version="SP_49"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR003226" secondary="Metdp_prot_hydro"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-709754" secondary="myg1_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>MGHRFLRGLLTLLLPPPPLYTRHRMLGPESVPPPKRSRSKLMAPPRIGTHNGTFHCDEALACALLRLLPEYRDAEIVRTRDPEKLASCDIVVDVGGEYDPRRHRYDHHQRSFTETMSSLSPGKPWQTKLSSAGLIYLHFGHKLLAQLLGPSEEDSMVGTLYDKMYENFVEEVDAVDNGISQWAEGEPRYALTTTLSARVARLNPTWNHPDQDTEAGFKRAMDLVQEEFLQRLDFYQHSWLPARALVEEALAQRFQVDPSGEIVELAKGACPWKEHLYHLESGLSPPVAIFFVIYTDQAGQWRIQCVPKEPHSFQSRLPLPEPWRGLRDEALDQVSGIPGCIFVHASGFIGGHPTREGALSMARATLAQRSYLPQIS</sequence>
+ </interactor>
+ <interactor id="82">
+ <names>
+ <shortLabel>q96km8_human</shortLabel>
+ <fullName>DJ69B10.1</fullName>
+ <alias type="gene name" typeAc="MI:0301">dJ69B10.1</alias>
+ <alias type="gene name synonym" typeAc="MI:0302">GA17</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="Q96KM8" refType="identity" refTypeAc="MI:0356" secondary="q96km8_human" version="31"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR000717" secondary="PCI"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-373200" secondary="q96km8_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>MSVPAFIDISEEDQAAELRAYLKSKGAEISEENSEGGLHVDLAQIIEACDVCLKEDDKDVESVMNSVVSLLLILEPDKQEALIESLCEKLVKFREGERPSLRLQLLSNLFHGMDKNTPVRYTVYCSLIKVAASCGAIQYIPTELDQVRKWISDWNLTTEKKHTLLRLLYEALVDCKKSDAASKVMVELLGSYTEDNASQARVDAHRCIVRALKDPNAFLFDHLLTLKPVKFLEGELIHDLLTIFVSAKLASYVKFYQNNKDFIDSLGLLHEQNMAKMRLLTFMGMAVENKEISFDTMQQELQIGADDVEAFVIDAVRTKMVYCKIDQTQRKVVVSHSTHRTFGKQQWQQLYDTLNAWKQNLNKVKNSLLSLSDT</sequence>
+ </interactor>
+ </interactorList>
+ <interactionList>
+ <interaction id="1">
+ <names>
+ <shortLabel>hspcb-aars</shortLabel>
+ <fullName>In vivo Co-IP: bait= Hsp90</fullName>
+ </names>
+ <xref>
+ <primaryRef db="intact" dbAc="MI:0469" id="EBI-709762" secondary="hspcb-aars"/>
+ </xref>
+ <experimentList>
+ <experimentRef>2</experimentRef>
+ </experimentList>
+ <participantList>
+ <participant id="3">
+ <interactorRef>4</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>bait</shortLabel>
+ <fullName>bait</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0496" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="5">
+ <interactorRef>6</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="7">
+ <interactorRef>8</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="9">
+ <interactorRef>10</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="11">
+ <interactorRef>12</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="13">
+ <interactorRef>14</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="15">
+ <interactorRef>16</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="17">
+ <interactorRef>18</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="19">
+ <interactorRef>20</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="21">
+ <interactorRef>22</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="23">
+ <interactorRef>24</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="25">
+ <interactorRef>26</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="27">
+ <interactorRef>28</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="29">
+ <interactorRef>30</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="31">
+ <interactorRef>32</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="33">
+ <interactorRef>34</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="35">
+ <interactorRef>36</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="37">
+ <interactorRef>38</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="39">
+ <interactorRef>40</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="41">
+ <interactorRef>42</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="43">
+ <interactorRef>44</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="45">
+ <interactorRef>46</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="47">
+ <interactorRef>48</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="49">
+ <interactorRef>50</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="51">
+ <interactorRef>52</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="53">
+ <interactorRef>54</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="55">
+ <interactorRef>56</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="57">
+ <interactorRef>58</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="59">
+ <interactorRef>60</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="61">
+ <interactorRef>62</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="63">
+ <interactorRef>64</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="65">
+ <interactorRef>66</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="67">
+ <interactorRef>68</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="69">
+ <interactorRef>70</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="71">
+ <interactorRef>72</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="73">
+ <interactorRef>74</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="75">
+ <interactorRef>76</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="77">
+ <interactorRef>78</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="79">
+ <interactorRef>80</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="81">
+ <interactorRef>82</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>physical interaction</shortLabel>
+ <fullName>physical interaction</fullName>
+ <alias>aggregation</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0218" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactionType>
+ <attributeList>
+ <attribute name="caution">The AC68 antibody is specific for both hsp90 alpha and beta which may have the same interactors. Only Hsp90 beta was identified.</attribute>
+ <attribute name="kd">0.0</attribute>
+ </attributeList>
+ </interaction>
+ </interactionList>
+ </entry>
+ </entrySet>
diff --git a/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/cyto_mapper/MapFromCytoscape.java b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/cyto_mapper/MapFromCytoscape.java
new file mode 100755
index 0000000..c89fd90
--- /dev/null
+++ b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/cyto_mapper/MapFromCytoscape.java
@@ -0,0 +1,196 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.psi_mi.cyto_mapper;
+
+import cytoscape.CyEdge;
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+
+import cytoscape.data.AttributeValueVisitor;
+import cytoscape.data.CyAttributes;
+import cytoscape.data.CyAttributesUtils;
+import cytoscape.data.attr.CountedIterator;
+import cytoscape.data.attr.MultiHashMap;
+import cytoscape.data.attr.MultiHashMapDefinition;
+
+import org.cytoscape.coreplugin.psi_mi.data_mapper.Mapper;
+import org.cytoscape.coreplugin.psi_mi.model.AttributeBag;
+import org.cytoscape.coreplugin.psi_mi.model.ExternalReference;
+import org.cytoscape.coreplugin.psi_mi.model.Interaction;
+import org.cytoscape.coreplugin.psi_mi.model.Interactor;
+import org.cytoscape.coreplugin.psi_mi.model.vocab.CommonVocab;
+
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+
+
+/**
+ * Maps Cytoscape Graph Objects to Data Service Interaction objects.
+ * This class performs the inverse mapping of the MapToCytoscape
+ * class.
+ *
+ * @author Ethan Cerami
+ */
+public class MapFromCytoscape implements Mapper {
+ private CyNetwork cyNetwork;
+ private CyAttributes nodeAttributes;
+ private CyAttributes edgeAttributes;
+
+ /**
+ * All new interactions.
+ */
+ private ArrayList interactions;
+
+ /**
+ * Constructor.
+ *
+ * @param cyNetwork CyNetwork Object.
+ */
+ public MapFromCytoscape(CyNetwork cyNetwork) {
+ this.cyNetwork = cyNetwork;
+ this.nodeAttributes = Cytoscape.getNodeAttributes();
+ this.edgeAttributes = Cytoscape.getEdgeAttributes();
+ }
+
+ /**
+ * Perform Mapping.
+ */
+ public void doMapping() {
+ interactions = new ArrayList();
+
+ Iterator edgesIterator = cyNetwork.edgesIterator();
+
+ while (edgesIterator.hasNext()) {
+ Interaction interaction = new Interaction();
+ CyEdge edge = (CyEdge) edgesIterator.next();
+
+ if (edge != null) {
+ CyNode sourceNode = (CyNode) edge.getSource();
+ CyNode targetNode = (CyNode) edge.getTarget();
+ Interactor sourceInteractor = new Interactor();
+ Interactor targetInteractor = new Interactor();
+ transferNodeAttributes(sourceNode, sourceInteractor);
+ transferNodeAttributes(targetNode, targetInteractor);
+
+ ArrayList interactors = new ArrayList();
+ interactors.add(sourceInteractor);
+ interactors.add(targetInteractor);
+ interaction.setInteractors(interactors);
+ transferEdgeAttributes(edge, interaction);
+ interactions.add(interaction);
+ }
+ }
+ }
+
+ /**
+ * Gets an ArrayList of Interaction objects.
+ *
+ * @return ArrayList of Interaction objects.
+ */
+ public ArrayList getInteractions() {
+ return this.interactions;
+ }
+
+ /**
+ * Transfers all Edge Attributes from Cytoscape to Data Service Objects.
+ *
+ * @param edge Cytoscape Edge.
+ * @param interaction Data Service Interaction Object.
+ */
+ private void transferEdgeAttributes(CyEdge edge, Interaction interaction) {
+ String[] attributeNames = edgeAttributes.getAttributeNames();
+ transferAllAttributes(attributeNames, edgeAttributes, edge.getIdentifier(), interaction);
+ }
+
+ /**
+ * Transfers all Node Attributes from Cytoscape to Data Service objects.
+ *
+ * @param node Cytoscape Node.
+ * @param interactor Data Service Interactor object.
+ */
+ private void transferNodeAttributes(CyNode node, Interactor interactor) {
+ interactor.setName(node.getIdentifier());
+
+ String[] attributeNames = nodeAttributes.getAttributeNames();
+ transferAllAttributes(attributeNames, nodeAttributes, node.getIdentifier(), interactor);
+ }
+
+ /**
+ * Transfers all Node / Edge Attributes.
+ */
+ private void transferAllAttributes(String[] attributeNames, CyAttributes attributes,
+ String nodeName, final AttributeBag bag) {
+ List dbNames = null;
+ List dbIds = null;
+
+ for (int i = 0; i < attributeNames.length; i++) {
+ String attributeName = attributeNames[i];
+
+ if (attributeName.equals(CommonVocab.XREF_DB_NAME)) {
+ dbNames = attributes.getListAttribute(nodeName, attributeName);
+ } else if (attributeName.equals(CommonVocab.XREF_DB_ID)) {
+ dbIds = attributes.getListAttribute(nodeName, attributeName);
+ } else {
+ CyAttributesUtils.traverseAttributeValues(nodeName, attributeName, attributes, new AttributeValueVisitor() {
+ @Override
+ public void visitingAttributeValue(String objTraverseID, String attrName, CyAttributes attrs, Object[] keySpace, Object visitedValue) {
+ bag.addAttribute(attrName, visitedValue);
+ }
+ });
+ }
+ }
+
+ addExternalReferences(dbNames, dbIds, bag);
+ }
+
+ /**
+ * Adds External References.
+ */
+ private void addExternalReferences(List dbNames, List dbIds, AttributeBag bag) {
+ if ((dbNames != null) && (dbIds != null)) {
+ ExternalReference[] refs = new ExternalReference[dbNames.size()];
+
+ for (int i = 0; i < dbNames.size(); i++) {
+ String dbName = (String) dbNames.get(i);
+ String dbId = (String) dbIds.get(i);
+ refs[i] = new ExternalReference(dbName, dbId);
+ }
+
+ bag.setExternalRefs(refs);
+ }
+ }
+}
diff --git a/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/cyto_mapper/MapToCytoscape.java b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/cyto_mapper/MapToCytoscape.java
new file mode 100755
index 0000000..148e728
--- /dev/null
+++ b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/cyto_mapper/MapToCytoscape.java
@@ -0,0 +1,754 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.psi_mi.cyto_mapper;
+
+import giny.model.Node;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import org.cytoscape.coreplugin.psi_mi.data_mapper.Mapper;
+import org.cytoscape.coreplugin.psi_mi.data_mapper.MapperException;
+import org.cytoscape.coreplugin.psi_mi.model.ExternalReference;
+import org.cytoscape.coreplugin.psi_mi.model.Interaction;
+import org.cytoscape.coreplugin.psi_mi.model.Interactor;
+import org.cytoscape.coreplugin.psi_mi.model.vocab.CommonVocab;
+import org.cytoscape.coreplugin.psi_mi.model.vocab.InteractionVocab;
+import org.cytoscape.coreplugin.psi_mi.model.vocab.InteractorVocab;
+import org.cytoscape.coreplugin.psi_mi.schema.mi25.CvType;
+import org.cytoscape.coreplugin.psi_mi.schema.mi25.DbReferenceType;
+import org.cytoscape.coreplugin.psi_mi.schema.mi25.NamesType;
+import org.cytoscape.coreplugin.psi_mi.schema.mi25.XrefType;
+import org.cytoscape.coreplugin.psi_mi.util.AttributeUtil;
+import org.cytoscape.coreplugin.psi_mi.util.ListUtil;
+
+import cytoscape.CyEdge;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+import cytoscape.data.Semantics;
+
+
+/**
+ * Maps Interaction objects to Cytoscape Node/Edge Objects.
+ * This data_mapper will work on a new empty CyNetwork, or an existing CyNetwork
+ * with pre-existing data. If the CyNetwork has pre-existing nodes/edges,
+ * the data_mapper will automatically check for duplicates when new interactions
+ * are added.
+ *
+ * @author Ethan Cerami
+ * @author Nisha Vinod
+ */
+public class MapToCytoscape implements Mapper {
+ /**
+ * Spoke View.
+ */
+ public static final int SPOKE_VIEW = 1;
+
+ /**
+ * Matrix View.
+ */
+ public static final int MATRIX_VIEW = 2;
+
+ /**
+ * ROOT_GRAPH_INDEXES Attribute Name.
+ */
+ public static final String ROOT_GRAPH_INDEXES = "ROOT_GRAPH_INDEXES";
+
+ /**
+ * Data Service Interactor Reference
+ */
+ public static final String DS_INTERACTOR = "DS_INTERACTOR";
+
+ /**
+ * Data Service Interaction Reference
+ */
+ public static final String DS_INTERACTION = "DS_INTERACTION";
+
+ /**
+ * Node List
+ */
+ private List<CyNode> nodeList = new ArrayList<CyNode>();
+
+ /**
+ * Edge List
+ */
+ private List<CyEdge> edgeList = new ArrayList<CyEdge>();
+
+ /**
+ * CyMap Object.
+ */
+ private Map<String, Object> cyMap;
+
+ /**
+ * ArrayList of Interaction Objects.
+ */
+ private List interactions;
+
+ /**
+ * Graph Type, e.g. SPOKE_VIEW or MATRIX_VIEW.
+ */
+ private int graphType;
+
+ /**
+ * List of Warnings.
+ */
+ private ArrayList warnings = new ArrayList();
+
+ /**
+ * If Number of Intearctors <= MATRIX_CUT_OFF then
+ * do Matrix View. Otherwise, report a warning.
+ */
+ private static final int MATRIX_CUT_OFF = 5;
+
+ /**
+ * Open Paren Constant.
+ */
+ protected static final String OPEN_PAREN = " (";
+
+ /**
+ * Close Paren Constant.
+ */
+ protected static final String CLOSE_PAREN = ") ";
+ private Map intMap;
+ private static final boolean DEBUG = false;
+
+ /**
+ * Constructor.
+ * The graphType parameter determines the method of drawing interactions
+ * when the number of interactors > 2.
+ * <p/>
+ * For example, consider we have an interaction defined for (A, B, C).
+ * <p/>
+ * If graphType is set to SPOKE_VIEW and A is the "bait" interactor, the
+ * data_mapper will draw the following graph:
+ * <p/>
+ * A <--> B
+ * A <--> C
+ * <p/>
+ * This looks like a "spoke", with A at the center of the spoke. Note that
+ * the data_mapper will not draw an edge between B and C. In order to properly
+ * draw a spoke view, one of the interactors must be designated as "bait".
+ * If graphType is set to SPOKE_VIEW, but there is no "bait" interactor,
+ * a MapperException will be thrown.
+ * Modified the code such that if there is no bait, bait is determined from the
+ * names sorted alphanumerically, and the first one is selected as bait.
+ * <p/>
+ * If graphType is set to MATRIX_VIEW, the data_mapper will draw the following
+ * graph:
+ * <p/>
+ * A <--> B
+ * A <--> C
+ * B <--> C
+ * <p/>
+ * In the matrix view, each node interacts with all other nodes, and
+ * therefore there is now an edge between B and C. The matrix view does
+ * not require a "bait" interactor.
+ *
+ * @param interactionList interactionList ArrayList of Interaction objects.
+ * @param graphType graphType (SPOKE_VIEW or MATRIX_VIEW).
+ */
+ public MapToCytoscape(List interactionList, int graphType) {
+ if ((graphType < SPOKE_VIEW) || (graphType > MATRIX_VIEW)) {
+ throw new IllegalArgumentException("Illegal GraphType Parameter.");
+ }
+
+ this.cyMap = new HashMap<String, Object>();
+ this.interactions = interactionList;
+ this.graphType = graphType;
+ }
+
+ /**
+ * Gets a Map of all Interactors/Interactions indexed by Node/Edge ID.
+ *
+ * @return HashMap Object.
+ */
+ public Map<String, Object> getCyMap() {
+ return this.cyMap;
+ }
+
+ /**
+ * Perform Mapping.
+ *
+ * @throws MapperException Indicates Error in mapping.
+ */
+ public final void doMapping() throws MapperException {
+ final Map nodeMap = new HashMap();
+ final Map edgeMap = new HashMap();
+ intMap = new HashMap();
+ // Validate Interaction Data
+ validateInteractions();
+
+ // First pass, add all new nodes.
+ addNewNodes(nodeMap);
+
+ // Second pass, add all new interactions.
+ addNewEdges(nodeMap, edgeMap);
+ }
+
+ /**
+ * Gets all node indices.
+ *
+ * @return array of root graph indices.
+ */
+ public int[] getNodeIndices() {
+ int[] nodeIndices = new int[nodeList.size()];
+
+ for (int i = 0; i < nodeList.size(); i++) {
+ CyNode node = (CyNode) nodeList.get(i);
+ nodeIndices[i] = node.getRootGraphIndex();
+ }
+
+ return nodeIndices;
+ }
+
+ /**
+ * Gets all edge indices.
+ *
+ * @return array of root graph indices.
+ */
+ public int[] getEdgeIndices() {
+ int[] edgeIndices = new int[edgeList.size()];
+
+ for (int i = 0; i < edgeList.size(); i++) {
+ CyEdge edge = (CyEdge) edgeList.get(i);
+ edgeIndices[i] = edge.getRootGraphIndex();
+ }
+
+ return edgeIndices;
+ }
+
+ /**
+ * Gets Mapping Warnings.
+ *
+ * @return Mapping Warnings.
+ */
+ public ArrayList getWarnings() {
+ return this.warnings;
+ }
+
+ /**
+ * Validates Interactions.
+ *
+ * @throws MapperException Mapping Exception.
+ */
+ private void validateInteractions() throws MapperException {
+ String errorMsg = "In order to correctly graph your interactions, "
+ + "each interaction must specify exactly " + "one bait value.";
+
+ if (graphType == SPOKE_VIEW) {
+ for (int i = 0; i < interactions.size(); i++) {
+ Interaction interaction = (Interaction) interactions.get(i);
+ List interactors = interaction.getInteractors();
+
+ if (interactors.size() > 2) {
+ HashMap baitMap = (HashMap) interaction.getAttribute(InteractionVocab.BAIT_MAP);
+
+ if (baitMap == null) {
+ throw new MapperException(errorMsg);
+ } else {
+ Interactor bait = determineBait(interactors, baitMap);
+
+ if (bait == null) {
+ throw new MapperException(errorMsg);
+ }
+ }
+ }
+ }
+ }
+ }
+
+ /**
+ * Adds New Nodes to Network.
+ *
+ * @param nodeMap HashMap of current nodes.
+ */
+ private void addNewNodes(Map nodeMap) {
+ for (int i = 0; i < interactions.size(); i++) {
+ Interaction interaction = (Interaction) interactions.get(i);
+ List interactors = interaction.getInteractors();
+
+ for (int j = 0; j < interactors.size(); j++) {
+ Interactor interactor = (Interactor) interactors.get(j);
+ addNode(interactor, nodeMap);
+ }
+ }
+ }
+
+ /**
+ * Adds New edges to Network.
+ *
+ * @param nodeMap Current Nodes.
+ * @param edgeMap Current Edges.
+ */
+ private void addNewEdges(Map nodeMap, Map edgeMap) {
+ for (int i = 0; i < interactions.size(); i++) {
+ Interaction interaction = (Interaction) interactions.get(i);
+ List interactors = interaction.getInteractors();
+
+ if (graphType == MATRIX_VIEW) {
+ doMatrixView(interactors, nodeMap, interaction, edgeMap);
+ } else {
+ doSpokeView(interactors, nodeMap, interaction, edgeMap);
+ }
+ }
+ }
+
+ /**
+ * Map to MATRIX_VIEW Graph Type
+ */
+ private void doMatrixView(List interactors, Map nodeMap, Interaction interaction,
+ Map edgeMap) {
+ if (interactors.size() <= MATRIX_CUT_OFF) {
+ for (int j = 0; j < interactors.size(); j++) {
+ for (int k = j + 1; k < interactors.size(); k++) {
+ // Get Interactors
+ Interactor interactor1 = (Interactor) interactors.get(j);
+ Interactor interactor2 = (Interactor) interactors.get(k);
+
+ // Conditionally Create Edge
+ createEdge(interactor1, interactor2, interaction, nodeMap, edgeMap);
+ }
+ }
+ } else {
+ ExternalReference[] refs = interaction.getExternalRefs();
+ StringBuffer refList = new StringBuffer();
+
+ if ((refs != null) && (refs.length > 0)) {
+ for (int i = 0; i < refs.length; i++) {
+ String db = refs[i].getDatabase();
+ String id = refs[i].getId();
+ refList.append("[" + db + ":" + id + "] ");
+ }
+ } else {
+ refList.append("[No Ids available]");
+ }
+
+ String warningMsg = new String("Interaction contains more" + " than " + MATRIX_CUT_OFF
+ + " interactors. The interaction will not be mapped to "
+ + " any Cytoscape edges. The offending interaction is"
+ + " identified with the following identifiers: "
+ + refList);
+ warnings.add(warningMsg);
+ }
+ }
+
+ /**
+ * Map to SPOKE_VIEW Graph Type
+ */
+ private void doSpokeView(List interactors, Map nodeMap, Interaction interaction,
+ Map edgeMap) {
+ Map baitMap = (Map) interaction.getAttribute(InteractionVocab.BAIT_MAP);
+
+ if (interactors.size() > 2) {
+ // Determine bait interactor
+ Interactor bait = determineBait(interactors, baitMap);
+
+ // Create Edges between Bait and all other interactors.
+ for (int i = 0; i < interactors.size(); i++) {
+ Interactor interactor = (Interactor) interactors.get(i);
+
+ String role = (String) baitMap.get(interactor.getName());
+ int eliminateInteractorflag = 0;
+
+ if ((role == null) || (!(role.equalsIgnoreCase("bait")))) {
+ if ((role != null) && !role.equalsIgnoreCase("prey")) {
+ if (!(bait.getName().equalsIgnoreCase(interactor.getName()))) {
+ createEdge(bait, interactor, interaction, nodeMap, edgeMap);
+ } else {
+ if (eliminateInteractorflag == 1) {
+ createEdge(bait, interactor, interaction, nodeMap, edgeMap);
+ } else if (eliminateInteractorflag == 0) {
+ eliminateInteractorflag = 1;
+ }
+ }
+ } else {
+ createEdge(bait, interactor, interaction, nodeMap, edgeMap);
+ }
+ }
+ }
+ } else if (interactors.size() == 2) {
+ Interactor interactor0 = (Interactor) interactors.get(0);
+ Interactor interactor1 = (Interactor) interactors.get(1);
+
+ if ((interactor0 != null) && (interactor1 != null)) {
+ createEdge(interactor0, interactor1, interaction, nodeMap, edgeMap);
+ }
+ }
+
+ ListUtil.setInteractionMap(intMap);
+ }
+
+ /*
+ * Determines a bait
+ */
+ private Interactor determineBait(List interactors, Map baitMap) {
+ Interactor bait = null;
+
+ for (int i = 0; i < interactors.size(); i++) {
+ Interactor interactor = (Interactor) interactors.get(i);
+ String name = interactor.getName();
+
+ String role = (String) baitMap.get(interactor.getName());
+
+ if ((role != null) && role.equalsIgnoreCase("bait")) {
+ bait = interactor;
+ AttributeUtil.setbaitStatus(0);
+
+ break;
+ }
+ }
+
+ // If a bait is not found, get a bait by sorting its name and gets the
+ //first one as bait
+ if (bait == null) {
+ bait = determineBaitByName(interactors);
+ AttributeUtil.setbaitStatus(1);
+ }
+
+ return bait;
+ }
+
+ /**
+ * If there is no bait defined, then it is determined by
+ * interactor name sorted alphanumerically and then the first in the
+ * list is selected as bait.
+ */
+ private Interactor determineBaitByName(List interactors) {
+ for (int i = 0; i < interactors.size(); i++) {
+ Interactor temp;
+
+ for (int j = 0; j < (interactors.size() - 1); j++) {
+ Interactor interactor1 = (Interactor) interactors.get(j);
+ Interactor interactor2 = (Interactor) interactors.get(j + 1);
+
+ if (interactor1.getName().compareTo(interactor2.getName()) > 0) {
+ temp = interactor1;
+ interactor1 = interactor2;
+ interactor2 = temp;
+ }
+ }
+ }
+
+ return (Interactor) interactors.get(0);
+ }
+
+ /**
+ * Creates Edge Between Node1 and Node2.
+ */
+ private void createEdge(Interactor interactor1, Interactor interactor2,
+ Interaction interaction, Map nodeMap, Map edgeMap) {
+ // Get Matching Nodes
+ CyNode node1 = (CyNode) nodeMap.get(interactor1.getName());
+ CyNode node2 = (CyNode) nodeMap.get(interactor2.getName());
+
+ // Create node1 --> node2 edge key
+ String key = this.createEdgeKey(node1, node2, interaction);
+ log("Creating edge: " + key);
+
+ // Create Edge between node1 and node2.
+ CyEdge edge = Cytoscape.getCyEdge(node1, node2, Semantics.INTERACTION, key, true);
+
+ // Now get the new edge and set the edge identifier.
+ edge.setIdentifier(key);
+
+ // If no edge exists then create a new one
+ if ((!edgeExists(node1, node2, interaction, edgeMap))) {
+ edgeList.add(edge);
+ mapEdgeAttributes(interaction, edge);
+
+ int edgeRootGraphIndex = edge.getRootGraphIndex();
+ ArrayList indexes = (ArrayList) interaction.getAttribute(ROOT_GRAPH_INDEXES);
+
+ if (indexes == null) {
+ indexes = new ArrayList();
+ interaction.addAttribute(ROOT_GRAPH_INDEXES, indexes);
+ }
+
+ indexes.add(new Integer(edgeRootGraphIndex));
+
+ // Add to CyMap
+ cyMap.put(key, interaction);
+
+ // Add to Edge Map
+ edgeMap.put(key, edge);
+ intMap.put(new Integer(interaction.getInteractionId()), interaction);
+ }
+ }
+
+ /**
+ * Determines if an edge already exists between the two nodes.
+ */
+ private boolean edgeExists(CyNode node1, CyNode node2, Interaction interaction, Map edgeMap) {
+ // Create node1 --> node2 edge key
+ String key1 = this.createEdgeKey(node1, node2, interaction);
+
+ // Create node2 --> node2 edge key
+ String key2 = this.createEdgeKey(node2, node1, interaction);
+
+ // Check to see if either key already exists
+ boolean exists1 = edgeMap.containsKey(key1);
+ boolean exists2 = edgeMap.containsKey(key2);
+ boolean exists3 = exists1 | exists2;
+
+ return exists3;
+ }
+
+ /**
+ * Conditionally adds new node to graph.
+ *
+ * @param interactor Interactor object.
+ * @param map HashMap of current nodes.
+ */
+ private void addNode(Interactor interactor, Map map) {
+ String name = interactor.getName();
+ boolean inGraph = map.containsKey(name);
+
+ //HashMap nodemap;
+ if (!inGraph) {
+ // Create New Node via getCyNode Method.
+ final CyNode node = Cytoscape.getCyNode(name, true);
+ // Add New Node to Network
+ nodeList.add(node);
+
+ // Set Node Identifier, Canonical Name, and Common Name.
+ node.setIdentifier(name);
+
+ // Add to CyMap
+ cyMap.put(name, interactor);
+
+ // Map Node Attributes, e.g. species, xrefs, and/or sequence.
+ mapNodeAttributes(interactor, node);
+
+ // Add Node to Node Map.
+ map.put(name, node);
+ }
+ }
+
+ /**
+ * Maps Node Attributes to Cytoscape GraphObj Attributes.
+ * Can be subclassed.
+ *
+ * @param interactor Interactor object.
+ * @param cyNode CyNode.
+ */
+ protected void mapNodeAttributes(Interactor interactor, CyNode cyNode) {
+ // Map All Interactor Attributes
+ Map<String, Object> attributeMap = interactor.getAllAttributes();
+
+ Object value = null;
+ for(String key : attributeMap.keySet()) {
+ value = attributeMap.get(key);
+
+ if (value != null && value instanceof String) {
+ Cytoscape.getNodeAttributes().setAttribute(cyNode.getIdentifier(), key, (String)value);
+ } else if(value != null && value instanceof List) {
+ Cytoscape.getNodeAttributes()
+ .setListAttribute(cyNode.getIdentifier(), key, (List)value);
+ }
+ }
+
+ // Map interactor type
+ final CvType type = interactor.getCvType();
+ if(type != null) mapCvType(type, interactor, cyNode);
+
+ // Map All External References
+ ExternalReference[] refs = interactor.getExternalRefs();
+
+ if (refs != null) {
+ List dbsList = new ArrayList(refs.length);
+ List idsList = new ArrayList(refs.length);
+
+ for (int i = 0; i < refs.length; i++) {
+ ExternalReference ref = refs[i];
+ dbsList.add(ref.getDatabase());
+ idsList.add(ref.getId());
+ }
+
+ if ((dbsList != null) && (dbsList.size() != 0)) {
+ Cytoscape.getNodeAttributes()
+ .setListAttribute(cyNode.getIdentifier(), CommonVocab.XREF_DB_NAME, dbsList);
+ }
+
+ if ((idsList != null) && (idsList.size() != 0)) {
+ Cytoscape.getNodeAttributes()
+ .setListAttribute(cyNode.getIdentifier(), CommonVocab.XREF_DB_ID, idsList);
+ }
+ }
+ }
+
+ private void mapCvType(CvType type, Interactor interactor, CyNode node) {
+ final NamesType names = type.getNames();
+ if(names != null) {
+ final String fullName = names.getFullName();
+ if(fullName != null)
+ Cytoscape.getNodeAttributes()
+ .setAttribute(node.getIdentifier(), InteractorVocab.INTERACTOR_TYPE, fullName);
+ else if (names.getShortLabel() != null) {
+ Cytoscape.getNodeAttributes()
+ .setAttribute(node.getIdentifier(), InteractorVocab.INTERACTOR_TYPE, names.getShortLabel());
+ }
+ }
+
+ // Currently, use primary reference only.
+ final XrefType xref = type.getXref();
+ if(xref != null) {
+ final DbReferenceType pRef = xref.getPrimaryRef();
+ if(pRef != null) {
+ Cytoscape.getNodeAttributes()
+ .setAttribute(node.getIdentifier(), InteractorVocab.INTERACTOR_TYPE_DEF, pRef.getId());
+ }
+ }
+
+
+ }
+
+ /**
+ * Maps Edge Attributes to Cytoscape Attributes.
+ * Can be subclassed.
+ *
+ * @param interaction Interaction object.
+ * @param cyEdge CyEdge object.
+ */
+ protected void mapEdgeAttributes(Interaction interaction, CyEdge cyEdge) {
+ final Map<String, Object> attributeMap = interaction.getAllAttributes();
+
+ Object attrObject = null;
+ for (String key: attributeMap.keySet()) {
+
+ attrObject = attributeMap.get(key);
+
+ if (attrObject instanceof String) {
+ final String str = (String) attrObject;
+ Object object = Cytoscape.getEdgeAttributes()
+ .getStringAttribute(key, cyEdge.getIdentifier());
+
+ if (object != null) {
+ final String[] values = AttributeUtil.appendString(object, str);
+
+ if ((values != null) && (values.toString().length() != 0)) {
+ Cytoscape.getEdgeAttributes()
+ .setAttribute(cyEdge.getIdentifier(), key, values.toString());
+ }
+ } else {
+ if ((str != null) && (str.length() != 0)) {
+ Cytoscape.getEdgeAttributes().setAttribute(cyEdge.getIdentifier(), key, str);
+ }
+ }
+ } else if (attrObject instanceof Number) {
+ final Number numeric = (Number) attrObject;
+ Cytoscape.getEdgeAttributes().setAttribute(cyEdge.getIdentifier(), key, numeric.doubleValue());
+ }
+ }
+
+ // Map All External References
+ ExternalReference[] refs = interaction.getExternalRefs();
+
+ if (refs != null) {
+ List dbsList = new ArrayList(refs.length);
+ List idsList = new ArrayList(refs.length);
+
+ for (int i = 0; i < refs.length; i++) {
+ ExternalReference ref = refs[i];
+ dbsList.add(ref.getDatabase());
+ idsList.add(ref.getId());
+ }
+
+ if ((dbsList != null) && (dbsList.size() != 0)) {
+ Cytoscape.getEdgeAttributes()
+ .setListAttribute(cyEdge.getIdentifier(), CommonVocab.XREF_DB_NAME, dbsList);
+ }
+
+ if ((idsList != null) && (idsList.size() != 0)) {
+ Cytoscape.getEdgeAttributes()
+ .setListAttribute(cyEdge.getIdentifier(), CommonVocab.XREF_DB_ID, idsList);
+ }
+ }
+ }
+
+ /**
+ * Create Canonical name for Interaction type.
+ * Can be subclassed.
+ *
+ * @param interaction Interaction to be named.
+ * @return canonical name of interaction type.
+ */
+ protected String getInteractionTypeId(Interaction interaction) {
+ StringBuffer key = new StringBuffer(OPEN_PAREN);
+ String expType = (String) interaction.getAttribute(InteractionVocab.EXPERIMENTAL_SYSTEM_NAME);
+ String shortName = (String) interaction.getAttribute(InteractionVocab.INTERACTION_SHORT_NAME);
+ String pmid = (String) interaction.getAttribute(InteractionVocab.PUB_MED_ID);
+
+ if (expType == null) {
+ key.append(" <--> ");
+ } else {
+ key.append(expType);
+ }
+
+ if (shortName != null) {
+ key.append(":" + shortName);
+ }
+
+ if (pmid != null) {
+ key.append(":" + pmid);
+ }
+
+ key.append(CLOSE_PAREN);
+
+ return key.toString();
+ }
+
+ /**
+ * Create Hashkey for Edges.
+ *
+ * @param node1 First node.
+ * @param node2 Second node.
+ * @return HashKey.
+ */
+ private String createEdgeKey(Node node1, Node node2, Interaction interaction) {
+ String node1Ident = node1.getIdentifier();
+ String node2Ident = node2.getIdentifier();
+ String interactionType = getInteractionTypeId(interaction);
+
+ return new String(node1Ident + interactionType + node2Ident);
+ }
+
+ private void log(String msg) {
+ if (DEBUG) {
+ System.out.println(msg);
+ }
+ }
+}
diff --git a/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/cyto_mapper/package.html b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/cyto_mapper/package.html
new file mode 100644
index 0000000..08401c0
--- /dev/null
+++ b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/cyto_mapper/package.html
@@ -0,0 +1,8 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+<html>
+<head></head>
+
+<body bgcolor="white">
+Maps data to/from Cytoscape nodes/edges.
+</body>
+</html>
diff --git a/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/data_mapper/MapInteractionsToPsiOne.java b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/data_mapper/MapInteractionsToPsiOne.java
new file mode 100755
index 0000000..90260be
--- /dev/null
+++ b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/data_mapper/MapInteractionsToPsiOne.java
@@ -0,0 +1,545 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.psi_mi.data_mapper;
+
+import org.cytoscape.coreplugin.psi_mi.model.AttributeBag;
+import org.cytoscape.coreplugin.psi_mi.model.ExternalReference;
+import org.cytoscape.coreplugin.psi_mi.model.Interaction;
+import org.cytoscape.coreplugin.psi_mi.model.Interactor;
+import org.cytoscape.coreplugin.psi_mi.model.vocab.InteractionVocab;
+import org.cytoscape.coreplugin.psi_mi.model.vocab.InteractorVocab;
+import org.cytoscape.coreplugin.psi_mi.schema.mi1.*;
+
+import java.math.BigInteger;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.List;
+
+
+/**
+ * Converts Data Services Object Model to the PSI-MI, Level 1 Format.
+ *
+ * @author Ethan Cerami
+ */
+public class MapInteractionsToPsiOne implements Mapper {
+ private static final String EXP_AFFINITY_PRECIPITATION = "Affinity Precipitation";
+ private static final String EXP_AFFINITY_CHROMOTOGRAPHY = "Affinity Chromatography";
+ private static final String EXP_TWO_HYBRID = "Two Hybrid";
+ private static final String EXP_PURIFIED_COMPLEX = "Purified Complex";
+
+ /**
+ * Pub Med Database.
+ */
+ private static final String PUB_MED_DB = "pubmed";
+ private EntrySet entrySet;
+
+ /**
+ * ArrayList of Protein-Protein Interactions.
+ */
+ private ArrayList interactions;
+
+ /**
+ * Constructor.
+ *
+ * @param interactions ArrayList of Interactions.
+ */
+ public MapInteractionsToPsiOne(ArrayList interactions) {
+ this.interactions = interactions;
+ }
+
+ /**
+ * Perform Mapping.
+ */
+ public void doMapping() {
+ // Create Entry Set and Entry
+ entrySet = new EntrySet();
+ entrySet.setLevel(new BigInteger("1"));
+ entrySet.setVersion(new BigInteger("1"));
+
+ EntrySet.Entry entry = new EntrySet.Entry();
+
+ // Get Interactor List
+ EntrySet.Entry.InteractorList interactorList = getInteractorList();
+
+ // Get Interaction List
+ EntrySet.Entry.InteractionList interactionList = getInteractionList();
+
+ // Add to Entry node
+ entry.setInteractorList(interactorList);
+ entry.setInteractionList(interactionList);
+ entrySet.getEntry().add(entry);
+ }
+
+ /**
+ * Gets PSI XML.
+ *
+ * @return Root PSI Element.
+ */
+ public EntrySet getPsiXml() {
+ return entrySet;
+ }
+
+ /**
+ * Gets Interactor List.
+ *
+ * @return Castor InteractorList.
+ */
+ private EntrySet.Entry.InteractorList getInteractorList() {
+ HashMap proteinSet = getNonRedundantInteractors();
+ EntrySet.Entry.InteractorList interactorList = new EntrySet.Entry.InteractorList();
+
+ // Iterate through all Interactors
+ Iterator iterator = proteinSet.values().iterator();
+
+ while (iterator.hasNext()) {
+ // Create new Interactor
+ Interactor interactor = (Interactor) iterator.next();
+ ProteinInteractorType jaxbInteractor = new ProteinInteractorType();
+ setNameId(interactor, jaxbInteractor);
+ setOrganism(interactor, jaxbInteractor);
+ setSequence(interactor, jaxbInteractor);
+
+ XrefType xref = createExternalRefs(interactor);
+
+ if (xref != null) {
+ jaxbInteractor.setXref(xref);
+ }
+
+ // Add to Interactor List
+ interactorList.getProteinInteractor().add(jaxbInteractor);
+ }
+
+ return interactorList;
+ }
+
+ /**
+ * Sets Sequence Data.
+ */
+ private void setSequence(Interactor interactor, ProteinInteractorType jaxbInteractor) {
+ String seqData = (String) interactor.getAttribute(InteractorVocab.SEQUENCE_DATA);
+
+ if (seqData != null) {
+ jaxbInteractor.setSequence(seqData);
+ }
+ }
+
+ /**
+ * Sets Interactor Name and ID.
+ *
+ * @param interactor Data Services Interactor object.
+ * @param jaxbInteractor JAXB Protein Interactor Object.
+ */
+ private void setNameId(Interactor interactor, ProteinInteractorType jaxbInteractor) {
+ NamesType names = new NamesType();
+ names.setShortLabel(interactor.getName());
+
+ String fullName = (String) interactor.getAttribute(InteractorVocab.FULL_NAME);
+
+ if (fullName != null) {
+ names.setFullName(fullName);
+ }
+
+ jaxbInteractor.setNames(names);
+ jaxbInteractor.setId(interactor.getName());
+ }
+
+ /**
+ * Sets Interactor Organism.
+ *
+ * @param interactor Data Services Interactor Object.
+ * @param jaxbInteractor JAXB Protein Interactor Object.
+ */
+ private void setOrganism(Interactor interactor, ProteinInteractorType jaxbInteractor) {
+ ProteinInteractorType.Organism organism = new ProteinInteractorType.Organism();
+ String taxonomyID = (String) interactor.getAttribute(InteractorVocab.ORGANISM_NCBI_TAXONOMY_ID);
+
+ if (taxonomyID != null) {
+ organism.setNcbiTaxId(new BigInteger(taxonomyID));
+ }
+
+ NamesType orgNames = new NamesType();
+ String commonName = (String) interactor.getAttribute(InteractorVocab.ORGANISM_COMMON_NAME);
+
+ if (commonName != null) {
+ orgNames.setShortLabel(commonName);
+ }
+
+ String speciesName = (String) interactor.getAttribute(InteractorVocab.ORGANISM_SPECIES_NAME);
+
+ if (speciesName != null) {
+ orgNames.setFullName(speciesName);
+ }
+
+ organism.setNames(orgNames);
+ jaxbInteractor.setOrganism(organism);
+ }
+
+ /**
+ * Sets Interactor External References.
+ * Filters out any redundant external references.
+ */
+ private XrefType createExternalRefs(AttributeBag bag) {
+ HashSet set = new HashSet();
+ ExternalReference[] refs = bag.getExternalRefs();
+ XrefType xref = new XrefType();
+
+ if ((refs != null) && (refs.length > 0)) {
+ // Add Primary Reference
+ createPrimaryKey(refs[0], xref);
+
+ // All others become Secondary References
+ if (refs.length > 1) {
+ for (int i = 1; i < refs.length; i++) {
+ String key = this.generateXRefKey(refs[i]);
+
+ if (!set.contains(key)) {
+ createSecondaryKey(refs[i], xref);
+ set.add(key);
+ }
+ }
+ }
+ }
+
+ if (xref.getPrimaryRef() != null) {
+ return xref;
+ } else {
+ return null;
+ }
+ }
+
+ /**
+ * Generates XRef Key.
+ *
+ * @param ref External Reference
+ * @return Hash Key.
+ */
+ private String generateXRefKey(ExternalReference ref) {
+ return ref.getDatabase() + "." + ref.getId();
+ }
+
+ /**
+ * Creates Primary Key.
+ *
+ * @param ref External Reference.
+ * @param xref Castor XRef.
+ */
+ private void createPrimaryKey(ExternalReference ref, XrefType xref) {
+ DbReferenceType primaryRef = new DbReferenceType();
+ primaryRef.setDb(ref.getDatabase());
+ primaryRef.setId(ref.getId());
+ xref.setPrimaryRef(primaryRef);
+ }
+
+ /**
+ * Creates Secondary Key.
+ *
+ * @param ref External Reference
+ * @param xref Castro XRef.
+ */
+ private void createSecondaryKey(ExternalReference ref, XrefType xref) {
+ DbReferenceType secondaryRef = new DbReferenceType();
+ secondaryRef.setDb(ref.getDatabase());
+ secondaryRef.setId(ref.getId());
+ xref.getSecondaryRef().add(secondaryRef);
+ }
+
+ /**
+ * Gets a complete list of NonRedundant Proteins.
+ *
+ * @return HashMap of NonRedundant Proteins.
+ */
+ private HashMap getNonRedundantInteractors() {
+ HashMap interactorMap = new HashMap();
+
+ for (int i = 0; i < interactions.size(); i++) {
+ Interaction interaction = (Interaction) interactions.get(i);
+ List interactors = interaction.getInteractors();
+
+ for (int j = 0; j < interactors.size(); j++) {
+ Interactor interactor = (Interactor) interactors.get(j);
+ addToHashMap(interactor, interactorMap);
+ }
+ }
+
+ return interactorMap;
+ }
+
+ /**
+ * Conditionally adds Protein to HashMap.
+ *
+ * @param interactor Interactor Object.
+ * @param interactorMap HashMap of NonRedundant Interactors.
+ */
+ private void addToHashMap(Interactor interactor, HashMap interactorMap) {
+ String orfName = interactor.getName();
+
+ if (!interactorMap.containsKey(orfName)) {
+ interactorMap.put(orfName, interactor);
+ }
+ }
+
+ /**
+ * Gets Interaction List.
+ *
+ * @return Castor InteractionList.
+ */
+ private EntrySet.Entry.InteractionList getInteractionList() {
+ EntrySet.Entry.InteractionList interactionList = new EntrySet.Entry.InteractionList();
+
+ // Iterate through all interactions
+ for (int i = 0; i < interactions.size(); i++) {
+ // Create New Interaction
+ InteractionElementType jaxbInteraction = new InteractionElementType();
+ Interaction interaction = (Interaction) interactions.get(i);
+
+ // Add Experiment List
+ InteractionElementType.ExperimentList expList = getExperimentDescription(interaction, i);
+ jaxbInteraction.setExperimentList(expList);
+
+ // Add Participants
+ InteractionElementType.ParticipantList participantList = getParticipantList(interaction);
+ jaxbInteraction.setParticipantList(participantList);
+
+ // Add to Interaction List
+ interactionList.getInteraction().add(jaxbInteraction);
+
+ // Add Xrefs
+ XrefType xref = createExternalRefs(interaction);
+
+ if (xref != null) {
+ jaxbInteraction.setXref(xref);
+ }
+ }
+
+ return interactionList;
+ }
+
+ /**
+ * Gets Experiment Description.
+ *
+ * @param interaction Interaction object.
+ * @return Castor InteractionElementTypeChoice object.
+ */
+ private InteractionElementType.ExperimentList getExperimentDescription(Interaction interaction,
+ int index) {
+ // Create New Experiment List
+ InteractionElementType.ExperimentList expList = new InteractionElementType.ExperimentList();
+
+ // Create New Experiment Description
+ ExperimentType expType = new ExperimentType();
+
+ // Set Experimental ID
+ expType.setId("exp" + index);
+
+ // Set Bibliographic Reference
+ BibrefType bibRef = null;
+
+ Object pmid = interaction.getAttribute(InteractionVocab.PUB_MED_ID);
+
+ if ((pmid != null) && pmid instanceof String) {
+ bibRef = createBibRef(PUB_MED_DB, (String) pmid);
+ expType.setBibref(bibRef);
+ }
+
+ // Set Interaction Detection
+ CvType interactionDetection = getInteractionDetection(interaction);
+ expType.setInteractionDetection(interactionDetection);
+
+ // Set Choice Element
+ expList.getExperimentRefOrExperimentDescription().add(expType);
+
+ return expList;
+ }
+
+ /**
+ * Creates a Bibliography Reference.
+ *
+ * @param database Database.
+ * @param id ID String.
+ * @return Castor Bibref Object.
+ */
+ private BibrefType createBibRef(String database, String id) {
+ XrefType xref = createXRef(database, id);
+ BibrefType bibRef = new BibrefType();
+ bibRef.setXref(xref);
+
+ return bibRef;
+ }
+
+ /**
+ * Creates a Primary Reference.
+ *
+ * @param database Database.
+ * @param id ID String.
+ * @return Castor XRef object
+ */
+ private XrefType createXRef(String database, String id) {
+ XrefType xref = new XrefType();
+ DbReferenceType primaryRef = new DbReferenceType();
+ primaryRef.setDb(database);
+ primaryRef.setId(id);
+ xref.setPrimaryRef(primaryRef);
+
+ return xref;
+ }
+
+ /**
+ * Gets Interaction Detection element.
+ * It is possible that an interaction is missing important attributes,
+ * such as Experimental System Name, XRef DB, and XRef ID. All of these
+ * attributes are required by PSI. Rather than throwing an exception
+ * here, the data_mapper manually specifies "Not Specified" for all missing
+ * attributes.
+ *
+ * @param interaction Interaction.
+ * @return InteractionDetection Object.
+ */
+ private CvType getInteractionDetection(Interaction interaction) {
+ CvType interactionDetection = new CvType();
+ String idStr = null;
+
+ try {
+ idStr = (String) interaction.getAttribute(InteractionVocab.EXPERIMENTAL_SYSTEM_NAME);
+ } catch (ClassCastException e) {
+ idStr = null;
+ }
+
+ if (idStr == null) {
+ idStr = "Not Specified";
+ }
+
+ String idRef = null;
+
+ try {
+ idRef = (String) interaction.getAttribute(InteractionVocab.EXPERIMENTAL_SYSTEM_XREF_ID);
+ } catch (ClassCastException e) {
+ idRef = null;
+ }
+
+ // If there is no ID Ref, find a best match.
+ if (idRef == null) {
+ if (idStr.equals(EXP_AFFINITY_PRECIPITATION)
+ || idStr.equals(EXP_AFFINITY_CHROMOTOGRAPHY)) {
+ idStr = "affinity chromatography technologies";
+ idRef = "MI:0004";
+ } else if (idStr.equals(EXP_TWO_HYBRID)) {
+ idStr = "classical two hybrid";
+ idRef = "MI:0018";
+ } else if (idStr.equals(EXP_PURIFIED_COMPLEX)) {
+ idStr = "copurification";
+ idRef = "MI:0025";
+ } else {
+ idRef = "Not Specified";
+ }
+ }
+
+ NamesType names = createName(idStr, null);
+ interactionDetection.setNames(names);
+
+ String dbRef = null;
+
+ try {
+ dbRef = (String) interaction.getAttribute(InteractionVocab.EXPERIMENTAL_SYSTEM_XREF_DB);
+ } catch (ClassCastException e) {
+ dbRef = null;
+ }
+
+ if (dbRef == null) {
+ dbRef = "PSI-MI";
+ }
+
+ XrefType xref = createXRef(dbRef, idRef);
+ interactionDetection.setXref(xref);
+
+ return interactionDetection;
+ }
+
+ /**
+ * Creates a new Names Object.
+ *
+ * @param shortLabel Short Name Label.
+ * @param fullName Full Name/Description.
+ * @return Castor Names Object.
+ */
+ private NamesType createName(String shortLabel, String fullName) {
+ NamesType names = new NamesType();
+ names.setShortLabel(shortLabel);
+
+ if (fullName != null) {
+ names.setFullName(fullName);
+ }
+
+ return names;
+ }
+
+ /**
+ * Gets the Interaction Participant List.
+ *
+ * @param interaction Interaction object.
+ * @return Castor Participant List.
+ */
+ private InteractionElementType.ParticipantList getParticipantList(Interaction interaction) {
+ InteractionElementType.ParticipantList participantList = new InteractionElementType.ParticipantList();
+
+ List interactors = interaction.getInteractors();
+
+ for (int i = 0; i < interactors.size(); i++) {
+ Interactor interactor = (Interactor) interactors.get(i);
+ String name = interactor.getName();
+ ProteinParticipantType participant1 = createParticipant(name);
+ participantList.getProteinParticipant().add(participant1);
+ }
+
+ return participantList;
+ }
+
+ /**
+ * Create New Protein Participant.
+ *
+ * @param id Protein ID.
+ * @return Castor Protein Participant Object.
+ */
+ private ProteinParticipantType createParticipant(String id) {
+ ProteinParticipantType participant = new ProteinParticipantType();
+ RefType ref = new RefType();
+ ref.setRef(id);
+ participant.setProteinInteractorRef(ref);
+
+ return participant;
+ }
+}
diff --git a/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/data_mapper/MapInteractionsToPsiTwoFive.java b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/data_mapper/MapInteractionsToPsiTwoFive.java
new file mode 100755
index 0000000..f9fae26
--- /dev/null
+++ b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/data_mapper/MapInteractionsToPsiTwoFive.java
@@ -0,0 +1,553 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.psi_mi.data_mapper;
+
+import org.cytoscape.coreplugin.psi_mi.model.AttributeBag;
+import org.cytoscape.coreplugin.psi_mi.model.ExternalReference;
+import org.cytoscape.coreplugin.psi_mi.model.Interactor;
+import org.cytoscape.coreplugin.psi_mi.model.vocab.InteractionVocab;
+import org.cytoscape.coreplugin.psi_mi.model.vocab.InteractorVocab;
+import org.cytoscape.coreplugin.psi_mi.schema.mi25.*;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.List;
+
+
+/**
+ * Converts Data Servics Object Model to the PSI-MI, Level 2.5 Format.
+ *
+ * @author Ethan Cerami
+ */
+public class MapInteractionsToPsiTwoFive implements Mapper {
+ private static final String EXP_AFFINITY_PRECIPITATION = "Affinity Precipitation";
+ private static final String EXP_AFFINITY_CHROMOTOGRAPHY = "Affinity Chromatography";
+ private static final String EXP_TWO_HYBRID = "Two Hybrid";
+ private static final String EXP_PURIFIED_COMPLEX = "Purified Complex";
+ private int interactorId = 0;
+ private int interactionId = 0;
+ private int participantId = 0;
+ private HashMap interactorMap = new HashMap();
+
+ /**
+ * Pub Med Database.
+ */
+ private static final String PUB_MED_DB = "pubmed";
+ private EntrySet entrySet;
+
+ /**
+ * ArrayList of Protein-Protein Interactions.
+ */
+ private ArrayList interactions;
+
+ /**
+ * Constructor.
+ *
+ * @param interactions ArrayList of Interactions.
+ */
+ public MapInteractionsToPsiTwoFive(ArrayList interactions) {
+ this.interactions = interactions;
+ }
+
+ /**
+ * Perform Mapping.
+ */
+ public void doMapping() {
+ // Create Entry Set and Entry
+ entrySet = new EntrySet();
+ entrySet.setLevel(2);
+ entrySet.setVersion(5);
+
+ EntrySet.Entry entry = new EntrySet.Entry();
+
+ // Get Interactor List
+ EntrySet.Entry.InteractorList interactorList = getInteractorList();
+
+ // Get Interaction List
+ EntrySet.Entry.InteractionList interactionList = getInteractionList();
+
+ // Add to Entry node
+ entry.setInteractorList(interactorList);
+ entry.setInteractionList(interactionList);
+ entrySet.getEntry().add(entry);
+ }
+
+ /**
+ * Gets PSI XML.
+ *
+ * @return Root PSI Element.
+ */
+ public EntrySet getPsiXml() {
+ return entrySet;
+ }
+
+ /**
+ * Gets Interactor List.
+ *
+ * @return Castor InteractorList.
+ */
+ private EntrySet.Entry.InteractorList getInteractorList() {
+ HashMap proteinSet = getNonRedundantInteractors();
+ EntrySet.Entry.InteractorList interactorList = new EntrySet.Entry.InteractorList();
+
+ // Iterate through all Interactors
+ Iterator iterator = proteinSet.values().iterator();
+
+ while (iterator.hasNext()) {
+ // Create new Interactor
+ Interactor interactor = (Interactor) iterator.next();
+ InteractorElementType jaxbInteractor = new InteractorElementType();
+ setNameId(interactor, jaxbInteractor);
+ setOrganism(interactor, jaxbInteractor);
+ setSequence(interactor, jaxbInteractor);
+
+ XrefType xref = createExternalRefs(interactor);
+
+ if (xref != null) {
+ jaxbInteractor.setXref(xref);
+ }
+
+ // Add to Interactor List
+ interactorList.getInteractor().add(jaxbInteractor);
+ }
+
+ return interactorList;
+ }
+
+ /**
+ * Sets Sequence Data.
+ */
+ private void setSequence(Interactor interactor, InteractorElementType jaxbInteractor) {
+ String seqData = (String) interactor.getAttribute(InteractorVocab.SEQUENCE_DATA);
+
+ if (seqData != null) {
+ jaxbInteractor.setSequence(seqData);
+ }
+ }
+
+ /**
+ * Sets Interactor Name and ID.
+ *
+ * @param interactor Data Services Interactor object.
+ * @param jaxbInteractor JAXB Protein Interactor Object.
+ */
+ private void setNameId(Interactor interactor, InteractorElementType jaxbInteractor) {
+ NamesType names = new NamesType();
+ names.setShortLabel(interactor.getName());
+
+ String fullName = (String) interactor.getAttribute(InteractorVocab.FULL_NAME);
+
+ if (fullName != null) {
+ names.setFullName(fullName);
+ }
+
+ jaxbInteractor.setNames(names);
+ jaxbInteractor.setId(interactorId);
+ interactorMap.put(interactor.getName(), interactorId);
+ interactorId++;
+ }
+
+ /**
+ * Sets Interactor Organism.
+ *
+ * @param interactor Data Services Interactor Object.
+ * @param jaxbInteractor JAXB Protein Interactor Object.
+ */
+ private void setOrganism(Interactor interactor, InteractorElementType jaxbInteractor) {
+ InteractorElementType.Organism organism = new InteractorElementType.Organism();
+ String taxonomyID = (String) interactor.getAttribute(InteractorVocab.ORGANISM_NCBI_TAXONOMY_ID);
+
+ if (taxonomyID != null) {
+ int taxId = Integer.parseInt(taxonomyID);
+ organism.setNcbiTaxId(taxId);
+ }
+
+ NamesType orgNames = new NamesType();
+ String commonName = (String) interactor.getAttribute(InteractorVocab.ORGANISM_COMMON_NAME);
+
+ if (commonName != null) {
+ orgNames.setShortLabel(commonName);
+ }
+
+ String speciesName = (String) interactor.getAttribute(InteractorVocab.ORGANISM_SPECIES_NAME);
+
+ if (speciesName != null) {
+ orgNames.setFullName(speciesName);
+ }
+
+ organism.setNames(orgNames);
+ jaxbInteractor.setOrganism(organism);
+ }
+
+ /**
+ * Sets Interactor External References.
+ * Filters out any redundant external references.
+ */
+ private XrefType createExternalRefs(AttributeBag bag) {
+ HashSet set = new HashSet();
+ ExternalReference[] refs = bag.getExternalRefs();
+ XrefType xref = new XrefType();
+
+ if ((refs != null) && (refs.length > 0)) {
+ // Add Primary Reference
+ createPrimaryKey(refs[0], xref);
+
+ // All others become Secondary References
+ if (refs.length > 1) {
+ for (int i = 1; i < refs.length; i++) {
+ String key = this.generateXRefKey(refs[i]);
+
+ if (!set.contains(key)) {
+ createSecondaryKey(refs[i], xref);
+ set.add(key);
+ }
+ }
+ }
+ }
+
+ if (xref.getPrimaryRef() != null) {
+ return xref;
+ } else {
+ return null;
+ }
+ }
+
+ /**
+ * Generates XRef Key.
+ *
+ * @param ref External Reference
+ * @return Hash Key.
+ */
+ private String generateXRefKey(ExternalReference ref) {
+ return ref.getDatabase() + "." + ref.getId();
+ }
+
+ /**
+ * Creates Primary Key.
+ *
+ * @param ref External Reference.
+ * @param xref Castor XRef.
+ */
+ private void createPrimaryKey(ExternalReference ref, XrefType xref) {
+ DbReferenceType primaryRef = new DbReferenceType();
+ primaryRef.setDb(ref.getDatabase());
+ primaryRef.setId(ref.getId());
+ xref.setPrimaryRef(primaryRef);
+ }
+
+ /**
+ * Creates Secondary Key.
+ *
+ * @param ref External Reference
+ * @param xref Castro XRef.
+ */
+ private void createSecondaryKey(ExternalReference ref, XrefType xref) {
+ DbReferenceType secondaryRef = new DbReferenceType();
+ secondaryRef.setDb(ref.getDatabase());
+ secondaryRef.setId(ref.getId());
+ xref.getSecondaryRef().add(secondaryRef);
+ }
+
+ /**
+ * Gets a complete list of NonRedundant Proteins.
+ *
+ * @return HashMap of NonRedundant Proteins.
+ */
+ private HashMap getNonRedundantInteractors() {
+ HashMap interactorMap = new HashMap();
+
+ for (int i = 0; i < interactions.size(); i++) {
+ org.cytoscape.coreplugin.psi_mi.model.Interaction interaction = (org.cytoscape.coreplugin.psi_mi.model.Interaction) interactions
+ .get(i);
+ List interactors = interaction.getInteractors();
+
+ for (int j = 0; j < interactors.size(); j++) {
+ Interactor interactor = (Interactor) interactors.get(j);
+ addToHashMap(interactor, interactorMap);
+ }
+ }
+
+ return interactorMap;
+ }
+
+ /**
+ * Conditionally adds Protein to HashMap.
+ *
+ * @param interactor Interactor Object.
+ * @param interactorMap HashMap of NonRedundant Interactors.
+ */
+ private void addToHashMap(Interactor interactor, HashMap interactorMap) {
+ String orfName = interactor.getName();
+
+ if (!interactorMap.containsKey(orfName)) {
+ interactorMap.put(orfName, interactor);
+ }
+ }
+
+ /**
+ * Gets Interaction List.
+ *
+ * @return Castor InteractionList.
+ */
+ private EntrySet.Entry.InteractionList getInteractionList() {
+ EntrySet.Entry.InteractionList interactionList = new EntrySet.Entry.InteractionList();
+
+ // Iterate through all interactions
+ for (int i = 0; i < interactions.size(); i++) {
+ // Create New Interaction
+ EntrySet.Entry.InteractionList.Interaction jaxbInteraction = new EntrySet.Entry.InteractionList.Interaction();
+ jaxbInteraction.setId(interactionId++);
+
+ org.cytoscape.coreplugin.psi_mi.model.Interaction interaction = (org.cytoscape.coreplugin.psi_mi.model.Interaction) interactions
+ .get(i);
+
+ // Add Experiment List
+ InteractionElementType.ExperimentList expList = getExperimentDescription(interaction, i);
+ jaxbInteraction.setExperimentList(expList);
+
+ // Add Participants
+ InteractionElementType.ParticipantList participantList = getParticipantList(interaction);
+ jaxbInteraction.setParticipantList(participantList);
+
+ // Add to Interaction List
+ interactionList.getInteraction().add(jaxbInteraction);
+
+ // Add Xrefs
+ XrefType xref = createExternalRefs(interaction);
+
+ if (xref != null) {
+ jaxbInteraction.setXref(xref);
+ }
+ }
+
+ return interactionList;
+ }
+
+ /**
+ * Gets Experiment Description.
+ *
+ * @param interaction Interaction object.
+ * @return Castor InteractionElementTypeChoice object.
+ */
+ private InteractionElementType.ExperimentList getExperimentDescription(org.cytoscape.coreplugin.psi_mi.model.Interaction interaction,
+ int index) {
+ // Create New Experiment List
+ InteractionElementType.ExperimentList expList = new InteractionElementType.ExperimentList();
+
+ // Create New Experiment Description
+ ExperimentType expType = new ExperimentType();
+
+ // Set Experimental ID
+ expType.setId(index);
+
+ // Set Bibliographic Reference
+ BibrefType bibRef = null;
+
+ Object pmid = interaction.getAttribute(InteractionVocab.PUB_MED_ID);
+
+ if ((pmid != null) && pmid instanceof String) {
+ bibRef = createBibRef(PUB_MED_DB, (String) pmid);
+ expType.setBibref(bibRef);
+ }
+
+ // Set Interaction Detection
+ CvType interactionDetection = getInteractionDetection(interaction);
+ expType.setInteractionDetectionMethod(interactionDetection);
+
+ // Set Choice Element
+ expList.getExperimentRefOrExperimentDescription().add(expType);
+
+ return expList;
+ }
+
+ /**
+ * Creates a Bibliography Reference.
+ *
+ * @param database Database.
+ * @param id ID String.
+ * @return Castor Bibref Object.
+ */
+ private BibrefType createBibRef(String database, String id) {
+ XrefType xref = createXRef(database, id);
+ BibrefType bibRef = new BibrefType();
+ bibRef.setXref(xref);
+
+ return bibRef;
+ }
+
+ /**
+ * Creates a Primary Reference.
+ *
+ * @param database Database.
+ * @param id ID String.
+ * @return Castor XRef object
+ */
+ private XrefType createXRef(String database, String id) {
+ XrefType xref = new XrefType();
+ DbReferenceType primaryRef = new DbReferenceType();
+ primaryRef.setDb(database);
+ primaryRef.setId(id);
+ xref.setPrimaryRef(primaryRef);
+
+ return xref;
+ }
+
+ /**
+ * Gets Interaction Detection element.
+ * It is possible that an interaction is missing important attributes,
+ * such as Experimental System Name, XRef DB, and XRef ID. All of these
+ * attributes are required by PSI. Rather than throwing an exception
+ * here, the data_mapper manually specifies "Not Specified" for all missing
+ * attributes.
+ *
+ * @param interaction Interaction.
+ * @return InteractionDetection Object.
+ */
+ private CvType getInteractionDetection(org.cytoscape.coreplugin.psi_mi.model.Interaction interaction) {
+ CvType interactionDetection = new CvType();
+ String idStr = null;
+
+ try {
+ idStr = (String) interaction.getAttribute(InteractionVocab.EXPERIMENTAL_SYSTEM_NAME);
+ } catch (ClassCastException e) {
+ idStr = null;
+ }
+
+ if (idStr == null) {
+ idStr = "Not Specified";
+ }
+
+ String idRef = null;
+
+ try {
+ idRef = (String) interaction.getAttribute(InteractionVocab.EXPERIMENTAL_SYSTEM_XREF_ID);
+ } catch (ClassCastException e) {
+ idRef = null;
+ }
+
+ // If there is no ID Ref, find a best match.
+ if (idRef == null) {
+ if (idStr.equals(EXP_AFFINITY_PRECIPITATION)
+ || idStr.equals(EXP_AFFINITY_CHROMOTOGRAPHY)) {
+ idStr = "affinity chromatography technologies";
+ idRef = "MI:0004";
+ } else if (idStr.equals(EXP_TWO_HYBRID)) {
+ idStr = "classical two hybrid";
+ idRef = "MI:0018";
+ } else if (idStr.equals(EXP_PURIFIED_COMPLEX)) {
+ idStr = "copurification";
+ idRef = "MI:0025";
+ } else {
+ idRef = "Not Specified";
+ }
+ }
+
+ NamesType names = createName(idStr, null);
+ interactionDetection.setNames(names);
+
+ String dbRef = null;
+
+ try {
+ dbRef = (String) interaction.getAttribute(InteractionVocab.EXPERIMENTAL_SYSTEM_XREF_DB);
+ } catch (ClassCastException e) {
+ dbRef = null;
+ }
+
+ if (dbRef == null) {
+ dbRef = "PSI-MI";
+ }
+
+ XrefType xref = createXRef(dbRef, idRef);
+ interactionDetection.setXref(xref);
+
+ return interactionDetection;
+ }
+
+ /**
+ * Creates a new Names Object.
+ *
+ * @param shortLabel Short Name Label.
+ * @param fullName Full Name/Description.
+ * @return Castor Names Object.
+ */
+ private NamesType createName(String shortLabel, String fullName) {
+ NamesType names = new NamesType();
+ names.setShortLabel(shortLabel);
+
+ if (fullName != null) {
+ names.setFullName(fullName);
+ }
+
+ return names;
+ }
+
+ /**
+ * Gets the Interaction Participant List.
+ *
+ * @param interaction Interaction object.
+ * @return Castor Participant List.
+ */
+ private InteractionElementType.ParticipantList getParticipantList(org.cytoscape.coreplugin.psi_mi.model.Interaction interaction) {
+ InteractionElementType.ParticipantList participantList = new InteractionElementType.ParticipantList();
+
+ List interactors = interaction.getInteractors();
+
+ for (int i = 0; i < interactors.size(); i++) {
+ Interactor interactor = (Interactor) interactors.get(i);
+ String name = interactor.getName();
+ ParticipantType participant1 = createParticipant(name);
+ participantList.getParticipant().add(participant1);
+ }
+
+ return participantList;
+ }
+
+ /**
+ * Create New Protein Participant.
+ *
+ * @param idStr Protein ID.
+ * @return Castor Protein Participant Object.
+ */
+ private ParticipantType createParticipant(String idStr) {
+ int id = (Integer) interactorMap.get(idStr);
+ ParticipantType participant = new ParticipantType();
+ participant.setId(participantId++);
+ participant.setInteractorRef(id);
+
+ return participant;
+ }
+}
diff --git a/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/data_mapper/MapPsiOneToInteractions.java b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/data_mapper/MapPsiOneToInteractions.java
new file mode 100755
index 0000000..c4d2483
--- /dev/null
+++ b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/data_mapper/MapPsiOneToInteractions.java
@@ -0,0 +1,529 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.psi_mi.data_mapper;
+
+import java.io.StringReader;
+import java.math.BigInteger;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBException;
+import javax.xml.bind.Unmarshaller;
+
+import org.cytoscape.coreplugin.psi_mi.model.ExternalReference;
+import org.cytoscape.coreplugin.psi_mi.model.Interaction;
+import org.cytoscape.coreplugin.psi_mi.model.Interactor;
+import org.cytoscape.coreplugin.psi_mi.model.vocab.InteractionVocab;
+import org.cytoscape.coreplugin.psi_mi.model.vocab.InteractorVocab;
+import org.cytoscape.coreplugin.psi_mi.schema.mi1.BibrefType;
+import org.cytoscape.coreplugin.psi_mi.schema.mi1.CvType;
+import org.cytoscape.coreplugin.psi_mi.schema.mi1.DbReferenceType;
+import org.cytoscape.coreplugin.psi_mi.schema.mi1.EntrySet;
+import org.cytoscape.coreplugin.psi_mi.schema.mi1.ExperimentType;
+import org.cytoscape.coreplugin.psi_mi.schema.mi1.InteractionElementType;
+import org.cytoscape.coreplugin.psi_mi.schema.mi1.NamesType;
+import org.cytoscape.coreplugin.psi_mi.schema.mi1.ObjectFactory;
+import org.cytoscape.coreplugin.psi_mi.schema.mi1.ProteinInteractorType;
+import org.cytoscape.coreplugin.psi_mi.schema.mi1.ProteinParticipantType;
+import org.cytoscape.coreplugin.psi_mi.schema.mi1.RefType;
+import org.cytoscape.coreplugin.psi_mi.schema.mi1.XrefType;
+import org.cytoscape.coreplugin.psi_mi.util.ListUtil;
+import org.jdom.Text;
+
+
+/**
+ * Maps PSI-MI Level 1 Document to Interaction Objects.
+ *
+ * @author Ethan Cerami
+ * @author Nisha Vinod
+ */
+public class MapPsiOneToInteractions implements Mapper {
+ private Map interactorMap;
+ private Map experimentMap;
+ private List interactions;
+ private String xml;
+
+ /**
+ * Constructor.
+ *
+ * @param xml XML Document.
+ * @param interactions ArrayList of Interaction objects.
+ */
+ public MapPsiOneToInteractions(String xml, List interactions) {
+ this.xml = xml;
+ this.interactions = interactions;
+ }
+
+ /**
+ * Perform Mapping.
+ *
+ * @throws MapperException Problem Performing mapping.
+ */
+ public void doMapping() throws MapperException {
+ parseXml(xml);
+ }
+
+ /**
+ * Parses the PSI XML Document.
+ */
+ private void parseXml(String content) throws MapperException {
+ try {
+ interactorMap = new HashMap();
+ experimentMap = new HashMap();
+
+ StringReader reader = new StringReader(content);
+
+ // Note to self. The following method will not work
+ // JAXBContext jc = JAXBContext.newInstance(
+ // "org.cytoscape.coreplugin.psi_mi.schema.mi1");
+ // Using the line above results in the following exception:
+ // javax.xml.bind.JAXBException: "org.cytoscape.coreplugin.psi_mi.schema.mi1"
+ // doesnt contain ObjectFactory.class or jaxb.index
+
+ // The alternative is to use the syntax below. I don't know why this works,
+ // but the tip is described online here:
+ // http://forums.java.net/jive/thread.jspa?forumID=46&threadID=20124&messageID=174472
+ Class[] classes = new Class[2];
+ classes[0] = org.cytoscape.coreplugin.psi_mi.schema.mi1.EntrySet.class;
+ classes[1] = ObjectFactory.class;
+
+ JAXBContext jc = JAXBContext.newInstance(classes);
+ Unmarshaller u = jc.createUnmarshaller();
+ org.cytoscape.coreplugin.psi_mi.schema.mi1.EntrySet entrySet = (org.cytoscape.coreplugin.psi_mi.schema.mi1.EntrySet) u
+ .unmarshal(reader);
+ ListUtil.setPsiOneEntrySet(entrySet);
+
+ int entryCount = entrySet.getEntry().size();
+
+ for (int i = 0; i < entryCount; i++) {
+ EntrySet.Entry entry = entrySet.getEntry().get(i);
+ extractEntry(entry);
+ }
+ } catch (JAXBException e) {
+ throw new MapperException(e, "PSI-MI XML File is invalid: " + e.getMessage());
+ }
+ }
+
+ /**
+ * Extracts PSI Entry Root Element.
+ */
+ private void extractEntry(EntrySet.Entry entry) throws MapperException {
+ EntrySet.Entry.ExperimentList expList = entry.getExperimentList();
+ extractExperimentList(expList);
+
+ EntrySet.Entry.InteractorList interactorList = entry.getInteractorList();
+ extractInteractorList(interactorList);
+
+ EntrySet.Entry.InteractionList interactionList = entry.getInteractionList();
+ extractInteractionList(interactionList);
+ }
+
+ /**
+ * Extracts Experiment List, and places into HashMap.
+ */
+ private void extractExperimentList(EntrySet.Entry.ExperimentList expList) {
+ if (expList != null) {
+ int count = expList.getExperimentDescription().size();
+
+ for (int i = 0; i < count; i++) {
+ ExperimentType expType = expList.getExperimentDescription().get(i);
+ String id = expType.getId();
+ experimentMap.put(id, expType);
+ }
+ }
+ }
+
+ /**
+ * Extracts PSI InteractorList, and places into HashMap.
+ */
+ private void extractInteractorList(EntrySet.Entry.InteractorList interactorList) {
+ if (interactorList != null) {
+ int count = interactorList.getProteinInteractor().size();
+ ListUtil.setInteractorCount(count);
+
+ for (int i = 0; i < count; i++) {
+ ProteinInteractorType cProtein = interactorList.getProteinInteractor().get(i);
+ String id = cProtein.getId();
+ interactorMap.put(id, cProtein);
+ }
+ }
+ }
+
+ /**
+ * Extracts PSI Interaction List
+ */
+ private void extractInteractionList(EntrySet.Entry.InteractionList interactionList)
+ throws MapperException {
+ int count = interactionList.getInteraction().size();
+
+ for (int i = 0; i < count; i++) {
+ Interaction interaction = new Interaction();
+ InteractionElementType cInteraction = interactionList.getInteraction().get(i);
+ interaction.setInteractionId(cInteraction.getInteractionType().size());
+
+ InteractionElementType.ParticipantList pList = cInteraction.getParticipantList();
+ int pCount = pList.getProteinParticipant().size();
+ ArrayList interactorList = new ArrayList();
+ HashMap interactorRoles = new HashMap();
+
+ for (int j = 0; j < pCount; j++) {
+ Interactor interactor = extractInteractorRefOrElement(pList, j);
+ interactorList.add(interactor);
+
+ ProteinParticipantType participant = pList.getProteinParticipant().get(j);
+ String role = participant.getRole();
+
+ if (role != null) {
+ interactorRoles.put(interactor.getName(), role);
+ }
+ }
+
+ interaction.setInteractors(interactorList);
+
+ ArrayList list = extractExperimentalData(cInteraction, interaction);
+
+ // Add BAIT MAP / Names To all Interactions.
+ for (int j = 0; j < list.size(); j++) {
+ interaction = (Interaction) list.get(j);
+ interaction.addAttribute(InteractionVocab.BAIT_MAP, interactorRoles);
+ extractInteractionNamesXrefs(cInteraction, interaction);
+ }
+
+ interactions.addAll(list);
+ }
+ }
+
+ /**
+ * Extracts Interaction Names.
+ */
+ private void extractInteractionNamesXrefs(InteractionElementType cInteraction,
+ Interaction interaction) {
+ NamesType names = cInteraction.getNames();
+
+ if (names != null) {
+ String shortLabel = names.getShortLabel();
+ String fullName = names.getFullName();
+
+ if (shortLabel != null) {
+ interaction.addAttribute(InteractionVocab.INTERACTION_SHORT_NAME, shortLabel);
+ }
+
+ if (fullName != null) {
+ interaction.addAttribute(InteractionVocab.INTERACTION_FULL_NAME, fullName);
+ }
+ }
+
+ XrefType xref = cInteraction.getXref();
+ ExternalReference[] refs = this.extractExternalRefs(xref);
+
+ if ((refs != null) && (refs.length > 0)) {
+ interaction.setExternalRefs(refs);
+ }
+ }
+
+ /**
+ * Extracts Interactor From Reference or Element.
+ */
+ private Interactor extractInteractorRefOrElement(InteractionElementType.ParticipantList pList,
+ int j) throws MapperException {
+ Interactor interactor = null;
+ ProteinInteractorType cInteractor;
+ ProteinParticipantType participant = pList.getProteinParticipant().get(j);
+ RefType ref = participant.getProteinInteractorRef();
+
+ if (ref != null) {
+ String key = ref.getRef();
+ cInteractor = (ProteinInteractorType) interactorMap.get(key);
+
+ if (cInteractor == null) {
+ throw new MapperException("No Interactor Found for " + "proteinInteractorRef: "
+ + key);
+ }
+ } else {
+ cInteractor = participant.getProteinInteractor();
+ }
+
+ if (cInteractor != null) {
+ interactor = createInteractor(cInteractor);
+ }
+
+ return interactor;
+ }
+
+ /**
+ * Extracts Interactor Name
+ */
+ private void extractInteractorName(ProteinInteractorType cProtein, Interactor interactor)
+ throws MapperException {
+ NamesType names = cProtein.getNames();
+
+ if (names != null) {
+ String name = MapperUtil.extractName(cProtein, interactor.getExternalRefs());
+
+ // Remove all surrounding and internal white space.
+ Text jdomText = new Text(name);
+ name = jdomText.getTextNormalize();
+
+ interactor.setName(name);
+
+ String fullName = names.getFullName();
+ interactor.addAttribute(InteractorVocab.FULL_NAME, fullName);
+ }
+ }
+
+ /**
+ * Extracts All Interactor External References.
+ */
+ private ExternalReference[] extractExternalRefs(XrefType xref) {
+ ArrayList refList = new ArrayList();
+
+ if (xref != null) {
+ DbReferenceType primaryRef = xref.getPrimaryRef();
+ if (primaryRef != null) {
+ createExternalReference(primaryRef.getDb(), primaryRef.getId(), refList);
+ }
+
+ int count = xref.getSecondaryRef().size();
+
+ for (int i = 0; i < count; i++) {
+ DbReferenceType secondaryRef = xref.getSecondaryRef().get(i);
+ createExternalReference(secondaryRef.getDb(), secondaryRef.getId(), refList);
+ }
+
+ ExternalReference[] refs = new ExternalReference[refList.size()];
+ refs = (ExternalReference[]) refList.toArray(refs);
+
+ return refs;
+ } else {
+ return null;
+ }
+ }
+
+ /**
+ * Creates ExternalReference.
+ */
+ private void createExternalReference(String db, String id, ArrayList refList) {
+ ExternalReference ref = new ExternalReference(db, id);
+ refList.add(ref);
+ }
+
+ /**
+ * Extracts Experimental Data.
+ * <p/>
+ * Notes: In PSI-MI, each interaction element can have 1 or more
+ * experimentDescriptions. For each experimentDescription, we
+ * create a new DataServices Interaction object.
+ * <p/>
+ * In other words, a Data Services Interaction object contains
+ * data for one interaction, determined under exactly one experimental
+ * condition.
+ */
+ private ArrayList extractExperimentalData(InteractionElementType cInteraction,
+ Interaction interactionTemplate)
+ throws MapperException {
+ InteractionElementType.ExperimentList expList = cInteraction.getExperimentList();
+ ArrayList list = new ArrayList();
+
+ if (expList != null) {
+ int expCount = expList.getExperimentRefOrExperimentDescription().size();
+
+ for (int i = 0; i < expCount; i++) {
+ Interaction interaction = cloneInteractionTemplate(interactionTemplate);
+ Object expItem = expList.getExperimentRefOrExperimentDescription().get(i);
+ ExperimentType expType = extractExperimentReferenceOrElement(expItem);
+ String id = getPubMedId(expType);
+
+ if (id != null) {
+ interaction.addAttribute(InteractionVocab.PUB_MED_ID, id);
+ }
+
+ extractInteractionDetection(expType, interaction);
+ list.add(interaction);
+ }
+ } else {
+ throw new MapperException("Could not determine experimental "
+ + "data for one of the PSI-MI interactions");
+ }
+
+ return list;
+ }
+
+ /**
+ * Clones the InteractionTemplate. Only clones the Interactors
+ * contained within the interaction, and none of the Interaction
+ * attributes.
+ */
+ private Interaction cloneInteractionTemplate(Interaction interactionTemplate) {
+ Interaction interaction = new Interaction();
+ List interactors = interactionTemplate.getInteractors();
+ interaction.setInteractors(interactors);
+
+ return interaction;
+ }
+
+ /**
+ * Extracts an Experiment Reference or Sub-Element.
+ */
+ private ExperimentType extractExperimentReferenceOrElement(Object expItem) {
+ if (expItem instanceof RefType) {
+ RefType refType = (RefType) expItem;
+
+ return (ExperimentType) experimentMap.get(refType.getRef());
+ } else {
+ return (ExperimentType) expItem;
+ }
+ }
+
+ /**
+ * Gets Interaction Detection.
+ */
+ private void extractInteractionDetection(ExperimentType expDesc, Interaction interaction) {
+ String expSystem = null;
+
+ if (expDesc != null) {
+ CvType detection = expDesc.getInteractionDetection();
+ if (detection != null) {
+ NamesType names = detection.getNames();
+ if (names != null) {
+ expSystem = names.getShortLabel();
+
+ if (expSystem != null) {
+ interaction.addAttribute(InteractionVocab.EXPERIMENTAL_SYSTEM_NAME, expSystem);
+ }
+ }
+ XrefType xref = detection.getXref();
+
+ if (xref != null) {
+ DbReferenceType primaryRef = xref.getPrimaryRef();
+
+ if (primaryRef != null) {
+ interaction.addAttribute(InteractionVocab.EXPERIMENTAL_SYSTEM_XREF_DB,
+ primaryRef.getDb());
+ interaction.addAttribute(InteractionVocab.EXPERIMENTAL_SYSTEM_XREF_ID,
+ primaryRef.getId());
+ }
+ }
+ }
+ }
+ }
+
+ /**
+ * Extracts Pub Med ID.
+ */
+ private String getPubMedId(ExperimentType expDesc) {
+ String id = null;
+
+ if (expDesc != null) {
+ BibrefType bibRef = expDesc.getBibref();
+
+ if (bibRef != null) {
+ XrefType xRef = bibRef.getXref();
+
+ if (xRef != null) {
+ DbReferenceType primaryRef = xRef.getPrimaryRef();
+
+ if (primaryRef != null) {
+ id = primaryRef.getId();
+ }
+ }
+ }
+ }
+
+ return id;
+ }
+
+ /**
+ * Extracts Single PSI Interactor.
+ */
+ private Interactor createInteractor(ProteinInteractorType cProtein) throws MapperException {
+ org.cytoscape.coreplugin.psi_mi.model.Interactor interactor = new org.cytoscape.coreplugin.psi_mi.model.Interactor();
+ extractOrganismInfo(cProtein, interactor);
+ extractSequenceData(cProtein, interactor);
+
+ ExternalReference[] refs = extractExternalRefs(cProtein.getXref());
+
+ if ((refs != null) && (refs.length > 0)) {
+ interactor.setExternalRefs(refs);
+ }
+
+ // Set Local Id.
+ String localId = cProtein.getId();
+ interactor.addAttribute(InteractorVocab.LOCAL_ID, localId);
+
+ // Set Interactor Name Last, as it may be dependent on
+ // external references.
+ extractInteractorName(cProtein, interactor);
+
+ return interactor;
+ }
+
+ /**
+ * Extracts Sequence Data.
+ */
+ private void extractSequenceData(ProteinInteractorType cProtein, Interactor interactor) {
+ String sequence = cProtein.getSequence();
+
+ if (sequence != null) {
+ interactor.addAttribute(InteractorVocab.SEQUENCE_DATA, sequence);
+ }
+ }
+
+ /**
+ * Extracts Organism Information.
+ */
+ private void extractOrganismInfo(ProteinInteractorType cProtein, Interactor interactor) {
+ ProteinInteractorType.Organism organism = cProtein.getOrganism();
+
+ if (organism != null) {
+ NamesType names = organism.getNames();
+ String commonName = names.getShortLabel();
+ String fullName = names.getFullName();
+ BigInteger ncbiTaxID = organism.getNcbiTaxId();
+ if (commonName != null && commonName.length() > 0) {
+ interactor.addAttribute(InteractorVocab.ORGANISM_COMMON_NAME, commonName);
+ }
+ if (fullName != null && fullName.length() > 0) {
+ interactor.addAttribute(InteractorVocab.ORGANISM_SPECIES_NAME, fullName);
+ }
+ if (ncbiTaxID != null) {
+ interactor.addAttribute(InteractorVocab.ORGANISM_NCBI_TAXONOMY_ID,
+ ncbiTaxID.toString());
+ }
+ }
+ }
+}
diff --git a/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/data_mapper/MapPsiTwoFiveToInteractions.java b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/data_mapper/MapPsiTwoFiveToInteractions.java
new file mode 100755
index 0000000..4f2acfe
--- /dev/null
+++ b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/data_mapper/MapPsiTwoFiveToInteractions.java
@@ -0,0 +1,641 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package org.cytoscape.coreplugin.psi_mi.data_mapper;
+
+import org.cytoscape.coreplugin.psi_mi.model.ExternalReference;
+import org.cytoscape.coreplugin.psi_mi.model.Interaction;
+import org.cytoscape.coreplugin.psi_mi.model.Interactor;
+import org.cytoscape.coreplugin.psi_mi.model.vocab.InteractionVocab;
+import org.cytoscape.coreplugin.psi_mi.model.vocab.InteractorVocab;
+import org.cytoscape.coreplugin.psi_mi.schema.mi25.BibrefType;
+import org.cytoscape.coreplugin.psi_mi.schema.mi25.ConfidenceListType;
+import org.cytoscape.coreplugin.psi_mi.schema.mi25.ConfidenceListType.Confidence;
+import org.cytoscape.coreplugin.psi_mi.schema.mi25.CvType;
+import org.cytoscape.coreplugin.psi_mi.schema.mi25.DbReferenceType;
+import org.cytoscape.coreplugin.psi_mi.schema.mi25.EntrySet;
+import org.cytoscape.coreplugin.psi_mi.schema.mi25.EntrySet.Entry;
+import org.cytoscape.coreplugin.psi_mi.schema.mi25.EntrySet.Entry.ExperimentList;
+import org.cytoscape.coreplugin.psi_mi.schema.mi25.EntrySet.Entry.InteractionList;
+import org.cytoscape.coreplugin.psi_mi.schema.mi25.EntrySet.Entry.InteractorList;
+import org.cytoscape.coreplugin.psi_mi.schema.mi25.ExperimentType;
+import org.cytoscape.coreplugin.psi_mi.schema.mi25.InteractionElementType;
+import org.cytoscape.coreplugin.psi_mi.schema.mi25.InteractorElementType;
+import org.cytoscape.coreplugin.psi_mi.schema.mi25.NamesType;
+import org.cytoscape.coreplugin.psi_mi.schema.mi25.OpenCvType;
+import org.cytoscape.coreplugin.psi_mi.schema.mi25.ParticipantType;
+import org.cytoscape.coreplugin.psi_mi.schema.mi25.XrefType;
+import org.cytoscape.coreplugin.psi_mi.util.ListUtil;
+
+import org.jdom.Text;
+
+import java.io.StringReader;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBException;
+import javax.xml.bind.Unmarshaller;
+
+
+/**
+ * Maps PSI-MI Level 2.5 to Interaction Objects.
+ *
+ * @author Ethan Cerami
+ * @author Nisha Vinod
+ */
+public class MapPsiTwoFiveToInteractions implements Mapper {
+ private Map<String, InteractorElementType> interactorMap;
+ private Map<String, ExperimentType> experimentMap;
+ private List<Interaction> interactions;
+ private String xml;
+ private static final boolean DEBUG = false;
+
+ /**
+ * Constructor.
+ *
+ * @param xml
+ * XML Document.
+ * @param interactions
+ * ArrayList of Interaction objects.
+ */
+ public MapPsiTwoFiveToInteractions(String xml, List<Interaction> interactions) {
+ this.xml = xml;
+ this.interactions = interactions;
+ }
+
+ /**
+ * Perform Mapping.
+ *
+ * @throws MapperException
+ * Problem Performing mapping.
+ */
+ public void doMapping() throws MapperException {
+ parseXml(xml);
+ }
+
+ /**
+ * Parses the PSI XML Document.
+ */
+ private void parseXml(String content) throws MapperException {
+ try {
+ interactorMap = new HashMap<String, InteractorElementType>();
+ experimentMap = new HashMap<String, ExperimentType>();
+
+ StringReader reader = new StringReader(content);
+
+ // Note to self. The following method will not work
+ // JAXBContext jc = JAXBContext.newInstance(
+ // "org.cytoscape.coreplugin.psi_mi.schema.mi25");
+ // Using the line above results in the following exception:
+ // javax.xml.bind.JAXBException:
+ // "org.cytoscape.coreplugin.psi_mi.schema.mi1"
+ // doesnt contain ObjectFactory.class or jaxb.index
+
+ // The alternative is to use the syntax below. I don't know why this
+ // works,
+ // but the tip is described online here:
+ // http://forums.java.net/jive/thread.jspa?forumID=46&threadID=20124&messageID=174472
+ Class<?>[] classes = new Class[2];
+ classes[0] = org.cytoscape.coreplugin.psi_mi.schema.mi25.EntrySet.class;
+ classes[1] = org.cytoscape.coreplugin.psi_mi.schema.mi25.ObjectFactory.class;
+
+ JAXBContext jc = JAXBContext.newInstance(classes);
+ Unmarshaller u = jc.createUnmarshaller();
+
+ final EntrySet entrySet = (EntrySet) u.unmarshal(reader);
+ final List<Entry> entryList = entrySet.getEntry();
+
+ for (Entry entry : entryList)
+ extractEntry(entry);
+ } catch (JAXBException e) {
+ throw new MapperException(e, "PSI-MI XML File is invalid: " + e.getMessage());
+ }
+ }
+
+ /**
+ * Extracts PSI Entry Root Element.
+ */
+ private void extractEntry(Entry entry) throws MapperException {
+ final ExperimentList expList = entry.getExperimentList();
+ extractExperimentList(expList);
+
+ final InteractorList interactorList = entry.getInteractorList();
+ extractInteractorList(interactorList);
+
+ final InteractionList interactionList = entry.getInteractionList();
+ extractInteractionList(interactionList);
+ }
+
+ /**
+ * Extracts Experiment List, and places into HashMap.
+ */
+ private void extractExperimentList(EntrySet.Entry.ExperimentList expList) {
+ log("Extracting Experiment List: Start");
+
+ if (expList != null) {
+ int count = expList.getExperimentDescription().size();
+
+ for (int i = 0; i < count; i++) {
+ ExperimentType expType = expList.getExperimentDescription().get(i);
+ String id = "" + expType.getId();
+ experimentMap.put(id, expType);
+ }
+ }
+
+ log("Extracting Experiment List: End");
+ }
+
+ /**
+ * Extracts PSI InteractorList, and places into HashMap.
+ */
+ private void extractInteractorList(EntrySet.Entry.InteractorList interactorList) {
+ log("Extracting Interactor List: Start");
+
+ if (interactorList != null) {
+ int count = interactorList.getInteractor().size();
+ ListUtil.setInteractorCount(count);
+
+ List<InteractorElementType> list = interactorList.getInteractor();
+
+ String id;
+
+ for (InteractorElementType cProtein : list) {
+ id = "" + cProtein.getId();
+ log("Extracting: " + id + " --> " + cProtein);
+ interactorMap.put(id, cProtein);
+ }
+ }
+
+ log("Extracting Interactor List: End");
+ }
+
+ /**
+ * Extracts PSI Interaction List
+ */
+ private void extractInteractionList(InteractionList interactionList) throws MapperException {
+ log("Extracting Interaction List: Start");
+
+ List<org.cytoscape.coreplugin.psi_mi.schema.mi25.EntrySet.Entry.InteractionList.Interaction> list = interactionList
+ .getInteraction();
+
+ for (InteractionList.Interaction cInteraction : list) {
+ Interaction interaction = new org.cytoscape.coreplugin.psi_mi.model.Interaction();
+
+ InteractionElementType.ParticipantList pList = cInteraction.getParticipantList();
+ int pCount = pList.getParticipant().size();
+ final List<Interactor> interactorList = new ArrayList<Interactor>();
+ Map interactorRoles = new HashMap();
+
+ for (int j = 0; j < pCount; j++) {
+ Interactor interactor = extractInteractorRefOrElement(pList, j);
+ log("Getting interactor: " + interactor);
+ interactorList.add(interactor);
+
+ ParticipantType participant = pList.getParticipant().get(j);
+ ParticipantType.ExperimentalRoleList role = participant.getExperimentalRoleList();
+
+ if (role != null) {
+ for (ParticipantType.ExperimentalRoleList.ExperimentalRole expRole : role
+ .getExperimentalRole()) {
+ NamesType namesType = expRole.getNames();
+ String roleName = namesType.getShortLabel();
+ log("Storing role for: " + interactor.getName() + " --> " + roleName);
+ interactorRoles.put(interactor.getName(), roleName);
+ }
+ }
+ }
+
+ interaction.setInteractors(interactorList);
+ interaction.setInteractionId(cInteraction.getId());
+
+ List expDatalist = extractExperimentalData(cInteraction, interaction);
+
+ // Add BAIT MAP / Names To all Interactions.
+ for (int j = 0; j < expDatalist.size(); j++) {
+ interaction = (org.cytoscape.coreplugin.psi_mi.model.Interaction) expDatalist.get(j);
+ interaction.addAttribute(InteractionVocab.BAIT_MAP, interactorRoles);
+ extractInteractionNamesXrefs(cInteraction, interaction);
+
+ // Extract Confidence Values
+ extractConfidence(cInteraction, interaction);
+ }
+
+ log("Adding num interactions: " + expDatalist.size());
+ interactions.addAll(expDatalist);
+ }
+
+ log("Extracting Interaction List: End");
+ }
+
+ private void extractConfidence(InteractionElementType cInteraction,
+ org.cytoscape.coreplugin.psi_mi.model.Interaction interaction) {
+ final ConfidenceListType conf = cInteraction.getConfidenceList();
+
+ if (conf == null)
+ return;
+
+ List<Confidence> confList = conf.getConfidence();
+
+ // Pick first one only (for now)
+ if (confList != null) {
+ Confidence c = confList.get(0);
+
+ try {
+ interaction.addAttribute(InteractionVocab.CONFIDENCE_VALUE,
+ Double.valueOf(c.getValue()));
+ } catch (NumberFormatException e) {
+ return;
+ }
+
+ final OpenCvType unit = c.getUnit();
+
+ if ((unit != null) && (unit.getNames() != null)) {
+ if (c.getUnit().getNames().getShortLabel() != null)
+ interaction.addAttribute(InteractionVocab.CONFIDENCE_UNIT_SHORT_NAME,
+ c.getUnit().getNames().getShortLabel());
+
+ if (c.getUnit().getNames().getFullName() != null)
+ interaction.addAttribute(InteractionVocab.CONFIDENCE_UNIT_FULL_NAME,
+ c.getUnit().getNames().getFullName());
+ }
+ }
+ }
+
+ /**
+ * Extracts Interaction Names.
+ */
+ private void extractInteractionNamesXrefs(InteractionElementType cInteraction,
+ org.cytoscape.coreplugin.psi_mi.model.Interaction interaction) {
+ NamesType names = cInteraction.getNames();
+
+ if (names != null) {
+ String shortLabel = names.getShortLabel();
+ String fullName = names.getFullName();
+
+ if (shortLabel != null) {
+ interaction.addAttribute(InteractionVocab.INTERACTION_SHORT_NAME, shortLabel);
+ }
+
+ if (fullName != null) {
+ interaction.addAttribute(InteractionVocab.INTERACTION_FULL_NAME, fullName);
+ }
+ }
+
+ XrefType xref = cInteraction.getXref();
+ ExternalReference[] refs = extractExternalRefs(xref);
+
+ if ((refs != null) && (refs.length > 0)) {
+ log("Got refs: " + refs.length);
+ interaction.setExternalRefs(refs);
+ }
+ }
+
+ /**
+ * Extracts Interactor From Reference or Element.
+ */
+ private Interactor extractInteractorRefOrElement(InteractionElementType.ParticipantList pList,
+ int j) throws MapperException {
+ Interactor interactor;
+ org.cytoscape.coreplugin.psi_mi.schema.mi25.InteractorElementType cInteractor = null;
+ ParticipantType participant = pList.getParticipant().get(j);
+ Integer ref = participant.getInteractorRef();
+
+ if (ref != null) {
+ cInteractor = (org.cytoscape.coreplugin.psi_mi.schema.mi25.InteractorElementType) interactorMap
+ .get(""
+ + ref);
+ } else {
+ cInteractor = participant.getInteractor();
+ }
+
+ interactor = createInteractor(cInteractor);
+
+ return interactor;
+ }
+
+ /**
+ * Extracts Interactor Name
+ */
+ private void extractInteractorName(InteractorElementType cProtein, Interactor interactor)
+ throws MapperException {
+ NamesType names = cProtein.getNames();
+
+ if (names != null) {
+ String name = MapperUtil.extractName(cProtein, interactor.getExternalRefs());
+
+ // Remove all surrounding and internal white space.
+ Text jdomText = new Text(name);
+ name = jdomText.getTextNormalize();
+
+ interactor.setName(name);
+
+ String fullName = names.getFullName();
+ interactor.addAttribute(InteractorVocab.FULL_NAME, fullName);
+ }
+ }
+
+ /**
+ * Extracts All Interactor External References.
+ */
+ private ExternalReference[] extractExternalRefs(XrefType xref) {
+ final List<ExternalReference> refList = new ArrayList<ExternalReference>();
+
+ if (xref != null) {
+ DbReferenceType primaryRef = xref.getPrimaryRef();
+ createExternalReference(primaryRef.getDb(), primaryRef.getId(), refList);
+
+ for (DbReferenceType secondaryRef : xref.getSecondaryRef()) {
+ createExternalReference(secondaryRef.getDb(), secondaryRef.getId(), refList);
+ }
+
+ ExternalReference[] refs = new ExternalReference[refList.size()];
+ refs = (ExternalReference[]) refList.toArray(refs);
+
+ return refs;
+ } else {
+ return null;
+ }
+ }
+
+ /**
+ * Creates ExternalReference.
+ */
+ private void createExternalReference(String db, String id, List<ExternalReference> refList) {
+ ExternalReference ref = new ExternalReference(db, id);
+ refList.add(ref);
+ }
+
+ /**
+ * Extracts Experimental Data. <p/> Notes: In PSI-MI, each interaction
+ * element can have 1 or more experimentDescriptions. For each
+ * experimentDescription, we create a new DataServices Interaction object.
+ * <p/> In other words, a Data Services Interaction object contains data for
+ * one interaction, determined under exactly one experimental condition.
+ */
+ private List<org.cytoscape.coreplugin.psi_mi.model.Interaction> extractExperimentalData(InteractionElementType cInteraction,
+ org.cytoscape.coreplugin.psi_mi.model.Interaction interactionTemplate)
+ throws MapperException {
+ InteractionElementType.ExperimentList expList = cInteraction.getExperimentList();
+ List<org.cytoscape.coreplugin.psi_mi.model.Interaction> list = new ArrayList<org.cytoscape.coreplugin.psi_mi.model.Interaction>();
+
+ if (expList != null) {
+ int expCount = expList.getExperimentRefOrExperimentDescription().size();
+
+ for (int i = 0; i < expCount; i++) {
+ org.cytoscape.coreplugin.psi_mi.model.Interaction interaction = cloneInteractionTemplate(interactionTemplate);
+ Object expItem = expList.getExperimentRefOrExperimentDescription().get(i);
+ ExperimentType expType = extractExperimentReferenceOrElement(expItem);
+ String id = getPubMedId(expType);
+
+ if (id != null) {
+ interaction.addAttribute(InteractionVocab.PUB_MED_ID, id);
+ }
+
+ extractInteractionDetection(expType, interaction);
+ list.add(interaction);
+ }
+ } else {
+ throw new MapperException("Could not determine experimental "
+ + "data for one of the PSI-MI interactions");
+ }
+
+ return list;
+ }
+
+ /**
+ * Clones the InteractionTemplate. Only clones the Interactors contained
+ * within the interaction, and none of the Interaction attributes.
+ */
+ private org.cytoscape.coreplugin.psi_mi.model.Interaction cloneInteractionTemplate(org.cytoscape.coreplugin.psi_mi.model.Interaction interactionTemplate) {
+ org.cytoscape.coreplugin.psi_mi.model.Interaction interaction = new org.cytoscape.coreplugin.psi_mi.model.Interaction();
+ List interactors = interactionTemplate.getInteractors();
+ interaction.setInteractors(interactors);
+
+ return interaction;
+ }
+
+ /**
+ * Extracts an Experiment Reference or Sub-Element.
+ */
+ private ExperimentType extractExperimentReferenceOrElement(Object expItem) {
+ if (expItem instanceof Integer) {
+ String ref = "" + expItem;
+
+ return (ExperimentType) experimentMap.get(ref);
+ } else {
+ return (ExperimentType) expItem;
+ }
+ }
+
+ /**
+ * Gets Interaction Detection.
+ */
+ private void extractInteractionDetection(ExperimentType expDesc,
+ org.cytoscape.coreplugin.psi_mi.model.Interaction interaction) {
+ String expSystem;
+
+ if (expDesc != null) {
+ CvType detection = expDesc.getInteractionDetectionMethod();
+ // In some files, this field is empty.
+ if(detection == null)
+ return;
+
+ NamesType names = detection.getNames();
+ expSystem = names.getShortLabel();
+
+ if (expSystem != null) {
+ interaction.addAttribute(InteractionVocab.EXPERIMENTAL_SYSTEM_NAME, expSystem);
+ }
+
+ XrefType xref = detection.getXref();
+
+ if (xref != null) {
+ DbReferenceType primaryRef = xref.getPrimaryRef();
+
+ if (primaryRef != null) {
+ interaction.addAttribute(InteractionVocab.EXPERIMENTAL_SYSTEM_XREF_DB,
+ primaryRef.getDb());
+ interaction.addAttribute(InteractionVocab.EXPERIMENTAL_SYSTEM_XREF_ID,
+ primaryRef.getId());
+ }
+ }
+ }
+ }
+
+ /**
+ * Extracts Pub Med ID.
+ */
+ private String getPubMedId(ExperimentType expDesc) {
+ String id = null;
+
+ if (expDesc != null) {
+ BibrefType bibRef = expDesc.getBibref();
+
+ if (bibRef != null) {
+ XrefType xRef = bibRef.getXref();
+
+ if (xRef != null) {
+ DbReferenceType primaryRef = xRef.getPrimaryRef();
+
+ if (primaryRef != null) {
+ id = primaryRef.getId();
+ }
+ }
+ }
+ }
+
+ return id;
+ }
+
+ /**
+ * Extracts Single PSI Interactor.
+ */
+ private Interactor createInteractor(InteractorElementType cProtein) throws MapperException {
+ Interactor interactor = new Interactor();
+ extractOrganismInfo(cProtein, interactor);
+ extractSequenceData(cProtein, interactor);
+
+ // Create ID sets
+ extractIndividualXrefs(cProtein, interactor);
+
+ ExternalReference[] refs = extractExternalRefs(cProtein.getXref());
+
+ if ((refs != null) && (refs.length > 0)) {
+ interactor.setExternalRefs(refs);
+ }
+
+ // Set Local Id.
+ String localId = "" + cProtein.getId();
+ interactor.addAttribute(InteractorVocab.LOCAL_ID, localId);
+
+ // Set Interactor Name Last, as it may be dependent on
+ // external references.
+ extractInteractorName(cProtein, interactor);
+ extractCvType(cProtein, interactor);
+
+ return interactor;
+ }
+
+ private void extractInteractorType(InteractorElementType cProtein, Interactor interactor) {
+ final CvType type = cProtein.getInteractorType();
+
+ if(type == null) return;
+ }
+
+ private void extractIndividualXrefs(InteractorElementType cProtein, Interactor interactor) {
+ final XrefType xrefs = cProtein.getXref();
+
+ if (xrefs != null) {
+ final DbReferenceType pRef = xrefs.getPrimaryRef();
+
+ List<String> newList = null;
+
+ if (pRef != null) {
+ Object value = interactor.getAttribute(pRef.getDb());
+
+ if (value == null) {
+ newList = new ArrayList<String>();
+ } else if ((value != null) && value instanceof List) {
+ newList = (List<String>) value;
+ }
+
+ newList.add(pRef.getId());
+ interactor.addAttribute(pRef.getDb(), newList);
+ }
+
+ final List<DbReferenceType> sRef = xrefs.getSecondaryRef();
+
+ if (sRef != null) {
+ for (DbReferenceType ref : sRef) {
+ Object value = interactor.getAttribute(ref.getDb());
+
+ if (value == null) {
+ newList = new ArrayList<String>();
+ } else if ((value != null) && value instanceof List) {
+ newList = (List<String>) value;
+ }
+
+ newList.add(ref.getId());
+ interactor.addAttribute(ref.getDb(), newList);
+ }
+ }
+ }
+ }
+
+ private void extractCvType(InteractorElementType cProtein, Interactor interactor) {
+ final CvType cvType = cProtein.getInteractorType();
+
+ if (cvType != null)
+ interactor.setCvType(cvType);
+ }
+
+ /**
+ * Extracts Sequence Data.
+ */
+ private void extractSequenceData(InteractorElementType cProtein, Interactor interactor) {
+ String sequence = cProtein.getSequence();
+
+ if (sequence != null) {
+ interactor.addAttribute(InteractorVocab.SEQUENCE_DATA, sequence);
+ }
+ }
+
+ /**
+ * Extracts Organism Information.
+ */
+ private void extractOrganismInfo(InteractorElementType cProtein, Interactor interactor) {
+ InteractorElementType.Organism organism = cProtein.getOrganism();
+
+ if (organism != null) {
+ NamesType names = organism.getNames();
+ String commonName = names.getShortLabel();
+ String fullName = names.getFullName();
+ int ncbiTaxID = organism.getNcbiTaxId();
+ interactor.addAttribute(InteractorVocab.ORGANISM_COMMON_NAME, commonName);
+ interactor.addAttribute(InteractorVocab.ORGANISM_SPECIES_NAME, fullName);
+ interactor.addAttribute(InteractorVocab.ORGANISM_NCBI_TAXONOMY_ID,
+ Integer.toString(ncbiTaxID));
+ }
+ }
+
+ private void log(String msg) {
+ if (DEBUG) {
+ System.out.println(msg);
+ }
+ }
+}
diff --git a/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/data_mapper/Mapper.java b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/data_mapper/Mapper.java
new file mode 100755
index 0000000..916d0d9
--- /dev/null
+++ b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/data_mapper/Mapper.java
@@ -0,0 +1,50 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.psi_mi.data_mapper;
+
+
+/**
+ * Mapper Interface.
+ *
+ * @author Ethan Cerami
+ */
+public interface Mapper {
+ /**
+ * Perform Mapping.
+ *
+ * @throws MapperException Problem Performing mapping.
+ */
+ void doMapping() throws MapperException;
+}
diff --git a/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/data_mapper/MapperException.java b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/data_mapper/MapperException.java
new file mode 100755
index 0000000..cc1039f
--- /dev/null
+++ b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/data_mapper/MapperException.java
@@ -0,0 +1,74 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.psi_mi.data_mapper;
+
+
+/**
+ * Encapsulates a Mapping Exception.
+ *
+ * @author Ethan Cerami
+ */
+public class MapperException extends Exception {
+ private String humanReadableErrorMessage;
+
+ /**
+ * Constructor.
+ *
+ * @param rootCause Root Cause.
+ * @param humanReadableErrorMessage HumanReadableErrorMessage
+ */
+ public MapperException(Throwable rootCause, String humanReadableErrorMessage) {
+ super(rootCause);
+ this.humanReadableErrorMessage = humanReadableErrorMessage;
+ }
+
+ /**
+ * Constructor.
+ *
+ * @param humanReadableErrorMessage HumanReadableErrorMessage
+ */
+ public MapperException(String humanReadableErrorMessage) {
+ this.humanReadableErrorMessage = humanReadableErrorMessage;
+ }
+
+ /**
+ * Gets Human Readable Error Message.
+ *
+ * @return msg Message
+ */
+ public String getHumanReadableErrorMessage() {
+ return this.humanReadableErrorMessage;
+ }
+}
diff --git a/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/data_mapper/MapperUtil.java b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/data_mapper/MapperUtil.java
new file mode 100755
index 0000000..a433f21
--- /dev/null
+++ b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/data_mapper/MapperUtil.java
@@ -0,0 +1,148 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.psi_mi.data_mapper;
+
+import org.cytoscape.coreplugin.psi_mi.model.ExternalReference;
+import org.cytoscape.coreplugin.psi_mi.schema.mi1.ProteinInteractorType;
+import org.cytoscape.coreplugin.psi_mi.schema.mi25.InteractorElementType;
+import org.cytoscape.coreplugin.psi_mi.schema.mi25.NamesType;
+
+
+/**
+ * Mapper Utility Class.
+ *
+ * @author Ethan Cerami.
+ */
+public class MapperUtil {
+ /**
+ * If there is no short label, we need to determine an interactor
+ * name from an External Reference or the full name.
+ * <p/>
+ * Here are the rules:
+ * <OL>
+ * <LI>If an interactor has a short label, we use it.
+ * <LI>Otherwise, try to use a SWISS-PROT or UNIPROT ID.
+ * <LI>Otherwise, try to use the FullName.
+ * <LI>Otherwise, try to use XML ID.
+ * <LI>Otherwise, throw a MapperException.
+ * </OL>
+ *
+ * @param interactor ProteinInteractor
+ * @param refs Array of External Reference Objects.
+ * @return Name Substitute.
+ * @throws MapperException Error in Mapping.
+ */
+ public static String extractName(InteractorElementType interactor, ExternalReference[] refs)
+ throws MapperException {
+ String shortLabel = null;
+ String fullName = null;
+ NamesType names = interactor.getNames();
+
+ if (names != null) {
+ shortLabel = names.getShortLabel();
+ fullName = names.getFullName();
+ }
+
+ if ((shortLabel != null) && (shortLabel.trim().length() > 0)) {
+ return shortLabel;
+ } else {
+ if (refs != null) {
+ for (int i = 0; i < refs.length; i++) {
+ String dbName = refs[i].getDatabase();
+
+ if (dbName.equals("SWP") || dbName.equals("SWISS-PROT")
+ || dbName.equalsIgnoreCase("SwissProt")
+ || dbName.equalsIgnoreCase("UniProt")) {
+ return refs[i].getId();
+ }
+ }
+ }
+ }
+
+ if ((fullName != null) && (fullName.trim().length() > 0)) {
+ return fullName;
+ } else if ((("" + interactor.getId()) != null)
+ && (("" + interactor.getId()).trim().length() > 0)) {
+ return "" + interactor.getId();
+ } else {
+ throw new MapperException("Unable to determine name" + "for interactor: "
+ + interactor.getId());
+ }
+ }
+
+ /**
+ * Exracts Interactor Name.
+ * @param interactor Interactor Object.
+ * @param refs Array of External References.
+ * @return Interaction name.
+ * @throws MapperException Mapper Error.
+ */
+ public static String extractName(ProteinInteractorType interactor, ExternalReference[] refs)
+ throws MapperException {
+ String shortLabel = null;
+ String fullName = null;
+ org.cytoscape.coreplugin.psi_mi.schema.mi1.NamesType names = interactor.getNames();
+
+ if (names != null) {
+ shortLabel = names.getShortLabel();
+ fullName = names.getFullName();
+ }
+
+ if ((shortLabel != null) && (shortLabel.trim().length() > 0)) {
+ return shortLabel;
+ } else {
+ if (refs != null) {
+ for (int i = 0; i < refs.length; i++) {
+ String dbName = refs[i].getDatabase();
+
+ if (dbName.equals("SWP") || dbName.equals("SWISS-PROT")
+ || dbName.equalsIgnoreCase("SwissProt")
+ || dbName.equalsIgnoreCase("UniProt")) {
+ return refs[i].getId();
+ }
+ }
+ }
+ }
+
+ if ((fullName != null) && (fullName.trim().length() > 0)) {
+ return fullName;
+ } else if ((interactor.getId() != null) && (interactor.getId().trim().length() > 0)) {
+ return interactor.getId();
+ } else {
+ throw new MapperException("Unable to determine name" + "for interactor: "
+ + interactor.getId());
+ }
+ }
+}
diff --git a/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/data_mapper/package.html b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/data_mapper/package.html
new file mode 100755
index 0000000..46b5b8c
--- /dev/null
+++ b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/data_mapper/package.html
@@ -0,0 +1,8 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+<html>
+<head></head>
+
+<body bgcolor="white">
+Maps data from multiple data formats to biological objects.
+</body>
+</html>
diff --git a/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/model/AttributeBag.java b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/model/AttributeBag.java
new file mode 100755
index 0000000..37af493
--- /dev/null
+++ b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/model/AttributeBag.java
@@ -0,0 +1,132 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.psi_mi.model;
+
+import org.cytoscape.coreplugin.psi_mi.schema.mi25.CvType;
+
+import java.util.HashMap;
+import java.util.Map;
+
+
+/**
+ * Encapsulates a Generic Bag of Attributes.
+ *
+ * @author Ethan Cerami
+ */
+public class AttributeBag {
+ private Map<String, Object> attributes = new HashMap<String, Object>();
+ private ExternalReference[] externalRefs;
+ private CvType cvType;
+ private int interactionId;
+
+ /**
+ * Gets Interaction ID;
+ * @return Interaction ID.
+ */
+ public int getInteractionId() {
+ return interactionId;
+ }
+
+ /**
+ * Sets Interaction ID.
+ * @param interactionId Interaction ID.
+ */
+ public void setInteractionId(int interactionId) {
+ this.interactionId = interactionId;
+ }
+
+ /**
+ * Gets CV Type.
+ * @return CV Type Object.
+ */
+ public CvType getCvType() {
+ return cvType;
+ }
+
+ /**
+ * Sets CV Type.
+ * @param cvType CV Type Object.
+ */
+ public void setCvType(CvType cvType) {
+ this.cvType = cvType;
+ }
+
+ /**
+ * Gets Attribute with specified key.
+ *
+ * @param key Attribute Key.
+ * @return Attribute object value.
+ */
+ public Object getAttribute(String key) {
+ return attributes.get(key);
+ }
+
+ /**
+ * Gets all Attributes.
+ *
+ * @return HashMap of all attributes.
+ */
+ public Map<String, Object> getAllAttributes() {
+ return attributes;
+ }
+
+ /**
+ * Adds new Attribute.
+ *
+ * @param name Attribute key.
+ * @param value Object value.
+ */
+ public void addAttribute(String name, Object value) {
+ attributes.put(name, value);
+ }
+
+ /**
+ * Gets the External References.
+ *
+ * @return Array of External Reference objects.
+ */
+ public ExternalReference[] getExternalRefs() {
+ return externalRefs;
+ }
+
+ /**
+ * Sets the External References.
+ *
+ * @param externalRefs Array of External Reference objects.
+ */
+ public void setExternalRefs(ExternalReference[] externalRefs) {
+ this.externalRefs = externalRefs;
+ }
+}
diff --git a/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/model/ExternalReference.java b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/model/ExternalReference.java
new file mode 100755
index 0000000..dab5d04
--- /dev/null
+++ b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/model/ExternalReference.java
@@ -0,0 +1,153 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.psi_mi.model;
+
+
+/**
+ * Encapsulates a Single External Reference.
+ *
+ * @author Ethan Cerami
+ */
+public class ExternalReference implements Comparable {
+ /**
+ * Database Name.
+ */
+ private String database;
+
+ /**
+ * Database ID.
+ */
+ private String id;
+
+ /**
+ * Constructor.
+ *
+ * @param db Database name.
+ * @param id Database id.
+ */
+ public ExternalReference(String db, String id) {
+ this.database = db;
+ this.id = id;
+ }
+
+ /**
+ * Gets the Database Name.
+ *
+ * @return Database name.
+ */
+ public String getDatabase() {
+ return database;
+ }
+
+ /**
+ * Sets the Database Name.
+ *
+ * @param db Database name.
+ */
+ public void setDatabase(String db) {
+ this.database = db;
+ }
+
+ /**
+ * Gets the Database ID.
+ *
+ * @return Database ID.
+ */
+ public String getId() {
+ return id;
+ }
+
+ /**
+ * Overrides default equals() method.
+ * Two external references are considered equal if they share the same
+ * database and id.
+ *
+ * @param obj Object to test.
+ * @return true or false.
+ */
+ public boolean equals(Object obj) {
+ if (obj instanceof ExternalReference) {
+ ExternalReference other = (ExternalReference) obj;
+
+ return (database.equals(other.getDatabase()) && id.equals(other.getId()));
+ } else {
+ return super.equals(obj);
+ }
+ }
+
+ /**
+ * Gets Hash Code.
+ *
+ * @return Integer Hash Code.
+ */
+ public int hashCode() {
+ String str = new String(database + ":" + id);
+
+ return str.hashCode();
+ }
+
+ /**
+ * Overrides default toString() method.
+ *
+ * @return String Representation.
+ */
+ public String toString() {
+ return new String("External Reference --> Database: [" + database + "], ID: [" + id
+ + "]");
+ }
+
+ /**
+ * Comparison Operator.
+ *
+ * @param o Other Object.
+ * @return integer value.
+ */
+ public int compareTo(Object o) {
+ if (o instanceof ExternalReference) {
+ ExternalReference other = (ExternalReference) o;
+ String otherDbName = other.getDatabase();
+
+ if (!otherDbName.equals(database)) {
+ return otherDbName.compareToIgnoreCase(database);
+ } else {
+ String otherId = other.getId();
+
+ return otherId.compareToIgnoreCase(id);
+ }
+ } else {
+ return 0;
+ }
+ }
+}
diff --git a/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/model/Interaction.java b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/model/Interaction.java
new file mode 100755
index 0000000..3954f06
--- /dev/null
+++ b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/model/Interaction.java
@@ -0,0 +1,108 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.psi_mi.model;
+
+import java.util.List;
+
+
+/**
+ * Encapsulates a Single Interaction.
+ *
+ * @author Ethan Cerami
+ */
+public class Interaction extends AttributeBag {
+ private List interactors;
+
+ /**
+ * Gets All Interactors
+ *
+ * @return ArrayList of Interactors.
+ */
+ public List getInteractors() {
+ return interactors;
+ }
+
+ /**
+ * Sets All Interactors.
+ *
+ * @param interactors ArrayList of Interactors.
+ */
+ public void setInteractors(List interactors) {
+ this.interactors = interactors;
+ }
+
+ /**
+ * To String Method.
+ *
+ * @return Interaction Description.
+ */
+ public String toString() {
+ StringBuffer buffer = new StringBuffer("Interaction: ");
+ String description = this.getDescription();
+ buffer.append(description);
+
+ return buffer.toString();
+ }
+
+ /**
+ * Gets Interaction Description.
+ *
+ * @return Interaction Description.
+ */
+ public String getDescription() {
+ StringBuffer buffer = new StringBuffer();
+
+ for (int i = 0; i < interactors.size(); i++) {
+ Interactor interactor = (Interactor) interactors.get(i);
+ String name = interactor.getName();
+ buffer.append(" [" + name + "]");
+ }
+
+ ExternalReference[] xrefs = getExternalRefs();
+ buffer.append(" [Interaction XREFs --> ");
+
+ if ((xrefs == null) || (xrefs.length == 0)) {
+ buffer.append("None");
+ } else {
+ for (int i = 0; i < xrefs.length; i++) {
+ buffer.append(xrefs[i].toString() + " ");
+ }
+ }
+
+ buffer.append("]");
+
+ return buffer.toString();
+ }
+}
diff --git a/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/model/Interactor.java b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/model/Interactor.java
new file mode 100755
index 0000000..014baa2
--- /dev/null
+++ b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/model/Interactor.java
@@ -0,0 +1,91 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.psi_mi.model;
+
+
+/**
+ * Encapsulates data for a single Interactor.
+ *
+ * @author Ethan Cerami
+ */
+public class Interactor extends AttributeBag {
+ private String name;
+ private String description;
+
+ /**
+ * Gets Interactor Name.
+ *
+ * @return Interactor Name.
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * Sets Interactor Name.
+ *
+ * @param name Interactor Name.
+ */
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ /**
+ * Gets Interactor Description.
+ *
+ * @return Interactor Description.
+ */
+ public String getDescription() {
+ return description;
+ }
+
+ /**
+ * Sets Interactor Description.
+ *
+ * @param description Interactor Descriptor.
+ */
+ public void setDescription(String description) {
+ this.description = description;
+ }
+
+ /**
+ * Provides Interactor Name.
+ *
+ * @return Interactor String Name.
+ */
+ public String toString() {
+ return "Interactor: " + this.getName();
+ }
+}
diff --git a/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/model/package.html b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/model/package.html
new file mode 100755
index 0000000..9ce7511
--- /dev/null
+++ b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/model/package.html
@@ -0,0 +1,8 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+<html>
+<head></head>
+
+<body bgcolor="white">
+Core classes for encapsulating Biological data.
+</body>
+</html>
diff --git a/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/model/vocab/CommonVocab.java b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/model/vocab/CommonVocab.java
new file mode 100755
index 0000000..3c2b81f
--- /dev/null
+++ b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/model/vocab/CommonVocab.java
@@ -0,0 +1,53 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.psi_mi.model.vocab;
+
+
+/**
+ * Common Vocab Terms.
+ *
+ * @author Ethan Cerami
+ */
+public class CommonVocab {
+ /**
+ * XREF_DB_NAME.
+ */
+ public static final String XREF_DB_NAME = "XREF_DB_NAME";
+
+ /**
+ * XREF_DB_NAME.
+ */
+ public static final String XREF_DB_ID = "XREF_DB_ID";
+}
diff --git a/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/model/vocab/GoVocab.java b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/model/vocab/GoVocab.java
new file mode 100755
index 0000000..6b78cf7
--- /dev/null
+++ b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/model/vocab/GoVocab.java
@@ -0,0 +1,73 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.psi_mi.model.vocab;
+
+
+/**
+ * Package Comments
+ *
+ * @author cerami
+ */
+public class GoVocab {
+ /**
+ * GO ID.
+ */
+ public static final String GO_ID = "GO_ID";
+
+ /**
+ * GO Name.
+ */
+ public static final String GO_NAME = "GO_NAME";
+
+ /**
+ * GO Category: Process.
+ */
+ public static final String GO_CATEGORY_PROCESS = "GO_CATEGORY_PROCESS";
+
+ /**
+ * GO Category: Function.
+ */
+ public static final String GO_CATEGORY_FUNCTION = "GO_CATEGORY_FUNCTION";
+
+ /**
+ * GO Category: Component.
+ */
+ public static final String GO_CATEGORY_COMPONENT = "GO_CATEGORY_COMPONENT";
+
+ /**
+ * GO Category: Special.
+ */
+ public static final String GO_CATEGORY_SPECIAL = "GO_CATEGORY_SPECIAL";
+}
diff --git a/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/model/vocab/InteractionVocab.java b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/model/vocab/InteractionVocab.java
new file mode 100755
index 0000000..380a304
--- /dev/null
+++ b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/model/vocab/InteractionVocab.java
@@ -0,0 +1,115 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.psi_mi.model.vocab;
+
+
+/**
+ * Controlled Vocabulary for Interactions.
+ *
+ * @author Ethan Cerami
+ */
+public class InteractionVocab extends CommonVocab {
+ /**
+ * Interaction Short Name.
+ */
+ public static final String INTERACTION_SHORT_NAME = "INTERACTION_SHORT_NAME";
+
+ /**
+ * Interaction Full Name.
+ */
+ public static final String INTERACTION_FULL_NAME = "INTERACTION_FULL_NAME";
+
+ /**
+ * Experimental System Name.
+ */
+ public static final String EXPERIMENTAL_SYSTEM_NAME = "EXPERIMENTAL_SYSTEM_NAME";
+
+ /**
+ * Experimental System Name.
+ */
+ public static final String INTERACTION_TYPE_NAME = "INTERACTION_TYPE_NAME";
+
+ /**
+ * Experimental System XRef Database.
+ */
+ public static final String EXPERIMENTAL_SYSTEM_XREF_DB = "EXPERIMENTAL_SYSTEM_XREF_DB";
+
+ /**
+ * Experimental System XRef Database.
+ */
+ public static final String EXPERIMENTAL_SYSTEM_XREF_ID = "EXPERIMENTAL_SYSTEM_XREF_ID";
+
+ /**
+ * Interaction Direction.
+ */
+ public static final String DIRECTION = "DIRECTION";
+
+ /**
+ * Interaction Owner.
+ */
+ public static final String OWNER = "OWNER";
+
+ /**
+ * Interaction PubMed ID
+ */
+ public static final String PUB_MED_ID = "PUB_MED_ID";
+
+ /**
+ * Bait Map.
+ */
+ public static final String BAIT_MAP = "BAIT_MAP";
+
+ /**
+ * Interaction Type
+ */
+ public static final String INTERACTION_TYPE = "interaction";
+
+ /**
+ * Confidence Unit Short Name.
+ */
+ public static final String CONFIDENCE_UNIT_SHORT_NAME = "CONFIDENCE_UNIT_SHORT_NAME";
+
+ /**
+ * Confidence Unit Full Name.
+ */
+ public static final String CONFIDENCE_UNIT_FULL_NAME = "CONFIDENCE_UNIT_FULL_NAME";
+
+ /**
+ * Confidence Value.
+ */
+ public static final String CONFIDENCE_VALUE = "CONFIDENCE_VALUE";
+
+
+}
diff --git a/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/model/vocab/InteractorVocab.java b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/model/vocab/InteractorVocab.java
new file mode 100755
index 0000000..3145cf5
--- /dev/null
+++ b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/model/vocab/InteractorVocab.java
@@ -0,0 +1,103 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.psi_mi.model.vocab;
+
+
+/**
+ * Controlled Vocabularly for Interactors.
+ *
+ * @author Ethan Cerami
+ */
+public class InteractorVocab extends CommonVocab {
+ /**
+ * Gene Name.
+ */
+ public static final String GENE_NAME = "GENE_NAME";
+
+ /**
+ * Go Term.
+ */
+ public static final String GO_TERM = "GO_TERM";
+
+ /**
+ * Organism (Species Name).
+ */
+ public static final String ORGANISM_SPECIES_NAME = "ORGANISM_SPECIES";
+
+ /**
+ * Organism (Common Name).
+ */
+ public static final String ORGANISM_COMMON_NAME = "ORGANISM_COMMON_NAME";
+
+ /**
+ * Organism (NCBI Taxonomy ID).
+ */
+ public static final String ORGANISM_NCBI_TAXONOMY_ID = "ORGANISM_NCBI_TAXON_ID";
+
+ /**
+ * Local ID.
+ */
+ public static final String LOCAL_ID = "LOCAL_ID";
+
+ /**
+ * GenBank Flat File.
+ */
+ public static final String GEN_BANK_FLAT_FILE = "GEN_BANK_FLAT_FILE";
+
+ /**
+ * Bio Java Sequence.
+ */
+ public static final String BIO_JAVA_SEQUENCE_LIST = "BIO_JAVA_SEQUENCE_LIST";
+
+ /**
+ * Full Name.
+ */
+ public static final String FULL_NAME = "FULL_NAME";
+
+ /**
+ * Sequence Data.
+ */
+ public static final String SEQUENCE_DATA = "SEQUENCE_DATA";
+
+ /**
+ * XML Document is Result Set Format.
+ */
+ public static final String XML_RESULT_SET = "XML_RESULT_SET";
+
+ public static final String INTERACTOR_TYPE = "INTERACTOR_TYPE";
+ public static final String INTERACTOR_TYPE_DEF = "INTERACTOR_TYPE_DEF";
+
+
+}
diff --git a/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/model/vocab/package.html b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/model/vocab/package.html
new file mode 100755
index 0000000..fb6622b
--- /dev/null
+++ b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/model/vocab/package.html
@@ -0,0 +1,8 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+<html>
+<head></head>
+
+<body bgcolor="white">
+Controlled Vocabulary for Attributes.
+</body>
+</html>
diff --git a/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/plugin/ExportNetworkAsPsiMiOne.java b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/plugin/ExportNetworkAsPsiMiOne.java
new file mode 100644
index 0000000..cd0152e
--- /dev/null
+++ b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/plugin/ExportNetworkAsPsiMiOne.java
@@ -0,0 +1,106 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.psi_mi.plugin;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.task.ui.JTaskConfig;
+
+import cytoscape.task.util.TaskManager;
+
+import cytoscape.util.CyFileFilter;
+import cytoscape.util.CytoscapeAction;
+import cytoscape.util.FileUtil;
+
+import java.awt.event.ActionEvent;
+
+import java.io.File;
+
+
+/**
+ * Action to Export Network as PSI-MI Level 1.
+ *
+ * @author Ethan Cerami
+ */
+public class ExportNetworkAsPsiMiOne extends CytoscapeAction {
+ /**
+ * Constructor.
+ */
+ public ExportNetworkAsPsiMiOne() {
+ super("Network as PSI-MI Level 1.0 File...");
+ setPreferredMenu("File.Export");
+ }
+
+ /**
+ * User-initiated action to save the current network in PSI-MI format
+ * to a user-specified file. If successfully saved, fires a
+ * PropertyChange event with property=Cytoscape.NETWORK_SAVED,
+ * old_value=null, and new_value=a three element Object array containing:
+ * <OL>
+ * <LI>first element = CyNetwork saved
+ * <LI>second element = URI of the location where saved
+ * <LI>third element = an Integer representing the format in which the
+ * Network was saved (e.g., Cytoscape.FILE_PSI_MI).
+ * </OL>
+ *
+ * @param e ActionEvent Object.
+ */
+ public void actionPerformed(ActionEvent e) {
+ // get the file name
+ File file = FileUtil.getFile("Save Network as PSI-MI Level 1.0", FileUtil.SAVE,
+ new CyFileFilter[] { });
+
+ if (file != null) {
+ String fileName = file.getAbsolutePath();
+
+ if (!fileName.endsWith(".xml")) {
+ fileName = fileName + ".xml";
+ }
+
+ // Create LoadNetwork Task
+ SaveAsPsiTask task = new SaveAsPsiTask(fileName, SaveAsPsiTask.EXPORT_PSI_MI_LEVEL_1);
+
+ // Configure JTask Dialog Pop-Up Box
+ JTaskConfig jTaskConfig = new JTaskConfig();
+ jTaskConfig.setOwner(Cytoscape.getDesktop());
+ jTaskConfig.displayCloseButton(true);
+ jTaskConfig.displayStatus(true);
+ jTaskConfig.setAutoDispose(false);
+
+ // Execute Task in New Thread; pop open JTask Dialog Box.
+ TaskManager.executeTask(task, jTaskConfig);
+ }
+ }
+}
diff --git a/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/plugin/ExportNetworkAsPsiMiTwoFive.java b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/plugin/ExportNetworkAsPsiMiTwoFive.java
new file mode 100644
index 0000000..b025fc5
--- /dev/null
+++ b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/plugin/ExportNetworkAsPsiMiTwoFive.java
@@ -0,0 +1,106 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.psi_mi.plugin;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.task.ui.JTaskConfig;
+
+import cytoscape.task.util.TaskManager;
+
+import cytoscape.util.CyFileFilter;
+import cytoscape.util.CytoscapeAction;
+import cytoscape.util.FileUtil;
+
+import java.awt.event.ActionEvent;
+
+import java.io.File;
+
+
+/**
+ * Action to Export Network as PSI-MI Level 2.5
+ *
+ * @author Ethan Cerami
+ */
+public class ExportNetworkAsPsiMiTwoFive extends CytoscapeAction {
+ /**
+ * Constructor.
+ */
+ public ExportNetworkAsPsiMiTwoFive() {
+ super("Network as PSI-MI Level 2.5 File...");
+ setPreferredMenu("File.Export");
+ }
+
+ /**
+ * User-initiated action to save the current network in PSI-MI format
+ * to a user-specified file. If successfully saved, fires a
+ * PropertyChange event with property=Cytoscape.NETWORK_SAVED,
+ * old_value=null, and new_value=a three element Object array containing:
+ * <OL>
+ * <LI>first element = CyNetwork saved
+ * <LI>second element = URI of the location where saved
+ * <LI>third element = an Integer representing the format in which the
+ * Network was saved (e.g., Cytoscape.FILE_PSI_MI).
+ * </OL>
+ *
+ * @param e ActionEvent Object.
+ */
+ public void actionPerformed(ActionEvent e) {
+ // get the file name
+ File file = FileUtil.getFile("Save Network as PSI-MI Level 2.5", FileUtil.SAVE,
+ new CyFileFilter[] { });
+
+ if (file != null) {
+ String fileName = file.getAbsolutePath();
+
+ if (!fileName.endsWith(".xml")) {
+ fileName = fileName + ".xml";
+ }
+
+ // Create LoadNetwork Task
+ SaveAsPsiTask task = new SaveAsPsiTask(fileName, SaveAsPsiTask.EXPORT_PSI_MI_LEVEL_2_5);
+
+ // Configure JTask Dialog Pop-Up Box
+ JTaskConfig jTaskConfig = new JTaskConfig();
+ jTaskConfig.setOwner(Cytoscape.getDesktop());
+ jTaskConfig.displayCloseButton(true);
+ jTaskConfig.displayStatus(true);
+ jTaskConfig.setAutoDispose(false);
+
+ // Execute Task in New Thread; pop open JTask Dialog Box.
+ TaskManager.executeTask(task, jTaskConfig);
+ }
+ }
+}
diff --git a/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/plugin/PsiMiFilter.java b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/plugin/PsiMiFilter.java
new file mode 100644
index 0000000..1660d62
--- /dev/null
+++ b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/plugin/PsiMiFilter.java
@@ -0,0 +1,165 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.psi_mi.plugin;
+
+import cytoscape.data.ImportHandler;
+
+import cytoscape.data.readers.GraphReader;
+
+import cytoscape.util.CyFileFilter;
+
+import java.io.File;
+import java.io.IOException;
+
+import java.net.URL;
+import java.net.URLConnection;
+
+
+/**
+ * PsiMi Filter class. Extends CyFileFilter for integration into the Cytoscape ImportHandler
+ * framework.
+ *
+ * @author Ethan Cerami.
+ */
+public class PsiMiFilter extends CyFileFilter {
+ /**
+ * PSI-MI Files are Graphs.
+ */
+ private static String fileNature = ImportHandler.GRAPH_NATURE;
+
+ /**
+ * File Extensions.
+ */
+ private static String[] fileExtensions = { "xml" };
+
+ /**
+ * Filter Description.
+ */
+ private static String description = "PSI-MI files";
+
+ /**
+ * Constructor.
+ */
+ public PsiMiFilter() {
+ super(fileExtensions, description, fileNature);
+ }
+
+ /**
+ * Indicates which files the PsiMiFilter accepts.
+ * <p/>
+ * This method will return true only if:
+ * <UL>
+ * <LI>File ends in .xml; and
+ * <LI>File header includes the root entrySet element.
+ * </UL>
+ *
+ * @param file File
+ * @return true or false.
+ */
+ public boolean accept(File file) {
+ String fileName = file.getName();
+ boolean firstPass = false;
+
+ // First test: file must end with one of the registered file extensions.
+ for (int i = 0; i < fileExtensions.length; i++) {
+ if (fileName.endsWith(fileExtensions[i])) {
+ firstPass = true;
+ }
+ }
+
+ if (firstPass) {
+ // Second test: file header must contain the root PSI-MI entry set
+ try {
+ String header = getHeader(file);
+
+ if (header.indexOf("<entrySet") > -1) {
+ return true;
+ }
+ } catch (IOException e) {
+ firstPass = false;
+ }
+ }
+
+ return false;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param url DOCUMENT ME!
+ * @param contentType DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean accept(URL url, String contentType) {
+ // Check for matching content type
+ if ((contentType != null) && (contentTypes != null)
+ && (contentTypes.get(contentType) != null))
+ return true;
+
+ try {
+ final String header = getHeader(url);
+
+ if (header.indexOf("<entrySet") > -1)
+ return true;
+ } catch (IOException e) {
+ return false;
+ }
+
+ return false;
+ }
+
+ /**
+ * Gets the appropirate GraphReader object.
+ *
+ * @param fileName File Name.
+ * @return GraphReader Object.
+ */
+ public GraphReader getReader(String fileName) {
+ return new PsiMiGraphReader(fileName);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param url DOCUMENT ME!
+ * @param conn DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public GraphReader getReader(URL url, URLConnection conn) {
+ return new PsiMiGraphReader(url.toString());
+ }
+}
diff --git a/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/plugin/PsiMiGraphReader.java b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/plugin/PsiMiGraphReader.java
new file mode 100644
index 0000000..c2f3e26
--- /dev/null
+++ b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/plugin/PsiMiGraphReader.java
@@ -0,0 +1,134 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.psi_mi.plugin;
+
+import cytoscape.data.readers.AbstractGraphReader;
+
+import org.cytoscape.coreplugin.psi_mi.cyto_mapper.MapToCytoscape;
+import org.cytoscape.coreplugin.psi_mi.data_mapper.MapPsiOneToInteractions;
+import org.cytoscape.coreplugin.psi_mi.data_mapper.MapPsiTwoFiveToInteractions;
+import org.cytoscape.coreplugin.psi_mi.util.ContentReader;
+
+import java.io.IOException;
+
+import java.util.ArrayList;
+import java.util.List;
+
+
+/**
+ * GraphReader Implementation for PSI-MI Files.
+ *
+ * @author Ethan Cerami.
+ */
+public class PsiMiGraphReader extends AbstractGraphReader {
+ private int[] nodeIndices;
+ private int[] edgeIndices;
+ private String networkName;
+
+ /**
+ * Constructor
+ *
+ * @param fileName File Name.
+ */
+ public PsiMiGraphReader(String fileName) {
+ super(fileName);
+ }
+
+ /**
+ * Read file.
+ *
+ * @throws IOException IO Error.
+ */
+ public void read() throws IOException {
+ try {
+ // set network name - use pathway name
+ networkName = fileName;
+
+ ContentReader reader = new ContentReader();
+ String xml = reader.retrieveContent(fileName);
+
+ // Map BioPAX Data to Cytoscape Nodes/Edges
+ List interactions = new ArrayList();
+
+ // Pick one of two mappers
+ int level2 = xml.indexOf("level=\"2\"");
+
+ if ((level2 > 0) && (level2 < 500)) {
+ MapPsiTwoFiveToInteractions mapper = new MapPsiTwoFiveToInteractions(xml,
+ interactions);
+ mapper.doMapping();
+ } else {
+ MapPsiOneToInteractions mapper = new MapPsiOneToInteractions(xml, interactions);
+ mapper.doMapping();
+ }
+
+ // Now Map to Cytocape Network Objects.
+ MapToCytoscape mapper2 = new MapToCytoscape(interactions, MapToCytoscape.SPOKE_VIEW);
+ mapper2.doMapping();
+ nodeIndices = mapper2.getNodeIndices();
+ edgeIndices = mapper2.getEdgeIndices();
+ } catch (Throwable e) {
+ e.printStackTrace();
+ throw new IOException(e.getMessage());
+ }
+ }
+
+ /**
+ * Get Node Indices.
+ *
+ * @return array of root graph node indices.
+ */
+ public int[] getNodeIndicesArray() {
+ return nodeIndices;
+ }
+
+ /**
+ * Get Edge Indices.
+ *
+ * @return array of root graph edge indices.
+ */
+ public int[] getEdgeIndicesArray() {
+ return edgeIndices;
+ }
+
+ /**
+ * Gets network name.
+ *
+ * @return network name.
+ */
+ public String getNetworkName() {
+ return networkName;
+ }
+}
diff --git a/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/plugin/PsiMiPlugIn.java b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/plugin/PsiMiPlugIn.java
new file mode 100644
index 0000000..b8a3678
--- /dev/null
+++ b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/plugin/PsiMiPlugIn.java
@@ -0,0 +1,62 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.psi_mi.plugin;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.data.ImportHandler;
+
+import cytoscape.plugin.CytoscapePlugin;
+
+
+/**
+ * PSI-MI PlugIn.
+ *
+ * @author Ethan Cerami.
+ * @author Nisha Vinod.
+ */
+public class PsiMiPlugIn extends CytoscapePlugin {
+ /**
+ * PSI-MI Plugin
+ */
+ public PsiMiPlugIn() {
+ // Register PsiMiFilter
+ ImportHandler importHandler = new ImportHandler();
+ importHandler.addFilter(new PsiMiFilter());
+
+ Cytoscape.getDesktop().getCyMenus().addAction(new ExportNetworkAsPsiMiOne());
+ Cytoscape.getDesktop().getCyMenus().addAction(new ExportNetworkAsPsiMiTwoFive());
+ }
+}
diff --git a/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/plugin/SaveAsPsiTask.java b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/plugin/SaveAsPsiTask.java
new file mode 100644
index 0000000..6be870a
--- /dev/null
+++ b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/plugin/SaveAsPsiTask.java
@@ -0,0 +1,182 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.psi_mi.plugin;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+
+import cytoscape.task.Task;
+import cytoscape.task.TaskMonitor;
+
+import org.cytoscape.coreplugin.psi_mi.cyto_mapper.MapFromCytoscape;
+import org.cytoscape.coreplugin.psi_mi.data_mapper.MapInteractionsToPsiOne;
+import org.cytoscape.coreplugin.psi_mi.data_mapper.MapInteractionsToPsiTwoFive;
+
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.StringWriter;
+
+import java.util.ArrayList;
+
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBException;
+import javax.xml.bind.Marshaller;
+
+
+/**
+ * Task to Export to PSI-MI.
+ *
+ * @author Ethan Cerami
+ */
+public class SaveAsPsiTask implements Task {
+ /**
+ * Export to PSI-MI Level 1.
+ */
+ public static final int EXPORT_PSI_MI_LEVEL_1 = 0;
+
+ /**
+ * Export to PSI-MI Level 2.5.
+ */
+ public static final int EXPORT_PSI_MI_LEVEL_2_5 = 1;
+ private String fileName;
+ private TaskMonitor taskMonitor;
+ private int exportOption;
+
+ /**
+ * Constructor.
+ *
+ * @param fileName Filename to save to
+ * @param exportOption EXPORT_PSI_MI_LEVEL_1 or EXPORT_PSI_MI_LEVEL_2_5.
+ */
+ public SaveAsPsiTask(String fileName, int exportOption) {
+ this.fileName = fileName;
+ this.exportOption = exportOption;
+ }
+
+ /**
+ * Executes the Task.
+ */
+ public void run() {
+ taskMonitor.setStatus("Saving to PSI-MI...");
+
+ try {
+ StringWriter writer = new StringWriter();
+
+ if (Cytoscape.getCurrentNetwork().getNodeCount() == 0) {
+ throw new IllegalArgumentException("Network is empty.");
+ }
+
+ FileWriter f = new FileWriter(fileName);
+ CyNetwork netToSave = Cytoscape.getCurrentNetwork();
+
+ // First, map to Data Service Objects
+ MapFromCytoscape mapper1 = new MapFromCytoscape(netToSave);
+ mapper1.doMapping();
+
+ ArrayList interactions = mapper1.getInteractions();
+
+ // Second, map to PSI-MI
+ if (exportOption == SaveAsPsiTask.EXPORT_PSI_MI_LEVEL_1) {
+ MapInteractionsToPsiOne mapper2 = new MapInteractionsToPsiOne(interactions);
+ mapper2.doMapping();
+
+ org.cytoscape.coreplugin.psi_mi.schema.mi1.EntrySet entrySet = mapper2.getPsiXml();
+ Marshaller marshaller = createMarshaller("org.cytoscape.coreplugin.psi_mi.schema.mi1");
+ marshaller.marshal(entrySet, writer);
+ } else {
+ MapInteractionsToPsiTwoFive mapper2 = new MapInteractionsToPsiTwoFive(interactions);
+ mapper2.doMapping();
+
+ org.cytoscape.coreplugin.psi_mi.schema.mi25.EntrySet entrySet = mapper2.getPsiXml();
+ Marshaller marshaller = createMarshaller("org.cytoscape.coreplugin.psi_mi.schema.mi25");
+ marshaller.marshal(entrySet, writer);
+ }
+
+ f.write(writer.toString());
+ f.close();
+
+ Object[] retValue = new Object[3];
+ retValue[0] = netToSave;
+ retValue[1] = new File(fileName).toURI();
+ retValue[2] = new Integer(Cytoscape.FILE_PSI_MI);
+ Cytoscape.firePropertyChange(Cytoscape.NETWORK_SAVED, null, retValue);
+
+ taskMonitor.setPercentCompleted(100);
+ taskMonitor.setStatus("Network successfully saved to: " + fileName);
+ } catch (IllegalArgumentException e) {
+ taskMonitor.setException(e, "Network is Empty. Cannot be saved.");
+ } catch (IOException e) {
+ taskMonitor.setException(e, "Unable to save network.");
+ } catch (JAXBException e) {
+ taskMonitor.setException(e, "Unable to save network.");
+ }
+ }
+
+ private Marshaller createMarshaller(String schema) throws JAXBException {
+ JAXBContext jc = JAXBContext.newInstance(schema);
+ Marshaller marshaller = jc.createMarshaller();
+ marshaller.setProperty(Marshaller.JAXB_ENCODING, "UTF-8");
+ marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, Boolean.TRUE);
+
+ return marshaller;
+ }
+
+ /**
+ * Halts the Task: Not Currently Implemented.
+ */
+ public void halt() {
+ // Task can not currently be halted.
+ }
+
+ /**
+ * Sets the Task Monitor.
+ *
+ * @param taskMonitor TaskMonitor Object.
+ * @throws IllegalThreadStateException Illegal Thread State Error.
+ */
+ public void setTaskMonitor(TaskMonitor taskMonitor) throws IllegalThreadStateException {
+ this.taskMonitor = taskMonitor;
+ }
+
+ /**
+ * Gets the Task Title.
+ *
+ * @return Task Title.
+ */
+ public String getTitle() {
+ return new String("Saving Network");
+ }
+}
diff --git a/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/plugin/package.html b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/plugin/package.html
new file mode 100644
index 0000000..eecbc0a
--- /dev/null
+++ b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/plugin/package.html
@@ -0,0 +1,8 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+<html>
+<head></head>
+
+<body bgcolor="white">
+PSI-MI Level 1, 2.5 Import/Export PlugIn.
+</body>
+</html>
diff --git a/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/util/AttributeUtil.java b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/util/AttributeUtil.java
new file mode 100755
index 0000000..a43b2c5
--- /dev/null
+++ b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/util/AttributeUtil.java
@@ -0,0 +1,109 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.psi_mi.util;
+
+import org.cytoscape.coreplugin.psi_mi.model.Interaction;
+
+
+/**
+ * Misc Utility Class for Extracting / Manipulating Attributes and Attribute
+ * Values.
+ *
+ * @author Ethan Cerami
+ */
+public class AttributeUtil {
+ private static int baitStatus = 0;
+
+ /**
+ * Gets Interaction Attribute with specified key.
+ *
+ * @param interaction Interaction Object.
+ * @param key Key.
+ * @return Attribute Value.
+ */
+ public static String getAttribute(Interaction interaction, String key) {
+ String value = (String) interaction.getAttribute(key);
+
+ if (value == null) {
+ value = "";
+ }
+
+ return value;
+ }
+
+ /**
+ * Appends a String to the specified Object.
+ *
+ * @param object Object (either a String or a String[]).
+ * @param value String to append.
+ * @return Array of Strings.
+ */
+ public static String[] appendString(Object object, String value) {
+ String[] newValues = null;
+
+ if (object instanceof String) {
+ newValues = new String[2];
+ newValues[0] = (String) object;
+ newValues[1] = value;
+ } else if (object instanceof String[]) {
+ String[] strs = (String[]) object;
+ newValues = new String[strs.length + 1];
+
+ for (int i = 0; i < strs.length; i++) {
+ newValues[i] = strs[i];
+ }
+
+ newValues[strs.length] = value;
+ }
+
+ return newValues;
+ }
+
+ /**
+ * Sets the Bait Status.
+ * @param s Bait Status.
+ */
+ public static void setbaitStatus(int s) {
+ baitStatus = s;
+ }
+
+ /**
+ * Gets the Bait Status.
+ * @return Bait Status.
+ */
+ public static int getbaitStatus() {
+ return baitStatus;
+ }
+}
diff --git a/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/util/ConfigLogger.java b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/util/ConfigLogger.java
new file mode 100755
index 0000000..372f42b
--- /dev/null
+++ b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/util/ConfigLogger.java
@@ -0,0 +1,56 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.psi_mi.util;
+
+
+/**
+ * Configures the Apache Commons Logging.
+ *
+ * @author Ethan Cerami
+ */
+public class ConfigLogger {
+ /**
+ * Configures the Apache Commons Logger Logger.
+ */
+ public static void configureLogger() {
+ // Use the Apache Simple Log
+ System.setProperty("org.apache.commons.logging.Log",
+ "org.apache.commons.logging.impl.SimpleLog");
+
+ // Set Logging Level: Must be one of ("trace", "debug", "info",
+ // "warn", "error", or "fatal"). If not specified, defaults to "info".
+ System.setProperty("org.apache.commons.logging.simplelog.defaultlog", "error");
+ }
+}
diff --git a/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/util/ContentReader.java b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/util/ContentReader.java
new file mode 100755
index 0000000..d4c5c7a
--- /dev/null
+++ b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/util/ContentReader.java
@@ -0,0 +1,267 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.psi_mi.util;
+
+import java.io.*;
+
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.net.UnknownHostException;
+
+import java.util.zip.GZIPInputStream;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipInputStream;
+
+
+/**
+ * Retrieves Content from Local File System, Web Site, or FTP Site.
+ *
+ * @author Ethan Cerami
+ */
+public class ContentReader {
+ private static final String HTTP = "http";
+ private static final String FTP = "ftp";
+
+ /**
+ * Retrieves Content from Local System, Web Site or FTP site.
+ *
+ * @param urlStr URL String.
+ * @return File contents.
+ * @throws DataServiceException Error Retrieving file.
+ */
+ public String retrieveContent(String urlStr) throws DataServiceException {
+ String content = null;
+ URL url = null;
+
+ try {
+ if (urlStr.startsWith(HTTP) || urlStr.startsWith(FTP)) {
+ url = new URL(urlStr);
+
+ if (url.getProtocol().equalsIgnoreCase(HTTP)) {
+ content = retrieveContentFromWeb(url);
+ }
+
+ if (url.getProtocol().equalsIgnoreCase(FTP)) {
+ content = retrieveContentFromFtp(url);
+ }
+ } else {
+ File file = new File(urlStr);
+ InputStreamReader reader = new InputStreamReader(new FileInputStream(file));
+ content = this.retrieveContentFromFile(reader);
+ }
+ } catch (MalformedURLException e) {
+ throw new DataServiceException(e, "URL is malformed: " + url + ". Please try again.");
+ } catch (UnknownHostException e) {
+ String msg = "Network error occurred while trying to "
+ + "make network connection. Could not find server: " + e.getMessage()
+ + ". Please check your server and network settings, " + "and try again.";
+ throw new DataServiceException(e, msg);
+ } catch (IOException e) {
+ throw new DataServiceException(e,
+ "Error occurred "
+ + " while trying to retrieve data from: " + urlStr);
+ }
+
+ return content;
+ }
+
+ /**
+ * Retrieves Content from Web.
+ *
+ * @param url URL String.
+ * @return File contents.
+ */
+ private String retrieveContentFromWeb(URL url) throws IOException {
+ InputStreamReader isr = new InputStreamReader(url.openStream());
+ final int bufSize = 65536;
+ char[] buf = new char[bufSize];
+ String content = "";
+ int charsread = 0;
+
+ while (true) {
+ charsread = isr.read(buf, 0, bufSize);
+
+ if (charsread == -1) {
+ break;
+ }
+
+ String bufstring = new String(buf, 0, charsread);
+ content += bufstring;
+ }
+
+ return content;
+ }
+
+ private URL addAuthorizationToUrl(URL url) throws MalformedURLException, IOException {
+ String protocol = url.getProtocol();
+ String userinfo = url.getUserInfo();
+ String host = url.getHost();
+ int port = url.getPort();
+ String file = url.getFile();
+ URL authorizedurl;
+
+ if ((userinfo == null) || (userinfo.length() == 0)) {
+ userinfo = "anonymous:anon at ftp.net";
+ authorizedurl = url;
+ } else {
+ authorizedurl = new URL(protocol + "://" + userinfo + "@" + host + ":" + port + file);
+ }
+
+ return authorizedurl;
+ }
+
+ /**
+ * Retrieves Content from FTP site.
+ *
+ * @param url URL String.
+ * @return File contents.
+ * @throws IOException Error Retrieving file.
+ */
+ private String retrieveContentFromFtp(URL url) throws IOException {
+ InputStreamReader isr = new InputStreamReader(url.openStream());
+ final int bufSize = 65536;
+ char[] buf = new char[bufSize];
+ String content = "";
+ int charsread = 0;
+
+ while (true) {
+ charsread = isr.read(buf, 0, bufSize);
+
+ if (charsread == -1) {
+ break;
+ }
+
+ String bufstring = new String(buf, 0, charsread);
+ content += bufstring;
+ }
+
+ return content;
+ }
+
+ /**
+ * Retrieves Content from local File System.
+ *
+ * @param reader Reader Object
+ * @return File contents.
+ * @throws IOException Error Retrieving file. //File file
+ */
+ private String retrieveContentFromFile(InputStreamReader reader) throws IOException {
+ final int bufSize = 65536;
+ char[] buf = new char[bufSize];
+ StringBuffer content = new StringBuffer("");
+ int charsread = 0;
+
+ int totalcharsread = 0;
+ while (true) {
+ charsread = reader.read(buf, 0, bufSize);
+ totalcharsread += charsread;
+
+ if (charsread == -1) {
+ break;
+ }
+
+ String bufstring = new String(buf, 0, charsread);
+ content.append(bufstring);
+
+ }
+
+ return content.toString();
+ }
+
+ /**
+ * This method will try to determine whether this stream is connected to a zip file,
+ * a gzipped file, a possible text file or a possible binary file, in that order.
+ * It will return an appropriate Reader for the identified filetype,
+ * or 'null' if the type was not recognizable (ie: we could not read the four
+ * bytes constituting the magic number).
+ *
+ * @param aStream InputStream to determine the nature of
+ * @return Reader with a Reader into the converted stream.
+ */
+ public static InputStreamReader determineFileType(InputStream aStream) {
+ InputStreamReader result = null;
+
+ try {
+ // Reading the first four bytes.
+ byte[] firstFour = new byte[4];
+ PushbackInputStream pbi = new PushbackInputStream(aStream, 4);
+ int count = pbi.read(firstFour, 0, 4);
+
+ // If we couldn't even read 4 bytes, it cannot be good. In that case
+ // we 'll therefore return 'null'.
+ if (count == 4) {
+ /*System.out.println( "Read magic numbers (first four bytes: " +
+ firstFour[ 0 ] + " " +
+ firstFour[ 1 ] + " " +
+ firstFour[ 2 ] + " " +
+ firstFour[ 3 ] + " " + ")." ); */
+
+ // Now unread our bytes.
+ pbi.unread(firstFour);
+
+ // Okay, let's check these magic numbers, shall we?
+ if ((firstFour[0] == (byte) 0x1F) && (firstFour[1] == (byte) 0x8b)) {
+ // GZIP!
+ //System.out.println( "Detected GZIP format." );
+ result = new InputStreamReader(new GZIPInputStream(pbi));
+ } else if ((firstFour[0] == (byte) 0x50) && (firstFour[1] == (byte) 0x4b)
+ && (firstFour[2] == (byte) 0x03) && (firstFour[3] == (byte) 0x04)) {
+ // (pk)ZIP!
+ //System.out.println( "Detected ZIP format." );
+ ZipInputStream zis = new ZipInputStream(pbi);
+
+ ZipEntry ze = zis.getNextEntry();
+
+ // Extra check: ze cannot be 'null'!
+ if (ze != null) {
+ result = new InputStreamReader(zis);
+ }
+ }
+
+ // If we are here and result is still 'null', we weren't able to identify it
+ // as either GZIP or ZIP.
+ // So create a regular reader and go from here.
+ if (result == null) {
+ System.out.println("Defaulted to standard Reader.");
+ result = new InputStreamReader(pbi);
+ }
+ }
+ } catch (Exception ioe) {
+ System.out.println("IOException while attempting to determine filetype." + ioe);
+ }
+
+ return result;
+ }
+}
diff --git a/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/util/DataServiceException.java b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/util/DataServiceException.java
new file mode 100755
index 0000000..1b8e0b8
--- /dev/null
+++ b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/util/DataServiceException.java
@@ -0,0 +1,74 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.psi_mi.util;
+
+
+/**
+ * Indicates communication error with the data service.
+ *
+ * @author Ethan Cerami
+ */
+public class DataServiceException extends Exception {
+ private String humanReadableErrorMessage;
+
+ /**
+ * Constructor.
+ *
+ * @param rootCause Root Cause.
+ * @param humanReadableErrorMessage Human Readable Error Message.
+ */
+ public DataServiceException(Throwable rootCause, String humanReadableErrorMessage) {
+ super(rootCause);
+ this.humanReadableErrorMessage = humanReadableErrorMessage;
+ }
+
+ /**
+ * Constructor.
+ *
+ * @param humanReadableErrorMessage Message.
+ */
+ public DataServiceException(String humanReadableErrorMessage) {
+ this.humanReadableErrorMessage = humanReadableErrorMessage;
+ }
+
+ /**
+ * Gets Exception Message.
+ *
+ * @return Error Message.
+ */
+ public String getMessage() {
+ return this.humanReadableErrorMessage;
+ }
+}
diff --git a/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/util/ListUtil.java b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/util/ListUtil.java
new file mode 100755
index 0000000..ede5bb7
--- /dev/null
+++ b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/util/ListUtil.java
@@ -0,0 +1,167 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.psi_mi.util;
+
+import org.cytoscape.coreplugin.psi_mi.schema.mi25.EntrySet;
+
+import java.util.Map;
+
+
+/**
+ * Misc. List Utilities.
+ *
+ * @author Nisha Vinod
+ */
+public class ListUtil {
+ private static int totalInteractors;
+ private static String level;
+ private static String version;
+ private static int fileCount;
+ private static EntrySet entrySet;
+ private static org.cytoscape.coreplugin.psi_mi.schema.mi1.EntrySet psiOneEntrySet;
+ private static Map interactionMap;
+
+ /**
+ * Gets PSI One Entry Set.
+ * @return PSI One Entry Set.
+ */
+ public static org.cytoscape.coreplugin.psi_mi.schema.mi1.EntrySet getPsiOneEntrySet() {
+ return psiOneEntrySet;
+ }
+
+ /**
+ * Set PSI One Entry Set.
+ * @param psiOneEntrySet PSI One Entry Set.
+ */
+ public static void setPsiOneEntrySet(org.cytoscape.coreplugin.psi_mi.schema.mi1.EntrySet psiOneEntrySet) {
+ ListUtil.psiOneEntrySet = psiOneEntrySet;
+ }
+
+ /**
+ * Gets the Interaction Map.
+ * @return Interaction Map.
+ */
+ public static Map getInteractionMap() {
+ return interactionMap;
+ }
+
+ /**
+ * Sets the Interaction Map.
+ * @param interactionMap Interaction Map.
+ */
+ public static void setInteractionMap(Map interactionMap) {
+ ListUtil.interactionMap = interactionMap;
+ }
+
+ /**
+ * Gets the Entry Set.
+ * @return EntrySet Object.
+ */
+ public static EntrySet getEntrySet() {
+ return entrySet;
+ }
+
+ /**
+ * Sets the Entry Set.
+ * @param eSet Entry Set Object.
+ */
+ public static void setEntrySet(EntrySet eSet) {
+ entrySet = eSet;
+ }
+
+ /**
+ * Sets the Interactor Count.
+ * @param interactorCount interactor count.
+ */
+ public static void setInteractorCount(int interactorCount) {
+ totalInteractors = interactorCount;
+ }
+
+ /**
+ * Gets the Interactor Count.
+ * @return interactorCount.
+ */
+ public static int getInteractorCount() {
+ return totalInteractors;
+ }
+
+ /**
+ * Sets the PSI-MI Level.
+ * @param l PSI-MI Level.
+ */
+ public static void setLevel(String l) {
+ level = l;
+ }
+
+ /**
+ * Gets the PSI-MI Level.
+ * @return PSI-MI Level.
+ */
+ public static String getLevel() {
+ return level;
+ }
+
+ /**
+ * Sets the PSI-MI Version #.
+ * @param v PSI-MI Version #.
+ */
+ public static void setVersion(String v) {
+ version = v;
+ }
+
+ /**
+ * Gets the PSI-MI Version #.
+ * @return PSI-MI Version #.
+ */
+ public static String getVersion() {
+ return version;
+ }
+
+ /**
+ * Sets the File Entry Count.
+ * @param count file entry count.
+ */
+ public static void setFileEntryCount(int count) {
+ fileCount = count;
+ }
+
+ /**
+ * Gets the File Entry Count.
+ * @return file entry count.
+ */
+ public static int getFileEntryCount() {
+ return fileCount;
+ }
+}
diff --git a/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/util/PropertyManager.java b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/util/PropertyManager.java
new file mode 100755
index 0000000..0065586
--- /dev/null
+++ b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/util/PropertyManager.java
@@ -0,0 +1,134 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.psi_mi.util;
+
+import java.util.Properties;
+
+
+/**
+ * Centralized Property Manager.
+ *
+ * @author Ethan Cerami
+ */
+public class PropertyManager extends Properties {
+ /**
+ * Property: Database Location
+ */
+ public static final String DB_LOCATION = new String("dataservice.db_location");
+
+ /**
+ * Property: Database User Name.
+ */
+ public static final String DB_USER = new String("dataservice.db_user");
+
+ /**
+ * Property: Database Password.
+ */
+ public static final String DB_PASSWORD = new String("dataservice.db_password");
+
+ /**
+ * Property: SeqHound Location.
+ */
+ public static final String SEQ_HOUND_LOCATION = new String("dataservice.seqhound_location");
+
+ /**
+ * Property: CPath Read Location.
+ */
+ public static final String CPATH_READ_LOCATION = new String("dataservice.cpath_read_location");
+
+ /**
+ * Property: DataService Proxy Host.
+ */
+ public static final String DATASERVICE_PROXY_HOST = new String("dataservice.proxy_host");
+
+ /**
+ * Property: DataService Proxy Port.
+ */
+ public static final String DATASERVICE_PROXY_PORT = new String("dataservice.proxy_port");
+
+ /**
+ * Property: CPath Write Location.
+ */
+ public static final String CPATH_WRITE_LOCATION = new String("dataservice.cpath_write_location");
+
+ /**
+ * Property: NCBI Location.
+ */
+ public static final String NCBI_LOCATION = new String("dataservice.ncbi_location");
+
+ /**
+ * Property: Log Config File.
+ */
+ public static final String LOG_CONFIG_FILE = new String("LOG_CONFIG_FILE");
+
+ /**
+ * Singelton Property Manager.
+ */
+ private static PropertyManager manager;
+
+ /**
+ * Private Constructor.
+ */
+ private PropertyManager() {
+ }
+
+ /**
+ * Gets Instance of Singleton.
+ *
+ * @return PropertyManager.
+ */
+ public static PropertyManager getInstance() {
+ if (manager == null) {
+ manager = new PropertyManager();
+ manager.bootStrap();
+ }
+
+ return manager;
+ }
+
+ /**
+ * Initializes Property Manager with Hard Coded Default Values.
+ */
+ private void bootStrap() {
+ manager.setProperty(DB_USER, "tomcat");
+ manager.setProperty(DB_PASSWORD, "kitty");
+ manager.setProperty(DB_LOCATION, "localhost");
+ manager.setProperty(LOG_CONFIG_FILE, "config/config-JDBC.properties");
+ manager.setProperty(CPATH_READ_LOCATION, "http://cbio.mskcc.org/cpath/webservice.do");
+ manager.setProperty(CPATH_WRITE_LOCATION, "http://cbio.mskcc.org/ds/xmlrpc");
+ manager.setProperty(SEQ_HOUND_LOCATION, "http://zaphod.mshri.on.ca/cgi-bin/seqhound/seqrem");
+ manager.setProperty(NCBI_LOCATION, "http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi");
+ }
+}
diff --git a/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/util/StringParser.java b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/util/StringParser.java
new file mode 100755
index 0000000..52c1dd3
--- /dev/null
+++ b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/util/StringParser.java
@@ -0,0 +1,92 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.psi_mi.util;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.StringReader;
+
+import java.util.ArrayList;
+import java.util.StringTokenizer;
+
+
+/**
+ * General String Parsing Utility Methods.
+ *
+ * @author Ethan Cerami
+ */
+public class StringParser {
+ /**
+ * Creates ArrayList of all Lines in File.
+ *
+ * @param content String content.
+ * @return ArrayList of all lines in File.
+ * @throws java.io.IOException Input Output Exception.
+ */
+ public static ArrayList createArrayList(String content) throws IOException {
+ StringReader strReader = new StringReader(content);
+ BufferedReader bufReader = new BufferedReader(strReader);
+ String line = bufReader.readLine();
+ ArrayList lines = new ArrayList();
+
+ while (line != null) {
+ lines.add(line);
+ line = bufReader.readLine();
+ }
+
+ return lines;
+ }
+
+ /**
+ * Counts Total Number of Columns.
+ * Note: This method determines number of columns by examining the first
+ * line of data only.
+ *
+ * @param lines ArrayList of Tab Delimited Lines.
+ * @return Number of Columns.
+ */
+ public static int countColumns(ArrayList lines) {
+ int counter = 0;
+ String line = (String) lines.get(0);
+ StringTokenizer tokenizer = new StringTokenizer(line, "\t");
+
+ while (tokenizer.hasMoreElements()) {
+ tokenizer.nextElement();
+ counter++;
+ }
+
+ return counter;
+ }
+}
diff --git a/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/util/XmlValidator.java b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/util/XmlValidator.java
new file mode 100755
index 0000000..693f125
--- /dev/null
+++ b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/util/XmlValidator.java
@@ -0,0 +1,143 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.psi_mi.util;
+
+import org.xml.sax.*;
+import org.xml.sax.helpers.DefaultHandler;
+import org.xml.sax.helpers.XMLReaderFactory;
+
+import java.io.IOException;
+import java.io.StringReader;
+
+
+/**
+ * provides XML validation for mi1 documents against schema.
+ *
+ * @author Robert Sheridan modified from Ethan Cerami
+ */
+public class XmlValidator extends DefaultHandler {
+ // Validation feature id
+ protected static final String VALIDATION_FEATURE_ID = "http://xml.org/sax/features/validation";
+
+ // Schema validation feature id.
+ protected static final String SCHEMA_VALIDATION_FEATURE_ID = "http://apache.org/xml/features/validation/schema";
+
+ // Dynamic validation feature id
+ protected static final String DYNAMIC_VALIDATION_FEATURE_ID = "http://apache.org/xml/features/validation/dynamic";
+
+ /**
+ * Warning.
+ *
+ * @param ex SAXParseException Object.
+ * @throws org.xml.sax.SAXException SAXException.
+ */
+ public void warning(SAXParseException ex) throws SAXException {
+ System.out.println(makeErrorMessage("Warning", ex));
+ }
+
+ /**
+ * Error.
+ *
+ * @param ex SAXParseException Object.
+ * @throws org.xml.sax.SAXException SAXException.
+ */
+ public void error(SAXParseException ex) throws SAXException {
+ throw new SAXException(makeErrorMessage("Error", ex));
+ }
+
+ /**
+ * Fatal Error.
+ *
+ * @param ex SAXParseException Object.
+ * @throws org.xml.sax.SAXException SAXException.
+ */
+ public void fatalError(SAXParseException ex) throws SAXException {
+ throw new SAXException(makeErrorMessage("Fatal Error", ex));
+ }
+
+ /**
+ * formats an error message.
+ */
+ protected String makeErrorMessage(String type, SAXParseException ex) {
+ if (ex == null) {
+ return "[" + type + "] " + "!!!";
+ }
+
+ String systemId = ex.getSystemId();
+
+ if (systemId != null) {
+ int index = systemId.lastIndexOf('/');
+
+ if (index != -1) {
+ systemId = systemId.substring(index + 1);
+ }
+ }
+
+ return "[" + type + "] " + ':' + ex.getLineNumber() + ':' + ex.getColumnNumber() + ": "
+ + ex.getMessage();
+ }
+
+ /**
+ * validates the content of an XML document according to a schema.
+ * Errors or fatal errors cause exceptions to be thrown.
+ * Warnings are printed to System.out and then ignored.
+ *
+ * @param content a string containing the XML content to validate.
+ * @throws DataServiceException DataServiceException.
+ */
+ public static void validate(String content) throws DataServiceException {
+ XmlValidator validator = new XmlValidator();
+
+ try {
+ XMLReader parser = XMLReaderFactory.createXMLReader();
+ parser.setFeature(VALIDATION_FEATURE_ID, true);
+ parser.setFeature(SCHEMA_VALIDATION_FEATURE_ID, true);
+ parser.setFeature(DYNAMIC_VALIDATION_FEATURE_ID, true);
+ parser.setContentHandler(validator);
+ parser.setErrorHandler(validator);
+ parser.parse(new InputSource(new StringReader(content)));
+ } catch (SAXNotRecognizedException e) {
+ throw new DataServiceException(e, e.toString());
+ } catch (SAXNotSupportedException e) {
+ throw new DataServiceException(e, e.toString());
+ } catch (SAXParseException e) {
+ throw new DataServiceException(e, e.toString());
+ } catch (SAXException e) {
+ throw new DataServiceException(e, e.toString());
+ } catch (IOException e) {
+ throw new DataServiceException(e, e.toString());
+ }
+ }
+}
diff --git a/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/util/package.html b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/util/package.html
new file mode 100755
index 0000000..c1d321f
--- /dev/null
+++ b/coreplugins/PSI-MI/src/main/java/org/cytoscape/coreplugin/psi_mi/util/package.html
@@ -0,0 +1,8 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+<html>
+<head></head>
+
+<body bgcolor="white">
+Miscellaneous Utility Classes.
+</body>
+</html>
diff --git a/coreplugins/PSI-MI/src/main/resources/org/cytoscape/coreplugin/psi_mi/plugin/plugin.props b/coreplugins/PSI-MI/src/main/resources/org/cytoscape/coreplugin/psi_mi/plugin/plugin.props
new file mode 100644
index 0000000..7850c51
--- /dev/null
+++ b/coreplugins/PSI-MI/src/main/resources/org/cytoscape/coreplugin/psi_mi/plugin/plugin.props
@@ -0,0 +1,30 @@
+# This props file would be filled out and included in the plugin jar file. This props file will be used
+# to put information into the Plugin Manager about the plugin
+
+# -- The following properties are REQUIRED -- #
+
+# The plugin name that will be displayed to users
+pluginName=PSI-MI
+
+# Description used to give users information about the plugin such as what it does.
+# Html tags are encouraged for formatting purposes.
+pluginDescription=Allows importing of PSI-MI 2.5 file format
+
+# Plugin version number, this must be two numbers separated by a decimlal. Ex. 0.2, 14.03
+pluginVersion=0.3
+
+# Compatible Cytoscape version
+cytoscapeVersion=2.5,2.6,2.7,2.8
+
+# Category, use one of the categories listed on the website or create your own
+pluginCategory=Core
+
+
+# List of authors. Note each author and institution pair are separated by a : (colon)
+# each additional author institution pair must be separated from other pairs bye a ; (semicolon)
+pluginAuthorsIntsitutions=Ethan Cerami:Memorial Sloan-Kettering Cancer Center
+
+# -- The following properties should be set ONLY BY CORE PLUGINS -- #
+downloadURL=http://cytoscape.org/plugins/plugins.xml
+uniqueID=13
+
diff --git a/coreplugins/PSI-MI/src/main/resources/xsd/MIF1.xsd b/coreplugins/PSI-MI/src/main/resources/xsd/MIF1.xsd
new file mode 100755
index 0000000..1cce6ce
--- /dev/null
+++ b/coreplugins/PSI-MI/src/main/resources/xsd/MIF1.xsd
@@ -0,0 +1,623 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- edited with XMLSPY v5 rel. 2 U (http://www.xmlspy.com) by Swiss-Prot (EMBL OUTSTATION THE EBI WELLCOME TRUST GENOME CAMPUS) -->
+<xs:schema targetNamespace="net:sf:psidev:mi" xmlns="net:sf:psidev:mi" xmlns:xs="http://www.w3.org/2001/XMLSchema" elementFormDefault="qualified" attributeFormDefault="unqualified">
+ <xs:element name="entrySet">
+ <xs:annotation>
+ <xs:documentation>Root element of the Molecular Interaction Format</xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="entry" maxOccurs="unbounded">
+ <xs:annotation>
+ <xs:documentation>Describes one or more interactions as a self-contained unit. Multiple entries from different files can be concatenated into a single entrySet.</xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="source" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Desciption of the source of the entry, usually an organisation</xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="names" type="namesType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Name(s) of the data source, for example the organisation name.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="bibref" type="bibrefType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Bibliographic reference for the data source. Example: A paper which describes all interactions of the entry.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="xref" type="xrefType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Cross reference for the data source. Example: Entry in a database of databases. </xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="attributeList" type="attributeListType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Further description of the source.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ </xs:sequence>
+ <xs:attribute name="release" type="xs:string" use="optional"/>
+ <xs:attribute name="releaseDate" type="xs:date" use="optional"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="availabilityList" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Data availability statements, for example copyrights</xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="availability" type="availabilityType" default="free" minOccurs="0" maxOccurs="unbounded">
+ <xs:annotation>
+ <xs:documentation>Describes data availability, e.g. through a copyright statement. If no availability is given, the data is assumed to be freely available.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="experimentList" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>All experiments in which the interactions of this entry have been determined</xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="experimentDescription" type="experimentType" minOccurs="0" maxOccurs="unbounded">
+ <xs:annotation>
+ <xs:documentation>Describes one set of experimental parameters, usually associated with a single publication.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="interactorList" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>List of all interactors occurring in the entry</xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:sequence>
+ <xs:annotation>
+ <xs:documentation>Will be extended in future levels to include other interactor types e.g. small molecules.</xs:documentation>
+ </xs:annotation>
+ <xs:element name="proteinInteractor" type="proteinInteractorType" minOccurs="0" maxOccurs="unbounded">
+ <xs:annotation>
+ <xs:documentation>A protein object participating in an interaction.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="interactionList">
+ <xs:annotation>
+ <xs:documentation>List of interactions</xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:sequence>
+ <xs:annotation>
+ <xs:documentation>Will be extended in future levels to include other interaction types e.g. biochemical reactions.</xs:documentation>
+ </xs:annotation>
+ <xs:element name="interaction" type="interactionElementType" maxOccurs="unbounded">
+ <xs:annotation>
+ <xs:documentation>A set of molecules interacting.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="attributeList" type="attributeListType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Semi-structured additional description of the data contained in the entry.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ </xs:sequence>
+ </xs:complexType>
+ <xs:key name="experimentKey">
+ <xs:selector xpath="experimentList/experimentDescription"/>
+ <xs:field xpath="@id"/>
+ </xs:key>
+ <xs:keyref name="experimentRef" refer="experimentKey">
+ <xs:selector xpath="interactionList/interaction/experimentsList/experimentRef"/>
+ <xs:field xpath="@ref"/>
+ </xs:keyref>
+ <xs:key name="interactorKey">
+ <xs:selector xpath="interactorList/proteinInteractor"/>
+ <xs:field xpath="@id"/>
+ </xs:key>
+ <xs:keyref name="interactorRef" refer="interactorKey">
+ <xs:selector xpath="interactionList/interaction/participantList/proteinParticipant/proteinInteractorRef"/>
+ <xs:field xpath="@ref"/>
+ </xs:keyref>
+ <xs:key name="availabilityKey">
+ <xs:selector xpath="availabilityList/availabilityDescription"/>
+ <xs:field xpath="@id"/>
+ </xs:key>
+ <xs:keyref name="availabilityRef" refer="availabilityKey">
+ <xs:selector xpath="availabilityList/availability"/>
+ <xs:field xpath="@ref"/>
+ </xs:keyref>
+ </xs:element>
+ </xs:sequence>
+ <xs:attribute name="level" type="xs:integer" use="required"/>
+ <xs:attribute name="version" type="xs:integer" use="required"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:complexType name="dbReferenceType">
+ <xs:annotation>
+ <xs:documentation>Refers to a unique object in an external database.</xs:documentation>
+ </xs:annotation>
+ <xs:attribute name="db" type="xs:string" use="required"/>
+ <xs:attribute name="id" type="xs:string" use="required"/>
+ <xs:attribute name="secondary" type="xs:string" use="optional"/>
+ <xs:attribute name="version" type="xs:string" use="optional"/>
+ </xs:complexType>
+ <xs:complexType name="labelType">
+ <xs:annotation>
+ <xs:documentation>A short alphanumeric label identifying an object. Not necessarily unique.</xs:documentation>
+ </xs:annotation>
+ <xs:simpleContent>
+ <xs:extension base="xs:string"/>
+ </xs:simpleContent>
+ </xs:complexType>
+ <xs:complexType name="fullNameType">
+ <xs:annotation>
+ <xs:documentation>Full, descriptive object name.</xs:documentation>
+ </xs:annotation>
+ <xs:simpleContent>
+ <xs:extension base="xs:string"/>
+ </xs:simpleContent>
+ </xs:complexType>
+ <xs:complexType name="bioSourceType">
+ <xs:annotation>
+ <xs:documentation>Describes the biological source of an object, in simple form only the NCBI taxid.</xs:documentation>
+ </xs:annotation>
+ <xs:sequence>
+ <xs:element name="names" type="namesType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>The names of the organism. The short label should be a common name if it exists. The full name should be the full name of the species (i.e. genus species).</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="cellType" type="openCvType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Description of the cell type. Currently no species-independent controlled vocabulary for cell types is available, therefore the choice of reference database(s) is open to the data provider.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="compartment" type="openCvType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>The subcellular compartement of the object. It is strongly recommended to refer to the Gene Ontology cellular component in this element.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="tissue" type="openCvType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Description of the source tissue. Currently no species-independent controlled vocabulary for tissues is available, therefore the choice of reference database(s) is open to the data provider.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ </xs:sequence>
+ </xs:complexType>
+ <xs:complexType name="featureType">
+ <xs:annotation>
+ <xs:documentation>A feature, e.g. domain, on a sequence.</xs:documentation>
+ </xs:annotation>
+ <xs:sequence>
+ <xs:element name="xref" type="xrefType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Reference to an external feature description, for example InterPro entry.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="featureDescription" type="cvType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Description and classification of the feature</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="location" type="baseLocationType">
+ <xs:annotation>
+ <xs:documentation>Location of the feature on the sequence of the interactor</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="featureDetection" type="cvType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Experimental method used to identify the feature.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ </xs:sequence>
+ </xs:complexType>
+ <xs:complexType name="xrefType">
+ <xs:annotation>
+ <xs:documentation>Crossreference to an external database.</xs:documentation>
+ </xs:annotation>
+ <xs:sequence>
+ <xs:element name="primaryRef" type="dbReferenceType">
+ <xs:annotation>
+ <xs:documentation>Primary reference to an external database.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="secondaryRef" type="dbReferenceType" minOccurs="0" maxOccurs="unbounded">
+ <xs:annotation>
+ <xs:documentation>Further external objects describing the object.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ </xs:sequence>
+ </xs:complexType>
+ <!-- Feature location definition begins -->
+ <xs:complexType name="positionType">
+ <xs:annotation>
+ <xs:documentation>A specified position a a sequence.</xs:documentation>
+ </xs:annotation>
+ <xs:attribute name="position" type="xs:long" use="required"/>
+ </xs:complexType>
+ <xs:complexType name="intervalType">
+ <xs:annotation>
+ <xs:documentation>A interval on a sequence.</xs:documentation>
+ </xs:annotation>
+ <xs:attribute name="begin" type="xs:long" use="required"/>
+ <xs:attribute name="end" type="xs:long" use="required"/>
+ </xs:complexType>
+ <xs:complexType name="baseLocationType">
+ <xs:annotation>
+ <xs:documentation>A location can be either a position, site or have a start and end, only start, only end or is an empty element if the position is unknown.</xs:documentation>
+ </xs:annotation>
+ <xs:choice>
+ <xs:sequence>
+ <xs:choice minOccurs="0">
+ <xs:element name="begin" type="positionType"/>
+ <xs:element name="beginInterval" type="intervalType"/>
+ </xs:choice>
+ <xs:choice minOccurs="0">
+ <xs:element name="end" type="positionType"/>
+ <xs:element name="endInterval" type="intervalType"/>
+ </xs:choice>
+ </xs:sequence>
+ <xs:element name="position" type="positionType"/>
+ <xs:element name="positionInterval" type="intervalType"/>
+ <xs:element name="site" type="positionType"/>
+ </xs:choice>
+ </xs:complexType>
+ <!-- Feature location definition ends -->
+ <xs:complexType name="experimentType">
+ <xs:annotation>
+ <xs:documentation>Describes one set of experimental parameters.</xs:documentation>
+ </xs:annotation>
+ <xs:sequence>
+ <xs:element name="names" type="namesType" minOccurs="0"/>
+ <xs:element name="bibref" type="bibrefType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Publication describing the experiment.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="xref" type="xrefType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Refers to external database description of the experiment.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="hostOrganism" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>The host organism in which the experiment has been performed.</xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:complexContent>
+ <xs:extension base="bioSourceType">
+ <xs:attribute name="ncbiTaxId" type="xs:integer" use="required"/>
+ </xs:extension>
+ </xs:complexContent>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="interactionDetection" type="cvType">
+ <xs:annotation>
+ <xs:documentation>Experimental method to determine the interaction. External controlled vocabulary.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="participantDetection" type="cvType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Experimental method to determine the interactors involved in the interaction. External controlled vocabulary.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="featureDetection" type="cvType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Experimental method to determine the features of interactors. External controlled vocabulary.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="confidence" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Confidence in this experiment. Usually a statistical measure.</xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:attribute name="unit" type="xs:string" use="required"/>
+ <xs:attribute name="value" type="xs:string" use="required"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="attributeList" type="attributeListType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Semi-structured additional description of the experiment.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:ID" use="required"/>
+ </xs:complexType>
+ <xs:complexType name="refType">
+ <xs:annotation>
+ <xs:documentation>Refers to an object within the same file by its id.</xs:documentation>
+ </xs:annotation>
+ <xs:attribute name="ref" type="xs:string" use="required"/>
+ </xs:complexType>
+ <xs:complexType name="attributeListType">
+ <xs:annotation>
+ <xs:documentation>A list of additional attributes. Open tag-value list to allow the inclusion of additional data.</xs:documentation>
+ </xs:annotation>
+ <xs:sequence>
+ <xs:element name="attribute" maxOccurs="unbounded">
+ <xs:complexType>
+ <xs:simpleContent>
+ <xs:extension base="xs:string">
+ <xs:attribute name="name" type="xs:string" use="required"/>
+ </xs:extension>
+ </xs:simpleContent>
+ </xs:complexType>
+ </xs:element>
+ </xs:sequence>
+ </xs:complexType>
+ <xs:complexType name="bibrefType">
+ <xs:annotation>
+ <xs:documentation>Bibliographic reference.</xs:documentation>
+ </xs:annotation>
+ <xs:choice>
+ <xs:element name="xref" type="xrefType">
+ <xs:annotation>
+ <xs:documentation>Bibliographic reference in external database, usually PubMed.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="attributeList" type="attributeListType">
+ <xs:annotation>
+ <xs:documentation>Alternative description of bibliographic reference if no external database entry is available.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ </xs:choice>
+ </xs:complexType>
+ <xs:complexType name="namesType">
+ <xs:annotation>
+ <xs:documentation>Names for an object.</xs:documentation>
+ </xs:annotation>
+ <xs:sequence>
+ <xs:element name="shortLabel" type="xs:string"/>
+ <xs:element name="fullName" type="xs:string" minOccurs="0"/>
+ </xs:sequence>
+ </xs:complexType>
+ <xs:complexType name="cvType">
+ <xs:annotation>
+ <xs:documentation>Reference to an external controlled vocabulary.</xs:documentation>
+ </xs:annotation>
+ <xs:sequence>
+ <xs:element name="names" type="namesType">
+ <xs:annotation>
+ <xs:documentation>Name of the controlled vocabulary term.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="xref" type="xrefType">
+ <xs:annotation>
+ <xs:documentation>Source of the controlled vocabulary term. E.g. the name of the CV and the term ID.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ </xs:sequence>
+ </xs:complexType>
+ <xs:complexType name="openCvType">
+ <xs:annotation>
+ <xs:documentation>Allows to reference an external controlled vocabulary, or to directly include a value if no suitable external definition is available.</xs:documentation>
+ </xs:annotation>
+ <xs:sequence>
+ <xs:element name="names" type="namesType">
+ <xs:annotation>
+ <xs:documentation>This contains the controlled vocabulary terms, as a short and optionally as a long form.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="xref" type="xrefType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Refers to the term of the controlled vocabulary in an external database.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="attributeList" type="attributeListType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>If no suitable external controlled vocabulary is available, this attributeList can be used to describe the term. Example: Attribute name: Mouse atlas tissue name; attribute value: spinal cord, day 30.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ </xs:sequence>
+ </xs:complexType>
+ <xs:complexType name="proteinInteractorType">
+ <xs:annotation>
+ <xs:documentation>Describes a protein interactor.</xs:documentation>
+ </xs:annotation>
+ <xs:sequence>
+ <xs:element name="names" type="namesType">
+ <xs:annotation>
+ <xs:documentation>Protein name(s). The short label is typically a short name that could appear as a label on a diagram.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="xref" type="xrefType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>An interactor should have an xref whenever possible. If the interactor is not available in external databases, it must be characterised within this proteinInteractor object e.g. by its sequence.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="organism" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>The normal source organism of the interactor. If a human protein has been expressed in yeast, this attribute would describe human.</xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:complexContent>
+ <xs:extension base="bioSourceType">
+ <xs:attribute name="ncbiTaxId" type="xs:integer" use="required"/>
+ </xs:extension>
+ </xs:complexContent>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="sequence" type="xs:string" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Amino acid sequence in uppercase</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:ID" use="required"/>
+ </xs:complexType>
+ <xs:complexType name="availabilityType">
+ <xs:annotation>
+ <xs:documentation>A text describing the availability of data, e.g. a copyright statement.</xs:documentation>
+ </xs:annotation>
+ <xs:simpleContent>
+ <xs:extension base="xs:string">
+ <xs:attribute name="id" type="xs:ID" use="required"/>
+ </xs:extension>
+ </xs:simpleContent>
+ </xs:complexType>
+ <xs:complexType name="interactionElementType">
+ <xs:annotation>
+ <xs:documentation>A molecular interaction.</xs:documentation>
+ </xs:annotation>
+ <xs:sequence>
+ <xs:element name="names" type="namesType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Name(s) of the interaction.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:choice minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Either refer to an already defined availability statement in this entry or insert description.</xs:documentation>
+ </xs:annotation>
+ <xs:element name="availabilityRef" type="refType">
+ <xs:annotation>
+ <xs:documentation>References an availability statement already present in this entry.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="availabilityDescription" type="availabilityType">
+ <xs:annotation>
+ <xs:documentation>Describes the availability of the interaction data. If no availability is given, the data is assumed to be freely available.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ </xs:choice>
+ <xs:element name="experimentList">
+ <xs:annotation>
+ <xs:documentation>List of experiments in which this interaction has been determined.</xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:choice maxOccurs="unbounded">
+ <xs:annotation>
+ <xs:documentation>Either refer to an already defined experiment in this entry or insert description.</xs:documentation>
+ </xs:annotation>
+ <xs:element name="experimentRef" type="refType">
+ <xs:annotation>
+ <xs:documentation>References an experiment already present in this entry.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="experimentDescription" type="experimentType">
+ <xs:annotation>
+ <xs:documentation>An experiment in which this interaction has been determined.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ </xs:choice>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="participantList">
+ <xs:annotation>
+ <xs:documentation>A list of molecules participating in this interaction.</xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:sequence>
+ <xs:annotation>
+ <xs:documentation>Will be extended in future levels to include other types of participant molecules.</xs:documentation>
+ </xs:annotation>
+ <xs:element name="proteinParticipant" type="proteinParticipantType" minOccurs="2" maxOccurs="unbounded">
+ <xs:annotation>
+ <xs:documentation>An interaction has two or more participants, thereby covering binary and n-ary interactions.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="interactionType" type="cvType" minOccurs="0" maxOccurs="unbounded">
+ <xs:annotation>
+ <xs:documentation>External controlled vocabulary characterising the interaction type, for example "aggregation".</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="confidence" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Confidence in this interaction. Usually a statistical measure.</xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:attribute name="unit" type="xs:string" use="required"/>
+ <xs:attribute name="value" type="xs:string" use="required"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="xref" type="xrefType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Interaction database ID</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="attributeList" type="attributeListType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Semi-structured additional description of the data contained in the entry.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ </xs:sequence>
+ </xs:complexType>
+ <xs:complexType name="proteinParticipantType">
+ <xs:annotation>
+ <xs:documentation>A protein participating in an interaction.</xs:documentation>
+ </xs:annotation>
+ <xs:sequence>
+ <xs:choice>
+ <xs:annotation>
+ <xs:documentation>Either refer to an already defined protein interactor in this entry or insert description.</xs:documentation>
+ </xs:annotation>
+ <xs:element name="proteinInteractorRef" type="refType">
+ <xs:annotation>
+ <xs:documentation>References an interactor described in the interactorList of the entry</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="proteinInteractor" type="proteinInteractorType">
+ <xs:annotation>
+ <xs:documentation>Fully describes an interactor</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ </xs:choice>
+ <xs:element name="featureList" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Sequence features relevant for the interaction, for example binding domains</xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="feature" type="featureType" maxOccurs="unbounded"/>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="confidence" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Confidence in participant detection.</xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:attribute name="unit" type="xs:string" use="required"/>
+ <xs:attribute name="value" type="xs:string" use="required"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="role" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>The role of the participant in the interaction, e.g. "bait". Choose an enumerated value.</xs:documentation>
+ </xs:annotation>
+ <xs:simpleType>
+ <xs:restriction base="xs:string">
+ <xs:enumeration value="bait"/>
+ <xs:enumeration value="prey"/>
+ <xs:enumeration value="neutral"/>
+ <xs:enumeration value="unspecified"/>
+ </xs:restriction>
+ </xs:simpleType>
+ </xs:element>
+ <xs:element name="isTaggedProtein" type="xs:boolean" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>True if the protein has been tagged in the experiment.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="isOverexpressedProtein" type="xs:boolean" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>True if the protein has been overexpressed in the experiment.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ </xs:sequence>
+ </xs:complexType>
+</xs:schema>
diff --git a/coreplugins/PSI-MI/src/main/resources/xsd/MIF25.xsd b/coreplugins/PSI-MI/src/main/resources/xsd/MIF25.xsd
new file mode 100755
index 0000000..04c13b1
--- /dev/null
+++ b/coreplugins/PSI-MI/src/main/resources/xsd/MIF25.xsd
@@ -0,0 +1,1155 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- edited with XMLSpy v2006 sp2 U (http://www.altova.com) by EBI Proteomics Services (EMBL Outstation) -->
+<!-- edited with XMLSPY v2004 rel. 3 U (http://www.xmlspy.com) by HENNING HERMJAKOB (EMBL OUTSTATION THE EBI) -->
+<xs:schema xmlns="net:sf:psidev:mi" xmlns:xs="http://www.w3.org/2001/XMLSchema" targetNamespace="net:sf:psidev:mi" elementFormDefault="qualified" attributeFormDefault="unqualified">
+ <!--Root element-->
+ <xs:element name="entrySet">
+ <xs:annotation>
+ <xs:documentation>Root element of the Molecular Interaction Format</xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="entry" maxOccurs="unbounded">
+ <xs:annotation>
+ <xs:documentation>Describes one or more interactions as a self-contained unit. Multiple entries from different files can be concatenated into a single entrySet.</xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="source" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Desciption of the source of the entry, usually an organisation</xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="names" type="namesType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Name(s) of the data source, for example the organisation name.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="bibref" type="bibrefType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Bibliographic reference for the data source. Example: A paper which describes all interactions of the entry.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="xref" type="xrefType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Cross reference for the data source. Example: Entry in a database of databases. </xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="attributeList" type="attributeListType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Further description of the source.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ </xs:sequence>
+ <xs:attribute name="release" use="optional">
+ <xs:simpleType>
+ <xs:restriction base="xs:string">
+ <xs:minLength value="1"/>
+ </xs:restriction>
+ </xs:simpleType>
+ </xs:attribute>
+ <xs:attribute name="releaseDate" type="xs:date" use="optional"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="availabilityList" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Data availability statements, for example copyrights</xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="availability" type="availabilityType" minOccurs="0" maxOccurs="unbounded">
+ <xs:annotation>
+ <xs:documentation>Describes data availability, e.g. through a copyright statement. If no availability is given, the data is assumed to be freely available.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="experimentList" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>All experiments in which the interactions of this entry have been determined</xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="experimentDescription" type="experimentType" minOccurs="0" maxOccurs="unbounded">
+ <xs:annotation>
+ <xs:documentation>Describes one set of experimental parameters, usually associated with a single publication.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="interactorList" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>List of all interactors occurring in the entry</xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="interactor" type="interactorElementType" minOccurs="0" maxOccurs="unbounded">
+ <xs:annotation>
+ <xs:documentation>A molecule object in its native state, as described in databases.</xs:documentation>
+ <xs:documentation>Usage: A protein interactor must contain an xref to UniProt and NCBI-GI where possible. </xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="interactionList">
+ <xs:annotation>
+ <xs:documentation>List of interactions</xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="interaction" maxOccurs="unbounded">
+ <xs:annotation>
+ <xs:documentation>A set of molecules interacting. </xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:complexContent>
+ <xs:extension base="interactionElementType"/>
+ </xs:complexContent>
+ </xs:complexType>
+ </xs:element>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="attributeList" type="attributeListType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Semi-structured additional description of the data contained in the entry.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ </xs:sequence>
+ <xs:attribute name="level" type="xs:int" use="required" fixed="2">
+ <xs:annotation>
+ <xs:documentation>PSI MI level</xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="version" type="xs:int" use="required" fixed="5">
+ <xs:annotation>
+ <xs:documentation>PSI MI version within given level</xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="minorVersion" type="xs:int" use="optional" fixed="3"/>
+ </xs:complexType>
+ </xs:element>
+ <!--aministrative elements-->
+ <xs:complexType name="labelType">
+ <xs:annotation>
+ <xs:documentation>A short alphanumeric label identifying an object. Not necessarily unique.</xs:documentation>
+ </xs:annotation>
+ <xs:simpleContent>
+ <xs:extension base="xs:string"/>
+ </xs:simpleContent>
+ </xs:complexType>
+ <xs:complexType name="fullNameType">
+ <xs:annotation>
+ <xs:documentation>Full, descriptive object name.</xs:documentation>
+ </xs:annotation>
+ <xs:simpleContent>
+ <xs:extension base="xs:string"/>
+ </xs:simpleContent>
+ </xs:complexType>
+ <xs:complexType name="experimentRefListType">
+ <xs:annotation>
+ <xs:documentation>Refers to a list of experiments within the same entry.</xs:documentation>
+ </xs:annotation>
+ <xs:sequence>
+ <xs:element name="experimentRef" type="xs:int" maxOccurs="unbounded">
+ <xs:annotation>
+ <xs:documentation>References an experiment already present in this entry.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ </xs:sequence>
+ </xs:complexType>
+ <xs:complexType name="xrefType">
+ <xs:annotation>
+ <xs:documentation>Crossreference to an external database. Crossreferences to literature databases, e.g. PubMed, should not be put into this structure, but into the bibRef element where possible.</xs:documentation>
+ </xs:annotation>
+ <xs:sequence>
+ <xs:element name="primaryRef" type="dbReferenceType">
+ <xs:annotation>
+ <xs:documentation>Primary reference to an external database.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="secondaryRef" type="dbReferenceType" minOccurs="0" maxOccurs="unbounded">
+ <xs:annotation>
+ <xs:documentation>Further external objects describing the object.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ </xs:sequence>
+ </xs:complexType>
+ <xs:complexType name="dbReferenceType">
+ <xs:annotation>
+ <xs:documentation>Refers to a unique object in an external database.</xs:documentation>
+ </xs:annotation>
+ <xs:sequence minOccurs="0">
+ <xs:element name="attributeList" type="attributeListType"/>
+ </xs:sequence>
+ <xs:attribute name="db" use="required">
+ <xs:annotation>
+ <xs:documentation>Name of the external database. Taken from the controlled vocabulary of databases.</xs:documentation>
+ </xs:annotation>
+ <xs:simpleType>
+ <xs:restriction base="xs:string">
+ <xs:minLength value="1"/>
+ </xs:restriction>
+ </xs:simpleType>
+ </xs:attribute>
+ <xs:attribute name="dbAc" use="optional">
+ <xs:annotation>
+ <xs:documentation>Accession number of the database in the database CV. This element is controlled by the PSI-MI controlled vocabulary "database citation", root term id MI:0444.</xs:documentation>
+ </xs:annotation>
+ <xs:simpleType>
+ <xs:restriction base="xs:string">
+ <xs:minLength value="1"/>
+ </xs:restriction>
+ </xs:simpleType>
+ </xs:attribute>
+ <xs:attribute name="id" use="required">
+ <xs:annotation>
+ <xs:documentation>Primary identifier of the object in the external database, e.g. UniProt accession number.</xs:documentation>
+ </xs:annotation>
+ <xs:simpleType>
+ <xs:restriction base="xs:string">
+ <xs:minLength value="1"/>
+ </xs:restriction>
+ </xs:simpleType>
+ </xs:attribute>
+ <xs:attribute name="secondary" use="optional">
+ <xs:annotation>
+ <xs:documentation>Secondary identifier of the object in the external database, e.g. UniProt ID.</xs:documentation>
+ </xs:annotation>
+ <xs:simpleType>
+ <xs:restriction base="xs:string">
+ <xs:minLength value="1"/>
+ </xs:restriction>
+ </xs:simpleType>
+ </xs:attribute>
+ <xs:attribute name="version" use="optional">
+ <xs:annotation>
+ <xs:documentation>The version number of the object in the external database.</xs:documentation>
+ </xs:annotation>
+ <xs:simpleType>
+ <xs:restriction base="xs:string">
+ <xs:minLength value="1"/>
+ </xs:restriction>
+ </xs:simpleType>
+ </xs:attribute>
+ <xs:attribute name="refType" use="optional">
+ <xs:annotation>
+ <xs:documentation>Reference type, e.g. "identity" if this reference referes to an identical object in the external database, or "see-also" for additional information. Controlled by CV.</xs:documentation>
+ </xs:annotation>
+ <xs:simpleType>
+ <xs:restriction base="xs:string">
+ <xs:minLength value="1"/>
+ </xs:restriction>
+ </xs:simpleType>
+ </xs:attribute>
+ <xs:attribute name="refTypeAc" use="optional">
+ <xs:annotation>
+ <xs:documentation>Reference type accession number from the CV of reference types. This element is controlled by the PSI-MI controlled vocabulary "xref type", root term id MI:0353. </xs:documentation>
+ </xs:annotation>
+ <xs:simpleType>
+ <xs:restriction base="xs:string">
+ <xs:minLength value="1"/>
+ </xs:restriction>
+ </xs:simpleType>
+ </xs:attribute>
+ </xs:complexType>
+ <xs:complexType name="bibrefType">
+ <xs:annotation>
+ <xs:documentation>Bibliographic reference.</xs:documentation>
+ </xs:annotation>
+ <xs:choice>
+ <xs:element name="xref" type="xrefType">
+ <xs:annotation>
+ <xs:documentation>Bibliographic reference in external database, usually PubMed.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="attributeList" type="attributeListType">
+ <xs:annotation>
+ <xs:documentation>Alternative description of bibliographic reference if no external database entry is available.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ </xs:choice>
+ </xs:complexType>
+ <xs:complexType name="attributeListType">
+ <xs:annotation>
+ <xs:documentation>A list of additional attributes. Open tag-value list to allow the inclusion of additional data.</xs:documentation>
+ </xs:annotation>
+ <xs:sequence>
+ <xs:element name="attribute" maxOccurs="unbounded">
+ <xs:complexType>
+ <xs:simpleContent>
+ <xs:extension base="xs:string">
+ <xs:attribute name="name" use="required">
+ <xs:annotation>
+ <xs:documentation>The name of the attribute.</xs:documentation>
+ </xs:annotation>
+ <xs:simpleType>
+ <xs:restriction base="xs:string">
+ <xs:minLength value="1"/>
+ </xs:restriction>
+ </xs:simpleType>
+ </xs:attribute>
+ <xs:attribute name="nameAc" use="optional">
+ <xs:annotation>
+ <xs:documentation>Enables control of the attribute type through reference to an external controlled vocabulary. Root element in the PSI MI CV is MI:0590.</xs:documentation>
+ </xs:annotation>
+ <xs:simpleType>
+ <xs:restriction base="xs:string">
+ <xs:minLength value="1"/>
+ </xs:restriction>
+ </xs:simpleType>
+ </xs:attribute>
+ </xs:extension>
+ </xs:simpleContent>
+ </xs:complexType>
+ </xs:element>
+ </xs:sequence>
+ </xs:complexType>
+ <xs:complexType name="confidenceType">
+ <xs:annotation>
+ <xs:documentation>A confidence value.</xs:documentation>
+ </xs:annotation>
+ <xs:sequence>
+ <xs:element name="unit" type="openCvType"/>
+ <xs:element name="value">
+ <xs:simpleType>
+ <xs:restriction base="xs:string">
+ <xs:minLength value="1"/>
+ </xs:restriction>
+ </xs:simpleType>
+ </xs:element>
+ </xs:sequence>
+ </xs:complexType>
+ <xs:complexType name="bioSourceType">
+ <xs:annotation>
+ <xs:documentation>Describes the biological source of an object, in simple form only the NCBI taxid.</xs:documentation>
+ </xs:annotation>
+ <xs:sequence>
+ <xs:element name="names" type="namesType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>The names of the organism. The short label should be a common name if it exists. The full name should be the full name of the species (i.e. genus species).</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="cellType" type="openCvType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Description of the cell type. Currently no species-independent controlled vocabulary for cell types is available, therefore the choice of reference database(s) is open to the data provider.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="compartment" type="openCvType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>The subcellular compartment of the object. It is strongly recommended to refer to the Gene Ontology cellular component in this element.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="tissue" type="openCvType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Description of the source tissue. Currently no species-independent controlled vocabulary for tissues is available, therefore the choice of reference database(s) is open to the data provider.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ </xs:sequence>
+ <xs:attribute name="ncbiTaxId" type="xs:int" use="required"/>
+ </xs:complexType>
+ <xs:complexType name="confidenceListType">
+ <xs:annotation>
+ <xs:documentation>A list of confidence values.</xs:documentation>
+ </xs:annotation>
+ <xs:sequence>
+ <xs:element name="confidence" maxOccurs="unbounded">
+ <xs:complexType>
+ <xs:complexContent>
+ <xs:extension base="confidenceType">
+ <xs:sequence minOccurs="0">
+ <xs:element name="experimentRefList" type="experimentRefListType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Each experiment might assign a different confidence to this object. If no experimentRef is given, it is assumed this confidence refers to all experiments linked to the object.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ </xs:sequence>
+ </xs:extension>
+ </xs:complexContent>
+ </xs:complexType>
+ </xs:element>
+ </xs:sequence>
+ </xs:complexType>
+ <xs:complexType name="cvType">
+ <xs:annotation>
+ <xs:documentation>Reference to an external controlled vocabulary.</xs:documentation>
+ </xs:annotation>
+ <xs:sequence>
+ <xs:element name="names" type="namesType">
+ <xs:annotation>
+ <xs:documentation>Name of the controlled vocabulary term.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="xref" type="xrefType">
+ <xs:annotation>
+ <xs:documentation>Source of the controlled vocabulary term. E.g. the name of the CV and the term ID.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ </xs:sequence>
+ </xs:complexType>
+ <xs:complexType name="openCvType">
+ <xs:annotation>
+ <xs:documentation>Allows to reference an external controlled vocabulary, or to directly include a value if no suitable external definition is available.</xs:documentation>
+ </xs:annotation>
+ <xs:sequence>
+ <xs:element name="names" type="namesType">
+ <xs:annotation>
+ <xs:documentation>This contains the controlled vocabulary terms, as a short and optionally as a long form.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="xref" type="xrefType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Refers to the term of the controlled vocabulary in an external database.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="attributeList" type="attributeListType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>If no suitable external controlled vocabulary is available, this attributeList can be used to describe the term. Example: Attribute name: Mouse atlas tissue name; attribute value: spinal cord, day 30.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ </xs:sequence>
+ </xs:complexType>
+ <xs:complexType name="namesType">
+ <xs:annotation>
+ <xs:documentation>Names for an object.</xs:documentation>
+ </xs:annotation>
+ <xs:sequence>
+ <xs:element name="shortLabel" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>A short string, suitable to remember the object. Can be e.g. a gene name, the first author of a paper, etc.</xs:documentation>
+ </xs:annotation>
+ <xs:simpleType>
+ <xs:restriction base="xs:string">
+ <xs:minLength value="1"/>
+ </xs:restriction>
+ </xs:simpleType>
+ </xs:element>
+ <xs:element name="fullName" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>A full, detailed name or description of the object. Can be e.g. the full title of a publication, or the scientific name of a species.</xs:documentation>
+ </xs:annotation>
+ <xs:simpleType>
+ <xs:restriction base="xs:string">
+ <xs:minLength value="1"/>
+ </xs:restriction>
+ </xs:simpleType>
+ </xs:element>
+ <xs:element name="alias" minOccurs="0" maxOccurs="unbounded">
+ <xs:complexType>
+ <xs:simpleContent>
+ <xs:extension base="xs:string">
+ <xs:attribute name="typeAc" use="optional">
+ <xs:simpleType>
+ <xs:restriction base="xs:string">
+ <xs:minLength value="1"/>
+ </xs:restriction>
+ </xs:simpleType>
+ </xs:attribute>
+ <xs:attribute name="type" use="optional">
+ <xs:simpleType>
+ <xs:restriction base="xs:string">
+ <xs:minLength value="1"/>
+ </xs:restriction>
+ </xs:simpleType>
+ </xs:attribute>
+ </xs:extension>
+ </xs:simpleContent>
+ </xs:complexType>
+ </xs:element>
+ </xs:sequence>
+ </xs:complexType>
+ <xs:complexType name="parameterType">
+ <xs:annotation>
+ <xs:documentation>A numeric parameter, e.g. for a kinetic value</xs:documentation>
+ </xs:annotation>
+ <xs:attribute name="term" use="required">
+ <xs:annotation>
+ <xs:documentation>The kind of parameter, e.g. "dissociation constant".</xs:documentation>
+ </xs:annotation>
+ <xs:simpleType>
+ <xs:restriction base="xs:string">
+ <xs:minLength value="1"/>
+ </xs:restriction>
+ </xs:simpleType>
+ </xs:attribute>
+ <xs:attribute name="termAc" use="optional">
+ <xs:annotation>
+ <xs:documentation>Accession number of the term in the associated controlled vocabulary.</xs:documentation>
+ </xs:annotation>
+ <xs:simpleType>
+ <xs:restriction base="xs:string">
+ <xs:minLength value="1"/>
+ </xs:restriction>
+ </xs:simpleType>
+ </xs:attribute>
+ <xs:attribute name="unit" use="optional">
+ <xs:annotation>
+ <xs:documentation>The unit of the term, e.g. "kiloDalton".</xs:documentation>
+ </xs:annotation>
+ <xs:simpleType>
+ <xs:restriction base="xs:string">
+ <xs:minLength value="1"/>
+ </xs:restriction>
+ </xs:simpleType>
+ </xs:attribute>
+ <xs:attribute name="unitAc" use="optional">
+ <xs:annotation>
+ <xs:documentation>Accession number of the unit in the associated controlled vocabulary.</xs:documentation>
+ </xs:annotation>
+ <xs:simpleType>
+ <xs:restriction base="xs:string">
+ <xs:minLength value="1"/>
+ </xs:restriction>
+ </xs:simpleType>
+ </xs:attribute>
+ <xs:attribute name="base" type="xs:short" use="optional" default="10">
+ <xs:annotation>
+ <xs:documentation>Base of the parameter expression. Defaults to 10.</xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="exponent" type="xs:short" use="optional" default="0">
+ <xs:annotation>
+ <xs:documentation>Exponent of the value.</xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="factor" type="xs:decimal" use="required">
+ <xs:annotation>
+ <xs:documentation>The "main" value of the parameter.</xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ </xs:complexType>
+ <!--Feature description-->
+ <xs:complexType name="featureElementType">
+ <xs:annotation>
+ <xs:documentation>A feature, e.g. domain, on a sequence.</xs:documentation>
+ </xs:annotation>
+ <xs:sequence>
+ <xs:element name="names" type="namesType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Names for the feature, e.g. SH3 domain.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="xref" type="xrefType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Reference to an external feature description, for example InterPro entry.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="featureType" type="cvType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Description and classification of the feature. This element is controlled by the PSI-MI controlled vocabulary "featureType", root term id MI:0116.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="featureDetectionMethod" type="cvType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Experimental method used to identify the feature. A setting here overrides the global setting given in the experimentDescription. External controlled vocabulary. </xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="experimentRefList" type="experimentRefListType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>If no experimentRef is given, it is assumed this refers to all experiments linked to the interaction.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="featureRangeList">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="featureRange" type="baseLocationType" maxOccurs="unbounded">
+ <xs:annotation>
+ <xs:documentation>Location of the feature on the sequence of the interactor. One feature may have more than one featureRange, used e.g. for features which involve sequence positions close in the folded, three-dimensional state of a protein, but non-continuous along the sequence.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="attributeList" type="attributeListType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Semi-structured additional description of the data contained in the entry.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int" use="required"/>
+ </xs:complexType>
+ <xs:complexType name="intervalType">
+ <xs:annotation>
+ <xs:documentation>A interval on a sequence.</xs:documentation>
+ </xs:annotation>
+ <xs:attribute name="begin" type="xs:long" use="required"/>
+ <xs:attribute name="end" type="xs:long" use="required"/>
+ </xs:complexType>
+ <xs:complexType name="baseLocationType">
+ <xs:annotation>
+ <xs:documentation>A location on a sequence. Both begin and end can be a defined position, a fuzzy position, or undetermined.</xs:documentation>
+ </xs:annotation>
+ <xs:sequence>
+ <xs:sequence>
+ <xs:element name="startStatus" type="cvType">
+ <xs:annotation>
+ <xs:documentation>Attribute of the start positions, e.g. "certain" or "n-terminal"</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:choice minOccurs="0">
+ <xs:element name="begin" type="positionType">
+ <xs:annotation>
+ <xs:documentation>The integer position gives the begin position of the feature. The first base or amino acid is position 1. In combination with the numeric value, the attribute 'status' allows to express fuzzy positions, e.g. 'less than 4'.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="beginInterval" type="intervalType">
+ <xs:annotation>
+ <xs:documentation>The begin position may be varying or unclear, but localisable to a certain range. Usually written as e.g. 3..5.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ </xs:choice>
+ </xs:sequence>
+ <xs:sequence>
+ <xs:element name="endStatus" type="cvType">
+ <xs:annotation>
+ <xs:documentation>Attribute of the end positions, e.g. "certain" or "c-terminal"</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:choice minOccurs="0">
+ <xs:element name="end" type="positionType">
+ <xs:annotation>
+ <xs:documentation>The integer position gives the end position of the feature. The first base or amino acid is position 1. In combination with the numeric value, the attribute 'status' allows to express fuzzy positions, e.g. 'more than 400'.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="endInterval" type="intervalType">
+ <xs:annotation>
+ <xs:documentation>The end position may be varying or unclear, but localisable to a certain range. Usually written as e.g. 3..5.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ </xs:choice>
+ </xs:sequence>
+ <xs:element name="isLink" type="xs:boolean" default="false" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>True if the described feature is a linking feature connecting two amino acids rather than extending along the sequence. 'begin' references the first amino acid, 'end' the second. Standard example is a disulfide bridge. Does not reference another feature, therefore is only suitable for linking features on the same amino acid chain. </xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ </xs:sequence>
+ </xs:complexType>
+ <xs:complexType name="positionType">
+ <xs:attribute name="position" type="xs:long" use="required"/>
+ </xs:complexType>
+ <!--Top level types-->
+ <xs:complexType name="availabilityType">
+ <xs:annotation>
+ <xs:documentation>A text describing the availability of data, e.g. a copyright statement.</xs:documentation>
+ </xs:annotation>
+ <xs:simpleContent>
+ <xs:extension base="xs:string">
+ <xs:attribute name="id" type="xs:int" use="required"/>
+ </xs:extension>
+ </xs:simpleContent>
+ </xs:complexType>
+ <xs:complexType name="experimentType">
+ <xs:annotation>
+ <xs:documentation>Describes one set of experimental parameters.</xs:documentation>
+ </xs:annotation>
+ <xs:sequence>
+ <xs:element name="names" type="namesType" minOccurs="0"/>
+ <xs:element name="bibref" type="bibrefType">
+ <xs:annotation>
+ <xs:documentation>Publication describing the experiment.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="xref" type="xrefType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Refers to external database description of the experiment.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="hostOrganismList" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>The host organism(s) in which the experiment has been performed.</xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="hostOrganism" maxOccurs="unbounded">
+ <xs:complexType>
+ <xs:complexContent>
+ <xs:extension base="bioSourceType"/>
+ </xs:complexContent>
+ </xs:complexType>
+ </xs:element>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="interactionDetectionMethod" type="cvType">
+ <xs:annotation>
+ <xs:documentation>Experimental method to determine the interaction. This element is controlled by the PSI-MI controlled vocabulary "interaction detection method", root term id MI:0001.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="participantIdentificationMethod" type="cvType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Experimental method to determine the interactors involved in the interaction. This element is controlled by the PSI-MI controlled vocabulary "participant identification method", root term id MI:0002.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="featureDetectionMethod" type="cvType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Experimental method to determine the features of interactors. If this element is filled it is assumed to apply to all features described in the experiment. But can be overridden by the featureDetectionMethod given in the individual feature. This element is controlled by the PSI-MI controlled vocabulary "feature detection method", root term id MI:0003.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="confidenceList" type="confidenceListType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Confidence in this experiment. Usually a statistical measure.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="attributeList" type="attributeListType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Semi-structured additional description of the experiment.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int" use="required">
+ <xs:annotation>
+ <xs:documentation>All major objects have a numerical id which must be unique to that object within an entry. The object may be repeated, though, e.g. in the denormalised representation.</xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ </xs:complexType>
+ <xs:complexType name="interactionElementType">
+ <xs:annotation>
+ <xs:documentation>A molecular interaction.</xs:documentation>
+ </xs:annotation>
+ <xs:sequence>
+ <xs:element name="names" type="namesType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Name(s) of the interaction.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="xref" type="xrefType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Interaction database ID</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:choice minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Either refer to an already defined availability statement in this entry or insert description.</xs:documentation>
+ </xs:annotation>
+ <xs:element name="availabilityRef" type="xs:int">
+ <xs:annotation>
+ <xs:documentation>References an availability statement already present in this entry.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="availability" type="availabilityType">
+ <xs:annotation>
+ <xs:documentation>Describes the availability of the interaction data. If no availability is given, the data is assumed to be freely available.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ </xs:choice>
+ <xs:element name="experimentList">
+ <xs:annotation>
+ <xs:documentation>List of experiments in which this interaction has been determined.</xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:choice maxOccurs="unbounded">
+ <xs:annotation>
+ <xs:documentation>Either refer to an already defined experiment in this entry or insert description.</xs:documentation>
+ </xs:annotation>
+ <xs:element name="experimentRef" type="xs:int">
+ <xs:annotation>
+ <xs:documentation>References an experiment already present in this entry.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="experimentDescription" type="experimentType">
+ <xs:annotation>
+ <xs:documentation>An experiment in which this interaction has been determined.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ </xs:choice>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="participantList">
+ <xs:annotation>
+ <xs:documentation>A list of molecules participating in this interaction. An interaction has one (intramolecular), two (binary), or more (n-ary, complexes) participants.</xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="participant" type="participantType" maxOccurs="unbounded"/>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="inferredInteractionList" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Describes inferred interactions, usually combining data from more than one experiment. Examples: 1: Show the topology of binary interactions within a complex. 2: Interaction inferred from multiple experiments which on their own would not support the interaction. Example: A-B in experiment 1, B-C- in experiment 2, A-C is the inferred interaction.</xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="inferredInteraction" maxOccurs="unbounded">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="participant" minOccurs="2" maxOccurs="unbounded">
+ <xs:annotation>
+ <xs:documentation>Participant of the inferred interaction.</xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:choice>
+ <xs:element name="participantRef" type="xs:int"/>
+ <xs:element name="participantFeatureRef" type="xs:int"/>
+ </xs:choice>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="experimentRefList" type="experimentRefListType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>If no experimentRef is given, it is assumed this refers to all experiments linked to the interaction.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="interactionType" type="cvType" minOccurs="0" maxOccurs="unbounded">
+ <xs:annotation>
+ <xs:documentation>External controlled vocabulary characterising the interaction type, for example "physical interaction".</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="modelled" type="xs:boolean" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>If true, this element describes an interaction in a species of interest, e.g. human, but has actually been investigated in another organism, e.g. mouse. The transfer will usually be based on a homology statement made by the data producer. If this optional element is missing, it is assumed to be set to false.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="intraMolecular" type="xs:boolean" default="false" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>If true, this interaction is an intramolecular interaction, e.g. an autophosphorylation. If missing, this element is assumed to be false.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="negative" type="xs:boolean" default="false" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>If true, this interaction has been shown NOT to occur under the described experimental conditions. Default false. If this optional element is missing, it is assumed to be set to false.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="confidenceList" type="confidenceListType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Confidence in this interaction. Usually a statistical measure.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="parameterList" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Lists parameters which are relevant for the Interaction, e.g. kinetics.</xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="parameter" maxOccurs="unbounded">
+ <xs:complexType>
+ <xs:complexContent>
+ <xs:extension base="parameterType">
+ <xs:sequence>
+ <xs:element name="experimentRef" type="xs:int">
+ <xs:annotation>
+ <xs:documentation>Reference to the experiment in which this parameter has been determined. If not given, it is assumed that this is valid for all experiments attached to the interaction.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ </xs:sequence>
+ <xs:attribute name="uncertainty" type="xs:decimal" use="optional"/>
+ </xs:extension>
+ </xs:complexContent>
+ </xs:complexType>
+ </xs:element>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="attributeList" type="attributeListType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Semi-structured additional description of the data contained in the entry.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ </xs:sequence>
+ <xs:attribute name="imexId" type="xs:string" use="optional">
+ <xs:annotation>
+ <xs:documentation>Interaction identifier assigned by the IMEx consortium. Will be unique for an interaction determined in one publication. Details defined in the IMEx documents.</xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="id" type="xs:int" use="required">
+ <xs:annotation>
+ <xs:documentation>All major objects have a numerical id which is unique to that object within a PSI MI file. The object may be repeated, though, e.g. in the denormalised representation.</xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ </xs:complexType>
+ <!--interactors and participants-->
+ <xs:complexType name="interactorElementType">
+ <xs:annotation>
+ <xs:documentation>Describes a molecular interactor.</xs:documentation>
+ </xs:annotation>
+ <xs:sequence>
+ <xs:element name="names" type="namesType">
+ <xs:annotation>
+ <xs:documentation>Name(s). The short label is typically a short name that could appear as a label on a diagram.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="xref" type="xrefType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>An interactor should have an xref whenever possible. If the interactor is not available in external databases, it must be characterised within this object e.g. by its sequence.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="interactorType" type="cvType">
+ <xs:annotation>
+ <xs:documentation>The molecule type of the participant, e.g. protein. This element is controlled by the PSI-MI controlled vocabulary "interactorType", root term id MI:0313.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="organism" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>The normal source organism of the interactor.</xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:complexContent>
+ <xs:extension base="bioSourceType"/>
+ </xs:complexContent>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="sequence" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Sequence in uppercase</xs:documentation>
+ <xs:documentation>Usage:</xs:documentation>
+ </xs:annotation>
+ <xs:simpleType>
+ <xs:restriction base="xs:string">
+ <xs:minLength value="1"/>
+ </xs:restriction>
+ </xs:simpleType>
+ </xs:element>
+ <xs:element name="attributeList" type="attributeListType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Allows semi-structured additional annotation of the interactor.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int" use="required">
+ <xs:annotation>
+ <xs:documentation>All major objects have a numerical id which is unique to that object within a PSI MI file. The object may be repeated, though, e.g. in the denormalised representation.</xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ </xs:complexType>
+ <xs:complexType name="participantType">
+ <xs:annotation>
+ <xs:documentation>A molecule participating in an interaction.</xs:documentation>
+ </xs:annotation>
+ <xs:sequence>
+ <xs:element name="names" type="namesType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>This contains the name(s) for the participant given by the authors of a publication.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="xref" type="xrefType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Contains the xref(s) for the participant given by the authors of a publication.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:choice>
+ <xs:annotation>
+ <xs:documentation>Description of the Interactor. Refers to an already defined interactor in this entry, fully describes an interactor, or references another interaction defined in this entry, to allow the hierarchical building up of complexes from subunits. </xs:documentation>
+ </xs:annotation>
+ <xs:element name="interactorRef" type="xs:int">
+ <xs:annotation>
+ <xs:documentation>References an interactor described in the interactorList of the entry</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="interactor" type="interactorElementType">
+ <xs:annotation>
+ <xs:documentation>Fully describes an interactor</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="interactionRef" type="xs:int">
+ <xs:annotation>
+ <xs:documentation>References an interaction described in this entry. Used for the hierarchical buildup of complexes.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ </xs:choice>
+ <xs:element name="participantIdentificationMethodList" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>The method(s) by which this participant has been determined. If this element is present, its value supersedes experimentDescription/ participantIdentificationMethod.</xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="participantIdentificationMethod" maxOccurs="unbounded">
+ <xs:annotation>
+ <xs:documentation>Experimental method to determine the interactors involved in the interaction. This element is controlled by the PSI-MI controlled vocabulary "participant identification method", root term id MI:0002.</xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:complexContent>
+ <xs:extension base="cvType">
+ <xs:sequence minOccurs="0">
+ <xs:element name="experimentRefList" type="experimentRefListType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>If no experimentRef is given, it is assumed this refers to all experiments linked to the interaction.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ </xs:sequence>
+ </xs:extension>
+ </xs:complexContent>
+ </xs:complexType>
+ </xs:element>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="biologicalRole" type="cvType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>The role of the participant in the interaction. This describes the biological role, e.g. enzyme or enzyme target. The experimental role of the participant, e.g. 'bait', is shown in experimentalForm. This element is controlled by the PSI-MI controlled vocabulary "biologicalRole", root term id MI:0500.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="experimentalRoleList" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>The role(s) of the participant in the interaction, e.g. bait. </xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="experimentalRole" maxOccurs="unbounded">
+ <xs:annotation>
+ <xs:documentation>This element is controlled by the PSI-MI controlled vocabulary "experimentalRole", root term id MI:0495.</xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:complexContent>
+ <xs:extension base="cvType">
+ <xs:sequence minOccurs="0">
+ <xs:element name="experimentRefList" type="experimentRefListType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>If no experimentRef is given, it is assumed this refers to all experiments linked to the interaction.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ </xs:sequence>
+ </xs:extension>
+ </xs:complexContent>
+ </xs:complexType>
+ </xs:element>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="experimentalPreparationList" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Terms describing the experimental sample preparation. </xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="experimentalPreparation" maxOccurs="unbounded">
+ <xs:annotation>
+ <xs:documentation>This element is controlled by the PSI-MI controlled vocabulary "experimentalPreparation", root term id MI:0346.</xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:complexContent>
+ <xs:extension base="cvType">
+ <xs:sequence minOccurs="0">
+ <xs:element name="experimentRefList" type="experimentRefListType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>If no experimentRef is given, it is assumed this refers to all experiments linked to the interaction.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ </xs:sequence>
+ </xs:extension>
+ </xs:complexContent>
+ </xs:complexType>
+ </xs:element>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="experimentalInteractorList" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Describes molecules which have been used in specific experiments if these molecules are different from the one listed as interactors. Example: The author of a paper makes a statement about human proteins, but has really worked with mouse proteins. In this case the human protein would be the main interactor, while the experimentalForm would be the mouse protein listed in this element. Optionally this can refer to the experiment(s) in which this form has been used. < [...]
+ </xs:annotation>
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="experimentalInteractor" maxOccurs="unbounded">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:choice>
+ <xs:annotation>
+ <xs:documentation>Either refer to an already defined protein interactor in this entry or insert description.</xs:documentation>
+ </xs:annotation>
+ <xs:element name="interactorRef" type="xs:int">
+ <xs:annotation>
+ <xs:documentation>References an interactor described in the interactorList of the entry</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="interactor" type="interactorElementType">
+ <xs:annotation>
+ <xs:documentation>Fully describes an interactor</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ </xs:choice>
+ <xs:element name="experimentRefList" type="experimentRefListType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>If no experimentRef is given, it is assumed this refers to all experiments linked to the interaction.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="featureList" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Sequence features relevant for the interaction, for example binding domains, and experimental modifications, e.g. protein tags. </xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="feature" type="featureElementType" maxOccurs="unbounded"/>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="hostOrganismList" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>The host organism(s) in which the protein has been expressed. If not given, it is assumed to be the native species of the protein.</xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="hostOrganism" minOccurs="0" maxOccurs="unbounded">
+ <xs:complexType>
+ <xs:complexContent>
+ <xs:extension base="bioSourceType">
+ <xs:sequence minOccurs="0">
+ <xs:element name="experimentRefList" type="experimentRefListType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>If no experimentRef is given, it is assumed this refers to all experiments linked to the interaction.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ </xs:sequence>
+ </xs:extension>
+ </xs:complexContent>
+ </xs:complexType>
+ </xs:element>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="confidenceList" type="confidenceListType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Confidence in participant detection.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="parameterList" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Lists parameters which are relevant for the Interaction, e.g. kinetics.</xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="parameter" maxOccurs="unbounded">
+ <xs:complexType>
+ <xs:complexContent>
+ <xs:extension base="parameterType">
+ <xs:sequence>
+ <xs:element name="experimentRef" type="xs:int">
+ <xs:annotation>
+ <xs:documentation>Reference to the experiment in which this parameter has been determined. If not given, it is assumed that this is valid for all experiments attached to the interaction.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ </xs:sequence>
+ <xs:attribute name="uncertainty" type="xs:decimal" use="optional"/>
+ </xs:extension>
+ </xs:complexContent>
+ </xs:complexType>
+ </xs:element>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="attributeList" type="attributeListType" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation>Semi-structured additional description of the data contained in the entry.</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:int" use="required"/>
+ </xs:complexType>
+</xs:schema>
\ No newline at end of file
diff --git a/coreplugins/PSI-MI/src/test/java/org/cytoscape/coreplugin/psi_mi/test/bio/BioSuite.java b/coreplugins/PSI-MI/src/test/java/org/cytoscape/coreplugin/psi_mi/test/bio/BioSuite.java
new file mode 100755
index 0000000..db4611f
--- /dev/null
+++ b/coreplugins/PSI-MI/src/test/java/org/cytoscape/coreplugin/psi_mi/test/bio/BioSuite.java
@@ -0,0 +1,60 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.psi_mi.test.bio;
+
+import junit.framework.Test;
+import junit.framework.TestCase;
+import junit.framework.TestSuite;
+
+
+/**
+ * Suite of all Cache Unit Tests.
+ *
+ * @author Ethan Cerami
+ */
+public class BioSuite extends TestCase {
+ /**
+ * The suite method runs all the tests.
+ *
+ * @return Suite of JUnit tests.
+ */
+ public static Test suite() {
+ TestSuite suite = new TestSuite();
+ suite.addTestSuite(TestInteractor.class);
+ suite.setName("Bio Unit Tests");
+
+ return suite;
+ }
+}
diff --git a/coreplugins/PSI-MI/src/test/java/org/cytoscape/coreplugin/psi_mi/test/bio/TestInteractor.java b/coreplugins/PSI-MI/src/test/java/org/cytoscape/coreplugin/psi_mi/test/bio/TestInteractor.java
new file mode 100755
index 0000000..142e9a6
--- /dev/null
+++ b/coreplugins/PSI-MI/src/test/java/org/cytoscape/coreplugin/psi_mi/test/bio/TestInteractor.java
@@ -0,0 +1,97 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.psi_mi.test.bio;
+
+import junit.framework.TestCase;
+
+import org.cytoscape.coreplugin.psi_mi.model.Interactor;
+import org.cytoscape.coreplugin.psi_mi.model.vocab.GoVocab;
+import org.cytoscape.coreplugin.psi_mi.model.vocab.InteractorVocab;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+
+
+/**
+ * Tests the Interactor Class.
+ *
+ * @author Ethan Cerami
+ */
+public class TestInteractor extends TestCase {
+ /**
+ * Tests the Interactor Class.
+ *
+ * @throws Exception All Exceptions.
+ */
+ public void testInteractor() throws Exception {
+ Interactor interactor = new Interactor();
+ interactor.setName("YHR119W");
+ interactor.setDescription("Gene has a SET or TROMO domain at its "
+ + "carboxyterminus like the trithorax gene family from human "
+ + "and Drosophila with postulated function in chromatin-"
+ + "mediated gene regulation.");
+
+ // Set Gene Names
+ ArrayList geneNameList = new ArrayList();
+ geneNameList.add("SET1");
+ geneNameList.add("YTX1");
+ interactor.addAttribute(InteractorVocab.GENE_NAME, geneNameList);
+
+ // Set GO Process Terms
+ ArrayList goProcessTerms = new ArrayList();
+ HashMap goTerm = new HashMap();
+ goTerm.put(GoVocab.GO_ID, "GO:0006348");
+ goTerm.put(GoVocab.GO_NAME, "chromatin silencing at telomere");
+ goProcessTerms.add(goTerm);
+ goTerm = new HashMap();
+ goTerm.put(GoVocab.GO_ID, "GO:0016571");
+ goTerm.put(GoVocab.GO_NAME, "histone methylation");
+ goProcessTerms.add(goTerm);
+ interactor.addAttribute(GoVocab.GO_CATEGORY_PROCESS, goProcessTerms);
+ validateAttributes(interactor);
+ }
+
+ /**
+ * Validates the First Go Term.
+ */
+ private void validateAttributes(Interactor interactor) {
+ ArrayList list = (ArrayList) interactor.getAttribute(GoVocab.GO_CATEGORY_PROCESS);
+ HashMap map = (HashMap) list.get(0);
+ String id = (String) map.get(GoVocab.GO_ID);
+ String name = (String) map.get(GoVocab.GO_NAME);
+ assertEquals("GO:0006348", id);
+ assertEquals("chromatin silencing at telomere", name);
+ }
+}
diff --git a/coreplugins/PSI-MI/src/test/java/org/cytoscape/coreplugin/psi_mi/test/bio/package.html b/coreplugins/PSI-MI/src/test/java/org/cytoscape/coreplugin/psi_mi/test/bio/package.html
new file mode 100755
index 0000000..55e4046
--- /dev/null
+++ b/coreplugins/PSI-MI/src/test/java/org/cytoscape/coreplugin/psi_mi/test/bio/package.html
@@ -0,0 +1,8 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+<html>
+<head></head>
+
+<body bgcolor="white">
+JUnit tests for testing the Core Biological Objects.
+</body>
+</html>
diff --git a/coreplugins/PSI-MI/src/test/java/org/cytoscape/coreplugin/psi_mi/test/cyto_mapper/CytoMapperSuite.java b/coreplugins/PSI-MI/src/test/java/org/cytoscape/coreplugin/psi_mi/test/cyto_mapper/CytoMapperSuite.java
new file mode 100755
index 0000000..2553fcb
--- /dev/null
+++ b/coreplugins/PSI-MI/src/test/java/org/cytoscape/coreplugin/psi_mi/test/cyto_mapper/CytoMapperSuite.java
@@ -0,0 +1,61 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.psi_mi.test.cyto_mapper;
+
+import junit.framework.Test;
+import junit.framework.TestCase;
+import junit.framework.TestSuite;
+
+
+/**
+ * Suite of Mapper JUnit Tests.
+ *
+ * @author Ethan Cerami.
+ */
+public class CytoMapperSuite extends TestCase {
+ /**
+ * The suite method runs all the tests.
+ *
+ * @return Suite of JUnit tests.
+ */
+ public static Test suite() {
+ TestSuite suite = new TestSuite();
+ suite.addTestSuite(TestMapToCytoscape.class);
+ suite.addTestSuite(TestMapFromCytoscape.class);
+ suite.setName("CytoMapper Tests");
+
+ return suite;
+ }
+}
diff --git a/coreplugins/PSI-MI/src/test/java/org/cytoscape/coreplugin/psi_mi/test/cyto_mapper/TestMapFromCytoscape.java b/coreplugins/PSI-MI/src/test/java/org/cytoscape/coreplugin/psi_mi/test/cyto_mapper/TestMapFromCytoscape.java
new file mode 100755
index 0000000..f0ab28b
--- /dev/null
+++ b/coreplugins/PSI-MI/src/test/java/org/cytoscape/coreplugin/psi_mi/test/cyto_mapper/TestMapFromCytoscape.java
@@ -0,0 +1,115 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.psi_mi.test.cyto_mapper;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+
+import junit.framework.TestCase;
+
+import org.cytoscape.coreplugin.psi_mi.cyto_mapper.MapFromCytoscape;
+import org.cytoscape.coreplugin.psi_mi.cyto_mapper.MapToCytoscape;
+import org.cytoscape.coreplugin.psi_mi.data_mapper.MapPsiOneToInteractions;
+import org.cytoscape.coreplugin.psi_mi.model.ExternalReference;
+import org.cytoscape.coreplugin.psi_mi.model.Interaction;
+import org.cytoscape.coreplugin.psi_mi.model.Interactor;
+import org.cytoscape.coreplugin.psi_mi.util.ContentReader;
+
+import java.util.ArrayList;
+
+
+/**
+ * Tests the MapFromCytoscape Class.
+ *
+ * @author Ethan Cerami.
+ */
+public class TestMapFromCytoscape extends TestCase {
+ /**
+ * Tests the Mapper.
+ *
+ * @throws Exception All Exceptions.
+ */
+ public void testMapper1() throws Exception {
+ // First, get some interactions from sample data file.
+ ArrayList interactions = new ArrayList();
+ ContentReader reader = new ContentReader();
+ String xml = reader.retrieveContent("src/test/resources/testData/psi_sample1.xml");
+
+ // Map from PSI 1.5 --> DataService Interaction Objects.
+ MapPsiOneToInteractions mapper1 = new MapPsiOneToInteractions(xml, interactions);
+ mapper1.doMapping();
+
+ // Now Map from Data Service Objects --> Cytocape Network Objects.
+ CyNetwork cyNetwork = Cytoscape.createNetwork("network1");
+ MapToCytoscape mapper2 = new MapToCytoscape(interactions, MapToCytoscape.MATRIX_VIEW);
+ mapper2.doMapping();
+
+ // Add new nodes/edges to network
+ int[] nodeIndices = mapper2.getNodeIndices();
+ int[] edgeIndices = mapper2.getEdgeIndices();
+
+ for (int i = 0; i < nodeIndices.length; i++) {
+ cyNetwork.addNode(nodeIndices[i]);
+ }
+
+ for (int i = 0; i < edgeIndices.length; i++) {
+ cyNetwork.addEdge(edgeIndices[i]);
+ }
+
+ // And, now map back from Cytoscape --> DataService Interaction Objects
+ MapFromCytoscape mapper3 = new MapFromCytoscape(cyNetwork);
+ mapper3.doMapping();
+
+ // Verify that we have 6 interactions still
+ interactions = mapper3.getInteractions();
+ assertEquals(6, interactions.size());
+
+ // Verify that Sample Interaction with XRefs is mapped over.
+ Interaction interaction = (Interaction) interactions.get(3);
+ assertTrue(interaction.toString().startsWith("Interaction: [YCR038C] [YDR532C]"));
+
+ ExternalReference[] refs = interaction.getExternalRefs();
+ assertEquals(2, refs.length);
+ assertEquals("DIP", refs[0].getDatabase());
+ assertEquals("61E", refs[0].getId());
+ assertEquals("CPATH", refs[1].getDatabase());
+ assertEquals("12345", refs[1].getId());
+
+ // Validate sample interactor with XRefs
+ Interactor interactor = (Interactor) interaction.getInteractors().get(0);
+ assertEquals("YCR038C", interactor.getName());
+ assertEquals(15, interactor.getExternalRefs().length);
+ }
+}
diff --git a/coreplugins/PSI-MI/src/test/java/org/cytoscape/coreplugin/psi_mi/test/cyto_mapper/TestMapToCytoscape.java b/coreplugins/PSI-MI/src/test/java/org/cytoscape/coreplugin/psi_mi/test/cyto_mapper/TestMapToCytoscape.java
new file mode 100755
index 0000000..bec835e
--- /dev/null
+++ b/coreplugins/PSI-MI/src/test/java/org/cytoscape/coreplugin/psi_mi/test/cyto_mapper/TestMapToCytoscape.java
@@ -0,0 +1,458 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.psi_mi.test.cyto_mapper;
+
+import cytoscape.CyEdge;
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+
+import cytoscape.data.CyAttributes;
+import cytoscape.data.Semantics;
+
+import giny.model.Edge;
+
+import junit.framework.TestCase;
+
+import org.cytoscape.coreplugin.psi_mi.cyto_mapper.MapToCytoscape;
+import org.cytoscape.coreplugin.psi_mi.data_mapper.MapPsiOneToInteractions;
+import org.cytoscape.coreplugin.psi_mi.data_mapper.MapPsiTwoFiveToInteractions;
+import org.cytoscape.coreplugin.psi_mi.model.vocab.CommonVocab;
+import org.cytoscape.coreplugin.psi_mi.model.vocab.InteractorVocab;
+import org.cytoscape.coreplugin.psi_mi.util.ContentReader;
+
+import java.util.ArrayList;
+import java.util.Date;
+import java.util.Iterator;
+import java.util.List;
+
+
+/**
+ * Tests the MapToCytoscape Class.
+ *
+ * @author Ethan Cerami.
+ */
+public class TestMapToCytoscape extends TestCase {
+ /**
+ * Tests the MapPsiInteractionsTo Graph mapper.
+ * This test assumes a new empty CyNetwork.
+ *
+ * @throws Exception All Exceptions.
+ */
+ public void testMapper1() throws Exception {
+ // First, get some interactions from sample data file.
+ ArrayList interactions = new ArrayList();
+ ContentReader reader = new ContentReader();
+ String xml = reader.retrieveContent("src/test/resources/testData/psi_sample1.xml");
+
+ // Map from PSI One to DataService Interaction Objects.
+ MapPsiOneToInteractions mapper1 = new MapPsiOneToInteractions(xml, interactions);
+ mapper1.doMapping();
+
+ // Now Map to Cytocape Network Objects.
+ CyNetwork network = Cytoscape.createNetwork("network1");
+ MapToCytoscape mapper2 = new MapToCytoscape(interactions, MapToCytoscape.MATRIX_VIEW);
+ mapper2.doMapping();
+ addToCyNetwork(mapper2, network);
+
+ // Verify Number of Nodes and Number of Edges
+ int nodeCount = network.getNodeCount();
+ int edgeCount = network.getEdgeCount();
+ assertEquals(7, nodeCount);
+ assertEquals(6, edgeCount);
+
+ Iterator nodeIterator = network.nodesIterator();
+ Iterator edgeIterator = network.edgesIterator();
+
+ // Verify one of the nodes in the graph
+ // First find correct index value
+ CyNode node1 = null;
+
+ while (nodeIterator.hasNext()) {
+ CyNode node = (CyNode) nodeIterator.next();
+
+ if (node.getIdentifier().equals("YDL065C")) {
+ node1 = node;
+ }
+ }
+
+ String nodeId1 = node1.getIdentifier();
+ assertEquals("YDL065C", nodeId1);
+
+ // Verify edge in the graph
+ // First find correct index value
+ CyEdge edge1 = null;
+
+ while (edgeIterator.hasNext()) {
+ CyEdge edge = (CyEdge) edgeIterator.next();
+
+ if (edge.getIdentifier().equals("YCR038C (classical two hybrid:11283351) YDR532C")) {
+ edge1 = edge;
+ }
+ }
+
+ String edgeId1 = edge1.getIdentifier();
+ assertEquals("YCR038C (classical two hybrid:11283351) YDR532C", edgeId1);
+
+ // Verify source / target nodes of edge
+ CyNode sourceNode = (CyNode) edge1.getSource();
+ CyNode targetNode = (CyNode) edge1.getTarget();
+ assertEquals("YCR038C", sourceNode.getIdentifier());
+ assertEquals("YDR532C", targetNode.getIdentifier());
+
+ // Verify that Attributes were mapped over too...
+ CyAttributes nodeAttributes = Cytoscape.getNodeAttributes();
+ String taxonomyId = nodeAttributes.getStringAttribute(sourceNode.getIdentifier(),
+ InteractorVocab.ORGANISM_NCBI_TAXONOMY_ID);
+ assertEquals("4932", taxonomyId);
+
+ String fullName = (String) nodeAttributes.getStringAttribute(sourceNode.getIdentifier(),
+ InteractorVocab.FULL_NAME);
+ assertTrue(fullName.indexOf("GTP/GDP exchange factor") > -1);
+
+ // Verify that DB Names were mapped over correctly.
+ // There are multiple DB Names in an array of Strings.
+ List dbNameList = nodeAttributes.getListAttribute(sourceNode.getIdentifier(),
+ CommonVocab.XREF_DB_NAME);
+ assertEquals(15, dbNameList.size());
+ assertEquals("RefSeq GI", dbNameList.get(0));
+
+ // Verify that Interaction Xrefs were mapped over correctly.
+ CyAttributes edgeAttributes = Cytoscape.getEdgeAttributes();
+ dbNameList = edgeAttributes.getListAttribute(edge1.getIdentifier(), CommonVocab.XREF_DB_NAME);
+
+ List dbIdList = edgeAttributes.getListAttribute(edge1.getIdentifier(),
+ CommonVocab.XREF_DB_ID);
+ assertEquals(2, dbNameList.size());
+ assertEquals(2, dbIdList.size());
+ assertEquals("DIP", dbNameList.get(0));
+ assertEquals("CPATH", dbNameList.get(1));
+ assertEquals("61E", dbIdList.get(0));
+ assertEquals("12345", dbIdList.get(1));
+ }
+
+ /**
+ * Tests the MapPsiInteractionsTo Graph mapper.
+ * This test assumes a pre-existing CyNetwork with existing nodes/edges.
+ *
+ * @throws Exception All Exceptions.
+ */
+ public void testMapper2() throws Exception {
+ // First, get some interactions from sample data file.
+ ArrayList interactions = new ArrayList();
+ ContentReader reader = new ContentReader();
+ String xml = reader.retrieveContent("src/test/resources/testData/psi_sample1.xml");
+
+ // Map from PSI to DataService Interaction Objects.
+ MapPsiOneToInteractions mapper1 = new MapPsiOneToInteractions(xml, interactions);
+ mapper1.doMapping();
+
+ // Create CyNetwork, and pre-populate it with some existing data.
+ CyNetwork network = Cytoscape.createNetwork("network2");
+ CyNode node1 = Cytoscape.getCyNode("YDL065C", true);
+ CyNode node2 = Cytoscape.getCyNode("YCR038C", true);
+ network.addNode(node1);
+ network.addNode(node2);
+
+ // Create Edge between node1 and node2.
+ CyEdge edge = Cytoscape.getCyEdge(node1, node2, Semantics.INTERACTION, "pp", true);
+ edge.setIdentifier("YDL065C (classical two hybrid, pmid: 11283351) " + "YCR038C");
+
+ // Now map interactions to cyNetwork.
+ MapToCytoscape mapper2 = new MapToCytoscape(interactions, MapToCytoscape.MATRIX_VIEW);
+ mapper2.doMapping();
+ addToCyNetwork(mapper2, network);
+
+ // Verify Number of Nodes; it should still be 7.
+ // If the mapper failed to check for pre-existing nodes, it would be 9.
+ int nodeCount = network.getNodeCount();
+ assertEquals(7, nodeCount);
+
+ // Verify Number of Edges; it should still be 6.
+ // If the mapper failed to check for pre-existing edges, it would be 7.
+ int edgeCount = network.getEdgeCount();
+ assertEquals(6, edgeCount);
+ }
+
+ /**
+ * Tests the MapPsiInteractionsTo Graph mapper.
+ * This time, we test that the MATRIX_VIEW works with # interactors > 2.
+ *
+ * @throws Exception All Exceptions.
+ */
+ public void testMapper3() throws Exception {
+ // First, get some interactions from sample data file.
+ ArrayList interactions = new ArrayList();
+ ContentReader reader = new ContentReader();
+ String xml = reader.retrieveContent("src/test/resources/testData/psi_sample2.xml");
+
+ // Map from PSI to DataService Interaction Objects.
+ MapPsiOneToInteractions mapper1 = new MapPsiOneToInteractions(xml, interactions);
+ mapper1.doMapping();
+
+ // Create CyNetwork
+ CyNetwork network = Cytoscape.createNetwork("network3");
+
+ // Now map interactions to cyNetwork.
+ MapToCytoscape mapper2 = new MapToCytoscape(interactions, MapToCytoscape.MATRIX_VIEW);
+ mapper2.doMapping();
+ addToCyNetwork(mapper2, network);
+
+ // Verify Number of Nodes; there should be 4.
+ int nodeCount = network.getNodeCount();
+ assertEquals(4, nodeCount);
+
+ // Verify Number of Edges; there should be 6
+ int edgeCount = network.getEdgeCount();
+ assertEquals(6, edgeCount);
+
+ Iterator edgeIterator = network.edgesIterator();
+ int counter = 0;
+
+ while (edgeIterator.hasNext()) {
+ Edge edge = (Edge) edgeIterator.next();
+ String id = edge.getIdentifier();
+
+ if (id.equals("A (classical two hybrid:11283351) C")) {
+ counter++;
+ } else if (id.equals("A (classical two hybrid:11283351) D")) {
+ counter++;
+ } else if (id.equals("B (classical two hybrid:11283351) C")) {
+ counter++;
+ } else if (id.equals("B (classical two hybrid:11283351) D")) {
+ counter++;
+ } else if (id.equals("C (classical two hybrid:11283351) D")) {
+ counter++;
+ } else if (id.equals("A (classical two hybrid:11283351) B")) {
+ counter++;
+ }
+ }
+
+ assertEquals(6, counter);
+ }
+
+ /**
+ * Tests the MapPsiInteractionsTo Graph mapper.
+ * This time, we test that the SPOKE_VIEW works with # interactors > 2.
+ *
+ * @throws Exception All Exceptions.
+ */
+ public void testMapper4() throws Exception {
+ // First, get some interactions from sample data file.
+ ArrayList interactions = new ArrayList();
+ ContentReader reader = new ContentReader();
+ String xml = reader.retrieveContent("src/test/resources/testData/psi_sample2.xml");
+
+ // Map from PSI to DataService Interaction Objects.
+ MapPsiOneToInteractions mapper1 = new MapPsiOneToInteractions(xml, interactions);
+ mapper1.doMapping();
+
+ // Create CyNetwork
+ CyNetwork network = Cytoscape.createNetwork("network3");
+
+ // Now map interactions to cyNetwork.
+ MapToCytoscape mapper2 = new MapToCytoscape(interactions, MapToCytoscape.SPOKE_VIEW);
+ mapper2.doMapping();
+ addToCyNetwork(mapper2, network);
+
+ // Verify Number of Nodes; there should be 4.
+ int nodeCount = network.getNodeCount();
+ assertEquals(4, nodeCount);
+
+ // Verify Number of Edges; there should be 3
+ int edgeCount = network.getEdgeCount();
+ assertEquals(3, edgeCount);
+
+ Iterator edgeIterator = network.edgesIterator();
+ int counter = 0;
+
+ while (edgeIterator.hasNext()) {
+ Edge edge = (Edge) edgeIterator.next();
+ String id = edge.getIdentifier();
+
+ if (id.equals("A (classical two hybrid:11283351) B")) {
+ counter++;
+ } else if (id.equals("A (classical two hybrid:11283351) C")) {
+ counter++;
+ } else if (id.equals("A (classical two hybrid:11283351) D")) {
+ counter++;
+ }
+ }
+
+ assertEquals(3, counter);
+ }
+
+ /**
+ * Test PSI-MI Level 2.5.
+ * @throws Exception All Errors.
+ */
+ public void testMapper5() throws Exception {
+ // First, get some interactions from sample data file.
+ ArrayList interactions = new ArrayList();
+ ContentReader reader = new ContentReader();
+ String xml = reader.retrieveContent("src/test/resources/testData/psi_sample_2_5_2.xml");
+
+ // Map from PSI to DataService Interaction Objects.
+ MapPsiTwoFiveToInteractions mapper1 = new MapPsiTwoFiveToInteractions(xml, interactions);
+ mapper1.doMapping();
+
+ // Create CyNetwork
+ CyNetwork network = Cytoscape.createNetwork("network");
+
+ // Now map interactions to cyNetwork.
+ MapToCytoscape mapper2 = new MapToCytoscape(interactions, MapToCytoscape.SPOKE_VIEW);
+ mapper2.doMapping();
+ addToCyNetwork(mapper2, network);
+
+ // Verify Number of Nodes; there should be 3.
+ int nodeCount = network.getNodeCount();
+ assertEquals(3, nodeCount);
+
+ // Verify Number of Edges; there should be 35
+ int edgeCount = network.getEdgeCount();
+ assertEquals(35, edgeCount);
+
+ Iterator edgeIterator = network.edgesIterator();
+ int counter = 0;
+
+ while (edgeIterator.hasNext()) {
+ Edge edge = (Edge) edgeIterator.next();
+ String id = edge.getIdentifier().trim();
+
+ if (id.equals("kaib_synp7 (pull down:kaib-kaia-2:10064581) kaia_synp7")) {
+ counter++;
+ } else if (id.equals("kaib_synp7 (pull down:kaib-kaic-5:10064581) kaic_synp7")) {
+ counter++;
+ } else if (id.equals("kaic_synp7 (two hybrid:kaic-kaia-1:10064581) kaia_synp7")) {
+ counter++;
+ }
+ }
+
+ assertEquals(3, counter);
+ }
+
+ /**
+ * Tests BioGrid Data defined in Bug: 0001126
+ *
+ * @throws Exception All Errors
+ */
+ public void testBioGridData() throws Exception {
+ // First, get some interactions from sample data file.
+ ArrayList interactions = new ArrayList();
+ ContentReader reader = new ContentReader();
+ String xml = reader.retrieveContent("src/test/resources/testData/bio_grid.xml");
+
+ // Map from PSI to DataService Interaction Objects.
+ MapPsiOneToInteractions mapper1 = new MapPsiOneToInteractions(xml, interactions);
+ mapper1.doMapping();
+
+ // Create CyNetwork
+ CyNetwork network = Cytoscape.createNetwork("network");
+
+ // Now map interactions to cyNetwork.
+ MapToCytoscape mapper2 = new MapToCytoscape(interactions, MapToCytoscape.SPOKE_VIEW);
+ mapper2.doMapping();
+ addToCyNetwork(mapper2, network);
+
+ CyNode node = Cytoscape.getCyNode("HGNC:7733", false);
+ assertEquals("HGNC:7733", node.getIdentifier());
+
+ int[] edges = network.getAdjacentEdgeIndicesArray(node.getRootGraphIndex(), true, true, true);
+
+ // validate that we have 9 edges.
+ assertEquals(9, edges.length);
+ }
+
+ /**
+ * Profile Loading of HPRD Data.
+ *
+ * @throws Exception All Exceptions.
+ */
+ public void profileHprd() throws Exception {
+ ArrayList allInteractions = new ArrayList();
+
+ // First, get some interactions from sample data file.
+ ContentReader reader = new ContentReader();
+ String xml = reader.retrieveContent("src/test/resources/testData/hprd.xml");
+
+ // Map from PSI to DataService Interaction Objects.
+ for (int i = 0; i < 25; i++) {
+ ArrayList interactions = new ArrayList();
+ MapPsiOneToInteractions mapper1 = new MapPsiOneToInteractions(xml, interactions);
+ mapper1.doMapping();
+ allInteractions.addAll(interactions);
+ }
+
+ // Now Map to Cytocape Network Objects.
+ System.out.println("Mapping to Cytoscape Network");
+ System.out.println("Number of Interactions: " + allInteractions.size());
+
+ CyNetwork network = Cytoscape.createNetwork("network1");
+ MapToCytoscape mapper2 = new MapToCytoscape(allInteractions, MapToCytoscape.MATRIX_VIEW);
+ addToCyNetwork(mapper2, network);
+ mapper2.doMapping();
+ System.out.println("DONE");
+ }
+
+ private void addToCyNetwork(MapToCytoscape mapper, CyNetwork cyNetwork) {
+ // Add new nodes/edges to network
+ int[] nodeIndices = mapper.getNodeIndices();
+ int[] edgeIndices = mapper.getEdgeIndices();
+
+ for (int i = 0; i < nodeIndices.length; i++) {
+ cyNetwork.addNode(nodeIndices[i]);
+ }
+
+ for (int i = 0; i < edgeIndices.length; i++) {
+ cyNetwork.addEdge(edgeIndices[i]);
+ }
+ }
+
+ /**
+ * Main Method. Used for JProfiler.
+ *
+ * @param args Command Line Arguments.
+ * @throws Exception All Exceptions.
+ */
+ public static void main(String[] args) throws Exception {
+ Date start = new Date();
+ TestMapToCytoscape test = new TestMapToCytoscape();
+ test.profileHprd();
+
+ Date stop = new Date();
+ long time = stop.getTime() - start.getTime();
+ System.out.println("Time: " + time);
+ }
+}
diff --git a/coreplugins/PSI-MI/src/test/java/org/cytoscape/coreplugin/psi_mi/test/cyto_mapper/package.html b/coreplugins/PSI-MI/src/test/java/org/cytoscape/coreplugin/psi_mi/test/cyto_mapper/package.html
new file mode 100644
index 0000000..f7df3da
--- /dev/null
+++ b/coreplugins/PSI-MI/src/test/java/org/cytoscape/coreplugin/psi_mi/test/cyto_mapper/package.html
@@ -0,0 +1,8 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+<html>
+<head></head>
+
+<body bgcolor="white">
+JUnit tests for testing mapping to/from Cytoscape.
+</body>
+</html>
diff --git a/coreplugins/PSI-MI/src/test/java/org/cytoscape/coreplugin/psi_mi/test/data_mapper/DataMapperSuite.java b/coreplugins/PSI-MI/src/test/java/org/cytoscape/coreplugin/psi_mi/test/data_mapper/DataMapperSuite.java
new file mode 100755
index 0000000..adf7c92
--- /dev/null
+++ b/coreplugins/PSI-MI/src/test/java/org/cytoscape/coreplugin/psi_mi/test/data_mapper/DataMapperSuite.java
@@ -0,0 +1,63 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.psi_mi.test.data_mapper;
+
+import junit.framework.Test;
+import junit.framework.TestCase;
+import junit.framework.TestSuite;
+
+
+/**
+ * Suite of all Cache Unit Tests.
+ *
+ * @author Ethan Cerami
+ */
+public class DataMapperSuite extends TestCase {
+ /**
+ * The suite method runs all the tests.
+ *
+ * @return Suite of JUnit tests.
+ */
+ public static Test suite() {
+ TestSuite suite = new TestSuite();
+ suite.addTestSuite(TestMapPsiOneToInteractions.class);
+ suite.addTestSuite(TestMapPsiTwoFiveToInteractions.class);
+ suite.addTestSuite(TestMapInteractionsToPsiOne.class);
+ suite.addTestSuite(TestMapInteractionsToPsiTwoFive.class);
+ suite.setName("Data Mapper Unit Tests");
+
+ return suite;
+ }
+}
diff --git a/coreplugins/PSI-MI/src/test/java/org/cytoscape/coreplugin/psi_mi/test/data_mapper/TestMapInteractionsToPsiOne.java b/coreplugins/PSI-MI/src/test/java/org/cytoscape/coreplugin/psi_mi/test/data_mapper/TestMapInteractionsToPsiOne.java
new file mode 100755
index 0000000..82b97d7
--- /dev/null
+++ b/coreplugins/PSI-MI/src/test/java/org/cytoscape/coreplugin/psi_mi/test/data_mapper/TestMapInteractionsToPsiOne.java
@@ -0,0 +1,210 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.psi_mi.test.data_mapper;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+
+import junit.framework.TestCase;
+
+import org.cytoscape.coreplugin.psi_mi.cyto_mapper.MapFromCytoscape;
+import org.cytoscape.coreplugin.psi_mi.cyto_mapper.MapToCytoscape;
+import org.cytoscape.coreplugin.psi_mi.data_mapper.MapInteractionsToPsiOne;
+import org.cytoscape.coreplugin.psi_mi.data_mapper.MapPsiOneToInteractions;
+import org.cytoscape.coreplugin.psi_mi.schema.mi1.*;
+import org.cytoscape.coreplugin.psi_mi.util.ContentReader;
+
+import java.io.File;
+import java.io.StringWriter;
+
+import java.math.BigInteger;
+
+import java.util.ArrayList;
+
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.Marshaller;
+
+
+/**
+ * Tests MapInteractionsToPsiOne.
+ *
+ * @author Ethan Cerami
+ */
+public class TestMapInteractionsToPsiOne extends TestCase {
+ /**
+ * Tests Mapper with Sample PSI Data File.
+ *
+ * @throws Exception All Exceptions.
+ */
+ public void testMapper() throws Exception { assertTrue(true); }
+ public void dont_testMapper() throws Exception {
+ File file = new File("src/test/resources/testData/psi_sample1.xml");
+ ContentReader reader = new ContentReader();
+ String xml = reader.retrieveContent(file.toString());
+ ArrayList interactions = new ArrayList();
+
+ // First map PSI-MI Level 1 to interaction objects
+ MapPsiOneToInteractions mapper1 = new MapPsiOneToInteractions(xml, interactions);
+ mapper1.doMapping();
+ assertEquals(6, interactions.size());
+
+ // Second, map to Cytoscape objects
+ CyNetwork network = Cytoscape.createNetwork("network1");
+ MapToCytoscape mapper2 = new MapToCytoscape(interactions, MapToCytoscape.SPOKE_VIEW);
+ mapper2.doMapping();
+ addToCyNetwork(mapper2, network);
+
+ // Verify Number of Nodes and Number of Edges
+ int nodeCount = network.getNodeCount();
+ int edgeCount = network.getEdgeCount();
+ assertEquals(7, nodeCount);
+ assertEquals(6, edgeCount);
+
+ // Third, map back to interaction Objects
+ MapFromCytoscape mapper3 = new MapFromCytoscape(network);
+ mapper3.doMapping();
+ interactions = mapper3.getInteractions();
+ assertEquals(6, interactions.size());
+
+ // Fourth, map to PSI-MI Level 1
+ MapInteractionsToPsiOne mapper4 = new MapInteractionsToPsiOne(interactions);
+ mapper4.doMapping();
+
+ EntrySet entrySet = mapper4.getPsiXml();
+ validateInteractors(entrySet.getEntry().get(0).getInteractorList());
+
+ validateInteractions(entrySet.getEntry().get(0).getInteractionList());
+
+ StringWriter writer = new StringWriter();
+ JAXBContext jc = JAXBContext.newInstance("org.cytoscape.coreplugin.psi_mi.schema.mi1");
+ Marshaller marshaller = jc.createMarshaller();
+ marshaller.setProperty(Marshaller.JAXB_ENCODING, "UTF-8");
+ marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, Boolean.TRUE);
+ marshaller.marshal(entrySet, writer);
+
+ // Verify that XML indentation is turned on.
+ String expected = "<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"yes\"?>\n"
+ + "<entrySet version=\"1\" level=\"1\" xmlns=\"net:sf:psidev:mi\">\n"
+ + " <entry>\n" + " <interactorList>";
+ assertTrue("XML Indentation Test has failed. ", writer.toString().startsWith(expected));
+
+ // System.out.println(writer.toString());
+ }
+
+ private void addToCyNetwork(MapToCytoscape mapper, CyNetwork cyNetwork) {
+ // Add new nodes/edges to network
+ int[] nodeIndices = mapper.getNodeIndices();
+ int[] edgeIndices = mapper.getEdgeIndices();
+
+ for (int i = 0; i < nodeIndices.length; i++) {
+ cyNetwork.addNode(nodeIndices[i]);
+ }
+
+ for (int i = 0; i < edgeIndices.length; i++) {
+ cyNetwork.addEdge(edgeIndices[i]);
+ }
+ }
+
+ /**
+ * Validates Interactor Objects.
+ *
+ * @param interactorList Castor InteractorList Object.
+ */
+ private void validateInteractors(EntrySet.Entry.InteractorList interactorList) {
+ ProteinInteractorType interactor = interactorList.getProteinInteractor().get(0);
+ NamesType name = interactor.getNames();
+ assertEquals("YHR119W", name.getShortLabel());
+ assertTrue(name.getFullName().startsWith("Gene has a SET or TROMO"));
+
+ ProteinInteractorType.Organism organism = interactor.getOrganism();
+ assertEquals(new BigInteger("4932"), organism.getNcbiTaxId());
+ assertEquals("baker's yeast", organism.getNames().getShortLabel());
+ assertEquals("Saccharomyces cerevisiae", organism.getNames().getFullName());
+
+ assertEquals("YHR119W", interactor.getId());
+
+ XrefType xrefType = interactor.getXref();
+ DbReferenceType xref = xrefType.getPrimaryRef();
+ assertEquals("Entrez GI", xref.getDb());
+ assertEquals("529135", xref.getId());
+
+ xref = xrefType.getSecondaryRef().get(0);
+ assertEquals("RefSeq GI", xref.getDb());
+ assertEquals("6321911", xref.getId());
+
+ String sequence = interactor.getSequence();
+ assertTrue(sequence.startsWith("MNTYAQESKLRLKTKIGAD"));
+ }
+
+ /**
+ * Validates Interaction Objects.
+ *
+ * @param interactionList Castor Interaction Object.
+ */
+ private void validateInteractions(EntrySet.Entry.InteractionList interactionList) {
+ InteractionElementType interaction = interactionList.getInteraction().get(3);
+ InteractionElementType.ExperimentList expList = interaction.getExperimentList();
+ ExperimentType expType = (ExperimentType) expList.getExperimentRefOrExperimentDescription()
+ .get(0);
+ BibrefType bibRef = expType.getBibref();
+ XrefType xref = bibRef.getXref();
+ DbReferenceType primaryRef = xref.getPrimaryRef();
+ assertEquals("pubmed", primaryRef.getDb());
+ assertEquals("11283351", primaryRef.getId());
+
+ CvType cvType = expType.getInteractionDetection();
+ NamesType name = cvType.getNames();
+ assertEquals("classical two hybrid", name.getShortLabel());
+ xref = cvType.getXref();
+ primaryRef = xref.getPrimaryRef();
+ assertEquals("PSI-MI", primaryRef.getDb());
+ assertEquals("MI:0018", primaryRef.getId());
+
+ InteractionElementType.ParticipantList pList = interaction.getParticipantList();
+ ProteinParticipantType participant = pList.getProteinParticipant().get(0);
+ RefType ref = participant.getProteinInteractorRef();
+ String reference = ref.getRef();
+ assertEquals("YCR038C", reference);
+
+ // Verify Interaction XRefs.
+ xref = interaction.getXref();
+ primaryRef = xref.getPrimaryRef();
+
+ String db = primaryRef.getDb();
+ String id = primaryRef.getId();
+ assertEquals("DIP", db);
+ assertEquals("61E", id);
+ }
+}
diff --git a/coreplugins/PSI-MI/src/test/java/org/cytoscape/coreplugin/psi_mi/test/data_mapper/TestMapInteractionsToPsiTwoFive.java b/coreplugins/PSI-MI/src/test/java/org/cytoscape/coreplugin/psi_mi/test/data_mapper/TestMapInteractionsToPsiTwoFive.java
new file mode 100644
index 0000000..55f061e
--- /dev/null
+++ b/coreplugins/PSI-MI/src/test/java/org/cytoscape/coreplugin/psi_mi/test/data_mapper/TestMapInteractionsToPsiTwoFive.java
@@ -0,0 +1,207 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.psi_mi.test.data_mapper;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+
+import junit.framework.TestCase;
+
+import org.cytoscape.coreplugin.psi_mi.cyto_mapper.MapFromCytoscape;
+import org.cytoscape.coreplugin.psi_mi.cyto_mapper.MapToCytoscape;
+import org.cytoscape.coreplugin.psi_mi.data_mapper.MapInteractionsToPsiTwoFive;
+import org.cytoscape.coreplugin.psi_mi.data_mapper.MapPsiOneToInteractions;
+import org.cytoscape.coreplugin.psi_mi.schema.mi25.*;
+import org.cytoscape.coreplugin.psi_mi.util.ContentReader;
+
+import java.io.File;
+import java.io.StringWriter;
+
+import java.util.ArrayList;
+
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.Marshaller;
+
+
+/**
+ * Tests MapInteractionsToPsiTwoFive.
+ *
+ * @author Ethan Cerami
+ */
+public class TestMapInteractionsToPsiTwoFive extends TestCase {
+ /**
+ * Tests Mapper with Sample PSI Data File.
+ *
+ * @throws Exception All Exceptions.
+ */
+ public void testMapper() throws Exception { assertTrue(true); }
+ public void dont_testMapper() throws Exception {
+ File file = new File("src/test/resources/testData/psi_sample1.xml");
+ ContentReader reader = new ContentReader();
+ String xml = reader.retrieveContent(file.toString());
+ ArrayList interactions = new ArrayList();
+
+ // First map PSI-MI Level 1 to interaction objects
+ MapPsiOneToInteractions mapper1 = new MapPsiOneToInteractions(xml, interactions);
+ mapper1.doMapping();
+ assertEquals(6, interactions.size());
+
+ // Second, map to Cytoscape objects
+ CyNetwork network = Cytoscape.createNetwork("network1");
+ MapToCytoscape mapper2 = new MapToCytoscape(interactions, MapToCytoscape.SPOKE_VIEW);
+ mapper2.doMapping();
+ addToCyNetwork(mapper2, network);
+
+ // Verify Number of Nodes and Number of Edges
+ int nodeCount = network.getNodeCount();
+ int edgeCount = network.getEdgeCount();
+ assertEquals(7, nodeCount);
+ assertEquals(6, edgeCount);
+
+ // Third, map back to interaction Objects
+ MapFromCytoscape mapper3 = new MapFromCytoscape(network);
+ mapper3.doMapping();
+ interactions = mapper3.getInteractions();
+ assertEquals(6, interactions.size());
+
+ // Fourth, map to PSI-MI Level 2.5
+ MapInteractionsToPsiTwoFive mapper4 = new MapInteractionsToPsiTwoFive(interactions);
+ mapper4.doMapping();
+
+ EntrySet entrySet = mapper4.getPsiXml();
+ validateInteractors(entrySet.getEntry().get(0).getInteractorList());
+
+ validateInteractions(entrySet.getEntry().get(0).getInteractionList());
+
+ StringWriter writer = new StringWriter();
+ JAXBContext jc = JAXBContext.newInstance("org.cytoscape.coreplugin.psi_mi.schema.mi25");
+ Marshaller marshaller = jc.createMarshaller();
+ marshaller.setProperty(Marshaller.JAXB_ENCODING, "UTF-8");
+ marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, Boolean.TRUE);
+ marshaller.marshal(entrySet, writer);
+
+ // System.out.println(writer.toString());
+
+ // Verify that XML indentation is turned on.
+ String expected = "<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"yes\"?>\n"
+ + "<entrySet version=\"5\" level=\"2\" xmlns=\"net:sf:psidev:mi\">\n"
+ + " <entry>\n" + " <interactorList>";
+ assertTrue("XML Indentation Test has failed. ", writer.toString().startsWith(expected));
+ }
+
+ private void addToCyNetwork(MapToCytoscape mapper, CyNetwork cyNetwork) {
+ // Add new nodes/edges to network
+ int[] nodeIndices = mapper.getNodeIndices();
+ int[] edgeIndices = mapper.getEdgeIndices();
+
+ for (int i = 0; i < nodeIndices.length; i++) {
+ cyNetwork.addNode(nodeIndices[i]);
+ }
+
+ for (int i = 0; i < edgeIndices.length; i++) {
+ cyNetwork.addEdge(edgeIndices[i]);
+ }
+ }
+
+ /**
+ * Validates Interactor Objects.
+ *
+ * @param interactorList Castor InteractorList Object.
+ */
+ private void validateInteractors(EntrySet.Entry.InteractorList interactorList) {
+ InteractorElementType interactor = interactorList.getInteractor().get(0);
+ NamesType name = interactor.getNames();
+ assertEquals("YHR119W", name.getShortLabel());
+ assertTrue(name.getFullName().startsWith("Gene has a SET or TROMO"));
+
+ InteractorElementType.Organism organism = interactor.getOrganism();
+ assertEquals(4932, organism.getNcbiTaxId());
+ assertEquals("baker's yeast", organism.getNames().getShortLabel());
+ assertEquals("Saccharomyces cerevisiae", organism.getNames().getFullName());
+
+ assertEquals(0, interactor.getId());
+
+ XrefType xrefType = interactor.getXref();
+ DbReferenceType xref = xrefType.getPrimaryRef();
+ assertEquals("Entrez GI", xref.getDb());
+ assertEquals("529135", xref.getId());
+
+ xref = xrefType.getSecondaryRef().get(0);
+ assertEquals("RefSeq GI", xref.getDb());
+ assertEquals("6321911", xref.getId());
+
+ String sequence = interactor.getSequence();
+ assertTrue(sequence.startsWith("MNTYAQESKLRLKTKIGAD"));
+ }
+
+ /**
+ * Validates Interaction Objects.
+ *
+ * @param interactionList Castor Interaction Object.
+ */
+ private void validateInteractions(EntrySet.Entry.InteractionList interactionList) {
+ InteractionElementType interaction = interactionList.getInteraction().get(3);
+ InteractionElementType.ExperimentList expList = interaction.getExperimentList();
+ ExperimentType expType = (ExperimentType) expList.getExperimentRefOrExperimentDescription()
+ .get(0);
+ BibrefType bibRef = expType.getBibref();
+ XrefType xref = bibRef.getXref();
+ DbReferenceType primaryRef = xref.getPrimaryRef();
+ assertEquals("pubmed", primaryRef.getDb());
+ assertEquals("11283351", primaryRef.getId());
+
+ CvType cvType = expType.getInteractionDetectionMethod();
+ NamesType name = cvType.getNames();
+ assertEquals("classical two hybrid", name.getShortLabel());
+ xref = cvType.getXref();
+ primaryRef = xref.getPrimaryRef();
+ assertEquals("PSI-MI", primaryRef.getDb());
+ assertEquals("MI:0018", primaryRef.getId());
+
+ InteractionElementType.ParticipantList pList = interaction.getParticipantList();
+ ParticipantType participant = pList.getParticipant().get(0);
+ Integer ref = participant.getInteractorRef();
+ assertEquals(new Integer(2), ref);
+
+ // Verify Interaction XRefs.
+ xref = interaction.getXref();
+ primaryRef = xref.getPrimaryRef();
+
+ String db = primaryRef.getDb();
+ String id = primaryRef.getId();
+ assertEquals("DIP", db);
+ assertEquals("61E", id);
+ }
+}
diff --git a/coreplugins/PSI-MI/src/test/java/org/cytoscape/coreplugin/psi_mi/test/data_mapper/TestMapPsiOneToInteractions.java b/coreplugins/PSI-MI/src/test/java/org/cytoscape/coreplugin/psi_mi/test/data_mapper/TestMapPsiOneToInteractions.java
new file mode 100755
index 0000000..7207dd3
--- /dev/null
+++ b/coreplugins/PSI-MI/src/test/java/org/cytoscape/coreplugin/psi_mi/test/data_mapper/TestMapPsiOneToInteractions.java
@@ -0,0 +1,295 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.psi_mi.test.data_mapper;
+
+import junit.framework.TestCase;
+
+import org.cytoscape.coreplugin.psi_mi.data_mapper.MapPsiOneToInteractions;
+import org.cytoscape.coreplugin.psi_mi.model.ExternalReference;
+import org.cytoscape.coreplugin.psi_mi.model.Interaction;
+import org.cytoscape.coreplugin.psi_mi.model.Interactor;
+import org.cytoscape.coreplugin.psi_mi.model.vocab.InteractionVocab;
+import org.cytoscape.coreplugin.psi_mi.model.vocab.InteractorVocab;
+import org.cytoscape.coreplugin.psi_mi.util.ContentReader;
+
+import java.io.File;
+
+import java.util.ArrayList;
+import java.util.List;
+
+
+/**
+ * Tests the MapPsiOneToInteractions Mapper.
+ *
+ * @author Ethan Cerami
+ */
+public class TestMapPsiOneToInteractions extends TestCase {
+ /**
+ * Test the PSI Mapper, Case 1.
+ *
+ * @throws Exception All Exceptions.
+ */
+ public void testPsiMapper1() throws Exception {
+ File file = new File("src/test/resources/testData/psi_sample2.xml");
+ ContentReader reader = new ContentReader();
+ String xml = reader.retrieveContent(file.toString());
+ ArrayList interactions = new ArrayList();
+ MapPsiOneToInteractions mapper = new MapPsiOneToInteractions(xml, interactions);
+ mapper.doMapping();
+
+ // Validate Interaction at index = 0.
+ Interaction interaction = (Interaction) interactions.get(0);
+ validateSample1(interaction);
+ }
+
+ /**
+ * Test the PSI Mapper, Case 2.
+ *
+ * @throws Exception All Exceptions.
+ */
+ public void testPsiMapper2() throws Exception {
+ File file = new File("src/test/resources/testData/yeast_normalised.xml");
+ ContentReader reader = new ContentReader();
+ String xml = reader.retrieveContent(file.toString());
+ ArrayList interactions = new ArrayList();
+ MapPsiOneToInteractions mapper = new MapPsiOneToInteractions(xml, interactions);
+ mapper.doMapping();
+
+ // Validate Interaction at index = 0.
+ Interaction interaction = (Interaction) interactions.get(0);
+ validateSample2(interaction);
+ }
+
+ /**
+ * Test the PSI Mapper, Case 3.
+ *
+ * @throws Exception All Exceptions.
+ */
+ public void testPsiMapper3() throws Exception {
+ File file = new File("src/test/resources/testData/yeast_denormalised.xml");
+ ContentReader reader = new ContentReader();
+ String xml = reader.retrieveContent(file.toString());
+ ArrayList interactions = new ArrayList();
+ MapPsiOneToInteractions mapper = new MapPsiOneToInteractions(xml, interactions);
+ mapper.doMapping();
+
+ // Validate Interaction at index = 0.
+ Interaction interaction = (Interaction) interactions.get(0);
+ validateSample3(interaction);
+ }
+
+ /**
+ * Test the PSI Mapper with Sample DIP Data.
+ * Tests Specifically for Changes in ShortLabel Data.
+ *
+ * @throws Exception All Exceptions.
+ */
+ public void testDipData1() throws Exception {
+ File file = new File("src/test/resources/testData/dip_sample.xml");
+ ContentReader reader = new ContentReader();
+ String xml = reader.retrieveContent(file.toString());
+ ArrayList interactions = new ArrayList();
+ MapPsiOneToInteractions mapper = new MapPsiOneToInteractions(xml, interactions);
+ mapper.doMapping();
+
+ Interaction interaction = (Interaction) interactions.get(0);
+ List interactors = interaction.getInteractors();
+
+ // The first interactor does not have a short label.
+ // In the absence of a short label, the SwissProt.
+ // These tests verifies this fact.
+ Interactor interactor = (Interactor) interactors.get(0);
+ String name = interactor.getName();
+ assertEquals("P06139", name);
+
+ interactor = (Interactor) interactors.get(1);
+ name = interactor.getName();
+ assertEquals("major prion PrP-Sc protein precursor", name);
+
+ // Verify Interaction Xrefs
+ ExternalReference[] refs = interaction.getExternalRefs();
+ assertEquals(1, refs.length);
+ assertEquals("DIP", refs[0].getDatabase());
+ assertEquals("61E", refs[0].getId());
+ }
+
+ /**
+ * Test the PSI Mapper with Sample DIP Data.
+ * Tests Specifically for Multiple Experimental Results
+ *
+ * @throws Exception All Exceptions.
+ */
+ public void testDipData2() throws Exception {
+ File file = new File("src/test/resources/testData/dip_sample.xml");
+ ContentReader reader = new ContentReader();
+ String xml = reader.retrieveContent(file.toString());
+ ArrayList interactions = new ArrayList();
+ MapPsiOneToInteractions mapper = new MapPsiOneToInteractions(xml, interactions);
+ mapper.doMapping();
+
+ // The sample data file has one PSI interaction.
+ // with 5 experimentDescriptions. This will map to
+ // 5 data service Interaction objects.
+ assertEquals(5, interactions.size());
+
+ Interaction interaction = (Interaction) interactions.get(0);
+ this.validateDipInteractions(interaction, "11821039", "Genetic", "PSI", "MI:0045");
+ interaction = (Interaction) interactions.get(1);
+ this.validateDipInteractions(interaction, "9174345", "x-ray crystallography", "PSI",
+ "MI:0114");
+ interaction = (Interaction) interactions.get(4);
+ this.validateDipInteractions(interaction, "10089390", "x-ray crystallography", "PSI",
+ "MI:0114");
+ }
+
+ /**
+ * Tests sample cPath File.
+ * @throws Exception All Errors.
+ */
+ public void testcPathData() throws Exception {
+ File file = new File("src/test/resources/testData/cpath_p53.xml");
+ ContentReader reader = new ContentReader();
+ String xml = reader.retrieveContent(file.toString());
+ ArrayList interactions = new ArrayList();
+ MapPsiOneToInteractions mapper = new MapPsiOneToInteractions(xml, interactions);
+ mapper.doMapping();
+ assertEquals(10, interactions.size());
+ }
+
+ /**
+ * Validates Specific Interaction.
+ */
+ private void validateSample1(Interaction interaction) {
+ assertEquals("11283351", interaction.getAttribute(InteractionVocab.PUB_MED_ID));
+ assertEquals("classical two hybrid",
+ interaction.getAttribute(InteractionVocab.EXPERIMENTAL_SYSTEM_NAME));
+ assertEquals("MI:0018",
+ interaction.getAttribute(InteractionVocab.EXPERIMENTAL_SYSTEM_XREF_ID));
+
+ List interactors = interaction.getInteractors();
+ assertEquals(4, interactors.size());
+
+ Interactor interactor0 = (Interactor) interactors.get(0);
+ Interactor interactor1 = (Interactor) interactors.get(1);
+ Interactor interactor2 = (Interactor) interactors.get(2);
+ Interactor interactor3 = (Interactor) interactors.get(3);
+
+ assertEquals("A", interactor0.getName());
+ assertEquals("B", interactor1.getName());
+ assertEquals("C", interactor2.getName());
+ assertEquals("D", interactor3.getName());
+
+ String fullName0 = (String) interactor0.getAttribute(InteractorVocab.FULL_NAME);
+ String fullName1 = (String) interactor1.getAttribute(InteractorVocab.FULL_NAME);
+ String fullName2 = (String) interactor2.getAttribute(InteractorVocab.FULL_NAME);
+ String fullName3 = (String) interactor3.getAttribute(InteractorVocab.FULL_NAME);
+ assertTrue(fullName0.startsWith("Gene has a SET"));
+ assertTrue(fullName1.startsWith("Kinesin-related"));
+ assertTrue(fullName2.startsWith("SH3-domain"));
+ assertTrue(fullName3.startsWith("SH3-domain"));
+ }
+
+ private void validateDipInteractions(Interaction interaction, String expectedPmid,
+ String expectedSystemName, String expectedDbName,
+ String expectedDbId) {
+ String pmid = (String) interaction.getAttribute(InteractionVocab.PUB_MED_ID);
+ String expName = (String) interaction.getAttribute(InteractionVocab.EXPERIMENTAL_SYSTEM_NAME);
+ String dbName = (String) interaction.getAttribute(InteractionVocab.EXPERIMENTAL_SYSTEM_XREF_DB);
+ String dbId = (String) interaction.getAttribute(InteractionVocab.EXPERIMENTAL_SYSTEM_XREF_ID);
+ assertEquals(expectedPmid, pmid);
+ assertEquals(expectedSystemName, expName);
+ assertEquals(expectedDbName, dbName);
+ assertEquals(expectedDbId, dbId);
+
+ List interactors = interaction.getInteractors();
+ assertEquals(2, interactors.size());
+
+ Interactor interactor = (Interactor) interactors.get(0);
+ assertEquals("P06139", interactor.getName());
+ interactor = (Interactor) interactors.get(1);
+ assertEquals("major prion PrP-Sc protein precursor", interactor.getName());
+ }
+
+ /**
+ * Validates Specific Interaction.
+ */
+ private void validateSample2(Interaction interaction) {
+ List interactors = interaction.getInteractors();
+ Interactor interactor0 = (Interactor) interactors.get(0);
+ assertEquals("MAK10", interactor0.getName());
+
+ Interactor interactor1 = (Interactor) interactors.get(1);
+ assertEquals("MAK3", interactor1.getName());
+ }
+
+ /**
+ * Validates Specific Interaction.
+ */
+ private void validateSample3(Interaction interaction) {
+ List interactors = interaction.getInteractors();
+ Interactor interactor0 = (Interactor) interactors.get(0);
+ assertEquals("MAK10", interactor0.getName());
+
+ Interactor interactor1 = (Interactor) interactors.get(1);
+ assertEquals("MAK3", interactor1.getName());
+ }
+
+ /**
+ * Outputs Interaction (used for debugging purposes).
+ */
+ private void outputInteraction(Interaction interaction) {
+ System.out.println("Interaction:");
+
+ String pubMedID = (String) interaction.getAttribute(InteractionVocab.PUB_MED_ID);
+ String expSystem = (String) interaction.getAttribute(InteractionVocab.EXPERIMENTAL_SYSTEM_NAME);
+ System.out.println(".. PubMedID: " + pubMedID);
+ System.out.println(".. Experimental System: " + expSystem);
+
+ List interactors = interaction.getInteractors();
+
+ for (int i = 0; i < interactors.size(); i++) {
+ Interactor interactor = (Interactor) interactors.get(i);
+ outputInteractor(interactor);
+ }
+ }
+
+ /**
+ * Outputs Interactor.
+ */
+ private void outputInteractor(Interactor interactor) {
+ System.out.println(".. Interactor: " + interactor.getName());
+ System.out.println("..... Description: " + interactor.getDescription());
+ }
+}
diff --git a/coreplugins/PSI-MI/src/test/java/org/cytoscape/coreplugin/psi_mi/test/data_mapper/TestMapPsiTwoFiveToInteractions.java b/coreplugins/PSI-MI/src/test/java/org/cytoscape/coreplugin/psi_mi/test/data_mapper/TestMapPsiTwoFiveToInteractions.java
new file mode 100644
index 0000000..9e2cef4
--- /dev/null
+++ b/coreplugins/PSI-MI/src/test/java/org/cytoscape/coreplugin/psi_mi/test/data_mapper/TestMapPsiTwoFiveToInteractions.java
@@ -0,0 +1,184 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.psi_mi.test.data_mapper;
+
+import junit.framework.TestCase;
+
+import org.cytoscape.coreplugin.psi_mi.data_mapper.MapPsiTwoFiveToInteractions;
+import org.cytoscape.coreplugin.psi_mi.model.ExternalReference;
+import org.cytoscape.coreplugin.psi_mi.model.Interaction;
+import org.cytoscape.coreplugin.psi_mi.model.Interactor;
+import org.cytoscape.coreplugin.psi_mi.model.vocab.InteractionVocab;
+import org.cytoscape.coreplugin.psi_mi.model.vocab.InteractorVocab;
+import org.cytoscape.coreplugin.psi_mi.util.ContentReader;
+
+import java.io.File;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+
+
+/**
+ * Tests the MapPsiTwoFiveToInteractions Mapper.
+ *
+ * @author Ethan Cerami
+ */
+public class TestMapPsiTwoFiveToInteractions extends TestCase {
+ /**
+ * Test the PSI Mapper, Case 2.
+ * Sample Data: PSI-MI Level 2.5 File
+ *
+ * @throws Exception All Exceptions.
+ */
+ public void testPsiMapper1() throws Exception {
+ File file = new File("src/test/resources/testData/psi_sample_2_5_1.xml");
+ ContentReader reader = new ContentReader();
+ String xml = reader.retrieveContent(file.toString());
+ ArrayList interactions = new ArrayList();
+ MapPsiTwoFiveToInteractions mapper = new MapPsiTwoFiveToInteractions(xml, interactions);
+ mapper.doMapping();
+
+ // Validate that we got all interactions
+ assertEquals(1, interactions.size());
+
+ // Validate Interaction at index = 0.
+ Interaction interaction = (Interaction) interactions.get(0);
+ List interactorList = interaction.getInteractors();
+ Interactor interactor = (Interactor) interactorList.get(0);
+ assertEquals("hs90b_human", interactor.getName());
+
+ // Verify bait map
+ HashMap baitMap = (HashMap) interaction.getAttribute(InteractionVocab.BAIT_MAP);
+ String role = (String) baitMap.get(interactor.getName());
+ assertEquals("bait", role);
+ }
+
+ /**
+ * Test the PSI Mapper, Case 2.
+ * Sample Data: PSI-MI Level 2.5 File
+ *
+ * @throws Exception All Exceptions.
+ */
+ public void testPsiMapper2() throws Exception {
+ File file = new File("src/test/resources/testData/psi_sample_2_5_2.xml");
+ ContentReader reader = new ContentReader();
+ String xml = reader.retrieveContent(file.toString());
+ ArrayList interactions = new ArrayList();
+ MapPsiTwoFiveToInteractions mapper = new MapPsiTwoFiveToInteractions(xml, interactions);
+ mapper.doMapping();
+
+ // Validate that we got all interactions
+ assertEquals(35, interactions.size());
+
+ // Validate Interaction at index = 0.
+ Interaction interaction = (Interaction) interactions.get(0);
+ validateInteractionCase1(interaction);
+ }
+
+ private void validateInteractionCase1(Interaction interaction) {
+ HashMap baitMap = (HashMap) interaction.getAttribute(InteractionVocab.BAIT_MAP);
+ assertEquals(2, baitMap.size());
+ assertEquals("bait", baitMap.get("kaic_synp7"));
+ assertEquals("prey", baitMap.get("kaia_synp7"));
+
+ assertEquals("10064581", interaction.getAttribute(InteractionVocab.PUB_MED_ID));
+ assertEquals("yeast two hybrid kaiC kaiA interaction",
+ interaction.getAttribute(InteractionVocab.INTERACTION_FULL_NAME));
+ assertEquals("kaic-kaia-1",
+ interaction.getAttribute(InteractionVocab.INTERACTION_SHORT_NAME));
+ assertEquals("MI:0018",
+ interaction.getAttribute(InteractionVocab.EXPERIMENTAL_SYSTEM_XREF_ID));
+ assertEquals("two hybrid",
+ interaction.getAttribute(InteractionVocab.EXPERIMENTAL_SYSTEM_NAME));
+ assertEquals("psi-mi",
+ interaction.getAttribute(InteractionVocab.EXPERIMENTAL_SYSTEM_XREF_DB));
+
+ // Validate interactors
+ List interactors = interaction.getInteractors();
+ Interactor interactor0 = (Interactor) interactors.get(0);
+ Interactor interactor1 = (Interactor) interactors.get(1);
+
+ // Validate short name, full name
+ assertEquals("kaic_synp7", interactor0.getName());
+ assertEquals("kaia_synp7", interactor1.getName());
+
+ assertEquals("Circadian clock protein kinase kaiC",
+ interactor0.getAttribute(InteractorVocab.FULL_NAME));
+ assertEquals("Circadian clock protein kaiA",
+ interactor1.getAttribute(InteractorVocab.FULL_NAME));
+
+ // Validate organism data
+ assertEquals("synp7", interactor0.getAttribute(InteractorVocab.ORGANISM_COMMON_NAME));
+ assertEquals("synp7", interactor1.getAttribute(InteractorVocab.ORGANISM_COMMON_NAME));
+
+ assertEquals("Synechococcus sp. (strain PCC 7942)",
+ interactor0.getAttribute(InteractorVocab.ORGANISM_SPECIES_NAME));
+ assertEquals("Synechococcus sp. (strain PCC 7942)",
+ interactor1.getAttribute(InteractorVocab.ORGANISM_SPECIES_NAME));
+
+ assertEquals("1140", interactor0.getAttribute(InteractorVocab.ORGANISM_NCBI_TAXONOMY_ID));
+ assertEquals("1140", interactor1.getAttribute(InteractorVocab.ORGANISM_NCBI_TAXONOMY_ID));
+
+ // Validate Sequence Data
+ String sequence0 = (String) interactor0.getAttribute(InteractorVocab.SEQUENCE_DATA);
+ assertTrue(sequence0.startsWith("MTSAEMTS"));
+
+ String sequence1 = (String) interactor1.getAttribute(InteractorVocab.SEQUENCE_DATA);
+ assertTrue(sequence1.startsWith("MLSQIAIC"));
+
+ // Validate all Xrefs for Interactor 0
+ ExternalReference[] xrefs = interactor0.getExternalRefs();
+ assertEquals(6, xrefs.length);
+ assertEquals("uniprotkb", xrefs[0].getDatabase());
+ assertEquals("Q79PF4", xrefs[0].getId());
+ assertEquals("interpro", xrefs[1].getDatabase());
+ assertEquals("IPR010624", xrefs[1].getId());
+ assertEquals("uniprotkb", xrefs[2].getDatabase());
+ assertEquals("Q9Z3H2", xrefs[2].getId());
+ assertEquals("go", xrefs[3].getDatabase());
+ assertEquals("GO:0005515", xrefs[3].getId());
+ assertEquals("go", xrefs[4].getDatabase());
+ assertEquals("GO:0042754", xrefs[4].getId());
+ assertEquals("intact", xrefs[5].getDatabase());
+ assertEquals("EBI-592287", xrefs[5].getId());
+
+ // Validate Xrefs for Interaction
+ xrefs = interaction.getExternalRefs();
+ assertEquals(1, xrefs.length);
+ assertEquals("intact", xrefs[0].getDatabase());
+ assertEquals("EBI-781017", xrefs[0].getId());
+ }
+}
diff --git a/coreplugins/PSI-MI/src/test/java/org/cytoscape/coreplugin/psi_mi/test/data_mapper/package.html b/coreplugins/PSI-MI/src/test/java/org/cytoscape/coreplugin/psi_mi/test/data_mapper/package.html
new file mode 100755
index 0000000..1ff997a
--- /dev/null
+++ b/coreplugins/PSI-MI/src/test/java/org/cytoscape/coreplugin/psi_mi/test/data_mapper/package.html
@@ -0,0 +1,8 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+<html>
+<head></head>
+
+<body bgcolor="white">
+JUnit tests for testing all Mappers.
+</body>
+</html>
diff --git a/coreplugins/PSI-MI/src/test/java/org/cytoscape/coreplugin/psi_mi/test/package.html b/coreplugins/PSI-MI/src/test/java/org/cytoscape/coreplugin/psi_mi/test/package.html
new file mode 100755
index 0000000..6d2b56a
--- /dev/null
+++ b/coreplugins/PSI-MI/src/test/java/org/cytoscape/coreplugin/psi_mi/test/package.html
@@ -0,0 +1,8 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+<html>
+<head></head>
+
+<body bgcolor="white">
+JUnit tests for testing the dataservices framework.
+</body>
+</html>
diff --git a/coreplugins/PSI-MI/src/test/resources/testData/bio_grid.xml b/coreplugins/PSI-MI/src/test/resources/testData/bio_grid.xml
new file mode 100644
index 0000000..360c421
--- /dev/null
+++ b/coreplugins/PSI-MI/src/test/resources/testData/bio_grid.xml
@@ -0,0 +1,8353 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- created using PSIFileMaker @ The BioGRID v.2.0 -->
+<entrySet level="1" version="1" xmlns="net:sf:psidev:mi" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="net:sf:psidev:mi http://psidev.sourceforge.net/mi/xml/src/MIF.xsd">
+ <entry>
+ <source release="2.0.20" releaseDate="2006-05-29">
+ <names>
+ <shortLabel>Interaction Data for BIOGRID-GENE-111719</shortLabel>
+ <fullName>The BioGRID: A General Repository for Interaction Datasets, The Samuel Lunenfeld Research Institute, Toronto, Ontario, Canada, http://www.thebiogrid.org</fullName>
+ </names>
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="16381927" secondary="The BioGRID: A General Repository for Interaction Datasets, The Samuel Lunenfeld Research Institute, Toronto, Ontario, Canada, http://www.thebiogrid.org" version="" />
+ </xref>
+ </bibref>
+ </source>
+ <availabilityList>
+ <availability id="BIOGRID">This data is freely available to both commercial and academic users for research purposes only. In any articles making use of this data, please refer to Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M. BioGRID: A General Repository for Interaction Datasets. Nucleic Acids Res. Jan1;34:D535-9. This data is distributed for research purposes only, and is provided WITHOUT ANY WARRANTY.</availability>
+ </availabilityList>
+ <experimentList>
+ <experimentDescription id="BIOGRID-PUBLICATION-910">
+ <names>
+ <shortLabel>Schlaepfer DD et al.</shortLabel>
+ <fullName>Integrin-mediated signal transduction linked to Ras pathway by GRB2 binding to focal adhesion kinase-</fullName>
+ </names>
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="7997267" secondary="" version="" />
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>Invivo</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="" id="" secondary="" version="" />
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ <experimentDescription id="BIOGRID-PUBLICATION-2525">
+ <names>
+ <shortLabel>Poullet P et al.</shortLabel>
+ <fullName>Ezrin interacts with focal adhesion kinase and induces its activation independently of cell-matrix adhesion-</fullName>
+ </names>
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="11468295" secondary="" version="" />
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>Invivo</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="" id="" secondary="" version="" />
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ <experimentDescription id="BIOGRID-PUBLICATION-2582">
+ <names>
+ <shortLabel>Bergman M et al.</shortLabel>
+ <fullName>Overexpressed Csk tyrosine kinase is localized in focal adhesions, causes reorganization of alpha v beta 5 integrin, and interferes with HeLa cell spreading-</fullName>
+ </names>
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="7529872" secondary="" version="" />
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>Invivo</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="" id="" secondary="" version="" />
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ <experimentDescription id="BIOGRID-PUBLICATION-78">
+ <names>
+ <shortLabel>Yoshida M et al.</shortLabel>
+ <fullName>Leukocyte adhesion to vascular endothelium induces E-selectin linkage to the actin cytoskeleton-</fullName>
+ </names>
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="8609175" secondary="" version="" />
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>Invitro</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="" id="" secondary="" version="" />
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ <experimentDescription id="BIOGRID-PUBLICATION-2918">
+ <names>
+ <shortLabel>Sieg DJ et al.</shortLabel>
+ <fullName>FAK integrates growth-factor and integrin signals to promote cell migration-</fullName>
+ </names>
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="10806474" secondary="" version="" />
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>Invivo</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="" id="" secondary="" version="" />
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ <experimentDescription id="BIOGRID-PUBLICATION-3326">
+ <names>
+ <shortLabel>Hildebrand JD et al.</shortLabel>
+ <fullName>An SH3 domain-containing GTPase-activating protein for Rho and Cdc42 associates with focal adhesion kinase-</fullName>
+ </names>
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="8649427" secondary="" version="" />
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>Invitro</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="" id="" secondary="" version="" />
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ <experimentDescription id="BIOGRID-PUBLICATION-3419">
+ <names>
+ <shortLabel>Arold ST et al.</shortLabel>
+ <fullName>The role of the Src homology 3-Src homology 2 interface in the regulation of Src kinases-</fullName>
+ </names>
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="11278857" secondary="" version="" />
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>Invitro</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="" id="" secondary="" version="" />
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ <experimentDescription id="BIOGRID-PUBLICATION-4515">
+ <names>
+ <shortLabel>Lebrun P et al.</shortLabel>
+ <fullName>Insulin receptor substrate-1 as a signaling molecule for focal adhesion kinase pp125-FAK- and pp60-src--</fullName>
+ </names>
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="9822703" secondary="" version="" />
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>Two-hybrid</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="" id="" secondary="" version="" />
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ <experimentDescription id="BIOGRID-PUBLICATION-4668">
+ <names>
+ <shortLabel>Zhu T et al.</shortLabel>
+ <fullName>Growth hormone stimulates the tyrosine phosphorylation and association of p125 focal adhesion kinase -FAK- with JAK2- Fak is not required for stat-mediated transcription-</fullName>
+ </names>
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="9553131" secondary="" version="" />
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>Invivo</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="" id="" secondary="" version="" />
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ <experimentDescription id="BIOGRID-PUBLICATION-180">
+ <names>
+ <shortLabel>Ryu H et al.</shortLabel>
+ <fullName>Regulation of neutrophil adhesion by pituitary growth hormone accompanies tyrosine phosphorylation of Jak2, p125FAK, and paxillin-</fullName>
+ </names>
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="10925297" secondary="" version="" />
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>Invivo</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="" id="" secondary="" version="" />
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ <experimentDescription id="BIOGRID-PUBLICATION-5705">
+ <names>
+ <shortLabel>Unknown</shortLabel>
+ <fullName>Unknown</fullName>
+ </names>
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="1" secondary="" version="" />
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>Invitro</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="" id="" secondary="" version="" />
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ <experimentDescription id="BIOGRID-PUBLICATION-5856">
+ <names>
+ <shortLabel>Vadlamudi RK et al.</shortLabel>
+ <fullName>Differential regulation of components of the focal adhesion complex by heregulin- role of phosphatase SHP-2-</fullName>
+ </names>
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="11807823" secondary="" version="" />
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>Invivo</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="" id="" secondary="" version="" />
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ <experimentDescription id="BIOGRID-PUBLICATION-5926">
+ <names>
+ <shortLabel>Relou IA et al.</shortLabel>
+ <fullName>Site-specific phosphorylation of platelet focal adhesion kinase by low-density lipoprotein-</fullName>
+ </names>
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="12387730" secondary="" version="" />
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>Invivo</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="" id="" secondary="" version="" />
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ <experimentDescription id="BIOGRID-PUBLICATION-6220">
+ <names>
+ <shortLabel>Guinebault C et al.</shortLabel>
+ <fullName>Integrin-dependent translocation of phosphoinositide 3-kinase to the cytoskeleton of thrombin-activated platelets involves specific interactions of p85 alpha with actin filaments and focal adhesion kinase-</fullName>
+ </names>
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="7537275" secondary="" version="" />
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>Invivo</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="" id="" secondary="" version="" />
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ <experimentDescription id="BIOGRID-PUBLICATION-6287">
+ <names>
+ <shortLabel>Kanner SB et al.</shortLabel>
+ <fullName>Focal adhesion kinase-related fakB is regulated by the integrin LFA-1 and interacts with the SH3 domain of phospholipase C gamma 1-</fullName>
+ </names>
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="8660853" secondary="" version="" />
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>Invivo</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="" id="" secondary="" version="" />
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ <experimentDescription id="BIOGRID-PUBLICATION-6292">
+ <names>
+ <shortLabel>Zhang X et al.</shortLabel>
+ <fullName>Focal adhesion kinase promotes phospholipase C-gamma1 activity-</fullName>
+ </names>
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="10430888" secondary="" version="" />
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>Invivo</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="" id="" secondary="" version="" />
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ <experimentDescription id="BIOGRID-PUBLICATION-6462">
+ <names>
+ <shortLabel>Hamawy MM et al.</shortLabel>
+ <fullName>A 77-kDa protein associates with pp125FAK in mast cells and becomes tyrosine-phosphorylated by high affinity IgE receptor aggregation-</fullName>
+ </names>
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="7744883" secondary="" version="" />
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>Invivo</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="" id="" secondary="" version="" />
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ <experimentDescription id="BIOGRID-PUBLICATION-6628">
+ <names>
+ <shortLabel>Miao H et al.</shortLabel>
+ <fullName>Activation of EphA2 kinase suppresses integrin function and causes focal-adhesion-kinase dephosphorylation-</fullName>
+ </names>
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="10655584" secondary="" version="" />
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>Invivo</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="" id="" secondary="" version="" />
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ <experimentDescription id="BIOGRID-PUBLICATION-6656">
+ <names>
+ <shortLabel>Defilippi P et al.</shortLabel>
+ <fullName>p125FAK tyrosine phosphorylation and focal adhesion assembly- studies with phosphotyrosine phosphatase inhibitors-</fullName>
+ </names>
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="7589239" secondary="" version="" />
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>Invivo</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="" id="" secondary="" version="" />
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ <experimentDescription id="BIOGRID-PUBLICATION-6629">
+ <names>
+ <shortLabel>Retta SF et al.</shortLabel>
+ <fullName>Focal adhesion and stress fiber formation is regulated by tyrosine phosphatase activity-</fullName>
+ </names>
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="8986614" secondary="" version="" />
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>Invivo</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="" id="" secondary="" version="" />
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ <experimentDescription id="BIOGRID-PUBLICATION-6630">
+ <names>
+ <shortLabel>Manes S et al.</shortLabel>
+ <fullName>Concerted activity of tyrosine phosphatase SHP-2 and focal adhesion kinase in regulation of cell motility-</fullName>
+ </names>
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="10082579" secondary="" version="" />
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>Invivo</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="" id="" secondary="" version="" />
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ <experimentDescription id="BIOGRID-PUBLICATION-7496">
+ <names>
+ <shortLabel>Chen HC et al.</shortLabel>
+ <fullName>Interaction of focal adhesion kinase with cytoskeletal protein talin-</fullName>
+ </names>
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="7622520" secondary="" version="" />
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>Invivo</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="" id="" secondary="" version="" />
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ <experimentDescription id="BIOGRID-PUBLICATION-7552">
+ <names>
+ <shortLabel>Cicala C et al.</shortLabel>
+ <fullName>Induction of phosphorylation and intracellular association of CC chemokine receptor 5 and focal adhesion kinase in primary human CD4- T cells by macrophage-tropic HIV envelope-</fullName>
+ </names>
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="10384144" secondary="" version="" />
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>Invivo</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="" id="" secondary="" version="" />
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ <experimentDescription id="BIOGRID-PUBLICATION-7909">
+ <names>
+ <shortLabel>Calalb MB et al.</shortLabel>
+ <fullName>Tyrosine phosphorylation of focal adhesion kinase at sites in the catalytic domain regulates kinase activity- a role for Src family kinases-</fullName>
+ </names>
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="7529876" secondary="" version="" />
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>Invivo</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="" id="" secondary="" version="" />
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ <experimentDescription id="BIOGRID-PUBLICATION-7910">
+ <names>
+ <shortLabel>Xing Z et al.</shortLabel>
+ <fullName>Direct interaction of v-Src with the focal adhesion kinase mediated by the Src SH2 domain-</fullName>
+ </names>
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="8054685" secondary="" version="" />
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>Invivo</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="" id="" secondary="" version="" />
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ <experimentDescription id="BIOGRID-PUBLICATION-8295">
+ <names>
+ <shortLabel>Eliceiri BP et al.</shortLabel>
+ <fullName>Src-mediated coupling of focal adhesion kinase to integrin alpha-v-beta5 in vascular endothelial growth factor signaling-</fullName>
+ </names>
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="11927607" secondary="" version="" />
+ </xref>
+ </bibref>
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+ <primaryRef db="pubmed" id="16189514" secondary="" version="" />
+ </xref>
+ </interaction>
+ <interaction>
+ <names>
+ <shortLabel>124715</shortLabel>
+ </names>
+ <availabilityRef ref="1"/>
+ <experimentList>
+ <experimentRef ref="BIOGRID-PUBLICATION-20558" />
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="BIOGRID-111719" />
+ <role>bait</role>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="BIOGRID-113056" />
+ <role>prey</role>
+ </proteinParticipant>
+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>Affinity Capture-MS</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="" id="" secondary="" version=""/>
+ </xref>
+ </interactionType>
+ <xref>
+ <primaryRef db="pubmed" id="16189514" secondary="" version="" />
+ </xref>
+ </interaction>
+ <interaction>
+ <names>
+ <shortLabel>124905</shortLabel>
+ </names>
+ <availabilityRef ref="1"/>
+ <experimentList>
+ <experimentRef ref="BIOGRID-PUBLICATION-20558" />
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="BIOGRID-109895" />
+ <role>bait</role>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="BIOGRID-111719" />
+ <role>prey</role>
+ </proteinParticipant>
+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>Affinity Capture-MS</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="" id="" secondary="" version=""/>
+ </xref>
+ </interactionType>
+ <xref>
+ <primaryRef db="pubmed" id="16189514" secondary="" version="" />
+ </xref>
+ </interaction>
+ <interaction>
+ <names>
+ <shortLabel>125062</shortLabel>
+ </names>
+ <availabilityRef ref="1"/>
+ <experimentList>
+ <experimentRef ref="BIOGRID-PUBLICATION-20558" />
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="BIOGRID-107128" />
+ <role>bait</role>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="BIOGRID-111719" />
+ <role>prey</role>
+ </proteinParticipant>
+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>Affinity Capture-MS</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="" id="" secondary="" version=""/>
+ </xref>
+ </interactionType>
+ <xref>
+ <primaryRef db="pubmed" id="16189514" secondary="" version="" />
+ </xref>
+ </interaction>
+ <interaction>
+ <names>
+ <shortLabel>125121</shortLabel>
+ </names>
+ <availabilityRef ref="1"/>
+ <experimentList>
+ <experimentRef ref="BIOGRID-PUBLICATION-20558" />
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="BIOGRID-111719" />
+ <role>bait</role>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="BIOGRID-112649" />
+ <role>prey</role>
+ </proteinParticipant>
+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>Affinity Capture-MS</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="" id="" secondary="" version=""/>
+ </xref>
+ </interactionType>
+ <xref>
+ <primaryRef db="pubmed" id="16189514" secondary="" version="" />
+ </xref>
+ </interaction>
+ <interaction>
+ <names>
+ <shortLabel>125162</shortLabel>
+ </names>
+ <availabilityRef ref="1"/>
+ <experimentList>
+ <experimentRef ref="BIOGRID-PUBLICATION-20558" />
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="BIOGRID-111719" />
+ <role>bait</role>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="BIOGRID-115567" />
+ <role>prey</role>
+ </proteinParticipant>
+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>Affinity Capture-MS</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="" id="" secondary="" version=""/>
+ </xref>
+ </interactionType>
+ <xref>
+ <primaryRef db="pubmed" id="16189514" secondary="" version="" />
+ </xref>
+ </interaction>
+ <interaction>
+ <names>
+ <shortLabel>125318</shortLabel>
+ </names>
+ <availabilityRef ref="1"/>
+ <experimentList>
+ <experimentRef ref="BIOGRID-PUBLICATION-20558" />
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="BIOGRID-111719" />
+ <role>bait</role>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="BIOGRID-112361" />
+ <role>prey</role>
+ </proteinParticipant>
+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>Affinity Capture-MS</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="" id="" secondary="" version=""/>
+ </xref>
+ </interactionType>
+ <xref>
+ <primaryRef db="pubmed" id="16189514" secondary="" version="" />
+ </xref>
+ </interaction>
+ <interaction>
+ <names>
+ <shortLabel>125331</shortLabel>
+ </names>
+ <availabilityRef ref="1"/>
+ <experimentList>
+ <experimentRef ref="BIOGRID-PUBLICATION-20558" />
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="BIOGRID-108377" />
+ <role>bait</role>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="BIOGRID-111719" />
+ <role>prey</role>
+ </proteinParticipant>
+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>Affinity Capture-MS</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="" id="" secondary="" version=""/>
+ </xref>
+ </interactionType>
+ <xref>
+ <primaryRef db="pubmed" id="16189514" secondary="" version="" />
+ </xref>
+ </interaction>
+ <interaction>
+ <names>
+ <shortLabel>125398</shortLabel>
+ </names>
+ <availabilityRef ref="1"/>
+ <experimentList>
+ <experimentRef ref="BIOGRID-PUBLICATION-20558" />
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="BIOGRID-107399" />
+ <role>bait</role>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="BIOGRID-111719" />
+ <role>prey</role>
+ </proteinParticipant>
+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>Affinity Capture-MS</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="" id="" secondary="" version=""/>
+ </xref>
+ </interactionType>
+ <xref>
+ <primaryRef db="pubmed" id="16189514" secondary="" version="" />
+ </xref>
+ </interaction>
+ </interactionList>
+ </entry>
+</entrySet>
diff --git a/coreplugins/PSI-MI/src/test/resources/testData/cpath_p53.xml b/coreplugins/PSI-MI/src/test/resources/testData/cpath_p53.xml
new file mode 100644
index 0000000..55dad04
--- /dev/null
+++ b/coreplugins/PSI-MI/src/test/resources/testData/cpath_p53.xml
@@ -0,0 +1,953 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<entrySet xsi:schemaLocation="net:sf:psidev:mi http://psidev.sourceforge.net/mi/xml/src/MIF.xsd" level="1" version="1" xmlns="net:sf:psidev:mi" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+ <entry>
+ <interactorList>
+ <proteinInteractor id="CPATH-42484">
+ <names>
+ <shortLabel>dpb3_yeast</shortLabel>
+ <fullName>DNA polymerase epsilon subunit C</fullName>
+ </names>
+ <xref>
+ <primaryRef db="UNIPROT" id="P27344" secondary="dpb3_yeast" version="45"/>
+ <secondaryRef db="SGD" id="S000000482" secondary="DPB3" version=""/>
+ <secondaryRef db="GO" id="GO:0008622" secondary="C:epsilon DNA polymerase compl" version=""/>
+ <secondaryRef db="GO" id="GO:0006348" secondary="P:chromatin silencing at telom" version=""/>
+ <secondaryRef db="PROSITE" id="IPR009072" secondary="Histone-fold" version=""/>
+ </xref>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>s cerevisiae</shortLabel>
+ <fullName>Saccharomyces cerevisiae</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-39103">
+ <names>
+ <shortLabel>smb2_human</shortLabel>
+ <fullName>DNA-binding protein SMUBP-2</fullName>
+ </names>
+ <xref>
+ <primaryRef db="UNIPROT" id="P38935" secondary="smb2_human" version="45"/>
+ <secondaryRef db="GO" id="GO:0003678" secondary="F:DNA helicase activity" version=""/>
+ <secondaryRef db="GO" id="GO:0003697" secondary="F:single-stranded DNA binding" version=""/>
+ <secondaryRef db="GO" id="GO:0006310" secondary="P:DNA recombination" version=""/>
+ <secondaryRef db="GO" id="GO:0006281" secondary="P:DNA repair" version=""/>
+ <secondaryRef db="GO" id="GO:0006260" secondary="P:DNA replication" version=""/>
+ <secondaryRef db="PROSITE" id="IPR004483" secondary="put_DNA_helic" version=""/>
+ <secondaryRef db="PROSITE" id="IPR001374" secondary="R3H" version=""/>
+ <secondaryRef db="UNIPROT" id="Q00443" secondary="smb2_human" version="45"/>
+ <secondaryRef db="UNIPROT" id="Q14177" secondary="smb2_human" version="45"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-7971">
+ <names>
+ <shortLabel>q9gsr1</shortLabel>
+ <fullName>DNA polymerase zeta catalytic subunit</fullName>
+ </names>
+ <xref>
+ <primaryRef db="UNIPROT" id="Q9GSR1" secondary="q9gsr1" version="28"/>
+ <secondaryRef db="GO" id="GO:0019985" secondary="P:bypass DNA synthesis" version=""/>
+ <secondaryRef db="PROSITE" id="IPR006172" secondary="DNA_pol_B" version=""/>
+ <secondaryRef db="PROSITE" id="IPR006134" secondary="DNA_pol_B_dom" version=""/>
+ <secondaryRef db="PROSITE" id="IPR006133" secondary="DNA_pol_B_exo" version=""/>
+ <secondaryRef db="FLYBASE" id="FBgn0002891" secondary="mus205" version=""/>
+ <secondaryRef db="UNIPROT" id="Q9V319" secondary="q9gsr1" version="28"/>
+ </xref>
+ <organism ncbiTaxId="7227">
+ <names>
+ <shortLabel>drome</shortLabel>
+ <fullName>Drosophila melanogaster</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-43006">
+ <names>
+ <shortLabel>dpoa_yeast</shortLabel>
+ <fullName>DNA polymerase alpha catalytic subunit</fullName>
+ </names>
+ <xref>
+ <primaryRef db="UNIPROT" id="P13382" secondary="dpoa_yeast" version="44"/>
+ <secondaryRef db="SGD" id="S000005046" secondary="POL1" version=""/>
+ <secondaryRef db="GO" id="GO:0000731" secondary="P:DNA repair synthesis" version=""/>
+ <secondaryRef db="PROSITE" id="IPR006172" secondary="DNA_pol_B" version=""/>
+ <secondaryRef db="PROSITE" id="IPR006134" secondary="DNA_pol_B_dom" version=""/>
+ <secondaryRef db="PROSITE" id="IPR006133" secondary="DNA_pol_B_exo" version=""/>
+ <secondaryRef db="PROSITE" id="IPR004578" secondary="Pol2" version=""/>
+ </xref>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>s cerevisiae</shortLabel>
+ <fullName>Saccharomyces cerevisiae</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-42444">
+ <names>
+ <shortLabel>ch12_yeast</shortLabel>
+ <fullName>CHL12 protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="UNIPROT" id="P49956" secondary="ch12_yeast" version="45"/>
+ <secondaryRef db="SGD" id="S0004683" secondary="CTF18" version=""/>
+ <secondaryRef db="GO" id="GO:0005663" secondary="C:DNA replication factor C com" version=""/>
+ <secondaryRef db="GO" id="GO:0007062" secondary="P:sister chromatid cohesion" version=""/>
+ <secondaryRef db="PROSITE" id="IPR003593" secondary="AAA_ATPase" version=""/>
+ <secondaryRef db="PROSITE" id="IPR003959" secondary="AAA_ATPase_centr" version=""/>
+ <secondaryRef db="PROSITE" id="IPR000862" secondary="RFCdomain" version=""/>
+ </xref>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>s cerevisiae</shortLabel>
+ <fullName>Saccharomyces cerevisiae</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-42306">
+ <names>
+ <shortLabel>dpoe_yeast</shortLabel>
+ <fullName>DNA polymerase epsilon, catalytic subunit A</fullName>
+ </names>
+ <xref>
+ <primaryRef db="UNIPROT" id="P21951" secondary="dpoe_yeast" version="44"/>
+ <secondaryRef db="SGD" id="S000005206" secondary="POL2" version=""/>
+ <secondaryRef db="GO" id="GO:0000731" secondary="P:DNA repair synthesis" version=""/>
+ <secondaryRef db="PROSITE" id="IPR006172" secondary="DNA_pol_B" version=""/>
+ <secondaryRef db="PROSITE" id="IPR006134" secondary="DNA_pol_B_dom" version=""/>
+ <secondaryRef db="PROSITE" id="IPR006133" secondary="DNA_pol_B_exo" version=""/>
+ <secondaryRef db="GO" id="GO:0008622" secondary="C:epsilon DNA polymerase compl" version=""/>
+ <secondaryRef db="GO" id="GO:0006348" secondary="P:chromatin silencing at telom" version=""/>
+ </xref>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>s cerevisiae</shortLabel>
+ <fullName>Saccharomyces cerevisiae</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-43005">
+ <names>
+ <shortLabel>dpo2_yeast</shortLabel>
+ <fullName>DNA polymerase alpha subunit B</fullName>
+ </names>
+ <xref>
+ <primaryRef db="UNIPROT" id="P38121" secondary="dpo2_yeast" version="44"/>
+ <secondaryRef db="SGD" id="S000000131" secondary="POL12" version=""/>
+ <secondaryRef db="PROSITE" id="IPR007200" secondary="DNA_pol_alpha_B" version=""/>
+ </xref>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>s cerevisiae</shortLabel>
+ <fullName>Saccharomyces cerevisiae</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-42475">
+ <names>
+ <shortLabel>dna2_yeast</shortLabel>
+ <fullName>DNA replication helicase DNA2</fullName>
+ </names>
+ <xref>
+ <primaryRef db="UNIPROT" id="P38859" secondary="dna2_yeast" version="44"/>
+ <secondaryRef db="SGD" id="S000001207" secondary="DNA2" version=""/>
+ <secondaryRef db="GO" id="GO:0004003" secondary="F:ATP dependent DNA helicase a" version=""/>
+ <secondaryRef db="GO" id="GO:0000014" secondary="F:single-stranded DNA specific" version=""/>
+ <secondaryRef db="GO" id="GO:0006261" secondary="P:DNA dependent DNA replicatio" version=""/>
+ <secondaryRef db="GO" id="GO:0006281" secondary="P:DNA repair" version=""/>
+ <secondaryRef db="GO" id="GO:0006273" secondary="P:lagging strand elongation" version=""/>
+ <secondaryRef db="GO" id="GO:0001302" secondary="P:replicative cell aging" version=""/>
+ </xref>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>s cerevisiae</shortLabel>
+ <fullName>Saccharomyces cerevisiae</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-8031">
+ <names>
+ <shortLabel>q9vc50</shortLabel>
+ <fullName>CG13627-PA</fullName>
+ </names>
+ <xref>
+ <primaryRef db="UNIPROT" id="Q9VC50" secondary="q9vc50" version="22"/>
+ <secondaryRef db="FLYBASE" id="FBgn0039217" secondary="CG13627" version=""/>
+ </xref>
+ <organism ncbiTaxId="7227">
+ <names>
+ <shortLabel>drome</shortLabel>
+ <fullName>Drosophila melanogaster</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-42483">
+ <names>
+ <shortLabel>q04603</shortLabel>
+ <fullName>Hypothetical protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="UNIPROT" id="Q04603" secondary="q04603" version="27"/>
+ <secondaryRef db="SGD" id="S000002528" secondary="DPB4" version=""/>
+ <secondaryRef db="GO" id="GO:0008622" secondary="C:epsilon DNA polymerase compl" version=""/>
+ <secondaryRef db="GO" id="GO:0003893" secondary="F:epsilon DNA polymerase activ" version=""/>
+ <secondaryRef db="GO" id="GO:0006273" secondary="P:lagging strand elongation" version=""/>
+ <secondaryRef db="GO" id="GO:0006272" secondary="P:leading strand elongation" version=""/>
+ <secondaryRef db="PROSITE" id="IPR007124" secondary="Hist_TAF" version=""/>
+ <secondaryRef db="GO" id="GO:0008623" secondary="C:chromatin accessibility comp" version=""/>
+ <secondaryRef db="GO" id="GO:0006348" secondary="P:chromatin silencing at telom" version=""/>
+ <secondaryRef db="PROSITE" id="IPR009072" secondary="Histone-fold" version=""/>
+ </xref>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>s cerevisiae</shortLabel>
+ <fullName>Saccharomyces cerevisiae</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-38752">
+ <names>
+ <shortLabel>lsm8_human</shortLabel>
+ <fullName>U6 snRNA-associated Sm-like protein LSm8</fullName>
+ </names>
+ <xref>
+ <primaryRef db="UNIPROT" id="O95777" secondary="lsm8_human" version="44"/>
+ <secondaryRef db="GO" id="GO:0005634" secondary="C:nucleus" version=""/>
+ <secondaryRef db="GO" id="GO:0017070" secondary="F:U6 snRNA binding" version=""/>
+ <secondaryRef db="GO" id="GO:0000398" secondary="P:nuclear mRNA splicing, via s" version=""/>
+ <secondaryRef db="PROSITE" id="IPR001163" secondary="snRNP_Sm" version=""/>
+ <secondaryRef db="PROSITE" id="IPR010920" secondary="Sm_like_riboprot" version=""/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-16196">
+ <names>
+ <shortLabel>q9w3r3</shortLabel>
+ <fullName>CG1999-PA</fullName>
+ </names>
+ <xref>
+ <primaryRef db="UNIPROT" id="Q9W3R3" secondary="q9w3r3" version="22"/>
+ <secondaryRef db="FLYBASE" id="FBgn0029947" secondary="CG1999" version=""/>
+ </xref>
+ <organism ncbiTaxId="7227">
+ <names>
+ <shortLabel>drome</shortLabel>
+ <fullName>Drosophila melanogaster</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-43008">
+ <names>
+ <shortLabel>pri2_yeast</shortLabel>
+ <fullName>DNA primase large subunit</fullName>
+ </names>
+ <xref>
+ <primaryRef db="UNIPROT" id="P20457" secondary="pri2_yeast" version="44"/>
+ <secondaryRef db="SGD" id="S000001528" secondary="PRI2" version=""/>
+ <secondaryRef db="GO" id="GO:0000731" secondary="P:DNA repair synthesis" version=""/>
+ <secondaryRef db="PROSITE" id="IPR007238" secondary="DNA_primase_lrg" version=""/>
+ </xref>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>s cerevisiae</shortLabel>
+ <fullName>Saccharomyces cerevisiae</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-42446">
+ <names>
+ <shortLabel>dpb2_yeast</shortLabel>
+ <fullName>DNA polymerase epsilon subunit B</fullName>
+ </names>
+ <xref>
+ <primaryRef db="UNIPROT" id="P24482" secondary="dpb2_yeast" version="44"/>
+ <secondaryRef db="SGD" id="S000006379" secondary="DPB2" version=""/>
+ <secondaryRef db="UNIPROT" id="Q06622" secondary="dpb2_yeast" version="44"/>
+ <secondaryRef db="PROSITE" id="IPR007185" secondary="DNA_pol_E_B" version=""/>
+ <secondaryRef db="GO" id="GO:0008622" secondary="C:epsilon DNA polymerase compl" version=""/>
+ </xref>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>s cerevisiae</shortLabel>
+ <fullName>Saccharomyces cerevisiae</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ </interactorList>
+ <interactionList>
+ <interaction>
+ <names>
+ <shortLabel>mint_9569</shortLabel>
+ </names>
+ <experimentList>
+ <experimentDescription id="NO_ID">
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="11805826"/>
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>tap tag coimmunoprecipitation</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="PSI-MI" id="MI:0109" secondary="tap tag coimmunoprecipitation"/>
+ </xref>
+ </interactionDetection>
+ <participantDetection>
+ <names>
+ <shortLabel>peptide massfingerprinting</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="PSI-MI" id="MI:0082" secondary="peptide massfingerprinting"/>
+ </xref>
+ </participantDetection>
+ <attributeList>
+ <attribute name="other references"/>
+ <attribute name="vivo/vitro">vivo</attribute>
+ </attributeList>
+ </experimentDescription>
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-42446"/>
+ <role>bait</role>
+ <isTaggedProtein>true</isTaggedProtein>
+ <isOverexpressedProtein>true</isOverexpressedProtein>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-42306"/>
+ <role>prey</role>
+ <isTaggedProtein>false</isTaggedProtein>
+ <isOverexpressedProtein>true</isOverexpressedProtein>
+ </proteinParticipant>
+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>aggregation</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="PSI-MI" id="MI:0191" secondary="aggregation"/>
+ </xref>
+ </interactionType>
+ <xref>
+ <primaryRef db="MINT" id="mint_9569"/>
+ <secondaryRef db="CPATH" id="65346"/>
+ </xref>
+ <attributeList>
+ <attribute name="dissociation constant">1</attribute>
+ <attribute name="comments"/>
+ </attributeList>
+ </interaction>
+ <interaction>
+ <names>
+ <shortLabel>mint_9261</shortLabel>
+ </names>
+ <experimentList>
+ <experimentDescription id="NO_ID">
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="11805826"/>
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>tap tag coimmunoprecipitation</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="PSI-MI" id="MI:0109" secondary="tap tag coimmunoprecipitation"/>
+ </xref>
+ </interactionDetection>
+ <participantDetection>
+ <names>
+ <shortLabel>peptide massfingerprinting</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="PSI-MI" id="MI:0082" secondary="peptide massfingerprinting"/>
+ </xref>
+ </participantDetection>
+ <attributeList>
+ <attribute name="other references"/>
+ <attribute name="vivo/vitro">vivo</attribute>
+ </attributeList>
+ </experimentDescription>
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-42475"/>
+ <role>bait</role>
+ <isTaggedProtein>true</isTaggedProtein>
+ <isOverexpressedProtein>true</isOverexpressedProtein>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-42475"/>
+ <role>prey</role>
+ <isTaggedProtein>false</isTaggedProtein>
+ <isOverexpressedProtein>true</isOverexpressedProtein>
+ </proteinParticipant>
+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>aggregation</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="PSI-MI" id="MI:0191" secondary="aggregation"/>
+ </xref>
+ </interactionType>
+ <xref>
+ <primaryRef db="MINT" id="mint_9261"/>
+ <secondaryRef db="CPATH" id="70695"/>
+ </xref>
+ <attributeList>
+ <attribute name="dissociation constant">1</attribute>
+ <attribute name="comments"/>
+ </attributeList>
+ </interaction>
+ <interaction>
+ <names>
+ <shortLabel>mint_7445</shortLabel>
+ </names>
+ <experimentList>
+ <experimentDescription id="NO_ID">
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="11805826"/>
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>tap tag coimmunoprecipitation</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="PSI-MI" id="MI:0109" secondary="tap tag coimmunoprecipitation"/>
+ </xref>
+ </interactionDetection>
+ <participantDetection>
+ <names>
+ <shortLabel>peptide massfingerprinting</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="PSI-MI" id="MI:0082" secondary="peptide massfingerprinting"/>
+ </xref>
+ </participantDetection>
+ <attributeList>
+ <attribute name="other references"/>
+ <attribute name="vivo/vitro">vivo</attribute>
+ </attributeList>
+ </experimentDescription>
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-42484"/>
+ <role>bait</role>
+ <isTaggedProtein>true</isTaggedProtein>
+ <isOverexpressedProtein>true</isOverexpressedProtein>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-42306"/>
+ <role>prey</role>
+ <isTaggedProtein>false</isTaggedProtein>
+ <isOverexpressedProtein>true</isOverexpressedProtein>
+ </proteinParticipant>
+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>aggregation</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="PSI-MI" id="MI:0191" secondary="aggregation"/>
+ </xref>
+ </interactionType>
+ <xref>
+ <primaryRef db="MINT" id="mint_7445"/>
+ <secondaryRef db="CPATH" id="65345"/>
+ </xref>
+ <attributeList>
+ <attribute name="dissociation constant">1</attribute>
+ <attribute name="comments"/>
+ </attributeList>
+ </interaction>
+ <interaction>
+ <names>
+ <shortLabel>mint_9397</shortLabel>
+ </names>
+ <experimentList>
+ <experimentDescription id="NO_ID">
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="11805826"/>
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>tap tag coimmunoprecipitation</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="PSI-MI" id="MI:0109" secondary="tap tag coimmunoprecipitation"/>
+ </xref>
+ </interactionDetection>
+ <participantDetection>
+ <names>
+ <shortLabel>peptide massfingerprinting</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="PSI-MI" id="MI:0082" secondary="peptide massfingerprinting"/>
+ </xref>
+ </participantDetection>
+ <attributeList>
+ <attribute name="other references"/>
+ <attribute name="vivo/vitro">vivo</attribute>
+ </attributeList>
+ </experimentDescription>
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-43005"/>
+ <role>bait</role>
+ <isTaggedProtein>true</isTaggedProtein>
+ <isOverexpressedProtein>true</isOverexpressedProtein>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-43008"/>
+ <role>prey</role>
+ <isTaggedProtein>false</isTaggedProtein>
+ <isOverexpressedProtein>true</isOverexpressedProtein>
+ </proteinParticipant>
+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>aggregation</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="PSI-MI" id="MI:0191" secondary="aggregation"/>
+ </xref>
+ </interactionType>
+ <xref>
+ <primaryRef db="MINT" id="mint_9397"/>
+ <secondaryRef db="CPATH" id="65028"/>
+ </xref>
+ <attributeList>
+ <attribute name="dissociation constant">1</attribute>
+ <attribute name="comments"/>
+ </attributeList>
+ </interaction>
+ <interaction>
+ <names>
+ <shortLabel>mint_37989</shortLabel>
+ </names>
+ <experimentList>
+ <experimentDescription id="NO_ID">
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="14605208"/>
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>two hybrid pooling approach</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="PSI-MI" id="MI:0398" secondary="two hybrid pooling approach"/>
+ </xref>
+ </interactionDetection>
+ <participantDetection>
+ <names>
+ <shortLabel>nucleotide sequence identification</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="PSI-MI" id="MI:0078" secondary="nucleotide sequence identification"/>
+ </xref>
+ </participantDetection>
+ <attributeList>
+ <attribute name="other references"/>
+ <attribute name="vivo/vitro">vivo</attribute>
+ </attributeList>
+ </experimentDescription>
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-16196"/>
+ <role>bait</role>
+ <isTaggedProtein>true</isTaggedProtein>
+ <isOverexpressedProtein>false</isOverexpressedProtein>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-7971"/>
+ <role>prey</role>
+ <isTaggedProtein>true</isTaggedProtein>
+ <isOverexpressedProtein>false</isOverexpressedProtein>
+ </proteinParticipant>
+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>aggregation</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="PSI-MI" id="MI:0191" secondary="aggregation"/>
+ </xref>
+ </interactionType>
+ <xref>
+ <primaryRef db="MINT" id="mint_37989"/>
+ <secondaryRef db="CPATH" id="88776"/>
+ </xref>
+ <attributeList>
+ <attribute name="dissociation constant">1</attribute>
+ <attribute name="comments"/>
+ </attributeList>
+ </interaction>
+ <interaction>
+ <names>
+ <shortLabel>mint_32538</shortLabel>
+ </names>
+ <experimentList>
+ <experimentDescription id="NO_ID">
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="14605208"/>
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>two hybrid pooling approach</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="PSI-MI" id="MI:0398" secondary="two hybrid pooling approach"/>
+ </xref>
+ </interactionDetection>
+ <participantDetection>
+ <names>
+ <shortLabel>nucleotide sequence identification</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="PSI-MI" id="MI:0078" secondary="nucleotide sequence identification"/>
+ </xref>
+ </participantDetection>
+ <attributeList>
+ <attribute name="other references"/>
+ <attribute name="vivo/vitro">vivo</attribute>
+ </attributeList>
+ </experimentDescription>
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-8031"/>
+ <role>bait</role>
+ <isTaggedProtein>true</isTaggedProtein>
+ <isOverexpressedProtein>false</isOverexpressedProtein>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-7971"/>
+ <role>prey</role>
+ <isTaggedProtein>true</isTaggedProtein>
+ <isOverexpressedProtein>false</isOverexpressedProtein>
+ </proteinParticipant>
+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>aggregation</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="PSI-MI" id="MI:0191" secondary="aggregation"/>
+ </xref>
+ </interactionType>
+ <xref>
+ <primaryRef db="MINT" id="mint_32538"/>
+ <secondaryRef db="CPATH" id="88779"/>
+ </xref>
+ <attributeList>
+ <attribute name="dissociation constant">4</attribute>
+ <attribute name="comments"/>
+ </attributeList>
+ </interaction>
+ <interaction>
+ <names>
+ <shortLabel>ga-103</shortLabel>
+ </names>
+ <experimentList>
+ <experimentDescription id="NO_ID">
+ <names>
+ <shortLabel>gavin-2002</shortLabel>
+ <fullName>Functional organization of the
+ yeast proteome by
+ systematic analysis of protein complexes.</fullName>
+ </names>
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="11805826" secondary="" version=""/>
+ <secondaryRef db="pubmed" id="15044803" secondary="" version=""/>
+ </xref>
+ </bibref>
+ <hostOrganism ncbiTaxId="4932">
+ <names>
+ <shortLabel>s cerevisiae</shortLabel>
+ <fullName>Saccharomyces cerevisiae</fullName>
+ </names>
+ </hostOrganism>
+ <interactionDetection>
+ <names>
+ <shortLabel>tandem affinity puri</shortLabel>
+ <fullName>tandem affinity purification</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" id="MI:0109" secondary="" version=""/>
+ <secondaryRef db="pubmed" id="10504710" secondary="" version=""/>
+ </xref>
+ </interactionDetection>
+ <participantDetection>
+ <names>
+ <shortLabel>peptide massfingerpr</shortLabel>
+ <fullName>peptide massfingerprinting</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" id="MI:0082" secondary="" version=""/>
+ <secondaryRef db="pubmed" id="10967324" secondary="" version=""/>
+ <secondaryRef db="pubmed" id="11752590" secondary="" version=""/>
+ </xref>
+ </participantDetection>
+ <attributeList>
+ <attribute name="comment">589 bait proteins TAP-tagged.</attribute>
+ </attributeList>
+ </experimentDescription>
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-42446"/>
+ <role>bait</role>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-42446"/>
+ <role>prey</role>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-42483"/>
+ <role>prey</role>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-42306"/>
+ <role>prey</role>
+ </proteinParticipant>
+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>aggregation</shortLabel>
+ <fullName>aggregation</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" id="MI:0191" secondary="" version=""/>
+ </xref>
+ </interactionType>
+ <xref>
+ <primaryRef db="intact" id="EBI-39966" secondary="ga-103"/>
+ <secondaryRef db="CPATH" id="43636"/>
+ </xref>
+ </interaction>
+ <interaction>
+ <names>
+ <shortLabel>lsm8-ighmbp2</shortLabel>
+ </names>
+ <experimentList>
+ <experimentDescription id="NO_ID">
+ <names>
+ <shortLabel>lehner-2004b-2</shortLabel>
+ <fullName>A Protein Interaction Framework
+ for Human mRNA Degradation</fullName>
+ </names>
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="15231747" secondary="" version=""/>
+ </xref>
+ </bibref>
+ <hostOrganism ncbiTaxId="4932">
+ <names>
+ <shortLabel>s cerevisiae</shortLabel>
+ <fullName>Saccharomyces cerevisiae</fullName>
+ </names>
+ </hostOrganism>
+ <interactionDetection>
+ <names>
+ <shortLabel>classical two hybrid</shortLabel>
+ <fullName>classical two hybrid</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" id="MI:0018" secondary="" version=""/>
+ <secondaryRef db="pubmed" id="10967325" secondary="" version=""/>
+ </xref>
+ </interactionDetection>
+ <participantDetection>
+ <names>
+ <shortLabel>nucleotide sequence</shortLabel>
+ <fullName>nucleotide sequence identification</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" id="MI:0078" secondary="" version=""/>
+ </xref>
+ </participantDetection>
+ </experimentDescription>
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-38752"/>
+ <role>bait</role>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-39103"/>
+ <role>prey</role>
+ </proteinParticipant>
+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>aggregation</shortLabel>
+ <fullName>aggregation</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" id="MI:0191" secondary="" version=""/>
+ </xref>
+ </interactionType>
+ <xref>
+ <primaryRef db="intact" id="EBI-374019" secondary="lsm8-ighmbp2"/>
+ <secondaryRef db="CPATH" id="40481"/>
+ </xref>
+ <attributeList>
+ <attribute name="author-confidence">high</attribute>
+ </attributeList>
+ </interaction>
+ <interaction>
+ <names>
+ <shortLabel>mint_7857</shortLabel>
+ </names>
+ <experimentList>
+ <experimentDescription id="NO_ID">
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="11805826"/>
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>tap tag coimmunoprecipitation</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="PSI-MI" id="MI:0109" secondary="tap tag coimmunoprecipitation"/>
+ </xref>
+ </interactionDetection>
+ <participantDetection>
+ <names>
+ <shortLabel>peptide massfingerprinting</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="PSI-MI" id="MI:0082" secondary="peptide massfingerprinting"/>
+ </xref>
+ </participantDetection>
+ <attributeList>
+ <attribute name="other references"/>
+ <attribute name="vivo/vitro">vivo</attribute>
+ </attributeList>
+ </experimentDescription>
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-43005"/>
+ <role>bait</role>
+ <isTaggedProtein>true</isTaggedProtein>
+ <isOverexpressedProtein>true</isOverexpressedProtein>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-43006"/>
+ <role>prey</role>
+ <isTaggedProtein>false</isTaggedProtein>
+ <isOverexpressedProtein>true</isOverexpressedProtein>
+ </proteinParticipant>
+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>aggregation</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="PSI-MI" id="MI:0191" secondary="aggregation"/>
+ </xref>
+ </interactionType>
+ <xref>
+ <primaryRef db="MINT" id="mint_7857"/>
+ <secondaryRef db="CPATH" id="63478"/>
+ </xref>
+ <attributeList>
+ <attribute name="dissociation constant">1</attribute>
+ <attribute name="comments"/>
+ </attributeList>
+ </interaction>
+ <interaction>
+ <names>
+ <shortLabel>mint_8668</shortLabel>
+ </names>
+ <experimentList>
+ <experimentDescription id="NO_ID">
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="11805826"/>
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>tap tag coimmunoprecipitation</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="PSI-MI" id="MI:0109" secondary="tap tag coimmunoprecipitation"/>
+ </xref>
+ </interactionDetection>
+ <participantDetection>
+ <names>
+ <shortLabel>peptide massfingerprinting</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="PSI-MI" id="MI:0082" secondary="peptide massfingerprinting"/>
+ </xref>
+ </participantDetection>
+ <attributeList>
+ <attribute name="other references"/>
+ <attribute name="vivo/vitro">vivo</attribute>
+ </attributeList>
+ </experimentDescription>
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-42444"/>
+ <role>bait</role>
+ <isTaggedProtein>true</isTaggedProtein>
+ <isOverexpressedProtein>true</isOverexpressedProtein>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-42306"/>
+ <role>prey</role>
+ <isTaggedProtein>false</isTaggedProtein>
+ <isOverexpressedProtein>true</isOverexpressedProtein>
+ </proteinParticipant>
+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>aggregation</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="PSI-MI" id="MI:0191" secondary="aggregation"/>
+ </xref>
+ </interactionType>
+ <xref>
+ <primaryRef db="MINT" id="mint_8668"/>
+ <secondaryRef db="CPATH" id="65341"/>
+ </xref>
+ <attributeList>
+ <attribute name="dissociation constant">1</attribute>
+ <attribute name="comments"/>
+ </attributeList>
+ </interaction>
+ </interactionList>
+ </entry>
+</entrySet>
\ No newline at end of file
diff --git a/coreplugins/PSI-MI/src/test/resources/testData/dip_sample.xml b/coreplugins/PSI-MI/src/test/resources/testData/dip_sample.xml
new file mode 100755
index 0000000..4a57340
--- /dev/null
+++ b/coreplugins/PSI-MI/src/test/resources/testData/dip_sample.xml
@@ -0,0 +1,137 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<entrySet level="1" version="1" xmlns="net:sf:psidev:mi" xmlns:psi="net:sf:psidev:mi"
+ xmlns:xin="http://dip.doe-mbi.ucla.edu/xml/XIN"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="net:sf:psidev:mi ../xml/MIF.xsd">
+ <entry>
+ <interactorList>
+ <proteinInteractor id="G_1">
+ <names>
+ <shortLabel/>
+ <fullName>60 kDa chaperonin (Protein Cpn60) (groEL protein) (AMS)</fullName>
+ </names>
+ <xref>
+ <primaryRef db="DIP" id="339N"/>
+ <secondaryRef db="PIR" id="BVECGL"/>
+ <secondaryRef db="SWP" id="P06139"/>
+ <secondaryRef db="GI" id="7429025"/>
+ <secondaryRef db="RefSeq" id="NP_313151"/>
+ </xref>
+ <organism ncbiTaxId="562">
+ <names>
+ <shortLabel/>
+ <fullName>Escherichia coli</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="G_2">
+ <names>
+ <shortLabel/>
+ <fullName>major prion PrP-Sc protein precursor</fullName>
+ </names>
+ <xref>
+ <primaryRef db="DIP" id="1081N"/>
+ <secondaryRef db="PIR" id="UJHYIH"/>
+ <secondaryRef db="GI" id="2144854"/>
+ </xref>
+ <organism ncbiTaxId="10036">
+ <names>
+ <shortLabel/>
+ <fullName>Mesocricetus auratus</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ </interactorList>
+ <interactionList>
+ <interaction>
+ <experimentList>
+ <experimentDescription id="DIP_22043X">
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="11821039"/>
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>Genetic</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="PSI" id="MI:0045"/>
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ <experimentDescription id="DIP_22120X">
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="9174345"/>
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>x-ray crystallography</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="PSI" id="MI:0114"/>
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ <experimentDescription id="DIP_70X">
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="9174345"/>
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>x-ray crystallography</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="PSI" id="MI:0114"/>
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ <experimentDescription id="DIP_22018X">
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="10587438"/>
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>x-ray crystallography</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="PSI" id="MI:0114"/>
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ <experimentDescription id="DIP_22044X">
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="10089390"/>
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>x-ray crystallography</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="PSI" id="MI:0114"/>
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="G_1"/>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="G_2"/>
+ </proteinParticipant>
+ </participantList>
+ <xref>
+ <primaryRef db="DIP" id="61E"/>
+ </xref>
+ </interaction>
+ </interactionList>
+ </entry>
+</entrySet>
diff --git a/coreplugins/PSI-MI/src/test/resources/testData/hprd.xml b/coreplugins/PSI-MI/src/test/resources/testData/hprd.xml
new file mode 100755
index 0000000..e3087dc
--- /dev/null
+++ b/coreplugins/PSI-MI/src/test/resources/testData/hprd.xml
@@ -0,0 +1,7662 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<entrySet
+ xsi:schemaLocation="net:sf:psidev:mi http://psidev.sourceforge.net/mi/xml/src/MIF.xsd"
+ level="1" version="1" xmlns="net:sf:psidev:mi" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+ <entry>
+ <interactorList>
+ <proteinInteractor id="CPATH-1561">
+ <names>
+ <shortLabel>GNAI3</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00765"/>
+ <secondaryRef db="RefSeq" id="NP_006487"/>
+ <secondaryRef db="Affymetrix" id="201179_s_at"/>
+ <secondaryRef db="Affymetrix" id="201180_s_at"/>
+ <secondaryRef db="Affymetrix" id="201181_at"/>
+ <secondaryRef db="Affymetrix" id="876_at"/>
+ <secondaryRef db="Affymetrix" id="g183183_3p_a_at"/>
+ <secondaryRef db="Affymetrix" id="g183224_3p_a_at"/>
+ <secondaryRef db="Affymetrix" id="g5729849_3p_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mgctlsaedk aaverskmid rnlredgeka akevkllllg
+ agesgkstiv kqmkiihedg ysedeckqyk vvvysntiqs
+ iiaiiramgr lkidfgeaar addarqlfvl agsaeegvmt
+ pelagvikrl wrdggvqacf srsreyqlnd sasyylndld
+ risqsnyipt qqdvlrtrvk ttgivethft fkdlyfkmfd
+ vggqrserkk wihcfegvta iifcvalsdy dlvlaedeem
+ nrmhesmklf dsicnnkwft etsiilflnk kdlfeekikr
+ splticypey tgsntyeeaa ayiqcqfedl nrrkdtkeiy
+ thftcatdtk nvqfvfdavt dviiknnlke cgly </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-3705">
+ <names>
+ <shortLabel>Hepatocyte growth factor</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00799"/>
+ <secondaryRef db="RefSeq" id="NP_000592"/>
+ <secondaryRef db="Affymetrix" id="209960_at"/>
+ <secondaryRef db="Affymetrix" id="209961_s_at"/>
+ <secondaryRef db="Affymetrix" id="210755_at"/>
+ <secondaryRef db="Affymetrix" id="210997_at"/>
+ <secondaryRef db="Affymetrix" id="210998_s_at"/>
+ <secondaryRef db="Affymetrix" id="1095_s_at"/>
+ <secondaryRef db="Affymetrix" id="1340_s_at"/>
+ <secondaryRef db="Affymetrix" id="210997_3p_at"/>
+ <secondaryRef db="Affymetrix" id="g1378041_3p_at"/>
+ <secondaryRef db="Affymetrix" id="g184029_3p_at"/>
+ <secondaryRef db="Affymetrix" id="g184029_3p_a_at"/>
+ <secondaryRef db="Affymetrix" id="g184031_3p_a_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.809.0.S3_3p_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mwvtkllpal llqhvllhll llpiaipyae gqrkrrntih
+ efkksakttl ikidpalkik tkkvntadqc anrctrnkgl
+ pftckafvfd karkqclwfp fnsmssgvkk efghefdlye
+ nkdyirncii gkgrsykgtv sitksgikcq pwssmipheh
+ sflpssyrgk dlqenycrnp rgeeggpwcf tsnpevryev
+ cdipqcseve cmtcngesyr glmdhtesgk icqrwdhqtp
+ hrhkflpery pdkgfddnyc rnpdgqprpw cytldphtrw
+ eycaiktcad ntmndtdvpl etteciqgqg egyrgtvnti
+ wngipcqrwd sqyphehdmt penfkckdlr enycrnpdgs
+ espwcfttdp nirvgycsqi pncdmshgqd cyrgngknym
+ gnlsqtrsgl tcsmwdknme dlhrhifwep dasklnenyc
+ rnpdddahgp wcytgnplip wdycpisrce gdttptivnl
+ dhpviscakt kqlrvvngip trtnigwmvs lryrnkhicg
+ gslikeswvl tarqcfpsrd lkdyeawlgi hdvhgrgdek
+ ckqvlnvsql vygpegsdlv lmklarpavl ddfvstidlp
+ nygctipekt scsvygwgyt glinydgllr vahlyimgne
+ kcsqhhrgkv tlneseicag aekigsgpce gdyggplvce
+ qhkmrmvlgv ivpgrgcaip nrpgifvrva yyakwihkii
+ ltykvpqs </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-2209">
+ <names>
+ <shortLabel>CD46</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00406"/>
+ <secondaryRef db="PubMed" id="3260937"/>
+ <secondaryRef db="RefSeq" id="NP_002380"/>
+ <secondaryRef db="Affymetrix" id="207549_x_at"/>
+ <secondaryRef db="Affymetrix" id="208783_s_at"/>
+ <secondaryRef db="Affymetrix" id="211574_s_at"/>
+ <secondaryRef db="Affymetrix" id="237126_at"/>
+ <secondaryRef db="Affymetrix" id="38441_s_at"/>
+ <secondaryRef db="Affymetrix" id="g11321566_3p_a_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.83532.1.A2_3p_a_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>meppgrrecp fpswrfpgll laamvlllys fsdaceeppt
+ feameligkp kpyyeigerv dykckkgyfy ipplathtic
+ drnhtwlpvs ddacyretcp yirdplngqa vpangtyefg
+ yqmhficneg yyligeeily celkgsvaiw sgkppicekv
+ lctpppkikn gkhtfsevev feyldavtys cdpapgpdpf
+ sligestiyc gdnsvwsraa peckvvkcrf pvvengkqis
+ gfgkkfyyka tvmfecdkgf yldgsdtivc dsnstwdppv
+ pkclkvlpps stkppalshs vstssttksp assasgprpt
+ ykppvsnypg ypkpeegild sldvwviavi viaivvgvav
+ icvvpyrylq rrkkkgtylt dethrevkft sl </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-446">
+ <names>
+ <shortLabel>Interleukin 10</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00495"/>
+ <secondaryRef db="PubMed" id="9162098"/>
+ <secondaryRef db="RefSeq" id="NP_000563"/>
+ <secondaryRef db="Affymetrix" id="207433_at"/>
+ <secondaryRef db="Affymetrix" id="1548_s_at"/>
+ <secondaryRef db="Affymetrix" id="g10835140_3p_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mhssallccl vlltgvrasp gqgtqsensc thfpgnlpnm
+ lrdlrdafsr vktffqmkdq ldnlllkesl ledfkgylgc
+ qalsemiqfy leevmpqaen qdpdikahvn slgenlktlr
+ lrlrrchrfl pcenkskave qvknafnklq ekgiykamse
+ fdifinyiea ymtmkirn </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-3838">
+ <names>
+ <shortLabel>HOXA10</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00845"/>
+ <secondaryRef db="RefSeq" id="NP_061824"/>
+ <secondaryRef db="Affymetrix" id="213147_at"/>
+ <secondaryRef db="Affymetrix" id="213150_at"/>
+ <secondaryRef db="Affymetrix" id="41448_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.110637.0.A2_3p_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.110637.0.A3_3p_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mscsespaan sflvdsliss grgeaggggg gagggggggy
+ yahggvylpp aadlpyglqs cglfptlggk rneaaspgsg
+ ggggglgpga hgygpspidl wldaprscrm eppdgppppp
+ qqqpppppqp pqpapqatsc sfaqnikees syclydsadk
+ cpkvsataae lapfprgppp dgcalgtssg vpvpgyfrls
+ qaygtakgyg sggggaqqlg agpfpaqppg rgfdlppala
+ sgsadaarke raldsppppt lacgsgggsq gdeeahasss
+ aaeelspaps esskaspekd slgnskgena anwltaksgr
+ kkrcpytkhq tlelekeflf nmyltrerrl eisrsvhltd
+ rqvkiwfqnr rmklkkmnre nrireltanf nfs </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-737">
+ <names>
+ <shortLabel>Apolipoprotein A II</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00129"/>
+ <secondaryRef db="PubMed" id="3136074"/>
+ <secondaryRef db="RefSeq" id="NP_001634"/>
+ <secondaryRef db="Affymetrix" id="219465_at"/>
+ <secondaryRef db="Affymetrix" id="219466_s_at"/>
+ <secondaryRef db="Affymetrix" id="g4502148_3p_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mkllaatvll lticslegal vrrqakepcv eslvsqyfqt
+ vtdygkdlme kvkspelqae aksyfekske qltplikkag
+ telvnflsyf velgtqpatq </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-1752">
+ <names>
+ <shortLabel>Cdc28 protein kinase 1B</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00299"/>
+ <secondaryRef db="RefSeq" id="NP_001817"/>
+ <secondaryRef db="Affymetrix" id="201897_s_at"/>
+ <secondaryRef db="Affymetrix" id="37347_at"/>
+ <secondaryRef db="Affymetrix" id="g4502856_3p_a_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mshkqiyysd kyddeefeyr hvmlpkdiak lvpkthlmse
+ sewrnlgvqq sqgwvhymih epephillfr rplpkkpkk </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-3409">
+ <names>
+ <shortLabel>GART</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00716"/>
+ <secondaryRef db="PubMed" id="2050105"/>
+ <secondaryRef db="RefSeq" id="NP_000810"/>
+ <secondaryRef db="Affymetrix" id="210005_at"/>
+ <secondaryRef db="Affymetrix" id="212378_at"/>
+ <secondaryRef db="Affymetrix" id="212379_at"/>
+ <secondaryRef db="Affymetrix" id="216990_at"/>
+ <secondaryRef db="Affymetrix" id="217445_s_at"/>
+ <secondaryRef db="Affymetrix" id="230097_at"/>
+ <secondaryRef db="Affymetrix" id="236969_at"/>
+ <secondaryRef db="Affymetrix" id="38384_at"/>
+ <secondaryRef db="Affymetrix" id="g509032_3p_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.144097.0.A1_3p_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.82285.1.S1_3p_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.82285.1.S2_3p_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.82285.2.A1_3p_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.82285.2.S1_3p_a_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>maarvliigs ggrehtlawk laqshhvkqv lvapgnagta
+ csekisntai sisdhtalaq fckekkiefv vvgpeaplaa
+ givgnlrsag vqcfgptaea aqlesskrfa kefmdrhgip
+ taqwkaftkp eeacsfilsa dfpalvvkas glaagkgviv
+ akskeeacka vqeimqekaf gaagetivie elldgeevsc
+ lcftdgktva pmppaqdhkr llegdggpnt ggmgaycpap
+ qvsndlllki kdtvlqrtvd gmqqegtpyt gilyagimlt
+ kngpkvlefn crfgdpecqv ilpllksdly eviqstldgl
+ lctslpvwle nhtaltvvma skgypgdytk gveitgfpea
+ qalglevfha gtalkngkvv thggrvlavt airenlisal
+ eeakkglaai kfegaiyrkd vgfraiaflq qprsltykes
+ gvdiaagnml vkkiqplaka tsrsgckvdl ggfaglfdlk
+ aagfkdplla sgtdgvgtkl kiaqlcnkhd tigqdlvamc
+ vndilaqgae plffldyfsc gkldlsvtea vvagiakacg
+ kagcallgge taempdmypp geydlagfav gamerdqklp
+ hleritegdv vvgiassglh sngfslvrki vaksslqyss
+ papdgcgdqt lgdllltptr iyshsllpvl rsghvkafah
+ itggglleni prvlpeklgv dldaqtwrip rvfswlqqeg
+ hlseeemart fncgvgavlv vskeqteqil rdiqqhkeea
+ wvigsvvara egsprvkvkn liesmqings vlkngsltnh
+ fsfekkkarv avlisgtgsn lqalidstre pnssaqidiv
+ isnkaavagl dkaeragipt rvinhklykn rvefdsaidl
+ vleefsidiv clagfmrils gpfvqkwngk mlnihpsllp
+ sfkgsnaheq aletgvtvtg ctvhfvaedv dagqiilqea
+ vpvkrgdtva tlservklae hkifpaalql vasgtvqlge
+ ngkicwvkee </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-1259">
+ <names>
+ <shortLabel>Collagen, type II, alpha 1</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00361"/>
+ <secondaryRef db="PubMed" id="3004202"/>
+ <secondaryRef db="RefSeq" id="NP_001835"/>
+ <secondaryRef db="Affymetrix" id="213492_at"/>
+ <secondaryRef db="Affymetrix" id="217404_s_at"/>
+ <secondaryRef db="Affymetrix" id="37605_at"/>
+ <secondaryRef db="Affymetrix" id="598_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.81343.0.S2_3p_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.81343.1.S1_3p_a_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mirlgapqsl vlltllvaav lrcqgqdvqe agscvqdgqr
+ yndkdvwkpe pcricvcdtg tvlcddiice dvkdclspei
+ pfgeccpicp tdlatasgqp gpkgqkgepg dikdivgpkg
+ ppgpqgpage qgprgdrgdk gekgapgprg rdgepgtpgn
+ pgppgppgpp gppglggnfa aqmaggfdek aggaqlgvmq
+ gpmgpmgprg ppgpagapgp qgfqgnpgep gepgvsgpmg
+ prgppgppgk pgddgeagkp gkagergppg pqgargfpgt
+ pglpgvkghr gypgldgakg eagapgvkge sgspgengsp
+ gpmgprglpg ergrtgpaga agargndgqp gpagppgpvg
+ paggpgfpga pgakgeagpt gargpegaqg prgepgtpgs
+ pgpagasgnp gtdgipgakg sagapgiaga pgfpgprgpp
+ gpqgatgplg pkgqtgepgi agfkgeqgpk gepgpagpqg
+ apgpageegk rgargepggv gpigppgerg apgnrgfpgq
+ dglagpkgap gergpsglag pkgangdpgr pgepglpgar
+ gltgrpgdag pqgkvgpsga pgedgrpgpp gpqgargqpg
+ vmgfpgpkga ngepgkagek glpgapglrg lpgkdgetga
+ agppgpagpa gergeqgapg psgfqglpgp pgppgeggkp
+ gdqgvpgeag apglvgprge rgfpgergsp gaqglqgprg
+ lpgtpgtdgp kgasgpagpp gaqgppglqg mpgergaagi
+ agpkgdrgdv gekgpegapg kdggrgltgp igppgpagan
+ gekgevgppg pagsagarga pgergetgpp gpagfagppg
+ adgqpgakge qgeagqkgda gapgpqgpsg apgpqgptgv
+ tgpkgargaq gppgatgfpg aagrvgppgs ngnpgppgpp
+ gpsgkdgpkg argdsgppgr agepglqgpa gppgekgepg
+ ddgpsgaegp pgpqglagqr givglpgqrg ergfpglpgp
+ sgepgkqgap gasgdrgppg pvgppgltgp agepgregsp
+ gadgppgrdg aagvkgdrge tgavgapgap gppgspgpag
+ ptgkqgdrge agaqgpmgps gpagargiqg pqgprgdkge
+ agepgerglk ghrgftglqg lpgppgpsgd qgasgpagps
+ gprgppgpvg psgkdgangi pgpigppgpr grsgetgpag
+ ppgnpgppgp pgppgpgidm safaglgpre kgpdplqymr
+ adqaagglrq hdaevdatlk slnnqiesir spegsrknpa
+ rtcrdlklch pewksgdywi dpnqgctlda mkvfcnmetg
+ etcvypnpan vpkknwwssk skekkhiwfg etinggfhfs
+ ygddnlapnt anvqmtflrl lstegsqnit yhcknsiayl
+ deaagnlkka lliqgsndve iraegnsrft ytalkdgctk
+ htgkwgktvi eyrsqktsrl piidiapmdi ggpeqefgvd
+ igpvcfl </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-1111">
+ <names>
+ <shortLabel>Solute carrier family 4, anion
+ exchanger, member 1</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00175"/>
+ <secondaryRef db="PubMed" id="2575590"/>
+ <secondaryRef db="RefSeq" id="NP_000333"/>
+ <secondaryRef db="Affymetrix" id="1552713_a_at"/>
+ <secondaryRef db="Affymetrix" id="205592_at"/>
+ <secondaryRef db="Affymetrix" id="33336_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.185923.0.S2_3p_at"/>
+ <secondaryRef db="Affymetrix" id="Hs2.185923.1.S1_3p_s_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>meelqddyed mmeenleqee yedpdipesq meepaahdte
+ atatdyhtts hpgthkvyve lqelvmdekn qelrwmeaar
+ wvqleenlge ngawgrphls hltfwsllel rrvftkgtvl
+ ldlqetslag vanqlldrfi fedqirpqdr eellralllk
+ hshageleal ggvkpavltr sgdpsqpllp qhssletqlf
+ ceqgdggteg hspsgileki ppdseatlvl vgradfleqp
+ vlgfvrlqea aeleavelpv pirflfvllg peaphidytq
+ lgraaatlms ervfridaym aqsrgellhs legfldcslv
+ lpptdapseq allslvpvqr ellrrryqss pakpdssfyk
+ gldlnggpdd plqqtgqlfg glvrdirrry pyylsditda
+ fspqvlaavi fiyfaalspa itfggllgek trnqmgvsel
+ listavqgil fallgaqpll vvgfsgpllv feeaffsfce
+ tngleyivgr vwigfwlill vvlvvafegs flvrfisryt
+ qeifsflisl ifiyetfskl ikifqdhplq ktynynvlmv
+ pkpqgplpnt allslvlmag tfffammlrk fknssyfpgk
+ lrrvigdfgv pisilimvlv dffiqdtytq klsvpdgfkv
+ snssargwvi hplglrsefp iwmmfasalp allvfilifl
+ esqittlivs kperkmvkgs gfhldlllvv gmggvaalfg
+ mpwlsattvr svthanaltv mgkastpgaa aqiqevkeqr
+ isgllvavlv glsilmepil sriplavlfg iflymgvtsl
+ sgiqlfdril llfkppkyhp dvpyvkrvkt wrmhlftgiq
+ iiclavlwvv kstpaslalp fvliltvplr rvllplifrn
+ velqcldadd akatfdeeeg rdeydevamp v </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-1730">
+ <names>
+ <shortLabel>Cyclin dependent kinase inhibitor 3</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00450"/>
+ <secondaryRef db="PubMed" id="7698009"/>
+ <secondaryRef db="RefSeq" id="NP_005183"/>
+ <secondaryRef db="Affymetrix" id="1555758_a_at"/>
+ <secondaryRef db="Affymetrix" id="209714_s_at"/>
+ <secondaryRef db="Affymetrix" id="1599_at"/>
+ <secondaryRef db="Affymetrix" id="g12734643_3p_a_at"/>
+ <secondaryRef db="Affymetrix" id="Hs2.84113.5.S1_3p_s_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mkppssiqts efdssdeepi edeqtpihis wlslsrvncs
+ qflglcalpg ckfkdvrrnv qkdteelksc giqdifvfct
+ rgelskyrvp nlldlyqqcg iithhhpiad ggtpdiascc
+ eimeelttcl knyrktlihc ygglgrsclv aaclllylsd
+ tispeqaids lrdlrgsgai qtikqynylh efrdklaahl
+ ssrdsqsrsv sr </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-1024">
+ <names>
+ <shortLabel>Epidermal growth factor</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00578"/>
+ <secondaryRef db="PubMed" id="3486749"/>
+ <secondaryRef db="RefSeq" id="NP_001954"/>
+ <secondaryRef db="Affymetrix" id="206254_at"/>
+ <secondaryRef db="Affymetrix" id="1542_at"/>
+ <secondaryRef db="Affymetrix" id="g6031163_3p_at"/>
+ <secondaryRef db="Affymetrix" id="g6031163_3p_x_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mlltliillp vvskfsfvsl sapqhwscpe gtlagngnst
+ cvgpapflif shgnsifrid tegtnyeqlv vdagvsvimd
+ fhynekriyw vdlerqllqr vflngsrqer vcnieknvsg
+ mainwineev iwsnqqegii tvtdmkgnns hillsalkyp
+ anvavdpver fifwssevag slyradldgv gvkalletse
+ kitavsldvl dkrlfwiqyn regsnslics cdydggsvhi
+ skhptqhnlf amslfgdrif ystwkmktiw iankhtgkdm
+ vrinlhssfv plgelkvvhp laqpkaeddt wepeqklckl
+ rkgncsstvc gqdlqshlcm caegyalsrd rkycedvnec
+ afwnhgctlg ckntpgsyyc tcpvgfvllp dgkrchqlvs
+ cprnvsecsh dcvltsegpl cfcpegsvle rdgktcsgcs
+ spdnggcsql cvplspvswe cdcfpgydlq ldekscaasg
+ pqpfllfans qdirhmhfdg tdygtllsqq mgmvyaldhd
+ pvenkiyfah talkwieran mdgsqrerli eegvdvpegl
+ avdwigrrfy wtdrgkslig rsdlngkrsk iitkenisqp
+ rgiavhpmak rlfwtdtgin priessslqg lgrlviassd
+ liwpsgitid fltdklywcd akqsvieman ldgskrrrlt
+ qndvghpfav avfedyvwfs dwampsvirv nkrtgkdrvr
+ lqgsmlkpss lvvvhplakp gadpclyqng gcehickkrl
+ gtawcscreg fmkasdgktc laldghqlla ggevdlknqv
+ tpldilsktr vsednitesq hmlvaeimvs dqddcapvgc
+ smyarciseg edatcqclkg fagdgklcsd idecemgvpv
+ cppasskcin teggyvcrcs egyqgdgihc ldidecqlgv
+ hscgenasct nteggytcmc agrlsepgli cpdstppphl
+ reddhhysvr nsdsecplsh dgyclhdgvc myiealdkya
+ cncvvgyige rcqyrdlkww elrhaghgqq qkvivvavcv
+ vvlvmlllls lwgahyyrtq kllsknpknp yeessrdvrs
+ rrpadtedgm sscpqpwfvv ikehqdlkng gqpvagedgq
+ aadgsmqpts wrqepqlcgm gteqgcwipv ssdkgscpqv
+ mersfhmpsy gtqtleggve kphsllsanp lwqqraldpp hqmeltq </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-1565">
+ <names>
+ <shortLabel>Carboxylesterase 1</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00268"/>
+ <secondaryRef db="GenBank" id="AAC60631"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mwlrafilat lsasaawgah pssppvvdtv hgkvlgkfvs
+ legfaqpvai flgipfakpp lgplrftppq paepwsfvkn
+ atsyppmctq dpkagqllse lftnrkenip lklsedclyl
+ niytpadltk knrlpvmvwi hggglmvgaa stydglalaa
+ henvvvvtiq yrlgiwgffs tgdehsrgnw ghldqvaalr
+ wvqdniasfg gnpgsvtifg esaggesvsv lvlsplaknl
+ fhraisesgv altsvlvkkg dvkplaeqia itagckttts
+ avmvhclrqk teeellettl kmkflsldlq gdpresqpll
+ gtvidgmlll ktpeelqaer nfhtvpymvg inkqefgwli
+ pmqlmsypls egqldqktam sllwksyplv ciakelipea
+ tekylggtdd tvkkkdlfld liadvmfgvp svivarnhrd
+ agaptymyef qyrpsfssdm kpktvigdhg delfsvfgap
+ flkegaseee irlskmvmkf wanfarngnp ngeglphwpe
+ ynqkegylqi gantqaaqkl kdkevafwtn lfakkavekp
+ pqtehiel </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-1268">
+ <names>
+ <shortLabel>Bone morphogenetic protein 4</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00207"/>
+ <secondaryRef db="PubMed" id="7558046"/>
+ <secondaryRef db="RefSeq" id="NP_001193"/>
+ <secondaryRef db="Affymetrix" id="211518_s_at"/>
+ <secondaryRef db="Affymetrix" id="1114_at"/>
+ <secondaryRef db="Affymetrix" id="40333_at"/>
+ <secondaryRef db="Affymetrix" id="g576934_3p_a_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mipgnrmlmv vllcqvllgg ashaslipet gkkkvaeiqg
+ haggrrsgqs hellrdfeat llqmfglrrr pqpsksavip
+ dymrdlyrlq sgeeeeeqih stgleyperp asrantvrsf
+ hheehlenip gtsensafrf lfnlssipen eaissaelrl
+ freqvdqgpd wergfhrini yevmkppaev vpghlitrll
+ dtrlvhhnvt rwetfdvspa vlrwtrekqp nyglaievth
+ lhqtrthqgq hvrisrslpq gsgnwaqlrp llvtfghdgr
+ ghaltrrrra krspkhhsqr arkknkncrr hslyvdfsdv
+ gwndwivapp gyqafychgd cpfpladhln stnhaivqtl
+ vnsvnssipk accvptelsa ismlyldeyd kvvlknyqem vvegcgcr </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-2120">
+ <names>
+ <shortLabel>Collagen, type XIII, alpha 1</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00383"/>
+ <secondaryRef db="PubMed" id="2767682"/>
+ <secondaryRef db="RefSeq" id="NP_005194"/>
+ <secondaryRef db="Affymetrix" id="208535_x_at"/>
+ <secondaryRef db="Affymetrix" id="211343_s_at"/>
+ <secondaryRef db="Affymetrix" id="211809_x_at"/>
+ <secondaryRef db="Affymetrix" id="38951_at"/>
+ <secondaryRef db="Affymetrix" id="38952_s_at"/>
+ <secondaryRef db="Affymetrix" id="g178319_3p_a_at"/>
+ <secondaryRef db="Affymetrix" id="g178319_3p_x_at"/>
+ <secondaryRef db="Affymetrix" id="g180828_3p_a_at"/>
+ <secondaryRef db="Affymetrix" id="g4885144_3p_x_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mvaerthkaa atgargpgel gapgtvalva araergarlp
+ spgscglltl alcslalsll ahfrtaelqa rvlrleaerg
+ eqqmetailg rvnqlldekw klhsrrrrea pktspgcncp
+ pafqgptgrp glpgdkgaig mpgrvgspgd aglsiigprg
+ ppgqpgtrgf pgfpgpigld gkpghpgpkg dmgltgppgq
+ pgpqgqkgek gqcgeyphre clssmpaalr ssqiialkll
+ pllnsvrlap ppvikrrtfq geqsqasiqg ppgppgppgp
+ sgplghpglp gpmgppglpg ppgpkgdpgi qgyhgrkger
+ gmpgmpgkhg akgapgiava gmkgepgipg tkgekgaegs
+ pglpgllgqk gekgdagnsi gggrgepgpp glpgppgpkg
+ eagvdgqvgp pgqpgdkger gaageqgpdg pkgskgepgk
+ gemvdyngni nealqeirtl almgppglpg qigppgapgi
+ pgqkgeiglp gppghdgekg prgkpgdmgp pgpqgppgkd
+ gppgvkgeng hpgspgekge kgetgqagsp gekgeagekg
+ npgaevpglp gpegppgppg lqgvpgpkge agldgakgek
+ gfqgekgdrg plglpgasgl dgrpgppgtp gpigvpgpag
+ pkgergskgd pgmtgptgaa glpglhgppg dkgnrgergk
+ kgsrgpkgdk gdqgapglda pcplgedglp vqgcwnk </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-2796">
+ <names>
+ <shortLabel>Fibrinogen, alpha chain</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00619"/>
+ <secondaryRef db="PubMed" id="6500566"/>
+ <secondaryRef db="RefSeq" id="NP_000499"/>
+ <secondaryRef db="Affymetrix" id="205649_s_at"/>
+ <secondaryRef db="Affymetrix" id="205650_s_at"/>
+ <secondaryRef db="Affymetrix" id="231671_at"/>
+ <secondaryRef db="Affymetrix" id="38825_at"/>
+ <secondaryRef db="Affymetrix" id="g11761627_3p_s_at"/>
+ <secondaryRef db="Affymetrix" id="g11761628_3p_s_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.326487.0.A1_3p_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mfsmrivclv lsvvgtawta dsgegdflae gggvrgprvv
+ erhqsackds dwpfcsdedw nykcpsgcrm kglidevnqd
+ ftnrinklkn slfeyqknnk dshslttnim eilrgdfssa
+ nnrdntynrv sedlrsriev lkrkviekvq hiqllqknvr
+ aqlvdmkrle vdidikirsc rgscsralar evdlkdyedq
+ qkqleqviak dllpsrdrqh lplikmkpvp dlvpgnfksq
+ lqkvppewka ltdmpqmrme lerpggneit rggstsygtg
+ setesprnps sagswnsgss gpgstgnrnp gssgtggtat
+ wkpgssgpgs tgswnsgssg tgstgnqnpg sprpgstgtw
+ npgssergsa ghwtsessvs gstgqwhses gsfrpdspgs
+ gnarpnnpdw gtfeevsgnv spgtrreyht eklvtskgdk
+ elrtgkekvt sgsttttrrs csktvtktvi gpdghkevtk
+ evvtsedgsd cpeamdlgtl sgigtldgfr hrhpdeaaff
+ dtastgktfp gffspmlgef vsetesrgse sgiftntkes
+ sshhpgiaef psrgksssys kqftsstsyn rgdstfesks
+ ykmadeagse adhegthstk rghaksrpvr dcddvlqthp
+ sgtqsgifni klpgsskifs vycdqetslg gwlliqqrmd
+ gslnfnrtwq dykrgfgsln degegefwlg ndylhlltqr
+ gsvlrveled wagneayaey hfrvgseaeg yalqvssyeg
+ tagdaliegs veegaeytsh nnmqfstfdr dadqweenca
+ evygggwwyn ncqaanlngi yypggsydpr nnspyeieng
+ vvwvsfrgad yslravrmki rplvtq </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-2425">
+ <names>
+ <shortLabel>S100 Calcium binding protein A9</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00472"/>
+ <secondaryRef db="PubMed" id="7759097"/>
+ <secondaryRef db="RefSeq" id="NP_002956"/>
+ <secondaryRef db="Affymetrix" id="203535_at"/>
+ <secondaryRef db="Affymetrix" id="41471_at"/>
+ <secondaryRef db="Affymetrix" id="g9845520_3p_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mtckmsqler nietiintfh qysvklghpd tlnqgefkel
+ vrkdlqnflk kenknekvie himedldtna dkqlsfeefi
+ mlmarltwas hekmhegdeg pghhhkpglg egtp </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-1064">
+ <names>
+ <shortLabel>NPR-C</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00167"/>
+ <secondaryRef db="RefSeq" id="NP_000899"/>
+ <secondaryRef db="Affymetrix" id="219789_at"/>
+ <secondaryRef db="Affymetrix" id="219790_s_at"/>
+ <secondaryRef db="Affymetrix" id="34519_at"/>
+ <secondaryRef db="Affymetrix" id="g4505440_3p_a_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.123655.0.S2_3p_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mpsllvltfs pcvllgwall aggtggggvg gggggagigg
+ grqerealpp qkievlvllp qddsylfslt rvrpaieyal
+ rsvegngtgr rllppgtrfq vayedsdcgn ralfslvdrv
+ aaargakpdl ilgpvceyaa apvarlashw dlpmlsagal
+ aagfqhkdse yshltrvapa yakmgemmla lfrhhhwsra
+ alvysddkle rncyftlegv hevfqeeglh tsiysfdetk
+ dldledivrn iqaservvim cassdtirsi mlvahrhgmt
+ sgdyaffnie lfnsssygdg swkrgdkhdf eakqaysslq
+ tvtllrtvkp efekfsmevk ssvekqglnm edyvnmfveg
+ fhdaillyvl alhevlragy skkdggkiiq qtwnrtfegi
+ agqvsidang drygdfsvia mtdveagtqe vigdyfgkeg
+ rfemrpnvky pwgplklrid enrivehtns spckscglee
+ savtgivvga llgagllmaf yffrkkyrit ierrtqqees
+ nlgkhrelre dsirshfsva </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-2345">
+ <names>
+ <shortLabel>Cyclin dependent kinase 5</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00449"/>
+ <secondaryRef db="PubMed" id="8275715"/>
+ <secondaryRef db="RefSeq" id="NP_004926"/>
+ <secondaryRef db="Affymetrix" id="204247_s_at"/>
+ <secondaryRef db="Affymetrix" id="1206_at"/>
+ <secondaryRef db="Affymetrix" id="40549_at"/>
+ <secondaryRef db="Affymetrix" id="g4826674_3p_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mqkyekleki gegtygtvfk aknretheiv alkrvrlddd
+ degvpssalr eicllkelkh knivrlhdvl hsdkkltlvf
+ efcdqdlkky fdscngdldp eivksflfql lkglgfchsr
+ nvlhrdlkpq nllinrngel kladfglara fgipvrcysa
+ evvtlwyrpp dvlfgaklys tsidmwsagc ifaelanagr
+ plfpgndvdd qlkrifrllg tpteeqwpsm tklpdykpyp
+ mypattslvn vvpklnatgr dllqnllkcn pvqrisaeea
+ lqhpyfsdfc pp </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-2972">
+ <names>
+ <shortLabel>Exostosin 1</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00598"/>
+ <secondaryRef db="PubMed" id="1757967"/>
+ <secondaryRef db="RefSeq" id="NP_000118"/>
+ <secondaryRef db="Affymetrix" id="201995_at"/>
+ <secondaryRef db="Affymetrix" id="222_at"/>
+ <secondaryRef db="Affymetrix" id="32164_at"/>
+ <secondaryRef db="Affymetrix" id="g4557570_3p_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mqakkryfil lsagsclall fyfgglqfra srshsrreeh
+ sgrnglhhps pdhfwprfpe plrpfvpwdq lenedssvhi
+ sprqkrdans siykgkkcrm escfdftlck kngfkvyvyp
+ qqkgekiaes yqnilaaieg srfytsdpsq aclfvlsldt
+ ldrdqlspqy vhnlrskvqs lhlwnngrnh lifnlysgtw
+ pdytedvgfd igqamlakas istenfrpnf dvsiplfskd
+ hprtggergf lkfntipplr kymlvfkgkr yltgigsdtr
+ nalyhvhnge dvvllttckh gkdwqkhkds rcdrdnteye
+ kydyremlhn atfclvprgr rlgsfrflea lqaacvpvml
+ sngwelpfse vinwnqaavi gderlllqip stirsihqdk
+ ilalrqqtqf lweayfssve kivlttleii qdrifkhisr
+ nsliwnkhpg glfvlpqyss ylgdfpyyya nlglkppskf
+ tavihavtpl vsqsqpvlkl lvaaaksqyc aqiivlwncd
+ kplpakhrwp atavpvvvie geskvmssrf lpydniitda
+ vlsldedtvl sttevdfaft vwqsfperiv gyparshfwd
+ nskerwgyts kwtndysmvl tgaaiyhkyy hylyshylpa
+ slknmvdqla ncedilmnfl vsavtklppi kvtqkkqyke
+ tmmgqtsras rwadpdhfaq rqscmntfas wfgymplihs
+ qmrldpvlfk dqvsilrkky rdierl </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-2280">
+ <names>
+ <shortLabel>Creatine kinase sarcomeric mitochondrial</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00425"/>
+ <secondaryRef db="RefSeq" id="NP_001816"/>
+ <secondaryRef db="Affymetrix" id="205295_at"/>
+ <secondaryRef db="Affymetrix" id="37592_at"/>
+ <secondaryRef db="Affymetrix" id="g4502854_3p_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>masifskllt grnasllfat mgtsvlttgy llnrqkvcae
+ vreqprlfpp sadypdlrkh nncmaecltp aiysklrnkv
+ tpngytldqc iqtgvdnpgh pfiktvgmva gdeesyevfa
+ dlfdpviklr hngydprvmk httdldaski tqgqfdehyv
+ lssrvrtgrs irglslppac traerreven vaitaleglk
+ gdlagryykl semteqdqqr liddhflfdk pvsplltcag
+ mardwpdarg iwhnydktfl iwineedhtr vismekggnm
+ krvferfcrg lkeverliqe rgwefmwner lgyiltcpsn
+ lgtglragvh vripklskdp rfskilenlr lqkrgtggvd
+ taavadvydi snidrigrse velvqividg vnylvdcekk
+ lergqdikvp pplpqfgkk </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-1184">
+ <names>
+ <shortLabel>17-Beta hydroxysteroid dehydrogenase I</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00185"/>
+ <secondaryRef db="PubMed" id="1977681"/>
+ <secondaryRef db="RefSeq" id="NP_000404"/>
+ <secondaryRef db="Affymetrix" id="205829_at"/>
+ <secondaryRef db="Affymetrix" id="228595_at"/>
+ <secondaryRef db="Affymetrix" id="33141_at"/>
+ <secondaryRef db="Affymetrix" id="602_s_at"/>
+ <secondaryRef db="Affymetrix" id="g4504500_3p_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.85279.1.A1_3p_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>martvvlitg cssgiglhla vrlasdpsqs fkvyatlrdl
+ ktqgrlweaa ralacppgsl etlqldvrds ksvaaarerv
+ tegrvdvlvc naglgllgpl ealgedavas vldvnvvgtv
+ rmlqaflpdm krrgsgrvlv tgsvgglmgl pfndvycask
+ faleglcesl avlllpfgvh lsliecgpvh tafmekvlgs
+ peevldrtdi htfhrfyqyl ahskqvfrea aqnpeevaev
+ fltalrapkp tlryftterf lpllrmrldd psgsnyvtam
+ hrevfgdvpa kaeagaeagg gagpgaedea grsavgdpel
+ gdppaapq </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-3025">
+ <names>
+ <shortLabel>Glutathione S transferase 3</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00614"/>
+ <secondaryRef db="PubMed" id="7587384"/>
+ <secondaryRef db="RefSeq" id="NP_000843"/>
+ <secondaryRef db="Affymetrix" id="200824_at"/>
+ <secondaryRef db="Affymetrix" id="33396_at"/>
+ <secondaryRef db="Affymetrix" id="829_s_at"/>
+ <secondaryRef db="Affymetrix" id="200824_3p_at"/>
+ <secondaryRef db="Affymetrix" id="g6552334_3p_at"/>
+ <secondaryRef db="Affymetrix" id="g6552334_3p_s_at"/>
+ <secondaryRef db="Affymetrix" id="g6552334_3p_x_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mppytvvyfp vrgrcaalrm lladqgqswk eevvtvetwq
+ egslkascly gqlpkfqdgd ltlyqsntil rhlgrtlgly
+ gkdqqeaalv dmvndgvedl rckyisliyt nyeagkddyv
+ kalpgqlkpf etllsqnqgg ktfivgdqis fadynlldll
+ lihevlapgc ldafpllsay vgrlsarpkl kaflaspeyv
+ nlpingngkq </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-1989">
+ <names>
+ <shortLabel>Fibulin 1</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00629"/>
+ <secondaryRef db="PubMed" id="7842734"/>
+ <secondaryRef db="RefSeq" id="NP_006477"/>
+ <secondaryRef db="Affymetrix" id="201787_at"/>
+ <secondaryRef db="Affymetrix" id="202994_s_at"/>
+ <secondaryRef db="Affymetrix" id="202995_s_at"/>
+ <secondaryRef db="Affymetrix" id="207834_at"/>
+ <secondaryRef db="Affymetrix" id="207835_at"/>
+ <secondaryRef db="Affymetrix" id="38026_at"/>
+ <secondaryRef db="Affymetrix" id="38027_at"/>
+ <secondaryRef db="Affymetrix" id="g4503662_3p_at"/>
+ <secondaryRef db="Affymetrix" id="g5922006_3p_at"/>
+ <secondaryRef db="Affymetrix" id="g5922008_3p_s_at"/>
+ <secondaryRef db="Affymetrix" id="g5922010_3p_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.79732.0.S2_3p_s_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>meraapsrrv plpllllggl allaagvdad vlleaccadg
+ hrmathqkdc slpyateske crmvqeqcch sqleelhcat
+ gislaneqdr catphgdnas leatfvkrcc hccllgraaq
+ aqgqsceysl mvgyqcgqvf raccvksqet gdldvgglqe
+ tdkiieveee qedpylndrc rgggpckqqc rdtgdevvcs
+ cfvgyqllsd gvscedvnec itgshscrlg escintvgsf
+ rcqrdsscgt gyeltednsc kdidecesgi hnclpdficq
+ ntlgsfrcrp klqcksgfiq dalgncidin eclsisapcp
+ ightcinteg sytcqknvpn cgrgyhlnee gtrcvdvdec
+ appaepcgkg hrcvnspgsf rcecktgyyf dgisrmcvdv
+ necqrypgrl cghkcentlg sylcscsvgf rlsvdgrsce
+ dinecssspc sqecanvygs yqcycrrgyq lsdvdgvtce
+ didecalptg ghicsyrcin ipgsfqcscp ssgyrlapng
+ rncqdidecv tgihncsine tcfniqgafr clafecpeny
+ rrsaatlqqe ktdtvrciks crpndvtcvf dpvhtishtv
+ islptfreft rpeeiiflra itpphpasqa niifditegn
+ lrdsfdiikr ymdgmtvgvv rqvrpivgpf havlklemny
+ vvggvvshrn vvnvrifvse ywf </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-2792">
+ <names>
+ <shortLabel>Nidogen 1</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00574"/>
+ <secondaryRef db="PubMed" id="2471408"/>
+ <secondaryRef db="RefSeq" id="NP_002499"/>
+ <secondaryRef db="Affymetrix" id="1561082_at"/>
+ <secondaryRef db="Affymetrix" id="202007_at"/>
+ <secondaryRef db="Affymetrix" id="202008_s_at"/>
+ <secondaryRef db="Affymetrix" id="35366_at"/>
+ <secondaryRef db="Affymetrix" id="g4505394_3p_a_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.62041.0.S2_3p_at"/>
+ <secondaryRef db="Affymetrix" id="Hs2.396253.1.S1_3p_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mlasssrira awtralllpl llagpvgcls rqelfpfgpg
+ qgdleledgd dfvspalels galrfydrsd idavyvttng
+ iiatseppak eshpglfppt fgavapflad ldttdglgkv
+ yyredlspsi tqraaecvhr gfpeisfqps savvvtwesv
+ apyqgpsrdp dqkgkrntfq avlassdsss yaiflypedg
+ lqfhttfskk ennqvpavva fsqgsvgflw ksngaynifa
+ ndresienla kssnsgqqgv wvfeigspat tngvvpadvi
+ lgtedgaeyd dededydlat trlgledvgt tpfsykalrr
+ ggadtysvps vlsprraate rplgpptert rsfqlavetf
+ hqqhpqvidv deveetgvvf syntdsrqtc annrhqcsvh
+ aecrdyatgf ccscvagytg ngrqcvaegs pqrvngkvkg
+ rifvgssqvp ivfentdlhs yvvmnhgrsy taistipetv
+ gysllplapv ggiigwmfav eqdgfkngfs itggeftrqa
+ evtfvghpgn lvikqrfsgi dehghltidt elegrvpqip
+ fgssvhiepy telyhystsv itssstreyt vteperdgas
+ psriytyqwr qtitfqecvh ddsrpalpst qqlsvdsvfv
+ lynqeekilr yafsnsigpv regspdalqn pcyigthgcd
+ tnaacrpgpr tqftcecsig frgdgrtcyd idecseqpsv
+ cgshticnnh pgtfrcecve gyqfsdegtc vavvdqrpin
+ ycetglhncd ipqraqciyt ggssytcscl pgfsgdgqac
+ qdvdecqpsr chpdafcynt pgsftcqckp gyqgdgfrcv
+ pgevektrcq herehilgaa gatdpqrpip pglfvpecda
+ hghyaptqch gstgycwcvd rdgrevegtr trpgmtppcl
+ stvappihqg pavptavipl ppgthllfaq tgkierlple
+ gntmrkteak aflhvpakvi iglafdcvdk mvywtditep
+ sigraslhgg epttiirqdl gspegiavdh lgrnifwtds
+ nldrievakl dgtqrrvlfe tdlvnprgiv tdsvrgnlyw
+ tdwnrdnpki etsymdgtnr rilvqddlgl pnglhfdafs
+ sqlcwvdagt nraeclnpsq psrrkalegl qypfavtsyg
+ knlyftdwkm nsvvaldlai sketdafqph kqtrlygitt
+ alsqcpqghn ycsvnnggct hlclatpgsr tcrcpdntlg vdcierk </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-1225">
+ <names>
+ <shortLabel>Interleukin 8</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00909"/>
+ <secondaryRef db="PubMed" id="10343098"/>
+ <secondaryRef db="RefSeq" id="NP_000575"/>
+ <secondaryRef db="Affymetrix" id="202859_x_at"/>
+ <secondaryRef db="Affymetrix" id="211506_s_at"/>
+ <secondaryRef db="Affymetrix" id="1369_s_at"/>
+ <secondaryRef db="Affymetrix" id="35372_r_at"/>
+ <secondaryRef db="Affymetrix" id="g10834977_3p_at"/>
+ <secondaryRef db="Affymetrix" id="g10834977_3p_x_at"/>
+ <secondaryRef db="Affymetrix" id="g12641914_3p_a_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mtsklavall aaflisaalc egavlprsak elrcqcikty
+ skpfhpkfik elrviesgph canteiivkl sdgrelcldp
+ kenwvqrvve kflkraens </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-545">
+ <names>
+ <shortLabel>Glyceraldehyde 3 phosphate dehydrogenase</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00713"/>
+ <secondaryRef db="RefSeq" id="NP_002037"/>
+ <secondaryRef db="Affymetrix" id="212581_x_at"/>
+ <secondaryRef db="Affymetrix" id="213453_x_at"/>
+ <secondaryRef db="Affymetrix" id="217398_x_at"/>
+ <secondaryRef db="Affymetrix" id="234954_at"/>
+ <secondaryRef db="Affymetrix" id="AFFX-HUMGAPDH/M33197_3_at"/>
+ <secondaryRef db="Affymetrix" id="AFFX-HUMGAPDH/M33197_5_at"/>
+ <secondaryRef db="Affymetrix" id="AFFX-HUMGAPDH/M33197_M_at"/>
+ <secondaryRef db="Affymetrix" id="35905_s_at"/>
+ <secondaryRef db="Affymetrix" id="AFFX-HUMGAPDH/M33197_3_st"/>
+ <secondaryRef db="Affymetrix" id="AFFX-HUMGAPDH/M33197_5_st"/>
+ <secondaryRef db="Affymetrix" id="AFFX-HUMGAPDH/M33197_M_st"/>
+ <secondaryRef db="Affymetrix" id="217398_3p_x_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.169476.4.A1_3p_s_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.169476.5.A1_3p_s_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.247894.0.S1_3p_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mgkvkvgvng fgrigrlvtr aafnsgkvdi vaindpfidl
+ nymvymfqyd sthgkfhgtv kaengklvin gnpitifqer
+ dpskikwgda gaeyvvestg vfttmekaga hlqggakrvi
+ isapsadapm fvmgvnheky dnslkiisna scttnclapl
+ akvihdnfgi veglmttvha itatqktvdg psgklwrdgr
+ galqniipas tgaakavgkv ipeldgkltg mafrvptanv
+ svvdltcrle kpakyddikk vvkqasegpl kgilgytehq
+ vvssdfnsdt hsstfdagag ialndhfvkl iswydnefgy
+ snrvvdlmah maske </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-2423">
+ <names>
+ <shortLabel>S100 Calcium binding protein A8</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00471"/>
+ <secondaryRef db="PubMed" id="7759097"/>
+ <secondaryRef db="RefSeq" id="NP_002955"/>
+ <secondaryRef db="Affymetrix" id="202917_s_at"/>
+ <secondaryRef db="Affymetrix" id="214370_at"/>
+ <secondaryRef db="Affymetrix" id="41096_at"/>
+ <secondaryRef db="Affymetrix" id="202917_3p_s_at"/>
+ <secondaryRef db="Affymetrix" id="g9845519_3p_s_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.100000.1.A1_3p_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mltelekaln siidvyhkys likgnfhavy rddlkkllet
+ ecpqyirkkg advwfkeldi ntdgavnfqe flilvikmgv
+ aahkkshees hke </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-2973">
+ <names>
+ <shortLabel>Exostosin 2</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00599"/>
+ <secondaryRef db="PubMed" id="8162019"/>
+ <secondaryRef db="RefSeq" id="NP_000392"/>
+ <secondaryRef db="Affymetrix" id="202012_s_at"/>
+ <secondaryRef db="Affymetrix" id="202013_s_at"/>
+ <secondaryRef db="Affymetrix" id="36593_at"/>
+ <secondaryRef db="Affymetrix" id="36594_s_at"/>
+ <secondaryRef db="Affymetrix" id="g4557572_3p_a_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.75334.0.S1_3p_a_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mcasvkynir gpaliprmkt khriyyitlf sivllgliat
+ gmfqfwphsi essndwnvek rsirdvpvvr lpadspiper
+ gdlscrmhtc fdvyrcgfnp knkikvyiya lkkyvddfgv
+ svsntisrey nellmaisds dyytddinra clfvpsidvl
+ nqntlriket aqamaqlsrw drgtnhllfn mlpggppdyn
+ taldvprdra llagggfstw tyrqgydvsi pvysplsaev
+ dlpekgpgpr qyfllssqvg lhpeyredle alqvkhgesv
+ lvldkctnls egvlsvrkrc hkhqvfdypq vlqeatfcvv
+ lrgarlgqav lsdvlqagcv pvviadsyil pfsevldwkr
+ asvvvpeekm sdvysilqsi pqrqieemqr qarwfweayf
+ qsikaialat lqiindriyp yaaisyeewn dppavkwgsv
+ snplflplip pqsqgftaiv ltydrveslf rvitevskvp
+ slskllvvwn nqnknppeds lwpkirvplk vvrtaenkls
+ nrffpydeie teavlaiddd iimltsdelq fgyevwrefp
+ drlvgypgrl hlwdhemnkw kyesewtnev smvltgaafy
+ hkyfnylyty kmpgdiknwv dahmncedia mnflvanvtg
+ kavikvtprk kfkcpectai dglsldqthm versecinkf
+ asvfgtmplk vvehradpvl ykddfpeklk sfpnigsl </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-2061">
+ <names>
+ <shortLabel>Collagen, type X, alpha-1</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00357"/>
+ <secondaryRef db="PubMed" id="1764025"/>
+ <secondaryRef db="RefSeq" id="NP_000484"/>
+ <secondaryRef db="Affymetrix" id="205941_s_at"/>
+ <secondaryRef db="Affymetrix" id="217428_s_at"/>
+ <secondaryRef db="Affymetrix" id="38566_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.179729.0.S1_3p_a_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.179729.1.S1_3p_a_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mlpqipflll vslnlvhgvf yaeryqmptg ikgplpntkt
+ qffipytiks kgiavrgeqg tpgppgpagp rghpgpsgpp
+ gkpgygspgl qgepglpgpp gpsavgkpgv pglpgkpger
+ gpygpkgdvg paglpgprgp pgppgipgpa gisvpgkpgq
+ qgptgapgpr gfpgekgapg vpgmngqkge mgygapgrpg
+ erglpgpqgp tgpsgppgvg krgengvpgq pgikgdrgfp
+ gemgpigppg pqgppgergp egigkpgaag apgqpgipgt
+ kglpgapgia gppgppgfgk pglpglkger gpaglpggpg
+ akgeqgpagl pgkpgltgpp gnmgpqgpkg ipgshglpgp
+ kgetgpagpa gypgakgerg spgsdgkpgy pgkpgldgpk
+ gnpglpgpkg dpgvggppgl pgpvgpagak gmpghngeag
+ prgapgipgt rgpigppgip gfpgskgdpg spgppgpagi
+ atkglngptg ppgppgprgh sgepglpgpp gppgppgqav
+ mpegfikagq rpslsgtplv sanqgvtgmp vsaftvilsk
+ aypaigtpip fdkilynrqq hydprtgift cqipgiyyfs
+ yhvhvkgthv wvglykngtp vmytydeytk gyldqasgsa
+ iidltendqv wlqlpnaesn glysseyvhs sfsgflvapm </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-1206">
+ <names>
+ <shortLabel>HLA-E</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00877"/>
+ <secondaryRef db="RefSeq" id="NP_005507"/>
+ <secondaryRef db="Affymetrix" id="200904_at"/>
+ <secondaryRef db="Affymetrix" id="200905_x_at"/>
+ <secondaryRef db="Affymetrix" id="217456_x_at"/>
+ <secondaryRef db="Affymetrix" id="32321_at"/>
+ <secondaryRef db="Affymetrix" id="217456_3p_x_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.181392.0.A2_3p_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.181392.1.A1_3p_a_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.181392.1.A1_3p_x_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mvdgtlllll sealaltqtw agshslkyfh tsvsrpgrge
+ prfisvgyvd dtqfvrfdnd aasprmvpra pwmeqegsey
+ wdretrsard taqifrvnlr tlrgyynqse agshtlqwmh
+ gcelgpdgrf lrgyeqfayd gkdyltlned lrswtavdta
+ aqiseqksnd aseaehqray ledtcvewlh kylekgketl
+ lhleppkthv thhpisdhea tlrcwalgfy paeitltwqq
+ dgeghtqdte lvetrpagdg tfqkwaavvv psgeeqrytc
+ hvqheglpep vtlrwkpasq ptipivgiia glvllgsvvs
+ gavvaaviwr kkssghflpt ggkggsyska ewsdsaqgse
+ shsl </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-1183">
+ <names>
+ <shortLabel>Sialyltransferase 1</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00184"/>
+ <secondaryRef db="PubMed" id="7786324"/>
+ <secondaryRef db="RefSeq" id="NP_775323"/>
+ <secondaryRef db="Affymetrix" id="201998_at"/>
+ <secondaryRef db="Affymetrix" id="214970_s_at"/>
+ <secondaryRef db="Affymetrix" id="214971_s_at"/>
+ <secondaryRef db="Affymetrix" id="41352_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.2554.0.A2_3p_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.2554.1.A1_3p_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.2554.1.A1_3p_x_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.2554.1.S1_3p_a_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mihtnlkkkf sccvlvfllf avicvwkekk kgsyydsfkl
+ qtkefqvlks lgklamgsds qsvsssstqd phrgrqtlgs
+ lrglakakpe asfqvwnkds ssknliprlq kiwknylsmn
+ kykvsykgpg pgikfsaeal rchlrdhvnv smvevtdfpf
+ ntsewegylp kesirtkagp wgrcavvssa gslkssqlgr
+ eiddhdavlr fngaptanfq qdvgtkttir lmnsqlvtte
+ krflkdslyn egilivwdps vyhsdipkwy qnpdynffnn
+ yktyrklhpn qpfyilkpqm pwelwdilqe ispeeiqpnp
+ pssgmlgiii mmtlcdqvdi yeflpskrkt dvcyyyqkff
+ dsactmgayh pllyeknlvk hlnqgtdedi yllgkatlpg frtihc </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-321">
+ <names>
+ <shortLabel>Grb2</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00150"/>
+ <secondaryRef db="PubMed" id="7806213"/>
+ <secondaryRef db="RefSeq" id="NP_002077"/>
+ <secondaryRef db="Affymetrix" id="215075_s_at"/>
+ <secondaryRef db="Affymetrix" id="223049_at"/>
+ <secondaryRef db="Affymetrix" id="228572_at"/>
+ <secondaryRef db="Affymetrix" id="1565_s_at"/>
+ <secondaryRef db="Affymetrix" id="33855_at"/>
+ <secondaryRef db="Affymetrix" id="g12005510_3p_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.296381.1.A1_3p_a_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.6289.1.A1_3p_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>meaiakydfk ataddelsfk rgdilkvlne ecdqnwykae
+ lngkdgfipk nyiemkphpw ffgkipraka eemlskqrhd
+ gaflireses apgdfslsvk fgndvqhfkv lrdgagkyfl
+ wvvkfnslne lvdyhrstsv srnqqiflrd ieqvpqqpty
+ vqalfdfdpq edgelgfrrg dfihvmdnsd pnwwkgachg
+ qtgmfprnyv tpvnrnv </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-1379">
+ <names>
+ <shortLabel>Trefoil factor 1</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00219"/>
+ <secondaryRef db="PubMed" id="9070946"/>
+ <secondaryRef db="RefSeq" id="NP_003216"/>
+ <secondaryRef db="Affymetrix" id="205009_at"/>
+ <secondaryRef db="Affymetrix" id="31798_at"/>
+ <secondaryRef db="Affymetrix" id="g4507450_3p_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>matmenkvic alvlvsmlal gtlaeaqtet ctvaprerqn
+ cgfpgvtpsq cankgccfdd tvrgvpwcfy pntidvppee
+ ecef </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-3776">
+ <names>
+ <shortLabel>H2AZ histone</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00823"/>
+ <secondaryRef db="PubMed" id="8020992"/>
+ <secondaryRef db="RefSeq" id="NP_002097"/>
+ <secondaryRef db="Affymetrix" id="200853_at"/>
+ <secondaryRef db="Affymetrix" id="213911_s_at"/>
+ <secondaryRef db="Affymetrix" id="39337_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.119192.1.A1_3p_a_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>maggkagkds gkaktkavsr sqraglqfpv grihrhlksr
+ ttshgrvgat aavysaaile yltaevlela gnaskdlkvk
+ ritprhlqla irgdeeldsl ikatiagggv iphihkslig
+ kkgqqktv </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-3688">
+ <names>
+ <shortLabel>Hemoglobin beta chain</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00786"/>
+ <secondaryRef db="PubMed" id="4053691"/>
+ <secondaryRef db="RefSeq" id="NP_000509"/>
+ <secondaryRef db="Affymetrix" id="1562981_at"/>
+ <secondaryRef db="Affymetrix" id="209116_x_at"/>
+ <secondaryRef db="Affymetrix" id="211696_x_at"/>
+ <secondaryRef db="Affymetrix" id="217232_x_at"/>
+ <secondaryRef db="Affymetrix" id="31687_f_at"/>
+ <secondaryRef db="Affymetrix" id="32052_at"/>
+ <secondaryRef db="Affymetrix" id="g13549111_3p_at"/>
+ <secondaryRef db="Affymetrix" id="g179408_3p_s_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.155376.1.A1_3p_s_at"/>
+ <secondaryRef db="Affymetrix" id="Hs2.339844.1.S1_3p_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mvhltpeeks avtalwgkvn vdevggealg rllvvypwtq
+ rffesfgdls tpdavmgnpk vkahgkkvlg afsdglahld
+ nlkgtfatls elhcdklhvd penfrllgnv lvcvlahhfg
+ keftppvqaa yqkvvagvan alahkyh </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-518">
+ <names>
+ <shortLabel>Collagen, type IV, alpha 1</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00359"/>
+ <secondaryRef db="PubMed" id="2891465"/>
+ <secondaryRef db="RefSeq" id="NP_001836"/>
+ <secondaryRef db="Affymetrix" id="211980_at"/>
+ <secondaryRef db="Affymetrix" id="211981_at"/>
+ <secondaryRef db="Affymetrix" id="39333_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.119129.0.A1_3p_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.119129.0.A2_3p_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mgprlsvwll llpaalllhe ehsraaakgg cagsgcgkcd
+ chgvkgqkge rglpglqgvi gfpgmqgpeg pqgppgqkgd
+ tgepglpgtk gtrgppgasg ypgnpglpgi pgqdgppgpp
+ gipgcngtkg ergplgppgl pgfagnpgpp glpgmkgdpg
+ eilghvpgml lkgergfpgi pgtpgppglp glqgpvgppg
+ ftgppgppgp pgppgekgqm glsfqgpkgd kgdqgvsgpp
+ gvpgqaqvqe kgdfatkgek gqkgepgfqg mpgvgekgep
+ gkpgprgkpg kdgdkgekgs pgfpgepgyp gligrqgpqg
+ ekgeagppgp pgivigtgpl gekgergypg tpgprgepgp
+ kgfpglpgqp gppglpvpgq agapgfpger gekgdrgfpg
+ tslpgpsgrd glpgppgspg ppgqpgytng ivecqpgppg
+ dqgppgipgq pgfigeigek gqkgesclic didgyrgppg
+ pqgppgeigf pgqpgakgdr glpgrdgvag vpgpqgtpgl
+ igqpgakgep gefyfdlrlk gdkgdpgfpg qpgmpgrags
+ pgrdghpglp gpkgspgsvg lkgergppgg vgfpgsrgdt
+ gppgppgygp agpigdkgqa gfpggpgspg lpgpkgepgk
+ ivplpgppga eglpgspgfp gpqgdrgfpg tpgrpglpge
+ kgavgqpgig fpgppgpkgv dglpgdmgpp gtpgrpgfng
+ lpgnpgvqgq kgepgvglpg lkglpglpgi pgtpgekgsi
+ gvpgvpgehg aigppglqgi rgepgppglp gsvgspgvpg
+ igppgargpp ggqgppglsg ppgikgekgf pgfpgldmpg
+ pkgdkgaqgl pgitgqsglp glpgqqgapg ipgfpgskge
+ mgvmgtpgqp gspgpvgapg lpgekgdhgf pgssgprgdp
+ glkgdkgdvg lpgkpgsmdk vdmgsmkgqk gdqgekgqig
+ pigekgsrgd pgtpgvpgkd gqagqpgqpg pkgdpgisgt
+ pgapglpgpk gsvggmglpg tpgekgvpgi pgpqgspglp
+ gdkgakgekg qagppgigip glrgekgdqg iagfpgspge
+ kgekgsigip gmpgspglkg spgsvgypgs pglpgekgdk
+ glpgldgipg vkgeaglpgt pgptgpagqk gepgsdgipg
+ sagekgepgl pgrgfpgfpg akgdkgskge vgfpglagsp
+ gipgskgeqg fmgppgpqgq pglpgspgha tegpkgdrgp
+ qgqpglpglp gpmgppglpg idgvkgdkgn pgwpgapgvp
+ gpkgdpgfqg mpgiggspgi tgskgdmgpp gvpgfqgpkg
+ lpglqgikgd qgdqgvpgak glpgppgppg pydiikgepg
+ lpgpegppgl kglqglpgpk gqqgvtglvg ipgppgipgf
+ dgapgqkgem gpagptgprg fpgppgpdgl pgsmgppgtp
+ svdhgflvtr hsqtiddpqc psgtkilyhg ysllyvqgne
+ rahgqdlgta gsclrkfstm pflfcninnv cnfasrndys
+ ywlstpepmp msmapitgen irpfisrcav ceapamvmav
+ hsqtiqippc psgwsslwig ysfvmhtsag aegsgqalas
+ pgscleefrs apfiechgrg tcnyyanays fwlatierse
+ mfkkptpstl kagelrthvs rcqvcmrrt </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-1995">
+ <names>
+ <shortLabel>Fibulin 2</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00630"/>
+ <secondaryRef db="PubMed" id="7806230"/>
+ <secondaryRef db="RefSeq" id="NP_001989"/>
+ <secondaryRef db="Affymetrix" id="203886_s_at"/>
+ <secondaryRef db="Affymetrix" id="32783_at"/>
+ <secondaryRef db="Affymetrix" id="g4503664_3p_a_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mvllwepaga wlalglalal gpsvaaaapr qdctgvecpp
+ lencieeale pgaccatcvq qgcacegyqy ydclqggfvr
+ grvpagqsyf vdfgstecsc ppgggkiscq fmlcpelppn
+ cieavvvads cpqcgqvgcv hagheyaagh tvhlppcrac
+ hcpdaggeli cyqlpgchgn fsdaeegdpe rhyedpysyd
+ qevaeveaat alggevqaga vqagaggppa algggsqpls
+ tiqappwpav lprptaaaal gppapvqaka rrvtedseee
+ eeeeeereem avteqlaagg hrgldglptt apagpslpiq
+ eeraeagara eagarpeenl ildaqatsrs tgpegvthap
+ slgkaalvpt qavpgsprdp vkpsphnils tslpdaawip
+ ptrevprkpq vlphshveed tdpnsvhsip rsspegstkd
+ lietccaagq qwaidndecl eipesgtedn vcrtaqrhcc
+ vsylqekscm agvlgakege tcgaedndsc gislykqccd
+ ccglglrvra egqscesnpn lgypcnhvml sccegeepli
+ vpevrrppep aaaprrvsea emagrealsl gteaelpnsl
+ pgddqdecll lpgelcqhlc intvgsyhca cfpgfslqdd
+ grtcrpeghp pqpeapqepa lksefsqvas ntiplplpqp
+ ntckdngpck qvcstvggsa icscfpgyai madgvscedi
+ necvtdlhtc srgehcvntl gsfhcykalt cepgyalkdg
+ ecedvdecam gthtcqpgfl cqntkgsfyc qarqrcmdgf
+ lqdpegncvd inectslsep crpgfscint vgsytcqrnp
+ licargyhas ddgakcvdvn ecetgvhrcg egqvchnlpg
+ syrcdckagf qrdafgrgci dvnecwaspg rlcqhtcent
+ lgsyrcscas gfllaadgkr cedvneceaq rcsqecaniy
+ gsyqcycrqg yqlaedghtc tdidecaqga gilctfrcln
+ vpgsyqcacp eqgytmtang rsckdvdeca lgthncseae
+ tchniqgsfr clrfecppny vqvsktkcer ttchdflecq
+ nsparithyq lnfqtgllvp ahifrigpap aftgdtialn
+ iikgneegyf gtrrlnaytg vvylqravle prdfaldvem
+ klwrqgsvtt flakmhifft tfal </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-3694">
+ <names>
+ <shortLabel>Hemoglobin zeta</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00794"/>
+ <secondaryRef db="RefSeq" id="NP_005323"/>
+ <secondaryRef db="Affymetrix" id="206647_at"/>
+ <secondaryRef db="Affymetrix" id="g6633805_3p_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>msltkterti ivsmwakist qadtigtetl erlflshpqt
+ ktyfphfdlh pgsaqlrahg skvvaavgda vksiddigga
+ lsklselhay ilrvdpvnfk llshcllvtl aarfpadfta
+ eahaawdkfl svvssvltek yr </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-2988">
+ <names>
+ <shortLabel>Coagulation factor XIII, A1</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00604"/>
+ <secondaryRef db="PubMed" id="2903011"/>
+ <secondaryRef db="RefSeq" id="NP_000120"/>
+ <secondaryRef db="Affymetrix" id="203305_at"/>
+ <secondaryRef db="Affymetrix" id="38052_at"/>
+ <secondaryRef db="Affymetrix" id="g9961355_3p_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>msetsrtafg grravppnns naaeddlptv elqgvvprgv
+ nlqeflnvts vhlfkerwdt nkvdhhtdky ennklivrrg
+ qsfyvqidls rpydprrdlf rveyvigryp qenkgtyipv
+ pivselqsgk wgakivmred rsvrlsiqss pkcivgkfrm
+ yvavwtpygv lrtsrnpetd tyilfnpwce ddavyldnek
+ ereeyvlndi gvifygevnd iktrswsygq fedgildtcl
+ yvmdraqmdl sgrgnpikvs rvgsamvnak ddegvlvgsw
+ dniyaygvpp sawtgsvdil leyrssenpv rygqcwvfag
+ vfntflrclg iparivtnyf sahdndanlq mdifleedgn
+ vnskltkdsv wnyhcwneaw mtrpdlpvgf ggwqavdstp
+ qensdgmyrc gpasvqaikh ghvcfqfdap fvfaevnsdl
+ iyitakkdgt hvvenvdath igklivtkqi ggdgmmditd
+ tykfqegqee erlaletalm ygakkplnte gvmksrsnvd
+ mdfevenavl gkdfklsitf rnnshnryti taylsanitf
+ ytgvpkaefk ketfdvtlep lsfkkeavli qageymgqll
+ eqaslhffvt arinetrdvl akqkstvlti peiiikvrgt
+ qvvgsdmtvt vqftnplket lrnvwvhldg pgvtrpmkkm
+ freirpnstv qweevcrpwv sghrkliasm ssdslrhvyg
+ eldvqiqrrp sm </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-1218">
+ <names>
+ <shortLabel>Carcinoembryonic antigen related cell
+ adhesion molecule 1</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00191"/>
+ <secondaryRef db="RefSeq" id="NP_001703"/>
+ <secondaryRef db="Affymetrix" id="206576_s_at"/>
+ <secondaryRef db="Affymetrix" id="209498_at"/>
+ <secondaryRef db="Affymetrix" id="210610_at"/>
+ <secondaryRef db="Affymetrix" id="211883_x_at"/>
+ <secondaryRef db="Affymetrix" id="211889_x_at"/>
+ <secondaryRef db="Affymetrix" id="36082_at"/>
+ <secondaryRef db="Affymetrix" id="988_at"/>
+ <secondaryRef db="Affymetrix" id="g179434_3p_at"/>
+ <secondaryRef db="Affymetrix" id="g4502404_3p_a_at"/>
+ <secondaryRef db="Affymetrix" id="g4502404_3p_x_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.50964.3.S2_3p_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mghlsaplhr vrvpwqglll taslltfwnp pttaqlttes
+ mpfnvaegke vlllvhnlpq qlfgyswykg ervdgnrqiv
+ gyaigtqqat pgpansgret iypnaslliq nvtqndtgfy
+ tlqviksdlv neeatgqfhv ypelpkpsis snnsnpvedk
+ davaftcepe tqdttylwwi nnqslpvspr lqlsngnrtl
+ tllsvtrndt gpyeceiqnp vsanrsdpvt lnvtygpdtp
+ tispsdtyyr pganlslscy aasnppaqys wlingtfqqs
+ tqelfipnit vnnsgsytch annsvtgcnr ttvktiivte
+ lspvvakpqi kaskttvtgd kdsvnltcst ndtgisirwf
+ fknqslpsse rmklsqgntt lsinpvkred agtywcevfn
+ pisknqsdpi mlnvnynalp qenglspgai agivigvval
+ valiavalac flhfgktgra sdqrdltehk psvsnhtqdh
+ sndppnkmne vtystlnfea qqptqptsas psltateiiy
+ sevkkq </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-3395">
+ <names>
+ <shortLabel>Glutathione S-transferase Mu-2</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00710"/>
+ <secondaryRef db="RefSeq" id="NP_000839"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mpmtlgywni rglahsirll leytdssyee kkytmgdapd
+ ydrsqwlnek fklgldfpnl pylidgthki tqsnailryi
+ arkhnlcges ekeqiredil enqfmdsrmq laklcydpdf
+ eklkpeylqa lpemlklysq flgkqpwflg dkitfvdfia
+ ydvlernqvf epscldafpn lkdfisrfeg lekisaymks
+ srflprpvft kmavwgnk </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-1630">
+ <names>
+ <shortLabel>Catalase</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00282"/>
+ <secondaryRef db="PubMed" id="6252821"/>
+ <secondaryRef db="RefSeq" id="NP_001743"/>
+ <secondaryRef db="Affymetrix" id="201432_at"/>
+ <secondaryRef db="Affymetrix" id="211922_s_at"/>
+ <secondaryRef db="Affymetrix" id="215573_at"/>
+ <secondaryRef db="Affymetrix" id="238363_at"/>
+ <secondaryRef db="Affymetrix" id="37009_at"/>
+ <secondaryRef db="Affymetrix" id="g13562131_3p_s_at"/>
+ <secondaryRef db="Affymetrix" id="g4557013_3p_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.287482.0.S1_3p_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>madsrdpasd qmqhwkeqra aqkadvlttg agnpvgdkln
+ vitvgprgpl lvqdvvftde mahfdrerip ervvhakgag
+ afgyfevthd itkyskakvf ehigkktpia vrfstvages
+ gsadtvrdpr gfavkfyted gnwdlvgnnt piffirdpil
+ fpsfihsqkr npqthlkdpd mvwdfwslrp eslhqvsflf
+ sdrgipdghr hmngygshtf klvnangeav yckfhyktdq
+ giknlsveda arlsqedpdy girdlfnaia tgkypswtfy
+ iqvmtfnqae tfpfnpfdlt kvwphkdypl ipvgklvlnr
+ npvnyfaeve qiafdpsnmp pgieaspdkm lqgrlfaypd
+ thrhrlgpny lhipvncpyr arvanyqrdg pmcmqdnqgg
+ apnyypnsfg apeqqpsale hsiqysgevr rfntanddnv
+ tqvrafyvnv lneeqrkrlc eniaghlkda qifiqkkavk
+ nftevhpdyg shiqalldky naekpknaih tfvqsgshla
+ arekanl </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-2422">
+ <names>
+ <shortLabel>CRP1</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00470"/>
+ <secondaryRef db="PubMed" id="9925910"/>
+ <secondaryRef db="RefSeq" id="NP_004069"/>
+ <secondaryRef db="Affymetrix" id="200621_at"/>
+ <secondaryRef db="Affymetrix" id="38700_at"/>
+ <secondaryRef db="Affymetrix" id="g4758085_3p_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mpnwgggkkc gvcqktvyfa eevqcegnsf hkscflcmvc
+ kknldsttva vhgeeiycks cygkkygpkg ygygqgagtl
+ stdkgeslgi kheeapghrp ttnpnaskfa qkiggsercp
+ rcsqavyaae kvigagkswh kacfrcakcg kglesttlad
+ kdgeiyckgc yaknfgpkgf gfgqgagalv hse </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-1210">
+ <names>
+ <shortLabel>5-hydroxytryptamine receptor, 1A</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00190"/>
+ <secondaryRef db="PubMed" id="1685484"/>
+ <secondaryRef db="RefSeq" id="NP_000515"/>
+ <secondaryRef db="Affymetrix" id="221351_at"/>
+ <secondaryRef db="Affymetrix" id="g4504530_3p_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mdvlspgqgn nttsppapfe tggnttgisd vtvsyqvits
+ lllgtlifca vlgnacvvaa ialerslqnv anyligslav
+ tdlmvsvlvl pmaalyqvln kwtlgqvtcd lfialdvlcc
+ tssilhlcai aldrywaitd pidyvnkrtp rpralisltw
+ ligflisipp ilgwrtpedr sdpdactisk dhgytiystf
+ gafyiplllm lvlygrifra arfrirktvk kvektgadtr
+ hgaspapqpk ksvngesgsr nwrlgveska ggalcangav
+ rqgddgaale vievhrvgns kehlplpsea gptpcapasf
+ erknernaea krkmalarer ktvktlgiim gtfilcwlpf
+ fivalvlpfc esschmptll gaiinwlgys nsllnpviya
+ yfnkdfqnaf kkiikcnfcr q </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-3962">
+ <names>
+ <shortLabel>CD179b</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00905"/>
+ <secondaryRef db="PubMed" id="1903358"/>
+ <secondaryRef db="RefSeq" id="NP_064455"/>
+ <secondaryRef db="Affymetrix" id="206660_at"/>
+ <secondaryRef db="Affymetrix" id="38514_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mrpgtgqggl eapgepgpnl rqrwpllllg lavvthgllr
+ ptaasqsral gpgapggssr sslrsrwgrf llqrgswtgp
+ rcwprgfqsk hnsvthvfgs gtqltvlsqp katpsvtlfp
+ psseelqank atlvclmndf ypgiltvtwk adgtpitqgv
+ emttpskqsn nkyaassyls ltpeqwrsrr syscqvmheg
+ stvektvapa ecs </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-2768">
+ <names>
+ <shortLabel>Fibroblast growth factor 1</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00567"/>
+ <secondaryRef db="RefSeq" id="NP_000791"/>
+ <secondaryRef db="Affymetrix" id="1552721_a_at"/>
+ <secondaryRef db="Affymetrix" id="205117_at"/>
+ <secondaryRef db="Affymetrix" id="208240_s_at"/>
+ <secondaryRef db="Affymetrix" id="996_at"/>
+ <secondaryRef db="Affymetrix" id="g7019394_3p_s_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.75297.0.S3_3p_at"/>
+ <secondaryRef db="Affymetrix" id="Hs2.75297.2.S1_3p_s_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>maegeittft altekfnlpp gnykkpklly csngghflri
+ lpdgtvdgtr drsdqhiqlq lsaesvgevy ikstetgqyl
+ amdtdgllyg sqtpneeclf lerleenhyn tyiskkhaek
+ nwfvglkkng sckrgprthy gqkailflpl pvssd </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-699">
+ <names>
+ <shortLabel>Elastase, leukocyte</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00554"/>
+ <secondaryRef db="PubMed" id="7713495"/>
+ <secondaryRef db="RefSeq" id="NP_001963"/>
+ <secondaryRef db="Affymetrix" id="206871_at"/>
+ <secondaryRef db="Affymetrix" id="37096_at"/>
+ <secondaryRef db="Affymetrix" id="g4503548_3p_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mtlgrrlacl flacvlpall lggtalasei vggrrarpha
+ wpfmvslqlr gghfcgatli apnfvmsaah cvanvnvrav
+ rvvlgahnls rreptrqvfa vqrifengyd pvnllndivi
+ lqlngsatin anvqvaqlpa qgrrlgngvq clamgwgllg
+ rnrgiasvlq elnvtvvtsl crrsnvctlv rgrqagvcfg
+ dsgsplvcng lihgiasfvr ggcasglypd afapvaqfvn
+ widsiiqrse dnpcphprdp dpasrth </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-3391">
+ <names>
+ <shortLabel>Glutathione S-transferase Mu-1</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00707"/>
+ <secondaryRef db="RefSeq" id="NP_000552"/>
+ <secondaryRef db="Affymetrix" id="204550_x_at"/>
+ <secondaryRef db="Affymetrix" id="215333_x_at"/>
+ <secondaryRef db="Affymetrix" id="39054_at"/>
+ <secondaryRef db="Affymetrix" id="556_s_at"/>
+ <secondaryRef db="Affymetrix" id="g10835126_3p_s_at"/>
+ <secondaryRef db="Affymetrix" id="g4504178_3p_s_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mpmilgywdi rglahairll leytdssyee kkytmgdapd
+ ydrsqwlnek fklgldfpnl pylidgahki tqsnailcyi
+ arkhnlcget eeekirvdil enqtmdnhmq lgmicynpef
+ eklkpkylee lpeklklyse flgkrpwfag nkitfvdflv
+ ydvldlhrif epkcldafpn lkdfisrfeg lekisaymks
+ srflprpvfs kmavwgnk </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-1034">
+ <names>
+ <shortLabel>FGF receptor 1</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00634"/>
+ <secondaryRef db="PubMed" id="7789168"/>
+ <secondaryRef db="RefSeq" id="NP_000595"/>
+ <secondaryRef db="Affymetrix" id="207822_at"/>
+ <secondaryRef db="Affymetrix" id="207937_x_at"/>
+ <secondaryRef db="Affymetrix" id="210973_s_at"/>
+ <secondaryRef db="Affymetrix" id="211535_s_at"/>
+ <secondaryRef db="Affymetrix" id="215404_x_at"/>
+ <secondaryRef db="Affymetrix" id="226705_at"/>
+ <secondaryRef db="Affymetrix" id="2056_at"/>
+ <secondaryRef db="Affymetrix" id="2057_g_at"/>
+ <secondaryRef db="Affymetrix" id="36168_at"/>
+ <secondaryRef db="Affymetrix" id="424_s_at"/>
+ <secondaryRef db="Affymetrix" id="215404_3p_x_at"/>
+ <secondaryRef db="Affymetrix" id="g13186237_3p_x_at"/>
+ <secondaryRef db="Affymetrix" id="g13186246_3p_a_at"/>
+ <secondaryRef db="Affymetrix" id="g182560_3p_a_at"/>
+ <secondaryRef db="Affymetrix" id="g183882_3p_a_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.306678.0.S1_3p_x_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.748.8.A1_3p_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mwswkcllfw avlvtatlct arpsptlpeq aqpwgapvev
+ esflvhpgdl lqlrcrlrdd vqsinwlrdg vqlaesnrtr
+ itgeevevqd svpadsglya cvtsspsgsd ttyfsvnvsd
+ alpssedddd dddssseeke tdntkpnrmp vapywtspek
+ mekklhavpa aktvkfkcps sgtpnptlrw lkngkefkpd
+ hriggykvry atwsiimdsv vpsdkgnytc iveneygsin
+ htyqldvver sphrpilqag lpanktvalg snvefmckvy
+ sdpqphiqwl khievngski gpdnlpyvqi lktagvnttd
+ kemevlhlrn vsfedageyt clagnsigls hhsawltvle
+ aleerpavmt splyleiiiy ctgafliscm vgsvivykmk
+ sgtkksdfhs qmavhklaks iplrrqvtvs adssasmnsg
+ vllvrpsrls ssgtpmlagv seyelpedpr welprdrlvl
+ gkplgegcfg qvvlaeaigl dkdkpnrvtk vavkmlksda
+ tekdlsdlis ememmkmigk hkniinllga ctqdgplyvi
+ veyaskgnlr eylqarrppg leycynpshn peeqlsskdl
+ vscayqvarg meylaskkci hrdlaarnvl vtednvmkia
+ dfglardihh idyykkttng rlpvkwmape alfdriythq
+ sdvwsfgvll weiftlggsp ypgvpveelf kllkeghrmd
+ kpsnctnely mmmrdcwhav psqrptfkql vedldrival
+ tsnqeyldls mpldqyspsf pdtrsstcss gedsvfshep
+ lpeepclprh paqlangglk rr </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-3444">
+ <names>
+ <shortLabel>CCAAT/Enhancer binding protein gamma</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00738"/>
+ <secondaryRef db="RefSeq" id="NP_001797"/>
+ <secondaryRef db="Affymetrix" id="204203_at"/>
+ <secondaryRef db="Affymetrix" id="225527_at"/>
+ <secondaryRef db="Affymetrix" id="39219_at"/>
+ <secondaryRef db="Affymetrix" id="g4502768_3p_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.7887.0.A1_3p_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mskisqqnst pgvngisvih tqahasglqq vpqlvpagpg
+ gggkavapsk qskksspmdr nsdeyrqrre rnnmavkksr
+ lkskqkaqdt lqrvnqlkee nerleakikl ltkelsvlkd
+ lflehahnla dnvqsisten ttadgdnagq </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-251">
+ <names>
+ <shortLabel>Vitamin D binding protein</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00749"/>
+ <secondaryRef db="PubMed" id="3015768"/>
+ <secondaryRef db="RefSeq" id="NP_000574"/>
+ <secondaryRef db="Affymetrix" id="204965_at"/>
+ <secondaryRef db="Affymetrix" id="32771_at"/>
+ <secondaryRef db="Affymetrix" id="g9845254_3p_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mkrvlvllla vafghalerg rdyeknkvck efshlgkedf
+ tslslvlysr kfpsgtfeqv sqlvkevvsl teaccaegad
+ pdcydtrtsa lsakscesns pfpvhpgtae cctkeglerk
+ lcmaalkhqp qefptyvept ndeiceafrk dpkeyanqfm
+ weystnyeqa plsllvsytk sylsmvgscc tsasptvcfl
+ kerlqlkhls llttlsnrvc sqyaaygekk srlsnlikla
+ qkvptadled vlplaeditn ilskccesas edcmakelpe
+ htvklcdnls tknskfedcc qektamdvfv ctyfmpaaql
+ pelpdvrlpt nkdvcdpgnt kvmdkytfel srrthlpevf
+ lskvleptlk slgeccdved sttcfnakgp llkkelssfi
+ dkgqelcady sentfteykk klaerlkakl peatptelak
+ lvnkrsdfas nccsinsppl ycdseidael knil </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-3695">
+ <names>
+ <shortLabel>Heparin cofactor II</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00795"/>
+ <secondaryRef db="PubMed" id="1671335"/>
+ <secondaryRef db="RefSeq" id="NP_000176"/>
+ <secondaryRef db="Affymetrix" id="205576_at"/>
+ <secondaryRef db="Affymetrix" id="31825_at"/>
+ <secondaryRef db="Affymetrix" id="g7262380_3p_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mkhslnalli fliitsawgg skgpldqlek ggetaqsadp
+ qweqlnnknl smpllpadfh kentvtndwi pegeedddyl
+ dlekifsedd dyidivdsls vsptdsdvsa gnilqlfhgk
+ sriqrlniln akfafnlyrv lkdqvntfdn ifiapvgist
+ amgmislglk getheqvhsi lhfkdfvnas skyeittihn
+ lfrklthrlf rrnfgytlrs vndlyiqkqf pilldfrtkv
+ reyyfaeaqi adfsdpafis ktnnhimklt kglikdalen
+ idpatqmmil nciyfkgswv nkfpvemthn hnfrlnerev
+ vkvsmmqtkg nflaandqel dcdilqleyv ggismlivvp
+ hkmsgmktle aqltprvver wqksmtnrtr evllpkfkle
+ knynlveslk lmgirmlfdk ngnmagisdq riaidlfkhq
+ gtitvneegt qattvttvgf mplstqvrft vdrpflfliy
+ ehrtscllfm grvanpsrs </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-1755">
+ <names>
+ <shortLabel>Cdc2 associated protein CKS2</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00300"/>
+ <secondaryRef db="PubMed" id="8697818"/>
+ <secondaryRef db="RefSeq" id="NP_001818"/>
+ <secondaryRef db="Affymetrix" id="204170_s_at"/>
+ <secondaryRef db="Affymetrix" id="40690_at"/>
+ <secondaryRef db="Affymetrix" id="g4502858_3p_s_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mahkqiyysd kyfdehyeyr hvmlprelsk qvpkthlmse
+ eewrrlgvqq slgwvhymih epephillfr rplpkdqqk </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-2011">
+ <names>
+ <shortLabel>Ciliary neurotrophic factor</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00347"/>
+ <secondaryRef db="PubMed" id="2294592"/>
+ <secondaryRef db="RefSeq" id="NP_000605"/>
+ <secondaryRef db="Affymetrix" id="208597_at"/>
+ <secondaryRef db="Affymetrix" id="34590_at"/>
+ <secondaryRef db="Affymetrix" id="g4758019_3p_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>maftehsplt phrrdlcsrs iwlarkirsd ltaltesyvk
+ hqglnkninl dsadgmpvas tdqwseltea erlqenlqay
+ rtfhvllarl ledqqvhftp tegdfhqaih tlllqvaafa
+ yqieelmill eykiprnead gmpinvgdgg lfekklwglk
+ vlqelsqwtv rsihdlrfis shqtgiparg shyiannkkm </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-3781">
+ <names>
+ <shortLabel>CD74 antigen</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00825"/>
+ <secondaryRef db="PubMed" id="3132422"/>
+ <secondaryRef db="RefSeq" id="NP_004346"/>
+ <secondaryRef db="Affymetrix" id="1567627_at"/>
+ <secondaryRef db="Affymetrix" id="1567628_at"/>
+ <secondaryRef db="Affymetrix" id="209619_at"/>
+ <secondaryRef db="Affymetrix" id="35016_at"/>
+ <secondaryRef db="Affymetrix" id="g188469_3p_at"/>
+ <secondaryRef db="Affymetrix" id="g188469_3p_x_at"/>
+ <secondaryRef db="Affymetrix" id="Hs2.438626.1.A1_3p_at"/>
+ <secondaryRef db="Affymetrix" id="Hs2.438626.1.S1_3p_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mhrrrsrscr edqkpvmddq rdlisnneql pmlgrrpgap
+ eskcsrgaly tgfsilvtll lagqattayf lyqqqgrldk
+ ltvtsqnlql enlrmklpkp pkpvskmrma tpllmqalpm
+ galpqgpmqn atkygnmted hvmhllqnad plkvypplkg
+ sfpenlrhlk ntmetidwkv feswmhhwll femsrhsleq
+ kptdappkes leledpssgl gvtkqdlgpv pm </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-2534">
+ <names>
+ <shortLabel>Desmoplakin</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00513"/>
+ <secondaryRef db="PubMed" id="1889810"/>
+ <secondaryRef db="RefSeq" id="NP_004406"/>
+ <secondaryRef db="Affymetrix" id="200606_at"/>
+ <secondaryRef db="Affymetrix" id="36133_at"/>
+ <secondaryRef db="Affymetrix" id="g4758199_3p_at"/>
+ <secondaryRef db="Affymetrix" id="g4758199_3p_s_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mscnggshpr intlgrmira esgpdlryev tsggggtsrm
+ yysrrgvitd qnsdgycqtg tmsrhqnqnt iqellqncsd
+ clmraelivq pelkygdgiq ltrsreldec faqandqmei
+ ldsliremrq mgqpcdayqk rllqlqeqmr alykaisvpr
+ vrrasskggg gytcqsgsgw deftkhvtse clgwmrqqra
+ emdmvawgvd lasveqhins hrgihnsigd yrwqldkika
+ dlreksaiyq leeeyenllk asfermdhlr qlqniiqats
+ reimwindce eeellydwsd kntniaqkqe afsirmsqle
+ vkekelnklk qesdqlvlnq hpasdkieay mdtlqtqwsw
+ ilqitkcidv hlkenaayfq ffeeaqstea ylkglqdsir
+ kkypcdknmp lqhlleqike lekerekile ykrqvqnlvn
+ kskkivqlkp rnpdyrsnkp iilralcdyk qdqkivhkgd
+ ecilkdnner skwyvtgpgg vdmlvpsvgl iipppnplav
+ dlsckieqyy eailalwnql yinmkslvsw hycmidieki
+ ramtiaklkt mrqedymkti adlelhyqef irnsqgsemf
+ gdddkrkiqs qftdaqkhyq tlviqlpgyp qhqtvtttei
+ thhgtcqdvn hnkvietnre ndkqetwmlm elqkirrqie
+ hcegrmtlkn lpladqgssh hitvkinelk svqndsqaia
+ evlnqlkdml anfrgsekyc ylqnevfglf qkleningvt
+ dgylnslctv rallqailqt edmlkvyear lteeetvcld
+ ldkveayrcg lkkikndlnl kksllatmkt elqkaqqihs
+ qtsqqyplyd ldlgkfgekv tqltdrwqri dkqidfrlwd
+ lekqikqlrn yrdnyqafck wlydrkrrqd slesmkfgds
+ ntvmrflneq knlhseisgk rdkseevqki aelcansikd
+ yelqlasyts gletllnipi krtmiqspsg vilqeaadvh
+ aryielltrs gdyyrflsem lksledlklk ntkievleee
+ lrlardanse ncnknkfldq nlqkyqaecs qfkaklasle
+ elkrqaeldg ksakqnldkc ygqikelnek itrltyeied
+ ekrrrksved rfdqqkndyd qlqkarqcek enlgwqkles
+ ekaikekeye ierlrvllqe egtrkreyen elakvrnhyn
+ eemsnlrnky eteinitktt ikeismqked dsknlrnqld
+ rlsrenrdlk deivrlndsi lqateqrrra eenalqqkac
+ gseimqkkqh leielkqvmq qrsednarhk qsleeaakti
+ qdknkeierl kaefqeeakr rweyenelsk vrnnydeeii
+ slknqfetei nitkttihql tmqkeedtsg yraqidnltr
+ enrslseeik rlkntltqtt enlrrveedi qqqkatgsev
+ sqrkqqleve lrqvtqmrte esvrykqsld daaktiqdkn
+ keierlkqli dketndrkcl edenarlqrv qydlqkanss
+ atetinklkv qeqeltrlri dyervsqert vkdqditrfq
+ nslkelqlqk qkveeelnrl krtasedsck rkkleeeleg
+ mrrslkeqai kitnltqqle qasivkkrse ddlrqqrdvl
+ dghlrekqrt qeelrrlsse vealrrqllq eqesvkqahl
+ rnehfqkaie dksrslnesk ieierlqslt enltkehlml
+ eeelrnlrle yddlrrgrse adsdknatil elrsqlqisn
+ nrtlelqgli ndlqrerenl rqeiekfqkq aleasnriqe
+ sknqctqvvq eresllvkik vleqdkarlq rledelnrak
+ stleaetrvk qrlecekqqi qndlnqwktq ysrkeeairk
+ ieserekser eknslrseie rlqaeikrie ercrrkleds
+ tretqsqlet ersryqreid klrqrpygsh retqtecewt
+ vdtsklvfdg lrkkvtamql yecqlidktt ldkllkgkks
+ veevaseiqp flrgagsiag asaspkekys lveakrkkli
+ spestvmlle aqaatggiid phrnekltvd saiardlidf
+ ddrqqiyaae kaitgfddpf sgktvsvsea ikknlidret
+ gmrlleaqia sggvvdpvns vflpkdvala rglidrdlyr
+ slndprdsqk nfvdpvtkkk vsyvqlkerc riephtglll
+ lsvqkrsmsf qgirqpvtvt elvdsgilrp stvnelesgq
+ isydevgeri kdflqgssci agiynettkq klgiyeamki
+ glvrpgtale lleaqaatgf ivdpvsnlrl pveeaykrgl
+ vgiefkekll saeravtgyn dpetgniisl fqamnkelie
+ kghgirllea qiatggiidp keshrlpvdi aykrgyfnee
+ lseilsdpsd dtkgffdpnt eenltylqlk ercikdeetg
+ lcllplkekk kqvqtsqknt lrkrrvvivd petnkemsvq
+ eaykkglidy etfkelceqe ceweeititg sdgstrvvlv
+ drktgsqydi qdaidkglvd rkffdqyrsg slsltqfadm
+ islkngvgts ssmgsgvsdd vfsssrhesv skistissvr
+ nltirsssfs dtleesspia aifdtenlek isitegierg
+ ivdsitgqrl leaqactggi ihpttgqkls lqdavsqgvi
+ dqdmatsvkp aqkafigfeg vkgkkkmsaa eavkekwlpy
+ eagqrflefq yltgglvdpe vhgristeea irkgfidgra
+ aqrlqdtssy akiltcpktk lkisykdain rsmveditgl
+ rlleaasvss kglpspynms sapgsrsgsr sgsrsgsrsg
+ srsgsrrgsf datgnssysy sysfssssig h </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-2004">
+ <names>
+ <shortLabel>Chorionic gonadotropin, alpha chain</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00342"/>
+ <secondaryRef db="PubMed" id="6581542"/>
+ <secondaryRef db="RefSeq" id="NP_000726"/>
+ <secondaryRef db="Affymetrix" id="204637_at"/>
+ <secondaryRef db="Affymetrix" id="233615_at"/>
+ <secondaryRef db="Affymetrix" id="39352_at"/>
+ <secondaryRef db="Affymetrix" id="g10800407_3p_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.301294.0.S1_3p_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mdyyrkyaai flvtlsvflh vlhsapdvqd cpectlqenp
+ ffsqpgapil qcmgccfsra yptplrskkt mlvqknvtse
+ stccvaksyn rvtvmggfkv enhtachcst cyyhks </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-1390">
+ <names>
+ <shortLabel>Complement component 5 receptor 1</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00224"/>
+ <secondaryRef db="PubMed" id="1612600"/>
+ <secondaryRef db="RefSeq" id="NP_001727"/>
+ <secondaryRef db="Affymetrix" id="220088_at"/>
+ <secondaryRef db="Affymetrix" id="g4502508_3p_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mnsfnyttpd yghyddkdtl dlntpvdkts ntlrvpdila
+ lvifavvflv gvlgnalvvw vtafeakrti naiwflnlav
+ adflsclalp ilftsivqhh hwpfggaacs ilpslillnm
+ yasilllati sadrfllvfk piwcqnfrga glawiacava
+ wglallltip sflyrvvree yfppkvlcgv dyshdkrrer
+ avaivrlvlg flwplltlti cytfillrtw srratrstkt
+ lkvvvavvas ffifwlpyqv tgimmsflep ssptflllnk
+ ldslcvsfay inccinpiiy vvagqgfqgr lrkslpsllr
+ nvlteesvvr esksftrstv dtmaqktqav </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-3448">
+ <names>
+ <shortLabel>Interleukin 3 receptor, beta</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00739"/>
+ <secondaryRef db="PubMed" id="1424804"/>
+ <secondaryRef db="RefSeq" id="NP_000386"/>
+ <secondaryRef db="Affymetrix" id="205159_at"/>
+ <secondaryRef db="Affymetrix" id="1086_at"/>
+ <secondaryRef db="Affymetrix" id="37493_at"/>
+ <secondaryRef db="Affymetrix" id="37494_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.285401.0.S2_3p_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mvlaqgllsm allalcwers lagaeetipl qtlrcyndyt
+ shitcrwadt qdaqrlvnvt lirrvnedll epvscdlsdd
+ mpwsacphpr cvprrcvipc qsfvvtdvdy fsfqpdrplg
+ trltvtltqh vqppeprdlq istdqdhfll twsvalgspq
+ shwlspgdle fevvykrlqd swedaaills ntsqatlgpe
+ hlmpsstyva rvrtrlapgs rlsgrpskws pevcwdsqpg
+ deaqpqnlec ffdgaavlsc swevrkevas svsfglfykp
+ spdageeecs pvlreglgsl htrhhcqipv pdpathgqyi
+ vsvqprraek hikssvniqm appslnvtkd gdsyslrwet
+ mkmryehidh tfeiqyrkdt atwkdsktet lqnahsmalp
+ alepstrywa rvrvrtsrtg yngiwsewse arswdtesvl
+ pmwvlalivi fltiavllal rfcgiygyrl rrkweekipn
+ pskshlfqng saelwppgsm saftsgspph qgpwgsrfpe
+ legvfpvgfg dsevspltie dpkhvcdpps gpdttpaasd
+ lpteqppspq pgppaashtp ekqassfdfn gpylgpphsr
+ slpdilgqpe ppqeggsqks pppgsleylc lpaggqvqlv
+ plaqamgpgq aveverrpsq gaagspsles gggpappalg
+ prvggqdqkd spvaipmssg dtedpgvasg yvssadlvft
+ pnsgassvsl vpslglpsdq tpslcpglas gppgapgpvk
+ sgfegyvelp piegrsprsp rnnpvppeak spvlnpgerp
+ advsptspqp egllvlqqvg dycflpglgp gplslrskps
+ spgpgpeikn ldqafqvkkp pgqavpqvpv iqlfkalkqq
+ dylslppwev nkpgevc </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-3387">
+ <names>
+ <shortLabel>Glutathione reductase</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00704"/>
+ <secondaryRef db="RefSeq" id="NP_000628"/>
+ <secondaryRef db="Affymetrix" id="205770_at"/>
+ <secondaryRef db="Affymetrix" id="225609_at"/>
+ <secondaryRef db="Affymetrix" id="35130_at"/>
+ <secondaryRef db="Affymetrix" id="g10835188_3p_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.193974.0.S1_3p_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>macrqepqpq gpppaagava sydylviggg sgglasarra
+ aelgaraavv eshklggtcv nvgcvpkkvm wntavhsefm
+ hdhadygfps cegkfnwrvi kekrdayvsr lnaiyqnnlt
+ kshieiirgh aaftsdpkpt ievsgkkyta philiatggm
+ pstphesqip gaslgitsdg ffqleelpgr svivgagyia
+ vemagilsal gsktslmirh dkvlrsfdsm istncteele
+ nagvevlkfs qvkevkktls glevsmvtav pgrlpvmtmi
+ pdvdcllwai grvpntkdls lnklgiqtdd kghiivdefq
+ ntnvkgiyav gdvcgkallt pvaiaagrkl ahrlfeyked
+ skldynnipt vvfshppigt vgltedeaih kygienvkty
+ stsftpmyha vtkrktkcvm kmvcankeek vvgihmqglg
+ cdemlqgfav avkmgatkad fdntvaihpt sseelvtlr </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-3686">
+ <names>
+ <shortLabel>Heme oxygenase 1</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00782"/>
+ <secondaryRef db="PubMed" id="8034330"/>
+ <secondaryRef db="RefSeq" id="NP_002124"/>
+ <secondaryRef db="Affymetrix" id="203665_at"/>
+ <secondaryRef db="Affymetrix" id="33802_at"/>
+ <secondaryRef db="Affymetrix" id="g4504436_3p_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>merpqpdsmp qdlsealkea tkevhtqaen aefmrnfqkg
+ qvtrdgfklv maslyhiyva leeeiernke spvfapvyfp
+ eelhrkaale qdlafwygpr wqevipytpa mqryvkrlhe
+ vgrtepellv ahaytrylgd lsggqvlkki aqkaldlpss
+ geglafftfp niasatkfkq lyrsrmnsle mtpavrqrvi
+ eeaktaflln iqlfeelqel lthdtkdqsp srapglrqra
+ snkvqdsapv etprgkppln trsqapllrw vltlsflvat
+ vavglyam </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-1799">
+ <names>
+ <shortLabel>Minichromosome maintenance protein 2</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00303"/>
+ <secondaryRef db="PubMed" id="8258304"/>
+ <secondaryRef db="RefSeq" id="NP_004517"/>
+ <secondaryRef db="Affymetrix" id="202107_s_at"/>
+ <secondaryRef db="Affymetrix" id="35312_at"/>
+ <secondaryRef db="Affymetrix" id="g4758705_3p_s_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>maessesftm asspaqrrrg ndpltsspgr ssrrtdalts
+ spgrdlppfe desegllgte gpleeeedge eligdgmerd
+ yraipelday eaeglaldde dveeltasqr eaaeramrqr
+ dreagrglgr mrrgllydsd eedeerpark rrqverated
+ geedeemies ienledlkgh svrewvsmag prleihhrfk
+ nflrthvdsh ghnvfkeris dmckenresl vvnyedlaar
+ ehvlayflpe apaellqifd eaalevvlam ypkydritnh
+ ihvrishlpl veelrslrql hlnqlirtsg vvtsctgvlp
+ qlsmvkyncn kcnfvlgpfc qsqnqevkpg scpecqsagp
+ fevnmeetiy qnyqririqe spgkvaagrl prskdailla
+ dlvdsckpgd eieltgiyhn nydgslntan gfpvfatvil
+ anhvakkdnk vavgeltded vkmitslskd qqigekifas
+ iapsiyghed ikrglalalf ggepknpggk hkvrgdinvl
+ lcgdpgtaks qflkyiekvs sraifttgqg asavgltayv
+ qrhpvsrewt leagalvlad rgvclidefd kmndqdrtsi
+ heameqqsis iskagivtsl qarctviaaa npiggrydps
+ ltfsenvdlt epiisrfdil cvvrdtvdpv qdemlarfvv
+ gshvrhhpsn keeeglangs aaepampnty gveplpqevl
+ kkyiiyaker vhpklnqmdq dkvakmysdl rkesmatgsi
+ pitvrhiesm irmaeahari hlrdyviedd vnmairvmle
+ sfidtqkfsv mrsmrktfar ylsfrrdnne lllfilkqlv
+ aeqvtyqrnr fgaqqdtiev pekdlvdkar qinihnlsaf
+ ydselfrmnk fshdlkrkmi lqqf </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-2666">
+ <names>
+ <shortLabel>Utrophin</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00547"/>
+ <secondaryRef db="PubMed" id="2203673"/>
+ <secondaryRef db="RefSeq" id="NP_009055"/>
+ <secondaryRef db="Affymetrix" id="213022_s_at"/>
+ <secondaryRef db="Affymetrix" id="213023_at"/>
+ <secondaryRef db="Affymetrix" id="225093_at"/>
+ <secondaryRef db="Affymetrix" id="41390_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.251967.0.A1_3p_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.286161.0.S1_3p_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>makygeheas pdngqnefsd iiksrsdehn dvqkktftkw
+ inarfsksgk ppindmftdl kdgrklldll egltgtslpk
+ ergstrvhal nnvnrvlqvl hqnnvelvni ggtdivdgnh
+ kltlgllwsi ilhwqvkdvm kdvmsdlqqt nsekillswv
+ rqttrpysqv nvlnfttswt dglafnavlh rhkpdlfswd
+ kvvkmspier lehafskaqt ylgieklldp edvavrlpdk
+ ksiimyltsl fevlpqqvti dairevetlp rkykkeceee
+ ainiqstape eehespraet pstvtevdmd ldsyqialee
+ vltwllsaed tfqeqddisd dveevkdqfa theafmmelt
+ ahqssvgsvl qagnqlitqg tlsdeeefei qeqmtllnar
+ wealrvesmd rqsrlhdvlm elqkkqlqql sawltlteer
+ iqkmetcpld ddvkslqkll eehkslqsdl eaeqvkvnsl
+ thmvvivden sgesataile dqlqklgerw tavcrwteer
+ wnrlqeinil wqelleeqcl lkawltekee alnkvqtsnf
+ kdqkelsvsv rrlailkedm emkrqtldql seigqdvgql
+ ldnskaskki nsdseeltqr wdslvqrled ssnqvtqava
+ klgmsqipqk dlletvrvre qaitkkskqe lppppppkkr
+ qihvdieakk kfdaisaell nwilkwktai qtteikeymk
+ mqdtsemkkk lkalekeqre ripradelnq tgqilveqmg
+ keglpteeik nvlekvssew knvsqhledl erkiqlqedi
+ nayfkqldel ekviktkeew vkhtsisess rqslpslkds
+ cqreltnllg lhpkiemara scsalmsqps apdfvqrgfd
+ sflgryqavq eavedrqqhl enelkgqpgh ayletlktlk
+ dvlndsenka qvslnvlndl akvekalqek ktldeilenq
+ kpalhklaee tkaleknvhp dveklykqef ddvqgkwnkl
+ kvlvskdlhl leeialtlra feadstviek wmdgvkdflm
+ kqqaaqgdda glqrqldqcs afvneietie sslknmkeie
+ tnlrsgpvag iktwvqtrlg dyqtqlekls keiatqksrl
+ sesqekaanl kkdlaemqew mtqaeeeyle rdfeykspee
+ lesaveemkr akedvlqkev rvkilkdnik llaakvpsgg
+ qeltselnvv lenyqllcnr irgkchtlee vwscwiellh
+ yldlettwln tleermkste vlpektdavn ealeslesvl
+ rhpadnrtqi relgqtlidg gilddiisek leafnsryed
+ lshlaeskqi slekqlqvlr etdqmlqvlq eslgeldkql
+ ttyltdrida fqvpqeaqki qaeisahelt leelrrnmrs
+ qpltspesrt arggsqmdvl qrklrevstk fqlfqkpanf
+ eqrmldckrv ldgvkaelhv ldvkdvdpdv iqthldkcmk
+ lyktlsevkl evetviktgr hivqkqqtdn pkgmdeqlts
+ lkvlyndlga qvtegkqdle rasqlarkmk keaaslsewl
+ satetelvqk stsegllgdl dteiswaknv lkdlekrkad
+ lntitessaa lqnliegsep ileerlcvln agwsrvrtwt
+ edwcntlmnh qnqleifdgn vahistwlyq aealldeiek
+ kptskqeeiv krlvseldda nlqvenvrdq alilmnargs
+ ssrelvepkl aelnrnfekv sqhiksakll iaqeplyqcl
+ vttetfetgv pfsdleklen dienmlkfve khlessdede
+ kmdeesaqie evlqrgeeml hqpmednkke kirlqllllh
+ trynkikaip iqqrkmgqla sgirssllpt dylveinkil
+ lcmddvelsl nvpelntaiy edfsfqedsl knikdqldkl
+ geqiavihek qpdvileasg peaiqirdtl tqlnakwdri
+ nrmysdrkgc fdrameewrq fhcdlndltq witeaeellv
+ dtcapggsld lekarihqqe levgisshqp sfaalnrtgd
+ givqklsqad gsflkeklag lnqrwdaiva evkdrqprlk
+ geskqvmkyr hqldeiicwl tkaehamqkr sttelgenlq
+ elrdltqeme vhaeklkwln rtelemlsdk slslperdki
+ seslrtvnmt wnkicrevpt tlkeciqeps svsqtriaah
+ pnvqkvvlvs sasdipvqsh rtseisipad ldktitelad
+ wlvlidqmlk snivtvgdve einktvsrmk itkadleqrh
+ pqldyvftla qnlknkasss dmrtaitekl ervknqwdgt
+ qhgvelrqqq ledmiidslq wddhreetee lmrkyearly
+ ilqqarrdpl tkqisdnqil lqelgpgdgi vmafdnvlqk
+ lleeygsddt rnvketteyl ktswinlkqs iadrqnalea
+ ewrtvqasrr dlenflkwiq eaettvnvlv dashrenalq
+ dsilarelkq qmqdiqaeid ahndifksid gnrqkmvkal
+ gnseeatmlq hrlddmnqrw ndlkaksasi rahleasaek
+ wnrllmslee likwlnmkde elkkqmpigg dvpalqlqyd
+ hckalrrelk ekeysvlnav dqarvfladq pieapeeprr
+ nlqskteltp eeraqkiaka mrkqssevke kweslnavts
+ nwqkqvdkal eklrdlqgam ddldadmkea esvrngwkpv
+ gdllidslqd hiekimafre eiapinfkvk tvndlssqls
+ pldlhpslkm srqlddlnmr wkllqvsvdd rlkqlqeahr
+ dfgpssqhfl stsvqlpwqr sishnkvpyy inhqtqttcw
+ dhpkmtelfq sladlnnvrf sayrtaikir rlqkalcldl
+ lelsttneif kqhklnqndq llsvpdvinc ltttydgleq
+ mhkdlvnvpl cvdmclnwll nvydtgrtgk irvqslkigl
+ mslskgllee kyrylfkeva gptemcdqrq lglllhdaiq
+ iprqlgevaa fggsniepsv rscfqqnnnk peisvkefid
+ wmhlepqsmv wlpvlhrvaa aetakhqakc nickecpivg
+ fryrslkhfn ydvcqscffs grtakghklh ypmveycipt
+ tsgedvrdft kvlknkfrsk kyfakhprlg ylpvqtvleg
+ dnletpitli smwpehydps qspqlfhddt hsrieqyatr
+ laqmertngs fltdsssttg svedehaliq qycqtlgges
+ pvsqpqspaq ilksvereer geleriiadl eeeqrnlqve
+ yeqlkdqhlr rglpvgsppe siisphhtse dseliaeakl
+ lrqhkgrlea rmqiledhnk qlesqlhrlr qlleqpesds
+ ringvspwas pqhsalsysl dpdasgpqfh qaagedllap
+ phdtstdlte vmeqihstfp sccpnvpsrp qam </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-2758">
+ <names>
+ <shortLabel>Emilin</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00563"/>
+ <secondaryRef db="RefSeq" id="NP_008977"/>
+ <secondaryRef db="Affymetrix" id="204163_at"/>
+ <secondaryRef db="Affymetrix" id="35740_at"/>
+ <secondaryRef db="Affymetrix" id="204163_3p_at"/>
+ <secondaryRef db="Affymetrix" id="g5901943_3p_at"/>
+ <secondaryRef db="Affymetrix" id="g5901943_3p_s_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>maprtlwscy lcclltaaag aasypprgfs lytgssgals
+ pggpqaqiap rpasrhrnwc ayvvtrtvsc vledgvetyv
+ kyqpcawgqp qcpqsimyrr flrpryrvay ktvtdmewrc
+ cqgyggddca espapalgpa sstprplarp arpnlsgssa
+ gsplsglgge gpgesekvqq leeqvqsltk elqglrgvlq
+ glsgrlaedv qravetafng rqqpadaaar pgvhetlnei
+ qhqlqlldtr vsthdqelgh lnnhhggsss sggsrapapa
+ sappgpseel lrqleqrlqe scsvclagld gfrrqqqedr
+ erlramekll asveerqrhl aglavgrrpp qeccspelgr
+ rlaelerrld vvagsvtvls grrgtelgga agqgghppgy
+ tslasrlsrl edrfnstlgp seeqeeswpg apgglshwlp
+ aargrleqlg gllanvsgel ggrldlleeq vagamqacgq
+ lcsgapgeqd sqvseilsal errvldsegq lrlvgsglht
+ veaagearqa tleglqevvg rlqdrvdaqd etaaeftlrl
+ nltaarlgql egllqahgde gcgacggvqe elgrlrdgve
+ rcscpllppr gpgagpgvgg psrgpldgfs vfggssgsal
+ qalqgelsev ilsfsslnds lnelqttveg qgadladlga
+ tkdriisein rlqqeateha teseerfrgl eegqaqagqc
+ pslegrlgrl egvcerldtv agglqglreg lsrhvaglwa
+ glretnttsq mqaalleklv ggqaglgrrl galnsslqll
+ edrlhqlslk dltgpageag ppgppglqgp pgpagppgsp
+ gkdgqegpig ppgpqgeqgv egapaapvpq vafsaalslp
+ rsepgtvpfd rvllndggyy dpetgvftap lagryllsav
+ ltghrhekve avlsrsnqgv arvdsggyep eglenkpvae
+ sqpspgtlgv fslilplqag dtvcvdlvmg qlahseeplt
+ ifsgallygd peleha </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-2873">
+ <names>
+ <shortLabel>Stomatin</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00585"/>
+ <secondaryRef db="RefSeq" id="NP_004090"/>
+ <secondaryRef db="Affymetrix" id="201060_x_at"/>
+ <secondaryRef db="Affymetrix" id="201061_s_at"/>
+ <secondaryRef db="Affymetrix" id="201062_at"/>
+ <secondaryRef db="Affymetrix" id="210824_at"/>
+ <secondaryRef db="Affymetrix" id="210825_s_at"/>
+ <secondaryRef db="Affymetrix" id="40419_at"/>
+ <secondaryRef db="Affymetrix" id="g181183_3p_a_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.160483.0.S2_3p_a_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>maekrhtrds eaqrlpdsfk dspskglgpc gwilvafsfl
+ ftvitfpisi wmcikiikey eraiifrlgr ilqggakgpg
+ lffilpctds fikvdmrtis fdippqeilt kdsvtisvdg
+ vvyyrvqnat lavanitnad satrllaqtt lrnvlgtknl
+ sqilsdreei ahnmqstldd atdawgikve rveikdvklp
+ vqlqramaae aeasrearak viaaegemna sralkeasmv
+ itespaalql rylqtlttia aeknstivfp lpidmlqgii
+ gakhshlg </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-687">
+ <names>
+ <shortLabel>CD69 antigen</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00119"/>
+ <secondaryRef db="PubMed" id="8340758"/>
+ <secondaryRef db="RefSeq" id="NP_001772"/>
+ <secondaryRef db="Affymetrix" id="209795_at"/>
+ <secondaryRef db="Affymetrix" id="37645_at"/>
+ <secondaryRef db="Affymetrix" id="g291897_3p_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mssencfvae nsslhpesgq endatsphfs trhegsfqvp
+ vlcavmnvvf itiliialia lsvgqyncpg qytfsmpsds
+ hvsscsedwv gyqrkcyfis tvkrswtsaq nacsehgatl
+ avidsekdmn flkryagree hwvglkkepg hpwkwsngke
+ fnnwfnvtgs dkcvflknte vssmeceknl ywicnkpyk </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-1447">
+ <names>
+ <shortLabel>Calcyclin</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00237"/>
+ <secondaryRef db="GenBank" id="AAH09017"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>macpldqaig llvaifhkys gregdkhtls kkelkeliqk
+ eltigsklqd aeiarlmedl drnkdqevnf qeyvtflgal
+ aliynealkg </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-822">
+ <names>
+ <shortLabel>Aquaporin 1</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00140"/>
+ <secondaryRef db="PubMed" id="8340403"/>
+ <secondaryRef db="RefSeq" id="NP_000376"/>
+ <secondaryRef db="Affymetrix" id="207542_s_at"/>
+ <secondaryRef db="Affymetrix" id="209047_at"/>
+ <secondaryRef db="Affymetrix" id="36156_at"/>
+ <secondaryRef db="Affymetrix" id="g4755121_3p_a_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.74602.1.S2_3p_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>masefkkklf wravvaefla ttlfvfisig salgfkypvg
+ nnqtavqdnv kvslafglsi atlaqsvghi sgahlnpavt
+ lglllscqis ifralmyiia qcvgaivata ilsgitsslt
+ gnslgrndla dgvnsgqglg ieiigtlqlv lcvlattdrr
+ rrdlggsapl aiglsvalgh llaidytgcg inparsfgsa
+ vithnfsnhw ifwvgpfigg alavliydfi laprssdltd
+ rvkvwtsgqv eeydldaddi nsrvemkpk </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-740">
+ <names>
+ <shortLabel>Apolipoprotein C-I</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00131"/>
+ <secondaryRef db="PubMed" id="8804993"/>
+ <secondaryRef db="RefSeq" id="NP_001636"/>
+ <secondaryRef db="Affymetrix" id="204416_x_at"/>
+ <secondaryRef db="Affymetrix" id="213553_x_at"/>
+ <secondaryRef db="Affymetrix" id="41764_at"/>
+ <secondaryRef db="Affymetrix" id="213553_3p_x_at"/>
+ <secondaryRef db="Affymetrix" id="g5174774_3p_a_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.268571.1.A1_3p_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.268571.1.A1_3p_a_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.268571.1.A1_3p_x_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mrlflslpvl vvvlsivleg papaqgtpdv ssaldklkef
+ gntledkare lisrikqsel sakmrewfse tfqkvkeklk
+ ids </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-3394">
+ <names>
+ <shortLabel>Glutathione S-transferase alpha 1</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00708"/>
+ <secondaryRef db="RefSeq" id="NP_665683"/>
+ <secondaryRef db="Affymetrix" id="203924_at"/>
+ <secondaryRef db="Affymetrix" id="215766_at"/>
+ <secondaryRef db="Affymetrix" id="1260_s_at"/>
+ <secondaryRef db="Affymetrix" id="33062_at"/>
+ <secondaryRef db="Affymetrix" id="38781_at"/>
+ <secondaryRef db="Affymetrix" id="g4504170_3p_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.146581.0.A1_3p_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>maekpklhyf nargrmestr wllaaagvef eekfiksaed
+ ldklrndgyl mfqqvpmvei dgmklvqtra ilnyiaskyn
+ lygkdikera lidmyiegia dlgemilllp vcppeekdak
+ lalikekikn ryfpafekvl kshgqdylvg nklsradihl
+ vellyyveel dsslissfpl lkalktrisn lptvkkflqp
+ gsprkppmde ksleearkif rf </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-2930">
+ <names>
+ <shortLabel>ETO</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00590"/>
+ <secondaryRef db="RefSeq" id="NP_783552"/>
+ <secondaryRef db="Affymetrix" id="205528_s_at"/>
+ <secondaryRef db="Affymetrix" id="205529_s_at"/>
+ <secondaryRef db="Affymetrix" id="216831_s_at"/>
+ <secondaryRef db="Affymetrix" id="216832_at"/>
+ <secondaryRef db="Affymetrix" id="228827_at"/>
+ <secondaryRef db="Affymetrix" id="242845_at"/>
+ <secondaryRef db="Affymetrix" id="35638_at"/>
+ <secondaryRef db="Affymetrix" id="35641_g_at"/>
+ <secondaryRef db="Affymetrix" id="g4757915_3p_a_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.144995.0.A1_3p_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.307345.0.S1_3p_s_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.31551.0.S1_3p_s_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.90858.0.S1_3p_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>misvkrntwr alslvigdcr kkgnfeycqd rtekhstmpd
+ spvdvktqsr ltpptmpppp ttqgaprtss ftpttltngt
+ shsptalnga psppngfsng psssssssla nqqlppacga
+ rqlsklkrfl ttlqqfgndi speigervrt lvlglvnstl
+ tieefhsklq eatnfplrpf vipflkanlp llqrellhca
+ rlakqnpaqy laqheqllld asttspvdss ellldvneng
+ krrtpdrtke ngfdreplhs ehpskrpcti spgqryspnn
+ glsyqpnglp hptppppqhy rlddmaiahh yrdsyrhpsh
+ rdlrdrnrpm glhgtrqeem idhrltdrew aeewkhldhl
+ lncimdmvek trrsltvlrr cqeadreeln ywirrysdae
+ dlkkgggsss shsrqqspvn pdpvaldahr eflhrpasgy
+ vpeeiwkkae eavnevkrqa mtelqkavse aerkahdmit
+ terakmertv aeakrqaaed alavinqqed ssescwncgr
+ kasetcsgcn tarycgsfcq hkdwekhhhi cgqtlqaqqq
+ gdtpavsssv tpnsgagspm dtppaatprs ttpgtpstie ttpr </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-2251">
+ <names>
+ <shortLabel>Core binding factor, beta subunit</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00418"/>
+ <secondaryRef db="PubMed" id="10914550"/>
+ <secondaryRef db="RefSeq" id="NP_074036"/>
+ <secondaryRef db="Affymetrix" id="202370_s_at"/>
+ <secondaryRef db="Affymetrix" id="206788_s_at"/>
+ <secondaryRef db="Affymetrix" id="41175_at"/>
+ <secondaryRef db="Affymetrix" id="g13124872_3p_a_at"/>
+ <secondaryRef db="Affymetrix" id="g9885832_3p_a_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mprvvpdqrs kfeneeffrk lsreceikyt gfrdrpheer
+ qarfqnacrd grseiafvat gtnlslqffp aswqgeqrqt
+ psreyvdler eagkvylkap milngvcviw kgwidlqrld
+ gmgclefdee raqqedalaq qafeearrrt refedrdrsh
+ reemearrqq dpspgsnlgg gddlklr </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-2435">
+ <names>
+ <shortLabel>Ezrin</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00475"/>
+ <secondaryRef db="PubMed" id="8162705"/>
+ <secondaryRef db="RefSeq" id="NP_003370"/>
+ <secondaryRef db="Affymetrix" id="208621_s_at"/>
+ <secondaryRef db="Affymetrix" id="208622_s_at"/>
+ <secondaryRef db="Affymetrix" id="208623_s_at"/>
+ <secondaryRef db="Affymetrix" id="217230_at"/>
+ <secondaryRef db="Affymetrix" id="217234_s_at"/>
+ <secondaryRef db="Affymetrix" id="238645_at"/>
+ <secondaryRef db="Affymetrix" id="40103_at"/>
+ <secondaryRef db="Affymetrix" id="g340216_3p_a_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.155191.0.S1_3p_a_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.155191.0.S2_3p_a_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.155191.1.A1_3p_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.155191.1.S1_3p_a_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mpkpinvrvt tmdaelefai qpnttgkqlf dqvvktiglr
+ evwyfglhyv dnkgfptwlk ldkkvsaqev rkenplqfkf
+ rakfypedva eeliqditqk lfflqvkegi lsdeiycppe
+ tavllgsyav qakfgdynke vhksgylsse rlipqrvmdq
+ hkltrdqwed riqvwhaehr gmlkdnamle ylkiaqdlem
+ yginyfeikn kkgtdlwlgv dalglniyek ddkltpkigf
+ pwseirnisf ndkkfvikpi dkkapdfvfy aprlrinkri
+ lqlcmgnhel ymrrrkpdti evqqmkaqar eekhqkqler
+ qqletekkrr etverekeqm mrekeelmlr lqdyeektkk
+ aerelseqiq ralqleeerk raqeeaerle adrmaalrak
+ eelerqavdq iksqeqlaae laeytakial leearrrked
+ eveewqhrak eaqddlvktk eelhlvmtap ppppppvyep
+ vsyhvqeslq degaeptgys aelssegird drneekrite
+ aeknervqrq lltlsselsq ardenkrthn diihnenmrq
+ grdkyktlrq irqgntkqri defeal </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-104">
+ <names>
+ <shortLabel>Collagen XVII</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00223"/>
+ <secondaryRef db="PubMed" id="2045679"/>
+ <secondaryRef db="RefSeq" id="NP_000485"/>
+ <secondaryRef db="Affymetrix" id="204636_at"/>
+ <secondaryRef db="Affymetrix" id="41618_at"/>
+ <secondaryRef db="Affymetrix" id="g4502942_3p_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mdvtkknkrd gtevterivt etvttrltsl ppkggtsngy
+ aktaslgggs rlekqslthg ssgyinstgs trghastssy
+ rrahspastl pnspgstfer kthvtrhaye gsssgnsspe
+ yprkefasss trgrsqtres eirvrlqsas pstrwteldd
+ vkrllkgsrs asvsptrnss ntlpipkkgt vetkivtass
+ qsvsgtydat ildanlpshv wsstlpagss mgtyhnnmtt
+ qsssllntna ysagsvfgvp nnmascsptl hpglstsssv
+ fgmqnnlaps lttlshgttt tstaygvkkn mpqspaavnt
+ gvstsaactt svqsddllhk dckflilekd ntpakkemel
+ limtkdsgkv ftaspasiaa tsfsedtlkk ekqaaynads
+ glkaeangdl ktvstkgktt tadihsysss ggggsggggg
+ vggagggpwg papawcpcgs ccswwkwllg llltwllllg
+ llfglialae evrklkarvd elerirrsil pygdsmdrie
+ kdrlqgmapa agadldkigl hsdsqeelwm fvrkklmmeq
+ engnlrgspg pkgdmgspgp kgdrgfpgtp gipgplghpg
+ pqgpkgqkgs vgdpgmegpm gqrgregpmg prgeagppgs
+ gekgergaag epgphgppgv pgsvgpkgss gspgpqgppg
+ pvglqglrge vglpgvkgdk gpmgppgpkg dqgekgprgl
+ tgepgmrglp gavgepgakg amgpagpdgh qgprgeqglt
+ gmpgirgppg psgdpgkpgl tgpqgpqglp gtpgrpgikg
+ epgapgkivt segssmltvp gppgppgamg ppgppgapgp
+ agpaglpghq evlnlqgppg ppgprgppgp sipgppgprg
+ ppgeglpgpp gppgsflsns etflfgppgp pgppgpkgdq
+ gppgprghqg eqglpgfsts gsssfglnlq gppgppgpqg
+ pkgdkgdpgv pgalgipsgp seggssstmy vsgppgppgp
+ pgppgsisss gqeiqqyise ymqsdsirsy lsgvqgppgp
+ pgppgpvtti tgetfdysel ashvvsylrt sgygvslfss
+ sissedilav lqrddvrqyl rqylmgprgp pgppgasgdg
+ sllsldyael ssrilsymss sgisiglpgp pgppglpgts
+ yeellsllrg sefrgivgpp gppgppgipg nvwssisved
+ lssylhtagl sfipgppgpp gppgprgppg vsgalatyaa
+ ensdsfrsel isyltspdvr sfivgppgpp gpqgppgdsr
+ llstdashsr gssssshsss vrrgssysss mstggggags
+ lgaggafgea agdrgpygtd igpgggygaa aeggmyagng
+ gllgadfagd ldynelavrv sesmqrqgll qgmaytvqgp
+ pgqpgpqgpp giskvfsays nvtadlmdff qtygaiqgpp
+ gqkgemgtpg pkgdrgpagp pghpgppgpr ghkgekgdkg
+ dqvyagrrrr rsiavkp </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-1862">
+ <names>
+ <shortLabel>CDC42</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00309"/>
+ <secondaryRef db="PubMed" id="7665558"/>
+ <secondaryRef db="RefSeq" id="NP_001782"/>
+ <secondaryRef db="Affymetrix" id="207273_at"/>
+ <secondaryRef db="Affymetrix" id="208727_s_at"/>
+ <secondaryRef db="Affymetrix" id="208728_s_at"/>
+ <secondaryRef db="Affymetrix" id="210232_at"/>
+ <secondaryRef db="Affymetrix" id="214230_at"/>
+ <secondaryRef db="Affymetrix" id="226400_at"/>
+ <secondaryRef db="Affymetrix" id="39736_at"/>
+ <secondaryRef db="Affymetrix" id="40192_at"/>
+ <secondaryRef db="Affymetrix" id="208728_3p_s_at"/>
+ <secondaryRef db="Affymetrix" id="g12803746_3p_a_at"/>
+ <secondaryRef db="Affymetrix" id="g13277547_3p_at"/>
+ <secondaryRef db="Affymetrix" id="g13277547_3p_s_at"/>
+ <secondaryRef db="Affymetrix" id="g182856_3p_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.146409.2.S1_3p_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mqtikcvvvg dgavgktcll isyttnkfps eyvptvfdny
+ avtvmiggep ytlglfdtag qedydrlrpl sypqtdvflv
+ cfsvvspssf envkekwvpe ithhcpktpf llvgtqidlr
+ ddpstiekla knkqkpitpe taeklardlk avkyvecsal
+ tqkglknvfd eailaalepp epkksrrcvl l </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-1589">
+ <names>
+ <shortLabel>Casein kinase II, beta</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00278"/>
+ <secondaryRef db="PubMed" id="2276748"/>
+ <secondaryRef db="RefSeq" id="NP_001311"/>
+ <secondaryRef db="Affymetrix" id="201390_s_at"/>
+ <secondaryRef db="Affymetrix" id="32843_s_at"/>
+ <secondaryRef db="Affymetrix" id="410_s_at"/>
+ <secondaryRef db="Affymetrix" id="g10334850_3p_s_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mssseevswi swfcglrgne ffcevdedyi qdkfnltgln
+ eqvphyrqal dmildlepde elednpnqsd lieqaaemly
+ gliharyilt nrgiaqmlek yqqgdfgycp rvycenqpml
+ piglsdipge amvklycpkc mdvytpkssr hhhtdgayfg
+ tgfphmlfmv hpeyrpkrpa nqfvprlygf kihpmayqlq
+ lqaasnfksp vktir </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-2674">
+ <names>
+ <shortLabel>Small nuclear ribonucleoprotein
+ polypeptide E</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00548"/>
+ <secondaryRef db="PubMed" id="2143747"/>
+ <secondaryRef db="RefSeq" id="NP_003085"/>
+ <secondaryRef db="Affymetrix" id="203316_s_at"/>
+ <secondaryRef db="Affymetrix" id="215450_at"/>
+ <secondaryRef db="Affymetrix" id="231112_at"/>
+ <secondaryRef db="Affymetrix" id="38678_at"/>
+ <secondaryRef db="Affymetrix" id="38679_g_at"/>
+ <secondaryRef db="Affymetrix" id="38680_at"/>
+ <secondaryRef db="Affymetrix" id="g4507128_3p_a_at"/>
+ <secondaryRef db="Affymetrix" id="g4507128_3p_x_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.1066.1.A1_3p_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.1066.2.A1_3p_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mayrgqgqkv qkvmvqpinl ifrylqnrsr iqvwlyeqvn
+ mriegciigf deymnlvldd aeeihsktks rkqlgrimlk
+ gdnitllqsv sn </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-2189">
+ <names>
+ <shortLabel>CD55</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00500"/>
+ <secondaryRef db="PubMed" id="2438369"/>
+ <secondaryRef db="RefSeq" id="NP_000565"/>
+ <secondaryRef db="Affymetrix" id="1555950_a_at"/>
+ <secondaryRef db="Affymetrix" id="201925_s_at"/>
+ <secondaryRef db="Affymetrix" id="201926_s_at"/>
+ <secondaryRef db="Affymetrix" id="241615_x_at"/>
+ <secondaryRef db="Affymetrix" id="241616_at"/>
+ <secondaryRef db="Affymetrix" id="39695_at"/>
+ <secondaryRef db="Affymetrix" id="g10835142_3p_a_at"/>
+ <secondaryRef db="Affymetrix" id="g12654888_3p_a_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.145830.0.A1_3p_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.145830.0.S1_3p_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mtvarpsvpa alpllgelpr llllvllclp avwgdcglpp
+ dvpnaqpale grtsfpedtv itykceesfv kipgekdsvi
+ clkgsqwsdi eefcnrscev ptrlnsaslk qpyitqnyfp
+ vgtvveyecr pgyrrepsls pkltclqnlk wstavefckk
+ kscpnpgeir ngqidvpggi lfgatisfsc ntgyklfgst
+ ssfclisgss vqwsdplpec reiycpappq idngiiqger
+ dhygyrqsvt yacnkgftmi gehsiyctvn ndegewsgpp
+ pecrgkslts kvpptvqkpt tvnvpttevs ptsqktttkt
+ ttpnaqatrs tpvsrttkhf hettpnkgsg ttsgttrlls
+ ghtcftltgl lgtlvtmgll t </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-2551">
+ <names>
+ <shortLabel>Transcription factor 1</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00800"/>
+ <secondaryRef db="PubMed" id="9075819"/>
+ <secondaryRef db="RefSeq" id="NP_000536"/>
+ <secondaryRef db="Affymetrix" id="210515_at"/>
+ <secondaryRef db="Affymetrix" id="216930_at"/>
+ <secondaryRef db="Affymetrix" id="34639_at"/>
+ <secondaryRef db="Affymetrix" id="34640_at"/>
+ <secondaryRef db="Affymetrix" id="216930_3p_at"/>
+ <secondaryRef db="Affymetrix" id="g184264_3p_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.73888.1.S1_3p_x_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mvsklsqlqt ellaallesg lskealiqal gepgpyllag
+ egpldkgesc gggrgelael pnglgetrgs edetdddged
+ ftppilkele nlspeeaahq kavvetllqe dpwrvakmvk
+ sylqqhnipq revvdttgln qshlsqhlnk gtpmktqkra
+ alytwyvrkq revaqqftha gqgglieept gdelptkkgr
+ rnrfkwgpas qqilfqayer qknpskeere tlveecnrae
+ ciqrgvspsq aqglgsnlvt evrvynwfan rrkeeafrhk
+ lamdtysgpp pgpgpgpalp ahsspglppp alspskvhgv
+ rygqpatset aevpsssggp lvtvstplhq vsptglepsh
+ sllsteaklv saaggplppv stltalhsle qtspglnqqp
+ qnlimaslpg vmtigpgepa slgptftntg astlviglas
+ tqaqsvpvin smgsslttlq pvqfsqplhp syqqplmppv
+ qshvtqspfm atmaqlqsph alyshkpeva qythtgllpq
+ tmlitdttnl salasltptk qvftsdteas sesglhtpas
+ qattlhvpsq dpagiqhlqp ahrlsasptv sssslvlyqs
+ sdssngqshl lpsnhsviet fistqmasss q </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-1207">
+ <names>
+ <shortLabel>HLA G</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00834"/>
+ <secondaryRef db="RefSeq" id="NP_002118"/>
+ <secondaryRef db="Affymetrix" id="211529_x_at"/>
+ <secondaryRef db="Affymetrix" id="211530_x_at"/>
+ <secondaryRef db="Affymetrix" id="40369_f_at"/>
+ <secondaryRef db="Affymetrix" id="40370_f_at"/>
+ <secondaryRef db="Affymetrix" id="g184213_3p_x_at"/>
+ <secondaryRef db="Affymetrix" id="g188467_3p_x_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mvvmaprtlf lllsgaltlt etwagshsmr yfsaavsrpg
+ rgeprfiamg yvddtqfvrf dsdsacprme prapwveqeg
+ peyweeetrn tkahaqtdrm nlqtlrgyyn qseasshtlq
+ wmigcdlgsd grllrgyeqy aydgkdylal nedlrswtaa
+ dtaaqiskrk ceaanvaeqr raylegtcve wlhrylengk
+ emlqradppk thvthhpvfd yeatlrcwal gfypaeiilt
+ wqrdgedqtq dvelvetrpa gdgtfqkwaa vvvpsgeeqr
+ ytchvqhegl peplmlrwkq sslptipimg ivaglvvlaa
+ vvtgaavaav lwrkkssd </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-2663">
+ <names>
+ <shortLabel>Dystroglycan</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00546"/>
+ <secondaryRef db="PubMed" id="8268918"/>
+ <secondaryRef db="RefSeq" id="NP_004384"/>
+ <secondaryRef db="Affymetrix" id="205417_s_at"/>
+ <secondaryRef db="Affymetrix" id="212128_s_at"/>
+ <secondaryRef db="Affymetrix" id="36989_at"/>
+ <secondaryRef db="Affymetrix" id="g4758115_3p_a_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.76111.1.A1_3p_a_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mrmsvglsll lplwgrtfll llsvvmaqsh wpsepseavr
+ dwenqleasm hsvlsdlhea vptvvgipdg tavvgrsfrv
+ tiptdliass gdiikvsaag kealpswlhw dsqshtlegl
+ pldtdkgvhy isvsatrlga ngshipqtss vfsievyped
+ hsdlqsvrta spdpgevvss acaadepvtv ltvildadlt
+ kmtpkqridl lhrmrsfsev elhnmklvpv vnnrlfdmsa
+ fmagpgnpkk vvengallsw klgcslnqns vpdihgveap
+ aregamsaql gypvvgwhia nkkpplpkrv rrqihatptp
+ vtaigpptta iqeppsrivp tptspaiapp tetmappvrd
+ pvpgkptvti rtrgaiiqtp tlgpiqptrv seagttvpgq
+ irptmtipgy veptavatpp ttttkkprvs tpkpatpstd
+ stttttrrpt kkprtprpvp rvttkvsitr letaspptri
+ rtttsgvprg gepnqrpelk nhidrvdawv gtyfevkips
+ dtfydhedtt tdklkltlkl reqqlvgeks wvqfnsnsql
+ myglpdsshv gkheyfmhat dkgglsavda feihvhrrpq
+ gdraparfka kfvgdpalvl ndihkkialv kklafafgdr
+ ncstitlqni trgsivvewt nntlplepcp keqiaglsrr
+ iaeddgkprp afsnalepdf katsitvtgs gscrhlqfip
+ vvpprrvpse apptevpdrd peksseddvy lhtvipavvv
+ aailliagii amicyrkkrk gkltledqat fikkgvpiif
+ adelddskpp psssmplilq eekaplpppe ypnqsvpett
+ plnqdtmgey tplrdedpna ppyqppppft vpmegkgsrp
+ knmtpyrspp pyvpp </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-1242">
+ <names>
+ <shortLabel>CD80 antigen</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00202"/>
+ <secondaryRef db="RefSeq" id="NP_005182"/>
+ <secondaryRef db="Affymetrix" id="1554519_at"/>
+ <secondaryRef db="Affymetrix" id="1555689_at"/>
+ <secondaryRef db="Affymetrix" id="207176_s_at"/>
+ <secondaryRef db="Affymetrix" id="35015_at"/>
+ <secondaryRef db="Affymetrix" id="g4885122_3p_s_at"/>
+ <secondaryRef db="Affymetrix" id="Hs2.838.2.S1_3p_at"/>
+ <secondaryRef db="Affymetrix" id="Hs2.838.3.S1_3p_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mghtrrqgts pskcpylnff qllvlaglsh fcsgvihvtk
+ evkevatlsc ghnvsveela qtriywqkek kmvltmmsgd
+ mniwpeyknr tifditnnls ivilalrpsd egtyecvvlk
+ yekdafkreh laevtlsvka dfptpsisdf eiptsnirri
+ icstsggfpe phlswlenge elnainttvs qdpetelyav
+ sskldfnmtt nhsfmcliky ghlrvnqtfn wnttkqehfp
+ dnllpswait lisvngifvi ccltycfapr crerrrnerl
+ rresvrpv </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-1409">
+ <names>
+ <shortLabel>Cadherin 3</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00227"/>
+ <secondaryRef db="PubMed" id="9615235"/>
+ <secondaryRef db="RefSeq" id="NP_001784"/>
+ <secondaryRef db="Affymetrix" id="203256_at"/>
+ <secondaryRef db="Affymetrix" id="160031_at"/>
+ <secondaryRef db="Affymetrix" id="g4502722_3p_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mglprgplas llllqvcwlq caasepcrav freaevtlea
+ ggaeqepgqa lgkvfmgcpg qepalfstdn ddftvrnget
+ vqerrslker nplkifpskr ilrrhkrdwv vapisvpeng
+ kgpfpqrlnq lksnkdrdtk ifysitgpga dsppegvfav
+ eketgwllln kpldreeiak yelfghavse ngasvedpmn
+ isiivtdqnd hkpkftqdtf rgsvlegvlp gtsvmqvtat
+ deddaiytyn gvvaysihsq epkdphdlmf tihrstgtis
+ vissgldrek vpeytltiqa tdmdgdgstt tavavveild
+ andnapmfdp qkyeahvpen avghevqrlt vtdldapnsp
+ awratylimg gddgdhftit thpesnqgil ttrkgldfea
+ knqhtlyvev tneapfvlkl ptstativvh vedvneapvf
+ vppskvvevq egiptgepvc vytaedpdke nqkisyrilr
+ dpagwlamdp dsgqvtavgt ldredeqfvr nniyevmvla
+ mdngsppttg tgtllltlid vndhgpvpep rqiticnqsp
+ vrqvlnitdk dlsphtspfq aqltddsdiy wtaevneegd
+ tvvlslkkfl kqdtydvhls lsdhgnkeql tviratvcdc
+ hghvetcpgp wkggfilpvl gavlallfll lvllllvrkk
+ rkikeplllp eddtrdnvfy ygeegggeed qdyditqlhr
+ glearpevvl rndvaptiip tpmyrprpan pdeignfiie
+ nlkaantdpt appydtllvf dyegsgsdaa slssltssas
+ dqdqdydyln ewgsrfkkla dmygggedd </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-564">
+ <names>
+ <shortLabel>C reactive protein</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00422"/>
+ <secondaryRef db="RefSeq" id="NP_000558"/>
+ <secondaryRef db="Affymetrix" id="205753_at"/>
+ <secondaryRef db="Affymetrix" id="37020_at"/>
+ <secondaryRef db="Affymetrix" id="4901355_3p_at"/>
+ <secondaryRef db="Affymetrix" id="g10835134_3p_at"/>
+ <secondaryRef db="Affymetrix" id="g10835134_3p_x_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mekllcflvl tslshafgqt dmsrkafvfp kesdtsyvsl
+ kapltkplka ftvclhfyte lsstrgtvfs rmpprdktmr
+ ffifwskdig ysftvggsei lfevpevtva pvhictswes
+ asgivefwvd gkprvrkslk kgytvgaeas iilgqeqdsf
+ ggnfegsqsl vgdignvnmw dfvlspdein tiylggpfsp
+ nvlnwralky evqgevftkp qlwp </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-1321">
+ <names>
+ <shortLabel>Branched-chain aminotransferase 2</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00217"/>
+ <secondaryRef db="PubMed" id="9657861"/>
+ <secondaryRef db="RefSeq" id="NP_001181"/>
+ <secondaryRef db="Affymetrix" id="203576_at"/>
+ <secondaryRef db="Affymetrix" id="215654_at"/>
+ <secondaryRef db="Affymetrix" id="41111_at"/>
+ <secondaryRef db="Affymetrix" id="g4502374_3p_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.306660.0.S1_3p_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>maaaalgqiw arkllsvpwl lcgprryass sfkaadlqle
+ mtqkphkkpg pgeplvfgkt ftdhmlmvew ndkgwgqpri
+ qpfqnltlhp assslhyslq lfegmkafkg kdqqvrlfrp
+ wlnmdrmlrs amrlclpsfd klellecirr lievdkdwvp
+ daagtslyvr pvlignepsl gvsqprrall fvilcpvgay
+ fpggsvtpvs lladpafira wvggvgnykl ggnygptvlv
+ qqealkrgce qvlwlygpdh qltevgtmni fvywthedgv
+ lelvtpplng vilpgvvrqs lldmaqtwge frvvertitm
+ kqllraleeg rvrevfgsgt acqvcpvhri lykdrnlhip
+ tmengpelil rfqkelkeiq ygirahewmf pv </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-2545">
+ <names>
+ <shortLabel>NAD(P)H dehydrogenase, quinone 1</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00518"/>
+ <secondaryRef db="PubMed" id="2071140"/>
+ <secondaryRef db="RefSeq" id="NP_000894"/>
+ <secondaryRef db="Affymetrix" id="201467_s_at"/>
+ <secondaryRef db="Affymetrix" id="201468_s_at"/>
+ <secondaryRef db="Affymetrix" id="210519_s_at"/>
+ <secondaryRef db="Affymetrix" id="38066_at"/>
+ <secondaryRef db="Affymetrix" id="g4505414_3p_a_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.80706.0.A1_3p_a_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mvgrralivl ahsertsfny amkeaaaaal kkkgwevves
+ dlyamnfnpi isrkditgkl kdpanfqypa esvlaykegh
+ lspdivaeqk kleaadlvif qfplqwfgvp ailkgwferv
+ figefaytya amydkgpfrs kkavlsittg gsgsmyslqg
+ ihgdmnvilw piqsgilhfc gfqvlepqlt ysightpada
+ riqilegwkk rleniwdetp lyfapsslfd lnfqagflmk
+ kevqdeeknk kfglsvghhl gksiptdnqi kark </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-2747">
+ <names>
+ <shortLabel>Eukaryotic translation elongation factor 1,delta</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00560"/>
+ <secondaryRef db="RefSeq" id="NP_115754"/>
+ <secondaryRef db="Affymetrix" id="203113_s_at"/>
+ <secondaryRef db="Affymetrix" id="214394_x_at"/>
+ <secondaryRef db="Affymetrix" id="41256_at"/>
+ <secondaryRef db="Affymetrix" id="g4503478_3p_x_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.223241.1.A1_3p_x_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mrsgkasctl etvwedkhky eeaerrfyeh eatqaaasaq
+ qlpaegpamn gpgqddpeda deaeapdggs rrdprksqds
+ rkplqkkrkr spksglgpad lallglsaer vwldkslfdq
+ aessyrqkla dvaaqaawpp alapwglcth gnqvachhvt
+ wgiwvnkssf dqaerafvew sqalllapdg srrqgtpntg
+ qqvavpdlah qpsppvngqp plgslqalvr evwlekpryd
+ aaergfyeal fdghppgkvr lqeraglaeg arrgrrdrrg
+ rnilgnkrag lrradgeaps alpycyflqk daeapwlskp
+ aydsaecrhh aaealrvawc leaaslshrp gprsglsvss
+ lrpnrkmatn flahekiwfd kfkyddaerr fyeqmngpva
+ gasrqengas vilrdiarar eniqkslags sgpgassgts
+ gdhgelvvri aslevenqsl rgvvqelqqa isklearlnv
+ leksspghra tapqtqhvsp mrqveppakk patpaedded
+ ddidlfgsdn eeedkeaaql reerlrqyae kkakkpalva
+ kssilldvkp wddetdmaql eacvrsiqld glvwgasklv
+ pvgygirklq iqcvveddkv gtdlleeeit kfeehvqsvd iaafnki </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-3691">
+ <names>
+ <shortLabel>Hemoglobin gamma G</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00792"/>
+ <secondaryRef db="RefSeq" id="NP_000175"/>
+ <secondaryRef db="Affymetrix" id="213515_x_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mghfteedka titslwgkvn vedaggetlg rllvvypwtq
+ rffdsfgnls sasaimgnpk vkahgkkvlt slgdaikhld
+ dlkgtfaqls elhcdklhvd penfkllgnv lvtvlaihfg
+ keftpevqas wqkmvtgvas alssryh </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-851">
+ <names>
+ <shortLabel>Interleukin 8 receptor, beta</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00907"/>
+ <secondaryRef db="PubMed" id="1427896"/>
+ <secondaryRef db="RefSeq" id="NP_001548"/>
+ <secondaryRef db="Affymetrix" id="207008_at"/>
+ <secondaryRef db="Affymetrix" id="1032_at"/>
+ <secondaryRef db="Affymetrix" id="1033_g_at"/>
+ <secondaryRef db="Affymetrix" id="664_at"/>
+ <secondaryRef db="Affymetrix" id="g4504682_3p_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>medfnmesds fedfwkgedl snysysstlp pflldaapce
+ pesleinkyf vviiyalvfl lsllgnslvm lvilysrvgr
+ svtdvyllnl aladllfalt lpiwaaskvn gwifgtflck
+ vvsllkevnf ysgilllaci svdrylaivh atrtltqkry
+ lvkficlsiw glslllalpv llfrrtvyss nvspacyedm
+ gnntanwrml lrilpqsfgf ivpllimlfc ygftlrtlfk
+ ahmgqkhram rvifavvlif llcwlpynlv lladtlmrtq
+ viqetcerrn hidraldate ilgilhscln pliyafigqk
+ frhgllkila ihgliskdsl pkdsrpsfvg sssghtsttl </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-636">
+ <names>
+ <shortLabel>Fyn</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00655"/>
+ <secondaryRef db="PubMed" id="3330788"/>
+ <secondaryRef db="RefSeq" id="NP_002028"/>
+ <secondaryRef db="Affymetrix" id="1559101_at"/>
+ <secondaryRef db="Affymetrix" id="210105_s_at"/>
+ <secondaryRef db="Affymetrix" id="212486_s_at"/>
+ <secondaryRef db="Affymetrix" id="216033_s_at"/>
+ <secondaryRef db="Affymetrix" id="2039_s_at"/>
+ <secondaryRef db="Affymetrix" id="40479_at"/>
+ <secondaryRef db="Affymetrix" id="40480_s_at"/>
+ <secondaryRef db="Affymetrix" id="40481_r_at"/>
+ <secondaryRef db="Affymetrix" id="1559101_3p_at"/>
+ <secondaryRef db="Affymetrix" id="g181171_3p_a_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.169370.1.A2_3p_a_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.169370.3.A1_3p_a_at"/>
+ <secondaryRef db="Affymetrix" id="Hs2.209652.1.S1_3p_x_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mgcvqckdke atklteerdg slnqssgyry gtdptpqhyp
+ sfgvtsipny nnfhaaggqg ltvfggvnss shtgtlrtrg
+ gtgvtlfval ydyeartedd lsfhkgekfq ilnssegdww
+ earslttget gyipsnyvap vdsiqaeewy fgklgrkdae
+ rqllsfgnpr gtflireset tkgayslsir dwddmkgdhv
+ khykirkldn ggyyittraq fetlqqlvqh yseraaglcc
+ rlvvpchkgm prltdlsvkt kdvweipres lqlikrlgng
+ qfgevwmgtw ngntkvaikt lkpgtmspes fleeaqimkk
+ lkhdklvqly avvseepiyi vteymnkgsl ldflkdgegr
+ alklpnlvdm aaqvaagmay iermnyihrd lrsanilvgn
+ glickiadfg larliedney tarqgakfpi kwtapeaaly
+ grftiksdvw sfgilltelv tkgrvpypgm nnrevleqve
+ rgyrmpcpqd cpislhelmi hcwkkdpeer ptfeylqsfl
+ edyftatepq yqpgenl </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-2289">
+ <names>
+ <shortLabel>Crystallin, beta A3</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00429"/>
+ <secondaryRef db="PubMed" id="3770741"/>
+ <secondaryRef db="RefSeq" id="NP_005199"/>
+ <secondaryRef db="Affymetrix" id="206982_at"/>
+ <secondaryRef db="Affymetrix" id="36325_at"/>
+ <secondaryRef db="Affymetrix" id="g12056460_3p_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>metqaeqqel etlpttkmaq tnptpgslgp wkitiydqen
+ fqgkrmefts scpnvsersf dnvrslkves gawigyehts
+ fcgqqfiler geyprwdaws gsnayhierl msfrpicsan
+ hkeskmtife kenfigrqwe isddypslqa mgwfnnevgs
+ mkiqsgawvc yqypgyrgyq yilecdhhgg dykhwrewgs
+ haqtsqiqsi rriqq </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-858">
+ <names>
+ <shortLabel>Clathrin, heavy polypeptide</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00350"/>
+ <secondaryRef db="RefSeq" id="NP_004850"/>
+ <secondaryRef db="Affymetrix" id="200614_at"/>
+ <secondaryRef db="Affymetrix" id="210498_at"/>
+ <secondaryRef db="Affymetrix" id="220855_at"/>
+ <secondaryRef db="Affymetrix" id="239871_at"/>
+ <secondaryRef db="Affymetrix" id="41159_at"/>
+ <secondaryRef db="Affymetrix" id="g11493430_RC_3p_at"/>
+ <secondaryRef db="Affymetrix" id="g4758011_3p_at"/>
+ <secondaryRef db="Affymetrix" id="g7662551_3p_x_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.187416.0.A1_3p_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>maqilpirfq ehlqlqnlgi npanigfstl tmesdkfici
+ rekvgeqaqv viidmndpsn pirrpisads aimnpaskvi
+ alkagktlqi fniemkskmk ahtmtddvtf wkwislntva
+ lvtdnavyhw smegesqpvk mfdrhsslag cqiinyrtda
+ kqkwllltgi saqqnrvvga mqlysvdrkv sqpieghaas
+ faqfkmegna eestlfcfav rgqaggklhi ievgtpptgn
+ qpfpkkavdv ffppeaqndf pvamqisekh dvvflitkyg
+ yihlydletg tciymnrisg etifvtaphe atagiigvnr
+ kgqvlsvcve eeniipyitn vlqnpdlalr mavrnnlaga
+ eelfarkfna lfaqgnysea akvaanapkg ilrtpdtirr
+ fqsvpaqpgq tspllqyfgi lldqgqlnky eslelcrpvl
+ qqgrkqllek wlkedklecs eelgdlvksv dptlalsvyl
+ ranvpnkviq cfaetgqvqk ivlyakkvgy tpdwifllrn
+ vmrispdqgq qfaqmlvqde epladitqiv dvfmeynliq
+ qctaflldal knnrpsegpl qtrllemnlm hapqvadail
+ gnqmfthydr ahiaqlceka gllqralehf tdlydikrav
+ vhthllnpew lvnyfgslsv edsleclram lsanirqnlq
+ icvqvaskyh eqlstqslie lfesfksfeg lfyflgsivn
+ fsqdpdvhfk yiqaacktgq ikevericre sncydpervk
+ nflkeakltd qlpliivcdr fdfvhdlvly lyrnnlqkyi
+ eiyvqkvnps rlpvviggll dvdcsedvik nlilvvrgqf
+ stdelvaeve krnrlklllp wlearihegc eepathnala
+ kiyidsnnnp erflrenpyy dsrvvgkyce krdphlacva
+ yergqcdlel invcnenslf kslsrylvrr kdpelwgsvl
+ lesnpyrrpl idqvvqtals etqdpeevsv tvkafmtadl
+ pneliellek ivldnsvfse hrnlqnllil taikadrtrv
+ meyinrldny dapdianiai snelfeeafa ifrkfdvnts
+ avqvliehig nldrayefae rcnepavwsq lakaqlqkgm
+ vkeaidsyik addpssymev vqaantsgnw eelvkylqma
+ rkkaresyve telifalakt nrlaeleefi ngpnnahiqq
+ vgdrcydekm ydaakllynn vsnfgrlast lvhlgeyqaa
+ vdgarkanst rtwkevcfac vdgkefrlaq mcglhivvha
+ deleelinyy qdrgyfeeli tmleaalgle rahmgmftel
+ ailyskfkpq kmrehlelfw srvnipkvlr aaeqahlwae
+ lvflydkyee ydnaiitmmn hptdawkegq fkdiitkvan
+ velyyraiqf ylefkpllln dllmvlsprl dhtravnyfs
+ kvkqlplvkp ylrsvqnhnn ksvneslnnl fiteedyqal
+ rtsidaydnf dnislaqrle kheliefrri aaylfkgnnr
+ wkqsvelckk dslykdamqy aseskdtela eellqwflqe
+ ekrecfgacl ftcydllrpd vvletawrhn imdfampyfi
+ qvmkeyltkv dkldaseslr keeeqatetq pivygqpqlm
+ ltagpsvavp pqapfgygyt appygqpqpg fgysm </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-2225">
+ <names>
+ <shortLabel>Fibrinogen, gamma chain</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00621"/>
+ <secondaryRef db="PubMed" id="6957371"/>
+ <secondaryRef db="RefSeq" id="NP_068656"/>
+ <secondaryRef db="Affymetrix" id="219612_s_at"/>
+ <secondaryRef db="Affymetrix" id="226621_at"/>
+ <secondaryRef db="Affymetrix" id="36622_at"/>
+ <secondaryRef db="Affymetrix" id="g11761634_3p_at"/>
+ <secondaryRef db="Affymetrix" id="g11761634_3p_x_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.75431.3.S1_3p_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mswslhprnl ilyfyallfl sstcvayvat rdnccilder
+ fgsycpttcg iadflstyqt kvdkdlqsle dilhqvenkt
+ sevkqlikai qltynpdess kpnmidaatl ksrimleeim
+ kyeasilthd ssirylqeiy nsnnqkivnl kekvaqleaq
+ cqepckdtvq ihditgkdcq diankgakqs glyfikplka
+ nqqflvycei dgsgngwtvf qkrldgsvdf kknwiqykeg
+ fghlsptgtt efwlgnekih listqsaipy alrveledwn
+ grtstadyam fkvgpeadky rltyayfagg dagdafdgfd
+ fgddpsdkff tshngmqfst wdndndkfeg ncaeqdgsgw
+ wmnkchaghl ngvyyqggty skastpngyd ngiiwatwkt
+ rwysmkkttm kiipfnrlti gegqqhhlgg akqvrpehpa
+ eteydslype ddl </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-513">
+ <names>
+ <shortLabel>Matrix metalloproteinase 9</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00387"/>
+ <secondaryRef db="PubMed" id="7762981"/>
+ <secondaryRef db="RefSeq" id="NP_004985"/>
+ <secondaryRef db="Affymetrix" id="203936_s_at"/>
+ <secondaryRef db="Affymetrix" id="31859_at"/>
+ <secondaryRef db="Affymetrix" id="g4826835_3p_s_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mslwqplvlv llvlgccfaa prqrqstlvl fpgdlrtnlt
+ drqlaeeyly rygytrvaem rgeskslgpa llllqkqlsl
+ petgeldsat lkamrtprcg vpdlgrfqtf egdlkwhhhn
+ itywiqnyse dlpravidda farafalwsa vtpltftrvy
+ srdadiviqf gvaehgdgyp fdgkdgllah afppgpgiqg
+ dahfdddelw slgkgvvvpt rfgnadgaac hfpfifegrs
+ ysacttdgrs dglpwcstta nydtddrfgf cpserlytrd
+ gnadgkpcqf pfifqgqsys acttdgrsdg yrwcattany
+ drdklfgfcp tradstvmgg nsagelcvfp ftflgkeyst
+ ctsegrgdgr lwcattsnfd sdkkwgfcpd qgyslflvaa
+ hefghalgld hssvpealmy pmyrftegpp lhkddvngir
+ hlygprpepe prppttttpq ptapptvcpt gpptvhpser
+ ptagptgpps agptgpptag pstattvpls pvddacnvni
+ fdaiaeignq lylfkdgkyw rfsegrgsrp qgpfliadkw
+ palprkldsv feeplskklf ffsgrqvwvy tgasvlgprr
+ ldklglgadv aqvtgalrsg rgkmllfsgr rlwrfdvkaq
+ mvdprsasev drmfpgvpld thdvfqyrek ayfcqdrfyw
+ rvssrselnq vdqvgyvtyd ilqcped </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-3390">
+ <names>
+ <shortLabel>Glutathione S-transferase M4</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00706"/>
+ <secondaryRef db="RefSeq" id="NP_000841"/>
+ <secondaryRef db="Affymetrix" id="204149_s_at"/>
+ <secondaryRef db="Affymetrix" id="204418_x_at"/>
+ <secondaryRef db="Affymetrix" id="210912_x_at"/>
+ <secondaryRef db="Affymetrix" id="204149_3p_s_at"/>
+ <secondaryRef db="Affymetrix" id="g183662_3p_s_at"/>
+ <secondaryRef db="Affymetrix" id="g4504178_3p_at"/>
+ <secondaryRef db="Affymetrix" id="g4504178_3p_x_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>msmtlgywdi rglahairll leytdssyee kkytmgdapd
+ ydrsqwlnek fklgldfpnl pylidgahki tqsnailcyi
+ arkhnlcget eeekirvdil enqamdvsnq larvcyspdf
+ eklkpeylee lptmmqhfsq flgkrpwfvg dkitfvdfla
+ ydvldlhrif epncldafpn lkdfisrfeg lekisaymks
+ srflpkplyt rvavwgnk </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-522">
+ <names>
+ <shortLabel>Collagen, type IV, alpha 2</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00355"/>
+ <secondaryRef db="PubMed" id="3025878"/>
+ <secondaryRef db="RefSeq" id="NP_001837"/>
+ <secondaryRef db="Affymetrix" id="211964_at"/>
+ <secondaryRef db="Affymetrix" id="211966_at"/>
+ <secondaryRef db="Affymetrix" id="36659_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.75617.0.A1_3p_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.75617.0.A2_3p_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mgrdqravag palrrwlllg tvtvgflaqs vlagvkkfdv
+ pcggrdcsgg cqcypekggr gqpgpvgpqg yngppglqgf
+ pglqgrkgdk gergapgvtg pkgdvgargv sgfpgadgip
+ ghpgqggprg rpgydgcngt qgdsgpqgpp gsegftgppg
+ pqgpkgqkge pyalpkeerd ryrgepgepg lvgfqgppgr
+ pghvgqmgpv gapgrpgppg ppgpkgqqgn rglgfygvkg
+ ekgdvgqpgp ngipsdtlhp iiaptgvtfh pdqykgekgs
+ egepgirgis lkgeegimgf pglrgypgls gekgspgqkg
+ srgldgyqgp dgprgpkgea gdpgppglpa ysphpslakg
+ argdpgfpga qgepgsqgep gdpglpgppg lsigdgdqrr
+ glpgemgpkg figdpgipal yggppgpdgk rgppgppglp
+ gppgpdgflf glkgakgrag fpglpgspga pgpkgwkgda
+ gecrctegde aikglpglpg pkgfaginge pgrkgdkgdp
+ gqhglpgfpg lkgvpgniga pgpkgakgds rtittkgerg
+ qpgvpgvpgm kgddgspgrd gldgfpglpg ppgdgikgpp
+ gdpgypgipg tkgtpgemgp pglglpglkg qrgfpgdagl
+ pgppgflgpp gpagtpgqid cdtdvkravg gdrqeaiqpg
+ ciggpkglpg lpgppgptga kglrgipgfa gadggpgprg
+ lpgdagregf pgppgfigpr gskgavglpg pdgspgpigl
+ pgpdgppger glpgevlgaq pgprgdagvp gqpglkglpg
+ drgppgfrgs qgmpgmpglk gqpglpgpsg qpglygppgl
+ hgfpgapgqe gplglpgipg reglpgdrgd pgdtgapgpv
+ gmkglsgdrg dagftgeqgh pgspgfkgid gmpgtpglkg
+ drgspgmdgf qgmpglkgrp gfpgskgeag ffgipglkgl
+ agepgfkgsr gdpgppgppp vilpgmkdik gekgdegpmg
+ lkgylgakgi qgmpgipgls gipglpgrpg hikgvkgdig
+ vpgipglpgf pgvagppgit gfpgfigsrg dkgapgragl
+ ygeigatgdf gdigdtinlp grpglkgerg ttgipglkgf
+ fgekgtegdi gfpgitgvtg vqgppglkgq tgfpgltgpp
+ gsqgelgrig lpggkgddgw pgapglpgfp glrgirglhg
+ lpgtkgfpgs pgsdihgdpg fpgppgergd pgeantlpgp
+ vgvpgqkgdq gapgergppg spglqgfpgi tppsnisgap
+ gdkgapgifg lkgyrgppgp pgsaalpgsk gdtgnpgapg
+ tpgtkgwagd sgpqgrpgvf glpgekgprg eqgfmgntgp
+ tgavgdrgpk gpkgdpgfpg apgtvgapgi agipqkiavq
+ pgtvgpqgrr gppgapgemg pqgppgepgf rgapgkagpq
+ grggvsavpg frgdegpigh qgpigqegap grpgspglpg
+ mpgrsvsigy llvkhsqtdq epmcpvgmnk lwsgysllyf
+ egqekahnqd lglagsclar fstmpflycn pgdvcyyasr
+ ndksywlstt aplpmmpvae deikpyisrc svceapaiai
+ avhsqdvsip hcpagwrslw igysflmhta agdegggqsl
+ vspgscledf ratpfiecng grgtchyyan kysfwlttip
+ eqsfqgspsa dtlkaglirt hisrcqvcmk nl </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-1423">
+ <names>
+ <shortLabel>Calpactin I, light chain</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00232"/>
+ <secondaryRef db="PubMed" id="8276421"/>
+ <secondaryRef db="RefSeq" id="NP_002957"/>
+ <secondaryRef db="Affymetrix" id="200872_at"/>
+ <secondaryRef db="Affymetrix" id="238909_at"/>
+ <secondaryRef db="Affymetrix" id="39338_at"/>
+ <secondaryRef db="Affymetrix" id="g4506760_3p_s_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.143873.0.A1_3p_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mpsqmehame tmmftfhkfa gdkgyltked lrvlmekefp
+ gflenqkdpl avdkimkdld qcrdgkvgfq sffsliaglt
+ iacndyfvvh mkqkgkk </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-2254">
+ <names>
+ <shortLabel>MSX2</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00421"/>
+ <secondaryRef db="RefSeq" id="NP_002440"/>
+ <secondaryRef db="Affymetrix" id="205555_s_at"/>
+ <secondaryRef db="Affymetrix" id="205556_at"/>
+ <secondaryRef db="Affymetrix" id="210319_x_at"/>
+ <secondaryRef db="Affymetrix" id="40733_f_at"/>
+ <secondaryRef db="Affymetrix" id="40734_r_at"/>
+ <secondaryRef db="Affymetrix" id="205556_3p_at"/>
+ <secondaryRef db="Affymetrix" id="210319_3p_x_at"/>
+ <secondaryRef db="Affymetrix" id="g1321637_3p_a_at"/>
+ <secondaryRef db="Affymetrix" id="g1722693_3p_at"/>
+ <secondaryRef db="Affymetrix" id="g1722693_3p_a_at"/>
+ <secondaryRef db="Affymetrix" id="g1722693_3p_x_at"/>
+ <secondaryRef db="Affymetrix" id="g6996018_3p_at"/>
+ <secondaryRef db="Affymetrix" id="g6996018_3p_a_at"/>
+ <secondaryRef db="Affymetrix" id="g6996018_3p_x_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>maspskgndl fspdeegpav vagpgpgpgg aegaaeerrv
+ kvsslpfsve almsdkkppk easplpaesa sagatlrpll
+ lsghgareah spgplvkpfe tasvksense dgaawmqepg
+ rysppprhms pttctlrkhk tnrkprtpft tsqllalerk
+ frqkqylsia eraefsssln ltetqvkiwf qnrrakakrl
+ qeaeleklkm aakpmlpssf slpfpisspl qaasiygasy
+ pfhrpvlpip pvglyatpvg ygmyhls </sequence>
+ </proteinInteractor>
+ <proteinInteractor id="CPATH-2007">
+ <names>
+ <shortLabel>Follicle stimulating hormone, beta polypeptide</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="HPRD" id="HPRD_00644"/>
+ <secondaryRef db="PubMed" id="2885163"/>
+ <secondaryRef db="RefSeq" id="NP_000501"/>
+ <secondaryRef db="Affymetrix" id="214489_at"/>
+ <secondaryRef db="Affymetrix" id="230_s_at"/>
+ <secondaryRef db="Affymetrix" id="Hs.36975.0.S1_3p_at"/>
+ </xref>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>Human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>mktlqffflf ccwkaiccns celtnitiai ekeecrfcis
+ inttwcagyc ytrdlvykdp arpkiqktct fkelvyetvr
+ vpgcahhads lytypvatqc hcgkcdsdst dctvrglgps
+ ycsfgemke </sequence>
+ </proteinInteractor>
+ </interactorList>
+ <interactionList>
+ <interaction>
+ <availabilityDescription id="NO_ID">
+ This data is copyrighted by Johns Hopkins
+ University. Commercial entities may not use
+ this without prior licensing authorization.
+ Other databases must agree to enforce the same
+ licensing guidelines before making this data public
+ on their website. </availabilityDescription>
+ <experimentList>
+ <experimentDescription id="I10656759756034_vt">
+ <bibref>
+ <xref>
+ <primaryRef db="PubMed" id="8340758"/>
+ <secondaryRef db="PubMed" id="7887967"/>
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>vt</shortLabel>
+ <fullName>in vitro</fullName>
+ </names>
+ <xref>
+ <primaryRef db="IOB" id="IOB:0002"/>
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+ </interactionDetection>
+ </experimentDescription>
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-687"/>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-687"/>
+ </proteinParticipant>
+ </participantList>
+ <attributeList>
+ <attribute name="HPRD Author">shibani</attribute>
+ <attribute name="last_updated">10_11_2004</attribute>
+ </attributeList>
+ </interaction>
+ <interaction>
+ <availabilityDescription id="NO_ID">
+ This data is copyrighted by Johns Hopkins
+ University. Commercial entities may not use
+ this without prior licensing authorization.
+ Other databases must agree to enforce the same
+ licensing guidelines before making this data public
+ on their website. </availabilityDescription>
+ <experimentList>
+ <experimentDescription id="I10972462160729_vt">
+ <bibref>
+ <xref>
+ <primaryRef db="PubMed" id="12269810"/>
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+ </bibref>
+ <interactionDetection>
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+ <shortLabel>vt</shortLabel>
+ <fullName>in vitro</fullName>
+ </names>
+ <xref>
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+ </interactionDetection>
+ </experimentDescription>
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-737"/>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-737"/>
+ </proteinParticipant>
+ </participantList>
+ <attributeList>
+ <attribute name="HPRD Author">dipanwita</attribute>
+ <attribute name="last_updated">10_11_2004</attribute>
+ </attributeList>
+ </interaction>
+ <interaction>
+ <availabilityDescription id="NO_ID">
+ This data is copyrighted by Johns Hopkins
+ University. Commercial entities may not use
+ this without prior licensing authorization.
+ Other databases must agree to enforce the same
+ licensing guidelines before making this data public
+ on their website. </availabilityDescription>
+ <experimentList>
+ <experimentDescription id="I10971649441428_vt">
+ <bibref>
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+ </bibref>
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+ <shortLabel>vt</shortLabel>
+ <fullName>in vitro</fullName>
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+ <xref>
+ <primaryRef db="IOB" id="IOB:0002"/>
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+ </interactionDetection>
+ </experimentDescription>
+ </experimentList>
+ <participantList>
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+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-740"/>
+ </proteinParticipant>
+ </participantList>
+ <attributeList>
+ <attribute name="HPRD Author">shibani</attribute>
+ <attribute name="last_updated">10_11_2004</attribute>
+ </attributeList>
+ </interaction>
+ <interaction>
+ <availabilityDescription id="NO_ID">
+ This data is copyrighted by Johns Hopkins
+ University. Commercial entities may not use
+ this without prior licensing authorization.
+ Other databases must agree to enforce the same
+ licensing guidelines before making this data public
+ on their website. </availabilityDescription>
+ <experimentList>
+ <experimentDescription id="I10513884369020_vv">
+ <bibref>
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+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>vv</shortLabel>
+ <fullName>in vivo</fullName>
+ </names>
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+ </interactionDetection>
+ </experimentDescription>
+ <experimentDescription id="I10513884369020_vt">
+ <bibref>
+ <xref>
+ <primaryRef db="PubMed" id="10872456"/>
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+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>vt</shortLabel>
+ <fullName>in vitro</fullName>
+ </names>
+ <xref>
+ <primaryRef db="IOB" id="IOB:0002"/>
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ </experimentList>
+ <participantList>
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+ <proteinInteractorRef ref="CPATH-822"/>
+ </proteinParticipant>
+ <proteinParticipant>
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+ </participantList>
+ <attributeList>
+ <attribute name="HPRD Author">dipanwita</attribute>
+ <attribute name="last_updated">10_11_2004</attribute>
+ </attributeList>
+ </interaction>
+ <interaction>
+ <availabilityDescription id="NO_ID">
+ This data is copyrighted by Johns Hopkins
+ University. Commercial entities may not use
+ this without prior licensing authorization.
+ Other databases must agree to enforce the same
+ licensing guidelines before making this data public
+ on their website. </availabilityDescription>
+ <experimentList>
+ <experimentDescription id="I10972438138774_vt">
+ <bibref>
+ <xref>
+ <primaryRef db="PubMed" id="7716522"/>
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+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>vt</shortLabel>
+ <fullName>in vitro</fullName>
+ </names>
+ <xref>
+ <primaryRef db="IOB" id="IOB:0002"/>
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ </experimentList>
+ <participantList>
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+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-321"/>
+ </proteinParticipant>
+ </participantList>
+ <attributeList>
+ <attribute name="HPRD Author">babylakshmi</attribute>
+ <attribute name="last_updated">10_11_2004</attribute>
+ </attributeList>
+ </interaction>
+ <interaction>
+ <availabilityDescription id="NO_ID">
+ This data is copyrighted by Johns Hopkins
+ University. Commercial entities may not use
+ this without prior licensing authorization.
+ Other databases must agree to enforce the same
+ licensing guidelines before making this data public
+ on their website. </availabilityDescription>
+ <experimentList>
+ <experimentDescription id="I10654193031139_vv">
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+ <interactionDetection>
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+ <shortLabel>vv</shortLabel>
+ <fullName>in vivo</fullName>
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+ </interactionDetection>
+ </experimentDescription>
+ <experimentDescription id="I10654193031139_vt">
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+ <fullName>in vitro</fullName>
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+ </experimentDescription>
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+ <attribute name="HPRD Author">julie</attribute>
+ <attribute name="last_updated">10_11_2004</attribute>
+ </attributeList>
+ </interaction>
+ <interaction>
+ <availabilityDescription id="NO_ID">
+ This data is copyrighted by Johns Hopkins
+ University. Commercial entities may not use
+ this without prior licensing authorization.
+ Other databases must agree to enforce the same
+ licensing guidelines before making this data public
+ on their website. </availabilityDescription>
+ <experimentList>
+ <experimentDescription id="I10969975027055_vt">
+ <bibref>
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+ <primaryRef db="PubMed" id="11049968"/>
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+ </experimentDescription>
+ </experimentList>
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+ <proteinParticipant>
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+ </proteinParticipant>
+ </participantList>
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+ <attribute name="HPRD Author">yathish</attribute>
+ <attribute name="last_updated">10_11_2004</attribute>
+ </attributeList>
+ </interaction>
+ <interaction>
+ <availabilityDescription id="NO_ID">
+ This data is copyrighted by Johns Hopkins
+ University. Commercial entities may not use
+ this without prior licensing authorization.
+ Other databases must agree to enforce the same
+ licensing guidelines before making this data public
+ on their website. </availabilityDescription>
+ <experimentList>
+ <experimentDescription id="I10908992623244_vv">
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+ </experimentDescription>
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+ </participantList>
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+ <attribute name="last_updated">10_11_2004</attribute>
+ </attributeList>
+ </interaction>
+ <interaction>
+ <availabilityDescription id="NO_ID">
+ This data is copyrighted by Johns Hopkins
+ University. Commercial entities may not use
+ this without prior licensing authorization.
+ Other databases must agree to enforce the same
+ licensing guidelines before making this data public
+ on their website. </availabilityDescription>
+ <experimentList>
+ <experimentDescription id="I10971554499736_vt">
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+ </bibref>
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+ <fullName>in vitro</fullName>
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+ <xref>
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+ </experimentDescription>
+ </experimentList>
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+ <proteinParticipant>
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+ </participantList>
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+ <attribute name="last_updated">10_11_2004</attribute>
+ </attributeList>
+ </interaction>
+ <interaction>
+ <availabilityDescription id="NO_ID">
+ This data is copyrighted by Johns Hopkins
+ University. Commercial entities may not use
+ this without prior licensing authorization.
+ Other databases must agree to enforce the same
+ licensing guidelines before making this data public
+ on their website. </availabilityDescription>
+ <experimentList>
+ <experimentDescription id="I10899047772252_vv">
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+ </bibref>
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+ <names>
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+ <fullName>in vivo</fullName>
+ </names>
+ <xref>
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+ </interactionDetection>
+ </experimentDescription>
+ <experimentDescription id="I10899047772252_vt">
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+ </bibref>
+ <interactionDetection>
+ <names>
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+ <fullName>in vitro</fullName>
+ </names>
+ <xref>
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+ </interactionDetection>
+ </experimentDescription>
+ </experimentList>
+ <participantList>
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+ <proteinParticipant>
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+ </proteinParticipant>
+ </participantList>
+ <attributeList>
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+ <attribute name="last_updated">10_11_2004</attribute>
+ </attributeList>
+ </interaction>
+ <interaction>
+ <availabilityDescription id="NO_ID">
+ This data is copyrighted by Johns Hopkins
+ University. Commercial entities may not use
+ this without prior licensing authorization.
+ Other databases must agree to enforce the same
+ licensing guidelines before making this data public
+ on their website. </availabilityDescription>
+ <experimentList>
+ <experimentDescription id="I10770335365272_vt">
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+ </bibref>
+ <interactionDetection>
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+ <fullName>in vitro</fullName>
+ </names>
+ <xref>
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+ </interactionDetection>
+ </experimentDescription>
+ </experimentList>
+ <participantList>
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+ </proteinParticipant>
+ <proteinParticipant>
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+ </proteinParticipant>
+ </participantList>
+ <attributeList>
+ <attribute name="HPRD Author">srinivas</attribute>
+ <attribute name="last_updated">10_11_2004</attribute>
+ </attributeList>
+ </interaction>
+ <interaction>
+ <availabilityDescription id="NO_ID">
+ This data is copyrighted by Johns Hopkins
+ University. Commercial entities may not use
+ this without prior licensing authorization.
+ Other databases must agree to enforce the same
+ licensing guidelines before making this data public
+ on their website. </availabilityDescription>
+ <experimentList>
+ <experimentDescription id="I10969854525036_vt">
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+ </bibref>
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+ <fullName>in vitro</fullName>
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+ </interactionDetection>
+ </experimentDescription>
+ </experimentList>
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+ </proteinParticipant>
+ <proteinParticipant>
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+ </proteinParticipant>
+ </participantList>
+ <attributeList>
+ <attribute name="HPRD Author">karthick</attribute>
+ <attribute name="last_updated">10_11_2004</attribute>
+ </attributeList>
+ </interaction>
+ <interaction>
+ <availabilityDescription id="NO_ID">
+ This data is copyrighted by Johns Hopkins
+ University. Commercial entities may not use
+ this without prior licensing authorization.
+ Other databases must agree to enforce the same
+ licensing guidelines before making this data public
+ on their website. </availabilityDescription>
+ <experimentList>
+ <experimentDescription id="I10435200757337_vv">
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+ <xref>
+ <primaryRef db="PubMed" id="7673243"/>
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+ </bibref>
+ <interactionDetection>
+ <names>
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+ <fullName>in vivo</fullName>
+ </names>
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+ </experimentDescription>
+ </experimentList>
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+ <proteinParticipant>
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+ </proteinParticipant>
+ </participantList>
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+ <attribute name="last_updated">10_11_2004</attribute>
+ </attributeList>
+ </interaction>
+ <interaction>
+ <availabilityDescription id="NO_ID">
+ This data is copyrighted by Johns Hopkins
+ University. Commercial entities may not use
+ this without prior licensing authorization.
+ Other databases must agree to enforce the same
+ licensing guidelines before making this data public
+ on their website. </availabilityDescription>
+ <experimentList>
+ <experimentDescription id="I10969815845673_vt">
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+ </experimentDescription>
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+ </participantList>
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+ </interaction>
+ <interaction>
+ <availabilityDescription id="NO_ID">
+ This data is copyrighted by Johns Hopkins
+ University. Commercial entities may not use
+ this without prior licensing authorization.
+ Other databases must agree to enforce the same
+ licensing guidelines before making this data public
+ on their website. </availabilityDescription>
+ <experimentList>
+ <experimentDescription id="I10603212086284_vt">
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+ </attributeList>
+ </interaction>
+ <interaction>
+ <availabilityDescription id="NO_ID">
+ This data is copyrighted by Johns Hopkins
+ University. Commercial entities may not use
+ this without prior licensing authorization.
+ Other databases must agree to enforce the same
+ licensing guidelines before making this data public
+ on their website. </availabilityDescription>
+ <experimentList>
+ <experimentDescription id="I10770780371776_vt">
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+ <proteinParticipant>
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+ <attribute name="last_updated">10_11_2004</attribute>
+ </attributeList>
+ </interaction>
+ <interaction>
+ <availabilityDescription id="NO_ID">
+ This data is copyrighted by Johns Hopkins
+ University. Commercial entities may not use
+ this without prior licensing authorization.
+ Other databases must agree to enforce the same
+ licensing guidelines before making this data public
+ on their website. </availabilityDescription>
+ <experimentList>
+ <experimentDescription id="I10435201745757_vv">
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+ Other databases must agree to enforce the same
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+ Other databases must agree to enforce the same
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+ Other databases must agree to enforce the same
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+ Other databases must agree to enforce the same
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+ Other databases must agree to enforce the same
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+ </experimentDescription>
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-1207"/>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-1207"/>
+ </proteinParticipant>
+ </participantList>
+ <attributeList>
+ <attribute name="HPRD Author">sriranjini</attribute>
+ <attribute name="last_updated">10_11_2004</attribute>
+ </attributeList>
+ </interaction>
+ <interaction>
+ <availabilityDescription id="NO_ID">
+ This data is copyrighted by Johns Hopkins
+ University. Commercial entities may not use
+ this without prior licensing authorization.
+ Other databases must agree to enforce the same
+ licensing guidelines before making this data public
+ on their website. </availabilityDescription>
+ <experimentList>
+ <experimentDescription id="I10920506872301_vt">
+ <bibref>
+ <xref>
+ <primaryRef db="PubMed" id="12145285"/>
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>vt</shortLabel>
+ <fullName>in vitro</fullName>
+ </names>
+ <xref>
+ <primaryRef db="IOB" id="IOB:0002"/>
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-3838"/>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-3838"/>
+ </proteinParticipant>
+ </participantList>
+ <attributeList>
+ <attribute name="HPRD Author">sriranjini</attribute>
+ <attribute name="last_updated">10_11_2004</attribute>
+ </attributeList>
+ </interaction>
+ <interaction>
+ <availabilityDescription id="NO_ID">
+ This data is copyrighted by Johns Hopkins
+ University. Commercial entities may not use
+ this without prior licensing authorization.
+ Other databases must agree to enforce the same
+ licensing guidelines before making this data public
+ on their website. </availabilityDescription>
+ <experimentList>
+ <experimentDescription id="I10974258642391_vt">
+ <bibref>
+ <xref>
+ <primaryRef db="PubMed" id="9605335"/>
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>vt</shortLabel>
+ <fullName>in vitro</fullName>
+ </names>
+ <xref>
+ <primaryRef db="IOB" id="IOB:0002"/>
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-1206"/>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-1206"/>
+ </proteinParticipant>
+ </participantList>
+ <attributeList>
+ <attribute name="HPRD Author">sriranjini</attribute>
+ <attribute name="last_updated">10_11_2004</attribute>
+ </attributeList>
+ </interaction>
+ <interaction>
+ <availabilityDescription id="NO_ID">
+ This data is copyrighted by Johns Hopkins
+ University. Commercial entities may not use
+ this without prior licensing authorization.
+ Other databases must agree to enforce the same
+ licensing guidelines before making this data public
+ on their website. </availabilityDescription>
+ <experimentList>
+ <experimentDescription id="I10970548108583_vt">
+ <bibref>
+ <xref>
+ <primaryRef db="PubMed" id="11976493"/>
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>vt</shortLabel>
+ <fullName>in vitro</fullName>
+ </names>
+ <xref>
+ <primaryRef db="IOB" id="IOB:0002"/>
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-3962"/>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-3962"/>
+ </proteinParticipant>
+ </participantList>
+ <attributeList>
+ <attribute name="HPRD Author">saravana</attribute>
+ <attribute name="last_updated">10_11_2004</attribute>
+ </attributeList>
+ </interaction>
+ <interaction>
+ <availabilityDescription id="NO_ID">
+ This data is copyrighted by Johns Hopkins
+ University. Commercial entities may not use
+ this without prior licensing authorization.
+ Other databases must agree to enforce the same
+ licensing guidelines before making this data public
+ on their website. </availabilityDescription>
+ <experimentList>
+ <experimentDescription id="I10649269236454_vv">
+ <bibref>
+ <xref>
+ <primaryRef db="PubMed" id="12888558"/>
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>vv</shortLabel>
+ <fullName>in vivo</fullName>
+ </names>
+ <xref>
+ <primaryRef db="IOB" id="IOB:0001"/>
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-851"/>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-851"/>
+ </proteinParticipant>
+ </participantList>
+ <attributeList>
+ <attribute name="HPRD Author">reshmi</attribute>
+ <attribute name="last_updated">10_11_2004</attribute>
+ </attributeList>
+ </interaction>
+ <interaction>
+ <availabilityDescription id="NO_ID">
+ This data is copyrighted by Johns Hopkins
+ University. Commercial entities may not use
+ this without prior licensing authorization.
+ Other databases must agree to enforce the same
+ licensing guidelines before making this data public
+ on their website. </availabilityDescription>
+ <experimentList>
+ <experimentDescription id="I10971669463111_vt">
+ <bibref>
+ <xref>
+ <primaryRef db="PubMed" id="2184886"/>
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>vt</shortLabel>
+ <fullName>in vitro</fullName>
+ </names>
+ <xref>
+ <primaryRef db="IOB" id="IOB:0002"/>
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-1225"/>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CPATH-1225"/>
+ </proteinParticipant>
+ </participantList>
+ <attributeList>
+ <attribute name="HPRD Author">shubha</attribute>
+ <attribute name="last_updated">10_11_2004</attribute>
+ </attributeList>
+ </interaction>
+ </interactionList>
+ </entry>
+</entrySet>
+
diff --git a/coreplugins/PSI-MI/src/test/resources/testData/psi_malformed.xml b/coreplugins/PSI-MI/src/test/resources/testData/psi_malformed.xml
new file mode 100755
index 0000000..5336dc5
--- /dev/null
+++ b/coreplugins/PSI-MI/src/test/resources/testData/psi_malformed.xml
@@ -0,0 +1,358 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<entrySet level="1" version="1" xmlns="net:sf:psidev:mi"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="net:sf:psidev:mi /Users/cerami/dev/sander/cytoscape/xml/MIF.xsd">
+ <entry>
+ <interactorList>
+ <proteinInteractor id="YHR119W">
+ <names>
+ <shortLabel>YHR119W</shortLabel>
+ <fullName>Gene has a SET or TROMO domain at its carboxyterminus like the
+ trithorax gene family from human and Drosophila with postulated function in
+ chromatin-mediated gene regulation.</fullNames>
+ </names>
+ <xref>
+ <primaryRef db="Entrez GI" id="529135"/>
+ <secondaryRef db="RefSeq GI" id="6321911"/>
+ <secondaryRef db="Entrez Protein_ID" id="AAB68867.1"/>
+ <secondaryRef db="CandidaDB" id="CA2985"/>
+ <secondaryRef db="InterPro" id="IPR001214"/>
+ <secondaryRef db="RefSeq Version" id="NP_011987.1"/>
+ <secondaryRef db="SwissProt" id="P38827"/>
+ <secondaryRef db="PIR" id="S48961"/>
+ <secondaryRef db="GenBank DNA Version" id="U00059.1"/>
+ <secondaryRef db="MIPS" id="YHR119W"/>
+ </xref>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>baker's yeast</shortLabel>
+ <fullName>Saccharomyces cerevisiae</fullName>
+ </names>
+ </organism>
+ <sequence>MNTYAQESKLRLKTKIGADGRCVIEDNFFTPPFKLMAPFYPKDDLAEIMLLAVSPGMMRGDAQDVQLNIGPNCKLRITSQSFEKIHNTEDGFASRDMHIVVGENAFLDFAPFPLIPFENAHFKGNTTISLRSSSQLLYSEIIVAGRVARNELFKFNRLHTKISILQDEKPIYYDNTILDPKTTDLNNMCMFDGYTHYLNLVLVNCPIELSGVRECIEESEGVDGAVSETASSHLCVKALAKGSEPLLHLREKIARLVTQTTTQKV</sequence>
+ </proteinInteractor>
+ <proteinInteractor id="YEL061C">
+ <names>
+ <shortLabel>YEL061C</shortLabel>
+ <fullName>Kinesin-related protein involved in establishment and maintenance of
+ mitotic spindle</fullName>
+ </names>
+ <xref>
+ <primaryRef db="Entrez GI" id="603257"/>
+ <secondaryRef db="RefSeq GI" id="6320774"/>
+ <secondaryRef db="Entrez Protein_ID" id="AAB65026.1"/>
+ <secondaryRef db="PIR" id="B42641"/>
+ <secondaryRef db="CandidaDB" id="CA4985"/>
+ <secondaryRef db="InterPro" id="IPR001752"/>
+ <secondaryRef db="GenBank DNA Version" id="M90522.1"/>
+ <secondaryRef db="RefSeq Version" id="NP_010853.1"/>
+ <secondaryRef db="SwissProt" id="P27895"/>
+ <secondaryRef db="GenBank DNA Version" id="U18795.1"/>
+ <secondaryRef db="MIPS" id="YEL061C"/>
+ <secondaryRef db="GenBank DNA Version" id="Z11859.1"/>
+ </xref>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>baker's yeast</shortLabel>
+ <fullName>Saccharomyces cerevisiae</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="YBR200W">
+ <names>
+ <shortLabel>YBR200W</shortLabel>
+ <fullName>SH3-domain protein that binds Cdc24p, Ste5p and Ste20p, and the
+ Rsr1p/Bud2p/Bup5p GTPase</fullName>
+ </names>
+ <xref>
+ <primaryRef db="Entrez GI" id="536573"/>
+ <secondaryRef db="RefSeq GI" id="6319677"/>
+ <secondaryRef db="CandidaDB" id="CA0514"/>
+ <secondaryRef db="Entrez Protein_ID" id="CAA85162.1"/>
+ <secondaryRef db="InterPro" id="IPR001452"/>
+ <secondaryRef db="InterPro" id="IPR001683"/>
+ <secondaryRef db="RefSeq Version" id="NP_009759.1"/>
+ <secondaryRef db="SwissProt" id="P29366"/>
+ <secondaryRef db="PIR" id="S23400"/>
+ <secondaryRef db="GenBank DNA Version" id="X63826.1"/>
+ <secondaryRef db="MIPS" id="YBR200W"/>
+ <secondaryRef db="GenBank DNA Version" id="Z21487.1"/>
+ <secondaryRef db="GenBank DNA Version" id="Z36069.1"/>
+ </xref>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>baker's yeast</shortLabel>
+ <fullName>Saccharomyces cerevisiae</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="YCR038C">
+ <names>
+ <shortLabel>YCR038C</shortLabel>
+ <fullName>GTP/GDP exchange factor for Rsr1 protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="RefSeq GI" id="10383799"/>
+ <secondaryRef db="Entrez GI" id="1907180"/>
+ <secondaryRef db="PIR" id="BWBYD5"/>
+ <secondaryRef db="CandidaDB" id="CA0382"/>
+ <secondaryRef db="Entrez Protein_ID" id="CAA42305.1"/>
+ <secondaryRef db="InterPro" id="IPR001895"/>
+ <secondaryRef db="GenBank DNA Version" id="M63552.1"/>
+ <secondaryRef db="GenBank DNA Version" id="M68938.1"/>
+ <secondaryRef db="RefSeq Version" id="NP_009967.2"/>
+ <secondaryRef db="SwissProt" id="P25300"/>
+ <secondaryRef db="SwissProt/TrEMBL" id="Q06729"/>
+ <secondaryRef db="GenBank DNA Version" id="X56909.1"/>
+ <secondaryRef db="GenBank DNA Version" id="X59720.2"/>
+ <secondaryRef db="GenBank DNA Version" id="X63853.1"/>
+ <secondaryRef db="MIPS" id="YCR038C"/>
+ </xref>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>baker's yeast</shortLabel>
+ <fullName>Saccharomyces cerevisiae</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="YAL036C">
+ <names>
+ <shortLabel>YAL036C</shortLabel>
+ <fullName>Function Unknown Now; similar to Xenopus GTP-binding protein DRG</fullName>
+ </names>
+ <xref>
+ <primaryRef db="Entrez GI" id="595548"/>
+ <secondaryRef db="RefSeq GI" id="6319281"/>
+ <secondaryRef db="Entrez Protein_ID" id="AAC04995.1"/>
+ <secondaryRef db="GenBank DNA Version" id="AQ876073.1"/>
+ <secondaryRef db="CandidaDB" id="CA3893"/>
+ <secondaryRef db="InterPro" id="IPR000765"/>
+ <secondaryRef db="RefSeq Version" id="NP_009364.1"/>
+ <secondaryRef db="SwissProt" id="P39729"/>
+ <secondaryRef db="PIR" id="S51983"/>
+ <secondaryRef db="GenBank DNA Version" id="U12980.1"/>
+ <secondaryRef db="MIPS" id="YAL036C"/>
+ </xref>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>baker's yeast</shortLabel>
+ <fullName>Saccharomyces cerevisiae</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="YDL065C">
+ <names>
+ <shortLabel>YDL065C</shortLabel>
+ <fullName>40 kDa farnesylated protein associated with peroxisomes</fullName>
+ </names>
+ <xref>
+ <primaryRef db="Entrez GI" id="1431072"/>
+ <secondaryRef db="RefSeq GI" id="6320138"/>
+ <secondaryRef db="CandidaDB" id="CA5105"/>
+ <secondaryRef db="Entrez Protein_ID" id="CAA98630.1"/>
+ <secondaryRef db="RefSeq Version" id="NP_010218.1"/>
+ <secondaryRef db="SwissProt" id="Q07418"/>
+ <secondaryRef db="PIR" id="S67600"/>
+ <secondaryRef db="MIPS" id="YDL065C"/>
+ <secondaryRef db="GenBank DNA Version" id="Z74113.1"/>
+ </xref>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>baker's yeast</shortLabel>
+ <fullName>Saccharomyces cerevisiae</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="YDR532C">
+ <names>
+ <shortLabel>YDR532C</shortLabel>
+ <fullName>Killer toxin REsistant</fullName>
+ </names>
+ <xref>
+ <primaryRef db="RefSeq GI" id="6320741"/>
+ <secondaryRef db="Entrez GI" id="927799"/>
+ <secondaryRef db="Entrez Protein_ID" id="AAB64971.1"/>
+ <secondaryRef db="CandidaDB" id="CA0383"/>
+ <secondaryRef db="RefSeq Version" id="NP_010821.1"/>
+ <secondaryRef db="SwissProt" id="Q04431"/>
+ <secondaryRef db="PIR" id="S69587"/>
+ <secondaryRef db="GenBank DNA Version" id="U33057.1"/>
+ <secondaryRef db="MIPS" id="YDR532C"/>
+ </xref>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>baker's yeast</shortLabel>
+ <fullName>Saccharomyces cerevisiae</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ </interactorList>
+ <interactionList>
+ <interaction>
+ <experimentList>
+ <experimentDescription id="no_id">
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="11283351"/>
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>classical two hybrid</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="PSI-MI" id="MI:0018"/>
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="YCR038C"/>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="YAL036C"/>
+ </proteinParticipant>
+ </participantList>
+ </interaction>
+ <interaction>
+ <experimentList>
+ <experimentDescription id="no_id">
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="11283351"/>
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>classical two hybrid</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="PSI-MI" id="MI:0018"/>
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="YCR038C"/>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="YDL065C"/>
+ </proteinParticipant>
+ </participantList>
+ </interaction>
+ <interaction>
+ <experimentList>
+ <experimentDescription id="no_id">
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="11283351"/>
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>classical two hybrid</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="PSI-MI" id="MI:0018"/>
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="YCR038C"/>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="YDR532C"/>
+ </proteinParticipant>
+ </participantList>
+ <xref>
+ <primaryRef db="DIP" id="61E"/>
+ <secondaryRef db="CPATH" id="12345"/>
+ </xref>
+ </interaction>
+ <interaction>
+ <experimentList>
+ <experimentDescription id="no_id">
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="11283351"/>
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>classical two hybrid</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="PSI-MI" id="MI:0018"/>
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="YCR038C"/>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="YEL061C"/>
+ </proteinParticipant>
+ </participantList>
+ </interaction>
+ <interaction>
+ <experimentList>
+ <experimentDescription id="no_id">
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="11283351"/>
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>classical two hybrid</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="PSI-MI" id="MI:0018"/>
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="YCR038C"/>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="YHR119W"/>
+ </proteinParticipant>
+ </participantList>
+ </interaction>
+ <interaction>
+ <experimentList>
+ <experimentDescription id="no_id">
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="91292524"/>
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>Synthetic Lethality</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="N/A" id="N/A"/>
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="YBR200W"/>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="YCR038C"/>
+ </proteinParticipant>
+ </participantList>
+ </interaction>
+ </interactionList>
+ </entry>
+</entrySet>
diff --git a/coreplugins/PSI-MI/src/test/resources/testData/psi_sample1.xml b/coreplugins/PSI-MI/src/test/resources/testData/psi_sample1.xml
new file mode 100755
index 0000000..397cb26
--- /dev/null
+++ b/coreplugins/PSI-MI/src/test/resources/testData/psi_sample1.xml
@@ -0,0 +1,358 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<entrySet level="1" version="1" xmlns="net:sf:psidev:mi"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="net:sf:psidev:mi /Users/cerami/dev/sander/cytoscape/xml/MIF.xsd">
+ <entry>
+ <interactorList>
+ <proteinInteractor id="YHR119W">
+ <names>
+ <shortLabel>YHR119W</shortLabel>
+ <fullName>Gene has a SET or TROMO domain at its carboxyterminus like the
+ trithorax gene family from human and Drosophila with postulated function in
+ chromatin-mediated gene regulation.</fullName>
+ </names>
+ <xref>
+ <primaryRef db="Entrez GI" id="529135"/>
+ <secondaryRef db="RefSeq GI" id="6321911"/>
+ <secondaryRef db="Entrez Protein_ID" id="AAB68867.1"/>
+ <secondaryRef db="CandidaDB" id="CA2985"/>
+ <secondaryRef db="InterPro" id="IPR001214"/>
+ <secondaryRef db="RefSeq Version" id="NP_011987.1"/>
+ <secondaryRef db="SwissProt" id="P38827"/>
+ <secondaryRef db="PIR" id="S48961"/>
+ <secondaryRef db="GenBank DNA Version" id="U00059.1"/>
+ <secondaryRef db="MIPS" id="YHR119W"/>
+ </xref>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>baker's yeast</shortLabel>
+ <fullName>Saccharomyces cerevisiae</fullName>
+ </names>
+ </organism>
+ <sequence>MNTYAQESKLRLKTKIGADGRCVIEDNFFTPPFKLMAPFYPKDDLAEIMLLAVSPGMMRGDAQDVQLNIGPNCKLRITSQSFEKIHNTEDGFASRDMHIVVGENAFLDFAPFPLIPFENAHFKGNTTISLRSSSQLLYSEIIVAGRVARNELFKFNRLHTKISILQDEKPIYYDNTILDPKTTDLNNMCMFDGYTHYLNLVLVNCPIELSGVRECIEESEGVDGAVSETASSHLCVKALAKGSEPLLHLREKIARLVTQTTTQKV</sequence>
+ </proteinInteractor>
+ <proteinInteractor id="YEL061C">
+ <names>
+ <shortLabel>YEL061C</shortLabel>
+ <fullName>Kinesin-related protein involved in establishment and maintenance of
+ mitotic spindle</fullName>
+ </names>
+ <xref>
+ <primaryRef db="Entrez GI" id="603257"/>
+ <secondaryRef db="RefSeq GI" id="6320774"/>
+ <secondaryRef db="Entrez Protein_ID" id="AAB65026.1"/>
+ <secondaryRef db="PIR" id="B42641"/>
+ <secondaryRef db="CandidaDB" id="CA4985"/>
+ <secondaryRef db="InterPro" id="IPR001752"/>
+ <secondaryRef db="GenBank DNA Version" id="M90522.1"/>
+ <secondaryRef db="RefSeq Version" id="NP_010853.1"/>
+ <secondaryRef db="SwissProt" id="P27895"/>
+ <secondaryRef db="GenBank DNA Version" id="U18795.1"/>
+ <secondaryRef db="MIPS" id="YEL061C"/>
+ <secondaryRef db="GenBank DNA Version" id="Z11859.1"/>
+ </xref>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>baker's yeast</shortLabel>
+ <fullName>Saccharomyces cerevisiae</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="YBR200W">
+ <names>
+ <shortLabel>YBR200W</shortLabel>
+ <fullName>SH3-domain protein that binds Cdc24p, Ste5p and Ste20p, and the
+ Rsr1p/Bud2p/Bup5p GTPase</fullName>
+ </names>
+ <xref>
+ <primaryRef db="Entrez GI" id="536573"/>
+ <secondaryRef db="RefSeq GI" id="6319677"/>
+ <secondaryRef db="CandidaDB" id="CA0514"/>
+ <secondaryRef db="Entrez Protein_ID" id="CAA85162.1"/>
+ <secondaryRef db="InterPro" id="IPR001452"/>
+ <secondaryRef db="InterPro" id="IPR001683"/>
+ <secondaryRef db="RefSeq Version" id="NP_009759.1"/>
+ <secondaryRef db="SwissProt" id="P29366"/>
+ <secondaryRef db="PIR" id="S23400"/>
+ <secondaryRef db="GenBank DNA Version" id="X63826.1"/>
+ <secondaryRef db="MIPS" id="YBR200W"/>
+ <secondaryRef db="GenBank DNA Version" id="Z21487.1"/>
+ <secondaryRef db="GenBank DNA Version" id="Z36069.1"/>
+ </xref>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>baker's yeast</shortLabel>
+ <fullName>Saccharomyces cerevisiae</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="YCR038C">
+ <names>
+ <shortLabel>YCR038C</shortLabel>
+ <fullName>GTP/GDP exchange factor for Rsr1 protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="RefSeq GI" id="10383799"/>
+ <secondaryRef db="Entrez GI" id="1907180"/>
+ <secondaryRef db="PIR" id="BWBYD5"/>
+ <secondaryRef db="CandidaDB" id="CA0382"/>
+ <secondaryRef db="Entrez Protein_ID" id="CAA42305.1"/>
+ <secondaryRef db="InterPro" id="IPR001895"/>
+ <secondaryRef db="GenBank DNA Version" id="M63552.1"/>
+ <secondaryRef db="GenBank DNA Version" id="M68938.1"/>
+ <secondaryRef db="RefSeq Version" id="NP_009967.2"/>
+ <secondaryRef db="SwissProt" id="P25300"/>
+ <secondaryRef db="SwissProt/TrEMBL" id="Q06729"/>
+ <secondaryRef db="GenBank DNA Version" id="X56909.1"/>
+ <secondaryRef db="GenBank DNA Version" id="X59720.2"/>
+ <secondaryRef db="GenBank DNA Version" id="X63853.1"/>
+ <secondaryRef db="MIPS" id="YCR038C"/>
+ </xref>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>baker's yeast</shortLabel>
+ <fullName>Saccharomyces cerevisiae</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="YAL036C">
+ <names>
+ <shortLabel>YAL036C</shortLabel>
+ <fullName>Function Unknown Now; similar to Xenopus GTP-binding protein DRG</fullName>
+ </names>
+ <xref>
+ <primaryRef db="Entrez GI" id="595548"/>
+ <secondaryRef db="RefSeq GI" id="6319281"/>
+ <secondaryRef db="Entrez Protein_ID" id="AAC04995.1"/>
+ <secondaryRef db="GenBank DNA Version" id="AQ876073.1"/>
+ <secondaryRef db="CandidaDB" id="CA3893"/>
+ <secondaryRef db="InterPro" id="IPR000765"/>
+ <secondaryRef db="RefSeq Version" id="NP_009364.1"/>
+ <secondaryRef db="SwissProt" id="P39729"/>
+ <secondaryRef db="PIR" id="S51983"/>
+ <secondaryRef db="GenBank DNA Version" id="U12980.1"/>
+ <secondaryRef db="MIPS" id="YAL036C"/>
+ </xref>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>baker's yeast</shortLabel>
+ <fullName>Saccharomyces cerevisiae</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="YDL065C">
+ <names>
+ <shortLabel>YDL065C</shortLabel>
+ <fullName>40 kDa farnesylated protein associated with peroxisomes</fullName>
+ </names>
+ <xref>
+ <primaryRef db="Entrez GI" id="1431072"/>
+ <secondaryRef db="RefSeq GI" id="6320138"/>
+ <secondaryRef db="CandidaDB" id="CA5105"/>
+ <secondaryRef db="Entrez Protein_ID" id="CAA98630.1"/>
+ <secondaryRef db="RefSeq Version" id="NP_010218.1"/>
+ <secondaryRef db="SwissProt" id="Q07418"/>
+ <secondaryRef db="PIR" id="S67600"/>
+ <secondaryRef db="MIPS" id="YDL065C"/>
+ <secondaryRef db="GenBank DNA Version" id="Z74113.1"/>
+ </xref>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>baker's yeast</shortLabel>
+ <fullName>Saccharomyces cerevisiae</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="YDR532C">
+ <names>
+ <shortLabel>YDR532C</shortLabel>
+ <fullName>Killer toxin REsistant</fullName>
+ </names>
+ <xref>
+ <primaryRef db="RefSeq GI" id="6320741"/>
+ <secondaryRef db="Entrez GI" id="927799"/>
+ <secondaryRef db="Entrez Protein_ID" id="AAB64971.1"/>
+ <secondaryRef db="CandidaDB" id="CA0383"/>
+ <secondaryRef db="RefSeq Version" id="NP_010821.1"/>
+ <secondaryRef db="SwissProt" id="Q04431"/>
+ <secondaryRef db="PIR" id="S69587"/>
+ <secondaryRef db="GenBank DNA Version" id="U33057.1"/>
+ <secondaryRef db="MIPS" id="YDR532C"/>
+ </xref>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>baker's yeast</shortLabel>
+ <fullName>Saccharomyces cerevisiae</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ </interactorList>
+ <interactionList>
+ <interaction>
+ <experimentList>
+ <experimentDescription id="no_id">
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="11283351"/>
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>classical two hybrid</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="PSI-MI" id="MI:0018"/>
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="YCR038C"/>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="YAL036C"/>
+ </proteinParticipant>
+ </participantList>
+ </interaction>
+ <interaction>
+ <experimentList>
+ <experimentDescription id="no_id">
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="11283351"/>
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>classical two hybrid</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="PSI-MI" id="MI:0018"/>
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="YCR038C"/>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="YDL065C"/>
+ </proteinParticipant>
+ </participantList>
+ </interaction>
+ <interaction>
+ <experimentList>
+ <experimentDescription id="no_id">
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="11283351"/>
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>classical two hybrid</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="PSI-MI" id="MI:0018"/>
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="YCR038C"/>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="YDR532C"/>
+ </proteinParticipant>
+ </participantList>
+ <xref>
+ <primaryRef db="DIP" id="61E"/>
+ <secondaryRef db="CPATH" id="12345"/>
+ </xref>
+ </interaction>
+ <interaction>
+ <experimentList>
+ <experimentDescription id="no_id">
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="11283351"/>
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>classical two hybrid</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="PSI-MI" id="MI:0018"/>
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="YCR038C"/>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="YEL061C"/>
+ </proteinParticipant>
+ </participantList>
+ </interaction>
+ <interaction>
+ <experimentList>
+ <experimentDescription id="no_id">
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="11283351"/>
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>classical two hybrid</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="PSI-MI" id="MI:0018"/>
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="YCR038C"/>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="YHR119W"/>
+ </proteinParticipant>
+ </participantList>
+ </interaction>
+ <interaction>
+ <experimentList>
+ <experimentDescription id="no_id">
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="91292524"/>
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>Synthetic Lethality</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="N/A" id="N/A"/>
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="YBR200W"/>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="YCR038C"/>
+ </proteinParticipant>
+ </participantList>
+ </interaction>
+ </interactionList>
+ </entry>
+</entrySet>
diff --git a/coreplugins/PSI-MI/src/test/resources/testData/psi_sample2.xml b/coreplugins/PSI-MI/src/test/resources/testData/psi_sample2.xml
new file mode 100755
index 0000000..b581547
--- /dev/null
+++ b/coreplugins/PSI-MI/src/test/resources/testData/psi_sample2.xml
@@ -0,0 +1,97 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<entrySet level="1" version="1" xmlns="net:sf:psidev:mi"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="net:sf:psidev:mi /Users/cerami/dev/sander/cytoscape/xml/MIF.xsd">
+ <entry>
+ <interactorList>
+ <proteinInteractor id="A">
+ <names>
+ <shortLabel>A</shortLabel>
+ <fullName>Gene has a SET or TROMO domain at its carboxyterminus like the
+ trithorax gene family from human and Drosophila with postulated function in
+ chromatin-mediated gene regulation.</fullName>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>baker's yeast</shortLabel>
+ <fullName>Saccharomyces cerevisiae</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="B">
+ <names>
+ <shortLabel>B</shortLabel>
+ <fullName>Kinesin-related protein involved in establishment and maintenance of
+ mitotic spindle</fullName>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>baker's yeast</shortLabel>
+ <fullName>Saccharomyces cerevisiae</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="C">
+ <names>
+ <shortLabel>C</shortLabel>
+ <fullName>SH3-domain protein that binds Cdc24p, Ste5p and Ste20p, and the
+ Rsr1p/Bud2p/Bup5p GTPase</fullName>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>baker's yeast</shortLabel>
+ <fullName>Saccharomyces cerevisiae</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="D">
+ <names>
+ <shortLabel>D</shortLabel>
+ <fullName>SH3-domain protein that binds Cdc24p, Ste5p and Ste20p, and the
+ Rsr1p/Bud2p/Bup5p GTPase</fullName>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>baker's yeast</shortLabel>
+ <fullName>Saccharomyces cerevisiae</fullName>
+ </names>
+ </organism>
+ </proteinInteractor>
+ </interactorList>
+ <interactionList>
+ <interaction>
+ <experimentList>
+ <experimentDescription id="no_id">
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" id="11283351"/>
+ </xref>
+ </bibref>
+ <interactionDetection>
+ <names>
+ <shortLabel>classical two hybrid</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="PSI-MI" id="MI:0018"/>
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ </experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="A"/>
+ <role>bait</role>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="B"/>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="C"/>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="D"/>
+ </proteinParticipant>
+ </participantList>
+ </interaction>
+ </interactionList>
+ </entry>
+</entrySet>
diff --git a/coreplugins/PSI-MI/src/test/resources/testData/psi_sample_2_5_1.xml b/coreplugins/PSI-MI/src/test/resources/testData/psi_sample_2_5_1.xml
new file mode 100755
index 0000000..e9f521a
--- /dev/null
+++ b/coreplugins/PSI-MI/src/test/resources/testData/psi_sample_2_5_1.xml
@@ -0,0 +1,2624 @@
+<?xml version="1.0" encoding="UTF-8"?>
+ <entrySet level="2" version="5" xmlns="net:sf:psidev:mi" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="net:sf:psidev:mi http://psidev.sourceforge.net/mi/rel25/src/MIF25.xsd">
+ <entry>
+ <source releaseDate="2006-02-19">
+ <names>
+ <shortLabel>European Bioinformatics Institute</shortLabel>
+ </names>
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" dbAc="MI:0446" id="14681455" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </bibref>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0469" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ <attributeList>
+ <attribute name="postalAddress">Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom</attribute>
+ <attribute name="url">http://www.ebi.ac.uk</attribute>
+ </attributeList>
+ </source>
+ <experimentList>
+ <experimentDescription id="2">
+ <names>
+ <shortLabel>falsone-2005-1</shortLabel>
+ <fullName>A proteomic snapshot of the human heat shock protein 90 interactome.</fullName>
+ </names>
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" dbAc="MI:0446" id="16263121" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </bibref>
+ <xref>
+ <primaryRef db="intact" dbAc="MI:0469" id="EBI-709759" secondary="falsone-2005-1"/>
+ <secondaryRef db="newt" dbAc="MI:0247" id="9606" refType="target-species" secondary="human"/>
+ </xref>
+ <hostOrganismList>
+ <hostOrganism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human-293</shortLabel>
+ <fullName>Homo sapiens transformed primary embryonal kidney cells</fullName>
+ </names>
+ <cellType>
+ <names>
+ <shortLabel>293</shortLabel>
+ <fullName>Transformed human primary embryonal kidney cells.</fullName>
+ </names>
+ <xref>
+ <primaryRef db="cabri" dbAc="MI:0246" id="ACC 305" refType="identity" refTypeAc="MI:0356"/>
+ </xref>
+ </cellType>
+ </hostOrganism>
+ </hostOrganismList>
+ <interactionDetectionMethod>
+ <names>
+ <shortLabel>anti bait coip</shortLabel>
+ <fullName>anti bait coimmunoprecipitation</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0006" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="7708014" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactionDetectionMethod>
+ <participantIdentificationMethod>
+ <names>
+ <shortLabel>fingerprinting</shortLabel>
+ <fullName>peptide massfingerprinting</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0082" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="10967324" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="11752590" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="11805826" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </participantIdentificationMethod>
+ <attributeList>
+ <attribute name="exp-modification">Anti-Hsp90 antibody (clone AC68) was used to immunopreciptate endogenous Hsp90 in HEK293 cell line. Co-immunoprecipitated proteins were analyzed by SDS-PAGE folllowed by silver staining. The bands were cut, dried, subjected to tryptic digestion and peptides were gel-extracted. Nano-HPLC-MS/MS sequencing was then used for protein identification.</attribute>
+ <attribute name="contact-email">andreas.kungl at uni-graz.at</attribute>
+ <attribute name="figure-legend">Table 1</attribute>
+ <attribute name="author-list">Falsone SF., Gesslbauer B., Tirk F., Piccinini AM., Kungl AJ.</attribute>
+ </attributeList>
+ </experimentDescription>
+ </experimentList>
+ <interactorList>
+ <interactor id="4">
+ <names>
+ <shortLabel>hs90b_human</shortLabel>
+ <fullName>Heat shock protein HSP 90-beta</fullName>
+ <alias type="gene name" typeAc="MI:0301">HSPCB</alias>
+ <alias type="gene name synonym" typeAc="MI:0302">HSP90B</alias>
+ <alias type="gene name synonym" typeAc="MI:0302">HSPC2</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="P08238" refType="identity" refTypeAc="MI:0356" secondary="hs90b_human" version="SP_77"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005737" secondary="C:cytoplasm"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0030235" secondary="F:nitric-oxide synthase regula"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR003594" secondary="ATPbind_ATPase"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR001404" secondary="Hsp90"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q9NQW0" refType="secondary-ac" refTypeAc="MI:0360" secondary="hs90b_human" version="SP_77"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0030911" secondary="F:TPR domain binding"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0051082" secondary="F:unfolded protein binding"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0045429" secondary="P:positive regulation of nitri"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0006986" secondary="P:response to unfolded protein"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-352572" secondary="hs90b_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>PEEVHHGEEEVETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNASDALDKIRYESLTDPSKLDSGKELKIDIIPNPQERTLTLVDTGIGMTKADLINNLGTIAKSGTKAFMEALQAGADISMIGQFGVGFYSAYLVAEKVVVITKHNDDEQYAWESSAGGSFTVRADHGEPIGRGTKVILHLKEDQTEYLEERRVKEVVKKHSQFIGYPITLYLEKEREKEISDDEAEEEKGEKEEEDKDDEEKPKIEDVGSDEEDDSGKDKKKKTKKIKEKYIDQEELNKTKPIWTRNPDDITQEEYGEFYKSLTNDWEDHLAVKHFSVEGQLEFRALLFIPRRAPFDLFENKKKKNNIKLYVRRVFIMDSCDELIPEYLNFIRGVVDSEDLPLNISREMLQQSKILKVIRKNIVKKCLELFSELAEDKENYKKFYEAFSKNLKLGIHEDSTNRRRLSELLRYHTSQSGDEMTSLSEY [...]
+ </interactor>
+ <interactor id="6">
+ <names>
+ <shortLabel>hsp71_human</shortLabel>
+ <fullName>Heat shock 70 kDa protein 1</fullName>
+ <alias type="gene name" typeAc="MI:0301">HSPA1A</alias>
+ <alias type="gene name synonym" typeAc="MI:0302">HSPA1</alias>
+ <alias type="gene name" typeAc="MI:0301">HSPA1B</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="P08107" refType="identity" refTypeAc="MI:0356" secondary="hsp71_human" version="SP_71"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005737" secondary="C:cytoplasm"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005634" secondary="C:nucleus"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0006402" secondary="P:mRNA catabolism"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0006986" secondary="P:response to unfolded protein"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR001023" secondary="Hsp70"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="P19790" refType="secondary-ac" refTypeAc="MI:0360" secondary="hsp71_human" version="SP_71"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q9UQL9" refType="secondary-ac" refTypeAc="MI:0360" secondary="hsp71_human" version="SP_71"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q9UQM0" refType="secondary-ac" refTypeAc="MI:0360" secondary="hsp71_human" version="SP_71"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-629985" secondary="hsp71_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>MAKAAAIGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQVALNPQNTVFDAKRLIGRKFGDPVVQSDMKHWPFQVINDGDKPKVQVSYKGETKAFYPEEISSMVLTKMKEIAEAYLGYPVTNAVITVPAYFNDSQRQATKDAGVIAGLNVLRIINEPTAAAIAYGLDRTGKGERNVLIFDLGGGTFDVSILTIDDGIFEVKATAGDTHLGGEDFDNRLVNHFVEEFKRKHKKDISQNKRAVRRLRTACERAKRTLSSSTQASLEIDSLFEGIDFYTSITRARFEELCSDLFRSTLEPVEKALRDAKLDKAQIHDLVLVGGSTRIPKVQKLLQDFFNGRDLNKSINPDEAVAYGAAVQAAILMGDKSENVQDLLLLDVAPLSLGLETAGGVMTALIKRNSTIPTKQTQIFTTYSDNQPGVLIQVYEGERAMTKDNNLLGRFELSGIPPAPRGV [...]
+ </interactor>
+ <interactor id="8">
+ <names>
+ <shortLabel>tcpa_human</shortLabel>
+ <fullName>T-complex protein 1, alpha subunit</fullName>
+ <alias type="gene name" typeAc="MI:0301">CCT1</alias>
+ <alias type="gene name synonym" typeAc="MI:0302">CCTA</alias>
+ <alias type="gene name synonym" typeAc="MI:0302">TCP1</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="P17987" refType="identity" refTypeAc="MI:0356" secondary="tcpa_human" version="SP_48"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005829" secondary="C:cytosol"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0051082" secondary="F:unfolded protein binding"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0007021" secondary="P:tubulin folding"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR002194" secondary="Chaperonin_TCP-1"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR001844" secondary="Chaprnin_Cpn60"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR002423" secondary="Cpn60/TCP-1"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR012715" secondary="Chap_CCT_alpha"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q15556" refType="secondary-ac" refTypeAc="MI:0360" secondary="tcpa_human" version="SP_48"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q5TCM3" refType="secondary-ac" refTypeAc="MI:0360" secondary="tcpa_human" version="SP_48"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-356553" secondary="tcpa_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>MEGPLSVFGDRSTGETIRSQNVMAAASIANIVKSSLGPVGLDKMLVDDIGDVTITNDGATILKLLEVEHPAAKVLCELADLQDKEVGDGTTSVVIIAAELLKNADELVKQKIHPTSVISGYRLACKEAVRYINENLIVNTDELGRDCLINAAKTSMSSKIIGINGDFFANMVVDAVLAIKYTDIRGQPRYPVNSVNILKAHGRSQMESMLISGYALNCVVGSQGMPKRIVNAKIACLDFSLQKTKMKLGVQVVITDPEKLDQIRQRESDITKERIQKILATGANVILTTGGIDDMCLKYFVEAGAMAVRRVLKRDLKRIAKASGATILSTLANLEGEETFEAAMLGQAEEVVQERICDDELILIKNTKARTSASIILRGANDFMCDEMERSLHDALCVVKRVLESKSVVPGGGAVEAALSIYLENYATSMGSREQLAIAEFARSLLVIPNTLAVNAAQDSTDLVAKLRAFH [...]
+ </interactor>
+ <interactor id="10">
+ <names>
+ <shortLabel>hs105_human</shortLabel>
+ <fullName>Heat-shock protein 105 kDa</fullName>
+ <alias type="gene name" typeAc="MI:0301">HSPH1</alias>
+ <alias type="gene name synonym" typeAc="MI:0302">HSP105</alias>
+ <alias type="gene name synonym" typeAc="MI:0302">HSP110</alias>
+ <alias type="gene name synonym" typeAc="MI:0302">KIAA0201</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="Q92598" refType="identity" refTypeAc="MI:0356" secondary="hs105_human" version="SP_48"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005737" secondary="C:cytoplasm"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0006986" secondary="P:response to unfolded protein"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR001023" secondary="Hsp70"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="O95739" refType="secondary-ac" refTypeAc="MI:0360" secondary="hs105_human" version="SP_48"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q9UPC4" refType="secondary-ac" refTypeAc="MI:0360" secondary="hs105_human" version="SP_48"/>
+ <secondaryRef db="huge" dbAc="MI:0249" id="KIAA0201"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-356829" secondary="hs105_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>MSVVGLDVGSQSCYIAVARAGGIETIANEFSDRCTPSVISFGSKNRTIGVAAKNQQITHANNTVSNFKRFHGRAFNDPFIQKEKENLSYDLVPLKNGGVGIKVMYMGEEHLFSVEQITAMLLTKLKETAENSLKKPVTDCVISVPSFFTDAERRSVLDAAQIVGLNCLRLMNDMTAVALNYGIYKQDLPSLDEKPRIVVFVDMGHSAFQVSACAFNKGKLKVLGTAFDPFLGGKNFDEKLVEHFCAEFKTKYKLDAKSKIRALLRLYQECEKLKKLMSSNSTDLPLNIECFMNDKDVSGKMNRSQFEELCAELLQKIEVPLYSLLEQTHLKVEDVSAVEIVGGATRIPAVKERIAKFFGKDISTTLNADEAVARGCALQCAILSPAFKVREFSVTDAVPFPISLIWNHDSEDTEGVHEVFSRNHAAPFSKVLTFLRRGPFELEAFYSDPQGVPYPEAKIGRFVVQNVSAQK [...]
+ </interactor>
+ <interactor id="12">
+ <names>
+ <shortLabel>prkdc_human</shortLabel>
+ <fullName>DNA-dependent protein kinase catalytic subunit</fullName>
+ <alias type="gene name" typeAc="MI:0301">PRKDC</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="P78527" refType="identity" refTypeAc="MI:0356" secondary="prkdc_human" version="SP_48"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0004672" secondary="F:protein kinase activity"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0006464" secondary="P:protein modification"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR003151" secondary="FAT"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR003152" secondary="FATC"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR000403" secondary="PI3_PI4_kinase"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="P78528" refType="secondary-ac" refTypeAc="MI:0360" secondary="prkdc_human" version="SP_48"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q13327" refType="secondary-ac" refTypeAc="MI:0360" secondary="prkdc_human" version="SP_48"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q13337" refType="secondary-ac" refTypeAc="MI:0360" secondary="prkdc_human" version="SP_48"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q14175" refType="secondary-ac" refTypeAc="MI:0360" secondary="prkdc_human" version="SP_48"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q7Z611" refType="secondary-ac" refTypeAc="MI:0360" secondary="prkdc_human" version="SP_48"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q96SE6" refType="secondary-ac" refTypeAc="MI:0360" secondary="prkdc_human" version="SP_48"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q9UME3" refType="secondary-ac" refTypeAc="MI:0360" secondary="prkdc_human" version="SP_48"/>
+ <secondaryRef db="reactome protein" dbAc="MI:0245" id="P78527"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005515" secondary="F:protein binding"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR011989" secondary="ARM-like"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR000357" secondary="HEAT"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR012582" secondary="NUC194"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR002885" secondary="PPR"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR011990" secondary="TPR-like_helical"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-352053" secondary="prkdc_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>MAGSGAGVRCSLLRLQETLSAADRCGAALAGHQLIRGLGQECVLSSSPAVLALQTSLVFSRDFGLLVFVRKSLNSIEFRECREEILKFLCIFLEKMGQKIAPYSVEIKNTCTSVYTKDRAAKCKIPALDLLIKLLQTFRSSRLMDEFKIGELFSKFYGELALKKKIPDTVLEKVYELLGLLGEVHPSEMINNAENLFRAFLGELKTQMTSAVREPKLPVLAGCLKGLSSLLCNFTKSMEEDPQTSREIFNFVLKAIRPQIDLKRYAVPSAGLRLFALHASQFSTCLLDNYVSLFEVLLKWCAHTNVELKKAALSALESFLKQVSNMVAKNAEMHKNKLQYFMEQFYGIIRNVDSNNKELSIAIRGYGLFAGPCKVINAKDVDFMYVELIQRCKQMFLTQTDTGDDRVYQMPSFLQSVASVLLYLDTVPEVYTPVLEHLVVMQIDSFPQYSPKMQLVCCRAIVKVFLALAAK [...]
+ </interactor>
+ <interactor id="14">
+ <names>
+ <shortLabel>gnai2_human</shortLabel>
+ <fullName>Guanine nucleotide-binding protein G(i), alpha-2 subunit</fullName>
+ <alias type="gene name" typeAc="MI:0301">GNAI2</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="P04899" refType="identity" refTypeAc="MI:0356" secondary="gnai2_human" version="SP_48"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0003924" secondary="F:GTPase activity"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0007186" secondary="P:G-protein coupled receptor p"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0007194" secondary="P:negative regulation of adeny"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0007584" secondary="P:response to nutrients"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0007165" secondary="P:signal transduction"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR001019" secondary="Gprotein_alpha"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR001408" secondary="Gprotein_alphaI"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR011025" secondary="Transducn_insert"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-353997" secondary="gnai2_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>GCTVSAEDKAAAERSKMIDKNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEDGYSEEECRQYRAVVYSNTIQSIMAIVKAMGNLQIDFADPSRADDARQLFALSCTAEEQGVLPDDLSGVIRRLWADHGVQACFGRSREYQLNDSAAYYLNDLERIAQSDYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSAYDLVLAEDEEMNRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKITHSPLTICFPEYTGANKYDEAASYIQSKFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF</sequence>
+ </interactor>
+ <interactor id="16">
+ <names>
+ <shortLabel>xpo1_human</shortLabel>
+ <fullName>Exportin-1</fullName>
+ <alias type="gene name" typeAc="MI:0301">XPO1</alias>
+ <alias type="gene name synonym" typeAc="MI:0302">CRM1</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="O14980" refType="identity" refTypeAc="MI:0356" secondary="xpo1_human" version="SP_48"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005737" secondary="C:cytoplasm"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005635" secondary="C:nuclear membrane"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005654" secondary="C:nucleoplasm"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR001494" secondary="Importinb_N"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q63HP8" refType="secondary-ac" refTypeAc="MI:0360" secondary="xpo1_human" version="SP_48"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005515" secondary="F:protein binding"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR011989" secondary="ARM-like"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR000357" secondary="HEAT"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q68CP3" refType="secondary-ac" refTypeAc="MI:0360" secondary="xpo1_human" version="SP_48"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q99433" refType="secondary-ac" refTypeAc="MI:0360" secondary="xpo1_human" version="SP_48"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-355867" secondary="xpo1_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>MPAIMTMLADHAARQLLDFSQKLDINLLDNVVNCLYHGEGAQQRMAQEVLTHLKEHPDAWTRVDTILEFSQNMNTKYYGLQILENVIKTRWKILPRNQCEGIKKYVVGLIIKTSSDPTCVEKEKVYIGKLNMILVQILKQEWPKHWPTFISDIVGASRTSESLCQNNMVILKLLSEEVFDFSSGQITQVKSKHLKDSMCNEFSQIFQLCQFVMENSQNAPLVHATLETLLRFLNWIPLGYIFETKLISTLIYKFLNVPMFRNVSLKCLTEIAGVSVSQYEEQFVTLFTLTMMQLKQMLPLNTNIRLAYSNGKDDEQNFIQNLSLFLCTFLKEHDQLIEKRLNLRETLMEALHYMLLVSEVEETEIFKICLEYWNHLAAELYRESPFSTSASPLLSGSQHFDVPPRRQLYLPMLFKVRLLMVSRMAKPEEVLVVENDQGEVVREFMKDTDSINLYKNMRETLVYLTHLDYVD [...]
+ </interactor>
+ <interactor id="18">
+ <names>
+ <shortLabel>kpym_human</shortLabel>
+ <fullName>Pyruvate kinase, isozymes M1/M2</fullName>
+ <alias type="gene name" typeAc="MI:0301">PKM2</alias>
+ <alias type="gene name synonym" typeAc="MI:0302">PKM</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="P14618" refType="identity" refTypeAc="MI:0356" secondary="kpym_human" version="SP_48"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005829" secondary="C:cytosol"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0004743" secondary="F:pyruvate kinase activity"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0006096" secondary="P:glycolysis"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR001697" secondary="Pyruvate_kinase"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="P14786" refType="secondary-ac" refTypeAc="MI:0360" secondary="kpym_human" version="SP_48"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q96E76" refType="secondary-ac" refTypeAc="MI:0360" secondary="kpym_human" version="SP_48"/>
+ <secondaryRef db="reactome protein" dbAc="MI:0245" id="P14618"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q9BWB5" refType="secondary-ac" refTypeAc="MI:0360" secondary="kpym_human" version="SP_48"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q9UPF2" refType="secondary-ac" refTypeAc="MI:0360" secondary="kpym_human" version="SP_48"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005515" secondary="F:protein binding"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-353408" secondary="kpym_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>SKPHSEAGTAFIQTQQLHAAMADTFLEHMCRLDIDSPPITARNTGIICTIGPASRSVETLKEMIKSGMNVARLNFSHGTHEYHAETIKNVRTATESFASDPILYRPVAVALDTKGPEIRTGLIKGSGTAEVELKKGATLKITLDNAYMEKCDENILWLDYKNICKVVEVGSKIYVDDGLISLQVKQKGADFLVTEVENGGSLGSKKGVNLPGAAVDLPAVSEKDIQDLKFGVEQDVDMVFASFIRKASDVHEVRKVLGEKGKNIKIISKIENHEGVRRFDEILEASDGIMVARGDLGIEIPAEKVFLAQKMMIGRCNRAGKPVICATQMLESMIKKPRPTRAEGSDVANAVLDGADCIMLSGETAKGDYPLEAVRMQHLIAREAEAAIYHLQLFEELRRLAPITSDPTEATAVGAVEASFKCCSGAIIVLTKSGRSAHQVARYRPRAPIIAVTRNPQTARQAHLYRGIFPV [...]
+ </interactor>
+ <interactor id="20">
+ <names>
+ <shortLabel>g3p1_human</shortLabel>
+ <fullName>Glyceraldehyde-3-phosphate dehydrogenase, muscle</fullName>
+ <alias type="gene name" typeAc="MI:0301">GAPD</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="P00354" refType="identity" refTypeAc="MI:0356" secondary="g3p1_human" version="SP_47"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0004365" secondary="F:glyceraldehyde-3-phosphate d"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005737" secondary="C:cytoplasm"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0006096" secondary="P:glycolysis"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR000173" secondary="GAP_dhdrogenase"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR006424" secondary="GAPDH-I"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-709590" secondary="g3p1_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>GKVKVGVDGFGRIGRLVTRAAFNSGKVDIVAINDPFIDLHYMVYMFQYDSTHGKFHGTVKAEDGKLVIDGKAITIFQERDPENIKWGDAGTAYVVESTGVFTTMEKAGAHLKGGAKRIVISAPSADAPMFVMGVNHFKYANSLKIISNASCTTNCLAPLAKVIHDHFGIVEGLMTTVHAITATQKTVDSPSGKLWRGGRGAAQNLIPASTGAAKAVGKVIPELDGKLTGMAFRVPTANVSVLDLTCRLEKPAKYDDIKKVVKEASEGPLKGILGYTEDEVVSDDFNGSNHSSIFDAGAGIELNDTFVKLVSWYDNEFGYSERVVDLMAHMASKE</sequence>
+ </interactor>
+ <interactor id="22">
+ <names>
+ <shortLabel>pgk1_human</shortLabel>
+ <fullName>Phosphoglycerate kinase 1</fullName>
+ <alias type="gene name" typeAc="MI:0301">PGK1</alias>
+ <alias type="gene name synonym" typeAc="MI:0302">PGKA</alias>
+ <alias type="orf name" typeAc="MI:0306">OK/SW-cl.110</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="P00558" refType="identity" refTypeAc="MI:0356" secondary="pgk1_human" version="SP_48"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005524" secondary="F:ATP binding"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0004618" secondary="F:phosphoglycerate kinase acti"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0006096" secondary="P:glycolysis"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0016310" secondary="P:phosphorylation"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR001576" secondary="PGK"/>
+ <secondaryRef db="reactome protein" dbAc="MI:0245" id="P00558"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q6IBT6" refType="secondary-ac" refTypeAc="MI:0360" secondary="pgk1_human" version="SP_48"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q8NI87" refType="secondary-ac" refTypeAc="MI:0360" secondary="pgk1_human" version="SP_48"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-709599" secondary="pgk1_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>SLSNKLTLDKLDVKGKRVVMRVDFNVPMKNNQITNNQRIKAAVPSIKFCLDNGAKSVVLMSHLGRPDGVPMPDKYSLEPVAVELKSLLGKDVLFLKDCVGPEVEKACANPAAGSVILLENLRFHVEEEGKGKDASGNKVKAEPAKIEAFRASLSKLGDVYVNDAFGTAHRAHSSMVGVNLPQKAGGFLMKKELNYFAKALESPERPFLAILGGAKVADKIQLINNMLDKVNEMIIGGGMAFTFLKVLNNMEIGTSLFDEEGAKIVKDLMSKAEKNGVKITLPVDFVTADKFDENAKTGQATVASGIPAGWMGLDCGPESSKKYAEAVTRAKQIVWNGPVGVFEWEAFARGTKALMDEVVKATSRGCITIIGGGDTATCCAKWNTEDKVSHVSTGGGASLELLEGKVLPGVDALSNI</sequence>
+ </interactor>
+ <interactor id="24">
+ <names>
+ <shortLabel>ldha_human</shortLabel>
+ <fullName>L-lactate dehydrogenase A chain</fullName>
+ <alias type="gene name" typeAc="MI:0301">LDHA</alias>
+ <alias type="gene name synonym" typeAc="MI:0302">PIG19</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="P00338" refType="identity" refTypeAc="MI:0356" secondary="ldha_human" version="SP_48"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005829" secondary="C:cytosol"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0004459" secondary="F:L-lactate dehydrogenase acti"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR001236" secondary="ldh"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR001557" secondary="L_LDH_MDH"/>
+ <secondaryRef db="reactome protein" dbAc="MI:0245" id="P00338"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR011304" secondary="L-LDH-NAD"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005515" secondary="F:protein binding"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q53G53" refType="secondary-ac" refTypeAc="MI:0360" secondary="ldha_human" version="SP_48"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q6IBM7" refType="secondary-ac" refTypeAc="MI:0360" secondary="ldha_human" version="SP_48"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q6ZNV1" refType="secondary-ac" refTypeAc="MI:0360" secondary="ldha_human" version="SP_48"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-372327" secondary="ldha_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>ATLKDQLIYNLLKEEQTPQNKITVVGVGAVGMACAISILMKDLADELALVDVIEDKLKGEMMDLQHGSLFLRTPKIVSGKDYNVTANSKLVIITAGARQQEGESRLNLVQRNVNIFKFIIPNVVKYSPNCKLLIVSNPVDILTYVAWKISGFPKNRVIGSGCNLDSARFRYLMGERLGVHPLSCHGWVLGEHGDSSVPVWSGMNVAGVSLKTLHPDLGTDKDKEQWKEVHKQVVESAYEVIKLKGYTSWAIGLSVADLAESIMKNLRRVHPVSTMIKGLYGIKDDVFLSVPCILGQNGISDLVKVTLTSEEEARLKKSADTLWGIQKELQF</sequence>
+ </interactor>
+ <interactor id="26">
+ <names>
+ <shortLabel>aldoa_human</shortLabel>
+ <fullName>Fructose-bisphosphate aldolase A</fullName>
+ <alias type="gene name" typeAc="MI:0301">ALDOA</alias>
+ <alias type="gene name synonym" typeAc="MI:0302">ALDA</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="P04075" refType="identity" refTypeAc="MI:0356" secondary="aldoa_human" version="SP_49"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0004332" secondary="F:fructose-bisphosphate aldola"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0006000" secondary="P:fructose metabolism"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0006096" secondary="P:glycolysis"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0006941" secondary="P:striated muscle contraction"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR000741" secondary="Aldolase_I"/>
+ <secondaryRef db="reactome protein" dbAc="MI:0245" id="P04075"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q6FH76" refType="secondary-ac" refTypeAc="MI:0360" secondary="aldoa_human" version="SP_49"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-709613" secondary="aldoa_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>PYQYPALTPEQKKELSDIAHRIVAPGKGILAADESTGSIAKRLQSIGTENTEENRRFYRQLLLTADDRVNPCIGGVILFHETLYQKADDGRPFPQVIKSKGGVVGIKVDKGVVPLAGTNGETTTQGLDGLSERCAQYKKDGADFAKWRCVLKIGEHTPSALAIMENANVLARYASICQQNGIVPIVEPEILPDGDHDLKRCQYVTEKVLAAVYKALSDHHIYLEGTLLKPNMVTPGHACTQKFSHEEIAMATVTALRRTVPPAVTGITFLSGGQSEEEASINLNAINKCPLLKPWALTFSYGRALQASALKAWGGKKENLKAAQEEYVKRALANSLACQGKYTPSGQAGAAASESLFVSNHAY</sequence>
+ </interactor>
+ <interactor id="28">
+ <names>
+ <shortLabel>mdhc_human</shortLabel>
+ <fullName>Malate dehydrogenase, cytoplasmic</fullName>
+ <alias type="gene name" typeAc="MI:0301">MDH1</alias>
+ <alias type="gene name synonym" typeAc="MI:0302">MDHA</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="P40925" refType="identity" refTypeAc="MI:0356" secondary="mdhc_human" version="SP_49"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005829" secondary="C:cytosol"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0004470" secondary="F:malic enzyme activity"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR001557" secondary="L_LDH_MDH"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR001236" secondary="ldh"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR008267" secondary="Mal_dehydrog"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR010945" secondary="MalateDH_SF1"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR001252" secondary="Mdh_AS"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR011274" secondary="MDH_euk_cyt"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-709625" secondary="mdhc_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>SEPIRVLVTGAAGQIAYSLLYSIGNGSVFGKDQPIILVLLDITPMMGVLDGVLMELQDCALPLLKDVIATDKEDVAFKDLDVAILVGSMPRREGMERKDLLKANVKIFKSQGAALDKYAKKSVKVIVVGNPANTNCLTASKSAPSIPKENFSCLTRLDHNRAKAQIALKLGVTANDVKNVIIWGNHSSTQYPDVNHAKVKLQGKEVGVYEALKDDSWLKGEFVTTVQQRGAAVIKARKLSSAMSAAKAICDHVRDIWFGTPEGEFVSMGVISDGNSYGVPDDLLYSFPVVIKNKTWKFVEGLPINDFSREKMDLTAKELTEEKESAFEFLSSA</sequence>
+ </interactor>
+ <interactor id="30">
+ <names>
+ <shortLabel>fas_human</shortLabel>
+ <fullName>Fatty acid synthase</fullName>
+ <alias type="gene name" typeAc="MI:0301">FASN</alias>
+ <alias type="gene name synonym" typeAc="MI:0302">FAS</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="P49327" refType="identity" refTypeAc="MI:0356" secondary="fas_human" version="SP_48"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0006631" secondary="P:fatty acid metabolism"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR001227" secondary="Ac_trans"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR002085" secondary="Adh_zn_family"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR000794" secondary="Ketoacyl_synth"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR006162" secondary="Ppantne_S"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR006163" secondary="Pp_bind"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR000051" secondary="SAM_bind"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR001031" secondary="Thioesterase"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR002198" secondary="ADH_short"/>
+ <secondaryRef db="reactome protein" dbAc="MI:0245" id="P49327"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q13479" refType="secondary-ac" refTypeAc="MI:0360" secondary="fas_human" version="SP_48"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q16702" refType="secondary-ac" refTypeAc="MI:0360" secondary="fas_human" version="SP_48"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q6P4U5" refType="secondary-ac" refTypeAc="MI:0360" secondary="fas_human" version="SP_48"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q6SS02" refType="secondary-ac" refTypeAc="MI:0360" secondary="fas_human" version="SP_48"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q969R1" refType="secondary-ac" refTypeAc="MI:0360" secondary="fas_human" version="SP_48"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q96C68" refType="secondary-ac" refTypeAc="MI:0360" secondary="fas_human" version="SP_48"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q96IT0" refType="secondary-ac" refTypeAc="MI:0360" secondary="fas_human" version="SP_48"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR009081" secondary="ACP_like"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-356658" secondary="fas_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>MEEVVIAGMSGKLPESENLQEFWDNLIGGVDMVTDDDRRWKAGLYGLPRRSGKLKDLSRFDASFFGVHPKQAHTMDPQLRLLLEVTYEAIVDGGINPDSLRGTHTGVWVGVSGSETSEALSRDPETLVGYSMVGCQRAMMANRLSFFFDFRGPSIALDTACSSSLMALQNAYQAIHSGQCPAAIVGGINVLLKPNTSVQFLRLGMLSPEGTCKAFDTAGNGYCRSEGVVAVLLTKKSLARRVYATILNAGTNTDGFKEQGVTFPSGDIQEQLIRSLYQSAGVAPESFEYIEAHGTGTKVGDPQELNGITRALCATRQEPLLIGSTKSNMGHPEPASGLAALAKVLLSLEHGLWAPNLHFHSPNPEIPALLDGRLQVVDQPLPVRGGNVGINSFGFGGSNVHIILRPNTQPPPAPAPHATLPRLLRASGRTPEAVQKLLEQGLRHSQDLAFLSMLNDIAAVPATAMPFRGYA [...]
+ </interactor>
+ <interactor id="32">
+ <names>
+ <shortLabel>c1tc_human</shortLabel>
+ <fullName>C-1-tetrahydrofolate synthase, cytoplasmic</fullName>
+ <alias type="gene name" typeAc="MI:0301">MTHFD1</alias>
+ <alias type="gene name synonym" typeAc="MI:0302">MTHFC</alias>
+ <alias type="gene name synonym" typeAc="MI:0302">MTHFD</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="P11586" refType="identity" refTypeAc="MI:0356" secondary="c1tc_human" version="SP_49"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005739" secondary="C:mitochondrion"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0004329" secondary="F:formate-tetrahydrofolate lig"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0004477" secondary="F:methenyltetrahydrofolate cyc"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0004486" secondary="F:methylenetetrahydrofolate de"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR000559" secondary="Fmtethyd_synth"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR000672" secondary="THFDhg/Cyc_hydro"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q86VC9" refType="secondary-ac" refTypeAc="MI:0360" secondary="c1tc_human" version="SP_49"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q9BVP5" refType="secondary-ac" refTypeAc="MI:0360" secondary="c1tc_human" version="SP_49"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-709638" secondary="c1tc_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>APAEILNGKEISAQIRARLKNQVTQLKEQVPGFTPRLAILQVGNRDDSNLYINVKLKAAEEIGIKATHIKLPRTTTESEVMKYITSLNEDSTVHGFLVQLPLDSENSINTEEVINAIAPEKDVDGLTSINAGRLARGDLNDCFIPCTPKGCLELIKETGVPIAGRHAVVVGRSKIVGAPMHDLLLWNNATVTTCHSKTAHLDEEVNKGDILVVATGQPEMVKGEWIKPGAIVIDCGINYVPDDKKPNGRKVVGDVAYDEAKERASFITPVPGGVGPMTVAMLMQSTVESAKRFLEKFKPGKWMIQYNNLNLKTPVPSDIDISRSCKPKPIGKLAREIGLLSEEVELYGETKAKVLLSALERLKHRPDGKYVVVTGITPTPLGEGKSTTTIGLVQALGAHLYQNVFACVRQPSQGPTFGIKGGAAGGGYSQVIPMEEFNLHLTGDIHAITAANNLVAAAIDARIFHELTQTD [...]
+ </interactor>
+ <interactor id="34">
+ <names>
+ <shortLabel>serc_human</shortLabel>
+ <fullName>Phosphoserine aminotransferase</fullName>
+ <alias type="gene name" typeAc="MI:0301">PSAT1</alias>
+ <alias type="gene name synonym" typeAc="MI:0302">PSA</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="Q9Y617" refType="identity" refTypeAc="MI:0356" secondary="serc_human" version="SP_49"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0004648" secondary="F:phosphoserine transaminase a"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0006564" secondary="P:L-serine biosynthesis"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0008615" secondary="P:pyridoxine biosynthesis"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR000192" secondary="Aminotrans_V"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR003248" secondary="Pser_amintransf"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q96AW2" refType="secondary-ac" refTypeAc="MI:0360" secondary="serc_human" version="SP_49"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q9BQ12" refType="secondary-ac" refTypeAc="MI:0360" secondary="serc_human" version="SP_49"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-709652" secondary="serc_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>MDAPRQVVNFGPGPAKLPHSVLLEIQKELLDYKGVGISVLEMSHRSSDFAKIINNTENLVRELLAVPDNYKVIFLQGGGCGQFSAVPLNLIGLKAGRCADYVVTGAWSAKAAEEAKKFGTINIVHPKLGSYTKIPDPSTWNLNPDASYVYYCANETVHGVEFDFIPDVKGAVLVCDMSSNFLSKPVDVSKFGVIFAGAQKNVGSAGVTVVIVRDDLLGFALRECPSVLEYKVQAGNSSLYNTPPCFSIYVMGLVLEWIKNNGGAAAMEKLSSIKSQTIYEIIDNSQGFYVCPVEPQNRSKMNIPFRIGNAKGDDALEKRFLDKALELNMLSLKGHRSVGGIRASLYNAVTIEDVQKLAAFMKKFLEMHQL</sequence>
+ </interactor>
+ <interactor id="36">
+ <names>
+ <shortLabel>sias_human</shortLabel>
+ <fullName>Sialic acid synthase (N-acetylneuraminate synthase)</fullName>
+ <alias type="gene name" typeAc="MI:0301">NANS</alias>
+ <alias type="gene name synonym" typeAc="MI:0302">SAS</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="Q9NR45" refType="identity" refTypeAc="MI:0356" secondary="sias_human" version="SP_47"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005737" secondary="C:cytoplasm"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0008781" secondary="F:N-acylneuraminate cytidylylt"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0009103" secondary="P:lipopolysaccharide biosynthe"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR006190" secondary="Antifreeze_like"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR004144" secondary="NeuB"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q8WUV9" refType="secondary-ac" refTypeAc="MI:0360" secondary="sias_human" version="SP_47"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q9BWS6" refType="secondary-ac" refTypeAc="MI:0360" secondary="sias_human" version="SP_47"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q9NVD4" refType="secondary-ac" refTypeAc="MI:0360" secondary="sias_human" version="SP_47"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-709675" secondary="sias_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>MPLELELCPGRWVGGQHPCFIIAEIGQNHQGDLDVAKRMIRMAKECGADCAKFQKSELEFKFNRKALERPYTSKHSWGKTYGEHKRHLEFSHDQYRELQRYAEEVGIFFTASGMDEMAVEFLHELNVPFFKVGSGDTNNFPYLEKTAKKGRPMVISSGMQSMDTMKQVYQIVKPLNPNFCFLQCTSAYPLQPEDVNLRVISEYQKLFPDIPIGYSGHETGIAISVAAVALGAKVLERHITLDKTWKGSDHSASLEPGELAELVRSVRLVERALGSPTKQLLPCEMACNEKLGKSVVAKVKIPEGTILTMDMLTVKVGEPKGYPPEDIFNLVGKKVLVTVEEDDTIMEELVDNHGKKIKS</sequence>
+ </interactor>
+ <interactor id="38">
+ <names>
+ <shortLabel>actg_human</shortLabel>
+ <fullName>Actin, cytoplasmic 2</fullName>
+ <alias type="gene name" typeAc="MI:0301">ACTG1</alias>
+ <alias type="gene name synonym" typeAc="MI:0302">ACTG</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="P63261" refType="identity" refTypeAc="MI:0356" secondary="actg_human" version="SP_48"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR004001" secondary="Actin"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR004000" secondary="Actin_like"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="P02571" refType="secondary-ac" refTypeAc="MI:0360" secondary="actg_human" version="SP_48"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="P14104" refType="secondary-ac" refTypeAc="MI:0360" secondary="actg_human" version="SP_48"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="P99022" refType="secondary-ac" refTypeAc="MI:0360" secondary="actg_human" version="SP_48"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-351292" secondary="actg_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>MEEEIAALVIDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVLSLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFNSIMKCDVDIRKDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQEYDESGPSIVHRKCF</sequence>
+ </interactor>
+ <interactor id="40">
+ <names>
+ <shortLabel>tpm3_human</shortLabel>
+ <fullName>Tropomyosin alpha 3 chain</fullName>
+ <alias type="gene name" typeAc="MI:0301">TPM3</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="P06753" refType="identity" refTypeAc="MI:0356" secondary="tpm3_human" version="SP_48"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005856" secondary="C:cytoskeleton"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005862" secondary="C:muscle thin filament tropomy"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0006937" secondary="P:regulation of muscle contrac"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR002017" secondary="Spectrin"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR000533" secondary="Tropomyosin"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="P12324" refType="secondary-ac" refTypeAc="MI:0360" secondary="tpm3_human" version="SP_48"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q969Q2" refType="secondary-ac" refTypeAc="MI:0360" secondary="tpm3_human" version="SP_48"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q9NQH8" refType="secondary-ac" refTypeAc="MI:0360" secondary="tpm3_human" version="SP_48"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-355607" secondary="tpm3_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>MEAIKKKMQMLKLDKENALDRAEQAEAEQKQAEERSKQLEDELAAMQKKLKGTEDELDKYSEALKDAQEKLELAEKKAADAEAEVASLNRRIQLVEEELDRAQERLATALQKLEEAEKAADESERGMKVIENRALKDEEKMELQEIQLKEAKHIAEEADRKYEEVARKLVIIEGDLERTEERAELAESKCSELEEELKNVTNNLKSLEAQAEKYSQKEDKYEEEIKILTDKLKEAETRAEFAERSVAKLEKTIDDLEDELYAQKLKYKAISEELDHALNDMTSI</sequence>
+ </interactor>
+ <interactor id="42">
+ <names>
+ <shortLabel>flna_human</shortLabel>
+ <fullName>Filamin-A</fullName>
+ <alias type="gene name" typeAc="MI:0301">FLNA</alias>
+ <alias type="gene name synonym" typeAc="MI:0302">FLN</alias>
+ <alias type="gene name synonym" typeAc="MI:0302">FLN1</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="P21333" refType="identity" refTypeAc="MI:0356" secondary="flna_human" version="SP_68"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0015629" secondary="C:actin cytoskeleton"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0051015" secondary="F:actin filament binding"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0004871" secondary="F:signal transducer activity"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0030036" secondary="P:actin cytoskeleton organizat"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0007399" secondary="P:neurogenesis"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0043123" secondary="P:positive regulation of I-kap"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR001589" secondary="Actbind_actnin"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR001715" secondary="Calponin-like"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR001298" secondary="Filamin"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-350432" secondary="flna_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>SSSHSRAGQSAAGAAPGGGVDTRDAEMPATEKDLAEDAPWKKIQQNTFTRWCNEHLKCVSKRIANLQTDLSDGLRLIALLEVLSQKKMHRKHNQRPTFRQMQLENVSVALEFLDRESIKLVSIDSKAIVDGNLKLILGLIWTLILHYSISMPMWDEEEDEEAKKQTPKQRLLGWIQNKLPQLPITNFSRDWQSGRALGALVDSCAPGLCPDWDSWDASKPVTNAREAMQQADDWLGIPQVITPEEIVDPNVDEHSVMTYLSQFPKAKLKPGAPLRPKLNPKKARAYGPGIEPTGNMVKKRAEFTVETRSAGQGEVLVYVEDPAGHQEEAKVTANNDKNRTFSVWYVPEVTGTHKVTVLFAGQHIAKSPFEVYVDKSQGDASKVTAQGPGLEPSGNIANKTTYFEIFTAGAGTGEVEVVIQDPMGQKGTVEPQLEARGDSTYRCSYQPTMEGVHTVHVTFAGVPIPRSPYTV [...]
+ </interactor>
+ <interactor id="44">
+ <names>
+ <shortLabel>myh9_human</shortLabel>
+ <fullName>Myosin-9</fullName>
+ <alias type="gene name" typeAc="MI:0301">MYH9</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="P35579" refType="identity" refTypeAc="MI:0356" secondary="myh9_human" version="SP_48"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR000048" secondary="IQ_region"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR001609" secondary="myosin_head"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR004009" secondary="Myosin_N"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR002928" secondary="Myosin_tail"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR002017" secondary="Spectrin"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="O60805" refType="secondary-ac" refTypeAc="MI:0360" secondary="myh9_human" version="SP_48"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR000861" secondary="REM_rpt_rho_bd"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-350338" secondary="myh9_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>AQQAADKYLYVDKNFINNPLAQADWAAKKLVWVPSDKSGFEPASLKEEVGEEAIVELVENGKKVKVNKDDIQKMNPPKFSKVEDMAELTCLNEASVLHNLKERYYSGLIYTYSGLFCVVINPYKNLPIYSEEIVEMYKGKKRHEMPPHIYAITDTAYRSMMQDREDQSILCTGESGAGKTENTKKVIQYLAYVASSHKSKKDQGELERQLLQANPILEAFGNAKTVKNDNSSRFGKFIRINFDVNGYIVGANIETYLLEKSRAIRQAKEERTFHIFYYLLSGAGEHLKTDLLLEPYNKYRFLSNGHVTIPGQQDKDMFQETMEAMRIMGIPEEEQMGLLRVISGVLQLGNIVFKKERNTDQASMPDNTAAQKVSHLLGINVTDFTRGILTPRIKVGRDYVQKAQTKEQADFAIEALAKATYERMFRWLVLRINKALDKTKRQGASFIGILDIAGFEIFDLNSFEQLCINYT [...]
+ </interactor>
+ <interactor id="46">
+ <names>
+ <shortLabel>spta2_human</shortLabel>
+ <fullName>Spectrin alpha chain, brain</fullName>
+ <alias type="gene name" typeAc="MI:0301">SPTAN1</alias>
+ <alias type="gene name synonym" typeAc="MI:0302">SPTA2</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="Q13813" refType="identity" refTypeAc="MI:0356" secondary="spta2_human" version="SP_48"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005624" secondary="C:membrane fraction"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0008091" secondary="C:spectrin"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0003779" secondary="F:actin binding"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005200" secondary="F:structural constituent of cy"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR002048" secondary="EF-hand"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR001452" secondary="SH3"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR002017" secondary="Spectrin"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q13186" refType="secondary-ac" refTypeAc="MI:0360" secondary="spta2_human" version="SP_48"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q15324" refType="secondary-ac" refTypeAc="MI:0360" secondary="spta2_human" version="SP_48"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q16606" refType="secondary-ac" refTypeAc="MI:0360" secondary="spta2_human" version="SP_48"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR011992" secondary="EF-Hand_type"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q7Z6M5" refType="secondary-ac" refTypeAc="MI:0360" secondary="spta2_human" version="SP_48"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q9P0V0" refType="secondary-ac" refTypeAc="MI:0360" secondary="spta2_human" version="SP_48"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-351450" secondary="spta2_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>MDPSGVKVLETAEDIQERRQQVLDRYHRFKELSTLRRQKLEDSYRFQFFQRDAEELEKWIQEKLQIASDENYKDPTNLQGKLQKHQAFEAEVQANSGAIVKLDETGNLMISEGHFASETIRTRLMELHRQWELLLEKMREKGIKLLQAQKLVQYLRECEDVMDWINDKEAIVTSEELGQDLEHVEVLQKKFEEFQTDMAAHEERVNEVNQFAAKLIQEQHPEEELIKTKQDEVNAAWQRLKGLALQRQGKLFGAAEVQRFNRDVDETISWIKEKEQLMASDDFGRDLASVQALLRKHEGLERDLAALEDKVKALCAEADRLQQSHPLSATQIQVKREELITNWEQIRTLAAERHARLNDSYRLQRFLADFRDLTSWVTEMKALINADELASDVAGAEALLDRHQEHKGEIDAHEDSFKSADESGQALLAAGHYASDEVREKLTVLSEERAALLELWELRRQQYEQCMDLQL [...]
+ </interactor>
+ <interactor id="48">
+ <names>
+ <shortLabel>q14981</shortLabel>
+ <fullName>NuMA protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="Q14981" refType="identity" refTypeAc="MI:0356" secondary="q14981" version="25"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005634" secondary="C:nucleus"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005876" secondary="C:spindle microtubule"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005198" secondary="F:structural molecule activity"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0000090" secondary="P:mitotic anaphase"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0006997" secondary="P:nuclear organization and bio"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR002017" secondary="Spectrin"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-395496" secondary="q14981"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>MTLHATRGAALLSWVNSLHVADPVEAVLQLQDCSIFIKIIDRIHGTEEGQQILKQPVSERLDFVCSFLQKNRKHPSSPECLVSAQKVLEGSELELAKMTMLLLYHSTMSSKSPRDWEQFEYKIQAELAVILKFVLDHEDGLNLNEDLENFLQKAPVPSTCSSTFPEELSPPSHQAKREIRFLELQKVASSSSGNNFLSGSPASPMGDILQTPQFQMRRLKKQLADERSNRDELELELAENRKLLTEKDAQIAMMQQRIDRLALLNEKQAASPLEPKELEELRDKNESLTMRLHETLKQCQDLKTEKSQMDRKINQLSEENGDLSFKLREFASHLQQLQDALNELTEEHSKATQEWLEKQAQLEKELSAALQDKKCLEEKNEILQGKLSQLEEHLSQLQDNPPQEKGEVLGDVLQLETLKQEAATLAANNTQLQARVEMLETERGQQEAKLLAERGHFEEEKQQLSSLITDL [...]
+ </interactor>
+ <interactor id="50">
+ <names>
+ <shortLabel>actn1_human</shortLabel>
+ <fullName>Alpha-actinin 1</fullName>
+ <alias type="gene name" typeAc="MI:0301">ACTN1</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="P12814" refType="identity" refTypeAc="MI:0356" secondary="actn1_human" version="SP_48"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0015629" secondary="C:actin cytoskeleton"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005200" secondary="F:structural constituent of cy"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR001589" secondary="Actbind_actnin"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR001715" secondary="Calponin-like"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR002048" secondary="EF-hand"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR002017" secondary="Spectrin"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q9BTN1" refType="secondary-ac" refTypeAc="MI:0360" secondary="actn1_human" version="SP_48"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR011992" secondary="EF-Hand_type"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-351710" secondary="actn1_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>MDHYDSQQTNDYMQPEEDWDRDLLLDPAWEKQQRKTFTAWCNSHLRKAGTQIENIEEDFRDGLKLMLLLEVISGERLAKPERGKMRVHKISNVNKALDFIASKGVKLVSIGAEEIVDGNVKMTLGMIWTIILRFAIQDISVEETSAKEGLLLWCQRKTAPYKNVNIQNFHISWKDGLGFCALIHRHRPELIDYGKLRKDDPLTNLNTAFDVAEKYLDIPKMLDAEDIVGTARPDEKAIMTYVSSFYHAFSGAQKAETAANRICKVLAVNQENEQLMEDYEKLASDLLEWIRRTIPWLENRVPENTMHAMQQKLEDFRDYRRLHKPPKVQEKCQLEINFNTLQTKLRLSNRPAFMPSEGRMVSDINNAWGCLEQVEKGYEEWLLNEIRRLERLDHLAEKFRQKASIHEAWTDGKEAMLRQKDYETATLSEIKALLKKHEAFESDLAAHQDRVEQIAAIAQELNELDYYDSPS [...]
+ </interactor>
+ <interactor id="52">
+ <names>
+ <shortLabel>ube1_human</shortLabel>
+ <fullName>Ubiquitin-activating enzyme E1</fullName>
+ <alias type="gene name" typeAc="MI:0301">UBE1</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="P22314" refType="identity" refTypeAc="MI:0356" secondary="ube1_human" version="SP_49"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005524" secondary="F:ATP binding"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0046872" secondary="F:metal ion binding"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR000594" secondary="ThiF_NAD_FAD_bd"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR000127" secondary="UBact_repeat"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR000011" secondary="UBQ-activ_enz_E1"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q96E13" refType="secondary-ac" refTypeAc="MI:0360" secondary="ube1_human" version="SP_49"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-709688" secondary="ube1_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>MSSSPLSKKRRVSGPDPKPGSNCSPAQSVLSEVPSVPTNGMAKNGSEADIDEGLYSRQLYVLGHEAMKRLQTSSVLVSGLRGLGVEIAKNIILGGVKAVTLHDQGTAQWADLSSQFYLREEDIGKNRAEVSQPRLAELNSYVPVTAYTGPLVEDFLSGFQVVVLTNTPLEDQLRVGEFCHNRGIKLVVADTRGLFGQLFCDFGEEMILTDSNGEQPLSAMVSMVTKDNPGVVTCLDEARHGFESGDFVSFSEVQGMVELNGNQPMEIKVLGPYTFSICDTSNFSDYIRGGIVSQVKVPKKISFKSLVASLAEPDFVVTDFAKFSRPAQLHIGFQALHQFCAQHGRPPRPRNEEDAAELVALAQAVNARALPAVQQNNLDEDLIRKLAYVAAGDLAPINAFIGGLAAQEVMKACSGKFMPIMQWLYFDALECLPEDKEVLTEDKCLQRQNRYDGQVAVFGSDLQEKLGKQKY [...]
+ </interactor>
+ <interactor id="54">
+ <names>
+ <shortLabel>psd1_human</shortLabel>
+ <fullName>26S proteasome non-ATPase regulatory subunit 1</fullName>
+ <alias type="gene name" typeAc="MI:0301">PSMD1</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="Q99460" refType="identity" refTypeAc="MI:0356" secondary="psd1_human" version="SP_47"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005838" secondary="C:proteasome regulatory partic"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR002015" secondary="APC_proteasome"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR011989" secondary="ARM-like"/>
+ <secondaryRef db="reactome protein" dbAc="MI:0245" id="Q99460"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q6GMU5" refType="secondary-ac" refTypeAc="MI:0360" secondary="psd1_human" version="SP_47"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q6P2P4" refType="secondary-ac" refTypeAc="MI:0360" secondary="psd1_human" version="SP_47"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q6PJM7" refType="secondary-ac" refTypeAc="MI:0360" secondary="psd1_human" version="SP_47"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q6PKG9" refType="secondary-ac" refTypeAc="MI:0360" secondary="psd1_human" version="SP_47"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q86VU1" refType="secondary-ac" refTypeAc="MI:0360" secondary="psd1_human" version="SP_47"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q8IV79" refType="secondary-ac" refTypeAc="MI:0360" secondary="psd1_human" version="SP_47"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005515" secondary="F:protein binding"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-357874" secondary="psd1_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>MITSAAGIISLLDEDEPQLKEFALHKLNAVVNDFWAEISESVDKIEVLYEDEGFRSRQFAALVASKVFYHLGAFEESLNYALGAGDLFNVNDNSEYVETIIAKCIDHYTKQCVENADLPEGEKKPIDQRLEGIVNKMFQRCLDDHKYKQAIGIALETRRLDVFEKTILESNDVPGMLAYSLKLCMSLMQNKQFRNKVLRVLVKIYMNLEKPDFINVCQCLIFLDDPQAVSDILEKLVKEDNLLMAYQICFDLYESASQQFLSSVIQNLRTVGTPIASVPGSTNTGTVPGSEKDSDSMETEEKTSSAFVGKTPEASPEPKDQTLKMIKILSGEMAIELHLQFLIRNNNTDLMILKNTKDAVRNSVCHTATVIANSFMHCGTTSDQFLRDNLEWLARATNWAKFTATASLGVIHKGHEKEALQLMATYLPKDTSPGSAYQEGGGLYALGLIHANHGGDIIDYLLNQLKNASND [...]
+ </interactor>
+ <interactor id="56">
+ <names>
+ <shortLabel>q6pew2_human</shortLabel>
+ <fullName>Proteasome beta 5 subunit</fullName>
+ <alias type="gene name" typeAc="MI:0301">PSMB5</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="Q6PEW2" refType="identity" refTypeAc="MI:0356" secondary="q6pew2_human" version="TrEMBL_27"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0043234" secondary="C:protein complex"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0004298" secondary="F:threonine endopeptidase acti"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0006511" secondary="P:ubiquitin-dependent protein "/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR000243" secondary="Pept_T1A_subB"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR001353" secondary="Proteasome_A_B"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005829" secondary="C:cytosol"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005839" secondary="C:proteasome core complex (sen"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-709699" secondary="q6pew2_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>MALASVLERPLPVNQRGFFGLGGRADLLDLGPGSLSDGLSLAAPGWGVPEEPGIEMLHGTTTLAFKFRHGVIVAADSRATAGAYIASQTVKKVIEINPYLLGTMAGGAADCSFWERLLARQCRIYELRNKERISVAAASKLLANMVYQYKGMGLSMGTMICGWDKRGPGLYYVDSEGNRISGATFSVGSGSVYAYGVMDRGYSYDLEVEQAYDLARRAIYQATYRDAYSGGAVNLYHVREDGWIRVSSDNVADLHEKYSGSTP</sequence>
+ </interactor>
+ <interactor id="58">
+ <names>
+ <shortLabel>sya_human</shortLabel>
+ <fullName>Alanyl-tRNA synthetase</fullName>
+ <alias type="gene name" typeAc="MI:0301">AARS</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="P49588" refType="identity" refTypeAc="MI:0356" secondary="sya_human" version="SP_49"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005737" secondary="C:cytoplasm"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005625" secondary="C:soluble fraction"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0000049" secondary="F:tRNA binding"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0006419" secondary="P:alanyl-tRNA aminoacylation"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0008033" secondary="P:tRNA processing"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR003156" secondary="Pesterase_DHHA1"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR002318" secondary="tRNA-synt_2c"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR012947" secondary="tRNA_SAD"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q96FA0" refType="secondary-ac" refTypeAc="MI:0360" secondary="sya_human" version="SP_49"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-709710" secondary="sya_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>MDSTLTASEIRQRFIDFFKRNEHTYVHSSATIPLDDPTLLFANAGMNQFKPIFLNTIDPSHPMAKLSRAANTQKCIRAGGKQNDLDDVGKDVYHHTFFEMLGSWSFGDYFKELACKMALELLTQEFGIPIERLYVTYFGGDEAAGLEADLECKQIWQNLGLDDTKILPGNMKDNFWEMGDTGPCGPCSEIHYDRIGGRDAAHLVNQDDPNVLEIWNLVFIQYNREADGILKPLPKKSIDTGMGLERLVSVLQNKMSNYDTDLFVPYFEAIQKGTGARPYTGKVGAEDADGIDMAYRVLADHARTITVALADGGRPDNTGRGYVLRRILRRAVRYAHEKLNASRGFFATLVDVVVQSLGDAFPELKKDPDMVKDIINEEEVQFLKTLSRGRRILDRKIQSLGDSKTIPGDTAWLLYDTYGFPVDLTGLIAEEKGLVVDMDGFEEERKLAQLKSQGKGAGGEDLIMLDIYAIE [...]
+ </interactor>
+ <interactor id="60">
+ <names>
+ <shortLabel>q6pi85_human</shortLabel>
+ <fullName>IARS2 protein</fullName>
+ <alias type="gene name" typeAc="MI:0301">IARS2</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="Q6PI85" refType="identity" refTypeAc="MI:0356" secondary="q6pi85_human" version="TrEMBL_27"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005524" secondary="F:ATP binding"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0004822" secondary="F:isoleucine-tRNA ligase activ"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0008270" secondary="F:zinc ion binding"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0006428" secondary="P:isoleucyl-tRNA aminoacylatio"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR002300" secondary="tRNA-synt_1a"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR001412" secondary="tRNA-synt_I"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR002301" secondary="tRNA-synt_ile"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR010663" secondary="Znf_Fpg"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-709723" secondary="q6pi85_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>MKLLGRQQPDTELEIQQKCGFSELYSWQRERKVKTEFCLHDGPPYANGDPHVGHALNKILKDIANRFHMMNGSKIHFVPGWDCHGLPIEIKVLSELGREAQNLSAMEIRKKARSFAKAAIEKQKSAFIRWGIMADWNNCYYTFDGKYEAKQLRTFYQMYDKGLVYRSYKPVFWSPSSRTALAEAELEYNPEHVSRSIYVKFPLLKPSPKLASLIDGSSPVSILVWTTQPWTIPANEAVCYMPESKYAVVKCSKSGDLYVLAADKVASVASTLETTFETISTLSGVDLENGTCSHPLIPDKASPLLPANHVTMAKGTGLVHTAPAHGMEDYGVASQHNLPMDCLVDEDGVFTDVAGPELQNKAVLEEGTDVVIKMLQTAKNLLKEEKLVHSYPYDWRTKKPVVIRASKQWFINITDIKTAAKELLKKVKFIPGSALNGMVEMMDRRPYWCISRQRVWGVPIPVFHHKTKDEY [...]
+ </interactor>
+ <interactor id="62">
+ <names>
+ <shortLabel>ef2_human</shortLabel>
+ <fullName>Elongation factor 2</fullName>
+ <alias type="gene name" typeAc="MI:0301">EEF2</alias>
+ <alias type="gene name synonym" typeAc="MI:0302">EF2</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="P13639" refType="identity" refTypeAc="MI:0356" secondary="ef2_human" version="SP_48"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR000795" secondary="EF_GTPbind"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR000640" secondary="EFG_C"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR005517" secondary="EFG_IV"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR004161" secondary="EFTU_D2"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR005225" secondary="Small_GTP"/>
+ <secondaryRef db="reactome protein" dbAc="MI:0245" id="P13639"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-352560" secondary="ef2_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>VNFTVDQIRAIMDKKANIRNMSVIAHVDHGKSTLTDSLVCKAGIIASARAGETRFTDTRKDEQERCITIKSTAISLFYELSENDLNFIKQSKDGAGFLINLIDSPGHVDFSSEVTAALRVTDGALVVVDCVSGVCVQTETVLRQAIAERIKPVLMMNKMDRALLELQLEPEELYQTFQRIVENVNVIISTYGEGESGPMGNIMIDPVLGTVGFGSGLHGWAFTLKQFAEMYVAKFAAKGEGQLGPAERAKKVEDMMKKLWGDRYFDPANGKFSKSATSPEGKKLPRTFCQLILDPIFKVFDAIMNFKKEETAKLIEKLDIKLDSEDKDKEGKPLLKAVMRRWLPAGDALLQMITIHLPSPVTAQKYRCELLYEGPPDDEAAMGIKSCDPKGPLMMYISKMVPTSDKGRFYAFGRVFSGLVSTGLKVRIMGPNYTPGKKEDLYLKPIQRTILMMGRYVEPIEDVPCGNIVGL [...]
+ </interactor>
+ <interactor id="64">
+ <names>
+ <shortLabel>if33_human</shortLabel>
+ <fullName>Eukaryotic translation initiation factor 3 subunit 3</fullName>
+ <alias type="gene name" typeAc="MI:0301">EIF3S3</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="O15372" refType="identity" refTypeAc="MI:0356" secondary="if33_human" version="SP_47"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005852" secondary="C:eukaryotic translation initi"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0008135" secondary="F:translation factor activity,"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0006446" secondary="P:regulation of translational "/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR000555" secondary="Mov34_MPN_PAD1"/>
+ <secondaryRef db="reactome protein" dbAc="MI:0245" id="O15372"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-709735" secondary="if33_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>MASRKEGTGSTATSSSSTAGAAGKGKGKGGSGDSAVKQVQIDGLVVLKIIKHYQEEGQGTEVVQGVLLGLVVEDRLEITNCFPFPQHTEDDADFDEVQYQMEMMRSLRHVNIDHLHVGWYQSTYYGSFVTRALLDSQFSYQHAIEESVVLIYDPIKTAQGSLSLKAYRLTPKLMEVCKEKDFSPEALKKANITFEYMFEEVPIVIKNSHLINVLMWELEKKSAVADKHELLSLASSNHLGKNLQLLMDRVDEMSQDIVKYNTYMRNTSKQQQQKHQYQQRRQQENMQRQSRGEPPLPEEDLSKLFKPPQPPARMDSLLIAGQINTYCQNIKEFTAQNLGKLFMAQALQEYNN</sequence>
+ </interactor>
+ <interactor id="66">
+ <names>
+ <shortLabel>q6ipd1_human</shortLabel>
+ <fullName>Similar to Laminin receptor 1</fullName>
+ <alias type="gene name" typeAc="MI:0301">LOC388524</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="Q6IPD1" refType="identity" refTypeAc="MI:0356" secondary="q6ipd1_human" version="TrEMBL_27"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0015935" secondary="C:small ribosomal subunit"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0004872" secondary="F:receptor activity"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0003735" secondary="F:structural constituent of ri"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0006412" secondary="P:protein biosynthesis"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR001865" secondary="Ribosomal_S2"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR005707" secondary="Ribosomal_S2_e/a"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-709744" secondary="q6ipd1_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>MSGALDVLQMKEEDVLKFLAAGTHLGGTNLDFQMEQYIYKRKSDGIYIINLKRTWEKLLLAARAIVAIENPADVSVISSRNTGQRAVLKFAAATGATPIAGRFTPGTFTNQIQAAFWEPRLLVVTDPRADHQPLTEASYVNLPTIALCNTDSPLRYVDIAIPCNNKGAHSVGLMWWMLAREVLRMRGTISREHPWEVMPDLYFYRDPEEIEKEEQAAAEKAVTKEEFQGEWTAPAPEFTATQPEVADWSEGVQVPSVPIQQFPTEDWSAQPAMEDWSAAPTAQATEWVGATTDWS</sequence>
+ </interactor>
+ <interactor id="68">
+ <names>
+ <shortLabel>rla0_human</shortLabel>
+ <fullName>60S acidic ribosomal protein P0</fullName>
+ <alias type="gene name" typeAc="MI:0301">RPLP0</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="P05388" refType="identity" refTypeAc="MI:0356" secondary="rla0_human" version="SP_48"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005842" secondary="C:cytosolic large ribosomal su"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0003723" secondary="F:RNA binding"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0003735" secondary="F:structural constituent of ri"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0006412" secondary="P:protein biosynthesis"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR001813" secondary="Ribosomal_60S"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR001790" secondary="Ribosomal_L10"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q9BVK4" refType="secondary-ac" refTypeAc="MI:0360" secondary="rla0_human" version="SP_48"/>
+ <secondaryRef db="reactome protein" dbAc="MI:0245" id="P05388"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005515" secondary="F:protein binding"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-354101" secondary="rla0_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>MPREDRATWKSNYFLKIIQLLDDYPKCFIVGADNVGSKQMQQIRMSLRGKAVVLMGKNTMMRKAIRGHLENNPALEKLLPHIRGNVGFVFTKEDLTEIRDMLLANKVPAAARAGAIAPCEVTVPAQNTGLGPEKTSFFQALGITTKISRGTIEILSDVQLIKTGDKVGASEATLLNMLNISPFSFGLVIQQVFDNGSIYNPEVLDITEETLHSRFLEGVRNVASVCLQIGYPTVASVPHSIINGYKRVLALSVETDYTFPLAEKVKAFLADPSAFVAAAPVAAATTAAPAAAAAPAKVEAKEESEESDEDMGFGLFD</sequence>
+ </interactor>
+ <interactor id="70">
+ <names>
+ <shortLabel>rs6_human</shortLabel>
+ <fullName>40S ribosomal protein S6</fullName>
+ <alias type="orf name" typeAc="MI:0306">OK/SW-cl.2</alias>
+ <alias type="gene name" typeAc="MI:0301">RPS6</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="P62753" refType="identity" refTypeAc="MI:0356" secondary="rs6_human" version="SP_48"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR001377" secondary="Ribosomal_S6E"/>
+ <secondaryRef db="reactome protein" dbAc="MI:0245" id="P62753"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="P08227" refType="secondary-ac" refTypeAc="MI:0360" secondary="rs6_human" version="SP_48"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="P10660" refType="secondary-ac" refTypeAc="MI:0360" secondary="rs6_human" version="SP_48"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-356625" secondary="rs6_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>MKLNISFPATGCQKLIEVDDERKLRTFYEKRMATEVAADALGEEWKGYVVRISGGNDKQGFPMKQGVLTHGRVRLLLSKGHSCYRPRRTGERKRKSVRGCIVDANLSVLNLVIVKKGEKDIPGLTDTTVPRRLGPKRASRIRKLFNLSKEDDVRQYVVRKPLNKEGKKPRTKAPKIQRLVTPRVLQHKRRRIALKKQRTKKNKEEAAEYAKLLAKRMKEAKEKRQEQIAKRRRLSSLRASTSKSESSQK</sequence>
+ </interactor>
+ <interactor id="72">
+ <names>
+ <shortLabel>rs4x_human</shortLabel>
+ <fullName>40S ribosomal protein S4, X isoform</fullName>
+ <alias type="gene name" typeAc="MI:0301">RPS4X</alias>
+ <alias type="gene name synonym" typeAc="MI:0302">CCG2</alias>
+ <alias type="gene name synonym" typeAc="MI:0302">RPS4</alias>
+ <alias type="gene name synonym" typeAc="MI:0302">SCAR</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="P62701" refType="identity" refTypeAc="MI:0356" secondary="rs4x_human" version="SP_47"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR005824" secondary="KOW"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR000876" secondary="Ribosomal_S4E"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR002942" secondary="S4"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="P12631" refType="secondary-ac" refTypeAc="MI:0360" secondary="rs4x_human" version="SP_47"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="P12750" refType="secondary-ac" refTypeAc="MI:0360" secondary="rs4x_human" version="SP_47"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="P27576" refType="secondary-ac" refTypeAc="MI:0360" secondary="rs4x_human" version="SP_47"/>
+ <secondaryRef db="reactome protein" dbAc="MI:0245" id="P62701"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="P55831" refType="secondary-ac" refTypeAc="MI:0360" secondary="rs4x_human" version="SP_47"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q14727" refType="secondary-ac" refTypeAc="MI:0360" secondary="rs4x_human" version="SP_47"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-354303" secondary="rs4x_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>ARGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDEVKKICMQRFIKIDGKVRTDITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAKYKLCKVRKIFVGTKGIPHLVTHDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNLCMVTGGANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWISLPRGKGIRLTIAEERDKRLAAKQSSG</sequence>
+ </interactor>
+ <interactor id="74">
+ <names>
+ <shortLabel>rl7_human</shortLabel>
+ <fullName>60S ribosomal protein L7</fullName>
+ <alias type="gene name" typeAc="MI:0301">RPL7</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="P18124" refType="identity" refTypeAc="MI:0356" secondary="rl7_human" version="SP_47"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005842" secondary="C:cytosolic large ribosomal su"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0003723" secondary="F:RNA binding"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0003735" secondary="F:structural constituent of ri"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0006412" secondary="P:protein biosynthesis"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR000517" secondary="Ribosomal_L30"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR005998" secondary="Ribosomal_L7_euk"/>
+ <secondaryRef db="reactome protein" dbAc="MI:0245" id="P18124"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q6IBM9" refType="secondary-ac" refTypeAc="MI:0360" secondary="rl7_human" version="SP_47"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR012988" secondary="Ribosomal_L30_N"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-350806" secondary="rl7_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>MEGVEEKKKEVPAVPETLKKKRRNFAELKIKRLRKKFAQKMLRKARRKLIYEKAKHYHKEYRQMYRTEIRMARMARKAGNFYVPAEPKLAFVIRIRGINGVSPKVRKVLQLLRLRQIFNGTFVKLNKASINMLRIVEPYIAWGYPNLKSVNELIYKRGYGKINKKRIALTDNALIARSLGKYGIICMEDLIHEIYTVGKRFKEANNFLWPFKLSSPRGGMKKKTTHFVEGGDAGNREDQINRLIRRMN</sequence>
+ </interactor>
+ <interactor id="76">
+ <names>
+ <shortLabel>rs3a_human</shortLabel>
+ <fullName>40S ribosomal protein S3a</fullName>
+ <alias type="gene name" typeAc="MI:0301">RPS3A</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="P61247" refType="identity" refTypeAc="MI:0356" secondary="rs3a_human" version="SP_47"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR001593" secondary="Ribosomal_S3AE"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="P33443" refType="secondary-ac" refTypeAc="MI:0360" secondary="rs3a_human" version="SP_47"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="P49241" refType="secondary-ac" refTypeAc="MI:0360" secondary="rs3a_human" version="SP_47"/>
+ <secondaryRef db="reactome protein" dbAc="MI:0245" id="P61247"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-352378" secondary="rs3a_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>AVGKNKRLTKGGKKGAKKKVVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASDGLKGRVFEVSLADLQNDEVAFRKFKLITEDVQGKNCLTNFHGMDLTRDKMCSMVKKWQTMIEAHVDVKTTDGYLLRLFCVGFTKKRNNQIRKTSYAQHQQVRQIRKKMMEIMTREVQTNDLKEVVNKLIPDSIGKDIEKACQSIYPLHDVFVRKVKMLKKPKFELGKLMELHGEGSSSGKATGDETGAKVERADGYEPPVQESV</sequence>
+ </interactor>
+ <interactor id="78">
+ <names>
+ <shortLabel>rl5_human</shortLabel>
+ <fullName>60S ribosomal protein L5</fullName>
+ <alias type="gene name" typeAc="MI:0301">RPL5</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="P46777" refType="identity" refTypeAc="MI:0356" secondary="rl5_human" version="SP_47"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005842" secondary="C:cytosolic large ribosomal su"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0003723" secondary="F:RNA binding"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0003735" secondary="F:structural constituent of ri"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0006412" secondary="P:protein biosynthesis"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR005484" secondary="Ribosomal_L18p"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR005485" secondary="Ribosomal_L5euk"/>
+ <secondaryRef db="reactome protein" dbAc="MI:0245" id="P46777"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005515" secondary="F:protein binding"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-358018" secondary="rl5_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>GFVKVVKNKAYFKRYQVKFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVTNRDIICQIAYARIEGDMIVCARYAHELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYEGQVEVTGDEYNVESIDGQPGAFTCYLDAGLARTTTGNKVFGALKGAVDGGLSIPHSTKRFPGYDSESKEFNAEVHRKHIMGQNVADYMRYLMEEDEDAYKKQFSQYIKNSVTPDMMEEMYKKAHAAIRENPVYEKKPKKEVKKKRWNRPKMSLAQKKDRVAQKKASFLRAQERAAES</sequence>
+ </interactor>
+ <interactor id="80">
+ <names>
+ <shortLabel>myg1_human</shortLabel>
+ <fullName>MYG1 protein</fullName>
+ <alias type="gene name" typeAc="MI:0301">C12orf10</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="Q9HB07" refType="identity" refTypeAc="MI:0356" secondary="myg1_human" version="SP_49"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR003226" secondary="Metdp_prot_hydro"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-709754" secondary="myg1_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>MGHRFLRGLLTLLLPPPPLYTRHRMLGPESVPPPKRSRSKLMAPPRIGTHNGTFHCDEALACALLRLLPEYRDAEIVRTRDPEKLASCDIVVDVGGEYDPRRHRYDHHQRSFTETMSSLSPGKPWQTKLSSAGLIYLHFGHKLLAQLLGPSEEDSMVGTLYDKMYENFVEEVDAVDNGISQWAEGEPRYALTTTLSARVARLNPTWNHPDQDTEAGFKRAMDLVQEEFLQRLDFYQHSWLPARALVEEALAQRFQVDPSGEIVELAKGACPWKEHLYHLESGLSPPVAIFFVIYTDQAGQWRIQCVPKEPHSFQSRLPLPEPWRGLRDEALDQVSGIPGCIFVHASGFIGGHPTREGALSMARATLAQRSYLPQIS</sequence>
+ </interactor>
+ <interactor id="82">
+ <names>
+ <shortLabel>q96km8_human</shortLabel>
+ <fullName>DJ69B10.1</fullName>
+ <alias type="gene name" typeAc="MI:0301">dJ69B10.1</alias>
+ <alias type="gene name synonym" typeAc="MI:0302">GA17</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="Q96KM8" refType="identity" refTypeAc="MI:0356" secondary="q96km8_human" version="31"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR000717" secondary="PCI"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-373200" secondary="q96km8_human"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="9606">
+ <names>
+ <shortLabel>human</shortLabel>
+ <fullName>Homo sapiens</fullName>
+ </names>
+ </organism>
+ <sequence>MSVPAFIDISEEDQAAELRAYLKSKGAEISEENSEGGLHVDLAQIIEACDVCLKEDDKDVESVMNSVVSLLLILEPDKQEALIESLCEKLVKFREGERPSLRLQLLSNLFHGMDKNTPVRYTVYCSLIKVAASCGAIQYIPTELDQVRKWISDWNLTTEKKHTLLRLLYEALVDCKKSDAASKVMVELLGSYTEDNASQARVDAHRCIVRALKDPNAFLFDHLLTLKPVKFLEGELIHDLLTIFVSAKLASYVKFYQNNKDFIDSLGLLHEQNMAKMRLLTFMGMAVENKEISFDTMQQELQIGADDVEAFVIDAVRTKMVYCKIDQTQRKVVVSHSTHRTFGKQQWQQLYDTLNAWKQNLNKVKNSLLSLSDT</sequence>
+ </interactor>
+ </interactorList>
+ <interactionList>
+ <interaction id="1">
+ <names>
+ <shortLabel>hspcb-aars</shortLabel>
+ <fullName>In vivo Co-IP: bait= Hsp90</fullName>
+ </names>
+ <xref>
+ <primaryRef db="intact" dbAc="MI:0469" id="EBI-709762" secondary="hspcb-aars"/>
+ </xref>
+ <experimentList>
+ <experimentRef>2</experimentRef>
+ </experimentList>
+ <participantList>
+ <participant id="3">
+ <interactorRef>4</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>bait</shortLabel>
+ <fullName>bait</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0496" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="5">
+ <interactorRef>6</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="7">
+ <interactorRef>8</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="9">
+ <interactorRef>10</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="11">
+ <interactorRef>12</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="13">
+ <interactorRef>14</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="15">
+ <interactorRef>16</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="17">
+ <interactorRef>18</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="19">
+ <interactorRef>20</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="21">
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+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
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+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
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+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="23">
+ <interactorRef>24</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="25">
+ <interactorRef>26</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="27">
+ <interactorRef>28</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="29">
+ <interactorRef>30</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="31">
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+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="33">
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+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="35">
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+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="37">
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+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="39">
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+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="41">
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+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="43">
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+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="45">
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+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="47">
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+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="49">
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+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
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+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
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+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
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+ <xref>
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+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="51">
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+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="53">
+ <interactorRef>54</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="55">
+ <interactorRef>56</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="57">
+ <interactorRef>58</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="59">
+ <interactorRef>60</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="61">
+ <interactorRef>62</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="63">
+ <interactorRef>64</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="65">
+ <interactorRef>66</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="67">
+ <interactorRef>68</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="69">
+ <interactorRef>70</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="71">
+ <interactorRef>72</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="73">
+ <interactorRef>74</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="75">
+ <interactorRef>76</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="77">
+ <interactorRef>78</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="79">
+ <interactorRef>80</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="81">
+ <interactorRef>82</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>physical interaction</shortLabel>
+ <fullName>physical interaction</fullName>
+ <alias>aggregation</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0218" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactionType>
+ <attributeList>
+ <attribute name="caution">The AC68 antibody is specific for both hsp90 alpha and beta which may have the same interactors. Only Hsp90 beta was identified.</attribute>
+ <attribute name="kd">0.0</attribute>
+ </attributeList>
+ </interaction>
+ </interactionList>
+ </entry>
+ </entrySet>
diff --git a/coreplugins/PSI-MI/src/test/resources/testData/psi_sample_2_5_2.xml b/coreplugins/PSI-MI/src/test/resources/testData/psi_sample_2_5_2.xml
new file mode 100755
index 0000000..ad5337d
--- /dev/null
+++ b/coreplugins/PSI-MI/src/test/resources/testData/psi_sample_2_5_2.xml
@@ -0,0 +1,6396 @@
+ <entrySet level="2" version="5" xmlns="net:sf:psidev:mi" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="net:sf:psidev:mi http://psidev.sourceforge.net/mi/rel25/src/MIF25.xsd">
+ <entry>
+ <source releaseDate="2006-02-19">
+ <names>
+ <shortLabel>European Bioinformatics Institute</shortLabel>
+ </names>
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" dbAc="MI:0446" id="14681455" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </bibref>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0469" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ <attributeList>
+ <attribute name="postalAddress">Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom</attribute>
+ <attribute name="url">http://www.ebi.ac.uk</attribute>
+ </attributeList>
+ </source>
+ <experimentList>
+ <experimentDescription id="2">
+ <names>
+ <shortLabel>iwasaki-1999-1</shortLabel>
+ <fullName>Physical interactions among circadian clock proteins KaiA, KaiB and KaiC in cyanobacteria.</fullName>
+ </names>
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" dbAc="MI:0446" id="10064581" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </bibref>
+ <xref>
+ <primaryRef db="intact" dbAc="MI:0469" id="EBI-701778" secondary="iwasaki-1999-1"/>
+ <secondaryRef db="newt" dbAc="MI:0247" id="1140" refType="target-species" secondary="synp7"/>
+ </xref>
+ <hostOrganismList>
+ <hostOrganism ncbiTaxId="4932">
+ <names>
+ <shortLabel>yeast</shortLabel>
+ <fullName>Saccharomyces cerevisiae</fullName>
+ </names>
+ </hostOrganism>
+ </hostOrganismList>
+ <interactionDetectionMethod>
+ <names>
+ <shortLabel>two hybrid</shortLabel>
+ <fullName>two hybrid</fullName>
+ <alias>2H</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0018" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="10967325" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="12634794" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactionDetectionMethod>
+ <participantIdentificationMethod>
+ <names>
+ <shortLabel>predetermined</shortLabel>
+ <fullName>predetermined participant</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0396" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="7940758" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </participantIdentificationMethod>
+ <attributeList>
+ <attribute name="author-list">Iwasaki H., Taniguchi Y., Ishiura M., Kondo T.</attribute>
+ <attribute name="contact-email">kondo at bio.nagoya-u.ac.jp , ishiura at bio.nagoya-u.ac.jp</attribute>
+ <attribute name="dataset">Dataset on Cyanobacteria and related species</attribute>
+ <attribute name="figure-legend">Fig.1 and fig.4.A</attribute>
+ <attribute name="exp-modification">The two hybrid experiment is carried out using LexA fusions on the bait and VP16 on the prey.</attribute>
+ </attributeList>
+ </experimentDescription>
+ <experimentDescription id="24">
+ <names>
+ <shortLabel>iwasaki-1999-3</shortLabel>
+ <fullName>Physical interactions among circadian clock proteins KaiA, KaiB and KaiC in cyanobacteria.</fullName>
+ </names>
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" dbAc="MI:0446" id="10064581" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </bibref>
+ <xref>
+ <primaryRef db="intact" dbAc="MI:0469" id="EBI-781794" secondary="iwasaki-1999-3"/>
+ <secondaryRef db="newt" dbAc="MI:0247" id="1140" refType="target-species" secondary="synp7"/>
+ </xref>
+ <hostOrganismList>
+ <hostOrganism ncbiTaxId="1140">
+ <names>
+ <shortLabel>synp7</shortLabel>
+ <fullName>Synechococcus sp. (strain PCC 7942)</fullName>
+ </names>
+ </hostOrganism>
+ </hostOrganismList>
+ <interactionDetectionMethod>
+ <names>
+ <shortLabel>pull down</shortLabel>
+ <fullName>pull down</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0096" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactionDetectionMethod>
+ <participantIdentificationMethod>
+ <names>
+ <shortLabel>western blot</shortLabel>
+ <fullName>western blot</fullName>
+ <alias>Immuno blot</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0113" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </participantIdentificationMethod>
+ <attributeList>
+ <attribute name="author-list">Iwasaki H., Taniguchi Y., Ishiura M., Kondo T.</attribute>
+ <attribute name="contact-email">kondo at bio.nagoya-u.ac.jp , ishiura at bio.nagoya-u.ac.jp</attribute>
+ <attribute name="dataset">Dataset on Cyanobacteria and related species</attribute>
+ <attribute name="figure-legend">fig.3.C</attribute>
+ </attributeList>
+ </experimentDescription>
+ <experimentDescription id="61">
+ <names>
+ <shortLabel>iwasaki-1999-4</shortLabel>
+ <fullName>Physical interactions among circadian clock proteins KaiA, KaiB and KaiC in cyanobacteria.</fullName>
+ </names>
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" dbAc="MI:0446" id="10064581" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </bibref>
+ <xref>
+ <primaryRef db="intact" dbAc="MI:0469" id="EBI-781988" secondary="iwasaki-1999-4"/>
+ <secondaryRef db="newt" dbAc="MI:0247" id="1140" refType="target-species" secondary="synp7"/>
+ </xref>
+ <hostOrganismList>
+ <hostOrganism ncbiTaxId="-1">
+ <names>
+ <shortLabel>in vitro</shortLabel>
+ </names>
+ </hostOrganism>
+ </hostOrganismList>
+ <interactionDetectionMethod>
+ <names>
+ <shortLabel>pull down</shortLabel>
+ <fullName>pull down</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0096" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactionDetectionMethod>
+ <participantIdentificationMethod>
+ <names>
+ <shortLabel>western blot</shortLabel>
+ <fullName>western blot</fullName>
+ <alias>Immuno blot</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0113" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </participantIdentificationMethod>
+ <attributeList>
+ <attribute name="author-list">Iwasaki H., Taniguchi Y., Ishiura M., Kondo T.</attribute>
+ <attribute name="contact-email">kondo at bio.nagoya-u.ac.jp , ishiura at bio.nagoya-u.ac.jp</attribute>
+ <attribute name="dataset">Dataset on Cyanobacteria and related species</attribute>
+ <attribute name="figure-legend">Fig.2.D</attribute>
+ </attributeList>
+ </experimentDescription>
+ <experimentDescription id="77">
+ <names>
+ <shortLabel>iwasaki-1999-2</shortLabel>
+ <fullName>Physical interactions among circadian clock proteins KaiA, KaiB and KaiC in cyanobacteria.</fullName>
+ </names>
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" dbAc="MI:0446" id="10064581" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </bibref>
+ <xref>
+ <primaryRef db="intact" dbAc="MI:0469" id="EBI-781202" secondary="iwasaki-1999-2"/>
+ <secondaryRef db="newt" dbAc="MI:0247" id="1140" refType="target-species" secondary="synp7"/>
+ </xref>
+ <hostOrganismList>
+ <hostOrganism ncbiTaxId="-1">
+ <names>
+ <shortLabel>in vitro</shortLabel>
+ </names>
+ </hostOrganism>
+ </hostOrganismList>
+ <interactionDetectionMethod>
+ <names>
+ <shortLabel>pull down</shortLabel>
+ <fullName>pull down</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0096" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactionDetectionMethod>
+ <participantIdentificationMethod>
+ <names>
+ <shortLabel>predetermined</shortLabel>
+ <fullName>predetermined participant</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0396" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="7940758" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </participantIdentificationMethod>
+ <attributeList>
+ <attribute name="author-list">Iwasaki H., Taniguchi Y., Ishiura M., Kondo T.</attribute>
+ <attribute name="contact-email">kondo at bio.nagoya-u.ac.jp , ishiura at bio.nagoya-u.ac.jp</attribute>
+ <attribute name="dataset">Dataset on Cyanobacteria and related species</attribute>
+ <attribute name="figure-legend">Fig.2.C and Fig.6.D</attribute>
+ <attribute name="comment">Binding assays with KaiC domains C1 and C2 show that each of this two moieties have the same binding abilities of KaiC and bind each other.</attribute>
+ </attributeList>
+ </experimentDescription>
+ <experimentDescription id="172">
+ <names>
+ <shortLabel>iwasaki-1999-5</shortLabel>
+ <fullName>Physical interactions among circadian clock proteins KaiA, KaiB and KaiC in cyanobacteria.</fullName>
+ </names>
+ <bibref>
+ <xref>
+ <primaryRef db="pubmed" dbAc="MI:0446" id="10064581" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </bibref>
+ <xref>
+ <primaryRef db="intact" dbAc="MI:0469" id="EBI-782029" secondary="iwasaki-1999-5"/>
+ <secondaryRef db="newt" dbAc="MI:0247" id="1140" refType="target-species" secondary="synp7"/>
+ </xref>
+ <hostOrganismList>
+ <hostOrganism ncbiTaxId="-1">
+ <names>
+ <shortLabel>in vitro</shortLabel>
+ </names>
+ </hostOrganism>
+ </hostOrganismList>
+ <interactionDetectionMethod>
+ <names>
+ <shortLabel>pull down</shortLabel>
+ <fullName>pull down</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0096" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactionDetectionMethod>
+ <participantIdentificationMethod>
+ <names>
+ <shortLabel>predetermined</shortLabel>
+ <fullName>predetermined participant</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0396" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="7940758" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </participantIdentificationMethod>
+ <attributeList>
+ <attribute name="author-list">Iwasaki H., Taniguchi Y., Ishiura M., Kondo T.</attribute>
+ <attribute name="contact-email">kondo at bio.nagoya-u.ac.jp , ishiura at bio.nagoya-u.ac.jp</attribute>
+ <attribute name="dataset">Dataset on Cyanobacteria and related species</attribute>
+ <attribute name="figure-legend">Fig.4.B and Fig.5.A and Fig.6.E</attribute>
+ </attributeList>
+ </experimentDescription>
+ </experimentList>
+ <interactorList>
+ <interactor id="4">
+ <names>
+ <shortLabel>kaic_synp7</shortLabel>
+ <fullName>Circadian clock protein kinase kaiC</fullName>
+ <alias type="orf name" typeAc="MI:0306">see0011</alias>
+ <alias type="gene name" typeAc="MI:0301">kaiC</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="Q79PF4" refType="identity" refTypeAc="MI:0356" secondary="kaic_synp7" version="SP_49"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR010624" secondary="KaiC"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q9Z3H2" refType="secondary-ac" refTypeAc="MI:0360" secondary="kaic_synp7" version="SP_49"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005515" secondary="F:protein binding"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0042754" secondary="P:negative regulation of circa"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-592287" secondary="kaic_synp7"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="1140">
+ <names>
+ <shortLabel>synp7</shortLabel>
+ <fullName>Synechococcus sp. (strain PCC 7942)</fullName>
+ </names>
+ </organism>
+ <sequence>MTSAEMTSPNNNSEHQAIAKMRTMIEGFDDISHGGLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVTFEETPQDIIKNARSFGWDLAKLVDEGKLFILDASPDPEGQEVVGGFDLSALIERINYAIQKYRARRVSIDSVTSVFQQYDASSVVRRELFRLVARLKQIGATTVMTTERIEEYGPIARYGVEEFVSDNVVILRNVLEGERRRRTLEILKLRGTSHMKGEYPFTITDHGINIFPLGAMRLTQRSSNVRVSSGVVRLDEMCGGGFFKDSIILATGATGTGKTLLVSRFVENACANKERAILFAYEESRAQLLRNAYSWGMDFEEMERQNLLKIVCAYPESAGLEDHLQIIKSEINDFKPARIAIDSLSALARGVSNNAFRQFVIGVTGYAKQEEITGLFTNTSDQFMGAHSITDSHISTITDTIILLQYVEIRGEMSRAINVFKMRGSWHDKAIREFM [...]
+ </interactor>
+ <interactor id="6">
+ <names>
+ <shortLabel>kaia_synp7</shortLabel>
+ <fullName>Circadian clock protein kaiA</fullName>
+ <alias type="orf name" typeAc="MI:0306">see0009</alias>
+ <alias type="gene name" typeAc="MI:0301">kaiA</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="Q79PF6" refType="identity" refTypeAc="MI:0356" secondary="kaia_synp7" version="SP_49"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR011648" secondary="KaiA"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q9Z3H4" refType="secondary-ac" refTypeAc="MI:0360" secondary="kaia_synp7" version="SP_49"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0042753" secondary="P:positive regulation of circa"/>
+ <secondaryRef db="go" dbAc="MI:0448" id="GO:0005515" secondary="F:protein binding"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-592281" secondary="kaia_synp7"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="1140">
+ <names>
+ <shortLabel>synp7</shortLabel>
+ <fullName>Synechococcus sp. (strain PCC 7942)</fullName>
+ </names>
+ </organism>
+ <sequence>MLSQIAICIWVESTAILQDCQRALSADRYQLQVCESGEMLLEYAQTHRDQIDCLILVAANPSFRAVVQQLCFEGVVVPAIVVGDRDSEDPDEPAKEQLYHSAELHLGIHQLEQLPYQVDAALAEFLRLAPVETMADHIMLMGANHDPELSSQQRDLAQRLQERLGYLGVYYKRDPDRFLRNLPAYESQKLHQAMQTSYREIVLSYFSPNSNLNQSIDNFVNMAFFADVPVTKVVEIHMELMDEFAKKLRVEGRSEDILLDYRLTLIDVIAHLCEMYRRSIPRET</sequence>
+ </interactor>
+ <interactor id="10">
+ <names>
+ <shortLabel>kaib_synp7</shortLabel>
+ <fullName>Circadian clock protein kaiB</fullName>
+ <alias type="gene name" typeAc="MI:0301">kaiB</alias>
+ <alias type="orf name" typeAc="MI:0306">see0010</alias>
+ </names>
+ <xref>
+ <primaryRef db="uniprotkb" dbAc="MI:0486" id="Q79PF5" refType="identity" refTypeAc="MI:0356" secondary="kaib_synp7" version="SP_49"/>
+ <secondaryRef db="interpro" dbAc="MI:0449" id="IPR011649" secondary="KaiB"/>
+ <secondaryRef db="uniprotkb" dbAc="MI:0486" id="Q9Z3H3" refType="secondary-ac" refTypeAc="MI:0360" secondary="kaib_synp7" version="SP_49"/>
+ <secondaryRef db="intact" dbAc="MI:0469" id="EBI-619150" secondary="kaib_synp7"/>
+ </xref>
+ <interactorType>
+ <names>
+ <shortLabel>protein</shortLabel>
+ <fullName>protein</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactorType>
+ <organism ncbiTaxId="1140">
+ <names>
+ <shortLabel>synp7</shortLabel>
+ <fullName>Synechococcus sp. (strain PCC 7942)</fullName>
+ </names>
+ </organism>
+ <sequence>MSPRKTYILKLYVAGNTPNSVRALKTLKNILEVEFQGVYALKVIDVLKNPQLAEEDKILATPTLAKVLPLPVRRIIGDLSDREKVLIGLDLLYGELQDSDDF</sequence>
+ </interactor>
+ </interactorList>
+ <interactionList>
+ <interaction id="1">
+ <names>
+ <shortLabel>kaic-kaia-1</shortLabel>
+ <fullName>yeast two hybrid kaiC kaiA interaction</fullName>
+ </names>
+ <xref>
+ <primaryRef db="intact" dbAc="MI:0469" id="EBI-781017" secondary="kaic-kaia-1"/>
+ </xref>
+ <experimentList>
+ <experimentRef>2</experimentRef>
+ </experimentList>
+ <participantList>
+ <participant id="3">
+ <interactorRef>4</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>bait</shortLabel>
+ <fullName>bait</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0496" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="5">
+ <interactorRef>6</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>physical interaction</shortLabel>
+ <fullName>physical interaction</fullName>
+ <alias>aggregation</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0218" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactionType>
+ <attributeList>
+ <attribute name="kd">1.0</attribute>
+ </attributeList>
+ </interaction>
+ <interaction id="7">
+ <names>
+ <shortLabel>kaic-kaib-1</shortLabel>
+ <fullName>yeast two hybrid kaiC kaiB interaction</fullName>
+ </names>
+ <xref>
+ <primaryRef db="intact" dbAc="MI:0469" id="EBI-781020" secondary="kaic-kaib-1"/>
+ </xref>
+ <experimentList>
+ <experimentRef>2</experimentRef>
+ </experimentList>
+ <participantList>
+ <participant id="8">
+ <interactorRef>4</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>bait</shortLabel>
+ <fullName>bait</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0496" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="9">
+ <interactorRef>10</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>physical interaction</shortLabel>
+ <fullName>physical interaction</fullName>
+ <alias>aggregation</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0218" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactionType>
+ <attributeList>
+ <attribute name="kd">1.0</attribute>
+ </attributeList>
+ </interaction>
+ <interaction id="11">
+ <names>
+ <shortLabel>kaic-kaic-3</shortLabel>
+ <fullName>yeast two hybrid kaiC kaiC interaction</fullName>
+ </names>
+ <xref>
+ <primaryRef db="intact" dbAc="MI:0469" id="EBI-781024" secondary="kaic-kaic-3"/>
+ </xref>
+ <experimentList>
+ <experimentRef>2</experimentRef>
+ </experimentList>
+ <participantList>
+ <participant id="12">
+ <interactorRef>4</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="13">
+ <interactorRef>4</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>bait</shortLabel>
+ <fullName>bait</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0496" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>physical interaction</shortLabel>
+ <fullName>physical interaction</fullName>
+ <alias>aggregation</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0218" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactionType>
+ <attributeList>
+ <attribute name="kd">1.0</attribute>
+ </attributeList>
+ </interaction>
+ <interaction id="14">
+ <names>
+ <shortLabel>kaib-kaic-1</shortLabel>
+ <fullName>yeast two hybrid kaiB kaiC interaction</fullName>
+ </names>
+ <xref>
+ <primaryRef db="intact" dbAc="MI:0469" id="EBI-781100" secondary="kaib-kaic-1"/>
+ </xref>
+ <experimentList>
+ <experimentRef>2</experimentRef>
+ </experimentList>
+ <participantList>
+ <participant id="15">
+ <interactorRef>10</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>bait</shortLabel>
+ <fullName>bait</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0496" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="16">
+ <interactorRef>4</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>physical interaction</shortLabel>
+ <fullName>physical interaction</fullName>
+ <alias>aggregation</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0218" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactionType>
+ <attributeList>
+ <attribute name="kd">1.0</attribute>
+ </attributeList>
+ </interaction>
+ <interaction id="17">
+ <names>
+ <shortLabel>kaib-kaib-4</shortLabel>
+ <fullName>yeast two hybrid kaiB kaiB interaction</fullName>
+ </names>
+ <xref>
+ <primaryRef db="intact" dbAc="MI:0469" id="EBI-781194" secondary="kaib-kaib-4"/>
+ </xref>
+ <experimentList>
+ <experimentRef>2</experimentRef>
+ </experimentList>
+ <participantList>
+ <participant id="18">
+ <interactorRef>10</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>bait</shortLabel>
+ <fullName>bait</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0496" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="19">
+ <interactorRef>10</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>physical interaction</shortLabel>
+ <fullName>physical interaction</fullName>
+ <alias>aggregation</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0218" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactionType>
+ <attributeList>
+ <attribute name="kd">1.0</attribute>
+ </attributeList>
+ </interaction>
+ <interaction id="20">
+ <names>
+ <shortLabel>kaib-kaia-6</shortLabel>
+ <fullName>yeast two hybrid kaiB kaiA interaction</fullName>
+ </names>
+ <xref>
+ <primaryRef db="intact" dbAc="MI:0469" id="EBI-781867" secondary="kaib-kaia-6"/>
+ </xref>
+ <experimentList>
+ <experimentRef>2</experimentRef>
+ </experimentList>
+ <participantList>
+ <participant id="21">
+ <interactorRef>10</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>bait</shortLabel>
+ <fullName>bait</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0496" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="22">
+ <interactorRef>6</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>physical interaction</shortLabel>
+ <fullName>physical interaction</fullName>
+ <alias>aggregation</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0218" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactionType>
+ <attributeList>
+ <attribute name="caution">The very weak interaction between KaiA and KAiB is strongly enhanced by the expression of KaiC in the same yeast cells that carry the double hybrid constructs.</attribute>
+ <attribute name="kd">1.0</attribute>
+ </attributeList>
+ </interaction>
+ <interaction id="23">
+ <names>
+ <shortLabel>kaia-kaia-3</shortLabel>
+ <fullName>pull down HIS KaiA - kaiA in vivo</fullName>
+ </names>
+ <xref>
+ <primaryRef db="intact" dbAc="MI:0469" id="EBI-781797" secondary="kaia-kaia-3"/>
+ </xref>
+ <experimentList>
+ <experimentRef>24</experimentRef>
+ </experimentList>
+ <participantList>
+ <participant id="25">
+ <interactorRef>6</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="26">
+ <interactorRef>6</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>bait</shortLabel>
+ <fullName>bait</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0496" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ <featureList>
+ <feature id="27">
+ <names>
+ <shortLabel>region</shortLabel>
+ </names>
+ <featureType>
+ <names>
+ <shortLabel>his tagged</shortLabel>
+ <fullName>his tagged</fullName>
+ <alias>6-His-tagged</alias>
+ <alias>Hexa-His-tagged</alias>
+ <alias>Histidine-tagged</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0521" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </featureType>
+ <featureRangeList>
+ <featureRange>
+ <startStatus>
+ <names>
+ <shortLabel>n-terminal</shortLabel>
+ <fullName>n-terminal position</fullName>
+ <alias>n-terminus</alias>
+ <alias>amino-terminus</alias>
+ <alias>n-term</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0340" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </startStatus>
+ <begin position="0"/>
+ <endStatus>
+ <names>
+ <shortLabel>n-terminal</shortLabel>
+ <fullName>n-terminal position</fullName>
+ <alias>n-terminus</alias>
+ <alias>amino-terminus</alias>
+ <alias>n-term</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0340" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </endStatus>
+ <end position="0"/>
+ </featureRange>
+ </featureRangeList>
+ </feature>
+ </featureList>
+ </participant>
+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>physical interaction</shortLabel>
+ <fullName>physical interaction</fullName>
+ <alias>aggregation</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0218" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactionType>
+ <attributeList>
+ <attribute name="kd">1.0</attribute>
+ </attributeList>
+ </interaction>
+ <interaction id="28">
+ <names>
+ <shortLabel>kaia-kaib-1</shortLabel>
+ <fullName>pull down HIS kaiA - kaiB in vivo</fullName>
+ </names>
+ <xref>
+ <primaryRef db="intact" dbAc="MI:0469" id="EBI-781807" secondary="kaia-kaib-1"/>
+ </xref>
+ <experimentList>
+ <experimentRef>24</experimentRef>
+ </experimentList>
+ <participantList>
+ <participant id="29">
+ <interactorRef>10</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="30">
+ <interactorRef>6</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>bait</shortLabel>
+ <fullName>bait</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0496" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ <featureList>
+ <feature id="31">
+ <names>
+ <shortLabel>region</shortLabel>
+ </names>
+ <featureType>
+ <names>
+ <shortLabel>his tagged</shortLabel>
+ <fullName>his tagged</fullName>
+ <alias>6-His-tagged</alias>
+ <alias>Hexa-His-tagged</alias>
+ <alias>Histidine-tagged</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0521" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </featureType>
+ <featureRangeList>
+ <featureRange>
+ <startStatus>
+ <names>
+ <shortLabel>n-terminal</shortLabel>
+ <fullName>n-terminal position</fullName>
+ <alias>n-terminus</alias>
+ <alias>amino-terminus</alias>
+ <alias>n-term</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0340" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </startStatus>
+ <begin position="0"/>
+ <endStatus>
+ <names>
+ <shortLabel>n-terminal</shortLabel>
+ <fullName>n-terminal position</fullName>
+ <alias>n-terminus</alias>
+ <alias>amino-terminus</alias>
+ <alias>n-term</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0340" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </endStatus>
+ <end position="0"/>
+ </featureRange>
+ </featureRangeList>
+ </feature>
+ </featureList>
+ </participant>
+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>physical interaction</shortLabel>
+ <fullName>physical interaction</fullName>
+ <alias>aggregation</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0218" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactionType>
+ <attributeList>
+ <attribute name="caution">Weak interaction</attribute>
+ <attribute name="kd">1.0</attribute>
+ </attributeList>
+ </interaction>
+ <interaction id="32">
+ <names>
+ <shortLabel>kaia-kaia-4</shortLabel>
+ <fullName>pull down HIS KaiA - kaiC in vivo</fullName>
+ </names>
+ <xref>
+ <primaryRef db="intact" dbAc="MI:0469" id="EBI-781813" secondary="kaia-kaia-4"/>
+ </xref>
+ <experimentList>
+ <experimentRef>24</experimentRef>
+ </experimentList>
+ <participantList>
+ <participant id="33">
+ <interactorRef>6</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>bait</shortLabel>
+ <fullName>bait</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0496" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ <featureList>
+ <feature id="34">
+ <names>
+ <shortLabel>region</shortLabel>
+ </names>
+ <featureType>
+ <names>
+ <shortLabel>his tagged</shortLabel>
+ <fullName>his tagged</fullName>
+ <alias>6-His-tagged</alias>
+ <alias>Hexa-His-tagged</alias>
+ <alias>Histidine-tagged</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0521" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </featureType>
+ <featureRangeList>
+ <featureRange>
+ <startStatus>
+ <names>
+ <shortLabel>n-terminal</shortLabel>
+ <fullName>n-terminal position</fullName>
+ <alias>n-terminus</alias>
+ <alias>amino-terminus</alias>
+ <alias>n-term</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0340" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </startStatus>
+ <begin position="0"/>
+ <endStatus>
+ <names>
+ <shortLabel>n-terminal</shortLabel>
+ <fullName>n-terminal position</fullName>
+ <alias>n-terminus</alias>
+ <alias>amino-terminus</alias>
+ <alias>n-term</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0340" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </endStatus>
+ <end position="0"/>
+ </featureRange>
+ </featureRangeList>
+ </feature>
+ </featureList>
+ </participant>
+ <participant id="35">
+ <interactorRef>4</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>physical interaction</shortLabel>
+ <fullName>physical interaction</fullName>
+ <alias>aggregation</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0218" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactionType>
+ <attributeList>
+ <attribute name="kd">1.0</attribute>
+ </attributeList>
+ </interaction>
+ <interaction id="36">
+ <names>
+ <shortLabel>kaib-kaib-5</shortLabel>
+ <fullName>pull down HIS kaiB - kaiB in vivo</fullName>
+ </names>
+ <xref>
+ <primaryRef db="intact" dbAc="MI:0469" id="EBI-781820" secondary="kaib-kaib-5"/>
+ </xref>
+ <experimentList>
+ <experimentRef>24</experimentRef>
+ </experimentList>
+ <participantList>
+ <participant id="37">
+ <interactorRef>10</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>bait</shortLabel>
+ <fullName>bait</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0496" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ <featureList>
+ <feature id="38">
+ <names>
+ <shortLabel>region</shortLabel>
+ </names>
+ <featureType>
+ <names>
+ <shortLabel>his tagged</shortLabel>
+ <fullName>his tagged</fullName>
+ <alias>6-His-tagged</alias>
+ <alias>Hexa-His-tagged</alias>
+ <alias>Histidine-tagged</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0521" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </featureType>
+ <featureRangeList>
+ <featureRange>
+ <startStatus>
+ <names>
+ <shortLabel>n-terminal</shortLabel>
+ <fullName>n-terminal position</fullName>
+ <alias>n-terminus</alias>
+ <alias>amino-terminus</alias>
+ <alias>n-term</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0340" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </startStatus>
+ <begin position="0"/>
+ <endStatus>
+ <names>
+ <shortLabel>n-terminal</shortLabel>
+ <fullName>n-terminal position</fullName>
+ <alias>n-terminus</alias>
+ <alias>amino-terminus</alias>
+ <alias>n-term</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0340" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </endStatus>
+ <end position="0"/>
+ </featureRange>
+ </featureRangeList>
+ </feature>
+ </featureList>
+ </participant>
+ <participant id="39">
+ <interactorRef>10</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>physical interaction</shortLabel>
+ <fullName>physical interaction</fullName>
+ <alias>aggregation</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0218" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactionType>
+ <attributeList>
+ <attribute name="kd">1.0</attribute>
+ </attributeList>
+ </interaction>
+ <interaction id="40">
+ <names>
+ <shortLabel>kaib-kaia-1</shortLabel>
+ <fullName>pull down HIS kaiB - kaiA in vivo</fullName>
+ </names>
+ <xref>
+ <primaryRef db="intact" dbAc="MI:0469" id="EBI-781828" secondary="kaib-kaia-1"/>
+ </xref>
+ <experimentList>
+ <experimentRef>24</experimentRef>
+ </experimentList>
+ <participantList>
+ <participant id="41">
+ <interactorRef>10</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>bait</shortLabel>
+ <fullName>bait</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0496" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ <featureList>
+ <feature id="42">
+ <names>
+ <shortLabel>region</shortLabel>
+ </names>
+ <featureType>
+ <names>
+ <shortLabel>his tagged</shortLabel>
+ <fullName>his tagged</fullName>
+ <alias>6-His-tagged</alias>
+ <alias>Hexa-His-tagged</alias>
+ <alias>Histidine-tagged</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0521" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </featureType>
+ <featureRangeList>
+ <featureRange>
+ <startStatus>
+ <names>
+ <shortLabel>n-terminal</shortLabel>
+ <fullName>n-terminal position</fullName>
+ <alias>n-terminus</alias>
+ <alias>amino-terminus</alias>
+ <alias>n-term</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0340" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </startStatus>
+ <begin position="0"/>
+ <endStatus>
+ <names>
+ <shortLabel>n-terminal</shortLabel>
+ <fullName>n-terminal position</fullName>
+ <alias>n-terminus</alias>
+ <alias>amino-terminus</alias>
+ <alias>n-term</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0340" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </endStatus>
+ <end position="0"/>
+ </featureRange>
+ </featureRangeList>
+ </feature>
+ </featureList>
+ </participant>
+ <participant id="43">
+ <interactorRef>6</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>physical interaction</shortLabel>
+ <fullName>physical interaction</fullName>
+ <alias>aggregation</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0218" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactionType>
+ <attributeList>
+ <attribute name="kd">1.0</attribute>
+ </attributeList>
+ </interaction>
+ <interaction id="44">
+ <names>
+ <shortLabel>kaib-kaic-3</shortLabel>
+ <fullName>pull down HIS kaiB - kaiC in vivo</fullName>
+ </names>
+ <xref>
+ <primaryRef db="intact" dbAc="MI:0469" id="EBI-781834" secondary="kaib-kaic-3"/>
+ </xref>
+ <experimentList>
+ <experimentRef>24</experimentRef>
+ </experimentList>
+ <participantList>
+ <participant id="45">
+ <interactorRef>4</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="46">
+ <interactorRef>10</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>bait</shortLabel>
+ <fullName>bait</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0496" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ <featureList>
+ <feature id="47">
+ <names>
+ <shortLabel>region</shortLabel>
+ </names>
+ <featureType>
+ <names>
+ <shortLabel>his tagged</shortLabel>
+ <fullName>his tagged</fullName>
+ <alias>6-His-tagged</alias>
+ <alias>Hexa-His-tagged</alias>
+ <alias>Histidine-tagged</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0521" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </featureType>
+ <featureRangeList>
+ <featureRange>
+ <startStatus>
+ <names>
+ <shortLabel>n-terminal</shortLabel>
+ <fullName>n-terminal position</fullName>
+ <alias>n-terminus</alias>
+ <alias>amino-terminus</alias>
+ <alias>n-term</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0340" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </startStatus>
+ <begin position="0"/>
+ <endStatus>
+ <names>
+ <shortLabel>n-terminal</shortLabel>
+ <fullName>n-terminal position</fullName>
+ <alias>n-terminus</alias>
+ <alias>amino-terminus</alias>
+ <alias>n-term</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0340" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </endStatus>
+ <end position="0"/>
+ </featureRange>
+ </featureRangeList>
+ </feature>
+ </featureList>
+ </participant>
+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>physical interaction</shortLabel>
+ <fullName>physical interaction</fullName>
+ <alias>aggregation</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0218" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactionType>
+ <attributeList>
+ <attribute name="kd">1.0</attribute>
+ </attributeList>
+ </interaction>
+ <interaction id="48">
+ <names>
+ <shortLabel>kaic-kaic-5</shortLabel>
+ <fullName>pull down HIS kaiC - kaiC in vivo</fullName>
+ </names>
+ <xref>
+ <primaryRef db="intact" dbAc="MI:0469" id="EBI-781840" secondary="kaic-kaic-5"/>
+ </xref>
+ <experimentList>
+ <experimentRef>24</experimentRef>
+ </experimentList>
+ <participantList>
+ <participant id="49">
+ <interactorRef>4</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="50">
+ <interactorRef>4</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>bait</shortLabel>
+ <fullName>bait</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0496" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ <featureList>
+ <feature id="51">
+ <names>
+ <shortLabel>region</shortLabel>
+ </names>
+ <featureType>
+ <names>
+ <shortLabel>his tagged</shortLabel>
+ <fullName>his tagged</fullName>
+ <alias>6-His-tagged</alias>
+ <alias>Hexa-His-tagged</alias>
+ <alias>Histidine-tagged</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0521" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </featureType>
+ <featureRangeList>
+ <featureRange>
+ <startStatus>
+ <names>
+ <shortLabel>n-terminal</shortLabel>
+ <fullName>n-terminal position</fullName>
+ <alias>n-terminus</alias>
+ <alias>amino-terminus</alias>
+ <alias>n-term</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0340" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </startStatus>
+ <begin position="0"/>
+ <endStatus>
+ <names>
+ <shortLabel>n-terminal</shortLabel>
+ <fullName>n-terminal position</fullName>
+ <alias>n-terminus</alias>
+ <alias>amino-terminus</alias>
+ <alias>n-term</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0340" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </endStatus>
+ <end position="0"/>
+ </featureRange>
+ </featureRangeList>
+ </feature>
+ </featureList>
+ </participant>
+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>physical interaction</shortLabel>
+ <fullName>physical interaction</fullName>
+ <alias>aggregation</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0218" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactionType>
+ <attributeList>
+ <attribute name="kd">1.0</attribute>
+ </attributeList>
+ </interaction>
+ <interaction id="52">
+ <names>
+ <shortLabel>kaic-kaib-2</shortLabel>
+ <fullName>pull down HIS kaiC - kaiB in vivo</fullName>
+ </names>
+ <xref>
+ <primaryRef db="intact" dbAc="MI:0469" id="EBI-781849" secondary="kaic-kaib-2"/>
+ </xref>
+ <experimentList>
+ <experimentRef>24</experimentRef>
+ </experimentList>
+ <participantList>
+ <participant id="53">
+ <interactorRef>10</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="54">
+ <interactorRef>4</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>bait</shortLabel>
+ <fullName>bait</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0496" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ <featureList>
+ <feature id="55">
+ <names>
+ <shortLabel>region</shortLabel>
+ </names>
+ <featureType>
+ <names>
+ <shortLabel>his tagged</shortLabel>
+ <fullName>his tagged</fullName>
+ <alias>6-His-tagged</alias>
+ <alias>Hexa-His-tagged</alias>
+ <alias>Histidine-tagged</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0521" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </featureType>
+ <featureRangeList>
+ <featureRange>
+ <startStatus>
+ <names>
+ <shortLabel>n-terminal</shortLabel>
+ <fullName>n-terminal position</fullName>
+ <alias>n-terminus</alias>
+ <alias>amino-terminus</alias>
+ <alias>n-term</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0340" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </startStatus>
+ <begin position="0"/>
+ <endStatus>
+ <names>
+ <shortLabel>n-terminal</shortLabel>
+ <fullName>n-terminal position</fullName>
+ <alias>n-terminus</alias>
+ <alias>amino-terminus</alias>
+ <alias>n-term</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0340" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </endStatus>
+ <end position="0"/>
+ </featureRange>
+ </featureRangeList>
+ </feature>
+ </featureList>
+ </participant>
+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>physical interaction</shortLabel>
+ <fullName>physical interaction</fullName>
+ <alias>aggregation</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0218" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactionType>
+ <attributeList>
+ <attribute name="caution">Weak interaction</attribute>
+ <attribute name="kd">1.0</attribute>
+ </attributeList>
+ </interaction>
+ <interaction id="56">
+ <names>
+ <shortLabel>kaic-kaia-3</shortLabel>
+ <fullName>pull down HIS kaiC - kaiA in vivo</fullName>
+ </names>
+ <xref>
+ <primaryRef db="intact" dbAc="MI:0469" id="EBI-781856" secondary="kaic-kaia-3"/>
+ </xref>
+ <experimentList>
+ <experimentRef>24</experimentRef>
+ </experimentList>
+ <participantList>
+ <participant id="57">
+ <interactorRef>6</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ </participant>
+ <participant id="58">
+ <interactorRef>4</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>bait</shortLabel>
+ <fullName>bait</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0496" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ <featureList>
+ <feature id="59">
+ <names>
+ <shortLabel>region</shortLabel>
+ </names>
+ <featureType>
+ <names>
+ <shortLabel>his tagged</shortLabel>
+ <fullName>his tagged</fullName>
+ <alias>6-His-tagged</alias>
+ <alias>Hexa-His-tagged</alias>
+ <alias>Histidine-tagged</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0521" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </featureType>
+ <featureRangeList>
+ <featureRange>
+ <startStatus>
+ <names>
+ <shortLabel>n-terminal</shortLabel>
+ <fullName>n-terminal position</fullName>
+ <alias>n-terminus</alias>
+ <alias>amino-terminus</alias>
+ <alias>n-term</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0340" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </startStatus>
+ <begin position="0"/>
+ <endStatus>
+ <names>
+ <shortLabel>n-terminal</shortLabel>
+ <fullName>n-terminal position</fullName>
+ <alias>n-terminus</alias>
+ <alias>amino-terminus</alias>
+ <alias>n-term</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0340" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </endStatus>
+ <end position="0"/>
+ </featureRange>
+ </featureRangeList>
+ </feature>
+ </featureList>
+ </participant>
+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>physical interaction</shortLabel>
+ <fullName>physical interaction</fullName>
+ <alias>aggregation</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0218" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactionType>
+ <attributeList>
+ <attribute name="caution">Weak interaction</attribute>
+ <attribute name="kd">1.0</attribute>
+ </attributeList>
+ </interaction>
+ <interaction id="60">
+ <names>
+ <shortLabel>kaib-kaib-7</shortLabel>
+ <fullName>pull down HIS KaiB GST kaiB</fullName>
+ </names>
+ <xref>
+ <primaryRef db="intact" dbAc="MI:0469" id="EBI-781992" secondary="kaib-kaib-7"/>
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+ <participant id="62">
+ <interactorRef>10</interactorRef>
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+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
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+ </biologicalRole>
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+ <fullName>bait</fullName>
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+ <featureType>
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+ <shortLabel>his tagged</shortLabel>
+ <fullName>his tagged</fullName>
+ <alias>6-His-tagged</alias>
+ <alias>Hexa-His-tagged</alias>
+ <alias>Histidine-tagged</alias>
+ </names>
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+ <fullName>n-terminal position</fullName>
+ <alias>n-terminus</alias>
+ <alias>amino-terminus</alias>
+ <alias>n-term</alias>
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+ <xref>
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+ <begin position="0"/>
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+ <fullName>n-terminal position</fullName>
+ <alias>n-terminus</alias>
+ <alias>amino-terminus</alias>
+ <alias>n-term</alias>
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+ <fullName>Synechococcus sp. (strain PCC 7942)</fullName>
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+ <fullName>unspecified</fullName>
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+ <experimentalRoleList>
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+ <fullName>prey</fullName>
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+ <names>
+ <shortLabel>region</shortLabel>
+ </names>
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+ <shortLabel>gst tagged</shortLabel>
+ <fullName>gst tagged</fullName>
+ <alias>glutathione S-tranferase tag</alias>
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+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0519" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
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+ <shortLabel>n-terminal</shortLabel>
+ <fullName>n-terminal position</fullName>
+ <alias>n-terminus</alias>
+ <alias>amino-terminus</alias>
+ <alias>n-term</alias>
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+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0340" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
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+ <begin position="0"/>
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+ <names>
+ <shortLabel>n-terminal</shortLabel>
+ <fullName>n-terminal position</fullName>
+ <alias>n-terminus</alias>
+ <alias>amino-terminus</alias>
+ <alias>n-term</alias>
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+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0340" refType="identity" refTypeAc="MI:0356"/>
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+ </featureRange>
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+ <hostOrganism ncbiTaxId="1140">
+ <names>
+ <shortLabel>synp7</shortLabel>
+ <fullName>Synechococcus sp. (strain PCC 7942)</fullName>
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+ </hostOrganism>
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+ </participant>
+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>direct interaction</shortLabel>
+ <fullName>direct interaction</fullName>
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+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
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+ <attributeList>
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+ </interaction>
+ <interaction id="66">
+ <names>
+ <shortLabel>kaib-kaia-8</shortLabel>
+ <fullName>pull down HIS KaiB GST kaiA</fullName>
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+ <xref>
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+ <participant id="67">
+ <interactorRef>10</interactorRef>
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+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
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+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
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+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>bait</shortLabel>
+ <fullName>bait</fullName>
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+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
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+ <featureList>
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+ <shortLabel>region</shortLabel>
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+ <featureType>
+ <names>
+ <shortLabel>his tagged</shortLabel>
+ <fullName>his tagged</fullName>
+ <alias>6-His-tagged</alias>
+ <alias>Hexa-His-tagged</alias>
+ <alias>Histidine-tagged</alias>
+ </names>
+ <xref>
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+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
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+ <alias>n-terminus</alias>
+ <alias>amino-terminus</alias>
+ <alias>n-term</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0340" refType="identity" refTypeAc="MI:0356"/>
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+ <fullName>n-terminal position</fullName>
+ <alias>n-terminus</alias>
+ <alias>amino-terminus</alias>
+ <alias>n-term</alias>
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+ </featureRange>
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+ <shortLabel>synp7</shortLabel>
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+ <alias>glutathione S-tranferase tag</alias>
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+ <shortLabel>synp7</shortLabel>
+ <fullName>Synechococcus sp. (strain PCC 7942)</fullName>
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+ </participant>
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+ <interactionType>
+ <names>
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+ <fullName>direct interaction</fullName>
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+ <attributeList>
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+ <attribute name="kd">1.0</attribute>
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+ </interaction>
+ <interaction id="71">
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+ <shortLabel>kaib-kaic-6</shortLabel>
+ <fullName>pull down HIS KaiB GST kaiC</fullName>
+ </names>
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+ <shortLabel>unspecified</shortLabel>
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+ <names>
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+ <experimentalRoleList>
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+ <shortLabel>bait</shortLabel>
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+ <shortLabel>region</shortLabel>
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+ <featureType>
+ <names>
+ <shortLabel>his tagged</shortLabel>
+ <fullName>his tagged</fullName>
+ <alias>6-His-tagged</alias>
+ <alias>Hexa-His-tagged</alias>
+ <alias>Histidine-tagged</alias>
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+ <alias>n-term</alias>
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+ <begin position="0"/>
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+ <fullName>n-terminal position</fullName>
+ <alias>n-terminus</alias>
+ <alias>amino-terminus</alias>
+ <alias>n-term</alias>
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+ <hostOrganism ncbiTaxId="1140">
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+ <shortLabel>synp7</shortLabel>
+ <fullName>Synechococcus sp. (strain PCC 7942)</fullName>
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+ </participant>
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+ <interactionType>
+ <names>
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+ <fullName>direct interaction</fullName>
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+ <attribute name="kd">1.0</attribute>
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+ <interaction id="76">
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+ <shortLabel>kaia-kaic-13</shortLabel>
+ <fullName>pull down bait GST KaiA - prey 35S kaiC in vitro</fullName>
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+ <primaryRef db="intact" dbAc="MI:0469" id="EBI-781221" secondary="kaia-kaic-13"/>
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+ <participant id="78">
+ <interactorRef>6</interactorRef>
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+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
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+ <experimentalRoleList>
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+ <names>
+ <shortLabel>bait</shortLabel>
+ <fullName>bait</fullName>
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+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0496" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
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+ <featureList>
+ <feature id="79">
+ <names>
+ <shortLabel>region</shortLabel>
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+ <featureType>
+ <names>
+ <shortLabel>gst tagged</shortLabel>
+ <fullName>gst tagged</fullName>
+ <alias>glutathione S-tranferase tag</alias>
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+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0519" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </featureType>
+ <featureRangeList>
+ <featureRange>
+ <startStatus>
+ <names>
+ <shortLabel>n-terminal</shortLabel>
+ <fullName>n-terminal position</fullName>
+ <alias>n-terminus</alias>
+ <alias>amino-terminus</alias>
+ <alias>n-term</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0340" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </startStatus>
+ <begin position="0"/>
+ <endStatus>
+ <names>
+ <shortLabel>n-terminal</shortLabel>
+ <fullName>n-terminal position</fullName>
+ <alias>n-terminus</alias>
+ <alias>amino-terminus</alias>
+ <alias>n-term</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0340" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </endStatus>
+ <end position="0"/>
+ </featureRange>
+ </featureRangeList>
+ </feature>
+ </featureList>
+ <hostOrganismList>
+ <hostOrganism ncbiTaxId="1140">
+ <names>
+ <shortLabel>synp7</shortLabel>
+ <fullName>Synechococcus sp. (strain PCC 7942)</fullName>
+ </names>
+ </hostOrganism>
+ </hostOrganismList>
+ </participant>
+ <participant id="80">
+ <interactorRef>4</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ <featureList>
+ <feature id="81">
+ <names>
+ <shortLabel>region</shortLabel>
+ </names>
+ <featureType>
+ <names>
+ <shortLabel>35s radiolabelled</shortLabel>
+ <fullName>35s radiolabelled</fullName>
+ <alias>35S</alias>
+ <alias>S35</alias>
+ <alias>s35 radiolabelled</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0371" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </featureType>
+ <featureRangeList>
+ <featureRange>
+ <startStatus>
+ <names>
+ <shortLabel>undetermined</shortLabel>
+ <fullName>undetermined sequence position</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0339" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </startStatus>
+ <begin position="0"/>
+ <endStatus>
+ <names>
+ <shortLabel>undetermined</shortLabel>
+ <fullName>undetermined sequence position</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0339" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </endStatus>
+ <end position="0"/>
+ </featureRange>
+ </featureRangeList>
+ </feature>
+ </featureList>
+ <hostOrganismList>
+ <hostOrganism ncbiTaxId="1140">
+ <names>
+ <shortLabel>synp7</shortLabel>
+ <fullName>Synechococcus sp. (strain PCC 7942)</fullName>
+ </names>
+ </hostOrganism>
+ </hostOrganismList>
+ </participant>
+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>physical interaction</shortLabel>
+ <fullName>physical interaction</fullName>
+ <alias>aggregation</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0218" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactionType>
+ <attributeList>
+ <attribute name="kd">1.0</attribute>
+ </attributeList>
+ </interaction>
+ <interaction id="82">
+ <names>
+ <shortLabel>kaia-kaia-2</shortLabel>
+ <fullName>pull down bait GST KaiA - prey 35S kaiA in vitro</fullName>
+ </names>
+ <xref>
+ <primaryRef db="intact" dbAc="MI:0469" id="EBI-781236" secondary="kaia-kaia-2"/>
+ </xref>
+ <experimentList>
+ <experimentRef>77</experimentRef>
+ </experimentList>
+ <participantList>
+ <participant id="83">
+ <interactorRef>6</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>bait</shortLabel>
+ <fullName>bait</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0496" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ <featureList>
+ <feature id="84">
+ <names>
+ <shortLabel>region</shortLabel>
+ </names>
+ <featureType>
+ <names>
+ <shortLabel>gst tagged</shortLabel>
+ <fullName>gst tagged</fullName>
+ <alias>glutathione S-tranferase tag</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0519" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </featureType>
+ <featureRangeList>
+ <featureRange>
+ <startStatus>
+ <names>
+ <shortLabel>n-terminal</shortLabel>
+ <fullName>n-terminal position</fullName>
+ <alias>n-terminus</alias>
+ <alias>amino-terminus</alias>
+ <alias>n-term</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0340" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </startStatus>
+ <begin position="0"/>
+ <endStatus>
+ <names>
+ <shortLabel>n-terminal</shortLabel>
+ <fullName>n-terminal position</fullName>
+ <alias>n-terminus</alias>
+ <alias>amino-terminus</alias>
+ <alias>n-term</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0340" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </endStatus>
+ <end position="0"/>
+ </featureRange>
+ </featureRangeList>
+ </feature>
+ </featureList>
+ <hostOrganismList>
+ <hostOrganism ncbiTaxId="1140">
+ <names>
+ <shortLabel>synp7</shortLabel>
+ <fullName>Synechococcus sp. (strain PCC 7942)</fullName>
+ </names>
+ </hostOrganism>
+ </hostOrganismList>
+ </participant>
+ <participant id="85">
+ <interactorRef>6</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ <featureList>
+ <feature id="86">
+ <names>
+ <shortLabel>region</shortLabel>
+ </names>
+ <featureType>
+ <names>
+ <shortLabel>35s radiolabelled</shortLabel>
+ <fullName>35s radiolabelled</fullName>
+ <alias>35S</alias>
+ <alias>S35</alias>
+ <alias>s35 radiolabelled</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0371" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </featureType>
+ <featureRangeList>
+ <featureRange>
+ <startStatus>
+ <names>
+ <shortLabel>undetermined</shortLabel>
+ <fullName>undetermined sequence position</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0339" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </startStatus>
+ <begin position="0"/>
+ <endStatus>
+ <names>
+ <shortLabel>undetermined</shortLabel>
+ <fullName>undetermined sequence position</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0339" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </endStatus>
+ <end position="0"/>
+ </featureRange>
+ </featureRangeList>
+ </feature>
+ </featureList>
+ <hostOrganismList>
+ <hostOrganism ncbiTaxId="1140">
+ <names>
+ <shortLabel>synp7</shortLabel>
+ <fullName>Synechococcus sp. (strain PCC 7942)</fullName>
+ </names>
+ </hostOrganism>
+ </hostOrganismList>
+ </participant>
+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>physical interaction</shortLabel>
+ <fullName>physical interaction</fullName>
+ <alias>aggregation</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0218" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactionType>
+ <attributeList>
+ <attribute name="kd">1.0</attribute>
+ </attributeList>
+ </interaction>
+ <interaction id="87">
+ <names>
+ <shortLabel>kaic-kaia-2</shortLabel>
+ <fullName>pull down bait GST KaiC - prey 35S kaiA in vitro</fullName>
+ </names>
+ <xref>
+ <primaryRef db="intact" dbAc="MI:0469" id="EBI-781277" secondary="kaic-kaia-2"/>
+ </xref>
+ <experimentList>
+ <experimentRef>77</experimentRef>
+ </experimentList>
+ <participantList>
+ <participant id="88">
+ <interactorRef>6</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ <featureList>
+ <feature id="89">
+ <names>
+ <shortLabel>region</shortLabel>
+ </names>
+ <featureType>
+ <names>
+ <shortLabel>35s radiolabelled</shortLabel>
+ <fullName>35s radiolabelled</fullName>
+ <alias>35S</alias>
+ <alias>S35</alias>
+ <alias>s35 radiolabelled</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0371" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </featureType>
+ <featureRangeList>
+ <featureRange>
+ <startStatus>
+ <names>
+ <shortLabel>undetermined</shortLabel>
+ <fullName>undetermined sequence position</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0339" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </startStatus>
+ <begin position="0"/>
+ <endStatus>
+ <names>
+ <shortLabel>undetermined</shortLabel>
+ <fullName>undetermined sequence position</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0339" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </endStatus>
+ <end position="0"/>
+ </featureRange>
+ </featureRangeList>
+ </feature>
+ </featureList>
+ <hostOrganismList>
+ <hostOrganism ncbiTaxId="1140">
+ <names>
+ <shortLabel>synp7</shortLabel>
+ <fullName>Synechococcus sp. (strain PCC 7942)</fullName>
+ </names>
+ </hostOrganism>
+ </hostOrganismList>
+ </participant>
+ <participant id="90">
+ <interactorRef>4</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>bait</shortLabel>
+ <fullName>bait</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0496" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ <featureList>
+ <feature id="91">
+ <names>
+ <shortLabel>region</shortLabel>
+ </names>
+ <featureType>
+ <names>
+ <shortLabel>gst tagged</shortLabel>
+ <fullName>gst tagged</fullName>
+ <alias>glutathione S-tranferase tag</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0519" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </featureType>
+ <featureRangeList>
+ <featureRange>
+ <startStatus>
+ <names>
+ <shortLabel>n-terminal</shortLabel>
+ <fullName>n-terminal position</fullName>
+ <alias>n-terminus</alias>
+ <alias>amino-terminus</alias>
+ <alias>n-term</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0340" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </startStatus>
+ <begin position="0"/>
+ <endStatus>
+ <names>
+ <shortLabel>n-terminal</shortLabel>
+ <fullName>n-terminal position</fullName>
+ <alias>n-terminus</alias>
+ <alias>amino-terminus</alias>
+ <alias>n-term</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0340" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </endStatus>
+ <end position="0"/>
+ </featureRange>
+ </featureRangeList>
+ </feature>
+ </featureList>
+ <hostOrganismList>
+ <hostOrganism ncbiTaxId="1140">
+ <names>
+ <shortLabel>synp7</shortLabel>
+ <fullName>Synechococcus sp. (strain PCC 7942)</fullName>
+ </names>
+ </hostOrganism>
+ </hostOrganismList>
+ </participant>
+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>physical interaction</shortLabel>
+ <fullName>physical interaction</fullName>
+ <alias>aggregation</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0218" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactionType>
+ <attributeList>
+ <attribute name="kd">1.0</attribute>
+ </attributeList>
+ </interaction>
+ <interaction id="92">
+ <names>
+ <shortLabel>kaic-kaic-4</shortLabel>
+ <fullName>pull down bait GST KaiC - prey 35S kaiC in vitro</fullName>
+ </names>
+ <xref>
+ <primaryRef db="intact" dbAc="MI:0469" id="EBI-781752" secondary="kaic-kaic-4"/>
+ </xref>
+ <experimentList>
+ <experimentRef>77</experimentRef>
+ </experimentList>
+ <participantList>
+ <participant id="93">
+ <interactorRef>4</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ <featureList>
+ <feature id="94">
+ <names>
+ <shortLabel>region</shortLabel>
+ </names>
+ <featureType>
+ <names>
+ <shortLabel>35s radiolabelled</shortLabel>
+ <fullName>35s radiolabelled</fullName>
+ <alias>35S</alias>
+ <alias>S35</alias>
+ <alias>s35 radiolabelled</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0371" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </featureType>
+ <featureRangeList>
+ <featureRange>
+ <startStatus>
+ <names>
+ <shortLabel>undetermined</shortLabel>
+ <fullName>undetermined sequence position</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0339" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </startStatus>
+ <begin position="0"/>
+ <endStatus>
+ <names>
+ <shortLabel>undetermined</shortLabel>
+ <fullName>undetermined sequence position</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0339" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </endStatus>
+ <end position="0"/>
+ </featureRange>
+ </featureRangeList>
+ </feature>
+ </featureList>
+ <hostOrganismList>
+ <hostOrganism ncbiTaxId="1140">
+ <names>
+ <shortLabel>synp7</shortLabel>
+ <fullName>Synechococcus sp. (strain PCC 7942)</fullName>
+ </names>
+ </hostOrganism>
+ </hostOrganismList>
+ </participant>
+ <participant id="95">
+ <interactorRef>4</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>bait</shortLabel>
+ <fullName>bait</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0496" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ <featureList>
+ <feature id="96">
+ <names>
+ <shortLabel>region</shortLabel>
+ </names>
+ <featureType>
+ <names>
+ <shortLabel>gst tagged</shortLabel>
+ <fullName>gst tagged</fullName>
+ <alias>glutathione S-tranferase tag</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0519" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </featureType>
+ <featureRangeList>
+ <featureRange>
+ <startStatus>
+ <names>
+ <shortLabel>n-terminal</shortLabel>
+ <fullName>n-terminal position</fullName>
+ <alias>n-terminus</alias>
+ <alias>amino-terminus</alias>
+ <alias>n-term</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0340" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </startStatus>
+ <begin position="0"/>
+ <endStatus>
+ <names>
+ <shortLabel>n-terminal</shortLabel>
+ <fullName>n-terminal position</fullName>
+ <alias>n-terminus</alias>
+ <alias>amino-terminus</alias>
+ <alias>n-term</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0340" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </endStatus>
+ <end position="0"/>
+ </featureRange>
+ </featureRangeList>
+ </feature>
+ </featureList>
+ <hostOrganismList>
+ <hostOrganism ncbiTaxId="1140">
+ <names>
+ <shortLabel>synp7</shortLabel>
+ <fullName>Synechococcus sp. (strain PCC 7942)</fullName>
+ </names>
+ </hostOrganism>
+ </hostOrganismList>
+ </participant>
+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>physical interaction</shortLabel>
+ <fullName>physical interaction</fullName>
+ <alias>aggregation</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0218" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactionType>
+ <attributeList>
+ <attribute name="kd">1.0</attribute>
+ </attributeList>
+ </interaction>
+ <interaction id="97">
+ <names>
+ <shortLabel>kaib-kaia-3</shortLabel>
+ <fullName>pull down bait GST KaiB - prey 35S kaiA in vitro</fullName>
+ </names>
+ <xref>
+ <primaryRef db="intact" dbAc="MI:0469" id="EBI-781764" secondary="kaib-kaia-3"/>
+ </xref>
+ <experimentList>
+ <experimentRef>77</experimentRef>
+ </experimentList>
+ <participantList>
+ <participant id="98">
+ <interactorRef>6</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ <featureList>
+ <feature id="99">
+ <names>
+ <shortLabel>region</shortLabel>
+ </names>
+ <featureType>
+ <names>
+ <shortLabel>35s radiolabelled</shortLabel>
+ <fullName>35s radiolabelled</fullName>
+ <alias>35S</alias>
+ <alias>S35</alias>
+ <alias>s35 radiolabelled</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0371" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </featureType>
+ <featureRangeList>
+ <featureRange>
+ <startStatus>
+ <names>
+ <shortLabel>undetermined</shortLabel>
+ <fullName>undetermined sequence position</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0339" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </startStatus>
+ <begin position="0"/>
+ <endStatus>
+ <names>
+ <shortLabel>undetermined</shortLabel>
+ <fullName>undetermined sequence position</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0339" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </endStatus>
+ <end position="0"/>
+ </featureRange>
+ </featureRangeList>
+ </feature>
+ </featureList>
+ <hostOrganismList>
+ <hostOrganism ncbiTaxId="1140">
+ <names>
+ <shortLabel>synp7</shortLabel>
+ <fullName>Synechococcus sp. (strain PCC 7942)</fullName>
+ </names>
+ </hostOrganism>
+ </hostOrganismList>
+ </participant>
+ <participant id="100">
+ <interactorRef>10</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>bait</shortLabel>
+ <fullName>bait</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0496" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ <featureList>
+ <feature id="101">
+ <names>
+ <shortLabel>region</shortLabel>
+ </names>
+ <featureType>
+ <names>
+ <shortLabel>gst tagged</shortLabel>
+ <fullName>gst tagged</fullName>
+ <alias>glutathione S-tranferase tag</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0519" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </featureType>
+ <featureRangeList>
+ <featureRange>
+ <startStatus>
+ <names>
+ <shortLabel>n-terminal</shortLabel>
+ <fullName>n-terminal position</fullName>
+ <alias>n-terminus</alias>
+ <alias>amino-terminus</alias>
+ <alias>n-term</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0340" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </startStatus>
+ <begin position="0"/>
+ <endStatus>
+ <names>
+ <shortLabel>n-terminal</shortLabel>
+ <fullName>n-terminal position</fullName>
+ <alias>n-terminus</alias>
+ <alias>amino-terminus</alias>
+ <alias>n-term</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0340" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </endStatus>
+ <end position="0"/>
+ </featureRange>
+ </featureRangeList>
+ </feature>
+ </featureList>
+ <hostOrganismList>
+ <hostOrganism ncbiTaxId="1140">
+ <names>
+ <shortLabel>synp7</shortLabel>
+ <fullName>Synechococcus sp. (strain PCC 7942)</fullName>
+ </names>
+ </hostOrganism>
+ </hostOrganismList>
+ </participant>
+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>physical interaction</shortLabel>
+ <fullName>physical interaction</fullName>
+ <alias>aggregation</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0218" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactionType>
+ <attributeList>
+ <attribute name="caution">Weak interaction compare to the others detected in the same experiment.</attribute>
+ <attribute name="kd">1.0</attribute>
+ </attributeList>
+ </interaction>
+ <interaction id="102">
+ <names>
+ <shortLabel>kaib-kaic-2</shortLabel>
+ <fullName>pull down bait GST KaiB - prey 35S kaiC in vitro</fullName>
+ </names>
+ <xref>
+ <primaryRef db="intact" dbAc="MI:0469" id="EBI-781780" secondary="kaib-kaic-2"/>
+ </xref>
+ <experimentList>
+ <experimentRef>77</experimentRef>
+ </experimentList>
+ <participantList>
+ <participant id="103">
+ <interactorRef>10</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>bait</shortLabel>
+ <fullName>bait</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0496" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ <featureList>
+ <feature id="104">
+ <names>
+ <shortLabel>region</shortLabel>
+ </names>
+ <featureType>
+ <names>
+ <shortLabel>gst tagged</shortLabel>
+ <fullName>gst tagged</fullName>
+ <alias>glutathione S-tranferase tag</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0519" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </featureType>
+ <featureRangeList>
+ <featureRange>
+ <startStatus>
+ <names>
+ <shortLabel>n-terminal</shortLabel>
+ <fullName>n-terminal position</fullName>
+ <alias>n-terminus</alias>
+ <alias>amino-terminus</alias>
+ <alias>n-term</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0340" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </startStatus>
+ <begin position="0"/>
+ <endStatus>
+ <names>
+ <shortLabel>n-terminal</shortLabel>
+ <fullName>n-terminal position</fullName>
+ <alias>n-terminus</alias>
+ <alias>amino-terminus</alias>
+ <alias>n-term</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0340" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </endStatus>
+ <end position="0"/>
+ </featureRange>
+ </featureRangeList>
+ </feature>
+ </featureList>
+ <hostOrganismList>
+ <hostOrganism ncbiTaxId="1140">
+ <names>
+ <shortLabel>synp7</shortLabel>
+ <fullName>Synechococcus sp. (strain PCC 7942)</fullName>
+ </names>
+ </hostOrganism>
+ </hostOrganismList>
+ </participant>
+ <participant id="105">
+ <interactorRef>4</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ <featureList>
+ <feature id="106">
+ <names>
+ <shortLabel>region</shortLabel>
+ </names>
+ <featureType>
+ <names>
+ <shortLabel>35s radiolabelled</shortLabel>
+ <fullName>35s radiolabelled</fullName>
+ <alias>35S</alias>
+ <alias>S35</alias>
+ <alias>s35 radiolabelled</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0371" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </featureType>
+ <featureRangeList>
+ <featureRange>
+ <startStatus>
+ <names>
+ <shortLabel>undetermined</shortLabel>
+ <fullName>undetermined sequence position</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0339" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </startStatus>
+ <begin position="0"/>
+ <endStatus>
+ <names>
+ <shortLabel>undetermined</shortLabel>
+ <fullName>undetermined sequence position</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0339" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </endStatus>
+ <end position="0"/>
+ </featureRange>
+ </featureRangeList>
+ </feature>
+ </featureList>
+ <hostOrganismList>
+ <hostOrganism ncbiTaxId="1140">
+ <names>
+ <shortLabel>synp7</shortLabel>
+ <fullName>Synechococcus sp. (strain PCC 7942)</fullName>
+ </names>
+ </hostOrganism>
+ </hostOrganismList>
+ </participant>
+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>physical interaction</shortLabel>
+ <fullName>physical interaction</fullName>
+ <alias>aggregation</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0218" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactionType>
+ <attributeList>
+ <attribute name="kd">1.0</attribute>
+ </attributeList>
+ </interaction>
+ <interaction id="107">
+ <names>
+ <shortLabel>kaia-kaic-14</shortLabel>
+ <fullName>pull down bait GST KaiA - prey 35S kaiC1 (1-250) in vitro</fullName>
+ </names>
+ <xref>
+ <primaryRef db="intact" dbAc="MI:0469" id="EBI-781873" secondary="kaia-kaic-14"/>
+ </xref>
+ <experimentList>
+ <experimentRef>77</experimentRef>
+ </experimentList>
+ <participantList>
+ <participant id="108">
+ <interactorRef>4</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ <featureList>
+ <feature id="109">
+ <names>
+ <shortLabel>region</shortLabel>
+ </names>
+ <featureType>
+ <names>
+ <shortLabel>35s radiolabelled</shortLabel>
+ <fullName>35s radiolabelled</fullName>
+ <alias>35S</alias>
+ <alias>S35</alias>
+ <alias>s35 radiolabelled</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0371" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </featureType>
+ <featureRangeList>
+ <featureRange>
+ <startStatus>
+ <names>
+ <shortLabel>undetermined</shortLabel>
+ <fullName>undetermined sequence position</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0339" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </startStatus>
+ <begin position="0"/>
+ <endStatus>
+ <names>
+ <shortLabel>undetermined</shortLabel>
+ <fullName>undetermined sequence position</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0339" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </endStatus>
+ <end position="0"/>
+ </featureRange>
+ </featureRangeList>
+ </feature>
+ <feature id="110">
+ <names>
+ <shortLabel>region</shortLabel>
+ </names>
+ <featureType>
+ <names>
+ <shortLabel>binding site</shortLabel>
+ <fullName>binding site</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0117" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </featureType>
+ <featureRangeList>
+ <featureRange>
+ <startStatus>
+ <names>
+ <shortLabel>certain</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0335" refType="identity" refTypeAc="MI:0356"/>
+ </xref>
+ </startStatus>
+ <begin position="1"/>
+ <endStatus>
+ <names>
+ <shortLabel>certain</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0335" refType="identity" refTypeAc="MI:0356"/>
+ </xref>
+ </endStatus>
+ <end position="250"/>
+ </featureRange>
+ </featureRangeList>
+ </feature>
+ </featureList>
+ <hostOrganismList>
+ <hostOrganism ncbiTaxId="1140">
+ <names>
+ <shortLabel>synp7</shortLabel>
+ <fullName>Synechococcus sp. (strain PCC 7942)</fullName>
+ </names>
+ </hostOrganism>
+ </hostOrganismList>
+ </participant>
+ <participant id="111">
+ <interactorRef>6</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>bait</shortLabel>
+ <fullName>bait</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0496" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ <featureList>
+ <feature id="112">
+ <names>
+ <shortLabel>region</shortLabel>
+ </names>
+ <featureType>
+ <names>
+ <shortLabel>gst tagged</shortLabel>
+ <fullName>gst tagged</fullName>
+ <alias>glutathione S-tranferase tag</alias>
+ </names>
+ <xref>
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+ <alias>amino-terminus</alias>
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+ <hostOrganism ncbiTaxId="1140">
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+ <shortLabel>unspecified</shortLabel>
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+ <alias>n-terminus</alias>
+ <alias>amino-terminus</alias>
+ <alias>n-term</alias>
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+ <begin position="0"/>
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+ <fullName>n-terminal position</fullName>
+ <alias>n-terminus</alias>
+ <alias>amino-terminus</alias>
+ <alias>n-term</alias>
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+ <hostOrganism ncbiTaxId="1140">
+ <names>
+ <shortLabel>synp7</shortLabel>
+ <fullName>Synechococcus sp. (strain PCC 7942)</fullName>
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+ <participant id="116">
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+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
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+ <experimentalRoleList>
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+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
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+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
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+ <shortLabel>region</shortLabel>
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+ <featureType>
+ <names>
+ <shortLabel>binding site</shortLabel>
+ <fullName>binding site</fullName>
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+ </feature>
+ <feature id="118">
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+ <shortLabel>region</shortLabel>
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+ <names>
+ <shortLabel>35s radiolabelled</shortLabel>
+ <fullName>35s radiolabelled</fullName>
+ <alias>35S</alias>
+ <alias>S35</alias>
+ <alias>s35 radiolabelled</alias>
+ </names>
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+ <fullName>undetermined sequence position</fullName>
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+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
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+ <shortLabel>synp7</shortLabel>
+ <fullName>Synechococcus sp. (strain PCC 7942)</fullName>
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+ </participant>
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+ <names>
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+ <fullName>physical interaction</fullName>
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+ </interaction>
+ <interaction id="119">
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+ <shortLabel>kaic-kaic-6</shortLabel>
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+ <primaryRef db="intact" dbAc="MI:0469" id="EBI-781893" secondary="kaic-kaic-6"/>
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+ <shortLabel>unspecified</shortLabel>
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+ <alias>n-term</alias>
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+ <fullName>Synechococcus sp. (strain PCC 7942)</fullName>
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+ <participant id="122">
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+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
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+ <fullName>35s radiolabelled</fullName>
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+ <alias>s35 radiolabelled</alias>
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+ <shortLabel>synp7</shortLabel>
+ <fullName>Synechococcus sp. (strain PCC 7942)</fullName>
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+ </participant>
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+ <interactionType>
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+ <shortLabel>physical interaction</shortLabel>
+ <fullName>physical interaction</fullName>
+ <alias>aggregation</alias>
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+ <attribute name="kd">1.0</attribute>
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+ </interaction>
+ <interaction id="125">
+ <names>
+ <shortLabel>kaic-kaic-7</shortLabel>
+ <fullName>pull down bait GST KaiC - prey 35S kaiC2 (252-519) in vitro</fullName>
+ </names>
+ <xref>
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+ <participantList>
+ <participant id="126">
+ <interactorRef>4</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
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+ <fullName>bait</fullName>
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+ <shortLabel>region</shortLabel>
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+ <featureType>
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+ <shortLabel>gst tagged</shortLabel>
+ <fullName>gst tagged</fullName>
+ <alias>glutathione S-tranferase tag</alias>
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+ <alias>n-terminus</alias>
+ <alias>amino-terminus</alias>
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+ <hostOrganism ncbiTaxId="1140">
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+ <fullName>Synechococcus sp. (strain PCC 7942)</fullName>
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+ <participant id="128">
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+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
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+ <experimentalRoleList>
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+ <fullName>prey</fullName>
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+ <xref>
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+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ <featureList>
+ <feature id="129">
+ <names>
+ <shortLabel>region</shortLabel>
+ </names>
+ <featureType>
+ <names>
+ <shortLabel>binding site</shortLabel>
+ <fullName>binding site</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0117" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </featureType>
+ <featureRangeList>
+ <featureRange>
+ <startStatus>
+ <names>
+ <shortLabel>certain</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0335" refType="identity" refTypeAc="MI:0356"/>
+ </xref>
+ </startStatus>
+ <begin position="252"/>
+ <endStatus>
+ <names>
+ <shortLabel>certain</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0335" refType="identity" refTypeAc="MI:0356"/>
+ </xref>
+ </endStatus>
+ <end position="519"/>
+ </featureRange>
+ </featureRangeList>
+ </feature>
+ <feature id="130">
+ <names>
+ <shortLabel>region</shortLabel>
+ </names>
+ <featureType>
+ <names>
+ <shortLabel>35s radiolabelled</shortLabel>
+ <fullName>35s radiolabelled</fullName>
+ <alias>35S</alias>
+ <alias>S35</alias>
+ <alias>s35 radiolabelled</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0371" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </featureType>
+ <featureRangeList>
+ <featureRange>
+ <startStatus>
+ <names>
+ <shortLabel>undetermined</shortLabel>
+ <fullName>undetermined sequence position</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0339" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </startStatus>
+ <begin position="0"/>
+ <endStatus>
+ <names>
+ <shortLabel>undetermined</shortLabel>
+ <fullName>undetermined sequence position</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0339" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </endStatus>
+ <end position="0"/>
+ </featureRange>
+ </featureRangeList>
+ </feature>
+ </featureList>
+ <hostOrganismList>
+ <hostOrganism ncbiTaxId="1140">
+ <names>
+ <shortLabel>synp7</shortLabel>
+ <fullName>Synechococcus sp. (strain PCC 7942)</fullName>
+ </names>
+ </hostOrganism>
+ </hostOrganismList>
+ </participant>
+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>physical interaction</shortLabel>
+ <fullName>physical interaction</fullName>
+ <alias>aggregation</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0218" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactionType>
+ <attributeList>
+ <attribute name="kd">1.0</attribute>
+ </attributeList>
+ </interaction>
+ <interaction id="131">
+ <names>
+ <shortLabel>kaib-kaic-4</shortLabel>
+ <fullName>pull down bait GST KaiB - prey 35S kaiC1 (1-250) in vitro</fullName>
+ </names>
+ <xref>
+ <primaryRef db="intact" dbAc="MI:0469" id="EBI-781912" secondary="kaib-kaic-4"/>
+ </xref>
+ <experimentList>
+ <experimentRef>77</experimentRef>
+ </experimentList>
+ <participantList>
+ <participant id="132">
+ <interactorRef>4</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ <featureList>
+ <feature id="133">
+ <names>
+ <shortLabel>region</shortLabel>
+ </names>
+ <featureType>
+ <names>
+ <shortLabel>35s radiolabelled</shortLabel>
+ <fullName>35s radiolabelled</fullName>
+ <alias>35S</alias>
+ <alias>S35</alias>
+ <alias>s35 radiolabelled</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0371" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </featureType>
+ <featureRangeList>
+ <featureRange>
+ <startStatus>
+ <names>
+ <shortLabel>undetermined</shortLabel>
+ <fullName>undetermined sequence position</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0339" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </startStatus>
+ <begin position="0"/>
+ <endStatus>
+ <names>
+ <shortLabel>undetermined</shortLabel>
+ <fullName>undetermined sequence position</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0339" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </endStatus>
+ <end position="0"/>
+ </featureRange>
+ </featureRangeList>
+ </feature>
+ <feature id="134">
+ <names>
+ <shortLabel>region</shortLabel>
+ </names>
+ <featureType>
+ <names>
+ <shortLabel>binding site</shortLabel>
+ <fullName>binding site</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0117" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </featureType>
+ <featureRangeList>
+ <featureRange>
+ <startStatus>
+ <names>
+ <shortLabel>certain</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0335" refType="identity" refTypeAc="MI:0356"/>
+ </xref>
+ </startStatus>
+ <begin position="1"/>
+ <endStatus>
+ <names>
+ <shortLabel>certain</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0335" refType="identity" refTypeAc="MI:0356"/>
+ </xref>
+ </endStatus>
+ <end position="250"/>
+ </featureRange>
+ </featureRangeList>
+ </feature>
+ </featureList>
+ <hostOrganismList>
+ <hostOrganism ncbiTaxId="1140">
+ <names>
+ <shortLabel>synp7</shortLabel>
+ <fullName>Synechococcus sp. (strain PCC 7942)</fullName>
+ </names>
+ </hostOrganism>
+ </hostOrganismList>
+ </participant>
+ <participant id="135">
+ <interactorRef>10</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>bait</shortLabel>
+ <fullName>bait</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0496" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ <featureList>
+ <feature id="136">
+ <names>
+ <shortLabel>region</shortLabel>
+ </names>
+ <featureType>
+ <names>
+ <shortLabel>gst tagged</shortLabel>
+ <fullName>gst tagged</fullName>
+ <alias>glutathione S-tranferase tag</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0519" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </featureType>
+ <featureRangeList>
+ <featureRange>
+ <startStatus>
+ <names>
+ <shortLabel>n-terminal</shortLabel>
+ <fullName>n-terminal position</fullName>
+ <alias>n-terminus</alias>
+ <alias>amino-terminus</alias>
+ <alias>n-term</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0340" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </startStatus>
+ <begin position="0"/>
+ <endStatus>
+ <names>
+ <shortLabel>n-terminal</shortLabel>
+ <fullName>n-terminal position</fullName>
+ <alias>n-terminus</alias>
+ <alias>amino-terminus</alias>
+ <alias>n-term</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0340" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </endStatus>
+ <end position="0"/>
+ </featureRange>
+ </featureRangeList>
+ </feature>
+ </featureList>
+ <hostOrganismList>
+ <hostOrganism ncbiTaxId="1140">
+ <names>
+ <shortLabel>synp7</shortLabel>
+ <fullName>Synechococcus sp. (strain PCC 7942)</fullName>
+ </names>
+ </hostOrganism>
+ </hostOrganismList>
+ </participant>
+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>physical interaction</shortLabel>
+ <fullName>physical interaction</fullName>
+ <alias>aggregation</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0218" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactionType>
+ <attributeList>
+ <attribute name="kd">1.0</attribute>
+ </attributeList>
+ </interaction>
+ <interaction id="137">
+ <names>
+ <shortLabel>kaib-kaic-5</shortLabel>
+ <fullName>pull down bait GST KaiB - prey 35S kaiC2 (252-519) in vitro</fullName>
+ </names>
+ <xref>
+ <primaryRef db="intact" dbAc="MI:0469" id="EBI-781924" secondary="kaib-kaic-5"/>
+ </xref>
+ <experimentList>
+ <experimentRef>77</experimentRef>
+ </experimentList>
+ <participantList>
+ <participant id="138">
+ <interactorRef>10</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>bait</shortLabel>
+ <fullName>bait</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0496" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ <featureList>
+ <feature id="139">
+ <names>
+ <shortLabel>region</shortLabel>
+ </names>
+ <featureType>
+ <names>
+ <shortLabel>gst tagged</shortLabel>
+ <fullName>gst tagged</fullName>
+ <alias>glutathione S-tranferase tag</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0519" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </featureType>
+ <featureRangeList>
+ <featureRange>
+ <startStatus>
+ <names>
+ <shortLabel>n-terminal</shortLabel>
+ <fullName>n-terminal position</fullName>
+ <alias>n-terminus</alias>
+ <alias>amino-terminus</alias>
+ <alias>n-term</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0340" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </startStatus>
+ <begin position="0"/>
+ <endStatus>
+ <names>
+ <shortLabel>n-terminal</shortLabel>
+ <fullName>n-terminal position</fullName>
+ <alias>n-terminus</alias>
+ <alias>amino-terminus</alias>
+ <alias>n-term</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0340" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </endStatus>
+ <end position="0"/>
+ </featureRange>
+ </featureRangeList>
+ </feature>
+ </featureList>
+ <hostOrganismList>
+ <hostOrganism ncbiTaxId="1140">
+ <names>
+ <shortLabel>synp7</shortLabel>
+ <fullName>Synechococcus sp. (strain PCC 7942)</fullName>
+ </names>
+ </hostOrganism>
+ </hostOrganismList>
+ </participant>
+ <participant id="140">
+ <interactorRef>4</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ <featureList>
+ <feature id="141">
+ <names>
+ <shortLabel>region</shortLabel>
+ </names>
+ <featureType>
+ <names>
+ <shortLabel>binding site</shortLabel>
+ <fullName>binding site</fullName>
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+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0117" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </featureType>
+ <featureRangeList>
+ <featureRange>
+ <startStatus>
+ <names>
+ <shortLabel>certain</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0335" refType="identity" refTypeAc="MI:0356"/>
+ </xref>
+ </startStatus>
+ <begin position="252"/>
+ <endStatus>
+ <names>
+ <shortLabel>certain</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0335" refType="identity" refTypeAc="MI:0356"/>
+ </xref>
+ </endStatus>
+ <end position="519"/>
+ </featureRange>
+ </featureRangeList>
+ </feature>
+ <feature id="142">
+ <names>
+ <shortLabel>region</shortLabel>
+ </names>
+ <featureType>
+ <names>
+ <shortLabel>35s radiolabelled</shortLabel>
+ <fullName>35s radiolabelled</fullName>
+ <alias>35S</alias>
+ <alias>S35</alias>
+ <alias>s35 radiolabelled</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0371" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </featureType>
+ <featureRangeList>
+ <featureRange>
+ <startStatus>
+ <names>
+ <shortLabel>undetermined</shortLabel>
+ <fullName>undetermined sequence position</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0339" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </startStatus>
+ <begin position="0"/>
+ <endStatus>
+ <names>
+ <shortLabel>undetermined</shortLabel>
+ <fullName>undetermined sequence position</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0339" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </endStatus>
+ <end position="0"/>
+ </featureRange>
+ </featureRangeList>
+ </feature>
+ </featureList>
+ <hostOrganismList>
+ <hostOrganism ncbiTaxId="1140">
+ <names>
+ <shortLabel>synp7</shortLabel>
+ <fullName>Synechococcus sp. (strain PCC 7942)</fullName>
+ </names>
+ </hostOrganism>
+ </hostOrganismList>
+ </participant>
+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>physical interaction</shortLabel>
+ <fullName>physical interaction</fullName>
+ <alias>aggregation</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0218" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactionType>
+ <attributeList>
+ <attribute name="kd">1.0</attribute>
+ </attributeList>
+ </interaction>
+ <interaction id="143">
+ <names>
+ <shortLabel>kaic-kaic-8</shortLabel>
+ <fullName>pull down bait GST KaiC2 (253-519) - prey 35S kaiC1 (1-250) in vitro</fullName>
+ </names>
+ <xref>
+ <primaryRef db="intact" dbAc="MI:0469" id="EBI-781935" secondary="kaic-kaic-8"/>
+ </xref>
+ <experimentList>
+ <experimentRef>77</experimentRef>
+ </experimentList>
+ <participantList>
+ <participant id="144">
+ <interactorRef>4</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ <featureList>
+ <feature id="145">
+ <names>
+ <shortLabel>region</shortLabel>
+ </names>
+ <featureType>
+ <names>
+ <shortLabel>35s radiolabelled</shortLabel>
+ <fullName>35s radiolabelled</fullName>
+ <alias>35S</alias>
+ <alias>S35</alias>
+ <alias>s35 radiolabelled</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0371" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </featureType>
+ <featureRangeList>
+ <featureRange>
+ <startStatus>
+ <names>
+ <shortLabel>undetermined</shortLabel>
+ <fullName>undetermined sequence position</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0339" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </startStatus>
+ <begin position="0"/>
+ <endStatus>
+ <names>
+ <shortLabel>undetermined</shortLabel>
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+ </featureRange>
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+ <hostOrganismList>
+ <hostOrganism ncbiTaxId="1140">
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+ <shortLabel>synp7</shortLabel>
+ <fullName>Synechococcus sp. (strain PCC 7942)</fullName>
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+ <fullName>n-terminal position</fullName>
+ <alias>n-terminus</alias>
+ <alias>amino-terminus</alias>
+ <alias>n-term</alias>
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+ <hostOrganism ncbiTaxId="1140">
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+ <shortLabel>synp7</shortLabel>
+ <fullName>Synechococcus sp. (strain PCC 7942)</fullName>
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+ <names>
+ <shortLabel>physical interaction</shortLabel>
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+ <interaction id="150">
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+ <shortLabel>kaic-kaic-9</shortLabel>
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+ </feature>
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+ <shortLabel>region</shortLabel>
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+ <shortLabel>35s radiolabelled</shortLabel>
+ <fullName>35s radiolabelled</fullName>
+ <alias>35S</alias>
+ <alias>S35</alias>
+ <alias>s35 radiolabelled</alias>
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+ <shortLabel>synp7</shortLabel>
+ <fullName>Synechococcus sp. (strain PCC 7942)</fullName>
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+ <interactionType>
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+ <shortLabel>kaic-kaic-10</shortLabel>
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+ <shortLabel>synp7</shortLabel>
+ <fullName>Synechococcus sp. (strain PCC 7942)</fullName>
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+ </feature>
+ <feature id="163">
+ <names>
+ <shortLabel>region</shortLabel>
+ </names>
+ <featureType>
+ <names>
+ <shortLabel>35s radiolabelled</shortLabel>
+ <fullName>35s radiolabelled</fullName>
+ <alias>35S</alias>
+ <alias>S35</alias>
+ <alias>s35 radiolabelled</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0371" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </featureType>
+ <featureRangeList>
+ <featureRange>
+ <startStatus>
+ <names>
+ <shortLabel>undetermined</shortLabel>
+ <fullName>undetermined sequence position</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0339" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </startStatus>
+ <begin position="0"/>
+ <endStatus>
+ <names>
+ <shortLabel>undetermined</shortLabel>
+ <fullName>undetermined sequence position</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0339" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </endStatus>
+ <end position="0"/>
+ </featureRange>
+ </featureRangeList>
+ </feature>
+ </featureList>
+ <hostOrganismList>
+ <hostOrganism ncbiTaxId="1140">
+ <names>
+ <shortLabel>synp7</shortLabel>
+ <fullName>Synechococcus sp. (strain PCC 7942)</fullName>
+ </names>
+ </hostOrganism>
+ </hostOrganismList>
+ </participant>
+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>physical interaction</shortLabel>
+ <fullName>physical interaction</fullName>
+ <alias>aggregation</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0218" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactionType>
+ <attributeList>
+ <attribute name="kd">1.0</attribute>
+ </attributeList>
+ </interaction>
+ <interaction id="164">
+ <names>
+ <shortLabel>kaic-kaic-11</shortLabel>
+ <fullName>pull down bait GST KaiC1 (2-250) - prey 35S kaiC2 (252-519) in vitro</fullName>
+ </names>
+ <xref>
+ <primaryRef db="intact" dbAc="MI:0469" id="EBI-781970" secondary="kaic-kaic-11"/>
+ </xref>
+ <experimentList>
+ <experimentRef>77</experimentRef>
+ </experimentList>
+ <participantList>
+ <participant id="165">
+ <interactorRef>4</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>bait</shortLabel>
+ <fullName>bait</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0496" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ <featureList>
+ <feature id="166">
+ <names>
+ <shortLabel>region</shortLabel>
+ </names>
+ <featureType>
+ <names>
+ <shortLabel>gst tagged</shortLabel>
+ <fullName>gst tagged</fullName>
+ <alias>glutathione S-tranferase tag</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0519" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </featureType>
+ <featureRangeList>
+ <featureRange>
+ <startStatus>
+ <names>
+ <shortLabel>n-terminal</shortLabel>
+ <fullName>n-terminal position</fullName>
+ <alias>n-terminus</alias>
+ <alias>amino-terminus</alias>
+ <alias>n-term</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0340" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </startStatus>
+ <begin position="0"/>
+ <endStatus>
+ <names>
+ <shortLabel>n-terminal</shortLabel>
+ <fullName>n-terminal position</fullName>
+ <alias>n-terminus</alias>
+ <alias>amino-terminus</alias>
+ <alias>n-term</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0340" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </endStatus>
+ <end position="0"/>
+ </featureRange>
+ </featureRangeList>
+ </feature>
+ <feature id="167">
+ <names>
+ <shortLabel>region</shortLabel>
+ </names>
+ <featureType>
+ <names>
+ <shortLabel>binding site</shortLabel>
+ <fullName>binding site</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0117" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </featureType>
+ <featureRangeList>
+ <featureRange>
+ <startStatus>
+ <names>
+ <shortLabel>certain</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0335" refType="identity" refTypeAc="MI:0356"/>
+ </xref>
+ </startStatus>
+ <begin position="2"/>
+ <endStatus>
+ <names>
+ <shortLabel>certain</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0335" refType="identity" refTypeAc="MI:0356"/>
+ </xref>
+ </endStatus>
+ <end position="250"/>
+ </featureRange>
+ </featureRangeList>
+ </feature>
+ </featureList>
+ <hostOrganismList>
+ <hostOrganism ncbiTaxId="1140">
+ <names>
+ <shortLabel>synp7</shortLabel>
+ <fullName>Synechococcus sp. (strain PCC 7942)</fullName>
+ </names>
+ </hostOrganism>
+ </hostOrganismList>
+ </participant>
+ <participant id="168">
+ <interactorRef>4</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ <featureList>
+ <feature id="169">
+ <names>
+ <shortLabel>region</shortLabel>
+ </names>
+ <featureType>
+ <names>
+ <shortLabel>binding site</shortLabel>
+ <fullName>binding site</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0117" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </featureType>
+ <featureRangeList>
+ <featureRange>
+ <startStatus>
+ <names>
+ <shortLabel>certain</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0335" refType="identity" refTypeAc="MI:0356"/>
+ </xref>
+ </startStatus>
+ <begin position="252"/>
+ <endStatus>
+ <names>
+ <shortLabel>certain</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0335" refType="identity" refTypeAc="MI:0356"/>
+ </xref>
+ </endStatus>
+ <end position="519"/>
+ </featureRange>
+ </featureRangeList>
+ </feature>
+ <feature id="170">
+ <names>
+ <shortLabel>region</shortLabel>
+ </names>
+ <featureType>
+ <names>
+ <shortLabel>35s radiolabelled</shortLabel>
+ <fullName>35s radiolabelled</fullName>
+ <alias>35S</alias>
+ <alias>S35</alias>
+ <alias>s35 radiolabelled</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0371" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </featureType>
+ <featureRangeList>
+ <featureRange>
+ <startStatus>
+ <names>
+ <shortLabel>undetermined</shortLabel>
+ <fullName>undetermined sequence position</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0339" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </startStatus>
+ <begin position="0"/>
+ <endStatus>
+ <names>
+ <shortLabel>undetermined</shortLabel>
+ <fullName>undetermined sequence position</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0339" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </endStatus>
+ <end position="0"/>
+ </featureRange>
+ </featureRangeList>
+ </feature>
+ </featureList>
+ <hostOrganismList>
+ <hostOrganism ncbiTaxId="1140">
+ <names>
+ <shortLabel>synp7</shortLabel>
+ <fullName>Synechococcus sp. (strain PCC 7942)</fullName>
+ </names>
+ </hostOrganism>
+ </hostOrganismList>
+ </participant>
+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>physical interaction</shortLabel>
+ <fullName>physical interaction</fullName>
+ <alias>aggregation</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0218" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactionType>
+ <attributeList>
+ <attribute name="kd">1.0</attribute>
+ </attributeList>
+ </interaction>
+ <interaction id="171">
+ <names>
+ <shortLabel>kaib-kaia-2</shortLabel>
+ <fullName>pull down HIS KaiB 35S kaiA with or without GST kaiC</fullName>
+ </names>
+ <xref>
+ <primaryRef db="intact" dbAc="MI:0469" id="EBI-782033" secondary="kaib-kaia-2"/>
+ </xref>
+ <experimentList>
+ <experimentRef>172</experimentRef>
+ </experimentList>
+ <participantList>
+ <participant id="173">
+ <interactorRef>10</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>bait</shortLabel>
+ <fullName>bait</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0496" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ <featureList>
+ <feature id="174">
+ <names>
+ <shortLabel>region</shortLabel>
+ </names>
+ <featureType>
+ <names>
+ <shortLabel>his tagged</shortLabel>
+ <fullName>his tagged</fullName>
+ <alias>6-His-tagged</alias>
+ <alias>Hexa-His-tagged</alias>
+ <alias>Histidine-tagged</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0521" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </featureType>
+ <featureRangeList>
+ <featureRange>
+ <startStatus>
+ <names>
+ <shortLabel>n-terminal</shortLabel>
+ <fullName>n-terminal position</fullName>
+ <alias>n-terminus</alias>
+ <alias>amino-terminus</alias>
+ <alias>n-term</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0340" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </startStatus>
+ <begin position="0"/>
+ <endStatus>
+ <names>
+ <shortLabel>n-terminal</shortLabel>
+ <fullName>n-terminal position</fullName>
+ <alias>n-terminus</alias>
+ <alias>amino-terminus</alias>
+ <alias>n-term</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0340" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </endStatus>
+ <end position="0"/>
+ </featureRange>
+ </featureRangeList>
+ </feature>
+ </featureList>
+ <hostOrganismList>
+ <hostOrganism ncbiTaxId="1140">
+ <names>
+ <shortLabel>synp7</shortLabel>
+ <fullName>Synechococcus sp. (strain PCC 7942)</fullName>
+ </names>
+ </hostOrganism>
+ </hostOrganismList>
+ </participant>
+ <participant id="175">
+ <interactorRef>6</interactorRef>
+ <biologicalRole>
+ <names>
+ <shortLabel>unspecified</shortLabel>
+ <fullName>unspecified</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </biologicalRole>
+ <experimentalRoleList>
+ <experimentalRole>
+ <names>
+ <shortLabel>prey</shortLabel>
+ <fullName>prey</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0498" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </experimentalRole>
+ </experimentalRoleList>
+ <featureList>
+ <feature id="176">
+ <names>
+ <shortLabel>glu103lys</shortLabel>
+ </names>
+ <featureType>
+ <names>
+ <shortLabel>mutation increasing</shortLabel>
+ <fullName>mutation increasing interaction</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0382" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14577292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </featureType>
+ <featureRangeList>
+ <featureRange>
+ <startStatus>
+ <names>
+ <shortLabel>certain</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0335" refType="identity" refTypeAc="MI:0356"/>
+ </xref>
+ </startStatus>
+ <begin position="103"/>
+ <endStatus>
+ <names>
+ <shortLabel>certain</shortLabel>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0335" refType="identity" refTypeAc="MI:0356"/>
+ </xref>
+ </endStatus>
+ <end position="103"/>
+ </featureRange>
+ </featureRangeList>
+ </feature>
+ <feature id="177">
+ <names>
+ <shortLabel>region</shortLabel>
+ </names>
+ <featureType>
+ <names>
+ <shortLabel>35s radiolabelled</shortLabel>
+ <fullName>35s radiolabelled</fullName>
+ <alias>35S</alias>
+ <alias>S35</alias>
+ <alias>s35 radiolabelled</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0371" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </featureType>
+ <featureRangeList>
+ <featureRange>
+ <startStatus>
+ <names>
+ <shortLabel>undetermined</shortLabel>
+ <fullName>undetermined sequence position</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0339" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </startStatus>
+ <begin position="0"/>
+ <endStatus>
+ <names>
+ <shortLabel>undetermined</shortLabel>
+ <fullName>undetermined sequence position</fullName>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0339" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
+ </xref>
+ </endStatus>
+ <end position="0"/>
+ </featureRange>
+ </featureRangeList>
+ </feature>
+ </featureList>
+ <hostOrganismList>
+ <hostOrganism ncbiTaxId="1140">
+ <names>
+ <shortLabel>synp7</shortLabel>
+ <fullName>Synechococcus sp. (strain PCC 7942)</fullName>
+ </names>
+ </hostOrganism>
+ </hostOrganismList>
+ </participant>
+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>physical interaction</shortLabel>
+ <fullName>physical interaction</fullName>
+ <alias>aggregation</alias>
+ </names>
+ <xref>
+ <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0218" refType="identity" refTypeAc="MI:0356"/>
+ <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="go-definition-ref" refTypeAc="MI:0242"/>
+ </xref>
+ </interactionType>
+ <attributeList>
+ <attribute name="caution">Weak interaction</attribute>
+ <attribute name="stimulation">The very weak interaction between KaiA and KAiB is strongly enhanced by the presence of GST-KaiC. The KaiC moiety 2-250 is sufficient to enhance KaiA-KaiB interaction</attribute>
+ <attribute name="kd">1.0</attribute>
+ </attributeList>
+ </interaction>
+ </interactionList>
+ </entry>
+ </entrySet>
diff --git a/coreplugins/PSI-MI/src/test/resources/testData/yeast_denormalised.xml b/coreplugins/PSI-MI/src/test/resources/testData/yeast_denormalised.xml
new file mode 100755
index 0000000..a6f9ead
--- /dev/null
+++ b/coreplugins/PSI-MI/src/test/resources/testData/yeast_denormalised.xml
@@ -0,0 +1,10390 @@
+<!-- edited with XMLSPY v5 rel. 4 U (http://www.xmlspy.com) by Chris Sander (Memorial Sloan Kettering) -->
+<entrySet xmlns="net:sf:psidev:mi" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="net:sf:psidev:mi
+/Users/cerami/dev/sander/cytoscape/xml/MIF.xsd" level="1" version="1">
+ <entry>
+ <interactionList>
+ <interaction>
+ <experimentList><experimentDescription id="lcms-maldi">
+ <interactionDetection>
+ <names>
+ <shortLabel>IX:0063,IX:0066</shortLabel>
+ <fullName>Liquid Chromatography-Mass Spectroscopy, MALDI-TOF</fullName>
+ </names>
+ <xref>
+ <primaryRef id="0" db=""/>
+ </xref>
+ </interactionDetection>
+ </experimentDescription></experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractor id="MAK10">
+ <names>
+ <shortLabel>MAK10</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <role>bait</role>
+ <isTaggedProtein>true</isTaggedProtein>
+ <isOverexpressedProtein>true</isOverexpressedProtein>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractor id="MAK3">
+ <names>
+ <shortLabel>MAK3</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <role>neutral</role>
+ <isTaggedProtein>false</isTaggedProtein>
+ <isOverexpressedProtein>false</isOverexpressedProtein>
+ </proteinParticipant>
+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>aggregation</shortLabel>
+ </names>
+ <xref>
+ <primaryRef id="0" db=""/>
+ </xref>
+ </interactionType>
+ </interaction>
+ <interaction>
+ <experimentList><experimentDescription id="lcms-maldi">
+ <interactionDetection>
+ <names>
+ <shortLabel>IX:0063,IX:0066</shortLabel>
+ <fullName>Liquid Chromatography-Mass Spectroscopy, MALDI-TOF</fullName>
+ </names>
+ <xref>
+ <primaryRef id="0" db=""/>
+ </xref>
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+ <isOverexpressedProtein>false</isOverexpressedProtein>
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+ <isOverexpressedProtein>false</isOverexpressedProtein>
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+ <organism ncbiTaxId="4932">
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+ <proteinParticipant>
+ <proteinInteractor id="RPN3">
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+ <organism ncbiTaxId="4932">
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+ <isOverexpressedProtein>false</isOverexpressedProtein>
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+ <proteinInteractor id="RPN6">
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+ </interactionType>
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+ <experimentList><experimentDescription id="lcms-maldi">
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+ <names>
+ <shortLabel>IX:0063,IX:0066</shortLabel>
+ <fullName>Liquid Chromatography-Mass Spectroscopy, MALDI-TOF</fullName>
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+ </experimentDescription></experimentList>
+ <participantList>
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+ <isTaggedProtein>true</isTaggedProtein>
+ <isOverexpressedProtein>true</isOverexpressedProtein>
+ </proteinParticipant>
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+ <proteinInteractor id="STI1">
+ <names>
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+ <organism ncbiTaxId="4932">
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+ <role>neutral</role>
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+ <isOverexpressedProtein>false</isOverexpressedProtein>
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+ <fullName>Liquid Chromatography-Mass Spectroscopy, MALDI-TOF</fullName>
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+ <isOverexpressedProtein>true</isOverexpressedProtein>
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+ <proteinParticipant>
+ <proteinInteractor id="YPL110C">
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+ <organism ncbiTaxId="4932">
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+ <experimentList><experimentDescription id="lcms-maldi">
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+ <proteinInteractor id="RVS167">
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+ <organism ncbiTaxId="4932">
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+ <isOverexpressedProtein>true</isOverexpressedProtein>
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+ <proteinParticipant>
+ <proteinInteractor id="YPL249C">
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+ <organism ncbiTaxId="4932">
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+ <shortLabel>Sce</shortLabel>
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+ </organism>
+ </proteinInteractor>
+ <role>neutral</role>
+ <isTaggedProtein>false</isTaggedProtein>
+ <isOverexpressedProtein>false</isOverexpressedProtein>
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+ <interactionType>
+ <names>
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+ <interaction>
+ <experimentList><experimentDescription id="lcms-maldi">
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+ <fullName>Liquid Chromatography-Mass Spectroscopy, MALDI-TOF</fullName>
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+ <xref>
+ <primaryRef id="0" db=""/>
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+ </interactionDetection>
+ </experimentDescription></experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractor id="YDL085W">
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+ <shortLabel>YDL085W</shortLabel>
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+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
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+ </proteinInteractor>
+ <role>bait</role>
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+ <isOverexpressedProtein>true</isOverexpressedProtein>
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+ <proteinParticipant>
+ <proteinInteractor id="dummy">
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+ <shortLabel>aggregation</shortLabel>
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+ <experimentList><experimentDescription id="lcms-maldi">
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+ <names>
+ <shortLabel>IX:0063,IX:0066</shortLabel>
+ <fullName>Liquid Chromatography-Mass Spectroscopy, MALDI-TOF</fullName>
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+ <xref>
+ <primaryRef id="0" db=""/>
+ </xref>
+ </interactionDetection>
+ </experimentDescription></experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractor id="YMR145C">
+ <names>
+ <shortLabel>YMR145C</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <role>bait</role>
+ <isTaggedProtein>true</isTaggedProtein>
+ <isOverexpressedProtein>true</isOverexpressedProtein>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractor id="dummy">
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+ <shortLabel>dummy</shortLabel>
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+ <shortLabel>aggregation</shortLabel>
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+ <xref>
+ <primaryRef id="0" db=""/>
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+ </interactionType>
+ </interaction>
+ <interaction>
+ <experimentList><experimentDescription id="lcms-maldi">
+ <interactionDetection>
+ <names>
+ <shortLabel>IX:0063,IX:0066</shortLabel>
+ <fullName>Liquid Chromatography-Mass Spectroscopy, MALDI-TOF</fullName>
+ </names>
+ <xref>
+ <primaryRef id="0" db=""/>
+ </xref>
+ </interactionDetection>
+ </experimentDescription></experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractor id="YPK1">
+ <names>
+ <shortLabel>YPK1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <role>bait</role>
+ <isTaggedProtein>true</isTaggedProtein>
+ <isOverexpressedProtein>true</isOverexpressedProtein>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractor id="dummy">
+ <names>
+ <shortLabel>dummy</shortLabel>
+ </names>
+ </proteinInteractor>
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+ <shortLabel>aggregation</shortLabel>
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+ <primaryRef id="0" db=""/>
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+ </interactionType>
+ </interaction>
+ <interaction>
+ <experimentList><experimentDescription id="lcms-maldi">
+ <interactionDetection>
+ <names>
+ <shortLabel>IX:0063,IX:0066</shortLabel>
+ <fullName>Liquid Chromatography-Mass Spectroscopy, MALDI-TOF</fullName>
+ </names>
+ <xref>
+ <primaryRef id="0" db=""/>
+ </xref>
+ </interactionDetection>
+ </experimentDescription></experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractor id="BAS1">
+ <names>
+ <shortLabel>BAS1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <role>bait</role>
+ <isTaggedProtein>true</isTaggedProtein>
+ <isOverexpressedProtein>true</isOverexpressedProtein>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractor id="dummy">
+ <names>
+ <shortLabel>dummy</shortLabel>
+ </names>
+ </proteinInteractor>
+ </proteinParticipant>
+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>aggregation</shortLabel>
+ </names>
+ <xref>
+ <primaryRef id="0" db=""/>
+ </xref>
+ </interactionType>
+ </interaction>
+ <interaction>
+ <experimentList><experimentDescription id="lcms-maldi">
+ <interactionDetection>
+ <names>
+ <shortLabel>IX:0063,IX:0066</shortLabel>
+ <fullName>Liquid Chromatography-Mass Spectroscopy, MALDI-TOF</fullName>
+ </names>
+ <xref>
+ <primaryRef id="0" db=""/>
+ </xref>
+ </interactionDetection>
+ </experimentDescription></experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractor id="GRF10">
+ <names>
+ <shortLabel>GRF10</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <role>bait</role>
+ <isTaggedProtein>true</isTaggedProtein>
+ <isOverexpressedProtein>true</isOverexpressedProtein>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractor id="dummy">
+ <names>
+ <shortLabel>dummy</shortLabel>
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+ </proteinInteractor>
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+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>aggregation</shortLabel>
+ </names>
+ <xref>
+ <primaryRef id="0" db=""/>
+ </xref>
+ </interactionType>
+ </interaction>
+ <interaction>
+ <experimentList><experimentDescription id="lcms-maldi">
+ <interactionDetection>
+ <names>
+ <shortLabel>IX:0063,IX:0066</shortLabel>
+ <fullName>Liquid Chromatography-Mass Spectroscopy, MALDI-TOF</fullName>
+ </names>
+ <xref>
+ <primaryRef id="0" db=""/>
+ </xref>
+ </interactionDetection>
+ </experimentDescription></experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractor id="YOR155C">
+ <names>
+ <shortLabel>YOR155C</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <role>bait</role>
+ <isTaggedProtein>true</isTaggedProtein>
+ <isOverexpressedProtein>true</isOverexpressedProtein>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractor id="dummy">
+ <names>
+ <shortLabel>dummy</shortLabel>
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+ </proteinParticipant>
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+ <names>
+ <shortLabel>aggregation</shortLabel>
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+ <xref>
+ <primaryRef id="0" db=""/>
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+ </interactionType>
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+ <experimentList><experimentDescription id="lcms-maldi">
+ <interactionDetection>
+ <names>
+ <shortLabel>IX:0063,IX:0066</shortLabel>
+ <fullName>Liquid Chromatography-Mass Spectroscopy, MALDI-TOF</fullName>
+ </names>
+ <xref>
+ <primaryRef id="0" db=""/>
+ </xref>
+ </interactionDetection>
+ </experimentDescription></experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractor id="BOI1">
+ <names>
+ <shortLabel>BOI1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <role>bait</role>
+ <isTaggedProtein>true</isTaggedProtein>
+ <isOverexpressedProtein>true</isOverexpressedProtein>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractor id="dummy">
+ <names>
+ <shortLabel>dummy</shortLabel>
+ </names>
+ </proteinInteractor>
+ </proteinParticipant>
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+ <primaryRef id="0" db=""/>
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+ </interaction>
+ <interaction>
+ <experimentList><experimentDescription id="lcms-maldi">
+ <interactionDetection>
+ <names>
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+ <fullName>Liquid Chromatography-Mass Spectroscopy, MALDI-TOF</fullName>
+ </names>
+ <xref>
+ <primaryRef id="0" db=""/>
+ </xref>
+ </interactionDetection>
+ </experimentDescription></experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractor id="BOI2">
+ <names>
+ <shortLabel>BOI2</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <role>bait</role>
+ <isTaggedProtein>true</isTaggedProtein>
+ <isOverexpressedProtein>true</isOverexpressedProtein>
+ </proteinParticipant>
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+ <experimentList><experimentDescription id="lcms-maldi">
+ <interactionDetection>
+ <names>
+ <shortLabel>IX:0063,IX:0066</shortLabel>
+ <fullName>Liquid Chromatography-Mass Spectroscopy, MALDI-TOF</fullName>
+ </names>
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+ <primaryRef id="0" db=""/>
+ </xref>
+ </interactionDetection>
+ </experimentDescription></experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractor id="SRA1">
+ <names>
+ <shortLabel>SRA1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <role>bait</role>
+ <isTaggedProtein>true</isTaggedProtein>
+ <isOverexpressedProtein>true</isOverexpressedProtein>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractor id="dummy">
+ <names>
+ <shortLabel>dummy</shortLabel>
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+ </proteinInteractor>
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+ <interactionType>
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+ </names>
+ <xref>
+ <primaryRef id="0" db=""/>
+ </xref>
+ </interactionType>
+ </interaction>
+ <interaction>
+ <experimentList><experimentDescription id="lcms-maldi">
+ <interactionDetection>
+ <names>
+ <shortLabel>IX:0063,IX:0066</shortLabel>
+ <fullName>Liquid Chromatography-Mass Spectroscopy, MALDI-TOF</fullName>
+ </names>
+ <xref>
+ <primaryRef id="0" db=""/>
+ </xref>
+ </interactionDetection>
+ </experimentDescription></experimentList>
+ <participantList>
+ <proteinParticipant>
+ <proteinInteractor id="ACT1">
+ <names>
+ <shortLabel>ACT1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <role>neutral</role>
+ <isTaggedProtein>false</isTaggedProtein>
+ <isOverexpressedProtein>false</isOverexpressedProtein>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractor id="CYR1">
+ <names>
+ <shortLabel>CYR1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <role>bait</role>
+ <isTaggedProtein>true</isTaggedProtein>
+ <isOverexpressedProtein>true</isOverexpressedProtein>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractor id="PHO81">
+ <names>
+ <shortLabel>PHO81</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <role>neutral</role>
+ <isTaggedProtein>false</isTaggedProtein>
+ <isOverexpressedProtein>false</isOverexpressedProtein>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractor id="RNR2">
+ <names>
+ <shortLabel>RNR2</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <role>neutral</role>
+ <isTaggedProtein>false</isTaggedProtein>
+ <isOverexpressedProtein>false</isOverexpressedProtein>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractor id="SRV2">
+ <names>
+ <shortLabel>SRV2</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <role>neutral</role>
+ <isTaggedProtein>false</isTaggedProtein>
+ <isOverexpressedProtein>false</isOverexpressedProtein>
+ </proteinParticipant>
+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>aggregation</shortLabel>
+ </names>
+ <xref>
+ <primaryRef id="0" db=""/>
+ </xref>
+ </interactionType>
+ </interaction>
+ </interactionList>
+ </entry>
+</entrySet>
diff --git a/coreplugins/PSI-MI/src/test/resources/testData/yeast_normalised.xml b/coreplugins/PSI-MI/src/test/resources/testData/yeast_normalised.xml
new file mode 100755
index 0000000..00324e3
--- /dev/null
+++ b/coreplugins/PSI-MI/src/test/resources/testData/yeast_normalised.xml
@@ -0,0 +1,8253 @@
+<?xml version="1.0"?>
+<!-- edited with XMLSPY v5 rel. 4 U (http://www.xmlspy.com) by Chris Sander (Memorial Sloan Kettering) -->
+<entrySet xmlns="net:sf:psidev:mi" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="net:sf:psidev:mi
+/Users/cerami/dev/sander/cytoscape/xml/MIF.xsd" level="1" version="1">
+ <entry>
+ <experimentList>
+ <experimentDescription id="dummy">
+ <interactionDetection>
+ <names>
+ <shortLabel>dummy</shortLabel>
+ <fullName/>
+ </names>
+ <xref>
+ <primaryRef id="0" db=""/>
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ <experimentDescription id="lcms-maldi">
+ <interactionDetection>
+ <names>
+ <shortLabel>IX:0063,IX:0066</shortLabel>
+ <fullName>Liquid Chromatography-Mass Spectroscopy, MALDI-TOF</fullName>
+ </names>
+ <xref>
+ <primaryRef id="0" db=""/>
+ </xref>
+ </interactionDetection>
+ </experimentDescription>
+ </experimentList>
+ <interactorList>
+ <proteinInteractor id="AAC1">
+ <names>
+ <shortLabel>AAC1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="AAC3">
+ <names>
+ <shortLabel>AAC3</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="ACH1">
+ <names>
+ <shortLabel>ACH1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="ACO1">
+ <names>
+ <shortLabel>ACO1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="ACT1">
+ <names>
+ <shortLabel>ACT1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="ADE4">
+ <names>
+ <shortLabel>ADE4</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="ADH1">
+ <names>
+ <shortLabel>ADH1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="ADH4">
+ <names>
+ <shortLabel>ADH4</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="ADR1">
+ <names>
+ <shortLabel>ADR1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="ALD5">
+ <names>
+ <shortLabel>ALD5</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="ARC1">
+ <names>
+ <shortLabel>ARC1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="ARO1">
+ <names>
+ <shortLabel>ARO1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="ARP2">
+ <names>
+ <shortLabel>ARP2</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="ASC1">
+ <names>
+ <shortLabel>ASC1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="ASF1">
+ <names>
+ <shortLabel>ASF1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="AUT2">
+ <names>
+ <shortLabel>AUT2</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="BAS1">
+ <names>
+ <shortLabel>BAS1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="BBC1">
+ <names>
+ <shortLabel>BBC1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="BDF1">
+ <names>
+ <shortLabel>BDF1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="BDF2">
+ <names>
+ <shortLabel>BDF2</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="BIO3">
+ <names>
+ <shortLabel>BIO3</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="BOI1">
+ <names>
+ <shortLabel>BOI1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="BOI2">
+ <names>
+ <shortLabel>BOI2</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="BOP2">
+ <names>
+ <shortLabel>BOP2</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="BRE2">
+ <names>
+ <shortLabel>BRE2</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="BUR2">
+ <names>
+ <shortLabel>BUR2</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="BZZ1">
+ <names>
+ <shortLabel>BZZ1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CAR2">
+ <names>
+ <shortLabel>CAR2</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CBK1">
+ <names>
+ <shortLabel>CBK1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CCL1">
+ <names>
+ <shortLabel>CCL1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CCT3">
+ <names>
+ <shortLabel>CCT3</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CCT6">
+ <names>
+ <shortLabel>CCT6</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CCT8">
+ <names>
+ <shortLabel>CCT8</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CDC12">
+ <names>
+ <shortLabel>CDC12</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CDC13">
+ <names>
+ <shortLabel>CDC13</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CDC15">
+ <names>
+ <shortLabel>CDC15</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CDC33">
+ <names>
+ <shortLabel>CDC33</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CDC34">
+ <names>
+ <shortLabel>CDC34</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CDC39">
+ <names>
+ <shortLabel>CDC39</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CDC4">
+ <names>
+ <shortLabel>CDC4</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CDC53">
+ <names>
+ <shortLabel>CDC53</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CDC95">
+ <names>
+ <shortLabel>CDC95</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CHC1">
+ <names>
+ <shortLabel>CHC1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CLU1">
+ <names>
+ <shortLabel>CLU1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="COF1">
+ <names>
+ <shortLabel>COF1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CPH1">
+ <names>
+ <shortLabel>CPH1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CRM1">
+ <names>
+ <shortLabel>CRM1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CTF4">
+ <names>
+ <shortLabel>CTF4</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="CYR1">
+ <names>
+ <shortLabel>CYR1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="DNA2">
+ <names>
+ <shortLabel>DNA2</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="DUN1">
+ <names>
+ <shortLabel>DUN1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="ECM10">
+ <names>
+ <shortLabel>ECM10</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="ECM25">
+ <names>
+ <shortLabel>ECM25</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="ECM29">
+ <names>
+ <shortLabel>ECM29</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="ECM33">
+ <names>
+ <shortLabel>ECM33</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="EDE1">
+ <names>
+ <shortLabel>EDE1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="END3">
+ <names>
+ <shortLabel>END3</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="ENO1">
+ <names>
+ <shortLabel>ENO1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="ESR1">
+ <names>
+ <shortLabel>ESR1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="FAP1">
+ <names>
+ <shortLabel>FAP1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="FAR1">
+ <names>
+ <shortLabel>FAR1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="FOL2">
+ <names>
+ <shortLabel>FOL2</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="FPR1">
+ <names>
+ <shortLabel>FPR1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="FUM1">
+ <names>
+ <shortLabel>FUM1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="FZF1">
+ <names>
+ <shortLabel>FZF1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="GCN1">
+ <names>
+ <shortLabel>GCN1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="GCN20">
+ <names>
+ <shortLabel>GCN20</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="GDI1">
+ <names>
+ <shortLabel>GDI1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="GFA1">
+ <names>
+ <shortLabel>GFA1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="GND1">
+ <names>
+ <shortLabel>GND1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="GPD1">
+ <names>
+ <shortLabel>GPD1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="GPD2">
+ <names>
+ <shortLabel>GPD2</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="GPH1">
+ <names>
+ <shortLabel>GPH1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="GRF10">
+ <names>
+ <shortLabel>GRF10</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="GRR1">
+ <names>
+ <shortLabel>GRR1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="GUT1">
+ <names>
+ <shortLabel>GUT1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="HDA1">
+ <names>
+ <shortLabel>HDA1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="HHF1">
+ <names>
+ <shortLabel>HHF1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="HOM2">
+ <names>
+ <shortLabel>HOM2</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="HRT1">
+ <names>
+ <shortLabel>HRT1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="HSC82">
+ <names>
+ <shortLabel>HSC82</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="HTA1">
+ <names>
+ <shortLabel>HTA1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="HTA2">
+ <names>
+ <shortLabel>HTA2</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="HTB2">
+ <names>
+ <shortLabel>HTB2</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="HTZ1">
+ <names>
+ <shortLabel>HTZ1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="HXT6">
+ <names>
+ <shortLabel>HXT6</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="HXT7">
+ <names>
+ <shortLabel>HXT7</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="HYP2">
+ <names>
+ <shortLabel>HYP2</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="IPP1">
+ <names>
+ <shortLabel>IPP1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="IRA2">
+ <names>
+ <shortLabel>IRA2</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="KAP123">
+ <names>
+ <shortLabel>KAP123</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="KAP95">
+ <names>
+ <shortLabel>KAP95</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="KEX2">
+ <names>
+ <shortLabel>KEX2</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="KIM3">
+ <names>
+ <shortLabel>KIM3</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="KIN28">
+ <names>
+ <shortLabel>KIN28</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="LAS17">
+ <names>
+ <shortLabel>LAS17</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="LAT1">
+ <names>
+ <shortLabel>LAT1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="LCD1">
+ <names>
+ <shortLabel>LCD1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="LPD1">
+ <names>
+ <shortLabel>LPD1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="LSC1">
+ <names>
+ <shortLabel>LSC1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="MAK10">
+ <names>
+ <shortLabel>MAK10</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="MAK3">
+ <names>
+ <shortLabel>MAK3</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="MAK31">
+ <names>
+ <shortLabel>MAK31</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="MDH1">
+ <names>
+ <shortLabel>MDH1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="MEC1">
+ <names>
+ <shortLabel>MEC1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="MET18">
+ <names>
+ <shortLabel>MET18</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="MET30">
+ <names>
+ <shortLabel>MET30</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="MET31">
+ <names>
+ <shortLabel>MET31</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="MET4">
+ <names>
+ <shortLabel>MET4</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="MGE1">
+ <names>
+ <shortLabel>MGE1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="MGM101">
+ <names>
+ <shortLabel>MGM101</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="MIP1">
+ <names>
+ <shortLabel>MIP1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="MIR1">
+ <names>
+ <shortLabel>MIR1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="MIS1">
+ <names>
+ <shortLabel>MIS1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="MKK2">
+ <names>
+ <shortLabel>MKK2</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="MLH1">
+ <names>
+ <shortLabel>MLH1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="MOB2">
+ <names>
+ <shortLabel>MOB2</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="MRE11">
+ <names>
+ <shortLabel>MRE11</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="MRPL23">
+ <names>
+ <shortLabel>MRPL23</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="MRPS28">
+ <names>
+ <shortLabel>MRPS28</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="MSH2">
+ <names>
+ <shortLabel>MSH2</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="MSH3">
+ <names>
+ <shortLabel>MSH3</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="MSH4">
+ <names>
+ <shortLabel>MSH4</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="MSH6">
+ <names>
+ <shortLabel>MSH6</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="MSI1">
+ <names>
+ <shortLabel>MSI1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="MUD13">
+ <names>
+ <shortLabel>MUD13</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="MYO4">
+ <names>
+ <shortLabel>MYO4</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="NAB3">
+ <names>
+ <shortLabel>NAB3</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="NCR1">
+ <names>
+ <shortLabel>NCR1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="NPL3">
+ <names>
+ <shortLabel>NPL3</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="NRD1">
+ <names>
+ <shortLabel>NRD1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="PDA1">
+ <names>
+ <shortLabel>PDA1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="PDC1">
+ <names>
+ <shortLabel>PDC1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="PDC5">
+ <names>
+ <shortLabel>PDC5</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="PDC6">
+ <names>
+ <shortLabel>PDC6</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="PDX1">
+ <names>
+ <shortLabel>PDX1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="PDX3">
+ <names>
+ <shortLabel>PDX3</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="PEP4">
+ <names>
+ <shortLabel>PEP4</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="PEX15">
+ <names>
+ <shortLabel>PEX15</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="PFK1">
+ <names>
+ <shortLabel>PFK1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="PFK2">
+ <names>
+ <shortLabel>PFK2</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="PGK1">
+ <names>
+ <shortLabel>PGK1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="PGM2">
+ <names>
+ <shortLabel>PGM2</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="PHO81">
+ <names>
+ <shortLabel>PHO81</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="PHO84">
+ <names>
+ <shortLabel>PHO84</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="PLO1">
+ <names>
+ <shortLabel>PLO1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="PLO2">
+ <names>
+ <shortLabel>PLO2</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="PMA1">
+ <names>
+ <shortLabel>PMA1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="PMA2">
+ <names>
+ <shortLabel>PMA2</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="PMS1">
+ <names>
+ <shortLabel>PMS1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="POL30">
+ <names>
+ <shortLabel>POL30</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="POR1">
+ <names>
+ <shortLabel>POR1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="PRB1">
+ <names>
+ <shortLabel>PRB1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="PRO1">
+ <names>
+ <shortLabel>PRO1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="PRP40">
+ <names>
+ <shortLabel>PRP40</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="PRP42">
+ <names>
+ <shortLabel>PRP42</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="PTC1">
+ <names>
+ <shortLabel>PTC1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="PTC2">
+ <names>
+ <shortLabel>PTC2</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="PTC3">
+ <names>
+ <shortLabel>PTC3</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="PYC1">
+ <names>
+ <shortLabel>PYC1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="PYC2">
+ <names>
+ <shortLabel>PYC2</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="QCR2">
+ <names>
+ <shortLabel>QCR2</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="RAD1">
+ <names>
+ <shortLabel>RAD1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="RAD10">
+ <names>
+ <shortLabel>RAD10</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="RAD14">
+ <names>
+ <shortLabel>RAD14</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="RAD16">
+ <names>
+ <shortLabel>RAD16</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="RAD17">
+ <names>
+ <shortLabel>RAD17</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="RAD18">
+ <names>
+ <shortLabel>RAD18</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="RAD2">
+ <names>
+ <shortLabel>RAD2</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="RAD23">
+ <names>
+ <shortLabel>RAD23</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="RAD24">
+ <names>
+ <shortLabel>RAD24</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="RAD26">
+ <names>
+ <shortLabel>RAD26</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="RAD27">
+ <names>
+ <shortLabel>RAD27</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="RAD28">
+ <names>
+ <shortLabel>RAD28</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="RAD3">
+ <names>
+ <shortLabel>RAD3</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="RAD30">
+ <names>
+ <shortLabel>RAD30</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="RAD4">
+ <names>
+ <shortLabel>RAD4</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="RAD5">
+ <names>
+ <shortLabel>RAD5</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="RAD50">
+ <names>
+ <shortLabel>RAD50</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="RAD51">
+ <names>
+ <shortLabel>RAD51</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="RAD52">
+ <names>
+ <shortLabel>RAD52</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="RAD53">
+ <names>
+ <shortLabel>RAD53</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="RAD54">
+ <names>
+ <shortLabel>RAD54</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="RAD55">
+ <names>
+ <shortLabel>RAD55</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="RAD57">
+ <names>
+ <shortLabel>RAD57</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="RAD59">
+ <names>
+ <shortLabel>RAD59</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="RAD6">
+ <names>
+ <shortLabel>RAD6</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="RAD7">
+ <names>
+ <shortLabel>RAD7</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="RAD9">
+ <names>
+ <shortLabel>RAD9</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="RFA1">
+ <names>
+ <shortLabel>RFA1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="RFA2">
+ <names>
+ <shortLabel>RFA2</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="RFA3">
+ <names>
+ <shortLabel>RFA3</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="RFC2">
+ <names>
+ <shortLabel>RFC2</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="RFC3">
+ <names>
+ <shortLabel>RFC3</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="RFC5">
+ <names>
+ <shortLabel>RFC5</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="RGD1">
+ <names>
+ <shortLabel>RGD1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="RHR2">
+ <names>
+ <shortLabel>RHR2</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="RIM1">
+ <names>
+ <shortLabel>RIM1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="RLR1">
+ <names>
+ <shortLabel>RLR1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="RNH1">
+ <names>
+ <shortLabel>RNH1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="RNR2">
+ <names>
+ <shortLabel>RNR2</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="ROM2">
+ <names>
+ <shortLabel>ROM2</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="RPA135">
+ <names>
+ <shortLabel>RPA135</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="RPN1">
+ <names>
+ <shortLabel>RPN1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="RPN10">
+ <names>
+ <shortLabel>RPN10</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="RPN12">
+ <names>
+ <shortLabel>RPN12</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="RPN3">
+ <names>
+ <shortLabel>RPN3</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="RPN6">
+ <names>
+ <shortLabel>RPN6</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="RPN9">
+ <names>
+ <shortLabel>RPN9</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="RPT2">
+ <names>
+ <shortLabel>RPT2</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="RPT3">
+ <names>
+ <shortLabel>RPT3</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="RPT6">
+ <names>
+ <shortLabel>RPT6</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="RSC8">
+ <names>
+ <shortLabel>RSC8</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="RSE1">
+ <names>
+ <shortLabel>RSE1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="RTT101">
+ <names>
+ <shortLabel>RTT101</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="RUB1">
+ <names>
+ <shortLabel>RUB1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="RVB2">
+ <names>
+ <shortLabel>RVB2</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="RVS161">
+ <names>
+ <shortLabel>RVS161</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="RVS167">
+ <names>
+ <shortLabel>RVS167</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="SAH1">
+ <names>
+ <shortLabel>SAH1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="SCH9">
+ <names>
+ <shortLabel>SCH9</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="SCP160">
+ <names>
+ <shortLabel>SCP160</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="SEC27">
+ <names>
+ <shortLabel>SEC27</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="SEC4">
+ <names>
+ <shortLabel>SEC4</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="SEC53">
+ <names>
+ <shortLabel>SEC53</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="SEC6">
+ <names>
+ <shortLabel>SEC6</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="SEN1">
+ <names>
+ <shortLabel>SEN1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="SET1">
+ <names>
+ <shortLabel>SET1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="SGS1">
+ <names>
+ <shortLabel>SGS1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="SGT1">
+ <names>
+ <shortLabel>SGT1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="SGT2">
+ <names>
+ <shortLabel>SGT2</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="SGV1">
+ <names>
+ <shortLabel>SGV1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="SHP1">
+ <names>
+ <shortLabel>SHP1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="SIS1">
+ <names>
+ <shortLabel>SIS1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="SKP1">
+ <names>
+ <shortLabel>SKP1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="SLA1">
+ <names>
+ <shortLabel>SLA1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="SLA2">
+ <names>
+ <shortLabel>SLA2</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="SMC3">
+ <names>
+ <shortLabel>SMC3</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="SNP1">
+ <names>
+ <shortLabel>SNP1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="SNU56">
+ <names>
+ <shortLabel>SNU56</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="SOD1">
+ <names>
+ <shortLabel>SOD1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="SOD2">
+ <names>
+ <shortLabel>SOD2</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="SPT7">
+ <names>
+ <shortLabel>SPT7</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="SRA1">
+ <names>
+ <shortLabel>SRA1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="SRO7">
+ <names>
+ <shortLabel>SRO7</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="SRO9">
+ <names>
+ <shortLabel>SRO9</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="SRP1">
+ <names>
+ <shortLabel>SRP1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="SRV2">
+ <names>
+ <shortLabel>SRV2</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="SSC1">
+ <names>
+ <shortLabel>SSC1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="SSL1">
+ <names>
+ <shortLabel>SSL1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="SSL2">
+ <names>
+ <shortLabel>SSL2</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="STE11">
+ <names>
+ <shortLabel>STE11</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="STE20">
+ <names>
+ <shortLabel>STE20</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="STI1">
+ <names>
+ <shortLabel>STI1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="STM1">
+ <names>
+ <shortLabel>STM1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="STO1">
+ <names>
+ <shortLabel>STO1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="SUI3">
+ <names>
+ <shortLabel>SUI3</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="SUP35">
+ <names>
+ <shortLabel>SUP35</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="SUP45">
+ <names>
+ <shortLabel>SUP45</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="SUR2">
+ <names>
+ <shortLabel>SUR2</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="SWI4">
+ <names>
+ <shortLabel>SWI4</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="TAO3">
+ <names>
+ <shortLabel>TAO3</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="TBF1">
+ <names>
+ <shortLabel>TBF1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="TCP1">
+ <names>
+ <shortLabel>TCP1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="TDH3">
+ <names>
+ <shortLabel>TDH3</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="TEF4">
+ <names>
+ <shortLabel>TEF4</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="TEL1">
+ <names>
+ <shortLabel>TEL1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="TFA1">
+ <names>
+ <shortLabel>TFA1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="TFB1">
+ <names>
+ <shortLabel>TFB1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="TFB3">
+ <names>
+ <shortLabel>TFB3</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
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+ <shortLabel>TFB4</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
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+ </names>
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+ <shortLabel>TFC1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
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+ </names>
+ </organism>
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+ <shortLabel>TFP1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
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+ <proteinInteractor id="THI21">
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+ <organism ncbiTaxId="4932">
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+ <proteinInteractor id="TIF2">
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+ </names>
+ <organism ncbiTaxId="4932">
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+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="TKL1">
+ <names>
+ <shortLabel>TKL1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
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+ <proteinInteractor id="TOP3">
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+ <shortLabel>TOP3</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
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+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="TPI1">
+ <names>
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+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
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+ <proteinInteractor id="TRP1">
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+ <shortLabel>TRP1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
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+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
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+ <proteinInteractor id="TUB3">
+ <names>
+ <shortLabel>TUB3</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
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+ <proteinInteractor id="UBA1">
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+ <organism ncbiTaxId="4932">
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+ </organism>
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+ <organism ncbiTaxId="4932">
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+ <proteinInteractor id="UBP15">
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+ <organism ncbiTaxId="4932">
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+ <proteinInteractor id="UFO1">
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+ <shortLabel>UFO1</shortLabel>
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+ <organism ncbiTaxId="4932">
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+ <organism ncbiTaxId="4932">
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+ <organism ncbiTaxId="4932">
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+ <proteinInteractor id="VMA4">
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+ <organism ncbiTaxId="4932">
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+ <proteinInteractor id="VMA6">
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+ <organism ncbiTaxId="4932">
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+ <organism ncbiTaxId="4932">
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+ <organism ncbiTaxId="4932">
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+ <proteinInteractor id="VPS5">
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+ <shortLabel>VPS5</shortLabel>
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+ <organism ncbiTaxId="4932">
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+ <proteinInteractor id="VRP1">
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+ </names>
+ <organism ncbiTaxId="4932">
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+ <proteinInteractor id="WRS1">
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+ <organism ncbiTaxId="4932">
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+ <proteinInteractor id="YAL027W">
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+ <organism ncbiTaxId="4932">
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+ <proteinInteractor id="YAR009C">
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+ <organism ncbiTaxId="4932">
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+ <proteinInteractor id="YBR280C">
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+ <organism ncbiTaxId="4932">
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+ <proteinInteractor id="YCR030C">
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+ <organism ncbiTaxId="4932">
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+ <proteinInteractor id="YCR102C">
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+ <organism ncbiTaxId="4932">
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+ <organism ncbiTaxId="4932">
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+ <proteinInteractor id="YDL085W">
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+ <organism ncbiTaxId="4932">
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+ <proteinInteractor id="YDL148C">
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+ <organism ncbiTaxId="4932">
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+ <organism ncbiTaxId="4932">
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+ <proteinInteractor id="YDL175C">
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+ <organism ncbiTaxId="4932">
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+ <organism ncbiTaxId="4932">
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+ <organism ncbiTaxId="4932">
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+ <organism ncbiTaxId="4932">
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+ <organism ncbiTaxId="4932">
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+ <organism ncbiTaxId="4932">
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+ <organism ncbiTaxId="4932">
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+ <organism ncbiTaxId="4932">
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+ <organism ncbiTaxId="4932">
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+ <organism ncbiTaxId="4932">
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+ <organism ncbiTaxId="4932">
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+ <organism ncbiTaxId="4932">
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+ <organism ncbiTaxId="4932">
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+ <organism ncbiTaxId="4932">
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+ <organism ncbiTaxId="4932">
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+ <organism ncbiTaxId="4932">
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+ <organism ncbiTaxId="4932">
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+ <organism ncbiTaxId="4932">
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+ </names>
+ <organism ncbiTaxId="4932">
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+ </names>
+ <organism ncbiTaxId="4932">
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+ </proteinInteractor>
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+ <shortLabel>YMR315W</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
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+ <shortLabel>Sce</shortLabel>
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+ </proteinInteractor>
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+ <organism ncbiTaxId="4932">
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+ </names>
+ <organism ncbiTaxId="4932">
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+ <shortLabel>YNL132W</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
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+ </names>
+ <organism ncbiTaxId="4932">
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+ </names>
+ <organism ncbiTaxId="4932">
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+ <shortLabel>YOR173W</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
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+ <shortLabel>Sce</shortLabel>
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+ <shortLabel>YPK1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
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+ </proteinInteractor>
+ <proteinInteractor id="YPL004C">
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+ <shortLabel>YPL004C</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
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+ <shortLabel>Sce</shortLabel>
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+ </proteinInteractor>
+ <proteinInteractor id="YPL110C">
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+ <shortLabel>YPL110C</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
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+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="YPL249C">
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+ <shortLabel>YPL249C</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
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+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="YPT1">
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+ <shortLabel>YPT1</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="YPT10">
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+ <shortLabel>YPT10</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
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+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="YPT31">
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+ <shortLabel>YPT31</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="YPT32">
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+ <shortLabel>YPT32</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="YPT52">
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+ <shortLabel>YPT52</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="YPT6">
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+ <shortLabel>YPT6</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="YPT7">
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+ <shortLabel>YPT7</shortLabel>
+ </names>
+ <organism ncbiTaxId="4932">
+ <names>
+ <shortLabel>Sce</shortLabel>
+ </names>
+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="YSC84">
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+ <shortLabel>YSC84</shortLabel>
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+ <organism ncbiTaxId="4932">
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+ <shortLabel>Sce</shortLabel>
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+ </organism>
+ </proteinInteractor>
+ <proteinInteractor id="YTA7">
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+ <shortLabel>YTA7</shortLabel>
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+ <isOverexpressedProtein>false</isOverexpressedProtein>
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+ <proteinParticipant>
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+ <proteinParticipant>
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+ <isTaggedProtein>true</isTaggedProtein>
+ <isOverexpressedProtein>true</isOverexpressedProtein>
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+ <proteinParticipant>
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+ <isTaggedProtein>true</isTaggedProtein>
+ <isOverexpressedProtein>true</isOverexpressedProtein>
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+ <proteinInteractorRef ref="ECM29"/>
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+ <isTaggedProtein>false</isTaggedProtein>
+ <isOverexpressedProtein>false</isOverexpressedProtein>
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+ <proteinParticipant>
+ <proteinInteractorRef ref="PGK1"/>
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+ <isTaggedProtein>false</isTaggedProtein>
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+ <isOverexpressedProtein>false</isOverexpressedProtein>
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+ <isOverexpressedProtein>false</isOverexpressedProtein>
+ </proteinParticipant>
+ <proteinParticipant>
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+ <isOverexpressedProtein>false</isOverexpressedProtein>
+ </proteinParticipant>
+ <proteinParticipant>
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+ <isOverexpressedProtein>false</isOverexpressedProtein>
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+ <proteinParticipant>
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+ <isOverexpressedProtein>false</isOverexpressedProtein>
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+ <proteinParticipant>
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+ <isOverexpressedProtein>false</isOverexpressedProtein>
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+ <isOverexpressedProtein>false</isOverexpressedProtein>
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+ <isOverexpressedProtein>false</isOverexpressedProtein>
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+ <proteinParticipant>
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+ <isOverexpressedProtein>false</isOverexpressedProtein>
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+ <proteinParticipant>
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+ <isOverexpressedProtein>false</isOverexpressedProtein>
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+ <proteinParticipant>
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+ <isTaggedProtein>false</isTaggedProtein>
+ <isOverexpressedProtein>false</isOverexpressedProtein>
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+ <proteinParticipant>
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+ <isOverexpressedProtein>true</isOverexpressedProtein>
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+ <isOverexpressedProtein>false</isOverexpressedProtein>
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+ <isOverexpressedProtein>false</isOverexpressedProtein>
+ </proteinParticipant>
+ <proteinParticipant>
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+ <isOverexpressedProtein>true</isOverexpressedProtein>
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+ <proteinParticipant>
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+ <isOverexpressedProtein>false</isOverexpressedProtein>
+ </proteinParticipant>
+ <proteinParticipant>
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+ <proteinParticipant>
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+ <proteinParticipant>
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+ <isOverexpressedProtein>false</isOverexpressedProtein>
+ </proteinParticipant>
+ <proteinParticipant>
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+ <isTaggedProtein>false</isTaggedProtein>
+ <isOverexpressedProtein>false</isOverexpressedProtein>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="YDR214W"/>
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+ <isTaggedProtein>false</isTaggedProtein>
+ <isOverexpressedProtein>false</isOverexpressedProtein>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="YJR072C"/>
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+ <isTaggedProtein>false</isTaggedProtein>
+ <isOverexpressedProtein>false</isOverexpressedProtein>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="YLR413W"/>
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+ <isOverexpressedProtein>false</isOverexpressedProtein>
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+ <isOverexpressedProtein>false</isOverexpressedProtein>
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+ <isOverexpressedProtein>false</isOverexpressedProtein>
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+ <proteinParticipant>
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+ <proteinParticipant>
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+ <isOverexpressedProtein>false</isOverexpressedProtein>
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+ <proteinParticipant>
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+ <isOverexpressedProtein>true</isOverexpressedProtein>
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+ <isOverexpressedProtein>false</isOverexpressedProtein>
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+ <proteinParticipant>
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+ <isTaggedProtein>false</isTaggedProtein>
+ <isOverexpressedProtein>false</isOverexpressedProtein>
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+ <proteinParticipant>
+ <proteinInteractorRef ref="YDR326C"/>
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+ <isTaggedProtein>false</isTaggedProtein>
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+ <proteinInteractorRef ref="YMR318C"/>
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+ <isTaggedProtein>false</isTaggedProtein>
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+ <isTaggedProtein>true</isTaggedProtein>
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+ <isTaggedProtein>false</isTaggedProtein>
+ <isOverexpressedProtein>false</isOverexpressedProtein>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="YGL245W"/>
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+ <isTaggedProtein>false</isTaggedProtein>
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+ <proteinParticipant>
+ <proteinInteractorRef ref="YHB1"/>
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+ <isTaggedProtein>false</isTaggedProtein>
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+ <proteinInteractorRef ref="TCP1"/>
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+ <isTaggedProtein>true</isTaggedProtein>
+ <isOverexpressedProtein>true</isOverexpressedProtein>
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+ <proteinParticipant>
+ <proteinInteractorRef ref="dummy"/>
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+ <names>
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+ <proteinParticipant>
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+ <proteinParticipant>
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+ <proteinParticipant>
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+ <proteinParticipant>
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+ <isOverexpressedProtein>true</isOverexpressedProtein>
+ </proteinParticipant>
+ <proteinParticipant>
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+ <isOverexpressedProtein>false</isOverexpressedProtein>
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+ <proteinParticipant>
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+ <proteinParticipant>
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+ <proteinParticipant>
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+ <proteinParticipant>
+ <proteinInteractorRef ref="YDR071C"/>
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+ <isOverexpressedProtein>false</isOverexpressedProtein>
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+ <proteinParticipant>
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+ <isTaggedProtein>false</isTaggedProtein>
+ <isOverexpressedProtein>false</isOverexpressedProtein>
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+ <proteinParticipant>
+ <proteinInteractorRef ref="YMR135C"/>
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+ <isTaggedProtein>false</isTaggedProtein>
+ <isOverexpressedProtein>false</isOverexpressedProtein>
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+ <proteinParticipant>
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+ <isOverexpressedProtein>true</isOverexpressedProtein>
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+ <isOverexpressedProtein>true</isOverexpressedProtein>
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+ <isOverexpressedProtein>true</isOverexpressedProtein>
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+ <proteinParticipant>
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+ <isTaggedProtein>false</isTaggedProtein>
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+ <isTaggedProtein>false</isTaggedProtein>
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+ <isTaggedProtein>false</isTaggedProtein>
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+ <isTaggedProtein>false</isTaggedProtein>
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+ <proteinInteractorRef ref="YPT7"/>
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+ <isTaggedProtein>false</isTaggedProtein>
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+ <proteinInteractorRef ref="GUT1"/>
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+ <isTaggedProtein>true</isTaggedProtein>
+ <isOverexpressedProtein>true</isOverexpressedProtein>
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+ <proteinParticipant>
+ <proteinInteractorRef ref="dummy"/>
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+ <proteinParticipant>
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+ <isOverexpressedProtein>false</isOverexpressedProtein>
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+ <proteinParticipant>
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+ <proteinParticipant>
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+ <proteinParticipant>
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+ <isOverexpressedProtein>false</isOverexpressedProtein>
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+ <proteinParticipant>
+ <proteinInteractorRef ref="YDL156W"/>
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+ <proteinParticipant>
+ <proteinInteractorRef ref="YHR122W"/>
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+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="YOR155C"/>
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+ <isOverexpressedProtein>false</isOverexpressedProtein>
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+ <isOverexpressedProtein>false</isOverexpressedProtein>
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+ <isOverexpressedProtein>false</isOverexpressedProtein>
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+ <proteinParticipant>
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+ <proteinInteractorRef ref="YHR122W"/>
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+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="STI1"/>
+ <role>neutral</role>
+ <isTaggedProtein>false</isTaggedProtein>
+ <isOverexpressedProtein>false</isOverexpressedProtein>
+ </proteinParticipant>
+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>aggregation</shortLabel>
+ </names>
+ <xref>
+ <primaryRef id="0" db=""/>
+ </xref>
+ </interactionType>
+ </interaction>
+ <interaction>
+ <experimentList>
+<experimentRef ref="lcms-maldi"/>
+</experimentList> <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="TEL1"/>
+ <role>bait</role>
+ <isTaggedProtein>true</isTaggedProtein>
+ <isOverexpressedProtein>true</isOverexpressedProtein>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="YPL110C"/>
+ <role>neutral</role>
+ <isTaggedProtein>false</isTaggedProtein>
+ <isOverexpressedProtein>false</isOverexpressedProtein>
+ </proteinParticipant>
+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>aggregation</shortLabel>
+ </names>
+ <xref>
+ <primaryRef id="0" db=""/>
+ </xref>
+ </interactionType>
+ </interaction>
+ <interaction>
+ <experimentList>
+<experimentRef ref="lcms-maldi"/>
+</experimentList> <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="RVS161"/>
+ <role>neutral</role>
+ <isTaggedProtein>false</isTaggedProtein>
+ <isOverexpressedProtein>false</isOverexpressedProtein>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="RVS167"/>
+ <role>bait</role>
+ <isTaggedProtein>true</isTaggedProtein>
+ <isOverexpressedProtein>true</isOverexpressedProtein>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="YPL249C"/>
+ <role>neutral</role>
+ <isTaggedProtein>false</isTaggedProtein>
+ <isOverexpressedProtein>false</isOverexpressedProtein>
+ </proteinParticipant>
+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>aggregation</shortLabel>
+ </names>
+ <xref>
+ <primaryRef id="0" db=""/>
+ </xref>
+ </interactionType>
+ </interaction>
+ <interaction>
+ <experimentList>
+<experimentRef ref="lcms-maldi"/>
+</experimentList> <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="YDL085W"/>
+ <role>bait</role>
+ <isTaggedProtein>true</isTaggedProtein>
+ <isOverexpressedProtein>true</isOverexpressedProtein>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="dummy"/>
+ </proteinParticipant>
+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>aggregation</shortLabel>
+ </names>
+ <xref>
+ <primaryRef id="0" db=""/>
+ </xref>
+ </interactionType>
+ </interaction>
+ <interaction>
+ <experimentList>
+<experimentRef ref="lcms-maldi"/>
+</experimentList> <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="YMR145C"/>
+ <role>bait</role>
+ <isTaggedProtein>true</isTaggedProtein>
+ <isOverexpressedProtein>true</isOverexpressedProtein>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="dummy"/>
+ </proteinParticipant>
+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>aggregation</shortLabel>
+ </names>
+ <xref>
+ <primaryRef id="0" db=""/>
+ </xref>
+ </interactionType>
+ </interaction>
+ <interaction>
+ <experimentList>
+<experimentRef ref="lcms-maldi"/>
+</experimentList> <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="YPK1"/>
+ <role>bait</role>
+ <isTaggedProtein>true</isTaggedProtein>
+ <isOverexpressedProtein>true</isOverexpressedProtein>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="dummy"/>
+ </proteinParticipant>
+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>aggregation</shortLabel>
+ </names>
+ <xref>
+ <primaryRef id="0" db=""/>
+ </xref>
+ </interactionType>
+ </interaction>
+ <interaction>
+ <experimentList>
+<experimentRef ref="lcms-maldi"/>
+</experimentList> <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="BAS1"/>
+ <role>bait</role>
+ <isTaggedProtein>true</isTaggedProtein>
+ <isOverexpressedProtein>true</isOverexpressedProtein>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="dummy"/>
+ </proteinParticipant>
+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>aggregation</shortLabel>
+ </names>
+ <xref>
+ <primaryRef id="0" db=""/>
+ </xref>
+ </interactionType>
+ </interaction>
+ <interaction>
+ <experimentList>
+<experimentRef ref="lcms-maldi"/>
+</experimentList> <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="GRF10"/>
+ <role>bait</role>
+ <isTaggedProtein>true</isTaggedProtein>
+ <isOverexpressedProtein>true</isOverexpressedProtein>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="dummy"/>
+ </proteinParticipant>
+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>aggregation</shortLabel>
+ </names>
+ <xref>
+ <primaryRef id="0" db=""/>
+ </xref>
+ </interactionType>
+ </interaction>
+ <interaction>
+ <experimentList>
+<experimentRef ref="lcms-maldi"/>
+</experimentList> <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="YOR155C"/>
+ <role>bait</role>
+ <isTaggedProtein>true</isTaggedProtein>
+ <isOverexpressedProtein>true</isOverexpressedProtein>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="dummy"/>
+ </proteinParticipant>
+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>aggregation</shortLabel>
+ </names>
+ <xref>
+ <primaryRef id="0" db=""/>
+ </xref>
+ </interactionType>
+ </interaction>
+ <interaction>
+ <experimentList>
+<experimentRef ref="lcms-maldi"/>
+</experimentList> <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="BOI1"/>
+ <role>bait</role>
+ <isTaggedProtein>true</isTaggedProtein>
+ <isOverexpressedProtein>true</isOverexpressedProtein>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="dummy"/>
+ </proteinParticipant>
+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>aggregation</shortLabel>
+ </names>
+ <xref>
+ <primaryRef id="0" db=""/>
+ </xref>
+ </interactionType>
+ </interaction>
+ <interaction>
+ <experimentList>
+<experimentRef ref="lcms-maldi"/>
+</experimentList> <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="BOI2"/>
+ <role>bait</role>
+ <isTaggedProtein>true</isTaggedProtein>
+ <isOverexpressedProtein>true</isOverexpressedProtein>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="dummy"/>
+ </proteinParticipant>
+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>aggregation</shortLabel>
+ </names>
+ <xref>
+ <primaryRef id="0" db=""/>
+ </xref>
+ </interactionType>
+ </interaction>
+ <interaction>
+ <experimentList>
+<experimentRef ref="lcms-maldi"/>
+</experimentList> <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="SRA1"/>
+ <role>bait</role>
+ <isTaggedProtein>true</isTaggedProtein>
+ <isOverexpressedProtein>true</isOverexpressedProtein>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="dummy"/>
+ </proteinParticipant>
+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>aggregation</shortLabel>
+ </names>
+ <xref>
+ <primaryRef id="0" db=""/>
+ </xref>
+ </interactionType>
+ </interaction>
+ <interaction>
+ <experimentList>
+<experimentRef ref="lcms-maldi"/>
+</experimentList> <participantList>
+ <proteinParticipant>
+ <proteinInteractorRef ref="ACT1"/>
+ <role>neutral</role>
+ <isTaggedProtein>false</isTaggedProtein>
+ <isOverexpressedProtein>false</isOverexpressedProtein>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="CYR1"/>
+ <role>bait</role>
+ <isTaggedProtein>true</isTaggedProtein>
+ <isOverexpressedProtein>true</isOverexpressedProtein>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="PHO81"/>
+ <role>neutral</role>
+ <isTaggedProtein>false</isTaggedProtein>
+ <isOverexpressedProtein>false</isOverexpressedProtein>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="RNR2"/>
+ <role>neutral</role>
+ <isTaggedProtein>false</isTaggedProtein>
+ <isOverexpressedProtein>false</isOverexpressedProtein>
+ </proteinParticipant>
+ <proteinParticipant>
+ <proteinInteractorRef ref="SRV2"/>
+ <role>neutral</role>
+ <isTaggedProtein>false</isTaggedProtein>
+ <isOverexpressedProtein>false</isOverexpressedProtein>
+ </proteinParticipant>
+ </participantList>
+ <interactionType>
+ <names>
+ <shortLabel>aggregation</shortLabel>
+ </names>
+ <xref>
+ <primaryRef id="0" db=""/>
+ </xref>
+ </interactionType>
+ </interaction>
+ </interactionList>
+ </entry>
+</entrySet>
diff --git a/coreplugins/QuickFind/README.txt b/coreplugins/QuickFind/README.txt
new file mode 100644
index 0000000..1227cb4
--- /dev/null
+++ b/coreplugins/QuickFind/README.txt
@@ -0,0 +1,8 @@
+This directory contains the QuickFind core plugin for Cytoscape.
+
+In order to compile this plugin, you must have cytoscape checked out,
+compiled and located here:
+
+../../cytoscape
+
+For questions, please email Ethan Cerami: cerami at cbio.mskcc.org
diff --git a/coreplugins/QuickFind/UI_Testing.txt b/coreplugins/QuickFind/UI_Testing.txt
new file mode 100644
index 0000000..5df97c0
--- /dev/null
+++ b/coreplugins/QuickFind/UI_Testing.txt
@@ -0,0 +1,32 @@
+The following document describes UI testing that can only be done manually.
+
+Run: RunTextIndexComboBox.java
+
+1. At startup, press the down arrow key. Verify that all hits fit
+within the pop-up window.
+2. Test up/down arrow keys
+ a. enter b
+ b. press down arrow key: "bat" should be selected in the textbox.
+ c. press the up arrow key: "bag" should be selected in the textbox.
+3. Test page up / page down keys
+ a. enter b
+ b. press page down key: "boom" should be selected in the textbox.
+ c. press page up key: "bag" should be selected in the textbox.
+4. Verify hit selection via Enter key
+ a. enter b
+ b. press down array key: "bat" should be selected in the textbox.
+ c. press enter. Pop-up box should display with final selection: "bat".
+5. Verify hit selection via Mouse
+ a. enter b.
+ b. using mouse, select "bat"
+ c. Pop-up box should display with final selection: "bat".
+6. Verify paste works
+ a. upon startup, page "bat" into text box.
+ b. should see "bat", 3 hits
+7. Verify copy works
+ a. enter a
+ b. select "apple"
+ c. paste into new document. verify apple was copied over.
+8. Verify no-matches
+ a. enter something silly like: "ffafafdsa"
+ b. verify box is turns red and 0 hits found.
diff --git a/coreplugins/QuickFind/pom.xml b/coreplugins/QuickFind/pom.xml
new file mode 100644
index 0000000..3a7db40
--- /dev/null
+++ b/coreplugins/QuickFind/pom.xml
@@ -0,0 +1,56 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>parent</artifactId>
+ <version>2.8.4-SNAPSHOT</version>
+ </parent>
+
+ <artifactId>quickfind</artifactId>
+ <packaging>jar</packaging>
+
+ <name>QuickFind</name>
+
+ <!-- bootstrap for cytoscape dependencies, namely the parent POM snapshots -->
+ <repositories>
+ <repository>
+ <id>cytoscape_snapshots</id>
+ <snapshots>
+ <enabled>true</enabled>
+ </snapshots>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <name>Cytoscape Snapshots</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/</url>
+ </repository>
+ <repository>
+ <id>cytoscape_releases</id>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ <name>Cytoscape Releases</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/releases/</url>
+ </repository>
+ </repositories>
+
+ <build>
+ <plugins>
+ <plugin>
+ <artifactId>maven-assembly-plugin</artifactId>
+ <configuration>
+ <archive>
+ <manifestEntries>
+ <Cytoscape-Plugin>csplugins.quickfind.plugin.QuickFindPlugIn</Cytoscape-Plugin>
+ </manifestEntries>
+ </archive>
+ </configuration>
+ </plugin>
+ </plugins>
+ </build>
+
+</project>
+
diff --git a/coreplugins/QuickFind/src/main/java/csplugins/quickfind/package.html b/coreplugins/QuickFind/src/main/java/csplugins/quickfind/package.html
new file mode 100644
index 0000000..21513ff
--- /dev/null
+++ b/coreplugins/QuickFind/src/main/java/csplugins/quickfind/package.html
@@ -0,0 +1,8 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+<html>
+<head></head>
+
+<body bgcolor="white">
+Cytoscape QuickFind Plugin.
+</body>
+</html>
diff --git a/coreplugins/QuickFind/src/main/java/csplugins/quickfind/plugin/QuickFindPlugIn.java b/coreplugins/QuickFind/src/main/java/csplugins/quickfind/plugin/QuickFindPlugIn.java
new file mode 100644
index 0000000..353604e
--- /dev/null
+++ b/coreplugins/QuickFind/src/main/java/csplugins/quickfind/plugin/QuickFindPlugIn.java
@@ -0,0 +1,550 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package csplugins.quickfind.plugin;
+
+import csplugins.quickfind.util.QuickFind;
+import csplugins.quickfind.util.QuickFindFactory;
+import csplugins.quickfind.util.QuickFindListener;
+
+import csplugins.quickfind.view.QuickFindPanel;
+
+import csplugins.quickfind.util.TaskMonitorBase;
+
+import csplugins.widgets.autocomplete.index.GenericIndex;
+import csplugins.widgets.autocomplete.index.Hit;
+import csplugins.widgets.autocomplete.index.NumberIndex;
+import csplugins.widgets.autocomplete.index.TextIndex;
+import csplugins.widgets.autocomplete.view.TextIndexComboBox;
+
+import csplugins.widgets.slider.JRangeSliderExtended;
+
+import cytoscape.CyEdge;
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+
+import cytoscape.ding.DingNetworkView;
+
+import cytoscape.plugin.CytoscapePlugin;
+
+import cytoscape.util.CytoscapeToolBar;
+
+import cytoscape.view.CyMenus;
+import cytoscape.view.CyNetworkView;
+import cytoscape.view.CytoscapeDesktop;
+
+import ding.view.DGraphView;
+import ding.view.InnerCanvas;
+
+import giny.view.NodeView;
+
+import prefuse.data.query.NumberRangeModel;
+
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+
+import java.util.*;
+
+import javax.swing.*;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+
+
+/**
+ * Quick Find PlugIn.
+ *
+ * @author Ethan Cerami.
+ */
+public class QuickFindPlugIn extends CytoscapePlugin implements PropertyChangeListener,
+ QuickFindListener {
+ static final int REINDEX_THRESHOLD = 1000;
+ private QuickFindPanel quickFindToolBar;
+ private static final int NODE_SIZE_MULTIPLER = 10;
+
+ /**
+ * Constructor.
+ */
+ public QuickFindPlugIn() {
+ initListeners();
+ initToolBar();
+ initIndex();
+ }
+
+ /**
+ * Initializes All Cytoscape Listeners.
+ */
+ private void initListeners() {
+ // to catch network create/destroy/focus events
+ Cytoscape.getDesktop().getSwingPropertyChangeSupport().addPropertyChangeListener(this);
+
+ // to catch network modified events
+ NetworkModifiedListener networkModifiedListener = new NetworkModifiedListener();
+ Cytoscape.getPropertyChangeSupport().addPropertyChangeListener(networkModifiedListener);
+
+ QuickFind quickFind = QuickFindFactory.getGlobalQuickFindInstance();
+ quickFind.addQuickFindListener(this);
+ }
+
+ /**
+ * Initalizes Tool Bar.
+ */
+ private void initToolBar() {
+ CytoscapeDesktop desktop = Cytoscape.getDesktop();
+ CyMenus cyMenus = desktop.getCyMenus();
+ CytoscapeToolBar toolBar = cyMenus.getToolBar();
+ quickFindToolBar = new QuickFindPanel();
+
+ TextIndexComboBox comboBox = quickFindToolBar.getTextIndexComboBox();
+ ActionListener listener = new UserSelectionListener(comboBox);
+ comboBox.addFinalSelectionListener(listener);
+
+ JRangeSliderExtended slider = quickFindToolBar.getSlider();
+ RangeSelectionListener rangeSelectionListener = new RangeSelectionListener(slider);
+ slider.addChangeListener(rangeSelectionListener);
+ toolBar.add(quickFindToolBar);
+ toolBar.validate();
+ }
+
+ /**
+ * Initializes index, if network already exists.
+ * This condition may occur if a user loads up a network from the command
+ * line, and the network is already loaded prior to any plugins being loaded
+ */
+ private void initIndex() {
+ final QuickFind quickFind = QuickFindFactory.getGlobalQuickFindInstance();
+
+ // If a network already exists within Cytoscape, index it
+ final CyNetwork cyNetwork = Cytoscape.getCurrentNetwork();
+
+ if ((cyNetwork != null) && (cyNetwork.getNodeCount() > 0)) {
+ // Run Indexer in separate background daemon thread.
+ Thread thread = new Thread() {
+ public void run() {
+ quickFind.addNetwork(cyNetwork, new TaskMonitorBase());
+ }
+ };
+
+ thread.start();
+ }
+ }
+
+ /**
+ * Property change listener - to get network/network view destroy events.
+ *
+ * @param event PropertyChangeEvent
+ */
+ public void propertyChange(PropertyChangeEvent event) {
+ final QuickFind quickFind = QuickFindFactory.getGlobalQuickFindInstance();
+
+ if (event.getPropertyName() != null) {
+ if (event.getPropertyName().equals(CytoscapeDesktop.NETWORK_VIEW_CREATED)) {
+ final CyNetwork cyNetwork = Cytoscape.getCurrentNetwork();
+
+ // Run Indexer in separate background daemon thread.
+ Thread thread = new Thread() {
+ public void run() {
+ quickFind.addNetwork(cyNetwork, new TaskMonitorBase());
+ }
+ };
+
+ thread.start();
+ } else if (event.getPropertyName().equals(CytoscapeDesktop.NETWORK_VIEW_DESTROYED)) {
+ CyNetworkView networkView = (CyNetworkView) event.getNewValue();
+ CyNetwork cyNetwork = networkView.getNetwork();
+ quickFind.removeNetwork(cyNetwork);
+ swapCurrentNetwork(quickFind);
+ } else if (event.getPropertyName().equals(CytoscapeDesktop.NETWORK_VIEW_FOCUS)) {
+ swapCurrentNetwork(quickFind);
+ }
+ }
+ }
+
+ /**
+ * Determine which network view now has focus.
+ * If no network view has focus, disable quick find.
+ */
+ private void swapCurrentNetwork(QuickFind quickFind) {
+ CyNetwork network = Cytoscape.getCurrentNetwork();
+ boolean networkHasFocus = false;
+
+ if (network != null) {
+ CyNetworkView networkView = Cytoscape.getNetworkView(network.getIdentifier());
+
+ if (networkView != Cytoscape.getNullNetworkView()) {
+ GenericIndex textIndex = quickFind.getIndex(network);
+
+ if (textIndex != null) {
+ quickFindToolBar.setIndex(textIndex);
+ networkHasFocus = true;
+ }
+ }
+ }
+
+ if (!networkHasFocus) {
+ quickFindToolBar.noNetworkLoaded();
+ }
+ }
+
+ /**
+ * Event: Network Added to Index.
+ *
+ * @param network CyNetwork Object.
+ */
+ public void networkAddedToIndex(CyNetwork network) {
+ // No-op
+ }
+
+ /**
+ * Event: Network Removed from Index.
+ *
+ * @param network CyNetwork Object.
+ */
+ public void networkRemovedfromIndex(CyNetwork network) {
+ // No-op
+ }
+
+ /**
+ * Indexing started.
+ *
+ * @param cyNetwork CyNetwork.
+ * @param indexType QuickFind.INDEX_NODES or QuickFind.INDEX_EDGES.
+ * @param controllingAttribute Controlling Attribute.
+ */
+ public void indexingStarted(CyNetwork cyNetwork, int indexType, String controllingAttribute) {
+ quickFindToolBar.indexingInProgress();
+ }
+
+ /**
+ * Indexing ended.
+ */
+ public void indexingEnded() {
+ QuickFind quickFind = QuickFindFactory.getGlobalQuickFindInstance();
+ CyNetwork cyNetwork = Cytoscape.getCurrentNetwork();
+ GenericIndex index = quickFind.getIndex(cyNetwork);
+ if (index != null){
+ quickFindToolBar.setIndex(index);
+ quickFindToolBar.enableAllQuickFindButtons();
+ }
+ }
+
+ /**
+ * Indicates that the user has selected a text item within the QuickFind
+ * Search Box.
+ *
+ * @param network the current CyNetwork.
+ * @param hit hit value chosen by the user.
+ */
+ public void onUserSelection(final CyNetwork network, Hit hit) {
+ network.unselectAllNodes();
+ network.unselectAllEdges();
+
+ // Assemble Hit Objects
+ final Object[] graphObjects = hit.getAssociatedObjects();
+ final ArrayList list = new ArrayList();
+
+ for (int i = 0; i < graphObjects.length; i++) {
+ list.add(graphObjects[i]);
+ }
+
+ // Fit Selected Content
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ QuickFind quickFind = QuickFindFactory.getGlobalQuickFindInstance();
+ final CyNetwork cyNetwork = Cytoscape.getCurrentNetwork();
+ GenericIndex index = quickFind.getIndex(cyNetwork);
+
+ if (index.getIndexType() == QuickFind.INDEX_NODES) {
+ network.setSelectedNodeState(list, true);
+ ((DingNetworkView) Cytoscape.getCurrentNetworkView()).fitSelected();
+ } else {
+ network.setSelectedEdgeState(list, true);
+
+ List nodeList = new ArrayList();
+
+ for (int i = 0; i < list.size(); i++) {
+ CyEdge edge = (CyEdge) list.get(i);
+ CyNode sourceNode = (CyNode) edge.getSource();
+ CyNode targetNode = (CyNode) edge.getTarget();
+ nodeList.add(sourceNode);
+ nodeList.add(targetNode);
+ }
+
+ network.setSelectedNodeState(nodeList, true);
+ ((DingNetworkView) Cytoscape.getCurrentNetworkView()).fitSelected();
+ }
+
+ // If only one node is selected, auto-adjust zoom factor
+ // so that node does not take up whole screen.
+ if (graphObjects.length == 1) {
+ if (graphObjects[0] instanceof CyNode) {
+ CyNode node = (CyNode) graphObjects[0];
+
+ // Obtain dimensions of current InnerCanvas
+ DGraphView graphView = (DGraphView) Cytoscape.getCurrentNetworkView();
+ InnerCanvas innerCanvas = graphView.getCanvas();
+
+ NodeView nodeView = Cytoscape.getCurrentNetworkView().getNodeView(node);
+
+ double width = nodeView.getWidth() * NODE_SIZE_MULTIPLER;
+ double height = nodeView.getHeight() * NODE_SIZE_MULTIPLER;
+ double scaleFactor = Math.min(innerCanvas.getWidth() / width,
+ (innerCanvas.getHeight() / height));
+ Cytoscape.getCurrentNetworkView().setZoom(scaleFactor);
+ }
+ }
+
+ Cytoscape.getCurrentNetworkView().updateView();
+ }
+ });
+ }
+
+ /**
+ * Indicates that the user has selected a number range within the QuickFind
+ * Range selector.
+ *
+ * @param network the current CyNetwork.
+ * @param lowValue the low value of the range.
+ * @param highValue the high value of the range.
+ */
+ public void onUserRangeSelection(CyNetwork network, Number lowValue, Number highValue) {
+ try {
+ QuickFind quickFind = QuickFindFactory.getGlobalQuickFindInstance();
+ GenericIndex index = quickFind.getIndex(network);
+ NumberIndex numberIndex = (NumberIndex) index;
+ final java.util.List rangeList = numberIndex.getRange(lowValue, highValue);
+
+ if (index.getIndexType() == QuickFind.INDEX_NODES) {
+ selectNodes(network, rangeList);
+ } else {
+ selectEdges(network, rangeList);
+ }
+ } catch (IllegalArgumentException exc) {
+ }
+ }
+
+ private void selectNodes(final CyNetwork cyNetwork, List rangeList) {
+ // First, do we have any edges selected? If so, unselect them all
+ Set selectedEdgeSet = cyNetwork.getSelectFilter().getSelectedEdges();
+
+ if (selectedEdgeSet.size() > 0) {
+ cyNetwork.setSelectedEdgeState(selectedEdgeSet, false);
+ }
+
+ // Then, determine the current set of selected nodes
+ Set selectedNodeSet = cyNetwork.getSelectFilter().getSelectedNodes();
+
+ // Then, figure out which new nodes to select
+ // This is the set operation: R - S
+ final List toBeSelected = new ArrayList();
+ toBeSelected.addAll(rangeList);
+ toBeSelected.removeAll(selectedNodeSet);
+
+ // Then, figure out which current nodes to unselect
+ // This is the set operation: S - R
+ final List toBeUnselected = new ArrayList();
+ toBeUnselected.addAll(selectedNodeSet);
+ toBeUnselected.removeAll(rangeList);
+
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ cyNetwork.setSelectedNodeState(toBeSelected, true);
+ cyNetwork.setSelectedNodeState(toBeUnselected, false);
+ Cytoscape.getCurrentNetworkView().updateView();
+ }
+ });
+ }
+
+ private void selectEdges(final CyNetwork cyNetwork, List rangeList) {
+ // First, do we have any nodes selected? If so, unselect them all
+ Set selectedNodeSet = cyNetwork.getSelectFilter().getSelectedNodes();
+
+ if (selectedNodeSet.size() > 0) {
+ cyNetwork.setSelectedNodeState(selectedNodeSet, false);
+ }
+
+ // Then, determine the current set of selected edge
+ Set selectedEdgeSet = cyNetwork.getSelectFilter().getSelectedEdges();
+
+ // Then, figure out which new nodes to select
+ // This is the set operation: R - S
+ final List toBeSelected = new ArrayList();
+ toBeSelected.addAll(rangeList);
+ toBeSelected.removeAll(selectedEdgeSet);
+
+ // Then, figure out which current nodes to unselect
+ // This is the set operation: S - R
+ final List toBeUnselected = new ArrayList();
+ toBeUnselected.addAll(selectedEdgeSet);
+ toBeUnselected.removeAll(rangeList);
+
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ cyNetwork.setSelectedEdgeState(toBeSelected, true);
+ cyNetwork.setSelectedEdgeState(toBeUnselected, false);
+ Cytoscape.getCurrentNetworkView().updateView();
+ }
+ });
+ }
+}
+
+
+/**
+ * Listens for Final Selection from User.
+ *
+ * @author Ethan Cerami.
+ */
+class UserSelectionListener implements ActionListener {
+ private TextIndexComboBox comboBox;
+
+ /**
+ * Constructor.
+ *
+ * @param comboBox TextIndexComboBox.
+ */
+ public UserSelectionListener(TextIndexComboBox comboBox) {
+ this.comboBox = comboBox;
+ }
+
+ /**
+ * User has made final selection.
+ *
+ * @param e ActionEvent Object.
+ */
+ public void actionPerformed(ActionEvent e) {
+ // Get Current Network
+ final CyNetwork currentNetwork = Cytoscape.getCurrentNetwork();
+
+ // Get Current User Selection
+ Object o = comboBox.getSelectedItem();
+
+ if ((o != null) && o instanceof Hit) {
+ QuickFind quickFind = QuickFindFactory.getGlobalQuickFindInstance();
+ Hit hit = (Hit) comboBox.getSelectedItem();
+ quickFind.selectHit(currentNetwork, hit);
+ }
+ }
+}
+
+
+/**
+ * Action to select a range of nodes.
+ *
+ * @author Ethan Cerami.
+ */
+class RangeSelectionListener implements ChangeListener {
+ private JRangeSliderExtended slider;
+
+ /**
+ * Constructor.
+ *
+ * @param slider JRangeSliderExtended Object.
+ */
+ public RangeSelectionListener(JRangeSliderExtended slider) {
+ this.slider = slider;
+ }
+
+ /**
+ * State Change Event.
+ *
+ * @param e ChangeEvent Object.
+ */
+ public void stateChanged(ChangeEvent e) {
+ QuickFind quickFind = QuickFindFactory.getGlobalQuickFindInstance();
+ final CyNetwork cyNetwork = Cytoscape.getCurrentNetwork();
+ GenericIndex index = quickFind.getIndex(cyNetwork);
+ NumberRangeModel model = (NumberRangeModel) slider.getModel();
+
+ if (slider.isVisible()) {
+ if (index instanceof NumberIndex) {
+ Number lowValue = (Number) model.getLowValue();
+ Number highValue = (Number) model.getHighValue();
+ quickFind.selectRange(cyNetwork, lowValue, highValue);
+ }
+ }
+ }
+}
+
+class NetworkModifiedListener implements PropertyChangeListener {
+
+ /**
+ * Property change listener - to get network modified events.
+ *
+ * @param event PropertyChangeEvent
+ */
+ public void propertyChange(PropertyChangeEvent event) {
+ final QuickFind quickFind = QuickFindFactory.getGlobalQuickFindInstance();
+
+ if (event.getPropertyName() != null) {
+ if (event.getPropertyName().equals(Cytoscape.NETWORK_MODIFIED)) {
+
+ final CyNetwork cyNetwork = Cytoscape.getCurrentNetwork();
+ if (cyNetwork.nodesList() != null) {
+
+ // this network may not have been added to quick find -
+ // this can happen if an empty network was added
+ if (quickFind.getIndex(cyNetwork) == null) {
+ // Run Indexer in separate background daemon thread.
+ Thread thread = new Thread() {
+ public void run() {
+ quickFind.addNetwork(cyNetwork, new TaskMonitorBase());
+ }
+ };
+ thread.start();
+ }
+ // Only re-index if network has fewer than REINDEX_THRESHOLD nodes
+ // I put this in to prevent quick find from auto re-indexing
+ // very large networks.
+ else if (cyNetwork.nodesList().size() < QuickFindPlugIn.REINDEX_THRESHOLD) {
+ // Run Indexer in separate background daemon thread.
+ Thread thread = new Thread() {
+ public void run() {
+ GenericIndex index = quickFind.getIndex(cyNetwork);
+ quickFind.reindexNetwork(cyNetwork, index.getIndexType(),
+ index.getControllingAttribute(), new TaskMonitorBase());
+ }
+ };
+ thread.start();
+ }
+ }
+ }
+ }
+ }
+
+}
diff --git a/coreplugins/QuickFind/src/main/java/csplugins/quickfind/plugin/package.html b/coreplugins/QuickFind/src/main/java/csplugins/quickfind/plugin/package.html
new file mode 100644
index 0000000..b40b25c
--- /dev/null
+++ b/coreplugins/QuickFind/src/main/java/csplugins/quickfind/plugin/package.html
@@ -0,0 +1,8 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+<html>
+<head></head>
+
+<body bgcolor="white">
+Cytoscape QuickFind PlugIn.
+</body>
+</html>
diff --git a/coreplugins/QuickFind/src/main/java/csplugins/quickfind/util/CyAttributesUtil.java b/coreplugins/QuickFind/src/main/java/csplugins/quickfind/util/CyAttributesUtil.java
new file mode 100644
index 0000000..5250f7c
--- /dev/null
+++ b/coreplugins/QuickFind/src/main/java/csplugins/quickfind/util/CyAttributesUtil.java
@@ -0,0 +1,188 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package csplugins.quickfind.util;
+
+import cytoscape.data.CyAttributes;
+
+import giny.model.GraphObject;
+
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+
+
+/**
+ * A set of Misc. Utility Methods for Accesssing CyAttribute data.
+ *
+ * @author Ethan Cerami
+ */
+public class CyAttributesUtil {
+ /**
+ * Regardless of attribute type, this method will always return attribute
+ * values as an array of String objects. For example, given an attribute of
+ * type: CyAttributes.TYPE_INTEGER with a single value = 25, this method
+ * will return an array of size 1 = ["25"]. The method will return null if
+ * no attribute value is found, or if the attribute is of type
+ * {@link CyAttributes#TYPE_COMPLEX}.
+ *
+ * @param attributes CyAttributes Object.
+ * @param graphObjectId Graph Object ID.
+ * @param attributeKey Attribute Key.
+ * @return array of String Objects or null.
+ */
+ public static String[] getAttributeValues(CyAttributes attributes, String graphObjectId,
+ String attributeKey) {
+ String[] terms = new String[1];
+
+ if (attributeKey.equals(QuickFind.UNIQUE_IDENTIFIER)) {
+ terms[0] = graphObjectId;
+ } else {
+ boolean hasAttribute = attributes.hasAttribute(graphObjectId, attributeKey);
+
+ if (hasAttribute) {
+ // Convert all types to String array.
+ byte type = attributes.getType(attributeKey);
+
+ if (type == CyAttributes.TYPE_BOOLEAN) {
+ terms[0] = attributes.getBooleanAttribute(graphObjectId, attributeKey).toString();
+ } else if (type == CyAttributes.TYPE_INTEGER) {
+ terms[0] = attributes.getIntegerAttribute(graphObjectId, attributeKey).toString();
+ } else if (type == CyAttributes.TYPE_FLOATING) {
+ terms[0] = attributes.getDoubleAttribute(graphObjectId, attributeKey).toString();
+ } else if (type == CyAttributes.TYPE_STRING) {
+ terms[0] = attributes.getStringAttribute(graphObjectId, attributeKey);
+ } else if (type == CyAttributes.TYPE_SIMPLE_LIST) {
+ List list = attributes.getListAttribute(graphObjectId, attributeKey);
+
+ // Iterate through all elements in the list
+ if ((list != null) && (list.size() > 0)) {
+ terms = new String[list.size()];
+
+ for (int i = 0; i < list.size(); i++) {
+ Object o = list.get(i);
+ terms[i] = o.toString();
+ }
+ }
+ } else if (type == CyAttributes.TYPE_SIMPLE_MAP) {
+ Map map = attributes.getMapAttribute(graphObjectId, attributeKey);
+
+ // Iterate through all values in the map
+ if ((map != null) && (map.size() > 0)) {
+ terms = new String[map.size()];
+
+ Iterator mapIterator = map.values().iterator();
+ int index = 0;
+
+ while (mapIterator.hasNext()) {
+ Object o = mapIterator.next();
+ terms[index++] = o.toString();
+ }
+ }
+ } else if (type == CyAttributes.TYPE_COMPLEX) {
+ return null;
+ }
+ } else {
+ return null;
+ }
+ }
+
+ // Remove all new line chars
+ for (int i = 0; i < terms.length; i++) {
+ terms[i] = terms[i].replaceAll("\n", " ");
+ }
+
+ return terms;
+ }
+
+ /**
+ * Method returns the first X distinct attribute values.
+ *
+ * @param iterator Iterator of nodes or edges.
+ * @param attributes Node or Edge Attributes.
+ * @param attributeKey Attribute Key.
+ * @param numDistinctValues Number of Distinct Values.
+ * @return Array of Distinct Value Strings.
+ */
+ public static String[] getDistinctAttributeValues(Iterator iterator, CyAttributes attributes,
+ String attributeKey, int numDistinctValues) {
+ HashSet set = new HashSet();
+ int counter = 0;
+
+ while (iterator.hasNext() && (counter < numDistinctValues)) {
+ GraphObject graphObject = (GraphObject) iterator.next();
+ String[] values = CyAttributesUtil.getAttributeValues(attributes,
+ graphObject.getIdentifier(),
+ attributeKey);
+
+ if ((values != null) && (values.length > 0)) {
+ String singleStr = join(values);
+
+ if (!set.contains(singleStr)) {
+ set.add(singleStr);
+ counter++;
+ }
+ }
+ }
+
+ if (set.size() > 0) {
+ return (String[]) set.toArray(new String[0]);
+ } else {
+ return null;
+ }
+ }
+
+ /**
+ * Joins a list of Strings with ,
+ *
+ * @param values Array of String Objects.
+ * @return One string with each value separate by a comma.
+ */
+ private static String join(String[] values) {
+ StringBuffer buf = new StringBuffer();
+
+ for (int i = 0; i < values.length; i++) {
+ buf.append(values[i]);
+
+ if (i < (values.length - 1)) {
+ buf.append(", ");
+ }
+ }
+
+ return buf.toString();
+ }
+}
diff --git a/coreplugins/QuickFind/src/main/java/csplugins/quickfind/util/IndexType.java b/coreplugins/QuickFind/src/main/java/csplugins/quickfind/util/IndexType.java
new file mode 100644
index 0000000..4a26fe3
--- /dev/null
+++ b/coreplugins/QuickFind/src/main/java/csplugins/quickfind/util/IndexType.java
@@ -0,0 +1,77 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package csplugins.quickfind.util;
+
+
+/**
+ * IndexType Type.
+ * <p/>
+ * Used to indicate whether we are currently indexing nodes or edges.
+ *
+ * @author Ethan Cerami.
+ */
+public class IndexType {
+ private String name;
+
+ /**
+ * Private Constructor. Enumeration Pattern.
+ *
+ * @param name Type Name.
+ */
+ private IndexType(String name) {
+ this.name = name;
+ }
+
+ /**
+ * Gets Type Name.
+ *
+ * @return Type Name.
+ */
+ public String toString() {
+ return name;
+ }
+
+ /**
+ * IndexType Type: NODE_INDEX.
+ */
+ public static final IndexType NODE_INDEX = new IndexType("NODE_INDEX");
+
+ /**
+ * IndexType Type: EDGE_INDEX.
+ */
+ public static final IndexType EDGE_INDEX = new IndexType("EDGE_INDEX");
+}
diff --git a/coreplugins/QuickFind/src/main/java/csplugins/quickfind/util/QuickFind.java b/coreplugins/QuickFind/src/main/java/csplugins/quickfind/util/QuickFind.java
new file mode 100644
index 0000000..3ad5103
--- /dev/null
+++ b/coreplugins/QuickFind/src/main/java/csplugins/quickfind/util/QuickFind.java
@@ -0,0 +1,233 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package csplugins.quickfind.util;
+
+import csplugins.widgets.autocomplete.index.GenericIndex;
+import csplugins.widgets.autocomplete.index.Hit;
+
+import cytoscape.CyNetwork;
+
+import cytoscape.task.TaskMonitor;
+
+
+/**
+ * Cytoscape Quick Find.
+ * <p/>
+ * The Cytoscape Quick Find class provides a convenient utility class for
+ * quickly searching nodes or edges by any attribute.
+ * <p/>
+ * The following example illustrates the utility of this class. To begin,
+ * consider that network 1 is defined by the following SIF File:
+ * <br/>
+ * <pre>
+ * YKR026C pp YGL122C
+ * YGR218W pp YGL097W
+ * YGL097W pp YOR204W
+ * YLR249W pp YPR080W
+ * YLR249W pp YBR118W
+ * YLR293C pp YGL097W
+ * </pre>
+ * After this network is loaded, it can be automatically added to the quick
+ * find index via the
+ * {@link QuickFind#addNetwork(cytoscape.CyNetwork, cytoscape.task.TaskMonitor)}
+ * method. By default, this method iterates through each node in the network,
+ * and indexes each node by its unique identifier, e.g. node.getIdentifier().
+ * <p/>
+ * A few minutes later, the end-user enters the String: "YLR" in the Cytoscape
+ * quick search box, and we want to quickly find all matching nodes that begin
+ * with this prefix.
+ * <p/>
+ * To do so, we must first obtain the text index associated with this network
+ * via the
+ * {@link QuickFind#getIndex(cytoscape.CyNetwork)} method. For example:
+ * <BR/>
+ * <PRE>
+ * CyNetwork currentNetwork = Cytoscape.getCurrentNetwork();
+ * TextIndex textIndex = QuickFind.getIndex (currentNetwork);
+ * </PRE>
+ * We can then retrieve all hits that begin with the prefix: "YLR" via the
+ * {@link csplugins.widgets.autocomplete.index.TextIndex#getHits(String, int)}
+ * method.
+ * <BR/>
+ * <PRE>
+ * Hit hits[] = textIndex.getHits ("YLR");
+ * </PRE>
+ * Technical Details:
+ * <UL>
+ * <LI>By default, this class will automatically index node objects based on the
+ * their unique node identifier, e.g. node.getIdentifier().</LI>
+ * <LI>You can index by a different attribute by calling the
+ * {@link QuickFind#reindexNetwork(CyNetwork, int, String,
+ * cytoscape.task.TaskMonitor)}.
+ * <LI>You can specify any attribute name you like. However, QuickFind
+ * is not yet capable of indexing attributes of type CyAttributes.TYPE_COMPLEX.
+ * <LI>QuickFind uses a {@link csplugins.widgets.autocomplete.index.Trie}
+ * data structure for very fast look-ups.</LI>
+ * </UL>
+ * <p/>
+ *
+ * @author Ethan Cerami.
+ */
+public interface QuickFind {
+ /**
+ * Index Nodes
+ */
+ int INDEX_NODES = 0;
+
+ /**
+ * Index Edges
+ */
+ int INDEX_EDGES = 1;
+
+ /**
+ * Node / Edge Unique Identifier.
+ */
+ String UNIQUE_IDENTIFIER = "Unique Identifier";
+
+ /**
+ * Index all attributes.
+ */
+ String INDEX_ALL_ATTRIBUTES = "[ Index all attributes ]";
+
+ /**
+ * Network attribute, used to set default index.
+ */
+ String DEFAULT_INDEX = "quickfind.default_index";
+
+ /**
+ * Adds a new network to the global index, and indexes all nodes
+ * described by this network.
+ * <P>By default, this class will first determine if the network includes
+ * a default index setting. It does so by determining if the network
+ * has a network attribute named: quickfind.default_index. For
+ * example, if you would like your network to be indexed by
+ * "biopax.short_name" by default, you would use the following code:
+ *
+ * <P>
+ * <CODE>
+ * CyAttributes networkAttributes = Cytoscape.getNetworkAttributes();
+ * <BR>networkAttributes.setAttribute(cyNetwork.getIdentifier(),
+ * "quickfind.default_index", "biopax.short_name");
+ * </CODE>
+ *
+ * <P>If no default index is found, this class will automatically
+ * index node objects based on their unique identifier,
+ * e.g. node.getIdentifier().
+ *
+ * @param network Cytoscape Network.
+ * @param taskMonitor TaskMonitor Object.
+ */
+ void addNetwork(CyNetwork network, TaskMonitor taskMonitor);
+
+ /**
+ * Removes the specified network from the global index.
+ * <p/>
+ * To free up memory, this method should be called whenever a network
+ * is destroyed.
+ *
+ * @param network CyNetwork Object.
+ */
+ void removeNetwork(CyNetwork network);
+
+ /**
+ * Gets the index associated with the specified network.
+ *
+ * @param network Cytoscape Network.
+ * @return Index Object.
+ */
+ GenericIndex getIndex(CyNetwork network);
+
+ /**
+ * Reindexes a network with the specified controlling attribute.
+ * <p/>
+ * This method will iterate through all nodes/edges within the
+ * registered network, and add each node/edge to the text index.
+ * For each node/edge, the attribute specified will be used to create the
+ * text index.
+ * <p/>For example, if you want to index all nodes by their
+ * "BIOPAX_NAME" attribute, you would use this code:
+ * <br/>
+ * <pre>reindexNetwork (cyNetwork, QuickFind.INDEX_NODES, "BIOPAX_NAME", tm);</pre>
+ *
+ * @param cyNetwork Cytoscape network.
+ * @param indexType INDEX_NODES or INDEX_EDGES.
+ * @param controllingAttribute Attribute used to index all nodes.
+ * @param taskMonitor Task Monitor, used to monitor long-term
+ * progress of task.
+ * @return GenericIndex Object.
+ */
+ GenericIndex reindexNetwork(CyNetwork cyNetwork, int indexType, String controllingAttribute,
+ TaskMonitor taskMonitor);
+
+ /**
+ * Select a specific text item in QuickFind.
+ *
+ * @param network the current CyNetwork.
+ * @param hit Hit chosen by the user.
+ */
+ void selectHit(CyNetwork network, Hit hit);
+
+ /**
+ * Select a range in QuickFind.
+ *
+ * @param network the current CyNetwork.
+ * @param low the low value of the range.
+ * @param high the high value of the range.
+ */
+ void selectRange(CyNetwork network, Number low, Number high);
+
+ /**
+ * Adds a new QuickFind Listener.
+ *
+ * @param listener QuickFindListener Object.
+ */
+ void addQuickFindListener(QuickFindListener listener);
+
+ /**
+ * Removes the specified QuickFind Listener Object.
+ *
+ * @param listener QuickFindListener Object.
+ */
+ void removeQuickFindListener(QuickFindListener listener);
+
+ /**
+ * Gets an array of all registered QuickFind Listener Objects.
+ *
+ * @return Array of QuickFindListener Objects.
+ */
+ QuickFindListener[] getQuickFindListeners();
+}
diff --git a/coreplugins/QuickFind/src/main/java/csplugins/quickfind/util/QuickFindFactory.java b/coreplugins/QuickFind/src/main/java/csplugins/quickfind/util/QuickFindFactory.java
new file mode 100644
index 0000000..7255a0a
--- /dev/null
+++ b/coreplugins/QuickFind/src/main/java/csplugins/quickfind/util/QuickFindFactory.java
@@ -0,0 +1,63 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package csplugins.quickfind.util;
+
+import cytoscape.Cytoscape;
+
+
+/**
+ * Factory for Creating QuickFind Classes.
+ *
+ * @author Ethan Cerami.
+ */
+public class QuickFindFactory {
+ private static QuickFind quickFind;
+
+ /**
+ * Gets instance of Global QuickFind Singleton.
+ *
+ * @return Global QuickFind Class.
+ */
+ public static QuickFind getGlobalQuickFindInstance() {
+ if (quickFind == null) {
+ quickFind = new QuickFindImpl(Cytoscape.getNodeAttributes(),
+ Cytoscape.getEdgeAttributes());
+ }
+
+ return quickFind;
+ }
+}
diff --git a/coreplugins/QuickFind/src/main/java/csplugins/quickfind/util/QuickFindImpl.java b/coreplugins/QuickFind/src/main/java/csplugins/quickfind/util/QuickFindImpl.java
new file mode 100644
index 0000000..3da9aa1
--- /dev/null
+++ b/coreplugins/QuickFind/src/main/java/csplugins/quickfind/util/QuickFindImpl.java
@@ -0,0 +1,482 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package csplugins.quickfind.util;
+
+import csplugins.widgets.autocomplete.index.GenericIndex;
+import csplugins.widgets.autocomplete.index.Hit;
+import csplugins.widgets.autocomplete.index.IndexFactory;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import cytoscape.CyNode;
+
+import cytoscape.data.CyAttributes;
+
+import cytoscape.task.TaskMonitor;
+
+import giny.model.GraphObject;
+
+import java.util.ArrayList;
+import java.util.Date;
+import java.util.HashMap;
+import java.util.Iterator;
+// import cytoscape.data.CyAttributesUtils;
+
+
+/**
+ * Default implementation of the QuickFind interface. For details, see
+ * {@link QuickFind}.
+ *
+ * @author Ethan Cerami.
+ */
+class QuickFindImpl implements QuickFind {
+ private ArrayList listenerList = new ArrayList();
+ private HashMap networkMap = new HashMap();
+ private CyAttributes nodeAttributes;
+ private CyAttributes edgeAttributes;
+ private int maxProgress;
+ private int currentProgress;
+ private static final boolean OUTPUT_PERFORMANCE_STATS = false;
+
+ /**
+ * Creates a new QuickFindImpl object.
+ *
+ * @param nodeAttributes DOCUMENT ME!
+ * @param edgeAttributes DOCUMENT ME!
+ */
+ public QuickFindImpl(CyAttributes nodeAttributes, CyAttributes edgeAttributes) {
+ this.nodeAttributes = nodeAttributes;
+ this.edgeAttributes = edgeAttributes;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param network DOCUMENT ME!
+ * @param taskMonitor DOCUMENT ME!
+ */
+ public synchronized void addNetwork(CyNetwork network, TaskMonitor taskMonitor) {
+ // check args - short circuit if necessary
+ if (network.getNodeCount() == 0) {
+ return;
+ }
+
+ // We need to update our node and edge attributes if the network changes
+ nodeAttributes = Cytoscape.getNodeAttributes();
+ edgeAttributes = Cytoscape.getEdgeAttributes();
+
+ // Use default index specified by network, if available.
+ // Otherwise, index by UNIQUE_IDENTIFIER.
+ String controllingAttribute = null;
+ CyAttributes networkAttributes = Cytoscape.getNetworkAttributes();
+
+ if (networkAttributes != null) {
+ controllingAttribute = networkAttributes.getStringAttribute(network.getIdentifier(),
+ QuickFind.DEFAULT_INDEX);
+ }
+
+ if (controllingAttribute == null) {
+ // Small hack to index BioPAX Networks by default with node_label.
+
+ Iterator nodesIterator = network.nodesIterator();
+ if (nodesIterator.hasNext())
+ {
+ CyNode node = (CyNode) nodesIterator.next();
+ String bioPaxFlag = nodeAttributes.getStringAttribute
+ (node.getIdentifier(), "biopax.node_label");
+ if (bioPaxFlag != null) {
+ controllingAttribute = "biopax.node_label";
+ } else {
+ controllingAttribute = QuickFind.UNIQUE_IDENTIFIER;
+ }
+ }
+ }
+
+ if (controllingAttribute.equalsIgnoreCase(QuickFind.UNIQUE_IDENTIFIER)||
+ controllingAttribute.equalsIgnoreCase(QuickFind.INDEX_ALL_ATTRIBUTES)||
+ controllingAttribute.equalsIgnoreCase("biopax.node_label")){
+ // do nothing
+ }
+ else if (cytoscape.data.CyAttributesUtils.isNullAttribute("node", controllingAttribute)){
+ return;
+ }
+
+ // Determine maxProgress
+ currentProgress = 0;
+ maxProgress = getGraphObjectCount(network, QuickFind.INDEX_NODES);
+
+ // Notify all listeners of add event
+ for (int i = 0; i < listenerList.size(); i++) {
+ QuickFindListener listener = (QuickFindListener) listenerList.get(i);
+ listener.networkAddedToIndex(network);
+ }
+
+ // Notify all listeners of index start event
+ for (int i = 0; i < listenerList.size(); i++) {
+ QuickFindListener listener = (QuickFindListener) listenerList.get(i);
+ listener.indexingStarted(network, QuickFind.INDEX_NODES, controllingAttribute);
+ }
+
+ // Create Appropriate Index Type, based on attribute type.
+ int attributeType = nodeAttributes.getType(controllingAttribute);
+ GenericIndex index = createIndex(QuickFind.INDEX_NODES, attributeType, controllingAttribute);
+ indexNetwork(network, QuickFind.INDEX_NODES, nodeAttributes, attributeType,
+ controllingAttribute, index, taskMonitor);
+ networkMap.put(network, index);
+
+ // Notify all listeners of end index event
+ for (int i = 0; i < listenerList.size(); i++) {
+ QuickFindListener listener = (QuickFindListener) listenerList.get(i);
+ listener.indexingEnded();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param network DOCUMENT ME!
+ */
+ public synchronized void removeNetwork(CyNetwork network) {
+ if (networkMap.containsKey(network)){
+ networkMap.remove(networkMap);
+ }
+
+ // Notify all listeners of remove event
+ for (int i = 0; i < listenerList.size(); i++) {
+ QuickFindListener listener = (QuickFindListener) listenerList.get(i);
+ listener.networkRemovedfromIndex(network);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param network DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public synchronized GenericIndex getIndex(CyNetwork network) {
+ if (networkMap.containsKey(network)){
+ return (GenericIndex) networkMap.get(network);
+ }
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param cyNetwork DOCUMENT ME!
+ * @param indexType DOCUMENT ME!
+ * @param controllingAttribute DOCUMENT ME!
+ * @param taskMonitor DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public synchronized GenericIndex reindexNetwork(CyNetwork cyNetwork, int indexType,
+ String controllingAttribute,
+ TaskMonitor taskMonitor) {
+
+ // If all the values for the controllingAttribute are NULL, return null
+ String _type = "node";
+ if (indexType == QuickFind.INDEX_EDGES){
+ _type = "edge";
+ }
+
+ if (controllingAttribute.equalsIgnoreCase(QuickFind.UNIQUE_IDENTIFIER)||
+ controllingAttribute.equalsIgnoreCase(QuickFind.INDEX_ALL_ATTRIBUTES)||
+ controllingAttribute.equalsIgnoreCase("biopax.node_label")){
+ // do nothing
+ }
+ else if (cytoscape.data.CyAttributesUtils.isNullAttribute(_type, controllingAttribute)){
+ return null;
+ }
+
+ //
+ Date start = new Date();
+ if ((indexType != QuickFind.INDEX_NODES) && (indexType != QuickFind.INDEX_EDGES)) {
+ throw new IllegalArgumentException("indexType must be set to: "
+ + "QuickFind.INDEX_NODES or QuickFind.INDEX_EDGES");
+ }
+
+ // Notify all listeners of index start event
+ for (int i = 0; i < listenerList.size(); i++) {
+ QuickFindListener listener = (QuickFindListener) listenerList.get(i);
+ listener.indexingStarted(cyNetwork, indexType, controllingAttribute);
+ }
+
+ // Determine maxProgress
+ currentProgress = 0;
+ maxProgress = 0;
+
+ CyAttributes attributes;
+
+ if (indexType == QuickFind.INDEX_NODES) {
+ attributes = nodeAttributes;
+ } else {
+ attributes = edgeAttributes;
+ }
+
+ if (controllingAttribute.equals(QuickFind.INDEX_ALL_ATTRIBUTES)) {
+ String[] attributeNames = attributes.getAttributeNames();
+
+ for (int i = 0; i < attributeNames.length; i++) {
+ if (attributes.getUserVisible(attributeNames[i])) {
+ maxProgress += getGraphObjectCount(cyNetwork, indexType);
+ }
+ }
+ } else {
+ maxProgress = getGraphObjectCount(cyNetwork, indexType);
+ }
+
+ GenericIndex index = null;
+
+ if (controllingAttribute.equals(QuickFind.INDEX_ALL_ATTRIBUTES)) {
+ // Option 1: Index all attributes
+ index = createIndex(indexType, CyAttributes.TYPE_STRING, controllingAttribute);
+
+ String[] attributeNames = attributes.getAttributeNames();
+
+ for (int i = 0; i < attributeNames.length; i++) {
+ if (attributes.getUserVisible(attributeNames[i])) {
+ indexNetwork(cyNetwork, indexType, attributes, CyAttributes.TYPE_STRING,
+ attributeNames[i], index, taskMonitor);
+ }
+ }
+ } else {
+ // Option 2: Index single attribute.
+ // Create appropriate index type, based on attribute type.
+ int attributeType = attributes.getType(controllingAttribute);
+ index = createIndex(indexType, attributeType, controllingAttribute);
+ indexNetwork(cyNetwork, indexType, attributes, attributeType, controllingAttribute,
+ index, taskMonitor);
+ }
+
+ networkMap.put(cyNetwork, index);
+
+ // Notify all listeners of index end event
+ for (int i = 0; i < listenerList.size(); i++) {
+ QuickFindListener listener = (QuickFindListener) listenerList.get(i);
+ listener.indexingEnded();
+ }
+
+ Date stop = new Date();
+ long duration = stop.getTime() - start.getTime();
+ // System.out.println("Time to re-index: " + duration + " ms");
+ return index;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param network DOCUMENT ME!
+ * @param hit DOCUMENT ME!
+ */
+ public synchronized void selectHit(CyNetwork network, Hit hit) {
+ // Notify all listeners of event
+ for (int i = 0; i < listenerList.size(); i++) {
+ QuickFindListener listener = (QuickFindListener) listenerList.get(i);
+ listener.onUserSelection(network, hit);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param network DOCUMENT ME!
+ * @param low DOCUMENT ME!
+ * @param high DOCUMENT ME!
+ */
+ public synchronized void selectRange(CyNetwork network, Number low, Number high) {
+ // Notify all listeners of event
+ for (int i = 0; i < listenerList.size(); i++) {
+ QuickFindListener listener = (QuickFindListener) listenerList.get(i);
+ listener.onUserRangeSelection(network, low, high);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param listener DOCUMENT ME!
+ */
+ public synchronized void addQuickFindListener(QuickFindListener listener) {
+ this.listenerList.add(listener);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param listener DOCUMENT ME!
+ */
+ public synchronized void removeQuickFindListener(QuickFindListener listener) {
+ this.listenerList.remove(listener);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public synchronized QuickFindListener[] getQuickFindListeners() {
+ return (QuickFindListener[]) listenerList.toArray(new QuickFindListener[listenerList.size()]);
+ }
+
+ private synchronized int getGraphObjectCount(CyNetwork network, int indexType) {
+ if (indexType == QuickFind.INDEX_NODES) {
+ return network.getNodeCount();
+ } else {
+ return network.getEdgeCount();
+ }
+ }
+
+ private void indexNetwork(CyNetwork network, int indexType, CyAttributes attributes,
+ int attributeType, String controllingAttribute, GenericIndex index,
+ TaskMonitor taskMonitor) {
+
+ //
+ Date start = new Date();
+ Iterator iterator;
+
+ if (indexType == QuickFind.INDEX_NODES) {
+ taskMonitor.setStatus("Indexing node attributes");
+ iterator = network.nodesIterator();
+ } else if (indexType == QuickFind.INDEX_EDGES) {
+ taskMonitor.setStatus("Indexing edge attributes");
+ iterator = network.edgesIterator();
+ } else {
+ throw new IllegalArgumentException("indexType must be set to: "
+ + "QuickFind.INDEX_NODES or QuickFind.INDEX_EDGES");
+ }
+
+ // Iterate through all nodes or edges
+ while (iterator.hasNext()) {
+ currentProgress++;
+
+ GraphObject graphObject = (GraphObject) iterator.next();
+ addToIndex(attributeType, attributes, graphObject, controllingAttribute, index);
+
+ // Determine percent complete
+ int percentComplete = 100 * (int) (currentProgress / (double) maxProgress);
+ taskMonitor.setPercentCompleted(percentComplete);
+ }
+
+ Date stop = new Date();
+ long interval = stop.getTime() - start.getTime();
+
+ if (OUTPUT_PERFORMANCE_STATS) {
+ System.out.println("Time to index network: " + interval + " ms");
+ }
+
+ networkMap.put(network, index);
+ }
+
+ /**
+ * Creates appropriate index, based on attribute type.
+ * @param indexType QuickFind.INDEX_NODES or QuickFind.INDEX_EDGES
+ * @param attributeType CyAttributes type.
+ * @param controllingAttribute Controlling attribute.
+ * @return GenericIndex Object.
+ */
+ private GenericIndex createIndex(int indexType, int attributeType, String controllingAttribute) {
+ GenericIndex index;
+
+ // If all the values for the controllingAttribute are NULL, return null
+ String _type = "node";
+ if (indexType == QuickFind.INDEX_EDGES){
+ _type = "edge";
+ }
+ //
+ if ((attributeType == CyAttributes.TYPE_INTEGER)
+ || (attributeType == CyAttributes.TYPE_FLOATING)) {
+ index = IndexFactory.createDefaultNumberIndex(indexType);
+ } else {
+ index = IndexFactory.createDefaultTextIndex(indexType);
+ }
+
+ index.setControllingAttribute(controllingAttribute);
+
+ return index;
+ }
+
+ /**
+ * Adds new items to index.
+ * @param attributeType CyAttributes type.
+ * @param graphObject Graph Object.
+ * @param controllingAttribute Controlling attribute.
+ * @param index Index to add to.
+ */
+ private void addToIndex(int attributeType, CyAttributes attributes, GraphObject graphObject,
+ String controllingAttribute, GenericIndex index) {
+ // Get attribute values, and index
+ if (attributeType == CyAttributes.TYPE_INTEGER) {
+ Integer value = attributes.getIntegerAttribute(graphObject.getIdentifier(),
+ controllingAttribute);
+
+ if (value != null) {
+ index.addToIndex(value, graphObject);
+ }
+ } else if (attributeType == CyAttributes.TYPE_FLOATING) {
+ Double value = attributes.getDoubleAttribute(graphObject.getIdentifier(),
+ controllingAttribute);
+
+ if (value != null) {
+ index.addToIndex(value, graphObject);
+ }
+ } else {
+ String[] values = CyAttributesUtil.getAttributeValues(attributes,
+ graphObject.getIdentifier(),
+ controllingAttribute);
+
+ if (values != null) {
+ addStringsToIndex(values, graphObject, index);
+ }
+ }
+ }
+
+ /**
+ * Adds multiple strings to an index.
+ * @param value Array of Strings.
+ * @param graphObject Graph Object.
+ * @param index Index to add to.
+ */
+ private void addStringsToIndex(String[] value, GraphObject graphObject, GenericIndex index) {
+ // Add to index
+ for (int i = 0; i < value.length; i++) {
+ index.addToIndex(value[i], graphObject);
+ }
+ }
+}
diff --git a/coreplugins/QuickFind/src/main/java/csplugins/quickfind/util/QuickFindListener.java b/coreplugins/QuickFind/src/main/java/csplugins/quickfind/util/QuickFindListener.java
new file mode 100644
index 0000000..b110561
--- /dev/null
+++ b/coreplugins/QuickFind/src/main/java/csplugins/quickfind/util/QuickFindListener.java
@@ -0,0 +1,96 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package csplugins.quickfind.util;
+
+import csplugins.widgets.autocomplete.index.Hit;
+
+import cytoscape.CyNetwork;
+
+
+/**
+ * Quick Find Listener Interface.
+ *
+ * @author Ethan Cerami.
+ */
+public interface QuickFindListener {
+ /**
+ * Network has been added to the Quick Find Index.
+ *
+ * @param network CyNetwork Object.
+ */
+ void networkAddedToIndex(CyNetwork network);
+
+ /**
+ * Network has been removed from the Quick Find Index.
+ *
+ * @param network CyNetwork Object.
+ */
+ void networkRemovedfromIndex(CyNetwork network);
+
+ /**
+ * Indexing started.
+ *
+ * @param cyNetwork CyNetwork.
+ * @param indexType QuickFind.INDEX_NODES or QuickFind.INDEX_EDGES.
+ * @param controllingAttribute Controlling Attribute.
+ */
+ void indexingStarted(CyNetwork cyNetwork, int indexType, String controllingAttribute);
+
+ /**
+ * Indexing operation ended.
+ */
+ void indexingEnded();
+
+ /**
+ * Indicates that the user has selected a hit within the QuickFind
+ * search box.
+ *
+ * @param network the current CyNetwork.
+ * @param hit hit value chosen by the user.
+ */
+ void onUserSelection(CyNetwork network, Hit hit);
+
+ /**
+ * Indicates that the user has selected a range within the QuickFind
+ * range selector.
+ *
+ * @param network the current CyNetwork.
+ * @param low the low value of the range.
+ * @param high the high value of the range.
+ */
+ void onUserRangeSelection(CyNetwork network, Number low, Number high);
+}
diff --git a/coreplugins/QuickFind/src/main/java/csplugins/quickfind/util/TaskMonitorBase.java b/coreplugins/QuickFind/src/main/java/csplugins/quickfind/util/TaskMonitorBase.java
new file mode 100644
index 0000000..a3579aa
--- /dev/null
+++ b/coreplugins/QuickFind/src/main/java/csplugins/quickfind/util/TaskMonitorBase.java
@@ -0,0 +1,121 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package csplugins.quickfind.util;
+
+import cytoscape.task.TaskMonitor;
+
+
+/**
+ * Task Monitor Stub.
+ *
+ * @author Ethan Cerami
+ */
+public class TaskMonitorBase implements TaskMonitor {
+ private String status;
+ private int percentComplete;
+
+ /**
+ * Sets Percent Completed.
+ *
+ * @param percentComplete Percent Completed.
+ * @throws IllegalThreadStateException Illegal Thread State.
+ * @throws IllegalArgumentException Illegal Argument.
+ */
+ public void setPercentCompleted(int percentComplete)
+ throws IllegalThreadStateException, IllegalArgumentException {
+ this.percentComplete = percentComplete;
+ }
+
+ /**
+ * Sets estimated time remaining: no-op.
+ *
+ * @param l time remaining.
+ * @throws IllegalThreadStateException Illegal Thread State.
+ */
+ public void setEstimatedTimeRemaining(long l) throws IllegalThreadStateException {
+ }
+
+ /**
+ * Sets Exception: no-op.
+ *
+ * @param throwable Throwable Object.
+ * @param string Human readable error message.
+ * @throws IllegalThreadStateException Illegal Thread State.
+ */
+ public void setException(Throwable throwable, String string) throws IllegalThreadStateException {
+ }
+
+ /**
+ * Sets Exception: no-op.
+ *
+ * @param throwable Throwable Object.
+ * @param str1 Human readable error message.
+ * @param str2 Recovery Tip.
+ */
+ public void setException(Throwable throwable, String str1, String str2)
+ throws IllegalThreadStateException {
+ }
+
+ /**
+ * Sets Status: no-op.
+ *
+ * @param status Status Message.
+ * @throws IllegalThreadStateException Illegal Thread State.
+ * @throws NullPointerException NullPointer Error.
+ */
+ public void setStatus(String status) throws IllegalThreadStateException, NullPointerException {
+ this.status = status;
+ }
+
+ /**
+ * Gets Status.
+ *
+ * @return Status Message.
+ */
+ public String getStatus() {
+ return status;
+ }
+
+ /**
+ * Gets Percent Complete.
+ *
+ * @return percent complete.
+ */
+ public int getPercentComplete() {
+ return percentComplete;
+ }
+}
diff --git a/coreplugins/QuickFind/src/main/java/csplugins/quickfind/util/package.html b/coreplugins/QuickFind/src/main/java/csplugins/quickfind/util/package.html
new file mode 100644
index 0000000..8b17ca4
--- /dev/null
+++ b/coreplugins/QuickFind/src/main/java/csplugins/quickfind/util/package.html
@@ -0,0 +1,8 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+<html>
+<head></head>
+
+<body bgcolor="white">
+Core Utility Classes for the Cytoscape QuickFind Functionality.
+</body>
+</html>
diff --git a/coreplugins/QuickFind/src/main/java/csplugins/quickfind/view/QuickFindConfigDialog.java b/coreplugins/QuickFind/src/main/java/csplugins/quickfind/view/QuickFindConfigDialog.java
new file mode 100644
index 0000000..fd7e47e
--- /dev/null
+++ b/coreplugins/QuickFind/src/main/java/csplugins/quickfind/view/QuickFindConfigDialog.java
@@ -0,0 +1,714 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package csplugins.quickfind.view;
+
+import csplugins.quickfind.util.*;
+
+import csplugins.widgets.autocomplete.index.GenericIndex;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+
+import cytoscape.data.CyAttributes;
+import cytoscape.data.Semantics;
+
+import cytoscape.task.Task;
+import cytoscape.task.TaskMonitor;
+
+import cytoscape.task.ui.JTaskConfig;
+
+import cytoscape.task.util.TaskManager;
+
+import java.awt.*;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import java.util.Collections;
+import java.util.Iterator;
+import java.util.Vector;
+
+import javax.swing.*;
+import javax.swing.border.EmptyBorder;
+import javax.swing.border.TitledBorder;
+import javax.swing.table.DefaultTableModel;
+import javax.swing.table.TableModel;
+
+
+/**
+ * Quick Find Config Dialog Box.
+ *
+ * @author Ethan Cerami.
+ */
+public class QuickFindConfigDialog extends JDialog {
+ /**
+ * Attribute ComboBox
+ */
+ private JComboBox attributeComboBox;
+
+ /**
+ * Table of Sample Attribute Values
+ */
+ private JTable sampleAttributeValuesTable;
+
+ /**
+ * Attribute description text area.
+ */
+ private JTextArea attributeDescriptionBox;
+
+ /**
+ * Current Network
+ */
+ private CyNetwork currentNetwork;
+
+ /**
+ * Current Index
+ */
+ private GenericIndex currentIndex;
+
+ /**
+ * Index Type.
+ */
+ private int indexType;
+
+ /**
+ * Apply Text.
+ */
+ private static final String BUTTON_INDEX_TEXT = "Apply";
+
+ /**
+ * Reindex Text.
+ */
+ private static final String BUTTON_REINDEX_TEXT = "Apply";
+
+ /**
+ * Apply Button.
+ */
+ private JButton applyButton;
+
+ /**
+ * Flag to indicate that we are currently adding new attributes.
+ */
+ private boolean addingNewAttributeList = false;
+
+ /**
+ * Constructor.
+ */
+ public QuickFindConfigDialog() {
+ // Initialize, based on currently selected network
+ currentNetwork = Cytoscape.getCurrentNetwork();
+
+ QuickFind quickFind = QuickFindFactory.getGlobalQuickFindInstance();
+ currentIndex = quickFind.getIndex(currentNetwork);
+ indexType = currentIndex.getIndexType();
+
+ Container container = getContentPane();
+ container.setLayout(new BoxLayout(container, BoxLayout.Y_AXIS));
+ this.setTitle("Configure Search Options for: " + currentNetwork.getTitle());
+
+ // If we are working on Linux, set always on top to true.
+ // This is a hack to deal with numerous z-ordering bugs on Linux.
+ String os = System.getProperty("os.name");
+
+ if (os != null) {
+ if (os.toLowerCase().startsWith("linux")) {
+ this.setAlwaysOnTop(true);
+ }
+ }
+
+ // Create Master Panel
+ JPanel masterPanel = new JPanel();
+ masterPanel.setBorder(new EmptyBorder(10, 10, 10, 10));
+ masterPanel.setLayout(new BoxLayout(masterPanel, BoxLayout.Y_AXIS));
+
+ // Add Node/Edge Selection Panel
+ JPanel nodeEdgePanel = createNodeEdgePanel();
+ masterPanel.add(nodeEdgePanel);
+
+ // Add Attribute ComboBox Panel
+ JPanel attributePanel = createAttributeSelectionPanel();
+ masterPanel.add(attributePanel);
+
+ // Add Attribute Description Panel
+ JPanel attributeDescriptionPanel = createAttributeDescriptionPanel();
+ masterPanel.add(attributeDescriptionPanel);
+
+ // Add Sample Attribute Values Panel
+ JPanel attributeValuePanel = createAttributeValuePanel();
+ masterPanel.add(attributeValuePanel);
+
+ // Add Button Panel
+ masterPanel.add(Box.createVerticalGlue());
+
+ JPanel buttonPanel = createButtonPanel();
+ masterPanel.add(buttonPanel);
+ container.add(masterPanel);
+
+ // Pack, set modality, and center on screen
+ pack();
+ setModal(true);
+ setLocationRelativeTo(Cytoscape.getDesktop());
+ setVisible(true);
+ }
+
+ /**
+ * Gets Index Type.
+ *
+ * @return QuickFind.INDEX_NODES or QuickFind.INDEX_EDGES.
+ */
+ int getIndexType() {
+ return this.indexType;
+ }
+
+ /**
+ * Enable / Disable Apply Button.
+ *
+ * @param enable Enable flag;
+ */
+ void enableApplyButton(boolean enable) {
+ if (applyButton != null) {
+ applyButton.setEnabled(enable);
+ }
+ }
+
+ /**
+ * Creates Button Panel.
+ *
+ * @return JPanel Object.
+ */
+ private JPanel createButtonPanel() {
+ JPanel buttonPanel = new JPanel();
+ buttonPanel.setLayout(new BoxLayout(buttonPanel, BoxLayout.X_AXIS));
+
+ // Cancel Button
+ JButton cancelButton = new JButton("Cancel");
+ cancelButton.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ QuickFindConfigDialog.this.setVisible(false);
+ QuickFindConfigDialog.this.dispose();
+ }
+ });
+
+ // Apply Button
+ applyButton = new JButton(BUTTON_REINDEX_TEXT);
+ applyButton.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ QuickFindConfigDialog.this.setVisible(false);
+ QuickFindConfigDialog.this.dispose();
+
+ String newAttribute = (String) attributeComboBox.getSelectedItem();
+ ReindexQuickFind task = new ReindexQuickFind(currentNetwork, indexType,
+ newAttribute);
+ JTaskConfig config = new JTaskConfig();
+ config.setAutoDispose(true);
+ config.displayStatus(true);
+ config.displayTimeElapsed(false);
+ config.displayCloseButton(true);
+ config.setOwner(Cytoscape.getDesktop());
+ config.setModal(true);
+
+ // Execute Task via TaskManager
+ // This automatically pops-open a JTask Dialog Box.
+ // This method will block until the JTask Dialog Box
+ // is disposed.
+ TaskManager.executeTask(task, config);
+ }
+ });
+ buttonPanel.add(Box.createHorizontalGlue());
+ buttonPanel.add(cancelButton);
+ buttonPanel.add(applyButton);
+
+ return buttonPanel;
+ }
+
+ /**
+ * Creates a Panel to show the currently selected attribute description.
+ *
+ * @return JPanel Object.
+ */
+ private JPanel createAttributeDescriptionPanel() {
+ JPanel panel = new JPanel();
+ panel.setBorder(new TitledBorder("Attribute Description:"));
+ panel.setLayout(new BorderLayout());
+ attributeDescriptionBox = new JTextArea(5, 40);
+ attributeDescriptionBox.setEditable(false);
+ attributeDescriptionBox.setLineWrap(true);
+ attributeDescriptionBox.setWrapStyleWord(true);
+
+ JScrollPane scrollPane = new JScrollPane(attributeDescriptionBox);
+ panel.add(scrollPane, BorderLayout.CENTER);
+ setAttributeDescription();
+
+ return panel;
+ }
+
+ /**
+ * Creates a Panel of Sample Attribute Values.
+ *
+ * @return JPanel Object.
+ */
+ private JPanel createAttributeValuePanel() {
+ JPanel panel = new JPanel();
+ panel.setBorder(new TitledBorder("Sample Attribute Values:"));
+ panel.setLayout(new GridLayout(1, 0));
+
+ // Table Cells are not editable
+ sampleAttributeValuesTable = new JTable() {
+ public boolean isCellEditable(int row, int column) {
+ return false;
+ }
+ };
+ addTableModel(sampleAttributeValuesTable);
+ this.setVisibleRowCount(sampleAttributeValuesTable, 5);
+ panel.add(sampleAttributeValuesTable);
+
+ return panel;
+ }
+
+ /**
+ * Sets Text for Attribute Description Box.
+ */
+ private void setAttributeDescription() {
+ Object selectedAttribute = attributeComboBox.getSelectedItem();
+ CyAttributes attributes = getCyAttributes();
+ String attributeKey;
+
+ if (selectedAttribute != null) {
+ attributeKey = selectedAttribute.toString();
+ } else {
+ attributeKey = currentIndex.getControllingAttribute();
+ }
+
+ String description;
+
+ if (attributeKey.equals(QuickFind.UNIQUE_IDENTIFIER)) {
+ description = "Each node and edge in Cytoscape is assigned a "
+ + "unique identifier. This is an alphanumeric value.";
+ } else if (attributeKey.equals(QuickFind.INDEX_ALL_ATTRIBUTES)) {
+ description = "Index all attributes. Use this option for the "
+ + "widest search scope possible. Note that indexing "
+ + "all attributes on very large networks may take a few " + "seconds.";
+ } else {
+ description = attributes.getAttributeDescription(attributeKey);
+ }
+
+ if (description == null) {
+ description = "No description available.";
+ }
+
+ attributeDescriptionBox.setText(description);
+ attributeDescriptionBox.setCaretPosition(0);
+ }
+
+ /**
+ * Creates TableModel consisting of Distinct Attribute Values.
+ */
+ private void addTableModel(JTable table) {
+ Object selectedAttribute = attributeComboBox.getSelectedItem();
+
+ // Determine current attribute key
+ String attributeKey;
+
+ if (selectedAttribute != null) {
+ attributeKey = selectedAttribute.toString();
+ } else {
+ attributeKey = currentIndex.getControllingAttribute();
+ }
+
+ // Create column names
+ Vector columnNames = new Vector();
+ columnNames.add(attributeKey);
+
+ TableModel model = new DefaultTableModel(columnNames, 5);
+
+ DetermineDistinctValuesTask task = new DetermineDistinctValuesTask(model, attributeKey, this);
+
+ JTaskConfig config = new JTaskConfig();
+ config.setAutoDispose(true);
+ config.displayStatus(true);
+ config.displayTimeElapsed(false);
+ config.displayCloseButton(true);
+ config.setOwner(Cytoscape.getDesktop());
+ config.setModal(true);
+
+ // Execute Task via TaskManager
+ // This automatically pops-open a JTask Dialog Box.
+ // This method will block until the JTask Dialog Box
+ // is disposed.
+ table.setModel(model);
+ TaskManager.executeTask(task, config);
+ }
+
+ private JPanel createNodeEdgePanel() {
+ JPanel nodeEdgePanel = new JPanel();
+ nodeEdgePanel.setBorder(new TitledBorder("Search:"));
+ nodeEdgePanel.setLayout(new BoxLayout(nodeEdgePanel, BoxLayout.X_AXIS));
+
+ JRadioButton nodeButton = new JRadioButton("Nodes");
+ nodeButton.setActionCommand(Integer.toString(QuickFind.INDEX_NODES));
+
+ JRadioButton edgeButton = new JRadioButton("Edges");
+ edgeButton.setActionCommand(Integer.toString(QuickFind.INDEX_EDGES));
+
+ if (indexType == QuickFind.INDEX_NODES) {
+ nodeButton.setSelected(true);
+ } else {
+ edgeButton.setSelected(true);
+ }
+
+ ButtonGroup group = new ButtonGroup();
+ group.add(nodeButton);
+ group.add(edgeButton);
+ nodeEdgePanel.add(nodeButton);
+ nodeEdgePanel.add(edgeButton);
+ nodeEdgePanel.add(Box.createHorizontalGlue());
+
+ // User has switched index type.
+ ActionListener indexTypeListener = new ActionListener() {
+ public void actionPerformed(ActionEvent actionEvent) {
+ String actionCommand = actionEvent.getActionCommand();
+ int type = Integer.parseInt(actionCommand);
+
+ if (type != indexType) {
+ indexType = type;
+ addingNewAttributeList = true;
+
+ Vector attributeList = createAttributeList();
+ attributeComboBox.removeAllItems();
+
+ for (int i = 0; i < attributeList.size(); i++) {
+ attributeComboBox.addItem(attributeList.get(i));
+ }
+
+ addingNewAttributeList = false;
+
+ // Simulate attribute combo box selection.
+ // Invoke via SwingUtilities, so that radio button
+ // selection is not delayed.
+ if (attributeList.size() > 0) {
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ attributeComboBox.setSelectedIndex(0);
+ }
+ });
+ }
+ }
+ }
+ };
+
+ nodeButton.addActionListener(indexTypeListener);
+ edgeButton.addActionListener(indexTypeListener);
+
+ return nodeEdgePanel;
+ }
+
+ /**
+ * Creates the Attribute Selection Panel.
+ *
+ * @return JPanel Object.
+ */
+ private JPanel createAttributeSelectionPanel() {
+ JPanel attributePanel = new JPanel();
+
+ attributePanel.setBorder(new TitledBorder("Select Attribute:"));
+ attributePanel.setLayout(new BoxLayout(attributePanel, BoxLayout.X_AXIS));
+
+ // Create ComboBox
+ Vector attributeList = createAttributeList();
+ attributeComboBox = new JComboBox(attributeList);
+
+ String currentAttribute = currentIndex.getControllingAttribute();
+
+ if (currentAttribute != null) {
+ attributeComboBox.setSelectedItem(currentAttribute);
+ }
+
+ attributePanel.add(attributeComboBox);
+ attributePanel.add(Box.createHorizontalGlue());
+
+ // Add Action Listener
+ attributeComboBox.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ // If we are adding new attributes to combox box, ignore the event
+ if (addingNewAttributeList) {
+ return;
+ }
+
+ // First, set text of apply button
+ String currentAttribute = currentIndex.getControllingAttribute();
+ String newAttribute = (String) attributeComboBox.getSelectedItem();
+
+ if (currentAttribute.equalsIgnoreCase(newAttribute)) {
+ applyButton.setText(BUTTON_REINDEX_TEXT);
+ } else {
+ applyButton.setText(BUTTON_INDEX_TEXT);
+ }
+
+ addTableModel(sampleAttributeValuesTable);
+ setAttributeDescription();
+ }
+ });
+
+ return attributePanel;
+ }
+
+ private Vector createAttributeList() {
+ Vector attributeList = new Vector();
+ CyAttributes attributes = getCyAttributes();
+ String[] attributeNames = attributes.getAttributeNames();
+
+ if (attributeNames != null) {
+ // Show all attributes, except those of TYPE_COMPLEX
+ for (int i = 0; i < attributeNames.length; i++) {
+ int type = attributes.getType(attributeNames[i]);
+
+ // only show user visible attributes
+ if (attributes.getUserVisible(attributeNames[i])) {
+ if (type != CyAttributes.TYPE_COMPLEX) {
+ attributeList.add(attributeNames[i]);
+ }
+ }
+ }
+
+ // Alphabetical sort
+ Collections.sort(attributeList);
+
+ // Add default: Unique Identifier
+ attributeList.insertElementAt(QuickFind.UNIQUE_IDENTIFIER, 0);
+
+ // Add option to index by all attributes
+ // Not yet sure if I want to add this yet. Keep code below.
+ // if (attributeList.size() > 1) {
+ // attributeList.add(QuickFind.INDEX_ALL_ATTRIBUTES);
+ // }
+ }
+
+ return attributeList;
+ }
+
+ CyAttributes getCyAttributes() {
+ CyAttributes attributes;
+
+ if (indexType == QuickFind.INDEX_NODES) {
+ attributes = Cytoscape.getNodeAttributes();
+ } else {
+ attributes = Cytoscape.getEdgeAttributes();
+ }
+
+ return attributes;
+ }
+
+ /**
+ * Sets the Visible Row Count.
+ *
+ * @param table JTable Object.
+ * @param rows Number of Visible Rows.
+ */
+ private void setVisibleRowCount(JTable table, int rows) {
+ int height = 0;
+
+ for (int row = 0; row < rows; row++) {
+ height += table.getRowHeight(row);
+ }
+
+ table.setPreferredScrollableViewportSize(new Dimension(table
+ [...]
+ height));
+ }
+
+ /**
+ * Main method: used for local debugging purposes only.
+ *
+ * @param args No command line arguments expected.
+ */
+ public static void main(String[] args) {
+ new QuickFindConfigDialog();
+ }
+}
+
+
+/**
+ * Long-term task to Reindex QuickFind.
+ *
+ * @author Ethan Cerami.
+ */
+class ReindexQuickFind implements Task {
+ private String newAttributeKey;
+ private CyNetwork cyNetwork;
+ private int indexType;
+ private TaskMonitor taskMonitor;
+
+ /**
+ * Constructor.
+ *
+ * @param indexType Index Type.
+ * @param newAttributeKey New Attribute Key for Indexing.
+ */
+ ReindexQuickFind(CyNetwork cyNetwork, int indexType, String newAttributeKey) {
+ this.cyNetwork = cyNetwork;
+ this.indexType = indexType;
+ this.newAttributeKey = newAttributeKey;
+ }
+
+ /**
+ * Executes Task: Reindex.
+ */
+ public void run() {
+ QuickFind quickFind = QuickFindFactory.getGlobalQuickFindInstance();
+ quickFind.reindexNetwork(cyNetwork, indexType, newAttributeKey, taskMonitor);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void halt() {
+ // No-op
+ }
+
+ /**
+ * Sets the TaskMonitor.
+ *
+ * @param taskMonitor TaskMonitor Object.
+ * @throws IllegalThreadStateException Illegal Thread State.
+ */
+ public void setTaskMonitor(TaskMonitor taskMonitor) throws IllegalThreadStateException {
+ this.taskMonitor = taskMonitor;
+ }
+
+ /**
+ * Gets Title of Task.
+ *
+ * @return Title of Task.
+ */
+ public String getTitle() {
+ return "ReIndexing";
+ }
+}
+
+
+/**
+ * Long-term task to determine distinct attribute values.
+ *
+ * @author Ethan Cerami.
+ */
+class DetermineDistinctValuesTask implements Task {
+ private TableModel tableModel;
+ private String attributeKey;
+ private QuickFindConfigDialog parentDialog;
+ private TaskMonitor taskMonitor;
+
+ /**
+ * Creates a new DetermineDistinctValuesTask object.
+ *
+ * @param tableModel DOCUMENT ME!
+ * @param attributeKey DOCUMENT ME!
+ * @param parentDialog DOCUMENT ME!
+ */
+ public DetermineDistinctValuesTask(TableModel tableModel, String attributeKey,
+ QuickFindConfigDialog parentDialog) {
+ this.tableModel = tableModel;
+
+ if (attributeKey.equals(QuickFind.INDEX_ALL_ATTRIBUTES)) {
+ attributeKey = QuickFind.UNIQUE_IDENTIFIER;
+ }
+
+ this.attributeKey = attributeKey;
+
+ // Disable apply button, while task is in progress.
+ parentDialog.enableApplyButton(false);
+ this.parentDialog = parentDialog;
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void run() {
+ taskMonitor.setPercentCompleted(-1);
+
+ // Obtain distinct attribute values
+ CyNetwork network = Cytoscape.getCurrentNetwork();
+ CyAttributes attributes = parentDialog.getCyAttributes();
+
+ Iterator iterator;
+
+ if (parentDialog.getIndexType() == QuickFind.INDEX_NODES) {
+ iterator = network.nodesIterator();
+ } else {
+ iterator = network.edgesIterator();
+ }
+
+ String[] values = CyAttributesUtil.getDistinctAttributeValues(iterator, attributes,
+ attributeKey, 5);
+
+ if ((values != null) && (values.length > 0)) {
+ for (int i = 0; i < values.length; i++) {
+ tableModel.setValueAt(values[i], i, 0);
+ }
+
+ parentDialog.enableApplyButton(true);
+ } else {
+ tableModel.setValueAt("No values found in network: " + network.getTitle()
+ + ". Cannot create index.", 0, 0);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void halt() {
+ // No-op
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param taskMonitor DOCUMENT ME!
+ *
+ * @throws IllegalThreadStateException DOCUMENT ME!
+ */
+ public void setTaskMonitor(TaskMonitor taskMonitor) throws IllegalThreadStateException {
+ this.taskMonitor = taskMonitor;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getTitle() {
+ return "Accessing sample attribute data";
+ }
+}
diff --git a/coreplugins/QuickFind/src/main/java/csplugins/quickfind/view/QuickFindPanel.java b/coreplugins/QuickFind/src/main/java/csplugins/quickfind/view/QuickFindPanel.java
new file mode 100644
index 0000000..505d246
--- /dev/null
+++ b/coreplugins/QuickFind/src/main/java/csplugins/quickfind/view/QuickFindPanel.java
@@ -0,0 +1,291 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package csplugins.quickfind.view;
+
+import csplugins.quickfind.plugin.QuickFindPlugIn;
+
+import csplugins.quickfind.util.QuickFind;
+
+import csplugins.widgets.autocomplete.index.GenericIndex;
+import csplugins.widgets.autocomplete.index.IndexFactory;
+import csplugins.widgets.autocomplete.index.NumberIndex;
+import csplugins.widgets.autocomplete.index.TextIndex;
+import csplugins.widgets.autocomplete.view.ComboBoxFactory;
+import csplugins.widgets.autocomplete.view.TextIndexComboBox;
+
+import csplugins.widgets.slider.JRangeSliderExtended;
+
+import prefuse.data.query.NumberRangeModel;
+
+import prefuse.util.ui.JRangeSlider;
+
+import java.awt.*;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import java.net.URL;
+
+import javax.swing.*;
+import javax.swing.border.EmptyBorder;
+import javax.swing.border.LineBorder;
+
+
+/**
+ * Quick Find UI Panel.
+ *
+ * @author Ethan Cerami.
+ */
+public class QuickFindPanel extends JPanel {
+ private TextIndexComboBox comboBox;
+ private JButton configButton;
+ private JRangeSliderExtended rangeSlider;
+ private NumberRangeModel rangeModel;
+ private JLabel label;
+ private static final String SEARCH_STRING = "Search: ";
+ private static final String SELECT_STRING = "Select: ";
+
+ /**
+ * Constructor.
+ */
+ public QuickFindPanel() {
+ // Must use BoxLayout, as we want to control width
+ // of all components.
+ setLayout(new BoxLayout(this, BoxLayout.X_AXIS));
+
+ comboBox = createTextIndexComboBox();
+ configButton = createConfigButton();
+ label = createSearchLabel();
+ rangeModel = new NumberRangeModel(0.0, 0.0, 0.0, 0.0);
+ rangeSlider = createSlider(rangeModel, comboBox);
+
+ add(label);
+ add(comboBox);
+ add(rangeSlider);
+ add(configButton);
+
+ // Add Right Buffer, to prevent config button from occassionally
+ // being partially obscured.
+ add(Box.createHorizontalStrut(5));
+ }
+
+ /**
+ * Sets Current Index.
+ *
+ * @param index Generic Index Object.
+ */
+ public void setIndex(GenericIndex index) {
+ if (index instanceof TextIndex) {
+ comboBox.setVisible(true);
+ rangeSlider.setVisible(false);
+ label.setText(SEARCH_STRING);
+ comboBox.setTextIndex((TextIndex) index);
+ } else if (index instanceof NumberIndex) {
+ NumberIndex numberIndex = (NumberIndex) index;
+ // by creating a new NumberRangeModel, the model retains the
+ // number setting, e.g. double or integer; otherwise, you get
+ // the bug described in #1315.
+ rangeModel = new NumberRangeModel(numberIndex.getMinimumValue(),
+ numberIndex.getMinimumValue(), numberIndex.getMinimumValue(),
+ numberIndex.getMaximumValue());
+ rangeSlider.setModel(rangeModel);
+ comboBox.setVisible(false);
+ rangeSlider.setVisible(true);
+ label.setText(SELECT_STRING);
+ }
+ else {
+ // index = null, because there is no enough time to create the index, before switch to other network
+ // just ignore it.
+ return;
+ }
+
+ enableAllQuickFindButtons();
+ }
+
+ /**
+ * No Network Current Available.
+ */
+ public void noNetworkLoaded() {
+ disableAllQuickFindButtons();
+ comboBox.setToolTipText("Please select or load a network");
+ rangeSlider.setToolTipText("Please select or load a network");
+ }
+
+ /**
+ * Indexing Operating in Progress.
+ */
+ public void indexingInProgress() {
+ disableAllQuickFindButtons();
+ comboBox.setToolTipText("Indexing network. Please wait...");
+ rangeSlider.setToolTipText("Indexing network. Please wait...");
+ }
+
+ /**
+ * Gets the TextIndexComboBox Widget.
+ *
+ * @return TextIndexComboBox Widget.
+ */
+ public TextIndexComboBox getTextIndexComboBox() {
+ return comboBox;
+ }
+
+ /**
+ * Gets the Range Slider Widget.
+ *
+ * @return JRangeSliderExtended Object.
+ */
+ public JRangeSliderExtended getSlider() {
+ return this.rangeSlider;
+ }
+
+ /**
+ * Disables all Quick Find Buttons.
+ */
+ private void disableAllQuickFindButtons() {
+ comboBox.removeAllText();
+ comboBox.setEnabled(false);
+ rangeSlider.setEnabled(false);
+ comboBox.setVisible(true);
+ rangeSlider.setVisible(false);
+ configButton.setEnabled(false);
+ label.setForeground(Color.GRAY);
+ }
+
+ /**
+ * Enables all Quick Find Buttons.
+ */
+ public void enableAllQuickFindButtons() {
+ comboBox.setToolTipText("Enter search string");
+ rangeSlider.setToolTipText("Select range");
+ comboBox.setEnabled(true);
+ rangeSlider.setEnabled(true);
+ configButton.setEnabled(true);
+ label.setForeground(Color.BLACK);
+ }
+
+ /**
+ * Creates Configure QuickFind Button.
+ *
+ * @return JButton Object.
+ */
+ private JButton createConfigButton() {
+ URL configIconUrl = QuickFindPlugIn.class.getResource("/resources/config.png");
+ ImageIcon configIcon = new ImageIcon(configIconUrl, "Configure search options");
+ JButton button = new JButton(configIcon);
+ button.setToolTipText("Configure search options");
+ button.setEnabled(false);
+ button.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ new QuickFindConfigDialog();
+ }
+ });
+ button.setBorderPainted(false);
+
+ return button;
+ }
+
+ /**
+ * Creates TextIndex ComboBox.
+ *
+ * @return TextIndexComboBox Object.
+ */
+ private TextIndexComboBox createTextIndexComboBox() {
+ TextIndexComboBox box = null;
+
+ try {
+ TextIndex textIndex = IndexFactory.createDefaultTextIndex(QuickFind.INDEX_NODES);
+ box = ComboBoxFactory.createTextIndexComboBox(textIndex, 2.0);
+ box.setEnabled(false);
+
+ // Set Size of ComboBox Display, based on # of specific chars
+ box.setPrototypeDisplayValue("01234567");
+ box.setToolTipText("Please select or load a network to "
+ + "activate search functionality.");
+
+ // Set Max Size of ComboBox to match preferred size
+ box.setMaximumSize(box.getPreferredSize());
+
+ return box;
+ } catch (Exception e) {
+ }
+
+ return box;
+ }
+
+ /**
+ * Creates Search Label.
+ */
+ private JLabel createSearchLabel() {
+ JLabel label = new JLabel(SEARCH_STRING);
+ label.setBorder(new EmptyBorder(0, 5, 0, 0));
+ label.setForeground(Color.GRAY);
+
+ // Fix width of label
+ label.setMaximumSize(label.getPreferredSize());
+
+ return label;
+ }
+
+ /**
+ * Creates Slider Widget.
+ *
+ * @param box TextIndexComboBox (used to tweak size of slider).
+ * @return JRangeSliderExteneded Object
+ */
+ private JRangeSliderExtended createSlider(BoundedRangeModel model, TextIndexComboBox box) {
+ JRangeSliderExtended slider = new JRangeSliderExtended(model, JRangeSlider.HORIZONTAL,
+ JRangeSlider.LEFTRIGHT_TOPBOTTOM);
+
+ // Hide slider range for now.
+ slider.setVisible(false);
+
+ // Create Border
+ slider.setBorder(new LineBorder(Color.GRAY, 1));
+
+ // Box Layout will respect the components' max size.
+ // Therefore set max size to match preferred size.
+ Dimension dComboBox = box.getPreferredSize();
+ Dimension dSlider = slider.getPreferredSize();
+
+ // Set RangeSlider to match width of combo box.
+ dSlider.width = dComboBox.width;
+ dSlider.height = dSlider.height + 3;
+ slider.setMaximumSize(dSlider);
+ slider.setPreferredSize(dSlider);
+
+ return slider;
+ }
+}
diff --git a/coreplugins/QuickFind/src/main/java/csplugins/quickfind/view/package.html b/coreplugins/QuickFind/src/main/java/csplugins/quickfind/view/package.html
new file mode 100644
index 0000000..9074cce
--- /dev/null
+++ b/coreplugins/QuickFind/src/main/java/csplugins/quickfind/view/package.html
@@ -0,0 +1,8 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+<html>
+<head></head>
+
+<body bgcolor="white">
+View classes for the Cytoscape QuickFind Functionality.
+</body>
+</html>
diff --git a/coreplugins/QuickFind/src/main/java/csplugins/widgets/autocomplete/index/GenericIndex.java b/coreplugins/QuickFind/src/main/java/csplugins/widgets/autocomplete/index/GenericIndex.java
new file mode 100644
index 0000000..1aa7fb7
--- /dev/null
+++ b/coreplugins/QuickFind/src/main/java/csplugins/widgets/autocomplete/index/GenericIndex.java
@@ -0,0 +1,111 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package csplugins.widgets.autocomplete.index;
+
+
+/**
+ * Generic Index Interface.
+ *
+ * @author Ethan Cerami
+ */
+public interface GenericIndex {
+ /**
+ * Gets Index Type: QuickFind.INDEX_NODES or QuickFind.INDEX_EDGES.
+ *
+ * @return QuickFind.INDEX_NODES or QuickFind.INDEX_EDGES.
+ */
+ int getIndexType();
+
+ /**
+ * Resets the index, wipes everything clean.
+ */
+ void resetIndex();
+
+ /**
+ * Sets the controlling attribute.
+ *
+ * <P>For example, if the controlling attribute is: biopax.short_name,
+ * that means that the index contains all values for this attribute.
+ *
+ * @param attributeName Controlling attribute name.
+ *
+ */
+ void setControllingAttribute(String attributeName);
+
+ /**
+ * Gets the controlling attribute.
+ *
+ * <P>For example, if the controlling attribute is: biopax.short_name,
+ * that means that the index contains all values for this attribute.
+ *
+ * @return attribute name.
+ */
+ String getControllingAttribute();
+
+ /**
+ * Adds new object to index.
+ *
+ * @param key Object Key.
+ * @param o Any Java Object.
+ */
+ void addToIndex(Object key, Object o);
+
+ /**
+ * Adds a new IndexListener object.
+ * <P>The IndexListener object will be notified each time the text
+ * index is modified.
+ *
+ * @param listener IndexListener Object.
+ */
+ void addIndexListener(IndexListener listener);
+
+ /**
+ * Deletes the specified IndexListener Object.
+ * <P>After being deleted, this listener will no longer receive any
+ * notification events.
+ *
+ * @param listener IndexListener Object.
+ */
+ void deleteIndexListener(IndexListener listener);
+
+ /**
+ * Gets number of registered listeners who are receving notification events.
+ *
+ * @return number of registered listeners.
+ */
+ int getNumListeners();
+}
diff --git a/coreplugins/QuickFind/src/main/java/csplugins/widgets/autocomplete/index/GenericIndexImpl.java b/coreplugins/QuickFind/src/main/java/csplugins/widgets/autocomplete/index/GenericIndexImpl.java
new file mode 100644
index 0000000..93d6b7d
--- /dev/null
+++ b/coreplugins/QuickFind/src/main/java/csplugins/widgets/autocomplete/index/GenericIndexImpl.java
@@ -0,0 +1,146 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package csplugins.widgets.autocomplete.index;
+
+import csplugins.quickfind.util.QuickFind;
+
+import java.util.ArrayList;
+
+
+/**
+ * Abstract Base class for all Index implementations.
+ *
+ * @author Ethan Cerami
+ */
+public abstract class GenericIndexImpl implements GenericIndex {
+ private int indexType;
+ private String attributeName = QuickFind.UNIQUE_IDENTIFIER;
+ private ArrayList observerList;
+
+ /**
+ * Default constructor.
+ *
+ * @param indexType QuickFind.INDEX_NODES or QuickFind.INDEX_EDGES.
+ */
+ public GenericIndexImpl(int indexType) {
+ this.indexType = indexType;
+ observerList = new ArrayList();
+ }
+
+ /**
+ * Gets Index Type: QuickFind.INDEX_NODES or QuickFind.INDEX_EDGES.
+ *
+ * @return QuickFind.INDEX_NODES or QuickFind.INDEX_EDGES.
+ */
+ public int getIndexType() {
+ return indexType;
+ }
+
+ /**
+ * Resets the index, e.g. wipes everything clean.
+ */
+ public void resetIndex() {
+ // Explicitly notify all observers
+ for (int i = 0; i < observerList.size(); i++) {
+ IndexListener observer = (IndexListener) observerList.get(i);
+ observer.indexReset();
+ }
+ }
+
+ /**
+ * Adds new item to index.
+ * @param key Key value.
+ * @param o Object value.
+ */
+ public void addToIndex(Object key, Object o) {
+ // Explicitly notify all observers
+ for (int i = 0; i < observerList.size(); i++) {
+ IndexListener observer = (IndexListener) observerList.get(i);
+ observer.itemAddedToIndex(key, o);
+ }
+ }
+
+ /**
+ * Sets the controlling attribute.
+ *
+ * @param attributeName Attribute name.
+ */
+ public void setControllingAttribute(String attributeName) {
+ this.attributeName = attributeName;
+ }
+
+ /**
+ * Gets the controlling attribute.
+ *
+ * @return attribute name.
+ */
+ public String getControllingAttribute() {
+ return this.attributeName;
+ }
+
+ /**
+ * Adds a new IndexListener Object.
+ * <P>Each IndexListener object will be notified each time the text
+ * index is modified.
+ *
+ * @param listener IndexListener Object.
+ */
+ public void addIndexListener(IndexListener listener) {
+ observerList.add(listener);
+ }
+
+ /**
+ * Deletes the specified IndexListener Object.
+ * <P>After being deleted, this listener will no longer receive any
+ * notification events.
+ *
+ * @param listener IndexListener Object.
+ */
+ public void deleteIndexListener(IndexListener listener) {
+ observerList.remove(listener);
+ }
+
+ /**
+ * Gets number of registered listeners who are receving notification
+ * events.
+ *
+ * @return number of registered listeners.
+ */
+ public int getNumListeners() {
+ return observerList.size();
+ }
+}
diff --git a/coreplugins/QuickFind/src/main/java/csplugins/widgets/autocomplete/index/Hit.java b/coreplugins/QuickFind/src/main/java/csplugins/widgets/autocomplete/index/Hit.java
new file mode 100644
index 0000000..e7b146b
--- /dev/null
+++ b/coreplugins/QuickFind/src/main/java/csplugins/widgets/autocomplete/index/Hit.java
@@ -0,0 +1,95 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package csplugins.widgets.autocomplete.index;
+
+
+/**
+ * Encapsulates a hit within the text index.
+ * <p/>
+ * Each hit has two pieces of data:
+ * <UL>
+ * <LI>a String keyword.
+ * <LI>1 or more associated Objects.
+ * </UL>
+ * For example, we may index two Objects with the same name, "YRC00441".
+ * If we subsequently search for "YRC00441", we get back one Hit object with
+ * the following data: keyword = "YRC00441", objects = [Object1][Object2].
+ *
+ * @author Ethan Cerami.
+ */
+public class Hit {
+ private String keyword;
+ private Object[] objects;
+
+ /**
+ * Constructor.
+ *
+ * @param keyword Keyword String.
+ * @param objects Objects associated with this hit.
+ */
+ public Hit(String keyword, Object[] objects) {
+ this.keyword = keyword;
+ this.objects = objects;
+ }
+
+ /**
+ * Gets keyword value of hit.
+ *
+ * @return String keyword.
+ */
+ public String getKeyword() {
+ return keyword;
+ }
+
+ /**
+ * Gets objects associated with this hit.
+ *
+ * @return Objects associated with this hit.
+ */
+ public Object[] getAssociatedObjects() {
+ return objects;
+ }
+
+ /**
+ * toString() method.
+ *
+ * @return Same as getKeyword().
+ */
+ public String toString() {
+ return getKeyword();
+ }
+}
diff --git a/coreplugins/QuickFind/src/main/java/csplugins/widgets/autocomplete/index/IndexFactory.java b/coreplugins/QuickFind/src/main/java/csplugins/widgets/autocomplete/index/IndexFactory.java
new file mode 100644
index 0000000..18b4a47
--- /dev/null
+++ b/coreplugins/QuickFind/src/main/java/csplugins/widgets/autocomplete/index/IndexFactory.java
@@ -0,0 +1,65 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package csplugins.widgets.autocomplete.index;
+
+
+/**
+ * Factory for creating Index objects.
+ *
+ * @author Ethan Cerami.
+ */
+public class IndexFactory {
+ /**
+ * Gets the default implementation of the TextIndex interface.
+ *
+ * @param indexType QuickFind.INDEX_NODES or QuickFind.INDEX_EDGES.
+ * @return TextIndex Object.
+ */
+ public static TextIndex createDefaultTextIndex(int indexType) {
+ return new TextIndexImpl(indexType);
+ }
+
+ /**
+ * Gets the default implementation of the NumberIndex interface.
+ *
+ * @param indexType QuickFind.INDEX_NODES or QuickFind.INDEX_EDGES.
+ * @return NumberIndex Object.
+ */
+ public static NumberIndex createDefaultNumberIndex(int indexType) {
+ return new NumberIndexImpl(indexType);
+ }
+}
diff --git a/coreplugins/QuickFind/src/main/java/csplugins/widgets/autocomplete/index/IndexListener.java b/coreplugins/QuickFind/src/main/java/csplugins/widgets/autocomplete/index/IndexListener.java
new file mode 100644
index 0000000..94b664d
--- /dev/null
+++ b/coreplugins/QuickFind/src/main/java/csplugins/widgets/autocomplete/index/IndexListener.java
@@ -0,0 +1,58 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package csplugins.widgets.autocomplete.index;
+
+
+/**
+ * Interface for listening to Index events.
+ *
+ * @author Ethan Cerami.
+ */
+public interface IndexListener {
+ /**
+ * Index has been reset.
+ */
+ void indexReset();
+
+ /**
+ * Item has been added to the index.
+ *
+ * @param key Object key.
+ * @param o Object o.
+ */
+ void itemAddedToIndex(Object key, Object o);
+}
diff --git a/coreplugins/QuickFind/src/main/java/csplugins/widgets/autocomplete/index/NumberIndex.java b/coreplugins/QuickFind/src/main/java/csplugins/widgets/autocomplete/index/NumberIndex.java
new file mode 100644
index 0000000..1cfb1e3
--- /dev/null
+++ b/coreplugins/QuickFind/src/main/java/csplugins/widgets/autocomplete/index/NumberIndex.java
@@ -0,0 +1,74 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package csplugins.widgets.autocomplete.index;
+
+import java.util.List;
+
+
+/**
+ * Number index interface.
+ * <p/>
+ * This is a core data structure for indexing arbitrary Objects, based on a
+ * numeric value, e.g. Integer or Double.
+ *
+ * @author Ethan Cerami.
+ */
+public interface NumberIndex extends GenericIndex {
+ /**
+ * Gets a closed range of indexed values between lower and upper.
+ *
+ * Returns a view of the portion of this set whose elements range from
+ * lower, inclusive, to upper, inclusive.
+ *
+ * @param lower lower bound.
+ * @param upper upper bound.
+ * @return List of Objects.
+ */
+ List getRange(Number lower, Number upper);
+
+ /**
+ * Gets minimum value in index.
+ * @return min value.
+ */
+ Number getMinimumValue();
+
+ /**
+ * Gets maximum value in index.
+ * @return max value.
+ */
+ Number getMaximumValue();
+}
diff --git a/coreplugins/QuickFind/src/main/java/csplugins/widgets/autocomplete/index/NumberIndexImpl.java b/coreplugins/QuickFind/src/main/java/csplugins/widgets/autocomplete/index/NumberIndexImpl.java
new file mode 100644
index 0000000..6659a89
--- /dev/null
+++ b/coreplugins/QuickFind/src/main/java/csplugins/widgets/autocomplete/index/NumberIndexImpl.java
@@ -0,0 +1,146 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package csplugins.widgets.autocomplete.index;
+
+import java.util.*;
+
+
+/**
+ * Basic implementation of the Number Index Interface.
+ *
+ * @author Ethan Cerami.
+ */
+class NumberIndexImpl extends GenericIndexImpl implements NumberIndex {
+ private TreeMap treeMap;
+
+ /**
+ * Creates a new NumberIndexImpl object.
+ *
+ * @param indexType DOCUMENT ME!
+ */
+ public NumberIndexImpl(int indexType) {
+ super(indexType);
+ treeMap = new TreeMap();
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void resetIndex() {
+ treeMap = new TreeMap();
+ super.resetIndex();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param key DOCUMENT ME!
+ * @param o DOCUMENT ME!
+ */
+ public void addToIndex(Object key, Object o) {
+ if (key instanceof Integer || key instanceof Double) {
+ List list;
+
+ if (treeMap.containsKey(key)) {
+ list = (List) treeMap.get(key);
+ } else {
+ list = new ArrayList();
+ treeMap.put(key, list);
+ }
+
+ list.add(o);
+ } else {
+ throw new IllegalArgumentException("key parameter must be of "
+ + "type Integer or Double.");
+ }
+
+ super.addToIndex(key, o);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param lower DOCUMENT ME!
+ * @param upper DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public List getRange(Number lower, Number upper) {
+ ArrayList list = new ArrayList();
+
+ // Calculate successor of upper via IEEE 754 method.
+ // Used to create a closed range between lower (inclusive) and
+ // upper (inclusive).
+ // For background, see:
+ // http://www.cygnus-software.com/papers/comparingfloats/
+ // comparingfloats.htm
+ if (upper instanceof Double) {
+ long bits = Double.doubleToLongBits(upper.doubleValue());
+ upper = new Double(Double.longBitsToDouble(bits + 1));
+ } else if (upper instanceof Integer) {
+ upper = new Integer(upper.intValue() + 1);
+ }
+
+ SortedMap map = treeMap.subMap(lower, upper);
+ Iterator iterator = map.values().iterator();
+
+ while (iterator.hasNext()) {
+ List subList = (List) iterator.next();
+ list.addAll(subList);
+ }
+
+ return list;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Number getMinimumValue() {
+ return (Number) treeMap.firstKey();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Number getMaximumValue() {
+ return (Number) treeMap.lastKey();
+ }
+}
diff --git a/coreplugins/QuickFind/src/main/java/csplugins/widgets/autocomplete/index/TextIndex.java b/coreplugins/QuickFind/src/main/java/csplugins/widgets/autocomplete/index/TextIndex.java
new file mode 100644
index 0000000..d09f179
--- /dev/null
+++ b/coreplugins/QuickFind/src/main/java/csplugins/widgets/autocomplete/index/TextIndex.java
@@ -0,0 +1,95 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package csplugins.widgets.autocomplete.index;
+
+
+/**
+ * Text index interface.
+ * <p/>
+ * This is a core data structure for indexing arbitrary Objects, based on a
+ * key string.
+ *
+ * @author Ethan Cerami.
+ */
+public interface TextIndex extends GenericIndex {
+ /**
+ * Default Max Key Length
+ */
+ int DEFAULT_MAX_KEY_LENGTH = 100;
+
+ /**
+ * Set max key length; all keys greater than this length will
+ * be automatically truncated.
+ *
+ * <P>Default is set to {@link TextIndex#DEFAULT_MAX_KEY_LENGTH}
+ * @param len max key length.
+ */
+ void setMaxKeyLength(int len);
+
+ /**
+ * Gets max key length; all keys greater than this length will
+ * be automatically truncated.
+ * <P>Default is set to {@link TextIndex#DEFAULT_MAX_KEY_LENGTH}
+ *
+ * @return max key length.
+ */
+ int getMaxKeyLength();
+
+ /**
+ * Gets all hits which begin with the specified prefix.
+ *
+ * @param prefix String prefix.
+ * @param maxHits Maximum number of hits.
+ * @return Array of Hits.
+ */
+ Hit[] getHits(String prefix, int maxHits);
+
+ /**
+ * Gets total number of keys in index.
+ *
+ * @return number of keys in index.
+ */
+ int getNumKeys();
+
+ /**
+ * Gets a text description of the text index, primarily used for debugging
+ * purposes.
+ *
+ * @return text description of the text index.
+ */
+ String toString();
+}
diff --git a/coreplugins/QuickFind/src/main/java/csplugins/widgets/autocomplete/index/TextIndexImpl.java b/coreplugins/QuickFind/src/main/java/csplugins/widgets/autocomplete/index/TextIndexImpl.java
new file mode 100644
index 0000000..6d8ea50
--- /dev/null
+++ b/coreplugins/QuickFind/src/main/java/csplugins/widgets/autocomplete/index/TextIndexImpl.java
@@ -0,0 +1,268 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package csplugins.widgets.autocomplete.index;
+
+import java.text.ParseException;
+import java.text.RuleBasedCollator;
+
+import java.util.*;
+
+
+/**
+ * Basic implementation of the Text Index Interface.
+ *
+ * @author Ethan Cerami.
+ */
+class TextIndexImpl extends GenericIndexImpl implements TextIndex {
+ private Trie trie;
+ private HashMap map;
+ private static final boolean OUTPUT_PERFORMANCE_STATS = false;
+ private HashMap cache = new HashMap();
+ private static final String WILD_CARD = "*";
+ private int maxKeyLength;
+
+ /**
+ * Constructor.
+ * @param indexType QuickFind.INDEX_NODES or QuickFind.INDEX_EDGES.
+ */
+ public TextIndexImpl(int indexType) {
+ super(indexType);
+ maxKeyLength = TextIndex.DEFAULT_MAX_KEY_LENGTH;
+ init();
+ }
+
+ /**
+ * Resets the index, e.g. wipes everything clean.
+ */
+ public void resetIndex() {
+ init();
+ super.resetIndex();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param len DOCUMENT ME!
+ */
+ public void setMaxKeyLength(int len) {
+ maxKeyLength = len;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getMaxKeyLength() {
+ return maxKeyLength;
+ }
+
+ /**
+ * Adds new object to index.
+ *
+ * @param key String Hit.
+ * @param o Any Java Object.
+ */
+ public void addToIndex(Object key, Object o) {
+ // convert all keys to lowercase
+ String keyString = (String) key;
+ keyString = keyString.toLowerCase();
+
+ // truncate key, if necessary
+ if (keyString.length() > maxKeyLength) {
+ keyString = keyString.substring(0, maxKeyLength);
+ }
+
+ // Add to Trie and HashMap
+ trie.add(keyString);
+
+ ArrayList objectList = (ArrayList) map.get(keyString);
+
+ if (objectList == null) {
+ objectList = new ArrayList();
+ map.put(keyString, objectList);
+ }
+
+ objectList.add(o);
+ super.addToIndex(key, o);
+ }
+
+ /**
+ * Gets all hits which begin with the specified prefix.
+ *
+ * @param prefix String prefix.
+ * @param maxHits Maximum number of hits
+ * @return Array of Strings, which begin with the specified prefix.
+ */
+ public Hit[] getHits(String prefix, int maxHits) {
+ Date start = new Date();
+ Hit[] hits = null;
+
+ // Deal with wild card cases.
+ if (prefix.equals("")) {
+ hits = (Hit[]) cache.get(prefix);
+ } else if (prefix.endsWith(WILD_CARD)) {
+ hits = getWildCardHits(prefix);
+ }
+
+ if (hits == null) {
+ String[] keys = trie.getWords(prefix.toLowerCase());
+ int size = Math.min(keys.length, maxHits);
+ hits = new Hit[size];
+
+ // By default, strings are ordered lexicographically -- meaning
+ // that the unicode value for each character is used for
+ // comparison. Therefore, in the world of QuickFind, strings
+ // beginning with non-alphanumeric and digits appear before those
+ // strings that begin with letters. This is not really want we
+ // want. Rather, we would like those strings beginning with
+ // letters to appear first. The collator rules below do the trick.
+ // This rule essentially says that a-z should appear before all
+ // other characters.
+ String collatorRules = "<a<b<c<d<e<f<g<h<i<j<k<l<m<n<o<p<q<r<s<t" + "<u<v<w<x<y<z";
+
+ try {
+ RuleBasedCollator collator = new RuleBasedCollator(collatorRules);
+ Arrays.sort(keys, collator);
+ } catch (ParseException e) {
+ }
+
+ // Create the Hits
+ for (int i = 0; i < size; i++) {
+ hits[i] = new Hit(keys[i], getObjectsByKey(keys[i]));
+ }
+ }
+
+ if (prefix.equals("")) {
+ cache.put(prefix, hits);
+ }
+
+ Date stop = new Date();
+
+ if (OUTPUT_PERFORMANCE_STATS) {
+ long interval = stop.getTime() - start.getTime();
+ System.out.println("Time to look up: " + interval + " ms");
+ }
+
+ return hits;
+ }
+
+ /**
+ * Gets total number of keys in index.
+ *
+ * @return number of keys in index.
+ */
+ public int getNumKeys() {
+ return map.size();
+ }
+
+ /**
+ * Gets a text description of the text index, primarily used for
+ * debugging purposes.
+ *
+ * @return text description of the text index.
+ */
+ public String toString() {
+ return "Text Index: [Total number of keys: " + map.size() + "]";
+ }
+
+ /**
+ * Executes basic wild card search. Prefix must end with *.
+ * For example: "YDR*".
+ *
+ * @param prefix prefix ending in *.
+ * @return An array containing 1 hit object or null.
+ */
+ private Hit[] getWildCardHits(String prefix) {
+ Hit[] hits = null;
+
+ // Remove wildcard.
+ String regex = prefix.toLowerCase().substring(0, prefix.length() - 1);
+
+ // Find all matching words
+ String[] keys = trie.getWords(regex);
+
+ // Find all associated graph objects; avoid redundant objects.
+ Set graphObjectSet = new HashSet();
+
+ for (int i = 0; i < keys.length; i++) {
+ Object[] graphObjects = getObjectsByKey(keys[i]);
+
+ for (int j = 0; j < graphObjects.length; j++) {
+ graphObjectSet.add(graphObjects[j]);
+ }
+ }
+
+ // Return result set
+ if (graphObjectSet.size() > 0) {
+ hits = new Hit[1];
+
+ Object[] graphObjects = graphObjectSet.toArray(new Object[graphObjectSet.size()]);
+ hits[0] = new Hit(prefix, graphObjects);
+ }
+
+ return hits;
+ }
+
+ /**
+ * Gets all objects associated with the specified key.
+ * <p/>
+ * Each key can be associated with multiple objects. This method therefore
+ * returns an array of Objects.
+ *
+ * @param key String Hit.
+ * @return Array of Java Objects.
+ */
+ private Object[] getObjectsByKey(String key) {
+ if (map.containsKey(key)) {
+ ArrayList list = (ArrayList) map.get(key);
+
+ return list.toArray();
+ } else {
+ throw new IllegalArgumentException("No objects exist for key: " + key);
+ }
+ }
+
+ /**
+ * Initializes the Text Index.
+ */
+ private void init() {
+ trie = new Trie();
+ map = new HashMap();
+ cache = new HashMap();
+ }
+}
diff --git a/coreplugins/QuickFind/src/main/java/csplugins/widgets/autocomplete/index/Trie.java b/coreplugins/QuickFind/src/main/java/csplugins/widgets/autocomplete/index/Trie.java
new file mode 100644
index 0000000..9686a45
--- /dev/null
+++ b/coreplugins/QuickFind/src/main/java/csplugins/widgets/autocomplete/index/Trie.java
@@ -0,0 +1,684 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package csplugins.widgets.autocomplete.index;
+
+
+/**
+ * <p>A Trie can be used for fast prefix matching of strings. The word
+ * "trie", pronounced "try", comes from the middle of the word retrieval.
+ * A Trie can be thought of as a container of strings, but in the
+ * implementation, a Trie is a node of a tree structure, where each node
+ * has a reference to a character, and 0 or more Trie children.
+ * The following figure shows an example of two Trie tree structures:
+ * <p/>
+ * <p><center><img align="center" src="doc-files/trie.gif"/>
+ * <br><font size="1">Figure 1 - Two example Trie structures</font>
+ * </center>
+ * <p/>
+ * <p>The following code can be used to create the above tree structures:
+ * <p/>
+ * <pre>
+ * Trie trie1 = new Trie(); Trie trie2 = new Trie();
+ * trie1.add("rain"); trie2.add("bat");
+ * trie1.add("rainbow"); trie2.add("bed");
+ * trie1.add("apple"); trie2.add("bear");
+ * trie1.add("apples"); trie2.add("boat");
+ * trie2.add("boats");
+ * trie2.add("cat");
+ * </pre>
+ * <p/>
+ * <p>The nodes with a green dot beside them indicate that the isWord flag is
+ * true for that node, and nodes with no green dot have the isWord flag
+ * set to false. To get all the words beginning with the prefix "be"
+ * from trie2, calling trie2.getWords("be") will return an array containing
+ * bed and bear. To see if trie1 contains any words beginning with "app",
+ * calling trie1.hasPrefix("app") will return true.
+ * <p/>
+ * <p>The speed of a prefix match depends on the number of children each node
+ * in the search path has. If the maximum number of children is bound
+ * by a constant, then the time to perform a query is O(m), where m is the
+ * length of the input string. The following data* represents statistics
+ * for the English language:
+ * <p/>
+ * <p><center><table border="1">
+ * <tr><td><b>Number of Children</b></td><td><b>Number of Nodes</b></td>
+ * <td><b>Number of Children</b></td><td><b>Number of Nodes</b></td></tr>
+ * <tr align="right"><td>0</td><td>101808</td><td>14</td><td>84</td></tr>
+ * <tr align="right"><td>1</td><td>199377</td><td>15</td><td>67</td></tr>
+ * <tr align="right"><td>2</td><td>31032</td><td>16</td><td>40</td></tr>
+ * <tr align="right"><td>3</td><td>10538</td><td>17</td><td>38</td></tr>
+ * <tr align="right"><td>4</td><td>4272</td><td>18</td><td>30</td></tr>
+ * <tr align="right"><td>5</td><td>2125</td><td>19</td><td>22</td></tr>
+ * <tr align="right"><td>6</td><td>1178</td><td>20</td><td>17</td></tr>
+ * <tr align="right"><td>7</td><td>739</td><td>21</td><td>13</td></tr>
+ * <tr align="right"><td>8</td><td>424</td><td>22</td><td>16</td></tr>
+ * <tr align="right"><td>9</td><td>329</td><td>23</td><td>10</td></tr>
+ * <tr align="right"><td>10</td><td>242</td><td>24</td><td>16</td></tr>
+ * <tr align="right"><td>11</td><td>163</td><td>25</td><td>9</td></tr>
+ * <tr align="right"><td>12</td><td>117</td><td>26</td><td>9</td></tr>
+ * <tr align="right"><td>13</td><td>106</td></tr>
+ * </table>
+ * <font size="1">Table 1 - Node statistics for the English language</font>
+ * </center>
+ * <p/>
+ * <p>The "Number of Nodes" column is a count of number of nodes with the
+ * specified number of children. Thus, about 99% of the nodes in the Trie
+ * structure have 5 or less children. The maximum number of children is 26
+ * since that is the size of the English alphabet. The above data was
+ * collected using a word list of 128,617 words obtained from an online
+ * dictionary site. Results will vary depending on the word list used.
+ * <p/>
+ * <p>The methods of a Trie fall into two broad categories, tree level
+ * operations and string operations. Tree level operations provide control of
+ * the tree structure, such as adding or removing children. String level
+ * operations are higher-level methods that do the work of adding or removing
+ * nodes from the Trie. For example, the add(String), contains(String),
+ * remove(String) and removeAll(String) are higher-level operations.
+ * <p/>
+ * <p>When words are removed using the remove(String) or removeAll(String)
+ * then the trie is left in a state where all leaf nodes have the isWord flag
+ * set to true. This is achieved by repeatedly removing any leaf
+ * node on the remove path that has the isWord flag set to false. However,
+ * tree level operations do not enforce this property.
+ * <p/>
+ * <P>This code has been placed in the public domain under a FreeBSD license
+ * (courtesy of Randall Kippen).
+ *
+ * @author GraphBuilder.com
+ */
+public class Trie {
+ protected Trie parent = null;
+ protected Trie[] child = new Trie[1];
+ protected int numChildren = 0;
+ protected char ch;
+ protected boolean isWord = false;
+
+ /**
+ * Creates a Trie using the root symbol as the character.
+ */
+ public Trie() {
+ this((char) 251);
+ }
+
+ /**
+ * Creates a Trie using the specified character.
+ *
+ * @param c Character.
+ */
+ public Trie(char c) {
+ ch = c;
+ }
+
+ /**
+ * Returns the character of this trie.
+ *
+ * @return char.
+ */
+ public char getChar() {
+ return ch;
+ }
+
+ /**
+ * Sets the character of this trie.
+ *
+ * @param c Character.
+ * @throws IllegalArgumentException if this trie has a sibling with
+ * the same character.
+ */
+ public void setChar(char c) throws IllegalArgumentException {
+ if (c == ch) {
+ return;
+ }
+
+ if ((parent != null) && parent.hasChar(c)) {
+ throw new IllegalArgumentException("duplicate chars not allowed");
+ }
+
+ ch = c;
+ }
+
+ /**
+ * Returns the value of the isWord flag.
+ *
+ * @return true or false.
+ */
+ public boolean isWord() {
+ return isWord;
+ }
+
+ /**
+ * Sets the value of the isWord flag.
+ *
+ * @param b true or false.
+ */
+ public void setWord(boolean b) {
+ isWord = b;
+ }
+
+ /**
+ * Used to create the trie nodes when a string is added to a trie.
+ *
+ * @param c Character.
+ * @return Trie Object.
+ */
+ protected Trie createNode(char c) {
+ return new Trie(c);
+ }
+
+ /**
+ * Inserts the trie as the last child.
+ *
+ * @param t Trie Object.
+ * @see #insertChild(Trie, int).
+ */
+ public void addChild(Trie t) {
+ insertChild(t, numChildren);
+ }
+
+ /**
+ * Inserts the trie at the specified index. If successful, the parent
+ * of the specified trie
+ * is updated to be this trie.
+ *
+ * @param t Trie Object.
+ * @param index Index integer value.
+ * @throws IllegalArgumentException if index < 0 or index > numChildren.
+ * @throws IllegalArgumentException if the specified trie is null.
+ * @throws IllegalArgumentException if the specified trie is still a
+ * child of another trie.
+ * @throws IllegalArgumentException if this trie already has a trie
+ * child with the same character.
+ * @throws IllegalArgumentException if this trie is a descendent of
+ * the specified trie.
+ */
+ public void insertChild(Trie t, int index) throws IllegalArgumentException {
+ if ((index < 0) || (index > numChildren)) {
+ throw new IllegalArgumentException("required: (index >= 0 && index <= numChildren) "
+ + "but: (index = " + index + ", numChildren = "
+ + numChildren + ")");
+ }
+
+ if (t == null) {
+ throw new IllegalArgumentException("cannot add null child");
+ }
+
+ if (t.parent != null) {
+ throw new IllegalArgumentException("specified child still belongs to parent");
+ }
+
+ if (hasChar(t.ch)) {
+ throw new IllegalArgumentException("duplicate chars not allowed");
+ }
+
+ if (isDescendent(t)) {
+ throw new IllegalArgumentException("cannot add cyclic reference");
+ }
+
+ t.parent = this;
+
+ if (numChildren == child.length) {
+ Trie[] arr = new Trie[2 * (numChildren + 1)];
+
+ for (int i = 0; i < numChildren; i++) {
+ arr[i] = child[i];
+ }
+
+ child = arr;
+ }
+
+ for (int i = numChildren; i > index; i--) {
+ child[i] = child[i - 1];
+ }
+
+ child[index] = t;
+ numChildren++;
+ }
+
+ /**
+ * Removes the specified trie from the child array. Does nothing if the
+ * specified trie is not a child of this trie. Otherwise the parent of
+ * the trie is set to null.
+ *
+ * @param t Trie Object.
+ */
+ public void removeChild(Trie t) {
+ for (int i = 0; i < numChildren; i++) {
+ if (t == child[i]) {
+ for (int j = i + 1; j < numChildren; j++) {
+ child[j - 1] = child[j];
+ }
+
+ numChildren--;
+ child[numChildren] = null;
+ t.parent = null;
+
+ break;
+ }
+ }
+ }
+
+ /**
+ * Returns the number of children this trie has.
+ *
+ * @return number of children.
+ */
+ public int numChildren() {
+ return numChildren;
+ }
+
+ /**
+ * Returns the child at the specified index.
+ *
+ * @param index Integer index value.
+ * @return Trie object.
+ * @throws IllegalArgumentException if index < 0 or index >= numChildren.
+ */
+ public Trie child(int index) throws IllegalArgumentException {
+ if ((index < 0) || (index >= numChildren)) {
+ throw new IllegalArgumentException("required: (index >= 0 && index < numChildren) "
+ + "but: (index = " + index + ", numChildren = "
+ + numChildren + ")");
+ }
+
+ return child[index];
+ }
+
+ /**
+ * Returns the parent node.
+ *
+ * @return Trie Object.
+ */
+ public Trie getParent() {
+ return parent;
+ }
+
+ /**
+ * Returns true if this node is a descendent of the specified node or
+ * this node and the specified node are the same node, false otherwise.
+ *
+ * @param t Trie Object.
+ * @return true or false.
+ */
+ public boolean isDescendent(Trie t) {
+ Trie r = this;
+
+ while (r != null) {
+ if (r == t) {
+ return true;
+ }
+
+ r = r.parent;
+ }
+
+ return false;
+ }
+
+ //-End of tree-level operations. Start of string operations. -------
+
+ /**
+ * Adds the string to the trie. Returns true if the string is added or
+ * false if the string is already contained in the trie.
+ *
+ * @param s String.
+ * @return true or false.
+ */
+ public boolean add(String s) {
+ return add(s, 0);
+ }
+
+ private boolean add(String s, int index) {
+ if (index == s.length()) {
+ if (isWord) {
+ return false;
+ }
+
+ isWord = true;
+
+ return true;
+ }
+
+ char c = s.charAt(index);
+
+ for (int i = 0; i < numChildren; i++) {
+ if (child[i].ch == c) {
+ return child[i].add(s, index + 1);
+ }
+ }
+
+ // this code adds from the bottom to the top because the addChild method
+ // checks for cyclic references. This prevents quadratic runtime.
+ int i = s.length() - 1;
+ Trie t = createNode(s.charAt(i--));
+ t.isWord = true;
+
+ while (i >= index) {
+ Trie n = createNode(s.charAt(i--));
+ n.addChild(t);
+ t = n;
+ }
+
+ addChild(t);
+
+ return true;
+ }
+
+ /**
+ * Returns the child that has the specified character or null if no
+ * child has the specified character.
+ *
+ * @param c Character.
+ * @return Trie Object.
+ */
+ public Trie getNode(char c) {
+ for (int i = 0; i < numChildren; i++) {
+ if (child[i].ch == c) {
+ return child[i];
+ }
+ }
+
+ return null;
+ }
+
+ /**
+ * Returns the last trie in the path that prefix matches the
+ * specified prefix string rooted at this node, or null if there is no
+ * such prefix path.
+ *
+ * @param prefix String prefix.
+ * @return Trie Object.
+ */
+ public Trie getNode(String prefix) {
+ return getNode(prefix, 0);
+ }
+
+ private Trie getNode(String prefix, int index) {
+ if (index == prefix.length()) {
+ return this;
+ }
+
+ char c = prefix.charAt(index);
+
+ for (int i = 0; i < numChildren; i++) {
+ if (child[i].ch == c) {
+ return child[i].getNode(prefix, index + 1);
+ }
+ }
+
+ return null;
+ }
+
+ /**
+ * Removes the specified string from the trie. Returns true if the
+ * string was removed or false if the string was not a word in the trie.
+ *
+ * @param s String.
+ * @return true or false.
+ */
+ public boolean remove(String s) {
+ Trie t = getNode(s);
+
+ if ((t == null) || !t.isWord) {
+ return false;
+ }
+
+ t.isWord = false;
+
+ while ((t != null) && (t.numChildren == 0) && !t.isWord) {
+ Trie p = t.parent;
+
+ if (p != null) {
+ p.removeChild(t);
+ }
+
+ t = p;
+ }
+
+ return true;
+ }
+
+ /**
+ * Removes all words from the trie that begin with the specified prefix.
+ * Returns true if the trie contained the prefix, false otherwise.
+ *
+ * @param prefix String.
+ * @return true or false.
+ */
+ public boolean removeAll(String prefix) {
+ Trie t = getNode(prefix);
+
+ if (t == null) {
+ return false;
+ }
+
+ if (t.parent == null) {
+ if ((t.numChildren == 0) && !t.isWord) {
+ return false;
+ }
+
+ for (int i = 0; i < t.numChildren; i++) {
+ t.child[i].parent = null;
+ t.child[i] = null;
+ }
+
+ t.numChildren = 0;
+ t.isWord = false;
+
+ return true;
+ }
+
+ Trie p = t.parent;
+ p.removeChild(t);
+ t = p;
+
+ while ((t != null) && (t.numChildren == 0) && !t.isWord) {
+ p = t.parent;
+
+ if (p != null) {
+ p.removeChild(t);
+ }
+
+ t = p;
+ }
+
+ return true;
+ }
+
+ /**
+ * Returns the number of nodes that define isWord as true, starting at
+ * this node and including all of its descendents. This operation requires
+ * traversing the tree rooted at this node.
+ *
+ * @return integer size.
+ */
+ public int size() {
+ int size = 0;
+
+ if (isWord) {
+ size++;
+ }
+
+ for (int i = 0; i < numChildren; i++) {
+ size += child[i].size();
+ }
+
+ return size;
+ }
+
+ /**
+ * Returns all of the words in the trie rooted at this node.
+ *
+ * @return Array of Strings.
+ */
+ public String[] getWords() {
+ return getWords("");
+ }
+
+ /**
+ * Returns all of the words in the trie that begin with the specified
+ * prefix rooted at this node. An array of length 0 is returned if there
+ * are no words that begin with the specified prefix.
+ *
+ * @param prefix String prefix.
+ * @return Array of Strings.
+ */
+ public String[] getWords(String prefix) {
+ Trie n = getNode(prefix);
+
+ if (n == null) {
+ return new String[0];
+ }
+
+ String[] arr = new String[n.size()];
+ n.getWords(arr, 0);
+
+ return arr;
+ }
+
+ private int getWords(String[] arr, int x) {
+ if (isWord) {
+ arr[x++] = toString();
+ }
+
+ for (int i = 0; i < numChildren; i++) {
+ x = child[i].getWords(arr, x);
+ }
+
+ return x;
+ }
+
+ /**
+ * Returns true if the specified string has a prefix path, starting at
+ * this node, where the last node on the path has the isWord flag set to
+ * true. Otherwise false is returned.
+ *
+ * @param s String.
+ * @return true or false.
+ */
+ public boolean hasWord(String s) {
+ return contains(s, false);
+ }
+
+ /**
+ * Returns true if the specified string has a prefix path starting at
+ * this node. Otherwise false is returned.
+ *
+ * @param s String.
+ * @return true or false.
+ */
+ public boolean hasPrefix(String s) {
+ return contains(s, true);
+ }
+
+ /**
+ * This method is the same as the hasWord(String) method.
+ *
+ * @param s String.
+ * @return true or false.
+ * @see #hasWord(String)
+ */
+ public boolean contains(String s) {
+ return contains(s, false);
+ }
+
+ private boolean contains(String s, boolean prefix) {
+ Trie t = getNode(s);
+
+ if (t == null) {
+ return false;
+ }
+
+ if (prefix) {
+ return true;
+ }
+
+ return t.isWord;
+ }
+
+ /**
+ * Returns true if this node has a child with the specified character.
+ *
+ * @param c Character.
+ * @return true or false.
+ */
+ public boolean hasChar(char c) {
+ for (int i = 0; i < numChildren; i++) {
+ if (child[i].ch == c) {
+ return true;
+ }
+ }
+
+ return false;
+ }
+
+ /**
+ * Returns the number of nodes from this node up to the root node.
+ * The root node has height 0.
+ *
+ * @return height integer.
+ */
+ public int getHeight() {
+ int h = -1;
+
+ Trie t = this;
+
+ while (t != null) {
+ h++;
+ t = t.parent;
+ }
+
+ return h;
+ }
+
+ /**
+ * Returns a string containing the characters on the path from this node to
+ * the root, but not including the root character. The last character in
+ * the returned string is the character at this node.
+ *
+ * @return String.
+ */
+ public String toString() {
+ StringBuffer sb = new StringBuffer(getHeight());
+ Trie t = this;
+
+ while (t.parent != null) {
+ sb.append(t.ch);
+ t = t.parent;
+ }
+
+ return sb.reverse().toString();
+ }
+}
diff --git a/coreplugins/QuickFind/src/main/java/csplugins/widgets/autocomplete/index/package.html b/coreplugins/QuickFind/src/main/java/csplugins/widgets/autocomplete/index/package.html
new file mode 100644
index 0000000..6536436
--- /dev/null
+++ b/coreplugins/QuickFind/src/main/java/csplugins/widgets/autocomplete/index/package.html
@@ -0,0 +1,8 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+<html>
+<head></head>
+
+<body bgcolor="white">
+Text Index Utility Package.
+</body>
+</html>
diff --git a/coreplugins/QuickFind/src/main/java/csplugins/widgets/autocomplete/view/AutoCompleteDocument.java b/coreplugins/QuickFind/src/main/java/csplugins/widgets/autocomplete/view/AutoCompleteDocument.java
new file mode 100644
index 0000000..760239d
--- /dev/null
+++ b/coreplugins/QuickFind/src/main/java/csplugins/widgets/autocomplete/view/AutoCompleteDocument.java
@@ -0,0 +1,446 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package csplugins.widgets.autocomplete.view;
+
+import csplugins.widgets.autocomplete.index.Hit;
+
+import java.awt.*;
+
+import javax.swing.*;
+import javax.swing.text.AttributeSet;
+import javax.swing.text.BadLocationException;
+import javax.swing.text.JTextComponent;
+import javax.swing.text.PlainDocument;
+
+
+/**
+ * PlainDocument used by the TextIndexComboBox.
+ * <p/>
+ * Most of this code is based on:
+ * <A href="http://www.orbital-computer.de/JComboBox/">
+ * http://www.orbital-computer.de/JComboBox/</A>, which is in the public
+ * domain.
+ *
+ * @author Thomas Bierhance, Ethan Cerami.
+ */
+public class AutoCompleteDocument extends PlainDocument {
+ // flag to indicate if setSelectedItem has been called
+ // subsequent calls to remove/insertString should be ignored
+ private boolean selecting = false;
+
+ // The container component
+ private TextIndexComboBox comboBox;
+
+ // The editor component
+ private JTextComponent editor;
+
+ // User has pressed the backspace key
+ private boolean hitBackspace;
+
+ // Cursor key pressed
+ private boolean cursorKeyPressed = false;
+
+ // User has pressed the backspace key, while a piece of text was selected
+ private boolean hitBackspaceOnSelection;
+
+ // Debug flag
+ private static final boolean DEBUG_MODE = false;
+
+ /**
+ * Constructor.
+ *
+ * @param comboBox TextIndexComboBox.
+ */
+ public AutoCompleteDocument(TextIndexComboBox comboBox) {
+ this.comboBox = comboBox;
+ this.editor = (JTextComponent) comboBox.getEditor().getEditorComponent();
+ }
+
+ /**
+ * Indicates that text input has triggered a JComboBox setSelectedItem()
+ * call.
+ *
+ * @return true or false.
+ */
+ public boolean getSelecting() {
+ return this.selecting;
+ }
+
+ /**
+ * Indicates if user has just pressed the backspace key.
+ *
+ * @param hitBackspace true or false.
+ */
+ public void setHitBackspace(boolean hitBackspace) {
+ this.hitBackspace = hitBackspace;
+ }
+
+ /**
+ * Sets that the user has pressed a cursor key.
+ *
+ * @param flag cursor key pressed.
+ */
+ public void setCursorKeyPressed(boolean flag) {
+ this.cursorKeyPressed = flag;
+ }
+
+ /**
+ * Indicates that user has pressed a cursor key.
+ *
+ * @return flag cursor key pressed.
+ */
+ public boolean getCursorKeyPressed() {
+ return cursorKeyPressed;
+ }
+
+ /**
+ * Indicates if the user has just pressed the backspace key while a
+ * specific section of text was selected.
+ *
+ * @param hitBackspaceOnSelection true or false.
+ */
+ public void setHitBackspaceOnSelection(boolean hitBackspaceOnSelection) {
+ this.hitBackspaceOnSelection = hitBackspaceOnSelection;
+ }
+
+ /**
+ * Replaces existing text.
+ *
+ * @param offset offset value.
+ * @param length length value.
+ * @param text replacement text.
+ * @param attrs text attributes.
+ * @throws BadLocationException Bad Location Error.
+ */
+ public void replace(int offset, int length, String text, AttributeSet attrs)
+ throws BadLocationException {
+ text = extractAscciCharsOnly(text);
+ debug("replace(), text=" + text + ", cursorKeyPressed=" + cursorKeyPressed);
+
+ int caretPosition = editor.getCaretPosition();
+ super.replace(offset, length, text, attrs);
+
+ if (cursorKeyPressed) {
+ highlightCompletedText(caretPosition);
+ }
+ }
+
+ /**
+ * Removes all text from TextBox; take no other action.
+ *
+ * @throws BadLocationException Bad Location Error.
+ */
+ public void removeAllText() throws BadLocationException {
+ if (getLength() > 0) {
+ super.remove(0, getLength());
+ }
+ }
+
+ /**
+ * Removes some content from the document.
+ * <p/>
+ * Overrides: remove() in class AbstractDocument
+ *
+ * @param offs offset
+ * @param len length
+ * @throws javax.swing.text.BadLocationException
+ * Bad Location Error.
+ */
+ public void remove(int offs, int len) throws BadLocationException {
+ // return immediately when selecting an item; prevents infinite loop
+ if (selecting) {
+ debug("remove(), offs=" + offs + ", len=" + len + " --> Exit");
+
+ return;
+ }
+
+ debug("remove(), offs=" + offs + ", len=" + len + " --> Process");
+
+ // Handle Backspace Key
+ if (hitBackspace) {
+ // user hit backspace => move the selection backwards
+ // old item keeps being selected
+ if (offs > 0) {
+ if (hitBackspaceOnSelection) {
+ offs--;
+ }
+ }
+ }
+
+ // Assume we have the following text: "butter".
+ // Now, we call remove (2, 1), we want the new text to be:
+ // "bu", not "buter".
+ int numCharsToRemove = getLength() - offs;
+ super.remove(offs, numCharsToRemove);
+
+ // Look up new items; calling this method causes the pull-down menu
+ // to be populated with new items.
+ lookUpItem(0, getText(0, getLength()));
+ }
+
+ /**
+ * Inserts String into document.
+ *
+ * @param offs Offset value.
+ * @param str String value.
+ * @param a AttributeSet Object.
+ * @throws BadLocationException Bad Location Error.
+ */
+ public void insertString(int offs, String str, AttributeSet a) throws BadLocationException {
+ // return immediately when selecting an item; prevents infinite loops
+ if (selecting) {
+ debug("insertString(), str=" + str + " --> Exit");
+
+ return;
+ }
+ str = extractAscciCharsOnly(str);
+ debug("insertString(), str=" + str + " --> Process");
+
+ // Assume we have the following text: "butter".
+ // We now call insert (2, "g");
+ // We want the text to now be set to "bug", not "bugtter".
+ // First, insert new string.
+ super.insertString(offs, str, a);
+
+ int newEnd = offs + str.length();
+
+ // Then, remove everything past the newly inserted word
+ if ((getLength() - newEnd) > 0) {
+ super.remove(newEnd, getLength() - (newEnd));
+ }
+
+ // Perform item lookup
+ lookUpItem(offs, str);
+ }
+
+ /**
+ * Populates the Pull-Down menu with all words that begin with the
+ * specific pattern.
+ *
+ * @param pattern String pattern.
+ */
+ public void populatePullDownMenu(String pattern) {
+ debug("Start : populatePullDownMenu(), pattern=" + pattern);
+
+ Hit[] hits = comboBox.getTextIndex()
+ .getHits(pattern, TextIndexComboBox.DEFAULT_MAX_HITS_SHOWN);
+
+ // Populate Pull-Down Menu with matching items derived from TextIndex
+ // Must set selecting flag to true, as modifying the model will
+ // result is multiple calls to setSelectedItem(), which results
+ // in an infinite loop.
+ setSelecting(true);
+
+ DefaultComboBoxModel model = (DefaultComboBoxModel) comboBox.getModel();
+ debug("Start: Remove all elements");
+ model.removeAllElements();
+ debug("End: Remove all elements");
+
+ if (hits.length > 0) {
+ int stopHits = Math.min(hits.length, TextIndexComboBox.DEFAULT_MAX_HITS_SHOWN);
+
+ for (int i = 0; i < stopHits; i++) {
+ // When we call addElement and there is only one item in
+ // the list, the DefaultComboBox will automatically call
+ // setSelected(); this can result in an inifinte loop.
+ // To prevent this, we set the set selecting flag to true.
+ model.addElement(hits[i]);
+ }
+
+ editor.setBackground(Color.WHITE);
+ editor.setForeground(Color.BLACK);
+ } else {
+ if ((comboBox.getTextIndex() != null) && (comboBox.getTextIndex().getNumKeys() > 0)) {
+ model.addElement(new Hit(pattern, new Object[0]));
+ editor.setBackground(new Color(212, 153, 159));
+ editor.setForeground(Color.WHITE);
+ }
+ }
+
+ // Set Max Row Count; this automatically resizes the pop-up
+ // menu window.
+ if (model.getSize() < TextIndexComboBox.DEFAULT_MAX_ROWS_VISIBLE) {
+ comboBox.setMaximumRowCount(model.getSize());
+ } else {
+ comboBox.setMaximumRowCount(TextIndexComboBox.DEFAULT_MAX_ROWS_VISIBLE);
+ }
+
+ // Must set selected item to null; otherwise, zeroeth
+ // item in model is selected, and we don't want it to be.
+ setSelectedItem(null);
+ setSelecting(false);
+ debug("End: populatePullDownMenu(), pattern=" + pattern);
+ }
+
+ /**
+ * Looks up item from the Pull-Down menu.
+ *
+ * @param offs Offset into document.
+ * @param str Newly inserted addition to the document.
+ * @throws BadLocationException Bad Location Error.
+ */
+ private void lookUpItem(int offs, String str) throws BadLocationException {
+ if (cursorKeyPressed) {
+ debug("lookUpItem(), str=" + str + ", cursorKeyPressed: " + cursorKeyPressed
+ + " --> Exit");
+
+ return;
+ }
+
+ debug("lookUpItem(), str=" + str + ", cursorKeyPressed: " + cursorKeyPressed
+ + " --> Process");
+
+ String pattern = getText(0, getLength());
+
+ if (pattern != null) {
+ populatePullDownMenu(pattern);
+
+ // Make pop-up visible; must be done b/c model has been reset
+ if (!comboBox.getUI().isPopupVisible(comboBox)) {
+ if (comboBox.isDisplayable()) {
+ comboBox.setPopupVisible(true);
+ }
+ }
+
+ // Iterate through all items in pull-down menu
+ Object item = null;
+ ComboBoxModel model = comboBox.getModel();
+
+ for (int i = 0, n = model.getSize(); i < n; i++) {
+ Object currentItem = model.getElementAt(i);
+
+ // current item starts with the pattern?
+ if ((currentItem != null) && startsWithIgnoreCase(currentItem.toString(), pattern)) {
+ item = currentItem;
+
+ break;
+ }
+ }
+
+ if (item != null) {
+ setSelectedItem(item);
+ // select the completed part
+ highlightCompletedText(offs + str.length());
+ }
+ }
+ }
+
+ /**
+ * Sets Document Text.
+ *
+ * @param text Document Text.
+ */
+ private void setText(String text) {
+ debug("setText(), text=" + text);
+
+ try {
+ // remove all text and insert the completed string
+ super.remove(0, getLength());
+ super.insertString(0, text, null);
+ } catch (BadLocationException e) {
+ throw new RuntimeException(e.toString());
+ }
+ }
+
+ /**
+ * Highlights Completed Text, so that it is clear which text was entered
+ * by the user, and which text was auto-completed.
+ *
+ * @param start start index.
+ */
+ private void highlightCompletedText(int start) {
+ debug("highlightCompletedText, start= " + start);
+ editor.setCaretPosition(getLength());
+ editor.moveCaretPosition(start);
+ }
+
+ /**
+ * Sets Selected Item.
+ *
+ * @param item Object selected.
+ */
+ private void setSelectedItem(Object item) {
+ debug("setSelectedItem(), item=" + item);
+
+ if (item != null) {
+ setSelecting(true);
+
+ ComboBoxModel model = comboBox.getModel();
+ model.setSelectedItem(item);
+ setText(item.toString());
+ setSelecting(false);
+ }
+ }
+
+ /**
+ * Indicates whether item is being selected from the pull-down menu.
+ *
+ * @param selecting true or false.
+ */
+ public void setSelecting(boolean selecting) {
+ this.selecting = selecting;
+ }
+
+ // checks if str1 starts with str2 - ignores case
+ protected boolean startsWithIgnoreCase(String str1, String str2) {
+ return str1.toUpperCase().startsWith(str2.toUpperCase());
+ }
+
+ private void debug(String str) {
+ if (DEBUG_MODE) {
+ System.out.println(str);
+ }
+ }
+
+ /**
+ * Enables users to only enter ASCII chars <= 255.
+ * This prevents users from entering Unicode values via, e.g. the ALT/Option key
+ * combination. Part of fix for bug #1310.
+ * @param text
+ * @return text containing only ASCII characters; all other chars are filered out.
+ */
+ private String extractAscciCharsOnly (String text) {
+ StringBuffer newText = new StringBuffer();
+ for (int i=0; i<text.length(); i++) {
+ char c = text.charAt(i);
+ if (c <= 126) {
+ newText.append(c);
+ }
+ }
+ return newText.toString();
+ }
+}
diff --git a/coreplugins/QuickFind/src/main/java/csplugins/widgets/autocomplete/view/ComboBoxFactory.java b/coreplugins/QuickFind/src/main/java/csplugins/widgets/autocomplete/view/ComboBoxFactory.java
new file mode 100644
index 0000000..6adbd11
--- /dev/null
+++ b/coreplugins/QuickFind/src/main/java/csplugins/widgets/autocomplete/view/ComboBoxFactory.java
@@ -0,0 +1,87 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package csplugins.widgets.autocomplete.view;
+
+import csplugins.widgets.autocomplete.index.TextIndex;
+
+import javax.swing.*;
+
+
+/**
+ * Factory for creating TextIndexComboBoxes.
+ *
+ * @author Ethan Cerami
+ */
+public class ComboBoxFactory {
+ /**
+ * Creates a new TextIndex Combo Box.
+ *
+ * @param textIndex Text Index Object.
+ * @param popupWindowSizeMultiple Indicates the size multiple used
+ * to resize the popup window.
+ * @return TextIndexComboBox Object.
+ * @throws IllegalAccessException Could not set Cross Platform
+ * Look and Feel.
+ * @throws UnsupportedLookAndFeelException
+ * Could not set Cross Platform
+ * Look and Feel.
+ * @throws InstantiationException Could not set Cross Platform
+ * Look and Feel.
+ * @throws ClassNotFoundException Could not set Cross Platform
+ * Look and Feel.
+ */
+ public static TextIndexComboBox createTextIndexComboBox(TextIndex textIndex,
+ double popupWindowSizeMultiple)
+ throws IllegalAccessException, UnsupportedLookAndFeelException, InstantiationException,
+ ClassNotFoundException {
+ // Obtain the current L & F
+ LookAndFeel currentLookAndFeel = UIManager.getLookAndFeel();
+
+ // Set to Default Java Cross Platform L & F
+ // UIManager.setLookAndFeel
+ // ("com.sun.java.swing.plaf.gtk.GTKLookAndFeel");
+ UIManager.setLookAndFeel(UIManager.getCrossPlatformLookAndFeelClassName());
+
+ // Create the ToDelete
+ TextIndexComboBox comboBox = new TextIndexComboBox(textIndex, popupWindowSizeMultiple);
+
+ // Return to original L & F
+ UIManager.setLookAndFeel(currentLookAndFeel);
+
+ return comboBox;
+ }
+}
diff --git a/coreplugins/QuickFind/src/main/java/csplugins/widgets/autocomplete/view/TextBoxRenderer.java b/coreplugins/QuickFind/src/main/java/csplugins/widgets/autocomplete/view/TextBoxRenderer.java
new file mode 100644
index 0000000..0b971b0
--- /dev/null
+++ b/coreplugins/QuickFind/src/main/java/csplugins/widgets/autocomplete/view/TextBoxRenderer.java
@@ -0,0 +1,225 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package csplugins.widgets.autocomplete.view;
+
+import csplugins.widgets.autocomplete.index.Hit;
+
+import java.awt.*;
+
+import javax.swing.*;
+import javax.swing.border.EmptyBorder;
+
+
+/**
+ * Custom Renderer for the TextIndexComboBox.
+ *
+ * @author Ethan Cerami
+ */
+public class TextBoxRenderer implements ListCellRenderer {
+ private JComboBox box;
+ private double popupSizeMultiple;
+ private static final int HGAP = 10;
+ private static final boolean DEBUG = false;
+
+ /**
+ * Constructor.
+ *
+ * @param box JComboBox.
+ * @param popupSizeMultiple Popup size multiple.
+ */
+ public TextBoxRenderer(JComboBox box, double popupSizeMultiple) {
+ this.box = box;
+ this.popupSizeMultiple = popupSizeMultiple;
+ }
+
+ /**
+ * This method finds the image and text corresponding
+ * to the selected value and returns the label, set up
+ * to display the text and image.
+ *
+ * @param list JList Object.
+ * @param value Object value.
+ * @param index Index value.
+ * @param isSelected is item selected flag.
+ * @param cellHasFocus call has focus flag.
+ * @return Component Object.
+ */
+ public Component getListCellRendererComponent(JList list, Object value, int index,
+ boolean isSelected, boolean cellHasFocus) {
+ // Create a JPanel Object
+ JPanel panel = new JPanel();
+ panel.setOpaque(true);
+
+ // Set different colors, depending on state
+ if (isSelected) {
+ panel.setBackground(list.getSelectionBackground());
+ panel.setForeground(list.getSelectionForeground());
+ } else {
+ panel.setBackground(list.getBackground());
+ panel.setForeground(list.getForeground());
+ }
+
+ // Use Box Layout, X-AXIS
+ panel.setLayout(new BoxLayout(panel, BoxLayout.X_AXIS));
+ panel.setBorder(new EmptyBorder(2, 2, 2, 2));
+
+ // Create text match label, but do not (yet) set final text,
+ // as we may need to truncate it.
+ JLabel textMatchLabel = new JLabel("TEMP", JLabel.LEFT);
+ panel.setToolTipText(value.toString());
+
+ String numResults = getNumResults(value);
+ JLabel numResultsLabel = new JLabel(numResults, JLabel.RIGHT);
+ numResultsLabel.setFont(new Font("Monospaced", Font.PLAIN,
+ numResultsLabel.getFont().getSize() - 1));
+
+ // Set color to green (matches exist) or red (no matches exist);
+ Color color = new Color(51, 102, 51);
+
+ if (value instanceof Hit) {
+ Hit hit = (Hit) value;
+
+ if (hit.getAssociatedObjects() != null) {
+ int numHits = hit.getAssociatedObjects().length;
+
+ if (numHits == 0) {
+ color = new Color(150, 0, 0);
+ }
+ }
+ }
+
+ numResultsLabel.setForeground(color);
+
+ // Resize Labels
+ resizeLabels(numResultsLabel, textMatchLabel, value.toString());
+
+ // Add Label 1, then glue, then Label 2
+ // The glue forces Label 1 to be left aligned, and Label 2 to be
+ // right aligned
+ panel.add(textMatchLabel);
+ panel.add(Box.createHorizontalGlue());
+ panel.add(numResultsLabel);
+
+ return panel;
+ }
+
+ /**
+ * Resizes the Labels, as needed.
+ *
+ * @param numResultsLabel Number of Results Label.
+ * @param textMatchLabel Text Match Label.
+ */
+ private void resizeLabels(JLabel numResultsLabel, JLabel textMatchLabel, String textString) {
+ if (box.isPopupVisible()) {
+ // How wide is the popup window?
+ int widthOfPopUpWindow = (int) (box.getSize().width * this.popupSizeMultiple);
+
+ // How wide is numResultsLabel?
+ FontMetrics fontMetrics = numResultsLabel.getFontMetrics(numResultsLabel.getFont());
+ int widthOfNumResultsText = fontMetrics.stringWidth(numResultsLabel.getText());
+
+ // How wide is the vertical scrollbar?
+ int widthOfVerticalScrollBar = 0;
+ Object comp = box.getUI().getAccessibleChild(box, 0);
+
+ if (comp instanceof JPopupMenu) {
+ JScrollPane scrollPane = (JScrollPane) ((JPopupMenu) comp).getComponent(0);
+ JScrollBar verticalScrollBar = scrollPane.getVerticalScrollBar();
+
+ if ((verticalScrollBar != null) && verticalScrollBar.isVisible()) {
+ widthOfVerticalScrollBar = verticalScrollBar.getPreferredSize().width;
+ }
+ }
+
+ // Truncate label text, as needed
+ int maxWidthOfTextValue = widthOfPopUpWindow
+ - (HGAP + widthOfNumResultsText + widthOfVerticalScrollBar);
+ fontMetrics = textMatchLabel.getFontMetrics(textMatchLabel.getFont());
+
+ int currentWidth = fontMetrics.stringWidth(textString);
+
+ if ((currentWidth + HGAP) > maxWidthOfTextValue) {
+ textMatchLabel.setText(textMatchLabel.getText() + "...");
+
+ // while loop: truncate string one letter at a time
+ // until we have the right size string.
+ while ((currentWidth + HGAP) > maxWidthOfTextValue) {
+ textString = textString.substring(0, textString.length() - 4) + "...";
+ currentWidth = fontMetrics.stringWidth(textString);
+ }
+ }
+
+ textMatchLabel.setText(textString);
+
+ if (DEBUG) {
+ System.out.println("Width of window: " + widthOfPopUpWindow);
+ System.out.println("Width of num results text: " + widthOfNumResultsText);
+ System.out.println("Bar: " + widthOfVerticalScrollBar);
+ System.out.println("Width of text: " + maxWidthOfTextValue);
+ }
+ }
+ }
+
+ /**
+ * Gets Number of Matching Results.
+ *
+ * @param value Object Value.
+ * @return Number of Results String.
+ */
+ private String getNumResults(Object value) {
+ String numResults = null;
+
+ if (value instanceof Hit) {
+ Hit hit = (Hit) value;
+ Object[] objects = hit.getAssociatedObjects();
+
+ if (objects != null) {
+ if (objects.length == 1) {
+ numResults = "1 hit ";
+ } else {
+ numResults = objects.length + " hits ";
+ }
+ }
+ }
+
+ if (numResults == null) {
+ numResults = " -- ";
+ }
+
+ return numResults;
+ }
+}
diff --git a/coreplugins/QuickFind/src/main/java/csplugins/widgets/autocomplete/view/TextIndexComboBox.java b/coreplugins/QuickFind/src/main/java/csplugins/widgets/autocomplete/view/TextIndexComboBox.java
new file mode 100644
index 0000000..339cde5
--- /dev/null
+++ b/coreplugins/QuickFind/src/main/java/csplugins/widgets/autocomplete/view/TextIndexComboBox.java
@@ -0,0 +1,459 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package csplugins.widgets.autocomplete.view;
+
+import csplugins.widgets.autocomplete.index.TextIndex;
+
+import javax.swing.*;
+import javax.swing.event.EventListenerList;
+import javax.swing.event.PopupMenuEvent;
+import javax.swing.event.PopupMenuListener;
+import javax.swing.text.BadLocationException;
+import javax.swing.text.JTextComponent;
+import java.awt.*;
+import java.awt.event.*;
+
+
+/**
+ * JComboBox, which provides a built-in auto complete feature.
+ * <p/>
+ * Most of this code is based on:
+ * <A href="http://www.orbital-computer.de/JComboBox/">
+ * http://www.orbital-computer.de/JComboBox/</A>, which is in the public
+ * domain.
+ * <p/>
+ *
+ * @author Ethan Cerami.
+ */
+public class TextIndexComboBox extends JComboBox {
+ private AutoCompleteDocument doc;
+ private TextIndex textIndex;
+ private boolean firingFinalSelectionEvent;
+ private double popupWindowSizeMultiple;
+
+ /**
+ * A list of final selection event listeners for this component.
+ */
+ protected EventListenerList finalSelectionListenerList = new EventListenerList();
+
+ /**
+ * Default: Maximum Row Count Visible
+ */
+ public static final int DEFAULT_MAX_ROWS_VISIBLE = 5;
+
+ /**
+ * Default: Max number of hits to show in pull-down menu
+ */
+ public static final int DEFAULT_MAX_HITS_SHOWN = 20;
+
+ /**
+ * Package-Level Constructor.
+ * <P>To instantiate a TextIndexComoboBox, you must use the
+ * {@link
+ * ComboBoxFactory#createTextIndexComboBox
+ * (csplugins.widgets.autocomplete.index.TextIndex)}
+ * method.
+ *
+ * @param textIndex TextIndex Object.
+ * @param popupWindowSizeMultiple Indicates the size multiple used
+ * to resize the popup window.
+ */
+ TextIndexComboBox(TextIndex textIndex, double popupWindowSizeMultiple) {
+ this.textIndex = textIndex;
+ this.popupWindowSizeMultiple = popupWindowSizeMultiple;
+ init();
+
+ // Populate menu with first X items
+ doc.populatePullDownMenu("");
+ }
+
+ /**
+ * Sets the Text Index Object.
+ *
+ * @param textIndex TextIndex Object.
+ */
+ public void setTextIndex(TextIndex textIndex) {
+ this.textIndex = textIndex;
+
+ // Remove Existing Text in Text Box
+ try {
+ doc.removeAllText();
+ } catch (BadLocationException e) {
+ }
+
+ // Populate menu with first X items
+ doc.populatePullDownMenu("");
+ }
+
+ /**
+ * Removes all text from combo box.
+ */
+ public void removeAllText() {
+ try {
+ doc.removeAllText();
+ } catch (BadLocationException e) {
+ }
+ }
+
+ /**
+ * Gets the Text Index Object.
+ *
+ * @return Text Index Object.
+ */
+ public TextIndex getTextIndex() {
+ return this.textIndex;
+ }
+
+ /**
+ * Sets selected item.
+ *
+ * @param object Selected Item Object.
+ */
+ public void setSelectedItem(Object object) {
+ super.setSelectedItem(object);
+
+ // Only fire final selection event if this is a mouse selection
+ if (!doc.getSelecting() && !doc.getCursorKeyPressed()) {
+ this.fireFinalSelectionEvent();
+ }
+ }
+
+ /**
+ * Adds an <code>ActionListener</code>.
+ * <p/>
+ * The <code>ActionListener</code> will receive an <code>ActionEvent</code>
+ * when a <b>final</b> selection has been made by the user. A final
+ * selection occurs when:
+ * <UL>
+ * <LI>A user hits Enter; or
+ * <LI>A user clicks on an item in the pull-down menu.
+ * </UL>
+ *
+ * @param l the <code>ActionListener</code> that is to be notified
+ * @see #setSelectedItem
+ */
+ public void addFinalSelectionListener(ActionListener l) {
+ finalSelectionListenerList.add(ActionListener.class, l);
+ }
+
+ /**
+ * Returns an array of all the <code>ActionListener</code>s added
+ * to this TextComboBox with addFinalSelectionListener().
+ *
+ * @return all of the <code>ActionListener</code>s added or an empty
+ * array if no listeners have been added
+ * @since 1.4
+ */
+ public ActionListener[] getFinalSelectionListeners() {
+ return (ActionListener[]) finalSelectionListenerList.getListeners(ActionListener.class);
+ }
+
+ /**
+ * Removes an <code>ActionListener</code> added to this TextComboBox
+ * with addFinalSelectionListener().
+ *
+ * @param l the <code>ActionListener</code> to remove
+ */
+ public void removeFinalSelectionListener(ActionListener l) {
+ finalSelectionListenerList.remove(ActionListener.class, l);
+ }
+
+ /**
+ * Notifies all listeners that have registered interest for
+ * notification on this event type.
+ *
+ * @see EventListenerList
+ */
+ protected void fireFinalSelectionEvent() {
+ if (!firingFinalSelectionEvent) {
+ // Set flag to ensure that an infinite loop is not created
+ firingFinalSelectionEvent = true;
+
+ ActionEvent e = null;
+
+ // Guaranteed to return a non-null array
+ Object[] listeners = finalSelectionListenerList.getListenerList();
+ long mostRecentEventTime = EventQueue.getMostRecentEventTime();
+ int modifiers = 0;
+ AWTEvent currentEvent = EventQueue.getCurrentEvent();
+
+ if (currentEvent instanceof InputEvent) {
+ modifiers = ((InputEvent) currentEvent).getModifiers();
+ } else if (currentEvent instanceof ActionEvent) {
+ modifiers = ((ActionEvent) currentEvent).getModifiers();
+ }
+
+ // Process the listeners last to first, notifying
+ // those that are interested in this event
+ for (int i = listeners.length - 2; i >= 0; i -= 2) {
+ if (listeners[i] == ActionListener.class) {
+ // Lazily create the event:
+ if (e == null) {
+ e = new ActionEvent(this, ActionEvent.ACTION_PERFORMED, getActionCommand(),
+ mostRecentEventTime, modifiers);
+ }
+
+ ((ActionListener) listeners[i + 1]).actionPerformed(e);
+ }
+ }
+
+ firingFinalSelectionEvent = false;
+ }
+ }
+
+ /**
+ * Initializes the Component.
+ */
+ private void init() {
+ // Enable Editing on ComboBox
+ setEditable(true);
+
+ // Set Max Rows Displayed
+ setMaximumRowCount(DEFAULT_MAX_ROWS_VISIBLE);
+
+ // Set Custom Document for processing user input
+ final JTextComponent editor = (JTextComponent) getEditor().getEditorComponent();
+ doc = new AutoCompleteDocument(this);
+ editor.setDocument(doc);
+
+ // Set Custom Renderer
+ setRenderer(new TextBoxRenderer(this, popupWindowSizeMultiple));
+ setBackground(Color.WHITE);
+
+ // Add Hit Listener, to auto pop-up the menu, and to detect
+ // specific keystrokes.
+ KeyAdapter editorKeyListener = new UserKeyListener(doc, editor, this);
+ editor.addKeyListener(editorKeyListener);
+
+ try {
+ // Over-ride default key mappings in JTextField, as these conflict
+ // with menu-item key mappings in the main Cytoscape tool bar.
+ // See bug: #1310.
+
+ // For future reference, built-in key mappings for JTextField are:
+ // pressed END
+ // ctrl pressed O
+ // pressed KP_LEFT
+ // pressed RIGHT
+ // pressed HOME
+ // pressed V
+ // pressed H (*)
+ // pressed KP_LEFT
+ // pressed LEFT
+ // pressed X
+ // pressed KP_RIGHT
+ // ctrl pressed KP_RIGHT
+ // pressed COPY
+ // shift pressed HOME
+ // pressed RIGHT
+ // shift ctrl pressed LEFT
+ // ctrl pressed KP_LEFT
+ // ctrl pressed KP_RIGHT
+ // pressed PASTE
+ // shift ctrl pressed RIGHT
+ // ctrl pressed BACK_SLASH
+ // ctrl pressed A
+ // shift pressed KP_RIGHT
+ // pressed CUT
+ // ctrl pressed LEFT
+ // pressed BACK_SPACE
+ // shift ctrl pressed KP_LEFT
+ // ctrl pressed C
+ // shift pressed END
+ // ctrl pressed RIGHT
+ // pressed DELETE
+ // pressed ENTER
+ // shift pressed LEFT
+ //
+ // * = indicates conflict with Cytsoscape Menu Item
+
+ JTextField textField = (JTextField) this.getEditor().getEditorComponent();
+
+ // By setting to "none", these keystrokes are passed up the containment
+ // hierarchy, and eventually make their way up to the Cytoscape Desktop.
+ KeyStroke keyStroke = javax.swing.KeyStroke.getKeyStroke
+ (java.awt.event.KeyEvent.VK_H, ActionEvent.CTRL_MASK);
+ textField.getInputMap().put(keyStroke, "none");
+
+ keyStroke = javax.swing.KeyStroke.getKeyStroke
+ (java.awt.event.KeyEvent.VK_H, ActionEvent.ALT_MASK);
+ textField.getInputMap().put(keyStroke, "none");
+ } catch (ClassCastException e) {
+ // Ignore it.
+ }
+
+ // Add PopupMenuListener, in order to resize size of popup window
+ addPopupMenuListener(new UserPopupListener(popupWindowSizeMultiple));
+ }
+}
+
+
+/**
+ * KeyListener for listening to specific key press / release events.
+ *
+ * @author Ethan Cerami
+ */
+class UserKeyListener extends KeyAdapter {
+ private AutoCompleteDocument doc;
+ private JTextComponent editor;
+ private TextIndexComboBox comboBox;
+
+ /**
+ * Constructor.
+ *
+ * @param doc Document.
+ * @param editor Editor.
+ * @param comboBox JComboBox.
+ */
+ UserKeyListener(AutoCompleteDocument doc, JTextComponent editor, TextIndexComboBox comboBox) {
+ this.doc = doc;
+ this.editor = editor;
+ this.comboBox = comboBox;
+ }
+
+ /**
+ * User has pressed a key.
+ *
+ * @param e KeyEvent Object.
+ */
+ public void keyPressed(KeyEvent e) {
+ doc.setHitBackspace(false);
+
+ switch (e.getKeyCode()) {
+ // determine if the pressed key is backspace
+ // (needed by the remove method)
+ case KeyEvent.VK_BACK_SPACE:
+ doc.setHitBackspace(true);
+ doc.setHitBackspaceOnSelection(editor.getSelectionStart() != editor.getSelectionEnd());
+
+ break;
+
+ case KeyEvent.VK_UP:
+ case KeyEvent.VK_DOWN:
+ case KeyEvent.VK_PAGE_DOWN:
+ case KeyEvent.VK_PAGE_UP:
+ doc.setCursorKeyPressed(true);
+
+ break;
+
+ case KeyEvent.VK_ENTER:
+ comboBox.fireFinalSelectionEvent();
+
+ break;
+ }
+ }
+
+ /**
+ * User has released a key.
+ *
+ * @param e KeyEvent Object.
+ */
+ public void keyReleased(KeyEvent e) {
+ if ((e.getKeyCode() == KeyEvent.VK_UP) || (e.getKeyCode() == KeyEvent.VK_DOWN)
+ || (e.getKeyCode() == KeyEvent.VK_PAGE_UP) || (e.getKeyCode() == KeyEvent.VK_PAGE_DOWN)) {
+ doc.setCursorKeyPressed(false);
+ }
+ }
+}
+
+
+/**
+ * PopupMenu Listener.
+ * <p/>
+ * Hack used to make the size of the pop-up menu bigger than the size
+ * of the JComboBox, to which it is attached.
+ * Hack is described here:
+ * http://forums.java.net/jive/thread.jspa?threadID=9017&messageID=61267
+ *
+ * @author Ethan Cerami.
+ */
+class UserPopupListener implements PopupMenuListener {
+ private double popupWindowSizeMultiple;
+
+ /**
+ * Constructor.
+ *
+ * @param popupWindowSizeMultiple Indicates the size multiple used
+ * to resize the popup window.
+ */
+ public UserPopupListener(double popupWindowSizeMultiple) {
+ this.popupWindowSizeMultiple = popupWindowSizeMultiple;
+ }
+
+ /**
+ * PopupMenu Will Become Visible: Resize.
+ *
+ * @param e PopupMenuEvent.
+ */
+ public void popupMenuWillBecomeVisible(PopupMenuEvent e) {
+ JComboBox box = (JComboBox) e.getSource();
+ Object comp = box.getUI().getAccessibleChild(box, 0);
+
+ if (!(comp instanceof JPopupMenu)) {
+ return;
+ }
+
+ JPopupMenu popUpMenu = (JPopupMenu) comp;
+ // Set to Flow Layout, fixes bug in Mac OS X, Java 1.5
+ popUpMenu.setLayout(new FlowLayout(FlowLayout.LEFT));
+
+ // Set size of ScrollPane
+ JScrollPane scrollPane = (JScrollPane) popUpMenu.getComponent(0);
+ scrollPane.setOpaque(true);
+
+ Dimension size = scrollPane.getPreferredSize();
+ size.width = (int) (size.width * popupWindowSizeMultiple);
+ scrollPane.setPreferredSize(size);
+ }
+
+ /**
+ * PopupMenu Will Become Invisible: No-op.
+ *
+ * @param e PopupMenuEvent.
+ */
+ public void popupMenuWillBecomeInvisible(PopupMenuEvent e) {
+ // No-op
+ }
+
+ /**
+ * PopupMenu Canceled: No-op.
+ *
+ * @param e PopupMenuEvent.
+ */
+ public void popupMenuCanceled(PopupMenuEvent e) {
+ // No-op
+ }
+}
diff --git a/coreplugins/QuickFind/src/main/java/csplugins/widgets/autocomplete/view/package.html b/coreplugins/QuickFind/src/main/java/csplugins/widgets/autocomplete/view/package.html
new file mode 100644
index 0000000..259e52a
--- /dev/null
+++ b/coreplugins/QuickFind/src/main/java/csplugins/widgets/autocomplete/view/package.html
@@ -0,0 +1,8 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+<html>
+<head></head>
+
+<body bgcolor="white">
+AutoCompleteComboBox Package.
+</body>
+</html>
diff --git a/coreplugins/QuickFind/src/main/java/csplugins/widgets/slider/JRangeSliderExtended.java b/coreplugins/QuickFind/src/main/java/csplugins/widgets/slider/JRangeSliderExtended.java
new file mode 100644
index 0000000..6b8f126
--- /dev/null
+++ b/coreplugins/QuickFind/src/main/java/csplugins/widgets/slider/JRangeSliderExtended.java
@@ -0,0 +1,225 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package csplugins.widgets.slider;
+
+import prefuse.data.query.NumberRangeModel;
+
+import prefuse.util.ui.JRangeSlider;
+
+import java.awt.*;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseEvent;
+
+import java.text.DecimalFormat;
+
+import javax.swing.*;
+import javax.swing.border.EmptyBorder;
+import javax.swing.border.LineBorder;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+
+
+/**
+ * Extension of the Prefuse JRangeSlider.
+ *
+ * @author Ethan Cerami.
+ * @see prefuse.util.ui.JRangeSlider
+ */
+public class JRangeSliderExtended extends JRangeSlider implements ChangeListener {
+ private Dimension preferredSize;
+ private Popup popup;
+ private JLabel popupLow;
+ private JLabel popupHigh;
+ private PopupDaemon popupDaemon;
+
+ /**
+ * Create a new range slider.
+ *
+ * @param model - a BoundedRangeModel specifying the slider's range
+ * @param orientation - construct a horizontal or vertical slider?
+ * @param direction - Is the slider left-to-right/top-to-bottom or
+ * right-to-left/bottom-to-top
+ */
+ public JRangeSliderExtended(BoundedRangeModel model, int orientation, int direction) {
+ super(model, orientation, direction);
+ addChangeListener(this);
+ }
+
+ /**
+ * Overrides default preferred size of JRangeSlider.
+ * <P>JRangeSlider is hard-coded to always be 300 px wide, and that is
+ * a bit constrained.
+ *
+ * @return Preferred Dimension.
+ */
+ public Dimension getPreferredSize() {
+ if (preferredSize == null) {
+ return super.getPreferredSize();
+ } else {
+ return preferredSize;
+ }
+ }
+
+ /**
+ * Sets the preferred size of the component.
+ *
+ * @param preferredSize Preferred Size.
+ */
+ public void setPreferredSize(Dimension preferredSize) {
+ this.preferredSize = preferredSize;
+ }
+
+ /**
+ * Placeholder.
+ *
+ * @param mouseEvent Mouse Event Object.
+ */
+ public void mouseReleased(MouseEvent mouseEvent) {
+ super.mouseReleased(mouseEvent);
+ }
+
+ /**
+ * Resets / hides Popup window.
+ */
+ public void resetPopup() {
+ if (popup != null) {
+ popup.hide();
+ }
+
+ this.popup = null;
+ }
+
+ /**
+ * Upon state change, pop-up a tiny window with low-high.
+ *
+ * @param e ChangeEvent Object.
+ */
+ public void stateChanged(ChangeEvent e) {
+ NumberRangeModel model = (NumberRangeModel) getModel();
+ Number low = (Number) model.getLowValue();
+ Number high = (Number) model.getHighValue();
+ Number min = (Number) model.getMinValue();
+ Number max = (Number) model.getMaxValue();
+
+ DecimalFormat format;
+
+ String lowStr = null;
+ String highStr = null;
+ if (low instanceof Integer) {
+ lowStr = Integer.toString((Integer) low);
+ highStr = Integer.toString((Integer) high);
+ } else {
+ if ((max.doubleValue() - min.doubleValue()) < .001) {
+ format = new DecimalFormat("0.###E0");
+ } else if ((max.doubleValue() - min.doubleValue()) > 100000) {
+ format = new DecimalFormat("0.###E0");
+ } else {
+ format = new DecimalFormat("###,###.000");
+ }
+ lowStr = format.format(low);
+ highStr = format.format(high);
+ }
+
+ if (isVisible()) {
+ if (popup == null) {
+ PopupFactory popupFactory = PopupFactory.getSharedInstance();
+ JPanel panel = new JPanel();
+ panel.setBorder(new LineBorder(Color.LIGHT_GRAY, 1));
+ panel.setPreferredSize(getPreferredSize());
+ panel.setLayout(new BoxLayout(panel, BoxLayout.X_AXIS));
+ popupLow = new JLabel(lowStr);
+ popupLow.setBorder(new EmptyBorder(6, 2, 6, 2));
+ popupHigh = new JLabel(highStr);
+ popupHigh.setBorder(new EmptyBorder(6, 2, 6, 2));
+ panel.add(popupLow);
+ panel.add(Box.createHorizontalGlue());
+ panel.add(popupHigh);
+ popup = popupFactory.getPopup(this, panel, getLocationOnScreen().x,
+ getLocationOnScreen().y + getPreferredSize().height
+ + 2);
+ popupDaemon = new PopupDaemon(this, 2000);
+
+ popup.show();
+ popupDaemon.restart();
+ } else {
+ popupLow.setText(lowStr);
+ popupHigh.setText(highStr);
+ popupDaemon.restart();
+ }
+ }
+ }
+}
+
+
+/**
+ * Daemon Thread to automatically hide Pop-up Window after xxx milliseconds.
+ *
+ * @author Ethan Cerami
+ */
+class PopupDaemon implements ActionListener {
+ private Timer timer;
+ private JRangeSliderExtended slider;
+
+ /**
+ * Constructor.
+ *
+ * @param slider JRangeSliderExtended Object.
+ * @param delay Delay until pop-up window is hidden.
+ */
+ public PopupDaemon(JRangeSliderExtended slider, int delay) {
+ timer = new Timer(delay, this);
+ timer.setRepeats(false);
+ this.slider = slider;
+ }
+
+ /**
+ * Restart timer.
+ */
+ public void restart() {
+ timer.restart();
+ }
+
+ /**
+ * Timer Event: Hide popup now.
+ *
+ * @param e ActionEvent Object.
+ */
+ public void actionPerformed(ActionEvent e) {
+ slider.resetPopup();
+ }
+}
diff --git a/coreplugins/QuickFind/src/main/java/csplugins/widgets/slider/package.html b/coreplugins/QuickFind/src/main/java/csplugins/widgets/slider/package.html
new file mode 100644
index 0000000..76c83cb
--- /dev/null
+++ b/coreplugins/QuickFind/src/main/java/csplugins/widgets/slider/package.html
@@ -0,0 +1,8 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+<html>
+<head></head>
+
+<body bgcolor="white">
+Slider Widget Package.
+</body>
+</html>
diff --git a/coreplugins/QuickFind/src/main/java/prefuse/data/query/NumberRangeModel.java b/coreplugins/QuickFind/src/main/java/prefuse/data/query/NumberRangeModel.java
new file mode 100644
index 0000000..ec12434
--- /dev/null
+++ b/coreplugins/QuickFind/src/main/java/prefuse/data/query/NumberRangeModel.java
@@ -0,0 +1,343 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package prefuse.data.query;
+
+import prefuse.util.TypeLib;
+
+import prefuse.util.ui.ValuedRangeModel;
+
+import javax.swing.DefaultBoundedRangeModel;
+
+
+/**
+ * Range model for numerical data. Designed to support range-based dynamic
+ * queries.
+ *
+ * @author <a href="http://jheer.org">jeffrey heer</a>
+ */
+public class NumberRangeModel extends DefaultBoundedRangeModel implements ValuedRangeModel {
+ protected Class m_type;
+ protected Number m_min;
+ protected Number m_max;
+ protected Number m_lo;
+ protected Number m_hi;
+
+ // ------------------------------------------------------------------------
+
+ /**
+ * Create a new NumberRangeModel for the given range.
+ * @param lo the low value of the selected range
+ * @param hi the high value of the selected range
+ * @param min the minimum value allowed for ranges
+ * @param max the maximum value allowed for ranges
+ */
+ public NumberRangeModel(int lo, int hi, int min, int max) {
+ this(new Integer(lo), new Integer(hi), new Integer(min), new Integer(max));
+ }
+
+ /**
+ * Create a new NumberRangeModel for the given range.
+ * @param lo the low value of the selected range
+ * @param hi the high value of the selected range
+ * @param min the minimum value allowed for ranges
+ * @param max the maximum value allowed for ranges
+ */
+ public NumberRangeModel(long lo, long hi, long min, long max) {
+ this(new Long(lo), new Long(hi), new Long(min), new Long(max));
+ }
+
+ /**
+ * Create a new NumberRangeModel for the given range.
+ * @param lo the low value of the selected range
+ * @param hi the high value of the selected range
+ * @param min the minimum value allowed for ranges
+ * @param max the maximum value allowed for ranges
+ */
+ public NumberRangeModel(float lo, float hi, float min, float max) {
+ this(new Float(lo), new Float(hi), new Float(min), new Float(max));
+ }
+
+ /**
+ * Create a new NumberRangeModel for the given range.
+ * @param lo the low value of the selected range
+ * @param hi the high value of the selected range
+ * @param min the minimum value allowed for ranges
+ * @param max the maximum value allowed for ranges
+ */
+ public NumberRangeModel(double lo, double hi, double min, double max) {
+ this(new Double(lo), new Double(hi), new Double(min), new Double(max));
+ }
+
+ /**
+ * Create a new NumberRangeModel for the given range.
+ * @param lo the low value of the selected range
+ * @param hi the high value of the selected range
+ * @param min the minimum value allowed for ranges
+ * @param max the maximum value allowed for ranges
+ */
+ public NumberRangeModel(Number lo, Number hi, Number min, Number max) {
+ m_type = TypeLib.getPrimitiveType(min.getClass());
+ setValueRange(lo, hi, min, max);
+ }
+
+ // ------------------------------------------------------------------------
+
+ /**
+ * Update the range settings based on current values.
+ */
+ protected void updateRange() {
+ if (m_type == int.class) {
+ setRange(m_lo.intValue(), m_hi.intValue() - m_lo.intValue(), m_min.intValue(),
+ m_max.intValue());
+ } else if (m_type == long.class) {
+ int v = 10000 * (int) ((m_lo.longValue() - m_min.longValue()) / (m_max.longValue()
+ - m_min.longValue()));
+ int e = (10000 * (int) ((m_hi.longValue() - m_min.longValue()) / (m_max.longValue()
+ - m_min.longValue())))
+ - v;
+ setRange(v, e, 0, 10000);
+ } else {
+ int v = (int) Math.round(10000 * ((m_lo.doubleValue() - m_min.doubleValue()) / (m_max.doubleValue()
+ - m_min.doubleValue())));
+ int e = (int) Math.round(10000 * ((m_hi.doubleValue() - m_min.doubleValue()) / (m_max.doubleValue()
+ - m_min.doubleValue())))
+ - v;
+
+ setRange(v, e, 0, 10000);
+ }
+ }
+
+ /**
+ * Set the range settings in the pixel-space coordinates.
+ */
+ protected void setRange(int val, int ext, int min, int max) {
+ super.setRangeProperties(val, ext, min, max, false);
+ }
+
+ /**
+ * @see javax.swing.BoundedRangeModel#setRangeProperties(int, int, int, int, boolean)
+ */
+ public void setRangeProperties(int val, int extent, int min, int max, boolean adj) {
+ if ((min != getMinimum()) || (max != getMaximum())) {
+ throw new IllegalArgumentException("Can not change min or max.");
+ }
+
+ m_lo = null;
+ m_hi = null;
+ super.setRangeProperties(val, extent, min, max, adj);
+ }
+
+ /**
+ * Set the range model's backing values.
+ * @param lo the low value of the selected range
+ * @param hi the high value of the selected range
+ * @param min the minimum value allowed for ranges
+ * @param max the maximum value allowed for ranges
+ */
+ public void setValueRange(Number lo, Number hi, Number min, Number max) {
+ m_lo = lo;
+ m_hi = hi;
+ m_min = min;
+ m_max = max;
+ updateRange();
+ }
+
+ /**
+ * Set the range model's backing values.
+ * @param lo the low value of the selected range
+ * @param hi the high value of the selected range
+ * @param min the minimum value allowed for ranges
+ * @param max the maximum value allowed for ranges
+ */
+ public void setValueRange(double lo, double hi, double min, double max) {
+ m_lo = new Double(lo);
+ m_hi = new Double(hi);
+ m_min = new Double(min);
+ m_max = new Double(max);
+ updateRange();
+ }
+
+ /**
+ * Set the range model's backing values.
+ * @param lo the low value of the selected range
+ * @param hi the high value of the selected range
+ * @param min the minimum value allowed for ranges
+ * @param max the maximum value allowed for ranges
+ */
+ public void setValueRange(int lo, int hi, int min, int max) {
+ m_lo = new Integer(lo);
+ m_hi = new Integer(hi);
+ m_min = new Integer(min);
+ m_max = new Integer(max);
+ updateRange();
+ }
+
+ /**
+ * Set the range model's backing values.
+ * @param lo the low value of the selected range
+ * @param hi the high value of the selected range
+ * @param min the minimum value allowed for ranges
+ * @param max the maximum value allowed for ranges
+ */
+ public void setValueRange(long lo, long hi, long min, long max) {
+ m_lo = new Long(lo);
+ m_hi = new Long(hi);
+ m_min = new Long(min);
+ m_max = new Long(max);
+ updateRange();
+ }
+
+ /**
+ * @see prefuse.util.ui.ValuedRangeModel#getMinValue()
+ */
+ public Object getMinValue() {
+ return m_min;
+ }
+
+ /**
+ * Set the minimum range value.
+ * @param n the minimum range value.
+ */
+ public void setMinValue(Number n) {
+ setValueRange((Number) getLowValue(), (Number) getHighValue(), n, m_max);
+ }
+
+ /**
+ * @see prefuse.util.ui.ValuedRangeModel#getMaxValue()
+ */
+ public Object getMaxValue() {
+ return m_max;
+ }
+
+ /**
+ * Set the maximum range value.
+ * @param n the maximum range value.
+ */
+ public void setMaxValue(Number n) {
+ setValueRange((Number) getLowValue(), (Number) getHighValue(), m_min, n);
+ }
+
+ /**
+ * @see prefuse.util.ui.ValuedRangeModel#getLowValue()
+ */
+ public Object getLowValue() {
+ if (m_lo == null)
+ m_lo = (Number) value(getValue());
+
+ return m_lo;
+ }
+
+ /**
+ * Set the lowest selected range value.
+ * @param n the low value of the selected range.
+ */
+ public void setLowValue(Number n) {
+ setValueRange(n, (Number) getHighValue(), m_min, m_max);
+ }
+
+ /**
+ * @see prefuse.util.ui.ValuedRangeModel#getHighValue()
+ */
+ public Object getHighValue() {
+ if (m_hi == null)
+ m_hi = (Number) value(getValue() + getExtent());
+
+ return m_hi;
+ }
+
+ /**
+ * Set the highest selected range value.
+ * @param n the high value of the selected range.
+ */
+ public void setHighValue(Number n) {
+ setValueRange((Number) getLowValue(), n, m_min, m_max);
+ }
+
+ protected Object value(int val) {
+ int min = getMinimum();
+ int max = getMaximum();
+
+ if ((m_type == double.class) || (m_type == float.class)) {
+ double f = (val - min) / (double) (max - min);
+ double m = m_min.doubleValue();
+ double v = m + (f * (m_max.doubleValue() - m));
+
+ return ((m_type == float.class) ? (Number) new Float((float) v) : new Double(v));
+ } else if (m_type == long.class) {
+ long m = m_min.longValue();
+ long v = m + (((val - min) * (m_max.longValue() - m)) / (max - min));
+
+ return new Long(v);
+ } else {
+ return new Integer(val);
+ }
+ }
+
+ /**
+ * Not supported, throws an exception.
+ * @throws UnsupportedOperationException
+ * @see javax.swing.BoundedRangeModel#setMinimum(int)
+ */
+ public void setMinimum(int min) {
+ throw new UnsupportedOperationException();
+ }
+
+ /**
+ * Not supported, throws an exception.
+ * @throws UnsupportedOperationException
+ * @see javax.swing.BoundedRangeModel#setMaximum(int)
+ */
+ public void setMaximum(int max) {
+ throw new UnsupportedOperationException();
+ }
+
+ /**
+ * @see javax.swing.BoundedRangeModel#setValue(int)
+ */
+ public void setValue(int val) {
+ m_lo = null;
+ super.setValue(val);
+ }
+
+ /**
+ * @see javax.swing.BoundedRangeModel#setExtent(int)
+ */
+ public void setExtent(int extent) {
+ m_hi = null;
+ super.setExtent(extent);
+ }
+} // end of class NumberRangeModel
diff --git a/coreplugins/QuickFind/src/main/java/prefuse/util/TypeLib.java b/coreplugins/QuickFind/src/main/java/prefuse/util/TypeLib.java
new file mode 100644
index 0000000..e70d5e7
--- /dev/null
+++ b/coreplugins/QuickFind/src/main/java/prefuse/util/TypeLib.java
@@ -0,0 +1,237 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package prefuse.util;
+
+
+/**
+ * Library routines dealing with Java Class types.
+ *
+ * @author <a href="http://jheer.org">jeffrey heer</a>
+ */
+public class TypeLib {
+ private TypeLib() {
+ // prevent instantiation
+ }
+
+ // ------------------------------------------------------------------------
+
+ /**
+ * Check if an object is an instance of a given class, or, if the class
+ * is a primitive type, if the Object is an instance of the wrapper class
+ * for that primitive (e.g., as Integer is a wrapper for int).
+ * @param type the Class type
+ * @param instance the Object instance
+ * @return true if the object is an instance of the given class, or if
+ * of the appropriate primitive wrapper type.
+ */
+ public static boolean typeCheck(Class type, Object instance) {
+ return type.isAssignableFrom(instance.getClass()) || isWrapperInstance(type, instance);
+ }
+
+ /**
+ * Get the nearest shared ancestor class of two objects. Note: this
+ * currently does not compute the actual least common ancestor, but
+ * only looks up one level in the inheritance tree and quits if
+ * it does not find a match.
+ * @param o1 the first object
+ * @param o2 the second object
+ * @return the nearest class instance of which both objects
+ * are instances
+ */
+ public static Class getSharedType(Object o1, Object o2) {
+ return getSharedType(o1.getClass(), o2.getClass());
+ }
+
+ /**
+ * Get the nearest shared ancestor class of two classes. Note: this
+ * currently does not compute the actual least common ancestor, but
+ * only looks up one level in the inheritance tree and quits if
+ * it does not find a match.
+ * @param type1 the first type
+ * @param type2 the second type
+ * @return the nearest class instance which is equal to or a
+ * superclass of the two class instances
+ */
+ public static Class getSharedType(Class type1, Class type2) {
+ if (type1 == type2) {
+ return type1;
+ } else if (type1.isAssignableFrom(type2)) {
+ return type1;
+ } else if (type2.isAssignableFrom(type1)) {
+ return type2;
+ } else {
+ return null;
+ }
+ }
+
+ /**
+ * Indicates if an object is an instance of a wrapper class for a given
+ * primitive type.
+ * @param type the primitive Class type
+ * @param instance the object to test as wrapper (e.g., as Integer is a
+ * wrapper type for int)
+ * @return true if the object is a wrapper instance of the given
+ * primitive type
+ */
+ public static boolean isWrapperInstance(Class type, Object instance) {
+ if (!type.isPrimitive())
+ throw new IllegalArgumentException("Input type must be a primitive");
+
+ if ((int.class == type) && instance instanceof Integer) {
+ return true;
+ } else if ((long.class == type) && instance instanceof Long) {
+ return true;
+ } else if ((float.class == type) && instance instanceof Float) {
+ return true;
+ } else if ((double.class == type) && instance instanceof Double) {
+ return true;
+ } else if ((boolean.class == type) && instance instanceof Boolean) {
+ return true;
+ } else if ((short.class == type) && instance instanceof Short) {
+ return true;
+ } else if ((byte.class == type) && instance instanceof Byte) {
+ return true;
+ } else if ((char.class == type) && instance instanceof Character) {
+ return true;
+ } else {
+ return false;
+ }
+ }
+
+ /**
+ * Given a numeric (byte, short, int, long, float, or double) class type or
+ * associated wrapper class type, return the primitive class type
+ * @param type the type to look up, must be a numerical type, but can be
+ * either primitive or a wrapper.
+ * @return the primitive class type
+ */
+ public static Class getPrimitiveType(Class type) {
+ if (Integer.class.equals(type) || (type == int.class)) {
+ return int.class;
+ } else if (Long.class.equals(type) || (type == long.class)) {
+ return long.class;
+ } else if (Float.class.equals(type) || (type == float.class)) {
+ return float.class;
+ } else if (Double.class.equals(type) || (type == double.class)) {
+ return double.class;
+ } else if (Byte.class.equals(type) || (type == byte.class)) {
+ return byte.class;
+ } else if (Short.class.equals(type) || (type == short.class)) {
+ return short.class;
+ } else {
+ throw new IllegalArgumentException("Input class must be a numeric type");
+ }
+ }
+
+ /**
+ * Get the wrapper class type for a primitive class type.
+ * @param type a class type
+ * @return the wrapper class for the input type if it is a
+ * primitive class type, otherwise returns the input type
+ */
+ public static Class getWrapperType(Class type) {
+ if (!type.isPrimitive()) {
+ return type;
+ } else if (int.class == type) {
+ return Integer.class;
+ } else if (long.class == type) {
+ return Long.class;
+ } else if (float.class == type) {
+ return Float.class;
+ } else if (double.class == type) {
+ return Double.class;
+ } else if (boolean.class == type) {
+ return Boolean.class;
+ } else if (short.class == type) {
+ return Short.class;
+ } else if (char.class == type) {
+ return Character.class;
+ } else if (byte.class == type) {
+ return Byte.class;
+ } else if (short.class == type) {
+ return Short.class;
+ } else {
+ throw new IllegalArgumentException();
+ }
+ }
+
+ /**
+ * Indicates if a given class type is a primitive integer type
+ * (one of byte, short, int, or long).
+ * @param type the type to check
+ * @return true if it is a primitive numeric type, false otherwise
+ */
+ public static boolean isIntegerType(Class type) {
+ return ((type == byte.class) || (type == short.class) || (type == int.class)
+ || (type == long.class));
+ }
+
+ /**
+ * Indicates if a given class type is a primitive numeric one type
+ * (one of byte, short, int, long, float, or double).
+ * @param type the type to check
+ * @return true if it is a primitive numeric type, false otherwise
+ */
+ public static boolean isNumericType(Class type) {
+ return ((type == byte.class) || (type == short.class) || (type == int.class)
+ || (type == long.class) || (type == double.class) || (type == float.class));
+ }
+
+ /**
+ * Get a compatible numeric type for two primitive numeric
+ * class types. Any of (byte, short, int) will resolve to int.
+ * @param c1 a numeric primitive class type (int, long, float, or double)
+ * @param c2 a numeric primitive class type (int, long, float, or double)
+ * @return the compatible numeric type for binary operations involving
+ * both types.
+ */
+ public static Class getNumericType(Class c1, Class c2) {
+ if (!isNumericType(c1) || !isNumericType(c2)) {
+ throw new IllegalArgumentException("Input types must be primitive number types");
+ }
+
+ if ((c1 == double.class) || (c2 == double.class)) {
+ return double.class;
+ } else if ((c1 == float.class) || (c1 == float.class)) {
+ return float.class;
+ } else if ((c1 == long.class) || (c2 == long.class)) {
+ return long.class;
+ } else {
+ return int.class;
+ }
+ }
+} // end of class TypeLib
diff --git a/coreplugins/QuickFind/src/main/java/prefuse/util/ui/JRangeSlider.java b/coreplugins/QuickFind/src/main/java/prefuse/util/ui/JRangeSlider.java
new file mode 100644
index 0000000..fc8bb2d
--- /dev/null
+++ b/coreplugins/QuickFind/src/main/java/prefuse/util/ui/JRangeSlider.java
@@ -0,0 +1,920 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package prefuse.util.ui;
+
+import java.awt.BasicStroke;
+import java.awt.Color;
+import java.awt.Cursor;
+import java.awt.Dimension;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.Rectangle;
+import java.awt.event.KeyEvent;
+import java.awt.event.KeyListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+
+import java.util.ArrayList;
+import java.util.Iterator;
+
+import javax.swing.BoundedRangeModel;
+import javax.swing.DefaultBoundedRangeModel;
+import javax.swing.JComponent;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+
+
+/**
+ * <p>Implements a Swing-based Range slider, which allows the user to enter a
+ * range (minimum and maximum) value.</p>
+ *
+ * @author Ben Bederson
+ * @author Jesse Grosjean
+ * @author Jon Meyer
+ * @author Lance Good
+ * @author jeffrey heer
+ */
+public class JRangeSlider extends JComponent implements MouseListener, MouseMotionListener,
+ KeyListener {
+ /*
+ * NOTE: This is a modified version of the original class distributed by
+ * Ben Bederson, Jesse Grosjean, and Jon Meyer as part of an HCIL Tech
+ * Report. It is modified to allow both vertical and horitonal modes.
+ * It also fixes a bug with offset on the buttons. Also fixed a bug with
+ * rendering using (x,y) instead of (0,0) as origin. Also modified to
+ * render arrows as a series of lines rather than as a GeneralPath.
+ * Also modified to fix rounding errors on toLocal and toScreen.
+ *
+ * With inclusion in prefuse, this class has been further modified to use a
+ * bounded range model, support keyboard commands and more extensize
+ * parameterization of rendering/appearance options. Furthermore, a stub
+ * method has been introduced to allow subclasses to perform custom
+ * rendering within the slider through.
+ */
+ /**
+ *
+ */
+ final public static int VERTICAL = 0;
+
+ /**
+ *
+ */
+ final public static int HORIZONTAL = 1;
+
+ /**
+ *
+ */
+ final public static int LEFTRIGHT_TOPBOTTOM = 0;
+
+ /**
+ *
+ */
+ final public static int RIGHTLEFT_BOTTOMTOP = 1;
+
+ /**
+ *
+ */
+ final public static int PREFERRED_BREADTH = 16;
+
+ /**
+ *
+ */
+ final public static int PREFERRED_LENGTH = 300;
+ final protected static int ARROW_SZ = 16;
+ final protected static int ARROW_WIDTH = 8;
+ final protected static int ARROW_HEIGHT = 4;
+ protected BoundedRangeModel model;
+ protected int orientation;
+ protected int direction;
+ protected boolean empty;
+ protected int increment = 1;
+ protected int minExtent = 0; // min extent, in pixels
+ protected ArrayList listeners = new ArrayList();
+ protected ChangeEvent changeEvent = null;
+ protected ChangeListener lstnr;
+ protected Color thumbColor = new Color(150, 180, 220);
+
+ // ------------------------------------------------------------------------
+
+ /**
+ * Create a new range slider.
+ *
+ * @param minimum - the minimum value of the range.
+ * @param maximum - the maximum value of the range.
+ * @param lowValue - the current low value shown by the range slider's bar.
+ * @param highValue - the current high value shown by the range slider's bar.
+ * @param orientation - construct a horizontal or vertical slider?
+ */
+ public JRangeSlider(int minimum, int maximum, int lowValue, int highValue, int orientation) {
+ this(new DefaultBoundedRangeModel(lowValue, highValue, minimum, maximum), orientation,
+ LEFTRIGHT_TOPBOTTOM);
+ }
+
+ /**
+ * Create a new range slider.
+ *
+ * @param minimum - the minimum value of the range.
+ * @param maximum - the maximum value of the range.
+ * @param lowValue - the current low value shown by the range slider's bar.
+ * @param highValue - the current high value shown by the range slider's bar.
+ * @param orientation - construct a horizontal or vertical slider?
+ * @param direction - Is the slider left-to-right/top-to-bottom or right-to-left/bottom-to-top
+ */
+ public JRangeSlider(int minimum, int maximum, int lowValue, int highValue, int orientation,
+ int direction) {
+ this(new DefaultBoundedRangeModel(lowValue, highValue, minimum, maximum), orientation,
+ direction);
+ }
+
+ /**
+ * Create a new range slider.
+ *
+ * @param model - a BoundedRangeModel specifying the slider's range
+ * @param orientation - construct a horizontal or vertical slider?
+ * @param direction - Is the slider left-to-right/top-to-bottom or right-to-left/bottom-to-top
+ */
+ public JRangeSlider(BoundedRangeModel model, int orientation, int direction) {
+ super.setFocusable(true);
+ this.model = model;
+ this.orientation = orientation;
+ this.direction = direction;
+
+ setForeground(Color.LIGHT_GRAY);
+
+ this.lstnr = createListener();
+ model.addChangeListener(lstnr);
+
+ addMouseListener(this);
+ addMouseMotionListener(this);
+ addKeyListener(this);
+ }
+
+ /**
+ * Create a listener to relay change events from the bounded range model.
+ * @return a ChangeListener to relay events from the range model
+ */
+ protected ChangeListener createListener() {
+ return new RangeSliderChangeListener();
+ }
+
+ /**
+ * Listener that fires a change event when it receives change event from
+ * the slider list model.
+ */
+ protected class RangeSliderChangeListener implements ChangeListener {
+ public void stateChanged(ChangeEvent e) {
+ fireChangeEvent();
+ }
+ }
+
+ /**
+ * Returns the current "low" value shown by the range slider's bar. The low
+ * value meets the constraint minimum <= lowValue <= highValue <= maximum.
+ */
+ public int getLowValue() {
+ return model.getValue();
+ }
+
+ /**
+ * Sets the low value shown by this range slider. This causes the range slider to be
+ * repainted and a ChangeEvent to be fired.
+ * @param lowValue the low value to use
+ */
+ public void setLowValue(int lowValue) {
+ int e = (model.getValue() - lowValue) + model.getExtent();
+ model.setRangeProperties(lowValue, e, model.getMinimum(), model.getMaximum(), false);
+ model.setValue(lowValue);
+ }
+
+ /**
+ * Returns the current "high" value shown by the range slider's bar. The high
+ * value meets the constraint minimum <= lowValue <= highValue <= maximum.
+ */
+ public int getHighValue() {
+ return model.getValue() + model.getExtent();
+ }
+
+ /**
+ * Sets the high value shown by this range slider. This causes the range slider to be
+ * repainted and a ChangeEvent to be fired.
+ * @param highValue the high value to use
+ */
+ public void setHighValue(int highValue) {
+ model.setExtent(highValue - model.getValue());
+ }
+
+ /**
+ * Set the slider range span.
+ * @param lowValue the low value of the slider range
+ * @param highValue the high value of the slider range
+ */
+ public void setRange(int lowValue, int highValue) {
+ model.setRangeProperties(lowValue, highValue - lowValue, model.getMinimum(),
+ model.getMaximum(), false);
+ }
+
+ /**
+ * Gets the minimum possible value for either the low value or the high value.
+ * @return the minimum possible range value
+ */
+ public int getMinimum() {
+ return model.getMinimum();
+ }
+
+ /**
+ * Sets the minimum possible value for either the low value or the high value.
+ * @param minimum the minimum possible range value
+ */
+ public void setMinimum(int minimum) {
+ model.setMinimum(minimum);
+ }
+
+ /**
+ * Gets the maximum possible value for either the low value or the high value.
+ * @return the maximum possible range value
+ */
+ public int getMaximum() {
+ return model.getMaximum();
+ }
+
+ /**
+ * Sets the maximum possible value for either the low value or the high value.
+ * @param maximum the maximum possible range value
+ */
+ public void setMaximum(int maximum) {
+ model.setMaximum(maximum);
+ }
+
+ /**
+ * Sets the minimum extent (difference between low and high values).
+ * This method <strong>does not</strong> change the current state of the
+ * model, but can affect all subsequent interaction.
+ * @param minExtent the minimum extent allowed in subsequent interaction
+ */
+ public void setMinExtent(int minExtent) {
+ this.minExtent = minExtent;
+ }
+
+ /**
+ * Sets whether this slider is empty.
+ * @param empty true if set to empty, false otherwise
+ */
+ public void setEmpty(boolean empty) {
+ this.empty = empty;
+ repaint();
+ }
+
+ /**
+ * Get the slider thumb color. This is the part of the slider between
+ * the range resize buttons.
+ * @return the slider thumb color
+ */
+ public Color getThumbColor() {
+ return thumbColor;
+ }
+
+ /**
+ * Set the slider thumb color. This is the part of the slider between
+ * the range resize buttons.
+ * @param thumbColor the slider thumb color
+ */
+ public void setThumbColor(Color thumbColor) {
+ this.thumbColor = thumbColor;
+ }
+
+ /**
+ * Get the BoundedRangeModel backing this slider.
+ * @return the slider's range model
+ */
+ public BoundedRangeModel getModel() {
+ return model;
+ }
+
+ /**
+ * Set the BoundedRangeModel backing this slider.
+ * @param brm the slider range model to use
+ */
+ public void setModel(BoundedRangeModel brm) {
+ model.removeChangeListener(lstnr);
+ model = brm;
+ model.addChangeListener(lstnr);
+ repaint();
+ }
+
+ /**
+ * Registers a listener for ChangeEvents.
+ * @param cl the ChangeListener to add
+ */
+ public void addChangeListener(ChangeListener cl) {
+ if (!listeners.contains(cl))
+ listeners.add(cl);
+ }
+
+ /**
+ * Removes a listener for ChangeEvents.
+ * @param cl the ChangeListener to remove
+ */
+ public void removeChangeListener(ChangeListener cl) {
+ listeners.remove(cl);
+ }
+
+ /**
+ * Fire a change event to all listeners.
+ */
+ protected void fireChangeEvent() {
+ repaint();
+
+ if (changeEvent == null)
+ changeEvent = new ChangeEvent(this);
+
+ Iterator iter = listeners.iterator();
+
+ while (iter.hasNext())
+ ((ChangeListener) iter.next()).stateChanged(changeEvent);
+ }
+
+ /**
+ * @see java.awt.Component#getPreferredSize()
+ */
+ public Dimension getPreferredSize() {
+ if (orientation == VERTICAL) {
+ return new Dimension(PREFERRED_BREADTH, PREFERRED_LENGTH);
+ } else {
+ return new Dimension(PREFERRED_LENGTH, PREFERRED_BREADTH);
+ }
+ }
+
+ // ------------------------------------------------------------------------
+ // Rendering
+
+ /**
+ * Override this method to perform custom painting of the slider trough.
+ * @param g a Graphics2D context for rendering
+ * @param width the width of the slider trough
+ * @param height the height of the slider trough
+ */
+ protected void customPaint(Graphics2D g, int width, int height) {
+ // does nothing in this class
+ // subclasses can override to perform custom painting
+ }
+
+ /**
+ * @see javax.swing.JComponent#paintComponent(java.awt.Graphics)
+ */
+ public void paintComponent(Graphics g) {
+ Rectangle bounds = getBounds();
+ int width = (int) bounds.getWidth() - 1;
+ int height = (int) bounds.getHeight() - 1;
+
+ int min = toScreen(getLowValue());
+ int max = toScreen(getHighValue());
+
+ // Paint the full slider if the slider is marked as empty
+ if (empty) {
+ if (direction == LEFTRIGHT_TOPBOTTOM) {
+ min = ARROW_SZ;
+ max = (orientation == VERTICAL) ? (height - ARROW_SZ) : (width - ARROW_SZ);
+ } else {
+ min = (orientation == VERTICAL) ? (height - ARROW_SZ) : (width - ARROW_SZ);
+ max = ARROW_SZ;
+ }
+ }
+
+ Graphics2D g2 = (Graphics2D) g;
+ g2.setColor(getBackground());
+ g2.fillRect(0, 0, width, height);
+ g2.setColor(getForeground());
+ g2.drawRect(0, 0, width, height);
+
+ customPaint(g2, width, height);
+
+ // Draw arrow and thumb backgrounds
+ g2.setStroke(new BasicStroke(1));
+
+ if (orientation == VERTICAL) {
+ if (direction == LEFTRIGHT_TOPBOTTOM) {
+ g2.setColor(getForeground());
+ g2.fillRect(0, min - ARROW_SZ, width, ARROW_SZ - 1);
+ paint3DRectLighting(g2, 0, min - ARROW_SZ, width, ARROW_SZ - 1);
+
+ if (thumbColor != null) {
+ g2.setColor(thumbColor);
+ g2.fillRect(0, min, width, max - min - 1);
+ paint3DRectLighting(g2, 0, min, width, max - min - 1);
+ }
+
+ g2.setColor(getForeground());
+ g2.fillRect(0, max, width, ARROW_SZ - 1);
+ paint3DRectLighting(g2, 0, max, width, ARROW_SZ - 1);
+
+ // Draw arrows
+ g2.setColor(Color.black);
+ paintArrow(g2, (width - ARROW_WIDTH) / 2.0,
+ min - ARROW_SZ + ((ARROW_SZ - ARROW_HEIGHT) / 2.0), ARROW_WIDTH,
+ ARROW_HEIGHT, true);
+ paintArrow(g2, (width - ARROW_WIDTH) / 2.0,
+ max + ((ARROW_SZ - ARROW_HEIGHT) / 2.0), ARROW_WIDTH, ARROW_HEIGHT, false);
+ } else {
+ g2.setColor(getForeground());
+ g2.fillRect(0, min, width, ARROW_SZ - 1);
+ paint3DRectLighting(g2, 0, min, width, ARROW_SZ - 1);
+
+ if (thumbColor != null) {
+ g2.setColor(thumbColor);
+ g2.fillRect(0, max, width, min - max - 1);
+ paint3DRectLighting(g2, 0, max, width, min - max - 1);
+ }
+
+ g2.setColor(getForeground());
+ g2.fillRect(0, max - ARROW_SZ, width, ARROW_SZ - 1);
+ paint3DRectLighting(g2, 0, max - ARROW_SZ, width, ARROW_SZ - 1);
+
+ // Draw arrows
+ g2.setColor(Color.black);
+ paintArrow(g2, (width - ARROW_WIDTH) / 2.0,
+ min + ((ARROW_SZ - ARROW_HEIGHT) / 2.0), ARROW_WIDTH, ARROW_HEIGHT, false);
+ paintArrow(g2, (width - ARROW_WIDTH) / 2.0,
+ max - ARROW_SZ + ((ARROW_SZ - ARROW_HEIGHT) / 2.0), ARROW_WIDTH,
+ ARROW_HEIGHT, true);
+ }
+ } else {
+ if (direction == LEFTRIGHT_TOPBOTTOM) {
+ g2.setColor(getForeground());
+ g2.fillRect(min - ARROW_SZ, 0, ARROW_SZ - 1, height);
+ paint3DRectLighting(g2, min - ARROW_SZ, 0, ARROW_SZ - 1, height);
+
+ if (thumbColor != null) {
+ g2.setColor(thumbColor);
+ g2.fillRect(min, 0, max - min - 1, height);
+ paint3DRectLighting(g2, min, 0, max - min - 1, height);
+ }
+
+ g2.setColor(getForeground());
+ g2.fillRect(max, 0, ARROW_SZ - 1, height);
+ paint3DRectLighting(g2, max, 0, ARROW_SZ - 1, height);
+
+ // Draw arrows
+ g2.setColor(Color.black);
+ paintArrow(g2, min - ARROW_SZ + ((ARROW_SZ - ARROW_HEIGHT) / 2.0),
+ (height - ARROW_WIDTH) / 2.0, ARROW_HEIGHT, ARROW_WIDTH, true);
+ paintArrow(g2, max + ((ARROW_SZ - ARROW_HEIGHT) / 2.0),
+ (height - ARROW_WIDTH) / 2.0, ARROW_HEIGHT, ARROW_WIDTH, false);
+ } else {
+ g2.setColor(getForeground());
+ g2.fillRect(min, 0, ARROW_SZ - 1, height);
+ paint3DRectLighting(g2, min, 0, ARROW_SZ - 1, height);
+
+ if (thumbColor != null) {
+ g2.setColor(thumbColor);
+ g2.fillRect(max, 0, min - max - 1, height);
+ paint3DRectLighting(g2, max, 0, min - max - 1, height);
+ }
+
+ g2.setColor(getForeground());
+ g2.fillRect(max - ARROW_SZ, 0, ARROW_SZ - 1, height);
+ paint3DRectLighting(g2, max - ARROW_SZ, 0, ARROW_SZ - 1, height);
+
+ // Draw arrows
+ g2.setColor(Color.black);
+ paintArrow(g2, min + ((ARROW_SZ - ARROW_HEIGHT) / 2.0),
+ (height - ARROW_WIDTH) / 2.0, ARROW_HEIGHT, ARROW_WIDTH, true);
+ paintArrow(g2, max - ARROW_SZ + ((ARROW_SZ - ARROW_HEIGHT) / 2.0),
+ (height - ARROW_WIDTH) / 2.0, ARROW_HEIGHT, ARROW_WIDTH, false);
+ }
+ }
+ }
+
+ /**
+ * This draws an arrow as a series of lines within the specified box.
+ * The last boolean specifies whether the point should be at the
+ * right/bottom or left/top.
+ */
+ protected void paintArrow(Graphics2D g2, double x, double y, int w, int h, boolean topDown) {
+ int intX = (int) (x + 0.5);
+ int intY = (int) (y + 0.5);
+
+ if (orientation == VERTICAL) {
+ if ((w % 2) == 0) {
+ w = w - 1;
+ }
+
+ if (topDown) {
+ for (int i = 0; i < ((w / 2) + 1); i++) {
+ g2.drawLine(intX + i, intY + i, (intX + w) - i - 1, intY + i);
+ }
+ } else {
+ for (int i = 0; i < ((w / 2) + 1); i++) {
+ g2.drawLine((intX + (w / 2)) - i, intY + i, ((intX + w) - (w / 2) + i) - 1,
+ intY + i);
+ }
+ }
+ } else {
+ if ((h % 2) == 0) {
+ h = h - 1;
+ }
+
+ if (topDown) {
+ for (int i = 0; i < ((h / 2) + 1); i++) {
+ g2.drawLine(intX + i, intY + i, intX + i, (intY + h) - i - 1);
+ }
+ } else {
+ for (int i = 0; i < ((h / 2) + 1); i++) {
+ g2.drawLine(intX + i, (intY + (h / 2)) - i, intX + i,
+ ((intY + h) - (h / 2) + i) - 1);
+ }
+ }
+ }
+ }
+
+ /**
+ * Adds Windows2K type 3D lighting effects
+ */
+ protected void paint3DRectLighting(Graphics2D g2, int x, int y, int width, int height) {
+ g2.setColor(Color.white);
+ g2.drawLine(x + 1, y + 1, x + 1, (y + height) - 1);
+ g2.drawLine(x + 1, y + 1, (x + width) - 1, y + 1);
+ g2.setColor(Color.gray);
+ g2.drawLine(x + 1, (y + height) - 1, (x + width) - 1, (y + height) - 1);
+ g2.drawLine((x + width) - 1, y + 1, (x + width) - 1, (y + height) - 1);
+ g2.setColor(Color.darkGray);
+ g2.drawLine(x, y + height, x + width, y + height);
+ g2.drawLine(x + width, y, x + width, y + height);
+ }
+
+ /**
+ * Converts from screen coordinates to a range value.
+ */
+ protected int toLocal(int xOrY) {
+ Dimension sz = getSize();
+ int min = getMinimum();
+ double scale;
+
+ if (orientation == VERTICAL) {
+ scale = (sz.height - (2 * ARROW_SZ)) / (double) (getMaximum() - min);
+ } else {
+ scale = (sz.width - (2 * ARROW_SZ)) / (double) (getMaximum() - min);
+ }
+
+ if (direction == LEFTRIGHT_TOPBOTTOM) {
+ return (int) (((xOrY - ARROW_SZ) / scale) + min + 0.5);
+ } else {
+ if (orientation == VERTICAL) {
+ return (int) (((sz.height - xOrY - ARROW_SZ) / scale) + min + 0.5);
+ } else {
+ return (int) (((sz.width - xOrY - ARROW_SZ) / scale) + min + 0.5);
+ }
+ }
+ }
+
+ /**
+ * Converts from a range value to screen coordinates.
+ */
+ protected int toScreen(int xOrY) {
+ Dimension sz = getSize();
+ int min = getMinimum();
+ double scale;
+
+ if (orientation == VERTICAL) {
+ scale = (sz.height - (2 * ARROW_SZ)) / (double) (getMaximum() - min);
+ } else {
+ scale = (sz.width - (2 * ARROW_SZ)) / (double) (getMaximum() - min);
+ }
+
+ // If the direction is left/right_top/bottom then we subtract the min and multiply times scale
+ // Otherwise, we have to invert the number by subtracting the value from the height
+ if (direction == LEFTRIGHT_TOPBOTTOM) {
+ return (int) (ARROW_SZ + ((xOrY - min) * scale) + 0.5);
+ } else {
+ if (orientation == VERTICAL) {
+ return (int) (sz.height - ((xOrY - min) * scale) - ARROW_SZ + 0.5);
+ } else {
+ return (int) (sz.width - ((xOrY - min) * scale) - ARROW_SZ + 0.5);
+ }
+ }
+ }
+
+ /**
+ * Converts from a range value to screen coordinates.
+ */
+ protected double toScreenDouble(int xOrY) {
+ Dimension sz = getSize();
+ int min = getMinimum();
+ double scale;
+
+ if (orientation == VERTICAL) {
+ scale = (sz.height - (2 * ARROW_SZ)) / (double) ((getMaximum() + 1) - min);
+ } else {
+ scale = (sz.width - (2 * ARROW_SZ)) / (double) ((getMaximum() + 1) - min);
+ }
+
+ // If the direction is left/right_top/bottom then we subtract the min and multiply times scale
+ // Otherwise, we have to invert the number by subtracting the value from the height
+ if (direction == LEFTRIGHT_TOPBOTTOM) {
+ return ARROW_SZ + ((xOrY - min) * scale);
+ } else {
+ if (orientation == VERTICAL) {
+ return sz.height - ((xOrY - min) * scale) - ARROW_SZ;
+ } else {
+ return sz.width - ((xOrY - min) * scale) - ARROW_SZ;
+ }
+ }
+ }
+
+ // ------------------------------------------------------------------------
+ // Event Handling
+ static final int PICK_NONE = 0;
+ static final int PICK_LEFT_OR_TOP = 1;
+ static final int PICK_THUMB = 2;
+ static final int PICK_RIGHT_OR_BOTTOM = 3;
+ int pick;
+ int pickOffsetLow;
+ int pickOffsetHigh;
+ int mouse;
+
+ private int pickHandle(int xOrY) {
+ int min = toScreen(getLowValue());
+ int max = toScreen(getHighValue());
+ int pick = PICK_NONE;
+
+ if (direction == LEFTRIGHT_TOPBOTTOM) {
+ if ((xOrY > (min - ARROW_SZ)) && (xOrY < min)) {
+ pick = PICK_LEFT_OR_TOP;
+ } else if ((xOrY >= min) && (xOrY <= max)) {
+ pick = PICK_THUMB;
+ } else if ((xOrY > max) && (xOrY < (max + ARROW_SZ))) {
+ pick = PICK_RIGHT_OR_BOTTOM;
+ }
+ } else {
+ if ((xOrY > min) && (xOrY < (min + ARROW_SZ))) {
+ pick = PICK_LEFT_OR_TOP;
+ } else if ((xOrY <= min) && (xOrY >= max)) {
+ pick = PICK_THUMB;
+ } else if (((xOrY > (max - ARROW_SZ)) && (xOrY < max))) {
+ pick = PICK_RIGHT_OR_BOTTOM;
+ }
+ }
+
+ return pick;
+ }
+
+ private void offset(int dxOrDy) {
+ model.setValue(model.getValue() + dxOrDy);
+ }
+
+ /**
+ * @see java.awt.event.MouseListener#mousePressed(java.awt.event.MouseEvent)
+ */
+ public void mousePressed(MouseEvent e) {
+ if (orientation == VERTICAL) {
+ pick = pickHandle(e.getY());
+ pickOffsetLow = e.getY() - toScreen(getLowValue());
+ pickOffsetHigh = e.getY() - toScreen(getHighValue());
+ mouse = e.getY();
+ } else {
+ pick = pickHandle(e.getX());
+ pickOffsetLow = e.getX() - toScreen(getLowValue());
+ pickOffsetHigh = e.getX() - toScreen(getHighValue());
+ mouse = e.getX();
+ }
+
+ repaint();
+ }
+
+ /**
+ * @see java.awt.event.MouseMotionListener#mouseDragged(java.awt.event.MouseEvent)
+ */
+ public void mouseDragged(MouseEvent e) {
+ requestFocus();
+
+ int value = (orientation == VERTICAL) ? e.getY() : e.getX();
+
+ int minimum = getMinimum();
+ int maximum = getMaximum();
+ int lowValue = getLowValue();
+ int highValue = getHighValue();
+
+ switch (pick) {
+ case PICK_LEFT_OR_TOP:
+
+ int low = toLocal(value - pickOffsetLow);
+
+ if (low < minimum) {
+ low = minimum;
+ }
+
+ if (low > maximum) {
+ low = maximum;
+ }
+
+ if (low > (highValue - minExtent)) {
+ low = highValue - minExtent;
+ }
+
+ setLowValue(low);
+
+ break;
+
+ case PICK_RIGHT_OR_BOTTOM:
+
+ int high = toLocal(value - pickOffsetHigh);
+
+ if (high < minimum) {
+ high = minimum;
+ }
+
+ if (high > maximum) {
+ high = maximum;
+ }
+
+ if (high < (lowValue + minExtent)) {
+ high = lowValue + minExtent;
+ }
+
+ setHighValue(high);
+
+ break;
+
+ case PICK_THUMB:
+
+ int dxOrDy = toLocal(value - pickOffsetLow) - lowValue;
+
+ if ((dxOrDy < 0) && ((lowValue + dxOrDy) < minimum)) {
+ dxOrDy = minimum - lowValue;
+ }
+
+ if ((dxOrDy > 0) && ((highValue + dxOrDy) > maximum)) {
+ dxOrDy = maximum - highValue;
+ }
+
+ if (dxOrDy != 0) {
+ offset(dxOrDy);
+ }
+
+ break;
+ }
+ }
+
+ /**
+ * @see java.awt.event.MouseListener#mouseReleased(java.awt.event.MouseEvent)
+ */
+ public void mouseReleased(MouseEvent e) {
+ pick = PICK_NONE;
+ repaint();
+ }
+
+ /**
+ * @see java.awt.event.MouseMotionListener#mouseMoved(java.awt.event.MouseEvent)
+ */
+ public void mouseMoved(MouseEvent e) {
+ if (orientation == VERTICAL) {
+ switch (pickHandle(e.getY())) {
+ case PICK_LEFT_OR_TOP:
+ setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR));
+
+ break;
+
+ case PICK_RIGHT_OR_BOTTOM:
+ setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR));
+
+ break;
+
+ case PICK_THUMB:
+ setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR));
+
+ break;
+
+ case PICK_NONE:
+ setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR));
+
+ break;
+ }
+ } else {
+ switch (pickHandle(e.getX())) {
+ case PICK_LEFT_OR_TOP:
+ setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR));
+
+ break;
+
+ case PICK_RIGHT_OR_BOTTOM:
+ setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR));
+
+ break;
+
+ case PICK_THUMB:
+ setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR));
+
+ break;
+
+ case PICK_NONE:
+ setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR));
+
+ break;
+ }
+ }
+ }
+
+ /**
+ * @see java.awt.event.MouseListener#mouseClicked(java.awt.event.MouseEvent)
+ */
+ public void mouseClicked(MouseEvent e) {
+ }
+
+ /**
+ * @see java.awt.event.MouseListener#mouseEntered(java.awt.event.MouseEvent)
+ */
+ public void mouseEntered(MouseEvent e) {
+ }
+
+ /**
+ * @see java.awt.event.MouseListener#mouseExited(java.awt.event.MouseEvent)
+ */
+ public void mouseExited(MouseEvent e) {
+ }
+
+ private void grow(int increment) {
+ model.setRangeProperties(model.getValue() - increment, model.getExtent() + (2 * increment),
+ model.getMinimum(), model.getMaximum(), false);
+ }
+
+ /**
+ * @see java.awt.event.KeyListener#keyPressed(java.awt.event.KeyEvent)
+ */
+ public void keyPressed(KeyEvent e) {
+ int kc = e.getKeyCode();
+ boolean v = (orientation == VERTICAL);
+ boolean d = (kc == KeyEvent.VK_DOWN);
+ boolean u = (kc == KeyEvent.VK_UP);
+ boolean l = (kc == KeyEvent.VK_LEFT);
+ boolean r = (kc == KeyEvent.VK_RIGHT);
+
+ int minimum = getMinimum();
+ int maximum = getMaximum();
+ int lowValue = getLowValue();
+ int highValue = getHighValue();
+
+ if ((v && r) || (!v && u)) {
+ if (((lowValue - increment) >= minimum) && ((highValue + increment) <= maximum)) {
+ grow(increment);
+ }
+ } else if ((v && l) || (!v && d)) {
+ if ((highValue - lowValue) >= (2 * increment)) {
+ grow(-1 * increment);
+ }
+ } else if ((v && d) || (!v && l)) {
+ if ((lowValue - increment) >= minimum) {
+ offset(-increment);
+ }
+ } else if ((v && u) || (!v && r)) {
+ if ((highValue + increment) <= maximum) {
+ offset(increment);
+ }
+ }
+ }
+
+ /**
+ * @see java.awt.event.KeyListener#keyReleased(java.awt.event.KeyEvent)
+ */
+ public void keyReleased(KeyEvent e) {
+ }
+
+ /**
+ * @see java.awt.event.KeyListener#keyTyped(java.awt.event.KeyEvent)
+ */
+ public void keyTyped(KeyEvent e) {
+ }
+} // end of class JRangeSlider
diff --git a/coreplugins/QuickFind/src/main/java/prefuse/util/ui/ValuedRangeModel.java b/coreplugins/QuickFind/src/main/java/prefuse/util/ui/ValuedRangeModel.java
new file mode 100644
index 0000000..12f878b
--- /dev/null
+++ b/coreplugins/QuickFind/src/main/java/prefuse/util/ui/ValuedRangeModel.java
@@ -0,0 +1,76 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package prefuse.util.ui;
+
+import javax.swing.BoundedRangeModel;
+
+
+/**
+ * BoundedRangeModel that additionally supports a mapping between the integer
+ * range used by interface components and a richer range of values, such
+ * as numbers or arbitrary objects.
+ *
+ * @author <a href="http://jheer.org">jeffrey heer</a>
+ * @see javax.swing.BoundedRangeModel
+ */
+public interface ValuedRangeModel extends BoundedRangeModel {
+ /**
+ * Get the minimum value backing the range model. This is
+ * the absolute minimum value possible for the range span.
+ * @return the minimum value
+ */
+ public Object getMinValue();
+
+ /**
+ * Get the maximum value backing the range model. This is
+ * the absolute maximum value possible for the range span.
+ * @return the maximum value
+ */
+ public Object getMaxValue();
+
+ /**
+ * Get the value at the low point of the range span.
+ * @return the lowest value of the current range
+ */
+ public Object getLowValue();
+
+ /**
+ * Get the value at the high point of the range span.
+ * @return the highest value of the current range
+ */
+ public Object getHighValue();
+} // end of interface ValuedRangeModel
diff --git a/coreplugins/QuickFind/src/main/resources/csplugins/quickfind/plugin/plugin.props b/coreplugins/QuickFind/src/main/resources/csplugins/quickfind/plugin/plugin.props
new file mode 100644
index 0000000..222d7f2
--- /dev/null
+++ b/coreplugins/QuickFind/src/main/resources/csplugins/quickfind/plugin/plugin.props
@@ -0,0 +1,30 @@
+# This props file would be filled out and included in the plugin jar file. This props file will be used
+# to put information into the Plugin Manager about the plugin
+
+# -- The following properties are REQUIRED -- #
+
+# The plugin name that will be displayed to users
+pluginName=QuickFind
+
+# Description used to give users information about the plugin such as what it does.
+# Html tags are encouraged for formatting purposes.
+pluginDescription=Provides a search dialog in the toolbar that can used to search for nodes and edges based on attributes.
+
+# Plugin version number, this must be two numbers separated by a decimlal. Ex. 0.2, 14.03
+pluginVersion=0.5
+
+# Compatible Cytoscape version
+cytoscapeVersion=2.5,2.6,2.7,2.8
+
+# Category, use one of the categories listed on the website or create your own
+pluginCategory=Core
+
+
+# List of authors. Note each author and institution pair are separated by a : (colon)
+# each additional author institution pair must be separated from other pairs bye a ; (semicolon)
+pluginAuthorsIntsitutions=Ethan Cerami:Memorial Sloan-Kettering Cancer Center
+
+# -- The following properties should be set ONLY BY CORE PLUGINS -- #
+downloadURL=http://cytoscape.org/plugins/plugins.xml
+uniqueID=14
+
diff --git a/coreplugins/QuickFind/src/main/resources/resources/config.png b/coreplugins/QuickFind/src/main/resources/resources/config.png
new file mode 100644
index 0000000..49da06b
Binary files /dev/null and b/coreplugins/QuickFind/src/main/resources/resources/config.png differ
diff --git a/coreplugins/QuickFind/src/test/java/csplugins/test/package.html b/coreplugins/QuickFind/src/test/java/csplugins/test/package.html
new file mode 100644
index 0000000..2299ebb
--- /dev/null
+++ b/coreplugins/QuickFind/src/test/java/csplugins/test/package.html
@@ -0,0 +1,8 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+<html>
+<head></head>
+
+<body bgcolor="white">
+Master JUnit Suite for running all Unit Tests.
+</body>
+</html>
diff --git a/coreplugins/QuickFind/src/test/java/csplugins/test/quickfind/test/TestCyAttributesUtil.java b/coreplugins/QuickFind/src/test/java/csplugins/test/quickfind/test/TestCyAttributesUtil.java
new file mode 100644
index 0000000..32d0efe
--- /dev/null
+++ b/coreplugins/QuickFind/src/test/java/csplugins/test/quickfind/test/TestCyAttributesUtil.java
@@ -0,0 +1,200 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package csplugins.test.quickfind.test;
+
+import csplugins.quickfind.util.CyAttributesUtil;
+
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+
+import cytoscape.data.CyAttributes;
+import cytoscape.data.CyAttributesImpl;
+
+import junit.framework.TestCase;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+
+
+/**
+ * Tests the CyAttributes Util class.
+ *
+ * @author Ethan Cerami.
+ */
+public class TestCyAttributesUtil extends TestCase {
+ private static final String ID = "id1";
+ private static final String BOOLEAN_TYPE = "boolean_type";
+ private static final String INTEGER_TYPE = "integer_type";
+ private static final String FLOATING_TYPE = "floating_type";
+ private static final String STRING_TYPE = "string_type";
+ private static final String LIST_TYPE = "list_type";
+ private static final String MAP_TYPE = "map_type";
+
+ /**
+ * Tests the getAttributeValues() method.
+ */
+ public void testGetAttributeValues() {
+ CyAttributes cyAttributes = new CyAttributesImpl();
+
+ // Test with Boolean value
+ cyAttributes.setAttribute(ID, BOOLEAN_TYPE, Boolean.TRUE);
+
+ String[] values = CyAttributesUtil.getAttributeValues(cyAttributes, ID, BOOLEAN_TYPE);
+ assertEquals(1, values.length);
+ assertEquals("true", values[0]);
+
+ // Test with Integer value
+ cyAttributes.setAttribute(ID, INTEGER_TYPE, new Integer(25));
+ values = CyAttributesUtil.getAttributeValues(cyAttributes, ID, INTEGER_TYPE);
+ assertEquals(1, values.length);
+ assertEquals("25", values[0]);
+
+ // Test with Floating value
+ cyAttributes.setAttribute(ID, FLOATING_TYPE, new Double(25.0));
+ values = CyAttributesUtil.getAttributeValues(cyAttributes, ID, FLOATING_TYPE);
+ assertEquals(1, values.length);
+ assertEquals("25.0", values[0]);
+
+ // Test with Simple List
+ ArrayList list = new ArrayList();
+ list.add("apple");
+ list.add("banana");
+ cyAttributes.setListAttribute(ID, LIST_TYPE, list);
+ values = CyAttributesUtil.getAttributeValues(cyAttributes, ID, LIST_TYPE);
+ assertEquals(2, values.length);
+ assertEquals("apple", values[0]);
+ assertEquals("banana", values[1]);
+
+ // Test with Simple Map
+ HashMap map = new HashMap();
+ map.put("first_name", "Ethan");
+ map.put("last_name", "Cerami");
+ cyAttributes.setMapAttribute(ID, MAP_TYPE, map);
+ values = CyAttributesUtil.getAttributeValues(cyAttributes, ID, MAP_TYPE);
+ assertEquals(2, values.length);
+
+ boolean firstNameCheck = false;
+ boolean lastNameCheck = false;
+
+ for (int i = 0; i < values.length; i++) {
+ if (values[i].equals("Ethan")) {
+ firstNameCheck = true;
+ } else if (values[i].equals("Cerami")) {
+ lastNameCheck = true;
+ }
+ }
+
+ assertTrue(firstNameCheck);
+ assertTrue(lastNameCheck);
+
+ // Test with invalid attribute key
+ values = CyAttributesUtil.getAttributeValues(cyAttributes, ID, "CELLULAR_LOCATION");
+ assertEquals(null, values);
+ }
+
+ /**
+ * Tests the getDistinctAttributeValues method, Take 1.
+ */
+ public static void testGetDistinctAttributeValues1() {
+ CyAttributes cyAttributes = new CyAttributesImpl();
+ cyAttributes.setAttribute("ID1", STRING_TYPE, "A");
+ cyAttributes.setAttribute("ID2", STRING_TYPE, "A");
+ cyAttributes.setAttribute("ID3", STRING_TYPE, "B");
+ cyAttributes.setAttribute("ID4", STRING_TYPE, "B");
+ cyAttributes.setAttribute("ID5", STRING_TYPE, "C");
+ cyAttributes.setAttribute("ID6", STRING_TYPE, "C");
+
+ CyNetwork network = Cytoscape.createNetwork("csplugins.test");
+
+ createNode("ID1", network);
+ createNode("ID2", network);
+ createNode("ID3", network);
+ createNode("ID4", network);
+ createNode("ID5", network);
+ createNode("ID6", network);
+
+ String[] values = CyAttributesUtil.getDistinctAttributeValues(network.nodesIterator(),
+ cyAttributes, STRING_TYPE, 5);
+ assertEquals(3, values.length);
+
+ boolean aCheck = false;
+ boolean bCheck = false;
+ boolean cCheck = false;
+
+ for (int i = 0; i < values.length; i++) {
+ if (values[i].equals("A")) {
+ aCheck = true;
+ } else if (values[i].equals("B")) {
+ bCheck = true;
+ } else if (values[i].equals("C")) {
+ cCheck = true;
+ }
+ }
+
+ assertTrue(aCheck);
+ assertTrue(bCheck);
+ assertTrue(cCheck);
+ }
+
+ /**
+ * Tests the getDistinctAttributeValues method, Take 2.
+ */
+ public static void testGetDistinctAttributeValues2() {
+ CyAttributes cyAttributes = new CyAttributesImpl();
+
+ // Test with Simple List
+ ArrayList list = new ArrayList();
+ list.add("apple");
+ list.add("banana");
+
+ cyAttributes.setListAttribute("ID1", LIST_TYPE, list);
+
+ CyNetwork network = Cytoscape.createNetwork("csplugins.test");
+ createNode("ID1", network);
+
+ String[] values = CyAttributesUtil.getDistinctAttributeValues(network.nodesIterator(),
+ cyAttributes, LIST_TYPE, 5);
+ assertEquals(1, values.length);
+ assertEquals("apple, banana", values[0]);
+ }
+
+ private static void createNode(String id, CyNetwork network) {
+ CyNode node = Cytoscape.getCyNode(id, true);
+ network.addNode(node);
+ }
+}
diff --git a/coreplugins/QuickFind/src/test/java/csplugins/test/quickfind/test/TestQuickFind.java b/coreplugins/QuickFind/src/test/java/csplugins/test/quickfind/test/TestQuickFind.java
new file mode 100644
index 0000000..bfa9f0b
--- /dev/null
+++ b/coreplugins/QuickFind/src/test/java/csplugins/test/quickfind/test/TestQuickFind.java
@@ -0,0 +1,275 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package csplugins.test.quickfind.test;
+
+import csplugins.quickfind.util.QuickFind;
+import csplugins.quickfind.util.QuickFindFactory;
+import csplugins.quickfind.util.TaskMonitorBase;
+
+import csplugins.widgets.autocomplete.index.Hit;
+import csplugins.widgets.autocomplete.index.NumberIndex;
+import csplugins.widgets.autocomplete.index.TextIndex;
+
+import cytoscape.CyEdge;
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+
+import cytoscape.data.CyAttributes;
+import cytoscape.data.Semantics;
+
+import junit.framework.TestCase;
+
+import java.util.List;
+
+
+/**
+ * Unit Test for Quick Find.
+ *
+ * @author Ethan Cerami.
+ */
+public class TestQuickFind extends TestCase {
+ private static final String LOCATION = "location";
+ private static final String NUCLEUS = "nucleus";
+ private static final String CYTOPLASM = "cytoplasm";
+ private static final String RANK = "rank";
+ private static final String SCORE = "score";
+ private static final String PMID = "pmid";
+
+ /**
+ * Runs basic tests to verify node indexing.
+ */
+ public void testNodeIndexing() {
+ // Create Sample Network
+ CyNetwork cyNetwork = Cytoscape.createNetwork("network1");
+ CyNode node0 = Cytoscape.getCyNode("rain", true);
+ CyNode node1 = Cytoscape.getCyNode("rainbow", true);
+ CyNode node2 = Cytoscape.getCyNode("rabbit", true);
+ CyNode node3 = Cytoscape.getCyNode("yellow", true);
+ cyNetwork.addNode(node0);
+ cyNetwork.addNode(node1);
+ cyNetwork.addNode(node2);
+ cyNetwork.addNode(node3);
+
+ CyEdge edge0 = Cytoscape.getCyEdge(node0, node1, Semantics.INTERACTION, "pp", true);
+ CyEdge edge1 = Cytoscape.getCyEdge(node0, node2, Semantics.INTERACTION, "pp", true);
+ CyEdge edge2 = Cytoscape.getCyEdge(node0, node3, Semantics.INTERACTION, "pp", true);
+ cyNetwork.addEdge(edge0);
+ cyNetwork.addEdge(edge1);
+ cyNetwork.addEdge(edge2);
+
+ // Add node/edge attributes
+ addNodeAttributes(node0, node1, node2, node3);
+ addEdgeAttributes(edge0, edge1, edge2);
+
+ Cytoscape.setCurrentNetwork(cyNetwork.getIdentifier());
+
+ // Index this network by Node:UNIQUE_IDENTIFIER
+ TaskMonitorBase monitor = new TaskMonitorBase();
+ QuickFind quickFind = QuickFindFactory.getGlobalQuickFindInstance();
+ quickFind.addNetwork(cyNetwork, monitor);
+
+ // Verify default values
+ TextIndex textIndex = (TextIndex) quickFind.getIndex(cyNetwork);
+ assertNotNull(textIndex);
+ String attributeKey = textIndex.getControllingAttribute();
+ assertEquals(QuickFind.UNIQUE_IDENTIFIER, attributeKey);
+
+ // Verify that nodes have been indexed
+ Hit[] hits = textIndex.getHits("ra", Integer.MAX_VALUE);
+ assertEquals(3, hits.length);
+ assertEquals("rabbit", hits[0].getKeyword());
+ assertEquals("rain", hits[1].getKeyword());
+ assertEquals("rainbow", hits[2].getKeyword());
+
+ // Verify Embedded Nodes
+ hits = textIndex.getHits("rain", Integer.MAX_VALUE);
+ assertEquals(1, hits[0].getAssociatedObjects().length);
+ assertEquals(node0, hits[0].getAssociatedObjects()[0]);
+
+ // Verify TaskMonitor data
+ assertEquals("Indexing node attributes", monitor.getStatus());
+ assertEquals(100, monitor.getPercentComplete());
+
+ // Now, try reindexing by Node:LOCATION
+ textIndex = (TextIndex) quickFind.reindexNetwork(cyNetwork, QuickFind.INDEX_NODES,
+ LOCATION, monitor);
+
+ // Verify Index type
+ assertEquals(QuickFind.INDEX_NODES, textIndex.getIndexType());
+
+ // Verify that nodes have been indexed
+ hits = textIndex.getHits("nu", Integer.MAX_VALUE);
+ assertEquals(1, hits.length);
+ assertEquals(NUCLEUS, hits[0].getKeyword());
+
+ // Verify Embedded Nodes
+ hits = textIndex.getHits(NUCLEUS, Integer.MAX_VALUE);
+ assertEquals(2, hits[0].getAssociatedObjects().length);
+ assertEquals(node3, hits[0].getAssociatedObjects()[0]);
+ assertEquals(node2, hits[0].getAssociatedObjects()[1]);
+
+ validateIndexAllAttributes(quickFind, cyNetwork, monitor);
+ validateIntegerIndex(quickFind, cyNetwork, monitor);
+ validateDoubleIndex(quickFind, cyNetwork, monitor);
+
+ // Now, try indexing edge attributes
+ textIndex = (TextIndex) quickFind.reindexNetwork(cyNetwork, QuickFind.INDEX_EDGES, PMID,
+ monitor);
+
+ // Verify Index type
+ assertEquals(QuickFind.INDEX_EDGES, textIndex.getIndexType());
+
+ // Verify that edges have been indexed
+ hits = textIndex.getHits("12", Integer.MAX_VALUE);
+ assertEquals(2, hits.length);
+ assertEquals("12345", hits[0].getKeyword());
+ assertEquals("12666", hits[1].getKeyword());
+
+ // Verify Embedded Edges
+ assertEquals(2, hits[0].getAssociatedObjects().length);
+
+ CyEdge edge = (CyEdge) hits[1].getAssociatedObjects()[0];
+ assertEquals("rain (pp) yellow", edge.getIdentifier());
+ }
+
+ private void addNodeAttributes(CyNode node0, CyNode node1, CyNode node2, CyNode node3) {
+ // Create Sample String Attributes
+ CyAttributes nodeAttributes = Cytoscape.getNodeAttributes();
+ nodeAttributes.setAttribute(node0.getIdentifier(), LOCATION, CYTOPLASM);
+ nodeAttributes.setAttribute(node1.getIdentifier(), LOCATION, CYTOPLASM);
+ nodeAttributes.setAttribute(node2.getIdentifier(), LOCATION, NUCLEUS);
+ nodeAttributes.setAttribute(node3.getIdentifier(), LOCATION, NUCLEUS);
+
+ // Create Sample Integer Attributes
+ nodeAttributes.setAttribute(node0.getIdentifier(), RANK, 4);
+ nodeAttributes.setAttribute(node1.getIdentifier(), RANK, 3);
+ nodeAttributes.setAttribute(node2.getIdentifier(), RANK, 1);
+ nodeAttributes.setAttribute(node3.getIdentifier(), RANK, 2);
+
+ // Create Sample Double Attributes
+ nodeAttributes.setAttribute(node0.getIdentifier(), SCORE, 45.2);
+ nodeAttributes.setAttribute(node1.getIdentifier(), SCORE, 3.211);
+ nodeAttributes.setAttribute(node2.getIdentifier(), SCORE, 22.2);
+ nodeAttributes.setAttribute(node3.getIdentifier(), SCORE, 2.1);
+
+ // make sure UNIQUE_IDENTIFIER attr is set
+ nodeAttributes.setAttribute(node0.getIdentifier(), QuickFind.UNIQUE_IDENTIFIER, "a");
+ nodeAttributes.setAttribute(node1.getIdentifier(), QuickFind.UNIQUE_IDENTIFIER, "b");
+ nodeAttributes.setAttribute(node2.getIdentifier(), QuickFind.UNIQUE_IDENTIFIER, "c");
+ nodeAttributes.setAttribute(node3.getIdentifier(), QuickFind.UNIQUE_IDENTIFIER, "d");
+ }
+
+ private void addEdgeAttributes(CyEdge edge0, CyEdge edge1, CyEdge edge2) {
+ // Create Sample String Attributes
+ CyAttributes edgeAttributes = Cytoscape.getEdgeAttributes();
+ edgeAttributes.setAttribute(edge0.getIdentifier(), PMID, "12345");
+ edgeAttributes.setAttribute(edge1.getIdentifier(), PMID, "12345");
+ edgeAttributes.setAttribute(edge2.getIdentifier(), PMID, "12666");
+ }
+
+ /**
+ * Validate that we can index all attributes.
+ */
+ private void validateIndexAllAttributes(QuickFind quickFind, CyNetwork cyNetwork,
+ TaskMonitorBase monitor) {
+ TextIndex textIndex;
+ Hit[] hits;
+ // Try indexing on a non-existent attribute key. This should
+ // do nothing silently, and should not throw any exceptions.
+ textIndex = (TextIndex) quickFind.reindexNetwork(cyNetwork, QuickFind.INDEX_NODES, "TYPE",
+ monitor);
+ assertNull(textIndex);
+
+ // Try indexing all attributes
+ textIndex = (TextIndex) quickFind.reindexNetwork(cyNetwork, QuickFind.INDEX_NODES,
+ QuickFind.INDEX_ALL_ATTRIBUTES, monitor);
+ assertNotNull(textIndex);
+
+ // First, try unique identifiers
+ hits = textIndex.getHits("ra", Integer.MAX_VALUE);
+ assertEquals(3, hits.length);
+ assertEquals("rabbit", hits[0].getKeyword());
+ assertEquals("rain", hits[1].getKeyword());
+ assertEquals("rainbow", hits[2].getKeyword());
+
+ // Then, try cellular location.
+ hits = textIndex.getHits("nu", Integer.MAX_VALUE);
+ assertEquals(1, hits.length);
+ assertEquals(NUCLEUS, hits[0].getKeyword());
+ }
+
+ private void validateIntegerIndex(QuickFind quickFind, CyNetwork cyNetwork,
+ TaskMonitorBase monitor) {
+ NumberIndex numberIndex = (NumberIndex) quickFind.reindexNetwork(cyNetwork,
+ QuickFind.INDEX_NODES,
+ RANK, monitor);
+ assertEquals(1, numberIndex.getMinimumValue());
+ assertEquals(4, numberIndex.getMaximumValue());
+
+ List list = numberIndex.getRange(1, 2);
+ assertEquals(2, list.size());
+
+ CyNode node0 = (CyNode) list.get(0);
+ assertEquals("rabbit", node0.getIdentifier());
+
+ CyNode node1 = (CyNode) list.get(1);
+ assertEquals("yellow", node1.getIdentifier());
+ }
+
+ private void validateDoubleIndex(QuickFind quickFind, CyNetwork cyNetwork,
+ TaskMonitorBase monitor) {
+ NumberIndex numberIndex = (NumberIndex) quickFind.reindexNetwork(cyNetwork,
+ QuickFind.INDEX_NODES,
+ SCORE, monitor);
+ assertEquals(2.1, numberIndex.getMinimumValue());
+ assertEquals(45.2, numberIndex.getMaximumValue());
+
+ List list = numberIndex.getRange(0.0, 5.0);
+ assertEquals(2, list.size());
+
+ CyNode node0 = (CyNode) list.get(0);
+ assertEquals("yellow", node0.getIdentifier());
+
+ CyNode node1 = (CyNode) list.get(1);
+ assertEquals("rainbow", node1.getIdentifier());
+
+ // Validate that upper bound is inclusive
+ list = numberIndex.getRange(0.0, 45.2);
+ assertEquals(4, list.size());
+ }
+}
diff --git a/coreplugins/QuickFind/src/test/java/csplugins/test/quickfind/test/package.html b/coreplugins/QuickFind/src/test/java/csplugins/test/quickfind/test/package.html
new file mode 100644
index 0000000..1ea582f
--- /dev/null
+++ b/coreplugins/QuickFind/src/test/java/csplugins/test/quickfind/test/package.html
@@ -0,0 +1,8 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+<html>
+<head></head>
+
+<body bgcolor="white">
+JUnit Tests for the Cytoscape QuickFind Functionality.
+</body>
+</html>
diff --git a/coreplugins/QuickFind/src/test/java/csplugins/test/widgets/test/package.html b/coreplugins/QuickFind/src/test/java/csplugins/test/widgets/test/package.html
new file mode 100644
index 0000000..ab74cb3
--- /dev/null
+++ b/coreplugins/QuickFind/src/test/java/csplugins/test/widgets/test/package.html
@@ -0,0 +1,8 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+<html>
+<head></head>
+
+<body bgcolor="white">
+Test Package.
+</body>
+</html>
diff --git a/coreplugins/QuickFind/src/test/java/csplugins/test/widgets/test/uiTests/package.html b/coreplugins/QuickFind/src/test/java/csplugins/test/widgets/test/uiTests/package.html
new file mode 100644
index 0000000..1d7ae2e
--- /dev/null
+++ b/coreplugins/QuickFind/src/test/java/csplugins/test/widgets/test/uiTests/package.html
@@ -0,0 +1,8 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+<html>
+<head></head>
+
+<body bgcolor="white">
+Usability / UI Tests.
+</body>
+</html>
diff --git a/coreplugins/QuickFind/src/test/java/csplugins/test/widgets/test/uiTests/view/RunQuickFindPanel.java b/coreplugins/QuickFind/src/test/java/csplugins/test/widgets/test/uiTests/view/RunQuickFindPanel.java
new file mode 100644
index 0000000..ff41d81
--- /dev/null
+++ b/coreplugins/QuickFind/src/test/java/csplugins/test/widgets/test/uiTests/view/RunQuickFindPanel.java
@@ -0,0 +1,142 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package csplugins.test.widgets.test.uiTests.view;
+
+import csplugins.quickfind.view.QuickFindPanel;
+
+import csplugins.test.widgets.test.unitTests.text.TestNumberIndex;
+import csplugins.test.widgets.test.unitTests.view.TestTextIndexComboBox;
+
+import csplugins.widgets.autocomplete.index.NumberIndex;
+import csplugins.widgets.autocomplete.index.TextIndex;
+import csplugins.widgets.autocomplete.view.TextIndexComboBox;
+
+import prefuse.data.query.NumberRangeModel;
+
+import prefuse.util.ui.JRangeSlider;
+
+import java.awt.*;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import javax.swing.*;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+
+
+/**
+ * Used to Test QuickFindPanel from the command line.
+ *
+ * @author Ethan Cerami
+ */
+public class RunQuickFindPanel {
+ private static JTextArea textArea;
+
+ /**
+ * Creates and shows GUI.
+ */
+ private static void createAndShowGUI() {
+ JFrame frame = new JFrame();
+ final QuickFindPanel panel = new QuickFindPanel();
+ panel.enableAllQuickFindButtons();
+ frame.getContentPane().add(panel, BorderLayout.NORTH);
+
+ // Create Sample Indexes
+ final TextIndex textIndex = TestTextIndexComboBox.createSampleTextIndex();
+ final NumberIndex numberIndex = TestNumberIndex.createSampleNumberIndex();
+ panel.setIndex(textIndex);
+
+ textArea = new JTextArea();
+
+ JScrollPane scrollPane = new JScrollPane(textArea);
+ frame.getContentPane().add(scrollPane, BorderLayout.CENTER);
+
+ final JComboBox box = new JComboBox();
+ box.addItem("Text index");
+ box.addItem("Number index");
+ box.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ String selection = (String) box.getSelectedItem();
+
+ if (selection.equals("Text index")) {
+ panel.setIndex(textIndex);
+ } else {
+ panel.setIndex(numberIndex);
+ }
+ }
+ });
+
+ final TextIndexComboBox comboBox = panel.getTextIndexComboBox();
+ comboBox.addFinalSelectionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ textArea.append("Select: " + comboBox.getSelectedItem() + "\n");
+ }
+ });
+
+ final JRangeSlider slider = panel.getSlider();
+ slider.addChangeListener(new ChangeListener() {
+ public void stateChanged(ChangeEvent e) {
+ NumberRangeModel model = (NumberRangeModel) slider.getModel();
+ Number low = (Number) model.getLowValue();
+ Number high = (Number) model.getHighValue();
+ textArea.append("Select: " + low + " - " + high + "\n");
+ }
+ });
+
+ frame.getContentPane().add(box, BorderLayout.SOUTH);
+ frame.setDefaultCloseOperation(3);
+ frame.setSize(300, 200);
+ frame.setVisible(true);
+ }
+
+ /**
+ * Main method, invoked for testing purposes only.
+ *
+ * @param args Command line arguments (none expected).
+ */
+ public static void main(String[] args) {
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ try {
+ RunQuickFindPanel.createAndShowGUI();
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+ }
+ });
+ }
+}
diff --git a/coreplugins/QuickFind/src/test/java/csplugins/test/widgets/test/uiTests/view/RunTextIndexComboBox.java b/coreplugins/QuickFind/src/test/java/csplugins/test/widgets/test/uiTests/view/RunTextIndexComboBox.java
new file mode 100644
index 0000000..38de69c
--- /dev/null
+++ b/coreplugins/QuickFind/src/test/java/csplugins/test/widgets/test/uiTests/view/RunTextIndexComboBox.java
@@ -0,0 +1,104 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package csplugins.test.widgets.test.uiTests.view;
+
+import csplugins.test.widgets.test.unitTests.view.TestTextIndexComboBox;
+
+import csplugins.widgets.autocomplete.index.TextIndex;
+import csplugins.widgets.autocomplete.view.ComboBoxFactory;
+import csplugins.widgets.autocomplete.view.TextIndexComboBox;
+
+import java.awt.*;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import javax.swing.*;
+
+
+/**
+ * Used to Test TextIndexComboBox from the command line.
+ *
+ * @author Ethan Cerami
+ */
+public class RunTextIndexComboBox {
+ private static JFrame frame;
+
+ /**
+ * Creates and shows GUI.
+ */
+ private static void createAndShowGUI()
+ throws IllegalAccessException, UnsupportedLookAndFeelException, ClassNotFoundException,
+ InstantiationException {
+ // Create Text Index, and populate with sample data.
+ TextIndex textIndex = TestTextIndexComboBox.createSampleTextIndex();
+
+ TextIndexComboBox comboBox = ComboBoxFactory.createTextIndexComboBox(textIndex, 1.2);
+ comboBox.setPrototypeDisplayValue("0123456790");
+
+ comboBox.addFinalSelectionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ TextIndexComboBox box = (TextIndexComboBox) e.getSource();
+ Object item = box.getSelectedItem();
+ JOptionPane.showMessageDialog(frame, "Final Selection: " + item.toString());
+ }
+ });
+
+ // create and show a window containing the combo box
+ frame = new JFrame();
+ frame.setDefaultCloseOperation(3);
+ frame.getContentPane().add(comboBox, BorderLayout.NORTH);
+ frame.setSize(200, 200);
+ frame.setVisible(true);
+ }
+
+ /**
+ * Main method, invoked for testing purposes only.
+ *
+ * @param args Command line arguments (none expected).
+ */
+ public static void main(String[] args) {
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ try {
+ RunTextIndexComboBox.createAndShowGUI();
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+ }
+ });
+ }
+}
diff --git a/coreplugins/QuickFind/src/test/java/csplugins/test/widgets/test/uiTests/view/package.html b/coreplugins/QuickFind/src/test/java/csplugins/test/widgets/test/uiTests/view/package.html
new file mode 100644
index 0000000..0b44a56
--- /dev/null
+++ b/coreplugins/QuickFind/src/test/java/csplugins/test/widgets/test/uiTests/view/package.html
@@ -0,0 +1,8 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+<html>
+<head></head>
+
+<body bgcolor="white">
+Tests the AutoCompleteComboBox.
+</body>
+</html>
diff --git a/coreplugins/QuickFind/src/test/java/csplugins/test/widgets/test/unitTests/package.html b/coreplugins/QuickFind/src/test/java/csplugins/test/widgets/test/unitTests/package.html
new file mode 100644
index 0000000..3199df4
--- /dev/null
+++ b/coreplugins/QuickFind/src/test/java/csplugins/test/widgets/test/unitTests/package.html
@@ -0,0 +1,8 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+<html>
+<head></head>
+
+<body bgcolor="white">
+JUnit Tests.
+</body>
+</html>
diff --git a/coreplugins/QuickFind/src/test/java/csplugins/test/widgets/test/unitTests/text/TestNumberIndex.java b/coreplugins/QuickFind/src/test/java/csplugins/test/widgets/test/unitTests/text/TestNumberIndex.java
new file mode 100644
index 0000000..ec99c0d
--- /dev/null
+++ b/coreplugins/QuickFind/src/test/java/csplugins/test/widgets/test/unitTests/text/TestNumberIndex.java
@@ -0,0 +1,130 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package csplugins.test.widgets.test.unitTests.text;
+
+import csplugins.quickfind.util.QuickFind;
+
+import csplugins.widgets.autocomplete.index.IndexFactory;
+import csplugins.widgets.autocomplete.index.NumberIndex;
+
+import junit.framework.TestCase;
+
+import java.util.List;
+
+
+/**
+ * Unit Tests for NumberIndexImpl.
+ *
+ * @author Ethan Cerami.
+ */
+public class TestNumberIndex extends TestCase {
+ /**
+ * Test Number Index with Integer Values.
+ */
+ public void testNumberIndexInteger() {
+ NumberIndex numberIndex = IndexFactory.createDefaultNumberIndex(QuickFind.INDEX_NODES);
+ numberIndex.addToIndex(new Integer(5), "a");
+ numberIndex.addToIndex(new Integer(2), "b");
+ numberIndex.addToIndex(new Integer(50), "c");
+ numberIndex.addToIndex(new Integer(15), "d");
+ numberIndex.addToIndex(new Integer(3), "e");
+ numberIndex.addToIndex(new Integer(5), "f");
+ numberIndex.addToIndex(new Integer(2), "g");
+
+ // Test Min / Max values
+ Number min = numberIndex.getMinimumValue();
+ assertEquals(2, min);
+
+ Number max = numberIndex.getMaximumValue();
+ assertEquals(50, max);
+
+ List list = numberIndex.getRange(10, 51);
+ assertEquals(2, list.size());
+ assertEquals("d", list.get(0));
+ assertEquals("c", list.get(1));
+
+ list = numberIndex.getRange(5, 6);
+ assertEquals(2, list.size());
+ assertEquals("a", list.get(0));
+ assertEquals("f", list.get(1));
+ }
+
+ /**
+ * Test Number Index with Double values.
+ */
+ public void testNumberIndexDouble() {
+ NumberIndex numberIndex = IndexFactory.createDefaultNumberIndex(QuickFind.INDEX_NODES);
+ numberIndex.addToIndex(new Double(0.1), "a");
+ numberIndex.addToIndex(new Double(0.2), "b");
+ numberIndex.addToIndex(new Double(0.8), "c");
+ numberIndex.addToIndex(new Double(0.9), "d");
+ numberIndex.addToIndex(new Double(0.99), "e");
+ numberIndex.addToIndex(new Double(0.7), "f");
+ numberIndex.addToIndex(new Double(0.88), "g");
+
+ // Test Min / Max values
+ Number min = numberIndex.getMinimumValue();
+ assertEquals(0.1, min);
+ assertEquals(0.1, min.doubleValue(), 0.001);
+
+ Number max = numberIndex.getMaximumValue();
+ assertEquals(.99, max.doubleValue(), 0.001);
+
+ List list = numberIndex.getRange(0.1, 0.3);
+ assertEquals(2, list.size());
+ assertEquals("a", list.get(0));
+ assertEquals("b", list.get(1));
+
+ list = numberIndex.getRange(0.0, 1.0);
+ assertEquals(7, list.size());
+ }
+
+ /**
+ * Creates a Sample Number Index.
+ *
+ * @return NumberIndex Object.
+ */
+ public static NumberIndex createSampleNumberIndex() {
+ NumberIndex numberIndex = IndexFactory.createDefaultNumberIndex(QuickFind.INDEX_NODES);
+
+ for (double d = 0; d < 100; d += .2) {
+ numberIndex.addToIndex(d, d);
+ }
+
+ return numberIndex;
+ }
+}
diff --git a/coreplugins/QuickFind/src/test/java/csplugins/test/widgets/test/unitTests/text/TestTextIndex.java b/coreplugins/QuickFind/src/test/java/csplugins/test/widgets/test/unitTests/text/TestTextIndex.java
new file mode 100644
index 0000000..ca1e271
--- /dev/null
+++ b/coreplugins/QuickFind/src/test/java/csplugins/test/widgets/test/unitTests/text/TestTextIndex.java
@@ -0,0 +1,170 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package csplugins.test.widgets.test.unitTests.text;
+
+import csplugins.quickfind.util.QuickFind;
+
+import csplugins.widgets.autocomplete.index.Hit;
+import csplugins.widgets.autocomplete.index.IndexFactory;
+import csplugins.widgets.autocomplete.index.TextIndex;
+
+import junit.framework.TestCase;
+
+
+/**
+ * Unit Tests for TextIndexImpl.
+ *
+ * @author Ethan Cerami.
+ */
+public class TestTextIndex extends TestCase {
+ /**
+ * First Round of Test Cases.
+ */
+ public void testTextIndex0() {
+ TextIndex textIndex = IndexFactory.createDefaultTextIndex(QuickFind.INDEX_NODES);
+ textIndex.addToIndex("rain", new Integer(1));
+ textIndex.addToIndex("rain", new Integer(2));
+ textIndex.addToIndex("rainbow", new Integer(3));
+ textIndex.addToIndex("rainbow trout", new Integer(4));
+ textIndex.addToIndex("RABBIT", new Integer(5));
+
+ assertEquals(4, textIndex.getNumKeys());
+
+ // Test with prefix: "ra"
+ Hit[] hits = textIndex.getHits("ra", Integer.MAX_VALUE);
+ assertEquals(4, hits.length);
+ assertEquals("rabbit", hits[0].getKeyword());
+ assertEquals("rain", hits[1].getKeyword());
+ assertEquals("rainbow", hits[2].getKeyword());
+ assertEquals("rainbow trout", hits[3].getKeyword());
+
+ // Test with prefix "rain"
+ hits = textIndex.getHits("rain", Integer.MAX_VALUE);
+ assertEquals(3, hits.length);
+ assertEquals("rain", hits[0].getKeyword());
+ assertEquals("rainbow", hits[1].getKeyword());
+ assertEquals("rainbow trout", hits[2].getKeyword());
+
+ // Test with prefix "RAIN". Verifies that search is
+ // case *insensitive*.
+ hits = textIndex.getHits("RAIN", Integer.MAX_VALUE);
+ assertEquals(3, hits.length);
+ assertEquals("rain", hits[0].getKeyword());
+ assertEquals("rainbow", hits[1].getKeyword());
+ assertEquals("rainbow trout", hits[2].getKeyword());
+
+ // Test Existence of Embedded Objects
+ hits = textIndex.getHits("rain", Integer.MAX_VALUE);
+ assertEquals(2, hits[0].getAssociatedObjects().length);
+ assertEquals("1", hits[0].getAssociatedObjects()[0].toString());
+ assertEquals("2", hits[0].getAssociatedObjects()[1].toString());
+
+ hits = textIndex.getHits("rainbow", Integer.MAX_VALUE);
+ assertEquals(1, hits[0].getAssociatedObjects().length);
+ assertEquals("3", hits[0].getAssociatedObjects()[0].toString());
+
+ // Try getting hits for an undefined key
+ hits = textIndex.getHits("cytoscape", Integer.MAX_VALUE);
+ assertEquals(0, hits.length);
+
+ // Now, try resetting the index
+ textIndex.resetIndex();
+
+ // Verify that keys are no longer available
+ hits = textIndex.getHits("rain", Integer.MAX_VALUE);
+ assertEquals(0, hits.length);
+
+ // Verify toString() makes sense
+ assertEquals("Text Index: [Total number of keys: 0]", textIndex.toString());
+ }
+
+ /**
+ * Tests wild card searches.
+ */
+ public void testWildCardSearches() {
+ TextIndex textIndex = IndexFactory.createDefaultTextIndex(QuickFind.INDEX_NODES);
+ textIndex.addToIndex("rain", new Integer(1));
+ textIndex.addToIndex("rain", new Integer(2));
+ textIndex.addToIndex("rainbow", new Integer(3));
+ textIndex.addToIndex("rainbow trout", new Integer(4));
+ textIndex.addToIndex("RABBIT", new Integer(5));
+
+ Hit[] hits = textIndex.getHits("ra*", Integer.MAX_VALUE);
+ assertEquals(1, hits.length);
+ assertEquals("ra*", hits[0].getKeyword());
+ assertEquals(5, hits[0].getAssociatedObjects().length);
+ }
+
+ /**
+ * Test max key length.
+ */
+ public void testMaxKeyLength() {
+ TextIndex textIndex = IndexFactory.createDefaultTextIndex(QuickFind.INDEX_NODES);
+ assertEquals(TextIndex.DEFAULT_MAX_KEY_LENGTH, textIndex.getMaxKeyLength());
+ textIndex.addToIndex("The Associated Press and the New York Times "
+ + "are now reporting that Atlantis will not launch Sunday.",
+ new Integer(1));
+
+ Hit[] hits = textIndex.getHits("the", Integer.MAX_VALUE);
+ assertEquals(1, hits.length);
+ assertEquals("the associated press and the new york times are now "
+ + "reporting that atlantis will not launch sunday.", hits[0].getKeyword());
+ assertEquals(1, hits[0].getAssociatedObjects().length);
+ }
+
+ /**
+ * Test modified sort order.
+ * @throws Exception All Errors.
+ */
+ public void testSortOrder() throws Exception {
+ TextIndex textIndex = IndexFactory.createDefaultTextIndex(QuickFind.INDEX_NODES);
+ textIndex.addToIndex("?", new Integer(1));
+ textIndex.addToIndex("1rain", new Integer(2));
+ textIndex.addToIndex("rainbow", new Integer(3));
+ textIndex.addToIndex("rainbow trout", new Integer(4));
+ textIndex.addToIndex("RABBIT", new Integer(5));
+
+ // Verify that strings starting beginning with letters appear
+ // at beginning of list.
+ Hit[] hits = textIndex.getHits("", Integer.MAX_VALUE);
+ assertEquals("rabbit", hits[0].getKeyword());
+ assertEquals("rainbow", hits[1].getKeyword());
+ assertEquals("rainbow trout", hits[2].getKeyword());
+ assertEquals("1rain", hits[3].getKeyword());
+ assertEquals("?", hits[4].getKeyword());
+ }
+}
diff --git a/coreplugins/QuickFind/src/test/java/csplugins/test/widgets/test/unitTests/text/package.html b/coreplugins/QuickFind/src/test/java/csplugins/test/widgets/test/unitTests/text/package.html
new file mode 100644
index 0000000..b0550d0
--- /dev/null
+++ b/coreplugins/QuickFind/src/test/java/csplugins/test/widgets/test/unitTests/text/package.html
@@ -0,0 +1,8 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+<html>
+<head></head>
+
+<body bgcolor="white">
+JUnit Tests for TextIndex Package.
+</body>
+</html>
diff --git a/coreplugins/QuickFind/src/test/java/csplugins/test/widgets/test/unitTests/view/TestTextIndexComboBox.java b/coreplugins/QuickFind/src/test/java/csplugins/test/widgets/test/unitTests/view/TestTextIndexComboBox.java
new file mode 100644
index 0000000..27d34e5
--- /dev/null
+++ b/coreplugins/QuickFind/src/test/java/csplugins/test/widgets/test/unitTests/view/TestTextIndexComboBox.java
@@ -0,0 +1,272 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package csplugins.test.widgets.test.unitTests.view;
+
+import csplugins.quickfind.util.QuickFind;
+
+import csplugins.widgets.autocomplete.index.Hit;
+import csplugins.widgets.autocomplete.index.IndexFactory;
+import csplugins.widgets.autocomplete.index.TextIndex;
+import csplugins.widgets.autocomplete.view.AutoCompleteDocument;
+import csplugins.widgets.autocomplete.view.ComboBoxFactory;
+import csplugins.widgets.autocomplete.view.TextIndexComboBox;
+
+import junit.framework.TestCase;
+
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import java.util.ArrayList;
+
+import javax.swing.text.Document;
+import javax.swing.text.JTextComponent;
+import javax.swing.text.SimpleAttributeSet;
+
+
+/**
+ * JUnit Tests for the TextIndexComboBox.
+ *
+ * @author Ethan Cerami.
+ */
+public class TestTextIndexComboBox extends TestCase {
+ /**
+ * Tests various user operations on the TextIndexComboBox.
+ *
+ * @throws Exception All Errors.
+ */
+ public void testComboBox() throws Exception {
+ TextIndex textIndex = createSampleTextIndex();
+ TextIndexComboBox comboBox = ComboBoxFactory.createTextIndexComboBox(textIndex, 1.0);
+ JTextComponent editor = (JTextComponent) comboBox.getEditor().getEditorComponent();
+
+ // Assuming no user input, what do I see in the pull-down?
+ assertEquals(TextIndexComboBox.DEFAULT_MAX_HITS_SHOWN, comboBox.getItemCount());
+ assertEquals("apple", comboBox.getItemAt(0).toString());
+ assertEquals("bag", comboBox.getItemAt(2).toString());
+ assertEquals("bat", comboBox.getItemAt(3).toString());
+ assertEquals("burn", comboBox.getItemAt(10).toString());
+
+ // Assuming user enters "B", what do I see in the pull-down menu?
+ Document doc = editor.getDocument();
+ doc.insertString(0, "B", new SimpleAttributeSet());
+ assertEquals(12, comboBox.getItemCount());
+ assertEquals("bag", comboBox.getItemAt(0).toString());
+ assertEquals("bat", comboBox.getItemAt(1).toString());
+ assertEquals("beef", comboBox.getItemAt(2).toString());
+ assertEquals("bust", comboBox.getItemAt(9).toString());
+
+ // What do I see in the text box? should be first item in the list
+ assertEquals("bag", editor.getText());
+
+ // Assuming user now enters "o", what do I see?
+ doc.insertString(1, "o", new SimpleAttributeSet());
+ assertEquals("bone", editor.getText());
+ assertEquals(4, comboBox.getItemCount());
+ assertEquals("bone", comboBox.getItemAt(0).toString());
+ assertEquals("boney", comboBox.getItemAt(1).toString());
+ assertEquals("boom", comboBox.getItemAt(2).toString());
+ assertEquals("boon", comboBox.getItemAt(3).toString());
+
+ // Assuming user now deletes the last "o", possibly via backspace,
+ // what do I see?
+ doc.remove(1, 1);
+ assertEquals("bag", editor.getText());
+ assertEquals(12, comboBox.getItemCount());
+ assertEquals("bag", comboBox.getItemAt(0).toString());
+ assertEquals("bat", comboBox.getItemAt(1).toString());
+ assertEquals("beef", comboBox.getItemAt(2).toString());
+ assertEquals("bust", comboBox.getItemAt(9).toString());
+
+ // Start over; Assuming user enters "but", what do I see in
+ // the pull-down?
+ doc.remove(0, doc.getLength());
+ doc.insertString(0, "but", new SimpleAttributeSet());
+ assertEquals(2, comboBox.getItemCount());
+ assertEquals("butter", comboBox.getItemAt(0).toString());
+ assertEquals("button", comboBox.getItemAt(1).toString());
+
+ // What do I see in the text box; should be first item in the list
+ assertEquals("butter", editor.getText());
+
+ // Assuming user hits Backspace a few times,
+ // e.g. erases the last 'tter', then what?
+ doc.remove(2, 4);
+ assertEquals(5, comboBox.getItemCount());
+ assertEquals("bug", comboBox.getItemAt(0).toString());
+ assertEquals("burn", comboBox.getItemAt(1).toString());
+ assertEquals("bust", comboBox.getItemAt(2).toString());
+ assertEquals("butter", comboBox.getItemAt(3).toString());
+ assertEquals("button", comboBox.getItemAt(4).toString());
+
+ // Start over; Assuming user enters "y", what do I see in the menu?
+ doc.remove(0, doc.getLength());
+ doc.insertString(0, "y", new SimpleAttributeSet());
+ assertEquals(1, comboBox.getItemCount());
+
+ Hit hit = (Hit) comboBox.getItemAt(0);
+ assertEquals(0, hit.getAssociatedObjects().length);
+ assertEquals("y", hit.getKeyword());
+ }
+
+ /**
+ * Test explicit functionality re: selecting items via cursor keys.
+ *
+ * @throws Exception All Errors.
+ */
+ public void testSelectionViaCursorKeys() throws Exception {
+ TextIndex textIndex = createSampleTextIndex();
+ TextIndexComboBox comboBox = ComboBoxFactory.createTextIndexComboBox(textIndex, 1.0);
+ JTextComponent editor = (JTextComponent) comboBox.getEditor().getEditorComponent();
+ AutoCompleteDocument doc = (AutoCompleteDocument) editor.getDocument();
+
+ // w/o cursor key selection;
+ // before selection: there should be 10 items in the pull-down
+ // after selection: there should be 1 item in the pull-down
+ doc.insertString(0, "B", new SimpleAttributeSet());
+
+ int before = comboBox.getItemCount();
+ comboBox.setSelectedItem("beef");
+
+ int after = comboBox.getItemCount();
+ assertEquals(12, before);
+ assertEquals(1, after);
+
+ // w/o cursor key selection;
+ // before selection: there should be 10 items in the pull-down
+ // after selection: there should still be 10 items in the pull-down
+ doc.remove(0, doc.getLength());
+ doc.insertString(0, "B", new SimpleAttributeSet());
+ before = comboBox.getItemCount();
+ doc.setCursorKeyPressed(true);
+ comboBox.setSelectedItem("beef");
+ after = comboBox.getItemCount();
+ assertEquals(12, before);
+ assertEquals(12, after);
+ }
+
+ /**
+ * Tests the FinalSelectionListener Framework.
+ *
+ * @throws Exception All Errors.
+ */
+ public void testFinalSelectionListenerFramework() throws Exception {
+ TextIndex textIndex = createSampleTextIndex();
+ TextIndexComboBox comboBox = ComboBoxFactory.createTextIndexComboBox(textIndex, 1.0);
+ final ArrayList eventList = new ArrayList();
+ comboBox.addFinalSelectionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ eventList.add(e);
+
+ TextIndexComboBox comboBox = (TextIndexComboBox) e.getSource();
+ Hit hit = (Hit) comboBox.getSelectedItem();
+ assertEquals("apple", hit.getKeyword());
+ }
+ });
+ // Select an item from the pull-down menu
+ comboBox.setSelectedIndex(0);
+
+ // Verify that event was received my listener
+ assertEquals(1, eventList.size());
+ }
+
+ /**
+ * Creates a Sample Text Index.
+ *
+ * @return TextIndex Object.
+ */
+ public static TextIndex createSampleTextIndex() {
+ TextIndex textIndex = IndexFactory.createDefaultTextIndex(QuickFind.INDEX_NODES);
+ textIndex.addToIndex("Apple", new String());
+ textIndex.addToIndex("Apple Long Long Long Long Long Label", new String());
+ textIndex.addToIndex("Bat", new String());
+ textIndex.addToIndex("Bat", new String());
+ textIndex.addToIndex("Bat", new String());
+ textIndex.addToIndex("Butter", new String());
+ textIndex.addToIndex("Butter", new String());
+ textIndex.addToIndex("Butter", new String());
+ textIndex.addToIndex("Butter", new String());
+ textIndex.addToIndex("Butter", new String());
+ textIndex.addToIndex("Button", new String());
+ textIndex.addToIndex("Button", new String());
+ textIndex.addToIndex("Button", new String());
+ textIndex.addToIndex("Button", new String());
+ textIndex.addToIndex("Button", new String());
+ textIndex.addToIndex("Button", new String());
+ textIndex.addToIndex("Button", new String());
+ textIndex.addToIndex("Button", new String());
+ textIndex.addToIndex("Button", new String());
+ textIndex.addToIndex("Button", new String());
+ textIndex.addToIndex("Button", new String());
+ textIndex.addToIndex("Button", new String());
+ textIndex.addToIndex("Button", new String());
+ textIndex.addToIndex("Button", new String());
+ textIndex.addToIndex("Button", new String());
+ textIndex.addToIndex("Button", new String());
+ textIndex.addToIndex("Bug", new String());
+ textIndex.addToIndex("Bag", new String());
+ textIndex.addToIndex("Bust", new String());
+ textIndex.addToIndex("Burn", new String());
+ textIndex.addToIndex("Beef", new String());
+ textIndex.addToIndex("Bone", new String());
+ textIndex.addToIndex("Boon", new String());
+ textIndex.addToIndex("Boney", new String());
+ textIndex.addToIndex("Boom", new String());
+ textIndex.addToIndex("Jello", new String());
+ textIndex.addToIndex("Kramer", new String());
+ textIndex.addToIndex("Lion", new String());
+ textIndex.addToIndex("Mary", new String());
+ textIndex.addToIndex("Nancy", new String());
+ textIndex.addToIndex("Oprah", new String());
+ textIndex.addToIndex("Queen", new String());
+ textIndex.addToIndex("Round", new String());
+ textIndex.addToIndex("Sam", new String());
+ textIndex.addToIndex("Sweet", new String());
+ textIndex.addToIndex("Swoon", new String());
+ textIndex.addToIndex("Swimmer", new String());
+ textIndex.addToIndex("Swish", new String());
+ textIndex.addToIndex("Swig", new String());
+ textIndex.addToIndex("Sammy", new String());
+ textIndex.addToIndex("Tomorrow", new String());
+ textIndex.addToIndex("Underground", new String());
+ textIndex.addToIndex("Vector", new String());
+ textIndex.addToIndex("World", new String());
+ textIndex.addToIndex("Zoo", new String());
+ textIndex.addToIndex("Zoo_REALLY_REALLY_REALLY_REALLY_REALY_" + "LONG NAME", new String());
+
+ return textIndex;
+ }
+}
diff --git a/coreplugins/QuickFind/src/test/java/csplugins/test/widgets/test/unitTests/view/package.html b/coreplugins/QuickFind/src/test/java/csplugins/test/widgets/test/unitTests/view/package.html
new file mode 100644
index 0000000..d66a87b
--- /dev/null
+++ b/coreplugins/QuickFind/src/test/java/csplugins/test/widgets/test/unitTests/view/package.html
@@ -0,0 +1,8 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+<html>
+<head></head>
+
+<body bgcolor="white">
+JUnit Tests for View Components.
+</body>
+</html>
diff --git a/coreplugins/RFilters/AUTHOR b/coreplugins/RFilters/AUTHOR
new file mode 100644
index 0000000..1e54e1b
--- /dev/null
+++ b/coreplugins/RFilters/AUTHOR
@@ -0,0 +1,5 @@
+This is a new Filter Plugin that is designed to be used non-exclusively with Y-Files or GINY graphs. This Filter plugin aims to be very extendable and very useful.
+
+Contact: Rowan Christmas
+E-Mail : xmas at systemsbiology.org
+Phone : (206) 732-1328
\ No newline at end of file
diff --git a/coreplugins/RFilters/pom.xml b/coreplugins/RFilters/pom.xml
new file mode 100644
index 0000000..7208af9
--- /dev/null
+++ b/coreplugins/RFilters/pom.xml
@@ -0,0 +1,56 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>parent</artifactId>
+ <version>2.8.4-SNAPSHOT</version>
+ </parent>
+
+ <artifactId>rfilters</artifactId>
+ <packaging>jar</packaging>
+
+ <name>RFilters</name>
+
+ <!-- bootstrap for cytoscape dependencies, namely the parent POM snapshots -->
+ <repositories>
+ <repository>
+ <id>cytoscape_snapshots</id>
+ <snapshots>
+ <enabled>true</enabled>
+ </snapshots>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <name>Cytoscape Snapshots</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/</url>
+ </repository>
+ <repository>
+ <id>cytoscape_releases</id>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ <name>Cytoscape Releases</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/releases/</url>
+ </repository>
+ </repositories>
+
+ <build>
+ <plugins>
+ <plugin>
+ <artifactId>maven-assembly-plugin</artifactId>
+ <configuration>
+ <archive>
+ <manifestEntries>
+ <Cytoscape-Plugin>filter.cytoscape.FilterPlugin</Cytoscape-Plugin>
+ </manifestEntries>
+ </archive>
+ </configuration>
+ </plugin>
+ </plugins>
+ </build>
+
+</project>
+
diff --git a/coreplugins/RFilters/src/main/java/filter/cytoscape/AttributeComboBoxModel.java b/coreplugins/RFilters/src/main/java/filter/cytoscape/AttributeComboBoxModel.java
new file mode 100644
index 0000000..17d21e4
--- /dev/null
+++ b/coreplugins/RFilters/src/main/java/filter/cytoscape/AttributeComboBoxModel.java
@@ -0,0 +1,286 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package filter.cytoscape;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.data.CyAttributes;
+
+import filter.view.*;
+
+import java.beans.*;
+
+import java.util.*;
+
+import javax.swing.*;
+import javax.swing.event.*;
+
+
+/**
+ *
+ */
+public abstract class AttributeComboBoxModel implements ComboBoxModel, PropertyChangeListener {
+ protected Object selectedObject;
+ protected Vector attributeList;
+ protected Class[] type2Class = new Class[] {
+ Boolean.class, Double.class, Integer.class, String.class
+ };
+
+ protected AttributeComboBoxModel() {
+ attributeList = new Vector();
+ Cytoscape.getSwingPropertyChangeSupport().addPropertyChangeListener(this);
+ }
+
+ /**
+ * This function will map from a type in the CyAttributes class to an actual
+ * class instance
+ */
+ protected Class type2Class(int type) {
+ switch (type) {
+ case CyAttributes.TYPE_BOOLEAN:
+ return Boolean.class;
+
+ case CyAttributes.TYPE_COMPLEX:
+ return Object.class;
+
+ case CyAttributes.TYPE_FLOATING:
+ return Double.class;
+
+ case CyAttributes.TYPE_INTEGER:
+ return Integer.class;
+
+ case CyAttributes.TYPE_SIMPLE_LIST:
+ return java.util.List.class;
+
+ case CyAttributes.TYPE_SIMPLE_MAP:
+ return java.util.Map.class;
+
+ case CyAttributes.TYPE_STRING:
+ return String.class;
+
+ case CyAttributes.TYPE_UNDEFINED:
+ return Object.class;
+
+ default:
+ return Object.class;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void notifyListeners() {
+ for (Iterator listenIt = listeners.iterator(); listenIt.hasNext();) {
+ ((ListDataListener) listenIt.next()).contentsChanged(new ListDataEvent(this,
+ ListDataEvent.CONTENTS_CHANGED,
+ 0,
+ attributeList
+ .size()));
+ }
+ }
+
+ //implements PropertyChange
+ /**
+ * DOCUMENT ME!
+ *
+ * @param pce DOCUMENT ME!
+ */
+ public abstract void propertyChange(PropertyChangeEvent pce);
+
+ //implements ListModel
+ Vector listeners = new Vector();
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param l DOCUMENT ME!
+ */
+ public void addListDataListener(ListDataListener l) {
+ listeners.add(l);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param index DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getElementAt(int index) {
+ return attributeList.elementAt(index);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getSize() {
+ return attributeList.size();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param l DOCUMENT ME!
+ */
+ public void removeListDataListener(ListDataListener l) {
+ listeners.remove(l);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param item DOCUMENT ME!
+ */
+ public void setSelectedItem(Object item) {
+ selectedObject = item;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getSelectedItem() {
+ return selectedObject;
+ }
+}
+
+
+class NodeAttributeComboBoxModel extends AttributeComboBoxModel {
+ Class attributeClass;
+ CyAttributes nodeAttributes;
+
+ /**
+ * Creates a new NodeAttributeComboBoxModel object.
+ *
+ * @param attributeClass DOCUMENT ME!
+ */
+ public NodeAttributeComboBoxModel(Class attributeClass) {
+ super();
+ nodeAttributes = Cytoscape.getNodeAttributes();
+ this.attributeClass = attributeClass;
+ updateAttributes();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param pce DOCUMENT ME!
+ */
+ public void propertyChange(PropertyChangeEvent pce) {
+ updateAttributes();
+ }
+
+ protected void updateAttributes() {
+ /*byte type;
+ if ( attributeClass == Double.class )
+ type = CyAttributes.TYPE_FLOATING;
+ else if ( attributeClass == Integer.class )
+ type = CyAttributes.TYPE_INTEGER;
+ else if ( attributeClass == String.class )
+ type = CyAttributes.TYPE_STRING;
+ else
+ return;
+ */
+ String[] na = Cytoscape.getNodeAttributes().getAttributeNames();
+ attributeList = new Vector();
+
+ for (int idx = 0; idx < na.length; idx++) {
+ if (attributeClass.isAssignableFrom(type2Class(nodeAttributes.getType(na[idx])))) {
+ attributeList.add(na[idx]);
+ }
+
+ notifyListeners();
+ }
+ }
+}
+
+
+class EdgeAttributeComboBoxModel extends AttributeComboBoxModel {
+ Class attributeClass;
+ CyAttributes edgeAttributes;
+
+ /**
+ * Creates a new EdgeAttributeComboBoxModel object.
+ *
+ * @param attributeClass DOCUMENT ME!
+ */
+ public EdgeAttributeComboBoxModel(Class attributeClass) {
+ super();
+ edgeAttributes = Cytoscape.getEdgeAttributes();
+ this.attributeClass = attributeClass;
+ updateAttributes();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param pce DOCUMENT ME!
+ */
+ public void propertyChange(PropertyChangeEvent pce) {
+ updateAttributes();
+ }
+
+ protected void updateAttributes() {
+ /*
+ * This part isn't really necessary anymore
+ * now that we have the class lookup
+ * table
+ byte type;
+ if ( attributeClass == String.class )
+ type = CyAttributes.TYPE_STRING;
+ else if ( attributeClass == Double.class )
+ type = CyAttributes.TYPE_FLOATING;
+ else if ( attributeClass == Integer.class )
+ type = CyAttributes.TYPE_INTEGER;
+ else
+ return;
+ */
+ String[] ea = Cytoscape.getEdgeAttributes().getAttributeNames();
+ attributeList = new Vector();
+
+ for (int idx = 0; idx < ea.length; idx++) {
+ if (attributeClass.isAssignableFrom(type2Class(edgeAttributes.getType(ea[idx])))) {
+ attributeList.add(ea[idx]);
+ }
+
+ notifyListeners();
+ }
+ }
+}
diff --git a/coreplugins/RFilters/src/main/java/filter/cytoscape/BooleanMetaFilter.java b/coreplugins/RFilters/src/main/java/filter/cytoscape/BooleanMetaFilter.java
new file mode 100644
index 0000000..fa566d7
--- /dev/null
+++ b/coreplugins/RFilters/src/main/java/filter/cytoscape/BooleanMetaFilter.java
@@ -0,0 +1,401 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package filter.cytoscape;
+
+import ViolinStrings.Strings;
+
+import cytoscape.*;
+import cytoscape.CyNetwork;
+
+import cytoscape.data.*;
+
+import filter.model.*;
+
+import giny.model.*;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import java.beans.*;
+
+import java.util.*;
+
+import javax.swing.*;
+import javax.swing.border.*;
+import javax.swing.event.*;
+import javax.swing.event.SwingPropertyChangeSupport;
+
+
+/**
+ * This is a Cytoscape specific filter that will pass nodes if
+ * a selected attribute matches a specific value.
+ */
+public class BooleanMetaFilter implements Filter {
+ //----------------------------------------//
+ // Filter specific properties
+ //----------------------------------------//
+ protected int[] filters;
+ protected String comparison;
+ protected boolean negation;
+
+ /**
+ *
+ */
+ public static String AND = "ALL";
+
+ /**
+ *
+ */
+ public static String OR = "AT LEAST ONE";
+
+ /**
+ *
+ */
+ public static String XOR = "ONLY ONE";
+
+ /**
+ *
+ */
+ public static String FILTER_NAME_EVENT = "FILTER_NAME_EVENT";
+
+ /**
+ *
+ */
+ public static String FILTER_ID = "Boolean Meta-Filter";
+
+ /**
+ *
+ */
+ public static String FILTER_DESCRIPTION = "Select nodes based on a combination of other filters";
+
+ /**
+ *
+ */
+ public static String COMPARISON_EVENT = "COMPARISON_EVENT";
+
+ /**
+ *
+ */
+ public static String FILTER_EVENT = "FILTER_EVENT";
+
+ /**
+ *
+ */
+ public static String FILTER_BOX_EVENT = "FILTER_BOX";
+
+ /**
+ *
+ */
+ public static String NEGATION_EVENT = "NEGATION_EVENT";
+
+ //----------------------------------------//
+ // Needed Variables
+ //----------------------------------------//
+ protected String identifier = "default";
+ protected SwingPropertyChangeSupport pcs = new SwingPropertyChangeSupport(this);
+
+ //---------------------------------------//
+ // Constructor
+ //----------------------------------------//
+
+ /**
+ * Creates a new BooleanMetaFilter
+ */
+ public BooleanMetaFilter(int[] filters, String comparison, String identifier, boolean negation) {
+ this.filters = filters;
+ this.comparison = comparison;
+ this.identifier = identifier;
+ this.negation = negation;
+ }
+
+ /**
+ * Creates a new BooleanMetaFilter object.
+ *
+ * @param desc DOCUMENT ME!
+ */
+ public BooleanMetaFilter(String desc) {
+ input(desc);
+ }
+
+ //----------------------------------------//
+ // Implements Filter
+ //----------------------------------------//
+
+ /**
+ * Returns the name for this Filter
+ */
+ public String toString() {
+ return identifier;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getDescription() {
+ return FILTER_DESCRIPTION;
+ }
+
+ /**
+ * sets a new name for this filter
+ */
+ public void setIdentifier(String new_id) {
+ this.identifier = new_id;
+ pcs.firePropertyChange(FILTER_NAME_EVENT, null, new_id);
+ }
+
+ /**
+ * This is usually the same as the class name
+ */
+ public String getFilterID() {
+ return FILTER_ID;
+ }
+
+ /**
+ * An Object Passes this Filter if its "toString" method
+ * matches any of the Text from the TextField
+ */
+ public boolean passesFilter(Object object) {
+ if (filters.length == 0) {
+ return false ^ negation;
+ }
+
+ int count = 0;
+
+ for (int idx = 0; idx < filters.length; idx++) {
+ //System.err.println(""+filters[idx]);
+ Filter f = FilterManager.defaultManager().getFilter(filters[idx]);
+ boolean filterResult = false;
+
+ if (f != null) {
+ filterResult = f.passesFilter(object);
+ } // end of if ()
+
+ if ((comparison == AND) && !filterResult) {
+ return false ^ negation;
+ }
+
+ if ((comparison == OR) && filterResult) {
+ return true ^ negation;
+ }
+
+ if ((comparison == XOR) && filterResult) {
+ if (++count > 1) {
+ return false ^ negation;
+ }
+ }
+ }
+
+ if ((comparison == XOR) && (count == 1)) {
+ return true ^ negation;
+ }
+
+ if (comparison == AND) {
+ return true ^ negation;
+ } else {
+ return false ^ negation;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Class[] getPassingTypes() {
+ Vector passingTypes = new Vector(2);
+
+ for (int idx = 0; idx < filters.length; idx++) {
+ Filter filter = FilterManager.defaultManager().getFilter(filters[idx]);
+ Class[] filterPassingTypes = filter.getPassingTypes();
+
+ for (int idy = 0; idy < filterPassingTypes.length; idy++) {
+ if (!passingTypes.contains(filterPassingTypes[idy])) {
+ passingTypes.add(filterPassingTypes[idy]);
+ }
+ }
+ }
+
+ return (Class[]) passingTypes.toArray(new Class[] { });
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param other_object DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean equals(Object other_object) {
+ return super.equals(other_object);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object clone() {
+ return new BooleanMetaFilter(filters, comparison, identifier + "_new", negation);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public SwingPropertyChangeSupport getSwingPropertyChangeSupport() {
+ return pcs;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param comparison DOCUMENT ME!
+ */
+ public void setComparison(String comparison) {
+ this.comparison = comparison;
+ pcs.firePropertyChange(COMPARISON_EVENT, null, comparison);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getComparison() {
+ return comparison;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param negation DOCUMENT ME!
+ */
+ public void setNegation(boolean negation) {
+ this.negation = negation;
+ pcs.firePropertyChange(NEGATION_EVENT, null, null);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean getNegation() {
+ return negation;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param filters DOCUMENT ME!
+ */
+ public void setFilters(int[] filters) {
+ this.filters = filters;
+ pcs.firePropertyChange(FILTER_BOX_EVENT, null, filters);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] getFilters() {
+ return filters;
+ }
+
+ //----------------------------------------//
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String output() {
+ StringBuffer buffer = new StringBuffer();
+
+ for (int i = 0; i < filters.length; ++i) {
+ buffer.append(filters[i]);
+
+ if (i != (filters.length - 1))
+ buffer.append(":");
+ }
+
+ buffer.append("," + getComparison());
+ buffer.append("," + negation + ",");
+ buffer.append(toString());
+
+ return buffer.toString();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param desc DOCUMENT ME!
+ */
+ public void input(String desc) {
+ String[] array = desc.split(",");
+ String[] filterStrings = array[0].split(":");
+ int[] selectedFilters = null;
+
+ if (filterStrings[0].equals("")) {
+ selectedFilters = new int[0];
+ } else {
+ selectedFilters = new int[filterStrings.length];
+ }
+
+ for (int idx = 0; idx < selectedFilters.length; idx++) {
+ selectedFilters[idx] = (new Integer(filterStrings[idx])).intValue();
+ } // end of for ()
+
+ setFilters(selectedFilters);
+
+ if (array[1].equals(AND)) {
+ setComparison(AND);
+ } else if (array[1].equals(OR)) {
+ setComparison(OR);
+ } else if (array[1].equals(XOR)) {
+ setComparison(XOR);
+ } else {
+ throw new IllegalArgumentException(array[1] + " is not a valid type of comparison");
+ }
+
+ setIdentifier(array[3]);
+ setNegation((new Boolean(array[2])).booleanValue());
+ }
+}
diff --git a/coreplugins/RFilters/src/main/java/filter/cytoscape/BooleanMetaFilterEditor.java b/coreplugins/RFilters/src/main/java/filter/cytoscape/BooleanMetaFilterEditor.java
new file mode 100644
index 0000000..32f4001
--- /dev/null
+++ b/coreplugins/RFilters/src/main/java/filter/cytoscape/BooleanMetaFilterEditor.java
@@ -0,0 +1,419 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package filter.cytoscape;
+
+import ViolinStrings.Strings;
+
+import cytoscape.*;
+import cytoscape.CyNetwork;
+
+import cytoscape.data.*;
+
+import filter.model.*;
+
+import filter.view.*;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import java.beans.*;
+
+import java.util.*;
+
+import javax.swing.*;
+import javax.swing.border.*;
+import javax.swing.event.*;
+import javax.swing.event.SwingPropertyChangeSupport;
+
+
+/**
+ * This is a Cytoscape specific filter that will pass nodes if
+ * a selected attribute matches a specific value.
+ */
+public class BooleanMetaFilterEditor extends FilterEditor implements ItemListener, FocusListener,
+ ActionListener,
+ ListSelectionListener {
+ /**
+ * This is the Name that will go in the Tab
+ * and is returned by the "toString" method
+ */
+ protected String identifier;
+ protected JTextField nameField;
+ protected JList filterList;
+ protected JComboBox comparisonBox;
+ protected JCheckBox negationBox;
+ protected Set filters;
+ protected Vector listModel;
+ protected BooleanMetaFilter filter;
+ protected String DEFAULT_FILTER_NAME = "BooleanMeta: ";
+ protected String DEFAULT_COMPARISON = BooleanMetaFilter.AND;
+ protected int[] DEFAULT_FILTERS = new int[0];
+ protected boolean DEFAULT_NEGATION = false;
+ protected Class filterClass;
+
+ /**
+ * Creates a new BooleanMetaFilterEditor object.
+ */
+ public BooleanMetaFilterEditor() {
+ super();
+
+ try {
+ filterClass = Class.forName("filter.cytoscape.BooleanMetaFilter");
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ this.filters = filters;
+ identifier = "Boolean Meta-Filter";
+ setBorder(new TitledBorder("Boolean Meta-Filter"));
+
+ setLayout(new java.awt.GridBagLayout());
+
+ JLabel lbFilterName = new JLabel("Filter Name");
+ nameField = new JTextField(15);
+ nameField.setMaximumSize(new Dimension(131, 19));
+ nameField.setText(identifier);
+ nameField.addActionListener(this);
+ nameField.addFocusListener(this);
+
+ JLabel lb_Select_objects_that_pass = new JLabel("Select objects that pass ");
+
+ comparisonBox = new JComboBox();
+ comparisonBox.setMinimumSize(new Dimension(105, 19));
+ comparisonBox.setPreferredSize(new Dimension(105, 19));
+
+ comparisonBox.addItem(BooleanMetaFilter.AND);
+ comparisonBox.addItem(BooleanMetaFilter.OR);
+ comparisonBox.addItem(BooleanMetaFilter.XOR);
+ comparisonBox.setSelectedIndex(0);
+ comparisonBox.setEditable(false);
+ comparisonBox.addItemListener(this);
+
+ JLabel lb_of_the_selected_filters = new JLabel(" of the selected filters");
+
+ filterList = new JList(FilterManager.defaultManager());
+ filterList.addListSelectionListener(this);
+
+ JScrollPane scrollPane = new JScrollPane(filterList);
+
+ negationBox = new JCheckBox("Negate?");
+
+ java.awt.GridBagConstraints gridBagConstraints;
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.EAST;
+ gridBagConstraints.insets = new java.awt.Insets(10, 5, 5, 5);
+ add(lbFilterName, gridBagConstraints);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridwidth = 2;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
+ gridBagConstraints.insets = new java.awt.Insets(10, 5, 5, 5);
+ gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.weightx = 1.0;
+ add(nameField, gridBagConstraints);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = 1;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.EAST;
+ gridBagConstraints.insets = new java.awt.Insets(0, 5, 5, 5);
+ add(lb_Select_objects_that_pass, gridBagConstraints);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = 1;
+ gridBagConstraints.insets = new java.awt.Insets(5, 5, 10, 5);
+ add(comparisonBox, gridBagConstraints);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = 1;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
+ add(lb_of_the_selected_filters, gridBagConstraints);
+
+ scrollPane.setViewportView(filterList);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = 2;
+ gridBagConstraints.gridwidth = 3;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.BOTH;
+ gridBagConstraints.weightx = 1.0;
+ gridBagConstraints.weighty = 1.0;
+ gridBagConstraints.insets = new java.awt.Insets(0, 5, 0, 5);
+ add(scrollPane, gridBagConstraints);
+
+ negationBox.setBorder(javax.swing.BorderFactory.createEmptyBorder(0, 0, 0, 0));
+ negationBox.setMargin(new java.awt.Insets(0, 0, 0, 0));
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = 3;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
+ gridBagConstraints.insets = new java.awt.Insets(10, 5, 10, 0);
+ add(negationBox, gridBagConstraints);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String toString() {
+ return identifier;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getDescription() {
+ return BooleanMetaFilter.FILTER_DESCRIPTION;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Class getFilterClass() {
+ return filterClass;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getFilterID() {
+ return BooleanMetaFilter.FILTER_ID;
+ }
+
+ /**
+ * Accepts a Filter for editing
+ * Note that this Filter must be a Filter that can be edited
+ * by this Filter editor.
+ */
+ public void editFilter(Filter filter) {
+ if (filter instanceof BooleanMetaFilter) {
+ // good, this Filter is of the right type
+ this.filter = (BooleanMetaFilter) filter;
+ setFilters(this.filter.getFilters());
+ setComparison(this.filter.getComparison());
+ setFilterName(this.filter.toString());
+ setNegation(this.filter.getNegation());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Filter createDefaultFilter() {
+ return new BooleanMetaFilter(DEFAULT_FILTERS, DEFAULT_COMPARISON, DEFAULT_FILTER_NAME,
+ DEFAULT_NEGATION);
+ }
+
+ //----------------------------------------//
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getFilterName() {
+ return filter.toString();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param name DOCUMENT ME!
+ */
+ public void setFilterName(String name) {
+ nameField.setText(name);
+ filter.setIdentifier(name);
+ }
+
+ // Search String /////////////////////////////////////
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] getFilters() {
+ return filter.getFilters();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param array DOCUMENT ME!
+ */
+ public void setFilters(int[] array) {
+ filterList.removeListSelectionListener(this);
+ filterList.clearSelection();
+
+ for (int idx = 0; idx < array.length; idx++) {
+ int index = FilterManager.defaultManager()
+ .indexOf(FilterManager.defaultManager().getFilter(array[idx]));
+
+ if (index > -1) {
+ filterList.addSelectionInterval(index, index);
+ }
+ }
+
+ filterList.addListSelectionListener(this);
+
+ Object[] selectedObjects = filterList.getSelectedValues();
+ int[] selectedFilters = new int[selectedObjects.length];
+
+ for (int idx = 0; idx < selectedFilters.length; idx++) {
+ selectedFilters[idx] = FilterManager.defaultManager()
+ .getFilterID((Filter) selectedObjects[idx]);
+ } // end of for ()
+
+ filter.setFilters(selectedFilters);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean getNegation() {
+ return negationBox.isSelected();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param negation DOCUMENT ME!
+ */
+ public void setNegation(boolean negation) {
+ filter.setNegation(negation);
+ negationBox.removeItemListener(this);
+ negationBox.setSelected(negation);
+ negationBox.addItemListener(this);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getComparison() {
+ return filter.getComparison();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param comparison DOCUMENT ME!
+ */
+ public void setComparison(String comparison) {
+ filter.setComparison(comparison);
+ comparisonBox.removeItemListener(this);
+ comparisonBox.setSelectedItem(comparison);
+ comparisonBox.addItemListener(this);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ handleEvent(e);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void focusGained(FocusEvent e) {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void focusLost(FocusEvent e) {
+ handleEvent(e);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void itemStateChanged(ItemEvent e) {
+ handleEvent(e);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void handleEvent(EventObject e) {
+ if (e.getSource() == nameField) {
+ setFilterName(nameField.getText());
+ } else if (e.getSource() == filterList) {
+ Object[] selectedObjects = filterList.getSelectedValues();
+ int[] selectedFilters = new int[selectedObjects.length];
+
+ for (int idx = 0; idx < selectedFilters.length; idx++) {
+ selectedFilters[idx] = FilterManager.defaultManager()
+ .getFilterID((Filter) selectedObjects[idx]);
+ } // end of for ()
+
+ setFilters(selectedFilters);
+ } else if (e.getSource() == comparisonBox) {
+ setComparison((String) comparisonBox.getSelectedItem());
+ } else if (e.getSource() == negationBox) {
+ setNegation(negationBox.isSelected());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void valueChanged(ListSelectionEvent e) {
+ handleEvent(e);
+ }
+}
diff --git a/coreplugins/RFilters/src/main/java/filter/cytoscape/CsFilter.java b/coreplugins/RFilters/src/main/java/filter/cytoscape/CsFilter.java
new file mode 100644
index 0000000..cc63a63
--- /dev/null
+++ b/coreplugins/RFilters/src/main/java/filter/cytoscape/CsFilter.java
@@ -0,0 +1,201 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package filter.cytoscape;
+
+import cytoscape.*;
+import cytoscape.data.*;
+import cytoscape.plugin.*;
+import cytoscape.util.*;
+import cytoscape.view.*;
+import filter.model.*;
+import filter.view.*;
+import java.awt.event.*;
+import java.beans.*;
+import java.io.*;
+import java.util.*;
+import javax.swing.*;
+
+
+/**
+ *
+ */
+public class CsFilter extends CytoscapePlugin { //implements PropertyChangeListener {
+ protected JFrame frame;
+ protected FilterUsePanel filterUsePanel;
+
+ /**
+ * Creates a new CsFilter object.
+ */
+ public CsFilter() {
+ initialize();
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void initialize() {
+
+ // create icons
+ ImageIcon icon = new ImageIcon(getClass().getResource("/stock_filter-data-by-criteria.png"));
+ ImageIcon icon2 = new ImageIcon(getClass()
+ .getResource("/stock_filter-data-by-criteria-16.png"));
+
+ //FilterPlugin action = new FilterPlugin(icon, this);
+ FilterMenuItem menu_action = new FilterMenuItem(icon2, this);
+ //Cytoscape.getDesktop().getCyMenus().addCytoscapeAction( ( CytoscapeAction )action );
+ Cytoscape.getDesktop().getCyMenus().addCytoscapeAction((CytoscapeAction) menu_action);
+
+ FilterEditorManager.defaultManager().addEditor(new NumericAttributeFilterEditor());
+ FilterEditorManager.defaultManager().addEditor(new StringPatternFilterEditor());
+ FilterEditorManager.defaultManager().addEditor(new NodeTopologyFilterEditor());
+ FilterEditorManager.defaultManager().addEditor(new BooleanMetaFilterEditor());
+ FilterEditorManager.defaultManager().addEditor(new NodeInteractionFilterEditor());
+ FilterEditorManager.defaultManager().addEditor(new EdgeInteractionFilterEditor());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public FilterUsePanel getFilterUsePanel() {
+ if (filterUsePanel == null) {
+ filterUsePanel = new FilterUsePanel(frame);
+ }
+
+ return filterUsePanel;
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void show() {
+ if (frame == null) {
+ frame = new JFrame("Use Filters");
+ frame.getContentPane().add(getFilterUsePanel());
+ frame.pack();
+ }
+
+ frame.setVisible(true);
+ }
+
+ // override the following two methods to save state.
+ /**
+ * DOCUMENT ME!
+ *
+ * @param pStateFileList
+ * DOCUMENT ME!
+ */
+ public void restoreSessionState(List<File> pStateFileList) {
+
+ if ((pStateFileList == null) || (pStateFileList.size() == 0)) {
+ cytoscape.logger.CyLogger.getLogger(CsFilter.class).warn("\tNo previous old filter state to restore.");
+ return;
+ }
+
+ try {
+ File filter_file = pStateFileList.get(0);
+ BufferedReader in = new BufferedReader(new FileReader(filter_file));
+ String oneLine = in.readLine();
+
+ while (oneLine != null) {
+ if (oneLine.startsWith("#")) {
+ // comment
+ } else {
+ FilterManager.defaultManager().createFilterFromString(oneLine);
+ }
+
+ oneLine = in.readLine();
+ }
+ in.close();
+ } catch (Exception ex) {
+ cytoscape.logger.CyLogger.getLogger(CsFilter.class).error("Filter Read error",ex);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param pFileList
+ * DOCUMENT ME!
+ */
+ public void saveSessionStateFiles(List<File> pFileList) {
+
+ Iterator i = FilterManager.defaultManager().getFilters();
+
+ // If not filter defined, do nothing
+ if (!i.hasNext()){
+ return;
+ }
+
+ // There are filters, save them now
+
+ // Create an empty file on system temp directory
+ String tmpDir = System.getProperty("java.io.tmpdir");
+ File session_filter_file = new File(tmpDir, "old_filters.props");
+
+ BufferedWriter writer = null;
+ try {
+ writer = new BufferedWriter(new FileWriter(session_filter_file));
+ while (i.hasNext()) {
+ Filter f = (Filter) i.next();
+ writer.write(FilterManager.defaultManager().getFilterID(f) + "\t"
+ + f.getClass() + "\t" + f.output());
+ writer.newLine();
+ }
+ }
+
+ catch (Exception ex) {
+ cytoscape.logger.CyLogger.getLogger(CsFilter.class).error("Session old filter Write error",ex);
+ }
+
+ finally {
+ if ( writer != null) {
+ try {
+ writer.close();
+ }
+ catch (Exception ex){
+ cytoscape.logger.CyLogger.getLogger(CsFilter.class).error("Session old filter Write error",ex);
+ }
+ }
+ }
+
+ if ((session_filter_file != null) && (session_filter_file.exists())) {
+ pFileList.add(session_filter_file);
+ }
+ }
+}
diff --git a/coreplugins/RFilters/src/main/java/filter/cytoscape/EdgeInteractionFilter.java b/coreplugins/RFilters/src/main/java/filter/cytoscape/EdgeInteractionFilter.java
new file mode 100644
index 0000000..207198d
--- /dev/null
+++ b/coreplugins/RFilters/src/main/java/filter/cytoscape/EdgeInteractionFilter.java
@@ -0,0 +1,324 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package filter.cytoscape;
+
+import cytoscape.*;
+import cytoscape.CyNetwork;
+
+import cytoscape.data.*;
+
+import filter.model.*;
+
+import giny.model.*;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import java.beans.*;
+
+import java.util.*;
+import java.util.List;
+
+import javax.swing.*;
+import javax.swing.border.*;
+import javax.swing.event.*;
+import javax.swing.event.SwingPropertyChangeSupport;
+
+
+/**
+ * This filter will pass nodes based on the edges that
+ * they have.
+ */
+public class EdgeInteractionFilter implements Filter {
+ //----------------------------------------//
+ // Filter specific properties
+ //----------------------------------------//
+ protected int filter;
+ protected String target;
+
+ /**
+ *
+ */
+ public static String FILTER_NAME_EVENT = "FILTER_NAME_EVENT";
+
+ /**
+ *
+ */
+ public static String FILTER_BOX_EVENT = "FILTER_BOX_EVENT";
+
+ /**
+ *
+ */
+ public static String TARGET_BOX_EVENT = "TARGET_BOX_EVENT";
+
+ /**
+ *
+ */
+ public static String FILTER_ID = "EdgeInteractionFilter";
+
+ /**
+ *
+ */
+ public static String FILTER_DESCRIPTION = "Select edges based on adjacent nodes";
+
+ /**
+ *
+ */
+ public static String SOURCE = "source";
+
+ /**
+ *
+ */
+ public static String TARGET = "target";
+
+ /**
+ *
+ */
+ public static String EITHER = "source or target";
+
+ //----------------------------------------//
+ // Cytoscape specific Variables
+ //----------------------------------------//
+
+ //----------------------------------------//
+ // Needed Variables
+ //----------------------------------------//
+ protected String identifier = "EdgeInteractionFilter";
+ protected SwingPropertyChangeSupport pcs = new SwingPropertyChangeSupport(this);
+
+ //---------------------------------------//
+ // Constructor
+ //----------------------------------------//
+
+ /**
+ * Creates a new InteractionFilter
+ */
+ public EdgeInteractionFilter(int filter, String target, String identifier) {
+ this.filter = filter;
+ this.target = target;
+ this.identifier = identifier;
+ }
+
+ /**
+ * Creates a new EdgeInteractionFilter object.
+ *
+ * @param desc DOCUMENT ME!
+ */
+ public EdgeInteractionFilter(String desc) {
+ input(desc);
+ }
+
+ //----------------------------------------//
+ // Implements Filter
+ //----------------------------------------//
+
+ /**
+ * Returns the name for this Filter
+ */
+ public String toString() {
+ return identifier;
+ }
+
+ /**
+ * sets a new name for this filter
+ */
+ public void setIdentifier(String new_id) {
+ this.identifier = new_id;
+ pcs.firePropertyChange(FILTER_NAME_EVENT, null, new_id);
+ }
+
+ /**
+ * This is usually the same as the class name
+ */
+ public String getFilterID() {
+ return FILTER_ID;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getDescription() {
+ return FILTER_DESCRIPTION;
+ }
+
+ /**
+ * An object passes this Filter if it is the source/target
+ * node for an edge that has a matching property for
+ * the given Edge atttribute.
+ */
+ public boolean passesFilter(Object object) {
+ Filter filter = FilterManager.defaultManager().getFilter(this.filter);
+
+ if (filter == null) {
+ return false;
+ }
+
+ if (!(object instanceof Edge)) {
+ return false;
+ }
+
+ Edge edge = (Edge) object;
+
+ //get the list of all relevant edges
+ Node adjacentNode;
+
+ if (target == SOURCE) {
+ return filter.passesFilter(edge.getSource());
+ } else if (target == TARGET) {
+ return filter.passesFilter(edge.getTarget());
+ } else {
+ return filter.passesFilter(edge.getSource()) || filter.passesFilter(edge.getTarget());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Class[] getPassingTypes() {
+ return new Class[] { Edge.class };
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param other_object DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean equals(Object other_object) {
+ return super.equals(other_object);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object clone() {
+ return new EdgeInteractionFilter(filter, target, identifier + "_new");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public SwingPropertyChangeSupport getSwingPropertyChangeSupport() {
+ return pcs;
+ }
+
+ //----------------------------------------//
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getTarget() {
+ return target;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param target DOCUMENT ME!
+ */
+ public void setTarget(String target) {
+ this.target = target;
+ pcs.firePropertyChange(TARGET_BOX_EVENT, null, target);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param filter DOCUMENT ME!
+ */
+ public void setFilter(int filter) {
+ int oldvalue = this.filter;
+ this.filter = filter;
+ pcs.firePropertyChange(FILTER_BOX_EVENT, oldvalue, filter);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getFilter() {
+ return filter;
+ }
+
+ //----------------------------------------//
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String output() {
+ StringBuffer buffer = new StringBuffer();
+ buffer.append(getFilter() + ",");
+ buffer.append(getTarget() + ",");
+ buffer.append(toString());
+
+ return buffer.toString();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param desc DOCUMENT ME!
+ */
+ public void input(String desc) {
+ String[] array = desc.split(",");
+ setFilter((new Integer(array[0])).intValue());
+
+ if (array[1].equals(TARGET)) {
+ setTarget(TARGET);
+ } else if (array[1].equals(SOURCE)) {
+ setTarget(SOURCE);
+ } else if (array[1].equals(EITHER)) {
+ setTarget(EITHER);
+ } else {
+ throw new IllegalArgumentException(array[1] + " is not a valid interaction type");
+ }
+
+ setIdentifier(array[2]);
+ }
+}
diff --git a/coreplugins/RFilters/src/main/java/filter/cytoscape/EdgeInteractionFilterEditor.java b/coreplugins/RFilters/src/main/java/filter/cytoscape/EdgeInteractionFilterEditor.java
new file mode 100644
index 0000000..8dbc728
--- /dev/null
+++ b/coreplugins/RFilters/src/main/java/filter/cytoscape/EdgeInteractionFilterEditor.java
@@ -0,0 +1,348 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package filter.cytoscape;
+
+import ViolinStrings.Strings;
+
+import cytoscape.*;
+import cytoscape.CyNetwork;
+
+import cytoscape.data.*;
+
+import filter.model.*;
+
+import filter.view.*;
+
+import giny.model.GraphPerspective;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import java.beans.*;
+
+import java.util.*;
+
+import javax.swing.*;
+import javax.swing.border.*;
+import javax.swing.event.*;
+import javax.swing.event.SwingPropertyChangeSupport;
+
+
+/**
+ * This filter will pass nodes based on the edges that
+ * they have.
+ */
+public class EdgeInteractionFilterEditor extends FilterEditor implements ActionListener,
+ FocusListener,
+ ItemListener {
+ /**
+ * This is the Name that will go in the Tab
+ * and is returned by the "toString" method
+ */
+ protected String identifier;
+ protected Class filterClass;
+ protected JTextField nameField;
+ protected JComboBox filterBox;
+ protected JComboBox targetBox;
+ protected EdgeInteractionFilter filter;
+ protected String DEFAULT_FILTER_NAME = "Edge Interaction: ";
+ protected int DEFAULT_FILTER = -1;
+ protected String DEFAULT_TARGET = EdgeInteractionFilter.SOURCE;
+
+ /**
+ * Creates a new EdgeInteractionFilterEditor object.
+ */
+ public EdgeInteractionFilterEditor() {
+ super();
+
+ try {
+ filterClass = Class.forName("filter.cytoscape.EdgeInteractionFilter");
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ identifier = "Edge Interactions";
+ setBorder(new TitledBorder("Edge Interaction Filter"));
+ setLayout(new GridBagLayout());
+ setPreferredSize(new Dimension(450, 125));
+
+ GridBagConstraints gridBagConstraints;
+
+ JLabel lbFilterName = new JLabel("Filter Name");
+ lbFilterName.setFocusable(false);
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 0;
+ gridBagConstraints.gridy = 0;
+ gridBagConstraints.anchor = GridBagConstraints.WEST;
+ gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
+ add(lbFilterName, gridBagConstraints);
+
+ nameField = new JTextField(15);
+ gridBagConstraints = new GridBagConstraints();
+ gridBagConstraints.gridx = 1;
+ gridBagConstraints.gridy = 0;
+ gridBagConstraints.fill = GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.weightx = 1.0;
+ gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
+ add(nameField, gridBagConstraints);
+
+ nameField.addActionListener(this);
+ nameField.addFocusListener(this);
+
+ JLabel SelectEdge = new JLabel("Select edges with a node ");
+ SelectEdge.setFocusable(false);
+ gridBagConstraints = new GridBagConstraints();
+ gridBagConstraints.gridx = 0;
+ gridBagConstraints.gridy = 1;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
+ gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
+ add(SelectEdge, gridBagConstraints);
+
+ targetBox = new JComboBox();
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 1;
+ gridBagConstraints.gridy = 1;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
+ add(targetBox, gridBagConstraints);
+
+ targetBox.addItem(EdgeInteractionFilter.SOURCE);
+ targetBox.addItem(EdgeInteractionFilter.TARGET);
+ targetBox.addItem(EdgeInteractionFilter.EITHER);
+ targetBox.addItemListener(this);
+
+ JLabel lbPassesFilter = new JLabel("which passes the filter ");
+ lbPassesFilter.setFocusable(false);
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 0;
+ gridBagConstraints.gridy = 2;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
+ gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
+ add(lbPassesFilter, gridBagConstraints);
+
+ filterBox = new JComboBox(FilterManager.defaultManager().getComboBoxModel());
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 1;
+ gridBagConstraints.gridy = 2;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
+ add(filterBox, gridBagConstraints);
+
+ filterBox.addItemListener(this);
+ }
+
+ //----------------------------------------//
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String toString() {
+ return identifier;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getFilterID() {
+ return EdgeInteractionFilter.FILTER_ID;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getDescription() {
+ return EdgeInteractionFilter.FILTER_DESCRIPTION;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Class getFilterClass() {
+ return filterClass;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Filter createDefaultFilter() {
+ return new EdgeInteractionFilter(DEFAULT_FILTER, DEFAULT_TARGET, DEFAULT_FILTER_NAME);
+ }
+
+ /**
+ * Accepts a Filter for editing
+ * Note that this Filter must be a Filter that can be edited
+ * by this Filter editor.
+ */
+ public void editFilter(Filter filter) {
+ if (this.filter == null) {
+ } // end of if ()
+
+ if (filter instanceof EdgeInteractionFilter) {
+ // good, this Filter is of the right type
+ this.filter = (EdgeInteractionFilter) filter;
+ setFilterName(this.filter.toString());
+ setSelectedFilter(this.filter.getFilter());
+ setTarget(this.filter.getTarget());
+ }
+ }
+
+ //----------------------------------------//
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getFilterName() {
+ return filter.toString();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param name DOCUMENT ME!
+ */
+ public void setFilterName(String name) {
+ nameField.setText(name);
+ filter.setIdentifier(name);
+ }
+
+ // Search String /////////////////////////////////////
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getTarget() {
+ return filter.getTarget();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param target DOCUMENT ME!
+ */
+ public void setTarget(String target) {
+ filter.setTarget(target);
+ targetBox.removeItemListener(this);
+ targetBox.setSelectedItem(target);
+ targetBox.addItemListener(this);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getSelectedFilter() {
+ return filter.getFilter();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param newFilter DOCUMENT ME!
+ */
+ public void setSelectedFilter(int newFilter) {
+ if (filter != null) {
+ filterBox.removeItemListener(this);
+ filterBox.setSelectedItem(FilterManager.defaultManager().getFilter(newFilter));
+ filterBox.addItemListener(this);
+ filter.setFilter(FilterManager.defaultManager()
+ .getFilterID((Filter) filterBox.getSelectedItem()));
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ handleEvent(e);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void itemStateChanged(ItemEvent e) {
+ handleEvent(e);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void focusGained(FocusEvent e) {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void focusLost(FocusEvent e) {
+ handleEvent(e);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void handleEvent(EventObject e) {
+ if (e.getSource() == nameField) {
+ setFilterName(nameField.getText());
+ } else if (e.getSource() == filterBox) {
+ setSelectedFilter(FilterManager.defaultManager()
+ .getFilterID((Filter) filterBox.getSelectedItem()));
+ } else if (e.getSource() == targetBox) {
+ setTarget((String) targetBox.getSelectedItem());
+ }
+ }
+}
diff --git a/coreplugins/RFilters/src/main/java/filter/cytoscape/EditorAction.java b/coreplugins/RFilters/src/main/java/filter/cytoscape/EditorAction.java
new file mode 100644
index 0000000..a5a9b5d
--- /dev/null
+++ b/coreplugins/RFilters/src/main/java/filter/cytoscape/EditorAction.java
@@ -0,0 +1,90 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package filter.cytoscape;
+
+import cytoscape.*;
+import cytoscape.CyNetwork;
+
+import cytoscape.data.*;
+
+import cytoscape.util.*;
+
+import cytoscape.view.*;
+
+import filter.view.FilterView;
+
+import java.awt.event.*;
+
+import javax.swing.*;
+
+
+/**
+ *
+ */
+public class EditorAction extends CytoscapeAction {
+ protected FilterView filterView;
+ protected JFrame frame;
+
+ /**
+ * Creates a new EditorAction object.
+ */
+ public EditorAction() {
+ super("Edit Filters");
+ setPreferredMenu("Select");
+ setAcceleratorCombo(java.awt.event.KeyEvent.VK_E,
+ ActionEvent.CTRL_MASK | ActionEvent.SHIFT_MASK);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ if (filterView == null) {
+ filterView = new FilterView();
+ }
+
+ if (frame == null) {
+ frame = new JFrame("Edit Filters");
+ frame.getContentPane().add(filterView);
+ frame.pack();
+ }
+
+ frame.setVisible(true);
+ }
+}
diff --git a/coreplugins/RFilters/src/main/java/filter/cytoscape/FilterManagerAction.java b/coreplugins/RFilters/src/main/java/filter/cytoscape/FilterManagerAction.java
new file mode 100644
index 0000000..f0284a8
--- /dev/null
+++ b/coreplugins/RFilters/src/main/java/filter/cytoscape/FilterManagerAction.java
@@ -0,0 +1,92 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package filter.cytoscape;
+
+import cytoscape.*;
+import cytoscape.CyNetwork;
+
+import cytoscape.data.*;
+
+import cytoscape.util.*;
+
+import cytoscape.view.*;
+
+import filter.model.*;
+
+import filter.view.*;
+
+import java.awt.event.*;
+
+import javax.swing.*;
+
+
+/**
+ *
+ */
+public class FilterManagerAction extends CytoscapeAction {
+ protected FilterView filterView;
+ protected JFrame frame;
+
+ /**
+ * Creates a new FilterManagerAction object.
+ */
+ public FilterManagerAction() {
+ super("Edit Filters");
+ setPreferredMenu("Select");
+ setAcceleratorCombo(java.awt.event.KeyEvent.VK_E,
+ ActionEvent.CTRL_MASK | ActionEvent.SHIFT_MASK);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ if (filterView == null) {
+ filterView = new FilterView();
+ }
+
+ if (frame == null) {
+ frame = new JFrame("Edit Filters");
+ frame.getContentPane().add(filterView);
+ frame.pack();
+ }
+
+ frame.setVisible(true);
+ }
+}
diff --git a/coreplugins/RFilters/src/main/java/filter/cytoscape/FilterMenuItem.java b/coreplugins/RFilters/src/main/java/filter/cytoscape/FilterMenuItem.java
new file mode 100644
index 0000000..692fbb1
--- /dev/null
+++ b/coreplugins/RFilters/src/main/java/filter/cytoscape/FilterMenuItem.java
@@ -0,0 +1,107 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package filter.cytoscape;
+
+import cytoscape.*;
+
+import cytoscape.data.*;
+
+import cytoscape.util.*;
+
+import cytoscape.view.*;
+
+import java.awt.event.*;
+
+import javax.swing.*;
+
+
+/**
+ *
+ */
+public class FilterMenuItem extends CytoscapeAction {
+ protected JFrame frame;
+ protected CsFilter csfilter;
+
+ /**
+ * Creates a new FilterMenuItem object.
+ *
+ * @param icon DOCUMENT ME!
+ * @param csfilter DOCUMENT ME!
+ */
+ public FilterMenuItem(ImageIcon icon, CsFilter csfilter) {
+ super("Use Old Filters", icon);
+ this.csfilter = csfilter;
+ setPreferredMenu("Select");
+ //setAcceleratorCombo(java.awt.event.KeyEvent.VK_F7, 0);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public FilterUsePanel getFilterUsePanel() {
+ return csfilter.getFilterUsePanel();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ csfilter.show();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isInToolBar() {
+ return false;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isInMenuBar() {
+ return true;
+ }
+}
diff --git a/coreplugins/RFilters/src/main/java/filter/cytoscape/FilterPlugin.java b/coreplugins/RFilters/src/main/java/filter/cytoscape/FilterPlugin.java
new file mode 100644
index 0000000..b06d5b9
--- /dev/null
+++ b/coreplugins/RFilters/src/main/java/filter/cytoscape/FilterPlugin.java
@@ -0,0 +1,110 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package filter.cytoscape;
+
+import cytoscape.*;
+
+import cytoscape.data.*;
+
+import cytoscape.util.*;
+
+import cytoscape.view.*;
+
+import java.awt.event.*;
+
+import javax.swing.*;
+
+
+/**
+ *
+ */
+public class FilterPlugin extends CytoscapeAction {
+ protected JFrame frame;
+ protected CsFilter csfilter;
+
+ /**
+ * Creates a new FilterPlugin object.
+ *
+ * @param icon DOCUMENT ME!
+ * @param csfilter DOCUMENT ME!
+ */
+ public FilterPlugin(ImageIcon icon, CsFilter csfilter) {
+ super("", icon);
+ // Set SHORT_DESCRIPTION; used to create tool-tip
+ this.putValue(Action.SHORT_DESCRIPTION, "Use Filters");
+ this.csfilter = csfilter;
+ setPreferredMenu("Select");
+ //setAcceleratorCombo(java.awt.event.KeyEvent.VK_A,
+ // ActionEvent.CTRL_MASK | ActionEvent.SHIFT_MASK);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public FilterUsePanel getFilterUsePanel() {
+ return csfilter.getFilterUsePanel();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ csfilter.show();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isInToolBar() {
+ return true;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isInMenuBar() {
+ return false;
+ }
+}
diff --git a/coreplugins/RFilters/src/main/java/filter/cytoscape/FilterUsePanel.java b/coreplugins/RFilters/src/main/java/filter/cytoscape/FilterUsePanel.java
new file mode 100644
index 0000000..4f7b9ec
--- /dev/null
+++ b/coreplugins/RFilters/src/main/java/filter/cytoscape/FilterUsePanel.java
@@ -0,0 +1,449 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package filter.cytoscape;
+
+import cytoscape.*;
+
+import cytoscape.data.*;
+
+import cytoscape.view.*;
+
+import filter.model.*;
+
+import filter.view.*;
+
+import giny.model.*;
+
+import giny.view.*;
+
+import phoebe.*;
+
+import java.awt.*;
+import java.awt.event.*;
+import java.awt.geom.*;
+
+import java.beans.*;
+
+import java.util.*;
+import java.util.List;
+
+import javax.swing.*;
+import javax.swing.border.*;
+
+
+/**
+ *
+ */
+public class FilterUsePanel extends JPanel implements PropertyChangeListener, ActionListener {
+ private FilterEditorPanel filterEditorPanel;
+ private FilterListPanel filterListPanel;
+ private JRadioButton hideFailed;
+ private JRadioButton grayFailed;
+ private JRadioButton selectPassed;
+ private JButton apply;
+ private JButton addFilters;
+ private JButton removeFilters;
+ private JList selectedFilters;
+ private JDialog createFilterDialog;
+ private JButton addButton;
+ private JButton removeButton;
+ private JCheckBox select;
+ private JCheckBox gray;
+ private JCheckBox hide;
+ private JCheckBox overwrite;
+ private JRadioButton pulsate;
+ private JRadioButton spiral;
+ private JFrame frame;
+ private Runnable updateProgMon;
+ private Runnable closeProgMon;
+ private Runnable setMinAndMax;
+ private int progressCount = 0;
+ private int minCount = 0;
+ private int maxCount = 100;
+ private String progressNote = "";
+ private String progressTitle = "Applying filter";
+ private boolean applyFilterCanceled = false;
+ private static final int TYPE_NODE = 1;
+ private static final int TYPE_EDGE = 2;
+
+ /**
+ *
+ */
+ public static final String NEW_FILTER_ADDED = "NEW_FILTER_ADDED";
+
+ /**
+ * Creates a new FilterUsePanel object.
+ *
+ * @param frame DOCUMENT ME!
+ */
+ public FilterUsePanel(JFrame frame) {
+ super();
+ this.frame = frame;
+ frame.setPreferredSize(new Dimension(700, 300));
+
+ setLayout(new BorderLayout());
+ // --------------------//
+ // FilterEditorPanel
+ filterEditorPanel = new FilterEditorPanel();
+ filterEditorPanel.getPropertyChangeSupport().addPropertyChangeListener(this);
+
+ // --------------------//
+ // Selected Filter Panel
+ JPanel selected_filter_panel = new JPanel();
+ selected_filter_panel.setLayout(new BorderLayout());
+ filterListPanel = new FilterListPanel();
+ selected_filter_panel.add(filterListPanel, BorderLayout.CENTER);
+ selected_filter_panel.add(createManagePanel(), BorderLayout.NORTH);
+ selected_filter_panel.add(createActionPanel(), BorderLayout.SOUTH);
+
+ JSplitPane pane0 = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT, selected_filter_panel,
+ filterEditorPanel);
+ add(pane0);
+ filterListPanel.getSwingPropertyChangeSupport().addPropertyChangeListener(filterEditorPanel);
+ filterListPanel.getSwingPropertyChangeSupport().addPropertyChangeListener(this);
+ initProgressMonitor();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public FilterListPanel getFilterListPanel() {
+ return filterListPanel;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void propertyChange(PropertyChangeEvent e) {
+ if (e.getPropertyName() == FilterListPanel.FILTER_SELECTED) {
+ removeButton.setEnabled(true);
+ apply.setEnabled(true);
+
+ // do something on a Filter Selected
+ } else if (e.getPropertyName() == FilterListPanel.NO_SELECTION) {
+ removeButton.setEnabled(false);
+ apply.setEnabled(false);
+ } // end of if ()
+ else if (e.getPropertyName() == FilterEditorPanel.ACTIVE_PANEL_CHANGED) {
+ frame.setPreferredSize(new Dimension(700, 300));
+ frame.pack();
+ } else if (e.getPropertyName() == NEW_FILTER_ADDED) {
+ // Select the new filter just created
+ // New filter created is always added at the end of a vector
+ int lastIndex = filterListPanel.getFilterList().getModel().getSize() - 1;
+ filterListPanel.getFilterList().setSelectedIndex(lastIndex);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public JPanel createManagePanel() {
+ JPanel result = new JPanel();
+ result.setBorder(new TitledBorder("Manage Filters"));
+ addButton = new JButton("Create new filter");
+ addButton.addActionListener(this);
+ removeButton = new JButton("Remove selected filter");
+ removeButton.addActionListener(this);
+ removeButton.setEnabled(false);
+ result.add(addButton);
+ result.add(removeButton);
+
+ return result;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ if (e.getSource() == addButton) {
+ if (createFilterDialog == null) {
+ createFilterDialog = new CreateFilterDialog(FilterEditorManager.defaultManager());
+ }
+
+ int pre_filterCount = filterListPanel.getFilterList().getModel().getSize();
+ createFilterDialog.setVisible(true);
+
+ int post_filterCount = filterListPanel.getFilterList().getModel().getSize();
+
+ /*
+ * Fire an event to notify the JList to select it, if new filter is
+ * added
+ */
+ if ((post_filterCount - pre_filterCount) > 0) {
+ java.beans.PropertyChangeEvent evt = new java.beans.PropertyChangeEvent(this,
+ NEW_FILTER_ADDED,
+ null, null);
+ filterListPanel.getSwingPropertyChangeSupport().firePropertyChange(evt);
+ }
+ }
+
+ if (e.getSource() == removeButton) {
+ Filter filter = filterListPanel.getSelectedFilter();
+
+ if (filter != null) {
+ FilterManager.defaultManager().removeFilter(filter);
+ }
+ }
+ }
+
+ private void initProgressMonitor() {
+ progressTitle = "Applying filter";
+ progressNote = "";
+
+ final ProgressMonitor pm = new ProgressMonitor(frame, progressTitle, progressNote, 0, 100);
+ pm.setMillisToDecideToPopup(500);
+ pm.setMillisToPopup(2000);
+
+ // Create these as inner classes to minimize the amount of thread
+ // creation (expensive!)...
+ updateProgMon = new Runnable() {
+ double dCount = 0;
+
+ public void run() {
+ if (pm.isCanceled()) {
+ applyFilterCanceled = true;
+ pm.close();
+ } else {
+ dCount = ((double) progressCount / (double) pm.getMaximum());
+ progressNote = ((int) (dCount * 100.0) + "% complete");
+ pm.setProgress(progressCount);
+ pm.setNote(progressNote);
+ }
+ }
+ };
+
+ closeProgMon = new Runnable() {
+ public void run() {
+ pm.close();
+ }
+ };
+
+ setMinAndMax = new Runnable() {
+ public void run() {
+ pm.setMinimum(minCount);
+ pm.setMaximum(maxCount);
+ }
+ };
+ }
+
+ /**
+ * This method will take an object and do whatever it is supposed to
+ * according to what the available actions are.
+ */
+ protected void passObject(Object object, boolean passes) {
+ // Should not use this... Event should fire only once in the filtering
+ // process!
+ if (passes) {
+ if (object instanceof Node) {
+ Cytoscape.getCurrentNetwork().setSelectedNodeState((Node) object, true);
+ } else if (object instanceof Edge) {
+ Cytoscape.getCurrentNetwork().setSelectedEdgeState((Edge) object, true);
+ }
+ }
+ }
+
+ private void fireEvent(final List selectedObjList, final int type) {
+ if (type == TYPE_NODE) {
+ Cytoscape.getCurrentNetwork().setSelectedNodeState(selectedObjList, true);
+ } else if (type == TYPE_EDGE) {
+ Cytoscape.getCurrentNetwork().setSelectedEdgeState(selectedObjList, true);
+ }
+ }
+
+ protected void testObjects() {
+ final Filter filter = filterListPanel.getSelectedFilter();
+ final CyNetwork network = Cytoscape.getCurrentNetwork();
+
+ final List<Node> nodes_list = network.nodesList();
+ final List<Edge> edges_list = network.edgesList();
+
+ if (filter != null) {
+ final Class[] passingTypes = filter.getPassingTypes();
+
+ minCount = 0;
+ maxCount = getTaskEstimation(passingTypes, nodes_list, edges_list);
+ progressCount = 0;
+ applyFilterCanceled = false;
+
+ try {
+ SwingUtilities.invokeAndWait(setMinAndMax);
+ } catch (Exception _e) {
+ _e.printStackTrace();
+ }
+
+ for (int idx = 0; idx < passingTypes.length; idx++) {
+ if (passingTypes[idx].equals(Node.class)) {
+ final List<Node> passedNodes = new ArrayList<Node>();
+
+ for (Node node : nodes_list) {
+ try {
+ if (filter.passesFilter(node)) {
+ passedNodes.add(node);
+ }
+
+ // passObject(node, filter.passesFilter(node));
+ } catch (StackOverflowError soe) {
+ soe.printStackTrace();
+
+ return;
+ }
+
+ progressCount++;
+
+ try {
+ SwingUtilities.invokeAndWait(updateProgMon);
+ } catch (Exception _e) {
+ _e.printStackTrace();
+ }
+
+ if (applyFilterCanceled) {
+ progressNote = "Please wait...";
+
+ try {
+ SwingUtilities.invokeAndWait(updateProgMon);
+ } catch (Exception _e) {
+ }
+
+ break;
+ }
+ }
+
+ fireEvent(passedNodes, TYPE_NODE);
+ } else if (passingTypes[idx].equals(Edge.class)) {
+ final List<Edge> passedEdges = new ArrayList<Edge>();
+
+ for (Edge edge : edges_list) {
+ try {
+ if (filter.passesFilter(edge)) {
+ passedEdges.add(edge);
+ }
+
+ // passObject(edge, filter.passesFilter(edge));
+ } catch (StackOverflowError soe) {
+ soe.printStackTrace();
+
+ return;
+ }
+
+ progressCount++;
+
+ try {
+ SwingUtilities.invokeAndWait(updateProgMon);
+ } catch (Exception _e) {
+ }
+
+ if (applyFilterCanceled) {
+ progressNote = "Please wait...";
+
+ try {
+ SwingUtilities.invokeAndWait(updateProgMon);
+ } catch (Exception _e) {
+ }
+
+ break;
+ }
+ }
+
+ fireEvent(passedEdges, TYPE_EDGE);
+ }
+ } // for loop
+
+ try {
+ SwingUtilities.invokeAndWait(closeProgMon);
+ } catch (Exception _e) {
+ _e.printStackTrace();
+ }
+ }
+ }
+
+ // Calculate the total tasks for the progress monitor
+ private int getTaskEstimation(Class[] pClassTypes, List pNodeList, List pEdgeList) {
+ int taskCount = 0;
+
+ for (int idx = 0; idx < pClassTypes.length; idx++) {
+ if (pClassTypes[idx].equals(Node.class)) {
+ taskCount += pNodeList.size();
+ } else if (pClassTypes[idx].equals(Edge.class)) {
+ taskCount += pEdgeList.size();
+ }
+ }
+
+ return taskCount;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public JPanel createActionPanel() {
+ final JPanel actionPanel = new JPanel();
+
+ apply = new JButton(new AbstractAction("Apply selected filter") {
+ public void actionPerformed(ActionEvent e) {
+ /*
+ * We have to run "Apply filter" in a seperate thread, becasue
+ * we want to monitor the progress
+ */
+ ApplyFilterThread applyFilterThread = new ApplyFilterThread();
+ applyFilterThread.start();
+ }
+ });
+
+ apply.setEnabled(false);
+
+ actionPanel.add(apply);
+
+ return actionPanel;
+ }
+
+ private class ApplyFilterThread extends Thread {
+ public void run() {
+ testObjects();
+ Cytoscape.getCurrentNetworkView().updateView();
+ }
+ }
+}
diff --git a/coreplugins/RFilters/src/main/java/filter/cytoscape/NodeInteractionFilter.java b/coreplugins/RFilters/src/main/java/filter/cytoscape/NodeInteractionFilter.java
new file mode 100644
index 0000000..82bfd70
--- /dev/null
+++ b/coreplugins/RFilters/src/main/java/filter/cytoscape/NodeInteractionFilter.java
@@ -0,0 +1,336 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package filter.cytoscape;
+
+import cytoscape.*;
+import cytoscape.CyNetwork;
+
+import cytoscape.data.*;
+
+import filter.model.*;
+
+import giny.model.*;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import java.beans.*;
+
+import java.util.*;
+import java.util.List;
+
+import javax.swing.*;
+import javax.swing.border.*;
+import javax.swing.event.*;
+import javax.swing.event.SwingPropertyChangeSupport;
+
+
+/**
+ * This filter will pass nodes based on the edges that
+ * they have.
+ */
+public class NodeInteractionFilter implements Filter {
+ //----------------------------------------//
+ // Filter specific properties
+ //----------------------------------------//
+ protected int filter;
+ protected String target;
+
+ /**
+ *
+ */
+ public static String FILTER_NAME_EVENT = "FILTER_NAME_EVENT";
+
+ /**
+ *
+ */
+ public static String FILTER_BOX_EVENT = "FILTER_BOX_EVENT";
+
+ /**
+ *
+ */
+ public static String TARGET_BOX_EVENT = "TARGET_BOX_EVENT";
+
+ /**
+ *
+ */
+ public static String FILTER_ID = "NodeInteractionFilter";
+
+ /**
+ *
+ */
+ public static String FILTER_DESCRIPTION = "Select nodes based on adjacent edges";
+
+ /**
+ *
+ */
+ public static String SOURCE = "source";
+
+ /**
+ *
+ */
+ public static String TARGET = "target";
+
+ /**
+ *
+ */
+ public static String EITHER = "source or target";
+
+ //----------------------------------------//
+ // Cytoscape specific Variables
+ //----------------------------------------//
+
+ //----------------------------------------//
+ // Needed Variables
+ //----------------------------------------//
+ protected String identifier = "NodeInteractionFilter";
+ protected SwingPropertyChangeSupport pcs = new SwingPropertyChangeSupport(this);
+
+ //---------------------------------------//
+ // Constructor
+ //----------------------------------------//
+
+ /**
+ * Creates a new InteractionFilter
+ */
+ public NodeInteractionFilter(int filter, String target, String identifier) {
+ this.filter = filter;
+ this.target = target;
+ this.identifier = identifier;
+ }
+
+ /**
+ * Creates a new NodeInteractionFilter object.
+ *
+ * @param desc DOCUMENT ME!
+ */
+ public NodeInteractionFilter(String desc) {
+ input(desc);
+ }
+
+ //----------------------------------------//
+ // Implements Filter
+ //----------------------------------------//
+
+ /**
+ * Returns the name for this Filter
+ */
+ public String toString() {
+ return identifier;
+ }
+
+ /**
+ * sets a new name for this filter
+ */
+ public void setIdentifier(String new_id) {
+ this.identifier = new_id;
+ pcs.firePropertyChange(FILTER_NAME_EVENT, null, new_id);
+ }
+
+ /**
+ * This is usually the same as the class name
+ */
+ public String getFilterID() {
+ return FILTER_ID;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getDescription() {
+ return FILTER_DESCRIPTION;
+ }
+
+ /**
+ * An object passes this Filter if it is the source/target
+ * node for an edge that has a matching property for
+ * the given Edge atttribute.
+ */
+ public boolean passesFilter(Object object) {
+ Filter filter = FilterManager.defaultManager().getFilter(this.filter);
+
+ if (filter == null) {
+ return false;
+ }
+
+ if (!(object instanceof Node)) {
+ return false;
+ }
+
+ Node node = (Node) object;
+
+ //get the list of all relevant edges
+ List adjacentEdges;
+ GraphPerspective myPerspective = Cytoscape.getCurrentNetwork();
+
+ if (target == SOURCE) {
+ adjacentEdges = myPerspective.getAdjacentEdgesList(node, true, false, true);
+ } else if (target == TARGET) {
+ adjacentEdges = myPerspective.getAdjacentEdgesList(node, true, true, false);
+ } else {
+ adjacentEdges = adjacentEdges = myPerspective.getAdjacentEdgesList(node, true, true,
+ true);
+ }
+
+ Iterator edgeIt = adjacentEdges.iterator();
+
+ while (edgeIt.hasNext()) {
+ if (filter.passesFilter(edgeIt.next())) {
+ return true;
+ }
+ }
+
+ return false;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Class[] getPassingTypes() {
+ return new Class[] { Node.class };
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param other_object DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean equals(Object other_object) {
+ return super.equals(other_object);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object clone() {
+ return new NodeInteractionFilter(filter, target, identifier + "_new");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public SwingPropertyChangeSupport getSwingPropertyChangeSupport() {
+ return pcs;
+ }
+
+ //----------------------------------------//
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getTarget() {
+ return target;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param target DOCUMENT ME!
+ */
+ public void setTarget(String target) {
+ this.target = target;
+ pcs.firePropertyChange(TARGET_BOX_EVENT, null, target);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param filter DOCUMENT ME!
+ */
+ public void setFilter(int filter) {
+ int oldvalue = this.filter;
+ this.filter = filter;
+ pcs.firePropertyChange(FILTER_BOX_EVENT, oldvalue, filter);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getFilter() {
+ return filter;
+ }
+
+ //----------------------------------------//
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String output() {
+ StringBuffer buffer = new StringBuffer();
+ buffer.append(getFilter() + ",");
+ buffer.append(getTarget() + ",");
+ buffer.append(toString());
+
+ return buffer.toString();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param desc DOCUMENT ME!
+ */
+ public void input(String desc) {
+ String[] array = desc.split(",");
+ setFilter((new Integer(array[0])).intValue());
+
+ if (array[1].equals(TARGET)) {
+ setTarget(TARGET);
+ } else if (array[1].equals(SOURCE)) {
+ setTarget(SOURCE);
+ } else if (array[1].equals(EITHER)) {
+ setTarget(EITHER);
+ } else {
+ throw new IllegalArgumentException(array[1] + " is not a valid interaction type");
+ }
+
+ setIdentifier(array[2]);
+ }
+}
diff --git a/coreplugins/RFilters/src/main/java/filter/cytoscape/NodeInteractionFilterEditor.java b/coreplugins/RFilters/src/main/java/filter/cytoscape/NodeInteractionFilterEditor.java
new file mode 100644
index 0000000..3f8218b
--- /dev/null
+++ b/coreplugins/RFilters/src/main/java/filter/cytoscape/NodeInteractionFilterEditor.java
@@ -0,0 +1,348 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package filter.cytoscape;
+
+import ViolinStrings.Strings;
+
+import cytoscape.*;
+import cytoscape.CyNetwork;
+
+import cytoscape.data.*;
+
+import filter.model.*;
+
+import filter.view.*;
+
+import giny.model.GraphPerspective;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import java.beans.*;
+
+import java.util.*;
+
+import javax.swing.*;
+import javax.swing.border.*;
+import javax.swing.event.*;
+import javax.swing.event.SwingPropertyChangeSupport;
+
+
+/**
+ * This filter will pass nodes based on the edges that
+ * they have.
+ */
+public class NodeInteractionFilterEditor extends FilterEditor implements ActionListener,
+ FocusListener,
+ ItemListener {
+ /**
+ * This is the Name that will go in the Tab
+ * and is returned by the "toString" method
+ */
+ protected String identifier;
+ protected Class filterClass;
+ protected JTextField nameField;
+ protected JComboBox filterBox;
+ protected JComboBox targetBox;
+ protected NodeInteractionFilter filter;
+ protected String DEFAULT_FILTER_NAME = "Node Interaction: ";
+ protected int DEFAULT_FILTER = -1;
+ protected String DEFAULT_TARGET = NodeInteractionFilter.SOURCE;
+
+ /**
+ * Creates a new NodeInteractionFilterEditor object.
+ */
+ public NodeInteractionFilterEditor() {
+ super();
+
+ try {
+ filterClass = Class.forName("filter.cytoscape.NodeInteractionFilter");
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ identifier = "Node Interactions";
+ setBorder(new TitledBorder("Node Interaction Filter"));
+ setLayout(new GridBagLayout());
+ setPreferredSize(new Dimension(450, 125));
+
+ GridBagConstraints gridBagConstraints;
+
+ JLabel lbFilterName = new JLabel("Filter Name");
+ lbFilterName.setFocusable(false);
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 0;
+ gridBagConstraints.gridy = 0;
+ gridBagConstraints.anchor = GridBagConstraints.WEST;
+ gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
+ add(lbFilterName, gridBagConstraints);
+
+ nameField = new JTextField(15);
+ gridBagConstraints = new GridBagConstraints();
+ gridBagConstraints.gridx = 1;
+ gridBagConstraints.gridy = 0;
+ gridBagConstraints.fill = GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.weightx = 1.0;
+ gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
+ add(nameField, gridBagConstraints);
+
+ nameField.addActionListener(this);
+ nameField.addFocusListener(this);
+
+ JLabel lbSelectNodes = new JLabel("Select nodes which are the ");
+ lbSelectNodes.setFocusable(false);
+ gridBagConstraints = new GridBagConstraints();
+ gridBagConstraints.gridx = 0;
+ gridBagConstraints.gridy = 1;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
+ gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
+ add(lbSelectNodes, gridBagConstraints);
+
+ targetBox = new JComboBox();
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 1;
+ gridBagConstraints.gridy = 1;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
+ add(targetBox, gridBagConstraints);
+
+ targetBox.addItem(NodeInteractionFilter.SOURCE);
+ targetBox.addItem(NodeInteractionFilter.TARGET);
+ targetBox.addItem(NodeInteractionFilter.EITHER);
+ targetBox.addItemListener(this);
+
+ JLabel lbEdgePassesTheFilter = new JLabel("of at least one edge which passes the filter ");
+ lbEdgePassesTheFilter.setFocusable(false);
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 0;
+ gridBagConstraints.gridy = 2;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
+ gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
+ add(lbEdgePassesTheFilter, gridBagConstraints);
+
+ filterBox = new JComboBox(FilterManager.defaultManager().getComboBoxModel());
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 1;
+ gridBagConstraints.gridy = 2;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
+ add(filterBox, gridBagConstraints);
+
+ filterBox.addItemListener(this);
+ }
+
+ //----------------------------------------//
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String toString() {
+ return identifier;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getFilterID() {
+ return NodeInteractionFilter.FILTER_ID;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getDescription() {
+ return NodeInteractionFilter.FILTER_DESCRIPTION;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Class getFilterClass() {
+ return filterClass;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Filter createDefaultFilter() {
+ return new NodeInteractionFilter(DEFAULT_FILTER, DEFAULT_TARGET, DEFAULT_FILTER_NAME);
+ }
+
+ /**
+ * Accepts a Filter for editing
+ * Note that this Filter must be a Filter that can be edited
+ * by this Filter editor.
+ */
+ public void editFilter(Filter filter) {
+ if (this.filter == null) {
+ } // end of if ()
+
+ if (filter instanceof NodeInteractionFilter) {
+ // good, this Filter is of the right type
+ this.filter = (NodeInteractionFilter) filter;
+ setFilterName(this.filter.toString());
+ setSelectedFilter(this.filter.getFilter());
+ setTarget(this.filter.getTarget());
+ }
+ }
+
+ //----------------------------------------//
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getFilterName() {
+ return filter.toString();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param name DOCUMENT ME!
+ */
+ public void setFilterName(String name) {
+ nameField.setText(name);
+ filter.setIdentifier(name);
+ }
+
+ // Search String /////////////////////////////////////
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getTarget() {
+ return filter.getTarget();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param target DOCUMENT ME!
+ */
+ public void setTarget(String target) {
+ filter.setTarget(target);
+ targetBox.removeItemListener(this);
+ targetBox.setSelectedItem(target);
+ targetBox.addItemListener(this);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getSelectedFilter() {
+ return filter.getFilter();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param newFilter DOCUMENT ME!
+ */
+ public void setSelectedFilter(int newFilter) {
+ if (filter != null) {
+ filterBox.removeItemListener(this);
+ filterBox.setSelectedItem(FilterManager.defaultManager().getFilter(newFilter));
+ filterBox.addItemListener(this);
+ filter.setFilter(FilterManager.defaultManager()
+ .getFilterID((Filter) filterBox.getSelectedItem()));
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ handleEvent(e);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void itemStateChanged(ItemEvent e) {
+ handleEvent(e);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void focusGained(FocusEvent e) {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void focusLost(FocusEvent e) {
+ handleEvent(e);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void handleEvent(EventObject e) {
+ if (e.getSource() == nameField) {
+ setFilterName(nameField.getText());
+ } else if (e.getSource() == filterBox) {
+ setSelectedFilter(FilterManager.defaultManager()
+ .getFilterID((Filter) filterBox.getSelectedItem()));
+ } else if (e.getSource() == targetBox) {
+ setTarget((String) targetBox.getSelectedItem());
+ }
+ }
+}
diff --git a/coreplugins/RFilters/src/main/java/filter/cytoscape/NodeTopologyFilter.java b/coreplugins/RFilters/src/main/java/filter/cytoscape/NodeTopologyFilter.java
new file mode 100644
index 0000000..0de2624
--- /dev/null
+++ b/coreplugins/RFilters/src/main/java/filter/cytoscape/NodeTopologyFilter.java
@@ -0,0 +1,365 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package filter.cytoscape;
+
+import ViolinStrings.Strings;
+
+import cytoscape.*;
+import cytoscape.CyNetwork;
+
+import cytoscape.data.*;
+
+import filter.model.*;
+
+import giny.model.*;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import java.beans.*;
+
+import java.util.*;
+
+import javax.swing.*;
+import javax.swing.border.*;
+import javax.swing.event.*;
+import javax.swing.event.SwingPropertyChangeSupport;
+
+
+/**
+ * This is a Cytoscape specific filter that will pass nodes if
+ * a selected attribute matches a specific value.
+ */
+public class NodeTopologyFilter implements Filter {
+ //----------------------------------------//
+ // Filter specific properties
+ //----------------------------------------//
+ protected int filter;
+ protected Integer count;
+ protected Integer distance;
+ protected HashSet seenNodes;
+ protected GraphPerspective myPerspective;
+
+ /**
+ *
+ */
+ public static String FILTER_NAME_EVENT = "FILTER_NAME_EVENT";
+
+ /**
+ *
+ */
+ public static String FILTER_ID = "Node Topology Filter";
+
+ /**
+ *
+ */
+ public static String FILTER_DESCRIPTION = "Select nodes based on the attributes of surrounding nodes";
+
+ /**
+ *
+ */
+ public static String FILTER_EVENT = "FILTER_EVENT";
+
+ /**
+ *
+ */
+ public static String FILTER_BOX_EVENT = "FILTER_BOX";
+
+ /**
+ *
+ */
+ public static String COUNT_EVENT = "COUNT";
+
+ /**
+ *
+ */
+ public static String DISTANCE_EVENT = "DISTANCE";
+
+ //----------------------------------------//
+ // Needed Variables
+ //----------------------------------------//
+ protected String identifier = "default";
+ protected SwingPropertyChangeSupport pcs = new SwingPropertyChangeSupport(this);
+
+ //---------------------------------------//
+ // Constructor
+ //----------------------------------------//
+
+ /**
+ * Creates a new NodeTopologyFilter
+ */
+ public NodeTopologyFilter(Integer count, Integer distance, int filter, String identifier) {
+ this.count = count;
+ this.distance = distance;
+ this.filter = filter;
+ this.identifier = identifier;
+ }
+
+ /**
+ * Creates a new NodeTopologyFilter
+ */
+ public NodeTopologyFilter(String desc) {
+ input(desc);
+ }
+
+ //----------------------------------------//
+ // Implements Filter
+ //----------------------------------------//
+
+ /**
+ * Returns the name for this Filter
+ */
+ public String toString() {
+ return identifier;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getDescription() {
+ return FILTER_DESCRIPTION;
+ }
+
+ /**
+ * sets a new name for this filter
+ */
+ public void setIdentifier(String new_id) {
+ this.identifier = new_id;
+ pcs.firePropertyChange(FILTER_NAME_EVENT, null, new_id);
+ }
+
+ /**
+ * This is usually the same as the class name
+ */
+ public String getFilterID() {
+ return FILTER_ID;
+ }
+
+ /**
+ * An Object Passes this Filter if its "toString" method
+ * matches any of the Text from the TextField
+ */
+ public boolean passesFilter(Object object) {
+ if (object instanceof Node) {
+ seenNodes = new HashSet();
+ seenNodes.add(object);
+ myPerspective = Cytoscape.getCurrentNetwork();
+
+ int totalSum = countNeighbors((Node) object, 0);
+ Filter filter = FilterManager.defaultManager().getFilter(this.filter);
+
+ if (filter.passesFilter((Node) object)) {
+ totalSum -= 1;
+ }
+
+ return totalSum >= count.intValue();
+ } else {
+ return false;
+ }
+ }
+
+ private int countNeighbors(Node currentNode, int currentDistance) {
+ Filter filter = FilterManager.defaultManager().getFilter(this.filter);
+ int sum = 0;
+
+ if (filter == null) {
+ return sum;
+ }
+
+ if (sum >= count.intValue()) {
+ return sum;
+ }
+
+ if (currentDistance == distance.intValue()) {
+ if (filter.passesFilter(currentNode)) {
+ return 1;
+ } else {
+ return 0;
+ }
+ } else {
+ java.util.List neighbors = myPerspective.neighborsList(currentNode);
+ Iterator nodeIt = neighbors.iterator();
+
+ while (nodeIt.hasNext() && (sum < count.intValue())) {
+ Node nextNode = (Node) nodeIt.next();
+
+ if (!seenNodes.contains(nextNode)) {
+ seenNodes.add(nextNode);
+ sum += countNeighbors(nextNode, currentDistance + 1);
+ }
+
+ if (sum > count.intValue()) {
+ return sum;
+ }
+ }
+
+ if (filter.passesFilter(currentNode)) {
+ return sum + 1;
+ } else {
+ return sum;
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Class[] getPassingTypes() {
+ return new Class[] { Node.class };
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param other_object DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean equals(Object other_object) {
+ return super.equals(other_object);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object clone() {
+ return new NodeTopologyFilter(count, distance, filter, identifier + "_new");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public SwingPropertyChangeSupport getSwingPropertyChangeSupport() {
+ return pcs;
+ }
+
+ //----------------------------------------//
+ /**
+ * DOCUMENT ME!
+ *
+ * @param filter DOCUMENT ME!
+ */
+ public void setFilter(int filter) {
+ int oldvalue = this.filter;
+ this.filter = filter;
+ pcs.firePropertyChange(FILTER_BOX_EVENT, oldvalue, filter);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getFilter() {
+ return filter;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param count DOCUMENT ME!
+ */
+ public void setCount(Integer count) {
+ this.count = count;
+ pcs.firePropertyChange(COUNT_EVENT, null, count);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Integer getCount() {
+ return count;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param distance DOCUMENT ME!
+ */
+ public void setDistance(Integer distance) {
+ this.distance = distance;
+ pcs.firePropertyChange(DISTANCE_EVENT, null, distance);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Integer getDistance() {
+ return distance;
+ }
+
+ //----------------------------------------//
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String output() {
+ StringBuffer buffer = new StringBuffer();
+ buffer.append(getCount() + ",");
+ buffer.append(getDistance() + ",");
+ buffer.append(getFilter() + ",");
+ buffer.append(toString());
+
+ return buffer.toString();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param desc DOCUMENT ME!
+ */
+ public void input(String desc) {
+ String[] array = desc.split(",");
+ setCount(new Integer(array[0]));
+ setDistance(new Integer(array[1]));
+ setFilter((new Integer(array[2])).intValue());
+ setIdentifier(array[3]);
+ }
+}
diff --git a/coreplugins/RFilters/src/main/java/filter/cytoscape/NodeTopologyFilterEditor.java b/coreplugins/RFilters/src/main/java/filter/cytoscape/NodeTopologyFilterEditor.java
new file mode 100644
index 0000000..6f17a32
--- /dev/null
+++ b/coreplugins/RFilters/src/main/java/filter/cytoscape/NodeTopologyFilterEditor.java
@@ -0,0 +1,441 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package filter.cytoscape;
+
+import ViolinStrings.Strings;
+
+import cytoscape.*;
+import cytoscape.CyNetwork;
+
+import cytoscape.data.*;
+
+import filter.model.*;
+
+import filter.view.*;
+
+import giny.model.GraphPerspective;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import java.beans.*;
+
+import java.util.*;
+
+import javax.swing.*;
+import javax.swing.border.*;
+import javax.swing.event.*;
+import javax.swing.event.SwingPropertyChangeSupport;
+
+
+/**
+ * This is a Cytoscape specific filter that will pass nodes if
+ * a selected attribute matches a specific value.
+ */
+public class NodeTopologyFilterEditor extends FilterEditor implements ActionListener, FocusListener,
+ ItemListener {
+ /**
+ * This is the Name that will go in the Tab
+ * and is returned by the "toString" method
+ */
+ protected String identifier;
+ protected NodeTopologyFilter filter;
+ protected JTextField nameField;
+ protected JComboBox filterBox;
+ protected JTextField distanceField;
+ protected JTextField countField;
+ protected String DEFAULT_FILTER_NAME = "NodeTopology: ";
+ protected Integer DEFAULT_DISTANCE = new Integer(1);
+ protected Integer DEFAULT_COUNT = new Integer(1);
+ protected int DEFAULT_FILTER = 0; // this is the SelectAllFilter
+ protected Class NODE_CLASS;
+ protected Class EDGE_CLASS;
+ protected Class NUMBER_CLASS;
+ protected Class DEFAULT_CLASS;
+ protected Class filterClass;
+
+ /**
+ * Creates a new NodeTopologyFilterEditor object.
+ */
+ public NodeTopologyFilterEditor() {
+ super();
+
+ try {
+ filterClass = Class.forName("filter.cytoscape.NodeTopologyFilter");
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ identifier = "Topology Filter";
+ setBorder(new TitledBorder("Node Topology Filter"));
+
+ setLayout(new GridBagLayout());
+
+ java.awt.GridBagConstraints gridBagConstraints;
+
+ JLabel lbFilterName = new JLabel("Filter Name");
+ lbFilterName.setFocusable(false);
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 0;
+ gridBagConstraints.gridy = 0;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
+ gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
+ add(lbFilterName, gridBagConstraints);
+
+ nameField = new JTextField(15);
+ nameField.setEditable(false);
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 1;
+ gridBagConstraints.gridy = 0;
+ gridBagConstraints.gridwidth = 2;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.weightx = 1.0;
+ gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
+ add(nameField, gridBagConstraints);
+
+ nameField.setText(identifier);
+ nameField.addActionListener(this);
+ nameField.addFocusListener(this);
+
+ JLabel lbSelectWith = new JLabel("Select nodes with at least");
+ lbSelectWith.setFocusable(false);
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 0;
+ gridBagConstraints.gridy = 1;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
+ gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
+ add(lbSelectWith, gridBagConstraints);
+
+ countField = new JTextField(10);
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 1;
+ gridBagConstraints.gridy = 1;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.weightx = 0.5;
+ gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
+ add(countField, gridBagConstraints);
+
+ countField.setEditable(true);
+ countField.addActionListener(this);
+ countField.addFocusListener(this);
+
+ JLabel lbNeighbors = new JLabel("neighbors ");
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 2;
+ gridBagConstraints.gridy = 1;
+ gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 20);
+ add(lbNeighbors, gridBagConstraints);
+
+ JLabel lbWithinDistance = new JLabel("within distance ");
+ lbWithinDistance.setFocusable(false);
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 0;
+ gridBagConstraints.gridy = 2;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
+ gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
+ add(lbWithinDistance, gridBagConstraints);
+
+ distanceField = new JTextField(10);
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 1;
+ gridBagConstraints.gridy = 2;
+ gridBagConstraints.gridwidth = 2;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
+ add(distanceField, gridBagConstraints);
+
+ distanceField.setEditable(true);
+ distanceField.addActionListener(this);
+ distanceField.addFocusListener(this);
+
+ JLabel lbPassFilter = new JLabel("that pass the filter ");
+ lbPassFilter.setFocusable(false);
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 0;
+ gridBagConstraints.gridy = 3;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
+ gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
+ add(lbPassFilter, gridBagConstraints);
+
+ filterBox = new JComboBox();
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 1;
+ gridBagConstraints.gridy = 3;
+ gridBagConstraints.gridwidth = 2;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
+ add(filterBox, gridBagConstraints);
+
+ filterBox.addItemListener(this);
+ filterBox.setModel(FilterManager.defaultManager().getComboBoxModel());
+ filterBox.setEditable(false);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void resetFilterBoxModel() {
+ filterBox.setModel(FilterManager.defaultManager().getComboBoxModel());
+ }
+
+ //----------------------------------------//
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Class getFilterClass() {
+ return filterClass;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String toString() {
+ return identifier;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getFilterID() {
+ return NodeTopologyFilter.FILTER_ID;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getDescription() {
+ return NodeTopologyFilter.FILTER_DESCRIPTION;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Filter createDefaultFilter() {
+ return new NodeTopologyFilter(DEFAULT_COUNT, DEFAULT_DISTANCE, DEFAULT_FILTER,
+ DEFAULT_FILTER_NAME);
+ }
+
+ /**
+ * Accepts a Filter for editing
+ * Note that this Filter must be a Filter that can be edited
+ * by this Filter editor.
+ */
+ public void editFilter(Filter filter) {
+ if (filter instanceof NodeTopologyFilter) {
+ // good, this Filter is of the right type
+ resetFilterBoxModel();
+ this.filter = (NodeTopologyFilter) filter;
+ setFilterName(this.filter.toString());
+ setSelectedFilter(this.filter.getFilter());
+ setDistance(this.filter.getDistance());
+ setCount(this.filter.getCount());
+ updateName();
+ }
+ }
+
+ //----------------------------------------//
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getFilterName() {
+ return filter.toString();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param name DOCUMENT ME!
+ */
+ public void setFilterName(String name) {
+ filter.setIdentifier(name);
+ nameField.setText(name);
+ }
+
+ // Search String /////////////////////////////////////
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getSelectedFilter() {
+ return filter.getFilter();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param newFilter DOCUMENT ME!
+ */
+ public void setSelectedFilter(int newFilter) {
+ if (filter != null) {
+ filter.setFilter(newFilter);
+ filterBox.removeItemListener(this);
+ filterBox.setSelectedItem(FilterManager.defaultManager().getFilter(newFilter));
+ filterBox.addItemListener(this);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Integer getCount() {
+ return filter.getCount();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param count DOCUMENT ME!
+ */
+ public void setCount(Integer count) {
+ filter.setCount(count);
+ countField.setText(count.toString());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Integer getDistance() {
+ return filter.getDistance();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param distance DOCUMENT ME!
+ */
+ public void setDistance(Integer distance) {
+ filter.setDistance(distance);
+ distanceField.setText(distance.toString());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ handleEvent(e);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void focusGained(FocusEvent e) {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void focusLost(FocusEvent e) {
+ handleEvent(e);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void itemStateChanged(ItemEvent e) {
+ handleEvent(e);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void handleEvent(AWTEvent e) {
+ if (e.getSource() == nameField) {
+ setFilterName(nameField.getText());
+ } else if (e.getSource() == filterBox) {
+ setSelectedFilter(FilterManager.defaultManager()
+ .getFilterID((Filter) filterBox.getSelectedItem()));
+ } else if (e.getSource() == countField) {
+ Integer count = null;
+
+ try {
+ count = new Integer(countField.getText());
+ } catch (NumberFormatException nfe) {
+ count = DEFAULT_COUNT;
+ }
+
+ setCount(count);
+ } else if (e.getSource() == distanceField) {
+ Integer distance = null;
+
+ try {
+ distance = new Integer(distanceField.getText());
+ } catch (NumberFormatException nfe) {
+ distance = DEFAULT_DISTANCE;
+ }
+
+ setDistance(distance);
+ }
+
+ updateName();
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void updateName() {
+ String newName = "NodeTopology:>=" + countField.getText().trim() + "~"
+ + distanceField.getText().trim();
+ setFilterName(newName);
+ }
+}
diff --git a/coreplugins/RFilters/src/main/java/filter/cytoscape/NumericAttributeFilter.java b/coreplugins/RFilters/src/main/java/filter/cytoscape/NumericAttributeFilter.java
new file mode 100644
index 0000000..d3d9c5c
--- /dev/null
+++ b/coreplugins/RFilters/src/main/java/filter/cytoscape/NumericAttributeFilter.java
@@ -0,0 +1,436 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package filter.cytoscape;
+
+import ViolinStrings.Strings;
+
+import cytoscape.*;
+import cytoscape.CyNetwork;
+
+import cytoscape.data.CyAttributes;
+
+import filter.model.*;
+
+import giny.model.*;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import java.beans.*;
+
+import java.util.*;
+
+import javax.swing.*;
+import javax.swing.border.*;
+import javax.swing.event.*;
+import javax.swing.event.SwingPropertyChangeSupport;
+
+
+/**
+ * This is a Cytoscape specific filter that will pass nodes if
+ * a selected attribute matches a specific value.
+ */
+public class NumericAttributeFilter implements Filter {
+ //----------------------------------------//
+ // Filter specific properties
+ //----------------------------------------//
+ protected String selectedAttribute;
+ protected Number searchNumber;
+ protected String comparison;
+ protected Class classType;
+ protected Class NODE_CLASS;
+ protected Class EDGE_CLASS;
+
+ /**
+ *
+ */
+ public static String EQUAL = "=";
+
+ /**
+ *
+ */
+ public static String LESS = "<";
+
+ /**
+ *
+ */
+ public static String GREATER = ">";
+
+ /**
+ *
+ */
+ public static String NODE = "Node";
+
+ /**
+ *
+ */
+ public static String EDGE = "Edge";
+
+ /**
+ *
+ */
+ public static String SEARCH_NUMBER_EVENT = "SEARCH_STRING_EVENT";
+
+ /**
+ *
+ */
+ public static String SELECTED_ATTRIBUTE_EVENT = "SELECTED_ATTRIBUTE_EVENT";
+
+ /**
+ *
+ */
+ public static String FILTER_NAME_EVENT = "FILTER_NAME_EVENT";
+
+ /**
+ *
+ */
+ public static String CLASS_TYPE_EVENT = "CLASS_TYPE";
+
+ /**
+ *
+ */
+ public static String FILTER_ID = "Numeric Attribute Filter";
+
+ /**
+ *
+ */
+ public static String FILTER_DESCRIPTION = "Select nodes or edges based on the value of a numeric attribute";
+
+ /**
+ *
+ */
+ public static String COMPARISON_EVENT = "COMPARISON_EVENT";
+
+ //----------------------------------------//
+ // Needed Variables
+ //----------------------------------------//
+ protected String identifier = "default";
+ protected SwingPropertyChangeSupport pcs = new SwingPropertyChangeSupport(this);
+
+ //---------------------------------------//
+ // Constructor
+ //----------------------------------------//
+
+ /**
+ * Creates a new NumericAttributeFilter
+ */
+ public NumericAttributeFilter(String comparison, String classString, String selectedAttribute,
+ Number searchNumber, String identifier) {
+ this.comparison = comparison;
+
+ try {
+ NODE_CLASS = Class.forName("giny.model.Node");
+ EDGE_CLASS = Class.forName("giny.model.Edge");
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ this.selectedAttribute = selectedAttribute;
+ this.searchNumber = searchNumber;
+ this.identifier = identifier;
+ setClassType(classString);
+ }
+
+ /**
+ * Creates a new NumericAttributeFilter
+ */
+ public NumericAttributeFilter(String desc) {
+ try {
+ NODE_CLASS = Node.class;
+ EDGE_CLASS = Edge.class;
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ input(desc);
+ }
+
+ //----------------------------------------//
+ // Implements Filter
+ //----------------------------------------//
+
+ /**
+ * Returns the name for this Filter
+ */
+ public String toString() {
+ return identifier;
+ }
+
+ /**
+ * sets a new name for this filter
+ */
+ public void setIdentifier(String new_id) {
+ this.identifier = new_id;
+ pcs.firePropertyChange(FILTER_NAME_EVENT, null, new_id);
+ }
+
+ /**
+ * This is usually the same as the class name
+ */
+ public String getFilterID() {
+ return FILTER_ID;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getDescription() {
+ return FILTER_DESCRIPTION;
+ }
+
+ /**
+ * An Object Passes this Filter if its "toString" method
+ * matches any of the Text from the TextField
+ */
+ public boolean passesFilter(Object object) {
+ if (!classType.isInstance(object)) {
+ return false;
+ }
+
+ CyAttributes data = null;
+
+ if (classType.equals(NODE_CLASS)) {
+ data = Cytoscape.getNodeAttributes();
+ } else {
+ data = Cytoscape.getEdgeAttributes();
+ }
+
+ String name = ((GraphObject) object).getIdentifier();
+
+ if (name == null) {
+ return false;
+ }
+
+ Number value;
+
+ if (data.getType(selectedAttribute) == CyAttributes.TYPE_FLOATING)
+ value = (Number) data.getDoubleAttribute(name, selectedAttribute);
+ else
+ value = (Number) data.getIntegerAttribute(name, selectedAttribute);
+
+ if (value == null) {
+ return false;
+ }
+
+ if (comparison == EQUAL) {
+ return searchNumber.doubleValue() == value.doubleValue();
+ } else if (comparison == LESS) {
+ return searchNumber.doubleValue() > value.doubleValue();
+ } else if (comparison == GREATER) {
+ return searchNumber.doubleValue() < value.doubleValue();
+ } else {
+ //System.err.println("Comparison not identified");
+ return false;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Class[] getPassingTypes() {
+ return new Class[] { classType };
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param other_object DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean equals(Object other_object) {
+ return super.equals(other_object);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object clone() {
+ return new NumericAttributeFilter(comparison, getClassType(), selectedAttribute,
+ searchNumber, identifier + "_new");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public SwingPropertyChangeSupport getSwingPropertyChangeSupport() {
+ return pcs;
+ }
+
+ // SearchString /////////////////////////////////
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Number getSearchNumber() {
+ return searchNumber;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param searchNumber DOCUMENT ME!
+ */
+ public void setSearchNumber(Number searchNumber) {
+ this.searchNumber = searchNumber;
+ pcs.firePropertyChange(SEARCH_NUMBER_EVENT, null, searchNumber);
+ }
+
+ // Selected_Attribute ///////////////////////////
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getSelectedAttribute() {
+ return selectedAttribute;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param new_attr DOCUMENT ME!
+ */
+ public void setSelectedAttribute(String new_attr) {
+ this.selectedAttribute = new_attr;
+ pcs.firePropertyChange(SELECTED_ATTRIBUTE_EVENT, null, selectedAttribute);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param classString DOCUMENT ME!
+ */
+ public void setClassType(String classString) {
+ if ((classString == NODE) || classString.equals("Node")) {
+ this.classType = NODE_CLASS;
+ } else {
+ this.classType = EDGE_CLASS;
+ }
+
+ pcs.firePropertyChange(CLASS_TYPE_EVENT, null, classString);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getClassType() {
+ if (classType == NODE_CLASS) {
+ return NODE;
+ } else {
+ return EDGE;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param comparison DOCUMENT ME!
+ */
+ public void setComparison(String comparison) {
+ this.comparison = comparison;
+ pcs.firePropertyChange(COMPARISON_EVENT, null, comparison);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getComparison() {
+ return comparison;
+ }
+
+ //----------------------------------------//
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String output() {
+ StringBuffer buffer = new StringBuffer();
+ buffer.append(getComparison() + ",");
+ buffer.append(getClassType() + ",");
+ buffer.append(getSelectedAttribute() + ",");
+ buffer.append(getSearchNumber() + ",");
+ buffer.append(toString());
+
+ return buffer.toString();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param desc DOCUMENT ME!
+ */
+ public void input(String desc) {
+ String[] array = desc.split(",");
+
+ if (array[0].equals(GREATER)) {
+ setComparison(GREATER);
+ } else if (array[0].equals(LESS)) {
+ setComparison(LESS);
+ } else if (array[0].equals(EQUAL)) {
+ setComparison(EQUAL);
+ } else {
+ throw new IllegalArgumentException(array[0] + " is not a valid type of comparison");
+ }
+
+ setSelectedAttribute(array[2]);
+ setSearchNumber(new Double(array[3]));
+ setIdentifier(array[4]);
+
+ if (array[1].equals(NODE)) {
+ setClassType(NODE);
+ } else if (array[1].equals(EDGE)) {
+ setClassType(EDGE);
+ } else {
+ throw new IllegalArgumentException(array[0] + " is not a valid type of class");
+ }
+ }
+}
diff --git a/coreplugins/RFilters/src/main/java/filter/cytoscape/NumericAttributeFilterEditor.java b/coreplugins/RFilters/src/main/java/filter/cytoscape/NumericAttributeFilterEditor.java
new file mode 100644
index 0000000..41e15d0
--- /dev/null
+++ b/coreplugins/RFilters/src/main/java/filter/cytoscape/NumericAttributeFilterEditor.java
@@ -0,0 +1,475 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package filter.cytoscape;
+
+import cytoscape.*;
+import cytoscape.CyNetwork;
+
+import cytoscape.data.*;
+
+import filter.model.*;
+
+import filter.view.*;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import java.beans.*;
+
+import java.util.*;
+
+import javax.swing.*;
+import javax.swing.border.*;
+import javax.swing.event.*;
+import javax.swing.event.SwingPropertyChangeSupport;
+
+
+/**
+ * This is a Cytoscape specific filter that will pass nodes if
+ * a selected attribute matches a specific value.
+ */
+public class NumericAttributeFilterEditor extends FilterEditor implements ActionListener,
+ FocusListener,
+ ItemListener {
+ /**
+ * This is the Name that will go in the Tab
+ * and is returned by the "toString" method
+ */
+ protected JTextField nameField;
+ protected JComboBox classBox;
+ protected JTextField searchField;
+ protected JComboBox attributeBox;
+ protected JComboBox comparisonBox;
+ protected String identifier;
+ protected NumericAttributeFilter filter;
+ protected Number DEFAULT_SEARCH_NUMBER = new Double(0);
+ protected String DEFAULT_FILTER_NAME = "Numeric: ";
+ protected String DEFAULT_SELECTED_ATTRIBUTE = "";
+ protected String DEFAULT_COMPARISON = NumericAttributeFilter.EQUAL;
+ protected String DEFAULT_CLASS = NumericAttributeFilter.NODE;
+ protected Class NODE_CLASS;
+ protected Class EDGE_CLASS;
+ protected Class NUMBER_CLASS;
+ protected Class filterClass;
+ protected ComboBoxModel nodeAttributeModel;
+ protected ComboBoxModel edgeAttributeModel;
+
+ /**
+ * Creates a new NumericAttributeFilterEditor object.
+ */
+ public NumericAttributeFilterEditor() {
+ super();
+
+ try {
+ NUMBER_CLASS = Class.forName("java.lang.Number");
+ NODE_CLASS = Class.forName("giny.model.Node");
+ EDGE_CLASS = Class.forName("giny.model.Edge");
+ filterClass = Class.forName("filter.cytoscape.NumericAttributeFilter");
+ nodeAttributeModel = new NodeAttributeComboBoxModel(NUMBER_CLASS);
+ edgeAttributeModel = new EdgeAttributeComboBoxModel(NUMBER_CLASS);
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ //this.objectAttributes = network.getNodeAttributes();
+ setLayout(new GridBagLayout());
+ identifier = "Numeric Filter";
+ setBorder(new TitledBorder(getFilterID()));
+
+ GridBagConstraints gridBagConstraints = new java.awt.GridBagConstraints();
+
+ JLabel lbFilterName = new JLabel("Filter Name");
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 0;
+ gridBagConstraints.gridy = 0;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
+ gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
+ add(lbFilterName, gridBagConstraints);
+
+ nameField = new JTextField(15);
+ nameField.setEditable(false);
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridwidth = 2;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.weightx = 1.0;
+ gridBagConstraints.insets = new java.awt.Insets(0, 0, 0, 10);
+ add(nameField, gridBagConstraints);
+
+ nameField.addActionListener(this);
+ nameField.addFocusListener(this);
+
+ JLabel lbSelectType = new JLabel("Select graph objects of type ");
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 0;
+ gridBagConstraints.gridy = 1;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
+ gridBagConstraints.insets = new java.awt.Insets(0, 10, 10, 10);
+ add(lbSelectType, gridBagConstraints);
+
+ classBox = new JComboBox();
+ //classBox.setPreferredSize(new Dimension(50,22));
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 1;
+ gridBagConstraints.gridy = 1;
+ gridBagConstraints.gridwidth = 2;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.insets = new java.awt.Insets(0, 0, 10, 10);
+ add(classBox, gridBagConstraints);
+
+ classBox.addItem(NumericAttributeFilter.NODE);
+ classBox.addItem(NumericAttributeFilter.EDGE);
+ classBox.setEditable(false);
+ classBox.addItemListener(this);
+
+ JLabel lbNumberAttr = new JLabel(" with a value for numeric attribute ");
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 0;
+ gridBagConstraints.gridy = 2;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
+ gridBagConstraints.insets = new java.awt.Insets(0, 10, 10, 10);
+ add(lbNumberAttr, gridBagConstraints);
+
+ attributeBox = new JComboBox();
+ attributeBox.setMinimumSize(new java.awt.Dimension(100, 18));
+ attributeBox.setPreferredSize(new java.awt.Dimension(100, 22));
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 1;
+ gridBagConstraints.gridy = 2;
+ gridBagConstraints.gridwidth = 2;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.weightx = 0.5;
+ gridBagConstraints.insets = new java.awt.Insets(0, 0, 10, 10);
+ add(attributeBox, gridBagConstraints);
+
+ attributeBox.setEditable(false);
+ attributeBox.addItemListener(this);
+
+ JLabel lbThatIs = new JLabel(" that is ");
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 0;
+ gridBagConstraints.gridy = 3;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
+ gridBagConstraints.insets = new java.awt.Insets(0, 10, 0, 10);
+ add(lbThatIs, gridBagConstraints);
+
+ comparisonBox = new JComboBox();
+ comparisonBox.setPreferredSize(new Dimension(50, 22));
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 1;
+ gridBagConstraints.gridy = 3;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
+ add(comparisonBox, gridBagConstraints);
+
+ comparisonBox.addItem(NumericAttributeFilter.LESS);
+ comparisonBox.addItem(NumericAttributeFilter.EQUAL);
+ comparisonBox.addItem(NumericAttributeFilter.GREATER);
+ comparisonBox.setSelectedIndex(0);
+ comparisonBox.setEditable(false);
+ comparisonBox.addItemListener(this);
+
+ searchField = new JTextField(10);
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 2;
+ gridBagConstraints.gridy = 3;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.weightx = 1.0;
+ gridBagConstraints.insets = new java.awt.Insets(0, 10, 0, 10);
+ add(searchField, gridBagConstraints);
+
+ searchField.setEditable(true);
+ searchField.addActionListener(this);
+ searchField.addFocusListener(this);
+ }
+
+ //----------------------------------------//
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Class getFilterClass() {
+ return filterClass;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String toString() {
+ return identifier;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getFilterID() {
+ return NumericAttributeFilter.FILTER_ID;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getDescription() {
+ return NumericAttributeFilter.FILTER_DESCRIPTION;
+ }
+
+ /**
+ * Create a new filter with the given name initialized to the default values
+ */
+ public Filter createDefaultFilter() {
+ return new NumericAttributeFilter(DEFAULT_COMPARISON, DEFAULT_CLASS,
+ DEFAULT_SELECTED_ATTRIBUTE, DEFAULT_SEARCH_NUMBER,
+ DEFAULT_FILTER_NAME);
+ }
+
+ /**
+ * Accepts a Filter for editing
+ * Note that this Filter must be a Filter that can be edited
+ * by this Filter editor.
+ */
+ public void editFilter(Filter filter) {
+ if (filter instanceof NumericAttributeFilter) {
+ // good, this Filter is of the right type
+ this.filter = (NumericAttributeFilter) filter;
+ setFilterName(this.filter.toString());
+ setSearchNumber(this.filter.getSearchNumber());
+ setSelectedAttribute(this.filter.getSelectedAttribute());
+ setSelectedClass(this.filter.getClassType());
+ setSelectedComparison(this.filter.getComparison());
+ updateName();
+ }
+ }
+
+ //----------------------------------------//
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getFilterName() {
+ return filter.toString();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param name DOCUMENT ME!
+ */
+ public void setFilterName(String name) {
+ nameField.setText(name);
+ filter.setIdentifier(name);
+ }
+
+ // Search String /////////////////////////////////////
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Number getSearchNumber() {
+ return filter.getSearchNumber();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param searchNumber DOCUMENT ME!
+ */
+ public void setSearchNumber(Number searchNumber) {
+ filter.setSearchNumber(searchNumber);
+ searchField.setText(searchNumber.toString());
+ }
+
+ // Selected Attribute ////////////////////////////////
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getSelectedAttribute() {
+ return filter.getSelectedAttribute();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param new_attr DOCUMENT ME!
+ */
+ public void setSelectedAttribute(String new_attr) {
+ filter.setSelectedAttribute(new_attr);
+ attributeBox.removeItemListener(this);
+ attributeBox.setSelectedItem(new_attr);
+ attributeBox.addItemListener(this);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getSelectedClass() {
+ return filter.getClassType();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param newClass DOCUMENT ME!
+ */
+ public void setSelectedClass(String newClass) {
+ filter.setClassType(newClass);
+ attributeBox.removeItemListener(this);
+
+ if (newClass == NumericAttributeFilter.NODE) {
+ attributeBox.setModel(nodeAttributeModel);
+ attributeBox.setSelectedItem(getSelectedAttribute());
+ } // end of if ()
+ else {
+ attributeBox.setModel(edgeAttributeModel);
+ attributeBox.setSelectedItem(getSelectedAttribute());
+ } // end of else
+
+ attributeBox.addItemListener(this);
+ classBox.removeItemListener(this);
+ classBox.setSelectedItem(newClass);
+ classBox.addItemListener(this);
+ setSelectedAttribute((String) attributeBox.getSelectedItem());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getSelectedComparison() {
+ return filter.getComparison();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param comparison DOCUMENT ME!
+ */
+ public void setSelectedComparison(String comparison) {
+ filter.setComparison(comparison);
+ comparisonBox.removeItemListener(this);
+ comparisonBox.setSelectedItem(comparison);
+ comparisonBox.addItemListener(this);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ handleEvent(e);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void itemStateChanged(ItemEvent e) {
+ handleEvent(e);
+ }
+
+ private void handleEvent(AWTEvent e) {
+ if (e.getSource() == nameField) {
+ setFilterName(nameField.getText());
+ } // end of if ()
+ else {
+ if (e.getSource() == searchField) {
+ String numberString = searchField.getText();
+ Number searchNumber = null;
+
+ try {
+ searchNumber = new Double(numberString);
+ } catch (Exception except) {
+ searchNumber = DEFAULT_SEARCH_NUMBER;
+ searchField.setText(searchNumber.toString());
+ }
+
+ setSearchNumber(searchNumber);
+ } else if (e.getSource() == attributeBox) {
+ setSelectedAttribute((String) attributeBox.getSelectedItem());
+ } else if (e.getSource() == classBox) {
+ setSelectedClass((String) classBox.getSelectedItem());
+ } else if (e.getSource() == comparisonBox) {
+ setSelectedComparison((String) comparisonBox.getSelectedItem());
+ }
+
+ updateName();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void focusGained(FocusEvent e) {
+ }
+ ;
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void focusLost(FocusEvent e) {
+ handleEvent(e);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void updateName() {
+ StringBuffer buffer = new StringBuffer();
+ buffer.append(getSelectedClass() + " : ");
+ buffer.append(getSelectedAttribute());
+ buffer.append(getSelectedComparison());
+ buffer.append(getSearchNumber());
+ setFilterName(buffer.toString());
+ }
+}
diff --git a/coreplugins/RFilters/src/main/java/filter/cytoscape/SelectAllFilter.java b/coreplugins/RFilters/src/main/java/filter/cytoscape/SelectAllFilter.java
new file mode 100644
index 0000000..5844af8
--- /dev/null
+++ b/coreplugins/RFilters/src/main/java/filter/cytoscape/SelectAllFilter.java
@@ -0,0 +1,191 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package filter.cytoscape;
+
+import ViolinStrings.Strings;
+
+import cytoscape.*;
+
+import cytoscape.data.*;
+
+import filter.model.*;
+
+import giny.model.*;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import java.beans.*;
+
+import java.util.*;
+
+import javax.swing.*;
+import javax.swing.border.*;
+import javax.swing.event.*;
+import javax.swing.event.SwingPropertyChangeSupport;
+
+
+/**
+ * This is a Cytoscape specific filter that will pass nodes if
+ * a selected attribute matches a specific value.
+ */
+public class SelectAllFilter implements Filter {
+ //----------------------------------------//
+ /**
+ *
+ */
+ public static String FILTER_ID = "[ No Filter ]";
+
+ /**
+ *
+ */
+ public static String FILTER_DESCRIPTION = "Selects all nodes and edges";
+
+ //----------------------------------------//
+ // Needed Variables
+ //----------------------------------------//
+ protected SwingPropertyChangeSupport pcs = new SwingPropertyChangeSupport(this);
+
+ //---------------------------------------//
+ // Constructor
+ //----------------------------------------//
+
+ /**
+ * Creates a new SelectAllFilter
+ */
+ public SelectAllFilter() {
+ }
+
+ //----------------------------------------//
+ // Implements Filter
+ //----------------------------------------//
+
+ /**
+ * Returns the name for this Filter
+ */
+ public String toString() {
+ return FILTER_ID;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getDescription() {
+ return FILTER_DESCRIPTION;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getFilterID() {
+ return FILTER_ID;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param object DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean passesFilter(Object object) {
+ if (object instanceof Node || object instanceof Edge) {
+ return true;
+ } else {
+ return false;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Class[] getPassingTypes() {
+ return new Class[] { Node.class, Edge.class };
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param other_object DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean equals(Object other_object) {
+ return super.equals(other_object);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object clone() {
+ return new SelectAllFilter();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public SwingPropertyChangeSupport getSwingPropertyChangeSupport() {
+ return pcs;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String output() {
+ return FILTER_ID;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param desc DOCUMENT ME!
+ */
+ public void input(String desc) {
+ }
+}
diff --git a/coreplugins/RFilters/src/main/java/filter/cytoscape/StringPatternFilter.java b/coreplugins/RFilters/src/main/java/filter/cytoscape/StringPatternFilter.java
new file mode 100644
index 0000000..1876353
--- /dev/null
+++ b/coreplugins/RFilters/src/main/java/filter/cytoscape/StringPatternFilter.java
@@ -0,0 +1,421 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package filter.cytoscape;
+
+import ViolinStrings.Strings;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.data.CyAttributes;
+
+import filter.model.*;
+
+import giny.model.*;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import java.beans.*;
+
+import java.util.*;
+
+import javax.swing.*;
+import javax.swing.border.*;
+import javax.swing.event.*;
+import javax.swing.event.SwingPropertyChangeSupport;
+
+
+/**
+ * This is a Cytoscape specific filter that will pass nodes if
+ * a selected attribute matches a specific value.
+ */
+public class StringPatternFilter implements Filter {
+ //----------------------------------------//
+ // Filter specific properties
+ //----------------------------------------//
+ protected String selectedAttribute;
+ protected String searchString;
+ protected Class classType;
+ protected Class NODE_CLASS;
+ protected Class EDGE_CLASS;
+
+ /**
+ *
+ */
+ public static String NODE = "Node";
+
+ /**
+ *
+ */
+ public static String EDGE = "Edge";
+
+ /**
+ *
+ */
+ public static String SEARCH_STRING_EVENT = "SEARCH_STRING_EVENT";
+
+ /**
+ *
+ */
+ public static String SELECTED_ATTRIBUTE_EVENT = "SELECTED_ATTRIBUTE_EVENT";
+
+ /**
+ *
+ */
+ public static String FILTER_NAME_EVENT = "FILTER_NAME_EVENT";
+
+ /**
+ *
+ */
+ public static String CLASS_TYPE_EVENT = "CLASS_TYPE";
+
+ /**
+ *
+ */
+ public static String FILTER_ID = "String Pattern Filter";
+
+ /**
+ *
+ */
+ public static String FILTER_DESCRIPTION = "Select nodes or edges based on the value of a text attribute";
+
+ //----------------------------------------//
+ // Needed Variables
+ //----------------------------------------//
+ protected String identifier = "default";
+ protected SwingPropertyChangeSupport pcs = new SwingPropertyChangeSupport(this);
+
+ //---------------------------------------//
+ // Constructor
+ //----------------------------------------//
+
+ /**
+ * Creates a new StringPatternFilter
+ */
+ public StringPatternFilter(String classString, String selectedAttribute, String searchString,
+ String identifier) {
+ try {
+ NODE_CLASS = Node.class;
+ EDGE_CLASS = Edge.class;
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ this.selectedAttribute = selectedAttribute;
+ this.searchString = searchString;
+ this.identifier = identifier;
+ setClassType(classString);
+ }
+
+ /**
+ * Creates a new StringPatternFilter object.
+ *
+ * @param desc DOCUMENT ME!
+ */
+ public StringPatternFilter(String desc) {
+ try {
+ NODE_CLASS = Class.forName("giny.model.Node");
+ EDGE_CLASS = Class.forName("giny.model.Edge");
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ input(desc);
+ }
+
+ //----------------------------------------//
+ // Implements Filter
+ //----------------------------------------//
+
+ /**
+ * Returns the name for this Filter
+ */
+ public String toString() {
+ return identifier;
+ }
+
+ /**
+ * sets a new name for this filter
+ */
+ public void setIdentifier(String new_id) {
+ this.identifier = new_id;
+ pcs.firePropertyChange(FILTER_NAME_EVENT, null, new_id);
+ }
+
+ /**
+ * This is usually the same as the class name
+ */
+ public String getFilterID() {
+ return FILTER_ID;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getDescription() {
+ return FILTER_DESCRIPTION;
+ }
+
+ /**
+ * An Object Passes this Filter if its "toString" method
+ * matches any of the Text from the TextField
+ */
+ public boolean passesFilter(Object object) {
+ String value = "";
+
+ if (!classType.isInstance(object)) {
+ return false;
+ }
+
+ CyAttributes data = null;
+
+ if (classType.equals(NODE_CLASS)) {
+ data = Cytoscape.getNodeAttributes();
+ } else {
+ data = Cytoscape.getEdgeAttributes();
+ }
+
+ String name = ((GraphObject) object).getIdentifier();
+
+ if (name == null) {
+ return false;
+ }
+
+ value = data.getStringAttribute(name, selectedAttribute); //.toString();
+
+ if (value == null) {
+ return false;
+ }
+
+ // I think that * and ? are better for now....
+ String[] pattern = searchString.split("\\s");
+
+ for (int p = 0; p < pattern.length; ++p) {
+ if (Strings.isLike((String) value, pattern[p], 0, true)) {
+ // this is an OR function
+ return true;
+ }
+ }
+
+ return false;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Class[] getPassingTypes() {
+ return new Class[] { classType };
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param other_object DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean equals(Object other_object) {
+ if (other_object instanceof StringPatternFilter) {
+ if (((StringPatternFilter) other_object).getSearchString().equals(getSearchString())) {
+ return true;
+ }
+ }
+
+ return false;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object clone() {
+ return new StringPatternFilter(getClassType(), selectedAttribute, searchString,
+ identifier + "_new");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public SwingPropertyChangeSupport getSwingPropertyChangeSupport() {
+ return pcs;
+ }
+
+ //----------------------------------------//
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void propertyChange(PropertyChangeEvent e) {
+ if (e.getPropertyName() == SEARCH_STRING_EVENT) {
+ //System.out.println( "Search String Changed to "+( String )e.getNewValue() );
+ setSearchString((String) e.getNewValue());
+ } else if (e.getPropertyName() == FILTER_NAME_EVENT) {
+ setIdentifier((String) e.getNewValue());
+ } else if (e.getPropertyName() == SELECTED_ATTRIBUTE_EVENT) {
+ setSelectedAttribute((String) e.getNewValue());
+ } else if (e.getPropertyName() == CLASS_TYPE_EVENT) {
+ setClassType((String) e.getNewValue());
+ }
+ }
+
+ // SearchString /////////////////////////////////
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getSearchString() {
+ return searchString;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param search_string DOCUMENT ME!
+ */
+ public void setSearchString(String search_string) {
+ this.searchString = search_string;
+ fireSearchStringChanged();
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void fireSearchStringChanged() {
+ pcs.firePropertyChange(SEARCH_STRING_EVENT, null, searchString);
+ }
+
+ // Selected_Attribute ///////////////////////////
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getSelectedAttribute() {
+ return selectedAttribute;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param new_attr DOCUMENT ME!
+ */
+ public void setSelectedAttribute(String new_attr) {
+ this.selectedAttribute = new_attr;
+ fireSelectedAttributeModified();
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void fireSelectedAttributeModified() {
+ pcs.firePropertyChange(SELECTED_ATTRIBUTE_EVENT, null, selectedAttribute);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param classString DOCUMENT ME!
+ */
+ public void setClassType(String classString) {
+ if ((classString == NODE) || classString.equals("Node")) {
+ classType = NODE_CLASS;
+ } else {
+ classType = EDGE_CLASS;
+ }
+
+ pcs.firePropertyChange(CLASS_TYPE_EVENT, null, classType);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getClassType() {
+ if (classType == NODE_CLASS) {
+ return NODE;
+ } else {
+ return EDGE;
+ }
+ }
+
+ //----------------------------------------//
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String output() {
+ StringBuffer buffer = new StringBuffer();
+ buffer.append(getClassType() + ",");
+ buffer.append(getSelectedAttribute() + ",");
+ buffer.append(getSearchString() + ",");
+ buffer.append(toString());
+
+ return buffer.toString();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param desc DOCUMENT ME!
+ */
+ public void input(String desc) {
+ String[] array = desc.split(",");
+
+ if (array[0].equals(NODE)) {
+ setClassType(NODE);
+ } else if (array[0].equals(EDGE)) {
+ setClassType(EDGE);
+ } else {
+ throw new IllegalArgumentException(array[0] + " is not a valid type of class");
+ }
+
+ setSelectedAttribute(array[1]);
+ setSearchString(array[2]);
+ setIdentifier(array[3]);
+ }
+}
diff --git a/coreplugins/RFilters/src/main/java/filter/cytoscape/StringPatternFilterEditor.java b/coreplugins/RFilters/src/main/java/filter/cytoscape/StringPatternFilterEditor.java
new file mode 100644
index 0000000..42424b9
--- /dev/null
+++ b/coreplugins/RFilters/src/main/java/filter/cytoscape/StringPatternFilterEditor.java
@@ -0,0 +1,429 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package filter.cytoscape;
+
+import ViolinStrings.Strings;
+
+import cytoscape.*;
+
+import cytoscape.data.CyAttributes;
+
+import filter.model.*;
+
+import filter.view.*;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import java.beans.*;
+
+import java.util.*;
+
+import javax.swing.*;
+import javax.swing.border.*;
+import javax.swing.event.*;
+import javax.swing.event.SwingPropertyChangeSupport;
+
+
+/**
+ * This is a Cytoscape specific filter that will pass nodes if
+ * a selected attribute matches a specific value.
+ */
+public class StringPatternFilterEditor extends FilterEditor implements ActionListener,
+ FocusListener, ItemListener {
+ /**
+ * This is the Name that will go in the Tab
+ * and is returned by the "toString" method
+ */
+ protected String identifier;
+ protected JTextField nameField;
+ protected JComboBox classBox;
+ protected JTextField searchField;
+ protected JComboBox attributeBox;
+ protected StringPatternFilter filter;
+ protected String DEFAULT_SEARCH_STRING = "";
+ protected String DEFAULT_FILTER_NAME = "Pattern: ";
+ protected String DEFAULT_SELECTED_ATTRIBUTE = "";
+ protected Class NODE_CLASS;
+ protected Class EDGE_CLASS;
+ protected Class STRING_CLASS;
+ protected String DEFAULT_CLASS = StringPatternFilter.NODE;
+ protected Class filterClass;
+ protected ComboBoxModel nodeAttributeModel;
+ protected ComboBoxModel edgeAttributeModel;
+
+ /**
+ * Creates a new StringPatternFilterEditor object.
+ */
+ public StringPatternFilterEditor() {
+ super();
+
+ try {
+ STRING_CLASS = Class.forName("java.lang.String");
+ NODE_CLASS = Class.forName("giny.model.Node");
+ EDGE_CLASS = Class.forName("giny.model.Edge");
+ filterClass = Class.forName("filter.cytoscape.StringPatternFilter");
+ nodeAttributeModel = new NodeAttributeComboBoxModel(STRING_CLASS);
+ edgeAttributeModel = new EdgeAttributeComboBoxModel(STRING_CLASS);
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ setLayout(new GridBagLayout());
+ identifier = "String Filter";
+ setBorder(new TitledBorder(getFilterID()));
+
+ java.awt.GridBagConstraints gridBagConstraints;
+
+ JLabel lbFilterName = new JLabel("Filter Name");
+ lbFilterName.setFocusable(false);
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 0;
+ gridBagConstraints.gridy = 0;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
+ gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
+ add(lbFilterName, gridBagConstraints);
+
+ nameField = new JTextField(15);
+ nameField.setEditable(false);
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 1;
+ gridBagConstraints.gridy = 0;
+ //gridBagConstraints.gridwidth = 2;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.weightx = 1.0;
+ gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
+ add(nameField, gridBagConstraints);
+
+ nameField.addActionListener(this);
+ nameField.addFocusListener(this);
+
+ JLabel lbSelectType = new JLabel("Select graph objects of type ");
+ lbSelectType.setFocusable(false);
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 0;
+ gridBagConstraints.gridy = 1;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
+ gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
+ add(lbSelectType, gridBagConstraints);
+
+ classBox = new JComboBox();
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 1;
+ gridBagConstraints.gridy = 1;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ //gridBagConstraints.weightx = 0.5;
+ gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
+ add(classBox, gridBagConstraints);
+
+ classBox.addItem(StringPatternFilter.NODE);
+ classBox.addItem(StringPatternFilter.EDGE);
+ classBox.setEditable(false);
+ classBox.addItemListener(this);
+
+ JLabel lbTextAttr = new JLabel(" with a value for text attribute ");
+ lbTextAttr.setFocusable(false);
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 0;
+ gridBagConstraints.gridy = 2;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
+ gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
+ add(lbTextAttr, gridBagConstraints);
+
+ attributeBox = new JComboBox();
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 1;
+ gridBagConstraints.gridy = 2;
+ //gridBagConstraints.gridwidth = 2;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
+ add(attributeBox, gridBagConstraints);
+
+ attributeBox.setEditable(false);
+ attributeBox.addItemListener(this);
+
+ JLabel lbMatchesPattern = new JLabel(" that matches the pattern ");
+ lbMatchesPattern.setFocusable(false);
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 0;
+ gridBagConstraints.gridy = 3;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
+ gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
+ add(lbMatchesPattern, gridBagConstraints);
+
+ searchField = new JTextField(10);
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 1;
+ gridBagConstraints.gridy = 3;
+ //gridBagConstraints.gridwidth = 2;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
+ add(searchField, gridBagConstraints);
+
+ searchField.setEditable(true);
+ searchField.addActionListener(this);
+ searchField.addFocusListener(this);
+ }
+
+ //----------------------------------------//
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Class getFilterClass() {
+ return filterClass;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String toString() {
+ return identifier;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getDescription() {
+ return StringPatternFilter.FILTER_DESCRIPTION;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getFilterID() {
+ return StringPatternFilter.FILTER_ID;
+ }
+
+ /**
+ * Creates a new filter initialized to the default values with the given name
+ */
+ public Filter createDefaultFilter() {
+ return new StringPatternFilter(DEFAULT_CLASS, DEFAULT_SELECTED_ATTRIBUTE,
+ DEFAULT_SEARCH_STRING, DEFAULT_FILTER_NAME);
+ }
+
+ /**
+ * Accepts a Filter for editing
+ * Note that this Filter must be a Filter that can be edited
+ * by this Filter editor.
+ */
+ public void editFilter(Filter filter) {
+ if (filter instanceof StringPatternFilter) {
+ // good, this Filter is of the right type
+ this.filter = (StringPatternFilter) filter;
+ setSearchString(this.filter.getSearchString());
+ setFilterName(this.filter.toString());
+ setSelectedAttribute(this.filter.getSelectedAttribute());
+ setSelectedClass(this.filter.getClassType());
+ updateName();
+ }
+ }
+
+ //----------------------------------------//
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getFilterName() {
+ return identifier;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param name DOCUMENT ME!
+ */
+ public void setFilterName(String name) {
+ nameField.setText(name);
+ filter.setIdentifier(name);
+ }
+
+ // Search String /////////////////////////////////////
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getSearchString() {
+ return filter.getSearchString();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param search_string DOCUMENT ME!
+ */
+ public void setSearchString(String search_string) {
+ filter.setSearchString(search_string);
+ searchField.setText(search_string);
+ }
+
+ // Selected Attribute ////////////////////////////////
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getSelectedAttribute() {
+ return filter.getSelectedAttribute();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param new_attr DOCUMENT ME!
+ */
+ public void setSelectedAttribute(String new_attr) {
+ filter.setSelectedAttribute(new_attr);
+ attributeBox.removeItemListener(this);
+ attributeBox.setSelectedItem(new_attr);
+ attributeBox.addItemListener(this);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getSelectedClass() {
+ return filter.getClassType();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param newClass DOCUMENT ME!
+ */
+ public void setSelectedClass(String newClass) {
+ filter.setClassType(newClass);
+ attributeBox.removeItemListener(this);
+
+ if (newClass == NumericAttributeFilter.NODE) {
+ attributeBox.setModel(nodeAttributeModel);
+ attributeBox.setSelectedItem(filter.getSelectedAttribute());
+ } // end of if ()
+ else {
+ attributeBox.setModel(edgeAttributeModel);
+ attributeBox.setSelectedItem(filter.getSelectedAttribute());
+ } // end of else
+
+ attributeBox.addItemListener(this);
+ classBox.removeItemListener(this);
+ classBox.setSelectedItem(newClass);
+ classBox.addItemListener(this);
+ setSelectedAttribute((String) attributeBox.getSelectedItem());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void handleEvent(AWTEvent e) {
+ if (e.getSource() == nameField) {
+ setFilterName(nameField.getText());
+ } else {
+ if (e.getSource() == searchField) {
+ setSearchString(searchField.getText());
+ } else if (e.getSource() == nameField) {
+ setFilterName(nameField.getText());
+ } else if (e.getSource() == attributeBox) {
+ setSelectedAttribute((String) attributeBox.getSelectedItem());
+ } else if (e.getSource() == classBox) {
+ setSelectedClass((String) classBox.getSelectedItem());
+ }
+
+ updateName();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param ae DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent ae) {
+ handleEvent(ae);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void itemStateChanged(ItemEvent e) {
+ handleEvent(e);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void focusGained(FocusEvent e) {
+ }
+ ;
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void focusLost(FocusEvent e) {
+ handleEvent(e);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void updateName() {
+ StringBuffer buffer = new StringBuffer();
+ buffer.append(getSelectedClass() + " : ");
+ buffer.append(getSelectedAttribute() + " ~ ");
+ buffer.append(getSearchString());
+ setFilterName(buffer.toString());
+ }
+}
diff --git a/coreplugins/RFilters/src/main/java/filter/model/Filter.java b/coreplugins/RFilters/src/main/java/filter/model/Filter.java
new file mode 100644
index 0000000..f943385
--- /dev/null
+++ b/coreplugins/RFilters/src/main/java/filter/model/Filter.java
@@ -0,0 +1,126 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package filter.model;
+
+import filter.view.FilterEditor;
+
+import java.beans.PropertyChangeListener;
+
+import javax.swing.event.SwingPropertyChangeSupport;
+
+
+/**
+ *
+ */
+public interface Filter {
+ /**
+ *
+ */
+ public static String FILTER_MODIFIED = "FILTER_MODIFIED";
+
+ /**
+ * Note that to truly pass this Filter an object must <b>both</b> be an
+ * instance of at least one of the passingTypes (unless {@link
+ * #getPassingTypes()} returns null) <i>and</i> passesFilter( object ).
+ * @see FilterUtilities#passesFilter( Filter, Object )
+ * @return true iff the given Object passes the filter.
+ */
+ public boolean passesFilter(Object object);
+
+ /**
+ * @return an array of Classes; all passers of this filter must be an
+ * instance of at least one of these classes; null if all object types could
+ * potentially pass this filter.
+ */
+ public Class[] getPassingTypes();
+
+ /**
+ * @return the name of this Filter.
+ */
+ public String toString();
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getFilterID();
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getDescription();
+
+ /**
+ * Every filter needs to know how to output itself in such a way that
+ * it knows how to re-create itself from a flat file.<BR>
+ * The required format is: <BR>
+ * Filter <I>class name</I> <B><small>whatever a filter wants</small></B>
+ */
+ public String output();
+
+ /**
+ * By passing a String that was ouput by this Filter it will create and return
+ * a new Filter that is equivalent to the instance that was output. Note that
+ * the output is modifiable, so that one could change how a Filter behaves if
+ * they wanted to.
+ */
+ public void input(String desc);
+
+ /**
+ * All filters should override the Object equals(..) method to return true
+ * when compared to an equivalent filter. This method should <b>not</b> call
+ * passesFilter(..) on this or on the given object.
+ * @see #hashCode()
+ */
+ public boolean equals(Object other_object);
+
+ /**
+ * All filters should implement the clone() method, as Filters will be
+ * cloned.
+ */
+ public Object clone();
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public SwingPropertyChangeSupport getSwingPropertyChangeSupport();
+} // interface Filter
diff --git a/coreplugins/RFilters/src/main/java/filter/model/FilterEditorManager.java b/coreplugins/RFilters/src/main/java/filter/model/FilterEditorManager.java
new file mode 100644
index 0000000..70a0d13
--- /dev/null
+++ b/coreplugins/RFilters/src/main/java/filter/model/FilterEditorManager.java
@@ -0,0 +1,136 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package filter.model;
+
+import filter.view.*;
+
+import java.util.*;
+
+import javax.swing.*;
+import javax.swing.event.SwingPropertyChangeSupport;
+
+
+/**
+ *
+ */
+public class FilterEditorManager {
+ protected static FilterEditorManager DEFAULT_MANAGER;
+ protected Vector editorList;
+ protected HashMap class2Editor;
+
+ /**
+ * PCS support
+ */
+ protected SwingPropertyChangeSupport pcs = new SwingPropertyChangeSupport(this);
+
+ /**
+ * Returns the Default Filter Manager
+ */
+ public static FilterEditorManager defaultManager() {
+ if (DEFAULT_MANAGER == null) {
+ DEFAULT_MANAGER = new FilterEditorManager();
+ }
+
+ return DEFAULT_MANAGER;
+ }
+
+ private FilterEditorManager() {
+ editorList = new Vector();
+ class2Editor = new HashMap();
+ }
+
+ /**
+ * PCS Support
+ */
+ public SwingPropertyChangeSupport getSwingPropertyChangeSupport() {
+ return pcs;
+ }
+
+ // Editor Methods
+ /**
+ * DOCUMENT ME!
+ *
+ * @param editor DOCUMENT ME!
+ */
+ public void addEditor(FilterEditor editor) {
+ editorList.add(editor);
+ class2Editor.put(editor.getFilterClass(), editor);
+
+ // fireEditorEvent();
+ //pcs.firePropertyChange( EDITOR_ADDED, null, editor );
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param editor DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean removeEditor(FilterEditor editor) {
+ return editorList.remove(editor);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Iterator getEditors() {
+ return editorList.iterator();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getEditorCount() {
+ return editorList.size();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param f DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public FilterEditor getEditorForFilter(Filter f) {
+ return (FilterEditor) class2Editor.get(f.getClass());
+ }
+}
diff --git a/coreplugins/RFilters/src/main/java/filter/model/FilterManager.java b/coreplugins/RFilters/src/main/java/filter/model/FilterManager.java
new file mode 100644
index 0000000..542b954
--- /dev/null
+++ b/coreplugins/RFilters/src/main/java/filter/model/FilterManager.java
@@ -0,0 +1,393 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package filter.model;
+
+import cern.colt.map.OpenIntObjectHashMap;
+
+import filter.view.*;
+
+import java.beans.*;
+
+import java.util.*;
+
+import javax.swing.*;
+import javax.swing.event.*;
+
+
+/**
+ *
+ */
+public class FilterManager implements ListModel, PropertyChangeListener {
+ protected static FilterManager DEFAULT_MANAGER;
+
+ /**
+ *
+ */
+ public static String FILTER_EVENT = "FILTER_EVENT";
+ protected Vector filterList;
+ protected OpenIntObjectHashMap ID2Filter;
+ protected HashMap Filter2ID;
+ Object selectedItem;
+
+ /**
+ * PCS support
+ */
+ protected SwingPropertyChangeSupport pcs = new SwingPropertyChangeSupport(this);
+
+ /**
+ * Returns the Default Filter Manager
+ */
+ public static FilterManager defaultManager() {
+ if (DEFAULT_MANAGER == null) {
+ DEFAULT_MANAGER = new FilterManager();
+ }
+
+ return DEFAULT_MANAGER;
+ }
+
+ private FilterManager() {
+ filterList = new Vector();
+ ID2Filter = new OpenIntObjectHashMap();
+ Filter2ID = new HashMap();
+
+ // Add the Select All filter before anything else.
+ // This is needed by the NodeTopologyFilter
+ addFilter(new filter.cytoscape.SelectAllFilter());
+ }
+
+ //----------------------------------------//
+ // PCS Methods
+
+ /**
+ * PCS Support
+ */
+ public SwingPropertyChangeSupport getSwingPropertyChangeSupport() {
+ return pcs;
+ }
+
+ /**
+ *Create a new combobox model
+ *that other classes can use to display
+ *the list of filters in a combobox. Note that we
+ *want a separate model for each combobox, because the data
+ *model keeps track of the selected item. The returned combobox will
+ * basically be a wrapper around the list model which they all will share
+ */
+ public ComboBoxModel getComboBoxModel() {
+ return new ComboBoxModel() {
+ Object selectedItem;
+
+ //implements ListModel
+ Vector listeners = new Vector();
+
+ public void addListDataListener(ListDataListener l) {
+ listeners.add(l);
+ }
+
+ public void removeListDataListener(ListDataListener l) {
+ listeners.remove(l);
+ }
+
+ public Object getSelectedItem() {
+ return selectedItem;
+ }
+
+ public void setSelectedItem(java.lang.Object anItem) {
+ selectedItem = anItem;
+ }
+
+ public Object getElementAt(int index) {
+ return FilterManager.this.getElementAt(index);
+ }
+
+ public int getSize() {
+ return FilterManager.this.getSize();
+ }
+ };
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void fireFilterEvent() {
+ pcs.firePropertyChange(FILTER_EVENT, null, null);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void notifyListeners(ListDataEvent e) {
+ for (Iterator listenIt = listeners.iterator(); listenIt.hasNext();) {
+ if (e.getType() == ListDataEvent.CONTENTS_CHANGED) {
+ ((ListDataListener) listenIt.next()).contentsChanged(e);
+ } else if (e.getType() == ListDataEvent.INTERVAL_ADDED) {
+ ((ListDataListener) listenIt.next()).intervalAdded(e);
+ } else if (e.getType() == ListDataEvent.INTERVAL_REMOVED) {
+ ((ListDataListener) listenIt.next()).intervalRemoved(e);
+ }
+ }
+ }
+
+ /**
+ * Add a filter and assign it the given unique ID
+ */
+ public void addFilter(Filter filter, int ID) {
+ if (ID < 0) {
+ throw new IllegalArgumentException("ID must be greater than 0");
+ }
+
+ if (ID2Filter.containsKey(ID)) {
+ throw new IllegalArgumentException("ID map already contains that ID");
+ }
+
+ ID2Filter.put(ID, filter);
+ Filter2ID.put(filter, new Integer(ID));
+ filterList.add(filter);
+ //System.out.println( "Filter list added: "+filter );
+ filter.getSwingPropertyChangeSupport().addPropertyChangeListener(this);
+ notifyListeners(new ListDataEvent(this, ListDataEvent.INTERVAL_ADDED, filterList.size(),
+ filterList.size()));
+ fireFilterEvent();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param filter DOCUMENT ME!
+ */
+ public void addFilter(Filter filter) {
+ //let's hope we don't have many filters, otherwise
+ int ID = 0;
+
+ while (ID2Filter.containsKey(ID)) {
+ ID++;
+ }
+
+ addFilter(filter, ID);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param filter DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean removeFilter(Filter filter) {
+ int index = filterList.indexOf(filter);
+
+ // If it's 0, assume that it's the SelectAllFilter, which we don't want to delete.
+ if (index <= 0) {
+ return false;
+ }
+
+ int ID = ((Integer) Filter2ID.get(filter)).intValue();
+ ID2Filter.removeKey(ID);
+ Filter2ID.remove(filter);
+ filterList.remove(filter);
+ notifyListeners(new ListDataEvent(this, ListDataEvent.INTERVAL_REMOVED, index, index));
+ filter.getSwingPropertyChangeSupport().removePropertyChangeListener(this);
+ fireFilterEvent();
+
+ return true;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param f DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getFilterID(Filter f) {
+ if (f == null) {
+ return -1;
+ }
+
+ return ((Integer) Filter2ID.get(f)).intValue();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param ID DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Filter getFilter(int ID) {
+ return (Filter) ID2Filter.get(ID);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Iterator getFilters() {
+ return filterList.iterator();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getFilterCount() {
+ return filterList.size();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param item DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int indexOf(Object item) {
+ return filterList.indexOf(item);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param desc DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Filter createFilterFromString(String desc) {
+ String[] array = desc.split("\t");
+
+ if (array[1].equals("class filter.cytoscape.StringPatternFilter")) {
+ //System.out.println( "Found String Filter" );
+ Filter new_filter = new filter.cytoscape.StringPatternFilter(array[2]);
+ addFilter(new_filter); //, (new Integer(array[0])).intValue() );
+
+ return new_filter;
+ } else if (array[1].equals("class filter.cytoscape.NumericAttributeFilter")) {
+ //System.out.println( "Found Numeric Filter" );
+ Filter new_filter = new filter.cytoscape.NumericAttributeFilter(array[2]);
+ addFilter(new_filter); //, (new Integer(array[0])).intValue());
+
+ return new_filter;
+ } else if (array[1].equals("class filter.cytoscape.NodeInteractionFilter")) {
+ Filter new_filter = new filter.cytoscape.NodeInteractionFilter(array[2]);
+ addFilter(new_filter); //, (new Integer(array[0])).intValue());
+
+ return new_filter;
+ } else if (array[1].equals("class filter.cytoscape.EdgeInteractionFilter")) {
+ Filter new_filter = new filter.cytoscape.EdgeInteractionFilter(array[2]);
+ addFilter(new_filter); //, (new Integer(array[0])).intValue());
+
+ return new_filter;
+ } else if (array[1].equals("class filter.cytoscape.NodeTopologyFilter")) {
+ Filter new_filter = new filter.cytoscape.NodeTopologyFilter(array[2]);
+ addFilter(new_filter); //, (new Integer(array[0])).intValue());
+
+ return new_filter;
+ } else if (array[1].equals("class filter.cytoscape.BooleanMetaFilter")) {
+ Filter new_filter = new filter.cytoscape.BooleanMetaFilter(array[2]);
+ addFilter(new_filter); //, (new Integer(array[0])).intValue());
+
+ return new_filter;
+ } // end of if ()
+
+ return null;
+ }
+
+ //implements PropertyChange
+ /**
+ * DOCUMENT ME!
+ *
+ * @param pce DOCUMENT ME!
+ */
+ public void propertyChange(PropertyChangeEvent pce) {
+ //the only thing we're really listening to here shoudl be the filters,
+ //we check which one is sending the event, and then let the list know that
+ //the contents of that filter have possibly changed
+ Filter filter = (Filter) pce.getSource();
+ int index = filterList.indexOf(filter);
+
+ if (index > -1) {
+ notifyListeners(new ListDataEvent(this, ListDataEvent.CONTENTS_CHANGED, 0,
+ filterList.size()));
+ fireFilterEvent();
+ }
+ }
+
+ //implements ListModel
+ Vector listeners = new Vector();
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param l DOCUMENT ME!
+ */
+ public void addListDataListener(ListDataListener l) {
+ listeners.add(l);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param index DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getElementAt(int index) {
+ return filterList.elementAt(index);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getSize() {
+ return getFilterCount();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param l DOCUMENT ME!
+ */
+ public void removeListDataListener(ListDataListener l) {
+ listeners.remove(l);
+ }
+}
diff --git a/coreplugins/RFilters/src/main/java/filter/view/CreateFilterDialog.java b/coreplugins/RFilters/src/main/java/filter/view/CreateFilterDialog.java
new file mode 100644
index 0000000..735a1eb
--- /dev/null
+++ b/coreplugins/RFilters/src/main/java/filter/view/CreateFilterDialog.java
@@ -0,0 +1,154 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package filter.view;
+
+import filter.model.*;
+
+import java.awt.BorderLayout;
+import java.awt.Dimension;
+import java.awt.event.*;
+
+import java.util.Iterator;
+import java.util.Vector;
+
+import javax.swing.JButton;
+import javax.swing.JDialog;
+import javax.swing.JList;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTextArea;
+import javax.swing.JTextField;
+import javax.swing.border.TitledBorder;
+import javax.swing.event.ListSelectionEvent;
+import javax.swing.event.ListSelectionListener;
+
+
+/**
+ *
+ */
+public class CreateFilterDialog extends JDialog {
+ FilterEditorManager filterManager;
+ JList filterEditorList;
+ JTextField nameField;
+
+ /**
+ * Creates a new CreateFilterDialog object.
+ *
+ * @param filterManager DOCUMENT ME!
+ */
+ public CreateFilterDialog(FilterEditorManager filterManager) {
+ this.filterManager = filterManager;
+ initializeDialog();
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void initializeDialog() {
+ setModal(true);
+ setTitle("Filter Creation Dialog");
+ getContentPane().setLayout(new BorderLayout());
+ filterEditorList = new JList();
+
+ Vector listItems = new Vector();
+
+ for (Iterator editorIt = filterManager.getEditors(); editorIt.hasNext();) {
+ listItems.add(editorIt.next());
+ }
+
+ filterEditorList = new JList(listItems);
+
+ JPanel westPanel = new JPanel(new BorderLayout());
+ westPanel.add(new JScrollPane(filterEditorList), BorderLayout.CENTER);
+ westPanel.setBorder(new TitledBorder("Filter types"));
+ getContentPane().add(westPanel, BorderLayout.WEST);
+
+ //westPanel.setPreferredSize(new Dimension(100,150));
+ DescriptionPanel descriptionPanel = new DescriptionPanel(filterEditorList);
+ filterEditorList.addListSelectionListener(descriptionPanel);
+ getContentPane().add(descriptionPanel, BorderLayout.CENTER);
+
+ JPanel southPanel = new JPanel();
+ JButton goButton = new JButton("OK");
+ //getContentPane().add(goButton,BorderLayout.SOUTH);
+ goButton.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent ae) {
+ //first get the selected editor type
+ FilterEditor selectedEditor = (FilterEditor) filterEditorList.getSelectedValue();
+ Filter newFilter = selectedEditor.createDefaultFilter();
+ FilterManager.defaultManager().addFilter(newFilter);
+ CreateFilterDialog.this.setVisible(false);
+
+ //NodeTopologyFilterEditor is a special case, since there is only one instance for each editor,
+ //and the model for the combobox in NodeTopologyFilterEditor must keep update if more than one filter
+ //is created
+ if (selectedEditor.getClass().getName()
+ .equals("filter.cytoscape.NodeTopologyFilterEditor")) {
+ ((filter.cytoscape.NodeTopologyFilterEditor) filterEditorList
+ .getSelectedValue())
+ .resetFilterBoxModel();
+ }
+ }
+ });
+ southPanel.add(goButton);
+ getContentPane().add(southPanel, BorderLayout.SOUTH);
+ pack();
+ filterEditorList.setSelectedIndex(0);
+ }
+
+ class DescriptionPanel extends JPanel implements ListSelectionListener {
+ JTextArea descriptionField;
+
+ public DescriptionPanel(JList filterEditorList) {
+ filterEditorList.addListSelectionListener(this);
+ descriptionField = new JTextArea();
+ descriptionField.setLineWrap(true);
+ descriptionField.setWrapStyleWord(true);
+ descriptionField.setBackground(getBackground());
+ setLayout(new BorderLayout());
+ add(descriptionField, BorderLayout.CENTER);
+ setBorder(new TitledBorder("Filter Type Description"));
+ setPreferredSize(new Dimension(200, 150));
+ }
+
+ public void valueChanged(ListSelectionEvent e) {
+ JList filterEditorList = (JList) e.getSource();
+ FilterEditor currentEditor = (FilterEditor) filterEditorList.getSelectedValue();
+ descriptionField.setText(currentEditor.getDescription());
+ }
+ }
+}
diff --git a/coreplugins/RFilters/src/main/java/filter/view/FilterEditor.java b/coreplugins/RFilters/src/main/java/filter/view/FilterEditor.java
new file mode 100644
index 0000000..b92a351
--- /dev/null
+++ b/coreplugins/RFilters/src/main/java/filter/view/FilterEditor.java
@@ -0,0 +1,102 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package filter.view;
+
+import filter.model.*;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import java.beans.*;
+
+import java.util.*;
+
+import javax.swing.*;
+import javax.swing.border.*;
+import javax.swing.event.*;
+
+
+/**
+ *
+ */
+public abstract class FilterEditor extends JPanel {
+ protected SwingPropertyChangeSupport pcs = new SwingPropertyChangeSupport(this);
+
+ /**
+ * Creates a new FilterEditor object.
+ */
+ public FilterEditor() {
+ super();
+ }
+
+ /**
+ * Return the Description of this Editor that will
+ * go into its tab
+ */
+ public abstract String getFilterID();
+
+ /**
+ * Return a user friendly description of the class of filters edited by this editor
+ */
+ public abstract String getDescription();
+
+ /**
+ * This Editor should be able to read in a Filter that it produced
+ * and redisplay that Filter in the Editor, so that the Filter can be
+ * edited.
+ */
+ public abstract void editFilter(Filter filter);
+
+ /**
+ * Create a filter initialized to the proper default values
+ */
+ public abstract Filter createDefaultFilter();
+
+ /**
+ * Return the class of filter subclass that I actually want to edit
+ */
+ public abstract Class getFilterClass();
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public SwingPropertyChangeSupport getSwingPropertyChangeSupport() {
+ return pcs;
+ }
+}
diff --git a/coreplugins/RFilters/src/main/java/filter/view/FilterEditorPanel.java b/coreplugins/RFilters/src/main/java/filter/view/FilterEditorPanel.java
new file mode 100644
index 0000000..d6d6518
--- /dev/null
+++ b/coreplugins/RFilters/src/main/java/filter/view/FilterEditorPanel.java
@@ -0,0 +1,156 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package filter.view;
+
+import ViolinStrings.Strings;
+
+import filter.model.*;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import java.beans.*;
+
+import java.util.*;
+
+import javax.swing.*;
+import javax.swing.border.*;
+import javax.swing.event.*;
+import javax.swing.event.SwingPropertyChangeSupport;
+
+
+/**
+ * Provides a tabbed Interface for creating filters of all available
+ * filter editors that have been provided.
+ */
+public class FilterEditorPanel extends JPanel implements PropertyChangeListener {
+ /**
+ *
+ */
+ public FilterEditor nullEdit;
+
+ /**
+ *
+ */
+ public static String ACTIVE_PANEL_CHANGED = "Active Panel Changed";
+ JPanel currentEditor;
+ JPanel defaultPanel;
+ PropertyChangeSupport pcs;
+
+ /**
+ * Creates a new FilterEditorPanel object.
+ */
+ public FilterEditorPanel() {
+ super();
+ initialize();
+ pcs = new PropertyChangeSupport(this);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void initialize() {
+ defaultPanel = new DefaultPanel();
+ currentEditor = defaultPanel;
+ nullEdit = new NullFilterEditor();
+ //Change the layout manager,to let the panel stretch to fill the available space
+ setLayout(new BorderLayout());
+ add(currentEditor);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public PropertyChangeSupport getPropertyChangeSupport() {
+ return pcs;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param editor DOCUMENT ME!
+ */
+ public void setActivePanel(JPanel editor) {
+ remove(currentEditor);
+ add(editor);
+ validate();
+ paint(getGraphics());
+ currentEditor = editor;
+ pcs.firePropertyChange(ACTIVE_PANEL_CHANGED, null, null);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void propertyChange(PropertyChangeEvent e) {
+ if (e.getPropertyName() == FilterListPanel.FILTER_SELECTED) {
+ Filter f = ((FilterListPanel) e.getSource()).getSelectedFilter();
+ FilterEditor editor = FilterEditorManager.defaultManager().getEditorForFilter(f);
+
+ if (editor == null) {
+ editor = nullEdit;
+ }
+
+ editor.editFilter(f);
+ setActivePanel(editor);
+ } else if (e.getPropertyName() == FilterListPanel.NO_SELECTION) {
+ setActivePanel(defaultPanel);
+ }
+ }
+}
+
+
+class DefaultPanel extends JPanel {
+ /**
+ * Creates a new DefaultPanel object.
+ */
+ public DefaultPanel() {
+ JTextArea text = new JTextArea();
+ text.setLineWrap(true);
+ text.setWrapStyleWord(true);
+ text.setEditable(false);
+ text.setText("There is no filter currently selected. To edit a filter, select it from the \"Available filters\" list. If the list is empty, you can create a new filter with the \"Create new filter\" button.");
+ text.setColumns(25);
+ text.setBackground(this.getBackground());
+ setLayout(new BorderLayout());
+ add(text, BorderLayout.CENTER);
+ }
+}
diff --git a/coreplugins/RFilters/src/main/java/filter/view/FilterListBox.java b/coreplugins/RFilters/src/main/java/filter/view/FilterListBox.java
new file mode 100644
index 0000000..c01c5e5
--- /dev/null
+++ b/coreplugins/RFilters/src/main/java/filter/view/FilterListBox.java
@@ -0,0 +1,177 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package filter.view;
+
+import ViolinStrings.Strings;
+
+import filter.model.*;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import java.beans.*;
+
+import java.util.*;
+
+import javax.swing.*;
+import javax.swing.border.*;
+import javax.swing.event.*;
+import javax.swing.event.SwingPropertyChangeSupport;
+
+
+/**
+ * A FilterListPanel will
+ * be able to search through its contents based on the Filter title using
+ * wildcard search
+ */
+public class FilterListBox extends JPanel implements PropertyChangeListener, ListSelectionListener,
+ ListDataListener {
+ JComboBox filterBox;
+
+ /**
+ *
+ */
+ public static String FILTER_SELECTED = "FILTER_SELECTED";
+
+ /**
+ *
+ */
+ public static String NO_SELECTION = "NO_SELECTION";
+ protected SwingPropertyChangeSupport pcs = new SwingPropertyChangeSupport(this);
+
+ /**
+ * Creates a new FilterListBox object.
+ */
+ public FilterListBox() {
+ super();
+ initialize();
+ }
+
+ protected void initialize() {
+ FilterManager.defaultManager().getSwingPropertyChangeSupport()
+ .addPropertyChangeListener(this);
+
+ JPanel listPanel = new JPanel();
+ //listPanel.setBorder( new TitledBorder( "Available Filters" ) );
+
+ //FilterManager.defaultManager().addListDataListener(this);
+ filterBox = new JComboBox(FilterManager.defaultManager().getComboBoxModel());
+ //filterBox.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
+ //filterBox.addListSelectionListener( this );
+
+ //JScrollPane scroll = new JScrollPane( filterBox );
+ //listPanel.add( scroll, BorderLayout.CENTER);
+ //setLayout( new BorderLayout() );
+ //add( listPanel, BorderLayout.CENTER );
+ //scroll.setPreferredSize(new Dimension(250,100));
+ add(filterBox);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public SwingPropertyChangeSupport getSwingPropertyChangeSupport() {
+ return pcs;
+ }
+
+ protected void fireFilterSelected() {
+ pcs.firePropertyChange(FILTER_SELECTED, null, null);
+ }
+
+ protected void handleEvent(EventObject e) {
+ if (filterBox.getSelectedItem() == null) {
+ pcs.firePropertyChange(NO_SELECTION, null, null);
+ } else {
+ pcs.firePropertyChange(FILTER_SELECTED, null, null);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void valueChanged(ListSelectionEvent e) {
+ handleEvent(e);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void contentsChanged(ListDataEvent e) {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void intervalAdded(ListDataEvent e) {
+ handleEvent(e);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void intervalRemoved(ListDataEvent e) {
+ handleEvent(e);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Filter getSelectedFilter() {
+ return (Filter) filterBox.getSelectedItem();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void propertyChange(PropertyChangeEvent e) {
+ //updateLists();
+ }
+}
diff --git a/coreplugins/RFilters/src/main/java/filter/view/FilterListPanel.java b/coreplugins/RFilters/src/main/java/filter/view/FilterListPanel.java
new file mode 100644
index 0000000..89bc627
--- /dev/null
+++ b/coreplugins/RFilters/src/main/java/filter/view/FilterListPanel.java
@@ -0,0 +1,187 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package filter.view;
+
+import ViolinStrings.Strings;
+
+import filter.model.*;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import java.beans.*;
+
+import java.util.*;
+
+import javax.swing.*;
+import javax.swing.border.*;
+import javax.swing.event.*;
+import javax.swing.event.SwingPropertyChangeSupport;
+
+
+/**
+ * A FilterListPanel will
+ * be able to search through its contents based on the Filter title using
+ * wildcard search
+ */
+public class FilterListPanel extends JPanel implements PropertyChangeListener,
+ ListSelectionListener, ListDataListener {
+ JList filterList;
+ DefaultListModel filterModel;
+
+ /**
+ *
+ */
+ public static String FILTER_SELECTED = "FILTER_SELECTED";
+
+ /**
+ *
+ */
+ public static String NO_SELECTION = "NO_SELECTION";
+ protected SwingPropertyChangeSupport pcs = new SwingPropertyChangeSupport(this);
+
+ /**
+ * Creates a new FilterListPanel object.
+ */
+ public FilterListPanel() {
+ super();
+ initialize();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public JList getFilterList() {
+ return filterList;
+ }
+
+ protected void initialize() {
+ FilterManager.defaultManager().getSwingPropertyChangeSupport()
+ .addPropertyChangeListener(this);
+
+ JPanel listPanel = new JPanel(new BorderLayout());
+ listPanel.setBorder(new TitledBorder("Available Filters"));
+
+ //FilterManager.defaultManager().addListDataListener(this);
+ filterList = new JList(FilterManager.defaultManager());
+ filterList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
+ filterList.addListSelectionListener(this);
+
+ JScrollPane scroll = new JScrollPane(filterList);
+ listPanel.add(scroll, BorderLayout.CENTER);
+ setLayout(new BorderLayout());
+ add(listPanel, BorderLayout.CENTER);
+
+ //scroll.setPreferredSize(new Dimension(250,100));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public SwingPropertyChangeSupport getSwingPropertyChangeSupport() {
+ return pcs;
+ }
+
+ protected void fireFilterSelected() {
+ pcs.firePropertyChange(FILTER_SELECTED, null, null);
+ }
+
+ protected void handleEvent(EventObject e) {
+ if (filterList.getSelectedValue() == null) {
+ pcs.firePropertyChange(NO_SELECTION, null, null);
+ } else {
+ pcs.firePropertyChange(FILTER_SELECTED, null, null);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void valueChanged(ListSelectionEvent e) {
+ handleEvent(e);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void contentsChanged(ListDataEvent e) {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void intervalAdded(ListDataEvent e) {
+ handleEvent(e);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void intervalRemoved(ListDataEvent e) {
+ handleEvent(e);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Filter getSelectedFilter() {
+ return (Filter) filterList.getSelectedValue();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void propertyChange(PropertyChangeEvent e) {
+ //updateLists();
+ }
+}
diff --git a/coreplugins/RFilters/src/main/java/filter/view/FilterView.java b/coreplugins/RFilters/src/main/java/filter/view/FilterView.java
new file mode 100644
index 0000000..17731ef
--- /dev/null
+++ b/coreplugins/RFilters/src/main/java/filter/view/FilterView.java
@@ -0,0 +1,108 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package filter.view;
+
+import filter.model.*;
+
+import javax.swing.*;
+import javax.swing.tree.*;
+
+
+//import giny.model.*;
+/**
+ *
+ */
+public class FilterView extends JPanel {
+ //FilterEditorPanel filterEditorPanel;
+ FilterListPanel filterListPanel;
+
+ /**
+ * Creates a new FilterView object.
+ */
+ public FilterView() {
+ super();
+
+ initialize();
+ }
+
+ protected void initialize() {
+ //filterEditorPanel = new FilterEditorPanel();
+ filterListPanel = new FilterListPanel();
+ //JSplitPane pane0 = new JSplitPane( JSplitPane.VERTICAL_SPLIT, filterEditorPanel, filterListPanel );
+
+ //add( pane0 );
+ add(filterListPanel);
+
+ //filterListPanel.getSwingPropertyChangeSupport().addPropertyChangeListener( filterEditorPanel );
+ //FilterManager.defaultManager().addEditor( new DefaultFilterEditor() );
+ //FilterManager.defaultManager().addEditor( new FilterTreeEditor() );
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ */
+ public static void main(String[] args) {
+ if (System.getProperty("os.name").startsWith("Windows")) {
+ try {
+ UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
+ } catch (Exception e) {
+ // TODO: Error handling.
+ System.err.println("Hey. Error loading L&F: on Windows");
+
+ // TODO: REMOVE
+ // e.printStackTrace();
+ }
+ } else {
+ try {
+ UIManager.setLookAndFeel("com.sun.java.swing.plaf.gtk.GTKLookAndFeel");
+ } catch (Exception e) {
+ // TODO: Error handling.
+ System.err.println("Hey. Error loading L&F: on NOT Windows");
+
+ // TODO: REMOVE
+ //e.printStackTrace();
+ }
+ }
+
+ JFrame frame = new JFrame("Filters");
+ frame.getContentPane().add(new FilterView());
+ frame.pack();
+ frame.setVisible(true);
+ }
+}
diff --git a/coreplugins/RFilters/src/main/java/filter/view/NullFilterEditor.java b/coreplugins/RFilters/src/main/java/filter/view/NullFilterEditor.java
new file mode 100644
index 0000000..9918bd2
--- /dev/null
+++ b/coreplugins/RFilters/src/main/java/filter/view/NullFilterEditor.java
@@ -0,0 +1,100 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package filter.view;
+
+import filter.model.*;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import java.beans.*;
+
+import java.util.*;
+
+import javax.swing.*;
+import javax.swing.border.*;
+import javax.swing.event.*;
+
+
+/**
+ *
+ */
+public class NullFilterEditor extends FilterEditor {
+ /**
+ * Creates a new NullFilterEditor object.
+ */
+ public NullFilterEditor() {
+ add(new JLabel("There is no Editor for this Filter"));
+ }
+
+ /**
+ * Return the Description of this Editor that will
+ * go into its tab
+ */
+ public String getFilterID() {
+ return "";
+ }
+
+ /**
+ * Return a user friendly description of the class of filters edited by this editor
+ */
+ public String getDescription() {
+ return "";
+ }
+
+ /**
+ * This Editor should be able to read in a Filter that it produced
+ * and redisplay that Filter in the Editor, so that the Filter can be
+ * edited.
+ */
+ public void editFilter(Filter filter) {
+ }
+
+ /**
+ * Create a filter initialized to the proper default values
+ */
+ public Filter createDefaultFilter() {
+ return null;
+ }
+
+ /**
+ * Return the class of filter subclass that I actually want to edit
+ */
+ public Class getFilterClass() {
+ return null;
+ }
+}
diff --git a/coreplugins/RFilters/src/main/resources/filter/cytoscape/plugin.props b/coreplugins/RFilters/src/main/resources/filter/cytoscape/plugin.props
new file mode 100644
index 0000000..eda1358
--- /dev/null
+++ b/coreplugins/RFilters/src/main/resources/filter/cytoscape/plugin.props
@@ -0,0 +1,29 @@
+# This props file would be filled out and included in the plugin jar file. This props file will be used
+# to put information into the Plugin Manager about the plugin
+
+# -- The following properties are REQUIRED -- #
+
+# The plugin name that will be displayed to users
+pluginName=Old Filters
+
+# Description used to give users information about the plugin such as what it does.
+# Html tags are encouraged for formatting purposes.
+pluginDescription=Cytoscape's old filter functionality.
+
+# Plugin version number, this must be two numbers separated by a decimlal. Ex. 0.2, 14.03
+pluginVersion=2.0
+
+# Compatible Cytoscape version
+cytoscapeVersion=2.5,2.6,2.7,2.8
+
+# Category, use one of the categories listed on the website or create your own
+pluginCategory=Core
+
+
+# List of authors. Note each author and institution pair are separated by a : (colon)
+# each additional author institution pair must be separated from other pairs bye a ; (semicolon)
+pluginAuthorsIntsitutions=Rowan Christmas:ISB;Ryan Kelley:UCSD
+
+# -- The following properties should be set ONLY BY CORE PLUGINS -- #
+downloadURL=http://cytoscape.org/plugins/plugins.xml
+uniqueID=7
diff --git a/coreplugins/RFilters/src/main/resources/filter16.gif b/coreplugins/RFilters/src/main/resources/filter16.gif
new file mode 100755
index 0000000..cfc477b
Binary files /dev/null and b/coreplugins/RFilters/src/main/resources/filter16.gif differ
diff --git a/coreplugins/RFilters/src/main/resources/filter36.gif b/coreplugins/RFilters/src/main/resources/filter36.gif
new file mode 100755
index 0000000..631ee93
Binary files /dev/null and b/coreplugins/RFilters/src/main/resources/filter36.gif differ
diff --git a/coreplugins/RFilters/src/main/resources/stock_filter-data-by-criteria-16.png b/coreplugins/RFilters/src/main/resources/stock_filter-data-by-criteria-16.png
new file mode 100644
index 0000000..ba4d92e
Binary files /dev/null and b/coreplugins/RFilters/src/main/resources/stock_filter-data-by-criteria-16.png differ
diff --git a/coreplugins/RFilters/src/main/resources/stock_filter-data-by-criteria.png b/coreplugins/RFilters/src/main/resources/stock_filter-data-by-criteria.png
new file mode 100644
index 0000000..bcf0fbb
Binary files /dev/null and b/coreplugins/RFilters/src/main/resources/stock_filter-data-by-criteria.png differ
diff --git a/coreplugins/SBMLReader/pom.xml b/coreplugins/SBMLReader/pom.xml
new file mode 100644
index 0000000..44daa7a
--- /dev/null
+++ b/coreplugins/SBMLReader/pom.xml
@@ -0,0 +1,64 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>parent</artifactId>
+ <version>2.8.4-SNAPSHOT</version>
+ </parent>
+
+ <artifactId>sbml-reader</artifactId>
+ <packaging>jar</packaging>
+
+ <name>SBML Reader</name>
+
+ <!-- bootstrap for cytoscape dependencies, namely the parent POM snapshots -->
+ <repositories>
+ <repository>
+ <id>cytoscape_snapshots</id>
+ <snapshots>
+ <enabled>true</enabled>
+ </snapshots>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <name>Cytoscape Snapshots</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/</url>
+ </repository>
+ <repository>
+ <id>cytoscape_releases</id>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ <name>Cytoscape Releases</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/releases/</url>
+ </repository>
+ </repositories>
+
+ <build>
+ <plugins>
+ <plugin>
+ <artifactId>maven-assembly-plugin</artifactId>
+ <configuration>
+ <archive>
+ <manifestEntries>
+ <Cytoscape-Plugin>sbmlreader.SBMLReaderPlugin</Cytoscape-Plugin>
+ </manifestEntries>
+ </archive>
+ </configuration>
+ </plugin>
+ </plugins>
+ </build>
+
+ <dependencies>
+ <dependency>
+ <groupId>cytoscape-temp</groupId>
+ <artifactId>sbml2</artifactId>
+ <version>1.0</version>
+ </dependency>
+ </dependencies>
+
+</project>
+
diff --git a/coreplugins/SBMLReader/src/main/java/sbmlreader/SBMLFilter.java b/coreplugins/SBMLReader/src/main/java/sbmlreader/SBMLFilter.java
new file mode 100644
index 0000000..ab3c7c8
--- /dev/null
+++ b/coreplugins/SBMLReader/src/main/java/sbmlreader/SBMLFilter.java
@@ -0,0 +1,124 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package sbmlreader;
+
+import cytoscape.data.ImportHandler;
+
+import cytoscape.data.readers.GraphReader;
+
+import cytoscape.util.CyFileFilter;
+
+import java.io.File;
+import java.io.IOException;
+
+
+/**
+ * SBMLReader extends CyFileFilter for integration into the Cytoscape ImportHandler
+ * framework.
+ *
+ */
+public class SBMLFilter extends CyFileFilter {
+ /**
+ * XGMML Files are Graphs.
+ */
+ private static String fileNature = ImportHandler.GRAPH_NATURE;
+
+ /**
+ * File Extensions.
+ */
+ private static String[] fileExtensions = { "xml", "sbml" };
+
+ /**
+ * Filter Description.
+ */
+ private static String description = "SBML files";
+
+ /**
+ * Constructor.
+ */
+ public SBMLFilter() {
+ super(fileExtensions, description, fileNature);
+ }
+
+ /**
+ * Indicates which files the SBMLFilter accepts.
+ * <p/>
+ * This method will return true only if:
+ * <UL>
+ * <LI>File ends in .xml or .sbml; and
+ * <LI>File headers includes the www.sbml.org namespace declaration.
+ * </UL>
+ *
+ * @param file File
+ * @return true or false.
+ */
+ public boolean accept(File file) {
+ String fileName = file.getName();
+ boolean firstPass = false;
+
+ // First test: file must end with one of the registered file extensions.
+ for (int i = 0; i < fileExtensions.length; i++) {
+ if (fileName.endsWith(fileExtensions[i])) {
+ firstPass = true;
+ }
+ }
+
+ if (firstPass) {
+ // Second test: file header must contain the biopax declaration
+ try {
+ String header = getHeader(file);
+
+ if (header.indexOf("www.sbml.org") > 0) {
+ return true;
+ }
+ } catch (IOException e) {
+ }
+ }
+
+ return false;
+ }
+
+ /**
+ * Gets the appropirate GraphReader object.
+ *
+ * @param fileName File Name.
+ * @return GraphReader Object.
+ */
+ public GraphReader getReader(String fileName) {
+ return new SBMLGraphReader(fileName);
+ }
+}
diff --git a/coreplugins/SBMLReader/src/main/java/sbmlreader/SBMLGraphReader.java b/coreplugins/SBMLReader/src/main/java/sbmlreader/SBMLGraphReader.java
new file mode 100644
index 0000000..4508204
--- /dev/null
+++ b/coreplugins/SBMLReader/src/main/java/sbmlreader/SBMLGraphReader.java
@@ -0,0 +1,290 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package sbmlreader;
+
+import cytoscape.CyEdge;
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+
+import cytoscape.data.CyAttributes;
+import cytoscape.data.Semantics;
+
+import cytoscape.data.readers.AbstractGraphReader;
+import cytoscape.data.readers.GraphReader;
+
+import cytoscape.view.CyNetworkView;
+import cytoscape.view.CytoscapeDesktop;
+
+import cytoscape.visual.*;
+
+import giny.model.Node;
+
+import giny.view.GraphView;
+import giny.view.NodeView;
+
+import jigcell.sbml2.*;
+
+import java.awt.Dimension;
+import java.awt.Toolkit;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+
+import java.net.URL;
+
+import java.util.*;
+
+import javax.swing.JFileChooser;
+import javax.swing.JOptionPane;
+
+
+/*
+ * Created on September 27, 2005, 9:23 AM
+ * This generates the Dialog for the loading of an SBML file and does the processing
+ * of the SBML file using the java SBML2 library.
+ */
+
+/**
+ * @author W.P.A. Ligtenberg, Eindhoven University of Technology
+ * @author Mike Smoot
+ */
+public class SBMLGraphReader extends AbstractGraphReader implements GraphReader {
+ ArrayList<Integer> nodeIds;
+ ArrayList<Integer> edgeIds;
+ URL fileURL;
+
+ /**
+ * Creates a new SBMLGraphReader object.
+ *
+ * @param filename DOCUMENT ME!
+ */
+ public SBMLGraphReader(String filename) {
+ super(filename);
+ fileURL = null;
+ }
+
+ /**
+ * Creates a new SBMLGraphReader object.
+ *
+ * @param url DOCUMENT ME!
+ */
+ public SBMLGraphReader(URL url) {
+ super(null);
+ fileURL = url;
+ fileName = null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws IOException DOCUMENT ME!
+ */
+ public void read() throws IOException {
+ InputStream instream;
+
+ if ((fileURL == null) && (fileName != null))
+ instream = new FileInputStream(fileName);
+ else if ((fileURL != null) && (fileName == null))
+ instream = fileURL.openStream();
+ else
+ throw new IOException("No file to open!");
+
+ // proces file
+ CyAttributes nodeAttributes = Cytoscape.getNodeAttributes();
+ CyAttributes edgeAttributes = Cytoscape.getEdgeAttributes();
+
+ nodeIds = new ArrayList<Integer>();
+ edgeIds = new ArrayList<Integer>();
+
+ SBMLLevel2Document document;
+
+ try {
+ document = SBMLLevel2Document.readDocument(instream);
+ } catch (IOException ioe) {
+ ioe.printStackTrace();
+ throw (ioe);
+ }
+
+ Model model = document.getModel();
+
+ // Get all the species in the network
+ List listOfSpecies = model.getSpecies();
+
+ for (Iterator i = listOfSpecies.iterator(); i.hasNext();) {
+ Species species = (Species) i.next();
+ CyNode node = Cytoscape.getCyNode(species.getId(), true);
+ nodeAttributes.setAttribute(species.getId(), "sbml name", species.getName());
+ nodeAttributes.setAttribute(species.getId(), "sbml type", "species");
+ nodeAttributes.setAttribute(species.getId(), "sbml id", species.getId());
+
+ // optional attrs, but they'll never be null
+ nodeAttributes.setAttribute(species.getId(), "sbml initial concentration",
+ new Double(species.getInitialConcentration()));
+ nodeAttributes.setAttribute(species.getId(), "sbml initial amount",
+ new Double(species.getInitialAmount()));
+ nodeAttributes.setAttribute(species.getId(), "sbml charge",
+ new Integer(species.getCharge()));
+
+ String comp = species.getCompartment();
+ if ( comp != null )
+ nodeAttributes.setAttribute(species.getId(), "sbml compartment", comp);
+
+ nodeIds.add(node.getRootGraphIndex());
+ }
+
+ // Get all reactions and create a node
+ List listOfReactions = model.getReactions();
+
+ for (Iterator i = listOfReactions.iterator(); i.hasNext();) {
+ Reaction reaction = (Reaction) i.next();
+ CyNode node = Cytoscape.getCyNode(reaction.getId(), true);
+ nodeAttributes.setAttribute(reaction.getId(), "sbml type", "reaction");
+ nodeAttributes.setAttribute(reaction.getId(), "sbml id", reaction.getId());
+
+ String rname = reaction.getName();
+ if ( rname != null )
+ nodeAttributes.setAttribute(reaction.getId(), "sbml name", rname);
+
+ nodeIds.add(node.getRootGraphIndex());
+
+ //Get all products and link them to the reaction node
+ List products = reaction.getProduct();
+
+ for (Iterator j = products.iterator(); j.hasNext();) {
+ SpeciesReference species = (SpeciesReference) j.next();
+ CyNode product = Cytoscape.getCyNode(species.getSpecies(), false);
+ CyEdge edge = Cytoscape.getCyEdge(node, product, Semantics.INTERACTION,
+ "reaction-product", true);
+ edgeIds.add(edge.getRootGraphIndex());
+ }
+
+ //Get all reactants and link them to the reaction node
+ List reactants = reaction.getReactant();
+
+ for (Iterator j = reactants.iterator(); j.hasNext();) {
+ SpeciesReference species = (SpeciesReference) j.next();
+ CyNode reactant = Cytoscape.getCyNode(species.getSpecies(), false);
+ CyEdge edge = Cytoscape.getCyEdge(node, reactant, Semantics.INTERACTION,
+ "reaction-reactant", true);
+ edgeIds.add(edge.getRootGraphIndex());
+ }
+
+ //Get all modifiers and link them to the reaction node
+ List modifiers = reaction.getModifier();
+
+ for (Iterator j = modifiers.iterator(); j.hasNext();) {
+ ModifierSpeciesReference species = (ModifierSpeciesReference) j.next();
+ CyNode modifier = Cytoscape.getCyNode(species.getSpecies(), false);
+ CyEdge edge = Cytoscape.getCyEdge(modifier, node, Semantics.INTERACTION,
+ "reaction-modifier", true);
+ edgeIds.add(edge.getRootGraphIndex());
+ }
+
+ KineticLaw law = reaction.getKineticLaw();
+
+ if ( law == null )
+ continue;
+
+ List<Parameter> parameters = law.getParameter();
+
+ if ( parameters == null )
+ continue;
+
+ for (Parameter p: parameters) {
+ String id = p.getName();
+ String units = p.getUnits();
+ double value = p.getValue();
+ nodeAttributes.setAttribute(reaction.getId(), "kineticLaw-"+id, new Double(value));
+ if (units != null)
+ nodeAttributes.setAttribute(reaction.getId(), "kineticLaw-"+id+"-units", units);
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param network DOCUMENT ME!
+ */
+ public void doPostProcessing(CyNetwork network) {
+ // Set SBML specific visual style
+ VisualMappingManager manager = Cytoscape.getVisualMappingManager();
+ CalculatorCatalog catalog = manager.getCalculatorCatalog();
+
+ VisualStyle vs = catalog.getVisualStyle(SBMLVisualStyleFactory.SBMLReader_VS);
+
+ if (vs == null) {
+ vs = SBMLVisualStyleFactory.createVisualStyle(network);
+ catalog.addVisualStyle(vs);
+ }
+
+ manager.setVisualStyle(vs);
+ Cytoscape.getCurrentNetworkView().setVisualStyle(vs.getName());
+ Cytoscape.getCurrentNetworkView().applyVizmapper(vs);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] getNodeIndicesArray() {
+ int[] nodes = new int[nodeIds.size()];
+
+ for (int i = 0; i < nodes.length; i++)
+ nodes[i] = nodeIds.get(i).intValue();
+
+ return nodes;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] getEdgeIndicesArray() {
+ int[] edges = new int[edgeIds.size()];
+
+ for (int i = 0; i < edges.length; i++)
+ edges[i] = edgeIds.get(i).intValue();
+
+ return edges;
+ }
+}
diff --git a/coreplugins/SBMLReader/src/main/java/sbmlreader/SBMLReaderPlugin.java b/coreplugins/SBMLReader/src/main/java/sbmlreader/SBMLReaderPlugin.java
new file mode 100644
index 0000000..673a771
--- /dev/null
+++ b/coreplugins/SBMLReader/src/main/java/sbmlreader/SBMLReaderPlugin.java
@@ -0,0 +1,63 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package sbmlreader;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.data.ImportHandler;
+
+import cytoscape.plugin.CytoscapePlugin;
+
+import java.awt.event.ActionEvent;
+
+import java.util.*;
+
+
+/**
+ This plugin will allow the reading of an SBML level 2 file.
+ *
+ *W.P.A. Ligtenberg, Eindhoven University of Technology
+ */
+public class SBMLReaderPlugin extends CytoscapePlugin {
+ /**
+ * This constructor creates an action and adds it to the Plugins menu.
+ */
+ public SBMLReaderPlugin() {
+ ImportHandler ih = Cytoscape.getImportHandler();
+ ih.addFilter(new SBMLFilter());
+ }
+}
diff --git a/coreplugins/SBMLReader/src/main/java/sbmlreader/SBMLVisualStyleFactory.java b/coreplugins/SBMLReader/src/main/java/sbmlreader/SBMLVisualStyleFactory.java
new file mode 100644
index 0000000..6fb686b
--- /dev/null
+++ b/coreplugins/SBMLReader/src/main/java/sbmlreader/SBMLVisualStyleFactory.java
@@ -0,0 +1,165 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package sbmlreader;
+
+import cytoscape.*;
+
+import cytoscape.data.Semantics;
+
+import cytoscape.view.CytoscapeDesktop;
+
+import cytoscape.visual.*;
+
+import cytoscape.visual.calculators.*;
+
+import cytoscape.visual.mappings.*;
+
+import cytoscape.visual.ui.*;
+
+import giny.view.EdgeView;
+
+import java.awt.Color;
+
+
+/**
+ * VisualStyleFactory.java
+ * This class defines the visualstyle in Cytoscape for the SBMLReader plugin.
+ *
+ * @author W.P.A. Ligtenberg, Eindhoven University of Technology
+ */
+public class SBMLVisualStyleFactory {
+ /**
+ *
+ */
+ public static final String SBMLReader_VS = "SBMLReader Style";
+
+ /**
+ *
+ */
+ public static final String NODE_TYPE_ATT = "sbml type";
+
+ /**
+ *
+ */
+ public static final String EDGE_TYPE_ATT = "interaction";
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param network DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static VisualStyle createVisualStyle(CyNetwork network) {
+ VisualMappingManager vmManager = Cytoscape.getVisualMappingManager();
+ NodeAppearanceCalculator nodeAppCalc = new NodeAppearanceCalculator();
+ EdgeAppearanceCalculator edgeAppCalc = new EdgeAppearanceCalculator();
+ CalculatorCatalog calculatorCatalog = vmManager.getCalculatorCatalog();
+
+ // ------------------------------ Set node shapes ---------------------------//
+ DiscreteMapping disMapping = new DiscreteMapping(NodeShape.RECT,
+ ObjectMapping.NODE_MAPPING);
+ disMapping.setControllingAttributeName(NODE_TYPE_ATT, network, false);
+ disMapping.putMapValue("species", NodeShape.DIAMOND);
+ disMapping.putMapValue("reaction", NodeShape.ELLIPSE);
+
+ Calculator shapeCalculator = new BasicCalculator("SBMLReader Shape Calculator",
+ disMapping,
+ VisualPropertyType.NODE_SHAPE);
+ nodeAppCalc.setCalculator(shapeCalculator);
+
+ // ------------------------------ Set the label ------------------------------//
+ // Display the value for geneName as a label
+ String cName = "sbml name";
+ Calculator nlc = calculatorCatalog.getCalculator(VisualPropertyType.NODE_LABEL, cName);
+
+ if (nlc == null) {
+ PassThroughMapping m = new PassThroughMapping(new String(), cName);
+ nlc = new BasicCalculator(cName, m, VisualPropertyType.NODE_LABEL);
+ }
+
+ nodeAppCalc.setCalculator(nlc);
+
+ //--------------------- Set the size of the nodes --------------------------//
+ //Discrete mapping on nodeType
+ Double speciesNodeSize = new Double(30);
+ Double reactionNodeSize = new Double(30);
+ DiscreteMapping sizeMapping = new DiscreteMapping(reactionNodeSize,
+ ObjectMapping.NODE_MAPPING);
+ sizeMapping.setControllingAttributeName(NODE_TYPE_ATT, network, false);
+ sizeMapping.putMapValue("species", speciesNodeSize);
+ sizeMapping.putMapValue("reaction", reactionNodeSize);
+
+ Calculator sizeCalculator = new BasicCalculator("SBMLReader Size Calculator",
+ sizeMapping,
+ VisualPropertyType.NODE_SIZE);
+ nodeAppCalc.setCalculator(sizeCalculator);
+ nodeAppCalc.setNodeSizeLocked(true);
+
+ // ------------------------------ Set edge arrow shape ---------------------------//
+ DiscreteMapping arrowMapping = new DiscreteMapping(ArrowShape.DELTA,
+ ObjectMapping.NODE_MAPPING);
+ arrowMapping.setControllingAttributeName(EDGE_TYPE_ATT, network, false);
+ arrowMapping.putMapValue("reaction-product", ArrowShape.ARROW);
+ arrowMapping.putMapValue("reaction-reactant", ArrowShape.NONE);
+ arrowMapping.putMapValue("reaction-modifier", ArrowShape.CIRCLE);
+
+ Calculator edgeArrowCalculator = new BasicCalculator("SBMLReader Edge Arrow Calculator",
+ arrowMapping,
+ VisualPropertyType.EDGE_SRCARROW_SHAPE);
+ edgeAppCalc.setCalculator(edgeArrowCalculator);
+
+ // ------------------------------ Set edge colour ---------------------------//
+ DiscreteMapping edgeColorMapping = new DiscreteMapping(Color.BLACK,
+ ObjectMapping.NODE_MAPPING);
+ edgeColorMapping.setControllingAttributeName(EDGE_TYPE_ATT, network, false);
+ edgeColorMapping.putMapValue("reaction-product", Color.GREEN);
+ edgeColorMapping.putMapValue("reaction-reactant", Color.RED);
+ edgeColorMapping.putMapValue("reaction-modifier", Color.BLACK);
+
+ Calculator edgeColorCalculator = new BasicCalculator("SBMLReader Edge Color Calculator",
+ edgeColorMapping,
+ VisualPropertyType.EDGE_COLOR);
+ edgeAppCalc.setCalculator(edgeColorCalculator);
+
+ //------------------------- Create a visual style -------------------------------//
+ GlobalAppearanceCalculator gac = vmManager.getVisualStyle().getGlobalAppearanceCalculator();
+ VisualStyle visualStyle = new VisualStyle(SBMLReader_VS, nodeAppCalc, edgeAppCalc, gac);
+
+ return visualStyle;
+ }
+}
diff --git a/coreplugins/SBMLReader/src/main/resources/sbmlreader/plugin.props b/coreplugins/SBMLReader/src/main/resources/sbmlreader/plugin.props
new file mode 100644
index 0000000..2292ea1
--- /dev/null
+++ b/coreplugins/SBMLReader/src/main/resources/sbmlreader/plugin.props
@@ -0,0 +1,30 @@
+# This props file would be filled out and included in the plugin jar file. This props file will be used
+# to put information into the Plugin Manager about the plugin
+
+# -- The following properties are REQUIRED -- #
+
+# The plugin name that will be displayed to users
+pluginName=SBML Reader
+
+# Description used to give users information about the plugin such as what it does.
+# Html tags are encouraged for formatting purposes.
+pluginDescription=Provides the ability to import SBML (Systems Biology Markup Language) formatted files.
+
+# Plugin version number, this must be two numbers separated by a decimlal. Ex. 0.2, 14.03
+pluginVersion=0.5
+
+# Compatible Cytoscape version
+cytoscapeVersion=2.5,2.6,2.7,2.8
+
+# Category, use one of the categories listed on the website or create your own
+pluginCategory=Core
+
+
+# List of authors. Note each author and institution pair are separated by a : (colon)
+# each additional author institution pair must be separated from other pairs bye a ; (semicolon)
+pluginAuthorsIntsitutions=Willem Ligtenberg:Eindhoven University of Technology
+
+# -- The following properties should be set ONLY BY CORE PLUGINS -- #
+downloadURL=http://cytoscape.org/plugins/plugins.xml
+uniqueID=15
+
diff --git a/coreplugins/TableImport/pom.xml b/coreplugins/TableImport/pom.xml
new file mode 100644
index 0000000..1adcf5c
--- /dev/null
+++ b/coreplugins/TableImport/pom.xml
@@ -0,0 +1,89 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>parent</artifactId>
+ <version>2.8.4-SNAPSHOT</version>
+ </parent>
+
+ <artifactId>table-import</artifactId>
+ <packaging>jar</packaging>
+
+ <name>Table Import</name>
+
+ <!-- bootstrap for cytoscape dependencies, namely the parent POM snapshots -->
+ <repositories>
+ <repository>
+ <id>cytoscape_snapshots</id>
+ <snapshots>
+ <enabled>true</enabled>
+ </snapshots>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <name>Cytoscape Snapshots</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/</url>
+ </repository>
+ <repository>
+ <id>cytoscape_releases</id>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ <name>Cytoscape Releases</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/releases/</url>
+ </repository>
+ </repositories>
+
+ <build>
+ <plugins>
+ <plugin>
+ <artifactId>maven-assembly-plugin</artifactId>
+ <configuration>
+ <archive>
+ <manifestEntries>
+ <Cytoscape-Plugin>edu.ucsd.bioeng.coreplugin.tableImport.TableImportPlugin</Cytoscape-Plugin>
+ </manifestEntries>
+ </archive>
+ </configuration>
+ </plugin>
+ </plugins>
+ </build>
+
+ <dependencies>
+ <dependency>
+ <groupId>org.apache.xmlbeans</groupId>
+ <artifactId>xmlbeans</artifactId>
+ <version>2.4.0</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.poi</groupId>
+ <artifactId>poi</artifactId>
+ <version>3.6</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.poi</groupId>
+ <artifactId>poi-contrib</artifactId>
+ <version>3.6</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.poi</groupId>
+ <artifactId>poi-ooxml</artifactId>
+ <version>3.6</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.poi</groupId>
+ <artifactId>poi-ooxml-schemas</artifactId>
+ <version>3.6</version>
+ </dependency>
+ <dependency>
+ <groupId>dom4j</groupId>
+ <artifactId>dom4j</artifactId>
+ <version>1.6.1</version>
+ </dependency>
+ </dependencies>
+
+</project>
+
diff --git a/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/TableImportPlugin.java b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/TableImportPlugin.java
new file mode 100644
index 0000000..4dcc2c7
--- /dev/null
+++ b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/TableImportPlugin.java
@@ -0,0 +1,71 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+package edu.ucsd.bioeng.coreplugin.tableImport;
+
+import cytoscape.Cytoscape;
+import cytoscape.plugin.CytoscapePlugin;
+import cytoscape.view.CyMenus;
+import edu.ucsd.bioeng.coreplugin.tableImport.actions.ImportAnnotationAndOntologyAction;
+import edu.ucsd.bioeng.coreplugin.tableImport.actions.ImportAttributeTableAction;
+import edu.ucsd.bioeng.coreplugin.tableImport.actions.ImportNetworkTableAction;
+
+/**
+ * Main class for Table Import plugin.
+ *
+ * @version 0.7
+ * @since Cytoscape 2.4
+ * @author Keiichiro Ono
+ *
+ */
+public class TableImportPlugin extends CytoscapePlugin {
+ /**
+ * Constructor for Table Import plugin.
+ *
+ */
+ public TableImportPlugin() {
+
+ final CyMenus cyMenus = Cytoscape.getDesktop().getCyMenus();
+
+ // Register each menu item
+ if (cyMenus != null) {
+ cyMenus.addAction(new ImportNetworkTableAction(), 1);
+ cyMenus.addAction(new ImportAttributeTableAction(), 5);
+ cyMenus.addAction(new ImportAnnotationAndOntologyAction(), 7);
+ } else
+ throw new IllegalStateException(
+ "Could not register Table Import Plugin to the menu bar.");
+ }
+}
diff --git a/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/actions/ImportAnnotationAndOntologyAction.java b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/actions/ImportAnnotationAndOntologyAction.java
new file mode 100644
index 0000000..0811b69
--- /dev/null
+++ b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/actions/ImportAnnotationAndOntologyAction.java
@@ -0,0 +1,95 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+package edu.ucsd.bioeng.coreplugin.tableImport.actions;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.util.CytoscapeAction;
+
+import edu.ucsd.bioeng.coreplugin.tableImport.ui.ImportTextTableDialog;
+
+import java.awt.event.ActionEvent;
+
+import java.io.IOException;
+
+import javax.xml.bind.JAXBException;
+
+/**
+ * Display Ontology and Annotation import dialog.<br>
+ *
+ * @since Cytoscape 2.4
+ * @version 1.0
+ * @author kono
+ *
+ */
+public class ImportAnnotationAndOntologyAction extends CytoscapeAction {
+
+ private static final long serialVersionUID = -7250841983164927184L;
+
+ /**
+ * Creates a new ImportAnnotationAndOntologyAction object.
+ */
+ public ImportAnnotationAndOntologyAction() {
+ super("Ontology and Annotation...");
+ setPreferredMenu("File.Import");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void actionPerformed(ActionEvent e) {
+
+ try {
+ ImportTextTableDialog iad = new ImportTextTableDialog(Cytoscape
+ .getDesktop(), true,
+ ImportTextTableDialog.ONTOLOGY_AND_ANNOTATION_IMPORT);
+ iad.pack();
+ iad.setLocationRelativeTo(Cytoscape.getDesktop());
+ iad.setVisible(true);
+ } catch (JAXBException e1) {
+ e1.printStackTrace();
+ throw new IllegalStateException("");
+ } catch (IOException e1) {
+ // TODO Auto-generated catch block
+ e1.printStackTrace();
+ }
+
+ }
+}
diff --git a/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/actions/ImportAttributeTableAction.java b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/actions/ImportAttributeTableAction.java
new file mode 100644
index 0000000..93c94f2
--- /dev/null
+++ b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/actions/ImportAttributeTableAction.java
@@ -0,0 +1,92 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package edu.ucsd.bioeng.coreplugin.tableImport.actions;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.util.CytoscapeAction;
+
+import edu.ucsd.bioeng.coreplugin.tableImport.ui.ImportTextTableDialog;
+
+import java.awt.event.ActionEvent;
+
+import java.io.IOException;
+
+import javax.xml.bind.JAXBException;
+
+
+/**
+ * Display dialog for importing attribute text/Excel file.<br>
+ *
+ * @since Cytoscape 2.4
+ * @version 1.0
+ * @author kono
+ *
+ */
+public class ImportAttributeTableAction extends CytoscapeAction {
+ /**
+ * Creates a new ImportAttributeTableAction object.
+ */
+ public ImportAttributeTableAction() {
+ super("Attribute from Table (Text/MS Excel)...");
+ setPreferredMenu("File.Import");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ ImportTextTableDialog iad;
+
+ try {
+ iad = new ImportTextTableDialog(Cytoscape.getDesktop(), true,
+ ImportTextTableDialog.SIMPLE_ATTRIBUTE_IMPORT);
+ iad.pack();
+ iad.setLocationRelativeTo(Cytoscape.getDesktop());
+ iad.setVisible(true);
+ } catch (JAXBException e1) {
+ // TODO Auto-generated catch block
+ e1.printStackTrace();
+ } catch (IOException e1) {
+ // TODO Auto-generated catch block
+ e1.printStackTrace();
+ }
+ }
+}
diff --git a/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/actions/ImportNetworkTableAction.java b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/actions/ImportNetworkTableAction.java
new file mode 100644
index 0000000..3a5384c
--- /dev/null
+++ b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/actions/ImportNetworkTableAction.java
@@ -0,0 +1,87 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package edu.ucsd.bioeng.coreplugin.tableImport.actions;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.util.CytoscapeAction;
+
+import edu.ucsd.bioeng.coreplugin.tableImport.ui.ImportTextTableDialog;
+
+import java.awt.event.ActionEvent;
+
+import java.io.IOException;
+
+import javax.xml.bind.JAXBException;
+
+
+/**
+ *
+ */
+public class ImportNetworkTableAction extends CytoscapeAction {
+ /**
+ * Creates a new ImportNetworkTableAction object.
+ */
+ public ImportNetworkTableAction() {
+ super("Network from Table (Text/MS Excel)...");
+ setPreferredMenu("File.Import");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ ImportTextTableDialog iad;
+
+ try {
+ iad = new ImportTextTableDialog(Cytoscape.getDesktop(), true,
+ ImportTextTableDialog.NETWORK_IMPORT);
+ iad.pack();
+ iad.setLocationRelativeTo(Cytoscape.getDesktop());
+ iad.setVisible(true);
+ } catch (JAXBException e1) {
+ // TODO Auto-generated catch block
+ e1.printStackTrace();
+ } catch (IOException e1) {
+ // TODO Auto-generated catch block
+ e1.printStackTrace();
+ }
+ }
+}
diff --git a/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/reader/AttributeAndOntologyMappingParameters.java b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/reader/AttributeAndOntologyMappingParameters.java
new file mode 100644
index 0000000..f864f6b
--- /dev/null
+++ b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/reader/AttributeAndOntologyMappingParameters.java
@@ -0,0 +1,145 @@
+
+/*
+ Copyright (c) 2006, 2007, 2009, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package edu.ucsd.bioeng.coreplugin.tableImport.reader;
+
+import cytoscape.Cytoscape;
+
+import edu.ucsd.bioeng.coreplugin.tableImport.reader.TextTableReader.ObjectType;
+
+import org.biojava.ontology.Ontology;
+
+import java.util.List;
+
+
+/**
+ *
+ */
+public class AttributeAndOntologyMappingParameters extends AttributeMappingParameters {
+ private final int ontologyIndex;
+ private final String ontologyName;
+
+ /**
+ * Creates a new AttributeAndOntologyMappingParameters object.
+ *
+ * @param objectType DOCUMENT ME!
+ * @param delimiters DOCUMENT ME!
+ * @param listDelimiter DOCUMENT ME!
+ * @param keyIndex DOCUMENT ME!
+ * @param mappingAttribute DOCUMENT ME!
+ * @param aliasIndex DOCUMENT ME!
+ * @param attributeNames DOCUMENT ME!
+ * @param attributeTypes DOCUMENT ME!
+ * @param listAttributeTypes DOCUMENT ME!
+ * @param importFlag DOCUMENT ME!
+ * @param ontologyIndex DOCUMENT ME!
+ * @param ontologyName DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public AttributeAndOntologyMappingParameters(ObjectType objectType, List<String> delimiters,
+ String listDelimiter, int keyIndex,
+ String mappingAttribute, List<Integer> aliasIndex,
+ String[] attributeNames, Byte[] attributeTypes,
+ Byte[] listAttributeTypes, boolean[] importFlag,
+ int ontologyIndex, final String ontologyName)
+ throws Exception {
+ this(objectType, delimiters, listDelimiter, keyIndex, mappingAttribute,
+ aliasIndex, attributeNames, attributeTypes, listAttributeTypes,
+ importFlag, ontologyIndex, ontologyName, true);
+ }
+
+ /**
+ * Creates a new AttributeAndOntologyMappingParameters object.
+ * This constructor takes an additional parameter to allow case sensitivity
+ * to be specified.
+ *
+ * @param objectType DOCUMENT ME!
+ * @param delimiters DOCUMENT ME!
+ * @param listDelimiter DOCUMENT ME!
+ * @param keyIndex DOCUMENT ME!
+ * @param mappingAttribute DOCUMENT ME!
+ * @param aliasIndex DOCUMENT ME!
+ * @param attributeNames DOCUMENT ME!
+ * @param attributeTypes DOCUMENT ME!
+ * @param listAttributeTypes DOCUMENT ME!
+ * @param importFlag DOCUMENT ME!
+ * @param ontologyIndex DOCUMENT ME!
+ * @param ontologyName DOCUMENT ME!
+ * @param caseSensitive DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public AttributeAndOntologyMappingParameters(ObjectType objectType, List<String> delimiters,
+ String listDelimiter, int keyIndex,
+ String mappingAttribute, List<Integer> aliasIndex,
+ String[] attributeNames, Byte[] attributeTypes,
+ Byte[] listAttributeTypes, boolean[] importFlag,
+ int ontologyIndex, final String ontologyName,
+ boolean caseSensitive)
+ throws Exception {
+ super(objectType, delimiters, listDelimiter, keyIndex, mappingAttribute, aliasIndex,
+ attributeNames, attributeTypes, listAttributeTypes, importFlag, caseSensitive);
+ this.ontologyName = ontologyName;
+ this.ontologyIndex = ontologyIndex;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getOntologyIndex() {
+ return ontologyIndex;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Ontology getOntology() {
+ final Ontology testOntology;
+
+ if (Cytoscape.getOntologyServer() != null) {
+ testOntology = Cytoscape.getOntologyServer().getOntologies().get(ontologyName);
+ } else {
+ testOntology = null;
+ }
+
+ return testOntology;
+ }
+}
diff --git a/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/reader/AttributeLineParser.java b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/reader/AttributeLineParser.java
new file mode 100644
index 0000000..b3fe36c
--- /dev/null
+++ b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/reader/AttributeLineParser.java
@@ -0,0 +1,538 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package edu.ucsd.bioeng.coreplugin.tableImport.reader;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.data.CyAttributes;
+
+import cytoscape.giny.CytoscapeRootGraph;
+
+import edu.ucsd.bioeng.coreplugin.tableImport.reader.TextTableReader.ObjectType;
+
+import giny.model.Edge;
+import giny.model.Node;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.TreeSet;
+
+
+/**
+ * Take a line of data, analyze it, and map to CyAttributes.
+ *
+ * @since Cytoscape 2.4
+ * @version 0.8
+ * @author Keiichiro Ono
+ *
+ */
+public class AttributeLineParser {
+ private AttributeMappingParameters mapping;
+ private Map<String, Object> invalid = new HashMap<String, Object>();
+
+ /**
+ * Creates a new AttributeLineParser object.
+ *
+ * @param mapping DOCUMENT ME!
+ */
+ public AttributeLineParser(AttributeMappingParameters mapping) {
+ this.mapping = mapping;
+ }
+
+ /**
+ * Import everything regardless associated nodes/edges exist or not.
+ *
+ * @param parts entries in a line.
+ */
+ public void parseAll(String[] parts) {
+ // Get key
+ final String primaryKey = parts[mapping.getKeyIndex()].trim();
+ final int partsLen = parts.length;
+
+ for (int i = 0; i < partsLen; i++) {
+ if ((i != mapping.getKeyIndex()) && !mapping.getAliasIndexList().contains(i)
+ && mapping.getImportFlag()[i]) {
+ if (parts[i] == null) {
+ continue;
+ } else if (mapping.getObjectType() == ObjectType.NETWORK) {
+ //mapAttribute(targetNetworkID, parts[i].trim(), i);
+ } else {
+ mapAttribute(primaryKey, parts[i].trim(), i);
+ }
+ }
+ }
+ }
+
+ /**
+ * Takes an array of entries, which is one line of text file, and maps them
+ * to CyAttributes.
+ *
+ * @param parts
+ */
+ public void parseEntry(String[] parts) {
+ /*
+ * Split the line and extract values
+ */
+ final String primaryKey = parts[mapping.getKeyIndex()].trim();
+
+ /*
+ * Set aliases In this case, "aliases" means alias entries in the TEXT
+ * TABLE, not the ones returned by Cytoscape.getNodeAliases()
+ *
+ * The variable aliasSet has non-redundant set of object names.
+ */
+ final Set<String> aliasSet = new TreeSet<String>();
+
+ if (mapping.getAliasIndexList().size() != 0) {
+ /*
+ * Alias column exists. Extract those keys.
+ */
+ String aliasCell = null;
+
+ for (int aliasIndex : mapping.getAliasIndexList()) {
+ if (parts.length > aliasIndex) {
+ aliasCell = parts[aliasIndex];
+
+ if ((aliasCell != null) && (aliasCell.trim().length() != 0)) {
+ aliasSet.addAll(buildList(aliasCell, CyAttributes.TYPE_STRING));
+ }
+ }
+ }
+ }
+ aliasSet.add(primaryKey);
+
+ /*
+ * Case 1: use node ID as the key
+ */
+ if (mapping.getMappingAttribute().equals(mapping.ID)) {
+ transfer2cyattributes(primaryKey, aliasSet, parts);
+ } else {
+ /*
+ * Case 2: use an attribute as the key.
+ */
+ List<String> objectIDs = null;
+
+ for (String id : aliasSet) {
+ // Normal Mapping. Case sensitive.
+
+ if (mapping.getAttributeToIDMap().containsKey(id)) {
+ objectIDs = mapping.toID(id);
+
+ for (String objectID : objectIDs) {
+ mapping.getAlias().add(objectID, new ArrayList<String>(aliasSet));
+ }
+
+ break;
+ } else if (mapping.getCaseSensitive() == false) {
+
+ Set<String> keySet = mapping.getAttributeToIDMap().keySet();
+
+ String newKey = null;
+
+ for (String key : keySet) {
+ if (key.equalsIgnoreCase(id)) {
+ newKey = key;
+
+ break;
+ }
+ }
+
+ if (newKey != null) {
+ objectIDs = mapping.toID(newKey);
+
+ for (String objectID : objectIDs) {
+ mapping.getAlias().add(objectID, new ArrayList<String>(aliasSet));
+ }
+
+ break;
+ }
+ }
+ }
+
+ if (objectIDs != null) {
+ for (String key : objectIDs) {
+ transfer2cyattributes(key, aliasSet, parts);
+ }
+ }
+ }
+ }
+
+ private void transfer2cyattributes(String primaryKey, Set<String> aliasSet, String[] parts) {
+ String altKey = null;
+ String targetNetworkID = null;
+
+ /*
+ * Search the key
+ */
+ switch (mapping.getObjectType()) {
+ case NODE:
+
+ Node node = Cytoscape.getCyNode(primaryKey);
+
+ if ((mapping.getCaseSensitive() == false) && (node == null)) {
+ // This is extremely slow, but we have no choice.
+ final CytoscapeRootGraph rg = Cytoscape.getRootGraph();
+ int[] nodes = Cytoscape.getRootGraph().getNodeIndicesArray();
+ int nodeCount = nodes.length;
+
+ for (int i = 0; i < nodeCount; i++) {
+ if (rg.getNode(nodes[i]).getIdentifier().equalsIgnoreCase(primaryKey)) {
+ node = rg.getNode(nodes[i]);
+ primaryKey = node.getIdentifier();
+
+ break;
+ }
+ }
+ }
+
+ if (node == null) {
+ for (String alias : aliasSet) {
+ node = Cytoscape.getCyNode(alias);
+
+ if ((mapping.getCaseSensitive() == false) && (node == null)) {
+ // This is extremely slow, but we have no choice.
+ final CytoscapeRootGraph rg = Cytoscape.getRootGraph();
+ int[] nodes = Cytoscape.getRootGraph().getNodeIndicesArray();
+ int nodeCount = nodes.length;
+
+ for (int i = 0; i < nodeCount; i++) {
+ if (rg.getNode(nodes[i]).getIdentifier().equalsIgnoreCase(alias)) {
+ node = rg.getNode(nodes[i]);
+ alias = node.getIdentifier();
+
+ break;
+ }
+ }
+ }
+
+ if (node != null) {
+ altKey = alias;
+
+ break;
+ }
+ }
+
+ if (node == null) {
+ return;
+ }
+ }
+
+ break;
+
+ case EDGE:
+
+ Edge edge = Cytoscape.getRootGraph().getEdge(primaryKey);
+
+ if ((mapping.getCaseSensitive() == false) && (edge == null)) {
+ // This is extremely slow, but we have no choice.
+ final CytoscapeRootGraph rg = Cytoscape.getRootGraph();
+ int[] edges = Cytoscape.getRootGraph().getEdgeIndicesArray();
+ int edgeCount = edges.length;
+
+ for (int i = 0; i < edgeCount; i++) {
+ if (rg.getEdge(edges[i]).getIdentifier().equalsIgnoreCase(primaryKey)) {
+ edge = rg.getEdge(edges[i]);
+ primaryKey = edge.getIdentifier();
+
+ break;
+ }
+ }
+ }
+
+ if (edge == null) {
+ for (String alias : aliasSet) {
+ edge = Cytoscape.getRootGraph().getEdge(alias);
+
+ if ((mapping.getCaseSensitive() == false) && (edge == null)) {
+ // This is extremely slow, but we have no choice.
+ final CytoscapeRootGraph rg = Cytoscape.getRootGraph();
+ int[] edges = Cytoscape.getRootGraph().getEdgeIndicesArray();
+ int edgeCount = edges.length;
+
+ for (int i = 0; i < edgeCount; i++) {
+ if (rg.getEdge(edges[i]).getIdentifier().equalsIgnoreCase(alias)) {
+ edge = rg.getEdge(edges[i]);
+ alias = edge.getIdentifier();
+
+ break;
+ }
+ }
+ }
+
+ if (edge != null) {
+ altKey = alias;
+
+ break;
+ }
+ }
+
+ if (edge == null) {
+ return;
+ }
+ } else {
+ break;
+ }
+
+ break;
+
+ case NETWORK:
+
+ /*
+ * This is a special case: Since network IDs are only integers and
+ * not always the same, we need to use title instead of ID.
+ */
+ if (mapping.getnetworkTitleMap().containsKey(primaryKey)) {
+ targetNetworkID = mapping.getnetworkTitleMap().get(primaryKey);
+
+ break;
+ }
+
+ if (targetNetworkID == null) {
+ for (String alias : aliasSet) {
+ if (mapping.getnetworkTitleMap().containsKey(alias)) {
+ targetNetworkID = mapping.getnetworkTitleMap().get(alias);
+
+ break;
+ }
+ }
+ }
+
+ if (targetNetworkID == null) {
+ /*
+ * Network not found: just ignore this line.
+ */
+ return;
+ }
+
+ break;
+
+ default:
+ }
+
+ /*
+ * Now, transfer entries into CyAttributes.
+ */
+ for (int i = 0; i < parts.length; i++) {
+ if ((i != mapping.getKeyIndex()) && !mapping.getAliasIndexList().contains(i)
+ && mapping.getImportFlag()[i]) {
+ if (parts[i] == null) {
+ // Do nothing
+ } else if (mapping.getObjectType() == ObjectType.NETWORK) {
+ mapAttribute(targetNetworkID, parts[i].trim(), i);
+ }
+ /*
+ * First, check the node exists or not with the primary key
+ */
+ else if (altKey == null) {
+ mapAttribute(primaryKey, parts[i].trim(), i);
+ } else {
+ mapAttribute(altKey, parts[i].trim(), i);
+ }
+ }
+ }
+
+ /*
+ * Finally, add aliases and primary key.
+ */
+ mapping.getAlias().add(primaryKey, new ArrayList<String>(aliasSet));
+ mapping.getAttributes()
+ .setAttribute(primaryKey, mapping.getAttributeNames()[mapping.getKeyIndex()],
+ parts[mapping.getKeyIndex()]);
+
+ /*
+ * Add primary key as an attribute
+ */
+ }
+
+ /**
+ * Based on the attribute types, map the entry to CyAttributes.<br>
+ *
+ * @param key
+ * @param entry
+ * @param index
+ */
+ private void mapAttribute(final String key, final String entry, final int index) {
+ final Byte type = mapping.getAttributeTypes()[index];
+
+ // System.out.println("Index = " + mapping.getAttributeNames()[index] + ", " + key + " = "
+ // + entry);
+ switch (type) {
+ case CyAttributes.TYPE_BOOLEAN:
+
+ Boolean newBool;
+
+ try {
+ newBool = new Boolean(entry);
+ mapping.getAttributes()
+ .setAttribute(key, mapping.getAttributeNames()[index], newBool);
+ } catch (Exception e) {
+ invalid.put(key, entry);
+ }
+
+ break;
+
+ case CyAttributes.TYPE_INTEGER:
+
+ Integer newInt;
+
+ try {
+ newInt = new Integer(entry);
+ mapping.getAttributes()
+ .setAttribute(key, mapping.getAttributeNames()[index], newInt);
+ } catch (Exception e) {
+ invalid.put(key, entry);
+ }
+
+ break;
+
+ case CyAttributes.TYPE_FLOATING:
+
+ Double newDouble;
+
+ try {
+ newDouble = new Double(entry);
+ mapping.getAttributes()
+ .setAttribute(key, mapping.getAttributeNames()[index], newDouble);
+ } catch (Exception e) {
+ invalid.put(key, entry);
+ }
+
+ break;
+
+ case CyAttributes.TYPE_STRING:
+ try {
+ mapping.getAttributes().setAttribute(key, mapping.getAttributeNames()[index], entry);
+ } catch (Exception e) {
+ invalid.put(key, entry);
+ }
+
+ break;
+
+ case CyAttributes.TYPE_SIMPLE_LIST:
+
+ /*
+ * In case of list, not overwrite the attribute. Get the existing
+ * list, and add it to the list.
+ *
+ * Since list has data types for their data types, so we need to
+ * extract it first.
+ *
+ */
+ final Byte[] listTypes = mapping.getListAttributeTypes();
+ final Byte listType;
+
+ if (listTypes != null) {
+ listType = listTypes[index];
+ } else {
+ listType = CyAttributes.TYPE_STRING;
+ }
+
+ List curList = mapping.getAttributes()
+ .getListAttribute(key, mapping.getAttributeNames()[index]);
+
+ if (curList == null) {
+ curList = new ArrayList();
+ }
+
+ curList.addAll(buildList(entry, listType));
+ try {
+ mapping.getAttributes()
+ .setListAttribute(key, mapping.getAttributeNames()[index], curList);
+ } catch (Exception e) {
+ invalid.put(key, entry);
+ }
+
+ break;
+
+ default:
+ try {
+ mapping.getAttributes().setAttribute(key, mapping.getAttributeNames()[index], entry);
+ } catch (Exception e) {
+ invalid.put(key, entry);
+ }
+ }
+ }
+
+ protected Map getInvalidMap() {
+ return invalid;
+ }
+
+ /**
+ * If an entry is a list, split the string and create new List Attribute.
+ *
+ * @return
+ */
+ private List buildList(final String entry, final Byte dataType) {
+ if (entry == null) {
+ return null;
+ }
+
+ final String[] parts = (entry.replace("\"", "")).split(mapping.getListDelimiter());
+
+ final List listAttr = new ArrayList();
+
+ for (String listItem : parts) {
+ switch (dataType) {
+ case CyAttributes.TYPE_BOOLEAN:
+ listAttr.add(Boolean.parseBoolean(listItem.trim()));
+
+ break;
+
+ case CyAttributes.TYPE_INTEGER:
+ listAttr.add(Integer.parseInt(listItem.trim()));
+
+ break;
+
+ case CyAttributes.TYPE_FLOATING:
+ listAttr.add(Double.parseDouble(listItem.trim()));
+
+ break;
+
+ case CyAttributes.TYPE_STRING:
+ listAttr.add(listItem.trim());
+
+ break;
+
+ default:
+ break;
+ }
+ }
+
+ return listAttr;
+ }
+}
diff --git a/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/reader/AttributeMappingParameters.java b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/reader/AttributeMappingParameters.java
new file mode 100644
index 0000000..dd4654a
--- /dev/null
+++ b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/reader/AttributeMappingParameters.java
@@ -0,0 +1,539 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package edu.ucsd.bioeng.coreplugin.tableImport.reader;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+
+import cytoscape.data.CyAttributes;
+import cytoscape.data.CyAttributesUtils;
+
+import cytoscape.data.synonyms.Aliases;
+import static edu.ucsd.bioeng.coreplugin.tableImport.reader.TextFileDelimiters.*;
+import edu.ucsd.bioeng.coreplugin.tableImport.reader.TextTableReader.ObjectType;
+import static edu.ucsd.bioeng.coreplugin.tableImport.reader.TextTableReader.ObjectType.*;
+
+import giny.model.Edge;
+import giny.model.Node;
+
+import java.io.IOException;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+
+/**
+ * Parameter object for text table <---> CyAttributes mapping.<br>
+ * <p>
+ * This object will be used by all attribute readers.
+ * </p>
+ *
+ * @since Cytoscape 2.4
+ * @version 0.9
+ * @author Keiichiro Ono
+ *
+ */
+public class AttributeMappingParameters implements MappingParameter {
+ /**
+ *
+ */
+ public static final String ID = "ID";
+ private static final String DEF_LIST_DELIMITER = PIPE.toString();
+ private static final String DEF_DELIMITER = TAB.toString();
+ private final ObjectType objectType;
+ private final int keyIndex;
+ private final List<Integer> aliasIndex;
+ private String[] attributeNames;
+ private Byte[] attributeTypes;
+ private Byte[] listAttributeTypes;
+ private final String mappingAttribute;
+ private List<String> delimiters;
+ private String listDelimiter;
+ private boolean[] importFlag;
+ private Map<String, List<String>> attr2id;
+ private CyAttributes attributes;
+ private Aliases existingAliases;
+ private final Map<String, String> networkTitle2ID;
+
+ // Case sensitivity
+ private Boolean caseSensitive;
+
+ /**
+ * Creates a new AttributeMappingParameters object.
+ *
+ * @param objectType DOCUMENT ME!
+ * @param delimiters DOCUMENT ME!
+ * @param listDelimiter DOCUMENT ME!
+ * @param keyIndex DOCUMENT ME!
+ * @param mappingAttribute DOCUMENT ME!
+ * @param aliasIndex DOCUMENT ME!
+ * @param attrNames DOCUMENT ME!
+ * @param attributeTypes DOCUMENT ME!
+ * @param listAttributeTypes DOCUMENT ME!
+ * @param importFlag DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public AttributeMappingParameters(final ObjectType objectType, final List<String> delimiters,
+ final String listDelimiter, final int keyIndex,
+ final String mappingAttribute,
+ final List<Integer> aliasIndex, final String[] attrNames,
+ Byte[] attributeTypes, Byte[] listAttributeTypes,
+ boolean[] importFlag) throws Exception {
+ this(objectType, delimiters, listDelimiter, keyIndex, mappingAttribute, aliasIndex,
+ attrNames, attributeTypes, listAttributeTypes, importFlag, true);
+ }
+
+ /**
+ * Creates a new AttributeMappingParameters object.
+ *
+ * @param objectType DOCUMENT ME!
+ * @param delimiters DOCUMENT ME!
+ * @param listDelimiter DOCUMENT ME!
+ * @param keyIndex DOCUMENT ME!
+ * @param mappingAttribute DOCUMENT ME!
+ * @param aliasIndex DOCUMENT ME!
+ * @param attrNames DOCUMENT ME!
+ * @param attributeTypes DOCUMENT ME!
+ * @param listAttributeTypes DOCUMENT ME!
+ * @param importFlag DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ * @throws IOException DOCUMENT ME!
+ */
+ public AttributeMappingParameters(final ObjectType objectType, final List<String> delimiters,
+ final String listDelimiter, final int keyIndex,
+ final String mappingAttribute,
+ final List<Integer> aliasIndex, final String[] attrNames,
+ Byte[] attributeTypes, Byte[] listAttributeTypes,
+ boolean[] importFlag, Boolean caseSensitive)
+ throws Exception {
+ this.listAttributeTypes = listAttributeTypes;
+ this.caseSensitive = caseSensitive;
+
+ if (attrNames == null) {
+ throw new Exception("attributeNames should not be null.");
+ }
+
+ /*
+ * Error check: Key column number should be smaller than actual number
+ * of columns in the text table.
+ */
+ if (attrNames.length < keyIndex) {
+ throw new IOException("Key is out of range.");
+ }
+
+ /*
+ * These calues should not be null!
+ */
+ this.objectType = objectType;
+ this.keyIndex = keyIndex;
+ this.attributeNames = attrNames;
+
+ if (this.objectType == NETWORK) {
+ networkTitle2ID = new HashMap<String, String>();
+
+ Set<CyNetwork> networkSet = Cytoscape.getNetworkSet();
+
+ for (CyNetwork net : networkSet) {
+ networkTitle2ID.put(net.getTitle(), net.getIdentifier());
+ }
+ } else {
+ networkTitle2ID = null;
+ }
+
+ /*
+ * If attribute mapping is null, use ID for mapping.
+ */
+ if (mappingAttribute == null) {
+ this.mappingAttribute = ID;
+ } else {
+ this.mappingAttribute = mappingAttribute;
+ }
+
+ /*
+ * If delimiter is not available, use default value (TAB)
+ */
+ if (delimiters == null) {
+ this.delimiters = new ArrayList<String>();
+ this.delimiters.add(DEF_DELIMITER);
+ } else {
+ this.delimiters = delimiters;
+ }
+
+ /*
+ * If list delimiter is null, use default "|"
+ */
+ if (listDelimiter == null) {
+ this.listDelimiter = DEF_LIST_DELIMITER;
+ } else {
+ this.listDelimiter = listDelimiter;
+ }
+
+ if (aliasIndex == null) {
+ this.aliasIndex = new ArrayList<Integer>();
+ } else {
+ this.aliasIndex = aliasIndex;
+ }
+
+ /*
+ * If not specified, import everything as String attributes.
+ */
+ if (attributeTypes == null) {
+ this.attributeTypes = new Byte[attrNames.length];
+
+ for (int i = 0; i < attrNames.length; i++) {
+ this.attributeTypes[i] = CyAttributes.TYPE_STRING;
+ }
+ } else {
+ this.attributeTypes = attributeTypes;
+ }
+
+ /*
+ * If not specified, import everything.
+ */
+ if (importFlag == null) {
+ this.importFlag = new boolean[attrNames.length];
+
+ for (int i = 0; i < this.importFlag.length; i++) {
+ this.importFlag[i] = true;
+ }
+ } else {
+ this.importFlag = importFlag;
+ }
+
+ final Iterator it;
+
+ switch (objectType) {
+ case NODE:
+ attributes = Cytoscape.getNodeAttributes();
+ existingAliases = Cytoscape.getOntologyServer().getNodeAliases();
+ it = Cytoscape.getRootGraph().nodesIterator();
+
+ break;
+
+ case EDGE:
+ attributes = Cytoscape.getEdgeAttributes();
+ existingAliases = Cytoscape.getOntologyServer().getEdgeAliases();
+ it = Cytoscape.getRootGraph().edgesIterator();
+
+ break;
+
+ case NETWORK:
+ attributes = Cytoscape.getNetworkAttributes();
+ existingAliases = Cytoscape.getOntologyServer().getNetworkAliases();
+ it = Cytoscape.getNetworkSet().iterator();
+
+ break;
+
+ default:
+ attributes = null;
+ it = null;
+ }
+
+ if ((this.mappingAttribute != null) && !this.mappingAttribute.equals(ID)) {
+ buildAttribute2IDMap(it);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Aliases getAlias() {
+ return existingAliases;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public CyAttributes getAttributes() {
+ return attributes;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public List<Integer> getAliasIndexList() {
+ return aliasIndex;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String[] getAttributeNames() {
+ // TODO Auto-generated method stub
+ return attributeNames;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Byte[] getAttributeTypes() {
+ return attributeTypes;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Byte[] getListAttributeTypes() {
+ return listAttributeTypes;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean[] getImportFlag() {
+ // TODO Auto-generated method stub
+ return importFlag;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getKeyIndex() {
+ // TODO Auto-generated method stub
+ return keyIndex;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getListDelimiter() {
+ // TODO Auto-generated method stub
+ return listDelimiter;
+ }
+
+ /**
+ * Returns attribute name for mapping.
+ *
+ * @return Key CyAttribute name for mapping.
+ */
+ public String getMappingAttribute() {
+ return mappingAttribute;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public ObjectType getObjectType() {
+ // TODO Auto-generated method stub
+ return objectType;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public List<String> getDelimiters() {
+ return delimiters;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getDelimiterRegEx() {
+ StringBuffer delimiterBuffer = new StringBuffer();
+ delimiterBuffer.append("[");
+
+ for (String delimiter : delimiters) {
+ if (delimiter.equals(" += +")) {
+ return " += +";
+ }
+
+ delimiterBuffer.append(delimiter);
+ }
+
+ delimiterBuffer.append("]");
+
+ return delimiterBuffer.toString();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param attributeValue DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public List<String> toID(String attributeValue) {
+ return attr2id.get(attributeValue);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Map<String, List<String>> getAttributeToIDMap() {
+ return attr2id;
+ }
+
+ /**
+ * Building hashmap for attribute <--> object ID mapping.
+ *
+ */
+ private void buildAttribute2IDMap(Iterator it) {
+ // Mapping from attribute value to object ID.
+ attr2id = new HashMap<String, List<String>>();
+
+ String objectID = null;
+ Object valObj = null;
+
+ while (it.hasNext()) {
+ switch (objectType) {
+ case NODE:
+
+ Node node = (Node) it.next();
+ objectID = node.getIdentifier();
+
+ if (CyAttributesUtils.getClass(mappingAttribute, attributes) == List.class) {
+ valObj = attributes.getListAttribute(objectID, mappingAttribute);
+ } else if (CyAttributesUtils.getClass(mappingAttribute, attributes) != Map.class) {
+ valObj = attributes.getAttribute(objectID, mappingAttribute);
+ }
+
+ break;
+
+ case EDGE:
+
+ Edge edge = (Edge) it.next();
+ objectID = edge.getIdentifier();
+
+ if (CyAttributesUtils.getClass(mappingAttribute, attributes) == List.class) {
+ valObj = attributes.getListAttribute(objectID, mappingAttribute);
+ } else if (CyAttributesUtils.getClass(mappingAttribute, attributes) != Map.class) {
+ valObj = attributes.getAttribute(objectID, mappingAttribute);
+ }
+
+ break;
+
+ case NETWORK:
+ // Not supported yet.
+ it.next();
+
+ break;
+
+ default:
+ }
+
+ // Put the <attribute value>-<object ID list> pair to the Map object.
+ if (valObj != null) {
+ if (valObj instanceof List) {
+ List keys = (List) valObj;
+
+ for (Object key : keys) {
+ if (key != null) {
+ putAttrValue(key.toString(), objectID);
+ }
+ }
+ } else {
+ putAttrValue(valObj.toString(), objectID);
+ }
+
+ // if (attr2id.containsKey(attributeValue)) {
+ // objIdList = (List<String>) attr2id.get(attributeValue);
+ // } else {
+ // objIdList = new ArrayList<String>();
+ // }
+ //
+ // objIdList.add(objectID);
+ // attr2id.put(attributeValue, objIdList);
+ }
+ }
+ }
+
+ private void putAttrValue(String attributeValue, String objectID) {
+ List<String> objIdList = null;
+
+ if (attr2id.containsKey(attributeValue)) {
+ objIdList = attr2id.get(attributeValue);
+ } else {
+ objIdList = new ArrayList<String>();
+ }
+
+ objIdList.add(objectID);
+ attr2id.put(attributeValue, objIdList);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getColumnCount() {
+ // TODO Auto-generated method stub
+ return attributeNames.length;
+ }
+
+ protected Map<String, String> getnetworkTitleMap() {
+ return networkTitle2ID;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Boolean getCaseSensitive() {
+ return caseSensitive;
+ }
+}
diff --git a/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/reader/DefaultAttributeTableReader.java b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/reader/DefaultAttributeTableReader.java
new file mode 100644
index 0000000..6ce60a0
--- /dev/null
+++ b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/reader/DefaultAttributeTableReader.java
@@ -0,0 +1,267 @@
+
+/*
+ Copyright (c) 2006, 2007, 2009, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package edu.ucsd.bioeng.coreplugin.tableImport.reader;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+
+import cytoscape.util.URLUtil;
+import cytoscape.logger.CyLogger;
+
+
+/**
+ * Basic text table reader for attributes.<br>
+ *
+ * <p>
+ * based on the given parameters, map the text table to CyAttributes.
+ * </p>
+ *
+ * @author kono
+ *
+ */
+public class DefaultAttributeTableReader implements TextTableReader {
+ /**
+ * Lines begin with this charactor will be considered as comment lines.
+ */
+ private static final int DEF_KEY_COLUMN = 0;
+ private final URL source;
+ private AttributeMappingParameters mapping;
+ private final AttributeLineParser parser;
+ private static CyLogger logger = CyLogger.getLogger(DefaultAttributeTableReader.class);
+
+ // Number of mapped attributes.
+ private int globalCounter = 0;
+
+ /*
+ * Reader will read entries from this line.
+ */
+ private final int startLineNumber;
+ private String commentChar = null;
+
+ // If this is on, import everything using ID as the key.
+ private boolean importAll = false;
+
+ /**
+ * Constructor.<br>
+ *
+ * @param source
+ * @param objectType
+ * @param delimiters
+ * @throws Exception
+ */
+ public DefaultAttributeTableReader(final URL source, final ObjectType objectType,
+ final List<String> delimiters) throws Exception {
+ this(source, objectType, delimiters, null, DEF_KEY_COLUMN, null, null, null, null, null, 0);
+ }
+
+ /**
+ * Creates a new DefaultAttributeTableReader object.
+ *
+ * @param source DOCUMENT ME!
+ * @param objectType DOCUMENT ME!
+ * @param delimiters DOCUMENT ME!
+ * @param key DOCUMENT ME!
+ * @param columnNames DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public DefaultAttributeTableReader(final URL source, final ObjectType objectType,
+ final List<String> delimiters, final int key,
+ final String[] columnNames) throws Exception {
+ this(source, objectType, delimiters, null, DEF_KEY_COLUMN, null, null, columnNames, null,
+ null, 0);
+ }
+
+ /**
+ * Constructor with full options.<br>
+ *
+ * @param source
+ * Source file URL (can be remote or local)
+ * @param objectType
+ * @param delimiter
+ * @param listDelimiter
+ * @param key
+ * @param aliases
+ * @param columnNames
+ * @param toBeImported
+ * @throws Exception
+ */
+ public DefaultAttributeTableReader(final URL source, final ObjectType objectType,
+ final List<String> delimiters, final String listDelimiter,
+ final int keyIndex, final String mappingAttribute,
+ final List<Integer> aliasIndexList,
+ final String[] attributeNames, final Byte[] attributeTypes,
+ final boolean[] importFlag, final int startLineNumber)
+ throws Exception {
+ this.source = source;
+ this.startLineNumber = startLineNumber;
+ this.mapping = new AttributeMappingParameters(objectType, delimiters, listDelimiter,
+ keyIndex, mappingAttribute, aliasIndexList,
+ attributeNames, attributeTypes, null,
+ importFlag);
+ this.parser = new AttributeLineParser(mapping);
+ }
+
+ /**
+ * Creates a new DefaultAttributeTableReader object.
+ *
+ * @param source DOCUMENT ME!
+ * @param mapping DOCUMENT ME!
+ * @param startLineNumber DOCUMENT ME!
+ * @param commentChar DOCUMENT ME!
+ */
+ public DefaultAttributeTableReader(final URL source, AttributeMappingParameters mapping,
+ final int startLineNumber, final String commentChar) {
+ this(source, mapping, startLineNumber, commentChar, false);
+ }
+
+ public DefaultAttributeTableReader(final URL source, AttributeMappingParameters mapping,
+ final int startLineNumber, final String commentChar, boolean importAll) {
+ this.source = source;
+ this.mapping = mapping;
+ this.startLineNumber = startLineNumber;
+ this.parser = new AttributeLineParser(mapping);
+ this.commentChar = commentChar;
+ this.importAll = importAll;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public List getColumnNames() {
+ List<String> colNamesList = new ArrayList<String>();
+
+ for (String name : mapping.getAttributeNames()) {
+ colNamesList.add(name);
+ }
+
+ return colNamesList;
+ }
+
+ /**
+ * Read table from the data source.
+ */
+ public void readTable() throws IOException {
+ InputStream is = null;
+
+ try {
+ BufferedReader bufRd = null;
+
+ is = URLUtil.getInputStream(source);
+ try {
+ String line;
+ int lineCount = 0;
+
+ bufRd = new BufferedReader(new InputStreamReader(is));
+ /*
+ * Read & extract one line at a time. The line can be Tab delimited,
+ */
+ String[] parts = null;
+
+ final String delimiter = mapping.getDelimiterRegEx();
+ while ((line = bufRd.readLine()) != null) {
+ /*
+ * Ignore Empty & Commnet lines.
+ */
+ if ((commentChar != null) && line.startsWith(commentChar)) {
+ // Do nothing
+ } else if ((lineCount >= startLineNumber) && (line.trim().length() > 0)) {
+ parts = line.split(delimiter);
+ // If key dos not exists, ignore the line.
+ if(parts.length>=mapping.getKeyIndex()+1) {
+ try {
+ if(importAll) {
+ parser.parseAll(parts);
+ } else
+ parser.parseEntry(parts);
+ } catch (Exception ex) {
+ logger.warn("Couldn't parse row: "+ lineCount);
+ }
+ globalCounter++;
+ }
+ }
+
+ lineCount++;
+ }
+ }
+ finally {
+ if (bufRd != null) {
+ bufRd.close();
+ }
+ }
+ }
+ finally {
+ if (is != null) {
+ is.close();
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getReport() {
+ final StringBuilder sb = new StringBuilder();
+ final Map<String, Object> invalid = parser.getInvalidMap();
+ sb.append(globalCounter + " entries are loaded and mapped onto\n");
+ sb.append(mapping.getObjectType().toString() + " attributes.");
+
+ if(invalid.size() > 0) {
+ sb.append("\n\nThe following enties are invalid and were not imported:\n");
+ int limit = 10;
+ for(String key: invalid.keySet()) {
+ sb.append(key + " = " + invalid.get(key) + "\n");
+ if ( limit-- <= 0 ) {
+ sb.append("Approximately " + (invalid.size() - 10) +
+ " additional entries were not imported...");
+ break;
+ }
+ }
+ }
+ return sb.toString();
+ }
+}
diff --git a/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/reader/ExcelAttributeSheetReader.java b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/reader/ExcelAttributeSheetReader.java
new file mode 100644
index 0000000..93abdda
--- /dev/null
+++ b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/reader/ExcelAttributeSheetReader.java
@@ -0,0 +1,205 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package edu.ucsd.bioeng.coreplugin.tableImport.reader;
+
+import java.io.IOException;
+import java.util.Arrays;
+import java.util.List;
+import java.util.Map;
+
+import org.apache.poi.ss.usermodel.Cell;
+import org.apache.poi.ss.usermodel.Row;
+import org.apache.poi.ss.usermodel.Sheet;
+
+import cytoscape.data.CyAttributes;
+import cytoscape.logger.CyLogger;
+
+
+/**
+ * Reader for Excel attribute workbook.<br>
+ * This class creates string array and pass it to the AttributeLineParser.<br>
+ *
+ * <p>
+ * This reader takes one sheet at a time.
+ * </p>
+ *
+ * @version 0.7
+ * @since Cytoscape 2.4
+ * @author kono
+ *
+ */
+public class ExcelAttributeSheetReader implements TextTableReader {
+ private final Sheet sheet;
+ private final AttributeMappingParameters mapping;
+ private final AttributeLineParser parser;
+ private final int startLineNumber;
+ private int globalCounter = 0;
+ private boolean importAll = false;
+ private CyLogger logger = CyLogger.getLogger(ExcelAttributeSheetReader.class);
+
+ /**
+ * Constructor.<br>
+ *
+ * Takes one Excel sheet as parameter.
+ *
+ * @param sheet
+ * @param mapping
+ */
+ public ExcelAttributeSheetReader(final Sheet sheet,
+ final AttributeMappingParameters mapping,
+ final int startLineNumber) {
+ this(sheet, mapping, startLineNumber, false);
+ }
+
+ /**
+ * Creates a new ExcelAttributeSheetReader object.
+ *
+ * @param sheet DOCUMENT ME!
+ * @param mapping DOCUMENT ME!
+ * @param startLineNumber DOCUMENT ME!
+ * @param importAll DOCUMENT ME!
+ */
+ public ExcelAttributeSheetReader(final Sheet sheet,
+ final AttributeMappingParameters mapping,
+ final int startLineNumber, boolean importAll) {
+ this.sheet = sheet;
+ this.mapping = mapping;
+ this.startLineNumber = startLineNumber;
+ this.parser = new AttributeLineParser(mapping);
+ this.importAll = importAll;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public List<String> getColumnNames() {
+ return Arrays.asList(mapping.getAttributeNames());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws IOException DOCUMENT ME!
+ */
+ public void readTable() throws IOException {
+ Row row;
+ int rowCount = startLineNumber;
+ String[] cellsInOneRow;
+
+ while ((row = sheet.getRow(rowCount)) != null) {
+ cellsInOneRow = createElementStringArray(row);
+ try {
+ if(importAll)
+ parser.parseAll(cellsInOneRow);
+ else
+ parser.parseEntry(cellsInOneRow);
+ } catch (Exception ex) {
+ logger.warn("Couldn't parse row: " + rowCount, ex);
+ }
+
+ rowCount++;
+ globalCounter++;
+ }
+ }
+
+ /**
+ * For a given Excell row, convert the cells into String.
+ *
+ * @param row
+ * @return
+ */
+ private String[] createElementStringArray(Row row) {
+ String[] cells = new String[mapping.getColumnCount()];
+ Cell cell = null;
+
+ for (short i = 0; i < mapping.getColumnCount(); i++) {
+ cell = row.getCell(i);
+
+ if (cell == null) {
+ cells[i] = null;
+ } else if (cell.getCellType() == Cell.CELL_TYPE_STRING) {
+ cells[i] = cell.getRichStringCellValue().getString();
+ } else if (cell.getCellType() == Cell.CELL_TYPE_NUMERIC) {
+ if (mapping.getAttributeTypes()[i] == CyAttributes.TYPE_INTEGER) {
+ Double dblValue = cell.getNumericCellValue();
+ Integer intValue = dblValue.intValue();
+ cells[i] = intValue.toString();
+ } else {
+ cells[i] = Double.toString(cell.getNumericCellValue());
+ }
+ } else if (cell.getCellType() == Cell.CELL_TYPE_BOOLEAN) {
+ cells[i] = Boolean.toString(cell.getBooleanCellValue());
+ } else if (cell.getCellType() == Cell.CELL_TYPE_BLANK) {
+ cells[i] = null;
+ } else if (cell.getCellType() == Cell.CELL_TYPE_ERROR) {
+ cells[i] = null;
+ logger.warn("Error found when reading a cell!");
+ }
+ }
+
+ return cells;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getReport() {
+ final StringBuilder sb = new StringBuilder();
+ final Map<String, Object> invalid = parser.getInvalidMap();
+ sb.append(globalCounter + " entries are loaded and mapped onto\n");
+ sb.append(mapping.getObjectType().toString() + " attributes.");
+
+ int limit = 10;
+ if (invalid.size() > 0) {
+ sb.append("\n\nThe following enties are invalid and were not imported:\n");
+
+ for (String key : invalid.keySet()) {
+ sb.append(key + " = " + invalid.get(key) + "\n");
+ if ( limit-- <= 0 ) {
+ sb.append("Approximately " + (invalid.size() - 10) +
+ " additional entries were not imported...");
+ break;
+ }
+
+ }
+ }
+
+ return sb.toString();
+ }
+}
diff --git a/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/reader/ExcelNetworkSheetReader.java b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/reader/ExcelNetworkSheetReader.java
new file mode 100644
index 0000000..7bc01b7
--- /dev/null
+++ b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/reader/ExcelNetworkSheetReader.java
@@ -0,0 +1,152 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package edu.ucsd.bioeng.coreplugin.tableImport.reader;
+
+import java.io.IOException;
+
+import org.apache.poi.ss.usermodel.Cell;
+import org.apache.poi.ss.usermodel.Row;
+import org.apache.poi.ss.usermodel.Sheet;
+
+import cytoscape.data.CyAttributes;
+import cytoscape.logger.CyLogger;
+
+
+/**
+ * Reader for Network file in Excel (.xls) format.<br>
+ *
+ * <p>
+ * Currently supports only one sheet.
+ * </p>
+ *
+ * @since Cytoscape 2.4
+ * @version 0.6
+ * @author Keiichiro Ono
+ */
+public class ExcelNetworkSheetReader extends NetworkTableReader {
+ private final Sheet sheet;
+ private CyLogger logger = CyLogger.getLogger(ExcelNetworkSheetReader.class);
+
+ /*
+ * Reader will read entries from this line.
+ */
+ /**
+ * Creates a new ExcelNetworkSheetReader object.
+ *
+ * @param networkName DOCUMENT ME!
+ * @param sheet DOCUMENT ME!
+ * @param nmp DOCUMENT ME!
+ */
+ public ExcelNetworkSheetReader(final String networkName, final Sheet sheet,
+ final NetworkTableMappingParameters nmp) {
+ this(networkName, sheet, nmp, 0);
+ }
+
+ /**
+ * Creates a new ExcelNetworkSheetReader object.
+ *
+ * @param networkName DOCUMENT ME!
+ * @param sheet DOCUMENT ME!
+ * @param nmp DOCUMENT ME!
+ * @param startLineNumber DOCUMENT ME!
+ */
+ public ExcelNetworkSheetReader(final String networkName, final Sheet sheet,
+ final NetworkTableMappingParameters nmp, final int startLineNumber) {
+ super(networkName, null, nmp, startLineNumber, null);
+ this.sheet = sheet;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws IOException DOCUMENT ME!
+ */
+ @Override
+ public void readTable() throws IOException {
+ Row row;
+ int rowCount = startLineNumber;
+ String[] cellsInOneRow;
+
+ while ((row = sheet.getRow(rowCount)) != null) {
+ cellsInOneRow = createElementStringArray(row);
+ try {
+ parser.parseEntry(cellsInOneRow);
+ } catch (Exception e) {
+ logger.warn("Couldn't parse row: " + rowCount, e);
+ }
+ rowCount++;
+ }
+ }
+
+ /**
+ * For a given Excell row, convert the cells into String.
+ *
+ * @param row
+ * @return
+ */
+ private String[] createElementStringArray(final Row row) {
+ String[] cells = new String[nmp.getColumnCount()];
+ Cell cell = null;
+
+ for (short i = 0; i < nmp.getColumnCount(); i++) {
+ cell = row.getCell(i);
+
+ if (cell == null) {
+ cells[i] = null;
+ } else if (cell.getCellType() == Cell.CELL_TYPE_STRING) {
+ cells[i] = cell.getRichStringCellValue().getString();
+ } else if (cell.getCellType() == Cell.CELL_TYPE_NUMERIC) {
+ if (nmp.getAttributeTypes()[i] == CyAttributes.TYPE_INTEGER) {
+ Double dblValue = cell.getNumericCellValue();
+ Integer intValue = dblValue.intValue();
+ cells[i] = intValue.toString();
+ } else {
+ cells[i] = Double.toString(cell.getNumericCellValue());
+ }
+ } else if (cell.getCellType() == Cell.CELL_TYPE_BOOLEAN) {
+ cells[i] = Boolean.toString(cell.getBooleanCellValue());
+ } else if (cell.getCellType() == Cell.CELL_TYPE_BLANK) {
+ cells[i] = null;
+ } else if (cell.getCellType() == Cell.CELL_TYPE_ERROR) {
+ cells[i] = null;
+ logger.warn("Error found when reading a cell!");
+ }
+ }
+
+ return cells;
+ }
+}
diff --git a/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/reader/GeneAssociationReader.java b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/reader/GeneAssociationReader.java
new file mode 100644
index 0000000..f8b0d9b
--- /dev/null
+++ b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/reader/GeneAssociationReader.java
@@ -0,0 +1,540 @@
+/*
+ Copyright (c) 2006, 2007, 2009, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+package edu.ucsd.bioeng.coreplugin.tableImport.reader;
+
+import static edu.ucsd.bioeng.coreplugin.tableImport.reader.TextFileDelimiters.PIPE;
+import static edu.ucsd.bioeng.coreplugin.tableImport.reader.TextFileDelimiters.TAB;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.TreeSet;
+
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+import cytoscape.data.CyAttributes;
+import cytoscape.data.ontology.GeneOntology;
+import cytoscape.data.ontology.Ontology;
+import cytoscape.data.synonyms.Aliases;
+import cytoscape.util.BioDataServerUtil;
+import edu.ucsd.bioeng.coreplugin.tableImport.TableImportPlugin;
+import giny.model.Node;
+
+/**
+ * <p>
+ * Gene Association (GA) file reader.<br>
+ * This is a special reader only for valid GA files.<br>
+ * </p>
+ *
+ * <p>
+ * Gene Association file is an annotation file for Gene Ontology. A valid GA
+ * file is:<br>
+ * <ul>
+ * <li>Should have 15 columns</li>
+ * <li>Tab delimited</li>
+ * <li>Key is column3, GO term is column5, and alias is column11.</li>
+ * </ul>
+ * <br>
+ * This reader accepts only valid GA file.<br>
+ * For more detail, please visit the following web site: <href
+ * a="http://www.geneontology.org/GO.current.annotations.shtml"/>
+ * </p>
+ *
+ * <p>
+ * Since Cytoscape do not use Annotation class any more, CyAtteibutes imported
+ * by this reader will be tagged with a special hidden attribute called
+ * "isAnnotation." This is a boolean value to distinguish these values from
+ * other regular attributes.
+ * </p>
+ *
+ * @version 0.8
+ * @since Cytoscape 2.4
+ * @author Keiichiro Ono
+ *
+ */
+public class GeneAssociationReader implements TextTableReader {
+
+ private static final String GO_PREFIX = "GO";
+ private static final String ANNOTATION_PREFIX = "annotation";
+ private static final String GA_DELIMITER = TAB.toString();
+ private static final String ID = "ID";
+ private static final int EXPECTED_COL_COUNT = GeneAssociationTags.values().length;
+
+ /*
+ * Default key columns
+ */
+ private static final int DB_OBJ_ID = 1;
+ private static int key = 2;
+ private static final int OBJ_NAME = 9;
+ private static final int SYNONYM = 10;
+ private static final int GOID = 4;
+ private static final String TAXON_RESOURCE_FILE = "resources/tax_report.txt";
+ private InputStream is;
+ private final String keyAttributeName;
+ private Aliases nodeAliases;
+ private Map<String, List<String>> attr2id;
+ private CyAttributes nodeAttributes;
+ private GeneOntology geneOntology;
+ private Map<String, String> speciesMap;
+ private boolean importAll = false;
+
+ private final boolean caseSensitive;
+ private Map<String, String> uppercaseIDMap;
+
+ public GeneAssociationReader(final String ontologyName,
+ final InputStream is, final String keyAttributeName,
+ final boolean importAll, final int mappingKey,
+ final boolean caseSensitive) throws IOException {
+ this(ontologyName, is, keyAttributeName, importAll, mappingKey,
+ caseSensitive, TAXON_RESOURCE_FILE);
+ }
+
+ /**
+ * Package protected because only in unit testing do we need to specify the
+ * taxon resource file. Normal operation should use one of the other
+ * constructors.
+ */
+ public GeneAssociationReader(final String ontologyName,
+ final InputStream is, final String keyAttributeName,
+ final boolean importAll, final int mappingKey,
+ final boolean caseSensitive, final String taxonResourceFile)
+ throws IOException {
+ this.importAll = importAll;
+ this.is = is;
+ this.keyAttributeName = keyAttributeName;
+ this.caseSensitive = caseSensitive;
+
+ key = mappingKey;
+
+ System.out.println("!!!! Case sensitivity is " + this.caseSensitive);
+
+ // GA file is only for nodes!
+ this.nodeAliases = Cytoscape.getOntologyServer().getNodeAliases();
+ this.nodeAttributes = Cytoscape.getNodeAttributes();
+
+ final Ontology testOntology = Cytoscape.getOntologyServer()
+ .getOntologies().get(ontologyName);
+ /*
+ * Ontology type should be GO.
+ */
+ if (testOntology == null)
+ throw new IOException("Could not find ontology data for "
+ + ontologyName + " in memory.");
+
+ if (testOntology.getClass() == GeneOntology.class)
+ this.geneOntology = (GeneOntology) testOntology;
+ else
+ throw new IllegalArgumentException(
+ "Given ontology is not Gene Ontology. Gene Assiciation File can be used with GO only.");
+
+ // get URL for resource file.
+ URL taxUrl = TableImportPlugin.class
+ .getResource(taxonResourceFile);
+ if (taxUrl == null)
+ taxUrl = TableImportPlugin.class.getClassLoader().getResource(taxonResourceFile);
+ if (taxUrl == null)
+ throw new IllegalStateException("Could not find taxonomy ID conversion table.");
+
+ BufferedReader taxonFileReader = null;
+
+ try {
+ taxonFileReader = new BufferedReader(new InputStreamReader(taxUrl
+ .openStream()));
+ final BioDataServerUtil bdsu = new BioDataServerUtil();
+ this.speciesMap = bdsu.getTaxonMap(taxonFileReader);
+ } finally {
+ if (taxonFileReader != null) {
+ taxonFileReader.close();
+ }
+ }
+
+ // If key is NOT ID, create mapping.
+ if ((this.keyAttributeName != null)
+ && !this.keyAttributeName.equals(ID))
+ buildMap();
+
+ if (!caseSensitive) {
+ // Create all uppercase ID map
+ uppercaseIDMap = new HashMap<String, String>();
+ List<CyNode> nodes = Cytoscape.getRootGraph().nodesList();
+ for (CyNode node : nodes)
+ uppercaseIDMap.put(node.getIdentifier().toUpperCase(), node
+ .getIdentifier());
+
+ nodes.clear();
+ nodes = null;
+ }
+
+ }
+
+ /**
+ * Create mapping from key attribute value to IDs
+ */
+ private void buildMap() {
+ attr2id = new HashMap<String, List<String>>();
+
+ final Iterator<CyNode> it = Cytoscape.getRootGraph().nodesIterator();
+
+ String nodeID = null;
+ Node node = null;
+ String attributeValue = null;
+ List<String> nodeIdList = null;
+
+ while (it.hasNext()) {
+ node = it.next();
+ nodeID = node.getIdentifier();
+ attributeValue = nodeAttributes.getStringAttribute(nodeID,
+ keyAttributeName);
+
+ if (attributeValue != null) {
+ if (attr2id.containsKey(attributeValue))
+ nodeIdList = attr2id.get(attributeValue);
+ else
+ nodeIdList = new ArrayList<String>();
+
+ nodeIdList.add(nodeID);
+ attr2id.put(attributeValue, nodeIdList);
+ }
+ }
+ }
+
+ /**
+ * Read Gene Association file
+ *
+ * @throws IOException
+ * DOCUMENT ME!
+ */
+ public void readTable() throws IOException {
+ try {
+ try {
+ BufferedReader bufRd = null;
+
+ try {
+ String line = null;
+ String[] parts;
+
+ int global = 0;
+
+ bufRd = new BufferedReader(new InputStreamReader(is));
+ while ((line = bufRd.readLine()) != null) {
+ global++;
+ parts = line.split(GA_DELIMITER);
+
+ if (parts.length == EXPECTED_COL_COUNT)
+ parseGA(parts);
+ }
+ } finally {
+ if (bufRd != null) {
+ bufRd.close();
+ }
+ }
+ } finally {
+ if (is != null) {
+ is.close();
+ }
+ }
+ } finally {
+ is = null;
+ if (uppercaseIDMap != null) {
+ uppercaseIDMap.clear();
+ uppercaseIDMap = null;
+ }
+ }
+ }
+
+ /**
+ *
+ * @param key
+ * @param synoString
+ * @return
+ */
+ private String setAlias(final String key, final String objName,
+ final String synoString, final String dbSpecificId) {
+
+ final String[] synos = synoString.split(PIPE.toString());
+ final String[] objNames;
+ final Set<String> idSet = new TreeSet<String>();
+
+ if ((objName != null) && (objName.length() != 0)) {
+ String[] tempObj = objName.split(":");
+
+ if (tempObj.length != 0) {
+ objNames = tempObj[0].split(",");
+
+ for (String name : objNames)
+ idSet.add(name);
+ }
+ }
+
+ idSet.add(key);
+
+ if ((dbSpecificId != null) && (dbSpecificId.length() != 0)) {
+ idSet.add(dbSpecificId);
+ }
+
+ /*
+ * Build a Set of node names which includes all aliases and id.
+ */
+ for (String synonym : synos)
+ idSet.add(synonym);
+
+ for (String id : idSet) {
+
+ if (Cytoscape.getCyNode(id) != null) {
+ // Match found
+ if (idSet.size() != 1)
+ idSet.remove(id);
+
+ nodeAliases.add(id, new ArrayList<String>(idSet));
+
+ return id;
+ } else if (!caseSensitive) {
+ final String originalID = uppercaseIDMap.get(id.toUpperCase());
+ if (originalID == null)
+ continue;
+
+ if (idSet.size() != 1)
+ idSet.remove(originalID);
+
+ nodeAliases.add(originalID, new ArrayList<String>(idSet));
+ return originalID;
+
+ }
+ }
+
+ return null;
+ }
+
+ private List<String> setMultipleAliases(String key, String synoString) {
+ final String[] synos = synoString.split(PIPE.toString());
+ final Set<String> idSet = new TreeSet<String>();
+ idSet.add(key);
+
+ for (String synonym : synos) {
+ idSet.add(synonym);
+ }
+
+ String targetID = null;
+ for (String id : idSet) {
+ if (!caseSensitive) {
+ targetID = uppercaseIDMap.get(id.toUpperCase());
+ if (targetID == null)
+ continue;
+ } else
+ targetID = id;
+
+ if (attr2id.containsKey(targetID)) {
+ List<String> nodeIDs = attr2id.get(targetID);
+
+ for (String nodeID : nodeIDs) {
+ nodeAliases.add(nodeID, new ArrayList<String>(idSet));
+ }
+
+ return nodeIDs;
+ }
+ }
+
+ return null;
+ }
+
+ /**
+ * All fields are saved as Strings.
+ *
+ */
+ private void parseGA(String[] entries) {
+ if (geneOntology.getAspect(entries[GOID]) == null)
+ return;
+
+ /*
+ * Create attribute name based on GO Aspect (a.k.a. Name Space)
+ */
+ final String attributeName = ANNOTATION_PREFIX + "." + GO_PREFIX + " "
+ + geneOntology.getAspect(entries[GOID]).name();
+
+ /*
+ * If importAll option is selected, just import everything even if the
+ * node does not exists in the memmory.
+ */
+ if (importAll) {
+ // Add all aliases
+ if ((entries[SYNONYM] != null) && (entries[SYNONYM].length() != 0)) {
+ final String[] alias = entries[SYNONYM].split(PIPE.toString());
+ nodeAliases.add(entries[key], Arrays.asList(alias));
+ }
+
+ mapEntry(entries, entries[key], attributeName);
+ } else {
+ /*
+ * Case 1: use node ID as the key
+ */
+ if (keyAttributeName.equals(ID)) {
+ final String newKey = setAlias(entries[key], entries[OBJ_NAME],
+ entries[SYNONYM], entries[DB_OBJ_ID]);
+
+ if (newKey != null)
+ mapEntry(entries, newKey, attributeName);
+ } else {
+ /*
+ * Case 2: use an attribute as the key.
+ */
+ List<String> keys = setMultipleAliases(entries[key],
+ entries[SYNONYM]);
+
+ if (keys != null) {
+ for (String key : keys)
+ mapEntry(entries, key, attributeName);
+ }
+ }
+ }
+ }
+
+ private void mapEntry(final String[] entries, final String key,
+ final String attributeName) {
+ String fullName = null;
+
+ for (int i = 0; i < GeneAssociationTags.values().length; i++) {
+ final GeneAssociationTags tag = GeneAssociationTags.values()[i];
+
+ switch (tag) {
+ case GO_ID:
+
+ Set<String> goTermSet = new TreeSet<String>();
+
+ if (nodeAttributes.getListAttribute(key, attributeName) != null) {
+ goTermSet.addAll(nodeAttributes.getListAttribute(key,
+ attributeName));
+ }
+
+ if ((fullName = geneOntology.getGOTerm(entries[i])
+ .getFullName()) != null) {
+ goTermSet.add(fullName);
+ }
+
+ nodeAttributes.setListAttribute(key, attributeName,
+ new ArrayList(goTermSet));
+
+ break;
+
+ case TAXON:
+ if (speciesMap.get(entries[i].split(":")[1]) != null) {
+ nodeAttributes.setAttribute(key, ANNOTATION_PREFIX + "."
+ + tag.toString(), (String) speciesMap
+ .get(entries[i].split(":")[1]));
+ }
+
+ break;
+
+ case EVIDENCE:
+
+ Map<String, String> evidences = nodeAttributes.getMapAttribute(
+ key, ANNOTATION_PREFIX + "." + tag.toString());
+
+ if (evidences == null) {
+ evidences = new HashMap<String, String>();
+ }
+
+ evidences.put(entries[GOID], entries[i]);
+ nodeAttributes.setMapAttribute(key, ANNOTATION_PREFIX + "."
+ + tag.toString(), evidences);
+
+ break;
+
+ case DB_REFERENCE:
+
+ Map<String, String> references = nodeAttributes
+ .getMapAttribute(key, ANNOTATION_PREFIX + "."
+ + tag.toString());
+
+ if (references == null) {
+ references = new HashMap<String, String>();
+ }
+
+ references.put(entries[GOID], entries[i]);
+ nodeAttributes.setMapAttribute(key, ANNOTATION_PREFIX + "."
+ + tag.toString(), references);
+
+ break;
+
+ case DB_OBJECT_SYMBOL:
+ case ASPECT:
+ case DB_OBJECT_SYNONYM:
+
+ // Ignore these lines
+ break;
+
+ default:
+ nodeAttributes.setAttribute(key, ANNOTATION_PREFIX + "."
+ + tag.toString(), entries[i]);
+
+ break;
+ }
+ }
+ }
+
+ /**
+ * Return column names as List onject.
+ */
+ public List<String> getColumnNames() {
+ final List<String> colNames = new ArrayList<String>();
+
+ for (GeneAssociationTags tag : GeneAssociationTags.values()) {
+ colNames.add(tag.toString());
+ }
+
+ return colNames;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getReport() {
+ // TODO Auto-generated method stub
+ final StringBuffer sb = new StringBuffer();
+
+ return sb.toString();
+ }
+}
diff --git a/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/reader/GeneAssociationTags.java b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/reader/GeneAssociationTags.java
new file mode 100644
index 0000000..a5fcb78
--- /dev/null
+++ b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/reader/GeneAssociationTags.java
@@ -0,0 +1,98 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package edu.ucsd.bioeng.coreplugin.tableImport.reader;
+
+
+/**
+ * Reserved keywords for Gene Association files.<br>
+ * <p>
+ * For more information about GA format, please visit:<br>
+ * http://www.geneontology.org/GO.annotation.shtml#file
+ * </p>
+ * @author kono
+ *
+ */
+public enum GeneAssociationTags {
+ DB("DB"),
+ DB_OBJECT_ID("DB_Object_ID"),
+ DB_OBJECT_SYMBOL("DB_Object_Symbol"),
+ QUALIFIER("Qualifier"),
+ GO_ID("GO ID"),
+ DB_REFERENCE("DB:Reference"),
+ EVIDENCE("Evidence"),
+ WITH_OR_FROM("With (or) From"),
+ ASPECT("Aspect"),
+ DB_OBJECT_NAME("DB_Object_Name"),
+ DB_OBJECT_SYNONYM("DB_Object_Synonym"),
+ DB_OBJECT_TYPE("DB_Object_Type"),
+ TAXON("Taxon"),
+ DATE("Date"),
+ ASSIGNED_BY("Assigned_by");
+
+ private String tag;
+
+ private GeneAssociationTags(String tag) {
+ this.tag = tag;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String toString() {
+ return tag;
+ }
+
+ /**
+ * Since this enum represents a column names, we can find the index of the tag
+ * by using this method.
+ * <br>
+ * @return
+ */
+ public int getPosition() {
+ GeneAssociationTags[] tags = values();
+
+ for (int i = 0; i < tags.length; i++) {
+ if (tags[i] == this) {
+ return i;
+ }
+ }
+
+ return 0;
+ }
+}
diff --git a/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/reader/MappingParameter.java b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/reader/MappingParameter.java
new file mode 100644
index 0000000..7afe974
--- /dev/null
+++ b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/reader/MappingParameter.java
@@ -0,0 +1,115 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package edu.ucsd.bioeng.coreplugin.tableImport.reader;
+
+import edu.ucsd.bioeng.coreplugin.tableImport.reader.TextTableReader.ObjectType;
+
+import java.util.List;
+
+
+/**
+ *
+ */
+public interface MappingParameter {
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getColumnCount();
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getKeyIndex();
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public ObjectType getObjectType();
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getMappingAttribute();
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean[] getImportFlag();
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public List<Integer> getAliasIndexList();
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String[] getAttributeNames();
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Byte[] getAttributeTypes();
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getListDelimiter();
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Boolean getCaseSensitive();
+}
diff --git a/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/reader/NetworkLineParser.java b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/reader/NetworkLineParser.java
new file mode 100644
index 0000000..d9ff216
--- /dev/null
+++ b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/reader/NetworkLineParser.java
@@ -0,0 +1,218 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package edu.ucsd.bioeng.coreplugin.tableImport.reader;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.data.CyAttributes;
+import cytoscape.data.Semantics;
+
+import giny.model.Edge;
+import giny.model.Node;
+
+import java.util.ArrayList;
+import java.util.List;
+
+
+/**
+ * Parse one line for network text table
+ *
+ * @author kono
+ *
+ */
+public class NetworkLineParser {
+ private final NetworkTableMappingParameters nmp;
+ private final List<Integer> nodeList;
+ private final List<Integer> edgeList;
+
+ /**
+ * Creates a new NetworkLineParser object.
+ *
+ * @param nodeList DOCUMENT ME!
+ * @param edgeList DOCUMENT ME!
+ * @param nmp DOCUMENT ME!
+ */
+ public NetworkLineParser(List<Integer> nodeList, List<Integer> edgeList,
+ final NetworkTableMappingParameters nmp) {
+ this.nmp = nmp;
+ this.nodeList = nodeList;
+ this.edgeList = edgeList;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param parts DOCUMENT ME!
+ */
+ public void parseEntry(String[] parts) {
+ final Edge edge = addNodeAndEdge(parts);
+
+ if (edge != null)
+ addEdgeAttributes(edge, parts);
+ }
+
+
+ private Edge addNodeAndEdge(final String[] parts) {
+
+ final Node source = createNode(parts, nmp.getSourceIndex());
+ final Node target = createNode(parts, nmp.getTargetIndex());
+
+ // Single column nodes list. Just add nodes.
+ if(source == null || target == null)
+ return null;
+
+ final String interaction;
+
+ if ((nmp.getInteractionIndex() == -1) || (nmp.getInteractionIndex() > (parts.length - 1))
+ || (parts[nmp.getInteractionIndex()] == null)) {
+ interaction = nmp.getDefaultInteraction();
+ } else
+ interaction = parts[nmp.getInteractionIndex()];
+
+ final Edge edge;
+ edge = Cytoscape.getCyEdge(source, target, Semantics.INTERACTION, interaction, true, true);
+ edgeList.add(edge.getRootGraphIndex());
+
+ return edge;
+ }
+
+
+ private Node createNode(final String[] parts, final Integer nodeIndex) {
+ final Node node;
+ if (nodeIndex.equals(-1) == false && (nodeIndex <= (parts.length - 1)) && (parts[nodeIndex] != null)) {
+ node = Cytoscape.getCyNode(parts[nodeIndex], true);
+ nodeList.add(node.getRootGraphIndex());
+ } else
+ node = null;
+
+ return node;
+ }
+
+ private void addEdgeAttributes(final Edge edge, final String[] parts) {
+ for (int i = 0; i < parts.length; i++) {
+ if ((i != nmp.getSourceIndex()) && (i != nmp.getTargetIndex())
+ && (i != nmp.getInteractionIndex()) && parts[i] != null ) {
+ if ((nmp.getImportFlag().length > i) && (nmp.getImportFlag()[i] == true)) {
+ mapAttribute(edge.getIdentifier(), parts[i].trim(), i);
+ }
+ }
+ }
+ }
+
+ /**
+ * Based on the attribute types, map the entry to CyAttributes.<br>
+ *
+ * @param key
+ * @param entry
+ * @param index
+ */
+ private void mapAttribute(final String key, final String entry, final int index) {
+ Byte type = nmp.getAttributeTypes()[index];
+
+ if (entry == null || entry.length() == 0) {
+ return;
+ }
+
+ switch (type) {
+ case CyAttributes.TYPE_BOOLEAN:
+ nmp.getAttributes()
+ .setAttribute(key, nmp.getAttributeNames()[index], new Boolean(entry));
+
+ break;
+
+ case CyAttributes.TYPE_INTEGER:
+ nmp.getAttributes()
+ .setAttribute(key, nmp.getAttributeNames()[index], new Integer(entry));
+
+ break;
+
+ case CyAttributes.TYPE_FLOATING:
+ nmp.getAttributes()
+ .setAttribute(key, nmp.getAttributeNames()[index], new Double(entry));
+
+ break;
+
+ case CyAttributes.TYPE_STRING:
+ nmp.getAttributes().setAttribute(key, nmp.getAttributeNames()[index], entry);
+
+ break;
+
+ case CyAttributes.TYPE_SIMPLE_LIST:
+
+ /*
+ * In case of list, not overwrite the attribute. Get the existing
+ * list, and add it to the list.
+ */
+ List curList = nmp.getAttributes()
+ .getListAttribute(key, nmp.getAttributeNames()[index]);
+
+ if (curList == null) {
+ curList = new ArrayList();
+ }
+
+ curList.addAll(buildList(entry));
+
+ nmp.getAttributes().setListAttribute(key, nmp.getAttributeNames()[index], curList);
+
+ break;
+
+ default:
+ nmp.getAttributes().setAttribute(key, nmp.getAttributeNames()[index], entry);
+ }
+ }
+
+ /**
+ * If an entry is a list, split the string and create new List Attribute.
+ *
+ * @return
+ */
+ private List buildList(final String entry) {
+ if (entry == null) {
+ return null;
+ }
+
+ final List<String> listAttr = new ArrayList<String>();
+
+ final String[] parts = (entry.replace("\"", "")).split(nmp.getListDelimiter());
+
+ for (String listItem : parts) {
+ listAttr.add(listItem.trim());
+ }
+
+ return listAttr;
+ }
+}
diff --git a/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/reader/NetworkTableMappingParameters.java b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/reader/NetworkTableMappingParameters.java
new file mode 100644
index 0000000..fe3b541
--- /dev/null
+++ b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/reader/NetworkTableMappingParameters.java
@@ -0,0 +1,130 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package edu.ucsd.bioeng.coreplugin.tableImport.reader;
+
+import static edu.ucsd.bioeng.coreplugin.tableImport.reader.TextTableReader.ObjectType.*;
+
+import java.util.List;
+
+/**
+ * Text table <---> CyAttribute & CyNetwork mapping parameters for network
+ * table.
+ *
+ * @since Cytoscape 2.4
+ * @version 0.9
+ *
+ * @author Keiichiro Ono
+ *
+ */
+public class NetworkTableMappingParameters extends AttributeMappingParameters {
+ private static final String DEF_INTERACTION = "pp";
+ private final Integer source;
+ private final Integer target;
+ private final Integer interaction;
+ private final String defInteraction;
+
+ /**
+ * Creates a new NetworkTableMappingParameters object.
+ *
+ * @param delimiters DOCUMENT ME!
+ * @param listDelimiter DOCUMENT ME!
+ * @param attributeNames DOCUMENT ME!
+ * @param attributeTypes DOCUMENT ME!
+ * @param listAttributeTypes DOCUMENT ME!
+ * @param importFlag DOCUMENT ME!
+ * @param source DOCUMENT ME!
+ * @param target DOCUMENT ME!
+ * @param interaction DOCUMENT ME!
+ * @param defInteraction DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public NetworkTableMappingParameters(List<String> delimiters, String listDelimiter,
+ String[] attributeNames, Byte[] attributeTypes,
+ Byte[] listAttributeTypes, boolean[] importFlag,
+ Integer source, Integer target, Integer interaction,
+ final String defInteraction) throws Exception {
+ super(EDGE, delimiters, listDelimiter, -1, null, null, attributeNames, attributeTypes,
+ listAttributeTypes, importFlag);
+
+ this.source = source;
+ this.target = target;
+ this.interaction = interaction;
+
+ this.defInteraction = defInteraction;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Integer getSourceIndex() {
+ return source;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Integer getTargetIndex() {
+ return target;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Integer getInteractionIndex() {
+ return interaction;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getDefaultInteraction() {
+ if (defInteraction == null) {
+ return DEF_INTERACTION;
+ } else {
+ return defInteraction;
+ }
+ }
+}
diff --git a/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/reader/NetworkTableReader.java b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/reader/NetworkTableReader.java
new file mode 100644
index 0000000..457fc4e
--- /dev/null
+++ b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/reader/NetworkTableReader.java
@@ -0,0 +1,225 @@
+
+/*
+ Copyright (c) 2006, 2007, 2009, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package edu.ucsd.bioeng.coreplugin.tableImport.reader;
+
+import cytoscape.data.readers.AbstractGraphReader;
+import cytoscape.logger.CyLogger;
+
+import cytoscape.util.URLUtil;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+
+import java.net.URL;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Set;
+import java.util.TreeSet;
+
+
+/**
+ * Network text table reader. This implemets GraphReader just like other network
+ * file readers.<br>
+ *
+ * @since Cytoscape 2.4
+ * @version 0.8
+ * @author Keiichiro Ono
+ *
+ */
+public class NetworkTableReader extends AbstractGraphReader implements TextTableReader {
+ protected static final String COMMENT_CHAR = "!";
+ protected final NetworkTableMappingParameters nmp;
+ protected final URL sourceURL;
+ protected final NetworkLineParser parser;
+ protected final List<Integer> nodeList;
+ protected final List<Integer> edgeList;
+ protected final int startLineNumber;
+ protected final String commentChar;
+ private CyLogger logger = CyLogger.getLogger(NetworkTableReader.class);
+
+ /**
+ * Creates a new NetworkTableReader object.
+ *
+ * @param networkName DOCUMENT ME!
+ * @param sourceURL DOCUMENT ME!
+ * @param nmp DOCUMENT ME!
+ * @param startLineNumber DOCUMENT ME!
+ * @param commentChar DOCUMENT ME!
+ */
+ public NetworkTableReader(final String networkName, final URL sourceURL,
+ final NetworkTableMappingParameters nmp, final int startLineNumber,
+ final String commentChar) {
+ super(networkName);
+ this.sourceURL = sourceURL;
+ this.nmp = nmp;
+ this.startLineNumber = startLineNumber;
+ this.nodeList = new ArrayList<Integer>();
+ this.edgeList = new ArrayList<Integer>();
+ this.commentChar = commentChar;
+
+ parser = new NetworkLineParser(nodeList, edgeList, nmp);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public List getColumnNames() {
+ List<String> colNames = new ArrayList<String>();
+
+ for (String name : nmp.getAttributeNames()) {
+ colNames.add(name);
+ }
+
+ return colNames;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws IOException DOCUMENT ME!
+ */
+ public void readTable() throws IOException {
+ InputStream is = null;
+ String line;
+
+ try {
+ BufferedReader bufRd = null;
+
+ is = URLUtil.getInputStream(sourceURL);
+ try {
+ bufRd = new BufferedReader(new InputStreamReader(is));
+ /*
+ * Read & extract one line at a time. The line can be Tab delimited,
+ */
+ int lineCount = 0;
+ int skipped = 0;
+
+ while ((line = bufRd.readLine()) != null) {
+ /*
+ * Ignore Empty & Commnet lines.
+ */
+ if ((commentChar != null) && (commentChar.trim().length() != 0)
+ && line.startsWith(commentChar)) {
+ skipped++;
+ } else if ((line.trim().length() > 0) && ((startLineNumber + skipped) <= lineCount)) {
+ String[] parts = line.split(nmp.getDelimiterRegEx());
+ try {
+ parser.parseEntry(parts);
+ } catch (Exception ex) {
+ logger.warn("Couldn't parse row: " + lineCount, ex);
+ }
+ }
+
+ lineCount++;
+ }
+ }
+ finally {
+ if (bufRd != null) {
+ bufRd.close();
+ }
+ }
+ }
+ finally {
+ if (is != null) {
+ is.close();
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ public int[] getNodeIndicesArray() {
+ final int[] nodeArray = new int[nodeList.size()];
+
+ for (int i = 0; i < nodeArray.length; i++) {
+ nodeArray[i] = nodeList.get(i);
+ }
+
+ return nodeArray;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ public int[] getEdgeIndicesArray() {
+ final int[] edgeArray = new int[edgeList.size()];
+
+ for (int i = 0; i < edgeArray.length; i++) {
+ edgeArray[i] = edgeList.get(i);
+ }
+
+ return edgeArray;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws IOException DOCUMENT ME!
+ */
+ @Override
+ public void read() throws IOException {
+ readTable();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getReport() {
+ final StringBuffer sb = new StringBuffer();
+ final Set<Integer> uniqueNodes = new TreeSet<Integer>(nodeList);
+ final Set<Integer> uniqueEdges = new TreeSet<Integer>(edgeList);
+
+ sb.append(uniqueNodes.size() + " nodes and " + uniqueEdges.size() + " edges are loaded.\n");
+ sb.append("New network name is " + super.getNetworkName() + "\n\n");
+
+ return sb.toString();
+ }
+}
diff --git a/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/reader/OntologyAndAnnotationLineParser.java b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/reader/OntologyAndAnnotationLineParser.java
new file mode 100644
index 0000000..6fc75cf
--- /dev/null
+++ b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/reader/OntologyAndAnnotationLineParser.java
@@ -0,0 +1,375 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package edu.ucsd.bioeng.coreplugin.tableImport.reader;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.data.CyAttributes;
+
+import edu.ucsd.bioeng.coreplugin.tableImport.reader.TextTableReader.ObjectType;
+
+import giny.model.Edge;
+import giny.model.Node;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Set;
+import java.util.TreeSet;
+
+
+/**
+ *
+ */
+public class OntologyAndAnnotationLineParser {
+ private final AttributeAndOntologyMappingParameters mapping;
+
+ /**
+ * Creates a new OntologyAndAnnotationLineParser object.
+ *
+ * @param mapping DOCUMENT ME!
+ */
+ public OntologyAndAnnotationLineParser(AttributeAndOntologyMappingParameters mapping) {
+ this.mapping = mapping;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param parts DOCUMENT ME!
+ */
+ public void parseEntry(String[] parts) {
+ /*
+ * Split the line and extract values
+ */
+ final String primaryKey = parts[mapping.getKeyIndex()].trim();
+
+ /*
+ * Set aliases In this case, "aliases" means alias entries in the TEXT
+ * TABLE, not the ones returned by Cytoscape.getNodeAliases()
+ *
+ * The variable aliasSet has non-redundant set of object names.
+ */
+ final Set<String> aliasSet = new TreeSet<String>();
+
+ if (mapping.getAliasIndexList().size() != 0) {
+ /*
+ * Alias column exists. Extract those keys.
+ */
+ String aliasCell = null;
+
+ for (int aliasIndex : mapping.getAliasIndexList()) {
+ if (parts.length > aliasIndex) {
+ aliasCell = parts[aliasIndex];
+
+ if ((aliasCell != null) && (aliasCell.trim().length() != 0)) {
+ aliasSet.addAll(buildList(aliasCell, CyAttributes.TYPE_STRING));
+ }
+ }
+ }
+ }
+
+ aliasSet.add(primaryKey);
+
+ /*
+ * Case 1: use node ID as the key
+ */
+ if (mapping.getMappingAttribute().equals(mapping.ID)) {
+ transfer2cyattributes(primaryKey, aliasSet, parts);
+ } else {
+ /*
+ * Case 2: use an attribute as the key.
+ */
+ List<String> objectIDs = null;
+
+ for (String id : aliasSet) {
+ if (mapping.getAttributeToIDMap().containsKey(id)) {
+ objectIDs = mapping.toID(id);
+
+ for (String objectID : objectIDs) {
+ mapping.getAlias().add(objectID, new ArrayList<String>(aliasSet));
+ }
+
+ break;
+ }
+ }
+
+ if (objectIDs != null) {
+ for (String key : objectIDs) {
+ transfer2cyattributes(key, aliasSet, parts);
+ }
+ }
+ }
+ }
+
+ private void transfer2cyattributes(String primaryKey, Set<String> aliasSet, String[] parts) {
+ String altKey = null;
+ String targetNetworkID = null;
+
+ /*
+ * Search the key
+ */
+ switch (mapping.getObjectType()) {
+ case NODE:
+
+ Node node = Cytoscape.getCyNode(primaryKey);
+
+ if (node == null) {
+ for (String alias : aliasSet) {
+ node = Cytoscape.getCyNode(alias);
+
+ if (node != null) {
+ altKey = alias;
+
+ break;
+ }
+ }
+
+ if (node == null) {
+ return;
+ }
+ } else {
+ break;
+ }
+
+ break;
+
+ case EDGE:
+
+ Edge edge = Cytoscape.getRootGraph().getEdge(primaryKey);
+
+ if (edge == null) {
+ for (String alias : aliasSet) {
+ edge = Cytoscape.getRootGraph().getEdge(alias);
+
+ if (edge != null) {
+ altKey = alias;
+
+ break;
+ }
+ }
+
+ if (edge == null) {
+ return;
+ }
+ } else {
+ break;
+ }
+
+ break;
+
+ case NETWORK:
+
+ /*
+ * This is a special case: Since network IDs are only integers and
+ * not always the same, we need to use title instead of ID.
+ */
+ if (mapping.getnetworkTitleMap().containsKey(primaryKey)) {
+ targetNetworkID = mapping.getnetworkTitleMap().get(primaryKey);
+
+ break;
+ }
+
+ if (targetNetworkID == null) {
+ for (String alias : aliasSet) {
+ if (mapping.getnetworkTitleMap().containsKey(alias)) {
+ targetNetworkID = mapping.getnetworkTitleMap().get(alias);
+
+ break;
+ }
+ }
+ }
+
+ if (targetNetworkID == null) {
+ /*
+ * Network not found: just ignore this line.
+ */
+ return;
+ }
+
+ break;
+
+ default:
+ }
+
+ /*
+ * Now, transfer entries into CyAttributes.
+ */
+ for (int i = 0; i < parts.length; i++) {
+ if ((i != mapping.getKeyIndex()) && !mapping.getAliasIndexList().contains(i)
+ && mapping.getImportFlag()[i]) {
+ if (parts[i] == null) {
+ // Do nothing
+ } else if (mapping.getObjectType() == ObjectType.NETWORK) {
+ mapAttribute(targetNetworkID, parts[i].trim(), i);
+ }
+ /*
+ * Frist, check the node exists or not with the primary key
+ */
+ else if (altKey == null) {
+ mapAttribute(primaryKey, parts[i].trim(), i);
+ } else {
+ mapAttribute(altKey, parts[i].trim(), i);
+ }
+ }
+ }
+
+ /*
+ * Finally, add aliases
+ */
+ if (altKey == null) {
+ mapping.getAlias().add(primaryKey, new ArrayList<String>(aliasSet));
+ } else {
+ mapping.getAlias().add(altKey, new ArrayList<String>(aliasSet));
+ }
+ }
+
+ private void mapAttribute(final String key, final String entry, final int index) {
+ final Byte type;
+
+ if (index == mapping.getOntologyIndex()) {
+ type = CyAttributes.TYPE_SIMPLE_LIST;
+ } else {
+ type = mapping.getAttributeTypes()[index];
+ }
+
+ switch (type) {
+ case CyAttributes.TYPE_BOOLEAN:
+ mapping.getAttributes()
+ .setAttribute(key, mapping.getAttributeNames()[index], new Boolean(entry));
+
+ break;
+
+ case CyAttributes.TYPE_INTEGER:
+ mapping.getAttributes()
+ .setAttribute(key, mapping.getAttributeNames()[index], new Integer(entry));
+
+ break;
+
+ case CyAttributes.TYPE_FLOATING:
+ mapping.getAttributes()
+ .setAttribute(key, mapping.getAttributeNames()[index], new Double(entry));
+
+ break;
+
+ case CyAttributes.TYPE_STRING:
+ mapping.getAttributes().setAttribute(key, mapping.getAttributeNames()[index], entry);
+
+ break;
+
+ case CyAttributes.TYPE_SIMPLE_LIST:
+
+ /*
+ * In case of list, not overwrite the attribute. Get the existing
+ * list, and add it to the list.
+ *
+ * Since list has data types for their data types, so we need to
+ * extract it first.
+ *
+ */
+ final Byte[] listTypes = mapping.getListAttributeTypes();
+ final Byte listType;
+
+ if (index == mapping.getOntologyIndex()) {
+ listType = CyAttributes.TYPE_STRING;
+ } else if (listTypes != null) {
+ listType = listTypes[index];
+ } else {
+ listType = CyAttributes.TYPE_STRING;
+ }
+
+ List curList = mapping.getAttributes()
+ .getListAttribute(key, mapping.getAttributeNames()[index]);
+
+ if (curList == null) {
+ curList = new ArrayList();
+ }
+
+ curList.addAll(buildList(entry, listType));
+ mapping.getAttributes()
+ .setListAttribute(key, mapping.getAttributeNames()[index], curList);
+
+ break;
+
+ default:
+ mapping.getAttributes().setAttribute(key, mapping.getAttributeNames()[index], entry);
+ }
+ }
+
+ /**
+ * If an entry is a list, split the string and create new List Attribute.
+ *
+ * @return
+ */
+ private List buildList(final String entry, final Byte dataType) {
+ if (entry == null) {
+ return null;
+ }
+
+ final String[] parts = (entry.replace("\"", "")).split(mapping.getListDelimiter());
+
+ final List listAttr = new ArrayList();
+
+ for (String listItem : parts) {
+ switch (dataType) {
+ case CyAttributes.TYPE_BOOLEAN:
+ listAttr.add(Boolean.parseBoolean(listItem.trim()));
+
+ break;
+
+ case CyAttributes.TYPE_INTEGER:
+ listAttr.add(Integer.parseInt(listItem.trim()));
+
+ break;
+
+ case CyAttributes.TYPE_FLOATING:
+ listAttr.add(Double.parseDouble(listItem.trim()));
+
+ break;
+
+ case CyAttributes.TYPE_STRING:
+ listAttr.add(listItem.trim());
+
+ break;
+
+ default:
+ break;
+ }
+ }
+
+ return listAttr;
+ }
+}
diff --git a/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/reader/OntologyAnnotationReader.java b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/reader/OntologyAnnotationReader.java
new file mode 100644
index 0000000..b3af719
--- /dev/null
+++ b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/reader/OntologyAnnotationReader.java
@@ -0,0 +1,154 @@
+
+/*
+ Copyright (c) 2006, 2007, 2009, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package edu.ucsd.bioeng.coreplugin.tableImport.reader;
+
+import cytoscape.logger.CyLogger;
+import cytoscape.util.URLUtil;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+
+import java.net.URL;
+
+import java.util.List;
+
+
+/**
+ *
+ */
+public class OntologyAnnotationReader implements TextTableReader {
+ private final AttributeAndOntologyMappingParameters mapping;
+ private final URL source;
+ private final String commentChar;
+ private final int startLineNumber;
+ private final OntologyAndAnnotationLineParser parser;
+ private CyLogger logger = CyLogger.getLogger(OntologyAnnotationReader.class);
+
+ /**
+ * Creates a new OntologyAnnotationReader object.
+ *
+ * @param source DOCUMENT ME!
+ * @param mapping DOCUMENT ME!
+ * @param commentChar DOCUMENT ME!
+ * @param startLineNumber DOCUMENT ME!
+ */
+ public OntologyAnnotationReader(URL source, AttributeAndOntologyMappingParameters mapping,
+ final String commentChar, final int startLineNumber) {
+ this.source = source;
+ this.mapping = mapping;
+ this.commentChar = commentChar;
+ this.startLineNumber = startLineNumber;
+
+ parser = new OntologyAndAnnotationLineParser(mapping);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public List getColumnNames() {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws IOException DOCUMENT ME!
+ */
+ public void readTable() throws IOException {
+ InputStream is = null;
+
+ try {
+ BufferedReader bufRd = null;
+
+ is = URLUtil.getInputStream(source);
+ try {
+ bufRd = new BufferedReader(new InputStreamReader(is));
+
+ String line;
+ int lineCount = 0;
+
+ /*
+ * Read & extract one line at a time. The line can be Tab delimited,
+ */
+ while ((line = bufRd.readLine()) != null) {
+ /*
+ * Ignore Empty & Commnet lines.
+ */
+ if ((commentChar != null) && line.startsWith(commentChar)) {
+ // Do nothing
+ } else if ((lineCount > startLineNumber) && (line.trim().length() > 0)) {
+ String[] parts = line.split(mapping.getDelimiterRegEx());
+ try {
+ parser.parseEntry(parts);
+ } catch (Exception ex) {
+ logger.warn("Couldn't parse line: " + lineCount, ex);
+ }
+ }
+
+ lineCount++;
+ }
+ }
+ finally {
+ if (bufRd != null) {
+ bufRd.close();
+ }
+ }
+ }
+ finally {
+ if (is != null) {
+ is.close();
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getReport() {
+ // TODO Auto-generated method stub
+ final StringBuffer sb = new StringBuffer();
+
+ return sb.toString();
+ }
+}
diff --git a/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/reader/SupportedFileType.java b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/reader/SupportedFileType.java
new file mode 100644
index 0000000..ebb66bb
--- /dev/null
+++ b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/reader/SupportedFileType.java
@@ -0,0 +1,19 @@
+package edu.ucsd.bioeng.coreplugin.tableImport.reader;
+
+public enum SupportedFileType {
+ EXCEL("xls"), OOXML("xlsx"), TEXT("txt");
+
+ private final String extension;
+
+ private SupportedFileType(final String extension) {
+ this.extension = extension;
+ }
+
+ /**
+ *
+ * @return file extension with dot.
+ */
+ public String getExtension() {
+ return "." + extension;
+ }
+}
diff --git a/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/reader/TextFileDelimiters.java b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/reader/TextFileDelimiters.java
new file mode 100644
index 0000000..d4e8d6c
--- /dev/null
+++ b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/reader/TextFileDelimiters.java
@@ -0,0 +1,72 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package edu.ucsd.bioeng.coreplugin.tableImport.reader;
+
+
+/**
+ * Define text file delimiters as enum.
+ *
+ * @since Cytoscape 2.4
+ * @version 0.9
+ * @author Keiichiro Ono
+ *
+ */
+public enum TextFileDelimiters {
+ TAB("\\t"),
+ COMMA(","),
+ SEMICOLON(";"),
+ SPACE(" "),
+ PIPE("\\|"),
+ COLON(":"),
+ SLASH("/"),
+ BACKSLASH("\\");
+
+ private String delimiter;
+
+ private TextFileDelimiters(String delimiter) {
+ this.delimiter = delimiter;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String toString() {
+ return delimiter;
+ }
+}
diff --git a/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/reader/TextTableReader.java b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/reader/TextTableReader.java
new file mode 100644
index 0000000..9b557e8
--- /dev/null
+++ b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/reader/TextTableReader.java
@@ -0,0 +1,66 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+package edu.ucsd.bioeng.coreplugin.tableImport.reader;
+
+import java.io.IOException;
+
+import java.util.List;
+
+/**
+ * Interface of all text table readers.<br>
+ *
+ * @since Cytoscape 2.4
+ * @version 1.0
+ * @author kono
+ *
+ */
+public interface TextTableReader {
+
+ public enum ObjectType {
+ NODE, EDGE, NETWORK;
+ }
+
+ public void readTable() throws IOException;
+
+ public List<String> getColumnNames();
+
+ /**
+ * Report the result of import as a string.
+ *
+ * @return Description of
+ */
+ public String getReport();
+}
diff --git a/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/ui/AliasTableRenderer.java b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/ui/AliasTableRenderer.java
new file mode 100644
index 0000000..c150ca7
--- /dev/null
+++ b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/ui/AliasTableRenderer.java
@@ -0,0 +1,156 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package edu.ucsd.bioeng.coreplugin.tableImport.ui;
+
+import cytoscape.data.CyAttributes;
+import static edu.ucsd.bioeng.coreplugin.tableImport.ui.theme.ImportDialogFontTheme.KEY_FONT;
+import static edu.ucsd.bioeng.coreplugin.tableImport.ui.theme.ImportDialogIconSets.BOOLEAN_ICON;
+import static edu.ucsd.bioeng.coreplugin.tableImport.ui.theme.ImportDialogIconSets.FLOAT_ICON;
+import static edu.ucsd.bioeng.coreplugin.tableImport.ui.theme.ImportDialogIconSets.INT_ICON;
+import static edu.ucsd.bioeng.coreplugin.tableImport.ui.theme.ImportDialogIconSets.LIST_ICON;
+import static edu.ucsd.bioeng.coreplugin.tableImport.ui.theme.ImportDialogIconSets.STRING_ICON;
+
+import java.awt.Color;
+import java.awt.Component;
+
+import java.util.List;
+
+import javax.swing.BorderFactory;
+import javax.swing.JLabel;
+import javax.swing.JTable;
+import javax.swing.SwingConstants;
+import javax.swing.table.DefaultTableCellRenderer;
+
+
+/**
+ * Cell renderer for alias table in Import Dialog.<br>
+ *
+ * @author kono
+ *
+ */
+class AliasTableRenderer extends DefaultTableCellRenderer {
+ private List<Byte> dataTypes;
+ private int primaryKey;
+ private final JLabel iconLabel = new JLabel();
+ private final JLabel label = new JLabel();
+
+ /**
+ * Creates a new AliasTableRenderer object.
+ *
+ * @param dataTypes DOCUMENT ME!
+ * @param primaryKey DOCUMENT ME!
+ */
+ public AliasTableRenderer(List<Byte> dataTypes, int primaryKey) {
+ this.dataTypes = dataTypes;
+ this.primaryKey = primaryKey;
+
+ label.setBorder(BorderFactory.createEmptyBorder(0, 2, 0, 0));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param dataTypes DOCUMENT ME!
+ */
+ public void setDataTypes(List<Byte> dataTypes) {
+ this.dataTypes = dataTypes;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param newKey DOCUMENT ME!
+ */
+ public void setPrimaryKey(int newKey) {
+ this.primaryKey = newKey;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param table DOCUMENT ME!
+ * @param value DOCUMENT ME!
+ * @param isSelected DOCUMENT ME!
+ * @param hasFocus DOCUMENT ME!
+ * @param row DOCUMENT ME!
+ * @param column DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected,
+ boolean hasFocus, int row, int column) {
+ setBackground(Color.white);
+
+ if (column != 2) {
+ label.setText((value == null) ? "" : value.toString());
+ label.setFont(table.getFont());
+
+ if (((Boolean) table.getValueAt(row, 0) == true) && (primaryKey != row)) {
+ label.setForeground(Color.green);
+ label.setFont(KEY_FONT.getFont());
+ } else if (primaryKey == row) {
+ label.setForeground(Color.blue);
+ label.setFont(KEY_FONT.getFont());
+ } else {
+ label.setForeground(Color.black);
+ }
+
+ return label;
+ } else {
+ if (dataTypes.get(row) == CyAttributes.TYPE_STRING) {
+ iconLabel.setIcon(STRING_ICON.getIcon());
+ iconLabel.setText("String");
+ } else if (dataTypes.get(row) == CyAttributes.TYPE_INTEGER) {
+ iconLabel.setIcon(INT_ICON.getIcon());
+ iconLabel.setText("Integer");
+ } else if (dataTypes.get(row) == CyAttributes.TYPE_FLOATING) {
+ iconLabel.setIcon(FLOAT_ICON.getIcon());
+ iconLabel.setText("Float");
+ } else if (dataTypes.get(row) == CyAttributes.TYPE_BOOLEAN) {
+ iconLabel.setIcon(BOOLEAN_ICON.getIcon());
+ iconLabel.setText("Boolean");
+ } else if (dataTypes.get(row) == CyAttributes.TYPE_SIMPLE_LIST) {
+ iconLabel.setIcon(LIST_ICON.getIcon());
+ iconLabel.setText("List");
+ }
+
+ iconLabel.setHorizontalAlignment(SwingConstants.CENTER);
+
+ return iconLabel;
+ }
+ }
+}
diff --git a/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/ui/AttributePreviewTableCellRenderer.java b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/ui/AttributePreviewTableCellRenderer.java
new file mode 100644
index 0000000..9761b00
--- /dev/null
+++ b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/ui/AttributePreviewTableCellRenderer.java
@@ -0,0 +1,445 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package edu.ucsd.bioeng.coreplugin.tableImport.ui;
+
+import cytoscape.data.CyAttributes;
+import static edu.ucsd.bioeng.coreplugin.tableImport.reader.TextFileDelimiters.*;
+import static edu.ucsd.bioeng.coreplugin.tableImport.ui.theme.ImportDialogColorTheme.ALIAS_COLOR;
+import static edu.ucsd.bioeng.coreplugin.tableImport.ui.theme.ImportDialogColorTheme.EDGE_ATTR_COLOR;
+import static edu.ucsd.bioeng.coreplugin.tableImport.ui.theme.ImportDialogColorTheme.HEADER_BACKGROUND_COLOR;
+import static edu.ucsd.bioeng.coreplugin.tableImport.ui.theme.ImportDialogColorTheme.HEADER_UNSELECTED_BACKGROUND_COLOR;
+import static edu.ucsd.bioeng.coreplugin.tableImport.ui.theme.ImportDialogColorTheme.INTERACTION_COLOR;
+import static edu.ucsd.bioeng.coreplugin.tableImport.ui.theme.ImportDialogColorTheme.NOT_SELECTED_COL_COLOR;
+import static edu.ucsd.bioeng.coreplugin.tableImport.ui.theme.ImportDialogColorTheme.ONTOLOGY_COLOR;
+import static edu.ucsd.bioeng.coreplugin.tableImport.ui.theme.ImportDialogColorTheme.PRIMARY_KEY_COLOR;
+import static edu.ucsd.bioeng.coreplugin.tableImport.ui.theme.ImportDialogColorTheme.SELECTED_COLOR;
+import static edu.ucsd.bioeng.coreplugin.tableImport.ui.theme.ImportDialogColorTheme.SOURCE_COLOR;
+import static edu.ucsd.bioeng.coreplugin.tableImport.ui.theme.ImportDialogColorTheme.SPECIES_COLOR;
+import static edu.ucsd.bioeng.coreplugin.tableImport.ui.theme.ImportDialogColorTheme.TARGET_COLOR;
+import static edu.ucsd.bioeng.coreplugin.tableImport.ui.theme.ImportDialogColorTheme.UNSELECTED_COLOR;
+import static edu.ucsd.bioeng.coreplugin.tableImport.ui.theme.ImportDialogFontTheme.SELECTED_COL_FONT;
+import static edu.ucsd.bioeng.coreplugin.tableImport.ui.theme.ImportDialogFontTheme.SELECTED_FONT;
+import static edu.ucsd.bioeng.coreplugin.tableImport.ui.theme.ImportDialogFontTheme.UNSELECTED_FONT;
+import static edu.ucsd.bioeng.coreplugin.tableImport.ui.theme.ImportDialogIconSets.BOOLEAN_ICON;
+import static edu.ucsd.bioeng.coreplugin.tableImport.ui.theme.ImportDialogIconSets.CHECKED_ICON;
+import static edu.ucsd.bioeng.coreplugin.tableImport.ui.theme.ImportDialogIconSets.FLOAT_ICON;
+import static edu.ucsd.bioeng.coreplugin.tableImport.ui.theme.ImportDialogIconSets.INTEGER_ICON;
+import static edu.ucsd.bioeng.coreplugin.tableImport.ui.theme.ImportDialogIconSets.LIST_ICON;
+import static edu.ucsd.bioeng.coreplugin.tableImport.ui.theme.ImportDialogIconSets.STRING_ICON;
+import static edu.ucsd.bioeng.coreplugin.tableImport.ui.theme.ImportDialogIconSets.UNCHECKED_ICON;
+
+import java.awt.Color;
+import java.awt.Component;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.swing.BorderFactory;
+import javax.swing.ImageIcon;
+import javax.swing.JLabel;
+import javax.swing.JTable;
+import javax.swing.table.DefaultTableCellRenderer;
+import javax.swing.table.TableCellRenderer;
+
+
+/**
+ * Cell and table header renderer for preview table.
+ *
+ * @author kono
+ *
+ */
+public class AttributePreviewTableCellRenderer extends DefaultTableCellRenderer {
+
+ private static final long serialVersionUID = -8441554470062692796L;
+
+ public static final int PARAMETER_NOT_EXIST = -1;
+
+ private final static String DEF_LIST_DELIMITER = PIPE.toString();
+ private int keyInFile;
+ private List<Integer> aliases;
+ private int ontologyColumn;
+ private int species;
+ private boolean[] importFlag;
+ private String listDelimiter;
+
+ /*
+ * For network import
+ */
+ private int source;
+ private int target;
+ private int interaction;
+
+ /*
+ * Constructors.<br>
+ *
+ * Primary Key is required.
+ */
+ /**
+ * Creates a new AttributePreviewTableCellRenderer object.
+ *
+ * @param primaryKey DOCUMENT ME!
+ * @param aliases DOCUMENT ME!
+ * @param listDelimiter DOCUMENT ME!
+ */
+ public AttributePreviewTableCellRenderer(int primaryKey, List<Integer> aliases,
+ final String listDelimiter) {
+ this(primaryKey, aliases, PARAMETER_NOT_EXIST, PARAMETER_NOT_EXIST, null, listDelimiter);
+ }
+
+ /**
+ * Creates a new AttributePreviewTableCellRenderer object.
+ *
+ * @param primaryKey DOCUMENT ME!
+ * @param aliases DOCUMENT ME!
+ * @param ontologyColumn DOCUMENT ME!
+ */
+ public AttributePreviewTableCellRenderer(int primaryKey, List<Integer> aliases,
+ int ontologyColumn) {
+ this(primaryKey, aliases, ontologyColumn, PARAMETER_NOT_EXIST, null, DEF_LIST_DELIMITER);
+ }
+
+ /**
+ * Creates a new AttributePreviewTableCellRenderer object.
+ *
+ * @param primaryKey DOCUMENT ME!
+ * @param aliases DOCUMENT ME!
+ * @param ontologyColumn DOCUMENT ME!
+ * @param species DOCUMENT ME!
+ */
+ public AttributePreviewTableCellRenderer(int primaryKey, List<Integer> aliases,
+ int ontologyColumn, int species) {
+ this(primaryKey, aliases, ontologyColumn, species, null, DEF_LIST_DELIMITER);
+ }
+
+ /**
+ * Creates a new AttributePreviewTableCellRenderer object.
+ *
+ * @param primaryKey DOCUMENT ME!
+ * @param aliases DOCUMENT ME!
+ * @param ontologyColumn DOCUMENT ME!
+ * @param species DOCUMENT ME!
+ * @param importFlag DOCUMENT ME!
+ * @param listDelimiter DOCUMENT ME!
+ */
+ public AttributePreviewTableCellRenderer(int primaryKey, List<Integer> aliases,
+ int ontologyColumn, int species, boolean[] importFlag,
+ final String listDelimiter) {
+ super();
+ setOpaque(true);
+ setBorder(BorderFactory.createEmptyBorder(0, 5, 0, 5));
+
+ this.source = PARAMETER_NOT_EXIST;
+ this.target = PARAMETER_NOT_EXIST;
+ this.interaction = PARAMETER_NOT_EXIST;
+
+ this.keyInFile = primaryKey;
+ this.ontologyColumn = ontologyColumn;
+
+ if (aliases == null) {
+ this.aliases = new ArrayList<Integer>();
+ } else {
+ this.aliases = aliases;
+ }
+
+ this.species = species;
+
+ if (importFlag != null)
+ this.importFlag = importFlag;
+
+ if (listDelimiter == null) {
+ this.listDelimiter = DEF_LIST_DELIMITER;
+ } else {
+ this.listDelimiter = listDelimiter;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param index DOCUMENT ME!
+ * @param flag DOCUMENT ME!
+ */
+ public void setImportFlag(int index, boolean flag) {
+ if ((importFlag != null) && (importFlag.length > index)) {
+ importFlag[index] = flag;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param index DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean getImportFlag(int index) {
+ if ((importFlag != null) && (importFlag.length > index)) {
+ return importFlag[index];
+ }
+
+ return false;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param i DOCUMENT ME!
+ * @param flag DOCUMENT ME!
+ */
+ public void setAliasFlag(Integer i, boolean flag) {
+ if (aliases.contains(i) && (flag == false)) {
+ aliases.remove(i);
+ } else if (!aliases.contains(i) && (flag == true)) {
+ aliases.add(i);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param idx DOCUMENT ME!
+ */
+ public void setSourceIndex(int idx) {
+ source = idx;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param idx DOCUMENT ME!
+ */
+ public void setInteractionIndex(int idx) {
+ interaction = idx;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param idx DOCUMENT ME!
+ */
+ public void setTargetIndex(int idx) {
+ target = idx;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getSourceIndex() {
+ return source;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getInteractionIndex() {
+ return interaction;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getTargetIndex() {
+ return target;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param table DOCUMENT ME!
+ * @param value DOCUMENT ME!
+ * @param isSelected DOCUMENT ME!
+ * @param hasFocus DOCUMENT ME!
+ * @param row DOCUMENT ME!
+ * @param column DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected,
+ boolean hasFocus, int row, int column) {
+ setHorizontalAlignment(DefaultTableCellRenderer.CENTER);
+
+ if ((importFlag == null) || (table.getModel().getColumnCount() != importFlag.length)) {
+ importFlag = new boolean[table.getColumnCount()];
+
+ for (int i = 0; i < importFlag.length; i++) {
+ importFlag[i] = true;
+ }
+ }
+
+ if (column == keyInFile) {
+ setForeground(PRIMARY_KEY_COLOR.getColor());
+ } else if (column == ontologyColumn) {
+ setForeground(ONTOLOGY_COLOR.getColor());
+ } else if (aliases.contains(column)) {
+ setForeground(ALIAS_COLOR.getColor());
+ } else if (column == species) {
+ setForeground(SPECIES_COLOR.getColor());
+ } else if (column == source) {
+ setForeground(SOURCE_COLOR.getColor());
+ importFlag[column] = true;
+ } else if (column == target) {
+ setForeground(TARGET_COLOR.getColor());
+ importFlag[column] = true;
+ } else if (column == interaction) {
+ setForeground(INTERACTION_COLOR.getColor());
+ importFlag[column] = true;
+ } else if ((column != source) && (column != target) && (column != interaction)
+ && (source != PARAMETER_NOT_EXIST) && (importFlag[column] == true)) {
+ setForeground(EDGE_ATTR_COLOR.getColor());
+ } else {
+ setForeground(Color.BLACK);
+ }
+
+ setText((value == null) ? "" : value.toString());
+
+ if (importFlag[column] == true) {
+ setBackground(Color.WHITE);
+ setFont(SELECTED_COL_FONT.getFont());
+ } else {
+ setBackground(NOT_SELECTED_COL_COLOR.getColor());
+ setFont(table.getFont());
+ }
+
+ return this;
+ }
+}
+
+
+/**
+ * For rendering table header.
+ *
+ * @author kono
+ *
+ */
+class HeaderRenderer implements TableCellRenderer {
+ private static final int PARAMETER_NOT_EXIST = -1;
+ private final TableCellRenderer tcr;
+
+ /**
+ * Creates a new HeaderRenderer object.
+ *
+ * @param tcr DOCUMENT ME!
+ * @param dataTypes DOCUMENT ME!
+ */
+ public HeaderRenderer(TableCellRenderer tcr, Byte[] dataTypes) {
+ this.tcr = tcr;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param tbl DOCUMENT ME!
+ * @param val DOCUMENT ME!
+ * @param isS DOCUMENT ME!
+ * @param hasF DOCUMENT ME!
+ * @param row DOCUMENT ME!
+ * @param col DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Component getTableCellRendererComponent(JTable tbl, Object val, boolean isS,
+ boolean hasF, int row, int col) {
+ final JLabel columnName = (JLabel) tcr.getTableCellRendererComponent(tbl, val, isS, hasF,
+ row, col);
+ final AttributePreviewTableCellRenderer rend = (AttributePreviewTableCellRenderer) tbl
+ .getCellRenderer(0,
+ col);
+ final boolean flag = rend.getImportFlag(col);
+ final int source = rend.getSourceIndex();
+ final int interaction = rend.getInteractionIndex();
+ final int target = rend.getTargetIndex();
+
+ if (flag) {
+ columnName.setFont(SELECTED_FONT.getFont());
+ columnName.setForeground(SELECTED_COLOR.getColor());
+ columnName.setBackground(HEADER_BACKGROUND_COLOR.getColor());
+ } else {
+ columnName.setFont(UNSELECTED_FONT.getFont());
+ columnName.setForeground(UNSELECTED_COLOR.getColor());
+ columnName.setBackground(HEADER_UNSELECTED_BACKGROUND_COLOR.getColor());
+ }
+
+ if (col == source) {
+ columnName.setFont(SELECTED_FONT.getFont());
+ columnName.setForeground(SOURCE_COLOR.getColor());
+ columnName.setBackground(HEADER_BACKGROUND_COLOR.getColor());
+ } else if (col == target) {
+ columnName.setFont(SELECTED_FONT.getFont());
+ columnName.setBackground(HEADER_BACKGROUND_COLOR.getColor());
+ columnName.setForeground(TARGET_COLOR.getColor());
+ } else if (col == interaction) {
+ columnName.setFont(SELECTED_FONT.getFont());
+ columnName.setBackground(HEADER_BACKGROUND_COLOR.getColor());
+ columnName.setForeground(INTERACTION_COLOR.getColor());
+ } else if ((col != target) && (col != source) && (col != interaction)
+ && (source != PARAMETER_NOT_EXIST) && (flag == true)) {
+ columnName.setForeground(EDGE_ATTR_COLOR.getColor());
+ }
+
+ if (flag || (source == col) || (target == col) || (interaction == col)) {
+ columnName.setIcon(CHECKED_ICON.getIcon());
+ } else {
+ columnName.setIcon(UNCHECKED_ICON.getIcon());
+ }
+
+ return columnName;
+ }
+
+ private static ImageIcon getDataTypeIcon(byte dataType) {
+ ImageIcon dataTypeIcon = null;
+
+ if (dataType == CyAttributes.TYPE_STRING) {
+ dataTypeIcon = STRING_ICON.getIcon();
+ } else if (dataType == CyAttributes.TYPE_INTEGER) {
+ dataTypeIcon = INTEGER_ICON.getIcon();
+ } else if (dataType == CyAttributes.TYPE_FLOATING) {
+ dataTypeIcon = FLOAT_ICON.getIcon();
+ } else if (dataType == CyAttributes.TYPE_BOOLEAN) {
+ dataTypeIcon = BOOLEAN_ICON.getIcon();
+ } else if (dataType == CyAttributes.TYPE_SIMPLE_LIST) {
+ dataTypeIcon = LIST_ICON.getIcon();
+ }
+
+ return dataTypeIcon;
+ }
+}
diff --git a/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/ui/AttributeTypeDialog.java b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/ui/AttributeTypeDialog.java
new file mode 100644
index 0000000..95151ec
--- /dev/null
+++ b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/ui/AttributeTypeDialog.java
@@ -0,0 +1,531 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package edu.ucsd.bioeng.coreplugin.tableImport.ui;
+
+import cytoscape.data.CyAttributes;
+import static edu.ucsd.bioeng.coreplugin.tableImport.reader.TextFileDelimiters.*;
+
+import java.awt.Frame;
+import java.awt.event.ActionEvent;
+
+import javax.swing.DefaultComboBoxModel;
+
+/**
+ *
+ * @author kono
+ */
+public class AttributeTypeDialog extends javax.swing.JDialog {
+ private static final String STRING = "List of Strings";
+ private static final String INTEGER = "List of Integers";
+ private static final String FLOAT = "List of Floating Point Numbers";
+ private static final String BOOLEAN = "List of Booleans";
+ private byte dataType;
+ private String name;
+ private static final String[] LIST_DATA_TYPES = { STRING, INTEGER, FLOAT, BOOLEAN };
+
+ /** Creates new form AttributeTypeDialog
+ * @param delimiter TODO*/
+ public AttributeTypeDialog(Frame parent, boolean modal, final String name, final byte dataType,
+ int index, String delimiter) {
+ super(parent, true);
+
+ this.name = name;
+ this.dataType = dataType;
+
+ initComponents(index);
+ updateComponents(delimiter);
+ }
+
+ /**
+ * This method is called from within the constructor to initialize the form.
+ * WARNING: Do NOT modify this code. The content of this method is always
+ * regenerated by the Form Editor.
+ */
+
+ // <editor-fold defaultstate="collapsed" desc=" Generated Code">
+ private void initComponents(int index) {
+ delimiterButtonGroup = new javax.swing.ButtonGroup();
+ listDelimiterButtonGroup = new javax.swing.ButtonGroup();
+
+ titleLabel = new javax.swing.JLabel();
+ titleSeparator = new javax.swing.JSeparator();
+ attributeNameLabel = new javax.swing.JLabel();
+ attributeNameTextField = new javax.swing.JTextField();
+ cancelButton = new javax.swing.JButton();
+ okButton = new javax.swing.JButton();
+ dataTypePanel = new javax.swing.JPanel();
+ stringRadioButton = new javax.swing.JRadioButton();
+ integerRadioButton = new javax.swing.JRadioButton();
+ floatingPointRadioButton = new javax.swing.JRadioButton();
+ booleanRadioButton = new javax.swing.JRadioButton();
+ listRadioButton = new javax.swing.JRadioButton();
+ listTypeComboBox = new javax.swing.JComboBox();
+ listDelimiterComboBox = new javax.swing.JComboBox();
+ otherTextField = new javax.swing.JTextField();
+ otherRadioButton = new javax.swing.JRadioButton();
+ listDelimiterRadioButton = new javax.swing.JRadioButton();
+ listDelimiterLabel = new javax.swing.JLabel();
+
+ setDefaultCloseOperation(javax.swing.WindowConstants.DISPOSE_ON_CLOSE);
+ setTitle("Set Attribute Name and Type");
+ titleLabel.setFont(new java.awt.Font("SansSerif", 1, 14));
+ titleLabel.setText("Attribute Name and Type");
+
+ attributeNameLabel.setText("Attribute name for Column " + (index + 1) + " entry:");
+
+ cancelButton.setText("Cancel");
+ cancelButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ cancelButtonActionPerformed(evt);
+ }
+ });
+
+ okButton.setText("OK");
+ okButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ okButtonActionPerformed(evt);
+ }
+ });
+
+ dataTypePanel.setBorder(javax.swing.BorderFactory.createTitledBorder(null,
+ "Attribute Data Type",
+ javax.swing.border.TitledBorder.DEFAULT_JUSTIFICATION,
+ javax.swing.border.TitledBorder.DEFAULT_POSITION,
+ new java.awt.Font("SansSerif",
+ 1, 11)));
+ stringRadioButton.setText("String");
+ stringRadioButton.setBorder(javax.swing.BorderFactory.createEmptyBorder(0, 0, 0, 0));
+ stringRadioButton.setMargin(new java.awt.Insets(0, 0, 0, 0));
+ stringRadioButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ dataTypeRadioButtonActionPerformed(evt);
+ }
+ });
+
+ integerRadioButton.setText("Integer");
+ integerRadioButton.setBorder(javax.swing.BorderFactory.createEmptyBorder(0, 0, 0, 0));
+ integerRadioButton.setMargin(new java.awt.Insets(0, 0, 0, 0));
+ integerRadioButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ dataTypeRadioButtonActionPerformed(evt);
+ }
+ });
+
+ floatingPointRadioButton.setText("Floating Point");
+ floatingPointRadioButton.setBorder(javax.swing.BorderFactory.createEmptyBorder(0, 0, 0, 0));
+ floatingPointRadioButton.setMargin(new java.awt.Insets(0, 0, 0, 0));
+ floatingPointRadioButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ dataTypeRadioButtonActionPerformed(evt);
+ }
+ });
+
+ booleanRadioButton.setText("Boolean");
+ booleanRadioButton.setBorder(javax.swing.BorderFactory.createEmptyBorder(0, 0, 0, 0));
+ booleanRadioButton.setMargin(new java.awt.Insets(0, 0, 0, 0));
+ booleanRadioButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ dataTypeRadioButtonActionPerformed(evt);
+ }
+ });
+
+ listRadioButton.setText("List:");
+ listRadioButton.setBorder(javax.swing.BorderFactory.createEmptyBorder(0, 0, 0, 0));
+ listRadioButton.setMargin(new java.awt.Insets(0, 0, 0, 0));
+ listRadioButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ listRadioButtonActionPerformed(evt);
+ }
+ });
+
+ listTypeComboBox.setModel(new javax.swing.DefaultComboBoxModel(LIST_DATA_TYPES));
+
+ listDelimiterLabel.setText("List delimiter is:");
+
+ listDelimiterComboBox.setModel(new DefaultComboBoxModel(new String[] {
+ "|",
+ COLON.toString(),
+ SLASH.toString(),
+ BACKSLASH.toString(),
+ COMMA.toString()
+ }));
+ listDelimiterComboBox.setName("listDelimiterComboBox");
+
+ otherRadioButton.setText("Other");
+ otherRadioButton.setBorder(javax.swing.BorderFactory.createEmptyBorder(0, 0, 0, 0));
+ otherRadioButton.setMargin(new java.awt.Insets(0, 0, 0, 0));
+ otherRadioButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ otherRadioButtonActionPerformed(evt);
+ }
+ });
+
+ listDelimiterRadioButton.setBorder(javax.swing.BorderFactory.createEmptyBorder(0, 0, 0, 0));
+ listDelimiterRadioButton.setMargin(new java.awt.Insets(0, 0, 0, 0));
+ listDelimiterRadioButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ listDelimiterRadioButtonActionPerformed(evt);
+ }
+ });
+ listDelimiterRadioButton.setSelected(true);
+
+ listDelimiterButtonGroup.add(listDelimiterRadioButton);
+ listDelimiterButtonGroup.add(otherRadioButton);
+
+ listDelimiterLabel.setText("List Delimiter is:");
+
+ org.jdesktop.layout.GroupLayout dataTypePanelLayout = new org.jdesktop.layout.GroupLayout(dataTypePanel);
+ dataTypePanel.setLayout(dataTypePanelLayout);
+
+ dataTypePanelLayout.setHorizontalGroup(dataTypePanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(dataTypePanelLayout.createSequentialGroup()
+ .addContainerGap()
+ .add(dataTypePanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(dataTypePanelLayout.createSequentialGroup()
+ .add(stringRadioButton)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(integerRadioButton)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(floatingPointRadioButton)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(booleanRadioButton))
+ .add(dataTypePanelLayout.createSequentialGroup()
+ .add(listRadioButton)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(dataTypePanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(listTypeComboBox,
+ 0,
+ 328,
+ Short.MAX_VALUE)
+ .add(dataTypePanelLayout.createSequentialGroup()
+ .add(listDelimiterLabel)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(dataTypePanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(dataTypePanelLayout.createSequentialGroup()
+ .add(otherRadioButton)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(otherTextField,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 155,
+ Short.MAX_VALUE))
+ .add(dataTypePanelLayout.createSequentialGroup()
+ .add(listDelimiterRadioButton)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(listDelimiterComboBox,
+ 0,
+ 194,
+ Short.MAX_VALUE)))))))
+ .addContainerGap()));
+ dataTypePanelLayout.setVerticalGroup(dataTypePanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(dataTypePanelLayout.createSequentialGroup()
+ .add(dataTypePanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE)
+ .add(stringRadioButton)
+ .add(integerRadioButton)
+ .add(floatingPointRadioButton)
+ .add(booleanRadioButton))
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(dataTypePanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE)
+ .add(listRadioButton)
+ .add(listTypeComboBox,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE))
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(dataTypePanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(dataTypePanelLayout.createSequentialGroup()
+ .add(30,
+ 30,
+ 30)
+ .add(dataTypePanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE)
+ .add(otherRadioButton)
+ .add(otherTextField,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)))
+ .add(dataTypePanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE)
+ .add(listDelimiterLabel)
+ .add(listDelimiterRadioButton)
+ .add(listDelimiterComboBox,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)))
+ .addContainerGap(org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE)));
+
+ org.jdesktop.layout.GroupLayout layout = new org.jdesktop.layout.GroupLayout(getContentPane());
+ getContentPane().setLayout(layout);
+ layout.setHorizontalGroup(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(layout.createSequentialGroup().addContainerGap()
+ .add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(layout.createSequentialGroup()
+ .add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(titleSeparator,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 340,
+ Short.MAX_VALUE)
+ .add(titleLabel)
+ .add(attributeNameLabel))
+ .addContainerGap())
+ .add(layout.createSequentialGroup()
+ .add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.TRAILING)
+ .add(org.jdesktop.layout.GroupLayout.LEADING,
+ dataTypePanel,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE)
+ .add(org.jdesktop.layout.GroupLayout.LEADING,
+ attributeNameTextField,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 340,
+ Short.MAX_VALUE))
+ .addContainerGap()))
+ .add(org.jdesktop.layout.GroupLayout.TRAILING,
+ layout.createSequentialGroup()
+ .add(okButton)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(cancelButton)
+ .addContainerGap()))));
+ layout.setVerticalGroup(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(layout.createSequentialGroup().addContainerGap()
+ .add(titleLabel)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(titleSeparator,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ 10,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(attributeNameLabel)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(attributeNameTextField,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(dataTypePanel,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE)
+ .add(cancelButton).add(okButton))
+ .addContainerGap(org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE)));
+ pack();
+ } // </editor-fold>
+
+ private void cancelButtonActionPerformed(java.awt.event.ActionEvent evt) {
+ name = null;
+ dispose();
+ }
+
+ private void okButtonActionPerformed(java.awt.event.ActionEvent evt) {
+ name = attributeNameTextField.getText();
+ dispose();
+ }
+
+ private void listRadioButtonActionPerformed(java.awt.event.ActionEvent evt) {
+ if (listRadioButton.isSelected()) {
+ if (otherRadioButton.isSelected()) {
+ otherTextField.setEnabled(true);
+ } else {
+ listDelimiterComboBox.setEnabled(true);
+ listTypeComboBox.setEnabled(true);
+ }
+
+ listDelimiterRadioButton.setEnabled(true);
+ otherRadioButton.setEnabled(true);
+ }
+ }
+
+ private void dataTypeRadioButtonActionPerformed(java.awt.event.ActionEvent evt) {
+ listDelimiterComboBox.setEnabled(false);
+ listTypeComboBox.setEnabled(false);
+ otherTextField.setEnabled(false);
+ listDelimiterRadioButton.setEnabled(false);
+ otherRadioButton.setEnabled(false);
+ }
+
+ private void otherRadioButtonActionPerformed(ActionEvent evt) {
+ if (otherRadioButton.isSelected()) {
+ otherTextField.setEnabled(true);
+ listDelimiterComboBox.setEnabled(false);
+ }
+ }
+
+ private void listDelimiterRadioButtonActionPerformed(ActionEvent evt) {
+ if (listDelimiterRadioButton.isSelected()) {
+ listDelimiterComboBox.setEnabled(true);
+ otherTextField.setEnabled(false);
+ }
+ }
+
+ /* =========================================================================================== */
+ private void updateComponents(String delimiter) {
+ attributeNameTextField.setText(name);
+ listDelimiterComboBox.setEnabled(false);
+
+ if (delimiter == null) {
+ listDelimiterComboBox.setSelectedIndex(0);
+ } else {
+ for (int i = 0; i < listDelimiterComboBox.getItemCount(); i++) {
+ if (delimiter.equals(listDelimiterComboBox.getItemAt(i))) {
+ listDelimiterComboBox.setSelectedIndex(i);
+
+ break;
+ }
+ }
+ }
+
+ listTypeComboBox.setEnabled(false);
+ otherTextField.setEnabled(false);
+ setButtonGroup();
+ }
+
+ private void setButtonGroup() {
+ delimiterButtonGroup.add(stringRadioButton);
+ delimiterButtonGroup.add(integerRadioButton);
+ delimiterButtonGroup.add(floatingPointRadioButton);
+ delimiterButtonGroup.add(booleanRadioButton);
+ delimiterButtonGroup.add(listRadioButton);
+
+ if (dataType == CyAttributes.TYPE_STRING) {
+ delimiterButtonGroup.setSelected(stringRadioButton.getModel(), true);
+ } else if (dataType == CyAttributes.TYPE_INTEGER) {
+ delimiterButtonGroup.setSelected(integerRadioButton.getModel(), true);
+ } else if (dataType == CyAttributes.TYPE_FLOATING) {
+ delimiterButtonGroup.setSelected(floatingPointRadioButton.getModel(), true);
+ } else if (dataType == CyAttributes.TYPE_BOOLEAN) {
+ delimiterButtonGroup.setSelected(booleanRadioButton.getModel(), true);
+ } else if (dataType == CyAttributes.TYPE_SIMPLE_LIST) {
+ delimiterButtonGroup.setSelected(booleanRadioButton.getModel(), true);
+ listDelimiterComboBox.setEnabled(true);
+ listTypeComboBox.setEnabled(true);
+ otherTextField.setEnabled(false);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public byte getAttType() {
+ if (delimiterButtonGroup.getSelection().equals(stringRadioButton.getModel())) {
+ return CyAttributes.TYPE_STRING;
+ } else if (delimiterButtonGroup.getSelection().equals(integerRadioButton.getModel())) {
+ return CyAttributes.TYPE_INTEGER;
+ } else if (delimiterButtonGroup.getSelection().equals(floatingPointRadioButton.getModel())) {
+ return CyAttributes.TYPE_FLOATING;
+ } else if (delimiterButtonGroup.getSelection().equals(booleanRadioButton.getModel())) {
+ return CyAttributes.TYPE_BOOLEAN;
+ } else if (delimiterButtonGroup.getSelection().equals(listRadioButton.getModel())) {
+ return CyAttributes.TYPE_SIMPLE_LIST;
+ }
+
+ return CyAttributes.TYPE_STRING;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getListDelimiterType() {
+ if (listDelimiterRadioButton.isSelected()) {
+ if(listDelimiterComboBox.getSelectedItem().toString().equals("|")) {
+ return PIPE.toString();
+ } else
+ return listDelimiterComboBox.getSelectedItem().toString();
+ } else {
+ return otherTextField.getText().trim();
+ }
+ }
+
+ /**
+ * Returns data type of the entries in the list object.
+ * Complex type is not supported.
+ *
+ * @return
+ */
+ public byte getListDataType() {
+ if (listTypeComboBox.getSelectedItem().equals(STRING)) {
+ return CyAttributes.TYPE_STRING;
+ } else if (listTypeComboBox.getSelectedItem().equals(INTEGER)) {
+ return CyAttributes.TYPE_INTEGER;
+ } else if (listTypeComboBox.getSelectedItem().equals(FLOAT)) {
+ return CyAttributes.TYPE_FLOATING;
+ } else if (listTypeComboBox.getSelectedItem().equals(BOOLEAN)) {
+ return CyAttributes.TYPE_BOOLEAN;
+ }
+
+ return CyAttributes.TYPE_STRING;
+ }
+
+ // Variables declaration - do not modify
+ private javax.swing.JLabel attributeNameLabel;
+ private javax.swing.JTextField attributeNameTextField;
+ private javax.swing.JRadioButton booleanRadioButton;
+ private javax.swing.JButton cancelButton;
+ private javax.swing.JPanel dataTypePanel;
+ private javax.swing.ButtonGroup delimiterButtonGroup;
+ private javax.swing.JRadioButton floatingPointRadioButton;
+ private javax.swing.JRadioButton integerRadioButton;
+ private javax.swing.JComboBox listDelimiterComboBox;
+ private javax.swing.JLabel listDelimiterLabel;
+ private javax.swing.JRadioButton listDelimiterRadioButton;
+ private javax.swing.JRadioButton listRadioButton;
+ private javax.swing.JComboBox listTypeComboBox;
+ private javax.swing.JButton okButton;
+ private javax.swing.JRadioButton otherRadioButton;
+ private javax.swing.JTextField otherTextField;
+ private javax.swing.JRadioButton stringRadioButton;
+ private javax.swing.JLabel titleLabel;
+ private javax.swing.JSeparator titleSeparator;
+ private javax.swing.ButtonGroup listDelimiterButtonGroup;
+
+ // End of variables declaration
+}
diff --git a/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/ui/DataSourceSelectDialog.java b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/ui/DataSourceSelectDialog.java
new file mode 100644
index 0000000..01db9ec
--- /dev/null
+++ b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/ui/DataSourceSelectDialog.java
@@ -0,0 +1,330 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package edu.ucsd.bioeng.coreplugin.tableImport.ui;
+
+import cytoscape.util.CyFileFilter;
+import cytoscape.util.FileUtil;
+
+import java.awt.Frame;
+
+import java.io.File;
+
+import java.net.MalformedURLException;
+
+import javax.swing.JDialog;
+
+
+/*
+ * OntologySourceSelectDialog.java
+ *
+ * Created on 2006/08/04, 17:32
+ */
+
+/**
+ *
+ * @author kono
+ */
+public class DataSourceSelectDialog extends JDialog {
+ private int sourceType;
+ private String sourceName;
+ private String sourceFileName;
+ private String sourceUrlString;
+
+ /**
+ *
+ */
+ public final static int ANNOTATION_TYPE = 1;
+
+ /**
+ *
+ */
+ public final static int ONTOLOGY_TYPE = 2;
+
+ /** Creates new form OntologySourceSelectDialog */
+ public DataSourceSelectDialog(Frame parent, boolean modal) {
+ this(ANNOTATION_TYPE, parent, modal);
+ }
+
+ /**
+ * Creates a new DataSourceSelectDialog object.
+ *
+ * @param sourceType DOCUMENT ME!
+ * @param parent DOCUMENT ME!
+ * @param modal DOCUMENT ME!
+ */
+ public DataSourceSelectDialog(int sourceType, Frame parent, boolean modal) {
+ super(parent, modal);
+ this.sourceType = sourceType;
+ sourceName = null;
+ sourceUrlString = null;
+ sourceFileName = null;
+ initComponents();
+ }
+
+ /**
+ * This method is called from within the constructor to initialize the form.
+ * WARNING: Do NOT modify this code. The content of this method is always
+ * regenerated by the Form Editor.
+ */
+
+ // <editor-fold defaultstate="collapsed" desc=" Generated Code">
+ private void initComponents() {
+ titleLabel = new javax.swing.JLabel();
+ jSeparator1 = new javax.swing.JSeparator();
+ ontologyNameTextField = new javax.swing.JTextField();
+ dataSourceTextField = new javax.swing.JTextField();
+ cancelButton = new javax.swing.JButton();
+ addButton = new javax.swing.JButton();
+ browseButton = new javax.swing.JButton();
+ nameLabel = new javax.swing.JLabel();
+ sourceLabel = new javax.swing.JLabel();
+
+ setDefaultCloseOperation(javax.swing.WindowConstants.DISPOSE_ON_CLOSE);
+ setTitle("Add new ontology data source");
+ titleLabel.setFont(new java.awt.Font("SansSerif", 1, 14));
+ titleLabel.setText("Add New Data Source");
+
+ ontologyNameTextField.setToolTipText("Add data source from local file system...");
+ ontologyNameTextField.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ ontologyNameTextFieldActionPerformed(evt);
+ }
+ });
+
+ dataSourceTextField.setText("http://");
+ dataSourceTextField.setToolTipText("http, ftp, and file are supported.");
+
+ cancelButton.setText("Cancel");
+ cancelButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ cancelButtonActionPerformed(evt);
+ }
+ });
+
+ addButton.setText("Add");
+ addButton.setMaximumSize(new java.awt.Dimension(75, 25));
+ addButton.setMinimumSize(new java.awt.Dimension(75, 25));
+ addButton.setPreferredSize(new java.awt.Dimension(75, 25));
+ addButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ addButtonActionPerformed(evt);
+ }
+ });
+
+ browseButton.setText("Browse Local Files");
+ browseButton.setToolTipText("Add data source from local file system...");
+ browseButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ browseButtonActionPerformed(evt);
+ }
+ });
+
+ nameLabel.setText("Data Source Name:");
+
+ sourceLabel.setText("Data Source URL:");
+
+ org.jdesktop.layout.GroupLayout layout = new org.jdesktop.layout.GroupLayout(getContentPane());
+ getContentPane().setLayout(layout);
+ layout.setHorizontalGroup(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(layout.createSequentialGroup().addContainerGap()
+ .add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(jSeparator1,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 681, Short.MAX_VALUE)
+ .add(titleLabel)
+ .add(org.jdesktop.layout.GroupLayout.TRAILING,
+ layout.createSequentialGroup()
+ .add(addButton,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(cancelButton)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED))
+ .add(layout.createSequentialGroup()
+ .add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(sourceLabel)
+ .add(nameLabel))
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.TRAILING)
+ .add(layout.createSequentialGroup()
+ .add(dataSourceTextField,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 378,
+ Short.MAX_VALUE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(browseButton,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 169,
+ Short.MAX_VALUE))
+ .add(ontologyNameTextField,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 553,
+ Short.MAX_VALUE))))
+ .addContainerGap()));
+ layout.setVerticalGroup(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(layout.createSequentialGroup().addContainerGap()
+ .add(titleLabel).add(8, 8, 8)
+ .add(jSeparator1,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE)
+ .add(nameLabel)
+ .add(ontologyNameTextField,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE))
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE)
+ .add(sourceLabel)
+ .add(dataSourceTextField,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .add(browseButton))
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE)
+ .add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE)
+ .add(addButton,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .add(cancelButton)).addContainerGap()));
+ pack();
+ } // </editor-fold>
+
+ private void cancelButtonActionPerformed(java.awt.event.ActionEvent evt) {
+ dispose();
+ }
+
+ private void addButtonActionPerformed(java.awt.event.ActionEvent evt) {
+ final String name = ontologyNameTextField.getText();
+ final String source = this.dataSourceTextField.getText();
+
+ if ((name == null) || (source == null) || (name.length() == 0) || (source.length() == 0)) {
+ return;
+ } else {
+ sourceName = name;
+ sourceUrlString = source;
+ }
+
+ setVisible(false);
+ }
+
+ private void browseButtonActionPerformed(java.awt.event.ActionEvent evt) {
+ CyFileFilter oboFilter = new CyFileFilter();
+ File file = null;
+
+ if (sourceType == ONTOLOGY_TYPE) {
+ oboFilter.addExtension("obo");
+ oboFilter.setDescription("Ontology files in OBO format");
+ file = FileUtil.getFile("Select local OBO file", FileUtil.LOAD,
+ new CyFileFilter[] { oboFilter });
+ } else {
+ file = FileUtil.getFile("Select local annotation file", FileUtil.LOAD,
+ new CyFileFilter[] { });
+ }
+
+ /*
+ * Do nothing if the file is null.
+ */
+ if (file == null) {
+ return;
+ }
+
+ sourceFileName = file.getName();
+
+ if (sourceType == ONTOLOGY_TYPE) {
+ ontologyNameTextField.setText("Local Ontology File: " + sourceFileName);
+ } else {
+ ontologyNameTextField.setText("Local Annotation File: " + sourceFileName);
+ }
+
+ try {
+ dataSourceTextField.setText(file.toURI().toURL().toString());
+ } catch (MalformedURLException e) {
+ e.printStackTrace();
+ }
+ }
+
+ private void ontologyNameTextFieldActionPerformed(java.awt.event.ActionEvent evt) {
+ // TODO add your handling code here:
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getSourceUrlString() {
+ return sourceUrlString;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getSourceName() {
+ return sourceName;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getSourceFileName() {
+ return sourceFileName;
+ }
+
+ // Variables declaration - do not modify
+ private javax.swing.JButton addButton;
+ private javax.swing.JButton browseButton;
+ private javax.swing.JButton cancelButton;
+ private javax.swing.JTextField dataSourceTextField;
+ private javax.swing.JSeparator jSeparator1;
+ private javax.swing.JLabel nameLabel;
+ private javax.swing.JTextField ontologyNameTextField;
+ private javax.swing.JLabel sourceLabel;
+ private javax.swing.JLabel titleLabel;
+
+ // End of variables declaration
+}
diff --git a/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/ui/DataTypeUtil.java b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/ui/DataTypeUtil.java
new file mode 100644
index 0000000..9ce8149
--- /dev/null
+++ b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/ui/DataTypeUtil.java
@@ -0,0 +1,151 @@
+
+/*
+ Copyright (c) 2006, 2007, 2009, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package edu.ucsd.bioeng.coreplugin.tableImport.ui;
+
+import cytoscape.Cytoscape;
+import cytoscape.data.CyAttributes;
+
+import java.util.Map;
+import java.util.regex.Pattern;
+import javax.swing.table.TableModel;
+
+/**
+ *
+ */
+class DataTypeUtil {
+
+ private static Pattern truePattern = Pattern.compile("^true$", Pattern.CASE_INSENSITIVE);
+ private static Pattern falsePattern = Pattern.compile("^false$", Pattern.CASE_INSENSITIVE);
+
+ private DataTypeUtil() {}
+
+ static void guessTypes(final TableModel model, final String tableName,
+ Map<String,Byte[]> dataTypeMap) {
+
+ //System.out.println("model row count: " + model.getRowCount() );
+ //System.out.println("model column count: " + model.getColumnCount() );
+
+ // 0 = Boolean, 1 = Integer, 2 = Double, 3 = String
+ final Integer[][] typeChecker = new Integer[4][model.getColumnCount()];
+
+ for (int i = 0; i < 4; i++) {
+ for (int j = 0; j < model.getColumnCount(); j++) {
+ typeChecker[i][j] = 0;
+ }
+ }
+
+ String cell = null;
+
+ for (int i = 0; i < model.getRowCount(); i++) {
+ for (int j = 0; j < model.getColumnCount(); j++) {
+ cell = (String) model.getValueAt(i, j);
+ //System.out.print( i + " " + j + " " + cell + " ");
+
+ boolean found = false;
+
+ if (cell != null) {
+ // boolean
+ if ( truePattern.matcher(cell).matches() ||
+ falsePattern.matcher(cell).matches() ) {
+ typeChecker[0][j]++;
+ found = true;
+ //System.out.println("boolean");
+ } else {
+
+ // integers
+ try {
+ Integer.valueOf(cell);
+ typeChecker[1][j]++;
+ found = true;
+ //System.out.println("integer");
+ } catch (NumberFormatException e) {
+ }
+
+
+ // floats
+ try {
+ Double.valueOf(cell);
+ typeChecker[2][j]++;
+ found = true;
+ //System.out.println("float");
+ } catch (NumberFormatException e) {
+ }
+ }
+ }
+
+ // default to string
+ if (found == false) {
+ typeChecker[3][j]++;
+ //System.out.println("string");
+ }
+ }
+ }
+
+ Byte[] dataType = dataTypeMap.get(tableName);
+
+ if ((dataType == null) || (dataType.length != model.getColumnCount())) {
+ dataType = new Byte[model.getColumnCount()];
+ }
+
+ for (int i = 0; i < dataType.length; i++) {
+ int maxVal = 0;
+ int maxIndex = 0;
+
+ for (int j = 0; j < 4; j++) {
+ //System.out.println("col: " + i + " byte: " + j + " count: " + typeChecker[j][i]);
+ if (maxVal < typeChecker[j][i]) {
+ maxVal = typeChecker[j][i];
+ maxIndex = j;
+ }
+ }
+
+ //System.out.println(" max index: " + maxIndex);
+
+ if (maxIndex == 0)
+ dataType[i] = CyAttributes.TYPE_BOOLEAN;
+ else if (maxIndex == 1)
+ dataType[i] = CyAttributes.TYPE_INTEGER;
+ else if (maxIndex == 2)
+ dataType[i] = CyAttributes.TYPE_FLOATING;
+ else
+ dataType[i] = CyAttributes.TYPE_STRING;
+
+ //System.out.println(" resulting data type: " + dataType[i]);
+ }
+
+ dataTypeMap.put(tableName, dataType);
+ }
+}
diff --git a/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/ui/ImportAttributeTableTask.java b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/ui/ImportAttributeTableTask.java
new file mode 100644
index 0000000..76a5cad
--- /dev/null
+++ b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/ui/ImportAttributeTableTask.java
@@ -0,0 +1,114 @@
+/*
+ Copyright (c) 2006, 2007, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package edu.ucsd.bioeng.coreplugin.tableImport.ui;
+
+
+import cytoscape.Cytoscape;
+import cytoscape.task.Task;
+import cytoscape.task.TaskMonitor;
+import edu.ucsd.bioeng.coreplugin.tableImport.reader.TextTableReader;
+
+
+public class ImportAttributeTableTask implements Task {
+ private TextTableReader reader;
+ private String source;
+ private TaskMonitor taskMonitor;
+
+ /**
+ * Constructor.
+ *
+ * @param file
+ * File.
+ * @param fileType
+ * FileType, e.g. Cytoscape.FILE_SIF or Cytoscape.FILE_GML.
+ */
+ public ImportAttributeTableTask(TextTableReader reader, String source) {
+ this.reader = reader;
+ this.source = source;
+ }
+
+ /**
+ * Executes Task.
+ */
+ public void run() {
+ taskMonitor.setStatus("Loading attribute data file...");
+ taskMonitor.setPercentCompleted(-1);
+
+ try {
+ reader.readTable();
+ taskMonitor.setPercentCompleted(100);
+ Cytoscape.firePropertyChange(Cytoscape.ATTRIBUTES_CHANGED, null, null);
+ informUserOfAnnotationStats();
+ Cytoscape.firePropertyChange(Cytoscape.NEW_ATTRS_LOADED, null, null);
+ } catch (Exception e) {
+ e.printStackTrace();
+ taskMonitor.setException(e, "Unable to import annotation data.");
+ }
+ }
+
+ /**
+ * Inform User of Network Stats.
+ */
+ private void informUserOfAnnotationStats() {
+ StringBuffer sb = new StringBuffer();
+
+ // Give the user some confirmation
+ sb.append("Succesfully loaded attribute data from:\n\n");
+ sb.append(source + "\n\n");
+
+ sb.append(reader.getReport());
+
+ taskMonitor.setStatus(sb.toString());
+ }
+
+ /**
+ * Halts the Task: Not Currently Implemented.
+ */
+ public void halt() {
+ // Task can not currently be halted.
+ }
+
+ /**
+ * Sets the Task Monitor.
+ *
+ * @param taskMonitor
+ * TaskMonitor Object.
+ */
+ public void setTaskMonitor(TaskMonitor taskMonitor) throws IllegalThreadStateException {
+ this.taskMonitor = taskMonitor;
+ }
+
+ /**
+ * Gets the Task Title.
+ *
+ * @return Task Title.
+ */
+ public String getTitle() {
+ return new String("Loading Attributes");
+ }
+}
diff --git a/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/ui/ImportNetworkTask.java b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/ui/ImportNetworkTask.java
new file mode 100644
index 0000000..dcb2edf
--- /dev/null
+++ b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/ui/ImportNetworkTask.java
@@ -0,0 +1,129 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package edu.ucsd.bioeng.coreplugin.tableImport.ui;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+
+import cytoscape.data.readers.GraphReader;
+
+import cytoscape.task.Task;
+import cytoscape.task.TaskMonitor;
+
+import edu.ucsd.bioeng.coreplugin.tableImport.reader.TextTableReader;
+
+import java.io.IOException;
+
+import java.net.URL;
+
+
+/**
+ *
+ */
+public class ImportNetworkTask implements Task {
+ private final GraphReader reader;
+ private final URL source;
+ private TaskMonitor taskMonitor;
+
+ /**
+ * Creates a new ImportNetworkTask object.
+ *
+ * @param reader DOCUMENT ME!
+ * @param source DOCUMENT ME!
+ */
+ public ImportNetworkTask(final GraphReader reader, final URL source) {
+ this.reader = reader;
+ this.source = source;
+ }
+
+ /**
+ * Executes Task.
+ */
+ public void run() {
+ taskMonitor.setStatus("Loading network and edge attributes...");
+ taskMonitor.setPercentCompleted(-1);
+
+ CyNetwork network = Cytoscape.createNetwork(reader, true, null);
+ Object[] ret_val = new Object[2];
+ ret_val[0] = network;
+ ret_val[1] = source.toString();
+ Cytoscape.firePropertyChange(Cytoscape.NETWORK_LOADED, null, ret_val);
+
+ taskMonitor.setPercentCompleted(100);
+
+ informUserOfAnnotationStats();
+ }
+
+ /**
+ * Inform User of Network Stats.
+ */
+ private void informUserOfAnnotationStats() {
+ StringBuffer sb = new StringBuffer();
+
+ // Give the user some confirmation
+ sb.append("Succesfully loaded network and edge attributes from:\n");
+ sb.append(source.toString() + "\n");
+ sb.append(((TextTableReader) reader).getReport());
+ taskMonitor.setStatus(sb.toString());
+ }
+
+ /**
+ * Halts the Task: Not Currently Implemented.
+ */
+ public void halt() {
+ // Task can not currently be halted.
+ }
+
+ /**
+ * Sets the Task Monitor.
+ *
+ * @param taskMonitor
+ * TaskMonitor Object.
+ */
+ public void setTaskMonitor(TaskMonitor taskMonitor) throws IllegalThreadStateException {
+ this.taskMonitor = taskMonitor;
+ }
+
+ /**
+ * Gets the Task Title.
+ *
+ * @return Task Title.
+ */
+ public String getTitle() {
+ return new String("Loading Network and Edge Attributes");
+ }
+}
diff --git a/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/ui/ImportOntologyAnnotationTask.java b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/ui/ImportOntologyAnnotationTask.java
new file mode 100644
index 0000000..f913abc
--- /dev/null
+++ b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/ui/ImportOntologyAnnotationTask.java
@@ -0,0 +1,126 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package edu.ucsd.bioeng.coreplugin.tableImport.ui;
+
+import cytoscape.task.Task;
+import cytoscape.task.TaskMonitor;
+
+import edu.ucsd.bioeng.coreplugin.tableImport.reader.TextTableReader;
+
+import java.io.IOException;
+
+
+/**
+ *
+ */
+public class ImportOntologyAnnotationTask implements Task {
+ private TextTableReader reader;
+ private String ontology;
+ private String source;
+ private TaskMonitor taskMonitor;
+
+ /**
+ * Constructor.
+ *
+ * @param file
+ * File.
+ * @param fileType
+ * FileType, e.g. Cytoscape.FILE_SIF or Cytoscape.FILE_GML.
+ */
+ public ImportOntologyAnnotationTask(TextTableReader reader, String ontology, String source) {
+ this.reader = reader;
+ this.ontology = ontology;
+ this.source = source;
+ }
+
+ /**
+ * Executes Task.
+ */
+ public void run() {
+ taskMonitor.setStatus("Loading annotation for " + ontology + "...");
+ taskMonitor.setPercentCompleted(-1);
+
+ try {
+ reader.readTable();
+ taskMonitor.setPercentCompleted(100);
+ } catch (IOException e) {
+ e.printStackTrace();
+ taskMonitor.setException(e, "Unable to import annotation data.");
+ }
+
+ informUserOfAnnotationStats();
+ }
+
+ /**
+ * Inform User of Network Stats.
+ */
+ private void informUserOfAnnotationStats() {
+ StringBuffer sb = new StringBuffer();
+
+ // Give the user some confirmation
+ sb.append("Succesfully loaded annotation file for " + ontology);
+ sb.append(" from: \n\n" + source);
+
+ taskMonitor.setStatus(sb.toString());
+ }
+
+ /**
+ * Halts the Task: Not Currently Implemented.
+ */
+ public void halt() {
+ // Task can not currently be halted.
+ }
+
+ /**
+ * Sets the Task Monitor.
+ *
+ * @param taskMonitor
+ * TaskMonitor Object.
+ */
+ public void setTaskMonitor(TaskMonitor taskMonitor) throws IllegalThreadStateException {
+ this.taskMonitor = taskMonitor;
+ }
+
+ /**
+ * Gets the Task Title.
+ *
+ * @return Task Title.
+ */
+ public String getTitle() {
+ return new String("Loading Annotation");
+ }
+}
diff --git a/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/ui/ImportOntologyTask.java b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/ui/ImportOntologyTask.java
new file mode 100644
index 0000000..8492e78
--- /dev/null
+++ b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/ui/ImportOntologyTask.java
@@ -0,0 +1,159 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package edu.ucsd.bioeng.coreplugin.tableImport.ui;
+
+import static cytoscape.data.servers.OntologyServer.OntologyType.BASIC;
+import static cytoscape.data.servers.OntologyServer.OntologyType.GO;
+
+import java.io.IOException;
+import java.net.URL;
+
+import cytoscape.Cytoscape;
+import cytoscape.task.Task;
+import cytoscape.task.TaskMonitor;
+
+
+/**
+ * Task to import OBO file<br>
+ *
+ * @since Cytoscape 2.4
+ * @version 0.8
+ * @author Keiichiro Ono
+ *
+ */
+public class ImportOntologyTask implements Task {
+ private String dataSource;
+ private String ontologyType;
+ private String ontologyName;
+ private String ontologyDescription;
+ private TaskMonitor taskMonitor;
+
+ /**
+ * Constructor of the task.<br>
+ * <p>
+ *
+ * </p>
+ *
+ * @param dataSource
+ * URL of the data source as String.
+ * @param type
+ * Type of Ontology.
+ * @param name
+ * Name of Ontology.
+ * @param description
+ * Description for this ontology.
+ */
+ public ImportOntologyTask(String dataSource, String type, String name, String description) {
+ this.dataSource = dataSource;
+ this.ontologyType = type;
+ this.ontologyName = name;
+ this.ontologyDescription = description;
+ }
+
+ /**
+ * Executes Task.
+ */
+ public void run() {
+ taskMonitor.setStatus("Loading Ontology Data...");
+
+ try {
+ URL targetUrl = new URL(dataSource);
+ taskMonitor.setPercentCompleted(-1);
+
+ if ((ontologyType != null) && ontologyType.equals(GO.toString())) {
+ Cytoscape.getOntologyServer()
+ .addOntology(targetUrl, GO, ontologyName, ontologyDescription);
+ } else {
+ Cytoscape.getOntologyServer()
+ .addOntology(targetUrl, BASIC, ontologyName, ontologyDescription);
+ }
+
+ if (Cytoscape.getOntologyServer().getOntologies().get(ontologyName) != null) {
+ informUserOfOntologyStats(ontologyName, targetUrl);
+ } else {
+ StringBuffer sb = new StringBuffer();
+ sb.append("Could not load ontology from the data source: " + targetUrl.toString());
+ sb.append("\nThis URL may not contain the correct ontology data.");
+ taskMonitor.setException(new IOException(sb.toString()), sb.toString());
+ }
+
+ taskMonitor.setPercentCompleted(100);
+ } catch (Exception e) {
+ taskMonitor.setException(e, "Unable to load ontology data.");
+ }
+ }
+
+ /**
+ * Display result of ontology import.<br>
+ *
+ * @param ontologyName
+ * @param source
+ */
+ private void informUserOfOntologyStats(String ontologyName, URL source) {
+ StringBuffer sb = new StringBuffer();
+
+ // Give the user some confirmation
+ sb.append("Succesfully loaded ontology from: " + source.toString());
+ sb.append("\n\nThis ontology DAG is called " + ontologyName);
+
+ taskMonitor.setStatus(sb.toString());
+ }
+
+ /**
+ * Halts the Task: Not Currently Implemented.
+ */
+ public void halt() {
+ // Task can not currently be halted.
+ }
+
+ /**
+ * Sets the Task Monitor.
+ *
+ * @param taskMonitor
+ * TaskMonitor Object.
+ */
+ public void setTaskMonitor(TaskMonitor taskMonitor) throws IllegalThreadStateException {
+ this.taskMonitor = taskMonitor;
+ }
+
+ /**
+ * Gets the Task Title.
+ *
+ * @return Task Title.
+ */
+ public String getTitle() {
+ return new String("Loading Ontology");
+ }
+}
diff --git a/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/ui/ImportTextTableDialog.java b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/ui/ImportTextTableDialog.java
new file mode 100644
index 0000000..fd80684
--- /dev/null
+++ b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/ui/ImportTextTableDialog.java
@@ -0,0 +1,3729 @@
+/*
+ Copyright (c) 2006, 2007, 2009, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package edu.ucsd.bioeng.coreplugin.tableImport.ui;
+
+import static edu.ucsd.bioeng.coreplugin.tableImport.reader.GeneAssociationTags.DB_OBJECT_SYMBOL;
+import static edu.ucsd.bioeng.coreplugin.tableImport.reader.GeneAssociationTags.DB_OBJECT_SYNONYM;
+import static edu.ucsd.bioeng.coreplugin.tableImport.reader.GeneAssociationTags.GO_ID;
+import static edu.ucsd.bioeng.coreplugin.tableImport.reader.GeneAssociationTags.TAXON;
+import static edu.ucsd.bioeng.coreplugin.tableImport.reader.TextFileDelimiters.PIPE;
+import static edu.ucsd.bioeng.coreplugin.tableImport.reader.TextTableReader.ObjectType.EDGE;
+import static edu.ucsd.bioeng.coreplugin.tableImport.reader.TextTableReader.ObjectType.NETWORK;
+import static edu.ucsd.bioeng.coreplugin.tableImport.reader.TextTableReader.ObjectType.NODE;
+import static edu.ucsd.bioeng.coreplugin.tableImport.ui.theme.ImportDialogColorTheme.NOT_LOADED_COLOR;
+import static edu.ucsd.bioeng.coreplugin.tableImport.ui.theme.ImportDialogColorTheme.ONTOLOGY_COLOR;
+import static edu.ucsd.bioeng.coreplugin.tableImport.ui.theme.ImportDialogFontTheme.ITEM_FONT;
+import static edu.ucsd.bioeng.coreplugin.tableImport.ui.theme.ImportDialogFontTheme.LABEL_FONT;
+import static edu.ucsd.bioeng.coreplugin.tableImport.ui.theme.ImportDialogFontTheme.TITLE_FONT;
+import static edu.ucsd.bioeng.coreplugin.tableImport.ui.theme.ImportDialogIconSets.BOOLEAN_ICON;
+import static edu.ucsd.bioeng.coreplugin.tableImport.ui.theme.ImportDialogIconSets.FLOAT_ICON;
+import static edu.ucsd.bioeng.coreplugin.tableImport.ui.theme.ImportDialogIconSets.ID_ICON;
+import static edu.ucsd.bioeng.coreplugin.tableImport.ui.theme.ImportDialogIconSets.INT_ICON;
+import static edu.ucsd.bioeng.coreplugin.tableImport.ui.theme.ImportDialogIconSets.LIST_ICON;
+import static edu.ucsd.bioeng.coreplugin.tableImport.ui.theme.ImportDialogIconSets.LOCAL_SOURCE_ICON;
+import static edu.ucsd.bioeng.coreplugin.tableImport.ui.theme.ImportDialogIconSets.REMOTE_SOURCE_ICON;
+import static edu.ucsd.bioeng.coreplugin.tableImport.ui.theme.ImportDialogIconSets.REMOTE_SOURCE_ICON_LARGE;
+import static edu.ucsd.bioeng.coreplugin.tableImport.ui.theme.ImportDialogIconSets.RIGHT_ARROW_ICON;
+import static edu.ucsd.bioeng.coreplugin.tableImport.ui.theme.ImportDialogIconSets.SPREADSHEET_ICON_LARGE;
+import static edu.ucsd.bioeng.coreplugin.tableImport.ui.theme.ImportDialogIconSets.STRING_ICON;
+
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Frame;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.KeyEvent;
+import java.awt.event.KeyListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.beans.PropertyChangeSupport;
+import java.io.BufferedInputStream;
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.TreeSet;
+import java.util.Vector;
+
+import javax.swing.ButtonGroup;
+import javax.swing.ImageIcon;
+import javax.swing.JCheckBox;
+import javax.swing.JComboBox;
+import javax.swing.JDialog;
+import javax.swing.JLabel;
+import javax.swing.JList;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JSpinner;
+import javax.swing.JTable;
+import javax.swing.JTextField;
+import javax.swing.ListCellRenderer;
+import javax.swing.SpinnerNumberModel;
+import javax.swing.SwingConstants;
+import javax.swing.ToolTipManager;
+import javax.swing.event.TableModelEvent;
+import javax.swing.event.TableModelListener;
+import javax.swing.table.DefaultTableModel;
+import javax.swing.table.TableCellRenderer;
+import javax.swing.table.TableModel;
+import javax.xml.bind.JAXBException;
+
+import org.apache.poi.ss.usermodel.Sheet;
+import org.apache.poi.ss.usermodel.Workbook;
+import org.apache.poi.ss.usermodel.WorkbookFactory;
+import org.jdesktop.layout.GroupLayout;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import cytoscape.bookmarks.Attribute;
+import cytoscape.bookmarks.Bookmarks;
+import cytoscape.bookmarks.DataSource;
+import cytoscape.data.CyAttributes;
+import cytoscape.data.readers.GraphReader;
+import cytoscape.logger.CyLogger;
+import cytoscape.task.ui.JTaskConfig;
+import cytoscape.task.util.TaskManager;
+import cytoscape.util.BookmarksUtil;
+import cytoscape.util.CyFileFilter;
+import cytoscape.util.FileUtil;
+import cytoscape.util.URLUtil;
+import cytoscape.util.swing.ColumnResizer;
+import cytoscape.util.swing.JStatusBar;
+import edu.ucsd.bioeng.coreplugin.tableImport.reader.AttributeAndOntologyMappingParameters;
+import edu.ucsd.bioeng.coreplugin.tableImport.reader.AttributeMappingParameters;
+import edu.ucsd.bioeng.coreplugin.tableImport.reader.DefaultAttributeTableReader;
+import edu.ucsd.bioeng.coreplugin.tableImport.reader.ExcelAttributeSheetReader;
+import edu.ucsd.bioeng.coreplugin.tableImport.reader.ExcelNetworkSheetReader;
+import edu.ucsd.bioeng.coreplugin.tableImport.reader.GeneAssociationReader;
+import edu.ucsd.bioeng.coreplugin.tableImport.reader.NetworkTableMappingParameters;
+import edu.ucsd.bioeng.coreplugin.tableImport.reader.NetworkTableReader;
+import edu.ucsd.bioeng.coreplugin.tableImport.reader.OntologyAnnotationReader;
+import edu.ucsd.bioeng.coreplugin.tableImport.reader.SupportedFileType;
+import edu.ucsd.bioeng.coreplugin.tableImport.reader.TextFileDelimiters;
+import edu.ucsd.bioeng.coreplugin.tableImport.reader.TextTableReader;
+import edu.ucsd.bioeng.coreplugin.tableImport.reader.TextTableReader.ObjectType;
+import giny.model.Edge;
+import giny.model.Node;
+
+
+/**
+ * Main UI for Table Import.
+ *
+ * @author kono
+ */
+public class ImportTextTableDialog extends JDialog implements PropertyChangeListener,
+ TableModelListener {
+
+ private static final long serialVersionUID = 7356378931577386260L;
+
+ /**
+ * This dialog GUI will be switched based on the following parameters:
+ *
+ * SIMPLE_ATTRIBUTE_IMPORT: Import attributes in text table.
+ *
+ * ONTOLOGY_AND_ANNOTATION_IMPORT: Load ontology and map attributes in text
+ * table.
+ *
+ * NETWORK_IMPORT: Import text table as a network.
+ */
+ public static final int SIMPLE_ATTRIBUTE_IMPORT = 1;
+
+ /**
+ *
+ */
+ public static final int ONTOLOGY_AND_ANNOTATION_IMPORT = 2;
+
+ /**
+ *
+ */
+ public static final int NETWORK_IMPORT = 3;
+
+ /**
+ * Enums for file types.
+ */
+ public static enum FileTypes {
+ ATTRIBUTE_FILE,
+ NETWORK_FILE,
+ GENE_ASSOCIATION_FILE,
+ CUSTOM_ANNOTATION_FILE;
+ }
+
+ /*
+ * Default value for Interaction edge attribute.
+ */
+ private static final String DEFAULT_INTERACTION = "pp";
+
+ /*
+ * Signals used among Swing components in this dialog:
+ */
+ public static final String LIST_DELIMITER_CHANGED = "listDelimiterChanged";
+ public static final String LIST_DATA_TYPE_CHANGED = "listDataTypeChanged";
+ public static final String ATTR_DATA_TYPE_CHANGED = "attrDataTypeChanged";
+ public static final String ATTRIBUTE_NAME_CHANGED = "aliasTableChanged";
+ public static final String SHEET_CHANGED = "sheetChanged";
+ public static final String NETWORK_IMPORT_TEMPLATE_CHANGED = "networkImportTemplateChanged";
+
+ /*
+ * HTML strings for tool tip text
+ */
+ private String ontologyHtml = "<html><body bgcolor=\"white\"><p><strong><font size=\"+1\" face=\"serif\"><u>%DataSourceName%</u></font></strong></p><br>"
+ + "<p><em>Data Source URL</em>: <br><font color=\"blue\">%SourceURL%</font></p><br><p><em>Description</em>:<br>"
+ + "<table width=\"300\" border=\"0\" cellspacing=\"3\" cellpadding=\"3\"><tr>"
+ + "<td rowspan=\"1\" colspan=\"1\">%Description%</td></tr></table></p></body></html>";
+ private String annotationHtml = "<html><body bgcolor=\"white\"><p><strong><font size=\"+1\" face=\"serif\"><u>%DataSourceName%</u></font></strong></p><br>"
+ + "<p><em>Annotation File URL</em>: <br><font color=\"blue\">%SourceURL%</font></p><br>"
+ + "<p><em>Data Format</em>: <font color=\"green\">%Format%</font></p><br>"
+ + "<p><em>Other Information</em>:<br>"
+ + "<table width=\"300\" border=\"0\" cellspacing=\"3\" cellpadding=\"3\">"
+ + "%AttributeTable%</table></p></body></html>";
+ private static final String DEF_ANNOTATION_ITEM = "Please select an annotation data source...";
+ private static final String[] keyTable = { "Alias?", "Column (Attribute Name)", "Data Type" };
+ private static final String ID = "ID";
+ private static final String GENE_ASSOCIATION = "gene_association";
+
+ // Key column index
+ private int keyInFile;
+
+ // Case sensitivity
+ private Boolean caseSensitive = true;
+
+ // Data Type
+ private edu.ucsd.bioeng.coreplugin.tableImport.reader.TextTableReader.ObjectType objType;
+ private final int dialogType;
+ private Map<String, String> annotationUrlMap;
+ private Map<String, String> annotationFormatMap;
+ private Map<String, Map<String, String>> annotationAttributesMap;
+ private Map<String, String> ontologyUrlMap;
+ private Map<String, String> ontologyTypeMap;
+ private Map<String, String> ontologyDescriptionMap;
+ private List<Byte> attributeDataTypes;
+
+ /*
+ * This is for storing data type in the list object.
+ */
+ private Byte[] listDataTypes;
+
+ /*
+ * Tracking multiple sheets.
+ */
+ private Map<String, AliasTableModel> aliasTableModelMap;
+ private Map<String, JTable> aliasTableMap;
+ private Map<String, Integer> primaryKeyMap;
+ private String[] columnHeaders;
+ private String listDelimiter;
+ private boolean[] importFlag;
+ private CyAttributes selectedAttributes;
+ private PropertyChangeSupport changes = new PropertyChangeSupport(this);
+ private File[] inputFiles;
+
+ private CyLogger logger;
+
+ /**
+ * Creates new form ImportAttributesDialog
+ *
+ * @throws IOException
+ * @throws JAXBException
+ */
+ public ImportTextTableDialog(Frame parent, boolean modal) throws JAXBException, IOException {
+ this(parent, modal, ImportTextTableDialog.SIMPLE_ATTRIBUTE_IMPORT);
+ }
+
+ public ImportTextTableDialog(final Frame parent, final File tableFile,
+ final String tableFileName, final int dialogType)
+ throws JAXBException, IOException
+ {
+ super(parent, /* modal = */ true);
+
+ // Default Attribute is node attr.
+ selectedAttributes = Cytoscape.getNodeAttributes();
+
+ this.objType = NODE;
+ this.dialogType = dialogType;
+ this.listDelimiter = PIPE.toString();
+
+ this.aliasTableModelMap = new HashMap<String, AliasTableModel>();
+ this.aliasTableMap = new HashMap<String, JTable>();
+ this.primaryKeyMap = new HashMap<String, Integer>();
+
+ annotationUrlMap = new HashMap<String, String>();
+ annotationFormatMap = new HashMap<String, String>();
+ annotationAttributesMap = new HashMap<String, Map<String, String>>();
+
+ ontologyUrlMap = new HashMap<String, String>();
+ ontologyDescriptionMap = new HashMap<String, String>();
+ ontologyTypeMap = new HashMap<String, String>();
+
+ attributeDataTypes = new ArrayList<Byte>();
+ initComponents(true);
+ updateComponents();
+
+ previewPanel.addPropertyChangeListener(this);
+
+ logger = CyLogger.getLogger( ImportTextTableDialog.class );
+
+ final File multiSource[] = { tableFile };
+ fileLoadAction(multiSource, tableFileName);
+ }
+
+ private void fileLoadAction(final File[] multiSource, final String displayName) throws IOException {
+ // Pick the first one and show preview.
+ this.inputFiles = multiSource;
+
+ final File sourceFile = multiSource[0];
+
+ targetDataSourceTextField.setText(displayName);
+
+ // Set tooltip as HTML
+ StringBuilder builder = new StringBuilder();
+ builder.append("<html><body><strong text=\"red\">File(s) to be imported</strong><ul>");
+
+ builder.append("<li>" + displayName + "</li>");
+ for (int i = 1; i < multiSource.length; i++)
+ builder.append("<li>" + multiSource[i].getName() + "</li>");
+
+ builder.append("</ul></body></html>");
+ targetDataSourceTextField.setToolTipText(builder.toString());
+
+ readAnnotationForPreview(multiSource[0].toURI().toURL(), checkDelimiter());
+
+ if (previewPanel.getPreviewTable() == null) {
+ JLabel label = new JLabel("File is broken or empty!");
+ label.setForeground(Color.RED);
+ JOptionPane.showMessageDialog(this, label);
+
+ return;
+ }
+
+ columnHeaders = new String[previewPanel.getPreviewTable().getColumnCount()];
+ transferNameCheckBox.setEnabled(true);
+ transferNameCheckBox.setSelected(false);
+
+ ColumnResizer.adjustColumnPreferredWidths(previewPanel.getPreviewTable());
+ previewPanel.getPreviewTable().repaint();
+ }
+
+ public ImportTextTableDialog(Frame parent, boolean modal, int dialogType)
+ throws JAXBException, IOException {
+ super(parent, modal);
+
+ // Default Attribute is node attr.
+ selectedAttributes = Cytoscape.getNodeAttributes();
+
+ this.objType = NODE;
+ this.dialogType = dialogType;
+ this.listDelimiter = PIPE.toString();
+
+ this.aliasTableModelMap = new HashMap<String, AliasTableModel>();
+ this.aliasTableMap = new HashMap<String, JTable>();
+ this.primaryKeyMap = new HashMap<String, Integer>();
+
+ annotationUrlMap = new HashMap<String, String>();
+ annotationFormatMap = new HashMap<String, String>();
+ annotationAttributesMap = new HashMap<String, Map<String, String>>();
+
+ ontologyUrlMap = new HashMap<String, String>();
+ ontologyDescriptionMap = new HashMap<String, String>();
+ ontologyTypeMap = new HashMap<String, String>();
+
+ attributeDataTypes = new ArrayList<Byte>();
+ initComponents(false);
+ updateComponents();
+
+ previewPanel.addPropertyChangeListener(this);
+
+ logger = CyLogger.getLogger( ImportTextTableDialog.class );
+ }
+
+ public void addPropertyChangeListener(PropertyChangeListener l) {
+ if(changes == null) return;
+ changes.addPropertyChangeListener(l);
+ }
+
+ public void removePropertyChangeListener(PropertyChangeListener l) {
+ changes.removePropertyChangeListener(l);
+ }
+
+ /**
+ * Listening to local signals used among Swing components in this dialog.
+ */
+ public void propertyChange(PropertyChangeEvent evt) {
+ if (evt.getPropertyName().equals(LIST_DELIMITER_CHANGED)) {
+ /*
+ * List delimiter has been changed by preview table GUI.
+ */
+ listDelimiter = evt.getNewValue().toString();
+ } else if (evt.getPropertyName().equals(LIST_DATA_TYPE_CHANGED)) {
+ listDataTypes = (Byte[]) evt.getNewValue();
+ } else if (evt.getPropertyName().equals(ATTR_DATA_TYPE_CHANGED)) {
+ /*
+ * Data type of an attribute has been chabged.
+ */
+ final Vector vec = (Vector) evt.getNewValue();
+ final Integer key = (Integer) vec.get(0);
+ final Byte newType = (Byte) vec.get(1);
+
+ if (key > attributeDataTypes.size()) {
+ attributeDataTypes = new ArrayList<Byte>();
+
+ for (Byte type : previewPanel.getCurrentDataTypes()) {
+ attributeDataTypes.add(type);
+ }
+ }
+
+ attributeDataTypes.set(key, newType);
+
+ if (dialogType != NETWORK_IMPORT) {
+ final JTable curTable = aliasTableMap.get(previewPanel.getSelectedSheetName());
+ curTable.setDefaultRenderer(Object.class,
+ new AliasTableRenderer(attributeDataTypes,
+ primaryKeyComboBox.getSelectedIndex()));
+ curTable.repaint();
+ }
+ } else if (evt.getPropertyName().equals(ATTRIBUTE_NAME_CHANGED)) {
+ /*
+ * Update Alias Table
+ */
+ if (dialogType != NETWORK_IMPORT) {
+ final Vector vec = (Vector) evt.getNewValue();
+ final String name = (String) vec.get(1);
+ final Integer column = (Integer) vec.get(0);
+
+ // Update cell in the attribute table
+ updateAliasTableCell(name, column);
+
+ // Update Primary Key combo box
+ updatePrimaryKeyComboBox();
+ }
+ } else if (evt.getPropertyName().equals(SHEET_CHANGED)) {
+ /*
+ * Only when the file is in Excel format.
+ */
+ final int columnCount = previewPanel.getPreviewTable().getColumnCount();
+ aliasTableModelMap.put(previewPanel.getSelectedSheetName(),
+ new AliasTableModel(keyTable, columnCount));
+
+ initializeAliasTable(columnCount, null);
+ updatePrimaryKeyComboBox();
+ } else if (evt.getPropertyName().equals(NETWORK_IMPORT_TEMPLATE_CHANGED)) {
+ /*
+ * This is a signal from network import options panel.
+ */
+ List<Integer> columnIdx = (List<Integer>) evt.getNewValue();
+
+ final AttributePreviewTableCellRenderer rend = (AttributePreviewTableCellRenderer) previewPanel.getPreviewTable()
+ .getCellRenderer(0,
+ 0);
+ rend.setSourceIndex(columnIdx.get(0));
+ rend.setTargetIndex(columnIdx.get(1));
+ rend.setInteractionIndex(columnIdx.get(2));
+
+ previewPanel.getPreviewTable().getTableHeader().resizeAndRepaint();
+ previewPanel.getPreviewTable().repaint();
+
+ //previewPanel.repaint();
+ }
+ }
+
+ /**
+ * This method is called from within the constructor to initialize the form.
+ * WARNING: Do NOT modify this code. The content of this method is always
+ * regenerated by the Form Editor.
+ */
+
+ // <editor-fold defaultstate="collapsed" desc=" Generated Code">
+ private void initComponents(final boolean fileHasBeenProvided) {
+ statusBar = new JStatusBar();
+
+ importAllCheckBox = new JCheckBox("Import everything (Key is always ID)");
+ importAllCheckBox.addActionListener(new ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ importAllCheckBoxActionPerformed(evt);
+ }
+ });
+
+ caseSensitiveCheckBox = new JCheckBox("Case Sensitive");
+ caseSensitiveCheckBox.setToolTipText("<html><strong><font color=\"red\">Caution! If you uncheck this, import can be extrelely slow.</font></strong></html>");
+ caseSensitiveCheckBox.setSelected(true);
+ caseSensitiveCheckBox.addActionListener(new ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ ignoreCaseCheckBoxActionPerformed(evt);
+ }
+
+ private void ignoreCaseCheckBoxActionPerformed(ActionEvent evt) {
+ caseSensitive = caseSensitiveCheckBox.isSelected();
+ }
+ });
+
+ importTypeButtonGroup = new ButtonGroup();
+
+ attrTypePanel = new JPanel();
+
+ counterSpinner = new javax.swing.JSpinner();
+ counterLabel = new javax.swing.JLabel();
+ reloadButton = new javax.swing.JButton();
+ showAllRadioButton = new javax.swing.JRadioButton();
+ counterRadioButton = new javax.swing.JRadioButton();
+
+ attrTypeButtonGroup = new javax.swing.ButtonGroup();
+ titleIconLabel1 = new javax.swing.JLabel();
+ titleIconLabel2 = new javax.swing.JLabel();
+ titleIconLabel3 = new javax.swing.JLabel();
+ titleLabel = new javax.swing.JLabel();
+ titleSeparator = new javax.swing.JSeparator();
+ importButton = new javax.swing.JButton();
+ cancelButton = new javax.swing.JButton();
+ helpButton = new javax.swing.JButton();
+ basicPanel = new javax.swing.JPanel();
+ attribuiteLabel = new javax.swing.JLabel();
+ nodeRadioButton = new javax.swing.JRadioButton();
+ edgeRadioButton = new javax.swing.JRadioButton();
+ networkRadioButton = new javax.swing.JRadioButton();
+ annotationAndOntologyImportPanel = new javax.swing.JPanel();
+ ontologyLabel = new javax.swing.JLabel();
+ ontologyComboBox = new javax.swing.JComboBox();
+ browseOntologyButton = new javax.swing.JButton();
+ sourceLabel = new javax.swing.JLabel();
+ annotationComboBox = new javax.swing.JComboBox();
+ browseAnnotationButton = new javax.swing.JButton();
+
+ targetDataSourceTextField = new javax.swing.JTextField();
+ if (fileHasBeenProvided)
+ targetDataSourceTextField.setEnabled(false);
+ selectAttributeFileButton = new javax.swing.JButton();
+ if (fileHasBeenProvided)
+ selectAttributeFileButton.setEnabled(false);
+ advancedPanel = new javax.swing.JPanel();
+ advancedOptionCheckBox = new javax.swing.JCheckBox();
+ textImportCheckBox = new javax.swing.JCheckBox();
+ attr2annotationPanel = new javax.swing.JPanel();
+ primaryKeyLabel = new javax.swing.JLabel();
+ nodeKeyLabel = new javax.swing.JLabel();
+ mappingAttributeComboBox = new javax.swing.JComboBox();
+ aliasScrollPane = new javax.swing.JScrollPane();
+ arrowButton1 = new javax.swing.JButton();
+ ontology2annotationPanel = new javax.swing.JPanel();
+ targetOntologyLabel = new javax.swing.JLabel();
+ ontologyTextField = new javax.swing.JTextField();
+ ontologyInAnnotationLabel = new javax.swing.JLabel();
+ ontologyInAnnotationComboBox = new javax.swing.JComboBox();
+ arrowButton2 = new javax.swing.JButton();
+ textImportOptionPanel = new javax.swing.JPanel();
+ delimiterPanel = new javax.swing.JPanel();
+ tabCheckBox = new javax.swing.JCheckBox();
+ commaCheckBox = new javax.swing.JCheckBox();
+ semicolonCheckBox = new javax.swing.JCheckBox();
+ spaceCheckBox = new javax.swing.JCheckBox();
+ otherCheckBox = new javax.swing.JCheckBox();
+ otherDelimiterTextField = new javax.swing.JTextField();
+ transferNameCheckBox = new javax.swing.JCheckBox();
+
+ attributeNamePanel = new JPanel();
+ previewOptionPanel = new JPanel();
+ networkImportOptionPanel = new JPanel();
+
+ defaultInteractionLabel = new JLabel();
+ defaultInteractionTextField = new JTextField();
+
+ simpleAttributeImportPanel = new javax.swing.JPanel();
+ attributeFileLabel = new javax.swing.JLabel();
+ if (fileHasBeenProvided)
+ attributeFileLabel.setEnabled(false);
+
+ startRowSpinner = new JSpinner();
+ startRowLabel = new JLabel();
+
+ commentLineLabel = new JLabel();
+ commentLineTextField = new JTextField();
+ commentLineTextField.setName("commentLineTextField");
+
+ titleLabel.setFont(TITLE_FONT.getFont());
+
+ if (dialogType == NETWORK_IMPORT) {
+ previewPanel = new PreviewTablePanel(null, PreviewTablePanel.NETWORK_PREVIEW);
+ } else if (dialogType == ONTOLOGY_AND_ANNOTATION_IMPORT) {
+ defaultInteractionLabel.setEnabled(false);
+ defaultInteractionTextField.setEnabled(false);
+ commentLineTextField.setText("!");
+ importAllCheckBox.setEnabled(false);
+ previewPanel = new PreviewTablePanel(null, PreviewTablePanel.ONTOLOGY_PREVIEW);
+ } else {
+ defaultInteractionLabel.setEnabled(false);
+ defaultInteractionTextField.setEnabled(false);
+
+ previewPanel = new PreviewTablePanel();
+ }
+
+ primaryLabel = new JLabel("Primary Key: ");
+ primaryKeyComboBox = new JComboBox();
+ primaryKeyComboBox.setEnabled(false);
+ primaryKeyComboBox.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent evt) {
+ primaryKeyComboBoxActionPerformed(evt);
+ }
+ });
+
+ /*
+ * Set tooltips options.
+ */
+ ToolTipManager tp = ToolTipManager.sharedInstance();
+ tp.setInitialDelay(40);
+ tp.setDismissDelay(50000);
+
+ setDefaultCloseOperation(javax.swing.WindowConstants.DISPOSE_ON_CLOSE);
+
+ titleIconLabel2.setIcon(RIGHT_ARROW_ICON.getIcon());
+
+ titleIconLabel3.setIcon(new ImageIcon(Cytoscape.class.getResource("images/icon48.png")));
+
+ titleSeparator.setForeground(java.awt.Color.blue);
+
+ importButton.setText("Import");
+ importButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ try {
+ importButtonActionPerformed(evt);
+ } catch (IOException e) {
+ e.printStackTrace();
+ } catch (Exception e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ }
+ });
+
+ cancelButton.setText("Cancel");
+ cancelButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ cancelButtonActionPerformed(evt);
+ }
+ });
+
+ helpButton.setBackground(new java.awt.Color(255, 255, 255));
+ helpButton.setText("?");
+ helpButton.setToolTipText("Display help page...");
+ helpButton.setMargin(new java.awt.Insets(1, 1, 1, 1));
+ helpButton.setPreferredSize(new java.awt.Dimension(14, 14));
+ helpButton.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent arg0) {
+ helpButtonActionPerformed(arg0);
+ }
+ });
+
+ /*
+ * Data Source Panel Layouts.
+ */
+ basicPanel.setBorder(javax.swing.BorderFactory.createTitledBorder(null, "Data Sources",
+ javax.swing.border.TitledBorder.DEFAULT_JUSTIFICATION,
+ javax.swing.border.TitledBorder.DEFAULT_POSITION,
+ new java.awt.Font("Dialog",
+ 1, 11)));
+
+ if ((dialogType == SIMPLE_ATTRIBUTE_IMPORT)
+ || (dialogType == ONTOLOGY_AND_ANNOTATION_IMPORT)) {
+ attribuiteLabel.setFont(new java.awt.Font("SansSerif", 1, 12));
+ attribuiteLabel.setText("Attributes");
+
+ nodeRadioButton.setText("Node");
+ nodeRadioButton.setBorder(javax.swing.BorderFactory.createEmptyBorder(0, 0, 0, 0));
+ nodeRadioButton.setMargin(new java.awt.Insets(0, 0, 0, 0));
+ nodeRadioButton.setSelected(true);
+ nodeRadioButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ attributeRadioButtonActionPerformed(evt);
+ }
+ });
+
+ edgeRadioButton.setText("Edge");
+ edgeRadioButton.setBorder(javax.swing.BorderFactory.createEmptyBorder(0, 0, 0, 0));
+ edgeRadioButton.setMargin(new java.awt.Insets(0, 0, 0, 0));
+ edgeRadioButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ attributeRadioButtonActionPerformed(evt);
+ }
+ });
+
+ networkRadioButton.setText("Network");
+ networkRadioButton.setBorder(javax.swing.BorderFactory.createEmptyBorder(0, 0, 0, 0));
+ networkRadioButton.setMargin(new java.awt.Insets(0, 0, 0, 0));
+ networkRadioButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ attributeRadioButtonActionPerformed(evt);
+ }
+ });
+
+ org.jdesktop.layout.GroupLayout attrTypePanelLayout = new org.jdesktop.layout.GroupLayout(attrTypePanel);
+ attrTypePanel.setLayout(attrTypePanelLayout);
+ attrTypePanelLayout.setHorizontalGroup(attrTypePanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(attrTypePanelLayout.createSequentialGroup()
+ .add(attribuiteLabel)
+ .add(24,
+ 24,
+ 24)
+ .add(nodeRadioButton)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(edgeRadioButton)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(networkRadioButton)
+ .addContainerGap(org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE)));
+ attrTypePanelLayout.setVerticalGroup(attrTypePanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(attrTypePanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE)
+ .add(attribuiteLabel)
+ .add(nodeRadioButton)
+ .add(edgeRadioButton)
+ .add(networkRadioButton)));
+ }
+
+ /*
+ * This panel is necessary only when this is an ontology import dialog.
+ */
+ if (dialogType == ONTOLOGY_AND_ANNOTATION_IMPORT) {
+ titleIconLabel1.setIcon(REMOTE_SOURCE_ICON_LARGE.getIcon());
+
+ ontologyLabel.setFont(LABEL_FONT.getFont());
+ ontologyLabel.setForeground(ONTOLOGY_COLOR.getColor());
+ ontologyLabel.setText("Ontology");
+
+ // ontologyComboBox.setFont(new java.awt.Font("SansSerif", 1, 14));
+ ontologyComboBox.setPreferredSize(new java.awt.Dimension(68, 25));
+
+ final ListCellRenderer ontologyLcr = ontologyComboBox.getRenderer();
+ ontologyComboBox.setFont(ITEM_FONT.getFont());
+ ontologyComboBox.setForeground(ONTOLOGY_COLOR.getColor());
+ ontologyComboBox.setRenderer(new ListCellRenderer() {
+ public Component getListCellRendererComponent(JList list, Object value,
+ int index, boolean isSelected,
+ boolean cellHasFocus) {
+ JLabel ontologyItem = (JLabel) ontologyLcr.getListCellRendererComponent(list,
+ value,
+ index,
+ isSelected,
+ cellHasFocus);
+ String url = ontologyUrlMap.get(value);
+
+ if (isSelected) {
+ ontologyItem.setBackground(list.getSelectionBackground());
+ ontologyItem.setForeground(list.getSelectionForeground());
+ } else {
+ ontologyItem.setBackground(list.getBackground());
+ ontologyItem.setForeground(list.getForeground());
+ }
+
+ if ((url != null) && url.startsWith("http://")) {
+ ontologyItem.setIcon(REMOTE_SOURCE_ICON.getIcon());
+ } else {
+ ontologyItem.setIcon(LOCAL_SOURCE_ICON.getIcon());
+ }
+
+ if (Cytoscape.getOntologyServer().getOntologyNames().contains(value)) {
+ ontologyItem.setForeground(ONTOLOGY_COLOR.getColor());
+ } else {
+ ontologyItem.setForeground(NOT_LOADED_COLOR.getColor());
+ }
+
+ return ontologyItem;
+ }
+ });
+
+ ontologyComboBox.addMouseListener(new MouseListener() {
+ public void mouseClicked(MouseEvent arg0) {
+ }
+
+ public void mouseEntered(MouseEvent arg0) {
+ }
+
+ public void mouseExited(MouseEvent arg0) {
+ }
+
+ public void mousePressed(MouseEvent arg0) {
+ }
+
+ public void mouseReleased(MouseEvent arg0) {
+ }
+ });
+
+ ontologyComboBox.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ ontologyComboBoxActionPerformed(evt);
+ }
+ });
+
+ browseOntologyButton.setText("Browse");
+ browseOntologyButton.setToolTipText("Browse local ontology file");
+ browseOntologyButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ browseOntologyButtonActionPerformed(evt);
+ }
+ });
+
+ sourceLabel.setFont(LABEL_FONT.getFont());
+ sourceLabel.setText("Annotation");
+
+ annotationComboBox.setName("annotationComboBox");
+ annotationComboBox.setFont(ITEM_FONT.getFont());
+ annotationComboBox.setPreferredSize(new java.awt.Dimension(68, 25));
+
+ final ListCellRenderer lcr = annotationComboBox.getRenderer();
+ annotationComboBox.setRenderer(new ListCellRenderer() {
+ public Component getListCellRendererComponent(JList list, Object value,
+ int index, boolean isSelected,
+ boolean cellHasFocus) {
+ JLabel cmp = (JLabel) lcr.getListCellRendererComponent(list, value, index,
+ isSelected,
+ cellHasFocus);
+ String url = annotationUrlMap.get(value);
+
+ if (isSelected) {
+ cmp.setBackground(list.getSelectionBackground());
+ cmp.setForeground(list.getSelectionForeground());
+ } else {
+ cmp.setBackground(list.getBackground());
+ cmp.setForeground(list.getForeground());
+ }
+
+ if (value.toString().equals(DEF_ANNOTATION_ITEM)) {
+ cmp.setIcon(null);
+ } else if ((url != null) && url.startsWith("http://")) {
+ cmp.setIcon(REMOTE_SOURCE_ICON.getIcon());
+ } else {
+ cmp.setIcon(LOCAL_SOURCE_ICON.getIcon());
+ }
+
+ return cmp;
+ }
+ });
+ annotationComboBox.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ annotationComboBoxActionPerformed(evt);
+ }
+ });
+
+ browseAnnotationButton.setText("Browse");
+ browseAnnotationButton.setToolTipText("Browse local annotation file...");
+ browseAnnotationButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ browseAnnotationButtonActionPerformed(evt);
+ }
+ });
+
+ GroupLayout annotationAndOntologyImportPanelLayout = new GroupLayout(annotationAndOntologyImportPanel);
+ annotationAndOntologyImportPanel.setLayout(annotationAndOntologyImportPanelLayout);
+
+ annotationAndOntologyImportPanelLayout.setHorizontalGroup(annotationAndOntologyImportPanelLayout.createParallelGroup(GroupLayout.LEADING)
+ .add(annotationAndOntologyImportPanelLayout.createSequentialGroup()
+ .addContainerGap()
+ .add(annotationAndOntologyImportPanelLayout.createParallelGroup(GroupLayout.LEADING)
+ .add(sourceLabel)
+ .add(ontologyLabel))
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(annotationAndOntologyImportPanelLayout.createParallelGroup(GroupLayout.TRAILING)
+ .add(annotationComboBox,
+ 0,
+ 100,
+ Short.MAX_VALUE)
+ .add(ontologyComboBox,
+ 0,
+ 100,
+ Short.MAX_VALUE))
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(annotationAndOntologyImportPanelLayout.createParallelGroup(GroupLayout.LEADING)
+ .add(browseAnnotationButton)
+ .add(browseOntologyButton))
+ .addContainerGap()));
+ annotationAndOntologyImportPanelLayout.setVerticalGroup(annotationAndOntologyImportPanelLayout.createParallelGroup(GroupLayout.LEADING)
+ .add(annotationAndOntologyImportPanelLayout.createSequentialGroup()
+ .addContainerGap()
+ .add(annotationAndOntologyImportPanelLayout.createParallelGroup(GroupLayout.CENTER)
+ .add(sourceLabel)
+ .add(browseAnnotationButton)
+ .add(annotationComboBox,
+ GroupLayout.PREFERRED_SIZE,
+ GroupLayout.DEFAULT_SIZE,
+ GroupLayout.PREFERRED_SIZE))
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(annotationAndOntologyImportPanelLayout.createParallelGroup(GroupLayout.CENTER)
+ .add(ontologyLabel)
+ .add(ontologyComboBox,
+ GroupLayout.PREFERRED_SIZE,
+ GroupLayout.DEFAULT_SIZE,
+ GroupLayout.PREFERRED_SIZE)
+ .add(browseOntologyButton))
+ .addContainerGap(GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE)));
+ }
+
+ if ((dialogType == SIMPLE_ATTRIBUTE_IMPORT) || (dialogType == NETWORK_IMPORT)) {
+ titleIconLabel1.setIcon(SPREADSHEET_ICON_LARGE.getIcon());
+
+ attributeFileLabel.setText("Input File");
+ attributeFileLabel.setFont(new java.awt.Font("SansSerif", 1, 12));
+ selectAttributeFileButton.setText("Select File(s)");
+ selectAttributeFileButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ try {
+ selectAttributeFileButtonActionPerformed(evt);
+ } catch (IOException e) {
+ JOptionPane.showMessageDialog(
+ ImportTextTableDialog.this,
+ "<html>Could not read selected file.<p>See <b>Help->Error Dialog</b> for further details.</html>",
+ "ERROR", JOptionPane.ERROR_MESSAGE);
+ logger.warn("Could not read selected file.", e);
+ }
+ }
+ });
+
+ GroupLayout simpleAttributeImportPanelLayout = new GroupLayout(simpleAttributeImportPanel);
+ simpleAttributeImportPanel.setLayout(simpleAttributeImportPanelLayout);
+ simpleAttributeImportPanelLayout.setHorizontalGroup(simpleAttributeImportPanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(simpleAttributeImportPanelLayout.createSequentialGroup()
+ .add(attributeFileLabel)
+ .add(24,
+ 24,
+ 24)
+ .add(targetDataSourceTextField,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 300,
+ Short.MAX_VALUE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(selectAttributeFileButton)
+ .addContainerGap()));
+ simpleAttributeImportPanelLayout.setVerticalGroup(simpleAttributeImportPanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(simpleAttributeImportPanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE)
+ .add(selectAttributeFileButton)
+ .add(targetDataSourceTextField,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .add(attributeFileLabel)));
+ }
+
+ GroupLayout basicPanelLayout = new GroupLayout(basicPanel);
+ basicPanel.setLayout(basicPanelLayout);
+
+ basicPanelLayout.setHorizontalGroup(basicPanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(basicPanelLayout.createSequentialGroup()
+ .addContainerGap()
+ .add(basicPanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(basicPanelLayout.createSequentialGroup()
+ .add(simpleAttributeImportPanel,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE)
+ .addContainerGap())
+ .add(basicPanelLayout.createSequentialGroup()
+ .add(annotationAndOntologyImportPanel,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE)
+ .addContainerGap())
+ .add(basicPanelLayout.createSequentialGroup()
+ .add(attrTypePanel,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .addContainerGap(50,
+ Short.MAX_VALUE)))));
+ basicPanelLayout.setVerticalGroup(basicPanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(basicPanelLayout.createSequentialGroup()
+ .add(attrTypePanel,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(simpleAttributeImportPanel,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE)
+ .add(annotationAndOntologyImportPanel,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)));
+
+ /*
+ * Layout data for advanced panel
+ */
+ advancedPanel.setBorder(javax.swing.BorderFactory.createTitledBorder(null, "Advanced",
+ javax.swing.border.TitledBorder.DEFAULT_JUSTIFICATION,
+ javax.swing.border.TitledBorder.DEFAULT_POSITION,
+ new java.awt.Font("Dialog",
+ 1, 11)));
+
+ if ((dialogType == SIMPLE_ATTRIBUTE_IMPORT)
+ || (dialogType == ONTOLOGY_AND_ANNOTATION_IMPORT)) {
+ advancedOptionCheckBox.setText("Show Mapping Options");
+ advancedOptionCheckBox.setBorder(javax.swing.BorderFactory.createEmptyBorder(0, 0, 0, 0));
+ advancedOptionCheckBox.setMargin(new java.awt.Insets(0, 0, 0, 0));
+ advancedOptionCheckBox.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ advancedOptionCheckBoxActionPerformed(evt);
+ }
+ });
+
+ attr2annotationPanel.setBackground(new java.awt.Color(250, 250, 250));
+ attr2annotationPanel.setBorder(javax.swing.BorderFactory.createTitledBorder(new javax.swing.border.SoftBevelBorder(javax.swing.border.BevelBorder.RAISED),
+ "Annotation File to Attribute Mapping",
+ javax.swing.border.TitledBorder.DEFAULT_JUSTIFICATION,
+ javax.swing.border.TitledBorder.DEFAULT_POSITION,
+ new java.awt.Font("Dialog",
+ 1,
+ 11)));
+ primaryKeyLabel.setFont(new java.awt.Font("SansSerif", 1, 12));
+ primaryKeyLabel.setForeground(new java.awt.Color(51, 51, 255));
+ primaryKeyLabel.setText("Key Column in Annotation File");
+
+ nodeKeyLabel.setFont(new java.awt.Font("SansSerif", 1, 12));
+ nodeKeyLabel.setForeground(new java.awt.Color(255, 0, 51));
+ nodeKeyLabel.setText("Key Attribute for Network");
+
+ mappingAttributeComboBox.setForeground(new java.awt.Color(255, 0, 51));
+ mappingAttributeComboBox.setEnabled(false);
+ mappingAttributeComboBox.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ nodeKeyComboBoxActionPerformed(evt);
+ }
+ });
+
+ arrowButton1.setBackground(new java.awt.Color(250, 250, 250));
+ arrowButton1.setOpaque(false);
+ arrowButton1.setIcon(RIGHT_ARROW_ICON.getIcon());
+ arrowButton1.setBorder(null);
+ arrowButton1.setBorderPainted(false);
+
+ GroupLayout attr2annotationPanelLayout = new GroupLayout(attr2annotationPanel);
+ attr2annotationPanel.setLayout(attr2annotationPanelLayout);
+ attr2annotationPanelLayout.setHorizontalGroup(attr2annotationPanelLayout.createParallelGroup(GroupLayout.LEADING)
+ .add(attr2annotationPanelLayout.createSequentialGroup()
+ .addContainerGap()
+ .add(attr2annotationPanelLayout.createParallelGroup(GroupLayout.LEADING)
+ .add(attr2annotationPanelLayout.createSequentialGroup()
+ .add(primaryKeyLabel)
+ .add(100,
+ 100,
+ 100))
+ .add(attr2annotationPanelLayout.createSequentialGroup()
+ .add(primaryLabel)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(primaryKeyComboBox,
+ 0,
+ 0,
+ Short.MAX_VALUE))
+ .add(aliasScrollPane,
+ GroupLayout.DEFAULT_SIZE,
+ 100,
+ Short.MAX_VALUE))
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(arrowButton1)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(attr2annotationPanelLayout.createParallelGroup(GroupLayout.LEADING)
+ .add(mappingAttributeComboBox,
+ 0,
+ 100,
+ Short.MAX_VALUE)
+ .add(nodeKeyLabel))
+ .addContainerGap()));
+ attr2annotationPanelLayout.setVerticalGroup(attr2annotationPanelLayout.createParallelGroup(GroupLayout.LEADING)
+ .add(attr2annotationPanelLayout.createSequentialGroup()
+ .add(attr2annotationPanelLayout.createParallelGroup(GroupLayout.BASELINE)
+ .add(primaryKeyLabel)
+ .add(nodeKeyLabel))
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(attr2annotationPanelLayout.createParallelGroup(GroupLayout.BASELINE)
+ .add(primaryLabel)
+ .add(primaryKeyComboBox,
+ GroupLayout.PREFERRED_SIZE,
+ GroupLayout.DEFAULT_SIZE,
+ GroupLayout.PREFERRED_SIZE))
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(attr2annotationPanelLayout.createParallelGroup(GroupLayout.LEADING)
+ .add(aliasScrollPane,
+ GroupLayout.DEFAULT_SIZE,
+ 100,
+ Short.MAX_VALUE)
+ .add(attr2annotationPanelLayout.createSequentialGroup()
+ .add(attr2annotationPanelLayout.createParallelGroup(GroupLayout.TRAILING)
+ .add(mappingAttributeComboBox,
+ GroupLayout.PREFERRED_SIZE,
+ GroupLayout.DEFAULT_SIZE,
+ GroupLayout.PREFERRED_SIZE)
+ .add(arrowButton1))
+ .addContainerGap()))));
+ }
+
+ textImportCheckBox.setText("Show Text File Import Options");
+ textImportCheckBox.setBorder(javax.swing.BorderFactory.createEmptyBorder(0, 0, 0, 0));
+ textImportCheckBox.setMargin(new java.awt.Insets(0, 0, 0, 0));
+ textImportCheckBox.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ textImportCheckBoxActionPerformed(evt);
+ }
+ });
+
+ if (dialogType == ONTOLOGY_AND_ANNOTATION_IMPORT) {
+ ontology2annotationPanel.setBackground(new java.awt.Color(250, 250, 250));
+ ontology2annotationPanel.setBorder(javax.swing.BorderFactory.createTitledBorder(new javax.swing.border.SoftBevelBorder(javax.swing.border.BevelBorder.RAISED),
+ "Annotation File to Ontology Mapping",
+ javax.swing.border.TitledBorder.DEFAULT_JUSTIFICATION,
+ javax.swing.border.TitledBorder.DEFAULT_POSITION,
+ new java.awt.Font("Dialog",
+ 1,
+ 11)));
+ targetOntologyLabel.setFont(new java.awt.Font("SansSerif", 1, 12));
+ targetOntologyLabel.setForeground(new java.awt.Color(73, 127, 235));
+ targetOntologyLabel.setText("Ontology");
+
+ ontologyTextField.setFont(new java.awt.Font("SansSerif", 1, 14));
+ ontologyTextField.setForeground(ONTOLOGY_COLOR.getColor());
+ ontologyTextField.setBackground(Color.WHITE);
+ ontologyTextField.setEditable(false);
+ ontologyTextField.setToolTipText("This ontology will be used for mapping.");
+
+ ontologyInAnnotationLabel.setFont(new java.awt.Font("SansSerif", 1, 12));
+ ontologyInAnnotationLabel.setForeground(new java.awt.Color(0, 255, 255));
+ ontologyInAnnotationLabel.setText("Key Column in Annotation File");
+
+ ontologyInAnnotationComboBox.setForeground(ONTOLOGY_COLOR.getColor());
+ ontologyInAnnotationComboBox.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ ontologyInAnnotationComboBoxActionPerformed(evt);
+ }
+ });
+
+ arrowButton2.setBackground(new java.awt.Color(250, 250, 250));
+ arrowButton2.setIcon(new javax.swing.ImageIcon(Cytoscape.class.getResource("images/ximian/stock_right-16.png")));
+ arrowButton2.setBorder(null);
+ arrowButton2.setBorderPainted(false);
+
+ GroupLayout ontology2annotationPanelLayout = new GroupLayout(ontology2annotationPanel);
+ ontology2annotationPanel.setLayout(ontology2annotationPanelLayout);
+ ontology2annotationPanelLayout.setHorizontalGroup(ontology2annotationPanelLayout.createParallelGroup(GroupLayout.LEADING)
+ .add(ontology2annotationPanelLayout.createSequentialGroup()
+ .addContainerGap()
+ .add(ontology2annotationPanelLayout.createParallelGroup(GroupLayout.LEADING)
+ .add(ontologyInAnnotationLabel)
+ .add(ontologyInAnnotationComboBox,
+ 0,
+ 100,
+ Short.MAX_VALUE))
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(arrowButton2)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(ontology2annotationPanelLayout.createParallelGroup(GroupLayout.TRAILING)
+ .add(GroupLayout.LEADING,
+ targetOntologyLabel)
+ .add(ontologyTextField,
+ GroupLayout.DEFAULT_SIZE,
+ 100,
+ Short.MAX_VALUE))
+ .addContainerGap()));
+ ontology2annotationPanelLayout.setVerticalGroup(ontology2annotationPanelLayout.createParallelGroup(GroupLayout.LEADING)
+ .add(ontology2annotationPanelLayout.createSequentialGroup()
+ .add(ontology2annotationPanelLayout.createParallelGroup(GroupLayout.BASELINE)
+ .add(ontologyInAnnotationLabel)
+ .add(targetOntologyLabel))
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(ontology2annotationPanelLayout.createParallelGroup(GroupLayout.BASELINE)
+ .add(ontologyInAnnotationComboBox,
+ GroupLayout.PREFERRED_SIZE,
+ GroupLayout.DEFAULT_SIZE,
+ GroupLayout.PREFERRED_SIZE)
+ .add(ontologyTextField,
+ GroupLayout.PREFERRED_SIZE,
+ GroupLayout.DEFAULT_SIZE,
+ GroupLayout.PREFERRED_SIZE)
+ .add(arrowButton2))
+ .addContainerGap(GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE)));
+ }
+
+ /*
+ * For Network Import
+ */
+ if (dialogType == NETWORK_IMPORT) {
+ networkImportPanel = new NetworkImportOptionsPanel();
+ networkImportPanel.addPropertyChangeListener(this);
+ caseSensitiveCheckBox.setVisible(false);
+ }
+
+ textImportOptionPanel.setBorder(javax.swing.BorderFactory.createTitledBorder(new javax.swing.border.SoftBevelBorder(javax.swing.border.BevelBorder.RAISED),
+ "Text File Import Options",
+ javax.swing.border.TitledBorder.DEFAULT_JUSTIFICATION,
+ javax.swing.border.TitledBorder.DEFAULT_POSITION,
+ new java.awt.Font("Dialog",
+ 1,
+ 11)));
+ delimiterPanel.setBorder(javax.swing.BorderFactory.createTitledBorder("Delimiter"));
+ tabCheckBox.setText("Tab");
+ tabCheckBox.setBorder(javax.swing.BorderFactory.createEmptyBorder(0, 0, 0, 0));
+ tabCheckBox.setMargin(new java.awt.Insets(0, 0, 0, 0));
+ tabCheckBox.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ try {
+ delimiterCheckBoxActionPerformed(evt);
+ } catch (IOException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ }
+ });
+
+ commaCheckBox.setText("Comma");
+ commaCheckBox.setBorder(javax.swing.BorderFactory.createEmptyBorder(0, 0, 0, 0));
+ commaCheckBox.setMargin(new java.awt.Insets(0, 0, 0, 0));
+ commaCheckBox.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ try {
+ delimiterCheckBoxActionPerformed(evt);
+ } catch (IOException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ }
+ });
+
+ semicolonCheckBox.setText("Semicolon");
+ semicolonCheckBox.setBorder(javax.swing.BorderFactory.createEmptyBorder(0, 0, 0, 0));
+ semicolonCheckBox.setMargin(new java.awt.Insets(0, 0, 0, 0));
+ semicolonCheckBox.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ try {
+ delimiterCheckBoxActionPerformed(evt);
+ } catch (IOException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ }
+ });
+
+ spaceCheckBox.setText("Space");
+ spaceCheckBox.setBorder(javax.swing.BorderFactory.createEmptyBorder(0, 0, 0, 0));
+ spaceCheckBox.setMargin(new java.awt.Insets(0, 0, 0, 0));
+ spaceCheckBox.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ try {
+ delimiterCheckBoxActionPerformed(evt);
+ } catch (IOException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ }
+ });
+
+ otherCheckBox.setText("Other");
+ otherCheckBox.setBorder(javax.swing.BorderFactory.createEmptyBorder(0, 0, 0, 0));
+ otherCheckBox.setMargin(new java.awt.Insets(0, 0, 0, 0));
+ otherCheckBox.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ try {
+ delimiterCheckBoxActionPerformed(evt);
+ } catch (IOException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ }
+ });
+
+ otherDelimiterTextField.addKeyListener(new KeyListener() {
+ public void keyPressed(KeyEvent evt) {
+ try {
+ otherTextFieldActionPerformed(evt);
+ } catch (IOException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ }
+
+ public void keyReleased(KeyEvent arg0) {
+ }
+
+ public void keyTyped(KeyEvent evt) {
+ }
+ });
+
+ GroupLayout delimiterPanelLayout = new GroupLayout(delimiterPanel);
+ delimiterPanel.setLayout(delimiterPanelLayout);
+ delimiterPanelLayout.setHorizontalGroup(delimiterPanelLayout.createParallelGroup(GroupLayout.LEADING)
+ .add(delimiterPanelLayout.createSequentialGroup()
+ .add(tabCheckBox)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(commaCheckBox)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(semicolonCheckBox)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(spaceCheckBox)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(otherCheckBox)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(otherDelimiterTextField,
+ GroupLayout.DEFAULT_SIZE,
+ 31,
+ Short.MAX_VALUE)));
+ delimiterPanelLayout.setVerticalGroup(delimiterPanelLayout.createParallelGroup(GroupLayout.LEADING)
+ .add(delimiterPanelLayout.createSequentialGroup()
+ .add(delimiterPanelLayout.createParallelGroup(GroupLayout.BASELINE)
+ .add(tabCheckBox)
+ .add(commaCheckBox)
+ .add(semicolonCheckBox)
+ .add(spaceCheckBox)
+ .add(otherCheckBox)
+ .add(otherDelimiterTextField,
+ GroupLayout.PREFERRED_SIZE,
+ GroupLayout.DEFAULT_SIZE,
+ GroupLayout.PREFERRED_SIZE))
+ .addContainerGap(GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE)));
+
+ transferNameCheckBox.setEnabled(false);
+
+ SpinnerNumberModel spinnerModel = new SpinnerNumberModel(100, 1, 10000000, 10);
+ counterSpinner.setModel(spinnerModel);
+ counterSpinner.addMouseWheelListener(new java.awt.event.MouseWheelListener() {
+ public void mouseWheelMoved(java.awt.event.MouseWheelEvent evt) {
+ counterSpinnerMouseWheelMoved(evt);
+ }
+ });
+ counterSpinner.setToolTipText("<html><body>Click <strong text=\"red\"><i>Refresh Preview</i></strong> button to update the table.</body></html>");
+
+ counterLabel.setText("entries.");
+
+ previewOptionPanel.setBorder(javax.swing.BorderFactory.createTitledBorder("Preview Options"));
+ reloadButton.setText("Refresh Preview");
+ reloadButton.setMargin(new java.awt.Insets(2, 2, 2, 2));
+ reloadButton.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ try {
+ reloadButtonActionPerformed(evt);
+ } catch (IOException e) {
+ e.printStackTrace();
+ throw new IllegalStateException("Could not reload target file.");
+ }
+ }
+ });
+
+ showAllRadioButton.setText("Show all entries in the file");
+ showAllRadioButton.setBorder(javax.swing.BorderFactory.createEmptyBorder(0, 0, 0, 0));
+ showAllRadioButton.setMargin(new java.awt.Insets(0, 0, 0, 0));
+
+ counterRadioButton.setText("Show first ");
+ counterRadioButton.setBorder(javax.swing.BorderFactory.createEmptyBorder(0, 0, 0, 0));
+ counterRadioButton.setMargin(new java.awt.Insets(0, 0, 0, 0));
+
+ org.jdesktop.layout.GroupLayout previewOptionPanelLayout = new org.jdesktop.layout.GroupLayout(previewOptionPanel);
+ previewOptionPanel.setLayout(previewOptionPanelLayout);
+
+ previewOptionPanelLayout.setHorizontalGroup(previewOptionPanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(previewOptionPanelLayout.createSequentialGroup()
+ .addContainerGap()
+ .add(showAllRadioButton)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(counterRadioButton)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(counterSpinner,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ 58,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(counterLabel)
+ .addContainerGap(76,
+ Short.MAX_VALUE)));
+ previewOptionPanelLayout.setVerticalGroup(previewOptionPanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE)
+ .add(counterRadioButton)
+ .add(counterSpinner,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .add(counterLabel)
+ .add(showAllRadioButton));
+
+ attributeNamePanel.setBorder(javax.swing.BorderFactory.createTitledBorder("Attribute Names"));
+
+ transferNameCheckBox.setText("Transfer first line as attribute names");
+
+ transferNameCheckBox.setBorder(null);
+ transferNameCheckBox.setMargin(new java.awt.Insets(0, 0, 0, 0));
+ transferNameCheckBox.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ transferNameCheckBoxActionPerformed(evt);
+ }
+ });
+
+ startRowLabel.setText("Start Import Row: ");
+ startRowLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+
+ startRowSpinner.setName("startRowSpinner");
+
+ SpinnerNumberModel startRowSpinnerModel = new SpinnerNumberModel(1, 1, 10000000, 1);
+ startRowSpinner.setModel(startRowSpinnerModel);
+ startRowSpinner.addMouseWheelListener(new java.awt.event.MouseWheelListener() {
+ public void mouseWheelMoved(java.awt.event.MouseWheelEvent evt) {
+ startRowSpinnerMouseWheelMoved(evt);
+ }
+ });
+ startRowSpinner.setToolTipText("<html>Load entries from this line. <p>"
+ + "(Click on the <strong><i>Refresh Preview</i></strong> button to refresh preview.)</p></html>");
+
+ commentLineLabel.setText("Comment Line:");
+
+ commentLineTextField.setToolTipText("<html>Lines start with this string will be ignored. <br>"
+ + "(Click on the <strong><i>Refresh Preview</i></strong> button to refresh preview.)</html>");
+
+ GroupLayout attributeNamePanelLayout = new org.jdesktop.layout.GroupLayout(attributeNamePanel);
+ attributeNamePanel.setLayout(attributeNamePanelLayout);
+
+ attributeNamePanelLayout.setHorizontalGroup(attributeNamePanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(attributeNamePanelLayout.createSequentialGroup()
+ .add(transferNameCheckBox)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(startRowLabel)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(startRowSpinner,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ 51,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(commentLineLabel)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(commentLineTextField,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ 24,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .addContainerGap(12,
+ Short.MAX_VALUE)));
+ attributeNamePanelLayout.setVerticalGroup(attributeNamePanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(attributeNamePanelLayout.createSequentialGroup()
+ .add(attributeNamePanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE)
+ .add(transferNameCheckBox,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 21,
+ Short.MAX_VALUE)
+ .add(startRowLabel)
+ .add(startRowSpinner,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .add(commentLineLabel)
+ .add(commentLineTextField,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE))
+ .addContainerGap()));
+
+ networkImportOptionPanel.setBorder(javax.swing.BorderFactory.createTitledBorder("Network Import Options"));
+ defaultInteractionLabel.setText("Default Interaction:");
+ defaultInteractionTextField.setText(DEFAULT_INTERACTION);
+ defaultInteractionTextField.setToolTipText("<html>If <font color=\"red\"><i>Default Interaction</i></font>"
+ + " is selected, this value will be used for <i>Interaction Type</i>.<br></html>");
+
+ org.jdesktop.layout.GroupLayout networkImportOptionPanelLayout = new org.jdesktop.layout.GroupLayout(networkImportOptionPanel);
+ networkImportOptionPanel.setLayout(networkImportOptionPanelLayout);
+
+ networkImportOptionPanelLayout.setHorizontalGroup(networkImportOptionPanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(networkImportOptionPanelLayout.createSequentialGroup()
+ .addContainerGap(org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE)
+ .add(defaultInteractionLabel)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(defaultInteractionTextField,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ 58,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)));
+ networkImportOptionPanelLayout.setVerticalGroup(networkImportOptionPanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(defaultInteractionLabel)
+ .add(defaultInteractionTextField,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE));
+
+ org.jdesktop.layout.GroupLayout textImportOptionPanelLayout = new org.jdesktop.layout.GroupLayout(textImportOptionPanel);
+ textImportOptionPanel.setLayout(textImportOptionPanelLayout);
+
+ textImportOptionPanelLayout.setHorizontalGroup(textImportOptionPanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(org.jdesktop.layout.GroupLayout.TRAILING,
+ textImportOptionPanelLayout.createSequentialGroup()
+ .add(attributeNamePanel,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(networkImportOptionPanel,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .add(29,
+ 29,
+ 29)
+ .add(reloadButton))
+ .add(org.jdesktop.layout.GroupLayout.TRAILING,
+ textImportOptionPanelLayout.createSequentialGroup()
+ .add(delimiterPanel,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(previewOptionPanel,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)));
+ textImportOptionPanelLayout.setVerticalGroup(textImportOptionPanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(textImportOptionPanelLayout.createSequentialGroup()
+ .add(textImportOptionPanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(delimiterPanel,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ 71,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .add(previewOptionPanel,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 50,
+ Short.MAX_VALUE))
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(textImportOptionPanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(networkImportOptionPanel,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 45,
+ Short.MAX_VALUE)
+ .add(attributeNamePanel,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ 71,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .add(org.jdesktop.layout.GroupLayout.TRAILING,
+ reloadButton))));
+
+ org.jdesktop.layout.GroupLayout advancedPanelLayout = new org.jdesktop.layout.GroupLayout(advancedPanel);
+ advancedPanel.setLayout(advancedPanelLayout);
+
+ advancedPanelLayout.setHorizontalGroup(advancedPanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(advancedPanelLayout.createSequentialGroup()
+ .addContainerGap()
+ .add(advancedOptionCheckBox)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(textImportCheckBox)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(importAllCheckBox)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(caseSensitiveCheckBox))
+ .add(attr2annotationPanel,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE)
+ .add(ontology2annotationPanel,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE)
+ .add(textImportOptionPanel,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE));
+ advancedPanelLayout.setVerticalGroup(advancedPanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(advancedPanelLayout.createSequentialGroup()
+ .add(advancedPanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE)
+ .add(advancedOptionCheckBox)
+ .add(textImportCheckBox)
+ .add(importAllCheckBox)
+ .add(caseSensitiveCheckBox))
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(attr2annotationPanel,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(ontology2annotationPanel,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(textImportOptionPanel,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)));
+
+ globalLayout();
+
+ attr2annotationPanel.setVisible(false);
+ basicPanel.repaint();
+ ontology2annotationPanel.setVisible(false);
+ textImportOptionPanel.setVisible(false);
+
+ pack();
+ } // </editor-fold>
+
+ /**
+ * Update UI based on the primary key selection.
+ * @param evt
+ */
+ private void primaryKeyComboBoxActionPerformed(ActionEvent evt) {
+ // Not necessary in Network Import.
+ if (dialogType == NETWORK_IMPORT)
+ return;
+
+ // Update primary key index.
+ keyInFile = primaryKeyComboBox.getSelectedIndex();
+
+ // Update
+ previewPanel.getPreviewTable()
+ .setDefaultRenderer(Object.class, getRenderer(previewPanel.getFileType()));
+
+ try {
+ if ((dialogType == SIMPLE_ATTRIBUTE_IMPORT) || (dialogType == NETWORK_IMPORT)) {
+ try {
+ setStatusBar(new URL(targetDataSourceTextField.getText()));
+ } catch (Exception e) {
+ setStatusBar(inputFiles[0].toURI().toURL());
+ }
+ } else {
+ setStatusBar(new URL(annotationUrlMap.get(annotationComboBox.getSelectedItem()
+ .toString())));
+ }
+ } catch (MalformedURLException e) {
+ e.printStackTrace();
+ }
+
+ previewPanel.repaint();
+
+ JTable curTable = aliasTableMap.get(previewPanel.getSelectedSheetName());
+ curTable.setModel(aliasTableModelMap.get(previewPanel.getSelectedSheetName()));
+
+ if (curTable.getCellRenderer(0, 1) != null) {
+ ((AliasTableRenderer) curTable.getCellRenderer(0, 1)).setPrimaryKey(keyInFile);
+ aliasScrollPane.setViewportView(curTable);
+
+ primaryKeyMap.put(previewPanel.getSelectedSheetName(),
+ primaryKeyComboBox.getSelectedIndex());
+
+ aliasScrollPane.setViewportView(curTable);
+ curTable.repaint();
+ }
+
+ // Update table view
+ ColumnResizer.adjustColumnPreferredWidths(previewPanel.getPreviewTable());
+ previewPanel.getPreviewTable().repaint();
+ }
+
+ private void helpButtonActionPerformed(ActionEvent evt) {
+ // Quick help should be implemented!
+ }
+
+ private void otherTextFieldActionPerformed(KeyEvent evt) throws IOException {
+ if (otherCheckBox.isSelected()) {
+ displayPreview();
+ }
+ }
+
+ private void attributeRadioButtonActionPerformed(ActionEvent evt) {
+ if (nodeRadioButton.isSelected()) {
+ selectedAttributes = Cytoscape.getNodeAttributes();
+ objType = NODE;
+ } else if (edgeRadioButton.isSelected()) {
+ selectedAttributes = Cytoscape.getEdgeAttributes();
+ objType = EDGE;
+ } else {
+ selectedAttributes = Cytoscape.getNetworkAttributes();
+ objType = NETWORK;
+ }
+
+ updateMappingAttributeComboBox();
+ setKeyList();
+ }
+
+ private void advancedOptionCheckBoxActionPerformed(ActionEvent evt) {
+ if (advancedOptionCheckBox.isSelected()) {
+ attr2annotationPanel.setVisible(true);
+ ontology2annotationPanel.setVisible(true);
+ } else {
+ attr2annotationPanel.setVisible(false);
+ ontology2annotationPanel.setVisible(false);
+ }
+
+ if (dialogType == ImportTextTableDialog.SIMPLE_ATTRIBUTE_IMPORT) {
+ ontology2annotationPanel.setVisible(false);
+ }
+
+ pack();
+ }
+
+ /**
+ * If Import All selected, ID combo box should be set to ID
+ * @param evt
+ */
+ private void importAllCheckBoxActionPerformed(ActionEvent evt) {
+ if (importAllCheckBox.isSelected()) {
+ // Lock key to ID
+ mappingAttributeComboBox.setSelectedItem(ID);
+ mappingAttributeComboBox.setEnabled(false);
+ } else {
+ mappingAttributeComboBox.setEnabled(true);
+ }
+ }
+
+ private void nodeKeyComboBoxActionPerformed(java.awt.event.ActionEvent evt) {
+ previewPanel.getPreviewTable()
+ .setDefaultRenderer(Object.class, getRenderer(previewPanel.getFileType()));
+
+ setKeyList();
+ }
+
+ private void browseOntologyButtonActionPerformed(java.awt.event.ActionEvent evt) {
+ DataSourceSelectDialog dssd = new DataSourceSelectDialog(DataSourceSelectDialog.ONTOLOGY_TYPE,
+ Cytoscape.getDesktop(), true);
+ dssd.setLocationRelativeTo(Cytoscape.getDesktop());
+ dssd.setVisible(true);
+
+ String key = dssd.getSourceName();
+
+ if (key != null) {
+ ontologyComboBox.insertItemAt(key, 0);
+ ontologyUrlMap.put(key, dssd.getSourceUrlString());
+ ontologyComboBox.setSelectedItem(key);
+ ontologyComboBox.setToolTipText(getOntologyTooltip());
+ }
+ }
+
+ private void transferNameCheckBoxActionPerformed(java.awt.event.ActionEvent evt) {
+ final DefaultTableModel model = (DefaultTableModel) previewPanel.getPreviewTable().getModel();
+
+ if (transferNameCheckBox.isSelected()) {
+ if ((previewPanel.getPreviewTable() != null) && (model != null)) {
+ columnHeaders = new String[previewPanel.getPreviewTable().getColumnCount()];
+
+ for (int i = 0; i < columnHeaders.length; i++) {
+ // Save the header
+ columnHeaders[i] = previewPanel.getPreviewTable().getColumnModel().getColumn(i)
+ .getHeaderValue().toString();
+ previewPanel.getPreviewTable().getColumnModel().getColumn(i)
+ .setHeaderValue((String) model.getValueAt(0, i));
+ }
+
+ model.removeRow(0);
+ previewPanel.getPreviewTable().getTableHeader().resizeAndRepaint();
+ }
+
+ startRowSpinner.setEnabled(false);
+ } else {
+ // Restore row
+ String currentName = null;
+ Object headerVal = null;
+
+ for (int i = 0; i < columnHeaders.length; i++) {
+ headerVal = previewPanel.getPreviewTable().getColumnModel().getColumn(i)
+ .getHeaderValue();
+
+ if (headerVal == null) {
+ currentName = "";
+ } else {
+ currentName = headerVal.toString();
+ }
+
+ previewPanel.getPreviewTable().getColumnModel().getColumn(i)
+ .setHeaderValue(columnHeaders[i]);
+ columnHeaders[i] = currentName;
+ }
+
+ model.insertRow(0, columnHeaders);
+ previewPanel.getPreviewTable().getTableHeader().resizeAndRepaint();
+ startRowSpinner.setEnabled(true);
+ }
+
+ updateAliasTable();
+ updatePrimaryKeyComboBox();
+ repaint();
+ }
+
+ private void cancelButtonActionPerformed(java.awt.event.ActionEvent evt) {
+ dispose();
+ }
+
+ /**
+ * Load from the data source.<br>
+ *
+ * @param evt
+ * @throws Exception
+ */
+ private void importButtonActionPerformed(ActionEvent evt) throws Exception {
+ if (checkDataSourceError() == false)
+ return;
+
+ boolean importAll = importAllCheckBox.isSelected();
+
+ /*
+ * Get start line number. If "transfer" check box is true, then start
+ * reading from the second line.
+ */
+ int startLineNumber;
+ final int spinnerNumber = Integer.parseInt(startRowSpinner.getValue().toString());
+
+ if (transferNameCheckBox.isSelected()) {
+ startLineNumber = spinnerNumber;
+ } else {
+ startLineNumber = spinnerNumber - 1;
+ }
+
+ final String commentChar = commentLineTextField.getText();
+
+ /*
+ * Get import flags
+ */
+ final int colCount = previewPanel.getPreviewTable().getColumnModel().getColumnCount();
+ importFlag = new boolean[colCount];
+
+ for (int i = 0; i < colCount; i++) {
+ importFlag[i] = ((AttributePreviewTableCellRenderer) previewPanel.getPreviewTable()
+ .getCellRenderer(0, i))
+ .getImportFlag(i);
+ }
+
+ /*
+ * Get Attribute Names
+ */
+ final String[] attributeNames;
+ final List<String> attrNameList = new ArrayList<String>();
+
+ Object curName = null;
+
+ for (int i = 0; i < colCount; i++) {
+ curName = previewPanel.getPreviewTable().getColumnModel().getColumn(i).getHeaderValue();
+
+ if (attrNameList.contains(curName)) {
+ int dupIndex = 0;
+
+ for (int idx = 0; idx < attrNameList.size(); idx++) {
+ if (curName.equals(attrNameList.get(idx))) {
+ dupIndex = idx;
+
+ break;
+ }
+ }
+
+ if (importFlag[i] && importFlag[dupIndex]) {
+ final JLabel label = new JLabel("Duplicate Attribute Name Found: " + curName);
+ label.setForeground(Color.RED);
+ JOptionPane.showMessageDialog(this, label);
+
+ return;
+ }
+ }
+
+ if (curName == null) {
+ attrNameList.add("Column " + i);
+ } else {
+ attrNameList.add(curName.toString());
+ }
+ }
+
+ attributeNames = attrNameList.toArray(new String[0]);
+
+ /*
+ * Get attribute data types
+ */
+
+ // final byte[] attributeTypes = new byte[previewPanel.getPreviewTable()
+ // .getColumnCount()];
+ final Byte[] test = previewPanel.getDataTypes(previewPanel.getSelectedSheetName());
+ final Byte[] attributeTypes = new Byte[test.length];
+
+ for (int i = 0; i < test.length; i++) {
+ attributeTypes[i] = test[i];
+ }
+
+ // for (int i = 0; i < attributeTypes.length; i++) {
+ // attributeTypes[i] = attributeDataTypes.get(i);
+ // }
+ final List<Integer> aliasList = new ArrayList<Integer>();
+ String mappingAttribute = ID;
+
+ if (dialogType != NETWORK_IMPORT) {
+ /*
+ * Get column indecies for alias
+ */
+ JTable curTable = aliasTableMap.get(previewPanel.getSelectedSheetName());
+
+ if (curTable != null) {
+ for (int i = 0; i < curTable.getModel().getRowCount(); i++) {
+ if ((Boolean) curTable.getModel().getValueAt(i, 0) == true) {
+ aliasList.add(i);
+ }
+ }
+ }
+
+ /*
+ * Get mapping attribute
+ */
+ mappingAttribute = mappingAttributeComboBox.getSelectedItem().toString();
+ }
+
+ ObjectType objType = null;
+
+ if (dialogType != NETWORK_IMPORT) {
+ if (nodeRadioButton.isSelected()) {
+ objType = NODE;
+ } else if (edgeRadioButton.isSelected()) {
+ objType = EDGE;
+ } else {
+ objType = NETWORK;
+ }
+ }
+
+ /*
+ * Switch readers based on the dialog type.
+ */
+ switch (dialogType) {
+ case SIMPLE_ATTRIBUTE_IMPORT:
+
+ /*
+ * Case 1: Attribute table import.
+ */
+ // Extract URL from the text table.
+ final URL source = new URL(targetDataSourceTextField.getText());
+ // Make sure primary key index is up-to-date.
+ keyInFile = primaryKeyComboBox.getSelectedIndex();
+
+ // Build mapping parameter object.
+ final AttributeMappingParameters mapping;
+ final List<String> del;
+
+ System.out.println("IsCytoscapeAttributeFile " + previewPanel.isCytoscapeAttributeFile(source));
+ if (previewPanel.isCytoscapeAttributeFile(source)) {
+ del = new ArrayList<String>();
+ del.add(" += +");
+ } else {
+ del = checkDelimiter();
+ }
+ mapping = new AttributeMappingParameters(objType, del,
+ listDelimiter, keyInFile,
+ mappingAttribute, aliasList,
+ attributeNames, attributeTypes,
+ listDataTypes, importFlag,
+ caseSensitive);
+
+ if (source.toString().endsWith(SupportedFileType.EXCEL.getExtension()) ||
+ source.toString().endsWith(SupportedFileType.OOXML.getExtension())) {
+ /*
+ * Read one sheet at a time
+ */
+ InputStream is = null;
+ Workbook wb = null;
+
+ try {
+ is = source.openStream();
+ wb = WorkbookFactory.create(is);
+ }
+ finally {
+ if (is != null) {
+ is.close();
+ }
+ }
+
+ // Load all sheets in the table
+ for (int i = 0; i < wb.getNumberOfSheets(); i++) {
+ final Sheet sheet = wb.getSheetAt(i);
+
+ loadAnnotation(new ExcelAttributeSheetReader(sheet, mapping,
+ startLineNumber,
+ importAll),
+ source.toString());
+ }
+ } else {
+ loadAnnotation(new DefaultAttributeTableReader(source, mapping,
+ startLineNumber,
+ null, importAll),
+ source.toString());
+ }
+
+ break;
+
+ case ONTOLOGY_AND_ANNOTATION_IMPORT:
+
+ /*
+ * Case 2: Import Ontology and its annotation.
+ */
+ final String selectedOntologyName = ontologyComboBox.getSelectedItem().toString();
+ final String ontologySourceLocation = ontologyUrlMap.get(selectedOntologyName);
+
+ /*
+ * If selected ontology is not loaded, load it first.
+ */
+ if (Cytoscape.getOntologyServer().getOntologyNames().contains(selectedOntologyName) == false)
+ loadOntology(ontologySourceLocation, selectedOntologyName);
+
+ /*
+ * Now, load & map annotation.
+ */
+ final String annotationSource = annotationUrlMap.get(annotationComboBox.getSelectedItem());
+ final URL annotationSourceUrl = new URL(annotationSource);
+
+ if (previewPanel.getFileType() == FileTypes.GENE_ASSOCIATION_FILE) {
+ /*
+ * This is a Gene Association file.
+ */
+ GeneAssociationReader gaReader = null;
+ keyInFile = this.primaryKeyComboBox.getSelectedIndex();
+
+ InputStream is = null;
+ try {
+ is = URLUtil.getInputStream(annotationSourceUrl);
+ gaReader = new GeneAssociationReader(selectedOntologyName,
+ is, mappingAttribute,
+ importAll, keyInFile,
+ caseSensitive);
+ }
+ catch (Exception e) {
+ if (is != null) {
+ is.close();
+ }
+ throw e;
+ }
+
+ loadGeneAssociation(gaReader, selectedOntologyName, annotationSource);
+ } else {
+ /*
+ * This is a custom annotation file.
+ */
+ final int ontologyIndex = ontologyInAnnotationComboBox.getSelectedIndex();
+
+ final AttributeAndOntologyMappingParameters aoMapping = new AttributeAndOntologyMappingParameters(objType,
+ checkDelimiter(),
+ listDelimiter,
+ keyInFile,
+ mappingAttribute,
+ aliasList,
+ attributeNames,
+ attributeTypes,
+ listDataTypes,
+ importFlag,
+ ontologyIndex,
+ selectedOntologyName,
+ caseSensitive);
+ final OntologyAnnotationReader oaReader = new OntologyAnnotationReader(annotationSourceUrl,
+ aoMapping,
+ commentChar,
+ startLineNumber);
+
+ loadAnnotation(oaReader, annotationSource);
+ }
+
+ break;
+
+ case NETWORK_IMPORT:
+
+ /*
+ * Case 3: read as network table (Network + Edge Attributes)
+ */
+
+ // Extract URL from the text table.
+ /*
+ * Now multiple files are supported.
+ */
+ URL[] sources = new URL[inputFiles.length];
+
+ for (int i = 0; i < sources.length; i++) {
+ sources[i] = inputFiles[i].toURI().toURL();
+ }
+
+ //final URL networkSource = new URL(targetDataSourceTextField.getText());
+ final int sourceColumnIndex = networkImportPanel.getSourceIndex();
+ final int targetColumnIndex = networkImportPanel.getTargetIndex();
+
+ final String defaultInteraction = defaultInteractionTextField.getText();
+
+ final int interactionColumnIndex = networkImportPanel.getInteractionIndex();
+
+ final NetworkTableMappingParameters nmp = new NetworkTableMappingParameters(checkDelimiter(),
+ listDelimiter,
+ attributeNames,
+ attributeTypes,
+ null,
+ importFlag,
+ sourceColumnIndex,
+ targetColumnIndex,
+ interactionColumnIndex,
+ defaultInteraction);
+
+ NetworkTableReader reader;
+ String networkName;
+ boolean multi = true;
+
+ if (sources.length == 1)
+ multi = false;
+
+ for (int i = 0; i < sources.length; i++) {
+ if (sources[i].toString().endsWith(SupportedFileType.EXCEL.getExtension()) || sources[i].toString().endsWith(SupportedFileType.OOXML.getExtension())) {
+ // Extract name from the sheet name.
+ InputStream is = null;
+ Workbook wb = null;
+ try {
+ is = sources[i].openStream();
+ wb = WorkbookFactory.create(is);
+ }
+ finally {
+ if (is != null) {
+ is.close();
+ }
+ }
+
+
+ Sheet sheet = wb.getSheetAt(0);
+ networkName = wb.getSheetName(0);
+
+ reader = new ExcelNetworkSheetReader(networkName, sheet, nmp,
+ startLineNumber);
+ } else {
+ // Get name from URL.
+ if ((commentChar != null) && (commentChar.length() != 0)
+ && transferNameCheckBox.isSelected()) {
+ startLineNumber++;
+ }
+
+ final String[] parts = sources[i].toString().split("/");
+ networkName = parts[parts.length - 1];
+ reader = new NetworkTableReader(networkName, sources[i], nmp,
+ startLineNumber, commentChar);
+ }
+
+ loadNetwork(networkName, reader, sources[i], multi);
+ }
+
+ if (multi) {
+ StringBuilder builder = new StringBuilder();
+ builder.append("The following networks are loaded:\n\n");
+
+ for (File f : inputFiles) {
+ builder.append(f.getName() + "\n");
+ }
+
+ JOptionPane.showMessageDialog(this, builder.toString(),
+ "Multiple Networks Loaded",
+ JOptionPane.INFORMATION_MESSAGE);
+ }
+
+ break;
+
+ default:
+ return;
+ }
+
+ Cytoscape.firePropertyChange(Cytoscape.ATTRIBUTES_CHANGED, null, null);
+
+ dispose();
+ }
+
+ private void ontologyInAnnotationComboBoxActionPerformed(java.awt.event.ActionEvent evt) {
+ /*
+ * Change color of the column in the preview panel.
+ */
+ int ontologyCol = ontologyInAnnotationComboBox.getSelectedIndex();
+ List<Integer> gaAlias = new ArrayList<Integer>();
+ gaAlias.add(DB_OBJECT_SYNONYM.getPosition());
+ previewPanel.getPreviewTable()
+ .setDefaultRenderer(Object.class,
+ new AttributePreviewTableCellRenderer(keyInFile, gaAlias,
+ ontologyCol,
+ TAXON.getPosition(),
+ importFlag,
+ listDelimiter));
+
+ try {
+ if ((dialogType == SIMPLE_ATTRIBUTE_IMPORT) || (dialogType == NETWORK_IMPORT)) {
+ setStatusBar(new URL(targetDataSourceTextField.getText()));
+ } else {
+ setStatusBar(new URL(annotationUrlMap.get(annotationComboBox.getSelectedItem()
+ .toString())));
+ }
+ } catch (MalformedURLException e) {
+ e.printStackTrace();
+ }
+
+ previewPanel.repaint();
+ }
+
+ private void browseAnnotationButtonActionPerformed(java.awt.event.ActionEvent evt) {
+ DataSourceSelectDialog dssd = new DataSourceSelectDialog(DataSourceSelectDialog.ANNOTATION_TYPE,
+ Cytoscape.getDesktop(), true);
+ dssd.setLocationRelativeTo(Cytoscape.getDesktop());
+ dssd.setVisible(true);
+
+ String key = dssd.getSourceName();
+
+ if (key != null) {
+ annotationComboBox.addItem(key);
+ annotationUrlMap.put(key, dssd.getSourceUrlString());
+ annotationComboBox.setSelectedItem(key);
+ annotationComboBox.setToolTipText(getAnnotationTooltip());
+ }
+ }
+
+ private void annotationComboBoxActionPerformed(java.awt.event.ActionEvent evt) {
+ if (annotationComboBox.getSelectedItem().toString().equals(DEF_ANNOTATION_ITEM)) {
+ annotationComboBox.setToolTipText(null);
+
+ return;
+ }
+
+ annotationComboBox.setToolTipText(getAnnotationTooltip());
+
+ try {
+ final String selectedSourceName = annotationComboBox.getSelectedItem().toString();
+ final URL sourceURL = new URL(annotationUrlMap.get(selectedSourceName));
+ readAnnotationForPreview(sourceURL, checkDelimiter());
+ } catch (IOException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ }
+
+ private void ontologyComboBoxActionPerformed(java.awt.event.ActionEvent evt) {
+ ontologyComboBox.setToolTipText(getOntologyTooltip());
+ ontologyTextField.setText(ontologyComboBox.getSelectedItem().toString());
+ }
+
+ private void selectAttributeFileButtonActionPerformed(ActionEvent evt)
+ throws IOException
+ {
+ final File[] multiSource = FileUtil.getFiles("Select local file", FileUtil.LOAD,
+ new CyFileFilter[] { });
+ if ((multiSource == null) || (multiSource[0] == null))
+ return;
+ fileLoadAction(multiSource, multiSource[0].toURI().toURL().toString());
+ }
+
+ private void delimiterCheckBoxActionPerformed(ActionEvent evt) throws IOException {
+ transferNameCheckBox.setSelected(false);
+ displayPreview();
+ }
+
+ private void textImportCheckBoxActionPerformed(java.awt.event.ActionEvent evt) {
+ if (textImportCheckBox.isSelected()) {
+ textImportOptionPanel.setVisible(true);
+ } else {
+ textImportOptionPanel.setVisible(false);
+ }
+
+ pack();
+ }
+
+
+ private void reloadButtonActionPerformed(java.awt.event.ActionEvent evt)
+ throws IOException {
+ displayPreview();
+
+ if (transferNameCheckBox.isSelected())
+ this.transferNameCheckBoxActionPerformed(null);
+ }
+
+ /**
+ * Actions for mouse wheel movement
+ *
+ * @param evt
+ */
+ private void counterSpinnerMouseWheelMoved(java.awt.event.MouseWheelEvent evt) {
+ JSpinner source = (JSpinner) evt.getSource();
+
+ SpinnerNumberModel model = (SpinnerNumberModel) source.getModel();
+ Integer oldValue = (Integer) source.getValue();
+ int intValue = oldValue.intValue()
+ - (evt.getWheelRotation() * model.getStepSize().intValue());
+ Integer newValue = new Integer(intValue);
+
+ if ((model.getMaximum().compareTo(newValue) >= 0)
+ && (model.getMinimum().compareTo(newValue) <= 0)) {
+ source.setValue(newValue);
+ }
+ }
+
+ /**
+ * Actions for selecting start line.
+ *
+ * @param evt
+ */
+ private void startRowSpinnerMouseWheelMoved(java.awt.event.MouseWheelEvent evt) {
+ JSpinner source = (JSpinner) evt.getSource();
+
+ SpinnerNumberModel model = (SpinnerNumberModel) source.getModel();
+ Integer oldValue = (Integer) source.getValue();
+ int intValue = oldValue.intValue()
+ - (evt.getWheelRotation() * model.getStepSize().intValue());
+ Integer newValue = new Integer(intValue);
+
+ if ((model.getMaximum().compareTo(newValue) >= 0)
+ && (model.getMinimum().compareTo(newValue) <= 0)) {
+ source.setValue(newValue);
+ }
+ }
+
+ /* =============================================================================================== */
+ private List<Integer> getAliasList() {
+ final List<Integer> aliasList = new ArrayList<Integer>();
+ AliasTableModel curModel = aliasTableModelMap.get(previewPanel.getSelectedSheetName());
+
+ if (curModel == null) {
+ return aliasList;
+ }
+
+ for (int i = 0; i < curModel.getRowCount(); i++) {
+ if ((Boolean) curModel.getValueAt(i, 0)) {
+ aliasList.add(i);
+ }
+ }
+
+ return aliasList;
+ }
+
+
+ private void displayPreview() throws IOException {
+ final String selectedSourceName;
+ final URL sourceURL;
+
+ if (dialogType == ONTOLOGY_AND_ANNOTATION_IMPORT) {
+ selectedSourceName = annotationComboBox.getSelectedItem().toString();
+ sourceURL = new URL(annotationUrlMap.get(selectedSourceName));
+ } else {
+ selectedSourceName = targetDataSourceTextField.getText();
+ sourceURL = new URL(selectedSourceName);
+ }
+
+ readAnnotationForPreview(sourceURL, checkDelimiter());
+ previewPanel.repaint();
+ }
+
+ private void updateComponents() throws JAXBException, IOException {
+ /*
+ * Do misc. GUI setups
+ */
+ if (dialogType == SIMPLE_ATTRIBUTE_IMPORT) {
+ setTitle("Import Annotation File");
+ titleLabel.setText("Import Attribute from Table");
+ annotationAndOntologyImportPanel.setVisible(false);
+ importAllCheckBox.setVisible(true);
+ } else if (dialogType == ONTOLOGY_AND_ANNOTATION_IMPORT) {
+ setTitle("Import Ontology Data and Annotations");
+ titleLabel.setText("Import Ontology and Annotation");
+ ontology2annotationPanel.setVisible(false);
+ /*
+ * Add items to Ontology Combobox
+ */
+ setOntologyComboBox();
+ /*
+ * Setup annotation Combo Box
+ */
+ setAnnotationComboBox();
+
+ ontologyTextField.setText(ontologyComboBox.getSelectedItem().toString());
+ } else if (dialogType == NETWORK_IMPORT) {
+ setTitle("Import Network and Edge Attributes from Table");
+ titleLabel.setText("Import Network from Table");
+ annotationAndOntologyImportPanel.setVisible(false);
+
+ importAllCheckBox.setVisible(false);
+ }
+
+ reloadButton.setEnabled(false);
+ startRowSpinner.setEnabled(false);
+ startRowLabel.setEnabled(false);
+ previewPanel.getPreviewTable().getTableHeader().setReorderingAllowed(false);
+ setRadioButtonGroup();
+ pack();
+
+ updateMappingAttributeComboBox();
+
+ setStatusBar("-", "-", "File Size: Unknown");
+ }
+
+ private void updatePrimaryKeyComboBox() {
+ final DefaultTableModel model = (DefaultTableModel) previewPanel.getPreviewTable().getModel();
+
+ primaryKeyComboBox.setRenderer(new ComboBoxRenderer(attributeDataTypes));
+
+ if ((model != null) && (model.getColumnCount() > 0)) {
+ primaryKeyComboBox.removeAllItems();
+
+ Object curValue = null;
+
+ for (int i = 0; i < model.getColumnCount(); i++) {
+ curValue = previewPanel.getPreviewTable().getColumnModel().getColumn(i)
+ .getHeaderValue();
+
+ if (curValue != null) {
+ primaryKeyComboBox.addItem(curValue.toString());
+ } else {
+ primaryKeyComboBox.addItem("");
+ }
+ }
+ }
+
+ primaryKeyComboBox.setEnabled(true);
+
+ Integer selectedIndex = primaryKeyMap.get(previewPanel.getSelectedSheetName());
+
+ if (selectedIndex == null) {
+ primaryKeyComboBox.setSelectedIndex(0);
+ } else {
+ primaryKeyComboBox.setSelectedIndex(selectedIndex);
+ }
+ }
+
+ protected static ImageIcon getDataTypeIcon(byte dataType) {
+ ImageIcon dataTypeIcon = null;
+
+ if (dataType == CyAttributes.TYPE_STRING) {
+ dataTypeIcon = STRING_ICON.getIcon();
+ } else if (dataType == CyAttributes.TYPE_INTEGER) {
+ dataTypeIcon = INT_ICON.getIcon();
+ } else if (dataType == CyAttributes.TYPE_FLOATING) {
+ dataTypeIcon = FLOAT_ICON.getIcon();
+ } else if (dataType == CyAttributes.TYPE_BOOLEAN) {
+ dataTypeIcon = BOOLEAN_ICON.getIcon();
+ } else if (dataType == CyAttributes.TYPE_SIMPLE_LIST) {
+ dataTypeIcon = LIST_ICON.getIcon();
+ }
+
+ return dataTypeIcon;
+ }
+
+ private void setRadioButtonGroup() {
+ attrTypeButtonGroup.add(nodeRadioButton);
+ attrTypeButtonGroup.add(edgeRadioButton);
+ attrTypeButtonGroup.add(networkRadioButton);
+ attrTypeButtonGroup.setSelected(nodeRadioButton.getModel(), true);
+
+ importTypeButtonGroup.add(showAllRadioButton);
+ importTypeButtonGroup.add(counterRadioButton);
+ importTypeButtonGroup.setSelected(counterRadioButton.getModel(), true);
+
+ tabCheckBox.setSelected(true);
+ tabCheckBox.setEnabled(false);
+ commaCheckBox.setEnabled(false);
+
+ spaceCheckBox.setEnabled(false);
+
+ if (dialogType == NETWORK_IMPORT) {
+ spaceCheckBox.setSelected(true);
+ } else {
+ spaceCheckBox.setSelected(false);
+ }
+
+ semicolonCheckBox.setEnabled(false);
+ otherCheckBox.setEnabled(false);
+ otherDelimiterTextField.setEnabled(false);
+ }
+
+ private void setOntologyInAnnotationComboBox() {
+ final DefaultTableModel model = (DefaultTableModel) previewPanel.getPreviewTable().getModel();
+
+ if ((model != null) && (model.getColumnCount() > 0)) {
+ ontologyInAnnotationComboBox.removeAllItems();
+
+ for (int i = 0; i < model.getColumnCount(); i++) {
+ ontologyInAnnotationComboBox.addItem(previewPanel.getPreviewTable().getColumnModel()
+ .getColumn(i).getHeaderValue()
+ .toString());
+ }
+ }
+
+ ontologyInAnnotationComboBox.setEnabled(true);
+ }
+
+ /**
+ * Setup ontology data source combo box.<br>
+ * Basically, this method just load informaiton from bookmark.
+ * @throws IOException
+ * @throws JAXBException
+ *
+ * @throws IOException
+ * @throws JAXBException
+ *
+ */
+ private void setOntologyComboBox() throws JAXBException, IOException {
+ Bookmarks bookmarks = Cytoscape.getBookmarks();
+ List<DataSource> annotations = BookmarksUtil.getDataSourceList("ontology",
+ bookmarks.getCategory());
+ String key = null;
+
+ Set<String> ontologyNames = Cytoscape.getOntologyServer().getOntologyNames();
+
+ for (DataSource source : annotations) {
+ key = source.getName();
+ ontologyComboBox.addItem(key);
+ ontologyUrlMap.put(key, source.getHref());
+ ontologyDescriptionMap.put(key, BookmarksUtil.getAttribute(source, "description"));
+ ontologyTypeMap.put(key, BookmarksUtil.getAttribute(source, "ontologyType"));
+ }
+
+ ontologyComboBox.setToolTipText(getOntologyTooltip());
+ }
+
+ private String getOntologyTooltip() {
+ final String key = ontologyComboBox.getSelectedItem().toString();
+ String tooltip = ontologyHtml.replace("%DataSourceName%", key);
+ final String description = ontologyDescriptionMap.get(key);
+
+ if (description == null) {
+ tooltip = tooltip.replace("%Description%", "N/A");
+ } else {
+ tooltip = tooltip.replace("%Description%", description);
+ }
+
+ if (ontologyUrlMap.get(key) != null) {
+ return tooltip.replace("%SourceURL%", ontologyUrlMap.get(key));
+ } else {
+ return tooltip.replace("%SourceURL%", "N/A");
+ }
+ }
+
+ private String getAnnotationTooltip() {
+ final String key = annotationComboBox.getSelectedItem().toString();
+ String tooltip = annotationHtml.replace("%DataSourceName%", key);
+
+ if (annotationUrlMap.get(key) == null) {
+ return "";
+ }
+
+ tooltip = tooltip.replace("%SourceURL%", annotationUrlMap.get(key));
+
+ if (annotationFormatMap.get(key) != null) {
+ tooltip = tooltip.replace("%Format%", annotationFormatMap.get(key));
+ } else {
+ String[] parts = annotationUrlMap.get(key).split("/");
+
+ if (parts[parts.length - 1].startsWith(GENE_ASSOCIATION)) {
+ tooltip = tooltip.replace("%Format%", "Gene Association");
+ }
+
+ tooltip = tooltip.replace("%Format%", "General Annotation Text Table");
+ }
+
+ if (annotationAttributesMap.get(key) != null) {
+ StringBuffer table = new StringBuffer();
+ final Map<String, String> annotations = annotationAttributesMap.get(key);
+
+ for (String anno : annotations.keySet()) {
+ table.append("<tr>");
+ table.append("<td><strong>" + anno + "</strong></td><td>" + annotations.get(anno)
+ + "</td>");
+ table.append("</tr>");
+ }
+
+ return tooltip.replace("%AttributeTable%", table.toString());
+ }
+
+ return tooltip.replace("%AttributeTable%", "");
+ }
+
+ private void setAnnotationComboBox() throws JAXBException, IOException {
+ Bookmarks bookmarks = Cytoscape.getBookmarks();
+ List<DataSource> annotations = BookmarksUtil.getDataSourceList("annotation",
+ bookmarks.getCategory());
+ String key = null;
+
+ annotationComboBox.addItem(DEF_ANNOTATION_ITEM);
+
+ for (DataSource source : annotations) {
+ key = source.getName();
+ annotationComboBox.addItem(key);
+ annotationUrlMap.put(key, source.getHref());
+ annotationFormatMap.put(key, source.getFormat());
+
+ final Map<String, String> attrMap = new HashMap<String, String>();
+
+ for (Attribute attr : source.getAttribute()) {
+ attrMap.put(attr.getName(), attr.getContent());
+ }
+
+ annotationAttributesMap.put(key, attrMap);
+ }
+
+ // annotationComboBox.setToolTipText(getAnnotationTooltip());
+ }
+
+ /**
+ * Generate preview table.<br>
+ *
+ * <p>
+ * </p>
+ *
+ * @throws IOException
+ */
+ private void readAnnotationForPreview(URL sourceURL, List<String> delimiters)
+ throws IOException {
+ /*
+ * Check number of lines we should load. if -1, load everything in the
+ * file.
+ */
+ final int previewSize;
+
+ if (showAllRadioButton.isSelected())
+ previewSize = -1;
+ else
+ previewSize = Integer.parseInt(counterSpinner.getValue().toString());
+
+ /*
+ * Load data from the given URL.
+ */
+ final String commentChar = commentLineTextField.getText();
+ final int startLine = Integer.parseInt(startRowSpinner.getValue().toString());
+ previewPanel.setPreviewTable(sourceURL, delimiters, null, previewSize, commentChar,
+ startLine - 1);
+
+ if (previewPanel.getPreviewTable() == null)
+ return;
+
+ // Initialize import flags.
+ final int colSize = previewPanel.getPreviewTable().getColumnCount();
+ importFlag = new boolean[colSize];
+
+ for (int i = 0; i < colSize; i++) {
+ importFlag[i] = true;
+ }
+
+ listDataTypes = previewPanel.getCurrentListDataTypes();
+
+ /*
+ * Initialize all Alias Tables
+ */
+ if (dialogType == NETWORK_IMPORT) {
+ final String[] columnNames = new String[previewPanel.getPreviewTable().getColumnCount()];
+
+ for (int i = 0; i < columnNames.length; i++) {
+ columnNames[i] = previewPanel.getPreviewTable().getColumnName(i);
+ }
+
+ networkImportPanel.setComboBoxes(columnNames);
+
+ if (sourceURL.toString().endsWith(SupportedFileType.EXCEL.getExtension()) || sourceURL.toString().endsWith(SupportedFileType.OOXML.getExtension())) {
+ switchDelimiterCheckBoxes(false);
+ } else {
+ switchDelimiterCheckBoxes(true);
+ }
+
+ AttributePreviewTableCellRenderer rend = (AttributePreviewTableCellRenderer) previewPanel.getPreviewTable()
+ .getCellRenderer(0,
+ 0);
+ rend.setSourceIndex(AttributePreviewTableCellRenderer.PARAMETER_NOT_EXIST);
+ rend.setTargetIndex(AttributePreviewTableCellRenderer.PARAMETER_NOT_EXIST);
+ rend.setInteractionIndex(AttributePreviewTableCellRenderer.PARAMETER_NOT_EXIST);
+ } else {
+ for (int i = 0; i < previewPanel.getTableCount(); i++) {
+ final int columnCount = previewPanel.getPreviewTable(i).getColumnCount();
+
+ aliasTableModelMap.put(previewPanel.getSheetName(i),
+ new AliasTableModel(keyTable, columnCount));
+
+ if (previewPanel.getFileType() == FileTypes.GENE_ASSOCIATION_FILE) {
+ TableModel previewModel = previewPanel.getPreviewTable(i).getModel();
+ String[] columnNames = new String[previewModel.getColumnCount()];
+
+ for (int j = 0; j < columnNames.length; j++) {
+ columnNames[j] = previewModel.getColumnName(j);
+ }
+
+ initializeAliasTable(columnCount, columnNames, i);
+
+ AliasTableModel curModel = aliasTableModelMap.get(previewPanel.getSheetName(i));
+ curModel.setValueAt(true, DB_OBJECT_SYNONYM.getPosition(), 0);
+ disableComponentsForGA();
+ } else {
+ initializeAliasTable(columnCount, null, i);
+ }
+
+ updatePrimaryKeyComboBox();
+ }
+
+ setOntologyInAnnotationComboBox();
+
+ /*
+ * If this is not an Excel file, enable delimiter checkboxes.
+ */
+ FileTypes type = checkFileType(sourceURL);
+
+ if (type == FileTypes.GENE_ASSOCIATION_FILE) {
+ primaryKeyComboBox.setSelectedIndex(DB_OBJECT_SYMBOL.getPosition());
+ ontologyInAnnotationComboBox.setSelectedIndex(GO_ID.getPosition());
+ disableComponentsForGA();
+ } else if (sourceURL.toString().endsWith(SupportedFileType.EXCEL.getExtension()) == false || sourceURL.toString().endsWith(SupportedFileType.OOXML.getExtension()) == false) {
+ switchDelimiterCheckBoxes(true);
+ nodeRadioButton.setEnabled(true);
+ edgeRadioButton.setEnabled(true);
+ networkRadioButton.setEnabled(true);
+ importAllCheckBox.setEnabled(true);
+ } else {
+ importAllCheckBox.setEnabled(true);
+ }
+
+ attributeRadioButtonActionPerformed(null);
+ /*
+ * Set Status bar
+ */
+ setStatusBar(sourceURL);
+ }
+
+ pack();
+ repaint();
+
+ reloadButton.setEnabled(true);
+ startRowSpinner.setEnabled(true);
+ startRowLabel.setEnabled(true);
+ }
+
+ private void disableComponentsForGA() {
+ primaryKeyComboBox.setEnabled(true);
+ aliasTableMap.get(previewPanel.getSelectedSheetName()).setEnabled(true);
+ ontologyInAnnotationComboBox.setEnabled(false);
+
+ nodeRadioButton.setSelected(true);
+ nodeRadioButton.setEnabled(false);
+ edgeRadioButton.setEnabled(false);
+ networkRadioButton.setEnabled(false);
+
+ tabCheckBox.setEnabled(false);
+ tabCheckBox.setSelected(true);
+ commaCheckBox.setEnabled(false);
+ commaCheckBox.setSelected(false);
+ spaceCheckBox.setEnabled(false);
+ spaceCheckBox.setSelected(false);
+ semicolonCheckBox.setEnabled(false);
+ semicolonCheckBox.setSelected(false);
+ otherCheckBox.setEnabled(false);
+ otherCheckBox.setSelected(false);
+ otherDelimiterTextField.setEnabled(false);
+
+ importAllCheckBox.setEnabled(true);
+ }
+
+ private void switchDelimiterCheckBoxes(Boolean state) {
+ tabCheckBox.setEnabled(state);
+ commaCheckBox.setEnabled(state);
+ spaceCheckBox.setEnabled(state);
+ semicolonCheckBox.setEnabled(state);
+ otherCheckBox.setEnabled(state);
+ otherDelimiterTextField.setEnabled(state);
+ }
+
+ private FileTypes checkFileType(URL source) {
+ String[] parts = source.toString().split("/");
+ final String fileName = parts[parts.length - 1];
+
+ if (fileName.startsWith("gene_association")
+ && (dialogType == ONTOLOGY_AND_ANNOTATION_IMPORT)) {
+ return FileTypes.GENE_ASSOCIATION_FILE;
+ } else if (dialogType == ONTOLOGY_AND_ANNOTATION_IMPORT) {
+ return FileTypes.CUSTOM_ANNOTATION_FILE;
+ } else if (dialogType == NETWORK_IMPORT) {
+ return FileTypes.NETWORK_FILE;
+ }
+
+ return FileTypes.ATTRIBUTE_FILE;
+ }
+
+ private void setStatusBar(URL sourceURL) {
+ final String centerMessage;
+ final String rightMessage;
+
+ if (showAllRadioButton.isSelected()) {
+ centerMessage = "All entries are loaded for preview.";
+ } else {
+ centerMessage = "First " + counterSpinner.getValue().toString()
+ + " entries are loaded for preview.";
+ }
+
+ if (sourceURL.toString().startsWith("file:")) {
+ int fileSize = 0;
+
+ try {
+ BufferedInputStream fis = (BufferedInputStream) sourceURL.openStream();
+ fileSize = fis.available();
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+
+ if ((fileSize / 1000) == 0) {
+ rightMessage = "File Size: " + fileSize + " Bytes";
+ } else {
+ rightMessage = "File Size: " + (fileSize / 1000) + " KBytes";
+ }
+ } else {
+ rightMessage = "File Size Unknown (Remote Data Source)";
+ }
+
+ setStatusBar("Key-Value Matched: "
+ + previewPanel.checkKeyMatch(primaryKeyComboBox.getSelectedIndex()),
+ centerMessage, rightMessage);
+ }
+
+ /**
+ * Update the list of mapping attributes.
+ *
+ */
+ private void setKeyList() {
+ if (mappingAttributeComboBox.getSelectedItem() == null) {
+ return;
+ }
+
+ String selectedKeyAttribute = mappingAttributeComboBox.getSelectedItem().toString();
+
+ Iterator it;
+
+ Set<Object> valueSet = new TreeSet<Object>();
+
+ if (selectedKeyAttribute.equals(ID)) {
+ if (objType == NODE) {
+ it = Cytoscape.getRootGraph().nodesIterator();
+
+ while (it.hasNext()) {
+ Node node = (Node) it.next();
+ valueSet.add(node.getIdentifier());
+ }
+ } else if (objType == EDGE) {
+ it = Cytoscape.getRootGraph().edgesIterator();
+
+ while (it.hasNext()) {
+ valueSet.add(((Edge) it.next()).getIdentifier());
+ }
+ } else {
+ it = Cytoscape.getNetworkSet().iterator();
+
+ while (it.hasNext()) {
+ valueSet.add(((CyNetwork) it.next()).getTitle());
+ }
+ }
+ } else {
+ final byte attrType = selectedAttributes.getType(selectedKeyAttribute);
+
+ Object value = null;
+
+ Iterator attrIt = selectedAttributes.getMultiHashMap()
+ .getObjectKeys(selectedKeyAttribute);
+
+ String stringValue = null;
+ Double dblValue = 0.;
+ Integer intValue = 0;
+ Boolean boolValue = false;
+ List listValue = null;
+
+ while (attrIt.hasNext()) {
+ value = attrIt.next();
+
+ switch (attrType) {
+ case CyAttributes.TYPE_STRING:
+ stringValue = selectedAttributes.getStringAttribute((String) value,
+ selectedKeyAttribute);
+ valueSet.add(stringValue);
+
+ break;
+
+ case CyAttributes.TYPE_FLOATING:
+ dblValue = selectedAttributes.getDoubleAttribute((String) value,
+ selectedKeyAttribute);
+ valueSet.add(dblValue);
+
+ break;
+
+ case CyAttributes.TYPE_INTEGER:
+ intValue = selectedAttributes.getIntegerAttribute((String) value,
+ selectedKeyAttribute);
+ valueSet.add(intValue);
+
+ break;
+
+ case CyAttributes.TYPE_BOOLEAN:
+ boolValue = selectedAttributes.getBooleanAttribute((String) value,
+ selectedKeyAttribute);
+ valueSet.add(boolValue);
+
+ break;
+
+ case CyAttributes.TYPE_SIMPLE_LIST:
+ listValue = selectedAttributes.getListAttribute((String) value,
+ selectedKeyAttribute);
+ valueSet.addAll(listValue);
+
+ break;
+
+ default:
+ break;
+ }
+ }
+ }
+
+ previewPanel.setKeyAttributeList(valueSet);
+
+ // nodeKeyList.setListData(valueSet.toArray());
+ }
+
+ private void updateAliasTableCell(String name, int columnIndex) {
+ JTable curTable = aliasTableMap.get(previewPanel.getSelectedSheetName());
+ curTable.setDefaultRenderer(Object.class,
+ new AliasTableRenderer(attributeDataTypes,
+ primaryKeyComboBox.getSelectedIndex()));
+
+ AliasTableModel curModel = aliasTableModelMap.get(previewPanel.getSelectedSheetName());
+ curModel.setValueAt(name, columnIndex, 1);
+ curTable.setModel(curModel);
+ curTable.repaint();
+ aliasScrollPane.repaint();
+ repaint();
+ }
+
+ private void updateAliasTable() {
+ if (dialogType == NETWORK_IMPORT) {
+ return;
+ }
+
+ JTable curTable = aliasTableMap.get(previewPanel.getSelectedSheetName());
+
+ curTable.setDefaultRenderer(Object.class,
+ new AliasTableRenderer(attributeDataTypes,
+ primaryKeyComboBox.getSelectedIndex()));
+
+ AliasTableModel curModel = aliasTableModelMap.get(previewPanel.getSelectedSheetName());
+
+ Object curValue = null;
+
+ for (int i = 0; i < previewPanel.getPreviewTable().getColumnCount(); i++) {
+ curValue = previewPanel.getPreviewTable().getColumnModel().getColumn(i).getHeaderValue();
+
+ if (curValue != null) {
+ curModel.setValueAt(curValue.toString(), i, 1);
+ } else {
+ previewPanel.getPreviewTable().getColumnModel().getColumn(i).setHeaderValue("");
+ curModel.setValueAt("", i, 1);
+ }
+ }
+
+ curTable.setModel(curModel);
+ aliasScrollPane.setViewportView(curTable);
+ aliasScrollPane.repaint();
+ }
+
+ private void initializeAliasTable(int rowCount, String[] columnNames) {
+ initializeAliasTable(rowCount, columnNames, -1);
+ }
+
+ private void initializeAliasTable(int rowCount, String[] columnNames, int sheetIndex) {
+ Object[][] keyTableData = new Object[rowCount][keyTable.length];
+
+ AliasTableModel curModel = null;
+ String tabName;
+
+ if (sheetIndex == -1) {
+ tabName = previewPanel.getSelectedSheetName();
+ } else {
+ tabName = previewPanel.getSheetName(sheetIndex);
+ }
+
+ curModel = aliasTableModelMap.get(tabName);
+
+ curModel = new AliasTableModel();
+
+ Byte[] dataTypeArray = previewPanel.getDataTypes(tabName);
+
+ for (int i = 0; i < rowCount; i++) {
+ keyTableData[i][0] = new Boolean(false);
+
+ if (columnNames == null) {
+ keyTableData[i][1] = "Column " + (i + 1);
+ } else {
+ keyTableData[i][1] = columnNames[i];
+ }
+
+ if (dataTypeArray.length <= i) {
+ attributeDataTypes.add(CyAttributes.TYPE_STRING);
+ } else {
+ attributeDataTypes.add(dataTypeArray[i]);
+ }
+
+ keyTableData[i][2] = "String";
+ }
+
+ curModel = new AliasTableModel(keyTableData, keyTable);
+
+ aliasTableModelMap.put(tabName, curModel);
+
+ curModel.addTableModelListener(this);
+ /*
+ * Set the list and combo box
+ */
+ mappingAttributeComboBox.setEnabled(true);
+
+ JTable curTable = new JTable();
+ curTable.setModel(curModel);
+ aliasTableMap.put(tabName, curTable);
+
+ curTable.setDefaultRenderer(Object.class,
+ new AliasTableRenderer(attributeDataTypes,
+ primaryKeyComboBox.getSelectedIndex()));
+ curTable.setEnabled(true);
+ curTable.setSelectionBackground(Color.white);
+ curTable.getTableHeader().setReorderingAllowed(false);
+
+ curTable.getColumnModel().getColumn(0).setPreferredWidth(55);
+ curTable.getColumnModel().getColumn(1).setPreferredWidth(300);
+ curTable.getColumnModel().getColumn(2).setPreferredWidth(100);
+
+ aliasScrollPane.setViewportView(curTable);
+ repaint();
+ }
+
+ private void updateMappingAttributeComboBox() {
+ mappingAttributeComboBox.removeAllItems();
+
+ final ListCellRenderer lcr = mappingAttributeComboBox.getRenderer();
+ mappingAttributeComboBox.setRenderer(new ListCellRenderer() {
+ public Component getListCellRendererComponent(JList list, Object value, int index,
+ boolean isSelected,
+ boolean cellHasFocus) {
+ JLabel cmp = (JLabel) lcr.getListCellRendererComponent(list, value, index,
+ isSelected, cellHasFocus);
+
+ if (value.equals(ID)) {
+ cmp.setIcon(ID_ICON.getIcon());
+ } else {
+ cmp.setIcon(getDataTypeIcon(selectedAttributes.getType(value.toString())));
+ }
+
+ return cmp;
+ }
+ });
+
+ mappingAttributeComboBox.addItem(ID);
+
+ for (String name : selectedAttributes.getAttributeNames()) {
+ if ((selectedAttributes.getType(name) != CyAttributes.TYPE_COMPLEX)
+ && (selectedAttributes.getType(name) != CyAttributes.TYPE_SIMPLE_MAP)
+ && (selectedAttributes.getType(name) != CyAttributes.TYPE_UNDEFINED)) {
+ mappingAttributeComboBox.addItem(name);
+ }
+ }
+ }
+
+ private TableCellRenderer getRenderer(FileTypes type) {
+ final TableCellRenderer rend;
+
+ if (type == FileTypes.GENE_ASSOCIATION_FILE) {
+ keyInFile = this.primaryKeyComboBox.getSelectedIndex();
+
+ int ontologyCol = this.ontologyInAnnotationComboBox.getSelectedIndex();
+ List<Integer> gaAlias = new ArrayList<Integer>();
+
+ AliasTableModel curModel = aliasTableModelMap.get(previewPanel.getSelectedSheetName());
+
+ for (int i = 0; i < curModel.getColumnCount(); i++) {
+ if ((Boolean) curModel.getValueAt(i, 0)) {
+ gaAlias.add(i);
+ }
+ }
+
+ gaAlias.add(DB_OBJECT_SYNONYM.getPosition());
+
+ rend = new AttributePreviewTableCellRenderer(keyInFile, gaAlias, ontologyCol,
+ TAXON.getPosition(), importFlag,
+ listDelimiter);
+ } else {
+ rend = new AttributePreviewTableCellRenderer(keyInFile, new ArrayList<Integer>(),
+ AttributePreviewTableCellRenderer.PARAMETER_NOT_EXIST,
+ AttributePreviewTableCellRenderer.PARAMETER_NOT_EXIST,
+ importFlag, listDelimiter);
+ }
+
+ return rend;
+ }
+
+ /**
+ * Create task for annotation reader and run it. tablechanged
+ *
+ * @param reader
+ * @param ontology
+ * @param source
+ */
+ private void loadAnnotation(TextTableReader reader, String source) {
+ // Create LoadNetwork Task
+ ImportAttributeTableTask task = new ImportAttributeTableTask(reader, source);
+
+ // Configure JTask Dialog Pop-Up Box
+ JTaskConfig jTaskConfig = new JTaskConfig();
+ jTaskConfig.setOwner(Cytoscape.getDesktop());
+ jTaskConfig.displayCloseButton(true);
+ jTaskConfig.displayStatus(true);
+ jTaskConfig.setAutoDispose(false);
+
+ // Execute Task in New Thread; pops open JTask Dialog Box.
+ TaskManager.executeTask(task, jTaskConfig);
+ }
+
+ /**
+ * Create task for ontology reader and run the task.<br>
+ *
+ * @param dataSource
+ * @param ontologyName
+ */
+ private void loadOntology(String dataSource, String ontologyName) {
+ // Create LoadNetwork Task
+ ImportOntologyTask task = new ImportOntologyTask(dataSource,
+ ontologyTypeMap.get(ontologyName),
+ ontologyName,
+ ontologyDescriptionMap.get(ontologyName));
+
+ // Configure JTask Dialog Pop-Up Box
+ JTaskConfig jTaskConfig = new JTaskConfig();
+ jTaskConfig.setOwner(Cytoscape.getDesktop());
+ jTaskConfig.displayCloseButton(true);
+ jTaskConfig.displayStatus(true);
+ jTaskConfig.setAutoDispose(true);
+
+ // Execute Task in New Thread; pops open JTask Dialog Box.
+ TaskManager.executeTask(task, jTaskConfig);
+ }
+
+ /**
+ * Create task for annotation reader and run it.
+ *
+ * @param reader
+ * @param ontology
+ * @param source
+ */
+ private void loadGeneAssociation(TextTableReader reader, String ontology, String source) {
+ // Create LoadNetwork Task
+ ImportOntologyAnnotationTask task = new ImportOntologyAnnotationTask(reader, ontology,
+ source);
+
+ // Configure JTask Dialog Pop-Up Box
+ JTaskConfig jTaskConfig = new JTaskConfig();
+ jTaskConfig.setOwner(Cytoscape.getDesktop());
+ jTaskConfig.displayCloseButton(true);
+ jTaskConfig.displayStatus(true);
+ jTaskConfig.setAutoDispose(false);
+
+ // Execute Task in New Thread; pops open JTask Dialog Box.
+ TaskManager.executeTask(task, jTaskConfig);
+ }
+
+ private void loadNetwork(final String networkName, final GraphReader reader, final URL source,
+ boolean multi) {
+ // Create LoadNetwork Task
+ ImportNetworkTask task = new ImportNetworkTask(reader, source);
+
+ // Configure JTask Dialog Pop-Up Box
+ JTaskConfig jTaskConfig = new JTaskConfig();
+ jTaskConfig.setOwner(Cytoscape.getDesktop());
+ jTaskConfig.displayCloseButton(true);
+ jTaskConfig.displayStatus(true);
+
+ if (multi)
+ jTaskConfig.setAutoDispose(true);
+ else
+ jTaskConfig.setAutoDispose(false);
+
+ // Execute Task in New Thread; pops open JTask Dialog Box.
+ TaskManager.executeTask(task, jTaskConfig);
+ }
+
+ private void setStatusBar(String message1, String message2, String message3) {
+ statusBar.setLeftLabel(message1);
+ statusBar.setCenterLabel(message2);
+ statusBar.setRightLabel(message3);
+ }
+
+ /**
+ * Alias table changed.
+ */
+ public void tableChanged(TableModelEvent evt) {
+ final int row = evt.getFirstRow();
+ final int col = evt.getColumn();
+ AliasTableModel curModel = aliasTableModelMap.get(previewPanel.getSelectedSheetName());
+
+ if (col == 0) {
+ previewPanel.setAliasColumn(row, (Boolean) curModel.getValueAt(row, col));
+ }
+
+ aliasScrollPane.repaint();
+ }
+
+ private List<String> checkDelimiter() {
+ final List<String> delList = new ArrayList<String>();
+
+ if (tabCheckBox.isSelected()) {
+ delList.add(TextFileDelimiters.TAB.toString());
+ }
+
+ if (commaCheckBox.isSelected()) {
+ delList.add(TextFileDelimiters.COMMA.toString());
+ }
+
+ if (spaceCheckBox.isSelected()) {
+ delList.add(TextFileDelimiters.SPACE.toString());
+ }
+
+ if (semicolonCheckBox.isSelected()) {
+ delList.add(TextFileDelimiters.SEMICOLON.toString());
+ }
+
+ if (otherCheckBox.isSelected()) {
+ delList.add(otherDelimiterTextField.getText());
+ }
+
+ return delList;
+ }
+
+ /**
+ * Error checker for imput table.<br>
+ *
+ * @return true if table looks OK.
+ */
+ private boolean checkDataSourceError() {
+ /*
+ * Number of ENABLED columns should be 2 or more.
+ *
+ */
+ final JTable table = previewPanel.getPreviewTable();
+
+ if ((table == null) || (table.getModel() == null) || (table.getColumnCount() == 0)) {
+ JOptionPane.showMessageDialog(this, "No table selected.", "Invalid Table!",
+ JOptionPane.INFORMATION_MESSAGE);
+
+ return false;
+ } else if ((table.getColumnCount() < 2) && (dialogType != NETWORK_IMPORT)) {
+ JOptionPane.showMessageDialog(this, "Table should contain at least 2 columns.",
+ "Invalid Table!", JOptionPane.INFORMATION_MESSAGE);
+
+ return false;
+ }
+
+ if (dialogType == NETWORK_IMPORT) {
+ final int sIdx = networkImportPanel.getSourceIndex();
+ final int tIdx = networkImportPanel.getTargetIndex();
+ final int iIdx = networkImportPanel.getInteractionIndex();
+
+ // if ((sIdx == -1) || (tIdx == -1)) {
+ // JOptionPane.showMessageDialog(this, "Source or Target index not selected.",
+ // "Please select both source & target index.",
+ // JOptionPane.INFORMATION_MESSAGE);
+ //
+ // return false;
+ // }
+ if ((sIdx == tIdx) || (((iIdx == sIdx) || (iIdx == tIdx)) && (iIdx != -1))) {
+ JOptionPane.showMessageDialog(this,
+ "Columns for source, target, and interaction type must be distinct.",
+ "Same column index!", JOptionPane.INFORMATION_MESSAGE);
+
+ return false;
+ }
+ }
+
+ return true;
+ }
+
+ /*
+ * Layout Information for the entire dialog.<br>
+ *
+ * <p> This layout will be switched by dialog type parameter. </p>
+ *
+ */
+ private void globalLayout() {
+ GroupLayout layout = new GroupLayout(getContentPane());
+ getContentPane().setLayout(layout);
+
+ /*
+ * Case 1: Simple Attribute Import
+ */
+ if (dialogType == SIMPLE_ATTRIBUTE_IMPORT) {
+ layout.setHorizontalGroup(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(layout.createSequentialGroup().addContainerGap()
+ .add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(org.jdesktop.layout.GroupLayout.TRAILING,
+ layout.createSequentialGroup()
+ .add(statusBar,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(importButton)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(cancelButton))
+ .add(previewPanel,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE)
+ .add(org.jdesktop.layout.GroupLayout.TRAILING,
+ advancedPanel,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE)
+ .add(basicPanel,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE)
+ .add(org.jdesktop.layout.GroupLayout.TRAILING,
+ layout.createSequentialGroup()
+ .add(titleIconLabel1)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(titleIconLabel2)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(titleIconLabel3)
+ .add(20, 20, 20)
+ .add(titleLabel)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED,
+ 350,
+ Short.MAX_VALUE)
+ .add(helpButton,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE))
+ .add(titleSeparator,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 700, Short.MAX_VALUE))
+ .addContainerGap()));
+ layout.setVerticalGroup(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(layout.createSequentialGroup().addContainerGap()
+ .add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.TRAILING)
+ .add(layout.createSequentialGroup()
+ .add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE)
+ .add(helpButton,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ 20,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .add(titleIconLabel1)
+ .add(titleIconLabel2)
+ .add(titleIconLabel3))
+ .add(2, 2, 2))
+ .add(layout.createSequentialGroup()
+ .add(titleLabel)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)))
+ .add(titleSeparator,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ 10,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(basicPanel,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(advancedPanel,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(previewPanel,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING,
+ false)
+ .add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE)
+ .add(cancelButton)
+ .add(importButton))
+ .add(statusBar,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE))
+ .addContainerGap()));
+ pack();
+ } else if (dialogType == ONTOLOGY_AND_ANNOTATION_IMPORT) {
+ layout.setHorizontalGroup(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(layout.createSequentialGroup().addContainerGap()
+ .add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(org.jdesktop.layout.GroupLayout.TRAILING,
+ layout.createSequentialGroup()
+ .add(statusBar,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(importButton)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(cancelButton))
+ .add(previewPanel,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE)
+ .add(org.jdesktop.layout.GroupLayout.TRAILING,
+ advancedPanel,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE)
+ .add(basicPanel,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE)
+ .add(org.jdesktop.layout.GroupLayout.TRAILING,
+ layout.createSequentialGroup()
+ .add(titleIconLabel1)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(titleIconLabel2)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(titleIconLabel3)
+ .add(20, 20, 20)
+ .add(titleLabel)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED,
+ 250,
+ Short.MAX_VALUE)
+ .add(helpButton,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE))
+ .add(titleSeparator,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 300, Short.MAX_VALUE))
+ .addContainerGap()));
+ layout.setVerticalGroup(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(layout.createSequentialGroup().addContainerGap()
+ .add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.TRAILING)
+ .add(layout.createSequentialGroup()
+ .add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE)
+ .add(helpButton,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ 20,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .add(titleIconLabel1)
+ .add(titleIconLabel2)
+ .add(titleIconLabel3))
+ .add(2, 2, 2))
+ .add(layout.createSequentialGroup()
+ .add(titleLabel)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)))
+ .add(titleSeparator,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ 10,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(basicPanel,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(advancedPanel,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(previewPanel,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING,
+ false)
+ .add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE)
+ .add(cancelButton)
+ .add(importButton))
+ .add(statusBar,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE))
+ .addContainerGap()));
+
+ annotationAndOntologyImportPanel.setVisible(true);
+ attrTypePanel.setVisible(true);
+ } else if (dialogType == NETWORK_IMPORT) {
+ /*
+ * Layout for network import.
+ */
+ layout.setHorizontalGroup(layout.createParallelGroup(GroupLayout.LEADING)
+ .add(layout.createSequentialGroup().addContainerGap()
+ .add(layout.createParallelGroup(GroupLayout.LEADING)
+ .add(GroupLayout.TRAILING,
+ previewPanel,
+ GroupLayout.DEFAULT_SIZE,
+ GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE)
+ .add(GroupLayout.TRAILING,
+ advancedPanel,
+ GroupLayout.DEFAULT_SIZE,
+ GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE)
+ .add(GroupLayout.TRAILING,
+ networkImportPanel,
+ GroupLayout.DEFAULT_SIZE,
+ GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE)
+ .add(basicPanel,
+ GroupLayout.DEFAULT_SIZE,
+ GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE)
+ .add(GroupLayout.TRAILING,
+ layout.createSequentialGroup()
+ .add(titleIconLabel1)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(titleIconLabel2)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(titleIconLabel3)
+ .add(20, 20, 20)
+ .add(titleLabel)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED,
+ 350,
+ Short.MAX_VALUE)
+ .add(helpButton,
+ GroupLayout.PREFERRED_SIZE,
+ GroupLayout.DEFAULT_SIZE,
+ GroupLayout.PREFERRED_SIZE))
+ .add(titleSeparator,
+ GroupLayout.DEFAULT_SIZE,
+ 700, Short.MAX_VALUE)
+ .add(GroupLayout.TRAILING,
+ layout.createSequentialGroup()
+ .add(importButton)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(cancelButton)))
+ .addContainerGap()));
+ layout.setVerticalGroup(layout.createParallelGroup(GroupLayout.LEADING)
+ .add(layout.createSequentialGroup().addContainerGap()
+ .add(layout.createParallelGroup(GroupLayout.TRAILING)
+ .add(layout.createSequentialGroup()
+ .add(layout.createParallelGroup(GroupLayout.BASELINE)
+ .add(helpButton,
+ GroupLayout.PREFERRED_SIZE,
+ 20,
+ GroupLayout.PREFERRED_SIZE)
+ .add(titleIconLabel1)
+ .add(titleIconLabel2)
+ .add(titleIconLabel3))
+ .add(2, 2, 2))
+ .add(layout.createSequentialGroup()
+ .add(titleLabel)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)))
+ .add(titleSeparator,
+ GroupLayout.PREFERRED_SIZE, 10,
+ GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(basicPanel, GroupLayout.PREFERRED_SIZE,
+ GroupLayout.DEFAULT_SIZE,
+ GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(networkImportPanel,
+ GroupLayout.PREFERRED_SIZE,
+ GroupLayout.DEFAULT_SIZE,
+ GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(advancedPanel,
+ GroupLayout.PREFERRED_SIZE,
+ GroupLayout.DEFAULT_SIZE,
+ GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(previewPanel, GroupLayout.DEFAULT_SIZE,
+ GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(layout.createParallelGroup(GroupLayout.BASELINE)
+ .add(cancelButton).add(importButton))
+ .addContainerGap()));
+
+ // annotationAndOntologyImportPanel.setVisible(false);
+ networkImportPanel.setVisible(true);
+ attrTypePanel.setVisible(false);
+ advancedOptionCheckBox.setVisible(false);
+
+ // advancedOptionPanel.setVisible(false);
+ }
+
+ pack();
+ }
+
+ // Variables declaration - do not modify
+ private javax.swing.JCheckBox advancedOptionCheckBox;
+ private javax.swing.JCheckBox caseSensitiveCheckBox;
+ private javax.swing.JPanel advancedPanel;
+
+ // private JTable aliasTable;
+ private javax.swing.JScrollPane aliasScrollPane;
+ private javax.swing.JPanel annotationAndOntologyImportPanel;
+ private javax.swing.JButton arrowButton1;
+ private javax.swing.JButton arrowButton2;
+ private javax.swing.JPanel attr2annotationPanel;
+ private javax.swing.JCheckBox transferNameCheckBox;
+ private javax.swing.ButtonGroup attrTypeButtonGroup;
+ private javax.swing.JLabel attribuiteLabel;
+ private javax.swing.JLabel attributeFileLabel;
+ private javax.swing.JPanel basicPanel;
+ private javax.swing.JButton browseAnnotationButton;
+ private javax.swing.JButton browseOntologyButton;
+ private javax.swing.JButton cancelButton;
+ private javax.swing.JCheckBox commaCheckBox;
+ private javax.swing.JPanel delimiterPanel;
+ private javax.swing.JRadioButton edgeRadioButton;
+ private javax.swing.JButton helpButton;
+ private javax.swing.JButton importButton;
+ private javax.swing.JRadioButton networkRadioButton;
+ private javax.swing.JComboBox mappingAttributeComboBox;
+ private javax.swing.JLabel nodeKeyLabel;
+ private javax.swing.JRadioButton nodeRadioButton;
+ private javax.swing.JPanel ontology2annotationPanel;
+ private javax.swing.JComboBox ontologyComboBox;
+ private javax.swing.JComboBox ontologyInAnnotationComboBox;
+ private javax.swing.JLabel ontologyInAnnotationLabel;
+ private javax.swing.JLabel ontologyLabel;
+ private javax.swing.JTextField otherDelimiterTextField;
+ private javax.swing.JCheckBox otherCheckBox;
+ private PreviewTablePanel previewPanel;
+ private javax.swing.JLabel primaryKeyLabel;
+ private javax.swing.JButton selectAttributeFileButton;
+ private javax.swing.JCheckBox semicolonCheckBox;
+ private javax.swing.JPanel simpleAttributeImportPanel;
+ private javax.swing.JComboBox annotationComboBox;
+ private javax.swing.JLabel sourceLabel;
+ private javax.swing.JCheckBox spaceCheckBox;
+ private javax.swing.JCheckBox tabCheckBox;
+ private javax.swing.JTextField targetDataSourceTextField;
+ private javax.swing.JLabel targetOntologyLabel;
+ private javax.swing.JTextField ontologyTextField;
+ private javax.swing.JCheckBox textImportCheckBox;
+ private javax.swing.JPanel textImportOptionPanel;
+ private javax.swing.JLabel titleIconLabel1;
+ private javax.swing.JLabel titleIconLabel2;
+ private javax.swing.JLabel titleIconLabel3;
+ private javax.swing.JLabel titleLabel;
+ private javax.swing.JSeparator titleSeparator;
+ private JComboBox primaryKeyComboBox;
+ private JLabel primaryLabel;
+ private JPanel attrTypePanel;
+ private javax.swing.JRadioButton showAllRadioButton;
+ private javax.swing.JLabel counterLabel;
+ private javax.swing.JRadioButton counterRadioButton;
+ private javax.swing.JButton reloadButton;
+ private javax.swing.JSpinner counterSpinner;
+ private javax.swing.ButtonGroup importTypeButtonGroup;
+ private JPanel attributeNamePanel;
+ private JPanel previewOptionPanel;
+ private JPanel networkImportOptionPanel;
+ private JLabel defaultInteractionLabel;
+ private JTextField defaultInteractionTextField;
+ private JLabel startRowLabel;
+ private JSpinner startRowSpinner;
+ private JLabel commentLineLabel;
+ private JTextField commentLineTextField;
+
+ // End of variables declaration
+ JStatusBar statusBar;
+ private NetworkImportOptionsPanel networkImportPanel;
+
+ // private DefaultTableModel model;
+ private AliasTableModel aliasTableModel;
+ private JTable aliasTable;
+ private JCheckBox importAllCheckBox;
+}
+
+
+class ComboBoxRenderer extends JLabel implements ListCellRenderer {
+ private List<Byte> attributeDataTypes;
+
+ /**
+ * Creates a new ComboBoxRenderer object.
+ *
+ * @param attributeDataTypes DOCUMENT ME!
+ */
+ public ComboBoxRenderer(List<Byte> attributeDataTypes) {
+ this.attributeDataTypes = attributeDataTypes;
+ setOpaque(true);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param list DOCUMENT ME!
+ * @param value DOCUMENT ME!
+ * @param index DOCUMENT ME!
+ * @param isSelected DOCUMENT ME!
+ * @param cellHasFocus DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Component getListCellRendererComponent(JList list, Object value, int index,
+ boolean isSelected, boolean cellHasFocus) {
+ setText(value.toString());
+ if (isSelected) {
+ setBackground(list.getSelectionBackground());
+ setForeground(list.getSelectionForeground());
+ } else {
+ setBackground(list.getBackground());
+ setForeground(list.getForeground());
+ }
+
+ if ((attributeDataTypes != null) && (attributeDataTypes.size() != 0)
+ && (index < attributeDataTypes.size()) && (index >= 0)) {
+ final Byte dataType = attributeDataTypes.get(index);
+
+ if (dataType == null) {
+ setIcon(null);
+ } else {
+ setIcon(ImportTextTableDialog.getDataTypeIcon(dataType));
+ }
+ } else if ((attributeDataTypes != null) && (attributeDataTypes.size() != 0)
+ && (index < attributeDataTypes.size())) {
+ setIcon(ImportTextTableDialog.getDataTypeIcon(attributeDataTypes.get(list.getSelectedIndex())));
+ }
+
+ return this;
+ }
+}
+
+
+class AliasTableModel extends DefaultTableModel {
+ AliasTableModel(String[] columnNames, int rowNum) {
+ super(columnNames, rowNum);
+ }
+
+ AliasTableModel(Object[][] data, Object[] colNames) {
+ super(data, colNames);
+ }
+
+ AliasTableModel() {
+ super();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param col DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Class getColumnClass(int col) {
+ return getValueAt(0, col).getClass();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param row DOCUMENT ME!
+ * @param column DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isCellEditable(int row, int column) {
+ if (column == 0) {
+ return true;
+ } else {
+ return false;
+ }
+ }
+}
diff --git a/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/ui/NetworkImportOptionsPanel.java b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/ui/NetworkImportOptionsPanel.java
new file mode 100644
index 0000000..ee2f838
--- /dev/null
+++ b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/ui/NetworkImportOptionsPanel.java
@@ -0,0 +1,313 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package edu.ucsd.bioeng.coreplugin.tableImport.ui;
+
+import static edu.ucsd.bioeng.coreplugin.tableImport.ui.theme.ImportDialogColorTheme.*;
+import static edu.ucsd.bioeng.coreplugin.tableImport.ui.theme.ImportDialogFontTheme.*;
+import static edu.ucsd.bioeng.coreplugin.tableImport.ui.theme.ImportDialogIconSets.*;
+
+import java.beans.PropertyChangeListener;
+import java.beans.PropertyChangeSupport;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.swing.JPanel;
+import javax.swing.SwingConstants;
+
+/**
+ * GUI Component for specify options for network table import.<br>
+ *
+ * @since Cytoscape 2.4
+ * @version 0.8
+ * @author Keiichiro Ono
+ */
+public class NetworkImportOptionsPanel extends JPanel {
+ //private PropertyChangeSupport changes = new PropertyChangeSupport(this);
+ private final PropertyChangeSupport changes;
+
+ /**
+ * Creates a new NetworkImportOptionsPanel object.
+ */
+ public NetworkImportOptionsPanel() {
+ initComponents();
+
+ initializeUIStates();
+ changes = new PropertyChangeSupport(this);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param l DOCUMENT ME!
+ */
+ public void addPropertyChangeListener(PropertyChangeListener l) {
+ if(changes != null)
+ changes.addPropertyChangeListener(l);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param l DOCUMENT ME!
+ */
+ public void removePropertyChangeListener(PropertyChangeListener l) {
+ changes.removePropertyChangeListener(l);
+ }
+
+ private void initComponents() {
+ sourceLabel = new javax.swing.JLabel();
+ sourceComboBox = new javax.swing.JComboBox();
+ interactionLabel = new javax.swing.JLabel();
+ interactionComboBox = new javax.swing.JComboBox();
+ targetLabel = new javax.swing.JLabel();
+ targetComboBox = new javax.swing.JComboBox();
+ iconLabel1 = new javax.swing.JLabel();
+ iconLabel2 = new javax.swing.JLabel();
+ edgeAttributesLabel = new javax.swing.JLabel();
+
+ setBorder(javax.swing.BorderFactory.createTitledBorder("Interaction Definition"));
+
+ sourceLabel.setText("Source Interaction");
+ sourceLabel.setForeground(SOURCE_COLOR.getColor());
+ sourceLabel.setFont(LABEL_FONT.getFont());
+ sourceComboBox.setName("sourceComboBox");
+ sourceComboBox.setForeground(SOURCE_COLOR.getColor());
+ sourceComboBox.setFont(ITEM_FONT_LARGE.getFont());
+ sourceComboBox.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ networkColumnsComboBoxActionPerformed(evt);
+ }
+ });
+
+ interactionLabel.setText("Interaction Type");
+ interactionLabel.setForeground(INTERACTION_COLOR.getColor());
+ interactionLabel.setFont(LABEL_FONT.getFont());
+
+ interactionComboBox.setName("interactionComboBox");
+ interactionComboBox.setForeground(INTERACTION_COLOR.getColor());
+ interactionComboBox.setFont(ITEM_FONT_LARGE.getFont());
+ interactionComboBox.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ networkColumnsComboBoxActionPerformed(evt);
+ }
+ });
+
+ targetLabel.setText("Target Interaction");
+ targetLabel.setForeground(TARGET_COLOR.getColor());
+ targetLabel.setFont(LABEL_FONT.getFont());
+
+ targetComboBox.setName("targetComboBox");
+ targetComboBox.setForeground(TARGET_COLOR.getColor());
+ targetComboBox.setFont(ITEM_FONT_LARGE.getFont());
+ targetComboBox.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ networkColumnsComboBoxActionPerformed(evt);
+ }
+ });
+
+ iconLabel1.setIcon(INTERACTION_ICON.getIcon());
+ iconLabel2.setIcon(INTERACTION_ICON.getIcon());
+
+ edgeAttributesLabel.setFont(LABEL_ITALIC_FONT.getFont());
+ edgeAttributesLabel.setForeground(EDGE_ATTR_COLOR.getColor());
+ edgeAttributesLabel.setHorizontalAlignment(SwingConstants.CENTER);
+ edgeAttributesLabel.setIcon(CAUTION_ICON.getIcon());
+ edgeAttributesLabel.setText("Columns in BLUE will be loaded as EDGE ATTRIBUTES.");
+
+ org.jdesktop.layout.GroupLayout layout = new org.jdesktop.layout.GroupLayout(this);
+ this.setLayout(layout);
+ layout.setHorizontalGroup(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(layout.createSequentialGroup().addContainerGap()
+ .add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(layout.createSequentialGroup()
+ .add(sourceComboBox, 0,
+ 100, Short.MAX_VALUE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(iconLabel1)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED))
+ .add(layout.createSequentialGroup()
+ .add(sourceLabel)
+ .add(100, 100, 100)))
+ .add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(layout.createSequentialGroup()
+ .add(interactionComboBox,
+ 0, 100,
+ Short.MAX_VALUE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(iconLabel2)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED))
+ .add(layout.createSequentialGroup()
+ .add(interactionLabel)
+ .add(100, 100, 100)))
+ .add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(layout.createSequentialGroup()
+ .add(targetLabel)
+ .addContainerGap(100,
+ Short.MAX_VALUE))
+ .add(layout.createSequentialGroup()
+ .add(targetComboBox, 0,
+ 100, Short.MAX_VALUE)
+ .add(22, 22, 22))))
+ .add(org.jdesktop.layout.GroupLayout.TRAILING,
+ edgeAttributesLabel,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 100,
+ Short.MAX_VALUE));
+ layout.setVerticalGroup(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(layout.createSequentialGroup()
+ .add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE)
+ .add(sourceLabel).add(interactionLabel)
+ .add(targetLabel))
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE)
+ .add(sourceComboBox,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .add(iconLabel1)
+ .add(interactionComboBox,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .add(iconLabel2)
+ .add(targetComboBox,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE))
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(edgeAttributesLabel)
+ .addContainerGap(org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ Short.MAX_VALUE)));
+ } // </editor-fold>
+
+ private void networkColumnsComboBoxActionPerformed(java.awt.event.ActionEvent e) {
+ final int sIdx = sourceComboBox.getSelectedIndex() - 1;
+ final int tIdx = targetComboBox.getSelectedIndex() - 1;
+ final int iIdx = interactionComboBox.getSelectedIndex() - 1;
+
+ List<Integer> colIdx = new ArrayList<Integer>();
+
+ colIdx.add(sIdx);
+ colIdx.add(tIdx);
+ colIdx.add(iIdx);
+
+ changes.firePropertyChange(ImportTextTableDialog.NETWORK_IMPORT_TEMPLATE_CHANGED, null,
+ colIdx);
+ }
+
+ /* ============================================================================================== */
+ private void initializeUIStates() {
+ sourceComboBox.setEnabled(false);
+ targetComboBox.setEnabled(false);
+ interactionComboBox.setEnabled(false);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param columnNames DOCUMENT ME!
+ */
+ public void setComboBoxes(String[] columnNames) {
+ /*
+ * Cleanup the combo boxes
+ */
+ sourceComboBox.removeAllItems();
+ targetComboBox.removeAllItems();
+ interactionComboBox.removeAllItems();
+
+ for (String item : columnNames) {
+ sourceComboBox.addItem(item);
+ targetComboBox.addItem(item);
+ interactionComboBox.addItem(item);
+ }
+
+ interactionComboBox.insertItemAt("Default Interaction", 0);
+ sourceComboBox.insertItemAt("Select Source node column...", 0);
+ targetComboBox.insertItemAt("Select Target node column...", 0);
+
+ sourceComboBox.setEnabled(true);
+ targetComboBox.setEnabled(true);
+ interactionComboBox.setEnabled(true);
+
+ sourceComboBox.setSelectedIndex(0);
+ targetComboBox.setSelectedIndex(0);
+ interactionComboBox.setSelectedIndex(0);
+ }
+
+ /*
+ * Get index from combo boxes.
+ */
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getSourceIndex() {
+ return sourceComboBox.getSelectedIndex() - 1;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getTargetIndex() {
+ return targetComboBox.getSelectedIndex() - 1;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getInteractionIndex() {
+ return interactionComboBox.getSelectedIndex() - 1;
+ }
+
+ // Variables declaration - do not modify
+ private javax.swing.JLabel edgeAttributesLabel;
+ private javax.swing.JLabel iconLabel1;
+ private javax.swing.JLabel iconLabel2;
+ private javax.swing.JComboBox interactionComboBox;
+ private javax.swing.JLabel interactionLabel;
+ private javax.swing.JComboBox sourceComboBox;
+ private javax.swing.JLabel sourceLabel;
+ private javax.swing.JComboBox targetComboBox;
+ private javax.swing.JLabel targetLabel;
+
+ // End of variables declaration
+}
diff --git a/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/ui/PreviewTablePanel.java b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/ui/PreviewTablePanel.java
new file mode 100644
index 0000000..95832f6
--- /dev/null
+++ b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/ui/PreviewTablePanel.java
@@ -0,0 +1,1352 @@
+/*
+ Copyright (c) 2006, 2007, 2009, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package edu.ucsd.bioeng.coreplugin.tableImport.ui;
+
+import static edu.ucsd.bioeng.coreplugin.tableImport.ui.theme.ImportDialogColorTheme.ALIAS_COLOR;
+import static edu.ucsd.bioeng.coreplugin.tableImport.ui.theme.ImportDialogColorTheme.ONTOLOGY_COLOR;
+import static edu.ucsd.bioeng.coreplugin.tableImport.ui.theme.ImportDialogColorTheme.PRIMARY_KEY_COLOR;
+import static edu.ucsd.bioeng.coreplugin.tableImport.ui.theme.ImportDialogColorTheme.SPECIES_COLOR;
+import static edu.ucsd.bioeng.coreplugin.tableImport.ui.theme.ImportDialogFontTheme.LABEL_FONT;
+import static edu.ucsd.bioeng.coreplugin.tableImport.ui.theme.ImportDialogIconSets.RIGHT_ARROW_ICON;
+import static edu.ucsd.bioeng.coreplugin.tableImport.ui.theme.ImportDialogIconSets.SPREADSHEET_ICON;
+import static edu.ucsd.bioeng.coreplugin.tableImport.ui.theme.ImportDialogIconSets.TEXT_FILE_ICON;
+
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Font;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.Insets;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.geom.AffineTransform;
+import java.awt.image.BufferedImage;
+import java.beans.PropertyChangeListener;
+import java.beans.PropertyChangeSupport;
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.Vector;
+
+import javax.imageio.ImageIO;
+import javax.swing.BorderFactory;
+import javax.swing.DefaultListModel;
+import javax.swing.ImageIcon;
+import javax.swing.JLabel;
+import javax.swing.JList;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTabbedPane;
+import javax.swing.JTable;
+import javax.swing.ListCellRenderer;
+import javax.swing.ListModel;
+import javax.swing.SwingConstants;
+import javax.swing.SwingUtilities;
+import javax.swing.border.Border;
+import javax.swing.table.DefaultTableModel;
+import javax.swing.table.JTableHeader;
+import javax.swing.table.TableCellRenderer;
+import javax.swing.table.TableModel;
+
+import org.apache.poi.openxml4j.exceptions.InvalidFormatException;
+import org.apache.poi.ss.usermodel.Cell;
+import org.apache.poi.ss.usermodel.Row;
+import org.apache.poi.ss.usermodel.Sheet;
+import org.apache.poi.ss.usermodel.Workbook;
+import org.apache.poi.ss.usermodel.WorkbookFactory;
+import org.jdesktop.layout.GroupLayout;
+
+import cytoscape.Cytoscape;
+import cytoscape.data.CyAttributes;
+import cytoscape.logger.CyLogger;
+import cytoscape.util.URLUtil;
+import cytoscape.util.swing.ColumnResizer;
+import edu.ucsd.bioeng.coreplugin.tableImport.reader.GeneAssociationTags;
+import edu.ucsd.bioeng.coreplugin.tableImport.reader.SupportedFileType;
+import edu.ucsd.bioeng.coreplugin.tableImport.reader.TextFileDelimiters;
+import edu.ucsd.bioeng.coreplugin.tableImport.ui.ImportTextTableDialog.FileTypes;
+
+/**
+ * General purpose preview table panel.
+ *
+ * @author kono
+ *
+ */
+public class PreviewTablePanel extends JPanel {
+
+ private static final long serialVersionUID = -7779176856705540150L;
+
+ /**
+ *
+ */
+ public static final int ATTRIBUTE_PREVIEW = 1;
+
+ /**
+ *
+ */
+ public static final int ONTOLOGY_PREVIEW = 2;
+
+ /**
+ *
+ */
+ public static final int NETWORK_PREVIEW = 3;
+
+ /*
+ * Default messages
+ */
+ private static final String DEF_MESSAGE = "Legend:";
+ private static final String DEF_TAB_MESSAGE = "Data File Preview Window";
+
+ // Lines start with this char will be ignored.
+ private String commentChar;
+ private final String message;
+ private boolean loadFlag = false;
+
+ // Tracking attribute data type.
+ // private Byte[] dataTypes;
+ private Map<String, Byte[]> dataTypeMap;
+ private Map<String, Byte[]> listDataTypeMap;
+
+ /*
+ * GUI Components
+ */
+ private JLabel legendLabel;
+ private JLabel aliasLabel;
+ private JLabel primaryKeyLabel;
+ private JLabel ontologyTermLabel;
+ private JLabel taxonomyLabel;
+ private JLabel instructionLabel;
+ private JLabel rightArrowLabel;
+ private JLabel fileTypeLabel;
+ private JScrollPane previewScrollPane;
+ private JTable previewTable;
+
+ // Tables for each worksheet.
+ private Map<String, JTable> previewTables;
+ private JTabbedPane tableTabbedPane;
+ private JScrollPane keyPreviewScrollPane;
+ private JList keyPreviewList;
+ private DefaultListModel keyListModel;
+ private PropertyChangeSupport changes = new PropertyChangeSupport(this);
+ private int panelType;
+ private String listDelimiter;
+
+ private CyLogger logger = CyLogger.getLogger(PreviewTablePanel.class);
+
+ /**
+ * Creates a new PreviewTablePanel object.
+ */
+ public PreviewTablePanel() {
+ this(DEF_MESSAGE, ATTRIBUTE_PREVIEW);
+ }
+
+ /**
+ * Creates a new PreviewTablePanel object.
+ *
+ * @param message
+ * DOCUMENT ME!
+ */
+ public PreviewTablePanel(String message) {
+ this(message, ATTRIBUTE_PREVIEW);
+ }
+
+ /**
+ * Creates a new PreviewTablePanel object.
+ *
+ * @param message
+ * DOCUMENT ME!
+ * @param panelType
+ * DOCUMENT ME!
+ */
+ public PreviewTablePanel(String message, int panelType) {
+ if (message == null) {
+ this.message = DEF_MESSAGE;
+ } else {
+ this.message = message;
+ }
+
+ this.panelType = panelType;
+
+ dataTypeMap = new HashMap<String, Byte[]>();
+ listDataTypeMap = new HashMap<String, Byte[]>();
+
+ initComponents();
+
+ hideUnnecessaryComponents();
+ }
+
+ private void hideUnnecessaryComponents() {
+ fileTypeLabel.setVisible(false);
+
+ if (panelType == NETWORK_PREVIEW) {
+ keyPreviewScrollPane.setVisible(false);
+ rightArrowLabel.setVisible(false);
+ legendLabel.setVisible(false);
+ primaryKeyLabel.setVisible(false);
+ aliasLabel.setVisible(false);
+ ontologyTermLabel.setVisible(false);
+ taxonomyLabel.setVisible(false);
+ } else if (panelType == ATTRIBUTE_PREVIEW) {
+ ontologyTermLabel.setVisible(false);
+ taxonomyLabel.setVisible(false);
+ }
+
+ repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param data
+ * DOCUMENT ME!
+ */
+ public void setKeyAttributeList(Set data) {
+ keyPreviewScrollPane.setBackground(Color.white);
+ keyListModel.clear();
+
+ for (Object item : data) {
+ keyListModel.addElement(item);
+ }
+
+ keyPreviewList.repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param l
+ * DOCUMENT ME!
+ */
+ public void addPropertyChangeListener(PropertyChangeListener l) {
+ if (changes == null) return;
+
+ changes.addPropertyChangeListener(l);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param l
+ * DOCUMENT ME!
+ */
+ public void removePropertyChangeListener(PropertyChangeListener l) {
+ changes.removePropertyChangeListener(l);
+ }
+
+ private void initComponents() {
+ legendLabel = new JLabel();
+ instructionLabel = new javax.swing.JLabel();
+
+ primaryKeyLabel = new javax.swing.JLabel();
+ aliasLabel = new javax.swing.JLabel();
+ ontologyTermLabel = new JLabel();
+ taxonomyLabel = new JLabel();
+ previewScrollPane = new JScrollPane();
+ rightArrowLabel = new JLabel();
+ tableTabbedPane = new JTabbedPane();
+ keyListModel = new DefaultListModel();
+ keyPreviewList = new JList(keyListModel);
+ keyPreviewScrollPane = new JScrollPane();
+
+ previewTables = new HashMap<String, JTable>();
+ previewTable = new JTable();
+ previewTable.setName("previewTable");
+ previewTable.setOpaque(false);
+ previewTable.setBackground(Color.white);
+
+ fileTypeLabel = new JLabel();
+ fileTypeLabel.setFont(new Font("Sans-Serif", Font.BOLD, 14));
+
+ keyPreviewScrollPane.setBorder(javax.swing.BorderFactory
+ .createTitledBorder("Key Attributes"));
+
+ keyPreviewList.setOpaque(false);
+ keyPreviewList.setCellRenderer(new KeyAttributeListRenderer());
+ keyPreviewScrollPane.setViewportView(keyPreviewList);
+
+ previewScrollPane.setOpaque(false);
+ previewScrollPane.setViewportView(previewTable);
+ previewScrollPane.setBackground(Color.WHITE);
+
+ final BufferedImage datasourceImage = getBufferedImage(Cytoscape.class
+ .getResource("images/ximian/data_sources_trans.png"));
+
+ final BufferedImage bi = getBufferedImage(Cytoscape.class
+ .getResource("images/icon100_trans.png"));
+
+ tableTabbedPane.setBackground(Color.white);
+ tableTabbedPane
+ .addChangeListener(new javax.swing.event.ChangeListener() {
+ public void stateChanged(javax.swing.event.ChangeEvent evt) {
+ tableTabbedPaneStateChanged(evt);
+ }
+ });
+
+ previewScrollPane.getViewport().setOpaque(false);
+ previewScrollPane.setViewportBorder(new CentredBackgroundBorder(
+ datasourceImage));
+ keyPreviewScrollPane.getViewport().setOpaque(false);
+ keyPreviewScrollPane.setViewportBorder(new CentredBackgroundBorder(bi));
+
+ tableTabbedPane.addTab(DEF_TAB_MESSAGE, previewScrollPane);
+
+ rightArrowLabel.setIcon(RIGHT_ARROW_ICON.getIcon());
+
+ JTableHeader hd = previewTable.getTableHeader();
+ hd.setReorderingAllowed(false);
+ hd
+ .setDefaultRenderer(new HeaderRenderer(hd.getDefaultRenderer(),
+ null));
+
+ /*
+ * Setting table properties
+ */
+ previewTable.setCellSelectionEnabled(false);
+ previewTable.setAutoResizeMode(JTable.AUTO_RESIZE_OFF);
+ previewTable.setDefaultEditor(Object.class, null);
+
+ this
+ .setBorder(BorderFactory
+ .createTitledBorder(
+ javax.swing.BorderFactory
+ .createBevelBorder(javax.swing.border.BevelBorder.RAISED),
+ "Preview",
+ javax.swing.border.TitledBorder.DEFAULT_JUSTIFICATION,
+ javax.swing.border.TitledBorder.DEFAULT_POSITION,
+ new java.awt.Font("Dialog", 1, 11)));
+
+ instructionLabel.setHorizontalAlignment(SwingConstants.CENTER);
+ instructionLabel
+ .setText("Left Click: Enable/Disable Column, Right Click: Edit Column");
+ instructionLabel.setFont(LABEL_FONT.getFont());
+ instructionLabel.setForeground(Color.red);
+
+ legendLabel.setFont(LABEL_FONT.getFont());
+ legendLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ legendLabel.setText(message);
+
+ primaryKeyLabel.setFont(LABEL_FONT.getFont());
+ primaryKeyLabel.setForeground(Color.WHITE);
+ primaryKeyLabel.setBackground(PRIMARY_KEY_COLOR.getColor());
+ primaryKeyLabel
+ .setHorizontalAlignment(javax.swing.SwingConstants.CENTER);
+ // onLabel
+ // .setIcon(CHECKED_ICON.getIcon());
+ primaryKeyLabel.setText("Key");
+ primaryKeyLabel
+ .setToolTipText("Column in this color is the Primary Key.");
+ // onLabel.setBorder(new javax.swing.border.LineBorder(new
+ // java.awt.Color(
+ // 0, 0, 0), 1, true));
+ primaryKeyLabel.setOpaque(true);
+
+ aliasLabel.setFont(LABEL_FONT.getFont());
+ aliasLabel.setForeground(Color.WHITE);
+ aliasLabel.setBackground(ALIAS_COLOR.getColor());
+ aliasLabel.setHorizontalAlignment(javax.swing.SwingConstants.CENTER);
+ // offLabel
+ // .setIcon(UNCHECKED_ICON.getIcon());
+ aliasLabel.setText("Alias");
+ aliasLabel.setToolTipText("Columns in this color are Aliases.");
+ // offLabel.setBorder(new javax.swing.border.LineBorder(
+ // new java.awt.Color(0, 0, 0), 1, true));
+ aliasLabel.setOpaque(true);
+
+ ontologyTermLabel.setFont(LABEL_FONT.getFont());
+ ontologyTermLabel.setForeground(Color.WHITE);
+ ontologyTermLabel.setBackground(ONTOLOGY_COLOR.getColor());
+ ontologyTermLabel
+ .setHorizontalAlignment(javax.swing.SwingConstants.CENTER);
+ ontologyTermLabel.setText("Ontology");
+ ontologyTermLabel
+ .setToolTipText("Column in this color is Ontology Term.");
+ ontologyTermLabel.setOpaque(true);
+
+ taxonomyLabel.setFont(LABEL_FONT.getFont());
+ taxonomyLabel.setForeground(Color.WHITE);
+ taxonomyLabel.setBackground(SPECIES_COLOR.getColor());
+ taxonomyLabel.setHorizontalAlignment(javax.swing.SwingConstants.CENTER);
+ taxonomyLabel.setText("Taxon");
+ taxonomyLabel
+ .setToolTipText("Columns in this color is Taxon (for Gene Association files only).");
+ taxonomyLabel.setOpaque(true);
+
+ GroupLayout previewPanelLayout = new GroupLayout(this);
+ this.setLayout(previewPanelLayout);
+
+ previewPanelLayout
+ .setHorizontalGroup(previewPanelLayout
+ .createParallelGroup(
+ org.jdesktop.layout.GroupLayout.LEADING)
+ .add(
+ org.jdesktop.layout.GroupLayout.TRAILING,
+ previewPanelLayout
+ .createSequentialGroup()
+ .add(
+ tableTabbedPane,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 250, Short.MAX_VALUE)
+ .addPreferredGap(
+ org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(rightArrowLabel)
+ .addPreferredGap(
+ org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(
+ keyPreviewScrollPane,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ 180,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE))
+ .add(
+ previewPanelLayout
+ .createSequentialGroup()
+ .add(fileTypeLabel)
+ .addPreferredGap(
+ org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(
+ instructionLabel,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 60, Short.MAX_VALUE)
+ .addPreferredGap(
+ org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(
+ legendLabel,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ 60,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(
+ org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(
+ primaryKeyLabel,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ 60,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(
+ org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(
+ aliasLabel,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ 60,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(
+ org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(
+ ontologyTermLabel,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ 70,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(
+ org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(
+ taxonomyLabel,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ 60,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .addContainerGap()));
+ previewPanelLayout
+ .setVerticalGroup(previewPanelLayout
+ .createParallelGroup(
+ org.jdesktop.layout.GroupLayout.LEADING)
+ .add(
+ previewPanelLayout
+ .createSequentialGroup()
+ .add(
+ previewPanelLayout
+ .createParallelGroup(
+ org.jdesktop.layout.GroupLayout.BASELINE)
+ .add(fileTypeLabel)
+ .add(primaryKeyLabel)
+ .add(aliasLabel)
+ .add(ontologyTermLabel)
+ .add(taxonomyLabel)
+ .add(legendLabel)
+ .add(instructionLabel))
+ .addPreferredGap(
+ org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(
+ previewPanelLayout
+ .createParallelGroup(
+ org.jdesktop.layout.GroupLayout.TRAILING)
+ .add(
+ tableTabbedPane,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 200,
+ Short.MAX_VALUE)
+ .add(
+ keyPreviewScrollPane,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 200,
+ Short.MAX_VALUE)
+ .add(
+ org.jdesktop.layout.GroupLayout.LEADING,
+ rightArrowLabel,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 200,
+ Short.MAX_VALUE))));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public JTable getPreviewTable() {
+ JScrollPane selected = (JScrollPane) tableTabbedPane
+ .getSelectedComponent();
+
+ if (selected == null) {
+ return null;
+ }
+
+ return (JTable) selected.getViewport().getComponent(0);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getTableCount() {
+ return tableTabbedPane.getTabCount();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param index
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getSheetName(int index) {
+ return tableTabbedPane.getTitleAt(index);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param selectedTabName
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Byte[] getDataTypes(final String selectedTabName) {
+ return dataTypeMap.get(selectedTabName);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Byte[] getCurrentDataTypes() {
+ return dataTypeMap.get(getSelectedSheetName());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Byte[] getCurrentListDataTypes() {
+ return listDataTypeMap.get(getSelectedSheetName());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public FileTypes getFileType() {
+ final String sheetName = getSheetName(tableTabbedPane
+ .getSelectedIndex());
+
+ if (sheetName.startsWith("gene_association")) {
+ return FileTypes.GENE_ASSOCIATION_FILE;
+ }
+
+ return FileTypes.ATTRIBUTE_FILE;
+ }
+
+ /**
+ * Get selected tab name.
+ *
+ * @return name of the selected tab (i.e., sheet name)
+ */
+ public String getSelectedSheetName() {
+ return tableTabbedPane.getTitleAt(tableTabbedPane.getSelectedIndex());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param index
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public JTable getPreviewTable(int index) {
+ JScrollPane selected = (JScrollPane) tableTabbedPane
+ .getComponentAt(index);
+
+ return (JTable) selected.getViewport().getComponent(0);
+ }
+
+ private void tableTabbedPaneStateChanged(javax.swing.event.ChangeEvent evt) {
+ if ((tableTabbedPane.getSelectedComponent() != null)
+ && (((JScrollPane) tableTabbedPane.getSelectedComponent())
+ .getViewport().getComponent(0) != null)
+ && (loadFlag == true)) {
+ changes.firePropertyChange(ImportTextTableDialog.SHEET_CHANGED,
+ null, null);
+ }
+ }
+
+ /**
+ * Get backgroung images for table & list.
+ *
+ * @param url
+ * @return
+ */
+ private BufferedImage getBufferedImage(URL url) {
+ BufferedImage image;
+
+ try {
+ image = ImageIO.read(url);
+ } catch (IOException ioe) {
+ logger.warn("could't create image from: " + url.toString(), ioe);
+
+ return new BufferedImage(1, 1, BufferedImage.TYPE_INT_RGB);
+ }
+
+ return image;
+ }
+
+ /**
+ * Load file and show preview.
+ *
+ * @param sourceURL
+ * @param delimiters
+ * @param renderer
+ * renderer for this table. Can be null.
+ * @param size
+ * @param commentLineChar
+ * TODO
+ * @param startLine
+ * TODO
+ * @throws IOException
+ */
+ public void setPreviewTable(URL sourceURL, List<String> delimiters,
+ TableCellRenderer renderer, int size, final String commentLineChar,
+ final int startLine) throws IOException {
+ TableCellRenderer curRenderer = renderer;
+
+ if ((commentLineChar != null) && (commentLineChar.trim().length() != 0))
+ this.commentChar = commentLineChar;
+ else
+ this.commentChar = null;
+ /*
+ * If rendrer is null, create default one.
+ */
+ if (curRenderer == null) {
+ curRenderer = new AttributePreviewTableCellRenderer(0,
+ new ArrayList<Integer>(),
+ AttributePreviewTableCellRenderer.PARAMETER_NOT_EXIST,
+ AttributePreviewTableCellRenderer.PARAMETER_NOT_EXIST,
+ null, TextFileDelimiters.PIPE.toString());
+ }
+
+ /*
+ * Reset current state
+ */
+ for (int i = 0; i < tableTabbedPane.getTabCount(); i++)
+ tableTabbedPane.removeTabAt(i);
+
+ previewTables = new HashMap<String, JTable>();
+
+ TableModel newModel;
+
+ fileTypeLabel.setVisible(true);
+
+ if (sourceURL.toString().endsWith(
+ SupportedFileType.EXCEL.getExtension())
+ || sourceURL.toString().endsWith(
+ SupportedFileType.OOXML.getExtension())) {
+
+ fileTypeLabel.setIcon(SPREADSHEET_ICON.getIcon());
+ fileTypeLabel.setText("Excel" + '\u2122' + " Workbook");
+
+ InputStream is = null;
+ final Workbook wb;
+
+ try {
+ is = sourceURL.openStream();
+ wb = WorkbookFactory.create(is);
+ } catch (InvalidFormatException e) {
+ e.printStackTrace();
+ throw new IllegalArgumentException("Could not read Excel file. Maybe the file is broken?");
+ } finally {
+ if (is != null)
+ is.close();
+ }
+
+ if (wb.getNumberOfSheets() == 0)
+ throw new IllegalStateException("No sheet found in the workbook.");
+
+ /*
+ * Load each sheet in the workbook.
+ */
+ logger.debug("# of Sheets = " + wb.getNumberOfSheets());
+
+ Sheet sheet = wb.getSheetAt(0);
+ logger.debug("Sheet name = " + wb.getSheetName(0) + ", ROW = "
+ + sheet.rowIterator().hasNext());
+
+ newModel = parseExcel(sourceURL, size, curRenderer, sheet,
+ startLine);
+
+ if (newModel.getRowCount() == 0)
+ throw new IllegalStateException("No data found in the Excel sheet.");
+
+ DataTypeUtil.guessTypes(newModel, wb.getSheetName(0), dataTypeMap);
+ listDataTypeMap
+ .put(wb.getSheetName(0), initListDataTypes(newModel));
+ addTableTab(newModel, wb.getSheetName(0), curRenderer);
+ } else {
+ if (isCytoscapeAttributeFile(sourceURL)) {
+ fileTypeLabel.setText("Cytoscape Attribute File");
+ fileTypeLabel.setIcon(new ImageIcon(Cytoscape.class
+ .getResource("images/icon48.png")));
+ newModel = parseText(sourceURL, size, curRenderer, null, 1);
+ } else {
+ fileTypeLabel.setText("Text File");
+ fileTypeLabel.setIcon(TEXT_FILE_ICON.getIcon());
+ newModel = parseText(sourceURL, size, curRenderer, delimiters,
+ startLine);
+ }
+
+ String[] urlParts = sourceURL.toString().split("/");
+ final String tabName = urlParts[urlParts.length - 1];
+ DataTypeUtil.guessTypes(newModel, tabName, dataTypeMap);
+ listDataTypeMap.put(tabName, initListDataTypes(newModel));
+ addTableTab(newModel, tabName, curRenderer);
+ }
+
+ if (getFileType() == FileTypes.GENE_ASSOCIATION_FILE) {
+ fileTypeLabel.setText("Gene Association");
+ fileTypeLabel
+ .setToolTipText("This is a fixed-format Gene Association file.");
+ }
+
+ loadFlag = true;
+ }
+
+ protected boolean isCytoscapeAttributeFile(final URL sourceURL)
+ throws IOException {
+ InputStream is = null;
+
+ boolean testResult = true;
+
+ try {
+ BufferedReader bufRd = null;
+
+ is = URLUtil.getInputStream(sourceURL);
+ try {
+ String line = null;
+ int i = 0;
+
+ bufRd = new BufferedReader(new InputStreamReader(is));
+ // Test first two lines to check the file type.
+ while ((line = bufRd.readLine()) != null) {
+ if (i == 0) {
+ String[] elements = line.split(" +");
+
+ if (elements.length == 1) {
+ // True so far.
+ } else {
+ elements = line.split("[(]");
+
+ if ((elements.length == 2)
+ && elements[1].startsWith("class=")) {
+ // true so far.
+ } else {
+ testResult = false;
+
+ break;
+ }
+ }
+ } else if (i == 1) {
+ String[] elements = line.split(" += +");
+
+ if (elements.length != 2)
+ testResult = false;
+ } else if (i >= 2) {
+ break;
+ }
+
+ i++;
+ }
+ } finally {
+ if (bufRd != null) {
+ bufRd.close();
+ }
+ }
+ } finally {
+ if (is != null) {
+ is.close();
+ }
+ }
+
+ return testResult;
+ }
+
+ private void addTableTab(TableModel newModel, final String tabName,
+ TableCellRenderer renderer) {
+ JTable newTable = new JTable(newModel);
+ previewTables.put(tabName, newTable);
+
+ JScrollPane newScrollPane = new JScrollPane();
+ newScrollPane.setViewportView(newTable);
+ newScrollPane.setBackground(Color.WHITE);
+
+ tableTabbedPane.add(tabName, newScrollPane);
+
+ /*
+ * Initialize data type atrray. By default, everything is a String.
+ */
+
+ // dataTypes = new Byte[newModel.getColumnCount()];
+ // dataTypeMap.put(tabName, new Byte[newModel.getColumnCount()]);
+ // for (int j = 0; j < newModel.getColumnCount(); j++) {
+ // dataTypes[j] = CyAttributes.TYPE_STRING;
+ // }
+
+ // Setting table properties
+ newTable.setCellSelectionEnabled(false);
+ newTable.setAutoResizeMode(JTable.AUTO_RESIZE_OFF);
+ newTable.setDefaultEditor(Object.class, null);
+
+ if (panelType == NETWORK_PREVIEW) {
+ final int colCount = newTable.getColumnCount();
+ final boolean[] importFlag = new boolean[colCount];
+
+ for (int i = 0; i < colCount; i++) {
+ importFlag[i] = false;
+ }
+
+ TableCellRenderer netRenderer = new AttributePreviewTableCellRenderer(
+ AttributePreviewTableCellRenderer.PARAMETER_NOT_EXIST,
+ new ArrayList<Integer>(),
+ AttributePreviewTableCellRenderer.PARAMETER_NOT_EXIST,
+ AttributePreviewTableCellRenderer.PARAMETER_NOT_EXIST,
+ importFlag, TextFileDelimiters.PIPE.toString());
+
+ newTable.setDefaultRenderer(Object.class, netRenderer);
+ } else {
+ newTable.setDefaultRenderer(Object.class, renderer);
+ }
+
+ JTableHeader hd = newTable.getTableHeader();
+ hd.setReorderingAllowed(false);
+ hd.setDefaultRenderer(new HeaderRenderer(hd.getDefaultRenderer(),
+ dataTypeMap.get(tabName)));
+
+ newTable.getTableHeader().addMouseListener(new TableHeaderListener());
+
+ ColumnResizer.adjustColumnPreferredWidths(newTable);
+
+ newTable.revalidate();
+ newTable.repaint();
+ newTable.getTableHeader().repaint();
+ }
+
+ private Byte[] initListDataTypes(final TableModel model) {
+ final Byte[] listTypes = new Byte[model.getColumnCount()];
+
+ for (int i = 0; i < listTypes.length; i++) {
+ listTypes[i] = null;
+ }
+
+ return listTypes;
+ }
+
+ /**
+ * Based on the file type, setup the initial column names.
+ * <p>
+ * </p>
+ *
+ * @param colCount
+ * @return
+ */
+ private Vector<String> getDefaultColumnNames(final int colCount,
+ final URL sourceURL) {
+
+ final Vector<String> colNames = new Vector<String>();
+
+ String[] parts = sourceURL.toString().split("/");
+ final String fileName = parts[parts.length - 1];
+
+ if ((colCount == GeneAssociationTags.values().length)
+ && fileName.startsWith("gene_association")) {
+ for (Object colName : GeneAssociationTags.values()) {
+ colNames.add(colName.toString());
+ }
+ } else {
+ for (int i = 0; i < colCount; i++) {
+ colNames.add("Column " + (i + 1));
+ }
+ }
+
+ return colNames;
+ }
+
+ private TableModel parseText(URL sourceURL, int size,
+ TableCellRenderer renderer, List<String> delimiters, int startLine)
+ throws IOException {
+ InputStream is = null;
+ String line;
+ String attrName = "Attr1";
+ Vector data;
+ int maxColumn;
+
+ try {
+ BufferedReader bufRd = null;
+
+ is = URLUtil.getInputStream(sourceURL);
+ try {
+ bufRd = new BufferedReader(new InputStreamReader(is));
+ /*
+ * Generate reg. exp. for delimiter.
+ */
+ final String delimiterRegEx;
+
+ if (delimiters != null) {
+ StringBuffer delimiterBuffer = new StringBuffer();
+
+ if (delimiters.size() != 0) {
+ delimiterBuffer.append("[");
+
+ for (String delimiter : delimiters) {
+ delimiterBuffer.append(delimiter);
+ }
+
+ delimiterBuffer.append("]");
+ }
+
+ delimiterRegEx = delimiterBuffer.toString();
+ } else {
+ // treat as cytoscape attribute files.
+ delimiterRegEx = " += +";
+ // Extract first column for attr name.
+ line = bufRd.readLine();
+ String[] line1 = line.split(" +");
+ attrName = line1[0];
+ }
+
+ /*
+ * Read & extract one line at a time. The line can be Tab
+ * delimited,
+ */
+ boolean importAll = false;
+
+ if (size == -1) {
+ importAll = true;
+ }
+
+ int counter = 0;
+ String[] parts;
+ maxColumn = 0;
+ data = new Vector();
+
+ while ((line = bufRd.readLine()) != null) {
+ if (((commentChar != null) && line.startsWith(commentChar))
+ || (line.trim().length() == 0)
+ || (counter < startLine)) {
+ // ignore
+ } else {
+ Vector row = new Vector();
+
+ if (delimiterRegEx.length() == 0) {
+ parts = new String[1];
+ parts[0] = line;
+ } else {
+ parts = line.split(delimiterRegEx);
+ }
+
+ for (String entry : parts) {
+ row.add(entry);
+ }
+
+ if (parts.length > maxColumn) {
+ maxColumn = parts.length;
+ }
+
+ data.add(row);
+ }
+
+ counter++;
+
+ if ((importAll == false) && (counter >= size)) {
+ break;
+ }
+ }
+ } finally {
+ if (bufRd != null) {
+ bufRd.close();
+ }
+ }
+ } finally {
+ if (is != null) {
+ is.close();
+ }
+ }
+
+ if (delimiters == null) {
+ // Cytoscape attr file.
+ Vector<String> columnNames = new Vector<String>();
+ columnNames.add("Key");
+ columnNames.add(attrName);
+ return new DefaultTableModel(data, columnNames);
+ } else
+ return new DefaultTableModel(data, getDefaultColumnNames(maxColumn,
+ sourceURL));
+ }
+
+ private TableModel parseExcel(final URL sourceURL, int size,
+ TableCellRenderer renderer, final Sheet sheet, int startLine)
+ throws IOException {
+
+ if(size == -1)
+ size = Integer.MAX_VALUE;
+
+
+ int maxCol = 0;
+ final Vector<Object> data = new Vector<Object>();
+
+ int rowCount = 0;
+ Row row;
+
+ while (((row = sheet.getRow(rowCount)) != null) && (rowCount < size)) {
+ if (rowCount >= startLine) {
+ Vector<Object> rowVector = new Vector<Object>();
+
+ if (maxCol < row.getPhysicalNumberOfCells()) {
+ maxCol = row.getPhysicalNumberOfCells();
+ }
+
+ for (short j = 0; j < maxCol; j++) {
+ Cell cell = row.getCell(j);
+
+ if (cell == null) {
+ rowVector.add(null);
+ } else if (cell.getCellType() == Cell.CELL_TYPE_STRING) {
+ rowVector
+ .add(cell.getRichStringCellValue().getString());
+ } else if (cell.getCellType() == Cell.CELL_TYPE_NUMERIC) {
+ final Double dblValue = cell.getNumericCellValue();
+ final Integer intValue = dblValue.intValue();
+
+ if (intValue.doubleValue() == dblValue) {
+ rowVector.add(intValue.toString());
+ } else {
+ rowVector.add(dblValue.toString());
+ }
+ } else if (cell.getCellType() == Cell.CELL_TYPE_BOOLEAN) {
+ rowVector.add(Boolean.toString(cell
+ .getBooleanCellValue()));
+ } else if ((cell.getCellType() == Cell.CELL_TYPE_BLANK)
+ || (cell.getCellType() == Cell.CELL_TYPE_ERROR)) {
+ rowVector.add(null);
+ } else {
+ rowVector.add(null);
+ }
+ }
+
+ data.add(rowVector);
+ }
+
+ rowCount++;
+ }
+
+ return new DefaultTableModel(data, this.getDefaultColumnNames(maxCol,
+ sourceURL));
+ }
+
+ /**
+ * Not yet implemented.
+ * <p>
+ * </p>
+ *
+ * @param targetColumn
+ * @return
+ */
+ public int checkKeyMatch(final int targetColumn) {
+ final DefaultListModel listModel = (DefaultListModel) keyPreviewList.getModel();
+ final Object[] data = listModel.toArray();
+
+ final List<Object> fileKeyList = Arrays.asList(data);
+
+ int matched = 0;
+
+ final TableModel curModel = getPreviewTable().getModel();
+
+ try {
+ curModel.getValueAt(0, targetColumn);
+ } catch (ArrayIndexOutOfBoundsException e) {
+ return 0;
+ }
+
+ final int rowCount = curModel.getRowCount();
+ for (int i = 0; i < rowCount; i++) {
+ final Object val = curModel.getValueAt(i, targetColumn);
+ if (val != null && fileKeyList.contains(val))
+ matched++;
+ }
+ return matched;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param column
+ * DOCUMENT ME!
+ * @param flag
+ * DOCUMENT ME!
+ */
+ public void setAliasColumn(int column, boolean flag) {
+ AttributePreviewTableCellRenderer rend = (AttributePreviewTableCellRenderer) getPreviewTable()
+ .getCellRenderer(0, column);
+ rend.setAliasFlag(column, flag);
+ // rend.setImportFlag(column, !rend.getImportFlag(column));
+ getPreviewTable().getTableHeader().resizeAndRepaint();
+ getPreviewTable().repaint();
+ }
+
+ private final class TableHeaderListener implements MouseListener {
+ public void mouseClicked(MouseEvent e) {
+ final JTable targetTable = getPreviewTable();
+ final String selectedTabName = getSelectedSheetName();
+ final Byte[] dataTypes = dataTypeMap.get(selectedTabName);
+ final Byte[] listDataTypes = listDataTypeMap.get(selectedTabName);
+
+ final int column = targetTable.getColumnModel().getColumnIndexAtX(
+ e.getX());
+
+ if (SwingUtilities.isRightMouseButton(e)) {
+ /*
+ * Right click: This action pops up an dialog to edit the
+ * attribute type and name.
+ */
+ AttributeTypeDialog atd = new AttributeTypeDialog(Cytoscape
+ .getDesktop(), true, targetTable.getColumnModel()
+ .getColumn(column).getHeaderValue().toString(),
+ dataTypes[column], column, listDelimiter);
+
+ atd.setLocationRelativeTo(targetTable.getParent());
+ atd.setVisible(true);
+
+ final String name = atd.getName();
+ final byte newType = atd.getAttType();
+ final byte newListType = atd.getListDataType();
+
+ if (name != null) {
+ targetTable.getColumnModel().getColumn(column)
+ .setHeaderValue(name);
+ targetTable.getTableHeader().resizeAndRepaint();
+
+ if (newType == CyAttributes.TYPE_SIMPLE_LIST) {
+ // listDelimiter = atd.getListDelimiterType();
+ listDelimiter = atd.getListDelimiterType();
+
+ changes.firePropertyChange(
+ ImportTextTableDialog.LIST_DELIMITER_CHANGED,
+ null, atd.getListDelimiterType());
+
+ listDataTypes[column] = newListType;
+ changes.firePropertyChange(
+ ImportTextTableDialog.LIST_DATA_TYPE_CHANGED,
+ null, listDataTypes);
+ listDataTypeMap.put(selectedTabName, listDataTypes);
+ }
+
+ final Vector keyValPair = new Vector();
+ keyValPair.add(column);
+ keyValPair.add(newType);
+ changes.firePropertyChange(
+ ImportTextTableDialog.ATTR_DATA_TYPE_CHANGED, null,
+ keyValPair);
+
+ final Vector colNamePair = new Vector();
+ colNamePair.add(column);
+ colNamePair.add(name);
+ changes.firePropertyChange(
+ ImportTextTableDialog.ATTRIBUTE_NAME_CHANGED, null,
+ colNamePair);
+
+ dataTypes[column] = newType;
+
+ targetTable.getTableHeader().setDefaultRenderer(
+ new HeaderRenderer(targetTable.getTableHeader()
+ .getDefaultRenderer(), dataTypes));
+ dataTypeMap.put(selectedTabName, dataTypes);
+ }
+ } else if (SwingUtilities.isLeftMouseButton(e)
+ && (e.getClickCount() == 1)) {
+ final AttributePreviewTableCellRenderer rend = (AttributePreviewTableCellRenderer) targetTable
+ .getCellRenderer(0, column);
+ rend.setImportFlag(column, !rend.getImportFlag(column));
+ targetTable.getTableHeader().resizeAndRepaint();
+ targetTable.repaint();
+ }
+ }
+
+ public void mouseEntered(MouseEvent arg0) {
+ }
+
+ public void mouseExited(MouseEvent arg0) {
+ }
+
+ public void mousePressed(MouseEvent arg0) {
+ }
+
+ public void mouseReleased(MouseEvent arg0) {
+ }
+ }
+}
+
+class KeyAttributeListRenderer extends JLabel implements ListCellRenderer {
+ private static final Font KEY_LIST_FONT = new Font("Sans-Serif", Font.BOLD,
+ 16);
+ private static final Color FONT_COLOR = Color.BLACK;
+
+ /**
+ * Creates a new KeyAttributeListRenderer object.
+ */
+ public KeyAttributeListRenderer() {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param list
+ * DOCUMENT ME!
+ * @param value
+ * DOCUMENT ME!
+ * @param index
+ * DOCUMENT ME!
+ * @param isSelected
+ * DOCUMENT ME!
+ * @param cellHasFocus
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Component getListCellRendererComponent(JList list, Object value,
+ int index, boolean isSelected, boolean cellHasFocus) {
+ setFont(KEY_LIST_FONT);
+ setForeground(FONT_COLOR);
+ setText(value.toString());
+
+ this.setOpaque(false);
+
+ return this;
+ }
+}
+
+class CentredBackgroundBorder implements Border {
+ private final BufferedImage image;
+
+ /**
+ * Creates a new CentredBackgroundBorder object.
+ *
+ * @param image
+ * DOCUMENT ME!
+ */
+ public CentredBackgroundBorder(BufferedImage image) {
+ this.image = image;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param c
+ * DOCUMENT ME!
+ * @param g
+ * DOCUMENT ME!
+ * @param x
+ * DOCUMENT ME!
+ * @param y
+ * DOCUMENT ME!
+ * @param width
+ * DOCUMENT ME!
+ * @param height
+ * DOCUMENT ME!
+ */
+ public void paintBorder(Component c, Graphics g, int x, int y, int width,
+ int height) {
+ x += ((width - image.getWidth()) / 2);
+ y += ((height - image.getHeight()) / 2);
+ ((Graphics2D) g).drawRenderedImage(image, AffineTransform
+ .getTranslateInstance(x, y));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param c
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Insets getBorderInsets(Component c) {
+ return new Insets(0, 0, 0, 0);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isBorderOpaque() {
+ return true;
+ }
+}
diff --git a/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/ui/SelectFormatPanel.java b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/ui/SelectFormatPanel.java
new file mode 100644
index 0000000..456e708
--- /dev/null
+++ b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/ui/SelectFormatPanel.java
@@ -0,0 +1,200 @@
+/*
+ * NewBioDataServerPanel.java
+ *
+ * Created on 2006/04/04, 11:47
+ */
+package edu.ucsd.bioeng.coreplugin.tableImport.ui;
+
+import cytoscape.util.OpenBrowser;
+
+import java.io.IOException;
+
+import java.net.MalformedURLException;
+import java.net.URL;
+
+import javax.swing.ImageIcon;
+import javax.swing.event.HyperlinkEvent;
+
+
+/**
+ * Start panel
+ *
+ * @author kono
+ */
+public class SelectFormatPanel extends javax.swing.JPanel {
+ // HTML document for the message box.
+ private static final String HTML_RESOURCE_FILE = "/cytoscape/resources/Gene_Ontology_Wizard.html";
+
+ /** Creates new form NewBioDataServerPanel */
+ public SelectFormatPanel() {
+ initComponents();
+ }
+
+ /**
+ * This method is called from within the constructor to initialize the form.
+ * WARNING: Do NOT modify this code. The content of this method is always
+ * regenerated by the Form Editor.
+ */
+
+ // <editor-fold defaultstate="collapsed" desc=" Generated Code ">
+ private void initComponents() {
+ fileTypeButtonGroup = new javax.swing.ButtonGroup();
+ titleLabel = new javax.swing.JLabel();
+ jSeparator1 = new javax.swing.JSeparator();
+ htmlScrollPane = new javax.swing.JScrollPane();
+ messageLabel = new javax.swing.JLabel();
+ bdsRadioButton = new javax.swing.JRadioButton();
+ oboRadioButton = new javax.swing.JRadioButton();
+
+ titleLabel.setFont(new java.awt.Font("Dialog", 1, 14));
+ titleLabel.setText("Welcome to Gene Ontology Wizard");
+
+ try {
+ URL descriptionDoc = getClass().getResource(HTML_RESOURCE_FILE);
+
+ descriptionEditorPane = new javax.swing.JEditorPane(descriptionDoc);
+ } catch (MalformedURLException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ } catch (IOException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+
+ descriptionEditorPane.setEditable(false);
+ descriptionEditorPane.addHyperlinkListener(new javax.swing.event.HyperlinkListener() {
+ public void hyperlinkUpdate(javax.swing.event.HyperlinkEvent evt) {
+ descriptionEditorPaneHyperlinkUpdate(evt);
+ }
+ });
+
+ htmlScrollPane.setHorizontalScrollBarPolicy(javax.swing.JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
+ htmlScrollPane.setViewportView(descriptionEditorPane);
+
+ messageLabel.setText("Which file format do you want to load?");
+
+ fileTypeButtonGroup.add(bdsRadioButton);
+ bdsRadioButton.setSelected(false);
+ bdsRadioButton.setText("Cytoscape BioDataServer (.anno and .onto)");
+ bdsRadioButton.setActionCommand("annoAndOnto");
+ bdsRadioButton.setBorder(javax.swing.BorderFactory.createEmptyBorder(0, 0, 0, 0));
+ bdsRadioButton.setMargin(new java.awt.Insets(0, 0, 0, 0));
+
+ fileTypeButtonGroup.add(oboRadioButton);
+ oboRadioButton.setText("Gene Ontology (.obo and gene_association)");
+ oboRadioButton.setActionCommand("oboAndGa");
+ oboRadioButton.setBorder(javax.swing.BorderFactory.createEmptyBorder(0, 0, 0, 0));
+ oboRadioButton.setMargin(new java.awt.Insets(0, 0, 0, 0));
+ oboRadioButton.setSelected(true);
+
+ org.jdesktop.layout.GroupLayout layout = new org.jdesktop.layout.GroupLayout(this);
+ this.setLayout(layout);
+ layout.setHorizontalGroup(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(layout.createSequentialGroup()
+ .add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.TRAILING)
+ .add(org.jdesktop.layout.GroupLayout.LEADING,
+ layout.createSequentialGroup()
+ .addContainerGap()
+ .add(htmlScrollPane,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 328, Short.MAX_VALUE))
+ .add(org.jdesktop.layout.GroupLayout.LEADING,
+ layout.createSequentialGroup()
+ .addContainerGap()
+ .add(titleLabel,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ 254,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE))
+ .add(org.jdesktop.layout.GroupLayout.LEADING,
+ layout.createSequentialGroup()
+ .add(65, 65, 65)
+ .add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.TRAILING)
+ .add(oboRadioButton)
+ .add(bdsRadioButton)))
+ .add(org.jdesktop.layout.GroupLayout.LEADING,
+ layout.createSequentialGroup()
+ .addContainerGap()
+ .add(jSeparator1,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ 328,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE))
+ .add(org.jdesktop.layout.GroupLayout.LEADING,
+ layout.createSequentialGroup()
+ .addContainerGap()
+ .add(messageLabel)))
+ .addContainerGap()));
+
+ layout.linkSize(new java.awt.Component[] { bdsRadioButton, oboRadioButton },
+ org.jdesktop.layout.GroupLayout.HORIZONTAL);
+
+ layout.setVerticalGroup(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(layout.createSequentialGroup().addContainerGap()
+ .add(titleLabel).add(8, 8, 8)
+ .add(jSeparator1,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ 14,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(messageLabel).add(21, 21, 21)
+ .add(bdsRadioButton,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ 16,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(oboRadioButton).add(19, 19, 19)
+ .add(htmlScrollPane,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 182, Short.MAX_VALUE).addContainerGap()));
+ } // </editor-fold>
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getFileFormatRadioButtonSelected() {
+ return fileTypeButtonGroup.getSelection().getActionCommand();
+ }
+
+ private void descriptionEditorPaneHyperlinkUpdate(javax.swing.event.HyperlinkEvent evt) {
+ // TODO add your handling code here:
+ if (evt.getEventType() == HyperlinkEvent.EventType.ACTIVATED) {
+ OpenBrowser.openURL(evt.getURL().toString());
+ }
+ }
+
+ private ImageIcon getImageIcon() {
+ // return new ImageIcon((URL)getResource("clouds.jpg"));
+ return null;
+ }
+
+ private Object getResource(String key) {
+ URL url = null;
+ String name = key;
+
+ if (name != null) {
+ try {
+ Class c = Class.forName("cytoscape.util.swing.BioDataServerWizard");
+ url = c.getResource(name);
+ } catch (ClassNotFoundException cnfe) {
+ System.err.println("Unable to find Parent class");
+ }
+
+ return url;
+ } else
+
+ return null;
+ }
+
+ // Variables declaration - do not modify
+ private javax.swing.ButtonGroup fileTypeButtonGroup;
+ private javax.swing.JEditorPane descriptionEditorPane;
+ private javax.swing.JLabel titleLabel;
+ private javax.swing.JLabel messageLabel;
+ private javax.swing.JRadioButton bdsRadioButton;
+ private javax.swing.JRadioButton oboRadioButton;
+ private javax.swing.JScrollPane htmlScrollPane;
+ private javax.swing.JSeparator jSeparator1;
+
+ // End of variables declaration
+}
diff --git a/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/ui/SpeciesPanel.java b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/ui/SpeciesPanel.java
new file mode 100644
index 0000000..cdf5800
--- /dev/null
+++ b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/ui/SpeciesPanel.java
@@ -0,0 +1,207 @@
+/*
+ * SpeciesPanel.java
+ *
+ * Created on 2006/04/13, 16:08
+ */
+package edu.ucsd.bioeng.coreplugin.tableImport.ui;
+
+import cytoscape.CytoscapeInit;
+import cytoscape.logger.CyLogger;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStreamReader;
+
+import java.net.URL;
+
+import java.util.StringTokenizer;
+
+import javax.swing.JPanel;
+
+
+/**
+ *
+ * @author kono
+ */
+public class SpeciesPanel extends JPanel {
+ // Resource Location
+ private static final String TAXON_RESOURCE_FILE = "/cytoscape/resources/tax_report.txt";
+ private String currentSpeciesName;
+ private CyLogger logger = CyLogger.getLogger(SpeciesPanel.class);
+
+ /** Creates new form SpeciesPanel */
+ public SpeciesPanel() {
+ currentSpeciesName = CytoscapeInit.getProperties().getProperty("defaultSpeciesName");
+ initComponents();
+ }
+
+ /**
+ * This method is called from within the constructor to initialize the form.
+ * WARNING: Do NOT modify this code. The content of this method is always
+ * regenerated by the Form Editor.
+ */
+
+ // <editor-fold defaultstate="collapsed" desc=" Generated Code ">
+ private void initComponents() {
+ jLabel1 = new javax.swing.JLabel();
+ jSeparator1 = new javax.swing.JSeparator();
+ overwriteCheckBox = new javax.swing.JCheckBox();
+ overwriteComboBox = new javax.swing.JComboBox();
+ messageScrollPane = new javax.swing.JScrollPane();
+ messageEditorPane = new javax.swing.JEditorPane();
+
+ setTaxonomyTable();
+ overwriteComboBox.setEditable(false);
+ overwriteComboBox.setEnabled(false);
+ overwriteComboBox.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ overwriteComboBoxActionPerformed(evt);
+ }
+ });
+
+ jLabel1.setFont(new java.awt.Font("Dialog", 1, 14));
+ jLabel1.setText("Default Species Name");
+
+ overwriteCheckBox.setFont(new java.awt.Font("Dialog", 1, 10));
+ overwriteCheckBox.setText("Overwrite default species name with:");
+ overwriteCheckBox.setBorder(javax.swing.BorderFactory.createEmptyBorder(0, 0, 0, 0));
+ overwriteCheckBox.setMargin(new java.awt.Insets(0, 0, 0, 0));
+ overwriteCheckBox.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ overwriteCheckBoxActionPerformed(evt);
+ }
+ });
+
+ messageScrollPane.setHorizontalScrollBarPolicy(javax.swing.JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
+ messageEditorPane.setEditable(false);
+ messageEditorPane.setContentType("text/html");
+ messageEditorPane.setText("<html><body><strong><u>Note</u></strong><br>"
+ + "The property <strong><i>defaultSpeciesName</i></strong>"
+ + " will be used <br>only when a node does not have an attribute <strong><i>species</i></strong>.<br><br>"
+ + "If you select a species name from this list, the value<br>"
+ + "will be used as the <strong><i>defaultSpeciesname</i></strong>."
+ + "</body></html>");
+
+ messageScrollPane.setViewportView(messageEditorPane);
+
+ // Layout
+ org.jdesktop.layout.GroupLayout layout = new org.jdesktop.layout.GroupLayout(this);
+ this.setLayout(layout);
+ layout.setHorizontalGroup(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(layout.createSequentialGroup().addContainerGap()
+ .add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(layout.createSequentialGroup()
+ .add(overwriteCheckBox,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 338, Short.MAX_VALUE)
+ .add(36, 36, 36))
+ .add(org.jdesktop.layout.GroupLayout.TRAILING,
+ layout.createSequentialGroup()
+ .add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.TRAILING)
+ .add(org.jdesktop.layout.GroupLayout.LEADING,
+ jSeparator1,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 362,
+ Short.MAX_VALUE)
+ .add(org.jdesktop.layout.GroupLayout.LEADING,
+ overwriteComboBox,
+ 0, 362,
+ Short.MAX_VALUE)
+ .add(org.jdesktop.layout.GroupLayout.LEADING,
+ messageScrollPane,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 362,
+ Short.MAX_VALUE)
+ .add(jLabel1,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 362,
+ Short.MAX_VALUE))
+ .addContainerGap()))));
+ layout.setVerticalGroup(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(layout.createSequentialGroup().addContainerGap()
+ .add(jLabel1)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(jSeparator1,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ 10,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(overwriteCheckBox,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ 13,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(overwriteComboBox,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ 25,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(messageScrollPane,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 103, Short.MAX_VALUE).addContainerGap()));
+ } // </editor-fold>
+
+ private void overwriteCheckBoxActionPerformed(java.awt.event.ActionEvent evt) {
+ // TODO add your handling code here:
+ if (overwriteComboBox.isEnabled() == false) {
+ overwriteComboBox.setEnabled(true);
+ CytoscapeInit.getProperties()
+ .setProperty("defaultSpeciesName",
+ (String) overwriteComboBox.getSelectedItem());
+ } else {
+ overwriteComboBox.setEnabled(false);
+ CytoscapeInit.getProperties().setProperty("defaultSpeciesName", currentSpeciesName);
+ }
+ }
+
+ private void overwriteComboBoxActionPerformed(java.awt.event.ActionEvent evt) {
+ String species = (String) overwriteComboBox.getSelectedItem();
+ CytoscapeInit.getProperties().setProperty("defaultSpeciesName", species);
+ }
+
+ private void setTaxonomyTable() {
+ BufferedReader spListReader = null;
+
+ try {
+ URL taxURL = getClass().getResource(TAXON_RESOURCE_FILE);
+ spListReader = new BufferedReader(new InputStreamReader(taxURL.openStream()));
+
+ logger.debug("Taxonomy table found in jar file...");
+ } catch (IOException e) {
+ logger.warn("I/O error while creating taxonomy table reader", e);
+ }
+
+ try {
+ setSpList(spListReader);
+ } catch (IOException e) {
+ // TODO Auto-generated catch block
+ logger.warn("I/O error while reading taxonomy table", e);
+ }
+ }
+
+ private void setSpList(final BufferedReader rd) throws IOException {
+ String curLine = null;
+ String name1 = null;
+
+ // remove the first line, which is a title
+ curLine = rd.readLine();
+
+ while ((curLine = rd.readLine()) != null) {
+ StringTokenizer st = new StringTokenizer(curLine, "|");
+ st.nextToken();
+ name1 = st.nextToken().trim();
+
+ overwriteComboBox.addItem(name1);
+ }
+ }
+
+ // Variables declaration - do not modify
+ private javax.swing.JComboBox overwriteComboBox;
+ private javax.swing.JLabel jLabel1;
+ private javax.swing.JSeparator jSeparator1;
+ private javax.swing.JCheckBox overwriteCheckBox;
+ private javax.swing.JEditorPane messageEditorPane;
+ private javax.swing.JScrollPane messageScrollPane;
+
+ // End of variables declaration
+}
diff --git a/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/ui/theme/ImportDialogColorTheme.java b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/ui/theme/ImportDialogColorTheme.java
new file mode 100644
index 0000000..6097085
--- /dev/null
+++ b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/ui/theme/ImportDialogColorTheme.java
@@ -0,0 +1,81 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package edu.ucsd.bioeng.coreplugin.tableImport.ui.theme;
+
+import java.awt.Color;
+
+/**
+ * Color theme for Import Dialogs.<br>
+ *
+ * @since Cytoscape 2.4
+ * @version 1.0
+ * @author kono
+ *
+ */
+public enum ImportDialogColorTheme {
+ LABEL_COLOR(Color.black),
+ KEY_ATTR_COLOR(Color.red),
+ PRIMARY_KEY_COLOR(new Color(51, 51, 255)),
+ ONTOLOGY_COLOR(new Color(0, 255, 255)),
+ ALIAS_COLOR(new Color(51, 204, 0)),
+ SPECIES_COLOR(new Color(182, 36, 212)),
+ ATTRIBUTE_NAME_COLOR(new Color(102, 102, 255)),
+ NOT_SELECTED_COL_COLOR(new Color(240, 240, 240)),
+ SELECTED_COLOR(Color.BLACK),
+ UNSELECTED_COLOR(Color.GRAY),
+
+ // HEADER_BACKGROUND_COLOR(new Color(165, 200, 254)),
+ HEADER_BACKGROUND_COLOR(Color.WHITE),
+ HEADER_UNSELECTED_BACKGROUND_COLOR(new Color(240, 240, 240)), NOT_LOADED_COLOR(Color.RED),
+ LOADED_COLOR(Color.GREEN),SOURCE_COLOR(new Color(204, 0, 204)),
+ INTERACTION_COLOR(new Color(255, 0, 51)),TARGET_COLOR(new Color(255, 102, 0)),
+ EDGE_ATTR_COLOR(Color.BLUE);
+ private Color color;
+
+ private ImportDialogColorTheme(Color color) {
+ this.color = color;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Color getColor() {
+ return color;
+ }
+}
diff --git a/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/ui/theme/ImportDialogFontTheme.java b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/ui/theme/ImportDialogFontTheme.java
new file mode 100644
index 0000000..a4a49be
--- /dev/null
+++ b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/ui/theme/ImportDialogFontTheme.java
@@ -0,0 +1,65 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package edu.ucsd.bioeng.coreplugin.tableImport.ui.theme;
+
+import java.awt.Font;
+public enum ImportDialogFontTheme {
+ TITLE_FONT(new Font("Sans-serif", Font.BOLD, 18)),
+ SELECTED_COL_FONT(new Font("Sans-serif", Font.BOLD, 14)),
+ SELECTED_FONT(new Font("Sans-serif", Font.BOLD, 14)),
+ UNSELECTED_FONT(new Font("Sans-serif", Font.PLAIN, 14)),
+ KEY_FONT(new Font("Sans-Serif", Font.BOLD, 14)),
+ LABEL_FONT(new Font("Sans-serif", Font.BOLD, 14)),
+ LABEL_ITALIC_FONT(new Font("Sans-serif", 3, 14)),
+ ITEM_FONT(new Font("Sans-serif", Font.BOLD, 12)),
+ ITEM_FONT_LARGE(new Font("Sans-serif", Font.BOLD, 14));
+
+ private Font font;
+
+ private ImportDialogFontTheme(Font font) {
+ this.font = font;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Font getFont() {
+ return font;
+ }
+}
diff --git a/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/ui/theme/ImportDialogIconSets.java b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/ui/theme/ImportDialogIconSets.java
new file mode 100644
index 0000000..c68442f
--- /dev/null
+++ b/coreplugins/TableImport/src/main/java/edu/ucsd/bioeng/coreplugin/tableImport/ui/theme/ImportDialogIconSets.java
@@ -0,0 +1,87 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package edu.ucsd.bioeng.coreplugin.tableImport.ui.theme;
+
+import edu.ucsd.bioeng.coreplugin.tableImport.TableImportPlugin;
+
+import javax.swing.ImageIcon;
+
+/**
+ * Iconset for Import Dialog GUI.<br>
+ *
+ * <p>
+ * By sharing these enums among GUIs, we can define Theme for the dialog.
+ * </p>
+ *
+ * @author kono
+ *
+ */
+public enum ImportDialogIconSets {
+ STRING_ICON("images/ximian/stock_font-16.png"),
+ INTEGER_ICON("images/ximian/stock_sort-row-ascending-16.png"),
+ FLOAT_ICON("images/ximian/stock_format-scientific-16.png"),
+ INT_ICON("images/ximian/stock_sort-row-ascending-16.png"),
+ LIST_ICON("images/ximian/stock_navigator-list-box-toggle-16.png"),
+ BOOLEAN_ICON("images/ximian/stock_form-radio-16.png"),
+ ID_ICON("images/ximian/stock_3d-light-on-16.png"),
+ INTERACTION_ICON("images/ximian/stock_interaction.png"),
+ SPREADSHEET_ICON_LARGE("images/ximian/stock_new-spreadsheet-48.png"),
+ REMOTE_SOURCE_ICON("images/ximian/stock_internet-16.png"),
+ REMOTE_SOURCE_ICON_LARGE("images/ximian/stock_internet-32.png"),
+ LOCAL_SOURCE_ICON("images/ximian/stock_data-sources-modified-16.png"),
+ SPREADSHEET_ICON("images/ximian/stock_new-spreadsheet.png"),
+ TEXT_FILE_ICON("images/ximian/stock_new-text-32.png"),
+ RIGHT_ARROW_ICON("images/ximian/stock_right-16.png"),
+ CAUTION_ICON("images/ximian/stock_dialog-warning-32.png"),
+ CHECKED_ICON("images/ximian/stock_3d-apply-16.png"),
+ UNCHECKED_ICON("images/ximian/stock_close-16.png");
+
+ private String resourceLoc;
+
+ private ImportDialogIconSets(String resourceLocation) {
+ this.resourceLoc = resourceLocation;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public ImageIcon getIcon() {
+ return new ImageIcon(getClass().getClassLoader().getResource(resourceLoc));
+ }
+}
diff --git a/coreplugins/TableImport/src/main/resources/edu/ucsd/bioeng/coreplugin/tableImport/plugin.props b/coreplugins/TableImport/src/main/resources/edu/ucsd/bioeng/coreplugin/tableImport/plugin.props
new file mode 100644
index 0000000..1ed5d05
--- /dev/null
+++ b/coreplugins/TableImport/src/main/resources/edu/ucsd/bioeng/coreplugin/tableImport/plugin.props
@@ -0,0 +1,30 @@
+# This props file would be filled out and included in the plugin jar file. This props file will be used
+# to put information into the Plugin Manager about the plugin
+
+# -- The following properties are REQUIRED -- #
+
+# The plugin name that will be displayed to users
+pluginName=Table Import
+
+# Description used to give users information about the plugin such as what it does.
+# Html tags are encouraged for formatting purposes.
+pluginDescription=Provides the ability to import network and attribute files from formatted text and Excel files (.xls and .xlsx).
+
+# Plugin version number, this must be two numbers separated by a decimlal. Ex. 0.2, 14.03
+pluginVersion=0.7
+
+# Compatible Cytoscape version
+cytoscapeVersion=2.5,2.6,2.7,2.8
+
+# Category, use one of the categories listed on the website or create your own
+pluginCategory=Core
+
+
+# List of authors. Note each author and institution pair are separated by a : (colon)
+# each additional author institution pair must be separated from other pairs bye a ; (semicolon)
+pluginAuthorsIntsitutions=Keiichiro Ono:UCSD Department of Medicine
+
+# -- The following properties should be set ONLY BY CORE PLUGINS -- #
+downloadURL=http://cytoscape.org/plugins/plugins.xml
+uniqueID=16
+
diff --git a/coreplugins/TableImport/src/main/resources/images/icon100.png b/coreplugins/TableImport/src/main/resources/images/icon100.png
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diff --git a/coreplugins/TableImport/src/main/resources/images/icon48.png b/coreplugins/TableImport/src/main/resources/images/icon48.png
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index 0000000..b876361
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diff --git a/coreplugins/TableImport/src/main/resources/images/microarrayIcon.png b/coreplugins/TableImport/src/main/resources/images/microarrayIcon.png
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index 0000000..2c2ae9b
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diff --git a/coreplugins/TableImport/src/main/resources/images/ximian/data_sources.png b/coreplugins/TableImport/src/main/resources/images/ximian/data_sources.png
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index 0000000..818f339
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index 0000000..acfe2cd
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diff --git a/coreplugins/TableImport/src/main/resources/images/ximian/net2.png b/coreplugins/TableImport/src/main/resources/images/ximian/net2.png
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index 0000000..64b554b
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diff --git a/coreplugins/TableImport/src/main/resources/images/ximian/network.png b/coreplugins/TableImport/src/main/resources/images/ximian/network.png
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index 0000000..a65ad3d
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diff --git a/coreplugins/TableImport/src/main/resources/images/ximian/stock_3d-apply-16.png b/coreplugins/TableImport/src/main/resources/images/ximian/stock_3d-apply-16.png
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diff --git a/coreplugins/TableImport/src/main/resources/images/ximian/stock_3d-light-16.png b/coreplugins/TableImport/src/main/resources/images/ximian/stock_3d-light-16.png
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diff --git a/coreplugins/TableImport/src/main/resources/images/ximian/stock_3d-light-on-16.png b/coreplugins/TableImport/src/main/resources/images/ximian/stock_3d-light-on-16.png
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diff --git a/coreplugins/TableImport/src/main/resources/images/ximian/stock_about-16.png b/coreplugins/TableImport/src/main/resources/images/ximian/stock_about-16.png
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diff --git a/coreplugins/TableImport/src/main/resources/images/ximian/stock_close-16.png b/coreplugins/TableImport/src/main/resources/images/ximian/stock_close-16.png
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diff --git a/coreplugins/TableImport/src/main/resources/images/ximian/stock_data-sources-modified-16.png b/coreplugins/TableImport/src/main/resources/images/ximian/stock_data-sources-modified-16.png
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diff --git a/coreplugins/TableImport/src/main/resources/images/ximian/stock_dialog-info-32.png b/coreplugins/TableImport/src/main/resources/images/ximian/stock_dialog-info-32.png
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diff --git a/coreplugins/TableImport/src/main/resources/images/ximian/stock_dialog-warning-32.png b/coreplugins/TableImport/src/main/resources/images/ximian/stock_dialog-warning-32.png
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diff --git a/coreplugins/TableImport/src/main/resources/images/ximian/stock_font-16.png b/coreplugins/TableImport/src/main/resources/images/ximian/stock_font-16.png
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diff --git a/coreplugins/TableImport/src/main/resources/images/ximian/stock_form-checkbox-16.png b/coreplugins/TableImport/src/main/resources/images/ximian/stock_form-checkbox-16.png
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diff --git a/coreplugins/TableImport/src/main/resources/images/ximian/stock_form-radio-16.png b/coreplugins/TableImport/src/main/resources/images/ximian/stock_form-radio-16.png
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diff --git a/coreplugins/TableImport/src/main/resources/images/ximian/stock_format-scientific-16.png b/coreplugins/TableImport/src/main/resources/images/ximian/stock_format-scientific-16.png
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diff --git a/coreplugins/TableImport/src/main/resources/images/ximian/stock_interaction.png b/coreplugins/TableImport/src/main/resources/images/ximian/stock_interaction.png
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diff --git a/coreplugins/TableImport/src/main/resources/images/ximian/stock_internet-16.png b/coreplugins/TableImport/src/main/resources/images/ximian/stock_internet-16.png
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diff --git a/coreplugins/TableImport/src/main/resources/images/ximian/stock_navigator-list-box-toggle-16.png b/coreplugins/TableImport/src/main/resources/images/ximian/stock_navigator-list-box-toggle-16.png
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diff --git a/coreplugins/TableImport/src/main/resources/images/ximian/stock_new-spreadsheet-16.png b/coreplugins/TableImport/src/main/resources/images/ximian/stock_new-spreadsheet-16.png
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diff --git a/coreplugins/TableImport/src/main/resources/images/ximian/stock_new-spreadsheet-48.png b/coreplugins/TableImport/src/main/resources/images/ximian/stock_new-spreadsheet-48.png
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diff --git a/coreplugins/TableImport/src/main/resources/images/ximian/stock_new-spreadsheet.png b/coreplugins/TableImport/src/main/resources/images/ximian/stock_new-spreadsheet.png
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diff --git a/coreplugins/TableImport/src/main/resources/images/ximian/stock_new-text-32.png b/coreplugins/TableImport/src/main/resources/images/ximian/stock_new-text-32.png
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diff --git a/coreplugins/TableImport/src/main/resources/images/ximian/stock_right-16.png b/coreplugins/TableImport/src/main/resources/images/ximian/stock_right-16.png
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index 0000000..42e783f
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diff --git a/coreplugins/TableImport/src/main/resources/images/ximian/stock_sort-row-ascending-16.png b/coreplugins/TableImport/src/main/resources/images/ximian/stock_sort-row-ascending-16.png
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index 0000000..3f4fb3a
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diff --git a/coreplugins/TableImport/src/main/resources/images/ximian/stock_toggle-info-16.png b/coreplugins/TableImport/src/main/resources/images/ximian/stock_toggle-info-16.png
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index 0000000..d548098
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diff --git a/coreplugins/TableImport/src/main/resources/resources/ontology_index.xml b/coreplugins/TableImport/src/main/resources/resources/ontology_index.xml
new file mode 100644
index 0000000..3f72109
--- /dev/null
+++ b/coreplugins/TableImport/src/main/resources/resources/ontology_index.xml
@@ -0,0 +1,10807 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<obo_metadata>
+ <time_started unix="1263595503">Fri Jan 15 14:45:03 2010</time_started>
+ <ont id="adult_mouse_anatomy">
+ <source>ftp://ftp.informatics.jax.org/pub/reports/adult_mouse_anatomy.obo</source>
+ <granularity>organismal</granularity>
+ <status>Production and review</status>
+ <subtypes_of>CARO:0000000</subtypes_of>
+ <contact>Anatomy at JAX anatomy informatics.jax.org</contact>
+ <foundry>Yes</foundry>
+ <domain>anatomy</domain>
+ <documentation></documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/mouse/adult_mouse_anatomy.obo</url>
+ <patho_type>canonical</patho_type>
+ <home>Mouse Anatomy Dictionary|http://www.informatics.jax.org/searches/AMA_form.shtml</home>
+ <namespace>MA</namespace>
+ <description>A structured controlled vocabulary of the adult anatomy of the mouse (Mus).</description>
+ <format>obo</format>
+ <title>Mouse adult gross anatomy</title>
+ <relevant_organism>NCBITaxon:10088|Mus</relevant_organism>
+ <download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/mouse/adult_mouse_anatomy.obo</download>
+ <export format="obo_xml" path="obo-all/adult_mouse_anatomy/adult_mouse_anatomy.obo_xml" md5="9c9c8da47433d7df6d25a09ecda3b598" timestamp="1260649507" time_generated="1263595504" time_taken_to_generate="0" size="657971">
+ </export>
+ <export format="obo" path="obo-all/adult_mouse_anatomy/adult_mouse_anatomy.obo" md5="acaf241406512d210e6ca53d2da90c42" timestamp="1263595504" time_generated="1263595504" time_taken_to_generate="0" size="316334">
+ </export>
+ <export format="owl" path="obo-all/adult_mouse_anatomy/adult_mouse_anatomy.owl" md5="c4cb66705eb21798ad76da7829aac890" timestamp="1260649561" time_generated="1263595504" time_taken_to_generate="0" size="1433557">
+ </export>
+ <export format="chadoxml" path="obo-all/adult_mouse_anatomy/adult_mouse_anatomy.chadoxml" md5="9c9110fc243df405a6465ea8941be315" timestamp="1260649573" time_generated="1263595504" time_taken_to_generate="0" size="1791315">
+ </export>
+ <export format="godb_prestore" path="obo-all/adult_mouse_anatomy/adult_mouse_anatomy.godb_prestore" md5="a393467a97046b2f68f34b3e1e460076" timestamp="1260649575" time_generated="1263595504" time_taken_to_generate="0" size="1659514">
+ </export>
+ <export format="rdf" path="obo-all/adult_mouse_anatomy/adult_mouse_anatomy.rdf" md5="c2194797608e1880cfdcc0a8ad7274a5" timestamp="1260649579" time_generated="1263595504" time_taken_to_generate="0" size="911201">
+ </export>
+ <export format="tbl" path="obo-all/adult_mouse_anatomy/adult_mouse_anatomy.tbl" md5="d676b9e13e1fb8336ab0b23e8cd9c8e1" timestamp="1260649581" time_generated="1263595504" time_taken_to_generate="0" size="104351">
+ </export>
+ <export format="prolog" path="obo-all/adult_mouse_anatomy/adult_mouse_anatomy.pro" md5="438e72249db5cee1b91f158066418ff6" timestamp="1263418630" time_generated="1263595504" time_taken_to_generate="0" size="749791">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/adult_mouse_anatomy/adult_mouse_anatomy.validation_report" md5="dd8677e865829f7ee201be5c4625e28f" timestamp="1260649590" time_generated="1263595507" time_taken_to_generate="0" size="2807">
+ </export>
+ <export format="stats" path="obo-all/adult_mouse_anatomy/adult_mouse_anatomy.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1260649592" time_generated="1263595507" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/adult_mouse_anatomy/adult_mouse_anatomy.obo.html" md5="51867f3fa5d3af5b104706f671b1a238" timestamp="1260649592" time_generated="1263595507" time_taken_to_generate="0" size="1911956">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="amphibian_anatomy">
+ <source></source>
+ <granularity>organismal</granularity>
+ <status>Discussion and review</status>
+ <subtypes_of>CARO:0000000</subtypes_of>
+ <contact>AmphiAnat mailing list sbhdbe mst.edu</contact>
+ <foundry>Yes</foundry>
+ <domain>anatomy</domain>
+ <documentation></documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/amphibian/amphibian_anatomy.obo</url>
+ <patho_type>canonical</patho_type>
+ <home>Amphibian Anatomy|http://www.amphibanat.org</home>
+ <namespace>AAO</namespace>
+ <description>A structured controlled vocabulary of the anatomy of Amphibians.</description>
+ <format>obo</format>
+ <title>Amphibian gross anatomy</title>
+ <relevant_organism>NCBITaxon:8292|Amphibia</relevant_organism>
+ <download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/amphibian/amphibian_anatomy.obo</download>
+ <export format="obo_xml" path="obo-all/amphibian_anatomy/amphibian_anatomy.obo_xml" md5="c6d9b255d4a8dd7a25da197a20e85c69" timestamp="1260649596" time_generated="1263595509" time_taken_to_generate="0" size="297452">
+ </export>
+ <export format="obo" path="obo-all/amphibian_anatomy/amphibian_anatomy.obo" md5="a8fa65c7443cfc5e22f82abfd1d33e70" timestamp="1263595509" time_generated="1263595509" time_taken_to_generate="0" size="151792">
+ </export>
+ <export format="owl" path="obo-all/amphibian_anatomy/amphibian_anatomy.owl" md5="c5d734169b731f8939204384969c174b" timestamp="1260649600" time_generated="1263595509" time_taken_to_generate="0" size="677654">
+ </export>
+ <export format="chadoxml" path="obo-all/amphibian_anatomy/amphibian_anatomy.chadoxml" md5="2c8d757f92f338b808a0de3c4cbbd81e" timestamp="1260649601" time_generated="1263595509" time_taken_to_generate="0" size="708142">
+ </export>
+ <export format="godb_prestore" path="obo-all/amphibian_anatomy/amphibian_anatomy.godb_prestore" md5="0795141f3a12d2c2f18225e171438ee2" timestamp="1260649602" time_generated="1263595509" time_taken_to_generate="0" size="602583">
+ </export>
+ <export format="rdf" path="obo-all/amphibian_anatomy/amphibian_anatomy.rdf" md5="8d32047f52e2ff5a4d48a1708ef8f09a" timestamp="1260649603" time_generated="1263595509" time_taken_to_generate="0" size="297086">
+ </export>
+ <export format="tbl" path="obo-all/amphibian_anatomy/amphibian_anatomy.tbl" md5="f1dbfad3b9e380d700f74a79beaba400" timestamp="1260649604" time_generated="1263595509" time_taken_to_generate="0" size="87746">
+ </export>
+ <export format="prolog" path="obo-all/amphibian_anatomy/amphibian_anatomy.pro" md5="d42044b9a10c967cd8606fe53f91d2ec" timestamp="1263427472" time_generated="1263595509" time_taken_to_generate="0" size="288638">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/amphibian_anatomy/amphibian_anatomy.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1260649607" time_generated="1263595510" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" path="obo-all/amphibian_anatomy/amphibian_anatomy.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1260649608" time_generated="1263595510" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/amphibian_anatomy/amphibian_anatomy.obo.html" md5="252bbe2a764a09dfd862395a3df6f55e" timestamp="1260649609" time_generated="1263595510" time_taken_to_generate="0" size="653286">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="amphibian_taxonomy">
+ <source></source>
+ <granularity>organismal</granularity>
+ <status>Discussion and review</status>
+ <subtypes_of>CARO:0000000</subtypes_of>
+ <contact>AmphiAnat mailing list sbhdbe mst.edu</contact>
+ <foundry>Yes</foundry>
+ <domain>anatomy</domain>
+ <documentation></documentation>
+ <url>http://ontology1.srv.mst.edu/sarah/amphibian_taxonomy.obo</url>
+ <home>Amphibian Anatomy|http://www.amphibanat.org</home>
+ <xrefs_to>ncbi_taxonomy</xrefs_to>
+ <namespace>ATO</namespace>
+ <description>A taxonomy of Amphibia</description>
+ <format>obo</format>
+ <title>Amphibian taxonomy</title>
+ <relevant_organism>NCBITaxon:8292|Amphibia</relevant_organism>
+ <download>http://ontology1.srv.mst.edu/sarah/amphibian_taxonomy.obo</download>
+ <export format="obo_xml" path="obo-all/amphibian_taxonomy/amphibian_taxonomy.obo_xml" md5="2e7e8d830410c0d69bbdc093eb830a3f" timestamp="1260649615" time_generated="1263595513" time_taken_to_generate="0" size="1719355">
+ </export>
+ <export format="obo" path="obo-all/amphibian_taxonomy/amphibian_taxonomy.obo" md5="349d73a08eccaebab23b2f77f5c819e6" timestamp="1263595513" time_generated="1263595513" time_taken_to_generate="0" size="1070331">
+ </export>
+ <export format="owl" problem="true">
+ </export>
+ <export format="chadoxml" path="obo-all/amphibian_taxonomy/amphibian_taxonomy.chadoxml" md5="c469fe399b402c3fdda2733dce226fd9" timestamp="1260650051" time_generated="1263595865" time_taken_to_generate="0" size="4470218">
+ </export>
+ <export format="godb_prestore" path="obo-all/amphibian_taxonomy/amphibian_taxonomy.godb_prestore" md5="89231f96d8bfda7cfaac0c960600b390" timestamp="1260650057" time_generated="1263595865" time_taken_to_generate="0" size="4840800">
+ </export>
+ <export format="rdf" path="obo-all/amphibian_taxonomy/amphibian_taxonomy.rdf" md5="0f9131ee8cf4f8204cddc9a581953c69" timestamp="1260650067" time_generated="1263595865" time_taken_to_generate="0" size="2384032">
+ </export>
+ <export format="tbl" path="obo-all/amphibian_taxonomy/amphibian_taxonomy.tbl" md5="26e5cfd7269cf99f2d057a01be9898ac" timestamp="1260650074" time_generated="1263595865" time_taken_to_generate="0" size="343471">
+ </export>
+ <export format="prolog" path="obo-all/amphibian_taxonomy/amphibian_taxonomy.pro" md5="d9fe4da05f44d2e46694c54283e19282" timestamp="1263250284" time_generated="1263595865" time_taken_to_generate="0" size="1983806">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/amphibian_taxonomy/amphibian_taxonomy.validation_report" md5="e5b91f6f2bdc7048f8af623885ea1889" timestamp="1260650093" time_generated="1263595870" time_taken_to_generate="0" size="227">
+ </export>
+ <export format="stats" path="obo-all/amphibian_taxonomy/amphibian_taxonomy.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1260650095" time_generated="1263595870" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/amphibian_taxonomy/amphibian_taxonomy.obo.html" md5="79dbe7b4191e14108044d5d8eaf9f659" timestamp="1260650095" time_generated="1263595870" time_taken_to_generate="0" size="5392629">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="sdiff" path="obo-all/amphibian_taxonomy/amphibian_taxonomy.sdiff" md5="d41d8cd98f00b204e9800998ecf8427e" timestamp="1263595870" time_generated="1263595887" time_taken_to_generate="17" size="0">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="animalhist">
+ <source>http://animaldiversity.ummz.umich.edu/site/about/technology/ADW_ontology_protege.zip/view.html</source>
+ <namespace>ADW</namespace>
+ <status>Inactive</status>
+ <contact>Animal Diversity Web technical staff adw_geeks umich.edu</contact>
+ <description>An ontology for animal life history and natural history characteristics suitable for populations and higher taxonomic entities.</description>
+ <foundry>No</foundry>
+ <format>protege</format>
+ <documentation>ADW Technology|http://animaldiversity.ummz.umich.edu/site/about/technology/index.html</documentation>
+ <url>http://animaldiversity.ummz.umich.edu/site/about/technology/ADW_ontology_protege.zip/view.html</url>
+ <title>Animal natural history and life history</title>
+ <is_obsolete>true</is_obsolete>
+ <home>Animal Diversity Web|http://www.animaldiversity.org</home>
+ <download></download>
+ </ont>
+ <ont id="ascomycete_phenotype">
+ <source></source>
+ <granularity>organismal</granularity>
+ <namespace>APO</namespace>
+ <status>Production and review</status>
+ <contact>SGD curators yeast-curator genome.stanford.edu</contact>
+ <description>A structured controlled vocabulary for the phenotypes of Ascomycete fungi</description>
+ <foundry>Yes</foundry>
+ <domain>phenotype</domain>
+ <format>obo</format>
+ <documentation></documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/ascomycete_phenotype.obo</url>
+ <title>Ascomycete phenotype ontology</title>
+ <relevant_organism>NCBITaxon:4890|Ascomycota</relevant_organism>
+ <home>Saccharomyces Genome Database|http://www.yeastgenome.org/ </home>
+ <download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/ascomycete_phenotype.obo</download>
+ <export format="obo_xml" path="obo-all/ascomycete_phenotype/ascomycete_phenotype.obo_xml" md5="0e53927a8cd53f6f8713e5311a6a8be7" timestamp="1263250294" time_generated="1263595889" time_taken_to_generate="0" size="135784">
+ </export>
+ <export format="obo" path="obo-all/ascomycete_phenotype/ascomycete_phenotype.obo" md5="832996c38db7fa2fad95115d6ed2c6ae" timestamp="1263595889" time_generated="1263595889" time_taken_to_generate="0" size="81867">
+ </export>
+ <export format="owl" path="obo-all/ascomycete_phenotype/ascomycete_phenotype.owl" md5="9838a5956258d1635ede2e4ab2ac2fcd" timestamp="1263250295" time_generated="1263595889" time_taken_to_generate="0" size="311815">
+ </export>
+ <export format="chadoxml" path="obo-all/ascomycete_phenotype/ascomycete_phenotype.chadoxml" md5="df31203fe60ee0d8208e176d6f3d719d" timestamp="1263250296" time_generated="1263595889" time_taken_to_generate="0" size="342118">
+ </export>
+ <export format="godb_prestore" path="obo-all/ascomycete_phenotype/ascomycete_phenotype.godb_prestore" md5="8d4032440b22adae660adb6e437bd96a" timestamp="1263250297" time_generated="1263595889" time_taken_to_generate="0" size="422042">
+ </export>
+ <export format="rdf" path="obo-all/ascomycete_phenotype/ascomycete_phenotype.rdf" md5="874a6cc42569a1a60a37f62cebb8514d" timestamp="1263250298" time_generated="1263595889" time_taken_to_generate="0" size="135605">
+ </export>
+ <export format="tbl" path="obo-all/ascomycete_phenotype/ascomycete_phenotype.tbl" md5="8a8382300e79465a363a8e6694fac932" timestamp="1263250298" time_generated="1263595889" time_taken_to_generate="0" size="30890">
+ </export>
+ <export format="prolog" path="obo-all/ascomycete_phenotype/ascomycete_phenotype.pro" md5="fa3944e0b9310c8b1f2ee32c67f5bc91" timestamp="1263250299" time_generated="1263595889" time_taken_to_generate="0" size="171239">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/ascomycete_phenotype/ascomycete_phenotype.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1263250300" time_generated="1263595890" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" path="obo-all/ascomycete_phenotype/ascomycete_phenotype.stats" md5="7ae7aaf83d188ac8830fad76a4acfeab" timestamp="1263250302" time_generated="1263595890" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/ascomycete_phenotype/ascomycete_phenotype.obo.html" md5="c710e5625b4467264f0db6283773ec15" timestamp="1263250302" time_generated="1263595890" time_taken_to_generate="0" size="444385">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="quality">
+ <source></source>
+ <granularity>all</granularity>
+ <status>Production and review</status>
+ <subtypes_of>bfo:DependentContinuant</subtypes_of>
+ <contact>George Gkoutos obo-phenotype lists.sourceforge.net</contact>
+ <foundry>Yes</foundry>
+ <domain>phenotype</domain>
+ <documentation></documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality.obo</url>
+ <patho_type>all</patho_type>
+ <home>PATO wiki|http://www.bioontology.org/wiki/index.php/PATO:Main_Page</home>
+ <namespace>PATO</namespace>
+ <description>Phenotypic qualities (properties). This ontology can be used in conjunction with other ontologies such as GO or anatomical ontologies to refer to phenotypes. Examples of qualities are red, ectopic, high temperature, fused, small, edematous and arrested.</description>
+ <format>obo</format>
+ <title>Phenotypic quality</title>
+ <relevant_organism>all</relevant_organism>
+ <download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality.obo</download>
+ <export format="obo_xml" path="obo-all/quality/quality.obo_xml" md5="6067c61f07de598c8bbd17d658824bb4" timestamp="1263595893" time_generated="1263595893" time_taken_to_generate="2" size="784855">
+ </export>
+ <export format="obo" path="obo-all/quality/quality.obo" md5="5a7a2cf761bc9e0e8d7f56202ac7b472" timestamp="1263595891" time_generated="1263595893" time_taken_to_generate="0" size="419476">
+ </export>
+ <export format="owl" path="obo-all/quality/quality.owl" md5="2e73a4ac45a409df9ed9b89db68b947b" timestamp="1263595921" time_generated="1263595921" time_taken_to_generate="28" size="1690346">
+ </export>
+ <export format="chadoxml" path="obo-all/quality/quality.chadoxml" md5="b818c2936d4fb825526a32f51755ab22" timestamp="1263595928" time_generated="1263595928" time_taken_to_generate="7" size="1834394">
+ </export>
+ <export format="godb_prestore" path="obo-all/quality/quality.godb_prestore" md5="fd7c387147072d296cbd3551148a11e6" timestamp="1263595931" time_generated="1263595931" time_taken_to_generate="3" size="1887392">
+ </export>
+ <export format="rdf" path="obo-all/quality/quality.rdf" md5="29de51dee0fcd394082c7020192c6732" timestamp="1263595934" time_generated="1263595934" time_taken_to_generate="3" size="775115">
+ </export>
+ <export format="tbl" path="obo-all/quality/quality.tbl" md5="c1ce73ec2343a2a872641d603e470640" timestamp="1263595937" time_generated="1263595937" time_taken_to_generate="3" size="203243">
+ </export>
+ <export format="prolog" path="obo-all/quality/quality.pro" md5="d167b2327f85a6069c5bf7ca1f90500d" timestamp="1263595942" time_generated="1263595942" time_taken_to_generate="5" size="833500">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/quality/quality.validation_report" md5="d462032903e9fe21df911108efcea9fe" timestamp="1263595944" time_generated="1263595944" time_taken_to_generate="1" size="946">
+ </export>
+ <export format="stats" path="obo-all/quality/quality.stats" md5="619a62d04ddf7c62cc6ebdc743938b12" timestamp="1263595946" time_generated="1263595946" time_taken_to_generate="2" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/quality/quality.obo.html" md5="9b6fff84cc431b8fea9b76ea84ce1576" timestamp="1263595946" time_generated="1263595946" time_taken_to_generate="0" size="2060626">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="bilateria_mrca">
+ <source>http://4dx.embl.de/4DXpress_4d/edocs/bilateria_mrca.obo</source>
+ <granularity>molecular,cellular,organismal,multi-organismal</granularity>
+ <status>Discussion and review</status>
+ <subtypes_of>bfo:IndependentContinuant,bfo:Occurrent</subtypes_of>
+ <contact>Thorsten Heinrich henrich embl.de</contact>
+ <foundry>No</foundry>
+ <domain>anatomy</domain>
+ <documentation></documentation>
+ <url>http://4dx.embl.de/4DXpress_4d/edocs/bilateria_mrca.obo</url>
+ <patho_type>canonical</patho_type>
+ <home>http://4dx.embl.de/4DXpress</home>
+ <additional_namespace>BILS</additional_namespace>
+ <xrefs_to>caro</xrefs_to>
+ <namespace>BILA</namespace>
+ <description></description>
+ <format>obo</format>
+ <title>Bilateria anatomy</title>
+ <relevant_organism>all</relevant_organism>
+ <download></download>
+ <export format="obo_xml" path="obo-all/bilateria_mrca/bilateria_mrca.obo_xml" md5="5943aa7e99145e9a71406c03d2e1f5ce" timestamp="1260650160" time_generated="1263595948" time_taken_to_generate="0" size="48469">
+ </export>
+ <export format="obo" path="obo-all/bilateria_mrca/bilateria_mrca.obo" md5="17d18e19b5a46e95cb87112c0a1a5320" timestamp="1263595948" time_generated="1263595948" time_taken_to_generate="0" size="27037">
+ </export>
+ <export format="owl" path="obo-all/bilateria_mrca/bilateria_mrca.owl" md5="cc01e00371ce9e9cb230194e8252aabb" timestamp="1260650160" time_generated="1263595948" time_taken_to_generate="0" size="97643">
+ </export>
+ <export format="chadoxml" path="obo-all/bilateria_mrca/bilateria_mrca.chadoxml" md5="e23db33d0d4b95c8fc37e9d9a545d066" timestamp="1260650160" time_generated="1263595948" time_taken_to_generate="0" size="106600">
+ </export>
+ <export format="godb_prestore" path="obo-all/bilateria_mrca/bilateria_mrca.godb_prestore" md5="fcb0396800dbd86787202a20220ab65d" timestamp="1260650161" time_generated="1263595948" time_taken_to_generate="0" size="92938">
+ </export>
+ <export format="rdf" path="obo-all/bilateria_mrca/bilateria_mrca.rdf" md5="9f28bdc499c2a38def656ddc4e3a11d7" timestamp="1260650161" time_generated="1263595948" time_taken_to_generate="0" size="55506">
+ </export>
+ <export format="tbl" path="obo-all/bilateria_mrca/bilateria_mrca.tbl" md5="48be023b968383d2700e877c3f76cb32" timestamp="1260650161" time_generated="1263595948" time_taken_to_generate="0" size="10600">
+ </export>
+ <export format="prolog" path="obo-all/bilateria_mrca/bilateria_mrca.pro" md5="8de351ec95354cdae12010d5835817f9" timestamp="1263250310" time_generated="1263595948" time_taken_to_generate="0" size="42936">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/bilateria_mrca/bilateria_mrca.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1260650162" time_generated="1263595948" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" path="obo-all/bilateria_mrca/bilateria_mrca.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1260650163" time_generated="1263595948" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/bilateria_mrca/bilateria_mrca.obo.html" md5="5d69056dd89923726462429b852fca98" timestamp="1260650163" time_generated="1263595948" time_taken_to_generate="0" size="128652">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="sdiff" path="obo-all/bilateria_mrca/bilateria_mrca.sdiff" md5="d41d8cd98f00b204e9800998ecf8427e" timestamp="1263595948" time_generated="1263595949" time_taken_to_generate="1" size="0">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="biological_process">
+ <source>ftp://ftp.geneontology.org/pub/go/ontology/gene_ontology_edit.obo</source>
+ <prerelease_download>ftp://ftp.geneontology.org/pub/go/ontology/obo_format_1_2/gene_ontology_ext.obo</prerelease_download>
+ <granularity>molecular,cellular,organismal,multi-organismal</granularity>
+ <status>Production and review</status>
+ <subtypes_of>bfo:Process</subtypes_of>
+ <contact>Gene Ontology go geneontology.org</contact>
+ <foundry>Yes</foundry>
+ <domain>biological process</domain>
+ <documentation>Gene Ontology documentation|http://www.geneontology.org/GO.doc.shtml</documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/gene_ontology_edit.obo</url>
+ <patho_type>canonical</patho_type>
+ <home>www.geneontology.org|http://www.geneontology.org</home>
+ <namespace>GO</namespace>
+ <description>Provides structured controlled vocabularies for the annotation of gene products with respect to their biological role. One of the three vocabularies of the Gene Ontology.</description>
+ <format>obo</format>
+ <title>Biological process</title>
+ <relevant_organism>all</relevant_organism>
+ <download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/gene_ontology_edit.obo</download>
+ <export format="obo_xml" path="obo-all/gene_ontology/gene_ontology.obo_xml" md5="12c6d75ca02b4580c1f1e632df16c3c6" timestamp="1263596025" time_generated="1263596025" time_taken_to_generate="60" size="29902564">
+ </export>
+ <export format="obo" path="obo-all/biological_process/biological_process.obo" md5="c1ddaea68676d387643d0e9b67105e1d" timestamp="1263596094" time_generated="1263596094" time_taken_to_generate="65" size="9602366">
+ </export>
+ <export format="obo_xml" path="obo-all/biological_process/biological_process.obo_xml" md5="5cd657b70c83b150b4a75fa6d7c05b8b" timestamp="1263596126" time_generated="1263596126" time_taken_to_generate="32" size="17398955">
+ </export>
+ <export format="obo" path="obo-all/biological_process/biological_process.obo" md5="c1ddaea68676d387643d0e9b67105e1d" timestamp="1263596094" time_generated="1263596126" time_taken_to_generate="0" size="9602366">
+ </export>
+ <export format="owl" path="obo-all/biological_process/biological_process.owl" md5="3cc918729cbcd1d7df8e4c974f8dc6de" timestamp="1263604615" time_generated="1263604616" time_taken_to_generate="8489" size="36654275">
+ </export>
+ <export format="chadoxml" path="obo-all/biological_process/biological_process.chadoxml" md5="84bbdfe87e7101b8893c510bac7510eb" timestamp="1263606250" time_generated="1263606250" time_taken_to_generate="1634" size="43064136">
+ </export>
+ <export format="godb_prestore" path="obo-all/biological_process/biological_process.godb_prestore" md5="40c33f7d83d2de408ccf29d4bd861902" timestamp="1263606299" time_generated="1263606299" time_taken_to_generate="49" size="37051395">
+ </export>
+ <export format="rdf" path="obo-all/biological_process/biological_process.rdf" md5="edb98f344f2f2059dd2f91b1b42a5aa9" timestamp="1263606359" time_generated="1263606359" time_taken_to_generate="60" size="15811513">
+ </export>
+ <export format="tbl" path="obo-all/biological_process/biological_process.tbl" md5="6d79c9f0e510f4509c43d315e56caff2" timestamp="1263606400" time_generated="1263606400" time_taken_to_generate="41" size="5770920">
+ </export>
+ <export format="prolog" path="obo-all/biological_process/biological_process.pro" md5="735dc4ea10112f7d37ec9fb3a58b02e5" timestamp="1263606468" time_generated="1263606468" time_taken_to_generate="68" size="18845266">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/biological_process/biological_process.validation_report" md5="83b51fa848e8ad1f57337f4799dea829" timestamp="1263606555" time_generated="1263606555" time_taken_to_generate="52" size="3282">
+ </export>
+ <export format="stats" path="obo-all/biological_process/biological_process.stats" md5="619a62d04ddf7c62cc6ebdc743938b12" timestamp="1263606557" time_generated="1263606557" time_taken_to_generate="2" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/biological_process/biological_process.obo.html" md5="57bd36ea24e6005bc98022cf9b29a40f" timestamp="1263606560" time_generated="1263606560" time_taken_to_generate="3" size="36493808">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="brenda">
+ <source>http://www.brenda-enzymes.info/ontology/tissue/tree/update/update_files/BrendaTissueOBO</source>
+ <namespace>BTO</namespace>
+ <status>Active</status>
+ <contact>BRENDA tissue ontology curators marion.gremse uni-koeln.de</contact>
+ <description>A structured controlled vocabulary for the source of an enzyme. It comprises terms for tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms.</description>
+ <foundry>No</foundry>
+ <domain>anatomy</domain>
+ <format>obo</format>
+ <documentation>BRENDA ontology help|http://www.brenda-enzymes.info</documentation>
+ <url>http://www.brenda-enzymes.info/ontology/tissue/tree/update/update_files/BrendaTissueOBO</url>
+ <title>BRENDA tissue / enzyme source</title>
+ <home>BRENDA enzyme database|http://www.brenda-enzymes.info</home>
+ <download></download>
+ <export format="obo_xml" path="obo-all/brenda/brenda.obo_xml" md5="e6ea495c52c96d745f6324cbb7d73df4" timestamp="1262917435" time_generated="1263606564" time_taken_to_generate="0" size="2123303">
+ </export>
+ <export format="obo" path="obo-all/brenda/brenda.obo" md5="04e2880582299c4963514a73ceb660b1" timestamp="1263606564" time_generated="1263606564" time_taken_to_generate="0" size="1354253">
+ </export>
+ <export format="owl" path="obo-all/brenda/brenda.owl" md5="4c7bf489d6155edb271a307d26d5cfe8" timestamp="1262917686" time_generated="1263606564" time_taken_to_generate="0" size="4627549">
+ </export>
+ <export format="chadoxml" path="obo-all/brenda/brenda.chadoxml" md5="325220e9e45aa2bc964696ad7bf6a081" timestamp="1262917748" time_generated="1263606564" time_taken_to_generate="0" size="4966709">
+ </export>
+ <export format="godb_prestore" path="obo-all/brenda/brenda.godb_prestore" md5="e86992f55c8836fead2c59ee36f3954b" timestamp="1262917755" time_generated="1263606564" time_taken_to_generate="0" size="4213620">
+ </export>
+ <export format="rdf" path="obo-all/brenda/brenda.rdf" md5="1ab0479b53dfeb4be5a5b2d78e599d17" timestamp="1262917763" time_generated="1263606564" time_taken_to_generate="0" size="1920479">
+ </export>
+ <export format="tbl" path="obo-all/brenda/brenda.tbl" md5="5576e4a19f67259f9d794411f2210a32" timestamp="1262917769" time_generated="1263606564" time_taken_to_generate="0" size="610618">
+ </export>
+ <export format="prolog" path="obo-all/brenda/brenda.pro" md5="ba51ddd020a5754c036631eb111ae2b9" timestamp="1262917778" time_generated="1263606565" time_taken_to_generate="0" size="2104417">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/brenda/brenda.validation_report" md5="865c015b708af7cd071816ce95feab8d" timestamp="1262917785" time_generated="1263606569" time_taken_to_generate="0" size="5794">
+ </export>
+ <export format="stats" path="obo-all/brenda/brenda.stats" md5="71666b8d5da5f0cdd71d1938865d3a1c" timestamp="1262917786" time_generated="1263606569" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/brenda/brenda.obo.html" md5="b5ddee4de2816a3d85b55df148c71622" timestamp="1262917787" time_generated="1263606569" time_taken_to_generate="0" size="5332112">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="caro">
+ <source></source>
+ <granularity>organismal</granularity>
+ <status>Discussion and review</status>
+ <subtypes_of>bfo:IndependentContinuant</subtypes_of>
+ <contact>Melissa Haendel obo-anatomy lists.sourceforge.net</contact>
+ <foundry>Yes</foundry>
+ <domain>anatomy</domain>
+ <documentation></documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/caro/caro.obo</url>
+ <patho_type>canonical</patho_type>
+ <home>CARO Wiki|http://www.bioontology.org/wiki/index.php/CARO:Main_Page</home>
+ <namespace>CARO</namespace>
+ <description>The Common Anatomy Reference Ontology (CARO) is being developed to facilitate interoperability between existing anatomy ontologies for different species, and will provide a template for building new anatomy ontologies. CARO will be described in Anatomy Ontologies for Bioinformatics: Principles and Practice Albert Burger, Duncan Davidson and Richard Baldock (Editors)</description>
+ <format>obo</format>
+ <title>Common Anatomy Reference Ontology</title>
+ <relevant_organism>all</relevant_organism>
+ <download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/caro/caro.obo</download>
+ <export format="obo_xml" path="obo-all/caro/caro.obo_xml" md5="e73acbeb24e28424c0bd1c6f27441af1" timestamp="1260658093" time_generated="1263606571" time_taken_to_generate="0" size="19409">
+ </export>
+ <export format="obo" path="obo-all/caro/caro.obo" md5="3b83de9259abe316afbfaa5037a8656d" timestamp="1263606571" time_generated="1263606571" time_taken_to_generate="0" size="10871">
+ </export>
+ <export format="owl" path="obo-all/caro/caro.owl" md5="3a134500be86266784cb61c60de9025b" timestamp="1260658094" time_generated="1263606571" time_taken_to_generate="0" size="56658">
+ </export>
+ <export format="chadoxml" path="obo-all/caro/caro.chadoxml" md5="898302308e6b205a1f171c98a003c4ac" timestamp="1260658094" time_generated="1263606571" time_taken_to_generate="0" size="47861">
+ </export>
+ <export format="godb_prestore" path="obo-all/caro/caro.godb_prestore" md5="50d3981f4cbe87573ddb8a5c2b1b3382" timestamp="1260658094" time_generated="1263606571" time_taken_to_generate="0" size="40077">
+ </export>
+ <export format="rdf" path="obo-all/caro/caro.rdf" md5="fd7431586aab1d0e72dab18a57ab606e" timestamp="1260658094" time_generated="1263606571" time_taken_to_generate="0" size="21141">
+ </export>
+ <export format="tbl" path="obo-all/caro/caro.tbl" md5="73256657f1848cca9b956dca3f57206e" timestamp="1260658094" time_generated="1263606571" time_taken_to_generate="0" size="6856">
+ </export>
+ <export format="prolog" path="obo-all/caro/caro.pro" md5="adf9d44df8dd85990ab5347fb831e6cc" timestamp="1263318806" time_generated="1263606571" time_taken_to_generate="0" size="18490">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/caro/caro.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1260658095" time_generated="1263606571" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" path="obo-all/caro/caro.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1260658096" time_generated="1263606571" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/caro/caro.obo.html" md5="39bf629b3ecb6aff78767caa9f1802f7" timestamp="1260658096" time_generated="1263606571" time_taken_to_generate="0" size="45283">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="spatial">
+ <source></source>
+ <granularity>organismal</granularity>
+ <status>Discussion and review</status>
+ <subtypes_of>bfo:DependentContinuant</subtypes_of>
+ <contact>Chris Mungall obo-anatomy lists.sourceforge.net</contact>
+ <foundry>Yes</foundry>
+ <domain>anatomy</domain>
+ <documentation></documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/caro/spatial.obo</url>
+ <patho_type>canonical</patho_type>
+ <home>CARO Wiki|http://www.bioontology.org/wiki/index.php/CARO:Main_Page</home>
+ <namespace>BSPO</namespace>
+ <description>A small ontology for anatomical spatiol references, such as dorsal, ventral, axis, and so forth.</description>
+ <format>obo</format>
+ <title>Spatial Ontology</title>
+ <relevant_organism>all</relevant_organism>
+ <download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/caro/spatial.obo</download>
+ <export format="obo_xml" path="obo-all/spatial/spatial.obo_xml" md5="3ed15d33c48b54d010d6d540a86d33a9" timestamp="1260658098" time_generated="1263606572" time_taken_to_generate="0" size="74884">
+ </export>
+ <export format="obo" path="obo-all/spatial/spatial.obo" md5="8b330b51ded38b876317ddba84f7cd86" timestamp="1263606572" time_generated="1263606572" time_taken_to_generate="0" size="38880">
+ </export>
+ <export format="owl" path="obo-all/spatial/spatial.owl" md5="374223e987059c1e01372f0e2513e04f" timestamp="1260658098" time_generated="1263606572" time_taken_to_generate="0" size="178213">
+ </export>
+ <export format="chadoxml" path="obo-all/spatial/spatial.chadoxml" md5="11df3439b67d1b69689575bb02a2d5ed" timestamp="1260658099" time_generated="1263606572" time_taken_to_generate="0" size="161041">
+ </export>
+ <export format="godb_prestore" path="obo-all/spatial/spatial.godb_prestore" md5="199feb799e981e450e69a21b217dbc06" timestamp="1260658099" time_generated="1263606572" time_taken_to_generate="0" size="181971">
+ </export>
+ <export format="rdf" path="obo-all/spatial/spatial.rdf" md5="4dc3c5bd8077dcd2a4a261725ac5f926" timestamp="1260658100" time_generated="1263606572" time_taken_to_generate="0" size="76699">
+ </export>
+ <export format="tbl" path="obo-all/spatial/spatial.tbl" md5="c8fc5696b2c5f740fb64056b71b4d09d" timestamp="1260658100" time_generated="1263606572" time_taken_to_generate="0" size="7251">
+ </export>
+ <export format="prolog" path="obo-all/spatial/spatial.pro" md5="8e01820f564dc9a2c789f98f41bcc914" timestamp="1260658100" time_generated="1263606572" time_taken_to_generate="0" size="71742">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/spatial/spatial.validation_report" md5="8cccd8bc8275db0b3dcbf173acdadd1c" timestamp="1260658101" time_generated="1263606573" time_taken_to_generate="0" size="121">
+ </export>
+ <export format="stats" path="obo-all/spatial/spatial.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1260658102" time_generated="1263606573" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/spatial/spatial.obo.html" md5="abb9287df6c2e6391c194cade927d2b2" timestamp="1260658102" time_generated="1263606573" time_taken_to_generate="0" size="192292">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="spider_anatomy">
+ <source></source>
+ <granularity>organismal</granularity>
+ <status>Discussion and review</status>
+ <subtypes_of>CARO:0000000</subtypes_of>
+ <contact>Martin Ramirez ramirez macn.gov.ar</contact>
+ <foundry>Yes</foundry>
+ <domain>anatomy</domain>
+ <documentation></documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/spider/spider_comparative_biology.obo</url>
+ <patho_type>canonical</patho_type>
+ <home>Phylogeny of Spiders|http://research.amnh.org/atol/files/</home>
+ <namespace>SPD</namespace>
+ <description>An ontology for spider comparative biology including anatomical parts (e.g. leg, claw), behavior (e.g. courtship, combing) and products (i.g. silk, web, borrow).</description>
+ <format>obo</format>
+ <title>Spider Ontology</title>
+ <relevant_organism>NCBITaxon:6893|spiders</relevant_organism>
+ <download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/spider/spider_comparative_biology.obo</download>
+ <export format="obo_xml" path="obo-all/spider_anatomy/spider_anatomy.obo_xml" md5="7e25556fee56c863b56433a61780d10b" timestamp="1260658105" time_generated="1263606574" time_taken_to_generate="0" size="233756">
+ </export>
+ <export format="obo" path="obo-all/spider_anatomy/spider_anatomy.obo" md5="94702ade3fdb408e931ee2b9bf16b9e0" timestamp="1263606574" time_generated="1263606574" time_taken_to_generate="0" size="120604">
+ </export>
+ <export format="owl" path="obo-all/spider_anatomy/spider_anatomy.owl" md5="16a27f077ef2785f82470b934e69e3e9" timestamp="1260658107" time_generated="1263606574" time_taken_to_generate="0" size="539793">
+ </export>
+ <export format="chadoxml" path="obo-all/spider_anatomy/spider_anatomy.chadoxml" md5="54183e05df360b2cc0c121636d6a8c5b" timestamp="1260658108" time_generated="1263606574" time_taken_to_generate="0" size="525797">
+ </export>
+ <export format="godb_prestore" path="obo-all/spider_anatomy/spider_anatomy.godb_prestore" md5="1d60a85104670e419b6f5206d5715001" timestamp="1260658108" time_generated="1263606574" time_taken_to_generate="0" size="490936">
+ </export>
+ <export format="rdf" path="obo-all/spider_anatomy/spider_anatomy.rdf" md5="2fe1228e6a6a0d8f3bc6ffde2595560a" timestamp="1260658109" time_generated="1263606574" time_taken_to_generate="0" size="239391">
+ </export>
+ <export format="tbl" path="obo-all/spider_anatomy/spider_anatomy.tbl" md5="acf7b6dd51294a2e8aa82404dca7e44e" timestamp="1260658110" time_generated="1263606574" time_taken_to_generate="0" size="54785">
+ </export>
+ <export format="prolog" path="obo-all/spider_anatomy/spider_anatomy.pro" md5="bd6b474805f99a51a764f4625875feb7" timestamp="1260658111" time_generated="1263606574" time_taken_to_generate="0" size="217761">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/spider_anatomy/spider_anatomy.validation_report" md5="a8fd5a58c807f861a2627adab8e4be27" timestamp="1260658113" time_generated="1263606575" time_taken_to_generate="0" size="1037">
+ </export>
+ <export format="stats" path="obo-all/spider_anatomy/spider_anatomy.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1260658114" time_generated="1263606575" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/spider_anatomy/spider_anatomy.obo.html" md5="240956be0e1b818fe3021382de9121a1" timestamp="1260658114" time_generated="1263606575" time_taken_to_generate="0" size="569299">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="cell">
+ <source></source>
+ <granularity>cellular</granularity>
+ <status>Production and review</status>
+ <subtypes_of>bfo:IndependentContinuant</subtypes_of>
+ <contact>Alex Diehl adiehl informatics.jax.org</contact>
+ <foundry>Yes</foundry>
+ <domain>anatomy</domain>
+ <documentation></documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/cell_type/cell.obo</url>
+ <patho_type>canonical</patho_type>
+ <home>Cell Type Ontology home|http://lists.sourceforge.net/lists/listinfo/obo-cell-type</home>
+ <xrefs_to>fly_anatomy</xrefs_to>
+ <namespace>CL</namespace>
+ <description>The Cell Ontology is designed as a structured controlled vocabulary for cell types. This ontology was constructed for use by the model organism and other bioinformatics databases, where there is a need for a controlled vocabulary of cell types. This ontology is not organism specific; indeed it includes cell types from prokaryotes to mammals, including plants and fungi. A full description of the Cell Ontology can be found in <a href="http://genomebiology.com/2005/6/2/R [...]
+ <format>obo</format>
+ <title>Cell type</title>
+ <relevant_organism>all</relevant_organism>
+ <download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/cell_type/cell.obo</download>
+ <export format="obo_xml" path="obo-all/cell/cell.obo_xml" md5="839412547b3154d2906939b531bb3a42" timestamp="1263606579" time_generated="1263606579" time_taken_to_generate="1" size="523305">
+ </export>
+ <export format="obo" path="obo-all/cell/cell.obo" md5="d0e09efc3d0718f00717b3d6c5c1c6c4" timestamp="1263606578" time_generated="1263606579" time_taken_to_generate="0" size="287292">
+ </export>
+ <export format="owl" path="obo-all/cell/cell.owl" md5="2986727f8a18d36bdfed754c73d41bb6" timestamp="1263606588" time_generated="1263606588" time_taken_to_generate="9" size="1199673">
+ </export>
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+ </export>
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+ </export>
+ <export format="tbl" path="obo-all/cell/cell.tbl" md5="db876d2c85c8922eb1ce2f6e19e697d7" timestamp="1263606596" time_generated="1263606596" time_taken_to_generate="1" size="149724">
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+ </export>
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+ </export>
+ <export format="validation_report" path="obo-all/cell/cell.validation_report" md5="7c9a194323b5fcecfb0e2f52d1f304c2" timestamp="1263606616" time_generated="1263606616" time_taken_to_generate="16" size="11394">
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+ <export format="stats" path="obo-all/cell/cell.stats" md5="619a62d04ddf7c62cc6ebdc743938b12" timestamp="1263606618" time_generated="1263606618" time_taken_to_generate="2" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/cell/cell.obo.html" md5="9a70f00834e9e71accd0e4bd97ac562f" timestamp="1263606618" time_generated="1263606618" time_taken_to_generate="0" size="1213479">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
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+ <export format="sdiff" path="obo-all/cell/cell.sdiff" md5="4ddfc189cae19b4fa9264eb7b1367618" timestamp="1263606620" time_generated="1263606620" time_taken_to_generate="2" size="3842">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="dendritic_cell">
+ <source></source>
+ <prerelease_download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/cell_type/DC-CL_editor.obo</prerelease_download>
+ <granularity>cellular</granularity>
+ <status>Production and review</status>
+ <subtypes_of>bfo:IndependentContinuant</subtypes_of>
+ <contact>Lindsay Cowell cowel001 mc.duke.edu</contact>
+ <foundry>No</foundry>
+ <domain>anatomy,immunology</domain>
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+ <patho_type>canonical</patho_type>
+ <home>http://www.dukeontologygroup.org/Projects.html</home>
+ <namespace>DC_CL</namespace>
+ <description>Representation of types of dendritic cell. Note that the domain of this ontology is wholly subsumed by the domain of the Cell ontology (CL).</description>
+ <format>obo</format>
+ <title>Dendritic cell</title>
+ <relevant_organism>all</relevant_organism>
+ <download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/cell_type/DC-CL_deployed.obo</download>
+ <export format="obo_xml" path="obo-all/dendritic_cell/dendritic_cell.obo_xml" md5="2e2019b188582ea25308740d5250ef13" timestamp="1260658154" time_generated="1263606621" time_taken_to_generate="0" size="97831">
+ </export>
+ <export format="obo" path="obo-all/dendritic_cell/dendritic_cell.obo" md5="30ed726749d8096ba7d8e7ebc250116e" timestamp="1263606621" time_generated="1263606621" time_taken_to_generate="0" size="58882">
+ </export>
+ <export format="owl" path="obo-all/dendritic_cell/dendritic_cell.owl" md5="399da2006dc98e33b551b71473a209bb" timestamp="1260658155" time_generated="1263606621" time_taken_to_generate="0" size="239168">
+ </export>
+ <export format="chadoxml" path="obo-all/dendritic_cell/dendritic_cell.chadoxml" md5="ef5f7c9395e84cf2f11402429a9a48e8" timestamp="1260658155" time_generated="1263606621" time_taken_to_generate="0" size="172364">
+ </export>
+ <export format="godb_prestore" path="obo-all/dendritic_cell/dendritic_cell.godb_prestore" md5="a6d9f05e74bcc1884f0c271b99e5d0dc" timestamp="1260658155" time_generated="1263606621" time_taken_to_generate="0" size="243921">
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+ <export format="tbl" path="obo-all/dendritic_cell/dendritic_cell.tbl" md5="0c55dda3c5c3b7044ef67f7dcba5734b" timestamp="1260658156" time_generated="1263606622" time_taken_to_generate="0" size="13268">
+ </export>
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+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/dendritic_cell/dendritic_cell.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1260658158" time_generated="1263606622" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" path="obo-all/dendritic_cell/dendritic_cell.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1260658159" time_generated="1263606622" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/dendritic_cell/dendritic_cell.obo.html" md5="dc63c37e753c157b88ceb49c7ad46632" timestamp="1260658159" time_generated="1263606622" time_taken_to_generate="0" size="233394">
+ </export>
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+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="cellular_component">
+ <source>ftp://ftp.geneontology.org/pub/go/ontology/gene_ontology_edit.obo</source>
+ <granularity>sub-cellular</granularity>
+ <status>Production and review</status>
+ <subtypes_of>bfo:IndependentContinuant</subtypes_of>
+ <contact>Gene Ontology go geneontology.org</contact>
+ <foundry>Yes</foundry>
+ <domain>anatomy</domain>
+ <documentation>Gene Ontology documentation|http://www.geneontology.org/GO.doc.shtml</documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/gene_ontology_edit.obo</url>
+ <patho_type>canonical</patho_type>
+ <home>www.geneontology.org|http://www.geneontology.org</home>
+ <namespace>GO</namespace>
+ <description>Provides structured controlled vocabularies for the annotation of gene products with respect to their cellular location. One of the three vocabularies of the Gene Ontology.</description>
+ <format>obo</format>
+ <title>Cellular component</title>
+ <relevant_organism>all</relevant_organism>
+ <download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/gene_ontology_edit.obo</download>
+ <export format="obo_xml" path="obo-all/gene_ontology/gene_ontology.obo_xml" md5="12c6d75ca02b4580c1f1e632df16c3c6" timestamp="1263596025" time_generated="1263606623" time_taken_to_generate="0" size="29902564">
+ </export>
+ <export format="obo" path="obo-all/cellular_component/cellular_component.obo" md5="9a5da44293e1862b49d5fa0c69a0d6e2" timestamp="1263606635" time_generated="1263606635" time_taken_to_generate="8" size="1153003">
+ </export>
+ <export format="obo_xml" path="obo-all/cellular_component/cellular_component.obo_xml" md5="a3e6f40c34d2e57afe25e7bc43caac0b" timestamp="1263606640" time_generated="1263606640" time_taken_to_generate="5" size="2045714">
+ </export>
+ <export format="obo" path="obo-all/cellular_component/cellular_component.obo" md5="9a5da44293e1862b49d5fa0c69a0d6e2" timestamp="1263606635" time_generated="1263606640" time_taken_to_generate="0" size="1153003">
+ </export>
+ <export format="owl" path="obo-all/cellular_component/cellular_component.owl" md5="51bd63581fdd9411b0bbc640fab5ff75" timestamp="1263606800" time_generated="1263606800" time_taken_to_generate="160" size="4505994">
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+ </export>
+ <export format="godb_prestore" path="obo-all/cellular_component/cellular_component.godb_prestore" md5="02238d980686dfeaf8f4ac0aff6cbc10" timestamp="1263606853" time_generated="1263606854" time_taken_to_generate="10" size="4336415">
+ </export>
+ <export format="rdf" path="obo-all/cellular_component/cellular_component.rdf" md5="431796a56a73c28a68d35297bd4053e0" timestamp="1263606866" time_generated="1263606867" time_taken_to_generate="13" size="1872799">
+ </export>
+ <export format="tbl" path="obo-all/cellular_component/cellular_component.tbl" md5="f45f4457a68d5008046c9014a88dddc8" timestamp="1263606875" time_generated="1263606875" time_taken_to_generate="8" size="688810">
+ </export>
+ <export format="prolog" path="obo-all/cellular_component/cellular_component.pro" md5="dcabdcc889c5b6871dce0c9beb92d2eb" timestamp="1263606889" time_generated="1263606889" time_taken_to_generate="14" size="2030212">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/cellular_component/cellular_component.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1263606905" time_generated="1263606905" time_taken_to_generate="10" size="20">
+ </export>
+ <export format="stats" path="obo-all/cellular_component/cellular_component.stats" md5="619a62d04ddf7c62cc6ebdc743938b12" timestamp="1263606907" time_generated="1263606907" time_taken_to_generate="2" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/cellular_component/cellular_component.obo.html" md5="72599df8c1a8c93cd8d1352ca017b731" timestamp="1263606908" time_generated="1263606908" time_taken_to_generate="1" size="4458655">
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+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="chebi">
+ <source>ftp://ftp.ebi.ac.uk/pub/databases/chebi/ontology/chebi.obo</source>
+ <granularity>molecular</granularity>
+ <status>Production and review</status>
+ <subtypes_of>bfo:IndependentContinuant</subtypes_of>
+ <contact>ChEBI help chebi-help ebi.ac.uk</contact>
+ <foundry>Yes</foundry>
+ <domain>biochemistry</domain>
+ <documentation>ChEBI user manual|http://www.ebi.ac.uk/chebi/init.do?toolBarForward=userManual</documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/chemical/chebi.obo</url>
+ <patho_type>canonical</patho_type>
+ <home>ChEBI home|http://www.ebi.ac.uk/chebi</home>
+ <namespace>CHEBI</namespace>
+ <description>A structured classification of chemical compounds of biological relevance.</description>
+ <format>obo</format>
+ <title>Chemical entities of biological interest</title>
+ <wiki>http://chebi.wiki.sourceforge.net/ </wiki>
+ <relevant_organism>all</relevant_organism>
+ <download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/chemical/chebi.obo</download>
+ <export format="obo_xml" path="obo-all/chebi/chebi.obo_xml" md5="de3166c7dcf00093b17d8a5385c60fdc" timestamp="1262918154" time_generated="1263606919" time_taken_to_generate="0" size="40377249">
+ </export>
+ <export format="obo" path="obo-all/chebi/chebi.obo" md5="2e86fb17ad7d0053edd7ecd298c0a88b" timestamp="1263606918" time_generated="1263606919" time_taken_to_generate="0" size="14919813">
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+ <export format="chadoxml" path="obo-all/chebi/chebi.chadoxml" md5="66c84c7d40787559cbc99d82026ecf47" timestamp="1262956606" time_generated="1263638481" time_taken_to_generate="0" size="84165233">
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+ <export format="godb_prestore" path="obo-all/chebi/chebi.godb_prestore" md5="b90262b9140cd8faea96bffefb7162f4" timestamp="1262956772" time_generated="1263638483" time_taken_to_generate="0" size="80425672">
+ </export>
+ <export format="rdf" path="obo-all/chebi/chebi.rdf" md5="4b2714d953f0f2c89ec14e795a807b1d" timestamp="1262956957" time_generated="1263638484" time_taken_to_generate="0" size="27710087">
+ </export>
+ <export format="tbl" path="obo-all/chebi/chebi.tbl" md5="683e024f8100d8842623a00219435510" timestamp="1262957107" time_generated="1263638485" time_taken_to_generate="0" size="6844586">
+ </export>
+ <export format="prolog" path="obo-all/chebi/chebi.pro" md5="3a5a79abbad0e135659520e09e3066ec" timestamp="1263423534" time_generated="1263638485" time_taken_to_generate="0" size="56774310">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/chebi/chebi.validation_report" md5="63d5b54bb4d2549f7f0c12cdeb9dc79b" timestamp="1262957511" time_generated="1263638629" time_taken_to_generate="0" size="133">
+ </export>
+ <export format="stats" path="obo-all/chebi/chebi.stats" md5="71666b8d5da5f0cdd71d1938865d3a1c" timestamp="1262957513" time_generated="1263638629" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/chebi/chebi.obo.html" md5="93399b5dc7893d5e68c78d8bb4548876" timestamp="1262957521" time_generated="1263638629" time_taken_to_generate="0" size="63243193">
+ </export>
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+ <export format="imports.owl" problem="true">
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+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="cob">
+ <source>ftp://ftp.ebi.ac.uk/pub/databases/RESID/RESIDUES.XML</source>
+ <namespace>RESID</namespace>
+ <status>Active</status>
+ <contact>John Garavelli john.garavelli ebi.ac.uk</contact>
+ <description>For the description of covalent bonds in proteins.</description>
+ <foundry>No</foundry>
+ <domain>proteins</domain>
+ <format>XML</format>
+ <url>ftp://ftp.ebi.ac.uk/pub/databases/RESID/RESIDUES.XML</url>
+ <documentation></documentation>
+ <title>Protein covalent bond</title>
+ <home>RESID Info|http://www.ebi.ac.uk/RESID/</home>
+ <download></download>
+ <export format="obo_xml" problem="true">
+ </export>
+ <export format="obo" problem="true">
+ </export>
+ <export format="owl" problem="true">
+ </export>
+ <export format="chadoxml" problem="true">
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+ <export format="godb_prestore" problem="true">
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+ <export format="rdf" problem="true">
+ </export>
+ <export format="tbl" problem="true">
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+ <export format="prolog" problem="true">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" problem="true">
+ </export>
+ <export format="stats" problem="true">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/cob/cob.obo.html" md5="d23ac85d66dd4db6a90d4ba49e89b4ba" timestamp="1260681955" time_generated="1263638645" time_taken_to_generate="0" size="437">
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+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="dictyostelium_discoideum_anatomy">
+ <source></source>
+ <granularity>organismal,cellular</granularity>
+ <status>Production and review</status>
+ <subtypes_of>CARO:0000000</subtypes_of>
+ <contact>Rex Chisholm dictybase northwestern.edu</contact>
+ <foundry>Yes</foundry>
+ <domain>anatomy</domain>
+ <documentation></documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/microbial_gross_anatomy/dictyostelium/dictyostelium_anatomy.obo</url>
+ <patho_type>canonical</patho_type>
+ <home>Dictybase|http://dictybase.org/</home>
+ <xrefs_to>cell</xrefs_to>
+ <namespace>DDANAT</namespace>
+ <description>A structured controlled vocabulary of the anatomy of the slime-mould <i>Dictyostelium discoideum</i>.</description>
+ <format>obo</format>
+ <publication>http://www.biomedcentral.com/1471-2164/9/130</publication>
+ <title>Dictyostelium discoideum anatomy</title>
+ <relevant_organism>NCBITaxon:44689|Dictyostelium discoideum</relevant_organism>
+ <download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/microbial_gross_anatomy/dictyostelium/dictyostelium_anatomy.obo</download>
+ <export format="obo_xml" path="obo-all/dictyostelium_discoideum_anatomy/dictyostelium_discoideum_anatomy.obo_xml" md5="648d2be2218e26ef3f2105bf8b43c633" timestamp="1260681957" time_generated="1263638650" time_taken_to_generate="0" size="116121">
+ </export>
+ <export format="obo" path="obo-all/dictyostelium_discoideum_anatomy/dictyostelium_discoideum_anatomy.obo" md5="7091d9f34376a2cf99d7ce4845b7030d" timestamp="1263638650" time_generated="1263638650" time_taken_to_generate="0" size="62417">
+ </export>
+ <export format="owl" path="obo-all/dictyostelium_discoideum_anatomy/dictyostelium_discoideum_anatomy.owl" md5="05b8a7f3bb1a73d02340b3406af0a15f" timestamp="1260681958" time_generated="1263638650" time_taken_to_generate="0" size="279843">
+ </export>
+ <export format="chadoxml" path="obo-all/dictyostelium_discoideum_anatomy/dictyostelium_discoideum_anatomy.chadoxml" md5="b86bff4bf53e6b2eddbbda4d9da744d1" timestamp="1260681958" time_generated="1263638650" time_taken_to_generate="0" size="273443">
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+ <export format="godb_prestore" path="obo-all/dictyostelium_discoideum_anatomy/dictyostelium_discoideum_anatomy.godb_prestore" md5="81c8b37e34f90ff8077c060af20697ae" timestamp="1260681958" time_generated="1263638651" time_taken_to_generate="0" size="268592">
+ </export>
+ <export format="rdf" path="obo-all/dictyostelium_discoideum_anatomy/dictyostelium_discoideum_anatomy.rdf" md5="7dfb3b1310192d3be2c3f982937a854e" timestamp="1260681959" time_generated="1263638651" time_taken_to_generate="0" size="107380">
+ </export>
+ <export format="tbl" path="obo-all/dictyostelium_discoideum_anatomy/dictyostelium_discoideum_anatomy.tbl" md5="00e3af3009446a9bb18d752c2aa8ee17" timestamp="1260681959" time_generated="1263638651" time_taken_to_generate="0" size="29614">
+ </export>
+ <export format="prolog" path="obo-all/dictyostelium_discoideum_anatomy/dictyostelium_discoideum_anatomy.pro" md5="78f1bb016b4eddadc33f0e4ebba7843a" timestamp="1263295124" time_generated="1263638651" time_taken_to_generate="0" size="114467">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/dictyostelium_discoideum_anatomy/dictyostelium_discoideum_anatomy.validation_report" md5="867857545f9669b9f8162b2423dda906" timestamp="1260681961" time_generated="1263638651" time_taken_to_generate="0" size="221">
+ </export>
+ <export format="stats" path="obo-all/dictyostelium_discoideum_anatomy/dictyostelium_discoideum_anatomy.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1260681962" time_generated="1263638651" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/dictyostelium_discoideum_anatomy/dictyostelium_discoideum_anatomy.obo.html" md5="58c6b3c0adf0a204ccbcc26fc79692e2" timestamp="1260681962" time_generated="1263638651" time_taken_to_generate="0" size="232328">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="sdiff" path="obo-all/dictyostelium_discoideum_anatomy/dictyostelium_discoideum_anatomy.sdiff" md5="a9b84fa4c368cb890bbf984efa12007e" timestamp="1263638653" time_generated="1263638653" time_taken_to_generate="2" size="1680">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="disease_ontology">
+ <source>http://diseaseontology.svn.sourceforge.net/viewvc/*checkout*/diseaseontology/trunk/HumanDO.obo</source>
+ <granularity>organismal,cellular</granularity>
+ <status>Discussion and review</status>
+ <subtypes_of>bfo:DependentContinuant</subtypes_of>
+ <contact>discussion list diseaseontology-discussion lists.sourceforge.net</contact>
+ <foundry>Yes</foundry>
+ <domain>health</domain>
+ <documentation>Disease Ontology|http://diseaseontology.sourceforge.net/</documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/human_disease.obo</url>
+ <patho_type>pathological</patho_type>
+ <home>Disease Ontology|http://diseaseontology.sourceforge.net/</home>
+ <namespace>DOID</namespace>
+ <description>Creating a comprehensive hierarchical controlled vocabulary for human disease representation.</description>
+ <format>obo</format>
+ <title>Human disease</title>
+ <relevant_organism>NCBITaxon:9606|Homo sapiens</relevant_organism>
+ <download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/human_disease.obo</download>
+ <export format="obo_xml" path="obo-all/disease_ontology/disease_ontology.obo_xml" md5="e0b05c1dbc4ddd3ee56484e1f7584373" timestamp="1263638818" time_generated="1263638818" time_taken_to_generate="141" size="48600551">
+ </export>
+ <export format="obo" path="obo-all/disease_ontology/disease_ontology.obo" md5="6beedfe24b7ec1a4a904d1b8f4895e52" timestamp="1263638677" time_generated="1263638818" time_taken_to_generate="0" size="15654077">
+ </export>
+ <export format="owl" path="obo-all/disease_ontology/disease_ontology.owl" md5="42bd40af675c2586fa1c314563405217" timestamp="1263655955" time_generated="1263655955" time_taken_to_generate="17136" size="146589786">
+ </export>
+ <export format="chadoxml" path="obo-all/disease_ontology/disease_ontology.chadoxml" md5="420f6f61ebf8e46910725fb78a226c2a" timestamp="1263660959" time_generated="1263660961" time_taken_to_generate="5005" size="126654041">
+ </export>
+ <export format="godb_prestore" path="obo-all/disease_ontology/disease_ontology.godb_prestore" md5="88465811e40e81ab214fffeb16b2861b" timestamp="1263661260" time_generated="1263661261" time_taken_to_generate="299" size="96312981">
+ </export>
+ <export format="rdf" path="obo-all/disease_ontology/disease_ontology.rdf" md5="00f9797d211132be73ee2b71a4d14919" timestamp="1263661716" time_generated="1263661716" time_taken_to_generate="454" size="85451064">
+ </export>
+ <export format="tbl" path="obo-all/disease_ontology/disease_ontology.tbl" md5="d91dd861618fb32c343fb9d79835c65c" timestamp="1263661954" time_generated="1263661954" time_taken_to_generate="237" size="1773852">
+ </export>
+ <export format="prolog" path="obo-all/disease_ontology/disease_ontology.pro" md5="e083763a9099a9511106111d207a9da1" timestamp="1263662342" time_generated="1263662342" time_taken_to_generate="388" size="37307046">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/disease_ontology/disease_ontology.validation_report" md5="ab91f1abca899e1e82403afd8f272d5f" timestamp="1263662645" time_generated="1263662645" time_taken_to_generate="62" size="42864">
+ </export>
+ <export format="stats" path="obo-all/disease_ontology/disease_ontology.stats" md5="619a62d04ddf7c62cc6ebdc743938b12" timestamp="1263662649" time_generated="1263662649" time_taken_to_generate="4" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/disease_ontology/disease_ontology.obo.html" md5="e6d3ea0226f1c62c7aadde8ff00ca767" timestamp="1263662670" time_generated="1263662670" time_taken_to_generate="21" size="105977888">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="infectious_disease_ontology">
+ <source></source>
+ <granularity>organismal,cellular</granularity>
+ <status>Discussion and review</status>
+ <contact>Lindsay Cowell ido duke.edu </contact>
+ <foundry>Yes</foundry>
+ <domain>health</domain>
+ <documentation></documentation>
+ <url>http://purl.obolibrary.org/obo/ido.owl</url>
+ <patho_type>pathological</patho_type>
+ <home>Infectious Disease Ontology|http://www.bioontology.org/wiki/index.php/Infectious_Disease_Ontology</home>
+ <metadata_ontology>IAO</metadata_ontology>
+ <namespace>IDO</namespace>
+ <description></description>
+ <format>owl</format>
+ <title>Infectious disease</title>
+ <relevant_organism>NCBITaxon:9606|Homo sapiens</relevant_organism>
+ <download>http://purl.obolibrary.org/obo/ido.owl</download>
+ <export format="pro" path="obo-all/infectious_disease_ontology/infectious_disease_ontology.pro" md5="1f7049f70fa5b1bc7bec725824adfd6c" timestamp="1260424405" time_generated="1263662675" time_taken_to_generate="0" size="381228">
+ </export>
+ <export format="obo" path="obo-all/infectious_disease_ontology/infectious_disease_ontology.obo" md5="8e994004091850cbc289927b2df451f9" timestamp="1260424400" time_generated="1263662675" time_taken_to_generate="0" size="260380">
+ </export>
+ <export format="obo_xml" path="obo-all/infectious_disease_ontology/infectious_disease_ontology.obo_xml" md5="dbfb032262832ea6e318dea0b0822580" timestamp="1260424401" time_generated="1263662675" time_taken_to_generate="0" size="387900">
+ </export>
+ <export format="owl" path="obo-all/infectious_disease_ontology/infectious_disease_ontology.owl" md5="3041961d77b595ccfa514015efe1a2a6" timestamp="1263662675" time_generated="1263662676" time_taken_to_generate="0" size="270791">
+ </export>
+ <export format="chadoxml" path="obo-all/infectious_disease_ontology/infectious_disease_ontology.chadoxml" md5="1317f518746e5f41da9a5a8d70bb8bc8" timestamp="1260424402" time_generated="1263662676" time_taken_to_generate="0" size="468484">
+ </export>
+ <export format="godb_prestore" path="obo-all/infectious_disease_ontology/infectious_disease_ontology.godb_prestore" md5="ac74376b7418ee0a6e93a2bded95238d" timestamp="1260424403" time_generated="1263662676" time_taken_to_generate="0" size="550676">
+ </export>
+ <export format="rdf" path="obo-all/infectious_disease_ontology/infectious_disease_ontology.rdf" md5="2a2c5b2d1fed717abd442d3357a28f43" timestamp="1260424404" time_generated="1263662676" time_taken_to_generate="0" size="143712">
+ </export>
+ <export format="tbl" path="obo-all/infectious_disease_ontology/infectious_disease_ontology.tbl" md5="8956c7d97dc9287e179c81485de6dd6b" timestamp="1260424404" time_generated="1263662676" time_taken_to_generate="0" size="27364">
+ </export>
+ <export format="prolog" path="obo-all/infectious_disease_ontology/infectious_disease_ontology.pro" md5="1f7049f70fa5b1bc7bec725824adfd6c" timestamp="1260424405" time_generated="1263662676" time_taken_to_generate="0" size="381228">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/infectious_disease_ontology/infectious_disease_ontology.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1260424406" time_generated="1263662677" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" path="obo-all/infectious_disease_ontology/infectious_disease_ontology.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1260696146" time_generated="1263662677" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/infectious_disease_ontology/infectious_disease_ontology.obo.html" md5="7ae737361559c49a474da4d0441a4f48" timestamp="1260696147" time_generated="1263662677" time_taken_to_generate="0" size="1120916">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="influenza_ontology">
+ <source></source>
+ <granularity>organismal,cellular</granularity>
+ <status>Discussion and review</status>
+ <contact>Burke Squires burkesquires gmail.com </contact>
+ <foundry>No</foundry>
+ <domain>health</domain>
+ <documentation></documentation>
+ <url>http://purl.obolibrary.org/obo/flu.owl</url>
+ <patho_type>pathological</patho_type>
+ <home>Influenza Ontology|http://purl.obolibrary.org/obo/flu/</home>
+ <metadata_ontology>IAO</metadata_ontology>
+ <namespace>FLU</namespace>
+ <description></description>
+ <format>owl</format>
+ <title>Influenza Ontology</title>
+ <relevant_organism></relevant_organism>
+ <download>http://purl.obolibrary.org/obo/flu.owl</download>
+ <problem>Source not available at specified URL as recognised format</problem>
+ </ont>
+ <ont id="malaria_ontology">
+ <source></source>
+ <namespace>IDOMAL</namespace>
+ <status>Discussion and review</status>
+ <contact>topalis mbb.forth.gr</contact>
+ <description>An application ontology to cover all aspects of malaria (clinical, epidemiological, biological, etc) as well as the intervention attempts to control it.</description>
+ <foundry>No</foundry>
+ <domain>health</domain>
+ <format>obo</format>
+ <documentation></documentation>
+ <url>http://anobase.vectorbase.org/idomal/IDOMAL.obo</url>
+ <patho_type>pathological</patho_type>
+ <title>Malaria Ontology</title>
+ <home>AnoBase / Vectorbase|http://anobase.vectorbase.org</home>
+ <download>http://anobase.vectorbase.org/idomal/IDOMAL.obo</download>
+ <export format="obo_xml" path="obo-all/malaria_ontology/malaria_ontology.obo_xml" md5="33cf530fb0d49abd1fcc96d156a72b1e" timestamp="1260696154" time_generated="1263662871" time_taken_to_generate="0" size="888886">
+ </export>
+ <export format="obo" path="obo-all/malaria_ontology/malaria_ontology.obo" md5="3add563223ac2c8a83b8442de9523430" timestamp="1263662871" time_generated="1263662871" time_taken_to_generate="0" size="514535">
+ </export>
+ <export format="owl" path="obo-all/malaria_ontology/malaria_ontology.owl" md5="ad8009767bda72fa1107a987768b675a" timestamp="1260696178" time_generated="1263662871" time_taken_to_generate="0" size="1803565">
+ </export>
+ <export format="chadoxml" path="obo-all/malaria_ontology/malaria_ontology.chadoxml" md5="1ff7829d2840901913d41be483f8d11e" timestamp="1260696184" time_generated="1263662871" time_taken_to_generate="0" size="1906150">
+ </export>
+ <export format="godb_prestore" path="obo-all/malaria_ontology/malaria_ontology.godb_prestore" md5="6283b45a642f6a95f817d6117552a9c0" timestamp="1260696187" time_generated="1263662871" time_taken_to_generate="0" size="1640205">
+ </export>
+ <export format="rdf" path="obo-all/malaria_ontology/malaria_ontology.rdf" md5="8ac6c46fa2866c9d4211e1b6c5aaddf3" timestamp="1260696191" time_generated="1263662871" time_taken_to_generate="0" size="871776">
+ </export>
+ <export format="tbl" path="obo-all/malaria_ontology/malaria_ontology.tbl" md5="a19abf3a6a07cd4325129c01bef9d1e2" timestamp="1260696193" time_generated="1263662871" time_taken_to_generate="0" size="247222">
+ </export>
+ <export format="prolog" path="obo-all/malaria_ontology/malaria_ontology.pro" md5="9a8795e397605dd033442d4cf1abacb0" timestamp="1260696197" time_generated="1263662871" time_taken_to_generate="0" size="813670">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/malaria_ontology/malaria_ontology.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1260696200" time_generated="1263662874" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" path="obo-all/malaria_ontology/malaria_ontology.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1260696201" time_generated="1263662874" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/malaria_ontology/malaria_ontology.obo.html" md5="06a5e910fad04a4ef241e6238453a0de" timestamp="1260696202" time_generated="1263662874" time_taken_to_generate="0" size="2040208">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="emap">
+ <source></source>
+ <granularity>organismal</granularity>
+ <status>Production and review</status>
+ <subtypes_of>CARO:0000000</subtypes_of>
+ <contact>Jonathan Bard J.Bard ed.ac.uk</contact>
+ <foundry>Yes</foundry>
+ <domain>anatomy</domain>
+ <documentation></documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/mouse/EMAP.obo</url>
+ <patho_type>canonical</patho_type>
+ <home>GeneX|http://genex.hgu.mrc.ac.uk/</home>
+ <namespace>EMAP</namespace>
+ <description>A structured controlled vocabulary of stage-specific anatomical structures of the mouse (Mus).</description>
+ <format>obo</format>
+ <title>Mouse gross anatomy and development</title>
+ <relevant_organism>NCBITaxon:10088|Mus</relevant_organism>
+ <download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/mouse/EMAP.obo</download>
+ <export format="obo_xml" path="obo-all/emap/emap.obo_xml" md5="55c40d1a0301dbe1b56e3343e7779c37" timestamp="1260696211" time_generated="1263662880" time_taken_to_generate="0" size="3314130">
+ </export>
+ <export format="obo" path="obo-all/emap/emap.obo" md5="8a61f1073431d329e8707858917b48de" timestamp="1263662880" time_generated="1263662880" time_taken_to_generate="0" size="1717529">
+ </export>
+ <export format="owl" path="obo-all/emap/emap.owl" md5="ded2c5afba183287236e0462d59e5413" timestamp="1260697358" time_generated="1263662880" time_taken_to_generate="0" size="7546422">
+ </export>
+ <export format="chadoxml" path="obo-all/emap/emap.chadoxml" md5="5b31b48e923ae178f96807f150bd4f7b" timestamp="1260697759" time_generated="1263662880" time_taken_to_generate="0" size="7084780">
+ </export>
+ <export format="godb_prestore" path="obo-all/emap/emap.godb_prestore" md5="aa8e5a8166db58cf73744fd39503300f" timestamp="1260697775" time_generated="1263662881" time_taken_to_generate="0" size="6887088">
+ </export>
+ <export format="rdf" path="obo-all/emap/emap.rdf" md5="c4ba33c31c2092bae00faa06f008a412" timestamp="1260697797" time_generated="1263662881" time_taken_to_generate="0" size="4097706">
+ </export>
+ <export format="tbl" path="obo-all/emap/emap.tbl" md5="bad5668b4355363533c09e395d246a45" timestamp="1260697812" time_generated="1263662881" time_taken_to_generate="0" size="645631">
+ </export>
+ <export format="prolog" path="obo-all/emap/emap.pro" md5="2e6f93d1b47d31c0f8e9e76ecaf5764e" timestamp="1263425122" time_generated="1263662881" time_taken_to_generate="0" size="3447482">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/emap/emap.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1260697861" time_generated="1263662894" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" path="obo-all/emap/emap.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1260697863" time_generated="1263662894" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/emap/emap.obo.html" md5="066cafca251fd7271b4c5e095837dd8c" timestamp="1260697865" time_generated="1263662894" time_taken_to_generate="0" size="8367663">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="envo">
+ <source></source>
+ <prerelease_download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/environmental/envo-edit.obo</prerelease_download>
+ <granularity>molecular,cellular,organismal,multi-organismal</granularity>
+ <status>Discussion and review</status>
+ <subtypes_of>bfo:IndependentContinuant</subtypes_of>
+ <contact>Norman Morrison obo-envo lists.sourceforge.net</contact>
+ <foundry>Yes</foundry>
+ <domain>environment</domain>
+ <documentation>http://www.envoc.org</documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/environmental/envo.obo</url>
+ <patho_type>all</patho_type>
+ <home>EnvO|http://environmentontology.org/</home>
+ <namespace>ENVO</namespace>
+ <description>Ontology of environmental features and habitats</description>
+ <format>obo</format>
+ <title>Environment Ontology</title>
+ <relevant_organism>all</relevant_organism>
+ <download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/environmental/envo.obo</download>
+ <export format="obo_xml" path="obo-all/envo/envo.obo_xml" md5="ed472155e9ecd29c7dbcdfc2a5239a65" timestamp="1260697871" time_generated="1263662900" time_taken_to_generate="0" size="896221">
+ </export>
+ <export format="obo" path="obo-all/envo/envo.obo" md5="d4496a4f63c40c346bab9655422e9e1b" timestamp="1263662900" time_generated="1263662900" time_taken_to_generate="0" size="352372">
+ </export>
+ <export format="owl" path="obo-all/envo/envo.owl" md5="0706e0f6c3d40940bc9c2dfd85b5bd7e" timestamp="1260697899" time_generated="1263662900" time_taken_to_generate="0" size="2296919">
+ </export>
+ <export format="chadoxml" path="obo-all/envo/envo.chadoxml" md5="36ad3fb559f44d6e12fbf2bb33b9800a" timestamp="1260697911" time_generated="1263662900" time_taken_to_generate="0" size="2251058">
+ </export>
+ <export format="godb_prestore" path="obo-all/envo/envo.godb_prestore" md5="955ab6cd5f0b0be9ff252824955e4711" timestamp="1260697916" time_generated="1263662900" time_taken_to_generate="0" size="1705775">
+ </export>
+ <export format="rdf" path="obo-all/envo/envo.rdf" md5="7991f4316e5d86b0d943cc95a767ece0" timestamp="1260697922" time_generated="1263662900" time_taken_to_generate="0" size="971403">
+ </export>
+ <export format="tbl" path="obo-all/envo/envo.tbl" md5="70886922fb1bb4e747e2b6c21f38dc84" timestamp="1260697926" time_generated="1263662900" time_taken_to_generate="0" size="163579">
+ </export>
+ <export format="prolog" path="obo-all/envo/envo.pro" md5="d9e169fa01e0a7e42907a540c57c78a7" timestamp="1263423635" time_generated="1263662900" time_taken_to_generate="0" size="913494">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/envo/envo.validation_report" md5="b51f15a866c6303ace753e7b1b601290" timestamp="1260697937" time_generated="1263662904" time_taken_to_generate="0" size="320">
+ </export>
+ <export format="stats" path="obo-all/envo/envo.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1260697939" time_generated="1263662904" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/envo/envo.obo.html" md5="3701b8d64b904f28d515bfd343f4b2ae" timestamp="1260697939" time_generated="1263662904" time_taken_to_generate="0" size="1916796">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="event">
+ <source>Event Ontology Download|http://www.inoh.org/ontologies/EventOntology.obo</source>
+ <namespace>IEV</namespace>
+ <status>Active</status>
+ <contact>INOH curators curator inoh.org</contact>
+ <description>A structured controlled vocabulary of pathway centric biological processes. This ontology is a INOH pathway annotation ontology, one of a set of ontologies intended to be used in pathway data annotation to ease data integration. This ontology is used to annotate biological processes, pathways, sub-pathways in the INOH pathway data.<br>INOH is part of the BioPAX working group.</description>
+ <foundry>No</foundry>
+ <domain>biological process</domain>
+ <format>obo</format>
+ <documentation>INOH Ontologies|http://www.inoh.org/info/ontologies/</documentation>
+ <url>http://www.inoh.org/ontologies/EventOntology.obo</url>
+ <title>Event (INOH pathway ontology)</title>
+ <source_label>Event Ontology Download</source_label>
+ <home>The INOH Pathway Database|http://www.inoh.org</home>
+ <download></download>
+ <export format="obo_xml" path="obo-all/event/event.obo_xml" md5="8e9e1d88a110070220aeec92b13f4d3c" timestamp="1260697949" time_generated="1263662909" time_taken_to_generate="0" size="1038203">
+ </export>
+ <export format="obo" path="obo-all/event/event.obo" md5="de6235966a009d95cb9e9ef33500cdc1" timestamp="1263662909" time_generated="1263662909" time_taken_to_generate="0" size="703211">
+ </export>
+ <export format="owl" path="obo-all/event/event.owl" md5="f6aff3d3073081bf1fcf92db96e22355" timestamp="1260698077" time_generated="1263662909" time_taken_to_generate="0" size="2452595">
+ </export>
+ <export format="chadoxml" path="obo-all/event/event.chadoxml" md5="7e6afe65728e2594e6c0a29a463ac9cf" timestamp="1260698119" time_generated="1263662909" time_taken_to_generate="0" size="2694759">
+ </export>
+ <export format="godb_prestore" path="obo-all/event/event.godb_prestore" md5="24b3ceaa9c6a050aeee15f45b86972f7" timestamp="1260698126" time_generated="1263662909" time_taken_to_generate="0" size="2641708">
+ </export>
+ <export format="rdf" path="obo-all/event/event.rdf" md5="bad08cea49b0887e78155549bc2cb77f" timestamp="1260698136" time_generated="1263662909" time_taken_to_generate="0" size="1469104">
+ </export>
+ <export format="tbl" path="obo-all/event/event.tbl" md5="3e6d6025b8a4e543efa5a06bbc07a425" timestamp="1260698142" time_generated="1263662909" time_taken_to_generate="0" size="247037">
+ </export>
+ <export format="prolog" path="obo-all/event/event.pro" md5="aea2550dacde6e597290c00f074be9d0" timestamp="1260698153" time_generated="1263662909" time_taken_to_generate="0" size="1144405">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/event/event.validation_report" md5="c1226942327514057a3da0ad9b32b933" timestamp="1260698165" time_generated="1263662914" time_taken_to_generate="0" size="23980">
+ </export>
+ <export format="stats" path="obo-all/event/event.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1260698167" time_generated="1263662914" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/event/event.obo.html" md5="476bed240b84bddba521a5839d6fc63d" timestamp="1260698167" time_generated="1263662914" time_taken_to_generate="0" size="3022187">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="evidence_code">
+ <source></source>
+ <granularity>molecular,cellular,organismal,multi-organismal</granularity>
+ <status>Production and review</status>
+ <subtypes_of>bfo:DependentContinuant</subtypes_of>
+ <contact>Michelle Gwinn Giglio mgiglio som.umaryland.edu</contact>
+ <foundry>Yes</foundry>
+ <domain>experiments</domain>
+ <documentation></documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/evidence_code.obo</url>
+ <patho_type>canonical</patho_type>
+ <home></home>
+ <namespace>ECO</namespace>
+ <description>A rich ontology for experimental and other evidence statements.</description>
+ <format>obo</format>
+ <title>Evidence codes</title>
+ <relevant_organism>all</relevant_organism>
+ <download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/evidence_code.obo</download>
+ <export format="obo_xml" path="obo-all/evidence_code/evidence_code.obo_xml" md5="22fec287f140b3a114fda31771973cf9" timestamp="1260698171" time_generated="1263662917" time_taken_to_generate="0" size="68185">
+ </export>
+ <export format="obo" path="obo-all/evidence_code/evidence_code.obo" md5="6e5bac4ed8635d99818f34877ffa9fbc" timestamp="1263662917" time_generated="1263662917" time_taken_to_generate="0" size="50307">
+ </export>
+ <export format="owl" path="obo-all/evidence_code/evidence_code.owl" md5="c3a54de03d8d5021273174b1e8ebec52" timestamp="1260698171" time_generated="1263662917" time_taken_to_generate="0" size="127940">
+ </export>
+ <export format="chadoxml" path="obo-all/evidence_code/evidence_code.chadoxml" md5="5cb2c447bb890e9a3df53e7f24c39368" timestamp="1260698171" time_generated="1263662917" time_taken_to_generate="0" size="167202">
+ </export>
+ <export format="godb_prestore" path="obo-all/evidence_code/evidence_code.godb_prestore" md5="f31e3a8942a81e8cb0e47c5bc066f1c9" timestamp="1260698172" time_generated="1263662917" time_taken_to_generate="0" size="135482">
+ </export>
+ <export format="rdf" path="obo-all/evidence_code/evidence_code.rdf" md5="3e9a375a7a478f973735d359dc4ac571" timestamp="1260698172" time_generated="1263662917" time_taken_to_generate="0" size="75594">
+ </export>
+ <export format="tbl" path="obo-all/evidence_code/evidence_code.tbl" md5="65706b4cfa5134974c55b4e9cb2944a0" timestamp="1260698172" time_generated="1263662917" time_taken_to_generate="0" size="30429">
+ </export>
+ <export format="prolog" path="obo-all/evidence_code/evidence_code.pro" md5="32bf9d57675daec5cce78aa7fd8da09c" timestamp="1260698173" time_generated="1263662917" time_taken_to_generate="0" size="77218">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/evidence_code/evidence_code.validation_report" md5="a1fe3d96637a32595f43805bcecba425" timestamp="1260698175" time_generated="1263662917" time_taken_to_generate="0" size="188">
+ </export>
+ <export format="stats" path="obo-all/evidence_code/evidence_code.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1260698176" time_generated="1263662917" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/evidence_code/evidence_code.obo.html" md5="cfd795a671022c496898ee27aa44ea88" timestamp="1260698176" time_generated="1263662917" time_taken_to_generate="0" size="172357">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="evoc">
+ <source>http://www.evocontology.org/uploads/Main/evoc_v2.7_obo.tar.gz</source>
+ <namespace>EV</namespace>
+ <status>Active</status>
+ <contact>eVOC mailing list evoc sanbi.ac.za</contact>
+ <description>Provides structured controlled vocabularies for the annotation of expressed sequences with respect to anatomical system, cell type, developmental stage, experimental technique, microarray platform, pathology, pooling, tissue preparation and treatment.</description>
+ <foundry>No</foundry>
+ <domain>experiments</domain>
+ <format>obo</format>
+ <documentation></documentation>
+ <url>http://www.evocontology.org/uploads/Main/evoc_v2.7_obo.tar.gz</url>
+ <title>eVOC (Expressed Sequence Annotation for Humans)</title>
+ <home>eVoc|http://www.evocontology.org/</home>
+ <download></download>
+ <export format="obo_xml" path="obo-all/evoc/evoc.obo_xml" md5="483af4b34d4f7990497c03d6336265fe" timestamp="1260698182" time_generated="1263662921" time_taken_to_generate="0" size="174987">
+ </export>
+ <export format="obo" path="obo-all/evoc/evoc.obo" md5="694b13b8115a272157b55ccc4a4ced54" timestamp="1263662921" time_generated="1263662921" time_taken_to_generate="0" size="71540">
+ </export>
+ <export format="owl" path="obo-all/evoc/evoc.owl" md5="6f3137ae98bdcc4f18dbe1fbb8c58a26" timestamp="1260698185" time_generated="1263662921" time_taken_to_generate="0" size="362380">
+ </export>
+ <export format="chadoxml" path="obo-all/evoc/evoc.chadoxml" md5="d05c2e46e69c0b2fdc6310a7e314f1d0" timestamp="1260698187" time_generated="1263662921" time_taken_to_generate="0" size="653352">
+ </export>
+ <export format="godb_prestore" path="obo-all/evoc/evoc.godb_prestore" md5="1a24cd8a805e1ec5808e5edab6a177b5" timestamp="1260698188" time_generated="1263662921" time_taken_to_generate="0" size="415890">
+ </export>
+ <export format="rdf" path="obo-all/evoc/evoc.rdf" md5="44ee04072fea3c02e06d245f69c8f3d4" timestamp="1260698190" time_generated="1263662921" time_taken_to_generate="0" size="291347">
+ </export>
+ <export format="tbl" path="obo-all/evoc/evoc.tbl" md5="df0010a590c4984f8e71452fbfa70bf5" timestamp="1260698192" time_generated="1263662921" time_taken_to_generate="0" size="31755">
+ </export>
+ <export format="prolog" path="obo-all/evoc/evoc.pro" md5="f5c3409fde81c43da8d3460c2446964e" timestamp="1260698194" time_generated="1263662921" time_taken_to_generate="0" size="209451">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/evoc/evoc.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1260698197" time_generated="1263662922" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" path="obo-all/evoc/evoc.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1260698198" time_generated="1263662922" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/evoc/evoc.obo.html" md5="17851c5058b0cbc138f2f54a84ca89d3" timestamp="1260698199" time_generated="1263662922" time_taken_to_generate="0" size="631337">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="fix">
+ <source>http://www.ebi.ac.uk/~kirill/FIX/fix.obo</source>
+ <namespace>FIX</namespace>
+ <status>Inactive</status>
+ <contact>Kirill Degtyarenko chebi-help ebi.ac.uk</contact>
+ <description>FIX consists of two ontologies: methods and properties (but not objects, which are subject of the chemical ontology). The methods are applied to study the properties.</description>
+ <foundry>No</foundry>
+ <format>obo</format>
+ <documentation></documentation>
+ <url>http://www.ebi.ac.uk/~kirill/FIX/fix.obo</url>
+ <title>Physico-chemical methods and properties</title>
+ <home></home>
+ <download></download>
+ <export format="obo_xml" path="obo-all/fix/fix.obo_xml" md5="adefe9f9f8afcab955147eff16e514e2" timestamp="1260698204" time_generated="1263662926" time_taken_to_generate="0" size="297898">
+ </export>
+ <export format="obo" path="obo-all/fix/fix.obo" md5="8c7693ace6f7eab4ba25f4aa87def287" timestamp="1263662926" time_generated="1263662926" time_taken_to_generate="0" size="178238">
+ </export>
+ <export format="owl" path="obo-all/fix/fix.owl" md5="5095575951c308639334e319d1ae7af3" timestamp="1260698213" time_generated="1263662926" time_taken_to_generate="0" size="644021">
+ </export>
+ <export format="chadoxml" path="obo-all/fix/fix.chadoxml" md5="cf4b62355d4d8d7a11dac1b13c25229b" timestamp="1260698215" time_generated="1263662926" time_taken_to_generate="0" size="1008975">
+ </export>
+ <export format="godb_prestore" path="obo-all/fix/fix.godb_prestore" md5="7105ba89237e860e171fb00701887f9a" timestamp="1260698217" time_generated="1263662926" time_taken_to_generate="0" size="749980">
+ </export>
+ <export format="rdf" path="obo-all/fix/fix.rdf" md5="029ec674416db0db392c25e7011d8040" timestamp="1260698220" time_generated="1263662926" time_taken_to_generate="0" size="486875">
+ </export>
+ <export format="tbl" path="obo-all/fix/fix.tbl" md5="536c0578b1ebb846297cba5720dc22be" timestamp="1260698221" time_generated="1263662926" time_taken_to_generate="0" size="57567">
+ </export>
+ <export format="prolog" path="obo-all/fix/fix.pro" md5="b85c771b69113308fe6cc34748db5481" timestamp="1260698224" time_generated="1263662926" time_taken_to_generate="0" size="351297">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/fix/fix.validation_report" md5="5f00db55a7a586e242bb344442c2bc80" timestamp="1260698228" time_generated="1263662928" time_taken_to_generate="0" size="381">
+ </export>
+ <export format="stats" path="obo-all/fix/fix.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1260698230" time_generated="1263662928" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/fix/fix.obo.html" md5="71d404ab24494df02c1ad9e22a1075dc" timestamp="1260698230" time_generated="1263662928" time_taken_to_generate="0" size="984545">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="fly_anatomy">
+ <source></source>
+ <prerelease_download></prerelease_download>
+ <granularity>organismal</granularity>
+ <status>Production and review</status>
+ <subtypes_of>CARO:0000000</subtypes_of>
+ <contact>David Osumi-Sutherland obo-anatomy lists.sourceforge.net</contact>
+ <foundry>Yes</foundry>
+ <domain>anatomy</domain>
+ <documentation></documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/fly/fly_anatomy.obo</url>
+ <patho_type>canonical</patho_type>
+ <home>FlyBase|https://cedar.bio.indiana.edu/trac/env/ontologies/wiki/PublicNewsletterIndex</home>
+ <xrefs_to>caro,cellular_component</xrefs_to>
+ <namespace>FBbt</namespace>
+ <description>A structured controlled vocabulary of the anatomy of <i>Drosophila melanogaster</i>.</description>
+ <prereasoned_ontology>fly_anatomy_xp</prereasoned_ontology>
+ <format>obo</format>
+ <title>Drosophila gross anatomy</title>
+ <relevant_organism>NCBITaxon:7227|Drosophila</relevant_organism>
+ <download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/fly/fly_anatomy.obo</download>
+ <export format="obo_xml" path="obo-all/fly_anatomy/fly_anatomy.obo_xml" md5="7e27109bf29cbc24024eac54e536ba1d" timestamp="1260698244" time_generated="1263662936" time_taken_to_generate="0" size="2612277">
+ </export>
+ <export format="obo" path="obo-all/fly_anatomy/fly_anatomy.obo" md5="8833243d952e06d4490a4b60dfa8da70" timestamp="1263662935" time_generated="1263662936" time_taken_to_generate="0" size="1520495">
+ </export>
+ <export format="owl" path="obo-all/fly_anatomy/fly_anatomy.owl" md5="c7990d10ab96ccbd8d7fa5c6fab722a9" timestamp="1260699042" time_generated="1263662936" time_taken_to_generate="0" size="5896251">
+ </export>
+ <export format="chadoxml" path="obo-all/fly_anatomy/fly_anatomy.chadoxml" md5="87b7a020a74be858f8632250025db1c5" timestamp="1260699159" time_generated="1263662936" time_taken_to_generate="0" size="6537551">
+ </export>
+ <export format="godb_prestore" path="obo-all/fly_anatomy/fly_anatomy.godb_prestore" md5="2a1ee682adf59c11f1adf77105cde21c" timestamp="1260699168" time_generated="1263662936" time_taken_to_generate="0" size="7083156">
+ </export>
+ <export format="rdf" path="obo-all/fly_anatomy/fly_anatomy.rdf" md5="5d1eafcbe3e052088cf43b999d435e5e" timestamp="1260699180" time_generated="1263662936" time_taken_to_generate="0" size="2879459">
+ </export>
+ <export format="tbl" path="obo-all/fly_anatomy/fly_anatomy.tbl" md5="5ac542778e69e1d2b1f3ec8bea771fb4" timestamp="1260699187" time_generated="1263662936" time_taken_to_generate="0" size="495142">
+ </export>
+ <export format="prolog" path="obo-all/fly_anatomy/fly_anatomy.pro" md5="09dcf65cc54d571865b88935aeb6b724" timestamp="1263318824" time_generated="1263662936" time_taken_to_generate="0" size="3179540">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/fly_anatomy/fly_anatomy.validation_report" md5="358fb8c814d6aa2c145d0294d1aa9fe7" timestamp="1260699331" time_generated="1263662948" time_taken_to_generate="0" size="117008">
+ </export>
+ <export format="stats" path="obo-all/fly_anatomy/fly_anatomy.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1260699332" time_generated="1263662948" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/fly_anatomy/fly_anatomy.obo.html" md5="264e37991fe836e65e377468f8847cc4" timestamp="1260699333" time_generated="1263662948" time_taken_to_generate="0" size="7198917">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="sdiff" path="obo-all/fly_anatomy/fly_anatomy.sdiff" md5="9a126a65b473a173af09f40a12987cf3" timestamp="1263662976" time_generated="1263662977" time_taken_to_generate="29" size="538">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="fly_development">
+ <source></source>
+ <granularity>organismal</granularity>
+ <status>Production and review</status>
+ <subtypes_of>bfo:Occurent</subtypes_of>
+ <contact>David Osumi-Sutherland obo-anatomy lists.sourceforge.net</contact>
+ <foundry>Yes</foundry>
+ <domain>anatomy</domain>
+ <documentation></documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/developmental/animal_development/fly/fly_development.obo</url>
+ <patho_type>canonical</patho_type>
+ <home>FlyBase|http://www.flybase.org/</home>
+ <namespace>FBdv</namespace>
+ <description>A structured controlled vocabulary of the development of <i>Drosophila melanogaster</i>.</description>
+ <format>obo</format>
+ <title>Drosophila development</title>
+ <relevant_organism>NCBITaxon:7227|Drosophila</relevant_organism>
+ <download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/developmental/animal_development/fly/fly_development.obo</download>
+ <export format="obo_xml" path="obo-all/fly_development/fly_development.obo_xml" md5="fc9137137e5e00f294ef262380f8ef9c" timestamp="1260699337" time_generated="1263662985" time_taken_to_generate="0" size="117750">
+ </export>
+ <export format="obo" path="obo-all/fly_development/fly_development.obo" md5="69ba2008b28679be0fca1e1e7992fe38" timestamp="1263662985" time_generated="1263662985" time_taken_to_generate="0" size="69873">
+ </export>
+ <export format="owl" path="obo-all/fly_development/fly_development.owl" md5="e1e561aef6b3c6502a55dd6715cc8a5e" timestamp="1260699337" time_generated="1263662985" time_taken_to_generate="0" size="275124">
+ </export>
+ <export format="chadoxml" path="obo-all/fly_development/fly_development.chadoxml" md5="c4fa923c00ae6df76d4092758ec32160" timestamp="1260699338" time_generated="1263662985" time_taken_to_generate="0" size="252451">
+ </export>
+ <export format="godb_prestore" path="obo-all/fly_development/fly_development.godb_prestore" md5="c7dccce71e177694a3f69e63623956ed" timestamp="1260699338" time_generated="1263662985" time_taken_to_generate="0" size="259494">
+ </export>
+ <export format="rdf" path="obo-all/fly_development/fly_development.rdf" md5="90600342813fc2f5c53223451f3904b6" timestamp="1260699339" time_generated="1263662985" time_taken_to_generate="0" size="108553">
+ </export>
+ <export format="tbl" path="obo-all/fly_development/fly_development.tbl" md5="caad7ee7baf48960fad7e230e46f72b8" timestamp="1260699339" time_generated="1263662985" time_taken_to_generate="0" size="29208">
+ </export>
+ <export format="prolog" path="obo-all/fly_development/fly_development.pro" md5="0a892f1ada900ec0d6eed8779d3bf615" timestamp="1260699340" time_generated="1263662985" time_taken_to_generate="0" size="114931">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" problem="true">
+ </export>
+ <export format="stats" problem="true">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/fly_development/fly_development.obo.html" md5="86ce28d4f1e7c78368d316f3c9fc9393" timestamp="1260699340" time_generated="1263662986" time_taken_to_generate="0" size="235817">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="fly_taxonomy">
+ <source></source>
+ <granularity>organismal</granularity>
+ <status>Discussion and review</status>
+ <subtypes_of>bfo:IndependentContinuant</subtypes_of>
+ <contact>Michael Ashburner ma11 gen.cam.ac.uk</contact>
+ <foundry>Yes</foundry>
+ <domain>taxonomy</domain>
+ <documentation></documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/taxonomy/fly_taxonomy.obo</url>
+ <patho_type>canonical</patho_type>
+ <home>FlyBase|http://www.flybase.org/</home>
+ <xrefs_to>ncbi_taxonomy</xrefs_to>
+ <namespace>FBsp</namespace>
+ <description>The taxonomy of the family <i>Drosophilidae</i> (largely after Baechli) and of other taxa referred to in FlyBase.</description>
+ <format>obo</format>
+ <title>Fly taxonomy</title>
+ <relevant_organism>NCBITaxon:7227|Drosophila</relevant_organism>
+ <download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/taxonomy/fly_taxonomy.obo</download>
+ <export format="obo_xml" path="obo-all/fly_taxonomy/fly_taxonomy.obo_xml" md5="f47334250ee0efdfcf498b514c3f1d17" timestamp="1260699348" time_generated="1263662996" time_taken_to_generate="0" size="1616040">
+ </export>
+ <export format="obo" path="obo-all/fly_taxonomy/fly_taxonomy.obo" md5="b5e606c63b83d37f6e20f8faf8993c8d" timestamp="1263662996" time_generated="1263662996" time_taken_to_generate="0" size="838705">
+ </export>
+ <export format="owl" path="obo-all/fly_taxonomy/fly_taxonomy.owl" md5="2cd26416d5b2947e4b4800781231fb8f" timestamp="1260699498" time_generated="1263662996" time_taken_to_generate="0" size="3234938">
+ </export>
+ <export format="chadoxml" path="obo-all/fly_taxonomy/fly_taxonomy.chadoxml" md5="ef2d3d5352b661e3a2abee50f7f1a49c" timestamp="1260699551" time_generated="1263662996" time_taken_to_generate="0" size="5232672">
+ </export>
+ <export format="godb_prestore" path="obo-all/fly_taxonomy/fly_taxonomy.godb_prestore" md5="8b2cc864ee62977af2803b67c4453f92" timestamp="1260699556" time_generated="1263662996" time_taken_to_generate="0" size="4106302">
+ </export>
+ <export format="rdf" path="obo-all/fly_taxonomy/fly_taxonomy.rdf" md5="3abcafbb478f7d3f73fda39832d8070a" timestamp="1260699566" time_generated="1263662996" time_taken_to_generate="0" size="2499659">
+ </export>
+ <export format="tbl" path="obo-all/fly_taxonomy/fly_taxonomy.tbl" md5="103e8c68b4e881836c21da1c3fec3fe8" timestamp="1260699571" time_generated="1263662996" time_taken_to_generate="0" size="333023">
+ </export>
+ <export format="prolog" path="obo-all/fly_taxonomy/fly_taxonomy.pro" md5="1edc5f7a2b0b74abc0a225a6f8a904ae" timestamp="1263318865" time_generated="1263662996" time_taken_to_generate="0" size="2159674">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/fly_taxonomy/fly_taxonomy.validation_report" md5="10c758609daea811ac66f0d3b1c4caac" timestamp="1260699592" time_generated="1263663005" time_taken_to_generate="0" size="1560">
+ </export>
+ <export format="stats" path="obo-all/fly_taxonomy/fly_taxonomy.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1260699593" time_generated="1263663005" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/fly_taxonomy/fly_taxonomy.obo.html" md5="d0b3a4fd1b0b4831dac96fbb90ff1620" timestamp="1260699594" time_generated="1263663005" time_taken_to_generate="0" size="4943177">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="sdiff" path="obo-all/fly_taxonomy/fly_taxonomy.sdiff" md5="d41d8cd98f00b204e9800998ecf8427e" timestamp="1263663005" time_generated="1263663041" time_taken_to_generate="36" size="0">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="flybase_vocab">
+ <source></source>
+ <namespace>FBcv</namespace>
+ <status>Inactive</status>
+ <contact>Michael Ashburner ma11 gen.cam.ac.uk</contact>
+ <description>A structured controlled vocabulary used for various aspects of annotation by FlyBase.<br>This ontology is maintained by FlyBase for various aspects of annotation not covered, or not yet covered, by other OBO ontologies. If and when community ontologies are available for the domains here covered FlyBase will use them.</description>
+ <foundry>No</foundry>
+ <format>obo</format>
+ <documentation>FlyBase Reference Manual|http://flybase.bio.indiana.edu/.data/docs/refman/refman-G.html#G.2</documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/vocabularies/flybase_controlled_vocabulary.obo</url>
+ <title>FlyBase Controlled Vocabulary</title>
+ <is_obsolete>true</is_obsolete>
+ <home>FlyBase|http://www.flybase.org/</home>
+ <download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/vocabularies/flybase_controlled_vocabulary.obo</download>
+ <export format="obo_xml" path="obo-all/flybase_vocab/flybase_vocab.obo_xml" md5="2a5f0aec5dd3e722514001f54d3a1414" timestamp="1260699597" time_generated="1263663046" time_taken_to_generate="0" size="223853">
+ </export>
+ <export format="obo" path="obo-all/flybase_vocab/flybase_vocab.obo" md5="e227c3428e55354c3fb0dae0fad7b1d4" timestamp="1263663046" time_generated="1263663046" time_taken_to_generate="0" size="156239">
+ </export>
+ <export format="owl" path="obo-all/flybase_vocab/flybase_vocab.owl" md5="42a63eb5a6643d1b6e5272f723638536" timestamp="1260699598" time_generated="1263663046" time_taken_to_generate="0" size="442861">
+ </export>
+ <export format="chadoxml" path="obo-all/flybase_vocab/flybase_vocab.chadoxml" md5="56ae452b7f3c8d92625036fa032de97c" timestamp="1260699599" time_generated="1263663046" time_taken_to_generate="0" size="571857">
+ </export>
+ <export format="godb_prestore" path="obo-all/flybase_vocab/flybase_vocab.godb_prestore" md5="876901c1715c2860e38c7919e6632aaa" timestamp="1260699600" time_generated="1263663046" time_taken_to_generate="0" size="454191">
+ </export>
+ <export format="rdf" path="obo-all/flybase_vocab/flybase_vocab.rdf" md5="33910a1c9a285fe49d3a6801961c6c94" timestamp="1260699601" time_generated="1263663046" time_taken_to_generate="0" size="288841">
+ </export>
+ <export format="tbl" path="obo-all/flybase_vocab/flybase_vocab.tbl" md5="6804620465024394a39fe694302c5cf7" timestamp="1260699602" time_generated="1263663046" time_taken_to_generate="0" size="38498">
+ </export>
+ <export format="prolog" path="obo-all/flybase_vocab/flybase_vocab.pro" md5="2ad7763e31932d73ef91dd103c00202c" timestamp="1260699604" time_generated="1263663046" time_taken_to_generate="0" size="288701">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/flybase_vocab/flybase_vocab.validation_report" md5="9422366decd126e23f71bb9d806d76cd" timestamp="1260699605" time_generated="1263663047" time_taken_to_generate="0" size="209">
+ </export>
+ <export format="stats" path="obo-all/flybase_vocab/flybase_vocab.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1260699606" time_generated="1263663047" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/flybase_vocab/flybase_vocab.obo.html" md5="ae0958908c82205a6866855f3aa7c856" timestamp="1260699606" time_generated="1263663047" time_taken_to_generate="0" size="708362">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="fma_lite">
+ <source></source>
+ <prerelease_download>http://obo.svn.sourceforge.net/viewvc/*checkout*/obo/fma-conversion/trunk/fma3.obo</prerelease_download>
+ <granularity>organismal</granularity>
+ <status>Production and review</status>
+ <subtypes_of>CARO:0000000</subtypes_of>
+ <contact>OBO Anatomy obo-anatomy lists.sourceforge.net</contact>
+ <foundry>Yes</foundry>
+ <domain>anatomy</domain>
+ <documentation></documentation>
+ <url>http://obo.svn.sourceforge.net/viewvc/*checkout*/obo/fma-conversion/trunk/fma2_obo.obo</url>
+ <patho_type>canonical</patho_type>
+ <home>FMA|http://sig.biostr.washington.edu/projects/fm/index.html</home>
+ <namespace>FMA</namespace>
+ <description>Obo format translation of the FMA, omitting all relationships other than is_a, part_of and has_part. Future versions of fma_obo will include more relationships</description>
+ <format>obo</format>
+ <previousrelease_download>http://obo.svn.sourceforge.net/viewvc/*checkout*/obo/fma-conversion/trunk/fma_obo.obo</previousrelease_download>
+ <title>Foundational Model of Anatomy (subset)</title>
+ <relevant_organism>NCBITaxon:9606|Homo sapiens</relevant_organism>
+ <download>http://obo.svn.sourceforge.net/viewvc/*checkout*/obo/fma-conversion/trunk/fma2_obo.obo</download>
+ <export format="obo_xml" path="obo-all/fma_lite/fma_lite.obo_xml" md5="64a79282bc40d5f38e56aebb5f26efad" timestamp="1260699694" time_generated="1263663087" time_taken_to_generate="0" size="22282002">
+ </export>
+ <export format="obo" path="obo-all/fma_lite/fma_lite.obo" md5="efe2b72573709277e317a16fe9b14a92" timestamp="1263663087" time_generated="1263663088" time_taken_to_generate="0" size="15705701">
+ </export>
+ <export format="owl" problem="true">
+ </export>
+ <export format="chadoxml" path="obo-all/fma_lite/fma_lite.chadoxml" md5="05a768ee8ac3ce9d2f04e5a4bb806876" timestamp="1260728484" time_generated="1263694571" time_taken_to_generate="0" size="65661665">
+ </export>
+ <export format="godb_prestore" path="obo-all/fma_lite/fma_lite.godb_prestore" md5="9ba576c192f94e32c627b714780434d9" timestamp="1260728558" time_generated="1263694572" time_taken_to_generate="0" size="59598893">
+ </export>
+ <export format="rdf" path="obo-all/fma_lite/fma_lite.rdf" md5="d50b6ca9bc6fdd5119ac0f925892b5ec" timestamp="1260728663" time_generated="1263694573" time_taken_to_generate="0" size="30438631">
+ </export>
+ <export format="tbl" path="obo-all/fma_lite/fma_lite.tbl" md5="4efc9175d25cfa3690aed63313c7eb51" timestamp="1260728728" time_generated="1263694574" time_taken_to_generate="0" size="6048806">
+ </export>
+ <export format="prolog" path="obo-all/fma_lite/fma_lite.pro" md5="ad4c66774a0ac567660ba0f25be33cb3" timestamp="1263425527" time_generated="1263694574" time_taken_to_generate="0" size="29272954">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/fma_lite/fma_lite.validation_report" md5="50a10156a7a76f4d7bf088751b11113b" timestamp="1260729064" time_generated="1263694628" time_taken_to_generate="0" size="105">
+ </export>
+ <export format="stats" path="obo-all/fma_lite/fma_lite.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1260729066" time_generated="1263694628" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/fma_lite/fma_lite.obo.html" md5="27aa92c74b000ef86c85a96b86b84f3c" timestamp="1260729073" time_generated="1263694628" time_taken_to_generate="0" size="66834799">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="fungal_anatomy">
+ <source></source>
+ <granularity>organismal</granularity>
+ <status>Production and review</status>
+ <subtypes_of>CARO:0000000</subtypes_of>
+ <contact>Maria Costanzo maria genome.stanford.edu</contact>
+ <foundry>Yes</foundry>
+ <domain>anatomy</domain>
+ <documentation>description|http://www.yeastgenome.org/fungi/fungal_anatomy_ontology/#description</documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/microbial_gross_anatomy/fungi/fungal_anatomy.obo</url>
+ <patho_type>canonical</patho_type>
+ <home>fungal gross anatomy|http://www.yeastgenome.org/fungi/fungal_anatomy_ontology/</home>
+ <namespace>FAO</namespace>
+ <description>A structured controlled vocabulary for the anatomy of fungi.</description>
+ <format>obo</format>
+ <title>Fungal gross anatomy</title>
+ <relevant_organism>NCBITaxon:4751|Fungal</relevant_organism>
+ <download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/microbial_gross_anatomy/fungi/fungal_anatomy.obo</download>
+ <export format="obo_xml" path="obo-all/fungal_anatomy/fungal_anatomy.obo_xml" md5="96fc528859159855b0c06ad7bc37af72" timestamp="1260729076" time_generated="1263694631" time_taken_to_generate="0" size="40063">
+ </export>
+ <export format="obo" path="obo-all/fungal_anatomy/fungal_anatomy.obo" md5="8a45ece7c0f12ac5b3495008ae633372" timestamp="1263694631" time_generated="1263694631" time_taken_to_generate="0" size="19831">
+ </export>
+ <export format="owl" path="obo-all/fungal_anatomy/fungal_anatomy.owl" md5="92a529c8a114d0e06d274e4675490bfc" timestamp="1260729076" time_generated="1263694631" time_taken_to_generate="0" size="95808">
+ </export>
+ <export format="chadoxml" path="obo-all/fungal_anatomy/fungal_anatomy.chadoxml" md5="a935b9d17b5ca57b4edfaf5bf889da98" timestamp="1260729076" time_generated="1263694631" time_taken_to_generate="0" size="101404">
+ </export>
+ <export format="godb_prestore" path="obo-all/fungal_anatomy/fungal_anatomy.godb_prestore" md5="74f58f17f429abcc0217a3d530e1471b" timestamp="1260729077" time_generated="1263694631" time_taken_to_generate="0" size="84804">
+ </export>
+ <export format="rdf" path="obo-all/fungal_anatomy/fungal_anatomy.rdf" md5="eb198871de1cf595121383b912390847" timestamp="1260729077" time_generated="1263694631" time_taken_to_generate="0" size="36822">
+ </export>
+ <export format="tbl" path="obo-all/fungal_anatomy/fungal_anatomy.tbl" md5="9e31ac0b681b0c9f6ee4b1fc51dadf86" timestamp="1260729077" time_generated="1263694631" time_taken_to_generate="0" size="11781">
+ </export>
+ <export format="prolog" path="obo-all/fungal_anatomy/fungal_anatomy.pro" md5="9936042f978aa5f219623bd730e780b1" timestamp="1260729078" time_generated="1263694631" time_taken_to_generate="0" size="36477">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/fungal_anatomy/fungal_anatomy.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1260729078" time_generated="1263694631" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" path="obo-all/fungal_anatomy/fungal_anatomy.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1260729079" time_generated="1263694631" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/fungal_anatomy/fungal_anatomy.obo.html" md5="5f400d8fe77a7a78f40a4fe1890d28ee" timestamp="1260729079" time_generated="1263694631" time_taken_to_generate="0" size="83528">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="yeast_phenotype">
+ <source></source>
+ <granularity>organismal</granularity>
+ <status>Production and review</status>
+ <subtypes_of>CARO:0000000</subtypes_of>
+ <contact>Mike Cherry cherry genome.stanford.edu</contact>
+ <foundry>Yes</foundry>
+ <domain>phenotype</domain>
+ <documentation></documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/yeast_phenotype.obo</url>
+ <patho_type>canonical</patho_type>
+ <is_obsolete>true</is_obsolete>
+ <home>Saccharomyces Genome Database|http://www.yeastgenome.org/ </home>
+ <namespace>YPO</namespace>
+ <replaced_by>ascomycete_phenotype</replaced_by>
+ <description>A structured controlled vocabulary for the phenotypes of budding yeast.</description>
+ <format>obo</format>
+ <title>Yeast phenotypes</title>
+ <relevant_organism>NCBITaxon:4932|Saccharomyces cerevisiae</relevant_organism>
+ <download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/yeast_phenotype.obo</download>
+ <export format="obo_xml" path="obo-all/yeast_phenotype/yeast_phenotype.obo_xml" md5="5fc4cab0ca0443ba6aaee7156a90e546" timestamp="1262993580" time_generated="1263694632" time_taken_to_generate="0" size="126337">
+ </export>
+ <export format="obo" path="obo-all/yeast_phenotype/yeast_phenotype.obo" md5="108bd1a426cde6c9905386b94f28c224" timestamp="1263694632" time_generated="1263694632" time_taken_to_generate="0" size="76296">
+ </export>
+ <export format="owl" path="obo-all/yeast_phenotype/yeast_phenotype.owl" md5="212a6b01d6d89f572e9fd60e2cdf6137" timestamp="1262993581" time_generated="1263694632" time_taken_to_generate="0" size="289815">
+ </export>
+ <export format="chadoxml" path="obo-all/yeast_phenotype/yeast_phenotype.chadoxml" md5="cb120b7f000cef299dbdfff1d71d46aa" timestamp="1262993581" time_generated="1263694632" time_taken_to_generate="0" size="320052">
+ </export>
+ <export format="godb_prestore" path="obo-all/yeast_phenotype/yeast_phenotype.godb_prestore" md5="d9d72d47d61e98578887f40b6291ddc9" timestamp="1262993582" time_generated="1263694633" time_taken_to_generate="0" size="400702">
+ </export>
+ <export format="rdf" path="obo-all/yeast_phenotype/yeast_phenotype.rdf" md5="43816bb506ec0b572d36ad2ee742c8ee" timestamp="1262993583" time_generated="1263694633" time_taken_to_generate="0" size="126140">
+ </export>
+ <export format="tbl" path="obo-all/yeast_phenotype/yeast_phenotype.tbl" md5="d99f0fef12fcbe61f09a6bc75ca19ce9" timestamp="1262993583" time_generated="1263694633" time_taken_to_generate="0" size="28054">
+ </export>
+ <export format="prolog" path="obo-all/yeast_phenotype/yeast_phenotype.pro" md5="4e11a90dc8579d458fbfd1a8e53030ac" timestamp="1262993584" time_generated="1263694633" time_taken_to_generate="0" size="161442">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/yeast_phenotype/yeast_phenotype.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1262993585" time_generated="1263694633" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" path="obo-all/yeast_phenotype/yeast_phenotype.stats" md5="71666b8d5da5f0cdd71d1938865d3a1c" timestamp="1262993586" time_generated="1263694633" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/yeast_phenotype/yeast_phenotype.obo.html" md5="a476a0ee1ef2459d441209cf6cb256ac" timestamp="1262993586" time_generated="1263694633" time_taken_to_generate="0" size="417642">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="gene_regulation">
+ <source>http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO_latest</source>
+ <namespace>BOOTStrep</namespace>
+ <status>Active</status>
+ <contact>Vivian Lee vlee ebi.ac.uk</contact>
+ <description>The BOOTStrep Ontology is a conceptual model for the domain of gene regulation. It covers processes that are linked to the regulation of gene expression as well as physical entities that are involved in these processes (such as genes and transcription factors) in terms of ontology classes and semantic relations between classes. GRO is intended to represent common knowledge about gene regulation in a formal way rather than representing extremely fine-grained classes as ca [...]
+ <foundry>No</foundry>
+ <domain>genomic</domain>
+ <format>owl</format>
+ <documentation></documentation>
+ <url>http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO_latest</url>
+ <title>Gene Regulation Ontology</title>
+ <home>http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO.html</home>
+ <download></download>
+ <export format="pro" path="obo-all/gene_regulation/gene_regulation.pro" md5="e378ab397511ebbc1f4e05b139b9cdc7" timestamp="1260729099" time_generated="1263694636" time_taken_to_generate="0" size="437649">
+ </export>
+ <export format="obo" path="obo-all/gene_regulation/gene_regulation.obo" md5="fa09af2743f9af470aba8023ba504c84" timestamp="1260729095" time_generated="1263694636" time_taken_to_generate="0" size="286398">
+ </export>
+ <export format="obo_xml" path="obo-all/gene_regulation/gene_regulation.obo_xml" md5="bd574ed603baa02d90bfdef4594b8002" timestamp="1260729095" time_generated="1263694636" time_taken_to_generate="0" size="377623">
+ </export>
+ <export format="owl" path="obo-all/gene_regulation/gene_regulation.owl" md5="263d0aa1a9d4a9553cf4a985eec8dbcb" timestamp="1263694636" time_generated="1263694636" time_taken_to_generate="0" size="389092">
+ </export>
+ <export format="chadoxml" path="obo-all/gene_regulation/gene_regulation.chadoxml" md5="04ed4d99e49d8000becaf7adbf3b4019" timestamp="1260729096" time_generated="1263694636" time_taken_to_generate="0" size="533257">
+ </export>
+ <export format="godb_prestore" path="obo-all/gene_regulation/gene_regulation.godb_prestore" md5="69fa2ad6ed999dfaa1bdf586342695e7" timestamp="1260729097" time_generated="1263694636" time_taken_to_generate="0" size="615429">
+ </export>
+ <export format="rdf" path="obo-all/gene_regulation/gene_regulation.rdf" md5="d441cf39061d5cf4fa6d5469fa2528b0" timestamp="1260729097" time_generated="1263694636" time_taken_to_generate="0" size="228485">
+ </export>
+ <export format="tbl" path="obo-all/gene_regulation/gene_regulation.tbl" md5="36bcfa461067f7ef8a62c6fc7b6320a8" timestamp="1260729098" time_generated="1263694636" time_taken_to_generate="0" size="35343">
+ </export>
+ <export format="prolog" path="obo-all/gene_regulation/gene_regulation.pro" md5="e378ab397511ebbc1f4e05b139b9cdc7" timestamp="1260729099" time_generated="1263694636" time_taken_to_generate="0" size="437649">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/gene_regulation/gene_regulation.validation_report" md5="414666675f4c8b6c842ebdeb2f33fe62" timestamp="1260729100" time_generated="1263694636" time_taken_to_generate="0" size="396">
+ </export>
+ <export format="stats" path="obo-all/gene_regulation/gene_regulation.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1260729101" time_generated="1263694636" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/gene_regulation/gene_regulation.obo.html" md5="5d12ef9d1f28ac04fe9acb14a56479b4" timestamp="1260729101" time_generated="1263694636" time_taken_to_generate="0" size="1088786">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="habronattus_courtship">
+ <source>protege source|http://www.mesquiteproject.org/ontology/Habronattus/Protege_source/</source>
+ <namespace></namespace>
+ <status>Inactive</status>
+ <contact>Peter Midford peteremidford yahoo.com</contact>
+ <description>A demonstration of ontology construction as a general technique for coding ethograms and other descriptions of behavior into machine understandable forms. An ontology for courtship behavior of the spider <i>Habronattus californicus</i>.</description>
+ <foundry>No</foundry>
+ <format>protege</format>
+ <documentation>Ontologies For Ethology|http://www.mesquiteproject.org/ontology/</documentation>
+ <url>http://www.mesquiteproject.org/ontology/Habronattus/Protege_source/</url>
+ <title>Habronattus courtship</title>
+ <is_obsolete>true</is_obsolete>
+ <source_label>protege source</source_label>
+ <home>Mesquite Project Habronattus Index|http://www.mesquiteproject.org/ontology/Habronattus/index.html</home>
+ <download></download>
+ <problem>Source not available at specified URL as recognised format</problem>
+ </ont>
+ <ont id="homology_ontology">
+ <source></source>
+ <namespace>HOM</namespace>
+ <status>Discussion and review</status>
+ <contact>julien.roux unil.ch</contact>
+ <description>This ontology represents concepts related to homology, as well as other concepts used to describe similarity and non-homology.</description>
+ <foundry>No</foundry>
+ <format>obo</format>
+ <documentation></documentation>
+ <url>http://bgee.unil.ch/download/homology_ontology.obo</url>
+ <title>homology_ontology</title>
+ <home>Bgee|http://bioinfo.unil.ch</home>
+ <download>http://bgee.unil.ch/download/homology_ontology.obo</download>
+ <export format="obo_xml" path="obo-all/homology_ontology/homology_ontology.obo_xml" md5="8d54fb8ab4c7aa582aba8ad623c26fd0" timestamp="1262993592" time_generated="1263694639" time_taken_to_generate="0" size="64823">
+ </export>
+ <export format="obo" path="obo-all/homology_ontology/homology_ontology.obo" md5="c813b8fac6c51eb2bd6565d49ea12d43" timestamp="1263694639" time_generated="1263694639" time_taken_to_generate="0" size="33271">
+ </export>
+ <export format="owl" path="obo-all/homology_ontology/homology_ontology.owl" md5="429645ee3426ca02072caf8694c2c354" timestamp="1262993593" time_generated="1263694639" time_taken_to_generate="0" size="141438">
+ </export>
+ <export format="chadoxml" path="obo-all/homology_ontology/homology_ontology.chadoxml" md5="9756f739b06ac7921637503f0d767421" timestamp="1262993593" time_generated="1263694639" time_taken_to_generate="0" size="151463">
+ </export>
+ <export format="godb_prestore" path="obo-all/homology_ontology/homology_ontology.godb_prestore" md5="7a73c6ed92ba66554e6f7bcdb025ed6f" timestamp="1262993593" time_generated="1263694639" time_taken_to_generate="0" size="115120">
+ </export>
+ <export format="rdf" path="obo-all/homology_ontology/homology_ontology.rdf" md5="e526caa69b7c3879635272717e4a45a7" timestamp="1262993594" time_generated="1263694639" time_taken_to_generate="0" size="40454">
+ </export>
+ <export format="tbl" path="obo-all/homology_ontology/homology_ontology.tbl" md5="190bd8cb8fadf2cdc6c6c72966f0d149" timestamp="1262993594" time_generated="1263694639" time_taken_to_generate="0" size="10060">
+ </export>
+ <export format="prolog" path="obo-all/homology_ontology/homology_ontology.pro" md5="100a5e3da6f59483a2d501e7c75665c3" timestamp="1262993594" time_generated="1263694639" time_taken_to_generate="0" size="53760">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/homology_ontology/homology_ontology.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1262993595" time_generated="1263694639" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" path="obo-all/homology_ontology/homology_ontology.stats" md5="71666b8d5da5f0cdd71d1938865d3a1c" timestamp="1262993596" time_generated="1263694639" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/homology_ontology/homology_ontology.obo.html" md5="15565b92d76c9e7617121580ec72a001" timestamp="1262993596" time_generated="1263694639" time_taken_to_generate="0" size="112537">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="human-dev-anat-abstract">
+ <source></source>
+ <granularity>organismal</granularity>
+ <status>Discussion and review</status>
+ <subtypes_of>CARO:0000000</subtypes_of>
+ <contact>Jonathan Bard J.Bard ed.ac.uk</contact>
+ <foundry>Yes</foundry>
+ <domain>anatomy</domain>
+ <documentation></documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/human/human-dev-anat-abstract.obo</url>
+ <patho_type>canonical</patho_type>
+ <home>GeneX|http://genex.hgu.mrc.ac.uk/</home>
+ <namespace>EHDAA</namespace>
+ <description>A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20). The abstract version of the human developmental anatomy ontology compresses all the tissues present over Carnegie stages 1-20 into a single hierarchy. The heart, for example, is present from Carnegie Stage 9 onwards and is thus represented by 12 EHDA IDs (one for each sta [...]
+ <format>obo</format>
+ <title>Human developmental anatomy, abstract version</title>
+ <relevant_organism>NCBITaxon:9606|Homo sapiens</relevant_organism>
+ <download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/human/human-dev-anat-abstract.obo</download>
+ <export format="obo_xml" path="obo-all/human-dev-anat-abstract/human-dev-anat-abstract.obo_xml" md5="33a429d347bf527cbe0fd7c1f07cf9ae" timestamp="1260729110" time_generated="1263694641" time_taken_to_generate="0" size="533722">
+ </export>
+ <export format="obo" path="obo-all/human-dev-anat-abstract/human-dev-anat-abstract.obo" md5="01cefb6b089f4eada89ce16e5bbf2565" timestamp="1263694641" time_generated="1263694641" time_taken_to_generate="0" size="220476">
+ </export>
+ <export format="owl" path="obo-all/human-dev-anat-abstract/human-dev-anat-abstract.owl" md5="4d41f49783399ba990c67a4504f2f34f" timestamp="1260729138" time_generated="1263694641" time_taken_to_generate="0" size="1267701">
+ </export>
+ <export format="chadoxml" path="obo-all/human-dev-anat-abstract/human-dev-anat-abstract.chadoxml" md5="3b72516f6de41111c0898f2d77d9355d" timestamp="1260729146" time_generated="1263694641" time_taken_to_generate="0" size="1187056">
+ </export>
+ <export format="godb_prestore" path="obo-all/human-dev-anat-abstract/human-dev-anat-abstract.godb_prestore" md5="a79b181cd55befd2f6295dbcd96f3c7c" timestamp="1260729148" time_generated="1263694641" time_taken_to_generate="0" size="1150219">
+ </export>
+ <export format="rdf" path="obo-all/human-dev-anat-abstract/human-dev-anat-abstract.rdf" md5="59874a5cb4d1fe4f2dbd8c58fc481825" timestamp="1260729150" time_generated="1263694641" time_taken_to_generate="0" size="665134">
+ </export>
+ <export format="tbl" path="obo-all/human-dev-anat-abstract/human-dev-anat-abstract.tbl" md5="8e1633a6723f426fd9518d94301137ef" timestamp="1260729152" time_generated="1263694641" time_taken_to_generate="0" size="67415">
+ </export>
+ <export format="prolog" path="obo-all/human-dev-anat-abstract/human-dev-anat-abstract.pro" md5="afdb9b7860cc74fe98473785e02b902f" timestamp="1260729156" time_generated="1263694641" time_taken_to_generate="0" size="527037">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/human-dev-anat-abstract/human-dev-anat-abstract.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1260729159" time_generated="1263694642" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" path="obo-all/human-dev-anat-abstract/human-dev-anat-abstract.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1260729160" time_generated="1263694642" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/human-dev-anat-abstract/human-dev-anat-abstract.obo.html" md5="788500834412f2cdde16aeb09a74c589" timestamp="1260729160" time_generated="1263694642" time_taken_to_generate="0" size="1357782">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="human-dev-anat-staged">
+ <source></source>
+ <granularity>organismal</granularity>
+ <status>Discussion and review</status>
+ <subtypes_of>bfo:Occurent</subtypes_of>
+ <contact>Jonathan Bard J.Bard ed.ac.uk</contact>
+ <foundry>Yes</foundry>
+ <domain>anatomy</domain>
+ <documentation></documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/human/human-dev-anat-staged.obo</url>
+ <patho_type>canonical</patho_type>
+ <home>GeneX|http://genex.hgu.mrc.ac.uk/</home>
+ <namespace>EHDA</namespace>
+ <description>A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20). The timed version of the human developmental anatomy ontology gives all the tissues present at each Carnegie Stage (CS) of human development (1-20) linked by a part-of rule. Each term is mentioned only once so that the embryo at each stage can be seen as the simple sum of [...]
+ <format>obo</format>
+ <title>Human developmental anatomy, timed version</title>
+ <relevant_organism>NCBITaxon:9606|Homo sapiens</relevant_organism>
+ <download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/human/human-dev-anat-staged.obo</download>
+ <export format="obo_xml" path="obo-all/human-dev-anat-staged/human-dev-anat-staged.obo_xml" md5="0e8597fa9a36a927ea1e6fa8e2f68cd3" timestamp="1260729169" time_generated="1263694646" time_taken_to_generate="0" size="3313221">
+ </export>
+ <export format="obo" path="obo-all/human-dev-anat-staged/human-dev-anat-staged.obo" md5="73b5f43ff1de07ffc5d3fbea171026fb" timestamp="1263694646" time_generated="1263694647" time_taken_to_generate="0" size="1148413">
+ </export>
+ <export format="owl" path="obo-all/human-dev-anat-staged/human-dev-anat-staged.owl" md5="a6b4a9bfff37dfd58080df0f1d778326" timestamp="1260729870" time_generated="1263694647" time_taken_to_generate="0" size="9115794">
+ </export>
+ <export format="chadoxml" path="obo-all/human-dev-anat-staged/human-dev-anat-staged.chadoxml" md5="2314ad7ba14665a41a7fd57922ec62ad" timestamp="1260730109" time_generated="1263694647" time_taken_to_generate="0" size="8404971">
+ </export>
+ <export format="godb_prestore" path="obo-all/human-dev-anat-staged/human-dev-anat-staged.godb_prestore" md5="eeddbcbe85550dbf9a44084bc54739aa" timestamp="1260730121" time_generated="1263694647" time_taken_to_generate="0" size="7183986">
+ </export>
+ <export format="rdf" path="obo-all/human-dev-anat-staged/human-dev-anat-staged.rdf" md5="f873b2c73733d2c012c41f6382ec7281" timestamp="1260730138" time_generated="1263694647" time_taken_to_generate="0" size="5431990">
+ </export>
+ <export format="tbl" path="obo-all/human-dev-anat-staged/human-dev-anat-staged.tbl" md5="eeeaff3df94b7dbd70417cdd286344b2" timestamp="1260730149" time_generated="1263694647" time_taken_to_generate="0" size="229483">
+ </export>
+ <export format="prolog" path="obo-all/human-dev-anat-staged/human-dev-anat-staged.pro" md5="aa98e10decee46080e2cee9d12f4bbc1" timestamp="1260730168" time_generated="1263694647" time_taken_to_generate="0" size="2682434">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/human-dev-anat-staged/human-dev-anat-staged.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1260730179" time_generated="1263694656" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" path="obo-all/human-dev-anat-staged/human-dev-anat-staged.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1260730180" time_generated="1263694656" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/human-dev-anat-staged/human-dev-anat-staged.obo.html" md5="aebaa9db53ac680d0d13ac2e6d08f049" timestamp="1260730181" time_generated="1263694656" time_taken_to_generate="0" size="7986058">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="human_phenotype">
+ <source>human-phenotype-ontology.obo.gz|http://www.human-phenotype-ontology.org/human-phenotype-ontology.obo.gz</source>
+ <granularity>organismal</granularity>
+ <status></status>
+ <subtypes_of></subtypes_of>
+ <contact>OBO Human Phenotype obo-human-phenotype lists.sourceforge.net</contact>
+ <foundry>No</foundry>
+ <domain>phenotype</domain>
+ <documentation>http://www.human-phenotype-ontology.org/</documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/human_phenotype.obo</url>
+ <patho_type>pathological</patho_type>
+ <home>http://www.human-phenotype-ontology.org/</home>
+ <namespace>HP</namespace>
+ <description>The Human Phenotype Ontology is being developed to provide a structured and controlled vocabulary for the phenotypic features encountered in human hereditary and other disease. Our goal is to provide resource for the computational analysis of the human phenome, with a current focus on monogenic diseases listed in the Online Mendelian Inheritance in Man (OMIM) database, for which annotations are also provided.</description>
+ <format>obo</format>
+ <title>human phenotype ontology</title>
+ <relevant_organism>NCBITaxon:9606|Homo sapiens</relevant_organism>
+ <download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/human_phenotype.obo</download>
+ <export format="obo_xml" path="obo-all/human_phenotype/human_phenotype.obo_xml" md5="bfa650505a916f3a32a7b61ee61bbee1" timestamp="1263694671" time_generated="1263694671" time_taken_to_generate="10" size="5149704">
+ </export>
+ <export format="obo" path="obo-all/human_phenotype/human_phenotype.obo" md5="b5c71db153c605f3fdd3163664b58ae7" timestamp="1263694661" time_generated="1263694671" time_taken_to_generate="0" size="2565321">
+ </export>
+ <export format="owl" path="obo-all/human_phenotype/human_phenotype.owl" md5="96ea9437f26276a35552071c45408c64" timestamp="1263695398" time_generated="1263695398" time_taken_to_generate="727" size="12634381">
+ </export>
+ <export format="chadoxml" path="obo-all/human_phenotype/human_phenotype.chadoxml" md5="324a033aa22ca081c76c146380b8f5d6" timestamp="1263695726" time_generated="1263695726" time_taken_to_generate="328" size="14664719">
+ </export>
+ <export format="godb_prestore" path="obo-all/human_phenotype/human_phenotype.godb_prestore" md5="a452a3aef132f03266a3d81de8c18707" timestamp="1263695760" time_generated="1263695761" time_taken_to_generate="35" size="11570158">
+ </export>
+ <export format="rdf" path="obo-all/human_phenotype/human_phenotype.rdf" md5="ea5eb38dca984d000cb530f0a34150c4" timestamp="1263695802" time_generated="1263695802" time_taken_to_generate="41" size="8548121">
+ </export>
+ <export format="tbl" path="obo-all/human_phenotype/human_phenotype.tbl" md5="75d0592993b87a0e76911198b151a3c0" timestamp="1263695827" time_generated="1263695827" time_taken_to_generate="25" size="785182">
+ </export>
+ <export format="prolog" path="obo-all/human_phenotype/human_phenotype.pro" md5="f2b8e831a464bb616d765333ac871017" timestamp="1263695870" time_generated="1263695870" time_taken_to_generate="43" size="4745402">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/human_phenotype/human_phenotype.validation_report" md5="6bd74be657533293385e04287a79d061" timestamp="1263695900" time_generated="1263695900" time_taken_to_generate="9" size="1368">
+ </export>
+ <export format="stats" path="obo-all/human_phenotype/human_phenotype.stats" md5="619a62d04ddf7c62cc6ebdc743938b12" timestamp="1263695902" time_generated="1263695902" time_taken_to_generate="2" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/human_phenotype/human_phenotype.obo.html" md5="b2f97aebcf0de6eb66c49786ceb9c99d" timestamp="1263695904" time_generated="1263695904" time_taken_to_generate="2" size="14533037">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="hymenoptera_anatomy">
+ <source></source>
+ <granularity>organismal</granularity>
+ <status>Production and review</status>
+ <subtypes_of>CARO:0000000</subtypes_of>
+ <contact>HAO developers diapriid gmail.com</contact>
+ <foundry>No</foundry>
+ <domain>anatomy</domain>
+ <documentation></documentation>
+ <url>http://obo.svn.sourceforge.net/viewvc/obo/ontologies/trunk/HAO/hao.obo</url>
+ <patho_type>canonical</patho_type>
+ <home>http://hymao.org</home>
+ <namespace>HAO</namespace>
+ <description>A structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, and ants)</description>
+ <format>obo</format>
+ <title>Hymenoptera Anatomy Ontology</title>
+ <relevant_organism>NCBITaxon:7399|Hymenoptera</relevant_organism>
+ <download>http://obo.svn.sourceforge.net/viewvc/obo/ontologies/trunk/HAO/hao.obo</download>
+ <export format="obo_xml" path="obo-all/hymenoptera_anatomy/hymenoptera_anatomy.obo_xml" md5="3e83547735542212eae14764aa0f7382" timestamp="1260731159" time_generated="1263695908" time_taken_to_generate="0" size="559087">
+ </export>
+ <export format="obo" path="obo-all/hymenoptera_anatomy/hymenoptera_anatomy.obo" md5="8befe29a002d78062a54ab9224f64d47" timestamp="1263695908" time_generated="1263695908" time_taken_to_generate="0" size="288243">
+ </export>
+ <export format="owl" path="obo-all/hymenoptera_anatomy/hymenoptera_anatomy.owl" md5="13ac714684bb15675c81c5650db2c3d2" timestamp="1260731173" time_generated="1263695908" time_taken_to_generate="0" size="1298942">
+ </export>
+ <export format="chadoxml" path="obo-all/hymenoptera_anatomy/hymenoptera_anatomy.chadoxml" md5="89f0d95ce6379ab4dbc7dda5b565889f" timestamp="1260731177" time_generated="1263695908" time_taken_to_generate="0" size="1324599">
+ </export>
+ <export format="godb_prestore" path="obo-all/hymenoptera_anatomy/hymenoptera_anatomy.godb_prestore" md5="bea257087e633fccacff6c368aec81ac" timestamp="1260731178" time_generated="1263695908" time_taken_to_generate="0" size="1201878">
+ </export>
+ <export format="rdf" path="obo-all/hymenoptera_anatomy/hymenoptera_anatomy.rdf" md5="7e8cf7163ec378e6a577442c981d29ff" timestamp="1260731181" time_generated="1263695908" time_taken_to_generate="0" size="583984">
+ </export>
+ <export format="tbl" path="obo-all/hymenoptera_anatomy/hymenoptera_anatomy.tbl" md5="38f0cb13169bb92c688425b900811004" timestamp="1260731183" time_generated="1263695908" time_taken_to_generate="0" size="134517">
+ </export>
+ <export format="prolog" path="obo-all/hymenoptera_anatomy/hymenoptera_anatomy.pro" md5="9993161ed30f25cca407d9b065e213cf" timestamp="1260731185" time_generated="1263695908" time_taken_to_generate="0" size="456027">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/hymenoptera_anatomy/hymenoptera_anatomy.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1260731188" time_generated="1263695911" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" path="obo-all/hymenoptera_anatomy/hymenoptera_anatomy.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1260731189" time_generated="1263695911" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/hymenoptera_anatomy/hymenoptera_anatomy.obo.html" md5="6b9423abf9a28d8c66d053583fa011a0" timestamp="1260731189" time_generated="1263695911" time_taken_to_generate="0" size="1284964">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="information_artifact">
+ <metadata_ontology>IAO</metadata_ontology>
+ <source>http://purl.obolibrary.org/obo/iao.owl</source>
+ <namespace>IAO</namespace>
+ <status></status>
+ <contact>Alan Ruttenberg alanruttenberg gmail.com</contact>
+ <description>The Information Artifact Ontology (IAO) is a new ontology of information entities, originally driven by work by the OBI digital entity and realizable information entity branch. The first workshop on the IAO took place in Boston at the MIT Stata Center, June 9, 2008.</description>
+ <foundry>No</foundry>
+ <domain>information</domain>
+ <format>owl</format>
+ <documentation>http://code.google.com/p/information-artifact-ontology/</documentation>
+ <url>http://purl.obolibrary.org/obo/iao.owl</url>
+ <title>Information Artifact Ontology</title>
+ <home>http://code.google.com/p/information-artifact-ontology/</home>
+ <download></download>
+ <export format="pro" path="obo-all/information_artifact/information_artifact.pro" md5="57e5cbb519f5661b317f93bf22682d12" timestamp="1260731198" time_generated="1263695914" time_taken_to_generate="0" size="79882">
+ </export>
+ <export format="obo" path="obo-all/information_artifact/information_artifact.obo" md5="5cadb7c3a4752e897382904568139eaf" timestamp="1260731196" time_generated="1263695914" time_taken_to_generate="0" size="55373">
+ </export>
+ <export format="obo_xml" path="obo-all/information_artifact/information_artifact.obo_xml" md5="2a504c5d9582582febc29d9fffdecc50" timestamp="1260731197" time_generated="1263695914" time_taken_to_generate="0" size="70382">
+ </export>
+ <export format="owl" path="obo-all/information_artifact/information_artifact.owl" md5="97d79c4a8b82938e0751420269640b7b" timestamp="1263695914" time_generated="1263695914" time_taken_to_generate="0" size="1925">
+ </export>
+ <export format="chadoxml" path="obo-all/information_artifact/information_artifact.chadoxml" md5="8da9a5d959a6bd8e3e4869c72b501b51" timestamp="1260731197" time_generated="1263695914" time_taken_to_generate="0" size="156971">
+ </export>
+ <export format="godb_prestore" path="obo-all/information_artifact/information_artifact.godb_prestore" md5="fd1464c58b90f26018ce9752c077cf27" timestamp="1260731197" time_generated="1263695914" time_taken_to_generate="0" size="120408">
+ </export>
+ <export format="rdf" path="obo-all/information_artifact/information_artifact.rdf" md5="37bf5a8d7dcf67c339f61a368e019b8b" timestamp="1260731197" time_generated="1263695914" time_taken_to_generate="0" size="99855">
+ </export>
+ <export format="tbl" path="obo-all/information_artifact/information_artifact.tbl" md5="f1afff6a86493f5e9bcf92af8c92fe63" timestamp="1260731198" time_generated="1263695914" time_taken_to_generate="0" size="21091">
+ </export>
+ <export format="prolog" path="obo-all/information_artifact/information_artifact.pro" md5="57e5cbb519f5661b317f93bf22682d12" timestamp="1260731198" time_generated="1263695914" time_taken_to_generate="0" size="79882">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/information_artifact/information_artifact.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1260731199" time_generated="1263695914" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" path="obo-all/information_artifact/information_artifact.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1260731200" time_generated="1263695914" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/information_artifact/information_artifact.obo.html" md5="725249403a1b70c42714ca043632af6c" timestamp="1260731200" time_generated="1263695914" time_taken_to_generate="0" size="224125">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="image">
+ <source></source>
+ <namespace>FBbi</namespace>
+ <status>Inactive</status>
+ <contact>Kathy Matthews matthewk indiana.edu</contact>
+ <description>A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research.</description>
+ <foundry>No</foundry>
+ <domain>experiments</domain>
+ <format>obo</format>
+ <documentation></documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/experimental_conditions/imaging_methods/image.obo</url>
+ <title>Biological imaging methods</title>
+ <home>FlyBase|http://www.flybase.org/</home>
+ <download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/experimental_conditions/imaging_methods/image.obo</download>
+ <export format="obo_xml" path="obo-all/image/image.obo_xml" md5="9888b772854b29d19d4340049911ed7c" timestamp="1260731203" time_generated="1263695917" time_taken_to_generate="0" size="46511">
+ </export>
+ <export format="obo" path="obo-all/image/image.obo" md5="7445adc134b33774c0cad9dec3768486" timestamp="1263695917" time_generated="1263695917" time_taken_to_generate="0" size="32553">
+ </export>
+ <export format="owl" path="obo-all/image/image.owl" md5="542b38ef8b1eba8a6fe60938d6706459" timestamp="1260731203" time_generated="1263695917" time_taken_to_generate="0" size="90701">
+ </export>
+ <export format="chadoxml" path="obo-all/image/image.chadoxml" md5="c1c135b0d596d6efb551c95aad40840a" timestamp="1260731204" time_generated="1263695917" time_taken_to_generate="0" size="149951">
+ </export>
+ <export format="godb_prestore" path="obo-all/image/image.godb_prestore" md5="43b5420758f2659745c0e587b465c8cd" timestamp="1260731204" time_generated="1263695917" time_taken_to_generate="0" size="110936">
+ </export>
+ <export format="rdf" path="obo-all/image/image.rdf" md5="fd758ea90ad2896c7cd1ea40766454f3" timestamp="1260731204" time_generated="1263695917" time_taken_to_generate="0" size="79732">
+ </export>
+ <export format="tbl" path="obo-all/image/image.tbl" md5="a671f129ade8aa42c7a98e3d820cb5c4" timestamp="1260731205" time_generated="1263695917" time_taken_to_generate="0" size="13610">
+ </export>
+ <export format="prolog" path="obo-all/image/image.pro" md5="06d8d49d1657a2bae500bdcb80536579" timestamp="1260731205" time_generated="1263695917" time_taken_to_generate="0" size="64087">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/image/image.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1260731206" time_generated="1263695917" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" path="obo-all/image/image.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1260731207" time_generated="1263695917" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/image/image.obo.html" md5="9d848ce02fee8e6934d5ae8bb43abcf6" timestamp="1260731207" time_generated="1263695917" time_taken_to_generate="0" size="166376">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="interpro">
+ <source>InterPro FTP directory|ftp://ftp.ebi.ac.uk/pub/databases/interpro/</source>
+ <namespace>IPR</namespace>
+ <status>Active</status>
+ <contact>InterPro Help interhelp ebi.ac.uk</contact>
+ <description>A database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences.</description>
+ <foundry>No</foundry>
+ <domain>proteins</domain>
+ <format>XML</format>
+ <documentation>InterPro documentation|http://www.ebi.ac.uk/interpro/documentation.html</documentation>
+ <url>ftp://ftp.ebi.ac.uk/pub/databases/interpro/</url>
+ <title>Protein Domains</title>
+ <source_label>InterPro FTP directory</source_label>
+ <home>InterPro home page|http://www.ebi.ac.uk/interpro/index.html</home>
+ <download></download>
+ <problem>Source not available at specified URL as recognised format</problem>
+ </ont>
+ <ont id="lipid">
+ <source></source>
+ <namespace>LiPrO</namespace>
+ <status>Active</status>
+ <contact>Christipher Baker bakerc unb.ca</contact>
+ <description>Lipid research is increasingly integrated within systems level biology such as lipidomics where lipid classification is required before appropriate annotation of chemical functions can be applied. The ontology describes the LIPIDMAPS nomenclature classification explicitly using description logics (OWL-DL). Lipid classes are organized hierarchically with the super-classes restricted by generic necessary conditions. More specific necessary conditions are used to define mem [...]
+ <foundry>No</foundry>
+ <domain>lipids</domain>
+ <format>owl</format>
+ <documentation></documentation>
+ <url>http://www.lipidprofiles.com/LipidOntology</url>
+ <title>Lipid Ontology</title>
+ <home></home>
+ <download>http://www.lipidprofiles.com/LipidOntology</download>
+ <export format="pro" path="obo-all/lipid/lipid.pro" md5="e7222e90af2bda83a7fa6dab05aefa6e" timestamp="1260731227" time_generated="1263695926" time_taken_to_generate="0" size="1060057">
+ </export>
+ <export format="obo" path="obo-all/lipid/lipid.obo" md5="ba8053724d8b70c2e24f4583c73525f5" timestamp="1260731222" time_generated="1263695926" time_taken_to_generate="0" size="572625">
+ </export>
+ <export format="obo_xml" path="obo-all/lipid/lipid.obo_xml" md5="93d3f8a84c476607bf6a0b7fb9f3c647" timestamp="1260731222" time_generated="1263695926" time_taken_to_generate="0" size="689285">
+ </export>
+ <export format="owl" path="obo-all/lipid/lipid.owl" md5="8c5f48b7b3185e743c2534261cce098e" timestamp="1263695926" time_generated="1263695926" time_taken_to_generate="0" size="1359853">
+ </export>
+ <export format="chadoxml" path="obo-all/lipid/lipid.chadoxml" md5="e9def9aa0b62674756a96735c3084cc2" timestamp="1260731223" time_generated="1263695926" time_taken_to_generate="0" size="689368">
+ </export>
+ <export format="godb_prestore" path="obo-all/lipid/lipid.godb_prestore" md5="5f142fdb8070749e0cd2071d8584483f" timestamp="1260731224" time_generated="1263695926" time_taken_to_generate="0" size="454260">
+ </export>
+ <export format="rdf" path="obo-all/lipid/lipid.rdf" md5="5e885672bc79d8d66915130fd5ec4082" timestamp="1260731225" time_generated="1263695926" time_taken_to_generate="0" size="374453">
+ </export>
+ <export format="tbl" path="obo-all/lipid/lipid.tbl" md5="acaf9fa6a2368979b87d2b90182e8df3" timestamp="1260731226" time_generated="1263695926" time_taken_to_generate="0" size="75126">
+ </export>
+ <export format="prolog" path="obo-all/lipid/lipid.pro" md5="e7222e90af2bda83a7fa6dab05aefa6e" timestamp="1260731227" time_generated="1263695926" time_taken_to_generate="0" size="1060057">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/lipid/lipid.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1260731228" time_generated="1263695927" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" path="obo-all/lipid/lipid.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1260731229" time_generated="1263695927" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/lipid/lipid.obo.html" md5="c03cd19698e65de4546c1b417e199332" timestamp="1260731229" time_generated="1263695927" time_taken_to_generate="0" size="1835805">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="loggerhead_nesting">
+ <source>B8467OBO|http://www.mesquiteproject.org/ontology/OBO/B8467OBO</source>
+ <namespace></namespace>
+ <status>Inactive</status>
+ <contact>Peter Midford peteremidford yahoo.com</contact>
+ <description>A demonstration of ontology construction as a general technique for coding ethograms and other descriptions of behavior into machine understandable forms. An ontology for Loggerhead sea turtle (<i>Caretta caretta</i>) nesting behavior, based on the published ethogram of Hailman and Elowson.</description>
+ <foundry>No</foundry>
+ <format>obo</format>
+ <documentation>Ontologies For Ethology|http://www.mesquiteproject.org/ontology/</documentation>
+ <url>http://www.mesquiteproject.org/ontology/OBO/B8467OBO</url>
+ <title>Loggerhead nesting</title>
+ <is_obsolete>true</is_obsolete>
+ <source_label>B8467OBO</source_label>
+ <home>Mesquite Project Loggerhead Index|http://www.mesquiteproject.org/ontology/Loggerhead/index.html</home>
+ <download></download>
+ <export format="obo_xml" path="obo-all/loggerhead_nesting/loggerhead_nesting.obo_xml" md5="dc0c96844bcc5c1463b14e17b85e3ed4" timestamp="1260731231" time_generated="1263695930" time_taken_to_generate="0" size="93296">
+ </export>
+ <export format="obo" path="obo-all/loggerhead_nesting/loggerhead_nesting.obo" md5="81b486ebdf2bd5133e865e35ce272ae1" timestamp="1263695930" time_generated="1263695930" time_taken_to_generate="0" size="43665">
+ </export>
+ <export format="owl" path="obo-all/loggerhead_nesting/loggerhead_nesting.owl" md5="39baf951f95ca8847611dec5edea732d" timestamp="1260731232" time_generated="1263695930" time_taken_to_generate="0" size="219901">
+ </export>
+ <export format="chadoxml" path="obo-all/loggerhead_nesting/loggerhead_nesting.chadoxml" md5="f5b8a8975b338e3469d502943599d16b" timestamp="1260731232" time_generated="1263695930" time_taken_to_generate="0" size="250472">
+ </export>
+ <export format="godb_prestore" path="obo-all/loggerhead_nesting/loggerhead_nesting.godb_prestore" md5="397e80cf3e279fd27d50bd01f0d542d4" timestamp="1260731233" time_generated="1263695930" time_taken_to_generate="0" size="210668">
+ </export>
+ <export format="rdf" path="obo-all/loggerhead_nesting/loggerhead_nesting.rdf" md5="24a3bf7861a01be7934085eefc304bb1" timestamp="1260731233" time_generated="1263695930" time_taken_to_generate="0" size="117045">
+ </export>
+ <export format="tbl" path="obo-all/loggerhead_nesting/loggerhead_nesting.tbl" md5="ae32406f39892686245c9e2899aed487" timestamp="1260731234" time_generated="1263695930" time_taken_to_generate="0" size="25286">
+ </export>
+ <export format="prolog" path="obo-all/loggerhead_nesting/loggerhead_nesting.pro" md5="1cf486908a855b399c119647406cc4dc" timestamp="1260731234" time_generated="1263695930" time_taken_to_generate="0" size="92492">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/loggerhead_nesting/loggerhead_nesting.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1260731235" time_generated="1263695930" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" path="obo-all/loggerhead_nesting/loggerhead_nesting.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1260731237" time_generated="1263695930" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/loggerhead_nesting/loggerhead_nesting.obo.html" md5="43c73cbe15568b5b5067b4486ebb2e04" timestamp="1260731237" time_generated="1263695930" time_taken_to_generate="0" size="249642">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="mammalian_phenotype">
+ <source>MPheno_OBO.ontology|ftp://ftp.informatics.jax.org/pub/reports/MPheno_OBO.ontology</source>
+ <granularity>organismal</granularity>
+ <status>Production and review</status>
+ <subtypes_of>PATO:0000000,MA:0000000,GO:0000000</subtypes_of>
+ <contact>JAX phenotype list pheno informatics.jax.org</contact>
+ <foundry>Yes</foundry>
+ <domain>phenotype</domain>
+ <documentation></documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/mammalian_phenotype.obo</url>
+ <patho_type>pathological</patho_type>
+ <home>Mammalian Phenotype Browser|http://www.informatics.jax.org/searches/MP_form.shtml</home>
+ <namespace>MP</namespace>
+ <description>The Mammalian Phenotype Ontology is under development as a community effort to provide standard terms for annotating mammalian phenotypic data.</description>
+ <format>obo</format>
+ <title>Mammalian phenotype</title>
+ <relevant_organism>NCBITaxon:10088|Mus</relevant_organism>
+ <download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/mammalian_phenotype.obo</download>
+ <export format="obo_xml" path="obo-all/mammalian_phenotype/mammalian_phenotype.obo_xml" md5="eb40f6bad0176f45b2c30e99fe335a11" timestamp="1261331357" time_generated="1263695937" time_taken_to_generate="0" size="5447930">
+ </export>
+ <export format="obo" path="obo-all/mammalian_phenotype/mammalian_phenotype.obo" md5="34aa7a2edc15f8adb257eb5b053b0747" timestamp="1263695937" time_generated="1263695937" time_taken_to_generate="0" size="2910798">
+ </export>
+ <export format="owl" path="obo-all/mammalian_phenotype/mammalian_phenotype.owl" md5="87438242284ec4ca8e016e4d92f6cb63" timestamp="1261331843" time_generated="1263695937" time_taken_to_generate="0" size="12432881">
+ </export>
+ <export format="chadoxml" path="obo-all/mammalian_phenotype/mammalian_phenotype.chadoxml" md5="12721238e8953fb28759b20f53c6bc92" timestamp="1261331991" time_generated="1263695937" time_taken_to_generate="0" size="14870046">
+ </export>
+ <export format="godb_prestore" path="obo-all/mammalian_phenotype/mammalian_phenotype.godb_prestore" md5="19c0bf860b5579da0e146c25b0b96181" timestamp="1261332007" time_generated="1263695938" time_taken_to_generate="0" size="11432548">
+ </export>
+ <export format="rdf" path="obo-all/mammalian_phenotype/mammalian_phenotype.rdf" md5="fe179427ba704c91ff9b510a76ce5edb" timestamp="1261332029" time_generated="1263695938" time_taken_to_generate="0" size="4222634">
+ </export>
+ <export format="tbl" path="obo-all/mammalian_phenotype/mammalian_phenotype.tbl" md5="58e0a1081a3ce9998ee62916148f8616" timestamp="1261332045" time_generated="1263695938" time_taken_to_generate="0" size="1537069">
+ </export>
+ <export format="prolog" path="obo-all/mammalian_phenotype/mammalian_phenotype.pro" md5="f8545b38159e06cfb757ff19516ccf58" timestamp="1263425168" time_generated="1263695938" time_taken_to_generate="0" size="5565407">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/mammalian_phenotype/mammalian_phenotype.validation_report" md5="a960e3f1ec895c5aa16420a3e1065e3d" timestamp="1261332093" time_generated="1263695957" time_taken_to_generate="0" size="13025">
+ </export>
+ <export format="stats" path="obo-all/mammalian_phenotype/mammalian_phenotype.stats" md5="7b6e8f1ae21de4404773ff97f9ae0ed3" timestamp="1261332095" time_generated="1263695957" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/mammalian_phenotype/mammalian_phenotype.obo.html" md5="5bb78dd03f490ac36d53c39eb63319e7" timestamp="1261332096" time_generated="1263695957" time_taken_to_generate="0" size="10487024">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="mao">
+ <source></source>
+ <namespace>MAO</namespace>
+ <status>Inactive</status>
+ <contact>Julie Thompson julie.thompson igbmc.u-strasbg.fr</contact>
+ <description>An ontology for data retrieval and exchange in the fields of multiple DNA/RNA alignment, protein sequence and protein structure alignment.</description>
+ <foundry>No</foundry>
+ <format>obo</format>
+ <documentation></documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/mao.obo</url>
+ <title>Multiple alignment</title>
+ <is_obsolete>true</is_obsolete>
+ <home>MAO Home|http://www-igbmc.u-strasbg.fr/BioInfo/MAO/mao.html</home>
+ <download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/mao.obo</download>
+ <export format="obo_xml" path="obo-all/mao/mao.obo_xml" md5="bfc24f4a155ab462b3ebc8614db32f82" timestamp="1260731898" time_generated="1263695960" time_taken_to_generate="0" size="66233">
+ </export>
+ <export format="obo" path="obo-all/mao/mao.obo" md5="1bab59dd4ddd9ab55fa5f219d316fb78" timestamp="1263695960" time_generated="1263695960" time_taken_to_generate="0" size="30437">
+ </export>
+ <export format="owl" path="obo-all/mao/mao.owl" md5="f0b2bbd629d37743614e1282e854be3b" timestamp="1260731899" time_generated="1263695960" time_taken_to_generate="0" size="157110">
+ </export>
+ <export format="chadoxml" path="obo-all/mao/mao.chadoxml" md5="567844d35c5e727a3e2446a23a0ca6a6" timestamp="1260731899" time_generated="1263695960" time_taken_to_generate="0" size="162387">
+ </export>
+ <export format="godb_prestore" path="obo-all/mao/mao.godb_prestore" md5="54e6fb2000eb9f1ff08feea9927675c6" timestamp="1260731899" time_generated="1263695960" time_taken_to_generate="0" size="130872">
+ </export>
+ <export format="rdf" path="obo-all/mao/mao.rdf" md5="d35791b83005a65a0c16dc08f41343db" timestamp="1260731900" time_generated="1263695960" time_taken_to_generate="0" size="69969">
+ </export>
+ <export format="tbl" path="obo-all/mao/mao.tbl" md5="de6eed9cc3e1e4d3cd1de45f33569138" timestamp="1260731900" time_generated="1263695960" time_taken_to_generate="0" size="19904">
+ </export>
+ <export format="prolog" path="obo-all/mao/mao.pro" md5="7cbd62ed46c8dd7d1ffde384b06f064f" timestamp="1260731900" time_generated="1263695960" time_taken_to_generate="0" size="59096">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/mao/mao.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1260731901" time_generated="1263695960" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" path="obo-all/mao/mao.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1260731902" time_generated="1263695960" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/mao/mao.obo.html" md5="913f6525a6b1db0b5a27b40c90870e64" timestamp="1260731902" time_generated="1263695961" time_taken_to_generate="0" size="151843">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="medaka_anatomy_development">
+ <source></source>
+ <granularity>organismal</granularity>
+ <status>Quiescent</status>
+ <subtypes_of>CARO:0000000</subtypes_of>
+ <contact>Thorsten Henrich Thorsten.Henrich embl-heidelberg.de</contact>
+ <foundry>Yes</foundry>
+ <domain>anatomy</domain>
+ <documentation></documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/fish/medaka_ontology.obo</url>
+ <patho_type>canonical</patho_type>
+ <home></home>
+ <namespace>MFO</namespace>
+ <description>A structured controlled vocabulary of the anatomy and development of the Japanese medaka fish, <i>Oryzias latipes</i>.</description>
+ <format>obo</format>
+ <title>Medaka fish anatomy and development</title>
+ <relevant_organism>NCBITaxon:8089|Oryzias</relevant_organism>
+ <download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/fish/medaka_ontology.obo</download>
+ <export format="obo_xml" path="obo-all/medaka_anatomy_development/medaka_anatomy_development.obo_xml" md5="eb0bc79cc3895e56e8272340d6d1c8ae" timestamp="1260731907" time_generated="1263695964" time_taken_to_generate="0" size="1043148">
+ </export>
+ <export format="obo" path="obo-all/medaka_anatomy_development/medaka_anatomy_development.obo" md5="68af8079d0e9e4a206e662f5fdc18fa4" timestamp="1263695964" time_generated="1263695964" time_taken_to_generate="0" size="512204">
+ </export>
+ <export format="owl" path="obo-all/medaka_anatomy_development/medaka_anatomy_development.owl" md5="72c07d9bab27d7b9e8f36e14f2fb3d16" timestamp="1260732017" time_generated="1263695964" time_taken_to_generate="0" size="2401230">
+ </export>
+ <export format="chadoxml" path="obo-all/medaka_anatomy_development/medaka_anatomy_development.chadoxml" md5="e553e04bca2a69019dd590fb9ad93221" timestamp="1260732051" time_generated="1263695964" time_taken_to_generate="0" size="2353411">
+ </export>
+ <export format="godb_prestore" path="obo-all/medaka_anatomy_development/medaka_anatomy_development.godb_prestore" md5="3fe7e155f61b8d78024cee4076aa053d" timestamp="1260732055" time_generated="1263695964" time_taken_to_generate="0" size="2202466">
+ </export>
+ <export format="rdf" path="obo-all/medaka_anatomy_development/medaka_anatomy_development.rdf" md5="e4fd783b00a4b289b67b0c2a0c8393df" timestamp="1260732063" time_generated="1263695964" time_taken_to_generate="0" size="1318617">
+ </export>
+ <export format="tbl" path="obo-all/medaka_anatomy_development/medaka_anatomy_development.tbl" md5="f395c32ecaf3eaaaeba9d2deaadf30cd" timestamp="1260732067" time_generated="1263695964" time_taken_to_generate="0" size="192885">
+ </export>
+ <export format="prolog" path="obo-all/medaka_anatomy_development/medaka_anatomy_development.pro" md5="efa737486cd962f037a80cf1b0803797" timestamp="1260732074" time_generated="1263695964" time_taken_to_generate="0" size="1080516">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/medaka_anatomy_development/medaka_anatomy_development.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1260732078" time_generated="1263695968" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" path="obo-all/medaka_anatomy_development/medaka_anatomy_development.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1260732079" time_generated="1263695968" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/medaka_anatomy_development/medaka_anatomy_development.obo.html" md5="bdbb1dde2304a0f77836a5363ef175d9" timestamp="1260732079" time_generated="1263695968" time_taken_to_generate="0" size="2695493">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="minimal_anatomical_terminology">
+ <source></source>
+ <granularity>organismal</granularity>
+ <status>Active</status>
+ <subtypes_of>CARO:0000000</subtypes_of>
+ <contact>Jonathan Bard j.bard ed.ac.uk</contact>
+ <foundry>No</foundry>
+ <domain>anatomy</domain>
+ <documentation></documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/multispecies/minimal_anatomical_terminology.obo</url>
+ <patho_type>canonical</patho_type>
+ <home></home>
+ <namespace>MAT</namespace>
+ <description>Minimal set of terms for anatomy</description>
+ <format>obo</format>
+ <title>Minimal anatomical terminology</title>
+ <download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/multispecies/minimal_anatomical_terminology.obo</download>
+ <export format="obo_xml" path="obo-all/minimal_anatomical_terminology/minimal_anatomical_terminology.obo_xml" md5="b0dbed9d2c5786dd47e543df6d488ead" timestamp="1260732081" time_generated="1263695971" time_taken_to_generate="0" size="194939">
+ </export>
+ <export format="obo" path="obo-all/minimal_anatomical_terminology/minimal_anatomical_terminology.obo" md5="7bcb8e84613c9891ec191edc4dd65a64" timestamp="1263695971" time_generated="1263695971" time_taken_to_generate="0" size="102344">
+ </export>
+ <export format="owl" path="obo-all/minimal_anatomical_terminology/minimal_anatomical_terminology.owl" md5="a581e6b6331f1f8042de6a4a4efa70e6" timestamp="1260732083" time_generated="1263695971" time_taken_to_generate="0" size="443370">
+ </export>
+ <export format="chadoxml" path="obo-all/minimal_anatomical_terminology/minimal_anatomical_terminology.chadoxml" md5="1693a113747ecc81b75673fc22e404b8" timestamp="1260732084" time_generated="1263695971" time_taken_to_generate="0" size="839840">
+ </export>
+ <export format="godb_prestore" path="obo-all/minimal_anatomical_terminology/minimal_anatomical_terminology.godb_prestore" md5="e5e790536e68ef7a89fb2572b79e2481" timestamp="1260732085" time_generated="1263695971" time_taken_to_generate="0" size="890134">
+ </export>
+ <export format="rdf" path="obo-all/minimal_anatomical_terminology/minimal_anatomical_terminology.rdf" md5="504326f1bb001a23535e8f25d952344c" timestamp="1260732086" time_generated="1263695971" time_taken_to_generate="0" size="234351">
+ </export>
+ <export format="tbl" path="obo-all/minimal_anatomical_terminology/minimal_anatomical_terminology.tbl" md5="d009efc9d1e1c0441e2290607b6ccd95" timestamp="1260732087" time_generated="1263695971" time_taken_to_generate="0" size="17794">
+ </export>
+ <export format="prolog" path="obo-all/minimal_anatomical_terminology/minimal_anatomical_terminology.pro" md5="c23675fde08adcad1c0172245a73d3f3" timestamp="1260732088" time_generated="1263695971" time_taken_to_generate="0" size="260988">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/minimal_anatomical_terminology/minimal_anatomical_terminology.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1260732091" time_generated="1263695972" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" path="obo-all/minimal_anatomical_terminology/minimal_anatomical_terminology.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1260732092" time_generated="1263695972" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/minimal_anatomical_terminology/minimal_anatomical_terminology.obo.html" md5="eb4a2209e0ee357c792d0a6e93ef2350" timestamp="1260732093" time_generated="1263695972" time_taken_to_generate="0" size="719234">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="mged">
+ <source>http://mged.sourceforge.net/ontologies/MGEDOntology.owl</source>
+ <namespace>MO</namespace>
+ <status>Active</status>
+ <contact>MGED mged-ontologies lists.sourceforge.net</contact>
+ <description>Concepts, definitions, terms, and resources for standardized description of a microarray experiment in support of MAGE v.1. The MGED ontology is divided into the MGED Core ontology which is intended to be stable and in synch with MAGE v.1; and the MGED Extended ontology which adds further associations and classes not found in MAGE v.1.</description>
+ <foundry>No</foundry>
+ <domain>experiments</domain>
+ <format>owl</format>
+ <documentation>MGED downloads|http://mged.sourceforge.net/software/downloads.php</documentation>
+ <url>http://mged.sourceforge.net/ontologies/MGEDOntology.owl</url>
+ <title>Microarray experimental conditions</title>
+ <home>MGED ontology|http://mged.sourceforge.net/ontologies/MGEDontology.php</home>
+ <download></download>
+ <export format="pro" path="obo-all/mged/mged.pro" md5="fc809755e1429433c79378868c9068b9" timestamp="1260732109" time_generated="1263695976" time_taken_to_generate="0" size="430183">
+ </export>
+ <export format="obo" path="obo-all/mged/mged.obo" md5="39f8e0c3274385bab8e030c70bfaa8ff" timestamp="1260732101" time_generated="1263695976" time_taken_to_generate="0" size="318361">
+ </export>
+ <export format="obo_xml" path="obo-all/mged/mged.obo_xml" md5="30ca99cb9375c609b9b2da8d3106caf7" timestamp="1260732102" time_generated="1263695976" time_taken_to_generate="0" size="560503">
+ </export>
+ <export format="owl" path="obo-all/mged/mged.owl" md5="5d417ac40add77c4424bf14109b8bd64" timestamp="1263695976" time_generated="1263695976" time_taken_to_generate="0" size="569802">
+ </export>
+ <export format="chadoxml" path="obo-all/mged/mged.chadoxml" md5="786b43f8b1637ffe1f186925aefd4189" timestamp="1260732105" time_generated="1263695976" time_taken_to_generate="0" size="695669">
+ </export>
+ <export format="godb_prestore" path="obo-all/mged/mged.godb_prestore" md5="d86bde7997e2adf2a5f741da3722c311" timestamp="1260732106" time_generated="1263695976" time_taken_to_generate="0" size="604497">
+ </export>
+ <export format="rdf" path="obo-all/mged/mged.rdf" md5="b9abb4b65efc48cbfde2e9061fa2b5f2" timestamp="1260732107" time_generated="1263695976" time_taken_to_generate="0" size="480412">
+ </export>
+ <export format="tbl" path="obo-all/mged/mged.tbl" md5="a7fd06abd4aa1eb39d94a61fc121c646" timestamp="1260732108" time_generated="1263695976" time_taken_to_generate="0" size="5311">
+ </export>
+ <export format="prolog" path="obo-all/mged/mged.pro" md5="fc809755e1429433c79378868c9068b9" timestamp="1260732109" time_generated="1263695976" time_taken_to_generate="0" size="430183">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/mged/mged.validation_report" md5="255a94523cb6a41cc5c479b993a4d7ea" timestamp="1260732111" time_generated="1263695977" time_taken_to_generate="0" size="277">
+ </export>
+ <export format="stats" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/mged/mged.obo.html" md5="a98bb68f79e9e6b920c546de7a892748" timestamp="1260732112" time_generated="1263695978" time_taken_to_generate="0" size="1377792">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="molecular_function">
+ <source>ftp://ftp.geneontology.org/pub/go/ontology/obo_format_1_2/gene_ontology.1_2.obo</source>
+ <granularity>molecular,cellular,organismal,multi-organismal</granularity>
+ <status>Production and review</status>
+ <subtypes_of>bfo:Process</subtypes_of>
+ <contact>Gene Ontology go geneontology.org</contact>
+ <foundry>Yes</foundry>
+ <domain>biological function</domain>
+ <documentation>Gene Ontology documentation|http://www.geneontology.org/GO.doc.shtml</documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/gene_ontology_edit.obo</url>
+ <patho_type>canonical</patho_type>
+ <home>www.geneontology.org|http://www.geneontology.org</home>
+ <namespace>GO</namespace>
+ <description>Provides structured controlled vocabularies for the annotation of gene products with respect to their molecular function. One of the three vocabularies of the Gene Ontology.</description>
+ <format>obo</format>
+ <title>Molecular function</title>
+ <relevant_organism>all</relevant_organism>
+ <download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/gene_ontology_edit.obo</download>
+ <export format="obo_xml" path="obo-all/gene_ontology/gene_ontology.obo_xml" md5="12c6d75ca02b4580c1f1e632df16c3c6" timestamp="1263596025" time_generated="1263695980" time_taken_to_generate="0" size="29902564">
+ </export>
+ <export format="obo" path="obo-all/molecular_function/molecular_function.obo" md5="193f36372b7aca4f57322bbe8585c3e8" timestamp="1263696053" time_generated="1263696053" time_taken_to_generate="67" size="4844680">
+ </export>
+ <export format="obo_xml" path="obo-all/molecular_function/molecular_function.obo_xml" md5="d01adb077c2fe5213d2e586d90e88405" timestamp="1263696096" time_generated="1263696096" time_taken_to_generate="43" size="10464263">
+ </export>
+ <export format="obo" path="obo-all/molecular_function/molecular_function.obo" md5="193f36372b7aca4f57322bbe8585c3e8" timestamp="1263696053" time_generated="1263696096" time_taken_to_generate="0" size="4844680">
+ </export>
+ <export format="owl" path="obo-all/molecular_function/molecular_function.owl" md5="162aca649b74149c2554d489b37be603" timestamp="1263698110" time_generated="1263698110" time_taken_to_generate="2014" size="24567383">
+ </export>
+ <export format="chadoxml" path="obo-all/molecular_function/molecular_function.chadoxml" md5="5855b9d252117293ef9cf3acd9e89da0" timestamp="1263698530" time_generated="1263698530" time_taken_to_generate="420" size="24022671">
+ </export>
+ <export format="godb_prestore" path="obo-all/molecular_function/molecular_function.godb_prestore" md5="ba4e8d4016636aa7500530dbf9904bf4" timestamp="1263698560" time_generated="1263698560" time_taken_to_generate="30" size="19005995">
+ </export>
+ <export format="rdf" path="obo-all/molecular_function/molecular_function.rdf" md5="25bc853156bcf8dc47666462838cb9db" timestamp="1263698597" time_generated="1263698597" time_taken_to_generate="36" size="8608237">
+ </export>
+ <export format="tbl" path="obo-all/molecular_function/molecular_function.tbl" md5="b91880e21b918c1e2e7132ef623484a0" timestamp="1263698626" time_generated="1263698626" time_taken_to_generate="29" size="2674506">
+ </export>
+ <export format="prolog" path="obo-all/molecular_function/molecular_function.pro" md5="b6facf6fb6abf8573f055ee673e54bde" timestamp="1263698670" time_generated="1263698670" time_taken_to_generate="44" size="12128850">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/molecular_function/molecular_function.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1263698703" time_generated="1263698703" time_taken_to_generate="8" size="20">
+ </export>
+ <export format="stats" path="obo-all/molecular_function/molecular_function.stats" md5="619a62d04ddf7c62cc6ebdc743938b12" timestamp="1263698705" time_generated="1263698705" time_taken_to_generate="2" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/molecular_function/molecular_function.obo.html" md5="e7e4655b1f882ef65f076b7867797c17" timestamp="1263698708" time_generated="1263698708" time_taken_to_generate="3" size="20854587">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="molecule_role">
+ <source>molecule_role.obo|http://www.inoh.org/ontologies/MoleculeRoleOntology.obo</source>
+ <namespace>IMR</namespace>
+ <status>Active</status>
+ <contact>INOH curators curator inoh.org</contact>
+ <description>A structured controlled vocabulary of concrete protein names and generic (abstract) protein names. This ontology is a INOH pathway annotation ontology, one of a set of ontologies intended to be used in pathway data annotation to ease data integration. This ontology is used to annotate protein names, protein family names, generic/concrete protein names in the INOH pathway data.<br>INOH is part of the BioPAX working group.</description>
+ <foundry>No</foundry>
+ <domain>proteins</domain>
+ <format>obo</format>
+ <documentation>INOH Ontologies|http://www.inoh.org/info/ontologies/</documentation>
+ <url>http://www.inoh.org/ontologies/MoleculeRoleOntology.obo</url>
+ <title>Molecule role (INOH Protein name/family name ontology)</title>
+ <source_label>molecule_role.obo</source_label>
+ <home>The INOH Pathway Database|http://www.inoh.org</home>
+ <export format="obo_xml" path="obo-all/molecule_role/molecule_role.obo_xml" md5="3b6ecab161f55a5fb6a7b3075c2d4df1" timestamp="1260733985" time_generated="1263698725" time_taken_to_generate="0" size="13587786">
+ </export>
+ <export format="obo" path="obo-all/molecule_role/molecule_role.obo" md5="9a409cb3baca5eed40475aafffe99d17" timestamp="1263698725" time_generated="1263698726" time_taken_to_generate="0" size="4152701">
+ </export>
+ <export format="owl" path="obo-all/molecule_role/molecule_role.owl" md5="8b265c0e10242a5ae1f3038dae087901" timestamp="1260736391" time_generated="1263698726" time_taken_to_generate="0" size="37176323">
+ </export>
+ <export format="chadoxml" path="obo-all/molecule_role/molecule_role.chadoxml" md5="6504d1056cf50e9f6927ae9924de1949" timestamp="1260737078" time_generated="1263698726" time_taken_to_generate="0" size="26504243">
+ </export>
+ <export format="godb_prestore" path="obo-all/molecule_role/molecule_role.godb_prestore" md5="2a905ec2ad4089383b200032c6102c2e" timestamp="1260737124" time_generated="1263698727" time_taken_to_generate="0" size="18688248">
+ </export>
+ <export format="rdf" path="obo-all/molecule_role/molecule_role.rdf" md5="4c9df2d346fe2aac90811f3b232024ba" timestamp="1260737175" time_generated="1263698727" time_taken_to_generate="0" size="6769105">
+ </export>
+ <export format="tbl" path="obo-all/molecule_role/molecule_role.tbl" md5="009ff047199589e83effccd2496caedf" timestamp="1260737212" time_generated="1263698727" time_taken_to_generate="0" size="1337762">
+ </export>
+ <export format="prolog" path="obo-all/molecule_role/molecule_role.pro" md5="6e3f65111057e91fbb556a36f396337f" timestamp="1260737273" time_generated="1263698727" time_taken_to_generate="0" size="15763973">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/molecule_role/molecule_role.validation_report" md5="6da87d863bb641bb7e288c388f007fb2" timestamp="1260737316" time_generated="1263698784" time_taken_to_generate="0" size="1429">
+ </export>
+ <export format="stats" path="obo-all/molecule_role/molecule_role.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1260737318" time_generated="1263698784" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/molecule_role/molecule_role.obo.html" md5="71ca508df2c0f6de92bd09cd8dd58528" timestamp="1260737320" time_generated="1263698784" time_taken_to_generate="0" size="23483237">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="mosquito_anatomy">
+ <source>http://www.anobase.org/anatomy/mosquito_anatomy.obo</source>
+ <granularity>organismal</granularity>
+ <status>Production and review</status>
+ <subtypes_of>CARO:0000000</subtypes_of>
+ <contact>C. Louis louis imbb.forth.gr</contact>
+ <foundry>Yes</foundry>
+ <domain>anatomy</domain>
+ <documentation></documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/mosquito_anatomy.obo</url>
+ <patho_type>canonical</patho_type>
+ <home>AnoBase / Vectorbase|http://www.anobase.org</home>
+ <namespace>TGMA</namespace>
+ <description>A structured controlled vocabulary of the anatomy of mosquitoes.</description>
+ <format>obo</format>
+ <title>Mosquito gross anatomy</title>
+ <relevant_organism>NCBITaxon:44484|Anopheles</relevant_organism>
+ <download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/mosquito_anatomy.obo</download>
+ <export format="obo_xml" path="obo-all/mosquito_anatomy/mosquito_anatomy.obo_xml" md5="b21532d60b7bae666cb89043d1ab7de9" timestamp="1260737328" time_generated="1263698789" time_taken_to_generate="0" size="2111776">
+ </export>
+ <export format="obo" path="obo-all/mosquito_anatomy/mosquito_anatomy.obo" md5="ce787cff4dd177007c2be5edbe3cff7a" timestamp="1263698789" time_generated="1263698789" time_taken_to_generate="0" size="970229">
+ </export>
+ <export format="owl" path="obo-all/mosquito_anatomy/mosquito_anatomy.owl" md5="7ac78b1035e3d539003b70acc1547220" timestamp="1260737421" time_generated="1263698789" time_taken_to_generate="0" size="5090374">
+ </export>
+ <export format="chadoxml" path="obo-all/mosquito_anatomy/mosquito_anatomy.chadoxml" md5="cd55e46f8037e239e97c48b8e1e63706" timestamp="1260737453" time_generated="1263698789" time_taken_to_generate="0" size="4286993">
+ </export>
+ <export format="godb_prestore" path="obo-all/mosquito_anatomy/mosquito_anatomy.godb_prestore" md5="53ac085f8db05cf15709197f87b9d96d" timestamp="1260737459" time_generated="1263698789" time_taken_to_generate="0" size="3439730">
+ </export>
+ <export format="rdf" path="obo-all/mosquito_anatomy/mosquito_anatomy.rdf" md5="789ef3ee6b46191e871ebc0642d133c3" timestamp="1260737466" time_generated="1263698789" time_taken_to_generate="0" size="1405125">
+ </export>
+ <export format="tbl" path="obo-all/mosquito_anatomy/mosquito_anatomy.tbl" md5="f031cfe20489af0d847310d3b4e11686" timestamp="1260737471" time_generated="1263698789" time_taken_to_generate="0" size="477289">
+ </export>
+ <export format="prolog" path="obo-all/mosquito_anatomy/mosquito_anatomy.pro" md5="363ffee130360778213f5e9bc8c87d5b" timestamp="1260737480" time_generated="1263698789" time_taken_to_generate="0" size="2278546">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/mosquito_anatomy/mosquito_anatomy.validation_report" md5="8f50f694487a20ff1128146be3146dfb" timestamp="1260737486" time_generated="1263698797" time_taken_to_generate="0" size="210">
+ </export>
+ <export format="stats" path="obo-all/mosquito_anatomy/mosquito_anatomy.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1260737487" time_generated="1263698797" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/mosquito_anatomy/mosquito_anatomy.obo.html" md5="fab7213c3fcef0e4d110008e52074a48" timestamp="1260737488" time_generated="1263698797" time_taken_to_generate="0" size="3880299">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="mosquito_insecticide_resistance">
+ <source>http://www.anobase.org/miro/miro_release.obo</source>
+ <granularity>organismal</granularity>
+ <status>Discussion and review</status>
+ <subtypes_of>bfo:DependentContinuant</subtypes_of>
+ <contact>C. Louis louis imbb.forth.gr</contact>
+ <foundry>Yes</foundry>
+ <domain>environment</domain>
+ <documentation></documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/mosquito_insecticide_resistance.obo</url>
+ <patho_type>canonical</patho_type>
+ <home>AnoBase / Vectorbase|http://www.anobase.org</home>
+ <namespace>MIRO</namespace>
+ <description>Application ontology for entities related to insecticide resistance in mosquitos</description>
+ <format>obo</format>
+ <title>Mosquito insecticide resistance</title>
+ <relevant_organism>NCBITaxon:44484|Anopheles</relevant_organism>
+ <download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/mosquito_insecticide_resistance.obo</download>
+ <export format="obo_xml" path="obo-all/mosquito_insecticide_resistance/mosquito_insecticide_resistance.obo_xml" md5="00b406353c74b68ea6c978f1767fb19a" timestamp="1263698808" time_generated="1263698808" time_taken_to_generate="7" size="2208443">
+ </export>
+ <export format="obo" path="obo-all/mosquito_insecticide_resistance/mosquito_insecticide_resistance.obo" md5="c2b73ab42630d6f5a7e2f39cdd9b07c8" timestamp="1263698800" time_generated="1263698808" time_taken_to_generate="0" size="993321">
+ </export>
+ <export format="owl" path="obo-all/mosquito_insecticide_resistance/mosquito_insecticide_resistance.owl" md5="7a3695eaca5f7246a8e096999e21b2fa" timestamp="1263698963" time_generated="1263698963" time_taken_to_generate="155" size="4668230">
+ </export>
+ <export format="chadoxml" path="obo-all/mosquito_insecticide_resistance/mosquito_insecticide_resistance.chadoxml" md5="0c84c686ded1debf5ec346c1486492ee" timestamp="1263699023" time_generated="1263699023" time_taken_to_generate="60" size="4724891">
+ </export>
+ <export format="godb_prestore" path="obo-all/mosquito_insecticide_resistance/mosquito_insecticide_resistance.godb_prestore" md5="ae29191394b740a33c04c7603ab45cee" timestamp="1263699033" time_generated="1263699033" time_taken_to_generate="10" size="3752224">
+ </export>
+ <export format="rdf" path="obo-all/mosquito_insecticide_resistance/mosquito_insecticide_resistance.rdf" md5="98656cef6382ffd33ff9291186af54d8" timestamp="1263699044" time_generated="1263699044" time_taken_to_generate="11" size="1731439">
+ </export>
+ <export format="tbl" path="obo-all/mosquito_insecticide_resistance/mosquito_insecticide_resistance.tbl" md5="35a2ce561d7e5104191da5f1c78fcf31" timestamp="1263699052" time_generated="1263699052" time_taken_to_generate="8" size="351351">
+ </export>
+ <export format="prolog" path="obo-all/mosquito_insecticide_resistance/mosquito_insecticide_resistance.pro" md5="4e9096cc6a1d7aca917096fa1f5bde2a" timestamp="1263699065" time_generated="1263699065" time_taken_to_generate="13" size="1962598">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/mosquito_insecticide_resistance/mosquito_insecticide_resistance.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1263699073" time_generated="1263699073" time_taken_to_generate="2" size="20">
+ </export>
+ <export format="stats" path="obo-all/mosquito_insecticide_resistance/mosquito_insecticide_resistance.stats" md5="619a62d04ddf7c62cc6ebdc743938b12" timestamp="1263699074" time_generated="1263699074" time_taken_to_generate="1" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/mosquito_insecticide_resistance/mosquito_insecticide_resistance.obo.html" md5="a352132d88a8077dad5f844b0b75ff02" timestamp="1263699075" time_generated="1263699075" time_taken_to_generate="1" size="5355798">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="mouse_pathology">
+ <source></source>
+ <granularity>organismal,cellular</granularity>
+ <status>Quiescent</status>
+ <subtypes_of>bfo:DependentContinuant</subtypes_of>
+ <contact>Paul Schofield PS mole.bio.cam.ac.uk</contact>
+ <foundry>Yes</foundry>
+ <domain>health</domain>
+ <documentation></documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/mouse_pathology/mouse_pathology.obo</url>
+ <patho_type>pathological</patho_type>
+ <home>Pathbase|http://www.pathbase.net</home>
+ <namespace>MPATH</namespace>
+ <description>A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes</description>
+ <format>obo</format>
+ <title>Mouse pathology</title>
+ <relevant_organism>NCBITaxon:10088|Mus</relevant_organism>
+ <download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/mouse_pathology/mouse_pathology.obo</download>
+ <export format="obo_xml" path="obo-all/mouse_pathology/mouse_pathology.obo_xml" md5="d2d12f5de54cf4cfcddb396bdd404e3e" timestamp="1263699078" time_generated="1263699078" time_taken_to_generate="0" size="344197">
+ </export>
+ <export format="obo" path="obo-all/mouse_pathology/mouse_pathology.obo" md5="eaaa3ec65e47766e68769271a23e4bd0" timestamp="1263699077" time_generated="1263699078" time_taken_to_generate="0" size="184315">
+ </export>
+ <export format="owl" path="obo-all/mouse_pathology/mouse_pathology.owl" md5="1e89c8a59fd90f13b8198c5f71bdab03" timestamp="1263699081" time_generated="1263699081" time_taken_to_generate="3" size="783608">
+ </export>
+ <export format="chadoxml" path="obo-all/mouse_pathology/mouse_pathology.chadoxml" md5="57f3a37739660e2fefa8cdefd6c68678" timestamp="1263699082" time_generated="1263699082" time_taken_to_generate="1" size="775089">
+ </export>
+ <export format="godb_prestore" path="obo-all/mouse_pathology/mouse_pathology.godb_prestore" md5="3222215924addef07c9bb802bdd078a2" timestamp="1263699083" time_generated="1263699083" time_taken_to_generate="1" size="648240">
+ </export>
+ <export format="rdf" path="obo-all/mouse_pathology/mouse_pathology.rdf" md5="9f01c8bbf01c12f79f129c678175c0f2" timestamp="1263699085" time_generated="1263699085" time_taken_to_generate="2" size="314101">
+ </export>
+ <export format="tbl" path="obo-all/mouse_pathology/mouse_pathology.tbl" md5="d39af1ffc7d3be49bd46b0370ae096ac" timestamp="1263699086" time_generated="1263699086" time_taken_to_generate="1" size="96540">
+ </export>
+ <export format="prolog" path="obo-all/mouse_pathology/mouse_pathology.pro" md5="e2d68fbba76150b9c0bef4e86450110c" timestamp="1263699088" time_generated="1263699088" time_taken_to_generate="2" size="344424">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/mouse_pathology/mouse_pathology.validation_report" md5="524851be6530e1910733d98c0b6bf480" timestamp="1263699090" time_generated="1263699090" time_taken_to_generate="2" size="303">
+ </export>
+ <export format="stats" path="obo-all/mouse_pathology/mouse_pathology.stats" md5="619a62d04ddf7c62cc6ebdc743938b12" timestamp="1263699092" time_generated="1263699092" time_taken_to_generate="2" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/mouse_pathology/mouse_pathology.obo.html" md5="afc697b72f2abee5c4f54bd676ff5195" timestamp="1263699092" time_generated="1263699092" time_taken_to_generate="0" size="677332">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="ncbi_taxonomy">
+ <source>taxonomy.dat|ftp://ftp.ebi.ac.uk/pub/databases/taxonomy/taxonomy.dat</source>
+ <namespace>NCBITaxon</namespace>
+ <status>Active</status>
+ <contact>NCBI information info ncbi.nlm.nih.gov</contact>
+ <description>A taxonomic classification of living organisms and associated artifacts for their controlled description within the context of databases.</description>
+ <foundry>No</foundry>
+ <domain>taxonomy</domain>
+ <format>ncbi_taxonomy</format>
+ <documentation></documentation>
+ <url>ftp://ftp.ebi.ac.uk/pub/databases/taxonomy/taxonomy.dat</url>
+ <title>NCBI organismal classification</title>
+ <source_label>taxonomy.dat</source_label>
+ <home>NCBI Taxonomy home page|http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/</home>
+ <download></download>
+ <export format="obo_xml" path="obo-all/ncbi_taxonomy/ncbi_taxonomy.obo_xml" md5="23664784818bb9382f06b322805fe66c" timestamp="1263699578" time_generated="1263699578" time_taken_to_generate="430" size="180493648">
+ </export>
+ <export format="obo" path="obo-all/ncbi_taxonomy/ncbi_taxonomy.obo" md5="c77a1e84d931a2c7ab4655281c149bff" timestamp="1263700949" time_generated="1263700949" time_taken_to_generate="1370" size="97154784">
+ </export>
+ <export format="owl" problem="true">
+ </export>
+ <export format="chadoxml" problem="true">
+ </export>
+ <export format="godb_prestore" path="obo-all/ncbi_taxonomy/ncbi_taxonomy.godb_prestore" md5="1dc7b3cd79a837004ede01818f46e449" timestamp="1263733594" time_generated="1263733598" time_taken_to_generate="982" size="519620686">
+ </export>
+ <export format="rdf" problem="true">
+ </export>
+ <export format="tbl" path="obo-all/ncbi_taxonomy/ncbi_taxonomy.tbl" md5="0065010c6d459c571c4975ec5d5d2770" timestamp="1263734319" time_generated="1263734319" time_taken_to_generate="718" size="32888664">
+ </export>
+ <export format="prolog" path="obo-all/ncbi_taxonomy/ncbi_taxonomy.pro" md5="61aecd32277d6ae9763f8aecad22b2ad" timestamp="1263735713" time_generated="1263735713" time_taken_to_generate="1393" size="196072403">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/ncbi_taxonomy/ncbi_taxonomy.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1263737370" time_generated="1263737370" time_taken_to_generate="849" size="20">
+ </export>
+ <export format="stats" problem="true">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/ncbi_taxonomy/ncbi_taxonomy.obo.html" md5="12b07999329f0544f436f9ae70b9e471" timestamp="1263737476" time_generated="1263737477" time_taken_to_generate="98" size="630624335">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="ncithesaurus">
+ <source>EVS ftp site|ftp://ftp1.nci.nih.gov/pub/cacore/EVS/</source>
+ <namespace>ncithesaurus</namespace>
+ <status>Active</status>
+ <contact>NCICB Support ncicb pop.nci.nih.gov</contact>
+ <description>The NCI Thesaurus is an ontology-like vocabulary that includes broad coverage of the cancer domain, including cancer related diseases, findings and abnormalities; anatomy; agents, drugs and chemicals; genes and gene products and so on. In certain areas, like cancer diseases and combination chemotherapies, it provides the most granular and consistent terminology available. It combines terminology from numerous cancer research related domains, and provides a way to integra [...]
+ <foundry>No</foundry>
+ <domain>health</domain>
+ <format>owl</format>
+ <documentation>NCI Terminology Browser|http://nciterms.nci.nih.gov/NCIBrowser/Dictionary.do</documentation>
+ <url>ftp://ftp1.nci.nih.gov/pub/cacore/EVS/</url>
+ <title>NCI Thesaurus</title>
+ <source_label>EVS ftp site</source_label>
+ <home>NCI Enterprise Vocabulary Services|http://ncicb.nci.nih.gov/core/EVS</home>
+ <download></download>
+ <export format="pro" path="obo-all/ncithesaurus/ncithesaurus.pro" md5="3464e1d0e82e8343a88b7d22b0270a91" timestamp="1260767860" time_generated="1263737900" time_taken_to_generate="0" size="193682781">
+ </export>
+ <export format="obo" path="obo-all/ncithesaurus/ncithesaurus.obo" md5="d33ba73fce2a88b5211c15022eb46ac6" timestamp="1260765438" time_generated="1263737902" time_taken_to_generate="0" size="137900646">
+ </export>
+ <export format="obo_xml" path="obo-all/ncithesaurus/ncithesaurus.obo_xml" md5="61e9d214d5537d567427e4f6d9786217" timestamp="1260765769" time_generated="1263737905" time_taken_to_generate="0" size="243876312">
+ </export>
+ <export format="owl" path="obo-all/ncithesaurus/ncithesaurus.owl" md5="d75822ea31e2a577ae7ff4b0bb49fd15" timestamp="1263737897" time_generated="1263737909" time_taken_to_generate="0" size="162578979">
+ </export>
+ <export format="chadoxml" problem="true">
+ </export>
+ <export format="godb_prestore" path="obo-all/ncithesaurus/ncithesaurus.godb_prestore" md5="38a78b047fb2402aa035d6262687139e" timestamp="1260766137" time_generated="1263737910" time_taken_to_generate="0" size="322301076">
+ </export>
+ <export format="rdf" path="obo-all/ncithesaurus/ncithesaurus.rdf" md5="dc7c6314da9d3963510e5f202a8d22db" timestamp="1260766594" time_generated="1263737914" time_taken_to_generate="0" size="107542176">
+ </export>
+ <export format="tbl" path="obo-all/ncithesaurus/ncithesaurus.tbl" md5="a94213cc5a3d73462962c7f83af88813" timestamp="1260767029" time_generated="1263737916" time_taken_to_generate="0" size="39469178">
+ </export>
+ <export format="prolog" path="obo-all/ncithesaurus/ncithesaurus.pro" md5="3464e1d0e82e8343a88b7d22b0270a91" timestamp="1260767860" time_generated="1263737916" time_taken_to_generate="0" size="193682781">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/ncithesaurus/ncithesaurus.validation_report" md5="f19883d9541527b17635edc54850f114" timestamp="1260768503" time_generated="1263738229" time_taken_to_generate="0" size="1085227">
+ </export>
+ <export format="stats" path="obo-all/ncithesaurus/ncithesaurus.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1260768508" time_generated="1263738229" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/ncithesaurus/ncithesaurus.obo.html" md5="0f9f3b31f7b9a8312c8a0287b1bc66c6" timestamp="1260768575" time_generated="1263738229" time_taken_to_generate="0" size="420504304">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="NIF_GrossAnatomy">
+ <source>http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-GrossAnatomy.owl</source>
+ <granularity>organismal</granularity>
+ <uriprefix>http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-GrossAnatomy.owl#</uriprefix>
+ <status>Production and review</status>
+ <subtypes_of>CARO:0000000</subtypes_of>
+ <contact>Fahim Imam smtifahim gmail.com</contact>
+ <foundry>No</foundry>
+ <domain>neuroscience</domain>
+ <documentation>http://neuinfo.org/about/vocabularies.shtml</documentation>
+ <url>http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-GrossAnatomy.owl</url>
+ <patho_type>canonical</patho_type>
+ <home>http://neuinfo.org/</home>
+ <metadata_ontology>NIF</metadata_ontology>
+ <namespace>NIF_GrossAnatomy</namespace>
+ <description>NIF-GrossAnatomy: anatomical entities of relevance to neuroscience. Contains most classes from BIRNLex-Anatomy</description>
+ <format>owl</format>
+ <title>NIF Gross Anatomy</title>
+ <download></download>
+ <export format="pro" problem="true">
+ </export>
+ <export format="obo" problem="true">
+ </export>
+ <export format="obo_xml" problem="true">
+ </export>
+ <export format="owl" path="obo-all/NIF_GrossAnatomy/NIF_GrossAnatomy.owl" md5="e1ad446c2edaba2714e0a0be39b5ecf8" timestamp="1263738237" time_generated="1263738247" time_taken_to_generate="0" size="2696073">
+ </export>
+ <export format="chadoxml" problem="true">
+ </export>
+ <export format="godb_prestore" problem="true">
+ </export>
+ <export format="rdf" problem="true">
+ </export>
+ <export format="tbl" problem="true">
+ </export>
+ <export format="prolog" problem="true">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" problem="true">
+ </export>
+ <export format="stats" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/NIF_GrossAnatomy/NIF_GrossAnatomy.obo.html" md5="137f216bcd648d249c8b7ba74ec9f972" timestamp="1260768597" time_generated="1263738250" time_taken_to_generate="1" size="450">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="NIF_Cell">
+ <source>http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Cell.owl</source>
+ <granularity>cellular</granularity>
+ <uriprefix>http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Cell.owl#</uriprefix>
+ <status>Production and review</status>
+ <subtypes_of>CL:0000000</subtypes_of>
+ <contact>Fahim Imam smtifahim gmail.com</contact>
+ <foundry>No</foundry>
+ <domain>neuroscience</domain>
+ <documentation>http://neuinfo.org/about/vocabularies.shtml</documentation>
+ <url>http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Cell.owl</url>
+ <patho_type>canonical</patho_type>
+ <home>http://neuinfo.org/</home>
+ <metadata_ontology>NIF</metadata_ontology>
+ <namespace>NIF_Cell</namespace>
+ <description>Cell types from NIFSTD</description>
+ <format>owl</format>
+ <title>NIF Cell</title>
+ <download></download>
+ <export format="pro" problem="true">
+ </export>
+ <export format="obo" problem="true">
+ </export>
+ <export format="obo_xml" problem="true">
+ </export>
+ <export format="owl" path="obo-all/NIF_Cell/NIF_Cell.owl" md5="e7f81387d0723aa6e3b7f8480f4f2d1a" timestamp="1263738251" time_generated="1263738255" time_taken_to_generate="0" size="390388">
+ </export>
+ <export format="chadoxml" problem="true">
+ </export>
+ <export format="godb_prestore" problem="true">
+ </export>
+ <export format="rdf" problem="true">
+ </export>
+ <export format="tbl" problem="true">
+ </export>
+ <export format="prolog" problem="true">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" problem="true">
+ </export>
+ <export format="stats" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/NIF_Cell/NIF_Cell.obo.html" md5="ae43859f99c90ff61f772a6e6ef9c707" timestamp="1260768606" time_generated="1263738258" time_taken_to_generate="0" size="442">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="NIF_Dysfunction">
+ <source>http://ontology.neuinfo.org/NIF/Dysfunction/NIF-Dysfunction.owl</source>
+ <uriprefix>http://ontology.neuinfo.org/NIF/Dysfunction/NIF-Dysfunction.owl#</uriprefix>
+ <status>Production and review</status>
+ <subtypes_of>bfo:DependentContinuant</subtypes_of>
+ <contact>Fahim Imam smtifahim gmail.com</contact>
+ <foundry>No</foundry>
+ <domain>neuroscience</domain>
+ <documentation>http://neuinfo.org/about/vocabularies.shtml</documentation>
+ <url>http://ontology.neuinfo.org/NIF/Dysfunction/NIF-Dysfunction.owl</url>
+ <patho_type>pathological</patho_type>
+ <home>http://neuinfo.org/</home>
+ <namespace>NIF_Dysfunction</namespace>
+ <description>This ontology contains the former BIRNLex-Disease, version 1.3.2. -- The BIRN Project lexicon will provide entities for data and database annotation for the BIRN project, covering anatomy, disease, data collection, project management and experimental design. It is built using the organizational framework provided by the foundational Basic Formal Ontology (BFO). It uses an abstract biomedical layer on top of that - OBO-UBO which has been constructed as a proposal to th [...]
+ <format>owl</format>
+ <title>NIF Dysfunction</title>
+ <download></download>
+ <export format="pro" problem="true">
+ </export>
+ <export format="obo" problem="true">
+ </export>
+ <export format="obo_xml" problem="true">
+ </export>
+ <export format="owl" path="obo-all/NIF_Dysfunction/NIF_Dysfunction.owl" md5="fb249624905879401486eb195537aa08" timestamp="1263738259" time_generated="1263738264" time_taken_to_generate="0" size="916082">
+ </export>
+ <export format="chadoxml" problem="true">
+ </export>
+ <export format="godb_prestore" problem="true">
+ </export>
+ <export format="rdf" problem="true">
+ </export>
+ <export format="tbl" problem="true">
+ </export>
+ <export format="prolog" problem="true">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" problem="true">
+ </export>
+ <export format="stats" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/NIF_Dysfunction/NIF_Dysfunction.obo.html" md5="9a83685b7b76df49c27a31bfac99d45b" timestamp="1260768617" time_generated="1263738267" time_taken_to_generate="0" size="449">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="nmr">
+ <source>https://msi-workgroups.svn.sourceforge.net/svnroot/msi-workgroups/ontology/NMR.owl</source>
+ <namespace>NMR</namespace>
+ <status>Inactive</status>
+ <contact>Daniel Schober via MSI OWG mailing list msi-workgroups-ontology lists.sourceforge.net</contact>
+ <description>Descriptors relevant to the experimental conditions of the Nuclear Magnetic Resonance (NMR) component in a metabolomics investigation.</description>
+ <foundry>Yes</foundry>
+ <domain>experiments</domain>
+ <format>owl</format>
+ <documentation>NMR.owlDocument.doc|http://msi-ontology.sourceforge.net/ontology/NMR.owlDocument.doc</documentation>
+ <url>https://msi-workgroups.svn.sourceforge.net/svnroot/msi-workgroups/ontology/NMR.owl</url>
+ <title>NMR-instrument specific component of metabolomics investigations</title>
+ <home>Metabolomics Standards Initiative - Ontology Working Group (MSI-OWG)|http://msi-ontology.sourceforge.net/</home>
+ <download></download>
+ <problem>Source not available at specified URL as recognised format</problem>
+ </ont>
+ <ont id="obi">
+ <source>http://purl.obofoundry.org/obo/obi.owl</source>
+ <granularity>molecular,cellular,organismal,multi-organismal</granularity>
+ <status>Discussion and review</status>
+ <subtypes_of>bfo</subtypes_of>
+ <contact>OBI Users obi-users googlegroups.com</contact>
+ <foundry>Yes</foundry>
+ <domain>experiments</domain>
+ <documentation>OBI Ontology Information|http://obi-ontology.org/page/Technical_Reports</documentation>
+ <url>http://purl.obofoundry.org/obo/obi.owl</url>
+ <patho_type>canonical</patho_type>
+ <home>OBI Home|http://purl.obofoundry.org/obo/obi</home>
+ <metadata_ontology>IAO</metadata_ontology>
+ <namespace>OBI</namespace>
+ <description>OBI models the design of an investigation, the protocols and instrumentation used, the material used, the data generated and the type analysis performed on it. This project was formerly titled the Functional Genomics Investigation Ontology (FuGO) project.</description>
+ <format>owl</format>
+ <title>Ontology for biomedical investigations</title>
+ <relevant_organism>all</relevant_organism>
+ <download></download>
+ <export format="pro" path="obo-all/obi/obi.pro" md5="289df83379e8da90727838bfbab7a6a7" timestamp="1260406462" time_generated="1263738278" time_taken_to_generate="0" size="1331870">
+ </export>
+ <export format="obo" path="obo-all/obi/obi.obo" md5="ad17b9aff6c895d4cc746debc7f2e480" timestamp="1260406438" time_generated="1263738278" time_taken_to_generate="0" size="1261779">
+ </export>
+ <export format="obo_xml" path="obo-all/obi/obi.obo_xml" md5="677becd41f669e60e2e0f508dab5e3b2" timestamp="1260406441" time_generated="1263738278" time_taken_to_generate="0" size="1313116">
+ </export>
+ <export format="owl" path="obo-all/obi/obi.owl" md5="fb9d7ae5f41a264f9eb28c099a3b8203" timestamp="1263738278" time_generated="1263738278" time_taken_to_generate="0" size="4105556">
+ </export>
+ <export format="chadoxml" path="obo-all/obi/obi.chadoxml" md5="3f45410605d235bd12264dd368835289" timestamp="1260406448" time_generated="1263738278" time_taken_to_generate="0" size="1752300">
+ </export>
+ <export format="godb_prestore" path="obo-all/obi/obi.godb_prestore" md5="31a9b645b229d89cd2eebba44dab6856" timestamp="1260406450" time_generated="1263738278" time_taken_to_generate="0" size="1636485">
+ </export>
+ <export format="rdf" path="obo-all/obi/obi.rdf" md5="0abf4fe4b613db9b9898785d909600c0" timestamp="1260406455" time_generated="1263738278" time_taken_to_generate="0" size="1178064">
+ </export>
+ <export format="tbl" path="obo-all/obi/obi.tbl" md5="9e6a89333faf3fa4795b87741e6780eb" timestamp="1260406457" time_generated="1263738278" time_taken_to_generate="0" size="375048">
+ </export>
+ <export format="prolog" path="obo-all/obi/obi.pro" md5="289df83379e8da90727838bfbab7a6a7" timestamp="1260406462" time_generated="1263738278" time_taken_to_generate="0" size="1331870">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/obi/obi.validation_report" md5="07a555ef46039ea77eb7bb37c776f093" timestamp="1260406466" time_generated="1263738280" time_taken_to_generate="0" size="115">
+ </export>
+ <export format="stats" path="obo-all/obi/obi.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1260768634" time_generated="1263738280" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/obi/obi.obo.html" md5="6078e4ddd5edef86ff52f0b0b75803af" timestamp="1260408396" time_generated="1263738280" time_taken_to_generate="0" size="4570078">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="OGMS">
+ <source>http://purl.obolibrary.org/obo/ogms.owl</source>
+ <granularity>molecular,cellular,organismal,multi-organismal</granularity>
+ <status>Discussion and review</status>
+ <subtypes_of>bfo</subtypes_of>
+ <contact>Albert Goldfain albertgoldfain gmail.com</contact>
+ <foundry>Yes</foundry>
+ <domain>medicine</domain>
+ <documentation>OGMS Home|http://code.google.com/p/ogms/</documentation>
+ <url>http://purl.obolibrary.org/obo/ogms.owl</url>
+ <patho_type>pathological</patho_type>
+ <home>OGMS Home|http://code.google.com/p/ogms/</home>
+ <metadata_ontology>IAO</metadata_ontology>
+ <namespace>OGMS</namespace>
+ <imports>bfo</imports>
+ <description>The Ontology for General Medical Science (OGMS) is based on the papers Toward an Ontological Treatment of Disease and Diagnosis and On Carcinomas and Other Pathological Entities. The ontology attempts to address some of the issues raised at the Workshop on Ontology of Diseases (Dallas, TX) and the Signs, Symptoms, and Findings Workshop(Milan, Italy). OGMS was formerly called the clinical phenotype ontology. Terms from OGMS hang from the Basic Formal Ontology. See http:// [...]
+ <format>owl</format>
+ <title>Ontology for General Medical Science</title>
+ <publication>http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf</publication>
+ <relevant_organism>NCBITaxon:9606|Homo sapiens</relevant_organism>
+ <download></download>
+ <export format="pro" path="obo-all/OGMS/OGMS.pro" md5="2391afe4482f58b62a8066000dba6208" timestamp="1260768642" time_generated="1263738283" time_taken_to_generate="0" size="18704">
+ </export>
+ <export format="obo" path="obo-all/OGMS/OGMS.obo" md5="5d94d8a2a7fa42993d89060011401176" timestamp="1260768640" time_generated="1263738283" time_taken_to_generate="0" size="13941">
+ </export>
+ <export format="obo_xml" path="obo-all/OGMS/OGMS.obo_xml" md5="a1dd78e0bfecf2d09381d60e66b18b0b" timestamp="1260768640" time_generated="1263738283" time_taken_to_generate="0" size="18758">
+ </export>
+ <export format="owl" path="obo-all/OGMS/OGMS.owl" md5="f5080d4a9697393f77562b545d1a4f75" timestamp="1263738283" time_generated="1263738283" time_taken_to_generate="0" size="47239">
+ </export>
+ <export format="chadoxml" path="obo-all/OGMS/OGMS.chadoxml" md5="b06ced3e9e8ca1adc0abfedc71bb36f7" timestamp="1260768641" time_generated="1263738283" time_taken_to_generate="0" size="44166">
+ </export>
+ <export format="godb_prestore" path="obo-all/OGMS/OGMS.godb_prestore" md5="a060847360466681530870587bf2c67f" timestamp="1260768641" time_generated="1263738283" time_taken_to_generate="0" size="39740">
+ </export>
+ <export format="rdf" path="obo-all/OGMS/OGMS.rdf" md5="989e0a152402b0d585be186af3c38ea9" timestamp="1260768641" time_generated="1263738283" time_taken_to_generate="0" size="30268">
+ </export>
+ <export format="tbl" path="obo-all/OGMS/OGMS.tbl" md5="cedf4b5c0ab3f247eeaa58a98c45e32b" timestamp="1260768642" time_generated="1263738283" time_taken_to_generate="0" size="10018">
+ </export>
+ <export format="prolog" path="obo-all/OGMS/OGMS.pro" md5="2391afe4482f58b62a8066000dba6208" timestamp="1260768642" time_generated="1263738283" time_taken_to_generate="0" size="18704">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/OGMS/OGMS.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1260768643" time_generated="1263738283" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/OGMS/OGMS.obo.html" md5="7e936dbbec33a020911a135397a638fc" timestamp="1260768645" time_generated="1263738284" time_taken_to_generate="0" size="57563">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="pathway">
+ <source>pathway.obo|ftp://rgd.mcw.edu/pub/data_release/pathway.obo</source>
+ <namespace>PW</namespace>
+ <status>Active</status>
+ <contact>Victoria Petri vpetri mcw.edu</contact>
+ <description>The Pathway Ontology is a controlled vocabulary for pathways that provides standard terms for the annotation of gene products. The Pathway Ontology is under development at <a href="http://rgd.mcw.edu">Rat Genome Database</a>.</description>
+ <foundry>No</foundry>
+ <domain>biological process</domain>
+ <format>obo</format>
+ <documentation>PW_Introduction.doc|ftp://rgd.mcw.edu/pub/data_release/PW_Introduction.doc</documentation>
+ <url>ftp://rgd.mcw.edu/pub/data_release/pathway.obo</url>
+ <title>Pathway ontology</title>
+ <source_label>pathway.obo</source_label>
+ <home>RGD ontology browser and viewer|http://rgd.mcw.edu/tools/ontology/ont_search.cgi</home>
+ <export format="obo_xml" path="obo-all/pathway/pathway.obo_xml" md5="6f0c4c72736861215f572d88c96cae9d" timestamp="1260768650" time_generated="1263738288" time_taken_to_generate="0" size="456973">
+ </export>
+ <export format="obo" path="obo-all/pathway/pathway.obo" md5="066eeae3a3c97efeadfd386ef66fb10f" timestamp="1263738288" time_generated="1263738288" time_taken_to_generate="0" size="306000">
+ </export>
+ <export format="owl" path="obo-all/pathway/pathway.owl" md5="e9087d15205bff32808a1f344be2654c" timestamp="1260768658" time_generated="1263738288" time_taken_to_generate="0" size="861587">
+ </export>
+ <export format="chadoxml" path="obo-all/pathway/pathway.chadoxml" md5="0f72fb45b50f723d85f7badf77b7fc55" timestamp="1260768661" time_generated="1263738288" time_taken_to_generate="0" size="944580">
+ </export>
+ <export format="godb_prestore" path="obo-all/pathway/pathway.godb_prestore" md5="cd3b0d50b1c1bd63fbf0d23d283f5155" timestamp="1260768663" time_generated="1263738288" time_taken_to_generate="0" size="791450">
+ </export>
+ <export format="rdf" path="obo-all/pathway/pathway.rdf" md5="b5391eb2732209b9e383ad5282fdf4ab" timestamp="1260768666" time_generated="1263738288" time_taken_to_generate="0" size="400959">
+ </export>
+ <export format="tbl" path="obo-all/pathway/pathway.tbl" md5="aa6b4f5bd2da2a66526357ec0d2cad0d" timestamp="1260768668" time_generated="1263738288" time_taken_to_generate="0" size="177778">
+ </export>
+ <export format="prolog" path="obo-all/pathway/pathway.pro" md5="c6aab144baa275254c880ae998d0ab37" timestamp="1260768672" time_generated="1263738288" time_taken_to_generate="0" size="412106">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/pathway/pathway.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1260768675" time_generated="1263738289" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" path="obo-all/pathway/pathway.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1260768677" time_generated="1263738289" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/pathway/pathway.obo.html" md5="df4c3f885a64ba2d6a7314e1b7b12a2b" timestamp="1260768677" time_generated="1263738289" time_taken_to_generate="0" size="905893">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="plant_environment">
+ <source></source>
+ <namespace>EO</namespace>
+ <status>Inactive</status>
+ <contact>Pankaj Jaiswal pj37 cornell.edu</contact>
+ <description>A structured controlled vocabulary for the representation of plant environmental conditions.</description>
+ <foundry>No</foundry>
+ <domain>environment</domain>
+ <format>obo</format>
+ <documentation>Gramene Ontology website|http://www.gramene.org/plant_ontology/index.html#eo</documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/environment/environment_ontology.obo</url>
+ <title>Plant environmental conditions</title>
+ <home>Gramene|http://www.gramene.org</home>
+ <download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/environment/environment_ontology.obo</download>
+ <export format="obo_xml" path="obo-all/plant_environment/plant_environment.obo_xml" md5="ef90da4a3120c51f8b76d9bc412b6ec8" timestamp="1260768682" time_generated="1263738294" time_taken_to_generate="0" size="240838">
+ </export>
+ <export format="obo" path="obo-all/plant_environment/plant_environment.obo" md5="46764d45eb076cb773a67a62d15e1eba" timestamp="1263738294" time_generated="1263738294" time_taken_to_generate="0" size="118427">
+ </export>
+ <export format="owl" path="obo-all/plant_environment/plant_environment.owl" md5="b4b0153fe7e4cc9855645cc758fbdf15" timestamp="1260768685" time_generated="1263738294" time_taken_to_generate="0" size="540827">
+ </export>
+ <export format="chadoxml" path="obo-all/plant_environment/plant_environment.chadoxml" md5="80525ca999eb6361fbb86f5612a09cd4" timestamp="1260768687" time_generated="1263738294" time_taken_to_generate="0" size="638612">
+ </export>
+ <export format="godb_prestore" path="obo-all/plant_environment/plant_environment.godb_prestore" md5="a90af100890e3d0b0e9e16fc1531604c" timestamp="1260768689" time_generated="1263738294" time_taken_to_generate="0" size="458672">
+ </export>
+ <export format="rdf" path="obo-all/plant_environment/plant_environment.rdf" md5="f87506745a635ca88497aa41d103657e" timestamp="1260768691" time_generated="1263738294" time_taken_to_generate="0" size="230758">
+ </export>
+ <export format="tbl" path="obo-all/plant_environment/plant_environment.tbl" md5="09091cd7c3ac6224d41022fd193d8ccc" timestamp="1260768692" time_generated="1263738294" time_taken_to_generate="0" size="74906">
+ </export>
+ <export format="prolog" path="obo-all/plant_environment/plant_environment.pro" md5="6c376132d128c6fdc8d787fd75bd4a7e" timestamp="1261003056" time_generated="1263738294" time_taken_to_generate="0" size="215322">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/plant_environment/plant_environment.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1260768697" time_generated="1263738295" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" path="obo-all/plant_environment/plant_environment.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1260768699" time_generated="1263738295" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/plant_environment/plant_environment.obo.html" md5="141457c613dbb2ab6d20fe74b8d8da43" timestamp="1260768699" time_generated="1263738295" time_taken_to_generate="0" size="526958">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="plant_trait">
+ <source>http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/collaborators_ontology/gramene/traits/trait.obo?view=co</source>
+ <namespace>TO</namespace>
+ <status>Discussion and review</status>
+ <contact>Gramene curators gramene gramene.org</contact>
+ <description>A controlled vocabulary of describe phenotypic traits in cereal plants. Each trait is a distinguishable feature, characteristic, quality or phenotypic feature of a developing or mature cereal plant.</description>
+ <foundry>Yes</foundry>
+ <domain>phenotype</domain>
+ <format>obo</format>
+ <documentation>Gramene Ontology database|http://www.gramene.org/plant_ontology/index.html#to</documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/plant_traits/plant_trait.obo</url>
+ <title>Cereal plant trait</title>
+ <home>Gramene Ontology database website|http://www.gramene.org/plant_ontology/</home>
+ <download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/plant_traits/plant_trait.obo</download>
+ <export format="obo_xml" path="obo-all/plant_trait/plant_trait.obo_xml" md5="80d0c01d42dc93b9cb54ccc2bb9f148c" timestamp="1263738301" time_generated="1263738301" time_taken_to_generate="2" size="521439">
+ </export>
+ <export format="obo" path="obo-all/plant_trait/plant_trait.obo" md5="e65b42d2179ad4577e6d8e767bf5610c" timestamp="1263738299" time_generated="1263738301" time_taken_to_generate="0" size="265753">
+ </export>
+ <export format="owl" path="obo-all/plant_trait/plant_trait.owl" md5="27640c55cec1935886a88ed3fe171661" timestamp="1263738312" time_generated="1263738312" time_taken_to_generate="11" size="1143836">
+ </export>
+ <export format="chadoxml" path="obo-all/plant_trait/plant_trait.chadoxml" md5="2012041bab60a32d1b461ad55163b877" timestamp="1263738316" time_generated="1263738316" time_taken_to_generate="4" size="1512195">
+ </export>
+ <export format="godb_prestore" path="obo-all/plant_trait/plant_trait.godb_prestore" md5="68bc87cb7ba41376ef661becb540462d" timestamp="1263738318" time_generated="1263738318" time_taken_to_generate="2" size="1136914">
+ </export>
+ <export format="rdf" path="obo-all/plant_trait/plant_trait.rdf" md5="99581252eeeae72ae9a77e7215d14d97" timestamp="1263738320" time_generated="1263738321" time_taken_to_generate="3" size="506017">
+ </export>
+ <export format="tbl" path="obo-all/plant_trait/plant_trait.tbl" md5="fda24cb24accb0b9943231b65bdb298b" timestamp="1263738323" time_generated="1263738323" time_taken_to_generate="2" size="135091">
+ </export>
+ <export format="prolog" path="obo-all/plant_trait/plant_trait.pro" md5="afb9a117b9ae1b80e72cb62c554aaefa" timestamp="1263738328" time_generated="1263738328" time_taken_to_generate="5" size="539549">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/plant_trait/plant_trait.validation_report" md5="c1d4a8bef067721d20ecec456b709778" timestamp="1263738333" time_generated="1263738333" time_taken_to_generate="2" size="1010">
+ </export>
+ <export format="stats" path="obo-all/plant_trait/plant_trait.stats" md5="619a62d04ddf7c62cc6ebdc743938b12" timestamp="1263738335" time_generated="1263738335" time_taken_to_generate="2" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/plant_trait/plant_trait.obo.html" md5="0ccdde3fabf82c01e6c9f344467aea3a" timestamp="1263738335" time_generated="1263738335" time_taken_to_generate="0" size="1206937">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="plasmodium_life_cycle">
+ <source>http://www.sanger.ac.uk/Users/mb4/PLO/PLO_ontology.txt</source>
+ <namespace>PLO</namespace>
+ <status>Inactive</status>
+ <contact>Matt Berriman mb4 sanger.ac.uk</contact>
+ <description>A structured controlled vocabulary for the life cycle of the malaria parasite <i>Plasmodium</i>.</description>
+ <definitions>http://www.sanger.ac.uk/Users/mb4/PLO/PLO_defs.shtml</definitions>
+ <foundry>No</foundry>
+ <domain>anatomy</domain>
+ <format>go</format>
+ <documentation></documentation>
+ <url>http://www.sanger.ac.uk/Users/mb4/PLO/PLO_ontology.txt</url>
+ <title>Plasmodium life cycle</title>
+ <relevant_organism>NCBITaxon:5820|Drosophila</relevant_organism>
+ <home>Parasite Life Cycle Ontology|http://www.sanger.ac.uk/Users/mb4/PLO/</home>
+ <download></download>
+ <export format="obo_xml" path="obo-all/plasmodium_life_cycle/plasmodium_life_cycle.obo_xml" md5="3dac78a892190642858fd7e3d542b2e0" timestamp="1263738339" time_generated="1263738339" time_taken_to_generate="1" size="724">
+ </export>
+ <export format="obo" problem="true">
+ </export>
+ <export format="owl" path="obo-all/plasmodium_life_cycle/plasmodium_life_cycle.owl" md5="2fd3701fafbbfff3cbc4318f7352c02f" timestamp="1263738339" time_generated="1263738339" time_taken_to_generate="0" size="3619">
+ </export>
+ <export format="chadoxml" path="obo-all/plasmodium_life_cycle/plasmodium_life_cycle.chadoxml" md5="667b02fc0e71b41d199504b7f509e188" timestamp="1263738340" time_generated="1263738340" time_taken_to_generate="1" size="2327">
+ </export>
+ <export format="godb_prestore" path="obo-all/plasmodium_life_cycle/plasmodium_life_cycle.godb_prestore" md5="85d40545d561e395265226eea247b4e8" timestamp="1263738340" time_generated="1263738340" time_taken_to_generate="0" size="2712">
+ </export>
+ <export format="rdf" problem="true">
+ </export>
+ <export format="tbl" problem="true">
+ </export>
+ <export format="prolog" problem="true">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" problem="true">
+ </export>
+ <export format="stats" problem="true">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/plasmodium_life_cycle/plasmodium_life_cycle.obo.html" md5="269be6ae955745c6a08153c706fc9182" timestamp="1260768756" time_generated="1263738343" time_taken_to_generate="0" size="40257">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="po_anatomy">
+ <source></source>
+ <granularity>organismal</granularity>
+ <status>Discussion and review</status>
+ <subtypes_of>CARO:0000000</subtypes_of>
+ <contact>Plant Ontology Consortium developers po-dev plantontology.org</contact>
+ <foundry>Yes</foundry>
+ <domain>anatomy</domain>
+ <documentation>Plant Ontology database|http://www.plantontology.org/docs/docs.html</documentation>
+ <url>http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/OBO_format/po_anatomy.obo?view=co</url>
+ <patho_type>canonical</patho_type>
+ <home>Plant Ontology Consortium|http://www.plantontology.org</home>
+ <namespace>PO</namespace>
+ <description>A controlled vocabulary of plant morphological and anatomical structures representing organs, tissues, cell types, and their biological relationships based on spatial and developmental organization.<br>The plant ontologies, which includes both the plant structure and growth and development stages can be downloaded as a <a href="http://brebiou.cshl.edu/viewcvs/Poc/ontology/OBO_format/plant_ontology.obo">single file in OBO format</a>.</description>
+ <format>obo</format>
+ <title>Plant structure</title>
+ <relevant_organism>NCBITaxon:33090|Viridiplantae</relevant_organism>
+ <download>http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/OBO_format/po_anatomy.obo?view=co</download>
+ <export format="obo_xml" path="obo-all/po_anatomy/po_anatomy.obo_xml" md5="fcfb82260259671c0dc6c478cc8d9ea6" timestamp="1260768761" time_generated="1263738346" time_taken_to_generate="0" size="446151">
+ </export>
+ <export format="obo" path="obo-all/po_anatomy/po_anatomy.obo" md5="1c2b7f57154888516e589a981a73bf07" timestamp="1263738346" time_generated="1263738346" time_taken_to_generate="0" size="247128">
+ </export>
+ <export format="owl" path="obo-all/po_anatomy/po_anatomy.owl" md5="c15fc4ac5643a4cbfce7729dd6c3bd49" timestamp="1260768779" time_generated="1263738346" time_taken_to_generate="0" size="1075251">
+ </export>
+ <export format="chadoxml" path="obo-all/po_anatomy/po_anatomy.chadoxml" md5="d053e2778830245a7bc979e024618605" timestamp="1260768784" time_generated="1263738346" time_taken_to_generate="0" size="1071798">
+ </export>
+ <export format="godb_prestore" path="obo-all/po_anatomy/po_anatomy.godb_prestore" md5="2f8c8f3cb49e365477bdb25bd6c8ca6b" timestamp="1260768787" time_generated="1263738346" time_taken_to_generate="0" size="977688">
+ </export>
+ <export format="rdf" path="obo-all/po_anatomy/po_anatomy.rdf" md5="454296b08b57525450138604fbe858bc" timestamp="1260768791" time_generated="1263738346" time_taken_to_generate="0" size="439316">
+ </export>
+ <export format="tbl" path="obo-all/po_anatomy/po_anatomy.tbl" md5="2233ea10cfbd1bfe092acb8ab6459fff" timestamp="1260768793" time_generated="1263738346" time_taken_to_generate="0" size="110868">
+ </export>
+ <export format="prolog" path="obo-all/po_anatomy/po_anatomy.pro" md5="50403ee592327b0778812da4577cb705" timestamp="1263423199" time_generated="1263738346" time_taken_to_generate="0" size="397249">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/po_anatomy/po_anatomy.validation_report" md5="20aa59ea80d0e3807a032851d02d3d3c" timestamp="1260768802" time_generated="1263738348" time_taken_to_generate="0" size="2454">
+ </export>
+ <export format="stats" path="obo-all/po_anatomy/po_anatomy.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1260768804" time_generated="1263738348" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/po_anatomy/po_anatomy.obo.html" md5="df9f654d115d57926aa08c68760a390a" timestamp="1260768804" time_generated="1263738348" time_taken_to_generate="0" size="1112053">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="po_temporal">
+ <source></source>
+ <granularity>organismal</granularity>
+ <status>Discussion and review</status>
+ <subtypes_of>bfo:Occurent</subtypes_of>
+ <contact>Plant Ontology Consortium developers po-dev plantontology.org</contact>
+ <foundry>Yes</foundry>
+ <domain>anatomy</domain>
+ <documentation>Plant Ontology database|http://www.plantontology.org/docs/docs.html</documentation>
+ <url>http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/OBO_format/po_temporal.obo?view=co</url>
+ <patho_type>canonical</patho_type>
+ <home>Plant Ontology Consortium|http://www.plantontology.org</home>
+ <namespace>PO</namespace>
+ <description>A controlled vocabulary of growth and developmental stages in various plants.<br>The plant ontologies, which includes both the plant structure and growth and development stages can be downloaded as a <a href="http://brebiou.cshl.edu/viewcvs/Poc/ontology/OBO_format/plant_ontology.obo">single file in OBO format</a>.</description>
+ <format>obo</format>
+ <title>Plant growth and developmental stage</title>
+ <relevant_organism>NCBITaxon:33090|Viridiplantae</relevant_organism>
+ <download>http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/OBO_format/po_temporal.obo?view=co</download>
+ <export format="obo_xml" path="obo-all/po_temporal/po_temporal.obo_xml" md5="70b25be17e7072570fbcb9a61bf1cbb9" timestamp="1260768808" time_generated="1263738351" time_taken_to_generate="0" size="317313">
+ </export>
+ <export format="obo" path="obo-all/po_temporal/po_temporal.obo" md5="d5d3f31e5eed595502d0c0489712e2b5" timestamp="1263738351" time_generated="1263738351" time_taken_to_generate="0" size="139734">
+ </export>
+ <export format="owl" path="obo-all/po_temporal/po_temporal.owl" md5="b69245208733d2d8d2304060e8e15e64" timestamp="1260768810" time_generated="1263738351" time_taken_to_generate="0" size="762901">
+ </export>
+ <export format="chadoxml" path="obo-all/po_temporal/po_temporal.chadoxml" md5="035a7c6d38012686e6881d187e4fcc57" timestamp="1260768812" time_generated="1263738351" time_taken_to_generate="0" size="703284">
+ </export>
+ <export format="godb_prestore" path="obo-all/po_temporal/po_temporal.godb_prestore" md5="3f90647dedc06cca863adc1bfa2a0a8b" timestamp="1260768814" time_generated="1263738351" time_taken_to_generate="0" size="366800">
+ </export>
+ <export format="rdf" path="obo-all/po_temporal/po_temporal.rdf" md5="b855cc88196377802402d0279a868a24" timestamp="1260768816" time_generated="1263738351" time_taken_to_generate="0" size="200961">
+ </export>
+ <export format="tbl" path="obo-all/po_temporal/po_temporal.tbl" md5="621ce4ae84f997d8efb598365ca715e1" timestamp="1260768817" time_generated="1263738351" time_taken_to_generate="0" size="68919">
+ </export>
+ <export format="prolog" path="obo-all/po_temporal/po_temporal.pro" md5="dfe2e5535620ece7f0d0ebc43ba18ff2" timestamp="1260768819" time_generated="1263738351" time_taken_to_generate="0" size="286879">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/po_temporal/po_temporal.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1260768821" time_generated="1263738352" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" path="obo-all/po_temporal/po_temporal.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1260768823" time_generated="1263738352" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/po_temporal/po_temporal.obo.html" md5="4ea49b518170a55e1ed28d2b9546da9f" timestamp="1260768823" time_generated="1263738352" time_taken_to_generate="0" size="612508">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="protein">
+ <source>pro.obo|ftp://ftp.pir.georgetown.edu/databases/ontology/pro_obo/pro.obo</source>
+ <granularity>molecular</granularity>
+ <status>Discussion and review</status>
+ <subtypes_of>bfo:IndependentContinuant</subtypes_of>
+ <contact>Darren Natale dan5 georgetown.edu</contact>
+ <foundry>Yes</foundry>
+ <domain>proteins</domain>
+ <documentation>PRO README|ftp://ftp.pir.georgetown.edu/databases/ontology/pro_obo/pro_readme.txt</documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/pro.obo</url>
+ <patho_type>canonical</patho_type>
+ <home>Protein Ontology|http://pir.georgetown.edu/pro/</home>
+ <namespace>PRO</namespace>
+ <description>PRotein Ontology (PRO) has been designed to describe the relationships of proteins and protein evolutionary classes (ontology for ProEvo), to delineate the multiple protein forms of a gene locus (ontology for protein forms), and to interconnect existing ontologies</description>
+ <format>obo</format>
+ <title>PRotein Ontology (PRO)</title>
+ <publication>http://www.biomedcentral.com/content/pdf/1471-2105-8-S9-S1.pdf</publication>
+ <wiki>https://pir5.georgetown.edu/wiki/PRO</wiki>
+ <relevant_organism>all</relevant_organism>
+ <download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/pro.obo</download>
+ <export format="obo_xml" path="obo-all/protein/protein.obo_xml" md5="78e5f6788a0c127326f648fcb63f6874" timestamp="1263738419" time_generated="1263738419" time_taken_to_generate="51" size="13901368">
+ </export>
+ <export format="obo" path="obo-all/protein/protein.obo" md5="522a932fc75b14cd45cb9be1300fc049" timestamp="1263738367" time_generated="1263738419" time_taken_to_generate="0" size="6852585">
+ </export>
+ <export format="owl" path="obo-all/protein/protein.owl" md5="61393ff3ddfc4a814bea14e2a977c425" timestamp="1263742412" time_generated="1263742412" time_taken_to_generate="3992" size="29532734">
+ </export>
+ <export format="chadoxml" path="obo-all/protein/protein.chadoxml" md5="92fef09e91e0056441669fc4dd3bee58" timestamp="1263743875" time_generated="1263743875" time_taken_to_generate="1463" size="43288943">
+ </export>
+ <export format="godb_prestore" path="obo-all/protein/protein.godb_prestore" md5="de61c4364b1265e91ee8a8bccb83dc4b" timestamp="1263743948" time_generated="1263743948" time_taken_to_generate="72" size="30958244">
+ </export>
+ <export format="rdf" path="obo-all/protein/protein.rdf" md5="ab02010e8785663748f28a256d9b09c6" timestamp="1263744043" time_generated="1263744043" time_taken_to_generate="94" size="12362863">
+ </export>
+ <export format="tbl" path="obo-all/protein/protein.tbl" md5="cce3c8cb625c9f620ea2525e00edf8f0" timestamp="1263744106" time_generated="1263744106" time_taken_to_generate="63" size="3812547">
+ </export>
+ <export format="prolog" path="obo-all/protein/protein.pro" md5="ea5e56140b49c065928b07c243e9d300" timestamp="1263744183" time_generated="1263744183" time_taken_to_generate="77" size="17092020">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/protein/protein.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1263744226" time_generated="1263744226" time_taken_to_generate="8" size="20">
+ </export>
+ <export format="stats" path="obo-all/protein/protein.stats" md5="619a62d04ddf7c62cc6ebdc743938b12" timestamp="1263744228" time_generated="1263744228" time_taken_to_generate="2" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/protein/protein.obo.html" md5="8e9dfd8f6644e6f01f2eea0136754f0f" timestamp="1263744231" time_generated="1263744231" time_taken_to_generate="3" size="32280387">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="provenance">
+ <source>http://lsdis.cs.uga.edu/projects/glycomics/propreo/ProPreO-060506.owl</source>
+ <namespace>ProPreO</namespace>
+ <status>Active</status>
+ <contact>Satya S. Sahoo satya30 uga.edu</contact>
+ <description>A comprehensive proteomics data and process provenance ontology.</description>
+ <foundry>No</foundry>
+ <domain>proteins</domain>
+ <format>owl</format>
+ <documentation>ProPreO Ontology home|http://lsdis.cs.uga.edu/projects/glycomics/propreo/</documentation>
+ <url>http://lsdis.cs.uga.edu/projects/glycomics/propreo/ProPreO-060506.owl</url>
+ <title>Proteomics data and process provenance</title>
+ <home>ProPreO Ontology home|http://lsdis.cs.uga.edu/projects/glycomics/propreo/</home>
+ <download></download>
+ <export format="pro" path="obo-all/provenance/provenance.pro" md5="02dfba598ee7a6aa1a1c6756cd753fe1" timestamp="1260769178" time_generated="1263744233" time_taken_to_generate="0" size="155732">
+ </export>
+ <export format="obo" path="obo-all/provenance/provenance.obo" md5="e8ddb9a863996b5a994640016edb9c64" timestamp="1260769176" time_generated="1263744233" time_taken_to_generate="0" size="113332">
+ </export>
+ <export format="obo_xml" path="obo-all/provenance/provenance.obo_xml" md5="a7d35b8e5da060c53cb324faf9e67563" timestamp="1260769176" time_generated="1263744233" time_taken_to_generate="0" size="151333">
+ </export>
+ <export format="owl" path="obo-all/provenance/provenance.owl" md5="7ec10e0ce39d0cb3921343fb0b0c0d60" timestamp="1263744233" time_generated="1263744233" time_taken_to_generate="0" size="234639">
+ </export>
+ <export format="chadoxml" path="obo-all/provenance/provenance.chadoxml" md5="20f48785c9bf3abd749c4c014724b2af" timestamp="1260769176" time_generated="1263744233" time_taken_to_generate="0" size="363992">
+ </export>
+ <export format="godb_prestore" path="obo-all/provenance/provenance.godb_prestore" md5="1f4387c8490305d49b9b85fac1510488" timestamp="1260769177" time_generated="1263744233" time_taken_to_generate="0" size="194140">
+ </export>
+ <export format="rdf" path="obo-all/provenance/provenance.rdf" md5="c487247b525a9ee1a485b24fa1f66235" timestamp="1260769177" time_generated="1263744233" time_taken_to_generate="0" size="226509">
+ </export>
+ <export format="tbl" path="obo-all/provenance/provenance.tbl" md5="0dd6d7ab657bcc75a2153355e3b5b6fd" timestamp="1260769178" time_generated="1263744233" time_taken_to_generate="0" size="14642">
+ </export>
+ <export format="prolog" path="obo-all/provenance/provenance.pro" md5="02dfba598ee7a6aa1a1c6756cd753fe1" timestamp="1260769178" time_generated="1263744233" time_taken_to_generate="0" size="155732">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/provenance/provenance.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1260769179" time_generated="1263744233" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/provenance/provenance.obo.html" md5="affb1313780611ae48f3521257fb57d7" timestamp="1260769180" time_generated="1263744234" time_taken_to_generate="0" size="431026">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="psi-mi">
+ <source>http://psidev.cvs.sourceforge.net/viewvc/*checkout*/psidev/psi/mi/rel25/data/psi-mi25.obo</source>
+ <granularity>molecular</granularity>
+ <status>Discussion and review</status>
+ <subtypes_of>bfo:IndependentContinuant</subtypes_of>
+ <contact>Henning Hermjakob Henning.Hermjakob ebi.ac.uk</contact>
+ <foundry>Yes</foundry>
+ <domain>experiments</domain>
+ <documentation>PSI documentation|http://psidev.sourceforge.net/mi/xml/doc/user/index.html</documentation>
+ <url>http://psidev.cvs.sourceforge.net/viewvc/*checkout*/psidev/psi/mi/rel25/data/psi-mi25.obo</url>
+ <patho_type>canonical</patho_type>
+ <home>Proteomics Standards Initiative for Molecular Interaction|http://psidev.sf.net</home>
+ <namespace>MI</namespace>
+ <description>A structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. Developed by the HUPO Proteomics Standards Initiative.</description>
+ <format>obo</format>
+ <title>Protein-protein interaction</title>
+ <relevant_organism>all</relevant_organism>
+ <download></download>
+ <export format="obo_xml" path="obo-all/psi-mi/psi-mi.obo_xml" md5="2ca4340dc937581b67233a38aa814c91" timestamp="1260769185" time_generated="1263744236" time_taken_to_generate="0" size="671872">
+ </export>
+ <export format="obo" path="obo-all/psi-mi/psi-mi.obo" md5="d1c5395f3a3a71615ae078217ac70b61" timestamp="1263744236" time_generated="1263744236" time_taken_to_generate="0" size="409159">
+ </export>
+ <export format="owl" path="obo-all/psi-mi/psi-mi.owl" md5="a2796127f8afaf29acf229b190ce4483" timestamp="1260769200" time_generated="1263744236" time_taken_to_generate="0" size="1400029">
+ </export>
+ <export format="chadoxml" path="obo-all/psi-mi/psi-mi.chadoxml" md5="306ea96b7a1601e0d1ba010850525a28" timestamp="1260769206" time_generated="1263744237" time_taken_to_generate="0" size="1632545">
+ </export>
+ <export format="godb_prestore" path="obo-all/psi-mi/psi-mi.godb_prestore" md5="f9a3d0bf8cdf45f9f2e351f833fe80f7" timestamp="1260769209" time_generated="1263744237" time_taken_to_generate="0" size="1422291">
+ </export>
+ <export format="rdf" path="obo-all/psi-mi/psi-mi.rdf" md5="4546ef5663a5a566ba9037b6ccf69a82" timestamp="1260769213" time_generated="1263744237" time_taken_to_generate="0" size="601031">
+ </export>
+ <export format="tbl" path="obo-all/psi-mi/psi-mi.tbl" md5="9fecd47b662b1b570d32d93c8003dc53" timestamp="1260769215" time_generated="1263744237" time_taken_to_generate="0" size="249626">
+ </export>
+ <export format="prolog" path="obo-all/psi-mi/psi-mi.pro" md5="9b0d9d973164067dd8ec435efb363b59" timestamp="1260769220" time_generated="1263744237" time_taken_to_generate="0" size="688107">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/psi-mi/psi-mi.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1260769224" time_generated="1263744238" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" path="obo-all/psi-mi/psi-mi.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1260769225" time_generated="1263744238" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/psi-mi/psi-mi.obo.html" md5="f3164cdcc2716dd49e6a991c9cdae560" timestamp="1260769226" time_generated="1263744238" time_taken_to_generate="0" size="1479651">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="psi-mod">
+ <source>http://psidev.sourceforge.net/mod/data/PSI-MOD.obo</source>
+ <granularity>molecular</granularity>
+ <status>Discussion and review</status>
+ <subtypes_of>bfo:IndependentContinuant</subtypes_of>
+ <contact>Luisa Montecchi luisa ebi.ac.uk</contact>
+ <foundry>Yes</foundry>
+ <domain>proteins</domain>
+ <documentation>Proteomic Standard Initiative for Protein Modification|http://psidev.sourceforge.net/mod/</documentation>
+ <url>http://psidev.sourceforge.net/mod/data/PSI-MOD.obo</url>
+ <patho_type>canonical</patho_type>
+ <home>Proteomic Standard Initiative for Protein Modification|http://psidev.sourceforge.net/mod/</home>
+ <namespace>MOD</namespace>
+ <description>PSI-MOD is an ontology consisting of terms that describe protein chemical modifications, logically linked by an is_a relationship in such a way as to form a direct acyclic graph (DAG). The PSI-MOD ontology has more than 45 top-level nodes, and provides alternative hierarchical paths for classifying protein modifications either by the molecular structure of the modification, or by the amino acid residue that is modified.</description>
+ <format>obo</format>
+ <title>Protein modification</title>
+ <relevant_organism>all</relevant_organism>
+ <download></download>
+ <export format="obo_xml" path="obo-all/psi-mod/psi-mod.obo_xml" md5="5c0e60d9f9a3c6b0b24ce5092a05d4ac" timestamp="1260769239" time_generated="1263744243" time_taken_to_generate="0" size="2510711">
+ </export>
+ <export format="obo" path="obo-all/psi-mod/psi-mod.obo" md5="905d1e4b3a56dd0687bc4a8a23624c58" timestamp="1263744243" time_generated="1263744243" time_taken_to_generate="0" size="1029989">
+ </export>
+ <export format="owl" problem="true">
+ </export>
+ <export format="chadoxml" path="obo-all/psi-mod/psi-mod.chadoxml" md5="1c5266d4d52d38aa942cc845d0d8ae1a" timestamp="1260769657" time_generated="1263744448" time_taken_to_generate="0" size="4733522">
+ </export>
+ <export format="godb_prestore" path="obo-all/psi-mod/psi-mod.godb_prestore" md5="ae45d603c71a212c35e6b7f978d7829f" timestamp="1260769667" time_generated="1263744449" time_taken_to_generate="0" size="4673794">
+ </export>
+ <export format="rdf" path="obo-all/psi-mod/psi-mod.rdf" md5="e6af22ee9d5197f7e735d14d1d16b66a" timestamp="1260769677" time_generated="1263744449" time_taken_to_generate="0" size="891986">
+ </export>
+ <export format="tbl" path="obo-all/psi-mod/psi-mod.tbl" md5="e3ee789fd9b12100979944fe0fa30857" timestamp="1260769684" time_generated="1263744449" time_taken_to_generate="0" size="259280">
+ </export>
+ <export format="prolog" path="obo-all/psi-mod/psi-mod.pro" md5="46763ecc8f0454ce8e5dcc934d6453df" timestamp="1260769694" time_generated="1263744449" time_taken_to_generate="0" size="1664425">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/psi-mod/psi-mod.validation_report" md5="6aafbcbb41c8f97aaa67c3bfe675490d" timestamp="1260769702" time_generated="1263744455" time_taken_to_generate="0" size="7633">
+ </export>
+ <export format="stats" path="obo-all/psi-mod/psi-mod.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1260769704" time_generated="1263744455" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/psi-mod/psi-mod.obo.html" md5="00b95dcad716853fa65dee12880be6dc" timestamp="1260769704" time_generated="1263744455" time_taken_to_generate="0" size="4283389">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="psi-ms">
+ <source>http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo</source>
+ <granularity>molecular</granularity>
+ <status>Discussion and review</status>
+ <subtypes_of>bfo:Continuant</subtypes_of>
+ <contact>Luisa Montecchi luisa ebi.ac.uk</contact>
+ <foundry>Yes</foundry>
+ <domain>experiments</domain>
+ <documentation>Proteomics Standards Initiative for Mass SpectrometryProteomic Standard Initiative for Mass Spectrometry|http://www.psidev.info/index.php?q=node/257</documentation>
+ <url>http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo</url>
+ <patho_type>canonical</patho_type>
+ <home>Proteomics Standards Initiative for Mass SpectrometryProteomic Standard Initiative for Mass Spectrometry|http://www.psidev.info/index.php?q=node/257</home>
+ <namespace>MS</namespace>
+ <description>A structured controlled vocabulary for the annotation of experiments concerned with proteomics mass spectrometry. Developed by the HUPO Proteomics Standards Initiative.</description>
+ <format>obo</format>
+ <title>Mass spectrometry</title>
+ <relevant_organism>all</relevant_organism>
+ <download></download>
+ <export format="obo_xml" path="obo-all/psi-ms/psi-ms.obo_xml" md5="8483e3d3031d25350365939d7fcffe30" timestamp="1263028971" time_generated="1263744457" time_taken_to_generate="0" size="583000">
+ </export>
+ <export format="obo" path="obo-all/psi-ms/psi-ms.obo" md5="50b28e130195e9293b388fdb74bf9b1d" timestamp="1263744457" time_generated="1263744457" time_taken_to_generate="0" size="327024">
+ </export>
+ <export format="owl" path="obo-all/psi-ms/psi-ms.owl" md5="f04a768c7db9c163aa88cdb167d273a2" timestamp="1263028995" time_generated="1263744457" time_taken_to_generate="0" size="1338848">
+ </export>
+ <export format="chadoxml" path="obo-all/psi-ms/psi-ms.chadoxml" md5="f9533cd9e2a1d9f8913a6faab774bfd9" timestamp="1263029003" time_generated="1263744457" time_taken_to_generate="0" size="1480716">
+ </export>
+ <export format="godb_prestore" path="obo-all/psi-ms/psi-ms.godb_prestore" md5="6e0acdee8cdb0b7b38a67b59ff842a0e" timestamp="1263029007" time_generated="1263744457" time_taken_to_generate="0" size="1268643">
+ </export>
+ <export format="rdf" path="obo-all/psi-ms/psi-ms.rdf" md5="f21f1dd5115889218945f8bdfa1161bc" timestamp="1263029011" time_generated="1263744457" time_taken_to_generate="0" size="686177">
+ </export>
+ <export format="tbl" path="obo-all/psi-ms/psi-ms.tbl" md5="79da1e9709cdb2d727937b861f27d908" timestamp="1263029015" time_generated="1263744457" time_taken_to_generate="0" size="166831">
+ </export>
+ <export format="prolog" path="obo-all/psi-ms/psi-ms.pro" md5="0bfa149289883e766c3d0899152e2f56" timestamp="1263029021" time_generated="1263744457" time_taken_to_generate="0" size="539461">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/psi-ms/psi-ms.validation_report" md5="97e69f103b529b1d13d72d498e49b872" timestamp="1263029025" time_generated="1263744459" time_taken_to_generate="0" size="5366">
+ </export>
+ <export format="stats" path="obo-all/psi-ms/psi-ms.stats" md5="71666b8d5da5f0cdd71d1938865d3a1c" timestamp="1263029027" time_generated="1263744459" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/psi-ms/psi-ms.obo.html" md5="94549fd05fa19ff3b1d0a3178abea8fb" timestamp="1263029028" time_generated="1263744459" time_taken_to_generate="0" size="1481263">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="relationship">
+ <source></source>
+ <granularity>all</granularity>
+ <status>Production and review</status>
+ <subtypes_of>bfo</subtypes_of>
+ <contact>Chris Mungall obo-relations lists.sourceforge.net</contact>
+ <foundry>Yes</foundry>
+ <domain>all</domain>
+ <documentation></documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo</url>
+ <patho_type>canonical</patho_type>
+ <home>OBO Relation Ontology|http://www.obofoundry.org/ro</home>
+ <namespace>OBO_REL</namespace>
+ <description>Defines core relations used in all OBO ontologies.</description>
+ <format>obo</format>
+ <title>OBO relationship types</title>
+ <relevant_organism>all</relevant_organism>
+ <download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo</download>
+ <export format="obo_xml" path="obo-all/relationship/relationship.obo_xml" md5="ac99c4dad19a49f53759d0cf2927a39d" timestamp="1260769743" time_generated="1263744461" time_taken_to_generate="0" size="24177">
+ </export>
+ <export format="obo" path="obo-all/relationship/relationship.obo" md5="c8098d52022f9beaee8a171dcbf5002b" timestamp="1263744461" time_generated="1263744461" time_taken_to_generate="0" size="17749">
+ </export>
+ <export format="owl" path="obo-all/relationship/relationship.owl" md5="775276c6069ffcb29a9c570205989f69" timestamp="1260769744" time_generated="1263744461" time_taken_to_generate="0" size="33745">
+ </export>
+ <export format="chadoxml" path="obo-all/relationship/relationship.chadoxml" md5="67c6322c8496664189eeb893ae8dfb2d" timestamp="1260769744" time_generated="1263744461" time_taken_to_generate="0" size="34682">
+ </export>
+ <export format="godb_prestore" path="obo-all/relationship/relationship.godb_prestore" md5="7eb5ce5417f2ad9f24979bcba1fcef6e" timestamp="1260769744" time_generated="1263744461" time_taken_to_generate="0" size="40691">
+ </export>
+ <export format="rdf" path="obo-all/relationship/relationship.rdf" md5="c35841913d1c7dad8713d083c206e76a" timestamp="1260769744" time_generated="1263744461" time_taken_to_generate="0" size="21356">
+ </export>
+ <export format="tbl" problem="true">
+ </export>
+ <export format="prolog" path="obo-all/relationship/relationship.pro" md5="0ad6fe29ba83ca14bd8372860a1f761c" timestamp="1263418982" time_generated="1263744461" time_taken_to_generate="0" size="25360">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/relationship/relationship.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1260769745" time_generated="1263744461" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" path="obo-all/relationship/relationship.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1260769747" time_generated="1263744461" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/relationship/relationship.obo.html" md5="e4eb75b004939850073d78c706bd52ab" timestamp="1260769747" time_generated="1263744461" time_taken_to_generate="0" size="43758">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="rex">
+ <source>http://www.ebi.ac.uk/~kirill/REX/rex.obo</source>
+ <namespace>REX</namespace>
+ <status>Active</status>
+ <contact>Kirill Degtyarenko chebi-help ebi.ac.uk</contact>
+ <description>REX is an ontology of physico-chemical processes, i.e. physico-chemical changes occurring in course of time. REX includes both microscopic processes (involving molecular entities or subatomic particles) and macroscopic processes. Some biochemical processes from Gene Ontology (GO Biological process) can be described as instances of REX.</description>
+ <foundry>No</foundry>
+ <format>obo</format>
+ <documentation></documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/physicochemical/rex.obo</url>
+ <title>Physico-chemical process</title>
+ <home>REX directory|http://www.ebi.ac.uk/~kirill/REX/</home>
+ <download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/physicochemical/rex.obo</download>
+ <export format="obo_xml" path="obo-all/rex/rex.obo_xml" md5="f548d0931b15c189f4c35f81f259c863" timestamp="1260769749" time_generated="1263744466" time_taken_to_generate="0" size="219909">
+ </export>
+ <export format="obo" path="obo-all/rex/rex.obo" md5="a18c4682170d341b82e487404eeac3da" timestamp="1263744466" time_generated="1263744466" time_taken_to_generate="0" size="130439">
+ </export>
+ <export format="owl" path="obo-all/rex/rex.owl" md5="6fb09d8d157f7a8c2401b883929c30b0" timestamp="1260769751" time_generated="1263744466" time_taken_to_generate="0" size="483977">
+ </export>
+ <export format="chadoxml" path="obo-all/rex/rex.chadoxml" md5="a350c4a90b04e2f9d2a3bc2e8f87605d" timestamp="1260769752" time_generated="1263744466" time_taken_to_generate="0" size="569960">
+ </export>
+ <export format="godb_prestore" path="obo-all/rex/rex.godb_prestore" md5="b4c6b764e613162d84125590977d1289" timestamp="1260769753" time_generated="1263744466" time_taken_to_generate="0" size="466895">
+ </export>
+ <export format="rdf" path="obo-all/rex/rex.rdf" md5="2ea923195bb0fc6478f9464a077b36d2" timestamp="1260769754" time_generated="1263744466" time_taken_to_generate="0" size="264807">
+ </export>
+ <export format="tbl" path="obo-all/rex/rex.tbl" md5="b34d4713ee0cc0d626103bf0724e7ab5" timestamp="1260769755" time_generated="1263744466" time_taken_to_generate="0" size="67496">
+ </export>
+ <export format="prolog" path="obo-all/rex/rex.pro" md5="0ffe1e6abc48ecf36c9b049cf9d32fac" timestamp="1260769756" time_generated="1263744466" time_taken_to_generate="0" size="216701">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/rex/rex.validation_report" md5="92342eb0a77da802ec0c836ebddf6727" timestamp="1260769758" time_generated="1263744467" time_taken_to_generate="0" size="1412">
+ </export>
+ <export format="stats" path="obo-all/rex/rex.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1260769759" time_generated="1263744467" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/rex/rex.obo.html" md5="a60403bc1c1f2cfbd36356d14933c69f" timestamp="1260769759" time_generated="1263744467" time_taken_to_generate="0" size="555786">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="sao">
+ <source>http://ccdb.ucsd.edu/SAO/1.2/SAO.owl</source>
+ <granularity>sub-cellular</granularity>
+ <uriprefix>http://ccdb.ucsd.edu/SAO/1.2#</uriprefix>
+ <status>Production and review</status>
+ <subtypes_of>bfo:IndependentContinuant</subtypes_of>
+ <contact>Stephen Larson slarson ncmir.ucsd.edu</contact>
+ <foundry>Yes</foundry>
+ <domain>anatomy</domain>
+ <documentation></documentation>
+ <url>http://ccdb.ucsd.edu/SAO/1.2/SAO.owl</url>
+ <patho_type>canonical</patho_type>
+ <home>http://ccdb.ucsd.edu/CCDBWebSite/sao.html</home>
+ <xrefs_to>cellular_component,cell</xrefs_to>
+ <namespace>SAO</namespace>
+ <description>We have developed the Subcellular Anatomy Ontology for the Nervous System (SAO) to provide a formal ontology to describe structures from the dimensional range known as the “mesoscale,” encompassing cellular and subcellular structure, supracellular domains, and macromolecules. The SAO describes the parts of neurons and glia and how these parts come together to define supracellular structures such as synapses and neuropil (Fong et al., submitted). Molecular specialization [...]
+ <format>owl</format>
+ <title>Subcellular anatomy ontology</title>
+ <relevant_organism>NCBITaxon:9606|Homo sapiens</relevant_organism>
+ <download></download>
+ <export format="pro" path="obo-all/sao/sao.pro" md5="1eceab133bc37a162a0133bdda1360ea" timestamp="1260769784" time_generated="1263744468" time_taken_to_generate="0" size="664229">
+ </export>
+ <export format="obo" path="obo-all/sao/sao.obo" md5="655797bdaecd9c674cc7155a86007dd0" timestamp="1260769766" time_generated="1263744468" time_taken_to_generate="0" size="539545">
+ </export>
+ <export format="obo_xml" path="obo-all/sao/sao.obo_xml" md5="c61bb16cd27e8300bbaf84eee7ec26b0" timestamp="1260769768" time_generated="1263744468" time_taken_to_generate="0" size="883195">
+ </export>
+ <export format="owl" path="obo-all/sao/sao.owl" md5="100f33866da1fe6b5ef0f60fab97fffa" timestamp="1263744468" time_generated="1263744468" time_taken_to_generate="0" size="877846">
+ </export>
+ <export format="chadoxml" path="obo-all/sao/sao.chadoxml" md5="dfe7dc25b6b76f3e836003ba9bdc8f03" timestamp="1260769777" time_generated="1263744468" time_taken_to_generate="0" size="921699">
+ </export>
+ <export format="godb_prestore" path="obo-all/sao/sao.godb_prestore" md5="9eaeddfcd6c2ded97e61344f8283ce4d" timestamp="1260769778" time_generated="1263744468" time_taken_to_generate="0" size="1132274">
+ </export>
+ <export format="rdf" path="obo-all/sao/sao.rdf" md5="95c443618b8a383e253bf1eb854c8b59" timestamp="1260769780" time_generated="1263744468" time_taken_to_generate="0" size="266164">
+ </export>
+ <export format="tbl" path="obo-all/sao/sao.tbl" md5="8327abdd9b428b62eb3cb0f984425be2" timestamp="1260769781" time_generated="1263744468" time_taken_to_generate="0" size="27864">
+ </export>
+ <export format="prolog" path="obo-all/sao/sao.pro" md5="1eceab133bc37a162a0133bdda1360ea" timestamp="1260769784" time_generated="1263744468" time_taken_to_generate="0" size="664229">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/sao/sao.validation_report" md5="fb4ea3f3c19c974223f984a4275c628e" timestamp="1260769786" time_generated="1263744469" time_taken_to_generate="0" size="148">
+ </export>
+ <export format="stats" path="obo-all/sao/sao.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1260769787" time_generated="1263744469" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/sao/sao.obo.html" md5="465adbb1fdca65e6bef5108f67709eab" timestamp="1260769788" time_generated="1263744469" time_taken_to_generate="0" size="2345363">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="sep">
+ <source>https://psidev.svn.sourceforge.net/svnroot/psidev/psi/sepcv/trunk/sep.obo</source>
+ <namespace>SEP</namespace>
+ <status>Active</status>
+ <contact>SEP developers via the PSI and MSI mailing lists psidev-gps-dev lists.sourceforge.net</contact>
+ <description>A structured controlled vocabulary for the annotation of sample processing and separation techniques in scientific experiments, such as, and including, gel electrophoresis, column chromatography, capillary electrophoresis, centrifugation and so on. Developed jointly by the HUPO Proteomics Standards Initiative and The Metabolomics Standards Initiative.</description>
+ <foundry>No</foundry>
+ <domain>provenance</domain>
+ <format>obo</format>
+ <documentation>SEP Ontology documentation|http://psidev.info/index.php?q=node/312</documentation>
+ <url>https://psidev.svn.sourceforge.net/svnroot/psidev/psi/sepcv/trunk/sep.obo</url>
+ <title>Sample processing and separation techniques</title>
+ <home>SEP Ontology|http://psidev.info/index.php?q=node/312</home>
+ <download></download>
+ <problem>Source not available at specified URL as recognised format</problem>
+ </ont>
+ <ont id="sequence">
+ <source>http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.obo</source>
+ <prerelease_download>http://song.cvs.sourceforge.net/*checkout*/song/ontology/so-xp.obo</prerelease_download>
+ <granularity>molecular</granularity>
+ <status>Production and review</status>
+ <contact>SONG developers song-devel lists.sourceforge.net</contact>
+ <foundry>Yes</foundry>
+ <domain>biological sequence</domain>
+ <documentation></documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/so.obo</url>
+ <patho_type>all</patho_type>
+ <home>SO home|http://song.sourceforge.net/</home>
+ <namespace>SO</namespace>
+ <description>The Sequence Ontology provides a structured controlled vocabulary for sequence annotation, for the exchange of annotation data and for the description of sequence objects in databases. <a href="http://obo.cvs.sourceforge.net/*checkout*/song/ontology/sofa.obo">SOFA</a> is a minimal version of SO for use in data exchange.</description>
+ <format>obo</format>
+ <title>Sequence types and features</title>
+ <relevant_organism>all</relevant_organism>
+ <download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/so.obo</download>
+ <export format="obo_xml" path="obo-all/sequence/sequence.obo_xml" md5="e373858c6677ecf0516e738ba3438821" timestamp="1263744476" time_generated="1263744476" time_taken_to_generate="2" size="1066358">
+ </export>
+ <export format="obo" path="obo-all/sequence/sequence.obo" md5="5e9d54a507f33cf4d753a7865f1f82e0" timestamp="1263744474" time_generated="1263744476" time_taken_to_generate="0" size="573356">
+ </export>
+ <export format="owl" path="obo-all/sequence/sequence.owl" md5="6f7f201c2f37e7b4c2db5f5cce8eef54" timestamp="1263744509" time_generated="1263744509" time_taken_to_generate="33" size="2299432">
+ </export>
+ <export format="chadoxml" path="obo-all/sequence/sequence.chadoxml" md5="49b31aa7901b009c120af6133c3ad103" timestamp="1263744518" time_generated="1263744518" time_taken_to_generate="9" size="2825476">
+ </export>
+ <export format="godb_prestore" path="obo-all/sequence/sequence.godb_prestore" md5="485851a27dc72a3c08be3736602c6f6b" timestamp="1263744521" time_generated="1263744521" time_taken_to_generate="3" size="2447483">
+ </export>
+ <export format="rdf" path="obo-all/sequence/sequence.rdf" md5="8b3fa66a267c1815421ade0a6d6e9388" timestamp="1263744526" time_generated="1263744526" time_taken_to_generate="5" size="1005104">
+ </export>
+ <export format="tbl" path="obo-all/sequence/sequence.tbl" md5="18b3b0f0ea2762a2f756faef881288f9" timestamp="1263744529" time_generated="1263744529" time_taken_to_generate="3" size="273855">
+ </export>
+ <export format="prolog" path="obo-all/sequence/sequence.pro" md5="cf57d5d034a047f2c533138a822c1cf8" timestamp="1263744534" time_generated="1263744534" time_taken_to_generate="5" size="1157082">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/sequence/sequence.validation_report" md5="d16167ab22061f8f939f2efccdd2da5f" timestamp="1263744538" time_generated="1263744538" time_taken_to_generate="2" size="1396">
+ </export>
+ <export format="stats" path="obo-all/sequence/sequence.stats" md5="619a62d04ddf7c62cc6ebdc743938b12" timestamp="1263744539" time_generated="1263744539" time_taken_to_generate="1" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/sequence/sequence.obo.html" md5="0159f53673754297d15922f95badee5b" timestamp="1263744539" time_generated="1263744539" time_taken_to_generate="0" size="2453703">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="systems_biology">
+ <source>http://www.ebi.ac.uk/sbo/exports/Main/SBO_OBO.obo</source>
+ <granularity>molecular</granularity>
+ <status>Discussion and review</status>
+ <subtypes_of>bfo:IndependentContinuant</subtypes_of>
+ <contact>Nicolas Le Novère lenov ebi.ac.uk</contact>
+ <foundry>Yes</foundry>
+ <domain>biochemistry</domain>
+ <documentation></documentation>
+ <url>http://www.ebi.ac.uk/sbo/exports/Main/SBO_OBO.obo</url>
+ <patho_type>canonical</patho_type>
+ <home>SBO : Systems Biology Ontology home|http://www.ebi.ac.uk/sbo/</home>
+ <namespace>SBO</namespace>
+ <description>The Systems Biology Ontology aims to strictly index and define terms used in quantitative biochemistry. The ontology is made up of four orthogonal vocabularies. A controlled vocabulary defines the roles of reaction participants, such as "substrate", "catalyst", etc. A taxonomy orders the quantitative parameters used in biochemistry such as "Michaelis constant", but also "first-order forward rate constant". A precise classification of rate laws defines them, such as "firs [...]
+ <format>obo</format>
+ <title>Systems Biology</title>
+ <relevant_organism>all</relevant_organism>
+ <alternate_download>http://www.ebi.ac.uk/sbo/exports/Main/SBO_OWL.owl</alternate_download>
+ <download></download>
+ <export format="obo_xml" path="obo-all/systems_biology/systems_biology.obo_xml" md5="29d61b0745e0404636a268862f608250" timestamp="1263744543" time_generated="1263744543" time_taken_to_generate="1" size="504479">
+ </export>
+ <export format="obo" path="obo-all/systems_biology/systems_biology.obo" md5="91f08967957b885a0e9a7521b9a397b4" timestamp="1263744542" time_generated="1263744543" time_taken_to_generate="0" size="385705">
+ </export>
+ <export format="owl" path="obo-all/systems_biology/systems_biology.owl" md5="5ccca15788724fa458f825131a84e992" timestamp="1263744544" time_generated="1263744544" time_taken_to_generate="1" size="759877">
+ </export>
+ <export format="chadoxml" path="obo-all/systems_biology/systems_biology.chadoxml" md5="3bd72263a6e9228e4c2c7df0625cac02" timestamp="1263744545" time_generated="1263744545" time_taken_to_generate="1" size="808132">
+ </export>
+ <export format="godb_prestore" path="obo-all/systems_biology/systems_biology.godb_prestore" md5="73bae619af38305bece7c5883eb3cd64" timestamp="1263744546" time_generated="1263744546" time_taken_to_generate="1" size="713529">
+ </export>
+ <export format="rdf" path="obo-all/systems_biology/systems_biology.rdf" md5="ff89f4de8acbcb87148e71ff02e61e77" timestamp="1263744547" time_generated="1263744547" time_taken_to_generate="1" size="526184">
+ </export>
+ <export format="tbl" path="obo-all/systems_biology/systems_biology.tbl" md5="4f579d89c269efe62bf2c12e6ae0da5d" timestamp="1263744548" time_generated="1263744548" time_taken_to_generate="1" size="322010">
+ </export>
+ <export format="prolog" path="obo-all/systems_biology/systems_biology.pro" md5="4af9d5151047d0f6b10de34148af3196" timestamp="1263744550" time_generated="1263744550" time_taken_to_generate="2" size="449751">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/systems_biology/systems_biology.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1263744551" time_generated="1263744551" time_taken_to_generate="1" size="20">
+ </export>
+ <export format="stats" path="obo-all/systems_biology/systems_biology.stats" md5="619a62d04ddf7c62cc6ebdc743938b12" timestamp="1263744552" time_generated="1263744552" time_taken_to_generate="1" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/systems_biology/systems_biology.obo.html" md5="a766e3f31c5b617c775acb2886e35a7c" timestamp="1263744552" time_generated="1263744552" time_taken_to_generate="0" size="795469">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="pharmacogenomics">
+ <source>http://purl.oclc.org/NET/loria/sopharm/owl/sopharm</source>
+ <granularity>molecular,cellular,organismal,multi-organismal</granularity>
+ <status>Discussion and review</status>
+ <subtypes_of>bfo</subtypes_of>
+ <contact>Adrien Coulet Adrien.Coulet loria.fr</contact>
+ <foundry>Yes</foundry>
+ <domain>health</domain>
+ <documentation>SO-Pharm documentation|http://www.loria.fr/~coulet/ontology/sopharm/version2.0/owlDoc/index.html</documentation>
+ <url>http://purl.oclc.org/NET/loria/sopharm/owl/sopharm</url>
+ <patho_type>pathological</patho_type>
+ <home>SO-Pharm description|http://www.loria.fr/~coulet/sopharm2.0_description.php</home>
+ <namespace>SOPHARM</namespace>
+ <description>SO-Pharm is a formal ontology that represent domain knowledge in pharmacogenomics. To achieve this goal SO-Pharm articulates ontologies from sub domains of phamacogenomics (i.e. genotype, phenotype, drug, trial representations). SO-Pharm enables to support knowledge about pharmacogenomic hypothesis, case study, and investigations in pharmacogenomics.</description>
+ <format>owl</format>
+ <title>Suggested Ontology for Pharmacogenomics</title>
+ <relevant_organism>NCBITaxon:9606|Homo sapiens</relevant_organism>
+ <download></download>
+ <export format="pro" path="obo-all/pharmacogenomics/pharmacogenomics.pro" md5="7188ed3b870d1064b32f693213e963a9" timestamp="1260769885" time_generated="1263744556" time_taken_to_generate="0" size="105965">
+ </export>
+ <export format="obo" path="obo-all/pharmacogenomics/pharmacogenomics.obo" md5="4d552976188a9e1f77f4d943081a79ba" timestamp="1260769884" time_generated="1263744556" time_taken_to_generate="0" size="59624">
+ </export>
+ <export format="obo_xml" path="obo-all/pharmacogenomics/pharmacogenomics.obo_xml" md5="9265cd0ba13bc806e0f589451efb9cdb" timestamp="1260769884" time_generated="1263744556" time_taken_to_generate="0" size="71236">
+ </export>
+ <export format="owl" path="obo-all/pharmacogenomics/pharmacogenomics.owl" md5="1c592ec988b075fb71b81276f9007695" timestamp="1263744556" time_generated="1263744556" time_taken_to_generate="0" size="130952">
+ </export>
+ <export format="chadoxml" path="obo-all/pharmacogenomics/pharmacogenomics.chadoxml" md5="7118a35377f6fae9a8db72984c7f02cc" timestamp="1260769884" time_generated="1263744556" time_taken_to_generate="0" size="130597">
+ </export>
+ <export format="godb_prestore" path="obo-all/pharmacogenomics/pharmacogenomics.godb_prestore" md5="996f731060bca4f7323a231021d8e453" timestamp="1260769884" time_generated="1263744556" time_taken_to_generate="0" size="89787">
+ </export>
+ <export format="rdf" path="obo-all/pharmacogenomics/pharmacogenomics.rdf" md5="507ad20935f0ba861e8195220a6f30e0" timestamp="1260769885" time_generated="1263744556" time_taken_to_generate="0" size="78838">
+ </export>
+ <export format="tbl" path="obo-all/pharmacogenomics/pharmacogenomics.tbl" md5="f25174de9def6f6a3ff808feda5030c1" timestamp="1260769885" time_generated="1263744556" time_taken_to_generate="0" size="6703">
+ </export>
+ <export format="prolog" path="obo-all/pharmacogenomics/pharmacogenomics.pro" md5="7188ed3b870d1064b32f693213e963a9" timestamp="1260769885" time_generated="1263744556" time_taken_to_generate="0" size="105965">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/pharmacogenomics/pharmacogenomics.validation_report" md5="acdc7f8aba63f5c19eb9e406fcb4a565" timestamp="1260769886" time_generated="1263744557" time_taken_to_generate="0" size="469">
+ </export>
+ <export format="stats" path="obo-all/pharmacogenomics/pharmacogenomics.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1260769887" time_generated="1263744557" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/pharmacogenomics/pharmacogenomics.obo.html" md5="ce6eb6bdbed756ee5eff9f88dd48ba94" timestamp="1260769887" time_generated="1263744557" time_taken_to_generate="0" size="181326">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="teleost_anatomy">
+ <source></source>
+ <granularity>organismal</granularity>
+ <status>Discussion and review</status>
+ <subtypes_of>bfo:IndependentContinuant</subtypes_of>
+ <contact>Wasila Dahdul wasila.dahdul usd.edu</contact>
+ <foundry>Yes</foundry>
+ <domain>anatomy</domain>
+ <documentation></documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/fish/teleost_anatomy.obo</url>
+ <patho_type>canonical</patho_type>
+ <home>PhenoScape|https://www.nescent.org/phenoscape/Main_Page</home>
+ <xrefs_to>zebrafish_anatomy</xrefs_to>
+ <namespace>TAO</namespace>
+ <description>Multispecies fish anatomy ontology. Originally seeded from ZFA, but intended to cover terms relevant to other taxa</description>
+ <format>obo</format>
+ <title>Teleost anatomy and development</title>
+ <relevant_organism>NCBITaxon:32443|Teleostei</relevant_organism>
+ <download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/fish/teleost_anatomy.obo</download>
+ <export format="obo_xml" path="obo-all/teleost_anatomy/teleost_anatomy.obo_xml" md5="c7297e0a6b8dde7d4ad573c165277af1" timestamp="1263029091" time_generated="1263744562" time_taken_to_generate="0" size="1636951">
+ </export>
+ <export format="obo" path="obo-all/teleost_anatomy/teleost_anatomy.obo" md5="8aaf531065dd81218566d2e04a89efc6" timestamp="1263744562" time_generated="1263744562" time_taken_to_generate="0" size="773477">
+ </export>
+ <export format="owl" path="obo-all/teleost_anatomy/teleost_anatomy.owl" md5="82558d071ffd2a02c37ff1c3f43ff416" timestamp="1263029277" time_generated="1263744562" time_taken_to_generate="0" size="4022356">
+ </export>
+ <export format="chadoxml" path="obo-all/teleost_anatomy/teleost_anatomy.chadoxml" md5="1455044ff71bee3fa201aed9c2620032" timestamp="1263029334" time_generated="1263744562" time_taken_to_generate="0" size="4137862">
+ </export>
+ <export format="godb_prestore" path="obo-all/teleost_anatomy/teleost_anatomy.godb_prestore" md5="e3c6b8df78bee1c693ecf671926604bb" timestamp="1263029345" time_generated="1263744562" time_taken_to_generate="0" size="3664979">
+ </export>
+ <export format="rdf" path="obo-all/teleost_anatomy/teleost_anatomy.rdf" md5="233af283414ff080626f9f5939295769" timestamp="1263029358" time_generated="1263744563" time_taken_to_generate="0" size="2163231">
+ </export>
+ <export format="tbl" path="obo-all/teleost_anatomy/teleost_anatomy.tbl" md5="052a848f6277fac464aaaf59bb61aa07" timestamp="1263029366" time_generated="1263744563" time_taken_to_generate="0" size="315065">
+ </export>
+ <export format="prolog" path="obo-all/teleost_anatomy/teleost_anatomy.pro" md5="780b3cdb0574208333d1768a6bb8a1da" timestamp="1263399585" time_generated="1263744563" time_taken_to_generate="0" size="1504374">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/teleost_anatomy/teleost_anatomy.validation_report" md5="290434dbbac9e1ef9ccb7e3652f33722" timestamp="1263029399" time_generated="1263744566" time_taken_to_generate="0" size="15424">
+ </export>
+ <export format="stats" path="obo-all/teleost_anatomy/teleost_anatomy.stats" md5="71666b8d5da5f0cdd71d1938865d3a1c" timestamp="1263029401" time_generated="1263744566" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/teleost_anatomy/teleost_anatomy.obo.html" md5="f7a8694fd263b877e5f2532018e24b49" timestamp="1263029402" time_generated="1263744567" time_taken_to_generate="1" size="3798839">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="sdiff" path="obo-all/teleost_anatomy/teleost_anatomy.sdiff" md5="6aa7cf03af3fb3cc643b443f208347db" timestamp="1263744591" time_generated="1263744591" time_taken_to_generate="24" size="153696">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="teleost_taxonomy">
+ <source></source>
+ <granularity>organismal</granularity>
+ <status>Discussion and review</status>
+ <subtypes_of>bfo:IndependentContinuant</subtypes_of>
+ <contact>Peter Midford peteremidford yahoo.com</contact>
+ <foundry>Yes</foundry>
+ <domain>taxonomy</domain>
+ <documentation></documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/taxonomy/teleost_taxonomy.obo</url>
+ <patho_type>canonical</patho_type>
+ <home>PhenoScape|https://www.nescent.org/phenoscape/Main_Page</home>
+ <namespace>TTO</namespace>
+ <description>The Teleost taxonomy ontology is being used to facilitate annotation of phenotypes, particularly for taxa that are not covered by NCBI because no submissions of molecular data have been made. Taxonomy ontologies can also be valuable in annotating legacy data, where authors make phenotype or ecological assertions (e.g., host-parasite associations) that refer to groups that are reorganized or no longer recognized. The taxonomy ontology serves as the source of taxa for our [...]
+ <format>obo</format>
+ <title>Teleost taxonomy</title>
+ <relevant_organism>NCBITaxon:32443|Teleostei</relevant_organism>
+ <download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/taxonomy/teleost_taxonomy.obo</download>
+ <export format="obo_xml" path="obo-all/teleost_taxonomy/teleost_taxonomy.obo_xml" md5="44ca315d766b2b348a0a96e54e9f55a2" timestamp="1260770148" time_generated="1263744626" time_taken_to_generate="0" size="17357119">
+ </export>
+ <export format="obo" path="obo-all/teleost_taxonomy/teleost_taxonomy.obo" md5="47e1aed1ffd1b1fd3ae10a793a41224a" timestamp="1263744626" time_generated="1263744626" time_taken_to_generate="0" size="6641520">
+ </export>
+ <export format="owl" problem="true">
+ </export>
+ <export format="chadoxml" path="obo-all/teleost_taxonomy/teleost_taxonomy.chadoxml" md5="590c4563d6b5cb7db3f72c297d1f3287" timestamp="1260800681" time_generated="1263757291" time_taken_to_generate="0" size="41503874">
+ </export>
+ <export format="godb_prestore" path="obo-all/teleost_taxonomy/teleost_taxonomy.godb_prestore" md5="3940510b5f37323be026a12a2f036081" timestamp="1260800790" time_generated="1263757292" time_taken_to_generate="0" size="31943214">
+ </export>
+ <export format="rdf" path="obo-all/teleost_taxonomy/teleost_taxonomy.rdf" md5="a94901a5208d52153f232611903b9589" timestamp="1260800915" time_generated="1263757292" time_taken_to_generate="0" size="12689887">
+ </export>
+ <export format="tbl" path="obo-all/teleost_taxonomy/teleost_taxonomy.tbl" md5="70a13eabf62f61dcbb89a3d5d2e640c8" timestamp="1260801016" time_generated="1263757292" time_taken_to_generate="0" size="2120266">
+ </export>
+ <export format="prolog" path="obo-all/teleost_taxonomy/teleost_taxonomy.pro" md5="c0b806329b88f8c2acdd0f5784586d9d" timestamp="1260801196" time_generated="1263757292" time_taken_to_generate="0" size="19250301">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/teleost_taxonomy/teleost_taxonomy.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1260801320" time_generated="1263757338" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" path="obo-all/teleost_taxonomy/teleost_taxonomy.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1260801323" time_generated="1263757338" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/teleost_taxonomy/teleost_taxonomy.obo.html" md5="cb5f1c8268159279239bf45676fefdb9" timestamp="1260801332" time_generated="1263757338" time_taken_to_generate="0" size="39576968">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="transmission">
+ <source>http://gemina.cvs.sourceforge.net/*checkout*/gemina/Gemina/ontologies/transmission_process.obo</source>
+ <granularity>organismal,cellular</granularity>
+ <status>Discussion and review</status>
+ <subtypes_of></subtypes_of>
+ <contact>Lynn Schriml diseaseontology-discussion lists.sourceforge.net</contact>
+ <foundry>Yes</foundry>
+ <domain>health</domain>
+ <documentation></documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/transmission_process.obo</url>
+ <patho_type>canonical</patho_type>
+ <home>Disease Ontology|http://diseaseontology.sourceforge.net/</home>
+ <namespace>TRANS</namespace>
+ <description>This vocabulary describes a process that is the means of how a pathogen is transmitted from one host, reservoir, or source to another host. This transmission may occur either directly or indirectly and may involve animate vectors or inanimate vehicles. </description>
+ <format>obo</format>
+ <title>Pathogen transmission</title>
+ <relevant_organism>NCBITaxon:9606|Homo sapiens</relevant_organism>
+ <download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/transmission_process.obo</download>
+ <export format="obo_xml" path="obo-all/transmission/transmission.obo_xml" md5="d4eb14046fa6a1add0d67a58e9bab5f0" timestamp="1260801336" time_generated="1263757340" time_taken_to_generate="0" size="18109">
+ </export>
+ <export format="obo" path="obo-all/transmission/transmission.obo" md5="a254e395544266623e50da1a8686cfed" timestamp="1263757340" time_generated="1263757340" time_taken_to_generate="0" size="10672">
+ </export>
+ <export format="owl" path="obo-all/transmission/transmission.owl" md5="5e41b42a001ebfcef3f68bfe51569161" timestamp="1260801336" time_generated="1263757340" time_taken_to_generate="0" size="36390">
+ </export>
+ <export format="chadoxml" path="obo-all/transmission/transmission.chadoxml" md5="f6c135a48493ff4ffae4d983b72cad4d" timestamp="1260801337" time_generated="1263757340" time_taken_to_generate="0" size="36460">
+ </export>
+ <export format="godb_prestore" path="obo-all/transmission/transmission.godb_prestore" md5="60c9c52c41d4821d0d7bcccab92b59a8" timestamp="1260801337" time_generated="1263757340" time_taken_to_generate="0" size="31054">
+ </export>
+ <export format="rdf" path="obo-all/transmission/transmission.rdf" md5="03361702bfef474942b8cba56a03c7e4" timestamp="1260801337" time_generated="1263757340" time_taken_to_generate="0" size="14619">
+ </export>
+ <export format="tbl" path="obo-all/transmission/transmission.tbl" md5="e005c9566cb153b3d1e4341c03d6c84f" timestamp="1260801338" time_generated="1263757340" time_taken_to_generate="0" size="6488">
+ </export>
+ <export format="prolog" path="obo-all/transmission/transmission.pro" md5="d06936283506c82e08e2438c1dab22f3" timestamp="1260801338" time_generated="1263757340" time_taken_to_generate="0" size="15234">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/transmission/transmission.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1260801339" time_generated="1263757340" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" path="obo-all/transmission/transmission.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1260801341" time_generated="1263757340" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/transmission/transmission.obo.html" md5="61c15cb5f18cc9160cef46ce67ad06ec" timestamp="1260801341" time_generated="1263757340" time_taken_to_generate="0" size="32541">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="gemina_symptom">
+ <source></source>
+ <granularity>organismal,cellular</granularity>
+ <status>Discussion and review</status>
+ <subtypes_of></subtypes_of>
+ <contact>Lynn Schriml lynn.schriml gmail.com</contact>
+ <foundry>No</foundry>
+ <domain>health</domain>
+ <documentation></documentation>
+ <url>http://gemina.cvs.sourceforge.net/*checkout*/gemina/Gemina/ontologies/gemina_symptom.obo</url>
+ <patho_type>pathological</patho_type>
+ <home>Wiki|http://symptomontologywiki.igs.umaryland.edu/wiki/index.php/Main_Page</home>
+ <namespace>SYMP</namespace>
+ <description>The symptom ontology was designed around the guiding concept of a symptom being: "A perceived change in function, sensation or appearance reported by a patient indicative of a disease". Understanding the close relationship of Signs and Symptoms, where Signs are the objective observation of an illness, the Symptom Ontology will work to broaden it's scope to capture and document in a more robust manor these two sets of terms. Understanding that at times, the same term may [...]
+ <format>obo</format>
+ <title>Symptom Ontology</title>
+ <relevant_organism>NCBITaxon:9606|Homo sapiens</relevant_organism>
+ <download>http://gemina.cvs.sourceforge.net/*checkout*/gemina/Gemina/ontologies/gemina_symptom.obo</download>
+ <export format="obo_xml" path="obo-all/gemina_symptom/gemina_symptom.obo_xml" md5="eb349cff1af7fbe84ef4132642e98eaf" timestamp="1260801346" time_generated="1263757342" time_taken_to_generate="0" size="205163">
+ </export>
+ <export format="obo" path="obo-all/gemina_symptom/gemina_symptom.obo" md5="8582feed5e700ab0863dbf1d93220ef5" timestamp="1263757342" time_generated="1263757342" time_taken_to_generate="0" size="98028">
+ </export>
+ <export format="owl" path="obo-all/gemina_symptom/gemina_symptom.owl" md5="cddd211c018e1de9032c3cd75413ccde" timestamp="1260801349" time_generated="1263757342" time_taken_to_generate="0" size="492434">
+ </export>
+ <export format="chadoxml" path="obo-all/gemina_symptom/gemina_symptom.chadoxml" md5="81200ac13d1744dbd23b2b21ade3dba7" timestamp="1260801351" time_generated="1263757342" time_taken_to_generate="0" size="655193">
+ </export>
+ <export format="godb_prestore" path="obo-all/gemina_symptom/gemina_symptom.godb_prestore" md5="d5e4b48b06671c14d71e4d2357e32e99" timestamp="1260801353" time_generated="1263757342" time_taken_to_generate="0" size="518671">
+ </export>
+ <export format="rdf" path="obo-all/gemina_symptom/gemina_symptom.rdf" md5="957b886b7b90d29d0f4ed4ebbd81c696" timestamp="1260801356" time_generated="1263757342" time_taken_to_generate="0" size="367238">
+ </export>
+ <export format="tbl" path="obo-all/gemina_symptom/gemina_symptom.tbl" md5="b0372195278fdba8312f75551d5cec6d" timestamp="1260801357" time_generated="1263757342" time_taken_to_generate="0" size="29654">
+ </export>
+ <export format="prolog" path="obo-all/gemina_symptom/gemina_symptom.pro" md5="b785a795280695208a478cce5d159043" timestamp="1260801360" time_generated="1263757342" time_taken_to_generate="0" size="224343">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/gemina_symptom/gemina_symptom.validation_report" md5="e5604a690f2fb618e454b25343eb4739" timestamp="1260801363" time_generated="1263757343" time_taken_to_generate="0" size="291">
+ </export>
+ <export format="stats" path="obo-all/gemina_symptom/gemina_symptom.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1260801365" time_generated="1263757343" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/gemina_symptom/gemina_symptom.obo.html" md5="d6fd4e050093b5dfee6ebcea7c14a217" timestamp="1260801365" time_generated="1263757343" time_taken_to_generate="0" size="650521">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="cereal_anatomy">
+ <source>http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/OBO_format/po_anatomy.obo?view=co</source>
+ <namespace>GRO</namespace>
+ <status>Inactive</status>
+ <contact>Gramene curators gramene gramene.org</contact>
+ <description>A structured controlled vocabulary for the anatomy of Graminae. Please note that this ontology has now been superseded by the <a href="http://obo.sf.net/cgi-bin/detail.cgi?po_anatomy">plant anatomy ontology</a>.</description>
+ <foundry>No</foundry>
+ <consider>po_anatomy</consider>
+ <domain>anatomy</domain>
+ <format>obo</format>
+ <documentation>Gramene Ontology database|http://www.gramene.org/plant_ontology/index.html#po</documentation>
+ <url>http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/OBO_format/po_anatomy.obo?view=co</url>
+ <title>Cereal plant gross anatomy</title>
+ <is_obsolete>true</is_obsolete>
+ <home>Gramene Ontology database website|http://www.gramene.org/plant_ontology/</home>
+ <download></download>
+ <export format="obo_xml" path="obo-all/cereal_anatomy/cereal_anatomy.obo_xml" md5="c57086aac7417e5e1f742b38ef07e1b9" timestamp="1260801370" time_generated="1263757344" time_taken_to_generate="0" size="446171">
+ </export>
+ <export format="obo" path="obo-all/cereal_anatomy/cereal_anatomy.obo" md5="1c2b7f57154888516e589a981a73bf07" timestamp="1263757344" time_generated="1263757344" time_taken_to_generate="0" size="247128">
+ </export>
+ <export format="owl" path="obo-all/cereal_anatomy/cereal_anatomy.owl" md5="19986350d3244606ad0aaf5ac35105d8" timestamp="1260801388" time_generated="1263757344" time_taken_to_generate="0" size="1075255">
+ </export>
+ <export format="chadoxml" path="obo-all/cereal_anatomy/cereal_anatomy.chadoxml" md5="604a10ebf1caf4c2af009444722c868f" timestamp="1260801393" time_generated="1263757344" time_taken_to_generate="0" size="1071802">
+ </export>
+ <export format="godb_prestore" path="obo-all/cereal_anatomy/cereal_anatomy.godb_prestore" md5="231c69b25cd3a120e5d9e526444201fd" timestamp="1260801396" time_generated="1263757344" time_taken_to_generate="0" size="977708">
+ </export>
+ <export format="rdf" path="obo-all/cereal_anatomy/cereal_anatomy.rdf" md5="454296b08b57525450138604fbe858bc" timestamp="1260801400" time_generated="1263757344" time_taken_to_generate="0" size="439316">
+ </export>
+ <export format="tbl" path="obo-all/cereal_anatomy/cereal_anatomy.tbl" md5="2233ea10cfbd1bfe092acb8ab6459fff" timestamp="1260801402" time_generated="1263757344" time_taken_to_generate="0" size="110868">
+ </export>
+ <export format="prolog" path="obo-all/cereal_anatomy/cereal_anatomy.pro" md5="d164ad7062d742a2bcfaa835ff26b31c" timestamp="1260801407" time_generated="1263757344" time_taken_to_generate="0" size="397190">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/cereal_anatomy/cereal_anatomy.validation_report" md5="20aa59ea80d0e3807a032851d02d3d3c" timestamp="1260801412" time_generated="1263757346" time_taken_to_generate="0" size="2454">
+ </export>
+ <export format="stats" path="obo-all/cereal_anatomy/cereal_anatomy.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1260801413" time_generated="1263757346" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/cereal_anatomy/cereal_anatomy.obo.html" md5="823f6c5329b4145aecc61949fcc986cf" timestamp="1260801414" time_generated="1263757346" time_taken_to_generate="0" size="1112057">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="temporal_gramene">
+ <source>http://brebiou.cshl.edu/viewcvs/Poc/ontology/collaborators_ontology/gramene/temporal_gramene.obo</source>
+ <namespace>GRO</namespace>
+ <status>Inactive</status>
+ <contact>Gramene curators gramene gramene.org</contact>
+ <description>A structured controlled vocabulary for expressing cereal plant development and growth stages.</description>
+ <foundry>No</foundry>
+ <consider>po_temporal</consider>
+ <format>obo</format>
+ <documentation>Gramene Ontology database|http://www.gramene.org/plant_ontology/index.html#po</documentation>
+ <url>http://brebiou.cshl.edu/viewcvs/Poc/ontology/collaborators_ontology/gramene/temporal_gramene.obo</url>
+ <title>Cereal plant development</title>
+ <is_obsolete>true</is_obsolete>
+ <home>Gramene Ontology database website|http://www.gramene.org/plant_ontology/</home>
+ <download></download>
+ <problem>Source not available at specified URL as recognised format</problem>
+ </ont>
+ <ont id="tick_anatomy">
+ <source>http://www.anobase.org/anatomy/tick_anatomy.obo</source>
+ <granularity>organismal</granularity>
+ <status>Discussion and review</status>
+ <subtypes_of>CARO:0000000</subtypes_of>
+ <contact>Daniel Sonenshine dsonensh odu.edu</contact>
+ <foundry>Yes</foundry>
+ <domain>anatomy</domain>
+ <documentation></documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/tick_anatomy.obo</url>
+ <patho_type>canonical</patho_type>
+ <home>AnoBase / VectorBase|http://www.anobase.org</home>
+ <namespace>TADS</namespace>
+ <description>The anatomy of the Tick, <i>Families: Ixodidae, Argassidae</i></description>
+ <format>obo</format>
+ <title>Tick gross anatomy</title>
+ <relevant_organism>NCBITaxon:6939|Ixodidae</relevant_organism>
+ <download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/tick_anatomy.obo</download>
+ <export format="obo_xml" path="obo-all/tick_anatomy/tick_anatomy.obo_xml" md5="bff5ebbe4e5080805aa67cccdef97718" timestamp="1260801600" time_generated="1263757533" time_taken_to_generate="0" size="415699">
+ </export>
+ <export format="obo" path="obo-all/tick_anatomy/tick_anatomy.obo" md5="ba0fd8d6a459c501485d3f97f933d857" timestamp="1263757533" time_generated="1263757533" time_taken_to_generate="0" size="259207">
+ </export>
+ <export format="owl" path="obo-all/tick_anatomy/tick_anatomy.owl" md5="aaccd436baafcf903120b2bdfae33d35" timestamp="1260801609" time_generated="1263757533" time_taken_to_generate="0" size="887736">
+ </export>
+ <export format="chadoxml" path="obo-all/tick_anatomy/tick_anatomy.chadoxml" md5="8c54d52fe8fb82f23259b872e8822907" timestamp="1260801612" time_generated="1263757533" time_taken_to_generate="0" size="831143">
+ </export>
+ <export format="godb_prestore" path="obo-all/tick_anatomy/tick_anatomy.godb_prestore" md5="75ef26b20abd4a25af18a4c37f21f45e" timestamp="1260801614" time_generated="1263757533" time_taken_to_generate="0" size="771089">
+ </export>
+ <export format="rdf" path="obo-all/tick_anatomy/tick_anatomy.rdf" md5="6fedba22bd75dfdc4cb7da6d22838f5f" timestamp="1260801617" time_generated="1263757533" time_taken_to_generate="0" size="411975">
+ </export>
+ <export format="tbl" path="obo-all/tick_anatomy/tick_anatomy.tbl" md5="b50d88a9fedf0bfb0d58bc39be6eee02" timestamp="1260801619" time_generated="1263757533" time_taken_to_generate="0" size="145572">
+ </export>
+ <export format="prolog" path="obo-all/tick_anatomy/tick_anatomy.pro" md5="381b0eb4b3cca62a7090e8d968ed231d" timestamp="1260801622" time_generated="1263757533" time_taken_to_generate="0" size="400201">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/tick_anatomy/tick_anatomy.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1260801626" time_generated="1263757535" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" path="obo-all/tick_anatomy/tick_anatomy.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1260801627" time_generated="1263757535" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/tick_anatomy/tick_anatomy.obo.html" md5="92785d18f5e2ecae61326e0e94d1742b" timestamp="1260801628" time_generated="1263757535" time_taken_to_generate="0" size="849720">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="uberon">
+ <source></source>
+ <granularity>organismal</granularity>
+ <status>Discussion and review</status>
+ <subtypes_of>bfo:IndependentContinuant</subtypes_of>
+ <contact>Chris Mungall obo-anatomy lists.sourceforge.net</contact>
+ <foundry>No</foundry>
+ <domain>anatomy</domain>
+ <documentation>http://www.bioontology.org/wiki/index.php/UBERON:Main_Page</documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/anatomy_xp/uberon.obo</url>
+ <patho_type>canonical</patho_type>
+ <home>http://www.bioontology.org/wiki/index.php/UBERON:Main_Page</home>
+ <namespace>UBERON</namespace>
+ <xrefs_to>cell,bila,caro,zebrafish_anatomy,xenopus_anatomy,fly_anatomy,adult_mouse_anatomy</xrefs_to>
+ <description>Uberon is a multi-species anatomy ontology created to facilitate comparison of phenotypes across multiple species. Uberon is generated semi-automatically from the union of existing species-centric anatomy ontologies.</description>
+ <format>obo</format>
+ <title>Uber anatomy ontology</title>
+ <download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/anatomy_xp/uberon.obo</download>
+ <export format="obo_xml" path="obo-all/uberon/uberon.obo_xml" md5="70fa819b305ffbb46a6bdb0e050ac451" timestamp="1260801648" time_generated="1263757539" time_taken_to_generate="0" size="3644646">
+ </export>
+ <export format="obo" path="obo-all/uberon/uberon.obo" md5="b4973af224cd6dd348e805b083afcdaf" timestamp="1263757539" time_generated="1263757539" time_taken_to_generate="0" size="1785451">
+ </export>
+ <export format="owl" path="obo-all/uberon/uberon.owl" md5="5300bc1dc4ba472b7912d648f4b3b233" timestamp="1260802231" time_generated="1263757539" time_taken_to_generate="0" size="9102331">
+ </export>
+ <export format="chadoxml" path="obo-all/uberon/uberon.chadoxml" md5="9d35a12e215dc1311f90108e5f58e7a7" timestamp="1260802415" time_generated="1263757539" time_taken_to_generate="0" size="10008759">
+ </export>
+ <export format="godb_prestore" path="obo-all/uberon/uberon.godb_prestore" md5="1458b254cc0aab49f7bc1bb5c21c0802" timestamp="1260802437" time_generated="1263757539" time_taken_to_generate="0" size="8673664">
+ </export>
+ <export format="rdf" path="obo-all/uberon/uberon.rdf" md5="cd20fa3eb4f45775b5daa1aeb8af2b8d" timestamp="1260802461" time_generated="1263757540" time_taken_to_generate="0" size="4409169">
+ </export>
+ <export format="tbl" path="obo-all/uberon/uberon.tbl" md5="1c99e0655c37e5b28db452330bfd01b0" timestamp="1260802476" time_generated="1263757540" time_taken_to_generate="0" size="470502">
+ </export>
+ <export format="prolog" path="obo-all/uberon/uberon.pro" md5="97539ef601115c19bf7a59c44ce3fc94" timestamp="1263418346" time_generated="1263757540" time_taken_to_generate="0" size="3838319">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/uberon/uberon.validation_report" md5="e1345444790830c8f82b5305b4aed544" timestamp="1260802519" time_generated="1263757557" time_taken_to_generate="0" size="128">
+ </export>
+ <export format="stats" path="obo-all/uberon/uberon.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1260802521" time_generated="1263757557" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/uberon/uberon.obo.html" md5="d7b032eb780449897878ff7dfbbe8437" timestamp="1260802522" time_generated="1263757557" time_taken_to_generate="0" size="8462480">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="sdiff" path="obo-all/uberon/uberon.sdiff" md5="ac62a4141fc991ae269c6d17f414e9c3" timestamp="1263758191" time_generated="1263758191" time_taken_to_generate="634" size="409202">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="unit">
+ <source></source>
+ <granularity>molecular,cellular,organismal,multi-organismal</granularity>
+ <status>Production and review</status>
+ <subtypes_of>bfo:DependentContinuant</subtypes_of>
+ <contact>OBO Unit list obo-unit lists.sourceforge.net</contact>
+ <foundry>Yes</foundry>
+ <domain>phenotype</domain>
+ <documentation></documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo</url>
+ <patho_type>canonical</patho_type>
+ <home>PATO wiki|http://www.bioontology.org/wiki/index.php/PATO:Main_Page</home>
+ <namespace>UO</namespace>
+ <description>Metrical units for use in conjunction with PATO</description>
+ <format>obo</format>
+ <title>Units of measurement</title>
+ <relevant_organism>all</relevant_organism>
+ <download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo</download>
+ <export format="obo_xml" path="obo-all/unit/unit.obo_xml" md5="5d1e025ec725cce49508026fc3790aa2" timestamp="1261396528" time_generated="1263758194" time_taken_to_generate="0" size="151987">
+ </export>
+ <export format="obo" path="obo-all/unit/unit.obo" md5="8685c0c45dd8c7d721f104b105136342" timestamp="1263758194" time_generated="1263758194" time_taken_to_generate="0" size="81842">
+ </export>
+ <export format="owl" path="obo-all/unit/unit.owl" md5="94832360ed09bdef10d9d969a2faa9c9" timestamp="1261396529" time_generated="1263758194" time_taken_to_generate="0" size="313213">
+ </export>
+ <export format="chadoxml" path="obo-all/unit/unit.chadoxml" md5="a5c930f0e8d1d46829d5e2d4fdd590e9" timestamp="1261396530" time_generated="1263758194" time_taken_to_generate="0" size="373737">
+ </export>
+ <export format="godb_prestore" path="obo-all/unit/unit.godb_prestore" md5="7ee3f5a6d5b0125fb25c14b37f850cb4" timestamp="1261396531" time_generated="1263758194" time_taken_to_generate="0" size="302265">
+ </export>
+ <export format="rdf" path="obo-all/unit/unit.rdf" md5="b6b3507990a881c19384ae452bced91b" timestamp="1261396532" time_generated="1263758194" time_taken_to_generate="0" size="138448">
+ </export>
+ <export format="tbl" path="obo-all/unit/unit.tbl" md5="141b403abf2c3d2380735308ea50cc87" timestamp="1261396532" time_generated="1263758194" time_taken_to_generate="0" size="37786">
+ </export>
+ <export format="prolog" path="obo-all/unit/unit.pro" md5="a086d183c7ff863769c415ee17ae7af9" timestamp="1261396534" time_generated="1263758194" time_taken_to_generate="0" size="137915">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/unit/unit.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1261396536" time_generated="1263758195" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" path="obo-all/unit/unit.stats" md5="7b6e8f1ae21de4404773ff97f9ae0ed3" timestamp="1261396537" time_generated="1263758195" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/unit/unit.obo.html" md5="c9294dbb4b3b3383236b994f97246269" timestamp="1261396538" time_generated="1263758195" time_taken_to_generate="0" size="365590">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="vaccine">
+ <source></source>
+ <granularity>molecular,cellular,organismal,multi-organismal</granularity>
+ <uriprefix>http://www.violinet.org/vo/VO_</uriprefix>
+ <status>Production and review</status>
+ <subtypes_of>bfo:entity</subtypes_of>
+ <contact>Yongqunh He yongqunh med.umich.edu</contact>
+ <foundry>No</foundry>
+ <domain>health</domain>
+ <documentation></documentation>
+ <url>http://www.violinet.org/vo</url>
+ <patho_type>pathological</patho_type>
+ <home>VO|http://www.violinet.org/vaccineontology</home>
+ <metadata_ontology>IAO</metadata_ontology>
+ <namespace>VO</namespace>
+ <description>To ensure consistent representation of vaccine knowledge and to support automated reasoning, a community-based effort to develop the Vaccine Ontology (VO) has been initiated. This international collaborative VO development effort has been joined by many institutes and disciplines around the world. The Vaccine Ontology is also being used in a variety of applications by many user groups in academia and industry.</description>
+ <format>owl</format>
+ <title>Vaccine ontology</title>
+ <relevant_organism>all</relevant_organism>
+ <download>http://www.violinet.org/vo</download>
+ <export format="pro" problem="true">
+ </export>
+ <export format="obo" problem="true">
+ </export>
+ <export format="obo_xml" problem="true">
+ </export>
+ <export format="owl" path="obo-all/vaccine/vaccine.owl" md5="5d655283c53e49bce7040effbf56e164" timestamp="1263758198" time_generated="1263758206" time_taken_to_generate="0" size="1212635">
+ </export>
+ <export format="chadoxml" problem="true">
+ </export>
+ <export format="godb_prestore" problem="true">
+ </export>
+ <export format="rdf" problem="true">
+ </export>
+ <export format="tbl" problem="true">
+ </export>
+ <export format="prolog" problem="true">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" problem="true">
+ </export>
+ <export format="stats" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/vaccine/vaccine.obo.html" md5="306bc03c93990ea101ad5e7039921f0e" timestamp="1260802717" time_generated="1263758211" time_taken_to_generate="0" size="441">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="worm_anatomy">
+ <source>http://brebiou.cshl.edu/viewcvs/*checkout*/Wao/WBbt.obo</source>
+ <granularity>organismal</granularity>
+ <status>Production and review</status>
+ <subtypes_of>bfo:IndependentContinuant</subtypes_of>
+ <contact>Raymond Lee raymond caltech.edu</contact>
+ <foundry>Yes</foundry>
+ <domain>anatomy</domain>
+ <documentation></documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/worm/worm_anatomy/WBbt.obo</url>
+ <patho_type>canonical</patho_type>
+ <home>Wormbase|http://www.wormbase.org/</home>
+ <namespace>WBbt</namespace>
+ <description>A structured controlled vocabulary of the anatomy of <i>Caenorhabditis elegans</i>.</description>
+ <format>obo</format>
+ <title>C. elegans gross anatomy</title>
+ <relevant_organism>NCBITaxon:6237|Caenorhabditis</relevant_organism>
+ <download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/worm/worm_anatomy/WBbt.obo</download>
+ <export format="obo_xml" path="obo-all/worm_anatomy/worm_anatomy.obo_xml" md5="987b1f21807c1c82c6530bb2c7d5c73d" timestamp="1261396573" time_generated="1263758221" time_taken_to_generate="0" size="3027013">
+ </export>
+ <export format="obo" path="obo-all/worm_anatomy/worm_anatomy.obo" md5="0fbe86b63024a6e0b1d852ce4bbb3dbe" timestamp="1263758221" time_generated="1263758222" time_taken_to_generate="0" size="1149887">
+ </export>
+ <export format="owl" path="obo-all/worm_anatomy/worm_anatomy.owl" md5="e0ba96c871932709e32b58ee4f548f03" timestamp="1261397554" time_generated="1263758222" time_taken_to_generate="0" size="7872310">
+ </export>
+ <export format="chadoxml" path="obo-all/worm_anatomy/worm_anatomy.chadoxml" md5="99d845adc9f7b4daa119514f72395e6f" timestamp="1261397846" time_generated="1263758222" time_taken_to_generate="0" size="7724744">
+ </export>
+ <export format="godb_prestore" path="obo-all/worm_anatomy/worm_anatomy.godb_prestore" md5="89b800b6410a7a0d752f688c2ff8054f" timestamp="1261397863" time_generated="1263758222" time_taken_to_generate="0" size="7237933">
+ </export>
+ <export format="rdf" path="obo-all/worm_anatomy/worm_anatomy.rdf" md5="9439d1ec57cb378e1b580f3c0f0f0761" timestamp="1261397880" time_generated="1263758222" time_taken_to_generate="0" size="3115137">
+ </export>
+ <export format="tbl" path="obo-all/worm_anatomy/worm_anatomy.tbl" md5="db56ab9a89d3ab30e556f0793fc9a306" timestamp="1261397892" time_generated="1263758222" time_taken_to_generate="0" size="482840">
+ </export>
+ <export format="prolog" path="obo-all/worm_anatomy/worm_anatomy.pro" md5="f1815e233ed5444b50c15919348c4645" timestamp="1261397911" time_generated="1263758222" time_taken_to_generate="0" size="2616475">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/worm_anatomy/worm_anatomy.validation_report" md5="c24ed26b37aa622af31de5559215ec7f" timestamp="1261397928" time_generated="1263758238" time_taken_to_generate="0" size="3130">
+ </export>
+ <export format="stats" path="obo-all/worm_anatomy/worm_anatomy.stats" md5="7b6e8f1ae21de4404773ff97f9ae0ed3" timestamp="1261397930" time_generated="1263758238" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/worm_anatomy/worm_anatomy.obo.html" md5="8fdf3db64b685b513faf031827057e26" timestamp="1261397931" time_generated="1263758238" time_taken_to_generate="0" size="7214973">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="worm_development">
+ <source>http://tazendra.caltech.edu/~azurebrd/var/work/phenote/worm_development.obo</source>
+ <granularity>organismal</granularity>
+ <status>Production and review</status>
+ <subtypes_of>bfo:Occurent</subtypes_of>
+ <contact>Wen J. Chen wchen its.caltech.edu</contact>
+ <foundry>Yes</foundry>
+ <domain>anatomy</domain>
+ <documentation></documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/developmental/animal_development/worm/worm_development.obo</url>
+ <patho_type>canonical</patho_type>
+ <home>WormBase|http://www.wormbase.org/</home>
+ <namespace>WBls</namespace>
+ <description>A structured controlled vocabulary of the development of <i>Caenorhabditis elegans</i>.</description>
+ <format>obo</format>
+ <title>C. elegans development</title>
+ <relevant_organism>NCBITaxon:6237|Caenorhabditis</relevant_organism>
+ <download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/developmental/animal_development/worm/worm_development.obo</download>
+ <export format="obo_xml" path="obo-all/worm_development/worm_development.obo_xml" md5="90d7774023cf3f2af06a300ce6f3a819" timestamp="1260804312" time_generated="1263758243" time_taken_to_generate="0" size="30644">
+ </export>
+ <export format="obo" path="obo-all/worm_development/worm_development.obo" md5="f37c8e9c16a1af0c0a0686ff20ed2d56" timestamp="1263758243" time_generated="1263758243" time_taken_to_generate="0" size="17239">
+ </export>
+ <export format="owl" path="obo-all/worm_development/worm_development.owl" md5="ce9db2ff94b05dbafed2750bd2e4307a" timestamp="1260804312" time_generated="1263758243" time_taken_to_generate="0" size="67535">
+ </export>
+ <export format="chadoxml" path="obo-all/worm_development/worm_development.chadoxml" md5="7f57696ddba3bc220645fe284ed6e0a0" timestamp="1260804312" time_generated="1263758243" time_taken_to_generate="0" size="71127">
+ </export>
+ <export format="godb_prestore" path="obo-all/worm_development/worm_development.godb_prestore" md5="ce4482f4f76c3d8ffe30b0a5bc7226e8" timestamp="1260804312" time_generated="1263758243" time_taken_to_generate="0" size="59799">
+ </export>
+ <export format="rdf" path="obo-all/worm_development/worm_development.rdf" md5="286dd0428779ac6ad7b1870d4e0eddb5" timestamp="1260804313" time_generated="1263758243" time_taken_to_generate="0" size="33129">
+ </export>
+ <export format="tbl" path="obo-all/worm_development/worm_development.tbl" md5="b479e8b3828d7bfeca6d6cbce14b3963" timestamp="1260804313" time_generated="1263758243" time_taken_to_generate="0" size="11942">
+ </export>
+ <export format="prolog" path="obo-all/worm_development/worm_development.pro" md5="634e7da45e03970173cb179c5183014e" timestamp="1261006538" time_generated="1263758243" time_taken_to_generate="0" size="29181">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/worm_development/worm_development.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1260804315" time_generated="1263758244" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" path="obo-all/worm_development/worm_development.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1260804316" time_generated="1263758244" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/worm_development/worm_development.obo.html" md5="c766dbdde606d96396ecadb8541228a2" timestamp="1260804317" time_generated="1263758244" time_taken_to_generate="0" size="68668">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="worm_phenotype">
+ <source>http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/phenotype_ontology_obo.cgi</source>
+ <granularity>organismal</granularity>
+ <status>Discussion and review</status>
+ <subtypes_of>bfo:DependentContinuant</subtypes_of>
+ <contact>Gary Schindelman garys caltech.edu</contact>
+ <foundry>Yes</foundry>
+ <domain>phenotype</domain>
+ <documentation></documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/worm_phenotype.obo</url>
+ <patho_type>pathological</patho_type>
+ <home>WormBase|http://www.wormbase.org/</home>
+ <namespace>WBPhenotype</namespace>
+ <description>A structured controlled vocabulary of <i>Caenorhabditis elegans</i> phenotypes</description>
+ <format>obo</format>
+ <title>C. elegans phenotype</title>
+ <relevant_organism>NCBITaxon:6237|Caenorhabditis</relevant_organism>
+ <download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/worm_phenotype.obo</download>
+ <export format="obo_xml" path="obo-all/worm_phenotype/worm_phenotype.obo_xml" md5="7dd135dadfd715099cf2fd328c0cd736" timestamp="1261397939" time_generated="1263758247" time_taken_to_generate="0" size="1254254">
+ </export>
+ <export format="obo" path="obo-all/worm_phenotype/worm_phenotype.obo" md5="25b481089a82babd44f25c8463bf6630" timestamp="1263758247" time_generated="1263758247" time_taken_to_generate="0" size="698246">
+ </export>
+ <export format="owl" path="obo-all/worm_phenotype/worm_phenotype.owl" md5="96e1cc51de294ca24d28dffe761832bc" timestamp="1261397975" time_generated="1263758247" time_taken_to_generate="0" size="2726471">
+ </export>
+ <export format="chadoxml" path="obo-all/worm_phenotype/worm_phenotype.chadoxml" md5="c77bd3c1235d317ac4d0a0c5a421afd2" timestamp="1261397989" time_generated="1263758247" time_taken_to_generate="0" size="3192170">
+ </export>
+ <export format="godb_prestore" path="obo-all/worm_phenotype/worm_phenotype.godb_prestore" md5="f8d780fb03a7b34aea6af86b78d96399" timestamp="1261397993" time_generated="1263758247" time_taken_to_generate="0" size="2542932">
+ </export>
+ <export format="rdf" path="obo-all/worm_phenotype/worm_phenotype.rdf" md5="e8c8da519d8e37040751aff6b8d26aeb" timestamp="1261397998" time_generated="1263758247" time_taken_to_generate="0" size="1082895">
+ </export>
+ <export format="tbl" path="obo-all/worm_phenotype/worm_phenotype.tbl" md5="dc440454a820a93819a8d9f2d60e27da" timestamp="1261398002" time_generated="1263758247" time_taken_to_generate="0" size="428175">
+ </export>
+ <export format="prolog" path="obo-all/worm_phenotype/worm_phenotype.pro" md5="ca3c5c5a4428cc4ded66e63463b6d400" timestamp="1263427442" time_generated="1263758247" time_taken_to_generate="0" size="1385166">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/worm_phenotype/worm_phenotype.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1261398014" time_generated="1263758252" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" path="obo-all/worm_phenotype/worm_phenotype.stats" md5="7b6e8f1ae21de4404773ff97f9ae0ed3" timestamp="1261398016" time_generated="1263758252" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/worm_phenotype/worm_phenotype.obo.html" md5="1c4df1c1c689ce68c57ddbc60d6be2e3" timestamp="1261398016" time_generated="1263758252" time_taken_to_generate="0" size="2576543">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="xenopus_anatomy">
+ <source>ftp://ftp.xenbase.org/pub/XenopusAnatomyOntology/xenopus_anatomy.obo</source>
+ <granularity>organismal</granularity>
+ <status>Discussion and review</status>
+ <subtypes_of>bfo:IndependentContinuant</subtypes_of>
+ <contact>Xenbase xenbase ucalgary.ca</contact>
+ <foundry>Yes</foundry>
+ <domain>anatomy</domain>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/frog/xenopus_anatomy.obo</url>
+ <patho_type>canonical</patho_type>
+ <home>Xenbase Atlas|http://www.xenbase.org/anatomy/atlas.do</home>
+ <namespace>XAO</namespace>
+ <description>A structured controlled vocabulary of the anatomy and development of the African clawed frog (<i>Xenopus laevis</i>).</description>
+ <format>obo</format>
+ <title>Xenopus anatomy and development</title>
+ <publication>http://www.biomedcentral.com/1471-213X/8/92/</publication>
+ <relevant_organism>NCBITaxon:8353|Xenopus</relevant_organism>
+ <download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/frog/xenopus_anatomy.obo</download>
+ <export format="obo_xml" path="obo-all/xenopus_anatomy/xenopus_anatomy.obo_xml" md5="aa535e16df47a0516def400fd9d45bdb" timestamp="1260804442" time_generated="1263758257" time_taken_to_generate="0" size="402928">
+ </export>
+ <export format="obo" path="obo-all/xenopus_anatomy/xenopus_anatomy.obo" md5="840ef327e2920baa55925b3528cb07b8" timestamp="1263758257" time_generated="1263758257" time_taken_to_generate="0" size="216639">
+ </export>
+ <export format="owl" path="obo-all/xenopus_anatomy/xenopus_anatomy.owl" md5="81a07eb4c6e3d04765a59a3ce0c40975" timestamp="1260804460" time_generated="1263758257" time_taken_to_generate="0" size="929185">
+ </export>
+ <export format="chadoxml" path="obo-all/xenopus_anatomy/xenopus_anatomy.chadoxml" md5="f08d92ae212a8adfa88fdbd3c248040a" timestamp="1260804464" time_generated="1263758257" time_taken_to_generate="0" size="899480">
+ </export>
+ <export format="godb_prestore" path="obo-all/xenopus_anatomy/xenopus_anatomy.godb_prestore" md5="d67aff84e35c746b04b0b692efe2386c" timestamp="1260804467" time_generated="1263758257" time_taken_to_generate="0" size="928941">
+ </export>
+ <export format="rdf" path="obo-all/xenopus_anatomy/xenopus_anatomy.rdf" md5="8b939d393399e90b8ebda598028fe373" timestamp="1260804471" time_generated="1263758257" time_taken_to_generate="0" size="438526">
+ </export>
+ <export format="tbl" path="obo-all/xenopus_anatomy/xenopus_anatomy.tbl" md5="6da4ab3e6ef5c48ab223378e67262b15" timestamp="1260804473" time_generated="1263758257" time_taken_to_generate="0" size="86755">
+ </export>
+ <export format="prolog" path="obo-all/xenopus_anatomy/xenopus_anatomy.pro" md5="829ab84100b319655775f0641226b8e9" timestamp="1263427470" time_generated="1263758257" time_taken_to_generate="0" size="363922">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/xenopus_anatomy/xenopus_anatomy.validation_report" md5="473b27549d2b2e9f35641db17431a249" timestamp="1260804492" time_generated="1263758259" time_taken_to_generate="0" size="25990">
+ </export>
+ <export format="stats" path="obo-all/xenopus_anatomy/xenopus_anatomy.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1260804493" time_generated="1263758259" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/xenopus_anatomy/xenopus_anatomy.obo.html" md5="38f95caf034fbcbd2fa2e79eea7babf0" timestamp="1260804494" time_generated="1263758260" time_taken_to_generate="0" size="979893">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="zea_mays_anatomy">
+ <source>http://brebiou.cshl.edu/viewcvs/Poc/ontology/collaborators_ontology/maizegdb/Zea_mays_anatomy_ontology.txt</source>
+ <granularity>organismal</granularity>
+ <status>Inactive</status>
+ <subtypes_of>bfo:IndependentContinuant</subtypes_of>
+ <contact>Leszek Vincent Leszek missouri.edu</contact>
+ <definitions>http://brebiou.cshl.edu/viewcvs/Poc/ontology/collaborators_ontology/maizegdb/Zea_mays_anatomy_ontology_definitions.txt</definitions>
+ <foundry>No</foundry>
+ <domain>anatomy</domain>
+ <documentation></documentation>
+ <url>http://brebiou.cshl.edu/viewcvs/Poc/ontology/collaborators_ontology/maizegdb/Zea_mays_anatomy_ontology.txt</url>
+ <patho_type>canonical</patho_type>
+ <is_obsolete>true</is_obsolete>
+ <home>Maizemap|http://www.maizemap.org/</home>
+ <namespace>ZEA</namespace>
+ <description>A structured controlled vocabulary for the anatomy of <i>Zea mays</i>.</description>
+ <format>legacy_go</format>
+ <title>Maize gross anatomy</title>
+ <relevant_organism>NCBITaxon:4575|Zea</relevant_organism>
+ <problem>Source not available at specified URL as recognised format</problem>
+ </ont>
+ <ont id="zebrafish_anatomy">
+ <prerelease_download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/fish/preversion.zfish.obo</prerelease_download>
+ <source></source>
+ <granularity>organismal</granularity>
+ <status>Production and review</status>
+ <subtypes_of>bfo:IndependentContinuant</subtypes_of>
+ <contact>ZFIN administrators zfinadmin zfin.org</contact>
+ <foundry>Yes</foundry>
+ <domain>anatomy</domain>
+ <documentation></documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/fish/zebrafish_anatomy.obo</url>
+ <patho_type>canonical</patho_type>
+ <home>ZFIN Summary|http://zfin.org/zf_info/anatomy/dict/sum.html</home>
+ <additional_namespace>ZFS</additional_namespace>
+ <xrefs_to>cell,caro,teleost_anatomy</xrefs_to>
+ <namespace>ZFA</namespace>
+ <description>A structured controlled vocabulary of the anatomy and development of the Zebrafish (<i>Danio rerio</i>).</description>
+ <format>obo</format>
+ <title>Zebrafish anatomy and development</title>
+ <relevant_organism>NCBITaxon:7954|Danio</relevant_organism>
+ <download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/fish/zebrafish_anatomy.obo</download>
+ <export format="obo_xml" path="obo-all/zebrafish_anatomy/zebrafish_anatomy.obo_xml" md5="079a55eeb91ba445e57aad680a19d7bf" timestamp="1261752251" time_generated="1263758450" time_taken_to_generate="0" size="2153354">
+ </export>
+ <export format="obo" path="obo-all/zebrafish_anatomy/zebrafish_anatomy.obo" md5="98cfadbc679f73388e5429fb46944b1a" timestamp="1263758450" time_generated="1263758450" time_taken_to_generate="0" size="1077469">
+ </export>
+ <export format="owl" path="obo-all/zebrafish_anatomy/zebrafish_anatomy.owl" md5="5c968459ad1d878b1fe12bf94debafda" timestamp="1261752543" time_generated="1263758450" time_taken_to_generate="0" size="5625697">
+ </export>
+ <export format="chadoxml" path="obo-all/zebrafish_anatomy/zebrafish_anatomy.chadoxml" md5="a540d2ea337fe0617a05a1ed48b3258c" timestamp="1261752616" time_generated="1263758450" time_taken_to_generate="0" size="5172037">
+ </export>
+ <export format="godb_prestore" path="obo-all/zebrafish_anatomy/zebrafish_anatomy.godb_prestore" md5="3363151f028f5f109eeaca4e5db43a1e" timestamp="1261752623" time_generated="1263758450" time_taken_to_generate="0" size="5573909">
+ </export>
+ <export format="rdf" path="obo-all/zebrafish_anatomy/zebrafish_anatomy.rdf" md5="a631926bfc15d68b1e853534181e4736" timestamp="1261752632" time_generated="1263758450" time_taken_to_generate="0" size="2590018">
+ </export>
+ <export format="tbl" path="obo-all/zebrafish_anatomy/zebrafish_anatomy.tbl" md5="44c41cd1f50df7f61ba3c6e2a5ad8bd0" timestamp="1261752639" time_generated="1263758450" time_taken_to_generate="0" size="335306">
+ </export>
+ <export format="prolog" path="obo-all/zebrafish_anatomy/zebrafish_anatomy.pro" md5="545bf0a008ccdd7c4e42f90c4faa440a" timestamp="1263418880" time_generated="1263758450" time_taken_to_generate="0" size="1895255">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/zebrafish_anatomy/zebrafish_anatomy.validation_report" md5="7e583435961fee0c3e4edfb7267d5587" timestamp="1261752678" time_generated="1263758461" time_taken_to_generate="0" size="5136767">
+ </export>
+ <export format="stats" path="obo-all/zebrafish_anatomy/zebrafish_anatomy.stats" md5="71666b8d5da5f0cdd71d1938865d3a1c" timestamp="1261752679" time_generated="1263758461" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/zebrafish_anatomy/zebrafish_anatomy.obo.html" md5="b7b3c7a5925f3ddacb75a50044d2e7a8" timestamp="1261752680" time_generated="1263758461" time_taken_to_generate="0" size="4978275">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="sdiff" path="obo-all/zebrafish_anatomy/zebrafish_anatomy.sdiff" md5="eadb305d9d490eb2b4ae0c9900890109" timestamp="1263758545" time_generated="1263758545" time_taken_to_generate="84" size="177636">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="go_xp_regulation">
+ <source></source>
+ <status>Draft</status>
+ <contact>Chris Mungall obo-crossproduct lists.sourceforge.net</contact>
+ <foundry>NA</foundry>
+ <documentation>http://wiki.geneontology.org/index.php/Regulation_cross-products</documentation>
+ <url>ftp://ftp.geneontology.org/pub/go/scratch/regulates_xp_live/go_reglive_withPosNeg_withPF.obo</url>
+ <extends>biological_process</extends>
+ <home>http://www.geneontology.org</home>
+ <namespace>biological_process_xp_regulation</namespace>
+ <description>Logical definitions for GO Biological Regulation types - regulation of BP and MF. Auto-generated by oboedit2 semantic parser. These are high quality due to the consistency in term name syntax for regulation terms. Also includes inter-ontology links. Note for regulation of biological qualities you should see the obol page - http://www.berkeleybop.org/obol</description>
+ <uses>biological_process</uses>
+ <format>obo</format>
+ <title>GO regulation logical definitions</title>
+ <type>logical_definitions</type>
+ <download>ftp://ftp.geneontology.org/pub/go/scratch/regulates_xp_live/go_reglive_withPosNeg_withPF.obo</download>
+ <export format="obo_xml" path="obo-all/go_xp_regulation/go_xp_regulation.obo_xml" md5="4311ce51ddd244245da7b8c16d27c33b" timestamp="1263758683" time_generated="1263758683" time_taken_to_generate="132" size="30960824">
+ </export>
+ <export format="obo" path="obo-all/go_xp_regulation/go_xp_regulation.obo" md5="04845087847c283811276f1baba678aa" timestamp="1263758550" time_generated="1263758683" time_taken_to_generate="0" size="18365316">
+ </export>
+ <export format="owl" problem="true">
+ </export>
+ <export format="chadoxml" path="obo-all/go_xp_regulation/go_xp_regulation.chadoxml" md5="ba7be4a3d35355ee301dee3ce7471aa1" timestamp="1263782921" time_generated="1263782922" time_taken_to_generate="4877" size="72068150">
+ </export>
+ <export format="godb_prestore" path="obo-all/go_xp_regulation/go_xp_regulation.godb_prestore" md5="1f365ec14b8a636671b833ad46427aeb" timestamp="1263783006" time_generated="1263783007" time_taken_to_generate="85" size="63232046">
+ </export>
+ <export format="rdf" path="obo-all/go_xp_regulation/go_xp_regulation.rdf" md5="1cf9f6f929459c3bb4dde618c11ce6ad" timestamp="1263783111" time_generated="1263783111" time_taken_to_generate="104" size="26372687">
+ </export>
+ <export format="tbl" path="obo-all/go_xp_regulation/go_xp_regulation.tbl" md5="88756a15f401623428fe1fd1669f1ce9" timestamp="1263783181" time_generated="1263783181" time_taken_to_generate="70" size="9136319">
+ </export>
+ <export format="prolog" path="obo-all/go_xp_regulation/go_xp_regulation.pro" md5="44d2142739cdec0c0c0750de31dec51e" timestamp="1263783300" time_generated="1263783300" time_taken_to_generate="119" size="33487761">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/go_xp_regulation/go_xp_regulation.validation_report" md5="78173ac43704ca15d591228535a3db2e" timestamp="1263783461" time_generated="1263783461" time_taken_to_generate="97" size="4391">
+ </export>
+ <export format="stats" path="obo-all/go_xp_regulation/go_xp_regulation.stats" md5="619a62d04ddf7c62cc6ebdc743938b12" timestamp="1263783463" time_generated="1263783463" time_taken_to_generate="2" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" path="obo-all/go_xp_regulation/go_xp_regulation.imports.obo" md5="38715a83606884812c2023ce7b695405" timestamp="1263783463" time_generated="1263783463" time_taken_to_generate="0" size="418">
+ </export>
+ <export format="obo.html" path="obo-all/go_xp_regulation/go_xp_regulation.obo.html" md5="bb2d0d826359531bc1dae5b1d8e82d88" timestamp="1263783469" time_generated="1263783470" time_taken_to_generate="7" size="66185974">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" path="obo-all/go_xp_regulation/go_xp_regulation.imports.owl" md5="823635f8f56099c2b41096aaa35d7825" timestamp="1260960739" time_generated="1263783470" time_taken_to_generate="0" size="692">
+ </export>
+ <export format="imports-local.obo" path="obo-all/go_xp_regulation/go_xp_regulation.imports-local.obo" md5="0daea8239963adccc5d0c98790a80e7e" timestamp="1263783470" time_generated="1263783470" time_taken_to_generate="0" size="373">
+ </export>
+ <export format="xp.html" path="obo-all/go_xp_regulation/go_xp_regulation.xp.html" md5="6dbb390c4970e5114f7819260728e5b5" timestamp="1263783502" time_generated="1263783502" time_taken_to_generate="32" size="22977403">
+ </export>
+ <export format="imports-local.owl" path="obo-all/go_xp_regulation/go_xp_regulation.imports-local.owl" md5="0214c0d11dae140e92b9f9569eb2bf3b" timestamp="1263783502" time_generated="1263783502" time_taken_to_generate="0" size="4400">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" path="obo-all/go_xp_regulation/go_xp_regulation.abduced-links.txt" md5="453674b76459b519374e23500da942b5" timestamp="1263785744" time_generated="1263785744" time_taken_to_generate="2241" size="35047">
+ </export>
+ </ont>
+ <ont id="biological_process_xp_cellular_component">
+ <source></source>
+ <status>Draft</status>
+ <contact>Chris Mungall obo-crossproduct lists.sourceforge.net</contact>
+ <foundry>NA</foundry>
+ <documentation>http://wiki.geneontology.org/index.php/XP:biological_process_xp_cellular_component</documentation>
+ <url>http://www.geneontology.org/scratch/xps/biological_process_xp_cellular_component.obo</url>
+ <extends>biological_process</extends>
+ <home>http://wiki.geneontology.org/index.php/XP:biological_process_xp_cellular_component</home>
+ <namespace>biological_process_xp_cellular_component</namespace>
+ <description>Logical definitions for GO Biological Processes using GO cellular component. These were sourced from auto-generated results, but then vetted manually. They may still be incomplete. The relations used may also change. These xps are internal to GO - no external OBO ontologies are used (with the exception of the OBO relation ontology and ro_proposed). Example: actin filament organization = organization and biogenesis THAT results_in_structural_change_to actin filament. </de [...]
+ <uses>cellular_component</uses>
+ <uses>relationship</uses>
+ <uses>ro_proposed</uses>
+ <format>obo</format>
+ <title>GO logical_definitions for BP in terms of CC</title>
+ <type>logical_definitions</type>
+ <download>http://www.geneontology.org/scratch/xps/biological_process_xp_cellular_component.obo</download>
+ <export format="obo_xml" path="obo-all/biological_process_xp_cellular_component/biological_process_xp_cellular_component.obo_xml" md5="fd216a086e183efb79c93b2741eba2d3" timestamp="1263785745" time_generated="1263785745" time_taken_to_generate="0" size="151451">
+ </export>
+ <export format="obo" path="obo-all/biological_process_xp_cellular_component/biological_process_xp_cellular_component.obo" md5="32ccdc95350484e99ac8ef2bc51a3dad" timestamp="1263785745" time_generated="1263785745" time_taken_to_generate="0" size="109123">
+ </export>
+ <export format="owl" path="obo-all/biological_process_xp_cellular_component/biological_process_xp_cellular_component.owl" md5="b5c7d6137718cd69819e1e657a167e32" timestamp="1263785749" time_generated="1263785749" time_taken_to_generate="4" size="377894">
+ </export>
+ <export format="chadoxml" path="obo-all/biological_process_xp_cellular_component/biological_process_xp_cellular_component.chadoxml" md5="717c838f3b9ab896c2734587bcaf85f3" timestamp="1263785750" time_generated="1263785750" time_taken_to_generate="1" size="167162">
+ </export>
+ <export format="godb_prestore" path="obo-all/biological_process_xp_cellular_component/biological_process_xp_cellular_component.godb_prestore" md5="e79043ab75e777b82d57d2ad419209b5" timestamp="1263785751" time_generated="1263785751" time_taken_to_generate="1" size="405834">
+ </export>
+ <export format="rdf" path="obo-all/biological_process_xp_cellular_component/biological_process_xp_cellular_component.rdf" md5="f16452c43f9b339c2bce5e6508aba1cb" timestamp="1263785753" time_generated="1263785753" time_taken_to_generate="2" size="101984">
+ </export>
+ <export format="tbl" path="obo-all/biological_process_xp_cellular_component/biological_process_xp_cellular_component.tbl" md5="76dcbbece4feb1a2b0d84aaf6ebe8f01" timestamp="1263785754" time_generated="1263785754" time_taken_to_generate="1" size="7566">
+ </export>
+ <export format="prolog" path="obo-all/biological_process_xp_cellular_component/biological_process_xp_cellular_component.pro" md5="3603c128db76004bed44f34d766f46a8" timestamp="1263785756" time_generated="1263785756" time_taken_to_generate="2" size="75710">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/biological_process_xp_cellular_component/biological_process_xp_cellular_component.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1263785758" time_generated="1263785758" time_taken_to_generate="1" size="20">
+ </export>
+ <export format="stats" problem="true">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" path="obo-all/biological_process_xp_cellular_component/biological_process_xp_cellular_component.imports.obo" md5="98366125738b2bb2484947384204631c" timestamp="1263785760" time_generated="1263785760" time_taken_to_generate="0" size="669">
+ </export>
+ <export format="obo.html" path="obo-all/biological_process_xp_cellular_component/biological_process_xp_cellular_component.obo.html" md5="49e6a18a93028bf80a5fd08b9be5fadb" timestamp="1263785760" time_generated="1263785760" time_taken_to_generate="0" size="507295">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" path="obo-all/biological_process_xp_cellular_component/biological_process_xp_cellular_component.imports.owl" md5="6ca568164947fcab7ef6432c3fcd684b" timestamp="1263785760" time_generated="1263785760" time_taken_to_generate="0" size="976">
+ </export>
+ <export format="imports-local.obo" path="obo-all/biological_process_xp_cellular_component/biological_process_xp_cellular_component.imports-local.obo" md5="f3c2590437b221a15a756e37769b1675" timestamp="1263785760" time_generated="1263785760" time_taken_to_generate="0" size="594">
+ </export>
+ <export format="xp.html" path="obo-all/biological_process_xp_cellular_component/biological_process_xp_cellular_component.xp.html" md5="8d997b31c3787666c7f525665a25f9d1" timestamp="1263785768" time_generated="1263785768" time_taken_to_generate="8" size="2205268">
+ </export>
+ <export format="imports-local.owl" path="obo-all/biological_process_xp_cellular_component/biological_process_xp_cellular_component.imports-local.owl" md5="fb78d9fab09ca33b3748ef7442168ef4" timestamp="1263785768" time_generated="1263785768" time_taken_to_generate="0" size="4921">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" path="obo-all/biological_process_xp_cellular_component/biological_process_xp_cellular_component.abduced-links.txt" md5="f2bbd52e99524e9326feb3372685200c" timestamp="1263786899" time_generated="1263786899" time_taken_to_generate="2" size="4246">
+ </export>
+ </ont>
+ <ont id="biological_process_xp_self">
+ <source></source>
+ <status>Draft</status>
+ <contact>Chris Mungall obo-crossproduct lists.sourceforge.net</contact>
+ <foundry>NA</foundry>
+ <documentation>http://wiki.geneontology.org/index.php/XP:biological_process_xp_self</documentation>
+ <url>http://www.geneontology.org/scratch/xps/biological_process_xp_self.obo</url>
+ <extends>biological_process</extends>
+ <home>http://wiki.geneontology.org/index.php/XP:biological_process_xp_self</home>
+ <namespace>biological_process_xp_self</namespace>
+ <description>Logical definitions for GO Biological Processes using terms from BP. Note that these exclude regulation XPs, which are maintained separately</description>
+ <uses>biological_process</uses>
+ <uses>relationship</uses>
+ <uses>ro_proposed</uses>
+ <format>obo</format>
+ <title>GO logical_definitions for BP in terms of BP</title>
+ <type>logical_definitions</type>
+ <download>http://www.geneontology.org/scratch/xps/biological_process_xp_self.obo</download>
+ <export format="obo_xml" path="obo-all/biological_process_xp_self/biological_process_xp_self.obo_xml" md5="d065c2c88374cc0bd1a64d34a4694dd7" timestamp="1260967980" time_generated="1263786900" time_taken_to_generate="0" size="123787">
+ </export>
+ <export format="obo" path="obo-all/biological_process_xp_self/biological_process_xp_self.obo" md5="ec68efa4ae7ab3701d9a34a6caa0cc06" timestamp="1263786899" time_generated="1263786900" time_taken_to_generate="0" size="101256">
+ </export>
+ <export format="owl" path="obo-all/biological_process_xp_self/biological_process_xp_self.owl" md5="18dcd20acd21ea83863cabde740d7c50" timestamp="1260967984" time_generated="1263786900" time_taken_to_generate="0" size="315011">
+ </export>
+ <export format="chadoxml" path="obo-all/biological_process_xp_self/biological_process_xp_self.chadoxml" md5="adc69a4d58abf7569be3e655a9f271f4" timestamp="1260967986" time_generated="1263786900" time_taken_to_generate="0" size="137856">
+ </export>
+ <export format="godb_prestore" path="obo-all/biological_process_xp_self/biological_process_xp_self.godb_prestore" md5="da5cd5d0d05edc4226d0fc83e37aaf58" timestamp="1260967987" time_generated="1263786900" time_taken_to_generate="0" size="339023">
+ </export>
+ <export format="rdf" path="obo-all/biological_process_xp_self/biological_process_xp_self.rdf" md5="c10bd4d69c50fa9c91c1c270c596ccf7" timestamp="1260967990" time_generated="1263786900" time_taken_to_generate="0" size="88334">
+ </export>
+ <export format="tbl" path="obo-all/biological_process_xp_self/biological_process_xp_self.tbl" md5="7a2c7ea26991a116ca46bf05a7390fb2" timestamp="1260967991" time_generated="1263786900" time_taken_to_generate="0" size="6539">
+ </export>
+ <export format="prolog" path="obo-all/biological_process_xp_self/biological_process_xp_self.pro" md5="edb477d3af63fb2e9125aca18c390dd5" timestamp="1260967993" time_generated="1263786900" time_taken_to_generate="0" size="59574">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/biological_process_xp_self/biological_process_xp_self.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1260967996" time_generated="1263786900" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" problem="true">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" path="obo-all/biological_process_xp_self/biological_process_xp_self.imports.obo" md5="328820e539d0551706f8d385768bb984" timestamp="1260967998" time_generated="1263786901" time_taken_to_generate="0" size="613">
+ </export>
+ <export format="obo.html" path="obo-all/biological_process_xp_self/biological_process_xp_self.obo.html" md5="676ef2e143b05e4a122abe56e561d41d" timestamp="1260967998" time_generated="1263786901" time_taken_to_generate="0" size="398988">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" path="obo-all/biological_process_xp_self/biological_process_xp_self.imports.owl" md5="2013484eabdae9c5ab301c5ad46d9140" timestamp="1260967998" time_generated="1263786901" time_taken_to_generate="0" size="948">
+ </export>
+ <export format="imports-local.obo" path="obo-all/biological_process_xp_self/biological_process_xp_self.imports-local.obo" md5="1f02bbfcf79fa41c9de35c4293ae28c1" timestamp="1260967998" time_generated="1263786901" time_taken_to_generate="0" size="553">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" path="obo-all/biological_process_xp_self/biological_process_xp_self.imports-local.owl" md5="5140195714db3aa72577ce1762d2e971" timestamp="1260968002" time_generated="1263786903" time_taken_to_generate="0" size="4839">
+ </export>
+ <export format="owl-classified-by-pellet2" path="obo-all/biological_process_xp_self/biological_process_xp_self.owl-classified-by-pellet2" md5="59eb47f06e76cb8877f4b9fcaec5cf16" timestamp="1260968519" time_generated="1263786903" time_taken_to_generate="0" size="1434">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="molecular_function_xp_regulators">
+ <source></source>
+ <status>Draft</status>
+ <contact>Chris Mungall obo-crossproduct lists.sourceforge.net</contact>
+ <foundry>NA</foundry>
+ <documentation>http://wiki.geneontology.org/index.php/XP:molecular_function_xp_regulators</documentation>
+ <url>http://www.geneontology.org/scratch/xps/molecular_function_xp_regulators.obo</url>
+ <extends>molecular_function</extends>
+ <home>http://www.geneontology.org</home>
+ <namespace>molecular_function_xp_regulators</namespace>
+ <description>Logical definitions for MF activator/regulator/inhibitor terms</description>
+ <uses>molecular_function</uses>
+ <uses>biological_process</uses>
+ <format>obo</format>
+ <title>GO logical_definitions for MF regulation terms</title>
+ <type>logical_definitions</type>
+ <download>http://www.geneontology.org/scratch/xps/molecular_function_xp_regulators.obo</download>
+ <export format="obo_xml" path="obo-all/molecular_function_xp_regulators/molecular_function_xp_regulators.obo_xml" md5="c54b1e1388fc596085fda075faa4dcd9" timestamp="1260968530" time_generated="1263786904" time_taken_to_generate="0" size="26197">
+ </export>
+ <export format="obo" path="obo-all/molecular_function_xp_regulators/molecular_function_xp_regulators.obo" md5="19816492de64c7eb5e8ba0a8f9dadec6" timestamp="1263786904" time_generated="1263786904" time_taken_to_generate="0" size="19998">
+ </export>
+ <export format="owl" path="obo-all/molecular_function_xp_regulators/molecular_function_xp_regulators.owl" md5="990e485a17f0aaccd91a85274b1963b8" timestamp="1260968531" time_generated="1263786904" time_taken_to_generate="0" size="68587">
+ </export>
+ <export format="chadoxml" path="obo-all/molecular_function_xp_regulators/molecular_function_xp_regulators.chadoxml" md5="8d7763b3d2070ee3fefd19f9866c1991" timestamp="1260968531" time_generated="1263786904" time_taken_to_generate="0" size="30567">
+ </export>
+ <export format="godb_prestore" path="obo-all/molecular_function_xp_regulators/molecular_function_xp_regulators.godb_prestore" md5="34905bd590d23de990c4a3121b892fa1" timestamp="1260968532" time_generated="1263786904" time_taken_to_generate="0" size="72257">
+ </export>
+ <export format="rdf" path="obo-all/molecular_function_xp_regulators/molecular_function_xp_regulators.rdf" md5="9b2a6305e3fa83a3a3f1bdd9e190e15a" timestamp="1260968532" time_generated="1263786904" time_taken_to_generate="0" size="18509">
+ </export>
+ <export format="tbl" path="obo-all/molecular_function_xp_regulators/molecular_function_xp_regulators.tbl" md5="5e116e80b4875d486a75a53c5216d876" timestamp="1260968533" time_generated="1263786904" time_taken_to_generate="0" size="1352">
+ </export>
+ <export format="prolog" path="obo-all/molecular_function_xp_regulators/molecular_function_xp_regulators.pro" md5="25c858a55913fbc0a47d345c678a28c0" timestamp="1263421901" time_generated="1263786904" time_taken_to_generate="0" size="12627">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/molecular_function_xp_regulators/molecular_function_xp_regulators.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1260968535" time_generated="1263786904" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" problem="true">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" path="obo-all/molecular_function_xp_regulators/molecular_function_xp_regulators.imports.obo" md5="b6fb2c31084f0622b6381235b86677f0" timestamp="1260968536" time_generated="1263786905" time_taken_to_generate="0" size="579">
+ </export>
+ <export format="obo.html" path="obo-all/molecular_function_xp_regulators/molecular_function_xp_regulators.obo.html" md5="aee6d59e5e64668a979d496098a3ca52" timestamp="1260968536" time_generated="1263786905" time_taken_to_generate="0" size="82042">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" path="obo-all/molecular_function_xp_regulators/molecular_function_xp_regulators.imports.owl" md5="21d09852e342a2b4eb16a3b82e7324a5" timestamp="1260968536" time_generated="1263786905" time_taken_to_generate="0" size="855">
+ </export>
+ <export format="imports-local.obo" path="obo-all/molecular_function_xp_regulators/molecular_function_xp_regulators.imports-local.obo" md5="480edb12b39bd93f422c6ed546b695d9" timestamp="1260968536" time_generated="1263786905" time_taken_to_generate="0" size="519">
+ </export>
+ <export format="xp.html" path="obo-all/molecular_function_xp_regulators/molecular_function_xp_regulators.xp.html" md5="e95384028b84bc33ead6b2751499a0b3" timestamp="1260968540" time_generated="1263786905" time_taken_to_generate="0" size="437826">
+ </export>
+ <export format="imports-local.owl" path="obo-all/molecular_function_xp_regulators/molecular_function_xp_regulators.imports-local.owl" md5="ada4abb1682aada213f178770daa9a30" timestamp="1260968540" time_generated="1263786905" time_taken_to_generate="0" size="4725">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" path="obo-all/molecular_function_xp_regulators/molecular_function_xp_regulators.abduced-links.txt" md5="6be9f1e9ea01944e2e9c4736bbe17cc1" timestamp="1260969086" time_generated="1263787511" time_taken_to_generate="0" size="449">
+ </export>
+ </ont>
+ <ont id="cellular_component_xp_self">
+ <source></source>
+ <status>Draft</status>
+ <contact>Chris Mungall obo-crossproduct lists.sourceforge.net</contact>
+ <foundry>NA</foundry>
+ <documentation>http://wiki.geneontology.org/index.php/XP:cellular_component_xp_self</documentation>
+ <url>http://www.geneontology.org/scratch/xps/cellular_component_xp_self.obo</url>
+ <extends>cellular_component</extends>
+ <home>http://www.geneontology.org</home>
+ <namespace>cellular_component_xp_self</namespace>
+ <description>Logical definitions for cellular component terms that reference only cellular component terms. </description>
+ <uses>cellular_component</uses>
+ <format>obo</format>
+ <title>GO cellular component internal logical definitions</title>
+ <type>logical_definitions</type>
+ <download>http://www.geneontology.org/scratch/xps/cellular_component_xp_self.obo</download>
+ <export format="obo_xml" path="obo-all/cellular_component_xp_self/cellular_component_xp_self.obo_xml" md5="93739d5f93f3343ee312244b2acdb270" timestamp="1260969086" time_generated="1263787511" time_taken_to_generate="0" size="69741">
+ </export>
+ <export format="obo" path="obo-all/cellular_component_xp_self/cellular_component_xp_self.obo" md5="1c2c68f633c65e8f0d6b978e869e9f93" timestamp="1263787511" time_generated="1263787511" time_taken_to_generate="0" size="47692">
+ </export>
+ <export format="owl" path="obo-all/cellular_component_xp_self/cellular_component_xp_self.owl" md5="2dd86f04224e2575f8233244ba84661e" timestamp="1260969087" time_generated="1263787511" time_taken_to_generate="0" size="178500">
+ </export>
+ <export format="chadoxml" path="obo-all/cellular_component_xp_self/cellular_component_xp_self.chadoxml" md5="a7b9d3fab7ddd494a51d32424b98c037" timestamp="1260969088" time_generated="1263787511" time_taken_to_generate="0" size="78384">
+ </export>
+ <export format="godb_prestore" path="obo-all/cellular_component_xp_self/cellular_component_xp_self.godb_prestore" md5="e3d88d1b9b3205155e7f5b0795d51e30" timestamp="1260969089" time_generated="1263787511" time_taken_to_generate="0" size="191472">
+ </export>
+ <export format="rdf" path="obo-all/cellular_component_xp_self/cellular_component_xp_self.rdf" md5="eb8962524e2a02d6bd42ee58fe346963" timestamp="1260969090" time_generated="1263787511" time_taken_to_generate="0" size="49659">
+ </export>
+ <export format="tbl" path="obo-all/cellular_component_xp_self/cellular_component_xp_self.tbl" md5="77b3540656e17611e4fb710110cef501" timestamp="1260969090" time_generated="1263787511" time_taken_to_generate="0" size="3666">
+ </export>
+ <export format="prolog" path="obo-all/cellular_component_xp_self/cellular_component_xp_self.pro" md5="ccabc9e7ad31cdd36787bd6067f4731b" timestamp="1263421900" time_generated="1263787511" time_taken_to_generate="0" size="33550">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/cellular_component_xp_self/cellular_component_xp_self.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1260969092" time_generated="1263787512" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" problem="true">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" path="obo-all/cellular_component_xp_self/cellular_component_xp_self.imports.obo" md5="3c6f55bbd76b3cc973522f692405fe51" timestamp="1260969094" time_generated="1263787513" time_taken_to_generate="0" size="458">
+ </export>
+ <export format="obo.html" path="obo-all/cellular_component_xp_self/cellular_component_xp_self.obo.html" md5="d03ae61f2549149f44914601f0841760" timestamp="1260969094" time_generated="1263787513" time_taken_to_generate="0" size="215283">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" path="obo-all/cellular_component_xp_self/cellular_component_xp_self.imports.owl" md5="8658d48aeda0864330d99ffd0f5e93bb" timestamp="1260969094" time_generated="1263787513" time_taken_to_generate="0" size="712">
+ </export>
+ <export format="imports-local.obo" path="obo-all/cellular_component_xp_self/cellular_component_xp_self.imports-local.obo" md5="e48aef351ff8e5a425f5946898974de4" timestamp="1260969094" time_generated="1263787513" time_taken_to_generate="0" size="413">
+ </export>
+ <export format="xp.html" path="obo-all/cellular_component_xp_self/cellular_component_xp_self.xp.html" md5="481a515729ce1fbe38b0429d2fd6b5b4" timestamp="1260969097" time_generated="1263787513" time_taken_to_generate="0" size="978562">
+ </export>
+ <export format="imports-local.owl" path="obo-all/cellular_component_xp_self/cellular_component_xp_self.imports-local.owl" md5="b26b9f543091f9a2a4b04dc8318d484e" timestamp="1260969098" time_generated="1263787513" time_taken_to_generate="0" size="4480">
+ </export>
+ <export format="owl-classified-by-pellet2" path="obo-all/cellular_component_xp_self/cellular_component_xp_self.owl-classified-by-pellet2" md5="691cb2d6ce0c553fa67a70ea795e23ae" timestamp="1260969149" time_generated="1263787513" time_taken_to_generate="0" size="1431">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" path="obo-all/cellular_component_xp_self/cellular_component_xp_self.abduced-links.txt" md5="893996b25fa72c395d4602c61af6a166" timestamp="1260969153" time_generated="1263787513" time_taken_to_generate="0" size="889">
+ </export>
+ </ont>
+ <ont id="cellular_component_xp_cell">
+ <source></source>
+ <status>Draft</status>
+ <contact>Chris Mungall obo-crossproduct lists.sourceforge.net</contact>
+ <foundry>NA</foundry>
+ <documentation>http://wiki.geneontology.org/index.php/XP:cellular_component_xp_cell</documentation>
+ <url>http://www.geneontology.org/scratch/xps/cellular_component_xp_cell.obo</url>
+ <extends>cellular_component</extends>
+ <home>http://www.geneontology.org</home>
+ <namespace>cellular_component_xp_cell</namespace>
+ <description>Logical definitions for cellular component terms that reference cell types</description>
+ <uses>cell</uses>
+ <format>obo</format>
+ <title>GO cellular component to Cell ontology logical definitions</title>
+ <type>logical_definitions</type>
+ <download>http://www.geneontology.org/scratch/xps/cellular_component_xp_cell.obo</download>
+ <export format="obo_xml" path="obo-all/cellular_component_xp_cell/cellular_component_xp_cell.obo_xml" md5="1166025e1568c0258b73de56b06b1690" timestamp="1260969153" time_generated="1263787514" time_taken_to_generate="0" size="7528">
+ </export>
+ <export format="obo" path="obo-all/cellular_component_xp_cell/cellular_component_xp_cell.obo" md5="ae59a5dc85b48dd35ca6e8c4ac80716c" timestamp="1263787514" time_generated="1263787514" time_taken_to_generate="0" size="4016">
+ </export>
+ <export format="owl" path="obo-all/cellular_component_xp_cell/cellular_component_xp_cell.owl" md5="7791ac0a159cfd591c3c644d35000c62" timestamp="1260969154" time_generated="1263787514" time_taken_to_generate="0" size="21237">
+ </export>
+ <export format="chadoxml" path="obo-all/cellular_component_xp_cell/cellular_component_xp_cell.chadoxml" md5="85306a72e3e46a4ae0070101286ee018" timestamp="1260969154" time_generated="1263787514" time_taken_to_generate="0" size="9843">
+ </export>
+ <export format="godb_prestore" path="obo-all/cellular_component_xp_cell/cellular_component_xp_cell.godb_prestore" md5="2d3481f9688f6bff1a6478048a245da7" timestamp="1260969154" time_generated="1263787514" time_taken_to_generate="0" size="21581">
+ </export>
+ <export format="rdf" path="obo-all/cellular_component_xp_cell/cellular_component_xp_cell.rdf" md5="7bbd21cc2a3c58610f6f22e0bf0ec374" timestamp="1260969154" time_generated="1263787514" time_taken_to_generate="0" size="5052">
+ </export>
+ <export format="tbl" path="obo-all/cellular_component_xp_cell/cellular_component_xp_cell.tbl" md5="0a24139fc049b1727a6f8fd17f611dd8" timestamp="1260969155" time_generated="1263787514" time_taken_to_generate="0" size="373">
+ </export>
+ <export format="prolog" path="obo-all/cellular_component_xp_cell/cellular_component_xp_cell.pro" md5="f96fb8c4de07237609de9a549bc41766" timestamp="1260969155" time_generated="1263787514" time_taken_to_generate="0" size="3613">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/cellular_component_xp_cell/cellular_component_xp_cell.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1260969156" time_generated="1263787514" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" problem="true">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" path="obo-all/cellular_component_xp_cell/cellular_component_xp_cell.imports.obo" md5="115320844fc31b6880f94bb6bca3f817" timestamp="1260969157" time_generated="1263787515" time_taken_to_generate="0" size="416">
+ </export>
+ <export format="obo.html" path="obo-all/cellular_component_xp_cell/cellular_component_xp_cell.obo.html" md5="b9e7ddfdaf7bda05e331b0645c0148da" timestamp="1260969157" time_generated="1263787515" time_taken_to_generate="0" size="21174">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" path="obo-all/cellular_component_xp_cell/cellular_component_xp_cell.imports.owl" md5="1df3d6fb66ec8e22f1167c44ceecc91e" timestamp="1260969158" time_generated="1263787515" time_taken_to_generate="0" size="684">
+ </export>
+ <export format="imports-local.obo" path="obo-all/cellular_component_xp_cell/cellular_component_xp_cell.imports-local.obo" md5="54a58f0a8545cffe3ae372ae88bc070c" timestamp="1260969158" time_generated="1263787515" time_taken_to_generate="0" size="371">
+ </export>
+ <export format="xp.html" path="obo-all/cellular_component_xp_cell/cellular_component_xp_cell.xp.html" md5="4b50adab46fcbabbdb89e89671aba505" timestamp="1260969159" time_generated="1263787515" time_taken_to_generate="0" size="97114">
+ </export>
+ <export format="imports-local.owl" path="obo-all/cellular_component_xp_cell/cellular_component_xp_cell.imports-local.owl" md5="b7ef8b0f8e441d72ca7fe51ad749fa21" timestamp="1260969160" time_generated="1263787515" time_taken_to_generate="0" size="4410">
+ </export>
+ <export format="owl-classified-by-pellet2" path="obo-all/cellular_component_xp_cell/cellular_component_xp_cell.owl-classified-by-pellet2" md5="25c7ca25a20717d1fbd836c40f914b0c" timestamp="1260969206" time_generated="1263787515" time_taken_to_generate="0" size="1428">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" path="obo-all/cellular_component_xp_cell/cellular_component_xp_cell.abduced-links.txt" md5="09eafa620688e2b75988e8b35e0c648a" timestamp="1260969210" time_generated="1263787515" time_taken_to_generate="0" size="130">
+ </export>
+ </ont>
+ <ont id="cellular_component_xp_go">
+ <source></source>
+ <status>Draft</status>
+ <contact>Chris Mungall obo-crossproduct lists.sourceforge.net</contact>
+ <foundry>NA</foundry>
+ <documentation>http://wiki.geneontology.org/index.php/XP:cellular_component_xp_go</documentation>
+ <url>http://www.geneontology.org/scratch/xps/cellular_component_xp_go.obo</url>
+ <extends>cellular_component</extends>
+ <home>http://www.geneontology.org</home>
+ <namespace>cellular_component_xp_go</namespace>
+ <description>logical definitions of CC cross-product classes, in terms of BP and MF. </description>
+ <uses>molecular_function</uses>
+ <uses>biological_process</uses>
+ <format>obo</format>
+ <title>GO cellular component logical definitions using BP and MF</title>
+ <type>logical_definitions</type>
+ <download>http://www.geneontology.org/scratch/xps/cellular_component_xp_go.obo</download>
+ <export format="obo_xml" path="obo-all/cellular_component_xp_go/cellular_component_xp_go.obo_xml" md5="e68cd4253092f3818b1772bd68171292" timestamp="1260969211" time_generated="1263787516" time_taken_to_generate="0" size="44994">
+ </export>
+ <export format="obo" path="obo-all/cellular_component_xp_go/cellular_component_xp_go.obo" md5="0f527bde563b5a05a3f0d950e2d3a953" timestamp="1263787516" time_generated="1263787516" time_taken_to_generate="0" size="34805">
+ </export>
+ <export format="owl" path="obo-all/cellular_component_xp_go/cellular_component_xp_go.owl" md5="47cdef1db209c04a343618ea4f82bc6b" timestamp="1260969212" time_generated="1263787516" time_taken_to_generate="0" size="114857">
+ </export>
+ <export format="chadoxml" path="obo-all/cellular_component_xp_go/cellular_component_xp_go.chadoxml" md5="b542ee7845a5aeeff0b09eea813f5a6a" timestamp="1260969212" time_generated="1263787516" time_taken_to_generate="0" size="50376">
+ </export>
+ <export format="godb_prestore" path="obo-all/cellular_component_xp_go/cellular_component_xp_go.godb_prestore" md5="c28a80d11d0eb7625529d54fe77ec74f" timestamp="1260969213" time_generated="1263787516" time_taken_to_generate="0" size="122603">
+ </export>
+ <export format="rdf" path="obo-all/cellular_component_xp_go/cellular_component_xp_go.rdf" md5="bb28992017c272d2bee494984b690f8c" timestamp="1260969213" time_generated="1263787516" time_taken_to_generate="0" size="31284">
+ </export>
+ <export format="tbl" path="obo-all/cellular_component_xp_go/cellular_component_xp_go.tbl" md5="19bbf68fdcc5eceb8dd7a46c760afaa5" timestamp="1260969214" time_generated="1263787516" time_taken_to_generate="0" size="2301">
+ </export>
+ <export format="prolog" path="obo-all/cellular_component_xp_go/cellular_component_xp_go.pro" md5="812a129252c03cf90f5a242267a3a237" timestamp="1263421901" time_generated="1263787516" time_taken_to_generate="0" size="22058">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/cellular_component_xp_go/cellular_component_xp_go.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1260969216" time_generated="1263787516" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" problem="true">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" path="obo-all/cellular_component_xp_go/cellular_component_xp_go.imports.obo" md5="bee57373d052411c5fa7182541caf022" timestamp="1260969218" time_generated="1263787518" time_taken_to_generate="0" size="547">
+ </export>
+ <export format="obo.html" path="obo-all/cellular_component_xp_go/cellular_component_xp_go.obo.html" md5="de590685da4c030ca1e2540ae4943c49" timestamp="1260969218" time_generated="1263787518" time_taken_to_generate="0" size="155816">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" path="obo-all/cellular_component_xp_go/cellular_component_xp_go.imports.owl" md5="a7391bf0c68fd9f9049ad0df2583df1b" timestamp="1260969218" time_generated="1263787518" time_taken_to_generate="0" size="839">
+ </export>
+ <export format="imports-local.obo" path="obo-all/cellular_component_xp_go/cellular_component_xp_go.imports-local.obo" md5="3507d1f951321dfc08f86c4e0092fde8" timestamp="1260969218" time_generated="1263787518" time_taken_to_generate="0" size="487">
+ </export>
+ <export format="xp.html" path="obo-all/cellular_component_xp_go/cellular_component_xp_go.xp.html" md5="d11d3ede5bd0307ecce1a3270a23708f" timestamp="1260969223" time_generated="1263787518" time_taken_to_generate="0" size="717347">
+ </export>
+ <export format="imports-local.owl" path="obo-all/cellular_component_xp_go/cellular_component_xp_go.imports-local.owl" md5="2a7b1ece17cb463e248f745f6c44e1e9" timestamp="1260969223" time_generated="1263787518" time_taken_to_generate="0" size="4661">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" path="obo-all/cellular_component_xp_go/cellular_component_xp_go.abduced-links.txt" md5="eb3e5b49100051b2ce37804a88a3ec18" timestamp="1260969818" time_generated="1263787930" time_taken_to_generate="0" size="154">
+ </export>
+ </ont>
+ <ont id="biological_process_xp_multi_organism_process">
+ <source></source>
+ <status>Draft</status>
+ <contact>Chris Mungall obo-crossproduct lists.sourceforge.net</contact>
+ <foundry>NA</foundry>
+ <documentation>http://wiki.geneontology.org/index.php/Category:Internal_Cross_Products</documentation>
+ <url>http://www.geneontology.org/scratch/xps/biological_process_xp_multi_organism_process.obo</url>
+ <extends>go_xp_regulation</extends>
+ <extends>biological_process</extends>
+ <home>http://www.geneontology.org</home>
+ <namespace>biological_process_xp_multi_organism_process</namespace>
+ <description>Logical definitions for multi-species regulation terms </description>
+ <uses>biological_process</uses>
+ <format>obo</format>
+ <title>GO logical definitions for multi-species regulation</title>
+ <type>logical_definitions</type>
+ <download>http://www.geneontology.org/scratch/xps/biological_process_xp_multi_organism_process.obo</download>
+ <export format="obo_xml" path="obo-all/biological_process_xp_multi_organism_process/biological_process_xp_multi_organism_process.obo_xml" md5="13a6210dbe0890525deec4e3c2588a41" timestamp="1260969819" time_generated="1263787930" time_taken_to_generate="0" size="151001">
+ </export>
+ <export format="obo" path="obo-all/biological_process_xp_multi_organism_process/biological_process_xp_multi_organism_process.obo" md5="30b05c07b0ac6551431ba4fc3a398012" timestamp="1263787930" time_generated="1263787930" time_taken_to_generate="0" size="116363">
+ </export>
+ <export format="owl" path="obo-all/biological_process_xp_multi_organism_process/biological_process_xp_multi_organism_process.owl" md5="42204891417422736818e403f45a5dc7" timestamp="1260969822" time_generated="1263787930" time_taken_to_generate="0" size="387972">
+ </export>
+ <export format="chadoxml" path="obo-all/biological_process_xp_multi_organism_process/biological_process_xp_multi_organism_process.chadoxml" md5="14bbd754bdf0f6373f246d47f188773b" timestamp="1260969823" time_generated="1263787930" time_taken_to_generate="0" size="119273">
+ </export>
+ <export format="godb_prestore" path="obo-all/biological_process_xp_multi_organism_process/biological_process_xp_multi_organism_process.godb_prestore" md5="bd02a5f9febbdc90aed2590c0277abd0" timestamp="1260969824" time_generated="1263787930" time_taken_to_generate="0" size="413322">
+ </export>
+ <export format="rdf" path="obo-all/biological_process_xp_multi_organism_process/biological_process_xp_multi_organism_process.rdf" md5="eb8f303cf9b632f5c22ba5430a9a0508" timestamp="1260969825" time_generated="1263787930" time_taken_to_generate="0" size="73192">
+ </export>
+ <export format="tbl" path="obo-all/biological_process_xp_multi_organism_process/biological_process_xp_multi_organism_process.tbl" md5="375608db0cd5132e1782fe7325228480" timestamp="1260969826" time_generated="1263787930" time_taken_to_generate="0" size="5402">
+ </export>
+ <export format="prolog" path="obo-all/biological_process_xp_multi_organism_process/biological_process_xp_multi_organism_process.pro" md5="d21884ae5d1a242ed9476c324720dc46" timestamp="1260969827" time_generated="1263787930" time_taken_to_generate="0" size="81019">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/biological_process_xp_multi_organism_process/biological_process_xp_multi_organism_process.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1260969829" time_generated="1263787931" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" path="obo-all/biological_process_xp_multi_organism_process/biological_process_xp_multi_organism_process.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1260969831" time_generated="1263787931" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" path="obo-all/biological_process_xp_multi_organism_process/biological_process_xp_multi_organism_process.imports.obo" md5="0a38285083fb5127e13fc4293d102566" timestamp="1260969831" time_generated="1263787931" time_taken_to_generate="0" size="621">
+ </export>
+ <export format="obo.html" path="obo-all/biological_process_xp_multi_organism_process/biological_process_xp_multi_organism_process.obo.html" md5="65210111c5a28b0fbb0dd21da3fba616" timestamp="1260969831" time_generated="1263787931" time_taken_to_generate="0" size="438842">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" path="obo-all/biological_process_xp_multi_organism_process/biological_process_xp_multi_organism_process.imports.owl" md5="bf7f66b0540507836fa856e20cc0f5ac" timestamp="1260969831" time_generated="1263787931" time_taken_to_generate="0" size="875">
+ </export>
+ <export format="imports-local.obo" path="obo-all/biological_process_xp_multi_organism_process/biological_process_xp_multi_organism_process.imports-local.obo" md5="b8158c30825c38897b065e9511437b2f" timestamp="1260969831" time_generated="1263787931" time_taken_to_generate="0" size="561">
+ </export>
+ <export format="xp.html" path="obo-all/biological_process_xp_multi_organism_process/biological_process_xp_multi_organism_process.xp.html" md5="dbfefbd5ea074ac4d33d58b1be26a6d4" timestamp="1260969885" time_generated="1263787931" time_taken_to_generate="0" size="24760940">
+ </export>
+ <export format="imports-local.owl" path="obo-all/biological_process_xp_multi_organism_process/biological_process_xp_multi_organism_process.imports-local.owl" md5="4e2a4e39490e31d9b9e1b4fd9b6380f3" timestamp="1260969886" time_generated="1263787932" time_taken_to_generate="0" size="4811">
+ </export>
+ <export format="owl-classified-by-pellet2" path="obo-all/biological_process_xp_multi_organism_process/biological_process_xp_multi_organism_process.owl-classified-by-pellet2" md5="6e2c17b6a15e4a9b7474455a41004cda" timestamp="1263788041" time_generated="1263788042" time_taken_to_generate="110" size="3950">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" path="obo-all/biological_process_xp_multi_organism_process/biological_process_xp_multi_organism_process.abduced-links.txt" md5="85903e9ae3a74ce089adf306a257ac9b" timestamp="1260976920" time_generated="1263788042" time_taken_to_generate="0" size="160802">
+ </export>
+ </ont>
+ <ont id="go_xp_internal">
+ <source></source>
+ <status>Draft</status>
+ <contact>Chris Mungall obo-crossproduct lists.sourceforge.net</contact>
+ <foundry>NA</foundry>
+ <documentation>http://wiki.geneontology.org/index.php/Category:Internal_Cross_Products</documentation>
+ <url>http://www.geneontology.org/scratch/xps/go_xp_internal-imports.obo</url>
+ <extends>go_xp_regulation</extends>
+ <home>http://www.geneontology.org</home>
+ <namespace>GO_XP_INTERNAL</namespace>
+ <description></description>
+ <uses>biological_process_xp_cellular_component</uses>
+ <uses>cellular_component_xp_self</uses>
+ <uses>cellular_component_xp_go</uses>
+ <uses>molecular_function_xp_regulators</uses>
+ <format>obo</format>
+ <title>GO internal logical definitions</title>
+ <type>logical_definitions</type>
+ <download>http://www.geneontology.org/scratch/xps/go_xp_internal-imports.obo</download>
+ <export format="obo_xml" path="obo-all/go_xp_internal/go_xp_internal.obo_xml" md5="e6c4400fc74ea9ed3a1f46526099098e" timestamp="1260976921" time_generated="1263788042" time_taken_to_generate="0" size="1455">
+ </export>
+ <export format="obo" path="obo-all/go_xp_internal/go_xp_internal.obo" md5="8cb5354caf682a5d5d95850146463bea" timestamp="1263788042" time_generated="1263788042" time_taken_to_generate="0" size="351">
+ </export>
+ <export format="owl" path="obo-all/go_xp_internal/go_xp_internal.owl" md5="b4dce5c8decabe2b8d090a422297e59d" timestamp="1260976921" time_generated="1263788042" time_taken_to_generate="0" size="4760">
+ </export>
+ <export format="chadoxml" path="obo-all/go_xp_internal/go_xp_internal.chadoxml" md5="84790ea20a08df860f456b1794956454" timestamp="1260976921" time_generated="1263788042" time_taken_to_generate="0" size="1832">
+ </export>
+ <export format="godb_prestore" path="obo-all/go_xp_internal/go_xp_internal.godb_prestore" md5="0868a9bb2c2e414c8bd8e9d60c9e5335" timestamp="1260976921" time_generated="1263788042" time_taken_to_generate="0" size="2456">
+ </export>
+ <export format="rdf" path="obo-all/go_xp_internal/go_xp_internal.rdf" md5="06d6c17326e130b1936d503eba8c6a89" timestamp="1260976922" time_generated="1263788042" time_taken_to_generate="0" size="304">
+ </export>
+ <export format="tbl" problem="true">
+ </export>
+ <export format="prolog" path="obo-all/go_xp_internal/go_xp_internal.pro" md5="44876d69a32c1bbbcb6dd6e2a9e43f27" timestamp="1263422109" time_generated="1263788042" time_taken_to_generate="0" size="1274">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/go_xp_internal/go_xp_internal.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1260976924" time_generated="1263788043" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" problem="true">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" path="obo-all/go_xp_internal/go_xp_internal.imports.obo" md5="63121018733332f5172ec9eeb0fa82ea" timestamp="1260976925" time_generated="1263788044" time_taken_to_generate="0" size="845">
+ </export>
+ <export format="obo.html" path="obo-all/go_xp_internal/go_xp_internal.obo.html" md5="adbb5d3ace41d51d1e087917f50983b3" timestamp="1260976925" time_generated="1263788044" time_taken_to_generate="0" size="448">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" path="obo-all/go_xp_internal/go_xp_internal.imports.owl" md5="6a8798e32f9afdca8476ae85dfafdbfc" timestamp="1260976925" time_generated="1263788044" time_taken_to_generate="0" size="1177">
+ </export>
+ <export format="imports-local.obo" path="obo-all/go_xp_internal/go_xp_internal.imports-local.obo" md5="c40e12466003656457778eb626a0aa1e" timestamp="1260976925" time_generated="1263788044" time_taken_to_generate="0" size="755">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" path="obo-all/go_xp_internal/go_xp_internal.imports-local.owl" md5="28e7042621dc423d54d998f53ef46c7e" timestamp="1260976929" time_generated="1263788050" time_taken_to_generate="0" size="5215">
+ </export>
+ <export format="owl-classified-by-pellet2" path="obo-all/go_xp_internal/go_xp_internal.owl-classified-by-pellet2" md5="c3a9774342ee715d0c6e08f0fbcf8894" timestamp="1260977130" time_generated="1263788050" time_taken_to_generate="0" size="6191">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="go_xp_all">
+ <source></source>
+ <namespace>GO_XP_ALL</namespace>
+ <status>Draft</status>
+ <contact>Chris Mungall obo-crossproduct lists.sourceforge.net</contact>
+ <description>This file combines GO, all logical definitions, plus MIREOTed terms from referenced ontologies</description>
+ <foundry>NA</foundry>
+ <format>obo</format>
+ <documentation>http://wiki.geneontology.org/index.php/Category:Cross_Products</documentation>
+ <url>http://www.geneontology.org/scratch/xps/go_xp_all-merged.obo</url>
+ <type>logical_definitions</type>
+ <title>GO all logical definitions</title>
+ <extends>go</extends>
+ <home>http://www.geneontology.org</home>
+ <download>http://www.geneontology.org/scratch/xps/go_xp_all-merged.obo</download>
+ <export format="obo_xml" path="obo-all/go_xp_all/go_xp_all.obo_xml" md5="5b488e10fcb4a88479a939f7a241d168" timestamp="1261754373" time_generated="1263788056" time_taken_to_generate="0" size="40995956">
+ </export>
+ <export format="obo" path="obo-all/go_xp_all/go_xp_all.obo" md5="cd4128f035f0aab30a3d20d62a065008" timestamp="1263788056" time_generated="1263788057" time_taken_to_generate="0" size="22787023">
+ </export>
+ <export format="owl" path="obo-all/go_xp_all/go_xp_all.owl" md5="0fe58e9cec65d39fc96dbabef571655a" timestamp="1261760698" time_generated="1263788057" time_taken_to_generate="0" size="93144393">
+ </export>
+ <export format="chadoxml" path="obo-all/go_xp_all/go_xp_all.chadoxml" md5="3c3c67acbd9aef280157f7af775b5089" timestamp="1261771784" time_generated="1263788059" time_taken_to_generate="0" size="93295752">
+ </export>
+ <export format="godb_prestore" path="obo-all/go_xp_all/go_xp_all.godb_prestore" md5="85d8a2bfb67cbb01db616ed0fee353ff" timestamp="1261771959" time_generated="1263788061" time_taken_to_generate="0" size="86822224">
+ </export>
+ <export format="rdf" path="obo-all/go_xp_all/go_xp_all.rdf" md5="983a7f3f79c4f3e8aabb361c0186b64a" timestamp="1261772162" time_generated="1263788062" time_taken_to_generate="0" size="33513155">
+ </export>
+ <export format="tbl" path="obo-all/go_xp_all/go_xp_all.tbl" md5="3ab7a376ab7fe84ef524277bacfa7aa9" timestamp="1261772256" time_generated="1263788062" time_taken_to_generate="0" size="10429976">
+ </export>
+ <export format="prolog" path="obo-all/go_xp_all/go_xp_all.pro" md5="097dc39166706d86466d16ddbf7e3cb4" timestamp="1261772424" time_generated="1263788062" time_taken_to_generate="0" size="46083733">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/go_xp_all/go_xp_all.validation_report" md5="1b9c80113d5bdb3f8cf0eac82c051350" timestamp="1261772535" time_generated="1263788217" time_taken_to_generate="0" size="158">
+ </export>
+ <export format="stats" path="obo-all/go_xp_all/go_xp_all.stats" md5="71666b8d5da5f0cdd71d1938865d3a1c" timestamp="1261772538" time_generated="1263788217" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" path="obo-all/go_xp_all/go_xp_all.imports.obo" md5="fc6148a1c16e16c91b8b9806bf16d31a" timestamp="1261772538" time_generated="1263788217" time_taken_to_generate="0" size="245">
+ </export>
+ <export format="obo.html" path="obo-all/go_xp_all/go_xp_all.obo.html" md5="fa6ae18c2ace861910706047d5c31f22" timestamp="1261772546" time_generated="1263788217" time_taken_to_generate="0" size="88252150">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" path="obo-all/go_xp_all/go_xp_all.imports.owl" md5="0441a99b4192546d8b73d18e849d2d91" timestamp="1261772547" time_generated="1263788218" time_taken_to_generate="0" size="515">
+ </export>
+ <export format="imports-local.obo" path="obo-all/go_xp_all/go_xp_all.imports-local.obo" md5="dfcbc95925b03d3ad2ca3f4ca0622115" timestamp="1261772547" time_generated="1263788218" time_taken_to_generate="0" size="230">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" path="obo-all/go_xp_all/go_xp_all.imports-local.owl" md5="d662d1e82ec7c21c3c8beb26122265e0" timestamp="1261772548" time_generated="1263788220" time_taken_to_generate="0" size="4097">
+ </export>
+ <export format="owl-classified-by-pellet2" path="obo-all/go_xp_all/go_xp_all.owl-classified-by-pellet2" md5="ec7c764855f2e87fd70e4e345cc0ca6b" timestamp="1261772549" time_generated="1263788220" time_taken_to_generate="0" size="3722">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="biological_process_xp_cell">
+ <source></source>
+ <status>Draft</status>
+ <contact>go-editors ontology-editors geneontology.org</contact>
+ <foundry>NA</foundry>
+ <documentation>http://wiki.geneontology.org/index.php/XP:biological_process_xp_cell</documentation>
+ <url>ftp://ftp.geneontology.org/pub/go/scratch/xps/biological_process_xp_cell.obo</url>
+ <extends>biological_process</extends>
+ <home>http://www.geneontology.org</home>
+ <namespace>biological_process_xp_cell</namespace>
+ <description>Logical definitions for GO Biological Processes using OBO-Cell. These were sourced from auto-generated results, but then vetted manually. They may still be incomplete. The relations used may also change. osteoblast differentiation = cell differentiation THAT results_in_acquisition_of_features_of osteoblast</description>
+ <uses>cell</uses>
+ <uses>relationship</uses>
+ <uses>ro_proposed</uses>
+ <format>obo</format>
+ <title>GO biological_process x cell logical definitions</title>
+ <type>logical_definitions</type>
+ <download>ftp://ftp.geneontology.org/pub/go/scratch/xps/biological_process_xp_cell.obo</download>
+ <export format="obo_xml" path="obo-all/biological_process_xp_cell/biological_process_xp_cell.obo_xml" md5="1ab658cc80189b67dfc78d2b728e01b3" timestamp="1261000586" time_generated="1263788222" time_taken_to_generate="0" size="175139">
+ </export>
+ <export format="obo" path="obo-all/biological_process_xp_cell/biological_process_xp_cell.obo" md5="ec28ddf40080f7eb2195ea4b39f82598" timestamp="1263788222" time_generated="1263788222" time_taken_to_generate="0" size="102950">
+ </export>
+ <export format="owl" path="obo-all/biological_process_xp_cell/biological_process_xp_cell.owl" md5="650cf66bbab38a5ff0befbae8147967c" timestamp="1261000588" time_generated="1263788222" time_taken_to_generate="0" size="400660">
+ </export>
+ <export format="chadoxml" path="obo-all/biological_process_xp_cell/biological_process_xp_cell.chadoxml" md5="8d4f50a6084fa045312689817bcf734e" timestamp="1261000589" time_generated="1263788222" time_taken_to_generate="0" size="186239">
+ </export>
+ <export format="godb_prestore" path="obo-all/biological_process_xp_cell/biological_process_xp_cell.godb_prestore" md5="3dceaac94f7f4bcae951ffa4769669c0" timestamp="1261000589" time_generated="1263788222" time_taken_to_generate="0" size="410460">
+ </export>
+ <export format="rdf" path="obo-all/biological_process_xp_cell/biological_process_xp_cell.rdf" md5="226e873029d429d2c1e5bd7463185c27" timestamp="1261000590" time_generated="1263788222" time_taken_to_generate="0" size="95509">
+ </export>
+ <export format="tbl" path="obo-all/biological_process_xp_cell/biological_process_xp_cell.tbl" md5="d9305ed8561f7b658cf31a6e7f75a86f" timestamp="1261000591" time_generated="1263788222" time_taken_to_generate="0" size="7085">
+ </export>
+ <export format="prolog" path="obo-all/biological_process_xp_cell/biological_process_xp_cell.pro" md5="cf1ab1373e4237b2b1771a8d1be27951" timestamp="1261000592" time_generated="1263788222" time_taken_to_generate="0" size="115296">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/biological_process_xp_cell/biological_process_xp_cell.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1261000593" time_generated="1263788223" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" path="obo-all/biological_process_xp_cell/biological_process_xp_cell.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1261000594" time_generated="1263788223" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" path="obo-all/biological_process_xp_cell/biological_process_xp_cell.imports.obo" md5="e9e850109aa184ef2e55787e3f4f6a2d" timestamp="1261000594" time_generated="1263788223" time_taken_to_generate="0" size="571">
+ </export>
+ <export format="obo.html" path="obo-all/biological_process_xp_cell/biological_process_xp_cell.obo.html" md5="e9c55553754a9f3fe433d7eefcffe3ab" timestamp="1261000594" time_generated="1263788223" time_taken_to_generate="0" size="483851">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" path="obo-all/biological_process_xp_cell/biological_process_xp_cell.imports.owl" md5="692a61b6cd36ad44df177c4ad2efeb6b" timestamp="1261000594" time_generated="1263788223" time_taken_to_generate="0" size="920">
+ </export>
+ <export format="imports-local.obo" path="obo-all/biological_process_xp_cell/biological_process_xp_cell.imports-local.obo" md5="ffa353c3666b5f86aba6cdfb60a237e4" timestamp="1261000594" time_generated="1263788223" time_taken_to_generate="0" size="511">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" path="obo-all/biological_process_xp_cell/biological_process_xp_cell.imports-local.owl" md5="a24d5ba50feb1b981c770ae9a788aa0e" timestamp="1261000596" time_generated="1263788224" time_taken_to_generate="0" size="4769">
+ </export>
+ <export format="owl-classified-by-pellet2" path="obo-all/biological_process_xp_cell/biological_process_xp_cell.owl-classified-by-pellet2" md5="7a96f32d68b660db97aeecf33cad217a" timestamp="1261000809" time_generated="1263788224" time_taken_to_generate="0" size="1430">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="biological_process_xp_uber_anatomy">
+ <source></source>
+ <status>Draft</status>
+ <contact>go-editors ontology-editors geneontology.org</contact>
+ <foundry>NA</foundry>
+ <documentation>http://wiki.geneontology.org/index.php/XP:biological_process_xp_anatomy</documentation>
+ <url>ftp://ftp.geneontology.org/pub/go/scratch/xps/biological_process_xp_uber_anatomy.obo</url>
+ <extends>biological_process</extends>
+ <home>http://www.geneontology.org</home>
+ <namespace>biological_process_xp_uber_anatomy</namespace>
+ <description>Defines GO biological processes in terms of a multi-species anatomy ontology (UBERON)</description>
+ <uses>uberon</uses>
+ <uses>quality</uses>
+ <uses>relationship</uses>
+ <uses>ro_proposed</uses>
+ <format>obo</format>
+ <title>GO biological_process x uberon definitions</title>
+ <type>logical_definitions</type>
+ <download>ftp://ftp.geneontology.org/pub/go/scratch/xps/biological_process_xp_uber_anatomy.obo</download>
+ <export format="obo_xml" path="obo-all/biological_process_xp_uber_anatomy/biological_process_xp_uber_anatomy.obo_xml" md5="756d12db2696a5c111d49d9bae89db4f" timestamp="1261000816" time_generated="1263788227" time_taken_to_generate="0" size="262279">
+ </export>
+ <export format="obo" path="obo-all/biological_process_xp_uber_anatomy/biological_process_xp_uber_anatomy.obo" md5="424d72b7a21aed9b29c29a164862f6a5" timestamp="1263788227" time_generated="1263788227" time_taken_to_generate="0" size="162177">
+ </export>
+ <export format="owl" path="obo-all/biological_process_xp_uber_anatomy/biological_process_xp_uber_anatomy.owl" md5="ad11f260070218477d855806bbf713d2" timestamp="1261000820" time_generated="1263788227" time_taken_to_generate="0" size="608425">
+ </export>
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+ <export format="obo.html" path="obo-all/biological_process_xp_uber_anatomy/biological_process_xp_uber_anatomy.obo.html" md5="a7e178af8d8199ffad82a5ca2e82bb1f" timestamp="1261000829" time_generated="1263788228" time_taken_to_generate="0" size="746726">
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+ <export format="xp.html" problem="true">
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+ <export format="imports-local.owl" path="obo-all/biological_process_xp_uber_anatomy/biological_process_xp_uber_anatomy.imports-local.owl" md5="c671ee3f4e01101889812b5c05875015" timestamp="1261000833" time_generated="1263788230" time_taken_to_generate="0" size="4985">
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+ <export format="obo-classified-by-oboedit" problem="true">
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+ <export format="obo-classified-by-blip" problem="true">
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+ <export format="abduced-links.txt" problem="true">
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+ <ont id="molecular_function_xp_uber_anatomy">
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+ <status>Draft</status>
+ <contact>go-editors ontology-editors geneontology.org</contact>
+ <foundry>NA</foundry>
+ <documentation>http://wiki.geneontology.org/index.php/XP:molecular_function_xp_anatomy</documentation>
+ <url>ftp://ftp.geneontology.org/pub/go/scratch/xps/molecular_function_xp_uber_anatomy.obo</url>
+ <extends>molecular_function</extends>
+ <home>http://www.geneontology.org</home>
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+ <description>Defines GO molecular functions in terms of a multi-species anatomy ontology (UBERON)</description>
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+ <uses>relationship</uses>
+ <uses>ro_proposed</uses>
+ <format>obo</format>
+ <title>GO molecular_function x uberon definitions</title>
+ <type>logical_definitions</type>
+ <download>ftp://ftp.geneontology.org/pub/go/scratch/xps/molecular_function_xp_uber_anatomy.obo</download>
+ <export format="obo_xml" path="obo-all/molecular_function_xp_uber_anatomy/molecular_function_xp_uber_anatomy.obo_xml" md5="72098683077f945762e0936d30c56208" timestamp="1261001139" time_generated="1263788730" time_taken_to_generate="0" size="3260">
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+ <export format="rdf" path="obo-all/molecular_function_xp_uber_anatomy/molecular_function_xp_uber_anatomy.rdf" md5="a0b7cb16e7bade0f4a900d91352357a5" timestamp="1261001140" time_generated="1263788730" time_taken_to_generate="0" size="1884">
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+ <export format="validation_report" path="obo-all/molecular_function_xp_uber_anatomy/molecular_function_xp_uber_anatomy.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1261001140" time_generated="1263788730" time_taken_to_generate="0" size="20">
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+ </export>
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+ <export format="obo-classified-by-blip" problem="true">
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+ <export format="abduced-links.txt" problem="true">
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+ <ont id="biological_process_xp_plant_anatomy">
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+ <status>Draft</status>
+ <contact>go-editors ontology-editors geneontology.org</contact>
+ <foundry>NA</foundry>
+ <documentation>http://wiki.geneontology.org/index.php/XP:biological_process_xp_anatomy</documentation>
+ <url>ftp://ftp.geneontology.org/pub/go/scratch/xps/biological_process_xp_plant_anatomy.obo</url>
+ <extends>biological_process</extends>
+ <home>http://www.geneontology.org</home>
+ <namespace>biological_process_xp_plant_anatomy</namespace>
+ <description>Defines GO biological processes in terms of a plant anatomical terms (from po_anatomy)</description>
+ <uses>po_anatomy</uses>
+ <uses>quality</uses>
+ <uses>relationship</uses>
+ <uses>ro_proposed</uses>
+ <format>obo</format>
+ <title>GO biological_process x planton definitions</title>
+ <type>logical_definitions</type>
+ <download>ftp://ftp.geneontology.org/pub/go/scratch/xps/biological_process_xp_plant_anatomy.obo</download>
+ <export format="obo_xml" path="obo-all/biological_process_xp_plant_anatomy/biological_process_xp_plant_anatomy.obo_xml" md5="254cb70d35f96cc404691e8afc6d3659" timestamp="1261001371" time_generated="1263788991" time_taken_to_generate="0" size="28430">
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+ </export>
+ <export format="error_report" problem="true">
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+ <export format="validation_report" path="obo-all/biological_process_xp_plant_anatomy/biological_process_xp_plant_anatomy.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1261001374" time_generated="1263788991" time_taken_to_generate="0" size="20">
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+ <export format="imports.obo" path="obo-all/biological_process_xp_plant_anatomy/biological_process_xp_plant_anatomy.imports.obo" md5="a89bac483aa7145fccfca90eb5f4136a" timestamp="1261001374" time_generated="1263788992" time_taken_to_generate="0" size="689">
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+ <export format="obo.html" path="obo-all/biological_process_xp_plant_anatomy/biological_process_xp_plant_anatomy.obo.html" md5="b0a1e68e206e0120ba0795e90d6231ee" timestamp="1261001374" time_generated="1263788992" time_taken_to_generate="0" size="92114">
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+ <export format="imports-local.obo" path="obo-all/biological_process_xp_plant_anatomy/biological_process_xp_plant_anatomy.imports-local.obo" md5="9eff8c291a7ca52ce3897b8bac02caed" timestamp="1261001374" time_generated="1263788992" time_taken_to_generate="0" size="614">
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+ <export format="xp.html" problem="true">
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+ <export format="owl-classified-by-pellet2" path="obo-all/biological_process_xp_plant_anatomy/biological_process_xp_plant_anatomy.owl-classified-by-pellet2" md5="194a5d6b30b836f5f1e0798cafcf8599" timestamp="1261001634" time_generated="1263788996" time_taken_to_generate="0" size="1478">
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+ <export format="abduced-links.txt" problem="true">
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+ </ont>
+ <ont id="biological_process_xp_chebi">
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+ <status>Draft</status>
+ <contact>go-editors ontology-editors geneontology.org</contact>
+ <foundry>NA</foundry>
+ <documentation>http://wiki.geneontology.org/index.php/XP:biological_process_xp_chebi</documentation>
+ <url>ftp://ftp.geneontology.org/pub/go/scratch/xps/biological_process_xp_chebi.obo</url>
+ <extends>biological_process</extends>
+ <home>http://www.geneontology.org</home>
+ <namespace>biological_process_xp_chebi</namespace>
+ <description>Defines GO biological processes in terms of chemical entities (CHEBI)</description>
+ <uses>chebi</uses>
+ <uses>relationship</uses>
+ <uses>ro_proposed</uses>
+ <format>obo</format>
+ <title>GO biological_process x CHEBI definitions</title>
+ <type>logical_definitions</type>
+ <download>ftp://ftp.geneontology.org/pub/go/scratch/xps/biological_process_xp_chebi.obo</download>
+ <export format="obo_xml" path="obo-all/biological_process_xp_chebi/biological_process_xp_chebi.obo_xml" md5="a8525a7efc93a99efe39acff44ee93dd" timestamp="1263056328" time_generated="1263788999" time_taken_to_generate="0" size="1026989">
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+ <export format="owl-classified-by-pellet2" path="obo-all/biological_process_xp_chebi/biological_process_xp_chebi.owl-classified-by-pellet2" md5="3aadbb2f7f6a2cbc2400ee812d94dd9a" timestamp="1263056638" time_generated="1263789005" time_taken_to_generate="0" size="3826">
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+ </export>
+ </ont>
+ <ont id="molecular_function_xp_chebi">
+ <source></source>
+ <status>Draft</status>
+ <contact>go-editors ontology-editors geneontology.org</contact>
+ <foundry>NA</foundry>
+ <documentation>http://wiki.geneontology.org/index.php/XP:molecular_function_xp_chebi</documentation>
+ <url>ftp://ftp.geneontology.org/pub/go/scratch/xps/molecular_function_xp_chebi.obo</url>
+ <extends>molecular_function</extends>
+ <home>http://www.geneontology.org</home>
+ <namespace>molecular_function_xp_chebi</namespace>
+ <description>Defines GO functions in terms of chemical entities (CHEBI)</description>
+ <uses>chebi</uses>
+ <uses>relationship</uses>
+ <uses>ro_proposed</uses>
+ <format>obo</format>
+ <title>GO molecular_function x CHEBI definitions</title>
+ <type>logical_definitions</type>
+ <download>ftp://ftp.geneontology.org/pub/go/scratch/xps/molecular_function_xp_chebi.obo</download>
+ <export format="obo_xml" path="obo-all/molecular_function_xp_chebi/molecular_function_xp_chebi.obo_xml" md5="acdc80e09c330b019518bd28593ea15f" timestamp="1263057031" time_generated="1263789006" time_taken_to_generate="0" size="1797906">
+ </export>
+ <export format="obo" path="obo-all/molecular_function_xp_chebi/molecular_function_xp_chebi.obo" md5="e6c8497ce0a64ba8d8362333d5a21f3b" timestamp="1263789006" time_generated="1263789006" time_taken_to_generate="0" size="1097334">
+ </export>
+ <export format="owl" path="obo-all/molecular_function_xp_chebi/molecular_function_xp_chebi.owl" md5="77fe7d01ccc7453f2594f6caab08bea2" timestamp="1263057727" time_generated="1263789006" time_taken_to_generate="0" size="4695260">
+ </export>
+ <export format="chadoxml" path="obo-all/molecular_function_xp_chebi/molecular_function_xp_chebi.chadoxml" md5="a9a4fd54bb385fcb326f7d940e5cfacb" timestamp="1263057798" time_generated="1263789006" time_taken_to_generate="0" size="1802655">
+ </export>
+ <export format="godb_prestore" path="obo-all/molecular_function_xp_chebi/molecular_function_xp_chebi.godb_prestore" md5="1dc8421b3433eba024789747d89d08e1" timestamp="1263057806" time_generated="1263789006" time_taken_to_generate="0" size="4433828">
+ </export>
+ <export format="rdf" path="obo-all/molecular_function_xp_chebi/molecular_function_xp_chebi.rdf" md5="ff24f70ca526738b77767a99d436a860" timestamp="1263057816" time_generated="1263789006" time_taken_to_generate="0" size="745729">
+ </export>
+ <export format="tbl" path="obo-all/molecular_function_xp_chebi/molecular_function_xp_chebi.tbl" md5="963dbd827d5fe1ccad40d93ad86a8798" timestamp="1263057821" time_generated="1263789006" time_taken_to_generate="0" size="197156">
+ </export>
+ <export format="prolog" path="obo-all/molecular_function_xp_chebi/molecular_function_xp_chebi.pro" md5="e2e4bf1fe40f856b31b4d8fcb316cad1" timestamp="1263423595" time_generated="1263789006" time_taken_to_generate="0" size="1023541">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/molecular_function_xp_chebi/molecular_function_xp_chebi.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1263057839" time_generated="1263789011" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" problem="true">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" path="obo-all/molecular_function_xp_chebi/molecular_function_xp_chebi.imports.obo" md5="a36d362bc92cee90d88619b3a6e746e2" timestamp="1263057841" time_generated="1263789012" time_taken_to_generate="0" size="578">
+ </export>
+ <export format="obo.html" path="obo-all/molecular_function_xp_chebi/molecular_function_xp_chebi.obo.html" md5="3694ed5b268558eeb3fbe2bf9aa352f3" timestamp="1263057842" time_generated="1263789012" time_taken_to_generate="0" size="4922192">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" path="obo-all/molecular_function_xp_chebi/molecular_function_xp_chebi.imports.owl" md5="b449cdf21c291846587bae33552cf35e" timestamp="1263057842" time_generated="1263789012" time_taken_to_generate="0" size="924">
+ </export>
+ <export format="imports-local.obo" path="obo-all/molecular_function_xp_chebi/molecular_function_xp_chebi.imports-local.obo" md5="241b211d1b80f3f16b0ca9dbb7403a08" timestamp="1263057842" time_generated="1263789012" time_taken_to_generate="0" size="503">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" path="obo-all/molecular_function_xp_chebi/molecular_function_xp_chebi.imports-local.owl" md5="6d27c0da8e446c44332165e6d6bd1f01" timestamp="1263057846" time_generated="1263789215" time_taken_to_generate="0" size="4752">
+ </export>
+ <export format="owl-classified-by-pellet2" path="obo-all/molecular_function_xp_chebi/molecular_function_xp_chebi.owl-classified-by-pellet2" md5="88322a13267810c9583f4c7d3d1bbf4b" timestamp="1263057848" time_generated="1263789215" time_taken_to_generate="0" size="3826">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" path="obo-all/molecular_function_xp_chebi/molecular_function_xp_chebi.abduced-links.txt" md5="f65d87084d323479a15a976a08224566" timestamp="1263057871" time_generated="1263789215" time_taken_to_generate="0" size="65178">
+ </export>
+ </ont>
+ <ont id="go_xp_chebi">
+ <source></source>
+ <status>Draft</status>
+ <contact>Mike Bada mike.bada uchsc.edu</contact>
+ <foundry>NA</foundry>
+ <documentation>http://wiki.geneontology.org/index.php/XP:biological_process_xp_chebi</documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/cross_products/go_chebi_xp/GO_to_ChEBI.obo</url>
+ <extends>biological_process</extends>
+ <extends>molecular_function</extends>
+ <home></home>
+ <namespace>go_to_chebi</namespace>
+ <description>Logical definitions for GO Biological Processes and CHEBI</description>
+ <uses>chebi</uses>
+ <uses>ro_ucdhsc</uses>
+ <uses>relationship</uses>
+ <format>obo</format>
+ <title>GO x chemical entity logical definitions</title>
+ <type>logical_definitions</type>
+ <download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/cross_products/go_chebi_xp/GO_to_ChEBI.obo</download>
+ <export format="obo_xml" path="obo-all/go_xp_chebi/go_xp_chebi.obo_xml" md5="a9977896c8beff66e5ea003e53968389" timestamp="1261002520" time_generated="1263789216" time_taken_to_generate="0" size="805119">
+ </export>
+ <export format="obo" path="obo-all/go_xp_chebi/go_xp_chebi.obo" md5="5ac499bbd3befe3e3fd51a4625ab5163" timestamp="1263789216" time_generated="1263789216" time_taken_to_generate="0" size="451926">
+ </export>
+ <export format="owl" path="obo-all/go_xp_chebi/go_xp_chebi.owl" md5="fb8fdb47d4b29aa9567db678d4a1b40e" timestamp="1261002591" time_generated="1263789216" time_taken_to_generate="0" size="1861583">
+ </export>
+ <export format="chadoxml" path="obo-all/go_xp_chebi/go_xp_chebi.chadoxml" md5="54f3c4b6c568ca9f47cf1179ec948210" timestamp="1261002600" time_generated="1263789216" time_taken_to_generate="0" size="806912">
+ </export>
+ <export format="godb_prestore" path="obo-all/go_xp_chebi/go_xp_chebi.godb_prestore" md5="ef2f08dda2a72a794a5b982e93901577" timestamp="1261002602" time_generated="1263789216" time_taken_to_generate="0" size="1901935">
+ </export>
+ <export format="rdf" path="obo-all/go_xp_chebi/go_xp_chebi.rdf" md5="528e5a6a46bf71c50e761a1175e82b3f" timestamp="1261002606" time_generated="1263789216" time_taken_to_generate="0" size="537958">
+ </export>
+ <export format="tbl" path="obo-all/go_xp_chebi/go_xp_chebi.tbl" md5="8eaf3468ca1415b00fab32a67c568c27" timestamp="1261002609" time_generated="1263789216" time_taken_to_generate="0" size="112030">
+ </export>
+ <export format="prolog" path="obo-all/go_xp_chebi/go_xp_chebi.pro" md5="0f7d1bc4e6cf385144f6270c2696a04f" timestamp="1261002614" time_generated="1263789216" time_taken_to_generate="0" size="539561">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/go_xp_chebi/go_xp_chebi.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1261002617" time_generated="1263789219" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" problem="true">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" path="obo-all/go_xp_chebi/go_xp_chebi.imports.obo" md5="134ee98478982bf1050b3009651949c5" timestamp="1261002617" time_generated="1263789220" time_taken_to_generate="0" size="605">
+ </export>
+ <export format="obo.html" path="obo-all/go_xp_chebi/go_xp_chebi.obo.html" md5="b6e37adc049040241afc7df64ab4cf9e" timestamp="1261002617" time_generated="1263789220" time_taken_to_generate="0" size="2262333">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" path="obo-all/go_xp_chebi/go_xp_chebi.imports.owl" md5="1fd82aa5ac6f1d915a9f45d7a08a9ed5" timestamp="1261002618" time_generated="1263789220" time_taken_to_generate="0" size="1019">
+ </export>
+ <export format="imports-local.obo" path="obo-all/go_xp_chebi/go_xp_chebi.imports-local.obo" md5="54c89867164c7e0357106a143490f0c9" timestamp="1261002618" time_generated="1263789220" time_taken_to_generate="0" size="530">
+ </export>
+ <export format="xp.html" path="obo-all/go_xp_chebi/go_xp_chebi.xp.html" md5="4e1f2beb4877f289f557c7404958a09c" timestamp="1261002638" time_generated="1263789220" time_taken_to_generate="0" size="11637700">
+ </export>
+ <export format="imports-local.owl" path="obo-all/go_xp_chebi/go_xp_chebi.imports-local.owl" md5="dbede7d22f55a8526b18593b1af7b41e" timestamp="1261002639" time_generated="1263789220" time_taken_to_generate="0" size="4841">
+ </export>
+ <export format="owl-classified-by-pellet2" path="obo-all/go_xp_chebi/go_xp_chebi.owl-classified-by-pellet2" md5="3ad84261b47e19c802028092332c759b" timestamp="1261002639" time_generated="1263789220" time_taken_to_generate="0" size="3730">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" path="obo-all/go_xp_chebi/go_xp_chebi.abduced-links.txt" md5="3dba424b157dcc3a8ac5d0336ee19cf3" timestamp="1261002873" time_generated="1263789220" time_taken_to_generate="0" size="347489">
+ </export>
+ </ont>
+ <ont id="ro_proposed">
+ <source></source>
+ <status>Draft</status>
+ <contact>Chris Mungall cjm berkeleybop.org</contact>
+ <foundry>NA</foundry>
+ <documentation></documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro_proposed.obo</url>
+ <home></home>
+ <extends>relationship</extends>
+ <namespace>ro_proposed</namespace>
+ <description>Relations under discussion. Candidates for inclusion in RO</description>
+ <filename>ro_proposed</filename>
+ <format>obo</format>
+ <title>Proposed new relations for RO</title>
+ <type>relations</type>
+ <download>ro_proposed|http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro_proposed.obo</download>
+ <export format="obo_xml" path="obo-all/ro_proposed/ro_proposed.obo_xml" md5="b4e3ec83fc30810f9bb3ec3c69332110" timestamp="1261002874" time_generated="1263789223" time_taken_to_generate="0" size="67862">
+ </export>
+ <export format="obo" path="obo-all/ro_proposed/ro_proposed.obo" md5="cdd0a646e75619254ed039393e981822" timestamp="1263789223" time_generated="1263789223" time_taken_to_generate="0" size="47262">
+ </export>
+ <export format="owl" path="obo-all/ro_proposed/ro_proposed.owl" md5="5153fd910ac9d5c8cca56fa1cdd062b4" timestamp="1261002874" time_generated="1263789223" time_taken_to_generate="0" size="116747">
+ </export>
+ <export format="chadoxml" path="obo-all/ro_proposed/ro_proposed.chadoxml" md5="3c6b65867e572bbded658fd298d52d92" timestamp="1261002874" time_generated="1263789223" time_taken_to_generate="0" size="106821">
+ </export>
+ <export format="godb_prestore" path="obo-all/ro_proposed/ro_proposed.godb_prestore" md5="77fd9cd5ec1f8d40bfad21dc399de453" timestamp="1261002874" time_generated="1263789223" time_taken_to_generate="0" size="122658">
+ </export>
+ <export format="rdf" path="obo-all/ro_proposed/ro_proposed.rdf" md5="d3a57d35df16a0424b0c544f66554b54" timestamp="1261002875" time_generated="1263789223" time_taken_to_generate="0" size="69748">
+ </export>
+ <export format="tbl" problem="true">
+ </export>
+ <export format="prolog" path="obo-all/ro_proposed/ro_proposed.pro" md5="129602cec12a8568a49bde6ba63ea9a6" timestamp="1263423610" time_generated="1263789223" time_taken_to_generate="0" size="82818">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/ro_proposed/ro_proposed.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1261002876" time_generated="1263789223" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" path="obo-all/ro_proposed/ro_proposed.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1261002877" time_generated="1263789223" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" path="obo-all/ro_proposed/ro_proposed.imports.obo" md5="989cc522b16b25677bbc76eb3cbc6e3e" timestamp="1261002877" time_generated="1263789223" time_taken_to_generate="0" size="283">
+ </export>
+ <export format="obo.html" path="obo-all/ro_proposed/ro_proposed.obo.html" md5="b96265825b2312b6051e87918c04ed7b" timestamp="1261002878" time_generated="1263789223" time_taken_to_generate="0" size="159534">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" path="obo-all/ro_proposed/ro_proposed.imports.owl" md5="a1acec016ab5f367faedca4567c50579" timestamp="1261002878" time_generated="1263789223" time_taken_to_generate="0" size="539">
+ </export>
+ <export format="imports-local.obo" path="obo-all/ro_proposed/ro_proposed.imports-local.obo" md5="7dd5eded5d6573f76eafb845bb9366d0" timestamp="1261002878" time_generated="1263789223" time_taken_to_generate="0" size="253">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" path="obo-all/ro_proposed/ro_proposed.imports-local.owl" md5="d5a8755a7865e31bbc75ab92566f8227" timestamp="1261002878" time_generated="1263789223" time_taken_to_generate="0" size="4133">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="ro_ucdhsc">
+ <source></source>
+ <status>Draft</status>
+ <contact>Mike Bada mike.bada uchsc.edu</contact>
+ <foundry>NA</foundry>
+ <documentation></documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/cross_products/go_chebi_xp/ro_ucdhsc.obo</url>
+ <home></home>
+ <extends>relationship</extends>
+ <namespace>ro_ucdhsc</namespace>
+ <description>Relations proposed by UCDHSC, potential RO inclusion candidates. Used in go_xp_chebi</description>
+ <filename>ro_ucdhsc</filename>
+ <format>obo</format>
+ <title>UCDHSC Relations</title>
+ <type>relations</type>
+ <download>ro_ucdhsc|http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/cross_products/go_chebi_xp/ro_ucdhsc.obo</download>
+ <export format="obo_xml" path="obo-all/ro_ucdhsc/ro_ucdhsc.obo_xml" md5="9edc9a94909afb611bbd0534e691bdb4" timestamp="1261002879" time_generated="1263789225" time_taken_to_generate="0" size="8592">
+ </export>
+ <export format="obo" path="obo-all/ro_ucdhsc/ro_ucdhsc.obo" md5="cbcc5c8358cc8c45c42797550eec7f25" timestamp="1263789225" time_generated="1263789225" time_taken_to_generate="0" size="6101">
+ </export>
+ <export format="owl" path="obo-all/ro_ucdhsc/ro_ucdhsc.owl" md5="d0a167a10330651ce92e215b15291766" timestamp="1261002879" time_generated="1263789225" time_taken_to_generate="0" size="18169">
+ </export>
+ <export format="chadoxml" path="obo-all/ro_ucdhsc/ro_ucdhsc.chadoxml" md5="4c60d23ade3fad066c9b4af5798d4474" timestamp="1261002879" time_generated="1263789225" time_taken_to_generate="0" size="16924">
+ </export>
+ <export format="godb_prestore" path="obo-all/ro_ucdhsc/ro_ucdhsc.godb_prestore" md5="b85b50860d32fee332cc24491c8681be" timestamp="1261002880" time_generated="1263789225" time_taken_to_generate="0" size="19197">
+ </export>
+ <export format="rdf" path="obo-all/ro_ucdhsc/ro_ucdhsc.rdf" md5="fabbda8b06c80ba104f7bc95859deff8" timestamp="1261002880" time_generated="1263789225" time_taken_to_generate="0" size="8757">
+ </export>
+ <export format="tbl" problem="true">
+ </export>
+ <export format="prolog" path="obo-all/ro_ucdhsc/ro_ucdhsc.pro" md5="dbc03f2ef7309f8c1561739043d2032c" timestamp="1263423614" time_generated="1263789225" time_taken_to_generate="0" size="10015">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/ro_ucdhsc/ro_ucdhsc.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1261002881" time_generated="1263789225" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" path="obo-all/ro_ucdhsc/ro_ucdhsc.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1261002882" time_generated="1263789226" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" path="obo-all/ro_ucdhsc/ro_ucdhsc.imports.obo" md5="7aa9a8ceb3d1d519b41aacf984a0587a" timestamp="1261002882" time_generated="1263789226" time_taken_to_generate="0" size="275">
+ </export>
+ <export format="obo.html" path="obo-all/ro_ucdhsc/ro_ucdhsc.obo.html" md5="ae3cb8d9c4ca98388e5a24eb2d0ce636" timestamp="1261002882" time_generated="1263789226" time_taken_to_generate="0" size="20367">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" path="obo-all/ro_ucdhsc/ro_ucdhsc.imports.owl" md5="8216aa628036ae04d96168756a2c75a8" timestamp="1261002882" time_generated="1263789226" time_taken_to_generate="0" size="535">
+ </export>
+ <export format="imports-local.obo" path="obo-all/ro_ucdhsc/ro_ucdhsc.imports-local.obo" md5="44fc7b331ef103b0a472ff7c05e90d9b" timestamp="1261002882" time_generated="1263789226" time_taken_to_generate="0" size="245">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" path="obo-all/ro_ucdhsc/ro_ucdhsc.imports-local.owl" md5="09f2c007250a4679924aeff61e8efc9b" timestamp="1261002882" time_generated="1263789226" time_taken_to_generate="0" size="4117">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="envo_xp">
+ <source></source>
+ <status>Draft</status>
+ <contact>Chris Mungall cjm fruitfly.org</contact>
+ <foundry>NA</foundry>
+ <documentation></documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/environmental/envo-edit.obo</url>
+ <extends>envo</extends>
+ <home></home>
+ <namespace>ENVO_XP</namespace>
+ <description>Mappings between ENVO terms and compositional descriptions that can be used for reasoning</description>
+ <uses>ro_proposed</uses>
+ <uses>relationship</uses>
+ <uses>quality</uses>
+ <uses>chebi</uses>
+ <format>obo</format>
+ <title>environmental entity logical definitions</title>
+ <type>logical_definitions</type>
+ <download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/environmental/envo-edit.obo</download>
+ <export format="obo_xml" path="obo-all/envo_xp/envo_xp.obo_xml" md5="0754858842f42fc64ff249b5e305f637" timestamp="1261002887" time_generated="1263789228" time_taken_to_generate="0" size="1102973">
+ </export>
+ <export format="obo" path="obo-all/envo_xp/envo_xp.obo" md5="eb7a6f46c5f9bd413e6d78f4cc433239" timestamp="1263789228" time_generated="1263789228" time_taken_to_generate="0" size="463442">
+ </export>
+ <export format="owl" path="obo-all/envo_xp/envo_xp.owl" md5="4f6174c5499acde2ce94978798f1c20a" timestamp="1261002915" time_generated="1263789228" time_taken_to_generate="0" size="2807569">
+ </export>
+ <export format="chadoxml" path="obo-all/envo_xp/envo_xp.chadoxml" md5="249c0242c4fb40481d88674b9d265273" timestamp="1261002928" time_generated="1263789229" time_taken_to_generate="0" size="2702196">
+ </export>
+ <export format="godb_prestore" path="obo-all/envo_xp/envo_xp.godb_prestore" md5="054ce105b9191af947cbd5bd9dd0de28" timestamp="1261002931" time_generated="1263789229" time_taken_to_generate="0" size="2150723">
+ </export>
+ <export format="rdf" path="obo-all/envo_xp/envo_xp.rdf" md5="0f36043425cfa8d3800ce73730d6a253" timestamp="1261002937" time_generated="1263789229" time_taken_to_generate="0" size="1120596">
+ </export>
+ <export format="tbl" path="obo-all/envo_xp/envo_xp.tbl" md5="c6f0305ab2f1ee7eb291e0b247e86bd3" timestamp="1261002940" time_generated="1263789229" time_taken_to_generate="0" size="195365">
+ </export>
+ <export format="prolog" path="obo-all/envo_xp/envo_xp.pro" md5="99358efcd672608e5e6b42bd85556b48" timestamp="1263423645" time_generated="1263789229" time_taken_to_generate="0" size="1157638">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/envo_xp/envo_xp.validation_report" md5="04b53854f45e689ff1f1e60b50c3ffe2" timestamp="1261002950" time_generated="1263789232" time_taken_to_generate="0" size="1558">
+ </export>
+ <export format="stats" path="obo-all/envo_xp/envo_xp.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1261002952" time_generated="1263789232" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" path="obo-all/envo_xp/envo_xp.imports.obo" md5="600d3710bee468827420109ba293ae00" timestamp="1261002952" time_generated="1263789232" time_taken_to_generate="0" size="520">
+ </export>
+ <export format="obo.html" path="obo-all/envo_xp/envo_xp.obo.html" md5="23582c64017158e4327fea51373e6663" timestamp="1261002952" time_generated="1263789232" time_taken_to_generate="0" size="2515149">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" path="obo-all/envo_xp/envo_xp.imports.owl" md5="6d3ce5c848777ff4dd9354dcc479c753" timestamp="1261002952" time_generated="1263789232" time_taken_to_generate="0" size="965">
+ </export>
+ <export format="imports-local.obo" path="obo-all/envo_xp/envo_xp.imports-local.obo" md5="0bf3e3adcb1f9cc0c8fdec6401abafa1" timestamp="1261002952" time_generated="1263789232" time_taken_to_generate="0" size="430">
+ </export>
+ <export format="xp.html" path="obo-all/envo_xp/envo_xp.xp.html" md5="ebc7f3642278706ec16fa375afa57443" timestamp="1261002959" time_generated="1263789232" time_taken_to_generate="0" size="523943">
+ </export>
+ <export format="imports-local.owl" path="obo-all/envo_xp/envo_xp.imports-local.owl" md5="b3c585fc4512ec59306fb061ce448f66" timestamp="1261002959" time_generated="1263789232" time_taken_to_generate="0" size="4664">
+ </export>
+ <export format="owl-classified-by-pellet2" path="obo-all/envo_xp/envo_xp.owl-classified-by-pellet2" md5="25c8d53f63becfc0a3ecb71fc6105c87" timestamp="1261002964" time_generated="1263789232" time_taken_to_generate="0" size="3706">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="plant_trait_xp">
+ <source></source>
+ <status>Draft</status>
+ <contact>OBO phenotype group obo-phenotype lists.sourceforge.net</contact>
+ <foundry>NA</foundry>
+ <documentation>http://www.bioontology.org/wiki/index.php/PATO:Pre_vs_Post_Coordinating</documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/plant_traits/plant_trait_xp.obo</url>
+ <home>Gramene Ontology database website|http://www.gramene.org/plant_ontology/</home>
+ <extends>plant_trait</extends>
+ <namespace>TO_XP</namespace>
+ <description>plant_trait is an ontology of pre-composed phenotype terms specifically for plants. This mapping decomposes these phenotypes into constituent terms using PATO</description>
+ <uses>ro_proposed</uses>
+ <uses>relationship</uses>
+ <uses>quality</uses>
+ <uses>po_anatomy</uses>
+ <uses>chebi</uses>
+ <uses>plant_environment</uses>
+ <uses>biological_process</uses>
+ <filename>plant_trait_xp.obo</filename>
+ <format>obo</format>
+ <title>plant_trait logical definitions</title>
+ <type>logical_definitions</type>
+ <download>plant_trait_xp.obo|http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/plant_traits/plant_trait_xp.obo</download>
+ <export format="obo_xml" path="obo-all/plant_trait_xp/plant_trait_xp.obo_xml" md5="9495dc49a09b938bb102a5b32a087273" timestamp="1261003047" time_generated="1263789346" time_taken_to_generate="0" size="126252">
+ </export>
+ <export format="obo" path="obo-all/plant_trait_xp/plant_trait_xp.obo" md5="961c2b721b653901b42e9f050b2ca9dc" timestamp="1263789346" time_generated="1263789346" time_taken_to_generate="0" size="62499">
+ </export>
+ <export format="owl" path="obo-all/plant_trait_xp/plant_trait_xp.owl" md5="b3dc9c8c10e183b125989a20d9dcd5d1" timestamp="1261003048" time_generated="1263789346" time_taken_to_generate="0" size="307132">
+ </export>
+ <export format="chadoxml" path="obo-all/plant_trait_xp/plant_trait_xp.chadoxml" md5="2ee9e09597360970ed974021b29fd159" timestamp="1261003048" time_generated="1263789346" time_taken_to_generate="0" size="126508">
+ </export>
+ <export format="godb_prestore" path="obo-all/plant_trait_xp/plant_trait_xp.godb_prestore" md5="02239aed88100ce78b2e37ef5f7c733d" timestamp="1261003049" time_generated="1263789346" time_taken_to_generate="0" size="313835">
+ </export>
+ <export format="rdf" path="obo-all/plant_trait_xp/plant_trait_xp.rdf" md5="895e6255060cb0a50cc3f694b1b31d14" timestamp="1261003050" time_generated="1263789346" time_taken_to_generate="0" size="69977">
+ </export>
+ <export format="tbl" path="obo-all/plant_trait_xp/plant_trait_xp.tbl" md5="eec1b0958c14d463a81d2834afb851b4" timestamp="1261003050" time_generated="1263789346" time_taken_to_generate="0" size="5161">
+ </export>
+ <export format="prolog" path="obo-all/plant_trait_xp/plant_trait_xp.pro" md5="038b83ce8185f1589f0600bdcae1a9ea" timestamp="1261003051" time_generated="1263789346" time_taken_to_generate="0" size="78739">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/plant_trait_xp/plant_trait_xp.validation_report" md5="58c0ac0edc13a859b0fc93fda25c934f" timestamp="1261003052" time_generated="1263789347" time_taken_to_generate="0" size="125">
+ </export>
+ <export format="stats" path="obo-all/plant_trait_xp/plant_trait_xp.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1261003053" time_generated="1263789347" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" path="obo-all/plant_trait_xp/plant_trait_xp.imports.obo" md5="62447528305a6110ed11179591b5fb16" timestamp="1261003053" time_generated="1263789347" time_taken_to_generate="0" size="833">
+ </export>
+ <export format="obo.html" path="obo-all/plant_trait_xp/plant_trait_xp.obo.html" md5="1081d7e88b2e79aae0d7ec8796029547" timestamp="1261003053" time_generated="1263789347" time_taken_to_generate="0" size="317752">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" path="obo-all/plant_trait_xp/plant_trait_xp.imports.owl" md5="165344c0ea2a807b1c76952cde2efe34" timestamp="1261003053" time_generated="1263789347" time_taken_to_generate="0" size="1368">
+ </export>
+ <export format="imports-local.obo" path="obo-all/plant_trait_xp/plant_trait_xp.imports-local.obo" md5="d53e978393def28b64296f7d86ec908e" timestamp="1261003053" time_generated="1263789347" time_taken_to_generate="0" size="698">
+ </export>
+ <export format="xp.html" path="obo-all/plant_trait_xp/plant_trait_xp.xp.html" md5="1250954d01432c16bf037586f82b2dc6" timestamp="1261003060" time_generated="1263789347" time_taken_to_generate="0" size="1791776">
+ </export>
+ <export format="imports-local.owl" path="obo-all/plant_trait_xp/plant_trait_xp.imports-local.owl" md5="3cc39cdead036fedb5b9e6b45f2876fb" timestamp="1261003060" time_generated="1263789347" time_taken_to_generate="0" size="5301">
+ </export>
+ <export format="owl-classified-by-pellet2" path="obo-all/plant_trait_xp/plant_trait_xp.owl-classified-by-pellet2" md5="d907115cec18ab07e68cd5a944277dc7" timestamp="1261003068" time_generated="1263789347" time_taken_to_generate="0" size="3748">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" path="obo-all/plant_trait_xp/plant_trait_xp.abduced-links.txt" md5="89efbcdf540e482ac6948d212042b698" timestamp="1261003073" time_generated="1263789347" time_taken_to_generate="0" size="10673">
+ </export>
+ </ont>
+ <ont id="mammalian_phenotype_xp">
+ <source></source>
+ <status>Draft</status>
+ <contact>OBO phenotype group obo-phenotype lists.sourceforge.net</contact>
+ <foundry>NA</foundry>
+ <documentation>http://www.bioontology.org/wiki/index.php/PATO:Pre_vs_Post_Coordinating</documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/mammalian_phenotype_xp.obo</url>
+ <home>Mammalian Phenotype Browser|http://www.informatics.jax.org/searches/MP_form.shtml</home>
+ <extends>mammalian_phenotype</extends>
+ <namespace>MP_XP</namespace>
+ <description>mammalian_phenotype is an ontology of pre-composed phenotype terms for mouse/mammals. This mapping decomposes these phenotypes into constituent terms using PATO. This mapping is at the alpha stage - it has not yet been approved by MP curators</description>
+ <uses>quality</uses>
+ <uses>ro_proposed</uses>
+ <uses>relationship</uses>
+ <uses>adult_mouse_anatomy</uses>
+ <uses>chebi</uses>
+ <uses>cell</uses>
+ <uses>biological_process</uses>
+ <uses>cellular_component</uses>
+ <uses>emap</uses>
+ <uses>mouse_pathology</uses>
+ <filename>mammalian_phenotype_xp.obo</filename>
+ <format>obo</format>
+ <title>mammalian_phenotype logical definitions</title>
+ <type>logical_definitions</type>
+ <download>mammalian_phenotype_xp.obo|http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/mammalian_phenotype_xp.obo</download>
+ <export format="obo_xml" path="obo-all/mammalian_phenotype_xp/mammalian_phenotype_xp.obo_xml" md5="07d799fd8a1e2e73cecb316d8624d2ea" timestamp="1263423826" time_generated="1263789350" time_taken_to_generate="0" size="1966818">
+ </export>
+ <export format="obo" path="obo-all/mammalian_phenotype_xp/mammalian_phenotype_xp.obo" md5="e4a162b37ee8f2e83a79fe622ad77cb5" timestamp="1263789350" time_generated="1263789350" time_taken_to_generate="0" size="1038901">
+ </export>
+ <export format="owl" path="obo-all/mammalian_phenotype_xp/mammalian_phenotype_xp.owl" md5="e843e77f1ecf4f84cc1aaff8425abc2f" timestamp="1263424757" time_generated="1263789350" time_taken_to_generate="0" size="4791314">
+ </export>
+ <export format="chadoxml" path="obo-all/mammalian_phenotype_xp/mammalian_phenotype_xp.chadoxml" md5="0be34c38217a2e3a634ac8eaa6b459c6" timestamp="1263425002" time_generated="1263789350" time_taken_to_generate="0" size="1687372">
+ </export>
+ <export format="godb_prestore" path="obo-all/mammalian_phenotype_xp/mammalian_phenotype_xp.godb_prestore" md5="6d8e472bc659b1fb810c4a87c4f6ed2b" timestamp="1263425016" time_generated="1263789350" time_taken_to_generate="0" size="4923457">
+ </export>
+ <export format="rdf" path="obo-all/mammalian_phenotype_xp/mammalian_phenotype_xp.rdf" md5="443f55aec5186a8c2a87660963301e86" timestamp="1263425034" time_generated="1263789350" time_taken_to_generate="0" size="926389">
+ </export>
+ <export format="tbl" path="obo-all/mammalian_phenotype_xp/mammalian_phenotype_xp.tbl" md5="73772391bd9c96a430bfbcd8373d284b" timestamp="1263425045" time_generated="1263789350" time_taken_to_generate="0" size="69867">
+ </export>
+ <export format="prolog" path="obo-all/mammalian_phenotype_xp/mammalian_phenotype_xp.pro" md5="7b986a03637038fd99f7604e01197ef2" timestamp="1263425068" time_generated="1263789350" time_taken_to_generate="0" size="1235444">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/mammalian_phenotype_xp/mammalian_phenotype_xp.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1263425081" time_generated="1263789355" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" path="obo-all/mammalian_phenotype_xp/mammalian_phenotype_xp.stats" md5="7ae7aaf83d188ac8830fad76a4acfeab" timestamp="1263425083" time_generated="1263789355" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" path="obo-all/mammalian_phenotype_xp/mammalian_phenotype_xp.imports.obo" md5="bed772ed61a1ac2a58835403805873f2" timestamp="1263425083" time_generated="1263789356" time_taken_to_generate="0" size="1117">
+ </export>
+ <export format="obo.html" path="obo-all/mammalian_phenotype_xp/mammalian_phenotype_xp.obo.html" md5="96b9607c4fedf85ce999b053e0658660" timestamp="1263425084" time_generated="1263789356" time_taken_to_generate="0" size="4808788">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" path="obo-all/mammalian_phenotype_xp/mammalian_phenotype_xp.imports.owl" md5="3cd92c866a594652b6e853532714439f" timestamp="1263425084" time_generated="1263789356" time_taken_to_generate="0" size="1751">
+ </export>
+ <export format="imports-local.obo" path="obo-all/mammalian_phenotype_xp/mammalian_phenotype_xp.imports-local.obo" md5="a731d3a1fc59c17e62e2533f4115852a" timestamp="1263425084" time_generated="1263789356" time_taken_to_generate="0" size="937">
+ </export>
+ <export format="xp.html" path="obo-all/mammalian_phenotype_xp/mammalian_phenotype_xp.xp.html" md5="b1a8b276ec0ca5823f16e316ae39dcd3" timestamp="1263425251" time_generated="1263789356" time_taken_to_generate="0" size="26831026">
+ </export>
+ <export format="imports-local.owl" path="obo-all/mammalian_phenotype_xp/mammalian_phenotype_xp.imports-local.owl" md5="945e84d1dbfbd1ec54ebc8ab84ce4bce" timestamp="1263425252" time_generated="1263789356" time_taken_to_generate="0" size="5891">
+ </export>
+ <export format="owl-classified-by-pellet2" path="obo-all/mammalian_phenotype_xp/mammalian_phenotype_xp.owl-classified-by-pellet2" md5="75b96e17b3a20466c58598b39672f155" timestamp="1263425264" time_generated="1263789356" time_taken_to_generate="0" size="3796">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" path="obo-all/mammalian_phenotype_xp/mammalian_phenotype_xp.abduced-links.txt" md5="27fbb607bfc42a085e6a6d370881fc6d" timestamp="1263425278" time_generated="1263789356" time_taken_to_generate="0" size="439890">
+ </export>
+ </ont>
+ <ont id="human_phenotype_xp">
+ <source></source>
+ <status>Draft</status>
+ <contact>OBO phenotype group obo-phenotype lists.sourceforge.net</contact>
+ <foundry>NA</foundry>
+ <documentation>http://www.bioontology.org/wiki/index.php/PATO:Pre_vs_Post_Coordinating</documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/phenotype_xp/human_phenotype_xp.obo</url>
+ <home></home>
+ <extends>human_phenotype</extends>
+ <namespace>HP_XP</namespace>
+ <description>human_phenotype is an ontology of pre-composed phenotype terms for humans. HP_XP is a set of logical definitions (cross-products) that describe these phenotypes using PATO and the FMA. </description>
+ <uses>quality</uses>
+ <uses>ro_proposed</uses>
+ <uses>relationship</uses>
+ <uses>fma_lite</uses>
+ <uses>chebi</uses>
+ <uses>cell</uses>
+ <uses>biological_process</uses>
+ <uses>cellular_component</uses>
+ <uses>mouse_pathology</uses>
+ <filename>human_phenotype_xp.obo</filename>
+ <format>obo</format>
+ <title>human_phenotype logical definitions</title>
+ <type>logical_definitions</type>
+ <download>human_phenotype_xp.obo|http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/phenotype_xp/human_phenotype_xp.obo</download>
+ <export format="obo_xml" path="obo-all/human_phenotype_xp/human_phenotype_xp.obo_xml" md5="a7aa8ec0ec41e2ee03c8722888463503" timestamp="1263789361" time_generated="1263789361" time_taken_to_generate="3" size="1154524">
+ </export>
+ <export format="obo" path="obo-all/human_phenotype_xp/human_phenotype_xp.obo" md5="8a0658873fc3cc73eb174734b66f7f8d" timestamp="1263789358" time_generated="1263789361" time_taken_to_generate="0" size="747936">
+ </export>
+ <export format="owl" path="obo-all/human_phenotype_xp/human_phenotype_xp.owl" md5="f136f3b359b99c3ca1e2f1cbb2c12762" timestamp="1263789550" time_generated="1263789550" time_taken_to_generate="189" size="2891904">
+ </export>
+ <export format="chadoxml" path="obo-all/human_phenotype_xp/human_phenotype_xp.chadoxml" md5="6b350806fd3cd3114b963596b47964e0" timestamp="1263789581" time_generated="1263789581" time_taken_to_generate="31" size="1098412">
+ </export>
+ <export format="godb_prestore" path="obo-all/human_phenotype_xp/human_phenotype_xp.godb_prestore" md5="06710c1fd7f8d33804a4e9aea6322c98" timestamp="1263789585" time_generated="1263789585" time_taken_to_generate="4" size="3088450">
+ </export>
+ <export format="rdf" path="obo-all/human_phenotype_xp/human_phenotype_xp.rdf" md5="484eb32ae673b79535f56188d91eb4f0" timestamp="1263789592" time_generated="1263789592" time_taken_to_generate="7" size="698222">
+ </export>
+ <export format="tbl" path="obo-all/human_phenotype_xp/human_phenotype_xp.tbl" md5="ca9ad9dadf393f3ca87e6a76cd574178" timestamp="1263789596" time_generated="1263789596" time_taken_to_generate="4" size="55919">
+ </export>
+ <export format="prolog" path="obo-all/human_phenotype_xp/human_phenotype_xp.pro" md5="b2c7832d91c68e1798c359062f68b7a8" timestamp="1263789604" time_generated="1263789604" time_taken_to_generate="8" size="615131">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/human_phenotype_xp/human_phenotype_xp.validation_report" md5="916f92d2bce0f351255794ed10162704" timestamp="1263789608" time_generated="1263789608" time_taken_to_generate="1" size="103">
+ </export>
+ <export format="stats" path="obo-all/human_phenotype_xp/human_phenotype_xp.stats" md5="619a62d04ddf7c62cc6ebdc743938b12" timestamp="1263789610" time_generated="1263789610" time_taken_to_generate="2" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" path="obo-all/human_phenotype_xp/human_phenotype_xp.imports.obo" md5="17dd0de806661de586405ea0237589f1" timestamp="1263789610" time_generated="1263789610" time_taken_to_generate="0" size="1001">
+ </export>
+ <export format="obo.html" path="obo-all/human_phenotype_xp/human_phenotype_xp.obo.html" md5="0beec3e523c666cbb60db880e3a131b9" timestamp="1263789610" time_generated="1263789610" time_taken_to_generate="0" size="3439756">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" path="obo-all/human_phenotype_xp/human_phenotype_xp.imports.owl" md5="90b02107c4305335416fe5deec14f532" timestamp="1263789610" time_generated="1263789610" time_taken_to_generate="0" size="1610">
+ </export>
+ <export format="imports-local.obo" path="obo-all/human_phenotype_xp/human_phenotype_xp.imports-local.obo" md5="b18c6c8111d4c27b9b2ad41e96885000" timestamp="1263789610" time_generated="1263789610" time_taken_to_generate="0" size="836">
+ </export>
+ <export format="xp.html" path="obo-all/human_phenotype_xp/human_phenotype_xp.xp.html" md5="19c1c0a2a85bd41dda786f680c4ac9ce" timestamp="1263789775" time_generated="1263789775" time_taken_to_generate="165" size="15536202">
+ </export>
+ <export format="imports-local.owl" path="obo-all/human_phenotype_xp/human_phenotype_xp.imports-local.owl" md5="d4a31e950916139600d90ca033eb1e4a" timestamp="1263789776" time_generated="1263789776" time_taken_to_generate="1" size="5657">
+ </export>
+ <export format="owl-classified-by-pellet2" path="obo-all/human_phenotype_xp/human_phenotype_xp.owl-classified-by-pellet2" md5="b4dcffac69413ea9c20a809b036f4309" timestamp="1263789782" time_generated="1263789782" time_taken_to_generate="6" size="3778">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="human_phenotype_xp_anatomy">
+ <source></source>
+ <status>Draft</status>
+ <contact>OBO human phenotype group obo-human-phenotype lists.sourceforge.net</contact>
+ <foundry>NA</foundry>
+ <documentation>http://www.obofoundry.org/wiki/index.php/PATO:XPs</documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/human_phenotype_xp/human-phenotype-ontology_xp_FMA.obo</url>
+ <home>http://www.obofoundry.org/wiki/index.php/PATO:human_phenotype_xp</home>
+ <extends>human_phenotype</extends>
+ <namespace>HP_XP_FMA</namespace>
+ <description>Logical definitions for HP terms that reference FMA, but *not* any other ontology (bar PATO and HP itself). This is a subset of HP_XP.</description>
+ <uses>quality</uses>
+ <uses>human_phenotype_xp_relations</uses>
+ <uses>fma_lite</uses>
+ <filename>human-phenotype-ontology_xp_FMA.obo</filename>
+ <format>obo</format>
+ <title>human_phenotype x anatomy logical definitions </title>
+ <type>logical_definitions</type>
+ <download>human-phenotype-ontology_xp_FMA.obo|http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/human_phenotype_xp/human-phenotype-ontology_xp_FMA.obo</download>
+ <export format="obo_xml" path="obo-all/human_phenotype_xp_anatomy/human_phenotype_xp_anatomy.obo_xml" md5="e77657385f8d19ca4009b9cbe0ecbdd9" timestamp="1261005241" time_generated="1263791679" time_taken_to_generate="0" size="630673">
+ </export>
+ <export format="obo" path="obo-all/human_phenotype_xp_anatomy/human_phenotype_xp_anatomy.obo" md5="fd135ddbdb88269e74e7fb3ec6dc0c98" timestamp="1263791679" time_generated="1263791679" time_taken_to_generate="0" size="392435">
+ </export>
+ <export format="owl" path="obo-all/human_phenotype_xp_anatomy/human_phenotype_xp_anatomy.owl" md5="80ba275d7566ac66ab8d72aa543cd995" timestamp="1261005289" time_generated="1263791679" time_taken_to_generate="0" size="1422277">
+ </export>
+ <export format="chadoxml" path="obo-all/human_phenotype_xp_anatomy/human_phenotype_xp_anatomy.chadoxml" md5="fac6c22956232f3b7308fead12dee769" timestamp="1261005294" time_generated="1263791679" time_taken_to_generate="0" size="543981">
+ </export>
+ <export format="godb_prestore" path="obo-all/human_phenotype_xp_anatomy/human_phenotype_xp_anatomy.godb_prestore" md5="5d5f9a3318fe785e164ecb1602a004d1" timestamp="1261005296" time_generated="1263791679" time_taken_to_generate="0" size="1520270">
+ </export>
+ <export format="rdf" problem="true">
+ </export>
+ <export format="tbl" problem="true">
+ </export>
+ <export format="prolog" problem="true">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" problem="true">
+ </export>
+ <export format="stats" problem="true">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" path="obo-all/human_phenotype_xp_anatomy/human_phenotype_xp_anatomy.imports.obo" md5="53beef5609bd5e7865e6d94941aef704" timestamp="1261005310" time_generated="1263791707" time_taken_to_generate="0" size="610">
+ </export>
+ <export format="obo.html" path="obo-all/human_phenotype_xp_anatomy/human_phenotype_xp_anatomy.obo.html" md5="53fb1736dfde59f5ac537d72315f4eaa" timestamp="1261005310" time_generated="1263791707" time_taken_to_generate="0" size="1860004">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" path="obo-all/human_phenotype_xp_anatomy/human_phenotype_xp_anatomy.imports.owl" md5="709d3f8e00270b277322c0ff7d15f780" timestamp="1261005310" time_generated="1263791707" time_taken_to_generate="0" size="946">
+ </export>
+ <export format="imports-local.obo" path="obo-all/human_phenotype_xp_anatomy/human_phenotype_xp_anatomy.imports-local.obo" md5="253d2e4d5b9627cd9efb4c0a4fab152f" timestamp="1261005310" time_generated="1263791707" time_taken_to_generate="0" size="550">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" path="obo-all/human_phenotype_xp_anatomy/human_phenotype_xp_anatomy.imports-local.owl" md5="403ddd87778c9afb80cf0d8bfceed015" timestamp="1261005311" time_generated="1263791709" time_taken_to_generate="0" size="4834">
+ </export>
+ <export format="owl-classified-by-pellet2" path="obo-all/human_phenotype_xp_anatomy/human_phenotype_xp_anatomy.owl-classified-by-pellet2" md5="af0b8906b32f03b817e9930817694bb0" timestamp="1261005317" time_generated="1263791709" time_taken_to_generate="0" size="3826">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="human_phenotype_xp_relations">
+ <source></source>
+ <namespace>HP_XP_REL</namespace>
+ <status>Draft</status>
+ <contact>OBO human phenotype group obo-human-phenotype lists.sourceforge.net</contact>
+ <description>Relations used in human_phenotype_xp_* mappings</description>
+ <foundry>NA</foundry>
+ <format>obo</format>
+ <filename>human-phenotype-ontology_xp_relations.obo</filename>
+ <documentation>http://www.obofoundry.org/wiki/index.php/PATO:XPs</documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/human_phenotype_xp/human-phenotype-ontology_xp_relations.obo</url>
+ <type>relations</type>
+ <title>relations for human_phenotype_xp</title>
+ <home>http://www.obofoundry.org/wiki/index.php/PATO:human_phenotype_xp</home>
+ <download>human-phenotype-ontology_xp_relations.obo|http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/human_phenotype_xp/human-phenotype-ontology_xp_relations.obo</download>
+ <export format="obo_xml" path="obo-all/human_phenotype_xp_relations/human_phenotype_xp_relations.obo_xml" md5="2e825205405641f108e9b0399e5227b7" timestamp="1261005318" time_generated="1263791712" time_taken_to_generate="0" size="1434">
+ </export>
+ <export format="obo" path="obo-all/human_phenotype_xp_relations/human_phenotype_xp_relations.obo" md5="a1dc0954e8f559793fbea49a5dfc801e" timestamp="1263791712" time_generated="1263791712" time_taken_to_generate="0" size="561">
+ </export>
+ <export format="owl" path="obo-all/human_phenotype_xp_relations/human_phenotype_xp_relations.owl" md5="08ce0737429291ab7e5579d9ae95bbc0" timestamp="1261005318" time_generated="1263791712" time_taken_to_generate="0" size="4760">
+ </export>
+ <export format="chadoxml" path="obo-all/human_phenotype_xp_relations/human_phenotype_xp_relations.chadoxml" md5="785692a6661980e23b37c4c81dbc6da3" timestamp="1261005318" time_generated="1263791712" time_taken_to_generate="0" size="3212">
+ </export>
+ <export format="godb_prestore" path="obo-all/human_phenotype_xp_relations/human_phenotype_xp_relations.godb_prestore" md5="223aa3c68924bc67232881d6b3f560f4" timestamp="1261005319" time_generated="1263791712" time_taken_to_generate="0" size="4250">
+ </export>
+ <export format="rdf" path="obo-all/human_phenotype_xp_relations/human_phenotype_xp_relations.rdf" md5="8bb568e8bdf0af30a46cb3fc14bd768a" timestamp="1261005319" time_generated="1263791712" time_taken_to_generate="0" size="1202">
+ </export>
+ <export format="tbl" problem="true">
+ </export>
+ <export format="prolog" path="obo-all/human_phenotype_xp_relations/human_phenotype_xp_relations.pro" md5="f6970e8f7d4c68bc986dc2fa7e887dd8" timestamp="1261005319" time_generated="1263791712" time_taken_to_generate="0" size="878">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/human_phenotype_xp_relations/human_phenotype_xp_relations.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1261005320" time_generated="1263791712" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" problem="true">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/human_phenotype_xp_relations/human_phenotype_xp_relations.obo.html" md5="110cc460ce787d6a8be9a1719ff4f552" timestamp="1261005320" time_generated="1263791714" time_taken_to_generate="0" size="2300">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="disease_xp_fma">
+ <source></source>
+ <status>Draft</status>
+ <contact>Chris Mungall cjm fruitfly.org</contact>
+ <foundry>NA</foundry>
+ <documentation>http://www.bioontology.org/wiki/index.php/PATO:Pre_vs_Post_Coordinating</documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/phenotype_xp/disease_xp_fma.obo</url>
+ <home></home>
+ <extends>disease_ontology</extends>
+ <namespace>DO_XP_FMA</namespace>
+ <description>Logical definitions for DO terms using the cross-product of DO and the FMA (Foundational Model of Anatomy)</description>
+ <uses>fma_lite</uses>
+ <uses>ro_proposed</uses>
+ <uses>relationship</uses>
+ <filename>disease_xp_fma.obo</filename>
+ <format>obo</format>
+ <title>Disease ontology logical definitions using FMA</title>
+ <type>logical_definitions</type>
+ <download>disease_xp_fma.obo|http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/phenotype_xp/disease_xp_fma.obo</download>
+ <export format="obo_xml" path="obo-all/disease_xp_fma/disease_xp_fma.obo_xml" md5="f414401539cadbcfc43011866faf90eb" timestamp="1261005323" time_generated="1263791717" time_taken_to_generate="0" size="369525">
+ </export>
+ <export format="obo" path="obo-all/disease_xp_fma/disease_xp_fma.obo" md5="825ddfd3cbaa1cac5d78fc8f0978bc77" timestamp="1263791717" time_generated="1263791717" time_taken_to_generate="0" size="232030">
+ </export>
+ <export format="owl" path="obo-all/disease_xp_fma/disease_xp_fma.owl" md5="dc09f433c7c570dc4c2b8e181b84d843" timestamp="1261005336" time_generated="1263791717" time_taken_to_generate="0" size="945794">
+ </export>
+ <export format="chadoxml" path="obo-all/disease_xp_fma/disease_xp_fma.chadoxml" md5="91a37aa3bb648a9f16f3080340165b9e" timestamp="1261005338" time_generated="1263791717" time_taken_to_generate="0" size="405960">
+ </export>
+ <export format="godb_prestore" path="obo-all/disease_xp_fma/disease_xp_fma.godb_prestore" md5="b0567ff8333b57767e716386af6fa3f7" timestamp="1261005340" time_generated="1263791717" time_taken_to_generate="0" size="1009865">
+ </export>
+ <export format="rdf" path="obo-all/disease_xp_fma/disease_xp_fma.rdf" md5="2d4d4ebbf05ae4a4c40bb0d896be0c6e" timestamp="1261005342" time_generated="1263791717" time_taken_to_generate="0" size="262160">
+ </export>
+ <export format="tbl" path="obo-all/disease_xp_fma/disease_xp_fma.tbl" md5="e1dc7ed7143d20c0cb31c63c9f503515" timestamp="1261005343" time_generated="1263791717" time_taken_to_generate="0" size="18181">
+ </export>
+ <export format="prolog" path="obo-all/disease_xp_fma/disease_xp_fma.pro" md5="6d2ee537f895b17f7ffa072335fdf923" timestamp="1263425650" time_generated="1263791717" time_taken_to_generate="0" size="174312">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/disease_xp_fma/disease_xp_fma.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1261005347" time_generated="1263791720" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" problem="true">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" path="obo-all/disease_xp_fma/disease_xp_fma.imports.obo" md5="7d9606d0a230aa9970de08021b6e21af" timestamp="1261005348" time_generated="1263791721" time_taken_to_generate="0" size="529">
+ </export>
+ <export format="obo.html" path="obo-all/disease_xp_fma/disease_xp_fma.obo.html" md5="f39dc4e91910470d585c1517f5db683c" timestamp="1261005348" time_generated="1263791721" time_taken_to_generate="0" size="1197471">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" path="obo-all/disease_xp_fma/disease_xp_fma.imports.owl" md5="861811fb1e8bc2952ff555a676e8bfa4" timestamp="1261005348" time_generated="1263791721" time_taken_to_generate="0" size="900">
+ </export>
+ <export format="imports-local.obo" path="obo-all/disease_xp_fma/disease_xp_fma.imports-local.obo" md5="50c3a76a04531a16a4310ab1f34730d1" timestamp="1261005348" time_generated="1263791721" time_taken_to_generate="0" size="454">
+ </export>
+ <export format="xp.html" path="obo-all/disease_xp_fma/disease_xp_fma.xp.html" md5="0c59a999bae1abeaac4eb7a200f153c0" timestamp="1261005500" time_generated="1263791721" time_taken_to_generate="0" size="6100014">
+ </export>
+ <export format="imports-local.owl" path="obo-all/disease_xp_fma/disease_xp_fma.imports-local.owl" md5="51e0589baa8b4e85e99d572e0b54e1a1" timestamp="1261005501" time_generated="1263791721" time_taken_to_generate="0" size="4653">
+ </export>
+ <export format="owl-classified-by-pellet2" path="obo-all/disease_xp_fma/disease_xp_fma.owl-classified-by-pellet2" md5="52717f0d8a59cafe9964a1ad9545e2eb" timestamp="1261005502" time_generated="1263791721" time_taken_to_generate="0" size="3754">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="worm_phenotype_xp">
+ <source></source>
+ <status>Draft</status>
+ <contact>OBO phenotype group obo-phenotype lists.sourceforge.net</contact>
+ <foundry>NA</foundry>
+ <documentation>http://www.bioontology.org/wiki/index.php/PATO:Pre_vs_Post_Coordinating</documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/worm_phenotype_xp.obo</url>
+ <home>http://wiki.geneontology.org/index.php/Obol</home>
+ <extends>worm_phenotype</extends>
+ <namespace>WP_XP</namespace>
+ <description>worm_phenotype is an ontology of pre-composed phenotype terms for C elegans. This mapping decomposes these phenotypes into constituent terms using PATO. This mapping is at the alpha stage - it has not yet been approved by WP curators</description>
+ <uses>quality</uses>
+ <uses>ro_proposed</uses>
+ <uses>relationship</uses>
+ <uses>worm_anatomy</uses>
+ <uses>worm_development</uses>
+ <uses>chebi</uses>
+ <uses>cell</uses>
+ <uses>biological_process</uses>
+ <uses>cellular_component</uses>
+ <filename>worm_phenotype_xp.obo</filename>
+ <format>obo</format>
+ <title>worm_phenotype logical definitions</title>
+ <type>logical_definitions</type>
+ <download>worm_phenotype_xp.obo|http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/worm_phenotype_xp.obo</download>
+ <export format="obo_xml" path="obo-all/worm_phenotype_xp/worm_phenotype_xp.obo_xml" md5="8c0046d5b69416e35465cbdfcae0d3e4" timestamp="1261006504" time_generated="1263793470" time_taken_to_generate="0" size="306331">
+ </export>
+ <export format="obo" path="obo-all/worm_phenotype_xp/worm_phenotype_xp.obo" md5="a85a141051f47ffe030587f72197de8f" timestamp="1263793470" time_generated="1263793470" time_taken_to_generate="0" size="193565">
+ </export>
+ <export format="owl" path="obo-all/worm_phenotype_xp/worm_phenotype_xp.owl" md5="a3aff96e1d8ef1faa74ef76c7c079e85" timestamp="1261006513" time_generated="1263793470" time_taken_to_generate="0" size="803980">
+ </export>
+ <export format="chadoxml" path="obo-all/worm_phenotype_xp/worm_phenotype_xp.chadoxml" md5="eed5170893acde25ce3e8154c760c21e" timestamp="1261006515" time_generated="1263793470" time_taken_to_generate="0" size="284946">
+ </export>
+ <export format="godb_prestore" path="obo-all/worm_phenotype_xp/worm_phenotype_xp.godb_prestore" md5="ab48fe4b530abeee636d9123dd0d2439" timestamp="1261006516" time_generated="1263793470" time_taken_to_generate="0" size="864837">
+ </export>
+ <export format="rdf" path="obo-all/worm_phenotype_xp/worm_phenotype_xp.rdf" md5="3ace648b22e5f171c4c82c2a80ba8a77" timestamp="1261006517" time_generated="1263793470" time_taken_to_generate="0" size="183519">
+ </export>
+ <export format="tbl" path="obo-all/worm_phenotype_xp/worm_phenotype_xp.tbl" md5="a4b5b4c6430a85cbd399acbbf161f548" timestamp="1261006518" time_generated="1263793470" time_taken_to_generate="0" size="20723">
+ </export>
+ <export format="prolog" path="obo-all/worm_phenotype_xp/worm_phenotype_xp.pro" md5="dd07abdc0cb971246b0f5733d29c77d3" timestamp="1261006520" time_generated="1263793470" time_taken_to_generate="0" size="179626">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/worm_phenotype_xp/worm_phenotype_xp.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1261006522" time_generated="1263793472" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" problem="true">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" path="obo-all/worm_phenotype_xp/worm_phenotype_xp.imports.obo" md5="4c4085b8e0564a409a117387b8350033" timestamp="1261006522" time_generated="1263793473" time_taken_to_generate="0" size="1009">
+ </export>
+ <export format="obo.html" path="obo-all/worm_phenotype_xp/worm_phenotype_xp.obo.html" md5="c2b9ae89ce9f4a88f0e53dc819c24453" timestamp="1261006523" time_generated="1263793473" time_taken_to_generate="0" size="882632">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" path="obo-all/worm_phenotype_xp/worm_phenotype_xp.imports.owl" md5="38a57fd82983890e3dc6d4d2f38f2807" timestamp="1261006523" time_generated="1263793473" time_taken_to_generate="0" size="1616">
+ </export>
+ <export format="imports-local.obo" path="obo-all/worm_phenotype_xp/worm_phenotype_xp.imports-local.obo" md5="3a91e9e6df879e8dd4bb44664552e8f6" timestamp="1261006523" time_generated="1263793473" time_taken_to_generate="0" size="844">
+ </export>
+ <export format="xp.html" path="obo-all/worm_phenotype_xp/worm_phenotype_xp.xp.html" md5="cb81bd426e4f3fab4ef84571274f04de" timestamp="1261006550" time_generated="1263793473" time_taken_to_generate="0" size="3795309">
+ </export>
+ <export format="imports-local.owl" path="obo-all/worm_phenotype_xp/worm_phenotype_xp.imports-local.owl" md5="5940699ea85f940ab0d53999fbadfff3" timestamp="1261006550" time_generated="1263793473" time_taken_to_generate="0" size="5669">
+ </export>
+ <export format="owl-classified-by-pellet2" path="obo-all/worm_phenotype_xp/worm_phenotype_xp.owl-classified-by-pellet2" md5="7ca1117e292cfe9fb2a4b853a178e081" timestamp="1261006564" time_generated="1263793473" time_taken_to_generate="0" size="3766">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" path="obo-all/worm_phenotype_xp/worm_phenotype_xp.abduced-links.txt" md5="39adc1e691bf9285a7a601c7fa5142e4" timestamp="1261006569" time_generated="1263793473" time_taken_to_generate="0" size="53828">
+ </export>
+ </ont>
+ <ont id="worm_phenotype_xp_relations">
+ <source></source>
+ <namespace>WP_XP_REL</namespace>
+ <status>Draft</status>
+ <contact>OBO phenotype group obo-phenotype lists.sourceforge.net</contact>
+ <description>Relations used in worm_phenotype_xp_* mappings</description>
+ <foundry>NA</foundry>
+ <format>obo</format>
+ <filename>worm_phenotype_xp_relations.obo</filename>
+ <documentation>http://www.bioontology.org/wiki/index.php/PATO:Pre_vs_Post_Coordinating</documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/worm_phenotype_xp/worm_phenotype_xp_relations.obo</url>
+ <type>relations</type>
+ <title>relations for worm_phenotype_xp</title>
+ <home>http://wiki.geneontology.org/index.php/Obol</home>
+ <download>worm_phenotype_xp_relations.obo|http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/worm_phenotype_xp/worm_phenotype_xp_relations.obo</download>
+ <export format="obo_xml" path="obo-all/worm_phenotype_xp_relations/worm_phenotype_xp_relations.obo_xml" md5="419119febbeefd496f69bedd326fca7a" timestamp="1261006569" time_generated="1263793476" time_taken_to_generate="0" size="1511">
+ </export>
+ <export format="obo" path="obo-all/worm_phenotype_xp_relations/worm_phenotype_xp_relations.obo" md5="3790ec5e8074d7b3719eec972579adf5" timestamp="1263793476" time_generated="1263793476" time_taken_to_generate="0" size="794">
+ </export>
+ <export format="owl" path="obo-all/worm_phenotype_xp_relations/worm_phenotype_xp_relations.owl" md5="5e58be504b1e187e51703025a0bcbafc" timestamp="1261006570" time_generated="1263793476" time_taken_to_generate="0" size="5397">
+ </export>
+ <export format="chadoxml" path="obo-all/worm_phenotype_xp_relations/worm_phenotype_xp_relations.chadoxml" md5="73e6f5ea50a97b6e9881795015deb8a2" timestamp="1261006570" time_generated="1263793476" time_taken_to_generate="0" size="4272">
+ </export>
+ <export format="godb_prestore" path="obo-all/worm_phenotype_xp_relations/worm_phenotype_xp_relations.godb_prestore" md5="c12e519474b421eaf68261497d7d92bb" timestamp="1261006570" time_generated="1263793476" time_taken_to_generate="0" size="5478">
+ </export>
+ <export format="rdf" path="obo-all/worm_phenotype_xp_relations/worm_phenotype_xp_relations.rdf" md5="2bda2e94e599b077467125e979d8d782" timestamp="1261006570" time_generated="1263793476" time_taken_to_generate="0" size="1963">
+ </export>
+ <export format="tbl" problem="true">
+ </export>
+ <export format="prolog" path="obo-all/worm_phenotype_xp_relations/worm_phenotype_xp_relations.pro" md5="380c1477cd418136f9f8be948374f96c" timestamp="1263427437" time_generated="1263793476" time_taken_to_generate="0" size="1291">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/worm_phenotype_xp_relations/worm_phenotype_xp_relations.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1261006571" time_generated="1263793476" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" problem="true">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/worm_phenotype_xp_relations/worm_phenotype_xp_relations.obo.html" md5="8cb2862be1292b094d5b81ae45554c3d" timestamp="1261006572" time_generated="1263793477" time_taken_to_generate="0" size="3948">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="worm_phenotype_xp_anatomy">
+ <source></source>
+ <status>Draft</status>
+ <contact>OBO phenotype group obo-phenotype lists.sourceforge.net</contact>
+ <foundry>NA</foundry>
+ <documentation>http://www.bioontology.org/wiki/index.php/PATO:Pre_vs_Post_Coordinating</documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/worm_phenotype_xp/worm_phenotype_xp_anatomy.obo</url>
+ <home>http://wiki.geneontology.org/index.php/Obol</home>
+ <extends>worm_phenotype</extends>
+ <namespace>WP_XP_WBbt</namespace>
+ <description>Logical definitions for WBP terms that reference WBbt, but *not* any other ontology (bar PATO and WBP itself)</description>
+ <uses>quality</uses>
+ <uses>worm_phenotype_xp_relations</uses>
+ <uses>worm_anatomy</uses>
+ <filename>worm_phenotype_xp_anatomy.obo</filename>
+ <format>obo</format>
+ <title>worm_phenotype x anatomy logical definitions </title>
+ <type>logical_definitions</type>
+ <download>worm_phenotype_xp_anatomy.obo|http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/worm_phenotype_xp/worm_phenotype_xp_anatomy.obo</download>
+ <export format="obo_xml" path="obo-all/worm_phenotype_xp_anatomy/worm_phenotype_xp_anatomy.obo_xml" md5="b8dce0d89d5d71fbc0710de37b972057" timestamp="1261006573" time_generated="1263793481" time_taken_to_generate="0" size="64063">
+ </export>
+ <export format="obo" path="obo-all/worm_phenotype_xp_anatomy/worm_phenotype_xp_anatomy.obo" md5="2e4cad2bcde08fa95205170270ea7762" timestamp="1263793481" time_generated="1263793481" time_taken_to_generate="0" size="40103">
+ </export>
+ <export format="owl" path="obo-all/worm_phenotype_xp_anatomy/worm_phenotype_xp_anatomy.owl" md5="a3a66af3b4801b307697897e43ebc02c" timestamp="1261006574" time_generated="1263793481" time_taken_to_generate="0" size="165596">
+ </export>
+ <export format="chadoxml" path="obo-all/worm_phenotype_xp_anatomy/worm_phenotype_xp_anatomy.chadoxml" md5="f1beafc044aa75c185030e144b890e75" timestamp="1261006574" time_generated="1263793481" time_taken_to_generate="0" size="75341">
+ </export>
+ <export format="godb_prestore" path="obo-all/worm_phenotype_xp_anatomy/worm_phenotype_xp_anatomy.godb_prestore" md5="cfd84b3c6d649e840b1367927f8dff89" timestamp="1261006575" time_generated="1263793481" time_taken_to_generate="0" size="177022">
+ </export>
+ <export format="rdf" path="obo-all/worm_phenotype_xp_anatomy/worm_phenotype_xp_anatomy.rdf" md5="0d6032d55dc288024cdcaa78ebd64c01" timestamp="1261006575" time_generated="1263793481" time_taken_to_generate="0" size="47200">
+ </export>
+ <export format="tbl" path="obo-all/worm_phenotype_xp_anatomy/worm_phenotype_xp_anatomy.tbl" md5="d266719691e88b0eb9dbef01e4b9d24f" timestamp="1261006575" time_generated="1263793481" time_taken_to_generate="0" size="5364">
+ </export>
+ <export format="prolog" path="obo-all/worm_phenotype_xp_anatomy/worm_phenotype_xp_anatomy.pro" md5="564ef42525be7aa1444b9d8ce862dab7" timestamp="1261006576" time_generated="1263793481" time_taken_to_generate="0" size="36383">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/worm_phenotype_xp_anatomy/worm_phenotype_xp_anatomy.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1261006577" time_generated="1263793482" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" problem="true">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" path="obo-all/worm_phenotype_xp_anatomy/worm_phenotype_xp_anatomy.imports.obo" md5="e2f366e802e28c960cf0f7ebee3679a8" timestamp="1261006577" time_generated="1263793482" time_taken_to_generate="0" size="612">
+ </export>
+ <export format="obo.html" path="obo-all/worm_phenotype_xp_anatomy/worm_phenotype_xp_anatomy.obo.html" md5="b45ab2e285f5a2fbf2e22671b6e8692c" timestamp="1261006577" time_generated="1263793482" time_taken_to_generate="0" size="191832">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" path="obo-all/worm_phenotype_xp_anatomy/worm_phenotype_xp_anatomy.imports.owl" md5="f1f777a85e0cb456671e313d51e1c652" timestamp="1261006578" time_generated="1263793482" time_taken_to_generate="0" size="948">
+ </export>
+ <export format="imports-local.obo" path="obo-all/worm_phenotype_xp_anatomy/worm_phenotype_xp_anatomy.imports-local.obo" md5="313c19a5ca23b3920cf992b677a24abd" timestamp="1261006578" time_generated="1263793482" time_taken_to_generate="0" size="537">
+ </export>
+ <export format="xp.html" path="obo-all/worm_phenotype_xp_anatomy/worm_phenotype_xp_anatomy.xp.html" md5="edacf4d00aeff3d2f7d37865b4e02c2c" timestamp="1261006579" time_generated="1263793482" time_taken_to_generate="0" size="720001">
+ </export>
+ <export format="imports-local.owl" path="obo-all/worm_phenotype_xp_anatomy/worm_phenotype_xp_anatomy.imports-local.owl" md5="e41d39d99194e34a80fe0407ef835929" timestamp="1261006579" time_generated="1263793482" time_taken_to_generate="0" size="4806">
+ </export>
+ <export format="owl-classified-by-pellet2" path="obo-all/worm_phenotype_xp_anatomy/worm_phenotype_xp_anatomy.owl-classified-by-pellet2" md5="56540498e1bf6af788e3ebb66d47d253" timestamp="1261006716" time_generated="1263793482" time_taken_to_generate="0" size="1426">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" path="obo-all/worm_phenotype_xp_anatomy/worm_phenotype_xp_anatomy.abduced-links.txt" md5="a453c15c9f903a9495c52995be382999" timestamp="1261006720" time_generated="1263793482" time_taken_to_generate="0" size="11012">
+ </export>
+ </ont>
+ <ont id="worm_phenotype_xp_anatomy_and_stages">
+ <source></source>
+ <status>Draft</status>
+ <contact>OBO phenotype group obo-phenotype lists.sourceforge.net</contact>
+ <foundry>NA</foundry>
+ <documentation>http://www.bioontology.org/wiki/index.php/PATO:Pre_vs_Post_Coordinating</documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/worm_phenotype_xp/worm_phenotype_xp_anatomy_and_stages.obo</url>
+ <home>http://wiki.geneontology.org/index.php/Obol</home>
+ <extends>worm_phenotype</extends>
+ <namespace>WP_XP_WBbt_WBls</namespace>
+ <description>Logical definitions for WBP terms that reference *both* WBbt and WBls, but *not* any other ontology (bar PATO and WBP itself)</description>
+ <uses>quality</uses>
+ <uses>worm_phenotype_xp_relations</uses>
+ <uses>worm_anatomy</uses>
+ <uses>worm_development</uses>
+ <filename>worm_phenotype_xp_anatomy_and_stages.obo</filename>
+ <format>obo</format>
+ <title>worm_phenotype x anatomy/stages logical definitions </title>
+ <type>logical_definitions</type>
+ <download>worm_phenotype_xp_anatomy_and_stages.obo|http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/worm_phenotype_xp/worm_phenotype_xp_anatomy_and_stages.obo</download>
+ <export format="obo_xml" path="obo-all/worm_phenotype_xp_anatomy_and_stages/worm_phenotype_xp_anatomy_and_stages.obo_xml" md5="54c22231dae3b6601c3e44689f632052" timestamp="1261006721" time_generated="1263793484" time_taken_to_generate="0" size="20552">
+ </export>
+ <export format="obo" path="obo-all/worm_phenotype_xp_anatomy_and_stages/worm_phenotype_xp_anatomy_and_stages.obo" md5="8a2282348091e10e330bb69d858b20a7" timestamp="1263793484" time_generated="1263793484" time_taken_to_generate="0" size="11592">
+ </export>
+ <export format="owl" path="obo-all/worm_phenotype_xp_anatomy_and_stages/worm_phenotype_xp_anatomy_and_stages.owl" md5="7bd6806ad2540e2f63d18905537d96e2" timestamp="1261006721" time_generated="1263793484" time_taken_to_generate="0" size="56335">
+ </export>
+ <export format="chadoxml" path="obo-all/worm_phenotype_xp_anatomy_and_stages/worm_phenotype_xp_anatomy_and_stages.chadoxml" md5="f54cd7923992e01665ce87d91fc4df72" timestamp="1261006721" time_generated="1263793484" time_taken_to_generate="0" size="18637">
+ </export>
+ <export format="godb_prestore" path="obo-all/worm_phenotype_xp_anatomy_and_stages/worm_phenotype_xp_anatomy_and_stages.godb_prestore" md5="e9cda3463dc9a6bbfff0bd1ead70f540" timestamp="1261006721" time_generated="1263793484" time_taken_to_generate="0" size="58855">
+ </export>
+ <export format="rdf" path="obo-all/worm_phenotype_xp_anatomy_and_stages/worm_phenotype_xp_anatomy_and_stages.rdf" md5="330f92d976666706c9009001918ca618" timestamp="1261006722" time_generated="1263793484" time_taken_to_generate="0" size="10536">
+ </export>
+ <export format="tbl" path="obo-all/worm_phenotype_xp_anatomy_and_stages/worm_phenotype_xp_anatomy_and_stages.tbl" md5="0c4ecd10ec8167cbdae7c43e6134b48c" timestamp="1261006722" time_generated="1263793484" time_taken_to_generate="0" size="1165">
+ </export>
+ <export format="prolog" path="obo-all/worm_phenotype_xp_anatomy_and_stages/worm_phenotype_xp_anatomy_and_stages.pro" md5="d3e456bbde45ff756e785b8448fb324d" timestamp="1261006722" time_generated="1263793484" time_taken_to_generate="0" size="11934">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/worm_phenotype_xp_anatomy_and_stages/worm_phenotype_xp_anatomy_and_stages.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1261006723" time_generated="1263793484" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" problem="true">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" path="obo-all/worm_phenotype_xp_anatomy_and_stages/worm_phenotype_xp_anatomy_and_stages.imports.obo" md5="4ece894920f2eb925d5df92685e7d271" timestamp="1261006723" time_generated="1263793484" time_taken_to_generate="0" size="747">
+ </export>
+ <export format="obo.html" path="obo-all/worm_phenotype_xp_anatomy_and_stages/worm_phenotype_xp_anatomy_and_stages.obo.html" md5="2eb0429ee7b2e3951cb24d82274cf08b" timestamp="1261006724" time_generated="1263793484" time_taken_to_generate="0" size="54869">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" path="obo-all/worm_phenotype_xp_anatomy_and_stages/worm_phenotype_xp_anatomy_and_stages.imports.owl" md5="6c3fb273796c0c3d0de8f704cee7d8a0" timestamp="1261006724" time_generated="1263793485" time_taken_to_generate="0" size="1097">
+ </export>
+ <export format="imports-local.obo" path="obo-all/worm_phenotype_xp_anatomy_and_stages/worm_phenotype_xp_anatomy_and_stages.imports-local.obo" md5="92a6f26bb5fa226575e4ed85292c4f9d" timestamp="1261006724" time_generated="1263793485" time_taken_to_generate="0" size="657">
+ </export>
+ <export format="xp.html" path="obo-all/worm_phenotype_xp_anatomy_and_stages/worm_phenotype_xp_anatomy_and_stages.xp.html" md5="2ec79c45ed741739259b9f39b0e315c2" timestamp="1261006725" time_generated="1263793485" time_taken_to_generate="0" size="209508">
+ </export>
+ <export format="imports-local.owl" path="obo-all/worm_phenotype_xp_anatomy_and_stages/worm_phenotype_xp_anatomy_and_stages.imports-local.owl" md5="591d46624ed6a090865fda675a2f2669" timestamp="1261006725" time_generated="1263793485" time_taken_to_generate="0" size="5081">
+ </export>
+ <export format="owl-classified-by-pellet2" path="obo-all/worm_phenotype_xp_anatomy_and_stages/worm_phenotype_xp_anatomy_and_stages.owl-classified-by-pellet2" md5="fa41011c3cf93da322c2c3cd815008d8" timestamp="1261006862" time_generated="1263793485" time_taken_to_generate="0" size="1480">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" path="obo-all/worm_phenotype_xp_anatomy_and_stages/worm_phenotype_xp_anatomy_and_stages.abduced-links.txt" md5="1550139d0bdf44d004fe22e93432c6c9" timestamp="1261006866" time_generated="1263793485" time_taken_to_generate="0" size="1673">
+ </export>
+ </ont>
+ <ont id="worm_phenotype_xp_go">
+ <source></source>
+ <status>Draft</status>
+ <contact>OBO phenotype group obo-phenotype lists.sourceforge.net</contact>
+ <foundry>NA</foundry>
+ <documentation>http://www.bioontology.org/wiki/index.php/PATO:Pre_vs_Post_Coordinating</documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/worm_phenotype_xp/worm_phenotype_xp_go.obo</url>
+ <home>http://wiki.geneontology.org/index.php/Obol</home>
+ <extends>worm_phenotype</extends>
+ <namespace>WP_XP_GO</namespace>
+ <description>Logical definitions for WBP terms that reference GO, but *not* any other ontology (bar PATO and WBP itself)</description>
+ <uses>quality</uses>
+ <uses>worm_phenotype_xp_relations</uses>
+ <uses>biological_process</uses>
+ <uses>cellular_component</uses>
+ <uses>molecular_function</uses>
+ <filename>worm_phenotype_xp_go.obo</filename>
+ <format>obo</format>
+ <title>worm_phenotype x GO logical definitions</title>
+ <type>logical_definitions</type>
+ <download>worm_phenotype_xp_go.obo|http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/worm_phenotype_xp/worm_phenotype_xp_go.obo</download>
+ <export format="obo_xml" path="obo-all/worm_phenotype_xp_go/worm_phenotype_xp_go.obo_xml" md5="42068f98c1264154b89a5dfcbb33477f" timestamp="1261006866" time_generated="1263793487" time_taken_to_generate="0" size="98142">
+ </export>
+ <export format="obo" path="obo-all/worm_phenotype_xp_go/worm_phenotype_xp_go.obo" md5="e66a965ca1e05fabea4113ac74a71b8a" timestamp="1263793487" time_generated="1263793487" time_taken_to_generate="0" size="64857">
+ </export>
+ <export format="owl" path="obo-all/worm_phenotype_xp_go/worm_phenotype_xp_go.owl" md5="24b512dd851ca1eb0a241634f21a7862" timestamp="1261006868" time_generated="1263793487" time_taken_to_generate="0" size="252305">
+ </export>
+ <export format="chadoxml" path="obo-all/worm_phenotype_xp_go/worm_phenotype_xp_go.chadoxml" md5="8a7485ce5f8eda815324e8b960010528" timestamp="1261006868" time_generated="1263793487" time_taken_to_generate="0" size="116354">
+ </export>
+ <export format="godb_prestore" path="obo-all/worm_phenotype_xp_go/worm_phenotype_xp_go.godb_prestore" md5="1269da7efcd159b18e1439f36bc0e424" timestamp="1261006869" time_generated="1263793487" time_taken_to_generate="0" size="271505">
+ </export>
+ <export format="rdf" path="obo-all/worm_phenotype_xp_go/worm_phenotype_xp_go.rdf" md5="d8740d9156ac8cd81d085622c9aa80a3" timestamp="1261006869" time_generated="1263793487" time_taken_to_generate="0" size="74031">
+ </export>
+ <export format="tbl" path="obo-all/worm_phenotype_xp_go/worm_phenotype_xp_go.tbl" md5="ad897d73a3abd4da1f3df4c32c535591" timestamp="1261006870" time_generated="1263793487" time_taken_to_generate="0" size="8424">
+ </export>
+ <export format="prolog" path="obo-all/worm_phenotype_xp_go/worm_phenotype_xp_go.pro" md5="2e1ea2d41e2ec770363b68f7f3e4016d" timestamp="1261006870" time_generated="1263793487" time_taken_to_generate="0" size="55522">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/worm_phenotype_xp_go/worm_phenotype_xp_go.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1261006871" time_generated="1263793488" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" problem="true">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" path="obo-all/worm_phenotype_xp_go/worm_phenotype_xp_go.imports.obo" md5="a3fe06a4a735892be1b22ec4d561bd94" timestamp="1261006872" time_generated="1263793488" time_taken_to_generate="0" size="804">
+ </export>
+ <export format="obo.html" path="obo-all/worm_phenotype_xp_go/worm_phenotype_xp_go.obo.html" md5="6930c2d04e321c096ba6caacb146ce17" timestamp="1261006872" time_generated="1263793488" time_taken_to_generate="0" size="298326">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" path="obo-all/worm_phenotype_xp_go/worm_phenotype_xp_go.imports.owl" md5="beb0b72c02c54d07cc8f9c7bf83a3795" timestamp="1261006872" time_generated="1263793488" time_taken_to_generate="0" size="1212">
+ </export>
+ <export format="imports-local.obo" path="obo-all/worm_phenotype_xp_go/worm_phenotype_xp_go.imports-local.obo" md5="d805c3615996c527396bc5c6b217d05a" timestamp="1261006872" time_generated="1263793488" time_taken_to_generate="0" size="699">
+ </export>
+ <export format="xp.html" path="obo-all/worm_phenotype_xp_go/worm_phenotype_xp_go.xp.html" md5="8c502da7fcbd743827cc9a4c5a02d663" timestamp="1261006875" time_generated="1263793488" time_taken_to_generate="0" size="1220224">
+ </export>
+ <export format="imports-local.owl" path="obo-all/worm_phenotype_xp_go/worm_phenotype_xp_go.imports-local.owl" md5="5342af77018c888274c195e946d571c0" timestamp="1261006875" time_generated="1263793488" time_taken_to_generate="0" size="5190">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" path="obo-all/worm_phenotype_xp_go/worm_phenotype_xp_go.abduced-links.txt" md5="6504534765f7075ed7e26250aef79947" timestamp="1261007215" time_generated="1263793954" time_taken_to_generate="0" size="12208">
+ </export>
+ </ont>
+ <ont id="worm_phenotype_xp_chebi">
+ <source></source>
+ <status>Draft</status>
+ <contact>OBO phenotype group obo-phenotype lists.sourceforge.net</contact>
+ <foundry>NA</foundry>
+ <documentation>http://www.bioontology.org/wiki/index.php/PATO:Pre_vs_Post_Coordinating</documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/worm_phenotype_xp/worm_phenotype_xp_chebi.obo</url>
+ <home>http://wiki.geneontology.org/index.php/Obol</home>
+ <extends>worm_phenotype</extends>
+ <namespace>WP_XP_CHEBI</namespace>
+ <description>Logical definitions for WBP terms that reference CHEBI, but *not* any other ontology (bar PATO and WBP itself)</description>
+ <uses>quality</uses>
+ <uses>worm_phenotype_xp_relations</uses>
+ <uses>chebi</uses>
+ <filename>worm_phenotype_xp_chebi.obo</filename>
+ <format>obo</format>
+ <title>worm_phenotype x CHEBI logical definitions</title>
+ <type>logical_definitions</type>
+ <download>worm_phenotype_xp_chebi.obo|http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/worm_phenotype_xp/worm_phenotype_xp_chebi.obo</download>
+ <export format="obo_xml" path="obo-all/worm_phenotype_xp_chebi/worm_phenotype_xp_chebi.obo_xml" md5="87e166eb71f371e9243934fb804d3638" timestamp="1261007215" time_generated="1263793955" time_taken_to_generate="0" size="13314">
+ </export>
+ <export format="obo" path="obo-all/worm_phenotype_xp_chebi/worm_phenotype_xp_chebi.obo" md5="8df3ce9428afd2ee0e5f0e0216b9afca" timestamp="1263793955" time_generated="1263793955" time_taken_to_generate="0" size="8014">
+ </export>
+ <export format="owl" path="obo-all/worm_phenotype_xp_chebi/worm_phenotype_xp_chebi.owl" md5="16a3208c7737e29b0f6a210bb02fcd26" timestamp="1261007216" time_generated="1263793955" time_taken_to_generate="0" size="36693">
+ </export>
+ <export format="chadoxml" path="obo-all/worm_phenotype_xp_chebi/worm_phenotype_xp_chebi.chadoxml" md5="6456350021e7ca4f7214c0d8b9965da2" timestamp="1261007216" time_generated="1263793955" time_taken_to_generate="0" size="15157">
+ </export>
+ <export format="godb_prestore" path="obo-all/worm_phenotype_xp_chebi/worm_phenotype_xp_chebi.godb_prestore" md5="d343d7c1f18682fbd832c540e1593b30" timestamp="1261007216" time_generated="1263793955" time_taken_to_generate="0" size="37854">
+ </export>
+ <export format="rdf" path="obo-all/worm_phenotype_xp_chebi/worm_phenotype_xp_chebi.rdf" md5="5c04dd3b83783c0f44c25b44a6321486" timestamp="1261007216" time_generated="1263793955" time_taken_to_generate="0" size="8608">
+ </export>
+ <export format="tbl" path="obo-all/worm_phenotype_xp_chebi/worm_phenotype_xp_chebi.tbl" md5="4910ada44df428b051db57218c3c0976" timestamp="1261007216" time_generated="1263793955" time_taken_to_generate="0" size="946">
+ </export>
+ <export format="prolog" path="obo-all/worm_phenotype_xp_chebi/worm_phenotype_xp_chebi.pro" md5="71fa9fd33385a9abbccd6059f2c9ab88" timestamp="1263427443" time_generated="1263793955" time_taken_to_generate="0" size="7488">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/worm_phenotype_xp_chebi/worm_phenotype_xp_chebi.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1261007217" time_generated="1263793956" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" problem="true">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" path="obo-all/worm_phenotype_xp_chebi/worm_phenotype_xp_chebi.imports.obo" md5="8f42b4f8bca87d5a531cef24be77705b" timestamp="1261007218" time_generated="1263793957" time_taken_to_generate="0" size="583">
+ </export>
+ <export format="obo.html" path="obo-all/worm_phenotype_xp_chebi/worm_phenotype_xp_chebi.obo.html" md5="0a256e7ee74e524a314d9e5054def273" timestamp="1261007218" time_generated="1263793957" time_taken_to_generate="0" size="37640">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" path="obo-all/worm_phenotype_xp_chebi/worm_phenotype_xp_chebi.imports.owl" md5="ac70d1c0c3c556633c238c20fb9bbd63" timestamp="1261007218" time_generated="1263793957" time_taken_to_generate="0" size="930">
+ </export>
+ <export format="imports-local.obo" path="obo-all/worm_phenotype_xp_chebi/worm_phenotype_xp_chebi.imports-local.obo" md5="7171085c1b51882b3fe8b1d44ec9036b" timestamp="1261007218" time_generated="1263793957" time_taken_to_generate="0" size="508">
+ </export>
+ <export format="xp.html" path="obo-all/worm_phenotype_xp_chebi/worm_phenotype_xp_chebi.xp.html" md5="0f8861a2440fdc06af4abac4905cc453" timestamp="1261007220" time_generated="1263793957" time_taken_to_generate="0" size="187810">
+ </export>
+ <export format="imports-local.owl" path="obo-all/worm_phenotype_xp_chebi/worm_phenotype_xp_chebi.imports-local.owl" md5="21531a518b71140cdfe340c9daf0d838" timestamp="1261007220" time_generated="1263793957" time_taken_to_generate="0" size="4755">
+ </export>
+ <export format="owl-classified-by-pellet2" path="obo-all/worm_phenotype_xp_chebi/worm_phenotype_xp_chebi.owl-classified-by-pellet2" md5="49f5682c589bd75b500413b7ac26be87" timestamp="1261007225" time_generated="1263793957" time_taken_to_generate="0" size="3802">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="worm_phenotype_xp_go_chebi">
+ <source></source>
+ <status>Draft</status>
+ <contact>OBO phenotype group obo-phenotype lists.sourceforge.net</contact>
+ <foundry>NA</foundry>
+ <documentation>http://www.bioontology.org/wiki/index.php/PATO:Pre_vs_Post_Coordinating</documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/worm_phenotype_xp/worm_phenotype_xp_go_chebi.obo</url>
+ <home>http://wiki.geneontology.org/index.php/Obol</home>
+ <extends>worm_phenotype</extends>
+ <namespace>WP_XP_GO_CHEBI</namespace>
+ <description>Logical definitions for WBP terms that reference *both* GO and CHEBI, but *not* any other ontology (bar PATO and WBP itself)</description>
+ <uses>quality</uses>
+ <uses>worm_phenotype_xp_relations</uses>
+ <uses>chebi</uses>
+ <uses>biological_process</uses>
+ <uses>cellular_component</uses>
+ <uses>molecular_function</uses>
+ <filename>worm_phenotype_xp_go_chebi.obo</filename>
+ <format>obo</format>
+ <title>worm_phenotype x GO+CHEBI logical definitions</title>
+ <type>logical_definitions</type>
+ <download>worm_phenotype_xp_go_chebi.obo|http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/worm_phenotype_xp/worm_phenotype_xp_go_chebi.obo</download>
+ <export format="obo_xml" path="obo-all/worm_phenotype_xp_go_chebi/worm_phenotype_xp_go_chebi.obo_xml" md5="b72238e270348aba1bbd0805e7161ff2" timestamp="1261007229" time_generated="1263793976" time_taken_to_generate="0" size="33288">
+ </export>
+ <export format="obo" path="obo-all/worm_phenotype_xp_go_chebi/worm_phenotype_xp_go_chebi.obo" md5="482873586c09c0c1f73e17a51dfe6789" timestamp="1263793976" time_generated="1263793976" time_taken_to_generate="0" size="20983">
+ </export>
+ <export format="owl" path="obo-all/worm_phenotype_xp_go_chebi/worm_phenotype_xp_go_chebi.owl" md5="ddfcce9aee2eecdd2087afb94cd699a0" timestamp="1261007229" time_generated="1263793976" time_taken_to_generate="0" size="89813">
+ </export>
+ <export format="chadoxml" path="obo-all/worm_phenotype_xp_go_chebi/worm_phenotype_xp_go_chebi.chadoxml" md5="943e74e8490d31c3f4ec0862870d137a" timestamp="1261007229" time_generated="1263793976" time_taken_to_generate="0" size="29733">
+ </export>
+ <export format="godb_prestore" path="obo-all/worm_phenotype_xp_go_chebi/worm_phenotype_xp_go_chebi.godb_prestore" md5="43ef7d3fa55a6c512b19b3ffc11d0ee8" timestamp="1261007229" time_generated="1263793976" time_taken_to_generate="0" size="94865">
+ </export>
+ <export format="rdf" path="obo-all/worm_phenotype_xp_go_chebi/worm_phenotype_xp_go_chebi.rdf" md5="807883e52d71a396904730dbaa194620" timestamp="1261007230" time_generated="1263793976" time_taken_to_generate="0" size="18065">
+ </export>
+ <export format="tbl" path="obo-all/worm_phenotype_xp_go_chebi/worm_phenotype_xp_go_chebi.tbl" md5="82da6f0f92b8a92d2d6754df34c30334" timestamp="1261007230" time_generated="1263793976" time_taken_to_generate="0" size="2024">
+ </export>
+ <export format="prolog" path="obo-all/worm_phenotype_xp_go_chebi/worm_phenotype_xp_go_chebi.pro" md5="6052eeff28ca1d4203541fcb3feaec6d" timestamp="1261007230" time_generated="1263793976" time_taken_to_generate="0" size="19429">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/worm_phenotype_xp_go_chebi/worm_phenotype_xp_go_chebi.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1261007231" time_generated="1263793977" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" problem="true">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" path="obo-all/worm_phenotype_xp_go_chebi/worm_phenotype_xp_go_chebi.imports.obo" md5="f5839d0c528bddd68892baaa19a03936" timestamp="1261007232" time_generated="1263793978" time_taken_to_generate="0" size="886">
+ </export>
+ <export format="obo.html" path="obo-all/worm_phenotype_xp_go_chebi/worm_phenotype_xp_go_chebi.obo.html" md5="1d667b581e0ced522e31412685daaff1" timestamp="1261007232" time_generated="1263793978" time_taken_to_generate="0" size="92530">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" path="obo-all/worm_phenotype_xp_go_chebi/worm_phenotype_xp_go_chebi.imports.owl" md5="4b6d31581a47727e56d5de9374877ded" timestamp="1261007232" time_generated="1263793978" time_taken_to_generate="0" size="1329">
+ </export>
+ <export format="imports-local.obo" path="obo-all/worm_phenotype_xp_go_chebi/worm_phenotype_xp_go_chebi.imports-local.obo" md5="5155b260b65ccb2951a38291ee399ceb" timestamp="1261007232" time_generated="1263793978" time_taken_to_generate="0" size="766">
+ </export>
+ <export format="xp.html" path="obo-all/worm_phenotype_xp_go_chebi/worm_phenotype_xp_go_chebi.xp.html" md5="29ab147441a77be443f50e89312b4c8c" timestamp="1261007235" time_generated="1263793978" time_taken_to_generate="0" size="467509">
+ </export>
+ <export format="imports-local.owl" path="obo-all/worm_phenotype_xp_go_chebi/worm_phenotype_xp_go_chebi.imports-local.owl" md5="28a952870e4a7cc973788737fe2b9bdb" timestamp="1261007235" time_generated="1263793978" time_taken_to_generate="0" size="5370">
+ </export>
+ <export format="owl-classified-by-pellet2" path="obo-all/worm_phenotype_xp_go_chebi/worm_phenotype_xp_go_chebi.owl-classified-by-pellet2" md5="99720f7c492ab6acdc53120e6fd8ff1f" timestamp="1261007240" time_generated="1263793978" time_taken_to_generate="0" size="3820">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" path="obo-all/worm_phenotype_xp_go_chebi/worm_phenotype_xp_go_chebi.abduced-links.txt" md5="5d3086393fbdf1f02cbf32a865a4a9f4" timestamp="1261007245" time_generated="1263793978" time_taken_to_generate="0" size="847">
+ </export>
+ </ont>
+ <ont id="sequence_xp">
+ <source>http://song.cvs.sourceforge.net/*checkout*/song/ontology/so-xp.obo</source>
+ <status>Implementation release</status>
+ <contact>SO developers song-devel lists.sourceforge.net</contact>
+ <foundry>NA</foundry>
+ <documentation></documentation>
+ <url>http://song.cvs.sourceforge.net/*checkout*/song/ontology/so-xp.obo</url>
+ <home>SO home|http://song.sourceforge.net/</home>
+ <extends>sequence</extends>
+ <namespace>SO_XP</namespace>
+ <description>Logical definitions (cross-products) for composite terms in SO. NOTE: these are now included in the main SO file. The so-xp file contains logical definitions WITHOUT implied links</description>
+ <uses>sequence</uses>
+ <filename>so-xp.obo</filename>
+ <format>obo</format>
+ <title>Sequence Ontology logical definitions</title>
+ <type>logical_definitions</type>
+ <download>so-xp.obo|http://song.cvs.sourceforge.net/*checkout*/song/ontology/so-xp.obo</download>
+ <export format="obo_xml" path="obo-all/sequence_xp/sequence_xp.obo_xml" md5="d883236306a05630bd6fd75b332a1ba5" timestamp="1263793985" time_generated="1263793985" time_taken_to_generate="5" size="1065003">
+ </export>
+ <export format="obo" path="obo-all/sequence_xp/sequence_xp.obo" md5="12fb773217babb6e74f22760875de8c9" timestamp="1263793980" time_generated="1263793985" time_taken_to_generate="0" size="557715">
+ </export>
+ <export format="owl" path="obo-all/sequence_xp/sequence_xp.owl" md5="e98d057c55cbefa7d6b02d25446cd043" timestamp="1263794060" time_generated="1263794060" time_taken_to_generate="75" size="2283095">
+ </export>
+ <export format="chadoxml" path="obo-all/sequence_xp/sequence_xp.chadoxml" md5="b1efe6585f9189dbda6f66d99c3f1c80" timestamp="1263794080" time_generated="1263794081" time_taken_to_generate="21" size="2790219">
+ </export>
+ <export format="godb_prestore" path="obo-all/sequence_xp/sequence_xp.godb_prestore" md5="515be843988c334f5ea84d67d9fed165" timestamp="1263794087" time_generated="1263794087" time_taken_to_generate="6" size="2394743">
+ </export>
+ <export format="rdf" path="obo-all/sequence_xp/sequence_xp.rdf" md5="0aeda69638f06e85ed218c8cd22abe55" timestamp="1263794093" time_generated="1263794093" time_taken_to_generate="6" size="987689">
+ </export>
+ <export format="tbl" path="obo-all/sequence_xp/sequence_xp.tbl" md5="18b3b0f0ea2762a2f756faef881288f9" timestamp="1263794098" time_generated="1263794098" time_taken_to_generate="5" size="273855">
+ </export>
+ <export format="prolog" path="obo-all/sequence_xp/sequence_xp.pro" md5="7a690311a705b7fbb05be9bde4ab3bd6" timestamp="1263794106" time_generated="1263794106" time_taken_to_generate="8" size="1146151">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/sequence_xp/sequence_xp.validation_report" md5="5891dc1a3b1a46646da277aacca6573c" timestamp="1263794113" time_generated="1263794113" time_taken_to_generate="3" size="1234">
+ </export>
+ <export format="stats" path="obo-all/sequence_xp/sequence_xp.stats" md5="619a62d04ddf7c62cc6ebdc743938b12" timestamp="1263794115" time_generated="1263794115" time_taken_to_generate="2" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" path="obo-all/sequence_xp/sequence_xp.imports.obo" md5="6d4e923655c79c1a58a1720de737eded" timestamp="1263794115" time_generated="1263794115" time_taken_to_generate="0" size="338">
+ </export>
+ <export format="obo.html" path="obo-all/sequence_xp/sequence_xp.obo.html" md5="bb1d35017dfdf55f323e09f6c0730863" timestamp="1263794115" time_generated="1263794115" time_taken_to_generate="0" size="2409255">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" path="obo-all/sequence_xp/sequence_xp.imports.owl" md5="034cd04233084d12d20309b5b01f199e" timestamp="1263794115" time_generated="1263794115" time_taken_to_generate="0" size="642">
+ </export>
+ <export format="imports-local.obo" path="obo-all/sequence_xp/sequence_xp.imports-local.obo" md5="3374e46afc5a6affb2849c8db50d4f38" timestamp="1263794116" time_generated="1263794116" time_taken_to_generate="1" size="293">
+ </export>
+ <export format="xp.html" path="obo-all/sequence_xp/sequence_xp.xp.html" md5="19c72042e27009153dc7066692e1be52" timestamp="1263794119" time_generated="1263794119" time_taken_to_generate="3" size="790154">
+ </export>
+ <export format="imports-local.owl" path="obo-all/sequence_xp/sequence_xp.imports-local.owl" md5="40d492c031b38551835ef47f21aacf70" timestamp="1263794119" time_generated="1263794119" time_taken_to_generate="0" size="4260">
+ </export>
+ <export format="owl-classified-by-pellet2" path="obo-all/sequence_xp/sequence_xp.owl-classified-by-pellet2" md5="03971f6dcb6553997191a1768b6f6c69" timestamp="1263794167" time_generated="1263794168" time_taken_to_generate="49" size="1354">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" path="obo-all/sequence_xp/sequence_xp.abduced-links.txt" md5="92ef68b015e3e02629242919b8e70bdf" timestamp="1263794171" time_generated="1263794171" time_taken_to_generate="2" size="517">
+ </export>
+ </ont>
+ <ont id="fly_anatomy_xp">
+ <source>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/fly/fly_anatomy_XP.obo</source>
+ <status>Implementation release</status>
+ <contact>David Osumi-Sutherland obo-anatomy lists.sourceforge.net</contact>
+ <foundry>NA</foundry>
+ <documentation></documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/fly/fly_anatomy_XP.obo</url>
+ <home>FlyBase|http://www.flybase.org/</home>
+ <extends>fly_anatomy</extends>
+ <namespace>FBbt_XP</namespace>
+ <description>Logical definitions (cross-products) for composite terms in fly_anatomy. Use of this ontology requires a reasoner. Recommended reasoners are - The OBO-Edit2 link-pile reasoner (but be careful of the redundancy calls) the OBO-Edit2 rule based reasoner, or FaCT++ via the OWL-API (e.g. within Protege4).</description>
+ <uses>fly_anatomy</uses>
+ <filename>fly_anatomy_XP.obo</filename>
+ <format>obo</format>
+ <title>Fly Anatomy Ontology, pre-reasoned version</title>
+ <type>logical_definitions</type>
+ <download>fly_anatomy_XP.obo|http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/fly/fly_anatomy_XP.obo</download>
+ <export format="obo_xml" path="obo-all/fly_anatomy_xp/fly_anatomy_xp.obo_xml" md5="c42baa85d97cb143fc3dcdc2e6faebf1" timestamp="1261007360" time_generated="1263794174" time_taken_to_generate="0" size="2591513">
+ </export>
+ <export format="obo" path="obo-all/fly_anatomy_xp/fly_anatomy_xp.obo" md5="29c8faa3ce76c2d7df57bab09d07b811" timestamp="1263794174" time_generated="1263794174" time_taken_to_generate="0" size="1473498">
+ </export>
+ <export format="owl" path="obo-all/fly_anatomy_xp/fly_anatomy_xp.owl" md5="b661cd7a635f6638966acb69b5147858" timestamp="1261007854" time_generated="1263794174" time_taken_to_generate="0" size="5806232">
+ </export>
+ <export format="chadoxml" path="obo-all/fly_anatomy_xp/fly_anatomy_xp.chadoxml" md5="91bdd05efc8fcada6711c5ecbbfe60f7" timestamp="1261007960" time_generated="1263794174" time_taken_to_generate="0" size="6209154">
+ </export>
+ <export format="godb_prestore" path="obo-all/fly_anatomy_xp/fly_anatomy_xp.godb_prestore" md5="ef7842715869de8263b7447223ae1e82" timestamp="1261007969" time_generated="1263794175" time_taken_to_generate="0" size="6909330">
+ </export>
+ <export format="rdf" path="obo-all/fly_anatomy_xp/fly_anatomy_xp.rdf" md5="5197a77c8aa726b34b66f07b3be2d2ad" timestamp="1261007981" time_generated="1263794175" time_taken_to_generate="0" size="2709309">
+ </export>
+ <export format="tbl" path="obo-all/fly_anatomy_xp/fly_anatomy_xp.tbl" md5="0fa09b70f87f0c42beb32eb94903bc96" timestamp="1261007988" time_generated="1263794175" time_taken_to_generate="0" size="453965">
+ </export>
+ <export format="prolog" path="obo-all/fly_anatomy_xp/fly_anatomy_xp.pro" md5="46d5b5c0cbc2078f60e30d23f6cc92e9" timestamp="1261008001" time_generated="1263794175" time_taken_to_generate="0" size="3111702">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/fly_anatomy_xp/fly_anatomy_xp.validation_report" md5="da1243896137b4c9f8b01fcffe55acca" timestamp="1261008114" time_generated="1263794188" time_taken_to_generate="0" size="43067">
+ </export>
+ <export format="stats" path="obo-all/fly_anatomy_xp/fly_anatomy_xp.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1261008115" time_generated="1263794188" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" path="obo-all/fly_anatomy_xp/fly_anatomy_xp.imports.obo" md5="f63db39ac1403c79a56372a8b743496c" timestamp="1261008115" time_generated="1263794188" time_taken_to_generate="0" size="368">
+ </export>
+ <export format="obo.html" path="obo-all/fly_anatomy_xp/fly_anatomy_xp.obo.html" md5="6083c282b074f71e36b964be6df81449" timestamp="1261008116" time_generated="1263794188" time_taken_to_generate="0" size="7028742">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" path="obo-all/fly_anatomy_xp/fly_anatomy_xp.imports.owl" md5="6b7386d483cbbd262e16b4019b95f949" timestamp="1261008116" time_generated="1263794188" time_taken_to_generate="0" size="660">
+ </export>
+ <export format="imports-local.obo" path="obo-all/fly_anatomy_xp/fly_anatomy_xp.imports-local.obo" md5="927d2f20ba7257eff146a1032c16f30f" timestamp="1261008116" time_generated="1263794188" time_taken_to_generate="0" size="323">
+ </export>
+ <export format="xp.html" path="obo-all/fly_anatomy_xp/fly_anatomy_xp.xp.html" md5="7f262ed748b1c9373f4bcb92c41ebaf9" timestamp="1261008119" time_generated="1263794188" time_taken_to_generate="0" size="1924040">
+ </export>
+ <export format="imports-local.owl" path="obo-all/fly_anatomy_xp/fly_anatomy_xp.imports-local.owl" md5="459e472cf2ec34078e8f11ee43a3f1e1" timestamp="1261008120" time_generated="1263794188" time_taken_to_generate="0" size="4314">
+ </export>
+ <export format="owl-classified-by-pellet2" path="obo-all/fly_anatomy_xp/fly_anatomy_xp.owl-classified-by-pellet2" md5="d8dc73d3195040ee29baabd4bd4d8347" timestamp="1261008167" time_generated="1263794188" time_taken_to_generate="0" size="1368">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" path="obo-all/fly_anatomy_xp/fly_anatomy_xp.abduced-links.txt" md5="5b6b2f0115921b309b3ab28e2dda25ba" timestamp="1261008229" time_generated="1263794188" time_taken_to_generate="0" size="259">
+ </export>
+ </ont>
+ <ont id="uberon_anatomy_ontologies_bridge">
+ <source></source>
+ <status>Draft</status>
+ <contact>Chris Mungall obo-anatomy lists.sourceforge.net</contact>
+ <foundry>NA</foundry>
+ <documentation>http://www.bioontology.org/wiki/index.php/UBERON:Main_Page</documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/anatomy_xp/uberon-bridge.obo</url>
+ <extends>uberon</extends>
+ <home>http://www.bioontology.org/wiki/index.php/UBERON:Main_Page</home>
+ <namespace>uberon_anatomy_ontologies_bridge</namespace>
+ <description>Mappings between species-specific anatomy ontologies and uberon multi-species anatomy ontology</description>
+ <uses>fma_lite</uses>
+ <uses>adult_mouse_anatomy</uses>
+ <uses>zebrafish_anatomy</uses>
+ <uses>fly_anatomy</uses>
+ <uses>teleost_anatomy</uses>
+ <uses>xenopus_anatomy</uses>
+ <uses>amphibian_anatomy</uses>
+ <uses>cell</uses>
+ <uses>caro</uses>
+ <format>obo</format>
+ <title>is_a links to uberon terms</title>
+ <type>bridge</type>
+ <download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/anatomy_xp/uberon-bridge.obo</download>
+ <export format="obo_xml" path="obo-all/uberon_anatomy_ontologies_bridge/uberon_anatomy_ontologies_bridge.obo_xml" md5="290863abd7b7afdde192010bace7c134" timestamp="1261008234" time_generated="1263794192" time_taken_to_generate="0" size="942144">
+ </export>
+ <export format="obo" path="obo-all/uberon_anatomy_ontologies_bridge/uberon_anatomy_ontologies_bridge.obo" md5="d30357355140e29ab7958f06400e0275" timestamp="1263794191" time_generated="1263794192" time_taken_to_generate="0" size="846040">
+ </export>
+ <export format="owl" path="obo-all/uberon_anatomy_ontologies_bridge/uberon_anatomy_ontologies_bridge.owl" md5="350f39ba1f00d0260686173246f50fbc" timestamp="1261008360" time_generated="1263794192" time_taken_to_generate="0" size="1705245">
+ </export>
+ <export format="chadoxml" path="obo-all/uberon_anatomy_ontologies_bridge/uberon_anatomy_ontologies_bridge.chadoxml" md5="108b882a17679be5923c8f7411a04274" timestamp="1261008415" time_generated="1263794192" time_taken_to_generate="0" size="6732379">
+ </export>
+ <export format="godb_prestore" path="obo-all/uberon_anatomy_ontologies_bridge/uberon_anatomy_ontologies_bridge.godb_prestore" md5="dbc75965d144a743728486adb647a324" timestamp="1261008418" time_generated="1263794192" time_taken_to_generate="0" size="3197191">
+ </export>
+ <export format="rdf" path="obo-all/uberon_anatomy_ontologies_bridge/uberon_anatomy_ontologies_bridge.rdf" md5="94ac74c8b105bfb3a395ff82092ccc2c" timestamp="1261008425" time_generated="1263794192" time_taken_to_generate="0" size="2665943">
+ </export>
+ <export format="tbl" path="obo-all/uberon_anatomy_ontologies_bridge/uberon_anatomy_ontologies_bridge.tbl" md5="3a7756b9b6ac90197f58258a54d39664" timestamp="1261008428" time_generated="1263794192" time_taken_to_generate="0" size="133074">
+ </export>
+ <export format="prolog" path="obo-all/uberon_anatomy_ontologies_bridge/uberon_anatomy_ontologies_bridge.pro" md5="32fb1fb4d676c164c4c3d070107995d1" timestamp="1263427479" time_generated="1263794192" time_taken_to_generate="0" size="853970">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/uberon_anatomy_ontologies_bridge/uberon_anatomy_ontologies_bridge.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1261008439" time_generated="1263794197" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" problem="true">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" path="obo-all/uberon_anatomy_ontologies_bridge/uberon_anatomy_ontologies_bridge.imports.obo" md5="b9a561e2e4a457587386877c259d280e" timestamp="1261008439" time_generated="1263794198" time_taken_to_generate="0" size="1066">
+ </export>
+ <export format="obo.html" path="obo-all/uberon_anatomy_ontologies_bridge/uberon_anatomy_ontologies_bridge.obo.html" md5="cd3d9421b0fa0f35cb919fa759980b44" timestamp="1261008440" time_generated="1263794198" time_taken_to_generate="0" size="5092276">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" path="obo-all/uberon_anatomy_ontologies_bridge/uberon_anatomy_ontologies_bridge.imports.owl" md5="1019ab37dedb07089e6af4406c2139e1" timestamp="1261008440" time_generated="1263794198" time_taken_to_generate="0" size="1644">
+ </export>
+ <export format="imports-local.obo" path="obo-all/uberon_anatomy_ontologies_bridge/uberon_anatomy_ontologies_bridge.imports-local.obo" md5="901968d23716aebefcd2d2f5bd848674" timestamp="1261008440" time_generated="1263794198" time_taken_to_generate="0" size="901">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" path="obo-all/uberon_anatomy_ontologies_bridge/uberon_anatomy_ontologies_bridge.imports-local.owl" md5="a71ba7bde8fa015c2d48b5ddcb7f4421" timestamp="1261008440" time_generated="1263794198" time_taken_to_generate="0" size="5784">
+ </export>
+ <export format="owl-classified-by-pellet2" path="obo-all/uberon_anatomy_ontologies_bridge/uberon_anatomy_ontologies_bridge.owl-classified-by-pellet2" md5="5549e44cf7a5d58e10a30ae77e07089a" timestamp="1261008441" time_generated="1263794198" time_taken_to_generate="0" size="3862">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="ro_bfo_bridge1_1">
+ <source>http://www.obofoundry.org/ro/ro_bfo1-1_bridge.obo</source>
+ <status>Draft</status>
+ <contact>Chris Mungall cjm fruitfly.org</contact>
+ <foundry>NA</foundry>
+ <documentation></documentation>
+ <url>http://www.obofoundry.org/ro/ro_bfo1-1_bridge.obo</url>
+ <extends>relationship</extends>
+ <home>OBO Relation Ontology|http://www.obofoundry.org/ro</home>
+ <namespace>OBO_REL_BFO_BRIDGE</namespace>
+ <description>specifies which OBO relations can be used with which BFO types</description>
+ <uses>bfo</uses>
+ <format>obo</format>
+ <title>RO BFO domain and range constraints</title>
+ <type>bridge</type>
+ <download></download>
+ <export format="obo_xml" path="obo-all/ro_bfo_bridge1_1/ro_bfo_bridge1_1.obo_xml" md5="0f6c74c8534839d892283ee130dee7fb" timestamp="1261009726" time_generated="1263796543" time_taken_to_generate="0" size="3541">
+ </export>
+ <export format="obo" path="obo-all/ro_bfo_bridge1_1/ro_bfo_bridge1_1.obo" md5="7fee3db80e04c454bac44aa5b4677142" timestamp="1263796543" time_generated="1263796543" time_taken_to_generate="0" size="1509">
+ </export>
+ <export format="owl" path="obo-all/ro_bfo_bridge1_1/ro_bfo_bridge1_1.owl" md5="9276c99d154d8a5ce773c90d8a8ac5d5" timestamp="1261009726" time_generated="1263796543" time_taken_to_generate="0" size="7990">
+ </export>
+ <export format="chadoxml" path="obo-all/ro_bfo_bridge1_1/ro_bfo_bridge1_1.chadoxml" md5="ae5fa1ffbc3e81a43a9eca4b5c06a8fd" timestamp="1261009726" time_generated="1263796543" time_taken_to_generate="0" size="6610">
+ </export>
+ <export format="godb_prestore" path="obo-all/ro_bfo_bridge1_1/ro_bfo_bridge1_1.godb_prestore" md5="0f3cc2dd6a9b26aeb7c192fc4edc49e1" timestamp="1261009726" time_generated="1263796543" time_taken_to_generate="0" size="6210">
+ </export>
+ <export format="rdf" path="obo-all/ro_bfo_bridge1_1/ro_bfo_bridge1_1.rdf" md5="74342ce76d6e20d79506f40a52dc07e0" timestamp="1261009727" time_generated="1263796543" time_taken_to_generate="0" size="2649">
+ </export>
+ <export format="tbl" problem="true">
+ </export>
+ <export format="prolog" path="obo-all/ro_bfo_bridge1_1/ro_bfo_bridge1_1.pro" md5="8a9eb9c3ee02976c8810cfb4dca82e0c" timestamp="1261009727" time_generated="1263796543" time_taken_to_generate="0" size="3176">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/ro_bfo_bridge1_1/ro_bfo_bridge1_1.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1261009728" time_generated="1263796544" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" path="obo-all/ro_bfo_bridge1_1/ro_bfo_bridge1_1.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1261009729" time_generated="1263796544" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" path="obo-all/ro_bfo_bridge1_1/ro_bfo_bridge1_1.imports.obo" md5="6528d1409a9786304cb182edf37b6ff4" timestamp="1261009729" time_generated="1263796544" time_taken_to_generate="0" size="355">
+ </export>
+ <export format="obo.html" path="obo-all/ro_bfo_bridge1_1/ro_bfo_bridge1_1.obo.html" md5="39ac3d5f6bf7931bcd0f3e16aacc3d2e" timestamp="1261009729" time_generated="1263796544" time_taken_to_generate="0" size="8797">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" path="obo-all/ro_bfo_bridge1_1/ro_bfo_bridge1_1.imports.owl" md5="9369d58d122cdd403bbf9eebb11bbd0c" timestamp="1261009729" time_generated="1263796544" time_taken_to_generate="0" size="650">
+ </export>
+ <export format="imports-local.obo" path="obo-all/ro_bfo_bridge1_1/ro_bfo_bridge1_1.imports-local.obo" md5="026024d5831afd08b6b3090fdbd2e887" timestamp="1261009729" time_generated="1263796544" time_taken_to_generate="0" size="325">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" path="obo-all/ro_bfo_bridge1_1/ro_bfo_bridge1_1.imports-local.owl" md5="c2051551590c60905eb90ebf0fb81315" timestamp="1261009729" time_generated="1263796544" time_taken_to_generate="0" size="4325">
+ </export>
+ <export format="owl-classified-by-pellet2" path="obo-all/ro_bfo_bridge1_1/ro_bfo_bridge1_1.owl-classified-by-pellet2" md5="2ab29e9b6cb62138c95e9eee2483f64d" timestamp="1261009732" time_generated="1263796544" time_taken_to_generate="0" size="1377">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="quality_bfo_bridge">
+ <source></source>
+ <status>Draft</status>
+ <contact>Chris Mungall cjm fruitfly.org</contact>
+ <foundry>NA</foundry>
+ <documentation></documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality_bfo_bridge.obo</url>
+ <home></home>
+ <extends>quality</extends>
+ <namespace>PATO_BFO_BRIDGE</namespace>
+ <description>Links upper level terms in PATO with BFO - eg quality of a continuant</description>
+ <uses>bfo</uses>
+ <filename>quality_bfo_bridge.obo</filename>
+ <format>obo</format>
+ <title>PATO BFO constraints</title>
+ <type>bridge</type>
+ <download>quality_bfo_bridge.obo|http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality_bfo_bridge.obo</download>
+ <export format="obo_xml" path="obo-all/quality_bfo_bridge/quality_bfo_bridge.obo_xml" md5="fc0cbe6b94200882d6d4a8fb71ff1452" timestamp="1261009734" time_generated="1263796546" time_taken_to_generate="0" size="3225">
+ </export>
+ <export format="obo" path="obo-all/quality_bfo_bridge/quality_bfo_bridge.obo" md5="89f0831349b20d8871b682cfd622950e" timestamp="1263796546" time_generated="1263796546" time_taken_to_generate="0" size="1608">
+ </export>
+ <export format="owl" path="obo-all/quality_bfo_bridge/quality_bfo_bridge.owl" md5="012def04c7bd6679fe03f50ea3b51937" timestamp="1261009734" time_generated="1263796546" time_taken_to_generate="0" size="7806">
+ </export>
+ <export format="chadoxml" path="obo-all/quality_bfo_bridge/quality_bfo_bridge.chadoxml" md5="4dce20be580ec6cc5cbd1db0a0ba921a" timestamp="1261009735" time_generated="1263796546" time_taken_to_generate="0" size="7191">
+ </export>
+ <export format="godb_prestore" path="obo-all/quality_bfo_bridge/quality_bfo_bridge.godb_prestore" md5="e404748359366ae5f28fe00a5b1bd38e" timestamp="1261009735" time_generated="1263796546" time_taken_to_generate="0" size="6500">
+ </export>
+ <export format="rdf" path="obo-all/quality_bfo_bridge/quality_bfo_bridge.rdf" md5="23ccf4e7d8199c62883a00d3684afece" timestamp="1261009735" time_generated="1263796546" time_taken_to_generate="0" size="2658">
+ </export>
+ <export format="tbl" path="obo-all/quality_bfo_bridge/quality_bfo_bridge.tbl" md5="877749e2558e6fc776cb56554624bcb7" timestamp="1261009735" time_generated="1263796546" time_taken_to_generate="0" size="75">
+ </export>
+ <export format="prolog" path="obo-all/quality_bfo_bridge/quality_bfo_bridge.pro" md5="e1d24d142a78373f9660df28e84ae836" timestamp="1261009735" time_generated="1263796546" time_taken_to_generate="0" size="2085">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/quality_bfo_bridge/quality_bfo_bridge.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1261009736" time_generated="1263796546" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" path="obo-all/quality_bfo_bridge/quality_bfo_bridge.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1261009737" time_generated="1263796546" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" path="obo-all/quality_bfo_bridge/quality_bfo_bridge.imports.obo" md5="50237c12edbd8b9552837291d3f2dd7f" timestamp="1261009737" time_generated="1263796546" time_taken_to_generate="0" size="348">
+ </export>
+ <export format="obo.html" path="obo-all/quality_bfo_bridge/quality_bfo_bridge.obo.html" md5="d86602ab7c29211d08b6942fdcb54a92" timestamp="1261009737" time_generated="1263796546" time_taken_to_generate="0" size="5724">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" path="obo-all/quality_bfo_bridge/quality_bfo_bridge.imports.owl" md5="2839682b9862c95fafbc82f29796789b" timestamp="1261009737" time_generated="1263796546" time_taken_to_generate="0" size="644">
+ </export>
+ <export format="imports-local.obo" path="obo-all/quality_bfo_bridge/quality_bfo_bridge.imports-local.obo" md5="56f419d56acd81ef735dfcf5eb60a3ea" timestamp="1261009737" time_generated="1263796546" time_taken_to_generate="0" size="318">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" path="obo-all/quality_bfo_bridge/quality_bfo_bridge.imports-local.owl" md5="5530c305262e3bd095986d015bff0fee" timestamp="1261009737" time_generated="1263796546" time_taken_to_generate="0" size="4316">
+ </export>
+ <export format="owl-classified-by-pellet2" path="obo-all/quality_bfo_bridge/quality_bfo_bridge.owl-classified-by-pellet2" md5="372e0bc8c9587327769227aab898c4dc" timestamp="1261009752" time_generated="1263796546" time_taken_to_generate="0" size="1387">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="caro_to_bfo">
+ <source></source>
+ <status>Draft</status>
+ <contact>Chris Mungall cjm fruitfly.org</contact>
+ <foundry>NA</foundry>
+ <documentation></documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/caro/caro_to_bfo.obo</url>
+ <home></home>
+ <extends>caro</extends>
+ <namespace>caro_to_bfo</namespace>
+ <description>CARO types are sub-types of more general BFO types; for example, cells are types of BFO:Object. This bridge file makes the is_a links explicit</description>
+ <uses>bfo</uses>
+ <filename>caro_to_bfo.obo</filename>
+ <format>obo</format>
+ <title>CARO to BFO is_a mappings</title>
+ <type>bridge</type>
+ <download>caro_to_bfo.obo|http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/caro/caro_to_bfo.obo</download>
+ <export format="obo_xml" path="obo-all/caro_to_bfo/caro_to_bfo.obo_xml" md5="acfc81f73a613db069b2782950dae2b2" timestamp="1261009755" time_generated="1263796549" time_taken_to_generate="0" size="2166">
+ </export>
+ <export format="obo" path="obo-all/caro_to_bfo/caro_to_bfo.obo" md5="dac5fc1ebf14137f9aa7d589d296a861" timestamp="1263796549" time_generated="1263796549" time_taken_to_generate="0" size="1453">
+ </export>
+ <export format="owl" path="obo-all/caro_to_bfo/caro_to_bfo.owl" md5="e6183c88b8996f2c275cb60a5ac79601" timestamp="1261009755" time_generated="1263796549" time_taken_to_generate="0" size="6598">
+ </export>
+ <export format="chadoxml" path="obo-all/caro_to_bfo/caro_to_bfo.chadoxml" md5="6d3f0f0470f352cd103800b7811274a1" timestamp="1261009756" time_generated="1263796549" time_taken_to_generate="0" size="9191">
+ </export>
+ <export format="godb_prestore" path="obo-all/caro_to_bfo/caro_to_bfo.godb_prestore" md5="f7778177b21f1f5691605ac2f627d1e6" timestamp="1261009756" time_generated="1263796549" time_taken_to_generate="0" size="6177">
+ </export>
+ <export format="rdf" path="obo-all/caro_to_bfo/caro_to_bfo.rdf" md5="8a5f1435a2ca2215d553197763f8c90c" timestamp="1261009756" time_generated="1263796549" time_taken_to_generate="0" size="3162">
+ </export>
+ <export format="tbl" path="obo-all/caro_to_bfo/caro_to_bfo.tbl" md5="fd9eccdd02776aee5d5365ef6df7d03e" timestamp="1261009756" time_generated="1263796549" time_taken_to_generate="0" size="150">
+ </export>
+ <export format="prolog" path="obo-all/caro_to_bfo/caro_to_bfo.pro" md5="dbf8f9d12a33e0901df7067453a9579c" timestamp="1261009756" time_generated="1263796549" time_taken_to_generate="0" size="1511">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/caro_to_bfo/caro_to_bfo.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1261009757" time_generated="1263796549" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" path="obo-all/caro_to_bfo/caro_to_bfo.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1261009758" time_generated="1263796549" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" path="obo-all/caro_to_bfo/caro_to_bfo.imports.obo" md5="ab797167ca09c975d4c0035a3f3070bf" timestamp="1261009758" time_generated="1263796549" time_taken_to_generate="0" size="311">
+ </export>
+ <export format="obo.html" path="obo-all/caro_to_bfo/caro_to_bfo.obo.html" md5="dd48bc13f191c811ebc84156f88275ff" timestamp="1261009758" time_generated="1263796549" time_taken_to_generate="0" size="6139">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" path="obo-all/caro_to_bfo/caro_to_bfo.imports.owl" md5="8a3020199b11be332ec4f402247f3aca" timestamp="1261009758" time_generated="1263796549" time_taken_to_generate="0" size="624">
+ </export>
+ <export format="imports-local.obo" path="obo-all/caro_to_bfo/caro_to_bfo.imports-local.obo" md5="c1ba8d29402e7273a9d5395dfe29baf6" timestamp="1261009758" time_generated="1263796549" time_taken_to_generate="0" size="281">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" path="obo-all/caro_to_bfo/caro_to_bfo.imports-local.owl" md5="73e75359fc83df2cd6d3f6f1cf7360a3" timestamp="1261009758" time_generated="1263796549" time_taken_to_generate="0" size="4245">
+ </export>
+ <export format="owl-classified-by-pellet2" path="obo-all/caro_to_bfo/caro_to_bfo.owl-classified-by-pellet2" md5="84c5982dc02fcae7ad64e94e881949b4" timestamp="1261009762" time_generated="1263796549" time_taken_to_generate="0" size="1350">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="bfo">
+ <source></source>
+ <status>Implementation</status>
+ <contact>BFO discuss bfo-discuss googlegroups.com</contact>
+ <foundry>NA</foundry>
+ <documentation></documentation>
+ <url>http://www.ifomis.org/bfo/1.1</url>
+ <home>BFO|http://www.ifomis.uni-saarland.de/bfo/</home>
+ <extends>relationship</extends>
+ <namespace>bfo</namespace>
+ <external>yes</external>
+ <description>The theory behind BFO has been developed and formulated by Barry Smith and Pierre Grenon in a series of publications. BFO grows out of a philosophical orientation which overlaps with that of DOLCE and SUMO. Unlike these, however, it is narrowly focused on the task of providing a genuine upper ontology which can be used in support of domain ontologies developed for scientific research, as for example in biomedicine within the framework of the OBO Foundry. Thus BFO does no [...]
+ <uses>bfo</uses>
+ <format>owl</format>
+ <filename>bfo.owl</filename>
+ <title>Basic Formal Ontology</title>
+ <type>ontology</type>
+ <download>bfo.owl|http://www.ifomis.org/bfo/1.1</download>
+ <export format="pro" path="obo-all/bfo/bfo.pro" md5="55515448e1d00d80af59c61b20fba818" timestamp="1261009766" time_generated="1263796553" time_taken_to_generate="0" size="81702">
+ </export>
+ <export format="obo" path="obo-all/bfo/bfo.obo" md5="6b3e1154b63feab2fe404733a7f9bbe4" timestamp="1261009766" time_generated="1263796553" time_taken_to_generate="0" size="54078">
+ </export>
+ <export format="obo_xml" path="obo-all/bfo/bfo.obo_xml" md5="b36b08fb8cb2d2f757b8e1e36530a165" timestamp="1261009767" time_generated="1263796553" time_taken_to_generate="0" size="75792">
+ </export>
+ <export format="owl" path="obo-all/bfo/bfo.owl" md5="53a3521073378369ea719e4779e495aa" timestamp="1263796553" time_generated="1263796553" time_taken_to_generate="0" size="45213">
+ </export>
+ <export format="chadoxml" path="obo-all/bfo/bfo.chadoxml" md5="89a38c74c7d304ea2b34c1d63ca2ab4d" timestamp="1261009767" time_generated="1263796553" time_taken_to_generate="0" size="86482">
+ </export>
+ <export format="godb_prestore" path="obo-all/bfo/bfo.godb_prestore" md5="b3f0279df446ca8d32b9b7be05698cf1" timestamp="1261009767" time_generated="1263796553" time_taken_to_generate="0" size="73390">
+ </export>
+ <export format="rdf" path="obo-all/bfo/bfo.rdf" md5="cab8ad8f99d966e6a726cd02222a3751" timestamp="1261009767" time_generated="1263796553" time_taken_to_generate="0" size="29505">
+ </export>
+ <export format="tbl" path="obo-all/bfo/bfo.tbl" md5="6a71ee8dd49f3bda47bbea925a098936" timestamp="1261009767" time_generated="1263796553" time_taken_to_generate="0" size="9007">
+ </export>
+ <export format="prolog" path="obo-all/bfo/bfo.pro" md5="55515448e1d00d80af59c61b20fba818" timestamp="1261009766" time_generated="1263796553" time_taken_to_generate="0" size="81702">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/bfo/bfo.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1261009768" time_generated="1263796554" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" path="obo-all/bfo/bfo.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1261009769" time_generated="1263796554" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="imports.obo" path="obo-all/bfo/bfo.imports.obo" md5="eccb3d9719a977bd87ddbbe669e2b583" timestamp="1261009769" time_generated="1263796554" time_taken_to_generate="0" size="303">
+ </export>
+ <export format="obo.html" path="obo-all/bfo/bfo.obo.html" md5="789c2c94662b4aee5f349062eb742a7d" timestamp="1261009769" time_generated="1263796554" time_taken_to_generate="0" size="154857">
+ </export>
+ <export format="imports.owl" path="obo-all/bfo/bfo.imports.owl" md5="cfe540cdb7625742942f016984dbb48a" timestamp="1261009769" time_generated="1263796554" time_taken_to_generate="0" size="624">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.obo" path="obo-all/bfo/bfo.imports-local.obo" md5="38f8595827459266d054f574f37e5ad7" timestamp="1261009769" time_generated="1263796554" time_taken_to_generate="0" size="258">
+ </export>
+ <export format="imports-local.owl" path="obo-all/bfo/bfo.imports-local.owl" md5="42e7c42d46a106419d6b22c42add2cbe" timestamp="1261009770" time_generated="1263796554" time_taken_to_generate="0" size="4191">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="map_CL-EMAPA">
+ <source></source>
+ <namespace>CL-EMAPA</namespace>
+ <status>Implementation release</status>
+ <contact>Jonathan Bard J.Bard ed.ac.uk</contact>
+ <description>Mappings of OBO cell ontology to EMAPA</description>
+ <foundry>NA</foundry>
+ <format>obo</format>
+ <filename>map_CL-EMAPA.obo</filename>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/anatomy_xp/map_CL-EMAPA.obo</url>
+ <type>mappings</type>
+ <title>CL to EMAPA mappings</title>
+ <home>http://www.xspan.org/obo/other.html</home>
+ <extends>CL</extends>
+ <download>map_CL-EMAPA.obo|http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/anatomy_xp/map_CL-EMAPA.obo</download>
+ <export format="obo_xml" path="obo-all/map_CL-EMAPA/map_CL-EMAPA.obo_xml" md5="3d34a5da591c80afebb8e7581705c48f" timestamp="1261009775" time_generated="1263796557" time_taken_to_generate="0" size="1664631">
+ </export>
+ <export format="obo" path="obo-all/map_CL-EMAPA/map_CL-EMAPA.obo" md5="5892fb8e97ca7a1f482012aa4ad4806e" timestamp="1263796557" time_generated="1263796557" time_taken_to_generate="0" size="895656">
+ </export>
+ <export format="owl" path="obo-all/map_CL-EMAPA/map_CL-EMAPA.owl" md5="786480f6ca419e7272adaf718634230b" timestamp="1261010090" time_generated="1263796557" time_taken_to_generate="0" size="4082472">
+ </export>
+ <export format="chadoxml" path="obo-all/map_CL-EMAPA/map_CL-EMAPA.chadoxml" md5="5c662fc2c84238bd0127ac1b6c139d38" timestamp="1261010175" time_generated="1263796557" time_taken_to_generate="0" size="4033040">
+ </export>
+ <export format="godb_prestore" path="obo-all/map_CL-EMAPA/map_CL-EMAPA.godb_prestore" md5="ca8904706c14f3a5d4cb45f828f06828" timestamp="1261010180" time_generated="1263796557" time_taken_to_generate="0" size="4433028">
+ </export>
+ <export format="rdf" path="obo-all/map_CL-EMAPA/map_CL-EMAPA.rdf" md5="6e8762b15f7ded3f8a0368fed98eb305" timestamp="1261010188" time_generated="1263796557" time_taken_to_generate="0" size="2281006">
+ </export>
+ <export format="tbl" path="obo-all/map_CL-EMAPA/map_CL-EMAPA.tbl" md5="6d94d8e5b4fc57ef7f9356697762c471" timestamp="1261010193" time_generated="1263796557" time_taken_to_generate="0" size="300624">
+ </export>
+ <export format="prolog" path="obo-all/map_CL-EMAPA/map_CL-EMAPA.pro" md5="de76da0af245e7c0af838b8f4e99c757" timestamp="1261010203" time_generated="1263796557" time_taken_to_generate="0" size="1777791">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/map_CL-EMAPA/map_CL-EMAPA.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1261010209" time_generated="1263796566" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" path="obo-all/map_CL-EMAPA/map_CL-EMAPA.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1261010210" time_generated="1263796566" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" path="obo-all/map_CL-EMAPA/map_CL-EMAPA.imports.obo" md5="67afc5c00c3cc27d23c063131a77aab1" timestamp="1261010210" time_generated="1263796566" time_taken_to_generate="0" size="257">
+ </export>
+ <export format="obo.html" path="obo-all/map_CL-EMAPA/map_CL-EMAPA.obo.html" md5="41cf26c8dd32a1ec0e4d5dc0cd868b51" timestamp="1261010210" time_generated="1263796566" time_taken_to_generate="0" size="5383204">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" path="obo-all/map_CL-EMAPA/map_CL-EMAPA.imports.owl" md5="f5e667204c34a97fff6d0bf7bd27e760" timestamp="1261010211" time_generated="1263796566" time_taken_to_generate="0" size="521">
+ </export>
+ <export format="imports-local.obo" path="obo-all/map_CL-EMAPA/map_CL-EMAPA.imports-local.obo" md5="0f8443115e3fdb92a8f05b5d1c691055" timestamp="1261010211" time_generated="1263796566" time_taken_to_generate="0" size="242">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" path="obo-all/map_CL-EMAPA/map_CL-EMAPA.imports-local.owl" md5="5bbe778bedebf6b4c5232479f5c701e9" timestamp="1261010211" time_generated="1263796566" time_taken_to_generate="0" size="4121">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="cog2go">
+ <source>ftp://ftp.geneontology.org/pub/go/external2go/cog2go</source>
+ <namespace>COG2GO</namespace>
+ <status>Implementation release</status>
+ <description>Mappings of cog2go to GO</description>
+ <foundry>NA</foundry>
+ <format>go_xref</format>
+ <documentation>contact Gene Ontology|go.org</documentation>
+ <url>ftp://ftp.geneontology.org/pub/go/external2go/cog2go</url>
+ <type>mappings</type>
+ <title>cog2go mapping</title>
+ <extends>GO</extends>
+ <home>GO|http://www.geneontology.org/</home>
+ <download></download>
+ <export format="obo_xml" path="obo-all/cog2go/cog2go.obo_xml" md5="6db71a46977aeb91673c54a69066c14f" timestamp="1261010212" time_generated="1263796568" time_taken_to_generate="0" size="17636">
+ </export>
+ <export format="obo" path="obo-all/cog2go/cog2go.obo" md5="551fb50a7d453c42ee46e2538f3d885d" timestamp="1261010212" time_generated="1263796568" time_taken_to_generate="0" size="6996">
+ </export>
+ <export format="owl" path="obo-all/cog2go/cog2go.owl" md5="63484b45f6688d8600af94ae3629830b" timestamp="1261010212" time_generated="1263796568" time_taken_to_generate="0" size="37985">
+ </export>
+ <export format="chadoxml" path="obo-all/cog2go/cog2go.chadoxml" md5="a7a7cc7f4b282ebe7f895df22927b02b" timestamp="1261010212" time_generated="1263796568" time_taken_to_generate="0" size="53362">
+ </export>
+ <export format="godb_prestore" path="obo-all/cog2go/cog2go.godb_prestore" md5="5536a5129bbc6a6bdea5e1804a67103e" timestamp="1261010213" time_generated="1263796568" time_taken_to_generate="0" size="24813">
+ </export>
+ <export format="rdf" path="obo-all/cog2go/cog2go.rdf" md5="d95c38e90ac3900b8153aa0f5d02a761" timestamp="1261010213" time_generated="1263796568" time_taken_to_generate="0" size="34597">
+ </export>
+ <export format="tbl" path="obo-all/cog2go/cog2go.tbl" md5="385068c1b690f7f3f1c51503323cc900" timestamp="1261010213" time_generated="1263796568" time_taken_to_generate="0" size="1287">
+ </export>
+ <export format="prolog" path="obo-all/cog2go/cog2go.pro" md5="ba27ce28739b6b8bd24e9e6701080950" timestamp="1261010213" time_generated="1263796568" time_taken_to_generate="0" size="7165">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/cog2go/cog2go.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1261010214" time_generated="1263796568" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" problem="true">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" path="obo-all/cog2go/cog2go.imports.obo" md5="c6a9a833acb18f67b03f308a2a67efef" timestamp="1261010215" time_generated="1263796569" time_taken_to_generate="0" size="233">
+ </export>
+ <export format="obo.html" path="obo-all/cog2go/cog2go.obo.html" md5="827cbea49066682415b1618988e72545" timestamp="1261010215" time_generated="1263796570" time_taken_to_generate="0" size="51846">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" path="obo-all/cog2go/cog2go.imports.owl" md5="1b5c39dd9d376f2ed2f1033050c809bf" timestamp="1261010215" time_generated="1263796570" time_taken_to_generate="0" size="509">
+ </export>
+ <export format="imports-local.obo" path="obo-all/cog2go/cog2go.imports-local.obo" md5="e645597e01ab021e21db29ed8a995f2b" timestamp="1261010215" time_generated="1263796570" time_taken_to_generate="0" size="218">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" path="obo-all/cog2go/cog2go.imports-local.owl" md5="0c7b0cf08c05315689c841301f548aef" timestamp="1261010215" time_generated="1263796570" time_taken_to_generate="0" size="4073">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="ec2go">
+ <source>ftp://ftp.geneontology.org/pub/go/external2go/ec2go</source>
+ <namespace>EC2GO</namespace>
+ <status>Implementation release</status>
+ <description>Mappings of ec2go to GO</description>
+ <foundry>NA</foundry>
+ <format>go_xref</format>
+ <documentation>contact Gene Ontology|go.org</documentation>
+ <url>ftp://ftp.geneontology.org/pub/go/external2go/ec2go</url>
+ <type>mappings</type>
+ <title>ec2go mapping</title>
+ <extends>GO</extends>
+ <home>GO|http://www.geneontology.org/</home>
+ <download></download>
+ <export format="obo_xml" path="obo-all/ec2go/ec2go.obo_xml" md5="8474f921d78e9a17fdd9a687d9254b94" timestamp="1261406465" time_generated="1263796571" time_taken_to_generate="0" size="518672">
+ </export>
+ <export format="obo" path="obo-all/ec2go/ec2go.obo" md5="8d0d490f36b1689c45f612d7ecdf700b" timestamp="1261406470" time_generated="1263796571" time_taken_to_generate="0" size="160895">
+ </export>
+ <export format="owl" path="obo-all/ec2go/ec2go.owl" md5="432a86ea8c4ee333e606eefab9761d8d" timestamp="1261406488" time_generated="1263796571" time_taken_to_generate="0" size="1421947">
+ </export>
+ <export format="chadoxml" path="obo-all/ec2go/ec2go.chadoxml" md5="5086f2f0409d0b08992fa6b27b532e31" timestamp="1261406492" time_generated="1263796572" time_taken_to_generate="0" size="2073526">
+ </export>
+ <export format="godb_prestore" path="obo-all/ec2go/ec2go.godb_prestore" md5="e94af4a05ac5778567b661353675d115" timestamp="1261406494" time_generated="1263796572" time_taken_to_generate="0" size="929575">
+ </export>
+ <export format="rdf" path="obo-all/ec2go/ec2go.rdf" md5="958fc17c208f63d2c236cafe10d2a496" timestamp="1261406500" time_generated="1263796572" time_taken_to_generate="0" size="1423963">
+ </export>
+ <export format="tbl" path="obo-all/ec2go/ec2go.tbl" md5="a28afa8bc479092627821733d234b6bd" timestamp="1261406503" time_generated="1263796572" time_taken_to_generate="0" size="51116">
+ </export>
+ <export format="prolog" path="obo-all/ec2go/ec2go.pro" md5="1029f93d0120330c73153f772ebf9f3a" timestamp="1261406510" time_generated="1263796572" time_taken_to_generate="0" size="298647">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/ec2go/ec2go.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1261406513" time_generated="1263796575" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" problem="true">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" path="obo-all/ec2go/ec2go.imports.obo" md5="f1e613b0a1703d74c240e28f7605f286" timestamp="1261406514" time_generated="1263796576" time_taken_to_generate="0" size="229">
+ </export>
+ <export format="obo.html" path="obo-all/ec2go/ec2go.obo.html" md5="7e3683b0e12f09c54fc38d7c1e6f2b11" timestamp="1261406515" time_generated="1263796576" time_taken_to_generate="0" size="1804822">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" path="obo-all/ec2go/ec2go.imports.owl" md5="5614e8117e72b86946c804ccc2ef9a68" timestamp="1261406515" time_generated="1263796576" time_taken_to_generate="0" size="507">
+ </export>
+ <export format="imports-local.obo" path="obo-all/ec2go/ec2go.imports-local.obo" md5="78b3be82c69efaf5d7de64e1d62ff565" timestamp="1261406515" time_generated="1263796576" time_taken_to_generate="0" size="214">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" path="obo-all/ec2go/ec2go.imports-local.owl" md5="9f8b4f1dfd786d04758bd9f29c06e36b" timestamp="1261406515" time_generated="1263796576" time_taken_to_generate="0" size="4065">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="egad2go">
+ <source>ftp://ftp.geneontology.org/pub/go/external2go/egad2go</source>
+ <namespace>EGAD2GO</namespace>
+ <status>Implementation release</status>
+ <description>Mappings of egad2go to GO</description>
+ <foundry>NA</foundry>
+ <format>go_xref</format>
+ <documentation>contact Gene Ontology|go.org</documentation>
+ <url>ftp://ftp.geneontology.org/pub/go/external2go/egad2go</url>
+ <type>mappings</type>
+ <title>egad2go mapping</title>
+ <extends>GO</extends>
+ <home>GO|http://www.geneontology.org/</home>
+ <download></download>
+ <export format="obo_xml" path="obo-all/egad2go/egad2go.obo_xml" md5="c0be83afe9815b93c9b2f27715316db0" timestamp="1261010258" time_generated="1263796578" time_taken_to_generate="0" size="9450">
+ </export>
+ <export format="obo" path="obo-all/egad2go/egad2go.obo" md5="5ea811b78f84387229584556cc675bcf" timestamp="1261010258" time_generated="1263796578" time_taken_to_generate="0" size="3601">
+ </export>
+ <export format="owl" path="obo-all/egad2go/egad2go.owl" md5="fc1e99018eb8b7382b884a0c70ce9d8c" timestamp="1261010259" time_generated="1263796578" time_taken_to_generate="0" size="25295">
+ </export>
+ <export format="chadoxml" path="obo-all/egad2go/egad2go.chadoxml" md5="6f865d3b905b45f293f3d7918aa0fe05" timestamp="1261010259" time_generated="1263796578" time_taken_to_generate="0" size="32315">
+ </export>
+ <export format="godb_prestore" path="obo-all/egad2go/egad2go.godb_prestore" md5="0610806ad65d0490a1a3e33508e0bead" timestamp="1261010259" time_generated="1263796578" time_taken_to_generate="0" size="15987">
+ </export>
+ <export format="rdf" path="obo-all/egad2go/egad2go.rdf" md5="437d4dc57f714b764f69a4c947ad9399" timestamp="1261010259" time_generated="1263796578" time_taken_to_generate="0" size="19642">
+ </export>
+ <export format="tbl" path="obo-all/egad2go/egad2go.tbl" md5="8adcfd8986cfba3d25ff3778fb491369" timestamp="1261010259" time_generated="1263796578" time_taken_to_generate="0" size="741">
+ </export>
+ <export format="prolog" path="obo-all/egad2go/egad2go.pro" md5="87e795565556cdda28e76b459036c421" timestamp="1261010259" time_generated="1263796578" time_taken_to_generate="0" size="5059">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/egad2go/egad2go.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1261010260" time_generated="1263796579" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" problem="true">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" path="obo-all/egad2go/egad2go.imports.obo" md5="13de83ec76b397e2b29cf2a0ffc815ed" timestamp="1261010261" time_generated="1263796580" time_taken_to_generate="0" size="237">
+ </export>
+ <export format="obo.html" path="obo-all/egad2go/egad2go.obo.html" md5="038a6e194ad54bca535e4955552dfedc" timestamp="1261010261" time_generated="1263796580" time_taken_to_generate="0" size="30159">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" path="obo-all/egad2go/egad2go.imports.owl" md5="3504dd992ea70d3ed401024f0c9d424d" timestamp="1261010261" time_generated="1263796580" time_taken_to_generate="0" size="511">
+ </export>
+ <export format="imports-local.obo" path="obo-all/egad2go/egad2go.imports-local.obo" md5="9146ef322a8d17076d14698613880877" timestamp="1261010261" time_generated="1263796580" time_taken_to_generate="0" size="222">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" path="obo-all/egad2go/egad2go.imports-local.owl" md5="56129f756858619a55a548b187aa75d4" timestamp="1261010261" time_generated="1263796580" time_taken_to_generate="0" size="4081">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="genprotec2go">
+ <source>ftp://ftp.geneontology.org/pub/go/external2go/genprotec2go</source>
+ <namespace>GENPROTECGO</namespace>
+ <status>Implementation release</status>
+ <description>Mappings of genprotec2go to GO</description>
+ <foundry>NA</foundry>
+ <format>go_xref</format>
+ <documentation>contact Gene Ontology|go.org</documentation>
+ <url>ftp://ftp.geneontology.org/pub/go/external2go/genprotec2go</url>
+ <type>mappings</type>
+ <title>genprotec2go mapping</title>
+ <extends>GO</extends>
+ <home>GO|http://www.geneontology.org/</home>
+ <download></download>
+ <export format="obo_xml" path="obo-all/genprotec2go/genprotec2go.obo_xml" md5="40152feded6ea20941633b053bed7db0" timestamp="1261010262" time_generated="1263796582" time_taken_to_generate="0" size="49737">
+ </export>
+ <export format="obo" path="obo-all/genprotec2go/genprotec2go.obo" md5="bc2b40c9a4145e4ab0bb5eb8d7f66d1a" timestamp="1261010263" time_generated="1263796582" time_taken_to_generate="0" size="20609">
+ </export>
+ <export format="owl" path="obo-all/genprotec2go/genprotec2go.owl" md5="5011f7c351d19187aa0245e187d2ec99" timestamp="1261010263" time_generated="1263796582" time_taken_to_generate="0" size="105359">
+ </export>
+ <export format="chadoxml" path="obo-all/genprotec2go/genprotec2go.chadoxml" md5="3d10d0e00822b598f58ac39c30907410" timestamp="1261010263" time_generated="1263796582" time_taken_to_generate="0" size="145411">
+ </export>
+ <export format="godb_prestore" path="obo-all/genprotec2go/genprotec2go.godb_prestore" md5="3f6b5d963f85ae6cc99a0a40b1fd28f6" timestamp="1261010264" time_generated="1263796582" time_taken_to_generate="0" size="67095">
+ </export>
+ <export format="rdf" path="obo-all/genprotec2go/genprotec2go.rdf" md5="aa5fef34e5000b0df5876e1d5f564c2c" timestamp="1261010264" time_generated="1263796582" time_taken_to_generate="0" size="94148">
+ </export>
+ <export format="tbl" path="obo-all/genprotec2go/genprotec2go.tbl" md5="54b8475c6aea260c95bd71211c1316bd" timestamp="1261010264" time_generated="1263796582" time_taken_to_generate="0" size="3510">
+ </export>
+ <export format="prolog" path="obo-all/genprotec2go/genprotec2go.pro" md5="a0c3d446b19729650c229c4e63b68bf2" timestamp="1261010265" time_generated="1263796582" time_taken_to_generate="0" size="22087">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/genprotec2go/genprotec2go.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1261010266" time_generated="1263796582" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" problem="true">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" path="obo-all/genprotec2go/genprotec2go.imports.obo" md5="c5a0bec27c6c4a68d602a6af1f8b2630" timestamp="1261010266" time_generated="1263796584" time_taken_to_generate="0" size="257">
+ </export>
+ <export format="obo.html" path="obo-all/genprotec2go/genprotec2go.obo.html" md5="22272f2e1025b8876f320dcfa316ef71" timestamp="1261010266" time_generated="1263796584" time_taken_to_generate="0" size="145814">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" path="obo-all/genprotec2go/genprotec2go.imports.owl" md5="38d9c3b85482a4a4b888a145176b514a" timestamp="1261010266" time_generated="1263796584" time_taken_to_generate="0" size="521">
+ </export>
+ <export format="imports-local.obo" path="obo-all/genprotec2go/genprotec2go.imports-local.obo" md5="08514b194a33a8be76a7819fcded45c5" timestamp="1261010266" time_generated="1263796584" time_taken_to_generate="0" size="242">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" path="obo-all/genprotec2go/genprotec2go.imports-local.owl" md5="bb07c6a14d81814ff1226dd95c4a46a8" timestamp="1261010267" time_generated="1263796584" time_taken_to_generate="0" size="4121">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="hamap2go">
+ <source>ftp://ftp.geneontology.org/pub/go/external2go/hamap2go</source>
+ <namespace>HAMAP2GO</namespace>
+ <status>Implementation release</status>
+ <description>Mappings of hamap2go to GO</description>
+ <foundry>NA</foundry>
+ <format>go_xref</format>
+ <documentation>contact Gene Ontology|go.org</documentation>
+ <url>ftp://ftp.geneontology.org/pub/go/external2go/hamap2go</url>
+ <type>mappings</type>
+ <title>hamap2go mapping</title>
+ <extends>GO</extends>
+ <home>GO|http://www.geneontology.org/</home>
+ <download></download>
+ <export format="obo_xml" path="obo-all/hamap2go/hamap2go.obo_xml" md5="4435f4d956afbf6c8a00b280890f6cb2" timestamp="1261406522" time_generated="1263796586" time_taken_to_generate="0" size="486187">
+ </export>
+ <export format="obo" path="obo-all/hamap2go/hamap2go.obo" md5="c92585624ca3b05b011fc458717d3406" timestamp="1261406526" time_generated="1263796586" time_taken_to_generate="0" size="158531">
+ </export>
+ <export format="owl" path="obo-all/hamap2go/hamap2go.owl" md5="4ff7e5d6e93dee2caf5a0176098dc7ee" timestamp="1261406542" time_generated="1263796586" time_taken_to_generate="0" size="1335673">
+ </export>
+ <export format="chadoxml" path="obo-all/hamap2go/hamap2go.chadoxml" md5="dee7a3005db2b2e82ae12bc78cdf780b" timestamp="1261406544" time_generated="1263796586" time_taken_to_generate="0" size="1910299">
+ </export>
+ <export format="godb_prestore" path="obo-all/hamap2go/hamap2go.godb_prestore" md5="66ea312b6e53f17b651686d80b00728f" timestamp="1261406546" time_generated="1263796586" time_taken_to_generate="0" size="862666">
+ </export>
+ <export format="rdf" path="obo-all/hamap2go/hamap2go.rdf" md5="f9fcf98db3d7e1fa84efa222ce55085c" timestamp="1261406549" time_generated="1263796586" time_taken_to_generate="0" size="402909">
+ </export>
+ <export format="tbl" path="obo-all/hamap2go/hamap2go.tbl" md5="151435593904b4bac11b331e34c564dd" timestamp="1261406551" time_generated="1263796586" time_taken_to_generate="0" size="46813">
+ </export>
+ <export format="prolog" path="obo-all/hamap2go/hamap2go.pro" md5="8629e50d2da4959e45363504147c91d5" timestamp="1261406555" time_generated="1263796586" time_taken_to_generate="0" size="284698">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/hamap2go/hamap2go.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1261406558" time_generated="1263796589" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" problem="true">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" path="obo-all/hamap2go/hamap2go.imports.obo" md5="03c6f5b474911208fb8c61750a97d943" timestamp="1261406558" time_generated="1263796590" time_taken_to_generate="0" size="241">
+ </export>
+ <export format="obo.html" path="obo-all/hamap2go/hamap2go.obo.html" md5="44113095de89a8c893d2bc589b8cb652" timestamp="1261406558" time_generated="1263796590" time_taken_to_generate="0" size="1710916">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" path="obo-all/hamap2go/hamap2go.imports.owl" md5="a95942b6ea0bd3c1daddcff4f7bea441" timestamp="1261406558" time_generated="1263796590" time_taken_to_generate="0" size="513">
+ </export>
+ <export format="imports-local.obo" path="obo-all/hamap2go/hamap2go.imports-local.obo" md5="7f203a2d6e14e80af6b1704b0cff2b14" timestamp="1261406558" time_generated="1263796590" time_taken_to_generate="0" size="226">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" path="obo-all/hamap2go/hamap2go.imports-local.owl" md5="c9c18f92bbde3355e756ae4086b925ea" timestamp="1261406559" time_generated="1263796590" time_taken_to_generate="0" size="4089">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="interpro2go">
+ <source>ftp://ftp.geneontology.org/pub/go/external2go/interpro2go</source>
+ <namespace>INTERPRO2GO</namespace>
+ <status>Implementation release</status>
+ <description>Mappings of interpro2go to GO</description>
+ <foundry>NA</foundry>
+ <format>go_xref</format>
+ <documentation>contact Gene Ontology|go.org</documentation>
+ <url>ftp://ftp.geneontology.org/pub/go/external2go/interpro2go</url>
+ <type>mappings</type>
+ <title>interpro2go mapping</title>
+ <extends>GO</extends>
+ <home>GO|http://www.geneontology.org/</home>
+ <download></download>
+ <export format="obo_xml" path="obo-all/interpro2go/interpro2go.obo_xml" md5="954df854a6f7dd96d0b95625367eefb9" timestamp="1261406568" time_generated="1263796592" time_taken_to_generate="0" size="4729461">
+ </export>
+ <export format="obo" path="obo-all/interpro2go/interpro2go.obo" md5="538ea22ba2f28f9f5dd08de0548d5e12" timestamp="1261406602" time_generated="1263796592" time_taken_to_generate="0" size="2106275">
+ </export>
+ <export format="owl" path="obo-all/interpro2go/interpro2go.owl" md5="56a4a9292ed64b1293d7444b845a65dc" timestamp="1261407455" time_generated="1263796592" time_taken_to_generate="0" size="9257412">
+ </export>
+ <export format="chadoxml" path="obo-all/interpro2go/interpro2go.chadoxml" md5="74b99332f806fb89b38341210de630c9" timestamp="1261407474" time_generated="1263796593" time_taken_to_generate="1" size="12972098">
+ </export>
+ <export format="godb_prestore" path="obo-all/interpro2go/interpro2go.godb_prestore" md5="0302fefff89c03e1e4cd21607278922e" timestamp="1261407492" time_generated="1263796593" time_taken_to_generate="0" size="5904254">
+ </export>
+ <export format="rdf" path="obo-all/interpro2go/interpro2go.rdf" md5="a0272a7ba9a3c25e1110af3d4f28891d" timestamp="1261407516" time_generated="1263796593" time_taken_to_generate="0" size="1216869">
+ </export>
+ <export format="tbl" path="obo-all/interpro2go/interpro2go.tbl" md5="2d7ced48f4ae4757991023948ccb60d8" timestamp="1261407534" time_generated="1263796593" time_taken_to_generate="0" size="315757">
+ </export>
+ <export format="prolog" path="obo-all/interpro2go/interpro2go.pro" md5="411dfe0098fb0cf8b7108d409bf1776c" timestamp="1261407563" time_generated="1263796593" time_taken_to_generate="0" size="2016206">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/interpro2go/interpro2go.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1261407578" time_generated="1263796617" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" problem="true">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" path="obo-all/interpro2go/interpro2go.imports.obo" md5="652270fc8991a43f193fe8f750722bb6" timestamp="1261407579" time_generated="1263796618" time_taken_to_generate="0" size="253">
+ </export>
+ <export format="obo.html" path="obo-all/interpro2go/interpro2go.obo.html" md5="879104d7c502bf804e4f81b74282b963" timestamp="1261407581" time_generated="1263796618" time_taken_to_generate="0" size="13447125">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" path="obo-all/interpro2go/interpro2go.imports.owl" md5="c816035bf5c8684dc86e6a72745e93c4" timestamp="1261407581" time_generated="1263796619" time_taken_to_generate="0" size="519">
+ </export>
+ <export format="imports-local.obo" path="obo-all/interpro2go/interpro2go.imports-local.obo" md5="1638c945c0a1258912d015c69cfe3bc4" timestamp="1261407581" time_generated="1263796619" time_taken_to_generate="0" size="238">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" path="obo-all/interpro2go/interpro2go.imports-local.owl" md5="95eb014ff786e08b239c68e837fef97e" timestamp="1261407582" time_generated="1263796619" time_taken_to_generate="0" size="4113">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="metacyc2go">
+ <source>ftp://ftp.geneontology.org/pub/go/external2go/metacyc2go</source>
+ <namespace>METACYC2GO</namespace>
+ <status>Implementation release</status>
+ <description>Mappings of metacyc2go to GO</description>
+ <foundry>NA</foundry>
+ <format>go_xref</format>
+ <documentation>contact Gene Ontology|go.org</documentation>
+ <url>ftp://ftp.geneontology.org/pub/go/external2go/metacyc2go</url>
+ <type>mappings</type>
+ <title>metacyc2go mapping</title>
+ <extends>GO</extends>
+ <home>GO|http://www.geneontology.org/</home>
+ <download></download>
+ <export format="obo_xml" path="obo-all/metacyc2go/metacyc2go.obo_xml" md5="b6bfd57fb5745538039079b0ad7bb78a" timestamp="1261011146" time_generated="1263796620" time_taken_to_generate="0" size="676379">
+ </export>
+ <export format="obo" path="obo-all/metacyc2go/metacyc2go.obo" md5="9ca5e34fe3e12d76d852622ff2d14f04" timestamp="1261011151" time_generated="1263796620" time_taken_to_generate="0" size="258724">
+ </export>
+ <export format="owl" path="obo-all/metacyc2go/metacyc2go.owl" md5="6b98e33e3dcf0f1ece1216cf581951b0" timestamp="1261011173" time_generated="1263796620" time_taken_to_generate="0" size="1824137">
+ </export>
+ <export format="chadoxml" path="obo-all/metacyc2go/metacyc2go.chadoxml" md5="050186f92ee46835d07636ddabefd744" timestamp="1261011175" time_generated="1263796620" time_taken_to_generate="0" size="2491148">
+ </export>
+ <export format="godb_prestore" path="obo-all/metacyc2go/metacyc2go.godb_prestore" md5="00fd5195f32dfff47cd021152177881d" timestamp="1261011178" time_generated="1263796621" time_taken_to_generate="0" size="1155714">
+ </export>
+ <export format="rdf" path="obo-all/metacyc2go/metacyc2go.rdf" md5="1f9f7d9aef7a81c47210dfa0436c9604" timestamp="1261011183" time_generated="1263796621" time_taken_to_generate="0" size="1671731">
+ </export>
+ <export format="tbl" path="obo-all/metacyc2go/metacyc2go.tbl" md5="2b0c27d51d90671f0e52e67036171ab2" timestamp="1261011185" time_generated="1263796621" time_taken_to_generate="0" size="59670">
+ </export>
+ <export format="prolog" path="obo-all/metacyc2go/metacyc2go.pro" md5="ca2e88662a651f2561cf3e10d7454d15" timestamp="1261011190" time_generated="1263796621" time_taken_to_generate="0" size="419506">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/metacyc2go/metacyc2go.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1261011192" time_generated="1263796625" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" problem="true">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" path="obo-all/metacyc2go/metacyc2go.imports.obo" md5="a278251920729472d2b06e51e8f18b72" timestamp="1261011193" time_generated="1263796626" time_taken_to_generate="0" size="249">
+ </export>
+ <export format="obo.html" path="obo-all/metacyc2go/metacyc2go.obo.html" md5="51bec214c86d532f9c8b47bd1b8cd8a0" timestamp="1261011193" time_generated="1263796626" time_taken_to_generate="0" size="2286343">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" path="obo-all/metacyc2go/metacyc2go.imports.owl" md5="7d816bed635ca1ab4514c92d7a5c740a" timestamp="1261011193" time_generated="1263796626" time_taken_to_generate="0" size="517">
+ </export>
+ <export format="imports-local.obo" path="obo-all/metacyc2go/metacyc2go.imports-local.obo" md5="51c3fd2036b22cc55efaa445e5f6f7c3" timestamp="1261011193" time_generated="1263796626" time_taken_to_generate="0" size="234">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" path="obo-all/metacyc2go/metacyc2go.imports-local.owl" md5="3ba7793a3f00edd7b68637eee8d16d9e" timestamp="1261011193" time_generated="1263796626" time_taken_to_generate="0" size="4105">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="mips2go">
+ <source>ftp://ftp.geneontology.org/pub/go/external2go/mips2go</source>
+ <namespace>MIPS2GO</namespace>
+ <status>Implementation release</status>
+ <description>Mappings of mips2go to GO</description>
+ <foundry>NA</foundry>
+ <format>go_xref</format>
+ <documentation>contact Gene Ontology|go.org</documentation>
+ <url>ftp://ftp.geneontology.org/pub/go/external2go/mips2go</url>
+ <type>mappings</type>
+ <title>mips2go mapping</title>
+ <extends>GO</extends>
+ <home>GO|http://www.geneontology.org/</home>
+ <download></download>
+ <export format="obo_xml" path="obo-all/mips2go/mips2go.obo_xml" md5="ccca9925d35c7961fb03aedc37b972fd" timestamp="1261011195" time_generated="1263796628" time_taken_to_generate="0" size="184855">
+ </export>
+ <export format="obo" path="obo-all/mips2go/mips2go.obo" md5="67467fd42bf6d0d20087a624163196c3" timestamp="1261011196" time_generated="1263796628" time_taken_to_generate="0" size="79914">
+ </export>
+ <export format="owl" path="obo-all/mips2go/mips2go.owl" md5="c371f8873391c91dcad0215f2b128228" timestamp="1261011197" time_generated="1263796628" time_taken_to_generate="0" size="383799">
+ </export>
+ <export format="chadoxml" path="obo-all/mips2go/mips2go.chadoxml" md5="836cbfab416e58aae2d79517bee37955" timestamp="1261011198" time_generated="1263796628" time_taken_to_generate="0" size="524440">
+ </export>
+ <export format="godb_prestore" path="obo-all/mips2go/mips2go.godb_prestore" md5="97f2eb74ed4b3185ba63c401732f6c35" timestamp="1261011199" time_generated="1263796628" time_taken_to_generate="0" size="241847">
+ </export>
+ <export format="rdf" path="obo-all/mips2go/mips2go.rdf" md5="2e733a9b264bceb9405020d0c773e59c" timestamp="1261011200" time_generated="1263796628" time_taken_to_generate="0" size="335295">
+ </export>
+ <export format="tbl" path="obo-all/mips2go/mips2go.tbl" md5="fb8094d1592f6633ed42a1201302c0fe" timestamp="1261011201" time_generated="1263796628" time_taken_to_generate="0" size="12636">
+ </export>
+ <export format="prolog" path="obo-all/mips2go/mips2go.pro" md5="ad515d1c390fa311c804e533fd499a74" timestamp="1261011202" time_generated="1263796628" time_taken_to_generate="0" size="84519">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/mips2go/mips2go.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1261011204" time_generated="1263796629" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" problem="true">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" path="obo-all/mips2go/mips2go.imports.obo" md5="84a2284cdb0bddbe9c96640413785a1a" timestamp="1261011205" time_generated="1263796630" time_taken_to_generate="0" size="237">
+ </export>
+ <export format="obo.html" path="obo-all/mips2go/mips2go.obo.html" md5="3183f32e16a9ab7a0c8940029333958e" timestamp="1261011205" time_generated="1263796630" time_taken_to_generate="0" size="532247">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" path="obo-all/mips2go/mips2go.imports.owl" md5="58957460a278b3faef0d58ecf1eead2b" timestamp="1261011205" time_generated="1263796630" time_taken_to_generate="0" size="511">
+ </export>
+ <export format="imports-local.obo" path="obo-all/mips2go/mips2go.imports-local.obo" md5="f8499b52833131af71aff1a7704e0526" timestamp="1261011205" time_generated="1263796630" time_taken_to_generate="0" size="222">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" path="obo-all/mips2go/mips2go.imports-local.owl" md5="e92031e961177b7397a366ea18dd4b8f" timestamp="1261011205" time_generated="1263796630" time_taken_to_generate="0" size="4081">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="multifun2go">
+ <source>ftp://ftp.geneontology.org/pub/go/external2go/multifun2go</source>
+ <namespace>MULTIFUN2GO</namespace>
+ <status>Implementation release</status>
+ <description>Mappings of multifun2go to GO</description>
+ <foundry>NA</foundry>
+ <format>go_xref</format>
+ <documentation>contact Gene Ontology|go.org</documentation>
+ <url>ftp://ftp.geneontology.org/pub/go/external2go/multifun2go</url>
+ <type>mappings</type>
+ <title>multifun2go mapping</title>
+ <extends>GO</extends>
+ <home>GO|http://www.geneontology.org/</home>
+ <download></download>
+ <export format="obo_xml" path="obo-all/multifun2go/multifun2go.obo_xml" md5="1cef5ee20b7b67cdef5d206333525324" timestamp="1261011206" time_generated="1263796632" time_taken_to_generate="0" size="130371">
+ </export>
+ <export format="obo" path="obo-all/multifun2go/multifun2go.obo" md5="0a931749105f72dd2767f5078a8a6619" timestamp="1261011207" time_generated="1263796632" time_taken_to_generate="0" size="50152">
+ </export>
+ <export format="owl" path="obo-all/multifun2go/multifun2go.owl" md5="dd67dd1258acf7ea7eb67e43c66947cc" timestamp="1261011208" time_generated="1263796632" time_taken_to_generate="0" size="282298">
+ </export>
+ <export format="chadoxml" path="obo-all/multifun2go/multifun2go.chadoxml" md5="c8f44205422381620bbe60049d04749a" timestamp="1261011209" time_generated="1263796632" time_taken_to_generate="0" size="396490">
+ </export>
+ <export format="godb_prestore" path="obo-all/multifun2go/multifun2go.godb_prestore" md5="c178fffb611cf2cb1c2bbf4c7fd199bc" timestamp="1261011209" time_generated="1263796632" time_taken_to_generate="0" size="180532">
+ </export>
+ <export format="rdf" path="obo-all/multifun2go/multifun2go.rdf" md5="08dd5ec3d3872e14e66f54599ff7fd02" timestamp="1261011210" time_generated="1263796632" time_taken_to_generate="0" size="230580">
+ </export>
+ <export format="tbl" path="obo-all/multifun2go/multifun2go.tbl" md5="615fe461daffee27f7b342ad510b3a70" timestamp="1261011211" time_generated="1263796632" time_taken_to_generate="0" size="9659">
+ </export>
+ <export format="prolog" path="obo-all/multifun2go/multifun2go.pro" md5="ba8950a0e4b95c23fd8f019078f39e7c" timestamp="1261011212" time_generated="1263796632" time_taken_to_generate="0" size="59844">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/multifun2go/multifun2go.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1261011213" time_generated="1263796633" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" problem="true">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" path="obo-all/multifun2go/multifun2go.imports.obo" md5="5bdec65fd282253101bb68b13c133ea3" timestamp="1261011213" time_generated="1263796635" time_taken_to_generate="0" size="253">
+ </export>
+ <export format="obo.html" path="obo-all/multifun2go/multifun2go.obo.html" md5="e4ea0e85b83c3821ed823d5f4632aa34" timestamp="1261011213" time_generated="1263796635" time_taken_to_generate="0" size="390843">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" path="obo-all/multifun2go/multifun2go.imports.owl" md5="733d778c754fe888ae198859776c5a2c" timestamp="1261011213" time_generated="1263796635" time_taken_to_generate="0" size="519">
+ </export>
+ <export format="imports-local.obo" path="obo-all/multifun2go/multifun2go.imports-local.obo" md5="b01fa6e8e0dcea7f43912483d1d5a141" timestamp="1261011213" time_generated="1263796635" time_taken_to_generate="0" size="238">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" path="obo-all/multifun2go/multifun2go.imports-local.owl" md5="88cb0ed573a6c98d7305b57cf411b7f9" timestamp="1261011214" time_generated="1263796635" time_taken_to_generate="0" size="4113">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="pfam2go">
+ <source>ftp://ftp.geneontology.org/pub/go/external2go/pfam2go</source>
+ <namespace>PFAM2GO</namespace>
+ <status>Implementation release</status>
+ <description>Mappings of pfam2go to GO</description>
+ <foundry>NA</foundry>
+ <format>go_xref</format>
+ <documentation>contact Gene Ontology|go.org</documentation>
+ <url>ftp://ftp.geneontology.org/pub/go/external2go/pfam2go</url>
+ <type>mappings</type>
+ <title>pfam2go mapping</title>
+ <extends>GO</extends>
+ <home>GO|http://www.geneontology.org/</home>
+ <download></download>
+ <export format="obo_xml" path="obo-all/pfam2go/pfam2go.obo_xml" md5="025741d032621c2827ec0f06f1822502" timestamp="1261407595" time_generated="1263796636" time_taken_to_generate="0" size="1651540">
+ </export>
+ <export format="obo" path="obo-all/pfam2go/pfam2go.obo" md5="a0944c38dbeb643afbc533a81307ca4e" timestamp="1261407609" time_generated="1263796636" time_taken_to_generate="0" size="549111">
+ </export>
+ <export format="owl" path="obo-all/pfam2go/pfam2go.owl" md5="e7d1943087cfe58c75364c866a4cf161" timestamp="1261407759" time_generated="1263796636" time_taken_to_generate="0" size="3729223">
+ </export>
+ <export format="chadoxml" path="obo-all/pfam2go/pfam2go.chadoxml" md5="5a02ee27eae0e4fe82a8ff4d96a8dc29" timestamp="1261407767" time_generated="1263796637" time_taken_to_generate="0" size="5391592">
+ </export>
+ <export format="godb_prestore" path="obo-all/pfam2go/pfam2go.godb_prestore" md5="a162c50b7c650fce7c3561de7182505a" timestamp="1261407775" time_generated="1263796637" time_taken_to_generate="0" size="2421323">
+ </export>
+ <export format="rdf" path="obo-all/pfam2go/pfam2go.rdf" md5="8a0e594c03d41197aefae021fad52771" timestamp="1261407787" time_generated="1263796637" time_taken_to_generate="0" size="750513">
+ </export>
+ <export format="tbl" path="obo-all/pfam2go/pfam2go.tbl" md5="aca8da5a2909e42853108ccc00c6f4b5" timestamp="1261407795" time_generated="1263796637" time_taken_to_generate="0" size="132704">
+ </export>
+ <export format="prolog" path="obo-all/pfam2go/pfam2go.pro" md5="b8ae180b5fba667c8d66123dcf85664b" timestamp="1261407809" time_generated="1263796637" time_taken_to_generate="0" size="786235">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/pfam2go/pfam2go.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1261407817" time_generated="1263796647" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" problem="true">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" path="obo-all/pfam2go/pfam2go.imports.obo" md5="58a0ac699858e6c66a10f1c3110573cf" timestamp="1261407818" time_generated="1263796648" time_taken_to_generate="0" size="237">
+ </export>
+ <export format="obo.html" path="obo-all/pfam2go/pfam2go.obo.html" md5="81cc389b6fae72d21c86c43677a4b5d9" timestamp="1261407819" time_generated="1263796648" time_taken_to_generate="0" size="5204312">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" path="obo-all/pfam2go/pfam2go.imports.owl" md5="c66aa7e1e414656c9c0bd7d860ac1bf5" timestamp="1261407819" time_generated="1263796648" time_taken_to_generate="0" size="511">
+ </export>
+ <export format="imports-local.obo" path="obo-all/pfam2go/pfam2go.imports-local.obo" md5="6dbd86c43d1e5be035d03e50614b5ba6" timestamp="1261407820" time_generated="1263796648" time_taken_to_generate="0" size="222">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" path="obo-all/pfam2go/pfam2go.imports-local.owl" md5="d2ce72d0db1ae035531807997e847240" timestamp="1261407820" time_generated="1263796648" time_taken_to_generate="0" size="4081">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="prints2go">
+ <source>ftp://ftp.geneontology.org/pub/go/external2go/prints2go</source>
+ <namespace>PRINTS2GO</namespace>
+ <status>Implementation release</status>
+ <description>Mappings of prints2go to GO</description>
+ <foundry>NA</foundry>
+ <format>go_xref</format>
+ <documentation>contact Gene Ontology|go.org</documentation>
+ <url>ftp://ftp.geneontology.org/pub/go/external2go/prints2go</url>
+ <type>mappings</type>
+ <title>prints2go mapping</title>
+ <extends>GO</extends>
+ <home>GO|http://www.geneontology.org/</home>
+ <download></download>
+ <export format="obo_xml" path="obo-all/prints2go/prints2go.obo_xml" md5="cc59f89d2decaf7520591e8363307eb5" timestamp="1261407823" time_generated="1263796650" time_taken_to_generate="0" size="747430">
+ </export>
+ <export format="obo" path="obo-all/prints2go/prints2go.obo" md5="ff46e7e810c5368fee59d980ccb09175" timestamp="1261407830" time_generated="1263796650" time_taken_to_generate="0" size="260709">
+ </export>
+ <export format="owl" path="obo-all/prints2go/prints2go.owl" md5="1ae3e94229a301380c681c1e70fd494d" timestamp="1261407863" time_generated="1263796650" time_taken_to_generate="0" size="1675400">
+ </export>
+ <export format="chadoxml" path="obo-all/prints2go/prints2go.chadoxml" md5="0ea71464c82973de8c0f28063e5b03d1" timestamp="1261407866" time_generated="1263796650" time_taken_to_generate="0" size="2390480">
+ </export>
+ <export format="godb_prestore" path="obo-all/prints2go/prints2go.godb_prestore" md5="2f23d545f133d6ee2736350e1530cf72" timestamp="1261407871" time_generated="1263796650" time_taken_to_generate="0" size="1079200">
+ </export>
+ <export format="rdf" path="obo-all/prints2go/prints2go.rdf" md5="374b320f9a85c0e8043c7e6cadc4a7c4" timestamp="1261407876" time_generated="1263796650" time_taken_to_generate="0" size="335199">
+ </export>
+ <export format="tbl" path="obo-all/prints2go/prints2go.tbl" md5="cb1659cd3480f87130d62cbf877a75ef" timestamp="1261407879" time_generated="1263796650" time_taken_to_generate="0" size="58591">
+ </export>
+ <export format="prolog" path="obo-all/prints2go/prints2go.pro" md5="f6f41d8bc07b80843dcaa800a7861980" timestamp="1261407887" time_generated="1263796650" time_taken_to_generate="0" size="356272">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/prints2go/prints2go.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1261407890" time_generated="1263796655" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" problem="true">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" path="obo-all/prints2go/prints2go.imports.obo" md5="e1140328d788932e00fd34d6df2b3a22" timestamp="1261407891" time_generated="1263796656" time_taken_to_generate="0" size="245">
+ </export>
+ <export format="obo.html" path="obo-all/prints2go/prints2go.obo.html" md5="4f153aa94f4cff4407c9ffd30b16ef54" timestamp="1261407892" time_generated="1263796656" time_taken_to_generate="0" size="2334284">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" path="obo-all/prints2go/prints2go.imports.owl" md5="8ab2ef940fa30f7c94fe78f580f4d51e" timestamp="1261407892" time_generated="1263796656" time_taken_to_generate="0" size="515">
+ </export>
+ <export format="imports-local.obo" path="obo-all/prints2go/prints2go.imports-local.obo" md5="8e2173178a32244ebe18f95bf2303d03" timestamp="1261407892" time_generated="1263796656" time_taken_to_generate="0" size="230">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" path="obo-all/prints2go/prints2go.imports-local.owl" md5="42948054ac0030b17de8ee5eb934945a" timestamp="1261407892" time_generated="1263796656" time_taken_to_generate="0" size="4097">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="prodom2go">
+ <source>ftp://ftp.geneontology.org/pub/go/external2go/prodom2go</source>
+ <namespace>PRODOM2GO</namespace>
+ <status>Implementation release</status>
+ <description>Mappings of prodom2go to GO</description>
+ <foundry>NA</foundry>
+ <format>go_xref</format>
+ <documentation>contact Gene Ontology|go.org</documentation>
+ <url>ftp://ftp.geneontology.org/pub/go/external2go/prodom2go</url>
+ <type>mappings</type>
+ <title>prodom2go mapping</title>
+ <extends>GO</extends>
+ <home>GO|http://www.geneontology.org/</home>
+ <download></download>
+ <export format="obo_xml" path="obo-all/prodom2go/prodom2go.obo_xml" md5="32ee09294868d663fa40f3c839a78980" timestamp="1261407894" time_generated="1263796658" time_taken_to_generate="0" size="146443">
+ </export>
+ <export format="obo" path="obo-all/prodom2go/prodom2go.obo" md5="77745c7da2659295d85c17b599aeef47" timestamp="1261407895" time_generated="1263796658" time_taken_to_generate="0" size="53598">
+ </export>
+ <export format="owl" path="obo-all/prodom2go/prodom2go.owl" md5="cb8cd3ef089995e00276dcaf5ad56837" timestamp="1261407897" time_generated="1263796658" time_taken_to_generate="0" size="324083">
+ </export>
+ <export format="chadoxml" path="obo-all/prodom2go/prodom2go.chadoxml" md5="f0723825e74afd82e0dea568fefd4d2c" timestamp="1261407898" time_generated="1263796658" time_taken_to_generate="0" size="458430">
+ </export>
+ <export format="godb_prestore" path="obo-all/prodom2go/prodom2go.godb_prestore" md5="11bb09132c4b6cc9eaed1be519e2e97f" timestamp="1261407899" time_generated="1263796658" time_taken_to_generate="0" size="208427">
+ </export>
+ <export format="rdf" path="obo-all/prodom2go/prodom2go.rdf" md5="b61076f165e4f8a8fa0eadd21508156f" timestamp="1261407900" time_generated="1263796658" time_taken_to_generate="0" size="137567">
+ </export>
+ <export format="tbl" path="obo-all/prodom2go/prodom2go.tbl" md5="50cf8a1ad6a3a17e9d9fa005a286410d" timestamp="1261407900" time_generated="1263796658" time_taken_to_generate="0" size="11180">
+ </export>
+ <export format="prolog" path="obo-all/prodom2go/prodom2go.pro" md5="cdc9398dbbb97cd2bcad1622de0ce2bb" timestamp="1261407902" time_generated="1263796658" time_taken_to_generate="0" size="69019">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/prodom2go/prodom2go.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1261407903" time_generated="1263796659" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" problem="true">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" path="obo-all/prodom2go/prodom2go.imports.obo" md5="ae0659717b199bab05812645d04bfbed" timestamp="1261407904" time_generated="1263796661" time_taken_to_generate="0" size="245">
+ </export>
+ <export format="obo.html" path="obo-all/prodom2go/prodom2go.obo.html" md5="d416981f82cfeb48b9af54846e4becf1" timestamp="1261407904" time_generated="1263796661" time_taken_to_generate="0" size="450413">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" path="obo-all/prodom2go/prodom2go.imports.owl" md5="7a7c6cb382b4555525766a778c37843f" timestamp="1261407904" time_generated="1263796661" time_taken_to_generate="0" size="515">
+ </export>
+ <export format="imports-local.obo" path="obo-all/prodom2go/prodom2go.imports-local.obo" md5="b32514d4f6f5a507a75bb66c382869be" timestamp="1261407904" time_generated="1263796661" time_taken_to_generate="0" size="230">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" path="obo-all/prodom2go/prodom2go.imports-local.owl" md5="139fecfbbe134a415d40f1201354f459" timestamp="1261407904" time_generated="1263796661" time_taken_to_generate="0" size="4097">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="prosite2go">
+ <source>ftp://ftp.geneontology.org/pub/go/external2go/prosite2go</source>
+ <namespace>PROSITE2GO</namespace>
+ <status>Implementation release</status>
+ <description>Mappings of prosite2go to GO</description>
+ <foundry>NA</foundry>
+ <format>go_xref</format>
+ <documentation>contact Gene Ontology|go.org</documentation>
+ <url>ftp://ftp.geneontology.org/pub/go/external2go/prosite2go</url>
+ <type>mappings</type>
+ <title>prosite2go mapping</title>
+ <extends>GO</extends>
+ <home>GO|http://www.geneontology.org/</home>
+ <download></download>
+ <export format="obo_xml" path="obo-all/prosite2go/prosite2go.obo_xml" md5="a167b9d769394778c58d45a7ed9a4a83" timestamp="1261407907" time_generated="1263796662" time_taken_to_generate="0" size="873126">
+ </export>
+ <export format="obo" path="obo-all/prosite2go/prosite2go.obo" md5="895567f5993ca5ba437ba6709598f0a3" timestamp="1261407914" time_generated="1263796662" time_taken_to_generate="0" size="309509">
+ </export>
+ <export format="owl" path="obo-all/prosite2go/prosite2go.owl" md5="0ea66bb0384abee3b5869b93df0dcf78" timestamp="1261407958" time_generated="1263796662" time_taken_to_generate="0" size="1958401">
+ </export>
+ <export format="chadoxml" path="obo-all/prosite2go/prosite2go.chadoxml" md5="eadecff9bee27486c37061c21645be96" timestamp="1261407962" time_generated="1263796663" time_taken_to_generate="0" size="2774656">
+ </export>
+ <export format="godb_prestore" path="obo-all/prosite2go/prosite2go.godb_prestore" md5="c62f2c400e0c0033447cf32b2c9af0cd" timestamp="1261407967" time_generated="1263796663" time_taken_to_generate="0" size="1256183">
+ </export>
+ <export format="rdf" path="obo-all/prosite2go/prosite2go.rdf" md5="488852381bf4f991b0bc6b008cbbbbd8" timestamp="1261407973" time_generated="1263796663" time_taken_to_generate="0" size="442892">
+ </export>
+ <export format="tbl" path="obo-all/prosite2go/prosite2go.tbl" md5="5dae5a0f85de6ad1738ff510efabd51c" timestamp="1261407977" time_generated="1263796663" time_taken_to_generate="0" size="67847">
+ </export>
+ <export format="prolog" path="obo-all/prosite2go/prosite2go.pro" md5="8581dc3840e9773b1147f04422c1c245" timestamp="1261407984" time_generated="1263796663" time_taken_to_generate="0" size="419335">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/prosite2go/prosite2go.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1261407988" time_generated="1263796668" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" problem="true">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" path="obo-all/prosite2go/prosite2go.imports.obo" md5="faf2985723b850b44de494d20c34261d" timestamp="1261407989" time_generated="1263796669" time_taken_to_generate="0" size="249">
+ </export>
+ <export format="obo.html" path="obo-all/prosite2go/prosite2go.obo.html" md5="7dca026eb55c7ebf6ef95ea44c4519b0" timestamp="1261407990" time_generated="1263796669" time_taken_to_generate="0" size="2722639">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" path="obo-all/prosite2go/prosite2go.imports.owl" md5="0bd7c3230764e88bce545717b3d4802e" timestamp="1261407990" time_generated="1263796669" time_taken_to_generate="0" size="517">
+ </export>
+ <export format="imports-local.obo" path="obo-all/prosite2go/prosite2go.imports-local.obo" md5="0d0b72f3193ca26c12e5e7f218fab674" timestamp="1261407990" time_generated="1263796669" time_taken_to_generate="0" size="234">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" path="obo-all/prosite2go/prosite2go.imports-local.owl" md5="ffe75b9cafa1a5dd254f411e5dfb3cf1" timestamp="1261407990" time_generated="1263796669" time_taken_to_generate="0" size="4105">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="reactome2go">
+ <source>ftp://ftp.geneontology.org/pub/go/external2go/reactome2go</source>
+ <namespace>REACTOM2GO</namespace>
+ <status>Implementation release</status>
+ <description>Mappings of reactome2go to GO</description>
+ <foundry>NA</foundry>
+ <format>go_xref</format>
+ <documentation>contact Gene Ontology|go.org</documentation>
+ <url>ftp://ftp.geneontology.org/pub/go/external2go/reactome2go</url>
+ <type>mappings</type>
+ <title>reactome2go mapping</title>
+ <extends>GO</extends>
+ <home>GO|http://www.geneontology.org/</home>
+ <download></download>
+ <export format="obo_xml" path="obo-all/reactome2go/reactome2go.obo_xml" md5="5dc4b467fe9123e249415e54cf6203f7" timestamp="1261011546" time_generated="1263796671" time_taken_to_generate="0" size="1370032">
+ </export>
+ <export format="obo" path="obo-all/reactome2go/reactome2go.obo" md5="6a617fcd2dc33fa426691a8b033a1a3f" timestamp="1261011554" time_generated="1263796671" time_taken_to_generate="0" size="603210">
+ </export>
+ <export format="owl" path="obo-all/reactome2go/reactome2go.owl" md5="54c6acbbcb65b08ba0987ca344c56606" timestamp="1261011618" time_generated="1263796671" time_taken_to_generate="0" size="2663307">
+ </export>
+ <export format="chadoxml" path="obo-all/reactome2go/reactome2go.chadoxml" md5="7010352f02821153e65c586b3bdb6d20" timestamp="1261011622" time_generated="1263796671" time_taken_to_generate="0" size="3769937">
+ </export>
+ <export format="godb_prestore" path="obo-all/reactome2go/reactome2go.godb_prestore" md5="5c8d97e6a34cbd0d1ca807be7d916584" timestamp="1261011627" time_generated="1263796671" time_taken_to_generate="0" size="1704674">
+ </export>
+ <export format="rdf" path="obo-all/reactome2go/reactome2go.rdf" md5="73230bbe8495ff6bc707a3a6d9ffc3a5" timestamp="1261011633" time_generated="1263796671" time_taken_to_generate="0" size="340766">
+ </export>
+ <export format="tbl" path="obo-all/reactome2go/reactome2go.tbl" md5="754ffb350c0b1b1c20f2f74a5d87400b" timestamp="1261011637" time_generated="1263796671" time_taken_to_generate="0" size="92274">
+ </export>
+ <export format="prolog" path="obo-all/reactome2go/reactome2go.pro" md5="2f44bd197a9cd244f8eb9092d825cf84" timestamp="1261011645" time_generated="1263796671" time_taken_to_generate="0" size="567186">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/reactome2go/reactome2go.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1261011649" time_generated="1263796679" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" problem="true">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" path="obo-all/reactome2go/reactome2go.imports.obo" md5="2710fb93376a00eee5cdc92472471fc7" timestamp="1261011650" time_generated="1263796680" time_taken_to_generate="0" size="253">
+ </export>
+ <export format="obo.html" path="obo-all/reactome2go/reactome2go.obo.html" md5="ef4355b193a24ac4ac63300bec78d234" timestamp="1261011650" time_generated="1263796680" time_taken_to_generate="0" size="3929092">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" path="obo-all/reactome2go/reactome2go.imports.owl" md5="9290046f6c19a28dff0ac04821d9a06e" timestamp="1261011650" time_generated="1263796680" time_taken_to_generate="0" size="519">
+ </export>
+ <export format="imports-local.obo" path="obo-all/reactome2go/reactome2go.imports-local.obo" md5="bb379cb359cef717f75ddde7774a3a15" timestamp="1261011650" time_generated="1263796680" time_taken_to_generate="0" size="238">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" path="obo-all/reactome2go/reactome2go.imports-local.owl" md5="a5185a2299b54f24344277376ec1ffa7" timestamp="1261011650" time_generated="1263796680" time_taken_to_generate="0" size="4113">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="rfam2go">
+ <source>ftp://ftp.geneontology.org/pub/go/external2go/rfam2go</source>
+ <namespace>RFAMGO</namespace>
+ <status>Implementation release</status>
+ <description>Mappings of rfam2go to GO</description>
+ <foundry>NA</foundry>
+ <format>go_xref</format>
+ <documentation>contact Gene Ontology|go.org</documentation>
+ <url>ftp://ftp.geneontology.org/pub/go/external2go/rfam2go</url>
+ <type>mappings</type>
+ <title>rfam2go mapping</title>
+ <extends>GO</extends>
+ <home>GO|http://www.geneontology.org/</home>
+ <download></download>
+ <export format="obo_xml" path="obo-all/rfam2go/rfam2go.obo_xml" md5="8264106333c4fdc8f963267971f8b783" timestamp="1261011652" time_generated="1263796682" time_taken_to_generate="0" size="130008">
+ </export>
+ <export format="obo" path="obo-all/rfam2go/rfam2go.obo" md5="b1a41c561fa43800155f3576613204a5" timestamp="1261011653" time_generated="1263796682" time_taken_to_generate="0" size="42563">
+ </export>
+ <export format="owl" path="obo-all/rfam2go/rfam2go.owl" md5="d7a1a174ed390d63769d4220ddb55d17" timestamp="1261011654" time_generated="1263796682" time_taken_to_generate="0" size="298953">
+ </export>
+ <export format="chadoxml" path="obo-all/rfam2go/rfam2go.chadoxml" md5="31d9e12851aa41b788bf228d04b954e7" timestamp="1261011655" time_generated="1263796682" time_taken_to_generate="0" size="429448">
+ </export>
+ <export format="godb_prestore" path="obo-all/rfam2go/rfam2go.godb_prestore" md5="865d22ab4276879836a6a54013a3a29e" timestamp="1261011655" time_generated="1263796682" time_taken_to_generate="0" size="193997">
+ </export>
+ <export format="rdf" path="obo-all/rfam2go/rfam2go.rdf" md5="1e48a9731fd23b28490240e711b214a8" timestamp="1261011656" time_generated="1263796682" time_taken_to_generate="0" size="23969">
+ </export>
+ <export format="tbl" path="obo-all/rfam2go/rfam2go.tbl" md5="b841e3571e9e2c06b157e2ad5886d36c" timestamp="1261011657" time_generated="1263796682" time_taken_to_generate="0" size="10530">
+ </export>
+ <export format="prolog" path="obo-all/rfam2go/rfam2go.pro" md5="988fbec2d2bd62b92ccb495c0c868d36" timestamp="1261011658" time_generated="1263796682" time_taken_to_generate="0" size="62589">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/rfam2go/rfam2go.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1261011659" time_generated="1263796683" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" problem="true">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" path="obo-all/rfam2go/rfam2go.imports.obo" md5="07d412fc6e7caef34da952e05f89c9de" timestamp="1261011659" time_generated="1263796684" time_taken_to_generate="0" size="237">
+ </export>
+ <export format="obo.html" path="obo-all/rfam2go/rfam2go.obo.html" md5="eaf2e247110524ca1d5adc751279b550" timestamp="1261011660" time_generated="1263796684" time_taken_to_generate="0" size="412276">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" path="obo-all/rfam2go/rfam2go.imports.owl" md5="9c33ad921fdbd9d4ed370b4f19bfcb05" timestamp="1261011660" time_generated="1263796685" time_taken_to_generate="0" size="511">
+ </export>
+ <export format="imports-local.obo" path="obo-all/rfam2go/rfam2go.imports-local.obo" md5="11ec6606eb716c86201bd185e2720b57" timestamp="1261011660" time_generated="1263796685" time_taken_to_generate="0" size="222">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" path="obo-all/rfam2go/rfam2go.imports-local.owl" md5="9bfff4484367796cb9344d6e8e52fcf3" timestamp="1261011660" time_generated="1263796685" time_taken_to_generate="0" size="4081">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="smart2go">
+ <source>ftp://ftp.geneontology.org/pub/go/external2go/smart2go</source>
+ <namespace>SMART2GO</namespace>
+ <status>Implementation release</status>
+ <description>Mappings of smart2go to GO</description>
+ <foundry>NA</foundry>
+ <format>go_xref</format>
+ <documentation>contact Gene Ontology|go.org</documentation>
+ <url>ftp://ftp.geneontology.org/pub/go/external2go/smart2go</url>
+ <type>mappings</type>
+ <title>smart2go mapping</title>
+ <extends>GO</extends>
+ <home>GO|http://www.geneontology.org/</home>
+ <download></download>
+ <export format="obo_xml" path="obo-all/smart2go/smart2go.obo_xml" md5="35a3621996f446bd1a385dd726b9bb29" timestamp="1261408002" time_generated="1263796686" time_taken_to_generate="0" size="176056">
+ </export>
+ <export format="obo" path="obo-all/smart2go/smart2go.obo" md5="0c8f1ad7c764b5a42e11bb0f0dc4e99b" timestamp="1261408004" time_generated="1263796686" time_taken_to_generate="0" size="56751">
+ </export>
+ <export format="owl" path="obo-all/smart2go/smart2go.owl" md5="61c8354aaf0b53dd2aa958b6a48b7d9c" timestamp="1261408006" time_generated="1263796686" time_taken_to_generate="0" size="409943">
+ </export>
+ <export format="chadoxml" path="obo-all/smart2go/smart2go.chadoxml" md5="78bcb22572c8684fd27f45be764cb579" timestamp="1261408007" time_generated="1263796686" time_taken_to_generate="0" size="586314">
+ </export>
+ <export format="godb_prestore" path="obo-all/smart2go/smart2go.godb_prestore" md5="a739e5b0c2b334f60a63a0b686cb3964" timestamp="1261408008" time_generated="1263796686" time_taken_to_generate="0" size="265017">
+ </export>
+ <export format="rdf" path="obo-all/smart2go/smart2go.rdf" md5="2fcddd9e97b8dc37df564f27cf4d924e" timestamp="1261408009" time_generated="1263796686" time_taken_to_generate="0" size="134994">
+ </export>
+ <export format="tbl" path="obo-all/smart2go/smart2go.tbl" md5="00b82e5f196eca3984a34fabe3cdf307" timestamp="1261408010" time_generated="1263796686" time_taken_to_generate="0" size="14365">
+ </export>
+ <export format="prolog" path="obo-all/smart2go/smart2go.pro" md5="ec8c36915ca8db11aa69f56da48d3e5b" timestamp="1261408012" time_generated="1263796686" time_taken_to_generate="0" size="86409">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/smart2go/smart2go.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1261408014" time_generated="1263796688" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" problem="true">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" path="obo-all/smart2go/smart2go.imports.obo" md5="4e8809df0094f5a6eb99eb29d9ed5e0b" timestamp="1261408014" time_generated="1263796689" time_taken_to_generate="0" size="241">
+ </export>
+ <export format="obo.html" path="obo-all/smart2go/smart2go.obo.html" md5="37a262afe66c3dfd2389c25900277050" timestamp="1261408014" time_generated="1263796689" time_taken_to_generate="0" size="563195">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" path="obo-all/smart2go/smart2go.imports.owl" md5="28bf0ce4486d65599f9ea70c4681819e" timestamp="1261408014" time_generated="1263796689" time_taken_to_generate="0" size="513">
+ </export>
+ <export format="imports-local.obo" path="obo-all/smart2go/smart2go.imports-local.obo" md5="83a29071a68f0529d8256d9a8a62bdfb" timestamp="1261408014" time_generated="1263796689" time_taken_to_generate="0" size="226">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" path="obo-all/smart2go/smart2go.imports-local.owl" md5="95f3913643c49c0d99860eeaabcb1697" timestamp="1261408014" time_generated="1263796689" time_taken_to_generate="0" size="4089">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="spkw2go">
+ <source>ftp://ftp.geneontology.org/pub/go/external2go/spkw2go</source>
+ <namespace>SPKW2GO</namespace>
+ <status>Implementation release</status>
+ <description>Mappings of spkw2go to GO</description>
+ <foundry>NA</foundry>
+ <format>go_xref</format>
+ <documentation>contact Gene Ontology|go.org</documentation>
+ <url>ftp://ftp.geneontology.org/pub/go/external2go/spkw2go</url>
+ <type>mappings</type>
+ <title>spkw2go mapping</title>
+ <extends>GO</extends>
+ <home>GO|http://www.geneontology.org/</home>
+ <download></download>
+ <export format="obo_xml" path="obo-all/spkw2go/spkw2go.obo_xml" md5="d64a94098326b10b18ee5e55abe41313" timestamp="1261408017" time_generated="1263796691" time_taken_to_generate="0" size="119446">
+ </export>
+ <export format="obo" path="obo-all/spkw2go/spkw2go.obo" md5="794e4e22cb376a3fb9ee326b06ac7677" timestamp="1261408018" time_generated="1263796691" time_taken_to_generate="0" size="43881">
+ </export>
+ <export format="owl" path="obo-all/spkw2go/spkw2go.owl" md5="36352086eec8356029f59b12a46553f7" timestamp="1261408019" time_generated="1263796691" time_taken_to_generate="0" size="260903">
+ </export>
+ <export format="chadoxml" path="obo-all/spkw2go/spkw2go.chadoxml" md5="11671cd7c04082265b21dfd2d70ddfac" timestamp="1261408020" time_generated="1263796691" time_taken_to_generate="0" size="372068">
+ </export>
+ <export format="godb_prestore" path="obo-all/spkw2go/spkw2go.godb_prestore" md5="12854372c03ff7bc9c47808386c4e636" timestamp="1261408021" time_generated="1263796691" time_taken_to_generate="0" size="168627">
+ </export>
+ <export format="rdf" path="obo-all/spkw2go/spkw2go.rdf" md5="6656931ef7f15c03a587c2445b42883b" timestamp="1261408022" time_generated="1263796691" time_taken_to_generate="0" size="236099">
+ </export>
+ <export format="tbl" path="obo-all/spkw2go/spkw2go.tbl" md5="1dd0d27954ad1741d1ebea0ffc3668a2" timestamp="1261408022" time_generated="1263796691" time_taken_to_generate="0" size="9100">
+ </export>
+ <export format="prolog" path="obo-all/spkw2go/spkw2go.pro" md5="245095c360aa5c35ee246bc1d713ea53" timestamp="1261408023" time_generated="1263796691" time_taken_to_generate="0" size="54819">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/spkw2go/spkw2go.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1261408024" time_generated="1263796692" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" problem="true">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" path="obo-all/spkw2go/spkw2go.imports.obo" md5="3ae065edd9d0cd41463296ed18cbb02b" timestamp="1261408025" time_generated="1263796693" time_taken_to_generate="0" size="237">
+ </export>
+ <export format="obo.html" path="obo-all/spkw2go/spkw2go.obo.html" md5="c34c2ea725c2875eb584a97657a36f60" timestamp="1261408025" time_generated="1263796693" time_taken_to_generate="0" size="364834">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" path="obo-all/spkw2go/spkw2go.imports.owl" md5="0f07e0597fb9aedee829e7445e1f494e" timestamp="1261408025" time_generated="1263796693" time_taken_to_generate="0" size="511">
+ </export>
+ <export format="imports-local.obo" path="obo-all/spkw2go/spkw2go.imports-local.obo" md5="4fb827396cb044374d5a54cca37a3ea0" timestamp="1261408025" time_generated="1263796693" time_taken_to_generate="0" size="222">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" path="obo-all/spkw2go/spkw2go.imports-local.owl" md5="aa8fb742ec73b9bb0e02cc8f3827e527" timestamp="1261408025" time_generated="1263796693" time_taken_to_generate="0" size="4081">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="tigr2go">
+ <source>ftp://ftp.geneontology.org/pub/go/external2go/tigr2go</source>
+ <namespace>TIGR2GO</namespace>
+ <status>Implementation release</status>
+ <description>Mappings of tigr2go to GO</description>
+ <foundry>NA</foundry>
+ <format>go_xref</format>
+ <documentation>contact Gene Ontology|go.org</documentation>
+ <url>ftp://ftp.geneontology.org/pub/go/external2go/tigr2go</url>
+ <type>mappings</type>
+ <title>tigr2go mapping</title>
+ <extends>GO</extends>
+ <home>GO|http://www.geneontology.org/</home>
+ <download></download>
+ <export format="obo_xml" path="obo-all/tigr2go/tigr2go.obo_xml" md5="eac068bbc4e481cbb031f70a9ac9bf04" timestamp="1261011681" time_generated="1263796695" time_taken_to_generate="0" size="47708">
+ </export>
+ <export format="obo" path="obo-all/tigr2go/tigr2go.obo" md5="503e1b7fab60132a29b2e78b0d81e2f8" timestamp="1261011681" time_generated="1263796695" time_taken_to_generate="0" size="23119">
+ </export>
+ <export format="owl" path="obo-all/tigr2go/tigr2go.owl" md5="e416d1431dc038081904c90c140fbb51" timestamp="1261011681" time_generated="1263796695" time_taken_to_generate="0" size="89031">
+ </export>
+ <export format="chadoxml" path="obo-all/tigr2go/tigr2go.chadoxml" md5="5d5f24f8bd32f7e68b2ab46e832147d2" timestamp="1261011682" time_generated="1263796695" time_taken_to_generate="0" size="122836">
+ </export>
+ <export format="godb_prestore" path="obo-all/tigr2go/tigr2go.godb_prestore" md5="b7c9f3dd32b56a721bc4850f6e64dab0" timestamp="1261011682" time_generated="1263796695" time_taken_to_generate="0" size="56747">
+ </export>
+ <export format="rdf" path="obo-all/tigr2go/tigr2go.rdf" md5="81bb4189f2e5e71a46791ea5adf9cb8a" timestamp="1261011682" time_generated="1263796695" time_taken_to_generate="0" size="79214">
+ </export>
+ <export format="tbl" path="obo-all/tigr2go/tigr2go.tbl" md5="73f6e2576db24cc75bce6340f8ab8b97" timestamp="1261011683" time_generated="1263796695" time_taken_to_generate="0" size="2964">
+ </export>
+ <export format="prolog" path="obo-all/tigr2go/tigr2go.pro" md5="510c647133dac1c33e52ee0f1d05dbdc" timestamp="1261011683" time_generated="1263796695" time_taken_to_generate="0" size="18459">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/tigr2go/tigr2go.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1261011684" time_generated="1263796695" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" problem="true">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" path="obo-all/tigr2go/tigr2go.imports.obo" md5="ca77525950c19fcea6964866bd8d9271" timestamp="1261011684" time_generated="1263796696" time_taken_to_generate="0" size="237">
+ </export>
+ <export format="obo.html" path="obo-all/tigr2go/tigr2go.obo.html" md5="20d482c87f9fa670f47492d6fc6dcb55" timestamp="1261011685" time_generated="1263796696" time_taken_to_generate="0" size="129264">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" path="obo-all/tigr2go/tigr2go.imports.owl" md5="e42ec9a7f789e152415693b4b3e2c19e" timestamp="1261011685" time_generated="1263796696" time_taken_to_generate="0" size="511">
+ </export>
+ <export format="imports-local.obo" path="obo-all/tigr2go/tigr2go.imports-local.obo" md5="9032985d00114d48f6f2595c0150be69" timestamp="1261011685" time_generated="1263796696" time_taken_to_generate="0" size="222">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" path="obo-all/tigr2go/tigr2go.imports-local.owl" md5="dc76ae88680ffb4ee7cea774c4305c2e" timestamp="1261011685" time_generated="1263796696" time_taken_to_generate="0" size="4081">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="tigrfams2go">
+ <source>ftp://ftp.geneontology.org/pub/go/external2go/tigrfams2go</source>
+ <namespace>TIGRFAMS2GO</namespace>
+ <status>Implementation release</status>
+ <description>Mappings of tigrfams2go to GO</description>
+ <foundry>NA</foundry>
+ <format>go_xref</format>
+ <documentation>contact Gene Ontology|go.org</documentation>
+ <url>ftp://ftp.geneontology.org/pub/go/external2go/tigrfams2go</url>
+ <type>mappings</type>
+ <title>tigrfams2go mapping</title>
+ <extends>GO</extends>
+ <home>GO|http://www.geneontology.org/</home>
+ <download></download>
+ <export format="obo_xml" path="obo-all/tigrfams2go/tigrfams2go.obo_xml" md5="d7de8a0ae2e1329412ce30dbf14a1b77" timestamp="1261011688" time_generated="1263796698" time_taken_to_generate="0" size="1046673">
+ </export>
+ <export format="obo" path="obo-all/tigrfams2go/tigrfams2go.obo" md5="db706b0797356c5780b3090db3d314ac" timestamp="1261011693" time_generated="1263796698" time_taken_to_generate="0" size="483704">
+ </export>
+ <export format="owl" path="obo-all/tigrfams2go/tigrfams2go.owl" md5="3c50f9e15eb0884b19149ca78fbe93e9" timestamp="1261011729" time_generated="1263796698" time_taken_to_generate="0" size="2067651">
+ </export>
+ <export format="chadoxml" path="obo-all/tigrfams2go/tigrfams2go.chadoxml" md5="5665041065e3813fc19622df3750de4d" timestamp="1261011732" time_generated="1263796698" time_taken_to_generate="0" size="2811579">
+ </export>
+ <export format="godb_prestore" path="obo-all/tigrfams2go/tigrfams2go.godb_prestore" md5="5a9fe65640acfad1f3225bcbb02480cb" timestamp="1261011736" time_generated="1263796698" time_taken_to_generate="0" size="1294851">
+ </export>
+ <export format="rdf" path="obo-all/tigrfams2go/tigrfams2go.rdf" md5="066bdf445384947961a712e052a01f7b" timestamp="1261011742" time_generated="1263796698" time_taken_to_generate="0" size="653934">
+ </export>
+ <export format="tbl" path="obo-all/tigrfams2go/tigrfams2go.tbl" md5="b29b942eaef4b3039117eaf6e696c2b6" timestamp="1261011745" time_generated="1263796698" time_taken_to_generate="0" size="67769">
+ </export>
+ <export format="prolog" path="obo-all/tigrfams2go/tigrfams2go.pro" md5="67b573f718c7a9cc2c1c10e8a625e472" timestamp="1261011750" time_generated="1263796698" time_taken_to_generate="0" size="458963">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/tigrfams2go/tigrfams2go.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1261011754" time_generated="1263796703" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" problem="true">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" path="obo-all/tigrfams2go/tigrfams2go.imports.obo" md5="3d245450cd01bb73665fa89d0e828956" timestamp="1261011754" time_generated="1263796704" time_taken_to_generate="0" size="253">
+ </export>
+ <export format="obo.html" path="obo-all/tigrfams2go/tigrfams2go.obo.html" md5="0e27587caff3e298bb538dac9901c321" timestamp="1261011755" time_generated="1263796704" time_taken_to_generate="0" size="2971734">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" path="obo-all/tigrfams2go/tigrfams2go.imports.owl" md5="ff38f9fd52bc58f9dfe110e1abadf7e7" timestamp="1261011755" time_generated="1263796704" time_taken_to_generate="0" size="519">
+ </export>
+ <export format="imports-local.obo" path="obo-all/tigrfams2go/tigrfams2go.imports-local.obo" md5="e6150660037b28ef8ad95e6a168dccef" timestamp="1261011755" time_generated="1263796704" time_taken_to_generate="0" size="238">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" path="obo-all/tigrfams2go/tigrfams2go.imports-local.owl" md5="3ca68f734865f623aa123e808f0ebc82" timestamp="1261011755" time_generated="1263796704" time_taken_to_generate="0" size="4113">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="um-bbd_enzymeid2go">
+ <source>ftp://ftp.geneontology.org/pub/go/external2go/um-bbd_enzymeid2go</source>
+ <namespace>UMBBDENZYMEID2GO</namespace>
+ <status>Implementation release</status>
+ <description>Mappings of um-bbd_enzymeid2go to GO</description>
+ <foundry>NA</foundry>
+ <format>go_xref</format>
+ <documentation>contact Gene Ontology|go.org</documentation>
+ <url>ftp://ftp.geneontology.org/pub/go/external2go/um-bbd_enzymeid2go</url>
+ <type>mappings</type>
+ <title>um-bbd_enzymeid2go mapping</title>
+ <extends>GO</extends>
+ <home>GO|http://www.geneontology.org/</home>
+ <download></download>
+ <export format="obo_xml" path="obo-all/um-bbd_enzymeid2go/um-bbd_enzymeid2go.obo_xml" md5="073051cf944a0cb5066b32256803f446" timestamp="1261011756" time_generated="1263796705" time_taken_to_generate="0" size="105586">
+ </export>
+ <export format="obo" path="obo-all/um-bbd_enzymeid2go/um-bbd_enzymeid2go.obo" md5="c0bb956fd7739654ae082787fc438108" timestamp="1261011757" time_generated="1263796705" time_taken_to_generate="0" size="38463">
+ </export>
+ <export format="owl" path="obo-all/um-bbd_enzymeid2go/um-bbd_enzymeid2go.owl" md5="10e16ca582d27021a3ab34c50169caaa" timestamp="1261011758" time_generated="1263796705" time_taken_to_generate="0" size="285957">
+ </export>
+ <export format="chadoxml" path="obo-all/um-bbd_enzymeid2go/um-bbd_enzymeid2go.chadoxml" md5="0ca78528b1d80e58394f7d9244924427" timestamp="1261011758" time_generated="1263796705" time_taken_to_generate="0" size="398823">
+ </export>
+ <export format="godb_prestore" path="obo-all/um-bbd_enzymeid2go/um-bbd_enzymeid2go.godb_prestore" md5="29b0c443f6103a3ee2fed5c1e9c758b4" timestamp="1261011759" time_generated="1263796706" time_taken_to_generate="0" size="184313">
+ </export>
+ <export format="rdf" path="obo-all/um-bbd_enzymeid2go/um-bbd_enzymeid2go.rdf" md5="e7e98f4ff89afdb92271b350669d42e0" timestamp="1261011760" time_generated="1263796706" time_taken_to_generate="0" size="276321">
+ </export>
+ <export format="tbl" path="obo-all/um-bbd_enzymeid2go/um-bbd_enzymeid2go.tbl" md5="990092de2a3d13eb43009c646d7df127" timestamp="1261011760" time_generated="1263796706" time_taken_to_generate="0" size="9594">
+ </export>
+ <export format="prolog" path="obo-all/um-bbd_enzymeid2go/um-bbd_enzymeid2go.pro" md5="d53ff789541793c56cd25c8e79b661ba" timestamp="1261011761" time_generated="1263796706" time_taken_to_generate="0" size="64425">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/um-bbd_enzymeid2go/um-bbd_enzymeid2go.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1261011762" time_generated="1263796706" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" problem="true">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" path="obo-all/um-bbd_enzymeid2go/um-bbd_enzymeid2go.imports.obo" md5="510017e4effb52932a98b2fb689f79c6" timestamp="1261011763" time_generated="1263796708" time_taken_to_generate="0" size="281">
+ </export>
+ <export format="obo.html" path="obo-all/um-bbd_enzymeid2go/um-bbd_enzymeid2go.obo.html" md5="3e8edb4c60df245c44d3a56e9c2f8d4f" timestamp="1261011763" time_generated="1263796708" time_taken_to_generate="0" size="356167">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" path="obo-all/um-bbd_enzymeid2go/um-bbd_enzymeid2go.imports.owl" md5="587c811965d156e830536944e1b6d47c" timestamp="1261011763" time_generated="1263796708" time_taken_to_generate="0" size="533">
+ </export>
+ <export format="imports-local.obo" path="obo-all/um-bbd_enzymeid2go/um-bbd_enzymeid2go.imports-local.obo" md5="9bc9a14cb5fff998ed9555a5627ab949" timestamp="1261011763" time_generated="1263796708" time_taken_to_generate="0" size="266">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" path="obo-all/um-bbd_enzymeid2go/um-bbd_enzymeid2go.imports-local.owl" md5="3da1f3ae82f9a2cbc7718aa78c29a8f6" timestamp="1261011763" time_generated="1263796708" time_taken_to_generate="0" size="4169">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="um-bbd_pathwayid2go">
+ <source>ftp://ftp.geneontology.org/pub/go/external2go/um-bbd_pathwayid2go</source>
+ <namespace>UMBBDPATHWAYID2GO</namespace>
+ <status>Implementation release</status>
+ <description>Mappings of um-bbd_pathwayid2go to GO</description>
+ <foundry>NA</foundry>
+ <format>go_xref</format>
+ <documentation>contact Gene Ontology|go.org</documentation>
+ <url>ftp://ftp.geneontology.org/pub/go/external2go/um-bbd_pathwayid2go</url>
+ <type>mappings</type>
+ <title>um-bbd_pathwayid2go mapping</title>
+ <extends>GO</extends>
+ <home>GO|http://www.geneontology.org/</home>
+ <download></download>
+ <export format="obo_xml" path="obo-all/um-bbd_pathwayid2go/um-bbd_pathwayid2go.obo_xml" md5="7aa458eb09ed9e1dd38102c22a52d817" timestamp="1261011764" time_generated="1263796709" time_taken_to_generate="0" size="18119">
+ </export>
+ <export format="obo" path="obo-all/um-bbd_pathwayid2go/um-bbd_pathwayid2go.obo" md5="335837d056411e8e4d6caab8109569e4" timestamp="1261011764" time_generated="1263796709" time_taken_to_generate="0" size="6597">
+ </export>
+ <export format="owl" path="obo-all/um-bbd_pathwayid2go/um-bbd_pathwayid2go.owl" md5="0588c424e1c43c076c08964471e2c951" timestamp="1261011765" time_generated="1263796709" time_taken_to_generate="0" size="51756">
+ </export>
+ <export format="chadoxml" path="obo-all/um-bbd_pathwayid2go/um-bbd_pathwayid2go.chadoxml" md5="a3df614cfa4745a0c3dda5a1a0066705" timestamp="1261011765" time_generated="1263796709" time_taken_to_generate="0" size="70012">
+ </export>
+ <export format="godb_prestore" path="obo-all/um-bbd_pathwayid2go/um-bbd_pathwayid2go.godb_prestore" md5="5c0749fa26f382d3e3ef5332dce98df5" timestamp="1261011765" time_generated="1263796709" time_taken_to_generate="0" size="33302">
+ </export>
+ <export format="rdf" path="obo-all/um-bbd_pathwayid2go/um-bbd_pathwayid2go.rdf" md5="7c806f852cfe01559d0eb0e158eb1324" timestamp="1261011765" time_generated="1263796709" time_taken_to_generate="0" size="47713">
+ </export>
+ <export format="tbl" path="obo-all/um-bbd_pathwayid2go/um-bbd_pathwayid2go.tbl" md5="adb9b31d050b6fc20c1297d846d46d2a" timestamp="1261011765" time_generated="1263796710" time_taken_to_generate="0" size="1651">
+ </export>
+ <export format="prolog" path="obo-all/um-bbd_pathwayid2go/um-bbd_pathwayid2go.pro" md5="0efb7af1befe907b5072cba2fbcac852" timestamp="1261011766" time_generated="1263796710" time_taken_to_generate="0" size="11174">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/um-bbd_pathwayid2go/um-bbd_pathwayid2go.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1261011766" time_generated="1263796710" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" problem="true">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" path="obo-all/um-bbd_pathwayid2go/um-bbd_pathwayid2go.imports.obo" md5="38434db1164691289787a928fbde297c" timestamp="1261011767" time_generated="1263796711" time_taken_to_generate="0" size="285">
+ </export>
+ <export format="obo.html" path="obo-all/um-bbd_pathwayid2go/um-bbd_pathwayid2go.obo.html" md5="19fcade1e54140e782018407257c04b7" timestamp="1261011767" time_generated="1263796711" time_taken_to_generate="0" size="61699">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" path="obo-all/um-bbd_pathwayid2go/um-bbd_pathwayid2go.imports.owl" md5="4764421a2f0c3a3055755cf505388d39" timestamp="1261011767" time_generated="1263796711" time_taken_to_generate="0" size="535">
+ </export>
+ <export format="imports-local.obo" path="obo-all/um-bbd_pathwayid2go/um-bbd_pathwayid2go.imports-local.obo" md5="6c4633e86266daaea78e4029eace7e87" timestamp="1261011767" time_generated="1263796711" time_taken_to_generate="0" size="270">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" path="obo-all/um-bbd_pathwayid2go/um-bbd_pathwayid2go.imports-local.owl" md5="1913cca2ff27b0c4bb781d2936eacc60" timestamp="1261011767" time_generated="1263796711" time_taken_to_generate="0" size="4177">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="go_xrf_metadata">
+ <source>ftp://ftp.geneontology.org/pub/go/doc/GO.xrf_abbs</source>
+ <namespace>GO_XRF_ABBS</namespace>
+ <status>Implementation release</status>
+ <contact></contact>
+ <description>metadata on the database authorities (MGI, EC, PubMed, UniProt, FlyBase etc) used in GO Consortium</description>
+ <foundry>NA</foundry>
+ <format>xrf_abbs</format>
+ <documentation>http://www.geneontology.org/cgi-bin/xrefs.cgi</documentation>
+ <url>ftp://ftp.geneontology.org/pub/go/doc/GO.xrf_abbs</url>
+ <type>metadata</type>
+ <title>GO database cross-references metadata</title>
+ <home>GO|http://www.geneontology.org/</home>
+ <download></download>
+ <export format="obo_xml" path="obo-all/go_xrf_metadata/go_xrf_metadata.obo_xml" md5="b88179ab10f2cfc767d3700703499c0b" timestamp="1263796714" time_generated="1263796714" time_taken_to_generate="1" size="239182">
+ </export>
+ <export format="obo" path="obo-all/go_xrf_metadata/go_xrf_metadata.obo" md5="15b1ee7ed33c5066e1ff87e40bf86fa9" timestamp="1263796715" time_generated="1263796715" time_taken_to_generate="1" size="119560">
+ </export>
+ <export format="owl" path="obo-all/go_xrf_metadata/go_xrf_metadata.owl" md5="90ac97c10cedec5b6dc166d746c40e1d" timestamp="1263796717" time_generated="1263796717" time_taken_to_generate="2" size="214256">
+ </export>
+ <export format="chadoxml" path="obo-all/go_xrf_metadata/go_xrf_metadata.chadoxml" md5="e4fc13f0c956cbdd24ba1656096dac9b" timestamp="1263796719" time_generated="1263796719" time_taken_to_generate="2" size="206727">
+ </export>
+ <export format="godb_prestore" path="obo-all/go_xrf_metadata/go_xrf_metadata.godb_prestore" md5="c90a3dcc3a22ab274a6058fc2df92f15" timestamp="1263796720" time_generated="1263796720" time_taken_to_generate="1" size="76105">
+ </export>
+ <export format="rdf" problem="true">
+ </export>
+ <export format="tbl" problem="true">
+ </export>
+ <export format="prolog" path="obo-all/go_xrf_metadata/go_xrf_metadata.pro" md5="08e46c2da5f6633bf0cbabe500742460" timestamp="1263796723" time_generated="1263796723" time_taken_to_generate="2" size="134066">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/go_xrf_metadata/go_xrf_metadata.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1263796725" time_generated="1263796725" time_taken_to_generate="1" size="20">
+ </export>
+ <export format="stats" problem="true">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/go_xrf_metadata/go_xrf_metadata.obo.html" md5="0d5fed4305d3b9a7759f25c4fb90f258" timestamp="1263796726" time_generated="1263796726" time_taken_to_generate="0" size="678926">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="oboInOwl">
+ <source>http://www.geneontology.org/formats/oboInOwl.obo</source>
+ <uriprefix>http://www.geneontology.org/formats/oboInOwl#</uriprefix>
+ <status>Implementation release</status>
+ <contact></contact>
+ <foundry>NA</foundry>
+ <documentation>http://www.bioontology.org/wiki/index.php/OboInOwl:Main_Page</documentation>
+ <url>http://www.geneontology.org/formats/oboInOwl.obo</url>
+ <home>GO|http://www.geneontology.org/</home>
+ <namespace>oboInOwl</namespace>
+ <description>description of the built-in OBO metamodel: synonyms, definitions, obsoletion</description>
+ <format>obo</format>
+ <title>OBO metamodel</title>
+ <type>metadata</type>
+ <owl_source>http://www.geneontology.org/formats/oboInOwl.owl</owl_source>
+ <download></download>
+ <export format="obo_xml" path="obo-all/oboInOwl/oboInOwl.obo_xml" md5="19fbc6e99c64f7b56ff156d046b1341e" timestamp="1261011777" time_generated="1263796729" time_taken_to_generate="0" size="13582">
+ </export>
+ <export format="obo" path="obo-all/oboInOwl/oboInOwl.obo" md5="f2cffbe0487b109e030e48c1bec98d01" timestamp="1263796729" time_generated="1263796729" time_taken_to_generate="0" size="6618">
+ </export>
+ <export format="owl" path="obo-all/oboInOwl/oboInOwl.owl" md5="9b93178dc37c14e724c83e7b0755ba8f" timestamp="1261011778" time_generated="1263796729" time_taken_to_generate="0" size="29560">
+ </export>
+ <export format="chadoxml" path="obo-all/oboInOwl/oboInOwl.chadoxml" md5="c02cd679b6ac669ee810ee4283e463d7" timestamp="1261011778" time_generated="1263796729" time_taken_to_generate="0" size="22619">
+ </export>
+ <export format="godb_prestore" path="obo-all/oboInOwl/oboInOwl.godb_prestore" md5="67123b5a4e8042d56517270a4ffeada2" timestamp="1261011778" time_generated="1263796729" time_taken_to_generate="0" size="24403">
+ </export>
+ <export format="rdf" path="obo-all/oboInOwl/oboInOwl.rdf" md5="14453a0e5230692181c3048fdc0c769d" timestamp="1261011778" time_generated="1263796729" time_taken_to_generate="0" size="14392">
+ </export>
+ <export format="tbl" path="obo-all/oboInOwl/oboInOwl.tbl" md5="38c5a4cc6ce081aa2679fa1ecf6f7573" timestamp="1261011778" time_generated="1263796729" time_taken_to_generate="0" size="717">
+ </export>
+ <export format="prolog" path="obo-all/oboInOwl/oboInOwl.pro" md5="618e4de5a79dc9275e684c388642eb0e" timestamp="1261011778" time_generated="1263796729" time_taken_to_generate="0" size="12920">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/oboInOwl/oboInOwl.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1261011779" time_generated="1263796729" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" path="obo-all/oboInOwl/oboInOwl.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1261011780" time_generated="1263796729" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/oboInOwl/oboInOwl.obo.html" md5="08edc33d6ec253438ba2c61da839fa62" timestamp="1261011780" time_generated="1263796729" time_taken_to_generate="0" size="27604">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="gazetteer">
+ <source></source>
+ <namespace>GAZ</namespace>
+ <status>Draft</status>
+ <contact>Michael Ashburner ma11 gen.cam.ac.uk</contact>
+ <description></description>
+ <foundry>NA</foundry>
+ <format>obo</format>
+ <documentation></documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/environmental/gaz.obo</url>
+ <type>instanceset</type>
+ <title></title>
+ <home></home>
+ <download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/environmental/gaz.obo</download>
+ <export format="obo_xml" path="obo-all/gazetteer/gazetteer.obo_xml" md5="9ecc5b701cfcbb42986032d6a2400d88" timestamp="1263797221" time_generated="1263797221" time_taken_to_generate="430" size="120895715">
+ </export>
+ <export format="obo" path="obo-all/gazetteer/gazetteer.obo" md5="0e420f06f30974c81d75978b5fbf61af" timestamp="1263796789" time_generated="1263797222" time_taken_to_generate="0" size="67394996">
+ </export>
+ <export format="owl" problem="true">
+ </export>
+ <export format="chadoxml" problem="true">
+ </export>
+ <export format="godb_prestore" problem="true">
+ </export>
+ <export format="rdf" problem="true">
+ </export>
+ <export format="tbl" problem="true">
+ </export>
+ <export format="prolog" path="obo-all/gazetteer/gazetteer.pro" md5="bbe6d1289147592e01279827a7baf08d" timestamp="1263831040" time_generated="1263831040" time_taken_to_generate="1014" size="106849759">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/gazetteer/gazetteer.validation_report" md5="5dad34a63ede79b3199888173432f22d" timestamp="1263832096" time_generated="1263832096" time_taken_to_generate="562" size="916">
+ </export>
+ <export format="stats" path="obo-all/gazetteer/gazetteer.stats" md5="619a62d04ddf7c62cc6ebdc743938b12" timestamp="1263832106" time_generated="1263832106" time_taken_to_generate="10" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/gazetteer/gazetteer.obo.html" md5="fadf4b7336646bbbf4f0b2cf32df57ce" timestamp="1263832159" time_generated="1263832159" time_taken_to_generate="53" size="264163798">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="genes-10090">
+ <source></source>
+ <namespace>MGI</namespace>
+ <status>Draft</status>
+ <contact>Chris Mungall cjm fruitfly.org</contact>
+ <description></description>
+ <foundry>NA</foundry>
+ <format>obo</format>
+ <documentation></documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/gene/genes-10090.obo</url>
+ <type>instanceset</type>
+ <title>mouse genes</title>
+ <home></home>
+ <download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/gene/genes-10090.obo</download>
+ <export format="obo_xml" path="obo-all/genes-10090/genes-10090.obo_xml" md5="a9d8a896c96ed0257e9183c2c8af388c" timestamp="1261033249" time_generated="1263832278" time_taken_to_generate="0" size="37213896">
+ </export>
+ <export format="obo" path="obo-all/genes-10090/genes-10090.obo" md5="29c4ee8b988948d1b6d7fcff45695eb5" timestamp="1263832278" time_generated="1263832279" time_taken_to_generate="0" size="15948313">
+ </export>
+ <export format="owl" problem="true">
+ </export>
+ <export format="chadoxml" problem="true">
+ </export>
+ <export format="godb_prestore" problem="true">
+ </export>
+ <export format="rdf" problem="true">
+ </export>
+ <export format="tbl" problem="true">
+ </export>
+ <export format="prolog" path="obo-all/genes-10090/genes-10090.pro" md5="4f7b455584c70db5328010d71c0c2cd5" timestamp="1261065556" time_generated="1263863801" time_taken_to_generate="0" size="33332899">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/genes-10090/genes-10090.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1261065695" time_generated="1263863963" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" problem="true">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/genes-10090/genes-10090.obo.html" md5="b3425da4f88d6ca7cec4062a87366362" timestamp="1261065712" time_generated="1263863966" time_taken_to_generate="0" size="100177475">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="genes-7955">
+ <source></source>
+ <namespace>ZFIN</namespace>
+ <status>Draft</status>
+ <contact>Chris Mungall cjm fruitfly.org</contact>
+ <description></description>
+ <foundry>NA</foundry>
+ <format>obo</format>
+ <documentation></documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/gene/genes-7955.obo</url>
+ <type>instanceset</type>
+ <title>zebrafish genes</title>
+ <home></home>
+ <download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/gene/genes-7955.obo</download>
+ <export format="obo_xml" path="obo-all/genes-7955/genes-7955.obo_xml" md5="f6ad6f748768065938d0b38a29d78628" timestamp="1261065767" time_generated="1263864023" time_taken_to_generate="0" size="18204458">
+ </export>
+ <export format="obo" path="obo-all/genes-7955/genes-7955.obo" md5="81b31e2efabe23a6053806eb48dcd746" timestamp="1263864023" time_generated="1263864024" time_taken_to_generate="0" size="7589900">
+ </export>
+ <export format="owl" path="obo-all/genes-7955/genes-7955.owl" md5="3da22d1f896ab80bee98d4d843a95bff" timestamp="1261469227" time_generated="1263864024" time_taken_to_generate="0" size="15864529">
+ </export>
+ <export format="chadoxml" problem="true">
+ </export>
+ <export format="godb_prestore" problem="true">
+ </export>
+ <export format="rdf" problem="true">
+ </export>
+ <export format="tbl" problem="true">
+ </export>
+ <export format="prolog" path="obo-all/genes-7955/genes-7955.pro" md5="73ef00f16b173503d2fcaf67ffe97d78" timestamp="1261094975" time_generated="1263864024" time_taken_to_generate="0" size="17880617">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/genes-7955/genes-7955.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1261095038" time_generated="1263864115" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" problem="true">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/genes-7955/genes-7955.obo.html" md5="92b994ad75ecd92ddc3b973dd4ad1aaa" timestamp="1261095047" time_generated="1263864117" time_taken_to_generate="0" size="52198884">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="genes-10090">
+ <source></source>
+ <namespace>MGI</namespace>
+ <status>Draft</status>
+ <contact>Chris Mungall cjm fruitfly.org</contact>
+ <description></description>
+ <foundry>NA</foundry>
+ <format>obo</format>
+ <documentation></documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/gene/genes-10090.obo</url>
+ <type>instanceset</type>
+ <title>mouse genes</title>
+ <home></home>
+ <download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/gene/genes-10090.obo</download>
+ <export format="obo_xml" path="obo-all/genes-10090/genes-10090.obo_xml" md5="a9d8a896c96ed0257e9183c2c8af388c" timestamp="1261033249" time_generated="1263864121" time_taken_to_generate="0" size="37213896">
+ </export>
+ <export format="obo" path="obo-all/genes-10090/genes-10090.obo" md5="29c4ee8b988948d1b6d7fcff45695eb5" timestamp="1263832278" time_generated="1263864121" time_taken_to_generate="0" size="15948313">
+ </export>
+ <export format="owl" problem="true">
+ </export>
+ <export format="chadoxml" problem="true">
+ </export>
+ <export format="godb_prestore" problem="true">
+ </export>
+ <export format="rdf" problem="true">
+ </export>
+ <export format="tbl" problem="true">
+ </export>
+ <export format="prolog" path="obo-all/genes-10090/genes-10090.pro" md5="4f7b455584c70db5328010d71c0c2cd5" timestamp="1261065556" time_generated="1263890229" time_taken_to_generate="0" size="33332899">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/genes-10090/genes-10090.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1261065695" time_generated="1263890434" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" problem="true">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/genes-10090/genes-10090.obo.html" md5="b3425da4f88d6ca7cec4062a87366362" timestamp="1261065712" time_generated="1263890438" time_taken_to_generate="0" size="100177475">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="genes-9096">
+ <source></source>
+ <namespace>NCBIGene</namespace>
+ <status>Draft</status>
+ <contact>Chris Mungall cjm fruitfly.org</contact>
+ <description></description>
+ <foundry>NA</foundry>
+ <format>obo</format>
+ <documentation></documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/gene/genes-9096.obo</url>
+ <type>instanceset</type>
+ <title>human genes</title>
+ <home></home>
+ <download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/gene/genes-9096.obo</download>
+ <problem>Source not available at specified URL as recognised format</problem>
+ </ont>
+ <ont id="genes-7227">
+ <source></source>
+ <namespace>FlyBase</namespace>
+ <status>Draft</status>
+ <contact>Chris Mungall cjm fruitfly.org</contact>
+ <description></description>
+ <foundry>NA</foundry>
+ <format>obo</format>
+ <documentation></documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/gene/genes-7227.obo</url>
+ <type>instanceset</type>
+ <title>fly genes</title>
+ <home></home>
+ <download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/gene/genes-7227.obo</download>
+ <export format="obo_xml" path="obo-all/genes-7227/genes-7227.obo_xml" md5="0b3a28db828ef1b221e427907b459b99" timestamp="1261121990" time_generated="1263890752" time_taken_to_generate="0" size="14719728">
+ </export>
+ <export format="obo" path="obo-all/genes-7227/genes-7227.obo" md5="19369c9d9574c6c54d3141bd8d0d2575" timestamp="1263890751" time_generated="1263890752" time_taken_to_generate="0" size="5807941">
+ </export>
+ <export format="owl" path="obo-all/genes-7227/genes-7227.owl" md5="3c785629e72d743b452a023ce47e94b3" timestamp="1261138446" time_generated="1263890752" time_taken_to_generate="0" size="9868706">
+ </export>
+ <export format="chadoxml" problem="true">
+ </export>
+ <export format="godb_prestore" problem="true">
+ </export>
+ <export format="rdf" problem="true">
+ </export>
+ <export format="tbl" problem="true">
+ </export>
+ <export format="prolog" path="obo-all/genes-7227/genes-7227.pro" md5="cd081c78bab8cf3f0a834d31a2fa94b8" timestamp="1261138556" time_generated="1263890752" time_taken_to_generate="0" size="15857990">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/genes-7227/genes-7227.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1261138627" time_generated="1263890853" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" problem="true">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/genes-7227/genes-7227.obo.html" md5="48ef69651c4b8726704c83ae03465670" timestamp="1261138634" time_generated="1263890857" time_taken_to_generate="0" size="38959138">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="zebrafish_anatomy_prerelease">
+ <prerelease_download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/fish/preversion.zfish.obo</prerelease_download>
+ <granularity>organismal</granularity>
+ <status>Production and review</status>
+ <contact>ZFIN administrators zfinadmin zfin.org</contact>
+ <subtypes_of>bfo:IndependentContinuant</subtypes_of>
+ <foundry>Yes</foundry>
+ <domain>anatomy</domain>
+ <is_prerelease>1</is_prerelease>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/fish/zebrafish_anatomy.obo</url>
+ <documentation></documentation>
+ <patho_type>canonical</patho_type>
+ <home>ZFIN Summary|http://zfin.org/zf_info/anatomy/dict/sum.html</home>
+ <additional_namespace>ZFS</additional_namespace>
+ <xrefs_to>cell,caro,teleost_anatomy</xrefs_to>
+ <namespace>ZFA</namespace>
+ <description>A structured controlled vocabulary of the anatomy and development of the Zebrafish (<i>Danio rerio</i>).</description>
+ <format>obo</format>
+ <title>Zebrafish anatomy and development PRERELEASE</title>
+ <relevant_organism>NCBITaxon:7954|Danio</relevant_organism>
+ <download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/fish/preversion.zfish.obo</download>
+ <export format="obo_xml" path="obo-all/zebrafish_anatomy_prerelease/zebrafish_anatomy_prerelease.obo_xml" md5="a56ad8d61dc2d87f7c672a00c059cfcf" timestamp="1261864063" time_generated="1263890870" time_taken_to_generate="0" size="2153409">
+ </export>
+ <export format="obo" path="obo-all/zebrafish_anatomy_prerelease/zebrafish_anatomy_prerelease.obo" md5="98cfadbc679f73388e5429fb46944b1a" timestamp="1263890870" time_generated="1263890870" time_taken_to_generate="0" size="1077469">
+ </export>
+ <export format="owl" path="obo-all/zebrafish_anatomy_prerelease/zebrafish_anatomy_prerelease.owl" md5="276ac6431982def1085abb3f487747cd" timestamp="1261864356" time_generated="1263890870" time_taken_to_generate="0" size="5625708">
+ </export>
+ <export format="chadoxml" path="obo-all/zebrafish_anatomy_prerelease/zebrafish_anatomy_prerelease.chadoxml" md5="09c3c63c2203b5e721739a13fbb7c4e4" timestamp="1261864429" time_generated="1263890870" time_taken_to_generate="0" size="5172048">
+ </export>
+ <export format="godb_prestore" path="obo-all/zebrafish_anatomy_prerelease/zebrafish_anatomy_prerelease.godb_prestore" md5="b5d58155af66b06c7e690ed90f3e7196" timestamp="1261864436" time_generated="1263890870" time_taken_to_generate="0" size="5573964">
+ </export>
+ <export format="rdf" path="obo-all/zebrafish_anatomy_prerelease/zebrafish_anatomy_prerelease.rdf" md5="a631926bfc15d68b1e853534181e4736" timestamp="1261864446" time_generated="1263890870" time_taken_to_generate="0" size="2590018">
+ </export>
+ <export format="tbl" path="obo-all/zebrafish_anatomy_prerelease/zebrafish_anatomy_prerelease.tbl" md5="44c41cd1f50df7f61ba3c6e2a5ad8bd0" timestamp="1261864451" time_generated="1263890870" time_taken_to_generate="0" size="335306">
+ </export>
+ <export format="prolog" path="obo-all/zebrafish_anatomy_prerelease/zebrafish_anatomy_prerelease.pro" md5="545bf0a008ccdd7c4e42f90c4faa440a" timestamp="1263527017" time_generated="1263890870" time_taken_to_generate="0" size="1895255">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/zebrafish_anatomy_prerelease/zebrafish_anatomy_prerelease.validation_report" md5="7e583435961fee0c3e4edfb7267d5587" timestamp="1261864490" time_generated="1263890884" time_taken_to_generate="0" size="5136767">
+ </export>
+ <export format="stats" path="obo-all/zebrafish_anatomy_prerelease/zebrafish_anatomy_prerelease.stats" md5="71666b8d5da5f0cdd71d1938865d3a1c" timestamp="1261864491" time_generated="1263890885" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/zebrafish_anatomy_prerelease/zebrafish_anatomy_prerelease.obo.html" md5="2536dd51b14c9832556f8a13f2f809a6" timestamp="1261864492" time_generated="1263890885" time_taken_to_generate="0" size="4978286">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="sdiff" path="obo-all/zebrafish_anatomy_prerelease/zebrafish_anatomy_prerelease.sdiff" md5="eadb305d9d490eb2b4ae0c9900890109" timestamp="1263891011" time_generated="1263891011" time_taken_to_generate="126" size="177636">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="fma_lite_prerelease">
+ <prerelease_download>http://obo.svn.sourceforge.net/viewvc/*checkout*/obo/fma-conversion/trunk/fma3.obo</prerelease_download>
+ <granularity>organismal</granularity>
+ <status>Production and review</status>
+ <contact>OBO Anatomy obo-anatomy lists.sourceforge.net</contact>
+ <subtypes_of>CARO:0000000</subtypes_of>
+ <foundry>Yes</foundry>
+ <domain>anatomy</domain>
+ <is_prerelease>1</is_prerelease>
+ <url>http://obo.svn.sourceforge.net/viewvc/*checkout*/obo/fma-conversion/trunk/fma2_obo.obo</url>
+ <documentation></documentation>
+ <patho_type>canonical</patho_type>
+ <home>FMA|http://sig.biostr.washington.edu/projects/fm/index.html</home>
+ <namespace>FMA</namespace>
+ <description>Obo format translation of the FMA, omitting all relationships other than is_a, part_of and has_part. Future versions of fma_obo will include more relationships</description>
+ <format>obo</format>
+ <title>Foundational Model of Anatomy (subset) PRERELEASE</title>
+ <previousrelease_download>http://obo.svn.sourceforge.net/viewvc/*checkout*/obo/fma-conversion/trunk/fma_obo.obo</previousrelease_download>
+ <relevant_organism>NCBITaxon:9606|Homo sapiens</relevant_organism>
+ <download>http://obo.svn.sourceforge.net/viewvc/*checkout*/obo/fma-conversion/trunk/fma3.obo</download>
+ <export format="obo_xml" path="obo-all/fma_lite_prerelease/fma_lite_prerelease.obo_xml" md5="bb2d7b13c7feab920971375af314920b" timestamp="1261139480" time_generated="1263891052" time_taken_to_generate="0" size="22282057">
+ </export>
+ <export format="obo" path="obo-all/fma_lite_prerelease/fma_lite_prerelease.obo" md5="efe2b72573709277e317a16fe9b14a92" timestamp="1263891052" time_generated="1263891052" time_taken_to_generate="0" size="15705701">
+ </export>
+ <export format="owl" problem="true">
+ </export>
+ <export format="chadoxml" path="obo-all/fma_lite_prerelease/fma_lite_prerelease.chadoxml" md5="5301a21da6a9236ff2bd78bfcacb0685" timestamp="1261172067" time_generated="1263926767" time_taken_to_generate="0" size="65661676">
+ </export>
+ <export format="godb_prestore" path="obo-all/fma_lite_prerelease/fma_lite_prerelease.godb_prestore" md5="11c73c0cecd1c0ec794ce0a82e9ac2c9" timestamp="1261172187" time_generated="1263926768" time_taken_to_generate="0" size="59598948">
+ </export>
+ <export format="rdf" path="obo-all/fma_lite_prerelease/fma_lite_prerelease.rdf" md5="d50b6ca9bc6fdd5119ac0f925892b5ec" timestamp="1261172388" time_generated="1263926769" time_taken_to_generate="0" size="30438631">
+ </export>
+ <export format="tbl" path="obo-all/fma_lite_prerelease/fma_lite_prerelease.tbl" md5="4efc9175d25cfa3690aed63313c7eb51" timestamp="1261172514" time_generated="1263926770" time_taken_to_generate="0" size="6048806">
+ </export>
+ <export format="prolog" path="obo-all/fma_lite_prerelease/fma_lite_prerelease.pro" md5="ad4c66774a0ac567660ba0f25be33cb3" timestamp="1261172758" time_generated="1263926770" time_taken_to_generate="0" size="29272954">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/fma_lite_prerelease/fma_lite_prerelease.validation_report" md5="50a10156a7a76f4d7bf088751b11113b" timestamp="1261173190" time_generated="1263926879" time_taken_to_generate="0" size="105">
+ </export>
+ <export format="stats" path="obo-all/fma_lite_prerelease/fma_lite_prerelease.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1261173194" time_generated="1263926879" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/fma_lite_prerelease/fma_lite_prerelease.obo.html" md5="3773bf37bbd291865fd7bf3fb8a495aa" timestamp="1261173209" time_generated="1263926879" time_taken_to_generate="0" size="66834810">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="sequence_prerelease">
+ <prerelease_download>http://song.cvs.sourceforge.net/*checkout*/song/ontology/so-xp.obo</prerelease_download>
+ <granularity>molecular</granularity>
+ <status>Production and review</status>
+ <contact>SONG developers song-devel lists.sourceforge.net</contact>
+ <foundry>Yes</foundry>
+ <domain>biological sequence</domain>
+ <is_prerelease>1</is_prerelease>
+ <documentation></documentation>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/so.obo</url>
+ <patho_type>all</patho_type>
+ <home>SO home|http://song.sourceforge.net/</home>
+ <namespace>SO</namespace>
+ <description>The Sequence Ontology provides a structured controlled vocabulary for sequence annotation, for the exchange of annotation data and for the description of sequence objects in databases. <a href="http://obo.cvs.sourceforge.net/*checkout*/song/ontology/sofa.obo">SOFA</a> is a minimal version of SO for use in data exchange.</description>
+ <format>obo</format>
+ <title>Sequence types and features PRERELEASE</title>
+ <relevant_organism>all</relevant_organism>
+ <download>http://song.cvs.sourceforge.net/*checkout*/song/ontology/so-xp.obo</download>
+ <export format="obo_xml" path="obo-all/sequence_prerelease/sequence_prerelease.obo_xml" md5="faff16f06b4c91dcd2736d5cf3f44a40" timestamp="1263555016" time_generated="1263926884" time_taken_to_generate="0" size="1066413">
+ </export>
+ <export format="obo" path="obo-all/sequence_prerelease/sequence_prerelease.obo" md5="5e9d54a507f33cf4d753a7865f1f82e0" timestamp="1263926884" time_generated="1263926884" time_taken_to_generate="0" size="573356">
+ </export>
+ <export format="owl" path="obo-all/sequence_prerelease/sequence_prerelease.owl" md5="8ba33e300bcbc5a29f6d1eaf4ebd369f" timestamp="1263555077" time_generated="1263926884" time_taken_to_generate="0" size="2299443">
+ </export>
+ <export format="chadoxml" path="obo-all/sequence_prerelease/sequence_prerelease.chadoxml" md5="943a27babf8e90cb5e6d602b368ec7a3" timestamp="1263555095" time_generated="1263926884" time_taken_to_generate="0" size="2825487">
+ </export>
+ <export format="godb_prestore" path="obo-all/sequence_prerelease/sequence_prerelease.godb_prestore" md5="10512e87d62168732eb54d92e0fca0e2" timestamp="1263555101" time_generated="1263926884" time_taken_to_generate="0" size="2447538">
+ </export>
+ <export format="rdf" path="obo-all/sequence_prerelease/sequence_prerelease.rdf" md5="8b3fa66a267c1815421ade0a6d6e9388" timestamp="1263555109" time_generated="1263926884" time_taken_to_generate="0" size="1005104">
+ </export>
+ <export format="tbl" path="obo-all/sequence_prerelease/sequence_prerelease.tbl" md5="18b3b0f0ea2762a2f756faef881288f9" timestamp="1263555115" time_generated="1263926884" time_taken_to_generate="0" size="273855">
+ </export>
+ <export format="prolog" path="obo-all/sequence_prerelease/sequence_prerelease.pro" md5="cf57d5d034a047f2c533138a822c1cf8" timestamp="1263555125" time_generated="1263926884" time_taken_to_generate="0" size="1157082">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/sequence_prerelease/sequence_prerelease.validation_report" md5="d16167ab22061f8f939f2efccdd2da5f" timestamp="1263555133" time_generated="1263926889" time_taken_to_generate="0" size="1396">
+ </export>
+ <export format="stats" path="obo-all/sequence_prerelease/sequence_prerelease.stats" md5="619a62d04ddf7c62cc6ebdc743938b12" timestamp="1263555135" time_generated="1263926889" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/sequence_prerelease/sequence_prerelease.obo.html" md5="c6bc6c55e81a1842cc228f7940392d0f" timestamp="1263555136" time_generated="1263926889" time_taken_to_generate="0" size="2453714">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="dendritic_cell_prerelease">
+ <prerelease_download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/cell_type/DC-CL_editor.obo</prerelease_download>
+ <granularity>cellular</granularity>
+ <status>Production and review</status>
+ <contact>Lindsay Cowell cowel001 mc.duke.edu</contact>
+ <subtypes_of>bfo:IndependentContinuant</subtypes_of>
+ <foundry>No</foundry>
+ <domain>anatomy,immunology</domain>
+ <is_prerelease>1</is_prerelease>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/cell_type/DC-CL_deployed.obo</url>
+ <documentation></documentation>
+ <patho_type>canonical</patho_type>
+ <home>http://www.dukeontologygroup.org/Projects.html</home>
+ <namespace>DC_CL</namespace>
+ <description>Representation of types of dendritic cell. Note that the domain of this ontology is wholly subsumed by the domain of the Cell ontology (CL).</description>
+ <format>obo</format>
+ <title>Dendritic cell PRERELEASE</title>
+ <relevant_organism>all</relevant_organism>
+ <download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/cell_type/DC-CL_editor.obo</download>
+ <export format="obo_xml" path="obo-all/dendritic_cell_prerelease/dendritic_cell_prerelease.obo_xml" md5="e5e3478390d77e2a4948bce88e48c675" timestamp="1261173355" time_generated="1263926892" time_taken_to_generate="0" size="97886">
+ </export>
+ <export format="obo" path="obo-all/dendritic_cell_prerelease/dendritic_cell_prerelease.obo" md5="30ed726749d8096ba7d8e7ebc250116e" timestamp="1263926892" time_generated="1263926892" time_taken_to_generate="0" size="58882">
+ </export>
+ <export format="owl" path="obo-all/dendritic_cell_prerelease/dendritic_cell_prerelease.owl" md5="4b9e86bff0ae669658e10f2731bcee73" timestamp="1261173356" time_generated="1263926892" time_taken_to_generate="0" size="239179">
+ </export>
+ <export format="chadoxml" path="obo-all/dendritic_cell_prerelease/dendritic_cell_prerelease.chadoxml" md5="4e7e6157444a1874723bf164fc8cb2cd" timestamp="1261173357" time_generated="1263926892" time_taken_to_generate="0" size="172375">
+ </export>
+ <export format="godb_prestore" path="obo-all/dendritic_cell_prerelease/dendritic_cell_prerelease.godb_prestore" md5="6348d27376303de4315c095f1d7a373b" timestamp="1261173359" time_generated="1263926892" time_taken_to_generate="0" size="243976">
+ </export>
+ <export format="rdf" path="obo-all/dendritic_cell_prerelease/dendritic_cell_prerelease.rdf" md5="c97a1cef40755191fb4ec851cee991ce" timestamp="1261173360" time_generated="1263926892" time_taken_to_generate="0" size="91222">
+ </export>
+ <export format="tbl" path="obo-all/dendritic_cell_prerelease/dendritic_cell_prerelease.tbl" md5="0c55dda3c5c3b7044ef67f7dcba5734b" timestamp="1261173361" time_generated="1263926892" time_taken_to_generate="0" size="13268">
+ </export>
+ <export format="prolog" path="obo-all/dendritic_cell_prerelease/dendritic_cell_prerelease.pro" md5="53983438a2f7f96be739ef799a5b55a1" timestamp="1261173362" time_generated="1263926892" time_taken_to_generate="0" size="92444">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/dendritic_cell_prerelease/dendritic_cell_prerelease.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1261173364" time_generated="1263926893" time_taken_to_generate="0" size="20">
+ </export>
+ <export format="stats" path="obo-all/dendritic_cell_prerelease/dendritic_cell_prerelease.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1261173366" time_generated="1263926893" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/dendritic_cell_prerelease/dendritic_cell_prerelease.obo.html" md5="5a9c31b6a11636c37fb8b4a7a2bb3387" timestamp="1261173366" time_generated="1263926893" time_taken_to_generate="0" size="233405">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="envo_prerelease">
+ <prerelease_download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/environmental/envo-edit.obo</prerelease_download>
+ <granularity>molecular,cellular,organismal,multi-organismal</granularity>
+ <status>Discussion and review</status>
+ <contact>Norman Morrison obo-envo lists.sourceforge.net</contact>
+ <subtypes_of>bfo:IndependentContinuant</subtypes_of>
+ <foundry>Yes</foundry>
+ <domain>environment</domain>
+ <is_prerelease>1</is_prerelease>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/environmental/envo.obo</url>
+ <documentation>http://www.envoc.org</documentation>
+ <patho_type>all</patho_type>
+ <home>EnvO|http://environmentontology.org/</home>
+ <namespace>ENVO</namespace>
+ <description>Ontology of environmental features and habitats</description>
+ <format>obo</format>
+ <title>Environment Ontology PRERELEASE</title>
+ <relevant_organism>all</relevant_organism>
+ <download>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/environmental/envo-edit.obo</download>
+ <export format="obo_xml" path="obo-all/envo_prerelease/envo_prerelease.obo_xml" md5="ef63d734bf2f88a506fd15a549f64bba" timestamp="1261173374" time_generated="1263926896" time_taken_to_generate="0" size="896276">
+ </export>
+ <export format="obo" path="obo-all/envo_prerelease/envo_prerelease.obo" md5="d4496a4f63c40c346bab9655422e9e1b" timestamp="1263926896" time_generated="1263926896" time_taken_to_generate="0" size="352372">
+ </export>
+ <export format="owl" path="obo-all/envo_prerelease/envo_prerelease.owl" md5="cf152f96758a6806924f9f426e3666c3" timestamp="1261173414" time_generated="1263926896" time_taken_to_generate="0" size="2296930">
+ </export>
+ <export format="chadoxml" path="obo-all/envo_prerelease/envo_prerelease.chadoxml" md5="992b103a33cffe2e270135bcbb33ae9e" timestamp="1261173435" time_generated="1263926896" time_taken_to_generate="0" size="2251069">
+ </export>
+ <export format="godb_prestore" path="obo-all/envo_prerelease/envo_prerelease.godb_prestore" md5="17c5d9dd02b6a194ad028e870432e4fc" timestamp="1261173441" time_generated="1263926896" time_taken_to_generate="0" size="1705830">
+ </export>
+ <export format="rdf" path="obo-all/envo_prerelease/envo_prerelease.rdf" md5="7991f4316e5d86b0d943cc95a767ece0" timestamp="1261173451" time_generated="1263926896" time_taken_to_generate="0" size="971403">
+ </export>
+ <export format="tbl" path="obo-all/envo_prerelease/envo_prerelease.tbl" md5="70886922fb1bb4e747e2b6c21f38dc84" timestamp="1261173456" time_generated="1263926896" time_taken_to_generate="0" size="163579">
+ </export>
+ <export format="prolog" path="obo-all/envo_prerelease/envo_prerelease.pro" md5="70666fbbbbd1e46df13924e72c0a0378" timestamp="1261173465" time_generated="1263926896" time_taken_to_generate="0" size="913491">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/envo_prerelease/envo_prerelease.validation_report" md5="b51f15a866c6303ace753e7b1b601290" timestamp="1261173473" time_generated="1263926901" time_taken_to_generate="0" size="320">
+ </export>
+ <export format="stats" path="obo-all/envo_prerelease/envo_prerelease.stats" md5="b6cd4b5a40819abb77a145d27dc31972" timestamp="1261173475" time_generated="1263926901" time_taken_to_generate="0" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/envo_prerelease/envo_prerelease.obo.html" md5="4bc1b29e805f32d0e2a6aa2127886a61" timestamp="1261173475" time_generated="1263926901" time_taken_to_generate="0" size="1916807">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ont id="biological_process_prerelease">
+ <prerelease_download>ftp://ftp.geneontology.org/pub/go/ontology/obo_format_1_2/gene_ontology_ext.obo</prerelease_download>
+ <granularity>molecular,cellular,organismal,multi-organismal</granularity>
+ <status>Production and review</status>
+ <contact>Gene Ontology go geneontology.org</contact>
+ <subtypes_of>bfo:Process</subtypes_of>
+ <foundry>Yes</foundry>
+ <domain>biological process</domain>
+ <is_prerelease>1</is_prerelease>
+ <url>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/gene_ontology_edit.obo</url>
+ <documentation>Gene Ontology documentation|http://www.geneontology.org/GO.doc.shtml</documentation>
+ <patho_type>canonical</patho_type>
+ <home>www.geneontology.org|http://www.geneontology.org</home>
+ <namespace>GO</namespace>
+ <description>Provides structured controlled vocabularies for the annotation of gene products with respect to their biological role. One of the three vocabularies of the Gene Ontology.</description>
+ <format>obo</format>
+ <title>Biological process PRERELEASE</title>
+ <relevant_organism>all</relevant_organism>
+ <download>ftp://ftp.geneontology.org/pub/go/ontology/obo_format_1_2/gene_ontology_ext.obo</download>
+ <export format="obo_xml" path="obo-all/biological_process_prerelease/biological_process_prerelease.obo_xml" md5="466d85b3bbe1d499c20f21721c19fd3d" timestamp="1263927047" time_generated="1263927047" time_taken_to_generate="122" size="29911950">
+ </export>
+ <export format="obo" path="obo-all/biological_process_prerelease/biological_process_prerelease.obo" md5="d57ac975d0bf40c5db7f15b03a6be83c" timestamp="1263926924" time_generated="1263927048" time_taken_to_generate="0" size="17631563">
+ </export>
+ <export format="owl" path="obo-all/biological_process_prerelease/biological_process_prerelease.owl" md5="157abee9f0ef60d64ffcfd974213a06a" timestamp="1263949168" time_generated="1263949169" time_taken_to_generate="22121" size="65732613">
+ </export>
+ <export format="chadoxml" path="obo-all/biological_process_prerelease/biological_process_prerelease.chadoxml" md5="075e069c48398e2eb61aec575a9c8f13" timestamp="1263956291" time_generated="1263956292" time_taken_to_generate="7122" size="71924633">
+ </export>
+ <export format="godb_prestore" path="obo-all/biological_process_prerelease/biological_process_prerelease.godb_prestore" md5="334285a046cbdc8a6eee28ac89ba21df" timestamp="1263956454" time_generated="1263956455" time_taken_to_generate="162" size="60393531">
+ </export>
+ <export format="rdf" path="obo-all/biological_process_prerelease/biological_process_prerelease.rdf" md5="6c87108b10ef867a992be866c2f62a7d" timestamp="1263956659" time_generated="1263956660" time_taken_to_generate="205" size="26293322">
+ </export>
+ <export format="tbl" path="obo-all/biological_process_prerelease/biological_process_prerelease.tbl" md5="88756a15f401623428fe1fd1669f1ce9" timestamp="1263956802" time_generated="1263956802" time_taken_to_generate="142" size="9136319">
+ </export>
+ <export format="prolog" path="obo-all/biological_process_prerelease/biological_process_prerelease.pro" md5="cb902e367888d3bcfb41f4510990fcb0" timestamp="1263957060" time_generated="1263957060" time_taken_to_generate="258" size="33012459">
+ </export>
+ <export format="error_report" problem="true">
+ </export>
+ <export format="validation_report" path="obo-all/biological_process_prerelease/biological_process_prerelease.validation_report" md5="201a3711c4c4c5291ddc78943b3254a2" timestamp="1263957262" time_generated="1263957262" time_taken_to_generate="94" size="20">
+ </export>
+ <export format="stats" path="obo-all/biological_process_prerelease/biological_process_prerelease.stats" md5="619a62d04ddf7c62cc6ebdc743938b12" timestamp="1263957265" time_generated="1263957265" time_taken_to_generate="3" size="52">
+ </export>
+ <export format="xref" problem="true">
+ </export>
+ <export format="imports.obo" problem="true">
+ </export>
+ <export format="obo.html" path="obo-all/biological_process_prerelease/biological_process_prerelease.obo.html" md5="351de67f5e73efd063691662a86b36fa" timestamp="1263957275" time_generated="1263957275" time_taken_to_generate="10" size="63600722">
+ </export>
+ <export format="linkfile" problem="true">
+ </export>
+ <export format="imports.owl" problem="true">
+ </export>
+ <export format="imports-local.obo" problem="true">
+ </export>
+ <export format="xp.html" problem="true">
+ </export>
+ <export format="imports-local.owl" problem="true">
+ </export>
+ <export format="owl-classified-by-pellet2" problem="true">
+ </export>
+ <export format="obo-classified-by-oboedit" problem="true">
+ </export>
+ <export format="obo-classified-by-blip" problem="true">
+ </export>
+ <export format="abduced-links.txt" problem="true">
+ </export>
+ </ont>
+ <ontologies_indexed>167</ontologies_indexed>
+ <ontologies_not_indexed>8</ontologies_not_indexed>
+ <time_completed unix="1263957278" total_time="361775">Tue Jan 19 19:14:38 2010</time_completed>
+</obo_metadata>
diff --git a/coreplugins/TableImport/src/main/resources/resources/tax_report.txt b/coreplugins/TableImport/src/main/resources/resources/tax_report.txt
new file mode 100644
index 0000000..c095751
--- /dev/null
+++ b/coreplugins/TableImport/src/main/resources/resources/tax_report.txt
@@ -0,0 +1,33 @@
+code | name | preferred name | taxid
+1 | Saccharomyces cerevisiae | | 4932
+1 | Drosophila melanogaster | | 7227
+1 | Mus musculus | | 10090
+1 | Arabidopsis thaliana | | 3702
+1 | Caenorhabditis elegans | | 6239
+1 | Rattus norvegicus | | 10116
+1 | Oryza sativa | | 4530
+1 | Danio rerio | | 7955
+1 | Dictyostelium discoideum | | 44689
+1 | Candida albicans | | 5476
+2 | Bacillus anthracis Ames | Bacillus anthracis str. Ames | 198094
+1 | Coxiella burnetii RSA 493 | | 227377
+1 | Campylobacter jejuni RM1221 | | 195099
+1 | Dehalococcoides ethenogenes 195 | | 243164
+1 | Geobacter sulfurreducens PCA | | 243231
+2 | Listeria monocytogenes 4b F2365 | Listeria monocytogenes str. 4b F2365 | 265669
+2 | Methylococcus capsulatus Bath | Methylococcus capsulatus str. Bath | 243233
+2 | Pseudomonas syringae DC3000 | Pseudomonas syringae pv. tomato str. DC3000 | 223283
+1 | Shewanella oneidensis MR-1 | | 211586
+1 | Silicibacter pomeroyi DSS-3 | | 246200
+1 | Trypanosoma brucei | | 5691
+1 | Vibrio cholerae | | 666
+1 | Arabidopsis | | 3701
+2 | Human | Homo sapiens | 9606
+2+ | Rat | Rattus | 10114
+2+ | Rat | Rattus norvegicus | 10116
+2 | Zebrafish | Danio rerio | 7955
+1 | Leishmania major | | 5664
+1 | Plasmodium falciparum | | 5833
+1 | Schizosaccharomyces pombe | | 4896
+1 | Trypanosoma brucei | | 5691
+1 | Glossina morsitans | | 7394
diff --git a/coreplugins/TableImport/src/test/java/edu/ucsd/bioeng/coreplugin/tableImport/reader/GeneAssociationReaderTest.java b/coreplugins/TableImport/src/test/java/edu/ucsd/bioeng/coreplugin/tableImport/reader/GeneAssociationReaderTest.java
new file mode 100644
index 0000000..5ef808c
--- /dev/null
+++ b/coreplugins/TableImport/src/test/java/edu/ucsd/bioeng/coreplugin/tableImport/reader/GeneAssociationReaderTest.java
@@ -0,0 +1,128 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package edu.ucsd.bioeng.coreplugin.tableImport.reader;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+
+import cytoscape.util.URLUtil;
+import cytoscape.data.CyAttributes;
+
+import cytoscape.data.ontology.GeneOntology;
+
+import cytoscape.data.servers.OntologyServer.OntologyType;
+
+import edu.ucsd.bioeng.coreplugin.tableImport.reader.GeneAssociationReader;
+
+import junit.framework.TestCase;
+
+import java.io.File;
+import java.io.IOException;
+
+import java.net.URISyntaxException;
+
+import java.util.Iterator;
+
+
+/**
+ * Test cases for GeneAssociationReader.java.
+ *
+ * @since Cytoscape 2.4
+ * @version 0.8
+ *
+ * @author Keiichiro Ono
+ *
+ */
+public class GeneAssociationReaderTest extends TestCase {
+ private static final String GO_SLIM = "/annotation/goslim_generic.obo";
+ private static final String GAL_NETWORK = "/galFiltered.sif";
+ private static final String GENE_ASSOCIATION = "/annotation/gene_association.sgd";
+
+ private static final String TAXON_FILE = "/resources/tax_report.txt";
+ private CyNetwork gal;
+ private CyAttributes nodeAttr;
+
+ protected void setUp() throws Exception {
+ super.setUp();
+ gal = Cytoscape.createNetworkFromURL(getClass().getResource(GAL_NETWORK),true);
+ Cytoscape.buildOntologyServer();
+ }
+
+ protected void tearDown() throws Exception {
+ super.tearDown();
+ Cytoscape.destroyNetwork(gal);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws IOException DOCUMENT ME!
+ * @throws URISyntaxException DOCUMENT ME!
+ */
+ public void testBuildMap() throws IOException, URISyntaxException {
+ assertNotNull(Cytoscape.getOntologyServer().getOntologyNames());
+
+ String ontologyName = null;
+ Iterator it = Cytoscape.getOntologyServer().getOntologyNames().iterator();
+
+ while (it.hasNext()) {
+ ontologyName = (String) it.next();
+ System.out.println("Ontology Name used for GA reader = " + ontologyName);
+ }
+
+ GeneOntology go = new GeneOntology("go1", "testCur", "testDesc", null);
+ Cytoscape.getOntologyServer().addOntology(go);
+
+ Cytoscape.getOntologyServer().addOntology(
+ getClass().getResource(GO_SLIM), OntologyType.GO, "GO Slim Test", "Test");
+
+ GeneAssociationReader gar = new GeneAssociationReader("GO Slim Test",
+ URLUtil.getInputStream(
+ getClass().getResource(GENE_ASSOCIATION)),
+ "ID", false, 2, true, TAXON_FILE);
+
+ gar.readTable();
+ nodeAttr = Cytoscape.getNodeAttributes();
+
+ for (String attrName : nodeAttr.getAttributeNames()) {
+ System.out.println("Deleting: " + attrName);
+ nodeAttr.deleteAttribute(attrName);
+ }
+
+ // TODO add some actual tests!!
+ }
+}
diff --git a/coreplugins/TableImport/src/test/java/edu/ucsd/bioeng/coreplugin/tableImport/tests/DefaultAttributeTableReaderTest.java b/coreplugins/TableImport/src/test/java/edu/ucsd/bioeng/coreplugin/tableImport/tests/DefaultAttributeTableReaderTest.java
new file mode 100644
index 0000000..5b1d6b8
--- /dev/null
+++ b/coreplugins/TableImport/src/test/java/edu/ucsd/bioeng/coreplugin/tableImport/tests/DefaultAttributeTableReaderTest.java
@@ -0,0 +1,174 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package edu.ucsd.bioeng.coreplugin.tableImport.tests;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+
+import cytoscape.data.CyAttributes;
+
+import edu.ucsd.bioeng.coreplugin.tableImport.reader.AttributeMappingParameters;
+import edu.ucsd.bioeng.coreplugin.tableImport.reader.DefaultAttributeTableReader;
+import edu.ucsd.bioeng.coreplugin.tableImport.reader.TextFileDelimiters;
+import static edu.ucsd.bioeng.coreplugin.tableImport.reader.TextFileDelimiters.*;
+import edu.ucsd.bioeng.coreplugin.tableImport.reader.TextTableReader;
+
+import junit.framework.TestCase;
+
+import java.io.File;
+
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ *
+ */
+public class DefaultAttributeTableReaderTest extends TestCase {
+ private DefaultAttributeTableReader tableReader;
+
+ /*
+ * Toy example created from galFiltered.sif and its attribute files.
+ */
+ private static final String DATA_FILE = "/annotation/galSubnetworkAnnotation2.txt";
+ private static final String NETWORK_FILE = "/galSubnetwork.sif";
+ private static final String DATA_FILE2 = "/annotation/annotationSampleForYeast.txt";
+ private static final String NETWORK_FILE2 = "/galFiltered.sif";
+
+ protected void setUp() throws Exception {
+ super.setUp();
+ Cytoscape.buildOntologyServer();
+ }
+
+ protected void tearDown() throws Exception {
+ super.tearDown();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testReadTable() throws Exception {
+ //
+ CyNetwork net = Cytoscape.createNetworkFromURL(getClass().getResource(NETWORK_FILE),true);
+ CyNetwork galNet = Cytoscape.createNetworkFromURL(getClass().getResource(NETWORK_FILE2),true);
+
+ /*
+ * Test1
+ */
+ List<String> delimiters = new ArrayList<String>();
+ delimiters.add(TextFileDelimiters.TAB.toString());
+
+ List<Integer> aliasList = new ArrayList<Integer>();
+ aliasList.add(2);
+
+ String[] galAttrName = {
+ "ID", "ID in SGD", "Synonyms", "Description of Genes", "Date",
+ "Sample Boolean Attr2", "gal1RGexp", "gal1RGsig", "String List"
+ };
+ Byte[] galAttrTypes = {
+ CyAttributes.TYPE_STRING, CyAttributes.TYPE_STRING,
+ CyAttributes.TYPE_STRING, CyAttributes.TYPE_STRING,
+ CyAttributes.TYPE_INTEGER, CyAttributes.TYPE_BOOLEAN,
+ CyAttributes.TYPE_FLOATING, CyAttributes.TYPE_FLOATING,
+ CyAttributes.TYPE_SIMPLE_LIST
+ };
+
+ for (int i = 0; i < galAttrTypes.length; i++) {
+ System.out.println("GAL Data Type " + i + " = " + galAttrTypes[i]);
+ }
+
+ // We need to delete the "String List" attribute because this one concatenates
+ // and if we've executed a previous test, we may have some junk lying around
+ Cytoscape.getNodeAttributes().deleteAttribute("String List");
+
+ AttributeMappingParameters mapping = new AttributeMappingParameters(TextTableReader.ObjectType.NODE,
+ null, COMMA.toString(),
+ 0, "ID", aliasList,
+ galAttrName,
+ galAttrTypes, null, null);
+ tableReader = new DefaultAttributeTableReader(getClass().getResource(DATA_FILE), mapping, 0, null);
+ tableReader.readTable();
+
+ assertEquals("ribosomal protein S28A (S33A) (YS27)",
+ Cytoscape.getNodeAttributes()
+ .getStringAttribute("YOR167C", "Description of Genes"));
+ assertEquals(new Integer(20010118),
+ Cytoscape.getNodeAttributes().getIntegerAttribute("YHR141C", "Date"));
+ //assertEquals(4, Cytoscape.getNodeAttributes().getListAttribute("YER112W", "alias").size());
+ assertEquals(7,
+ Cytoscape.getNodeAttributes().getListAttribute("YDR277C", "String List").size());
+
+ assertEquals("List",
+ Cytoscape.getNodeAttributes().getListAttribute("YDR277C", "String List").get(5));
+
+ /*
+ * Test2
+ */
+ List<Integer> aliases = new ArrayList<Integer>();
+ aliases.add(2);
+
+ String[] cols = { "Object Name in SGD", "key", "alias", "Taxon ID" };
+
+ tableReader = new DefaultAttributeTableReader(getClass().getResource(DATA_FILE2),
+ TextTableReader.ObjectType.NODE, delimiters,
+ PIPE.toString(), 1, "ID", aliases, cols,
+ null, null, 0);
+ tableReader.readTable();
+
+ System.out.println("* YOL123W Object Name in SGD = "
+ + Cytoscape.getNodeAttributes()
+ .getStringAttribute("YOL123W", "Object Name in SGD"));
+ assertEquals("S000005483",
+ Cytoscape.getNodeAttributes()
+ .getStringAttribute("YOL123W", "Object Name in SGD"));
+ assertEquals("S000006010",
+ Cytoscape.getNodeAttributes()
+ .getStringAttribute("YPL089C", "Object Name in SGD"));
+ assertEquals("taxon:4932",
+ Cytoscape.getNodeAttributes().getStringAttribute("YDR009W", "Taxon ID"));
+
+// assertTrue(Cytoscape.getNodeAttributes().getListAttribute("YOR315W", "alias")
+// .contains("SFG1"));
+
+// assertTrue(Cytoscape.getOntologyServer().getNodeAliases().getAliases("YLR319C")
+// .contains("AIP3"));
+
+ Cytoscape.destroyNetwork(galNet);
+ Cytoscape.destroyNetwork(net);
+ }
+}
diff --git a/coreplugins/TableImport/src/test/java/edu/ucsd/bioeng/coreplugin/tableImport/tests/ExcelAttributeSheetReaderTest.java b/coreplugins/TableImport/src/test/java/edu/ucsd/bioeng/coreplugin/tableImport/tests/ExcelAttributeSheetReaderTest.java
new file mode 100644
index 0000000..6830e60
--- /dev/null
+++ b/coreplugins/TableImport/src/test/java/edu/ucsd/bioeng/coreplugin/tableImport/tests/ExcelAttributeSheetReaderTest.java
@@ -0,0 +1,152 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package edu.ucsd.bioeng.coreplugin.tableImport.tests;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+
+import cytoscape.data.CyAttributes;
+
+import edu.ucsd.bioeng.coreplugin.tableImport.reader.AttributeMappingParameters;
+import edu.ucsd.bioeng.coreplugin.tableImport.reader.ExcelAttributeSheetReader;
+import edu.ucsd.bioeng.coreplugin.tableImport.reader.TextFileDelimiters;
+import static edu.ucsd.bioeng.coreplugin.tableImport.reader.TextFileDelimiters.*;
+import edu.ucsd.bioeng.coreplugin.tableImport.reader.TextTableReader;
+
+import junit.framework.TestCase;
+
+import org.apache.poi.hssf.usermodel.HSSFSheet;
+import org.apache.poi.hssf.usermodel.HSSFWorkbook;
+import org.apache.poi.poifs.filesystem.POIFSFileSystem;
+
+import java.io.File;
+import java.io.FileInputStream;
+
+import java.io.InputStream;
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ *
+ */
+public class ExcelAttributeSheetReaderTest extends TestCase {
+ private static final String WORKBOOK1 = "/annotation/galSubnetworkAnnotation3.xls";
+ private static final String NETWORK_FILE = "/galSubnetwork.sif";
+
+ protected void setUp() throws Exception {
+ super.setUp();
+ Cytoscape.buildOntologyServer();
+ }
+
+ protected void tearDown() throws Exception {
+ super.tearDown();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testReadTable() throws Exception {
+ /*
+ * Load test network
+ */
+ CyNetwork net = Cytoscape.createNetworkFromURL(getClass().getResource(NETWORK_FILE),true);
+
+ /*
+ * Single Sheet Test
+ */
+ InputStream is = null;
+ POIFSFileSystem excelIn;
+ try {
+ is = getClass().getResource(WORKBOOK1).openStream();
+ excelIn = new POIFSFileSystem(is);
+ }
+ finally {
+ if (is != null) {
+ is.close();
+ }
+ }
+
+ HSSFWorkbook wb = new HSSFWorkbook(excelIn);
+
+ HSSFSheet sheet = wb.getSheetAt(0);
+
+ List<String> delimiters = new ArrayList<String>();
+ delimiters.add(TextFileDelimiters.TAB.toString());
+
+ List<Integer> aliasList = new ArrayList<Integer>();
+ aliasList.add(2);
+
+ String[] galAttrName = {
+ "ID", "ID in SGD", "Synonyms", "Description of Genes", "Date",
+ "Sample Boolean Attr2", "gal1RGexp", "gal1RGsig", "String List"
+ };
+ Byte[] galAttrTypes = {
+ CyAttributes.TYPE_STRING, CyAttributes.TYPE_STRING,
+ CyAttributes.TYPE_STRING, CyAttributes.TYPE_STRING,
+ CyAttributes.TYPE_INTEGER, CyAttributes.TYPE_BOOLEAN,
+ CyAttributes.TYPE_FLOATING, CyAttributes.TYPE_FLOATING,
+ CyAttributes.TYPE_SIMPLE_LIST
+ };
+
+ for (int i = 0; i < galAttrTypes.length; i++) {
+ System.out.println("GAL Data Type " + i + " = " + galAttrTypes[i]);
+ }
+
+ AttributeMappingParameters mapping = new AttributeMappingParameters(TextTableReader.ObjectType.NODE,
+ null, COMMA.toString(),
+ 0, "ID", aliasList,
+ galAttrName,
+ galAttrTypes, null, null);
+
+ TextTableReader rd = new ExcelAttributeSheetReader(sheet, mapping, 0);
+ rd.readTable();
+
+ assertEquals("ribosomal protein S28A (S33A) (YS27)",
+ Cytoscape.getNodeAttributes()
+ .getStringAttribute("YOR167C", "Description of Genes"));
+ assertEquals(new Integer(20010118),
+ Cytoscape.getNodeAttributes().getIntegerAttribute("YHR141C", "Date"));
+ //assertEquals(4, Cytoscape.getNodeAttributes().getListAttribute("YER112W", "alias").size());
+
+ /*
+ * Multiple sheet test (not yet supported)
+ */
+ Cytoscape.destroyNetwork(net);
+ }
+}
diff --git a/coreplugins/TableImport/src/test/java/edu/ucsd/bioeng/coreplugin/tableImport/tests/ExcelNetworkSheetReaderTest.java b/coreplugins/TableImport/src/test/java/edu/ucsd/bioeng/coreplugin/tableImport/tests/ExcelNetworkSheetReaderTest.java
new file mode 100644
index 0000000..f813a7d
--- /dev/null
+++ b/coreplugins/TableImport/src/test/java/edu/ucsd/bioeng/coreplugin/tableImport/tests/ExcelNetworkSheetReaderTest.java
@@ -0,0 +1,211 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package edu.ucsd.bioeng.coreplugin.tableImport.tests;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+
+import cytoscape.data.CyAttributes;
+
+import edu.ucsd.bioeng.coreplugin.tableImport.reader.ExcelNetworkSheetReader;
+import edu.ucsd.bioeng.coreplugin.tableImport.reader.NetworkTableMappingParameters;
+import edu.ucsd.bioeng.coreplugin.tableImport.reader.NetworkTableReader;
+import edu.ucsd.bioeng.coreplugin.tableImport.reader.TextFileDelimiters;
+
+import junit.framework.TestCase;
+
+import org.apache.poi.hssf.usermodel.HSSFSheet;
+import org.apache.poi.hssf.usermodel.HSSFWorkbook;
+import org.apache.poi.poifs.filesystem.POIFSFileSystem;
+
+import java.io.File;
+import java.io.FileInputStream;
+
+import java.io.InputStream;
+import java.util.ArrayList;
+import java.util.List;
+
+
+/**
+ * Test cases for Excel network file import.<br>
+ *
+ * @since Cytoscape 2.4
+ *
+ * @version 0.6
+ * @author Keiichiro Ono
+ *
+ */
+public class ExcelNetworkSheetReaderTest extends TestCase {
+ private static final String NETWORK_FILE = "/galFiltered.xls";
+ private NetworkTableReader reader;
+
+ protected void setUp() throws Exception {
+ super.setUp();
+ Cytoscape.buildOntologyServer();
+ }
+
+ protected void tearDown() throws Exception {
+ super.tearDown();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testReadTable() throws Exception {
+
+ InputStream is =null;
+ POIFSFileSystem excelIn;
+
+ try {
+ is = getClass().getResource(NETWORK_FILE).openStream();
+ excelIn = new POIFSFileSystem(is);
+ }
+ finally {
+ if (is != null) {
+ is.close();
+ }
+ }
+
+ HSSFWorkbook wb = new HSSFWorkbook(excelIn);
+
+ HSSFSheet sheet = wb.getSheetAt(0);
+
+ List<String> delimiters = new ArrayList<String>();
+ delimiters.add(TextFileDelimiters.TAB.toString());
+
+ String[] galAttrName = {
+ "Source", "Target", "Interaction", "edge bool attr",
+ "edge string attr", "edge float attr"
+ };
+ Byte[] galAttrTypes = {
+ CyAttributes.TYPE_STRING, CyAttributes.TYPE_STRING,
+ CyAttributes.TYPE_STRING, CyAttributes.TYPE_BOOLEAN,
+ CyAttributes.TYPE_STRING, CyAttributes.TYPE_FLOATING
+ };
+ NetworkTableMappingParameters mapping = new NetworkTableMappingParameters(delimiters,
+ TextFileDelimiters.PIPE
+ .toString(),
+ galAttrName,
+ galAttrTypes,
+ null, null, 0, 1,
+ 2, null);
+
+ reader = new ExcelNetworkSheetReader(wb.getSheetName(0), sheet, mapping);
+
+ CyNetwork net = Cytoscape.createNetwork(reader, false, null);
+
+ /*
+ * test cases
+ */
+ assertEquals("Yeast Network Sheet 1", net.getTitle());
+ assertEquals(331, net.getNodeCount());
+ assertEquals(362, net.getEdgeCount());
+
+ CyAttributes attr = Cytoscape.getEdgeAttributes();
+ assertTrue(attr.getBooleanAttribute("YGL122C (pp) YOL123W", "edge bool attr"));
+ assertFalse(attr.getBooleanAttribute("YKR026C (pp) YGL122C", "edge bool attr"));
+
+ assertEquals(1.2344543, attr.getDoubleAttribute("YBL026W (pp) YOR167C", "edge float attr"));
+ assertEquals("abcd12706",
+ attr.getStringAttribute("YBL026W (pp) YOR167C", "edge string attr"));
+ assertEquals("abcd12584", attr.getStringAttribute("YPL248C (pd) ?", "edge string attr"));
+
+ Cytoscape.destroyNetwork(net);
+ }
+
+ public void testReadTableWithEmptyRows() throws Exception {
+ String network = "/empty_attr_row.xls";
+
+ InputStream is = null;
+ POIFSFileSystem excelIn;
+
+ try {
+ is = getClass().getResource(network).openStream();
+ excelIn = new POIFSFileSystem(is);
+ }
+ finally {
+ if (is != null) {
+ is.close();
+ }
+ }
+
+ HSSFWorkbook wb = new HSSFWorkbook(excelIn);
+
+ HSSFSheet sheet = wb.getSheetAt(0);
+
+ List<String> delimiters = new ArrayList<String>();
+ delimiters.add(TextFileDelimiters.TAB.toString());
+
+ String[] galAttrName = { "Gene 1", "Gene 2", "Interaction Type", "Gene", "GO Group" };
+ Byte[] galAttrTypes = { CyAttributes.TYPE_STRING, CyAttributes.TYPE_STRING,
+ CyAttributes.TYPE_STRING, CyAttributes.TYPE_STRING,
+ CyAttributes.TYPE_STRING };
+ NetworkTableMappingParameters mapping = new NetworkTableMappingParameters(delimiters,
+ TextFileDelimiters.PIPE
+ .toString(),
+ galAttrName,
+ galAttrTypes,
+ null, null, 0, 1,
+ 2, null);
+
+ CyNetwork net = null;
+ try {
+ reader = new ExcelNetworkSheetReader(wb.getSheetName(0), sheet, mapping, 1);
+ net = Cytoscape.createNetwork(reader, false, null);
+ } catch (Exception ee) {
+ ee.printStackTrace();
+ fail("Caught exception");
+ }
+
+ assertEquals(222, net.getNodeCount());
+ assertEquals(443, net.getEdgeCount());
+
+ CyAttributes attr = Cytoscape.getEdgeAttributes();
+
+ // test some random edges
+ assertEquals("cc", attr.getStringAttribute("YDR459C (cc) YNL271C", "interaction"));
+ assertEquals("Transport", attr.getStringAttribute("YDR459C (cc) YNL271C", "GO Group"));
+ assertEquals("YPR011C", attr.getStringAttribute("YDR459C (cc) YNL271C", "Gene"));
+
+ assertNull(attr.getStringAttribute("YEL040W (cc) YER016W","GO Group"));
+ assertNull(attr.getStringAttribute("YEL040W (cc) YER016W","Gene"));
+
+ Cytoscape.destroyNetwork(net);
+ }
+}
diff --git a/coreplugins/TableImport/src/test/java/edu/ucsd/bioeng/coreplugin/tableImport/tests/NetworkTableReaderTest.java b/coreplugins/TableImport/src/test/java/edu/ucsd/bioeng/coreplugin/tableImport/tests/NetworkTableReaderTest.java
new file mode 100644
index 0000000..147a8eb
--- /dev/null
+++ b/coreplugins/TableImport/src/test/java/edu/ucsd/bioeng/coreplugin/tableImport/tests/NetworkTableReaderTest.java
@@ -0,0 +1,130 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package edu.ucsd.bioeng.coreplugin.tableImport.tests;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+
+import cytoscape.data.CyAttributes;
+
+import edu.ucsd.bioeng.coreplugin.tableImport.reader.NetworkTableMappingParameters;
+import edu.ucsd.bioeng.coreplugin.tableImport.reader.NetworkTableReader;
+import edu.ucsd.bioeng.coreplugin.tableImport.reader.TextFileDelimiters;
+
+import junit.framework.TestCase;
+
+import java.io.File;
+
+import java.util.ArrayList;
+import java.util.List;
+
+
+/**
+ * Test cases for network & edge attributes table reader.
+ *
+ * @since Cytoscape 2.4
+ * @version 0.6
+ *
+ * @author kono
+ *
+ */
+public class NetworkTableReaderTest extends TestCase {
+ private NetworkTableReader reader;
+
+ /*
+ * Test file: galFiltered.sif + some edge attributes.
+ */
+ private static final String TEST_TABLE = "/galFiltered.txt";
+
+ protected void setUp() throws Exception {
+ super.setUp();
+ Cytoscape.buildOntologyServer();
+ }
+
+ protected void tearDown() throws Exception {
+ super.tearDown();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testReadTable() throws Exception {
+
+ List<String> delimiters = new ArrayList<String>();
+ delimiters.add(TextFileDelimiters.TAB.toString());
+
+ String[] galAttrName = {
+ "Source", "Target", "Interaction", "edge bool attr",
+ "edge string attr", "edge float attr"
+ };
+ Byte[] galAttrTypes = {
+ CyAttributes.TYPE_STRING, CyAttributes.TYPE_STRING,
+ CyAttributes.TYPE_STRING, CyAttributes.TYPE_BOOLEAN,
+ CyAttributes.TYPE_STRING, CyAttributes.TYPE_FLOATING
+ };
+ NetworkTableMappingParameters mapping = new NetworkTableMappingParameters(delimiters,
+ TextFileDelimiters.PIPE
+ .toString(),
+ galAttrName,
+ galAttrTypes,
+ null, null, 0, 1,
+ 2, null);
+
+ reader = new NetworkTableReader("test name", getClass().getResource(TEST_TABLE), mapping, 0, null);
+
+ CyNetwork net = Cytoscape.createNetwork(reader, false, null);
+
+ /*
+ * test cases
+ */
+ assertEquals(331, net.getNodeCount());
+ assertEquals(362, net.getEdgeCount());
+
+ CyAttributes attr = Cytoscape.getEdgeAttributes();
+ assertTrue(attr.getBooleanAttribute("YGL122C (pp) YOL123W", "edge bool attr"));
+ assertFalse(attr.getBooleanAttribute("YKR026C (pp) YGL122C", "edge bool attr"));
+
+ assertEquals(1.2344543, attr.getDoubleAttribute("YBL026W (pp) YOR167C", "edge float attr"));
+ assertEquals("abcd12706",
+ attr.getStringAttribute("YBL026W (pp) YOR167C", "edge string attr"));
+ assertEquals("abcd12584", attr.getStringAttribute("YPL248C (pd) ?", "edge string attr"));
+
+ Cytoscape.destroyNetwork(net);
+ }
+}
diff --git a/coreplugins/TableImport/src/test/java/edu/ucsd/bioeng/coreplugin/tableImport/ui/DataTypeUtilTest.java b/coreplugins/TableImport/src/test/java/edu/ucsd/bioeng/coreplugin/tableImport/ui/DataTypeUtilTest.java
new file mode 100644
index 0000000..a9fe0fb
--- /dev/null
+++ b/coreplugins/TableImport/src/test/java/edu/ucsd/bioeng/coreplugin/tableImport/ui/DataTypeUtilTest.java
@@ -0,0 +1,88 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package edu.ucsd.bioeng.coreplugin.tableImport.ui;
+
+import junit.framework.*;
+import javax.swing.table.TableModel;
+import javax.swing.table.DefaultTableModel;
+import java.util.Map;
+import java.util.HashMap;
+import cytoscape.data.CyAttributes;
+
+public class DataTypeUtilTest extends TestCase {
+
+ TableModel tableModel;
+ Map<String,Byte[]> dataTypeMap;
+
+ protected void setUp() throws Exception {
+ super.setUp();
+
+ Object[] columnNames =
+ {"allFalse","mostlyFalse","mostlyTrue","integer","double","string"};
+ Object[][] data = {
+ { "false", "false", "false", "1", "1.0", "homer" },
+ { "false", "true", "true", "5", "4.4", "marge" },
+ { "false", "false", "true", "18", "3.14", "bart" },
+ { "false", "false", "true", "123", "123", "lisa" },
+ { "false", "true", "true", "7", "5", "maggie" },
+ { "false", "false", "false", "9", "0.007", "smithers" }
+ };
+
+ tableModel = new DefaultTableModel(data, columnNames);
+ dataTypeMap = new HashMap<String,Byte[]>();
+ }
+
+ protected void tearDown() throws Exception {
+ super.tearDown();
+ }
+
+ public void testGuessTypes() throws Exception {
+ DataTypeUtil.guessTypes(tableModel,"test1",dataTypeMap);
+ Byte[] res = dataTypeMap.get("test1");
+
+ // CyAttributes.TYPE_BOOLEAN = 1
+ // CyAttributes.TYPE_FLOATING = 2
+ // CyAttributes.TYPE_INTEGER = 3
+ // CyAttributes.TYPE_STRING = 4
+ assertEquals( CyAttributes.TYPE_BOOLEAN, res[0].byteValue() ); // allFalse
+ assertEquals( CyAttributes.TYPE_BOOLEAN, res[1].byteValue() ); // mostlyFalse
+ assertEquals( CyAttributes.TYPE_BOOLEAN, res[2].byteValue() ); // mostlyTrue
+ assertEquals( CyAttributes.TYPE_INTEGER, res[3].byteValue() ); // integer
+ assertEquals( CyAttributes.TYPE_FLOATING, res[4].byteValue() ); // double
+ assertEquals( CyAttributes.TYPE_STRING, res[5].byteValue() ); // string
+ }
+}
diff --git a/coreplugins/TableImport/src/test/resources/TestSetting.properties b/coreplugins/TableImport/src/test/resources/TestSetting.properties
new file mode 100644
index 0000000..7777c4b
--- /dev/null
+++ b/coreplugins/TableImport/src/test/resources/TestSetting.properties
@@ -0,0 +1,16 @@
+delayRatio=1.0
+delayAdjust=0
+calmDelay=100
+keyBoardType=US101
+isScrollArrowPlaceTogether=true
+clickInterval=200
+singleClickTime=300
+doubleClickTime=100
+screenInsetTop=0
+screenInsetBottom=0
+screenInsetRight=0
+screenInsetLeft=0
+isCapturableWhenExceptionIsThrown=true
+useKeywordSubstitution=true
+hostsAllowed=localhost
+targetHost=notepc2
diff --git a/coreplugins/TableImport/src/test/resources/annotation/annotationSampleForYeast.txt b/coreplugins/TableImport/src/test/resources/annotation/annotationSampleForYeast.txt
new file mode 100755
index 0000000..e5d3f4b
--- /dev/null
+++ b/coreplugins/TableImport/src/test/resources/annotation/annotationSampleForYeast.txt
@@ -0,0 +1,33341 @@
+Object Name in SGD key alias Taxon ID
+S000007287 15S_RRNA 15S_rRNA|15S_RRNA_2 taxon:4932
+S000007287 15S_RRNA 15S_rRNA|15S_RRNA_2 taxon:4932
+S000007287 15S_RRNA 15S_rRNA|15S_RRNA_2 taxon:4932
+S000007287 15S_RRNA 15S_rRNA|15S_RRNA_2 taxon:4932
+S000007288 21S_RRNA 21S_rRNA|21S_rRNA_3|21S_rRNA_4 taxon:4932
+S000007288 21S_RRNA 21S_rRNA|21S_rRNA_3|21S_rRNA_4 taxon:4932
+S000007288 21S_RRNA 21S_rRNA|21S_rRNA_3|21S_rRNA_4 taxon:4932
+S000007288 21S_RRNA 21S_rRNA|21S_rRNA_3|21S_rRNA_4 taxon:4932
+S000007288 21S_RRNA 21S_rRNA|21S_rRNA_3|21S_rRNA_4 taxon:4932
+S000007288 21S_RRNA 21S_rRNA|21S_rRNA_3|21S_rRNA_4 taxon:4932
+S000004660 AAC1 YMR056C taxon:4932
+S000004660 AAC1 YMR056C taxon:4932
+S000004660 AAC1 YMR056C taxon:4932
+S000004660 AAC1 YMR056C taxon:4932
+S000000289 AAC3 YBR085W|ANC3 taxon:4932
+S000000289 AAC3 YBR085W|ANC3 taxon:4932
+S000000289 AAC3 YBR085W|ANC3 taxon:4932
+S000000289 AAC3 YBR085W|ANC3 taxon:4932
+S000000289 AAC3 YBR085W|ANC3 taxon:4932
+S000003916 AAD10 YJR155W taxon:4932
+S000003916 AAD10 YJR155W taxon:4932
+S000003916 AAD10 YJR155W taxon:4932
+S000005275 AAD14 YNL331C taxon:4932
+S000005275 AAD14 YNL331C taxon:4932
+S000005275 AAD14 YNL331C taxon:4932
+S000005525 AAD15 YOL165C taxon:4932
+S000005525 AAD15 YOL165C taxon:4932
+S000005525 AAD15 YOL165C taxon:4932
+S000001837 AAD16 YFL057C taxon:4932
+S000001837 AAD16 YFL057C taxon:4932
+S000001837 AAD16 YFL057C taxon:4932
+S000000704 AAD3 YCR107W taxon:4932
+S000000704 AAD3 YCR107W taxon:4932
+S000000704 AAD3 YCR107W taxon:4932
+S000002402 AAD4 YDL243C taxon:4932
+S000002402 AAD4 YDL243C taxon:4932
+S000002402 AAD4 YDL243C taxon:4932
+S000001838 AAD6 YFL056C taxon:4932
+S000001838 AAD6 YFL056C taxon:4932
+S000001838 AAD6 YFL056C taxon:4932
+S000005085 AAH1 YNL141W taxon:4932
+S000005085 AAH1 YNL141W taxon:4932
+S000005085 AAH1 YNL141W taxon:4932
+S000005085 AAH1 YNL141W taxon:4932
+S000001089 AAP1 YHR047C|AAP1' taxon:4932
+S000001089 AAP1 YHR047C|AAP1' taxon:4932
+S000001089 AAP1 YHR047C|AAP1' taxon:4932
+S000001089 AAP1 YHR047C|AAP1' taxon:4932
+S000001089 AAP1 YHR047C|AAP1' taxon:4932
+S000000170 AAR2 YBL074C taxon:4932
+S000000170 AAR2 YBL074C taxon:4932
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+S000000170 AAR2 YBL074C taxon:4932
+S000001589 AAT1 YKL106W taxon:4932
+S000001589 AAT1 YKL106W taxon:4932
+S000001589 AAT1 YKL106W taxon:4932
+S000001589 AAT1 YKL106W taxon:4932
+S000001589 AAT1 YKL106W taxon:4932
+S000001589 AAT1 YKL106W taxon:4932
+S000004017 AAT2 YLR027C|ASP5 taxon:4932
+S000004017 AAT2 YLR027C|ASP5 taxon:4932
+S000004017 AAT2 YLR027C|ASP5 taxon:4932
+S000004017 AAT2 YLR027C|ASP5 taxon:4932
+S000004017 AAT2 YLR027C|ASP5 taxon:4932
+S000004017 AAT2 YLR027C|ASP5 taxon:4932
+S000004017 AAT2 YLR027C|ASP5 taxon:4932
+S000004017 AAT2 YLR027C|ASP5 taxon:4932
+S000003087 ABC1 YGL119W|COQ8 taxon:4932
+S000003087 ABC1 YGL119W|COQ8 taxon:4932
+S000003087 ABC1 YGL119W|COQ8 taxon:4932
+S000003087 ABC1 YGL119W|COQ8 taxon:4932
+S000003087 ABC1 YGL119W|COQ8 taxon:4932
+S000003087 ABC1 YGL119W|COQ8 taxon:4932
+S000000440 ABD1 YBR236C taxon:4932
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+S000000440 ABD1 YBR236C taxon:4932
+S000000440 ABD1 YBR236C taxon:4932
+S000000440 ABD1 YBR236C taxon:4932
+S000001595 ABF1 YKL112W|BAF1|OBF1|REB2|SBF1 taxon:4932
+S000001595 ABF1 YKL112W|BAF1|OBF1|REB2|SBF1 taxon:4932
+S000001595 ABF1 YKL112W|BAF1|OBF1|REB2|SBF1 taxon:4932
+S000001595 ABF1 YKL112W|BAF1|OBF1|REB2|SBF1 taxon:4932
+S000001595 ABF1 YKL112W|BAF1|OBF1|REB2|SBF1 taxon:4932
+S000001595 ABF1 YKL112W|BAF1|OBF1|REB2|SBF1 taxon:4932
+S000001595 ABF1 YKL112W|BAF1|OBF1|REB2|SBF1 taxon:4932
+S000001595 ABF1 YKL112W|BAF1|OBF1|REB2|SBF1 taxon:4932
+S000001595 ABF1 YKL112W|BAF1|OBF1|REB2|SBF1 taxon:4932
+S000001595 ABF1 YKL112W|BAF1|OBF1|REB2|SBF1 taxon:4932
+S000001595 ABF1 YKL112W|BAF1|OBF1|REB2|SBF1 taxon:4932
+S000001595 ABF1 YKL112W|BAF1|OBF1|REB2|SBF1 taxon:4932
+S000001595 ABF1 YKL112W|BAF1|OBF1|REB2|SBF1 taxon:4932
+S000001595 ABF1 YKL112W|BAF1|OBF1|REB2|SBF1 taxon:4932
+S000001595 ABF1 YKL112W|BAF1|OBF1|REB2|SBF1 taxon:4932
+S000001595 ABF1 YKL112W|BAF1|OBF1|REB2|SBF1 taxon:4932
+S000001595 ABF1 YKL112W|BAF1|OBF1|REB2|SBF1 taxon:4932
+S000001595 ABF1 YKL112W|BAF1|OBF1|REB2|SBF1 taxon:4932
+S000001595 ABF1 YKL112W|BAF1|OBF1|REB2|SBF1 taxon:4932
+S000001595 ABF1 YKL112W|BAF1|OBF1|REB2|SBF1 taxon:4932
+S000001595 ABF1 YKL112W|BAF1|OBF1|REB2|SBF1 taxon:4932
+S000001595 ABF1 YKL112W|BAF1|OBF1|REB2|SBF1 taxon:4932
+S000001595 ABF1 YKL112W|BAF1|OBF1|REB2|SBF1 taxon:4932
+S000001595 ABF1 YKL112W|BAF1|OBF1|REB2|SBF1 taxon:4932
+S000004676 ABF2 YMR072W taxon:4932
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+S000003869 ABM1 YJR108W taxon:4932
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+S000000684 ABP1 YCR088W taxon:4932
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+S000000684 ABP1 YCR088W taxon:4932
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+S000000684 ABP1 YCR088W taxon:4932
+S000005765 ABP140 YOR239W|YOR240W taxon:4932
+S000005765 ABP140 YOR239W|YOR240W taxon:4932
+S000005765 ABP140 YOR239W|YOR240W taxon:4932
+S000005765 ABP140 YOR239W|YOR240W taxon:4932
+S000005765 ABP140 YOR239W|YOR240W taxon:4932
+S000005765 ABP140 YOR239W|YOR240W taxon:4932
+S000005316 ABZ1 YNR033W taxon:4932
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+S000004902 ABZ2 YMR289W taxon:4932
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+S000000847 ACA1 YER045C taxon:4932
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+S000005299 ACC1 YNR016C|ABP2|FAS3|MTR7 taxon:4932
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+S000005299 ACC1 YNR016C|ABP2|FAS3|MTR7 taxon:4932
+S000005299 ACC1 YNR016C|ABP2|FAS3|MTR7 taxon:4932
+S000005299 ACC1 YNR016C|ABP2|FAS3|MTR7 taxon:4932
+S000005299 ACC1 YNR016C|ABP2|FAS3|MTR7 taxon:4932
+S000005299 ACC1 YNR016C|ABP2|FAS3|MTR7 taxon:4932
+S000005299 ACC1 YNR016C|ABP2|FAS3|MTR7 taxon:4932
+S000005299 ACC1 YNR016C|ABP2|FAS3|MTR7 taxon:4932
+S000005299 ACC1 YNR016C|ABP2|FAS3|MTR7 taxon:4932
+S000004121 ACE2 YLR131C taxon:4932
+S000004121 ACE2 YLR131C taxon:4932
+S000004121 ACE2 YLR131C taxon:4932
+S000004121 ACE2 YLR131C taxon:4932
+S000004121 ACE2 YLR131C taxon:4932
+S000004121 ACE2 YLR131C taxon:4932
+S000004134 ACF2 YLR144C|ENG2|PCA1 taxon:4932
+S000004134 ACF2 YLR144C|ENG2|PCA1 taxon:4932
+S000004134 ACF2 YLR144C|ENG2|PCA1 taxon:4932
+S000003843 ACF4 YJR083C taxon:4932
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+S000002362 ACK1 YDL203C taxon:4932
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+S000002362 ACK1 YDL203C taxon:4932
+S000006188 ACM1 YPL267W taxon:4932
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+S000002919 ACN9 YDR511W taxon:4932
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+S000002919 ACN9 YDR511W taxon:4932
+S000002919 ACN9 YDR511W taxon:4932
+S000004295 ACO1 YLR304C|GLU1 taxon:4932
+S000004295 ACO1 YLR304C|GLU1 taxon:4932
+S000004295 ACO1 YLR304C|GLU1 taxon:4932
+S000004295 ACO1 YLR304C|GLU1 taxon:4932
+S000004295 ACO1 YLR304C|GLU1 taxon:4932
+S000004295 ACO1 YLR304C|GLU1 taxon:4932
+S000004295 ACO1 YLR304C|GLU1 taxon:4932
+S000004295 ACO1 YLR304C|GLU1 taxon:4932
+S000004295 ACO1 YLR304C|GLU1 taxon:4932
+S000003736 ACO2 YJL200C taxon:4932
+S000003736 ACO2 YJL200C taxon:4932
+S000003736 ACO2 YJL200C taxon:4932
+S000003736 ACO2 YJL200C taxon:4932
+S000001675 ACP1 YKL192C taxon:4932
+S000001675 ACP1 YKL192C taxon:4932
+S000001675 ACP1 YKL192C taxon:4932
+S000001675 ACP1 YKL192C taxon:4932
+S000000050 ACS1 YAL054C|FUN44 taxon:4932
+S000000050 ACS1 YAL054C|FUN44 taxon:4932
+S000000050 ACS1 YAL054C|FUN44 taxon:4932
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+S000004143 ACS2 YLR153C taxon:4932
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+S000001855 ACT1 YFL039C|ABY1|END7|actin taxon:4932
+S000001855 ACT1 YFL039C|ABY1|END7|actin taxon:4932
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+S000001855 ACT1 YFL039C|ABY1|END7|actin taxon:4932
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+S000001855 ACT1 YFL039C|ABY1|END7|actin taxon:4932
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+S000001855 ACT1 YFL039C|ABY1|END7|actin taxon:4932
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+S000001855 ACT1 YFL039C|ABY1|END7|actin taxon:4932
+S000001855 ACT1 YFL039C|ABY1|END7|actin taxon:4932
+S000001855 ACT1 YFL039C|ABY1|END7|actin taxon:4932
+S000001855 ACT1 YFL039C|ABY1|END7|actin taxon:4932
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+S000001855 ACT1 YFL039C|ABY1|END7|actin taxon:4932
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+S000000274 ALG14 YBR070C taxon:4932
+S000000274 ALG14 YBR070C taxon:4932
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+S000000178 ALG3 YBL082C|RHK1 taxon:4932
+S000000178 ALG3 YBL082C|RHK1 taxon:4932
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+S000000178 ALG3 YBL082C|RHK1 taxon:4932
+S000000178 ALG3 YBL082C|RHK1 taxon:4932
+S000000178 ALG3 YBL082C|RHK1 taxon:4932
+S000006148 ALG5 YPL227C taxon:4932
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+S000005593 ALG8 YOR067C|YOR29-18 taxon:4932
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+S000005214 ALP1 YNL270C|APL1 taxon:4932
+S000005214 ALP1 YNL270C|APL1 taxon:4932
+S000005214 ALP1 YNL270C|APL1 taxon:4932
+S000005490 ALR1 YOL130W|SWC3 taxon:4932
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+S000004079 ALT1 YLR089C taxon:4932
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+S000004079 ALT1 YLR089C taxon:4932
+S000002518 ALT2 YDR111C taxon:4932
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+S000003457 AMA1 YGR225W|SPO70 taxon:4932
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+S000000415 AME1 YBR211C|ARP100 taxon:4932
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+S000000362 AMN1 YBR158W|CST13|ICS4 taxon:4932
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+S000029033 ANC4 taxon:4932
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+S000000762 ANP1 YEL036C|GEM3|MNN8 taxon:4932
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+S000006384 AOS1 YPR180W taxon:4932
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+S000000555 APA1 YCL050C|DTP1 taxon:4932
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+S000002938 APA2 YDR530C taxon:4932
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+S000005116 APC1 YNL172W taxon:4932
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+S000002166 APC11 YDL008W taxon:4932
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+S000002166 APC11 YDL008W taxon:4932
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+S000002166 APC11 YDL008W taxon:4932
+S000004117 APC2 YLR127C|RSI1 taxon:4932
+S000004117 APC2 YLR127C|RSI1 taxon:4932
+S000004117 APC2 YLR127C|RSI1 taxon:4932
+S000004117 APC2 YLR127C|RSI1 taxon:4932
+S000004117 APC2 YLR127C|RSI1 taxon:4932
+S000004117 APC2 YLR127C|RSI1 taxon:4932
+S000004117 APC2 YLR127C|RSI1 taxon:4932
+S000004117 APC2 YLR127C|RSI1 taxon:4932
+S000004117 APC2 YLR127C|RSI1 taxon:4932
+S000002525 APC4 YDR118W taxon:4932
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+S000005775 APC5 YOR249C|RMC1 taxon:4932
+S000005775 APC5 YOR249C|RMC1 taxon:4932
+S000005775 APC5 YOR249C|RMC1 taxon:4932
+S000005775 APC5 YOR249C|RMC1 taxon:4932
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+S000005775 APC5 YOR249C|RMC1 taxon:4932
+S000005775 APC5 YOR249C|RMC1 taxon:4932
+S000005775 APC5 YOR249C|RMC1 taxon:4932
+S000005775 APC5 YOR249C|RMC1 taxon:4932
+S000005775 APC5 YOR249C|RMC1 taxon:4932
+S000004092 APC9 YLR102C taxon:4932
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+S000004092 APC9 YLR102C taxon:4932
+S000004092 APC9 YLR102C taxon:4932
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+S000004092 APC9 YLR102C taxon:4932
+S000004092 APC9 YLR102C taxon:4932
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+S000000355 APD1 YBR151W taxon:4932
+S000000355 APD1 YBR151W taxon:4932
+S000000355 APD1 YBR151W taxon:4932
+S000000355 APD1 YBR151W taxon:4932
+S000001640 APE2 YKL157W|LAP1|YKL158W taxon:4932
+S000001640 APE2 YKL157W|LAP1|YKL158W taxon:4932
+S000001640 APE2 YKL157W|LAP1|YKL158W taxon:4932
+S000001640 APE2 YKL157W|LAP1|YKL158W taxon:4932
+S000001640 APE2 YKL157W|LAP1|YKL158W taxon:4932
+S000001640 APE2 YKL157W|LAP1|YKL158W taxon:4932
+S000000490 APE3 YBR286W|APY1 taxon:4932
+S000000490 APE3 YBR286W|APY1 taxon:4932
+S000000490 APE3 YBR286W|APY1 taxon:4932
+S000000490 APE3 YBR286W|APY1 taxon:4932
+S000000490 APE3 YBR286W|APY1 taxon:4932
+S000029035 APG11 taxon:4932
+S000029035 APG11 taxon:4932
+S000029035 APG11 taxon:4932
+S000005021 APJ1 YNL077W taxon:4932
+S000005021 APJ1 YNL077W taxon:4932
+S000005021 APJ1 YNL077W taxon:4932
+S000005021 APJ1 YNL077W taxon:4932
+S000005021 APJ1 YNL077W taxon:4932
+S000005021 APJ1 YNL077W taxon:4932
+S000003765 APL1 YJR005W|YAP80 taxon:4932
+S000003765 APL1 YJR005W|YAP80 taxon:4932
+S000003765 APL1 YJR005W|YAP80 taxon:4932
+S000003765 APL1 YJR005W|YAP80 taxon:4932
+S000001618 APL2 YKL135C taxon:4932
+S000001618 APL2 YKL135C taxon:4932
+S000001618 APL2 YKL135C taxon:4932
+S000001618 APL2 YKL135C taxon:4932
+S000001618 APL2 YKL135C taxon:4932
+S000001618 APL2 YKL135C taxon:4932
+S000001618 APL2 YKL135C taxon:4932
+S000000133 APL3 YBL037W taxon:4932
+S000000133 APL3 YBL037W taxon:4932
+S000000133 APL3 YBL037W taxon:4932
+S000000133 APL3 YBL037W taxon:4932
+S000006233 APL4 YPR029C taxon:4932
+S000006233 APL4 YPR029C taxon:4932
+S000006233 APL4 YPR029C taxon:4932
+S000006233 APL4 YPR029C taxon:4932
+S000006233 APL4 YPR029C taxon:4932
+S000006233 APL4 YPR029C taxon:4932
+S000006233 APL4 YPR029C taxon:4932
+S000006116 APL5 YPL195W|YKS4 taxon:4932
+S000006116 APL5 YPL195W|YKS4 taxon:4932
+S000006116 APL5 YPL195W|YKS4 taxon:4932
+S000006116 APL5 YPL195W|YKS4 taxon:4932
+S000003493 APL6 YGR261C|YKS5 taxon:4932
+S000003493 APL6 YGR261C|YKS5 taxon:4932
+S000003493 APL6 YGR261C|YKS5 taxon:4932
+S000003493 APL6 YGR261C|YKS5 taxon:4932
+S000006180 APM1 YPL259C|YAP54 taxon:4932
+S000006180 APM1 YPL259C|YAP54 taxon:4932
+S000006180 APM1 YPL259C|YAP54 taxon:4932
+S000006180 APM1 YPL259C|YAP54 taxon:4932
+S000006180 APM1 YPL259C|YAP54 taxon:4932
+S000006180 APM1 YPL259C|YAP54 taxon:4932
+S000006180 APM1 YPL259C|YAP54 taxon:4932
+S000001011 APM2 YHL019C taxon:4932
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+S000001011 APM2 YHL019C taxon:4932
+S000001011 APM2 YHL019C taxon:4932
+S000000492 APM3 YBR288C|YKS6 taxon:4932
+S000000492 APM3 YBR288C|YKS6 taxon:4932
+S000000492 APM3 YBR288C|YKS6 taxon:4932
+S000000492 APM3 YBR288C|YKS6 taxon:4932
+S000005423 APM4 YOL062C|AMP1 taxon:4932
+S000005423 APM4 YOL062C|AMP1 taxon:4932
+S000005423 APM4 YOL062C|AMP1 taxon:4932
+S000005423 APM4 YOL062C|AMP1 taxon:4932
+S000005423 APM4 YOL062C|AMP1 taxon:4932
+S000001597 APN1 YKL114C taxon:4932
+S000001597 APN1 YKL114C taxon:4932
+S000001597 APN1 YKL114C taxon:4932
+S000001597 APN1 YKL114C taxon:4932
+S000001597 APN1 YKL114C taxon:4932
+S000001597 APN1 YKL114C taxon:4932
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+S000000115 APN2 YBL019W|ETH1 taxon:4932
+S000000115 APN2 YBL019W|ETH1 taxon:4932
+S000000115 APN2 YBL019W|ETH1 taxon:4932
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+S000005038 APP1 YNL094W taxon:4932
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+S000004160 APS1 YLR170C|YAP19 taxon:4932
+S000004160 APS1 YLR170C|YAP19 taxon:4932
+S000004160 APS1 YLR170C|YAP19 taxon:4932
+S000004160 APS1 YLR170C|YAP19 taxon:4932
+S000004160 APS1 YLR170C|YAP19 taxon:4932
+S000004160 APS1 YLR170C|YAP19 taxon:4932
+S000004160 APS1 YLR170C|YAP19 taxon:4932
+S000003819 APS2 YJR058C|YAP17 taxon:4932
+S000003819 APS2 YJR058C|YAP17 taxon:4932
+S000003819 APS2 YJR058C|YAP17 taxon:4932
+S000003819 APS2 YJR058C|YAP17 taxon:4932
+S000003561 APS3 YJL024C|YKS7 taxon:4932
+S000003561 APS3 YJL024C|YKS7 taxon:4932
+S000003561 APS3 YJL024C|YKS7 taxon:4932
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+S000006396 AQY1 YPR192W taxon:4932
+S000006396 AQY1 YPR192W taxon:4932
+S000006396 AQY1 YPR192W taxon:4932
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+S000003975 AQY2 YLL052C taxon:4932
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+S000000353 ARA1 YBR149W taxon:4932
+S000000353 ARA1 YBR149W taxon:4932
+S000000353 ARA1 YBR149W taxon:4932
+S000000353 ARA1 YBR149W taxon:4932
+S000000353 ARA1 YBR149W taxon:4932
+S000000353 ARA1 YBR149W taxon:4932
+S000000838 ARB1 YER036C taxon:4932
+S000000838 ARB1 YER036C taxon:4932
+S000000838 ARB1 YER036C taxon:4932
+S000000838 ARB1 YER036C taxon:4932
+S000000838 ARB1 YER036C taxon:4932
+S000000838 ARB1 YER036C taxon:4932
+S000003073 ARC1 YGL105W taxon:4932
+S000003073 ARC1 YGL105W taxon:4932
+S000003073 ARC1 YGL105W taxon:4932
+S000003073 ARC1 YGL105W taxon:4932
+S000003073 ARC1 YGL105W taxon:4932
+S000003073 ARC1 YGL105W taxon:4932
+S000003073 ARC1 YGL105W taxon:4932
+S000003073 ARC1 YGL105W taxon:4932
+S000001324 ARC15 YIL062C taxon:4932
+S000001324 ARC15 YIL062C taxon:4932
+S000001324 ARC15 YIL062C taxon:4932
+S000001324 ARC15 YIL062C taxon:4932
+S000001324 ARC15 YIL062C taxon:4932
+S000001324 ARC15 YIL062C taxon:4932
+S000001324 ARC15 YIL062C taxon:4932
+S000001324 ARC15 YIL062C taxon:4932
+S000004362 ARC18 YLR370C taxon:4932
+S000004362 ARC18 YLR370C taxon:4932
+S000004362 ARC18 YLR370C taxon:4932
+S000004362 ARC18 YLR370C taxon:4932
+S000001496 ARC19 YKL013C taxon:4932
+S000001496 ARC19 YKL013C taxon:4932
+S000001496 ARC19 YKL013C taxon:4932
+S000001496 ARC19 YKL013C taxon:4932
+S000001496 ARC19 YKL013C taxon:4932
+S000005318 ARC35 YNR035C|END9 taxon:4932
+S000005318 ARC35 YNR035C|END9 taxon:4932
+S000005318 ARC35 YNR035C|END9 taxon:4932
+S000005318 ARC35 YNR035C|END9 taxon:4932
+S000005318 ARC35 YNR035C|END9 taxon:4932
+S000005318 ARC35 YNR035C|END9 taxon:4932
+S000005318 ARC35 YNR035C|END9 taxon:4932
+S000005318 ARC35 YNR035C|END9 taxon:4932
+S000005318 ARC35 YNR035C|END9 taxon:4932
+S000005318 ARC35 YNR035C|END9 taxon:4932
+S000005318 ARC35 YNR035C|END9 taxon:4932
+S000005318 ARC35 YNR035C|END9 taxon:4932
+S000005318 ARC35 YNR035C|END9 taxon:4932
+S000000438 ARC40 YBR234C taxon:4932
+S000000438 ARC40 YBR234C taxon:4932
+S000000438 ARC40 YBR234C taxon:4932
+S000000438 ARC40 YBR234C taxon:4932
+S000000438 ARC40 YBR234C taxon:4932
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+S000001055 ARD1 YHR013C taxon:4932
+S000001055 ARD1 YHR013C taxon:4932
+S000001055 ARD1 YHR013C taxon:4932
+S000001055 ARD1 YHR013C taxon:4932
+S000001055 ARD1 YHR013C taxon:4932
+S000001055 ARD1 YHR013C taxon:4932
+S000001055 ARD1 YHR013C taxon:4932
+S000000644 ARE1 YCR048W|SAT2 taxon:4932
+S000000644 ARE1 YCR048W|SAT2 taxon:4932
+S000000644 ARE1 YCR048W|SAT2 taxon:4932
+S000005302 ARE2 YNR019W|SAT1 taxon:4932
+S000005302 ARE2 YNR019W|SAT1 taxon:4932
+S000005302 ARE2 YNR019W|SAT1 taxon:4932
+S000002351 ARF1 YDL192W taxon:4932
+S000002351 ARF1 YDL192W taxon:4932
+S000002351 ARF1 YDL192W taxon:4932
+S000002351 ARF1 YDL192W taxon:4932
+S000002351 ARF1 YDL192W taxon:4932
+S000002351 ARF1 YDL192W taxon:4932
+S000002351 ARF1 YDL192W taxon:4932
+S000002351 ARF1 YDL192W taxon:4932
+S000002351 ARF1 YDL192W taxon:4932
+S000002351 ARF1 YDL192W taxon:4932
+S000002351 ARF1 YDL192W taxon:4932
+S000002296 ARF2 YDL137W taxon:4932
+S000002296 ARF2 YDL137W taxon:4932
+S000002296 ARF2 YDL137W taxon:4932
+S000002296 ARF2 YDL137W taxon:4932
+S000002296 ARF2 YDL137W taxon:4932
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+S000002296 ARF2 YDL137W taxon:4932
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+S000005620 ARF3 YOR094W|ARL2 taxon:4932
+S000005620 ARF3 YOR094W|ARL2 taxon:4932
+S000005620 ARF3 YOR094W|ARL2 taxon:4932
+S000005419 ARG1 YOL058W|ARG10 taxon:4932
+S000005419 ARG1 YOL058W|ARG10 taxon:4932
+S000005419 ARG1 YOL058W|ARG10 taxon:4932
+S000005419 ARG1 YOL058W|ARG10 taxon:4932
+S000005419 ARG1 YOL058W|ARG10 taxon:4932
+S000003607 ARG2 YJL071W|HRB574 taxon:4932
+S000003607 ARG2 YJL071W|HRB574 taxon:4932
+S000003607 ARG2 YJL071W|HRB574 taxon:4932
+S000003607 ARG2 YJL071W|HRB574 taxon:4932
+S000003607 ARG2 YJL071W|HRB574 taxon:4932
+S000003607 ARG2 YJL071W|HRB574 taxon:4932
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+S000003624 ARG3 YJL088W taxon:4932
+S000003624 ARG3 YJL088W taxon:4932
+S000001060 ARG4 YHR018C taxon:4932
+S000001060 ARG4 YHR018C taxon:4932
+S000001060 ARG4 YHR018C taxon:4932
+S000000871 "ARG5,6" YER069W taxon:4932
+S000000871 "ARG5,6" YER069W taxon:4932
+S000000871 "ARG5,6" YER069W taxon:4932
+S000000871 "ARG5,6" YER069W taxon:4932
+S000000871 "ARG5,6" YER069W taxon:4932
+S000000871 "ARG5,6" YER069W taxon:4932
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+S000005500 ARG8 YOL140W taxon:4932
+S000005500 ARG8 YOL140W taxon:4932
+S000005500 ARG8 YOL140W taxon:4932
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+S000004645 ARG80 YMR042W|ARGR1 taxon:4932
+S000004645 ARG80 YMR042W|ARGR1 taxon:4932
+S000004645 ARG80 YMR042W|ARGR1 taxon:4932
+S000004645 ARG80 YMR042W|ARGR1 taxon:4932
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+S000004565 ARG81 YML099C|ARGR2 taxon:4932
+S000004565 ARG81 YML099C|ARGR2 taxon:4932
+S000004565 ARG81 YML099C|ARGR2 taxon:4932
+S000002580 ARG82 YDR173C|ARGR3|IPK2 taxon:4932
+S000002580 ARG82 YDR173C|ARGR3|IPK2 taxon:4932
+S000002580 ARG82 YDR173C|ARGR3|IPK2 taxon:4932
+S000002580 ARG82 YDR173C|ARGR3|IPK2 taxon:4932
+S000002580 ARG82 YDR173C|ARGR3|IPK2 taxon:4932
+S000029041 ARG84 taxon:4932
+S000029041 ARG84 taxon:4932
+S000029041 ARG84 taxon:4932
+S000002784 ARH1 YDR376W taxon:4932
+S000002784 ARH1 YDR376W taxon:4932
+S000002784 ARH1 YDR376W taxon:4932
+S000002784 ARH1 YDR376W taxon:4932
+S000002784 ARH1 YDR376W taxon:4932
+S000004965 ARK1 YNL020C taxon:4932
+S000004965 ARK1 YNL020C taxon:4932
+S000004965 ARK1 YNL020C taxon:4932
+S000004965 ARK1 YNL020C taxon:4932
+S000004965 ARK1 YNL020C taxon:4932
+S000004965 ARK1 YNL020C taxon:4932
+S000004965 ARK1 YNL020C taxon:4932
+S000004965 ARK1 YNL020C taxon:4932
+S000004965 ARK1 YNL020C taxon:4932
+S000004965 ARK1 YNL020C taxon:4932
+S000000368 ARL1 YBR164C|DLP2 taxon:4932
+S000000368 ARL1 YBR164C|DLP2 taxon:4932
+S000000368 ARL1 YBR164C|DLP2 taxon:4932
+S000000368 ARL1 YBR164C|DLP2 taxon:4932
+S000000368 ARL1 YBR164C|DLP2 taxon:4932
+S000000368 ARL1 YBR164C|DLP2 taxon:4932
+S000000368 ARL1 YBR164C|DLP2 taxon:4932
+S000000368 ARL1 YBR164C|DLP2 taxon:4932
+S000005972 ARL3 YPL051W taxon:4932
+S000005972 ARL3 YPL051W taxon:4932
+S000005972 ARL3 YPL051W taxon:4932
+S000005972 ARL3 YPL051W taxon:4932
+S000005972 ARL3 YPL051W taxon:4932
+S000005972 ARL3 YPL051W taxon:4932
+S000005972 ARL3 YPL051W taxon:4932
+S000001032 ARN1 YHL040C taxon:4932
+S000001032 ARN1 YHL040C taxon:4932
+S000001032 ARN1 YHL040C taxon:4932
+S000001032 ARN1 YHL040C taxon:4932
+S000001039 ARN2 YHL047C|TAF1 taxon:4932
+S000001039 ARN2 YHL047C|TAF1 taxon:4932
+S000001039 ARN2 YHL047C|TAF1 taxon:4932
+S000001039 ARN2 YHL047C|TAF1 taxon:4932
+S000001039 ARN2 YHL047C|TAF1 taxon:4932
+S000001039 ARN2 YHL047C|TAF1 taxon:4932
+S000001039 ARN2 YHL047C|TAF1 taxon:4932
+S000001039 ARN2 YHL047C|TAF1 taxon:4932
+S000001039 ARN2 YHL047C|TAF1 taxon:4932
+S000001039 ARN2 YHL047C|TAF1 taxon:4932
+S000001039 ARN2 YHL047C|TAF1 taxon:4932
+S000001039 ARN2 YHL047C|TAF1 taxon:4932
+S000002534 ARO1 YDR127W taxon:4932
+S000002534 ARO1 YDR127W taxon:4932
+S000002534 ARO1 YDR127W taxon:4932
+S000002534 ARO1 YDR127W taxon:4932
+S000002534 ARO1 YDR127W taxon:4932
+S000002534 ARO1 YDR127W taxon:4932
+S000002534 ARO1 YDR127W taxon:4932
+S000002788 ARO10 YDR380W taxon:4932
+S000002788 ARO10 YDR380W taxon:4932
+S000002788 ARO10 YDR380W taxon:4932
+S000002788 ARO10 YDR380W taxon:4932
+S000002788 ARO10 YDR380W taxon:4932
+S000002788 ARO10 YDR380W taxon:4932
+S000002788 ARO10 YDR380W taxon:4932
+S000003116 ARO2 YGL148W taxon:4932
+S000003116 ARO2 YGL148W taxon:4932
+S000003116 ARO2 YGL148W taxon:4932
+S000003116 ARO2 YGL148W taxon:4932
+S000002442 ARO3 YDR035W taxon:4932
+S000002442 ARO3 YDR035W taxon:4932
+S000002442 ARO3 YDR035W taxon:4932
+S000002442 ARO3 YDR035W taxon:4932
+S000002442 ARO3 YDR035W taxon:4932
+S000000453 ARO4 YBR249C taxon:4932
+S000000453 ARO4 YBR249C taxon:4932
+S000000453 ARO4 YBR249C taxon:4932
+S000000453 ARO4 YBR249C taxon:4932
+S000006264 ARO7 YPR060C|HGS1|OSM2|TYR7 taxon:4932
+S000006264 ARO7 YPR060C|HGS1|OSM2|TYR7 taxon:4932
+S000006264 ARO7 YPR060C|HGS1|OSM2|TYR7 taxon:4932
+S000006264 ARO7 YPR060C|HGS1|OSM2|TYR7 taxon:4932
+S000003170 ARO8 YGL202W taxon:4932
+S000003170 ARO8 YGL202W taxon:4932
+S000003170 ARO8 YGL202W taxon:4932
+S000003170 ARO8 YGL202W taxon:4932
+S000003170 ARO8 YGL202W taxon:4932
+S000002829 ARO80 YDR421W taxon:4932
+S000002829 ARO80 YDR421W taxon:4932
+S000002829 ARO80 YDR421W taxon:4932
+S000002829 ARO80 YDR421W taxon:4932
+S000002829 ARO80 YDR421W taxon:4932
+S000001179 ARO9 YHR137W taxon:4932
+S000001179 ARO9 YHR137W taxon:4932
+S000001179 ARO9 YHR137W taxon:4932
+S000001179 ARO9 YHR137W taxon:4932
+S000001179 ARO9 YHR137W taxon:4932
+S000001179 ARO9 YHR137W taxon:4932
+S000001171 ARP1 YHR129C|ACT5 taxon:4932
+S000001171 ARP1 YHR129C|ACT5 taxon:4932
+S000001171 ARP1 YHR129C|ACT5 taxon:4932
+S000001171 ARP1 YHR129C|ACT5 taxon:4932
+S000002513 ARP10 YDR106W taxon:4932
+S000002513 ARP10 YDR106W taxon:4932
+S000002513 ARP10 YDR106W taxon:4932
+S000002513 ARP10 YDR106W taxon:4932
+S000002187 ARP2 YDL029W|ACT2 taxon:4932
+S000002187 ARP2 YDL029W|ACT2 taxon:4932
+S000002187 ARP2 YDL029W|ACT2 taxon:4932
+S000002187 ARP2 YDL029W|ACT2 taxon:4932
+S000002187 ARP2 YDL029W|ACT2 taxon:4932
+S000002187 ARP2 YDL029W|ACT2 taxon:4932
+S000002187 ARP2 YDL029W|ACT2 taxon:4932
+S000002187 ARP2 YDL029W|ACT2 taxon:4932
+S000002187 ARP2 YDL029W|ACT2 taxon:4932
+S000003826 ARP3 YJR065C|ACT4 taxon:4932
+S000003826 ARP3 YJR065C|ACT4 taxon:4932
+S000003826 ARP3 YJR065C|ACT4 taxon:4932
+S000003826 ARP3 YJR065C|ACT4 taxon:4932
+S000003826 ARP3 YJR065C|ACT4 taxon:4932
+S000003826 ARP3 YJR065C|ACT4 taxon:4932
+S000003826 ARP3 YJR065C|ACT4 taxon:4932
+S000003617 ARP4 YJL081C|ACT3 taxon:4932
+S000003617 ARP4 YJL081C|ACT3 taxon:4932
+S000003617 ARP4 YJL081C|ACT3 taxon:4932
+S000003617 ARP4 YJL081C|ACT3 taxon:4932
+S000003617 ARP4 YJL081C|ACT3 taxon:4932
+S000003617 ARP4 YJL081C|ACT3 taxon:4932
+S000003617 ARP4 YJL081C|ACT3 taxon:4932
+S000003617 ARP4 YJL081C|ACT3 taxon:4932
+S000003617 ARP4 YJL081C|ACT3 taxon:4932
+S000003617 ARP4 YJL081C|ACT3 taxon:4932
+S000003617 ARP4 YJL081C|ACT3 taxon:4932
+S000003617 ARP4 YJL081C|ACT3 taxon:4932
+S000003617 ARP4 YJL081C|ACT3 taxon:4932
+S000003617 ARP4 YJL081C|ACT3 taxon:4932
+S000003617 ARP4 YJL081C|ACT3 taxon:4932
+S000005004 ARP5 YNL059C taxon:4932
+S000005004 ARP5 YNL059C taxon:4932
+S000005004 ARP5 YNL059C taxon:4932
+S000005004 ARP5 YNL059C taxon:4932
+S000005004 ARP5 YNL059C taxon:4932
+S000005004 ARP5 YNL059C taxon:4932
+S000005004 ARP5 YNL059C taxon:4932
+S000005004 ARP5 YNL059C taxon:4932
+S000005004 ARP5 YNL059C taxon:4932
+S000005004 ARP5 YNL059C taxon:4932
+S000005004 ARP5 YNL059C taxon:4932
+S000004075 ARP6 YLR085C taxon:4932
+S000004075 ARP6 YLR085C taxon:4932
+S000004075 ARP6 YLR085C taxon:4932
+S000004075 ARP6 YLR085C taxon:4932
+S000004075 ARP6 YLR085C taxon:4932
+S000004075 ARP6 YLR085C taxon:4932
+S000004075 ARP6 YLR085C taxon:4932
+S000004075 ARP6 YLR085C taxon:4932
+S000006238 ARP7 YPR034W|SWP61 taxon:4932
+S000006238 ARP7 YPR034W|SWP61 taxon:4932
+S000006238 ARP7 YPR034W|SWP61 taxon:4932
+S000006238 ARP7 YPR034W|SWP61 taxon:4932
+S000006238 ARP7 YPR034W|SWP61 taxon:4932
+S000005667 ARP8 YOR141C taxon:4932
+S000005667 ARP8 YOR141C taxon:4932
+S000005667 ARP8 YOR141C taxon:4932
+S000005667 ARP8 YOR141C taxon:4932
+S000005667 ARP8 YOR141C taxon:4932
+S000004636 ARP9 YMR033W|SWP59 taxon:4932
+S000004636 ARP9 YMR033W|SWP59 taxon:4932
+S000004636 ARP9 YMR033W|SWP59 taxon:4932
+S000004636 ARP9 YMR033W|SWP59 taxon:4932
+S000004636 ARP9 YMR033W|SWP59 taxon:4932
+S000006403 ARR1 YPR199C|ACR1|YAP8 taxon:4932
+S000006403 ARR1 YPR199C|ACR1|YAP8 taxon:4932
+S000006403 ARR1 YPR199C|ACR1|YAP8 taxon:4932
+S000006403 ARR1 YPR199C|ACR1|YAP8 taxon:4932
+S000006403 ARR1 YPR199C|ACR1|YAP8 taxon:4932
+S000006403 ARR1 YPR199C|ACR1|YAP8 taxon:4932
+S000006403 ARR1 YPR199C|ACR1|YAP8 taxon:4932
+S000006403 ARR1 YPR199C|ACR1|YAP8 taxon:4932
+S000006403 ARR1 YPR199C|ACR1|YAP8 taxon:4932
+S000006404 ARR2 YPR200C|ACR2 taxon:4932
+S000006404 ARR2 YPR200C|ACR2 taxon:4932
+S000006404 ARR2 YPR200C|ACR2 taxon:4932
+S000006404 ARR2 YPR200C|ACR2 taxon:4932
+S000006405 ARR3 YPR201W|ACR3 taxon:4932
+S000006405 ARR3 YPR201W|ACR3 taxon:4932
+S000006405 ARR3 YPR201W|ACR3 taxon:4932
+S000006405 ARR3 YPR201W|ACR3 taxon:4932
+S000004232 ARV1 YLR242C taxon:4932
+S000004232 ARV1 YLR242C taxon:4932
+S000004232 ARV1 YLR242C taxon:4932
+S000004232 ARV1 YLR242C taxon:4932
+S000004232 ARV1 YLR242C taxon:4932
+S000004232 ARV1 YLR242C taxon:4932
+S000004232 ARV1 YLR242C taxon:4932
+S000004232 ARV1 YLR242C taxon:4932
+S000002508 ARX1 YDR101C taxon:4932
+S000002508 ARX1 YDR101C taxon:4932
+S000002508 ARX1 YDR101C taxon:4932
+S000002508 ARX1 YDR101C taxon:4932
+S000004722 ASC1 YMR116C|CPC2 taxon:4932
+S000004722 ASC1 YMR116C|CPC2 taxon:4932
+S000004722 ASC1 YMR116C|CPC2 taxon:4932
+S000004722 ASC1 YMR116C|CPC2 taxon:4932
+S000004722 ASC1 YMR116C|CPC2 taxon:4932
+S000005584 ASE1 YOR058C|YOR29-09 taxon:4932
+S000005584 ASE1 YOR058C|YOR29-09 taxon:4932
+S000005584 ASE1 YOR058C|YOR29-09 taxon:4932
+S000005584 ASE1 YOR058C|YOR29-09 taxon:4932
+S000005584 ASE1 YOR058C|YOR29-09 taxon:4932
+S000005584 ASE1 YOR058C|YOR29-09 taxon:4932
+S000003651 ASF1 YJL115W|CIA1 taxon:4932
+S000003651 ASF1 YJL115W|CIA1 taxon:4932
+S000003651 ASF1 YJL115W|CIA1 taxon:4932
+S000003651 ASF1 YJL115W|CIA1 taxon:4932
+S000002356 ASF2 YDL197C taxon:4932
+S000002356 ASF2 YDL197C taxon:4932
+S000002356 ASF2 YDL197C taxon:4932
+S000002356 ASF2 YDL197C taxon:4932
+S000002356 ASF2 YDL197C taxon:4932
+S000001392 ASG1 YIL130W taxon:4932
+S000001392 ASG1 YIL130W taxon:4932
+S000001392 ASG1 YIL130W taxon:4932
+S000003706 ASG7 YJL170C taxon:4932
+S000003706 ASG7 YJL170C taxon:4932
+S000003706 ASG7 YJL170C taxon:4932
+S000001668 ASH1 YKL185W taxon:4932
+S000001668 ASH1 YKL185W taxon:4932
+S000001668 ASH1 YKL185W taxon:4932
+S000001668 ASH1 YKL185W taxon:4932
+S000001668 ASH1 YKL185W taxon:4932
+S000001668 ASH1 YKL185W taxon:4932
+S000001668 ASH1 YKL185W taxon:4932
+S000001668 ASH1 YKL185W taxon:4932
+S000001668 ASH1 YKL185W taxon:4932
+S000001668 ASH1 YKL185W taxon:4932
+S000001668 ASH1 YKL185W taxon:4932
+S000001668 ASH1 YKL185W taxon:4932
+S000001668 ASH1 YKL185W taxon:4932
+S000001668 ASH1 YKL185W taxon:4932
+S000001668 ASH1 YKL185W taxon:4932
+S000004725 ASI1 YMR119W taxon:4932
+S000004725 ASI1 YMR119W taxon:4932
+S000004725 ASI1 YMR119W taxon:4932
+S000004725 ASI1 YMR119W taxon:4932
+S000004725 ASI1 YMR119W taxon:4932
+S000005103 ASI2 YNL159C taxon:4932
+S000005103 ASI2 YNL159C taxon:4932
+S000005103 ASI2 YNL159C taxon:4932
+S000004953 ASI3 YNL008C taxon:4932
+S000004953 ASI3 YNL008C taxon:4932
+S000004953 ASI3 YNL008C taxon:4932
+S000004953 ASI3 YNL008C taxon:4932
+S000004953 ASI3 YNL008C taxon:4932
+S000001535 ASK1 YKL052C taxon:4932
+S000001535 ASK1 YKL052C taxon:4932
+S000001535 ASK1 YKL052C taxon:4932
+S000001535 ASK1 YKL052C taxon:4932
+S000001535 ASK1 YKL052C taxon:4932
+S000001535 ASK1 YKL052C taxon:4932
+S000001535 ASK1 YKL052C taxon:4932
+S000001535 ASK1 YKL052C taxon:4932
+S000001535 ASK1 YKL052C taxon:4932
+S000001535 ASK1 YKL052C taxon:4932
+S000001535 ASK1 YKL052C taxon:4932
+S000001535 ASK1 YKL052C taxon:4932
+S000001535 ASK1 YKL052C taxon:4932
+S000003329 ASK10 YGR097W taxon:4932
+S000003329 ASK10 YGR097W taxon:4932
+S000003329 ASK10 YGR097W taxon:4932
+S000003329 ASK10 YGR097W taxon:4932
+S000003329 ASK10 YGR097W taxon:4932
+S000003329 ASK10 YGR097W taxon:4932
+S000003329 ASK10 YGR097W taxon:4932
+S000002246 ASM4 YDL088C|NUP59 taxon:4932
+S000002246 ASM4 YDL088C|NUP59 taxon:4932
+S000002246 ASM4 YDL088C|NUP59 taxon:4932
+S000002246 ASM4 YDL088C|NUP59 taxon:4932
+S000002246 ASM4 YDL088C|NUP59 taxon:4932
+S000002246 ASM4 YDL088C|NUP59 taxon:4932
+S000002246 ASM4 YDL088C|NUP59 taxon:4932
+S000002246 ASM4 YDL088C|NUP59 taxon:4932
+S000002246 ASM4 YDL088C|NUP59 taxon:4932
+S000002246 ASM4 YDL088C|NUP59 taxon:4932
+S000002246 ASM4 YDL088C|NUP59 taxon:4932
+S000002246 ASM4 YDL088C|NUP59 taxon:4932
+S000006349 ASN1 YPR145W taxon:4932
+S000006349 ASN1 YPR145W taxon:4932
+S000006349 ASN1 YPR145W taxon:4932
+S000006349 ASN1 YPR145W taxon:4932
+S000003356 ASN2 YGR124W taxon:4932
+S000003356 ASN2 YGR124W taxon:4932
+S000003356 ASN2 YGR124W taxon:4932
+S000003356 ASN2 YGR124W taxon:4932
+S000002729 ASP1 YDR321W taxon:4932
+S000002729 ASP1 YDR321W taxon:4932
+S000002729 ASP1 YDR321W taxon:4932
+S000002729 ASP1 YDR321W taxon:4932
+S000002729 ASP1 YDR321W taxon:4932
+S000004145 ASP3-1 YLR155C|ASP3 taxon:4932
+S000004145 ASP3-1 YLR155C|ASP3 taxon:4932
+S000004145 ASP3-1 YLR155C|ASP3 taxon:4932
+S000004145 ASP3-1 YLR155C|ASP3 taxon:4932
+S000004145 ASP3-1 YLR155C|ASP3 taxon:4932
+S000004145 ASP3-1 YLR155C|ASP3 taxon:4932
+S000004147 ASP3-2 YLR157C|ASP3 taxon:4932
+S000004147 ASP3-2 YLR157C|ASP3 taxon:4932
+S000004147 ASP3-2 YLR157C|ASP3 taxon:4932
+S000004147 ASP3-2 YLR157C|ASP3 taxon:4932
+S000004148 ASP3-3 YLR158C|ASP3 taxon:4932
+S000004148 ASP3-3 YLR158C|ASP3 taxon:4932
+S000004148 ASP3-3 YLR158C|ASP3 taxon:4932
+S000004148 ASP3-3 YLR158C|ASP3 taxon:4932
+S000004150 ASP3-4 YLR160C|ASP3 taxon:4932
+S000004150 ASP3-4 YLR160C|ASP3 taxon:4932
+S000004150 ASP3-4 YLR160C|ASP3 taxon:4932
+S000004150 ASP3-4 YLR160C|ASP3 taxon:4932
+S000006297 ASR1 YPR093C taxon:4932
+S000006297 ASR1 YPR093C taxon:4932
+S000006297 ASR1 YPR093C taxon:4932
+S000006297 ASR1 YPR093C taxon:4932
+S000000165 AST1 YBL069W taxon:4932
+S000000165 AST1 YBL069W taxon:4932
+S000000165 AST1 YBL069W taxon:4932
+S000000165 AST1 YBL069W taxon:4932
+S000000903 AST2 YER101C taxon:4932
+S000000903 AST2 YER101C taxon:4932
+S000000903 AST2 YER101C taxon:4932
+S000000903 AST2 YER101C taxon:4932
+S000002592 ATC1 YDR184C|LIC4 taxon:4932
+S000002592 ATC1 YDR184C|LIC4 taxon:4932
+S000002592 ATC1 YDR184C|LIC4 taxon:4932
+S000002592 ATC1 YDR184C|LIC4 taxon:4932
+S000002985 ATE1 YGL017W taxon:4932
+S000002985 ATE1 YGL017W taxon:4932
+S000002985 ATE1 YGL017W taxon:4932
+S000002985 ATE1 YGL017W taxon:4932
+S000005904 ATF1 YOR377W taxon:4932
+S000005904 ATF1 YOR377W taxon:4932
+S000005904 ATF1 YOR377W taxon:4932
+S000005904 ATF1 YOR377W taxon:4932
+S000005904 ATF1 YOR377W taxon:4932
+S000005904 ATF1 YOR377W taxon:4932
+S000003409 ATF2 YGR177C taxon:4932
+S000003409 ATF2 YGR177C taxon:4932
+S000003409 ATF2 YGR177C taxon:4932
+S000003409 ATF2 YGR177C taxon:4932
+S000003148 ATG1 YGL180W|APG1|AUT3|CVT10 taxon:4932
+S000003148 ATG1 YGL180W|APG1|AUT3|CVT10 taxon:4932
+S000003148 ATG1 YGL180W|APG1|AUT3|CVT10 taxon:4932
+S000003148 ATG1 YGL180W|APG1|AUT3|CVT10 taxon:4932
+S000003148 ATG1 YGL180W|APG1|AUT3|CVT10 taxon:4932
+S000003965 ATG10 YLL042C|APG10 taxon:4932
+S000003965 ATG10 YLL042C|APG10 taxon:4932
+S000003965 ATG10 YLL042C|APG10 taxon:4932
+S000003965 ATG10 YLL042C|APG10 taxon:4932
+S000003965 ATG10 YLL042C|APG10 taxon:4932
+S000003965 ATG10 YLL042C|APG10 taxon:4932
+S000003965 ATG10 YLL042C|APG10 taxon:4932
+S000003965 ATG10 YLL042C|APG10 taxon:4932
+S000003965 ATG10 YLL042C|APG10 taxon:4932
+S000006253 ATG11 YPR049C|CVT9 taxon:4932
+S000006253 ATG11 YPR049C|CVT9 taxon:4932
+S000006253 ATG11 YPR049C|CVT9 taxon:4932
+S000006253 ATG11 YPR049C|CVT9 taxon:4932
+S000006253 ATG11 YPR049C|CVT9 taxon:4932
+S000000421 ATG12 YBR217W|APG12 taxon:4932
+S000000421 ATG12 YBR217W|APG12 taxon:4932
+S000000421 ATG12 YBR217W|APG12 taxon:4932
+S000000421 ATG12 YBR217W|APG12 taxon:4932
+S000000421 ATG12 YBR217W|APG12 taxon:4932
+S000000421 ATG12 YBR217W|APG12 taxon:4932
+S000006389 ATG13 YPR185W|APG13 taxon:4932
+S000006389 ATG13 YPR185W|APG13 taxon:4932
+S000006389 ATG13 YPR185W|APG13 taxon:4932
+S000006389 ATG13 YPR185W|APG13 taxon:4932
+S000000332 ATG14 YBR128C|APG14|CVT12 taxon:4932
+S000000332 ATG14 YBR128C|APG14|CVT12 taxon:4932
+S000000332 ATG14 YBR128C|APG14|CVT12 taxon:4932
+S000000332 ATG14 YBR128C|APG14|CVT12 taxon:4932
+S000000664 ATG15 YCR068W|AUT5|CVT17 taxon:4932
+S000000664 ATG15 YCR068W|AUT5|CVT17 taxon:4932
+S000000664 ATG15 YCR068W|AUT5|CVT17 taxon:4932
+S000000664 ATG15 YCR068W|AUT5|CVT17 taxon:4932
+S000000664 ATG15 YCR068W|AUT5|CVT17 taxon:4932
+S000000664 ATG15 YCR068W|AUT5|CVT17 taxon:4932
+S000000664 ATG15 YCR068W|AUT5|CVT17 taxon:4932
+S000000664 ATG15 YCR068W|AUT5|CVT17 taxon:4932
+S000000664 ATG15 YCR068W|AUT5|CVT17 taxon:4932
+S000000664 ATG15 YCR068W|AUT5|CVT17 taxon:4932
+S000000664 ATG15 YCR068W|AUT5|CVT17 taxon:4932
+S000000664 ATG15 YCR068W|AUT5|CVT17 taxon:4932
+S000000664 ATG15 YCR068W|AUT5|CVT17 taxon:4932
+S000004769 ATG16 YMR159C|APG15|APG16|CVT11|SAP18 taxon:4932
+S000004769 ATG16 YMR159C|APG15|APG16|CVT11|SAP18 taxon:4932
+S000004769 ATG16 YMR159C|APG15|APG16|CVT11|SAP18 taxon:4932
+S000004769 ATG16 YMR159C|APG15|APG16|CVT11|SAP18 taxon:4932
+S000004415 ATG17 YLR423C|APG17 taxon:4932
+S000004415 ATG17 YLR423C|APG17 taxon:4932
+S000004415 ATG17 YLR423C|APG17 taxon:4932
+S000001917 ATG18 YFR021W|AUT10|CVT18|NMR1|SVP1 taxon:4932
+S000001917 ATG18 YFR021W|AUT10|CVT18|NMR1|SVP1 taxon:4932
+S000001917 ATG18 YFR021W|AUT10|CVT18|NMR1|SVP1 taxon:4932
+S000001917 ATG18 YFR021W|AUT10|CVT18|NMR1|SVP1 taxon:4932
+S000001917 ATG18 YFR021W|AUT10|CVT18|NMR1|SVP1 taxon:4932
+S000001917 ATG18 YFR021W|AUT10|CVT18|NMR1|SVP1 taxon:4932
+S000001917 ATG18 YFR021W|AUT10|CVT18|NMR1|SVP1 taxon:4932
+S000001917 ATG18 YFR021W|AUT10|CVT18|NMR1|SVP1 taxon:4932
+S000001917 ATG18 YFR021W|AUT10|CVT18|NMR1|SVP1 taxon:4932
+S000001917 ATG18 YFR021W|AUT10|CVT18|NMR1|SVP1 taxon:4932
+S000001917 ATG18 YFR021W|AUT10|CVT18|NMR1|SVP1 taxon:4932
+S000001917 ATG18 YFR021W|AUT10|CVT18|NMR1|SVP1 taxon:4932
+S000005442 ATG19 YOL082W|CVT19 taxon:4932
+S000005442 ATG19 YOL082W|CVT19 taxon:4932
+S000005442 ATG19 YOL082W|CVT19 taxon:4932
+S000005442 ATG19 YOL082W|CVT19 taxon:4932
+S000005442 ATG19 YOL082W|CVT19 taxon:4932
+S000005442 ATG19 YOL082W|CVT19 taxon:4932
+S000005186 ATG2 YNL242W|APG2|AUT8|SPO72 taxon:4932
+S000005186 ATG2 YNL242W|APG2|AUT8|SPO72 taxon:4932
+S000005186 ATG2 YNL242W|APG2|AUT8|SPO72 taxon:4932
+S000005186 ATG2 YNL242W|APG2|AUT8|SPO72 taxon:4932
+S000005186 ATG2 YNL242W|APG2|AUT8|SPO72 taxon:4932
+S000005186 ATG2 YNL242W|APG2|AUT8|SPO72 taxon:4932
+S000005186 ATG2 YNL242W|APG2|AUT8|SPO72 taxon:4932
+S000005186 ATG2 YNL242W|APG2|AUT8|SPO72 taxon:4932
+S000005186 ATG2 YNL242W|APG2|AUT8|SPO72 taxon:4932
+S000005186 ATG2 YNL242W|APG2|AUT8|SPO72 taxon:4932
+S000002271 ATG20 YDL113C|CVT20|SNX42 taxon:4932
+S000002271 ATG20 YDL113C|CVT20|SNX42 taxon:4932
+S000002271 ATG20 YDL113C|CVT20|SNX42 taxon:4932
+S000002271 ATG20 YDL113C|CVT20|SNX42 taxon:4932
+S000002271 ATG20 YDL113C|CVT20|SNX42 taxon:4932
+S000002271 ATG20 YDL113C|CVT20|SNX42 taxon:4932
+S000006021 ATG21 YPL100W|HSV1|MAI1 taxon:4932
+S000006021 ATG21 YPL100W|HSV1|MAI1 taxon:4932
+S000006021 ATG21 YPL100W|HSV1|MAI1 taxon:4932
+S000006021 ATG21 YPL100W|HSV1|MAI1 taxon:4932
+S000006021 ATG21 YPL100W|HSV1|MAI1 taxon:4932
+S000006021 ATG21 YPL100W|HSV1|MAI1 taxon:4932
+S000006021 ATG21 YPL100W|HSV1|MAI1 taxon:4932
+S000000543 ATG22 YCL038C|AUT4 taxon:4932
+S000000543 ATG22 YCL038C|AUT4 taxon:4932
+S000000543 ATG22 YCL038C|AUT4 taxon:4932
+S000000543 ATG22 YCL038C|AUT4 taxon:4932
+S000000543 ATG22 YCL038C|AUT4 taxon:4932
+S000000543 ATG22 YCL038C|AUT4 taxon:4932
+S000000543 ATG22 YCL038C|AUT4 taxon:4932
+S000004423 ATG23 YLR431C|CVT23 taxon:4932
+S000004423 ATG23 YLR431C|CVT23 taxon:4932
+S000004423 ATG23 YLR431C|CVT23 taxon:4932
+S000004423 ATG23 YLR431C|CVT23 taxon:4932
+S000004179 ATG26 YLR189C|UGT51 taxon:4932
+S000004179 ATG26 YLR189C|UGT51 taxon:4932
+S000004179 ATG26 YLR189C|UGT51 taxon:4932
+S000003714 ATG27 YJL178C|ETF1 taxon:4932
+S000003714 ATG27 YJL178C|ETF1 taxon:4932
+S000003714 ATG27 YJL178C|ETF1 taxon:4932
+S000003714 ATG27 YJL178C|ETF1 taxon:4932
+S000006087 ATG29 YPL166W taxon:4932
+S000006087 ATG29 YPL166W taxon:4932
+S000006087 ATG29 YPL166W taxon:4932
+S000005290 ATG3 YNR007C|APG3|AUT1 taxon:4932
+S000005290 ATG3 YNR007C|APG3|AUT1 taxon:4932
+S000005290 ATG3 YNR007C|APG3|AUT1 taxon:4932
+S000005290 ATG3 YNR007C|APG3|AUT1 taxon:4932
+S000005290 ATG3 YNR007C|APG3|AUT1 taxon:4932
+S000005290 ATG3 YNR007C|APG3|AUT1 taxon:4932
+S000005290 ATG3 YNR007C|APG3|AUT1 taxon:4932
+S000005290 ATG3 YNR007C|APG3|AUT1 taxon:4932
+S000005290 ATG3 YNR007C|APG3|AUT1 taxon:4932
+S000005290 ATG3 YNR007C|APG3|AUT1 taxon:4932
+S000005167 ATG4 YNL223W|APG4|AUT2 taxon:4932
+S000005167 ATG4 YNL223W|APG4|AUT2 taxon:4932
+S000005167 ATG4 YNL223W|APG4|AUT2 taxon:4932
+S000005167 ATG4 YNL223W|APG4|AUT2 taxon:4932
+S000005167 ATG4 YNL223W|APG4|AUT2 taxon:4932
+S000005167 ATG4 YNL223W|APG4|AUT2 taxon:4932
+S000005167 ATG4 YNL223W|APG4|AUT2 taxon:4932
+S000005167 ATG4 YNL223W|APG4|AUT2 taxon:4932
+S000006070 ATG5 YPL149W|APG5 taxon:4932
+S000006070 ATG5 YPL149W|APG5 taxon:4932
+S000006070 ATG5 YPL149W|APG5 taxon:4932
+S000006070 ATG5 YPL149W|APG5 taxon:4932
+S000006070 ATG5 YPL149W|APG5 taxon:4932
+S000001214 ATG7 YHR171W|APG7|CVT2 taxon:4932
+S000001214 ATG7 YHR171W|APG7|CVT2 taxon:4932
+S000001214 ATG7 YHR171W|APG7|CVT2 taxon:4932
+S000001214 ATG7 YHR171W|APG7|CVT2 taxon:4932
+S000001214 ATG7 YHR171W|APG7|CVT2 taxon:4932
+S000001214 ATG7 YHR171W|APG7|CVT2 taxon:4932
+S000001214 ATG7 YHR171W|APG7|CVT2 taxon:4932
+S000001214 ATG7 YHR171W|APG7|CVT2 taxon:4932
+S000001214 ATG7 YHR171W|APG7|CVT2 taxon:4932
+S000001214 ATG7 YHR171W|APG7|CVT2 taxon:4932
+S000001214 ATG7 YHR171W|APG7|CVT2 taxon:4932
+S000001214 ATG7 YHR171W|APG7|CVT2 taxon:4932
+S000001214 ATG7 YHR171W|APG7|CVT2 taxon:4932
+S000001214 ATG7 YHR171W|APG7|CVT2 taxon:4932
+S000001214 ATG7 YHR171W|APG7|CVT2 taxon:4932
+S000001214 ATG7 YHR171W|APG7|CVT2 taxon:4932
+S000001214 ATG7 YHR171W|APG7|CVT2 taxon:4932
+S000001214 ATG7 YHR171W|APG7|CVT2 taxon:4932
+S000001214 ATG7 YHR171W|APG7|CVT2 taxon:4932
+S000001214 ATG7 YHR171W|APG7|CVT2 taxon:4932
+S000001214 ATG7 YHR171W|APG7|CVT2 taxon:4932
+S000001214 ATG7 YHR171W|APG7|CVT2 taxon:4932
+S000000174 ATG8 YBL078C|APG8|AUT7|CVT5 taxon:4932
+S000000174 ATG8 YBL078C|APG8|AUT7|CVT5 taxon:4932
+S000000174 ATG8 YBL078C|APG8|AUT7|CVT5 taxon:4932
+S000000174 ATG8 YBL078C|APG8|AUT7|CVT5 taxon:4932
+S000000174 ATG8 YBL078C|APG8|AUT7|CVT5 taxon:4932
+S000000174 ATG8 YBL078C|APG8|AUT7|CVT5 taxon:4932
+S000000174 ATG8 YBL078C|APG8|AUT7|CVT5 taxon:4932
+S000000174 ATG8 YBL078C|APG8|AUT7|CVT5 taxon:4932
+S000000174 ATG8 YBL078C|APG8|AUT7|CVT5 taxon:4932
+S000000174 ATG8 YBL078C|APG8|AUT7|CVT5 taxon:4932
+S000002308 ATG9 YDL149W|APG9|AUT9|CVT7 taxon:4932
+S000002308 ATG9 YDL149W|APG9|AUT9|CVT7 taxon:4932
+S000002308 ATG9 YDL149W|APG9|AUT9|CVT7 taxon:4932
+S000002308 ATG9 YDL149W|APG9|AUT9|CVT7 taxon:4932
+S000002308 ATG9 YDL149W|APG9|AUT9|CVT7 taxon:4932
+S000002308 ATG9 YDL149W|APG9|AUT9|CVT7 taxon:4932
+S000002308 ATG9 YDL149W|APG9|AUT9|CVT7 taxon:4932
+S000002308 ATG9 YDL149W|APG9|AUT9|CVT7 taxon:4932
+S000006230 ATH1 YPR026W taxon:4932
+S000006230 ATH1 YPR026W taxon:4932
+S000006230 ATH1 YPR026W taxon:4932
+S000006230 ATH1 YPR026W taxon:4932
+S000006230 ATH1 YPR026W taxon:4932
+S000006230 ATH1 YPR026W taxon:4932
+S000006230 ATH1 YPR026W taxon:4932
+S000006230 ATH1 YPR026W taxon:4932
+S000006230 ATH1 YPR026W taxon:4932
+S000004916 ATM1 YMR301C taxon:4932
+S000004916 ATM1 YMR301C taxon:4932
+S000004916 ATM1 YMR301C taxon:4932
+S000004916 ATM1 YMR301C taxon:4932
+S000005285 ATO2 YNR002C|FUN34 taxon:4932
+S000005285 ATO2 YNR002C|FUN34 taxon:4932
+S000005285 ATO2 YNR002C|FUN34 taxon:4932
+S000005285 ATO2 YNR002C|FUN34 taxon:4932
+S000005285 ATO2 YNR002C|FUN34 taxon:4932
+S000005285 ATO2 YNR002C|FUN34 taxon:4932
+S000005285 ATO2 YNR002C|FUN34 taxon:4932
+S000005285 ATO2 YNR002C|FUN34 taxon:4932
+S000005285 ATO2 YNR002C|FUN34 taxon:4932
+S000005285 ATO2 YNR002C|FUN34 taxon:4932
+S000005285 ATO2 YNR002C|FUN34 taxon:4932
+S000002792 ATO3 YDR384C taxon:4932
+S000002792 ATO3 YDR384C taxon:4932
+S000002792 ATO3 YDR384C taxon:4932
+S000002792 ATO3 YDR384C taxon:4932
+S000002792 ATO3 YDR384C taxon:4932
+S000002792 ATO3 YDR384C taxon:4932
+S000002792 ATO3 YDR384C taxon:4932
+S000002792 ATO3 YDR384C taxon:4932
+S000002792 ATO3 YDR384C taxon:4932
+S000000195 ATP1 YBL099W taxon:4932
+S000000195 ATP1 YBL099W taxon:4932
+S000000195 ATP1 YBL099W taxon:4932
+S000000195 ATP1 YBL099W taxon:4932
+S000000195 ATP1 YBL099W taxon:4932
+S000000195 ATP1 YBL099W taxon:4932
+S000000195 ATP1 YBL099W taxon:4932
+S000004385 ATP10 YLR393W taxon:4932
+S000004385 ATP10 YLR393W taxon:4932
+S000004385 ATP10 YLR393W taxon:4932
+S000005259 ATP11 YNL315C taxon:4932
+S000005259 ATP11 YNL315C taxon:4932
+S000005259 ATP11 YNL315C taxon:4932
+S000005259 ATP11 YNL315C taxon:4932
+S000005259 ATP11 YNL315C taxon:4932
+S000003716 ATP12 YJL180C taxon:4932
+S000003716 ATP12 YJL180C taxon:4932
+S000003716 ATP12 YJL180C taxon:4932
+S000003716 ATP12 YJL180C taxon:4932
+S000004286 ATP14 YLR295C taxon:4932
+S000004286 ATP14 YLR295C taxon:4932
+S000004286 ATP14 YLR295C taxon:4932
+S000004286 ATP14 YLR295C taxon:4932
+S000004286 ATP14 YLR295C taxon:4932
+S000004286 ATP14 YLR295C taxon:4932
+S000006192 ATP15 YPL271W|ATPEPSILON taxon:4932
+S000006192 ATP15 YPL271W|ATPEPSILON taxon:4932
+S000006192 ATP15 YPL271W|ATPEPSILON taxon:4932
+S000006192 ATP15 YPL271W|ATPEPSILON taxon:4932
+S000006192 ATP15 YPL271W|ATPEPSILON taxon:4932
+S000006192 ATP15 YPL271W|ATPEPSILON taxon:4932
+S000006192 ATP15 YPL271W|ATPEPSILON taxon:4932
+S000006192 ATP15 YPL271W|ATPEPSILON taxon:4932
+S000006192 ATP15 YPL271W|ATPEPSILON taxon:4932
+S000002162 ATP16 YDL004W taxon:4932
+S000002162 ATP16 YDL004W taxon:4932
+S000002162 ATP16 YDL004W taxon:4932
+S000002162 ATP16 YDL004W taxon:4932
+S000002162 ATP16 YDL004W taxon:4932
+S000002162 ATP16 YDL004W taxon:4932
+S000002162 ATP16 YDL004W taxon:4932
+S000002162 ATP16 YDL004W taxon:4932
+S000002162 ATP16 YDL004W taxon:4932
+S000002785 ATP17 YDR377W taxon:4932
+S000002785 ATP17 YDR377W taxon:4932
+S000002785 ATP17 YDR377W taxon:4932
+S000002785 ATP17 YDR377W taxon:4932
+S000002785 ATP17 YDR377W taxon:4932
+S000002785 ATP17 YDR377W taxon:4932
+S000007247 ATP18 YML081C-A taxon:4932
+S000007247 ATP18 YML081C-A taxon:4932
+S000007247 ATP18 YML081C-A taxon:4932
+S000007247 ATP18 YML081C-A taxon:4932
+S000007247 ATP18 YML081C-A taxon:4932
+S000007247 ATP18 YML081C-A taxon:4932
+S000007247 ATP18 YML081C-A taxon:4932
+S000007247 ATP18 YML081C-A taxon:4932
+S000007339 ATP19 YOL077W-A taxon:4932
+S000007339 ATP19 YOL077W-A taxon:4932
+S000007339 ATP19 YOL077W-A taxon:4932
+S000007339 ATP19 YOL077W-A taxon:4932
+S000007339 ATP19 YOL077W-A taxon:4932
+S000003882 ATP2 YJR121W taxon:4932
+S000003882 ATP2 YJR121W taxon:4932
+S000003882 ATP2 YJR121W taxon:4932
+S000003882 ATP2 YJR121W taxon:4932
+S000003882 ATP2 YJR121W taxon:4932
+S000003882 ATP2 YJR121W taxon:4932
+S000003882 ATP2 YJR121W taxon:4932
+S000006224 ATP20 YPR020W taxon:4932
+S000006224 ATP20 YPR020W taxon:4932
+S000006224 ATP20 YPR020W taxon:4932
+S000006224 ATP20 YPR020W taxon:4932
+S000006224 ATP20 YPR020W taxon:4932
+S000006224 ATP20 YPR020W taxon:4932
+S000006224 ATP20 YPR020W taxon:4932
+S000006224 ATP20 YPR020W taxon:4932
+S000006224 ATP20 YPR020W taxon:4932
+S000000243 ATP3 YBR039W taxon:4932
+S000000243 ATP3 YBR039W taxon:4932
+S000000243 ATP3 YBR039W taxon:4932
+S000000243 ATP3 YBR039W taxon:4932
+S000005999 ATP4 YPL078C|LPF7 taxon:4932
+S000005999 ATP4 YPL078C|LPF7 taxon:4932
+S000005999 ATP4 YPL078C|LPF7 taxon:4932
+S000005999 ATP4 YPL078C|LPF7 taxon:4932
+S000005999 ATP4 YPL078C|LPF7 taxon:4932
+S000005999 ATP4 YPL078C|LPF7 taxon:4932
+S000005999 ATP4 YPL078C|LPF7 taxon:4932
+S000002706 ATP5 YDR298C|OSC1 taxon:4932
+S000002706 ATP5 YDR298C|OSC1 taxon:4932
+S000002706 ATP5 YDR298C|OSC1 taxon:4932
+S000002706 ATP5 YDR298C|OSC1 taxon:4932
+S000002706 ATP5 YDR298C|OSC1 taxon:4932
+S000002706 ATP5 YDR298C|OSC1 taxon:4932
+S000002706 ATP5 YDR298C|OSC1 taxon:4932
+S000002706 ATP5 YDR298C|OSC1 taxon:4932
+S000007268 ATP6 Q0085|OLI2|OLI4|PHO1 taxon:4932
+S000007268 ATP6 Q0085|OLI2|OLI4|PHO1 taxon:4932
+S000007268 ATP6 Q0085|OLI2|OLI4|PHO1 taxon:4932
+S000007268 ATP6 Q0085|OLI2|OLI4|PHO1 taxon:4932
+S000007268 ATP6 Q0085|OLI2|OLI4|PHO1 taxon:4932
+S000001499 ATP7 YKL016C taxon:4932
+S000001499 ATP7 YKL016C taxon:4932
+S000001499 ATP7 YKL016C taxon:4932
+S000001499 ATP7 YKL016C taxon:4932
+S000001499 ATP7 YKL016C taxon:4932
+S000001499 ATP7 YKL016C taxon:4932
+S000001499 ATP7 YKL016C taxon:4932
+S000001499 ATP7 YKL016C taxon:4932
+S000001499 ATP7 YKL016C taxon:4932
+S000001499 ATP7 YKL016C taxon:4932
+S000007267 ATP8 Q0080|AAP1 taxon:4932
+S000007267 ATP8 Q0080|AAP1 taxon:4932
+S000007267 ATP8 Q0080|AAP1 taxon:4932
+S000004584 ATR1 YML116W|SNQ1 taxon:4932
+S000004584 ATR1 YML116W|SNQ1 taxon:4932
+S000004584 ATR1 YML116W|SNQ1 taxon:4932
+S000004584 ATR1 YML116W|SNQ1 taxon:4932
+S000000018 ATS1 YAL020C|FUN28|KTI13 taxon:4932
+S000000018 ATS1 YAL020C|FUN28|KTI13 taxon:4932
+S000000018 ATS1 YAL020C|FUN28|KTI13 taxon:4932
+S000000018 ATS1 YAL020C|FUN28|KTI13 taxon:4932
+S000000018 ATS1 YAL020C|FUN28|KTI13 taxon:4932
+S000000018 ATS1 YAL020C|FUN28|KTI13 taxon:4932
+S000000018 ATS1 YAL020C|FUN28|KTI13 taxon:4932
+S000000018 ATS1 YAL020C|FUN28|KTI13 taxon:4932
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+S000000019 CCR4 YAL021C|FUN27|NUT21 taxon:4932
+S000000019 CCR4 YAL021C|FUN27|NUT21 taxon:4932
+S000000019 CCR4 YAL021C|FUN27|NUT21 taxon:4932
+S000000019 CCR4 YAL021C|FUN27|NUT21 taxon:4932
+S000000019 CCR4 YAL021C|FUN27|NUT21 taxon:4932
+S000000019 CCR4 YAL021C|FUN27|NUT21 taxon:4932
+S000000019 CCR4 YAL021C|FUN27|NUT21 taxon:4932
+S000000019 CCR4 YAL021C|FUN27|NUT21 taxon:4932
+S000000019 CCR4 YAL021C|FUN27|NUT21 taxon:4932
+S000000019 CCR4 YAL021C|FUN27|NUT21 taxon:4932
+S000000019 CCR4 YAL021C|FUN27|NUT21 taxon:4932
+S000004641 CCS1 YMR038C|CCS|LYS7 taxon:4932
+S000004641 CCS1 YMR038C|CCS|LYS7 taxon:4932
+S000004641 CCS1 YMR038C|CCS|LYS7 taxon:4932
+S000004641 CCS1 YMR038C|CCS|LYS7 taxon:4932
+S000004641 CCS1 YMR038C|CCS|LYS7 taxon:4932
+S000004641 CCS1 YMR038C|CCS|LYS7 taxon:4932
+S000004641 CCS1 YMR038C|CCS|LYS7 taxon:4932
+S000001404 CCT2 YIL142W|BIN3|TCP2 taxon:4932
+S000001404 CCT2 YIL142W|BIN3|TCP2 taxon:4932
+S000001404 CCT2 YIL142W|BIN3|TCP2 taxon:4932
+S000001404 CCT2 YIL142W|BIN3|TCP2 taxon:4932
+S000001404 CCT2 YIL142W|BIN3|TCP2 taxon:4932
+S000001404 CCT2 YIL142W|BIN3|TCP2 taxon:4932
+S000001404 CCT2 YIL142W|BIN3|TCP2 taxon:4932
+S000001404 CCT2 YIL142W|BIN3|TCP2 taxon:4932
+S000003551 CCT3 YJL014W|BIN2|TCP3 taxon:4932
+S000003551 CCT3 YJL014W|BIN2|TCP3 taxon:4932
+S000003551 CCT3 YJL014W|BIN2|TCP3 taxon:4932
+S000003551 CCT3 YJL014W|BIN2|TCP3 taxon:4932
+S000003551 CCT3 YJL014W|BIN2|TCP3 taxon:4932
+S000003551 CCT3 YJL014W|BIN2|TCP3 taxon:4932
+S000003551 CCT3 YJL014W|BIN2|TCP3 taxon:4932
+S000002302 CCT4 YDL143W|TCP4 taxon:4932
+S000002302 CCT4 YDL143W|TCP4 taxon:4932
+S000002302 CCT4 YDL143W|TCP4 taxon:4932
+S000002302 CCT4 YDL143W|TCP4 taxon:4932
+S000002302 CCT4 YDL143W|TCP4 taxon:4932
+S000002302 CCT4 YDL143W|TCP4 taxon:4932
+S000002302 CCT4 YDL143W|TCP4 taxon:4932
+S000002302 CCT4 YDL143W|TCP4 taxon:4932
+S000003825 CCT5 YJR064W|TCP5 taxon:4932
+S000003825 CCT5 YJR064W|TCP5 taxon:4932
+S000003825 CCT5 YJR064W|TCP5 taxon:4932
+S000003825 CCT5 YJR064W|TCP5 taxon:4932
+S000003825 CCT5 YJR064W|TCP5 taxon:4932
+S000003825 CCT5 YJR064W|TCP5 taxon:4932
+S000003825 CCT5 YJR064W|TCP5 taxon:4932
+S000002596 CCT6 YDR188W|HTR3|TCP20|TCP6 taxon:4932
+S000002596 CCT6 YDR188W|HTR3|TCP20|TCP6 taxon:4932
+S000002596 CCT6 YDR188W|HTR3|TCP20|TCP6 taxon:4932
+S000002596 CCT6 YDR188W|HTR3|TCP20|TCP6 taxon:4932
+S000002596 CCT6 YDR188W|HTR3|TCP20|TCP6 taxon:4932
+S000002596 CCT6 YDR188W|HTR3|TCP20|TCP6 taxon:4932
+S000002596 CCT6 YDR188W|HTR3|TCP20|TCP6 taxon:4932
+S000003647 CCT7 YJL111W|TCP7 taxon:4932
+S000003647 CCT7 YJL111W|TCP7 taxon:4932
+S000003647 CCT7 YJL111W|TCP7 taxon:4932
+S000003647 CCT7 YJL111W|TCP7 taxon:4932
+S000003647 CCT7 YJL111W|TCP7 taxon:4932
+S000003647 CCT7 YJL111W|TCP7 taxon:4932
+S000003647 CCT7 YJL111W|TCP7 taxon:4932
+S000003647 CCT7 YJL111W|TCP7 taxon:4932
+S000003545 CCT8 YJL008C taxon:4932
+S000003545 CCT8 YJL008C taxon:4932
+S000003545 CCT8 YJL008C taxon:4932
+S000003545 CCT8 YJL008C taxon:4932
+S000003545 CCT8 YJL008C taxon:4932
+S000003545 CCT8 YJL008C taxon:4932
+S000003545 CCT8 YJL008C taxon:4932
+S000003545 CCT8 YJL008C taxon:4932
+S000029067 CCW1 taxon:4932
+S000029067 CCW1 taxon:4932
+S000029067 CCW1 taxon:4932
+S000029068 CCW10 taxon:4932
+S000029068 CCW10 taxon:4932
+S000029068 CCW10 taxon:4932
+S000004100 CCW12 YLR110C taxon:4932
+S000004100 CCW12 YLR110C taxon:4932
+S000004100 CCW12 YLR110C taxon:4932
+S000004100 CCW12 YLR110C taxon:4932
+S000004100 CCW12 YLR110C taxon:4932
+S000006429 CCW14 YLR390W-A|SSR1|YLR391W|YLR391W-A taxon:4932
+S000006429 CCW14 YLR390W-A|SSR1|YLR391W|YLR391W-A taxon:4932
+S000006429 CCW14 YLR390W-A|SSR1|YLR391W|YLR391W-A taxon:4932
+S000006429 CCW14 YLR390W-A|SSR1|YLR391W|YLR391W-A taxon:4932
+S000006429 CCW14 YLR390W-A|SSR1|YLR391W|YLR391W-A taxon:4932
+S000006429 CCW14 YLR390W-A|SSR1|YLR391W|YLR391W-A taxon:4932
+S000006429 CCW14 YLR390W-A|SSR1|YLR391W|YLR391W-A taxon:4932
+S000006429 CCW14 YLR390W-A|SSR1|YLR391W|YLR391W-A taxon:4932
+S000029069 CCW2 taxon:4932
+S000029069 CCW2 taxon:4932
+S000029069 CCW2 taxon:4932
+S000029070 CCW3 taxon:4932
+S000029070 CCW3 taxon:4932
+S000029070 CCW3 taxon:4932
+S000029071 CCW4 taxon:4932
+S000029071 CCW4 taxon:4932
+S000029071 CCW4 taxon:4932
+S000029073 CCW9 taxon:4932
+S000029073 CCW9 taxon:4932
+S000029073 CCW9 taxon:4932
+S000000335 CCZ1 YBR131W|CVT16 taxon:4932
+S000000335 CCZ1 YBR131W|CVT16 taxon:4932
+S000000335 CCZ1 YBR131W|CVT16 taxon:4932
+S000000335 CCZ1 YBR131W|CVT16 taxon:4932
+S000000335 CCZ1 YBR131W|CVT16 taxon:4932
+S000000335 CCZ1 YBR131W|CVT16 taxon:4932
+S000000335 CCZ1 YBR131W|CVT16 taxon:4932
+S000000335 CCZ1 YBR131W|CVT16 taxon:4932
+S000000335 CCZ1 YBR131W|CVT16 taxon:4932
+S000000335 CCZ1 YBR131W|CVT16 taxon:4932
+S000004298 CDA1 YLR307W taxon:4932
+S000004298 CDA1 YLR307W taxon:4932
+S000004298 CDA1 YLR307W taxon:4932
+S000004298 CDA1 YLR307W taxon:4932
+S000004298 CDA1 YLR307W taxon:4932
+S000004299 CDA2 YLR308W taxon:4932
+S000004299 CDA2 YLR308W taxon:4932
+S000004299 CDA2 YLR308W taxon:4932
+S000004299 CDA2 YLR308W taxon:4932
+S000004299 CDA2 YLR308W taxon:4932
+S000002590 CDC1 YDR182W|DSC1|DSR1|ESP2 taxon:4932
+S000002590 CDC1 YDR182W|DSC1|DSR1|ESP2 taxon:4932
+S000002590 CDC1 YDR182W|DSC1|DSR1|ESP2 taxon:4932
+S000002590 CDC1 YDR182W|DSC1|DSR1|ESP2 taxon:4932
+S000002590 CDC1 YDR182W|DSC1|DSR1|ESP2 taxon:4932
+S000002590 CDC1 YDR182W|DSC1|DSR1|ESP2 taxon:4932
+S000002590 CDC1 YDR182W|DSC1|DSR1|ESP2 taxon:4932
+S000000595 CDC10 YCR002C taxon:4932
+S000000595 CDC10 YCR002C taxon:4932
+S000000595 CDC10 YCR002C taxon:4932
+S000000595 CDC10 YCR002C taxon:4932
+S000000595 CDC10 YCR002C taxon:4932
+S000000595 CDC10 YCR002C taxon:4932
+S000000595 CDC10 YCR002C taxon:4932
+S000000595 CDC10 YCR002C taxon:4932
+S000000595 CDC10 YCR002C taxon:4932
+S000000595 CDC10 YCR002C taxon:4932
+S000000595 CDC10 YCR002C taxon:4932
+S000000595 CDC10 YCR002C taxon:4932
+S000000595 CDC10 YCR002C taxon:4932
+S000003837 CDC11 YJR076C|PSL9 taxon:4932
+S000003837 CDC11 YJR076C|PSL9 taxon:4932
+S000003837 CDC11 YJR076C|PSL9 taxon:4932
+S000003837 CDC11 YJR076C|PSL9 taxon:4932
+S000003837 CDC11 YJR076C|PSL9 taxon:4932
+S000003837 CDC11 YJR076C|PSL9 taxon:4932
+S000003837 CDC11 YJR076C|PSL9 taxon:4932
+S000003837 CDC11 YJR076C|PSL9 taxon:4932
+S000003837 CDC11 YJR076C|PSL9 taxon:4932
+S000003837 CDC11 YJR076C|PSL9 taxon:4932
+S000003837 CDC11 YJR076C|PSL9 taxon:4932
+S000003837 CDC11 YJR076C|PSL9 taxon:4932
+S000001149 CDC12 YHR107C|CLA10|PSL7 taxon:4932
+S000001149 CDC12 YHR107C|CLA10|PSL7 taxon:4932
+S000001149 CDC12 YHR107C|CLA10|PSL7 taxon:4932
+S000001149 CDC12 YHR107C|CLA10|PSL7 taxon:4932
+S000001149 CDC12 YHR107C|CLA10|PSL7 taxon:4932
+S000001149 CDC12 YHR107C|CLA10|PSL7 taxon:4932
+S000001149 CDC12 YHR107C|CLA10|PSL7 taxon:4932
+S000001149 CDC12 YHR107C|CLA10|PSL7 taxon:4932
+S000001149 CDC12 YHR107C|CLA10|PSL7 taxon:4932
+S000001149 CDC12 YHR107C|CLA10|PSL7 taxon:4932
+S000001149 CDC12 YHR107C|CLA10|PSL7 taxon:4932
+S000001149 CDC12 YHR107C|CLA10|PSL7 taxon:4932
+S000004205 CDC123 YLR215C taxon:4932
+S000004205 CDC123 YLR215C taxon:4932
+S000004205 CDC123 YLR215C taxon:4932
+S000002379 CDC13 YDL220C|EST4 taxon:4932
+S000002379 CDC13 YDL220C|EST4 taxon:4932
+S000002379 CDC13 YDL220C|EST4 taxon:4932
+S000002379 CDC13 YDL220C|EST4 taxon:4932
+S000001924 CDC14 YFR028C|OAF3 taxon:4932
+S000001924 CDC14 YFR028C|OAF3 taxon:4932
+S000001924 CDC14 YFR028C|OAF3 taxon:4932
+S000001924 CDC14 YFR028C|OAF3 taxon:4932
+S000001924 CDC14 YFR028C|OAF3 taxon:4932
+S000001924 CDC14 YFR028C|OAF3 taxon:4932
+S000001924 CDC14 YFR028C|OAF3 taxon:4932
+S000001924 CDC14 YFR028C|OAF3 taxon:4932
+S000000072 CDC15 YAR019C|LYT1 taxon:4932
+S000000072 CDC15 YAR019C|LYT1 taxon:4932
+S000000072 CDC15 YAR019C|LYT1 taxon:4932
+S000000072 CDC15 YAR019C|LYT1 taxon:4932
+S000000072 CDC15 YAR019C|LYT1 taxon:4932
+S000000072 CDC15 YAR019C|LYT1 taxon:4932
+S000001505 CDC16 YKL022C taxon:4932
+S000001505 CDC16 YKL022C taxon:4932
+S000001505 CDC16 YKL022C taxon:4932
+S000001505 CDC16 YKL022C taxon:4932
+S000001505 CDC16 YKL022C taxon:4932
+S000001505 CDC16 YKL022C taxon:4932
+S000001505 CDC16 YKL022C taxon:4932
+S000001505 CDC16 YKL022C taxon:4932
+S000001505 CDC16 YKL022C taxon:4932
+S000001505 CDC16 YKL022C taxon:4932
+S000000036 CDC19 YAL038W|PYK1 taxon:4932
+S000000036 CDC19 YAL038W|PYK1 taxon:4932
+S000000036 CDC19 YAL038W|PYK1 taxon:4932
+S000000036 CDC19 YAL038W|PYK1 taxon:4932
+S000000036 CDC19 YAL038W|PYK1 taxon:4932
+S000002260 CDC2 YDL102W|HPR6|POL3|TEX1 taxon:4932
+S000002260 CDC2 YDL102W|HPR6|POL3|TEX1 taxon:4932
+S000002260 CDC2 YDL102W|HPR6|POL3|TEX1 taxon:4932
+S000002260 CDC2 YDL102W|HPR6|POL3|TEX1 taxon:4932
+S000002260 CDC2 YDL102W|HPR6|POL3|TEX1 taxon:4932
+S000002260 CDC2 YDL102W|HPR6|POL3|TEX1 taxon:4932
+S000002260 CDC2 YDL102W|HPR6|POL3|TEX1 taxon:4932
+S000002260 CDC2 YDL102W|HPR6|POL3|TEX1 taxon:4932
+S000002260 CDC2 YDL102W|HPR6|POL3|TEX1 taxon:4932
+S000002260 CDC2 YDL102W|HPR6|POL3|TEX1 taxon:4932
+S000002260 CDC2 YDL102W|HPR6|POL3|TEX1 taxon:4932
+S000002260 CDC2 YDL102W|HPR6|POL3|TEX1 taxon:4932
+S000002260 CDC2 YDL102W|HPR6|POL3|TEX1 taxon:4932
+S000003084 CDC20 YGL116W|PAC5 taxon:4932
+S000003084 CDC20 YGL116W|PAC5 taxon:4932
+S000003084 CDC20 YGL116W|PAC5 taxon:4932
+S000003084 CDC20 YGL116W|PAC5 taxon:4932
+S000003084 CDC20 YGL116W|PAC5 taxon:4932
+S000003084 CDC20 YGL116W|PAC5 taxon:4932
+S000003084 CDC20 YGL116W|PAC5 taxon:4932
+S000003084 CDC20 YGL116W|PAC5 taxon:4932
+S000005600 CDC21 YOR074C|CRT9|TMP1|YOR29-25 taxon:4932
+S000005600 CDC21 YOR074C|CRT9|TMP1|YOR29-25 taxon:4932
+S000005600 CDC21 YOR074C|CRT9|TMP1|YOR29-25 taxon:4932
+S000005600 CDC21 YOR074C|CRT9|TMP1|YOR29-25 taxon:4932
+S000001209 CDC23 YHR166C taxon:4932
+S000001209 CDC23 YHR166C taxon:4932
+S000001209 CDC23 YHR166C taxon:4932
+S000001209 CDC23 YHR166C taxon:4932
+S000001209 CDC23 YHR166C taxon:4932
+S000001209 CDC23 YHR166C taxon:4932
+S000001209 CDC23 YHR166C taxon:4932
+S000001209 CDC23 YHR166C taxon:4932
+S000001209 CDC23 YHR166C taxon:4932
+S000001209 CDC23 YHR166C taxon:4932
+S000000039 CDC24 YAL041W|CLS4 taxon:4932
+S000000039 CDC24 YAL041W|CLS4 taxon:4932
+S000000039 CDC24 YAL041W|CLS4 taxon:4932
+S000000039 CDC24 YAL041W|CLS4 taxon:4932
+S000000039 CDC24 YAL041W|CLS4 taxon:4932
+S000000039 CDC24 YAL041W|CLS4 taxon:4932
+S000000039 CDC24 YAL041W|CLS4 taxon:4932
+S000000039 CDC24 YAL041W|CLS4 taxon:4932
+S000000039 CDC24 YAL041W|CLS4 taxon:4932
+S000000039 CDC24 YAL041W|CLS4 taxon:4932
+S000000039 CDC24 YAL041W|CLS4 taxon:4932
+S000000039 CDC24 YAL041W|CLS4 taxon:4932
+S000000039 CDC24 YAL041W|CLS4 taxon:4932
+S000000039 CDC24 YAL041W|CLS4 taxon:4932
+S000000039 CDC24 YAL041W|CLS4 taxon:4932
+S000000039 CDC24 YAL041W|CLS4 taxon:4932
+S000000039 CDC24 YAL041W|CLS4 taxon:4932
+S000000039 CDC24 YAL041W|CLS4 taxon:4932
+S000000039 CDC24 YAL041W|CLS4 taxon:4932
+S000004301 CDC25 YLR310C|CDC25'|CTN1 taxon:4932
+S000004301 CDC25 YLR310C|CDC25'|CTN1 taxon:4932
+S000004301 CDC25 YLR310C|CDC25'|CTN1 taxon:4932
+S000004301 CDC25 YLR310C|CDC25'|CTN1 taxon:4932
+S000004301 CDC25 YLR310C|CDC25'|CTN1 taxon:4932
+S000004301 CDC25 YLR310C|CDC25'|CTN1 taxon:4932
+S000004301 CDC25 YLR310C|CDC25'|CTN1 taxon:4932
+S000001932 CDC26 YFR036W|HIT3|SCD26 taxon:4932
+S000001932 CDC26 YFR036W|HIT3|SCD26 taxon:4932
+S000001932 CDC26 YFR036W|HIT3|SCD26 taxon:4932
+S000001932 CDC26 YFR036W|HIT3|SCD26 taxon:4932
+S000001932 CDC26 YFR036W|HIT3|SCD26 taxon:4932
+S000001932 CDC26 YFR036W|HIT3|SCD26 taxon:4932
+S000001932 CDC26 YFR036W|HIT3|SCD26 taxon:4932
+S000001932 CDC26 YFR036W|HIT3|SCD26 taxon:4932
+S000001932 CDC26 YFR036W|HIT3|SCD26 taxon:4932
+S000001932 CDC26 YFR036W|HIT3|SCD26 taxon:4932
+S000000180 CDC27 YBL084C|APC3|SNB1 taxon:4932
+S000000180 CDC27 YBL084C|APC3|SNB1 taxon:4932
+S000000180 CDC27 YBL084C|APC3|SNB1 taxon:4932
+S000000180 CDC27 YBL084C|APC3|SNB1 taxon:4932
+S000000180 CDC27 YBL084C|APC3|SNB1 taxon:4932
+S000000180 CDC27 YBL084C|APC3|SNB1 taxon:4932
+S000000180 CDC27 YBL084C|APC3|SNB1 taxon:4932
+S000000180 CDC27 YBL084C|APC3|SNB1 taxon:4932
+S000000180 CDC27 YBL084C|APC3|SNB1 taxon:4932
+S000000180 CDC27 YBL084C|APC3|SNB1 taxon:4932
+S000000364 CDC28 YBR160W|CDK1|HSL5|SRM5 taxon:4932
+S000000364 CDC28 YBR160W|CDK1|HSL5|SRM5 taxon:4932
+S000000364 CDC28 YBR160W|CDK1|HSL5|SRM5 taxon:4932
+S000000364 CDC28 YBR160W|CDK1|HSL5|SRM5 taxon:4932
+S000000364 CDC28 YBR160W|CDK1|HSL5|SRM5 taxon:4932
+S000000364 CDC28 YBR160W|CDK1|HSL5|SRM5 taxon:4932
+S000000364 CDC28 YBR160W|CDK1|HSL5|SRM5 taxon:4932
+S000000364 CDC28 YBR160W|CDK1|HSL5|SRM5 taxon:4932
+S000000364 CDC28 YBR160W|CDK1|HSL5|SRM5 taxon:4932
+S000000364 CDC28 YBR160W|CDK1|HSL5|SRM5 taxon:4932
+S000004306 CDC3 YLR314C taxon:4932
+S000004306 CDC3 YLR314C taxon:4932
+S000004306 CDC3 YLR314C taxon:4932
+S000004306 CDC3 YLR314C taxon:4932
+S000004306 CDC3 YLR314C taxon:4932
+S000004306 CDC3 YLR314C taxon:4932
+S000004306 CDC3 YLR314C taxon:4932
+S000004306 CDC3 YLR314C taxon:4932
+S000004306 CDC3 YLR314C taxon:4932
+S000004306 CDC3 YLR314C taxon:4932
+S000004306 CDC3 YLR314C taxon:4932
+S000005783 CDC31 YOR257W|DSK1 taxon:4932
+S000005783 CDC31 YOR257W|DSK1 taxon:4932
+S000005783 CDC31 YOR257W|DSK1 taxon:4932
+S000005783 CDC31 YOR257W|DSK1 taxon:4932
+S000005783 CDC31 YOR257W|DSK1 taxon:4932
+S000005499 CDC33 YOL139C|TIF45|eIF-4E taxon:4932
+S000005499 CDC33 YOL139C|TIF45|eIF-4E taxon:4932
+S000005499 CDC33 YOL139C|TIF45|eIF-4E taxon:4932
+S000005499 CDC33 YOL139C|TIF45|eIF-4E taxon:4932
+S000005499 CDC33 YOL139C|TIF45|eIF-4E taxon:4932
+S000005499 CDC33 YOL139C|TIF45|eIF-4E taxon:4932
+S000005499 CDC33 YOL139C|TIF45|eIF-4E taxon:4932
+S000005499 CDC33 YOL139C|TIF45|eIF-4E taxon:4932
+S000005499 CDC33 YOL139C|TIF45|eIF-4E taxon:4932
+S000005499 CDC33 YOL139C|TIF45|eIF-4E taxon:4932
+S000005499 CDC33 YOL139C|TIF45|eIF-4E taxon:4932
+S000002461 CDC34 YDR054C|DNA6|UBC3 taxon:4932
+S000002461 CDC34 YDR054C|DNA6|UBC3 taxon:4932
+S000002461 CDC34 YDR054C|DNA6|UBC3 taxon:4932
+S000002461 CDC34 YDR054C|DNA6|UBC3 taxon:4932
+S000002461 CDC34 YDR054C|DNA6|UBC3 taxon:4932
+S000002461 CDC34 YDR054C|DNA6|UBC3 taxon:4932
+S000002461 CDC34 YDR054C|DNA6|UBC3 taxon:4932
+S000002461 CDC34 YDR054C|DNA6|UBC3 taxon:4932
+S000002461 CDC34 YDR054C|DNA6|UBC3 taxon:4932
+S000002461 CDC34 YDR054C|DNA6|UBC3 taxon:4932
+S000002461 CDC34 YDR054C|DNA6|UBC3 taxon:4932
+S000002461 CDC34 YDR054C|DNA6|UBC3 taxon:4932
+S000002461 CDC34 YDR054C|DNA6|UBC3 taxon:4932
+S000002461 CDC34 YDR054C|DNA6|UBC3 taxon:4932
+S000002324 CDC36 YDL165W|DNA19|NOT2 taxon:4932
+S000002324 CDC36 YDL165W|DNA19|NOT2 taxon:4932
+S000002324 CDC36 YDL165W|DNA19|NOT2 taxon:4932
+S000002324 CDC36 YDL165W|DNA19|NOT2 taxon:4932
+S000002324 CDC36 YDL165W|DNA19|NOT2 taxon:4932
+S000002324 CDC36 YDL165W|DNA19|NOT2 taxon:4932
+S000002324 CDC36 YDL165W|DNA19|NOT2 taxon:4932
+S000002324 CDC36 YDL165W|DNA19|NOT2 taxon:4932
+S000002324 CDC36 YDL165W|DNA19|NOT2 taxon:4932
+S000002324 CDC36 YDL165W|DNA19|NOT2 taxon:4932
+S000002324 CDC36 YDL165W|DNA19|NOT2 taxon:4932
+S000002324 CDC36 YDL165W|DNA19|NOT2 taxon:4932
+S000002575 CDC37 YDR168W|SMO1 taxon:4932
+S000002575 CDC37 YDR168W|SMO1 taxon:4932
+S000002575 CDC37 YDR168W|SMO1 taxon:4932
+S000002575 CDC37 YDR168W|SMO1 taxon:4932
+S000002575 CDC37 YDR168W|SMO1 taxon:4932
+S000002575 CDC37 YDR168W|SMO1 taxon:4932
+S000000689 CDC39 YCR093W|NOT1|ROS1|SMD6 taxon:4932
+S000000689 CDC39 YCR093W|NOT1|ROS1|SMD6 taxon:4932
+S000000689 CDC39 YCR093W|NOT1|ROS1|SMD6 taxon:4932
+S000000689 CDC39 YCR093W|NOT1|ROS1|SMD6 taxon:4932
+S000000689 CDC39 YCR093W|NOT1|ROS1|SMD6 taxon:4932
+S000000689 CDC39 YCR093W|NOT1|ROS1|SMD6 taxon:4932
+S000000689 CDC39 YCR093W|NOT1|ROS1|SMD6 taxon:4932
+S000000689 CDC39 YCR093W|NOT1|ROS1|SMD6 taxon:4932
+S000000689 CDC39 YCR093W|NOT1|ROS1|SMD6 taxon:4932
+S000000689 CDC39 YCR093W|NOT1|ROS1|SMD6 taxon:4932
+S000000689 CDC39 YCR093W|NOT1|ROS1|SMD6 taxon:4932
+S000000689 CDC39 YCR093W|NOT1|ROS1|SMD6 taxon:4932
+S000001885 CDC4 YFL009W taxon:4932
+S000001885 CDC4 YFL009W taxon:4932
+S000001885 CDC4 YFL009W taxon:4932
+S000001885 CDC4 YFL009W taxon:4932
+S000001885 CDC4 YFL009W taxon:4932
+S000001885 CDC4 YFL009W taxon:4932
+S000001885 CDC4 YFL009W taxon:4932
+S000001885 CDC4 YFL009W taxon:4932
+S000001885 CDC4 YFL009W taxon:4932
+S000001885 CDC4 YFL009W taxon:4932
+S000002772 CDC40 YDR364C|PRP17|SLT15|SLU4 taxon:4932
+S000002772 CDC40 YDR364C|PRP17|SLT15|SLU4 taxon:4932
+S000002772 CDC40 YDR364C|PRP17|SLT15|SLU4 taxon:4932
+S000002772 CDC40 YDR364C|PRP17|SLT15|SLU4 taxon:4932
+S000002772 CDC40 YDR364C|PRP17|SLT15|SLU4 taxon:4932
+S000002772 CDC40 YDR364C|PRP17|SLT15|SLU4 taxon:4932
+S000002772 CDC40 YDR364C|PRP17|SLT15|SLU4 taxon:4932
+S000002772 CDC40 YDR364C|PRP17|SLT15|SLU4 taxon:4932
+S000002772 CDC40 YDR364C|PRP17|SLT15|SLU4 taxon:4932
+S000002772 CDC40 YDR364C|PRP17|SLT15|SLU4 taxon:4932
+S000004219 CDC42 YLR229C taxon:4932
+S000004219 CDC42 YLR229C taxon:4932
+S000004219 CDC42 YLR229C taxon:4932
+S000004219 CDC42 YLR229C taxon:4932
+S000004219 CDC42 YLR229C taxon:4932
+S000004219 CDC42 YLR229C taxon:4932
+S000004219 CDC42 YLR229C taxon:4932
+S000004219 CDC42 YLR229C taxon:4932
+S000004219 CDC42 YLR229C taxon:4932
+S000004219 CDC42 YLR229C taxon:4932
+S000004219 CDC42 YLR229C taxon:4932
+S000004219 CDC42 YLR229C taxon:4932
+S000004219 CDC42 YLR229C taxon:4932
+S000004219 CDC42 YLR229C taxon:4932
+S000004219 CDC42 YLR229C taxon:4932
+S000004219 CDC42 YLR229C taxon:4932
+S000004219 CDC42 YLR229C taxon:4932
+S000004219 CDC42 YLR229C taxon:4932
+S000003123 CDC43 YGL155W|CAL1 taxon:4932
+S000003123 CDC43 YGL155W|CAL1 taxon:4932
+S000003123 CDC43 YGL155W|CAL1 taxon:4932
+S000003123 CDC43 YGL155W|CAL1 taxon:4932
+S000003123 CDC43 YGL155W|CAL1 taxon:4932
+S000003123 CDC43 YGL155W|CAL1 taxon:4932
+S000003123 CDC43 YGL155W|CAL1 taxon:4932
+S000003123 CDC43 YGL155W|CAL1 taxon:4932
+S000003123 CDC43 YGL155W|CAL1 taxon:4932
+S000003123 CDC43 YGL155W|CAL1 taxon:4932
+S000004093 CDC45 YLR103C|SLD4 taxon:4932
+S000004093 CDC45 YLR103C|SLD4 taxon:4932
+S000004093 CDC45 YLR103C|SLD4 taxon:4932
+S000004093 CDC45 YLR103C|SLD4 taxon:4932
+S000004093 CDC45 YLR103C|SLD4 taxon:4932
+S000004093 CDC45 YLR103C|SLD4 taxon:4932
+S000004264 CDC46 YLR274W|BOB1|MCM5 taxon:4932
+S000004264 CDC46 YLR274W|BOB1|MCM5 taxon:4932
+S000004264 CDC46 YLR274W|BOB1|MCM5 taxon:4932
+S000004264 CDC46 YLR274W|BOB1|MCM5 taxon:4932
+S000004264 CDC46 YLR274W|BOB1|MCM5 taxon:4932
+S000004264 CDC46 YLR274W|BOB1|MCM5 taxon:4932
+S000004264 CDC46 YLR274W|BOB1|MCM5 taxon:4932
+S000004264 CDC46 YLR274W|BOB1|MCM5 taxon:4932
+S000004264 CDC46 YLR274W|BOB1|MCM5 taxon:4932
+S000004264 CDC46 YLR274W|BOB1|MCM5 taxon:4932
+S000000406 CDC47 YBR202W|MCM7 taxon:4932
+S000000406 CDC47 YBR202W|MCM7 taxon:4932
+S000000406 CDC47 YBR202W|MCM7 taxon:4932
+S000000406 CDC47 YBR202W|MCM7 taxon:4932
+S000000406 CDC47 YBR202W|MCM7 taxon:4932
+S000000406 CDC47 YBR202W|MCM7 taxon:4932
+S000000406 CDC47 YBR202W|MCM7 taxon:4932
+S000000406 CDC47 YBR202W|MCM7 taxon:4932
+S000000406 CDC47 YBR202W|MCM7 taxon:4932
+S000000406 CDC47 YBR202W|MCM7 taxon:4932
+S000000406 CDC47 YBR202W|MCM7 taxon:4932
+S000002284 CDC48 YDL126C taxon:4932
+S000002284 CDC48 YDL126C taxon:4932
+S000002284 CDC48 YDL126C taxon:4932
+S000002284 CDC48 YDL126C taxon:4932
+S000002284 CDC48 YDL126C taxon:4932
+S000002284 CDC48 YDL126C taxon:4932
+S000002284 CDC48 YDL126C taxon:4932
+S000002284 CDC48 YDL126C taxon:4932
+S000002284 CDC48 YDL126C taxon:4932
+S000002284 CDC48 YDL126C taxon:4932
+S000002284 CDC48 YDL126C taxon:4932
+S000002284 CDC48 YDL126C taxon:4932
+S000002284 CDC48 YDL126C taxon:4932
+S000002284 CDC48 YDL126C taxon:4932
+S000004603 CDC5 YMR001C|MSD2|PKX2 taxon:4932
+S000004603 CDC5 YMR001C|MSD2|PKX2 taxon:4932
+S000004603 CDC5 YMR001C|MSD2|PKX2 taxon:4932
+S000004603 CDC5 YMR001C|MSD2|PKX2 taxon:4932
+S000004603 CDC5 YMR001C|MSD2|PKX2 taxon:4932
+S000004603 CDC5 YMR001C|MSD2|PKX2 taxon:4932
+S000004603 CDC5 YMR001C|MSD2|PKX2 taxon:4932
+S000004603 CDC5 YMR001C|MSD2|PKX2 taxon:4932
+S000004603 CDC5 YMR001C|MSD2|PKX2 taxon:4932
+S000000690 CDC50 YCR094W taxon:4932
+S000000690 CDC50 YCR094W taxon:4932
+S000000690 CDC50 YCR094W taxon:4932
+S000000690 CDC50 YCR094W taxon:4932
+S000000690 CDC50 YCR094W taxon:4932
+S000000690 CDC50 YCR094W taxon:4932
+S000000690 CDC50 YCR094W taxon:4932
+S000000690 CDC50 YCR094W taxon:4932
+S000000690 CDC50 YCR094W taxon:4932
+S000000690 CDC50 YCR094W taxon:4932
+S000002290 CDC53 YDL132W taxon:4932
+S000002290 CDC53 YDL132W taxon:4932
+S000002290 CDC53 YDL132W taxon:4932
+S000002290 CDC53 YDL132W taxon:4932
+S000002290 CDC53 YDL132W taxon:4932
+S000002290 CDC53 YDL132W taxon:4932
+S000002290 CDC53 YDL132W taxon:4932
+S000002290 CDC53 YDL132W taxon:4932
+S000002290 CDC53 YDL132W taxon:4932
+S000002290 CDC53 YDL132W taxon:4932
+S000002290 CDC53 YDL132W taxon:4932
+S000006223 CDC54 YPR019W|HCD21|MCM4 taxon:4932
+S000006223 CDC54 YPR019W|HCD21|MCM4 taxon:4932
+S000006223 CDC54 YPR019W|HCD21|MCM4 taxon:4932
+S000006223 CDC54 YPR019W|HCD21|MCM4 taxon:4932
+S000006223 CDC54 YPR019W|HCD21|MCM4 taxon:4932
+S000006223 CDC54 YPR019W|HCD21|MCM4 taxon:4932
+S000006223 CDC54 YPR019W|HCD21|MCM4 taxon:4932
+S000006223 CDC54 YPR019W|HCD21|MCM4 taxon:4932
+S000006223 CDC54 YPR019W|HCD21|MCM4 taxon:4932
+S000006223 CDC54 YPR019W|HCD21|MCM4 taxon:4932
+S000003158 CDC55 YGL190C taxon:4932
+S000003158 CDC55 YGL190C taxon:4932
+S000003158 CDC55 YGL190C taxon:4932
+S000003158 CDC55 YGL190C taxon:4932
+S000003158 CDC55 YGL190C taxon:4932
+S000003158 CDC55 YGL190C taxon:4932
+S000003158 CDC55 YGL190C taxon:4932
+S000003158 CDC55 YGL190C taxon:4932
+S000003158 CDC55 YGL190C taxon:4932
+S000003158 CDC55 YGL190C taxon:4932
+S000003158 CDC55 YGL190C taxon:4932
+S000003730 CDC6 YJL194W taxon:4932
+S000003730 CDC6 YJL194W taxon:4932
+S000003730 CDC6 YJL194W taxon:4932
+S000003730 CDC6 YJL194W taxon:4932
+S000003730 CDC6 YJL194W taxon:4932
+S000006081 CDC60 YPL160W|LeuRS taxon:4932
+S000006081 CDC60 YPL160W|LeuRS taxon:4932
+S000006081 CDC60 YPL160W|LeuRS taxon:4932
+S000006690 CDC65 tQ(CUG)M|DNA33|SUP70 taxon:4932
+S000006690 CDC65 tQ(CUG)M|DNA33|SUP70 taxon:4932
+S000006690 CDC65 tQ(CUG)M|DNA33|SUP70 taxon:4932
+S000002175 CDC7 YDL017W|LSD6|SAS1 taxon:4932
+S000002175 CDC7 YDL017W|LSD6|SAS1 taxon:4932
+S000002175 CDC7 YDL017W|LSD6|SAS1 taxon:4932
+S000002175 CDC7 YDL017W|LSD6|SAS1 taxon:4932
+S000002175 CDC7 YDL017W|LSD6|SAS1 taxon:4932
+S000004410 CDC73 YLR418C taxon:4932
+S000004410 CDC73 YLR418C taxon:4932
+S000004410 CDC73 YLR418C taxon:4932
+S000004410 CDC73 YLR418C taxon:4932
+S000004410 CDC73 YLR418C taxon:4932
+S000004410 CDC73 YLR418C taxon:4932
+S000004410 CDC73 YLR418C taxon:4932
+S000004410 CDC73 YLR418C taxon:4932
+S000004410 CDC73 YLR418C taxon:4932
+S000004410 CDC73 YLR418C taxon:4932
+S000003818 CDC8 YJR057W taxon:4932
+S000003818 CDC8 YJR057W taxon:4932
+S000003818 CDC8 YJR057W taxon:4932
+S000003818 CDC8 YJR057W taxon:4932
+S000003818 CDC8 YJR057W taxon:4932
+S000003818 CDC8 YJR057W taxon:4932
+S000003818 CDC8 YJR057W taxon:4932
+S000003818 CDC8 YJR057W taxon:4932
+S000003818 CDC8 YJR057W taxon:4932
+S000003818 CDC8 YJR057W taxon:4932
+S000003818 CDC8 YJR057W taxon:4932
+S000003818 CDC8 YJR057W taxon:4932
+S000003818 CDC8 YJR057W taxon:4932
+S000003818 CDC8 YJR057W taxon:4932
+S000003818 CDC8 YJR057W taxon:4932
+S000002323 CDC9 YDL164C|MMS8 taxon:4932
+S000002323 CDC9 YDL164C|MMS8 taxon:4932
+S000002323 CDC9 YDL164C|MMS8 taxon:4932
+S000002323 CDC9 YDL164C|MMS8 taxon:4932
+S000002323 CDC9 YDL164C|MMS8 taxon:4932
+S000002323 CDC9 YDL164C|MMS8 taxon:4932
+S000002323 CDC9 YDL164C|MMS8 taxon:4932
+S000002323 CDC9 YDL164C|MMS8 taxon:4932
+S000002323 CDC9 YDL164C|MMS8 taxon:4932
+S000002323 CDC9 YDL164C|MMS8 taxon:4932
+S000002323 CDC9 YDL164C|MMS8 taxon:4932
+S000002323 CDC9 YDL164C|MMS8 taxon:4932
+S000002323 CDC9 YDL164C|MMS8 taxon:4932
+S000004235 CDD1 YLR245C taxon:4932
+S000004235 CDD1 YLR245C taxon:4932
+S000004235 CDD1 YLR245C taxon:4932
+S000004235 CDD1 YLR245C taxon:4932
+S000004235 CDD1 YLR245C taxon:4932
+S000004235 CDD1 YLR245C taxon:4932
+S000004235 CDD1 YLR245C taxon:4932
+S000004235 CDD1 YLR245C taxon:4932
+S000002971 CDH1 YGL003C|HCT1 taxon:4932
+S000002971 CDH1 YGL003C|HCT1 taxon:4932
+S000002971 CDH1 YGL003C|HCT1 taxon:4932
+S000002971 CDH1 YGL003C|HCT1 taxon:4932
+S000002971 CDH1 YGL003C|HCT1 taxon:4932
+S000002971 CDH1 YGL003C|HCT1 taxon:4932
+S000002971 CDH1 YGL003C|HCT1 taxon:4932
+S000002971 CDH1 YGL003C|HCT1 taxon:4932
+S000002971 CDH1 YGL003C|HCT1 taxon:4932
+S000002971 CDH1 YGL003C|HCT1 taxon:4932
+S000002971 CDH1 YGL003C|HCT1 taxon:4932
+S000000233 CDS1 YBR029C|CDG1 taxon:4932
+S000000233 CDS1 YBR029C|CDG1 taxon:4932
+S000000233 CDS1 YBR029C|CDG1 taxon:4932
+S000000233 CDS1 YBR029C|CDG1 taxon:4932
+S000000233 CDS1 YBR029C|CDG1 taxon:4932
+S000004826 CEF1 YMR213W|NTC85 taxon:4932
+S000004826 CEF1 YMR213W|NTC85 taxon:4932
+S000004826 CEF1 YMR213W|NTC85 taxon:4932
+S000004826 CEF1 YMR213W|NTC85 taxon:4932
+S000003098 CEG1 YGL130W taxon:4932
+S000003098 CEG1 YGL130W taxon:4932
+S000003098 CEG1 YGL130W taxon:4932
+S000003098 CEG1 YGL130W taxon:4932
+S000003098 CEG1 YGL130W taxon:4932
+S000003098 CEG1 YGL130W taxon:4932
+S000003098 CEG1 YGL130W taxon:4932
+S000000863 CEM1 YER061C taxon:4932
+S000000863 CEM1 YER061C taxon:4932
+S000000863 CEM1 YER061C taxon:4932
+S000004778 CEP3 YMR168C|CBF3|CBF3B|CSL1 taxon:4932
+S000004778 CEP3 YMR168C|CBF3|CBF3B|CSL1 taxon:4932
+S000004778 CEP3 YMR168C|CBF3|CBF3B|CSL1 taxon:4932
+S000004778 CEP3 YMR168C|CBF3|CBF3B|CSL1 taxon:4932
+S000004778 CEP3 YMR168C|CBF3|CBF3B|CSL1 taxon:4932
+S000004778 CEP3 YMR168C|CBF3|CBF3B|CSL1 taxon:4932
+S000006149 CET1 YPL228W|CES5 taxon:4932
+S000006149 CET1 YPL228W|CES5 taxon:4932
+S000006149 CET1 YPL228W|CES5 taxon:4932
+S000001265 CFD1 YIL003W|DRE3 taxon:4932
+S000001265 CFD1 YIL003W|DRE3 taxon:4932
+S000001265 CFD1 YIL003W|DRE3 taxon:4932
+S000002709 CFT1 YDR301W|YHH1 taxon:4932
+S000002709 CFT1 YDR301W|YHH1 taxon:4932
+S000002709 CFT1 YDR301W|YHH1 taxon:4932
+S000002709 CFT1 YDR301W|YHH1 taxon:4932
+S000002709 CFT1 YDR301W|YHH1 taxon:4932
+S000002709 CFT1 YDR301W|YHH1 taxon:4932
+S000002709 CFT1 YDR301W|YHH1 taxon:4932
+S000002709 CFT1 YDR301W|YHH1 taxon:4932
+S000002709 CFT1 YDR301W|YHH1 taxon:4932
+S000002709 CFT1 YDR301W|YHH1 taxon:4932
+S000004105 CFT2 YLR115W|YDH1 taxon:4932
+S000004105 CFT2 YLR115W|YDH1 taxon:4932
+S000004105 CFT2 YLR115W|YDH1 taxon:4932
+S000004105 CFT2 YLR115W|YDH1 taxon:4932
+S000004105 CFT2 YLR115W|YDH1 taxon:4932
+S000004105 CFT2 YLR115W|YDH1 taxon:4932
+S000004105 CFT2 YLR115W|YDH1 taxon:4932
+S000004105 CFT2 YLR115W|YDH1 taxon:4932
+S000004500 CGI121 YML036W taxon:4932
+S000004500 CGI121 YML036W taxon:4932
+S000004500 CGI121 YML036W taxon:4932
+S000002997 CGR1 YGL029W taxon:4932
+S000002997 CGR1 YGL029W taxon:4932
+S000002997 CGR1 YGL029W taxon:4932
+S000002997 CGR1 YGL029W taxon:4932
+S000000569 CHA1 YCL064C taxon:4932
+S000000569 CHA1 YCL064C taxon:4932
+S000000569 CHA1 YCL064C taxon:4932
+S000000569 CHA1 YCL064C taxon:4932
+S000000569 CHA1 YCL064C taxon:4932
+S000000569 CHA1 YCL064C taxon:4932
+S000000569 CHA1 YCL064C taxon:4932
+S000000569 CHA1 YCL064C taxon:4932
+S000004088 CHA4 YLR098C|SIL2|SIL3 taxon:4932
+S000004088 CHA4 YLR098C|SIL2|SIL3 taxon:4932
+S000004088 CHA4 YLR098C|SIL2|SIL3 taxon:4932
+S000004088 CHA4 YLR098C|SIL2|SIL3 taxon:4932
+S000004088 CHA4 YLR098C|SIL2|SIL3 taxon:4932
+S000004088 CHA4 YLR098C|SIL2|SIL3 taxon:4932
+S000004088 CHA4 YLR098C|SIL2|SIL3 taxon:4932
+S000003174 CHC1 YGL206C|SWA5 taxon:4932
+S000003174 CHC1 YGL206C|SWA5 taxon:4932
+S000003174 CHC1 YGL206C|SWA5 taxon:4932
+S000003174 CHC1 YGL206C|SWA5 taxon:4932
+S000000966 CHD1 YER164W taxon:4932
+S000000966 CHD1 YER164W taxon:4932
+S000000966 CHD1 YER164W taxon:4932
+S000000966 CHD1 YER164W taxon:4932
+S000000966 CHD1 YER164W taxon:4932
+S000000966 CHD1 YER164W taxon:4932
+S000000966 CHD1 YER164W taxon:4932
+S000000966 CHD1 YER164W taxon:4932
+S000000478 CHK1 YBR274W taxon:4932
+S000000478 CHK1 YBR274W taxon:4932
+S000000478 CHK1 YBR274W taxon:4932
+S000000478 CHK1 YBR274W taxon:4932
+S000000478 CHK1 YBR274W taxon:4932
+S000000478 CHK1 YBR274W taxon:4932
+S000005929 CHL1 YPL008W|CTF1|LPA9 taxon:4932
+S000005929 CHL1 YPL008W|CTF1|LPA9 taxon:4932
+S000005929 CHL1 YPL008W|CTF1|LPA9 taxon:4932
+S000005929 CHL1 YPL008W|CTF1|LPA9 taxon:4932
+S000005929 CHL1 YPL008W|CTF1|LPA9 taxon:4932
+S000005929 CHL1 YPL008W|CTF1|LPA9 taxon:4932
+S000005929 CHL1 YPL008W|CTF1|LPA9 taxon:4932
+S000005929 CHL1 YPL008W|CTF1|LPA9 taxon:4932
+S000002662 CHL4 YDR254W|CTF17|MCM17 taxon:4932
+S000002662 CHL4 YDR254W|CTF17|MCM17 taxon:4932
+S000002662 CHL4 YDR254W|CTF17|MCM17 taxon:4932
+S000002662 CHL4 YDR254W|CTF17|MCM17 taxon:4932
+S000000828 CHO1 YER026C|PSS1 taxon:4932
+S000000828 CHO1 YER026C|PSS1 taxon:4932
+S000000828 CHO1 YER026C|PSS1 taxon:4932
+S000000828 CHO1 YER026C|PSS1 taxon:4932
+S000000828 CHO1 YER026C|PSS1 taxon:4932
+S000000828 CHO1 YER026C|PSS1 taxon:4932
+S000000828 CHO1 YER026C|PSS1 taxon:4932
+S000003389 CHO2 YGR157W|PEM1 taxon:4932
+S000003389 CHO2 YGR157W|PEM1 taxon:4932
+S000003389 CHO2 YGR157W|PEM1 taxon:4932
+S000003389 CHO2 YGR157W|PEM1 taxon:4932
+S000003389 CHO2 YGR157W|PEM1 taxon:4932
+S000003389 CHO2 YGR157W|PEM1 taxon:4932
+S000003389 CHO2 YGR157W|PEM1 taxon:4932
+S000005136 CHS1 YNL192W|USA4 taxon:4932
+S000005136 CHS1 YNL192W|USA4 taxon:4932
+S000005136 CHS1 YNL192W|USA4 taxon:4932
+S000005136 CHS1 YNL192W|USA4 taxon:4932
+S000005136 CHS1 YNL192W|USA4 taxon:4932
+S000000242 CHS2 YBR038W taxon:4932
+S000000242 CHS2 YBR038W taxon:4932
+S000000242 CHS2 YBR038W taxon:4932
+S000000227 CHS3 YBR023C|CAL1|CSD2|DIT101|KTI2 taxon:4932
+S000000227 CHS3 YBR023C|CAL1|CSD2|DIT101|KTI2 taxon:4932
+S000000227 CHS3 YBR023C|CAL1|CSD2|DIT101|KTI2 taxon:4932
+S000000227 CHS3 YBR023C|CAL1|CSD2|DIT101|KTI2 taxon:4932
+S000000227 CHS3 YBR023C|CAL1|CSD2|DIT101|KTI2 taxon:4932
+S000000227 CHS3 YBR023C|CAL1|CSD2|DIT101|KTI2 taxon:4932
+S000000227 CHS3 YBR023C|CAL1|CSD2|DIT101|KTI2 taxon:4932
+S000000227 CHS3 YBR023C|CAL1|CSD2|DIT101|KTI2 taxon:4932
+S000000227 CHS3 YBR023C|CAL1|CSD2|DIT101|KTI2 taxon:4932
+S000000227 CHS3 YBR023C|CAL1|CSD2|DIT101|KTI2 taxon:4932
+S000000227 CHS3 YBR023C|CAL1|CSD2|DIT101|KTI2 taxon:4932
+S000004322 CHS5 YLR330W|CAL3 taxon:4932
+S000004322 CHS5 YLR330W|CAL3 taxon:4932
+S000004322 CHS5 YLR330W|CAL3 taxon:4932
+S000004322 CHS5 YLR330W|CAL3 taxon:4932
+S000004322 CHS5 YLR330W|CAL3 taxon:4932
+S000004322 CHS5 YLR330W|CAL3 taxon:4932
+S000004322 CHS5 YLR330W|CAL3 taxon:4932
+S000004322 CHS5 YLR330W|CAL3 taxon:4932
+S000004322 CHS5 YLR330W|CAL3 taxon:4932
+S000003635 CHS6 YJL099W|CSD3 taxon:4932
+S000003635 CHS6 YJL099W|CSD3 taxon:4932
+S000003635 CHS6 YJL099W|CSD3 taxon:4932
+S000003635 CHS6 YJL099W|CSD3 taxon:4932
+S000003635 CHS6 YJL099W|CSD3 taxon:4932
+S000003635 CHS6 YJL099W|CSD3 taxon:4932
+S000003635 CHS6 YJL099W|CSD3 taxon:4932
+S000001184 CHS7 YHR142W taxon:4932
+S000001184 CHS7 YHR142W taxon:4932
+S000001184 CHS7 YHR142W taxon:4932
+S000001184 CHS7 YHR142W taxon:4932
+S000001184 CHS7 YHR142W taxon:4932
+S000000832 CHZ1 YER030W taxon:4932
+S000000832 CHZ1 YER030W taxon:4932
+S000000832 CHZ1 YER030W taxon:4932
+S000002675 CIA1 YDR267C taxon:4932
+S000002675 CIA1 YDR267C taxon:4932
+S000002675 CIA1 YDR267C taxon:4932
+S000002675 CIA1 YDR267C taxon:4932
+S000002675 CIA1 YDR267C taxon:4932
+S000001094 CIC1 YHR052W|NSA3 taxon:4932
+S000001094 CIC1 YHR052W|NSA3 taxon:4932
+S000001094 CIC1 YHR052W|NSA3 taxon:4932
+S000001094 CIC1 YHR052W|NSA3 taxon:4932
+S000001094 CIC1 YHR052W|NSA3 taxon:4932
+S000001094 CIC1 YHR052W|NSA3 taxon:4932
+S000001094 CIC1 YHR052W|NSA3 taxon:4932
+S000001094 CIC1 YHR052W|NSA3 taxon:4932
+S000001094 CIC1 YHR052W|NSA3 taxon:4932
+S000004811 CIK1 YMR198W taxon:4932
+S000004811 CIK1 YMR198W taxon:4932
+S000004811 CIK1 YMR198W taxon:4932
+S000004811 CIK1 YMR198W taxon:4932
+S000004811 CIK1 YMR198W taxon:4932
+S000004811 CIK1 YMR198W taxon:4932
+S000004811 CIK1 YMR198W taxon:4932
+S000004811 CIK1 YMR198W taxon:4932
+S000004811 CIK1 YMR198W taxon:4932
+S000004811 CIK1 YMR198W taxon:4932
+S000004811 CIK1 YMR198W taxon:4932
+S000004811 CIK1 YMR198W taxon:4932
+S000005876 CIN1 YOR349W taxon:4932
+S000005876 CIN1 YOR349W taxon:4932
+S000005876 CIN1 YOR349W taxon:4932
+S000005876 CIN1 YOR349W taxon:4932
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+S000006162 CIN2 YPL241C taxon:4932
+S000006162 CIN2 YPL241C taxon:4932
+S000004746 CIN4 YMR138W|GTP1|UGX1 taxon:4932
+S000004746 CIN4 YMR138W|GTP1|UGX1 taxon:4932
+S000004746 CIN4 YMR138W|GTP1|UGX1 taxon:4932
+S000005554 CIN5 YOR028C|HAL6|YAP4 taxon:4932
+S000005554 CIN5 YOR028C|HAL6|YAP4 taxon:4932
+S000005554 CIN5 YOR028C|HAL6|YAP4 taxon:4932
+S000005554 CIN5 YOR028C|HAL6|YAP4 taxon:4932
+S000005554 CIN5 YOR028C|HAL6|YAP4 taxon:4932
+S000005554 CIN5 YOR028C|HAL6|YAP4 taxon:4932
+S000000787 CIN8 YEL061C|KSL2|SDS15 taxon:4932
+S000000787 CIN8 YEL061C|KSL2|SDS15 taxon:4932
+S000000787 CIN8 YEL061C|KSL2|SDS15 taxon:4932
+S000000787 CIN8 YEL061C|KSL2|SDS15 taxon:4932
+S000000787 CIN8 YEL061C|KSL2|SDS15 taxon:4932
+S000000787 CIN8 YEL061C|KSL2|SDS15 taxon:4932
+S000000787 CIN8 YEL061C|KSL2|SDS15 taxon:4932
+S000000787 CIN8 YEL061C|KSL2|SDS15 taxon:4932
+S000000787 CIN8 YEL061C|KSL2|SDS15 taxon:4932
+S000002429 CIS1 YDR022C taxon:4932
+S000002429 CIS1 YDR022C taxon:4932
+S000002429 CIS1 YDR022C taxon:4932
+S000003694 CIS3 YJL158C|CCW11|CCW5|PIR4 taxon:4932
+S000003694 CIS3 YJL158C|CCW11|CCW5|PIR4 taxon:4932
+S000003694 CIS3 YJL158C|CCW11|CCW5|PIR4 taxon:4932
+S000003694 CIS3 YJL158C|CCW11|CCW5|PIR4 taxon:4932
+S000003694 CIS3 YJL158C|CCW11|CCW5|PIR4 taxon:4932
+S000003694 CIS3 YJL158C|CCW11|CCW5|PIR4 taxon:4932
+S000003694 CIS3 YJL158C|CCW11|CCW5|PIR4 taxon:4932
+S000003694 CIS3 YJL158C|CCW11|CCW5|PIR4 taxon:4932
+S000005284 CIT1 YNR001C|CS1|LYS6 taxon:4932
+S000005284 CIT1 YNR001C|CS1|LYS6 taxon:4932
+S000005284 CIT1 YNR001C|CS1|LYS6 taxon:4932
+S000005284 CIT1 YNR001C|CS1|LYS6 taxon:4932
+S000005284 CIT1 YNR001C|CS1|LYS6 taxon:4932
+S000005284 CIT1 YNR001C|CS1|LYS6 taxon:4932
+S000005284 CIT1 YNR001C|CS1|LYS6 taxon:4932
+S000000598 CIT2 YCR005C taxon:4932
+S000000598 CIT2 YCR005C taxon:4932
+S000000598 CIT2 YCR005C taxon:4932
+S000000598 CIT2 YCR005C taxon:4932
+S000000598 CIT2 YCR005C taxon:4932
+S000006205 CIT3 YPR001W taxon:4932
+S000006205 CIT3 YPR001W taxon:4932
+S000006205 CIT3 YPR001W taxon:4932
+S000006205 CIT3 YPR001W taxon:4932
+S000006205 CIT3 YPR001W taxon:4932
+S000006205 CIT3 YPR001W taxon:4932
+S000001297 CKA1 YIL035C taxon:4932
+S000001297 CKA1 YIL035C taxon:4932
+S000001297 CKA1 YIL035C taxon:4932
+S000001297 CKA1 YIL035C taxon:4932
+S000001297 CKA1 YIL035C taxon:4932
+S000001297 CKA1 YIL035C taxon:4932
+S000001297 CKA1 YIL035C taxon:4932
+S000001297 CKA1 YIL035C taxon:4932
+S000001297 CKA1 YIL035C taxon:4932
+S000001297 CKA1 YIL035C taxon:4932
+S000001297 CKA1 YIL035C taxon:4932
+S000005587 CKA2 YOR061W|YOR29-12 taxon:4932
+S000005587 CKA2 YOR061W|YOR29-12 taxon:4932
+S000005587 CKA2 YOR061W|YOR29-12 taxon:4932
+S000005587 CKA2 YOR061W|YOR29-12 taxon:4932
+S000005587 CKA2 YOR061W|YOR29-12 taxon:4932
+S000005587 CKA2 YOR061W|YOR29-12 taxon:4932
+S000005587 CKA2 YOR061W|YOR29-12 taxon:4932
+S000005587 CKA2 YOR061W|YOR29-12 taxon:4932
+S000005587 CKA2 YOR061W|YOR29-12 taxon:4932
+S000005587 CKA2 YOR061W|YOR29-12 taxon:4932
+S000005587 CKA2 YOR061W|YOR29-12 taxon:4932
+S000002987 CKB1 YGL019W taxon:4932
+S000002987 CKB1 YGL019W taxon:4932
+S000002987 CKB1 YGL019W taxon:4932
+S000002987 CKB1 YGL019W taxon:4932
+S000002987 CKB1 YGL019W taxon:4932
+S000002987 CKB1 YGL019W taxon:4932
+S000002987 CKB1 YGL019W taxon:4932
+S000002987 CKB1 YGL019W taxon:4932
+S000002987 CKB1 YGL019W taxon:4932
+S000002987 CKB1 YGL019W taxon:4932
+S000002987 CKB1 YGL019W taxon:4932
+S000002987 CKB1 YGL019W taxon:4932
+S000005565 CKB2 YOR039W taxon:4932
+S000005565 CKB2 YOR039W taxon:4932
+S000005565 CKB2 YOR039W taxon:4932
+S000005565 CKB2 YOR039W taxon:4932
+S000005565 CKB2 YOR039W taxon:4932
+S000005565 CKB2 YOR039W taxon:4932
+S000005565 CKB2 YOR039W taxon:4932
+S000005565 CKB2 YOR039W taxon:4932
+S000005565 CKB2 YOR039W taxon:4932
+S000005565 CKB2 YOR039W taxon:4932
+S000005565 CKB2 YOR039W taxon:4932
+S000005565 CKB2 YOR039W taxon:4932
+S000004123 CKI1 YLR133W taxon:4932
+S000004123 CKI1 YLR133W taxon:4932
+S000004123 CKI1 YLR133W taxon:4932
+S000004123 CKI1 YLR133W taxon:4932
+S000000339 CKS1 YBR135W taxon:4932
+S000000339 CKS1 YBR135W taxon:4932
+S000000339 CKS1 YBR135W taxon:4932
+S000000339 CKS1 YBR135W taxon:4932
+S000000339 CKS1 YBR135W taxon:4932
+S000005242 CLA4 YNL298W|ERC10 taxon:4932
+S000005242 CLA4 YNL298W|ERC10 taxon:4932
+S000005242 CLA4 YNL298W|ERC10 taxon:4932
+S000005242 CLA4 YNL298W|ERC10 taxon:4932
+S000005242 CLA4 YNL298W|ERC10 taxon:4932
+S000005242 CLA4 YNL298W|ERC10 taxon:4932
+S000005242 CLA4 YNL298W|ERC10 taxon:4932
+S000005242 CLA4 YNL298W|ERC10 taxon:4932
+S000003340 CLB1 YGR108W|SCB1 taxon:4932
+S000003340 CLB1 YGR108W|SCB1 taxon:4932
+S000003340 CLB1 YGR108W|SCB1 taxon:4932
+S000003340 CLB1 YGR108W|SCB1 taxon:4932
+S000003340 CLB1 YGR108W|SCB1 taxon:4932
+S000003340 CLB1 YGR108W|SCB1 taxon:4932
+S000003340 CLB1 YGR108W|SCB1 taxon:4932
+S000003340 CLB1 YGR108W|SCB1 taxon:4932
+S000003340 CLB1 YGR108W|SCB1 taxon:4932
+S000003340 CLB1 YGR108W|SCB1 taxon:4932
+S000003340 CLB1 YGR108W|SCB1 taxon:4932
+S000003340 CLB1 YGR108W|SCB1 taxon:4932
+S000006323 CLB2 YPR119W taxon:4932
+S000006323 CLB2 YPR119W taxon:4932
+S000006323 CLB2 YPR119W taxon:4932
+S000006323 CLB2 YPR119W taxon:4932
+S000006323 CLB2 YPR119W taxon:4932
+S000006323 CLB2 YPR119W taxon:4932
+S000006323 CLB2 YPR119W taxon:4932
+S000006323 CLB2 YPR119W taxon:4932
+S000006323 CLB2 YPR119W taxon:4932
+S000006323 CLB2 YPR119W taxon:4932
+S000006323 CLB2 YPR119W taxon:4932
+S000006323 CLB2 YPR119W taxon:4932
+S000002314 CLB3 YDL155W taxon:4932
+S000002314 CLB3 YDL155W taxon:4932
+S000002314 CLB3 YDL155W taxon:4932
+S000002314 CLB3 YDL155W taxon:4932
+S000002314 CLB3 YDL155W taxon:4932
+S000002314 CLB3 YDL155W taxon:4932
+S000002314 CLB3 YDL155W taxon:4932
+S000002314 CLB3 YDL155W taxon:4932
+S000002314 CLB3 YDL155W taxon:4932
+S000002314 CLB3 YDL155W taxon:4932
+S000004200 CLB4 YLR210W taxon:4932
+S000004200 CLB4 YLR210W taxon:4932
+S000004200 CLB4 YLR210W taxon:4932
+S000004200 CLB4 YLR210W taxon:4932
+S000004200 CLB4 YLR210W taxon:4932
+S000004200 CLB4 YLR210W taxon:4932
+S000004200 CLB4 YLR210W taxon:4932
+S000004200 CLB4 YLR210W taxon:4932
+S000004200 CLB4 YLR210W taxon:4932
+S000004200 CLB4 YLR210W taxon:4932
+S000006324 CLB5 YPR120C taxon:4932
+S000006324 CLB5 YPR120C taxon:4932
+S000006324 CLB5 YPR120C taxon:4932
+S000006324 CLB5 YPR120C taxon:4932
+S000006324 CLB5 YPR120C taxon:4932
+S000006324 CLB5 YPR120C taxon:4932
+S000006324 CLB5 YPR120C taxon:4932
+S000006324 CLB5 YPR120C taxon:4932
+S000006324 CLB5 YPR120C taxon:4932
+S000003341 CLB6 YGR109C taxon:4932
+S000003341 CLB6 YGR109C taxon:4932
+S000003341 CLB6 YGR109C taxon:4932
+S000003341 CLB6 YGR109C taxon:4932
+S000003341 CLB6 YGR109C taxon:4932
+S000003341 CLB6 YGR109C taxon:4932
+S000003341 CLB6 YGR109C taxon:4932
+S000003399 CLC1 YGR167W|SCD4 taxon:4932
+S000003399 CLC1 YGR167W|SCD4 taxon:4932
+S000003399 CLC1 YGR167W|SCD4 taxon:4932
+S000003399 CLC1 YGR167W|SCD4 taxon:4932
+S000004107 CLF1 YLR117C|NTC77|SYF3 taxon:4932
+S000004107 CLF1 YLR117C|NTC77|SYF3 taxon:4932
+S000004107 CLF1 YLR117C|NTC77|SYF3 taxon:4932
+S000004107 CLF1 YLR117C|NTC77|SYF3 taxon:4932
+S000004107 CLF1 YLR117C|NTC77|SYF3 taxon:4932
+S000004107 CLF1 YLR117C|NTC77|SYF3 taxon:4932
+S000003183 CLG1 YGL215W taxon:4932
+S000003183 CLG1 YGL215W taxon:4932
+S000003183 CLG1 YGL215W taxon:4932
+S000004812 CLN1 YMR199W taxon:4932
+S000004812 CLN1 YMR199W taxon:4932
+S000004812 CLN1 YMR199W taxon:4932
+S000004812 CLN1 YMR199W taxon:4932
+S000006177 CLN2 YPL256C taxon:4932
+S000006177 CLN2 YPL256C taxon:4932
+S000006177 CLN2 YPL256C taxon:4932
+S000006177 CLN2 YPL256C taxon:4932
+S000006177 CLN2 YPL256C taxon:4932
+S000006177 CLN2 YPL256C taxon:4932
+S000006177 CLN2 YPL256C taxon:4932
+S000006177 CLN2 YPL256C taxon:4932
+S000006177 CLN2 YPL256C taxon:4932
+S000006177 CLN2 YPL256C taxon:4932
+S000006177 CLN2 YPL256C taxon:4932
+S000000038 CLN3 YAL040C|DAF1|FUN10|WHI1 taxon:4932
+S000000038 CLN3 YAL040C|DAF1|FUN10|WHI1 taxon:4932
+S000000038 CLN3 YAL040C|DAF1|FUN10|WHI1 taxon:4932
+S000000038 CLN3 YAL040C|DAF1|FUN10|WHI1 taxon:4932
+S000000038 CLN3 YAL040C|DAF1|FUN10|WHI1 taxon:4932
+S000000038 CLN3 YAL040C|DAF1|FUN10|WHI1 taxon:4932
+S000000038 CLN3 YAL040C|DAF1|FUN10|WHI1 taxon:4932
+S000000038 CLN3 YAL040C|DAF1|FUN10|WHI1 taxon:4932
+S000000038 CLN3 YAL040C|DAF1|FUN10|WHI1 taxon:4932
+S000000038 CLN3 YAL040C|DAF1|FUN10|WHI1 taxon:4932
+S000005776 CLP1 YOR250C taxon:4932
+S000005776 CLP1 YOR250C taxon:4932
+S000005776 CLP1 YOR250C taxon:4932
+S000005776 CLP1 YOR250C taxon:4932
+S000005776 CLP1 YOR250C taxon:4932
+S000004614 CLU1 YMR012W|TIF31 taxon:4932
+S000004614 CLU1 YMR012W|TIF31 taxon:4932
+S000004614 CLU1 YMR012W|TIF31 taxon:4932
+S000004614 CLU1 YMR012W|TIF31 taxon:4932
+S000004614 CLU1 YMR012W|TIF31 taxon:4932
+S000000313 CMD1 YBR109C taxon:4932
+S000000313 CMD1 YBR109C taxon:4932
+S000000313 CMD1 YBR109C taxon:4932
+S000000313 CMD1 YBR109C taxon:4932
+S000000313 CMD1 YBR109C taxon:4932
+S000000313 CMD1 YBR109C taxon:4932
+S000000313 CMD1 YBR109C taxon:4932
+S000000313 CMD1 YBR109C taxon:4932
+S000000313 CMD1 YBR109C taxon:4932
+S000000313 CMD1 YBR109C taxon:4932
+S000000313 CMD1 YBR109C taxon:4932
+S000000313 CMD1 YBR109C taxon:4932
+S000000313 CMD1 YBR109C taxon:4932
+S000000313 CMD1 YBR109C taxon:4932
+S000000313 CMD1 YBR109C taxon:4932
+S000001910 CMK1 YFR014C taxon:4932
+S000001910 CMK1 YFR014C taxon:4932
+S000001910 CMK1 YFR014C taxon:4932
+S000001910 CMK1 YFR014C taxon:4932
+S000005376 CMK2 YOL016C taxon:4932
+S000005376 CMK2 YOL016C taxon:4932
+S000005376 CMK2 YOL016C taxon:4932
+S000005376 CMK2 YOL016C taxon:4932
+S000004521 CMP2 YML057W|CNA2 taxon:4932
+S000004521 CMP2 YML057W|CNA2 taxon:4932
+S000004521 CMP2 YML057W|CNA2 taxon:4932
+S000004521 CMP2 YML057W|CNA2 taxon:4932
+S000004521 CMP2 YML057W|CNA2 taxon:4932
+S000004521 CMP2 YML057W|CNA2 taxon:4932
+S000004521 CMP2 YML057W|CNA2 taxon:4932
+S000004425 CNA1 YLR433C|CMP1 taxon:4932
+S000004425 CNA1 YLR433C|CMP1 taxon:4932
+S000004425 CNA1 YLR433C|CMP1 taxon:4932
+S000004425 CNA1 YLR433C|CMP1 taxon:4932
+S000004425 CNA1 YLR433C|CMP1 taxon:4932
+S000004425 CNA1 YLR433C|CMP1 taxon:4932
+S000004425 CNA1 YLR433C|CMP1 taxon:4932
+S000004425 CNA1 YLR433C|CMP1 taxon:4932
+S000004425 CNA1 YLR433C|CMP1 taxon:4932
+S000001673 CNB1 YKL190W|CRV1|YCN2 taxon:4932
+S000001673 CNB1 YKL190W|CRV1|YCN2 taxon:4932
+S000001673 CNB1 YKL190W|CRV1|YCN2 taxon:4932
+S000001673 CNB1 YKL190W|CRV1|YCN2 taxon:4932
+S000001673 CNB1 YKL190W|CRV1|YCN2 taxon:4932
+S000001673 CNB1 YKL190W|CRV1|YCN2 taxon:4932
+S000001673 CNB1 YKL190W|CRV1|YCN2 taxon:4932
+S000001673 CNB1 YKL190W|CRV1|YCN2 taxon:4932
+S000001673 CNB1 YKL190W|CRV1|YCN2 taxon:4932
+S000001673 CNB1 YKL190W|CRV1|YCN2 taxon:4932
+S000000054 CNE1 YAL058W|FUN48 taxon:4932
+S000000054 CNE1 YAL058W|FUN48 taxon:4932
+S000000054 CNE1 YAL058W|FUN48 taxon:4932
+S000000054 CNE1 YAL058W|FUN48 taxon:4932
+S000000054 CNE1 YAL058W|FUN48 taxon:4932
+S000005169 CNM67 YNL225C taxon:4932
+S000005169 CNM67 YNL225C taxon:4932
+S000005169 CNM67 YNL225C taxon:4932
+S000005169 CNM67 YNL225C taxon:4932
+S000005169 CNM67 YNL225C taxon:4932
+S000005169 CNM67 YNL225C taxon:4932
+S000001942 CNN1 YFR046C taxon:4932
+S000001942 CNN1 YFR046C taxon:4932
+S000001942 CNN1 YFR046C taxon:4932
+S000001942 CNN1 YFR046C taxon:4932
+S000001942 CNN1 YFR046C taxon:4932
+S000000359 CNS1 YBR155W taxon:4932
+S000000359 CNS1 YBR155W taxon:4932
+S000000359 CNS1 YBR155W taxon:4932
+S000000359 CNS1 YBR155W taxon:4932
+S000007270 COB Q0105|COB1|CYTB taxon:4932
+S000007270 COB Q0105|COB1|CYTB taxon:4932
+S000007270 COB Q0105|COB1|CYTB taxon:4932
+S000007270 COB Q0105|COB1|CYTB taxon:4932
+S000007270 COB Q0105|COB1|CYTB taxon:4932
+S000003973 COF1 YLL050C taxon:4932
+S000003973 COF1 YLL050C taxon:4932
+S000003973 COF1 YLL050C taxon:4932
+S000003973 COF1 YLL050C taxon:4932
+S000003973 COF1 YLL050C taxon:4932
+S000003973 COF1 YLL050C taxon:4932
+S000003973 COF1 YLL050C taxon:4932
+S000003191 COG1 YGL223C|COD3|LDB11|SEC36 taxon:4932
+S000003191 COG1 YGL223C|COD3|LDB11|SEC36 taxon:4932
+S000003191 COG1 YGL223C|COD3|LDB11|SEC36 taxon:4932
+S000003191 COG1 YGL223C|COD3|LDB11|SEC36 taxon:4932
+S000003191 COG1 YGL223C|COD3|LDB11|SEC36 taxon:4932
+S000003352 COG2 YGR120C|SEC35 taxon:4932
+S000003352 COG2 YGR120C|SEC35 taxon:4932
+S000003352 COG2 YGR120C|SEC35 taxon:4932
+S000003352 COG2 YGR120C|SEC35 taxon:4932
+S000003352 COG2 YGR120C|SEC35 taxon:4932
+S000003352 COG2 YGR120C|SEC35 taxon:4932
+S000003352 COG2 YGR120C|SEC35 taxon:4932
+S000003352 COG2 YGR120C|SEC35 taxon:4932
+S000003352 COG2 YGR120C|SEC35 taxon:4932
+S000000959 COG3 YER157W|GRD20|SEC34 taxon:4932
+S000000959 COG3 YER157W|GRD20|SEC34 taxon:4932
+S000000959 COG3 YER157W|GRD20|SEC34 taxon:4932
+S000000959 COG3 YER157W|GRD20|SEC34 taxon:4932
+S000000959 COG3 YER157W|GRD20|SEC34 taxon:4932
+S000000959 COG3 YER157W|GRD20|SEC34 taxon:4932
+S000000959 COG3 YER157W|GRD20|SEC34 taxon:4932
+S000000959 COG3 YER157W|GRD20|SEC34 taxon:4932
+S000000959 COG3 YER157W|GRD20|SEC34 taxon:4932
+S000006309 COG4 YPR105C|COD1|SEC38|SGF1 taxon:4932
+S000006309 COG4 YPR105C|COD1|SEC38|SGF1 taxon:4932
+S000006309 COG4 YPR105C|COD1|SEC38|SGF1 taxon:4932
+S000006309 COG4 YPR105C|COD1|SEC38|SGF1 taxon:4932
+S000006309 COG4 YPR105C|COD1|SEC38|SGF1 taxon:4932
+S000004996 COG5 YNL051W|API4|COD4 taxon:4932
+S000004996 COG5 YNL051W|API4|COD4 taxon:4932
+S000004996 COG5 YNL051W|API4|COD4 taxon:4932
+S000004996 COG5 YNL051W|API4|COD4 taxon:4932
+S000004986 COG6 YNL041C|COD2|SEC37 taxon:4932
+S000004986 COG6 YNL041C|COD2|SEC37 taxon:4932
+S000004986 COG6 YNL041C|COD2|SEC37 taxon:4932
+S000004986 COG6 YNL041C|COD2|SEC37 taxon:4932
+S000002973 COG7 YGL005C|COD5 taxon:4932
+S000002973 COG7 YGL005C|COD5 taxon:4932
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+S000002337 DLD2 YDL178W|AIP2 taxon:4932
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+S000002337 DLD2 YDL178W|AIP2 taxon:4932
+S000002337 DLD2 YDL178W|AIP2 taxon:4932
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+S000001157 DMA1 YHR115C|CHF1 taxon:4932
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+S000001157 DMA1 YHR115C|CHF1 taxon:4932
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+S000005060 DMA2 YNL116W|CHF2 taxon:4932
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+S000005060 DMA2 YNL116W|CHF2 taxon:4932
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+S000000981 DMC1 YER179W|ISC2 taxon:4932
+S000000981 DMC1 YER179W|ISC2 taxon:4932
+S000000981 DMC1 YER179W|ISC2 taxon:4932
+S000000981 DMC1 YER179W|ISC2 taxon:4932
+S000000981 DMC1 YER179W|ISC2 taxon:4932
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+S000004824 DML1 YMR211W taxon:4932
+S000004824 DML1 YMR211W taxon:4932
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+S000004824 DML1 YMR211W taxon:4932
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+S000001207 DNA2 YHR164C|WEB2 taxon:4932
+S000001207 DNA2 YHR164C|WEB2 taxon:4932
+S000001207 DNA2 YHR164C|WEB2 taxon:4932
+S000001207 DNA2 YHR164C|WEB2 taxon:4932
+S000001207 DNA2 YHR164C|WEB2 taxon:4932
+S000001207 DNA2 YHR164C|WEB2 taxon:4932
+S000001207 DNA2 YHR164C|WEB2 taxon:4932
+S000001207 DNA2 YHR164C|WEB2 taxon:4932
+S000001207 DNA2 YHR164C|WEB2 taxon:4932
+S000001207 DNA2 YHR164C|WEB2 taxon:4932
+S000001207 DNA2 YHR164C|WEB2 taxon:4932
+S000001207 DNA2 YHR164C|WEB2 taxon:4932
+S000001207 DNA2 YHR164C|WEB2 taxon:4932
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+S000000968 DNF1 YER166W taxon:4932
+S000000968 DNF1 YER166W taxon:4932
+S000000968 DNF1 YER166W taxon:4932
+S000000968 DNF1 YER166W taxon:4932
+S000000968 DNF1 YER166W taxon:4932
+S000000968 DNF1 YER166W taxon:4932
+S000000968 DNF1 YER166W taxon:4932
+S000002500 DNF2 YDR093W taxon:4932
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+S000002500 DNF2 YDR093W taxon:4932
+S000002500 DNF2 YDR093W taxon:4932
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+S000005531 DNL4 YOR005C|LIG4 taxon:4932
+S000005531 DNL4 YOR005C|LIG4 taxon:4932
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+S000001696 DOA1 YKL213C|UFD3|ZZZ4 taxon:4932
+S000001696 DOA1 YKL213C|UFD3|ZZZ4 taxon:4932
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+S000001696 DOA1 YKL213C|UFD3|ZZZ4 taxon:4932
+S000001696 DOA1 YKL213C|UFD3|ZZZ4 taxon:4932
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+S000001272 DOT5 YIL010W|nTPx taxon:4932
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+S000002702 DPL1 YDR294C|BST1 taxon:4932
+S000002702 DPL1 YDR294C|BST1 taxon:4932
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+S000002692 DPP1 YDR284C|ZRG1 taxon:4932
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+S000003941 DPS1 YLL018C|AspRS taxon:4932
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+S000003941 DPS1 YLL018C|AspRS taxon:4932
+S000003941 DPS1 YLL018C|AspRS taxon:4932
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+S000001779 DRE2 YKR071C taxon:4932
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+S000000926 DSE1 YER124C taxon:4932
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+S000000796 DSF1 YEL070W taxon:4932
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+S000000211 DSF2 YBR007C taxon:4932
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+S000004889 DSK2 YMR276W taxon:4932
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+S000005202 DSL1 YNL258C taxon:4932
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+S000001449 DSN1 YIR010W taxon:4932
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+S000001449 DSN1 YIR010W taxon:4932
+S000001449 DSN1 YIR010W taxon:4932
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+S000006221 DSS4 YPR017C taxon:4932
+S000006221 DSS4 YPR017C taxon:4932
+S000006221 DSS4 YPR017C taxon:4932
+S000006221 DSS4 YPR017C taxon:4932
+S000006221 DSS4 YPR017C taxon:4932
+S000006221 DSS4 YPR017C taxon:4932
+S000003011 DST1 YGL043W|P37|PPR2|S-II|SII|TFIIS taxon:4932
+S000003011 DST1 YGL043W|P37|PPR2|S-II|SII|TFIIS taxon:4932
+S000003011 DST1 YGL043W|P37|PPR2|S-II|SII|TFIIS taxon:4932
+S000003011 DST1 YGL043W|P37|PPR2|S-II|SII|TFIIS taxon:4932
+S000003011 DST1 YGL043W|P37|PPR2|S-II|SII|TFIIS taxon:4932
+S000003011 DST1 YGL043W|P37|PPR2|S-II|SII|TFIIS taxon:4932
+S000003011 DST1 YGL043W|P37|PPR2|S-II|SII|TFIIS taxon:4932
+S000002378 DTD1 YDL219W taxon:4932
+S000002378 DTD1 YDL219W taxon:4932
+S000002378 DTD1 YDL219W taxon:4932
+S000002378 DTD1 YDL219W taxon:4932
+S000000384 DTR1 YBR180W taxon:4932
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+S000003330 ESP1 YGR098C|separin taxon:4932
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+S000000858 FCY2 YER056C|BRA7 taxon:4932
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+S000001393 FKH1 YIL131C taxon:4932
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+S000000084 FLO1 YAR050W|FLO2|FLO4 taxon:4932
+S000000084 FLO1 YAR050W|FLO2|FLO4 taxon:4932
+S000000084 FLO1 YAR050W|FLO2|FLO4 taxon:4932
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+S000001254 FLO5 YHR211W taxon:4932
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+S000000911 FLO8 YER109C|PHD5|YER108C taxon:4932
+S000000911 FLO8 YER109C|PHD5|YER108C taxon:4932
+S000000911 FLO8 YER109C|PHD5|YER108C taxon:4932
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+S000000059 FLO9 YAL063C taxon:4932
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+S000029654 FLP1 taxon:4932
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+S000005704 GAC1 YOR178C taxon:4932
+S000005704 GAC1 YOR178C taxon:4932
+S000005704 GAC1 YOR178C taxon:4932
+S000005704 GAC1 YOR178C taxon:4932
+S000005704 GAC1 YOR178C taxon:4932
+S000005704 GAC1 YOR178C taxon:4932
+S000005704 GAC1 YOR178C taxon:4932
+S000005704 GAC1 YOR178C taxon:4932
+S000005704 GAC1 YOR178C taxon:4932
+S000004862 GAD1 YMR250W taxon:4932
+S000004862 GAD1 YMR250W taxon:4932
+S000004862 GAD1 YMR250W taxon:4932
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+S000004862 GAD1 YMR250W taxon:4932
+S000004862 GAD1 YMR250W taxon:4932
+S000004862 GAD1 YMR250W taxon:4932
+S000000224 GAL1 YBR020W taxon:4932
+S000000224 GAL1 YBR020W taxon:4932
+S000000224 GAL1 YBR020W taxon:4932
+S000000223 GAL10 YBR019C taxon:4932
+S000000223 GAL10 YBR019C taxon:4932
+S000000223 GAL10 YBR019C taxon:4932
+S000005411 GAL11 YOL051W|ABE1|MED15|RAR3|SDS4|SPT13 taxon:4932
+S000005411 GAL11 YOL051W|ABE1|MED15|RAR3|SDS4|SPT13 taxon:4932
+S000005411 GAL11 YOL051W|ABE1|MED15|RAR3|SDS4|SPT13 taxon:4932
+S000004071 GAL2 YLR081W taxon:4932
+S000004071 GAL2 YLR081W taxon:4932
+S000004071 GAL2 YLR081W taxon:4932
+S000004071 GAL2 YLR081W taxon:4932
+S000004071 GAL2 YLR081W taxon:4932
+S000002416 GAL3 YDR009W taxon:4932
+S000002416 GAL3 YDR009W taxon:4932
+S000002416 GAL3 YDR009W taxon:4932
+S000002416 GAL3 YDR009W taxon:4932
+S000006169 GAL4 YPL248C|GAL81 taxon:4932
+S000006169 GAL4 YPL248C|GAL81 taxon:4932
+S000006169 GAL4 YPL248C|GAL81 taxon:4932
+S000006169 GAL4 YPL248C|GAL81 taxon:4932
+S000000222 GAL7 YBR018C taxon:4932
+S000000222 GAL7 YBR018C taxon:4932
+S000000222 GAL7 YBR018C taxon:4932
+S000004515 GAL80 YML051W taxon:4932
+S000004515 GAL80 YML051W taxon:4932
+S000004515 GAL80 YML051W taxon:4932
+S000004515 GAL80 YML051W taxon:4932
+S000004515 GAL80 YML051W taxon:4932
+S000000829 GAL83 YER027C|SPM1 taxon:4932
+S000000829 GAL83 YER027C|SPM1 taxon:4932
+S000000829 GAL83 YER027C|SPM1 taxon:4932
+S000000829 GAL83 YER027C|SPM1 taxon:4932
+S000000829 GAL83 YER027C|SPM1 taxon:4932
+S000000829 GAL83 YER027C|SPM1 taxon:4932
+S000001747 GAP1 YKR039W taxon:4932
+S000001747 GAP1 YKR039W taxon:4932
+S000001747 GAP1 YKR039W taxon:4932
+S000001747 GAP1 YKR039W taxon:4932
+S000001747 GAP1 YKR039W taxon:4932
+S000001747 GAP1 YKR039W taxon:4932
+S000001747 GAP1 YKR039W taxon:4932
+S000001747 GAP1 YKR039W taxon:4932
+S000001747 GAP1 YKR039W taxon:4932
+S000001747 GAP1 YKR039W taxon:4932
+S000001747 GAP1 YKR039W taxon:4932
+S000001747 GAP1 YKR039W taxon:4932
+S000001131 GAR1 YHR089C taxon:4932
+S000001131 GAR1 YHR089C taxon:4932
+S000001131 GAR1 YHR089C taxon:4932
+S000001131 GAR1 YHR089C taxon:4932
+S000001131 GAR1 YHR089C taxon:4932
+S000004924 GAS1 YMR307W|CWH52|GGP1 taxon:4932
+S000004924 GAS1 YMR307W|CWH52|GGP1 taxon:4932
+S000004924 GAS1 YMR307W|CWH52|GGP1 taxon:4932
+S000004924 GAS1 YMR307W|CWH52|GGP1 taxon:4932
+S000004924 GAS1 YMR307W|CWH52|GGP1 taxon:4932
+S000004924 GAS1 YMR307W|CWH52|GGP1 taxon:4932
+S000004924 GAS1 YMR307W|CWH52|GGP1 taxon:4932
+S000004335 GAS2 YLR343W taxon:4932
+S000004335 GAS2 YLR343W taxon:4932
+S000004335 GAS2 YLR343W taxon:4932
+S000004828 GAS3 YMR215W taxon:4932
+S000004828 GAS3 YMR215W taxon:4932
+S000004828 GAS3 YMR215W taxon:4932
+S000004828 GAS3 YMR215W taxon:4932
+S000005492 GAS4 YOL132W taxon:4932
+S000005492 GAS4 YOL132W taxon:4932
+S000005492 GAS4 YOL132W taxon:4932
+S000005390 GAS5 YOL030W taxon:4932
+S000005390 GAS5 YOL030W taxon:4932
+S000005390 GAS5 YOL030W taxon:4932
+S000005390 GAS5 YOL030W taxon:4932
+S000001873 GAT1 YFL021W|MEP80|NIL1 taxon:4932
+S000001873 GAT1 YFL021W|MEP80|NIL1 taxon:4932
+S000001873 GAT1 YFL021W|MEP80|NIL1 taxon:4932
+S000001873 GAT1 YFL021W|MEP80|NIL1 taxon:4932
+S000001873 GAT1 YFL021W|MEP80|NIL1 taxon:4932
+S000001873 GAT1 YFL021W|MEP80|NIL1 taxon:4932
+S000001873 GAT1 YFL021W|MEP80|NIL1 taxon:4932
+S000001873 GAT1 YFL021W|MEP80|NIL1 taxon:4932
+S000001873 GAT1 YFL021W|MEP80|NIL1 taxon:4932
+S000004744 GAT2 YMR136W taxon:4932
+S000004744 GAT2 YMR136W taxon:4932
+S000004744 GAT2 YMR136W taxon:4932
+S000004003 GAT3 YLR013W taxon:4932
+S000004003 GAT3 YLR013W taxon:4932
+S000004003 GAT3 YLR013W taxon:4932
+S000001452 GAT4 YIR013C taxon:4932
+S000001452 GAT4 YIR013C taxon:4932
+S000001452 GAT4 YIR013C taxon:4932
+S000000517 GBP2 YCL011C|RLF6 taxon:4932
+S000000517 GBP2 YCL011C|RLF6 taxon:4932
+S000000517 GBP2 YCL011C|RLF6 taxon:4932
+S000000517 GBP2 YCL011C|RLF6 taxon:4932
+S000000517 GBP2 YCL011C|RLF6 taxon:4932
+S000000517 GBP2 YCL011C|RLF6 taxon:4932
+S000000517 GBP2 YCL011C|RLF6 taxon:4932
+S000000517 GBP2 YCL011C|RLF6 taxon:4932
+S000000517 GBP2 YCL011C|RLF6 taxon:4932
+S000000517 GBP2 YCL011C|RLF6 taxon:4932
+S000005786 GCD1 YOR260W|TRA3 taxon:4932
+S000005786 GCD1 YOR260W|TRA3 taxon:4932
+S000005786 GCD1 YOR260W|TRA3 taxon:4932
+S000005786 GCD1 YOR260W|TRA3 taxon:4932
+S000005786 GCD1 YOR260W|TRA3 taxon:4932
+S000005786 GCD1 YOR260W|TRA3 taxon:4932
+S000005006 GCD10 YNL062C|TRM6 taxon:4932
+S000005006 GCD10 YNL062C|TRM6 taxon:4932
+S000005006 GCD10 YNL062C|TRM6 taxon:4932
+S000005006 GCD10 YNL062C|TRM6 taxon:4932
+S000005006 GCD10 YNL062C|TRM6 taxon:4932
+S000005006 GCD10 YNL062C|TRM6 taxon:4932
+S000000827 GCD11 YER025W|SUI4|eIF2 gamma taxon:4932
+S000000827 GCD11 YER025W|SUI4|eIF2 gamma taxon:4932
+S000000827 GCD11 YER025W|SUI4|eIF2 gamma taxon:4932
+S000000827 GCD11 YER025W|SUI4|eIF2 gamma taxon:4932
+S000000827 GCD11 YER025W|SUI4|eIF2 gamma taxon:4932
+S000000827 GCD11 YER025W|SUI4|eIF2 gamma taxon:4932
+S000003661 GCD14 YJL125C|TRM61 taxon:4932
+S000003661 GCD14 YJL125C|TRM61 taxon:4932
+S000003661 GCD14 YJL125C|TRM61 taxon:4932
+S000003661 GCD14 YJL125C|TRM61 taxon:4932
+S000003661 GCD14 YJL125C|TRM61 taxon:4932
+S000003315 GCD2 YGR083C|GCD12 taxon:4932
+S000003315 GCD2 YGR083C|GCD12 taxon:4932
+S000003315 GCD2 YGR083C|GCD12 taxon:4932
+S000003315 GCD2 YGR083C|GCD12 taxon:4932
+S000003315 GCD2 YGR083C|GCD12 taxon:4932
+S000003315 GCD2 YGR083C|GCD12 taxon:4932
+S000029174 GCD3 taxon:4932
+S000029174 GCD3 taxon:4932
+S000029174 GCD3 taxon:4932
+S000002619 GCD6 YDR211W taxon:4932
+S000002619 GCD6 YDR211W taxon:4932
+S000002619 GCD6 YDR211W taxon:4932
+S000002619 GCD6 YDR211W taxon:4932
+S000002619 GCD6 YDR211W taxon:4932
+S000002619 GCD6 YDR211W taxon:4932
+S000004282 GCD7 YLR291C taxon:4932
+S000004282 GCD7 YLR291C taxon:4932
+S000004282 GCD7 YLR291C taxon:4932
+S000004282 GCD7 YLR291C taxon:4932
+S000004282 GCD7 YLR291C taxon:4932
+S000004282 GCD7 YLR291C taxon:4932
+S000004282 GCD7 YLR291C taxon:4932
+S000003163 GCN1 YGL195W taxon:4932
+S000003163 GCN1 YGL195W taxon:4932
+S000003163 GCN1 YGL195W taxon:4932
+S000003163 GCN1 YGL195W taxon:4932
+S000003163 GCN1 YGL195W taxon:4932
+S000003163 GCN1 YGL195W taxon:4932
+S000002691 GCN2 YDR283C|AAS1 taxon:4932
+S000002691 GCN2 YDR283C|AAS1 taxon:4932
+S000002691 GCN2 YDR283C|AAS1 taxon:4932
+S000002691 GCN2 YDR283C|AAS1 taxon:4932
+S000002691 GCN2 YDR283C|AAS1 taxon:4932
+S000002691 GCN2 YDR283C|AAS1 taxon:4932
+S000001905 GCN20 YFR009W taxon:4932
+S000001905 GCN20 YFR009W taxon:4932
+S000001905 GCN20 YFR009W taxon:4932
+S000001905 GCN20 YFR009W taxon:4932
+S000001905 GCN20 YFR009W taxon:4932
+S000001734 GCN3 YKR026C|AAS2 taxon:4932
+S000001734 GCN3 YKR026C|AAS2 taxon:4932
+S000001734 GCN3 YKR026C|AAS2 taxon:4932
+S000001734 GCN3 YKR026C|AAS2 taxon:4932
+S000001734 GCN3 YKR026C|AAS2 taxon:4932
+S000001734 GCN3 YKR026C|AAS2 taxon:4932
+S000000735 GCN4 YEL009C|AAS3|ARG9 taxon:4932
+S000000735 GCN4 YEL009C|AAS3|ARG9 taxon:4932
+S000000735 GCN4 YEL009C|AAS3|ARG9 taxon:4932
+S000000735 GCN4 YEL009C|AAS3|ARG9 taxon:4932
+S000000735 GCN4 YEL009C|AAS3|ARG9 taxon:4932
+S000003484 GCN5 YGR252W|ADA4|SWI9 taxon:4932
+S000003484 GCN5 YGR252W|ADA4|SWI9 taxon:4932
+S000003484 GCN5 YGR252W|ADA4|SWI9 taxon:4932
+S000003484 GCN5 YGR252W|ADA4|SWI9 taxon:4932
+S000003484 GCN5 YGR252W|ADA4|SWI9 taxon:4932
+S000003484 GCN5 YGR252W|ADA4|SWI9 taxon:4932
+S000003484 GCN5 YGR252W|ADA4|SWI9 taxon:4932
+S000005996 GCR1 YPL075W|LPF10 taxon:4932
+S000005996 GCR1 YPL075W|LPF10 taxon:4932
+S000005996 GCR1 YPL075W|LPF10 taxon:4932
+S000005996 GCR1 YPL075W|LPF10 taxon:4932
+S000005996 GCR1 YPL075W|LPF10 taxon:4932
+S000005996 GCR1 YPL075W|LPF10 taxon:4932
+S000005143 GCR2 YNL199C taxon:4932
+S000005143 GCR2 YNL199C taxon:4932
+S000005143 GCR2 YNL199C taxon:4932
+S000005143 GCR2 YNL199C taxon:4932
+S000005143 GCR2 YNL199C taxon:4932
+S000002385 GCS1 YDL226C taxon:4932
+S000002385 GCS1 YDL226C taxon:4932
+S000002385 GCS1 YDL226C taxon:4932
+S000002385 GCS1 YDL226C taxon:4932
+S000002385 GCS1 YDL226C taxon:4932
+S000002385 GCS1 YDL226C taxon:4932
+S000002385 GCS1 YDL226C taxon:4932
+S000002385 GCS1 YDL226C taxon:4932
+S000002385 GCS1 YDL226C taxon:4932
+S000002385 GCS1 YDL226C taxon:4932
+S000002385 GCS1 YDL226C taxon:4932
+S000002385 GCS1 YDL226C taxon:4932
+S000002385 GCS1 YDL226C taxon:4932
+S000002385 GCS1 YDL226C taxon:4932
+S000002426 GCV1 YDR019C|GSD1 taxon:4932
+S000002426 GCV1 YDR019C|GSD1 taxon:4932
+S000002426 GCV1 YDR019C|GSD1 taxon:4932
+S000002426 GCV1 YDR019C|GSD1 taxon:4932
+S000002426 GCV1 YDR019C|GSD1 taxon:4932
+S000002426 GCV1 YDR019C|GSD1 taxon:4932
+S000002426 GCV1 YDR019C|GSD1 taxon:4932
+S000002426 GCV1 YDR019C|GSD1 taxon:4932
+S000002426 GCV1 YDR019C|GSD1 taxon:4932
+S000004801 GCV2 YMR189W|GSD2 taxon:4932
+S000004801 GCV2 YMR189W|GSD2 taxon:4932
+S000004801 GCV2 YMR189W|GSD2 taxon:4932
+S000004801 GCV2 YMR189W|GSD2 taxon:4932
+S000004801 GCV2 YMR189W|GSD2 taxon:4932
+S000004801 GCV2 YMR189W|GSD2 taxon:4932
+S000004801 GCV2 YMR189W|GSD2 taxon:4932
+S000004801 GCV2 YMR189W|GSD2 taxon:4932
+S000000042 GCV3 YAL044C taxon:4932
+S000000042 GCV3 YAL044C taxon:4932
+S000000042 GCV3 YAL044C taxon:4932
+S000000042 GCV3 YAL044C taxon:4932
+S000000042 GCV3 YAL044C taxon:4932
+S000000042 GCV3 YAL044C taxon:4932
+S000000042 GCV3 YAL044C taxon:4932
+S000000042 GCV3 YAL044C taxon:4932
+S000000042 GCV3 YAL044C taxon:4932
+S000005646 GCY1 YOR120W|GCY taxon:4932
+S000005646 GCY1 YOR120W|GCY taxon:4932
+S000005646 GCY1 YOR120W|GCY taxon:4932
+S000005646 GCY1 YOR120W|GCY taxon:4932
+S000005646 GCY1 YOR120W|GCY taxon:4932
+S000005646 GCY1 YOR120W|GCY taxon:4932
+S000005646 GCY1 YOR120W|GCY taxon:4932
+S000000768 GDA1 YEL042W|GDPase taxon:4932
+S000000768 GDA1 YEL042W|GDPase taxon:4932
+S000000768 GDA1 YEL042W|GDPase taxon:4932
+S000000768 GDA1 YEL042W|GDPase taxon:4932
+S000006388 GDB1 YPR184W taxon:4932
+S000006388 GDB1 YPR184W taxon:4932
+S000006388 GDB1 YPR184W taxon:4932
+S000006388 GDB1 YPR184W taxon:4932
+S000006388 GDB1 YPR184W taxon:4932
+S000006388 GDB1 YPR184W taxon:4932
+S000006388 GDB1 YPR184W taxon:4932
+S000006388 GDB1 YPR184W taxon:4932
+S000006388 GDB1 YPR184W taxon:4932
+S000006031 GDE1 YPL110C taxon:4932
+S000006031 GDE1 YPL110C taxon:4932
+S000006031 GDE1 YPL110C taxon:4932
+S000006031 GDE1 YPL110C taxon:4932
+S000006031 GDE1 YPL110C taxon:4932
+S000005902 GDH1 YOR375C|GDH-A|GDHA|URE1 taxon:4932
+S000005902 GDH1 YOR375C|GDH-A|GDHA|URE1 taxon:4932
+S000005902 GDH1 YOR375C|GDH-A|GDHA|URE1 taxon:4932
+S000005902 GDH1 YOR375C|GDH-A|GDHA|URE1 taxon:4932
+S000002374 GDH2 YDL215C|GDH-B|GDHB taxon:4932
+S000002374 GDH2 YDL215C|GDH-B|GDHB taxon:4932
+S000002374 GDH2 YDL215C|GDH-B|GDHB taxon:4932
+S000002374 GDH2 YDL215C|GDH-B|GDHB taxon:4932
+S000002374 GDH2 YDL215C|GDH-B|GDHB taxon:4932
+S000000058 GDH3 YAL062W|FUN51 taxon:4932
+S000000058 GDH3 YAL062W|FUN51 taxon:4932
+S000000058 GDH3 YAL062W|FUN51 taxon:4932
+S000000058 GDH3 YAL062W|FUN51 taxon:4932
+S000000058 GDH3 YAL062W|FUN51 taxon:4932
+S000000058 GDH3 YAL062W|FUN51 taxon:4932
+S000000058 GDH3 YAL062W|FUN51 taxon:4932
+S000000938 GDI1 YER136W|SEC19 taxon:4932
+S000000938 GDI1 YER136W|SEC19 taxon:4932
+S000000938 GDI1 YER136W|SEC19 taxon:4932
+S000000938 GDI1 YER136W|SEC19 taxon:4932
+S000005882 GDS1 YOR355W taxon:4932
+S000005882 GDS1 YOR355W taxon:4932
+S000005882 GDS1 YOR355W taxon:4932
+S000005882 GDS1 YOR355W taxon:4932
+S000005882 GDS1 YOR355W taxon:4932
+S000005882 GDS1 YOR355W taxon:4932
+S000003792 GEA1 YJR031C taxon:4932
+S000003792 GEA1 YJR031C taxon:4932
+S000003792 GEA1 YJR031C taxon:4932
+S000003792 GEA1 YJR031C taxon:4932
+S000003792 GEA1 YJR031C taxon:4932
+S000003792 GEA1 YJR031C taxon:4932
+S000003792 GEA1 YJR031C taxon:4932
+S000000748 GEA2 YEL022W taxon:4932
+S000000748 GEA2 YEL022W taxon:4932
+S000000748 GEA2 YEL022W taxon:4932
+S000000748 GEA2 YEL022W taxon:4932
+S000000748 GEA2 YEL022W taxon:4932
+S000000748 GEA2 YEL022W taxon:4932
+S000000748 GEA2 YEL022W taxon:4932
+S000003801 GEF1 YJR040W|CLC taxon:4932
+S000003801 GEF1 YJR040W|CLC taxon:4932
+S000003801 GEF1 YJR040W|CLC taxon:4932
+S000003801 GEF1 YJR040W|CLC taxon:4932
+S000003801 GEF1 YJR040W|CLC taxon:4932
+S000003801 GEF1 YJR040W|CLC taxon:4932
+S000003801 GEF1 YJR040W|CLC taxon:4932
+S000000046 GEM1 YAL048C|GON1 taxon:4932
+S000000046 GEM1 YAL048C|GON1 taxon:4932
+S000000046 GEM1 YAL048C|GON1 taxon:4932
+S000000046 GEM1 YAL048C|GON1 taxon:4932
+S000000046 GEM1 YAL048C|GON1 taxon:4932
+S000002988 GET1 YGL020C|MDM39 taxon:4932
+S000002988 GET1 YGL020C|MDM39 taxon:4932
+S000002988 GET1 YGL020C|MDM39 taxon:4932
+S000002988 GET1 YGL020C|MDM39 taxon:4932
+S000002988 GET1 YGL020C|MDM39 taxon:4932
+S000002988 GET1 YGL020C|MDM39 taxon:4932
+S000002988 GET1 YGL020C|MDM39 taxon:4932
+S000002988 GET1 YGL020C|MDM39 taxon:4932
+S000002988 GET1 YGL020C|MDM39 taxon:4932
+S000002988 GET1 YGL020C|MDM39 taxon:4932
+S000000885 GET2 YER083C|HUR2|RMD7 taxon:4932
+S000000885 GET2 YER083C|HUR2|RMD7 taxon:4932
+S000000885 GET2 YER083C|HUR2|RMD7 taxon:4932
+S000000885 GET2 YER083C|HUR2|RMD7 taxon:4932
+S000000885 GET2 YER083C|HUR2|RMD7 taxon:4932
+S000000885 GET2 YER083C|HUR2|RMD7 taxon:4932
+S000000885 GET2 YER083C|HUR2|RMD7 taxon:4932
+S000000885 GET2 YER083C|HUR2|RMD7 taxon:4932
+S000002258 GET3 YDL100C|ARR4 taxon:4932
+S000002258 GET3 YDL100C|ARR4 taxon:4932
+S000002258 GET3 YDL100C|ARR4 taxon:4932
+S000002258 GET3 YDL100C|ARR4 taxon:4932
+S000002258 GET3 YDL100C|ARR4 taxon:4932
+S000002258 GET3 YDL100C|ARR4 taxon:4932
+S000002258 GET3 YDL100C|ARR4 taxon:4932
+S000002258 GET3 YDL100C|ARR4 taxon:4932
+S000001587 GFA1 YKL104C taxon:4932
+S000001587 GFA1 YKL104C taxon:4932
+S000001587 GFA1 YKL104C taxon:4932
+S000004868 GFD1 YMR255W taxon:4932
+S000004868 GFD1 YMR255W taxon:4932
+S000004868 GFD1 YMR255W taxon:4932
+S000004868 GFD1 YMR255W taxon:4932
+S000004868 GFD1 YMR255W taxon:4932
+S000004868 GFD1 YMR255W taxon:4932
+S000000541 GFD2 YCL036W taxon:4932
+S000000541 GFD2 YCL036W taxon:4932
+S000000541 GFD2 YCL036W taxon:4932
+S000002766 GGA1 YDR358W taxon:4932
+S000002766 GGA1 YDR358W taxon:4932
+S000002766 GGA1 YDR358W taxon:4932
+S000002766 GGA1 YDR358W taxon:4932
+S000002766 GGA1 YDR358W taxon:4932
+S000002766 GGA1 YDR358W taxon:4932
+S000001150 GGA2 YHR108W taxon:4932
+S000001150 GGA2 YHR108W taxon:4932
+S000001150 GGA2 YHR108W taxon:4932
+S000001150 GGA2 YHR108W taxon:4932
+S000001150 GGA2 YHR108W taxon:4932
+S000001150 GGA2 YHR108W taxon:4932
+S000002357 GGC1 YDL198C|YHM1 taxon:4932
+S000002357 GGC1 YDL198C|YHM1 taxon:4932
+S000002357 GGC1 YDL198C|YHM1 taxon:4932
+S000002357 GGC1 YDL198C|YHM1 taxon:4932
+S000002357 GGC1 YDL198C|YHM1 taxon:4932
+S000002357 GGC1 YDL198C|YHM1 taxon:4932
+S000001103 GIC1 YHR061C taxon:4932
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+S000001103 GIC1 YHR061C taxon:4932
+S000001103 GIC1 YHR061C taxon:4932
+S000001103 GIC1 YHR061C taxon:4932
+S000001103 GIC1 YHR061C taxon:4932
+S000001103 GIC1 YHR061C taxon:4932
+S000001103 GIC1 YHR061C taxon:4932
+S000001103 GIC1 YHR061C taxon:4932
+S000001103 GIC1 YHR061C taxon:4932
+S000001103 GIC1 YHR061C taxon:4932
+S000002717 GIC2 YDR309C taxon:4932
+S000002717 GIC2 YDR309C taxon:4932
+S000002717 GIC2 YDR309C taxon:4932
+S000002717 GIC2 YDR309C taxon:4932
+S000002717 GIC2 YDR309C taxon:4932
+S000002717 GIC2 YDR309C taxon:4932
+S000002717 GIC2 YDR309C taxon:4932
+S000002717 GIC2 YDR309C taxon:4932
+S000002717 GIC2 YDR309C taxon:4932
+S000002717 GIC2 YDR309C taxon:4932
+S000000544 GID7 YCL039W|MOH2 taxon:4932
+S000000544 GID7 YCL039W|MOH2 taxon:4932
+S000000544 GID7 YCL039W|MOH2 taxon:4932
+S000000544 GID7 YCL039W|MOH2 taxon:4932
+S000004742 GID8 YMR135C|DCR1 taxon:4932
+S000004742 GID8 YMR135C|DCR1 taxon:4932
+S000004742 GID8 YMR135C|DCR1 taxon:4932
+S000004742 GID8 YMR135C|DCR1 taxon:4932
+S000004742 GID8 YMR135C|DCR1 taxon:4932
+S000005097 GIM3 YNL153C|PFD4 taxon:4932
+S000005097 GIM3 YNL153C|PFD4 taxon:4932
+S000005097 GIM3 YNL153C|PFD4 taxon:4932
+S000005097 GIM3 YNL153C|PFD4 taxon:4932
+S000005097 GIM3 YNL153C|PFD4 taxon:4932
+S000005097 GIM3 YNL153C|PFD4 taxon:4932
+S000000729 GIM4 YEL003W|PFD2 taxon:4932
+S000000729 GIM4 YEL003W|PFD2 taxon:4932
+S000000729 GIM4 YEL003W|PFD2 taxon:4932
+S000000729 GIM4 YEL003W|PFD2 taxon:4932
+S000000729 GIM4 YEL003W|PFD2 taxon:4932
+S000000729 GIM4 YEL003W|PFD2 taxon:4932
+S000004559 GIM5 YML094W|PFD5 taxon:4932
+S000004559 GIM5 YML094W|PFD5 taxon:4932
+S000004559 GIM5 YML094W|PFD5 taxon:4932
+S000004559 GIM5 YML094W|PFD5 taxon:4932
+S000004559 GIM5 YML094W|PFD5 taxon:4932
+S000004559 GIM5 YML094W|PFD5 taxon:4932
+S000002915 GIN4 YDR507C|ERC47 taxon:4932
+S000002915 GIN4 YDR507C|ERC47 taxon:4932
+S000002915 GIN4 YDR507C|ERC47 taxon:4932
+S000002915 GIN4 YDR507C|ERC47 taxon:4932
+S000002915 GIN4 YDR507C|ERC47 taxon:4932
+S000002915 GIN4 YDR507C|ERC47 taxon:4932
+S000002915 GIN4 YDR507C|ERC47 taxon:4932
+S000002915 GIN4 YDR507C|ERC47 taxon:4932
+S000002915 GIN4 YDR507C|ERC47 taxon:4932
+S000002915 GIN4 YDR507C|ERC47 taxon:4932
+S000002915 GIN4 YDR507C|ERC47 taxon:4932
+S000000249 GIP1 YBR045C taxon:4932
+S000000249 GIP1 YBR045C taxon:4932
+S000000249 GIP1 YBR045C taxon:4932
+S000000249 GIP1 YBR045C taxon:4932
+S000000249 GIP1 YBR045C taxon:4932
+S000000249 GIP1 YBR045C taxon:4932
+S000000856 GIP2 YER054C taxon:4932
+S000000856 GIP2 YER054C taxon:4932
+S000000856 GIP2 YER054C taxon:4932
+S000000856 GIP2 YER054C taxon:4932
+S000000856 GIP2 YER054C taxon:4932
+S000000856 GIP2 YER054C taxon:4932
+S000006058 GIP3 YPL137C taxon:4932
+S000006058 GIP3 YPL137C taxon:4932
+S000006058 GIP3 YPL137C taxon:4932
+S000006058 GIP3 YPL137C taxon:4932
+S000006058 GIP3 YPL137C taxon:4932
+S000000029 GIP4 YAL031C|FUN21 taxon:4932
+S000000029 GIP4 YAL031C|FUN21 taxon:4932
+S000000029 GIP4 YAL031C|FUN21 taxon:4932
+S000002559 GIR2 YDR152W taxon:4932
+S000002559 GIR2 YDR152W taxon:4932
+S000002559 GIR2 YDR152W taxon:4932
+S000002503 GIS1 YDR096W taxon:4932
+S000002503 GIS1 YDR096W taxon:4932
+S000002503 GIS1 YDR096W taxon:4932
+S000002503 GIS1 YDR096W taxon:4932
+S000002503 GIS1 YDR096W taxon:4932
+S000002503 GIS1 YDR096W taxon:4932
+S000005199 GIS2 YNL255C taxon:4932
+S000005199 GIS2 YNL255C taxon:4932
+S000005199 GIS2 YNL255C taxon:4932
+S000004084 GIS3 YLR094C taxon:4932
+S000004084 GIS3 YLR094C taxon:4932
+S000004084 GIS3 YLR094C taxon:4932
+S000004084 GIS3 YLR094C taxon:4932
+S000004465 GIS4 YML006C taxon:4932
+S000004465 GIS4 YML006C taxon:4932
+S000004465 GIS4 YML006C taxon:4932
+S000000695 GIT1 YCR098C taxon:4932
+S000000695 GIT1 YCR098C taxon:4932
+S000000695 GIT1 YCR098C taxon:4932
+S000000695 GIT1 YCR098C taxon:4932
+S000000695 GIT1 YCR098C taxon:4932
+S000000737 GLC3 YEL011W|GHA1 taxon:4932
+S000000737 GLC3 YEL011W|GHA1 taxon:4932
+S000000737 GLC3 YEL011W|GHA1 taxon:4932
+S000000737 GLC3 YEL011W|GHA1 taxon:4932
+S000000935 GLC7 YER133W|CID1|DIS2|DIS2S1|PP1 taxon:4932
+S000000935 GLC7 YER133W|CID1|DIS2|DIS2S1|PP1 taxon:4932
+S000000935 GLC7 YER133W|CID1|DIS2|DIS2S1|PP1 taxon:4932
+S000000935 GLC7 YER133W|CID1|DIS2|DIS2S1|PP1 taxon:4932
+S000000935 GLC7 YER133W|CID1|DIS2|DIS2S1|PP1 taxon:4932
+S000000935 GLC7 YER133W|CID1|DIS2|DIS2S1|PP1 taxon:4932
+S000000935 GLC7 YER133W|CID1|DIS2|DIS2S1|PP1 taxon:4932
+S000000935 GLC7 YER133W|CID1|DIS2|DIS2S1|PP1 taxon:4932
+S000000935 GLC7 YER133W|CID1|DIS2|DIS2S1|PP1 taxon:4932
+S000000935 GLC7 YER133W|CID1|DIS2|DIS2S1|PP1 taxon:4932
+S000000935 GLC7 YER133W|CID1|DIS2|DIS2S1|PP1 taxon:4932
+S000000935 GLC7 YER133W|CID1|DIS2|DIS2S1|PP1 taxon:4932
+S000000935 GLC7 YER133W|CID1|DIS2|DIS2S1|PP1 taxon:4932
+S000000935 GLC7 YER133W|CID1|DIS2|DIS2S1|PP1 taxon:4932
+S000000935 GLC7 YER133W|CID1|DIS2|DIS2S1|PP1 taxon:4932
+S000000935 GLC7 YER133W|CID1|DIS2|DIS2S1|PP1 taxon:4932
+S000000935 GLC7 YER133W|CID1|DIS2|DIS2S1|PP1 taxon:4932
+S000000935 GLC7 YER133W|CID1|DIS2|DIS2S1|PP1 taxon:4932
+S000000935 GLC7 YER133W|CID1|DIS2|DIS2S1|PP1 taxon:4932
+S000000935 GLC7 YER133W|CID1|DIS2|DIS2S1|PP1 taxon:4932
+S000000935 GLC7 YER133W|CID1|DIS2|DIS2S1|PP1 taxon:4932
+S000000935 GLC7 YER133W|CID1|DIS2|DIS2S1|PP1 taxon:4932
+S000000935 GLC7 YER133W|CID1|DIS2|DIS2S1|PP1 taxon:4932
+S000000935 GLC7 YER133W|CID1|DIS2|DIS2S1|PP1 taxon:4932
+S000000935 GLC7 YER133W|CID1|DIS2|DIS2S1|PP1 taxon:4932
+S000000935 GLC7 YER133W|CID1|DIS2|DIS2S1|PP1 taxon:4932
+S000000935 GLC7 YER133W|CID1|DIS2|DIS2S1|PP1 taxon:4932
+S000000935 GLC7 YER133W|CID1|DIS2|DIS2S1|PP1 taxon:4932
+S000000935 GLC7 YER133W|CID1|DIS2|DIS2S1|PP1 taxon:4932
+S000000935 GLC7 YER133W|CID1|DIS2|DIS2S1|PP1 taxon:4932
+S000004928 GLC8 YMR311C taxon:4932
+S000004928 GLC8 YMR311C taxon:4932
+S000004928 GLC8 YMR311C taxon:4932
+S000004928 GLC8 YMR311C taxon:4932
+S000004928 GLC8 YMR311C taxon:4932
+S000004928 GLC8 YMR311C taxon:4932
+S000002366 GLE1 YDL207W|BRR3|RSS1 taxon:4932
+S000002366 GLE1 YDL207W|BRR3|RSS1 taxon:4932
+S000002366 GLE1 YDL207W|BRR3|RSS1 taxon:4932
+S000002366 GLE1 YDL207W|BRR3|RSS1 taxon:4932
+S000002366 GLE1 YDL207W|BRR3|RSS1 taxon:4932
+S000000909 GLE2 YER107C|RAE1 taxon:4932
+S000000909 GLE2 YER107C|RAE1 taxon:4932
+S000000909 GLE2 YER107C|RAE1 taxon:4932
+S000000909 GLE2 YER107C|RAE1 taxon:4932
+S000000909 GLE2 YER107C|RAE1 taxon:4932
+S000000909 GLE2 YER107C|RAE1 taxon:4932
+S000000909 GLE2 YER107C|RAE1 taxon:4932
+S000000909 GLE2 YER107C|RAE1 taxon:4932
+S000000909 GLE2 YER107C|RAE1 taxon:4932
+S000000909 GLE2 YER107C|RAE1 taxon:4932
+S000000909 GLE2 YER107C|RAE1 taxon:4932
+S000000909 GLE2 YER107C|RAE1 taxon:4932
+S000000909 GLE2 YER107C|RAE1 taxon:4932
+S000000909 GLE2 YER107C|RAE1 taxon:4932
+S000001766 GLG1 YKR058W taxon:4932
+S000001766 GLG1 YKR058W taxon:4932
+S000001766 GLG1 YKR058W taxon:4932
+S000001766 GLG1 YKR058W taxon:4932
+S000003673 GLG2 YJL137C taxon:4932
+S000003673 GLG2 YJL137C taxon:4932
+S000003673 GLG2 YJL137C taxon:4932
+S000003673 GLG2 YJL137C taxon:4932
+S000000545 GLK1 YCL040W|HOR3 taxon:4932
+S000000545 GLK1 YCL040W|HOR3 taxon:4932
+S000000545 GLK1 YCL040W|HOR3 taxon:4932
+S000000545 GLK1 YCL040W|HOR3 taxon:4932
+S000000545 GLK1 YCL040W|HOR3 taxon:4932
+S000006239 GLN1 YPR035W taxon:4932
+S000006239 GLN1 YPR035W taxon:4932
+S000006239 GLN1 YPR035W taxon:4932
+S000006239 GLN1 YPR035W taxon:4932
+S000006239 GLN1 YPR035W taxon:4932
+S000006239 GLN1 YPR035W taxon:4932
+S000006239 GLN1 YPR035W taxon:4932
+S000000842 GLN3 YER040W taxon:4932
+S000000842 GLN3 YER040W taxon:4932
+S000000842 GLN3 YER040W taxon:4932
+S000000842 GLN3 YER040W taxon:4932
+S000000842 GLN3 YER040W taxon:4932
+S000000842 GLN3 YER040W taxon:4932
+S000000842 GLN3 YER040W taxon:4932
+S000000842 GLN3 YER040W taxon:4932
+S000000842 GLN3 YER040W taxon:4932
+S000000842 GLN3 YER040W taxon:4932
+S000000842 GLN3 YER040W taxon:4932
+S000000842 GLN3 YER040W taxon:4932
+S000005694 GLN4 YOR168W taxon:4932
+S000005694 GLN4 YOR168W taxon:4932
+S000005694 GLN4 YOR168W taxon:4932
+S000005694 GLN4 YOR168W taxon:4932
+S000004463 GLO1 YML004C taxon:4932
+S000004463 GLO1 YML004C taxon:4932
+S000004463 GLO1 YML004C taxon:4932
+S000004463 GLO1 YML004C taxon:4932
+S000004463 GLO1 YML004C taxon:4932
+S000002680 GLO2 YDR272W taxon:4932
+S000002680 GLO2 YDR272W taxon:4932
+S000002680 GLO2 YDR272W taxon:4932
+S000002680 GLO2 YDR272W taxon:4932
+S000000924 GLO3 YER122C taxon:4932
+S000000924 GLO3 YER122C taxon:4932
+S000000924 GLO3 YER122C taxon:4932
+S000000924 GLO3 YER122C taxon:4932
+S000000924 GLO3 YER122C taxon:4932
+S000000924 GLO3 YER122C taxon:4932
+S000000924 GLO3 YER122C taxon:4932
+S000000924 GLO3 YER122C taxon:4932
+S000000924 GLO3 YER122C taxon:4932
+S000000924 GLO3 YER122C taxon:4932
+S000000924 GLO3 YER122C taxon:4932
+S000005566 GLO4 YOR040W taxon:4932
+S000005566 GLO4 YOR040W taxon:4932
+S000005566 GLO4 YOR040W taxon:4932
+S000005566 GLO4 YOR040W taxon:4932
+S000005566 GLO4 YOR040W taxon:4932
+S000005566 GLO4 YOR040W taxon:4932
+S000005566 GLO4 YOR040W taxon:4932
+S000006012 GLR1 YPL091W|LPG17 taxon:4932
+S000006012 GLR1 YPL091W|LPG17 taxon:4932
+S000006012 GLR1 YPL091W|LPG17 taxon:4932
+S000006012 GLR1 YPL091W|LPG17 taxon:4932
+S000006012 GLR1 YPL091W|LPG17 taxon:4932
+S000006012 GLR1 YPL091W|LPG17 taxon:4932
+S000002330 GLT1 YDL171C taxon:4932
+S000002330 GLT1 YDL171C taxon:4932
+S000002330 GLT1 YDL171C taxon:4932
+S000002330 GLT1 YDL171C taxon:4932
+S000000772 GLY1 YEL046C taxon:4932
+S000000772 GLY1 YEL046C taxon:4932
+S000000772 GLY1 YEL046C taxon:4932
+S000000772 GLY1 YEL046C taxon:4932
+S000001738 GMH1 YKR030W|MSG1 taxon:4932
+S000001738 GMH1 YKR030W|MSG1 taxon:4932
+S000001738 GMH1 YKR030W|MSG1 taxon:4932
+S000001877 GNA1 YFL017C|PAT1 taxon:4932
+S000001877 GNA1 YFL017C|PAT1 taxon:4932
+S000001877 GNA1 YFL017C|PAT1 taxon:4932
+S000001877 GNA1 YFL017C|PAT1 taxon:4932
+S000001877 GNA1 YFL017C|PAT1 taxon:4932
+S000001226 GND1 YHR183W taxon:4932
+S000001226 GND1 YHR183W taxon:4932
+S000001226 GND1 YHR183W taxon:4932
+S000001226 GND1 YHR183W taxon:4932
+S000001226 GND1 YHR183W taxon:4932
+S000001226 GND1 YHR183W taxon:4932
+S000003488 GND2 YGR256W taxon:4932
+S000003488 GND2 YGR256W taxon:4932
+S000003488 GND2 YGR256W taxon:4932
+S000003488 GND2 YGR256W taxon:4932
+S000002916 GNP1 YDR508C taxon:4932
+S000002916 GNP1 YDR508C taxon:4932
+S000002916 GNP1 YDR508C taxon:4932
+S000002916 GNP1 YDR508C taxon:4932
+S000002916 GNP1 YDR508C taxon:4932
+S000002916 GNP1 YDR508C taxon:4932
+S000005847 GNT1 YOR320C taxon:4932
+S000005847 GNT1 YOR320C taxon:4932
+S000005847 GNT1 YOR320C taxon:4932
+S000003720 GON7 YJL184W|LDB6 taxon:4932
+S000003720 GON7 YJL184W|LDB6 taxon:4932
+S000003720 GON7 YJL184W|LDB6 taxon:4932
+S000003720 GON7 YJL184W|LDB6 taxon:4932
+S000001023 GOS1 YHL031C taxon:4932
+S000001023 GOS1 YHL031C taxon:4932
+S000001023 GOS1 YHL031C taxon:4932
+S000001023 GOS1 YHL031C taxon:4932
+S000001023 GOS1 YHL031C taxon:4932
+S000004906 GOT1 YMR292W taxon:4932
+S000004906 GOT1 YMR292W taxon:4932
+S000004906 GOT1 YMR292W taxon:4932
+S000004906 GOT1 YMR292W taxon:4932
+S000001047 GPA1 YHR005C|CDC70|DAC1|SCG1 taxon:4932
+S000001047 GPA1 YHR005C|CDC70|DAC1|SCG1 taxon:4932
+S000001047 GPA1 YHR005C|CDC70|DAC1|SCG1 taxon:4932
+S000001047 GPA1 YHR005C|CDC70|DAC1|SCG1 taxon:4932
+S000000822 GPA2 YER020W|SSP101 taxon:4932
+S000000822 GPA2 YER020W|SSP101 taxon:4932
+S000000822 GPA2 YER020W|SSP101 taxon:4932
+S000000822 GPA2 YER020W|SSP101 taxon:4932
+S000000822 GPA2 YER020W|SSP101 taxon:4932
+S000000822 GPA2 YER020W|SSP101 taxon:4932
+S000000822 GPA2 YER020W|SSP101 taxon:4932
+S000005898 GPB1 YOR371C|KRH2 taxon:4932
+S000005898 GPB1 YOR371C|KRH2 taxon:4932
+S000005898 GPB1 YOR371C|KRH2 taxon:4932
+S000005898 GPB1 YOR371C|KRH2 taxon:4932
+S000000052 GPB2 YAL056W|KRH1 taxon:4932
+S000000052 GPB2 YAL056W|KRH1 taxon:4932
+S000000052 GPB2 YAL056W|KRH1 taxon:4932
+S000000052 GPB2 YAL056W|KRH1 taxon:4932
+S000000052 GPB2 YAL056W|KRH1 taxon:4932
+S000000052 GPB2 YAL056W|KRH1 taxon:4932
+S000002180 GPD1 YDL022W|DAR1|HOR1|OSG1|OSR5 taxon:4932
+S000002180 GPD1 YDL022W|DAR1|HOR1|OSG1|OSR5 taxon:4932
+S000002180 GPD1 YDL022W|DAR1|HOR1|OSG1|OSR5 taxon:4932
+S000002180 GPD1 YDL022W|DAR1|HOR1|OSG1|OSR5 taxon:4932
+S000005420 GPD2 YOL059W|GPD3 taxon:4932
+S000005420 GPD2 YOL059W|GPD3 taxon:4932
+S000005420 GPD2 YOL059W|GPD3 taxon:4932
+S000005420 GPD2 YOL059W|GPD3 taxon:4932
+S000003089 GPG1 YGL121C taxon:4932
+S000003089 GPG1 YGL121C taxon:4932
+S000003089 GPG1 YGL121C taxon:4932
+S000006364 GPH1 YPR160W taxon:4932
+S000006364 GPH1 YPR160W taxon:4932
+S000006364 GPH1 YPR160W taxon:4932
+S000003448 GPI1 YGR216C taxon:4932
+S000003448 GPI1 YGR216C taxon:4932
+S000003448 GPI1 YGR216C taxon:4932
+S000003448 GPI1 YGR216C taxon:4932
+S000003448 GPI1 YGR216C taxon:4932
+S000003448 GPI1 YGR216C taxon:4932
+S000003448 GPI1 YGR216C taxon:4932
+S000003110 GPI10 YGL142C taxon:4932
+S000003110 GPI10 YGL142C taxon:4932
+S000003110 GPI10 YGL142C taxon:4932
+S000002710 GPI11 YDR302W taxon:4932
+S000002710 GPI11 YDR302W taxon:4932
+S000002710 GPI11 YDR302W taxon:4932
+S000002710 GPI11 YDR302W taxon:4932
+S000004894 GPI12 YMR281W taxon:4932
+S000004894 GPI12 YMR281W taxon:4932
+S000004894 GPI12 YMR281W taxon:4932
+S000003954 GPI13 YLL031C|MPC1 taxon:4932
+S000003954 GPI13 YLL031C|MPC1 taxon:4932
+S000003954 GPI13 YLL031C|MPC1 taxon:4932
+S000003774 GPI14 YJR013W|PMH1 taxon:4932
+S000003774 GPI14 YJR013W|PMH1 taxon:4932
+S000003774 GPI14 YJR013W|PMH1 taxon:4932
+S000003774 GPI14 YJR013W|PMH1 taxon:4932
+S000003774 GPI14 YJR013W|PMH1 taxon:4932
+S000004983 GPI15 YNL038W taxon:4932
+S000004983 GPI15 YNL038W taxon:4932
+S000004983 GPI15 YNL038W taxon:4932
+S000004983 GPI15 YNL038W taxon:4932
+S000004983 GPI15 YNL038W taxon:4932
+S000001231 GPI16 YHR188C taxon:4932
+S000001231 GPI16 YHR188C taxon:4932
+S000001231 GPI16 YHR188C taxon:4932
+S000001231 GPI16 YHR188C taxon:4932
+S000002842 GPI17 YDR434W taxon:4932
+S000002842 GPI17 YDR434W taxon:4932
+S000002842 GPI17 YDR434W taxon:4932
+S000002842 GPI17 YDR434W taxon:4932
+S000002842 GPI17 YDR434W taxon:4932
+S000002842 GPI17 YDR434W taxon:4932
+S000000208 GPI18 YBR004C|FMP44 taxon:4932
+S000000208 GPI18 YBR004C|FMP44 taxon:4932
+S000000208 GPI18 YBR004C|FMP44 taxon:4932
+S000000208 GPI18 YBR004C|FMP44 taxon:4932
+S000000208 GPI18 YBR004C|FMP44 taxon:4932
+S000000208 GPI18 YBR004C|FMP44 taxon:4932
+S000000208 GPI18 YBR004C|FMP44 taxon:4932
+S000000208 GPI18 YBR004C|FMP44 taxon:4932
+S000000208 GPI18 YBR004C|FMP44 taxon:4932
+S000002845 GPI19 YDR437W taxon:4932
+S000002845 GPI19 YDR437W taxon:4932
+S000002845 GPI19 YDR437W taxon:4932
+S000002845 GPI19 YDR437W taxon:4932
+S000002845 GPI19 YDR437W taxon:4932
+S000002845 GPI19 YDR437W taxon:4932
+S000002845 GPI19 YDR437W taxon:4932
+S000002845 GPI19 YDR437W taxon:4932
+S000002845 GPI19 YDR437W taxon:4932
+S000002845 GPI19 YDR437W taxon:4932
+S000005997 GPI2 YPL076W|GCR4 taxon:4932
+S000005997 GPI2 YPL076W|GCR4 taxon:4932
+S000005997 GPI2 YPL076W|GCR4 taxon:4932
+S000005997 GPI2 YPL076W|GCR4 taxon:4932
+S000005997 GPI2 YPL076W|GCR4 taxon:4932
+S000005997 GPI2 YPL076W|GCR4 taxon:4932
+S000005997 GPI2 YPL076W|GCR4 taxon:4932
+S000002739 GPI8 YDR331W taxon:4932
+S000002739 GPI8 YDR331W taxon:4932
+S000002739 GPI8 YDR331W taxon:4932
+S000002739 GPI8 YDR331W taxon:4932
+S000001635 GPM1 YKL152C taxon:4932
+S000001635 GPM1 YKL152C taxon:4932
+S000001635 GPM1 YKL152C taxon:4932
+S000001635 GPM1 YKL152C taxon:4932
+S000002179 GPM2 YDL021W taxon:4932
+S000002179 GPM2 YDL021W taxon:4932
+S000002179 GPM2 YDL021W taxon:4932
+S000002179 GPM2 YDL021W taxon:4932
+S000002179 GPM2 YDL021W taxon:4932
+S000005417 GPM3 YOL056W taxon:4932
+S000005417 GPM3 YOL056W taxon:4932
+S000005417 GPM3 YOL056W taxon:4932
+S000005417 GPM3 YOL056W taxon:4932
+S000002193 GPR1 YDL035C taxon:4932
+S000002193 GPR1 YDL035C taxon:4932
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+S000001775 GPT2 YKR067W|GAT1 taxon:4932
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+S000001775 GPT2 YKR067W|GAT1 taxon:4932
+S000001775 GPT2 YKR067W|GAT1 taxon:4932
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+S000001509 GPX1 YKL026C taxon:4932
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+S000000448 GPX2 YBR244W|AMI1 taxon:4932
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+S000003958 GRC3 YLL035W taxon:4932
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+S000029189 GRD10 taxon:4932
+S000029189 GRD10 taxon:4932
+S000029189 GRD10 taxon:4932
+S000029190 GRD14 taxon:4932
+S000029190 GRD14 taxon:4932
+S000029190 GRD14 taxon:4932
+S000029191 GRD15 taxon:4932
+S000029191 GRD15 taxon:4932
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+S000029192 GRD16 taxon:4932
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+S000029193 GRD17 taxon:4932
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+S000029194 GRD18 taxon:4932
+S000029195 GRD3 taxon:4932
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+S000029195 GRD3 taxon:4932
+S000029196 GRD4 taxon:4932
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+S000029197 GRD5 taxon:4932
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+S000029197 GRD5 taxon:4932
+S000006144 GRE1 YPL223C taxon:4932
+S000006144 GRE1 YPL223C taxon:4932
+S000006144 GRE1 YPL223C taxon:4932
+S000006144 GRE1 YPL223C taxon:4932
+S000006144 GRE1 YPL223C taxon:4932
+S000005511 GRE2 YOL151W taxon:4932
+S000005511 GRE2 YOL151W taxon:4932
+S000005511 GRE2 YOL151W taxon:4932
+S000005511 GRE2 YOL151W taxon:4932
+S000005511 GRE2 YOL151W taxon:4932
+S000001146 GRE3 YHR104W taxon:4932
+S000001146 GRE3 YHR104W taxon:4932
+S000001146 GRE3 YHR104W taxon:4932
+S000001146 GRE3 YHR104W taxon:4932
+S000001146 GRE3 YHR104W taxon:4932
+S000001146 GRE3 YHR104W taxon:4932
+S000001146 GRE3 YHR104W taxon:4932
+S000001146 GRE3 YHR104W taxon:4932
+S000001146 GRE3 YHR104W taxon:4932
+S000001146 GRE3 YHR104W taxon:4932
+S000002925 GRH1 YDR517W taxon:4932
+S000002925 GRH1 YDR517W taxon:4932
+S000002925 GRH1 YDR517W taxon:4932
+S000002925 GRH1 YDR517W taxon:4932
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+S000003850 GRR1 YJR090C|CAT80|COT2|SDC1|SSU2 taxon:4932
+S000003850 GRR1 YJR090C|CAT80|COT2|SDC1|SSU2 taxon:4932
+S000003850 GRR1 YJR090C|CAT80|COT2|SDC1|SSU2 taxon:4932
+S000003850 GRR1 YJR090C|CAT80|COT2|SDC1|SSU2 taxon:4932
+S000003850 GRR1 YJR090C|CAT80|COT2|SDC1|SSU2 taxon:4932
+S000003850 GRR1 YJR090C|CAT80|COT2|SDC1|SSU2 taxon:4932
+S000003850 GRR1 YJR090C|CAT80|COT2|SDC1|SSU2 taxon:4932
+S000003850 GRR1 YJR090C|CAT80|COT2|SDC1|SSU2 taxon:4932
+S000003850 GRR1 YJR090C|CAT80|COT2|SDC1|SSU2 taxon:4932
+S000003850 GRR1 YJR090C|CAT80|COT2|SDC1|SSU2 taxon:4932
+S000003850 GRR1 YJR090C|CAT80|COT2|SDC1|SSU2 taxon:4932
+S000003850 GRR1 YJR090C|CAT80|COT2|SDC1|SSU2 taxon:4932
+S000003850 GRR1 YJR090C|CAT80|COT2|SDC1|SSU2 taxon:4932
+S000003850 GRR1 YJR090C|CAT80|COT2|SDC1|SSU2 taxon:4932
+S000000325 GRS1 YBR121C taxon:4932
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+S000000325 GRS1 YBR121C taxon:4932
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+S000006285 GRS2 YPR081C taxon:4932
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+S000000540 GRX1 YCL035C taxon:4932
+S000000540 GRX1 YCL035C taxon:4932
+S000000540 GRX1 YCL035C taxon:4932
+S000000540 GRX1 YCL035C taxon:4932
+S000000540 GRX1 YCL035C taxon:4932
+S000000540 GRX1 YCL035C taxon:4932
+S000000540 GRX1 YCL035C taxon:4932
+S000000540 GRX1 YCL035C taxon:4932
+S000000540 GRX1 YCL035C taxon:4932
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+S000002921 GRX2 YDR513W|TTR1 taxon:4932
+S000002921 GRX2 YDR513W|TTR1 taxon:4932
+S000002921 GRX2 YDR513W|TTR1 taxon:4932
+S000002921 GRX2 YDR513W|TTR1 taxon:4932
+S000002921 GRX2 YDR513W|TTR1 taxon:4932
+S000002921 GRX2 YDR513W|TTR1 taxon:4932
+S000002921 GRX2 YDR513W|TTR1 taxon:4932
+S000002921 GRX2 YDR513W|TTR1 taxon:4932
+S000002921 GRX2 YDR513W|TTR1 taxon:4932
+S000002921 GRX2 YDR513W|TTR1 taxon:4932
+S000002505 GRX3 YDR098C taxon:4932
+S000002505 GRX3 YDR098C taxon:4932
+S000002505 GRX3 YDR098C taxon:4932
+S000002505 GRX3 YDR098C taxon:4932
+S000002505 GRX3 YDR098C taxon:4932
+S000002505 GRX3 YDR098C taxon:4932
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+S000000976 GRX4 YER174C taxon:4932
+S000000976 GRX4 YER174C taxon:4932
+S000000976 GRX4 YER174C taxon:4932
+S000000976 GRX4 YER174C taxon:4932
+S000000976 GRX4 YER174C taxon:4932
+S000000976 GRX4 YER174C taxon:4932
+S000005980 GRX5 YPL059W taxon:4932
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+S000005980 GRX5 YPL059W taxon:4932
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+S000005980 GRX5 YPL059W taxon:4932
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+S000003264 GSC2 YGR032W|FKS2 taxon:4932
+S000003264 GSC2 YGR032W|FKS2 taxon:4932
+S000003264 GSC2 YGR032W|FKS2 taxon:4932
+S000003264 GSC2 YGR032W|FKS2 taxon:4932
+S000003264 GSC2 YGR032W|FKS2 taxon:4932
+S000003264 GSC2 YGR032W|FKS2 taxon:4932
+S000003264 GSC2 YGR032W|FKS2 taxon:4932
+S000004511 GSF2 YML048W|ECM6 taxon:4932
+S000004511 GSF2 YML048W|ECM6 taxon:4932
+S000004511 GSF2 YML048W|ECM6 taxon:4932
+S000004511 GSF2 YML048W|ECM6 taxon:4932
+S000004511 GSF2 YML048W|ECM6 taxon:4932
+S000004511 GSF2 YML048W|ECM6 taxon:4932
+S000004511 GSF2 YML048W|ECM6 taxon:4932
+S000004511 GSF2 YML048W|ECM6 taxon:4932
+S000002515 GSG1 YDR108W|MUM1|TRS85 taxon:4932
+S000002515 GSG1 YDR108W|MUM1|TRS85 taxon:4932
+S000002515 GSG1 YDR108W|MUM1|TRS85 taxon:4932
+S000002515 GSG1 YDR108W|MUM1|TRS85 taxon:4932
+S000002515 GSG1 YDR108W|MUM1|TRS85 taxon:4932
+S000002515 GSG1 YDR108W|MUM1|TRS85 taxon:4932
+S000002515 GSG1 YDR108W|MUM1|TRS85 taxon:4932
+S000003637 GSH1 YJL101C taxon:4932
+S000003637 GSH1 YJL101C taxon:4932
+S000003637 GSH1 YJL101C taxon:4932
+S000003637 GSH1 YJL101C taxon:4932
+S000005409 GSH2 YOL049W taxon:4932
+S000005409 GSH2 YOL049W taxon:4932
+S000005409 GSH2 YOL049W taxon:4932
+S000004284 GSP1 YLR293C|CNR1|CST17 taxon:4932
+S000004284 GSP1 YLR293C|CNR1|CST17 taxon:4932
+S000004284 GSP1 YLR293C|CNR1|CST17 taxon:4932
+S000004284 GSP1 YLR293C|CNR1|CST17 taxon:4932
+S000004284 GSP1 YLR293C|CNR1|CST17 taxon:4932
+S000004284 GSP1 YLR293C|CNR1|CST17 taxon:4932
+S000004284 GSP1 YLR293C|CNR1|CST17 taxon:4932
+S000004284 GSP1 YLR293C|CNR1|CST17 taxon:4932
+S000005711 GSP2 YOR185C|CNR2 taxon:4932
+S000005711 GSP2 YOR185C|CNR2 taxon:4932
+S000005711 GSP2 YOR185C|CNR2 taxon:4932
+S000005711 GSP2 YOR185C|CNR2 taxon:4932
+S000005711 GSP2 YOR185C|CNR2 taxon:4932
+S000005711 GSP2 YOR185C|CNR2 taxon:4932
+S000001911 GSY1 YFR015C taxon:4932
+S000001911 GSY1 YFR015C taxon:4932
+S000001911 GSY1 YFR015C taxon:4932
+S000001911 GSY1 YFR015C taxon:4932
+S000001911 GSY1 YFR015C taxon:4932
+S000001911 GSY1 YFR015C taxon:4932
+S000004248 GSY2 YLR258W taxon:4932
+S000004248 GSY2 YLR258W taxon:4932
+S000004248 GSY2 YLR258W taxon:4932
+S000004248 GSY2 YLR258W taxon:4932
+S000004248 GSY2 YLR258W taxon:4932
+S000004248 GSY2 YLR258W taxon:4932
+S000004248 GSY2 YLR258W taxon:4932
+S000004248 GSY2 YLR258W taxon:4932
+S000002629 GTB1 YDR221W taxon:4932
+S000002629 GTB1 YDR221W taxon:4932
+S000002629 GTB1 YDR221W taxon:4932
+S000002629 GTB1 YDR221W taxon:4932
+S000002629 GTB1 YDR221W taxon:4932
+S000002629 GTB1 YDR221W taxon:4932
+S000003386 GTO1 YGR154C taxon:4932
+S000003386 GTO1 YGR154C taxon:4932
+S000003386 GTO1 YGR154C taxon:4932
+S000004863 GTO3 YMR251W taxon:4932
+S000004863 GTO3 YMR251W taxon:4932
+S000004863 GTO3 YMR251W taxon:4932
+S000004590 GTR1 YML121W taxon:4932
+S000004590 GTR1 YML121W taxon:4932
+S000004590 GTR1 YML121W taxon:4932
+S000004590 GTR1 YML121W taxon:4932
+S000004590 GTR1 YML121W taxon:4932
+S000004590 GTR1 YML121W taxon:4932
+S000004590 GTR1 YML121W taxon:4932
+S000004590 GTR1 YML121W taxon:4932
+S000004590 GTR1 YML121W taxon:4932
+S000004590 GTR1 YML121W taxon:4932
+S000004590 GTR1 YML121W taxon:4932
+S000003395 GTR2 YGR163W taxon:4932
+S000003395 GTR2 YGR163W taxon:4932
+S000003395 GTR2 YGR163W taxon:4932
+S000003395 GTR2 YGR163W taxon:4932
+S000003395 GTR2 YGR163W taxon:4932
+S000003395 GTR2 YGR163W taxon:4932
+S000003395 GTR2 YGR163W taxon:4932
+S000003149 GTS1 YGL181W|FHT1|LSR1 taxon:4932
+S000003149 GTS1 YGL181W|FHT1|LSR1 taxon:4932
+S000003149 GTS1 YGL181W|FHT1|LSR1 taxon:4932
+S000003149 GTS1 YGL181W|FHT1|LSR1 taxon:4932
+S000003149 GTS1 YGL181W|FHT1|LSR1 taxon:4932
+S000003149 GTS1 YGL181W|FHT1|LSR1 taxon:4932
+S000003149 GTS1 YGL181W|FHT1|LSR1 taxon:4932
+S000003149 GTS1 YGL181W|FHT1|LSR1 taxon:4932
+S000003149 GTS1 YGL181W|FHT1|LSR1 taxon:4932
+S000003149 GTS1 YGL181W|FHT1|LSR1 taxon:4932
+S000003149 GTS1 YGL181W|FHT1|LSR1 taxon:4932
+S000003149 GTS1 YGL181W|FHT1|LSR1 taxon:4932
+S000003149 GTS1 YGL181W|FHT1|LSR1 taxon:4932
+S000001477 GTT1 YIR038C taxon:4932
+S000001477 GTT1 YIR038C taxon:4932
+S000001477 GTT1 YIR038C taxon:4932
+S000001477 GTT1 YIR038C taxon:4932
+S000001477 GTT1 YIR038C taxon:4932
+S000001477 GTT1 YIR038C taxon:4932
+S000003983 GTT2 YLL060C taxon:4932
+S000003983 GTT2 YLL060C taxon:4932
+S000003983 GTT2 YLL060C taxon:4932
+S000003983 GTT2 YLL060C taxon:4932
+S000000743 GTT3 YEL017W taxon:4932
+S000000743 GTT3 YEL017W taxon:4932
+S000000743 GTT3 YEL017W taxon:4932
+S000004830 GUA1 YMR217W taxon:4932
+S000004830 GUA1 YMR217W taxon:4932
+S000004830 GUA1 YMR217W taxon:4932
+S000004830 GUA1 YMR217W taxon:4932
+S000002397 GUD1 YDL238C taxon:4932
+S000002397 GUD1 YDL238C taxon:4932
+S000002397 GUD1 YDL238C taxon:4932
+S000002397 GUD1 YDL238C taxon:4932
+S000004280 GUF1 YLR289W taxon:4932
+S000004280 GUF1 YLR289W taxon:4932
+S000004280 GUF1 YLR289W taxon:4932
+S000004280 GUF1 YLR289W taxon:4932
+S000002862 GUK1 YDR454C|PUR5 taxon:4932
+S000002862 GUK1 YDR454C|PUR5 taxon:4932
+S000002862 GUK1 YDR454C|PUR5 taxon:4932
+S000002862 GUK1 YDR454C|PUR5 taxon:4932
+S000003052 GUP1 YGL084C taxon:4932
+S000003052 GUP1 YGL084C taxon:4932
+S000003052 GUP1 YGL084C taxon:4932
+S000003052 GUP1 YGL084C taxon:4932
+S000003052 GUP1 YGL084C taxon:4932
+S000003052 GUP1 YGL084C taxon:4932
+S000003052 GUP1 YGL084C taxon:4932
+S000003052 GUP1 YGL084C taxon:4932
+S000003052 GUP1 YGL084C taxon:4932
+S000003052 GUP1 YGL084C taxon:4932
+S000006110 GUP2 YPL189W taxon:4932
+S000006110 GUP2 YPL189W taxon:4932
+S000006110 GUP2 YPL189W taxon:4932
+S000003214 GUS1 YGL245W|GSN1|GluRS taxon:4932
+S000003214 GUS1 YGL245W|GSN1|GluRS taxon:4932
+S000003214 GUS1 YGL245W|GSN1|GluRS taxon:4932
+S000003214 GUS1 YGL245W|GSN1|GluRS taxon:4932
+S000001024 GUT1 YHL032C taxon:4932
+S000001024 GUT1 YHL032C taxon:4932
+S000001024 GUT1 YHL032C taxon:4932
+S000001024 GUT1 YHL032C taxon:4932
+S000001417 GUT2 YIL155C taxon:4932
+S000001417 GUT2 YIL155C taxon:4932
+S000001417 GUT2 YIL155C taxon:4932
+S000001417 GUT2 YIL155C taxon:4932
+S000001417 GUT2 YIL155C taxon:4932
+S000001417 GUT2 YIL155C taxon:4932
+S000001417 GUT2 YIL155C taxon:4932
+S000001417 GUT2 YIL155C taxon:4932
+S000001417 GUT2 YIL155C taxon:4932
+S000001303 GVP36 YIL041W taxon:4932
+S000001303 GVP36 YIL041W taxon:4932
+S000001303 GVP36 YIL041W taxon:4932
+S000001303 GVP36 YIL041W taxon:4932
+S000003627 GWT1 YJL091C taxon:4932
+S000003627 GWT1 YJL091C taxon:4932
+S000003627 GWT1 YJL091C taxon:4932
+S000003627 GWT1 YJL091C taxon:4932
+S000004804 GYL1 YMR192W|APP2 taxon:4932
+S000004804 GYL1 YMR192W|APP2 taxon:4932
+S000004804 GYL1 YMR192W|APP2 taxon:4932
+S000004804 GYL1 YMR192W|APP2 taxon:4932
+S000004804 GYL1 YMR192W|APP2 taxon:4932
+S000004804 GYL1 YMR192W|APP2 taxon:4932
+S000004804 GYL1 YMR192W|APP2 taxon:4932
+S000004804 GYL1 YMR192W|APP2 taxon:4932
+S000004804 GYL1 YMR192W|APP2 taxon:4932
+S000004804 GYL1 YMR192W|APP2 taxon:4932
+S000004804 GYL1 YMR192W|APP2 taxon:4932
+S000004804 GYL1 YMR192W|APP2 taxon:4932
+S000004804 GYL1 YMR192W|APP2 taxon:4932
+S000004804 GYL1 YMR192W|APP2 taxon:4932
+S000004804 GYL1 YMR192W|APP2 taxon:4932
+S000005596 GYP1 YOR070C|YOR29-21 taxon:4932
+S000005596 GYP1 YOR070C|YOR29-21 taxon:4932
+S000005596 GYP1 YOR070C|YOR29-21 taxon:4932
+S000005596 GYP1 YOR070C|YOR29-21 taxon:4932
+S000005596 GYP1 YOR070C|YOR29-21 taxon:4932
+S000005596 GYP1 YOR070C|YOR29-21 taxon:4932
+S000005596 GYP1 YOR070C|YOR29-21 taxon:4932
+S000006170 GYP5 YPL249C taxon:4932
+S000006170 GYP5 YPL249C taxon:4932
+S000006170 GYP5 YPL249C taxon:4932
+S000006170 GYP5 YPL249C taxon:4932
+S000006170 GYP5 YPL249C taxon:4932
+S000006170 GYP5 YPL249C taxon:4932
+S000006170 GYP5 YPL249C taxon:4932
+S000006170 GYP5 YPL249C taxon:4932
+S000006170 GYP5 YPL249C taxon:4932
+S000006170 GYP5 YPL249C taxon:4932
+S000006170 GYP5 YPL249C taxon:4932
+S000006170 GYP5 YPL249C taxon:4932
+S000006170 GYP5 YPL249C taxon:4932
+S000006170 GYP5 YPL249C taxon:4932
+S000006170 GYP5 YPL249C taxon:4932
+S000003580 GYP6 YJL044C taxon:4932
+S000003580 GYP6 YJL044C taxon:4932
+S000003580 GYP6 YJL044C taxon:4932
+S000003580 GYP6 YJL044C taxon:4932
+S000002393 GYP7 YDL234C taxon:4932
+S000002393 GYP7 YDL234C taxon:4932
+S000002393 GYP7 YDL234C taxon:4932
+S000002393 GYP7 YDL234C taxon:4932
+S000002393 GYP7 YDL234C taxon:4932
+S000002393 GYP7 YDL234C taxon:4932
+S000001867 GYP8 YFL027C taxon:4932
+S000001867 GYP8 YFL027C taxon:4932
+S000001867 GYP8 YFL027C taxon:4932
+S000001867 GYP8 YFL027C taxon:4932
+S000001867 GYP8 YFL027C taxon:4932
+S000003646 GZF3 YJL110C|DEH1|NIL2 taxon:4932
+S000003646 GZF3 YJL110C|DEH1|NIL2 taxon:4932
+S000003646 GZF3 YJL110C|DEH1|NIL2 taxon:4932
+S000003646 GZF3 YJL110C|DEH1|NIL2 taxon:4932
+S000003646 GZF3 YJL110C|DEH1|NIL2 taxon:4932
+S000003646 GZF3 YJL110C|DEH1|NIL2 taxon:4932
+S000003646 GZF3 YJL110C|DEH1|NIL2 taxon:4932
+S000003646 GZF3 YJL110C|DEH1|NIL2 taxon:4932
+S000003646 GZF3 YJL110C|DEH1|NIL2 taxon:4932
+S000003646 GZF3 YJL110C|DEH1|NIL2 taxon:4932
+S000006212 HAA1 YPR008W taxon:4932
+S000006212 HAA1 YPR008W taxon:4932
+S000006212 HAA1 YPR008W taxon:4932
+S000001863 HAC1 YFL031W|ERN4|IRE15 taxon:4932
+S000001863 HAC1 YFL031W|ERN4|IRE15 taxon:4932
+S000001863 HAC1 YFL031W|ERN4|IRE15 taxon:4932
+S000001863 HAC1 YFL031W|ERN4|IRE15 taxon:4932
+S000001863 HAC1 YFL031W|ERN4|IRE15 taxon:4932
+S000001863 HAC1 YFL031W|ERN4|IRE15 taxon:4932
+S000001863 HAC1 YFL031W|ERN4|IRE15 taxon:4932
+S000006209 HAL1 YPR005C taxon:4932
+S000006209 HAL1 YPR005C taxon:4932
+S000006209 HAL1 YPR005C taxon:4932
+S000006209 HAL1 YPR005C taxon:4932
+S000006209 HAL1 YPR005C taxon:4932
+S000003701 HAL5 YJL165C taxon:4932
+S000003701 HAL5 YJL165C taxon:4932
+S000003701 HAL5 YJL165C taxon:4932
+S000003701 HAL5 YJL165C taxon:4932
+S000005449 HAL9 YOL089C taxon:4932
+S000005449 HAL9 YOL089C taxon:4932
+S000005449 HAL9 YOL089C taxon:4932
+S000005449 HAL9 YOL089C taxon:4932
+S000005449 HAL9 YOL089C taxon:4932
+S000003830 HAM1 YJR069C taxon:4932
+S000003830 HAM1 YJR069C taxon:4932
+S000003830 HAM1 YJR069C taxon:4932
+S000003830 HAM1 YJR069C taxon:4932
+S000004246 HAP1 YLR256W|CYP1 taxon:4932
+S000004246 HAP1 YLR256W|CYP1 taxon:4932
+S000004246 HAP1 YLR256W|CYP1 taxon:4932
+S000004246 HAP1 YLR256W|CYP1 taxon:4932
+S000003206 HAP2 YGL237C taxon:4932
+S000003206 HAP2 YGL237C taxon:4932
+S000003206 HAP2 YGL237C taxon:4932
+S000003206 HAP2 YGL237C taxon:4932
+S000003206 HAP2 YGL237C taxon:4932
+S000000117 HAP3 YBL021C taxon:4932
+S000000117 HAP3 YBL021C taxon:4932
+S000000117 HAP3 YBL021C taxon:4932
+S000000117 HAP3 YBL021C taxon:4932
+S000000117 HAP3 YBL021C taxon:4932
+S000001592 HAP4 YKL109W taxon:4932
+S000001592 HAP4 YKL109W taxon:4932
+S000001592 HAP4 YKL109W taxon:4932
+S000001592 HAP4 YKL109W taxon:4932
+S000005885 HAP5 YOR358W taxon:4932
+S000005885 HAP5 YOR358W taxon:4932
+S000005885 HAP5 YOR358W taxon:4932
+S000005885 HAP5 YOR358W taxon:4932
+S000005885 HAP5 YOR358W taxon:4932
+S000005885 HAP5 YOR358W taxon:4932
+S000004903 HAS1 YMR290C taxon:4932
+S000004903 HAS1 YMR290C taxon:4932
+S000004903 HAS1 YMR290C taxon:4932
+S000004903 HAS1 YMR290C taxon:4932
+S000004903 HAS1 YMR290C taxon:4932
+S000004903 HAS1 YMR290C taxon:4932
+S000004903 HAS1 YMR290C taxon:4932
+S000004903 HAS1 YMR290C taxon:4932
+S000005922 HAT1 YPL001W taxon:4932
+S000005922 HAT1 YPL001W taxon:4932
+S000005922 HAT1 YPL001W taxon:4932
+S000005922 HAT1 YPL001W taxon:4932
+S000005922 HAT1 YPL001W taxon:4932
+S000005922 HAT1 YPL001W taxon:4932
+S000000782 HAT2 YEL056W taxon:4932
+S000000782 HAT2 YEL056W taxon:4932
+S000000782 HAT2 YEL056W taxon:4932
+S000000782 HAT2 YEL056W taxon:4932
+S000000782 HAT2 YEL056W taxon:4932
+S000000782 HAT2 YEL056W taxon:4932
+S000000782 HAT2 YEL056W taxon:4932
+S000001792 HBS1 YKR084C taxon:4932
+S000001792 HBS1 YKR084C taxon:4932
+S000001792 HBS1 YKR084C taxon:4932
+S000001792 HBS1 YKR084C taxon:4932
+S000002382 HBT1 YDL223C taxon:4932
+S000002382 HBT1 YDL223C taxon:4932
+S000002382 HBT1 YDL223C taxon:4932
+S000003570 HCA4 YJL033W|DBP4|ECM24 taxon:4932
+S000003570 HCA4 YJL033W|DBP4|ECM24 taxon:4932
+S000003570 HCA4 YJL033W|DBP4|ECM24 taxon:4932
+S000005225 HCH1 YNL281W taxon:4932
+S000005225 HCH1 YNL281W taxon:4932
+S000005225 HCH1 YNL281W taxon:4932
+S000005225 HCH1 YNL281W taxon:4932
+S000005225 HCH1 YNL281W taxon:4932
+S000005225 HCH1 YNL281W taxon:4932
+S000005225 HCH1 YNL281W taxon:4932
+S000005225 HCH1 YNL281W taxon:4932
+S000005225 HCH1 YNL281W taxon:4932
+S000005225 HCH1 YNL281W taxon:4932
+S000005225 HCH1 YNL281W taxon:4932
+S000000661 HCM1 YCR065W taxon:4932
+S000000661 HCM1 YCR065W taxon:4932
+S000000661 HCM1 YCR065W taxon:4932
+S000000661 HCM1 YCR065W taxon:4932
+S000000661 HCM1 YCR065W taxon:4932
+S000000661 HCM1 YCR065W taxon:4932
+S000004182 HCR1 YLR192C taxon:4932
+S000004182 HCR1 YLR192C taxon:4932
+S000004182 HCR1 YLR192C taxon:4932
+S000004182 HCR1 YLR192C taxon:4932
+S000004182 HCR1 YLR192C taxon:4932
+S000004182 HCR1 YLR192C taxon:4932
+S000004182 HCR1 YLR192C taxon:4932
+S000001500 HCS1 YKL017C|DIP1 taxon:4932
+S000001500 HCS1 YKL017C|DIP1 taxon:4932
+S000001500 HCS1 YKL017C|DIP1 taxon:4932
+S000004966 HDA1 YNL021W taxon:4932
+S000004966 HDA1 YNL021W taxon:4932
+S000004966 HDA1 YNL021W taxon:4932
+S000004966 HDA1 YNL021W taxon:4932
+S000004966 HDA1 YNL021W taxon:4932
+S000004966 HDA1 YNL021W taxon:4932
+S000004966 HDA1 YNL021W taxon:4932
+S000004966 HDA1 YNL021W taxon:4932
+S000004966 HDA1 YNL021W taxon:4932
+S000004966 HDA1 YNL021W taxon:4932
+S000004966 HDA1 YNL021W taxon:4932
+S000002703 HDA2 YDR295C|PLO2 taxon:4932
+S000002703 HDA2 YDR295C|PLO2 taxon:4932
+S000002703 HDA2 YDR295C|PLO2 taxon:4932
+S000002703 HDA2 YDR295C|PLO2 taxon:4932
+S000002703 HDA2 YDR295C|PLO2 taxon:4932
+S000002703 HDA2 YDR295C|PLO2 taxon:4932
+S000002703 HDA2 YDR295C|PLO2 taxon:4932
+S000006383 HDA3 YPR179C|PLO1 taxon:4932
+S000006383 HDA3 YPR179C|PLO1 taxon:4932
+S000006383 HDA3 YPR179C|PLO1 taxon:4932
+S000006383 HDA3 YPR179C|PLO1 taxon:4932
+S000006383 HDA3 YPR179C|PLO1 taxon:4932
+S000006383 HDA3 YPR179C|PLO1 taxon:4932
+S000006383 HDA3 YPR179C|PLO1 taxon:4932
+S000006383 HDA3 YPR179C|PLO1 taxon:4932
+S000113613 HED1 YDR014W-A taxon:4932
+S000113613 HED1 YDR014W-A taxon:4932
+S000113613 HED1 YDR014W-A taxon:4932
+S000004959 HEF3 YNL014W|EF-3|ZRG7 taxon:4932
+S000004959 HEF3 YNL014W|EF-3|ZRG7 taxon:4932
+S000004959 HEF3 YNL014W|EF-3|ZRG7 taxon:4932
+S000004959 HEF3 YNL014W|EF-3|ZRG7 taxon:4932
+S000004959 HEF3 YNL014W|EF-3|ZRG7 taxon:4932
+S000000128 HEK2 YBL032W|KHD1 taxon:4932
+S000000128 HEK2 YBL032W|KHD1 taxon:4932
+S000000128 HEK2 YBL032W|KHD1 taxon:4932
+S000000128 HEK2 YBL032W|KHD1 taxon:4932
+S000000128 HEK2 YBL032W|KHD1 taxon:4932
+S000000128 HEK2 YBL032W|KHD1 taxon:4932
+S000000128 HEK2 YBL032W|KHD1 taxon:4932
+S000002640 HEM1 YDR232W|CYD1 taxon:4932
+S000002640 HEM1 YDR232W|CYD1 taxon:4932
+S000002640 HEM1 YDR232W|CYD1 taxon:4932
+S000002454 HEM12 YDR047W|HEM6 taxon:4932
+S000002454 HEM12 YDR047W|HEM6 taxon:4932
+S000002454 HEM12 YDR047W|HEM6 taxon:4932
+S000002454 HEM12 YDR047W|HEM6 taxon:4932
+S000002454 HEM12 YDR047W|HEM6 taxon:4932
+S000002451 HEM13 YDR044W taxon:4932
+S000002451 HEM13 YDR044W taxon:4932
+S000002451 HEM13 YDR044W taxon:4932
+S000002451 HEM13 YDR044W taxon:4932
+S000000816 HEM14 YER014W taxon:4932
+S000000816 HEM14 YER014W taxon:4932
+S000000816 HEM14 YER014W taxon:4932
+S000000816 HEM14 YER014W taxon:4932
+S000000816 HEM14 YER014W taxon:4932
+S000005702 HEM15 YOR176W taxon:4932
+S000005702 HEM15 YOR176W taxon:4932
+S000005702 HEM15 YOR176W taxon:4932
+S000005702 HEM15 YOR176W taxon:4932
+S000005702 HEM15 YOR176W taxon:4932
+S000003008 HEM2 YGL040C|SLU1 taxon:4932
+S000003008 HEM2 YGL040C|SLU1 taxon:4932
+S000003008 HEM2 YGL040C|SLU1 taxon:4932
+S000003008 HEM2 YGL040C|SLU1 taxon:4932
+S000002364 HEM3 YDL205C taxon:4932
+S000002364 HEM3 YDL205C taxon:4932
+S000002364 HEM3 YDL205C taxon:4932
+S000002364 HEM3 YDL205C taxon:4932
+S000002364 HEM3 YDL205C taxon:4932
+S000002364 HEM3 YDL205C taxon:4932
+S000002364 HEM3 YDL205C taxon:4932
+S000005804 HEM4 YOR278W|SLU2 taxon:4932
+S000005804 HEM4 YOR278W|SLU2 taxon:4932
+S000005804 HEM4 YOR278W|SLU2 taxon:4932
+S000005804 HEM4 YOR278W|SLU2 taxon:4932
+S000005763 HES1 YOR237W|OSH5 taxon:4932
+S000005763 HES1 YOR237W|OSH5 taxon:4932
+S000005763 HES1 YOR237W|OSH5 taxon:4932
+S000005763 HES1 YOR237W|OSH5 taxon:4932
+S000002171 HEX3 YDL013W|SLX5 taxon:4932
+S000002171 HEX3 YDL013W|SLX5 taxon:4932
+S000002171 HEX3 YDL013W|SLX5 taxon:4932
+S000002171 HEX3 YDL013W|SLX5 taxon:4932
+S000002171 HEX3 YDL013W|SLX5 taxon:4932
+S000002171 HEX3 YDL013W|SLX5 taxon:4932
+S000004820 HFA1 YMR207C taxon:4932
+S000004820 HFA1 YMR207C taxon:4932
+S000004820 HFA1 YMR207C taxon:4932
+S000004820 HFA1 YMR207C taxon:4932
+S000004820 HFA1 YMR207C taxon:4932
+S000004820 HFA1 YMR207C taxon:4932
+S000004716 HFD1 YMR110C taxon:4932
+S000004716 HFD1 YMR110C taxon:4932
+S000004716 HFD1 YMR110C taxon:4932
+S000004716 HFD1 YMR110C taxon:4932
+S000004716 HFD1 YMR110C taxon:4932
+S000004716 HFD1 YMR110C taxon:4932
+S000004716 HFD1 YMR110C taxon:4932
+S000006175 HFI1 YPL254W|ADA1|GAN1|SRM12|SUP110 taxon:4932
+S000006175 HFI1 YPL254W|ADA1|GAN1|SRM12|SUP110 taxon:4932
+S000006175 HFI1 YPL254W|ADA1|GAN1|SRM12|SUP110 taxon:4932
+S000006175 HFI1 YPL254W|ADA1|GAN1|SRM12|SUP110 taxon:4932
+S000006175 HFI1 YPL254W|ADA1|GAN1|SRM12|SUP110 taxon:4932
+S000006175 HFI1 YPL254W|ADA1|GAN1|SRM12|SUP110 taxon:4932
+S000006175 HFI1 YPL254W|ADA1|GAN1|SRM12|SUP110 taxon:4932
+S000006175 HFI1 YPL254W|ADA1|GAN1|SRM12|SUP110 taxon:4932
+S000006175 HFI1 YPL254W|ADA1|GAN1|SRM12|SUP110 taxon:4932
+S000006175 HFI1 YPL254W|ADA1|GAN1|SRM12|SUP110 taxon:4932
+S000003220 HFM1 YGL251C|MER3 taxon:4932
+S000003220 HFM1 YGL251C|MER3 taxon:4932
+S000003220 HFM1 YGL251C|MER3 taxon:4932
+S000003220 HFM1 YGL251C|MER3 taxon:4932
+S000003220 HFM1 YGL251C|MER3 taxon:4932
+S000003220 HFM1 YGL251C|MER3 taxon:4932
+S000003419 HGH1 YGR187C taxon:4932
+S000003419 HGH1 YGR187C taxon:4932
+S000003419 HGH1 YGR187C taxon:4932
+S000000213 HHF1 YBR009C taxon:4932
+S000000213 HHF1 YBR009C taxon:4932
+S000000213 HHF1 YBR009C taxon:4932
+S000004975 HHF2 YNL030W taxon:4932
+S000004975 HHF2 YNL030W taxon:4932
+S000004975 HHF2 YNL030W taxon:4932
+S000006048 HHO1 YPL127C taxon:4932
+S000006048 HHO1 YPL127C taxon:4932
+S000006048 HHO1 YPL127C taxon:4932
+S000006048 HHO1 YPL127C taxon:4932
+S000006048 HHO1 YPL127C taxon:4932
+S000006048 HHO1 YPL127C taxon:4932
+S000006048 HHO1 YPL127C taxon:4932
+S000000214 HHT1 YBR010W|BUR5|SIN2 taxon:4932
+S000000214 HHT1 YBR010W|BUR5|SIN2 taxon:4932
+S000000214 HHT1 YBR010W|BUR5|SIN2 taxon:4932
+S000000214 HHT1 YBR010W|BUR5|SIN2 taxon:4932
+S000004976 HHT2 YNL031C taxon:4932
+S000004976 HHT2 YNL031C taxon:4932
+S000004976 HHT2 YNL031C taxon:4932
+S000003945 HIF1 YLL022C taxon:4932
+S000003945 HIF1 YLL022C taxon:4932
+S000003945 HIF1 YLL022C taxon:4932
+S000003945 HIF1 YLL022C taxon:4932
+S000003945 HIF1 YLL022C taxon:4932
+S000002725 HIM1 YDR317W taxon:4932
+S000002725 HIM1 YDR317W taxon:4932
+S000002725 HIM1 YDR317W taxon:4932
+S000003423 HIP1 YGR191W taxon:4932
+S000003423 HIP1 YGR191W taxon:4932
+S000003423 HIP1 YGR191W taxon:4932
+S000003423 HIP1 YGR191W taxon:4932
+S000003423 HIP1 YGR191W taxon:4932
+S000003423 HIP1 YGR191W taxon:4932
+S000000104 HIR1 YBL008W taxon:4932
+S000000104 HIR1 YBL008W taxon:4932
+S000000104 HIR1 YBL008W taxon:4932
+S000000104 HIR1 YBL008W taxon:4932
+S000005564 HIR2 YOR038C|SPT1 taxon:4932
+S000005564 HIR2 YOR038C|SPT1 taxon:4932
+S000005564 HIR2 YOR038C|SPT1 taxon:4932
+S000003901 HIR3 YJR140C|HPC1 taxon:4932
+S000003901 HIR3 YJR140C|HPC1 taxon:4932
+S000003901 HIR3 YJR140C|HPC1 taxon:4932
+S000029211 HIR4 taxon:4932
+S000029211 HIR4 taxon:4932
+S000029211 HIR4 taxon:4932
+S000000857 HIS1 YER055C taxon:4932
+S000000857 HIS1 YER055C taxon:4932
+S000000857 HIS1 YER055C taxon:4932
+S000001921 HIS2 YFR025C taxon:4932
+S000001921 HIS2 YFR025C taxon:4932
+S000001921 HIS2 YFR025C taxon:4932
+S000005728 HIS3 YOR202W|HIS10 taxon:4932
+S000005728 HIS3 YOR202W|HIS10 taxon:4932
+S000005728 HIS3 YOR202W|HIS10 taxon:4932
+S000000535 HIS4 YCL030C taxon:4932
+S000000535 HIS4 YCL030C taxon:4932
+S000000535 HIS4 YCL030C taxon:4932
+S000000535 HIS4 YCL030C taxon:4932
+S000000535 HIS4 YCL030C taxon:4932
+S000001378 HIS5 YIL116W taxon:4932
+S000001378 HIS5 YIL116W taxon:4932
+S000001378 HIS5 YIL116W taxon:4932
+S000001282 HIS6 YIL020C taxon:4932
+S000001282 HIS6 YIL020C taxon:4932
+S000001282 HIS6 YIL020C taxon:4932
+S000000452 HIS7 YBR248C taxon:4932
+S000000452 HIS7 YBR248C taxon:4932
+S000000452 HIS7 YBR248C taxon:4932
+S000000452 HIS7 YBR248C taxon:4932
+S000000452 HIS7 YBR248C taxon:4932
+S000003816 HIT1 YJR055W taxon:4932
+S000003816 HIT1 YJR055W taxon:4932
+S000003816 HIT1 YJR055W taxon:4932
+S000003816 HIT1 YJR055W taxon:4932
+S000002828 HKR1 YDR420W taxon:4932
+S000002828 HKR1 YDR420W taxon:4932
+S000002828 HKR1 YDR420W taxon:4932
+S000002828 HKR1 YDR420W taxon:4932
+S000002828 HKR1 YDR420W taxon:4932
+S000002828 HKR1 YDR420W taxon:4932
+S000004771 HLJ1 YMR161W taxon:4932
+S000004771 HLJ1 YMR161W taxon:4932
+S000004771 HLJ1 YMR161W taxon:4932
+S000004771 HLJ1 YMR161W taxon:4932
+S000004771 HLJ1 YMR161W taxon:4932
+S000004771 HLJ1 YMR161W taxon:4932
+S000004771 HLJ1 YMR161W taxon:4932
+S000004771 HLJ1 YMR161W taxon:4932
+S000004771 HLJ1 YMR161W taxon:4932
+S000002936 HLR1 YDR528W taxon:4932
+S000002936 HLR1 YDR528W taxon:4932
+S000002936 HLR1 YDR528W taxon:4932
+S000000859 HMF1 YER057C|HIG1 taxon:4932
+S000000859 HMF1 YER057C|HIG1 taxon:4932
+S000000859 HMF1 YER057C|HIG1 taxon:4932
+S000000859 HMF1 YER057C|HIG1 taxon:4932
+S000000859 HMF1 YER057C|HIG1 taxon:4932
+S000004540 HMG1 YML075C taxon:4932
+S000004540 HMG1 YML075C taxon:4932
+S000004540 HMG1 YML075C taxon:4932
+S000004540 HMG1 YML075C taxon:4932
+S000004540 HMG1 YML075C taxon:4932
+S000004442 HMG2 YLR450W taxon:4932
+S000004442 HMG2 YLR450W taxon:4932
+S000004442 HMG2 YLR450W taxon:4932
+S000004442 HMG2 YLR450W taxon:4932
+S000004442 HMG2 YLR450W taxon:4932
+S000005455 HMI1 YOL095C taxon:4932
+S000005455 HMI1 YOL095C taxon:4932
+S000005455 HMI1 YOL095C taxon:4932
+S000000571 HMLALPHA1 YCL066W|ALPHA1 taxon:4932
+S000000571 HMLALPHA1 YCL066W|ALPHA1 taxon:4932
+S000000571 HMLALPHA1 YCL066W|ALPHA1 taxon:4932
+S000000571 HMLALPHA1 YCL066W|ALPHA1 taxon:4932
+S000000572 HMLALPHA2 YCL067C|ALPHA2 taxon:4932
+S000000572 HMLALPHA2 YCL067C|ALPHA2 taxon:4932
+S000000572 HMLALPHA2 YCL067C|ALPHA2 taxon:4932
+S000000572 HMLALPHA2 YCL067C|ALPHA2 taxon:4932
+S000000572 HMLALPHA2 YCL067C|ALPHA2 taxon:4932
+S000002581 HMO1 YDR174W|HSM2 taxon:4932
+S000002581 HMO1 YDR174W|HSM2 taxon:4932
+S000002581 HMO1 YDR174W|HSM2 taxon:4932
+S000002581 HMO1 YDR174W|HSM2 taxon:4932
+S000002581 HMO1 YDR174W|HSM2 taxon:4932
+S000002581 HMO1 YDR174W|HSM2 taxon:4932
+S000002581 HMO1 YDR174W|HSM2 taxon:4932
+S000000694 HMRA1 YCR097W|YCR097WB taxon:4932
+S000000694 HMRA1 YCR097W|YCR097WB taxon:4932
+S000000694 HMRA1 YCR097W|YCR097WB taxon:4932
+S000000692 HMRA2 YCR096C|A2 taxon:4932
+S000000692 HMRA2 YCR096C|A2 taxon:4932
+S000000692 HMRA2 YCR096C|A2 taxon:4932
+S000005558 HMS1 YOR032C taxon:4932
+S000005558 HMS1 YOR032C taxon:4932
+S000005558 HMS1 YOR032C taxon:4932
+S000003908 HMS2 YJR147W taxon:4932
+S000003908 HMS2 YJR147W taxon:4932
+S000003908 HMS2 YJR147W taxon:4932
+S000003908 HMS2 YJR147W taxon:4932
+S000000238 HMT1 YBR034C|HCP1|ODP1|RMT1 taxon:4932
+S000000238 HMT1 YBR034C|HCP1|ODP1|RMT1 taxon:4932
+S000000238 HMT1 YBR034C|HCP1|ODP1|RMT1 taxon:4932
+S000000238 HMT1 YBR034C|HCP1|ODP1|RMT1 taxon:4932
+S000000238 HMT1 YBR034C|HCP1|ODP1|RMT1 taxon:4932
+S000000238 HMT1 YBR034C|HCP1|ODP1|RMT1 taxon:4932
+S000000238 HMT1 YBR034C|HCP1|ODP1|RMT1 taxon:4932
+S000000238 HMT1 YBR034C|HCP1|ODP1|RMT1 taxon:4932
+S000004195 HMX1 YLR205C taxon:4932
+S000004195 HMX1 YLR205C taxon:4932
+S000004195 HMX1 YLR205C taxon:4932
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+S000000994 HSE1 YHL002W taxon:4932
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+S000003041 HSF1 YGL073W|EXA3|MAS3 taxon:4932
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+S000004901 HSH155 YMR288W taxon:4932
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+S000005846 HSH49 YOR319W taxon:4932
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+S000001584 HSL1 YKL101W|NIK1 taxon:4932
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+S000001584 HSL1 YKL101W|NIK1 taxon:4932
+S000001584 HSL1 YKL101W|NIK1 taxon:4932
+S000001584 HSL1 YKL101W|NIK1 taxon:4932
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+S000001584 HSL1 YKL101W|NIK1 taxon:4932
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+S000001584 HSL1 YKL101W|NIK1 taxon:4932
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+S000000337 HSL7 YBR133C taxon:4932
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+S000000337 HSL7 YBR133C taxon:4932
+S000000337 HSL7 YBR133C taxon:4932
+S000000337 HSL7 YBR133C taxon:4932
+S000000337 HSL7 YBR133C taxon:4932
+S000000337 HSL7 YBR133C taxon:4932
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+S000000337 HSL7 YBR133C taxon:4932
+S000000337 HSL7 YBR133C taxon:4932
+S000000476 HSM3 YBR272C taxon:4932
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+S000000476 HSM3 YBR272C taxon:4932
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+S000003949 HSP104 YLL026W taxon:4932
+S000003949 HSP104 YLL026W taxon:4932
+S000003949 HSP104 YLL026W taxon:4932
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+S000003949 HSP104 YLL026W taxon:4932
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+S000000276 HSP26 YBR072W taxon:4932
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+S000002941 HSP31 YDR533C taxon:4932
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+S000002578 HSP42 YDR171W taxon:4932
+S000002578 HSP42 YDR171W taxon:4932
+S000002578 HSP42 YDR171W taxon:4932
+S000002578 HSP42 YDR171W taxon:4932
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+S000004249 HSP60 YLR259C|CPN60|MIF4 taxon:4932
+S000004249 HSP60 YLR259C|CPN60|MIF4 taxon:4932
+S000004249 HSP60 YLR259C|CPN60|MIF4 taxon:4932
+S000004249 HSP60 YLR259C|CPN60|MIF4 taxon:4932
+S000004249 HSP60 YLR259C|CPN60|MIF4 taxon:4932
+S000004249 HSP60 YLR259C|CPN60|MIF4 taxon:4932
+S000002666 HSP78 YDR258C taxon:4932
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+S000002984 KAP122 YGL016W|PDR6 taxon:4932
+S000000912 KAP123 YER110C|YRB4 taxon:4932
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+S000004339 KAP95 YLR347C|RSL1 taxon:4932
+S000004339 KAP95 YLR347C|RSL1 taxon:4932
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+S000003571 KAR2 YJL034W|BIP|GRP78 taxon:4932
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+S000006345 KAR3 YPR141C|OSR11 taxon:4932
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+S000004669 KAR5 YMR065W|FIG3 taxon:4932
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+S000001201 KEL1 YHR158C taxon:4932
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+S000001201 KEL1 YHR158C taxon:4932
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+S000003141 KEM1 YGL173C|DST2|RAR5|SEP1|SKI1|XRN1 taxon:4932
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+S000006066 KES1 YPL145C|LPI3|OSH4 taxon:4932
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+S000005182 KEX2 YNL238W|QDS1|SRB1|VMA45|kexin|yscF taxon:4932
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+S000001387 KGD1 YIL125W|OGD1 taxon:4932
+S000001387 KGD1 YIL125W|OGD1 taxon:4932
+S000001387 KGD1 YIL125W|OGD1 taxon:4932
+S000001387 KGD1 YIL125W|OGD1 taxon:4932
+S000001387 KGD1 YIL125W|OGD1 taxon:4932
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+S000001144 KIC1 YHR102W|NRK1 taxon:4932
+S000001144 KIC1 YHR102W|NRK1 taxon:4932
+S000001144 KIC1 YHR102W|NRK1 taxon:4932
+S000001144 KIC1 YHR102W|NRK1 taxon:4932
+S000001144 KIC1 YHR102W|NRK1 taxon:4932
+S000001144 KIC1 YHR102W|NRK1 taxon:4932
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+S000001144 KIC1 YHR102W|NRK1 taxon:4932
+S000001144 KIC1 YHR102W|NRK1 taxon:4932
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+S000002266 KIN28 YDL108W taxon:4932
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+S000001491 LAC1 YKL008C|DGT1 taxon:4932
+S000001491 LAC1 YKL008C|DGT1 taxon:4932
+S000001491 LAC1 YKL008C|DGT1 taxon:4932
+S000001491 LAC1 YKL008C|DGT1 taxon:4932
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+S000001491 LAC1 YKL008C|DGT1 taxon:4932
+S000001491 LAC1 YKL008C|DGT1 taxon:4932
+S000000995 LAG1 YHL003C taxon:4932
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+S000000995 LAG1 YHL003C taxon:4932
+S000000995 LAG1 YHL003C taxon:4932
+S000000995 LAG1 YHL003C taxon:4932
+S000000995 LAG1 YHL003C taxon:4932
+S000000995 LAG1 YHL003C taxon:4932
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+S000005385 LAG2 YOL025W|ECM36 taxon:4932
+S000005385 LAG2 YOL025W|ECM36 taxon:4932
+S000005385 LAG2 YOL025W|ECM36 taxon:4932
+S000005183 LAP3 YNL239W|BLH1|GAL6|YCP1 taxon:4932
+S000005183 LAP3 YNL239W|BLH1|GAL6|YCP1 taxon:4932
+S000005183 LAP3 YNL239W|BLH1|GAL6|YCP1 taxon:4932
+S000005183 LAP3 YNL239W|BLH1|GAL6|YCP1 taxon:4932
+S000005183 LAP3 YNL239W|BLH1|GAL6|YCP1 taxon:4932
+S000005183 LAP3 YNL239W|BLH1|GAL6|YCP1 taxon:4932
+S000005183 LAP3 YNL239W|BLH1|GAL6|YCP1 taxon:4932
+S000005183 LAP3 YNL239W|BLH1|GAL6|YCP1 taxon:4932
+S000001586 LAP4 YKL103C|APE1|API|YSC1 taxon:4932
+S000001586 LAP4 YKL103C|APE1|API|YSC1 taxon:4932
+S000001586 LAP4 YKL103C|APE1|API|YSC1 taxon:4932
+S000001586 LAP4 YKL103C|APE1|API|YSC1 taxon:4932
+S000001771 LAS1 YKR063C taxon:4932
+S000001771 LAS1 YKR063C taxon:4932
+S000001771 LAS1 YKR063C taxon:4932
+S000001771 LAS1 YKR063C taxon:4932
+S000001771 LAS1 YKR063C taxon:4932
+S000005707 LAS17 YOR181W|BEE1 taxon:4932
+S000005707 LAS17 YOR181W|BEE1 taxon:4932
+S000005707 LAS17 YOR181W|BEE1 taxon:4932
+S000005707 LAS17 YOR181W|BEE1 taxon:4932
+S000005707 LAS17 YOR181W|BEE1 taxon:4932
+S000005707 LAS17 YOR181W|BEE1 taxon:4932
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+S000005707 LAS17 YOR181W|BEE1 taxon:4932
+S000005707 LAS17 YOR181W|BEE1 taxon:4932
+S000005707 LAS17 YOR181W|BEE1 taxon:4932
+S000003598 LAS21 YJL062W|GPI7 taxon:4932
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+S000003598 LAS21 YJL062W|GPI7 taxon:4932
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+S000005015 LAT1 YNL071W|ODP2|PDA2 taxon:4932
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+S000005015 LAT1 YNL071W|ODP2|PDA2 taxon:4932
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+S000004911 LCB1 YMR296C|END8|TSC2 taxon:4932
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+S000005697 LCB4 YOR171C taxon:4932
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+S000005697 LCB4 YOR171C taxon:4932
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+S000004250 LCB5 YLR260W taxon:4932
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+S000004250 LCB5 YLR260W taxon:4932
+S000002907 LCD1 YDR499W|DDC2|PIE1 taxon:4932
+S000002907 LCD1 YDR499W|DDC2|PIE1 taxon:4932
+S000002907 LCD1 YDR499W|DDC2|PIE1 taxon:4932
+S000002907 LCD1 YDR499W|DDC2|PIE1 taxon:4932
+S000002907 LCD1 YDR499W|DDC2|PIE1 taxon:4932
+S000002907 LCD1 YDR499W|DDC2|PIE1 taxon:4932
+S000002907 LCD1 YDR499W|DDC2|PIE1 taxon:4932
+S000002907 LCD1 YDR499W|DDC2|PIE1 taxon:4932
+S000000929 LCP5 YER127W taxon:4932
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+S000000511 LDB16 YCL005W taxon:4932
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+S000002305 LDB17 YDL146W taxon:4932
+S000002305 LDB17 YDL146W taxon:4932
+S000002305 LDB17 YDL146W taxon:4932
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+S000000102 LDB7 YBL006C|RSC14 taxon:4932
+S000000102 LDB7 YBL006C|RSC14 taxon:4932
+S000000102 LDB7 YBL006C|RSC14 taxon:4932
+S000000102 LDB7 YBL006C|RSC14 taxon:4932
+S000000102 LDB7 YBL006C|RSC14 taxon:4932
+S000000102 LDB7 YBL006C|RSC14 taxon:4932
+S000006134 LEA1 YPL213W taxon:4932
+S000006134 LEA1 YPL213W taxon:4932
+S000006134 LEA1 YPL213W taxon:4932
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+S000005975 LEE1 YPL054W taxon:4932
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+S000005267 LEM3 YNL323W|BRE3|ROS3 taxon:4932
+S000005267 LEM3 YNL323W|BRE3|ROS3 taxon:4932
+S000005267 LEM3 YNL323W|BRE3|ROS3 taxon:4932
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+S000005267 LEM3 YNL323W|BRE3|ROS3 taxon:4932
+S000005267 LEM3 YNL323W|BRE3|ROS3 taxon:4932
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+S000005649 LEO1 YOR123C taxon:4932
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+S000005649 LEO1 YOR123C taxon:4932
+S000005649 LEO1 YOR123C taxon:4932
+S000005649 LEO1 YOR123C taxon:4932
+S000005649 LEO1 YOR123C taxon:4932
+S000005649 LEO1 YOR123C taxon:4932
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+S000002977 LEU1 YGL009C taxon:4932
+S000002977 LEU1 YGL009C taxon:4932
+S000002977 LEU1 YGL009C taxon:4932
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+S000000523 LEU2 YCL018W taxon:4932
+S000000523 LEU2 YCL018W taxon:4932
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+S000004443 LEU3 YLR451W taxon:4932
+S000004443 LEU3 YLR451W taxon:4932
+S000004443 LEU3 YLR451W taxon:4932
+S000005048 LEU4 YNL104C taxon:4932
+S000005048 LEU4 YNL104C taxon:4932
+S000005048 LEU4 YNL104C taxon:4932
+S000005048 LEU4 YNL104C taxon:4932
+S000005048 LEU4 YNL104C taxon:4932
+S000005048 LEU4 YNL104C taxon:4932
+S000005048 LEU4 YNL104C taxon:4932
+S000001044 LEU5 YHR002W taxon:4932
+S000001044 LEU5 YHR002W taxon:4932
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+S000029256 LEU7 taxon:4932
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+S000005634 LEU9 YOR108W taxon:4932
+S000005634 LEU9 YOR108W taxon:4932
+S000005634 LEU9 YOR108W taxon:4932
+S000005634 LEU9 YOR108W taxon:4932
+S000005976 LGE1 YPL055C taxon:4932
+S000005976 LGE1 YPL055C taxon:4932
+S000005976 LGE1 YPL055C taxon:4932
+S000005976 LGE1 YPL055C taxon:4932
+S000005976 LGE1 YPL055C taxon:4932
+S000005976 LGE1 YPL055C taxon:4932
+S000005976 LGE1 YPL055C taxon:4932
+S000005976 LGE1 YPL055C taxon:4932
+S000002209 LHP1 YDL051W|LAH1|La protein|YLA1 taxon:4932
+S000002209 LHP1 YDL051W|LAH1|La protein|YLA1 taxon:4932
+S000002209 LHP1 YDL051W|LAH1|La protein|YLA1 taxon:4932
+S000002209 LHP1 YDL051W|LAH1|La protein|YLA1 taxon:4932
+S000002209 LHP1 YDL051W|LAH1|La protein|YLA1 taxon:4932
+S000001556 LHS1 YKL073W|CER1|SSI1 taxon:4932
+S000001556 LHS1 YKL073W|CER1|SSI1 taxon:4932
+S000001556 LHS1 YKL073W|CER1|SSI1 taxon:4932
+S000001556 LHS1 YKL073W|CER1|SSI1 taxon:4932
+S000001556 LHS1 YKL073W|CER1|SSI1 taxon:4932
+S000001556 LHS1 YKL073W|CER1|SSI1 taxon:4932
+S000001556 LHS1 YKL073W|CER1|SSI1 taxon:4932
+S000001556 LHS1 YKL073W|CER1|SSI1 taxon:4932
+S000001556 LHS1 YKL073W|CER1|SSI1 taxon:4932
+S000001556 LHS1 YKL073W|CER1|SSI1 taxon:4932
+S000001556 LHS1 YKL073W|CER1|SSI1 taxon:4932
+S000001556 LHS1 YKL073W|CER1|SSI1 taxon:4932
+S000001556 LHS1 YKL073W|CER1|SSI1 taxon:4932
+S000001556 LHS1 YKL073W|CER1|SSI1 taxon:4932
+S000001556 LHS1 YKL073W|CER1|SSI1 taxon:4932
+S000001556 LHS1 YKL073W|CER1|SSI1 taxon:4932
+S000001556 LHS1 YKL073W|CER1|SSI1 taxon:4932
+S000001556 LHS1 YKL073W|CER1|SSI1 taxon:4932
+S000003831 LIA1 YJR070C|MMD1 taxon:4932
+S000003831 LIA1 YJR070C|MMD1 taxon:4932
+S000003831 LIA1 YJR070C|MMD1 taxon:4932
+S000003831 LIA1 YJR070C|MMD1 taxon:4932
+S000003831 LIA1 YJR070C|MMD1 taxon:4932
+S000003831 LIA1 YJR070C|MMD1 taxon:4932
+S000003831 LIA1 YJR070C|MMD1 taxon:4932
+S000003831 LIA1 YJR070C|MMD1 taxon:4932
+S000003831 LIA1 YJR070C|MMD1 taxon:4932
+S000003058 LIF1 YGL090W taxon:4932
+S000003058 LIF1 YGL090W taxon:4932
+S000003058 LIF1 YGL090W taxon:4932
+S000003058 LIF1 YGL090W taxon:4932
+S000001199 LIN1 YHR156C|SNU40 taxon:4932
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+S000004913 LIP1 YMR298W taxon:4932
+S000004913 LIP1 YMR298W taxon:4932
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+S000004913 LIP1 YMR298W taxon:4932
+S000004913 LIP1 YMR298W taxon:4932
+S000004913 LIP1 YMR298W taxon:4932
+S000004913 LIP1 YMR298W taxon:4932
+S000004229 LIP2 YLR239C taxon:4932
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+S000004229 LIP2 YLR239C taxon:4932
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+S000004229 LIP2 YLR239C taxon:4932
+S000004229 LIP2 YLR239C taxon:4932
+S000005722 LIP5 YOR196C taxon:4932
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+S000005722 LIP5 YOR196C taxon:4932
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+S000001897 LOC1 YFR001W taxon:4932
+S000001897 LOC1 YFR001W taxon:4932
+S000001897 LOC1 YFR001W taxon:4932
+S000001897 LOC1 YFR001W taxon:4932
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+S000001897 LOC1 YFR001W taxon:4932
+S000001688 LOS1 YKL205W taxon:4932
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+S000001666 LOT5 YKL183W taxon:4932
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+S000004001 LOT6 YLR011W taxon:4932
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+S000001876 LPD1 YFL018C|HPD1 taxon:4932
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+S000001876 LPD1 YFL018C|HPD1 taxon:4932
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+S000001876 LPD1 YFL018C|HPD1 taxon:4932
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+S000005981 LPE10 YPL060W taxon:4932
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+S000005981 LPE10 YPL060W taxon:4932
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+S000005981 LPE10 YPL060W taxon:4932
+S000005981 LPE10 YPL060W taxon:4932
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+S000002911 LPP1 YDR503C taxon:4932
+S000002911 LPP1 YDR503C taxon:4932
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+S000000556 LRE1 YCL051W taxon:4932
+S000000556 LRE1 YCL051W taxon:4932
+S000000556 LRE1 YCL051W taxon:4932
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+S000002399 LRG1 YDL240W taxon:4932
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+S000005291 LRO1 YNR008W taxon:4932
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+S000005291 LRO1 YNR008W taxon:4932
+S000005291 LRO1 YNR008W taxon:4932
+S000005291 LRO1 YNR008W taxon:4932
+S000001123 LRP1 YHR081W|RRP47|YC1D taxon:4932
+S000001123 LRP1 YHR081W|RRP47|YC1D taxon:4932
+S000001123 LRP1 YHR081W|RRP47|YC1D taxon:4932
+S000001123 LRP1 YHR081W|RRP47|YC1D taxon:4932
+S000001123 LRP1 YHR081W|RRP47|YC1D taxon:4932
+S000001123 LRP1 YHR081W|RRP47|YC1D taxon:4932
+S000001123 LRP1 YHR081W|RRP47|YC1D taxon:4932
+S000001123 LRP1 YHR081W|RRP47|YC1D taxon:4932
+S000001123 LRP1 YHR081W|RRP47|YC1D taxon:4932
+S000001123 LRP1 YHR081W|RRP47|YC1D taxon:4932
+S000002847 LRS4 YDR439W taxon:4932
+S000002847 LRS4 YDR439W taxon:4932
+S000002847 LRS4 YDR439W taxon:4932
+S000002847 LRS4 YDR439W taxon:4932
+S000002847 LRS4 YDR439W taxon:4932
+S000002847 LRS4 YDR439W taxon:4932
+S000002847 LRS4 YDR439W taxon:4932
+S000003368 LSB1 YGR136W taxon:4932
+S000003368 LSB1 YGR136W taxon:4932
+S000003368 LSB1 YGR136W taxon:4932
+S000003368 LSB1 YGR136W taxon:4932
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+S000002968 LSB3 YFR024C-A|YFR024C taxon:4932
+S000002968 LSB3 YFR024C-A|YFR024C taxon:4932
+S000002968 LSB3 YFR024C-A|YFR024C taxon:4932
+S000002968 LSB3 YFR024C-A|YFR024C taxon:4932
+S000002968 LSB3 YFR024C-A|YFR024C taxon:4932
+S000000539 LSB5 YCL034W taxon:4932
+S000000539 LSB5 YCL034W taxon:4932
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+S000003636 LSB6 YJL100W taxon:4932
+S000003636 LSB6 YJL100W taxon:4932
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+S000003636 LSB6 YJL100W taxon:4932
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+S000003636 LSB6 YJL100W taxon:4932
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+S000003636 LSB6 YJL100W taxon:4932
+S000003636 LSB6 YJL100W taxon:4932
+S000005668 LSC1 YOR142W taxon:4932
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+S000005668 LSC1 YOR142W taxon:4932
+S000005668 LSC1 YOR142W taxon:4932
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+S000005668 LSC1 YOR142W taxon:4932
+S000005668 LSC1 YOR142W taxon:4932
+S000005668 LSC1 YOR142W taxon:4932
+S000003476 LSC2 YGR244C taxon:4932
+S000003476 LSC2 YGR244C taxon:4932
+S000003476 LSC2 YGR244C taxon:4932
+S000003476 LSC2 YGR244C taxon:4932
+S000003476 LSC2 YGR244C taxon:4932
+S000003476 LSC2 YGR244C taxon:4932
+S000003476 LSC2 YGR244C taxon:4932
+S000003476 LSC2 YGR244C taxon:4932
+S000003067 LSG1 YGL099W|KRE35 taxon:4932
+S000003067 LSG1 YGL099W|KRE35 taxon:4932
+S000003067 LSG1 YGL099W|KRE35 taxon:4932
+S000003067 LSG1 YGL099W|KRE35 taxon:4932
+S000003067 LSG1 YGL099W|KRE35 taxon:4932
+S000003067 LSG1 YGL099W|KRE35 taxon:4932
+S000003660 LSM1 YJL124C|SPB8 taxon:4932
+S000003660 LSM1 YJL124C|SPB8 taxon:4932
+S000003660 LSM1 YJL124C|SPB8 taxon:4932
+S000003660 LSM1 YJL124C|SPB8 taxon:4932
+S000003660 LSM1 YJL124C|SPB8 taxon:4932
+S000003660 LSM1 YJL124C|SPB8 taxon:4932
+S000003660 LSM1 YJL124C|SPB8 taxon:4932
+S000003660 LSM1 YJL124C|SPB8 taxon:4932
+S000003660 LSM1 YJL124C|SPB8 taxon:4932
+S000003660 LSM1 YJL124C|SPB8 taxon:4932
+S000003660 LSM1 YJL124C|SPB8 taxon:4932
+S000003660 LSM1 YJL124C|SPB8 taxon:4932
+S000003660 LSM1 YJL124C|SPB8 taxon:4932
+S000003660 LSM1 YJL124C|SPB8 taxon:4932
+S000003660 LSM1 YJL124C|SPB8 taxon:4932
+S000001163 LSM12 YHR121W taxon:4932
+S000001163 LSM12 YHR121W taxon:4932
+S000001163 LSM12 YHR121W taxon:4932
+S000001163 LSM12 YHR121W taxon:4932
+S000001163 LSM12 YHR121W taxon:4932
+S000000122 LSM2 YBL026W|SMX5|SNP3 taxon:4932
+S000000122 LSM2 YBL026W|SMX5|SNP3 taxon:4932
+S000000122 LSM2 YBL026W|SMX5|SNP3 taxon:4932
+S000000122 LSM2 YBL026W|SMX5|SNP3 taxon:4932
+S000000122 LSM2 YBL026W|SMX5|SNP3 taxon:4932
+S000000122 LSM2 YBL026W|SMX5|SNP3 taxon:4932
+S000000122 LSM2 YBL026W|SMX5|SNP3 taxon:4932
+S000000122 LSM2 YBL026W|SMX5|SNP3 taxon:4932
+S000000122 LSM2 YBL026W|SMX5|SNP3 taxon:4932
+S000000122 LSM2 YBL026W|SMX5|SNP3 taxon:4932
+S000000122 LSM2 YBL026W|SMX5|SNP3 taxon:4932
+S000000122 LSM2 YBL026W|SMX5|SNP3 taxon:4932
+S000000122 LSM2 YBL026W|SMX5|SNP3 taxon:4932
+S000006434 LSM3 YLR438C-A|SMX4|USS2 taxon:4932
+S000006434 LSM3 YLR438C-A|SMX4|USS2 taxon:4932
+S000006434 LSM3 YLR438C-A|SMX4|USS2 taxon:4932
+S000006434 LSM3 YLR438C-A|SMX4|USS2 taxon:4932
+S000006434 LSM3 YLR438C-A|SMX4|USS2 taxon:4932
+S000006434 LSM3 YLR438C-A|SMX4|USS2 taxon:4932
+S000006434 LSM3 YLR438C-A|SMX4|USS2 taxon:4932
+S000006434 LSM3 YLR438C-A|SMX4|USS2 taxon:4932
+S000006434 LSM3 YLR438C-A|SMX4|USS2 taxon:4932
+S000006434 LSM3 YLR438C-A|SMX4|USS2 taxon:4932
+S000006434 LSM3 YLR438C-A|SMX4|USS2 taxon:4932
+S000006434 LSM3 YLR438C-A|SMX4|USS2 taxon:4932
+S000006434 LSM3 YLR438C-A|SMX4|USS2 taxon:4932
+S000000914 LSM4 YER112W|SDB23|USS1 taxon:4932
+S000000914 LSM4 YER112W|SDB23|USS1 taxon:4932
+S000000914 LSM4 YER112W|SDB23|USS1 taxon:4932
+S000000914 LSM4 YER112W|SDB23|USS1 taxon:4932
+S000000914 LSM4 YER112W|SDB23|USS1 taxon:4932
+S000000914 LSM4 YER112W|SDB23|USS1 taxon:4932
+S000000914 LSM4 YER112W|SDB23|USS1 taxon:4932
+S000000914 LSM4 YER112W|SDB23|USS1 taxon:4932
+S000000914 LSM4 YER112W|SDB23|USS1 taxon:4932
+S000000914 LSM4 YER112W|SDB23|USS1 taxon:4932
+S000000914 LSM4 YER112W|SDB23|USS1 taxon:4932
+S000000914 LSM4 YER112W|SDB23|USS1 taxon:4932
+S000000914 LSM4 YER112W|SDB23|USS1 taxon:4932
+S000000914 LSM4 YER112W|SDB23|USS1 taxon:4932
+S000000948 LSM5 YER146W taxon:4932
+S000000948 LSM5 YER146W taxon:4932
+S000000948 LSM5 YER146W taxon:4932
+S000000948 LSM5 YER146W taxon:4932
+S000000948 LSM5 YER146W taxon:4932
+S000000948 LSM5 YER146W taxon:4932
+S000000948 LSM5 YER146W taxon:4932
+S000000948 LSM5 YER146W taxon:4932
+S000000948 LSM5 YER146W taxon:4932
+S000000948 LSM5 YER146W taxon:4932
+S000000948 LSM5 YER146W taxon:4932
+S000000948 LSM5 YER146W taxon:4932
+S000000948 LSM5 YER146W taxon:4932
+S000002786 LSM6 YDR378C taxon:4932
+S000002786 LSM6 YDR378C taxon:4932
+S000002786 LSM6 YDR378C taxon:4932
+S000002786 LSM6 YDR378C taxon:4932
+S000002786 LSM6 YDR378C taxon:4932
+S000002786 LSM6 YDR378C taxon:4932
+S000002786 LSM6 YDR378C taxon:4932
+S000002786 LSM6 YDR378C taxon:4932
+S000002786 LSM6 YDR378C taxon:4932
+S000002786 LSM6 YDR378C taxon:4932
+S000002786 LSM6 YDR378C taxon:4932
+S000002786 LSM6 YDR378C taxon:4932
+S000002786 LSM6 YDR378C taxon:4932
+S000005091 LSM7 YNL147W taxon:4932
+S000005091 LSM7 YNL147W taxon:4932
+S000005091 LSM7 YNL147W taxon:4932
+S000005091 LSM7 YNL147W taxon:4932
+S000005091 LSM7 YNL147W taxon:4932
+S000005091 LSM7 YNL147W taxon:4932
+S000005091 LSM7 YNL147W taxon:4932
+S000005091 LSM7 YNL147W taxon:4932
+S000005091 LSM7 YNL147W taxon:4932
+S000005091 LSM7 YNL147W taxon:4932
+S000005091 LSM7 YNL147W taxon:4932
+S000005091 LSM7 YNL147W taxon:4932
+S000005091 LSM7 YNL147W taxon:4932
+S000005091 LSM7 YNL147W taxon:4932
+S000005091 LSM7 YNL147W taxon:4932
+S000005091 LSM7 YNL147W taxon:4932
+S000003783 LSM8 YJR022W taxon:4932
+S000003783 LSM8 YJR022W taxon:4932
+S000003783 LSM8 YJR022W taxon:4932
+S000003783 LSM8 YJR022W taxon:4932
+S000003783 LSM8 YJR022W taxon:4932
+S000003783 LSM8 YJR022W taxon:4932
+S000003783 LSM8 YJR022W taxon:4932
+S000003783 LSM8 YJR022W taxon:4932
+S000003783 LSM8 YJR022W taxon:4932
+S000003783 LSM8 YJR022W taxon:4932
+S000003783 LSM8 YJR022W taxon:4932
+S000005925 LSP1 YPL004C taxon:4932
+S000005925 LSP1 YPL004C taxon:4932
+S000005925 LSP1 YPL004C taxon:4932
+S000005925 LSP1 YPL004C taxon:4932
+S000005925 LSP1 YPL004C taxon:4932
+S000005925 LSP1 YPL004C taxon:4932
+S000005925 LSP1 YPL004C taxon:4932
+S000005925 LSP1 YPL004C taxon:4932
+S000006478 LSR1 snR20 taxon:4932
+S000006478 LSR1 snR20 taxon:4932
+S000006478 LSR1 snR20 taxon:4932
+S000001659 LST4 YKL176C taxon:4932
+S000001659 LST4 YKL176C taxon:4932
+S000001659 LST4 YKL176C taxon:4932
+S000001659 LST4 YKL176C taxon:4932
+S000001659 LST4 YKL176C taxon:4932
+S000001659 LST4 YKL176C taxon:4932
+S000003289 LST7 YGR057C taxon:4932
+S000003289 LST7 YGR057C taxon:4932
+S000003289 LST7 YGR057C taxon:4932
+S000003289 LST7 YGR057C taxon:4932
+S000003289 LST7 YGR057C taxon:4932
+S000003289 LST7 YGR057C taxon:4932
+S000003289 LST7 YGR057C taxon:4932
+S000004951 LST8 YNL006W taxon:4932
+S000004951 LST8 YNL006W taxon:4932
+S000004951 LST8 YNL006W taxon:4932
+S000004951 LST8 YNL006W taxon:4932
+S000004951 LST8 YNL006W taxon:4932
+S000004951 LST8 YNL006W taxon:4932
+S000004951 LST8 YNL006W taxon:4932
+S000004951 LST8 YNL006W taxon:4932
+S000004951 LST8 YNL006W taxon:4932
+S000004951 LST8 YNL006W taxon:4932
+S000004951 LST8 YNL006W taxon:4932
+S000004951 LST8 YNL006W taxon:4932
+S000004951 LST8 YNL006W taxon:4932
+S000004951 LST8 YNL006W taxon:4932
+S000000022 LTE1 YAL024C|MSI2 taxon:4932
+S000000022 LTE1 YAL024C|MSI2 taxon:4932
+S000000022 LTE1 YAL024C|MSI2 taxon:4932
+S000000022 LTE1 YAL024C|MSI2 taxon:4932
+S000000022 LTE1 YAL024C|MSI2 taxon:4932
+S000006277 LTP1 YPR073C taxon:4932
+S000006277 LTP1 YPR073C taxon:4932
+S000006277 LTP1 YPR073C taxon:4932
+S000006277 LTP1 YPR073C taxon:4932
+S000006277 LTP1 YPR073C taxon:4932
+S000006277 LTP1 YPR073C taxon:4932
+S000001626 LTV1 YKL143W|YKL2 taxon:4932
+S000001626 LTV1 YKL143W|YKL2 taxon:4932
+S000001626 LTV1 YKL143W|YKL2 taxon:4932
+S000001626 LTV1 YKL143W|YKL2 taxon:4932
+S000001626 LTV1 YKL143W|YKL2 taxon:4932
+S000002245 LUC7 YDL087C|EPE1|EXM2 taxon:4932
+S000002245 LUC7 YDL087C|EPE1|EXM2 taxon:4932
+S000002245 LUC7 YDL087C|EPE1|EXM2 taxon:4932
+S000002245 LUC7 YDL087C|EPE1|EXM2 taxon:4932
+S000002245 LUC7 YDL087C|EPE1|EXM2 taxon:4932
+S000002245 LUC7 YDL087C|EPE1|EXM2 taxon:4932
+S000002245 LUC7 YDL087C|EPE1|EXM2 taxon:4932
+S000005212 LYP1 YNL268W taxon:4932
+S000005212 LYP1 YNL268W taxon:4932
+S000005212 LYP1 YNL268W taxon:4932
+S000005212 LYP1 YNL268W taxon:4932
+S000001473 LYS1 YIR034C taxon:4932
+S000001473 LYS1 YIR034C taxon:4932
+S000001473 LYS1 YIR034C taxon:4932
+S000001473 LYS1 YIR034C taxon:4932
+S000001356 LYS12 YIL094C|LYS10|LYS11 taxon:4932
+S000001356 LYS12 YIL094C|LYS10|LYS11 taxon:4932
+S000001356 LYS12 YIL094C|LYS10|LYS11 taxon:4932
+S000001356 LYS12 YIL094C|LYS10|LYS11 taxon:4932
+S000001356 LYS12 YIL094C|LYS10|LYS11 taxon:4932
+S000002441 LYS14 YDR034C taxon:4932
+S000002441 LYS14 YDR034C taxon:4932
+S000002441 LYS14 YDR034C taxon:4932
+S000002441 LYS14 YDR034C taxon:4932
+S000000319 LYS2 YBR115C taxon:4932
+S000000319 LYS2 YBR115C taxon:4932
+S000000319 LYS2 YBR115C taxon:4932
+S000002341 LYS20 YDL182W taxon:4932
+S000002341 LYS20 YDL182W taxon:4932
+S000002341 LYS20 YDL182W taxon:4932
+S000002341 LYS20 YDL182W taxon:4932
+S000002341 LYS20 YDL182W taxon:4932
+S000002341 LYS20 YDL182W taxon:4932
+S000002341 LYS20 YDL182W taxon:4932
+S000002341 LYS20 YDL182W taxon:4932
+S000002341 LYS20 YDL182W taxon:4932
+S000002289 LYS21 YDL131W taxon:4932
+S000002289 LYS21 YDL131W taxon:4932
+S000002289 LYS21 YDL131W taxon:4932
+S000002289 LYS21 YDL131W taxon:4932
+S000002642 LYS4 YDR234W|LYS3 taxon:4932
+S000002642 LYS4 YDR234W|LYS3 taxon:4932
+S000002642 LYS4 YDR234W|LYS3 taxon:4932
+S000002642 LYS4 YDR234W|LYS3 taxon:4932
+S000003122 LYS5 YGL154C taxon:4932
+S000003122 LYS5 YGL154C taxon:4932
+S000003122 LYS5 YGL154C taxon:4932
+S000003122 LYS5 YGL154C taxon:4932
+S000005333 LYS9 YNR050C|LYS13 taxon:4932
+S000005333 LYS9 YNR050C|LYS13 taxon:4932
+S000005333 LYS9 YNR050C|LYS13 taxon:4932
+S000005333 LYS9 YNR050C|LYS13 taxon:4932
+S000004623 MAC1 YMR021C|CUA1 taxon:4932
+S000004623 MAC1 YMR021C|CUA1 taxon:4932
+S000004623 MAC1 YMR021C|CUA1 taxon:4932
+S000004623 MAC1 YMR021C|CUA1 taxon:4932
+S000004623 MAC1 YMR021C|CUA1 taxon:4932
+S000003054 MAD1 YGL086W taxon:4932
+S000003054 MAD1 YGL086W taxon:4932
+S000003054 MAD1 YGL086W taxon:4932
+S000003054 MAD1 YGL086W taxon:4932
+S000003054 MAD1 YGL086W taxon:4932
+S000003054 MAD1 YGL086W taxon:4932
+S000003054 MAD1 YGL086W taxon:4932
+S000003567 MAD2 YJL030W taxon:4932
+S000003567 MAD2 YJL030W taxon:4932
+S000003567 MAD2 YJL030W taxon:4932
+S000003567 MAD2 YJL030W taxon:4932
+S000003567 MAD2 YJL030W taxon:4932
+S000003550 MAD3 YJL013C taxon:4932
+S000003550 MAD3 YJL013C taxon:4932
+S000003550 MAD3 YJL013C taxon:4932
+S000003550 MAD3 YJL013C taxon:4932
+S000001512 MAE1 YKL029C taxon:4932
+S000001512 MAE1 YKL029C taxon:4932
+S000001512 MAE1 YKL029C taxon:4932
+S000001512 MAE1 YKL029C taxon:4932
+S000001512 MAE1 YKL029C taxon:4932
+S000001512 MAE1 YKL029C taxon:4932
+S000002412 MAF1 YDR005C taxon:4932
+S000002412 MAF1 YDR005C taxon:4932
+S000002412 MAF1 YDR005C taxon:4932
+S000002412 MAF1 YDR005C taxon:4932
+S000000944 MAG1 YER142C|MMS5 taxon:4932
+S000000944 MAG1 YER142C|MMS5 taxon:4932
+S000000944 MAG1 YER142C|MMS5 taxon:4932
+S000000944 MAG1 YER142C|MMS5 taxon:4932
+S000000944 MAG1 YER142C|MMS5 taxon:4932
+S000000944 MAG1 YER142C|MMS5 taxon:4932
+S000004419 MAG2 YLR427W taxon:4932
+S000004419 MAG2 YLR427W taxon:4932
+S000004419 MAG2 YLR427W taxon:4932
+S000000779 MAK10 YEL053C taxon:4932
+S000000779 MAK10 YEL053C taxon:4932
+S000000779 MAK10 YEL053C taxon:4932
+S000000779 MAK10 YEL053C taxon:4932
+S000000779 MAK10 YEL053C taxon:4932
+S000001504 MAK11 YKL021C taxon:4932
+S000001504 MAK11 YKL021C taxon:4932
+S000001504 MAK11 YKL021C taxon:4932
+S000000023 MAK16 YAL025C taxon:4932
+S000000023 MAK16 YAL025C taxon:4932
+S000000023 MAK16 YAL025C taxon:4932
+S000002467 MAK21 YDR060W|NOC1 taxon:4932
+S000002467 MAK21 YDR060W|NOC1 taxon:4932
+S000002467 MAK21 YDR060W|NOC1 taxon:4932
+S000006255 MAK3 YPR051W taxon:4932
+S000006255 MAK3 YPR051W taxon:4932
+S000006255 MAK3 YPR051W taxon:4932
+S000006255 MAK3 YPR051W taxon:4932
+S000000614 MAK31 YCR020C-A|LSM9|SMX1 taxon:4932
+S000000614 MAK31 YCR020C-A|LSM9|SMX1 taxon:4932
+S000000614 MAK31 YCR020C-A|LSM9|SMX1 taxon:4932
+S000000614 MAK31 YCR020C-A|LSM9|SMX1 taxon:4932
+S000000612 MAK32 YCR019W taxon:4932
+S000000612 MAK32 YCR019W taxon:4932
+S000000612 MAK32 YCR019W taxon:4932
+S000000346 MAK5 YBR142W taxon:4932
+S000000346 MAK5 YBR142W taxon:4932
+S000000346 MAK5 YBR142W taxon:4932
+S000000346 MAK5 YBR142W taxon:4932
+S000003521 MAL11 YGR289C|AGT1 taxon:4932
+S000003521 MAL11 YGR289C|AGT1 taxon:4932
+S000003521 MAL11 YGR289C|AGT1 taxon:4932
+S000003521 MAL11 YGR289C|AGT1 taxon:4932
+S000003521 MAL11 YGR289C|AGT1 taxon:4932
+S000003521 MAL11 YGR289C|AGT1 taxon:4932
+S000003521 MAL11 YGR289C|AGT1 taxon:4932
+S000003524 MAL12 YGR292W taxon:4932
+S000003524 MAL12 YGR292W taxon:4932
+S000003524 MAL12 YGR292W taxon:4932
+S000003520 MAL13 YGR288W taxon:4932
+S000003520 MAL13 YGR288W taxon:4932
+S000003520 MAL13 YGR288W taxon:4932
+S000003520 MAL13 YGR288W taxon:4932
+S000029681 MAL21 taxon:4932
+S000029681 MAL21 taxon:4932
+S000029681 MAL21 taxon:4932
+S000029681 MAL21 taxon:4932
+S000029681 MAL21 taxon:4932
+S000029681 MAL21 taxon:4932
+S000029682 MAL22 taxon:4932
+S000029682 MAL22 taxon:4932
+S000029682 MAL22 taxon:4932
+S000029657 MAL23 taxon:4932
+S000029657 MAL23 taxon:4932
+S000029657 MAL23 taxon:4932
+S000029657 MAL23 taxon:4932
+S000029657 MAL23 taxon:4932
+S000000502 MAL31 YBR298C|MAL3T taxon:4932
+S000000502 MAL31 YBR298C|MAL3T taxon:4932
+S000000502 MAL31 YBR298C|MAL3T taxon:4932
+S000000503 MAL32 YBR299W|MAL3S taxon:4932
+S000000503 MAL32 YBR299W|MAL3S taxon:4932
+S000000503 MAL32 YBR299W|MAL3S taxon:4932
+S000000501 MAL33 YBR297W|MAL3R taxon:4932
+S000000501 MAL33 YBR297W|MAL3R taxon:4932
+S000000501 MAL33 YBR297W|MAL3R taxon:4932
+S000000501 MAL33 YBR297W|MAL3R taxon:4932
+S000029686 MAL41 taxon:4932
+S000029686 MAL41 taxon:4932
+S000029686 MAL41 taxon:4932
+S000029687 MAL42 taxon:4932
+S000029687 MAL42 taxon:4932
+S000029687 MAL42 taxon:4932
+S000029688 MAL43 taxon:4932
+S000029688 MAL43 taxon:4932
+S000029688 MAL43 taxon:4932
+S000029688 MAL43 taxon:4932
+S000029658 MAL61 taxon:4932
+S000029658 MAL61 taxon:4932
+S000029658 MAL61 taxon:4932
+S000029658 MAL61 taxon:4932
+S000029658 MAL61 taxon:4932
+S000029690 MAL62 taxon:4932
+S000029690 MAL62 taxon:4932
+S000029690 MAL62 taxon:4932
+S000029659 MAL63 taxon:4932
+S000029659 MAL63 taxon:4932
+S000029659 MAL63 taxon:4932
+S000029659 MAL63 taxon:4932
+S000029659 MAL63 taxon:4932
+S000029659 MAL63 taxon:4932
+S000029659 MAL63 taxon:4932
+S000000908 MAM1 YER106W taxon:4932
+S000000908 MAM1 YER106W taxon:4932
+S000000908 MAM1 YER106W taxon:4932
+S000000908 MAM1 YER106W taxon:4932
+S000005421 MAM3 YOL060C taxon:4932
+S000005421 MAM3 YOL060C taxon:4932
+S000005421 MAM3 YOL060C taxon:4932
+S000005421 MAM3 YOL060C taxon:4932
+S000001332 MAM33 YIL070C taxon:4932
+S000001332 MAM33 YIL070C taxon:4932
+S000001332 MAM33 YIL070C taxon:4932
+S000004234 MAP1 YLR244C taxon:4932
+S000004234 MAP1 YLR244C taxon:4932
+S000004234 MAP1 YLR244C taxon:4932
+S000000187 MAP2 YBL091C taxon:4932
+S000000187 MAP2 YBL091C taxon:4932
+S000000187 MAP2 YBL091C taxon:4932
+S000004153 MAS1 YLR163C|MIF1 taxon:4932
+S000004153 MAS1 YLR163C|MIF1 taxon:4932
+S000004153 MAS1 YLR163C|MIF1 taxon:4932
+S000004153 MAS1 YLR163C|MIF1 taxon:4932
+S000001066 MAS2 YHR024C|MIF2 taxon:4932
+S000001066 MAS2 YHR024C|MIF2 taxon:4932
+S000001066 MAS2 YHR024C|MIF2 taxon:4932
+S000005300 MAS6 YNR017W|MIM23|MPI3|TIM23 taxon:4932
+S000005300 MAS6 YNR017W|MIM23|MPI3|TIM23 taxon:4932
+S000005300 MAS6 YNR017W|MIM23|MPI3|TIM23 taxon:4932
+S000005300 MAS6 YNR017W|MIM23|MPI3|TIM23 taxon:4932
+S000005300 MAS6 YNR017W|MIM23|MPI3|TIM23 taxon:4932
+S000029660 MATA1 A1 taxon:4932
+S000029660 MATA1 A1 taxon:4932
+S000029660 MATA1 A1 taxon:4932
+S000029661 MATA2 A2 taxon:4932
+S000029661 MATA2 A2 taxon:4932
+S000029661 MATA2 A2 taxon:4932
+S000000636 MATALPHA1 YCR040W|ALPHA1 taxon:4932
+S000000636 MATALPHA1 YCR040W|ALPHA1 taxon:4932
+S000000636 MATALPHA1 YCR040W|ALPHA1 taxon:4932
+S000000636 MATALPHA1 YCR040W|ALPHA1 taxon:4932
+S000000635 MATALPHA2 YCR039C|ALPHA2 taxon:4932
+S000000635 MATALPHA2 YCR039C|ALPHA2 taxon:4932
+S000000635 MATALPHA2 YCR039C|ALPHA2 taxon:4932
+S000000635 MATALPHA2 YCR039C|ALPHA2 taxon:4932
+S000000635 MATALPHA2 YCR039C|ALPHA2 taxon:4932
+S000000389 MBA1 YBR185C taxon:4932
+S000000389 MBA1 YBR185C taxon:4932
+S000000389 MBA1 YBR185C taxon:4932
+S000000389 MBA1 YBR185C taxon:4932
+S000007253 MBF1 YOR298C-A|SUF13 taxon:4932
+S000007253 MBF1 YOR298C-A|SUF13 taxon:4932
+S000007253 MBF1 YOR298C-A|SUF13 taxon:4932
+S000007253 MBF1 YOR298C-A|SUF13 taxon:4932
+S000002214 MBP1 YDL056W taxon:4932
+S000002214 MBP1 YDL056W taxon:4932
+S000002214 MBP1 YDL056W taxon:4932
+S000002214 MBP1 YDL056W taxon:4932
+S000002214 MBP1 YDL056W taxon:4932
+S000002214 MBP1 YDL056W taxon:4932
+S000002214 MBP1 YDL056W taxon:4932
+S000002214 MBP1 YDL056W taxon:4932
+S000002214 MBP1 YDL056W taxon:4932
+S000001576 MBR1 YKL093W taxon:4932
+S000001576 MBR1 YKL093W taxon:4932
+S000001576 MBR1 YKL093W taxon:4932
+S000005723 MCA1 YOR197W|YCA1 taxon:4932
+S000005723 MCA1 YOR197W|YCA1 taxon:4932
+S000005723 MCA1 YOR197W|YCA1 taxon:4932
+S000002161 MCD1 YDL003W|PDS3|RHC21|SCC1 taxon:4932
+S000002161 MCD1 YDL003W|PDS3|RHC21|SCC1 taxon:4932
+S000002161 MCD1 YDL003W|PDS3|RHC21|SCC1 taxon:4932
+S000002161 MCD1 YDL003W|PDS3|RHC21|SCC1 taxon:4932
+S000002161 MCD1 YDL003W|PDS3|RHC21|SCC1 taxon:4932
+S000002161 MCD1 YDL003W|PDS3|RHC21|SCC1 taxon:4932
+S000002161 MCD1 YDL003W|PDS3|RHC21|SCC1 taxon:4932
+S000001648 MCD4 YKL165C|FSR2|SSU21|ZRG16 taxon:4932
+S000001648 MCD4 YKL165C|FSR2|SSU21|ZRG16 taxon:4932
+S000001648 MCD4 YKL165C|FSR2|SSU21|ZRG16 taxon:4932
+S000001648 MCD4 YKL165C|FSR2|SSU21|ZRG16 taxon:4932
+S000001648 MCD4 YKL165C|FSR2|SSU21|ZRG16 taxon:4932
+S000001648 MCD4 YKL165C|FSR2|SSU21|ZRG16 taxon:4932
+S000002212 MCH1 YDL054C taxon:4932
+S000002212 MCH1 YDL054C taxon:4932
+S000002212 MCH1 YDL054C taxon:4932
+S000002212 MCH1 YDL054C taxon:4932
+S000002212 MCH1 YDL054C taxon:4932
+S000001704 MCH2 YKL221W taxon:4932
+S000001704 MCH2 YKL221W taxon:4932
+S000001704 MCH2 YKL221W taxon:4932
+S000001704 MCH2 YKL221W taxon:4932
+S000001704 MCH2 YKL221W taxon:4932
+S000005479 MCH4 YOL119C taxon:4932
+S000005479 MCH4 YOL119C taxon:4932
+S000005479 MCH4 YOL119C taxon:4932
+S000005479 MCH4 YOL119C taxon:4932
+S000005479 MCH4 YOL119C taxon:4932
+S000005833 MCH5 YOR306C taxon:4932
+S000005833 MCH5 YOR306C taxon:4932
+S000005833 MCH5 YOR306C taxon:4932
+S000005833 MCH5 YOR306C taxon:4932
+S000005833 MCH5 YOR306C taxon:4932
+S000005251 MCK1 YNL307C|YPK1 taxon:4932
+S000005251 MCK1 YNL307C|YPK1 taxon:4932
+S000005251 MCK1 YNL307C|YPK1 taxon:4932
+S000005251 MCK1 YNL307C|YPK1 taxon:4932
+S000005251 MCK1 YNL307C|YPK1 taxon:4932
+S000005251 MCK1 YNL307C|YPK1 taxon:4932
+S000005251 MCK1 YNL307C|YPK1 taxon:4932
+S000005251 MCK1 YNL307C|YPK1 taxon:4932
+S000005251 MCK1 YNL307C|YPK1 taxon:4932
+S000005251 MCK1 YNL307C|YPK1 taxon:4932
+S000005251 MCK1 YNL307C|YPK1 taxon:4932
+S000004646 MCM1 YMR043W|FUN80 taxon:4932
+S000004646 MCM1 YMR043W|FUN80 taxon:4932
+S000004646 MCM1 YMR043W|FUN80 taxon:4932
+S000004646 MCM1 YMR043W|FUN80 taxon:4932
+S000004646 MCM1 YMR043W|FUN80 taxon:4932
+S000004646 MCM1 YMR043W|FUN80 taxon:4932
+S000004646 MCM1 YMR043W|FUN80 taxon:4932
+S000004646 MCM1 YMR043W|FUN80 taxon:4932
+S000001412 MCM10 YIL150C|DNA43 taxon:4932
+S000001412 MCM10 YIL150C|DNA43 taxon:4932
+S000001412 MCM10 YIL150C|DNA43 taxon:4932
+S000001412 MCM10 YIL150C|DNA43 taxon:4932
+S000001412 MCM10 YIL150C|DNA43 taxon:4932
+S000001412 MCM10 YIL150C|DNA43 taxon:4932
+S000001412 MCM10 YIL150C|DNA43 taxon:4932
+S000001412 MCM10 YIL150C|DNA43 taxon:4932
+S000001412 MCM10 YIL150C|DNA43 taxon:4932
+S000001412 MCM10 YIL150C|DNA43 taxon:4932
+S000001412 MCM10 YIL150C|DNA43 taxon:4932
+S000001412 MCM10 YIL150C|DNA43 taxon:4932
+S000006250 MCM16 YPR046W taxon:4932
+S000006250 MCM16 YPR046W taxon:4932
+S000006250 MCM16 YPR046W taxon:4932
+S000000119 MCM2 YBL023C taxon:4932
+S000000119 MCM2 YBL023C taxon:4932
+S000000119 MCM2 YBL023C taxon:4932
+S000000119 MCM2 YBL023C taxon:4932
+S000000119 MCM2 YBL023C taxon:4932
+S000000119 MCM2 YBL023C taxon:4932
+S000000119 MCM2 YBL023C taxon:4932
+S000000119 MCM2 YBL023C taxon:4932
+S000000119 MCM2 YBL023C taxon:4932
+S000000119 MCM2 YBL023C taxon:4932
+S000002726 MCM21 YDR318W|CTF5 taxon:4932
+S000002726 MCM21 YDR318W|CTF5 taxon:4932
+S000002726 MCM21 YDR318W|CTF5 taxon:4932
+S000002726 MCM21 YDR318W|CTF5 taxon:4932
+S000003896 MCM22 YJR135C taxon:4932
+S000003896 MCM22 YJR135C taxon:4932
+S000003896 MCM22 YJR135C taxon:4932
+S000000758 MCM3 YEL032W taxon:4932
+S000000758 MCM3 YEL032W taxon:4932
+S000000758 MCM3 YEL032W taxon:4932
+S000000758 MCM3 YEL032W taxon:4932
+S000000758 MCM3 YEL032W taxon:4932
+S000000758 MCM3 YEL032W taxon:4932
+S000000758 MCM3 YEL032W taxon:4932
+S000000758 MCM3 YEL032W taxon:4932
+S000000758 MCM3 YEL032W taxon:4932
+S000000758 MCM3 YEL032W taxon:4932
+S000000758 MCM3 YEL032W taxon:4932
+S000003169 MCM6 YGL201C taxon:4932
+S000003169 MCM6 YGL201C taxon:4932
+S000003169 MCM6 YGL201C taxon:4932
+S000003169 MCM6 YGL201C taxon:4932
+S000003169 MCM6 YGL201C taxon:4932
+S000003169 MCM6 YGL201C taxon:4932
+S000003169 MCM6 YGL201C taxon:4932
+S000003169 MCM6 YGL201C taxon:4932
+S000003169 MCM6 YGL201C taxon:4932
+S000003169 MCM6 YGL201C taxon:4932
+S000001633 MCR1 YKL150W taxon:4932
+S000001633 MCR1 YKL150W taxon:4932
+S000001633 MCR1 YKL150W taxon:4932
+S000001633 MCR1 YKL150W taxon:4932
+S000001633 MCR1 YKL150W taxon:4932
+S000001633 MCR1 YKL150W taxon:4932
+S000001633 MCR1 YKL150W taxon:4932
+S000001633 MCR1 YKL150W taxon:4932
+S000005747 MCT1 YOR221C taxon:4932
+S000005747 MCT1 YOR221C taxon:4932
+S000005747 MCT1 YOR221C taxon:4932
+S000005747 MCT1 YOR221C taxon:4932
+S000005747 MCT1 YOR221C taxon:4932
+S000005747 MCT1 YOR221C taxon:4932
+S000005747 MCT1 YOR221C taxon:4932
+S000000431 MCX1 YBR227C taxon:4932
+S000000431 MCX1 YBR227C taxon:4932
+S000000431 MCX1 YBR227C taxon:4932
+S000000431 MCX1 YBR227C taxon:4932
+S000005117 MDG1 YNL173C taxon:4932
+S000005117 MDG1 YNL173C taxon:4932
+S000005117 MDG1 YNL173C taxon:4932
+S000001568 MDH1 YKL085W taxon:4932
+S000001568 MDH1 YKL085W taxon:4932
+S000001568 MDH1 YKL085W taxon:4932
+S000001568 MDH1 YKL085W taxon:4932
+S000005486 MDH2 YOL126C taxon:4932
+S000005486 MDH2 YOL126C taxon:4932
+S000005486 MDH2 YOL126C taxon:4932
+S000005486 MDH2 YOL126C taxon:4932
+S000005486 MDH2 YOL126C taxon:4932
+S000005486 MDH2 YOL126C taxon:4932
+S000005486 MDH2 YOL126C taxon:4932
+S000002236 MDH3 YDL078C taxon:4932
+S000002236 MDH3 YDL078C taxon:4932
+S000002236 MDH3 YDL078C taxon:4932
+S000002236 MDH3 YDL078C taxon:4932
+S000002236 MDH3 YDL078C taxon:4932
+S000002236 MDH3 YDL078C taxon:4932
+S000002236 MDH3 YDL078C taxon:4932
+S000002236 MDH3 YDL078C taxon:4932
+S000001878 MDJ1 YFL016C taxon:4932
+S000001878 MDJ1 YFL016C taxon:4932
+S000001878 MDJ1 YFL016C taxon:4932
+S000001878 MDJ1 YFL016C taxon:4932
+S000001878 MDJ1 YFL016C taxon:4932
+S000005272 MDJ2 YNL328C taxon:4932
+S000005272 MDJ2 YNL328C taxon:4932
+S000005272 MDJ2 YNL328C taxon:4932
+S000005272 MDJ2 YNL328C taxon:4932
+S000005272 MDJ2 YNL328C taxon:4932
+S000005272 MDJ2 YNL328C taxon:4932
+S000005272 MDJ2 YNL328C taxon:4932
+S000004178 MDL1 YLR188W taxon:4932
+S000004178 MDL1 YLR188W taxon:4932
+S000004178 MDL1 YLR188W taxon:4932
+S000004178 MDL1 YLR188W taxon:4932
+S000004178 MDL1 YLR188W taxon:4932
+S000004178 MDL1 YLR188W taxon:4932
+S000004178 MDL1 YLR188W taxon:4932
+S000006191 MDL2 YPL270W taxon:4932
+S000006191 MDL2 YPL270W taxon:4932
+S000006191 MDL2 YPL270W taxon:4932
+S000004572 MDM1 YML104C taxon:4932
+S000004572 MDM1 YML104C taxon:4932
+S000004572 MDM1 YML104C taxon:4932
+S000004572 MDM1 YML104C taxon:4932
+S000004572 MDM1 YML104C taxon:4932
+S000004572 MDM1 YML104C taxon:4932
+S000000008 MDM10 YAL010C|FUN37 taxon:4932
+S000000008 MDM10 YAL010C|FUN37 taxon:4932
+S000000008 MDM10 YAL010C|FUN37 taxon:4932
+S000000008 MDM10 YAL010C|FUN37 taxon:4932
+S000000008 MDM10 YAL010C|FUN37 taxon:4932
+S000000008 MDM10 YAL010C|FUN37 taxon:4932
+S000000008 MDM10 YAL010C|FUN37 taxon:4932
+S000000008 MDM10 YAL010C|FUN37 taxon:4932
+S000005369 MDM12 YOL009C taxon:4932
+S000005369 MDM12 YOL009C taxon:4932
+S000005369 MDM12 YOL009C taxon:4932
+S000005369 MDM12 YOL009C taxon:4932
+S000005436 MDM20 YOL076W|DEC1 taxon:4932
+S000005436 MDM20 YOL076W|DEC1 taxon:4932
+S000005436 MDM20 YOL076W|DEC1 taxon:4932
+S000005436 MDM20 YOL076W|DEC1 taxon:4932
+S000005436 MDM20 YOL076W|DEC1 taxon:4932
+S000005436 MDM20 YOL076W|DEC1 taxon:4932
+S000005436 MDM20 YOL076W|DEC1 taxon:4932
+S000005436 MDM20 YOL076W|DEC1 taxon:4932
+S000004360 MDM30 YLR368W|DSG1 taxon:4932
+S000004360 MDM30 YLR368W|DSG1 taxon:4932
+S000004360 MDM30 YLR368W|DSG1 taxon:4932
+S000004360 MDM30 YLR368W|DSG1 taxon:4932
+S000001237 MDM31 YHR194W taxon:4932
+S000001237 MDM31 YHR194W taxon:4932
+S000001237 MDM31 YHR194W taxon:4932
+S000001237 MDM31 YHR194W taxon:4932
+S000001237 MDM31 YHR194W taxon:4932
+S000001237 MDM31 YHR194W taxon:4932
+S000001237 MDM31 YHR194W taxon:4932
+S000005673 MDM32 YOR147W taxon:4932
+S000005673 MDM32 YOR147W taxon:4932
+S000005673 MDM32 YOR147W taxon:4932
+S000005673 MDM32 YOR147W taxon:4932
+S000005673 MDM32 YOR147W taxon:4932
+S000005673 MDM32 YOR147W taxon:4932
+S000005673 MDM32 YOR147W taxon:4932
+S000003187 MDM34 YGL219C|MMM2 taxon:4932
+S000003187 MDM34 YGL219C|MMM2 taxon:4932
+S000003187 MDM34 YGL219C|MMM2 taxon:4932
+S000003187 MDM34 YGL219C|MMM2 taxon:4932
+S000003187 MDM34 YGL219C|MMM2 taxon:4932
+S000007243 MDM35 YKL053C-A taxon:4932
+S000007243 MDM35 YKL053C-A taxon:4932
+S000007243 MDM35 YKL053C-A taxon:4932
+S000007243 MDM35 YKL053C-A taxon:4932
+S000006287 MDM36 YPR083W taxon:4932
+S000006287 MDM36 YPR083W taxon:4932
+S000006287 MDM36 YPR083W taxon:4932
+S000005387 MDM38 YOL027C|MKH1 taxon:4932
+S000005387 MDM38 YOL027C|MKH1 taxon:4932
+S000005387 MDM38 YOL027C|MKH1 taxon:4932
+S000005387 MDM38 YOL027C|MKH1 taxon:4932
+S000005387 MDM38 YOL027C|MKH1 taxon:4932
+S000005387 MDM38 YOL027C|MKH1 taxon:4932
+S000005387 MDM38 YOL027C|MKH1 taxon:4932
+S000005387 MDM38 YOL027C|MKH1 taxon:4932
+S000005387 MDM38 YOL027C|MKH1 taxon:4932
+S000004096 MDN1 YLR106C|REA1 taxon:4932
+S000004096 MDN1 YLR106C|REA1 taxon:4932
+S000004096 MDN1 YLR106C|REA1 taxon:4932
+S000004096 MDN1 YLR106C|REA1 taxon:4932
+S000004096 MDN1 YLR106C|REA1 taxon:4932
+S000004096 MDN1 YLR106C|REA1 taxon:4932
+S000004096 MDN1 YLR106C|REA1 taxon:4932
+S000004096 MDN1 YLR106C|REA1 taxon:4932
+S000004096 MDN1 YLR106C|REA1 taxon:4932
+S000003332 MDR1 YGR100W|GYP2|MIC1 taxon:4932
+S000003332 MDR1 YGR100W|GYP2|MIC1 taxon:4932
+S000003332 MDR1 YGR100W|GYP2|MIC1 taxon:4932
+S000003332 MDR1 YGR100W|GYP2|MIC1 taxon:4932
+S000003332 MDR1 YGR100W|GYP2|MIC1 taxon:4932
+S000003165 MDS3 YGL197W taxon:4932
+S000003165 MDS3 YGL197W taxon:4932
+S000003165 MDS3 YGL197W taxon:4932
+S000003165 MDS3 YGL197W taxon:4932
+S000003165 MDS3 YGL197W taxon:4932
+S000003165 MDS3 YGL197W taxon:4932
+S000003648 MDV1 YJL112W|FIS2|GAG3|NET2 taxon:4932
+S000003648 MDV1 YJL112W|FIS2|GAG3|NET2 taxon:4932
+S000003648 MDV1 YJL112W|FIS2|GAG3|NET2 taxon:4932
+S000003648 MDV1 YJL112W|FIS2|GAG3|NET2 taxon:4932
+S000003648 MDV1 YJL112W|FIS2|GAG3|NET2 taxon:4932
+S000003648 MDV1 YJL112W|FIS2|GAG3|NET2 taxon:4932
+S000003648 MDV1 YJL112W|FIS2|GAG3|NET2 taxon:4932
+S000003648 MDV1 YJL112W|FIS2|GAG3|NET2 taxon:4932
+S000003648 MDV1 YJL112W|FIS2|GAG3|NET2 taxon:4932
+S000003648 MDV1 YJL112W|FIS2|GAG3|NET2 taxon:4932
+S000003648 MDV1 YJL112W|FIS2|GAG3|NET2 taxon:4932
+S000003648 MDV1 YJL112W|FIS2|GAG3|NET2 taxon:4932
+S000003648 MDV1 YJL112W|FIS2|GAG3|NET2 taxon:4932
+S000003648 MDV1 YJL112W|FIS2|GAG3|NET2 taxon:4932
+S000003648 MDV1 YJL112W|FIS2|GAG3|NET2 taxon:4932
+S000003648 MDV1 YJL112W|FIS2|GAG3|NET2 taxon:4932
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+S000005471 MDY2 YOL111C|TMA24 taxon:4932
+S000005471 MDY2 YOL111C|TMA24 taxon:4932
+S000005471 MDY2 YOL111C|TMA24 taxon:4932
+S000005471 MDY2 YOL111C|TMA24 taxon:4932
+S000000340 MEC1 YBR136W|ESR1|SAD3 taxon:4932
+S000000340 MEC1 YBR136W|ESR1|SAD3 taxon:4932
+S000000340 MEC1 YBR136W|ESR1|SAD3 taxon:4932
+S000000340 MEC1 YBR136W|ESR1|SAD3 taxon:4932
+S000000340 MEC1 YBR136W|ESR1|SAD3 taxon:4932
+S000000340 MEC1 YBR136W|ESR1|SAD3 taxon:4932
+S000000340 MEC1 YBR136W|ESR1|SAD3 taxon:4932
+S000000340 MEC1 YBR136W|ESR1|SAD3 taxon:4932
+S000000340 MEC1 YBR136W|ESR1|SAD3 taxon:4932
+S000004279 MEC3 YLR288C|PIP3 taxon:4932
+S000004279 MEC3 YLR288C|PIP3 taxon:4932
+S000004279 MEC3 YLR288C|PIP3 taxon:4932
+S000004279 MEC3 YLR288C|PIP3 taxon:4932
+S000004279 MEC3 YLR288C|PIP3 taxon:4932
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+S000004718 MED11 YMR112C taxon:4932
+S000004718 MED11 YMR112C taxon:4932
+S000004718 MED11 YMR112C taxon:4932
+S000002163 MED2 YDL005C taxon:4932
+S000002163 MED2 YDL005C taxon:4932
+S000002163 MED2 YDL005C taxon:4932
+S000005700 MED4 YOR174W taxon:4932
+S000005700 MED4 YOR174W taxon:4932
+S000005700 MED4 YOR174W taxon:4932
+S000001100 MED6 YHR058C taxon:4932
+S000001100 MED6 YHR058C taxon:4932
+S000001100 MED6 YHR058C taxon:4932
+S000001100 MED6 YHR058C taxon:4932
+S000001100 MED6 YHR058C taxon:4932
+S000001100 MED6 YHR058C taxon:4932
+S000005495 MED7 YOL135C taxon:4932
+S000005495 MED7 YOL135C taxon:4932
+S000005495 MED7 YOL135C taxon:4932
+S000000397 MED8 YBR193C taxon:4932
+S000000397 MED8 YBR193C taxon:4932
+S000000397 MED8 YBR193C taxon:4932
+S000004059 MEF1 YLR069C taxon:4932
+S000004059 MEF1 YLR069C taxon:4932
+S000004059 MEF1 YLR069C taxon:4932
+S000004059 MEF1 YLR069C taxon:4932
+S000004059 MEF1 YLR069C taxon:4932
+S000004059 MEF1 YLR069C taxon:4932
+S000003638 MEF2 YJL102W taxon:4932
+S000003638 MEF2 YJL102W taxon:4932
+S000003638 MEF2 YJL102W taxon:4932
+S000003638 MEF2 YJL102W taxon:4932
+S000001715 MEH1 YKR007W|EGO1 taxon:4932
+S000001715 MEH1 YKR007W|EGO1 taxon:4932
+S000001715 MEH1 YKR007W|EGO1 taxon:4932
+S000001715 MEH1 YKR007W|EGO1 taxon:4932
+S000001715 MEH1 YKR007W|EGO1 taxon:4932
+S000001715 MEH1 YKR007W|EGO1 taxon:4932
+S000001715 MEH1 YKR007W|EGO1 taxon:4932
+S000001954 MEI4 YER044C-A taxon:4932
+S000001954 MEI4 YER044C-A taxon:4932
+S000001954 MEI4 YER044C-A taxon:4932
+S000001954 MEI4 YER044C-A taxon:4932
+S000001954 MEI4 YER044C-A taxon:4932
+S000006042 MEI5 YPL121C|LPH6 taxon:4932
+S000006042 MEI5 YPL121C|LPH6 taxon:4932
+S000006042 MEI5 YPL121C|LPH6 taxon:4932
+S000006042 MEI5 YPL121C|LPH6 taxon:4932
+S000006042 MEI5 YPL121C|LPH6 taxon:4932
+S000006042 MEI5 YPL121C|LPH6 taxon:4932
+S000006042 MEI5 YPL121C|LPH6 taxon:4932
+S000005878 MEK1 YOR351C|MRE4 taxon:4932
+S000005878 MEK1 YOR351C|MRE4 taxon:4932
+S000005878 MEK1 YOR351C|MRE4 taxon:4932
+S000005878 MEK1 YOR351C|MRE4 taxon:4932
+S000005878 MEK1 YOR351C|MRE4 taxon:4932
+S000005878 MEK1 YOR351C|MRE4 taxon:4932
+S000029662 MEL1 taxon:4932
+S000029662 MEL1 taxon:4932
+S000029662 MEL1 taxon:4932
+S000029692 MEL10 taxon:4932
+S000029692 MEL10 taxon:4932
+S000029692 MEL10 taxon:4932
+S000029663 MEL2 taxon:4932
+S000029663 MEL2 taxon:4932
+S000029663 MEL2 taxon:4932
+S000029693 MEL3 taxon:4932
+S000029693 MEL3 taxon:4932
+S000029693 MEL3 taxon:4932
+S000029694 MEL4 taxon:4932
+S000029694 MEL4 taxon:4932
+S000029694 MEL4 taxon:4932
+S000029664 MEL5 taxon:4932
+S000029664 MEL5 taxon:4932
+S000029664 MEL5 taxon:4932
+S000029665 MEL6 taxon:4932
+S000029665 MEL6 taxon:4932
+S000029665 MEL6 taxon:4932
+S000029695 MEL7 taxon:4932
+S000029695 MEL7 taxon:4932
+S000029695 MEL7 taxon:4932
+S000029696 MEL8 taxon:4932
+S000029696 MEL8 taxon:4932
+S000029696 MEL8 taxon:4932
+S000029697 MEL9 taxon:4932
+S000029697 MEL9 taxon:4932
+S000029697 MEL9 taxon:4932
+S000029697 MEL9 taxon:4932
+S000029697 MEL9 taxon:4932
+S000003353 MEP1 YGR121C|AMT1 taxon:4932
+S000003353 MEP1 YGR121C|AMT1 taxon:4932
+S000003353 MEP1 YGR121C|AMT1 taxon:4932
+S000003353 MEP1 YGR121C|AMT1 taxon:4932
+S000003353 MEP1 YGR121C|AMT1 taxon:4932
+S000003353 MEP1 YGR121C|AMT1 taxon:4932
+S000003353 MEP1 YGR121C|AMT1 taxon:4932
+S000005086 MEP2 YNL142W taxon:4932
+S000005086 MEP2 YNL142W taxon:4932
+S000005086 MEP2 YNL142W taxon:4932
+S000005086 MEP2 YNL142W taxon:4932
+S000006342 MEP3 YPR138C taxon:4932
+S000006342 MEP3 YPR138C taxon:4932
+S000006342 MEP3 YPR138C taxon:4932
+S000006342 MEP3 YPR138C taxon:4932
+S000006342 MEP3 YPR138C taxon:4932
+S000006342 MEP3 YPR138C taxon:4932
+S000006342 MEP3 YPR138C taxon:4932
+S000005154 MER1 YNL210W taxon:4932
+S000005154 MER1 YNL210W taxon:4932
+S000005154 MER1 YNL210W taxon:4932
+S000005154 MER1 YNL210W taxon:4932
+S000003496 MES1 YGR264C|MESI|MetRS taxon:4932
+S000003496 MES1 YGR264C|MESI|MetRS taxon:4932
+S000003496 MES1 YGR264C|MESI|MetRS taxon:4932
+S000003496 MES1 YGR264C|MESI|MetRS taxon:4932
+S000001777 MET1 YKR069W|MET20 taxon:4932
+S000001777 MET1 YKR069W|MET20 taxon:4932
+S000001777 MET1 YKR069W|MET20 taxon:4932
+S000001777 MET1 YKR069W|MET20 taxon:4932
+S000001777 MET1 YKR069W|MET20 taxon:4932
+S000001777 MET1 YKR069W|MET20 taxon:4932
+S000001777 MET1 YKR069W|MET20 taxon:4932
+S000001777 MET1 YKR069W|MET20 taxon:4932
+S000001926 MET10 YFR030W taxon:4932
+S000001926 MET10 YFR030W taxon:4932
+S000001926 MET10 YFR030W taxon:4932
+S000001926 MET10 YFR030W taxon:4932
+S000001926 MET10 YFR030W taxon:4932
+S000005944 MET12 YPL023C taxon:4932
+S000005944 MET12 YPL023C taxon:4932
+S000005944 MET12 YPL023C taxon:4932
+S000005944 MET12 YPL023C taxon:4932
+S000003093 MET13 YGL125W|MET11|MRPL45 taxon:4932
+S000003093 MET13 YGL125W|MET11|MRPL45 taxon:4932
+S000003093 MET13 YGL125W|MET11|MRPL45 taxon:4932
+S000003093 MET13 YGL125W|MET11|MRPL45 taxon:4932
+S000003093 MET13 YGL125W|MET11|MRPL45 taxon:4932
+S000003093 MET13 YGL125W|MET11|MRPL45 taxon:4932
+S000003093 MET13 YGL125W|MET11|MRPL45 taxon:4932
+S000003093 MET13 YGL125W|MET11|MRPL45 taxon:4932
+S000003093 MET13 YGL125W|MET11|MRPL45 taxon:4932
+S000003093 MET13 YGL125W|MET11|MRPL45 taxon:4932
+S000001484 MET14 YKL001C taxon:4932
+S000001484 MET14 YKL001C taxon:4932
+S000001484 MET14 YKL001C taxon:4932
+S000001484 MET14 YKL001C taxon:4932
+S000001484 MET14 YKL001C taxon:4932
+S000006371 MET16 YPR167C taxon:4932
+S000006371 MET16 YPR167C taxon:4932
+S000006371 MET16 YPR167C taxon:4932
+S000006371 MET16 YPR167C taxon:4932
+S000006371 MET16 YPR167C taxon:4932
+S000004294 MET17 YLR303W|MET15|MET25 taxon:4932
+S000004294 MET17 YLR303W|MET15|MET25 taxon:4932
+S000004294 MET17 YLR303W|MET15|MET25 taxon:4932
+S000004294 MET17 YLR303W|MET15|MET25 taxon:4932
+S000004294 MET17 YLR303W|MET15|MET25 taxon:4932
+S000004294 MET17 YLR303W|MET15|MET25 taxon:4932
+S000001390 MET18 YIL128W|MMS19 taxon:4932
+S000001390 MET18 YIL128W|MMS19 taxon:4932
+S000001390 MET18 YIL128W|MMS19 taxon:4932
+S000001390 MET18 YIL128W|MMS19 taxon:4932
+S000001390 MET18 YIL128W|MMS19 taxon:4932
+S000001390 MET18 YIL128W|MMS19 taxon:4932
+S000001390 MET18 YIL128W|MMS19 taxon:4932
+S000001390 MET18 YIL128W|MMS19 taxon:4932
+S000005221 MET2 YNL277W taxon:4932
+S000005221 MET2 YNL277W taxon:4932
+S000005221 MET2 YNL277W taxon:4932
+S000005221 MET2 YNL277W taxon:4932
+S000005425 MET22 YOL064C|HAL2 taxon:4932
+S000005425 MET22 YOL064C|HAL2 taxon:4932
+S000005425 MET22 YOL064C|HAL2 taxon:4932
+S000005425 MET22 YOL064C|HAL2 taxon:4932
+S000005425 MET22 YOL064C|HAL2 taxon:4932
+S000001456 MET28 YIR017C taxon:4932
+S000001456 MET28 YIR017C taxon:4932
+S000001456 MET28 YIR017C taxon:4932
+S000001456 MET28 YIR017C taxon:4932
+S000001456 MET28 YIR017C taxon:4932
+S000001456 MET28 YIR017C taxon:4932
+S000001456 MET28 YIR017C taxon:4932
+S000001456 MET28 YIR017C taxon:4932
+S000003771 MET3 YJR010W taxon:4932
+S000003771 MET3 YJR010W taxon:4932
+S000003771 MET3 YJR010W taxon:4932
+S000003771 MET3 YJR010W taxon:4932
+S000003771 MET3 YJR010W taxon:4932
+S000001308 MET30 YIL046W|ZRG11 taxon:4932
+S000001308 MET30 YIL046W|ZRG11 taxon:4932
+S000001308 MET30 YIL046W|ZRG11 taxon:4932
+S000001308 MET30 YIL046W|ZRG11 taxon:4932
+S000001308 MET30 YIL046W|ZRG11 taxon:4932
+S000001308 MET30 YIL046W|ZRG11 taxon:4932
+S000001308 MET30 YIL046W|ZRG11 taxon:4932
+S000001308 MET30 YIL046W|ZRG11 taxon:4932
+S000001308 MET30 YIL046W|ZRG11 taxon:4932
+S000005959 MET31 YPL038W taxon:4932
+S000005959 MET31 YPL038W taxon:4932
+S000005959 MET31 YPL038W taxon:4932
+S000005959 MET31 YPL038W taxon:4932
+S000005959 MET31 YPL038W taxon:4932
+S000005959 MET31 YPL038W taxon:4932
+S000005959 MET31 YPL038W taxon:4932
+S000005959 MET31 YPL038W taxon:4932
+S000005959 MET31 YPL038W taxon:4932
+S000002661 MET32 YDR253C taxon:4932
+S000002661 MET32 YDR253C taxon:4932
+S000002661 MET32 YDR253C taxon:4932
+S000002661 MET32 YDR253C taxon:4932
+S000005047 MET4 YNL103W taxon:4932
+S000005047 MET4 YNL103W taxon:4932
+S000005047 MET4 YNL103W taxon:4932
+S000005047 MET4 YNL103W taxon:4932
+S000005047 MET4 YNL103W taxon:4932
+S000005047 MET4 YNL103W taxon:4932
+S000000893 MET6 YER091C taxon:4932
+S000000893 MET6 YER091C taxon:4932
+S000000893 MET6 YER091C taxon:4932
+S000005767 MET7 YOR241W|MET23 taxon:4932
+S000005767 MET7 YOR241W|MET23 taxon:4932
+S000005767 MET7 YOR241W|MET23 taxon:4932
+S000005767 MET7 YOR241W|MET23 taxon:4932
+S000005767 MET7 YOR241W|MET23 taxon:4932
+S000000417 MET8 YBR213W taxon:4932
+S000000417 MET8 YBR213W taxon:4932
+S000000417 MET8 YBR213W taxon:4932
+S000000417 MET8 YBR213W taxon:4932
+S000000417 MET8 YBR213W taxon:4932
+S000004007 MEU1 YLR017W taxon:4932
+S000004007 MEU1 YLR017W taxon:4932
+S000004007 MEU1 YLR017W taxon:4932
+S000004007 MEU1 YLR017W taxon:4932
+S000004007 MEU1 YLR017W taxon:4932
+S000004007 MEU1 YLR017W taxon:4932
+S000006090 MEX67 YPL169C taxon:4932
+S000006090 MEX67 YPL169C taxon:4932
+S000006090 MEX67 YPL169C taxon:4932
+S000006090 MEX67 YPL169C taxon:4932
+S000006090 MEX67 YPL169C taxon:4932
+S000006090 MEX67 YPL169C taxon:4932
+S000006108 MF(ALPHA)1 YPL187W taxon:4932
+S000006108 MF(ALPHA)1 YPL187W taxon:4932
+S000006108 MF(ALPHA)1 YPL187W taxon:4932
+S000006108 MF(ALPHA)1 YPL187W taxon:4932
+S000006108 MF(ALPHA)1 YPL187W taxon:4932
+S000003057 MF(ALPHA)2 YGL089C taxon:4932
+S000003057 MF(ALPHA)2 YGL089C taxon:4932
+S000003057 MF(ALPHA)2 YGL089C taxon:4932
+S000003057 MF(ALPHA)2 YGL089C taxon:4932
+S000002869 MFA1 YDR461W taxon:4932
+S000002869 MFA1 YDR461W taxon:4932
+S000002869 MFA1 YDR461W taxon:4932
+S000002869 MFA1 YDR461W taxon:4932
+S000002869 MFA1 YDR461W taxon:4932
+S000005089 MFA2 YNL145W taxon:4932
+S000005089 MFA2 YNL145W taxon:4932
+S000005089 MFA2 YNL145W taxon:4932
+S000005089 MFA2 YNL145W taxon:4932
+S000002627 MFB1 YDR219C taxon:4932
+S000002627 MFB1 YDR219C taxon:4932
+S000002627 MFB1 YDR219C taxon:4932
+S000004527 MFT1 YML062C|MFT52 taxon:4932
+S000004527 MFT1 YML062C|MFT52 taxon:4932
+S000004527 MFT1 YML062C|MFT52 taxon:4932
+S000004527 MFT1 YML062C|MFT52 taxon:4932
+S000004527 MFT1 YML062C|MFT52 taxon:4932
+S000004527 MFT1 YML062C|MFT52 taxon:4932
+S000004527 MFT1 YML062C|MFT52 taxon:4932
+S000003481 MGA1 YGR249W taxon:4932
+S000003481 MGA1 YGR249W taxon:4932
+S000003481 MGA1 YGR249W taxon:4932
+S000001472 MGA2 YIR033W taxon:4932
+S000001472 MGA2 YIR033W taxon:4932
+S000001472 MGA2 YIR033W taxon:4932
+S000001472 MGA2 YIR033W taxon:4932
+S000001472 MGA2 YIR033W taxon:4932
+S000001472 MGA2 YIR033W taxon:4932
+S000005758 MGE1 YOR232W|GRPE|YGE1 taxon:4932
+S000005758 MGE1 YOR232W|GRPE|YGE1 taxon:4932
+S000005758 MGE1 YOR232W|GRPE|YGE1 taxon:4932
+S000005758 MGE1 YOR232W|GRPE|YGE1 taxon:4932
+S000005758 MGE1 YOR232W|GRPE|YGE1 taxon:4932
+S000005758 MGE1 YOR232W|GRPE|YGE1 taxon:4932
+S000005758 MGE1 YOR232W|GRPE|YGE1 taxon:4932
+S000005737 MGM1 YOR211C|MNA1 taxon:4932
+S000005737 MGM1 YOR211C|MNA1 taxon:4932
+S000005737 MGM1 YOR211C|MNA1 taxon:4932
+S000005737 MGM1 YOR211C|MNA1 taxon:4932
+S000005737 MGM1 YOR211C|MNA1 taxon:4932
+S000005737 MGM1 YOR211C|MNA1 taxon:4932
+S000005737 MGM1 YOR211C|MNA1 taxon:4932
+S000003905 MGM101 YJR144W|MGM9 taxon:4932
+S000003905 MGM101 YJR144W|MGM9 taxon:4932
+S000003905 MGM101 YJR144W|MGM9 taxon:4932
+S000003905 MGM101 YJR144W|MGM9 taxon:4932
+S000003905 MGM101 YJR144W|MGM9 taxon:4932
+S000000549 MGR1 YCL044C taxon:4932
+S000000549 MGR1 YCL044C taxon:4932
+S000000549 MGR1 YCL044C taxon:4932
+S000000549 MGR1 YCL044C taxon:4932
+S000000549 MGR1 YCL044C taxon:4932
+S000000549 MGR1 YCL044C taxon:4932
+S000006019 MGR2 YPL098C taxon:4932
+S000006019 MGR2 YPL098C taxon:4932
+S000006019 MGR2 YPL098C taxon:4932
+S000006019 MGR2 YPL098C taxon:4932
+S000005162 MGS1 YNL218W taxon:4932
+S000005162 MGS1 YNL218W taxon:4932
+S000005162 MGS1 YNL218W taxon:4932
+S000005162 MGS1 YNL218W taxon:4932
+S000005162 MGS1 YNL218W taxon:4932
+S000005162 MGS1 YNL218W taxon:4932
+S000005162 MGS1 YNL218W taxon:4932
+S000002359 MGT1 YDL200C|MGMT taxon:4932
+S000002359 MGT1 YDL200C|MGMT taxon:4932
+S000002359 MGT1 YDL200C|MGMT taxon:4932
+S000002359 MGT1 YDL200C|MGMT taxon:4932
+S000003578 MHP1 YJL042W taxon:4932
+S000003578 MHP1 YJL042W taxon:4932
+S000003578 MHP1 YJL042W taxon:4932
+S000003578 MHP1 YJL042W taxon:4932
+S000002704 MHR1 YDR296W|XTC1 taxon:4932
+S000002704 MHR1 YDR296W|XTC1 taxon:4932
+S000002704 MHR1 YDR296W|XTC1 taxon:4932
+S000002704 MHR1 YDR296W|XTC1 taxon:4932
+S000002704 MHR1 YDR296W|XTC1 taxon:4932
+S000003985 MHT1 YLL062C taxon:4932
+S000003985 MHT1 YLL062C taxon:4932
+S000003985 MHT1 YLL062C taxon:4932
+S000001678 MIA40 YKL195W|FMP15|TIM40 taxon:4932
+S000001678 MIA40 YKL195W|FMP15|TIM40 taxon:4932
+S000001678 MIA40 YKL195W|FMP15|TIM40 taxon:4932
+S000001678 MIA40 YKL195W|FMP15|TIM40 taxon:4932
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+S000003003 MIG1 YGL035C|CAT4|SSN1|TDS22 taxon:4932
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+S000002551 MKC7 YDR144C|YPS2 taxon:4932
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+S000005757 MKK1 YOR231W|SSP32 taxon:4932
+S000005757 MKK1 YOR231W|SSP32 taxon:4932
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+S000006061 MKK2 YPL140C|LPI6|SSP33 taxon:4932
+S000006061 MKK2 YPL140C|LPI6|SSP33 taxon:4932
+S000006061 MKK2 YPL140C|LPI6|SSP33 taxon:4932
+S000005020 MKS1 YNL076W|LYS80 taxon:4932
+S000005020 MKS1 YNL076W|LYS80 taxon:4932
+S000005020 MKS1 YNL076W|LYS80 taxon:4932
+S000005020 MKS1 YNL076W|LYS80 taxon:4932
+S000005029 MKT1 YNL085W taxon:4932
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+S000005029 MKT1 YNL085W taxon:4932
+S000005029 MKT1 YNL085W taxon:4932
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+S000003074 MLC1 YGL106W taxon:4932
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+S000003074 MLC1 YGL106W taxon:4932
+S000003074 MLC1 YGL106W taxon:4932
+S000003074 MLC1 YGL106W taxon:4932
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+S000003074 MLC1 YGL106W taxon:4932
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+S000003074 MLC1 YGL106W taxon:4932
+S000003074 MLC1 YGL106W taxon:4932
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+S000006392 MLC2 YPR188C taxon:4932
+S000006392 MLC2 YPR188C taxon:4932
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+S000005018 MLF3 YNL074C|YMK1 taxon:4932
+S000005018 MLF3 YNL074C|YMK1 taxon:4932
+S000004777 MLH1 YMR167W|PMS2 taxon:4932
+S000004777 MLH1 YMR167W|PMS2 taxon:4932
+S000004777 MLH1 YMR167W|PMS2 taxon:4932
+S000004777 MLH1 YMR167W|PMS2 taxon:4932
+S000004777 MLH1 YMR167W|PMS2 taxon:4932
+S000004777 MLH1 YMR167W|PMS2 taxon:4932
+S000004025 MLH2 YLR035C taxon:4932
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+S000006085 MLH3 YPL164C taxon:4932
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+S000001803 MLP1 YKR095W|MPL1 taxon:4932
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+S000001411 MLP2 YIL149C taxon:4932
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+S000001313 MMF1 YIL051C|IBM1 taxon:4932
+S000001313 MMF1 YIL051C|IBM1 taxon:4932
+S000001313 MMF1 YIL051C|IBM1 taxon:4932
+S000003929 MMM1 YLL006W|YME6 taxon:4932
+S000003929 MMM1 YLL006W|YME6 taxon:4932
+S000003929 MMM1 YLL006W|YME6 taxon:4932
+S000003929 MMM1 YLL006W|YME6 taxon:4932
+S000003929 MMM1 YLL006W|YME6 taxon:4932
+S000003929 MMM1 YLL006W|YME6 taxon:4932
+S000003984 MMP1 YLL061W taxon:4932
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+S000003984 MMP1 YLL061W taxon:4932
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+S000004180 MMR1 YLR190W taxon:4932
+S000004180 MMR1 YLR190W taxon:4932
+S000004180 MMR1 YLR190W taxon:4932
+S000004180 MMR1 YLR190W taxon:4932
+S000004180 MMR1 YLR190W taxon:4932
+S000004180 MMR1 YLR190W taxon:4932
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+S000006368 MMS1 YPR164W|RTT108|SLM6 taxon:4932
+S000006368 MMS1 YPR164W|RTT108|SLM6 taxon:4932
+S000006368 MMS1 YPR164W|RTT108|SLM6 taxon:4932
+S000006368 MMS1 YPR164W|RTT108|SLM6 taxon:4932
+S000006368 MMS1 YPR164W|RTT108|SLM6 taxon:4932
+S000003055 MMS2 YGL087C taxon:4932
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+S000003055 MMS2 YGL087C taxon:4932
+S000003055 MMS2 YGL087C taxon:4932
+S000003055 MMS2 YGL087C taxon:4932
+S000003055 MMS2 YGL087C taxon:4932
+S000003055 MMS2 YGL087C taxon:4932
+S000003055 MMS2 YGL087C taxon:4932
+S000003055 MMS2 YGL087C taxon:4932
+S000003055 MMS2 YGL087C taxon:4932
+S000003055 MMS2 YGL087C taxon:4932
+S000003055 MMS2 YGL087C taxon:4932
+S000003055 MMS2 YGL087C taxon:4932
+S000000745 MMS21 YEL019C taxon:4932
+S000000745 MMS21 YEL019C taxon:4932
+S000000745 MMS21 YEL019C taxon:4932
+S000000745 MMS21 YEL019C taxon:4932
+S000000745 MMS21 YEL019C taxon:4932
+S000000745 MMS21 YEL019C taxon:4932
+S000000745 MMS21 YEL019C taxon:4932
+S000000745 MMS21 YEL019C taxon:4932
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+S000004312 MMS22 YLR320W|SLM2 taxon:4932
+S000004312 MMS22 YLR320W|SLM2 taxon:4932
+S000000302 MMS4 YBR098W|SLX2|YBR100W taxon:4932
+S000000302 MMS4 YBR098W|SLX2|YBR100W taxon:4932
+S000000302 MMS4 YBR098W|SLX2|YBR100W taxon:4932
+S000000302 MMS4 YBR098W|SLX2|YBR100W taxon:4932
+S000000302 MMS4 YBR098W|SLX2|YBR100W taxon:4932
+S000004789 MMT1 YMR177W taxon:4932
+S000004789 MMT1 YMR177W taxon:4932
+S000004789 MMT1 YMR177W taxon:4932
+S000004789 MMT1 YMR177W taxon:4932
+S000004789 MMT1 YMR177W taxon:4932
+S000004789 MMT1 YMR177W taxon:4932
+S000006145 MMT2 YPL224C|MFT2 taxon:4932
+S000006145 MMT2 YPL224C|MFT2 taxon:4932
+S000006145 MMT2 YPL224C|MFT2 taxon:4932
+S000006145 MMT2 YPL224C|MFT2 taxon:4932
+S000006145 MMT2 YPL224C|MFT2 taxon:4932
+S000006145 MMT2 YPL224C|MFT2 taxon:4932
+S000003151 MND1 YGL183C taxon:4932
+S000003151 MND1 YGL183C taxon:4932
+S000003151 MND1 YGL183C taxon:4932
+S000003151 MND1 YGL183C taxon:4932
+S000003151 MND1 YGL183C taxon:4932
+S000001464 MND2 YIR025W taxon:4932
+S000001464 MND2 YIR025W taxon:4932
+S000001464 MND2 YIR025W taxon:4932
+S000001464 MND2 YIR025W taxon:4932
+S000001464 MND2 YIR025W taxon:4932
+S000001464 MND2 YIR025W taxon:4932
+S000001464 MND2 YIR025W taxon:4932
+S000001464 MND2 YIR025W taxon:4932
+S000001464 MND2 YIR025W taxon:4932
+S000005877 MNE1 YOR350C taxon:4932
+S000005877 MNE1 YOR350C taxon:4932
+S000005877 MNE1 YOR350C taxon:4932
+S000001247 MNL1 YHR204W|HTM1 taxon:4932
+S000001247 MNL1 YHR204W|HTM1 taxon:4932
+S000001247 MNL1 YHR204W|HTM1 taxon:4932
+S000001247 MNL1 YHR204W|HTM1 taxon:4932
+S000001247 MNL1 YHR204W|HTM1 taxon:4932
+S000000803 MNN1 YER001W taxon:4932
+S000000803 MNN1 YER001W taxon:4932
+S000000803 MNN1 YER001W taxon:4932
+S000000803 MNN1 YER001W taxon:4932
+S000002653 MNN10 YDR245W|BED1|REC41|SLC2 taxon:4932
+S000002653 MNN10 YDR245W|BED1|REC41|SLC2 taxon:4932
+S000002653 MNN10 YDR245W|BED1|REC41|SLC2 taxon:4932
+S000002653 MNN10 YDR245W|BED1|REC41|SLC2 taxon:4932
+S000002653 MNN10 YDR245W|BED1|REC41|SLC2 taxon:4932
+S000002653 MNN10 YDR245W|BED1|REC41|SLC2 taxon:4932
+S000003719 MNN11 YJL183W taxon:4932
+S000003719 MNN11 YJL183W taxon:4932
+S000003719 MNN11 YJL183W taxon:4932
+S000003719 MNN11 YJL183W taxon:4932
+S000000219 MNN2 YBR015C|CRV4|LDB8|TTP1 taxon:4932
+S000000219 MNN2 YBR015C|CRV4|LDB8|TTP1 taxon:4932
+S000000219 MNN2 YBR015C|CRV4|LDB8|TTP1 taxon:4932
+S000000219 MNN2 YBR015C|CRV4|LDB8|TTP1 taxon:4932
+S000001684 MNN4 YKL201C taxon:4932
+S000001684 MNN4 YKL201C taxon:4932
+S000001684 MNN4 YKL201C taxon:4932
+S000001684 MNN4 YKL201C taxon:4932
+S000001684 MNN4 YKL201C taxon:4932
+S000003722 MNN5 YJL186W taxon:4932
+S000003722 MNN5 YJL186W taxon:4932
+S000003722 MNN5 YJL186W taxon:4932
+S000005971 MNN9 YPL050C taxon:4932
+S000005971 MNN9 YPL050C taxon:4932
+S000005971 MNN9 YPL050C taxon:4932
+S000005971 MNN9 YPL050C taxon:4932
+S000005971 MNN9 YPL050C taxon:4932
+S000005971 MNN9 YPL050C taxon:4932
+S000005971 MNN9 YPL050C taxon:4932
+S000005971 MNN9 YPL050C taxon:4932
+S000003036 MNP1 YGL068W taxon:4932
+S000003036 MNP1 YGL068W taxon:4932
+S000003036 MNP1 YGL068W taxon:4932
+S000003036 MNP1 YGL068W taxon:4932
+S000003036 MNP1 YGL068W taxon:4932
+S000003036 MNP1 YGL068W taxon:4932
+S000003036 MNP1 YGL068W taxon:4932
+S000001547 MNR2 YKL064W taxon:4932
+S000001547 MNR2 YKL064W taxon:4932
+S000001547 MNR2 YKL064W taxon:4932
+S000003892 MNS1 YJR131W taxon:4932
+S000003892 MNS1 YJR131W taxon:4932
+S000003892 MNS1 YJR131W taxon:4932
+S000003892 MNS1 YJR131W taxon:4932
+S000003226 MNT2 YGL257C taxon:4932
+S000003226 MNT2 YGL257C taxon:4932
+S000003226 MNT2 YGL257C taxon:4932
+S000001276 MNT3 YIL014W taxon:4932
+S000001276 MNT3 YIL014W taxon:4932
+S000001276 MNT3 YIL014W taxon:4932
+S000005342 MNT4 YNR059W taxon:4932
+S000005342 MNT4 YNR059W taxon:4932
+S000005342 MNT4 YNR059W taxon:4932
+S000001368 MOB1 YIL106W taxon:4932
+S000001368 MOB1 YIL106W taxon:4932
+S000001368 MOB1 YIL106W taxon:4932
+S000001368 MOB1 YIL106W taxon:4932
+S000001368 MOB1 YIL106W taxon:4932
+S000001859 MOB2 YFL034C-B|YFL035C|YFL035C-A taxon:4932
+S000001859 MOB2 YFL034C-B|YFL035C|YFL035C-A taxon:4932
+S000001859 MOB2 YFL034C-B|YFL035C|YFL035C-A taxon:4932
+S000001859 MOB2 YFL034C-B|YFL035C|YFL035C-A taxon:4932
+S000001859 MOB2 YFL034C-B|YFL035C|YFL035C-A taxon:4932
+S000001859 MOB2 YFL034C-B|YFL035C|YFL035C-A taxon:4932
+S000001859 MOB2 YFL034C-B|YFL035C|YFL035C-A taxon:4932
+S000001859 MOB2 YFL034C-B|YFL035C|YFL035C-A taxon:4932
+S000001859 MOB2 YFL034C-B|YFL035C|YFL035C-A taxon:4932
+S000005800 MOD5 YOR274W taxon:4932
+S000005800 MOD5 YOR274W taxon:4932
+S000005800 MOD5 YOR274W taxon:4932
+S000005800 MOD5 YOR274W taxon:4932
+S000005800 MOD5 YOR274W taxon:4932
+S000005800 MOD5 YOR274W taxon:4932
+S000005800 MOD5 YOR274W taxon:4932
+S000003835 MOG1 YJR074W taxon:4932
+S000003835 MOG1 YJR074W taxon:4932
+S000003835 MOG1 YJR074W taxon:4932
+S000000145 MOH1 YBL049W taxon:4932
+S000000145 MOH1 YBL049W taxon:4932
+S000000145 MOH1 YBL049W taxon:4932
+S000003092 MON1 YGL124C|AUT12 taxon:4932
+S000003092 MON1 YGL124C|AUT12 taxon:4932
+S000003092 MON1 YGL124C|AUT12 taxon:4932
+S000003092 MON1 YGL124C|AUT12 taxon:4932
+S000003092 MON1 YGL124C|AUT12 taxon:4932
+S000003092 MON1 YGL124C|AUT12 taxon:4932
+S000005241 MON2 YNL297C|YSL2 taxon:4932
+S000005241 MON2 YNL297C|YSL2 taxon:4932
+S000005241 MON2 YNL297C|YSL2 taxon:4932
+S000005241 MON2 YNL297C|YSL2 taxon:4932
+S000005241 MON2 YNL297C|YSL2 taxon:4932
+S000005241 MON2 YNL297C|YSL2 taxon:4932
+S000005241 MON2 YNL297C|YSL2 taxon:4932
+S000005241 MON2 YNL297C|YSL2 taxon:4932
+S000005241 MON2 YNL297C|YSL2 taxon:4932
+S000005241 MON2 YNL297C|YSL2 taxon:4932
+S000006003 MOT1 YPL082C|BTAF1|BUR3|LPF4 taxon:4932
+S000006003 MOT1 YPL082C|BTAF1|BUR3|LPF4 taxon:4932
+S000006003 MOT1 YPL082C|BTAF1|BUR3|LPF4 taxon:4932
+S000006003 MOT1 YPL082C|BTAF1|BUR3|LPF4 taxon:4932
+S000006003 MOT1 YPL082C|BTAF1|BUR3|LPF4 taxon:4932
+S000000870 MOT2 YER068W|NOT4|SIG1 taxon:4932
+S000000870 MOT2 YER068W|NOT4|SIG1 taxon:4932
+S000000870 MOT2 YER068W|NOT4|SIG1 taxon:4932
+S000000870 MOT2 YER068W|NOT4|SIG1 taxon:4932
+S000000870 MOT2 YER068W|NOT4|SIG1 taxon:4932
+S000000870 MOT2 YER068W|NOT4|SIG1 taxon:4932
+S000000870 MOT2 YER068W|NOT4|SIG1 taxon:4932
+S000004674 MOT3 YMR070W|ROX7 taxon:4932
+S000004674 MOT3 YMR070W|ROX7 taxon:4932
+S000004674 MOT3 YMR070W|ROX7 taxon:4932
+S000004674 MOT3 YMR070W|ROX7 taxon:4932
+S000004674 MOT3 YMR070W|ROX7 taxon:4932
+S000004674 MOT3 YMR070W|ROX7 taxon:4932
+S000004674 MOT3 YMR070W|ROX7 taxon:4932
+S000004674 MOT3 YMR070W|ROX7 taxon:4932
+S000004674 MOT3 YMR070W|ROX7 taxon:4932
+S000005193 MPA43 YNL249C taxon:4932
+S000005193 MPA43 YNL249C taxon:4932
+S000005193 MPA43 YNL249C taxon:4932
+S000005703 MPC54 YOR177C taxon:4932
+S000005703 MPC54 YOR177C taxon:4932
+S000005703 MPC54 YOR177C taxon:4932
+S000005703 MPC54 YOR177C taxon:4932
+S000005814 MPD1 YOR288C taxon:4932
+S000005814 MPD1 YOR288C taxon:4932
+S000005814 MPD1 YOR288C taxon:4932
+S000005814 MPD1 YOR288C taxon:4932
+S000005448 MPD2 YOL088C taxon:4932
+S000005448 MPD2 YOL088C taxon:4932
+S000005448 MPD2 YOL088C taxon:4932
+S000005448 MPD2 YOL088C taxon:4932
+S000001542 MPE1 YKL059C taxon:4932
+S000001542 MPE1 YKL059C taxon:4932
+S000001542 MPE1 YKL059C taxon:4932
+S000001542 MPE1 YKL059C taxon:4932
+S000001542 MPE1 YKL059C taxon:4932
+S000001542 MPE1 YKL059C taxon:4932
+S000001542 MPE1 YKL059C taxon:4932
+S000001542 MPE1 YKL059C taxon:4932
+S000001542 MPE1 YKL059C taxon:4932
+S000001542 MPE1 YKL059C taxon:4932
+S000001441 MPH1 YIR002C taxon:4932
+S000001441 MPH1 YIR002C taxon:4932
+S000001441 MPH1 YIR002C taxon:4932
+S000001441 MPH1 YIR002C taxon:4932
+S000001441 MPH1 YIR002C taxon:4932
+S000002406 MPH2 YDL247W taxon:4932
+S000002406 MPH2 YDL247W taxon:4932
+S000002406 MPH2 YDL247W taxon:4932
+S000002406 MPH2 YDL247W taxon:4932
+S000002406 MPH2 YDL247W taxon:4932
+S000002406 MPH2 YDL247W taxon:4932
+S000003921 MPH3 YJR160C taxon:4932
+S000003921 MPH3 YJR160C taxon:4932
+S000003921 MPH3 YJR160C taxon:4932
+S000003921 MPH3 YJR160C taxon:4932
+S000003921 MPH3 YJR160C taxon:4932
+S000003602 MPM1 YJL066C taxon:4932
+S000003602 MPM1 YJL066C taxon:4932
+S000003602 MPM1 YJL066C taxon:4932
+S000003602 MPM1 YJL066C taxon:4932
+S000003602 MPM1 YJL066C taxon:4932
+S000003762 MPP10 YJR002W taxon:4932
+S000003762 MPP10 YJR002W taxon:4932
+S000003762 MPP10 YJR002W taxon:4932
+S000003762 MPP10 YJR002W taxon:4932
+S000003762 MPP10 YJR002W taxon:4932
+S000003762 MPP10 YJR002W taxon:4932
+S000003762 MPP10 YJR002W taxon:4932
+S000003762 MPP10 YJR002W taxon:4932
+S000003762 MPP10 YJR002W taxon:4932
+S000029666 MPR1 taxon:4932
+S000029666 MPR1 taxon:4932
+S000029666 MPR1 taxon:4932
+S000029666 MPR1 taxon:4932
+S000029666 MPR1 taxon:4932
+S000029666 MPR1 taxon:4932
+S000029666 MPR1 taxon:4932
+S000002186 MPS1 YDL028C|RPK1 taxon:4932
+S000002186 MPS1 YDL028C|RPK1 taxon:4932
+S000002186 MPS1 YDL028C|RPK1 taxon:4932
+S000002186 MPS1 YDL028C|RPK1 taxon:4932
+S000002186 MPS1 YDL028C|RPK1 taxon:4932
+S000002186 MPS1 YDL028C|RPK1 taxon:4932
+S000002186 MPS1 YDL028C|RPK1 taxon:4932
+S000002186 MPS1 YDL028C|RPK1 taxon:4932
+S000003043 MPS2 YGL075C|MMC1 taxon:4932
+S000003043 MPS2 YGL075C|MMC1 taxon:4932
+S000003043 MPS2 YGL075C|MMC1 taxon:4932
+S000003043 MPS2 YGL075C|MMC1 taxon:4932
+S000003043 MPS2 YGL075C|MMC1 taxon:4932
+S000003556 MPS3 YJL019W|NEP98|YJL018W taxon:4932
+S000003556 MPS3 YJL019W|NEP98|YJL018W taxon:4932
+S000003556 MPS3 YJL019W|NEP98|YJL018W taxon:4932
+S000003556 MPS3 YJL019W|NEP98|YJL018W taxon:4932
+S000003556 MPS3 YJL019W|NEP98|YJL018W taxon:4932
+S000003556 MPS3 YJL019W|NEP98|YJL018W taxon:4932
+S000003556 MPS3 YJL019W|NEP98|YJL018W taxon:4932
+S000003146 MPT5 YGL178W|HTR1|PUF5|UTH4 taxon:4932
+S000003146 MPT5 YGL178W|HTR1|PUF5|UTH4 taxon:4932
+S000003146 MPT5 YGL178W|HTR1|PUF5|UTH4 taxon:4932
+S000003146 MPT5 YGL178W|HTR1|PUF5|UTH4 taxon:4932
+S000003146 MPT5 YGL178W|HTR1|PUF5|UTH4 taxon:4932
+S000003146 MPT5 YGL178W|HTR1|PUF5|UTH4 taxon:4932
+S000003146 MPT5 YGL178W|HTR1|PUF5|UTH4 taxon:4932
+S000003146 MPT5 YGL178W|HTR1|PUF5|UTH4 taxon:4932
+S000003146 MPT5 YGL178W|HTR1|PUF5|UTH4 taxon:4932
+S000003146 MPT5 YGL178W|HTR1|PUF5|UTH4 taxon:4932
+S000000566 MRC1 YCL061C|YCL060C taxon:4932
+S000000566 MRC1 YCL061C|YCL060C taxon:4932
+S000000566 MRC1 YCL061C|YCL060C taxon:4932
+S000000566 MRC1 YCL061C|YCL060C taxon:4932
+S000000566 MRC1 YCL061C|YCL060C taxon:4932
+S000000566 MRC1 YCL061C|YCL060C taxon:4932
+S000000566 MRC1 YCL061C|YCL060C taxon:4932
+S000000566 MRC1 YCL061C|YCL060C taxon:4932
+S000000566 MRC1 YCL061C|YCL060C taxon:4932
+S000000566 MRC1 YCL061C|YCL060C taxon:4932
+S000000566 MRC1 YCL061C|YCL060C taxon:4932
+S000000566 MRC1 YCL061C|YCL060C taxon:4932
+S000006316 MRD1 YPR112C taxon:4932
+S000006316 MRD1 YPR112C taxon:4932
+S000006316 MRD1 YPR112C taxon:4932
+S000006316 MRD1 YPR112C taxon:4932
+S000004837 MRE11 YMR224C|NGS1|RAD58|XRS4 taxon:4932
+S000004837 MRE11 YMR224C|NGS1|RAD58|XRS4 taxon:4932
+S000004837 MRE11 YMR224C|NGS1|RAD58|XRS4 taxon:4932
+S000004837 MRE11 YMR224C|NGS1|RAD58|XRS4 taxon:4932
+S000004837 MRE11 YMR224C|NGS1|RAD58|XRS4 taxon:4932
+S000004837 MRE11 YMR224C|NGS1|RAD58|XRS4 taxon:4932
+S000004837 MRE11 YMR224C|NGS1|RAD58|XRS4 taxon:4932
+S000004837 MRE11 YMR224C|NGS1|RAD58|XRS4 taxon:4932
+S000004837 MRE11 YMR224C|NGS1|RAD58|XRS4 taxon:4932
+S000004837 MRE11 YMR224C|NGS1|RAD58|XRS4 taxon:4932
+S000004837 MRE11 YMR224C|NGS1|RAD58|XRS4 taxon:4932
+S000004837 MRE11 YMR224C|NGS1|RAD58|XRS4 taxon:4932
+S000004837 MRE11 YMR224C|NGS1|RAD58|XRS4 taxon:4932
+S000004837 MRE11 YMR224C|NGS1|RAD58|XRS4 taxon:4932
+S000004837 MRE11 YMR224C|NGS1|RAD58|XRS4 taxon:4932
+S000004837 MRE11 YMR224C|NGS1|RAD58|XRS4 taxon:4932
+S000003111 MRF1 YGL143C taxon:4932
+S000003111 MRF1 YGL143C taxon:4932
+S000003111 MRF1 YGL143C taxon:4932
+S000003111 MRF1 YGL143C taxon:4932
+S000003111 MRF1 YGL143C taxon:4932
+S000003111 MRF1 YGL143C taxon:4932
+S000003111 MRF1 YGL143C taxon:4932
+S000003111 MRF1 YGL143C taxon:4932
+S000003111 MRF1 YGL143C taxon:4932
+S000002440 MRH1 YDR033W taxon:4932
+S000002440 MRH1 YDR033W taxon:4932
+S000002440 MRH1 YDR033W taxon:4932
+S000002440 MRH1 YDR033W taxon:4932
+S000003032 MRH4 YGL064C taxon:4932
+S000003032 MRH4 YGL064C taxon:4932
+S000003032 MRH4 YGL064C taxon:4932
+S000003032 MRH4 YGL064C taxon:4932
+S000002237 MRK1 YDL079C taxon:4932
+S000002237 MRK1 YDL079C taxon:4932
+S000002237 MRK1 YDL079C taxon:4932
+S000002237 MRK1 YDL079C taxon:4932
+S000002237 MRK1 YDL079C taxon:4932
+S000002237 MRK1 YDL079C taxon:4932
+S000002237 MRK1 YDL079C taxon:4932
+S000002237 MRK1 YDL079C taxon:4932
+S000006283 MRL1 YPR079W taxon:4932
+S000006283 MRL1 YPR079W taxon:4932
+S000006283 MRL1 YPR079W taxon:4932
+S000006283 MRL1 YPR079W taxon:4932
+S000006283 MRL1 YPR079W taxon:4932
+S000006283 MRL1 YPR079W taxon:4932
+S000005727 MRM1 YOR201C|PET56 taxon:4932
+S000005727 MRM1 YOR201C|PET56 taxon:4932
+S000005727 MRM1 YOR201C|PET56 taxon:4932
+S000003104 MRM2 YGL136C taxon:4932
+S000003104 MRM2 YGL136C taxon:4932
+S000003104 MRM2 YGL136C taxon:4932
+S000003104 MRM2 YGL136C taxon:4932
+S000003104 MRM2 YGL136C taxon:4932
+S000003104 MRM2 YGL136C taxon:4932
+S000003104 MRM2 YGL136C taxon:4932
+S000002755 MRP1 YDR347W taxon:4932
+S000002755 MRP1 YDR347W taxon:4932
+S000002755 MRP1 YDR347W taxon:4932
+S000002755 MRP1 YDR347W taxon:4932
+S000002755 MRP1 YDR347W taxon:4932
+S000002755 MRP1 YDR347W taxon:4932
+S000006430 MRP10 YDL045W-A taxon:4932
+S000006430 MRP10 YDL045W-A taxon:4932
+S000006430 MRP10 YDL045W-A taxon:4932
+S000006430 MRP10 YDL045W-A taxon:4932
+S000006430 MRP10 YDL045W-A taxon:4932
+S000006430 MRP10 YDL045W-A taxon:4932
+S000003316 MRP13 YGR084C taxon:4932
+S000003316 MRP13 YGR084C taxon:4932
+S000003316 MRP13 YGR084C taxon:4932
+S000003316 MRP13 YGR084C taxon:4932
+S000001486 MRP17 YKL003C taxon:4932
+S000001486 MRP17 YKL003C taxon:4932
+S000001486 MRP17 YKL003C taxon:4932
+S000001486 MRP17 YKL003C taxon:4932
+S000006370 MRP2 YPR166C taxon:4932
+S000006370 MRP2 YPR166C taxon:4932
+S000006370 MRP2 YPR166C taxon:4932
+S000006370 MRP2 YPR166C taxon:4932
+S000006370 MRP2 YPR166C taxon:4932
+S000006370 MRP2 YPR166C taxon:4932
+S000002813 MRP20 YDR405W|MRPL41|YmL41 taxon:4932
+S000002813 MRP20 YDR405W|MRPL41|YmL41 taxon:4932
+S000002813 MRP20 YDR405W|MRPL41|YmL41 taxon:4932
+S000000186 MRP21 YBL090W|MRP50 taxon:4932
+S000000186 MRP21 YBL090W|MRP50 taxon:4932
+S000000186 MRP21 YBL090W|MRP50 taxon:4932
+S000000186 MRP21 YBL090W|MRP50 taxon:4932
+S000000996 MRP4 YHL004W taxon:4932
+S000000996 MRP4 YHL004W taxon:4932
+S000000996 MRP4 YHL004W taxon:4932
+S000000996 MRP4 YHL004W taxon:4932
+S000000996 MRP4 YHL004W taxon:4932
+S000000996 MRP4 YHL004W taxon:4932
+S000000996 MRP4 YHL004W taxon:4932
+S000001650 MRP49 YKL167C taxon:4932
+S000001650 MRP49 YKL167C taxon:4932
+S000001650 MRP49 YKL167C taxon:4932
+S000006039 MRP51 YPL118W taxon:4932
+S000006039 MRP51 YPL118W taxon:4932
+S000006039 MRP51 YPL118W taxon:4932
+S000006039 MRP51 YPL118W taxon:4932
+S000006039 MRP51 YPL118W taxon:4932
+S000006039 MRP51 YPL118W taxon:4932
+S000006039 MRP51 YPL118W taxon:4932
+S000004950 MRP7 YNL005C|MRPL2|YmL2 taxon:4932
+S000004950 MRP7 YNL005C|MRPL2|YmL2 taxon:4932
+S000004950 MRP7 YNL005C|MRPL2|YmL2 taxon:4932
+S000004950 MRP7 YNL005C|MRPL2|YmL2 taxon:4932
+S000001625 MRP8 YKL142W|YKL3 taxon:4932
+S000001625 MRP8 YKL142W|YKL3 taxon:4932
+S000001625 MRP8 YKL142W|YKL3 taxon:4932
+S000002523 MRPL1 YDR116C taxon:4932
+S000002523 MRPL1 YDR116C taxon:4932
+S000002523 MRPL1 YDR116C taxon:4932
+S000002523 MRPL1 YDR116C taxon:4932
+S000002523 MRPL1 YDR116C taxon:4932
+S000002523 MRPL1 YDR116C taxon:4932
+S000002523 MRPL1 YDR116C taxon:4932
+S000005228 MRPL10 YNL284C|MRPL18|YmL10|YmL18 taxon:4932
+S000005228 MRPL10 YNL284C|MRPL18|YmL10|YmL18 taxon:4932
+S000005228 MRPL10 YNL284C|MRPL18|YmL10|YmL18 taxon:4932
+S000002361 MRPL11 YDL202W|YmL11 taxon:4932
+S000002361 MRPL11 YDL202W|YmL11 taxon:4932
+S000002361 MRPL11 YDL202W|YmL11 taxon:4932
+S000001714 MRPL13 YKR006C|YK105|YmL13 taxon:4932
+S000001714 MRPL13 YKR006C|YK105|YmL13 taxon:4932
+S000001714 MRPL13 YKR006C|YK105|YmL13 taxon:4932
+S000004304 MRPL15 YLR312W-A|YmL15 taxon:4932
+S000004304 MRPL15 YLR312W-A|YmL15 taxon:4932
+S000004304 MRPL15 YLR312W-A|YmL15 taxon:4932
+S000004304 MRPL15 YLR312W-A|YmL15 taxon:4932
+S000000134 MRPL16 YBL038W taxon:4932
+S000000134 MRPL16 YBL038W taxon:4932
+S000000134 MRPL16 YBL038W taxon:4932
+S000000134 MRPL16 YBL038W taxon:4932
+S000005196 MRPL17 YNL252C|MRPL30|YmL30 taxon:4932
+S000005196 MRPL17 YNL252C|MRPL30|YmL30 taxon:4932
+S000005196 MRPL17 YNL252C|MRPL30|YmL30 taxon:4932
+S000005196 MRPL17 YNL252C|MRPL30|YmL30 taxon:4932
+S000005129 MRPL19 YNL185C|YmL19 taxon:4932
+S000005129 MRPL19 YNL185C|YmL19 taxon:4932
+S000005129 MRPL19 YNL185C|YmL19 taxon:4932
+S000001793 MRPL20 YKR085C|YmL20 taxon:4932
+S000001793 MRPL20 YKR085C|YmL20 taxon:4932
+S000001793 MRPL20 YKR085C|YmL20 taxon:4932
+S000001793 MRPL20 YKR085C|YmL20 taxon:4932
+S000001793 MRPL20 YKR085C|YmL20 taxon:4932
+S000005121 MRPL22 YNL177C taxon:4932
+S000005121 MRPL22 YNL177C taxon:4932
+S000005121 MRPL22 YNL177C taxon:4932
+S000005121 MRPL22 YNL177C taxon:4932
+S000005121 MRPL22 YNL177C taxon:4932
+S000005121 MRPL22 YNL177C taxon:4932
+S000005121 MRPL22 YNL177C taxon:4932
+S000005676 MRPL23 YOR150W|YmL23 taxon:4932
+S000005676 MRPL23 YOR150W|YmL23 taxon:4932
+S000005676 MRPL23 YOR150W|YmL23 taxon:4932
+S000005676 MRPL23 YOR150W|YmL23 taxon:4932
+S000005676 MRPL23 YOR150W|YmL23 taxon:4932
+S000004806 MRPL24 YMR193W|MRPL14|YmL14|YmL24 taxon:4932
+S000004806 MRPL24 YMR193W|MRPL14|YmL14|YmL24 taxon:4932
+S000004806 MRPL24 YMR193W|MRPL14|YmL14|YmL24 taxon:4932
+S000003308 MRPL25 YGR076C|YMR26|YmL25 taxon:4932
+S000003308 MRPL25 YGR076C|YMR26|YmL25 taxon:4932
+S000003308 MRPL25 YGR076C|YMR26|YmL25 taxon:4932
+S000003308 MRPL25 YGR076C|YMR26|YmL25 taxon:4932
+S000000486 MRPL27 YBR282W|YmL27 taxon:4932
+S000000486 MRPL27 YBR282W|YmL27 taxon:4932
+S000000486 MRPL27 YBR282W|YmL27 taxon:4932
+S000000486 MRPL27 YBR282W|YmL27 taxon:4932
+S000002870 MRPL28 YDR462W|YmL28 taxon:4932
+S000002870 MRPL28 YDR462W|YmL28 taxon:4932
+S000002870 MRPL28 YDR462W|YmL28 taxon:4932
+S000004626 MRPL3 YMR024W|YmL3 taxon:4932
+S000004626 MRPL3 YMR024W|YmL3 taxon:4932
+S000004626 MRPL3 YMR024W|YmL3 taxon:4932
+S000004626 MRPL3 YMR024W|YmL3 taxon:4932
+S000001621 MRPL31 YKL138C|YmL31 taxon:4932
+S000001621 MRPL31 YKL138C|YmL31 taxon:4932
+S000001621 MRPL31 YKL138C|YmL31 taxon:4932
+S000001621 MRPL31 YKL138C|YmL31 taxon:4932
+S000000596 MRPL32 YCR003W|YmL32 taxon:4932
+S000000596 MRPL32 YCR003W|YmL32 taxon:4932
+S000000596 MRPL32 YCR003W|YmL32 taxon:4932
+S000004899 MRPL33 YMR286W|YmL33 taxon:4932
+S000004899 MRPL33 YMR286W|YmL33 taxon:4932
+S000004899 MRPL33 YMR286W|YmL33 taxon:4932
+S000002730 MRPL35 YDR322W|YmL35 taxon:4932
+S000002730 MRPL35 YDR322W|YmL35 taxon:4932
+S000002730 MRPL35 YDR322W|YmL35 taxon:4932
+S000002730 MRPL35 YDR322W|YmL35 taxon:4932
+S000000326 MRPL36 YBR122C|YmL36 taxon:4932
+S000000326 MRPL36 YBR122C|YmL36 taxon:4932
+S000000326 MRPL36 YBR122C|YmL36 taxon:4932
+S000000326 MRPL36 YBR122C|YmL36 taxon:4932
+S000000472 MRPL37 YBR268W|YmL37 taxon:4932
+S000000472 MRPL37 YBR268W|YmL37 taxon:4932
+S000000472 MRPL37 YBR268W|YmL37 taxon:4932
+S000001653 MRPL38 YKL170W|MRPL34|YmL34|YmL38 taxon:4932
+S000001653 MRPL38 YKL170W|MRPL34|YmL34|YmL38 taxon:4932
+S000001653 MRPL38 YKL170W|MRPL34|YmL34|YmL38 taxon:4932
+S000001653 MRPL38 YKL170W|MRPL34|YmL34|YmL38 taxon:4932
+S000001653 MRPL38 YKL170W|MRPL34|YmL34|YmL38 taxon:4932
+S000004468 MRPL39 YML009C|YmL39 taxon:4932
+S000004468 MRPL39 YML009C|YmL39 taxon:4932
+S000004468 MRPL39 YML009C|YmL39 taxon:4932
+S000004431 MRPL4 YLR439W|YmL4 taxon:4932
+S000004431 MRPL4 YLR439W|YmL4 taxon:4932
+S000004431 MRPL4 YLR439W|YmL4 taxon:4932
+S000006094 MRPL40 YPL173W|YmL40 taxon:4932
+S000006094 MRPL40 YPL173W|YmL40 taxon:4932
+S000006094 MRPL40 YPL173W|YmL40 taxon:4932
+S000006094 MRPL40 YPL173W|YmL40 taxon:4932
+S000004838 MRPL44 YMR225C|YMR44|YmL44 taxon:4932
+S000004838 MRPL44 YMR225C|YMR44|YmL44 taxon:4932
+S000004838 MRPL44 YMR225C|YMR44|YmL44 taxon:4932
+S000004838 MRPL44 YMR225C|YMR44|YmL44 taxon:4932
+S000003632 MRPL49 YJL096W|YmL49 taxon:4932
+S000003632 MRPL49 YJL096W|YmL49 taxon:4932
+S000003632 MRPL49 YJL096W|YmL49 taxon:4932
+S000003632 MRPL49 YJL096W|YmL49 taxon:4932
+S000005305 MRPL50 YNR022C taxon:4932
+S000005305 MRPL50 YNR022C taxon:4932
+S000005305 MRPL50 YNR022C taxon:4932
+S000006304 MRPL51 YPR100W taxon:4932
+S000006304 MRPL51 YPR100W taxon:4932
+S000006304 MRPL51 YPR100W taxon:4932
+S000006304 MRPL51 YPR100W taxon:4932
+S000001190 MRPL6 YHR147C|YmL16 taxon:4932
+S000001190 MRPL6 YHR147C|YmL16 taxon:4932
+S000001190 MRPL6 YHR147C|YmL16 taxon:4932
+S000001190 MRPL6 YHR147C|YmL16 taxon:4932
+S000002645 MRPL7 YDR237W|YmL5/7 taxon:4932
+S000002645 MRPL7 YDR237W|YmL5/7 taxon:4932
+S000002645 MRPL7 YDR237W|YmL5/7 taxon:4932
+S000003599 MRPL8 YJL063C|HRD238|YmL8 taxon:4932
+S000003599 MRPL8 YJL063C|HRD238|YmL8 taxon:4932
+S000003599 MRPL8 YJL063C|HRD238|YmL8 taxon:4932
+S000003599 MRPL8 YJL063C|HRD238|YmL8 taxon:4932
+S000003599 MRPL8 YJL063C|HRD238|YmL8 taxon:4932
+S000003452 MRPL9 YGR220C|YmL9 taxon:4932
+S000003452 MRPL9 YGR220C|YmL9 taxon:4932
+S000003452 MRPL9 YGR220C|YmL9 taxon:4932
+S000003452 MRPL9 YGR220C|YmL9 taxon:4932
+S000003452 MRPL9 YGR220C|YmL9 taxon:4932
+S000005934 MRPS16 YPL013C taxon:4932
+S000005934 MRPS16 YPL013C taxon:4932
+S000005934 MRPS16 YPL013C taxon:4932
+S000005934 MRPS16 YPL013C taxon:4932
+S000005934 MRPS16 YPL013C taxon:4932
+S000004800 MRPS17 YMR188C taxon:4932
+S000004800 MRPS17 YMR188C taxon:4932
+S000004800 MRPS17 YMR188C taxon:4932
+S000004800 MRPS17 YMR188C taxon:4932
+S000004800 MRPS17 YMR188C taxon:4932
+S000004800 MRPS17 YMR188C taxon:4932
+S000004800 MRPS17 YMR188C taxon:4932
+S000005250 MRPS18 YNL306W|YmS18 taxon:4932
+S000005250 MRPS18 YNL306W|YmS18 taxon:4932
+S000005250 MRPS18 YNL306W|YmS18 taxon:4932
+S000005250 MRPS18 YNL306W|YmS18 taxon:4932
+S000002745 MRPS28 YDR337W taxon:4932
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+S000005686 MTR10 YOR160W|KAP111 taxon:4932
+S000005686 MTR10 YOR160W|KAP111 taxon:4932
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+S000000032 MTW1 YAL034W-A|DSN3|NSL2 taxon:4932
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+S000000032 MTW1 YAL034W-A|DSN3|NSL2 taxon:4932
+S000004706 MUB1 YMR100W taxon:4932
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+S000001458 MUC1 YIR019C|FLO11|STA4 taxon:4932
+S000001458 MUC1 YIR019C|FLO11|STA4 taxon:4932
+S000001458 MUC1 YIR019C|FLO11|STA4 taxon:4932
+S000001458 MUC1 YIR019C|FLO11|STA4 taxon:4932
+S000001458 MUC1 YIR019C|FLO11|STA4 taxon:4932
+S000001458 MUC1 YIR019C|FLO11|STA4 taxon:4932
+S000000323 MUD1 YBR119W|U1-A|U1A taxon:4932
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+S000001557 MUD2 YKL074C taxon:4932
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+S000005991 MUK1 YPL070W taxon:4932
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+S000000261 MUM2 YBR057C|SPOT8 taxon:4932
+S000000261 MUM2 YBR057C|SPOT8 taxon:4932
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+S000005824 MUM3 YOR298W taxon:4932
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+S000029316 MUP2 taxon:4932
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+S000003239 MUQ1 YGR007W|ECT1 taxon:4932
+S000003239 MUQ1 YGR007W|ECT1 taxon:4932
+S000003239 MUQ1 YGR007W|ECT1 taxon:4932
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+S000003239 MUQ1 YGR007W|ECT1 taxon:4932
+S000003239 MUQ1 YGR007W|ECT1 taxon:4932
+S000003239 MUQ1 YGR007W|ECT1 taxon:4932
+S000002794 MUS81 YDR386W|SLX3 taxon:4932
+S000002794 MUS81 YDR386W|SLX3 taxon:4932
+S000002794 MUS81 YDR386W|SLX3 taxon:4932
+S000002794 MUS81 YDR386W|SLX3 taxon:4932
+S000002794 MUS81 YDR386W|SLX3 taxon:4932
+S000005326 MVD1 YNR043W|ERG19 taxon:4932
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+S000005326 MVD1 YNR043W|ERG19 taxon:4932
+S000005326 MVD1 YNR043W|ERG19 taxon:4932
+S000004606 MVP1 YMR004W taxon:4932
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+S000004606 MVP1 YMR004W taxon:4932
+S000000844 MXR1 YER042W|MSRA taxon:4932
+S000000844 MXR1 YER042W|MSRA taxon:4932
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+S000000844 MXR1 YER042W|MSRA taxon:4932
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+S000000844 MXR1 YER042W|MSRA taxon:4932
+S000001065 MYO1 YHR023W taxon:4932
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+S000005853 MYO2 YOR326W|CDC66 taxon:4932
+S000005853 MYO2 YOR326W|CDC66 taxon:4932
+S000005853 MYO2 YOR326W|CDC66 taxon:4932
+S000005853 MYO2 YOR326W|CDC66 taxon:4932
+S000005853 MYO2 YOR326W|CDC66 taxon:4932
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+S000005853 MYO2 YOR326W|CDC66 taxon:4932
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+S000005853 MYO2 YOR326W|CDC66 taxon:4932
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+S000005853 MYO2 YOR326W|CDC66 taxon:4932
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+S000005853 MYO2 YOR326W|CDC66 taxon:4932
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+S000005853 MYO2 YOR326W|CDC66 taxon:4932
+S000001612 MYO3 YKL129C taxon:4932
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+S000000027 MYO4 YAL029C|FUN22|SHE1 taxon:4932
+S000000027 MYO4 YAL029C|FUN22|SHE1 taxon:4932
+S000000027 MYO4 YAL029C|FUN22|SHE1 taxon:4932
+S000000027 MYO4 YAL029C|FUN22|SHE1 taxon:4932
+S000000027 MYO4 YAL029C|FUN22|SHE1 taxon:4932
+S000004715 MYO5 YMR109W taxon:4932
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+S000004715 MYO5 YMR109W taxon:4932
+S000004715 MYO5 YMR109W taxon:4932
+S000003090 NAB2 YGL122C taxon:4932
+S000003090 NAB2 YGL122C taxon:4932
+S000003090 NAB2 YGL122C taxon:4932
+S000003090 NAB2 YGL122C taxon:4932
+S000003090 NAB2 YGL122C taxon:4932
+S000003090 NAB2 YGL122C taxon:4932
+S000003090 NAB2 YGL122C taxon:4932
+S000006111 NAB3 YPL190C|HMD1 taxon:4932
+S000006111 NAB3 YPL190C|HMD1 taxon:4932
+S000006111 NAB3 YPL190C|HMD1 taxon:4932
+S000006111 NAB3 YPL190C|HMD1 taxon:4932
+S000004585 NAB6 YML117W taxon:4932
+S000004585 NAB6 YML117W taxon:4932
+S000004585 NAB6 YML117W taxon:4932
+S000005068 NAF1 YNL124W taxon:4932
+S000005068 NAF1 YNL124W taxon:4932
+S000005068 NAF1 YNL124W taxon:4932
+S000005068 NAF1 YNL124W taxon:4932
+S000004374 NAM2 YLR382C|MSL1 taxon:4932
+S000004374 NAM2 YLR382C|MSL1 taxon:4932
+S000004374 NAM2 YLR382C|MSL1 taxon:4932
+S000004374 NAM2 YLR382C|MSL1 taxon:4932
+S000004374 NAM2 YLR382C|MSL1 taxon:4932
+S000004374 NAM2 YLR382C|MSL1 taxon:4932
+S000004685 NAM7 YMR080C|IFS2|MOF4|UPF1 taxon:4932
+S000004685 NAM7 YMR080C|IFS2|MOF4|UPF1 taxon:4932
+S000004685 NAM7 YMR080C|IFS2|MOF4|UPF1 taxon:4932
+S000004685 NAM7 YMR080C|IFS2|MOF4|UPF1 taxon:4932
+S000004685 NAM7 YMR080C|IFS2|MOF4|UPF1 taxon:4932
+S000004685 NAM7 YMR080C|IFS2|MOF4|UPF1 taxon:4932
+S000004685 NAM7 YMR080C|IFS2|MOF4|UPF1 taxon:4932
+S000004685 NAM7 YMR080C|IFS2|MOF4|UPF1 taxon:4932
+S000004685 NAM7 YMR080C|IFS2|MOF4|UPF1 taxon:4932
+S000004685 NAM7 YMR080C|IFS2|MOF4|UPF1 taxon:4932
+S000004685 NAM7 YMR080C|IFS2|MOF4|UPF1 taxon:4932
+S000001128 NAM8 YHR086W|MRE2|MUD15 taxon:4932
+S000001128 NAM8 YHR086W|MRE2|MUD15 taxon:4932
+S000001128 NAM8 YHR086W|MRE2|MUD15 taxon:4932
+S000001128 NAM8 YHR086W|MRE2|MUD15 taxon:4932
+S000001128 NAM8 YHR086W|MRE2|MUD15 taxon:4932
+S000001128 NAM8 YHR086W|MRE2|MUD15 taxon:4932
+S000001128 NAM8 YHR086W|MRE2|MUD15 taxon:4932
+S000005081 NAM9 YNL137C|MNA6 taxon:4932
+S000005081 NAM9 YNL137C|MNA6 taxon:4932
+S000005081 NAM9 YNL137C|MNA6 taxon:4932
+S000005081 NAM9 YNL137C|MNA6 taxon:4932
+S000005081 NAM9 YNL137C|MNA6 taxon:4932
+S000005081 NAM9 YNL137C|MNA6 taxon:4932
+S000006047 NAN1 YPL126W|UTP17 taxon:4932
+S000006047 NAN1 YPL126W|UTP17 taxon:4932
+S000006047 NAN1 YPL126W|UTP17 taxon:4932
+S000006047 NAN1 YPL126W|UTP17 taxon:4932
+S000006047 NAN1 YPL126W|UTP17 taxon:4932
+S000001756 NAP1 YKR048C taxon:4932
+S000001756 NAP1 YKR048C taxon:4932
+S000001756 NAP1 YKR048C taxon:4932
+S000001756 NAP1 YKR048C taxon:4932
+S000001756 NAP1 YKR048C taxon:4932
+S000001756 NAP1 YKR048C taxon:4932
+S000001756 NAP1 YKR048C taxon:4932
+S000001756 NAP1 YKR048C taxon:4932
+S000005184 NAR1 YNL240C taxon:4932
+S000005184 NAR1 YNL240C taxon:4932
+S000005184 NAR1 YNL240C taxon:4932
+S000005184 NAR1 YNL240C taxon:4932
+S000001269 NAS2 YIL007C taxon:4932
+S000001269 NAS2 YIL007C taxon:4932
+S000001269 NAS2 YIL007C taxon:4932
+S000003464 NAS6 YGR232W taxon:4932
+S000003464 NAS6 YGR232W taxon:4932
+S000003464 NAS6 YGR232W taxon:4932
+S000003464 NAS6 YGR232W taxon:4932
+S000002198 NAT1 YDL040C|AAA1 taxon:4932
+S000002198 NAT1 YDL040C|AAA1 taxon:4932
+S000002198 NAT1 YDL040C|AAA1 taxon:4932
+S000002198 NAT1 YDL040C|AAA1 taxon:4932
+S000002198 NAT1 YDL040C|AAA1 taxon:4932
+S000002198 NAT1 YDL040C|AAA1 taxon:4932
+S000002198 NAT1 YDL040C|AAA1 taxon:4932
+S000002198 NAT1 YDL040C|AAA1 taxon:4932
+S000002198 NAT1 YDL040C|AAA1 taxon:4932
+S000003379 NAT2 YGR147C taxon:4932
+S000003379 NAT2 YGR147C taxon:4932
+S000003379 NAT2 YGR147C taxon:4932
+S000003379 NAT2 YGR147C taxon:4932
+S000003379 NAT2 YGR147C taxon:4932
+S000006335 NAT3 YPR131C taxon:4932
+S000006335 NAT3 YPR131C taxon:4932
+S000006335 NAT3 YPR131C taxon:4932
+S000006335 NAT3 YPR131C taxon:4932
+S000006335 NAT3 YPR131C taxon:4932
+S000006335 NAT3 YPR131C taxon:4932
+S000006335 NAT3 YPR131C taxon:4932
+S000006335 NAT3 YPR131C taxon:4932
+S000006335 NAT3 YPR131C taxon:4932
+S000004673 NAT4 YMR069W taxon:4932
+S000004673 NAT4 YMR069W taxon:4932
+S000004673 NAT4 YMR069W taxon:4932
+S000004673 NAT4 YMR069W taxon:4932
+S000005779 NAT5 YOR253W|ARD2|ROG2 taxon:4932
+S000005779 NAT5 YOR253W|ARD2|ROG2 taxon:4932
+S000005779 NAT5 YOR253W|ARD2|ROG2 taxon:4932
+S000005779 NAT5 YOR253W|ARD2|ROG2 taxon:4932
+S000005779 NAT5 YOR253W|ARD2|ROG2 taxon:4932
+S000004449 NBP1 YLR457C taxon:4932
+S000004449 NBP1 YLR457C taxon:4932
+S000004449 NBP1 YLR457C taxon:4932
+S000004449 NBP1 YLR457C taxon:4932
+S000004449 NBP1 YLR457C taxon:4932
+S000004449 NBP1 YLR457C taxon:4932
+S000004449 NBP1 YLR457C taxon:4932
+S000002569 NBP2 YDR162C taxon:4932
+S000002569 NBP2 YDR162C taxon:4932
+S000002569 NBP2 YDR162C taxon:4932
+S000002569 NBP2 YDR162C taxon:4932
+S000002569 NBP2 YDR162C taxon:4932
+S000002569 NBP2 YDR162C taxon:4932
+S000002569 NBP2 YDR162C taxon:4932
+S000002569 NBP2 YDR162C taxon:4932
+S000003059 NBP35 YGL091C taxon:4932
+S000003059 NBP35 YGL091C taxon:4932
+S000003059 NBP35 YGL091C taxon:4932
+S000003059 NBP35 YGL091C taxon:4932
+S000006359 NCA2 YPR155C taxon:4932
+S000006359 NCA2 YPR155C taxon:4932
+S000006359 NCA2 YPR155C taxon:4932
+S000006359 NCA2 YPR155C taxon:4932
+S000006359 NCA2 YPR155C taxon:4932
+S000006359 NCA2 YPR155C taxon:4932
+S000003652 NCA3 YJL116C taxon:4932
+S000003652 NCA3 YJL116C taxon:4932
+S000003652 NCA3 YJL116C taxon:4932
+S000002805 NCB2 YDR397C|YDR1 taxon:4932
+S000002805 NCB2 YDR397C|YDR1 taxon:4932
+S000002805 NCB2 YDR397C|YDR1 taxon:4932
+S000002805 NCB2 YDR397C|YDR1 taxon:4932
+S000002805 NCB2 YDR397C|YDR1 taxon:4932
+S000003742 NCE101 YJL205C|NCE1|YJL205C-A|YJL206C-A taxon:4932
+S000003742 NCE101 YJL205C|NCE1|YJL205C-A|YJL206C-A taxon:4932
+S000003742 NCE101 YJL205C|NCE1|YJL205C-A|YJL206C-A taxon:4932
+S000006353 NCE102 YPR149W|NCE2 taxon:4932
+S000006353 NCE102 YPR149W|NCE2 taxon:4932
+S000006353 NCE102 YPR149W|NCE2 taxon:4932
+S000006353 NCE102 YPR149W|NCE2 taxon:4932
+S000006353 NCE102 YPR149W|NCE2 taxon:4932
+S000006353 NCE102 YPR149W|NCE2 taxon:4932
+S000006353 NCE102 YPR149W|NCE2 taxon:4932
+S000004981 NCE103 YNL036W|NCE3 taxon:4932
+S000004981 NCE103 YNL036W|NCE3 taxon:4932
+S000004981 NCE103 YNL036W|NCE3 taxon:4932
+S000004981 NCE103 YNL036W|NCE3 taxon:4932
+S000004981 NCE103 YNL036W|NCE3 taxon:4932
+S000004981 NCE103 YNL036W|NCE3 taxon:4932
+S000000120 NCL1 YBL024W|TRM4 taxon:4932
+S000000120 NCL1 YBL024W|TRM4 taxon:4932
+S000000120 NCL1 YBL024W|TRM4 taxon:4932
+S000001084 NCP1 YHR042W|CPR1 taxon:4932
+S000001084 NCP1 YHR042W|CPR1 taxon:4932
+S000001084 NCP1 YHR042W|CPR1 taxon:4932
+S000001084 NCP1 YHR042W|CPR1 taxon:4932
+S000001084 NCP1 YHR042W|CPR1 taxon:4932
+S000001084 NCP1 YHR042W|CPR1 taxon:4932
+S000005927 NCR1 YPL006W taxon:4932
+S000005927 NCR1 YPL006W taxon:4932
+S000005927 NCR1 YPL006W taxon:4932
+S000005927 NCR1 YPL006W taxon:4932
+S000005063 NCS2 YNL119W taxon:4932
+S000005063 NCS2 YNL119W taxon:4932
+S000005063 NCS2 YNL119W taxon:4932
+S000005063 NCS2 YNL119W taxon:4932
+S000005063 NCS2 YNL119W taxon:4932
+S000003179 NCS6 YGL211W|YGL210W-A taxon:4932
+S000003179 NCS6 YGL211W|YGL210W-A taxon:4932
+S000003179 NCS6 YGL211W|YGL210W-A taxon:4932
+S000004493 NDC1 YML031W taxon:4932
+S000004493 NDC1 YML031W taxon:4932
+S000004493 NDC1 YML031W taxon:4932
+S000004493 NDC1 YML031W taxon:4932
+S000004493 NDC1 YML031W taxon:4932
+S000004493 NDC1 YML031W taxon:4932
+S000004493 NDC1 YML031W taxon:4932
+S000004493 NDC1 YML031W taxon:4932
+S000004493 NDC1 YML031W taxon:4932
+S000004493 NDC1 YML031W taxon:4932
+S000004493 NDC1 YML031W taxon:4932
+S000005899 NDD1 YOR372C taxon:4932
+S000005899 NDD1 YOR372C taxon:4932
+S000005899 NDD1 YOR372C taxon:4932
+S000005899 NDD1 YOR372C taxon:4932
+S000004753 NDE1 YMR145C|NDH1 taxon:4932
+S000004753 NDE1 YMR145C|NDH1 taxon:4932
+S000004753 NDE1 YMR145C|NDH1 taxon:4932
+S000004753 NDE1 YMR145C|NDH1 taxon:4932
+S000004753 NDE1 YMR145C|NDH1 taxon:4932
+S000004753 NDE1 YMR145C|NDH1 taxon:4932
+S000004753 NDE1 YMR145C|NDH1 taxon:4932
+S000004753 NDE1 YMR145C|NDH1 taxon:4932
+S000004753 NDE1 YMR145C|NDH1 taxon:4932
+S000004753 NDE1 YMR145C|NDH1 taxon:4932
+S000004753 NDE1 YMR145C|NDH1 taxon:4932
+S000004753 NDE1 YMR145C|NDH1 taxon:4932
+S000004753 NDE1 YMR145C|NDH1 taxon:4932
+S000002243 NDE2 YDL085W|NDH2 taxon:4932
+S000002243 NDE2 YDL085W|NDH2 taxon:4932
+S000002243 NDE2 YDL085W|NDH2 taxon:4932
+S000002243 NDE2 YDL085W|NDH2 taxon:4932
+S000002243 NDE2 YDL085W|NDH2 taxon:4932
+S000002243 NDE2 YDL085W|NDH2 taxon:4932
+S000002243 NDE2 YDL085W|NDH2 taxon:4932
+S000002243 NDE2 YDL085W|NDH2 taxon:4932
+S000002243 NDE2 YDL085W|NDH2 taxon:4932
+S000004589 NDI1 YML120C taxon:4932
+S000004589 NDI1 YML120C taxon:4932
+S000004589 NDI1 YML120C taxon:4932
+S000004589 NDI1 YML120C taxon:4932
+S000004589 NDI1 YML120C taxon:4932
+S000004589 NDI1 YML120C taxon:4932
+S000005464 NDJ1 YOL104C|TAM1 taxon:4932
+S000005464 NDJ1 YOL104C|TAM1 taxon:4932
+S000005464 NDJ1 YOL104C|TAM1 taxon:4932
+S000005464 NDJ1 YOL104C|TAM1 taxon:4932
+S000005464 NDJ1 YOL104C|TAM1 taxon:4932
+S000005464 NDJ1 YOL104C|TAM1 taxon:4932
+S000004244 NDL1 YLR254C taxon:4932
+S000004244 NDL1 YLR254C taxon:4932
+S000004244 NDL1 YLR254C taxon:4932
+S000004244 NDL1 YLR254C taxon:4932
+S000004244 NDL1 YLR254C taxon:4932
+S000004244 NDL1 YLR254C taxon:4932
+S000001166 NDT80 YHR124W taxon:4932
+S000001166 NDT80 YHR124W taxon:4932
+S000001166 NDT80 YHR124W taxon:4932
+S000001166 NDT80 YHR124W taxon:4932
+S000001166 NDT80 YHR124W taxon:4932
+S000001166 NDT80 YHR124W taxon:4932
+S000001166 NDT80 YHR124W taxon:4932
+S000001166 NDT80 YHR124W taxon:4932
+S000001166 NDT80 YHR124W taxon:4932
+S000001166 NDT80 YHR124W taxon:4932
+S000001166 NDT80 YHR124W taxon:4932
+S000001166 NDT80 YHR124W taxon:4932
+S000004255 NEJ1 YLR265C|LIF2 taxon:4932
+S000004255 NEJ1 YLR265C|LIF2 taxon:4932
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+S000004255 NEJ1 YLR265C|LIF2 taxon:4932
+S000001046 NEM1 YHR004C taxon:4932
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+S000001310 NEO1 YIL048W taxon:4932
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+S000003612 NET1 YJL076W|CFI1|ESC5|SRM8 taxon:4932
+S000003612 NET1 YJL076W|CFI1|ESC5|SRM8 taxon:4932
+S000003612 NET1 YJL076W|CFI1|ESC5|SRM8 taxon:4932
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+S000006147 NEW1 YPL226W taxon:4932
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+S000006147 NEW1 YPL226W taxon:4932
+S000006147 NEW1 YPL226W taxon:4932
+S000005682 NFI1 YOR156C|SIZ2 taxon:4932
+S000005682 NFI1 YOR156C|SIZ2 taxon:4932
+S000005682 NFI1 YOR156C|SIZ2 taxon:4932
+S000005682 NFI1 YOR156C|SIZ2 taxon:4932
+S000005682 NFI1 YOR156C|SIZ2 taxon:4932
+S000005682 NFI1 YOR156C|SIZ2 taxon:4932
+S000000522 NFS1 YCL017C|SPL1 taxon:4932
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+S000000522 NFS1 YCL017C|SPL1 taxon:4932
+S000000522 NFS1 YCL017C|SPL1 taxon:4932
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+S000000522 NFS1 YCL017C|SPL1 taxon:4932
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+S000000522 NFS1 YCL017C|SPL1 taxon:4932
+S000000522 NFS1 YCL017C|SPL1 taxon:4932
+S000000522 NFS1 YCL017C|SPL1 taxon:4932
+S000001811 NFT1 YKR103W taxon:4932
+S000001811 NFT1 YKR103W taxon:4932
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+S000001523 NFU1 YKL040C|NUB1 taxon:4932
+S000001523 NFU1 YKL040C|NUB1 taxon:4932
+S000001523 NFU1 YKL040C|NUB1 taxon:4932
+S000001523 NFU1 YKL040C|NUB1 taxon:4932
+S000002583 NGG1 YDR176W|ADA3|SWI7 taxon:4932
+S000002583 NGG1 YDR176W|ADA3|SWI7 taxon:4932
+S000002583 NGG1 YDR176W|ADA3|SWI7 taxon:4932
+S000002583 NGG1 YDR176W|ADA3|SWI7 taxon:4932
+S000002583 NGG1 YDR176W|ADA3|SWI7 taxon:4932
+S000002583 NGG1 YDR176W|ADA3|SWI7 taxon:4932
+S000005402 NGL1 YOL042W taxon:4932
+S000005402 NGL1 YOL042W taxon:4932
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+S000004898 NGL2 YMR285C taxon:4932
+S000004898 NGL2 YMR285C taxon:4932
+S000004898 NGL2 YMR285C taxon:4932
+S000004898 NGL2 YMR285C taxon:4932
+S000004587 NGL3 YML118W taxon:4932
+S000004587 NGL3 YML118W taxon:4932
+S000004587 NGL3 YML118W taxon:4932
+S000000416 NGR1 YBR212W|RBP1 taxon:4932
+S000000416 NGR1 YBR212W|RBP1 taxon:4932
+S000000416 NGR1 YBR212W|RBP1 taxon:4932
+S000000416 NGR1 YBR212W|RBP1 taxon:4932
+S000000416 NGR1 YBR212W|RBP1 taxon:4932
+S000000416 NGR1 YBR212W|RBP1 taxon:4932
+S000000416 NGR1 YBR212W|RBP1 taxon:4932
+S000000416 NGR1 YBR212W|RBP1 taxon:4932
+S000004128 NHA1 YLR138W taxon:4932
+S000004128 NHA1 YLR138W taxon:4932
+S000004128 NHA1 YLR138W taxon:4932
+S000004128 NHA1 YLR138W taxon:4932
+S000004128 NHA1 YLR138W taxon:4932
+S000004128 NHA1 YLR138W taxon:4932
+S000004128 NHA1 YLR138W taxon:4932
+S000004128 NHA1 YLR138W taxon:4932
+S000002160 NHP10 YDL002C|HMO2 taxon:4932
+S000002160 NHP10 YDL002C|HMO2 taxon:4932
+S000002160 NHP10 YDL002C|HMO2 taxon:4932
+S000002160 NHP10 YDL002C|HMO2 taxon:4932
+S000002367 NHP2 YDL208W taxon:4932
+S000002367 NHP2 YDL208W taxon:4932
+S000002367 NHP2 YDL208W taxon:4932
+S000002367 NHP2 YDL208W taxon:4932
+S000002367 NHP2 YDL208W taxon:4932
+S000006256 NHP6A YPR052C taxon:4932
+S000006256 NHP6A YPR052C taxon:4932
+S000006256 NHP6A YPR052C taxon:4932
+S000006256 NHP6A YPR052C taxon:4932
+S000006256 NHP6A YPR052C taxon:4932
+S000006256 NHP6A YPR052C taxon:4932
+S000006256 NHP6A YPR052C taxon:4932
+S000006256 NHP6A YPR052C taxon:4932
+S000006256 NHP6A YPR052C taxon:4932
+S000006256 NHP6A YPR052C taxon:4932
+S000006256 NHP6A YPR052C taxon:4932
+S000006256 NHP6A YPR052C taxon:4932
+S000006256 NHP6A YPR052C taxon:4932
+S000006256 NHP6A YPR052C taxon:4932
+S000006256 NHP6A YPR052C taxon:4932
+S000002157 NHP6B YBR089C-A|YBR090C-A taxon:4932
+S000002157 NHP6B YBR089C-A|YBR090C-A taxon:4932
+S000002157 NHP6B YBR089C-A|YBR090C-A taxon:4932
+S000002157 NHP6B YBR089C-A|YBR090C-A taxon:4932
+S000002157 NHP6B YBR089C-A|YBR090C-A taxon:4932
+S000002157 NHP6B YBR089C-A|YBR090C-A taxon:4932
+S000002157 NHP6B YBR089C-A|YBR090C-A taxon:4932
+S000002157 NHP6B YBR089C-A|YBR090C-A taxon:4932
+S000002157 NHP6B YBR089C-A|YBR090C-A taxon:4932
+S000002157 NHP6B YBR089C-A|YBR090C-A taxon:4932
+S000002157 NHP6B YBR089C-A|YBR090C-A taxon:4932
+S000002157 NHP6B YBR089C-A|YBR090C-A taxon:4932
+S000002157 NHP6B YBR089C-A|YBR090C-A taxon:4932
+S000002864 NHX1 YDR456W|NHA2|VPS44 taxon:4932
+S000002864 NHX1 YDR456W|NHA2|VPS44 taxon:4932
+S000002864 NHX1 YDR456W|NHA2|VPS44 taxon:4932
+S000002864 NHX1 YDR456W|NHA2|VPS44 taxon:4932
+S000002864 NHX1 YDR456W|NHA2|VPS44 taxon:4932
+S000002864 NHX1 YDR456W|NHA2|VPS44 taxon:4932
+S000002864 NHX1 YDR456W|NHA2|VPS44 taxon:4932
+S000002864 NHX1 YDR456W|NHA2|VPS44 taxon:4932
+S000002864 NHX1 YDR456W|NHA2|VPS44 taxon:4932
+S000001898 NIC96 YFR002W taxon:4932
+S000001898 NIC96 YFR002W taxon:4932
+S000001898 NIC96 YFR002W taxon:4932
+S000001898 NIC96 YFR002W taxon:4932
+S000001898 NIC96 YFR002W taxon:4932
+S000001898 NIC96 YFR002W taxon:4932
+S000001898 NIC96 YFR002W taxon:4932
+S000001898 NIC96 YFR002W taxon:4932
+S000001898 NIC96 YFR002W taxon:4932
+S000001898 NIC96 YFR002W taxon:4932
+S000001898 NIC96 YFR002W taxon:4932
+S000001898 NIC96 YFR002W taxon:4932
+S000001898 NIC96 YFR002W taxon:4932
+S000003189 NIF3 YGL221C taxon:4932
+S000003189 NIF3 YGL221C taxon:4932
+S000003189 NIF3 YGL221C taxon:4932
+S000003189 NIF3 YGL221C taxon:4932
+S000004926 NIP1 YMR309C taxon:4932
+S000004926 NIP1 YMR309C taxon:4932
+S000004926 NIP1 YMR309C taxon:4932
+S000004926 NIP1 YMR309C taxon:4932
+S000004926 NIP1 YMR309C taxon:4932
+S000004926 NIP1 YMR309C taxon:4932
+S000004926 NIP1 YMR309C taxon:4932
+S000004926 NIP1 YMR309C taxon:4932
+S000004926 NIP1 YMR309C taxon:4932
+S000004926 NIP1 YMR309C taxon:4932
+S000006095 NIP100 YPL174C|PAC13 taxon:4932
+S000006095 NIP100 YPL174C|PAC13 taxon:4932
+S000006095 NIP100 YPL174C|PAC13 taxon:4932
+S000006095 NIP100 YPL174C|PAC13 taxon:4932
+S000006095 NIP100 YPL174C|PAC13 taxon:4932
+S000006132 NIP7 YPL211W taxon:4932
+S000006132 NIP7 YPL211W taxon:4932
+S000006132 NIP7 YPL211W taxon:4932
+S000006132 NIP7 YPL211W taxon:4932
+S000006132 NIP7 YPL211W taxon:4932
+S000006132 NIP7 YPL211W taxon:4932
+S000005022 NIS1 YNL078W|JIP1 taxon:4932
+S000005022 NIS1 YNL078W|JIP1 taxon:4932
+S000005022 NIS1 YNL078W|JIP1 taxon:4932
+S000005022 NIS1 YNL078W|JIP1 taxon:4932
+S000001426 NIT1 YIL164C taxon:4932
+S000001426 NIT1 YIL164C taxon:4932
+S000001426 NIT1 YIL164C taxon:4932
+S000003662 NIT2 YJL126W taxon:4932
+S000003662 NIT2 YJL126W taxon:4932
+S000003662 NIT2 YJL126W taxon:4932
+S000004343 NIT3 YLR351C taxon:4932
+S000004343 NIT3 YLR351C taxon:4932
+S000004343 NIT3 YLR351C taxon:4932
+S000004343 NIT3 YLR351C taxon:4932
+S000004343 NIT3 YLR351C taxon:4932
+S000002791 NKP1 YDR383C taxon:4932
+S000002791 NKP1 YDR383C taxon:4932
+S000002791 NKP1 YDR383C taxon:4932
+S000004307 NKP2 YLR315W taxon:4932
+S000004307 NKP2 YLR315W taxon:4932
+S000004307 NKP2 YLR315W taxon:4932
+S000004307 NKP2 YLR315W taxon:4932
+S000004320 NMA1 YLR328W taxon:4932
+S000004320 NMA1 YLR328W taxon:4932
+S000004320 NMA1 YLR328W taxon:4932
+S000004320 NMA1 YLR328W taxon:4932
+S000005067 NMA111 YNL123W|YNM3 taxon:4932
+S000005067 NMA111 YNL123W|YNM3 taxon:4932
+S000005067 NMA111 YNL123W|YNM3 taxon:4932
+S000005067 NMA111 YNL123W|YNM3 taxon:4932
+S000005067 NMA111 YNL123W|YNM3 taxon:4932
+S000005067 NMA111 YNL123W|YNM3 taxon:4932
+S000005067 NMA111 YNL123W|YNM3 taxon:4932
+S000005067 NMA111 YNL123W|YNM3 taxon:4932
+S000005067 NMA111 YNL123W|YNM3 taxon:4932
+S000003242 NMA2 YGR010W taxon:4932
+S000003242 NMA2 YGR010W taxon:4932
+S000003242 NMA2 YGR010W taxon:4932
+S000003242 NMA2 YGR010W taxon:4932
+S000001119 NMD2 YHR077C|IFS1|SUA1|UPF2 taxon:4932
+S000001119 NMD2 YHR077C|IFS1|SUA1|UPF2 taxon:4932
+S000001119 NMD2 YHR077C|IFS1|SUA1|UPF2 taxon:4932
+S000001119 NMD2 YHR077C|IFS1|SUA1|UPF2 taxon:4932
+S000001119 NMD2 YHR077C|IFS1|SUA1|UPF2 taxon:4932
+S000001119 NMD2 YHR077C|IFS1|SUA1|UPF2 taxon:4932
+S000001119 NMD2 YHR077C|IFS1|SUA1|UPF2 taxon:4932
+S000001213 NMD3 YHR170W|SRC5 taxon:4932
+S000001213 NMD3 YHR170W|SRC5 taxon:4932
+S000001213 NMD3 YHR170W|SRC5 taxon:4932
+S000001213 NMD3 YHR170W|SRC5 taxon:4932
+S000001213 NMD3 YHR170W|SRC5 taxon:4932
+S000001213 NMD3 YHR170W|SRC5 taxon:4932
+S000004355 NMD4 YLR363C taxon:4932
+S000004355 NMD4 YLR363C taxon:4932
+S000004355 NMD4 YLR363C taxon:4932
+S000003893 NMD5 YJR132W|KAP119 taxon:4932
+S000003893 NMD5 YJR132W|KAP119 taxon:4932
+S000003893 NMD5 YJR132W|KAP119 taxon:4932
+S000003893 NMD5 YJR132W|KAP119 taxon:4932
+S000003893 NMD5 YJR132W|KAP119 taxon:4932
+S000003893 NMD5 YJR132W|KAP119 taxon:4932
+S000007436 NME1 RRP2 taxon:4932
+S000007436 NME1 RRP2 taxon:4932
+S000007436 NME1 RRP2 taxon:4932
+S000004185 NMT1 YLR195C|CDC72 taxon:4932
+S000004185 NMT1 YLR195C|CDC72 taxon:4932
+S000004185 NMT1 YLR195C|CDC72 taxon:4932
+S000004185 NMT1 YLR195C|CDC72 taxon:4932
+S000003873 NNF1 YJR112W taxon:4932
+S000003873 NNF1 YJR112W taxon:4932
+S000003873 NNF1 YJR112W taxon:4932
+S000003873 NNF1 YJR112W taxon:4932
+S000003873 NNF1 YJR112W taxon:4932
+S000003321 NNF2 YGR089W taxon:4932
+S000003321 NNF2 YGR089W taxon:4932
+S000003321 NNF2 YGR089W taxon:4932
+S000004275 NNT1 YLR285W taxon:4932
+S000004275 NNT1 YLR285W taxon:4932
+S000004275 NNT1 YLR285W taxon:4932
+S000004275 NNT1 YLR285W taxon:4932
+S000005582 NOB1 YOR056C|YOR29-07 taxon:4932
+S000005582 NOB1 YOR056C|YOR29-07 taxon:4932
+S000005582 NOB1 YOR056C|YOR29-07 taxon:4932
+S000005582 NOB1 YOR056C|YOR29-07 taxon:4932
+S000005582 NOB1 YOR056C|YOR29-07 taxon:4932
+S000005582 NOB1 YOR056C|YOR29-07 taxon:4932
+S000005582 NOB1 YOR056C|YOR29-07 taxon:4932
+S000005582 NOB1 YOR056C|YOR29-07 taxon:4932
+S000005582 NOB1 YOR056C|YOR29-07 taxon:4932
+S000005582 NOB1 YOR056C|YOR29-07 taxon:4932
+S000005582 NOB1 YOR056C|YOR29-07 taxon:4932
+S000005582 NOB1 YOR056C|YOR29-07 taxon:4932
+S000005582 NOB1 YOR056C|YOR29-07 taxon:4932
+S000005582 NOB1 YOR056C|YOR29-07 taxon:4932
+S000005732 NOC2 YOR206W taxon:4932
+S000005732 NOC2 YOR206W taxon:4932
+S000005732 NOC2 YOR206W taxon:4932
+S000005732 NOC2 YOR206W taxon:4932
+S000005732 NOC2 YOR206W taxon:4932
+S000005732 NOC2 YOR206W taxon:4932
+S000005732 NOC2 YOR206W taxon:4932
+S000003992 NOC3 YLR002C taxon:4932
+S000003992 NOC3 YLR002C taxon:4932
+S000003992 NOC3 YLR002C taxon:4932
+S000003992 NOC3 YLR002C taxon:4932
+S000003992 NOC3 YLR002C taxon:4932
+S000003992 NOC3 YLR002C taxon:4932
+S000003992 NOC3 YLR002C taxon:4932
+S000006348 NOC4 YPR144C|UTP19 taxon:4932
+S000006348 NOC4 YPR144C|UTP19 taxon:4932
+S000006348 NOC4 YPR144C|UTP19 taxon:4932
+S000006348 NOC4 YPR144C|UTP19 taxon:4932
+S000006348 NOC4 YPR144C|UTP19 taxon:4932
+S000006348 NOC4 YPR144C|UTP19 taxon:4932
+S000006348 NOC4 YPR144C|UTP19 taxon:4932
+S000006348 NOC4 YPR144C|UTP19 taxon:4932
+S000006348 NOC4 YPR144C|UTP19 taxon:4932
+S000006348 NOC4 YPR144C|UTP19 taxon:4932
+S000006014 NOG1 YPL093W taxon:4932
+S000006014 NOG1 YPL093W taxon:4932
+S000006014 NOG1 YPL093W taxon:4932
+S000006014 NOG1 YPL093W taxon:4932
+S000005336 NOG2 YNR053C taxon:4932
+S000005336 NOG2 YNR053C taxon:4932
+S000005336 NOG2 YNR053C taxon:4932
+S000005336 NOG2 YNR053C taxon:4932
+S000005336 NOG2 YNR053C taxon:4932
+S000005336 NOG2 YNR053C taxon:4932
+S000005336 NOG2 YNR053C taxon:4932
+S000002172 NOP1 YDL014W|LOT3 taxon:4932
+S000002172 NOP1 YDL014W|LOT3 taxon:4932
+S000002172 NOP1 YDL014W|LOT3 taxon:4932
+S000002172 NOP1 YDL014W|LOT3 taxon:4932
+S000002172 NOP1 YDL014W|LOT3 taxon:4932
+S000002172 NOP1 YDL014W|LOT3 taxon:4932
+S000002172 NOP1 YDL014W|LOT3 taxon:4932
+S000002172 NOP1 YDL014W|LOT3 taxon:4932
+S000002172 NOP1 YDL014W|LOT3 taxon:4932
+S000002172 NOP1 YDL014W|LOT3 taxon:4932
+S000002172 NOP1 YDL014W|LOT3 taxon:4932
+S000002172 NOP1 YDL014W|LOT3 taxon:4932
+S000002172 NOP1 YDL014W|LOT3 taxon:4932
+S000007455 NOP10 YHR072W-A taxon:4932
+S000007455 NOP10 YHR072W-A taxon:4932
+S000007455 NOP10 YHR072W-A taxon:4932
+S000007455 NOP10 YHR072W-A taxon:4932
+S000007455 NOP10 YHR072W-A taxon:4932
+S000005401 NOP12 YOL041C taxon:4932
+S000005401 NOP12 YOL041C taxon:4932
+S000005401 NOP12 YOL041C taxon:4932
+S000005119 NOP13 YNL175C taxon:4932
+S000005119 NOP13 YNL175C taxon:4932
+S000005119 NOP13 YNL175C taxon:4932
+S000005119 NOP13 YNL175C taxon:4932
+S000002307 NOP14 YDL148C|UTP2 taxon:4932
+S000002307 NOP14 YDL148C|UTP2 taxon:4932
+S000002307 NOP14 YDL148C|UTP2 taxon:4932
+S000002307 NOP14 YDL148C|UTP2 taxon:4932
+S000002307 NOP14 YDL148C|UTP2 taxon:4932
+S000002307 NOP14 YDL148C|UTP2 taxon:4932
+S000002307 NOP14 YDL148C|UTP2 taxon:4932
+S000002307 NOP14 YDL148C|UTP2 taxon:4932
+S000002307 NOP14 YDL148C|UTP2 taxon:4932
+S000005054 NOP15 YNL110C taxon:4932
+S000005054 NOP15 YNL110C taxon:4932
+S000005054 NOP15 YNL110C taxon:4932
+S000005054 NOP15 YNL110C taxon:4932
+S000005054 NOP15 YNL110C taxon:4932
+S000005054 NOP15 YNL110C taxon:4932
+S000005054 NOP15 YNL110C taxon:4932
+S000000804 NOP16 YER002W taxon:4932
+S000000804 NOP16 YER002W taxon:4932
+S000000804 NOP16 YER002W taxon:4932
+S000000804 NOP16 YER002W taxon:4932
+S000000804 NOP16 YER002W taxon:4932
+S000000804 NOP16 YER002W taxon:4932
+S000005005 NOP2 YNL061W|YNA1 taxon:4932
+S000005005 NOP2 YNL061W|YNA1 taxon:4932
+S000005005 NOP2 YNL061W|YNA1 taxon:4932
+S000005005 NOP2 YNL061W|YNA1 taxon:4932
+S000005964 NOP4 YPL043W|NOP77 taxon:4932
+S000005964 NOP4 YPL043W|NOP77 taxon:4932
+S000005964 NOP4 YPL043W|NOP77 taxon:4932
+S000006067 NOP53 YPL146C|RRP16 taxon:4932
+S000006067 NOP53 YPL146C|RRP16 taxon:4932
+S000006067 NOP53 YPL146C|RRP16 taxon:4932
+S000006067 NOP53 YPL146C|RRP16 taxon:4932
+S000006067 NOP53 YPL146C|RRP16 taxon:4932
+S000006067 NOP53 YPL146C|RRP16 taxon:4932
+S000006067 NOP53 YPL146C|RRP16 taxon:4932
+S000006067 NOP53 YPL146C|RRP16 taxon:4932
+S000005837 NOP58 YOR310C|NOP5 taxon:4932
+S000005837 NOP58 YOR310C|NOP5 taxon:4932
+S000005837 NOP58 YOR310C|NOP5 taxon:4932
+S000005837 NOP58 YOR310C|NOP5 taxon:4932
+S000005837 NOP58 YOR310C|NOP5 taxon:4932
+S000005837 NOP58 YOR310C|NOP5 taxon:4932
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+S000003391 NSR1 YGR159C|SHE5 taxon:4932
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+S000003823 NTA1 YJR062C|DEA1 taxon:4932
+S000003823 NTA1 YJR062C|DEA1 taxon:4932
+S000003823 NTA1 YJR062C|DEA1 taxon:4932
+S000003823 NTA1 YJR062C|DEA1 taxon:4932
+S000003823 NTA1 YJR062C|DEA1 taxon:4932
+S000003823 NTA1 YJR062C|DEA1 taxon:4932
+S000000392 NTC20 YBR188C taxon:4932
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+S000000392 NTC20 YBR188C taxon:4932
+S000000392 NTC20 YBR188C taxon:4932
+S000004524 NTE1 YML059C taxon:4932
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+S000004524 NTE1 YML059C taxon:4932
+S000004524 NTE1 YML059C taxon:4932
+S000000811 NTF2 YER009W taxon:4932
+S000000811 NTF2 YER009W taxon:4932
+S000000811 NTF2 YER009W taxon:4932
+S000000811 NTF2 YER009W taxon:4932
+S000000013 NTG1 YAL015C|FUN33|SCR1 taxon:4932
+S000000013 NTG1 YAL015C|FUN33|SCR1 taxon:4932
+S000000013 NTG1 YAL015C|FUN33|SCR1 taxon:4932
+S000000013 NTG1 YAL015C|FUN33|SCR1 taxon:4932
+S000000013 NTG1 YAL015C|FUN33|SCR1 taxon:4932
+S000000013 NTG1 YAL015C|FUN33|SCR1 taxon:4932
+S000000013 NTG1 YAL015C|FUN33|SCR1 taxon:4932
+S000000013 NTG1 YAL015C|FUN33|SCR1 taxon:4932
+S000000013 NTG1 YAL015C|FUN33|SCR1 taxon:4932
+S000000013 NTG1 YAL015C|FUN33|SCR1 taxon:4932
+S000005403 NTG2 YOL043C|SCR2 taxon:4932
+S000005403 NTG2 YOL043C|SCR2 taxon:4932
+S000005403 NTG2 YOL043C|SCR2 taxon:4932
+S000005403 NTG2 YOL043C|SCR2 taxon:4932
+S000005403 NTG2 YOL043C|SCR2 taxon:4932
+S000005403 NTG2 YOL043C|SCR2 taxon:4932
+S000002408 NTH1 YDR001C taxon:4932
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+S000002408 NTH1 YDR001C taxon:4932
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+S000000205 NTH2 YBR001C taxon:4932
+S000000205 NTH2 YBR001C taxon:4932
+S000000205 NTH2 YBR001C taxon:4932
+S000000205 NTH2 YBR001C taxon:4932
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+S000006235 NTO1 YPR031W taxon:4932
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+S000006235 NTO1 YPR031W taxon:4932
+S000006235 NTO1 YPR031W taxon:4932
+S000001730 NTR2 YKR022C taxon:4932
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+S000001730 NTR2 YKR022C taxon:4932
+S000001730 NTR2 YKR022C taxon:4932
+S000001730 NTR2 YKR022C taxon:4932
+S000001730 NTR2 YKR022C taxon:4932
+S000003744 NUC1 YJL208C taxon:4932
+S000003744 NUC1 YJL208C taxon:4932
+S000003744 NUC1 YJL208C taxon:4932
+S000003744 NUC1 YJL208C taxon:4932
+S000003744 NUC1 YJL208C taxon:4932
+S000003744 NUC1 YJL208C taxon:4932
+S000003744 NUC1 YJL208C taxon:4932
+S000005900 NUD1 YOR373W taxon:4932
+S000005900 NUD1 YOR373W taxon:4932
+S000005900 NUD1 YOR373W taxon:4932
+S000005430 NUF2 YOL069W taxon:4932
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+S000005430 NUF2 YOL069W taxon:4932
+S000005430 NUF2 YOL069W taxon:4932
+S000005430 NUF2 YOL069W taxon:4932
+S000000808 NUG1 YER006W taxon:4932
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+S000000808 NUG1 YER006W taxon:4932
+S000000808 NUG1 YER006W taxon:4932
+S000002557 NUM1 YDR150W|PAC12 taxon:4932
+S000002557 NUM1 YDR150W|PAC12 taxon:4932
+S000002557 NUM1 YDR150W|PAC12 taxon:4932
+S000002557 NUM1 YDR150W|PAC12 taxon:4932
+S000002557 NUM1 YDR150W|PAC12 taxon:4932
+S000002557 NUM1 YDR150W|PAC12 taxon:4932
+S000005624 NUP1 YOR098C taxon:4932
+S000005624 NUP1 YOR098C taxon:4932
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+S000005624 NUP1 YOR098C taxon:4932
+S000005624 NUP1 YOR098C taxon:4932
+S000005624 NUP1 YOR098C taxon:4932
+S000005624 NUP1 YOR098C taxon:4932
+S000005624 NUP1 YOR098C taxon:4932
+S000005624 NUP1 YOR098C taxon:4932
+S000005624 NUP1 YOR098C taxon:4932
+S000005624 NUP1 YOR098C taxon:4932
+S000005624 NUP1 YOR098C taxon:4932
+S000005624 NUP1 YOR098C taxon:4932
+S000005624 NUP1 YOR098C taxon:4932
+S000005624 NUP1 YOR098C taxon:4932
+S000005624 NUP1 YOR098C taxon:4932
+S000001551 NUP100 YKL068W|NSP100 taxon:4932
+S000001551 NUP100 YKL068W|NSP100 taxon:4932
+S000001551 NUP100 YKL068W|NSP100 taxon:4932
+S000001551 NUP100 YKL068W|NSP100 taxon:4932
+S000001551 NUP100 YKL068W|NSP100 taxon:4932
+S000001551 NUP100 YKL068W|NSP100 taxon:4932
+S000001551 NUP100 YKL068W|NSP100 taxon:4932
+S000001551 NUP100 YKL068W|NSP100 taxon:4932
+S000001551 NUP100 YKL068W|NSP100 taxon:4932
+S000001551 NUP100 YKL068W|NSP100 taxon:4932
+S000001551 NUP100 YKL068W|NSP100 taxon:4932
+S000001551 NUP100 YKL068W|NSP100 taxon:4932
+S000004650 NUP116 YMR047C|NSP116 taxon:4932
+S000004650 NUP116 YMR047C|NSP116 taxon:4932
+S000004650 NUP116 YMR047C|NSP116 taxon:4932
+S000004650 NUP116 YMR047C|NSP116 taxon:4932
+S000004650 NUP116 YMR047C|NSP116 taxon:4932
+S000004650 NUP116 YMR047C|NSP116 taxon:4932
+S000004650 NUP116 YMR047C|NSP116 taxon:4932
+S000004650 NUP116 YMR047C|NSP116 taxon:4932
+S000004650 NUP116 YMR047C|NSP116 taxon:4932
+S000004650 NUP116 YMR047C|NSP116 taxon:4932
+S000004650 NUP116 YMR047C|NSP116 taxon:4932
+S000004650 NUP116 YMR047C|NSP116 taxon:4932
+S000004650 NUP116 YMR047C|NSP116 taxon:4932
+S000004650 NUP116 YMR047C|NSP116 taxon:4932
+S000004650 NUP116 YMR047C|NSP116 taxon:4932
+S000001540 NUP120 YKL057C|RAT2 taxon:4932
+S000001540 NUP120 YKL057C|RAT2 taxon:4932
+S000001540 NUP120 YKL057C|RAT2 taxon:4932
+S000001540 NUP120 YKL057C|RAT2 taxon:4932
+S000001540 NUP120 YKL057C|RAT2 taxon:4932
+S000001540 NUP120 YKL057C|RAT2 taxon:4932
+S000001540 NUP120 YKL057C|RAT2 taxon:4932
+S000001540 NUP120 YKL057C|RAT2 taxon:4932
+S000001540 NUP120 YKL057C|RAT2 taxon:4932
+S000001540 NUP120 YKL057C|RAT2 taxon:4932
+S000001540 NUP120 YKL057C|RAT2 taxon:4932
+S000001540 NUP120 YKL057C|RAT2 taxon:4932
+S000001540 NUP120 YKL057C|RAT2 taxon:4932
+S000001540 NUP120 YKL057C|RAT2 taxon:4932
+S000001790 NUP133 YKR082W|RAT3 taxon:4932
+S000001790 NUP133 YKR082W|RAT3 taxon:4932
+S000001790 NUP133 YKR082W|RAT3 taxon:4932
+S000001790 NUP133 YKR082W|RAT3 taxon:4932
+S000001790 NUP133 YKR082W|RAT3 taxon:4932
+S000001790 NUP133 YKR082W|RAT3 taxon:4932
+S000001790 NUP133 YKR082W|RAT3 taxon:4932
+S000001790 NUP133 YKR082W|RAT3 taxon:4932
+S000001790 NUP133 YKR082W|RAT3 taxon:4932
+S000001790 NUP133 YKR082W|RAT3 taxon:4932
+S000001790 NUP133 YKR082W|RAT3 taxon:4932
+S000001790 NUP133 YKR082W|RAT3 taxon:4932
+S000001790 NUP133 YKR082W|RAT3 taxon:4932
+S000001790 NUP133 YKR082W|RAT3 taxon:4932
+S000003060 NUP145 YGL092W|RAT10 taxon:4932
+S000003060 NUP145 YGL092W|RAT10 taxon:4932
+S000003060 NUP145 YGL092W|RAT10 taxon:4932
+S000003060 NUP145 YGL092W|RAT10 taxon:4932
+S000003060 NUP145 YGL092W|RAT10 taxon:4932
+S000003060 NUP145 YGL092W|RAT10 taxon:4932
+S000003060 NUP145 YGL092W|RAT10 taxon:4932
+S000003060 NUP145 YGL092W|RAT10 taxon:4932
+S000003060 NUP145 YGL092W|RAT10 taxon:4932
+S000003060 NUP145 YGL092W|RAT10 taxon:4932
+S000003060 NUP145 YGL092W|RAT10 taxon:4932
+S000003060 NUP145 YGL092W|RAT10 taxon:4932
+S000003060 NUP145 YGL092W|RAT10 taxon:4932
+S000003060 NUP145 YGL092W|RAT10 taxon:4932
+S000003060 NUP145 YGL092W|RAT10 taxon:4932
+S000000907 NUP157 YER105C taxon:4932
+S000000907 NUP157 YER105C taxon:4932
+S000000907 NUP157 YER105C taxon:4932
+S000000907 NUP157 YER105C taxon:4932
+S000000907 NUP157 YER105C taxon:4932
+S000000907 NUP157 YER105C taxon:4932
+S000000907 NUP157 YER105C taxon:4932
+S000000907 NUP157 YER105C taxon:4932
+S000000907 NUP157 YER105C taxon:4932
+S000000907 NUP157 YER105C taxon:4932
+S000000907 NUP157 YER105C taxon:4932
+S000000907 NUP157 YER105C taxon:4932
+S000000907 NUP157 YER105C taxon:4932
+S000001377 NUP159 YIL115C|NUP158|RAT7 taxon:4932
+S000001377 NUP159 YIL115C|NUP158|RAT7 taxon:4932
+S000001377 NUP159 YIL115C|NUP158|RAT7 taxon:4932
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+S000000613 PET18 YCR020C|HIT2 taxon:4932
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+S000000126 PET9 YBL030C|AAC2|ANC2|OP1 taxon:4932
+S000000126 PET9 YBL030C|AAC2|ANC2|OP1 taxon:4932
+S000000126 PET9 YBL030C|AAC2|ANC2|OP1 taxon:4932
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+S000001680 PEX1 YKL197C|PAS1 taxon:4932
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+S000002673 PEX10 YDR265W|PAS4 taxon:4932
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+S000005507 PEX11 YOL147C|PMP24|PMP27 taxon:4932
+S000005507 PEX11 YOL147C|PMP24|PMP27 taxon:4932
+S000005507 PEX11 YOL147C|PMP24|PMP27 taxon:4932
+S000005507 PEX11 YOL147C|PMP24|PMP27 taxon:4932
+S000005507 PEX11 YOL147C|PMP24|PMP27 taxon:4932
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+S000004628 PEX12 YMR026C|PAS11 taxon:4932
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+S000004181 PEX13 YLR191W|PAS20 taxon:4932
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+S000005648 PFY1 YOR122C|PRF1 taxon:4932
+S000005648 PFY1 YOR122C|PRF1 taxon:4932
+S000005648 PFY1 YOR122C|PRF1 taxon:4932
+S000005648 PFY1 YOR122C|PRF1 taxon:4932
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+S000000400 PGI1 YBR196C|CDC30 taxon:4932
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+S000004711 PGM2 YMR105C|GAL5 taxon:4932
+S000004711 PGM2 YMR105C|GAL5 taxon:4932
+S000004711 PGM2 YMR105C|GAL5 taxon:4932
+S000004711 PGM2 YMR105C|GAL5 taxon:4932
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+S000005444 PHM7 YOL084W taxon:4932
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+S000000094 PHO11 YAR071W taxon:4932
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+S000001258 PHO12 YHR215W|PHO10 taxon:4932
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+S000002264 PHO2 YDL106C|BAS2|GRF10 taxon:4932
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+S000000296 PHO3 YBR092C taxon:4932
+S000000296 PHO3 YBR092C taxon:4932
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+S000001930 PHO4 YFR034C taxon:4932
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+S000001930 PHO4 YFR034C taxon:4932
+S000001930 PHO4 YFR034C taxon:4932
+S000001930 PHO4 YFR034C taxon:4932
+S000000297 PHO5 YBR093C taxon:4932
+S000000297 PHO5 YBR093C taxon:4932
+S000000297 PHO5 YBR093C taxon:4932
+S000000297 PHO5 YBR093C taxon:4932
+S000000297 PHO5 YBR093C taxon:4932
+S000000297 PHO5 YBR093C taxon:4932
+S000000297 PHO5 YBR093C taxon:4932
+S000000297 PHO5 YBR093C taxon:4932
+S000000297 PHO5 YBR093C taxon:4932
+S000000297 PHO5 YBR093C taxon:4932
+S000000297 PHO5 YBR093C taxon:4932
+S000000297 PHO5 YBR093C taxon:4932
+S000002889 PHO8 YDR481C taxon:4932
+S000002889 PHO8 YDR481C taxon:4932
+S000002889 PHO8 YDR481C taxon:4932
+S000002889 PHO8 YDR481C taxon:4932
+S000002889 PHO8 YDR481C taxon:4932
+S000005361 PHO80 YOL001W|AGS3|TUP7|VAC5 taxon:4932
+S000005361 PHO80 YOL001W|AGS3|TUP7|VAC5 taxon:4932
+S000005361 PHO80 YOL001W|AGS3|TUP7|VAC5 taxon:4932
+S000005361 PHO80 YOL001W|AGS3|TUP7|VAC5 taxon:4932
+S000003465 PHO81 YGR233C taxon:4932
+S000003465 PHO81 YGR233C taxon:4932
+S000003465 PHO81 YGR233C taxon:4932
+S000003465 PHO81 YGR233C taxon:4932
+S000004592 PHO84 YML123C taxon:4932
+S000004592 PHO84 YML123C taxon:4932
+S000004592 PHO84 YML123C taxon:4932
+S000004592 PHO84 YML123C taxon:4932
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+S000005952 PHO85 YPL031C|LDB15 taxon:4932
+S000005952 PHO85 YPL031C|LDB15 taxon:4932
+S000005952 PHO85 YPL031C|LDB15 taxon:4932
+S000005952 PHO85 YPL031C|LDB15 taxon:4932
+S000005952 PHO85 YPL031C|LDB15 taxon:4932
+S000005952 PHO85 YPL031C|LDB15 taxon:4932
+S000005952 PHO85 YPL031C|LDB15 taxon:4932
+S000005952 PHO85 YPL031C|LDB15 taxon:4932
+S000005952 PHO85 YPL031C|LDB15 taxon:4932
+S000005952 PHO85 YPL031C|LDB15 taxon:4932
+S000005952 PHO85 YPL031C|LDB15 taxon:4932
+S000005952 PHO85 YPL031C|LDB15 taxon:4932
+S000005952 PHO85 YPL031C|LDB15 taxon:4932
+S000005952 PHO85 YPL031C|LDB15 taxon:4932
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+S000000500 PHO89 YBR296C|ITN1 taxon:4932
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+S000001076 PIH1 YHR034C|NOP17 taxon:4932
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+S000001076 PIH1 YHR034C|NOP17 taxon:4932
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+S000001076 PIH1 YHR034C|NOP17 taxon:4932
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+S000001076 PIH1 YHR034C|NOP17 taxon:4932
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+S000005211 PIK1 YNL267W|PIK120|PIK41 taxon:4932
+S000005211 PIK1 YNL267W|PIK120|PIK41 taxon:4932
+S000005211 PIK1 YNL267W|PIK120|PIK41 taxon:4932
+S000005211 PIK1 YNL267W|PIK120|PIK41 taxon:4932
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+S000005890 PIP2 YOR363C|OAF2 taxon:4932
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+S000001647 PIR1 YKL164C|CCW6 taxon:4932
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+S000000201 PKC1 YBL105C|CLY15|HPO2|STT1 taxon:4932
+S000000201 PKC1 YBL105C|CLY15|HPO2|STT1 taxon:4932
+S000000201 PKC1 YBL105C|CLY15|HPO2|STT1 taxon:4932
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+S000004730 PKR1 YMR123W taxon:4932
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+S000004608 PLB2 YMR006C taxon:4932
+S000004608 PLB2 YMR006C taxon:4932
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+S000005371 PLB3 YOL011W taxon:4932
+S000005371 PLB3 YOL011W taxon:4932
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+S000005371 PLB3 YOL011W taxon:4932
+S000005371 PLB3 YOL011W taxon:4932
+S000005371 PLB3 YOL011W taxon:4932
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+S000006189 PLC1 YPL268W taxon:4932
+S000006189 PLC1 YPL268W taxon:4932
+S000006189 PLC1 YPL268W taxon:4932
+S000006189 PLC1 YPL268W taxon:4932
+S000006189 PLC1 YPL268W taxon:4932
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+S000002591 PLP1 YDR183W taxon:4932
+S000002591 PLP1 YDR183W taxon:4932
+S000002591 PLP1 YDR183W taxon:4932
+S000002591 PLP1 YDR183W taxon:4932
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+S000005807 PLP2 YOR281C taxon:4932
+S000005807 PLP2 YOR281C taxon:4932
+S000005807 PLP2 YOR281C taxon:4932
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+S000002976 PMA1 YGL008C taxon:4932
+S000002976 PMA1 YGL008C taxon:4932
+S000002976 PMA1 YGL008C taxon:4932
+S000002976 PMA1 YGL008C taxon:4932
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+S000005957 PMA2 YPL036W taxon:4932
+S000005957 PMA2 YPL036W taxon:4932
+S000005957 PMA2 YPL036W taxon:4932
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+S000002974 PMC1 YGL006W taxon:4932
+S000002974 PMC1 YGL006W taxon:4932
+S000002974 PMC1 YGL006W taxon:4932
+S000002974 PMC1 YGL006W taxon:4932
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+S000000934 PMD1 YER132C taxon:4932
+S000000934 PMD1 YER132C taxon:4932
+S000000934 PMD1 YER132C taxon:4932
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+S000000805 PMI40 YER003C|PMI taxon:4932
+S000000805 PMI40 YER003C|PMI taxon:4932
+S000000805 PMI40 YER003C|PMI taxon:4932
+S000000805 PMI40 YER003C|PMI taxon:4932
+S000000805 PMI40 YER003C|PMI taxon:4932
+S000004006 PML1 YLR016C taxon:4932
+S000004006 PML1 YLR016C taxon:4932
+S000004006 PML1 YLR016C taxon:4932
+S000004006 PML1 YLR016C taxon:4932
+S000004006 PML1 YLR016C taxon:4932
+S000004006 PML1 YLR016C taxon:4932
+S000004006 PML1 YLR016C taxon:4932
+S000004575 PML39 YML107C taxon:4932
+S000004575 PML39 YML107C taxon:4932
+S000004575 PML39 YML107C taxon:4932
+S000004575 PML39 YML107C taxon:4932
+S000000619 PMP1 YCR024C-A taxon:4932
+S000000619 PMP1 YCR024C-A taxon:4932
+S000000619 PMP1 YCR024C-A taxon:4932
+S000000619 PMP1 YCR024C-A taxon:4932
+S000002103 PMP2 YEL017C-A taxon:4932
+S000002103 PMP2 YEL017C-A taxon:4932
+S000002103 PMP2 YEL017C-A taxon:4932
+S000002684 PMP3 YDR276C|SNA1 taxon:4932
+S000002684 PMP3 YDR276C|SNA1 taxon:4932
+S000002684 PMP3 YDR276C|SNA1 taxon:4932
+S000003135 PMR1 YGL167C|BSD1|LDB1 taxon:4932
+S000003135 PMR1 YGL167C|BSD1|LDB1 taxon:4932
+S000003135 PMR1 YGL167C|BSD1|LDB1 taxon:4932
+S000003135 PMR1 YGL167C|BSD1|LDB1 taxon:4932
+S000003135 PMR1 YGL167C|BSD1|LDB1 taxon:4932
+S000003135 PMR1 YGL167C|BSD1|LDB1 taxon:4932
+S000003135 PMR1 YGL167C|BSD1|LDB1 taxon:4932
+S000003135 PMR1 YGL167C|BSD1|LDB1 taxon:4932
+S000005026 PMS1 YNL082W taxon:4932
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+S000005026 PMS1 YNL082W taxon:4932
+S000005026 PMS1 YNL082W taxon:4932
+S000005026 PMS1 YNL082W taxon:4932
+S000002253 PMT1 YDL095W taxon:4932
+S000002253 PMT1 YDL095W taxon:4932
+S000002253 PMT1 YDL095W taxon:4932
+S000002253 PMT1 YDL095W taxon:4932
+S000002253 PMT1 YDL095W taxon:4932
+S000000021 PMT2 YAL023C|FUN25 taxon:4932
+S000000021 PMT2 YAL023C|FUN25 taxon:4932
+S000000021 PMT2 YAL023C|FUN25 taxon:4932
+S000000021 PMT2 YAL023C|FUN25 taxon:4932
+S000000021 PMT2 YAL023C|FUN25 taxon:4932
+S000005848 PMT3 YOR321W taxon:4932
+S000005848 PMT3 YOR321W taxon:4932
+S000005848 PMT3 YOR321W taxon:4932
+S000005848 PMT3 YOR321W taxon:4932
+S000005848 PMT3 YOR321W taxon:4932
+S000003904 PMT4 YJR143C taxon:4932
+S000003904 PMT4 YJR143C taxon:4932
+S000003904 PMT4 YJR143C taxon:4932
+S000003904 PMT4 YJR143C taxon:4932
+S000003904 PMT4 YJR143C taxon:4932
+S000002251 PMT5 YDL093W taxon:4932
+S000002251 PMT5 YDL093W taxon:4932
+S000002251 PMT5 YDL093W taxon:4932
+S000003431 PMT6 YGR199W taxon:4932
+S000003431 PMT6 YGR199W taxon:4932
+S000003431 PMT6 YGR199W taxon:4932
+S000029378 PMT7 taxon:4932
+S000029378 PMT7 taxon:4932
+S000029378 PMT7 taxon:4932
+S000001611 PMU1 YKL128C taxon:4932
+S000001611 PMU1 YKL128C taxon:4932
+S000001611 PMU1 YKL128C taxon:4932
+S000001611 PMU1 YKL128C taxon:4932
+S000003005 PNC1 YGL037C taxon:4932
+S000003005 PNC1 YGL037C taxon:4932
+S000003005 PNC1 YGL037C taxon:4932
+S000003005 PNC1 YGL037C taxon:4932
+S000003005 PNC1 YGL037C taxon:4932
+S000003005 PNC1 YGL037C taxon:4932
+S000003005 PNC1 YGL037C taxon:4932
+S000003005 PNC1 YGL037C taxon:4932
+S000003005 PNC1 YGL037C taxon:4932
+S000006017 PNG1 YPL096W|PNGase taxon:4932
+S000006017 PNG1 YPL096W|PNGase taxon:4932
+S000006017 PNG1 YPL096W|PNGase taxon:4932
+S000006017 PNG1 YPL096W|PNGase taxon:4932
+S000006017 PNG1 YPL096W|PNGase taxon:4932
+S000006017 PNG1 YPL096W|PNGase taxon:4932
+S000006017 PNG1 YPL096W|PNGase taxon:4932
+S000005671 PNO1 YOR145C|DIM2|RRP20 taxon:4932
+S000005671 PNO1 YOR145C|DIM2|RRP20 taxon:4932
+S000005671 PNO1 YOR145C|DIM2|RRP20 taxon:4932
+S000005671 PNO1 YOR145C|DIM2|RRP20 taxon:4932
+S000005671 PNO1 YOR145C|DIM2|RRP20 taxon:4932
+S000005671 PNO1 YOR145C|DIM2|RRP20 taxon:4932
+S000005671 PNO1 YOR145C|DIM2|RRP20 taxon:4932
+S000005671 PNO1 YOR145C|DIM2|RRP20 taxon:4932
+S000004199 PNP1 YLR209C taxon:4932
+S000004199 PNP1 YLR209C taxon:4932
+S000004199 PNP1 YLR209C taxon:4932
+S000004199 PNP1 YLR209C taxon:4932
+S000004199 PNP1 YLR209C taxon:4932
+S000005687 PNS1 YOR161C taxon:4932
+S000005687 PNS1 YOR161C taxon:4932
+S000005687 PNS1 YOR161C taxon:4932
+S000005687 PNS1 YOR161C taxon:4932
+S000005792 PNT1 YOR266W taxon:4932
+S000005792 PNT1 YOR266W taxon:4932
+S000005792 PNT1 YOR266W taxon:4932
+S000000226 POA1 YBR022W taxon:4932
+S000000226 POA1 YBR022W taxon:4932
+S000000226 POA1 YBR022W taxon:4932
+S000000226 POA1 YBR022W taxon:4932
+S000004534 POB3 YML069W taxon:4932
+S000004534 POB3 YML069W taxon:4932
+S000004534 POB3 YML069W taxon:4932
+S000004534 POB3 YML069W taxon:4932
+S000004534 POB3 YML069W taxon:4932
+S000004534 POB3 YML069W taxon:4932
+S000004534 POB3 YML069W taxon:4932
+S000004534 POB3 YML069W taxon:4932
+S000004534 POB3 YML069W taxon:4932
+S000004534 POB3 YML069W taxon:4932
+S000004534 POB3 YML069W taxon:4932
+S000001384 POG1 YIL122W taxon:4932
+S000001384 POG1 YIL122W taxon:4932
+S000001384 POG1 YIL122W taxon:4932
+S000001384 POG1 YIL122W taxon:4932
+S000001384 POG1 YIL122W taxon:4932
+S000001384 POG1 YIL122W taxon:4932
+S000005046 POL1 YNL102W|CDC17|CRT5|HPR3 taxon:4932
+S000005046 POL1 YNL102W|CDC17|CRT5|HPR3 taxon:4932
+S000005046 POL1 YNL102W|CDC17|CRT5|HPR3 taxon:4932
+S000005046 POL1 YNL102W|CDC17|CRT5|HPR3 taxon:4932
+S000005046 POL1 YNL102W|CDC17|CRT5|HPR3 taxon:4932
+S000005046 POL1 YNL102W|CDC17|CRT5|HPR3 taxon:4932
+S000005046 POL1 YNL102W|CDC17|CRT5|HPR3 taxon:4932
+S000000131 POL12 YBL035C taxon:4932
+S000000131 POL12 YBL035C taxon:4932
+S000000131 POL12 YBL035C taxon:4932
+S000000131 POL12 YBL035C taxon:4932
+S000000131 POL12 YBL035C taxon:4932
+S000000131 POL12 YBL035C taxon:4932
+S000000131 POL12 YBL035C taxon:4932
+S000005206 POL2 YNL262W|DUN2 taxon:4932
+S000005206 POL2 YNL262W|DUN2 taxon:4932
+S000005206 POL2 YNL262W|DUN2 taxon:4932
+S000005206 POL2 YNL262W|DUN2 taxon:4932
+S000005206 POL2 YNL262W|DUN2 taxon:4932
+S000005206 POL2 YNL262W|DUN2 taxon:4932
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+S000003238 PRP18 YGR006W taxon:4932
+S000003238 PRP18 YGR006W taxon:4932
+S000003238 PRP18 YGR006W taxon:4932
+S000003238 PRP18 YGR006W taxon:4932
+S000003959 PRP19 YLL036C|PSO4 taxon:4932
+S000003959 PRP19 YLL036C|PSO4 taxon:4932
+S000003959 PRP19 YLL036C|PSO4 taxon:4932
+S000003959 PRP19 YLL036C|PSO4 taxon:4932
+S000003959 PRP19 YLL036C|PSO4 taxon:4932
+S000003959 PRP19 YLL036C|PSO4 taxon:4932
+S000003959 PRP19 YLL036C|PSO4 taxon:4932
+S000003959 PRP19 YLL036C|PSO4 taxon:4932
+S000003959 PRP19 YLL036C|PSO4 taxon:4932
+S000003959 PRP19 YLL036C|PSO4 taxon:4932
+S000003959 PRP19 YLL036C|PSO4 taxon:4932
+S000003959 PRP19 YLL036C|PSO4 taxon:4932
+S000005294 PRP2 YNR011C|RNA2 taxon:4932
+S000005294 PRP2 YNR011C|RNA2 taxon:4932
+S000005294 PRP2 YNR011C|RNA2 taxon:4932
+S000005294 PRP2 YNR011C|RNA2 taxon:4932
+S000005294 PRP2 YNR011C|RNA2 taxon:4932
+S000005294 PRP2 YNR011C|RNA2 taxon:4932
+S000003739 PRP21 YJL203W|SPP91 taxon:4932
+S000003739 PRP21 YJL203W|SPP91 taxon:4932
+S000003739 PRP21 YJL203W|SPP91 taxon:4932
+S000003739 PRP21 YJL203W|SPP91 taxon:4932
+S000000815 PRP22 YER013W taxon:4932
+S000000815 PRP22 YER013W taxon:4932
+S000000815 PRP22 YER013W taxon:4932
+S000000815 PRP22 YER013W taxon:4932
+S000000815 PRP22 YER013W taxon:4932
+S000000815 PRP22 YER013W taxon:4932
+S000000815 PRP22 YER013W taxon:4932
+S000000815 PRP22 YER013W taxon:4932
+S000000815 PRP22 YER013W taxon:4932
+S000004881 PRP24 YMR268C taxon:4932
+S000004881 PRP24 YMR268C taxon:4932
+S000004881 PRP24 YMR268C taxon:4932
+S000004881 PRP24 YMR268C taxon:4932
+S000002651 PRP28 YDR243C taxon:4932
+S000002651 PRP28 YDR243C taxon:4932
+S000002651 PRP28 YDR243C taxon:4932
+S000002651 PRP28 YDR243C taxon:4932
+S000002651 PRP28 YDR243C taxon:4932
+S000002651 PRP28 YDR243C taxon:4932
+S000002881 PRP3 YDR473C|RNA3 taxon:4932
+S000002881 PRP3 YDR473C|RNA3 taxon:4932
+S000002881 PRP3 YDR473C|RNA3 taxon:4932
+S000002881 PRP3 YDR473C|RNA3 taxon:4932
+S000002881 PRP3 YDR473C|RNA3 taxon:4932
+S000003323 PRP31 YGR091W taxon:4932
+S000003323 PRP31 YGR091W taxon:4932
+S000003323 PRP31 YGR091W taxon:4932
+S000003323 PRP31 YGR091W taxon:4932
+S000003323 PRP31 YGR091W taxon:4932
+S000003323 PRP31 YGR091W taxon:4932
+S000003307 PRP38 YGR075C taxon:4932
+S000003307 PRP38 YGR075C taxon:4932
+S000003307 PRP38 YGR075C taxon:4932
+S000003307 PRP38 YGR075C taxon:4932
+S000003307 PRP38 YGR075C taxon:4932
+S000003307 PRP38 YGR075C taxon:4932
+S000004509 PRP39 YML046W taxon:4932
+S000004509 PRP39 YML046W taxon:4932
+S000004509 PRP39 YML046W taxon:4932
+S000004509 PRP39 YML046W taxon:4932
+S000004509 PRP39 YML046W taxon:4932
+S000004509 PRP39 YML046W taxon:4932
+S000004509 PRP39 YML046W taxon:4932
+S000006382 PRP4 YPR178W|RNA4 taxon:4932
+S000006382 PRP4 YPR178W|RNA4 taxon:4932
+S000006382 PRP4 YPR178W|RNA4 taxon:4932
+S000006382 PRP4 YPR178W|RNA4 taxon:4932
+S000006382 PRP4 YPR178W|RNA4 taxon:4932
+S000001495 PRP40 YKL012W taxon:4932
+S000001495 PRP40 YKL012W taxon:4932
+S000001495 PRP40 YKL012W taxon:4932
+S000001495 PRP40 YKL012W taxon:4932
+S000002643 PRP42 YDR235W|MUD16|SNU65 taxon:4932
+S000002643 PRP42 YDR235W|MUD16|SNU65 taxon:4932
+S000002643 PRP42 YDR235W|MUD16|SNU65 taxon:4932
+S000002643 PRP42 YDR235W|MUD16|SNU65 taxon:4932
+S000003088 PRP43 YGL120C|JA1 taxon:4932
+S000003088 PRP43 YGL120C|JA1 taxon:4932
+S000003088 PRP43 YGL120C|JA1 taxon:4932
+S000003088 PRP43 YGL120C|JA1 taxon:4932
+S000003088 PRP43 YGL120C|JA1 taxon:4932
+S000003088 PRP43 YGL120C|JA1 taxon:4932
+S000003088 PRP43 YGL120C|JA1 taxon:4932
+S000000030 PRP45 YAL032C|FUN20 taxon:4932
+S000000030 PRP45 YAL032C|FUN20 taxon:4932
+S000000030 PRP45 YAL032C|FUN20 taxon:4932
+S000006072 PRP46 YPL151C|NTC50 taxon:4932
+S000006072 PRP46 YPL151C|NTC50 taxon:4932
+S000006072 PRP46 YPL151C|NTC50 taxon:4932
+S000000441 PRP5 YBR237W|RNA5 taxon:4932
+S000000441 PRP5 YBR237W|RNA5 taxon:4932
+S000000441 PRP5 YBR237W|RNA5 taxon:4932
+S000000441 PRP5 YBR237W|RNA5 taxon:4932
+S000000441 PRP5 YBR237W|RNA5 taxon:4932
+S000000259 PRP6 YBR055C|RNA6|TSM7269 taxon:4932
+S000000259 PRP6 YBR055C|RNA6|TSM7269 taxon:4932
+S000000259 PRP6 YBR055C|RNA6|TSM7269 taxon:4932
+S000000259 PRP6 YBR055C|RNA6|TSM7269 taxon:4932
+S000000259 PRP6 YBR055C|RNA6|TSM7269 taxon:4932
+S000001208 PRP8 YHR165C|DBF3|DNA39|RNA8|SLT21|USA2 taxon:4932
+S000001208 PRP8 YHR165C|DBF3|DNA39|RNA8|SLT21|USA2 taxon:4932
+S000001208 PRP8 YHR165C|DBF3|DNA39|RNA8|SLT21|USA2 taxon:4932
+S000001208 PRP8 YHR165C|DBF3|DNA39|RNA8|SLT21|USA2 taxon:4932
+S000001208 PRP8 YHR165C|DBF3|DNA39|RNA8|SLT21|USA2 taxon:4932
+S000001208 PRP8 YHR165C|DBF3|DNA39|RNA8|SLT21|USA2 taxon:4932
+S000001208 PRP8 YHR165C|DBF3|DNA39|RNA8|SLT21|USA2 taxon:4932
+S000001208 PRP8 YHR165C|DBF3|DNA39|RNA8|SLT21|USA2 taxon:4932
+S000001208 PRP8 YHR165C|DBF3|DNA39|RNA8|SLT21|USA2 taxon:4932
+S000002188 PRP9 YDL030W taxon:4932
+S000002188 PRP9 YDL030W taxon:4932
+S000002188 PRP9 YDL030W taxon:4932
+S000002188 PRP9 YDL030W taxon:4932
+S000001599 PRR1 YKL116C taxon:4932
+S000001599 PRR1 YKL116C taxon:4932
+S000001599 PRR1 YKL116C taxon:4932
+S000001599 PRR1 YKL116C taxon:4932
+S000002373 PRR2 YDL214C taxon:4932
+S000002373 PRR2 YDL214C taxon:4932
+S000002373 PRR2 YDL214C taxon:4932
+S000002373 PRR2 YDL214C taxon:4932
+S000001664 PRS1 YKL181W|PRP1 taxon:4932
+S000001664 PRS1 YKL181W|PRP1 taxon:4932
+S000001664 PRS1 YKL181W|PRP1 taxon:4932
+S000001664 PRS1 YKL181W|PRP1 taxon:4932
+S000001664 PRS1 YKL181W|PRP1 taxon:4932
+S000001664 PRS1 YKL181W|PRP1 taxon:4932
+S000001664 PRS1 YKL181W|PRP1 taxon:4932
+S000000901 PRS2 YER099C taxon:4932
+S000000901 PRS2 YER099C taxon:4932
+S000000901 PRS2 YER099C taxon:4932
+S000000901 PRS2 YER099C taxon:4932
+S000000901 PRS2 YER099C taxon:4932
+S000000901 PRS2 YER099C taxon:4932
+S000000901 PRS2 YER099C taxon:4932
+S000001003 PRS3 YHL011C taxon:4932
+S000001003 PRS3 YHL011C taxon:4932
+S000001003 PRS3 YHL011C taxon:4932
+S000001003 PRS3 YHL011C taxon:4932
+S000001003 PRS3 YHL011C taxon:4932
+S000001003 PRS3 YHL011C taxon:4932
+S000001003 PRS3 YHL011C taxon:4932
+S000001003 PRS3 YHL011C taxon:4932
+S000001003 PRS3 YHL011C taxon:4932
+S000000164 PRS4 YBL068W taxon:4932
+S000000164 PRS4 YBL068W taxon:4932
+S000000164 PRS4 YBL068W taxon:4932
+S000000164 PRS4 YBL068W taxon:4932
+S000000164 PRS4 YBL068W taxon:4932
+S000000164 PRS4 YBL068W taxon:4932
+S000000164 PRS4 YBL068W taxon:4932
+S000005422 PRS5 YOL061W taxon:4932
+S000005422 PRS5 YOL061W taxon:4932
+S000005422 PRS5 YOL061W taxon:4932
+S000005422 PRS5 YOL061W taxon:4932
+S000005422 PRS5 YOL061W taxon:4932
+S000005422 PRS5 YOL061W taxon:4932
+S000005422 PRS5 YOL061W taxon:4932
+S000005888 PRT1 YOR361C|CDC63|DNA26 taxon:4932
+S000005888 PRT1 YOR361C|CDC63|DNA26 taxon:4932
+S000005888 PRT1 YOR361C|CDC63|DNA26 taxon:4932
+S000005888 PRT1 YOR361C|CDC63|DNA26 taxon:4932
+S000005888 PRT1 YOR361C|CDC63|DNA26 taxon:4932
+S000005888 PRT1 YOR361C|CDC63|DNA26 taxon:4932
+S000005888 PRT1 YOR361C|CDC63|DNA26 taxon:4932
+S000005888 PRT1 YOR361C|CDC63|DNA26 taxon:4932
+S000005888 PRT1 YOR361C|CDC63|DNA26 taxon:4932
+S000005888 PRT1 YOR361C|CDC63|DNA26 taxon:4932
+S000005888 PRT1 YOR361C|CDC63|DNA26 taxon:4932
+S000005888 PRT1 YOR361C|CDC63|DNA26 taxon:4932
+S000000160 PRX1 YBL064C|mTPx taxon:4932
+S000000160 PRX1 YBL064C|mTPx taxon:4932
+S000000160 PRX1 YBL064C|mTPx taxon:4932
+S000000160 PRX1 YBL064C|mTPx taxon:4932
+S000000160 PRX1 YBL064C|mTPx taxon:4932
+S000000160 PRX1 YBL064C|mTPx taxon:4932
+S000000160 PRX1 YBL064C|mTPx taxon:4932
+S000000160 PRX1 YBL064C|mTPx taxon:4932
+S000003615 PRY1 YJL079C taxon:4932
+S000003615 PRY1 YJL079C taxon:4932
+S000003615 PRY1 YJL079C taxon:4932
+S000003615 PRY1 YJL079C taxon:4932
+S000003615 PRY1 YJL079C taxon:4932
+S000003615 PRY1 YJL079C taxon:4932
+S000001721 PRY2 YKR013W|YFW12 taxon:4932
+S000001721 PRY2 YKR013W|YFW12 taxon:4932
+S000001721 PRY2 YKR013W|YFW12 taxon:4932
+S000001721 PRY2 YKR013W|YFW12 taxon:4932
+S000003614 PRY3 YJL078C taxon:4932
+S000003614 PRY3 YJL078C taxon:4932
+S000003614 PRY3 YJL078C taxon:4932
+S000003614 PRY3 YJL078C taxon:4932
+S000002213 PSA1 YDL055C|MPG1|SRB1|VIG9 taxon:4932
+S000002213 PSA1 YDL055C|MPG1|SRB1|VIG9 taxon:4932
+S000002213 PSA1 YDL055C|MPG1|SRB1|VIG9 taxon:4932
+S000002213 PSA1 YDL055C|MPG1|SRB1|VIG9 taxon:4932
+S000002213 PSA1 YDL055C|MPG1|SRB1|VIG9 taxon:4932
+S000002213 PSA1 YDL055C|MPG1|SRB1|VIG9 taxon:4932
+S000002213 PSA1 YDL055C|MPG1|SRB1|VIG9 taxon:4932
+S000002213 PSA1 YDL055C|MPG1|SRB1|VIG9 taxon:4932
+S000005113 PSD1 YNL169C taxon:4932
+S000005113 PSD1 YNL169C taxon:4932
+S000005113 PSD1 YNL169C taxon:4932
+S000005113 PSD1 YNL169C taxon:4932
+S000005113 PSD1 YNL169C taxon:4932
+S000003402 PSD2 YGR170W taxon:4932
+S000003402 PSD2 YGR170W taxon:4932
+S000003402 PSD2 YGR170W taxon:4932
+S000003402 PSD2 YGR170W taxon:4932
+S000004925 PSE1 YMR308C|KAP121 taxon:4932
+S000004925 PSE1 YMR308C|KAP121 taxon:4932
+S000004925 PSE1 YMR308C|KAP121 taxon:4932
+S000004925 PSE1 YMR308C|KAP121 taxon:4932
+S000004925 PSE1 YMR308C|KAP121 taxon:4932
+S000002420 PSF1 YDR013W|CDC101 taxon:4932
+S000002420 PSF1 YDR013W|CDC101 taxon:4932
+S000002420 PSF1 YDR013W|CDC101 taxon:4932
+S000002420 PSF1 YDR013W|CDC101 taxon:4932
+S000002420 PSF1 YDR013W|CDC101 taxon:4932
+S000003608 PSF2 YJL072C|CDC102 taxon:4932
+S000003608 PSF2 YJL072C|CDC102 taxon:4932
+S000003608 PSF2 YJL072C|CDC102 taxon:4932
+S000003608 PSF2 YJL072C|CDC102 taxon:4932
+S000003608 PSF2 YJL072C|CDC102 taxon:4932
+S000003608 PSF2 YJL072C|CDC102 taxon:4932
+S000005506 PSF3 YOL146W taxon:4932
+S000005506 PSF3 YOL146W taxon:4932
+S000005506 PSF3 YOL146W taxon:4932
+S000005506 PSF3 YOL146W taxon:4932
+S000005415 PSH1 YOL054W taxon:4932
+S000005415 PSH1 YOL054W taxon:4932
+S000005415 PSH1 YOL054W taxon:4932
+S000000015 PSK1 YAL017W|FUN31 taxon:4932
+S000000015 PSK1 YAL017W|FUN31 taxon:4932
+S000000015 PSK1 YAL017W|FUN31 taxon:4932
+S000000015 PSK1 YAL017W|FUN31 taxon:4932
+S000000015 PSK1 YAL017W|FUN31 taxon:4932
+S000000015 PSK1 YAL017W|FUN31 taxon:4932
+S000000015 PSK1 YAL017W|FUN31 taxon:4932
+S000000015 PSK1 YAL017W|FUN31 taxon:4932
+S000005405 PSK2 YOL045W taxon:4932
+S000005405 PSK2 YOL045W taxon:4932
+S000005405 PSK2 YOL045W taxon:4932
+S000005405 PSK2 YOL045W taxon:4932
+S000005405 PSK2 YOL045W taxon:4932
+S000005405 PSK2 YOL045W taxon:4932
+S000005405 PSK2 YOL045W taxon:4932
+S000005405 PSK2 YOL045W taxon:4932
+S000004745 PSO2 YMR137C|SNM1 taxon:4932
+S000004745 PSO2 YMR137C|SNM1 taxon:4932
+S000004745 PSO2 YMR137C|SNM1 taxon:4932
+S000004745 PSO2 YMR137C|SNM1 taxon:4932
+S000004745 PSO2 YMR137C|SNM1 taxon:4932
+S000004745 PSO2 YMR137C|SNM1 taxon:4932
+S000002913 PSP1 YDR505C|GIN5 taxon:4932
+S000002913 PSP1 YDR505C|GIN5 taxon:4932
+S000002913 PSP1 YDR505C|GIN5 taxon:4932
+S000002913 PSP1 YDR505C|GIN5 taxon:4932
+S000004479 PSP2 YML017W|MRS15 taxon:4932
+S000004479 PSP2 YML017W|MRS15 taxon:4932
+S000004479 PSP2 YML017W|MRS15 taxon:4932
+S000003933 PSR1 YLL010C taxon:4932
+S000003933 PSR1 YLL010C taxon:4932
+S000003933 PSR1 YLL010C taxon:4932
+S000003933 PSR1 YLL010C taxon:4932
+S000004009 PSR2 YLR019W taxon:4932
+S000004009 PSR2 YLR019W taxon:4932
+S000004009 PSR2 YLR019W taxon:4932
+S000002462 PST1 YDR055W taxon:4932
+S000002462 PST1 YDR055W taxon:4932
+S000002462 PST1 YDR055W taxon:4932
+S000002439 PST2 YDR032C taxon:4932
+S000002439 PST2 YDR032C taxon:4932
+S000002439 PST2 YDR032C taxon:4932
+S000002439 PST2 YDR032C taxon:4932
+S000005145 PSY2 YNL201C taxon:4932
+S000005145 PSY2 YNL201C taxon:4932
+S000005145 PSY2 YNL201C taxon:4932
+S000004368 PSY3 YLR376C taxon:4932
+S000004368 PSY3 YLR376C taxon:4932
+S000004368 PSY3 YLR376C taxon:4932
+S000004368 PSY3 YLR376C taxon:4932
+S000004368 PSY3 YLR376C taxon:4932
+S000000142 PSY4 YBL046W taxon:4932
+S000000142 PSY4 YBL046W taxon:4932
+S000000142 PSY4 YBL046W taxon:4932
+S000000041 PTA1 YAL043C|FUN39 taxon:4932
+S000000041 PTA1 YAL043C|FUN39 taxon:4932
+S000000041 PTA1 YAL043C|FUN39 taxon:4932
+S000000041 PTA1 YAL043C|FUN39 taxon:4932
+S000000041 PTA1 YAL043C|FUN39 taxon:4932
+S000000041 PTA1 YAL043C|FUN39 taxon:4932
+S000000041 PTA1 YAL043C|FUN39 taxon:4932
+S000000041 PTA1 YAL043C|FUN39 taxon:4932
+S000000041 PTA1 YAL043C|FUN39 taxon:4932
+S000002164 PTC1 YDL006W|CWH47|KCS2|TPD1 taxon:4932
+S000002164 PTC1 YDL006W|CWH47|KCS2|TPD1 taxon:4932
+S000002164 PTC1 YDL006W|CWH47|KCS2|TPD1 taxon:4932
+S000002164 PTC1 YDL006W|CWH47|KCS2|TPD1 taxon:4932
+S000002164 PTC1 YDL006W|CWH47|KCS2|TPD1 taxon:4932
+S000002164 PTC1 YDL006W|CWH47|KCS2|TPD1 taxon:4932
+S000002164 PTC1 YDL006W|CWH47|KCS2|TPD1 taxon:4932
+S000002164 PTC1 YDL006W|CWH47|KCS2|TPD1 taxon:4932
+S000002164 PTC1 YDL006W|CWH47|KCS2|TPD1 taxon:4932
+S000002164 PTC1 YDL006W|CWH47|KCS2|TPD1 taxon:4932
+S000002164 PTC1 YDL006W|CWH47|KCS2|TPD1 taxon:4932
+S000000891 PTC2 YER089C taxon:4932
+S000000891 PTC2 YER089C taxon:4932
+S000000891 PTC2 YER089C taxon:4932
+S000000891 PTC2 YER089C taxon:4932
+S000000891 PTC2 YER089C taxon:4932
+S000000891 PTC2 YER089C taxon:4932
+S000000891 PTC2 YER089C taxon:4932
+S000000891 PTC2 YER089C taxon:4932
+S000000891 PTC2 YER089C taxon:4932
+S000000891 PTC2 YER089C taxon:4932
+S000000891 PTC2 YER089C taxon:4932
+S000000891 PTC2 YER089C taxon:4932
+S000000891 PTC2 YER089C taxon:4932
+S000000891 PTC2 YER089C taxon:4932
+S000000891 PTC2 YER089C taxon:4932
+S000000152 PTC3 YBL056W taxon:4932
+S000000152 PTC3 YBL056W taxon:4932
+S000000152 PTC3 YBL056W taxon:4932
+S000000152 PTC3 YBL056W taxon:4932
+S000000152 PTC3 YBL056W taxon:4932
+S000000152 PTC3 YBL056W taxon:4932
+S000000152 PTC3 YBL056W taxon:4932
+S000000152 PTC3 YBL056W taxon:4932
+S000000329 PTC4 YBR125C|GCT1 taxon:4932
+S000000329 PTC4 YBR125C|GCT1 taxon:4932
+S000000329 PTC4 YBR125C|GCT1 taxon:4932
+S000000329 PTC4 YBR125C|GCT1 taxon:4932
+S000005616 PTC5 YOR090C taxon:4932
+S000005616 PTC5 YOR090C taxon:4932
+S000005616 PTC5 YOR090C taxon:4932
+S000005616 PTC5 YOR090C taxon:4932
+S000001118 PTC7 YHR076W taxon:4932
+S000001118 PTC7 YHR076W taxon:4932
+S000001118 PTC7 YHR076W taxon:4932
+S000001118 PTC7 YHR076W taxon:4932
+S000001232 PTH1 YHR189W|PTH taxon:4932
+S000001232 PTH1 YHR189W|PTH taxon:4932
+S000001232 PTH1 YHR189W|PTH taxon:4932
+S000001232 PTH1 YHR189W|PTH taxon:4932
+S000001232 PTH1 YHR189W|PTH taxon:4932
+S000001232 PTH1 YHR189W|PTH taxon:4932
+S000000153 PTH2 YBL057C taxon:4932
+S000000153 PTH2 YBL057C taxon:4932
+S000000153 PTH2 YBL057C taxon:4932
+S000000153 PTH2 YBL057C taxon:4932
+S000000153 PTH2 YBL057C taxon:4932
+S000000153 PTH2 YBL057C taxon:4932
+S000000153 PTH2 YBL057C taxon:4932
+S000003388 PTI1 YGR156W taxon:4932
+S000003388 PTI1 YGR156W taxon:4932
+S000003388 PTI1 YGR156W taxon:4932
+S000003388 PTI1 YGR156W taxon:4932
+S000003388 PTI1 YGR156W taxon:4932
+S000003388 PTI1 YGR156W taxon:4932
+S000003388 PTI1 YGR156W taxon:4932
+S000003388 PTI1 YGR156W taxon:4932
+S000003388 PTI1 YGR156W taxon:4932
+S000003388 PTI1 YGR156W taxon:4932
+S000003388 PTI1 YGR156W taxon:4932
+S000001681 PTK1 YKL198C|KKT8|POT1|STK1|YKL199C|YKT9 taxon:4932
+S000001681 PTK1 YKL198C|KKT8|POT1|STK1|YKL199C|YKT9 taxon:4932
+S000001681 PTK1 YKL198C|KKT8|POT1|STK1|YKL199C|YKT9 taxon:4932
+S000001681 PTK1 YKL198C|KKT8|POT1|STK1|YKL199C|YKT9 taxon:4932
+S000003820 PTK2 YJR059W|STK2 taxon:4932
+S000003820 PTK2 YJR059W|STK2 taxon:4932
+S000003820 PTK2 YJR059W|STK2 taxon:4932
+S000003820 PTK2 YJR059W|STK2 taxon:4932
+S000003820 PTK2 YJR059W|STK2 taxon:4932
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+S000005943 RAD1 YPL022W|LPB9 taxon:4932
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+S000005943 RAD1 YPL022W|LPB9 taxon:4932
+S000005943 RAD1 YPL022W|LPB9 taxon:4932
+S000005943 RAD1 YPL022W|LPB9 taxon:4932
+S000005943 RAD1 YPL022W|LPB9 taxon:4932
+S000005943 RAD1 YPL022W|LPB9 taxon:4932
+S000005943 RAD1 YPL022W|LPB9 taxon:4932
+S000005943 RAD1 YPL022W|LPB9 taxon:4932
+S000005943 RAD1 YPL022W|LPB9 taxon:4932
+S000005943 RAD1 YPL022W|LPB9 taxon:4932
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+S000005943 RAD1 YPL022W|LPB9 taxon:4932
+S000004560 RAD10 YML095C taxon:4932
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+S000000318 RAD16 YBR114W|PSO5 taxon:4932
+S000000318 RAD16 YBR114W|PSO5 taxon:4932
+S000000318 RAD16 YBR114W|PSO5 taxon:4932
+S000000318 RAD16 YBR114W|PSO5 taxon:4932
+S000000318 RAD16 YBR114W|PSO5 taxon:4932
+S000000318 RAD16 YBR114W|PSO5 taxon:4932
+S000005895 RAD17 YOR368W taxon:4932
+S000005895 RAD17 YOR368W taxon:4932
+S000005895 RAD17 YOR368W taxon:4932
+S000005895 RAD17 YOR368W taxon:4932
+S000000662 RAD18 YCR066W taxon:4932
+S000000662 RAD18 YCR066W taxon:4932
+S000000662 RAD18 YCR066W taxon:4932
+S000000662 RAD18 YCR066W taxon:4932
+S000000662 RAD18 YCR066W taxon:4932
+S000000662 RAD18 YCR066W taxon:4932
+S000003490 RAD2 YGR258C taxon:4932
+S000003490 RAD2 YGR258C taxon:4932
+S000003490 RAD2 YGR258C taxon:4932
+S000000763 RAD23 YEL037C taxon:4932
+S000000763 RAD23 YEL037C taxon:4932
+S000000763 RAD23 YEL037C taxon:4932
+S000000763 RAD23 YEL037C taxon:4932
+S000000763 RAD23 YEL037C taxon:4932
+S000000763 RAD23 YEL037C taxon:4932
+S000000763 RAD23 YEL037C taxon:4932
+S000000763 RAD23 YEL037C taxon:4932
+S000000763 RAD23 YEL037C taxon:4932
+S000000763 RAD23 YEL037C taxon:4932
+S000000763 RAD23 YEL037C taxon:4932
+S000000975 RAD24 YER173W|RS1 taxon:4932
+S000000975 RAD24 YER173W|RS1 taxon:4932
+S000000975 RAD24 YER173W|RS1 taxon:4932
+S000000975 RAD24 YER173W|RS1 taxon:4932
+S000000975 RAD24 YER173W|RS1 taxon:4932
+S000000975 RAD24 YER173W|RS1 taxon:4932
+S000003796 RAD26 YJR035W taxon:4932
+S000003796 RAD26 YJR035W taxon:4932
+S000003796 RAD26 YJR035W taxon:4932
+S000003796 RAD26 YJR035W taxon:4932
+S000001596 RAD27 YKL113C|ERC11|FEN1|RTH1 taxon:4932
+S000001596 RAD27 YKL113C|ERC11|FEN1|RTH1 taxon:4932
+S000001596 RAD27 YKL113C|ERC11|FEN1|RTH1 taxon:4932
+S000001596 RAD27 YKL113C|ERC11|FEN1|RTH1 taxon:4932
+S000001596 RAD27 YKL113C|ERC11|FEN1|RTH1 taxon:4932
+S000001596 RAD27 YKL113C|ERC11|FEN1|RTH1 taxon:4932
+S000001596 RAD27 YKL113C|ERC11|FEN1|RTH1 taxon:4932
+S000001596 RAD27 YKL113C|ERC11|FEN1|RTH1 taxon:4932
+S000002437 RAD28 YDR030C taxon:4932
+S000002437 RAD28 YDR030C taxon:4932
+S000002437 RAD28 YDR030C taxon:4932
+S000000973 RAD3 YER171W|REM1 taxon:4932
+S000000973 RAD3 YER171W|REM1 taxon:4932
+S000000973 RAD3 YER171W|REM1 taxon:4932
+S000000973 RAD3 YER171W|REM1 taxon:4932
+S000000973 RAD3 YER171W|REM1 taxon:4932
+S000000973 RAD3 YER171W|REM1 taxon:4932
+S000000973 RAD3 YER171W|REM1 taxon:4932
+S000000973 RAD3 YER171W|REM1 taxon:4932
+S000000973 RAD3 YER171W|REM1 taxon:4932
+S000002827 RAD30 YDR419W|DBH1 taxon:4932
+S000002827 RAD30 YDR419W|DBH1 taxon:4932
+S000002827 RAD30 YDR419W|DBH1 taxon:4932
+S000002827 RAD30 YDR419W|DBH1 taxon:4932
+S000002827 RAD30 YDR419W|DBH1 taxon:4932
+S000004472 RAD33 YML011C taxon:4932
+S000004472 RAD33 YML011C taxon:4932
+S000004472 RAD33 YML011C taxon:4932
+S000002722 RAD34 YDR314C taxon:4932
+S000002722 RAD34 YDR314C taxon:4932
+S000002722 RAD34 YDR314C taxon:4932
+S000000964 RAD4 YER162C taxon:4932
+S000000964 RAD4 YER162C taxon:4932
+S000000964 RAD4 YER162C taxon:4932
+S000000964 RAD4 YER162C taxon:4932
+S000000964 RAD4 YER162C taxon:4932
+S000004022 RAD5 YLR032W|REV2|SNM2 taxon:4932
+S000004022 RAD5 YLR032W|REV2|SNM2 taxon:4932
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+S000004022 RAD5 YLR032W|REV2|SNM2 taxon:4932
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+S000001502 RAM2 YKL019W taxon:4932
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+S000005160 RAP1 YNL216W|GRF1|TBA1|TUF1 taxon:4932
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+S000005042 RAS2 YNL098C|CTN5|CYR3|GLC5|TSL7 taxon:4932
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+S000006167 RBD2 YPL246C taxon:4932
+S000006167 RBD2 YPL246C taxon:4932
+S000006167 RBD2 YPL246C taxon:4932
+S000000034 RBG1 YAL036C|FUN11 taxon:4932
+S000000034 RBG1 YAL036C|FUN11 taxon:4932
+S000000034 RBG1 YAL036C|FUN11 taxon:4932
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+S000004238 RCK2 YLR248W|CLK1|CMK3 taxon:4932
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+S000004238 RCK2 YLR248W|CLK1|CMK3 taxon:4932
+S000004238 RCK2 YLR248W|CLK1|CMK3 taxon:4932
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+S000000277 RDH54 YBR073W|TID1 taxon:4932
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+S000000277 RDH54 YBR073W|TID1 taxon:4932
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+S000000277 RDH54 YBR073W|TID1 taxon:4932
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+S000002294 RDI1 YDL135C taxon:4932
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+S000006485 RDN25-2 RDN25 taxon:4932
+S000006479 RDN5-1 RDN5 taxon:4932
+S000006479 RDN5-1 RDN5 taxon:4932
+S000006479 RDN5-1 RDN5 taxon:4932
+S000006480 RDN5-2 RDN5 taxon:4932
+S000006480 RDN5-2 RDN5 taxon:4932
+S000006480 RDN5-2 RDN5 taxon:4932
+S000006481 RDN5-3 RDN5 taxon:4932
+S000006481 RDN5-3 RDN5 taxon:4932
+S000006481 RDN5-3 RDN5 taxon:4932
+S000029708 RDN5-4 RDN5 taxon:4932
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+S000029710 RDN5-5 RDN5 taxon:4932
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+S000029711 RDN5-6 RDN5 taxon:4932
+S000029711 RDN5-6 RDN5 taxon:4932
+S000006488 RDN58-1 RDN58 taxon:4932
+S000006488 RDN58-1 RDN58 taxon:4932
+S000006488 RDN58-1 RDN58 taxon:4932
+S000006489 RDN58-2 RDN58 taxon:4932
+S000006489 RDN58-2 RDN58 taxon:4932
+S000006489 RDN58-2 RDN58 taxon:4932
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+S000005907 RDR1 YOR380W taxon:4932
+S000005907 RDR1 YOR380W taxon:4932
+S000005907 RDR1 YOR380W taxon:4932
+S000005907 RDR1 YOR380W taxon:4932
+S000000703 RDS1 YCR106W taxon:4932
+S000000703 RDS1 YCR106W taxon:4932
+S000000703 RDS1 YCR106W taxon:4932
+S000000703 RDS1 YCR106W taxon:4932
+S000000703 RDS1 YCR106W taxon:4932
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+S000006054 RDS2 YPL133C taxon:4932
+S000006054 RDS2 YPL133C taxon:4932
+S000006054 RDS2 YPL133C taxon:4932
+S000006054 RDS2 YPL133C taxon:4932
+S000006298 RDS3 YPR094W taxon:4932
+S000006298 RDS3 YPR094W taxon:4932
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+S000006298 RDS3 YPR094W taxon:4932
+S000006298 RDS3 YPR094W taxon:4932
+S000006298 RDS3 YPR094W taxon:4932
+S000000253 REB1 YBR049C|GRF2 taxon:4932
+S000000253 REB1 YBR049C|GRF2 taxon:4932
+S000000253 REB1 YBR049C|GRF2 taxon:4932
+S000000253 REB1 YBR049C|GRF2 taxon:4932
+S000000253 REB1 YBR049C|GRF2 taxon:4932
+S000029412 REC1 taxon:4932
+S000029412 REC1 taxon:4932
+S000029412 REC1 taxon:4932
+S000004321 REC102 YLR329W taxon:4932
+S000004321 REC102 YLR329W taxon:4932
+S000004321 REC102 YLR329W taxon:4932
+S000004321 REC102 YLR329W taxon:4932
+S000004321 REC102 YLR329W taxon:4932
+S000001200 REC104 YHR157W taxon:4932
+S000001200 REC104 YHR157W taxon:4932
+S000001200 REC104 YHR157W taxon:4932
+S000001200 REC104 YHR157W taxon:4932
+S000003782 REC107 YJR021C|MER2 taxon:4932
+S000003782 REC107 YJR021C|MER2 taxon:4932
+S000003782 REC107 YJR021C|MER2 taxon:4932
+S000004740 REC114 YMR133W taxon:4932
+S000004740 REC114 YMR133W taxon:4932
+S000004740 REC114 YMR133W taxon:4932
+S000004740 REC114 YMR133W taxon:4932
+S000006211 REC8 YPR007C|SPO69 taxon:4932
+S000006211 REC8 YPR007C|SPO69 taxon:4932
+S000006211 REC8 YPR007C|SPO69 taxon:4932
+S000006211 REC8 YPR007C|SPO69 taxon:4932
+S000006211 REC8 YPR007C|SPO69 taxon:4932
+S000004253 RED1 YLR263W taxon:4932
+S000004253 RED1 YLR263W taxon:4932
+S000004253 RED1 YLR263W taxon:4932
+S000004253 RED1 YLR263W taxon:4932
+S000004253 RED1 YLR263W taxon:4932
+S000004253 RED1 YLR263W taxon:4932
+S000004253 RED1 YLR263W taxon:4932
+S000004253 RED1 YLR263W taxon:4932
+S000004253 RED1 YLR263W taxon:4932
+S000004253 RED1 YLR263W taxon:4932
+S000004253 RED1 YLR263W taxon:4932
+S000004253 RED1 YLR263W taxon:4932
+S000004253 RED1 YLR263W taxon:4932
+S000004253 RED1 YLR263W taxon:4932
+S000002603 REF2 YDR195W taxon:4932
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+S000002603 REF2 YDR195W taxon:4932
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+S000002603 REF2 YDR195W taxon:4932
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+S000002435 REG1 YDR028C|HEX2|PZF240|SPP43|SRN1 taxon:4932
+S000002435 REG1 YDR028C|HEX2|PZF240|SPP43|SRN1 taxon:4932
+S000002435 REG1 YDR028C|HEX2|PZF240|SPP43|SRN1 taxon:4932
+S000002435 REG1 YDR028C|HEX2|PZF240|SPP43|SRN1 taxon:4932
+S000002435 REG1 YDR028C|HEX2|PZF240|SPP43|SRN1 taxon:4932
+S000002435 REG1 YDR028C|HEX2|PZF240|SPP43|SRN1 taxon:4932
+S000002435 REG1 YDR028C|HEX2|PZF240|SPP43|SRN1 taxon:4932
+S000002435 REG1 YDR028C|HEX2|PZF240|SPP43|SRN1 taxon:4932
+S000002435 REG1 YDR028C|HEX2|PZF240|SPP43|SRN1 taxon:4932
+S000002435 REG1 YDR028C|HEX2|PZF240|SPP43|SRN1 taxon:4932
+S000000254 REG2 YBR050C taxon:4932
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+S000000254 REG2 YBR050C taxon:4932
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+S000004379 REH1 YLR387C taxon:4932
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+S000004379 REH1 YLR387C taxon:4932
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+S000000471 REI1 YBR267W taxon:4932
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+S000029675 REP1 taxon:4932
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+S000029675 REP1 taxon:4932
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+S000000507 RER1 YCL001W taxon:4932
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+S000000206 RER2 YBR002C taxon:4932
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+S000000206 RER2 YBR002C taxon:4932
+S000000206 RER2 YBR002C taxon:4932
+S000000206 RER2 YBR002C taxon:4932
+S000005733 RET1 YOR207C|C128|PDS2|RPC128|RPC2 taxon:4932
+S000005733 RET1 YOR207C|C128|PDS2|RPC128|RPC2 taxon:4932
+S000005733 RET1 YOR207C|C128|PDS2|RPC128|RPC2 taxon:4932
+S000001947 RET2 YFR051C taxon:4932
+S000001947 RET2 YFR051C taxon:4932
+S000001947 RET2 YFR051C taxon:4932
+S000001947 RET2 YFR051C taxon:4932
+S000001947 RET2 YFR051C taxon:4932
+S000005931 RET3 YPL010W taxon:4932
+S000005931 RET3 YPL010W taxon:4932
+S000005931 RET3 YPL010W taxon:4932
+S000005931 RET3 YPL010W taxon:4932
+S000005873 REV1 YOR346W taxon:4932
+S000005873 REV1 YOR346W taxon:4932
+S000005873 REV1 YOR346W taxon:4932
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+S000005873 REV1 YOR346W taxon:4932
+S000005873 REV1 YOR346W taxon:4932
+S000006088 REV3 YPL167C|PSO1 taxon:4932
+S000006088 REV3 YPL167C|PSO1 taxon:4932
+S000006088 REV3 YPL167C|PSO1 taxon:4932
+S000006088 REV3 YPL167C|PSO1 taxon:4932
+S000006088 REV3 YPL167C|PSO1 taxon:4932
+S000001401 REV7 YIL139C taxon:4932
+S000001401 REV7 YIL139C taxon:4932
+S000001401 REV7 YIL139C taxon:4932
+S000001401 REV7 YIL139C taxon:4932
+S000001401 REV7 YIL139C taxon:4932
+S000004049 REX2 YLR059C|YNT20 taxon:4932
+S000004049 REX2 YLR059C|YNT20 taxon:4932
+S000004049 REX2 YLR059C|YNT20 taxon:4932
+S000004049 REX2 YLR059C|YNT20 taxon:4932
+S000004049 REX2 YLR059C|YNT20 taxon:4932
+S000004049 REX2 YLR059C|YNT20 taxon:4932
+S000004097 REX3 YLR107W taxon:4932
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+S000004097 REX3 YLR107W taxon:4932
+S000004097 REX3 YLR107W taxon:4932
+S000005440 REX4 YOL080C taxon:4932
+S000005440 REX4 YOL080C taxon:4932
+S000005440 REX4 YOL080C taxon:4932
+S000005440 REX4 YOL080C taxon:4932
+S000005440 REX4 YOL080C taxon:4932
+S000005440 REX4 YOL080C taxon:4932
+S000029417 RF2 taxon:4932
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+S000029417 RF2 taxon:4932
+S000000065 RFA1 YAR007C|BUF2|FUN3|RPA1 taxon:4932
+S000000065 RFA1 YAR007C|BUF2|FUN3|RPA1 taxon:4932
+S000000065 RFA1 YAR007C|BUF2|FUN3|RPA1 taxon:4932
+S000000065 RFA1 YAR007C|BUF2|FUN3|RPA1 taxon:4932
+S000000065 RFA1 YAR007C|BUF2|FUN3|RPA1 taxon:4932
+S000000065 RFA1 YAR007C|BUF2|FUN3|RPA1 taxon:4932
+S000000065 RFA1 YAR007C|BUF2|FUN3|RPA1 taxon:4932
+S000000065 RFA1 YAR007C|BUF2|FUN3|RPA1 taxon:4932
+S000000065 RFA1 YAR007C|BUF2|FUN3|RPA1 taxon:4932
+S000000065 RFA1 YAR007C|BUF2|FUN3|RPA1 taxon:4932
+S000000065 RFA1 YAR007C|BUF2|FUN3|RPA1 taxon:4932
+S000000065 RFA1 YAR007C|BUF2|FUN3|RPA1 taxon:4932
+S000000065 RFA1 YAR007C|BUF2|FUN3|RPA1 taxon:4932
+S000005256 RFA2 YNL312W|BUF1|RPA2 taxon:4932
+S000005256 RFA2 YNL312W|BUF1|RPA2 taxon:4932
+S000005256 RFA2 YNL312W|BUF1|RPA2 taxon:4932
+S000005256 RFA2 YNL312W|BUF1|RPA2 taxon:4932
+S000005256 RFA2 YNL312W|BUF1|RPA2 taxon:4932
+S000005256 RFA2 YNL312W|BUF1|RPA2 taxon:4932
+S000005256 RFA2 YNL312W|BUF1|RPA2 taxon:4932
+S000005256 RFA2 YNL312W|BUF1|RPA2 taxon:4932
+S000005256 RFA2 YNL312W|BUF1|RPA2 taxon:4932
+S000005256 RFA2 YNL312W|BUF1|RPA2 taxon:4932
+S000003709 RFA3 YJL173C taxon:4932
+S000003709 RFA3 YJL173C taxon:4932
+S000003709 RFA3 YJL173C taxon:4932
+S000003709 RFA3 YJL173C taxon:4932
+S000003709 RFA3 YJL173C taxon:4932
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+S000003709 RFA3 YJL173C taxon:4932
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+S000005743 RFC1 YOR217W|CDC44 taxon:4932
+S000005743 RFC1 YOR217W|CDC44 taxon:4932
+S000005743 RFC1 YOR217W|CDC44 taxon:4932
+S000005743 RFC1 YOR217W|CDC44 taxon:4932
+S000003829 RFC2 YJR068W taxon:4932
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+S000003829 RFC2 YJR068W taxon:4932
+S000003829 RFC2 YJR068W taxon:4932
+S000003829 RFC2 YJR068W taxon:4932
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+S000005234 RFC3 YNL290W taxon:4932
+S000005234 RFC3 YNL290W taxon:4932
+S000005234 RFC3 YNL290W taxon:4932
+S000005234 RFC3 YNL290W taxon:4932
+S000005234 RFC3 YNL290W taxon:4932
+S000005234 RFC3 YNL290W taxon:4932
+S000005234 RFC3 YNL290W taxon:4932
+S000005234 RFC3 YNL290W taxon:4932
+S000005454 RFC4 YOL094C taxon:4932
+S000005454 RFC4 YOL094C taxon:4932
+S000005454 RFC4 YOL094C taxon:4932
+S000005454 RFC4 YOL094C taxon:4932
+S000005454 RFC4 YOL094C taxon:4932
+S000005454 RFC4 YOL094C taxon:4932
+S000005454 RFC4 YOL094C taxon:4932
+S000005454 RFC4 YOL094C taxon:4932
+S000000291 RFC5 YBR087W taxon:4932
+S000000291 RFC5 YBR087W taxon:4932
+S000000291 RFC5 YBR087W taxon:4932
+S000000291 RFC5 YBR087W taxon:4932
+S000000291 RFC5 YBR087W taxon:4932
+S000000291 RFC5 YBR087W taxon:4932
+S000000291 RFC5 YBR087W taxon:4932
+S000005805 RFM1 YOR279C taxon:4932
+S000005805 RFM1 YOR279C taxon:4932
+S000005805 RFM1 YOR279C taxon:4932
+S000005805 RFM1 YOR279C taxon:4932
+S000005805 RFM1 YOR279C taxon:4932
+S000005805 RFM1 YOR279C taxon:4932
+S000005805 RFM1 YOR279C taxon:4932
+S000005805 RFM1 YOR279C taxon:4932
+S000005805 RFM1 YOR279C taxon:4932
+S000000256 RFS1 YBR052C taxon:4932
+S000000256 RFS1 YBR052C taxon:4932
+S000000256 RFS1 YBR052C taxon:4932
+S000000116 RFT1 YBL020W taxon:4932
+S000000116 RFT1 YBL020W taxon:4932
+S000000116 RFT1 YBL020W taxon:4932
+S000000116 RFT1 YBL020W taxon:4932
+S000004166 RFX1 YLR176C|CRT1 taxon:4932
+S000004166 RFX1 YLR176C|CRT1 taxon:4932
+S000004166 RFX1 YLR176C|CRT1 taxon:4932
+S000004166 RFX1 YLR176C|CRT1 taxon:4932
+S000004166 RFX1 YLR176C|CRT1 taxon:4932
+S000004166 RFX1 YLR176C|CRT1 taxon:4932
+S000005653 RGA1 YOR127W|DBM1|THE1 taxon:4932
+S000005653 RGA1 YOR127W|DBM1|THE1 taxon:4932
+S000005653 RGA1 YOR127W|DBM1|THE1 taxon:4932
+S000005653 RGA1 YOR127W|DBM1|THE1 taxon:4932
+S000005653 RGA1 YOR127W|DBM1|THE1 taxon:4932
+S000005653 RGA1 YOR127W|DBM1|THE1 taxon:4932
+S000005653 RGA1 YOR127W|DBM1|THE1 taxon:4932
+S000005653 RGA1 YOR127W|DBM1|THE1 taxon:4932
+S000005653 RGA1 YOR127W|DBM1|THE1 taxon:4932
+S000005653 RGA1 YOR127W|DBM1|THE1 taxon:4932
+S000005653 RGA1 YOR127W|DBM1|THE1 taxon:4932
+S000005653 RGA1 YOR127W|DBM1|THE1 taxon:4932
+S000002787 RGA2 YDR379W taxon:4932
+S000002787 RGA2 YDR379W taxon:4932
+S000002787 RGA2 YDR379W taxon:4932
+S000002787 RGA2 YDR379W taxon:4932
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+S000002787 RGA2 YDR379W taxon:4932
+S000002787 RGA2 YDR379W taxon:4932
+S000002787 RGA2 YDR379W taxon:4932
+S000002787 RGA2 YDR379W taxon:4932
+S000002787 RGA2 YDR379W taxon:4932
+S000002787 RGA2 YDR379W taxon:4932
+S000000464 RGD1 YBR260C taxon:4932
+S000000464 RGD1 YBR260C taxon:4932
+S000000464 RGD1 YBR260C taxon:4932
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+S000001847 RGD2 YFL047W taxon:4932
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+S000004794 RGM1 YMR182C taxon:4932
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+S000004794 RGM1 YMR182C taxon:4932
+S000004794 RGM1 YMR182C taxon:4932
+S000002544 RGP1 YDR137W taxon:4932
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+S000002544 RGP1 YDR137W taxon:4932
+S000004061 RGR1 YLR071C|MED14 taxon:4932
+S000004061 RGR1 YLR071C|MED14 taxon:4932
+S000004061 RGR1 YLR071C|MED14 taxon:4932
+S000005633 RGS2 YOR107W taxon:4932
+S000005633 RGS2 YOR107W taxon:4932
+S000005633 RGS2 YOR107W taxon:4932
+S000005633 RGS2 YOR107W taxon:4932
+S000001521 RGT1 YKL038W taxon:4932
+S000001521 RGT1 YKL038W taxon:4932
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+S000002297 RGT2 YDL138W taxon:4932
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+S000002297 RGT2 YDL138W taxon:4932
+S000002297 RGT2 YDL138W taxon:4932
+S000002297 RGT2 YDL138W taxon:4932
+S000002297 RGT2 YDL138W taxon:4932
+S000002297 RGT2 YDL138W taxon:4932
+S000000622 RHB1 YCR027C|RSG1 taxon:4932
+S000000622 RHB1 YCR027C|RSG1 taxon:4932
+S000000622 RHB1 YCR027C|RSG1 taxon:4932
+S000000622 RHB1 YCR027C|RSG1 taxon:4932
+S000000622 RHB1 YCR027C|RSG1 taxon:4932
+S000006369 RHO1 YPR165W taxon:4932
+S000006369 RHO1 YPR165W taxon:4932
+S000006369 RHO1 YPR165W taxon:4932
+S000006369 RHO1 YPR165W taxon:4932
+S000006369 RHO1 YPR165W taxon:4932
+S000006369 RHO1 YPR165W taxon:4932
+S000006369 RHO1 YPR165W taxon:4932
+S000006369 RHO1 YPR165W taxon:4932
+S000006369 RHO1 YPR165W taxon:4932
+S000006369 RHO1 YPR165W taxon:4932
+S000006369 RHO1 YPR165W taxon:4932
+S000006369 RHO1 YPR165W taxon:4932
+S000006369 RHO1 YPR165W taxon:4932
+S000006369 RHO1 YPR165W taxon:4932
+S000006369 RHO1 YPR165W taxon:4932
+S000006369 RHO1 YPR165W taxon:4932
+S000005034 RHO2 YNL090W taxon:4932
+S000005034 RHO2 YNL090W taxon:4932
+S000005034 RHO2 YNL090W taxon:4932
+S000005034 RHO2 YNL090W taxon:4932
+S000005034 RHO2 YNL090W taxon:4932
+S000005034 RHO2 YNL090W taxon:4932
+S000005034 RHO2 YNL090W taxon:4932
+S000005034 RHO2 YNL090W taxon:4932
+S000001380 RHO3 YIL118W taxon:4932
+S000001380 RHO3 YIL118W taxon:4932
+S000001380 RHO3 YIL118W taxon:4932
+S000001380 RHO3 YIL118W taxon:4932
+S000001380 RHO3 YIL118W taxon:4932
+S000001380 RHO3 YIL118W taxon:4932
+S000001380 RHO3 YIL118W taxon:4932
+S000001380 RHO3 YIL118W taxon:4932
+S000001380 RHO3 YIL118W taxon:4932
+S000001763 RHO4 YKR055W taxon:4932
+S000001763 RHO4 YKR055W taxon:4932
+S000001763 RHO4 YKR055W taxon:4932
+S000001763 RHO4 YKR055W taxon:4932
+S000001763 RHO4 YKR055W taxon:4932
+S000001763 RHO4 YKR055W taxon:4932
+S000001763 RHO4 YKR055W taxon:4932
+S000001763 RHO4 YKR055W taxon:4932
+S000005124 RHO5 YNL180C taxon:4932
+S000005124 RHO5 YNL180C taxon:4932
+S000005124 RHO5 YNL180C taxon:4932
+S000005124 RHO5 YNL180C taxon:4932
+S000001315 RHR2 YIL053W|GPP1 taxon:4932
+S000001315 RHR2 YIL053W|GPP1 taxon:4932
+S000001315 RHR2 YIL053W|GPP1 taxon:4932
+S000001315 RHR2 YIL053W|GPP1 taxon:4932
+S000001315 RHR2 YIL053W|GPP1 taxon:4932
+S000005107 RIA1 YNL163C|EFL1 taxon:4932
+S000005107 RIA1 YNL163C|EFL1 taxon:4932
+S000005107 RIA1 YNL163C|EFL1 taxon:4932
+S000005107 RIA1 YNL163C|EFL1 taxon:4932
+S000005107 RIA1 YNL163C|EFL1 taxon:4932
+S000005107 RIA1 YNL163C|EFL1 taxon:4932
+S000000129 RIB1 YBL033C taxon:4932
+S000000129 RIB1 YBL033C taxon:4932
+S000000129 RIB1 YBL033C taxon:4932
+S000000129 RIB1 YBL033C taxon:4932
+S000000129 RIB1 YBL033C taxon:4932
+S000000129 RIB1 YBL033C taxon:4932
+S000005427 RIB2 YOL066C|PUS8 taxon:4932
+S000005427 RIB2 YOL066C|PUS8 taxon:4932
+S000005427 RIB2 YOL066C|PUS8 taxon:4932
+S000005427 RIB2 YOL066C|PUS8 taxon:4932
+S000005427 RIB2 YOL066C|PUS8 taxon:4932
+S000005427 RIB2 YOL066C|PUS8 taxon:4932
+S000005427 RIB2 YOL066C|PUS8 taxon:4932
+S000005427 RIB2 YOL066C|PUS8 taxon:4932
+S000005427 RIB2 YOL066C|PUS8 taxon:4932
+S000005427 RIB2 YOL066C|PUS8 taxon:4932
+S000002895 RIB3 YDR487C taxon:4932
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+S000002895 RIB3 YDR487C taxon:4932
+S000002895 RIB3 YDR487C taxon:4932
+S000005503 RIB4 YOL143C taxon:4932
+S000005503 RIB4 YOL143C taxon:4932
+S000005503 RIB4 YOL143C taxon:4932
+S000005503 RIB4 YOL143C taxon:4932
+S000005503 RIB4 YOL143C taxon:4932
+S000005503 RIB4 YOL143C taxon:4932
+S000000460 RIB5 YBR256C taxon:4932
+S000000460 RIB5 YBR256C taxon:4932
+S000000460 RIB5 YBR256C taxon:4932
+S000000460 RIB5 YBR256C taxon:4932
+S000000357 RIB7 YBR153W taxon:4932
+S000000357 RIB7 YBR153W taxon:4932
+S000000357 RIB7 YBR153W taxon:4932
+S000000357 RIB7 YBR153W taxon:4932
+S000004029 RIC1 YLR039C taxon:4932
+S000004029 RIC1 YLR039C taxon:4932
+S000004029 RIC1 YLR039C taxon:4932
+S000004029 RIC1 YLR039C taxon:4932
+S000004029 RIC1 YLR039C taxon:4932
+S000004029 RIC1 YLR039C taxon:4932
+S000004029 RIC1 YLR039C taxon:4932
+S000004029 RIC1 YLR039C taxon:4932
+S000004029 RIC1 YLR039C taxon:4932
+S000004029 RIC1 YLR039C taxon:4932
+S000000479 RIF1 YBR275C taxon:4932
+S000000479 RIF1 YBR275C taxon:4932
+S000000479 RIF1 YBR275C taxon:4932
+S000000479 RIF1 YBR275C taxon:4932
+S000000479 RIF1 YBR275C taxon:4932
+S000000479 RIF1 YBR275C taxon:4932
+S000004445 RIF2 YLR453C taxon:4932
+S000004445 RIF2 YLR453C taxon:4932
+S000004445 RIF2 YLR453C taxon:4932
+S000007222 RIM1 YCR028C-A taxon:4932
+S000007222 RIM1 YCR028C-A taxon:4932
+S000007222 RIM1 YCR028C-A taxon:4932
+S000007222 RIM1 YCR028C-A taxon:4932
+S000007222 RIM1 YCR028C-A taxon:4932
+S000001019 RIM101 YHL027W|RIM1 taxon:4932
+S000001019 RIM101 YHL027W|RIM1 taxon:4932
+S000001019 RIM101 YHL027W|RIM1 taxon:4932
+S000001019 RIM101 YHL027W|RIM1 taxon:4932
+S000001019 RIM101 YHL027W|RIM1 taxon:4932
+S000001019 RIM101 YHL027W|RIM1 taxon:4932
+S000004747 RIM11 YMR139W|GSK3|MDS1 taxon:4932
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+S000004747 RIM11 YMR139W|GSK3|MDS1 taxon:4932
+S000004763 RIM13 YMR154C|CPL1 taxon:4932
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+S000004763 RIM13 YMR154C|CPL1 taxon:4932
+S000004763 RIM13 YMR154C|CPL1 taxon:4932
+S000001861 RIM15 YFL033C|TAK1 taxon:4932
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+S000005801 RIM20 YOR275C taxon:4932
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+S000005238 RIM21 YNL294C|PAL2 taxon:4932
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+S000005645 RIO1 YOR119C|RRP10 taxon:4932
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+S000005645 RIO1 YOR119C|RRP10 taxon:4932
+S000005645 RIO1 YOR119C|RRP10 taxon:4932
+S000005645 RIO1 YOR119C|RRP10 taxon:4932
+S000005151 RIO2 YNL207W taxon:4932
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+S000005151 RIO2 YNL207W taxon:4932
+S000005151 RIO2 YNL207W taxon:4932
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+S000005151 RIO2 YNL207W taxon:4932
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+S000005717 RIS1 YOR191W|DIS1 taxon:4932
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+S000005717 RIS1 YOR191W|DIS1 taxon:4932
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+S000005717 RIS1 YOR191W|DIS1 taxon:4932
+S000004896 RIT1 YMR283C taxon:4932
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+S000004896 RIT1 YMR283C taxon:4932
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+S000004896 RIT1 YMR283C taxon:4932
+S000001240 RIX1 YHR197W|IPI2 taxon:4932
+S000001240 RIX1 YHR197W|IPI2 taxon:4932
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+S000001240 RIX1 YHR197W|IPI2 taxon:4932
+S000001240 RIX1 YHR197W|IPI2 taxon:4932
+S000001240 RIX1 YHR197W|IPI2 taxon:4932
+S000001240 RIX1 YHR197W|IPI2 taxon:4932
+S000001240 RIX1 YHR197W|IPI2 taxon:4932
+S000001240 RIX1 YHR197W|IPI2 taxon:4932
+S000003957 RIX7 YLL034C taxon:4932
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+S000003957 RIX7 YLL034C taxon:4932
+S000003957 RIX7 YLL034C taxon:4932
+S000003957 RIX7 YLL034C taxon:4932
+S000003957 RIX7 YLL034C taxon:4932
+S000005621 RKI1 YOR095C taxon:4932
+S000005621 RKI1 YOR095C taxon:4932
+S000005621 RKI1 YOR095C taxon:4932
+S000005621 RKI1 YOR095C taxon:4932
+S000005621 RKI1 YOR095C taxon:4932
+S000005621 RKI1 YOR095C taxon:4932
+S000006129 RKM1 YPL208W taxon:4932
+S000006129 RKM1 YPL208W taxon:4932
+S000006129 RKM1 YPL208W taxon:4932
+S000006129 RKM1 YPL208W taxon:4932
+S000006129 RKM1 YPL208W taxon:4932
+S000002606 RKM2 YDR198C taxon:4932
+S000002606 RKM2 YDR198C taxon:4932
+S000002606 RKM2 YDR198C taxon:4932
+S000004861 RKR1 YMR247C taxon:4932
+S000004861 RKR1 YMR247C taxon:4932
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+S000006222 RLF2 YPR018W|CAC1 taxon:4932
+S000006222 RLF2 YPR018W|CAC1 taxon:4932
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+S000002498 RLI1 YDR091C taxon:4932
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+S000002498 RLI1 YDR091C taxon:4932
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+S000002498 RLI1 YDR091C taxon:4932
+S000002498 RLI1 YDR091C taxon:4932
+S000002498 RLI1 YDR091C taxon:4932
+S000002498 RLI1 YDR091C taxon:4932
+S000002498 RLI1 YDR091C taxon:4932
+S000002498 RLI1 YDR091C taxon:4932
+S000002498 RLI1 YDR091C taxon:4932
+S000006010 RLM1 YPL089C taxon:4932
+S000006010 RLM1 YPL089C taxon:4932
+S000006010 RLM1 YPL089C taxon:4932
+S000006010 RLM1 YPL089C taxon:4932
+S000006010 RLM1 YPL089C taxon:4932
+S000006010 RLM1 YPL089C taxon:4932
+S000006010 RLM1 YPL089C taxon:4932
+S000006010 RLM1 YPL089C taxon:4932
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+S000003999 RLP24 YLR009W taxon:4932
+S000003999 RLP24 YLR009W taxon:4932
+S000003999 RLP24 YLR009W taxon:4932
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+S000004947 RLP7 YNL002C|RPL7 taxon:4932
+S000004947 RLP7 YNL002C|RPL7 taxon:4932
+S000004947 RLP7 YNL002C|RPL7 taxon:4932
+S000005083 RLR1 YNL139C|LDB5|THO2|ZRG13 taxon:4932
+S000005083 RLR1 YNL139C|LDB5|THO2|ZRG13 taxon:4932
+S000005083 RLR1 YNL139C|LDB5|THO2|ZRG13 taxon:4932
+S000005083 RLR1 YNL139C|LDB5|THO2|ZRG13 taxon:4932
+S000005083 RLR1 YNL139C|LDB5|THO2|ZRG13 taxon:4932
+S000005083 RLR1 YNL139C|LDB5|THO2|ZRG13 taxon:4932
+S000005083 RLR1 YNL139C|LDB5|THO2|ZRG13 taxon:4932
+S000005083 RLR1 YNL139C|LDB5|THO2|ZRG13 taxon:4932
+S000001615 RMA1 YKL132C taxon:4932
+S000001615 RMA1 YKL132C taxon:4932
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+S000002159 RMD1 YDL001W taxon:4932
+S000002159 RMD1 YDL001W taxon:4932
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+S000001015 RMD11 YHL023C taxon:4932
+S000001015 RMD11 YHL023C taxon:4932
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+S000002663 RMD5 YDR255C|GID2 taxon:4932
+S000002663 RMD5 YDR255C|GID2 taxon:4932
+S000002663 RMD5 YDR255C|GID2 taxon:4932
+S000000798 RMD6 YEL072W taxon:4932
+S000000798 RMD6 YEL072W taxon:4932
+S000000798 RMD6 YEL072W taxon:4932
+S000001944 RMD8 YFR048W taxon:4932
+S000001944 RMD8 YFR048W taxon:4932
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+S000003075 RMD9 YGL107C taxon:4932
+S000003075 RMD9 YGL107C taxon:4932
+S000003075 RMD9 YGL107C taxon:4932
+S000003075 RMD9 YGL107C taxon:4932
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+S000003276 RME1 YGR044C|CSP1 taxon:4932
+S000003276 RME1 YGR044C|CSP1 taxon:4932
+S000003276 RME1 YGR044C|CSP1 taxon:4932
+S000005945 RMI1 YPL024W|NCE4 taxon:4932
+S000005945 RMI1 YPL024W|NCE4 taxon:4932
+S000005945 RMI1 YPL024W|NCE4 taxon:4932
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+S000005945 RMI1 YPL024W|NCE4 taxon:4932
+S000000776 RML2 YEL050C taxon:4932
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+S000000776 RML2 YEL050C taxon:4932
+S000000776 RML2 YEL050C taxon:4932
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+S000004135 RMP1 YLR145W taxon:4932
+S000004135 RMP1 YLR145W taxon:4932
+S000004135 RMP1 YLR145W taxon:4932
+S000004135 RMP1 YLR145W taxon:4932
+S000004135 RMP1 YLR145W taxon:4932
+S000004135 RMP1 YLR145W taxon:4932
+S000004135 RMP1 YLR145W taxon:4932
+S000002873 RMT2 YDR465C taxon:4932
+S000002873 RMT2 YDR465C taxon:4932
+S000002873 RMT2 YDR465C taxon:4932
+S000002873 RMT2 YDR465C taxon:4932
+S000002873 RMT2 YDR465C taxon:4932
+S000004848 RNA1 YMR235C taxon:4932
+S000004848 RNA1 YMR235C taxon:4932
+S000004848 RNA1 YMR235C taxon:4932
+S000004848 RNA1 YMR235C taxon:4932
+S000004848 RNA1 YMR235C taxon:4932
+S000004848 RNA1 YMR235C taxon:4932
+S000004848 RNA1 YMR235C taxon:4932
+S000004665 RNA14 YMR061W taxon:4932
+S000004665 RNA14 YMR061W taxon:4932
+S000004665 RNA14 YMR061W taxon:4932
+S000004665 RNA14 YMR061W taxon:4932
+S000004665 RNA14 YMR061W taxon:4932
+S000004665 RNA14 YMR061W taxon:4932
+S000004665 RNA14 YMR061W taxon:4932
+S000003012 RNA15 YGL044C taxon:4932
+S000003012 RNA15 YGL044C taxon:4932
+S000003012 RNA15 YGL044C taxon:4932
+S000003012 RNA15 YGL044C taxon:4932
+S000003012 RNA15 YGL044C taxon:4932
+S000004847 RNH1 YMR234W taxon:4932
+S000004847 RNH1 YMR234W taxon:4932
+S000004847 RNH1 YMR234W taxon:4932
+S000004847 RNH1 YMR234W taxon:4932
+S000004847 RNH1 YMR234W taxon:4932
+S000005016 RNH201 YNL072W|RNH35|Rnh2A taxon:4932
+S000005016 RNH201 YNL072W|RNH35|Rnh2A taxon:4932
+S000005016 RNH201 YNL072W|RNH35|Rnh2A taxon:4932
+S000002687 RNH202 YDR279W|Rnh2B taxon:4932
+S000002687 RNH202 YDR279W|Rnh2B taxon:4932
+S000002687 RNH202 YDR279W|Rnh2B taxon:4932
+S000004144 RNH203 YLR154C|Rnh2C taxon:4932
+S000004144 RNH203 YLR154C|Rnh2C taxon:4932
+S000004144 RNH203 YLR154C|Rnh2C taxon:4932
+S000004144 RNH203 YLR154C|Rnh2C taxon:4932
+S000003508 RNH70 YGR276C|REX1 taxon:4932
+S000003508 RNH70 YGR276C|REX1 taxon:4932
+S000003508 RNH70 YGR276C|REX1 taxon:4932
+S000003508 RNH70 YGR276C|REX1 taxon:4932
+S000003969 RNP1 YLL046C taxon:4932
+S000003969 RNP1 YLL046C taxon:4932
+S000003969 RNP1 YLL046C taxon:4932
+S000000533 RNQ1 YCL028W|[PIN(+)] taxon:4932
+S000000533 RNQ1 YCL028W|[PIN(+)] taxon:4932
+S000000533 RNQ1 YCL028W|[PIN(+)] taxon:4932
+S000000872 RNR1 YER070W|CRT7|RIR1|SDS12 taxon:4932
+S000000872 RNR1 YER070W|CRT7|RIR1|SDS12 taxon:4932
+S000000872 RNR1 YER070W|CRT7|RIR1|SDS12 taxon:4932
+S000000872 RNR1 YER070W|CRT7|RIR1|SDS12 taxon:4932
+S000000872 RNR1 YER070W|CRT7|RIR1|SDS12 taxon:4932
+S000003563 RNR2 YJL026W|CRT6 taxon:4932
+S000003563 RNR2 YJL026W|CRT6 taxon:4932
+S000003563 RNR2 YJL026W|CRT6 taxon:4932
+S000003563 RNR2 YJL026W|CRT6 taxon:4932
+S000003563 RNR2 YJL026W|CRT6 taxon:4932
+S000003563 RNR2 YJL026W|CRT6 taxon:4932
+S000003563 RNR2 YJL026W|CRT6 taxon:4932
+S000001328 RNR3 YIL066C|DIN1|RIR3 taxon:4932
+S000001328 RNR3 YIL066C|DIN1|RIR3 taxon:4932
+S000001328 RNR3 YIL066C|DIN1|RIR3 taxon:4932
+S000001328 RNR3 YIL066C|DIN1|RIR3 taxon:4932
+S000001328 RNR3 YIL066C|DIN1|RIR3 taxon:4932
+S000003412 RNR4 YGR180C|CRT3 taxon:4932
+S000003412 RNR4 YGR180C|CRT3 taxon:4932
+S000003412 RNR4 YGR180C|CRT3 taxon:4932
+S000003412 RNR4 YGR180C|CRT3 taxon:4932
+S000003412 RNR4 YGR180C|CRT3 taxon:4932
+S000003412 RNR4 YGR180C|CRT3 taxon:4932
+S000003412 RNR4 YGR180C|CRT3 taxon:4932
+S000003412 RNR4 YGR180C|CRT3 taxon:4932
+S000003412 RNR4 YGR180C|CRT3 taxon:4932
+S000003412 RNR4 YGR180C|CRT3 taxon:4932
+S000004852 RNT1 YMR239C taxon:4932
+S000004852 RNT1 YMR239C taxon:4932
+S000004852 RNT1 YMR239C taxon:4932
+S000004852 RNT1 YMR239C taxon:4932
+S000006044 RNY1 YPL123C taxon:4932
+S000006044 RNY1 YPL123C taxon:4932
+S000006044 RNY1 YPL123C taxon:4932
+S000005544 ROD1 YOR018W taxon:4932
+S000005544 ROD1 YOR018W taxon:4932
+S000005544 ROD1 YOR018W taxon:4932
+S000003112 ROG1 YGL144C taxon:4932
+S000003112 ROG1 YGL144C taxon:4932
+S000003112 ROG1 YGL144C taxon:4932
+S000001918 ROG3 YFR022W taxon:4932
+S000001918 ROG3 YFR022W taxon:4932
+S000001918 ROG3 YFR022W taxon:4932
+S000003139 ROK1 YGL171W taxon:4932
+S000003139 ROK1 YGL171W taxon:4932
+S000003139 ROK1 YGL171W taxon:4932
+S000003139 ROK1 YGL171W taxon:4932
+S000003302 ROM1 YGR070W|SKC1 taxon:4932
+S000003302 ROM1 YGR070W|SKC1 taxon:4932
+S000003302 ROM1 YGR070W|SKC1 taxon:4932
+S000003302 ROM1 YGR070W|SKC1 taxon:4932
+S000003302 ROM1 YGR070W|SKC1 taxon:4932
+S000003302 ROM1 YGR070W|SKC1 taxon:4932
+S000003302 ROM1 YGR070W|SKC1 taxon:4932
+S000003302 ROM1 YGR070W|SKC1 taxon:4932
+S000004363 ROM2 YLR371W taxon:4932
+S000004363 ROM2 YLR371W taxon:4932
+S000004363 ROM2 YLR371W taxon:4932
+S000004363 ROM2 YLR371W taxon:4932
+S000004363 ROM2 YLR371W taxon:4932
+S000004363 ROM2 YLR371W taxon:4932
+S000004363 ROM2 YLR371W taxon:4932
+S000004363 ROM2 YLR371W taxon:4932
+S000004363 ROM2 YLR371W taxon:4932
+S000004363 ROM2 YLR371W taxon:4932
+S000004813 ROT1 YMR200W taxon:4932
+S000004813 ROT1 YMR200W taxon:4932
+S000004813 ROT1 YMR200W taxon:4932
+S000000433 ROT2 YBR229C|GLS2 taxon:4932
+S000000433 ROT2 YBR229C|GLS2 taxon:4932
+S000000433 ROT2 YBR229C|GLS2 taxon:4932
+S000000433 ROT2 YBR229C|GLS2 taxon:4932
+S000000433 ROT2 YBR229C|GLS2 taxon:4932
+S000006269 ROX1 YPR065W|REO1 taxon:4932
+S000006269 ROX1 YPR065W|REO1 taxon:4932
+S000006269 ROX1 YPR065W|REO1 taxon:4932
+S000006269 ROX1 YPR065W|REO1 taxon:4932
+S000000189 ROX3 YBL093C|MED19|NUT3|SSN7 taxon:4932
+S000000189 ROX3 YBL093C|MED19|NUT3|SSN7 taxon:4932
+S000000189 ROX3 YBL093C|MED19|NUT3|SSN7 taxon:4932
+S000000189 ROX3 YBL093C|MED19|NUT3|SSN7 taxon:4932
+S000003824 RPA12 YJR063W|A12.2|RRN4 taxon:4932
+S000003824 RPA12 YJR063W|A12.2|RRN4 taxon:4932
+S000003824 RPA12 YJR063W|A12.2|RRN4 taxon:4932
+S000006214 RPA135 YPR010C|A135|RPA2|RRN2|SRP3 taxon:4932
+S000006214 RPA135 YPR010C|A135|RPA2|RRN2|SRP3 taxon:4932
+S000006214 RPA135 YPR010C|A135|RPA2|RRN2|SRP3 taxon:4932
+S000002563 RPA14 YDR156W|A14 taxon:4932
+S000002563 RPA14 YDR156W|A14 taxon:4932
+S000002563 RPA14 YDR156W|A14 taxon:4932
+S000005868 RPA190 YOR341W|A190|RRN1 taxon:4932
+S000005868 RPA190 YOR341W|A190|RRN1 taxon:4932
+S000005868 RPA190 YOR341W|A190|RRN1 taxon:4932
+S000003684 RPA34 YJL148W|A34.5 taxon:4932
+S000003684 RPA34 YJL148W|A34.5 taxon:4932
+S000003684 RPA34 YJL148W|A34.5 taxon:4932
+S000003684 RPA34 YJL148W|A34.5 taxon:4932
+S000003684 RPA34 YJL148W|A34.5 taxon:4932
+S000005867 RPA43 YOR340C|A43 taxon:4932
+S000005867 RPA43 YOR340C|A43 taxon:4932
+S000005867 RPA43 YOR340C|A43 taxon:4932
+S000005192 RPA49 YNL248C|A49 taxon:4932
+S000005192 RPA49 YNL248C|A49 taxon:4932
+S000005192 RPA49 YNL248C|A49 taxon:4932
+S000005736 RPB10 YOR210W|ABC10-beta taxon:4932
+S000005736 RPB10 YOR210W|ABC10-beta taxon:4932
+S000005736 RPB10 YOR210W|ABC10-beta taxon:4932
+S000005736 RPB10 YOR210W|ABC10-beta taxon:4932
+S000005736 RPB10 YOR210W|ABC10-beta taxon:4932
+S000005736 RPB10 YOR210W|ABC10-beta taxon:4932
+S000005736 RPB10 YOR210W|ABC10-beta taxon:4932
+S000005365 RPB11 YOL005C|B12.5 taxon:4932
+S000005365 RPB11 YOL005C|B12.5 taxon:4932
+S000005365 RPB11 YOL005C|B12.5 taxon:4932
+S000005677 RPB2 YOR151C|B150|RPB150|RPO22|SIT2|SOH2 taxon:4932
+S000005677 RPB2 YOR151C|B150|RPB150|RPO22|SIT2|SOH2 taxon:4932
+S000005677 RPB2 YOR151C|B150|RPB150|RPO22|SIT2|SOH2 taxon:4932
+S000001283 RPB3 YIL021W|B44 taxon:4932
+S000001283 RPB3 YIL021W|B44 taxon:4932
+S000001283 RPB3 YIL021W|B44 taxon:4932
+S000003676 RPB4 YJL140W|B32|CTF15 taxon:4932
+S000003676 RPB4 YJL140W|B32|CTF15 taxon:4932
+S000003676 RPB4 YJL140W|B32|CTF15 taxon:4932
+S000003676 RPB4 YJL140W|B32|CTF15 taxon:4932
+S000003676 RPB4 YJL140W|B32|CTF15 taxon:4932
+S000003676 RPB4 YJL140W|B32|CTF15 taxon:4932
+S000003676 RPB4 YJL140W|B32|CTF15 taxon:4932
+S000000358 RPB5 YBR154C|ABC27 taxon:4932
+S000000358 RPB5 YBR154C|ABC27 taxon:4932
+S000000358 RPB5 YBR154C|ABC27 taxon:4932
+S000000358 RPB5 YBR154C|ABC27 taxon:4932
+S000000358 RPB5 YBR154C|ABC27 taxon:4932
+S000000358 RPB5 YBR154C|ABC27 taxon:4932
+S000000358 RPB5 YBR154C|ABC27 taxon:4932
+S000002812 RPB7 YDR404C|B16 taxon:4932
+S000002812 RPB7 YDR404C|B16 taxon:4932
+S000002812 RPB7 YDR404C|B16 taxon:4932
+S000005750 RPB8 YOR224C|ABC14.5 taxon:4932
+S000005750 RPB8 YOR224C|ABC14.5 taxon:4932
+S000005750 RPB8 YOR224C|ABC14.5 taxon:4932
+S000005750 RPB8 YOR224C|ABC14.5 taxon:4932
+S000005750 RPB8 YOR224C|ABC14.5 taxon:4932
+S000005750 RPB8 YOR224C|ABC14.5 taxon:4932
+S000005750 RPB8 YOR224C|ABC14.5 taxon:4932
+S000003038 RPB9 YGL070C|B12.6|SHI1|SSU73 taxon:4932
+S000003038 RPB9 YGL070C|B12.6|SHI1|SSU73 taxon:4932
+S000003038 RPB9 YGL070C|B12.6|SHI1|SSU73 taxon:4932
+S000003038 RPB9 YGL070C|B12.6|SHI1|SSU73 taxon:4932
+S000003038 RPB9 YGL070C|B12.6|SHI1|SSU73 taxon:4932
+S000001185 RPC10 YHR143W-A|ABC10-alpha|RPB12 taxon:4932
+S000001185 RPC10 YHR143W-A|ABC10-alpha|RPB12 taxon:4932
+S000001185 RPC10 YHR143W-A|ABC10-alpha|RPB12 taxon:4932
+S000001185 RPC10 YHR143W-A|ABC10-alpha|RPB12 taxon:4932
+S000001185 RPC10 YHR143W-A|ABC10-alpha|RPB12 taxon:4932
+S000001185 RPC10 YHR143W-A|ABC10-alpha|RPB12 taxon:4932
+S000001185 RPC10 YHR143W-A|ABC10-alpha|RPB12 taxon:4932
+S000002452 RPC11 YDR045C|C11 taxon:4932
+S000002452 RPC11 YDR045C|C11 taxon:4932
+S000002452 RPC11 YDR045C|C11 taxon:4932
+S000003548 RPC17 YJL011C|C17 taxon:4932
+S000003548 RPC17 YJL011C|C17 taxon:4932
+S000003548 RPC17 YJL011C|C17 taxon:4932
+S000003548 RPC17 YJL011C|C17 taxon:4932
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+S000005057 RPC19 YNL113W|AC19 taxon:4932
+S000005057 RPC19 YNL113W|AC19 taxon:4932
+S000005057 RPC19 YNL113W|AC19 taxon:4932
+S000005057 RPC19 YNL113W|AC19 taxon:4932
+S000005057 RPC19 YNL113W|AC19 taxon:4932
+S000001627 RPC25 YKL144C|C25|YKL1 taxon:4932
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+S000001627 RPC25 YKL144C|C25|YKL1 taxon:4932
+S000005095 RPC31 YNL151C|ACP2|C31|RPC8 taxon:4932
+S000005095 RPC31 YNL151C|ACP2|C31|RPC8 taxon:4932
+S000005095 RPC31 YNL151C|ACP2|C31|RPC8 taxon:4932
+S000005286 RPC34 YNR003C|C34 taxon:4932
+S000005286 RPC34 YNR003C|C34 taxon:4932
+S000005286 RPC34 YNR003C|C34 taxon:4932
+S000005286 RPC34 YNR003C|C34 taxon:4932
+S000005286 RPC34 YNR003C|C34 taxon:4932
+S000001733 RPC37 YKR025W|C37 taxon:4932
+S000001733 RPC37 YKR025W|C37 taxon:4932
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+S000006314 RPC40 YPR110C|AC40|RPC5 taxon:4932
+S000006314 RPC40 YPR110C|AC40|RPC5 taxon:4932
+S000006314 RPC40 YPR110C|AC40|RPC5 taxon:4932
+S000006314 RPC40 YPR110C|AC40|RPC5 taxon:4932
+S000006314 RPC40 YPR110C|AC40|RPC5 taxon:4932
+S000002309 RPC53 YDL150W|C53|RPC4 taxon:4932
+S000002309 RPC53 YDL150W|C53|RPC4 taxon:4932
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+S000006394 RPC82 YPR190C|C82|RPC3 taxon:4932
+S000006394 RPC82 YPR190C|C82|RPC3 taxon:4932
+S000006394 RPC82 YPR190C|C82|RPC3 taxon:4932
+S000005274 RPD3 YNL330C|MOF6|REC3|SDI2|SDS6 taxon:4932
+S000005274 RPD3 YNL330C|MOF6|REC3|SDI2|SDS6 taxon:4932
+S000005274 RPD3 YNL330C|MOF6|REC3|SDI2|SDS6 taxon:4932
+S000005274 RPD3 YNL330C|MOF6|REC3|SDI2|SDS6 taxon:4932
+S000005274 RPD3 YNL330C|MOF6|REC3|SDI2|SDS6 taxon:4932
+S000005274 RPD3 YNL330C|MOF6|REC3|SDI2|SDS6 taxon:4932
+S000005274 RPD3 YNL330C|MOF6|REC3|SDI2|SDS6 taxon:4932
+S000005274 RPD3 YNL330C|MOF6|REC3|SDI2|SDS6 taxon:4932
+S000005274 RPD3 YNL330C|MOF6|REC3|SDI2|SDS6 taxon:4932
+S000005274 RPD3 YNL330C|MOF6|REC3|SDI2|SDS6 taxon:4932
+S000005274 RPD3 YNL330C|MOF6|REC3|SDI2|SDS6 taxon:4932
+S000005274 RPD3 YNL330C|MOF6|REC3|SDI2|SDS6 taxon:4932
+S000005274 RPD3 YNL330C|MOF6|REC3|SDI2|SDS6 taxon:4932
+S000005274 RPD3 YNL330C|MOF6|REC3|SDI2|SDS6 taxon:4932
+S000005274 RPD3 YNL330C|MOF6|REC3|SDI2|SDS6 taxon:4932
+S000005274 RPD3 YNL330C|MOF6|REC3|SDI2|SDS6 taxon:4932
+S000005274 RPD3 YNL330C|MOF6|REC3|SDI2|SDS6 taxon:4932
+S000005274 RPD3 YNL330C|MOF6|REC3|SDI2|SDS6 taxon:4932
+S000003657 RPE1 YJL121C|EPI1|POS18 taxon:4932
+S000003657 RPE1 YJL121C|EPI1|POS18 taxon:4932
+S000003657 RPE1 YJL121C|EPI1|POS18 taxon:4932
+S000003657 RPE1 YJL121C|EPI1|POS18 taxon:4932
+S000003657 RPE1 YJL121C|EPI1|POS18 taxon:4932
+S000001130 RPF1 YHR088W taxon:4932
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+S000001130 RPF1 YHR088W taxon:4932
+S000001130 RPF1 YHR088W taxon:4932
+S000001789 RPF2 YKR081C taxon:4932
+S000001789 RPF2 YKR081C taxon:4932
+S000001789 RPF2 YKR081C taxon:4932
+S000001789 RPF2 YKR081C taxon:4932
+S000001789 RPF2 YKR081C taxon:4932
+S000001789 RPF2 YKR081C taxon:4932
+S000001789 RPF2 YKR081C taxon:4932
+S000001789 RPF2 YKR081C taxon:4932
+S000000283 RPG1 YBR079C|TIF32 taxon:4932
+S000000283 RPG1 YBR079C|TIF32 taxon:4932
+S000000283 RPG1 YBR079C|TIF32 taxon:4932
+S000000283 RPG1 YBR079C|TIF32 taxon:4932
+S000000283 RPG1 YBR079C|TIF32 taxon:4932
+S000000283 RPG1 YBR079C|TIF32 taxon:4932
+S000000283 RPG1 YBR079C|TIF32 taxon:4932
+S000000283 RPG1 YBR079C|TIF32 taxon:4932
+S000000283 RPG1 YBR079C|TIF32 taxon:4932
+S000000283 RPG1 YBR079C|TIF32 taxon:4932
+S000000971 RPH1 YER169W taxon:4932
+S000000971 RPH1 YER169W taxon:4932
+S000000971 RPH1 YER169W taxon:4932
+S000000971 RPH1 YER169W taxon:4932
+S000001381 RPI1 YIL119C taxon:4932
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+S000001381 RPI1 YIL119C taxon:4932
+S000004065 RPL10 YLR075W|GRC5|QSR1 taxon:4932
+S000004065 RPL10 YLR075W|GRC5|QSR1 taxon:4932
+S000004065 RPL10 YLR075W|GRC5|QSR1 taxon:4932
+S000004065 RPL10 YLR075W|GRC5|QSR1 taxon:4932
+S000004065 RPL10 YLR075W|GRC5|QSR1 taxon:4932
+S000006306 RPL11A YPR102C taxon:4932
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+S000004750 RPL13B YMR142C taxon:4932
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+S000001489 RPL14A YKL006W taxon:4932
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+S000000993 RPL14B YHL001W taxon:4932
+S000000993 RPL14B YHL001W taxon:4932
+S000000993 RPL14B YHL001W taxon:4932
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+S000004019 RPL15A YLR029C|RPL10A taxon:4932
+S000004019 RPL15A YLR029C|RPL10A taxon:4932
+S000004019 RPL15A YLR029C|RPL10A taxon:4932
+S000004728 RPL15B YMR121C taxon:4932
+S000004728 RPL15B YMR121C taxon:4932
+S000004728 RPL15B YMR121C taxon:4932
+S000004728 RPL15B YMR121C taxon:4932
+S000004728 RPL15B YMR121C taxon:4932
+S000001395 RPL16A YIL133C|RPL13 taxon:4932
+S000001395 RPL16A YIL133C|RPL13 taxon:4932
+S000001395 RPL16A YIL133C|RPL13 taxon:4932
+S000001395 RPL16A YIL133C|RPL13 taxon:4932
+S000001395 RPL16A YIL133C|RPL13 taxon:4932
+S000005013 RPL16B YNL069C|RP23 taxon:4932
+S000005013 RPL16B YNL069C|RP23 taxon:4932
+S000005013 RPL16B YNL069C|RP23 taxon:4932
+S000005013 RPL16B YNL069C|RP23 taxon:4932
+S000005013 RPL16B YNL069C|RP23 taxon:4932
+S000001663 RPL17A YKL180W|RPL17 taxon:4932
+S000001663 RPL17A YKL180W|RPL17 taxon:4932
+S000001663 RPL17A YKL180W|RPL17 taxon:4932
+S000001663 RPL17A YKL180W|RPL17 taxon:4932
+S000001663 RPL17A YKL180W|RPL17 taxon:4932
+S000003713 RPL17B YJL177W taxon:4932
+S000003713 RPL17B YJL177W taxon:4932
+S000003713 RPL17B YJL177W taxon:4932
+S000003713 RPL17B YJL177W taxon:4932
+S000005480 RPL18A YOL120C|RP28A taxon:4932
+S000005480 RPL18A YOL120C|RP28A taxon:4932
+S000005480 RPL18A YOL120C|RP28A taxon:4932
+S000005480 RPL18A YOL120C|RP28A taxon:4932
+S000005245 RPL18B YNL301C|RP28B taxon:4932
+S000005245 RPL18B YNL301C|RP28B taxon:4932
+S000005245 RPL18B YNL301C|RP28B taxon:4932
+S000005245 RPL18B YNL301C|RP28B taxon:4932
+S000002156 RPL19A YBR084C-A taxon:4932
+S000002156 RPL19A YBR084C-A taxon:4932
+S000002156 RPL19A YBR084C-A taxon:4932
+S000002156 RPL19A YBR084C-A taxon:4932
+S000000123 RPL19B YBL027W taxon:4932
+S000000123 RPL19B YBL027W taxon:4932
+S000000123 RPL19B YBL027W taxon:4932
+S000000123 RPL19B YBL027W taxon:4932
+S000006141 RPL1A YPL220W|SSM1 taxon:4932
+S000006141 RPL1A YPL220W|SSM1 taxon:4932
+S000006141 RPL1A YPL220W|SSM1 taxon:4932
+S000006141 RPL1A YPL220W|SSM1 taxon:4932
+S000003103 RPL1B YGL135W|SSM2 taxon:4932
+S000003103 RPL1B YGL135W|SSM2 taxon:4932
+S000003103 RPL1B YGL135W|SSM2 taxon:4932
+S000003103 RPL1B YGL135W|SSM2 taxon:4932
+S000003103 RPL1B YGL135W|SSM2 taxon:4932
+S000004855 RPL20A YMR242C|RPL18A2 taxon:4932
+S000004855 RPL20A YMR242C|RPL18A2 taxon:4932
+S000004855 RPL20A YMR242C|RPL18A2 taxon:4932
+S000004855 RPL20A YMR242C|RPL18A2 taxon:4932
+S000005839 RPL20B YOR312C|RPL18A1 taxon:4932
+S000005839 RPL20B YOR312C|RPL18A1 taxon:4932
+S000005839 RPL20B YOR312C|RPL18A1 taxon:4932
+S000005839 RPL20B YOR312C|RPL18A1 taxon:4932
+S000000395 RPL21A YBR191W|URP1 taxon:4932
+S000000395 RPL21A YBR191W|URP1 taxon:4932
+S000000395 RPL21A YBR191W|URP1 taxon:4932
+S000000395 RPL21A YBR191W|URP1 taxon:4932
+S000000395 RPL21A YBR191W|URP1 taxon:4932
+S000006000 RPL21B YPL079W taxon:4932
+S000006000 RPL21B YPL079W taxon:4932
+S000006000 RPL21B YPL079W taxon:4932
+S000006000 RPL21B YPL079W taxon:4932
+S000004051 RPL22A YLR061W taxon:4932
+S000004051 RPL22A YLR061W taxon:4932
+S000004051 RPL22A YLR061W taxon:4932
+S000004051 RPL22A YLR061W taxon:4932
+S000006436 RPL22B YFL034C-A|YFL035C-B taxon:4932
+S000006436 RPL22B YFL034C-A|YFL035C-B taxon:4932
+S000006436 RPL22B YFL034C-A|YFL035C-B taxon:4932
+S000006436 RPL22B YFL034C-A|YFL035C-B taxon:4932
+S000000183 RPL23A YBL087C taxon:4932
+S000000183 RPL23A YBL087C taxon:4932
+S000000183 RPL23A YBL087C taxon:4932
+S000000183 RPL23A YBL087C taxon:4932
+S000000919 RPL23B YER117W taxon:4932
+S000000919 RPL23B YER117W taxon:4932
+S000000919 RPL23B YER117W taxon:4932
+S000000919 RPL23B YER117W taxon:4932
+S000002999 RPL24A YGL031C|RPL30A taxon:4932
+S000002999 RPL24A YGL031C|RPL30A taxon:4932
+S000002999 RPL24A YGL031C|RPL30A taxon:4932
+S000002999 RPL24A YGL031C|RPL30A taxon:4932
+S000002999 RPL24A YGL031C|RPL30A taxon:4932
+S000003380 RPL24B YGR148C|RPL30B taxon:4932
+S000003380 RPL24B YGR148C|RPL30B taxon:4932
+S000003380 RPL24B YGR148C|RPL30B taxon:4932
+S000003380 RPL24B YGR148C|RPL30B taxon:4932
+S000003380 RPL24B YGR148C|RPL30B taxon:4932
+S000005487 RPL25 YOL127W taxon:4932
+S000005487 RPL25 YOL127W taxon:4932
+S000005487 RPL25 YOL127W taxon:4932
+S000005487 RPL25 YOL127W taxon:4932
+S000005487 RPL25 YOL127W taxon:4932
+S000005487 RPL25 YOL127W taxon:4932
+S000004336 RPL26A YLR344W taxon:4932
+S000004336 RPL26A YLR344W taxon:4932
+S000004336 RPL26A YLR344W taxon:4932
+S000004336 RPL26A YLR344W taxon:4932
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+S000003266 RPL26B YGR034W taxon:4932
+S000003266 RPL26B YGR034W taxon:4932
+S000003266 RPL26B YGR034W taxon:4932
+S000003266 RPL26B YGR034W taxon:4932
+S000003266 RPL26B YGR034W taxon:4932
+S000001052 RPL27A YHR010W|RPL27 taxon:4932
+S000001052 RPL27A YHR010W|RPL27 taxon:4932
+S000001052 RPL27A YHR010W|RPL27 taxon:4932
+S000001052 RPL27A YHR010W|RPL27 taxon:4932
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+S000002879 RPL27B YDR471W taxon:4932
+S000002879 RPL27B YDR471W taxon:4932
+S000002879 RPL27B YDR471W taxon:4932
+S000003071 RPL28 YGL103W|CYH2 taxon:4932
+S000003071 RPL28 YGL103W|CYH2 taxon:4932
+S000003071 RPL28 YGL103W|CYH2 taxon:4932
+S000003071 RPL28 YGL103W|CYH2 taxon:4932
+S000003071 RPL28 YGL103W|CYH2 taxon:4932
+S000003071 RPL28 YGL103W|CYH2 taxon:4932
+S000006437 RPL29 YFR032C-A taxon:4932
+S000006437 RPL29 YFR032C-A taxon:4932
+S000006437 RPL29 YFR032C-A taxon:4932
+S000006437 RPL29 YFR032C-A taxon:4932
+S000006437 RPL29 YFR032C-A taxon:4932
+S000002104 RPL2A YFR031C-A|RPL5B taxon:4932
+S000002104 RPL2A YFR031C-A|RPL5B taxon:4932
+S000002104 RPL2A YFR031C-A|RPL5B taxon:4932
+S000002104 RPL2A YFR031C-A|RPL5B taxon:4932
+S000001280 RPL2B YIL018W|LOT2|RPL5A taxon:4932
+S000001280 RPL2B YIL018W|LOT2|RPL5A taxon:4932
+S000001280 RPL2B YIL018W|LOT2|RPL5A taxon:4932
+S000001280 RPL2B YIL018W|LOT2|RPL5A taxon:4932
+S000005589 RPL3 YOR063W|MAK8|TCM1|YOR29-14 taxon:4932
+S000005589 RPL3 YOR063W|MAK8|TCM1|YOR29-14 taxon:4932
+S000005589 RPL3 YOR063W|MAK8|TCM1|YOR29-14 taxon:4932
+S000005589 RPL3 YOR063W|MAK8|TCM1|YOR29-14 taxon:4932
+S000005589 RPL3 YOR063W|MAK8|TCM1|YOR29-14 taxon:4932
+S000002998 RPL30 YGL030W taxon:4932
+S000002998 RPL30 YGL030W taxon:4932
+S000002998 RPL30 YGL030W taxon:4932
+S000002998 RPL30 YGL030W taxon:4932
+S000002998 RPL30 YGL030W taxon:4932
+S000002998 RPL30 YGL030W taxon:4932
+S000002998 RPL30 YGL030W taxon:4932
+S000002998 RPL30 YGL030W taxon:4932
+S000002998 RPL30 YGL030W taxon:4932
+S000002233 RPL31A YDL075W|RPL34 taxon:4932
+S000002233 RPL31A YDL075W|RPL34 taxon:4932
+S000002233 RPL31A YDL075W|RPL34 taxon:4932
+S000002233 RPL31A YDL075W|RPL34 taxon:4932
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+S000004398 RPL31B YLR406C taxon:4932
+S000004398 RPL31B YLR406C taxon:4932
+S000004398 RPL31B YLR406C taxon:4932
+S000000188 RPL32 YBL092W taxon:4932
+S000000188 RPL32 YBL092W taxon:4932
+S000000188 RPL32 YBL092W taxon:4932
+S000000188 RPL32 YBL092W taxon:4932
+S000006064 RPL33A YPL143W|RPL37A taxon:4932
+S000006064 RPL33A YPL143W|RPL37A taxon:4932
+S000006064 RPL33A YPL143W|RPL37A taxon:4932
+S000006064 RPL33A YPL143W|RPL37A taxon:4932
+S000005760 RPL33B YOR234C|RPL37B taxon:4932
+S000005760 RPL33B YOR234C|RPL37B taxon:4932
+S000005760 RPL33B YOR234C|RPL37B taxon:4932
+S000005760 RPL33B YOR234C|RPL37B taxon:4932
+S000002135 RPL34A YER056C-A taxon:4932
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+S000029426 RYE6 taxon:4932
+S000029426 RYE6 taxon:4932
+S000029427 RYE7 taxon:4932
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+S000029427 RYE7 taxon:4932
+S000029428 RYE8 taxon:4932
+S000029428 RYE8 taxon:4932
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+S000001695 SAC1 YKL212W|RSD1 taxon:4932
+S000001695 SAC1 YKL212W|RSD1 taxon:4932
+S000001695 SAC1 YKL212W|RSD1 taxon:4932
+S000001695 SAC1 YKL212W|RSD1 taxon:4932
+S000001695 SAC1 YKL212W|RSD1 taxon:4932
+S000001695 SAC1 YKL212W|RSD1 taxon:4932
+S000001695 SAC1 YKL212W|RSD1 taxon:4932
+S000001695 SAC1 YKL212W|RSD1 taxon:4932
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+S000001695 SAC1 YKL212W|RSD1 taxon:4932
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+S000002566 SAC3 YDR159W|LEP1 taxon:4932
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+S000002566 SAC3 YDR159W|LEP1 taxon:4932
+S000002566 SAC3 YDR159W|LEP1 taxon:4932
+S000002566 SAC3 YDR159W|LEP1 taxon:4932
+S000002566 SAC3 YDR159W|LEP1 taxon:4932
+S000002566 SAC3 YDR159W|LEP1 taxon:4932
+S000002566 SAC3 YDR159W|LEP1 taxon:4932
+S000002536 SAC6 YDR129C|ABP67 taxon:4932
+S000002536 SAC6 YDR129C|ABP67 taxon:4932
+S000002536 SAC6 YDR129C|ABP67 taxon:4932
+S000002536 SAC6 YDR129C|ABP67 taxon:4932
+S000002536 SAC6 YDR129C|ABP67 taxon:4932
+S000002536 SAC6 YDR129C|ABP67 taxon:4932
+S000002536 SAC6 YDR129C|ABP67 taxon:4932
+S000002536 SAC6 YDR129C|ABP67 taxon:4932
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+S000002797 SAC7 YDR389W taxon:4932
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+S000001901 SAD1 YFR005C taxon:4932
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+S000001901 SAD1 YFR005C taxon:4932
+S000003143 SAE2 YGL175C|COM1 taxon:4932
+S000003143 SAE2 YGL175C|COM1 taxon:4932
+S000003143 SAE2 YGL175C|COM1 taxon:4932
+S000003143 SAE2 YGL175C|COM1 taxon:4932
+S000001957 SAE3 YHR079C-A|YHR079BC|YHR079C-B taxon:4932
+S000001957 SAE3 YHR079C-A|YHR079BC|YHR079C-B taxon:4932
+S000001957 SAE3 YHR079C-A|YHR079BC|YHR079C-B taxon:4932
+S000001957 SAE3 YHR079C-A|YHR079BC|YHR079C-B taxon:4932
+S000001957 SAE3 YHR079C-A|YHR079BC|YHR079C-B taxon:4932
+S000001957 SAE3 YHR079C-A|YHR079BC|YHR079C-B taxon:4932
+S000001957 SAE3 YHR079C-A|YHR079BC|YHR079C-B taxon:4932
+S000003764 SAG1 YJR004C|AG(ALPHA)1 taxon:4932
+S000003764 SAG1 YJR004C|AG(ALPHA)1 taxon:4932
+S000003764 SAG1 YJR004C|AG(ALPHA)1 taxon:4932
+S000003764 SAG1 YJR004C|AG(ALPHA)1 taxon:4932
+S000003764 SAG1 YJR004C|AG(ALPHA)1 taxon:4932
+S000003764 SAG1 YJR004C|AG(ALPHA)1 taxon:4932
+S000000845 SAH1 YER043C taxon:4932
+S000000845 SAH1 YER043C taxon:4932
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+S000000931 SAK1 YER129W|PAK1 taxon:4932
+S000000931 SAK1 YER129W|PAK1 taxon:4932
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+S000000931 SAK1 YER129W|PAK1 taxon:4932
+S000000931 SAK1 YER129W|PAK1 taxon:4932
+S000000931 SAK1 YER129W|PAK1 taxon:4932
+S000005027 SAL1 YNL083W taxon:4932
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+S000005027 SAL1 YNL083W taxon:4932
+S000004170 SAM1 YLR180W|ETH10 taxon:4932
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+S000004170 SAM1 YLR180W|ETH10 taxon:4932
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+S000006195 SAM3 YPL274W taxon:4932
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+S000006195 SAM3 YPL274W taxon:4932
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+S000006195 SAM3 YPL274W taxon:4932
+S000001125 SAM35 YHR083W|FMP20|TOB38|TOM38 taxon:4932
+S000001125 SAM35 YHR083W|FMP20|TOB38|TOM38 taxon:4932
+S000001125 SAM35 YHR083W|FMP20|TOB38|TOM38 taxon:4932
+S000001125 SAM35 YHR083W|FMP20|TOB38|TOM38 taxon:4932
+S000001125 SAM35 YHR083W|FMP20|TOB38|TOM38 taxon:4932
+S000001125 SAM35 YHR083W|FMP20|TOB38|TOM38 taxon:4932
+S000001125 SAM35 YHR083W|FMP20|TOB38|TOM38 taxon:4932
+S000001125 SAM35 YHR083W|FMP20|TOB38|TOM38 taxon:4932
+S000001125 SAM35 YHR083W|FMP20|TOB38|TOM38 taxon:4932
+S000001125 SAM35 YHR083W|FMP20|TOB38|TOM38 taxon:4932
+S000004664 SAM37 YMR060C|MAS37|PET3027|TOM37 taxon:4932
+S000004664 SAM37 YMR060C|MAS37|PET3027|TOM37 taxon:4932
+S000004664 SAM37 YMR060C|MAS37|PET3027|TOM37 taxon:4932
+S000004664 SAM37 YMR060C|MAS37|PET3027|TOM37 taxon:4932
+S000004664 SAM37 YMR060C|MAS37|PET3027|TOM37 taxon:4932
+S000004664 SAM37 YMR060C|MAS37|PET3027|TOM37 taxon:4932
+S000006194 SAM4 YPL273W taxon:4932
+S000006194 SAM4 YPL273W taxon:4932
+S000006194 SAM4 YPL273W taxon:4932
+S000006194 SAM4 YPL273W taxon:4932
+S000004971 SAM50 YNL026W|OMP85|TOB55 taxon:4932
+S000004971 SAM50 YNL026W|OMP85|TOB55 taxon:4932
+S000004971 SAM50 YNL026W|OMP85|TOB55 taxon:4932
+S000004971 SAM50 YNL026W|OMP85|TOB55 taxon:4932
+S000004971 SAM50 YNL026W|OMP85|TOB55 taxon:4932
+S000004971 SAM50 YNL026W|OMP85|TOB55 taxon:4932
+S000004971 SAM50 YNL026W|OMP85|TOB55 taxon:4932
+S000004971 SAM50 YNL026W|OMP85|TOB55 taxon:4932
+S000004971 SAM50 YNL026W|OMP85|TOB55 taxon:4932
+S000004971 SAM50 YNL026W|OMP85|TOB55 taxon:4932
+S000002550 SAN1 YDR143C taxon:4932
+S000002550 SAN1 YDR143C taxon:4932
+S000002550 SAN1 YDR143C taxon:4932
+S000002550 SAN1 YDR143C taxon:4932
+S000002550 SAN1 YDR143C taxon:4932
+S000000849 SAP1 YER047C taxon:4932
+S000000849 SAP1 YER047C taxon:4932
+S000000849 SAP1 YER047C taxon:4932
+S000001936 SAP155 YFR040W taxon:4932
+S000001936 SAP155 YFR040W taxon:4932
+S000001936 SAP155 YFR040W taxon:4932
+S000001936 SAP155 YFR040W taxon:4932
+S000001936 SAP155 YFR040W taxon:4932
+S000003634 SAP185 YJL098W taxon:4932
+S000003634 SAP185 YJL098W taxon:4932
+S000003634 SAP185 YJL098W taxon:4932
+S000003634 SAP185 YJL098W taxon:4932
+S000003634 SAP185 YJL098W taxon:4932
+S000003634 SAP185 YJL098W taxon:4932
+S000001736 SAP190 YKR028W taxon:4932
+S000001736 SAP190 YKR028W taxon:4932
+S000001736 SAP190 YKR028W taxon:4932
+S000001736 SAP190 YKR028W taxon:4932
+S000001736 SAP190 YKR028W taxon:4932
+S000004876 SAP30 YMR263W taxon:4932
+S000004876 SAP30 YMR263W taxon:4932
+S000004876 SAP30 YMR263W taxon:4932
+S000004876 SAP30 YMR263W taxon:4932
+S000004876 SAP30 YMR263W taxon:4932
+S000004876 SAP30 YMR263W taxon:4932
+S000003198 SAP4 YGL229C taxon:4932
+S000003198 SAP4 YGL229C taxon:4932
+S000003198 SAP4 YGL229C taxon:4932
+S000003198 SAP4 YGL229C taxon:4932
+S000003198 SAP4 YGL229C taxon:4932
+S000006139 SAR1 YPL218W taxon:4932
+S000006139 SAR1 YPL218W taxon:4932
+S000006139 SAR1 YPL218W taxon:4932
+S000002312 SAS10 YDL153C|UTP3 taxon:4932
+S000002312 SAS10 YDL153C|UTP3 taxon:4932
+S000002312 SAS10 YDL153C|UTP3 taxon:4932
+S000002312 SAS10 YDL153C|UTP3 taxon:4932
+S000002312 SAS10 YDL153C|UTP3 taxon:4932
+S000002312 SAS10 YDL153C|UTP3 taxon:4932
+S000002312 SAS10 YDL153C|UTP3 taxon:4932
+S000002312 SAS10 YDL153C|UTP3 taxon:4932
+S000004734 SAS2 YMR127C taxon:4932
+S000004734 SAS2 YMR127C taxon:4932
+S000004734 SAS2 YMR127C taxon:4932
+S000004734 SAS2 YMR127C taxon:4932
+S000004734 SAS2 YMR127C taxon:4932
+S000000148 SAS3 YBL052C taxon:4932
+S000000148 SAS3 YBL052C taxon:4932
+S000000148 SAS3 YBL052C taxon:4932
+S000000148 SAS3 YBL052C taxon:4932
+S000000148 SAS3 YBL052C taxon:4932
+S000000148 SAS3 YBL052C taxon:4932
+S000000148 SAS3 YBL052C taxon:4932
+S000002589 SAS4 YDR181C taxon:4932
+S000002589 SAS4 YDR181C taxon:4932
+S000002589 SAS4 YDR181C taxon:4932
+S000002589 SAS4 YDR181C taxon:4932
+S000002589 SAS4 YDR181C taxon:4932
+S000005739 SAS5 YOR213C taxon:4932
+S000005739 SAS5 YOR213C taxon:4932
+S000005739 SAS5 YOR213C taxon:4932
+S000005739 SAS5 YOR213C taxon:4932
+S000005739 SAS5 YOR213C taxon:4932
+S000000601 SAT4 YCR008W|HAL4 taxon:4932
+S000000601 SAT4 YCR008W|HAL4 taxon:4932
+S000000601 SAT4 YCR008W|HAL4 taxon:4932
+S000000601 SAT4 YCR008W|HAL4 taxon:4932
+S000000601 SAT4 YCR008W|HAL4 taxon:4932
+S000001600 SBA1 YKL117W taxon:4932
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+S000001600 SBA1 YKL117W taxon:4932
+S000001600 SBA1 YKL117W taxon:4932
+S000001600 SBA1 YKL117W taxon:4932
+S000001600 SBA1 YKL117W taxon:4932
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+S000002759 SBE2 YDR351W taxon:4932
+S000002759 SBE2 YDR351W taxon:4932
+S000002759 SBE2 YDR351W taxon:4932
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+S000001145 SBE22 YHR103W taxon:4932
+S000001145 SBE22 YHR103W taxon:4932
+S000001145 SBE22 YHR103W taxon:4932
+S000002128 SBH1 YER087C-B|SEB1|YER087C-A taxon:4932
+S000002128 SBH1 YER087C-B|SEB1|YER087C-A taxon:4932
+S000002128 SBH1 YER087C-B|SEB1|YER087C-A taxon:4932
+S000002128 SBH1 YER087C-B|SEB1|YER087C-A taxon:4932
+S000002128 SBH1 YER087C-B|SEB1|YER087C-A taxon:4932
+S000002128 SBH1 YER087C-B|SEB1|YER087C-A taxon:4932
+S000002128 SBH1 YER087C-B|SEB1|YER087C-A taxon:4932
+S000002128 SBH1 YER087C-B|SEB1|YER087C-A taxon:4932
+S000002128 SBH1 YER087C-B|SEB1|YER087C-A taxon:4932
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+S000002127 SBH2 YER019C-A|SEB2 taxon:4932
+S000002127 SBH2 YER019C-A|SEB2 taxon:4932
+S000002127 SBH2 YER019C-A|SEB2 taxon:4932
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+S000001026 SBP1 YHL034C|SSB1|SSBR1 taxon:4932
+S000001026 SBP1 YHL034C|SSB1|SSBR1 taxon:4932
+S000001026 SBP1 YHL034C|SSB1|SSBR1 taxon:4932
+S000002588 SCC2 YDR180W taxon:4932
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+S000000949 SCC4 YER147C taxon:4932
+S000000949 SCC4 YER147C taxon:4932
+S000000949 SCC4 YER147C taxon:4932
+S000000949 SCC4 YER147C taxon:4932
+S000005856 SCD5 YOR329C|FTB1 taxon:4932
+S000005856 SCD5 YOR329C|FTB1 taxon:4932
+S000005856 SCD5 YOR329C|FTB1 taxon:4932
+S000005856 SCD5 YOR329C|FTB1 taxon:4932
+S000005856 SCD5 YOR329C|FTB1 taxon:4932
+S000005856 SCD5 YOR329C|FTB1 taxon:4932
+S000005856 SCD5 YOR329C|FTB1 taxon:4932
+S000005856 SCD5 YOR329C|FTB1 taxon:4932
+S000006333 SCD6 YPR129W|LSM13 taxon:4932
+S000006333 SCD6 YPR129W|LSM13 taxon:4932
+S000006333 SCD6 YPR129W|LSM13 taxon:4932
+S000007279 SCEI Q0160|I-SceI|OMEGA taxon:4932
+S000007279 SCEI Q0160|I-SceI|OMEGA taxon:4932
+S000007279 SCEI Q0160|I-SceI|OMEGA taxon:4932
+S000029678 SCH1 taxon:4932
+S000029678 SCH1 taxon:4932
+S000029678 SCH1 taxon:4932
+S000001248 SCH9 YHR205W|KOM1 taxon:4932
+S000001248 SCH9 YHR205W|KOM1 taxon:4932
+S000001248 SCH9 YHR205W|KOM1 taxon:4932
+S000001248 SCH9 YHR205W|KOM1 taxon:4932
+S000001248 SCH9 YHR205W|KOM1 taxon:4932
+S000001248 SCH9 YHR205W|KOM1 taxon:4932
+S000001248 SCH9 YHR205W|KOM1 taxon:4932
+S000001248 SCH9 YHR205W|KOM1 taxon:4932
+S000001248 SCH9 YHR205W|KOM1 taxon:4932
+S000001248 SCH9 YHR205W|KOM1 taxon:4932
+S000004827 SCJ1 YMR214W taxon:4932
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+S000002979 SCL1 YGL011C|PRC2 taxon:4932
+S000002979 SCL1 YGL011C|PRC2 taxon:4932
+S000002979 SCL1 YGL011C|PRC2 taxon:4932
+S000002979 SCL1 YGL011C|PRC2 taxon:4932
+S000002979 SCL1 YGL011C|PRC2 taxon:4932
+S000002979 SCL1 YGL011C|PRC2 taxon:4932
+S000002979 SCL1 YGL011C|PRC2 taxon:4932
+S000002298 SCM3 YDL139C taxon:4932
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+S000002298 SCM3 YDL139C taxon:4932
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+S000003281 SCM4 YGR049W taxon:4932
+S000003281 SCM4 YGR049W taxon:4932
+S000003281 SCM4 YGR049W taxon:4932
+S000003281 SCM4 YGR049W taxon:4932
+S000000241 SCO1 YBR037C|PET161 taxon:4932
+S000000241 SCO1 YBR037C|PET161 taxon:4932
+S000000241 SCO1 YBR037C|PET161 taxon:4932
+S000000241 SCO1 YBR037C|PET161 taxon:4932
+S000000241 SCO1 YBR037C|PET161 taxon:4932
+S000000241 SCO1 YBR037C|PET161 taxon:4932
+S000000241 SCO1 YBR037C|PET161 taxon:4932
+S000000228 SCO2 YBR024W taxon:4932
+S000000228 SCO2 YBR024W taxon:4932
+S000000228 SCO2 YBR024W taxon:4932
+S000005894 SCP1 YOR367W taxon:4932
+S000005894 SCP1 YOR367W taxon:4932
+S000005894 SCP1 YOR367W taxon:4932
+S000005894 SCP1 YOR367W taxon:4932
+S000005894 SCP1 YOR367W taxon:4932
+S000005894 SCP1 YOR367W taxon:4932
+S000003616 SCP160 YJL080C taxon:4932
+S000003616 SCP160 YJL080C taxon:4932
+S000003616 SCP160 YJL080C taxon:4932
+S000003616 SCP160 YJL080C taxon:4932
+S000003616 SCP160 YJL080C taxon:4932
+S000003616 SCP160 YJL080C taxon:4932
+S000003616 SCP160 YJL080C taxon:4932
+S000003616 SCP160 YJL080C taxon:4932
+S000003616 SCP160 YJL080C taxon:4932
+S000003616 SCP160 YJL080C taxon:4932
+S000003616 SCP160 YJL080C taxon:4932
+S000003616 SCP160 YJL080C taxon:4932
+S000006491 SCR1 taxon:4932
+S000006491 SCR1 taxon:4932
+S000006491 SCR1 taxon:4932
+S000006491 SCR1 taxon:4932
+S000000922 SCS2 YER120W taxon:4932
+S000000922 SCS2 YER120W taxon:4932
+S000000922 SCS2 YER120W taxon:4932
+S000000922 SCS2 YER120W taxon:4932
+S000000922 SCS2 YER120W taxon:4932
+S000000922 SCS2 YER120W taxon:4932
+S000000922 SCS2 YER120W taxon:4932
+S000000922 SCS2 YER120W taxon:4932
+S000007228 SCS22 YBL091C-A taxon:4932
+S000007228 SCS22 YBL091C-A taxon:4932
+S000007228 SCS22 YBL091C-A taxon:4932
+S000007228 SCS22 YBL091C-A taxon:4932
+S000007228 SCS22 YBL091C-A taxon:4932
+S000007228 SCS22 YBL091C-A taxon:4932
+S000003094 SCS3 YGL126W taxon:4932
+S000003094 SCS3 YGL126W taxon:4932
+S000003094 SCS3 YGL126W taxon:4932
+S000004885 SCS7 YMR272C|FAH1 taxon:4932
+S000004885 SCS7 YMR272C|FAH1 taxon:4932
+S000004885 SCS7 YMR272C|FAH1 taxon:4932
+S000004885 SCS7 YMR272C|FAH1 taxon:4932
+S000004885 SCS7 YMR272C|FAH1 taxon:4932
+S000000107 SCT1 YBL011W|GAT2 taxon:4932
+S000000107 SCT1 YBL011W|GAT2 taxon:4932
+S000000107 SCT1 YBL011W|GAT2 taxon:4932
+S000000107 SCT1 YBL011W|GAT2 taxon:4932
+S000000107 SCT1 YBL011W|GAT2 taxon:4932
+S000000107 SCT1 YBL011W|GAT2 taxon:4932
+S000029434 SCW1 taxon:4932
+S000029434 SCW1 taxon:4932
+S000029434 SCW1 taxon:4932
+S000004921 SCW10 YMR305C taxon:4932
+S000004921 SCW10 YMR305C taxon:4932
+S000004921 SCW10 YMR305C taxon:4932
+S000004921 SCW10 YMR305C taxon:4932
+S000004921 SCW10 YMR305C taxon:4932
+S000004921 SCW10 YMR305C taxon:4932
+S000002996 SCW11 YGL028C taxon:4932
+S000002996 SCW11 YGL028C taxon:4932
+S000002996 SCW11 YGL028C taxon:4932
+S000029435 SCW2 taxon:4932
+S000029435 SCW2 taxon:4932
+S000029435 SCW2 taxon:4932
+S000003511 SCW4 YGR279C taxon:4932
+S000003511 SCW4 YGR279C taxon:4932
+S000003511 SCW4 YGR279C taxon:4932
+S000003511 SCW4 YGR279C taxon:4932
+S000029436 SCW5 taxon:4932
+S000029436 SCW5 taxon:4932
+S000029436 SCW5 taxon:4932
+S000029437 SCW6 taxon:4932
+S000029437 SCW6 taxon:4932
+S000029437 SCW6 taxon:4932
+S000029438 SCW7 taxon:4932
+S000029438 SCW7 taxon:4932
+S000029438 SCW7 taxon:4932
+S000029439 SCW8 taxon:4932
+S000029439 SCW8 taxon:4932
+S000029439 SCW8 taxon:4932
+S000029440 SCW9 taxon:4932
+S000029440 SCW9 taxon:4932
+S000029440 SCW9 taxon:4932
+S000003051 SCY1 YGL083W taxon:4932
+S000003051 SCY1 YGL083W taxon:4932
+S000003051 SCY1 YGL083W taxon:4932
+S000003477 SDA1 YGR245C taxon:4932
+S000003477 SDA1 YGR245C taxon:4932
+S000003477 SDA1 YGR245C taxon:4932
+S000003477 SDA1 YGR245C taxon:4932
+S000003477 SDA1 YGR245C taxon:4932
+S000002877 SDC1 YDR469W|CPS25|SAF19 taxon:4932
+S000002877 SDC1 YDR469W|CPS25|SAF19 taxon:4932
+S000002877 SDC1 YDR469W|CPS25|SAF19 taxon:4932
+S000002877 SDC1 YDR469W|CPS25|SAF19 taxon:4932
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+S000004663 SEN15 YMR059W taxon:4932
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+S000004095 SEN2 YLR105C taxon:4932
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+S000000066 SEN34 YAR008W|FUN4 taxon:4932
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+S000000066 SEN34 YAR008W|FUN4 taxon:4932
+S000000066 SEN34 YAR008W|FUN4 taxon:4932
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+S000006004 SEN54 YPL083C taxon:4932
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+S000006004 SEN54 YPL083C taxon:4932
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+S000006004 SEN54 YPL083C taxon:4932
+S000006004 SEN54 YPL083C taxon:4932
+S000000062 SEO1 YAL067C taxon:4932
+S000000062 SEO1 YAL067C taxon:4932
+S000000062 SEO1 YAL067C taxon:4932
+S000005710 SER1 YOR184W|ADE9 taxon:4932
+S000005710 SER1 YOR184W|ADE9 taxon:4932
+S000005710 SER1 YOR184W|ADE9 taxon:4932
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+S000003440 SER2 YGR208W taxon:4932
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+S000000883 SER3 YER081W taxon:4932
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+S000001336 SER33 YIL074C taxon:4932
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+S000001336 SER33 YIL074C taxon:4932
+S000002430 SES1 YDR023W|SerRS taxon:4932
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+S000001161 SET1 YHR119W|YTX1 taxon:4932
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+S000003704 SET2 YJL168C|EZL1 taxon:4932
+S000003704 SET2 YJL168C|EZL1 taxon:4932
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+S000003704 SET2 YJL168C|EZL1 taxon:4932
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+S000003704 SET2 YJL168C|EZL1 taxon:4932
+S000003704 SET2 YJL168C|EZL1 taxon:4932
+S000001737 SET3 YKR029C taxon:4932
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+S000003641 SET4 YJL105W taxon:4932
+S000003641 SET4 YJL105W taxon:4932
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+S000001250 SET5 YHR207C taxon:4932
+S000001250 SET5 YHR207C taxon:4932
+S000001250 SET5 YHR207C taxon:4932
+S000001250 SET5 YHR207C taxon:4932
+S000006086 SET6 YPL165C taxon:4932
+S000006086 SET6 YPL165C taxon:4932
+S000006086 SET6 YPL165C taxon:4932
+S000002665 SET7 YDR257C|RMS1 taxon:4932
+S000002665 SET7 YDR257C|RMS1 taxon:4932
+S000002665 SET7 YDR257C|RMS1 taxon:4932
+S000005691 SEY1 YOR165W taxon:4932
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+S000002327 SFA1 YDL168W|ADH5 taxon:4932
+S000002327 SFA1 YDL168W|ADH5 taxon:4932
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+S000002327 SFA1 YDL168W|ADH5 taxon:4932
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+S000004994 SFB2 YNL049C taxon:4932
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+S000001140 SFB3 YHR098C|LST1 taxon:4932
+S000001140 SFB3 YHR098C|LST1 taxon:4932
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+S000001140 SFB3 YHR098C|LST1 taxon:4932
+S000001140 SFB3 YHR098C|LST1 taxon:4932
+S000001140 SFB3 YHR098C|LST1 taxon:4932
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+S000001140 SFB3 YHR098C|LST1 taxon:4932
+S000001140 SFB3 YHR098C|LST1 taxon:4932
+S000001140 SFB3 YHR098C|LST1 taxon:4932
+S000003856 SFC1 YJR095W|ACR1 taxon:4932
+S000003856 SFC1 YJR095W|ACR1 taxon:4932
+S000003856 SFC1 YJR095W|ACR1 taxon:4932
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+S000005842 SFG1 YOR315W taxon:4932
+S000005842 SFG1 YOR315W taxon:4932
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+S000003926 SFI1 YLL003W taxon:4932
+S000003926 SFI1 YLL003W taxon:4932
+S000003926 SFI1 YLL003W taxon:4932
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+S000001534 SFK1 YKL051W taxon:4932
+S000001534 SFK1 YKL051W taxon:4932
+S000001534 SFK1 YKL051W taxon:4932
+S000001534 SFK1 YKL051W taxon:4932
+S000001534 SFK1 YKL051W taxon:4932
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+S000005666 SFL1 YOR140W taxon:4932
+S000005666 SFL1 YOR140W taxon:4932
+S000005666 SFL1 YOR140W taxon:4932
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+S000004395 SFP1 YLR403W taxon:4932
+S000004395 SFP1 YLR403W taxon:4932
+S000004395 SFP1 YLR403W taxon:4932
+S000004395 SFP1 YLR403W taxon:4932
+S000004395 SFP1 YLR403W taxon:4932
+S000004395 SFP1 YLR403W taxon:4932
+S000004395 SFP1 YLR403W taxon:4932
+S000004395 SFP1 YLR403W taxon:4932
+S000004395 SFP1 YLR403W taxon:4932
+S000004395 SFP1 YLR403W taxon:4932
+S000004395 SFP1 YLR403W taxon:4932
+S000004395 SFP1 YLR403W taxon:4932
+S000002101 SFT1 YKL006C-A taxon:4932
+S000002101 SFT1 YKL006C-A taxon:4932
+S000002101 SFT1 YKL006C-A taxon:4932
+S000002101 SFT1 YKL006C-A taxon:4932
+S000002101 SFT1 YKL006C-A taxon:4932
+S000002101 SFT1 YKL006C-A taxon:4932
+S000002101 SFT1 YKL006C-A taxon:4932
+S000000198 SFT2 YBL102W taxon:4932
+S000000198 SFT2 YBL102W taxon:4932
+S000000198 SFT2 YBL102W taxon:4932
+S000000198 SFT2 YBL102W taxon:4932
+S000001361 SGA1 YIL099W taxon:4932
+S000001361 SGA1 YIL099W taxon:4932
+S000001361 SGA1 YIL099W taxon:4932
+S000001361 SGA1 YIL099W taxon:4932
+S000004328 SGD1 YLR336C taxon:4932
+S000004328 SGD1 YLR336C taxon:4932
+S000004328 SGD1 YLR336C taxon:4932
+S000004328 SGD1 YLR336C taxon:4932
+S000004328 SGD1 YLR336C taxon:4932
+S000004328 SGD1 YLR336C taxon:4932
+S000004328 SGD1 YLR336C taxon:4932
+S000004328 SGD1 YLR336C taxon:4932
+S000006402 SGE1 YPR198W|NOR1 taxon:4932
+S000006402 SGE1 YPR198W|NOR1 taxon:4932
+S000006402 SGE1 YPR198W|NOR1 taxon:4932
+S000006402 SGE1 YPR198W|NOR1 taxon:4932
+S000005968 SGF11 YPL047W taxon:4932
+S000005968 SGF11 YPL047W taxon:4932
+S000005968 SGF11 YPL047W taxon:4932
+S000005968 SGF11 YPL047W taxon:4932
+S000005968 SGF11 YPL047W taxon:4932
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+S000000516 SGF29 YCL010C taxon:4932
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+S000003034 SGF73 YGL066W|sca7 taxon:4932
+S000003034 SGF73 YGL066W|sca7 taxon:4932
+S000003034 SGF73 YGL066W|sca7 taxon:4932
+S000003034 SGF73 YGL066W|sca7 taxon:4932
+S000003034 SGF73 YGL066W|sca7 taxon:4932
+S000003034 SGF73 YGL066W|sca7 taxon:4932
+S000003034 SGF73 YGL066W|sca7 taxon:4932
+S000003034 SGF73 YGL066W|sca7 taxon:4932
+S000003034 SGF73 YGL066W|sca7 taxon:4932
+S000003895 SGM1 YJR134C taxon:4932
+S000003895 SGM1 YJR134C taxon:4932
+S000003895 SGM1 YJR134C taxon:4932
+S000003895 SGM1 YJR134C taxon:4932
+S000001440 SGN1 YIR001C|RBP1|RBP29 taxon:4932
+S000001440 SGN1 YIR001C|RBP1|RBP29 taxon:4932
+S000001440 SGN1 YIR001C|RBP1|RBP29 taxon:4932
+S000005599 SGO1 YOR073W|YOR29-24 taxon:4932
+S000005599 SGO1 YOR073W|YOR29-24 taxon:4932
+S000005599 SGO1 YOR073W|YOR29-24 taxon:4932
+S000005599 SGO1 YOR073W|YOR29-24 taxon:4932
+S000005599 SGO1 YOR073W|YOR29-24 taxon:4932
+S000005599 SGO1 YOR073W|YOR29-24 taxon:4932
+S000005599 SGO1 YOR073W|YOR29-24 taxon:4932
+S000005599 SGO1 YOR073W|YOR29-24 taxon:4932
+S000005599 SGO1 YOR073W|YOR29-24 taxon:4932
+S000005599 SGO1 YOR073W|YOR29-24 taxon:4932
+S000005599 SGO1 YOR073W|YOR29-24 taxon:4932
+S000005599 SGO1 YOR073W|YOR29-24 taxon:4932
+S000005599 SGO1 YOR073W|YOR29-24 taxon:4932
+S000004802 SGS1 YMR190C taxon:4932
+S000004802 SGS1 YMR190C taxon:4932
+S000004802 SGS1 YMR190C taxon:4932
+S000004802 SGS1 YMR190C taxon:4932
+S000004802 SGS1 YMR190C taxon:4932
+S000004802 SGS1 YMR190C taxon:4932
+S000004802 SGS1 YMR190C taxon:4932
+S000004802 SGS1 YMR190C taxon:4932
+S000004802 SGS1 YMR190C taxon:4932
+S000004802 SGS1 YMR190C taxon:4932
+S000005583 SGT1 YOR057W|YOR29-08 taxon:4932
+S000005583 SGT1 YOR057W|YOR29-08 taxon:4932
+S000005583 SGT1 YOR057W|YOR29-08 taxon:4932
+S000005583 SGT1 YOR057W|YOR29-08 taxon:4932
+S000005583 SGT1 YOR057W|YOR29-08 taxon:4932
+S000005583 SGT1 YOR057W|YOR29-08 taxon:4932
+S000005583 SGT1 YOR057W|YOR29-08 taxon:4932
+S000005583 SGT1 YOR057W|YOR29-08 taxon:4932
+S000005583 SGT1 YOR057W|YOR29-08 taxon:4932
+S000005583 SGT1 YOR057W|YOR29-08 taxon:4932
+S000005533 SGT2 YOR007C taxon:4932
+S000005533 SGT2 YOR007C taxon:4932
+S000005533 SGT2 YOR007C taxon:4932
+S000006365 SGV1 YPR161C|BUR1 taxon:4932
+S000006365 SGV1 YPR161C|BUR1 taxon:4932
+S000006365 SGV1 YPR161C|BUR1 taxon:4932
+S000006365 SGV1 YPR161C|BUR1 taxon:4932
+S000006365 SGV1 YPR161C|BUR1 taxon:4932
+S000006365 SGV1 YPR161C|BUR1 taxon:4932
+S000006365 SGV1 YPR161C|BUR1 taxon:4932
+S000006365 SGV1 YPR161C|BUR1 taxon:4932
+S000000898 SHC1 YER096W taxon:4932
+S000000898 SHC1 YER096W taxon:4932
+S000000898 SHC1 YER096W taxon:4932
+S000000898 SHC1 YER096W taxon:4932
+S000000127 SHE1 YBL031W taxon:4932
+S000000127 SHE1 YBL031W taxon:4932
+S000000127 SHE1 YBL031W taxon:4932
+S000003197 SHE10 YGL228W taxon:4932
+S000003197 SHE10 YGL228W taxon:4932
+S000003197 SHE10 YGL228W taxon:4932
+S000001613 SHE2 YKL130C taxon:4932
+S000001613 SHE2 YKL130C taxon:4932
+S000001613 SHE2 YKL130C taxon:4932
+S000000334 SHE3 YBR130C taxon:4932
+S000000334 SHE3 YBR130C taxon:4932
+S000000334 SHE3 YBR130C taxon:4932
+S000000334 SHE3 YBR130C taxon:4932
+S000000334 SHE3 YBR130C taxon:4932
+S000005561 SHE4 YOR035C|DIM1 taxon:4932
+S000005561 SHE4 YOR035C|DIM1 taxon:4932
+S000005561 SHE4 YOR035C|DIM1 taxon:4932
+S000005561 SHE4 YOR035C|DIM1 taxon:4932
+S000002801 SHE9 YDR393W|MDM33 taxon:4932
+S000002801 SHE9 YDR393W|MDM33 taxon:4932
+S000002801 SHE9 YDR393W|MDM33 taxon:4932
+S000002801 SHE9 YDR393W|MDM33 taxon:4932
+S000002801 SHE9 YDR393W|MDM33 taxon:4932
+S000000462 SHG1 YBR258C|CPS15 taxon:4932
+S000000462 SHG1 YBR258C|CPS15 taxon:4932
+S000000462 SHG1 YBR258C|CPS15 taxon:4932
+S000000462 SHG1 YBR258C|CPS15 taxon:4932
+S000000462 SHG1 YBR258C|CPS15 taxon:4932
+S000000462 SHG1 YBR258C|CPS15 taxon:4932
+S000000462 SHG1 YBR258C|CPS15 taxon:4932
+S000000467 SHM1 YBR263W|SHMT1|TMP3 taxon:4932
+S000000467 SHM1 YBR263W|SHMT1|TMP3 taxon:4932
+S000000467 SHM1 YBR263W|SHMT1|TMP3 taxon:4932
+S000000467 SHM1 YBR263W|SHMT1|TMP3 taxon:4932
+S000004048 SHM2 YLR058C|SHMT2 taxon:4932
+S000004048 SHM2 YLR058C|SHMT2 taxon:4932
+S000004048 SHM2 YLR058C|SHMT2 taxon:4932
+S000000920 SHO1 YER118C|SSU81 taxon:4932
+S000000920 SHO1 YER118C|SSU81 taxon:4932
+S000000920 SHO1 YER118C|SSU81 taxon:4932
+S000000920 SHO1 YER118C|SSU81 taxon:4932
+S000000920 SHO1 YER118C|SSU81 taxon:4932
+S000000154 SHP1 YBL058W|UBX1 taxon:4932
+S000000154 SHP1 YBL058W|UBX1 taxon:4932
+S000000154 SHP1 YBL058W|UBX1 taxon:4932
+S000000154 SHP1 YBL058W|UBX1 taxon:4932
+S000000154 SHP1 YBL058W|UBX1 taxon:4932
+S000000154 SHP1 YBL058W|UBX1 taxon:4932
+S000001366 SHQ1 YIL104C taxon:4932
+S000001366 SHQ1 YIL104C taxon:4932
+S000001366 SHQ1 YIL104C taxon:4932
+S000001366 SHQ1 YIL104C taxon:4932
+S000002371 SHR3 YDL212W|APF1 taxon:4932
+S000002371 SHR3 YDL212W|APF1 taxon:4932
+S000002371 SHR3 YDL212W|APF1 taxon:4932
+S000002371 SHR3 YDL212W|APF1 taxon:4932
+S000002371 SHR3 YDL212W|APF1 taxon:4932
+S000002371 SHR3 YDL212W|APF1 taxon:4932
+S000002371 SHR3 YDL212W|APF1 taxon:4932
+S000002371 SHR3 YDL212W|APF1 taxon:4932
+S000002371 SHR3 YDL212W|APF1 taxon:4932
+S000005470 SHR5 YOL110W|ERF4 taxon:4932
+S000005470 SHR5 YOL110W|ERF4 taxon:4932
+S000005470 SHR5 YOL110W|ERF4 taxon:4932
+S000005470 SHR5 YOL110W|ERF4 taxon:4932
+S000005470 SHR5 YOL110W|ERF4 taxon:4932
+S000005470 SHR5 YOL110W|ERF4 taxon:4932
+S000002384 SHS1 YDL225W|SEP7 taxon:4932
+S000002384 SHS1 YDL225W|SEP7 taxon:4932
+S000002384 SHS1 YDL225W|SEP7 taxon:4932
+S000002384 SHS1 YDL225W|SEP7 taxon:4932
+S000002384 SHS1 YDL225W|SEP7 taxon:4932
+S000002384 SHS1 YDL225W|SEP7 taxon:4932
+S000002384 SHS1 YDL225W|SEP7 taxon:4932
+S000002384 SHS1 YDL225W|SEP7 taxon:4932
+S000002384 SHS1 YDL225W|SEP7 taxon:4932
+S000002384 SHS1 YDL225W|SEP7 taxon:4932
+S000002384 SHS1 YDL225W|SEP7 taxon:4932
+S000002384 SHS1 YDL225W|SEP7 taxon:4932
+S000000998 SHU1 YHL006C taxon:4932
+S000000998 SHU1 YHL006C taxon:4932
+S000000998 SHU1 YHL006C taxon:4932
+S000002485 SHU2 YDR078C taxon:4932
+S000002485 SHU2 YDR078C taxon:4932
+S000002485 SHU2 YDR078C taxon:4932
+S000003344 SHY1 YGR112W taxon:4932
+S000003344 SHY1 YGR112W taxon:4932
+S000003344 SHY1 YGR112W taxon:4932
+S000003344 SHY1 YGR112W taxon:4932
+S000003344 SHY1 YGR112W taxon:4932
+S000005663 SIA1 YOR137C taxon:4932
+S000005663 SIA1 YOR137C taxon:4932
+S000005663 SIA1 YOR137C taxon:4932
+S000004069 SIC1 YLR079W|SDB25 taxon:4932
+S000004069 SIC1 YLR079W|SDB25 taxon:4932
+S000004069 SIC1 YLR079W|SDB25 taxon:4932
+S000004069 SIC1 YLR079W|SDB25 taxon:4932
+S000004069 SIC1 YLR079W|SDB25 taxon:4932
+S000004069 SIC1 YLR079W|SDB25 taxon:4932
+S000004069 SIC1 YLR079W|SDB25 taxon:4932
+S000004069 SIC1 YLR079W|SDB25 taxon:4932
+S000004069 SIC1 YLR079W|SDB25 taxon:4932
+S000004069 SIC1 YLR079W|SDB25 taxon:4932
+S000000307 SIF2 YBR103W|EMB1 taxon:4932
+S000000307 SIF2 YBR103W|EMB1 taxon:4932
+S000000307 SIF2 YBR103W|EMB1 taxon:4932
+S000000307 SIF2 YBR103W|EMB1 taxon:4932
+S000000307 SIF2 YBR103W|EMB1 taxon:4932
+S000000307 SIF2 YBR103W|EMB1 taxon:4932
+S000000307 SIF2 YBR103W|EMB1 taxon:4932
+S000000307 SIF2 YBR103W|EMB1 taxon:4932
+S000000307 SIF2 YBR103W|EMB1 taxon:4932
+S000000307 SIF2 YBR103W|EMB1 taxon:4932
+S000000307 SIF2 YBR103W|EMB1 taxon:4932
+S000004187 SIK1 YLR197W|NOP56 taxon:4932
+S000004187 SIK1 YLR197W|NOP56 taxon:4932
+S000004187 SIK1 YLR197W|NOP56 taxon:4932
+S000004187 SIK1 YLR197W|NOP56 taxon:4932
+S000004187 SIK1 YLR197W|NOP56 taxon:4932
+S000004187 SIK1 YLR197W|NOP56 taxon:4932
+S000004187 SIK1 YLR197W|NOP56 taxon:4932
+S000004187 SIK1 YLR197W|NOP56 taxon:4932
+S000004187 SIK1 YLR197W|NOP56 taxon:4932
+S000004187 SIK1 YLR197W|NOP56 taxon:4932
+S000005391 SIL1 YOL031C|SLS1 taxon:4932
+S000005391 SIL1 YOL031C|SLS1 taxon:4932
+S000005391 SIL1 YOL031C|SLS1 taxon:4932
+S000005391 SIL1 YOL031C|SLS1 taxon:4932
+S000001385 SIM1 YIL123W taxon:4932
+S000001385 SIM1 YIL123W taxon:4932
+S000001385 SIM1 YIL123W taxon:4932
+S000005364 SIN3 YOL004W|CPE1|GAM2|RPD1|SDI1|SDS16|UME4 taxon:4932
+S000005364 SIN3 YOL004W|CPE1|GAM2|RPD1|SDI1|SDS16|UME4 taxon:4932
+S000005364 SIN3 YOL004W|CPE1|GAM2|RPD1|SDI1|SDS16|UME4 taxon:4932
+S000005364 SIN3 YOL004W|CPE1|GAM2|RPD1|SDI1|SDS16|UME4 taxon:4932
+S000005364 SIN3 YOL004W|CPE1|GAM2|RPD1|SDI1|SDS16|UME4 taxon:4932
+S000005364 SIN3 YOL004W|CPE1|GAM2|RPD1|SDI1|SDS16|UME4 taxon:4932
+S000005364 SIN3 YOL004W|CPE1|GAM2|RPD1|SDI1|SDS16|UME4 taxon:4932
+S000005364 SIN3 YOL004W|CPE1|GAM2|RPD1|SDI1|SDS16|UME4 taxon:4932
+S000005364 SIN3 YOL004W|CPE1|GAM2|RPD1|SDI1|SDS16|UME4 taxon:4932
+S000005364 SIN3 YOL004W|CPE1|GAM2|RPD1|SDI1|SDS16|UME4 taxon:4932
+S000005180 SIN4 YNL236W|BEL2|GAL22|MED16|RYE1|SDI3|SSF5|SSN4|TSF3 taxon:4932
+S000005180 SIN4 YNL236W|BEL2|GAL22|MED16|RYE1|SDI3|SSF5|SSN4|TSF3 taxon:4932
+S000005180 SIN4 YNL236W|BEL2|GAL22|MED16|RYE1|SDI3|SSF5|SSN4|TSF3 taxon:4932
+S000002830 SIP1 YDR422C taxon:4932
+S000002830 SIP1 YDR422C taxon:4932
+S000002830 SIP1 YDR422C taxon:4932
+S000002830 SIP1 YDR422C taxon:4932
+S000004787 SIP18 YMR175W taxon:4932
+S000004787 SIP18 YMR175W taxon:4932
+S000004787 SIP18 YMR175W taxon:4932
+S000004787 SIP18 YMR175W taxon:4932
+S000003176 SIP2 YGL208W|SPM2 taxon:4932
+S000003176 SIP2 YGL208W|SPM2 taxon:4932
+S000003176 SIP2 YGL208W|SPM2 taxon:4932
+S000003176 SIP2 YGL208W|SPM2 taxon:4932
+S000003176 SIP2 YGL208W|SPM2 taxon:4932
+S000003176 SIP2 YGL208W|SPM2 taxon:4932
+S000003176 SIP2 YGL208W|SPM2 taxon:4932
+S000003176 SIP2 YGL208W|SPM2 taxon:4932
+S000003176 SIP2 YGL208W|SPM2 taxon:4932
+S000005201 SIP3 YNL257C taxon:4932
+S000005201 SIP3 YNL257C taxon:4932
+S000005201 SIP3 YNL257C taxon:4932
+S000003625 SIP4 YJL089W taxon:4932
+S000003625 SIP4 YJL089W taxon:4932
+S000003625 SIP4 YJL089W taxon:4932
+S000003625 SIP4 YJL089W taxon:4932
+S000003625 SIP4 YJL089W taxon:4932
+S000003625 SIP4 YJL089W taxon:4932
+S000003625 SIP4 YJL089W taxon:4932
+S000004748 SIP5 YMR140W taxon:4932
+S000004748 SIP5 YMR140W taxon:4932
+S000004748 SIP5 YMR140W taxon:4932
+S000004748 SIP5 YMR140W taxon:4932
+S000001809 SIR1 YKR101W taxon:4932
+S000001809 SIR1 YKR101W taxon:4932
+S000001809 SIR1 YKR101W taxon:4932
+S000001809 SIR1 YKR101W taxon:4932
+S000001809 SIR1 YKR101W taxon:4932
+S000002200 SIR2 YDL042C|MAR1 taxon:4932
+S000002200 SIR2 YDL042C|MAR1 taxon:4932
+S000002200 SIR2 YDL042C|MAR1 taxon:4932
+S000002200 SIR2 YDL042C|MAR1 taxon:4932
+S000002200 SIR2 YDL042C|MAR1 taxon:4932
+S000002200 SIR2 YDL042C|MAR1 taxon:4932
+S000002200 SIR2 YDL042C|MAR1 taxon:4932
+S000002200 SIR2 YDL042C|MAR1 taxon:4932
+S000002200 SIR2 YDL042C|MAR1 taxon:4932
+S000002200 SIR2 YDL042C|MAR1 taxon:4932
+S000002200 SIR2 YDL042C|MAR1 taxon:4932
+S000002200 SIR2 YDL042C|MAR1 taxon:4932
+S000002200 SIR2 YDL042C|MAR1 taxon:4932
+S000002200 SIR2 YDL042C|MAR1 taxon:4932
+S000002200 SIR2 YDL042C|MAR1 taxon:4932
+S000002200 SIR2 YDL042C|MAR1 taxon:4932
+S000002200 SIR2 YDL042C|MAR1 taxon:4932
+S000002200 SIR2 YDL042C|MAR1 taxon:4932
+S000002200 SIR2 YDL042C|MAR1 taxon:4932
+S000002200 SIR2 YDL042C|MAR1 taxon:4932
+S000002200 SIR2 YDL042C|MAR1 taxon:4932
+S000004434 SIR3 YLR442C|CMT1|MAR2|STE8 taxon:4932
+S000004434 SIR3 YLR442C|CMT1|MAR2|STE8 taxon:4932
+S000004434 SIR3 YLR442C|CMT1|MAR2|STE8 taxon:4932
+S000004434 SIR3 YLR442C|CMT1|MAR2|STE8 taxon:4932
+S000004434 SIR3 YLR442C|CMT1|MAR2|STE8 taxon:4932
+S000004434 SIR3 YLR442C|CMT1|MAR2|STE8 taxon:4932
+S000004434 SIR3 YLR442C|CMT1|MAR2|STE8 taxon:4932
+S000004434 SIR3 YLR442C|CMT1|MAR2|STE8 taxon:4932
+S000004434 SIR3 YLR442C|CMT1|MAR2|STE8 taxon:4932
+S000004434 SIR3 YLR442C|CMT1|MAR2|STE8 taxon:4932
+S000002635 SIR4 YDR227W|ASD1|STE9|UTH2 taxon:4932
+S000002635 SIR4 YDR227W|ASD1|STE9|UTH2 taxon:4932
+S000002635 SIR4 YDR227W|ASD1|STE9|UTH2 taxon:4932
+S000002635 SIR4 YDR227W|ASD1|STE9|UTH2 taxon:4932
+S000002635 SIR4 YDR227W|ASD1|STE9|UTH2 taxon:4932
+S000002635 SIR4 YDR227W|ASD1|STE9|UTH2 taxon:4932
+S000002635 SIR4 YDR227W|ASD1|STE9|UTH2 taxon:4932
+S000002635 SIR4 YDR227W|ASD1|STE9|UTH2 taxon:4932
+S000004952 SIS1 YNL007C taxon:4932
+S000004952 SIS1 YNL007C taxon:4932
+S000004952 SIS1 YNL007C taxon:4932
+S000004952 SIS1 YNL007C taxon:4932
+S000004952 SIS1 YNL007C taxon:4932
+S000004952 SIS1 YNL007C taxon:4932
+S000001780 SIS2 YKR072C|HAL3 taxon:4932
+S000001780 SIS2 YKR072C|HAL3 taxon:4932
+S000001780 SIS2 YKR072C|HAL3 taxon:4932
+S000001780 SIS2 YKR072C|HAL3 taxon:4932
+S000001780 SIS2 YKR072C|HAL3 taxon:4932
+S000001780 SIS2 YKR072C|HAL3 taxon:4932
+S000001780 SIS2 YKR072C|HAL3 taxon:4932
+S000001780 SIS2 YKR072C|HAL3 taxon:4932
+S000001780 SIS2 YKR072C|HAL3 taxon:4932
+S000001780 SIS2 YKR072C|HAL3 taxon:4932
+S000001780 SIS2 YKR072C|HAL3 taxon:4932
+S000000791 SIT1 YEL065W|ARN3 taxon:4932
+S000000791 SIT1 YEL065W|ARN3 taxon:4932
+S000000791 SIT1 YEL065W|ARN3 taxon:4932
+S000000791 SIT1 YEL065W|ARN3 taxon:4932
+S000000791 SIT1 YEL065W|ARN3 taxon:4932
+S000000791 SIT1 YEL065W|ARN3 taxon:4932
+S000000791 SIT1 YEL065W|ARN3 taxon:4932
+S000029447 SIT3 taxon:4932
+S000029447 SIT3 taxon:4932
+S000029447 SIT3 taxon:4932
+S000002205 SIT4 YDL047W|LGN4 taxon:4932
+S000002205 SIT4 YDL047W|LGN4 taxon:4932
+S000002205 SIT4 YDL047W|LGN4 taxon:4932
+S000002205 SIT4 YDL047W|LGN4 taxon:4932
+S000002205 SIT4 YDL047W|LGN4 taxon:4932
+S000002205 SIT4 YDL047W|LGN4 taxon:4932
+S000002205 SIT4 YDL047W|LGN4 taxon:4932
+S000002205 SIT4 YDL047W|LGN4 taxon:4932
+S000002205 SIT4 YDL047W|LGN4 taxon:4932
+S000002205 SIT4 YDL047W|LGN4 taxon:4932
+S000002205 SIT4 YDL047W|LGN4 taxon:4932
+S000004977 SIW14 YNL032W|OCA3 taxon:4932
+S000004977 SIW14 YNL032W|OCA3 taxon:4932
+S000004977 SIW14 YNL032W|OCA3 taxon:4932
+S000004977 SIW14 YNL032W|OCA3 taxon:4932
+S000004977 SIW14 YNL032W|OCA3 taxon:4932
+S000004977 SIW14 YNL032W|OCA3 taxon:4932
+S000002817 SIZ1 YDR409W|ULL1 taxon:4932
+S000002817 SIZ1 YDR409W|ULL1 taxon:4932
+S000002817 SIZ1 YDR409W|ULL1 taxon:4932
+S000002817 SIZ1 YDR409W|ULL1 taxon:4932
+S000002817 SIZ1 YDR409W|ULL1 taxon:4932
+S000002817 SIZ1 YDR409W|ULL1 taxon:4932
+S000002817 SIZ1 YDR409W|ULL1 taxon:4932
+S000001808 SKG1 YKR100C|YKR099C-A taxon:4932
+S000001808 SKG1 YKR100C|YKR099C-A taxon:4932
+S000001808 SKG1 YKR100C|YKR099C-A taxon:4932
+S000001808 SKG1 YKR100C|YKR099C-A taxon:4932
+S000001808 SKG1 YKR100C|YKR099C-A taxon:4932
+S000004177 SKG3 YLR187W taxon:4932
+S000004177 SKG3 YLR187W taxon:4932
+S000004177 SKG3 YLR187W taxon:4932
+S000004177 SKG3 YLR187W taxon:4932
+S000004177 SKG3 YLR187W taxon:4932
+S000001192 SKG6 YHR149C taxon:4932
+S000001192 SKG6 YHR149C taxon:4932
+S000001192 SKG6 YHR149C taxon:4932
+S000001192 SKG6 YHR149C taxon:4932
+S000004390 SKI2 YLR398C taxon:4932
+S000004390 SKI2 YLR398C taxon:4932
+S000004390 SKI2 YLR398C taxon:4932
+S000004390 SKI2 YLR398C taxon:4932
+S000004390 SKI2 YLR398C taxon:4932
+S000004390 SKI2 YLR398C taxon:4932
+S000004390 SKI2 YLR398C taxon:4932
+S000004390 SKI2 YLR398C taxon:4932
+S000004390 SKI2 YLR398C taxon:4932
+S000004390 SKI2 YLR398C taxon:4932
+S000004390 SKI2 YLR398C taxon:4932
+S000006393 SKI3 YPR189W|SKI5 taxon:4932
+S000006393 SKI3 YPR189W|SKI5 taxon:4932
+S000006393 SKI3 YPR189W|SKI5 taxon:4932
+S000006393 SKI3 YPR189W|SKI5 taxon:4932
+S000006393 SKI3 YPR189W|SKI5 taxon:4932
+S000006393 SKI3 YPR189W|SKI5 taxon:4932
+S000003427 SKI6 YGR195W|ECM20|RRP41 taxon:4932
+S000003427 SKI6 YGR195W|ECM20|RRP41 taxon:4932
+S000003427 SKI6 YGR195W|ECM20|RRP41 taxon:4932
+S000003427 SKI6 YGR195W|ECM20|RRP41 taxon:4932
+S000003427 SKI6 YGR195W|ECM20|RRP41 taxon:4932
+S000003427 SKI6 YGR195W|ECM20|RRP41 taxon:4932
+S000003427 SKI6 YGR195W|ECM20|RRP41 taxon:4932
+S000005602 SKI7 YOR076C|YOR29-27 taxon:4932
+S000005602 SKI7 YOR076C|YOR29-27 taxon:4932
+S000005602 SKI7 YOR076C|YOR29-27 taxon:4932
+S000005602 SKI7 YOR076C|YOR29-27 taxon:4932
+S000005602 SKI7 YOR076C|YOR29-27 taxon:4932
+S000003181 SKI8 YGL213C|REC103 taxon:4932
+S000003181 SKI8 YGL213C|REC103 taxon:4932
+S000003181 SKI8 YGL213C|REC103 taxon:4932
+S000003181 SKI8 YGL213C|REC103 taxon:4932
+S000003181 SKI8 YGL213C|REC103 taxon:4932
+S000003181 SKI8 YGL213C|REC103 taxon:4932
+S000003181 SKI8 YGL213C|REC103 taxon:4932
+S000003181 SKI8 YGL213C|REC103 taxon:4932
+S000005473 SKM1 YOL113W taxon:4932
+S000005473 SKM1 YOL113W taxon:4932
+S000005473 SKM1 YOL113W taxon:4932
+S000005473 SKM1 YOL113W taxon:4932
+S000005473 SKM1 YOL113W taxon:4932
+S000003375 SKN1 YGR143W taxon:4932
+S000003375 SKN1 YGR143W taxon:4932
+S000003375 SKN1 YGR143W taxon:4932
+S000003375 SKN1 YGR143W taxon:4932
+S000003375 SKN1 YGR143W taxon:4932
+S000003375 SKN1 YGR143W taxon:4932
+S000003375 SKN1 YGR143W taxon:4932
+S000003375 SKN1 YGR143W taxon:4932
+S000001249 SKN7 YHR206W|BRY1|POS9 taxon:4932
+S000001249 SKN7 YHR206W|BRY1|POS9 taxon:4932
+S000001249 SKN7 YHR206W|BRY1|POS9 taxon:4932
+S000001249 SKN7 YHR206W|BRY1|POS9 taxon:4932
+S000001249 SKN7 YHR206W|BRY1|POS9 taxon:4932
+S000001249 SKN7 YHR206W|BRY1|POS9 taxon:4932
+S000001249 SKN7 YHR206W|BRY1|POS9 taxon:4932
+S000001249 SKN7 YHR206W|BRY1|POS9 taxon:4932
+S000001249 SKN7 YHR206W|BRY1|POS9 taxon:4932
+S000001249 SKN7 YHR206W|BRY1|POS9 taxon:4932
+S000001249 SKN7 YHR206W|BRY1|POS9 taxon:4932
+S000001249 SKN7 YHR206W|BRY1|POS9 taxon:4932
+S000001249 SKN7 YHR206W|BRY1|POS9 taxon:4932
+S000005111 SKO1 YNL167C|ACR1 taxon:4932
+S000005111 SKO1 YNL167C|ACR1 taxon:4932
+S000005111 SKO1 YNL167C|ACR1 taxon:4932
+S000005111 SKO1 YNL167C|ACR1 taxon:4932
+S000005111 SKO1 YNL167C|ACR1 taxon:4932
+S000005111 SKO1 YNL167C|ACR1 taxon:4932
+S000002736 SKP1 YDR328C|CBF3D|MGO1 taxon:4932
+S000002736 SKP1 YDR328C|CBF3D|MGO1 taxon:4932
+S000002736 SKP1 YDR328C|CBF3D|MGO1 taxon:4932
+S000002736 SKP1 YDR328C|CBF3D|MGO1 taxon:4932
+S000002736 SKP1 YDR328C|CBF3D|MGO1 taxon:4932
+S000002736 SKP1 YDR328C|CBF3D|MGO1 taxon:4932
+S000002736 SKP1 YDR328C|CBF3D|MGO1 taxon:4932
+S000002736 SKP1 YDR328C|CBF3D|MGO1 taxon:4932
+S000002736 SKP1 YDR328C|CBF3D|MGO1 taxon:4932
+S000002736 SKP1 YDR328C|CBF3D|MGO1 taxon:4932
+S000002736 SKP1 YDR328C|CBF3D|MGO1 taxon:4932
+S000002736 SKP1 YDR328C|CBF3D|MGO1 taxon:4932
+S000002736 SKP1 YDR328C|CBF3D|MGO1 taxon:4932
+S000002736 SKP1 YDR328C|CBF3D|MGO1 taxon:4932
+S000002736 SKP1 YDR328C|CBF3D|MGO1 taxon:4932
+S000002736 SKP1 YDR328C|CBF3D|MGO1 taxon:4932
+S000002736 SKP1 YDR328C|CBF3D|MGO1 taxon:4932
+S000002736 SKP1 YDR328C|CBF3D|MGO1 taxon:4932
+S000002736 SKP1 YDR328C|CBF3D|MGO1 taxon:4932
+S000002736 SKP1 YDR328C|CBF3D|MGO1 taxon:4932
+S000002736 SKP1 YDR328C|CBF3D|MGO1 taxon:4932
+S000002736 SKP1 YDR328C|CBF3D|MGO1 taxon:4932
+S000002736 SKP1 YDR328C|CBF3D|MGO1 taxon:4932
+S000002736 SKP1 YDR328C|CBF3D|MGO1 taxon:4932
+S000002736 SKP1 YDR328C|CBF3D|MGO1 taxon:4932
+S000005255 SKP2 YNL311C taxon:4932
+S000005255 SKP2 YNL311C taxon:4932
+S000005255 SKP2 YNL311C taxon:4932
+S000005947 SKS1 YPL026C|SHA3 taxon:4932
+S000005947 SKS1 YPL026C|SHA3 taxon:4932
+S000005947 SKS1 YPL026C|SHA3 taxon:4932
+S000005947 SKS1 YPL026C|SHA3 taxon:4932
+S000005947 SKS1 YPL026C|SHA3 taxon:4932
+S000005947 SKS1 YPL026C|SHA3 taxon:4932
+S000000157 SKT5 YBL061C|CAL2|CHS4|CSD4 taxon:4932
+S000000157 SKT5 YBL061C|CAL2|CHS4|CSD4 taxon:4932
+S000000157 SKT5 YBL061C|CAL2|CHS4|CSD4 taxon:4932
+S000000157 SKT5 YBL061C|CAL2|CHS4|CSD4 taxon:4932
+S000000157 SKT5 YBL061C|CAL2|CHS4|CSD4 taxon:4932
+S000000157 SKT5 YBL061C|CAL2|CHS4|CSD4 taxon:4932
+S000000157 SKT5 YBL061C|CAL2|CHS4|CSD4 taxon:4932
+S000000157 SKT5 YBL061C|CAL2|CHS4|CSD4 taxon:4932
+S000004829 SKY1 YMR216C taxon:4932
+S000004829 SKY1 YMR216C taxon:4932
+S000004829 SKY1 YMR216C taxon:4932
+S000004829 SKY1 YMR216C taxon:4932
+S000004829 SKY1 YMR216C taxon:4932
+S000004829 SKY1 YMR216C taxon:4932
+S000004829 SKY1 YMR216C taxon:4932
+S000000103 SLA1 YBL007C taxon:4932
+S000000103 SLA1 YBL007C taxon:4932
+S000000103 SLA1 YBL007C taxon:4932
+S000000103 SLA1 YBL007C taxon:4932
+S000000103 SLA1 YBL007C taxon:4932
+S000000103 SLA1 YBL007C taxon:4932
+S000000103 SLA1 YBL007C taxon:4932
+S000000103 SLA1 YBL007C taxon:4932
+S000000103 SLA1 YBL007C taxon:4932
+S000000103 SLA1 YBL007C taxon:4932
+S000000103 SLA1 YBL007C taxon:4932
+S000005187 SLA2 YNL243W|END4|MOP2 taxon:4932
+S000005187 SLA2 YNL243W|END4|MOP2 taxon:4932
+S000005187 SLA2 YNL243W|END4|MOP2 taxon:4932
+S000005187 SLA2 YNL243W|END4|MOP2 taxon:4932
+S000005187 SLA2 YNL243W|END4|MOP2 taxon:4932
+S000005187 SLA2 YNL243W|END4|MOP2 taxon:4932
+S000005187 SLA2 YNL243W|END4|MOP2 taxon:4932
+S000005187 SLA2 YNL243W|END4|MOP2 taxon:4932
+S000005187 SLA2 YNL243W|END4|MOP2 taxon:4932
+S000002210 SLC1 YDL052C taxon:4932
+S000002210 SLC1 YDL052C taxon:4932
+S000002210 SLC1 YDL052C taxon:4932
+S000001591 SLD2 YKL108W|DRC1 taxon:4932
+S000001591 SLD2 YKL108W|DRC1 taxon:4932
+S000001591 SLD2 YKL108W|DRC1 taxon:4932
+S000001591 SLD2 YKL108W|DRC1 taxon:4932
+S000001591 SLD2 YKL108W|DRC1 taxon:4932
+S000003081 SLD3 YGL113W taxon:4932
+S000003081 SLD3 YGL113W taxon:4932
+S000003081 SLD3 YGL113W taxon:4932
+S000003081 SLD3 YGL113W taxon:4932
+S000003081 SLD3 YGL113W taxon:4932
+S000002897 SLD5 YDR489W|CDC105 taxon:4932
+S000002897 SLD5 YDR489W|CDC105 taxon:4932
+S000002897 SLD5 YDR489W|CDC105 taxon:4932
+S000002897 SLD5 YDR489W|CDC105 taxon:4932
+S000002897 SLD5 YDR489W|CDC105 taxon:4932
+S000002923 SLF1 YDR515W|SRO99 taxon:4932
+S000002923 SLF1 YDR515W|SRO99 taxon:4932
+S000002923 SLF1 YDR515W|SRO99 taxon:4932
+S000002923 SLF1 YDR515W|SRO99 taxon:4932
+S000002923 SLF1 YDR515W|SRO99 taxon:4932
+S000002923 SLF1 YDR515W|SRO99 taxon:4932
+S000002923 SLF1 YDR515W|SRO99 taxon:4932
+S000002923 SLF1 YDR515W|SRO99 taxon:4932
+S000005534 SLG1 YOR008C|HCS77|WSC1 taxon:4932
+S000005534 SLG1 YOR008C|HCS77|WSC1 taxon:4932
+S000005534 SLG1 YOR008C|HCS77|WSC1 taxon:4932
+S000005534 SLG1 YOR008C|HCS77|WSC1 taxon:4932
+S000005534 SLG1 YOR008C|HCS77|WSC1 taxon:4932
+S000005534 SLG1 YOR008C|HCS77|WSC1 taxon:4932
+S000005534 SLG1 YOR008C|HCS77|WSC1 taxon:4932
+S000005534 SLG1 YOR008C|HCS77|WSC1 taxon:4932
+S000005534 SLG1 YOR008C|HCS77|WSC1 taxon:4932
+S000005534 SLG1 YOR008C|HCS77|WSC1 taxon:4932
+S000005534 SLG1 YOR008C|HCS77|WSC1 taxon:4932
+S000005534 SLG1 YOR008C|HCS77|WSC1 taxon:4932
+S000005534 SLG1 YOR008C|HCS77|WSC1 taxon:4932
+S000005534 SLG1 YOR008C|HCS77|WSC1 taxon:4932
+S000005534 SLG1 YOR008C|HCS77|WSC1 taxon:4932
+S000005534 SLG1 YOR008C|HCS77|WSC1 taxon:4932
+S000003503 SLH1 YGR271W taxon:4932
+S000003503 SLH1 YGR271W taxon:4932
+S000003503 SLH1 YGR271W taxon:4932
+S000003503 SLH1 YGR271W taxon:4932
+S000003503 SLH1 YGR271W taxon:4932
+S000003503 SLH1 YGR271W taxon:4932
+S000003444 SLI1 YGR212W taxon:4932
+S000003444 SLI1 YGR212W taxon:4932
+S000003444 SLI1 YGR212W taxon:4932
+S000003444 SLI1 YGR212W taxon:4932
+S000003444 SLI1 YGR212W taxon:4932
+S000000360 SLI15 YBR156C taxon:4932
+S000000360 SLI15 YBR156C taxon:4932
+S000000360 SLI15 YBR156C taxon:4932
+S000000360 SLI15 YBR156C taxon:4932
+S000000360 SLI15 YBR156C taxon:4932
+S000000360 SLI15 YBR156C taxon:4932
+S000000360 SLI15 YBR156C taxon:4932
+S000000360 SLI15 YBR156C taxon:4932
+S000005721 SLK19 YOR195W taxon:4932
+S000005721 SLK19 YOR195W taxon:4932
+S000005721 SLK19 YOR195W taxon:4932
+S000005721 SLK19 YOR195W taxon:4932
+S000005721 SLK19 YOR195W taxon:4932
+S000005721 SLK19 YOR195W taxon:4932
+S000005721 SLK19 YOR195W taxon:4932
+S000005721 SLK19 YOR195W taxon:4932
+S000005721 SLK19 YOR195W taxon:4932
+S000001367 SLM1 YIL105C|LIT2 taxon:4932
+S000001367 SLM1 YIL105C|LIT2 taxon:4932
+S000001367 SLM1 YIL105C|LIT2 taxon:4932
+S000001367 SLM1 YIL105C|LIT2 taxon:4932
+S000001367 SLM1 YIL105C|LIT2 taxon:4932
+S000001367 SLM1 YIL105C|LIT2 taxon:4932
+S000001367 SLM1 YIL105C|LIT2 taxon:4932
+S000001367 SLM1 YIL105C|LIT2 taxon:4932
+S000001367 SLM1 YIL105C|LIT2 taxon:4932
+S000001367 SLM1 YIL105C|LIT2 taxon:4932
+S000001367 SLM1 YIL105C|LIT2 taxon:4932
+S000001367 SLM1 YIL105C|LIT2 taxon:4932
+S000001367 SLM1 YIL105C|LIT2 taxon:4932
+S000001367 SLM1 YIL105C|LIT2 taxon:4932
+S000004992 SLM2 YNL047C|LIT1 taxon:4932
+S000004992 SLM2 YNL047C|LIT1 taxon:4932
+S000004992 SLM2 YNL047C|LIT1 taxon:4932
+S000004992 SLM2 YNL047C|LIT1 taxon:4932
+S000004992 SLM2 YNL047C|LIT1 taxon:4932
+S000004992 SLM2 YNL047C|LIT1 taxon:4932
+S000004992 SLM2 YNL047C|LIT1 taxon:4932
+S000004992 SLM2 YNL047C|LIT1 taxon:4932
+S000004992 SLM2 YNL047C|LIT1 taxon:4932
+S000004992 SLM2 YNL047C|LIT1 taxon:4932
+S000002191 SLM3 YDL033C|MTO2|MTU1 taxon:4932
+S000002191 SLM3 YDL033C|MTO2|MTU1 taxon:4932
+S000002191 SLM3 YDL033C|MTO2|MTU1 taxon:4932
+S000002191 SLM3 YDL033C|MTO2|MTU1 taxon:4932
+S000002191 SLM3 YDL033C|MTO2|MTU1 taxon:4932
+S000002191 SLM3 YDL033C|MTO2|MTU1 taxon:4932
+S000000281 SLM4 YBR077C|EGO3|NIR1 taxon:4932
+S000000281 SLM4 YBR077C|EGO3|NIR1 taxon:4932
+S000000281 SLM4 YBR077C|EGO3|NIR1 taxon:4932
+S000000281 SLM4 YBR077C|EGO3|NIR1 taxon:4932
+S000000281 SLM4 YBR077C|EGO3|NIR1 taxon:4932
+S000000281 SLM4 YBR077C|EGO3|NIR1 taxon:4932
+S000000618 SLM5 YCR024C taxon:4932
+S000000618 SLM5 YCR024C taxon:4932
+S000000618 SLM5 YCR024C taxon:4932
+S000000618 SLM5 YCR024C taxon:4932
+S000000618 SLM5 YCR024C taxon:4932
+S000001409 SLN1 YIL147C|YPD2 taxon:4932
+S000001409 SLN1 YIL147C|YPD2 taxon:4932
+S000001409 SLN1 YIL147C|YPD2 taxon:4932
+S000001409 SLN1 YIL147C|YPD2 taxon:4932
+S000001409 SLN1 YIL147C|YPD2 taxon:4932
+S000001409 SLN1 YIL147C|YPD2 taxon:4932
+S000001409 SLN1 YIL147C|YPD2 taxon:4932
+S000001409 SLN1 YIL147C|YPD2 taxon:4932
+S000028437 SLO1 YER180C-A taxon:4932
+S000028437 SLO1 YER180C-A taxon:4932
+S000028437 SLO1 YER180C-A taxon:4932
+S000004129 SLS1 YLR139C taxon:4932
+S000004129 SLS1 YLR139C taxon:4932
+S000004129 SLS1 YLR139C taxon:4932
+S000004129 SLS1 YLR139C taxon:4932
+S000004129 SLS1 YLR139C taxon:4932
+S000004129 SLS1 YLR139C taxon:4932
+S000004129 SLS1 YLR139C taxon:4932
+S000004129 SLS1 YLR139C taxon:4932
+S000001072 SLT2 YHR030C|BYC2|MPK1|SLK2 taxon:4932
+S000001072 SLT2 YHR030C|BYC2|MPK1|SLK2 taxon:4932
+S000001072 SLT2 YHR030C|BYC2|MPK1|SLK2 taxon:4932
+S000001072 SLT2 YHR030C|BYC2|MPK1|SLK2 taxon:4932
+S000001072 SLT2 YHR030C|BYC2|MPK1|SLK2 taxon:4932
+S000001072 SLT2 YHR030C|BYC2|MPK1|SLK2 taxon:4932
+S000001072 SLT2 YHR030C|BYC2|MPK1|SLK2 taxon:4932
+S000001072 SLT2 YHR030C|BYC2|MPK1|SLK2 taxon:4932
+S000002495 SLU7 YDR088C|SLT17 taxon:4932
+S000002495 SLU7 YDR088C|SLT17 taxon:4932
+S000002495 SLU7 YDR088C|SLT17 taxon:4932
+S000002495 SLU7 YDR088C|SLT17 taxon:4932
+S000002495 SLU7 YDR088C|SLT17 taxon:4932
+S000000432 SLX1 YBR228W taxon:4932
+S000000432 SLX1 YBR228W taxon:4932
+S000000432 SLX1 YBR228W taxon:4932
+S000000432 SLX1 YBR228W taxon:4932
+S000004125 SLX4 YLR135W taxon:4932
+S000004125 SLX4 YLR135W taxon:4932
+S000004125 SLX4 YLR135W taxon:4932
+S000004125 SLX4 YLR135W taxon:4932
+S000004125 SLX4 YLR135W taxon:4932
+S000000918 SLX8 YER116C taxon:4932
+S000000918 SLX8 YER116C taxon:4932
+S000000918 SLX8 YER116C taxon:4932
+S000000918 SLX8 YER116C taxon:4932
+S000003313 SLX9 YGR081C taxon:4932
+S000003313 SLX9 YGR081C taxon:4932
+S000003313 SLX9 YGR081C taxon:4932
+S000003313 SLX9 YGR081C taxon:4932
+S000002597 SLY1 YDR189W taxon:4932
+S000002597 SLY1 YDR189W taxon:4932
+S000002597 SLY1 YDR189W taxon:4932
+S000002597 SLY1 YDR189W taxon:4932
+S000002597 SLY1 YDR189W taxon:4932
+S000005834 SLY41 YOR307C taxon:4932
+S000005834 SLY41 YOR307C taxon:4932
+S000005834 SLY41 YOR307C taxon:4932
+S000005948 SMA1 YPL027W taxon:4932
+S000005948 SMA1 YPL027W taxon:4932
+S000005948 SMA1 YPL027W taxon:4932
+S000004531 SMA2 YML066C taxon:4932
+S000004531 SMA2 YML066C taxon:4932
+S000004531 SMA2 YML066C taxon:4932
+S000000831 SMB1 YER029C|Sm B|SmB taxon:4932
+S000000831 SMB1 YER029C|Sm B|SmB taxon:4932
+S000000831 SMB1 YER029C|Sm B|SmB taxon:4932
+S000000831 SMB1 YER029C|Sm B|SmB taxon:4932
+S000000831 SMB1 YER029C|Sm B|SmB taxon:4932
+S000000831 SMB1 YER029C|Sm B|SmB taxon:4932
+S000000831 SMB1 YER029C|Sm B|SmB taxon:4932
+S000001886 SMC1 YFL008W|CHL10 taxon:4932
+S000001886 SMC1 YFL008W|CHL10 taxon:4932
+S000001886 SMC1 YFL008W|CHL10 taxon:4932
+S000001886 SMC1 YFL008W|CHL10 taxon:4932
+S000001886 SMC1 YFL008W|CHL10 taxon:4932
+S000001886 SMC1 YFL008W|CHL10 taxon:4932
+S000001886 SMC1 YFL008W|CHL10 taxon:4932
+S000001886 SMC1 YFL008W|CHL10 taxon:4932
+S000001886 SMC1 YFL008W|CHL10 taxon:4932
+S000001886 SMC1 YFL008W|CHL10 taxon:4932
+S000001927 SMC2 YFR031C taxon:4932
+S000001927 SMC2 YFR031C taxon:4932
+S000001927 SMC2 YFR031C taxon:4932
+S000001927 SMC2 YFR031C taxon:4932
+S000001927 SMC2 YFR031C taxon:4932
+S000001927 SMC2 YFR031C taxon:4932
+S000001927 SMC2 YFR031C taxon:4932
+S000001927 SMC2 YFR031C taxon:4932
+S000001927 SMC2 YFR031C taxon:4932
+S000001927 SMC2 YFR031C taxon:4932
+S000001927 SMC2 YFR031C taxon:4932
+S000001927 SMC2 YFR031C taxon:4932
+S000001927 SMC2 YFR031C taxon:4932
+S000003610 SMC3 YJL074C taxon:4932
+S000003610 SMC3 YJL074C taxon:4932
+S000003610 SMC3 YJL074C taxon:4932
+S000003610 SMC3 YJL074C taxon:4932
+S000003610 SMC3 YJL074C taxon:4932
+S000003610 SMC3 YJL074C taxon:4932
+S000003610 SMC3 YJL074C taxon:4932
+S000004076 SMC4 YLR086W taxon:4932
+S000004076 SMC4 YLR086W taxon:4932
+S000004076 SMC4 YLR086W taxon:4932
+S000004076 SMC4 YLR086W taxon:4932
+S000004076 SMC4 YLR086W taxon:4932
+S000004076 SMC4 YLR086W taxon:4932
+S000004076 SMC4 YLR086W taxon:4932
+S000004076 SMC4 YLR086W taxon:4932
+S000005394 SMC5 YOL034W taxon:4932
+S000005394 SMC5 YOL034W taxon:4932
+S000005394 SMC5 YOL034W taxon:4932
+S000005394 SMC5 YOL034W taxon:4932
+S000005394 SMC5 YOL034W taxon:4932
+S000005394 SMC5 YOL034W taxon:4932
+S000005394 SMC5 YOL034W taxon:4932
+S000004375 SMC6 YLR383W|RHC18 taxon:4932
+S000004375 SMC6 YLR383W|RHC18 taxon:4932
+S000004375 SMC6 YLR383W|RHC18 taxon:4932
+S000004375 SMC6 YLR383W|RHC18 taxon:4932
+S000004375 SMC6 YLR383W|RHC18 taxon:4932
+S000004375 SMC6 YLR383W|RHC18 taxon:4932
+S000004375 SMC6 YLR383W|RHC18 taxon:4932
+S000004375 SMC6 YLR383W|RHC18 taxon:4932
+S000003306 SMD1 YGR074W|SPP92|Sm D1 taxon:4932
+S000003306 SMD1 YGR074W|SPP92|Sm D1 taxon:4932
+S000003306 SMD1 YGR074W|SPP92|Sm D1 taxon:4932
+S000003306 SMD1 YGR074W|SPP92|Sm D1 taxon:4932
+S000003306 SMD1 YGR074W|SPP92|Sm D1 taxon:4932
+S000003306 SMD1 YGR074W|SPP92|Sm D1 taxon:4932
+S000003306 SMD1 YGR074W|SPP92|Sm D1 taxon:4932
+S000003306 SMD1 YGR074W|SPP92|Sm D1 taxon:4932
+S000003306 SMD1 YGR074W|SPP92|Sm D1 taxon:4932
+S000003306 SMD1 YGR074W|SPP92|Sm D1 taxon:4932
+S000003306 SMD1 YGR074W|SPP92|Sm D1 taxon:4932
+S000004265 SMD2 YLR275W|Sm D2 taxon:4932
+S000004265 SMD2 YLR275W|Sm D2 taxon:4932
+S000004265 SMD2 YLR275W|Sm D2 taxon:4932
+S000004265 SMD2 YLR275W|Sm D2 taxon:4932
+S000004265 SMD2 YLR275W|Sm D2 taxon:4932
+S000004265 SMD2 YLR275W|Sm D2 taxon:4932
+S000004265 SMD2 YLR275W|Sm D2 taxon:4932
+S000004265 SMD2 YLR275W|Sm D2 taxon:4932
+S000004137 SMD3 YLR147C|SLT16|Sm D3 taxon:4932
+S000004137 SMD3 YLR147C|SLT16|Sm D3 taxon:4932
+S000004137 SMD3 YLR147C|SLT16|Sm D3 taxon:4932
+S000004137 SMD3 YLR147C|SLT16|Sm D3 taxon:4932
+S000004137 SMD3 YLR147C|SLT16|Sm D3 taxon:4932
+S000004137 SMD3 YLR147C|SLT16|Sm D3 taxon:4932
+S000004137 SMD3 YLR147C|SLT16|Sm D3 taxon:4932
+S000004137 SMD3 YLR147C|SLT16|Sm D3 taxon:4932
+S000004137 SMD3 YLR147C|SLT16|Sm D3 taxon:4932
+S000004137 SMD3 YLR147C|SLT16|Sm D3 taxon:4932
+S000004137 SMD3 YLR147C|SLT16|Sm D3 taxon:4932
+S000005685 SME1 YOR159C|Sm E|SmE taxon:4932
+S000005685 SME1 YOR159C|Sm E|SmE taxon:4932
+S000005685 SME1 YOR159C|Sm E|SmE taxon:4932
+S000005685 SME1 YOR159C|Sm E|SmE taxon:4932
+S000005685 SME1 YOR159C|Sm E|SmE taxon:4932
+S000005685 SME1 YOR159C|Sm E|SmE taxon:4932
+S000005685 SME1 YOR159C|Sm E|SmE taxon:4932
+S000005685 SME1 YOR159C|Sm E|SmE taxon:4932
+S000029458 SME2 taxon:4932
+S000029458 SME2 taxon:4932
+S000029458 SME2 taxon:4932
+S000029459 SME3 taxon:4932
+S000029459 SME3 taxon:4932
+S000029459 SME3 taxon:4932
+S000005482 SMF1 YOL122C|SBS1 taxon:4932
+S000005482 SMF1 YOL122C|SBS1 taxon:4932
+S000005482 SMF1 YOL122C|SBS1 taxon:4932
+S000005482 SMF1 YOL122C|SBS1 taxon:4932
+S000005482 SMF1 YOL122C|SBS1 taxon:4932
+S000001092 SMF2 YHR050W taxon:4932
+S000001092 SMF2 YHR050W taxon:4932
+S000001092 SMF2 YHR050W taxon:4932
+S000001092 SMF2 YHR050W taxon:4932
+S000001092 SMF2 YHR050W taxon:4932
+S000001092 SMF2 YHR050W taxon:4932
+S000001092 SMF2 YHR050W taxon:4932
+S000004024 SMF3 YLR034C taxon:4932
+S000004024 SMF3 YLR034C taxon:4932
+S000004024 SMF3 YLR034C taxon:4932
+S000003461 SMI1 YGR229C|KNR4 taxon:4932
+S000003461 SMI1 YGR229C|KNR4 taxon:4932
+S000003461 SMI1 YGR229C|KNR4 taxon:4932
+S000003461 SMI1 YGR229C|KNR4 taxon:4932
+S000003461 SMI1 YGR229C|KNR4 taxon:4932
+S000003461 SMI1 YGR229C|KNR4 taxon:4932
+S000006258 SMK1 YPR054W taxon:4932
+S000006258 SMK1 YPR054W taxon:4932
+S000006258 SMK1 YPR054W taxon:4932
+S000006258 SMK1 YPR054W taxon:4932
+S000004523 SML1 YML058W taxon:4932
+S000004523 SML1 YML058W taxon:4932
+S000004523 SML1 YML058W taxon:4932
+S000004523 SML1 YML058W taxon:4932
+S000004523 SML1 YML058W taxon:4932
+S000005298 SMM1 YNR015W|DUS2 taxon:4932
+S000005298 SMM1 YNR015W|DUS2 taxon:4932
+S000005298 SMM1 YNR015W|DUS2 taxon:4932
+S000005298 SMM1 YNR015W|DUS2 taxon:4932
+S000005298 SMM1 YNR015W|DUS2 taxon:4932
+S000000386 SMP1 YBR182C taxon:4932
+S000000386 SMP1 YBR182C taxon:4932
+S000000386 SMP1 YBR182C taxon:4932
+S000000386 SMP1 YBR182C taxon:4932
+S000000386 SMP1 YBR182C taxon:4932
+S000000386 SMP1 YBR182C taxon:4932
+S000000386 SMP1 YBR182C taxon:4932
+S000000386 SMP1 YBR182C taxon:4932
+S000000386 SMP1 YBR182C taxon:4932
+S000000386 SMP1 YBR182C taxon:4932
+S000005675 SMP3 YOR149C|LAS2|SAP2 taxon:4932
+S000005675 SMP3 YOR149C|LAS2|SAP2 taxon:4932
+S000005675 SMP3 YOR149C|LAS2|SAP2 taxon:4932
+S000005675 SMP3 YOR149C|LAS2|SAP2 taxon:4932
+S000002918 SMT3 YDR510W taxon:4932
+S000002918 SMT3 YDR510W taxon:4932
+S000002918 SMT3 YDR510W taxon:4932
+S000002918 SMT3 YDR510W taxon:4932
+S000002918 SMT3 YDR510W taxon:4932
+S000002918 SMT3 YDR510W taxon:4932
+S000002918 SMT3 YDR510W taxon:4932
+S000002918 SMT3 YDR510W taxon:4932
+S000002965 SMX2 YFL017W-A|SNP2|Sm G|SmG|YFL018W-A taxon:4932
+S000002965 SMX2 YFL017W-A|SNP2|Sm G|SmG|YFL018W-A taxon:4932
+S000002965 SMX2 YFL017W-A|SNP2|Sm G|SmG|YFL018W-A taxon:4932
+S000002965 SMX2 YFL017W-A|SNP2|Sm G|SmG|YFL018W-A taxon:4932
+S000002965 SMX2 YFL017W-A|SNP2|Sm G|SmG|YFL018W-A taxon:4932
+S000002965 SMX2 YFL017W-A|SNP2|Sm G|SmG|YFL018W-A taxon:4932
+S000002965 SMX2 YFL017W-A|SNP2|Sm G|SmG|YFL018W-A taxon:4932
+S000002965 SMX2 YFL017W-A|SNP2|Sm G|SmG|YFL018W-A taxon:4932
+S000006386 SMX3 YPR182W|Sm F|SmF taxon:4932
+S000006386 SMX3 YPR182W|Sm F|SmF taxon:4932
+S000006386 SMX3 YPR182W|Sm F|SmF taxon:4932
+S000006386 SMX3 YPR182W|Sm F|SmF taxon:4932
+S000006386 SMX3 YPR182W|Sm F|SmF taxon:4932
+S000006386 SMX3 YPR182W|Sm F|SmF taxon:4932
+S000006386 SMX3 YPR182W|Sm F|SmF taxon:4932
+S000006386 SMX3 YPR182W|Sm F|SmF taxon:4932
+S000001562 SMY1 YKL079W taxon:4932
+S000001562 SMY1 YKL079W taxon:4932
+S000001562 SMY1 YKL079W taxon:4932
+S000001562 SMY1 YKL079W taxon:4932
+S000000376 SMY2 YBR172C taxon:4932
+S000000376 SMY2 YBR172C taxon:4932
+S000000376 SMY2 YBR172C taxon:4932
+S000007236 SNA2 YDR525W-A taxon:4932
+S000007236 SNA2 YDR525W-A taxon:4932
+S000007236 SNA2 YDR525W-A taxon:4932
+S000007236 SNA2 YDR525W-A taxon:4932
+S000003687 SNA3 YJL151C taxon:4932
+S000003687 SNA3 YJL151C taxon:4932
+S000003687 SNA3 YJL151C taxon:4932
+S000003687 SNA3 YJL151C taxon:4932
+S000002281 SNA4 YDL123W taxon:4932
+S000002281 SNA4 YDL123W taxon:4932
+S000002281 SNA4 YDL123W taxon:4932
+S000000028 SNC1 YAL030W taxon:4932
+S000000028 SNC1 YAL030W taxon:4932
+S000000028 SNC1 YAL030W taxon:4932
+S000000028 SNC1 YAL030W taxon:4932
+S000000028 SNC1 YAL030W taxon:4932
+S000000028 SNC1 YAL030W taxon:4932
+S000000028 SNC1 YAL030W taxon:4932
+S000005854 SNC2 YOR327C taxon:4932
+S000005854 SNC2 YOR327C taxon:4932
+S000005854 SNC2 YOR327C taxon:4932
+S000005854 SNC2 YOR327C taxon:4932
+S000005854 SNC2 YOR327C taxon:4932
+S000005854 SNC2 YOR327C taxon:4932
+S000002885 SNF1 YDR477W|CAT1|CCR1|GLC2|HAF3|PAS14 taxon:4932
+S000002885 SNF1 YDR477W|CAT1|CCR1|GLC2|HAF3|PAS14 taxon:4932
+S000002885 SNF1 YDR477W|CAT1|CCR1|GLC2|HAF3|PAS14 taxon:4932
+S000002885 SNF1 YDR477W|CAT1|CCR1|GLC2|HAF3|PAS14 taxon:4932
+S000002885 SNF1 YDR477W|CAT1|CCR1|GLC2|HAF3|PAS14 taxon:4932
+S000002885 SNF1 YDR477W|CAT1|CCR1|GLC2|HAF3|PAS14 taxon:4932
+S000002885 SNF1 YDR477W|CAT1|CCR1|GLC2|HAF3|PAS14 taxon:4932
+S000002885 SNF1 YDR477W|CAT1|CCR1|GLC2|HAF3|PAS14 taxon:4932
+S000002885 SNF1 YDR477W|CAT1|CCR1|GLC2|HAF3|PAS14 taxon:4932
+S000002885 SNF1 YDR477W|CAT1|CCR1|GLC2|HAF3|PAS14 taxon:4932
+S000002885 SNF1 YDR477W|CAT1|CCR1|GLC2|HAF3|PAS14 taxon:4932
+S000002885 SNF1 YDR477W|CAT1|CCR1|GLC2|HAF3|PAS14 taxon:4932
+S000002885 SNF1 YDR477W|CAT1|CCR1|GLC2|HAF3|PAS14 taxon:4932
+S000002885 SNF1 YDR477W|CAT1|CCR1|GLC2|HAF3|PAS14 taxon:4932
+S000002885 SNF1 YDR477W|CAT1|CCR1|GLC2|HAF3|PAS14 taxon:4932
+S000002480 SNF11 YDR073W taxon:4932
+S000002480 SNF11 YDR073W taxon:4932
+S000002480 SNF11 YDR073W taxon:4932
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+S000001196 SPO16 YHR153C taxon:4932
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+S000006051 SPO19 YPL130W taxon:4932
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+S000005451 SPO21 YOL091W|MPC70 taxon:4932
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+S000001335 SPO22 YIL073C taxon:4932
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+S000000007 SPO7 YAL009W taxon:4932
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+S000000007 SPO7 YAL009W taxon:4932
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+S000003928 SPO75 YLL005C taxon:4932
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+S000006059 SPP1 YPL138C|CPS40|SAF41 taxon:4932
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+S000006059 SPP1 YPL138C|CPS40|SAF41 taxon:4932
+S000006059 SPP1 YPL138C|CPS40|SAF41 taxon:4932
+S000006059 SPP1 YPL138C|CPS40|SAF41 taxon:4932
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+S000006059 SPP1 YPL138C|CPS40|SAF41 taxon:4932
+S000005674 SPP2 YOR148C taxon:4932
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+S000000356 SPP381 YBR152W taxon:4932
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+S000000356 SPP381 YBR152W taxon:4932
+S000000356 SPP381 YBR152W taxon:4932
+S000000356 SPP381 YBR152W taxon:4932
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+S000000356 SPP381 YBR152W taxon:4932
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+S000000356 SPP381 YBR152W taxon:4932
+S000004416 SPP382 YLR424W|CCF8|NTR1 taxon:4932
+S000004416 SPP382 YLR424W|CCF8|NTR1 taxon:4932
+S000004416 SPP382 YLR424W|CCF8|NTR1 taxon:4932
+S000004416 SPP382 YLR424W|CCF8|NTR1 taxon:4932
+S000004416 SPP382 YLR424W|CCF8|NTR1 taxon:4932
+S000004416 SPP382 YLR424W|CCF8|NTR1 taxon:4932
+S000002872 SPP41 YDR464W taxon:4932
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+S000005716 SPR1 YOR190W|SSG1 taxon:4932
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+S000005716 SPR1 YOR190W|SSG1 taxon:4932
+S000002626 SPR28 YDR218C taxon:4932
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+S000003291 SPR3 YGR059W taxon:4932
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+S000003291 SPR3 YGR059W taxon:4932
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+S000000917 SPR6 YER115C taxon:4932
+S000000917 SPR6 YER115C taxon:4932
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+S000002931 SPS1 YDR523C taxon:4932
+S000002931 SPS1 YDR523C taxon:4932
+S000002931 SPS1 YDR523C taxon:4932
+S000002931 SPS1 YDR523C taxon:4932
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+S000002931 SPS1 YDR523C taxon:4932
+S000002931 SPS1 YDR523C taxon:4932
+S000001181 SPS100 YHR139C taxon:4932
+S000001181 SPS100 YHR139C taxon:4932
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+S000001181 SPS100 YHR139C taxon:4932
+S000005148 SPS18 YNL204C|SPX18 taxon:4932
+S000005148 SPS18 YNL204C|SPX18 taxon:4932
+S000005148 SPS18 YNL204C|SPX18 taxon:4932
+S000005146 SPS19 YNL202W|SPX19 taxon:4932
+S000005146 SPS19 YNL202W|SPX19 taxon:4932
+S000005146 SPS19 YNL202W|SPX19 taxon:4932
+S000005146 SPS19 YNL202W|SPX19 taxon:4932
+S000005146 SPS19 YNL202W|SPX19 taxon:4932
+S000005146 SPS19 YNL202W|SPX19 taxon:4932
+S000005146 SPS19 YNL202W|SPX19 taxon:4932
+S000002930 SPS2 YDR522C taxon:4932
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+S000000553 SPS22 YCL048W taxon:4932
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+S000000553 SPS22 YCL048W taxon:4932
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+S000005840 SPS4 YOR313C taxon:4932
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+S000005840 SPS4 YOR313C taxon:4932
+S000005840 SPS4 YOR313C taxon:4932
+S000005840 SPS4 YOR313C taxon:4932
+S000003663 SPT10 YJL127C|CRE1|SUD1 taxon:4932
+S000003663 SPT10 YJL127C|CRE1|SUD1 taxon:4932
+S000003663 SPT10 YJL127C|CRE1|SUD1 taxon:4932
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+S000006096 SPT14 YPL175W|CWH6|GPI3 taxon:4932
+S000006096 SPT14 YPL175W|CWH6|GPI3 taxon:4932
+S000006096 SPT14 YPL175W|CWH6|GPI3 taxon:4932
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+S000000950 SPT15 YER148W|BTF1|TBP|TBP1 taxon:4932
+S000000950 SPT15 YER148W|BTF1|TBP|TBP1 taxon:4932
+S000000950 SPT15 YER148W|BTF1|TBP|TBP1 taxon:4932
+S000000950 SPT15 YER148W|BTF1|TBP|TBP1 taxon:4932
+S000000950 SPT15 YER148W|BTF1|TBP|TBP1 taxon:4932
+S000000950 SPT15 YER148W|BTF1|TBP|TBP1 taxon:4932
+S000000950 SPT15 YER148W|BTF1|TBP|TBP1 taxon:4932
+S000000950 SPT15 YER148W|BTF1|TBP|TBP1 taxon:4932
+S000000950 SPT15 YER148W|BTF1|TBP|TBP1 taxon:4932
+S000000950 SPT15 YER148W|BTF1|TBP|TBP1 taxon:4932
+S000000950 SPT15 YER148W|BTF1|TBP|TBP1 taxon:4932
+S000000950 SPT15 YER148W|BTF1|TBP|TBP1 taxon:4932
+S000000950 SPT15 YER148W|BTF1|TBP|TBP1 taxon:4932
+S000000950 SPT15 YER148W|BTF1|TBP|TBP1 taxon:4932
+S000000950 SPT15 YER148W|BTF1|TBP|TBP1 taxon:4932
+S000000950 SPT15 YER148W|BTF1|TBP|TBP1 taxon:4932
+S000000950 SPT15 YER148W|BTF1|TBP|TBP1 taxon:4932
+S000000950 SPT15 YER148W|BTF1|TBP|TBP1 taxon:4932
+S000000950 SPT15 YER148W|BTF1|TBP|TBP1 taxon:4932
+S000000950 SPT15 YER148W|BTF1|TBP|TBP1 taxon:4932
+S000000950 SPT15 YER148W|BTF1|TBP|TBP1 taxon:4932
+S000000950 SPT15 YER148W|BTF1|TBP|TBP1 taxon:4932
+S000000950 SPT15 YER148W|BTF1|TBP|TBP1 taxon:4932
+S000000950 SPT15 YER148W|BTF1|TBP|TBP1 taxon:4932
+S000003175 SPT16 YGL207W|CDC68|SSF1 taxon:4932
+S000003175 SPT16 YGL207W|CDC68|SSF1 taxon:4932
+S000003175 SPT16 YGL207W|CDC68|SSF1 taxon:4932
+S000003175 SPT16 YGL207W|CDC68|SSF1 taxon:4932
+S000003175 SPT16 YGL207W|CDC68|SSF1 taxon:4932
+S000003175 SPT16 YGL207W|CDC68|SSF1 taxon:4932
+S000003175 SPT16 YGL207W|CDC68|SSF1 taxon:4932
+S000003175 SPT16 YGL207W|CDC68|SSF1 taxon:4932
+S000003175 SPT16 YGL207W|CDC68|SSF1 taxon:4932
+S000003175 SPT16 YGL207W|CDC68|SSF1 taxon:4932
+S000003175 SPT16 YGL207W|CDC68|SSF1 taxon:4932
+S000003175 SPT16 YGL207W|CDC68|SSF1 taxon:4932
+S000000963 SPT2 YER161C|EXA1|SIN1 taxon:4932
+S000000963 SPT2 YER161C|EXA1|SIN1 taxon:4932
+S000000963 SPT2 YER161C|EXA1|SIN1 taxon:4932
+S000005508 SPT20 YOL148C|ADA5 taxon:4932
+S000005508 SPT20 YOL148C|ADA5 taxon:4932
+S000005508 SPT20 YOL148C|ADA5 taxon:4932
+S000005508 SPT20 YOL148C|ADA5 taxon:4932
+S000005508 SPT20 YOL148C|ADA5 taxon:4932
+S000005508 SPT20 YOL148C|ADA5 taxon:4932
+S000005508 SPT20 YOL148C|ADA5 taxon:4932
+S000004791 SPT21 YMR179W taxon:4932
+S000004791 SPT21 YMR179W taxon:4932
+S000004791 SPT21 YMR179W taxon:4932
+S000004791 SPT21 YMR179W taxon:4932
+S000001503 SPT23 YKL020C taxon:4932
+S000001503 SPT23 YKL020C taxon:4932
+S000001503 SPT23 YKL020C taxon:4932
+S000001503 SPT23 YKL020C taxon:4932
+S000001503 SPT23 YKL020C taxon:4932
+S000001503 SPT23 YKL020C taxon:4932
+S000001503 SPT23 YKL020C taxon:4932
+S000001503 SPT23 YKL020C taxon:4932
+S000001503 SPT23 YKL020C taxon:4932
+S000002800 SPT3 YDR392W taxon:4932
+S000002800 SPT3 YDR392W taxon:4932
+S000002800 SPT3 YDR392W taxon:4932
+S000002800 SPT3 YDR392W taxon:4932
+S000002800 SPT3 YDR392W taxon:4932
+S000002800 SPT3 YDR392W taxon:4932
+S000002800 SPT3 YDR392W taxon:4932
+S000002800 SPT3 YDR392W taxon:4932
+S000002800 SPT3 YDR392W taxon:4932
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+S000003295 SPT4 YGR063C taxon:4932
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+S000003295 SPT4 YGR063C taxon:4932
+S000003295 SPT4 YGR063C taxon:4932
+S000003295 SPT4 YGR063C taxon:4932
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+S000003295 SPT4 YGR063C taxon:4932
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+S000003295 SPT4 YGR063C taxon:4932
+S000003295 SPT4 YGR063C taxon:4932
+S000003295 SPT4 YGR063C taxon:4932
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+S000004470 SPT5 YML010W taxon:4932
+S000004470 SPT5 YML010W taxon:4932
+S000004470 SPT5 YML010W taxon:4932
+S000004470 SPT5 YML010W taxon:4932
+S000004470 SPT5 YML010W taxon:4932
+S000004470 SPT5 YML010W taxon:4932
+S000004470 SPT5 YML010W taxon:4932
+S000004470 SPT5 YML010W taxon:4932
+S000004470 SPT5 YML010W taxon:4932
+S000004470 SPT5 YML010W taxon:4932
+S000004470 SPT5 YML010W taxon:4932
+S000004470 SPT5 YML010W taxon:4932
+S000003348 SPT6 YGR116W|CRE2|SSN20 taxon:4932
+S000003348 SPT6 YGR116W|CRE2|SSN20 taxon:4932
+S000003348 SPT6 YGR116W|CRE2|SSN20 taxon:4932
+S000003348 SPT6 YGR116W|CRE2|SSN20 taxon:4932
+S000003348 SPT6 YGR116W|CRE2|SSN20 taxon:4932
+S000003348 SPT6 YGR116W|CRE2|SSN20 taxon:4932
+S000003348 SPT6 YGR116W|CRE2|SSN20 taxon:4932
+S000003348 SPT6 YGR116W|CRE2|SSN20 taxon:4932
+S000000285 SPT7 YBR081C|GIT2 taxon:4932
+S000000285 SPT7 YBR081C|GIT2 taxon:4932
+S000000285 SPT7 YBR081C|GIT2 taxon:4932
+S000000285 SPT7 YBR081C|GIT2 taxon:4932
+S000000285 SPT7 YBR081C|GIT2 taxon:4932
+S000000285 SPT7 YBR081C|GIT2 taxon:4932
+S000000285 SPT7 YBR081C|GIT2 taxon:4932
+S000000285 SPT7 YBR081C|GIT2 taxon:4932
+S000000285 SPT7 YBR081C|GIT2 taxon:4932
+S000000285 SPT7 YBR081C|GIT2 taxon:4932
+S000004045 SPT8 YLR055C taxon:4932
+S000004045 SPT8 YLR055C taxon:4932
+S000004045 SPT8 YLR055C taxon:4932
+S000004045 SPT8 YLR055C taxon:4932
+S000004045 SPT8 YLR055C taxon:4932
+S000004045 SPT8 YLR055C taxon:4932
+S000001451 SQT1 YIR012W taxon:4932
+S000001451 SQT1 YIR012W taxon:4932
+S000001451 SQT1 YIR012W taxon:4932
+S000001451 SQT1 YIR012W taxon:4932
+S000001451 SQT1 YIR012W taxon:4932
+S000001451 SQT1 YIR012W taxon:4932
+S000001083 SRB2 YHR041C|HRS2|MED20 taxon:4932
+S000001083 SRB2 YHR041C|HRS2|MED20 taxon:4932
+S000001083 SRB2 YHR041C|HRS2|MED20 taxon:4932
+S000001083 SRB2 YHR041C|HRS2|MED20 taxon:4932
+S000000824 SRB4 YER022W|MED17 taxon:4932
+S000000824 SRB4 YER022W|MED17 taxon:4932
+S000000824 SRB4 YER022W|MED17 taxon:4932
+S000003336 SRB5 YGR104C|MED18 taxon:4932
+S000003336 SRB5 YGR104C|MED18 taxon:4932
+S000003336 SRB5 YGR104C|MED18 taxon:4932
+S000003336 SRB5 YGR104C|MED18 taxon:4932
+S000000457 SRB6 YBR253W|MED22 taxon:4932
+S000000457 SRB6 YBR253W|MED22 taxon:4932
+S000000457 SRB6 YBR253W|MED22 taxon:4932
+S000002716 SRB7 YDR308C|MED21 taxon:4932
+S000002716 SRB7 YDR308C|MED21 taxon:4932
+S000002716 SRB7 YDR308C|MED21 taxon:4932
+S000000677 SRB8 YCR081W|GIG1|MED12|NUT6|SSN5|YCR080W taxon:4932
+S000000677 SRB8 YCR081W|GIG1|MED12|NUT6|SSN5|YCR080W taxon:4932
+S000000677 SRB8 YCR081W|GIG1|MED12|NUT6|SSN5|YCR080W taxon:4932
+S000004497 SRC1 YML034W|YML033W taxon:4932
+S000004497 SRC1 YML034W|YML033W taxon:4932
+S000004497 SRC1 YML034W|YML033W taxon:4932
+S000000611 SRD1 YCR018C taxon:4932
+S000000611 SRD1 YCR018C taxon:4932
+S000000611 SRD1 YCR018C taxon:4932
+S000000611 SRD1 YCR018C taxon:4932
+S000029010 SRG1 taxon:4932
+S000029010 SRG1 taxon:4932
+S000029010 SRG1 taxon:4932
+S000029010 SRG1 taxon:4932
+S000005773 SRL1 YOR247W taxon:4932
+S000005773 SRL1 YOR247W taxon:4932
+S000005773 SRL1 YOR247W taxon:4932
+S000005773 SRL1 YOR247W taxon:4932
+S000005773 SRL1 YOR247W taxon:4932
+S000005773 SRL1 YOR247W taxon:4932
+S000004072 SRL2 YLR082C taxon:4932
+S000004072 SRL2 YLR082C taxon:4932
+S000004072 SRL2 YLR082C taxon:4932
+S000004072 SRL2 YLR082C taxon:4932
+S000001799 SRL3 YKR091W taxon:4932
+S000001799 SRL3 YKR091W taxon:4932
+S000001799 SRL3 YKR091W taxon:4932
+S000003065 SRM1 YGL097W|MTR1|PRP20 taxon:4932
+S000003065 SRM1 YGL097W|MTR1|PRP20 taxon:4932
+S000003065 SRM1 YGL097W|MTR1|PRP20 taxon:4932
+S000003065 SRM1 YGL097W|MTR1|PRP20 taxon:4932
+S000003065 SRM1 YGL097W|MTR1|PRP20 taxon:4932
+S000004109 SRN2 YLR119W|SRN10|VPS37 taxon:4932
+S000004109 SRN2 YLR119W|SRN10|VPS37 taxon:4932
+S000004109 SRN2 YLR119W|SRN10|VPS37 taxon:4932
+S000004109 SRN2 YLR119W|SRN10|VPS37 taxon:4932
+S000004109 SRN2 YLR119W|SRN10|VPS37 taxon:4932
+S000004109 SRN2 YLR119W|SRN10|VPS37 taxon:4932
+S000004109 SRN2 YLR119W|SRN10|VPS37 taxon:4932
+S000004109 SRN2 YLR119W|SRN10|VPS37 taxon:4932
+S000004109 SRN2 YLR119W|SRN10|VPS37 taxon:4932
+S000006236 SRO7 YPR032W|SNI1|SOP1 taxon:4932
+S000006236 SRO7 YPR032W|SNI1|SOP1 taxon:4932
+S000006236 SRO7 YPR032W|SNI1|SOP1 taxon:4932
+S000006236 SRO7 YPR032W|SNI1|SOP1 taxon:4932
+S000006236 SRO7 YPR032W|SNI1|SOP1 taxon:4932
+S000006236 SRO7 YPR032W|SNI1|SOP1 taxon:4932
+S000006236 SRO7 YPR032W|SNI1|SOP1 taxon:4932
+S000006236 SRO7 YPR032W|SNI1|SOP1 taxon:4932
+S000000202 SRO77 YBL106C|SNI2|SOP2 taxon:4932
+S000000202 SRO77 YBL106C|SNI2|SOP2 taxon:4932
+S000000202 SRO77 YBL106C|SNI2|SOP2 taxon:4932
+S000000202 SRO77 YBL106C|SNI2|SOP2 taxon:4932
+S000000202 SRO77 YBL106C|SNI2|SOP2 taxon:4932
+S000000202 SRO77 YBL106C|SNI2|SOP2 taxon:4932
+S000000542 SRO9 YCL037C taxon:4932
+S000000542 SRO9 YCL037C taxon:4932
+S000000542 SRO9 YCL037C taxon:4932
+S000005133 SRP1 YNL189W|KAP60|SCM1 taxon:4932
+S000005133 SRP1 YNL189W|KAP60|SCM1 taxon:4932
+S000005133 SRP1 YNL189W|KAP60|SCM1 taxon:4932
+S000005133 SRP1 YNL189W|KAP60|SCM1 taxon:4932
+S000005133 SRP1 YNL189W|KAP60|SCM1 taxon:4932
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+S000002700 SRP101 YDR292C taxon:4932
+S000002700 SRP101 YDR292C taxon:4932
+S000002700 SRP101 YDR292C taxon:4932
+S000002700 SRP101 YDR292C taxon:4932
+S000002700 SRP101 YDR292C taxon:4932
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+S000001637 SRP102 YKL154W taxon:4932
+S000001637 SRP102 YKL154W taxon:4932
+S000001637 SRP102 YKL154W taxon:4932
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+S000001405 SSL2 YIL143C|LOM3|RAD25 taxon:4932
+S000001405 SSL2 YIL143C|LOM3|RAD25 taxon:4932
+S000001405 SSL2 YIL143C|LOM3|RAD25 taxon:4932
+S000001405 SSL2 YIL143C|LOM3|RAD25 taxon:4932
+S000001405 SSL2 YIL143C|LOM3|RAD25 taxon:4932
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+S000001292 SSM4 YIL030C|DOA10 taxon:4932
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+S000001292 SSM4 YIL030C|DOA10 taxon:4932
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+S000005963 SSN3 YPL042C|CDK8|GIG2|NUT7|RYE5|SRB10|UME5 taxon:4932
+S000005963 SSN3 YPL042C|CDK8|GIG2|NUT7|RYE5|SRB10|UME5 taxon:4932
+S000005963 SSN3 YPL042C|CDK8|GIG2|NUT7|RYE5|SRB10|UME5 taxon:4932
+S000005963 SSN3 YPL042C|CDK8|GIG2|NUT7|RYE5|SRB10|UME5 taxon:4932
+S000005963 SSN3 YPL042C|CDK8|GIG2|NUT7|RYE5|SRB10|UME5 taxon:4932
+S000004970 SSN8 YNL025C|CycC|GIG3|NUT9|RYE2|SRB11|UME3 taxon:4932
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+S000001227 SSP1 YHR184W|SPO3 taxon:4932
+S000001227 SSP1 YHR184W|SPO3 taxon:4932
+S000001227 SSP1 YHR184W|SPO3 taxon:4932
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+S000005768 SSP2 YOR242C taxon:4932
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+S000004361 SSQ1 YLR369W|SSC2 taxon:4932
+S000004361 SSQ1 YLR369W|SSC2 taxon:4932
+S000004361 SSQ1 YLR369W|SSC2 taxon:4932
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+S000006013 SSU1 YPL092W|LPG16 taxon:4932
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+S000002567 SSY1 YDR160W|SHR10 taxon:4932
+S000002567 SSY1 YDR160W|SHR10 taxon:4932
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+S000001106 SSZ1 YHR064C|PDR13 taxon:4932
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+S000001106 SSZ1 YHR064C|PDR13 taxon:4932
+S000001106 SSZ1 YHR064C|PDR13 taxon:4932
+S000001106 SSZ1 YHR064C|PDR13 taxon:4932
+S000001106 SSZ1 YHR064C|PDR13 taxon:4932
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+S000029522 STA1 DEX2|MAL5 taxon:4932
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+S000004354 STE11 YLR362W taxon:4932
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+S000004354 STE11 YLR362W taxon:4932
+S000004354 STE11 YLR362W taxon:4932
+S000004354 STE11 YLR362W taxon:4932
+S000004354 STE11 YLR362W taxon:4932
+S000001126 STE12 YHR084W taxon:4932
+S000001126 STE12 YHR084W taxon:4932
+S000001126 STE12 YHR084W taxon:4932
+S000001126 STE12 YHR084W taxon:4932
+S000001126 STE12 YHR084W taxon:4932
+S000001126 STE12 YHR084W taxon:4932
+S000005745 STE13 YOR219C|YCI1|yscIV taxon:4932
+S000005745 STE13 YOR219C|YCI1|yscIV taxon:4932
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+S000003424 TDH3 YGR192C|GLD1|HSP35|HSP36|SSS2 taxon:4932
+S000003424 TDH3 YGR192C|GLD1|HSP35|HSP36|SSS2 taxon:4932
+S000003424 TDH3 YGR192C|GLD1|HSP35|HSP36|SSS2 taxon:4932
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+S000000287 TEC1 YBR083W|ROC1 taxon:4932
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+S000000184 TEL1 YBL088C taxon:4932
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+S000000001 TFC3 YAL001C|FUN24|TSV115 taxon:4932
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+S000006155 TFP3 YPL234C|CLS9|VMA11 taxon:4932
+S000006155 TFP3 YPL234C|CLS9|VMA11 taxon:4932
+S000006155 TFP3 YPL234C|CLS9|VMA11 taxon:4932
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+S000004168 TFS1 YLR178C|DKA1 taxon:4932
+S000004168 TFS1 YLR178C|DKA1 taxon:4932
+S000004168 TFS1 YLR178C|DKA1 taxon:4932
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+S000001623 TGL1 YKL140W|YKL5 taxon:4932
+S000001623 TGL1 YKL140W|YKL5 taxon:4932
+S000001623 TGL1 YKL140W|YKL5 taxon:4932
+S000001623 TGL1 YKL140W|YKL5 taxon:4932
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+S000001797 TGL4 YKR089C|STC1 taxon:4932
+S000001797 TGL4 YKR089C|STC1 taxon:4932
+S000001797 TGL4 YKR089C|STC1 taxon:4932
+S000001797 TGL4 YKR089C|STC1 taxon:4932
+S000001797 TGL4 YKR089C|STC1 taxon:4932
+S000001797 TGL4 YKR089C|STC1 taxon:4932
+S000001797 TGL4 YKR089C|STC1 taxon:4932
+S000001797 TGL4 YKR089C|STC1 taxon:4932
+S000001797 TGL4 YKR089C|STC1 taxon:4932
+S000005607 TGL5 YOR081C|STC2 taxon:4932
+S000005607 TGL5 YOR081C|STC2 taxon:4932
+S000005607 TGL5 YOR081C|STC2 taxon:4932
+S000005607 TGL5 YOR081C|STC2 taxon:4932
+S000005607 TGL5 YOR081C|STC2 taxon:4932
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+S000000444 THI2 YBR240C|PHO6 taxon:4932
+S000000444 THI2 YBR240C|PHO6 taxon:4932
+S000000444 THI2 YBR240C|PHO6 taxon:4932
+S000000444 THI2 YBR240C|PHO6 taxon:4932
+S000000444 THI2 YBR240C|PHO6 taxon:4932
+S000000444 THI2 YBR240C|PHO6 taxon:4932
+S000000444 THI2 YBR240C|PHO6 taxon:4932
+S000000444 THI2 YBR240C|PHO6 taxon:4932
+S000000444 THI2 YBR240C|PHO6 taxon:4932
+S000005416 THI20 YOL055C taxon:4932
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+S000006179 THI21 YPL258C taxon:4932
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+S000002238 THI3 YDL080C|KID1 taxon:4932
+S000002238 THI3 YDL080C|KID1 taxon:4932
+S000002238 THI3 YDL080C|KID1 taxon:4932
+S000002238 THI3 YDL080C|KID1 taxon:4932
+S000002238 THI3 YDL080C|KID1 taxon:4932
+S000002238 THI3 YDL080C|KID1 taxon:4932
+S000002238 THI3 YDL080C|KID1 taxon:4932
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+S000003376 THI4 YGR144W|ESP35|MOL1 taxon:4932
+S000003376 THI4 YGR144W|ESP35|MOL1 taxon:4932
+S000003376 THI4 YGR144W|ESP35|MOL1 taxon:4932
+S000003376 THI4 YGR144W|ESP35|MOL1 taxon:4932
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+S000004227 THI7 YLR237W|THI10 taxon:4932
+S000004227 THI7 YLR237W|THI10 taxon:4932
+S000004227 THI7 YLR237W|THI10 taxon:4932
+S000004227 THI7 YLR237W|THI10 taxon:4932
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+S000005669 THI80 YOR143C taxon:4932
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+S000005433 THP1 YOL072W|BUD29 taxon:4932
+S000005433 THP1 YOL072W|BUD29 taxon:4932
+S000005433 THP1 YOL072W|BUD29 taxon:4932
+S000005433 THP1 YOL072W|BUD29 taxon:4932
+S000005433 THP1 YOL072W|BUD29 taxon:4932
+S000005433 THP1 YOL072W|BUD29 taxon:4932
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+S000001210 THP2 YHR167W taxon:4932
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+S000001067 THR1 YHR025W taxon:4932
+S000001067 THR1 YHR025W taxon:4932
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+S000001340 THS1 YIL078W taxon:4932
+S000001340 THS1 YIL078W taxon:4932
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+S000001406 TID3 YIL144W|HEC1|NDC80 taxon:4932
+S000001406 TID3 YIL144W|HEC1|NDC80 taxon:4932
+S000001406 TID3 YIL144W|HEC1|NDC80 taxon:4932
+S000001406 TID3 YIL144W|HEC1|NDC80 taxon:4932
+S000001406 TID3 YIL144W|HEC1|NDC80 taxon:4932
+S000001406 TID3 YIL144W|HEC1|NDC80 taxon:4932
+S000001406 TID3 YIL144W|HEC1|NDC80 taxon:4932
+S000001406 TID3 YIL144W|HEC1|NDC80 taxon:4932
+S000001406 TID3 YIL144W|HEC1|NDC80 taxon:4932
+S000001406 TID3 YIL144W|HEC1|NDC80 taxon:4932
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+S000029631 URR1 taxon:4932
+S000029631 URR1 taxon:4932
+S000029631 URR1 taxon:4932
+S000029632 URR3 taxon:4932
+S000029632 URR3 taxon:4932
+S000029632 URR3 taxon:4932
+S000029633 URR4 taxon:4932
+S000029633 URR4 taxon:4932
+S000029633 URR4 taxon:4932
+S000004491 USA1 YML029W taxon:4932
+S000004491 USA1 YML029W taxon:4932
+S000004491 USA1 YML029W taxon:4932
+S000003066 USE1 YGL098W|SLT1 taxon:4932
+S000003066 USE1 YGL098W|SLT1 taxon:4932
+S000003066 USE1 YGL098W|SLT1 taxon:4932
+S000003066 USE1 YGL098W|SLT1 taxon:4932
+S000003066 USE1 YGL098W|SLT1 taxon:4932
+S000003066 USE1 YGL098W|SLT1 taxon:4932
+S000003066 USE1 YGL098W|SLT1 taxon:4932
+S000002216 USO1 YDL058W|INT1 taxon:4932
+S000002216 USO1 YDL058W|INT1 taxon:4932
+S000002216 USO1 YDL058W|INT1 taxon:4932
+S000002216 USO1 YDL058W|INT1 taxon:4932
+S000001750 UTH1 YKR042W taxon:4932
+S000001750 UTH1 YKR042W taxon:4932
+S000001750 UTH1 YKR042W taxon:4932
+S000001750 UTH1 YKR042W taxon:4932
+S000001750 UTH1 YKR042W taxon:4932
+S000003645 UTP10 YJL109C taxon:4932
+S000003645 UTP10 YJL109C taxon:4932
+S000003645 UTP10 YJL109C taxon:4932
+S000003645 UTP10 YJL109C taxon:4932
+S000003645 UTP10 YJL109C taxon:4932
+S000001582 UTP11 YKL099C taxon:4932
+S000001582 UTP11 YKL099C taxon:4932
+S000001582 UTP11 YKL099C taxon:4932
+S000001582 UTP11 YKL099C taxon:4932
+S000004212 UTP13 YLR222C taxon:4932
+S000004212 UTP13 YLR222C taxon:4932
+S000004212 UTP13 YLR222C taxon:4932
+S000004212 UTP13 YLR222C taxon:4932
+S000004558 UTP14 YML093W taxon:4932
+S000004558 UTP14 YML093W taxon:4932
+S000004558 UTP14 YML093W taxon:4932
+S000004558 UTP14 YML093W taxon:4932
+S000004699 UTP15 YMR093W taxon:4932
+S000004699 UTP15 YMR093W taxon:4932
+S000004699 UTP15 YMR093W taxon:4932
+S000004699 UTP15 YMR093W taxon:4932
+S000003605 UTP18 YJL069C taxon:4932
+S000003605 UTP18 YJL069C taxon:4932
+S000003605 UTP18 YJL069C taxon:4932
+S000003605 UTP18 YJL069C taxon:4932
+S000003605 UTP18 YJL069C taxon:4932
+S000003605 UTP18 YJL069C taxon:4932
+S000000100 UTP20 YBL004W taxon:4932
+S000000100 UTP20 YBL004W taxon:4932
+S000000100 UTP20 YBL004W taxon:4932
+S000000100 UTP20 YBL004W taxon:4932
+S000000100 UTP20 YBL004W taxon:4932
+S000000100 UTP20 YBL004W taxon:4932
+S000000100 UTP20 YBL004W taxon:4932
+S000004401 UTP21 YLR409C taxon:4932
+S000004401 UTP21 YLR409C taxon:4932
+S000004401 UTP21 YLR409C taxon:4932
+S000004401 UTP21 YLR409C taxon:4932
+S000004401 UTP21 YLR409C taxon:4932
+S000004401 UTP21 YLR409C taxon:4932
+S000003322 UTP22 YGR090W taxon:4932
+S000003322 UTP22 YGR090W taxon:4932
+S000003322 UTP22 YGR090W taxon:4932
+S000003322 UTP22 YGR090W taxon:4932
+S000003322 UTP22 YGR090W taxon:4932
+S000003322 UTP22 YGR090W taxon:4932
+S000003322 UTP22 YGR090W taxon:4932
+S000005530 UTP23 YOR004W taxon:4932
+S000005530 UTP23 YOR004W taxon:4932
+S000005530 UTP23 YOR004W taxon:4932
+S000005530 UTP23 YOR004W taxon:4932
+S000005530 UTP23 YOR004W taxon:4932
+S000001768 UTP30 YKR060W taxon:4932
+S000001768 UTP30 YKR060W taxon:4932
+S000001768 UTP30 YKR060W taxon:4932
+S000001768 UTP30 YKR060W taxon:4932
+S000002732 UTP4 YDR324C taxon:4932
+S000002732 UTP4 YDR324C taxon:4932
+S000002732 UTP4 YDR324C taxon:4932
+S000002732 UTP4 YDR324C taxon:4932
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+S000002806 UTP5 YDR398W taxon:4932
+S000002806 UTP5 YDR398W taxon:4932
+S000002806 UTP5 YDR398W taxon:4932
+S000002857 UTP6 YDR449C taxon:4932
+S000002857 UTP6 YDR449C taxon:4932
+S000002857 UTP6 YDR449C taxon:4932
+S000002857 UTP6 YDR449C taxon:4932
+S000000884 UTP7 YER082C|KRE31 taxon:4932
+S000000884 UTP7 YER082C|KRE31 taxon:4932
+S000000884 UTP7 YER082C|KRE31 taxon:4932
+S000000884 UTP7 YER082C|KRE31 taxon:4932
+S000000884 UTP7 YER082C|KRE31 taxon:4932
+S000003360 UTP8 YGR128C taxon:4932
+S000003360 UTP8 YGR128C taxon:4932
+S000003360 UTP8 YGR128C taxon:4932
+S000003360 UTP8 YGR128C taxon:4932
+S000001239 UTP9 YHR196W taxon:4932
+S000001239 UTP9 YHR196W taxon:4932
+S000001239 UTP9 YHR196W taxon:4932
+S000001239 UTP9 YHR196W taxon:4932
+S000001239 UTP9 YHR196W taxon:4932
+S000001239 UTP9 YHR196W taxon:4932
+S000003810 UTR1 YJR049C taxon:4932
+S000003810 UTR1 YJR049C taxon:4932
+S000003810 UTR1 YJR049C taxon:4932
+S000003810 UTR1 YJR049C taxon:4932
+S000003810 UTR1 YJR049C taxon:4932
+S000003810 UTR1 YJR049C taxon:4932
+S000003810 UTR1 YJR049C taxon:4932
+S000000766 UTR2 YEL040W|CRH2 taxon:4932
+S000000766 UTR2 YEL040W|CRH2 taxon:4932
+S000000766 UTR2 YEL040W|CRH2 taxon:4932
+S000000766 UTR2 YEL040W|CRH2 taxon:4932
+S000000766 UTR2 YEL040W|CRH2 taxon:4932
+S000000764 UTR4 YEL038W taxon:4932
+S000000764 UTR4 YEL038W taxon:4932
+S000000764 UTR4 YEL038W taxon:4932
+S000000764 UTR4 YEL038W taxon:4932
+S000000761 UTR5 YEL035C taxon:4932
+S000000761 UTR5 YEL035C taxon:4932
+S000000761 UTR5 YEL035C taxon:4932
+S000000731 VAB2 YEL005C|VAB31 taxon:4932
+S000000731 VAB2 YEL005C|VAB31 taxon:4932
+S000000731 VAB2 YEL005C|VAB31 taxon:4932
+S000004378 VAC14 YLR386W taxon:4932
+S000004378 VAC14 YLR386W taxon:4932
+S000004378 VAC14 YLR386W taxon:4932
+S000004378 VAC14 YLR386W taxon:4932
+S000004378 VAC14 YLR386W taxon:4932
+S000004378 VAC14 YLR386W taxon:4932
+S000000568 VAC17 YCL063W taxon:4932
+S000000568 VAC17 YCL063W taxon:4932
+S000000568 VAC17 YCL063W taxon:4932
+S000004999 VAC7 YNL054W taxon:4932
+S000004999 VAC7 YNL054W taxon:4932
+S000004999 VAC7 YNL054W taxon:4932
+S000004999 VAC7 YNL054W taxon:4932
+S000004999 VAC7 YNL054W taxon:4932
+S000004999 VAC7 YNL054W taxon:4932
+S000004999 VAC7 YNL054W taxon:4932
+S000000739 VAC8 YEL013W|YEB3 taxon:4932
+S000000739 VAC8 YEL013W|YEB3 taxon:4932
+S000000739 VAC8 YEL013W|YEB3 taxon:4932
+S000000739 VAC8 YEL013W|YEB3 taxon:4932
+S000000739 VAC8 YEL013W|YEB3 taxon:4932
+S000000739 VAC8 YEL013W|YEB3 taxon:4932
+S000000739 VAC8 YEL013W|YEB3 taxon:4932
+S000029635 VAL1 taxon:4932
+S000029635 VAL1 taxon:4932
+S000029635 VAL1 taxon:4932
+S000005594 VAM10 YOR068C|YOR29-19 taxon:4932
+S000005594 VAM10 YOR068C|YOR29-19 taxon:4932
+S000005594 VAM10 YOR068C|YOR29-19 taxon:4932
+S000005632 VAM3 YOR106W|PTH1 taxon:4932
+S000005632 VAM3 YOR106W|PTH1 taxon:4932
+S000005632 VAM3 YOR106W|PTH1 taxon:4932
+S000005632 VAM3 YOR106W|PTH1 taxon:4932
+S000002235 VAM6 YDL077C|CVT4|VPL18|VPL22|VPS39 taxon:4932
+S000002235 VAM6 YDL077C|CVT4|VPL18|VPL22|VPS39 taxon:4932
+S000002235 VAM6 YDL077C|CVT4|VPL18|VPL22|VPS39 taxon:4932
+S000002235 VAM6 YDL077C|CVT4|VPL18|VPL22|VPS39 taxon:4932
+S000002235 VAM6 YDL077C|CVT4|VPL18|VPL22|VPS39 taxon:4932
+S000002235 VAM6 YDL077C|CVT4|VPL18|VPL22|VPS39 taxon:4932
+S000002235 VAM6 YDL077C|CVT4|VPL18|VPL22|VPS39 taxon:4932
+S000002235 VAM6 YDL077C|CVT4|VPL18|VPL22|VPS39 taxon:4932
+S000003180 VAM7 YGL212W|VPS43 taxon:4932
+S000003180 VAM7 YGL212W|VPS43 taxon:4932
+S000003180 VAM7 YGL212W|VPS43 taxon:4932
+S000003180 VAM7 YGL212W|VPS43 taxon:4932
+S000003180 VAM7 YGL212W|VPS43 taxon:4932
+S000004583 VAN1 YML115C|LDB13|VRG7|VRG8 taxon:4932
+S000004583 VAN1 YML115C|LDB13|VRG7|VRG8 taxon:4932
+S000004583 VAN1 YML115C|LDB13|VRG7|VRG8 taxon:4932
+S000004583 VAN1 YML115C|LDB13|VRG7|VRG8 taxon:4932
+S000004583 VAN1 YML115C|LDB13|VRG7|VRG8 taxon:4932
+S000004583 VAN1 YML115C|LDB13|VRG7|VRG8 taxon:4932
+S000007275 VAR1 Q0140|VARI taxon:4932
+S000007275 VAR1 Q0140|VARI taxon:4932
+S000007275 VAR1 Q0140|VARI taxon:4932
+S000007275 VAR1 Q0140|VARI taxon:4932
+S000007275 VAR1 Q0140|VARI taxon:4932
+S000007275 VAR1 Q0140|VARI taxon:4932
+S000007275 VAR1 Q0140|VARI taxon:4932
+S000003326 VAS1 YGR094W taxon:4932
+S000003326 VAS1 YGR094W taxon:4932
+S000003326 VAS1 YGR094W taxon:4932
+S000003326 VAS1 YGR094W taxon:4932
+S000003326 VAS1 YGR094W taxon:4932
+S000004694 VBA1 YMR088C taxon:4932
+S000004694 VBA1 YMR088C taxon:4932
+S000004694 VBA1 YMR088C taxon:4932
+S000004694 VBA1 YMR088C taxon:4932
+S000000497 VBA2 YBR293W taxon:4932
+S000000497 VBA2 YBR293W taxon:4932
+S000000497 VBA2 YBR293W taxon:4932
+S000000497 VBA2 YBR293W taxon:4932
+S000000497 VBA2 YBR293W taxon:4932
+S000000574 VBA3 YCL069W taxon:4932
+S000000574 VBA3 YCL069W taxon:4932
+S000000574 VBA3 YCL069W taxon:4932
+S000000574 VBA3 YCL069W taxon:4932
+S000002286 VCX1 YDL128W|HUM1|MNR1 taxon:4932
+S000002286 VCX1 YDL128W|HUM1|MNR1 taxon:4932
+S000002286 VCX1 YDL128W|HUM1|MNR1 taxon:4932
+S000002286 VCX1 YDL128W|HUM1|MNR1 taxon:4932
+S000002286 VCX1 YDL128W|HUM1|MNR1 taxon:4932
+S000002286 VCX1 YDL128W|HUM1|MNR1 taxon:4932
+S000002286 VCX1 YDL128W|HUM1|MNR1 taxon:4932
+S000002286 VCX1 YDL128W|HUM1|MNR1 taxon:4932
+S000002286 VCX1 YDL128W|HUM1|MNR1 taxon:4932
+S000002286 VCX1 YDL128W|HUM1|MNR1 taxon:4932
+S000003227 VEL1 YGL258W taxon:4932
+S000003227 VEL1 YGL258W taxon:4932
+S000003227 VEL1 YGL258W taxon:4932
+S000001318 VHR1 YIL056W taxon:4932
+S000001318 VHR1 YIL056W taxon:4932
+S000001318 VHR1 YIL056W taxon:4932
+S000001318 VHR1 YIL056W taxon:4932
+S000001318 VHR1 YIL056W taxon:4932
+S000001318 VHR1 YIL056W taxon:4932
+S000001318 VHR1 YIL056W taxon:4932
+S000002655 VHS1 YDR247W taxon:4932
+S000002655 VHS1 YDR247W taxon:4932
+S000002655 VHS1 YDR247W taxon:4932
+S000002655 VHS1 YDR247W taxon:4932
+S000002655 VHS1 YDR247W taxon:4932
+S000001397 VHS2 YIL135C taxon:4932
+S000001397 VHS2 YIL135C taxon:4932
+S000001397 VHS2 YIL135C taxon:4932
+S000005580 VHS3 YOR054C|YOR29-05 taxon:4932
+S000005580 VHS3 YOR054C|YOR29-05 taxon:4932
+S000005580 VHS3 YOR054C|YOR29-05 taxon:4932
+S000005580 VHS3 YOR054C|YOR29-05 taxon:4932
+S000005580 VHS3 YOR054C|YOR29-05 taxon:4932
+S000005580 VHS3 YOR054C|YOR29-05 taxon:4932
+S000005580 VHS3 YOR054C|YOR29-05 taxon:4932
+S000003297 VHT1 YGR065C taxon:4932
+S000003297 VHT1 YGR065C taxon:4932
+S000003297 VHT1 YGR065C taxon:4932
+S000002767 VID21 YDR359C|EAF1 taxon:4932
+S000002767 VID21 YDR359C|EAF1 taxon:4932
+S000002767 VID21 YDR359C|EAF1 taxon:4932
+S000002767 VID21 YDR359C|EAF1 taxon:4932
+S000002767 VID21 YDR359C|EAF1 taxon:4932
+S000004365 VID22 YLR373C taxon:4932
+S000004365 VID22 YLR373C taxon:4932
+S000004365 VID22 YLR373C taxon:4932
+S000000309 VID24 YBR105C|GID4 taxon:4932
+S000000309 VID24 YBR105C|GID4 taxon:4932
+S000000309 VID24 YBR105C|GID4 taxon:4932
+S000000309 VID24 YBR105C|GID4 taxon:4932
+S000000309 VID24 YBR105C|GID4 taxon:4932
+S000005156 VID27 YNL212W taxon:4932
+S000005156 VID27 YNL212W taxon:4932
+S000005156 VID27 YNL212W taxon:4932
+S000001279 VID28 YIL017C|GID5 taxon:4932
+S000001279 VID28 YIL017C|GID5 taxon:4932
+S000001279 VID28 YIL017C|GID5 taxon:4932
+S000001279 VID28 YIL017C|GID5 taxon:4932
+S000003196 VID30 YGL227W|GID1 taxon:4932
+S000003196 VID30 YGL227W|GID1 taxon:4932
+S000003196 VID30 YGL227W|GID1 taxon:4932
+S000003196 VID30 YGL227W|GID1 taxon:4932
+S000003196 VID30 YGL227W|GID1 taxon:4932
+S000003196 VID30 YGL227W|GID1 taxon:4932
+S000003196 VID30 YGL227W|GID1 taxon:4932
+S000006174 VIK1 YPL253C taxon:4932
+S000006174 VIK1 YPL253C taxon:4932
+S000006174 VIK1 YPL253C taxon:4932
+S000006174 VIK1 YPL253C taxon:4932
+S000006174 VIK1 YPL253C taxon:4932
+S000006174 VIK1 YPL253C taxon:4932
+S000006174 VIK1 YPL253C taxon:4932
+S000006174 VIK1 YPL253C taxon:4932
+S000004402 VIP1 YLR410W taxon:4932
+S000004402 VIP1 YLR410W taxon:4932
+S000004402 VIP1 YLR410W taxon:4932
+S000002100 VMA10 YHR039C-A|YHR039BC|YHR039C-B taxon:4932
+S000002100 VMA10 YHR039C-A|YHR039BC|YHR039C-B taxon:4932
+S000002100 VMA10 YHR039C-A|YHR039BC|YHR039C-B taxon:4932
+S000002100 VMA10 YHR039C-A|YHR039BC|YHR039C-B taxon:4932
+S000002100 VMA10 YHR039C-A|YHR039BC|YHR039C-B taxon:4932
+S000002100 VMA10 YHR039C-A|YHR039BC|YHR039C-B taxon:4932
+S000002100 VMA10 YHR039C-A|YHR039BC|YHR039C-B taxon:4932
+S000006240 VMA13 YPR036W|CLS11 taxon:4932
+S000006240 VMA13 YPR036W|CLS11 taxon:4932
+S000006240 VMA13 YPR036W|CLS11 taxon:4932
+S000006240 VMA13 YPR036W|CLS11 taxon:4932
+S000006240 VMA13 YPR036W|CLS11 taxon:4932
+S000006240 VMA13 YPR036W|CLS11 taxon:4932
+S000006240 VMA13 YPR036W|CLS11 taxon:4932
+S000000331 VMA2 YBR127C|ATPSV|VAT2 taxon:4932
+S000000331 VMA2 YBR127C|ATPSV|VAT2 taxon:4932
+S000000331 VMA2 YBR127C|ATPSV|VAT2 taxon:4932
+S000000331 VMA2 YBR127C|ATPSV|VAT2 taxon:4932
+S000000331 VMA2 YBR127C|ATPSV|VAT2 taxon:4932
+S000000331 VMA2 YBR127C|ATPSV|VAT2 taxon:4932
+S000000331 VMA2 YBR127C|ATPSV|VAT2 taxon:4932
+S000003337 VMA21 YGR105W taxon:4932
+S000003337 VMA21 YGR105W taxon:4932
+S000003337 VMA21 YGR105W taxon:4932
+S000003337 VMA21 YGR105W taxon:4932
+S000003337 VMA21 YGR105W taxon:4932
+S000001102 VMA22 YHR060W|CEV1|VPH6 taxon:4932
+S000001102 VMA22 YHR060W|CEV1|VPH6 taxon:4932
+S000001102 VMA22 YHR060W|CEV1|VPH6 taxon:4932
+S000001102 VMA22 YHR060W|CEV1|VPH6 taxon:4932
+S000001102 VMA22 YHR060W|CEV1|VPH6 taxon:4932
+S000001102 VMA22 YHR060W|CEV1|VPH6 taxon:4932
+S000001102 VMA22 YHR060W|CEV1|VPH6 taxon:4932
+S000001102 VMA22 YHR060W|CEV1|VPH6 taxon:4932
+S000005859 VMA4 YOR332W taxon:4932
+S000005859 VMA4 YOR332W taxon:4932
+S000005859 VMA4 YOR332W taxon:4932
+S000005859 VMA4 YOR332W taxon:4932
+S000005859 VMA4 YOR332W taxon:4932
+S000005859 VMA4 YOR332W taxon:4932
+S000005859 VMA4 YOR332W taxon:4932
+S000001563 VMA5 YKL080W|CSL5|VAT3 taxon:4932
+S000001563 VMA5 YKL080W|CSL5|VAT3 taxon:4932
+S000001563 VMA5 YKL080W|CSL5|VAT3 taxon:4932
+S000001563 VMA5 YKL080W|CSL5|VAT3 taxon:4932
+S000001563 VMA5 YKL080W|CSL5|VAT3 taxon:4932
+S000001563 VMA5 YKL080W|CSL5|VAT3 taxon:4932
+S000001563 VMA5 YKL080W|CSL5|VAT3 taxon:4932
+S000004439 VMA6 YLR447C taxon:4932
+S000004439 VMA6 YLR447C taxon:4932
+S000004439 VMA6 YLR447C taxon:4932
+S000004439 VMA6 YLR447C taxon:4932
+S000004439 VMA6 YLR447C taxon:4932
+S000004439 VMA6 YLR447C taxon:4932
+S000004439 VMA6 YLR447C taxon:4932
+S000004439 VMA6 YLR447C taxon:4932
+S000004439 VMA6 YLR447C taxon:4932
+S000003252 VMA7 YGR020C taxon:4932
+S000003252 VMA7 YGR020C taxon:4932
+S000003252 VMA7 YGR020C taxon:4932
+S000003252 VMA7 YGR020C taxon:4932
+S000003252 VMA7 YGR020C taxon:4932
+S000003252 VMA7 YGR020C taxon:4932
+S000003252 VMA7 YGR020C taxon:4932
+S000000777 VMA8 YEL051W taxon:4932
+S000000777 VMA8 YEL051W taxon:4932
+S000000777 VMA8 YEL051W taxon:4932
+S000000777 VMA8 YEL051W taxon:4932
+S000000777 VMA8 YEL051W taxon:4932
+S000000777 VMA8 YEL051W taxon:4932
+S000000777 VMA8 YEL051W taxon:4932
+S000028508 VMA9 YCL005W-A|CWH36|LDB10 taxon:4932
+S000028508 VMA9 YCL005W-A|CWH36|LDB10 taxon:4932
+S000028508 VMA9 YCL005W-A|CWH36|LDB10 taxon:4932
+S000028508 VMA9 YCL005W-A|CWH36|LDB10 taxon:4932
+S000028508 VMA9 YCL005W-A|CWH36|LDB10 taxon:4932
+S000028508 VMA9 YCL005W-A|CWH36|LDB10 taxon:4932
+S000001027 VMR1 YHL035C taxon:4932
+S000001027 VMR1 YHL035C taxon:4932
+S000001027 VMR1 YHL035C taxon:4932
+S000001027 VMR1 YHL035C taxon:4932
+S000005796 VPH1 YOR270C taxon:4932
+S000005796 VPH1 YOR270C taxon:4932
+S000005796 VPH1 YOR270C taxon:4932
+S000005796 VPH1 YOR270C taxon:4932
+S000005796 VPH1 YOR270C taxon:4932
+S000005796 VPH1 YOR270C taxon:4932
+S000005796 VPH1 YOR270C taxon:4932
+S000005796 VPH1 YOR270C taxon:4932
+S000005796 VPH1 YOR270C taxon:4932
+S000001602 VPH2 YKL119C|CLS10|VMA12 taxon:4932
+S000001602 VPH2 YKL119C|CLS10|VMA12 taxon:4932
+S000001602 VPH2 YKL119C|CLS10|VMA12 taxon:4932
+S000001602 VPH2 YKL119C|CLS10|VMA12 taxon:4932
+S000001709 VPS1 YKR001C|GRD1|LAM1|SPO15|VPL1|VPT26 taxon:4932
+S000001709 VPS1 YKR001C|GRD1|LAM1|SPO15|VPL1|VPT26 taxon:4932
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+S000005615 VPS21 YOR089C|VPS12|VPT12|YPT21|YPT51 taxon:4932
+S000005615 VPS21 YOR089C|VPS12|VPT12|YPT21|YPT51 taxon:4932
+S000005615 VPS21 YOR089C|VPS12|VPT12|YPT21|YPT51 taxon:4932
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+S000004352 VPS38 YLR360W|VPL17 taxon:4932
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+S000006377 VPS4 YPR173C|CSC1|DID6|END13|GRD13|VPL4|VPT10 taxon:4932
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+S000003063 VPS45 YGL095C|STT10|VPL28 taxon:4932
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+S000002434 VPS54 YDR027C|CGP1|LUV1|TCS3 taxon:4932
+S000002434 VPS54 YDR027C|CGP1|LUV1|TCS3 taxon:4932
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+S000002894 VPS60 YDR486C|CHM5|MOS10 taxon:4932
+S000002894 VPS60 YDR486C|CHM5|MOS10 taxon:4932
+S000002894 VPS60 YDR486C|CHM5|MOS10 taxon:4932
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+S000002608 VPS64 YDR200C|FAR9 taxon:4932
+S000002608 VPS64 YDR200C|FAR9 taxon:4932
+S000002608 VPS64 YDR200C|FAR9 taxon:4932
+S000002608 VPS64 YDR200C|FAR9 taxon:4932
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+S000004505 VPS71 YML041C|SWC6 taxon:4932
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+S000002893 VPS72 YDR485C|SWC2 taxon:4932
+S000002893 VPS72 YDR485C|SWC2 taxon:4932
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+S000000002 VPS8 YAL002W|FUN15|VPT8 taxon:4932
+S000000002 VPS8 YAL002W|FUN15|VPT8 taxon:4932
+S000004563 VPS9 YML097C|VPL31|VPT9 taxon:4932
+S000004563 VPS9 YML097C|VPL31|VPT9 taxon:4932
+S000004563 VPS9 YML097C|VPL31|VPT9 taxon:4932
+S000004563 VPS9 YML097C|VPL31|VPT9 taxon:4932
+S000003193 VRG4 YGL225W|GOG5|LDB3|VAN2|VIG4 taxon:4932
+S000003193 VRG4 YGL225W|GOG5|LDB3|VAN2|VIG4 taxon:4932
+S000003193 VRG4 YGL225W|GOG5|LDB3|VAN2|VIG4 taxon:4932
+S000003193 VRG4 YGL225W|GOG5|LDB3|VAN2|VIG4 taxon:4932
+S000003193 VRG4 YGL225W|GOG5|LDB3|VAN2|VIG4 taxon:4932
+S000003193 VRG4 YGL225W|GOG5|LDB3|VAN2|VIG4 taxon:4932
+S000003193 VRG4 YGL225W|GOG5|LDB3|VAN2|VIG4 taxon:4932
+S000003193 VRG4 YGL225W|GOG5|LDB3|VAN2|VIG4 taxon:4932
+S000004329 VRP1 YLR337C|END5|MDP2|YLR337W taxon:4932
+S000004329 VRP1 YLR337C|END5|MDP2|YLR337W taxon:4932
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+S000004262 YCS4 YLR272C|LOC7 taxon:4932
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diff --git a/coreplugins/TableImport/src/test/resources/annotation/galSubnetworkAnnotation2.txt b/coreplugins/TableImport/src/test/resources/annotation/galSubnetworkAnnotation2.txt
new file mode 100755
index 0000000..e221f24
--- /dev/null
+++ b/coreplugins/TableImport/src/test/resources/annotation/galSubnetworkAnnotation2.txt
@@ -0,0 +1,14 @@
+ID ID in SGD alias Column Description of Genes Date Sample Boolean Attr2 gal1RGexp gal1RGsig Sample String List
+YOR167C S000005693 "RPS28A, RPS33A, YOR167C" ribosomal protein S28A (S33A) (YS27) 20010118 TRUE -0.374 2.73E-06 "This, is, a, test, for, List, attribute."
+YOL149W S000005509 "DCP1, YOL149W" 20010124 FALSE 0.228 9.08E-05 "This, is, a, test, for, List, attribute."
+YNR050C S000005333 "LYS13, LYS9, YNR050C" 20020930 FALSE 0.223 1.18E-05 "This, is, a, test, for, List, attribute."
+YNL050C S000004995 YNL050C 20030422 FALSE 0.301 1.43E-05 "This, is, a, test, for, List, attribute."
+YMR138W S000004746 "CIN4, GTP1, UGX1, YMR138W" GTP-binding protein 20010118 TRUE 0.414 0.037256 "This, is, a, test, for, List, attribute."
+YLR264W S000004254 "RPS28B, RPS33B, YLR264W" ribosomal protein S28B (S33B) (YS27) 20010118 TRUE -0.259 1.61E-04 "This, is, a, test, for, List, attribute."
+YLR109W S000004099 "AHP1, YLR109W, cTPxIII" alkyl hydroperoxide reductase 20020411 TRUE -0.603 1.48E-09 "This, is, a, test, for, List, attribute."
+YJR022W S000003783 "LSM8, YJR022W" snRNP protein 20020620 TRUE 0.059 0.6011 "This, is, a, test, for, List, attribute."
+YHR141C S000001183 "MAK18, RPL42B, YHR141C" ribosomal protein L42B (YL27) (L41B) (YP44) 20010118 TRUE -0.359 7.74E-07 "This, is, a, test, for, List, attribute."
+YER112W S000000914 "LSM4, SDB23, USS1, YER112W" U6 snRNA associated protein 20050222 TRUE 0.193 7.05E-05 "This, is, a, test, for, List, attribute."
+YDR277C S000002685 "BPC1, DGT1, HTR1, MTH1, YDR277C" Msn3p homolog (61% identical) 20020408 TRUE 0.243 2.19E-05 "This, is, a, test, for, List, attribute."
+YDL194W S000002353 "SNF3, YDL194W" glucose sensor 20021003 TRUE 0.139 0.018043 "This, is, a, test, for, List, attribute."
+YBL026W S000000122 "LSM2, SMX5, SNP3, YBL026W" "snRNA-associated protein, Sm class" 20050222 TRUE -0.032 0.48423 "This, is, a, test, for, List, attribute."
diff --git a/coreplugins/TableImport/src/test/resources/annotation/galSubnetworkAnnotation3.xls b/coreplugins/TableImport/src/test/resources/annotation/galSubnetworkAnnotation3.xls
new file mode 100755
index 0000000..fd75bbe
Binary files /dev/null and b/coreplugins/TableImport/src/test/resources/annotation/galSubnetworkAnnotation3.xls differ
diff --git a/coreplugins/TableImport/src/test/resources/annotation/gene_association.sgd b/coreplugins/TableImport/src/test/resources/annotation/gene_association.sgd
new file mode 100644
index 0000000..9127015
--- /dev/null
+++ b/coreplugins/TableImport/src/test/resources/annotation/gene_association.sgd
@@ -0,0 +1,33366 @@
+!CVS Version: Revision: 1.1261 $
+!GOC Validation Date: 06/14/2006 $
+!Submission Date: 6/13/2006
+!
+! The above "Submission Date" is when the annotation project provided
+! this file to the Gene Ontology Consortium (GOC). The "GOC Validation
+! Date" indicates when this file was last changed as a result of a GOC
+! validation and filtering process. The "CVS Version" above is the
+! GOC version of this file.
+!
+! Note: The contents of this file may differ from that submitted to the
+! GOC. The identifiers and syntax of the file have been checked, rows of
+! data not meeting the standards set by the GOC have been removed. This
+! file may also have annotations removed because the annotations for the
+! listed Taxonomy identifier are only allowed in a file provided by
+! another annotation project. The original submitted file is available from:
+! http://www.geneontology.org/gene-associations/submission/
+!
+! For information on which taxon are allowed in which files please see:
+! http://www.geneontology.org/GO.annotation.shtml#script
+!
+!Project_name: Saccharomyces Genome Database (SGD)
+!URL: http://www.yeastgenome.org/
+!Contact Email: yeast-curator at yeastgenome.org
+!Funding: NHGRI of US National Institutes of Health, 5-P41-HG001315
+!
+SGD S000007287 15S_RRNA GO:0005763 SGD_REF:S000073642|PMID:6261980 ISS C 15S_rRNA|15S_RRNA_2 gene taxon:4932 20040202 SGD
+SGD S000007287 15S_RRNA GO:0003735 SGD_REF:S000073642|PMID:6261980 ISS F 15S_rRNA|15S_RRNA_2 gene taxon:4932 20030723 SGD
+SGD S000007287 15S_RRNA GO:0006412 SGD_REF:S000073643|PMID:6280192 IGI P 15S_rRNA|15S_RRNA_2 gene taxon:4932 20030723 SGD
+SGD S000007287 15S_RRNA GO:0042255 SGD_REF:S000051605|PMID:2167435 IGI P 15S_rRNA|15S_RRNA_2 gene taxon:4932 20030723 SGD
+SGD S000007288 21S_RRNA GO:0005762 SGD_REF:S000073372|PMID:6759872 IDA C 21S_rRNA|21S_rRNA_3|21S_rRNA_4 gene taxon:4932 20040202 SGD
+SGD S000007288 21S_RRNA GO:0003735 SGD_REF:S000073372|PMID:6759872 IMP F 21S_rRNA|21S_rRNA_3|21S_rRNA_4 gene taxon:4932 20030721 SGD
+SGD S000007288 21S_RRNA GO:0003735 SGD_REF:S000073372|PMID:6759872 ISS F 21S_rRNA|21S_rRNA_3|21S_rRNA_4 gene taxon:4932 20030721 SGD
+SGD S000007288 21S_RRNA GO:0006412 SGD_REF:S000073372|PMID:6759872 IMP P 21S_rRNA|21S_rRNA_3|21S_rRNA_4 gene taxon:4932 20030721 SGD
+SGD S000007288 21S_RRNA GO:0006412 SGD_REF:S000073372|PMID:6759872 ISS P 21S_rRNA|21S_rRNA_3|21S_rRNA_4 gene taxon:4932 20030721 SGD
+SGD S000007288 21S_RRNA GO:0042255 SGD_REF:S000073372|PMID:6759872 IMP P 21S_rRNA|21S_rRNA_3|21S_rRNA_4 gene taxon:4932 20030721 SGD
+SGD S000004660 AAC1 GO:0005743 SGD_REF:S000050955|PMID:2167309 TAS C ADP/ATP translocator YMR056C gene taxon:4932 20010118 SGD
+SGD S000004660 AAC1 GO:0005471 SGD_REF:S000050955|PMID:2167309 IDA F ADP/ATP translocator YMR056C gene taxon:4932 20010213 SGD
+SGD S000004660 AAC1 GO:0006839 SGD_REF:S000050955|PMID:2167309 IGI SGD:S000000126 P ADP/ATP translocator YMR056C gene taxon:4932 20040226 SGD
+SGD S000004660 AAC1 GO:0009060 SGD_REF:S000050955|PMID:2167309 IGI SGD:S000000126 P ADP/ATP translocator YMR056C gene taxon:4932 20040226 SGD
+SGD S000000289 AAC3 GO:0005743 SGD_REF:S000045889|PMID:2165073 ISS SGD:S000000126|SGD:S000004660 C ADP/ATP translocator YBR085W|ANC3 gene taxon:4932 20040226 SGD
+SGD S000000289 AAC3 GO:0005471 SGD_REF:S000045889|PMID:2165073 ISS SGD:S000000126|SGD:S000004660 F ADP/ATP translocator YBR085W|ANC3 gene taxon:4932 20040226 SGD
+SGD S000000289 AAC3 GO:0009061 SGD_REF:S000045889|PMID:2165073 IGI SGD:S000000126 P ADP/ATP translocator YBR085W|ANC3 gene taxon:4932 20040226 SGD
+SGD S000000289 AAC3 GO:0009061 SGD_REF:S000052497|PMID:1915842 IGI SGD:S000000126|SGD:S000004660 P ADP/ATP translocator YBR085W|ANC3 gene taxon:4932 20040226 SGD
+SGD S000000289 AAC3 GO:0009061 SGD_REF:S000045889|PMID:2165073 IEP P ADP/ATP translocator YBR085W|ANC3 gene taxon:4932 20040226 SGD
+SGD S000003916 AAD10 GO:0008372 SGD_REF:S000069584 ND C aryl-alcohol dehydrogenase (putative) YJR155W gene taxon:4932 20010119 SGD
+SGD S000003916 AAD10 GO:0018456 SGD_REF:S000042151|PMID:10572264 ISS F aryl-alcohol dehydrogenase (putative) YJR155W gene taxon:4932 20020902 SGD
+SGD S000003916 AAD10 GO:0006081 SGD_REF:S000042151|PMID:10572264 ISS P aryl-alcohol dehydrogenase (putative) YJR155W gene taxon:4932 20020902 SGD
+SGD S000005275 AAD14 GO:0008372 SGD_REF:S000069584 ND C aryl-alcohol dehydrogenase (putative) YNL331C gene taxon:4932 20010119 SGD
+SGD S000005275 AAD14 GO:0018456 SGD_REF:S000042151|PMID:10572264 ISS F aryl-alcohol dehydrogenase (putative) YNL331C gene taxon:4932 20020902 SGD
+SGD S000005275 AAD14 GO:0006081 SGD_REF:S000042151|PMID:10572264 ISS P aryl-alcohol dehydrogenase (putative) YNL331C gene taxon:4932 20020902 SGD
+SGD S000005525 AAD15 GO:0008372 SGD_REF:S000069584 ND C aryl-alcohol dehydrogenase (putative) YOL165C gene taxon:4932 20010119 SGD
+SGD S000005525 AAD15 GO:0018456 SGD_REF:S000042151|PMID:10572264 ISS F aryl-alcohol dehydrogenase (putative) YOL165C gene taxon:4932 20020902 SGD
+SGD S000005525 AAD15 GO:0006081 SGD_REF:S000042151|PMID:10572264 ISS P aryl-alcohol dehydrogenase (putative) YOL165C gene taxon:4932 20020902 SGD
+SGD S000001837 AAD16 GO:0008372 SGD_REF:S000069584 ND C YFL057C gene taxon:4932 20020902 SGD
+SGD S000001837 AAD16 GO:0018456 SGD_REF:S000042151|PMID:10572264 ISS F YFL057C gene taxon:4932 20020902 SGD
+SGD S000001837 AAD16 GO:0006081 SGD_REF:S000042151|PMID:10572264 ISS P YFL057C gene taxon:4932 20020902 SGD
+SGD S000000704 AAD3 GO:0008372 SGD_REF:S000069584 ND C aryl-alcohol dehydrogenase (putative) YCR107W gene taxon:4932 20010119 SGD
+SGD S000000704 AAD3 GO:0018456 SGD_REF:S000042151|PMID:10572264 ISS F aryl-alcohol dehydrogenase (putative) YCR107W gene taxon:4932 20020902 SGD
+SGD S000000704 AAD3 GO:0006081 SGD_REF:S000042151|PMID:10572264 ISS P aryl-alcohol dehydrogenase (putative) YCR107W gene taxon:4932 20020902 SGD
+SGD S000002402 AAD4 GO:0008372 SGD_REF:S000069584 ND C aryl-alcohol dehydrogenase (putative) YDL243C gene taxon:4932 20010119 SGD
+SGD S000002402 AAD4 GO:0018456 SGD_REF:S000042151|PMID:10572264 ISS F aryl-alcohol dehydrogenase (putative) YDL243C gene taxon:4932 20020902 SGD
+SGD S000002402 AAD4 GO:0006081 SGD_REF:S000042151|PMID:10572264 ISS P aryl-alcohol dehydrogenase (putative) YDL243C gene taxon:4932 20020902 SGD
+SGD S000001838 AAD6 GO:0008372 SGD_REF:S000069584 ND C aryl-alcohol dehydrogenase (putative) YFL056C gene taxon:4932 20010119 SGD
+SGD S000001838 AAD6 GO:0018456 SGD_REF:S000042151|PMID:10572264 ISS F aryl-alcohol dehydrogenase (putative) YFL056C gene taxon:4932 20020902 SGD
+SGD S000001838 AAD6 GO:0006081 SGD_REF:S000042151|PMID:10572264 ISS P aryl-alcohol dehydrogenase (putative) YFL056C gene taxon:4932 20020902 SGD
+SGD S000005085 AAH1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C adenine aminohydrolase (adenine deaminase) YNL141W gene taxon:4932 20031028 SGD
+SGD S000005085 AAH1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C adenine aminohydrolase (adenine deaminase) YNL141W gene taxon:4932 20031028 SGD
+SGD S000005085 AAH1 GO:0000034 SGD_REF:S000045033|PMID:6392474 IMP F adenine aminohydrolase (adenine deaminase) YNL141W gene taxon:4932 20010118 SGD
+SGD S000005085 AAH1 GO:0006146 SGD_REF:S000058499 TAS P adenine aminohydrolase (adenine deaminase) YNL141W gene taxon:4932 20010119 SGD
+SGD S000001089 AAP1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C arginine/alanine aminopeptidase YHR047C|AAP1' gene taxon:4932 20031028 SGD
+SGD S000001089 AAP1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C arginine/alanine aminopeptidase YHR047C|AAP1' gene taxon:4932 20031028 SGD
+SGD S000001089 AAP1 GO:0004177 SGD_REF:S000050813|PMID:8100228 ISS F arginine/alanine aminopeptidase YHR047C|AAP1' gene taxon:4932 20010118 SGD
+SGD S000001089 AAP1 GO:0005977 SGD_REF:S000050813|PMID:8100228 IMP P arginine/alanine aminopeptidase YHR047C|AAP1' gene taxon:4932 20031212 SGD
+SGD S000001089 AAP1 GO:0006508 SGD_REF:S000050813|PMID:8100228 IMP P arginine/alanine aminopeptidase YHR047C|AAP1' gene taxon:4932 20031212 SGD
+SGD S000000170 AAR2 GO:0005682 SGD_REF:S000066236|PMID:11720285 IDA C YBL074C gene taxon:4932 20030408 SGD
+SGD S000000170 AAR2 GO:0005682 SGD_REF:S000066236|PMID:11720285 IPI C YBL074C gene taxon:4932 20030408 SGD
+SGD S000000170 AAR2 GO:0005554 SGD_REF:S000069584 ND F YBL074C gene taxon:4932 20030408 SGD
+SGD S000000170 AAR2 GO:0000244 SGD_REF:S000066236|PMID:11720285 IDA P YBL074C gene taxon:4932 20030408 SGD
+SGD S000001589 AAT1 GO:0005739 SGD_REF:S000041949|PMID:1482685 TAS C aspartate aminotransferase YKL106W gene taxon:4932 20010118 SGD
+SGD S000001589 AAT1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C aspartate aminotransferase YKL106W gene taxon:4932 20040928 SGD
+SGD S000001589 AAT1 GO:0004069 SGD_REF:S000041949|PMID:1482685 ISS F aspartate aminotransferase YKL106W gene taxon:4932 20010118 SGD
+SGD S000001589 AAT1 GO:0006532 SGD_REF:S000070200 IC GO:0004069 P aspartate aminotransferase YKL106W gene taxon:4932 20030509 SGD
+SGD S000001589 AAT1 GO:0006533 SGD_REF:S000058499 TAS P aspartate aminotransferase YKL106W gene taxon:4932 20010119 SGD
+SGD S000001589 AAT1 GO:0019266 SGD_REF:S000070200 IC GO:0004069 P aspartate aminotransferase YKL106W gene taxon:4932 20030508 SGD
+SGD S000004017 AAT2 GO:0005737 SGD_REF:S000039792|PMID:9288922 TAS C aspartate aminotransferase YLR027C|ASP5 gene taxon:4932 20010118 SGD
+SGD S000004017 AAT2 GO:0005777 SGD_REF:S000039792|PMID:9288922 TAS C aspartate aminotransferase YLR027C|ASP5 gene taxon:4932 20010118 SGD
+SGD S000004017 AAT2 GO:0004069 SGD_REF:S000056664|PMID:1859361 IDA F aspartate aminotransferase YLR027C|ASP5 gene taxon:4932 20010118 SGD
+SGD S000004017 AAT2 GO:0006532 SGD_REF:S000070200 TAS P aspartate aminotransferase YLR027C|ASP5 gene taxon:4932 20030509 SGD
+SGD S000004017 AAT2 GO:0006533 SGD_REF:S000058499 TAS P aspartate aminotransferase YLR027C|ASP5 gene taxon:4932 20010119 SGD
+SGD S000004017 AAT2 GO:0006536 SGD_REF:S000056664|PMID:1859361 NAS P aspartate aminotransferase YLR027C|ASP5 gene taxon:4932 20010118 SGD
+SGD S000004017 AAT2 GO:0006807 SGD_REF:S000056664|PMID:1859361 NAS P aspartate aminotransferase YLR027C|ASP5 gene taxon:4932 20010118 SGD
+SGD S000004017 AAT2 GO:0019266 SGD_REF:S000070200 TAS P aspartate aminotransferase YLR027C|ASP5 gene taxon:4932 20030508 SGD
+SGD S000003087 ABC1 GO:0005739 SGD_REF:S000060371|PMID:11279158 IDA C YGL119W|COQ8 gene taxon:4932 20030204 SGD
+SGD S000003087 ABC1 GO:0005739 SGD_REF:S000048591|PMID:1648478 ISS C YGL119W|COQ8 gene taxon:4932 20030523 SGD
+SGD S000003087 ABC1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YGL119W|COQ8 gene taxon:4932 20040924 SGD
+SGD S000003087 ABC1 GO:0005554 SGD_REF:S000069584 ND F YGL119W|COQ8 gene taxon:4932 20050906 SGD
+SGD S000003087 ABC1 GO:0006744 SGD_REF:S000060371|PMID:11279158 IMP P YGL119W|COQ8 gene taxon:4932 20031218 SGD
+SGD S000003087 ABC1 GO:0009060 SGD_REF:S000048591|PMID:1648478 IMP P YGL119W|COQ8 gene taxon:4932 20050906 SGD
+SGD S000000440 ABD1 GO:0005634 SGD_REF:S000059699|PMID:11018011 IPI C RNA (guanine-7-)methyltransferase (cap methyltransferase) YBR236C gene taxon:4932 20030204 SGD
+SGD S000000440 ABD1 GO:0016591 SGD_REF:S000059699|PMID:11018011 IPI C RNA (guanine-7-)methyltransferase (cap methyltransferase) YBR236C gene taxon:4932 20030204 SGD
+SGD S000000440 ABD1 GO:0004482 SGD_REF:S000050516|PMID:7623811 ISS F RNA (guanine-7-)methyltransferase (cap methyltransferase) YBR236C gene taxon:4932 20010118 SGD
+SGD S000000440 ABD1 GO:0004482 SGD_REF:S000050516|PMID:7623811 IDA F RNA (guanine-7-)methyltransferase (cap methyltransferase) YBR236C gene taxon:4932 20010118 SGD
+SGD S000000440 ABD1 GO:0006370 SGD_REF:S000050516|PMID:7623811 IDA P RNA (guanine-7-)methyltransferase (cap methyltransferase) YBR236C gene taxon:4932 20010118 SGD
+SGD S000001595 ABF1 GO:0000113 SGD_REF:S000056193|PMID:10601031 IPI SGD:S000003813 C ARS1 binding protein, transcriptional activator YKL112W|BAF1|OBF1|REB2|SBF1 gene taxon:4932 20051020 SGD
+SGD S000001595 ABF1 GO:0000790 SGD_REF:S000069013|PMID:11756546 TAS C ARS1 binding protein, transcriptional activator YKL112W|BAF1|OBF1|REB2|SBF1 gene taxon:4932 20021002 SGD
+SGD S000001595 ABF1 GO:0005634 SGD_REF:S000080227|PMID:15522095 IDA C ARS1 binding protein, transcriptional activator YKL112W|BAF1|OBF1|REB2|SBF1 gene taxon:4932 20051020 SGD
+SGD S000001595 ABF1 GO:0005634 SGD_REF:S000080227|PMID:15522095 IMP C ARS1 binding protein, transcriptional activator YKL112W|BAF1|OBF1|REB2|SBF1 gene taxon:4932 20051020 SGD
+SGD S000001595 ABF1 GO:0003677 SGD_REF:S000048814|PMID:3046937 TAS F ARS1 binding protein, transcriptional activator YKL112W|BAF1|OBF1|REB2|SBF1 gene taxon:4932 20021124 SGD
+SGD S000001595 ABF1 GO:0003677 SGD_REF:S000050312|PMID:3275867 IDA F ARS1 binding protein, transcriptional activator YKL112W|BAF1|OBF1|REB2|SBF1 gene taxon:4932 20051019 SGD
+SGD S000001595 ABF1 GO:0003682 SGD_REF:S000069013|PMID:11756546 TAS F ARS1 binding protein, transcriptional activator YKL112W|BAF1|OBF1|REB2|SBF1 gene taxon:4932 20021002 SGD
+SGD S000001595 ABF1 GO:0003682 SGD_REF:S000077502|PMID:15456886 IDA F ARS1 binding protein, transcriptional activator YKL112W|BAF1|OBF1|REB2|SBF1 gene taxon:4932 20051024 SGD
+SGD S000001595 ABF1 GO:0003682 SGD_REF:S000040971|PMID:10684934 IMP F ARS1 binding protein, transcriptional activator YKL112W|BAF1|OBF1|REB2|SBF1 gene taxon:4932 20051024 SGD
+SGD S000001595 ABF1 GO:0003700 SGD_REF:S000070000|PMID:11937506 TAS F ARS1 binding protein, transcriptional activator YKL112W|BAF1|OBF1|REB2|SBF1 gene taxon:4932 20021124 SGD
+SGD S000001595 ABF1 GO:0008301 SGD_REF:S000053200|PMID:8206955 IDA F ARS1 binding protein, transcriptional activator YKL112W|BAF1|OBF1|REB2|SBF1 gene taxon:4932 20051019 SGD
+SGD S000001595 ABF1 GO:0016563 SGD_REF:S000069013|PMID:11756546 IDA F ARS1 binding protein, transcriptional activator YKL112W|BAF1|OBF1|REB2|SBF1 gene taxon:4932 20051020 SGD
+SGD S000001595 ABF1 GO:0016563 SGD_REF:S000076894|PMID:15192094 IMP F ARS1 binding protein, transcriptional activator YKL112W|BAF1|OBF1|REB2|SBF1 gene taxon:4932 20051020 SGD
+SGD S000001595 ABF1 GO:0016564 SGD_REF:S000076894|PMID:15192094 IMP F ARS1 binding protein, transcriptional activator YKL112W|BAF1|OBF1|REB2|SBF1 gene taxon:4932 20051020 SGD
+SGD S000001595 ABF1 GO:0000122 SGD_REF:S000076894|PMID:15192094 IMP P ARS1 binding protein, transcriptional activator YKL112W|BAF1|OBF1|REB2|SBF1 gene taxon:4932 20051020 SGD
+SGD S000001595 ABF1 GO:0000715 SGD_REF:S000077426|PMID:15177043 IDA P ARS1 binding protein, transcriptional activator YKL112W|BAF1|OBF1|REB2|SBF1 gene taxon:4932 20051018 SGD
+SGD S000001595 ABF1 GO:0000715 SGD_REF:S000056193|PMID:10601031 IPI SGD:S000003813 P ARS1 binding protein, transcriptional activator YKL112W|BAF1|OBF1|REB2|SBF1 gene taxon:4932 20051018 SGD
+SGD S000001595 ABF1 GO:0000715 SGD_REF:S000056193|PMID:10601031 IMP P ARS1 binding protein, transcriptional activator YKL112W|BAF1|OBF1|REB2|SBF1 gene taxon:4932 20051018 SGD
+SGD S000001595 ABF1 GO:0006260 SGD_REF:S000069013|PMID:11756546 TAS P ARS1 binding protein, transcriptional activator YKL112W|BAF1|OBF1|REB2|SBF1 gene taxon:4932 20021002 SGD
+SGD S000001595 ABF1 GO:0006260 SGD_REF:S000069013|PMID:11756546 IDA P ARS1 binding protein, transcriptional activator YKL112W|BAF1|OBF1|REB2|SBF1 gene taxon:4932 20051020 SGD
+SGD S000001595 ABF1 GO:0006338 SGD_REF:S000040971|PMID:10684934 IMP P ARS1 binding protein, transcriptional activator YKL112W|BAF1|OBF1|REB2|SBF1 gene taxon:4932 20051024 SGD
+SGD S000001595 ABF1 GO:0030466 SGD_REF:S000069013|PMID:11756546 TAS P ARS1 binding protein, transcriptional activator YKL112W|BAF1|OBF1|REB2|SBF1 gene taxon:4932 20021002 SGD
+SGD S000001595 ABF1 GO:0030466 SGD_REF:S000053123|PMID:8582634 IMP P ARS1 binding protein, transcriptional activator YKL112W|BAF1|OBF1|REB2|SBF1 gene taxon:4932 20051020 SGD
+SGD S000001595 ABF1 GO:0045944 SGD_REF:S000076894|PMID:15192094 IMP P ARS1 binding protein, transcriptional activator YKL112W|BAF1|OBF1|REB2|SBF1 gene taxon:4932 20051020 SGD
+SGD S000004676 ABF2 GO:0000262 SGD_REF:S000042213|PMID:9581629 IDA C HMG-1 homolog YMR072W gene taxon:4932 20020917 SGD
+SGD S000004676 ABF2 GO:0042645 SGD_REF:S000050870|PMID:10869431 IDA C HMG-1 homolog YMR072W gene taxon:4932 20050401 SGD
+SGD S000004676 ABF2 GO:0003677 SGD_REF:S000042213|PMID:9581629 IDA F HMG-1 homolog YMR072W gene taxon:4932 20020917 SGD
+SGD S000004676 ABF2 GO:0008301 SGD_REF:S000061139|PMID:1737790 IDA F HMG-1 homolog YMR072W gene taxon:4932 20040720 SGD
+SGD S000004676 ABF2 GO:0000001 SGD_REF:S000042213|PMID:9581629 IMP P HMG-1 homolog YMR072W gene taxon:4932 20020917 SGD
+SGD S000004676 ABF2 GO:0000002 SGD_REF:S000042213|PMID:9581629 IMP P HMG-1 homolog YMR072W gene taxon:4932 20020917 SGD
+SGD S000003869 ABM1 GO:0008372 SGD_REF:S000069584 ND C YJR108W gene taxon:4932 20020523 SGD
+SGD S000003869 ABM1 GO:0005554 SGD_REF:S000069584 ND F YJR108W gene taxon:4932 20020523 SGD
+SGD S000003869 ABM1 GO:0000226 SGD_REF:S000056413|PMID:10628851 IMP P YJR108W gene taxon:4932 20031211 SGD
+SGD S000000684 ABP1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C actin binding protein YCR088W gene taxon:4932 20020507 SGD
+SGD S000000684 ABP1 GO:0005856 SGD_REF:S000043720|PMID:2405279 TAS C actin binding protein YCR088W gene taxon:4932 20010118 SGD
+SGD S000000684 ABP1 GO:0005938 SGD_REF:S000072033|PMID:11950888 IDA C actin binding protein YCR088W gene taxon:4932 20030123 SGD
+SGD S000000684 ABP1 GO:0005515 SGD_REF:S000069184|PMID:11668184 IDA F actin binding protein YCR088W gene taxon:4932 20030123 SGD
+SGD S000000684 ABP1 GO:0000147 SGD_REF:S000043720|PMID:2405279 IMP P actin binding protein YCR088W gene taxon:4932 20010705 SGD
+SGD S000000684 ABP1 GO:0030447 SGD_REF:S000080384|PMID:15645503 IMP P actin binding protein YCR088W gene taxon:4932 20050621 SGD
+SGD S000000684 ABP1 GO:0030468 SGD_REF:S000043720|PMID:2405279 IMP P actin binding protein YCR088W gene taxon:4932 20010302 SGD
+SGD S000005765 ABP140 GO:0005884 SGD_REF:S000041861|PMID:9467951 IPI C actin filament binding protein YOR239W|YOR240W gene taxon:4932 20010411 SGD
+SGD S000005765 ABP140 GO:0005884 SGD_REF:S000041861|PMID:9467951 IDA C actin filament binding protein YOR239W|YOR240W gene taxon:4932 20010411 SGD
+SGD S000005765 ABP140 GO:0008757 SGD_REF:S000074033|PMID:12872006 ISS F actin filament binding protein YOR239W|YOR240W gene taxon:4932 20031001 SGD
+SGD S000005765 ABP140 GO:0030674 SGD_REF:S000041861|PMID:9467951 IDA F actin filament binding protein YOR239W|YOR240W gene taxon:4932 20040409 SGD
+SGD S000005765 ABP140 GO:0051015 SGD_REF:S000041861|PMID:9467951 IDA F actin filament binding protein YOR239W|YOR240W gene taxon:4932 20040409 SGD
+SGD S000005765 ABP140 GO:0030036 SGD_REF:S000041861|PMID:9467951 IDA P actin filament binding protein YOR239W|YOR240W gene taxon:4932 20010705 SGD
+SGD S000005316 ABZ1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C aminodeoxychorismate synthase YNR033W gene taxon:4932 20031028 SGD
+SGD S000005316 ABZ1 GO:0046820 SGD_REF:S000057703|PMID:8346682 IMP F aminodeoxychorismate synthase YNR033W gene taxon:4932 20030106 SGD
+SGD S000005316 ABZ1 GO:0046820 SGD_REF:S000057703|PMID:8346682 ISS CGSC:pabA|CGSC:pabB F aminodeoxychorismate synthase YNR033W gene taxon:4932 20030106 SGD
+SGD S000005316 ABZ1 GO:0046482 SGD_REF:S000057703|PMID:8346682 IMP P aminodeoxychorismate synthase YNR033W gene taxon:4932 20030106 SGD
+SGD S000004902 ABZ2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C 4-amino-4-deoxychorismate lyase YMR289W gene taxon:4932 20031028 SGD
+SGD S000004902 ABZ2 GO:0005554 SGD_REF:S000069584 ND F 4-amino-4-deoxychorismate lyase YMR289W gene taxon:4932 20030203 SGD
+SGD S000004902 ABZ2 GO:0000004 SGD_REF:S000069584 ND P 4-amino-4-deoxychorismate lyase YMR289W gene taxon:4932 20030203 SGD
+SGD S000000847 ACA1 GO:0005634 SGD_REF:S000046567|PMID:10825197 IPI C YER045C gene taxon:4932 20021011 SGD
+SGD S000000847 ACA1 GO:0003704 SGD_REF:S000046567|PMID:10825197 IDA F YER045C gene taxon:4932 20021011 SGD
+SGD S000000847 ACA1 GO:0006367 SGD_REF:S000046567|PMID:10825197 IDA P YER045C gene taxon:4932 20021011 SGD
+SGD S000003269 ACB1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C acyl-CoA-binding protein (ACBP)/diazepam binding inhibitor (DBI)/endozepine (EP) YGR037C gene taxon:4932 20031028 SGD
+SGD S000003269 ACB1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C acyl-CoA-binding protein (ACBP)/diazepam binding inhibitor (DBI)/endozepine (EP) YGR037C gene taxon:4932 20031028 SGD
+SGD S000003269 ACB1 GO:0000062 SGD_REF:S000056518|PMID:1454809 ISS F acyl-CoA-binding protein (ACBP)/diazepam binding inhibitor (DBI)/endozepine (EP) YGR037C gene taxon:4932 20010118 SGD
+SGD S000003269 ACB1 GO:0005324 SGD_REF:S000060237|PMID:11294913 IMP F acyl-CoA-binding protein (ACBP)/diazepam binding inhibitor (DBI)/endozepine (EP) YGR037C gene taxon:4932 20030319 SGD
+SGD S000003269 ACB1 GO:0006631 SGD_REF:S000041522|PMID:8798418 IMP P acyl-CoA-binding protein (ACBP)/diazepam binding inhibitor (DBI)/endozepine (EP) YGR037C gene taxon:4932 20010118 SGD
+SGD S000003269 ACB1 GO:0006631 SGD_REF:S000041522|PMID:8798418 IDA P acyl-CoA-binding protein (ACBP)/diazepam binding inhibitor (DBI)/endozepine (EP) YGR037C gene taxon:4932 20010118 SGD
+SGD S000003269 ACB1 GO:0015909 SGD_REF:S000060237|PMID:11294913 IMP P acyl-CoA-binding protein (ACBP)/diazepam binding inhibitor (DBI)/endozepine (EP) YGR037C gene taxon:4932 20030319 SGD
+SGD S000005299 ACC1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C acetyl CoA carboxylase YNR016C|ABP2|FAS3|MTR7 gene taxon:4932 20040928 SGD
+SGD S000005299 ACC1 GO:0005789 SGD_REF:S000046231|PMID:9438137 IDA C acetyl CoA carboxylase YNR016C|ABP2|FAS3|MTR7 gene taxon:4932 20010118 SGD
+SGD S000005299 ACC1 GO:0005829 SGD_REF:S000058499 TAS C acetyl CoA carboxylase YNR016C|ABP2|FAS3|MTR7 gene taxon:4932 20010119 SGD
+SGD S000005299 ACC1 GO:0003989 SGD_REF:S000039600|PMID:8098706 IMP F acetyl CoA carboxylase YNR016C|ABP2|FAS3|MTR7 gene taxon:4932 20010118 SGD
+SGD S000005299 ACC1 GO:0003989 SGD_REF:S000039600|PMID:8098706 ISS F acetyl CoA carboxylase YNR016C|ABP2|FAS3|MTR7 gene taxon:4932 20010118 SGD
+SGD S000005299 ACC1 GO:0004075 SGD_REF:S000047755|PMID:6108218 IMP F acetyl CoA carboxylase YNR016C|ABP2|FAS3|MTR7 gene taxon:4932 20010118 SGD
+SGD S000005299 ACC1 GO:0004075 SGD_REF:S000054508|PMID:1350093 ISS F acetyl CoA carboxylase YNR016C|ABP2|FAS3|MTR7 gene taxon:4932 20010118 SGD
+SGD S000005299 ACC1 GO:0006606 SGD_REF:S000068846|PMID:12730220 IMP P acetyl CoA carboxylase YNR016C|ABP2|FAS3|MTR7 gene taxon:4932 20030731 SGD
+SGD S000005299 ACC1 GO:0006633 SGD_REF:S000058499 TAS P acetyl CoA carboxylase YNR016C|ABP2|FAS3|MTR7 gene taxon:4932 20010119 SGD
+SGD S000005299 ACC1 GO:0006998 SGD_REF:S000058277|PMID:9442897 TAS P acetyl CoA carboxylase YNR016C|ABP2|FAS3|MTR7 gene taxon:4932 20010118 SGD
+SGD S000004121 ACE2 GO:0005634 SGD_REF:S000054707|PMID:1730413 IDA C zinc finger transcription factor YLR131C gene taxon:4932 20051012 SGD
+SGD S000004121 ACE2 GO:0005634 SGD_REF:S000081332|PMID:15200949 IDA C zinc finger transcription factor YLR131C gene taxon:4932 20051012 SGD
+SGD S000004121 ACE2 GO:0005829 SGD_REF:S000054707|PMID:1730413 IDA C zinc finger transcription factor YLR131C gene taxon:4932 20051012 SGD
+SGD S000004121 ACE2 GO:0005829 SGD_REF:S000081332|PMID:15200949 IDA C zinc finger transcription factor YLR131C gene taxon:4932 20051012 SGD
+SGD S000004121 ACE2 GO:0016563 SGD_REF:S000044727|PMID:10409653 IMP F zinc finger transcription factor YLR131C gene taxon:4932 20060420 SGD
+SGD S000004121 ACE2 GO:0000114 SGD_REF:S000044727|PMID:10409653 IDA P zinc finger transcription factor YLR131C gene taxon:4932 20010118 SGD
+SGD S000004134 ACF2 GO:0005622 SGD_REF:S000071737|PMID:12455695 TAS C YLR144C|ENG2|PCA1 gene taxon:4932 20021206 SGD
+SGD S000004134 ACF2 GO:0004338 SGD_REF:S000071737|PMID:12455695 TAS F YLR144C|ENG2|PCA1 gene taxon:4932 20021206 SGD
+SGD S000004134 ACF2 GO:0030036 SGD_REF:S000040513|PMID:9214384 IDA P YLR144C|ENG2|PCA1 gene taxon:4932 20020807 SGD
+SGD S000003843 ACF4 GO:0008372 SGD_REF:S000069584 ND C YJR083C gene taxon:4932 20060315 SGD
+SGD S000003843 ACF4 GO:0005554 SGD_REF:S000069584 ND F YJR083C gene taxon:4932 20060315 SGD
+SGD S000003843 ACF4 GO:0030036 SGD_REF:S000074191|PMID:14566057 RCA P YJR083C gene taxon:4932 20050608 SGD
+SGD S000000111 ACH1 GO:0005739 SGD_REF:S000073148|PMID:12606555 IDA C acetyl CoA hydrolase YBL015W gene taxon:4932 20030519 SGD
+SGD S000000111 ACH1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C acetyl CoA hydrolase YBL015W gene taxon:4932 20040924 SGD
+SGD S000000111 ACH1 GO:0005829 SGD_REF:S000068747|PMID:11746603 IDA C acetyl CoA hydrolase YBL015W gene taxon:4932 20021125 SGD
+SGD S000000111 ACH1 GO:0003986 SGD_REF:S000058496 TAS F acetyl CoA hydrolase YBL015W gene taxon:4932 20010119 SGD
+SGD S000000111 ACH1 GO:0003986 SGD_REF:S000073148|PMID:12606555 IDA F acetyl CoA hydrolase YBL015W gene taxon:4932 20030519 SGD
+SGD S000000111 ACH1 GO:0006083 SGD_REF:S000053049|PMID:8841387 IMP P acetyl CoA hydrolase YBL015W gene taxon:4932 20010118 SGD
+SGD S000000111 ACH1 GO:0006084 SGD_REF:S000058496 TAS P acetyl CoA hydrolase YBL015W gene taxon:4932 20010119 SGD
+SGD S000002362 ACK1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C a TRP/SEL-1 domain containing protein YDL203C gene taxon:4932 20040813 SGD
+SGD S000002362 ACK1 GO:0005554 SGD_REF:S000069584 ND F a TRP/SEL-1 domain containing protein YDL203C gene taxon:4932 20030203 SGD
+SGD S000002362 ACK1 GO:0000004 SGD_REF:S000069584 ND P a TRP/SEL-1 domain containing protein YDL203C gene taxon:4932 20030203 SGD
+SGD S000006188 ACM1 GO:0008372 SGD_REF:S000069584 ND C YPL267W gene taxon:4932 20021126 SGD
+SGD S000006188 ACM1 GO:0005554 SGD_REF:S000069584 ND F YPL267W gene taxon:4932 20021126 SGD
+SGD S000006188 ACM1 GO:0000004 SGD_REF:S000069584 ND P YPL267W gene taxon:4932 20021126 SGD
+SGD S000002919 ACN9 GO:0005758 SGD_REF:S000056338|PMID:10103055 IDA C YDR511W gene taxon:4932 20020716 SGD
+SGD S000002919 ACN9 GO:0005554 SGD_REF:S000069584 ND F YDR511W gene taxon:4932 20020716 SGD
+SGD S000002919 ACN9 GO:0006094 SGD_REF:S000056338|PMID:10103055 IMP P YDR511W gene taxon:4932 20020716 SGD
+SGD S000002919 ACN9 GO:0015978 SGD_REF:S000056338|PMID:10103055 IMP P YDR511W gene taxon:4932 20020716 SGD
+SGD S000004295 ACO1 GO:0005759 SGD_REF:S000058126|PMID:9175438 TAS C aconitase YLR304C|GLU1 gene taxon:4932 20021201 SGD
+SGD S000004295 ACO1 GO:0005829 SGD_REF:S000058126|PMID:9175438 TAS C aconitase YLR304C|GLU1 gene taxon:4932 20010118 SGD
+SGD S000004295 ACO1 GO:0042645 SGD_REF:S000050870|PMID:10869431 IDA C aconitase YLR304C|GLU1 gene taxon:4932 20050401 SGD
+SGD S000004295 ACO1 GO:0003994 SGD_REF:S000058126|PMID:9175438 TAS F aconitase YLR304C|GLU1 gene taxon:4932 20010118 SGD
+SGD S000004295 ACO1 GO:0000002 SGD_REF:S000080741|PMID:15692048 IMP P aconitase YLR304C|GLU1 gene taxon:4932 20050401 SGD
+SGD S000004295 ACO1 GO:0006099 SGD_REF:S000058126|PMID:9175438 TAS P aconitase YLR304C|GLU1 gene taxon:4932 20010118 SGD
+SGD S000004295 ACO1 GO:0006101 SGD_REF:S000058126|PMID:9175438 TAS P aconitase YLR304C|GLU1 gene taxon:4932 20010118 SGD
+SGD S000004295 ACO1 GO:0006537 SGD_REF:S000058126|PMID:9175438 TAS P aconitase YLR304C|GLU1 gene taxon:4932 20010118 SGD
+SGD S000004295 ACO1 GO:0019541 SGD_REF:S000059712|PMID:11179416 IEP P aconitase YLR304C|GLU1 gene taxon:4932 20011023 SGD
+SGD S000003736 ACO2 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YJL200C gene taxon:4932 20031028 SGD
+SGD S000003736 ACO2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YJL200C gene taxon:4932 20031210 SGD
+SGD S000003736 ACO2 GO:0003994 SGD_REF:S000072463|PMID:10592175 ISS F YJL200C gene taxon:4932 20030213 SGD
+SGD S000003736 ACO2 GO:0000004 SGD_REF:S000069584 ND P YJL200C gene taxon:4932 20021002 SGD
+SGD S000001675 ACP1 GO:0005739 SGD_REF:S000044091|PMID:8595652 TAS C acyl carrier protein YKL192C gene taxon:4932 20030212 SGD
+SGD S000001675 ACP1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C acyl carrier protein YKL192C gene taxon:4932 20040928 SGD
+SGD S000001675 ACP1 GO:0000036 SGD_REF:S000044091|PMID:8595652 TAS F acyl carrier protein YKL192C gene taxon:4932 20010118 SGD
+SGD S000001675 ACP1 GO:0006633 SGD_REF:S000058499 TAS P acyl carrier protein YKL192C gene taxon:4932 20010119 SGD
+SGD S000000050 ACS1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C acetyl CoA synthetase YAL054C|FUN44 gene taxon:4932 20040928 SGD
+SGD S000000050 ACS1 GO:0005829 SGD_REF:S000048464|PMID:9711835 IDA C acetyl CoA synthetase YAL054C|FUN44 gene taxon:4932 20020920 SGD
+SGD S000000050 ACS1 GO:0003987 SGD_REF:S000047927|PMID:8910545 IDA F acetyl CoA synthetase YAL054C|FUN44 gene taxon:4932 20020716 SGD
+SGD S000000050 ACS1 GO:0006085 SGD_REF:S000047927|PMID:8910545 IDA P acetyl CoA synthetase YAL054C|FUN44 gene taxon:4932 20020716 SGD
+SGD S000000050 ACS1 GO:0019654 SGD_REF:S000047705|PMID:1363452 IMP P acetyl CoA synthetase YAL054C|FUN44 gene taxon:4932 20020716 SGD
+SGD S000004143 ACS2 GO:0005829 SGD_REF:S000048464|PMID:9711835 IDA C acetyl CoA synthetase YLR153C gene taxon:4932 20020920 SGD
+SGD S000004143 ACS2 GO:0003987 SGD_REF:S000047927|PMID:8910545 IDA F acetyl CoA synthetase YLR153C gene taxon:4932 20020716 SGD
+SGD S000004143 ACS2 GO:0006085 SGD_REF:S000047927|PMID:8910545 IDA P acetyl CoA synthetase YLR153C gene taxon:4932 20020716 SGD
+SGD S000001855 ACT1 GO:0000123 SGD_REF:S000046619|PMID:10911987 IDA C actin YFL039C|ABY1|END7|actin gene taxon:4932 20020918 SGD
+SGD S000001855 ACT1 GO:0000142 SGD_REF:S000041005|PMID:10652251 TAS C actin YFL039C|ABY1|END7|actin gene taxon:4932 20041001 SGD
+SGD S000001855 ACT1 GO:0000812 SGD_REF:S000074662|PMID:14645854 IPI C actin YFL039C|ABY1|END7|actin gene taxon:4932 20040412 SGD
+SGD S000001855 ACT1 GO:0000812 SGD_REF:S000075430|PMID:14690608 IPI C actin YFL039C|ABY1|END7|actin gene taxon:4932 20040412 SGD
+SGD S000001855 ACT1 GO:0005884 SGD_REF:S000058492 TAS C actin YFL039C|ABY1|END7|actin gene taxon:4932 20010119 SGD
+SGD S000001855 ACT1 GO:0030479 SGD_REF:S000041005|PMID:10652251 TAS C actin YFL039C|ABY1|END7|actin gene taxon:4932 20041001 SGD
+SGD S000001855 ACT1 GO:0030482 SGD_REF:S000041005|PMID:10652251 TAS C actin YFL039C|ABY1|END7|actin gene taxon:4932 20041001 SGD
+SGD S000001855 ACT1 GO:0031011 SGD_REF:S000040657|PMID:10952318 IPI SGD:S000003118 C actin YFL039C|ABY1|END7|actin gene taxon:4932 20050411 SGD
+SGD S000001855 ACT1 GO:0043189 SGD_REF:S000079775|PMID:15485911 IPI C actin YFL039C|ABY1|END7|actin gene taxon:4932 20050207 SGD
+SGD S000001855 ACT1 GO:0005200 SGD_REF:S000058492 TAS F actin YFL039C|ABY1|END7|actin gene taxon:4932 20010119 SGD
+SGD S000001855 ACT1 GO:0000001 SGD_REF:S000046605|PMID:10639324 TAS P actin YFL039C|ABY1|END7|actin gene taxon:4932 20010118 SGD
+SGD S000001855 ACT1 GO:0000001 SGD_REF:S000041005|PMID:10652251 TAS P actin YFL039C|ABY1|END7|actin gene taxon:4932 20010118 SGD
+SGD S000001855 ACT1 GO:0000011 SGD_REF:S000046605|PMID:10639324 TAS P actin YFL039C|ABY1|END7|actin gene taxon:4932 20010118 SGD
+SGD S000001855 ACT1 GO:0000011 SGD_REF:S000041005|PMID:10652251 TAS P actin YFL039C|ABY1|END7|actin gene taxon:4932 20010118 SGD
+SGD S000001855 ACT1 GO:0000132 SGD_REF:S000041005|PMID:10652251 TAS P actin YFL039C|ABY1|END7|actin gene taxon:4932 20040128 SGD
+SGD S000001855 ACT1 GO:0000132 SGD_REF:S000046605|PMID:10639324 TAS P actin YFL039C|ABY1|END7|actin gene taxon:4932 20040128 SGD
+SGD S000001855 ACT1 GO:0000910 SGD_REF:S000058492 TAS P actin YFL039C|ABY1|END7|actin gene taxon:4932 20010119 SGD
+SGD S000001855 ACT1 GO:0000910 SGD_REF:S000046605|PMID:10639324 TAS P actin YFL039C|ABY1|END7|actin gene taxon:4932 20010119 SGD
+SGD S000001855 ACT1 GO:0000910 SGD_REF:S000041005|PMID:10652251 TAS P actin YFL039C|ABY1|END7|actin gene taxon:4932 20010119 SGD
+SGD S000001855 ACT1 GO:0001300 SGD_REF:S000077155|PMID:15024029 IMP P actin YFL039C|ABY1|END7|actin gene taxon:4932 20041001 SGD
+SGD S000001855 ACT1 GO:0006357 SGD_REF:S000046619|PMID:10911987 IDA P actin YFL039C|ABY1|END7|actin gene taxon:4932 20020918 SGD
+SGD S000001855 ACT1 GO:0006887 SGD_REF:S000058492 TAS P actin YFL039C|ABY1|END7|actin gene taxon:4932 20010119 SGD
+SGD S000001855 ACT1 GO:0006887 SGD_REF:S000041005|PMID:10652251 TAS P actin YFL039C|ABY1|END7|actin gene taxon:4932 20010118 SGD
+SGD S000001855 ACT1 GO:0006887 SGD_REF:S000046605|PMID:10639324 TAS P actin YFL039C|ABY1|END7|actin gene taxon:4932 20010118 SGD
+SGD S000001855 ACT1 GO:0006897 SGD_REF:S000058492 TAS P actin YFL039C|ABY1|END7|actin gene taxon:4932 20010119 SGD
+SGD S000001855 ACT1 GO:0006897 SGD_REF:S000041005|PMID:10652251 TAS P actin YFL039C|ABY1|END7|actin gene taxon:4932 20010118 SGD
+SGD S000001855 ACT1 GO:0006897 SGD_REF:S000046605|PMID:10639324 TAS P actin YFL039C|ABY1|END7|actin gene taxon:4932 20010118 SGD
+SGD S000001855 ACT1 GO:0006970 SGD_REF:S000058492 TAS P actin YFL039C|ABY1|END7|actin gene taxon:4932 20010119 SGD
+SGD S000001855 ACT1 GO:0006970 SGD_REF:S000046605|PMID:10639324 TAS P actin YFL039C|ABY1|END7|actin gene taxon:4932 20010118 SGD
+SGD S000001855 ACT1 GO:0006970 SGD_REF:S000041005|PMID:10652251 TAS P actin YFL039C|ABY1|END7|actin gene taxon:4932 20010118 SGD
+SGD S000001855 ACT1 GO:0007047 SGD_REF:S000046605|PMID:10639324 TAS P actin YFL039C|ABY1|END7|actin gene taxon:4932 20010118 SGD
+SGD S000001855 ACT1 GO:0007047 SGD_REF:S000041005|PMID:10652251 TAS P actin YFL039C|ABY1|END7|actin gene taxon:4932 20010118 SGD
+SGD S000001855 ACT1 GO:0007119 SGD_REF:S000041005|PMID:10652251 TAS P actin YFL039C|ABY1|END7|actin gene taxon:4932 20041001 SGD
+SGD S000001855 ACT1 GO:0009306 SGD_REF:S000058492 TAS P actin YFL039C|ABY1|END7|actin gene taxon:4932 20011217 SGD
+SGD S000001855 ACT1 GO:0016573 SGD_REF:S000046619|PMID:10911987 IDA P actin YFL039C|ABY1|END7|actin gene taxon:4932 20020918 SGD
+SGD S000001855 ACT1 GO:0030037 SGD_REF:S000058492 TAS P actin YFL039C|ABY1|END7|actin gene taxon:4932 20011217 SGD
+SGD S000001855 ACT1 GO:0030050 SGD_REF:S000041005|PMID:10652251 TAS P actin YFL039C|ABY1|END7|actin gene taxon:4932 20011217 SGD
+SGD S000001855 ACT1 GO:0030437 SGD_REF:S000058492 TAS P actin YFL039C|ABY1|END7|actin gene taxon:4932 20011217 SGD
+SGD S000001855 ACT1 GO:0030468 SGD_REF:S000058492 TAS P actin YFL039C|ABY1|END7|actin gene taxon:4932 20010302 SGD
+SGD S000002856 ADA2 GO:0000124 SGD_REF:S000048255|PMID:9674426 IDA C transcription factor YDR448W|SWI8 gene taxon:4932 20010221 SGD
+SGD S000002856 ADA2 GO:0005671 SGD_REF:S000042121|PMID:10490601 IPI C transcription factor YDR448W|SWI8 gene taxon:4932 20031215 SGD
+SGD S000002856 ADA2 GO:0046695 SGD_REF:S000071997|PMID:12446794 IPI C transcription factor YDR448W|SWI8 gene taxon:4932 20041024 SGD
+SGD S000002856 ADA2 GO:0003713 SGD_REF:S000069189|PMID:11857084 TAS F transcription factor YDR448W|SWI8 gene taxon:4932 20021102 SGD
+SGD S000002856 ADA2 GO:0016568 SGD_REF:S000061032|PMID:10839822 TAS P transcription factor YDR448W|SWI8 gene taxon:4932 20020426 SGD
+SGD S000002856 ADA2 GO:0016573 SGD_REF:S000061032|PMID:10839822 TAS P transcription factor YDR448W|SWI8 gene taxon:4932 20020426 SGD
+SGD S000004796 ADD37 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YMR184W gene taxon:4932 20031028 SGD
+SGD S000004796 ADD37 GO:0005554 SGD_REF:S000069584 ND F YMR184W gene taxon:4932 20021126 SGD
+SGD S000004796 ADD37 GO:0030433 SGD_REF:S000115312|PMID:12711700 IMP P YMR184W gene taxon:4932 20060511 SGD
+SGD S000001689 ADD66 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YKL206C gene taxon:4932 20031028 SGD
+SGD S000001689 ADD66 GO:0005554 SGD_REF:S000069584 ND F YKL206C gene taxon:4932 20021126 SGD
+SGD S000001689 ADD66 GO:0030433 SGD_REF:S000115312|PMID:12711700 IMP P YKL206C gene taxon:4932 20060511 SGD
+SGD S000000070 ADE1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C phosphoribosyl amino imidazolesuccinocarbozamide synthetase YAR015W gene taxon:4932 20031028 SGD
+SGD S000000070 ADE1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C phosphoribosyl amino imidazolesuccinocarbozamide synthetase YAR015W gene taxon:4932 20031028 SGD
+SGD S000000070 ADE1 GO:0004639 SGD_REF:S000039345|PMID:1756975 IDA F phosphoribosyl amino imidazolesuccinocarbozamide synthetase YAR015W gene taxon:4932 20021001 SGD
+SGD S000000070 ADE1 GO:0006144 SGD_REF:S000053972|PMID:8939809 IMP P phosphoribosyl amino imidazolesuccinocarbozamide synthetase YAR015W gene taxon:4932 20021001 SGD
+SGD S000000070 ADE1 GO:0006144 SGD_REF:S000053972|PMID:8939809 TAS P phosphoribosyl amino imidazolesuccinocarbozamide synthetase YAR015W gene taxon:4932 20021001 SGD
+SGD S000000070 ADE1 GO:0006164 SGD_REF:S000070200 TAS P phosphoribosyl amino imidazolesuccinocarbozamide synthetase YAR015W gene taxon:4932 20031219 SGD
+SGD S000000070 ADE1 GO:0006189 SGD_REF:S000070200 TAS P phosphoribosyl amino imidazolesuccinocarbozamide synthetase YAR015W gene taxon:4932 20050711 SGD
+SGD S000005164 ADE12 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C adenylosuccinate synthetase YNL220W|BRA9 gene taxon:4932 20031028 SGD
+SGD S000005164 ADE12 GO:0004019 SGD_REF:S000042931|PMID:10417315 IDA F adenylosuccinate synthetase YNL220W|BRA9 gene taxon:4932 20021212 SGD
+SGD S000005164 ADE12 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P adenylosuccinate synthetase YNL220W|BRA9 gene taxon:4932 20060227 SGD
+SGD S000005164 ADE12 GO:0006164 SGD_REF:S000070200 TAS P adenylosuccinate synthetase YNL220W|BRA9 gene taxon:4932 20031219 SGD
+SGD S000005164 ADE12 GO:0046086 SGD_REF:S000042931|PMID:10417315 TAS P adenylosuccinate synthetase YNL220W|BRA9 gene taxon:4932 20020927 SGD
+SGD S000004351 ADE13 GO:0008372 SGD_REF:S000069584 ND C adenylosuccinate lyase YLR359W|BRA1|BRA8 gene taxon:4932 20020927 SGD
+SGD S000004351 ADE13 GO:0004018 SGD_REF:S000070200 TAS F adenylosuccinate lyase YLR359W|BRA1|BRA8 gene taxon:4932 20021212 SGD
+SGD S000004351 ADE13 GO:0006144 SGD_REF:S000051099|PMID:7896125 TAS P adenylosuccinate lyase YLR359W|BRA1|BRA8 gene taxon:4932 20021001 SGD
+SGD S000004351 ADE13 GO:0006164 SGD_REF:S000070200 TAS P adenylosuccinate lyase YLR359W|BRA1|BRA8 gene taxon:4932 20031219 SGD
+SGD S000004351 ADE13 GO:0006189 SGD_REF:S000070200 TAS P adenylosuccinate lyase YLR359W|BRA1|BRA8 gene taxon:4932 20050711 SGD
+SGD S000004018 ADE16 GO:0005829 SGD_REF:S000053260|PMID:10877846 IDA C 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) transformylase/IMP cyclohydrolase YLR028C gene taxon:4932 20010626 SGD
+SGD S000004018 ADE16 GO:0003937 SGD_REF:S000053260|PMID:10877846 IDA F 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) transformylase/IMP cyclohydrolase YLR028C gene taxon:4932 20010626 SGD
+SGD S000004018 ADE16 GO:0004643 SGD_REF:S000053260|PMID:10877846 IDA F 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) transformylase/IMP cyclohydrolase YLR028C gene taxon:4932 20010626 SGD
+SGD S000004018 ADE16 GO:0006164 SGD_REF:S000053260|PMID:10877846 IDA P 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) transformylase/IMP cyclohydrolase YLR028C gene taxon:4932 20031219 SGD
+SGD S000004018 ADE16 GO:0006164 SGD_REF:S000053260|PMID:10877846 IMP P 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) transformylase/IMP cyclohydrolase YLR028C gene taxon:4932 20031219 SGD
+SGD S000004018 ADE16 GO:0006189 SGD_REF:S000053260|PMID:10877846 IMP P 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) transformylase/IMP cyclohydrolase YLR028C gene taxon:4932 20010626 SGD
+SGD S000004018 ADE16 GO:0006189 SGD_REF:S000053260|PMID:10877846 IDA P 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) transformylase/IMP cyclohydrolase YLR028C gene taxon:4932 20010626 SGD
+SGD S000004018 ADE16 GO:0009060 SGD_REF:S000053260|PMID:10877846 IEP P 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) transformylase/IMP cyclohydrolase YLR028C gene taxon:4932 20010626 SGD
+SGD S000004018 ADE16 GO:0030437 SGD_REF:S000053260|PMID:10877846 IEP P 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) transformylase/IMP cyclohydrolase YLR028C gene taxon:4932 20010626 SGD
+SGD S000004727 ADE17 GO:0005829 SGD_REF:S000053260|PMID:10877846 IDA C 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) transformylase/IMP cyclohydrolase YMR120C gene taxon:4932 20010626 SGD
+SGD S000004727 ADE17 GO:0003937 SGD_REF:S000053260|PMID:10877846 IDA F 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) transformylase/IMP cyclohydrolase YMR120C gene taxon:4932 20010626 SGD
+SGD S000004727 ADE17 GO:0004643 SGD_REF:S000053260|PMID:10877846 IDA F 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) transformylase/IMP cyclohydrolase YMR120C gene taxon:4932 20010626 SGD
+SGD S000004727 ADE17 GO:0006164 SGD_REF:S000053260|PMID:10877846 IDA P 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) transformylase/IMP cyclohydrolase YMR120C gene taxon:4932 20031219 SGD
+SGD S000004727 ADE17 GO:0006164 SGD_REF:S000053260|PMID:10877846 IMP P 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) transformylase/IMP cyclohydrolase YMR120C gene taxon:4932 20031219 SGD
+SGD S000004727 ADE17 GO:0006189 SGD_REF:S000053260|PMID:10877846 IMP P 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) transformylase/IMP cyclohydrolase YMR120C gene taxon:4932 20010626 SGD
+SGD S000004727 ADE17 GO:0006189 SGD_REF:S000053260|PMID:10877846 IDA P 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) transformylase/IMP cyclohydrolase YMR120C gene taxon:4932 20010626 SGD
+SGD S000005654 ADE2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C phosphoribosylamino-imidazole-carboxylase YOR128C gene taxon:4932 20031028 SGD
+SGD S000005654 ADE2 GO:0004638 SGD_REF:S000070200 TAS F phosphoribosylamino-imidazole-carboxylase YOR128C gene taxon:4932 20021212 SGD
+SGD S000005654 ADE2 GO:0006144 SGD_REF:S000053972|PMID:8939809 IMP P phosphoribosylamino-imidazole-carboxylase YOR128C gene taxon:4932 20021001 SGD
+SGD S000005654 ADE2 GO:0006144 SGD_REF:S000053972|PMID:8939809 TAS P phosphoribosylamino-imidazole-carboxylase YOR128C gene taxon:4932 20021001 SGD
+SGD S000005654 ADE2 GO:0006164 SGD_REF:S000070200 TAS P phosphoribosylamino-imidazole-carboxylase YOR128C gene taxon:4932 20031219 SGD
+SGD S000005654 ADE2 GO:0006189 SGD_REF:S000070200 TAS P phosphoribosylamino-imidazole-carboxylase YOR128C gene taxon:4932 20050428 SGD
+SGD S000003436 ADE3 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C C1-tetrahydrofolate synthase YGR204W gene taxon:4932 20031028 SGD
+SGD S000003436 ADE3 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C C1-tetrahydrofolate synthase YGR204W gene taxon:4932 20020507 SGD
+SGD S000003436 ADE3 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C C1-tetrahydrofolate synthase YGR204W gene taxon:4932 20031028 SGD
+SGD S000003436 ADE3 GO:0004329 SGD_REF:S000043392|PMID:8852837 TAS F C1-tetrahydrofolate synthase YGR204W gene taxon:4932 20020930 SGD
+SGD S000003436 ADE3 GO:0004329 SGD_REF:S000045356|PMID:8464869 IMP F C1-tetrahydrofolate synthase YGR204W gene taxon:4932 20031218 SGD
+SGD S000003436 ADE3 GO:0004477 SGD_REF:S000045356|PMID:8464869 IMP F C1-tetrahydrofolate synthase YGR204W gene taxon:4932 20031218 SGD
+SGD S000003436 ADE3 GO:0004488 SGD_REF:S000045356|PMID:8464869 IMP F C1-tetrahydrofolate synthase YGR204W gene taxon:4932 20031218 SGD
+SGD S000003436 ADE3 GO:0006760 SGD_REF:S000070200 TAS P C1-tetrahydrofolate synthase YGR204W gene taxon:4932 20031218 SGD
+SGD S000003436 ADE3 GO:0009113 SGD_REF:S000045356|PMID:8464869 IMP P C1-tetrahydrofolate synthase YGR204W gene taxon:4932 20020927 SGD
+SGD S000004915 ADE4 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C phosphoribosylpyrophosphate amidotransferase YMR300C gene taxon:4932 20031028 SGD
+SGD S000004915 ADE4 GO:0004044 SGD_REF:S000070200 TAS F phosphoribosylpyrophosphate amidotransferase YMR300C gene taxon:4932 20021212 SGD
+SGD S000004915 ADE4 GO:0006144 SGD_REF:S000068861|PMID:11689683 IMP P phosphoribosylpyrophosphate amidotransferase YMR300C gene taxon:4932 20021001 SGD
+SGD S000004915 ADE4 GO:0006144 SGD_REF:S000068861|PMID:11689683 TAS P phosphoribosylpyrophosphate amidotransferase YMR300C gene taxon:4932 20021001 SGD
+SGD S000004915 ADE4 GO:0006164 SGD_REF:S000070200 TAS P phosphoribosylpyrophosphate amidotransferase YMR300C gene taxon:4932 20031219 SGD
+SGD S000004915 ADE4 GO:0006189 SGD_REF:S000070200 TAS P phosphoribosylpyrophosphate amidotransferase YMR300C gene taxon:4932 20050711 SGD
+SGD S000003203 ADE5,7 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C aminoimidazole ribotide synthetase, glycinamide ribotide synthetase YGL234W gene taxon:4932 20020507 SGD
+SGD S000003203 ADE5,7 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C aminoimidazole ribotide synthetase, glycinamide ribotide synthetase YGL234W gene taxon:4932 20031028 SGD
+SGD S000003203 ADE5,7 GO:0004637 SGD_REF:S000070200 TAS F aminoimidazole ribotide synthetase, glycinamide ribotide synthetase YGL234W gene taxon:4932 20021212 SGD
+SGD S000003203 ADE5,7 GO:0004641 SGD_REF:S000070200 TAS F aminoimidazole ribotide synthetase, glycinamide ribotide synthetase YGL234W gene taxon:4932 20021212 SGD
+SGD S000003203 ADE5,7 GO:0006144 SGD_REF:S000055124|PMID:9148957 TAS P aminoimidazole ribotide synthetase, glycinamide ribotide synthetase YGL234W gene taxon:4932 20021001 SGD
+SGD S000003203 ADE5,7 GO:0006164 SGD_REF:S000070200 TAS P aminoimidazole ribotide synthetase, glycinamide ribotide synthetase YGL234W gene taxon:4932 20031219 SGD
+SGD S000003203 ADE5,7 GO:0006189 SGD_REF:S000070200 TAS P aminoimidazole ribotide synthetase, glycinamide ribotide synthetase YGL234W gene taxon:4932 20050711 SGD
+SGD S000003293 ADE6 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C 5'-phosphoribosylformyl glycinamidine synthetase YGR061C gene taxon:4932 20031028 SGD
+SGD S000003293 ADE6 GO:0004642 SGD_REF:S000046114|PMID:1743513 TAS F 5'-phosphoribosylformyl glycinamidine synthetase YGR061C gene taxon:4932 20020917 SGD
+SGD S000003293 ADE6 GO:0006164 SGD_REF:S000046114|PMID:1743513 IMP P 5'-phosphoribosylformyl glycinamidine synthetase YGR061C gene taxon:4932 20020917 SGD
+SGD S000003293 ADE6 GO:0006164 SGD_REF:S000070200 TAS P 5'-phosphoribosylformyl glycinamidine synthetase YGR061C gene taxon:4932 20031219 SGD
+SGD S000003293 ADE6 GO:0006189 SGD_REF:S000070200 TAS P 5'-phosphoribosylformyl glycinamidine synthetase YGR061C gene taxon:4932 20050711 SGD
+SGD S000002816 ADE8 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C glycinamide ribotide transformylase YDR408C gene taxon:4932 20031028 SGD
+SGD S000002816 ADE8 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C glycinamide ribotide transformylase YDR408C gene taxon:4932 20031028 SGD
+SGD S000002816 ADE8 GO:0004644 SGD_REF:S000070200 TAS F glycinamide ribotide transformylase YDR408C gene taxon:4932 20021212 SGD
+SGD S000002816 ADE8 GO:0006164 SGD_REF:S000070200 TAS P glycinamide ribotide transformylase YDR408C gene taxon:4932 20031219 SGD
+SGD S000002816 ADE8 GO:0006189 SGD_REF:S000070200 TAS P glycinamide ribotide transformylase YDR408C gene taxon:4932 20050711 SGD
+SGD S000002816 ADE8 GO:0046084 SGD_REF:S000053972|PMID:8939809 TAS P glycinamide ribotide transformylase YDR408C gene taxon:4932 20020927 SGD
+SGD S000005446 ADH1 GO:0005829 SGD_REF:S000071144 TAS C alcohol dehydrogenase YOL086C|ADC1 gene taxon:4932 20020920 SGD
+SGD S000005446 ADH1 GO:0004022 SGD_REF:S000071144 TAS F alcohol dehydrogenase YOL086C|ADC1 gene taxon:4932 20020920 SGD
+SGD S000005446 ADH1 GO:0004022 SGD_REF:S000061496|PMID:6985717 IDA F alcohol dehydrogenase YOL086C|ADC1 gene taxon:4932 20051212 SGD
+SGD S000005446 ADH1 GO:0006113 SGD_REF:S000071144 TAS P alcohol dehydrogenase YOL086C|ADC1 gene taxon:4932 20020920 SGD
+SGD S000005446 ADH1 GO:0006113 SGD_REF:S000113785 IMP P alcohol dehydrogenase YOL086C|ADC1 gene taxon:4932 20051214 SGD
+SGD S000004918 ADH2 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C alcohol dehydrogenase II YMR303C|ADR2 gene taxon:4932 20020507 SGD
+SGD S000004918 ADH2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C alcohol dehydrogenase II YMR303C|ADR2 gene taxon:4932 20031028 SGD
+SGD S000004918 ADH2 GO:0004022 SGD_REF:S000057123|PMID:3546317 IDA F alcohol dehydrogenase II YMR303C|ADR2 gene taxon:4932 20021002 SGD
+SGD S000004918 ADH2 GO:0006067 SGD_REF:S000057531|PMID:7900189 TAS P alcohol dehydrogenase II YMR303C|ADR2 gene taxon:4932 20020823 SGD
+SGD S000004918 ADH2 GO:0006067 SGD_REF:S000057123|PMID:3546317 IDA P alcohol dehydrogenase II YMR303C|ADR2 gene taxon:4932 20051215 SGD
+SGD S000004918 ADH2 GO:0006113 SGD_REF:S000071144 TAS P alcohol dehydrogenase II YMR303C|ADR2 gene taxon:4932 20020920 SGD
+SGD S000004918 ADH2 GO:0006113 SGD_REF:S000113785 IMP P alcohol dehydrogenase II YMR303C|ADR2 gene taxon:4932 20051214 SGD
+SGD S000004688 ADH3 GO:0005625 SGD_REF:S000068747|PMID:11746603 IDA C alcohol dehydrogenase isoenzyme III YMR083W gene taxon:4932 20030130 SGD
+SGD S000004688 ADH3 GO:0005759 SGD_REF:S000049393|PMID:3550419 IDA C alcohol dehydrogenase isoenzyme III YMR083W gene taxon:4932 20020920 SGD
+SGD S000004688 ADH3 GO:0004022 SGD_REF:S000049393|PMID:3550419 IDA F alcohol dehydrogenase isoenzyme III YMR083W gene taxon:4932 20020920 SGD
+SGD S000004688 ADH3 GO:0006113 SGD_REF:S000049393|PMID:3550419 ISS P alcohol dehydrogenase isoenzyme III YMR083W gene taxon:4932 20020920 SGD
+SGD S000003225 ADH4 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C alcohol dehydrogenase isoenzyme IV YGL256W|NRC465|ZRG5 gene taxon:4932 20031028 SGD
+SGD S000003225 ADH4 GO:0004024 SGD_REF:S000046776|PMID:3282541 IDA F alcohol dehydrogenase isoenzyme IV YGL256W|NRC465|ZRG5 gene taxon:4932 20020920 SGD
+SGD S000003225 ADH4 GO:0006113 SGD_REF:S000046776|PMID:3282541 IDA P alcohol dehydrogenase isoenzyme IV YGL256W|NRC465|ZRG5 gene taxon:4932 20020920 SGD
+SGD S000000349 ADH5 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C alcohol dehydrogenase isoenzyme V YBR145W gene taxon:4932 20031028 SGD
+SGD S000000349 ADH5 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C alcohol dehydrogenase isoenzyme V YBR145W gene taxon:4932 20031028 SGD
+SGD S000000349 ADH5 GO:0004022 SGD_REF:S000059094|PMID:10974568 ISS F alcohol dehydrogenase isoenzyme V YBR145W gene taxon:4932 20020917 SGD
+SGD S000000349 ADH5 GO:0006066 SGD_REF:S000059094|PMID:10974568 ISS P alcohol dehydrogenase isoenzyme V YBR145W gene taxon:4932 20020917 SGD
+SGD S000004937 ADH6 GO:0005625 SGD_REF:S000068777|PMID:11742541 IDA C medium chain alcohol dehydrogenase YMR318C|ADHVI gene taxon:4932 20020829 SGD
+SGD S000004937 ADH6 GO:0008106 SGD_REF:S000068777|PMID:11742541 IDA F medium chain alcohol dehydrogenase YMR318C|ADHVI gene taxon:4932 20020829 SGD
+SGD S000004937 ADH6 GO:0006066 SGD_REF:S000068777|PMID:11742541 IDA P medium chain alcohol dehydrogenase YMR318C|ADHVI gene taxon:4932 20020829 SGD
+SGD S000004937 ADH6 GO:0006081 SGD_REF:S000068777|PMID:11742541 IDA P medium chain alcohol dehydrogenase YMR318C|ADHVI gene taxon:4932 20020829 SGD
+SGD S000000702 ADH7 GO:0005625 SGD_REF:S000071752|PMID:12423374 IDA C medium chain alcohol dehydrogenase YCR105W|ADHVII gene taxon:4932 20021209 SGD
+SGD S000000702 ADH7 GO:0008106 SGD_REF:S000071752|PMID:12423374 IDA F medium chain alcohol dehydrogenase YCR105W|ADHVII gene taxon:4932 20021209 SGD
+SGD S000000702 ADH7 GO:0008106 SGD_REF:S000071752|PMID:12423374 ISS F medium chain alcohol dehydrogenase YCR105W|ADHVII gene taxon:4932 20021209 SGD
+SGD S000000702 ADH7 GO:0006066 SGD_REF:S000071752|PMID:12423374 IDA P medium chain alcohol dehydrogenase YCR105W|ADHVII gene taxon:4932 20021209 SGD
+SGD S000004611 ADI1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C Acireductone Dioxygenease YMR009W gene taxon:4932 20031028 SGD
+SGD S000004611 ADI1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C Acireductone Dioxygenease YMR009W gene taxon:4932 20031028 SGD
+SGD S000004611 ADI1 GO:0016702 SGD_REF:S000082083|PMID:15938715 IGI protein_id:AB158319 F Acireductone Dioxygenease YMR009W gene taxon:4932 20050630 SGD
+SGD S000004611 ADI1 GO:0016702 SGD_REF:S000082083|PMID:15938715 ISS protein_id:AB158319 F Acireductone Dioxygenease YMR009W gene taxon:4932 20050630 SGD
+SGD S000004611 ADI1 GO:0016702 SGD_REF:S000082083|PMID:15938715 IMP F Acireductone Dioxygenease YMR009W gene taxon:4932 20050630 SGD
+SGD S000004611 ADI1 GO:0019509 SGD_REF:S000082083|PMID:15938715 IGI protein_id:AB158319 P Acireductone Dioxygenease YMR009W gene taxon:4932 20050630 SGD
+SGD S000004611 ADI1 GO:0019509 SGD_REF:S000082083|PMID:15938715 IMP P Acireductone Dioxygenease YMR009W gene taxon:4932 20050630 SGD
+SGD S000004611 ADI1 GO:0019509 SGD_REF:S000082083|PMID:15938715 ISS protein_id:AB158319 P Acireductone Dioxygenease YMR009W gene taxon:4932 20050630 SGD
+SGD S000002634 ADK1 GO:0005737 SGD_REF:S000071123|PMID:12045196 TAS C adenylate kinase YDR226W|AKY1|AKY2 gene taxon:4932 20020918 SGD
+SGD S000002634 ADK1 GO:0005758 SGD_REF:S000071123|PMID:12045196 TAS C adenylate kinase YDR226W|AKY1|AKY2 gene taxon:4932 20020918 SGD
+SGD S000002634 ADK1 GO:0004017 SGD_REF:S000071123|PMID:12045196 TAS F adenylate kinase YDR226W|AKY1|AKY2 gene taxon:4932 20021223 SGD
+SGD S000002634 ADK1 GO:0006172 SGD_REF:S000052879|PMID:2848829 IDA P adenylate kinase YDR226W|AKY1|AKY2 gene taxon:4932 20050726 SGD
+SGD S000002634 ADK1 GO:0009117 SGD_REF:S000056004|PMID:2850178 IMP P adenylate kinase YDR226W|AKY1|AKY2 gene taxon:4932 20050314 SGD
+SGD S000000972 ADK2 GO:0005743 SGD_REF:S000043092|PMID:8537371 IDA C adenylate kinase, mitochondrial GTP:AMP phosphotransferase YER170W|AKY3|PAK3 gene taxon:4932 20020927 SGD
+SGD S000000972 ADK2 GO:0005743 SGD_REF:S000081003|PMID:15753074 IDA C adenylate kinase, mitochondrial GTP:AMP phosphotransferase YER170W|AKY3|PAK3 gene taxon:4932 20050314 SGD
+SGD S000000972 ADK2 GO:0004017 SGD_REF:S000043092|PMID:8537371 IDA F adenylate kinase, mitochondrial GTP:AMP phosphotransferase YER170W|AKY3|PAK3 gene taxon:4932 20021223 SGD
+SGD S000000972 ADK2 GO:0004017 SGD_REF:S000081003|PMID:15753074 IDA F adenylate kinase, mitochondrial GTP:AMP phosphotransferase YER170W|AKY3|PAK3 gene taxon:4932 20050314 SGD
+SGD S000000972 ADK2 GO:0009117 SGD_REF:S000081003|PMID:15753074 IDA P adenylate kinase, mitochondrial GTP:AMP phosphotransferase YER170W|AKY3|PAK3 gene taxon:4932 20050314 SGD
+SGD S000003866 ADO1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C adenosine kinase YJR105W gene taxon:4932 20031028 SGD
+SGD S000003866 ADO1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C adenosine kinase YJR105W gene taxon:4932 20031028 SGD
+SGD S000003866 ADO1 GO:0004001 SGD_REF:S000059917|PMID:11223943 IMP F adenosine kinase YJR105W gene taxon:4932 20011004 SGD
+SGD S000003866 ADO1 GO:0004001 SGD_REF:S000059917|PMID:11223943 IDA F adenosine kinase YJR105W gene taxon:4932 20011004 SGD
+SGD S000003866 ADO1 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P adenosine kinase YJR105W gene taxon:4932 20060227 SGD
+SGD S000003866 ADO1 GO:0006144 SGD_REF:S000059917|PMID:11223943 IMP P adenosine kinase YJR105W gene taxon:4932 20011004 SGD
+SGD S000000604 ADP1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YCR011C gene taxon:4932 20020507 SGD
+SGD S000000604 ADP1 GO:0005783 SGD_REF:S000069459|PMID:11914276 IDA C YCR011C gene taxon:4932 20020507 SGD
+SGD S000000604 ADP1 GO:0016021 SGD_REF:S000058031|PMID:9020838 ISS C YCR011C gene taxon:4932 20010306 SGD
+SGD S000000604 ADP1 GO:0042626 SGD_REF:S000058031|PMID:9020838 ISS F YCR011C gene taxon:4932 20010306 SGD
+SGD S000000604 ADP1 GO:0006810 SGD_REF:S000058031|PMID:9020838 ISS P YCR011C gene taxon:4932 20021223 SGD
+SGD S000002624 ADR1 GO:0005634 SGD_REF:S000055196|PMID:10608811 IDA C positive transcriptional regulator YDR216W gene taxon:4932 20020726 SGD
+SGD S000002624 ADR1 GO:0005634 SGD_REF:S000055196|PMID:10608811 ISS C positive transcriptional regulator YDR216W gene taxon:4932 20020726 SGD
+SGD S000002624 ADR1 GO:0005634 SGD_REF:S000055196|PMID:10608811 IPI C positive transcriptional regulator YDR216W gene taxon:4932 20020726 SGD
+SGD S000002624 ADR1 GO:0003700 SGD_REF:S000071682|PMID:12167649 IPI F positive transcriptional regulator YDR216W gene taxon:4932 20030402 SGD
+SGD S000002624 ADR1 GO:0003700 SGD_REF:S000071682|PMID:12167649 TAS F positive transcriptional regulator YDR216W gene taxon:4932 20030402 SGD
+SGD S000002624 ADR1 GO:0006109 SGD_REF:S000071682|PMID:12167649 IGI P positive transcriptional regulator YDR216W gene taxon:4932 20030402 SGD
+SGD S000002624 ADR1 GO:0006109 SGD_REF:S000071682|PMID:12167649 IPI P positive transcriptional regulator YDR216W gene taxon:4932 20030402 SGD
+SGD S000002624 ADR1 GO:0006109 SGD_REF:S000071682|PMID:12167649 TAS P positive transcriptional regulator YDR216W gene taxon:4932 20030402 SGD
+SGD S000002624 ADR1 GO:0006350 SGD_REF:S000071682|PMID:12167649 IGI P positive transcriptional regulator YDR216W gene taxon:4932 20030402 SGD
+SGD S000002624 ADR1 GO:0006350 SGD_REF:S000071682|PMID:12167649 IPI P positive transcriptional regulator YDR216W gene taxon:4932 20030402 SGD
+SGD S000002624 ADR1 GO:0006350 SGD_REF:S000071682|PMID:12167649 TAS P positive transcriptional regulator YDR216W gene taxon:4932 20030402 SGD
+SGD S000002624 ADR1 GO:0007031 SGD_REF:S000061271|PMID:11431484 IMP P positive transcriptional regulator YDR216W gene taxon:4932 20020726 SGD
+SGD S000002624 ADR1 GO:0045014 SGD_REF:S000073798|PMID:12676948 IMP P positive transcriptional regulator YDR216W gene taxon:4932 20051212 SGD
+SGD S000000603 ADY2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C transmembrane protein YCR010C|ATO1 gene taxon:4932 20040928 SGD
+SGD S000000603 ADY2 GO:0016020 SGD_REF:S000071765|PMID:12429834 ISS C transmembrane protein YCR010C|ATO1 gene taxon:4932 20021213 SGD
+SGD S000000603 ADY2 GO:0008519 SGD_REF:S000071765|PMID:12429834 IMP F transmembrane protein YCR010C|ATO1 gene taxon:4932 20051025 SGD
+SGD S000000603 ADY2 GO:0008519 SGD_REF:S000071765|PMID:12429834 ISS WB:amt-1 F transmembrane protein YCR010C|ATO1 gene taxon:4932 20051025 SGD
+SGD S000000603 ADY2 GO:0008519 SGD_REF:S000071765|PMID:12429834 IEP F transmembrane protein YCR010C|ATO1 gene taxon:4932 20051025 SGD
+SGD S000000603 ADY2 GO:0015123 SGD_REF:S000074898|PMID:14968426 IMP F transmembrane protein YCR010C|ATO1 gene taxon:4932 20040326 SGD
+SGD S000000603 ADY2 GO:0006259 SGD_REF:S000043176|PMID:10051619 IGI P transmembrane protein YCR010C|ATO1 gene taxon:4932 20020923 SGD
+SGD S000000603 ADY2 GO:0006846 SGD_REF:S000074898|PMID:14968426 IMP P transmembrane protein YCR010C|ATO1 gene taxon:4932 20040326 SGD
+SGD S000000603 ADY2 GO:0007126 SGD_REF:S000043176|PMID:10051619 IEP P transmembrane protein YCR010C|ATO1 gene taxon:4932 20020923 SGD
+SGD S000000603 ADY2 GO:0015696 SGD_REF:S000071765|PMID:12429834 IMP P transmembrane protein YCR010C|ATO1 gene taxon:4932 20051025 SGD
+SGD S000000603 ADY2 GO:0015696 SGD_REF:S000071765|PMID:12429834 IEP P transmembrane protein YCR010C|ATO1 gene taxon:4932 20051025 SGD
+SGD S000000603 ADY2 GO:0015696 SGD_REF:S000071765|PMID:12429834 ISS WB:amt-1 P transmembrane protein YCR010C|ATO1 gene taxon:4932 20051025 SGD
+SGD S000000603 ADY2 GO:0019740 SGD_REF:S000071765|PMID:12429834 IMP P transmembrane protein YCR010C|ATO1 gene taxon:4932 20021213 SGD
+SGD S000002398 ADY3 GO:0005628 SGD_REF:S000069721|PMID:11973299 IDA C YDL239C gene taxon:4932 20020920 SGD
+SGD S000002398 ADY3 GO:0005628 SGD_REF:S000069149|PMID:11742972 IDA C YDL239C gene taxon:4932 20020920 SGD
+SGD S000002398 ADY3 GO:0005819 SGD_REF:S000069721|PMID:11973299 IDA C YDL239C gene taxon:4932 20020920 SGD
+SGD S000002398 ADY3 GO:0005515 SGD_REF:S000069721|PMID:11973299 IMP F YDL239C gene taxon:4932 20020920 SGD
+SGD S000002398 ADY3 GO:0005515 SGD_REF:S000069721|PMID:11973299 IPI F YDL239C gene taxon:4932 20020920 SGD
+SGD S000002398 ADY3 GO:0006461 SGD_REF:S000069721|PMID:11973299 IMP P YDL239C gene taxon:4932 20020920 SGD
+SGD S000002398 ADY3 GO:0030435 SGD_REF:S000060989|PMID:11470404 IMP P YDL239C gene taxon:4932 20020925 SGD
+SGD S000002398 ADY3 GO:0030435 SGD_REF:S000060989|PMID:11470404 IEP P YDL239C gene taxon:4932 20020925 SGD
+SGD S000002398 ADY3 GO:0030476 SGD_REF:S000069721|PMID:11973299 IMP P YDL239C gene taxon:4932 20020920 SGD
+SGD S000004217 ADY4 GO:0005816 SGD_REF:S000073593|PMID:12796288 IDA C YLR227C gene taxon:4932 20030708 SGD
+SGD S000004217 ADY4 GO:0005816 SGD_REF:S000073593|PMID:12796288 IMP C YLR227C gene taxon:4932 20030708 SGD
+SGD S000004217 ADY4 GO:0005198 SGD_REF:S000073593|PMID:12796288 IDA F YLR227C gene taxon:4932 20030708 SGD
+SGD S000004217 ADY4 GO:0005198 SGD_REF:S000073593|PMID:12796288 IMP F YLR227C gene taxon:4932 20030708 SGD
+SGD S000004217 ADY4 GO:0030435 SGD_REF:S000060989|PMID:11470404 IMP P YLR227C gene taxon:4932 20020925 SGD
+SGD S000004217 ADY4 GO:0030435 SGD_REF:S000060989|PMID:11470404 IEP P YLR227C gene taxon:4932 20020925 SGD
+SGD S000004668 AEP1 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YMR064W|NCA1 gene taxon:4932 20031028 SGD
+SGD S000004668 AEP1 GO:0005554 SGD_REF:S000057943|PMID:8811190 TAS F YMR064W|NCA1 gene taxon:4932 20010118 SGD
+SGD S000004668 AEP1 GO:0006412 SGD_REF:S000057943|PMID:8811190 TAS P YMR064W|NCA1 gene taxon:4932 20010118 SGD
+SGD S000004895 AEP2 GO:0005739 SGD_REF:S000057943|PMID:8811190 TAS C YMR282C|ATP13 gene taxon:4932 20010118 SGD
+SGD S000004895 AEP2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YMR282C|ATP13 gene taxon:4932 20040928 SGD
+SGD S000004895 AEP2 GO:0005554 SGD_REF:S000057943|PMID:8811190 TAS F YMR282C|ATP13 gene taxon:4932 20010118 SGD
+SGD S000004895 AEP2 GO:0006412 SGD_REF:S000057943|PMID:8811190 TAS P YMR282C|ATP13 gene taxon:4932 20010118 SGD
+SGD S000005926 AEP3 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YPL005W gene taxon:4932 20020507 SGD
+SGD S000005926 AEP3 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YPL005W gene taxon:4932 20031028 SGD
+SGD S000005926 AEP3 GO:0005743 SGD_REF:S000076000|PMID:14742425 IDA C YPL005W gene taxon:4932 20040427 SGD
+SGD S000005926 AEP3 GO:0019898 SGD_REF:S000076000|PMID:14742425 IDA C YPL005W gene taxon:4932 20040427 SGD
+SGD S000005926 AEP3 GO:0005554 SGD_REF:S000069584 ND F YPL005W gene taxon:4932 20030203 SGD
+SGD S000005926 AEP3 GO:0016071 SGD_REF:S000076000|PMID:14742425 IMP P YPL005W gene taxon:4932 20040427 SGD
+SGD S000000778 AFG1 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C ATPase family YEL052W gene taxon:4932 20031028 SGD
+SGD S000000778 AFG1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C ATPase family YEL052W gene taxon:4932 20040924 SGD
+SGD S000000778 AFG1 GO:0016887 SGD_REF:S000044832|PMID:1441755 ISS F ATPase family YEL052W gene taxon:4932 20010411 SGD
+SGD S000000778 AFG1 GO:0000004 SGD_REF:S000069584 ND P ATPase family YEL052W gene taxon:4932 20010411 SGD
+SGD S000004389 AFG2 GO:0005622 SGD_REF:S000070262|PMID:12006565 IDA C similar to the CDC48 gene product YLR397C|DRG1 gene taxon:4932 20030108 SGD
+SGD S000004389 AFG2 GO:0016887 SGD_REF:S000070262|PMID:12006565 IDA F similar to the CDC48 gene product YLR397C|DRG1 gene taxon:4932 20021009 SGD
+SGD S000004389 AFG2 GO:0042493 SGD_REF:S000049799|PMID:9341149 IMP P similar to the CDC48 gene product YLR397C|DRG1 gene taxon:4932 20021111 SGD
+SGD S000000819 AFG3 GO:0005743 SGD_REF:S000050177|PMID:7926051 IDA C ATP dependent metalloprotease YER017C|YTA10 gene taxon:4932 20010118 SGD
+SGD S000000819 AFG3 GO:0005745 SGD_REF:S000055187|PMID:8681382 IDA C ATP dependent metalloprotease YER017C|YTA10 gene taxon:4932 20030430 SGD
+SGD S000000819 AFG3 GO:0008237 SGD_REF:S000055187|PMID:8681382 IMP F ATP dependent metalloprotease YER017C|YTA10 gene taxon:4932 20010118 SGD
+SGD S000000819 AFG3 GO:0016887 SGD_REF:S000053170|PMID:7900428 ISS F ATP dependent metalloprotease YER017C|YTA10 gene taxon:4932 20010118 SGD
+SGD S000000819 AFG3 GO:0006461 SGD_REF:S000055187|PMID:8681382 IMP P ATP dependent metalloprotease YER017C|YTA10 gene taxon:4932 20010118 SGD
+SGD S000000819 AFG3 GO:0006465 SGD_REF:S000071826|PMID:12417197 IMP P ATP dependent metalloprotease YER017C|YTA10 gene taxon:4932 20050503 SGD
+SGD S000000819 AFG3 GO:0006508 SGD_REF:S000055187|PMID:8681382 IMP P ATP dependent metalloprotease YER017C|YTA10 gene taxon:4932 20010118 SGD
+SGD S000000819 AFG3 GO:0045041 SGD_REF:S000071826|PMID:12417197 TAS P ATP dependent metalloprotease YER017C|YTA10 gene taxon:4932 20021212 SGD
+SGD S000002492 AFR1 GO:0001400 SGD_REF:S000044733|PMID:7823940 IDA C cytoskeletal protein, similar to arrestins YDR085C gene taxon:4932 20050124 SGD
+SGD S000002492 AFR1 GO:0005057 SGD_REF:S000039241|PMID:9504911 IMP F cytoskeletal protein, similar to arrestins YDR085C gene taxon:4932 20010118 SGD
+SGD S000002492 AFR1 GO:0005057 SGD_REF:S000039241|PMID:9504911 IPI F cytoskeletal protein, similar to arrestins YDR085C gene taxon:4932 20010118 SGD
+SGD S000002492 AFR1 GO:0000750 SGD_REF:S000039241|PMID:9504911 IGI P cytoskeletal protein, similar to arrestins YDR085C gene taxon:4932 20021206 SGD
+SGD S000002492 AFR1 GO:0000750 SGD_REF:S000039241|PMID:9504911 IMP P cytoskeletal protein, similar to arrestins YDR085C gene taxon:4932 20021206 SGD
+SGD S000002492 AFR1 GO:0000750 SGD_REF:S000039241|PMID:9504911 IPI P cytoskeletal protein, similar to arrestins YDR085C gene taxon:4932 20021206 SGD
+SGD S000002492 AFR1 GO:0000767 SGD_REF:S000041075|PMID:8413281 IMP P cytoskeletal protein, similar to arrestins YDR085C gene taxon:4932 20050421 SGD
+SGD S000002492 AFR1 GO:0008277 SGD_REF:S000039241|PMID:9504911 IMP P cytoskeletal protein, similar to arrestins YDR085C gene taxon:4932 20010118 SGD
+SGD S000002492 AFR1 GO:0008277 SGD_REF:S000039241|PMID:9504911 IPI P cytoskeletal protein, similar to arrestins YDR085C gene taxon:4932 20010118 SGD
+SGD S000006123 AFT2 GO:0005634 SGD_REF:S000065850|PMID:11448968 ISS C YPL202C gene taxon:4932 20021011 SGD
+SGD S000006123 AFT2 GO:0005634 SGD_REF:S000065850|PMID:11448968 IMP C YPL202C gene taxon:4932 20021011 SGD
+SGD S000006123 AFT2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YPL202C gene taxon:4932 20040928 SGD
+SGD S000006123 AFT2 GO:0003700 SGD_REF:S000066237|PMID:11734641 IDA F YPL202C gene taxon:4932 20050117 SGD
+SGD S000006123 AFT2 GO:0003704 SGD_REF:S000065850|PMID:11448968 ISS F YPL202C gene taxon:4932 20021011 SGD
+SGD S000006123 AFT2 GO:0003704 SGD_REF:S000065850|PMID:11448968 IMP F YPL202C gene taxon:4932 20021011 SGD
+SGD S000006123 AFT2 GO:0006367 SGD_REF:S000065850|PMID:11448968 ISS P YPL202C gene taxon:4932 20021011 SGD
+SGD S000006123 AFT2 GO:0006367 SGD_REF:S000065850|PMID:11448968 IMP P YPL202C gene taxon:4932 20021011 SGD
+SGD S000006123 AFT2 GO:0006879 SGD_REF:S000065850|PMID:11448968 ISS P YPL202C gene taxon:4932 20021011 SGD
+SGD S000006123 AFT2 GO:0006879 SGD_REF:S000065850|PMID:11448968 IMP P YPL202C gene taxon:4932 20021011 SGD
+SGD S000006123 AFT2 GO:0006979 SGD_REF:S000065850|PMID:11448968 ISS P YPL202C gene taxon:4932 20021011 SGD
+SGD S000006123 AFT2 GO:0006979 SGD_REF:S000065850|PMID:11448968 IMP P YPL202C gene taxon:4932 20021011 SGD
+SGD S000006123 AFT2 GO:0045941 SGD_REF:S000066237|PMID:11734641 IDA P YPL202C gene taxon:4932 20050117 SGD
+SGD S000005327 AGA1 GO:0009277 SGD_REF:S000044430|PMID:7957044 IDA C a-agglutinin anchorage subunit YNR044W gene taxon:4932 20010118 SGD
+SGD S000005327 AGA1 GO:0009277 SGD_REF:S000043878|PMID:2072914 IDA C a-agglutinin anchorage subunit YNR044W gene taxon:4932 20010118 SGD
+SGD S000005327 AGA1 GO:0050839 SGD_REF:S000044430|PMID:7957044 IMP F a-agglutinin anchorage subunit YNR044W gene taxon:4932 20010118 SGD
+SGD S000005327 AGA1 GO:0050839 SGD_REF:S000044430|PMID:7957044 ISS F a-agglutinin anchorage subunit YNR044W gene taxon:4932 20010118 SGD
+SGD S000005327 AGA1 GO:0050839 SGD_REF:S000061548|PMID:11292808 TAS F a-agglutinin anchorage subunit YNR044W gene taxon:4932 20040130 SGD
+SGD S000005327 AGA1 GO:0050839 SGD_REF:S000043878|PMID:2072914 IMP F a-agglutinin anchorage subunit YNR044W gene taxon:4932 20010118 SGD
+SGD S000005327 AGA1 GO:0000752 SGD_REF:S000043878|PMID:2072914 IMP P a-agglutinin anchorage subunit YNR044W gene taxon:4932 20021206 SGD
+SGD S000005327 AGA1 GO:0000752 SGD_REF:S000044430|PMID:7957044 IMP P a-agglutinin anchorage subunit YNR044W gene taxon:4932 20021206 SGD
+SGD S000003000 AGA2 GO:0009277 SGD_REF:S000044430|PMID:7957044 TAS C a-agglutinin adhesion subunit YGL032C gene taxon:4932 20010118 SGD
+SGD S000003000 AGA2 GO:0050839 SGD_REF:S000044430|PMID:7957044 TAS F a-agglutinin adhesion subunit YGL032C gene taxon:4932 20010118 SGD
+SGD S000003000 AGA2 GO:0050839 SGD_REF:S000061548|PMID:11292808 TAS F a-agglutinin adhesion subunit YGL032C gene taxon:4932 20040130 SGD
+SGD S000003000 AGA2 GO:0000752 SGD_REF:S000044430|PMID:7957044 TAS P a-agglutinin adhesion subunit YGL032C gene taxon:4932 20021206 SGD
+SGD S000006225 AGC1 GO:0005743 SGD_REF:S000049213|PMID:10930523 ISS C Aspartate-glutamate transporter YPR021C gene taxon:4932 20021017 SGD
+SGD S000006225 AGC1 GO:0005313 SGD_REF:S000074366|PMID:14622413 IDA F Aspartate-glutamate transporter YPR021C gene taxon:4932 20031204 SGD
+SGD S000006225 AGC1 GO:0015183 SGD_REF:S000074366|PMID:14622413 IDA F Aspartate-glutamate transporter YPR021C gene taxon:4932 20031204 SGD
+SGD S000006225 AGC1 GO:0015810 SGD_REF:S000074366|PMID:14622413 IDA P Aspartate-glutamate transporter YPR021C gene taxon:4932 20031204 SGD
+SGD S000006225 AGC1 GO:0015813 SGD_REF:S000074366|PMID:14622413 IDA P Aspartate-glutamate transporter YPR021C gene taxon:4932 20031204 SGD
+SGD S000002932 AGE1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C ARF GAP with effector function(s) YDR524C|SAT1 gene taxon:4932 20031028 SGD
+SGD S000002932 AGE1 GO:0008060 SGD_REF:S000053398|PMID:9677411 IGI F ARF GAP with effector function(s) YDR524C|SAT1 gene taxon:4932 20010411 SGD
+SGD S000002932 AGE1 GO:0008060 SGD_REF:S000053398|PMID:9677411 ISS F ARF GAP with effector function(s) YDR524C|SAT1 gene taxon:4932 20010411 SGD
+SGD S000002932 AGE1 GO:0008060 SGD_REF:S000068828|PMID:12627398 IDA F ARF GAP with effector function(s) YDR524C|SAT1 gene taxon:4932 20030509 SGD
+SGD S000002932 AGE1 GO:0006888 SGD_REF:S000053398|PMID:9677411 IGI P ARF GAP with effector function(s) YDR524C|SAT1 gene taxon:4932 20010411 SGD
+SGD S000002932 AGE1 GO:0006888 SGD_REF:S000053398|PMID:9677411 ISS P ARF GAP with effector function(s) YDR524C|SAT1 gene taxon:4932 20010411 SGD
+SGD S000002932 AGE1 GO:0006891 SGD_REF:S000053398|PMID:9677411 IGI P ARF GAP with effector function(s) YDR524C|SAT1 gene taxon:4932 20010411 SGD
+SGD S000002932 AGE1 GO:0006891 SGD_REF:S000053398|PMID:9677411 ISS P ARF GAP with effector function(s) YDR524C|SAT1 gene taxon:4932 20010411 SGD
+SGD S000001306 AGE2 colocalizes_with GO:0030136 SGD_REF:S000074185|PMID:14562095 IDA C ARF GAP with effector function(s) YIL044C|SAT2 gene taxon:4932 20031028 SGD
+SGD S000001306 AGE2 GO:0008060 SGD_REF:S000053398|PMID:9677411 IGI F ARF GAP with effector function(s) YIL044C|SAT2 gene taxon:4932 20010411 SGD
+SGD S000001306 AGE2 GO:0008060 SGD_REF:S000068828|PMID:12627398 IDA F ARF GAP with effector function(s) YIL044C|SAT2 gene taxon:4932 20030509 SGD
+SGD S000001306 AGE2 GO:0008060 SGD_REF:S000053398|PMID:9677411 ISS F ARF GAP with effector function(s) YIL044C|SAT2 gene taxon:4932 20010411 SGD
+SGD S000001306 AGE2 GO:0006888 SGD_REF:S000053398|PMID:9677411 IGI P ARF GAP with effector function(s) YIL044C|SAT2 gene taxon:4932 20010411 SGD
+SGD S000001306 AGE2 GO:0006888 SGD_REF:S000053398|PMID:9677411 ISS P ARF GAP with effector function(s) YIL044C|SAT2 gene taxon:4932 20010411 SGD
+SGD S000001306 AGE2 GO:0006891 SGD_REF:S000053398|PMID:9677411 IGI P ARF GAP with effector function(s) YIL044C|SAT2 gene taxon:4932 20010411 SGD
+SGD S000001306 AGE2 GO:0006891 SGD_REF:S000053398|PMID:9677411 ISS P ARF GAP with effector function(s) YIL044C|SAT2 gene taxon:4932 20010411 SGD
+SGD S000000530 AGP1 GO:0005886 SGD_REF:S000043244|PMID:10654085 ISS C amino acid permease YCL025C|YCC5 gene taxon:4932 20020805 SGD
+SGD S000000530 AGP1 GO:0005296 SGD_REF:S000074897|PMID:14968425 IGI SGD:S000002916|SGD:S000005875|SGD:S000001747 F amino acid permease YCL025C|YCC5 gene taxon:4932 20050428 SGD
+SGD S000000530 AGP1 GO:0015171 SGD_REF:S000043244|PMID:10654085 IDA F amino acid permease YCL025C|YCC5 gene taxon:4932 20020806 SGD
+SGD S000000530 AGP1 GO:0006865 SGD_REF:S000043244|PMID:10654085 IDA P amino acid permease YCL025C|YCC5 gene taxon:4932 20020806 SGD
+SGD S000000336 AGP2 GO:0005774 SGD_REF:S000053576|PMID:10545096 IDA C plasma membrane carnitine transporter YBR132C gene taxon:4932 20010118 SGD
+SGD S000000336 AGP2 GO:0005789 SGD_REF:S000053576|PMID:10545096 IDA C plasma membrane carnitine transporter YBR132C gene taxon:4932 20010118 SGD
+SGD S000000336 AGP2 GO:0005887 SGD_REF:S000053576|PMID:10545096 IDA C plasma membrane carnitine transporter YBR132C gene taxon:4932 20010118 SGD
+SGD S000000336 AGP2 GO:0015171 SGD_REF:S000075454|PMID:14697254 IMP F plasma membrane carnitine transporter YBR132C gene taxon:4932 20040224 SGD
+SGD S000000336 AGP2 GO:0015203 SGD_REF:S000081462|PMID:15855155 IMP F plasma membrane carnitine transporter YBR132C gene taxon:4932 20050503 SGD
+SGD S000000336 AGP2 GO:0015226 SGD_REF:S000053576|PMID:10545096 IDA F plasma membrane carnitine transporter YBR132C gene taxon:4932 20040210 SGD
+SGD S000000336 AGP2 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P plasma membrane carnitine transporter YBR132C gene taxon:4932 20060210 SGD
+SGD S000000336 AGP2 GO:0006631 SGD_REF:S000053576|PMID:10545096 IDA P plasma membrane carnitine transporter YBR132C gene taxon:4932 20010118 SGD
+SGD S000000336 AGP2 GO:0006865 SGD_REF:S000075454|PMID:14697254 IMP P plasma membrane carnitine transporter YBR132C gene taxon:4932 20040224 SGD
+SGD S000000336 AGP2 GO:0006970 SGD_REF:S000070193|PMID:12132580 IDA P plasma membrane carnitine transporter YBR132C gene taxon:4932 20020919 SGD
+SGD S000000336 AGP2 GO:0015846 SGD_REF:S000081462|PMID:15855155 IMP P plasma membrane carnitine transporter YBR132C gene taxon:4932 20050503 SGD
+SGD S000000336 AGP2 GO:0015879 SGD_REF:S000053576|PMID:10545096 IDA P plasma membrane carnitine transporter YBR132C gene taxon:4932 20040210 SGD
+SGD S000001839 AGP3 GO:0005886 SGD_REF:S000043244|PMID:10654085 ISS C YFL055W gene taxon:4932 20021002 SGD
+SGD S000001839 AGP3 GO:0015171 SGD_REF:S000043244|PMID:10654085 IDA F YFL055W gene taxon:4932 20021002 SGD
+SGD S000001839 AGP3 GO:0015171 SGD_REF:S000075454|PMID:14697254 IMP F YFL055W gene taxon:4932 20040224 SGD
+SGD S000001839 AGP3 GO:0006865 SGD_REF:S000043244|PMID:10654085 IDA P YFL055W gene taxon:4932 20021002 SGD
+SGD S000001839 AGP3 GO:0006865 SGD_REF:S000075454|PMID:14697254 IMP P YFL055W gene taxon:4932 20040224 SGD
+SGD S000001864 AGX1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YFL030W gene taxon:4932 20040923 SGD
+SGD S000001864 AGX1 GO:0008453 SGD_REF:S000075415|PMID:14745783 IMP F YFL030W gene taxon:4932 20040202 SGD
+SGD S000001864 AGX1 GO:0008453 SGD_REF:S000075415|PMID:14745783 ISS F YFL030W gene taxon:4932 20040202 SGD
+SGD S000001864 AGX1 GO:0008453 SGD_REF:S000086943|PMID:16226833 ISS F YFL030W gene taxon:4932 20051024 SGD
+SGD S000001864 AGX1 GO:0008453 SGD_REF:S000086943|PMID:16226833 IDA F YFL030W gene taxon:4932 20051024 SGD
+SGD S000001864 AGX1 GO:0006545 SGD_REF:S000075415|PMID:14745783 IGI P YFL030W gene taxon:4932 20040202 SGD
+SGD S000001864 AGX1 GO:0006545 SGD_REF:S000086943|PMID:16226833 ISS P YFL030W gene taxon:4932 20051024 SGD
+SGD S000001864 AGX1 GO:0006545 SGD_REF:S000075415|PMID:14745783 IMP P YFL030W gene taxon:4932 20040202 SGD
+SGD S000001864 AGX1 GO:0006545 SGD_REF:S000086943|PMID:16226833 IDA P YFL030W gene taxon:4932 20051024 SGD
+SGD S000002622 AHA1 GO:0005737 SGD_REF:S000072028|PMID:12504007 IPI SGD:S000006161 C Hsp90 system cochaperone; Aha1 binds to the middle domain of Hsp90 and improves client protein activation in vivo YDR214W gene taxon:4932 20030416 SGD
+SGD S000002622 AHA1 GO:0030189 SGD_REF:S000072028|PMID:12504007 IDA F Hsp90 system cochaperone; Aha1 binds to the middle domain of Hsp90 and improves client protein activation in vivo YDR214W gene taxon:4932 20030107 SGD
+SGD S000002622 AHA1 GO:0030189 SGD_REF:S000072028|PMID:12504007 IPI SGD:S000006161 F Hsp90 system cochaperone; Aha1 binds to the middle domain of Hsp90 and improves client protein activation in vivo YDR214W gene taxon:4932 20030107 SGD
+SGD S000002622 AHA1 GO:0006457 SGD_REF:S000072028|PMID:12504007 IMP P Hsp90 system cochaperone; Aha1 binds to the middle domain of Hsp90 and improves client protein activation in vivo YDR214W gene taxon:4932 20030107 SGD
+SGD S000002622 AHA1 GO:0006457 SGD_REF:S000072028|PMID:12504007 IPI SGD:S000006161 P Hsp90 system cochaperone; Aha1 binds to the middle domain of Hsp90 and improves client protein activation in vivo YDR214W gene taxon:4932 20030107 SGD
+SGD S000002622 AHA1 GO:0006950 SGD_REF:S000072028|PMID:12504007 IMP P Hsp90 system cochaperone; Aha1 binds to the middle domain of Hsp90 and improves client protein activation in vivo YDR214W gene taxon:4932 20030107 SGD
+SGD S000002622 AHA1 GO:0006950 SGD_REF:S000072028|PMID:12504007 IPI SGD:S000006161 P Hsp90 system cochaperone; Aha1 binds to the middle domain of Hsp90 and improves client protein activation in vivo YDR214W gene taxon:4932 20030107 SGD
+SGD S000002622 AHA1 GO:0006950 SGD_REF:S000072028|PMID:12504007 IEP P Hsp90 system cochaperone; Aha1 binds to the middle domain of Hsp90 and improves client protein activation in vivo YDR214W gene taxon:4932 20030107 SGD
+SGD S000005549 AHC1 GO:0005671 SGD_REF:S000042121|PMID:10490601 IPI C Ada histone acetyltransferase complex component YOR023C gene taxon:4932 20031215 SGD
+SGD S000005549 AHC1 contributes_to GO:0004402 SGD_REF:S000042121|PMID:10490601 IPI F Ada histone acetyltransferase complex component YOR023C gene taxon:4932 20050512 SGD
+SGD S000005549 AHC1 contributes_to GO:0004402 SGD_REF:S000042121|PMID:10490601 IDA F Ada histone acetyltransferase complex component YOR023C gene taxon:4932 20050926 SGD
+SGD S000005549 AHC1 GO:0016573 SGD_REF:S000042121|PMID:10490601 IPI P Ada histone acetyltransferase complex component YOR023C gene taxon:4932 20050512 SGD
+SGD S000005549 AHC1 GO:0016573 SGD_REF:S000042121|PMID:10490601 IMP P Ada histone acetyltransferase complex component YOR023C gene taxon:4932 20050912 SGD
+SGD S000000678 AHC2 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YCR082W gene taxon:4932 20031028 SGD
+SGD S000000678 AHC2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YCR082W gene taxon:4932 20031028 SGD
+SGD S000000678 AHC2 GO:0005554 SGD_REF:S000069584 ND F YCR082W gene taxon:4932 20021126 SGD
+SGD S000000678 AHC2 GO:0000004 SGD_REF:S000069584 ND P YCR082W gene taxon:4932 20021126 SGD
+SGD S000004099 AHP1 GO:0005737 SGD_REF:S000061563|PMID:10681558 IDA C alkyl hydroperoxide reductase YLR109W|cTPxIII gene taxon:4932 20020411 SGD
+SGD S000004099 AHP1 GO:0008379 SGD_REF:S000061563|PMID:10681558 IMP F alkyl hydroperoxide reductase YLR109W|cTPxIII gene taxon:4932 20020411 SGD
+SGD S000004099 AHP1 GO:0008379 SGD_REF:S000061563|PMID:10681558 IDA F alkyl hydroperoxide reductase YLR109W|cTPxIII gene taxon:4932 20020411 SGD
+SGD S000004099 AHP1 GO:0008379 SGD_REF:S000061563|PMID:10681558 ISS F alkyl hydroperoxide reductase YLR109W|cTPxIII gene taxon:4932 20020411 SGD
+SGD S000004099 AHP1 GO:0010038 SGD_REF:S000071459|PMID:12270680 IMP P alkyl hydroperoxide reductase YLR109W|cTPxIII gene taxon:4932 20030416 SGD
+SGD S000004099 AHP1 GO:0030503 SGD_REF:S000061563|PMID:10681558 IMP P alkyl hydroperoxide reductase YLR109W|cTPxIII gene taxon:4932 20020411 SGD
+SGD S000004099 AHP1 GO:0030503 SGD_REF:S000061563|PMID:10681558 IDA P alkyl hydroperoxide reductase YLR109W|cTPxIII gene taxon:4932 20020411 SGD
+SGD S000007261 AI1 GO:0005739 SGD_REF:S000065815|PMID:1648225 TAS C intron-specific reverse transcriptase activity, maturase aI1 Q0050 gene taxon:4932 20021024 SGD
+SGD S000007261 AI1 GO:0003676 SGD_REF:S000044486|PMID:9126836 TAS F intron-specific reverse transcriptase activity, maturase aI1 Q0050 gene taxon:4932 20021024 SGD
+SGD S000007261 AI1 GO:0004519 SGD_REF:S000065816|PMID:9118229 TAS F intron-specific reverse transcriptase activity, maturase aI1 Q0050 gene taxon:4932 20021024 SGD
+SGD S000007261 AI1 GO:0006315 SGD_REF:S000068950|PMID:11687644 IDA P intron-specific reverse transcriptase activity, maturase aI1 Q0050 gene taxon:4932 20030108 SGD
+SGD S000007261 AI1 GO:0006397 SGD_REF:S000068950|PMID:11687644 IDA P intron-specific reverse transcriptase activity, maturase aI1 Q0050 gene taxon:4932 20021119 SGD
+SGD S000007261 AI1 GO:0045333 SGD_REF:S000044486|PMID:9126836 IMP P intron-specific reverse transcriptase activity, maturase aI1 Q0050 gene taxon:4932 20030110 SGD
+SGD S000007262 AI2 GO:0005739 SGD_REF:S000065815|PMID:1648225 TAS C endonuclease (putative), intron-specific reverse transcriptase activity, maturase aI2 Q0055 gene taxon:4932 20021024 SGD
+SGD S000007262 AI2 GO:0003676 SGD_REF:S000044486|PMID:9126836 TAS F endonuclease (putative), intron-specific reverse transcriptase activity, maturase aI2 Q0055 gene taxon:4932 20021024 SGD
+SGD S000007262 AI2 GO:0003723 SGD_REF:S000065817|PMID:10356323 TAS F endonuclease (putative), intron-specific reverse transcriptase activity, maturase aI2 Q0055 gene taxon:4932 20021024 SGD
+SGD S000007262 AI2 GO:0003964 SGD_REF:S000065817|PMID:10356323 TAS F endonuclease (putative), intron-specific reverse transcriptase activity, maturase aI2 Q0055 gene taxon:4932 20021024 SGD
+SGD S000007262 AI2 GO:0004519 SGD_REF:S000065816|PMID:9118229 TAS F endonuclease (putative), intron-specific reverse transcriptase activity, maturase aI2 Q0055 gene taxon:4932 20021024 SGD
+SGD S000007262 AI2 GO:0008380 SGD_REF:S000065817|PMID:10356323 TAS P endonuclease (putative), intron-specific reverse transcriptase activity, maturase aI2 Q0055 gene taxon:4932 20021024 SGD
+SGD S000007263 AI3 GO:0005739 SGD_REF:S000049650|PMID:7797552 TAS C I-SceIII endonuclease activity, encoded by the 3' part of the aI3 intron Q0060 gene taxon:4932 20021118 SGD
+SGD S000007263 AI3 GO:0004519 SGD_REF:S000049650|PMID:7797552 IDA F I-SceIII endonuclease activity, encoded by the 3' part of the aI3 intron Q0060 gene taxon:4932 20021118 SGD
+SGD S000007263 AI3 GO:0000004 SGD_REF:S000069584 ND P I-SceIII endonuclease activity, encoded by the 3' part of the aI3 intron Q0060 gene taxon:4932 20030821 SGD
+SGD S000007264 AI4 GO:0005739 SGD_REF:S000054913|PMID:7588637 TAS C I-SceII endonuclease activity, encoded by the aI4 intron Q0065 gene taxon:4932 20021114 SGD
+SGD S000007264 AI4 GO:0004519 SGD_REF:S000054913|PMID:7588637 IDA F I-SceII endonuclease activity, encoded by the aI4 intron Q0065 gene taxon:4932 20021114 SGD
+SGD S000007264 AI4 GO:0006314 SGD_REF:S000060150|PMID:2536592 IMP P I-SceII endonuclease activity, encoded by the aI4 intron Q0065 gene taxon:4932 20040916 SGD
+SGD S000007264 AI4 GO:0008380 SGD_REF:S000054913|PMID:7588637 IDA P I-SceII endonuclease activity, encoded by the aI4 intron Q0065 gene taxon:4932 20021114 SGD
+SGD S000007265 AI5_ALPHA GO:0005739 SGD_REF:S000058438|PMID:9872396 TAS C DNA endonuclease involved in intron homing Q0070|I-SceIV gene taxon:4932 20021119 SGD
+SGD S000007265 AI5_ALPHA GO:0004519 SGD_REF:S000048803|PMID:1314207 IMP F DNA endonuclease involved in intron homing Q0070|I-SceIV gene taxon:4932 20021119 SGD
+SGD S000007265 AI5_ALPHA GO:0006316 SGD_REF:S000048803|PMID:1314207 IMP P DNA endonuclease involved in intron homing Q0070|I-SceIV gene taxon:4932 20021119 SGD
+SGD S000007266 AI5_BETA GO:0005739 SGD_REF:S000058438|PMID:9872396 TAS C Q0075 gene taxon:4932 20021119 SGD
+SGD S000007266 AI5_BETA GO:0005554 SGD_REF:S000069584 ND F Q0075 gene taxon:4932 20020925 SGD
+SGD S000007266 AI5_BETA GO:0000004 SGD_REF:S000069584 ND P Q0075 gene taxon:4932 20020925 SGD
+SGD S000005357 AIF1 GO:0005634 SGD_REF:S000079920|PMID:15381687 IDA C YNR074C|CPD1 gene taxon:4932 20050208 SGD
+SGD S000005357 AIF1 GO:0005739 SGD_REF:S000079920|PMID:15381687 IDA C YNR074C|CPD1 gene taxon:4932 20050208 SGD
+SGD S000005357 AIF1 GO:0005886 SGD_REF:S000060708|PMID:11409174 ISS C YNR074C|CPD1 gene taxon:4932 20011228 SGD
+SGD S000005357 AIF1 GO:0016654 SGD_REF:S000060708|PMID:11409174 ISS F YNR074C|CPD1 gene taxon:4932 20011228 SGD
+SGD S000005357 AIF1 GO:0000304 SGD_REF:S000060708|PMID:11409174 IMP P YNR074C|CPD1 gene taxon:4932 20011228 SGD
+SGD S000005357 AIF1 GO:0043065 SGD_REF:S000079920|PMID:15381687 IMP P YNR074C|CPD1 gene taxon:4932 20050208 SGD
+SGD S000004698 AIP1 GO:0005634 SGD_REF:S000069459|PMID:11914276 IDA C actin cortical patch component YMR092C gene taxon:4932 20020507 SGD
+SGD S000004698 AIP1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C actin cortical patch component YMR092C gene taxon:4932 20020507 SGD
+SGD S000004698 AIP1 GO:0030479 SGD_REF:S000041005|PMID:10652251 IDA C actin cortical patch component YMR092C gene taxon:4932 20010118 SGD
+SGD S000004698 AIP1 GO:0005515 SGD_REF:S000053733|PMID:10366597 IDA F actin cortical patch component YMR092C gene taxon:4932 20040403 SGD
+SGD S000004698 AIP1 GO:0006970 SGD_REF:S000041005|PMID:10652251 IMP P actin cortical patch component YMR092C gene taxon:4932 20010118 SGD
+SGD S000004698 AIP1 GO:0030042 SGD_REF:S000053733|PMID:10366597 IPI P actin cortical patch component YMR092C gene taxon:4932 20010705 SGD
+SGD S000004698 AIP1 GO:0030042 SGD_REF:S000053733|PMID:10366597 IGI P actin cortical patch component YMR092C gene taxon:4932 20010705 SGD
+SGD S000001341 AIR1 GO:0005634 SGD_REF:S000059204|PMID:10896665 IPI C YIL079C gene taxon:4932 20020820 SGD
+SGD S000001341 AIR1 GO:0005730 SGD_REF:S000061434|PMID:11489916 IDA C YIL079C gene taxon:4932 20030512 SGD
+SGD S000001341 AIR1 GO:0031499 SGD_REF:S000081438|PMID:15828860 IDA C YIL079C gene taxon:4932 20050621 SGD
+SGD S000001341 AIR1 GO:0031499 SGD_REF:S000081438|PMID:15828860 IPI SGD:S000005475 C YIL079C gene taxon:4932 20050621 SGD
+SGD S000001341 AIR1 GO:0005554 SGD_REF:S000069584 ND F YIL079C gene taxon:4932 20020820 SGD
+SGD S000001341 AIR1 GO:0006406 SGD_REF:S000059204|PMID:10896665 IMP P YIL079C gene taxon:4932 20020820 SGD
+SGD S000001341 AIR1 GO:0016075 SGD_REF:S000081843|PMID:15935758 IGI SGD:S000002334 P YIL079C gene taxon:4932 20050610 SGD
+SGD S000001341 AIR1 GO:0016077 SGD_REF:S000081843|PMID:15935758 IGI SGD:S000002334 P YIL079C gene taxon:4932 20050610 SGD
+SGD S000001341 AIR1 GO:0016078 SGD_REF:S000081438|PMID:15828860 IDA P YIL079C gene taxon:4932 20050610 SGD
+SGD S000002334 AIR2 GO:0005634 SGD_REF:S000059204|PMID:10896665 IPI C YDL175C gene taxon:4932 20020820 SGD
+SGD S000002334 AIR2 GO:0031499 SGD_REF:S000081843|PMID:15935758 IPI SGD:S000003586|SGD:S000005475 C YDL175C gene taxon:4932 20050621 SGD
+SGD S000002334 AIR2 GO:0031499 SGD_REF:S000081843|PMID:15935758 IDA C YDL175C gene taxon:4932 20050621 SGD
+SGD S000002334 AIR2 GO:0031499 SGD_REF:S000081438|PMID:15828860 IPI SGD:S000005475 C YDL175C gene taxon:4932 20050621 SGD
+SGD S000002334 AIR2 GO:0031499 SGD_REF:S000081438|PMID:15828860 IDA C YDL175C gene taxon:4932 20050621 SGD
+SGD S000002334 AIR2 GO:0005554 SGD_REF:S000069584 ND F YDL175C gene taxon:4932 20020820 SGD
+SGD S000002334 AIR2 GO:0006406 SGD_REF:S000059204|PMID:10896665 IMP P YDL175C gene taxon:4932 20020820 SGD
+SGD S000002334 AIR2 GO:0016075 SGD_REF:S000081843|PMID:15935758 IGI SGD:S000001341 P YDL175C gene taxon:4932 20050610 SGD
+SGD S000002334 AIR2 GO:0016077 SGD_REF:S000081843|PMID:15935758 IGI SGD:S000001341 P YDL175C gene taxon:4932 20050610 SGD
+SGD S000002334 AIR2 GO:0016078 SGD_REF:S000081438|PMID:15828860 IDA P YDL175C gene taxon:4932 20050610 SGD
+SGD S000002334 AIR2 GO:0016078 SGD_REF:S000081843|PMID:15935758 IDA P YDL175C gene taxon:4932 20050610 SGD
+SGD S000000263 AKL1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YBR059C gene taxon:4932 20031028 SGD
+SGD S000000263 AKL1 GO:0005935 SGD_REF:S000074185|PMID:14562095 IDA C YBR059C gene taxon:4932 20031028 SGD
+SGD S000000263 AKL1 GO:0004672 SGD_REF:S000043672|PMID:10087264 ISS F YBR059C gene taxon:4932 20020925 SGD
+SGD S000000263 AKL1 GO:0030036 SGD_REF:S000075418|PMID:12956961 IMP P YBR059C gene taxon:4932 20040520 SGD
+SGD S000000263 AKL1 GO:0030100 SGD_REF:S000075418|PMID:12956961 IMP P YBR059C gene taxon:4932 20040520 SGD
+SGD S000002672 AKR1 GO:0016020 SGD_REF:S000071693|PMID:12370247 IDA C ankyrin repeat-containing protein YDR264C gene taxon:4932 20021205 SGD
+SGD S000002672 AKR1 GO:0019706 SGD_REF:S000071693|PMID:12370247 IDA F ankyrin repeat-containing protein YDR264C gene taxon:4932 20050304 SGD
+SGD S000002672 AKR1 GO:0000750 SGD_REF:S000051630|PMID:8524293 IGI P ankyrin repeat-containing protein YDR264C gene taxon:4932 20021206 SGD
+SGD S000002672 AKR1 GO:0006897 SGD_REF:S000049884|PMID:9243510 IMP P ankyrin repeat-containing protein YDR264C gene taxon:4932 20010118 SGD
+SGD S000002672 AKR1 GO:0018318 SGD_REF:S000071693|PMID:12370247 IDA P ankyrin repeat-containing protein YDR264C gene taxon:4932 20021205 SGD
+SGD S000005560 AKR2 GO:0008372 SGD_REF:S000069584 ND C YOR034C gene taxon:4932 20051017 SGD
+SGD S000005560 AKR2 GO:0019706 SGD_REF:S000082414|PMID:15973437 ISS F YOR034C gene taxon:4932 20051017 SGD
+SGD S000005560 AKR2 GO:0006897 SGD_REF:S000049884|PMID:9243510 ISS P YOR034C gene taxon:4932 20050510 SGD
+SGD S000005560 AKR2 GO:0018318 SGD_REF:S000082414|PMID:15973437 ISS P YOR034C gene taxon:4932 20051017 SGD
+SGD S000005862 ALA1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YOR335C|CDC64 gene taxon:4932 20020507 SGD
+SGD S000005862 ALA1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YOR335C|CDC64 gene taxon:4932 20031028 SGD
+SGD S000005862 ALA1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YOR335C|CDC64 gene taxon:4932 20040813 SGD
+SGD S000005862 ALA1 GO:0004813 SGD_REF:S000046212|PMID:7761427 IGI F YOR335C|CDC64 gene taxon:4932 20020902 SGD
+SGD S000005862 ALA1 GO:0004813 SGD_REF:S000046212|PMID:7761427 ISS F YOR335C|CDC64 gene taxon:4932 20020902 SGD
+SGD S000005862 ALA1 GO:0006419 SGD_REF:S000046212|PMID:7761427 IGI P YOR335C|CDC64 gene taxon:4932 20020902 SGD
+SGD S000005862 ALA1 GO:0006419 SGD_REF:S000046212|PMID:7761427 IMP P YOR335C|CDC64 gene taxon:4932 20020902 SGD
+SGD S000003658 ALB1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YJL122W gene taxon:4932 20031028 SGD
+SGD S000003658 ALB1 GO:0005634 SGD_REF:S000115804|PMID:16651379 IDA C YJL122W gene taxon:4932 20060522 SGD
+SGD S000003658 ALB1 GO:0005737 SGD_REF:S000115804|PMID:16651379 IDA C YJL122W gene taxon:4932 20060522 SGD
+SGD S000003658 ALB1 GO:0005554 SGD_REF:S000069584 ND F YJL122W gene taxon:4932 20060522 SGD
+SGD S000003658 ALB1 GO:0042273 SGD_REF:S000115804|PMID:16651379 IGI SGD:S000002508 P YJL122W gene taxon:4932 20060522 SGD
+SGD S000003658 ALB1 GO:0042273 SGD_REF:S000115804|PMID:16651379 IPI SGD:S000002508 P YJL122W gene taxon:4932 20060522 SGD
+SGD S000029651 ALD1 GO:0005759 SGD_REF:S000058482|PMID:10592178 NAS C aldehyde dehydrogenase gene taxon:4932 20010118 SGD
+SGD S000029651 ALD1 GO:0004029 SGD_REF:S000058482|PMID:10592178 NAS F aldehyde dehydrogenase gene taxon:4932 20010118 SGD
+SGD S000029651 ALD1 GO:0006067 SGD_REF:S000058482|PMID:10592178 NAS P aldehyde dehydrogenase gene taxon:4932 20010118 SGD
+SGD S000004780 ALD2 GO:0005737 SGD_REF:S000040158|PMID:8801420 ISS C aldehyde dehydrogenase YMR170C gene taxon:4932 20010118 SGD
+SGD S000004780 ALD2 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C aldehyde dehydrogenase YMR170C gene taxon:4932 20020507 SGD
+SGD S000004780 ALD2 GO:0004028 SGD_REF:S000040158|PMID:8801420 ISS F aldehyde dehydrogenase YMR170C gene taxon:4932 20010118 SGD
+SGD S000004780 ALD2 GO:0006081 SGD_REF:S000039810|PMID:10407263 ISS P aldehyde dehydrogenase YMR170C gene taxon:4932 20030128 SGD
+SGD S000004780 ALD2 GO:0006598 SGD_REF:S000072585|PMID:12586697 IGI P aldehyde dehydrogenase YMR170C gene taxon:4932 20030619 SGD
+SGD S000004780 ALD2 GO:0006598 SGD_REF:S000072585|PMID:12586697 IMP P aldehyde dehydrogenase YMR170C gene taxon:4932 20030619 SGD
+SGD S000004780 ALD2 GO:0019483 SGD_REF:S000072585|PMID:12586697 IMP P aldehyde dehydrogenase YMR170C gene taxon:4932 20030225 SGD
+SGD S000004779 ALD3 GO:0005737 SGD_REF:S000039810|PMID:10407263 ISS C aldehyde dehydrogenase YMR169C gene taxon:4932 20010118 SGD
+SGD S000004779 ALD3 GO:0004028 SGD_REF:S000039810|PMID:10407263 ISS F aldehyde dehydrogenase YMR169C gene taxon:4932 20010118 SGD
+SGD S000004779 ALD3 GO:0006598 SGD_REF:S000072585|PMID:12586697 IGI P aldehyde dehydrogenase YMR169C gene taxon:4932 20030619 SGD
+SGD S000004779 ALD3 GO:0006598 SGD_REF:S000072585|PMID:12586697 IMP P aldehyde dehydrogenase YMR169C gene taxon:4932 20030619 SGD
+SGD S000004779 ALD3 GO:0006950 SGD_REF:S000052245|PMID:10641035 IEP P aldehyde dehydrogenase YMR169C gene taxon:4932 20010118 SGD
+SGD S000004779 ALD3 GO:0019483 SGD_REF:S000072585|PMID:12586697 IMP P aldehyde dehydrogenase YMR169C gene taxon:4932 20030225 SGD
+SGD S000005901 ALD4 GO:0005739 SGD_REF:S000052397|PMID:9675847 IMP C aldehyde dehydrogenase YOR374W|ALD7 gene taxon:4932 20010118 SGD
+SGD S000005901 ALD4 GO:0005739 SGD_REF:S000052397|PMID:9675847 ISS C aldehyde dehydrogenase YOR374W|ALD7 gene taxon:4932 20010118 SGD
+SGD S000005901 ALD4 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C aldehyde dehydrogenase YOR374W|ALD7 gene taxon:4932 20040928 SGD
+SGD S000005901 ALD4 GO:0042645 SGD_REF:S000050870|PMID:10869431 IDA C aldehyde dehydrogenase YOR374W|ALD7 gene taxon:4932 20050401 SGD
+SGD S000005901 ALD4 GO:0004029 SGD_REF:S000052397|PMID:9675847 IMP F aldehyde dehydrogenase YOR374W|ALD7 gene taxon:4932 20010118 SGD
+SGD S000005901 ALD4 GO:0004029 SGD_REF:S000052397|PMID:9675847 ISS F aldehyde dehydrogenase YOR374W|ALD7 gene taxon:4932 20010118 SGD
+SGD S000005901 ALD4 GO:0006067 SGD_REF:S000052397|PMID:9675847 IMP P aldehyde dehydrogenase YOR374W|ALD7 gene taxon:4932 20010118 SGD
+SGD S000000875 ALD5 GO:0005739 SGD_REF:S000050673|PMID:9473035 IDA C aldehyde dehydrogenase YER073W gene taxon:4932 20030211 SGD
+SGD S000000875 ALD5 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C aldehyde dehydrogenase YER073W gene taxon:4932 20040924 SGD
+SGD S000000875 ALD5 GO:0004028 SGD_REF:S000050673|PMID:9473035 IDA F aldehyde dehydrogenase YER073W gene taxon:4932 20030211 SGD
+SGD S000000875 ALD5 GO:0006118 SGD_REF:S000052315|PMID:10585550 IMP P aldehyde dehydrogenase YER073W gene taxon:4932 20030211 SGD
+SGD S000000875 ALD5 GO:0019413 SGD_REF:S000076746|PMID:15256563 IMP P aldehyde dehydrogenase YER073W gene taxon:4932 20040916 SGD
+SGD S000005982 ALD6 GO:0005737 SGD_REF:S000050185|PMID:9392076 ISS C aldehyde dehydrogenase YPL061W gene taxon:4932 20010118 SGD
+SGD S000005982 ALD6 GO:0005737 SGD_REF:S000050185|PMID:9392076 IMP C aldehyde dehydrogenase YPL061W gene taxon:4932 20010118 SGD
+SGD S000005982 ALD6 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C aldehyde dehydrogenase YPL061W gene taxon:4932 20040813 SGD
+SGD S000005982 ALD6 GO:0004028 SGD_REF:S000050185|PMID:9392076 IMP F aldehyde dehydrogenase YPL061W gene taxon:4932 20010118 SGD
+SGD S000005982 ALD6 GO:0004028 SGD_REF:S000050185|PMID:9392076 ISS F aldehyde dehydrogenase YPL061W gene taxon:4932 20010118 SGD
+SGD S000005982 ALD6 GO:0019413 SGD_REF:S000069449|PMID:11870853 IMP P aldehyde dehydrogenase YPL061W gene taxon:4932 20030213 SGD
+SGD S000005092 ALF1 GO:0005634 SGD_REF:S000069459|PMID:11914276 IDA C tubulin folding cofactor B YNL148C gene taxon:4932 20020507 SGD
+SGD S000005092 ALF1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C tubulin folding cofactor B YNL148C gene taxon:4932 20020507 SGD
+SGD S000005092 ALF1 GO:0008017 SGD_REF:S000058454|PMID:9885248 IPI F tubulin folding cofactor B YNL148C gene taxon:4932 20040715 SGD
+SGD S000005092 ALF1 GO:0043014 SGD_REF:S000058454|PMID:9885248 IPI SGD:S000004550 F tubulin folding cofactor B YNL148C gene taxon:4932 20040722 SGD
+SGD S000005092 ALF1 GO:0007023 SGD_REF:S000058454|PMID:9885248 IMP P tubulin folding cofactor B YNL148C gene taxon:4932 20010118 SGD
+SGD S000005092 ALF1 GO:0007023 SGD_REF:S000058454|PMID:9885248 IPI P tubulin folding cofactor B YNL148C gene taxon:4932 20010118 SGD
+SGD S000005092 ALF1 GO:0007024 SGD_REF:S000058454|PMID:9885248 IMP P tubulin folding cofactor B YNL148C gene taxon:4932 20010118 SGD
+SGD S000005092 ALF1 GO:0007024 SGD_REF:S000058454|PMID:9885248 IPI P tubulin folding cofactor B YNL148C gene taxon:4932 20010118 SGD
+SGD S000000314 ALG1 GO:0005783 SGD_REF:S000080875|PMID:15044395 IPI SGD:S000004993 C beta-1,4-mannosyltransferase YBR110W gene taxon:4932 20050301 SGD
+SGD S000000314 ALG1 GO:0016021 SGD_REF:S000050991|PMID:2182636 ISS C beta-1,4-mannosyltransferase YBR110W gene taxon:4932 20030204 SGD
+SGD S000000314 ALG1 GO:0019187 SGD_REF:S000045623|PMID:6368538 IDA F beta-1,4-mannosyltransferase YBR110W gene taxon:4932 20020902 SGD
+SGD S000000314 ALG1 GO:0006487 SGD_REF:S000046125|PMID:6369318 IMP P beta-1,4-mannosyltransferase YBR110W gene taxon:4932 20020902 SGD
+SGD S000000314 ALG1 GO:0006490 SGD_REF:S000044380|PMID:7037780 IMP P beta-1,4-mannosyltransferase YBR110W gene taxon:4932 20050301 SGD
+SGD S000004993 ALG11 GO:0005783 SGD_REF:S000060698|PMID:11278778 IDA C YNL048W gene taxon:4932 20010622 SGD
+SGD S000004993 ALG11 GO:0016020 SGD_REF:S000060698|PMID:11278778 ISS C YNL048W gene taxon:4932 20010622 SGD
+SGD S000004993 ALG11 GO:0000026 SGD_REF:S000060698|PMID:11278778 IGI F YNL048W gene taxon:4932 20010622 SGD
+SGD S000004993 ALG11 GO:0006486 SGD_REF:S000060698|PMID:11278778 IGI P YNL048W gene taxon:4932 20010622 SGD
+SGD S000005313 ALG12 GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C mannosyltransferase YNR030W|ECM39 gene taxon:4932 20031028 SGD
+SGD S000005313 ALG12 GO:0000009 SGD_REF:S000070115|PMID:10336995 ISS F mannosyltransferase YNR030W|ECM39 gene taxon:4932 20020709 SGD
+SGD S000005313 ALG12 GO:0000009 SGD_REF:S000070115|PMID:10336995 IMP F mannosyltransferase YNR030W|ECM39 gene taxon:4932 20020709 SGD
+SGD S000005313 ALG12 GO:0006486 SGD_REF:S000070115|PMID:10336995 ISS P mannosyltransferase YNR030W|ECM39 gene taxon:4932 20020709 SGD
+SGD S000005313 ALG12 GO:0006486 SGD_REF:S000070115|PMID:10336995 IMP P mannosyltransferase YNR030W|ECM39 gene taxon:4932 20020709 SGD
+SGD S000005313 ALG12 GO:0006488 SGD_REF:S000070115|PMID:10336995 IMP P mannosyltransferase YNR030W|ECM39 gene taxon:4932 20021220 SGD
+SGD S000003015 ALG13 GO:0005624 SGD_REF:S000086130|PMID:16100113 IDA C UDP-N-acetylglucosamine transferase YGL047W gene taxon:4932 20051109 SGD
+SGD S000003015 ALG13 GO:0005634 SGD_REF:S000075214|PMID:14690591 IDA C UDP-N-acetylglucosamine transferase YGL047W gene taxon:4932 20040105 SGD
+SGD S000003015 ALG13 GO:0005737 SGD_REF:S000075214|PMID:14690591 IDA C UDP-N-acetylglucosamine transferase YGL047W gene taxon:4932 20040105 SGD
+SGD S000003015 ALG13 GO:0005737 SGD_REF:S000086112|PMID:16100110 IDA C UDP-N-acetylglucosamine transferase YGL047W gene taxon:4932 20051109 SGD
+SGD S000003015 ALG13 GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C UDP-N-acetylglucosamine transferase YGL047W gene taxon:4932 20031028 SGD
+SGD S000003015 ALG13 GO:0005829 SGD_REF:S000086130|PMID:16100113 IDA C UDP-N-acetylglucosamine transferase YGL047W gene taxon:4932 20051109 SGD
+SGD S000003015 ALG13 GO:0042406 SGD_REF:S000086112|PMID:16100110 IDA C UDP-N-acetylglucosamine transferase YGL047W gene taxon:4932 20050817 SGD
+SGD S000003015 ALG13 GO:0043541 SGD_REF:S000086112|PMID:16100110 IPI SGD:S000000274 C UDP-N-acetylglucosamine transferase YGL047W gene taxon:4932 20051129 SGD
+SGD S000003015 ALG13 GO:0043541 SGD_REF:S000086130|PMID:16100113 IPI SGD:S000000274 C UDP-N-acetylglucosamine transferase YGL047W gene taxon:4932 20051129 SGD
+SGD S000003015 ALG13 contributes_to GO:0004577 SGD_REF:S000080148|PMID:15615718 ISS F UDP-N-acetylglucosamine transferase YGL047W gene taxon:4932 20051109 SGD
+SGD S000003015 ALG13 contributes_to GO:0004577 SGD_REF:S000086130|PMID:16100113 IDA F UDP-N-acetylglucosamine transferase YGL047W gene taxon:4932 20051109 SGD
+SGD S000003015 ALG13 contributes_to GO:0004577 SGD_REF:S000086130|PMID:16100113 IMP F UDP-N-acetylglucosamine transferase YGL047W gene taxon:4932 20051109 SGD
+SGD S000003015 ALG13 contributes_to GO:0004577 SGD_REF:S000086130|PMID:16100113 ISS F UDP-N-acetylglucosamine transferase YGL047W gene taxon:4932 20051109 SGD
+SGD S000003015 ALG13 contributes_to GO:0004577 SGD_REF:S000080148|PMID:15615718 IMP F UDP-N-acetylglucosamine transferase YGL047W gene taxon:4932 20051109 SGD
+SGD S000003015 ALG13 GO:0016758 SGD_REF:S000075214|PMID:14690591 ISS F UDP-N-acetylglucosamine transferase YGL047W gene taxon:4932 20040105 SGD
+SGD S000003015 ALG13 GO:0006488 SGD_REF:S000080148|PMID:15615718 IMP P UDP-N-acetylglucosamine transferase YGL047W gene taxon:4932 20051109 SGD
+SGD S000003015 ALG13 GO:0006488 SGD_REF:S000080148|PMID:15615718 ISS P UDP-N-acetylglucosamine transferase YGL047W gene taxon:4932 20051109 SGD
+SGD S000003015 ALG13 GO:0006488 SGD_REF:S000086130|PMID:16100113 IDA P UDP-N-acetylglucosamine transferase YGL047W gene taxon:4932 20051109 SGD
+SGD S000003015 ALG13 GO:0006488 SGD_REF:S000086130|PMID:16100113 ISS P UDP-N-acetylglucosamine transferase YGL047W gene taxon:4932 20051109 SGD
+SGD S000003015 ALG13 GO:0006488 SGD_REF:S000086130|PMID:16100113 IMP P UDP-N-acetylglucosamine transferase YGL047W gene taxon:4932 20051109 SGD
+SGD S000000274 ALG14 GO:0005624 SGD_REF:S000086130|PMID:16100113 IDA C UDP-GlcNAc transferase associated protein YBR070C gene taxon:4932 20051109 SGD
+SGD S000000274 ALG14 GO:0030176 SGD_REF:S000086112|PMID:16100110 IDA C UDP-GlcNAc transferase associated protein YBR070C gene taxon:4932 20050817 SGD
+SGD S000000274 ALG14 GO:0042175 SGD_REF:S000077144|PMID:15282802 IDA C UDP-GlcNAc transferase associated protein YBR070C gene taxon:4932 20041008 SGD
+SGD S000000274 ALG14 GO:0043541 SGD_REF:S000086130|PMID:16100113 IPI SGD:S000003015 C UDP-GlcNAc transferase associated protein YBR070C gene taxon:4932 20051129 SGD
+SGD S000000274 ALG14 GO:0043541 SGD_REF:S000086112|PMID:16100110 IPI SGD:S000003015 C UDP-GlcNAc transferase associated protein YBR070C gene taxon:4932 20051129 SGD
+SGD S000000274 ALG14 contributes_to GO:0004577 SGD_REF:S000086112|PMID:16100110 IPI SGD:S000003015 F UDP-GlcNAc transferase associated protein YBR070C gene taxon:4932 20051109 SGD
+SGD S000000274 ALG14 contributes_to GO:0004577 SGD_REF:S000080148|PMID:15615718 IMP F UDP-GlcNAc transferase associated protein YBR070C gene taxon:4932 20051109 SGD
+SGD S000000274 ALG14 contributes_to GO:0004577 SGD_REF:S000080148|PMID:15615718 ISS F UDP-GlcNAc transferase associated protein YBR070C gene taxon:4932 20051109 SGD
+SGD S000000274 ALG14 contributes_to GO:0004577 SGD_REF:S000086130|PMID:16100113 IDA F UDP-GlcNAc transferase associated protein YBR070C gene taxon:4932 20051109 SGD
+SGD S000000274 ALG14 contributes_to GO:0004577 SGD_REF:S000086130|PMID:16100113 IMP F UDP-GlcNAc transferase associated protein YBR070C gene taxon:4932 20051109 SGD
+SGD S000000274 ALG14 contributes_to GO:0004577 SGD_REF:S000086130|PMID:16100113 ISS F UDP-GlcNAc transferase associated protein YBR070C gene taxon:4932 20051109 SGD
+SGD S000000274 ALG14 GO:0043495 SGD_REF:S000086112|PMID:16100110 IMP F UDP-GlcNAc transferase associated protein YBR070C gene taxon:4932 20051109 SGD
+SGD S000000274 ALG14 GO:0043495 SGD_REF:S000086130|PMID:16100113 IMP F UDP-GlcNAc transferase associated protein YBR070C gene taxon:4932 20051109 SGD
+SGD S000000274 ALG14 GO:0006488 SGD_REF:S000080148|PMID:15615718 IMP P UDP-GlcNAc transferase associated protein YBR070C gene taxon:4932 20051109 SGD
+SGD S000000274 ALG14 GO:0006488 SGD_REF:S000086112|PMID:16100110 IPI SGD:S000003015 P UDP-GlcNAc transferase associated protein YBR070C gene taxon:4932 20051109 SGD
+SGD S000000274 ALG14 GO:0006488 SGD_REF:S000086130|PMID:16100113 IDA P UDP-GlcNAc transferase associated protein YBR070C gene taxon:4932 20051109 SGD
+SGD S000000274 ALG14 GO:0006488 SGD_REF:S000086130|PMID:16100113 ISS P UDP-GlcNAc transferase associated protein YBR070C gene taxon:4932 20051109 SGD
+SGD S000000274 ALG14 GO:0006488 SGD_REF:S000080148|PMID:15615718 ISS P UDP-GlcNAc transferase associated protein YBR070C gene taxon:4932 20051109 SGD
+SGD S000000274 ALG14 GO:0006488 SGD_REF:S000086130|PMID:16100113 IMP P UDP-GlcNAc transferase associated protein YBR070C gene taxon:4932 20051109 SGD
+SGD S000003033 ALG2 GO:0005783 SGD_REF:S000060698|PMID:11278778 TAS C glycosyltransferase YGL065C gene taxon:4932 20021115 SGD
+SGD S000003033 ALG2 GO:0004376 SGD_REF:S000058396|PMID:9878760 TAS F glycosyltransferase YGL065C gene taxon:4932 20021120 SGD
+SGD S000003033 ALG2 GO:0006490 SGD_REF:S000046125|PMID:6369318 TAS P glycosyltransferase YGL065C gene taxon:4932 20010118 SGD
+SGD S000000178 ALG3 GO:0005783 SGD_REF:S000039563|PMID:8842708 IMP C Dol-P-Man dependent alpha(1-3) mannosyltransferase (putative) YBL082C|RHK1 gene taxon:4932 20021114 SGD
+SGD S000000178 ALG3 GO:0005783 SGD_REF:S000039563|PMID:8842708 ISS C Dol-P-Man dependent alpha(1-3) mannosyltransferase (putative) YBL082C|RHK1 gene taxon:4932 20021114 SGD
+SGD S000000178 ALG3 GO:0000033 SGD_REF:S000071866|PMID:11308030 IDA F Dol-P-Man dependent alpha(1-3) mannosyltransferase (putative) YBL082C|RHK1 gene taxon:4932 20021220 SGD
+SGD S000000178 ALG3 GO:0000033 SGD_REF:S000071866|PMID:11308030 IMP F Dol-P-Man dependent alpha(1-3) mannosyltransferase (putative) YBL082C|RHK1 gene taxon:4932 20021220 SGD
+SGD S000000178 ALG3 GO:0006486 SGD_REF:S000039563|PMID:8842708 IMP P Dol-P-Man dependent alpha(1-3) mannosyltransferase (putative) YBL082C|RHK1 gene taxon:4932 20021114 SGD
+SGD S000000178 ALG3 GO:0006488 SGD_REF:S000070115|PMID:10336995 TAS P Dol-P-Man dependent alpha(1-3) mannosyltransferase (putative) YBL082C|RHK1 gene taxon:4932 20021220 SGD
+SGD S000006148 ALG5 GO:0005789 SGD_REF:S000048956|PMID:9560251 IDA C UDP-glucose:dolichyl-phosphate glucosyltransferase YPL227C gene taxon:4932 20020927 SGD
+SGD S000006148 ALG5 GO:0004581 SGD_REF:S000046164|PMID:8076653 IDA F UDP-glucose:dolichyl-phosphate glucosyltransferase YPL227C gene taxon:4932 20021010 SGD
+SGD S000006148 ALG5 GO:0006487 SGD_REF:S000046164|PMID:8076653 TAS P UDP-glucose:dolichyl-phosphate glucosyltransferase YPL227C gene taxon:4932 20020927 SGD
+SGD S000005528 ALG6 GO:0005783 SGD_REF:S000055554|PMID:8877369 IMP C glucosyltransferase YOR002W gene taxon:4932 20020830 SGD
+SGD S000005528 ALG6 GO:0016758 SGD_REF:S000055554|PMID:8877369 IMP F glucosyltransferase YOR002W gene taxon:4932 20020830 SGD
+SGD S000005528 ALG6 GO:0006486 SGD_REF:S000055554|PMID:8877369 IMP P glucosyltransferase YOR002W gene taxon:4932 20020830 SGD
+SGD S000005528 ALG6 GO:0006488 SGD_REF:S000070115|PMID:10336995 TAS P glucosyltransferase YOR002W gene taxon:4932 20021220 SGD
+SGD S000000447 ALG7 GO:0005783 SGD_REF:S000058396|PMID:9878760 IC GO:0006487 C UDP-N-acetyl-glucosamine-1-P transferase (GPT) YBR243C|TUR1 gene taxon:4932 20021113 SGD
+SGD S000000447 ALG7 GO:0003975 SGD_REF:S000052965|PMID:3031666 TAS F UDP-N-acetyl-glucosamine-1-P transferase (GPT) YBR243C|TUR1 gene taxon:4932 20010118 SGD
+SGD S000000447 ALG7 GO:0006487 SGD_REF:S000058396|PMID:9878760 TAS P UDP-N-acetyl-glucosamine-1-P transferase (GPT) YBR243C|TUR1 gene taxon:4932 20010118 SGD
+SGD S000005593 ALG8 GO:0005789 SGD_REF:S000040670|PMID:8016100 ISS C glycosyl transferase YOR067C|YOR29-18 gene taxon:4932 20021010 SGD
+SGD S000005593 ALG8 GO:0005789 SGD_REF:S000040670|PMID:8016100 IMP C glycosyl transferase YOR067C|YOR29-18 gene taxon:4932 20021010 SGD
+SGD S000005593 ALG8 GO:0042283 SGD_REF:S000055633|PMID:3536907 IMP F glycosyl transferase YOR067C|YOR29-18 gene taxon:4932 20050613 SGD
+SGD S000005593 ALG8 GO:0006487 SGD_REF:S000040670|PMID:8016100 IMP P glycosyl transferase YOR067C|YOR29-18 gene taxon:4932 20050511 SGD
+SGD S000005593 ALG8 GO:0006488 SGD_REF:S000070115|PMID:10336995 TAS P glycosyl transferase YOR067C|YOR29-18 gene taxon:4932 20021220 SGD
+SGD S000005593 ALG8 GO:0006490 SGD_REF:S000055633|PMID:3536907 IMP P glycosyl transferase YOR067C|YOR29-18 gene taxon:4932 20010118 SGD
+SGD S000005163 ALG9 GO:0005783 SGD_REF:S000046181|PMID:8692962 IMP C mannosyltransferase YNL219C gene taxon:4932 20021115 SGD
+SGD S000005163 ALG9 GO:0005783 SGD_REF:S000046181|PMID:8692962 ISS C mannosyltransferase YNL219C gene taxon:4932 20021115 SGD
+SGD S000005163 ALG9 GO:0000030 SGD_REF:S000046181|PMID:8692962 IMP F mannosyltransferase YNL219C gene taxon:4932 20021115 SGD
+SGD S000005163 ALG9 GO:0000030 SGD_REF:S000046181|PMID:8692962 ISS F mannosyltransferase YNL219C gene taxon:4932 20021115 SGD
+SGD S000005163 ALG9 GO:0006486 SGD_REF:S000046181|PMID:8692962 IMP P mannosyltransferase YNL219C gene taxon:4932 20021115 SGD
+SGD S000005163 ALG9 GO:0006488 SGD_REF:S000070115|PMID:10336995 TAS P mannosyltransferase YNL219C gene taxon:4932 20021220 SGD
+SGD S000002989 ALK1 GO:0005634 SGD_REF:S000073149|PMID:12737306 ISS C haspin YGL021W gene taxon:4932 20030527 SGD
+SGD S000002989 ALK1 GO:0004674 SGD_REF:S000073149|PMID:12737306 ISS F haspin YGL021W gene taxon:4932 20030527 SGD
+SGD S000002989 ALK1 GO:0007067 SGD_REF:S000073149|PMID:12737306 IEP P haspin YGL021W gene taxon:4932 20030527 SGD
+SGD S000004551 ALO1 GO:0005739 SGD_REF:S000044242|PMID:10094636 IDA C D-arabinono-1,4-lactone oxidase YML086C gene taxon:4932 20020801 SGD
+SGD S000004551 ALO1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C D-arabinono-1,4-lactone oxidase YML086C gene taxon:4932 20040924 SGD
+SGD S000004551 ALO1 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C D-arabinono-1,4-lactone oxidase YML086C gene taxon:4932 20060317 SGD
+SGD S000004551 ALO1 GO:0031307 SGD_REF:S000115559|PMID:16689936 IDA C D-arabinono-1,4-lactone oxidase YML086C gene taxon:4932 20060515 SGD
+SGD S000004551 ALO1 GO:0003885 SGD_REF:S000044242|PMID:10094636 IDA F D-arabinono-1,4-lactone oxidase YML086C gene taxon:4932 20020801 SGD
+SGD S000004551 ALO1 GO:0006979 SGD_REF:S000044242|PMID:10094636 IMP P D-arabinono-1,4-lactone oxidase YML086C gene taxon:4932 20020801 SGD
+SGD S000005214 ALP1 GO:0005886 SGD_REF:S000043244|PMID:10654085 ISS C basic amino acid permease YNL270C|APL1 gene taxon:4932 20020805 SGD
+SGD S000005214 ALP1 GO:0015174 SGD_REF:S000043244|PMID:10654085 IDA F basic amino acid permease YNL270C|APL1 gene taxon:4932 20020806 SGD
+SGD S000005214 ALP1 GO:0015802 SGD_REF:S000043244|PMID:10654085 IDA P basic amino acid permease YNL270C|APL1 gene taxon:4932 20020805 SGD
+SGD S000005490 ALR1 GO:0005886 SGD_REF:S000053741|PMID:9430719 IMP C YOL130W|SWC3 gene taxon:4932 20010412 SGD
+SGD S000005490 ALR1 GO:0015082 SGD_REF:S000053741|PMID:9430719 IMP F YOL130W|SWC3 gene taxon:4932 20010412 SGD
+SGD S000005490 ALR1 GO:0015082 SGD_REF:S000053741|PMID:9430719 ISS F YOL130W|SWC3 gene taxon:4932 20010412 SGD
+SGD S000005490 ALR1 GO:0015674 SGD_REF:S000053741|PMID:9430719 IMP P YOL130W|SWC3 gene taxon:4932 20010412 SGD
+SGD S000005490 ALR1 GO:0015674 SGD_REF:S000053741|PMID:9430719 ISS P YOL130W|SWC3 gene taxon:4932 20010412 SGD
+SGD S000005490 ALR1 GO:0015693 SGD_REF:S000070286|PMID:12167543 IDA P YOL130W|SWC3 gene taxon:4932 20020919 SGD
+SGD S000001844 ALR2 GO:0005886 SGD_REF:S000053741|PMID:9430719 IMP C YFL050C gene taxon:4932 20010412 SGD
+SGD S000001844 ALR2 GO:0015082 SGD_REF:S000053741|PMID:9430719 IMP F YFL050C gene taxon:4932 20010412 SGD
+SGD S000001844 ALR2 GO:0015082 SGD_REF:S000053741|PMID:9430719 ISS F YFL050C gene taxon:4932 20010412 SGD
+SGD S000001844 ALR2 GO:0015674 SGD_REF:S000053741|PMID:9430719 IMP P YFL050C gene taxon:4932 20010412 SGD
+SGD S000001844 ALR2 GO:0015674 SGD_REF:S000053741|PMID:9430719 ISS P YFL050C gene taxon:4932 20010412 SGD
+SGD S000001844 ALR2 GO:0015693 SGD_REF:S000070286|PMID:12167543 IDA P YFL050C gene taxon:4932 20020919 SGD
+SGD S000004079 ALT1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YLR089C gene taxon:4932 20031210 SGD
+SGD S000004079 ALT1 GO:0008483 SGD_REF:S000072463|PMID:10592175 ISS F YLR089C gene taxon:4932 20030213 SGD
+SGD S000004079 ALT1 GO:0000004 SGD_REF:S000069584 ND P YLR089C gene taxon:4932 20021002 SGD
+SGD S000002518 ALT2 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YDR111C gene taxon:4932 20031028 SGD
+SGD S000002518 ALT2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDR111C gene taxon:4932 20031028 SGD
+SGD S000002518 ALT2 GO:0008483 SGD_REF:S000072463|PMID:10592175 ISS F YDR111C gene taxon:4932 20030204 SGD
+SGD S000002518 ALT2 GO:0000004 SGD_REF:S000069584 ND P YDR111C gene taxon:4932 20021002 SGD
+SGD S000003457 AMA1 GO:0005680 SGD_REF:S000061000|PMID:11114178 IPI C YGR225W|SPO70 gene taxon:4932 20020807 SGD
+SGD S000003457 AMA1 GO:0008047 SGD_REF:S000061000|PMID:11114178 IMP F YGR225W|SPO70 gene taxon:4932 20050511 SGD
+SGD S000003457 AMA1 GO:0008047 SGD_REF:S000061000|PMID:11114178 IPI F YGR225W|SPO70 gene taxon:4932 20050511 SGD
+SGD S000003457 AMA1 GO:0007127 SGD_REF:S000061000|PMID:11114178 IMP P YGR225W|SPO70 gene taxon:4932 20020807 SGD
+SGD S000003457 AMA1 GO:0007127 SGD_REF:S000061000|PMID:11114178 IEP P YGR225W|SPO70 gene taxon:4932 20020807 SGD
+SGD S000003457 AMA1 GO:0030163 SGD_REF:S000061000|PMID:11114178 IMP P YGR225W|SPO70 gene taxon:4932 20020807 SGD
+SGD S000003457 AMA1 GO:0030163 SGD_REF:S000061000|PMID:11114178 IPI P YGR225W|SPO70 gene taxon:4932 20020807 SGD
+SGD S000003457 AMA1 GO:0030437 SGD_REF:S000061000|PMID:11114178 IMP P YGR225W|SPO70 gene taxon:4932 20020807 SGD
+SGD S000003457 AMA1 GO:0030476 SGD_REF:S000079982|PMID:15590821 IMP P YGR225W|SPO70 gene taxon:4932 20050127 SGD
+SGD S000004498 AMD1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C AMP deaminase YML035C|AMD3 gene taxon:4932 20031028 SGD
+SGD S000004498 AMD1 GO:0003876 SGD_REF:S000061598|PMID:8241153 IDA F AMP deaminase YML035C|AMD3 gene taxon:4932 20021212 SGD
+SGD S000004498 AMD1 GO:0006163 SGD_REF:S000061598|PMID:8241153 IC GO:0003876 P AMP deaminase YML035C|AMD3 gene taxon:4932 20021212 SGD
+SGD S000002650 AMD2 GO:0008372 SGD_REF:S000069584 ND C amidase (putative) YDR242W gene taxon:4932 20020925 SGD
+SGD S000002650 AMD2 GO:0004040 SGD_REF:S000056825|PMID:2263500 ISS F amidase (putative) YDR242W gene taxon:4932 20021223 SGD
+SGD S000002650 AMD2 GO:0000004 SGD_REF:S000069584 ND P amidase (putative) YDR242W gene taxon:4932 20021001 SGD
+SGD S000000415 AME1 GO:0000776 SGD_REF:S000075142|PMID:14633972 IDA C microtubule stability regulator YBR211C|ARP100 gene taxon:4932 20031230 SGD
+SGD S000000415 AME1 GO:0000817 SGD_REF:S000075142|PMID:14633972 IDA C microtubule stability regulator YBR211C|ARP100 gene taxon:4932 20040618 SGD
+SGD S000000415 AME1 GO:0005816 SGD_REF:S000066054|PMID:8990184 NAS C microtubule stability regulator YBR211C|ARP100 gene taxon:4932 20030122 SGD
+SGD S000000415 AME1 GO:0005554 SGD_REF:S000069584 ND F microtubule stability regulator YBR211C|ARP100 gene taxon:4932 20030122 SGD
+SGD S000000415 AME1 GO:0008608 SGD_REF:S000075142|PMID:14633972 IDA P microtubule stability regulator YBR211C|ARP100 gene taxon:4932 20040618 SGD
+SGD S000000415 AME1 GO:0008608 SGD_REF:S000075142|PMID:14633972 IPI SGD:S000002726|SGD:S000005939|SGD:S000003411 P microtubule stability regulator YBR211C|ARP100 gene taxon:4932 20040618 SGD
+SGD S000000362 AMN1 GO:0005634 SGD_REF:S000073106|PMID:12628189 IDA C YBR158W|CST13|ICS4 gene taxon:4932 20030513 SGD
+SGD S000000362 AMN1 GO:0005737 SGD_REF:S000073106|PMID:12628189 IDA C YBR158W|CST13|ICS4 gene taxon:4932 20030513 SGD
+SGD S000000362 AMN1 GO:0005933 SGD_REF:S000073106|PMID:12628189 IDA C YBR158W|CST13|ICS4 gene taxon:4932 20030513 SGD
+SGD S000000362 AMN1 GO:0005515 SGD_REF:S000073106|PMID:12628189 IPI SGD:S000004529 F YBR158W|CST13|ICS4 gene taxon:4932 20030528 SGD
+SGD S000000362 AMN1 GO:0001100 SGD_REF:S000073106|PMID:12628189 IMP P YBR158W|CST13|ICS4 gene taxon:4932 20030528 SGD
+SGD S000000362 AMN1 GO:0001100 SGD_REF:S000073106|PMID:12628189 IGI SGD:S000000022|SGD:S000003324|SGD:S000000072|SGD:S000003330|SGD:S000001368|SGD:S000004603|SGD:S000005721|SGD:S000004529 P YBR158W|CST13|ICS4 gene taxon:4932 20030528 SGD
+SGD S000000362 AMN1 GO:0007093 SGD_REF:S000073106|PMID:12628189 IMP P YBR158W|CST13|ICS4 gene taxon:4932 20030528 SGD
+SGD S000003124 AMS1 GO:0005774 SGD_REF:S000056829|PMID:2266133 IDA C alpha mannosidase YGL156W gene taxon:4932 20010118 SGD
+SGD S000003124 AMS1 GO:0004559 SGD_REF:S000046652|PMID:2675832 ISS F alpha mannosidase YGL156W gene taxon:4932 20010118 SGD
+SGD S000003124 AMS1 GO:0005975 SGD_REF:S000046652|PMID:2675832 ISS P alpha mannosidase YGL156W gene taxon:4932 20010118 SGD
+SGD S000003124 AMS1 GO:0009313 SGD_REF:S000073759|PMID:12723970 IMP P alpha mannosidase YGL156W gene taxon:4932 20050614 SGD
+SGD S000003808 ANB1 GO:0005840 SGD_REF:S000058753|PMID:9841679 TAS C translation initiation factor eIF-5A, anaerobically expressed form YJR047C|HYP1|TIF51B gene taxon:4932 20010124 SGD
+SGD S000003808 ANB1 GO:0003743 SGD_REF:S000058753|PMID:9841679 TAS F translation initiation factor eIF-5A, anaerobically expressed form YJR047C|HYP1|TIF51B gene taxon:4932 20010124 SGD
+SGD S000003808 ANB1 GO:0006413 SGD_REF:S000058753|PMID:9841679 TAS P translation initiation factor eIF-5A, anaerobically expressed form YJR047C|HYP1|TIF51B gene taxon:4932 20010124 SGD
+SGD S000029033 ANC4 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20021209 SGD
+SGD S000029033 ANC4 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20021209 SGD
+SGD S000029033 ANC4 GO:0030029 SGD_REF:S000044102|PMID:8243993 IGI P gene taxon:4932 20010620 SGD
+SGD S000000762 ANP1 GO:0000136 SGD_REF:S000053242|PMID:9430634 IPI C YEL036C|GEM3|MNN8 gene taxon:4932 20020213 SGD
+SGD S000000762 ANP1 GO:0000137 SGD_REF:S000053242|PMID:9430634 IDA C YEL036C|GEM3|MNN8 gene taxon:4932 20020213 SGD
+SGD S000000762 ANP1 contributes_to GO:0000009 SGD_REF:S000047367|PMID:10037752 IDA F YEL036C|GEM3|MNN8 gene taxon:4932 20050428 SGD
+SGD S000000762 ANP1 GO:0000030 SGD_REF:S000043074|PMID:9434768 ISS F YEL036C|GEM3|MNN8 gene taxon:4932 20020213 SGD
+SGD S000000762 ANP1 GO:0006487 SGD_REF:S000053242|PMID:9430634 IMP P YEL036C|GEM3|MNN8 gene taxon:4932 20020213 SGD
+SGD S000000762 ANP1 GO:0006487 SGD_REF:S000053242|PMID:9430634 IDA P YEL036C|GEM3|MNN8 gene taxon:4932 20020213 SGD
+SGD S000006332 ANT1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YPR128C gene taxon:4932 20020507 SGD
+SGD S000006332 ANT1 GO:0005779 SGD_REF:S000065926|PMID:11566870 IDA C YPR128C gene taxon:4932 20011004 SGD
+SGD S000006332 ANT1 GO:0000295 SGD_REF:S000065926|PMID:11566870 IDA F YPR128C gene taxon:4932 20011005 SGD
+SGD S000006332 ANT1 GO:0000295 SGD_REF:S000061003|PMID:11390660 IMP F YPR128C gene taxon:4932 20011005 SGD
+SGD S000006332 ANT1 GO:0006635 SGD_REF:S000065926|PMID:11566870 IMP P YPR128C gene taxon:4932 20011004 SGD
+SGD S000006332 ANT1 GO:0006635 SGD_REF:S000061003|PMID:11390660 IMP P YPR128C gene taxon:4932 20011004 SGD
+SGD S000006332 ANT1 GO:0006635 SGD_REF:S000061003|PMID:11390660 IGI P YPR128C gene taxon:4932 20011004 SGD
+SGD S000006332 ANT1 GO:0006635 SGD_REF:S000065926|PMID:11566870 IGI P YPR128C gene taxon:4932 20011004 SGD
+SGD S000006332 ANT1 GO:0007031 SGD_REF:S000061003|PMID:11390660 IMP P YPR128C gene taxon:4932 20011004 SGD
+SGD S000006332 ANT1 GO:0015867 SGD_REF:S000065926|PMID:11566870 IDA P YPR128C gene taxon:4932 20030320 SGD
+SGD S000006384 AOS1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YPR180W gene taxon:4932 20031028 SGD
+SGD S000006384 AOS1 GO:0019948 SGD_REF:S000040819|PMID:9312010 IDA F YPR180W gene taxon:4932 20020610 SGD
+SGD S000006384 AOS1 GO:0019948 SGD_REF:S000040819|PMID:9312010 IPI F YPR180W gene taxon:4932 20020610 SGD
+SGD S000006384 AOS1 GO:0016925 SGD_REF:S000040819|PMID:9312010 IDA P YPR180W gene taxon:4932 20020404 SGD
+SGD S000000555 APA1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C diadenosine 5',5'''-P1,P4-tetraphosphate phosphorylase I YCL050C|DTP1 gene taxon:4932 20031028 SGD
+SGD S000000555 APA1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C diadenosine 5',5'''-P1,P4-tetraphosphate phosphorylase I YCL050C|DTP1 gene taxon:4932 20031028 SGD
+SGD S000000555 APA1 GO:0008796 SGD_REF:S000061627|PMID:7642617 TAS F diadenosine 5',5'''-P1,P4-tetraphosphate phosphorylase I YCL050C|DTP1 gene taxon:4932 20021223 SGD
+SGD S000000555 APA1 GO:0009117 SGD_REF:S000061627|PMID:7642617 TAS P diadenosine 5',5'''-P1,P4-tetraphosphate phosphorylase I YCL050C|DTP1 gene taxon:4932 20021223 SGD
+SGD S000002938 APA2 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C 5',5'''-P-1,P-4-tetraphosphate phosphorylase II YDR530C gene taxon:4932 20031028 SGD
+SGD S000002938 APA2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C 5',5'''-P-1,P-4-tetraphosphate phosphorylase II YDR530C gene taxon:4932 20031028 SGD
+SGD S000002938 APA2 GO:0004081 SGD_REF:S000052301|PMID:2174863 IDA F 5',5'''-P-1,P-4-tetraphosphate phosphorylase II YDR530C gene taxon:4932 20021001 SGD
+SGD S000002938 APA2 GO:0004081 SGD_REF:S000052301|PMID:2174863 IMP F 5',5'''-P-1,P-4-tetraphosphate phosphorylase II YDR530C gene taxon:4932 20021001 SGD
+SGD S000002938 APA2 GO:0004081 SGD_REF:S000052301|PMID:2174863 IGI F 5',5'''-P-1,P-4-tetraphosphate phosphorylase II YDR530C gene taxon:4932 20021001 SGD
+SGD S000002938 APA2 GO:0008796 SGD_REF:S000061627|PMID:7642617 TAS F 5',5'''-P-1,P-4-tetraphosphate phosphorylase II YDR530C gene taxon:4932 20021223 SGD
+SGD S000002938 APA2 GO:0009117 SGD_REF:S000052301|PMID:2174863 IMP P 5',5'''-P-1,P-4-tetraphosphate phosphorylase II YDR530C gene taxon:4932 20021001 SGD
+SGD S000002938 APA2 GO:0009117 SGD_REF:S000052301|PMID:2174863 IGI P 5',5'''-P-1,P-4-tetraphosphate phosphorylase II YDR530C gene taxon:4932 20021001 SGD
+SGD S000005116 APC1 GO:0005680 SGD_REF:S000058476|PMID:10465783 TAS C ubiquitin ligase subunit YNL172W gene taxon:4932 20010118 SGD
+SGD S000005116 APC1 GO:0004842 SGD_REF:S000058476|PMID:10465783 TAS F ubiquitin ligase subunit YNL172W gene taxon:4932 20010118 SGD
+SGD S000005116 APC1 GO:0005515 SGD_REF:S000058476|PMID:10465783 TAS F ubiquitin ligase subunit YNL172W gene taxon:4932 20010118 SGD
+SGD S000005116 APC1 GO:0000022 SGD_REF:S000058476|PMID:10465783 TAS P ubiquitin ligase subunit YNL172W gene taxon:4932 20010118 SGD
+SGD S000005116 APC1 GO:0000070 SGD_REF:S000058476|PMID:10465783 TAS P ubiquitin ligase subunit YNL172W gene taxon:4932 20010118 SGD
+SGD S000005116 APC1 GO:0007091 SGD_REF:S000058476|PMID:10465783 TAS P ubiquitin ligase subunit YNL172W gene taxon:4932 20010118 SGD
+SGD S000005116 APC1 GO:0008054 SGD_REF:S000058476|PMID:10465783 TAS P ubiquitin ligase subunit YNL172W gene taxon:4932 20010118 SGD
+SGD S000005116 APC1 GO:0016567 SGD_REF:S000044570|PMID:9469814 IPI P ubiquitin ligase subunit YNL172W gene taxon:4932 20050408 SGD
+SGD S000005116 APC1 GO:0031145 SGD_REF:S000042065|PMID:8895471 IDA P ubiquitin ligase subunit YNL172W gene taxon:4932 20050404 SGD
+SGD S000005116 APC1 GO:0031145 SGD_REF:S000044570|PMID:9469814 IPI P ubiquitin ligase subunit YNL172W gene taxon:4932 20050404 SGD
+SGD S000002166 APC11 GO:0005680 SGD_REF:S000058476|PMID:10465783 TAS C anaphase promoting complex (APC) subunit YDL008W gene taxon:4932 20010118 SGD
+SGD S000002166 APC11 GO:0004842 SGD_REF:S000058476|PMID:10465783 TAS F anaphase promoting complex (APC) subunit YDL008W gene taxon:4932 20010118 SGD
+SGD S000002166 APC11 GO:0004842 SGD_REF:S000044681|PMID:10230407 IDA F anaphase promoting complex (APC) subunit YDL008W gene taxon:4932 20030708 SGD
+SGD S000002166 APC11 GO:0005515 SGD_REF:S000058476|PMID:10465783 TAS F anaphase promoting complex (APC) subunit YDL008W gene taxon:4932 20010118 SGD
+SGD S000002166 APC11 GO:0000022 SGD_REF:S000058476|PMID:10465783 TAS P anaphase promoting complex (APC) subunit YDL008W gene taxon:4932 20010118 SGD
+SGD S000002166 APC11 GO:0000070 SGD_REF:S000058476|PMID:10465783 TAS P anaphase promoting complex (APC) subunit YDL008W gene taxon:4932 20010118 SGD
+SGD S000002166 APC11 GO:0007091 SGD_REF:S000058476|PMID:10465783 TAS P anaphase promoting complex (APC) subunit YDL008W gene taxon:4932 20010118 SGD
+SGD S000002166 APC11 GO:0008054 SGD_REF:S000058476|PMID:10465783 TAS P anaphase promoting complex (APC) subunit YDL008W gene taxon:4932 20010118 SGD
+SGD S000002166 APC11 GO:0016567 SGD_REF:S000044570|PMID:9469814 IPI P anaphase promoting complex (APC) subunit YDL008W gene taxon:4932 20050408 SGD
+SGD S000002166 APC11 GO:0031145 SGD_REF:S000044570|PMID:9469814 IPI P anaphase promoting complex (APC) subunit YDL008W gene taxon:4932 20050404 SGD
+SGD S000004117 APC2 GO:0005680 SGD_REF:S000058476|PMID:10465783 TAS C anaphase promoting complex (APC) subunit YLR127C|RSI1 gene taxon:4932 20010118 SGD
+SGD S000004117 APC2 GO:0004842 SGD_REF:S000058476|PMID:10465783 TAS F anaphase promoting complex (APC) subunit YLR127C|RSI1 gene taxon:4932 20010118 SGD
+SGD S000004117 APC2 GO:0005515 SGD_REF:S000058476|PMID:10465783 TAS F anaphase promoting complex (APC) subunit YLR127C|RSI1 gene taxon:4932 20010118 SGD
+SGD S000004117 APC2 GO:0000022 SGD_REF:S000058476|PMID:10465783 TAS P anaphase promoting complex (APC) subunit YLR127C|RSI1 gene taxon:4932 20010118 SGD
+SGD S000004117 APC2 GO:0000070 SGD_REF:S000058476|PMID:10465783 TAS P anaphase promoting complex (APC) subunit YLR127C|RSI1 gene taxon:4932 20010118 SGD
+SGD S000004117 APC2 GO:0007091 SGD_REF:S000058476|PMID:10465783 TAS P anaphase promoting complex (APC) subunit YLR127C|RSI1 gene taxon:4932 20010118 SGD
+SGD S000004117 APC2 GO:0008054 SGD_REF:S000058476|PMID:10465783 TAS P anaphase promoting complex (APC) subunit YLR127C|RSI1 gene taxon:4932 20010118 SGD
+SGD S000004117 APC2 GO:0016567 SGD_REF:S000044570|PMID:9469814 IPI P anaphase promoting complex (APC) subunit YLR127C|RSI1 gene taxon:4932 20050408 SGD
+SGD S000004117 APC2 GO:0031145 SGD_REF:S000044570|PMID:9469814 IPI P anaphase promoting complex (APC) subunit YLR127C|RSI1 gene taxon:4932 20050404 SGD
+SGD S000002525 APC4 GO:0005680 SGD_REF:S000058476|PMID:10465783 TAS C anaphase promoting complex (APC) subunit YDR118W gene taxon:4932 20010118 SGD
+SGD S000002525 APC4 GO:0004842 SGD_REF:S000058476|PMID:10465783 TAS F anaphase promoting complex (APC) subunit YDR118W gene taxon:4932 20010118 SGD
+SGD S000002525 APC4 GO:0005515 SGD_REF:S000058476|PMID:10465783 TAS F anaphase promoting complex (APC) subunit YDR118W gene taxon:4932 20010118 SGD
+SGD S000002525 APC4 GO:0000022 SGD_REF:S000058476|PMID:10465783 TAS P anaphase promoting complex (APC) subunit YDR118W gene taxon:4932 20010118 SGD
+SGD S000002525 APC4 GO:0000070 SGD_REF:S000058476|PMID:10465783 TAS P anaphase promoting complex (APC) subunit YDR118W gene taxon:4932 20010118 SGD
+SGD S000002525 APC4 GO:0007091 SGD_REF:S000058476|PMID:10465783 TAS P anaphase promoting complex (APC) subunit YDR118W gene taxon:4932 20010118 SGD
+SGD S000002525 APC4 GO:0008054 SGD_REF:S000058476|PMID:10465783 TAS P anaphase promoting complex (APC) subunit YDR118W gene taxon:4932 20010118 SGD
+SGD S000002525 APC4 GO:0016567 SGD_REF:S000044570|PMID:9469814 IPI P anaphase promoting complex (APC) subunit YDR118W gene taxon:4932 20050408 SGD
+SGD S000002525 APC4 GO:0031145 SGD_REF:S000044570|PMID:9469814 IPI P anaphase promoting complex (APC) subunit YDR118W gene taxon:4932 20050404 SGD
+SGD S000005775 APC5 GO:0005680 SGD_REF:S000058476|PMID:10465783 TAS C anaphase promoting complex (APC) subunit YOR249C|RMC1 gene taxon:4932 20010118 SGD
+SGD S000005775 APC5 GO:0004842 SGD_REF:S000058476|PMID:10465783 TAS F anaphase promoting complex (APC) subunit YOR249C|RMC1 gene taxon:4932 20010118 SGD
+SGD S000005775 APC5 GO:0005515 SGD_REF:S000058476|PMID:10465783 TAS F anaphase promoting complex (APC) subunit YOR249C|RMC1 gene taxon:4932 20010118 SGD
+SGD S000005775 APC5 GO:0000022 SGD_REF:S000058476|PMID:10465783 TAS P anaphase promoting complex (APC) subunit YOR249C|RMC1 gene taxon:4932 20010118 SGD
+SGD S000005775 APC5 GO:0000070 SGD_REF:S000058476|PMID:10465783 TAS P anaphase promoting complex (APC) subunit YOR249C|RMC1 gene taxon:4932 20010118 SGD
+SGD S000005775 APC5 GO:0006333 SGD_REF:S000071545|PMID:12399376 IMP P anaphase promoting complex (APC) subunit YOR249C|RMC1 gene taxon:4932 20021115 SGD
+SGD S000005775 APC5 GO:0007091 SGD_REF:S000058476|PMID:10465783 TAS P anaphase promoting complex (APC) subunit YOR249C|RMC1 gene taxon:4932 20010118 SGD
+SGD S000005775 APC5 GO:0008054 SGD_REF:S000058476|PMID:10465783 TAS P anaphase promoting complex (APC) subunit YOR249C|RMC1 gene taxon:4932 20010118 SGD
+SGD S000005775 APC5 GO:0016567 SGD_REF:S000044570|PMID:9469814 IPI P anaphase promoting complex (APC) subunit YOR249C|RMC1 gene taxon:4932 20050408 SGD
+SGD S000005775 APC5 GO:0031145 SGD_REF:S000044570|PMID:9469814 IPI P anaphase promoting complex (APC) subunit YOR249C|RMC1 gene taxon:4932 20050404 SGD
+SGD S000004092 APC9 GO:0005680 SGD_REF:S000058476|PMID:10465783 TAS C anaphase promoting complex (APC) subunit YLR102C gene taxon:4932 20010118 SGD
+SGD S000004092 APC9 GO:0004842 SGD_REF:S000058476|PMID:10465783 TAS F anaphase promoting complex (APC) subunit YLR102C gene taxon:4932 20010118 SGD
+SGD S000004092 APC9 GO:0005515 SGD_REF:S000058476|PMID:10465783 TAS F anaphase promoting complex (APC) subunit YLR102C gene taxon:4932 20010118 SGD
+SGD S000004092 APC9 GO:0000022 SGD_REF:S000058476|PMID:10465783 TAS P anaphase promoting complex (APC) subunit YLR102C gene taxon:4932 20010118 SGD
+SGD S000004092 APC9 GO:0000070 SGD_REF:S000058476|PMID:10465783 TAS P anaphase promoting complex (APC) subunit YLR102C gene taxon:4932 20010118 SGD
+SGD S000004092 APC9 GO:0007091 SGD_REF:S000058476|PMID:10465783 TAS P anaphase promoting complex (APC) subunit YLR102C gene taxon:4932 20010118 SGD
+SGD S000004092 APC9 GO:0008054 SGD_REF:S000058476|PMID:10465783 TAS P anaphase promoting complex (APC) subunit YLR102C gene taxon:4932 20010118 SGD
+SGD S000004092 APC9 GO:0016567 SGD_REF:S000044570|PMID:9469814 IPI P anaphase promoting complex (APC) subunit YLR102C gene taxon:4932 20050408 SGD
+SGD S000004092 APC9 GO:0031145 SGD_REF:S000044570|PMID:9469814 IPI P anaphase promoting complex (APC) subunit YLR102C gene taxon:4932 20050404 SGD
+SGD S000000355 APD1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YBR151W gene taxon:4932 20031028 SGD
+SGD S000000355 APD1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YBR151W gene taxon:4932 20031028 SGD
+SGD S000000355 APD1 GO:0005554 SGD_REF:S000069584 ND F YBR151W gene taxon:4932 20020925 SGD
+SGD S000000355 APD1 GO:0000004 SGD_REF:S000069584 ND P YBR151W gene taxon:4932 20020925 SGD
+SGD S000001640 APE2 GO:0005737 SGD_REF:S000053939|PMID:1765107 NAS C aminopeptidase yscII YKL157W|LAP1|YKL158W gene taxon:4932 20010118 SGD
+SGD S000001640 APE2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C aminopeptidase yscII YKL157W|LAP1|YKL158W gene taxon:4932 20040813 SGD
+SGD S000001640 APE2 GO:0030287 SGD_REF:S000053939|PMID:1765107 NAS C aminopeptidase yscII YKL157W|LAP1|YKL158W gene taxon:4932 20010924 SGD
+SGD S000001640 APE2 GO:0004178 SGD_REF:S000050368|PMID:6352682 IMP F aminopeptidase yscII YKL157W|LAP1|YKL158W gene taxon:4932 20010118 SGD
+SGD S000001640 APE2 GO:0006518 SGD_REF:S000051861|PMID:3286257 IMP P aminopeptidase yscII YKL157W|LAP1|YKL158W gene taxon:4932 20010118 SGD
+SGD S000001640 APE2 GO:0006518 SGD_REF:S000050368|PMID:6352682 IMP P aminopeptidase yscII YKL157W|LAP1|YKL158W gene taxon:4932 20010118 SGD
+SGD S000000490 APE3 GO:0000324 SGD_REF:S000057628|PMID:8175799 IDA C aminopeptidase yscIII YBR286W|APY1 gene taxon:4932 20010118 SGD
+SGD S000000490 APE3 GO:0004177 SGD_REF:S000057629|PMID:8175800 IMP F aminopeptidase yscIII YBR286W|APY1 gene taxon:4932 20010118 SGD
+SGD S000000490 APE3 GO:0004177 SGD_REF:S000057628|PMID:8175799 IDA F aminopeptidase yscIII YBR286W|APY1 gene taxon:4932 20010118 SGD
+SGD S000000490 APE3 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P aminopeptidase yscIII YBR286W|APY1 gene taxon:4932 20060210 SGD
+SGD S000000490 APE3 GO:0007039 SGD_REF:S000057628|PMID:8175799 IDA P aminopeptidase yscIII YBR286W|APY1 gene taxon:4932 20010118 SGD
+SGD S000029035 APG11 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20010119 SGD
+SGD S000029035 APG11 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20040419 SGD
+SGD S000029035 APG11 GO:0006914 SGD_REF:S000051835|PMID:8224160 IMP P gene taxon:4932 20010118 SGD
+SGD S000005021 APJ1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C J-protein co-chaperone family 20 kDa YNL077W gene taxon:4932 20031028 SGD
+SGD S000005021 APJ1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C J-protein co-chaperone family 20 kDa YNL077W gene taxon:4932 20031028 SGD
+SGD S000005021 APJ1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C J-protein co-chaperone family 20 kDa YNL077W gene taxon:4932 20040813 SGD
+SGD S000005021 APJ1 GO:0051082 SGD_REF:S000070059|PMID:11923285 IMP F J-protein co-chaperone family 20 kDa YNL077W gene taxon:4932 20030120 SGD
+SGD S000005021 APJ1 GO:0051082 SGD_REF:S000070059|PMID:11923285 ISS F J-protein co-chaperone family 20 kDa YNL077W gene taxon:4932 20030120 SGD
+SGD S000005021 APJ1 GO:0000004 SGD_REF:S000069584 ND P J-protein co-chaperone family 20 kDa YNL077W gene taxon:4932 20030120 SGD
+SGD S000003765 APL1 GO:0030122 SGD_REF:S000061640|PMID:10564262 ISS C beta-adaptin, clathrin associated protein complex large subunit YJR005W|YAP80 gene taxon:4932 20020708 SGD
+SGD S000003765 APL1 GO:0005554 SGD_REF:S000069584 ND F beta-adaptin, clathrin associated protein complex large subunit YJR005W|YAP80 gene taxon:4932 20020708 SGD
+SGD S000003765 APL1 GO:0016192 SGD_REF:S000056754|PMID:2122239 ISS P beta-adaptin, clathrin associated protein complex large subunit YJR005W|YAP80 gene taxon:4932 20010412 SGD
+SGD S000003765 APL1 GO:0016192 SGD_REF:S000061172|PMID:11252894 TAS P beta-adaptin, clathrin associated protein complex large subunit YJR005W|YAP80 gene taxon:4932 20050427 SGD
+SGD S000001618 APL2 GO:0030121 SGD_REF:S000061640|PMID:10564262 ISS C beta-adaptin, clathrin associated protein complex large subunit YKL135C gene taxon:4932 20020522 SGD
+SGD S000001618 APL2 GO:0030121 SGD_REF:S000061640|PMID:10564262 IPI C beta-adaptin, clathrin associated protein complex large subunit YKL135C gene taxon:4932 20020522 SGD
+SGD S000001618 APL2 GO:0030276 SGD_REF:S000061640|PMID:10564262 ISS F beta-adaptin, clathrin associated protein complex large subunit YKL135C gene taxon:4932 20020522 SGD
+SGD S000001618 APL2 GO:0030276 SGD_REF:S000061640|PMID:10564262 IPI F beta-adaptin, clathrin associated protein complex large subunit YKL135C gene taxon:4932 20020522 SGD
+SGD S000001618 APL2 GO:0016192 SGD_REF:S000061640|PMID:10564262 ISS P beta-adaptin, clathrin associated protein complex large subunit YKL135C gene taxon:4932 20020708 SGD
+SGD S000001618 APL2 GO:0016192 SGD_REF:S000061172|PMID:11252894 TAS P beta-adaptin, clathrin associated protein complex large subunit YKL135C gene taxon:4932 20050427 SGD
+SGD S000001618 APL2 GO:0016192 SGD_REF:S000061640|PMID:10564262 IPI P beta-adaptin, clathrin associated protein complex large subunit YKL135C gene taxon:4932 20020708 SGD
+SGD S000000133 APL3 GO:0030122 SGD_REF:S000061640|PMID:10564262 ISS C clathrin associated protein complex large subunit YBL037W gene taxon:4932 20020708 SGD
+SGD S000000133 APL3 GO:0005554 SGD_REF:S000069584 ND F clathrin associated protein complex large subunit YBL037W gene taxon:4932 20020708 SGD
+SGD S000000133 APL3 GO:0016192 SGD_REF:S000061640|PMID:10564262 ISS P clathrin associated protein complex large subunit YBL037W gene taxon:4932 20020708 SGD
+SGD S000000133 APL3 GO:0016192 SGD_REF:S000061172|PMID:11252894 TAS P clathrin associated protein complex large subunit YBL037W gene taxon:4932 20050427 SGD
+SGD S000006233 APL4 GO:0030121 SGD_REF:S000061640|PMID:10564262 ISS C clathrin associated protein complex large subunit, gamma-adaptin YPR029C gene taxon:4932 20020522 SGD
+SGD S000006233 APL4 GO:0030121 SGD_REF:S000061640|PMID:10564262 IPI C clathrin associated protein complex large subunit, gamma-adaptin YPR029C gene taxon:4932 20020522 SGD
+SGD S000006233 APL4 GO:0030276 SGD_REF:S000061640|PMID:10564262 ISS F clathrin associated protein complex large subunit, gamma-adaptin YPR029C gene taxon:4932 20020522 SGD
+SGD S000006233 APL4 GO:0030276 SGD_REF:S000061640|PMID:10564262 IPI F clathrin associated protein complex large subunit, gamma-adaptin YPR029C gene taxon:4932 20020522 SGD
+SGD S000006233 APL4 GO:0016192 SGD_REF:S000061640|PMID:10564262 ISS P clathrin associated protein complex large subunit, gamma-adaptin YPR029C gene taxon:4932 20020708 SGD
+SGD S000006233 APL4 GO:0016192 SGD_REF:S000061172|PMID:11252894 TAS P clathrin associated protein complex large subunit, gamma-adaptin YPR029C gene taxon:4932 20050427 SGD
+SGD S000006233 APL4 GO:0016192 SGD_REF:S000061640|PMID:10564262 IPI P clathrin associated protein complex large subunit, gamma-adaptin YPR029C gene taxon:4932 20020708 SGD
+SGD S000006116 APL5 GO:0030123 SGD_REF:S000054355|PMID:9335339 ISS C clathrin assembly complex AP-3 adaptin component delta-like subunit YPL195W|YKS4 gene taxon:4932 20020708 SGD
+SGD S000006116 APL5 GO:0005515 SGD_REF:S000061641|PMID:10559961 IPI SGD:S000002487 F clathrin assembly complex AP-3 adaptin component delta-like subunit YPL195W|YKS4 gene taxon:4932 20050616 SGD
+SGD S000006116 APL5 GO:0006896 SGD_REF:S000054355|PMID:9335339 IMP P clathrin assembly complex AP-3 adaptin component delta-like subunit YPL195W|YKS4 gene taxon:4932 20020708 SGD
+SGD S000006116 APL5 GO:0016192 SGD_REF:S000061172|PMID:11252894 TAS P clathrin assembly complex AP-3 adaptin component delta-like subunit YPL195W|YKS4 gene taxon:4932 20050427 SGD
+SGD S000003493 APL6 GO:0030123 SGD_REF:S000054355|PMID:9335339 ISS C clathrin assembly complex beta adaptin component (putative) YGR261C|YKS5 gene taxon:4932 20020708 SGD
+SGD S000003493 APL6 GO:0005554 SGD_REF:S000069584 ND F clathrin assembly complex beta adaptin component (putative) YGR261C|YKS5 gene taxon:4932 20020708 SGD
+SGD S000003493 APL6 GO:0006896 SGD_REF:S000054355|PMID:9335339 IMP P clathrin assembly complex beta adaptin component (putative) YGR261C|YKS5 gene taxon:4932 20020708 SGD
+SGD S000003493 APL6 GO:0016192 SGD_REF:S000061172|PMID:11252894 TAS P clathrin assembly complex beta adaptin component (putative) YGR261C|YKS5 gene taxon:4932 20050427 SGD
+SGD S000006180 APM1 GO:0030121 SGD_REF:S000061640|PMID:10564262 ISS C clathrin associated protein complex medium subunit YPL259C|YAP54 gene taxon:4932 20020708 SGD
+SGD S000006180 APM1 GO:0030121 SGD_REF:S000061640|PMID:10564262 IPI C clathrin associated protein complex medium subunit YPL259C|YAP54 gene taxon:4932 20020708 SGD
+SGD S000006180 APM1 GO:0030276 SGD_REF:S000061640|PMID:10564262 ISS F clathrin associated protein complex medium subunit YPL259C|YAP54 gene taxon:4932 20020708 SGD
+SGD S000006180 APM1 GO:0030276 SGD_REF:S000061640|PMID:10564262 IPI F clathrin associated protein complex medium subunit YPL259C|YAP54 gene taxon:4932 20020708 SGD
+SGD S000006180 APM1 GO:0016192 SGD_REF:S000061640|PMID:10564262 ISS P clathrin associated protein complex medium subunit YPL259C|YAP54 gene taxon:4932 20020708 SGD
+SGD S000006180 APM1 GO:0016192 SGD_REF:S000061172|PMID:11252894 TAS P clathrin associated protein complex medium subunit YPL259C|YAP54 gene taxon:4932 20050427 SGD
+SGD S000006180 APM1 GO:0016192 SGD_REF:S000061640|PMID:10564262 IPI P clathrin associated protein complex medium subunit YPL259C|YAP54 gene taxon:4932 20020708 SGD
+SGD S000001011 APM2 GO:0030121 SGD_REF:S000061640|PMID:10564262 IPI C YHL019C gene taxon:4932 20020708 SGD
+SGD S000001011 APM2 GO:0030276 SGD_REF:S000061640|PMID:10564262 ISS F YHL019C gene taxon:4932 20020708 SGD
+SGD S000001011 APM2 GO:0016192 SGD_REF:S000061640|PMID:10564262 ISS P YHL019C gene taxon:4932 20020708 SGD
+SGD S000001011 APM2 GO:0016192 SGD_REF:S000061172|PMID:11252894 TAS P YHL019C gene taxon:4932 20050427 SGD
+SGD S000000492 APM3 GO:0030123 SGD_REF:S000054355|PMID:9335339 ISS C clathrin associated protein complex medium subunit YBR288C|YKS6 gene taxon:4932 20020708 SGD
+SGD S000000492 APM3 GO:0005554 SGD_REF:S000069584 ND F clathrin associated protein complex medium subunit YBR288C|YKS6 gene taxon:4932 20020708 SGD
+SGD S000000492 APM3 GO:0006896 SGD_REF:S000054355|PMID:9335339 IMP P clathrin associated protein complex medium subunit YBR288C|YKS6 gene taxon:4932 20020708 SGD
+SGD S000000492 APM3 GO:0016192 SGD_REF:S000061172|PMID:11252894 TAS P clathrin associated protein complex medium subunit YBR288C|YKS6 gene taxon:4932 20050427 SGD
+SGD S000005423 APM4 GO:0030122 SGD_REF:S000069980|PMID:11598180 ISS C clathrin associated protein complex medium subunit YOL062C|AMP1 gene taxon:4932 20020617 SGD
+SGD S000005423 APM4 GO:0030122 SGD_REF:S000061640|PMID:10564262 ISS C clathrin associated protein complex medium subunit YOL062C|AMP1 gene taxon:4932 20020708 SGD
+SGD S000005423 APM4 GO:0005554 SGD_REF:S000069584 ND F clathrin associated protein complex medium subunit YOL062C|AMP1 gene taxon:4932 20020708 SGD
+SGD S000005423 APM4 GO:0006886 SGD_REF:S000069980|PMID:11598180 ISS P clathrin associated protein complex medium subunit YOL062C|AMP1 gene taxon:4932 20020617 SGD
+SGD S000005423 APM4 GO:0016192 SGD_REF:S000061172|PMID:11252894 TAS P clathrin associated protein complex medium subunit YOL062C|AMP1 gene taxon:4932 20050427 SGD
+SGD S000001597 APN1 GO:0005634 SGD_REF:S000050884|PMID:7690756 IDA C major apurinic/apyrimidinic endonuclease/3'-repair diesterase YKL114C gene taxon:4932 20020927 SGD
+SGD S000001597 APN1 GO:0005739 SGD_REF:S000060116|PMID:11238901 IDA C major apurinic/apyrimidinic endonuclease/3'-repair diesterase YKL114C gene taxon:4932 20021223 SGD
+SGD S000001597 APN1 GO:0003906 SGD_REF:S000039558|PMID:1693433 IMP F major apurinic/apyrimidinic endonuclease/3'-repair diesterase YKL114C gene taxon:4932 20021223 SGD
+SGD S000001597 APN1 GO:0003906 SGD_REF:S000073336|PMID:12767225 IDA F major apurinic/apyrimidinic endonuclease/3'-repair diesterase YKL114C gene taxon:4932 20030624 SGD
+SGD S000001597 APN1 GO:0003906 SGD_REF:S000039558|PMID:1693433 ISS F major apurinic/apyrimidinic endonuclease/3'-repair diesterase YKL114C gene taxon:4932 20021223 SGD
+SGD S000001597 APN1 GO:0006281 SGD_REF:S000041997|PMID:10806210 TAS P major apurinic/apyrimidinic endonuclease/3'-repair diesterase YKL114C gene taxon:4932 20020927 SGD
+SGD S000001597 APN1 GO:0006284 SGD_REF:S000051442|PMID:9295360 IDA P major apurinic/apyrimidinic endonuclease/3'-repair diesterase YKL114C gene taxon:4932 20030306 SGD
+SGD S000000115 APN2 GO:0005634 SGD_REF:S000059907|PMID:11238902 IC GO:0006281 C AP endonuclease YBL019W|ETH1 gene taxon:4932 20021113 SGD
+SGD S000000115 APN2 GO:0004528 SGD_REF:S000059907|PMID:11238902 IDA F AP endonuclease YBL019W|ETH1 gene taxon:4932 20020902 SGD
+SGD S000000115 APN2 GO:0008311 SGD_REF:S000059907|PMID:11238902 IDA F AP endonuclease YBL019W|ETH1 gene taxon:4932 20020902 SGD
+SGD S000000115 APN2 GO:0006281 SGD_REF:S000059907|PMID:11238902 IMP P AP endonuclease YBL019W|ETH1 gene taxon:4932 20020902 SGD
+SGD S000005038 APP1 GO:0015629 SGD_REF:S000059091|PMID:10992286 IPI C YNL094W gene taxon:4932 20020718 SGD
+SGD S000005038 APP1 GO:0030479 SGD_REF:S000061434|PMID:11489916 IDA C YNL094W gene taxon:4932 20030512 SGD
+SGD S000005038 APP1 GO:0005554 SGD_REF:S000069584 ND F YNL094W gene taxon:4932 20060315 SGD
+SGD S000005038 APP1 GO:0030036 SGD_REF:S000059091|PMID:10992286 IPI P YNL094W gene taxon:4932 20020718 SGD
+SGD S000001302 APQ12 GO:0005635 SGD_REF:S000077177|PMID:15273328 IDA C YIL040W gene taxon:4932 20041005 SGD
+SGD S000001302 APQ12 GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YIL040W gene taxon:4932 20031028 SGD
+SGD S000001302 APQ12 GO:0005554 SGD_REF:S000069584 ND F YIL040W gene taxon:4932 20041005 SGD
+SGD S000001302 APQ12 GO:0006406 SGD_REF:S000077177|PMID:15273328 IMP P YIL040W gene taxon:4932 20041005 SGD
+SGD S000004160 APS1 GO:0030121 SGD_REF:S000061640|PMID:10564262 ISS C clathrin associated protein complex small subunit YLR170C|YAP19 gene taxon:4932 20020708 SGD
+SGD S000004160 APS1 GO:0030121 SGD_REF:S000061640|PMID:10564262 IPI C clathrin associated protein complex small subunit YLR170C|YAP19 gene taxon:4932 20020708 SGD
+SGD S000004160 APS1 GO:0030276 SGD_REF:S000061640|PMID:10564262 ISS F clathrin associated protein complex small subunit YLR170C|YAP19 gene taxon:4932 20020708 SGD
+SGD S000004160 APS1 GO:0030276 SGD_REF:S000061640|PMID:10564262 IPI F clathrin associated protein complex small subunit YLR170C|YAP19 gene taxon:4932 20020708 SGD
+SGD S000004160 APS1 GO:0016192 SGD_REF:S000061640|PMID:10564262 ISS P clathrin associated protein complex small subunit YLR170C|YAP19 gene taxon:4932 20020708 SGD
+SGD S000004160 APS1 GO:0016192 SGD_REF:S000061640|PMID:10564262 IPI P clathrin associated protein complex small subunit YLR170C|YAP19 gene taxon:4932 20020708 SGD
+SGD S000004160 APS1 GO:0016192 SGD_REF:S000061172|PMID:11252894 TAS P clathrin associated protein complex small subunit YLR170C|YAP19 gene taxon:4932 20050427 SGD
+SGD S000003819 APS2 GO:0030122 SGD_REF:S000061640|PMID:10564262 ISS C clathrin associated protein complex small subunit YJR058C|YAP17 gene taxon:4932 20020708 SGD
+SGD S000003819 APS2 GO:0005554 SGD_REF:S000069584 ND F clathrin associated protein complex small subunit YJR058C|YAP17 gene taxon:4932 20020708 SGD
+SGD S000003819 APS2 GO:0016192 SGD_REF:S000061640|PMID:10564262 ISS P clathrin associated protein complex small subunit YJR058C|YAP17 gene taxon:4932 20020708 SGD
+SGD S000003819 APS2 GO:0016192 SGD_REF:S000061172|PMID:11252894 TAS P clathrin associated protein complex small subunit YJR058C|YAP17 gene taxon:4932 20050427 SGD
+SGD S000003561 APS3 GO:0030123 SGD_REF:S000054355|PMID:9335339 ISS C YJL024C|YKS7 gene taxon:4932 20020708 SGD
+SGD S000003561 APS3 GO:0005554 SGD_REF:S000069584 ND F YJL024C|YKS7 gene taxon:4932 20020708 SGD
+SGD S000003561 APS3 GO:0006896 SGD_REF:S000054355|PMID:9335339 IMP P YJL024C|YKS7 gene taxon:4932 20020708 SGD
+SGD S000003561 APS3 GO:0016192 SGD_REF:S000061172|PMID:11252894 TAS P YJL024C|YKS7 gene taxon:4932 20050427 SGD
+SGD S000004484 APT1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C adenine phosphoribosyltransferase YML022W gene taxon:4932 20031028 SGD
+SGD S000004484 APT1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C adenine phosphoribosyltransferase YML022W gene taxon:4932 20031028 SGD
+SGD S000004484 APT1 GO:0003999 SGD_REF:S000055423|PMID:9864350 IDA F adenine phosphoribosyltransferase YML022W gene taxon:4932 20021111 SGD
+SGD S000004484 APT1 GO:0006167 SGD_REF:S000050460|PMID:9357956 TAS P adenine phosphoribosyltransferase YML022W gene taxon:4932 20010118 SGD
+SGD S000004484 APT1 GO:0006168 SGD_REF:S000055423|PMID:9864350 IMP P adenine phosphoribosyltransferase YML022W gene taxon:4932 20050425 SGD
+SGD S000002849 APT2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDR441C gene taxon:4932 20031028 SGD
+SGD S000002849 APT2 NOT GO:0003999 SGD_REF:S000055423|PMID:9864350 IDA F YDR441C gene taxon:4932 20020902 SGD
+SGD S000002849 APT2 GO:0005554 SGD_REF:S000069584 ND F YDR441C gene taxon:4932 20020902 SGD
+SGD S000002849 APT2 GO:0000004 SGD_REF:S000069584 ND P YDR441C gene taxon:4932 20020902 SGD
+SGD S000005009 AQR1 GO:0005886 SGD_REF:S000069477|PMID:11922628 IDA C multidrug resistance transporter YNL065W gene taxon:4932 20021212 SGD
+SGD S000005009 AQR1 GO:0008028 SGD_REF:S000069477|PMID:11922628 IMP F multidrug resistance transporter YNL065W gene taxon:4932 20021212 SGD
+SGD S000005009 AQR1 GO:0015238 SGD_REF:S000069477|PMID:11922628 IMP F multidrug resistance transporter YNL065W gene taxon:4932 20021212 SGD
+SGD S000005009 AQR1 GO:0015718 SGD_REF:S000069477|PMID:11922628 IMP P multidrug resistance transporter YNL065W gene taxon:4932 20021212 SGD
+SGD S000005009 AQR1 GO:0015893 SGD_REF:S000069477|PMID:11922628 IMP P multidrug resistance transporter YNL065W gene taxon:4932 20021212 SGD
+SGD S000006396 AQY1 GO:0005886 SGD_REF:S000040273|PMID:10092523 IDA C aquaporin YPR192W gene taxon:4932 20030108 SGD
+SGD S000006396 AQY1 GO:0015250 SGD_REF:S000051106|PMID:9765289 IMP F aquaporin YPR192W gene taxon:4932 20010118 SGD
+SGD S000006396 AQY1 GO:0015250 SGD_REF:S000051106|PMID:9765289 ISS F aquaporin YPR192W gene taxon:4932 20010118 SGD
+SGD S000006396 AQY1 GO:0015250 SGD_REF:S000051106|PMID:9765289 IGI F aquaporin YPR192W gene taxon:4932 20010118 SGD
+SGD S000006396 AQY1 GO:0006833 SGD_REF:S000051106|PMID:9765289 IMP P aquaporin YPR192W gene taxon:4932 20010118 SGD
+SGD S000006396 AQY1 GO:0030437 SGD_REF:S000079836|PMID:15583134 IMP P aquaporin YPR192W gene taxon:4932 20050805 SGD
+SGD S000003975 AQY2 GO:0005789 SGD_REF:S000059515|PMID:11168368 IDA C MIP family member, aquaporin (putative) YLL052C gene taxon:4932 20030108 SGD
+SGD S000003975 AQY2 GO:0005886 SGD_REF:S000059515|PMID:11168368 IDA C MIP family member, aquaporin (putative) YLL052C gene taxon:4932 20030108 SGD
+SGD S000003975 AQY2 GO:0015250 SGD_REF:S000054716|PMID:10870101 ISS F MIP family member, aquaporin (putative) YLL052C gene taxon:4932 20010302 SGD
+SGD S000003975 AQY2 GO:0006833 SGD_REF:S000054716|PMID:10870101 ISS P MIP family member, aquaporin (putative) YLL052C gene taxon:4932 20010118 SGD
+SGD S000000353 ARA1 GO:0005829 SGD_REF:S000041001|PMID:9920381 IDA C D-arabinose dehydrogenase YBR149W gene taxon:4932 20030912 SGD
+SGD S000000353 ARA1 GO:0004032 SGD_REF:S000060122|PMID:11306085 IDA F D-arabinose dehydrogenase YBR149W gene taxon:4932 20030912 SGD
+SGD S000000353 ARA1 GO:0004033 SGD_REF:S000060122|PMID:11306085 ISS F D-arabinose dehydrogenase YBR149W gene taxon:4932 20030912 SGD
+SGD S000000353 ARA1 GO:0045290 SGD_REF:S000041001|PMID:9920381 IDA F D-arabinose dehydrogenase YBR149W gene taxon:4932 20020611 SGD
+SGD S000000353 ARA1 GO:0005975 SGD_REF:S000041001|PMID:9920381 IDA P D-arabinose dehydrogenase YBR149W gene taxon:4932 20020529 SGD
+SGD S000000353 ARA1 GO:0005975 SGD_REF:S000041001|PMID:9920381 IMP P D-arabinose dehydrogenase YBR149W gene taxon:4932 20020529 SGD
+SGD S000000838 ARB1 GO:0005634 SGD_REF:S000087079|PMID:16260602 IDA C Shuttling protein, ATP binding cassette protein YER036C gene taxon:4932 20060105 SGD
+SGD S000000838 ARB1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C Shuttling protein, ATP binding cassette protein YER036C gene taxon:4932 20031028 SGD
+SGD S000000838 ARB1 GO:0042626 SGD_REF:S000058031|PMID:9020838 ISS F Shuttling protein, ATP binding cassette protein YER036C gene taxon:4932 20021202 SGD
+SGD S000000838 ARB1 GO:0042626 SGD_REF:S000087079|PMID:16260602 IMP F Shuttling protein, ATP binding cassette protein YER036C gene taxon:4932 20060105 SGD
+SGD S000000838 ARB1 GO:0000056 SGD_REF:S000087079|PMID:16260602 IMP P Shuttling protein, ATP binding cassette protein YER036C gene taxon:4932 20060105 SGD
+SGD S000000838 ARB1 GO:0007046 SGD_REF:S000087079|PMID:16260602 IMP P Shuttling protein, ATP binding cassette protein YER036C gene taxon:4932 20060105 SGD
+SGD S000003073 ARC1 GO:0005737 SGD_REF:S000069031|PMID:11726524 IDA C YGL105W gene taxon:4932 20020807 SGD
+SGD S000003073 ARC1 GO:0005737 SGD_REF:S000080889|PMID:15710377 IDA C YGL105W gene taxon:4932 20050318 SGD
+SGD S000003073 ARC1 GO:0017102 SGD_REF:S000061654|PMID:9659920 IMP C YGL105W gene taxon:4932 20020807 SGD
+SGD S000003073 ARC1 GO:0017102 SGD_REF:S000061654|PMID:9659920 IPI C YGL105W gene taxon:4932 20020807 SGD
+SGD S000003073 ARC1 GO:0000049 SGD_REF:S000069031|PMID:11726524 IMP F YGL105W gene taxon:4932 20020807 SGD
+SGD S000003073 ARC1 GO:0000049 SGD_REF:S000069031|PMID:11726524 IPI F YGL105W gene taxon:4932 20020807 SGD
+SGD S000003073 ARC1 GO:0006409 SGD_REF:S000069031|PMID:11726524 IMP P YGL105W gene taxon:4932 20020807 SGD
+SGD S000003073 ARC1 GO:0006418 SGD_REF:S000061654|PMID:9659920 IMP P YGL105W gene taxon:4932 20020807 SGD
+SGD S000001324 ARC15 GO:0005740 SGD_REF:S000061657|PMID:10047519 TAS C YIL062C gene taxon:4932 20030304 SGD
+SGD S000001324 ARC15 GO:0005885 SGD_REF:S000051208|PMID:9210376 IDA C YIL062C gene taxon:4932 20010118 SGD
+SGD S000001324 ARC15 GO:0005885 SGD_REF:S000040553|PMID:10377407 IDA C YIL062C gene taxon:4932 20010118 SGD
+SGD S000001324 ARC15 GO:0003779 SGD_REF:S000061657|PMID:10047519 TAS F YIL062C gene taxon:4932 20030304 SGD
+SGD S000001324 ARC15 GO:0005198 SGD_REF:S000040553|PMID:10377407 IMP F YIL062C gene taxon:4932 20030213 SGD
+SGD S000001324 ARC15 GO:0000001 SGD_REF:S000068995|PMID:11248049 IMP P YIL062C gene taxon:4932 20050221 SGD
+SGD S000001324 ARC15 GO:0000001 SGD_REF:S000068995|PMID:11248049 IPI P YIL062C gene taxon:4932 20050221 SGD
+SGD S000001324 ARC15 GO:0000147 SGD_REF:S000040553|PMID:10377407 IMP P YIL062C gene taxon:4932 20030213 SGD
+SGD S000004362 ARC18 GO:0005885 SGD_REF:S000040553|PMID:10377407 IDA C YLR370C gene taxon:4932 20010118 SGD
+SGD S000004362 ARC18 GO:0005200 SGD_REF:S000040553|PMID:10377407 TAS F YLR370C gene taxon:4932 20010118 SGD
+SGD S000004362 ARC18 GO:0000001 SGD_REF:S000068995|PMID:11248049 TAS P YLR370C gene taxon:4932 20050221 SGD
+SGD S000004362 ARC18 GO:0007015 SGD_REF:S000040553|PMID:10377407 IMP P YLR370C gene taxon:4932 20010118 SGD
+SGD S000001496 ARC19 GO:0005885 SGD_REF:S000051208|PMID:9210376 IDA C YKL013C gene taxon:4932 20010118 SGD
+SGD S000001496 ARC19 GO:0005885 SGD_REF:S000040553|PMID:10377407 IDA C YKL013C gene taxon:4932 20010118 SGD
+SGD S000001496 ARC19 GO:0005198 SGD_REF:S000040553|PMID:10377407 IMP F YKL013C gene taxon:4932 20030213 SGD
+SGD S000001496 ARC19 GO:0000001 SGD_REF:S000068995|PMID:11248049 TAS P YKL013C gene taxon:4932 20050221 SGD
+SGD S000001496 ARC19 GO:0000147 SGD_REF:S000040553|PMID:10377407 IMP P YKL013C gene taxon:4932 20030213 SGD
+SGD S000005318 ARC35 GO:0005829 SGD_REF:S000077208|PMID:14554195 IPI C YNR035C|END9 gene taxon:4932 20041031 SGD
+SGD S000005318 ARC35 GO:0005885 SGD_REF:S000051208|PMID:9210376 IDA C YNR035C|END9 gene taxon:4932 20010118 SGD
+SGD S000005318 ARC35 GO:0005885 SGD_REF:S000040553|PMID:10377407 IDA C YNR035C|END9 gene taxon:4932 20010118 SGD
+SGD S000005318 ARC35 GO:0005198 SGD_REF:S000040553|PMID:10377407 IMP F YNR035C|END9 gene taxon:4932 20030218 SGD
+SGD S000005318 ARC35 GO:0000001 SGD_REF:S000068995|PMID:11248049 TAS P YNR035C|END9 gene taxon:4932 20050221 SGD
+SGD S000005318 ARC35 GO:0000226 SGD_REF:S000077208|PMID:14554195 IGI P YNR035C|END9 gene taxon:4932 20041031 SGD
+SGD S000005318 ARC35 GO:0000226 SGD_REF:S000077208|PMID:14554195 IPI P YNR035C|END9 gene taxon:4932 20041031 SGD
+SGD S000005318 ARC35 GO:0000226 SGD_REF:S000077208|PMID:14554195 TAS P YNR035C|END9 gene taxon:4932 20041031 SGD
+SGD S000005318 ARC35 GO:0000226 SGD_REF:S000077208|PMID:14554195 IMP P YNR035C|END9 gene taxon:4932 20041031 SGD
+SGD S000005318 ARC35 GO:0030036 SGD_REF:S000077208|PMID:14554195 IGI P YNR035C|END9 gene taxon:4932 20041031 SGD
+SGD S000005318 ARC35 GO:0030036 SGD_REF:S000077208|PMID:14554195 TAS P YNR035C|END9 gene taxon:4932 20041031 SGD
+SGD S000005318 ARC35 GO:0030036 SGD_REF:S000077208|PMID:14554195 IMP P YNR035C|END9 gene taxon:4932 20041031 SGD
+SGD S000005318 ARC35 GO:0030036 SGD_REF:S000077208|PMID:14554195 IPI P YNR035C|END9 gene taxon:4932 20041031 SGD
+SGD S000000438 ARC40 GO:0005885 SGD_REF:S000040553|PMID:10377407 IDA C YBR234C gene taxon:4932 20010118 SGD
+SGD S000000438 ARC40 GO:0005885 SGD_REF:S000081024|PMID:15485833 IDA C YBR234C gene taxon:4932 20050328 SGD
+SGD S000000438 ARC40 GO:0005200 SGD_REF:S000040553|PMID:10377407 TAS F YBR234C gene taxon:4932 20010118 SGD
+SGD S000000438 ARC40 GO:0000001 SGD_REF:S000068995|PMID:11248049 TAS P YBR234C gene taxon:4932 20050221 SGD
+SGD S000000438 ARC40 GO:0007015 SGD_REF:S000040553|PMID:10377407 IMP P YBR234C gene taxon:4932 20010118 SGD
+SGD S000000438 ARC40 GO:0045010 SGD_REF:S000081024|PMID:15485833 IDA P YBR234C gene taxon:4932 20050328 SGD
+SGD S000001055 ARD1 colocalizes_with GO:0005830 SGD_REF:S000074487|PMID:14517307 IDA C N alpha-acetyltransferase major subunit, complexes with Nat1p YHR013C gene taxon:4932 20041201 SGD
+SGD S000001055 ARD1 GO:0031415 SGD_REF:S000073836|PMID:12890471 TAS C N alpha-acetyltransferase major subunit, complexes with Nat1p YHR013C gene taxon:4932 20051205 SGD
+SGD S000001055 ARD1 GO:0031415 SGD_REF:S000074487|PMID:14517307 IDA C N alpha-acetyltransferase major subunit, complexes with Nat1p YHR013C gene taxon:4932 20060119 SGD
+SGD S000001055 ARD1 contributes_to GO:0004596 SGD_REF:S000044111|PMID:2551674 IDA F N alpha-acetyltransferase major subunit, complexes with Nat1p YHR013C gene taxon:4932 20060120 SGD
+SGD S000001055 ARD1 contributes_to GO:0004596 SGD_REF:S000044111|PMID:2551674 IMP F N alpha-acetyltransferase major subunit, complexes with Nat1p YHR013C gene taxon:4932 20060120 SGD
+SGD S000001055 ARD1 GO:0006474 SGD_REF:S000044111|PMID:2551674 IDA P N alpha-acetyltransferase major subunit, complexes with Nat1p YHR013C gene taxon:4932 20060120 SGD
+SGD S000001055 ARD1 GO:0006474 SGD_REF:S000044111|PMID:2551674 IMP P N alpha-acetyltransferase major subunit, complexes with Nat1p YHR013C gene taxon:4932 20060120 SGD
+SGD S000000644 ARE1 GO:0005783 SGD_REF:S000046370|PMID:10672016 IDA C acyl-CoA cholesterol acyltransferase (sterol-ester synthetase) YCR048W|SAT2 gene taxon:4932 20020906 SGD
+SGD S000000644 ARE1 GO:0004772 SGD_REF:S000046370|PMID:10672016 IDA F acyl-CoA cholesterol acyltransferase (sterol-ester synthetase) YCR048W|SAT2 gene taxon:4932 20020906 SGD
+SGD S000000644 ARE1 GO:0016125 SGD_REF:S000046370|PMID:10672016 IMP P acyl-CoA cholesterol acyltransferase (sterol-ester synthetase) YCR048W|SAT2 gene taxon:4932 20020906 SGD
+SGD S000005302 ARE2 GO:0005783 SGD_REF:S000046370|PMID:10672016 IDA C acyl-CoA cholesterol acyltransferase (sterol-ester synthetase) YNR019W|SAT1 gene taxon:4932 20020906 SGD
+SGD S000005302 ARE2 GO:0004772 SGD_REF:S000046370|PMID:10672016 IDA F acyl-CoA cholesterol acyltransferase (sterol-ester synthetase) YNR019W|SAT1 gene taxon:4932 20020906 SGD
+SGD S000005302 ARE2 GO:0016125 SGD_REF:S000046370|PMID:10672016 IMP P acyl-CoA cholesterol acyltransferase (sterol-ester synthetase) YNR019W|SAT1 gene taxon:4932 20020906 SGD
+SGD S000002351 ARF1 GO:0005798 SGD_REF:S000058477|PMID:9705267 TAS C ADP-ribosylation factor YDL192W gene taxon:4932 20010118 SGD
+SGD S000002351 ARF1 GO:0005798 SGD_REF:S000053279|PMID:10331652 TAS C ADP-ribosylation factor YDL192W gene taxon:4932 20010118 SGD
+SGD S000002351 ARF1 GO:0005829 SGD_REF:S000058477|PMID:9705267 TAS C ADP-ribosylation factor YDL192W gene taxon:4932 20010118 SGD
+SGD S000002351 ARF1 GO:0005829 SGD_REF:S000053279|PMID:10331652 TAS C ADP-ribosylation factor YDL192W gene taxon:4932 20010118 SGD
+SGD S000002351 ARF1 GO:0003924 SGD_REF:S000057032|PMID:3133654 ISS F ADP-ribosylation factor YDL192W gene taxon:4932 20010118 SGD
+SGD S000002351 ARF1 GO:0006888 SGD_REF:S000058477|PMID:9705267 TAS P ADP-ribosylation factor YDL192W gene taxon:4932 20010118 SGD
+SGD S000002351 ARF1 GO:0006888 SGD_REF:S000053279|PMID:10331652 TAS P ADP-ribosylation factor YDL192W gene taxon:4932 20010118 SGD
+SGD S000002351 ARF1 GO:0006891 SGD_REF:S000058477|PMID:9705267 TAS P ADP-ribosylation factor YDL192W gene taxon:4932 20010118 SGD
+SGD S000002351 ARF1 GO:0006891 SGD_REF:S000053279|PMID:10331652 TAS P ADP-ribosylation factor YDL192W gene taxon:4932 20010118 SGD
+SGD S000002351 ARF1 GO:0006893 SGD_REF:S000114540|PMID:16498409 IGI P ADP-ribosylation factor YDL192W gene taxon:4932 20060531 SGD
+SGD S000002351 ARF1 GO:0006893 SGD_REF:S000114540|PMID:16498409 IPI SGD:S000003635|SGD:S000001735 P ADP-ribosylation factor YDL192W gene taxon:4932 20060531 SGD
+SGD S000002296 ARF2 GO:0005798 SGD_REF:S000058477|PMID:9705267 TAS C ADP-ribosylation factor 2 YDL137W gene taxon:4932 20010118 SGD
+SGD S000002296 ARF2 GO:0005798 SGD_REF:S000053279|PMID:10331652 TAS C ADP-ribosylation factor 2 YDL137W gene taxon:4932 20010118 SGD
+SGD S000002296 ARF2 GO:0005829 SGD_REF:S000058477|PMID:9705267 TAS C ADP-ribosylation factor 2 YDL137W gene taxon:4932 20010118 SGD
+SGD S000002296 ARF2 GO:0005829 SGD_REF:S000053279|PMID:10331652 TAS C ADP-ribosylation factor 2 YDL137W gene taxon:4932 20010118 SGD
+SGD S000002296 ARF2 GO:0003924 SGD_REF:S000047924|PMID:2123295 ISS F ADP-ribosylation factor 2 YDL137W gene taxon:4932 20010118 SGD
+SGD S000002296 ARF2 GO:0006888 SGD_REF:S000058477|PMID:9705267 TAS P ADP-ribosylation factor 2 YDL137W gene taxon:4932 20010118 SGD
+SGD S000002296 ARF2 GO:0006888 SGD_REF:S000053279|PMID:10331652 TAS P ADP-ribosylation factor 2 YDL137W gene taxon:4932 20010118 SGD
+SGD S000002296 ARF2 GO:0006891 SGD_REF:S000058477|PMID:9705267 TAS P ADP-ribosylation factor 2 YDL137W gene taxon:4932 20010118 SGD
+SGD S000002296 ARF2 GO:0006891 SGD_REF:S000053279|PMID:10331652 TAS P ADP-ribosylation factor 2 YDL137W gene taxon:4932 20010118 SGD
+SGD S000005620 ARF3 GO:0008372 SGD_REF:S000069584 ND C GTP-binding ADP-ribosylation factor YOR094W|ARL2 gene taxon:4932 20021118 SGD
+SGD S000005620 ARF3 GO:0003924 SGD_REF:S000055715|PMID:8063710 ISS F GTP-binding ADP-ribosylation factor YOR094W|ARL2 gene taxon:4932 20010118 SGD
+SGD S000005620 ARF3 GO:0006886 SGD_REF:S000055715|PMID:8063710 ISS P GTP-binding ADP-ribosylation factor YOR094W|ARL2 gene taxon:4932 20010118 SGD
+SGD S000005620 ARF3 GO:0030036 SGD_REF:S000075147|PMID:14668359 IGI SGD:S000005648 P GTP-binding ADP-ribosylation factor YOR094W|ARL2 gene taxon:4932 20050103 SGD
+SGD S000005419 ARG1 GO:0005829 SGD_REF:S000056736|PMID:205532 IDA C arginosuccinate synthetase YOL058W|ARG10 gene taxon:4932 20010118 SGD
+SGD S000005419 ARG1 GO:0004055 SGD_REF:S000046890|PMID:2897249 IDA F arginosuccinate synthetase YOL058W|ARG10 gene taxon:4932 20010118 SGD
+SGD S000005419 ARG1 GO:0000052 SGD_REF:S000046047|PMID:348678 NAS P arginosuccinate synthetase YOL058W|ARG10 gene taxon:4932 20010118 SGD
+SGD S000005419 ARG1 GO:0000053 SGD_REF:S000056736|PMID:205532 TAS P arginosuccinate synthetase YOL058W|ARG10 gene taxon:4932 20010118 SGD
+SGD S000005419 ARG1 GO:0006526 SGD_REF:S000056736|PMID:205532 TAS P arginosuccinate synthetase YOL058W|ARG10 gene taxon:4932 20010118 SGD
+SGD S000003607 ARG2 GO:0005759 SGD_REF:S000056736|PMID:205532 IDA C acetylglutamate synthase YJL071W|HRB574 gene taxon:4932 20010118 SGD
+SGD S000003607 ARG2 GO:0004042 SGD_REF:S000066207|PMID:11553611 IDA F acetylglutamate synthase YJL071W|HRB574 gene taxon:4932 20030617 SGD
+SGD S000003607 ARG2 GO:0004042 SGD_REF:S000066207|PMID:11553611 IMP F acetylglutamate synthase YJL071W|HRB574 gene taxon:4932 20030617 SGD
+SGD S000003607 ARG2 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P acetylglutamate synthase YJL071W|HRB574 gene taxon:4932 20060227 SGD
+SGD S000003607 ARG2 GO:0006526 SGD_REF:S000066207|PMID:11553611 TAS P acetylglutamate synthase YJL071W|HRB574 gene taxon:4932 20030508 SGD
+SGD S000003607 ARG2 GO:0006592 SGD_REF:S000058497 TAS P acetylglutamate synthase YJL071W|HRB574 gene taxon:4932 20010119 SGD
+SGD S000003624 ARG3 GO:0005829 SGD_REF:S000056736|PMID:205532 IDA C ornithine carbamoyltransferase YJL088W gene taxon:4932 20010118 SGD
+SGD S000003624 ARG3 GO:0004585 SGD_REF:S000043118|PMID:7029528 IDA F ornithine carbamoyltransferase YJL088W gene taxon:4932 20010118 SGD
+SGD S000003624 ARG3 GO:0006526 SGD_REF:S000056736|PMID:205532 TAS P ornithine carbamoyltransferase YJL088W gene taxon:4932 20010118 SGD
+SGD S000003624 ARG3 GO:0006591 SGD_REF:S000056736|PMID:205532 TAS P ornithine carbamoyltransferase YJL088W gene taxon:4932 20010118 SGD
+SGD S000001060 ARG4 GO:0005829 SGD_REF:S000056736|PMID:205532 IDA C argininosuccinate lyase YHR018C gene taxon:4932 20010118 SGD
+SGD S000001060 ARG4 GO:0004056 SGD_REF:S000049571|PMID:6386606 IDA F argininosuccinate lyase YHR018C gene taxon:4932 20010118 SGD
+SGD S000001060 ARG4 GO:0006526 SGD_REF:S000049571|PMID:6386606 TAS P argininosuccinate lyase YHR018C gene taxon:4932 20010118 SGD
+SGD S000000871 ARG5,6 GO:0005759 SGD_REF:S000056662|PMID:1851947 IDA C N-acetyl-gamma-glutamyl-phosphate reductase, acetylglutamate kinase YER069W gene taxon:4932 20010118 SGD
+SGD S000000871 ARG5,6 GO:0003942 SGD_REF:S000056662|PMID:1851947 IDA F N-acetyl-gamma-glutamyl-phosphate reductase, acetylglutamate kinase YER069W gene taxon:4932 20010118 SGD
+SGD S000000871 ARG5,6 GO:0003991 SGD_REF:S000056662|PMID:1851947 IDA F N-acetyl-gamma-glutamyl-phosphate reductase, acetylglutamate kinase YER069W gene taxon:4932 20010118 SGD
+SGD S000000871 ARG5,6 GO:0006526 SGD_REF:S000073096|PMID:12603335 TAS P N-acetyl-gamma-glutamyl-phosphate reductase, acetylglutamate kinase YER069W gene taxon:4932 20030508 SGD
+SGD S000000871 ARG5,6 GO:0006592 SGD_REF:S000056662|PMID:1851947 TAS P N-acetyl-gamma-glutamyl-phosphate reductase, acetylglutamate kinase YER069W gene taxon:4932 20010118 SGD
+SGD S000000871 ARG5,6 GO:0045449 SGD_REF:S000079740|PMID:15486299 IMP P N-acetyl-gamma-glutamyl-phosphate reductase, acetylglutamate kinase YER069W gene taxon:4932 20041128 SGD
+SGD S000005500 ARG8 GO:0005759 SGD_REF:S000056736|PMID:205532 NAS C acetylornithine aminotransferase YOL140W gene taxon:4932 20010118 SGD
+SGD S000005500 ARG8 GO:0005759 SGD_REF:S000046321|PMID:8643562 NAS C acetylornithine aminotransferase YOL140W gene taxon:4932 20010118 SGD
+SGD S000005500 ARG8 GO:0003992 SGD_REF:S000046942|PMID:2199330 IDA F acetylornithine aminotransferase YOL140W gene taxon:4932 20010118 SGD
+SGD S000005500 ARG8 GO:0006526 SGD_REF:S000073096|PMID:12603335 TAS P acetylornithine aminotransferase YOL140W gene taxon:4932 20030508 SGD
+SGD S000005500 ARG8 GO:0006592 SGD_REF:S000056736|PMID:205532 TAS P acetylornithine aminotransferase YOL140W gene taxon:4932 20010118 SGD
+SGD S000004645 ARG80 GO:0005634 SGD_REF:S000057072|PMID:3311884 IDA C transcription factor YMR042W|ARGR1 gene taxon:4932 20020729 SGD
+SGD S000004645 ARG80 GO:0003677 SGD_REF:S000070419|PMID:12138185 TAS F transcription factor YMR042W|ARGR1 gene taxon:4932 20021203 SGD
+SGD S000004645 ARG80 GO:0003704 SGD_REF:S000070419|PMID:12138185 IDA F transcription factor YMR042W|ARGR1 gene taxon:4932 20021212 SGD
+SGD S000004645 ARG80 GO:0006525 SGD_REF:S000057062|PMID:3298999 TAS P transcription factor YMR042W|ARGR1 gene taxon:4932 20021212 SGD
+SGD S000004645 ARG80 GO:0045944 SGD_REF:S000070419|PMID:12138185 IDA P transcription factor YMR042W|ARGR1 gene taxon:4932 20021212 SGD
+SGD S000004565 ARG81 GO:0005634 SGD_REF:S000057072|PMID:3311884 IDA C zinc finger transcription factor of the Zn(2)-Cys(6) binuclear cluster domain type YML099C|ARGR2 gene taxon:4932 20020729 SGD
+SGD S000004565 ARG81 GO:0003712 SGD_REF:S000045902|PMID:10688655 IDA F zinc finger transcription factor of the Zn(2)-Cys(6) binuclear cluster domain type YML099C|ARGR2 gene taxon:4932 20021212 SGD
+SGD S000004565 ARG81 GO:0006525 SGD_REF:S000057062|PMID:3298999 TAS P zinc finger transcription factor of the Zn(2)-Cys(6) binuclear cluster domain type YML099C|ARGR2 gene taxon:4932 20021212 SGD
+SGD S000004565 ARG81 GO:0045955 SGD_REF:S000045902|PMID:10688655 IDA P zinc finger transcription factor of the Zn(2)-Cys(6) binuclear cluster domain type YML099C|ARGR2 gene taxon:4932 20021212 SGD
+SGD S000002580 ARG82 GO:0005634 SGD_REF:S000057072|PMID:3311884 IDA C dual specificity inositol 1,4,5-trisphosphate 6-kinase/inositol 1,4,5,6-tetrakisphosphate 3-kinase (IP3 6-/IP4 3-kinase) YDR173C|ARGR3|IPK2 gene taxon:4932 20020729 SGD
+SGD S000002580 ARG82 GO:0004428 SGD_REF:S000060143|PMID:11311242 IDA F dual specificity inositol 1,4,5-trisphosphate 6-kinase/inositol 1,4,5,6-tetrakisphosphate 3-kinase (IP3 6-/IP4 3-kinase) YDR173C|ARGR3|IPK2 gene taxon:4932 20020729 SGD
+SGD S000002580 ARG82 GO:0006525 SGD_REF:S000045518|PMID:8043104 IMP P dual specificity inositol 1,4,5-trisphosphate 6-kinase/inositol 1,4,5,6-tetrakisphosphate 3-kinase (IP3 6-/IP4 3-kinase) YDR173C|ARGR3|IPK2 gene taxon:4932 20020729 SGD
+SGD S000002580 ARG82 GO:0016310 SGD_REF:S000060143|PMID:11311242 IDA P dual specificity inositol 1,4,5-trisphosphate 6-kinase/inositol 1,4,5,6-tetrakisphosphate 3-kinase (IP3 6-/IP4 3-kinase) YDR173C|ARGR3|IPK2 gene taxon:4932 20020729 SGD
+SGD S000002580 ARG82 GO:0019220 SGD_REF:S000081537|PMID:15866881 IMP P dual specificity inositol 1,4,5-trisphosphate 6-kinase/inositol 1,4,5,6-tetrakisphosphate 3-kinase (IP3 6-/IP4 3-kinase) YDR173C|ARGR3|IPK2 gene taxon:4932 20060425 SGD
+SGD S000029041 ARG84 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20030423 SGD
+SGD S000029041 ARG84 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20030423 SGD
+SGD S000029041 ARG84 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20030423 SGD
+SGD S000002784 ARH1 GO:0005743 SGD_REF:S000039924|PMID:9727014 IDA C adrenodoxin oxidoreductase homolog YDR376W gene taxon:4932 20020820 SGD
+SGD S000002784 ARH1 GO:0015039 SGD_REF:S000039924|PMID:9727014 IDA F adrenodoxin oxidoreductase homolog YDR376W gene taxon:4932 20020820 SGD
+SGD S000002784 ARH1 GO:0006784 SGD_REF:S000069465|PMID:11788607 IGI P adrenodoxin oxidoreductase homolog YDR376W gene taxon:4932 20020903 SGD
+SGD S000002784 ARH1 GO:0006784 SGD_REF:S000069465|PMID:11788607 IMP P adrenodoxin oxidoreductase homolog YDR376W gene taxon:4932 20020903 SGD
+SGD S000002784 ARH1 GO:0006879 SGD_REF:S000060033|PMID:11035018 IMP P adrenodoxin oxidoreductase homolog YDR376W gene taxon:4932 20020820 SGD
+SGD S000004965 ARK1 GO:0030479 SGD_REF:S000041005|PMID:10652251 IDA C serine/threonine kinase (putative) YNL020C gene taxon:4932 20010118 SGD
+SGD S000004965 ARK1 GO:0004674 SGD_REF:S000043672|PMID:10087264 IMP F serine/threonine kinase (putative) YNL020C gene taxon:4932 20010118 SGD
+SGD S000004965 ARK1 GO:0004674 SGD_REF:S000043672|PMID:10087264 ISS F serine/threonine kinase (putative) YNL020C gene taxon:4932 20010118 SGD
+SGD S000004965 ARK1 GO:0000147 SGD_REF:S000041005|PMID:10652251 TAS P serine/threonine kinase (putative) YNL020C gene taxon:4932 20010118 SGD
+SGD S000004965 ARK1 GO:0000910 SGD_REF:S000041005|PMID:10652251 IMP P serine/threonine kinase (putative) YNL020C gene taxon:4932 20010119 SGD
+SGD S000004965 ARK1 GO:0006468 SGD_REF:S000043672|PMID:10087264 ISS P serine/threonine kinase (putative) YNL020C gene taxon:4932 20010118 SGD
+SGD S000004965 ARK1 GO:0006468 SGD_REF:S000043672|PMID:10087264 IMP P serine/threonine kinase (putative) YNL020C gene taxon:4932 20010118 SGD
+SGD S000004965 ARK1 GO:0007015 SGD_REF:S000043672|PMID:10087264 IMP P serine/threonine kinase (putative) YNL020C gene taxon:4932 20010118 SGD
+SGD S000004965 ARK1 GO:0007015 SGD_REF:S000043672|PMID:10087264 IGI P serine/threonine kinase (putative) YNL020C gene taxon:4932 20010118 SGD
+SGD S000004965 ARK1 GO:0030100 SGD_REF:S000075418|PMID:12956961 IMP P serine/threonine kinase (putative) YNL020C gene taxon:4932 20040520 SGD
+SGD S000000368 ARL1 GO:0005625 SGD_REF:S000040646|PMID:9388248 IDA C ADP-ribosylation factor-like protein 1 YBR164C|DLP2 gene taxon:4932 20020529 SGD
+SGD S000000368 ARL1 GO:0005794 SGD_REF:S000076519|PMID:15077113 IDA C ADP-ribosylation factor-like protein 1 YBR164C|DLP2 gene taxon:4932 20050523 SGD
+SGD S000000368 ARL1 GO:0005794 SGD_REF:S000081743|PMID:15564045 IDA C ADP-ribosylation factor-like protein 1 YBR164C|DLP2 gene taxon:4932 20050615 SGD
+SGD S000000368 ARL1 GO:0003924 SGD_REF:S000040646|PMID:9388248 ISS F ADP-ribosylation factor-like protein 1 YBR164C|DLP2 gene taxon:4932 20020529 SGD
+SGD S000000368 ARL1 GO:0003924 SGD_REF:S000040646|PMID:9388248 IDA F ADP-ribosylation factor-like protein 1 YBR164C|DLP2 gene taxon:4932 20020529 SGD
+SGD S000000368 ARL1 GO:0006623 SGD_REF:S000071154|PMID:12210899 IMP P ADP-ribosylation factor-like protein 1 YBR164C|DLP2 gene taxon:4932 20030123 SGD
+SGD S000000368 ARL1 GO:0016192 SGD_REF:S000069211|PMID:11840166 IGI P ADP-ribosylation factor-like protein 1 YBR164C|DLP2 gene taxon:4932 20020529 SGD
+SGD S000000368 ARL1 GO:0016192 SGD_REF:S000069211|PMID:11840166 IMP P ADP-ribosylation factor-like protein 1 YBR164C|DLP2 gene taxon:4932 20020529 SGD
+SGD S000005972 ARL3 GO:0005625 SGD_REF:S000044373|PMID:9920936 IDA C YPL051W gene taxon:4932 20020529 SGD
+SGD S000005972 ARL3 GO:0005794 SGD_REF:S000076519|PMID:15077113 IDA C YPL051W gene taxon:4932 20050523 SGD
+SGD S000005972 ARL3 GO:0005794 SGD_REF:S000076293|PMID:15077114 IDA C YPL051W gene taxon:4932 20050523 SGD
+SGD S000005972 ARL3 GO:0042175 SGD_REF:S000044373|PMID:9920936 IDA C YPL051W gene taxon:4932 20020529 SGD
+SGD S000005972 ARL3 GO:0003924 SGD_REF:S000044373|PMID:9920936 ISS F YPL051W gene taxon:4932 20020529 SGD
+SGD S000005972 ARL3 GO:0003924 SGD_REF:S000044373|PMID:9920936 IDA F YPL051W gene taxon:4932 20020529 SGD
+SGD S000005972 ARL3 GO:0006886 SGD_REF:S000044373|PMID:9920936 IMP P YPL051W gene taxon:4932 20020529 SGD
+SGD S000001032 ARN1 GO:0005768 SGD_REF:S000070405|PMID:12196168 TAS C YHL040C gene taxon:4932 20020912 SGD
+SGD S000001032 ARN1 GO:0016023 SGD_REF:S000052120|PMID:10748025 IDA C YHL040C gene taxon:4932 20010118 SGD
+SGD S000001032 ARN1 GO:0015343 SGD_REF:S000052311|PMID:10802175 IMP F YHL040C gene taxon:4932 20011019 SGD
+SGD S000001032 ARN1 GO:0015892 SGD_REF:S000052311|PMID:10802175 IMP P YHL040C gene taxon:4932 20010118 SGD
+SGD S000001039 ARN2 GO:0005768 SGD_REF:S000070405|PMID:12196168 TAS C triacetylfusarinine C transporter YHL047C|TAF1 gene taxon:4932 20020912 SGD
+SGD S000001039 ARN2 GO:0005886 SGD_REF:S000048259|PMID:10816729 ISS C triacetylfusarinine C transporter YHL047C|TAF1 gene taxon:4932 20020314 SGD
+SGD S000001039 ARN2 GO:0016023 SGD_REF:S000070405|PMID:12196168 TAS C triacetylfusarinine C transporter YHL047C|TAF1 gene taxon:4932 20020912 SGD
+SGD S000001039 ARN2 GO:0015343 SGD_REF:S000048259|PMID:10816729 IMP F triacetylfusarinine C transporter YHL047C|TAF1 gene taxon:4932 20020314 SGD
+SGD S000001039 ARN2 GO:0015343 SGD_REF:S000052120|PMID:10748025 IGI F triacetylfusarinine C transporter YHL047C|TAF1 gene taxon:4932 20020314 SGD
+SGD S000001039 ARN2 GO:0015343 SGD_REF:S000052120|PMID:10748025 IMP F triacetylfusarinine C transporter YHL047C|TAF1 gene taxon:4932 20020314 SGD
+SGD S000001039 ARN2 GO:0015343 SGD_REF:S000048259|PMID:10816729 IDA F triacetylfusarinine C transporter YHL047C|TAF1 gene taxon:4932 20020314 SGD
+SGD S000001039 ARN2 GO:0015343 SGD_REF:S000048259|PMID:10816729 ISS F triacetylfusarinine C transporter YHL047C|TAF1 gene taxon:4932 20020314 SGD
+SGD S000001039 ARN2 GO:0006879 SGD_REF:S000048259|PMID:10816729 IMP P triacetylfusarinine C transporter YHL047C|TAF1 gene taxon:4932 20020314 SGD
+SGD S000001039 ARN2 GO:0009237 SGD_REF:S000048259|PMID:10816729 IMP P triacetylfusarinine C transporter YHL047C|TAF1 gene taxon:4932 20020314 SGD
+SGD S000001039 ARN2 GO:0015892 SGD_REF:S000048259|PMID:10816729 IMP P triacetylfusarinine C transporter YHL047C|TAF1 gene taxon:4932 20020314 SGD
+SGD S000001039 ARN2 GO:0015892 SGD_REF:S000048259|PMID:10816729 IDA P triacetylfusarinine C transporter YHL047C|TAF1 gene taxon:4932 20020314 SGD
+SGD S000002534 ARO1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C 3-dehydroquinate dehydratase (3-dehydroquinase), 3-dehydroquinate synthase, epsp synthase, pentafunctional arom polypeptide, shikimate 5-dehydrogenase, shikimate kinase YDR127W gene taxon:4932 20031028 SGD
+SGD S000002534 ARO1 GO:0003855 SGD_REF:S000039885|PMID:6355828 IDA F 3-dehydroquinate dehydratase (3-dehydroquinase), 3-dehydroquinate synthase, epsp synthase, pentafunctional arom polypeptide, shikimate 5-dehydrogenase, shikimate kinase YDR127W gene taxon:4932 20021211 SGD
+SGD S000002534 ARO1 GO:0003856 SGD_REF:S000039885|PMID:6355828 IDA F 3-dehydroquinate dehydratase (3-dehydroquinase), 3-dehydroquinate synthase, epsp synthase, pentafunctional arom polypeptide, shikimate 5-dehydrogenase, shikimate kinase YDR127W gene taxon:4932 20021211 SGD
+SGD S000002534 ARO1 GO:0003866 SGD_REF:S000039885|PMID:6355828 IDA F 3-dehydroquinate dehydratase (3-dehydroquinase), 3-dehydroquinate synthase, epsp synthase, pentafunctional arom polypeptide, shikimate 5-dehydrogenase, shikimate kinase YDR127W gene taxon:4932 20021211 SGD
+SGD S000002534 ARO1 GO:0004764 SGD_REF:S000039885|PMID:6355828 IDA F 3-dehydroquinate dehydratase (3-dehydroquinase), 3-dehydroquinate synthase, epsp synthase, pentafunctional arom polypeptide, shikimate 5-dehydrogenase, shikimate kinase YDR127W gene taxon:4932 20021211 SGD
+SGD S000002534 ARO1 GO:0004765 SGD_REF:S000039885|PMID:6355828 IDA F 3-dehydroquinate dehydratase (3-dehydroquinase), 3-dehydroquinate synthase, epsp synthase, pentafunctional arom polypeptide, shikimate 5-dehydrogenase, shikimate kinase YDR127W gene taxon:4932 20021211 SGD
+SGD S000002534 ARO1 GO:0009073 SGD_REF:S000070200 TAS P 3-dehydroquinate dehydratase (3-dehydroquinase), 3-dehydroquinate synthase, epsp synthase, pentafunctional arom polypeptide, shikimate 5-dehydrogenase, shikimate kinase YDR127W gene taxon:4932 20021211 SGD
+SGD S000002788 ARO10 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDR380W gene taxon:4932 20031028 SGD
+SGD S000002788 ARO10 GO:0004737 SGD_REF:S000061038|PMID:8962070 ISS F YDR380W gene taxon:4932 20021218 SGD
+SGD S000002788 ARO10 GO:0016831 SGD_REF:S000051759|PMID:10753893 ISS F YDR380W gene taxon:4932 20021011 SGD
+SGD S000002788 ARO10 GO:0016831 SGD_REF:S000051759|PMID:10753893 IMP F YDR380W gene taxon:4932 20021011 SGD
+SGD S000002788 ARO10 GO:0050177 SGD_REF:S000073909|PMID:12902239 IDA F YDR380W gene taxon:4932 20030912 SGD
+SGD S000002788 ARO10 GO:0006552 SGD_REF:S000051759|PMID:10753893 IMP P YDR380W gene taxon:4932 20021011 SGD
+SGD S000002788 ARO10 GO:0006559 SGD_REF:S000073909|PMID:12902239 IDA P YDR380W gene taxon:4932 20030912 SGD
+SGD S000003116 ARO2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C chorismate synthase YGL148W gene taxon:4932 20031028 SGD
+SGD S000003116 ARO2 GO:0004107 SGD_REF:S000070200 TAS F chorismate synthase YGL148W gene taxon:4932 20021211 SGD
+SGD S000003116 ARO2 GO:0042602 SGD_REF:S000061725|PMID:8971708 IDA F chorismate synthase YGL148W gene taxon:4932 20040504 SGD
+SGD S000003116 ARO2 GO:0009073 SGD_REF:S000070200 TAS P chorismate synthase YGL148W gene taxon:4932 20021211 SGD
+SGD S000002442 ARO3 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase isoenzyme YDR035W gene taxon:4932 20031028 SGD
+SGD S000002442 ARO3 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase isoenzyme YDR035W gene taxon:4932 20031028 SGD
+SGD S000002442 ARO3 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase isoenzyme YDR035W gene taxon:4932 20040813 SGD
+SGD S000002442 ARO3 GO:0003849 SGD_REF:S000049239|PMID:2880280 IDA F 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase isoenzyme YDR035W gene taxon:4932 20021212 SGD
+SGD S000002442 ARO3 GO:0009073 SGD_REF:S000070200 TAS P 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase isoenzyme YDR035W gene taxon:4932 20021212 SGD
+SGD S000000453 ARO4 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase isoenzyme YBR249C gene taxon:4932 20031028 SGD
+SGD S000000453 ARO4 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase isoenzyme YBR249C gene taxon:4932 20031028 SGD
+SGD S000000453 ARO4 GO:0003849 SGD_REF:S000049239|PMID:2880280 IDA F 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase isoenzyme YBR249C gene taxon:4932 20021212 SGD
+SGD S000000453 ARO4 GO:0009073 SGD_REF:S000070200 TAS P 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase isoenzyme YBR249C gene taxon:4932 20021212 SGD
+SGD S000006264 ARO7 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C chorismate mutase YPR060C|HGS1|OSM2|TYR7 gene taxon:4932 20031028 SGD
+SGD S000006264 ARO7 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C chorismate mutase YPR060C|HGS1|OSM2|TYR7 gene taxon:4932 20031028 SGD
+SGD S000006264 ARO7 GO:0004106 SGD_REF:S000041525|PMID:3027508 IDA F chorismate mutase YPR060C|HGS1|OSM2|TYR7 gene taxon:4932 20021212 SGD
+SGD S000006264 ARO7 GO:0009073 SGD_REF:S000070200 TAS P chorismate mutase YPR060C|HGS1|OSM2|TYR7 gene taxon:4932 20021212 SGD
+SGD S000003170 ARO8 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C aromatic amino acid aminotransferase YGL202W gene taxon:4932 20031028 SGD
+SGD S000003170 ARO8 GO:0008793 SGD_REF:S000054047|PMID:9491082 IDA F aromatic amino acid aminotransferase YGL202W gene taxon:4932 20020529 SGD
+SGD S000003170 ARO8 GO:0008793 SGD_REF:S000054049|PMID:9491083 ISS F aromatic amino acid aminotransferase YGL202W gene taxon:4932 20020529 SGD
+SGD S000003170 ARO8 GO:0009072 SGD_REF:S000054049|PMID:9491083 IGI P aromatic amino acid aminotransferase YGL202W gene taxon:4932 20020529 SGD
+SGD S000003170 ARO8 GO:0009072 SGD_REF:S000054049|PMID:9491083 IMP P aromatic amino acid aminotransferase YGL202W gene taxon:4932 20020529 SGD
+SGD S000002829 ARO80 GO:0005634 SGD_REF:S000044328|PMID:10207060 IC GO:0003704 C YDR421W gene taxon:4932 20030507 SGD
+SGD S000002829 ARO80 GO:0003704 SGD_REF:S000044328|PMID:10207060 IMP F YDR421W gene taxon:4932 20030507 SGD
+SGD S000002829 ARO80 GO:0003704 SGD_REF:S000044328|PMID:10207060 ISS F YDR421W gene taxon:4932 20030507 SGD
+SGD S000002829 ARO80 GO:0009074 SGD_REF:S000044328|PMID:10207060 IMP P YDR421W gene taxon:4932 20040616 SGD
+SGD S000002829 ARO80 GO:0045944 SGD_REF:S000044328|PMID:10207060 IMP P YDR421W gene taxon:4932 20030507 SGD
+SGD S000001179 ARO9 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C aromatic amino acid aminotransferase II YHR137W gene taxon:4932 20031028 SGD
+SGD S000001179 ARO9 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C aromatic amino acid aminotransferase II YHR137W gene taxon:4932 20031028 SGD
+SGD S000001179 ARO9 GO:0008793 SGD_REF:S000054047|PMID:9491082 IDA F aromatic amino acid aminotransferase II YHR137W gene taxon:4932 20020529 SGD
+SGD S000001179 ARO9 GO:0008793 SGD_REF:S000054049|PMID:9491083 ISS F aromatic amino acid aminotransferase II YHR137W gene taxon:4932 20020529 SGD
+SGD S000001179 ARO9 GO:0009072 SGD_REF:S000054049|PMID:9491083 IGI P aromatic amino acid aminotransferase II YHR137W gene taxon:4932 20020529 SGD
+SGD S000001179 ARO9 GO:0009072 SGD_REF:S000054049|PMID:9491083 IMP P aromatic amino acid aminotransferase II YHR137W gene taxon:4932 20020529 SGD
+SGD S000001171 ARP1 GO:0005869 SGD_REF:S000046660|PMID:9658168 IDA C YHR129C|ACT5 gene taxon:4932 20010118 SGD
+SGD S000001171 ARP1 GO:0005200 SGD_REF:S000046660|PMID:9658168 IPI F YHR129C|ACT5 gene taxon:4932 20010118 SGD
+SGD S000001171 ARP1 GO:0000132 SGD_REF:S000049667|PMID:8069915 IMP P YHR129C|ACT5 gene taxon:4932 20050512 SGD
+SGD S000001171 ARP1 GO:0007097 SGD_REF:S000049667|PMID:8069915 IMP P YHR129C|ACT5 gene taxon:4932 20050512 SGD
+SGD S000002513 ARP10 GO:0005737 SGD_REF:S000059257|PMID:11011149 IDA C YDR106W gene taxon:4932 20021127 SGD
+SGD S000002513 ARP10 GO:0005869 SGD_REF:S000113752|PMID:16291862 IPI SGD:S000001171|SGD:S000004908|SGD:S000006095 C YDR106W gene taxon:4932 20060424 SGD
+SGD S000002513 ARP10 GO:0005200 SGD_REF:S000113752|PMID:16291862 IPI SGD:S000001171|SGD:S000004908|SGD:S000006095 F YDR106W gene taxon:4932 20060424 SGD
+SGD S000002513 ARP10 GO:0007067 SGD_REF:S000113752|PMID:16291862 IGI SGD:S000001171 P YDR106W gene taxon:4932 20060424 SGD
+SGD S000002187 ARP2 GO:0005739 SGD_REF:S000061657|PMID:10047519 TAS C actin related protein YDL029W|ACT2 gene taxon:4932 20030304 SGD
+SGD S000002187 ARP2 GO:0005885 SGD_REF:S000040553|PMID:10377407 IDA C actin related protein YDL029W|ACT2 gene taxon:4932 20010118 SGD
+SGD S000002187 ARP2 GO:0003779 SGD_REF:S000040553|PMID:10377407 TAS F actin related protein YDL029W|ACT2 gene taxon:4932 20010118 SGD
+SGD S000002187 ARP2 GO:0005200 SGD_REF:S000040553|PMID:10377407 TAS F actin related protein YDL029W|ACT2 gene taxon:4932 20010118 SGD
+SGD S000002187 ARP2 GO:0005524 SGD_REF:S000080403|PMID:15657399 IDA F actin related protein YDL029W|ACT2 gene taxon:4932 20050822 SGD
+SGD S000002187 ARP2 GO:0005524 SGD_REF:S000080403|PMID:15657399 IMP F actin related protein YDL029W|ACT2 gene taxon:4932 20050822 SGD
+SGD S000002187 ARP2 GO:0000001 SGD_REF:S000068995|PMID:11248049 IMP P actin related protein YDL029W|ACT2 gene taxon:4932 20050221 SGD
+SGD S000002187 ARP2 GO:0000001 SGD_REF:S000068995|PMID:11248049 IPI P actin related protein YDL029W|ACT2 gene taxon:4932 20050221 SGD
+SGD S000002187 ARP2 GO:0007015 SGD_REF:S000040553|PMID:10377407 IMP P actin related protein YDL029W|ACT2 gene taxon:4932 20010118 SGD
+SGD S000003826 ARP3 GO:0005885 SGD_REF:S000040553|PMID:10377407 IDA C YJR065C|ACT4 gene taxon:4932 20010118 SGD
+SGD S000003826 ARP3 GO:0003779 SGD_REF:S000040553|PMID:10377407 TAS F YJR065C|ACT4 gene taxon:4932 20010118 SGD
+SGD S000003826 ARP3 GO:0005200 SGD_REF:S000040553|PMID:10377407 TAS F YJR065C|ACT4 gene taxon:4932 20010118 SGD
+SGD S000003826 ARP3 GO:0005524 SGD_REF:S000080403|PMID:15657399 IDA F YJR065C|ACT4 gene taxon:4932 20050822 SGD
+SGD S000003826 ARP3 GO:0005524 SGD_REF:S000080403|PMID:15657399 IMP F YJR065C|ACT4 gene taxon:4932 20050822 SGD
+SGD S000003826 ARP3 GO:0000001 SGD_REF:S000068995|PMID:11248049 TAS P YJR065C|ACT4 gene taxon:4932 20050221 SGD
+SGD S000003826 ARP3 GO:0007015 SGD_REF:S000040553|PMID:10377407 IMP P YJR065C|ACT4 gene taxon:4932 20010118 SGD
+SGD S000003617 ARP4 GO:0000790 SGD_REF:S000046089|PMID:10436015 IDA C actin related protein YJL081C|ACT3 gene taxon:4932 20010118 SGD
+SGD S000003617 ARP4 GO:0000812 SGD_REF:S000074662|PMID:14645854 IPI C actin related protein YJL081C|ACT3 gene taxon:4932 20040412 SGD
+SGD S000003617 ARP4 GO:0000812 SGD_REF:S000075430|PMID:14690608 IPI C actin related protein YJL081C|ACT3 gene taxon:4932 20040412 SGD
+SGD S000003617 ARP4 GO:0005634 SGD_REF:S000059257|PMID:11011149 IDA C actin related protein YJL081C|ACT3 gene taxon:4932 20021127 SGD
+SGD S000003617 ARP4 GO:0031011 SGD_REF:S000040657|PMID:10952318 IPI SGD:S000003118 C actin related protein YJL081C|ACT3 gene taxon:4932 20050411 SGD
+SGD S000003617 ARP4 GO:0043189 SGD_REF:S000046619|PMID:10911987 IPI C actin related protein YJL081C|ACT3 gene taxon:4932 20060321 SGD
+SGD S000003617 ARP4 GO:0003682 SGD_REF:S000046089|PMID:10436015 IDA F actin related protein YJL081C|ACT3 gene taxon:4932 20010118 SGD
+SGD S000003617 ARP4 contributes_to GO:0004402 SGD_REF:S000046619|PMID:10911987 IMP F actin related protein YJL081C|ACT3 gene taxon:4932 20060321 SGD
+SGD S000003617 ARP4 contributes_to GO:0043141 SGD_REF:S000040657|PMID:10952318 IDA F actin related protein YJL081C|ACT3 gene taxon:4932 20060320 SGD
+SGD S000003617 ARP4 GO:0006325 SGD_REF:S000046089|PMID:10436015 IMP P actin related protein YJL081C|ACT3 gene taxon:4932 20010118 SGD
+SGD S000003617 ARP4 GO:0006325 SGD_REF:S000046089|PMID:10436015 IPI P actin related protein YJL081C|ACT3 gene taxon:4932 20010118 SGD
+SGD S000003617 ARP4 GO:0006338 SGD_REF:S000074662|PMID:14645854 IDA P actin related protein YJL081C|ACT3 gene taxon:4932 20040322 SGD
+SGD S000003617 ARP4 GO:0006355 SGD_REF:S000046829|PMID:8598290 IMP P actin related protein YJL081C|ACT3 gene taxon:4932 20010118 SGD
+SGD S000003617 ARP4 GO:0006357 SGD_REF:S000046619|PMID:10911987 IDA P actin related protein YJL081C|ACT3 gene taxon:4932 20020918 SGD
+SGD S000003617 ARP4 GO:0016573 SGD_REF:S000046619|PMID:10911987 IDA P actin related protein YJL081C|ACT3 gene taxon:4932 20020918 SGD
+SGD S000005004 ARP5 GO:0005634 SGD_REF:S000061051|PMID:10878579 TAS C actin related protein YNL059C gene taxon:4932 20021115 SGD
+SGD S000005004 ARP5 GO:0005634 SGD_REF:S000059257|PMID:11011149 IDA C actin related protein YNL059C gene taxon:4932 20021127 SGD
+SGD S000005004 ARP5 GO:0031011 SGD_REF:S000079913|PMID:15525518 IDA C actin related protein YNL059C gene taxon:4932 20050317 SGD
+SGD S000005004 ARP5 GO:0031011 SGD_REF:S000073963|PMID:12887900 IPI SGD:S000003118 C actin related protein YNL059C gene taxon:4932 20050317 SGD
+SGD S000005004 ARP5 GO:0031011 SGD_REF:S000073963|PMID:12887900 IMP C actin related protein YNL059C gene taxon:4932 20050317 SGD
+SGD S000005004 ARP5 GO:0005554 SGD_REF:S000069584 ND F actin related protein YNL059C gene taxon:4932 20021016 SGD
+SGD S000005004 ARP5 contributes_to GO:0043141 SGD_REF:S000040657|PMID:10952318 IDA F actin related protein YNL059C gene taxon:4932 20060320 SGD
+SGD S000005004 ARP5 GO:0006338 SGD_REF:S000079913|PMID:15525518 IPI SGD:S000003118 P actin related protein YNL059C gene taxon:4932 20050317 SGD
+SGD S000005004 ARP5 GO:0006338 SGD_REF:S000073963|PMID:12887900 IMP P actin related protein YNL059C gene taxon:4932 20050317 SGD
+SGD S000005004 ARP5 GO:0006338 SGD_REF:S000073963|PMID:12887900 IPI SGD:S000003118 P actin related protein YNL059C gene taxon:4932 20050317 SGD
+SGD S000005004 ARP5 GO:0006623 SGD_REF:S000070264|PMID:12134085 IMP P actin related protein YNL059C gene taxon:4932 20021016 SGD
+SGD S000004075 ARP6 GO:0000812 SGD_REF:S000074662|PMID:14645854 IPI C YLR085C gene taxon:4932 20040412 SGD
+SGD S000004075 ARP6 GO:0000812 SGD_REF:S000075430|PMID:14690608 IPI C YLR085C gene taxon:4932 20040412 SGD
+SGD S000004075 ARP6 GO:0005737 SGD_REF:S000059257|PMID:11011149 IDA C YLR085C gene taxon:4932 20021127 SGD
+SGD S000004075 ARP6 GO:0005554 SGD_REF:S000069584 ND F YLR085C gene taxon:4932 20021016 SGD
+SGD S000004075 ARP6 GO:0006338 SGD_REF:S000074662|PMID:14645854 IDA P YLR085C gene taxon:4932 20040322 SGD
+SGD S000004075 ARP6 GO:0006338 SGD_REF:S000075430|PMID:14690608 IGI P YLR085C gene taxon:4932 20040323 SGD
+SGD S000004075 ARP6 GO:0006338 SGD_REF:S000075430|PMID:14690608 IPI P YLR085C gene taxon:4932 20040323 SGD
+SGD S000004075 ARP6 GO:0006623 SGD_REF:S000070264|PMID:12134085 IMP P YLR085C gene taxon:4932 20021016 SGD
+SGD S000006238 ARP7 GO:0005634 SGD_REF:S000059257|PMID:11011149 IDA C actin related protein, chromatin remodeling Snf/Swi complex subunit YPR034W|SWP61 gene taxon:4932 20021127 SGD
+SGD S000006238 ARP7 GO:0016514 SGD_REF:S000043500|PMID:9726966 IPI C actin related protein, chromatin remodeling Snf/Swi complex subunit YPR034W|SWP61 gene taxon:4932 20030513 SGD
+SGD S000006238 ARP7 GO:0016585 SGD_REF:S000058455|PMID:9048886 TAS C actin related protein, chromatin remodeling Snf/Swi complex subunit YPR034W|SWP61 gene taxon:4932 20010118 SGD
+SGD S000006238 ARP7 GO:0016251 SGD_REF:S000058455|PMID:9048886 TAS F actin related protein, chromatin remodeling Snf/Swi complex subunit YPR034W|SWP61 gene taxon:4932 20020528 SGD
+SGD S000006238 ARP7 GO:0006338 SGD_REF:S000058455|PMID:9048886 TAS P actin related protein, chromatin remodeling Snf/Swi complex subunit YPR034W|SWP61 gene taxon:4932 20010118 SGD
+SGD S000005667 ARP8 GO:0005634 SGD_REF:S000059257|PMID:11011149 IDA C YOR141C gene taxon:4932 20021127 SGD
+SGD S000005667 ARP8 GO:0031011 SGD_REF:S000040657|PMID:10952318 IPI SGD:S000003118 C YOR141C gene taxon:4932 20050411 SGD
+SGD S000005667 ARP8 GO:0005554 SGD_REF:S000069584 ND F YOR141C gene taxon:4932 20021127 SGD
+SGD S000005667 ARP8 contributes_to GO:0043141 SGD_REF:S000040657|PMID:10952318 IDA F YOR141C gene taxon:4932 20060320 SGD
+SGD S000005667 ARP8 GO:0000004 SGD_REF:S000069584 ND P YOR141C gene taxon:4932 20021127 SGD
+SGD S000004636 ARP9 GO:0005634 SGD_REF:S000059257|PMID:11011149 IDA C actin related protein, chromatin remodeling Snf/Swi complex subunit YMR033W|SWP59 gene taxon:4932 20021127 SGD
+SGD S000004636 ARP9 GO:0016514 SGD_REF:S000043500|PMID:9726966 IPI C actin related protein, chromatin remodeling Snf/Swi complex subunit YMR033W|SWP59 gene taxon:4932 20030513 SGD
+SGD S000004636 ARP9 GO:0016585 SGD_REF:S000058455|PMID:9048886 TAS C actin related protein, chromatin remodeling Snf/Swi complex subunit YMR033W|SWP59 gene taxon:4932 20010118 SGD
+SGD S000004636 ARP9 GO:0016251 SGD_REF:S000058455|PMID:9048886 TAS F actin related protein, chromatin remodeling Snf/Swi complex subunit YMR033W|SWP59 gene taxon:4932 20020528 SGD
+SGD S000004636 ARP9 GO:0006338 SGD_REF:S000058455|PMID:9048886 TAS P actin related protein, chromatin remodeling Snf/Swi complex subunit YMR033W|SWP59 gene taxon:4932 20010118 SGD
+SGD S000006403 ARR1 GO:0005634 SGD_REF:S000052767|PMID:1448073 IPI C YPR199C|ACR1|YAP8 gene taxon:4932 20021021 SGD
+SGD S000006403 ARR1 GO:0005634 SGD_REF:S000076257|PMID:15147884 IDA C YPR199C|ACR1|YAP8 gene taxon:4932 20051006 SGD
+SGD S000006403 ARR1 GO:0005737 SGD_REF:S000076257|PMID:15147884 IDA C YPR199C|ACR1|YAP8 gene taxon:4932 20051006 SGD
+SGD S000006403 ARR1 GO:0003702 SGD_REF:S000052767|PMID:1448073 IDA F YPR199C|ACR1|YAP8 gene taxon:4932 20021021 SGD
+SGD S000006403 ARR1 GO:0045944 SGD_REF:S000052767|PMID:1448073 IDA P YPR199C|ACR1|YAP8 gene taxon:4932 20021021 SGD
+SGD S000006403 ARR1 GO:0046685 SGD_REF:S000048851|PMID:9234670 IMP P YPR199C|ACR1|YAP8 gene taxon:4932 20041228 SGD
+SGD S000006403 ARR1 GO:0046685 SGD_REF:S000080191|PMID:15575969 IMP P YPR199C|ACR1|YAP8 gene taxon:4932 20050331 SGD
+SGD S000006403 ARR1 GO:0046685 SGD_REF:S000080191|PMID:15575969 IEP P YPR199C|ACR1|YAP8 gene taxon:4932 20050331 SGD
+SGD S000006403 ARR1 GO:0046685 SGD_REF:S000076257|PMID:15147884 IMP P YPR199C|ACR1|YAP8 gene taxon:4932 20051006 SGD
+SGD S000006404 ARR2 GO:0008372 SGD_REF:S000069584 ND C YPR200C|ACR2 gene taxon:4932 20020927 SGD
+SGD S000006404 ARR2 GO:0030611 SGD_REF:S000054698|PMID:10801893 IDA F YPR200C|ACR2 gene taxon:4932 20020927 SGD
+SGD S000006404 ARR2 GO:0030611 SGD_REF:S000054698|PMID:10801893 IMP F YPR200C|ACR2 gene taxon:4932 20020927 SGD
+SGD S000006404 ARR2 GO:0046685 SGD_REF:S000054698|PMID:10801893 TAS P YPR200C|ACR2 gene taxon:4932 20021106 SGD
+SGD S000006405 ARR3 GO:0005887 SGD_REF:S000058238|PMID:9374482 ISS C YPR201W|ACR3 gene taxon:4932 20020906 SGD
+SGD S000006405 ARR3 GO:0015105 SGD_REF:S000058238|PMID:9374482 IGI F YPR201W|ACR3 gene taxon:4932 20020906 SGD
+SGD S000006405 ARR3 GO:0015105 SGD_REF:S000058238|PMID:9374482 ISS F YPR201W|ACR3 gene taxon:4932 20020906 SGD
+SGD S000006405 ARR3 GO:0015700 SGD_REF:S000058238|PMID:9374482 IGI P YPR201W|ACR3 gene taxon:4932 20020906 SGD
+SGD S000004232 ARV1 GO:0005783 SGD_REF:S000071418|PMID:12145310 IDA C Protein involved in sterol distribution YLR242C gene taxon:4932 20030123 SGD
+SGD S000004232 ARV1 GO:0005794 SGD_REF:S000071418|PMID:12145310 IDA C Protein involved in sterol distribution YLR242C gene taxon:4932 20030123 SGD
+SGD S000004232 ARV1 GO:0016021 SGD_REF:S000059466|PMID:11063737 ISS C Protein involved in sterol distribution YLR242C gene taxon:4932 20020905 SGD
+SGD S000004232 ARV1 GO:0005554 SGD_REF:S000069584 ND F Protein involved in sterol distribution YLR242C gene taxon:4932 20020905 SGD
+SGD S000004232 ARV1 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P Protein involved in sterol distribution YLR242C gene taxon:4932 20060210 SGD
+SGD S000004232 ARV1 GO:0006665 SGD_REF:S000071418|PMID:12145310 IMP P Protein involved in sterol distribution YLR242C gene taxon:4932 20050309 SGD
+SGD S000004232 ARV1 GO:0015918 SGD_REF:S000059466|PMID:11063737 IMP P Protein involved in sterol distribution YLR242C gene taxon:4932 20020905 SGD
+SGD S000004232 ARV1 GO:0016125 SGD_REF:S000061664|PMID:11111085 ISS P Protein involved in sterol distribution YLR242C gene taxon:4932 20030123 SGD
+SGD S000002508 ARX1 GO:0005654 SGD_REF:S000071707|PMID:12374754 IDA C YDR101C gene taxon:4932 20030508 SGD
+SGD S000002508 ARX1 GO:0005737 SGD_REF:S000071707|PMID:12374754 IDA C YDR101C gene taxon:4932 20030508 SGD
+SGD S000002508 ARX1 GO:0005554 SGD_REF:S000069584 ND F YDR101C gene taxon:4932 20030514 SGD
+SGD S000002508 ARX1 GO:0042273 SGD_REF:S000071707|PMID:12374754 IDA P YDR101C gene taxon:4932 20030508 SGD
+SGD S000004722 ASC1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C G-beta like protein YMR116C|CPC2 gene taxon:4932 20020507 SGD
+SGD S000004722 ASC1 GO:0005843 SGD_REF:S000077324|PMID:15340087 IDA C G-beta like protein YMR116C|CPC2 gene taxon:4932 20051108 SGD
+SGD S000004722 ASC1 GO:0005554 SGD_REF:S000069584 ND F G-beta like protein YMR116C|CPC2 gene taxon:4932 20021001 SGD
+SGD S000004722 ASC1 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P G-beta like protein YMR116C|CPC2 gene taxon:4932 20060227 SGD
+SGD S000004722 ASC1 GO:0016478 SGD_REF:S000077324|PMID:15340087 IMP P G-beta like protein YMR116C|CPC2 gene taxon:4932 20051108 SGD
+SGD S000005584 ASE1 GO:0005876 SGD_REF:S000058447|PMID:9153752 TAS C spindle midzone component YOR058C|YOR29-09 gene taxon:4932 20010118 SGD
+SGD S000005584 ASE1 GO:0005880 SGD_REF:S000058447|PMID:9153752 TAS C spindle midzone component YOR058C|YOR29-09 gene taxon:4932 20010118 SGD
+SGD S000005584 ASE1 GO:0008017 SGD_REF:S000042364|PMID:9036857 TAS F spindle midzone component YOR058C|YOR29-09 gene taxon:4932 20010118 SGD
+SGD S000005584 ASE1 GO:0008017 SGD_REF:S000072934|PMID:12591913 IDA F spindle midzone component YOR058C|YOR29-09 gene taxon:4932 20040128 SGD
+SGD S000005584 ASE1 GO:0000092 SGD_REF:S000058447|PMID:9153752 TAS P spindle midzone component YOR058C|YOR29-09 gene taxon:4932 20010118 SGD
+SGD S000005584 ASE1 GO:0030472 SGD_REF:S000058447|PMID:9153752 TAS P spindle midzone component YOR058C|YOR29-09 gene taxon:4932 20040128 SGD
+SGD S000003651 ASF1 GO:0005678 SGD_REF:S000066269|PMID:11731479 IDA C YJL115W|CIA1 gene taxon:4932 20020601 SGD
+SGD S000003651 ASF1 GO:0030528 SGD_REF:S000080322|PMID:15632066 IMP F YJL115W|CIA1 gene taxon:4932 20050216 SGD
+SGD S000003651 ASF1 GO:0042393 SGD_REF:S000069174|PMID:11856374 TAS F YJL115W|CIA1 gene taxon:4932 20021113 SGD
+SGD S000003651 ASF1 GO:0008630 SGD_REF:S000068780|PMID:11737265 IMP P YJL115W|CIA1 gene taxon:4932 20020916 SGD
+SGD S000002356 ASF2 GO:0000784 SGD_REF:S000077144|PMID:15282802 IDA C YDL197C gene taxon:4932 20041008 SGD
+SGD S000002356 ASF2 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YDL197C gene taxon:4932 20031028 SGD
+SGD S000002356 ASF2 GO:0005634 SGD_REF:S000077144|PMID:15282802 IDA C YDL197C gene taxon:4932 20041008 SGD
+SGD S000002356 ASF2 GO:0005554 SGD_REF:S000069584 ND F YDL197C gene taxon:4932 20021104 SGD
+SGD S000002356 ASF2 GO:0030466 SGD_REF:S000042342|PMID:9290207 IGI P YDL197C gene taxon:4932 20021104 SGD
+SGD S000001392 ASG1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C transcriptional activator YIL130W gene taxon:4932 20031028 SGD
+SGD S000001392 ASG1 GO:0005554 SGD_REF:S000069584 ND F transcriptional activator YIL130W gene taxon:4932 20021122 SGD
+SGD S000001392 ASG1 GO:0000004 SGD_REF:S000069584 ND P transcriptional activator YIL130W gene taxon:4932 20021122 SGD
+SGD S000003706 ASG7 GO:0005886 SGD_REF:S000059571|PMID:11073983 IDA C YJL170C gene taxon:4932 20020916 SGD
+SGD S000003706 ASG7 GO:0005554 SGD_REF:S000069584 ND F YJL170C gene taxon:4932 20010119 SGD
+SGD S000003706 ASG7 GO:0000747 SGD_REF:S000051804|PMID:10568744 IEP P YJL170C gene taxon:4932 20010118 SGD
+SGD S000001668 ASH1 GO:0000118 SGD_REF:S000113697|PMID:16314178 IPI C zinc finger transcription factor YKL185W gene taxon:4932 20060428 SGD
+SGD S000001668 ASH1 GO:0005634 SGD_REF:S000042424|PMID:8625408 IDA C zinc finger transcription factor YKL185W gene taxon:4932 20010626 SGD
+SGD S000001668 ASH1 GO:0005634 SGD_REF:S000042425|PMID:8625409 IDA C zinc finger transcription factor YKL185W gene taxon:4932 20010626 SGD
+SGD S000001668 ASH1 GO:0005634 SGD_REF:S000045535|PMID:9566907 IDA C zinc finger transcription factor YKL185W gene taxon:4932 20010626 SGD
+SGD S000001668 ASH1 GO:0016566 SGD_REF:S000042424|PMID:8625408 IMP F zinc finger transcription factor YKL185W gene taxon:4932 20010626 SGD
+SGD S000001668 ASH1 GO:0016566 SGD_REF:S000042425|PMID:8625409 ISS F zinc finger transcription factor YKL185W gene taxon:4932 20010626 SGD
+SGD S000001668 ASH1 GO:0016566 SGD_REF:S000042424|PMID:8625408 ISS F zinc finger transcription factor YKL185W gene taxon:4932 20010626 SGD
+SGD S000001668 ASH1 GO:0016566 SGD_REF:S000079870|PMID:11171979 IDA F zinc finger transcription factor YKL185W gene taxon:4932 20050117 SGD
+SGD S000001668 ASH1 GO:0016566 SGD_REF:S000042425|PMID:8625409 IMP F zinc finger transcription factor YKL185W gene taxon:4932 20010626 SGD
+SGD S000001668 ASH1 GO:0007124 SGD_REF:S000045535|PMID:9566907 IMP P zinc finger transcription factor YKL185W gene taxon:4932 20010626 SGD
+SGD S000001668 ASH1 GO:0007124 SGD_REF:S000059111|PMID:11046133 IGI P zinc finger transcription factor YKL185W gene taxon:4932 20060428 SGD
+SGD S000001668 ASH1 GO:0007124 SGD_REF:S000059111|PMID:11046133 IMP P zinc finger transcription factor YKL185W gene taxon:4932 20060428 SGD
+SGD S000001668 ASH1 GO:0007532 SGD_REF:S000042424|PMID:8625408 IMP P zinc finger transcription factor YKL185W gene taxon:4932 20010626 SGD
+SGD S000001668 ASH1 GO:0007532 SGD_REF:S000042425|PMID:8625409 IMP P zinc finger transcription factor YKL185W gene taxon:4932 20010626 SGD
+SGD S000001668 ASH1 GO:0045892 SGD_REF:S000079870|PMID:11171979 IDA P zinc finger transcription factor YKL185W gene taxon:4932 20050117 SGD
+SGD S000004725 ASI1 GO:0005789 SGD_REF:S000061385|PMID:11454748 IGI C YMR119W gene taxon:4932 20010824 SGD
+SGD S000004725 ASI1 GO:0005789 SGD_REF:S000061385|PMID:11454748 ISS C YMR119W gene taxon:4932 20010824 SGD
+SGD S000004725 ASI1 GO:0004842 SGD_REF:S000061385|PMID:11454748 IGI F YMR119W gene taxon:4932 20010824 SGD
+SGD S000004725 ASI1 GO:0004842 SGD_REF:S000061385|PMID:11454748 ISS F YMR119W gene taxon:4932 20010824 SGD
+SGD S000004725 ASI1 GO:0006511 SGD_REF:S000061385|PMID:11454748 IGI P YMR119W gene taxon:4932 20010824 SGD
+SGD S000005103 ASI2 GO:0016021 SGD_REF:S000061385|PMID:11454748 ISS C YNL159C gene taxon:4932 20010824 SGD
+SGD S000005103 ASI2 GO:0005554 SGD_REF:S000069584 ND F YNL159C gene taxon:4932 20010824 SGD
+SGD S000005103 ASI2 GO:0006511 SGD_REF:S000061385|PMID:11454748 IGI P YNL159C gene taxon:4932 20010824 SGD
+SGD S000004953 ASI3 GO:0005789 SGD_REF:S000061385|PMID:11454748 IGI C YNL008C gene taxon:4932 20010824 SGD
+SGD S000004953 ASI3 GO:0005789 SGD_REF:S000061385|PMID:11454748 ISS C YNL008C gene taxon:4932 20010824 SGD
+SGD S000004953 ASI3 GO:0004842 SGD_REF:S000061385|PMID:11454748 IGI F YNL008C gene taxon:4932 20010824 SGD
+SGD S000004953 ASI3 GO:0004842 SGD_REF:S000061385|PMID:11454748 ISS F YNL008C gene taxon:4932 20010824 SGD
+SGD S000004953 ASI3 GO:0006511 SGD_REF:S000061385|PMID:11454748 IGI P YNL008C gene taxon:4932 20010824 SGD
+SGD S000001535 ASK1 GO:0000778 SGD_REF:S000069091|PMID:11756468 IDA C YKL052C gene taxon:4932 20021008 SGD
+SGD S000001535 ASK1 GO:0000780 SGD_REF:S000069220|PMID:11782438 IDA C YKL052C gene taxon:4932 20030404 SGD
+SGD S000001535 ASK1 GO:0005819 SGD_REF:S000069091|PMID:11756468 IDA C YKL052C gene taxon:4932 20021008 SGD
+SGD S000001535 ASK1 GO:0042729 SGD_REF:S000069052|PMID:11799062 IDA C YKL052C gene taxon:4932 20040122 SGD
+SGD S000001535 ASK1 GO:0042729 SGD_REF:S000080444|PMID:15640796 IDA C YKL052C gene taxon:4932 20050328 SGD
+SGD S000001535 ASK1 GO:0042729 SGD_REF:S000069052|PMID:11799062 IPI C YKL052C gene taxon:4932 20040122 SGD
+SGD S000001535 ASK1 GO:0042729 SGD_REF:S000080444|PMID:15640796 IPI C YKL052C gene taxon:4932 20050328 SGD
+SGD S000001535 ASK1 GO:0042729 SGD_REF:S000080667|PMID:15664196 IPI C YKL052C gene taxon:4932 20050328 SGD
+SGD S000001535 ASK1 GO:0042729 SGD_REF:S000080667|PMID:15664196 IDA C YKL052C gene taxon:4932 20050328 SGD
+SGD S000001535 ASK1 GO:0005200 SGD_REF:S000069091|PMID:11756468 IDA F YKL052C gene taxon:4932 20021008 SGD
+SGD S000001535 ASK1 GO:0030472 SGD_REF:S000069091|PMID:11756468 IMP P YKL052C gene taxon:4932 20021008 SGD
+SGD S000001535 ASK1 GO:0031110 SGD_REF:S000080667|PMID:15664196 IPI P YKL052C gene taxon:4932 20050328 SGD
+SGD S000001535 ASK1 GO:0031110 SGD_REF:S000080667|PMID:15664196 IDA P YKL052C gene taxon:4932 20050328 SGD
+SGD S000003329 ASK10 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C transcriptional activator of the SKN7 mediated 'two-component' regulatory system YGR097W gene taxon:4932 20031028 SGD
+SGD S000003329 ASK10 GO:0016591 SGD_REF:S000074242|PMID:14555478 IDA C transcriptional activator of the SKN7 mediated 'two-component' regulatory system YGR097W gene taxon:4932 20040120 SGD
+SGD S000003329 ASK10 GO:0030528 SGD_REF:S000050127|PMID:8904339 TAS F transcriptional activator of the SKN7 mediated 'two-component' regulatory system YGR097W gene taxon:4932 20030311 SGD
+SGD S000003329 ASK10 GO:0006350 SGD_REF:S000050127|PMID:8904339 IGI P transcriptional activator of the SKN7 mediated 'two-component' regulatory system YGR097W gene taxon:4932 20020925 SGD
+SGD S000003329 ASK10 GO:0006350 SGD_REF:S000074242|PMID:14555478 IPI P transcriptional activator of the SKN7 mediated 'two-component' regulatory system YGR097W gene taxon:4932 20040120 SGD
+SGD S000003329 ASK10 GO:0006979 SGD_REF:S000074242|PMID:14555478 IGI P transcriptional activator of the SKN7 mediated 'two-component' regulatory system YGR097W gene taxon:4932 20040120 SGD
+SGD S000003329 ASK10 GO:0006979 SGD_REF:S000074242|PMID:14555478 IMP P transcriptional activator of the SKN7 mediated 'two-component' regulatory system YGR097W gene taxon:4932 20040120 SGD
+SGD S000002246 ASM4 GO:0005643 SGD_REF:S000058277|PMID:9442897 IDA C nuclear pore complex subunit YDL088C|NUP59 gene taxon:4932 20010118 SGD
+SGD S000002246 ASM4 GO:0005198 SGD_REF:S000058277|PMID:9442897 TAS F nuclear pore complex subunit YDL088C|NUP59 gene taxon:4932 20010118 SGD
+SGD S000002246 ASM4 GO:0000059 SGD_REF:S000055428|PMID:9864357 IPI P nuclear pore complex subunit YDL088C|NUP59 gene taxon:4932 20010118 SGD
+SGD S000002246 ASM4 GO:0006406 SGD_REF:S000058277|PMID:9442897 IMP P nuclear pore complex subunit YDL088C|NUP59 gene taxon:4932 20010118 SGD
+SGD S000002246 ASM4 GO:0006407 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YDL088C|NUP59 gene taxon:4932 20010118 SGD
+SGD S000002246 ASM4 GO:0006408 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YDL088C|NUP59 gene taxon:4932 20010118 SGD
+SGD S000002246 ASM4 GO:0006607 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YDL088C|NUP59 gene taxon:4932 20010118 SGD
+SGD S000002246 ASM4 GO:0006608 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YDL088C|NUP59 gene taxon:4932 20010118 SGD
+SGD S000002246 ASM4 GO:0006609 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YDL088C|NUP59 gene taxon:4932 20010118 SGD
+SGD S000002246 ASM4 GO:0006610 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YDL088C|NUP59 gene taxon:4932 20010118 SGD
+SGD S000002246 ASM4 GO:0006611 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YDL088C|NUP59 gene taxon:4932 20010118 SGD
+SGD S000002246 ASM4 GO:0006999 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YDL088C|NUP59 gene taxon:4932 20010118 SGD
+SGD S000006349 ASN1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C asparagine synthetase YPR145W gene taxon:4932 20031028 SGD
+SGD S000006349 ASN1 GO:0004066 SGD_REF:S000047179|PMID:8951815 IMP F asparagine synthetase YPR145W gene taxon:4932 20021218 SGD
+SGD S000006349 ASN1 GO:0004066 SGD_REF:S000047179|PMID:8951815 ISS F asparagine synthetase YPR145W gene taxon:4932 20021218 SGD
+SGD S000006349 ASN1 GO:0006529 SGD_REF:S000047179|PMID:8951815 TAS P asparagine synthetase YPR145W gene taxon:4932 20020927 SGD
+SGD S000003356 ASN2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C asparagine synthetase YGR124W gene taxon:4932 20031028 SGD
+SGD S000003356 ASN2 GO:0004066 SGD_REF:S000047179|PMID:8951815 IMP F asparagine synthetase YGR124W gene taxon:4932 20021218 SGD
+SGD S000003356 ASN2 GO:0004066 SGD_REF:S000047179|PMID:8951815 ISS F asparagine synthetase YGR124W gene taxon:4932 20021218 SGD
+SGD S000003356 ASN2 GO:0006529 SGD_REF:S000047179|PMID:8951815 TAS P asparagine synthetase YGR124W gene taxon:4932 20020927 SGD
+SGD S000002729 ASP1 GO:0005622 SGD_REF:S000047596|PMID:8026756 IDA C asparaginase I YDR321W gene taxon:4932 20030625 SGD
+SGD S000002729 ASP1 GO:0005829 SGD_REF:S000073352 TAS C asparaginase I YDR321W gene taxon:4932 20040120 SGD
+SGD S000002729 ASP1 GO:0004067 SGD_REF:S000047596|PMID:8026756 ISS F asparaginase I YDR321W gene taxon:4932 20010703 SGD
+SGD S000002729 ASP1 GO:0006530 SGD_REF:S000045976|PMID:323221 IGI P asparaginase I YDR321W gene taxon:4932 20030625 SGD
+SGD S000002729 ASP1 GO:0006530 SGD_REF:S000045976|PMID:323221 IMP P asparaginase I YDR321W gene taxon:4932 20030625 SGD
+SGD S000004145 ASP3-1 GO:0005635 SGD_REF:S000069459|PMID:11914276 IDA C nitrogen catabolite-regulated cell-wall L-asparaginase II YLR155C|ASP3 gene taxon:4932 20020507 SGD
+SGD S000004145 ASP3-1 GO:0005783 SGD_REF:S000069459|PMID:11914276 IDA C nitrogen catabolite-regulated cell-wall L-asparaginase II YLR155C|ASP3 gene taxon:4932 20020507 SGD
+SGD S000004145 ASP3-1 GO:0030287 SGD_REF:S000047638|PMID:9170245 TAS C nitrogen catabolite-regulated cell-wall L-asparaginase II YLR155C|ASP3 gene taxon:4932 20010924 SGD
+SGD S000004145 ASP3-1 GO:0004067 SGD_REF:S000041101|PMID:3042786 TAS F nitrogen catabolite-regulated cell-wall L-asparaginase II YLR155C|ASP3 gene taxon:4932 20010118 SGD
+SGD S000004145 ASP3-1 GO:0006530 SGD_REF:S000073352 TAS P nitrogen catabolite-regulated cell-wall L-asparaginase II YLR155C|ASP3 gene taxon:4932 20030625 SGD
+SGD S000004145 ASP3-1 GO:0006995 SGD_REF:S000047638|PMID:9170245 TAS P nitrogen catabolite-regulated cell-wall L-asparaginase II YLR155C|ASP3 gene taxon:4932 20010118 SGD
+SGD S000004147 ASP3-2 GO:0030287 SGD_REF:S000047638|PMID:9170245 TAS C nitrogen catabolite-regulated cell-wall L-asparaginase II YLR157C|ASP3 gene taxon:4932 20010924 SGD
+SGD S000004147 ASP3-2 GO:0004067 SGD_REF:S000041101|PMID:3042786 TAS F nitrogen catabolite-regulated cell-wall L-asparaginase II YLR157C|ASP3 gene taxon:4932 20010118 SGD
+SGD S000004147 ASP3-2 GO:0006530 SGD_REF:S000073352 TAS P nitrogen catabolite-regulated cell-wall L-asparaginase II YLR157C|ASP3 gene taxon:4932 20030625 SGD
+SGD S000004147 ASP3-2 GO:0006995 SGD_REF:S000047638|PMID:9170245 TAS P nitrogen catabolite-regulated cell-wall L-asparaginase II YLR157C|ASP3 gene taxon:4932 20010118 SGD
+SGD S000004148 ASP3-3 GO:0030287 SGD_REF:S000047638|PMID:9170245 TAS C nitrogen catabolite-regulated cell-wall L-asparaginase II YLR158C|ASP3 gene taxon:4932 20010924 SGD
+SGD S000004148 ASP3-3 GO:0004067 SGD_REF:S000041101|PMID:3042786 TAS F nitrogen catabolite-regulated cell-wall L-asparaginase II YLR158C|ASP3 gene taxon:4932 20010118 SGD
+SGD S000004148 ASP3-3 GO:0006530 SGD_REF:S000073352 TAS P nitrogen catabolite-regulated cell-wall L-asparaginase II YLR158C|ASP3 gene taxon:4932 20030625 SGD
+SGD S000004148 ASP3-3 GO:0006995 SGD_REF:S000047638|PMID:9170245 TAS P nitrogen catabolite-regulated cell-wall L-asparaginase II YLR158C|ASP3 gene taxon:4932 20010118 SGD
+SGD S000004150 ASP3-4 GO:0030287 SGD_REF:S000047638|PMID:9170245 TAS C nitrogen catabolite-regulated cell-wall L-asparaginase II YLR160C|ASP3 gene taxon:4932 20010924 SGD
+SGD S000004150 ASP3-4 GO:0004067 SGD_REF:S000041101|PMID:3042786 TAS F nitrogen catabolite-regulated cell-wall L-asparaginase II YLR160C|ASP3 gene taxon:4932 20010118 SGD
+SGD S000004150 ASP3-4 GO:0006530 SGD_REF:S000073352 TAS P nitrogen catabolite-regulated cell-wall L-asparaginase II YLR160C|ASP3 gene taxon:4932 20030625 SGD
+SGD S000004150 ASP3-4 GO:0006995 SGD_REF:S000047638|PMID:9170245 TAS P nitrogen catabolite-regulated cell-wall L-asparaginase II YLR160C|ASP3 gene taxon:4932 20010118 SGD
+SGD S000006297 ASR1 GO:0005634 SGD_REF:S000076825|PMID:15117954 IDA C YPR093C gene taxon:4932 20041018 SGD
+SGD S000006297 ASR1 GO:0005737 SGD_REF:S000076825|PMID:15117954 IDA C YPR093C gene taxon:4932 20041018 SGD
+SGD S000006297 ASR1 GO:0005554 SGD_REF:S000069584 ND F YPR093C gene taxon:4932 20041018 SGD
+SGD S000006297 ASR1 GO:0045471 SGD_REF:S000076825|PMID:15117954 IMP P YPR093C gene taxon:4932 20041018 SGD
+SGD S000000165 AST1 GO:0019898 SGD_REF:S000069871|PMID:11739806 TAS C YBL069W gene taxon:4932 20020602 SGD
+SGD S000000165 AST1 GO:0005554 SGD_REF:S000069584 ND F YBL069W gene taxon:4932 20040116 SGD
+SGD S000000165 AST1 GO:0006612 SGD_REF:S000040210|PMID:7822420 IGI P YBL069W gene taxon:4932 20040116 SGD
+SGD S000000165 AST1 GO:0006612 SGD_REF:S000040210|PMID:7822420 IMP P YBL069W gene taxon:4932 20040116 SGD
+SGD S000000903 AST2 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YER101C gene taxon:4932 20020507 SGD
+SGD S000000903 AST2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YER101C gene taxon:4932 20031028 SGD
+SGD S000000903 AST2 GO:0005554 SGD_REF:S000069584 ND F YER101C gene taxon:4932 20021001 SGD
+SGD S000000903 AST2 GO:0000004 SGD_REF:S000069584 ND P YER101C gene taxon:4932 20021001 SGD
+SGD S000002592 ATC1 GO:0005634 SGD_REF:S000049546|PMID:10102375 IDA C YDR184C|LIC4 gene taxon:4932 20030415 SGD
+SGD S000002592 ATC1 GO:0005554 SGD_REF:S000069584 ND F YDR184C|LIC4 gene taxon:4932 20020807 SGD
+SGD S000002592 ATC1 GO:0006950 SGD_REF:S000049546|PMID:10102375 IGI P YDR184C|LIC4 gene taxon:4932 20030415 SGD
+SGD S000002592 ATC1 GO:0007121 SGD_REF:S000059390|PMID:11065362 IGI P YDR184C|LIC4 gene taxon:4932 20030415 SGD
+SGD S000002985 ATE1 GO:0005737 SGD_REF:S000053800|PMID:2185248 TAS C arginyl-tRNA-protein transferase YGL017W gene taxon:4932 20010118 SGD
+SGD S000002985 ATE1 GO:0004057 SGD_REF:S000053800|PMID:2185248 TAS F arginyl-tRNA-protein transferase YGL017W gene taxon:4932 20010118 SGD
+SGD S000002985 ATE1 GO:0006464 SGD_REF:S000042625|PMID:9858543 TAS P arginyl-tRNA-protein transferase YGL017W gene taxon:4932 20010118 SGD
+SGD S000002985 ATE1 GO:0016598 SGD_REF:S000053800|PMID:2185248 IDA P arginyl-tRNA-protein transferase YGL017W gene taxon:4932 20050404 SGD
+SGD S000005904 ATF1 GO:0005811 SGD_REF:S000075754|PMID:15042596 IDA C alcohol acetyltransferase YOR377W gene taxon:4932 20040403 SGD
+SGD S000005904 ATF1 GO:0012505 SGD_REF:S000061763|PMID:11015726 TAS C alcohol acetyltransferase YOR377W gene taxon:4932 20040120 SGD
+SGD S000005904 ATF1 GO:0004026 SGD_REF:S000048977|PMID:8085822 IDA F alcohol acetyltransferase YOR377W gene taxon:4932 20030110 SGD
+SGD S000005904 ATF1 GO:0006113 SGD_REF:S000045450|PMID:10653746 TAS P alcohol acetyltransferase YOR377W gene taxon:4932 20021001 SGD
+SGD S000005904 ATF1 GO:0006631 SGD_REF:S000061763|PMID:11015726 TAS P alcohol acetyltransferase YOR377W gene taxon:4932 20040120 SGD
+SGD S000005904 ATF1 GO:0030636 SGD_REF:S000075754|PMID:15042596 TAS P alcohol acetyltransferase YOR377W gene taxon:4932 20040403 SGD
+SGD S000003409 ATF2 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C alcohol acetyltransferase YGR177C gene taxon:4932 20020507 SGD
+SGD S000003409 ATF2 GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C alcohol acetyltransferase YGR177C gene taxon:4932 20031028 SGD
+SGD S000003409 ATF2 GO:0004026 SGD_REF:S000049334|PMID:9836419 IDA F alcohol acetyltransferase YGR177C gene taxon:4932 20030110 SGD
+SGD S000003409 ATF2 GO:0008202 SGD_REF:S000049485|PMID:10103065 IMP P alcohol acetyltransferase YGR177C gene taxon:4932 20020927 SGD
+SGD S000003148 ATG1 GO:0005829 SGD_REF:S000040285|PMID:9190802 IDA C protein kinase YGL180W|APG1|AUT3|CVT10 gene taxon:4932 20010118 SGD
+SGD S000003148 ATG1 GO:0004674 SGD_REF:S000040285|PMID:9190802 ISS F protein kinase YGL180W|APG1|AUT3|CVT10 gene taxon:4932 20010118 SGD
+SGD S000003148 ATG1 GO:0004674 SGD_REF:S000046735|PMID:9224897 IDA F protein kinase YGL180W|APG1|AUT3|CVT10 gene taxon:4932 20010118 SGD
+SGD S000003148 ATG1 GO:0006914 SGD_REF:S000051835|PMID:8224160 IMP P protein kinase YGL180W|APG1|AUT3|CVT10 gene taxon:4932 20010118 SGD
+SGD S000003148 ATG1 GO:0016050 SGD_REF:S000086066|PMID:16079147 IMP P protein kinase YGL180W|APG1|AUT3|CVT10 gene taxon:4932 20051018 SGD
+SGD S000003965 ATG10 GO:0005737 SGD_REF:S000045627|PMID:10508157 TAS C protein-conjugating enzyme YLL042C|APG10 gene taxon:4932 20021203 SGD
+SGD S000003965 ATG10 GO:0019777 SGD_REF:S000045627|PMID:10508157 IMP F protein-conjugating enzyme YLL042C|APG10 gene taxon:4932 20051017 SGD
+SGD S000003965 ATG10 GO:0019777 SGD_REF:S000045627|PMID:10508157 IPI SGD:S000000421|SGD:S000001214 F protein-conjugating enzyme YLL042C|APG10 gene taxon:4932 20051017 SGD
+SGD S000003965 ATG10 GO:0006464 SGD_REF:S000039962|PMID:9759731 IMP P protein-conjugating enzyme YLL042C|APG10 gene taxon:4932 20051017 SGD
+SGD S000003965 ATG10 GO:0006464 SGD_REF:S000045627|PMID:10508157 IMP P protein-conjugating enzyme YLL042C|APG10 gene taxon:4932 20051017 SGD
+SGD S000003965 ATG10 GO:0006464 SGD_REF:S000045627|PMID:10508157 IPI SGD:S000000421|SGD:S000001214 P protein-conjugating enzyme YLL042C|APG10 gene taxon:4932 20051017 SGD
+SGD S000003965 ATG10 GO:0006623 SGD_REF:S000045627|PMID:10508157 IMP P protein-conjugating enzyme YLL042C|APG10 gene taxon:4932 20010118 SGD
+SGD S000003965 ATG10 GO:0006914 SGD_REF:S000051835|PMID:8224160 IMP P protein-conjugating enzyme YLL042C|APG10 gene taxon:4932 20010118 SGD
+SGD S000003965 ATG10 GO:0006914 SGD_REF:S000045627|PMID:10508157 IMP P protein-conjugating enzyme YLL042C|APG10 gene taxon:4932 20051017 SGD
+SGD S000006253 ATG11 GO:0019898 SGD_REF:S000060133|PMID:11309418 IDA C Oligomeric, coiled-coil, peripheral membrane protein required for stable binding of precursor API to its target membrane. YPR049C|CVT9 gene taxon:4932 20020916 SGD
+SGD S000006253 ATG11 GO:0005554 SGD_REF:S000069584 ND F Oligomeric, coiled-coil, peripheral membrane protein required for stable binding of precursor API to its target membrane. YPR049C|CVT9 gene taxon:4932 20020916 SGD
+SGD S000006253 ATG11 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P Oligomeric, coiled-coil, peripheral membrane protein required for stable binding of precursor API to its target membrane. YPR049C|CVT9 gene taxon:4932 20060210 SGD
+SGD S000006253 ATG11 GO:0006623 SGD_REF:S000060133|PMID:11309418 IMP P Oligomeric, coiled-coil, peripheral membrane protein required for stable binding of precursor API to its target membrane. YPR049C|CVT9 gene taxon:4932 20020916 SGD
+SGD S000006253 ATG11 GO:0030242 SGD_REF:S000060133|PMID:11309418 IMP P Oligomeric, coiled-coil, peripheral membrane protein required for stable binding of precursor API to its target membrane. YPR049C|CVT9 gene taxon:4932 20020916 SGD
+SGD S000000421 ATG12 GO:0005624 SGD_REF:S000048111|PMID:10233148 IDA C YBR217W|APG12 gene taxon:4932 20010118 SGD
+SGD S000000421 ATG12 GO:0031386 SGD_REF:S000039962|PMID:9759731 IPI SGD:S000006070 F YBR217W|APG12 gene taxon:4932 20051017 SGD
+SGD S000000421 ATG12 GO:0031386 SGD_REF:S000048125|PMID:10233150 IPI SGD:S000001214 F YBR217W|APG12 gene taxon:4932 20051017 SGD
+SGD S000000421 ATG12 GO:0031386 SGD_REF:S000045627|PMID:10508157 IPI SGD:S000003965 F YBR217W|APG12 gene taxon:4932 20051017 SGD
+SGD S000000421 ATG12 GO:0006623 SGD_REF:S000039962|PMID:9759731 IMP P YBR217W|APG12 gene taxon:4932 20010118 SGD
+SGD S000000421 ATG12 GO:0006914 SGD_REF:S000039962|PMID:9759731 IMP P YBR217W|APG12 gene taxon:4932 20010118 SGD
+SGD S000006389 ATG13 GO:0019898 SGD_REF:S000054987|PMID:10837477 IDA C YPR185W|APG13 gene taxon:4932 20030204 SGD
+SGD S000006389 ATG13 GO:0005515 SGD_REF:S000039257|PMID:10888680 IPI F YPR185W|APG13 gene taxon:4932 20020927 SGD
+SGD S000006389 ATG13 GO:0006623 SGD_REF:S000057871|PMID:8663607 IMP P YPR185W|APG13 gene taxon:4932 20010118 SGD
+SGD S000006389 ATG13 GO:0006914 SGD_REF:S000046726|PMID:9224892 IMP P YPR185W|APG13 gene taxon:4932 20010118 SGD
+SGD S000000332 ATG14 GO:0005624 SGD_REF:S000050199|PMID:9712845 IDA C YBR128C|APG14|CVT12 gene taxon:4932 20010118 SGD
+SGD S000000332 ATG14 GO:0005554 SGD_REF:S000069584 ND F YBR128C|APG14|CVT12 gene taxon:4932 20010119 SGD
+SGD S000000332 ATG14 GO:0006914 SGD_REF:S000050199|PMID:9712845 IMP P YBR128C|APG14|CVT12 gene taxon:4932 20010118 SGD
+SGD S000000332 ATG14 GO:0006914 SGD_REF:S000051835|PMID:8224160 IMP P YBR128C|APG14|CVT12 gene taxon:4932 20010118 SGD
+SGD S000000664 ATG15 GO:0005775 SGD_REF:S000066067|PMID:11566994 IDA C YCR068W|AUT5|CVT17 gene taxon:4932 20011023 SGD
+SGD S000000664 ATG15 GO:0016021 SGD_REF:S000060121|PMID:11085977 IPI C YCR068W|AUT5|CVT17 gene taxon:4932 20011023 SGD
+SGD S000000664 ATG15 GO:0016021 SGD_REF:S000060121|PMID:11085977 ISS C YCR068W|AUT5|CVT17 gene taxon:4932 20011023 SGD
+SGD S000000664 ATG15 GO:0016298 SGD_REF:S000060121|PMID:11085977 IMP F YCR068W|AUT5|CVT17 gene taxon:4932 20011023 SGD
+SGD S000000664 ATG15 GO:0016298 SGD_REF:S000060121|PMID:11085977 ISS F YCR068W|AUT5|CVT17 gene taxon:4932 20011023 SGD
+SGD S000000664 ATG15 GO:0006624 SGD_REF:S000060121|PMID:11085977 IMP P YCR068W|AUT5|CVT17 gene taxon:4932 20011025 SGD
+SGD S000000664 ATG15 GO:0006624 SGD_REF:S000060121|PMID:11085977 IDA P YCR068W|AUT5|CVT17 gene taxon:4932 20011025 SGD
+SGD S000000664 ATG15 GO:0006914 SGD_REF:S000066067|PMID:11566994 IMP P YCR068W|AUT5|CVT17 gene taxon:4932 20011023 SGD
+SGD S000000664 ATG15 GO:0006914 SGD_REF:S000060121|PMID:11085977 IDA P YCR068W|AUT5|CVT17 gene taxon:4932 20011023 SGD
+SGD S000000664 ATG15 GO:0006914 SGD_REF:S000060121|PMID:11085977 IMP P YCR068W|AUT5|CVT17 gene taxon:4932 20011023 SGD
+SGD S000000664 ATG15 GO:0006914 SGD_REF:S000066067|PMID:11566994 IDA P YCR068W|AUT5|CVT17 gene taxon:4932 20011023 SGD
+SGD S000000664 ATG15 GO:0030397 SGD_REF:S000060121|PMID:11085977 IMP P YCR068W|AUT5|CVT17 gene taxon:4932 20011114 SGD
+SGD S000000664 ATG15 GO:0030397 SGD_REF:S000060121|PMID:11085977 IDA P YCR068W|AUT5|CVT17 gene taxon:4932 20011114 SGD
+SGD S000004769 ATG16 GO:0005624 SGD_REF:S000040381|PMID:10406794 IDA C YMR159C|APG15|APG16|CVT11|SAP18 gene taxon:4932 20010118 SGD
+SGD S000004769 ATG16 GO:0005554 SGD_REF:S000069584 ND F YMR159C|APG15|APG16|CVT11|SAP18 gene taxon:4932 20010119 SGD
+SGD S000004769 ATG16 GO:0006914 SGD_REF:S000040381|PMID:10406794 IMP P YMR159C|APG15|APG16|CVT11|SAP18 gene taxon:4932 20010118 SGD
+SGD S000004769 ATG16 GO:0006914 SGD_REF:S000051835|PMID:8224160 IMP P YMR159C|APG15|APG16|CVT11|SAP18 gene taxon:4932 20041217 SGD
+SGD S000004415 ATG17 GO:0005737 SGD_REF:S000061434|PMID:11489916 IDA C YLR423C|APG17 gene taxon:4932 20030512 SGD
+SGD S000004415 ATG17 GO:0019209 SGD_REF:S000042312|PMID:10995454 IMP F YLR423C|APG17 gene taxon:4932 20011005 SGD
+SGD S000004415 ATG17 GO:0006914 SGD_REF:S000042312|PMID:10995454 IMP P YLR423C|APG17 gene taxon:4932 20011005 SGD
+SGD S000001917 ATG18 GO:0000329 SGD_REF:S000076078|PMID:15103325 IDA C YFR021W|AUT10|CVT18|NMR1|SVP1 gene taxon:4932 20040511 SGD
+SGD S000001917 ATG18 GO:0005829 SGD_REF:S000066204|PMID:11707261 IDA C YFR021W|AUT10|CVT18|NMR1|SVP1 gene taxon:4932 20011119 SGD
+SGD S000001917 ATG18 GO:0035091 SGD_REF:S000076078|PMID:15103325 IDA F YFR021W|AUT10|CVT18|NMR1|SVP1 gene taxon:4932 20040511 SGD
+SGD S000001917 ATG18 GO:0006623 SGD_REF:S000066204|PMID:11707261 IMP P YFR021W|AUT10|CVT18|NMR1|SVP1 gene taxon:4932 20011119 SGD
+SGD S000001917 ATG18 GO:0006623 SGD_REF:S000066204|PMID:11707261 IDA P YFR021W|AUT10|CVT18|NMR1|SVP1 gene taxon:4932 20011119 SGD
+SGD S000001917 ATG18 GO:0006624 SGD_REF:S000066204|PMID:11707261 IMP P YFR021W|AUT10|CVT18|NMR1|SVP1 gene taxon:4932 20011119 SGD
+SGD S000001917 ATG18 GO:0006624 SGD_REF:S000066204|PMID:11707261 IDA P YFR021W|AUT10|CVT18|NMR1|SVP1 gene taxon:4932 20011119 SGD
+SGD S000001917 ATG18 GO:0006914 SGD_REF:S000066204|PMID:11707261 IMP P YFR021W|AUT10|CVT18|NMR1|SVP1 gene taxon:4932 20011119 SGD
+SGD S000001917 ATG18 GO:0006914 SGD_REF:S000066204|PMID:11707261 IDA P YFR021W|AUT10|CVT18|NMR1|SVP1 gene taxon:4932 20011119 SGD
+SGD S000001917 ATG18 GO:0007033 SGD_REF:S000076078|PMID:15103325 IMP P YFR021W|AUT10|CVT18|NMR1|SVP1 gene taxon:4932 20040511 SGD
+SGD S000001917 ATG18 GO:0030437 SGD_REF:S000060989|PMID:11470404 IMP P YFR021W|AUT10|CVT18|NMR1|SVP1 gene taxon:4932 20011026 SGD
+SGD S000001917 ATG18 GO:0030437 SGD_REF:S000060989|PMID:11470404 IDA P YFR021W|AUT10|CVT18|NMR1|SVP1 gene taxon:4932 20011026 SGD
+SGD S000005442 ATG19 GO:0000300 SGD_REF:S000060945|PMID:11430817 IDA C Receptor for biosynthetic cytoplasm to vacuole targeting YOL082W|CVT19 gene taxon:4932 20021002 SGD
+SGD S000005442 ATG19 GO:0005737 SGD_REF:S000065831|PMID:11382752 IDA C Receptor for biosynthetic cytoplasm to vacuole targeting YOL082W|CVT19 gene taxon:4932 20021002 SGD
+SGD S000005442 ATG19 GO:0005773 SGD_REF:S000060945|PMID:11430817 IDA C Receptor for biosynthetic cytoplasm to vacuole targeting YOL082W|CVT19 gene taxon:4932 20021002 SGD
+SGD S000005442 ATG19 GO:0005515 SGD_REF:S000065831|PMID:11382752 IMP F Receptor for biosynthetic cytoplasm to vacuole targeting YOL082W|CVT19 gene taxon:4932 20021002 SGD
+SGD S000005442 ATG19 GO:0005515 SGD_REF:S000065831|PMID:11382752 IPI F Receptor for biosynthetic cytoplasm to vacuole targeting YOL082W|CVT19 gene taxon:4932 20021002 SGD
+SGD S000005442 ATG19 GO:0006623 SGD_REF:S000060945|PMID:11430817 IMP P Receptor for biosynthetic cytoplasm to vacuole targeting YOL082W|CVT19 gene taxon:4932 20021002 SGD
+SGD S000005186 ATG2 GO:0005737 SGD_REF:S000061369|PMID:11382760 IDA C peripheral membrane protein YNL242W|APG2|AUT8|SPO72 gene taxon:4932 20060608 SGD
+SGD S000005186 ATG2 GO:0019898 SGD_REF:S000061369|PMID:11382760 IDA C peripheral membrane protein YNL242W|APG2|AUT8|SPO72 gene taxon:4932 20020104 SGD
+SGD S000005186 ATG2 GO:0005554 SGD_REF:S000069584 ND F peripheral membrane protein YNL242W|APG2|AUT8|SPO72 gene taxon:4932 20010604 SGD
+SGD S000005186 ATG2 GO:0006623 SGD_REF:S000061369|PMID:11382760 IMP P peripheral membrane protein YNL242W|APG2|AUT8|SPO72 gene taxon:4932 20011025 SGD
+SGD S000005186 ATG2 GO:0006623 SGD_REF:S000061369|PMID:11382760 IEP P peripheral membrane protein YNL242W|APG2|AUT8|SPO72 gene taxon:4932 20011025 SGD
+SGD S000005186 ATG2 GO:0006914 SGD_REF:S000051835|PMID:8224160 IMP P peripheral membrane protein YNL242W|APG2|AUT8|SPO72 gene taxon:4932 20010604 SGD
+SGD S000005186 ATG2 GO:0006914 SGD_REF:S000061369|PMID:11382760 IMP P peripheral membrane protein YNL242W|APG2|AUT8|SPO72 gene taxon:4932 20011025 SGD
+SGD S000005186 ATG2 GO:0030242 SGD_REF:S000061369|PMID:11382760 IMP P peripheral membrane protein YNL242W|APG2|AUT8|SPO72 gene taxon:4932 20011108 SGD
+SGD S000005186 ATG2 GO:0030242 SGD_REF:S000061369|PMID:11382760 IDA P peripheral membrane protein YNL242W|APG2|AUT8|SPO72 gene taxon:4932 20011108 SGD
+SGD S000005186 ATG2 GO:0030242 SGD_REF:S000061369|PMID:11382760 IEP P peripheral membrane protein YNL242W|APG2|AUT8|SPO72 gene taxon:4932 20011108 SGD
+SGD S000002271 ATG20 GO:0016020 SGD_REF:S000070289|PMID:12048214 IPI C PX domain-containing protein that binds Apg17 and Cvt13, and is required for import of precursor Ape1. YDL113C|CVT20|SNX42 gene taxon:4932 20021002 SGD
+SGD S000002271 ATG20 GO:0008289 SGD_REF:S000070289|PMID:12048214 IMP F PX domain-containing protein that binds Apg17 and Cvt13, and is required for import of precursor Ape1. YDL113C|CVT20|SNX42 gene taxon:4932 20021002 SGD
+SGD S000002271 ATG20 GO:0008289 SGD_REF:S000070289|PMID:12048214 IPI F PX domain-containing protein that binds Apg17 and Cvt13, and is required for import of precursor Ape1. YDL113C|CVT20|SNX42 gene taxon:4932 20021002 SGD
+SGD S000002271 ATG20 GO:0006623 SGD_REF:S000070289|PMID:12048214 IMP P PX domain-containing protein that binds Apg17 and Cvt13, and is required for import of precursor Ape1. YDL113C|CVT20|SNX42 gene taxon:4932 20021002 SGD
+SGD S000002271 ATG20 GO:0006623 SGD_REF:S000070289|PMID:12048214 IPI P PX domain-containing protein that binds Apg17 and Cvt13, and is required for import of precursor Ape1. YDL113C|CVT20|SNX42 gene taxon:4932 20021002 SGD
+SGD S000002271 ATG20 GO:0006914 SGD_REF:S000070289|PMID:12048214 IDA P PX domain-containing protein that binds Apg17 and Cvt13, and is required for import of precursor Ape1. YDL113C|CVT20|SNX42 gene taxon:4932 20020821 SGD
+SGD S000006021 ATG21 GO:0000329 SGD_REF:S000069469|PMID:11852075 IDA C YPL100W|HSV1|MAI1 gene taxon:4932 20020814 SGD
+SGD S000006021 ATG21 GO:0000329 SGD_REF:S000079910|PMID:15194695 IDA C YPL100W|HSV1|MAI1 gene taxon:4932 20041222 SGD
+SGD S000006021 ATG21 GO:0005829 SGD_REF:S000069469|PMID:11852075 IDA C YPL100W|HSV1|MAI1 gene taxon:4932 20020814 SGD
+SGD S000006021 ATG21 GO:0035091 SGD_REF:S000076078|PMID:15103325 IDA F YPL100W|HSV1|MAI1 gene taxon:4932 20040511 SGD
+SGD S000006021 ATG21 GO:0006624 SGD_REF:S000069469|PMID:11852075 IMP P YPL100W|HSV1|MAI1 gene taxon:4932 20020814 SGD
+SGD S000006021 ATG21 GO:0006914 SGD_REF:S000079910|PMID:15194695 IGI P YPL100W|HSV1|MAI1 gene taxon:4932 20041222 SGD
+SGD S000006021 ATG21 GO:0006914 SGD_REF:S000079910|PMID:15194695 IMP P YPL100W|HSV1|MAI1 gene taxon:4932 20041222 SGD
+SGD S000000543 ATG22 GO:0005774 SGD_REF:S000059686|PMID:11058089 IDA C YCL038C|AUT4 gene taxon:4932 20050218 SGD
+SGD S000000543 ATG22 GO:0016021 SGD_REF:S000059686|PMID:11058089 ISS C YCL038C|AUT4 gene taxon:4932 20050218 SGD
+SGD S000000543 ATG22 GO:0005554 SGD_REF:S000069584 ND F YCL038C|AUT4 gene taxon:4932 20010119 SGD
+SGD S000000543 ATG22 GO:0006623 SGD_REF:S000057871|PMID:8663607 IMP P YCL038C|AUT4 gene taxon:4932 20010118 SGD
+SGD S000000543 ATG22 GO:0006623 SGD_REF:S000057871|PMID:8663607 IGI P YCL038C|AUT4 gene taxon:4932 20010118 SGD
+SGD S000000543 ATG22 GO:0006914 SGD_REF:S000057871|PMID:8663607 IMP P YCL038C|AUT4 gene taxon:4932 20010118 SGD
+SGD S000000543 ATG22 GO:0006914 SGD_REF:S000057871|PMID:8663607 IGI P YCL038C|AUT4 gene taxon:4932 20010118 SGD
+SGD S000004423 ATG23 GO:0019898 SGD_REF:S000074543|PMID:14504273 IDA C YLR431C|CVT23 gene taxon:4932 20040115 SGD
+SGD S000004423 ATG23 GO:0005554 SGD_REF:S000069584 ND F YLR431C|CVT23 gene taxon:4932 20021126 SGD
+SGD S000004423 ATG23 GO:0006623 SGD_REF:S000074543|PMID:14504273 IMP P YLR431C|CVT23 gene taxon:4932 20040115 SGD
+SGD S000004423 ATG23 GO:0006914 SGD_REF:S000074543|PMID:14504273 IMP P YLR431C|CVT23 gene taxon:4932 20040115 SGD
+SGD S000004179 ATG26 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C UDP-glucose:sterol glucosyltransferase YLR189C|UGT51 gene taxon:4932 20031028 SGD
+SGD S000004179 ATG26 GO:0016906 SGD_REF:S000045791|PMID:10224056 IDA F UDP-glucose:sterol glucosyltransferase YLR189C|UGT51 gene taxon:4932 20021030 SGD
+SGD S000004179 ATG26 GO:0016125 SGD_REF:S000045791|PMID:10224056 IMP P UDP-glucose:sterol glucosyltransferase YLR189C|UGT51 gene taxon:4932 20021030 SGD
+SGD S000003714 ATG27 GO:0016020 SGD_REF:S000071450|PMID:12186856 IDA C YJL178C|ETF1 gene taxon:4932 20030225 SGD
+SGD S000003714 ATG27 GO:0016020 SGD_REF:S000071450|PMID:12186856 ISS C YJL178C|ETF1 gene taxon:4932 20030225 SGD
+SGD S000003714 ATG27 GO:0019887 SGD_REF:S000071450|PMID:12186856 IMP F YJL178C|ETF1 gene taxon:4932 20030225 SGD
+SGD S000003714 ATG27 GO:0016050 SGD_REF:S000071450|PMID:12186856 IMP P YJL178C|ETF1 gene taxon:4932 20030225 SGD
+SGD S000006087 ATG29 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YPL166W gene taxon:4932 20031028 SGD
+SGD S000006087 ATG29 GO:0005554 SGD_REF:S000069584 ND F YPL166W gene taxon:4932 20030203 SGD
+SGD S000006087 ATG29 GO:0000004 SGD_REF:S000069584 ND P YPL166W gene taxon:4932 20030203 SGD
+SGD S000005290 ATG3 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YNR007C|APG3|AUT1 gene taxon:4932 20031028 SGD
+SGD S000005290 ATG3 GO:0019776 SGD_REF:S000059720|PMID:11100732 ISS SGD:S000003965 F YNR007C|APG3|AUT1 gene taxon:4932 20051018 SGD
+SGD S000005290 ATG3 GO:0019776 SGD_REF:S000059720|PMID:11100732 IMP F YNR007C|APG3|AUT1 gene taxon:4932 20051018 SGD
+SGD S000005290 ATG3 GO:0019776 SGD_REF:S000059720|PMID:11100732 IPI SGD:S000000174 F YNR007C|APG3|AUT1 gene taxon:4932 20051018 SGD
+SGD S000005290 ATG3 GO:0006501 SGD_REF:S000059720|PMID:11100732 IMP P YNR007C|APG3|AUT1 gene taxon:4932 20051018 SGD
+SGD S000005290 ATG3 GO:0006501 SGD_REF:S000077450|PMID:15277523 IMP P YNR007C|APG3|AUT1 gene taxon:4932 20051021 SGD
+SGD S000005290 ATG3 GO:0006501 SGD_REF:S000077450|PMID:15277523 IDA P YNR007C|APG3|AUT1 gene taxon:4932 20051021 SGD
+SGD S000005290 ATG3 GO:0006623 SGD_REF:S000047449|PMID:9023185 IMP P YNR007C|APG3|AUT1 gene taxon:4932 20010118 SGD
+SGD S000005290 ATG3 GO:0006914 SGD_REF:S000047449|PMID:9023185 IMP P YNR007C|APG3|AUT1 gene taxon:4932 20010118 SGD
+SGD S000005290 ATG3 GO:0006914 SGD_REF:S000051835|PMID:8224160 IMP P YNR007C|APG3|AUT1 gene taxon:4932 20010316 SGD
+SGD S000005167 ATG4 GO:0005875 SGD_REF:S000046683|PMID:9649430 IPI C anchor protein, mediates attachment of autophagosomes to microtubules YNL223W|APG4|AUT2 gene taxon:4932 20010118 SGD
+SGD S000005167 ATG4 GO:0004197 SGD_REF:S000059897|PMID:11038174 IDA F anchor protein, mediates attachment of autophagosomes to microtubules YNL223W|APG4|AUT2 gene taxon:4932 20050224 SGD
+SGD S000005167 ATG4 GO:0004197 SGD_REF:S000059897|PMID:11038174 IMP F anchor protein, mediates attachment of autophagosomes to microtubules YNL223W|APG4|AUT2 gene taxon:4932 20051020 SGD
+SGD S000005167 ATG4 GO:0008017 SGD_REF:S000046683|PMID:9649430 IPI F anchor protein, mediates attachment of autophagosomes to microtubules YNL223W|APG4|AUT2 gene taxon:4932 20010118 SGD
+SGD S000005167 ATG4 GO:0006501 SGD_REF:S000059897|PMID:11038174 IMP P anchor protein, mediates attachment of autophagosomes to microtubules YNL223W|APG4|AUT2 gene taxon:4932 20051020 SGD
+SGD S000005167 ATG4 GO:0006623 SGD_REF:S000046683|PMID:9649430 IMP P anchor protein, mediates attachment of autophagosomes to microtubules YNL223W|APG4|AUT2 gene taxon:4932 20010118 SGD
+SGD S000005167 ATG4 GO:0006914 SGD_REF:S000046683|PMID:9649430 IGI P anchor protein, mediates attachment of autophagosomes to microtubules YNL223W|APG4|AUT2 gene taxon:4932 20010118 SGD
+SGD S000005167 ATG4 GO:0006914 SGD_REF:S000051835|PMID:8224160 IMP P anchor protein, mediates attachment of autophagosomes to microtubules YNL223W|APG4|AUT2 gene taxon:4932 20010316 SGD
+SGD S000006070 ATG5 GO:0005776 SGD_REF:S000080872|PMID:15155809 IDA C YPL149W|APG5 gene taxon:4932 20050228 SGD
+SGD S000006070 ATG5 GO:0005829 SGD_REF:S000069879|PMID:11897782 IDA C YPL149W|APG5 gene taxon:4932 20030410 SGD
+SGD S000006070 ATG5 GO:0005554 SGD_REF:S000069584 ND F YPL149W|APG5 gene taxon:4932 20010119 SGD
+SGD S000006070 ATG5 GO:0006623 SGD_REF:S000052325|PMID:10712513 IMP P YPL149W|APG5 gene taxon:4932 20010118 SGD
+SGD S000006070 ATG5 GO:0006914 SGD_REF:S000055121|PMID:8921905 IMP P YPL149W|APG5 gene taxon:4932 20010118 SGD
+SGD S000001214 ATG7 GO:0005737 SGD_REF:S000048111|PMID:10233148 IDA C YHR171W|APG7|CVT2 gene taxon:4932 20050224 SGD
+SGD S000001214 ATG7 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YHR171W|APG7|CVT2 gene taxon:4932 20040813 SGD
+SGD S000001214 ATG7 GO:0005829 SGD_REF:S000048125|PMID:10233150 IDA C YHR171W|APG7|CVT2 gene taxon:4932 20051017 SGD
+SGD S000001214 ATG7 GO:0016020 SGD_REF:S000048111|PMID:10233148 IDA C YHR171W|APG7|CVT2 gene taxon:4932 20050224 SGD
+SGD S000001214 ATG7 GO:0019778 SGD_REF:S000039962|PMID:9759731 ISS SGD:S000001693 F YHR171W|APG7|CVT2 gene taxon:4932 20051017 SGD
+SGD S000001214 ATG7 GO:0019778 SGD_REF:S000048125|PMID:10233150 IPI SGD:S000000421 F YHR171W|APG7|CVT2 gene taxon:4932 20051017 SGD
+SGD S000001214 ATG7 GO:0019778 SGD_REF:S000048125|PMID:10233150 IMP F YHR171W|APG7|CVT2 gene taxon:4932 20051017 SGD
+SGD S000001214 ATG7 GO:0019779 SGD_REF:S000059720|PMID:11100732 IMP F YHR171W|APG7|CVT2 gene taxon:4932 20051018 SGD
+SGD S000001214 ATG7 GO:0019779 SGD_REF:S000059720|PMID:11100732 IPI SGD:S000000174 F YHR171W|APG7|CVT2 gene taxon:4932 20051018 SGD
+SGD S000001214 ATG7 GO:0006464 SGD_REF:S000039962|PMID:9759731 IMP P YHR171W|APG7|CVT2 gene taxon:4932 20051017 SGD
+SGD S000001214 ATG7 GO:0006464 SGD_REF:S000048125|PMID:10233150 IMP P YHR171W|APG7|CVT2 gene taxon:4932 20051017 SGD
+SGD S000001214 ATG7 GO:0006464 SGD_REF:S000048125|PMID:10233150 IPI SGD:S000000421 P YHR171W|APG7|CVT2 gene taxon:4932 20051017 SGD
+SGD S000001214 ATG7 GO:0006464 SGD_REF:S000039962|PMID:9759731 ISS SGD:S000001693 P YHR171W|APG7|CVT2 gene taxon:4932 20051017 SGD
+SGD S000001214 ATG7 GO:0006501 SGD_REF:S000059720|PMID:11100732 IMP P YHR171W|APG7|CVT2 gene taxon:4932 20051018 SGD
+SGD S000001214 ATG7 GO:0006501 SGD_REF:S000059897|PMID:11038174 IMP P YHR171W|APG7|CVT2 gene taxon:4932 20051018 SGD
+SGD S000001214 ATG7 GO:0006501 SGD_REF:S000077450|PMID:15277523 IDA P YHR171W|APG7|CVT2 gene taxon:4932 20051021 SGD
+SGD S000001214 ATG7 GO:0006501 SGD_REF:S000077450|PMID:15277523 IMP P YHR171W|APG7|CVT2 gene taxon:4932 20051021 SGD
+SGD S000001214 ATG7 GO:0006501 SGD_REF:S000073971|PMID:12965207 IMP P YHR171W|APG7|CVT2 gene taxon:4932 20051021 SGD
+SGD S000001214 ATG7 GO:0006623 SGD_REF:S000048125|PMID:10233150 IMP P YHR171W|APG7|CVT2 gene taxon:4932 20010118 SGD
+SGD S000001214 ATG7 GO:0006623 SGD_REF:S000073971|PMID:12965207 IMP P YHR171W|APG7|CVT2 gene taxon:4932 20051021 SGD
+SGD S000001214 ATG7 GO:0006914 SGD_REF:S000048125|PMID:10233150 IMP P YHR171W|APG7|CVT2 gene taxon:4932 20010118 SGD
+SGD S000001214 ATG7 GO:0006914 SGD_REF:S000073971|PMID:12965207 IMP P YHR171W|APG7|CVT2 gene taxon:4932 20051021 SGD
+SGD S000000174 ATG8 GO:0005776 SGD_REF:S000049668|PMID:10525546 IDA C similar to LC3, a microtubule-associated protein from rat YBL078C|APG8|AUT7|CVT5 gene taxon:4932 20050225 SGD
+SGD S000000174 ATG8 GO:0005776 SGD_REF:S000086066|PMID:16079147 IDA C similar to LC3, a microtubule-associated protein from rat YBL078C|APG8|AUT7|CVT5 gene taxon:4932 20050808 SGD
+SGD S000000174 ATG8 GO:0005875 SGD_REF:S000046683|PMID:9649430 IPI C similar to LC3, a microtubule-associated protein from rat YBL078C|APG8|AUT7|CVT5 gene taxon:4932 20010118 SGD
+SGD S000000174 ATG8 GO:0005875 SGD_REF:S000046683|PMID:9649430 ISS C similar to LC3, a microtubule-associated protein from rat YBL078C|APG8|AUT7|CVT5 gene taxon:4932 20010118 SGD
+SGD S000000174 ATG8 GO:0008017 SGD_REF:S000046683|PMID:9649430 IPI F similar to LC3, a microtubule-associated protein from rat YBL078C|APG8|AUT7|CVT5 gene taxon:4932 20010118 SGD
+SGD S000000174 ATG8 GO:0006501 SGD_REF:S000059720|PMID:11100732 IDA P similar to LC3, a microtubule-associated protein from rat YBL078C|APG8|AUT7|CVT5 gene taxon:4932 20051018 SGD
+SGD S000000174 ATG8 GO:0006501 SGD_REF:S000059720|PMID:11100732 IPI SGD:S000001214 P similar to LC3, a microtubule-associated protein from rat YBL078C|APG8|AUT7|CVT5 gene taxon:4932 20051018 SGD
+SGD S000000174 ATG8 GO:0006501 SGD_REF:S000077450|PMID:15277523 IDA P similar to LC3, a microtubule-associated protein from rat YBL078C|APG8|AUT7|CVT5 gene taxon:4932 20051021 SGD
+SGD S000000174 ATG8 GO:0006623 SGD_REF:S000046683|PMID:9649430 IMP P similar to LC3, a microtubule-associated protein from rat YBL078C|APG8|AUT7|CVT5 gene taxon:4932 20010118 SGD
+SGD S000000174 ATG8 GO:0006914 SGD_REF:S000046683|PMID:9649430 IGI P similar to LC3, a microtubule-associated protein from rat YBL078C|APG8|AUT7|CVT5 gene taxon:4932 20010118 SGD
+SGD S000002308 ATG9 GO:0005624 SGD_REF:S000047296|PMID:10662773 IDA C integral membrane protein YDL149W|APG9|AUT9|CVT7 gene taxon:4932 20010118 SGD
+SGD S000002308 ATG9 GO:0005737 SGD_REF:S000048362|PMID:10735854 IDA C integral membrane protein YDL149W|APG9|AUT9|CVT7 gene taxon:4932 20030306 SGD
+SGD S000002308 ATG9 GO:0016021 SGD_REF:S000047296|PMID:10662773 IDA C integral membrane protein YDL149W|APG9|AUT9|CVT7 gene taxon:4932 20011024 SGD
+SGD S000002308 ATG9 GO:0016021 SGD_REF:S000047296|PMID:10662773 ISS C integral membrane protein YDL149W|APG9|AUT9|CVT7 gene taxon:4932 20011024 SGD
+SGD S000002308 ATG9 GO:0005554 SGD_REF:S000069584 ND F integral membrane protein YDL149W|APG9|AUT9|CVT7 gene taxon:4932 20010119 SGD
+SGD S000002308 ATG9 GO:0000045 SGD_REF:S000047296|PMID:10662773 IMP P integral membrane protein YDL149W|APG9|AUT9|CVT7 gene taxon:4932 20010118 SGD
+SGD S000002308 ATG9 GO:0006623 SGD_REF:S000047296|PMID:10662773 IMP P integral membrane protein YDL149W|APG9|AUT9|CVT7 gene taxon:4932 20010118 SGD
+SGD S000002308 ATG9 GO:0006914 SGD_REF:S000047296|PMID:10662773 IMP P integral membrane protein YDL149W|APG9|AUT9|CVT7 gene taxon:4932 20010118 SGD
+SGD S000006230 ATH1 GO:0000324 SGD_REF:S000052501|PMID:7502577 IMP C acid trehalase YPR026W gene taxon:4932 20010118 SGD
+SGD S000006230 ATH1 GO:0009277 SGD_REF:S000076473|PMID:15128531 IDA C acid trehalase YPR026W gene taxon:4932 20050812 SGD
+SGD S000006230 ATH1 GO:0030287 SGD_REF:S000076473|PMID:15128531 IDA C acid trehalase YPR026W gene taxon:4932 20050812 SGD
+SGD S000006230 ATH1 GO:0004555 SGD_REF:S000052501|PMID:7502577 IMP F acid trehalase YPR026W gene taxon:4932 20010118 SGD
+SGD S000006230 ATH1 GO:0005993 SGD_REF:S000052501|PMID:7502577 IMP P acid trehalase YPR026W gene taxon:4932 20020423 SGD
+SGD S000006230 ATH1 GO:0005993 SGD_REF:S000045138|PMID:8764988 IMP P acid trehalase YPR026W gene taxon:4932 20020423 SGD
+SGD S000006230 ATH1 GO:0005993 SGD_REF:S000045138|PMID:8764988 ISS P acid trehalase YPR026W gene taxon:4932 20020423 SGD
+SGD S000006230 ATH1 GO:0005993 SGD_REF:S000045138|PMID:8764988 IDA P acid trehalase YPR026W gene taxon:4932 20020423 SGD
+SGD S000006230 ATH1 GO:0006950 SGD_REF:S000044723|PMID:8633854 IMP P acid trehalase YPR026W gene taxon:4932 20010118 SGD
+SGD S000004916 ATM1 GO:0005743 SGD_REF:S000050985|PMID:7828591 IDA C ABC transporter YMR301C gene taxon:4932 20010118 SGD
+SGD S000004916 ATM1 GO:0042626 SGD_REF:S000050985|PMID:7828591 IMP F ABC transporter YMR301C gene taxon:4932 20010118 SGD
+SGD S000004916 ATM1 GO:0042626 SGD_REF:S000050985|PMID:7828591 ISS F ABC transporter YMR301C gene taxon:4932 20010118 SGD
+SGD S000004916 ATM1 GO:0006879 SGD_REF:S000046445|PMID:9428742 IMP P ABC transporter YMR301C gene taxon:4932 20010118 SGD
+SGD S000005285 ATO2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C transmembrane protein (putative) YNR002C|FUN34 gene taxon:4932 20040928 SGD
+SGD S000005285 ATO2 GO:0016020 SGD_REF:S000071765|PMID:12429834 ISS C transmembrane protein (putative) YNR002C|FUN34 gene taxon:4932 20021213 SGD
+SGD S000005285 ATO2 GO:0016020 SGD_REF:S000052536|PMID:7941739 ISS C transmembrane protein (putative) YNR002C|FUN34 gene taxon:4932 20020919 SGD
+SGD S000005285 ATO2 GO:0016021 SGD_REF:S000072825|PMID:12524434 ISS C transmembrane protein (putative) YNR002C|FUN34 gene taxon:4932 20030409 SGD
+SGD S000005285 ATO2 GO:0008519 SGD_REF:S000071765|PMID:12429834 IMP F transmembrane protein (putative) YNR002C|FUN34 gene taxon:4932 20051025 SGD
+SGD S000005285 ATO2 GO:0008519 SGD_REF:S000071765|PMID:12429834 IEP F transmembrane protein (putative) YNR002C|FUN34 gene taxon:4932 20051025 SGD
+SGD S000005285 ATO2 GO:0008519 SGD_REF:S000071765|PMID:12429834 ISS WB:amt-1 F transmembrane protein (putative) YNR002C|FUN34 gene taxon:4932 20051025 SGD
+SGD S000005285 ATO2 GO:0015696 SGD_REF:S000071765|PMID:12429834 IMP P transmembrane protein (putative) YNR002C|FUN34 gene taxon:4932 20051025 SGD
+SGD S000005285 ATO2 GO:0015696 SGD_REF:S000071765|PMID:12429834 ISS WB:amt-1 P transmembrane protein (putative) YNR002C|FUN34 gene taxon:4932 20051025 SGD
+SGD S000005285 ATO2 GO:0015696 SGD_REF:S000071765|PMID:12429834 IEP P transmembrane protein (putative) YNR002C|FUN34 gene taxon:4932 20051025 SGD
+SGD S000005285 ATO2 GO:0019740 SGD_REF:S000071765|PMID:12429834 IMP P transmembrane protein (putative) YNR002C|FUN34 gene taxon:4932 20021213 SGD
+SGD S000002792 ATO3 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C transmembrane protein YDR384C gene taxon:4932 20040928 SGD
+SGD S000002792 ATO3 GO:0005886 SGD_REF:S000075192|PMID:12966084 IDA C transmembrane protein YDR384C gene taxon:4932 20031228 SGD
+SGD S000002792 ATO3 GO:0008519 SGD_REF:S000071765|PMID:12429834 IMP F transmembrane protein YDR384C gene taxon:4932 20051025 SGD
+SGD S000002792 ATO3 GO:0008519 SGD_REF:S000071765|PMID:12429834 ISS WB:amt-1 F transmembrane protein YDR384C gene taxon:4932 20051025 SGD
+SGD S000002792 ATO3 GO:0008519 SGD_REF:S000071765|PMID:12429834 IEP F transmembrane protein YDR384C gene taxon:4932 20051025 SGD
+SGD S000002792 ATO3 GO:0015696 SGD_REF:S000071765|PMID:12429834 IMP P transmembrane protein YDR384C gene taxon:4932 20051025 SGD
+SGD S000002792 ATO3 GO:0015696 SGD_REF:S000071765|PMID:12429834 ISS WB:amt-1 P transmembrane protein YDR384C gene taxon:4932 20051025 SGD
+SGD S000002792 ATO3 GO:0015696 SGD_REF:S000071765|PMID:12429834 IEP P transmembrane protein YDR384C gene taxon:4932 20051025 SGD
+SGD S000002792 ATO3 GO:0019740 SGD_REF:S000071765|PMID:12429834 IMP P transmembrane protein YDR384C gene taxon:4932 20021213 SGD
+SGD S000000195 ATP1 GO:0005754 SGD_REF:S000042736|PMID:2876995 IMP C F1F0-ATPase alpha subunit YBL099W gene taxon:4932 20010118 SGD
+SGD S000000195 ATP1 GO:0005754 SGD_REF:S000042736|PMID:2876995 ISS C F1F0-ATPase alpha subunit YBL099W gene taxon:4932 20010118 SGD
+SGD S000000195 ATP1 GO:0042645 SGD_REF:S000050870|PMID:10869431 IDA C F1F0-ATPase alpha subunit YBL099W gene taxon:4932 20050401 SGD
+SGD S000000195 ATP1 GO:0046933 SGD_REF:S000042736|PMID:2876995 IMP F F1F0-ATPase alpha subunit YBL099W gene taxon:4932 20030710 SGD
+SGD S000000195 ATP1 GO:0046933 SGD_REF:S000042736|PMID:2876995 ISS F F1F0-ATPase alpha subunit YBL099W gene taxon:4932 20030710 SGD
+SGD S000000195 ATP1 GO:0015986 SGD_REF:S000042736|PMID:2876995 IMP P F1F0-ATPase alpha subunit YBL099W gene taxon:4932 20010118 SGD
+SGD S000000195 ATP1 GO:0015986 SGD_REF:S000042736|PMID:2876995 ISS P F1F0-ATPase alpha subunit YBL099W gene taxon:4932 20010118 SGD
+SGD S000004385 ATP10 GO:0005740 SGD_REF:S000076364|PMID:14998992 IPI SGD:S000007268 C YLR393W gene taxon:4932 20041005 SGD
+SGD S000004385 ATP10 GO:0051087 SGD_REF:S000076364|PMID:14998992 IDA F YLR393W gene taxon:4932 20041005 SGD
+SGD S000004385 ATP10 GO:0006461 SGD_REF:S000076364|PMID:14998992 IDA P YLR393W gene taxon:4932 20041005 SGD
+SGD S000005259 ATP11 GO:0005759 SGD_REF:S000051052|PMID:10681564 TAS C YNL315C gene taxon:4932 20010118 SGD
+SGD S000005259 ATP11 GO:0051082 SGD_REF:S000074128|PMID:12829692 IDA F YNL315C gene taxon:4932 20040107 SGD
+SGD S000005259 ATP11 GO:0051082 SGD_REF:S000051052|PMID:10681564 IPI F YNL315C gene taxon:4932 20010118 SGD
+SGD S000005259 ATP11 GO:0006461 SGD_REF:S000053378|PMID:2142305 IMP P YNL315C gene taxon:4932 20010118 SGD
+SGD S000005259 ATP11 GO:0006461 SGD_REF:S000051052|PMID:10681564 IPI P YNL315C gene taxon:4932 20010118 SGD
+SGD S000003716 ATP12 GO:0005759 SGD_REF:S000050374|PMID:10747017 TAS C YJL180C gene taxon:4932 20010118 SGD
+SGD S000003716 ATP12 GO:0051082 SGD_REF:S000050374|PMID:10747017 IPI F YJL180C gene taxon:4932 20010118 SGD
+SGD S000003716 ATP12 GO:0006461 SGD_REF:S000053378|PMID:2142305 IMP P YJL180C gene taxon:4932 20010118 SGD
+SGD S000003716 ATP12 GO:0006461 SGD_REF:S000050374|PMID:10747017 IPI P YJL180C gene taxon:4932 20010118 SGD
+SGD S000004286 ATP14 GO:0000276 SGD_REF:S000055419|PMID:8702761 IMP C ATP synthase subunit h YLR295C gene taxon:4932 20010118 SGD
+SGD S000004286 ATP14 GO:0000276 SGD_REF:S000055419|PMID:8702761 IPI C ATP synthase subunit h YLR295C gene taxon:4932 20010118 SGD
+SGD S000004286 ATP14 GO:0046933 SGD_REF:S000055419|PMID:8702761 IMP F ATP synthase subunit h YLR295C gene taxon:4932 20030710 SGD
+SGD S000004286 ATP14 GO:0046933 SGD_REF:S000055419|PMID:8702761 IPI F ATP synthase subunit h YLR295C gene taxon:4932 20030710 SGD
+SGD S000004286 ATP14 GO:0015986 SGD_REF:S000055419|PMID:8702761 IMP P ATP synthase subunit h YLR295C gene taxon:4932 20010118 SGD
+SGD S000004286 ATP14 GO:0015986 SGD_REF:S000055419|PMID:8702761 IPI P ATP synthase subunit h YLR295C gene taxon:4932 20010118 SGD
+SGD S000006192 ATP15 GO:0005756 SGD_REF:S000057737|PMID:8416924 IMP C ATP synthase epsilon subunit YPL271W|ATPEPSILON gene taxon:4932 20010118 SGD
+SGD S000006192 ATP15 GO:0005756 SGD_REF:S000056703|PMID:1985960 ISS C ATP synthase epsilon subunit YPL271W|ATPEPSILON gene taxon:4932 20010118 SGD
+SGD S000006192 ATP15 GO:0005756 SGD_REF:S000056703|PMID:1985960 IPI C ATP synthase epsilon subunit YPL271W|ATPEPSILON gene taxon:4932 20010118 SGD
+SGD S000006192 ATP15 GO:0046933 SGD_REF:S000056703|PMID:1985960 IPI F ATP synthase epsilon subunit YPL271W|ATPEPSILON gene taxon:4932 20030710 SGD
+SGD S000006192 ATP15 GO:0046933 SGD_REF:S000057737|PMID:8416924 IMP F ATP synthase epsilon subunit YPL271W|ATPEPSILON gene taxon:4932 20030710 SGD
+SGD S000006192 ATP15 GO:0046933 SGD_REF:S000056703|PMID:1985960 ISS F ATP synthase epsilon subunit YPL271W|ATPEPSILON gene taxon:4932 20030710 SGD
+SGD S000006192 ATP15 GO:0015986 SGD_REF:S000057737|PMID:8416924 IMP P ATP synthase epsilon subunit YPL271W|ATPEPSILON gene taxon:4932 20010118 SGD
+SGD S000006192 ATP15 GO:0015986 SGD_REF:S000056703|PMID:1985960 IPI P ATP synthase epsilon subunit YPL271W|ATPEPSILON gene taxon:4932 20010118 SGD
+SGD S000006192 ATP15 GO:0015986 SGD_REF:S000056703|PMID:1985960 ISS P ATP synthase epsilon subunit YPL271W|ATPEPSILON gene taxon:4932 20010118 SGD
+SGD S000002162 ATP16 GO:0005756 SGD_REF:S000057571|PMID:8026496 IMP C ATP synthase delta subunit YDL004W gene taxon:4932 20010118 SGD
+SGD S000002162 ATP16 GO:0005756 SGD_REF:S000057571|PMID:8026496 ISS C ATP synthase delta subunit YDL004W gene taxon:4932 20010118 SGD
+SGD S000002162 ATP16 GO:0005756 SGD_REF:S000057571|PMID:8026496 IPI C ATP synthase delta subunit YDL004W gene taxon:4932 20010118 SGD
+SGD S000002162 ATP16 GO:0046933 SGD_REF:S000057571|PMID:8026496 IMP F ATP synthase delta subunit YDL004W gene taxon:4932 20030710 SGD
+SGD S000002162 ATP16 GO:0046933 SGD_REF:S000057571|PMID:8026496 ISS F ATP synthase delta subunit YDL004W gene taxon:4932 20030710 SGD
+SGD S000002162 ATP16 GO:0046933 SGD_REF:S000057571|PMID:8026496 IPI F ATP synthase delta subunit YDL004W gene taxon:4932 20030710 SGD
+SGD S000002162 ATP16 GO:0015986 SGD_REF:S000057571|PMID:8026496 IMP P ATP synthase delta subunit YDL004W gene taxon:4932 20010118 SGD
+SGD S000002162 ATP16 GO:0015986 SGD_REF:S000057571|PMID:8026496 IPI P ATP synthase delta subunit YDL004W gene taxon:4932 20010118 SGD
+SGD S000002162 ATP16 GO:0015986 SGD_REF:S000057571|PMID:8026496 ISS P ATP synthase delta subunit YDL004W gene taxon:4932 20010118 SGD
+SGD S000002785 ATP17 GO:0000276 SGD_REF:S000039775|PMID:9288937 IMP C ATP synthase subunit f YDR377W gene taxon:4932 20010118 SGD
+SGD S000002785 ATP17 GO:0000276 SGD_REF:S000039775|PMID:9288937 IPI C ATP synthase subunit f YDR377W gene taxon:4932 20010118 SGD
+SGD S000002785 ATP17 GO:0046933 SGD_REF:S000039775|PMID:9288937 IMP F ATP synthase subunit f YDR377W gene taxon:4932 20030710 SGD
+SGD S000002785 ATP17 GO:0046933 SGD_REF:S000039775|PMID:9288937 IPI F ATP synthase subunit f YDR377W gene taxon:4932 20030710 SGD
+SGD S000002785 ATP17 GO:0015986 SGD_REF:S000039775|PMID:9288937 IMP P ATP synthase subunit f YDR377W gene taxon:4932 20010118 SGD
+SGD S000002785 ATP17 GO:0015986 SGD_REF:S000039775|PMID:9288937 IPI P ATP synthase subunit f YDR377W gene taxon:4932 20010118 SGD
+SGD S000007247 ATP18 GO:0000276 SGD_REF:S000045806|PMID:9867807 IMP C ATP synthase associated protein YML081C-A gene taxon:4932 20010118 SGD
+SGD S000007247 ATP18 GO:0000276 SGD_REF:S000045806|PMID:9867807 IPI C ATP synthase associated protein YML081C-A gene taxon:4932 20010118 SGD
+SGD S000007247 ATP18 GO:0046933 SGD_REF:S000045806|PMID:9867807 IMP F ATP synthase associated protein YML081C-A gene taxon:4932 20030710 SGD
+SGD S000007247 ATP18 GO:0046933 SGD_REF:S000045806|PMID:9867807 IPI F ATP synthase associated protein YML081C-A gene taxon:4932 20030710 SGD
+SGD S000007247 ATP18 GO:0015986 SGD_REF:S000045806|PMID:9867807 IMP P ATP synthase associated protein YML081C-A gene taxon:4932 20010118 SGD
+SGD S000007247 ATP18 GO:0015986 SGD_REF:S000045951|PMID:9867878 IMP P ATP synthase associated protein YML081C-A gene taxon:4932 20010118 SGD
+SGD S000007247 ATP18 GO:0015986 SGD_REF:S000045806|PMID:9867807 IPI P ATP synthase associated protein YML081C-A gene taxon:4932 20010118 SGD
+SGD S000007247 ATP18 GO:0015986 SGD_REF:S000045951|PMID:9867878 IPI P ATP synthase associated protein YML081C-A gene taxon:4932 20010118 SGD
+SGD S000007339 ATP19 GO:0000276 SGD_REF:S000055993|PMID:9857174 IMP C ATP synthase subunit k homolog YOL077W-A gene taxon:4932 20010118 SGD
+SGD S000007339 ATP19 GO:0000276 SGD_REF:S000055993|PMID:9857174 IPI C ATP synthase subunit k homolog YOL077W-A gene taxon:4932 20010118 SGD
+SGD S000007339 ATP19 GO:0046933 SGD_REF:S000055993|PMID:9857174 IPI F ATP synthase subunit k homolog YOL077W-A gene taxon:4932 20030710 SGD
+SGD S000007339 ATP19 GO:0015986 SGD_REF:S000055993|PMID:9857174 IMP P ATP synthase subunit k homolog YOL077W-A gene taxon:4932 20010118 SGD
+SGD S000007339 ATP19 GO:0015986 SGD_REF:S000055993|PMID:9857174 IPI P ATP synthase subunit k homolog YOL077W-A gene taxon:4932 20010118 SGD
+SGD S000003882 ATP2 GO:0005625 SGD_REF:S000068747|PMID:11746603 IDA C F(1)F(0)-ATPase complex beta subunit YJR121W gene taxon:4932 20030130 SGD
+SGD S000003882 ATP2 GO:0005754 SGD_REF:S000040453|PMID:6225776 IMP C F(1)F(0)-ATPase complex beta subunit YJR121W gene taxon:4932 20010118 SGD
+SGD S000003882 ATP2 GO:0046933 SGD_REF:S000040453|PMID:6225776 IMP F F(1)F(0)-ATPase complex beta subunit YJR121W gene taxon:4932 20030711 SGD
+SGD S000003882 ATP2 GO:0046933 SGD_REF:S000040453|PMID:6225776 ISS F F(1)F(0)-ATPase complex beta subunit YJR121W gene taxon:4932 20030711 SGD
+SGD S000003882 ATP2 GO:0001321 SGD_REF:S000071401|PMID:12242224 IMP P F(1)F(0)-ATPase complex beta subunit YJR121W gene taxon:4932 20030814 SGD
+SGD S000003882 ATP2 GO:0015986 SGD_REF:S000040453|PMID:6225776 IMP P F(1)F(0)-ATPase complex beta subunit YJR121W gene taxon:4932 20010118 SGD
+SGD S000003882 ATP2 GO:0015986 SGD_REF:S000040453|PMID:6225776 ISS P F(1)F(0)-ATPase complex beta subunit YJR121W gene taxon:4932 20010118 SGD
+SGD S000006224 ATP20 GO:0000276 SGD_REF:S000044163|PMID:10336613 IMP C ATP synthase subunit g homolog YPR020W gene taxon:4932 20010118 SGD
+SGD S000006224 ATP20 GO:0000276 SGD_REF:S000044163|PMID:10336613 ISS C ATP synthase subunit g homolog YPR020W gene taxon:4932 20010118 SGD
+SGD S000006224 ATP20 GO:0000276 SGD_REF:S000044163|PMID:10336613 IPI C ATP synthase subunit g homolog YPR020W gene taxon:4932 20010118 SGD
+SGD S000006224 ATP20 GO:0005198 SGD_REF:S000055993|PMID:9857174 IMP F ATP synthase subunit g homolog YPR020W gene taxon:4932 20010118 SGD
+SGD S000006224 ATP20 GO:0005198 SGD_REF:S000055993|PMID:9857174 IPI F ATP synthase subunit g homolog YPR020W gene taxon:4932 20010118 SGD
+SGD S000006224 ATP20 GO:0015986 SGD_REF:S000055993|PMID:9857174 IMP P ATP synthase subunit g homolog YPR020W gene taxon:4932 20010118 SGD
+SGD S000006224 ATP20 GO:0015986 SGD_REF:S000044163|PMID:10336613 ISS P ATP synthase subunit g homolog YPR020W gene taxon:4932 20010118 SGD
+SGD S000006224 ATP20 GO:0015986 SGD_REF:S000055993|PMID:9857174 IPI P ATP synthase subunit g homolog YPR020W gene taxon:4932 20010118 SGD
+SGD S000006224 ATP20 GO:0015986 SGD_REF:S000044163|PMID:10336613 IMP P ATP synthase subunit g homolog YPR020W gene taxon:4932 20010118 SGD
+SGD S000000243 ATP3 GO:0005756 SGD_REF:S000039415|PMID:7929329 IMP C ATP synthase gamma subunit YBR039W gene taxon:4932 20010118 SGD
+SGD S000000243 ATP3 GO:0005756 SGD_REF:S000058444|PMID:10838056 TAS C ATP synthase gamma subunit YBR039W gene taxon:4932 20010118 SGD
+SGD S000000243 ATP3 GO:0046933 SGD_REF:S000039415|PMID:7929329 IMP F ATP synthase gamma subunit YBR039W gene taxon:4932 20030711 SGD
+SGD S000000243 ATP3 GO:0015986 SGD_REF:S000039415|PMID:7929329 IMP P ATP synthase gamma subunit YBR039W gene taxon:4932 20010118 SGD
+SGD S000005999 ATP4 GO:0000274 SGD_REF:S000040849|PMID:2892678 ISS C F(1)F(0)-ATPase complex subunit b YPL078C|LPF7 gene taxon:4932 20010118 SGD
+SGD S000005999 ATP4 GO:0000274 SGD_REF:S000058444|PMID:10838056 TAS C F(1)F(0)-ATPase complex subunit b YPL078C|LPF7 gene taxon:4932 20010118 SGD
+SGD S000005999 ATP4 GO:0005198 SGD_REF:S000040849|PMID:2892678 ISS F F(1)F(0)-ATPase complex subunit b YPL078C|LPF7 gene taxon:4932 20030711 SGD
+SGD S000005999 ATP4 GO:0005198 SGD_REF:S000058444|PMID:10838056 TAS F F(1)F(0)-ATPase complex subunit b YPL078C|LPF7 gene taxon:4932 20030711 SGD
+SGD S000005999 ATP4 GO:0046933 SGD_REF:S000058444|PMID:10838056 TAS F F(1)F(0)-ATPase complex subunit b YPL078C|LPF7 gene taxon:4932 20030714 SGD
+SGD S000005999 ATP4 GO:0015986 SGD_REF:S000040849|PMID:2892678 ISS P F(1)F(0)-ATPase complex subunit b YPL078C|LPF7 gene taxon:4932 20010118 SGD
+SGD S000005999 ATP4 GO:0015986 SGD_REF:S000044471|PMID:2553130 IMP P F(1)F(0)-ATPase complex subunit b YPL078C|LPF7 gene taxon:4932 20010118 SGD
+SGD S000002706 ATP5 GO:0000274 SGD_REF:S000042136|PMID:2146269 IMP C ATP synthase subunit 5, oligomycin sensitivity-conferring protein YDR298C|OSC1 gene taxon:4932 20010118 SGD
+SGD S000002706 ATP5 GO:0000274 SGD_REF:S000042136|PMID:2146269 ISS C ATP synthase subunit 5, oligomycin sensitivity-conferring protein YDR298C|OSC1 gene taxon:4932 20010118 SGD
+SGD S000002706 ATP5 GO:0000274 SGD_REF:S000058444|PMID:10838056 TAS C ATP synthase subunit 5, oligomycin sensitivity-conferring protein YDR298C|OSC1 gene taxon:4932 20010118 SGD
+SGD S000002706 ATP5 GO:0005198 SGD_REF:S000042136|PMID:2146269 IMP F ATP synthase subunit 5, oligomycin sensitivity-conferring protein YDR298C|OSC1 gene taxon:4932 20030711 SGD
+SGD S000002706 ATP5 GO:0005198 SGD_REF:S000042136|PMID:2146269 ISS F ATP synthase subunit 5, oligomycin sensitivity-conferring protein YDR298C|OSC1 gene taxon:4932 20030711 SGD
+SGD S000002706 ATP5 GO:0046933 SGD_REF:S000058444|PMID:10838056 TAS F ATP synthase subunit 5, oligomycin sensitivity-conferring protein YDR298C|OSC1 gene taxon:4932 20030714 SGD
+SGD S000002706 ATP5 GO:0015986 SGD_REF:S000042136|PMID:2146269 IMP P ATP synthase subunit 5, oligomycin sensitivity-conferring protein YDR298C|OSC1 gene taxon:4932 20010118 SGD
+SGD S000002706 ATP5 GO:0015986 SGD_REF:S000042136|PMID:2146269 ISS P ATP synthase subunit 5, oligomycin sensitivity-conferring protein YDR298C|OSC1 gene taxon:4932 20010118 SGD
+SGD S000007268 ATP6 GO:0000276 SGD_REF:S000058444|PMID:10838056 TAS C ATP synthase subunit 6 Q0085|OLI2|OLI4|PHO1 gene taxon:4932 20010118 SGD
+SGD S000007268 ATP6 GO:0005198 SGD_REF:S000058444|PMID:10838056 TAS F ATP synthase subunit 6 Q0085|OLI2|OLI4|PHO1 gene taxon:4932 20030711 SGD
+SGD S000007268 ATP6 GO:0046933 SGD_REF:S000058444|PMID:10838056 TAS F ATP synthase subunit 6 Q0085|OLI2|OLI4|PHO1 gene taxon:4932 20030714 SGD
+SGD S000007268 ATP6 GO:0006461 SGD_REF:S000058444|PMID:10838056 TAS P ATP synthase subunit 6 Q0085|OLI2|OLI4|PHO1 gene taxon:4932 20030711 SGD
+SGD S000007268 ATP6 GO:0015986 SGD_REF:S000058444|PMID:10838056 TAS P ATP synthase subunit 6 Q0085|OLI2|OLI4|PHO1 gene taxon:4932 20010118 SGD
+SGD S000001499 ATP7 GO:0000274 SGD_REF:S000044474|PMID:1832157 IMP C ATP synthase d subunit YKL016C gene taxon:4932 20010118 SGD
+SGD S000001499 ATP7 GO:0000274 SGD_REF:S000044474|PMID:1832157 ISS C ATP synthase d subunit YKL016C gene taxon:4932 20010118 SGD
+SGD S000001499 ATP7 GO:0000274 SGD_REF:S000058444|PMID:10838056 TAS C ATP synthase d subunit YKL016C gene taxon:4932 20010118 SGD
+SGD S000001499 ATP7 GO:0005198 SGD_REF:S000044474|PMID:1832157 IMP F ATP synthase d subunit YKL016C gene taxon:4932 20030711 SGD
+SGD S000001499 ATP7 GO:0005198 SGD_REF:S000044474|PMID:1832157 IPI F ATP synthase d subunit YKL016C gene taxon:4932 20030711 SGD
+SGD S000001499 ATP7 GO:0046933 SGD_REF:S000044474|PMID:1832157 IMP F ATP synthase d subunit YKL016C gene taxon:4932 20030714 SGD
+SGD S000001499 ATP7 GO:0006461 SGD_REF:S000044474|PMID:1832157 IMP P ATP synthase d subunit YKL016C gene taxon:4932 20030711 SGD
+SGD S000001499 ATP7 GO:0006461 SGD_REF:S000044474|PMID:1832157 IPI P ATP synthase d subunit YKL016C gene taxon:4932 20030711 SGD
+SGD S000001499 ATP7 GO:0015986 SGD_REF:S000044474|PMID:1832157 IMP P ATP synthase d subunit YKL016C gene taxon:4932 20010118 SGD
+SGD S000001499 ATP7 GO:0015986 SGD_REF:S000044474|PMID:1832157 ISS P ATP synthase d subunit YKL016C gene taxon:4932 20010118 SGD
+SGD S000007267 ATP8 GO:0000276 SGD_REF:S000049532|PMID:8662204 TAS C ATP synthase subunit 8 Q0080|AAP1 gene taxon:4932 20010118 SGD
+SGD S000007267 ATP8 GO:0046933 SGD_REF:S000049532|PMID:8662204 TAS F ATP synthase subunit 8 Q0080|AAP1 gene taxon:4932 20030710 SGD
+SGD S000007267 ATP8 GO:0015986 SGD_REF:S000049532|PMID:8662204 TAS P ATP synthase subunit 8 Q0080|AAP1 gene taxon:4932 20010118 SGD
+SGD S000004584 ATR1 GO:0005886 SGD_REF:S000047210|PMID:2123132 ISS C YML116W|SNQ1 gene taxon:4932 20020712 SGD
+SGD S000004584 ATR1 GO:0005886 SGD_REF:S000047210|PMID:2123132 IMP C YML116W|SNQ1 gene taxon:4932 20020712 SGD
+SGD S000004584 ATR1 GO:0015559 SGD_REF:S000047210|PMID:2123132 IMP F YML116W|SNQ1 gene taxon:4932 20020712 SGD
+SGD S000004584 ATR1 GO:0006855 SGD_REF:S000047210|PMID:2123132 IMP P YML116W|SNQ1 gene taxon:4932 20020712 SGD
+SGD S000000018 ATS1 GO:0005737 SGD_REF:S000075265|PMID:13680156 IPI C YAL020C|FUN28|KTI13 gene taxon:4932 20040115 SGD
+SGD S000000018 ATS1 GO:0005554 SGD_REF:S000069584 ND F YAL020C|FUN28|KTI13 gene taxon:4932 20010119 SGD
+SGD S000000018 ATS1 GO:0000226 SGD_REF:S000075265|PMID:13680156 IGI P YAL020C|FUN28|KTI13 gene taxon:4932 20040115 SGD
+SGD S000000018 ATS1 GO:0000226 SGD_REF:S000075265|PMID:13680156 IMP P YAL020C|FUN28|KTI13 gene taxon:4932 20040115 SGD
+SGD S000000018 ATS1 GO:0007017 SGD_REF:S000053617|PMID:8070652 ISS P YAL020C|FUN28|KTI13 gene taxon:4932 20010118 SGD
+SGD S000000018 ATS1 GO:0007017 SGD_REF:S000053617|PMID:8070652 IGI P YAL020C|FUN28|KTI13 gene taxon:4932 20010118 SGD
+SGD S000000018 ATS1 GO:0007117 SGD_REF:S000075265|PMID:13680156 IGI P YAL020C|FUN28|KTI13 gene taxon:4932 20040115 SGD
+SGD S000000018 ATS1 GO:0007117 SGD_REF:S000075265|PMID:13680156 IMP P YAL020C|FUN28|KTI13 gene taxon:4932 20040115 SGD
+SGD S000005203 ATX1 GO:0005829 SGD_REF:S000049311|PMID:9083054 IDA C copper chaperone YNL259C gene taxon:4932 20020607 SGD
+SGD S000005203 ATX1 GO:0016531 SGD_REF:S000042600|PMID:9346482 IDA F copper chaperone YNL259C gene taxon:4932 20020607 SGD
+SGD S000005203 ATX1 GO:0006825 SGD_REF:S000049311|PMID:9083054 IMP P copper chaperone YNL259C gene taxon:4932 20020607 SGD
+SGD S000005203 ATX1 GO:0006879 SGD_REF:S000049311|PMID:9083054 IMP P copper chaperone YNL259C gene taxon:4932 20050720 SGD
+SGD S000005203 ATX1 GO:0006979 SGD_REF:S000039642|PMID:7731983 IMP P copper chaperone YNL259C gene taxon:4932 20020919 SGD
+SGD S000005605 ATX2 GO:0000139 SGD_REF:S000043267|PMID:8887660 IDA C manganese-trafficking protein YOR079C|YOR29-30 gene taxon:4932 20020919 SGD
+SGD S000005605 ATX2 GO:0005384 SGD_REF:S000043267|PMID:8887660 IGI F manganese-trafficking protein YOR079C|YOR29-30 gene taxon:4932 20020919 SGD
+SGD S000005605 ATX2 GO:0005384 SGD_REF:S000043267|PMID:8887660 IMP F manganese-trafficking protein YOR079C|YOR29-30 gene taxon:4932 20020919 SGD
+SGD S000005605 ATX2 GO:0030026 SGD_REF:S000043267|PMID:8887660 IGI P manganese-trafficking protein YOR079C|YOR29-30 gene taxon:4932 20020919 SGD
+SGD S000005605 ATX2 GO:0030026 SGD_REF:S000043267|PMID:8887660 IMP P manganese-trafficking protein YOR079C|YOR29-30 gene taxon:4932 20020919 SGD
+SGD S000001955 AUA1 GO:0008372 SGD_REF:S000069584 ND C YFL010W-A|YFL011W-A gene taxon:4932 20020807 SGD
+SGD S000001955 AUA1 GO:0005554 SGD_REF:S000069584 ND F YFL010W-A|YFL011W-A gene taxon:4932 20020807 SGD
+SGD S000001955 AUA1 GO:0006865 SGD_REF:S000039889|PMID:8497191 IMP P YFL010W-A|YFL011W-A gene taxon:4932 20020807 SGD
+SGD S000002133 AUP1 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YCR079W gene taxon:4932 20031028 SGD
+SGD S000002133 AUP1 GO:0004721 SGD_REF:S000042149|PMID:10572263 TAS F YCR079W gene taxon:4932 20021223 SGD
+SGD S000002133 AUP1 GO:0000004 SGD_REF:S000069584 ND P YCR079W gene taxon:4932 20021223 SGD
+SGD S000001487 AUR1 GO:0005794 SGD_REF:S000039304|PMID:10888667 IDA C YKL004W gene taxon:4932 20020711 SGD
+SGD S000001487 AUR1 GO:0045140 SGD_REF:S000053853|PMID:9092515 IDA F YKL004W gene taxon:4932 20020711 SGD
+SGD S000001487 AUR1 GO:0006665 SGD_REF:S000053853|PMID:9092515 IMP P YKL004W gene taxon:4932 20030110 SGD
+SGD S000005537 AUS1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C ATP-binding cassette (ABC) family YOR011W gene taxon:4932 20040928 SGD
+SGD S000005537 AUS1 GO:0016020 SGD_REF:S000058031|PMID:9020838 ISS C ATP-binding cassette (ABC) family YOR011W gene taxon:4932 20020614 SGD
+SGD S000005537 AUS1 GO:0042626 SGD_REF:S000058031|PMID:9020838 ISS F ATP-binding cassette (ABC) family YOR011W gene taxon:4932 20020614 SGD
+SGD S000005537 AUS1 GO:0015918 SGD_REF:S000071132|PMID:12077145 IMP P ATP-binding cassette (ABC) family YOR011W gene taxon:4932 20020918 SGD
+SGD S000029048 AUT6 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20010119 SGD
+SGD S000029048 AUT6 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20040419 SGD
+SGD S000029048 AUT6 GO:0006914 SGD_REF:S000057871|PMID:8663607 IMP P gene taxon:4932 20040419 SGD
+SGD S000004104 AVL9 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YLR114C gene taxon:4932 20031028 SGD
+SGD S000004104 AVL9 GO:0005554 SGD_REF:S000069584 ND F YLR114C gene taxon:4932 20030203 SGD
+SGD S000004104 AVL9 GO:0000004 SGD_REF:S000069584 ND P YLR114C gene taxon:4932 20030203 SGD
+SGD S000005438 AVO1 GO:0005737 SGD_REF:S000071528|PMID:12408816 IPI SGD:S000004672 C YOL078W gene taxon:4932 20021105 SGD
+SGD S000005438 AVO1 GO:0031932 SGD_REF:S000071528|PMID:12408816 IPI C YOL078W gene taxon:4932 20051130 SGD
+SGD S000005438 AVO1 GO:0005554 SGD_REF:S000071528|PMID:12408816 ND F YOL078W gene taxon:4932 20021105 SGD
+SGD S000005438 AVO1 GO:0001558 SGD_REF:S000071528|PMID:12408816 IPI SGD:S000001686 P YOL078W gene taxon:4932 20051108 SGD
+SGD S000005438 AVO1 GO:0030950 SGD_REF:S000071528|PMID:12408816 IMP P YOL078W gene taxon:4932 20051108 SGD
+SGD S000005438 AVO1 GO:0030950 SGD_REF:S000071528|PMID:12408816 IPI SGD:S000001686 P YOL078W gene taxon:4932 20051108 SGD
+SGD S000005438 AVO1 GO:0031505 SGD_REF:S000071528|PMID:12408816 IPI SGD:S000001686 P YOL078W gene taxon:4932 20051108 SGD
+SGD S000004672 AVO2 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YMR068W gene taxon:4932 20020507 SGD
+SGD S000004672 AVO2 GO:0031932 SGD_REF:S000071528|PMID:12408816 IPI C YMR068W gene taxon:4932 20051130 SGD
+SGD S000004672 AVO2 GO:0005554 SGD_REF:S000071528|PMID:12408816 ND F YMR068W gene taxon:4932 20021105 SGD
+SGD S000004672 AVO2 GO:0001558 SGD_REF:S000071528|PMID:12408816 IPI SGD:S000001686 P YMR068W gene taxon:4932 20051108 SGD
+SGD S000004672 AVO2 GO:0030950 SGD_REF:S000071528|PMID:12408816 IPI SGD:S000001686 P YMR068W gene taxon:4932 20051108 SGD
+SGD S000004672 AVO2 GO:0031505 SGD_REF:S000071528|PMID:12408816 IPI SGD:S000001686 P YMR068W gene taxon:4932 20051109 SGD
+SGD S000003761 AVT1 GO:0005773 SGD_REF:S000072326|PMID:11274162 IMP C Gln (Asn), Ile (Leu), Tyr transporter YJR001W gene taxon:4932 20030127 SGD
+SGD S000003761 AVT1 GO:0015175 SGD_REF:S000072326|PMID:11274162 IMP F Gln (Asn), Ile (Leu), Tyr transporter YJR001W gene taxon:4932 20030127 SGD
+SGD S000003761 AVT1 GO:0015175 SGD_REF:S000072326|PMID:11274162 IGI F Gln (Asn), Ile (Leu), Tyr transporter YJR001W gene taxon:4932 20030127 SGD
+SGD S000003761 AVT1 GO:0015175 SGD_REF:S000072326|PMID:11274162 ISS F Gln (Asn), Ile (Leu), Tyr transporter YJR001W gene taxon:4932 20030127 SGD
+SGD S000003761 AVT1 GO:0015804 SGD_REF:S000072326|PMID:11274162 IGI P Gln (Asn), Ile (Leu), Tyr transporter YJR001W gene taxon:4932 20030127 SGD
+SGD S000003761 AVT1 GO:0015804 SGD_REF:S000072326|PMID:11274162 IMP P Gln (Asn), Ile (Leu), Tyr transporter YJR001W gene taxon:4932 20030127 SGD
+SGD S000000790 AVT2 GO:0005783 SGD_REF:S000072326|PMID:11274162 NAS C transporter YEL064C gene taxon:4932 20030127 SGD
+SGD S000000790 AVT2 GO:0005215 SGD_REF:S000072326|PMID:11274162 ISS F transporter YEL064C gene taxon:4932 20030127 SGD
+SGD S000000790 AVT2 GO:0006810 SGD_REF:S000072326|PMID:11274162 ISS P transporter YEL064C gene taxon:4932 20030127 SGD
+SGD S000001629 AVT3 GO:0005773 SGD_REF:S000072326|PMID:11274162 IMP C Gln (Asn), Ile (Leu), Tyr transporter YKL146W gene taxon:4932 20030127 SGD
+SGD S000001629 AVT3 GO:0015175 SGD_REF:S000072326|PMID:11274162 IGI F Gln (Asn), Ile (Leu), Tyr transporter YKL146W gene taxon:4932 20030127 SGD
+SGD S000001629 AVT3 GO:0015175 SGD_REF:S000072326|PMID:11274162 ISS F Gln (Asn), Ile (Leu), Tyr transporter YKL146W gene taxon:4932 20030127 SGD
+SGD S000001629 AVT3 GO:0015175 SGD_REF:S000072326|PMID:11274162 IMP F Gln (Asn), Ile (Leu), Tyr transporter YKL146W gene taxon:4932 20030127 SGD
+SGD S000001629 AVT3 GO:0015804 SGD_REF:S000072326|PMID:11274162 IGI P Gln (Asn), Ile (Leu), Tyr transporter YKL146W gene taxon:4932 20030127 SGD
+SGD S000001629 AVT3 GO:0015804 SGD_REF:S000072326|PMID:11274162 IMP P Gln (Asn), Ile (Leu), Tyr transporter YKL146W gene taxon:4932 20030127 SGD
+SGD S000005045 AVT4 GO:0005773 SGD_REF:S000072326|PMID:11274162 IMP C Gln (Asn), Ile (Leu), Tyr transporter YNL101W gene taxon:4932 20030127 SGD
+SGD S000005045 AVT4 GO:0015175 SGD_REF:S000072326|PMID:11274162 IGI F Gln (Asn), Ile (Leu), Tyr transporter YNL101W gene taxon:4932 20030127 SGD
+SGD S000005045 AVT4 GO:0015175 SGD_REF:S000072326|PMID:11274162 ISS F Gln (Asn), Ile (Leu), Tyr transporter YNL101W gene taxon:4932 20030127 SGD
+SGD S000005045 AVT4 GO:0015175 SGD_REF:S000072326|PMID:11274162 IMP F Gln (Asn), Ile (Leu), Tyr transporter YNL101W gene taxon:4932 20030127 SGD
+SGD S000005045 AVT4 GO:0015804 SGD_REF:S000072326|PMID:11274162 IGI P Gln (Asn), Ile (Leu), Tyr transporter YNL101W gene taxon:4932 20030127 SGD
+SGD S000005045 AVT4 GO:0015804 SGD_REF:S000072326|PMID:11274162 IMP P Gln (Asn), Ile (Leu), Tyr transporter YNL101W gene taxon:4932 20030127 SGD
+SGD S000000185 AVT5 GO:0008372 SGD_REF:S000069584 ND C transporter YBL089W gene taxon:4932 20021120 SGD
+SGD S000000185 AVT5 GO:0005215 SGD_REF:S000072326|PMID:11274162 ISS F transporter YBL089W gene taxon:4932 20030127 SGD
+SGD S000000185 AVT5 GO:0006810 SGD_REF:S000072326|PMID:11274162 ISS P transporter YBL089W gene taxon:4932 20030127 SGD
+SGD S000000921 AVT6 GO:0005773 SGD_REF:S000072326|PMID:11274162 IMP C Asp, Glu transporter YER119C gene taxon:4932 20030127 SGD
+SGD S000000921 AVT6 GO:0015171 SGD_REF:S000072326|PMID:11274162 IMP F Asp, Glu transporter YER119C gene taxon:4932 20030127 SGD
+SGD S000000921 AVT6 GO:0015171 SGD_REF:S000072326|PMID:11274162 ISS F Asp, Glu transporter YER119C gene taxon:4932 20030127 SGD
+SGD S000000921 AVT6 GO:0006865 SGD_REF:S000072326|PMID:11274162 IGI P Asp, Glu transporter YER119C gene taxon:4932 20030127 SGD
+SGD S000000921 AVT6 GO:0006865 SGD_REF:S000072326|PMID:11274162 ISS P Asp, Glu transporter YER119C gene taxon:4932 20030127 SGD
+SGD S000001350 AVT7 GO:0005773 SGD_REF:S000072326|PMID:11274162 ND C transporter YIL088C gene taxon:4932 20030127 SGD
+SGD S000001350 AVT7 GO:0005215 SGD_REF:S000072326|PMID:11274162 ISS F transporter YIL088C gene taxon:4932 20030127 SGD
+SGD S000001350 AVT7 GO:0006810 SGD_REF:S000072326|PMID:11274162 ISS P transporter YIL088C gene taxon:4932 20030127 SGD
+SGD S000029703 AWA1 GO:0009277 SGD_REF:S000075428|PMID:11916725 IDA C gene taxon:4932 20040209 SGD
+SGD S000029703 AWA1 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20040209 SGD
+SGD S000029703 AWA1 GO:0007155 SGD_REF:S000075428|PMID:11916725 ISS SGD:S000000084|SGD:S000005327 P gene taxon:4932 20040209 SGD
+SGD S000006326 AXL1 GO:0005935 SGD_REF:S000072029|PMID:12176366 IDA C YPR122W|FUS5|STE22 gene taxon:4932 20030109 SGD
+SGD S000006326 AXL1 GO:0016021 SGD_REF:S000041192|PMID:9725832 TAS C YPR122W|FUS5|STE22 gene taxon:4932 20021007 SGD
+SGD S000006326 AXL1 GO:0043332 SGD_REF:S000072029|PMID:12176366 IDA C YPR122W|FUS5|STE22 gene taxon:4932 20030109 SGD
+SGD S000006326 AXL1 GO:0004222 SGD_REF:S000051760|PMID:7569998 IMP F YPR122W|FUS5|STE22 gene taxon:4932 20021202 SGD
+SGD S000006326 AXL1 GO:0004222 SGD_REF:S000051760|PMID:7569998 ISS F YPR122W|FUS5|STE22 gene taxon:4932 20021202 SGD
+SGD S000006326 AXL1 GO:0000282 SGD_REF:S000058399|PMID:9891811 TAS P YPR122W|FUS5|STE22 gene taxon:4932 20010201 SGD
+SGD S000006326 AXL1 GO:0000747 SGD_REF:S000046112|PMID:9744878 NAS P YPR122W|FUS5|STE22 gene taxon:4932 20020614 SGD
+SGD S000006326 AXL1 GO:0000747 SGD_REF:S000046809|PMID:9135999 NAS P YPR122W|FUS5|STE22 gene taxon:4932 20020614 SGD
+SGD S000006326 AXL1 GO:0007120 SGD_REF:S000058399|PMID:9891811 TAS P YPR122W|FUS5|STE22 gene taxon:4932 20010118 SGD
+SGD S000006326 AXL1 GO:0007323 SGD_REF:S000051760|PMID:7569998 IMP P YPR122W|FUS5|STE22 gene taxon:4932 20021202 SGD
+SGD S000006326 AXL1 GO:0007323 SGD_REF:S000051760|PMID:7569998 ISS P YPR122W|FUS5|STE22 gene taxon:4932 20021202 SGD
+SGD S000001402 AXL2 GO:0005887 SGD_REF:S000058399|PMID:9891811 TAS C YIL140W|BUD10|SRO4 gene taxon:4932 20010118 SGD
+SGD S000001402 AXL2 GO:0005935 SGD_REF:S000077144|PMID:15282802 IDA C YIL140W|BUD10|SRO4 gene taxon:4932 20041008 SGD
+SGD S000001402 AXL2 GO:0005940 SGD_REF:S000058399|PMID:9891811 TAS C YIL140W|BUD10|SRO4 gene taxon:4932 20010118 SGD
+SGD S000001402 AXL2 GO:0005554 SGD_REF:S000058399|PMID:9891811 TAS F YIL140W|BUD10|SRO4 gene taxon:4932 20010118 SGD
+SGD S000001402 AXL2 GO:0000282 SGD_REF:S000058399|PMID:9891811 TAS P YIL140W|BUD10|SRO4 gene taxon:4932 20010302 SGD
+SGD S000001402 AXL2 GO:0007120 SGD_REF:S000058399|PMID:9891811 TAS P YIL140W|BUD10|SRO4 gene taxon:4932 20010118 SGD
+SGD S000001386 AYR1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C 1-acyl dihydroxyacetone phosphate reductase YIL124W gene taxon:4932 20020507 SGD
+SGD S000001386 AYR1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C 1-acyl dihydroxyacetone phosphate reductase YIL124W gene taxon:4932 20040928 SGD
+SGD S000001386 AYR1 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C 1-acyl dihydroxyacetone phosphate reductase YIL124W gene taxon:4932 20060317 SGD
+SGD S000001386 AYR1 GO:0005783 SGD_REF:S000055653|PMID:10617610 IDA C 1-acyl dihydroxyacetone phosphate reductase YIL124W gene taxon:4932 20010118 SGD
+SGD S000001386 AYR1 GO:0005811 SGD_REF:S000055653|PMID:10617610 IDA C 1-acyl dihydroxyacetone phosphate reductase YIL124W gene taxon:4932 20010118 SGD
+SGD S000001386 AYR1 GO:0000140 SGD_REF:S000055653|PMID:10617610 IMP F 1-acyl dihydroxyacetone phosphate reductase YIL124W gene taxon:4932 20010118 SGD
+SGD S000001386 AYR1 GO:0006654 SGD_REF:S000055653|PMID:10617610 IMP P 1-acyl dihydroxyacetone phosphate reductase YIL124W gene taxon:4932 20010118 SGD
+SGD S000003986 AYT1 GO:0008372 SGD_REF:S000069584 ND C YLL063C gene taxon:4932 20020905 SGD
+SGD S000003986 AYT1 GO:0045462 SGD_REF:S000071945|PMID:12478589 IMP F YLL063C gene taxon:4932 20030107 SGD
+SGD S000003986 AYT1 GO:0045462 SGD_REF:S000071945|PMID:12478589 ISS F YLL063C gene taxon:4932 20030107 SGD
+SGD S000003986 AYT1 GO:0019748 SGD_REF:S000071945|PMID:12478589 IMP P YLL063C gene taxon:4932 20030107 SGD
+SGD S000003986 AYT1 GO:0019748 SGD_REF:S000071945|PMID:12478589 ISS P YLL063C gene taxon:4932 20030107 SGD
+SGD S000005639 AZF1 GO:0005634 SGD_REF:S000050968|PMID:9799362 IDA C YOR113W gene taxon:4932 20020807 SGD
+SGD S000005639 AZF1 GO:0005634 SGD_REF:S000114340|PMID:16467472 IDA C YOR113W gene taxon:4932 20060214 SGD
+SGD S000005639 AZF1 GO:0003677 SGD_REF:S000069522|PMID:11839825 IPI F YOR113W gene taxon:4932 20020807 SGD
+SGD S000005639 AZF1 GO:0003677 SGD_REF:S000114340|PMID:16467472 IPI F YOR113W gene taxon:4932 20060214 SGD
+SGD S000005639 AZF1 GO:0016563 SGD_REF:S000069522|PMID:11839825 IMP F YOR113W gene taxon:4932 20020807 SGD
+SGD S000005639 AZF1 GO:0016563 SGD_REF:S000069522|PMID:11839825 IDA F YOR113W gene taxon:4932 20050117 SGD
+SGD S000005639 AZF1 GO:0016563 SGD_REF:S000114340|PMID:16467472 IMP F YOR113W gene taxon:4932 20060214 SGD
+SGD S000005639 AZF1 GO:0006355 SGD_REF:S000069522|PMID:11839825 IDA P YOR113W gene taxon:4932 20020807 SGD
+SGD S000005639 AZF1 GO:0006355 SGD_REF:S000114340|PMID:16467472 IMP P YOR113W gene taxon:4932 20060214 SGD
+SGD S000005639 AZF1 GO:0006355 SGD_REF:S000069522|PMID:11839825 IMP P YOR113W gene taxon:4932 20020807 SGD
+SGD S000005639 AZF1 GO:0009743 SGD_REF:S000069522|PMID:11839825 IDA P YOR113W gene taxon:4932 20020807 SGD
+SGD S000005639 AZF1 GO:0009743 SGD_REF:S000069522|PMID:11839825 IMP P YOR113W gene taxon:4932 20020807 SGD
+SGD S000005639 AZF1 GO:0009743 SGD_REF:S000114340|PMID:16467472 IMP P YOR113W gene taxon:4932 20060214 SGD
+SGD S000003456 AZR1 GO:0005886 SGD_REF:S000059211|PMID:11113970 IDA C YGR224W gene taxon:4932 20040120 SGD
+SGD S000003456 AZR1 GO:0045118 SGD_REF:S000059211|PMID:11113970 IMP F YGR224W gene taxon:4932 20040120 SGD
+SGD S000003456 AZR1 GO:0045117 SGD_REF:S000059211|PMID:11113970 IMP P YGR224W gene taxon:4932 20040120 SGD
+SGD S000005660 BAG7 GO:0005622 SGD_REF:S000058399|PMID:9891811 TAS C GTPase activating protein (GAP) YOR134W gene taxon:4932 20010118 SGD
+SGD S000005660 BAG7 GO:0004871 SGD_REF:S000058399|PMID:9891811 ISS F GTPase activating protein (GAP) YOR134W gene taxon:4932 20010118 SGD
+SGD S000005660 BAG7 GO:0005100 SGD_REF:S000058399|PMID:9891811 ISS F GTPase activating protein (GAP) YOR134W gene taxon:4932 20010118 SGD
+SGD S000005660 BAG7 GO:0007264 SGD_REF:S000058399|PMID:9891811 ISS P GTPase activating protein (GAP) YOR134W gene taxon:4932 20010118 SGD
+SGD S000000272 BAP2 GO:0005886 SGD_REF:S000043244|PMID:10654085 ISS C YBR068C gene taxon:4932 20020806 SGD
+SGD S000000272 BAP2 GO:0015171 SGD_REF:S000043244|PMID:10654085 IDA F YBR068C gene taxon:4932 20020806 SGD
+SGD S000000272 BAP2 GO:0006865 SGD_REF:S000043244|PMID:10654085 IDA P YBR068C gene taxon:4932 20020806 SGD
+SGD S000002453 BAP3 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C valine transporter YDR046C|PAP1 gene taxon:4932 20040928 SGD
+SGD S000002453 BAP3 GO:0005886 SGD_REF:S000043244|PMID:10654085 ISS C valine transporter YDR046C|PAP1 gene taxon:4932 20020806 SGD
+SGD S000002453 BAP3 GO:0015171 SGD_REF:S000043244|PMID:10654085 IDA F valine transporter YDR046C|PAP1 gene taxon:4932 20020806 SGD
+SGD S000002453 BAP3 GO:0006865 SGD_REF:S000043244|PMID:10654085 IDA P valine transporter YDR046C|PAP1 gene taxon:4932 20020806 SGD
+SGD S000001277 BAR1 GO:0030287 SGD_REF:S000039259|PMID:9249020 TAS C protease, synthesized in a-cells; cleaves and inactivates alpha factor YIL015W|SST1 gene taxon:4932 20010924 SGD
+SGD S000001277 BAR1 GO:0004190 SGD_REF:S000039259|PMID:9249020 TAS F protease, synthesized in a-cells; cleaves and inactivates alpha factor YIL015W|SST1 gene taxon:4932 20010118 SGD
+SGD S000001277 BAR1 GO:0030163 SGD_REF:S000039259|PMID:9249020 TAS P protease, synthesized in a-cells; cleaves and inactivates alpha factor YIL015W|SST1 gene taxon:4932 20021206 SGD
+SGD S000001807 BAS1 GO:0005634 SGD_REF:S000061035|PMID:9705508 IDA C transcription factor YKR099W gene taxon:4932 20031218 SGD
+SGD S000001807 BAS1 GO:0003702 SGD_REF:S000052116|PMID:1495962 IDA F transcription factor YKR099W gene taxon:4932 20021112 SGD
+SGD S000001807 BAS1 GO:0003702 SGD_REF:S000052116|PMID:1495962 ISS F transcription factor YKR099W gene taxon:4932 20021112 SGD
+SGD S000001807 BAS1 GO:0000105 SGD_REF:S000052116|PMID:1495962 IDA P transcription factor YKR099W gene taxon:4932 20020926 SGD
+SGD S000001807 BAS1 GO:0000105 SGD_REF:S000052116|PMID:1495962 IMP P transcription factor YKR099W gene taxon:4932 20020926 SGD
+SGD S000001807 BAS1 GO:0006366 SGD_REF:S000052116|PMID:1495962 IDA P transcription factor YKR099W gene taxon:4932 20021112 SGD
+SGD S000001807 BAS1 GO:0006366 SGD_REF:S000052116|PMID:1495962 ISS P transcription factor YKR099W gene taxon:4932 20021112 SGD
+SGD S000001807 BAS1 GO:0009113 SGD_REF:S000052116|PMID:1495962 IDA P transcription factor YKR099W gene taxon:4932 20020926 SGD
+SGD S000001807 BAS1 GO:0009113 SGD_REF:S000052116|PMID:1495962 IMP P transcription factor YKR099W gene taxon:4932 20020926 SGD
+SGD S000001251 BAT1 GO:0005759 SGD_REF:S000043212|PMID:8798704 IDA C branched-chain amino acid transaminase, highly similar to mammalian ECA39, which is regulated by the oncogene myc YHR208W|ECA39|TWT1 gene taxon:4932 20020926 SGD
+SGD S000001251 BAT1 GO:0004084 SGD_REF:S000043212|PMID:8798704 IDA F branched-chain amino acid transaminase, highly similar to mammalian ECA39, which is regulated by the oncogene myc YHR208W|ECA39|TWT1 gene taxon:4932 20020926 SGD
+SGD S000001251 BAT1 GO:0004084 SGD_REF:S000043212|PMID:8798704 ISS F branched-chain amino acid transaminase, highly similar to mammalian ECA39, which is regulated by the oncogene myc YHR208W|ECA39|TWT1 gene taxon:4932 20020926 SGD
+SGD S000001251 BAT1 GO:0009063 SGD_REF:S000049425|PMID:9748245 TAS P branched-chain amino acid transaminase, highly similar to mammalian ECA39, which is regulated by the oncogene myc YHR208W|ECA39|TWT1 gene taxon:4932 20030130 SGD
+SGD S000001251 BAT1 GO:0009082 SGD_REF:S000043212|PMID:8798704 IDA P branched-chain amino acid transaminase, highly similar to mammalian ECA39, which is regulated by the oncogene myc YHR208W|ECA39|TWT1 gene taxon:4932 20020926 SGD
+SGD S000001251 BAT1 GO:0009082 SGD_REF:S000043212|PMID:8798704 IMP P branched-chain amino acid transaminase, highly similar to mammalian ECA39, which is regulated by the oncogene myc YHR208W|ECA39|TWT1 gene taxon:4932 20020926 SGD
+SGD S000003909 BAT2 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C branched-chain amino acid transaminase YJR148W|ECA40|TWT2 gene taxon:4932 20031028 SGD
+SGD S000003909 BAT2 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C branched-chain amino acid transaminase YJR148W|ECA40|TWT2 gene taxon:4932 20020507 SGD
+SGD S000003909 BAT2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C branched-chain amino acid transaminase YJR148W|ECA40|TWT2 gene taxon:4932 20031028 SGD
+SGD S000003909 BAT2 GO:0004084 SGD_REF:S000043212|PMID:8798704 IDA F branched-chain amino acid transaminase YJR148W|ECA40|TWT2 gene taxon:4932 20020926 SGD
+SGD S000003909 BAT2 GO:0004084 SGD_REF:S000043212|PMID:8798704 ISS F branched-chain amino acid transaminase YJR148W|ECA40|TWT2 gene taxon:4932 20020926 SGD
+SGD S000003909 BAT2 GO:0009063 SGD_REF:S000049425|PMID:9748245 TAS P branched-chain amino acid transaminase YJR148W|ECA40|TWT2 gene taxon:4932 20030130 SGD
+SGD S000003909 BAT2 GO:0009082 SGD_REF:S000043212|PMID:8798704 IMP P branched-chain amino acid transaminase YJR148W|ECA40|TWT2 gene taxon:4932 20020926 SGD
+SGD S000003909 BAT2 GO:0009082 SGD_REF:S000043212|PMID:8798704 IDA P branched-chain amino acid transaminase YJR148W|ECA40|TWT2 gene taxon:4932 20020926 SGD
+SGD S000003557 BBC1 GO:0030479 SGD_REF:S000069491|PMID:11901111 IDA C YJL020C|MTI1|YJL021C gene taxon:4932 20021126 SGD
+SGD S000003557 BBC1 GO:0030479 SGD_REF:S000069133|PMID:11743162 IDA C YJL020C|MTI1|YJL021C gene taxon:4932 20051107 SGD
+SGD S000003557 BBC1 GO:0017024 SGD_REF:S000069491|PMID:11901111 IDA F YJL020C|MTI1|YJL021C gene taxon:4932 20021126 SGD
+SGD S000003557 BBC1 GO:0030036 SGD_REF:S000069491|PMID:11901111 IGI P YJL020C|MTI1|YJL021C gene taxon:4932 20021126 SGD
+SGD S000003557 BBC1 GO:0030036 SGD_REF:S000069491|PMID:11901111 IPI P YJL020C|MTI1|YJL021C gene taxon:4932 20021126 SGD
+SGD S000006176 BBP1 GO:0005816 SGD_REF:S000047788|PMID:9585415 IDA C YPL255W gene taxon:4932 20010118 SGD
+SGD S000006176 BBP1 GO:0005200 SGD_REF:S000047788|PMID:9585415 IPI F YPL255W gene taxon:4932 20010118 SGD
+SGD S000006176 BBP1 GO:0007020 SGD_REF:S000058447|PMID:9153752 IPI P YPL255W gene taxon:4932 20010118 SGD
+SGD S000006176 BBP1 GO:0007103 SGD_REF:S000061837|PMID:10654940 IMP P YPL255W gene taxon:4932 20040422 SGD
+SGD S000001082 BCD1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YHR040W gene taxon:4932 20031028 SGD
+SGD S000001082 BCD1 GO:0005634 SGD_REF:S000075214|PMID:14690591 IDA C YHR040W gene taxon:4932 20040105 SGD
+SGD S000001082 BCD1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YHR040W gene taxon:4932 20031028 SGD
+SGD S000001082 BCD1 GO:0003676 SGD_REF:S000073750|PMID:12837249 NAS F YHR040W gene taxon:4932 20030804 SGD
+SGD S000001082 BCD1 GO:0016074 SGD_REF:S000073750|PMID:12837249 IMP P YHR040W gene taxon:4932 20030804 SGD
+SGD S000004850 BCH1 colocalizes_with GO:0030136 SGD_REF:S000074185|PMID:14562095 IDA C YMR237W gene taxon:4932 20031028 SGD
+SGD S000004850 BCH1 GO:0005554 SGD_REF:S000069584 ND F YMR237W gene taxon:4932 20021126 SGD
+SGD S000004850 BCH1 GO:0006038 SGD_REF:S000114540|PMID:16498409 IGI P YMR237W gene taxon:4932 20060609 SGD
+SGD S000004850 BCH1 GO:0006038 SGD_REF:S000114540|PMID:16498409 IPI SGD:S000000227 P YMR237W gene taxon:4932 20060609 SGD
+SGD S000004850 BCH1 GO:0006893 SGD_REF:S000114540|PMID:16498409 IGI SGD:S000005825 P YMR237W gene taxon:4932 20060531 SGD
+SGD S000001735 BCH2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YKR027W|FMP50 gene taxon:4932 20040928 SGD
+SGD S000001735 BCH2 colocalizes_with GO:0030136 SGD_REF:S000074185|PMID:14562095 IDA C YKR027W|FMP50 gene taxon:4932 20031028 SGD
+SGD S000001735 BCH2 colocalizes_with GO:0030140 SGD_REF:S000114540|PMID:16498409 IDA C YKR027W|FMP50 gene taxon:4932 20060531 SGD
+SGD S000001735 BCH2 GO:0005554 SGD_REF:S000069584 ND F YKR027W|FMP50 gene taxon:4932 20021126 SGD
+SGD S000001735 BCH2 GO:0006038 SGD_REF:S000114540|PMID:16498409 IPI SGD:S000000227 P YKR027W|FMP50 gene taxon:4932 20060609 SGD
+SGD S000001735 BCH2 GO:0006893 SGD_REF:S000114540|PMID:16498409 IGI SGD:S000002351 P YKR027W|FMP50 gene taxon:4932 20060531 SGD
+SGD S000003631 BCK1 GO:0005622 SGD_REF:S000043521|PMID:10361272 TAS C MEKK YJL095W|LAS3|SAP3|SLK1|SSP31 gene taxon:4932 20030327 SGD
+SGD S000003631 BCK1 GO:0004709 SGD_REF:S000060317|PMID:11283616 IGI F MEKK YJL095W|LAS3|SAP3|SLK1|SSP31 gene taxon:4932 20030204 SGD
+SGD S000003631 BCK1 GO:0004709 SGD_REF:S000060317|PMID:11283616 TAS F MEKK YJL095W|LAS3|SAP3|SLK1|SSP31 gene taxon:4932 20030204 SGD
+SGD S000003631 BCK1 GO:0006468 SGD_REF:S000044844|PMID:8190082 TAS P MEKK YJL095W|LAS3|SAP3|SLK1|SSP31 gene taxon:4932 20010118 SGD
+SGD S000003631 BCK1 GO:0007243 SGD_REF:S000044844|PMID:8190082 IMP P MEKK YJL095W|LAS3|SAP3|SLK1|SSP31 gene taxon:4932 20010118 SGD
+SGD S000003631 BCK1 GO:0007584 SGD_REF:S000044844|PMID:8190082 IMP P MEKK YJL095W|LAS3|SAP3|SLK1|SSP31 gene taxon:4932 20010118 SGD
+SGD S000003631 BCK1 GO:0030468 SGD_REF:S000039131|PMID:1545797 IMP P MEKK YJL095W|LAS3|SAP3|SLK1|SSP31 gene taxon:4932 20010302 SGD
+SGD S000000969 BCK2 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YER167W|CTR7 gene taxon:4932 20031028 SGD
+SGD S000000969 BCK2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YER167W|CTR7 gene taxon:4932 20031028 SGD
+SGD S000000969 BCK2 GO:0005554 SGD_REF:S000069584 ND F YER167W|CTR7 gene taxon:4932 20021209 SGD
+SGD S000000969 BCK2 GO:0000074 SGD_REF:S000045556|PMID:7891677 IMP P YER167W|CTR7 gene taxon:4932 20010118 SGD
+SGD S000000969 BCK2 GO:0000082 SGD_REF:S000072514|PMID:12518319 IGI P YER167W|CTR7 gene taxon:4932 20030217 SGD
+SGD S000002769 BCP1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YDR361C gene taxon:4932 20031028 SGD
+SGD S000002769 BCP1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDR361C gene taxon:4932 20031028 SGD
+SGD S000002769 BCP1 GO:0005554 SGD_REF:S000069584 ND F YDR361C gene taxon:4932 20021209 SGD
+SGD S000002769 BCP1 GO:0000004 SGD_REF:S000069584 ND P YDR361C gene taxon:4932 20021209 SGD
+SGD S000002783 BCS1 GO:0005743 SGD_REF:S000052579|PMID:8599931 IDA C ATPase (AAA family) YDR375C gene taxon:4932 20010118 SGD
+SGD S000002783 BCS1 GO:0016887 SGD_REF:S000042848|PMID:1327750 ISS F ATPase (AAA family) YDR375C gene taxon:4932 20010118 SGD
+SGD S000002783 BCS1 GO:0009060 SGD_REF:S000042848|PMID:1327750 IMP P ATPase (AAA family) YDR375C gene taxon:4932 20020604 SGD
+SGD S000002783 BCS1 GO:0051131 SGD_REF:S000061850|PMID:10508156 IMP P ATPase (AAA family) YDR375C gene taxon:4932 20050219 SGD
+SGD S000002783 BCS1 GO:0051131 SGD_REF:S000061850|PMID:10508156 IPI P ATPase (AAA family) YDR375C gene taxon:4932 20050219 SGD
+SGD S000001295 BCY1 GO:0005634 SGD_REF:S000056327|PMID:3288487 IDA C cAMP-dependent protein kinase regulatory subunit YIL033C|SRA1 gene taxon:4932 20010118 SGD
+SGD S000001295 BCY1 GO:0005634 SGD_REF:S000069459|PMID:11914276 IDA C cAMP-dependent protein kinase regulatory subunit YIL033C|SRA1 gene taxon:4932 20020507 SGD
+SGD S000001295 BCY1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C cAMP-dependent protein kinase regulatory subunit YIL033C|SRA1 gene taxon:4932 20020507 SGD
+SGD S000001295 BCY1 GO:0004862 SGD_REF:S000055679|PMID:6292221 IMP F cAMP-dependent protein kinase regulatory subunit YIL033C|SRA1 gene taxon:4932 20010118 SGD
+SGD S000001295 BCY1 GO:0006950 SGD_REF:S000043708|PMID:3037314 IMP P cAMP-dependent protein kinase regulatory subunit YIL033C|SRA1 gene taxon:4932 20010118 SGD
+SGD S000001295 BCY1 GO:0007124 SGD_REF:S000051906|PMID:10373537 IMP P cAMP-dependent protein kinase regulatory subunit YIL033C|SRA1 gene taxon:4932 20010118 SGD
+SGD S000001295 BCY1 GO:0007165 SGD_REF:S000043708|PMID:3037314 IMP P cAMP-dependent protein kinase regulatory subunit YIL033C|SRA1 gene taxon:4932 20010118 SGD
+SGD S000001295 BCY1 GO:0009408 SGD_REF:S000043708|PMID:3037314 IMP P cAMP-dependent protein kinase regulatory subunit YIL033C|SRA1 gene taxon:4932 20010118 SGD
+SGD S000004391 BDF1 GO:0000790 SGD_REF:S000040692|PMID:7791775 IDA C YLR399C gene taxon:4932 20050415 SGD
+SGD S000004391 BDF1 GO:0005634 SGD_REF:S000040692|PMID:7791775 IDA C YLR399C gene taxon:4932 20010118 SGD
+SGD S000004391 BDF1 GO:0030528 SGD_REF:S000044678|PMID:7816623 IMP F YLR399C gene taxon:4932 20030311 SGD
+SGD S000004391 BDF1 GO:0030528 SGD_REF:S000044678|PMID:7816623 ISS F YLR399C gene taxon:4932 20030311 SGD
+SGD S000004391 BDF1 GO:0006281 SGD_REF:S000040692|PMID:7791775 IMP P YLR399C gene taxon:4932 20050415 SGD
+SGD S000004391 BDF1 GO:0006338 SGD_REF:S000075430|PMID:14690608 IPI P YLR399C gene taxon:4932 20040322 SGD
+SGD S000004391 BDF1 GO:0007126 SGD_REF:S000040692|PMID:7791775 IMP P YLR399C gene taxon:4932 20050415 SGD
+SGD S000004391 BDF1 GO:0030437 SGD_REF:S000040692|PMID:7791775 IMP P YLR399C gene taxon:4932 20010118 SGD
+SGD S000002228 BDF2 GO:0005634 SGD_REF:S000039134|PMID:10077188 TAS C BDF1 homolog, bromodomain protein YDL070W gene taxon:4932 20010118 SGD
+SGD S000002228 BDF2 GO:0005554 SGD_REF:S000069584 ND F BDF1 homolog, bromodomain protein YDL070W gene taxon:4932 20010119 SGD
+SGD S000002228 BDF2 GO:0000004 SGD_REF:S000069584 ND P BDF1 homolog, bromodomain protein YDL070W gene taxon:4932 20010119 SGD
+SGD S000000056 BDH1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YAL060W gene taxon:4932 20020507 SGD
+SGD S000000056 BDH1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YAL060W gene taxon:4932 20031028 SGD
+SGD S000000056 BDH1 GO:0000721 SGD_REF:S000060105|PMID:11306064 IDA F YAL060W gene taxon:4932 20020905 SGD
+SGD S000000056 BDH1 GO:0019650 SGD_REF:S000060105|PMID:11306064 IDA P YAL060W gene taxon:4932 20020902 SGD
+SGD S000004984 BDP1 GO:0000126 SGD_REF:S000058323|PMID:9585500 TAS C TFIIIB 90 kDa subunit YNL039W|TFC5 gene taxon:4932 20010118 SGD
+SGD S000004984 BDP1 GO:0003709 SGD_REF:S000058323|PMID:9585500 TAS F TFIIIB 90 kDa subunit YNL039W|TFC5 gene taxon:4932 20010118 SGD
+SGD S000004984 BDP1 GO:0006384 SGD_REF:S000058323|PMID:9585500 TAS P TFIIIB 90 kDa subunit YNL039W|TFC5 gene taxon:4932 20010118 SGD
+SGD S000005524 BDS1 GO:0008372 SGD_REF:S000069584 ND C alkyl/aryl-sulfatase YOL164W gene taxon:4932 20021126 SGD
+SGD S000005524 BDS1 GO:0004065 SGD_REF:S000082122|PMID:15947202 IDA F alkyl/aryl-sulfatase YOL164W gene taxon:4932 20050810 SGD
+SGD S000005524 BDS1 GO:0004065 SGD_REF:S000082122|PMID:15947202 ISS F alkyl/aryl-sulfatase YOL164W gene taxon:4932 20050810 SGD
+SGD S000005524 BDS1 GO:0004065 SGD_REF:S000082122|PMID:15947202 IMP F alkyl/aryl-sulfatase YOL164W gene taxon:4932 20050810 SGD
+SGD S000005524 BDS1 GO:0018741 SGD_REF:S000082122|PMID:15947202 IMP F alkyl/aryl-sulfatase YOL164W gene taxon:4932 20050810 SGD
+SGD S000005524 BDS1 GO:0018741 SGD_REF:S000082122|PMID:15947202 ISS F alkyl/aryl-sulfatase YOL164W gene taxon:4932 20050810 SGD
+SGD S000005524 BDS1 GO:0018909 SGD_REF:S000082122|PMID:15947202 IMP P alkyl/aryl-sulfatase YOL164W gene taxon:4932 20050810 SGD
+SGD S000000404 BEM1 GO:0000131 SGD_REF:S000044417|PMID:9128251 IDA C YBR200W|SRO1 gene taxon:4932 20020807 SGD
+SGD S000000404 BEM1 GO:0005934 SGD_REF:S000069507|PMID:11927541 IDA C YBR200W|SRO1 gene taxon:4932 20020807 SGD
+SGD S000000404 BEM1 GO:0005935 SGD_REF:S000069507|PMID:11927541 IDA C YBR200W|SRO1 gene taxon:4932 20020807 SGD
+SGD S000000404 BEM1 GO:0043332 SGD_REF:S000041197|PMID:8754808 TAS C YBR200W|SRO1 gene taxon:4932 20050218 SGD
+SGD S000000404 BEM1 GO:0005515 SGD_REF:S000069507|PMID:11927541 IDA F YBR200W|SRO1 gene taxon:4932 20020807 SGD
+SGD S000000404 BEM1 GO:0005515 SGD_REF:S000069507|PMID:11927541 IMP F YBR200W|SRO1 gene taxon:4932 20020807 SGD
+SGD S000000404 BEM1 GO:0000753 SGD_REF:S000043671|PMID:10087263 IGI P YBR200W|SRO1 gene taxon:4932 20021206 SGD
+SGD S000000404 BEM1 GO:0000753 SGD_REF:S000043671|PMID:10087263 IMP P YBR200W|SRO1 gene taxon:4932 20021206 SGD
+SGD S000000404 BEM1 GO:0000753 SGD_REF:S000043671|PMID:10087263 TAS P YBR200W|SRO1 gene taxon:4932 20021206 SGD
+SGD S000000404 BEM1 GO:0030468 SGD_REF:S000070267|PMID:11113154 TAS P YBR200W|SRO1 gene taxon:4932 20020807 SGD
+SGD S000000957 BEM2 GO:0005622 SGD_REF:S000058399|PMID:9891811 TAS C rho GTPase activating protein (GAP) YER155C|IPL2|SUP9|TSL1 gene taxon:4932 20010118 SGD
+SGD S000000957 BEM2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C rho GTPase activating protein (GAP) YER155C|IPL2|SUP9|TSL1 gene taxon:4932 20041203 SGD
+SGD S000000957 BEM2 GO:0004871 SGD_REF:S000058399|PMID:9891811 IPI F rho GTPase activating protein (GAP) YER155C|IPL2|SUP9|TSL1 gene taxon:4932 20010118 SGD
+SGD S000000957 BEM2 GO:0005100 SGD_REF:S000058399|PMID:9891811 IDA F rho GTPase activating protein (GAP) YER155C|IPL2|SUP9|TSL1 gene taxon:4932 20010118 SGD
+SGD S000000957 BEM2 GO:0000226 SGD_REF:S000053805|PMID:7579704 IGI P rho GTPase activating protein (GAP) YER155C|IPL2|SUP9|TSL1 gene taxon:4932 20010705 SGD
+SGD S000000957 BEM2 GO:0007047 SGD_REF:S000058399|PMID:9891811 IPI P rho GTPase activating protein (GAP) YER155C|IPL2|SUP9|TSL1 gene taxon:4932 20010118 SGD
+SGD S000000957 BEM2 GO:0007117 SGD_REF:S000058399|PMID:9891811 IPI P rho GTPase activating protein (GAP) YER155C|IPL2|SUP9|TSL1 gene taxon:4932 20010118 SGD
+SGD S000000957 BEM2 GO:0007264 SGD_REF:S000058399|PMID:9891811 IPI P rho GTPase activating protein (GAP) YER155C|IPL2|SUP9|TSL1 gene taxon:4932 20010118 SGD
+SGD S000000957 BEM2 GO:0030036 SGD_REF:S000058399|PMID:9891811 IGI P rho GTPase activating protein (GAP) YER155C|IPL2|SUP9|TSL1 gene taxon:4932 20010705 SGD
+SGD S000000957 BEM2 GO:0030036 SGD_REF:S000053805|PMID:7579704 IGI P rho GTPase activating protein (GAP) YER155C|IPL2|SUP9|TSL1 gene taxon:4932 20010705 SGD
+SGD S000000957 BEM2 GO:0030468 SGD_REF:S000058399|PMID:9891811 IPI P rho GTPase activating protein (GAP) YER155C|IPL2|SUP9|TSL1 gene taxon:4932 20010302 SGD
+SGD S000006036 BEM3 GO:0005622 SGD_REF:S000058399|PMID:9891811 TAS C rho GTPase activating protein (GAP) YPL115C gene taxon:4932 20010118 SGD
+SGD S000006036 BEM3 GO:0004871 SGD_REF:S000058399|PMID:9891811 IPI F rho GTPase activating protein (GAP) YPL115C gene taxon:4932 20010118 SGD
+SGD S000006036 BEM3 GO:0005100 SGD_REF:S000058399|PMID:9891811 IDA F rho GTPase activating protein (GAP) YPL115C gene taxon:4932 20010118 SGD
+SGD S000006036 BEM3 GO:0001403 SGD_REF:S000056064|PMID:10066831 IPI P rho GTPase activating protein (GAP) YPL115C gene taxon:4932 20010118 SGD
+SGD S000006036 BEM3 GO:0007118 SGD_REF:S000056064|PMID:10066831 IPI P rho GTPase activating protein (GAP) YPL115C gene taxon:4932 20010118 SGD
+SGD S000006036 BEM3 GO:0007119 SGD_REF:S000056064|PMID:10066831 IPI P rho GTPase activating protein (GAP) YPL115C gene taxon:4932 20010118 SGD
+SGD S000006036 BEM3 GO:0007124 SGD_REF:S000056064|PMID:10066831 IPI P rho GTPase activating protein (GAP) YPL115C gene taxon:4932 20010118 SGD
+SGD S000006036 BEM3 GO:0007264 SGD_REF:S000058399|PMID:9891811 IPI P rho GTPase activating protein (GAP) YPL115C gene taxon:4932 20010118 SGD
+SGD S000006036 BEM3 GO:0030468 SGD_REF:S000058399|PMID:9891811 IPI P rho GTPase activating protein (GAP) YPL115C gene taxon:4932 20010302 SGD
+SGD S000006082 BEM4 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YPL161C|ROM7 gene taxon:4932 20031028 SGD
+SGD S000006082 BEM4 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YPL161C|ROM7 gene taxon:4932 20031028 SGD
+SGD S000006082 BEM4 GO:0005554 SGD_REF:S000069584 ND F YPL161C|ROM7 gene taxon:4932 20021209 SGD
+SGD S000006082 BEM4 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P YPL161C|ROM7 gene taxon:4932 20060202 SGD
+SGD S000006082 BEM4 GO:0007266 SGD_REF:S000041238|PMID:8754839 IGI P YPL161C|ROM7 gene taxon:4932 20010118 SGD
+SGD S000006082 BEM4 GO:0030036 SGD_REF:S000058399|PMID:9891811 TAS P YPL161C|ROM7 gene taxon:4932 20020103 SGD
+SGD S000006082 BEM4 GO:0030468 SGD_REF:S000041238|PMID:8754839 IMP P YPL161C|ROM7 gene taxon:4932 20010302 SGD
+SGD S000001266 BET1 GO:0005789 SGD_REF:S000045788|PMID:1396561 IDA C YIL004C|SLY12 gene taxon:4932 20020716 SGD
+SGD S000001266 BET1 GO:0030134 SGD_REF:S000061877|PMID:11157978 IDA C YIL004C|SLY12 gene taxon:4932 20020716 SGD
+SGD S000001266 BET1 GO:0005485 SGD_REF:S000044624|PMID:3312234 IMP F YIL004C|SLY12 gene taxon:4932 20020716 SGD
+SGD S000001266 BET1 GO:0006888 SGD_REF:S000061877|PMID:11157978 IPI P YIL004C|SLY12 gene taxon:4932 20020716 SGD
+SGD S000001266 BET1 GO:0006888 SGD_REF:S000044624|PMID:3312234 IMP P YIL004C|SLY12 gene taxon:4932 20020716 SGD
+SGD S000001266 BET1 GO:0006890 SGD_REF:S000052969|PMID:9813082 IDA P YIL004C|SLY12 gene taxon:4932 20020716 SGD
+SGD S000006380 BET2 GO:0005968 SGD_REF:S000044007|PMID:8756702 IDA C geranylgeranyltransferase type II beta subunit YPR176C gene taxon:4932 20020716 SGD
+SGD S000006380 BET2 GO:0004663 SGD_REF:S000044007|PMID:8756702 IDA F geranylgeranyltransferase type II beta subunit YPR176C gene taxon:4932 20020716 SGD
+SGD S000006380 BET2 GO:0018348 SGD_REF:S000044007|PMID:8756702 IDA P geranylgeranyltransferase type II beta subunit YPR176C gene taxon:4932 20020716 SGD
+SGD S000001776 BET3 GO:0005794 SGD_REF:S000080118|PMID:15608655 IDA C transport protein particle (TRAPP) component YKR068C gene taxon:4932 20050314 SGD
+SGD S000001776 BET3 GO:0030008 SGD_REF:S000043703|PMID:10727015 IDA C transport protein particle (TRAPP) component YKR068C gene taxon:4932 20020716 SGD
+SGD S000001776 BET3 GO:0005554 SGD_REF:S000069584 ND F transport protein particle (TRAPP) component YKR068C gene taxon:4932 20020716 SGD
+SGD S000001776 BET3 GO:0006888 SGD_REF:S000043703|PMID:10727015 IMP P transport protein particle (TRAPP) component YKR068C gene taxon:4932 20020716 SGD
+SGD S000003568 BET4 GO:0005968 SGD_REF:S000044007|PMID:8756702 IDA C geranylgeranyltransferase type II alpha subunit (PGGTase-II, alpha subunit) YJL031C gene taxon:4932 20020716 SGD
+SGD S000003568 BET4 GO:0004663 SGD_REF:S000044007|PMID:8756702 IDA F geranylgeranyltransferase type II alpha subunit (PGGTase-II, alpha subunit) YJL031C gene taxon:4932 20020716 SGD
+SGD S000003568 BET4 GO:0018348 SGD_REF:S000044007|PMID:8756702 IDA P geranylgeranyltransferase type II alpha subunit (PGGTase-II, alpha subunit) YJL031C gene taxon:4932 20020716 SGD
+SGD S000004542 BET5 GO:0030008 SGD_REF:S000043703|PMID:10727015 IDA C TRAPP 18kDa component YML077W gene taxon:4932 20020716 SGD
+SGD S000004542 BET5 GO:0005554 SGD_REF:S000069584 ND F TRAPP 18kDa component YML077W gene taxon:4932 20020716 SGD
+SGD S000004542 BET5 GO:0006888 SGD_REF:S000043703|PMID:10727015 IMP P TRAPP 18kDa component YML077W gene taxon:4932 20020716 SGD
+SGD S000003814 BFA1 GO:0005816 SGD_REF:S000056361|PMID:10220406 IDA C YJR053W|IBD1 gene taxon:4932 20010118 SGD
+SGD S000003814 BFA1 GO:0005096 SGD_REF:S000071885|PMID:12432084 TAS F YJR053W|IBD1 gene taxon:4932 20030131 SGD
+SGD S000003814 BFA1 GO:0007096 SGD_REF:S000086185|PMID:16039591 TAS P YJR053W|IBD1 gene taxon:4932 20060314 SGD
+SGD S000003814 BFA1 GO:0031578 SGD_REF:S000086185|PMID:16039591 IGI P YJR053W|IBD1 gene taxon:4932 20060314 SGD
+SGD S000003814 BFA1 GO:0031578 SGD_REF:S000086185|PMID:16039591 IMP P YJR053W|IBD1 gene taxon:4932 20060314 SGD
+SGD S000005724 BFR1 GO:0005844 SGD_REF:S000060730|PMID:11410665 IDA C YOR198C gene taxon:4932 20021204 SGD
+SGD S000005724 BFR1 GO:0030529 SGD_REF:S000060730|PMID:11410665 IDA C YOR198C gene taxon:4932 20050309 SGD
+SGD S000005724 BFR1 GO:0042175 SGD_REF:S000060730|PMID:11410665 IDA C YOR198C gene taxon:4932 20021204 SGD
+SGD S000005724 BFR1 GO:0003723 SGD_REF:S000060730|PMID:11410665 IDA F YOR198C gene taxon:4932 20021204 SGD
+SGD S000005724 BFR1 GO:0007088 SGD_REF:S000054125|PMID:8913743 IMP P YOR198C gene taxon:4932 20010118 SGD
+SGD S000005724 BFR1 GO:0007126 SGD_REF:S000054125|PMID:8913743 IMP P YOR198C gene taxon:4932 20010118 SGD
+SGD S000005724 BFR1 GO:0016071 SGD_REF:S000060730|PMID:11410665 IPI P YOR198C gene taxon:4932 20050620 SGD
+SGD S000002707 BFR2 GO:0005730 SGD_REF:S000074185|PMID:14562095 IDA C YDR299W gene taxon:4932 20031028 SGD
+SGD S000002707 BFR2 GO:0005554 SGD_REF:S000069584 ND F YDR299W gene taxon:4932 20020918 SGD
+SGD S000002707 BFR2 GO:0006888 SGD_REF:S000049018|PMID:9472076 IGI P YDR299W gene taxon:4932 20020918 SGD
+SGD S000003514 BGL2 GO:0009277 SGD_REF:S000048756|PMID:8458852 TAS C cell wall endo-beta-1,3-glucanase YGR282C gene taxon:4932 20010118 SGD
+SGD S000003514 BGL2 GO:0004338 SGD_REF:S000048756|PMID:8458852 TAS F cell wall endo-beta-1,3-glucanase YGR282C gene taxon:4932 20010118 SGD
+SGD S000003514 BGL2 GO:0007047 SGD_REF:S000048756|PMID:8458852 TAS P cell wall endo-beta-1,3-glucanase YGR282C gene taxon:4932 20010118 SGD
+SGD S000007271 BI2 GO:0005739 SGD_REF:S000058438|PMID:9872396 TAS C mRNA maturase bI2 Q0110 gene taxon:4932 20021119 SGD
+SGD S000007271 BI2 GO:0004518 SGD_REF:S000053184|PMID:8670880 IDA F mRNA maturase bI2 Q0110 gene taxon:4932 20010118 SGD
+SGD S000007271 BI2 GO:0008380 SGD_REF:S000053184|PMID:8670880 IDA P mRNA maturase bI2 Q0110 gene taxon:4932 20010118 SGD
+SGD S000007272 BI3 GO:0005739 SGD_REF:S000058438|PMID:9872396 TAS C mRNA maturase bI3 Q0115 gene taxon:4932 20021119 SGD
+SGD S000007272 BI3 GO:0003723 SGD_REF:S000068996|PMID:11773622 IDA F mRNA maturase bI3 Q0115 gene taxon:4932 20021119 SGD
+SGD S000007272 BI3 GO:0000372 SGD_REF:S000068996|PMID:11773622 IDA P mRNA maturase bI3 Q0115 gene taxon:4932 20030821 SGD
+SGD S000007273 BI4 GO:0005739 SGD_REF:S000039920|PMID:2875797 IDA C mitochondrial mRNA maturase bI4 Q0120 gene taxon:4932 20010118 SGD
+SGD S000007273 BI4 GO:0003723 SGD_REF:S000059609|PMID:11142386 IDA F mitochondrial mRNA maturase bI4 Q0120 gene taxon:4932 20021119 SGD
+SGD S000007273 BI4 GO:0000372 SGD_REF:S000059609|PMID:11142386 IDA P mitochondrial mRNA maturase bI4 Q0120 gene taxon:4932 20030821 SGD
+SGD S000007273 BI4 GO:0000372 SGD_REF:S000059609|PMID:11142386 IMP P mitochondrial mRNA maturase bI4 Q0120 gene taxon:4932 20030821 SGD
+SGD S000001143 BIG1 GO:0030176 SGD_REF:S000070122|PMID:12112232 IDA C YHR101C gene taxon:4932 20050623 SGD
+SGD S000001143 BIG1 GO:0005554 SGD_REF:S000069584 ND F YHR101C gene taxon:4932 20020807 SGD
+SGD S000001143 BIG1 GO:0009272 SGD_REF:S000070122|PMID:12112232 IGI P YHR101C gene taxon:4932 20020807 SGD
+SGD S000001143 BIG1 GO:0009272 SGD_REF:S000070122|PMID:12112232 IMP P YHR101C gene taxon:4932 20020807 SGD
+SGD S000000534 BIK1 GO:0000776 SGD_REF:S000069443|PMID:11756471 IDA C YCL029C|ARM5|PAC14 gene taxon:4932 20040922 SGD
+SGD S000000534 BIK1 GO:0000778 SGD_REF:S000080960|PMID:11511347 IDA C YCL029C|ARM5|PAC14 gene taxon:4932 20050307 SGD
+SGD S000000534 BIK1 GO:0005816 SGD_REF:S000058447|PMID:9153752 TAS C YCL029C|ARM5|PAC14 gene taxon:4932 20010118 SGD
+SGD S000000534 BIK1 GO:0005876 SGD_REF:S000058447|PMID:9153752 TAS C YCL029C|ARM5|PAC14 gene taxon:4932 20010118 SGD
+SGD S000000534 BIK1 GO:0005876 SGD_REF:S000080960|PMID:11511347 IDA C YCL029C|ARM5|PAC14 gene taxon:4932 20050307 SGD
+SGD S000000534 BIK1 GO:0005938 SGD_REF:S000080960|PMID:11511347 IDA C YCL029C|ARM5|PAC14 gene taxon:4932 20050307 SGD
+SGD S000000534 BIK1 GO:0008017 SGD_REF:S000040788|PMID:2277073 IGI F YCL029C|ARM5|PAC14 gene taxon:4932 20010118 SGD
+SGD S000000534 BIK1 GO:0000092 SGD_REF:S000058447|PMID:9153752 TAS P YCL029C|ARM5|PAC14 gene taxon:4932 20010118 SGD
+SGD S000000534 BIK1 GO:0030472 SGD_REF:S000058447|PMID:9153752 TAS P YCL029C|ARM5|PAC14 gene taxon:4932 20040128 SGD
+SGD S000000818 BIM1 GO:0000776 SGD_REF:S000076817|PMID:14570580 TAS C YER016W|EB1|YEB1 gene taxon:4932 20040922 SGD
+SGD S000000818 BIM1 GO:0005816 SGD_REF:S000047788|PMID:9585415 IDA C YER016W|EB1|YEB1 gene taxon:4932 20010118 SGD
+SGD S000000818 BIM1 GO:0005881 SGD_REF:S000040584|PMID:10352017 IDA C YER016W|EB1|YEB1 gene taxon:4932 20010118 SGD
+SGD S000000818 BIM1 GO:0005200 SGD_REF:S000047788|PMID:9585415 IPI F YER016W|EB1|YEB1 gene taxon:4932 20010118 SGD
+SGD S000000818 BIM1 GO:0007019 SGD_REF:S000040584|PMID:10352017 IMP P YER016W|EB1|YEB1 gene taxon:4932 20010118 SGD
+SGD S000000818 BIM1 GO:0007020 SGD_REF:S000058447|PMID:9153752 IPI P YER016W|EB1|YEB1 gene taxon:4932 20010118 SGD
+SGD S000000818 BIM1 GO:0007026 SGD_REF:S000040584|PMID:10352017 IMP P YER016W|EB1|YEB1 gene taxon:4932 20010118 SGD
+SGD S000000818 BIM1 GO:0007064 SGD_REF:S000076127|PMID:14742714 IGI SGD:S000001234 P YER016W|EB1|YEB1 gene taxon:4932 20050513 SGD
+SGD S000000818 BIM1 GO:0007064 SGD_REF:S000076127|PMID:14742714 IMP P YER016W|EB1|YEB1 gene taxon:4932 20050513 SGD
+SGD S000000818 BIM1 GO:0007094 SGD_REF:S000061889|PMID:10935617 TAS P YER016W|EB1|YEB1 gene taxon:4932 20021219 SGD
+SGD S000000818 BIM1 GO:0030473 SGD_REF:S000040584|PMID:10352017 IMP P YER016W|EB1|YEB1 gene taxon:4932 20010118 SGD
+SGD S000003518 BIO2 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C biotin synthase YGR286C gene taxon:4932 20031028 SGD
+SGD S000003518 BIO2 GO:0004076 SGD_REF:S000055833|PMID:10333520 TAS F biotin synthase YGR286C gene taxon:4932 20020927 SGD
+SGD S000003518 BIO2 GO:0009102 SGD_REF:S000055833|PMID:10333520 TAS P biotin synthase YGR286C gene taxon:4932 20020927 SGD
+SGD S000005341 BIO3 GO:0005737 SGD_REF:S000055833|PMID:10333520 ISS C 7,8-diamino-pelargonic acid aminotransferase (DAPA) aminotransferase YNR058W gene taxon:4932 20020927 SGD
+SGD S000005341 BIO3 GO:0004015 SGD_REF:S000055833|PMID:10333520 IDA F 7,8-diamino-pelargonic acid aminotransferase (DAPA) aminotransferase YNR058W gene taxon:4932 20020927 SGD
+SGD S000005341 BIO3 GO:0004015 SGD_REF:S000055833|PMID:10333520 ISS F 7,8-diamino-pelargonic acid aminotransferase (DAPA) aminotransferase YNR058W gene taxon:4932 20020927 SGD
+SGD S000005341 BIO3 GO:0009102 SGD_REF:S000055833|PMID:10333520 IDA P 7,8-diamino-pelargonic acid aminotransferase (DAPA) aminotransferase YNR058W gene taxon:4932 20020927 SGD
+SGD S000005341 BIO3 GO:0009102 SGD_REF:S000055833|PMID:10333520 IMP P 7,8-diamino-pelargonic acid aminotransferase (DAPA) aminotransferase YNR058W gene taxon:4932 20020927 SGD
+SGD S000005340 BIO4 GO:0005737 SGD_REF:S000055833|PMID:10333520 ISS C dethiobiotin synthetase YNR057C gene taxon:4932 20020927 SGD
+SGD S000005340 BIO4 GO:0004141 SGD_REF:S000055833|PMID:10333520 IDA F dethiobiotin synthetase YNR057C gene taxon:4932 20020927 SGD
+SGD S000005340 BIO4 GO:0004141 SGD_REF:S000055833|PMID:10333520 ISS F dethiobiotin synthetase YNR057C gene taxon:4932 20020927 SGD
+SGD S000005340 BIO4 GO:0009102 SGD_REF:S000055833|PMID:10333520 IDA P dethiobiotin synthetase YNR057C gene taxon:4932 20020927 SGD
+SGD S000005340 BIO4 GO:0009102 SGD_REF:S000055833|PMID:10333520 IMP P dethiobiotin synthetase YNR057C gene taxon:4932 20020927 SGD
+SGD S000005339 BIO5 GO:0005886 SGD_REF:S000055833|PMID:10333520 ISS C transmembrane regulator of KAPA/DAPA transport YNR056C gene taxon:4932 20020927 SGD
+SGD S000005339 BIO5 GO:0015646 SGD_REF:S000055833|PMID:10333520 IDA F transmembrane regulator of KAPA/DAPA transport YNR056C gene taxon:4932 20020927 SGD
+SGD S000005339 BIO5 GO:0015646 SGD_REF:S000055833|PMID:10333520 ISS F transmembrane regulator of KAPA/DAPA transport YNR056C gene taxon:4932 20020927 SGD
+SGD S000005339 BIO5 GO:0009102 SGD_REF:S000055833|PMID:10333520 IMP P transmembrane regulator of KAPA/DAPA transport YNR056C gene taxon:4932 20020927 SGD
+SGD S000005339 BIO5 GO:0051180 SGD_REF:S000055833|PMID:10333520 IDA P transmembrane regulator of KAPA/DAPA transport YNR056C gene taxon:4932 20041006 SGD
+SGD S000005339 BIO5 GO:0051180 SGD_REF:S000055833|PMID:10333520 IMP P transmembrane regulator of KAPA/DAPA transport YNR056C gene taxon:4932 20041006 SGD
+SGD S000029723 BIO6 GO:0008372 SGD_REF:S000069584 ND C biotin biosynthesis enzyme gene taxon:4932 20051109 SGD
+SGD S000029723 BIO6 GO:0008710 SGD_REF:S000087157|PMID:16269718 ISS F biotin biosynthesis enzyme gene taxon:4932 20051114 SGD
+SGD S000029723 BIO6 GO:0009102 SGD_REF:S000087157|PMID:16269718 IMP P biotin biosynthesis enzyme gene taxon:4932 20051109 SGD
+SGD S000003849 BIR1 GO:0000778 SGD_REF:S000044012|PMID:10557299 IGI C YJR089W gene taxon:4932 20021009 SGD
+SGD S000003849 BIR1 GO:0000778 SGD_REF:S000044012|PMID:10557299 IPI C YJR089W gene taxon:4932 20021009 SGD
+SGD S000003849 BIR1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YJR089W gene taxon:4932 20040928 SGD
+SGD S000003849 BIR1 GO:0005819 SGD_REF:S000113988|PMID:16381814 IDA C YJR089W gene taxon:4932 20060111 SGD
+SGD S000003849 BIR1 GO:0051233 SGD_REF:S000113988|PMID:16381814 IDA C YJR089W gene taxon:4932 20060111 SGD
+SGD S000003849 BIR1 GO:0005554 SGD_REF:S000069584 ND F YJR089W gene taxon:4932 20021009 SGD
+SGD S000003849 BIR1 GO:0000022 SGD_REF:S000113988|PMID:16381814 IMP P YJR089W gene taxon:4932 20060111 SGD
+SGD S000003849 BIR1 GO:0007059 SGD_REF:S000044012|PMID:10557299 IMP P YJR089W gene taxon:4932 20021009 SGD
+SGD S000000474 BIT2 GO:0008372 SGD_REF:S000069584 ND C YBR270C gene taxon:4932 20030203 SGD
+SGD S000000474 BIT2 GO:0005554 SGD_REF:S000069584 ND F YBR270C gene taxon:4932 20030203 SGD
+SGD S000000474 BIT2 GO:0000004 SGD_REF:S000069584 ND P YBR270C gene taxon:4932 20030203 SGD
+SGD S000003594 BIT61 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YJL058C gene taxon:4932 20031028 SGD
+SGD S000003594 BIT61 GO:0031932 SGD_REF:S000075967|PMID:14736892 IPI C YJL058C gene taxon:4932 20051130 SGD
+SGD S000003594 BIT61 GO:0005554 SGD_REF:S000069584 ND F YJL058C gene taxon:4932 20021001 SGD
+SGD S000003594 BIT61 GO:0001558 SGD_REF:S000075967|PMID:14736892 IPI SGD:S000001686 P YJL058C gene taxon:4932 20051108 SGD
+SGD S000003594 BIT61 GO:0030950 SGD_REF:S000075967|PMID:14736892 IPI SGD:S000001686 P YJL058C gene taxon:4932 20051108 SGD
+SGD S000003594 BIT61 GO:0031505 SGD_REF:S000075967|PMID:14736892 IPI SGD:S000001686 P YJL058C gene taxon:4932 20051108 SGD
+SGD S000001887 BLM10 colocalizes_with GO:0000502 SGD_REF:S000081108|PMID:15778719 IDA C YFL007W|YFL006W gene taxon:4932 20060216 SGD
+SGD S000001887 BLM10 GO:0005634 SGD_REF:S000076318|PMID:12973301 IDA C YFL007W|YFL006W gene taxon:4932 20041001 SGD
+SGD S000001887 BLM10 GO:0005634 SGD_REF:S000081108|PMID:15778719 IDA C YFL007W|YFL006W gene taxon:4932 20050715 SGD
+SGD S000001887 BLM10 colocalizes_with GO:0005839 SGD_REF:S000081108|PMID:15778719 IDA C YFL007W|YFL006W gene taxon:4932 20050927 SGD
+SGD S000001887 BLM10 colocalizes_with GO:0005839 SGD_REF:S000081108|PMID:15778719 IMP C YFL007W|YFL006W gene taxon:4932 20060216 SGD
+SGD S000001887 BLM10 contributes_to GO:0008538 SGD_REF:S000076318|PMID:12973301 IMP F YFL007W|YFL006W gene taxon:4932 20041001 SGD
+SGD S000001887 BLM10 GO:0008538 SGD_REF:S000081108|PMID:15778719 IMP F YFL007W|YFL006W gene taxon:4932 20060216 SGD
+SGD S000001887 BLM10 GO:0008538 SGD_REF:S000081108|PMID:15778719 IDA F YFL007W|YFL006W gene taxon:4932 20060216 SGD
+SGD S000001887 BLM10 GO:0030163 SGD_REF:S000076318|PMID:12973301 IMP P YFL007W|YFL006W gene taxon:4932 20050513 SGD
+SGD S000001887 BLM10 GO:0030163 SGD_REF:S000081108|PMID:15778719 IGI SGD:S000002178|SGD:S000001022 P YFL007W|YFL006W gene taxon:4932 20060216 SGD
+SGD S000001887 BLM10 GO:0030163 SGD_REF:S000081108|PMID:15778719 IMP P YFL007W|YFL006W gene taxon:4932 20060216 SGD
+SGD S000001887 BLM10 GO:0043248 SGD_REF:S000076318|PMID:12973301 IMP P YFL007W|YFL006W gene taxon:4932 20041115 SGD
+SGD S000086717 BLM3 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20060215 SGD
+SGD S000086717 BLM3 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20060215 SGD
+SGD S000086717 BLM3 GO:0042493 SGD_REF:S000049146|PMID:1710619 IMP P gene taxon:4932 20060215 SGD
+SGD S000000979 BMH1 GO:0005634 SGD_REF:S000071462|PMID:12167636 IDA C member of conserved eukaryotic 14-3-3 gene family YER177W|APR6 gene taxon:4932 20030127 SGD
+SGD S000000979 BMH1 GO:0003677 SGD_REF:S000071462|PMID:12167636 IDA F member of conserved eukaryotic 14-3-3 gene family YER177W|APR6 gene taxon:4932 20030127 SGD
+SGD S000000979 BMH1 GO:0005515 SGD_REF:S000061894|PMID:11447594 TAS F member of conserved eukaryotic 14-3-3 gene family YER177W|APR6 gene taxon:4932 20031003 SGD
+SGD S000000979 BMH1 GO:0000077 SGD_REF:S000075294|PMID:14704161 IMP P member of conserved eukaryotic 14-3-3 gene family YER177W|APR6 gene taxon:4932 20050513 SGD
+SGD S000000979 BMH1 GO:0001402 SGD_REF:S000043884|PMID:9215628 IGI P member of conserved eukaryotic 14-3-3 gene family YER177W|APR6 gene taxon:4932 20010829 SGD
+SGD S000000979 BMH1 GO:0005977 SGD_REF:S000043884|PMID:9215628 IGI P member of conserved eukaryotic 14-3-3 gene family YER177W|APR6 gene taxon:4932 20010829 SGD
+SGD S000000979 BMH1 GO:0007124 SGD_REF:S000043884|PMID:9215628 IGI P member of conserved eukaryotic 14-3-3 gene family YER177W|APR6 gene taxon:4932 20010829 SGD
+SGD S000000979 BMH1 GO:0007265 SGD_REF:S000043884|PMID:9215628 IGI P member of conserved eukaryotic 14-3-3 gene family YER177W|APR6 gene taxon:4932 20010829 SGD
+SGD S000000979 BMH1 GO:0030437 SGD_REF:S000043884|PMID:9215628 IGI P member of conserved eukaryotic 14-3-3 gene family YER177W|APR6 gene taxon:4932 20010829 SGD
+SGD S000002506 BMH2 GO:0005634 SGD_REF:S000071462|PMID:12167636 IDA C member of conserved eukaryotic 14-3-3 gene family YDR099W|SCD3 gene taxon:4932 20030127 SGD
+SGD S000002506 BMH2 GO:0003677 SGD_REF:S000071462|PMID:12167636 IDA F member of conserved eukaryotic 14-3-3 gene family YDR099W|SCD3 gene taxon:4932 20030127 SGD
+SGD S000002506 BMH2 GO:0005515 SGD_REF:S000061894|PMID:11447594 TAS F member of conserved eukaryotic 14-3-3 gene family YDR099W|SCD3 gene taxon:4932 20031003 SGD
+SGD S000002506 BMH2 GO:0000077 SGD_REF:S000075294|PMID:14704161 IMP P member of conserved eukaryotic 14-3-3 gene family YDR099W|SCD3 gene taxon:4932 20050513 SGD
+SGD S000002506 BMH2 GO:0001402 SGD_REF:S000043884|PMID:9215628 IGI P member of conserved eukaryotic 14-3-3 gene family YDR099W|SCD3 gene taxon:4932 20010829 SGD
+SGD S000002506 BMH2 GO:0005977 SGD_REF:S000043884|PMID:9215628 IGI P member of conserved eukaryotic 14-3-3 gene family YDR099W|SCD3 gene taxon:4932 20010829 SGD
+SGD S000002506 BMH2 GO:0007124 SGD_REF:S000043884|PMID:9215628 IGI P member of conserved eukaryotic 14-3-3 gene family YDR099W|SCD3 gene taxon:4932 20010829 SGD
+SGD S000002506 BMH2 GO:0007265 SGD_REF:S000043884|PMID:9215628 IGI P member of conserved eukaryotic 14-3-3 gene family YDR099W|SCD3 gene taxon:4932 20010829 SGD
+SGD S000002506 BMH2 GO:0030437 SGD_REF:S000043884|PMID:9215628 IGI P member of conserved eukaryotic 14-3-3 gene family YDR099W|SCD3 gene taxon:4932 20010829 SGD
+SGD S000006138 BMS1 GO:0005634 SGD_REF:S000056415|PMID:10684247 IDA C YPL217C gene taxon:4932 20010118 SGD
+SGD S000006138 BMS1 GO:0005730 SGD_REF:S000056415|PMID:10684247 IDA C YPL217C gene taxon:4932 20010118 SGD
+SGD S000006138 BMS1 GO:0005737 SGD_REF:S000056415|PMID:10684247 IDA C YPL217C gene taxon:4932 20010118 SGD
+SGD S000006138 BMS1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YPL217C gene taxon:4932 20040813 SGD
+SGD S000006138 BMS1 GO:0005525 SGD_REF:S000065947|PMID:11565749 TAS F YPL217C gene taxon:4932 20020603 SGD
+SGD S000006138 BMS1 GO:0006364 SGD_REF:S000065947|PMID:11565749 IDA P YPL217C gene taxon:4932 20020603 SGD
+SGD S000006138 BMS1 GO:0006365 SGD_REF:S000066033|PMID:11565748 IDA P YPL217C gene taxon:4932 20020603 SGD
+SGD S000006138 BMS1 GO:0042255 SGD_REF:S000065947|PMID:11565749 IDA P YPL217C gene taxon:4932 20020603 SGD
+SGD S000003786 BNA1 GO:0005737 SGD_REF:S000069524|PMID:11901108 IDA C 3-hydroxyanthranilic acid dioxygenase YJR025C|HAD1 gene taxon:4932 20020708 SGD
+SGD S000003786 BNA1 GO:0000334 SGD_REF:S000053587|PMID:9539135 IDA F 3-hydroxyanthranilic acid dioxygenase YJR025C|HAD1 gene taxon:4932 20020821 SGD
+SGD S000003786 BNA1 GO:0000334 SGD_REF:S000069977|PMID:12062417 TAS F 3-hydroxyanthranilic acid dioxygenase YJR025C|HAD1 gene taxon:4932 20020821 SGD
+SGD S000003786 BNA1 GO:0009435 SGD_REF:S000069524|PMID:11901108 IMP P 3-hydroxyanthranilic acid dioxygenase YJR025C|HAD1 gene taxon:4932 20020708 SGD
+SGD S000003839 BNA2 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C Tryptophan 2,3-dioxygenase YJR078W gene taxon:4932 20020507 SGD
+SGD S000003839 BNA2 GO:0004833 SGD_REF:S000069977|PMID:12062417 TAS F Tryptophan 2,3-dioxygenase YJR078W gene taxon:4932 20020821 SGD
+SGD S000003839 BNA2 GO:0009435 SGD_REF:S000069977|PMID:12062417 IMP P Tryptophan 2,3-dioxygenase YJR078W gene taxon:4932 20020821 SGD
+SGD S000003596 BNA3 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C Arylformamidase YJL060W gene taxon:4932 20031028 SGD
+SGD S000003596 BNA3 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C Arylformamidase YJL060W gene taxon:4932 20031028 SGD
+SGD S000003596 BNA3 GO:0004061 SGD_REF:S000069977|PMID:12062417 TAS F Arylformamidase YJL060W gene taxon:4932 20020821 SGD
+SGD S000003596 BNA3 GO:0009435 SGD_REF:S000069977|PMID:12062417 IMP P Arylformamidase YJL060W gene taxon:4932 20020821 SGD
+SGD S000000194 BNA4 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C Kynurenine 3-mono oxygenase YBL098W gene taxon:4932 20031028 SGD
+SGD S000000194 BNA4 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C Kynurenine 3-mono oxygenase YBL098W gene taxon:4932 20040924 SGD
+SGD S000000194 BNA4 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C Kynurenine 3-mono oxygenase YBL098W gene taxon:4932 20060317 SGD
+SGD S000000194 BNA4 GO:0004502 SGD_REF:S000069977|PMID:12062417 TAS F Kynurenine 3-mono oxygenase YBL098W gene taxon:4932 20020821 SGD
+SGD S000000194 BNA4 GO:0009435 SGD_REF:S000069977|PMID:12062417 IMP P Kynurenine 3-mono oxygenase YBL098W gene taxon:4932 20020821 SGD
+SGD S000004221 BNA5 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C Kynureninase YLR231C gene taxon:4932 20031028 SGD
+SGD S000004221 BNA5 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C Kynureninase YLR231C gene taxon:4932 20031028 SGD
+SGD S000004221 BNA5 GO:0030429 SGD_REF:S000069977|PMID:12062417 IDA F Kynureninase YLR231C gene taxon:4932 20020616 SGD
+SGD S000004221 BNA5 GO:0009435 SGD_REF:S000069977|PMID:12062417 IDA P Kynureninase YLR231C gene taxon:4932 20020821 SGD
+SGD S000004221 BNA5 GO:0009435 SGD_REF:S000069977|PMID:12062417 IMP P Kynureninase YLR231C gene taxon:4932 20020821 SGD
+SGD S000001943 BNA6 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C Quinolinate phosphoribosyl transferase YFR047C|QPT1 gene taxon:4932 20031028 SGD
+SGD S000001943 BNA6 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C Quinolinate phosphoribosyl transferase YFR047C|QPT1 gene taxon:4932 20031028 SGD
+SGD S000001943 BNA6 GO:0004514 SGD_REF:S000069977|PMID:12062417 IDA F Quinolinate phosphoribosyl transferase YFR047C|QPT1 gene taxon:4932 20020801 SGD
+SGD S000001943 BNA6 GO:0009435 SGD_REF:S000069977|PMID:12062417 IDA P Quinolinate phosphoribosyl transferase YFR047C|QPT1 gene taxon:4932 20020821 SGD
+SGD S000001943 BNA6 GO:0009435 SGD_REF:S000069977|PMID:12062417 IMP P Quinolinate phosphoribosyl transferase YFR047C|QPT1 gene taxon:4932 20020821 SGD
+SGD S000005215 BNI1 GO:0000131 SGD_REF:S000059323|PMID:11154270 IDA C formin, involved in spindle orientation YNL271C|PPF3|SHE5 gene taxon:4932 20030827 SGD
+SGD S000005215 BNI1 GO:0000133 SGD_REF:S000046605|PMID:10639324 TAS C formin, involved in spindle orientation YNL271C|PPF3|SHE5 gene taxon:4932 20010118 SGD
+SGD S000005215 BNI1 GO:0005884 SGD_REF:S000070351|PMID:12052901 IDA C formin, involved in spindle orientation YNL271C|PPF3|SHE5 gene taxon:4932 20030821 SGD
+SGD S000005215 BNI1 GO:0005934 SGD_REF:S000059323|PMID:11154270 IDA C formin, involved in spindle orientation YNL271C|PPF3|SHE5 gene taxon:4932 20030827 SGD
+SGD S000005215 BNI1 GO:0005935 SGD_REF:S000059323|PMID:11154270 IDA C formin, involved in spindle orientation YNL271C|PPF3|SHE5 gene taxon:4932 20030827 SGD
+SGD S000005215 BNI1 GO:0030478 SGD_REF:S000041005|PMID:10652251 IDA C formin, involved in spindle orientation YNL271C|PPF3|SHE5 gene taxon:4932 20010118 SGD
+SGD S000005215 BNI1 GO:0043332 SGD_REF:S000053007|PMID:9082982 IDA C formin, involved in spindle orientation YNL271C|PPF3|SHE5 gene taxon:4932 20030827 SGD
+SGD S000005215 BNI1 GO:0005519 SGD_REF:S000046605|PMID:10639324 IPI F formin, involved in spindle orientation YNL271C|PPF3|SHE5 gene taxon:4932 20010118 SGD
+SGD S000005215 BNI1 GO:0000132 SGD_REF:S000040363|PMID:10085293 IMP P formin, involved in spindle orientation YNL271C|PPF3|SHE5 gene taxon:4932 20040128 SGD
+SGD S000005215 BNI1 GO:0006970 SGD_REF:S000041005|PMID:10652251 TAS P formin, involved in spindle orientation YNL271C|PPF3|SHE5 gene taxon:4932 20010118 SGD
+SGD S000005215 BNI1 GO:0007015 SGD_REF:S000046605|PMID:10639324 IPI P formin, involved in spindle orientation YNL271C|PPF3|SHE5 gene taxon:4932 20010118 SGD
+SGD S000005215 BNI1 GO:0007117 SGD_REF:S000041005|PMID:10652251 TAS P formin, involved in spindle orientation YNL271C|PPF3|SHE5 gene taxon:4932 20010118 SGD
+SGD S000005215 BNI1 GO:0007121 SGD_REF:S000041005|PMID:10652251 TAS P formin, involved in spindle orientation YNL271C|PPF3|SHE5 gene taxon:4932 20010118 SGD
+SGD S000005215 BNI1 GO:0007266 SGD_REF:S000046605|PMID:10639324 IPI P formin, involved in spindle orientation YNL271C|PPF3|SHE5 gene taxon:4932 20010118 SGD
+SGD S000005215 BNI1 GO:0008298 SGD_REF:S000068954|PMID:11553699 IMP P formin, involved in spindle orientation YNL271C|PPF3|SHE5 gene taxon:4932 20021001 SGD
+SGD S000005215 BNI1 GO:0030447 SGD_REF:S000080384|PMID:15645503 IMP P formin, involved in spindle orientation YNL271C|PPF3|SHE5 gene taxon:4932 20050621 SGD
+SGD S000005215 BNI1 GO:0030468 SGD_REF:S000046605|PMID:10639324 IMP P formin, involved in spindle orientation YNL271C|PPF3|SHE5 gene taxon:4932 20010302 SGD
+SGD S000005215 BNI1 GO:0030468 SGD_REF:S000046605|PMID:10639324 IPI P formin, involved in spindle orientation YNL271C|PPF3|SHE5 gene taxon:4932 20010302 SGD
+SGD S000005215 BNI1 GO:0031384 SGD_REF:S000077102|PMID:14734532 IMP P formin, involved in spindle orientation YNL271C|PPF3|SHE5 gene taxon:4932 20050719 SGD
+SGD S000005215 BNI1 GO:0031385 SGD_REF:S000077102|PMID:14734532 IMP P formin, involved in spindle orientation YNL271C|PPF3|SHE5 gene taxon:4932 20050719 SGD
+SGD S000005215 BNI1 GO:0045010 SGD_REF:S000070351|PMID:12052901 IDA P formin, involved in spindle orientation YNL271C|PPF3|SHE5 gene taxon:4932 20030821 SGD
+SGD S000005177 BNI4 GO:0000131 SGD_REF:S000077520|PMID:15470103 IDA C scaffold protein YNL233W gene taxon:4932 20041112 SGD
+SGD S000005177 BNI4 GO:0005935 SGD_REF:S000077144|PMID:15282802 IDA C scaffold protein YNL233W gene taxon:4932 20041008 SGD
+SGD S000005177 BNI4 GO:0005940 SGD_REF:S000047109|PMID:9314530 IDA C scaffold protein YNL233W gene taxon:4932 20041112 SGD
+SGD S000005177 BNI4 GO:0005940 SGD_REF:S000047109|PMID:9314530 IPI C scaffold protein YNL233W gene taxon:4932 20041112 SGD
+SGD S000005177 BNI4 GO:0005515 SGD_REF:S000072489|PMID:12529424 IDA F scaffold protein YNL233W gene taxon:4932 20030218 SGD
+SGD S000005177 BNI4 GO:0000917 SGD_REF:S000077520|PMID:15470103 IGI P scaffold protein YNL233W gene taxon:4932 20041112 SGD
+SGD S000005177 BNI4 GO:0006031 SGD_REF:S000077520|PMID:15470103 IGI P scaffold protein YNL233W gene taxon:4932 20041112 SGD
+SGD S000005177 BNI4 GO:0006031 SGD_REF:S000077520|PMID:15470103 TAS P scaffold protein YNL233W gene taxon:4932 20041112 SGD
+SGD S000005177 BNI4 GO:0006031 SGD_REF:S000077520|PMID:15470103 IMP P scaffold protein YNL233W gene taxon:4932 20041112 SGD
+SGD S000005177 BNI4 GO:0008105 SGD_REF:S000072489|PMID:12529424 IDA P scaffold protein YNL233W gene taxon:4932 20050920 SGD
+SGD S000005177 BNI4 GO:0008105 SGD_REF:S000072489|PMID:12529424 IMP P scaffold protein YNL233W gene taxon:4932 20050920 SGD
+SGD S000005110 BNI5 GO:0000144 SGD_REF:S000071355|PMID:12215547 IDA C YNL166C gene taxon:4932 20020926 SGD
+SGD S000005110 BNI5 GO:0000144 SGD_REF:S000071355|PMID:12215547 IPI C YNL166C gene taxon:4932 20020926 SGD
+SGD S000005110 BNI5 GO:0005935 SGD_REF:S000071355|PMID:12215547 IDA C YNL166C gene taxon:4932 20020926 SGD
+SGD S000005110 BNI5 GO:0005554 SGD_REF:S000069584 ND F YNL166C gene taxon:4932 20020926 SGD
+SGD S000005110 BNI5 GO:0000910 SGD_REF:S000071355|PMID:12215547 IGI P YNL166C gene taxon:4932 20020926 SGD
+SGD S000005110 BNI5 GO:0000921 SGD_REF:S000071355|PMID:12215547 IGI P YNL166C gene taxon:4932 20030321 SGD
+SGD S000005110 BNI5 GO:0000921 SGD_REF:S000071355|PMID:12215547 IMP P YNL166C gene taxon:4932 20030321 SGD
+SGD S000005110 BNI5 GO:0000921 SGD_REF:S000071355|PMID:12215547 IPI P YNL166C gene taxon:4932 20030321 SGD
+SGD S000001421 BNR1 GO:0000142 SGD_REF:S000041005|PMID:10652251 IDA C YIL159W gene taxon:4932 20010118 SGD
+SGD S000001421 BNR1 GO:0008092 SGD_REF:S000071593|PMID:12419188 TAS F YIL159W gene taxon:4932 20021204 SGD
+SGD S000001421 BNR1 GO:0006970 SGD_REF:S000041005|PMID:10652251 IGI P YIL159W gene taxon:4932 20010118 SGD
+SGD S000001421 BNR1 GO:0007015 SGD_REF:S000071593|PMID:12419188 TAS P YIL159W gene taxon:4932 20021204 SGD
+SGD S000001421 BNR1 GO:0007120 SGD_REF:S000041005|PMID:10652251 IMP P YIL159W gene taxon:4932 20010118 SGD
+SGD S000003462 BNS1 GO:0008372 SGD_REF:S000069584 ND C YGR230W gene taxon:4932 20021001 SGD
+SGD S000003462 BNS1 GO:0005554 SGD_REF:S000069584 ND F YGR230W gene taxon:4932 20021001 SGD
+SGD S000003462 BNS1 GO:0007126 SGD_REF:S000061836|PMID:10564265 IGI P YGR230W gene taxon:4932 20021001 SGD
+SGD S000000181 BOI1 GO:0005933 SGD_REF:S000070309|PMID:12097146 IDA C YBL085W|BOB1|GIN7 gene taxon:4932 20020821 SGD
+SGD S000000181 BOI1 GO:0005935 SGD_REF:S000070309|PMID:12097146 IDA C YBL085W|BOB1|GIN7 gene taxon:4932 20020821 SGD
+SGD S000000181 BOI1 GO:0030427 SGD_REF:S000070309|PMID:12097146 IDA C YBL085W|BOB1|GIN7 gene taxon:4932 20020821 SGD
+SGD S000000181 BOI1 GO:0005543 SGD_REF:S000070309|PMID:12097146 IDA F YBL085W|BOB1|GIN7 gene taxon:4932 20021209 SGD
+SGD S000000181 BOI1 GO:0007266 SGD_REF:S000046605|PMID:10639324 IPI P YBL085W|BOB1|GIN7 gene taxon:4932 20010118 SGD
+SGD S000000181 BOI1 GO:0007266 SGD_REF:S000046605|PMID:10639324 IGI P YBL085W|BOB1|GIN7 gene taxon:4932 20010118 SGD
+SGD S000000181 BOI1 GO:0030468 SGD_REF:S000046605|PMID:10639324 IMP P YBL085W|BOB1|GIN7 gene taxon:4932 20010302 SGD
+SGD S000000181 BOI1 GO:0030468 SGD_REF:S000046605|PMID:10639324 IGI P YBL085W|BOB1|GIN7 gene taxon:4932 20010302 SGD
+SGD S000000181 BOI1 GO:0030468 SGD_REF:S000046605|PMID:10639324 IPI P YBL085W|BOB1|GIN7 gene taxon:4932 20010302 SGD
+SGD S000000916 BOI2 GO:0005933 SGD_REF:S000070309|PMID:12097146 IDA C YER114C|BEB1 gene taxon:4932 20020821 SGD
+SGD S000000916 BOI2 GO:0005935 SGD_REF:S000070309|PMID:12097146 IDA C YER114C|BEB1 gene taxon:4932 20020821 SGD
+SGD S000000916 BOI2 GO:0030427 SGD_REF:S000070309|PMID:12097146 IDA C YER114C|BEB1 gene taxon:4932 20020821 SGD
+SGD S000000916 BOI2 GO:0005543 SGD_REF:S000070309|PMID:12097146 ISS F YER114C|BEB1 gene taxon:4932 20021209 SGD
+SGD S000000916 BOI2 GO:0007266 SGD_REF:S000046605|PMID:10639324 IPI P YER114C|BEB1 gene taxon:4932 20010118 SGD
+SGD S000000916 BOI2 GO:0007266 SGD_REF:S000046605|PMID:10639324 IGI P YER114C|BEB1 gene taxon:4932 20010118 SGD
+SGD S000000916 BOI2 GO:0030468 SGD_REF:S000046605|PMID:10639324 IMP P YER114C|BEB1 gene taxon:4932 20010302 SGD
+SGD S000000916 BOI2 GO:0030468 SGD_REF:S000046605|PMID:10639324 IGI P YER114C|BEB1 gene taxon:4932 20010302 SGD
+SGD S000000916 BOI2 GO:0030468 SGD_REF:S000046605|PMID:10639324 IPI P YER114C|BEB1 gene taxon:4932 20010302 SGD
+SGD S000004257 BOP2 GO:0008372 SGD_REF:S000069584 ND C YLR267W gene taxon:4932 20021121 SGD
+SGD S000004257 BOP2 GO:0005554 SGD_REF:S000069584 ND F YLR267W gene taxon:4932 20021121 SGD
+SGD S000004257 BOP2 GO:0000004 SGD_REF:S000069584 ND P YLR267W gene taxon:4932 20021121 SGD
+SGD S000004987 BOP3 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YNL042W gene taxon:4932 20031028 SGD
+SGD S000004987 BOP3 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YNL042W gene taxon:4932 20031028 SGD
+SGD S000004987 BOP3 GO:0005554 SGD_REF:S000069584 ND F YNL042W gene taxon:4932 20021121 SGD
+SGD S000004987 BOP3 GO:0046689 SGD_REF:S000081267|PMID:15796894 IMP P YNL042W gene taxon:4932 20050415 SGD
+SGD S000005219 BOR1 GO:0005624 SGD_REF:S000061383|PMID:11401825 IDA C boron efflux transporter YNL275W gene taxon:4932 20030130 SGD
+SGD S000005219 BOR1 GO:0005886 SGD_REF:S000061383|PMID:11401825 IDA C boron efflux transporter YNL275W gene taxon:4932 20030130 SGD
+SGD S000005219 BOR1 GO:0005886 SGD_REF:S000080737|PMID:12447444 IDA C boron efflux transporter YNL275W gene taxon:4932 20050215 SGD
+SGD S000005219 BOR1 GO:0008509 SGD_REF:S000061383|PMID:11401825 IPI F boron efflux transporter YNL275W gene taxon:4932 20030130 SGD
+SGD S000005219 BOR1 GO:0008509 SGD_REF:S000061383|PMID:11401825 ISS F boron efflux transporter YNL275W gene taxon:4932 20030130 SGD
+SGD S000005219 BOR1 GO:0046714 SGD_REF:S000080737|PMID:12447444 IDA F boron efflux transporter YNL275W gene taxon:4932 20050215 SGD
+SGD S000005219 BOR1 GO:0046715 SGD_REF:S000080737|PMID:12447444 IMP F boron efflux transporter YNL275W gene taxon:4932 20050215 SGD
+SGD S000005219 BOR1 GO:0046715 SGD_REF:S000080737|PMID:12447444 ISS F boron efflux transporter YNL275W gene taxon:4932 20050215 SGD
+SGD S000005219 BOR1 GO:0006810 SGD_REF:S000061383|PMID:11401825 ISS P boron efflux transporter YNL275W gene taxon:4932 20030130 SGD
+SGD S000005219 BOR1 GO:0046713 SGD_REF:S000080737|PMID:12447444 IMP P boron efflux transporter YNL275W gene taxon:4932 20050215 SGD
+SGD S000005219 BOR1 GO:0046713 SGD_REF:S000080737|PMID:12447444 ISS P boron efflux transporter YNL275W gene taxon:4932 20050215 SGD
+SGD S000004068 BOS1 GO:0005789 SGD_REF:S000054988|PMID:8500167 IDA C v-SNARE YLR078C|SEC32 gene taxon:4932 20010118 SGD
+SGD S000004068 BOS1 GO:0005485 SGD_REF:S000041201|PMID:10547372 TAS F v-SNARE YLR078C|SEC32 gene taxon:4932 20010118 SGD
+SGD S000004068 BOS1 GO:0006888 SGD_REF:S000041201|PMID:10547372 TAS P v-SNARE YLR078C|SEC32 gene taxon:4932 20010118 SGD
+SGD S000000628 BPH1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YCR032W gene taxon:4932 20040813 SGD
+SGD S000000628 BPH1 GO:0005554 SGD_REF:S000069584 ND F YCR032W gene taxon:4932 20021003 SGD
+SGD S000000628 BPH1 GO:0007047 SGD_REF:S000077194|PMID:15296494 IMP P YCR032W gene taxon:4932 20041004 SGD
+SGD S000000628 BPH1 GO:0009268 SGD_REF:S000061751|PMID:9509574 IMP P YCR032W gene taxon:4932 20021003 SGD
+SGD S000002300 BPL1 GO:0005622 SGD_REF:S000059541|PMID:9847139 NAS C biotin:apoprotein ligase YDL141W|ACC2 gene taxon:4932 20010302 SGD
+SGD S000002300 BPL1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C biotin:apoprotein ligase YDL141W|ACC2 gene taxon:4932 20020507 SGD
+SGD S000002300 BPL1 GO:0004077 SGD_REF:S000047755|PMID:6108218 IMP F biotin:apoprotein ligase YDL141W|ACC2 gene taxon:4932 20010118 SGD
+SGD S000002300 BPL1 GO:0004077 SGD_REF:S000061900|PMID:10551847 IDA F biotin:apoprotein ligase YDL141W|ACC2 gene taxon:4932 20040519 SGD
+SGD S000002300 BPL1 GO:0004078 SGD_REF:S000059541|PMID:9847139 NAS F biotin:apoprotein ligase YDL141W|ACC2 gene taxon:4932 20010302 SGD
+SGD S000002300 BPL1 GO:0004079 SGD_REF:S000059541|PMID:9847139 NAS F biotin:apoprotein ligase YDL141W|ACC2 gene taxon:4932 20010302 SGD
+SGD S000002300 BPL1 GO:0004080 SGD_REF:S000059541|PMID:9847139 NAS F biotin:apoprotein ligase YDL141W|ACC2 gene taxon:4932 20010302 SGD
+SGD S000002300 BPL1 GO:0009305 SGD_REF:S000061900|PMID:10551847 IDA P biotin:apoprotein ligase YDL141W|ACC2 gene taxon:4932 20040519 SGD
+SGD S000003938 BPT1 GO:0000329 SGD_REF:S000071744|PMID:12455987 IDA C ABC transporter, highly homologous to human MRP1 and to C. elegans mrp-1 YLL015W gene taxon:4932 20030115 SGD
+SGD S000003938 BPT1 GO:0015086 SGD_REF:S000071744|PMID:12455987 IDA F ABC transporter, highly homologous to human MRP1 and to C. elegans mrp-1 YLL015W gene taxon:4932 20030115 SGD
+SGD S000003938 BPT1 GO:0015127 SGD_REF:S000041475|PMID:10790694 IMP F ABC transporter, highly homologous to human MRP1 and to C. elegans mrp-1 YLL015W gene taxon:4932 20010118 SGD
+SGD S000003938 BPT1 GO:0015127 SGD_REF:S000041475|PMID:10790694 IGI F ABC transporter, highly homologous to human MRP1 and to C. elegans mrp-1 YLL015W gene taxon:4932 20010118 SGD
+SGD S000003938 BPT1 GO:0015691 SGD_REF:S000071744|PMID:12455987 IDA P ABC transporter, highly homologous to human MRP1 and to C. elegans mrp-1 YLL015W gene taxon:4932 20030115 SGD
+SGD S000003938 BPT1 GO:0015723 SGD_REF:S000041475|PMID:10790694 IMP P ABC transporter, highly homologous to human MRP1 and to C. elegans mrp-1 YLL015W gene taxon:4932 20010118 SGD
+SGD S000003938 BPT1 GO:0015723 SGD_REF:S000041475|PMID:10790694 IGI P ABC transporter, highly homologous to human MRP1 and to C. elegans mrp-1 YLL015W gene taxon:4932 20010118 SGD
+SGD S000002232 BRE1 GO:0005634 SGD_REF:S000071811|PMID:12206772 IDA C YDL074C gene taxon:4932 20021210 SGD
+SGD S000002232 BRE1 GO:0004842 SGD_REF:S000072783|PMID:12535539 IMP F YDL074C gene taxon:4932 20030325 SGD
+SGD S000002232 BRE1 GO:0004842 SGD_REF:S000072664|PMID:12535538 ISS F YDL074C gene taxon:4932 20030519 SGD
+SGD S000002232 BRE1 GO:0004842 SGD_REF:S000072783|PMID:12535539 ISS F YDL074C gene taxon:4932 20030325 SGD
+SGD S000002232 BRE1 GO:0004842 SGD_REF:S000072783|PMID:12535539 IPI F YDL074C gene taxon:4932 20030325 SGD
+SGD S000002232 BRE1 GO:0004842 SGD_REF:S000072664|PMID:12535538 IMP F YDL074C gene taxon:4932 20030519 SGD
+SGD S000002232 BRE1 GO:0006348 SGD_REF:S000072783|PMID:12535539 IMP P YDL074C gene taxon:4932 20030325 SGD
+SGD S000002232 BRE1 GO:0006513 SGD_REF:S000072664|PMID:12535538 IMP P YDL074C gene taxon:4932 20030307 SGD
+SGD S000002232 BRE1 GO:0016571 SGD_REF:S000072664|PMID:12535538 IMP P YDL074C gene taxon:4932 20030307 SGD
+SGD S000002232 BRE1 GO:0016574 SGD_REF:S000072664|PMID:12535538 IMP P YDL074C gene taxon:4932 20030307 SGD
+SGD S000004005 BRE2 GO:0048188 SGD_REF:S000066156|PMID:11687631 IPI SGD:S000000064|SGD:S000001161|SGD:S000006059|SGD:S000001501|SGD:S000002877|SGD:S000000379 C compass (complex proteins associated with Set1p) component YLR015W|CPS60 gene taxon:4932 20050524 SGD
+SGD S000004005 BRE2 GO:0048188 SGD_REF:S000068991|PMID:11752412 IPI SGD:S000000064|SGD:S000000379|SGD:S000006059|SGD:S000001501|SGD:S000001161|SGD:S000002877 C compass (complex proteins associated with Set1p) component YLR015W|CPS60 gene taxon:4932 20050524 SGD
+SGD S000004005 BRE2 GO:0048188 SGD_REF:S000068755|PMID:11742990 IPI SGD:S000000064|SGD:S000000379|SGD:S000006059|SGD:S000001501|SGD:S000001161|SGD:S000002877|SGD:S000000462 C compass (complex proteins associated with Set1p) component YLR015W|CPS60 gene taxon:4932 20050524 SGD
+SGD S000004005 BRE2 GO:0030528 SGD_REF:S000061289|PMID:11169758 ISS F compass (complex proteins associated with Set1p) component YLR015W|CPS60 gene taxon:4932 20030402 SGD
+SGD S000004005 BRE2 contributes_to GO:0042800 SGD_REF:S000068991|PMID:11752412 IMP F compass (complex proteins associated with Set1p) component YLR015W|CPS60 gene taxon:4932 20050524 SGD
+SGD S000004005 BRE2 contributes_to GO:0042800 SGD_REF:S000068755|PMID:11742990 IDA F compass (complex proteins associated with Set1p) component YLR015W|CPS60 gene taxon:4932 20050525 SGD
+SGD S000004005 BRE2 contributes_to GO:0042800 SGD_REF:S000069538|PMID:11805083 IMP F compass (complex proteins associated with Set1p) component YLR015W|CPS60 gene taxon:4932 20050525 SGD
+SGD S000004005 BRE2 contributes_to GO:0042800 SGD_REF:S000069538|PMID:11805083 IDA F compass (complex proteins associated with Set1p) component YLR015W|CPS60 gene taxon:4932 20050525 SGD
+SGD S000004005 BRE2 GO:0000723 SGD_REF:S000068755|PMID:11742990 IMP P compass (complex proteins associated with Set1p) component YLR015W|CPS60 gene taxon:4932 20050525 SGD
+SGD S000004005 BRE2 GO:0006348 SGD_REF:S000066156|PMID:11687631 IMP P compass (complex proteins associated with Set1p) component YLR015W|CPS60 gene taxon:4932 20020212 SGD
+SGD S000004005 BRE2 GO:0006348 SGD_REF:S000069538|PMID:11805083 IMP P compass (complex proteins associated with Set1p) component YLR015W|CPS60 gene taxon:4932 20050525 SGD
+SGD S000004005 BRE2 GO:0006350 SGD_REF:S000061289|PMID:11169758 ISS P compass (complex proteins associated with Set1p) component YLR015W|CPS60 gene taxon:4932 20011018 SGD
+SGD S000004005 BRE2 GO:0016571 SGD_REF:S000068755|PMID:11742990 IDA P compass (complex proteins associated with Set1p) component YLR015W|CPS60 gene taxon:4932 20020212 SGD
+SGD S000004005 BRE2 GO:0016571 SGD_REF:S000069538|PMID:11805083 IMP P compass (complex proteins associated with Set1p) component YLR015W|CPS60 gene taxon:4932 20050525 SGD
+SGD S000004005 BRE2 GO:0016571 SGD_REF:S000068991|PMID:11752412 IDA P compass (complex proteins associated with Set1p) component YLR015W|CPS60 gene taxon:4932 20050524 SGD
+SGD S000004005 BRE2 GO:0016571 SGD_REF:S000069538|PMID:11805083 IDA P compass (complex proteins associated with Set1p) component YLR015W|CPS60 gene taxon:4932 20050525 SGD
+SGD S000004005 BRE2 GO:0016571 SGD_REF:S000068991|PMID:11752412 IMP P compass (complex proteins associated with Set1p) component YLR015W|CPS60 gene taxon:4932 20050524 SGD
+SGD S000002390 BRE4 GO:0016021 SGD_REF:S000061289|PMID:11169758 ISS C YDL231C gene taxon:4932 20011018 SGD
+SGD S000002390 BRE4 GO:0005554 SGD_REF:S000069584 ND F YDL231C gene taxon:4932 20030128 SGD
+SGD S000002390 BRE4 GO:0006897 SGD_REF:S000060817|PMID:11378903 IMP P YDL231C gene taxon:4932 20021004 SGD
+SGD S000005334 BRE5 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YNR051C gene taxon:4932 20031028 SGD
+SGD S000005334 BRE5 GO:0005554 SGD_REF:S000069584 ND F YNR051C gene taxon:4932 20011018 SGD
+SGD S000005334 BRE5 GO:0016579 SGD_REF:S000073727|PMID:12778054 IMP P YNR051C gene taxon:4932 20031229 SGD
+SGD S000003478 BRF1 GO:0000126 SGD_REF:S000058323|PMID:9585500 TAS C RNA polymerase III transcription factor, similar to TFIIB YGR246C|PCF4|TDS4|TFIIIB70 gene taxon:4932 20010118 SGD
+SGD S000003478 BRF1 GO:0003709 SGD_REF:S000058323|PMID:9585500 TAS F RNA polymerase III transcription factor, similar to TFIIB YGR246C|PCF4|TDS4|TFIIIB70 gene taxon:4932 20010118 SGD
+SGD S000003478 BRF1 GO:0006384 SGD_REF:S000058323|PMID:9585500 TAS P RNA polymerase III transcription factor, similar to TFIIB YGR246C|PCF4|TDS4|TFIIIB70 gene taxon:4932 20010118 SGD
+SGD S000001078 BRL1 GO:0005635 SGD_REF:S000082007|PMID:15882446 IDA C ER / nuclear envelope protein YHR036W gene taxon:4932 20050810 SGD
+SGD S000001078 BRL1 GO:0005783 SGD_REF:S000082007|PMID:15882446 IDA C ER / nuclear envelope protein YHR036W gene taxon:4932 20050810 SGD
+SGD S000001078 BRL1 GO:0005554 SGD_REF:S000069584 ND F ER / nuclear envelope protein YHR036W gene taxon:4932 20050810 SGD
+SGD S000001078 BRL1 GO:0006406 SGD_REF:S000082007|PMID:15882446 IMP P ER / nuclear envelope protein YHR036W gene taxon:4932 20050810 SGD
+SGD S000001078 BRL1 GO:0006611 SGD_REF:S000082007|PMID:15882446 IMP P ER / nuclear envelope protein YHR036W gene taxon:4932 20050810 SGD
+SGD S000001078 BRL1 GO:0006998 SGD_REF:S000082007|PMID:15882446 IMP P ER / nuclear envelope protein YHR036W gene taxon:4932 20050810 SGD
+SGD S000000193 BRN1 GO:0000799 SGD_REF:S000041579|PMID:10749931 IPI C YBL097W gene taxon:4932 20010118 SGD
+SGD S000000193 BRN1 GO:0000799 SGD_REF:S000046263|PMID:7698648 IPI C YBL097W gene taxon:4932 20010118 SGD
+SGD S000000193 BRN1 GO:0000799 SGD_REF:S000041579|PMID:10749931 ISS C YBL097W gene taxon:4932 20010118 SGD
+SGD S000000193 BRN1 GO:0000799 SGD_REF:S000046263|PMID:7698648 ISS C YBL097W gene taxon:4932 20010118 SGD
+SGD S000000193 BRN1 GO:0000799 SGD_REF:S000040443|PMID:10811823 TAS C YBL097W gene taxon:4932 20010118 SGD
+SGD S000000193 BRN1 GO:0005634 SGD_REF:S000041579|PMID:10749931 IDA C YBL097W gene taxon:4932 20010118 SGD
+SGD S000000193 BRN1 GO:0005554 SGD_REF:S000069584 ND F YBL097W gene taxon:4932 20010119 SGD
+SGD S000000193 BRN1 GO:0000070 SGD_REF:S000041579|PMID:10749931 IMP P YBL097W gene taxon:4932 20010118 SGD
+SGD S000000193 BRN1 GO:0007076 SGD_REF:S000040443|PMID:10811823 IMP P YBL097W gene taxon:4932 20010118 SGD
+SGD S000000193 BRN1 GO:0007076 SGD_REF:S000041579|PMID:10749931 IMP P YBL097W gene taxon:4932 20010118 SGD
+SGD S000000193 BRN1 GO:0007076 SGD_REF:S000041579|PMID:10749931 IGI P YBL097W gene taxon:4932 20010118 SGD
+SGD S000000193 BRN1 GO:0007076 SGD_REF:S000046263|PMID:7698648 IMP P YBL097W gene taxon:4932 20010118 SGD
+SGD S000006005 BRO1 GO:0005624 SGD_REF:S000076958|PMID:15326198 IDA C YPL084W|ASI6|LPF2|NPI3|VPS31 gene taxon:4932 20050107 SGD
+SGD S000006005 BRO1 GO:0005737 SGD_REF:S000073168|PMID:12668726 TAS C YPL084W|ASI6|LPF2|NPI3|VPS31 gene taxon:4932 20030528 SGD
+SGD S000006005 BRO1 GO:0005768 SGD_REF:S000073168|PMID:12668726 IDA C YPL084W|ASI6|LPF2|NPI3|VPS31 gene taxon:4932 20030528 SGD
+SGD S000006005 BRO1 GO:0005768 SGD_REF:S000082075|PMID:15935782 IDA C YPL084W|ASI6|LPF2|NPI3|VPS31 gene taxon:4932 20050715 SGD
+SGD S000006005 BRO1 GO:0005478 SGD_REF:S000073168|PMID:12668726 IDA F YPL084W|ASI6|LPF2|NPI3|VPS31 gene taxon:4932 20030528 SGD
+SGD S000006005 BRO1 GO:0005478 SGD_REF:S000073168|PMID:12668726 IMP F YPL084W|ASI6|LPF2|NPI3|VPS31 gene taxon:4932 20030528 SGD
+SGD S000006005 BRO1 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P YPL084W|ASI6|LPF2|NPI3|VPS31 gene taxon:4932 20060210 SGD
+SGD S000006005 BRO1 GO:0006511 SGD_REF:S000069978|PMID:12062418 IMP P YPL084W|ASI6|LPF2|NPI3|VPS31 gene taxon:4932 20021209 SGD
+SGD S000006005 BRO1 GO:0007034 SGD_REF:S000073168|PMID:12668726 IMP P YPL084W|ASI6|LPF2|NPI3|VPS31 gene taxon:4932 20030528 SGD
+SGD S000006005 BRO1 GO:0007034 SGD_REF:S000073168|PMID:12668726 TAS P YPL084W|ASI6|LPF2|NPI3|VPS31 gene taxon:4932 20030528 SGD
+SGD S000006005 BRO1 GO:0007165 SGD_REF:S000055289|PMID:8649366 IMP P YPL084W|ASI6|LPF2|NPI3|VPS31 gene taxon:4932 20010118 SGD
+SGD S000006005 BRO1 GO:0043328 SGD_REF:S000075331|PMID:14523026 IMP P YPL084W|ASI6|LPF2|NPI3|VPS31 gene taxon:4932 20051024 SGD
+SGD S000006261 BRR1 GO:0030532 SGD_REF:S000045536|PMID:8861964 IDA C spliceosomal snRNP component YPR057W gene taxon:4932 20021101 SGD
+SGD S000006261 BRR1 GO:0003723 SGD_REF:S000045536|PMID:8861964 IPI F spliceosomal snRNP component YPR057W gene taxon:4932 20021101 SGD
+SGD S000006261 BRR1 GO:0000245 SGD_REF:S000045536|PMID:8861964 IMP P spliceosomal snRNP component YPR057W gene taxon:4932 20021101 SGD
+SGD S000000974 BRR2 GO:0005682 SGD_REF:S000073846 TAS C DEIH-box ATPase YER172C|PRP44|RSS1|SLT22|SNU246 gene taxon:4932 20030825 SGD
+SGD S000000974 BRR2 GO:0005682 SGD_REF:S000066234|PMID:11720284 IPI C DEIH-box ATPase YER172C|PRP44|RSS1|SLT22|SNU246 gene taxon:4932 20051003 SGD
+SGD S000000974 BRR2 GO:0046540 SGD_REF:S000056376|PMID:10377396 IPI C DEIH-box ATPase YER172C|PRP44|RSS1|SLT22|SNU246 gene taxon:4932 20050219 SGD
+SGD S000000974 BRR2 GO:0046540 SGD_REF:S000039461|PMID:10449419 IDA C DEIH-box ATPase YER172C|PRP44|RSS1|SLT22|SNU246 gene taxon:4932 20050926 SGD
+SGD S000000974 BRR2 GO:0004004 SGD_REF:S000058281|PMID:9476892 TAS F DEIH-box ATPase YER172C|PRP44|RSS1|SLT22|SNU246 gene taxon:4932 20010118 SGD
+SGD S000000974 BRR2 GO:0031202 SGD_REF:S000058281|PMID:9476892 TAS F DEIH-box ATPase YER172C|PRP44|RSS1|SLT22|SNU246 gene taxon:4932 20010118 SGD
+SGD S000000974 BRR2 contributes_to GO:0031202 SGD_REF:S000039461|PMID:10449419 IDA F DEIH-box ATPase YER172C|PRP44|RSS1|SLT22|SNU246 gene taxon:4932 20051003 SGD
+SGD S000000974 BRR2 contributes_to GO:0031202 SGD_REF:S000056376|PMID:10377396 IPI F DEIH-box ATPase YER172C|PRP44|RSS1|SLT22|SNU246 gene taxon:4932 20051003 SGD
+SGD S000000974 BRR2 GO:0000396 SGD_REF:S000058281|PMID:9476892 TAS P DEIH-box ATPase YER172C|PRP44|RSS1|SLT22|SNU246 gene taxon:4932 20030825 SGD
+SGD S000000974 BRR2 GO:0000396 SGD_REF:S000073846 TAS P DEIH-box ATPase YER172C|PRP44|RSS1|SLT22|SNU246 gene taxon:4932 20030825 SGD
+SGD S000003216 BRR6 GO:0005635 SGD_REF:S000065919|PMID:11483521 IDA C nuclear envelope protein YGL247W gene taxon:4932 20020801 SGD
+SGD S000003216 BRR6 GO:0005554 SGD_REF:S000069584 ND F nuclear envelope protein YGL247W gene taxon:4932 20020801 SGD
+SGD S000003216 BRR6 GO:0006406 SGD_REF:S000065919|PMID:11483521 IMP P nuclear envelope protein YGL247W gene taxon:4932 20020801 SGD
+SGD S000003216 BRR6 GO:0006611 SGD_REF:S000065919|PMID:11483521 IMP P nuclear envelope protein YGL247W gene taxon:4932 20020801 SGD
+SGD S000003216 BRR6 GO:0006998 SGD_REF:S000065919|PMID:11483521 IMP P nuclear envelope protein YGL247W gene taxon:4932 20020801 SGD
+SGD S000005437 BRX1 GO:0005730 SGD_REF:S000069532|PMID:11864607 IPI C YOL077C gene taxon:4932 20020826 SGD
+SGD S000005437 BRX1 GO:0008097 SGD_REF:S000069545|PMID:11864606 IPI F YOL077C gene taxon:4932 20030219 SGD
+SGD S000005437 BRX1 GO:0042134 SGD_REF:S000069545|PMID:11864606 IPI F YOL077C gene taxon:4932 20030219 SGD
+SGD S000005437 BRX1 GO:0000027 SGD_REF:S000069532|PMID:11864607 IPI P YOL077C gene taxon:4932 20020826 SGD
+SGD S000002195 BSC1 GO:0008372 SGD_REF:S000069584 ND C YDL037C gene taxon:4932 20030513 SGD
+SGD S000002195 BSC1 GO:0005554 SGD_REF:S000069584 ND F YDL037C gene taxon:4932 20030513 SGD
+SGD S000002195 BSC1 GO:0000004 SGD_REF:S000069584 ND P YDL037C gene taxon:4932 20030513 SGD
+SGD S000002683 BSC2 GO:0005811 SGD_REF:S000074185|PMID:14562095 IDA C YDR275W gene taxon:4932 20031028 SGD
+SGD S000002683 BSC2 GO:0005554 SGD_REF:S000069584 ND F YDR275W gene taxon:4932 20030513 SGD
+SGD S000002683 BSC2 GO:0000004 SGD_REF:S000069584 ND P YDR275W gene taxon:4932 20030513 SGD
+SGD S000005213 BSC4 GO:0008372 SGD_REF:S000069584 ND C YNL269W gene taxon:4932 20030513 SGD
+SGD S000005213 BSC4 GO:0005554 SGD_REF:S000069584 ND F YNL269W gene taxon:4932 20030513 SGD
+SGD S000005213 BSC4 GO:0000004 SGD_REF:S000069584 ND P YNL269W gene taxon:4932 20030513 SGD
+SGD S000005352 BSC5 GO:0008372 SGD_REF:S000069584 ND C YNR069C gene taxon:4932 20030513 SGD
+SGD S000005352 BSC5 GO:0005554 SGD_REF:S000069584 ND F YNR069C gene taxon:4932 20030513 SGD
+SGD S000005352 BSC5 GO:0000004 SGD_REF:S000069584 ND P YNR069C gene taxon:4932 20030513 SGD
+SGD S000005497 BSC6 colocalizes_with GO:0030136 SGD_REF:S000074185|PMID:14562095 IDA C YOL137W gene taxon:4932 20031028 SGD
+SGD S000005497 BSC6 colocalizes_with GO:0030137 SGD_REF:S000074185|PMID:14562095 IDA C YOL137W gene taxon:4932 20031028 SGD
+SGD S000005497 BSC6 GO:0005554 SGD_REF:S000069584 ND F YOL137W gene taxon:4932 20030513 SGD
+SGD S000005497 BSC6 GO:0000004 SGD_REF:S000069584 ND P YOL137W gene taxon:4932 20030513 SGD
+SGD S000000494 BSD2 GO:0000329 SGD_REF:S000082212|PMID:14988731 IDA C YBR290W gene taxon:4932 20050715 SGD
+SGD S000000494 BSD2 GO:0005783 SGD_REF:S000053512|PMID:9115231 IDA C YBR290W gene taxon:4932 20020918 SGD
+SGD S000000494 BSD2 GO:0005515 SGD_REF:S000082212|PMID:14988731 IDA F YBR290W gene taxon:4932 20050715 SGD
+SGD S000000494 BSD2 GO:0005554 SGD_REF:S000069584 ND F YBR290W gene taxon:4932 20020918 SGD
+SGD S000000494 BSD2 GO:0006623 SGD_REF:S000041834|PMID:9988727 IMP P YBR290W gene taxon:4932 20020918 SGD
+SGD S000000494 BSD2 GO:0006623 SGD_REF:S000082212|PMID:14988731 IMP P YBR290W gene taxon:4932 20050715 SGD
+SGD S000000494 BSD2 GO:0030001 SGD_REF:S000053512|PMID:9115231 IMP P YBR290W gene taxon:4932 20030414 SGD
+SGD S000006375 BSP1 GO:0005624 SGD_REF:S000073043|PMID:12606027 IDA C YPR171W gene taxon:4932 20030429 SGD
+SGD S000006375 BSP1 GO:0005934 SGD_REF:S000073043|PMID:12606027 IDA C YPR171W gene taxon:4932 20030429 SGD
+SGD S000006375 BSP1 GO:0005935 SGD_REF:S000073043|PMID:12606027 IDA C YPR171W gene taxon:4932 20030429 SGD
+SGD S000006375 BSP1 GO:0030479 SGD_REF:S000073043|PMID:12606027 IDA C YPR171W gene taxon:4932 20030429 SGD
+SGD S000006375 BSP1 GO:0030674 SGD_REF:S000073043|PMID:12606027 IDA F YPR171W gene taxon:4932 20050425 SGD
+SGD S000006375 BSP1 GO:0048228 SGD_REF:S000073043|PMID:12606027 IMP P YPR171W gene taxon:4932 20060315 SGD
+SGD S000001869 BST1 GO:0005783 SGD_REF:S000044848|PMID:8862519 IDA C YFL025C gene taxon:4932 20010626 SGD
+SGD S000001869 BST1 GO:0016021 SGD_REF:S000044848|PMID:8862519 ISS C YFL025C gene taxon:4932 20010626 SGD
+SGD S000001869 BST1 GO:0016789 SGD_REF:S000076198|PMID:14734546 IGI protein_id:BAD08353 F YFL025C gene taxon:4932 20040805 SGD
+SGD S000001869 BST1 GO:0006505 SGD_REF:S000076198|PMID:14734546 IGI protein_id:BAD08353 P YFL025C gene taxon:4932 20040805 SGD
+SGD S000001869 BST1 GO:0006621 SGD_REF:S000044848|PMID:8862519 IMP P YFL025C gene taxon:4932 20050425 SGD
+SGD S000001869 BST1 GO:0006888 SGD_REF:S000044848|PMID:8862519 IMP P YFL025C gene taxon:4932 20050425 SGD
+SGD S000001869 BST1 GO:0016050 SGD_REF:S000044848|PMID:8862519 IMP P YFL025C gene taxon:4932 20010626 SGD
+SGD S000001869 BST1 GO:0016050 SGD_REF:S000044848|PMID:8862519 IGI P YFL025C gene taxon:4932 20010626 SGD
+SGD S000001869 BST1 GO:0030433 SGD_REF:S000071349|PMID:11673477 IMP P YFL025C gene taxon:4932 20020925 SGD
+SGD S000029062 BST3 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20010626 SGD
+SGD S000029062 BST3 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20010626 SGD
+SGD S000029062 BST3 GO:0006621 SGD_REF:S000044848|PMID:8862519 IMP P gene taxon:4932 20050425 SGD
+SGD S000029062 BST3 GO:0006888 SGD_REF:S000044848|PMID:8862519 IMP P gene taxon:4932 20050425 SGD
+SGD S000029062 BST3 GO:0016050 SGD_REF:S000044848|PMID:8862519 IMP P gene taxon:4932 20010626 SGD
+SGD S000029062 BST3 GO:0016050 SGD_REF:S000044848|PMID:8862519 IGI P gene taxon:4932 20010626 SGD
+SGD S000003374 BTN2 GO:0005829 SGD_REF:S000059219|PMID:11053386 IDA C YGR142W gene taxon:4932 20010206 SGD
+SGD S000003374 BTN2 GO:0005554 SGD_REF:S000069584 ND F YGR142W gene taxon:4932 20010119 SGD
+SGD S000003374 BTN2 GO:0006865 SGD_REF:S000080825|PMID:15701790 IMP P YGR142W gene taxon:4932 20050310 SGD
+SGD S000003374 BTN2 GO:0006885 SGD_REF:S000059219|PMID:11053386 IMP P YGR142W gene taxon:4932 20010206 SGD
+SGD S000003374 BTN2 GO:0006885 SGD_REF:S000059219|PMID:11053386 IGI P YGR142W gene taxon:4932 20010206 SGD
+SGD S000003374 BTN2 GO:0006885 SGD_REF:S000080825|PMID:15701790 IMP P YGR142W gene taxon:4932 20050310 SGD
+SGD S000003374 BTN2 GO:0006886 SGD_REF:S000072803|PMID:12615067 IMP P YGR142W gene taxon:4932 20030324 SGD
+SGD S000003374 BTN2 GO:0006886 SGD_REF:S000072803|PMID:12615067 IPI P YGR142W gene taxon:4932 20030324 SGD
+SGD S000005990 BTS1 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C EC 2.5.1.29, geranylgeranyl diphosphate synthase YPL069C gene taxon:4932 20031028 SGD
+SGD S000005990 BTS1 GO:0004311 SGD_REF:S000048587|PMID:7665600 IDA F EC 2.5.1.29, geranylgeranyl diphosphate synthase YPL069C gene taxon:4932 20020522 SGD
+SGD S000005990 BTS1 GO:0004311 SGD_REF:S000048587|PMID:7665600 ISS F EC 2.5.1.29, geranylgeranyl diphosphate synthase YPL069C gene taxon:4932 20020522 SGD
+SGD S000005990 BTS1 GO:0016114 SGD_REF:S000048587|PMID:7665600 IDA P EC 2.5.1.29, geranylgeranyl diphosphate synthase YPL069C gene taxon:4932 20020522 SGD
+SGD S000005990 BTS1 GO:0016114 SGD_REF:S000048587|PMID:7665600 IGI P EC 2.5.1.29, geranylgeranyl diphosphate synthase YPL069C gene taxon:4932 20020522 SGD
+SGD S000005990 BTS1 GO:0016114 SGD_REF:S000048587|PMID:7665600 IMP P EC 2.5.1.29, geranylgeranyl diphosphate synthase YPL069C gene taxon:4932 20020522 SGD
+SGD S000002660 BTT1 GO:0005830 SGD_REF:S000039338|PMID:9482879 IC GO:0005854 C YDR252W gene taxon:4932 20040408 SGD
+SGD S000002660 BTT1 GO:0005854 SGD_REF:S000056211|PMID:10219998 IDA C YDR252W gene taxon:4932 20010118 SGD
+SGD S000002660 BTT1 GO:0051082 SGD_REF:S000056211|PMID:10219998 IMP F YDR252W gene taxon:4932 20010327 SGD
+SGD S000002660 BTT1 GO:0051083 SGD_REF:S000056211|PMID:10219998 IPI P YDR252W gene taxon:4932 20010118 SGD
+SGD S000003420 BUB1 GO:0000776 SGD_REF:S000073469|PMID:12769845 IDA C YGR188C gene taxon:4932 20030725 SGD
+SGD S000003420 BUB1 GO:0000778 SGD_REF:S000071425|PMID:12221113 IDA C YGR188C gene taxon:4932 20021204 SGD
+SGD S000003420 BUB1 GO:0000780 SGD_REF:S000115004|PMID:16541024 IDA C YGR188C gene taxon:4932 20060525 SGD
+SGD S000003420 BUB1 GO:0005634 SGD_REF:S000051781|PMID:7969164 IDA C YGR188C gene taxon:4932 20010118 SGD
+SGD S000003420 BUB1 GO:0004672 SGD_REF:S000051781|PMID:7969164 IDA F YGR188C gene taxon:4932 20010118 SGD
+SGD S000003420 BUB1 GO:0005515 SGD_REF:S000073469|PMID:12769845 IPI SGD:S000002736 F YGR188C gene taxon:4932 20030725 SGD
+SGD S000003420 BUB1 GO:0006468 SGD_REF:S000051781|PMID:7969164 IDA P YGR188C gene taxon:4932 20030213 SGD
+SGD S000003420 BUB1 GO:0007094 SGD_REF:S000058279|PMID:9448456 TAS P YGR188C gene taxon:4932 20010118 SGD
+SGD S000004659 BUB2 GO:0005816 SGD_REF:S000040583|PMID:10352016 IDA C YMR055C|PAC7 gene taxon:4932 20010118 SGD
+SGD S000004659 BUB2 GO:0005816 SGD_REF:S000056361|PMID:10220406 IDA C YMR055C|PAC7 gene taxon:4932 20010118 SGD
+SGD S000004659 BUB2 GO:0005096 SGD_REF:S000071885|PMID:12432084 TAS F YMR055C|PAC7 gene taxon:4932 20030131 SGD
+SGD S000004659 BUB2 GO:0007096 SGD_REF:S000086185|PMID:16039591 TAS P YMR055C|PAC7 gene taxon:4932 20060314 SGD
+SGD S000004659 BUB2 GO:0031578 SGD_REF:S000086185|PMID:16039591 IGI P YMR055C|PAC7 gene taxon:4932 20060314 SGD
+SGD S000004659 BUB2 GO:0031578 SGD_REF:S000086185|PMID:16039591 IMP P YMR055C|PAC7 gene taxon:4932 20060314 SGD
+SGD S000005552 BUB3 GO:0000778 SGD_REF:S000071425|PMID:12221113 IPI C YOR026W gene taxon:4932 20021204 SGD
+SGD S000005552 BUB3 GO:0005554 SGD_REF:S000069584 ND F YOR026W gene taxon:4932 20021204 SGD
+SGD S000005552 BUB3 GO:0007094 SGD_REF:S000058279|PMID:9448456 TAS P YOR026W gene taxon:4932 20010118 SGD
+SGD S000003142 BUD13 GO:0005634 SGD_REF:S000061390|PMID:11452010 IDA C YGL174W|CWC26 gene taxon:4932 20021010 SGD
+SGD S000003142 BUD13 GO:0005554 SGD_REF:S000069584 ND F YGL174W|CWC26 gene taxon:4932 20020925 SGD
+SGD S000003142 BUD13 GO:0000282 SGD_REF:S000061390|PMID:11452010 IMP P YGL174W|CWC26 gene taxon:4932 20021010 SGD
+SGD S000003142 BUD13 GO:0000398 SGD_REF:S000080993|PMID:15565172 IDA P YGL174W|CWC26 gene taxon:4932 20051006 SGD
+SGD S000003142 BUD13 GO:0006406 SGD_REF:S000080993|PMID:15565172 IMP P YGL174W|CWC26 gene taxon:4932 20051006 SGD
+SGD S000000069 BUD14 GO:0000131 SGD_REF:S000061390|PMID:11452010 IDA C YAR014C gene taxon:4932 20021010 SGD
+SGD S000000069 BUD14 GO:0005934 SGD_REF:S000061390|PMID:11452010 IDA C YAR014C gene taxon:4932 20021010 SGD
+SGD S000000069 BUD14 GO:0005935 SGD_REF:S000061390|PMID:11452010 IDA C YAR014C gene taxon:4932 20021010 SGD
+SGD S000000069 BUD14 GO:0008599 SGD_REF:S000086411|PMID:16107882 IDA F YAR014C gene taxon:4932 20050926 SGD
+SGD S000000069 BUD14 GO:0008599 SGD_REF:S000086411|PMID:16107882 IPI F YAR014C gene taxon:4932 20050926 SGD
+SGD S000000069 BUD14 GO:0008599 SGD_REF:S000086411|PMID:16107882 IMP F YAR014C gene taxon:4932 20050926 SGD
+SGD S000000069 BUD14 GO:0000903 SGD_REF:S000071946|PMID:12477789 IGI P YAR014C gene taxon:4932 20030721 SGD
+SGD S000000069 BUD14 GO:0006355 SGD_REF:S000079965|PMID:15601868 IGI P YAR014C gene taxon:4932 20050926 SGD
+SGD S000000069 BUD14 GO:0006355 SGD_REF:S000079965|PMID:15601868 IMP P YAR014C gene taxon:4932 20050926 SGD
+SGD S000000069 BUD14 GO:0006355 SGD_REF:S000079965|PMID:15601868 IDA P YAR014C gene taxon:4932 20050926 SGD
+SGD S000000069 BUD14 GO:0007010 SGD_REF:S000086411|PMID:16107882 IGI P YAR014C gene taxon:4932 20050926 SGD
+SGD S000000069 BUD14 GO:0007010 SGD_REF:S000086411|PMID:16107882 IPI P YAR014C gene taxon:4932 20050926 SGD
+SGD S000000069 BUD14 GO:0007010 SGD_REF:S000086411|PMID:16107882 IMP P YAR014C gene taxon:4932 20050926 SGD
+SGD S000000755 BUD16 GO:0008372 SGD_REF:S000069584 ND C YEL029C gene taxon:4932 20051214 SGD
+SGD S000000755 BUD16 GO:0005554 SGD_REF:S000069584 ND F YEL029C gene taxon:4932 20020925 SGD
+SGD S000000755 BUD16 GO:0000282 SGD_REF:S000061390|PMID:11452010 IMP P YEL029C gene taxon:4932 20021010 SGD
+SGD S000000755 BUD16 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P YEL029C gene taxon:4932 20060202 SGD
+SGD S000005310 BUD17 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YNR027W gene taxon:4932 20031028 SGD
+SGD S000005310 BUD17 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YNR027W gene taxon:4932 20031028 SGD
+SGD S000005310 BUD17 GO:0005554 SGD_REF:S000069584 ND F YNR027W gene taxon:4932 20020925 SGD
+SGD S000005310 BUD17 GO:0000282 SGD_REF:S000061390|PMID:11452010 IMP P YNR027W gene taxon:4932 20021010 SGD
+SGD S000001575 BUD2 GO:0005622 SGD_REF:S000058399|PMID:9891811 TAS C GTPase activating protein (GAP) for Rsr1p/Bud1p YKL092C|CLA2|ERC25 gene taxon:4932 20010118 SGD
+SGD S000001575 BUD2 GO:0004871 SGD_REF:S000058399|PMID:9891811 TAS F GTPase activating protein (GAP) for Rsr1p/Bud1p YKL092C|CLA2|ERC25 gene taxon:4932 20010118 SGD
+SGD S000001575 BUD2 GO:0005096 SGD_REF:S000056175|PMID:8234337 TAS F GTPase activating protein (GAP) for Rsr1p/Bud1p YKL092C|CLA2|ERC25 gene taxon:4932 20010118 SGD
+SGD S000001575 BUD2 GO:0005096 SGD_REF:S000055049|PMID:8371782 TAS F GTPase activating protein (GAP) for Rsr1p/Bud1p YKL092C|CLA2|ERC25 gene taxon:4932 20010118 SGD
+SGD S000001575 BUD2 GO:0005099 SGD_REF:S000058399|PMID:9891811 TAS F GTPase activating protein (GAP) for Rsr1p/Bud1p YKL092C|CLA2|ERC25 gene taxon:4932 20010118 SGD
+SGD S000001575 BUD2 GO:0000282 SGD_REF:S000056175|PMID:8234337 TAS P GTPase activating protein (GAP) for Rsr1p/Bud1p YKL092C|CLA2|ERC25 gene taxon:4932 20010302 SGD
+SGD S000001575 BUD2 GO:0007120 SGD_REF:S000040385|PMID:2690082 TAS P GTPase activating protein (GAP) for Rsr1p/Bud1p YKL092C|CLA2|ERC25 gene taxon:4932 20010118 SGD
+SGD S000001575 BUD2 GO:0007120 SGD_REF:S000042162|PMID:2065354 TAS P GTPase activating protein (GAP) for Rsr1p/Bud1p YKL092C|CLA2|ERC25 gene taxon:4932 20010118 SGD
+SGD S000001575 BUD2 GO:0007121 SGD_REF:S000040385|PMID:2690082 TAS P GTPase activating protein (GAP) for Rsr1p/Bud1p YKL092C|CLA2|ERC25 gene taxon:4932 20010118 SGD
+SGD S000001575 BUD2 GO:0007121 SGD_REF:S000042162|PMID:2065354 TAS P GTPase activating protein (GAP) for Rsr1p/Bud1p YKL092C|CLA2|ERC25 gene taxon:4932 20010118 SGD
+SGD S000001575 BUD2 GO:0007264 SGD_REF:S000058399|PMID:9891811 TAS P GTPase activating protein (GAP) for Rsr1p/Bud1p YKL092C|CLA2|ERC25 gene taxon:4932 20010118 SGD
+SGD S000001575 BUD2 GO:0030447 SGD_REF:S000080384|PMID:15645503 IMP P GTPase activating protein (GAP) for Rsr1p/Bud1p YKL092C|CLA2|ERC25 gene taxon:4932 20050621 SGD
+SGD S000004064 BUD20 GO:0005634 SGD_REF:S000061390|PMID:11452010 IDA C YLR074C gene taxon:4932 20021010 SGD
+SGD S000004064 BUD20 GO:0005554 SGD_REF:S000069584 ND F YLR074C gene taxon:4932 20010213 SGD
+SGD S000004064 BUD20 GO:0000282 SGD_REF:S000061390|PMID:11452010 IMP P YLR074C gene taxon:4932 20021010 SGD
+SGD S000005604 BUD21 GO:0005732 SGD_REF:S000070145|PMID:12068309 IPI C U3 snoRNP protein YOR078W|UTP16|YOR29-29 gene taxon:4932 20030224 SGD
+SGD S000005604 BUD21 GO:0030515 SGD_REF:S000070145|PMID:12068309 IPI F U3 snoRNP protein YOR078W|UTP16|YOR29-29 gene taxon:4932 20030224 SGD
+SGD S000005604 BUD21 GO:0030490 SGD_REF:S000070145|PMID:12068309 IMP P U3 snoRNP protein YOR078W|UTP16|YOR29-29 gene taxon:4932 20020906 SGD
+SGD S000005604 BUD21 GO:0030490 SGD_REF:S000070145|PMID:12068309 IPI P U3 snoRNP protein YOR078W|UTP16|YOR29-29 gene taxon:4932 20020906 SGD
+SGD S000004616 BUD22 GO:0005634 SGD_REF:S000061390|PMID:11452010 IDA C YMR014W gene taxon:4932 20021010 SGD
+SGD S000004616 BUD22 GO:0005554 SGD_REF:S000069584 ND F YMR014W gene taxon:4932 20020925 SGD
+SGD S000004616 BUD22 GO:0000282 SGD_REF:S000061390|PMID:11452010 IMP P YMR014W gene taxon:4932 20021010 SGD
+SGD S000000643 BUD23 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YCR047C gene taxon:4932 20031028 SGD
+SGD S000000643 BUD23 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YCR047C gene taxon:4932 20031028 SGD
+SGD S000000643 BUD23 GO:0008757 SGD_REF:S000073093|PMID:9873020 ISS F YCR047C gene taxon:4932 20030507 SGD
+SGD S000000643 BUD23 GO:0000282 SGD_REF:S000061390|PMID:11452010 IMP P YCR047C gene taxon:4932 20021010 SGD
+SGD S000007590 BUD25 GO:0008372 SGD_REF:S000069584 ND C YER014C-A gene taxon:4932 20010302 SGD
+SGD S000007590 BUD25 GO:0005554 SGD_REF:S000069584 ND F YER014C-A gene taxon:4932 20010302 SGD
+SGD S000007590 BUD25 GO:0000282 SGD_REF:S000061390|PMID:11452010 IMP P YER014C-A gene taxon:4932 20021010 SGD
+SGD S000001871 BUD27 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YFL023W gene taxon:4932 20031028 SGD
+SGD S000001871 BUD27 GO:0005554 SGD_REF:S000069584 ND F YFL023W gene taxon:4932 20010314 SGD
+SGD S000001871 BUD27 GO:0000282 SGD_REF:S000061390|PMID:11452010 IMP P YFL023W gene taxon:4932 20021010 SGD
+SGD S000000520 BUD3 GO:0000142 SGD_REF:S000058399|PMID:9891811 TAS C YCL014W|YCL012W gene taxon:4932 20010118 SGD
+SGD S000000520 BUD3 GO:0005935 SGD_REF:S000074146|PMID:12972503 IDA C YCL014W|YCL012W gene taxon:4932 20050602 SGD
+SGD S000000520 BUD3 GO:0005554 SGD_REF:S000069584 ND F YCL014W|YCL012W gene taxon:4932 20010119 SGD
+SGD S000000520 BUD3 GO:0000282 SGD_REF:S000058399|PMID:9891811 TAS P YCL014W|YCL012W gene taxon:4932 20010302 SGD
+SGD S000000520 BUD3 GO:0000910 SGD_REF:S000058399|PMID:9891811 TAS P YCL014W|YCL012W gene taxon:4932 20010119 SGD
+SGD S000000520 BUD3 GO:0000910 SGD_REF:S000074146|PMID:12972503 IMP P YCL014W|YCL012W gene taxon:4932 20050602 SGD
+SGD S000000520 BUD3 GO:0007120 SGD_REF:S000058399|PMID:9891811 TAS P YCL014W|YCL012W gene taxon:4932 20010118 SGD
+SGD S000000659 BUD31 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YCR063W|CWC14 gene taxon:4932 20031028 SGD
+SGD S000000659 BUD31 GO:0005554 SGD_REF:S000069584 ND F YCR063W|CWC14 gene taxon:4932 20021010 SGD
+SGD S000000659 BUD31 GO:0000282 SGD_REF:S000061390|PMID:11452010 IMP P YCR063W|CWC14 gene taxon:4932 20021010 SGD
+SGD S000000659 BUD31 GO:0008380 SGD_REF:S000076833|PMID:15303280 IPI P YCR063W|CWC14 gene taxon:4932 20041031 SGD
+SGD S000003494 BUD32 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YGR262C|LDB14 gene taxon:4932 20031028 SGD
+SGD S000003494 BUD32 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YGR262C|LDB14 gene taxon:4932 20031028 SGD
+SGD S000003494 BUD32 GO:0004674 SGD_REF:S000056340|PMID:9305753 IDA F YGR262C|LDB14 gene taxon:4932 20021010 SGD
+SGD S000003494 BUD32 GO:0000282 SGD_REF:S000061390|PMID:11452010 IMP P YGR262C|LDB14 gene taxon:4932 20021010 SGD
+SGD S000003494 BUD32 GO:0006468 SGD_REF:S000056340|PMID:9305753 IDA P YGR262C|LDB14 gene taxon:4932 20021010 SGD
+SGD S000003852 BUD4 GO:0000142 SGD_REF:S000058399|PMID:9891811 TAS C YJR092W gene taxon:4932 20010118 SGD
+SGD S000003852 BUD4 GO:0005525 SGD_REF:S000046978|PMID:8707826 ISS F YJR092W gene taxon:4932 20021125 SGD
+SGD S000003852 BUD4 GO:0000282 SGD_REF:S000058399|PMID:9891811 TAS P YJR092W gene taxon:4932 20010302 SGD
+SGD S000003852 BUD4 GO:0007120 SGD_REF:S000058399|PMID:9891811 TAS P YJR092W gene taxon:4932 20010118 SGD
+SGD S000000634 BUD5 GO:0000131 SGD_REF:S000060338|PMID:11313501 IDA C GTP/GDP exchange factor for Rsr1 protein YCR038C gene taxon:4932 20030108 SGD
+SGD S000000634 BUD5 GO:0005935 SGD_REF:S000060338|PMID:11313501 IDA C GTP/GDP exchange factor for Rsr1 protein YCR038C gene taxon:4932 20030108 SGD
+SGD S000000634 BUD5 GO:0004871 SGD_REF:S000058399|PMID:9891811 TAS F GTP/GDP exchange factor for Rsr1 protein YCR038C gene taxon:4932 20010118 SGD
+SGD S000000634 BUD5 GO:0005085 SGD_REF:S000056175|PMID:8234337 TAS F GTP/GDP exchange factor for Rsr1 protein YCR038C gene taxon:4932 20010118 SGD
+SGD S000000634 BUD5 GO:0005085 SGD_REF:S000055049|PMID:8371782 TAS F GTP/GDP exchange factor for Rsr1 protein YCR038C gene taxon:4932 20010118 SGD
+SGD S000000634 BUD5 GO:0005088 SGD_REF:S000058399|PMID:9891811 TAS F GTP/GDP exchange factor for Rsr1 protein YCR038C gene taxon:4932 20010118 SGD
+SGD S000000634 BUD5 GO:0000282 SGD_REF:S000056175|PMID:8234337 TAS P GTP/GDP exchange factor for Rsr1 protein YCR038C gene taxon:4932 20010302 SGD
+SGD S000000634 BUD5 GO:0007120 SGD_REF:S000042162|PMID:2065354 TAS P GTP/GDP exchange factor for Rsr1 protein YCR038C gene taxon:4932 20010118 SGD
+SGD S000000634 BUD5 GO:0007120 SGD_REF:S000049760|PMID:1905981 TAS P GTP/GDP exchange factor for Rsr1 protein YCR038C gene taxon:4932 20010118 SGD
+SGD S000000634 BUD5 GO:0007120 SGD_REF:S000055049|PMID:8371782 TAS P GTP/GDP exchange factor for Rsr1 protein YCR038C gene taxon:4932 20010118 SGD
+SGD S000000634 BUD5 GO:0007121 SGD_REF:S000042162|PMID:2065354 TAS P GTP/GDP exchange factor for Rsr1 protein YCR038C gene taxon:4932 20010118 SGD
+SGD S000000634 BUD5 GO:0007121 SGD_REF:S000049760|PMID:1905981 TAS P GTP/GDP exchange factor for Rsr1 protein YCR038C gene taxon:4932 20010118 SGD
+SGD S000000634 BUD5 GO:0007121 SGD_REF:S000055049|PMID:8371782 TAS P GTP/GDP exchange factor for Rsr1 protein YCR038C gene taxon:4932 20010118 SGD
+SGD S000000634 BUD5 GO:0007124 SGD_REF:S000043647|PMID:9339344 TAS P GTP/GDP exchange factor for Rsr1 protein YCR038C gene taxon:4932 20010118 SGD
+SGD S000000634 BUD5 GO:0007264 SGD_REF:S000058399|PMID:9891811 TAS P GTP/GDP exchange factor for Rsr1 protein YCR038C gene taxon:4932 20010118 SGD
+SGD S000004311 BUD6 GO:0000133 SGD_REF:S000046605|PMID:10639324 TAS C YLR319C|AIP3 gene taxon:4932 20010118 SGD
+SGD S000004311 BUD6 GO:0030478 SGD_REF:S000041005|PMID:10652251 IDA C YLR319C|AIP3 gene taxon:4932 20010118 SGD
+SGD S000004311 BUD6 GO:0005519 SGD_REF:S000053007|PMID:9082982 IPI SGD:S000005215 F YLR319C|AIP3 gene taxon:4932 20050719 SGD
+SGD S000004311 BUD6 GO:0005519 SGD_REF:S000081831|PMID:15923184 IPI SGD:S000005215 F YLR319C|AIP3 gene taxon:4932 20050719 SGD
+SGD S000004311 BUD6 GO:0000282 SGD_REF:S000046605|PMID:10639324 IMP P YLR319C|AIP3 gene taxon:4932 20010302 SGD
+SGD S000004311 BUD6 GO:0000282 SGD_REF:S000046605|PMID:10639324 IPI P YLR319C|AIP3 gene taxon:4932 20010302 SGD
+SGD S000004311 BUD6 GO:0000910 SGD_REF:S000041005|PMID:10652251 TAS P YLR319C|AIP3 gene taxon:4932 20010119 SGD
+SGD S000004311 BUD6 GO:0006970 SGD_REF:S000041005|PMID:10652251 TAS P YLR319C|AIP3 gene taxon:4932 20010118 SGD
+SGD S000004311 BUD6 GO:0007015 SGD_REF:S000046605|PMID:10639324 IPI P YLR319C|AIP3 gene taxon:4932 20010118 SGD
+SGD S000004311 BUD6 GO:0007121 SGD_REF:S000041005|PMID:10652251 TAS P YLR319C|AIP3 gene taxon:4932 20010118 SGD
+SGD S000004311 BUD6 GO:0007266 SGD_REF:S000046605|PMID:10639324 IPI P YLR319C|AIP3 gene taxon:4932 20010118 SGD
+SGD S000004311 BUD6 GO:0030468 SGD_REF:S000046605|PMID:10639324 IMP P YLR319C|AIP3 gene taxon:4932 20010302 SGD
+SGD S000004311 BUD6 GO:0030468 SGD_REF:S000046605|PMID:10639324 IPI P YLR319C|AIP3 gene taxon:4932 20010302 SGD
+SGD S000005825 BUD7 colocalizes_with GO:0030136 SGD_REF:S000074185|PMID:14562095 IDA C YOR299W gene taxon:4932 20031028 SGD
+SGD S000005825 BUD7 colocalizes_with GO:0030140 SGD_REF:S000114540|PMID:16498409 IDA C YOR299W gene taxon:4932 20060531 SGD
+SGD S000005825 BUD7 GO:0005554 SGD_REF:S000069584 ND F YOR299W gene taxon:4932 20021001 SGD
+SGD S000005825 BUD7 GO:0000282 SGD_REF:S000054190|PMID:8657162 IMP P YOR299W gene taxon:4932 20020926 SGD
+SGD S000005825 BUD7 GO:0006038 SGD_REF:S000114540|PMID:16498409 IGI P YOR299W gene taxon:4932 20060609 SGD
+SGD S000005825 BUD7 GO:0006038 SGD_REF:S000114540|PMID:16498409 IPI SGD:S000000227 P YOR299W gene taxon:4932 20060609 SGD
+SGD S000005825 BUD7 GO:0006893 SGD_REF:S000114540|PMID:16498409 IGI SGD:S000004850 P YOR299W gene taxon:4932 20060531 SGD
+SGD S000004345 BUD8 GO:0000131 SGD_REF:S000061264|PMID:11514631 IDA C YLR353W gene taxon:4932 20021201 SGD
+SGD S000004345 BUD8 GO:0005934 SGD_REF:S000061264|PMID:11514631 IDA C YLR353W gene taxon:4932 20021201 SGD
+SGD S000004345 BUD8 GO:0005554 SGD_REF:S000069584 ND F YLR353W gene taxon:4932 20010119 SGD
+SGD S000004345 BUD8 GO:0000282 SGD_REF:S000054190|PMID:8657162 IMP P YLR353W gene taxon:4932 20020926 SGD
+SGD S000004345 BUD8 GO:0007124 SGD_REF:S000042772|PMID:9055077 IMP P YLR353W gene taxon:4932 20010118 SGD
+SGD S000003273 BUD9 GO:0005935 SGD_REF:S000061264|PMID:11514631 IDA C YGR041W gene taxon:4932 20021201 SGD
+SGD S000003273 BUD9 GO:0005554 SGD_REF:S000069584 ND F YGR041W gene taxon:4932 20010119 SGD
+SGD S000003273 BUD9 GO:0000282 SGD_REF:S000054190|PMID:8657162 IMP P YGR041W gene taxon:4932 20020926 SGD
+SGD S000002257 BUG1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDL099W gene taxon:4932 20031028 SGD
+SGD S000002257 BUG1 GO:0005554 SGD_REF:S000069584 ND F YDL099W gene taxon:4932 20030203 SGD
+SGD S000002257 BUG1 GO:0006888 SGD_REF:S000087084|PMID:16269340 IPI SGD:S000002216|SGD:S000002925 P YDL099W gene taxon:4932 20051111 SGD
+SGD S000004888 BUL1 GO:0000151 SGD_REF:S000060289|PMID:11352928 TAS C YMR275C|DAG1|RDS1|SMM2 gene taxon:4932 20041130 SGD
+SGD S000004888 BUL1 GO:0000151 SGD_REF:S000046442|PMID:9931424 IDA C YMR275C|DAG1|RDS1|SMM2 gene taxon:4932 20051009 SGD
+SGD S000004888 BUL1 GO:0005886 SGD_REF:S000041714|PMID:8668140 IPI C YMR275C|DAG1|RDS1|SMM2 gene taxon:4932 20010118 SGD
+SGD S000004888 BUL1 GO:0005515 SGD_REF:S000073661|PMID:12709439 TAS F YMR275C|DAG1|RDS1|SMM2 gene taxon:4932 20030730 SGD
+SGD S000004888 BUL1 GO:0005515 SGD_REF:S000046442|PMID:9931424 IDA F YMR275C|DAG1|RDS1|SMM2 gene taxon:4932 20051009 SGD
+SGD S000004888 BUL1 GO:0043130 SGD_REF:S000060289|PMID:11352928 TAS F YMR275C|DAG1|RDS1|SMM2 gene taxon:4932 20041130 SGD
+SGD S000004888 BUL1 GO:0000001 SGD_REF:S000053731|PMID:10366593 IGI P YMR275C|DAG1|RDS1|SMM2 gene taxon:4932 20010118 SGD
+SGD S000004888 BUL1 GO:0000209 SGD_REF:S000041714|PMID:8668140 IMP P YMR275C|DAG1|RDS1|SMM2 gene taxon:4932 20010118 SGD
+SGD S000004888 BUL1 GO:0000209 SGD_REF:S000041714|PMID:8668140 IPI P YMR275C|DAG1|RDS1|SMM2 gene taxon:4932 20010118 SGD
+SGD S000004888 BUL1 GO:0006513 SGD_REF:S000041714|PMID:8668140 IMP P YMR275C|DAG1|RDS1|SMM2 gene taxon:4932 20010118 SGD
+SGD S000004888 BUL1 GO:0006513 SGD_REF:S000041714|PMID:8668140 IPI P YMR275C|DAG1|RDS1|SMM2 gene taxon:4932 20010118 SGD
+SGD S000004579 BUL2 GO:0000151 SGD_REF:S000060289|PMID:11352928 IMP C YML111W gene taxon:4932 20051010 SGD
+SGD S000004579 BUL2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YML111W gene taxon:4932 20031028 SGD
+SGD S000004579 BUL2 GO:0005515 SGD_REF:S000046442|PMID:9931424 IGI F YML111W gene taxon:4932 20051009 SGD
+SGD S000004579 BUL2 GO:0005515 SGD_REF:S000046442|PMID:9931424 ISS F YML111W gene taxon:4932 20051009 SGD
+SGD S000004579 BUL2 GO:0000209 SGD_REF:S000046442|PMID:9931424 IMP P YML111W gene taxon:4932 20010118 SGD
+SGD S000004579 BUL2 GO:0000209 SGD_REF:S000046442|PMID:9931424 ISS P YML111W gene taxon:4932 20010118 SGD
+SGD S000004579 BUL2 GO:0006513 SGD_REF:S000046442|PMID:9931424 IMP P YML111W gene taxon:4932 20010118 SGD
+SGD S000004579 BUL2 GO:0006513 SGD_REF:S000046442|PMID:9931424 ISS P YML111W gene taxon:4932 20010118 SGD
+SGD S000004216 BUR2 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YLR226W|CST4 gene taxon:4932 20031028 SGD
+SGD S000004216 BUR2 GO:0016538 SGD_REF:S000053628|PMID:10982824 IDA F YLR226W|CST4 gene taxon:4932 20020930 SGD
+SGD S000004216 BUR2 GO:0016538 SGD_REF:S000053628|PMID:10982824 IPI F YLR226W|CST4 gene taxon:4932 20020930 SGD
+SGD S000004216 BUR2 GO:0016538 SGD_REF:S000053628|PMID:10982824 ISS F YLR226W|CST4 gene taxon:4932 20020930 SGD
+SGD S000004216 BUR2 GO:0000070 SGD_REF:S000052609|PMID:10454593 IGI P YLR226W|CST4 gene taxon:4932 20010118 SGD
+SGD S000004216 BUR2 GO:0006350 SGD_REF:S000053628|PMID:10982824 IDA P YLR226W|CST4 gene taxon:4932 20020930 SGD
+SGD S000004216 BUR2 GO:0006350 SGD_REF:S000053628|PMID:10982824 IMP P YLR226W|CST4 gene taxon:4932 20020930 SGD
+SGD S000004216 BUR2 GO:0006350 SGD_REF:S000053628|PMID:10982824 IPI P YLR226W|CST4 gene taxon:4932 20020930 SGD
+SGD S000004216 BUR2 GO:0006974 SGD_REF:S000076175|PMID:12482937 IMP P YLR226W|CST4 gene taxon:4932 20060406 SGD
+SGD S000000961 BUR6 GO:0005634 SGD_REF:S000051732|PMID:10713169 IPI C transcriptional regulator YER159C|NCB1 gene taxon:4932 20020918 SGD
+SGD S000000961 BUR6 GO:0003714 SGD_REF:S000051732|PMID:10713169 IGI F transcriptional regulator YER159C|NCB1 gene taxon:4932 20020918 SGD
+SGD S000000961 BUR6 GO:0003714 SGD_REF:S000051732|PMID:10713169 IMP F transcriptional regulator YER159C|NCB1 gene taxon:4932 20020918 SGD
+SGD S000000961 BUR6 GO:0000122 SGD_REF:S000051732|PMID:10713169 IGI P transcriptional regulator YER159C|NCB1 gene taxon:4932 20020918 SGD
+SGD S000000961 BUR6 GO:0000122 SGD_REF:S000051732|PMID:10713169 IMP P transcriptional regulator YER159C|NCB1 gene taxon:4932 20020918 SGD
+SGD S000001488 BYE1 GO:0005634 SGD_REF:S000075289|PMID:14704159 TAS C Negative regulator of transcription elongation YKL005C gene taxon:4932 20040113 SGD
+SGD S000001488 BYE1 GO:0003711 SGD_REF:S000075289|PMID:14704159 IGI F Negative regulator of transcription elongation YKL005C gene taxon:4932 20040113 SGD
+SGD S000001488 BYE1 GO:0000122 SGD_REF:S000075289|PMID:14704159 IGI P Negative regulator of transcription elongation YKL005C gene taxon:4932 20040113 SGD
+SGD S000001156 BZZ1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YHR114W|LSB7 gene taxon:4932 20020502 SGD
+SGD S000001156 BZZ1 GO:0030479 SGD_REF:S000071805|PMID:12391157 IDA C YHR114W|LSB7 gene taxon:4932 20021218 SGD
+SGD S000001156 BZZ1 GO:0005554 SGD_REF:S000069584 ND F YHR114W|LSB7 gene taxon:4932 20060315 SGD
+SGD S000001156 BZZ1 GO:0007015 SGD_REF:S000071805|PMID:12391157 IPI SGD:S000005707 P YHR114W|LSB7 gene taxon:4932 20021218 SGD
+SGD S000001156 BZZ1 GO:0009651 SGD_REF:S000071805|PMID:12391157 IGI SGD:S000004715 P YHR114W|LSB7 gene taxon:4932 20060315 SGD
+SGD S000001156 BZZ1 GO:0009651 SGD_REF:S000071805|PMID:12391157 IPI SGD:S000004715 P YHR114W|LSB7 gene taxon:4932 20060315 SGD
+SGD S000004570 CAC2 GO:0000775 SGD_REF:S000069112|PMID:11782447 IDA C chromatin assembly factor-I (CAF-I) p60 subunit YML102W gene taxon:4932 20030410 SGD
+SGD S000004570 CAC2 GO:0005678 SGD_REF:S000048516|PMID:9030687 IDA C chromatin assembly factor-I (CAF-I) p60 subunit YML102W gene taxon:4932 20020716 SGD
+SGD S000004570 CAC2 GO:0030528 SGD_REF:S000080322|PMID:15632066 IMP F chromatin assembly factor-I (CAF-I) p60 subunit YML102W gene taxon:4932 20050216 SGD
+SGD S000004570 CAC2 GO:0006281 SGD_REF:S000048516|PMID:9030687 IMP P chromatin assembly factor-I (CAF-I) p60 subunit YML102W gene taxon:4932 20020716 SGD
+SGD S000004570 CAC2 GO:0006334 SGD_REF:S000048516|PMID:9030687 IMP P chromatin assembly factor-I (CAF-I) p60 subunit YML102W gene taxon:4932 20020716 SGD
+SGD S000004570 CAC2 GO:0006342 SGD_REF:S000047698|PMID:9436982 IMP P chromatin assembly factor-I (CAF-I) p60 subunit YML102W gene taxon:4932 20020716 SGD
+SGD S000002831 CAD1 GO:0005634 SGD_REF:S000048602|PMID:9372930 IC GO:0003702 C basic leucine zipper transcription factor YDR423C|YAP2 gene taxon:4932 20021031 SGD
+SGD S000002831 CAD1 GO:0005634 SGD_REF:S000077186|PMID:15341652 IDA C basic leucine zipper transcription factor YDR423C|YAP2 gene taxon:4932 20050224 SGD
+SGD S000002831 CAD1 GO:0005737 SGD_REF:S000077186|PMID:15341652 IDA C basic leucine zipper transcription factor YDR423C|YAP2 gene taxon:4932 20050224 SGD
+SGD S000002831 CAD1 GO:0003702 SGD_REF:S000048602|PMID:9372930 IDA F basic leucine zipper transcription factor YDR423C|YAP2 gene taxon:4932 20021031 SGD
+SGD S000002831 CAD1 GO:0045944 SGD_REF:S000048602|PMID:9372930 IDA P basic leucine zipper transcription factor YDR423C|YAP2 gene taxon:4932 20021031 SGD
+SGD S000002831 CAD1 GO:0046686 SGD_REF:S000046513|PMID:8360174 IMP P basic leucine zipper transcription factor YDR423C|YAP2 gene taxon:4932 20021106 SGD
+SGD S000005222 CAF120 GO:0030014 SGD_REF:S000067484|PMID:11733989 IPI C YNL278W gene taxon:4932 20020808 SGD
+SGD S000005222 CAF120 GO:0005554 SGD_REF:S000069584 ND F YNL278W gene taxon:4932 20020808 SGD
+SGD S000005222 CAF120 GO:0006357 SGD_REF:S000067484|PMID:11733989 IPI P YNL278W gene taxon:4932 20020808 SGD
+SGD S000003366 CAF130 GO:0030014 SGD_REF:S000067484|PMID:11733989 IPI C YGR134W gene taxon:4932 20020808 SGD
+SGD S000003366 CAF130 GO:0005554 SGD_REF:S000069584 ND F YGR134W gene taxon:4932 20020808 SGD
+SGD S000003366 CAF130 GO:0006357 SGD_REF:S000067484|PMID:11733989 IPI P YGR134W gene taxon:4932 20020808 SGD
+SGD S000001866 CAF16 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C ABC ATPase YFL028C gene taxon:4932 20020507 SGD
+SGD S000001866 CAF16 GO:0030014 SGD_REF:S000061504|PMID:11113136 IPI C ABC ATPase YFL028C gene taxon:4932 20020522 SGD
+SGD S000001866 CAF16 GO:0016887 SGD_REF:S000044365|PMID:10581358 ISS F ABC ATPase YFL028C gene taxon:4932 20050726 SGD
+SGD S000001866 CAF16 GO:0006355 SGD_REF:S000061504|PMID:11113136 IMP P ABC ATPase YFL028C gene taxon:4932 20020522 SGD
+SGD S000001866 CAF16 GO:0006355 SGD_REF:S000061504|PMID:11113136 IPI P ABC ATPase YFL028C gene taxon:4932 20020522 SGD
+SGD S000003883 CAF17 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YJR122W gene taxon:4932 20031028 SGD
+SGD S000003883 CAF17 GO:0005554 SGD_REF:S000069584 ND F YJR122W gene taxon:4932 20020522 SGD
+SGD S000003883 CAF17 GO:0000004 SGD_REF:S000069584 ND P YJR122W gene taxon:4932 20020522 SGD
+SGD S000005802 CAF20 GO:0005845 SGD_REF:S000061947|PMID:9707439 IPI C 20 kDa protein, functional and limited sequence similarity to EAP1, functionally analogous to mammalian 4E-BPs YOR276W|CAF2|CAP20|p20 gene taxon:4932 20020724 SGD
+SGD S000005802 CAF20 GO:0045182 SGD_REF:S000061947|PMID:9707439 IGI F 20 kDa protein, functional and limited sequence similarity to EAP1, functionally analogous to mammalian 4E-BPs YOR276W|CAF2|CAP20|p20 gene taxon:4932 20021118 SGD
+SGD S000005802 CAF20 GO:0045182 SGD_REF:S000061947|PMID:9707439 IPI F 20 kDa protein, functional and limited sequence similarity to EAP1, functionally analogous to mammalian 4E-BPs YOR276W|CAF2|CAP20|p20 gene taxon:4932 20021118 SGD
+SGD S000005802 CAF20 GO:0016478 SGD_REF:S000044306|PMID:9144215 IGI P 20 kDa protein, functional and limited sequence similarity to EAP1, functionally analogous to mammalian 4E-BPs YOR276W|CAF2|CAP20|p20 gene taxon:4932 20020724 SGD
+SGD S000005802 CAF20 GO:0016478 SGD_REF:S000044306|PMID:9144215 IMP P 20 kDa protein, functional and limited sequence similarity to EAP1, functionally analogous to mammalian 4E-BPs YOR276W|CAF2|CAP20|p20 gene taxon:4932 20020724 SGD
+SGD S000001744 CAF4 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C CCR4 transcriptional complex component YKR036C gene taxon:4932 20040928 SGD
+SGD S000001744 CAF4 GO:0030014 SGD_REF:S000061504|PMID:11113136 IPI C CCR4 transcriptional complex component YKR036C gene taxon:4932 20020522 SGD
+SGD S000001744 CAF4 GO:0005515 SGD_REF:S000061504|PMID:11113136 ISS F CCR4 transcriptional complex component YKR036C gene taxon:4932 20020522 SGD
+SGD S000001744 CAF4 GO:0005515 SGD_REF:S000061504|PMID:11113136 IPI F CCR4 transcriptional complex component YKR036C gene taxon:4932 20020522 SGD
+SGD S000001744 CAF4 GO:0006355 SGD_REF:S000061504|PMID:11113136 IMP P CCR4 transcriptional complex component YKR036C gene taxon:4932 20020522 SGD
+SGD S000001744 CAF4 GO:0006355 SGD_REF:S000061504|PMID:11113136 IGI P CCR4 transcriptional complex component YKR036C gene taxon:4932 20020522 SGD
+SGD S000001744 CAF4 GO:0006355 SGD_REF:S000061504|PMID:11113136 IPI P CCR4 transcriptional complex component YKR036C gene taxon:4932 20020522 SGD
+SGD S000005232 CAF40 GO:0030014 SGD_REF:S000067484|PMID:11733989 IPI C YNL288W gene taxon:4932 20020808 SGD
+SGD S000005232 CAF40 GO:0005554 SGD_REF:S000069584 ND F YNL288W gene taxon:4932 20020808 SGD
+SGD S000005232 CAF40 GO:0006357 SGD_REF:S000067484|PMID:11733989 IPI P YNL288W gene taxon:4932 20020808 SGD
+SGD S000000850 CAJ1 GO:0005634 SGD_REF:S000076441|PMID:15170475 TAS C YER048C gene taxon:4932 20050107 SGD
+SGD S000000850 CAJ1 GO:0030188 SGD_REF:S000050769|PMID:8045411 ISS F YER048C gene taxon:4932 20021001 SGD
+SGD S000000850 CAJ1 GO:0000004 SGD_REF:S000069584 ND P YER048C gene taxon:4932 20021001 SGD
+SGD S000001865 CAK1 GO:0005737 SGD_REF:S000047254|PMID:9819350 IDA C cyclin-dependent kinase-activating kinase YFL029C|CIV1 gene taxon:4932 20020918 SGD
+SGD S000001865 CAK1 GO:0019912 SGD_REF:S000051770|PMID:8752210 IDA F cyclin-dependent kinase-activating kinase YFL029C|CIV1 gene taxon:4932 20051102 SGD
+SGD S000001865 CAK1 GO:0019912 SGD_REF:S000042721|PMID:8781234 IDA F cyclin-dependent kinase-activating kinase YFL029C|CIV1 gene taxon:4932 20051102 SGD
+SGD S000001865 CAK1 GO:0019912 SGD_REF:S000051771|PMID:8752211 IMP F cyclin-dependent kinase-activating kinase YFL029C|CIV1 gene taxon:4932 20051102 SGD
+SGD S000001865 CAK1 GO:0019912 SGD_REF:S000051889|PMID:10373527 IDA F cyclin-dependent kinase-activating kinase YFL029C|CIV1 gene taxon:4932 20051102 SGD
+SGD S000001865 CAK1 GO:0019912 SGD_REF:S000051889|PMID:10373527 IMP F cyclin-dependent kinase-activating kinase YFL029C|CIV1 gene taxon:4932 20051102 SGD
+SGD S000001865 CAK1 GO:0019912 SGD_REF:S000051771|PMID:8752211 IPI SGD:S000000364 F cyclin-dependent kinase-activating kinase YFL029C|CIV1 gene taxon:4932 20051102 SGD
+SGD S000001865 CAK1 GO:0019912 SGD_REF:S000051771|PMID:8752211 IDA F cyclin-dependent kinase-activating kinase YFL029C|CIV1 gene taxon:4932 20051102 SGD
+SGD S000001865 CAK1 GO:0019912 SGD_REF:S000042721|PMID:8781234 IMP F cyclin-dependent kinase-activating kinase YFL029C|CIV1 gene taxon:4932 20051102 SGD
+SGD S000001865 CAK1 GO:0019912 SGD_REF:S000051770|PMID:8752210 IMP F cyclin-dependent kinase-activating kinase YFL029C|CIV1 gene taxon:4932 20051102 SGD
+SGD S000001865 CAK1 GO:0000080 SGD_REF:S000051770|PMID:8752210 IMP P cyclin-dependent kinase-activating kinase YFL029C|CIV1 gene taxon:4932 20051102 SGD
+SGD S000001865 CAK1 GO:0000080 SGD_REF:S000051771|PMID:8752211 IMP P cyclin-dependent kinase-activating kinase YFL029C|CIV1 gene taxon:4932 20051102 SGD
+SGD S000001865 CAK1 GO:0000086 SGD_REF:S000051770|PMID:8752210 IMP P cyclin-dependent kinase-activating kinase YFL029C|CIV1 gene taxon:4932 20051102 SGD
+SGD S000001865 CAK1 GO:0000086 SGD_REF:S000051771|PMID:8752211 IMP P cyclin-dependent kinase-activating kinase YFL029C|CIV1 gene taxon:4932 20051102 SGD
+SGD S000001865 CAK1 GO:0006468 SGD_REF:S000051770|PMID:8752210 IDA P cyclin-dependent kinase-activating kinase YFL029C|CIV1 gene taxon:4932 20020918 SGD
+SGD S000001865 CAK1 GO:0006468 SGD_REF:S000051770|PMID:8752210 IMP P cyclin-dependent kinase-activating kinase YFL029C|CIV1 gene taxon:4932 20051102 SGD
+SGD S000001865 CAK1 GO:0006468 SGD_REF:S000042721|PMID:8781234 IDA P cyclin-dependent kinase-activating kinase YFL029C|CIV1 gene taxon:4932 20051102 SGD
+SGD S000001865 CAK1 GO:0006468 SGD_REF:S000051771|PMID:8752211 IMP P cyclin-dependent kinase-activating kinase YFL029C|CIV1 gene taxon:4932 20051102 SGD
+SGD S000001865 CAK1 GO:0006468 SGD_REF:S000051771|PMID:8752211 IDA P cyclin-dependent kinase-activating kinase YFL029C|CIV1 gene taxon:4932 20051102 SGD
+SGD S000001865 CAK1 GO:0006468 SGD_REF:S000042721|PMID:8781234 IMP P cyclin-dependent kinase-activating kinase YFL029C|CIV1 gene taxon:4932 20051102 SGD
+SGD S000001865 CAK1 GO:0007126 SGD_REF:S000069070|PMID:11739722 IGI P cyclin-dependent kinase-activating kinase YFL029C|CIV1 gene taxon:4932 20020918 SGD
+SGD S000001865 CAK1 GO:0007126 SGD_REF:S000069070|PMID:11739722 IMP P cyclin-dependent kinase-activating kinase YFL029C|CIV1 gene taxon:4932 20020918 SGD
+SGD S000005969 CAM1 GO:0005830 SGD_REF:S000045141|PMID:8041634 IGI C calcium and phospholipid binding protein homologous to translation elongation factor 1-gamma (EF-1gamma) YPL048W|EF-1 gamma|TEF3 gene taxon:4932 20020715 SGD
+SGD S000005969 CAM1 GO:0005830 SGD_REF:S000045141|PMID:8041634 ISS C calcium and phospholipid binding protein homologous to translation elongation factor 1-gamma (EF-1gamma) YPL048W|EF-1 gamma|TEF3 gene taxon:4932 20020715 SGD
+SGD S000005969 CAM1 GO:0003746 SGD_REF:S000045141|PMID:8041634 ISS F calcium and phospholipid binding protein homologous to translation elongation factor 1-gamma (EF-1gamma) YPL048W|EF-1 gamma|TEF3 gene taxon:4932 20020715 SGD
+SGD S000005969 CAM1 GO:0006448 SGD_REF:S000045141|PMID:8041634 IGI P calcium and phospholipid binding protein homologous to translation elongation factor 1-gamma (EF-1gamma) YPL048W|EF-1 gamma|TEF3 gene taxon:4932 20020715 SGD
+SGD S000005969 CAM1 GO:0006448 SGD_REF:S000045141|PMID:8041634 ISS P calcium and phospholipid binding protein homologous to translation elongation factor 1-gamma (EF-1gamma) YPL048W|EF-1 gamma|TEF3 gene taxon:4932 20020715 SGD
+SGD S000000789 CAN1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C arginine permease YEL063C gene taxon:4932 20040928 SGD
+SGD S000000789 CAN1 GO:0005886 SGD_REF:S000043244|PMID:10654085 ISS C arginine permease YEL063C gene taxon:4932 20020806 SGD
+SGD S000000789 CAN1 GO:0045121 SGD_REF:S000079755|PMID:15536122 IDA C arginine permease YEL063C gene taxon:4932 20041215 SGD
+SGD S000000789 CAN1 GO:0005288 SGD_REF:S000071670|PMID:12456008 TAS F arginine permease YEL063C gene taxon:4932 20021204 SGD
+SGD S000000789 CAN1 GO:0005293 SGD_REF:S000071670|PMID:12456008 TAS F arginine permease YEL063C gene taxon:4932 20021204 SGD
+SGD S000000789 CAN1 GO:0015174 SGD_REF:S000043244|PMID:10654085 IDA F arginine permease YEL063C gene taxon:4932 20020806 SGD
+SGD S000000789 CAN1 GO:0015802 SGD_REF:S000043244|PMID:10654085 IDA P arginine permease YEL063C gene taxon:4932 20020806 SGD
+SGD S000001490 CAP1 GO:0005884 SGD_REF:S000077157|PMID:14769858 IPI C capping protein YKL007W gene taxon:4932 20041001 SGD
+SGD S000001490 CAP1 GO:0008290 SGD_REF:S000077157|PMID:14769858 IGI C capping protein YKL007W gene taxon:4932 20040930 SGD
+SGD S000001490 CAP1 GO:0008290 SGD_REF:S000077157|PMID:14769858 IMP C capping protein YKL007W gene taxon:4932 20040930 SGD
+SGD S000001490 CAP1 GO:0008290 SGD_REF:S000077157|PMID:14769858 IDA C capping protein YKL007W gene taxon:4932 20040930 SGD
+SGD S000001490 CAP1 GO:0008290 SGD_REF:S000077157|PMID:14769858 ISS C capping protein YKL007W gene taxon:4932 20040930 SGD
+SGD S000001490 CAP1 GO:0008290 SGD_REF:S000077157|PMID:14769858 IPI C capping protein YKL007W gene taxon:4932 20040930 SGD
+SGD S000001490 CAP1 GO:0030479 SGD_REF:S000077157|PMID:14769858 IDA C capping protein YKL007W gene taxon:4932 20040930 SGD
+SGD S000001490 CAP1 GO:0051015 SGD_REF:S000077157|PMID:14769858 IGI F capping protein YKL007W gene taxon:4932 20041001 SGD
+SGD S000001490 CAP1 GO:0051015 SGD_REF:S000077157|PMID:14769858 IPI F capping protein YKL007W gene taxon:4932 20041001 SGD
+SGD S000001490 CAP1 GO:0051015 SGD_REF:S000077157|PMID:14769858 ISS F capping protein YKL007W gene taxon:4932 20041001 SGD
+SGD S000001490 CAP1 GO:0051015 SGD_REF:S000077157|PMID:14769858 IMP F capping protein YKL007W gene taxon:4932 20041001 SGD
+SGD S000001490 CAP1 GO:0051016 SGD_REF:S000077157|PMID:14769858 IDA P capping protein YKL007W gene taxon:4932 20041018 SGD
+SGD S000001296 CAP2 GO:0005884 SGD_REF:S000077157|PMID:14769858 IPI C capping protein beta subunit YIL034C gene taxon:4932 20041001 SGD
+SGD S000001296 CAP2 GO:0008290 SGD_REF:S000077157|PMID:14769858 IGI C capping protein beta subunit YIL034C gene taxon:4932 20040930 SGD
+SGD S000001296 CAP2 GO:0008290 SGD_REF:S000077157|PMID:14769858 IDA C capping protein beta subunit YIL034C gene taxon:4932 20040930 SGD
+SGD S000001296 CAP2 GO:0008290 SGD_REF:S000077157|PMID:14769858 IPI C capping protein beta subunit YIL034C gene taxon:4932 20040930 SGD
+SGD S000001296 CAP2 GO:0008290 SGD_REF:S000077157|PMID:14769858 ISS C capping protein beta subunit YIL034C gene taxon:4932 20040930 SGD
+SGD S000001296 CAP2 GO:0008290 SGD_REF:S000077157|PMID:14769858 IMP C capping protein beta subunit YIL034C gene taxon:4932 20040930 SGD
+SGD S000001296 CAP2 GO:0030479 SGD_REF:S000077157|PMID:14769858 IDA C capping protein beta subunit YIL034C gene taxon:4932 20040930 SGD
+SGD S000001296 CAP2 GO:0051015 SGD_REF:S000077157|PMID:14769858 IGI F capping protein beta subunit YIL034C gene taxon:4932 20041001 SGD
+SGD S000001296 CAP2 GO:0051015 SGD_REF:S000077157|PMID:14769858 ISS F capping protein beta subunit YIL034C gene taxon:4932 20041001 SGD
+SGD S000001296 CAP2 GO:0051015 SGD_REF:S000077157|PMID:14769858 IMP F capping protein beta subunit YIL034C gene taxon:4932 20041001 SGD
+SGD S000001296 CAP2 GO:0051015 SGD_REF:S000077157|PMID:14769858 IPI F capping protein beta subunit YIL034C gene taxon:4932 20041001 SGD
+SGD S000001296 CAP2 GO:0030447 SGD_REF:S000080384|PMID:15645503 IMP P capping protein beta subunit YIL034C gene taxon:4932 20050621 SGD
+SGD S000001296 CAP2 GO:0051016 SGD_REF:S000077157|PMID:14769858 IDA P capping protein beta subunit YIL034C gene taxon:4932 20041018 SGD
+SGD S000006032 CAR1 GO:0005829 SGD_REF:S000070200 TAS C arginase YPL111W|LPH15|cargA gene taxon:4932 20021105 SGD
+SGD S000006032 CAR1 GO:0004053 SGD_REF:S000052476|PMID:8816501 TAS F arginase YPL111W|LPH15|cargA gene taxon:4932 20030115 SGD
+SGD S000006032 CAR1 GO:0008270 SGD_REF:S000061971|PMID:1939179 IDA F arginase YPL111W|LPH15|cargA gene taxon:4932 20050914 SGD
+SGD S000006032 CAR1 GO:0030145 SGD_REF:S000061971|PMID:1939179 IDA F arginase YPL111W|LPH15|cargA gene taxon:4932 20050914 SGD
+SGD S000006032 CAR1 GO:0019547 SGD_REF:S000061758|PMID:10640599 TAS P arginase YPL111W|LPH15|cargA gene taxon:4932 20020927 SGD
+SGD S000004430 CAR2 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C ornithine aminotransferase YLR438W gene taxon:4932 20031028 SGD
+SGD S000004430 CAR2 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C ornithine aminotransferase YLR438W gene taxon:4932 20020507 SGD
+SGD S000004430 CAR2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C ornithine aminotransferase YLR438W gene taxon:4932 20031028 SGD
+SGD S000004430 CAR2 GO:0004587 SGD_REF:S000049560|PMID:10809695 TAS F ornithine aminotransferase YLR438W gene taxon:4932 20020927 SGD
+SGD S000004430 CAR2 GO:0006527 SGD_REF:S000049560|PMID:10809695 TAS P ornithine aminotransferase YLR438W gene taxon:4932 20020927 SGD
+SGD S000004506 CAT2 GO:0005739 SGD_REF:S000039668|PMID:7628448 ISS C carnitine O-acetyltransferase YML042W|YCAT gene taxon:4932 20010118 SGD
+SGD S000004506 CAT2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C carnitine O-acetyltransferase YML042W|YCAT gene taxon:4932 20040928 SGD
+SGD S000004506 CAT2 GO:0005777 SGD_REF:S000039668|PMID:7628448 ISS C carnitine O-acetyltransferase YML042W|YCAT gene taxon:4932 20010118 SGD
+SGD S000004506 CAT2 GO:0005782 SGD_REF:S000058494 TAS C carnitine O-acetyltransferase YML042W|YCAT gene taxon:4932 20010119 SGD
+SGD S000004506 CAT2 GO:0004092 SGD_REF:S000058474|PMID:8420957 IMP F carnitine O-acetyltransferase YML042W|YCAT gene taxon:4932 20010118 SGD
+SGD S000004506 CAT2 GO:0004092 SGD_REF:S000058474|PMID:8420957 ISS F carnitine O-acetyltransferase YML042W|YCAT gene taxon:4932 20010118 SGD
+SGD S000004506 CAT2 GO:0009437 SGD_REF:S000060344|PMID:11329169 IMP P carnitine O-acetyltransferase YML042W|YCAT gene taxon:4932 20021204 SGD
+SGD S000005651 CAT5 GO:0005743 SGD_REF:S000044605|PMID:9452453 TAS C may encode a protein involved in one or more monoxygenase or hydroxylase steps of ubiquinone biosynthesis YOR125C|COQ7 gene taxon:4932 20010118 SGD
+SGD S000005651 CAT5 GO:0005554 SGD_REF:S000069584 ND F may encode a protein involved in one or more monoxygenase or hydroxylase steps of ubiquinone biosynthesis YOR125C|COQ7 gene taxon:4932 20021114 SGD
+SGD S000005651 CAT5 GO:0006743 SGD_REF:S000044605|PMID:9452453 TAS P may encode a protein involved in one or more monoxygenase or hydroxylase steps of ubiquinone biosynthesis YOR125C|COQ7 gene taxon:4932 20010118 SGD
+SGD S000004893 CAT8 GO:0005634 SGD_REF:S000047272|PMID:9111319 IC GO:0003704 C zinc-cluster protein involved in activating gluconeogenic genes; related to Gal4p YMR280C|DIL1|MSP8 gene taxon:4932 20021112 SGD
+SGD S000004893 CAT8 GO:0003704 SGD_REF:S000047272|PMID:9111319 IDA F zinc-cluster protein involved in activating gluconeogenic genes; related to Gal4p YMR280C|DIL1|MSP8 gene taxon:4932 20021112 SGD
+SGD S000004893 CAT8 GO:0045722 SGD_REF:S000045582|PMID:7891685 IMP P zinc-cluster protein involved in activating gluconeogenic genes; related to Gal4p YMR280C|DIL1|MSP8 gene taxon:4932 20050525 SGD
+SGD S000004893 CAT8 GO:0045944 SGD_REF:S000047272|PMID:9111319 IDA P zinc-cluster protein involved in activating gluconeogenic genes; related to Gal4p YMR280C|DIL1|MSP8 gene taxon:4932 20021112 SGD
+SGD S000003268 CAX4 GO:0030176 SGD_REF:S000066176|PMID:11504728 IDA C contains 3 short stretches of amino acids that are characteristic for a wide variety of phosphatases, including lipid phosphatases and a protein phosphatase YGR036C|CWH8 gene taxon:4932 20020905 SGD
+SGD S000003268 CAX4 GO:0016462 SGD_REF:S000066176|PMID:11504728 IDA F contains 3 short stretches of amino acids that are characteristic for a wide variety of phosphatases, including lipid phosphatases and a protein phosphatase YGR036C|CWH8 gene taxon:4932 20020905 SGD
+SGD S000003268 CAX4 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P contains 3 short stretches of amino acids that are characteristic for a wide variety of phosphatases, including lipid phosphatases and a protein phosphatase YGR036C|CWH8 gene taxon:4932 20060209 SGD
+SGD S000003268 CAX4 GO:0006487 SGD_REF:S000055691|PMID:10024662 IMP P contains 3 short stretches of amino acids that are characteristic for a wide variety of phosphatases, including lipid phosphatases and a protein phosphatase YGR036C|CWH8 gene taxon:4932 20020905 SGD
+SGD S000003268 CAX4 GO:0008610 SGD_REF:S000066176|PMID:11504728 IGI P contains 3 short stretches of amino acids that are characteristic for a wide variety of phosphatases, including lipid phosphatases and a protein phosphatase YGR036C|CWH8 gene taxon:4932 20020905 SGD
+SGD S000003268 CAX4 GO:0008610 SGD_REF:S000066176|PMID:11504728 IMP P contains 3 short stretches of amino acids that are characteristic for a wide variety of phosphatases, including lipid phosphatases and a protein phosphatase YGR036C|CWH8 gene taxon:4932 20020905 SGD
+SGD S000006099 CBC2 GO:0000243 SGD_REF:S000056291|PMID:8682299 IDA C nuclear cap binding complex subunit YPL178W|CBP20|MUD13|SAE1 gene taxon:4932 20020730 SGD
+SGD S000006099 CBC2 GO:0005846 SGD_REF:S000057938|PMID:8811086 IDA C nuclear cap binding complex subunit YPL178W|CBP20|MUD13|SAE1 gene taxon:4932 20020730 SGD
+SGD S000006099 CBC2 GO:0000339 SGD_REF:S000056291|PMID:8682299 IDA F nuclear cap binding complex subunit YPL178W|CBP20|MUD13|SAE1 gene taxon:4932 20050226 SGD
+SGD S000006099 CBC2 GO:0000339 SGD_REF:S000056291|PMID:8682299 ISS F nuclear cap binding complex subunit YPL178W|CBP20|MUD13|SAE1 gene taxon:4932 20050226 SGD
+SGD S000006099 CBC2 GO:0000398 SGD_REF:S000056291|PMID:8682299 IMP P nuclear cap binding complex subunit YPL178W|CBP20|MUD13|SAE1 gene taxon:4932 20020730 SGD
+SGD S000003821 CBF1 GO:0000776 SGD_REF:S000073660|PMID:12756538 TAS C basic helix-loop-helix protein YJR060W|CEP1|CPF1 gene taxon:4932 20030731 SGD
+SGD S000003821 CBF1 GO:0005634 SGD_REF:S000069459|PMID:11914276 IDA C basic helix-loop-helix protein YJR060W|CEP1|CPF1 gene taxon:4932 20020507 SGD
+SGD S000003821 CBF1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C basic helix-loop-helix protein YJR060W|CEP1|CPF1 gene taxon:4932 20040928 SGD
+SGD S000003821 CBF1 GO:0003677 SGD_REF:S000059647|PMID:11222754 IDA F basic helix-loop-helix protein YJR060W|CEP1|CPF1 gene taxon:4932 20021104 SGD
+SGD S000003821 CBF1 GO:0019237 SGD_REF:S000059647|PMID:11222754 IDA F basic helix-loop-helix protein YJR060W|CEP1|CPF1 gene taxon:4932 20021104 SGD
+SGD S000003821 CBF1 GO:0006333 SGD_REF:S000059050|PMID:15111622 IDA P basic helix-loop-helix protein YJR060W|CEP1|CPF1 gene taxon:4932 20050104 SGD
+SGD S000003821 CBF1 GO:0007059 SGD_REF:S000039955|PMID:2185892 IMP P basic helix-loop-helix protein YJR060W|CEP1|CPF1 gene taxon:4932 20060130 SGD
+SGD S000003821 CBF1 GO:0009086 SGD_REF:S000039955|PMID:2185892 IMP P basic helix-loop-helix protein YJR060W|CEP1|CPF1 gene taxon:4932 20021104 SGD
+SGD S000003372 CBF2 GO:0000778 SGD_REF:S000046254|PMID:10097110 TAS C centromere binding factor CBF3 110 kDa subunit YGR140W|CBF3A|CEP2|CSL5|CTF14|NDC10 gene taxon:4932 20021017 SGD
+SGD S000003372 CBF2 GO:0000778 SGD_REF:S000051477|PMID:9407032 IDA C centromere binding factor CBF3 110 kDa subunit YGR140W|CBF3A|CEP2|CSL5|CTF14|NDC10 gene taxon:4932 20030403 SGD
+SGD S000003372 CBF2 GO:0005819 SGD_REF:S000113988|PMID:16381814 IDA C centromere binding factor CBF3 110 kDa subunit YGR140W|CBF3A|CEP2|CSL5|CTF14|NDC10 gene taxon:4932 20060111 SGD
+SGD S000003372 CBF2 GO:0031518 SGD_REF:S000056114|PMID:8682209 TAS C centromere binding factor CBF3 110 kDa subunit YGR140W|CBF3A|CEP2|CSL5|CTF14|NDC10 gene taxon:4932 20050722 SGD
+SGD S000003372 CBF2 GO:0051233 SGD_REF:S000078515|PMID:12566427 IDA C centromere binding factor CBF3 110 kDa subunit YGR140W|CBF3A|CEP2|CSL5|CTF14|NDC10 gene taxon:4932 20050407 SGD
+SGD S000003372 CBF2 GO:0008301 SGD_REF:S000046254|PMID:10097110 IDA F centromere binding factor CBF3 110 kDa subunit YGR140W|CBF3A|CEP2|CSL5|CTF14|NDC10 gene taxon:4932 20021017 SGD
+SGD S000003372 CBF2 GO:0019237 SGD_REF:S000051477|PMID:9407032 IDA F centromere binding factor CBF3 110 kDa subunit YGR140W|CBF3A|CEP2|CSL5|CTF14|NDC10 gene taxon:4932 20021003 SGD
+SGD S000003372 CBF2 GO:0000022 SGD_REF:S000113988|PMID:16381814 IMP P centromere binding factor CBF3 110 kDa subunit YGR140W|CBF3A|CEP2|CSL5|CTF14|NDC10 gene taxon:4932 20060111 SGD
+SGD S000003372 CBF2 GO:0007059 SGD_REF:S000054842|PMID:8486732 IMP P centromere binding factor CBF3 110 kDa subunit YGR140W|CBF3A|CEP2|CSL5|CTF14|NDC10 gene taxon:4932 20030110 SGD
+SGD S000004165 CBF5 GO:0005732 SGD_REF:S000048923|PMID:9472021 IPI C major low affinity 55 kDa centromere/microtubule binding protein YLR175W gene taxon:4932 20021203 SGD
+SGD S000004165 CBF5 GO:0004730 SGD_REF:S000058443|PMID:10690410 TAS F major low affinity 55 kDa centromere/microtubule binding protein YLR175W gene taxon:4932 20010118 SGD
+SGD S000004165 CBF5 GO:0000154 SGD_REF:S000058443|PMID:10690410 TAS P major low affinity 55 kDa centromere/microtubule binding protein YLR175W gene taxon:4932 20010118 SGD
+SGD S000004165 CBF5 GO:0006365 SGD_REF:S000058443|PMID:10690410 TAS P major low affinity 55 kDa centromere/microtubule binding protein YLR175W gene taxon:4932 20010118 SGD
+SGD S000005105 CBK1 GO:0005634 SGD_REF:S000070382|PMID:12196508 IDA C serine/threonine protein kinase YNL161W gene taxon:4932 20020930 SGD
+SGD S000005105 CBK1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C serine/threonine protein kinase YNL161W gene taxon:4932 20020507 SGD
+SGD S000005105 CBK1 GO:0005933 SGD_REF:S000070382|PMID:12196508 IDA C serine/threonine protein kinase YNL161W gene taxon:4932 20020930 SGD
+SGD S000005105 CBK1 GO:0005935 SGD_REF:S000070382|PMID:12196508 IDA C serine/threonine protein kinase YNL161W gene taxon:4932 20020930 SGD
+SGD S000005105 CBK1 GO:0043332 SGD_REF:S000074101|PMID:12972564 TAS C serine/threonine protein kinase YNL161W gene taxon:4932 20031016 SGD
+SGD S000005105 CBK1 GO:0004672 SGD_REF:S000053768|PMID:10411916 ISS F serine/threonine protein kinase YNL161W gene taxon:4932 20010118 SGD
+SGD S000005105 CBK1 GO:0000749 SGD_REF:S000053768|PMID:10411916 IDA P serine/threonine protein kinase YNL161W gene taxon:4932 20010118 SGD
+SGD S000005105 CBK1 GO:0000753 SGD_REF:S000053768|PMID:10411916 IDA P serine/threonine protein kinase YNL161W gene taxon:4932 20021206 SGD
+SGD S000005105 CBK1 GO:0000903 SGD_REF:S000074101|PMID:12972564 IGI P serine/threonine protein kinase YNL161W gene taxon:4932 20050420 SGD
+SGD S000005105 CBK1 GO:0007096 SGD_REF:S000070382|PMID:12196508 IMP P serine/threonine protein kinase YNL161W gene taxon:4932 20020930 SGD
+SGD S000005105 CBK1 GO:0030467 SGD_REF:S000070382|PMID:12196508 IMP P serine/threonine protein kinase YNL161W gene taxon:4932 20020930 SGD
+SGD S000003745 CBP1 GO:0005739 SGD_REF:S000046193|PMID:2104848 IDA C YJL209W gene taxon:4932 20020918 SGD
+SGD S000003745 CBP1 GO:0031314 SGD_REF:S000076558|PMID:15047869 IDA C YJL209W gene taxon:4932 20050801 SGD
+SGD S000003745 CBP1 GO:0003729 SGD_REF:S000054393|PMID:9343381 IGI F YJL209W gene taxon:4932 20020918 SGD
+SGD S000003745 CBP1 GO:0006402 SGD_REF:S000054393|PMID:9343381 IMP P YJL209W gene taxon:4932 20020918 SGD
+SGD S000003745 CBP1 GO:0009060 SGD_REF:S000054393|PMID:9343381 IMP P YJL209W gene taxon:4932 20020918 SGD
+SGD S000001030 CBP2 GO:0005739 SGD_REF:S000048319|PMID:2685564 IDA C YHL038C gene taxon:4932 20020804 SGD
+SGD S000001030 CBP2 GO:0031202 SGD_REF:S000051572|PMID:8524264 IDA F YHL038C gene taxon:4932 20020804 SGD
+SGD S000001030 CBP2 GO:0000372 SGD_REF:S000054517|PMID:9092668 IDA P YHL038C gene taxon:4932 20020804 SGD
+SGD S000006136 CBP3 GO:0005740 SGD_REF:S000057943|PMID:8811190 TAS C YPL215W gene taxon:4932 20010118 SGD
+SGD S000006136 CBP3 GO:0005554 SGD_REF:S000057943|PMID:8811190 TAS F YPL215W gene taxon:4932 20010118 SGD
+SGD S000006136 CBP3 GO:0006461 SGD_REF:S000057943|PMID:8811190 TAS P YPL215W gene taxon:4932 20010118 SGD
+SGD S000003406 CBP4 GO:0005740 SGD_REF:S000057943|PMID:8811190 TAS C YGR174C gene taxon:4932 20010118 SGD
+SGD S000003406 CBP4 GO:0005554 SGD_REF:S000057943|PMID:8811190 TAS F YGR174C gene taxon:4932 20010118 SGD
+SGD S000003406 CBP4 GO:0006461 SGD_REF:S000057943|PMID:8811190 TAS P YGR174C gene taxon:4932 20010118 SGD
+SGD S000000324 CBP6 GO:0005739 SGD_REF:S000057943|PMID:8811190 TAS C translational activator of COB mRNA YBR120C gene taxon:4932 20010118 SGD
+SGD S000000324 CBP6 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C translational activator of COB mRNA YBR120C gene taxon:4932 20040928 SGD
+SGD S000000324 CBP6 GO:0005554 SGD_REF:S000057943|PMID:8811190 TAS F translational activator of COB mRNA YBR120C gene taxon:4932 20010118 SGD
+SGD S000000324 CBP6 GO:0006412 SGD_REF:S000057943|PMID:8811190 TAS P translational activator of COB mRNA YBR120C gene taxon:4932 20010118 SGD
+SGD S000001305 CBR1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C cytochrome b reductase YIL043C|CBR5 gene taxon:4932 20040928 SGD
+SGD S000001305 CBR1 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C cytochrome b reductase YIL043C|CBR5 gene taxon:4932 20060317 SGD
+SGD S000001305 CBR1 GO:0005792 SGD_REF:S000062022|PMID:14930 IDA C cytochrome b reductase YIL043C|CBR5 gene taxon:4932 20021003 SGD
+SGD S000001305 CBR1 GO:0004128 SGD_REF:S000062022|PMID:14930 IDA F cytochrome b reductase YIL043C|CBR5 gene taxon:4932 20021003 SGD
+SGD S000001305 CBR1 GO:0006118 SGD_REF:S000062022|PMID:14930 IDA P cytochrome b reductase YIL043C|CBR5 gene taxon:4932 20021003 SGD
+SGD S000002227 CBS1 GO:0005743 SGD_REF:S000046988|PMID:9162108 TAS C translational activator of cytochrome B YDL069C gene taxon:4932 20010118 SGD
+SGD S000002227 CBS1 GO:0005761 SGD_REF:S000081814|PMID:15927884 IPI C translational activator of cytochrome B YDL069C gene taxon:4932 20050609 SGD
+SGD S000002227 CBS1 GO:0008135 SGD_REF:S000044739|PMID:7823946 IGI F translational activator of cytochrome B YDL069C gene taxon:4932 20021205 SGD
+SGD S000002227 CBS1 GO:0008135 SGD_REF:S000044739|PMID:7823946 IMP F translational activator of cytochrome B YDL069C gene taxon:4932 20021205 SGD
+SGD S000002227 CBS1 GO:0008135 SGD_REF:S000044739|PMID:7823946 IDA F translational activator of cytochrome B YDL069C gene taxon:4932 20021205 SGD
+SGD S000002227 CBS1 GO:0043037 SGD_REF:S000046988|PMID:9162108 TAS P translational activator of cytochrome B YDL069C gene taxon:4932 20010118 SGD
+SGD S000002605 CBS2 GO:0005743 SGD_REF:S000046988|PMID:9162108 TAS C cytochrome b translational activator YDR197W|CBP7 gene taxon:4932 20010118 SGD
+SGD S000002605 CBS2 GO:0005554 SGD_REF:S000046988|PMID:9162108 TAS F cytochrome b translational activator YDR197W|CBP7 gene taxon:4932 20010118 SGD
+SGD S000002605 CBS2 GO:0006412 SGD_REF:S000046988|PMID:9162108 TAS P cytochrome b translational activator YDR197W|CBP7 gene taxon:4932 20010118 SGD
+SGD S000001691 CBT1 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YKL208W|SOC1 gene taxon:4932 20031028 SGD
+SGD S000001691 CBT1 GO:0005554 SGD_REF:S000069584 ND F YKL208W|SOC1 gene taxon:4932 20021002 SGD
+SGD S000001691 CBT1 GO:0006397 SGD_REF:S000058221|PMID:9339340 IDA P YKL208W|SOC1 gene taxon:4932 20020927 SGD
+SGD S000001691 CBT1 GO:0006397 SGD_REF:S000058221|PMID:9339340 IMP P YKL208W|SOC1 gene taxon:4932 20020927 SGD
+SGD S000001691 CBT1 GO:0006397 SGD_REF:S000086295|PMID:16118200 IMP P YKL208W|SOC1 gene taxon:4932 20050909 SGD
+SGD S000001691 CBT1 GO:0017004 SGD_REF:S000058221|PMID:9339340 IDA P YKL208W|SOC1 gene taxon:4932 20020927 SGD
+SGD S000001691 CBT1 GO:0017004 SGD_REF:S000058221|PMID:9339340 IMP P YKL208W|SOC1 gene taxon:4932 20020927 SGD
+SGD S000001691 CBT1 GO:0048255 SGD_REF:S000086295|PMID:16118200 IMP P YKL208W|SOC1 gene taxon:4932 20050909 SGD
+SGD S000000970 CCA1 GO:0005634 SGD_REF:S000056592|PMID:1634528 NAS C tRNA nucleotidyltransferase (tRNA CCA-pyrophosphorylase) YER168C|TNT1 gene taxon:4932 20010118 SGD
+SGD S000000970 CCA1 GO:0005634 SGD_REF:S000050706|PMID:8175766 NAS C tRNA nucleotidyltransferase (tRNA CCA-pyrophosphorylase) YER168C|TNT1 gene taxon:4932 20010118 SGD
+SGD S000000970 CCA1 GO:0005634 SGD_REF:S000044248|PMID:8617732 NAS C tRNA nucleotidyltransferase (tRNA CCA-pyrophosphorylase) YER168C|TNT1 gene taxon:4932 20010118 SGD
+SGD S000000970 CCA1 GO:0005737 SGD_REF:S000056592|PMID:1634528 NAS C tRNA nucleotidyltransferase (tRNA CCA-pyrophosphorylase) YER168C|TNT1 gene taxon:4932 20010118 SGD
+SGD S000000970 CCA1 GO:0005737 SGD_REF:S000044248|PMID:8617732 NAS C tRNA nucleotidyltransferase (tRNA CCA-pyrophosphorylase) YER168C|TNT1 gene taxon:4932 20010118 SGD
+SGD S000000970 CCA1 GO:0005737 SGD_REF:S000050706|PMID:8175766 NAS C tRNA nucleotidyltransferase (tRNA CCA-pyrophosphorylase) YER168C|TNT1 gene taxon:4932 20010118 SGD
+SGD S000000970 CCA1 GO:0005759 SGD_REF:S000056592|PMID:1634528 IDA C tRNA nucleotidyltransferase (tRNA CCA-pyrophosphorylase) YER168C|TNT1 gene taxon:4932 20021202 SGD
+SGD S000000970 CCA1 GO:0004810 SGD_REF:S000056592|PMID:1634528 IDA F tRNA nucleotidyltransferase (tRNA CCA-pyrophosphorylase) YER168C|TNT1 gene taxon:4932 20021202 SGD
+SGD S000000970 CCA1 GO:0006400 SGD_REF:S000056592|PMID:1634528 IDA P tRNA nucleotidyltransferase (tRNA CCA-pyrophosphorylase) YER168C|TNT1 gene taxon:4932 20021202 SGD
+SGD S000004210 CCC1 GO:0000329 SGD_REF:S000061435|PMID:11390404 IDA C transmembrane Ca2+ transporter (putative) YLR220W gene taxon:4932 20050912 SGD
+SGD S000004210 CCC1 GO:0005624 SGD_REF:S000052533|PMID:7941738 ISS C transmembrane Ca2+ transporter (putative) YLR220W gene taxon:4932 20010608 SGD
+SGD S000004210 CCC1 GO:0005794 SGD_REF:S000051213|PMID:8866476 IDA C transmembrane Ca2+ transporter (putative) YLR220W gene taxon:4932 20010608 SGD
+SGD S000004210 CCC1 GO:0005384 SGD_REF:S000061435|PMID:11390404 IMP F transmembrane Ca2+ transporter (putative) YLR220W gene taxon:4932 20050912 SGD
+SGD S000004210 CCC1 GO:0015093 SGD_REF:S000061435|PMID:11390404 IMP F transmembrane Ca2+ transporter (putative) YLR220W gene taxon:4932 20050912 SGD
+SGD S000004210 CCC1 GO:0006874 SGD_REF:S000052533|PMID:7941738 IMP P transmembrane Ca2+ transporter (putative) YLR220W gene taxon:4932 20010608 SGD
+SGD S000004210 CCC1 GO:0006874 SGD_REF:S000052533|PMID:7941738 IGI P transmembrane Ca2+ transporter (putative) YLR220W gene taxon:4932 20010608 SGD
+SGD S000004210 CCC1 GO:0006879 SGD_REF:S000051167|PMID:10713071 IMP P transmembrane Ca2+ transporter (putative) YLR220W gene taxon:4932 20010608 SGD
+SGD S000004210 CCC1 GO:0006879 SGD_REF:S000051167|PMID:10713071 IGI P transmembrane Ca2+ transporter (putative) YLR220W gene taxon:4932 20010608 SGD
+SGD S000004210 CCC1 GO:0030026 SGD_REF:S000051213|PMID:8866476 IMP P transmembrane Ca2+ transporter (putative) YLR220W gene taxon:4932 20010611 SGD
+SGD S000004210 CCC1 GO:0030026 SGD_REF:S000051213|PMID:8866476 IGI P transmembrane Ca2+ transporter (putative) YLR220W gene taxon:4932 20010611 SGD
+SGD S000002678 CCC2 GO:0012510 SGD_REF:S000050925|PMID:9325307 IDA C YDR270W gene taxon:4932 20050720 SGD
+SGD S000002678 CCC2 GO:0019829 SGD_REF:S000039583|PMID:7708696 IMP F YDR270W gene taxon:4932 20050720 SGD
+SGD S000002678 CCC2 GO:0019829 SGD_REF:S000076726|PMID:15078884 IDA F YDR270W gene taxon:4932 20050720 SGD
+SGD S000002678 CCC2 GO:0006879 SGD_REF:S000039583|PMID:7708696 IMP P YDR270W gene taxon:4932 20050720 SGD
+SGD S000002678 CCC2 GO:0015680 SGD_REF:S000039583|PMID:7708696 IMP P YDR270W gene taxon:4932 20020905 SGD
+SGD S000001494 CCE1 GO:0005743 SGD_REF:S000040488|PMID:8413191 IDA C cruciform cutting endonuclease YKL011C|MGT1 gene taxon:4932 20021105 SGD
+SGD S000001494 CCE1 GO:0004520 SGD_REF:S000040488|PMID:8413191 IDA F cruciform cutting endonuclease YKL011C|MGT1 gene taxon:4932 20021105 SGD
+SGD S000001494 CCE1 GO:0006310 SGD_REF:S000070062|PMID:12024022 TAS P cruciform cutting endonuclease YKL011C|MGT1 gene taxon:4932 20020813 SGD
+SGD S000003449 CCH1 GO:0005886 SGD_REF:S000052677|PMID:10958666 IDA C calcium channel (putative) YGR217W gene taxon:4932 20021003 SGD
+SGD S000003449 CCH1 GO:0005262 SGD_REF:S000052677|PMID:10958666 IDA F calcium channel (putative) YGR217W gene taxon:4932 20021003 SGD
+SGD S000003449 CCH1 GO:0006816 SGD_REF:S000052677|PMID:10958666 IDA P calcium channel (putative) YGR217W gene taxon:4932 20021003 SGD
+SGD S000006229 CCL1 GO:0005675 SGD_REF:S000058446|PMID:9774381 TAS C TFIIK subunit, a subcomplex of transcription factor TFIIH, cyclin YPR025C gene taxon:4932 20010118 SGD
+SGD S000006229 CCL1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C TFIIK subunit, a subcomplex of transcription factor TFIIH, cyclin YPR025C gene taxon:4932 20040928 SGD
+SGD S000006229 CCL1 GO:0016251 SGD_REF:S000058446|PMID:9774381 TAS F TFIIK subunit, a subcomplex of transcription factor TFIIH, cyclin YPR025C gene taxon:4932 20010119 SGD
+SGD S000006229 CCL1 GO:0016538 SGD_REF:S000058446|PMID:9774381 TAS F TFIIK subunit, a subcomplex of transcription factor TFIIH, cyclin YPR025C gene taxon:4932 20020208 SGD
+SGD S000006229 CCL1 GO:0006367 SGD_REF:S000056378|PMID:10384286 TAS P TFIIK subunit, a subcomplex of transcription factor TFIIH, cyclin YPR025C gene taxon:4932 20010118 SGD
+SGD S000006229 CCL1 GO:0006367 SGD_REF:S000056377|PMID:10384273 TAS P TFIIK subunit, a subcomplex of transcription factor TFIIH, cyclin YPR025C gene taxon:4932 20010118 SGD
+SGD S000006229 CCL1 GO:0007070 SGD_REF:S000056377|PMID:10384273 TAS P TFIIK subunit, a subcomplex of transcription factor TFIIH, cyclin YPR025C gene taxon:4932 20010118 SGD
+SGD S000001774 CCP1 GO:0005739 SGD_REF:S000069459|PMID:11914276 IDA C cytochrome c peroxidase YKR066C gene taxon:4932 20020507 SGD
+SGD S000001774 CCP1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C cytochrome c peroxidase YKR066C gene taxon:4932 20040924 SGD
+SGD S000001774 CCP1 GO:0005758 SGD_REF:S000071826|PMID:12417197 TAS C cytochrome c peroxidase YKR066C gene taxon:4932 20021212 SGD
+SGD S000001774 CCP1 GO:0005758 SGD_REF:S000062048|PMID:6290489 IDA C cytochrome c peroxidase YKR066C gene taxon:4932 20041005 SGD
+SGD S000001774 CCP1 GO:0004130 SGD_REF:S000043279|PMID:10589830 IMP F cytochrome c peroxidase YKR066C gene taxon:4932 20030115 SGD
+SGD S000001774 CCP1 GO:0006979 SGD_REF:S000043279|PMID:10589830 IMP P cytochrome c peroxidase YKR066C gene taxon:4932 20020927 SGD
+SGD S000000019 CCR4 GO:0005737 SGD_REF:S000069437|PMID:11889048 IDA C YAL021C|FUN27|NUT21 gene taxon:4932 20020802 SGD
+SGD S000000019 CCR4 GO:0016593 SGD_REF:S000041293|PMID:9891041 IPI SGD:S000004410 C YAL021C|FUN27|NUT21 gene taxon:4932 20051108 SGD
+SGD S000000019 CCR4 GO:0030015 SGD_REF:S000042122|PMID:10490603 IPI C YAL021C|FUN27|NUT21 gene taxon:4932 20020802 SGD
+SGD S000000019 CCR4 GO:0000175 SGD_REF:S000069437|PMID:11889048 TAS F YAL021C|FUN27|NUT21 gene taxon:4932 20030922 SGD
+SGD S000000019 CCR4 GO:0000288 SGD_REF:S000069437|PMID:11889048 IGI P YAL021C|FUN27|NUT21 gene taxon:4932 20030922 SGD
+SGD S000000019 CCR4 GO:0000288 SGD_REF:S000069437|PMID:11889048 IDA P YAL021C|FUN27|NUT21 gene taxon:4932 20030922 SGD
+SGD S000000019 CCR4 GO:0000288 SGD_REF:S000069437|PMID:11889048 IMP P YAL021C|FUN27|NUT21 gene taxon:4932 20030922 SGD
+SGD S000000019 CCR4 GO:0000289 SGD_REF:S000069437|PMID:11889048 IDA P YAL021C|FUN27|NUT21 gene taxon:4932 20020802 SGD
+SGD S000000019 CCR4 GO:0000289 SGD_REF:S000073816|PMID:11410650 IMP P YAL021C|FUN27|NUT21 gene taxon:4932 20030818 SGD
+SGD S000000019 CCR4 GO:0006357 SGD_REF:S000042122|PMID:10490603 IPI P YAL021C|FUN27|NUT21 gene taxon:4932 20020802 SGD
+SGD S000000019 CCR4 GO:0007089 SGD_REF:S000076054|PMID:15075273 IMP P YAL021C|FUN27|NUT21 gene taxon:4932 20040526 SGD
+SGD S000004641 CCS1 GO:0005743 SGD_REF:S000068943|PMID:11500508 IDA C copper chaperone YMR038C|CCS|LYS7 gene taxon:4932 20040304 SGD
+SGD S000004641 CCS1 GO:0005829 SGD_REF:S000050869|PMID:9295278 IDA C copper chaperone YMR038C|CCS|LYS7 gene taxon:4932 20020919 SGD
+SGD S000004641 CCS1 GO:0016532 SGD_REF:S000050869|PMID:9295278 IGI F copper chaperone YMR038C|CCS|LYS7 gene taxon:4932 20020919 SGD
+SGD S000004641 CCS1 GO:0016532 SGD_REF:S000050869|PMID:9295278 IMP F copper chaperone YMR038C|CCS|LYS7 gene taxon:4932 20020919 SGD
+SGD S000004641 CCS1 GO:0016532 SGD_REF:S000050869|PMID:9295278 ISS F copper chaperone YMR038C|CCS|LYS7 gene taxon:4932 20020919 SGD
+SGD S000004641 CCS1 GO:0015680 SGD_REF:S000050869|PMID:9295278 ISS P copper chaperone YMR038C|CCS|LYS7 gene taxon:4932 20020919 SGD
+SGD S000004641 CCS1 GO:0015680 SGD_REF:S000050869|PMID:9295278 IMP P copper chaperone YMR038C|CCS|LYS7 gene taxon:4932 20020919 SGD
+SGD S000001404 CCT2 GO:0005737 SGD_REF:S000042209|PMID:8771707 TAS C YIL142W|BIN3|TCP2 gene taxon:4932 20010118 SGD
+SGD S000001404 CCT2 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YIL142W|BIN3|TCP2 gene taxon:4932 20020507 SGD
+SGD S000001404 CCT2 GO:0005832 SGD_REF:S000042209|PMID:8771707 TAS C YIL142W|BIN3|TCP2 gene taxon:4932 20031215 SGD
+SGD S000001404 CCT2 GO:0005832 SGD_REF:S000080727|PMID:15704212 IPI SGD:S000002596 C YIL142W|BIN3|TCP2 gene taxon:4932 20050307 SGD
+SGD S000001404 CCT2 GO:0005856 SGD_REF:S000042209|PMID:8771707 TAS C YIL142W|BIN3|TCP2 gene taxon:4932 20010118 SGD
+SGD S000001404 CCT2 GO:0051082 SGD_REF:S000042209|PMID:8771707 TAS F YIL142W|BIN3|TCP2 gene taxon:4932 20010118 SGD
+SGD S000001404 CCT2 GO:0006457 SGD_REF:S000042209|PMID:8771707 TAS P YIL142W|BIN3|TCP2 gene taxon:4932 20010118 SGD
+SGD S000001404 CCT2 GO:0007010 SGD_REF:S000042209|PMID:8771707 TAS P YIL142W|BIN3|TCP2 gene taxon:4932 20010118 SGD
+SGD S000003551 CCT3 GO:0005737 SGD_REF:S000042209|PMID:8771707 TAS C gamma chaperonin subunit YJL014W|BIN2|TCP3 gene taxon:4932 20010118 SGD
+SGD S000003551 CCT3 GO:0005832 SGD_REF:S000042209|PMID:8771707 TAS C gamma chaperonin subunit YJL014W|BIN2|TCP3 gene taxon:4932 20031215 SGD
+SGD S000003551 CCT3 GO:0005832 SGD_REF:S000080727|PMID:15704212 IPI SGD:S000002596 C gamma chaperonin subunit YJL014W|BIN2|TCP3 gene taxon:4932 20050307 SGD
+SGD S000003551 CCT3 GO:0005856 SGD_REF:S000042209|PMID:8771707 TAS C gamma chaperonin subunit YJL014W|BIN2|TCP3 gene taxon:4932 20010118 SGD
+SGD S000003551 CCT3 GO:0051082 SGD_REF:S000042209|PMID:8771707 TAS F gamma chaperonin subunit YJL014W|BIN2|TCP3 gene taxon:4932 20010118 SGD
+SGD S000003551 CCT3 GO:0006457 SGD_REF:S000042209|PMID:8771707 TAS P gamma chaperonin subunit YJL014W|BIN2|TCP3 gene taxon:4932 20010118 SGD
+SGD S000003551 CCT3 GO:0007010 SGD_REF:S000042209|PMID:8771707 TAS P gamma chaperonin subunit YJL014W|BIN2|TCP3 gene taxon:4932 20010118 SGD
+SGD S000002302 CCT4 GO:0005737 SGD_REF:S000042209|PMID:8771707 TAS C YDL143W|TCP4 gene taxon:4932 20010118 SGD
+SGD S000002302 CCT4 GO:0005832 SGD_REF:S000073234|PMID:12697815 TAS C YDL143W|TCP4 gene taxon:4932 20030619 SGD
+SGD S000002302 CCT4 GO:0005832 SGD_REF:S000042209|PMID:8771707 TAS C YDL143W|TCP4 gene taxon:4932 20031215 SGD
+SGD S000002302 CCT4 GO:0005832 SGD_REF:S000080727|PMID:15704212 IPI SGD:S000002596 C YDL143W|TCP4 gene taxon:4932 20050307 SGD
+SGD S000002302 CCT4 GO:0005856 SGD_REF:S000042209|PMID:8771707 TAS C YDL143W|TCP4 gene taxon:4932 20010118 SGD
+SGD S000002302 CCT4 GO:0051082 SGD_REF:S000042209|PMID:8771707 TAS F YDL143W|TCP4 gene taxon:4932 20010118 SGD
+SGD S000002302 CCT4 GO:0006457 SGD_REF:S000042209|PMID:8771707 TAS P YDL143W|TCP4 gene taxon:4932 20010118 SGD
+SGD S000002302 CCT4 GO:0007010 SGD_REF:S000042209|PMID:8771707 TAS P YDL143W|TCP4 gene taxon:4932 20010118 SGD
+SGD S000003825 CCT5 GO:0005737 SGD_REF:S000042209|PMID:8771707 TAS C chaperonin subunit epsilon subunit YJR064W|TCP5 gene taxon:4932 20010118 SGD
+SGD S000003825 CCT5 GO:0005832 SGD_REF:S000042209|PMID:8771707 TAS C chaperonin subunit epsilon subunit YJR064W|TCP5 gene taxon:4932 20031215 SGD
+SGD S000003825 CCT5 GO:0005832 SGD_REF:S000080727|PMID:15704212 IPI SGD:S000002596 C chaperonin subunit epsilon subunit YJR064W|TCP5 gene taxon:4932 20050307 SGD
+SGD S000003825 CCT5 GO:0005856 SGD_REF:S000042209|PMID:8771707 TAS C chaperonin subunit epsilon subunit YJR064W|TCP5 gene taxon:4932 20010118 SGD
+SGD S000003825 CCT5 GO:0051082 SGD_REF:S000042209|PMID:8771707 TAS F chaperonin subunit epsilon subunit YJR064W|TCP5 gene taxon:4932 20010118 SGD
+SGD S000003825 CCT5 GO:0006457 SGD_REF:S000042209|PMID:8771707 TAS P chaperonin subunit epsilon subunit YJR064W|TCP5 gene taxon:4932 20010118 SGD
+SGD S000003825 CCT5 GO:0007010 SGD_REF:S000042209|PMID:8771707 TAS P chaperonin subunit epsilon subunit YJR064W|TCP5 gene taxon:4932 20010118 SGD
+SGD S000002596 CCT6 GO:0005737 SGD_REF:S000042209|PMID:8771707 TAS C YDR188W|HTR3|TCP20|TCP6 gene taxon:4932 20010118 SGD
+SGD S000002596 CCT6 GO:0005832 SGD_REF:S000042209|PMID:8771707 TAS C YDR188W|HTR3|TCP20|TCP6 gene taxon:4932 20031215 SGD
+SGD S000002596 CCT6 GO:0005832 SGD_REF:S000080727|PMID:15704212 IPI C YDR188W|HTR3|TCP20|TCP6 gene taxon:4932 20050307 SGD
+SGD S000002596 CCT6 GO:0005856 SGD_REF:S000042209|PMID:8771707 TAS C YDR188W|HTR3|TCP20|TCP6 gene taxon:4932 20010118 SGD
+SGD S000002596 CCT6 GO:0051082 SGD_REF:S000042209|PMID:8771707 TAS F YDR188W|HTR3|TCP20|TCP6 gene taxon:4932 20010118 SGD
+SGD S000002596 CCT6 GO:0006457 SGD_REF:S000042209|PMID:8771707 TAS P YDR188W|HTR3|TCP20|TCP6 gene taxon:4932 20010118 SGD
+SGD S000002596 CCT6 GO:0007010 SGD_REF:S000042209|PMID:8771707 TAS P YDR188W|HTR3|TCP20|TCP6 gene taxon:4932 20010118 SGD
+SGD S000003647 CCT7 GO:0005737 SGD_REF:S000042209|PMID:8771707 TAS C chaperonin containing T-complex subunit seven component YJL111W|TCP7 gene taxon:4932 20010118 SGD
+SGD S000003647 CCT7 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C chaperonin containing T-complex subunit seven component YJL111W|TCP7 gene taxon:4932 20020507 SGD
+SGD S000003647 CCT7 GO:0005832 SGD_REF:S000042209|PMID:8771707 TAS C chaperonin containing T-complex subunit seven component YJL111W|TCP7 gene taxon:4932 20031215 SGD
+SGD S000003647 CCT7 GO:0005832 SGD_REF:S000080727|PMID:15704212 IPI SGD:S000002596 C chaperonin containing T-complex subunit seven component YJL111W|TCP7 gene taxon:4932 20050307 SGD
+SGD S000003647 CCT7 GO:0005856 SGD_REF:S000042209|PMID:8771707 TAS C chaperonin containing T-complex subunit seven component YJL111W|TCP7 gene taxon:4932 20010118 SGD
+SGD S000003647 CCT7 GO:0051082 SGD_REF:S000042209|PMID:8771707 TAS F chaperonin containing T-complex subunit seven component YJL111W|TCP7 gene taxon:4932 20010118 SGD
+SGD S000003647 CCT7 GO:0006457 SGD_REF:S000042209|PMID:8771707 TAS P chaperonin containing T-complex subunit seven component YJL111W|TCP7 gene taxon:4932 20010118 SGD
+SGD S000003647 CCT7 GO:0007010 SGD_REF:S000042209|PMID:8771707 TAS P chaperonin containing T-complex subunit seven component YJL111W|TCP7 gene taxon:4932 20010118 SGD
+SGD S000003545 CCT8 GO:0005737 SGD_REF:S000042209|PMID:8771707 TAS C chaperonin containing T-complex subunit eight component YJL008C gene taxon:4932 20010118 SGD
+SGD S000003545 CCT8 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C chaperonin containing T-complex subunit eight component YJL008C gene taxon:4932 20020507 SGD
+SGD S000003545 CCT8 GO:0005832 SGD_REF:S000042209|PMID:8771707 TAS C chaperonin containing T-complex subunit eight component YJL008C gene taxon:4932 20031215 SGD
+SGD S000003545 CCT8 GO:0005832 SGD_REF:S000080727|PMID:15704212 IPI SGD:S000002596 C chaperonin containing T-complex subunit eight component YJL008C gene taxon:4932 20050307 SGD
+SGD S000003545 CCT8 GO:0005856 SGD_REF:S000042209|PMID:8771707 TAS C chaperonin containing T-complex subunit eight component YJL008C gene taxon:4932 20010118 SGD
+SGD S000003545 CCT8 GO:0051082 SGD_REF:S000042209|PMID:8771707 TAS F chaperonin containing T-complex subunit eight component YJL008C gene taxon:4932 20010118 SGD
+SGD S000003545 CCT8 GO:0006457 SGD_REF:S000042209|PMID:8771707 TAS P chaperonin containing T-complex subunit eight component YJL008C gene taxon:4932 20010118 SGD
+SGD S000003545 CCT8 GO:0007010 SGD_REF:S000042209|PMID:8771707 TAS P chaperonin containing T-complex subunit eight component YJL008C gene taxon:4932 20010118 SGD
+SGD S000029067 CCW1 GO:0009277 SGD_REF:S000053320|PMID:9301021 IDA C released from SDS-extracted cell walls by laminarinase gene taxon:4932 20010607 SGD
+SGD S000029067 CCW1 GO:0005199 SGD_REF:S000053320|PMID:9301021 IPI F released from SDS-extracted cell walls by laminarinase gene taxon:4932 20010607 SGD
+SGD S000029067 CCW1 GO:0000004 SGD_REF:S000069584 ND P released from SDS-extracted cell walls by laminarinase gene taxon:4932 20010607 SGD
+SGD S000029068 CCW10 GO:0009277 SGD_REF:S000053320|PMID:9301021 IDA C released from SDS-extracted cell walls with mild alkali treatment gene taxon:4932 20010607 SGD
+SGD S000029068 CCW10 GO:0005199 SGD_REF:S000053320|PMID:9301021 IPI F released from SDS-extracted cell walls with mild alkali treatment gene taxon:4932 20010607 SGD
+SGD S000029068 CCW10 GO:0000004 SGD_REF:S000069584 ND P released from SDS-extracted cell walls with mild alkali treatment gene taxon:4932 20010607 SGD
+SGD S000004100 CCW12 GO:0009277 SGD_REF:S000040179|PMID:10383953 IDA C cell wall mannoprotein YLR110C gene taxon:4932 20020617 SGD
+SGD S000004100 CCW12 GO:0005554 SGD_REF:S000069584 ND F cell wall mannoprotein YLR110C gene taxon:4932 20021209 SGD
+SGD S000004100 CCW12 GO:0000747 SGD_REF:S000048008|PMID:10322008 IMP P cell wall mannoprotein YLR110C gene taxon:4932 20021210 SGD
+SGD S000004100 CCW12 GO:0000752 SGD_REF:S000048008|PMID:10322008 IMP P cell wall mannoprotein YLR110C gene taxon:4932 20021210 SGD
+SGD S000004100 CCW12 GO:0007047 SGD_REF:S000048008|PMID:10322008 IMP P cell wall mannoprotein YLR110C gene taxon:4932 20021210 SGD
+SGD S000006429 CCW14 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C cell wall mannoprotein YLR390W-A|SSR1|YLR391W|YLR391W-A gene taxon:4932 20031028 SGD
+SGD S000006429 CCW14 GO:0009277 SGD_REF:S000043414|PMID:9079899 IDA C cell wall mannoprotein YLR390W-A|SSR1|YLR391W|YLR391W-A gene taxon:4932 20020913 SGD
+SGD S000006429 CCW14 GO:0009277 SGD_REF:S000081097|PMID:15781460 IDA C cell wall mannoprotein YLR390W-A|SSR1|YLR391W|YLR391W-A gene taxon:4932 20050601 SGD
+SGD S000006429 CCW14 GO:0009277 SGD_REF:S000053320|PMID:9301021 IDA C cell wall mannoprotein YLR390W-A|SSR1|YLR391W|YLR391W-A gene taxon:4932 20020913 SGD
+SGD S000006429 CCW14 GO:0005199 SGD_REF:S000053320|PMID:9301021 IPI F cell wall mannoprotein YLR390W-A|SSR1|YLR391W|YLR391W-A gene taxon:4932 20010607 SGD
+SGD S000006429 CCW14 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P cell wall mannoprotein YLR390W-A|SSR1|YLR391W|YLR391W-A gene taxon:4932 20060214 SGD
+SGD S000006429 CCW14 GO:0007047 SGD_REF:S000043414|PMID:9079899 ISS P cell wall mannoprotein YLR390W-A|SSR1|YLR391W|YLR391W-A gene taxon:4932 20020913 SGD
+SGD S000006429 CCW14 GO:0007047 SGD_REF:S000043414|PMID:9079899 IMP P cell wall mannoprotein YLR390W-A|SSR1|YLR391W|YLR391W-A gene taxon:4932 20020913 SGD
+SGD S000029069 CCW2 GO:0009277 SGD_REF:S000053320|PMID:9301021 IDA C released from SDS-extracted cell walls by laminarinase gene taxon:4932 20010607 SGD
+SGD S000029069 CCW2 GO:0005199 SGD_REF:S000053320|PMID:9301021 IPI F released from SDS-extracted cell walls by laminarinase gene taxon:4932 20010607 SGD
+SGD S000029069 CCW2 GO:0000004 SGD_REF:S000069584 ND P released from SDS-extracted cell walls by laminarinase gene taxon:4932 20010607 SGD
+SGD S000029070 CCW3 GO:0009277 SGD_REF:S000053320|PMID:9301021 IDA C released from SDS-extracted cell walls by laminarinase gene taxon:4932 20010607 SGD
+SGD S000029070 CCW3 GO:0005199 SGD_REF:S000053320|PMID:9301021 IPI F released from SDS-extracted cell walls by laminarinase gene taxon:4932 20010607 SGD
+SGD S000029070 CCW3 GO:0000004 SGD_REF:S000069584 ND P released from SDS-extracted cell walls by laminarinase gene taxon:4932 20010607 SGD
+SGD S000029071 CCW4 GO:0009277 SGD_REF:S000053320|PMID:9301021 IDA C released from SDS-extracted cell walls by laminarinase gene taxon:4932 20010607 SGD
+SGD S000029071 CCW4 GO:0005199 SGD_REF:S000053320|PMID:9301021 IPI F released from SDS-extracted cell walls by laminarinase gene taxon:4932 20010607 SGD
+SGD S000029071 CCW4 GO:0000004 SGD_REF:S000069584 ND P released from SDS-extracted cell walls by laminarinase gene taxon:4932 20010607 SGD
+SGD S000029073 CCW9 GO:0009277 SGD_REF:S000053320|PMID:9301021 IDA C released from SDS-extracted cell walls with mild alkali treatment gene taxon:4932 20010607 SGD
+SGD S000029073 CCW9 GO:0005199 SGD_REF:S000053320|PMID:9301021 IPI F released from SDS-extracted cell walls with mild alkali treatment gene taxon:4932 20010607 SGD
+SGD S000029073 CCW9 GO:0000004 SGD_REF:S000069584 ND P released from SDS-extracted cell walls with mild alkali treatment gene taxon:4932 20010607 SGD
+SGD S000000335 CCZ1 GO:0005770 SGD_REF:S000059160|PMID:11069774 TAS C YBR131W|CVT16 gene taxon:4932 20021023 SGD
+SGD S000000335 CCZ1 GO:0005773 SGD_REF:S000066015|PMID:11590240 IDA C YBR131W|CVT16 gene taxon:4932 20020817 SGD
+SGD S000000335 CCZ1 GO:0016020 SGD_REF:S000059160|PMID:11069774 TAS C YBR131W|CVT16 gene taxon:4932 20021023 SGD
+SGD S000000335 CCZ1 GO:0005085 SGD_REF:S000066015|PMID:11590240 IPI F YBR131W|CVT16 gene taxon:4932 20021023 SGD
+SGD S000000335 CCZ1 GO:0000046 SGD_REF:S000071474|PMID:12208507 IDA P YBR131W|CVT16 gene taxon:4932 20021023 SGD
+SGD S000000335 CCZ1 GO:0006623 SGD_REF:S000072494|PMID:12364329 IMP P YBR131W|CVT16 gene taxon:4932 20030226 SGD
+SGD S000000335 CCZ1 GO:0006914 SGD_REF:S000071474|PMID:12208507 IDA P YBR131W|CVT16 gene taxon:4932 20021023 SGD
+SGD S000000335 CCZ1 GO:0007034 SGD_REF:S000066015|PMID:11590240 IGI P YBR131W|CVT16 gene taxon:4932 20020927 SGD
+SGD S000000335 CCZ1 GO:0007034 SGD_REF:S000066015|PMID:11590240 IMP P YBR131W|CVT16 gene taxon:4932 20020927 SGD
+SGD S000000335 CCZ1 GO:0048278 SGD_REF:S000074698|PMID:14662743 IMP P YBR131W|CVT16 gene taxon:4932 20051003 SGD
+SGD S000004298 CDA1 GO:0005631 SGD_REF:S000055522|PMID:8940152 ISS C chitin deacetylase YLR307W gene taxon:4932 20020927 SGD
+SGD S000004298 CDA1 GO:0004099 SGD_REF:S000055522|PMID:8940152 IDA F chitin deacetylase YLR307W gene taxon:4932 20020927 SGD
+SGD S000004298 CDA1 GO:0004099 SGD_REF:S000055522|PMID:8940152 ISS F chitin deacetylase YLR307W gene taxon:4932 20020927 SGD
+SGD S000004298 CDA1 GO:0030476 SGD_REF:S000055522|PMID:8940152 IDA P chitin deacetylase YLR307W gene taxon:4932 20020927 SGD
+SGD S000004298 CDA1 GO:0030476 SGD_REF:S000055522|PMID:8940152 IMP P chitin deacetylase YLR307W gene taxon:4932 20020927 SGD
+SGD S000004299 CDA2 GO:0005631 SGD_REF:S000055522|PMID:8940152 ISS C chitin deacetylase YLR308W gene taxon:4932 20020927 SGD
+SGD S000004299 CDA2 GO:0004099 SGD_REF:S000055522|PMID:8940152 IDA F chitin deacetylase YLR308W gene taxon:4932 20020927 SGD
+SGD S000004299 CDA2 GO:0004099 SGD_REF:S000055522|PMID:8940152 ISS F chitin deacetylase YLR308W gene taxon:4932 20020927 SGD
+SGD S000004299 CDA2 GO:0030476 SGD_REF:S000055522|PMID:8940152 IDA P chitin deacetylase YLR308W gene taxon:4932 20020927 SGD
+SGD S000004299 CDA2 GO:0030476 SGD_REF:S000055522|PMID:8940152 IMP P chitin deacetylase YLR308W gene taxon:4932 20020927 SGD
+SGD S000002590 CDC1 GO:0016021 SGD_REF:S000072825|PMID:12524434 ISS C YDR182W|DSC1|DSR1|ESP2 gene taxon:4932 20030409 SGD
+SGD S000002590 CDC1 GO:0005554 SGD_REF:S000069584 ND F YDR182W|DSC1|DSR1|ESP2 gene taxon:4932 20010119 SGD
+SGD S000002590 CDC1 GO:0000747 SGD_REF:S000049662|PMID:9560392 TAS P YDR182W|DSC1|DSR1|ESP2 gene taxon:4932 20010118 SGD
+SGD S000002590 CDC1 GO:0006281 SGD_REF:S000051725|PMID:7969142 IMP P YDR182W|DSC1|DSR1|ESP2 gene taxon:4932 20030917 SGD
+SGD S000002590 CDC1 GO:0030026 SGD_REF:S000049663|PMID:9560393 IGI P YDR182W|DSC1|DSR1|ESP2 gene taxon:4932 20030917 SGD
+SGD S000002590 CDC1 GO:0030026 SGD_REF:S000049663|PMID:9560393 IMP P YDR182W|DSC1|DSR1|ESP2 gene taxon:4932 20030917 SGD
+SGD S000002590 CDC1 GO:0030036 SGD_REF:S000060041|PMID:11285273 IMP P YDR182W|DSC1|DSR1|ESP2 gene taxon:4932 20030917 SGD
+SGD S000000595 CDC10 GO:0000144 SGD_REF:S000057920|PMID:8791410 TAS C septin YCR002C gene taxon:4932 20010118 SGD
+SGD S000000595 CDC10 GO:0003924 SGD_REF:S000077127|PMID:14993234 IDA F septin YCR002C gene taxon:4932 20041210 SGD
+SGD S000000595 CDC10 GO:0005200 SGD_REF:S000057920|PMID:8791410 TAS F septin YCR002C gene taxon:4932 20010118 SGD
+SGD S000000595 CDC10 GO:0005545 SGD_REF:S000072964|PMID:12665577 IDA F septin YCR002C gene taxon:4932 20030505 SGD
+SGD S000000595 CDC10 GO:0000747 SGD_REF:S000057920|PMID:8791410 TAS P septin YCR002C gene taxon:4932 20010118 SGD
+SGD S000000595 CDC10 GO:0000753 SGD_REF:S000057920|PMID:8791410 TAS P septin YCR002C gene taxon:4932 20021206 SGD
+SGD S000000595 CDC10 GO:0000902 SGD_REF:S000057920|PMID:8791410 TAS P septin YCR002C gene taxon:4932 20021108 SGD
+SGD S000000595 CDC10 GO:0000910 SGD_REF:S000057920|PMID:8791410 TAS P septin YCR002C gene taxon:4932 20010119 SGD
+SGD S000000595 CDC10 GO:0007047 SGD_REF:S000057920|PMID:8791410 TAS P septin YCR002C gene taxon:4932 20010118 SGD
+SGD S000000595 CDC10 GO:0007120 SGD_REF:S000058399|PMID:9891811 TAS P septin YCR002C gene taxon:4932 20010118 SGD
+SGD S000000595 CDC10 GO:0007121 SGD_REF:S000057920|PMID:8791410 TAS P septin YCR002C gene taxon:4932 20010118 SGD
+SGD S000000595 CDC10 GO:0030468 SGD_REF:S000057920|PMID:8791410 TAS P septin YCR002C gene taxon:4932 20010302 SGD
+SGD S000000595 CDC10 GO:0030476 SGD_REF:S000057920|PMID:8791410 TAS P septin YCR002C gene taxon:4932 20010118 SGD
+SGD S000003837 CDC11 GO:0000144 SGD_REF:S000057920|PMID:8791410 TAS C 10 nm filament component of mother-bud neck, septin YJR076C|PSL9 gene taxon:4932 20010118 SGD
+SGD S000003837 CDC11 GO:0001400 SGD_REF:S000057920|PMID:8791410 IDA C 10 nm filament component of mother-bud neck, septin YJR076C|PSL9 gene taxon:4932 20050124 SGD
+SGD S000003837 CDC11 GO:0005619 SGD_REF:S000057920|PMID:8791410 TAS C 10 nm filament component of mother-bud neck, septin YJR076C|PSL9 gene taxon:4932 20010118 SGD
+SGD S000003837 CDC11 GO:0005628 SGD_REF:S000057920|PMID:8791410 TAS C 10 nm filament component of mother-bud neck, septin YJR076C|PSL9 gene taxon:4932 20010118 SGD
+SGD S000003837 CDC11 GO:0005200 SGD_REF:S000057920|PMID:8791410 TAS F 10 nm filament component of mother-bud neck, septin YJR076C|PSL9 gene taxon:4932 20010118 SGD
+SGD S000003837 CDC11 GO:0005545 SGD_REF:S000072964|PMID:12665577 IDA F 10 nm filament component of mother-bud neck, septin YJR076C|PSL9 gene taxon:4932 20030505 SGD
+SGD S000003837 CDC11 GO:0000747 SGD_REF:S000057920|PMID:8791410 TAS P 10 nm filament component of mother-bud neck, septin YJR076C|PSL9 gene taxon:4932 20010118 SGD
+SGD S000003837 CDC11 GO:0000902 SGD_REF:S000057920|PMID:8791410 TAS P 10 nm filament component of mother-bud neck, septin YJR076C|PSL9 gene taxon:4932 20021108 SGD
+SGD S000003837 CDC11 GO:0000910 SGD_REF:S000057920|PMID:8791410 TAS P 10 nm filament component of mother-bud neck, septin YJR076C|PSL9 gene taxon:4932 20010119 SGD
+SGD S000003837 CDC11 GO:0007047 SGD_REF:S000057920|PMID:8791410 TAS P 10 nm filament component of mother-bud neck, septin YJR076C|PSL9 gene taxon:4932 20010118 SGD
+SGD S000003837 CDC11 GO:0007120 SGD_REF:S000058399|PMID:9891811 TAS P 10 nm filament component of mother-bud neck, septin YJR076C|PSL9 gene taxon:4932 20010118 SGD
+SGD S000003837 CDC11 GO:0030468 SGD_REF:S000057920|PMID:8791410 TAS P 10 nm filament component of mother-bud neck, septin YJR076C|PSL9 gene taxon:4932 20010302 SGD
+SGD S000001149 CDC12 GO:0000144 SGD_REF:S000057920|PMID:8791410 TAS C 10 nm filament component of mother-bud neck, septin YHR107C|CLA10|PSL7 gene taxon:4932 20010118 SGD
+SGD S000001149 CDC12 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C 10 nm filament component of mother-bud neck, septin YHR107C|CLA10|PSL7 gene taxon:4932 20020507 SGD
+SGD S000001149 CDC12 GO:0003924 SGD_REF:S000077127|PMID:14993234 IDA F 10 nm filament component of mother-bud neck, septin YHR107C|CLA10|PSL7 gene taxon:4932 20041210 SGD
+SGD S000001149 CDC12 GO:0005200 SGD_REF:S000057920|PMID:8791410 TAS F 10 nm filament component of mother-bud neck, septin YHR107C|CLA10|PSL7 gene taxon:4932 20010118 SGD
+SGD S000001149 CDC12 GO:0005545 SGD_REF:S000072964|PMID:12665577 IDA F 10 nm filament component of mother-bud neck, septin YHR107C|CLA10|PSL7 gene taxon:4932 20030505 SGD
+SGD S000001149 CDC12 GO:0000747 SGD_REF:S000057920|PMID:8791410 TAS P 10 nm filament component of mother-bud neck, septin YHR107C|CLA10|PSL7 gene taxon:4932 20010118 SGD
+SGD S000001149 CDC12 GO:0000902 SGD_REF:S000057920|PMID:8791410 TAS P 10 nm filament component of mother-bud neck, septin YHR107C|CLA10|PSL7 gene taxon:4932 20021108 SGD
+SGD S000001149 CDC12 GO:0000910 SGD_REF:S000057920|PMID:8791410 TAS P 10 nm filament component of mother-bud neck, septin YHR107C|CLA10|PSL7 gene taxon:4932 20010119 SGD
+SGD S000001149 CDC12 GO:0007047 SGD_REF:S000057920|PMID:8791410 TAS P 10 nm filament component of mother-bud neck, septin YHR107C|CLA10|PSL7 gene taxon:4932 20010118 SGD
+SGD S000001149 CDC12 GO:0007120 SGD_REF:S000058399|PMID:9891811 TAS P 10 nm filament component of mother-bud neck, septin YHR107C|CLA10|PSL7 gene taxon:4932 20010118 SGD
+SGD S000001149 CDC12 GO:0007121 SGD_REF:S000057920|PMID:8791410 TAS P 10 nm filament component of mother-bud neck, septin YHR107C|CLA10|PSL7 gene taxon:4932 20010118 SGD
+SGD S000001149 CDC12 GO:0030468 SGD_REF:S000057920|PMID:8791410 TAS P 10 nm filament component of mother-bud neck, septin YHR107C|CLA10|PSL7 gene taxon:4932 20010302 SGD
+SGD S000004205 CDC123 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YLR215C gene taxon:4932 20031028 SGD
+SGD S000004205 CDC123 GO:0005554 SGD_REF:S000069584 ND F YLR215C gene taxon:4932 20021121 SGD
+SGD S000004205 CDC123 GO:0007346 SGD_REF:S000113995|PMID:15319434 IMP P YLR215C gene taxon:4932 20060110 SGD
+SGD S000002379 CDC13 GO:0000783 SGD_REF:S000045567|PMID:9710643 IDA C single-stranded TG1-3 telomere G-tails binding protein YDL220C|EST4 gene taxon:4932 20030403 SGD
+SGD S000002379 CDC13 GO:0003697 SGD_REF:S000070037|PMID:11352055 TAS F single-stranded TG1-3 telomere G-tails binding protein YDL220C|EST4 gene taxon:4932 20020625 SGD
+SGD S000002379 CDC13 GO:0000723 SGD_REF:S000061450|PMID:11390652 IMP P single-stranded TG1-3 telomere G-tails binding protein YDL220C|EST4 gene taxon:4932 20021101 SGD
+SGD S000002379 CDC13 GO:0016233 SGD_REF:S000070037|PMID:11352055 TAS P single-stranded TG1-3 telomere G-tails binding protein YDL220C|EST4 gene taxon:4932 20020625 SGD
+SGD S000001924 CDC14 GO:0005634 SGD_REF:S000069459|PMID:11914276 IDA C protein phosphatase YFR028C|OAF3 gene taxon:4932 20020507 SGD
+SGD S000001924 CDC14 GO:0005730 SGD_REF:S000069957|PMID:12062061 IDA C protein phosphatase YFR028C|OAF3 gene taxon:4932 20020918 SGD
+SGD S000001924 CDC14 GO:0005816 SGD_REF:S000069957|PMID:12062061 IDA C protein phosphatase YFR028C|OAF3 gene taxon:4932 20020918 SGD
+SGD S000001924 CDC14 GO:0030869 SGD_REF:S000056360|PMID:10219244 IDA C protein phosphatase YFR028C|OAF3 gene taxon:4932 20040906 SGD
+SGD S000001924 CDC14 GO:0004721 SGD_REF:S000051434|PMID:9295359 IDA F protein phosphatase YFR028C|OAF3 gene taxon:4932 20020918 SGD
+SGD S000001924 CDC14 GO:0006470 SGD_REF:S000051434|PMID:9295359 IDA P protein phosphatase YFR028C|OAF3 gene taxon:4932 20020918 SGD
+SGD S000001924 CDC14 GO:0007096 SGD_REF:S000056360|PMID:10219244 IGI P protein phosphatase YFR028C|OAF3 gene taxon:4932 20020918 SGD
+SGD S000001924 CDC14 GO:0007096 SGD_REF:S000056360|PMID:10219244 IPI P protein phosphatase YFR028C|OAF3 gene taxon:4932 20020918 SGD
+SGD S000000072 CDC15 GO:0005816 SGD_REF:S000046027|PMID:10662594 IDA C protein kinase domain YAR019C|LYT1 gene taxon:4932 20020918 SGD
+SGD S000000072 CDC15 GO:0005935 SGD_REF:S000073737|PMID:12832486 TAS C protein kinase domain YAR019C|LYT1 gene taxon:4932 20030918 SGD
+SGD S000000072 CDC15 GO:0004672 SGD_REF:S000061406|PMID:11404483 IDA F protein kinase domain YAR019C|LYT1 gene taxon:4932 20020918 SGD
+SGD S000000072 CDC15 GO:0000910 SGD_REF:S000059953|PMID:11267871 IMP P protein kinase domain YAR019C|LYT1 gene taxon:4932 20020918 SGD
+SGD S000000072 CDC15 GO:0006468 SGD_REF:S000061406|PMID:11404483 IDA P protein kinase domain YAR019C|LYT1 gene taxon:4932 20020918 SGD
+SGD S000000072 CDC15 GO:0007096 SGD_REF:S000059953|PMID:11267871 IMP P protein kinase domain YAR019C|LYT1 gene taxon:4932 20020918 SGD
+SGD S000001505 CDC16 GO:0005680 SGD_REF:S000058476|PMID:10465783 TAS C metal-binding nucleic acid-binding protein, interacts with Cdc23p and Cdc27p to catalyze the conjugation of ubiquitin to cyclin B (putative) YKL022C gene taxon:4932 20010118 SGD
+SGD S000001505 CDC16 GO:0004842 SGD_REF:S000058476|PMID:10465783 TAS F metal-binding nucleic acid-binding protein, interacts with Cdc23p and Cdc27p to catalyze the conjugation of ubiquitin to cyclin B (putative) YKL022C gene taxon:4932 20010118 SGD
+SGD S000001505 CDC16 GO:0005515 SGD_REF:S000058476|PMID:10465783 TAS F metal-binding nucleic acid-binding protein, interacts with Cdc23p and Cdc27p to catalyze the conjugation of ubiquitin to cyclin B (putative) YKL022C gene taxon:4932 20010118 SGD
+SGD S000001505 CDC16 GO:0000022 SGD_REF:S000058476|PMID:10465783 TAS P metal-binding nucleic acid-binding protein, interacts with Cdc23p and Cdc27p to catalyze the conjugation of ubiquitin to cyclin B (putative) YKL022C gene taxon:4932 20010118 SGD
+SGD S000001505 CDC16 GO:0000070 SGD_REF:S000058476|PMID:10465783 TAS P metal-binding nucleic acid-binding protein, interacts with Cdc23p and Cdc27p to catalyze the conjugation of ubiquitin to cyclin B (putative) YKL022C gene taxon:4932 20010118 SGD
+SGD S000001505 CDC16 GO:0007091 SGD_REF:S000058476|PMID:10465783 TAS P metal-binding nucleic acid-binding protein, interacts with Cdc23p and Cdc27p to catalyze the conjugation of ubiquitin to cyclin B (putative) YKL022C gene taxon:4932 20010118 SGD
+SGD S000001505 CDC16 GO:0008054 SGD_REF:S000058476|PMID:10465783 TAS P metal-binding nucleic acid-binding protein, interacts with Cdc23p and Cdc27p to catalyze the conjugation of ubiquitin to cyclin B (putative) YKL022C gene taxon:4932 20010118 SGD
+SGD S000001505 CDC16 GO:0016567 SGD_REF:S000044570|PMID:9469814 IPI P metal-binding nucleic acid-binding protein, interacts with Cdc23p and Cdc27p to catalyze the conjugation of ubiquitin to cyclin B (putative) YKL022C gene taxon:4932 20050408 SGD
+SGD S000001505 CDC16 GO:0031145 SGD_REF:S000042065|PMID:8895471 IDA P metal-binding nucleic acid-binding protein, interacts with Cdc23p and Cdc27p to catalyze the conjugation of ubiquitin to cyclin B (putative) YKL022C gene taxon:4932 20050404 SGD
+SGD S000001505 CDC16 GO:0031145 SGD_REF:S000044570|PMID:9469814 IPI P metal-binding nucleic acid-binding protein, interacts with Cdc23p and Cdc27p to catalyze the conjugation of ubiquitin to cyclin B (putative) YKL022C gene taxon:4932 20050404 SGD
+SGD S000000036 CDC19 GO:0005829 SGD_REF:S000058491 TAS C pyruvate kinase YAL038W|PYK1 gene taxon:4932 20010119 SGD
+SGD S000000036 CDC19 GO:0004743 SGD_REF:S000045991|PMID:323230 IMP F pyruvate kinase YAL038W|PYK1 gene taxon:4932 20010118 SGD
+SGD S000000036 CDC19 GO:0004743 SGD_REF:S000070373|PMID:12063246 IDA F pyruvate kinase YAL038W|PYK1 gene taxon:4932 20030509 SGD
+SGD S000000036 CDC19 GO:0006090 SGD_REF:S000045991|PMID:323230 IMP P pyruvate kinase YAL038W|PYK1 gene taxon:4932 20050727 SGD
+SGD S000000036 CDC19 GO:0006096 SGD_REF:S000045991|PMID:323230 IMP P pyruvate kinase YAL038W|PYK1 gene taxon:4932 20050727 SGD
+SGD S000002260 CDC2 GO:0005657 SGD_REF:S000081149|PMID:15773893 IDA C DNA polymerase III catalytic (delta) subunit YDL102W|HPR6|POL3|TEX1 gene taxon:4932 20050708 SGD
+SGD S000002260 CDC2 GO:0043625 SGD_REF:S000058372|PMID:9745046 TAS C DNA polymerase III catalytic (delta) subunit YDL102W|HPR6|POL3|TEX1 gene taxon:4932 20010118 SGD
+SGD S000002260 CDC2 GO:0003891 SGD_REF:S000058372|PMID:9745046 TAS F DNA polymerase III catalytic (delta) subunit YDL102W|HPR6|POL3|TEX1 gene taxon:4932 20010118 SGD
+SGD S000002260 CDC2 GO:0008310 SGD_REF:S000058372|PMID:9745046 TAS F DNA polymerase III catalytic (delta) subunit YDL102W|HPR6|POL3|TEX1 gene taxon:4932 20060309 SGD
+SGD S000002260 CDC2 GO:0006272 SGD_REF:S000058372|PMID:9745046 TAS P DNA polymerase III catalytic (delta) subunit YDL102W|HPR6|POL3|TEX1 gene taxon:4932 20010118 SGD
+SGD S000002260 CDC2 GO:0006273 SGD_REF:S000058372|PMID:9745046 TAS P DNA polymerase III catalytic (delta) subunit YDL102W|HPR6|POL3|TEX1 gene taxon:4932 20010118 SGD
+SGD S000002260 CDC2 GO:0006280 SGD_REF:S000058372|PMID:9745046 TAS P DNA polymerase III catalytic (delta) subunit YDL102W|HPR6|POL3|TEX1 gene taxon:4932 20010118 SGD
+SGD S000002260 CDC2 GO:0006284 SGD_REF:S000058372|PMID:9745046 TAS P DNA polymerase III catalytic (delta) subunit YDL102W|HPR6|POL3|TEX1 gene taxon:4932 20010118 SGD
+SGD S000002260 CDC2 GO:0006289 SGD_REF:S000058372|PMID:9745046 TAS P DNA polymerase III catalytic (delta) subunit YDL102W|HPR6|POL3|TEX1 gene taxon:4932 20010118 SGD
+SGD S000002260 CDC2 GO:0006298 SGD_REF:S000058372|PMID:9745046 NAS P DNA polymerase III catalytic (delta) subunit YDL102W|HPR6|POL3|TEX1 gene taxon:4932 20010118 SGD
+SGD S000002260 CDC2 GO:0006298 SGD_REF:S000058456|PMID:10072354 NAS P DNA polymerase III catalytic (delta) subunit YDL102W|HPR6|POL3|TEX1 gene taxon:4932 20010118 SGD
+SGD S000002260 CDC2 GO:0006301 SGD_REF:S000058372|PMID:9745046 TAS P DNA polymerase III catalytic (delta) subunit YDL102W|HPR6|POL3|TEX1 gene taxon:4932 20010118 SGD
+SGD S000002260 CDC2 GO:0045005 SGD_REF:S000079974|PMID:15601866 IGI SGD:S000001596|SGD:S000005450|SGD:S000005559 P DNA polymerase III catalytic (delta) subunit YDL102W|HPR6|POL3|TEX1 gene taxon:4932 20060504 SGD
+SGD S000003084 CDC20 GO:0005680 SGD_REF:S000058476|PMID:10465783 TAS C anaphase promoting complex (APC) subunit YGL116W|PAC5 gene taxon:4932 20010118 SGD
+SGD S000003084 CDC20 GO:0008047 SGD_REF:S000058476|PMID:10465783 TAS F anaphase promoting complex (APC) subunit YGL116W|PAC5 gene taxon:4932 20010118 SGD
+SGD S000003084 CDC20 GO:0000022 SGD_REF:S000058476|PMID:10465783 TAS P anaphase promoting complex (APC) subunit YGL116W|PAC5 gene taxon:4932 20010118 SGD
+SGD S000003084 CDC20 GO:0000070 SGD_REF:S000058476|PMID:10465783 TAS P anaphase promoting complex (APC) subunit YGL116W|PAC5 gene taxon:4932 20010118 SGD
+SGD S000003084 CDC20 GO:0007091 SGD_REF:S000058476|PMID:10465783 TAS P anaphase promoting complex (APC) subunit YGL116W|PAC5 gene taxon:4932 20010118 SGD
+SGD S000003084 CDC20 GO:0007092 SGD_REF:S000039265|PMID:9504909 IMP P anaphase promoting complex (APC) subunit YGL116W|PAC5 gene taxon:4932 20050404 SGD
+SGD S000003084 CDC20 GO:0007092 SGD_REF:S000052656|PMID:9334304 IMP P anaphase promoting complex (APC) subunit YGL116W|PAC5 gene taxon:4932 20050404 SGD
+SGD S000003084 CDC20 GO:0008054 SGD_REF:S000058476|PMID:10465783 TAS P anaphase promoting complex (APC) subunit YGL116W|PAC5 gene taxon:4932 20010118 SGD
+SGD S000005600 CDC21 GO:0005634 SGD_REF:S000058478|PMID:8132557 IDA C thymidylate synthase YOR074C|CRT9|TMP1|YOR29-25 gene taxon:4932 20010118 SGD
+SGD S000005600 CDC21 GO:0004799 SGD_REF:S000043477|PMID:6287238 IDA F thymidylate synthase YOR074C|CRT9|TMP1|YOR29-25 gene taxon:4932 20010118 SGD
+SGD S000005600 CDC21 GO:0006231 SGD_REF:S000058499 TAS P thymidylate synthase YOR074C|CRT9|TMP1|YOR29-25 gene taxon:4932 20010119 SGD
+SGD S000005600 CDC21 GO:0006261 SGD_REF:S000058499 TAS P thymidylate synthase YOR074C|CRT9|TMP1|YOR29-25 gene taxon:4932 20010119 SGD
+SGD S000001209 CDC23 GO:0005680 SGD_REF:S000058476|PMID:10465783 TAS C YHR166C gene taxon:4932 20010118 SGD
+SGD S000001209 CDC23 GO:0004842 SGD_REF:S000058476|PMID:10465783 TAS F YHR166C gene taxon:4932 20010118 SGD
+SGD S000001209 CDC23 GO:0005515 SGD_REF:S000058476|PMID:10465783 TAS F YHR166C gene taxon:4932 20010118 SGD
+SGD S000001209 CDC23 GO:0000022 SGD_REF:S000058476|PMID:10465783 TAS P YHR166C gene taxon:4932 20010118 SGD
+SGD S000001209 CDC23 GO:0000070 SGD_REF:S000058476|PMID:10465783 TAS P YHR166C gene taxon:4932 20010118 SGD
+SGD S000001209 CDC23 GO:0007091 SGD_REF:S000058476|PMID:10465783 TAS P YHR166C gene taxon:4932 20010118 SGD
+SGD S000001209 CDC23 GO:0008054 SGD_REF:S000058476|PMID:10465783 TAS P YHR166C gene taxon:4932 20010118 SGD
+SGD S000001209 CDC23 GO:0016567 SGD_REF:S000044570|PMID:9469814 IPI P YHR166C gene taxon:4932 20050408 SGD
+SGD S000001209 CDC23 GO:0031145 SGD_REF:S000042065|PMID:8895471 IDA P YHR166C gene taxon:4932 20050404 SGD
+SGD S000001209 CDC23 GO:0031145 SGD_REF:S000044570|PMID:9469814 IPI P YHR166C gene taxon:4932 20050404 SGD
+SGD S000000039 CDC24 GO:0000131 SGD_REF:S000047882|PMID:10655592 IDA C guanine nucleotide exchange factor (a.k.a. GDP-release factor) for cdc42 YAL041W|CLS4 gene taxon:4932 20020710 SGD
+SGD S000000039 CDC24 GO:0005634 SGD_REF:S000047882|PMID:10655592 IDA C guanine nucleotide exchange factor (a.k.a. GDP-release factor) for cdc42 YAL041W|CLS4 gene taxon:4932 20020710 SGD
+SGD S000000039 CDC24 GO:0005935 SGD_REF:S000043671|PMID:10087263 IDA C guanine nucleotide exchange factor (a.k.a. GDP-release factor) for cdc42 YAL041W|CLS4 gene taxon:4932 20020807 SGD
+SGD S000000039 CDC24 GO:0043332 SGD_REF:S000043671|PMID:10087263 IDA C guanine nucleotide exchange factor (a.k.a. GDP-release factor) for cdc42 YAL041W|CLS4 gene taxon:4932 20020807 SGD
+SGD S000000039 CDC24 GO:0004871 SGD_REF:S000058399|PMID:9891811 TAS F guanine nucleotide exchange factor (a.k.a. GDP-release factor) for cdc42 YAL041W|CLS4 gene taxon:4932 20010118 SGD
+SGD S000000039 CDC24 GO:0005089 SGD_REF:S000058399|PMID:9891811 IDA F guanine nucleotide exchange factor (a.k.a. GDP-release factor) for cdc42 YAL041W|CLS4 gene taxon:4932 20010118 SGD
+SGD S000000039 CDC24 GO:0000750 SGD_REF:S000043671|PMID:10087263 IGI P guanine nucleotide exchange factor (a.k.a. GDP-release factor) for cdc42 YAL041W|CLS4 gene taxon:4932 20021206 SGD
+SGD S000000039 CDC24 GO:0000750 SGD_REF:S000043671|PMID:10087263 TAS P guanine nucleotide exchange factor (a.k.a. GDP-release factor) for cdc42 YAL041W|CLS4 gene taxon:4932 20021206 SGD
+SGD S000000039 CDC24 GO:0000750 SGD_REF:S000043671|PMID:10087263 IPI P guanine nucleotide exchange factor (a.k.a. GDP-release factor) for cdc42 YAL041W|CLS4 gene taxon:4932 20021206 SGD
+SGD S000000039 CDC24 GO:0000753 SGD_REF:S000047882|PMID:10655592 IMP P guanine nucleotide exchange factor (a.k.a. GDP-release factor) for cdc42 YAL041W|CLS4 gene taxon:4932 20021206 SGD
+SGD S000000039 CDC24 GO:0000753 SGD_REF:S000047882|PMID:10655592 IPI P guanine nucleotide exchange factor (a.k.a. GDP-release factor) for cdc42 YAL041W|CLS4 gene taxon:4932 20021206 SGD
+SGD S000000039 CDC24 GO:0001403 SGD_REF:S000056064|PMID:10066831 IPI P guanine nucleotide exchange factor (a.k.a. GDP-release factor) for cdc42 YAL041W|CLS4 gene taxon:4932 20010118 SGD
+SGD S000000039 CDC24 GO:0006033 SGD_REF:S000056064|PMID:10066831 IMP P guanine nucleotide exchange factor (a.k.a. GDP-release factor) for cdc42 YAL041W|CLS4 gene taxon:4932 20010118 SGD
+SGD S000000039 CDC24 GO:0007096 SGD_REF:S000071653|PMID:12234925 IMP P guanine nucleotide exchange factor (a.k.a. GDP-release factor) for cdc42 YAL041W|CLS4 gene taxon:4932 20050324 SGD
+SGD S000000039 CDC24 GO:0007118 SGD_REF:S000056064|PMID:10066831 IPI P guanine nucleotide exchange factor (a.k.a. GDP-release factor) for cdc42 YAL041W|CLS4 gene taxon:4932 20010118 SGD
+SGD S000000039 CDC24 GO:0007119 SGD_REF:S000056064|PMID:10066831 IPI P guanine nucleotide exchange factor (a.k.a. GDP-release factor) for cdc42 YAL041W|CLS4 gene taxon:4932 20010118 SGD
+SGD S000000039 CDC24 GO:0007124 SGD_REF:S000056064|PMID:10066831 IPI P guanine nucleotide exchange factor (a.k.a. GDP-release factor) for cdc42 YAL041W|CLS4 gene taxon:4932 20010118 SGD
+SGD S000000039 CDC24 GO:0007264 SGD_REF:S000058399|PMID:9891811 TAS P guanine nucleotide exchange factor (a.k.a. GDP-release factor) for cdc42 YAL041W|CLS4 gene taxon:4932 20010118 SGD
+SGD S000000039 CDC24 GO:0030468 SGD_REF:S000058399|PMID:9891811 IMP P guanine nucleotide exchange factor (a.k.a. GDP-release factor) for cdc42 YAL041W|CLS4 gene taxon:4932 20010302 SGD
+SGD S000004301 CDC25 GO:0005737 SGD_REF:S000039968|PMID:1334534 IDA C adenylate cyclase regulatory protein YLR310C|CDC25'|CTN1 gene taxon:4932 20010118 SGD
+SGD S000004301 CDC25 GO:0005886 SGD_REF:S000056081|PMID:8893498 IDA C adenylate cyclase regulatory protein YLR310C|CDC25'|CTN1 gene taxon:4932 20010118 SGD
+SGD S000004301 CDC25 GO:0005088 SGD_REF:S000039968|PMID:1334534 TAS F adenylate cyclase regulatory protein YLR310C|CDC25'|CTN1 gene taxon:4932 20010118 SGD
+SGD S000004301 CDC25 GO:0000074 SGD_REF:S000050740|PMID:3021894 IMP P adenylate cyclase regulatory protein YLR310C|CDC25'|CTN1 gene taxon:4932 20010118 SGD
+SGD S000004301 CDC25 GO:0001302 SGD_REF:S000047674|PMID:11000115 IMP P adenylate cyclase regulatory protein YLR310C|CDC25'|CTN1 gene taxon:4932 20050323 SGD
+SGD S000004301 CDC25 GO:0007089 SGD_REF:S000050740|PMID:3021894 IMP P adenylate cyclase regulatory protein YLR310C|CDC25'|CTN1 gene taxon:4932 20010213 SGD
+SGD S000004301 CDC25 GO:0007265 SGD_REF:S000039968|PMID:1334534 TAS P adenylate cyclase regulatory protein YLR310C|CDC25'|CTN1 gene taxon:4932 20010118 SGD
+SGD S000001932 CDC26 GO:0005680 SGD_REF:S000058476|PMID:10465783 TAS C YFR036W|HIT3|SCD26 gene taxon:4932 20010118 SGD
+SGD S000001932 CDC26 GO:0004842 SGD_REF:S000058476|PMID:10465783 TAS F YFR036W|HIT3|SCD26 gene taxon:4932 20010118 SGD
+SGD S000001932 CDC26 GO:0005515 SGD_REF:S000058476|PMID:10465783 TAS F YFR036W|HIT3|SCD26 gene taxon:4932 20010118 SGD
+SGD S000001932 CDC26 GO:0000022 SGD_REF:S000058476|PMID:10465783 TAS P YFR036W|HIT3|SCD26 gene taxon:4932 20010118 SGD
+SGD S000001932 CDC26 GO:0000070 SGD_REF:S000058476|PMID:10465783 TAS P YFR036W|HIT3|SCD26 gene taxon:4932 20010118 SGD
+SGD S000001932 CDC26 GO:0007091 SGD_REF:S000058476|PMID:10465783 TAS P YFR036W|HIT3|SCD26 gene taxon:4932 20010118 SGD
+SGD S000001932 CDC26 GO:0008054 SGD_REF:S000058476|PMID:10465783 TAS P YFR036W|HIT3|SCD26 gene taxon:4932 20010118 SGD
+SGD S000001932 CDC26 GO:0016567 SGD_REF:S000044570|PMID:9469814 IPI P YFR036W|HIT3|SCD26 gene taxon:4932 20050408 SGD
+SGD S000001932 CDC26 GO:0031145 SGD_REF:S000042065|PMID:8895471 IDA P YFR036W|HIT3|SCD26 gene taxon:4932 20050404 SGD
+SGD S000001932 CDC26 GO:0031145 SGD_REF:S000044570|PMID:9469814 IPI P YFR036W|HIT3|SCD26 gene taxon:4932 20050404 SGD
+SGD S000000180 CDC27 GO:0005680 SGD_REF:S000058476|PMID:10465783 TAS C anaphase promoting complex (APC) subunit YBL084C|APC3|SNB1 gene taxon:4932 20010118 SGD
+SGD S000000180 CDC27 GO:0004842 SGD_REF:S000058476|PMID:10465783 TAS F anaphase promoting complex (APC) subunit YBL084C|APC3|SNB1 gene taxon:4932 20010118 SGD
+SGD S000000180 CDC27 GO:0005515 SGD_REF:S000058476|PMID:10465783 TAS F anaphase promoting complex (APC) subunit YBL084C|APC3|SNB1 gene taxon:4932 20010118 SGD
+SGD S000000180 CDC27 GO:0000022 SGD_REF:S000058476|PMID:10465783 TAS P anaphase promoting complex (APC) subunit YBL084C|APC3|SNB1 gene taxon:4932 20010118 SGD
+SGD S000000180 CDC27 GO:0000070 SGD_REF:S000058476|PMID:10465783 TAS P anaphase promoting complex (APC) subunit YBL084C|APC3|SNB1 gene taxon:4932 20010118 SGD
+SGD S000000180 CDC27 GO:0007091 SGD_REF:S000058476|PMID:10465783 TAS P anaphase promoting complex (APC) subunit YBL084C|APC3|SNB1 gene taxon:4932 20010118 SGD
+SGD S000000180 CDC27 GO:0008054 SGD_REF:S000058476|PMID:10465783 TAS P anaphase promoting complex (APC) subunit YBL084C|APC3|SNB1 gene taxon:4932 20010118 SGD
+SGD S000000180 CDC27 GO:0016567 SGD_REF:S000044570|PMID:9469814 IPI P anaphase promoting complex (APC) subunit YBL084C|APC3|SNB1 gene taxon:4932 20050408 SGD
+SGD S000000180 CDC27 GO:0031145 SGD_REF:S000042065|PMID:8895471 IDA P anaphase promoting complex (APC) subunit YBL084C|APC3|SNB1 gene taxon:4932 20050404 SGD
+SGD S000000180 CDC27 GO:0031145 SGD_REF:S000044570|PMID:9469814 IPI P anaphase promoting complex (APC) subunit YBL084C|APC3|SNB1 gene taxon:4932 20050404 SGD
+SGD S000000364 CDC28 GO:0005634 SGD_REF:S000044622|PMID:3312233 IDA C cyclin-dependent protein kinase YBR160W|CDK1|HSL5|SRM5 gene taxon:4932 20020622 SGD
+SGD S000000364 CDC28 GO:0005737 SGD_REF:S000044622|PMID:3312233 IDA C cyclin-dependent protein kinase YBR160W|CDK1|HSL5|SRM5 gene taxon:4932 20020128 SGD
+SGD S000000364 CDC28 GO:0004693 SGD_REF:S000058495 TAS F cyclin-dependent protein kinase YBR160W|CDK1|HSL5|SRM5 gene taxon:4932 20010119 SGD
+SGD S000000364 CDC28 GO:0000074 SGD_REF:S000058495 TAS P cyclin-dependent protein kinase YBR160W|CDK1|HSL5|SRM5 gene taxon:4932 20010119 SGD
+SGD S000000364 CDC28 GO:0000082 SGD_REF:S000058495 TAS P cyclin-dependent protein kinase YBR160W|CDK1|HSL5|SRM5 gene taxon:4932 20010119 SGD
+SGD S000000364 CDC28 GO:0000084 SGD_REF:S000058495 TAS P cyclin-dependent protein kinase YBR160W|CDK1|HSL5|SRM5 gene taxon:4932 20020618 SGD
+SGD S000000364 CDC28 GO:0000086 SGD_REF:S000058495 TAS P cyclin-dependent protein kinase YBR160W|CDK1|HSL5|SRM5 gene taxon:4932 20010119 SGD
+SGD S000000364 CDC28 GO:0006350 SGD_REF:S000080329|PMID:15629725 IMP P cyclin-dependent protein kinase YBR160W|CDK1|HSL5|SRM5 gene taxon:4932 20050125 SGD
+SGD S000000364 CDC28 GO:0006468 SGD_REF:S000058495 TAS P cyclin-dependent protein kinase YBR160W|CDK1|HSL5|SRM5 gene taxon:4932 20030204 SGD
+SGD S000000364 CDC28 GO:0040020 SGD_REF:S000055580|PMID:10619027 TAS P cyclin-dependent protein kinase YBR160W|CDK1|HSL5|SRM5 gene taxon:4932 20020618 SGD
+SGD S000004306 CDC3 GO:0000144 SGD_REF:S000057920|PMID:8791410 TAS C septin YLR314C gene taxon:4932 20010118 SGD
+SGD S000004306 CDC3 GO:0001400 SGD_REF:S000057920|PMID:8791410 IDA C septin YLR314C gene taxon:4932 20050124 SGD
+SGD S000004306 CDC3 GO:0005619 SGD_REF:S000057920|PMID:8791410 TAS C septin YLR314C gene taxon:4932 20010118 SGD
+SGD S000004306 CDC3 GO:0005628 SGD_REF:S000057920|PMID:8791410 TAS C septin YLR314C gene taxon:4932 20010118 SGD
+SGD S000004306 CDC3 GO:0005200 SGD_REF:S000057920|PMID:8791410 TAS F septin YLR314C gene taxon:4932 20010118 SGD
+SGD S000004306 CDC3 GO:0005545 SGD_REF:S000072964|PMID:12665577 IDA F septin YLR314C gene taxon:4932 20030505 SGD
+SGD S000004306 CDC3 GO:0000902 SGD_REF:S000057920|PMID:8791410 TAS P septin YLR314C gene taxon:4932 20021108 SGD
+SGD S000004306 CDC3 GO:0000910 SGD_REF:S000057920|PMID:8791410 TAS P septin YLR314C gene taxon:4932 20010119 SGD
+SGD S000004306 CDC3 GO:0007047 SGD_REF:S000057920|PMID:8791410 TAS P septin YLR314C gene taxon:4932 20010118 SGD
+SGD S000004306 CDC3 GO:0007120 SGD_REF:S000058399|PMID:9891811 TAS P septin YLR314C gene taxon:4932 20010118 SGD
+SGD S000004306 CDC3 GO:0030468 SGD_REF:S000057920|PMID:8791410 TAS P septin YLR314C gene taxon:4932 20010302 SGD
+SGD S000005783 CDC31 GO:0005643 SGD_REF:S000069412|PMID:11343909 TAS C nuclear pore complex subunit, spindle pole body calcium-binding protein component YOR257W|DSK1 gene taxon:4932 20020313 SGD
+SGD S000005783 CDC31 GO:0005825 SGD_REF:S000058447|PMID:9153752 TAS C nuclear pore complex subunit, spindle pole body calcium-binding protein component YOR257W|DSK1 gene taxon:4932 20010118 SGD
+SGD S000005783 CDC31 GO:0005200 SGD_REF:S000058447|PMID:9153752 IPI F nuclear pore complex subunit, spindle pole body calcium-binding protein component YOR257W|DSK1 gene taxon:4932 20010118 SGD
+SGD S000005783 CDC31 GO:0007020 SGD_REF:S000058447|PMID:9153752 IPI P nuclear pore complex subunit, spindle pole body calcium-binding protein component YOR257W|DSK1 gene taxon:4932 20010118 SGD
+SGD S000005783 CDC31 GO:0007103 SGD_REF:S000058447|PMID:9153752 IMP P nuclear pore complex subunit, spindle pole body calcium-binding protein component YOR257W|DSK1 gene taxon:4932 20010118 SGD
+SGD S000005499 CDC33 GO:0005634 SGD_REF:S000057604|PMID:8119957 IDA C mRNA cap binding protein eIF-4E YOL139C|TIF45|eIF-4E gene taxon:4932 20010118 SGD
+SGD S000005499 CDC33 GO:0005737 SGD_REF:S000057604|PMID:8119957 IDA C mRNA cap binding protein eIF-4E YOL139C|TIF45|eIF-4E gene taxon:4932 20010118 SGD
+SGD S000005499 CDC33 GO:0005840 SGD_REF:S000058753|PMID:9841679 TAS C mRNA cap binding protein eIF-4E YOL139C|TIF45|eIF-4E gene taxon:4932 20010124 SGD
+SGD S000005499 CDC33 GO:0016281 SGD_REF:S000058753|PMID:9841679 TAS C mRNA cap binding protein eIF-4E YOL139C|TIF45|eIF-4E gene taxon:4932 20050105 SGD
+SGD S000005499 CDC33 GO:0003743 SGD_REF:S000045345|PMID:3062383 ISS F mRNA cap binding protein eIF-4E YOL139C|TIF45|eIF-4E gene taxon:4932 20010118 SGD
+SGD S000005499 CDC33 GO:0003743 SGD_REF:S000058753|PMID:9841679 TAS F mRNA cap binding protein eIF-4E YOL139C|TIF45|eIF-4E gene taxon:4932 20010124 SGD
+SGD S000005499 CDC33 GO:0000074 SGD_REF:S000055832|PMID:2540596 IMP P mRNA cap binding protein eIF-4E YOL139C|TIF45|eIF-4E gene taxon:4932 20010118 SGD
+SGD S000005499 CDC33 GO:0000184 SGD_REF:S000080989|PMID:15753296 IDA P mRNA cap binding protein eIF-4E YOL139C|TIF45|eIF-4E gene taxon:4932 20050315 SGD
+SGD S000005499 CDC33 GO:0000184 SGD_REF:S000080989|PMID:15753296 IPI P mRNA cap binding protein eIF-4E YOL139C|TIF45|eIF-4E gene taxon:4932 20050315 SGD
+SGD S000005499 CDC33 GO:0006413 SGD_REF:S000045345|PMID:3062383 ISS P mRNA cap binding protein eIF-4E YOL139C|TIF45|eIF-4E gene taxon:4932 20010118 SGD
+SGD S000005499 CDC33 GO:0006413 SGD_REF:S000058753|PMID:9841679 TAS P mRNA cap binding protein eIF-4E YOL139C|TIF45|eIF-4E gene taxon:4932 20010124 SGD
+SGD S000002461 CDC34 GO:0000152 SGD_REF:S000058469|PMID:9346231 TAS C ubiquitin-conjugating enzyme YDR054C|DNA6|UBC3 gene taxon:4932 20010118 SGD
+SGD S000002461 CDC34 GO:0005634 SGD_REF:S000059560|PMID:11080155 IDA C ubiquitin-conjugating enzyme YDR054C|DNA6|UBC3 gene taxon:4932 20030619 SGD
+SGD S000002461 CDC34 GO:0005737 SGD_REF:S000059560|PMID:11080155 IDA C ubiquitin-conjugating enzyme YDR054C|DNA6|UBC3 gene taxon:4932 20030619 SGD
+SGD S000002461 CDC34 GO:0019005 SGD_REF:S000058369|PMID:9736614 IMP C ubiquitin-conjugating enzyme YDR054C|DNA6|UBC3 gene taxon:4932 20050408 SGD
+SGD S000002461 CDC34 GO:0004840 SGD_REF:S000042774|PMID:2842867 ISS SGD:S000003026 F ubiquitin-conjugating enzyme YDR054C|DNA6|UBC3 gene taxon:4932 20051028 SGD
+SGD S000002461 CDC34 GO:0004840 SGD_REF:S000042774|PMID:2842867 IMP F ubiquitin-conjugating enzyme YDR054C|DNA6|UBC3 gene taxon:4932 20051028 SGD
+SGD S000002461 CDC34 GO:0004840 SGD_REF:S000056659|PMID:1848239 IDA F ubiquitin-conjugating enzyme YDR054C|DNA6|UBC3 gene taxon:4932 20051028 SGD
+SGD S000002461 CDC34 GO:0004840 SGD_REF:S000042774|PMID:2842867 IDA F ubiquitin-conjugating enzyme YDR054C|DNA6|UBC3 gene taxon:4932 20051028 SGD
+SGD S000002461 CDC34 GO:0000082 SGD_REF:S000058469|PMID:9346231 TAS P ubiquitin-conjugating enzyme YDR054C|DNA6|UBC3 gene taxon:4932 20010118 SGD
+SGD S000002461 CDC34 GO:0000086 SGD_REF:S000045265|PMID:10409741 IPI P ubiquitin-conjugating enzyme YDR054C|DNA6|UBC3 gene taxon:4932 20010118 SGD
+SGD S000002461 CDC34 GO:0000209 SGD_REF:S000056659|PMID:1848239 IDA P ubiquitin-conjugating enzyme YDR054C|DNA6|UBC3 gene taxon:4932 20051028 SGD
+SGD S000002461 CDC34 GO:0016567 SGD_REF:S000058289|PMID:9499404 IGI P ubiquitin-conjugating enzyme YDR054C|DNA6|UBC3 gene taxon:4932 20050408 SGD
+SGD S000002461 CDC34 GO:0016567 SGD_REF:S000058289|PMID:9499404 IPI P ubiquitin-conjugating enzyme YDR054C|DNA6|UBC3 gene taxon:4932 20050408 SGD
+SGD S000002461 CDC34 GO:0031146 SGD_REF:S000041398|PMID:9346239 IDA P ubiquitin-conjugating enzyme YDR054C|DNA6|UBC3 gene taxon:4932 20050404 SGD
+SGD S000002324 CDC36 GO:0005634 SGD_REF:S000054264|PMID:7926748 IDA C transcriptional regulator YDL165W|DNA19|NOT2 gene taxon:4932 20010118 SGD
+SGD S000002324 CDC36 GO:0005737 SGD_REF:S000069437|PMID:11889048 IDA C transcriptional regulator YDL165W|DNA19|NOT2 gene taxon:4932 20020802 SGD
+SGD S000002324 CDC36 GO:0030015 SGD_REF:S000042122|PMID:10490603 IPI C transcriptional regulator YDL165W|DNA19|NOT2 gene taxon:4932 20020802 SGD
+SGD S000002324 CDC36 GO:0000175 SGD_REF:S000069437|PMID:11889048 TAS F transcriptional regulator YDL165W|DNA19|NOT2 gene taxon:4932 20030922 SGD
+SGD S000002324 CDC36 GO:0000074 SGD_REF:S000042286|PMID:2111445 IMP P transcriptional regulator YDL165W|DNA19|NOT2 gene taxon:4932 20010118 SGD
+SGD S000002324 CDC36 GO:0000122 SGD_REF:S000054264|PMID:7926748 TAS P transcriptional regulator YDL165W|DNA19|NOT2 gene taxon:4932 20010118 SGD
+SGD S000002324 CDC36 GO:0000288 SGD_REF:S000069437|PMID:11889048 IGI P transcriptional regulator YDL165W|DNA19|NOT2 gene taxon:4932 20030922 SGD
+SGD S000002324 CDC36 GO:0000288 SGD_REF:S000069437|PMID:11889048 IDA P transcriptional regulator YDL165W|DNA19|NOT2 gene taxon:4932 20030922 SGD
+SGD S000002324 CDC36 GO:0000288 SGD_REF:S000069437|PMID:11889048 IMP P transcriptional regulator YDL165W|DNA19|NOT2 gene taxon:4932 20030922 SGD
+SGD S000002324 CDC36 GO:0000289 SGD_REF:S000069437|PMID:11889048 IDA P transcriptional regulator YDL165W|DNA19|NOT2 gene taxon:4932 20020802 SGD
+SGD S000002324 CDC36 GO:0000749 SGD_REF:S000042286|PMID:2111445 IMP P transcriptional regulator YDL165W|DNA19|NOT2 gene taxon:4932 20010118 SGD
+SGD S000002324 CDC36 GO:0006357 SGD_REF:S000042122|PMID:10490603 IPI P transcriptional regulator YDL165W|DNA19|NOT2 gene taxon:4932 20020802 SGD
+SGD S000002575 CDC37 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDR168W|SMO1 gene taxon:4932 20031028 SGD
+SGD S000002575 CDC37 GO:0051082 SGD_REF:S000058479|PMID:9242486 IDA F YDR168W|SMO1 gene taxon:4932 20010118 SGD
+SGD S000002575 CDC37 GO:0000074 SGD_REF:S000048663|PMID:7753858 IMP P YDR168W|SMO1 gene taxon:4932 20010118 SGD
+SGD S000002575 CDC37 GO:0007103 SGD_REF:S000039989|PMID:9060463 IMP P YDR168W|SMO1 gene taxon:4932 20010118 SGD
+SGD S000002575 CDC37 GO:0007103 SGD_REF:S000039989|PMID:9060463 IGI P YDR168W|SMO1 gene taxon:4932 20010118 SGD
+SGD S000002575 CDC37 GO:0007165 SGD_REF:S000058479|PMID:9242486 TAS P YDR168W|SMO1 gene taxon:4932 20010118 SGD
+SGD S000000689 CDC39 GO:0005634 SGD_REF:S000054264|PMID:7926748 IDA C transcriptional regulator YCR093W|NOT1|ROS1|SMD6 gene taxon:4932 20010118 SGD
+SGD S000000689 CDC39 GO:0005737 SGD_REF:S000069437|PMID:11889048 IDA C transcriptional regulator YCR093W|NOT1|ROS1|SMD6 gene taxon:4932 20020802 SGD
+SGD S000000689 CDC39 GO:0030015 SGD_REF:S000042122|PMID:10490603 IPI C transcriptional regulator YCR093W|NOT1|ROS1|SMD6 gene taxon:4932 20020802 SGD
+SGD S000000689 CDC39 GO:0000175 SGD_REF:S000069437|PMID:11889048 IDA F transcriptional regulator YCR093W|NOT1|ROS1|SMD6 gene taxon:4932 20020802 SGD
+SGD S000000689 CDC39 GO:0000074 SGD_REF:S000041086|PMID:2680756 IMP P transcriptional regulator YCR093W|NOT1|ROS1|SMD6 gene taxon:4932 20010118 SGD
+SGD S000000689 CDC39 GO:0000122 SGD_REF:S000054264|PMID:7926748 TAS P transcriptional regulator YCR093W|NOT1|ROS1|SMD6 gene taxon:4932 20010118 SGD
+SGD S000000689 CDC39 GO:0000288 SGD_REF:S000069437|PMID:11889048 IGI P transcriptional regulator YCR093W|NOT1|ROS1|SMD6 gene taxon:4932 20030922 SGD
+SGD S000000689 CDC39 GO:0000288 SGD_REF:S000069437|PMID:11889048 IMP P transcriptional regulator YCR093W|NOT1|ROS1|SMD6 gene taxon:4932 20030922 SGD
+SGD S000000689 CDC39 GO:0000288 SGD_REF:S000069437|PMID:11889048 IDA P transcriptional regulator YCR093W|NOT1|ROS1|SMD6 gene taxon:4932 20030922 SGD
+SGD S000000689 CDC39 GO:0000289 SGD_REF:S000069437|PMID:11889048 IDA P transcriptional regulator YCR093W|NOT1|ROS1|SMD6 gene taxon:4932 20020802 SGD
+SGD S000000689 CDC39 GO:0000749 SGD_REF:S000040388|PMID:2099190 IMP P transcriptional regulator YCR093W|NOT1|ROS1|SMD6 gene taxon:4932 20010118 SGD
+SGD S000000689 CDC39 GO:0006357 SGD_REF:S000042122|PMID:10490603 IPI P transcriptional regulator YCR093W|NOT1|ROS1|SMD6 gene taxon:4932 20020802 SGD
+SGD S000001885 CDC4 GO:0043224 SGD_REF:S000059560|PMID:11080155 IDA C ubiquitin ligase subunit YFL009W gene taxon:4932 20050421 SGD
+SGD S000001885 CDC4 GO:0004842 SGD_REF:S000058469|PMID:9346231 TAS F ubiquitin ligase subunit YFL009W gene taxon:4932 20010118 SGD
+SGD S000001885 CDC4 GO:0005515 SGD_REF:S000040889|PMID:9312054 IPI SGD:S000003730 F ubiquitin ligase subunit YFL009W gene taxon:4932 20030702 SGD
+SGD S000001885 CDC4 GO:0000082 SGD_REF:S000045265|PMID:10409741 IMP P ubiquitin ligase subunit YFL009W gene taxon:4932 20010118 SGD
+SGD S000001885 CDC4 GO:0000086 SGD_REF:S000045265|PMID:10409741 IGI P ubiquitin ligase subunit YFL009W gene taxon:4932 20010118 SGD
+SGD S000001885 CDC4 GO:0000086 SGD_REF:S000045265|PMID:10409741 IMP P ubiquitin ligase subunit YFL009W gene taxon:4932 20010118 SGD
+SGD S000001885 CDC4 GO:0007126 SGD_REF:S000055075|PMID:328339 IMP P ubiquitin ligase subunit YFL009W gene taxon:4932 20060209 SGD
+SGD S000001885 CDC4 GO:0016567 SGD_REF:S000058289|PMID:9499404 IGI P ubiquitin ligase subunit YFL009W gene taxon:4932 20050408 SGD
+SGD S000001885 CDC4 GO:0016567 SGD_REF:S000058289|PMID:9499404 IPI P ubiquitin ligase subunit YFL009W gene taxon:4932 20050408 SGD
+SGD S000001885 CDC4 GO:0031146 SGD_REF:S000041398|PMID:9346239 IDA P ubiquitin ligase subunit YFL009W gene taxon:4932 20050404 SGD
+SGD S000002772 CDC40 GO:0005635 SGD_REF:S000052822|PMID:9862477 IDA C beta transducin family YDR364C|PRP17|SLT15|SLU4 gene taxon:4932 20021024 SGD
+SGD S000002772 CDC40 GO:0005643 SGD_REF:S000052822|PMID:9862477 IDA C beta transducin family YDR364C|PRP17|SLT15|SLU4 gene taxon:4932 20021024 SGD
+SGD S000002772 CDC40 GO:0005681 SGD_REF:S000045092|PMID:10628969 IGI C beta transducin family YDR364C|PRP17|SLT15|SLU4 gene taxon:4932 20021021 SGD
+SGD S000002772 CDC40 GO:0003676 SGD_REF:S000039211|PMID:9769104 IPI F beta transducin family YDR364C|PRP17|SLT15|SLU4 gene taxon:4932 20021024 SGD
+SGD S000002772 CDC40 GO:0031202 SGD_REF:S000065954|PMID:11565750 TAS F beta transducin family YDR364C|PRP17|SLT15|SLU4 gene taxon:4932 20021024 SGD
+SGD S000002772 CDC40 GO:0000084 SGD_REF:S000052822|PMID:9862477 IDA P beta transducin family YDR364C|PRP17|SLT15|SLU4 gene taxon:4932 20021024 SGD
+SGD S000002772 CDC40 GO:0000398 SGD_REF:S000045092|PMID:10628969 IMP P beta transducin family YDR364C|PRP17|SLT15|SLU4 gene taxon:4932 20030115 SGD
+SGD S000002772 CDC40 GO:0006260 SGD_REF:S000045092|PMID:10628969 TAS P beta transducin family YDR364C|PRP17|SLT15|SLU4 gene taxon:4932 20020927 SGD
+SGD S000002772 CDC40 GO:0006974 SGD_REF:S000076175|PMID:12482937 IMP P beta transducin family YDR364C|PRP17|SLT15|SLU4 gene taxon:4932 20060406 SGD
+SGD S000002772 CDC40 GO:0030472 SGD_REF:S000045092|PMID:10628969 TAS P beta transducin family YDR364C|PRP17|SLT15|SLU4 gene taxon:4932 20030115 SGD
+SGD S000004219 CDC42 GO:0005625 SGD_REF:S000056064|PMID:10066831 IDA C Rho subfamily of Ras-like proteins YLR229C gene taxon:4932 20010118 SGD
+SGD S000004219 CDC42 GO:0005886 SGD_REF:S000056064|PMID:10066831 IDA C Rho subfamily of Ras-like proteins YLR229C gene taxon:4932 20010118 SGD
+SGD S000004219 CDC42 GO:0005934 SGD_REF:S000058399|PMID:9891811 IDA C Rho subfamily of Ras-like proteins YLR229C gene taxon:4932 20010118 SGD
+SGD S000004219 CDC42 GO:0005935 SGD_REF:S000058399|PMID:9891811 IDA C Rho subfamily of Ras-like proteins YLR229C gene taxon:4932 20010118 SGD
+SGD S000004219 CDC42 GO:0043332 SGD_REF:S000056064|PMID:10066831 IDA C Rho subfamily of Ras-like proteins YLR229C gene taxon:4932 20010118 SGD
+SGD S000004219 CDC42 GO:0003924 SGD_REF:S000058399|PMID:9891811 IDA F Rho subfamily of Ras-like proteins YLR229C gene taxon:4932 20010118 SGD
+SGD S000004219 CDC42 GO:0004871 SGD_REF:S000058399|PMID:9891811 TAS F Rho subfamily of Ras-like proteins YLR229C gene taxon:4932 20010118 SGD
+SGD S000004219 CDC42 GO:0000750 SGD_REF:S000059191|PMID:11003652 IGI P Rho subfamily of Ras-like proteins YLR229C gene taxon:4932 20021206 SGD
+SGD S000004219 CDC42 GO:0000750 SGD_REF:S000059191|PMID:11003652 IMP P Rho subfamily of Ras-like proteins YLR229C gene taxon:4932 20021206 SGD
+SGD S000004219 CDC42 GO:0001403 SGD_REF:S000056064|PMID:10066831 IMP P Rho subfamily of Ras-like proteins YLR229C gene taxon:4932 20010118 SGD
+SGD S000004219 CDC42 GO:0006887 SGD_REF:S000068748|PMID:11595741 IGI P Rho subfamily of Ras-like proteins YLR229C gene taxon:4932 20021105 SGD
+SGD S000004219 CDC42 GO:0007096 SGD_REF:S000071653|PMID:12234925 IMP P Rho subfamily of Ras-like proteins YLR229C gene taxon:4932 20050324 SGD
+SGD S000004219 CDC42 GO:0007118 SGD_REF:S000056064|PMID:10066831 IMP P Rho subfamily of Ras-like proteins YLR229C gene taxon:4932 20010118 SGD
+SGD S000004219 CDC42 GO:0007119 SGD_REF:S000056064|PMID:10066831 IMP P Rho subfamily of Ras-like proteins YLR229C gene taxon:4932 20010118 SGD
+SGD S000004219 CDC42 GO:0007124 SGD_REF:S000056064|PMID:10066831 IMP P Rho subfamily of Ras-like proteins YLR229C gene taxon:4932 20010118 SGD
+SGD S000004219 CDC42 GO:0007266 SGD_REF:S000058399|PMID:9891811 TAS P Rho subfamily of Ras-like proteins YLR229C gene taxon:4932 20010118 SGD
+SGD S000004219 CDC42 GO:0030468 SGD_REF:S000058399|PMID:9891811 IMP P Rho subfamily of Ras-like proteins YLR229C gene taxon:4932 20010302 SGD
+SGD S000004219 CDC42 GO:0031384 SGD_REF:S000077102|PMID:14734532 IMP P Rho subfamily of Ras-like proteins YLR229C gene taxon:4932 20050719 SGD
+SGD S000003123 CDC43 GO:0005622 SGD_REF:S000058399|PMID:9891811 TAS C protein geranylgeranyltransferase type 1 polypeptide subunit YGL155W|CAL1 gene taxon:4932 20010118 SGD
+SGD S000003123 CDC43 GO:0005953 SGD_REF:S000044942|PMID:1400380 IDA C protein geranylgeranyltransferase type 1 polypeptide subunit YGL155W|CAL1 gene taxon:4932 20050404 SGD
+SGD S000003123 CDC43 GO:0004661 SGD_REF:S000056064|PMID:10066831 IDA F protein geranylgeranyltransferase type 1 polypeptide subunit YGL155W|CAL1 gene taxon:4932 20010118 SGD
+SGD S000003123 CDC43 GO:0004661 SGD_REF:S000049697|PMID:2034682 IDA F protein geranylgeranyltransferase type 1 polypeptide subunit YGL155W|CAL1 gene taxon:4932 20030324 SGD
+SGD S000003123 CDC43 GO:0004662 SGD_REF:S000044942|PMID:1400380 IDA F protein geranylgeranyltransferase type 1 polypeptide subunit YGL155W|CAL1 gene taxon:4932 20051228 SGD
+SGD S000003123 CDC43 GO:0004871 SGD_REF:S000058399|PMID:9891811 TAS F protein geranylgeranyltransferase type 1 polypeptide subunit YGL155W|CAL1 gene taxon:4932 20010118 SGD
+SGD S000003123 CDC43 GO:0006874 SGD_REF:S000058399|PMID:9891811 IMP P protein geranylgeranyltransferase type 1 polypeptide subunit YGL155W|CAL1 gene taxon:4932 20010118 SGD
+SGD S000003123 CDC43 GO:0007264 SGD_REF:S000058399|PMID:9891811 TAS P protein geranylgeranyltransferase type 1 polypeptide subunit YGL155W|CAL1 gene taxon:4932 20010118 SGD
+SGD S000003123 CDC43 GO:0018348 SGD_REF:S000049697|PMID:2034682 IDA P protein geranylgeranyltransferase type 1 polypeptide subunit YGL155W|CAL1 gene taxon:4932 20030324 SGD
+SGD S000003123 CDC43 GO:0030468 SGD_REF:S000058399|PMID:9891811 IMP P protein geranylgeranyltransferase type 1 polypeptide subunit YGL155W|CAL1 gene taxon:4932 20010302 SGD
+SGD S000004093 CDC45 GO:0005656 SGD_REF:S000054350|PMID:9335335 IDA C chromosomal DNA replication initiation protein YLR103C|SLD4 gene taxon:4932 20021126 SGD
+SGD S000004093 CDC45 GO:0005657 SGD_REF:S000054350|PMID:9335335 IDA C chromosomal DNA replication initiation protein YLR103C|SLD4 gene taxon:4932 20021126 SGD
+SGD S000004093 CDC45 GO:0003677 SGD_REF:S000058275|PMID:9442876 TAS F chromosomal DNA replication initiation protein YLR103C|SLD4 gene taxon:4932 20021107 SGD
+SGD S000004093 CDC45 GO:0006267 SGD_REF:S000054350|PMID:9335335 IPI P chromosomal DNA replication initiation protein YLR103C|SLD4 gene taxon:4932 20021126 SGD
+SGD S000004093 CDC45 GO:0006270 SGD_REF:S000058400|PMID:9914182 TAS P chromosomal DNA replication initiation protein YLR103C|SLD4 gene taxon:4932 20010118 SGD
+SGD S000004093 CDC45 GO:0006271 SGD_REF:S000073092|PMID:12730134 TAS P chromosomal DNA replication initiation protein YLR103C|SLD4 gene taxon:4932 20030508 SGD
+SGD S000004264 CDC46 GO:0005656 SGD_REF:S000054350|PMID:9335335 IDA C YLR274W|BOB1|MCM5 gene taxon:4932 20021201 SGD
+SGD S000004264 CDC46 GO:0005657 SGD_REF:S000054350|PMID:9335335 IDA C YLR274W|BOB1|MCM5 gene taxon:4932 20021201 SGD
+SGD S000004264 CDC46 GO:0005737 SGD_REF:S000058275|PMID:9442876 TAS C YLR274W|BOB1|MCM5 gene taxon:4932 20010118 SGD
+SGD S000004264 CDC46 GO:0042555 SGD_REF:S000072578|PMID:12480933 IDA C YLR274W|BOB1|MCM5 gene taxon:4932 20041024 SGD
+SGD S000004264 CDC46 GO:0003682 SGD_REF:S000058275|PMID:9442876 TAS F YLR274W|BOB1|MCM5 gene taxon:4932 20010118 SGD
+SGD S000004264 CDC46 GO:0004003 SGD_REF:S000058400|PMID:9914182 TAS F YLR274W|BOB1|MCM5 gene taxon:4932 20010118 SGD
+SGD S000004264 CDC46 GO:0006267 SGD_REF:S000054350|PMID:9335335 IPI P YLR274W|BOB1|MCM5 gene taxon:4932 20021201 SGD
+SGD S000004264 CDC46 GO:0006268 SGD_REF:S000058400|PMID:9914182 TAS P YLR274W|BOB1|MCM5 gene taxon:4932 20010118 SGD
+SGD S000004264 CDC46 GO:0006270 SGD_REF:S000058275|PMID:9442876 TAS P YLR274W|BOB1|MCM5 gene taxon:4932 20010118 SGD
+SGD S000004264 CDC46 GO:0006343 SGD_REF:S000073701|PMID:12750362 IMP P YLR274W|BOB1|MCM5 gene taxon:4932 20030818 SGD
+SGD S000000406 CDC47 GO:0005634 SGD_REF:S000051716|PMID:10704410 IDA C YBR202W|MCM7 gene taxon:4932 20020625 SGD
+SGD S000000406 CDC47 GO:0005656 SGD_REF:S000054350|PMID:9335335 IDA C YBR202W|MCM7 gene taxon:4932 20021202 SGD
+SGD S000000406 CDC47 GO:0005737 SGD_REF:S000058275|PMID:9442876 TAS C YBR202W|MCM7 gene taxon:4932 20010118 SGD
+SGD S000000406 CDC47 GO:0005737 SGD_REF:S000051716|PMID:10704410 IDA C YBR202W|MCM7 gene taxon:4932 20020625 SGD
+SGD S000000406 CDC47 GO:0042555 SGD_REF:S000072578|PMID:12480933 IDA C YBR202W|MCM7 gene taxon:4932 20041024 SGD
+SGD S000000406 CDC47 GO:0003682 SGD_REF:S000058275|PMID:9442876 TAS F YBR202W|MCM7 gene taxon:4932 20010118 SGD
+SGD S000000406 CDC47 GO:0004003 SGD_REF:S000058400|PMID:9914182 TAS F YBR202W|MCM7 gene taxon:4932 20010118 SGD
+SGD S000000406 CDC47 GO:0005524 SGD_REF:S000072578|PMID:12480933 IDA F YBR202W|MCM7 gene taxon:4932 20030612 SGD
+SGD S000000406 CDC47 GO:0006267 SGD_REF:S000054350|PMID:9335335 IPI P YBR202W|MCM7 gene taxon:4932 20021202 SGD
+SGD S000000406 CDC47 GO:0006268 SGD_REF:S000058400|PMID:9914182 TAS P YBR202W|MCM7 gene taxon:4932 20010118 SGD
+SGD S000000406 CDC47 GO:0006270 SGD_REF:S000058275|PMID:9442876 TAS P YBR202W|MCM7 gene taxon:4932 20010118 SGD
+SGD S000002284 CDC48 GO:0005634 SGD_REF:S000047715|PMID:9436996 IDA C YDL126C gene taxon:4932 20010118 SGD
+SGD S000002284 CDC48 GO:0005789 SGD_REF:S000086063|PMID:15910746 IDA C YDL126C gene taxon:4932 20050808 SGD
+SGD S000002284 CDC48 GO:0005792 SGD_REF:S000055149|PMID:1860879 IDA C YDL126C gene taxon:4932 20010118 SGD
+SGD S000002284 CDC48 GO:0005829 SGD_REF:S000069082|PMID:11740563 IDA C YDL126C gene taxon:4932 20020906 SGD
+SGD S000002284 CDC48 GO:0005829 SGD_REF:S000086063|PMID:15910746 IDA C YDL126C gene taxon:4932 20050808 SGD
+SGD S000002284 CDC48 GO:0016887 SGD_REF:S000042102|PMID:7492595 IDA F YDL126C gene taxon:4932 20010118 SGD
+SGD S000002284 CDC48 GO:0006511 SGD_REF:S000049317|PMID:8890162 IPI P YDL126C gene taxon:4932 20010118 SGD
+SGD S000002284 CDC48 GO:0006511 SGD_REF:S000049317|PMID:8890162 IDA P YDL126C gene taxon:4932 20010118 SGD
+SGD S000002284 CDC48 GO:0006906 SGD_REF:S000057372|PMID:7553849 IDA P YDL126C gene taxon:4932 20010118 SGD
+SGD S000002284 CDC48 GO:0006915 SGD_REF:S000072937|PMID:11738144 TAS P YDL126C gene taxon:4932 20030414 SGD
+SGD S000002284 CDC48 GO:0007049 SGD_REF:S000055149|PMID:1860879 IMP P YDL126C gene taxon:4932 20010118 SGD
+SGD S000002284 CDC48 GO:0007049 SGD_REF:S000045449|PMID:6749598 IMP P YDL126C gene taxon:4932 20010118 SGD
+SGD S000002284 CDC48 GO:0015031 SGD_REF:S000069082|PMID:11740563 IDA P YDL126C gene taxon:4932 20020906 SGD
+SGD S000002284 CDC48 GO:0030433 SGD_REF:S000069104|PMID:11756557 IMP P YDL126C gene taxon:4932 20030130 SGD
+SGD S000004603 CDC5 GO:0000922 SGD_REF:S000050961|PMID:10594031 IDA C protein kinase YMR001C|MSD2|PKX2 gene taxon:4932 20030627 SGD
+SGD S000004603 CDC5 GO:0005634 SGD_REF:S000047786|PMID:9819423 IDA C protein kinase YMR001C|MSD2|PKX2 gene taxon:4932 20030213 SGD
+SGD S000004603 CDC5 GO:0005935 SGD_REF:S000050961|PMID:10594031 IDA C protein kinase YMR001C|MSD2|PKX2 gene taxon:4932 20030627 SGD
+SGD S000004603 CDC5 GO:0004672 SGD_REF:S000068838|PMID:12637549 IDA F protein kinase YMR001C|MSD2|PKX2 gene taxon:4932 20060612 SGD
+SGD S000004603 CDC5 GO:0004680 SGD_REF:S000052953|PMID:8321244 IDA F protein kinase YMR001C|MSD2|PKX2 gene taxon:4932 20060612 SGD
+SGD S000004603 CDC5 GO:0042801 SGD_REF:S000052953|PMID:8321244 ISS FLYBASE:FBgn0003124 F protein kinase YMR001C|MSD2|PKX2 gene taxon:4932 20060612 SGD
+SGD S000004603 CDC5 GO:0006261 SGD_REF:S000044356|PMID:8943332 IDA P protein kinase YMR001C|MSD2|PKX2 gene taxon:4932 20030213 SGD
+SGD S000004603 CDC5 GO:0006261 SGD_REF:S000044356|PMID:8943332 IMP P protein kinase YMR001C|MSD2|PKX2 gene taxon:4932 20030213 SGD
+SGD S000004603 CDC5 GO:0006468 SGD_REF:S000052953|PMID:8321244 IDA P protein kinase YMR001C|MSD2|PKX2 gene taxon:4932 20030213 SGD
+SGD S000000690 CDC50 GO:0000299 SGD_REF:S000072635|PMID:12589066 IDA C YCR094W gene taxon:4932 20030309 SGD
+SGD S000000690 CDC50 GO:0005770 SGD_REF:S000072635|PMID:12589066 IDA C YCR094W gene taxon:4932 20030309 SGD
+SGD S000000690 CDC50 GO:0005802 SGD_REF:S000076777|PMID:15090616 IDA C YCR094W gene taxon:4932 20051208 SGD
+SGD S000000690 CDC50 contributes_to GO:0004012 SGD_REF:S000076777|PMID:15090616 IPI SGD:S000000024 F YCR094W gene taxon:4932 20051212 SGD
+SGD S000000690 CDC50 GO:0000080 SGD_REF:S000059546|PMID:11180453 IDA P YCR094W gene taxon:4932 20020927 SGD
+SGD S000000690 CDC50 GO:0000080 SGD_REF:S000059546|PMID:11180453 IGI P YCR094W gene taxon:4932 20020927 SGD
+SGD S000000690 CDC50 GO:0000080 SGD_REF:S000059546|PMID:11180453 IMP P YCR094W gene taxon:4932 20020927 SGD
+SGD S000000690 CDC50 GO:0006897 SGD_REF:S000086880|PMID:16195350 IGI SGD:S000004046 P YCR094W gene taxon:4932 20051208 SGD
+SGD S000000690 CDC50 GO:0045332 SGD_REF:S000076777|PMID:15090616 IGI SGD:S000005267 P YCR094W gene taxon:4932 20051212 SGD
+SGD S000000690 CDC50 GO:0051666 SGD_REF:S000086880|PMID:16195350 IGI SGD:S000004046 P YCR094W gene taxon:4932 20051208 SGD
+SGD S000002290 CDC53 GO:0000152 SGD_REF:S000058469|PMID:9346231 TAS C YDL132W gene taxon:4932 20010118 SGD
+SGD S000002290 CDC53 GO:0019005 SGD_REF:S000054644|PMID:9716410 TAS C YDL132W gene taxon:4932 20030523 SGD
+SGD S000002290 CDC53 GO:0019005 SGD_REF:S000041398|PMID:9346239 IDA C YDL132W gene taxon:4932 20050408 SGD
+SGD S000002290 CDC53 GO:0003688 SGD_REF:S000114165|PMID:16421250 IPI F YDL132W gene taxon:4932 20060123 SGD
+SGD S000002290 CDC53 GO:0004842 SGD_REF:S000058469|PMID:9346231 TAS F YDL132W gene taxon:4932 20010118 SGD
+SGD S000002290 CDC53 GO:0005198 SGD_REF:S000045265|PMID:10409741 TAS F YDL132W gene taxon:4932 20010118 SGD
+SGD S000002290 CDC53 GO:0000082 SGD_REF:S000058469|PMID:9346231 TAS P YDL132W gene taxon:4932 20010118 SGD
+SGD S000002290 CDC53 GO:0000086 SGD_REF:S000045265|PMID:10409741 IPI P YDL132W gene taxon:4932 20010118 SGD
+SGD S000002290 CDC53 GO:0016567 SGD_REF:S000058289|PMID:9499404 IGI P YDL132W gene taxon:4932 20050408 SGD
+SGD S000002290 CDC53 GO:0016567 SGD_REF:S000058289|PMID:9499404 IPI P YDL132W gene taxon:4932 20050408 SGD
+SGD S000002290 CDC53 GO:0031146 SGD_REF:S000041398|PMID:9346239 IDA P YDL132W gene taxon:4932 20050404 SGD
+SGD S000006223 CDC54 GO:0005634 SGD_REF:S000051716|PMID:10704410 IDA C YPR019W|HCD21|MCM4 gene taxon:4932 20020625 SGD
+SGD S000006223 CDC54 GO:0005656 SGD_REF:S000054350|PMID:9335335 IDA C YPR019W|HCD21|MCM4 gene taxon:4932 20021202 SGD
+SGD S000006223 CDC54 GO:0005737 SGD_REF:S000058275|PMID:9442876 TAS C YPR019W|HCD21|MCM4 gene taxon:4932 20010118 SGD
+SGD S000006223 CDC54 GO:0005737 SGD_REF:S000051716|PMID:10704410 IDA C YPR019W|HCD21|MCM4 gene taxon:4932 20020625 SGD
+SGD S000006223 CDC54 GO:0042555 SGD_REF:S000072578|PMID:12480933 IDA C YPR019W|HCD21|MCM4 gene taxon:4932 20041024 SGD
+SGD S000006223 CDC54 GO:0003682 SGD_REF:S000058275|PMID:9442876 TAS F YPR019W|HCD21|MCM4 gene taxon:4932 20010118 SGD
+SGD S000006223 CDC54 GO:0004003 SGD_REF:S000058400|PMID:9914182 TAS F YPR019W|HCD21|MCM4 gene taxon:4932 20010118 SGD
+SGD S000006223 CDC54 GO:0006267 SGD_REF:S000054350|PMID:9335335 IPI P YPR019W|HCD21|MCM4 gene taxon:4932 20021202 SGD
+SGD S000006223 CDC54 GO:0006268 SGD_REF:S000058400|PMID:9914182 TAS P YPR019W|HCD21|MCM4 gene taxon:4932 20010118 SGD
+SGD S000006223 CDC54 GO:0006270 SGD_REF:S000058275|PMID:9442876 TAS P YPR019W|HCD21|MCM4 gene taxon:4932 20010118 SGD
+SGD S000003158 CDC55 GO:0000159 SGD_REF:S000045742|PMID:10329624 TAS C protein phosphatase 2A regulatory subunit B YGL190C gene taxon:4932 20010118 SGD
+SGD S000003158 CDC55 GO:0005634 SGD_REF:S000071578|PMID:12388751 IDA C protein phosphatase 2A regulatory subunit B YGL190C gene taxon:4932 20040513 SGD
+SGD S000003158 CDC55 GO:0005934 SGD_REF:S000071578|PMID:12388751 IDA C protein phosphatase 2A regulatory subunit B YGL190C gene taxon:4932 20040513 SGD
+SGD S000003158 CDC55 GO:0005935 SGD_REF:S000071578|PMID:12388751 IDA C protein phosphatase 2A regulatory subunit B YGL190C gene taxon:4932 20040513 SGD
+SGD S000003158 CDC55 GO:0000158 SGD_REF:S000045742|PMID:10329624 TAS F protein phosphatase 2A regulatory subunit B YGL190C gene taxon:4932 20010118 SGD
+SGD S000003158 CDC55 GO:0006412 SGD_REF:S000045742|PMID:10329624 IMP P protein phosphatase 2A regulatory subunit B YGL190C gene taxon:4932 20010118 SGD
+SGD S000003158 CDC55 GO:0006470 SGD_REF:S000055155|PMID:9001215 TAS P protein phosphatase 2A regulatory subunit B YGL190C gene taxon:4932 20030430 SGD
+SGD S000003158 CDC55 GO:0007015 SGD_REF:S000055155|PMID:9001215 TAS P protein phosphatase 2A regulatory subunit B YGL190C gene taxon:4932 20010118 SGD
+SGD S000003158 CDC55 GO:0007094 SGD_REF:S000055155|PMID:9001215 IMP P protein phosphatase 2A regulatory subunit B YGL190C gene taxon:4932 20010118 SGD
+SGD S000003158 CDC55 GO:0007117 SGD_REF:S000055155|PMID:9001215 TAS P protein phosphatase 2A regulatory subunit B YGL190C gene taxon:4932 20010118 SGD
+SGD S000003158 CDC55 GO:0007124 SGD_REF:S000042772|PMID:9055077 IMP P protein phosphatase 2A regulatory subunit B YGL190C gene taxon:4932 20010118 SGD
+SGD S000003730 CDC6 GO:0005656 SGD_REF:S000058275|PMID:9442876 TAS C pre-initiation complex component YJL194W gene taxon:4932 20010118 SGD
+SGD S000003730 CDC6 GO:0003689 SGD_REF:S000058275|PMID:9442876 TAS F pre-initiation complex component YJL194W gene taxon:4932 20010118 SGD
+SGD S000003730 CDC6 GO:0005515 SGD_REF:S000040889|PMID:9312054 IPI SGD:S000001885 F pre-initiation complex component YJL194W gene taxon:4932 20030702 SGD
+SGD S000003730 CDC6 GO:0016887 SGD_REF:S000058400|PMID:9914182 TAS F pre-initiation complex component YJL194W gene taxon:4932 20010118 SGD
+SGD S000003730 CDC6 GO:0006267 SGD_REF:S000058275|PMID:9442876 TAS P pre-initiation complex component YJL194W gene taxon:4932 20010118 SGD
+SGD S000006081 CDC60 GO:0005737 SGD_REF:S000058370|PMID:9742237 IDA C leucine--tRNA ligase YPL160W|LeuRS gene taxon:4932 20021202 SGD
+SGD S000006081 CDC60 GO:0004823 SGD_REF:S000058370|PMID:9742237 IDA F leucine--tRNA ligase YPL160W|LeuRS gene taxon:4932 20021202 SGD
+SGD S000006081 CDC60 GO:0006429 SGD_REF:S000058370|PMID:9742237 IDA P leucine--tRNA ligase YPL160W|LeuRS gene taxon:4932 20021202 SGD
+SGD S000006690 CDC65 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tRNA-Gln tQ(CUG)M|DNA33|SUP70 gene taxon:4932 20030507 SGD
+SGD S000006690 CDC65 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tRNA-Gln tQ(CUG)M|DNA33|SUP70 gene taxon:4932 20030507 SGD
+SGD S000006690 CDC65 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tRNA-Gln tQ(CUG)M|DNA33|SUP70 gene taxon:4932 20030507 SGD
+SGD S000002175 CDC7 GO:0005654 SGD_REF:S000058400|PMID:9914182 TAS C Cdc7p-Dbf4p kinase complex catalytic subunit YDL017W|LSD6|SAS1 gene taxon:4932 20010118 SGD
+SGD S000002175 CDC7 GO:0004674 SGD_REF:S000058275|PMID:9442876 TAS F Cdc7p-Dbf4p kinase complex catalytic subunit YDL017W|LSD6|SAS1 gene taxon:4932 20010118 SGD
+SGD S000002175 CDC7 GO:0006270 SGD_REF:S000058275|PMID:9442876 TAS P Cdc7p-Dbf4p kinase complex catalytic subunit YDL017W|LSD6|SAS1 gene taxon:4932 20010118 SGD
+SGD S000002175 CDC7 GO:0006275 SGD_REF:S000058275|PMID:9442876 TAS P Cdc7p-Dbf4p kinase complex catalytic subunit YDL017W|LSD6|SAS1 gene taxon:4932 20010118 SGD
+SGD S000002175 CDC7 GO:0006468 SGD_REF:S000058275|PMID:9442876 TAS P Cdc7p-Dbf4p kinase complex catalytic subunit YDL017W|LSD6|SAS1 gene taxon:4932 20010118 SGD
+SGD S000004410 CDC73 GO:0005634 SGD_REF:S000080456|PMID:15643076 IDA C YLR418C gene taxon:4932 20050228 SGD
+SGD S000004410 CDC73 GO:0005634 SGD_REF:S000058039|PMID:9032243 IDA C YLR418C gene taxon:4932 20051108 SGD
+SGD S000004410 CDC73 GO:0008023 SGD_REF:S000071357|PMID:12242279 IPI C YLR418C gene taxon:4932 20021004 SGD
+SGD S000004410 CDC73 GO:0016593 SGD_REF:S000073599|PMID:12773564 TAS C YLR418C gene taxon:4932 20040129 SGD
+SGD S000004410 CDC73 GO:0016593 SGD_REF:S000058039|PMID:9032243 IPI SGD:S000000483 C YLR418C gene taxon:4932 20051108 SGD
+SGD S000004410 CDC73 GO:0016944 SGD_REF:S000071357|PMID:12242279 IPI F YLR418C gene taxon:4932 20021004 SGD
+SGD S000004410 CDC73 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P YLR418C gene taxon:4932 20060203 SGD
+SGD S000004410 CDC73 GO:0006310 SGD_REF:S000041293|PMID:9891041 IMP P YLR418C gene taxon:4932 20051108 SGD
+SGD S000004410 CDC73 GO:0006368 SGD_REF:S000071357|PMID:12242279 IPI P YLR418C gene taxon:4932 20021004 SGD
+SGD S000004410 CDC73 GO:0016571 SGD_REF:S000073147|PMID:12667454 IMP P YLR418C gene taxon:4932 20050503 SGD
+SGD S000003818 CDC8 GO:0005634 SGD_REF:S000049877|PMID:6094555 IDA C thymidylate kinase YJR057W gene taxon:4932 20010118 SGD
+SGD S000003818 CDC8 GO:0005737 SGD_REF:S000049877|PMID:6094555 IDA C thymidylate kinase YJR057W gene taxon:4932 20010118 SGD
+SGD S000003818 CDC8 GO:0004798 SGD_REF:S000049877|PMID:6094555 IDA F thymidylate kinase YJR057W gene taxon:4932 20010118 SGD
+SGD S000003818 CDC8 GO:0004798 SGD_REF:S000053290|PMID:6088527 IDA F thymidylate kinase YJR057W gene taxon:4932 20010118 SGD
+SGD S000003818 CDC8 GO:0009041 SGD_REF:S000049877|PMID:6094555 IDA F thymidylate kinase YJR057W gene taxon:4932 20040514 SGD
+SGD S000003818 CDC8 GO:0006227 SGD_REF:S000049877|PMID:6094555 IDA P thymidylate kinase YJR057W gene taxon:4932 20040514 SGD
+SGD S000003818 CDC8 GO:0006233 SGD_REF:S000049877|PMID:6094555 IDA P thymidylate kinase YJR057W gene taxon:4932 20010118 SGD
+SGD S000003818 CDC8 GO:0006235 SGD_REF:S000049877|PMID:6094555 IDA P thymidylate kinase YJR057W gene taxon:4932 20010118 SGD
+SGD S000003818 CDC8 GO:0006261 SGD_REF:S000052759|PMID:6338494 IDA P thymidylate kinase YJR057W gene taxon:4932 20010118 SGD
+SGD S000003818 CDC8 GO:0006261 SGD_REF:S000051326|PMID:1098780 IMP P thymidylate kinase YJR057W gene taxon:4932 20010118 SGD
+SGD S000003818 CDC8 GO:0006261 SGD_REF:S000054138|PMID:6356128 IDA P thymidylate kinase YJR057W gene taxon:4932 20010118 SGD
+SGD S000003818 CDC8 GO:0006276 SGD_REF:S000050180|PMID:1657418 IMP P thymidylate kinase YJR057W gene taxon:4932 20010118 SGD
+SGD S000003818 CDC8 GO:0006280 SGD_REF:S000040197|PMID:1725090 IMP P thymidylate kinase YJR057W gene taxon:4932 20010118 SGD
+SGD S000003818 CDC8 GO:0006280 SGD_REF:S000055091|PMID:45608 IMP P thymidylate kinase YJR057W gene taxon:4932 20010118 SGD
+SGD S000003818 CDC8 GO:0006281 SGD_REF:S000052772|PMID:2249248 IMP P thymidylate kinase YJR057W gene taxon:4932 20010118 SGD
+SGD S000002323 CDC9 GO:0005634 SGD_REF:S000043286|PMID:10531002 IDA C DNA ligase YDL164C|MMS8 gene taxon:4932 20040514 SGD
+SGD S000002323 CDC9 GO:0005657 SGD_REF:S000058459|PMID:9759502 NAS C DNA ligase YDL164C|MMS8 gene taxon:4932 20010118 SGD
+SGD S000002323 CDC9 GO:0005739 SGD_REF:S000043286|PMID:10531002 IDA C DNA ligase YDL164C|MMS8 gene taxon:4932 20040514 SGD
+SGD S000002323 CDC9 GO:0005739 SGD_REF:S000043286|PMID:10531002 IMP C DNA ligase YDL164C|MMS8 gene taxon:4932 20040514 SGD
+SGD S000002323 CDC9 GO:0003910 SGD_REF:S000055408|PMID:6347688 IDA F DNA ligase YDL164C|MMS8 gene taxon:4932 20010118 SGD
+SGD S000002323 CDC9 GO:0003910 SGD_REF:S000052827|PMID:1445910 IDA F DNA ligase YDL164C|MMS8 gene taxon:4932 20010118 SGD
+SGD S000002323 CDC9 GO:0006266 SGD_REF:S000058459|PMID:9759502 IMP P DNA ligase YDL164C|MMS8 gene taxon:4932 20010118 SGD
+SGD S000002323 CDC9 GO:0006266 SGD_REF:S000058459|PMID:9759502 IDA P DNA ligase YDL164C|MMS8 gene taxon:4932 20010118 SGD
+SGD S000002323 CDC9 GO:0006273 SGD_REF:S000058459|PMID:9759502 IMP P DNA ligase YDL164C|MMS8 gene taxon:4932 20010118 SGD
+SGD S000002323 CDC9 GO:0006273 SGD_REF:S000058459|PMID:9759502 IDA P DNA ligase YDL164C|MMS8 gene taxon:4932 20010118 SGD
+SGD S000002323 CDC9 GO:0006284 SGD_REF:S000046630|PMID:10052932 IMP P DNA ligase YDL164C|MMS8 gene taxon:4932 20010118 SGD
+SGD S000002323 CDC9 GO:0006289 SGD_REF:S000046630|PMID:10052932 IMP P DNA ligase YDL164C|MMS8 gene taxon:4932 20010118 SGD
+SGD S000002323 CDC9 GO:0006310 SGD_REF:S000040324|PMID:9230305 IMP P DNA ligase YDL164C|MMS8 gene taxon:4932 20010118 SGD
+SGD S000004235 CDD1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C cytidine deaminase YLR245C gene taxon:4932 20031028 SGD
+SGD S000004235 CDD1 GO:0005634 SGD_REF:S000065997|PMID:11292850 IDA C cytidine deaminase YLR245C gene taxon:4932 20050215 SGD
+SGD S000004235 CDD1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C cytidine deaminase YLR245C gene taxon:4932 20031028 SGD
+SGD S000004235 CDD1 GO:0005737 SGD_REF:S000065997|PMID:11292850 IDA C cytidine deaminase YLR245C gene taxon:4932 20050215 SGD
+SGD S000004235 CDD1 GO:0004126 SGD_REF:S000055858|PMID:10501935 IDA F cytidine deaminase YLR245C gene taxon:4932 20010118 SGD
+SGD S000004235 CDD1 GO:0006216 SGD_REF:S000055858|PMID:10501935 IDA P cytidine deaminase YLR245C gene taxon:4932 20010118 SGD
+SGD S000004235 CDD1 GO:0006217 SGD_REF:S000055858|PMID:10501935 IDA P cytidine deaminase YLR245C gene taxon:4932 20010118 SGD
+SGD S000004235 CDD1 GO:0008655 SGD_REF:S000055858|PMID:10501935 IDA P cytidine deaminase YLR245C gene taxon:4932 20051219 SGD
+SGD S000002971 CDH1 GO:0005634 SGD_REF:S000072254|PMID:12456658 IDA C required for Clb2 and Ase1 degradation YGL003C|HCT1 gene taxon:4932 20030129 SGD
+SGD S000002971 CDH1 GO:0005680 SGD_REF:S000058476|PMID:10465783 TAS C required for Clb2 and Ase1 degradation YGL003C|HCT1 gene taxon:4932 20010118 SGD
+SGD S000002971 CDH1 GO:0005737 SGD_REF:S000072254|PMID:12456658 IDA C required for Clb2 and Ase1 degradation YGL003C|HCT1 gene taxon:4932 20030129 SGD
+SGD S000002971 CDH1 GO:0008047 SGD_REF:S000058476|PMID:10465783 TAS F required for Clb2 and Ase1 degradation YGL003C|HCT1 gene taxon:4932 20010118 SGD
+SGD S000002971 CDH1 GO:0000022 SGD_REF:S000058476|PMID:10465783 TAS P required for Clb2 and Ase1 degradation YGL003C|HCT1 gene taxon:4932 20010118 SGD
+SGD S000002971 CDH1 GO:0000070 SGD_REF:S000058476|PMID:10465783 TAS P required for Clb2 and Ase1 degradation YGL003C|HCT1 gene taxon:4932 20010118 SGD
+SGD S000002971 CDH1 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P required for Clb2 and Ase1 degradation YGL003C|HCT1 gene taxon:4932 20060221 SGD
+SGD S000002971 CDH1 GO:0007091 SGD_REF:S000058476|PMID:10465783 TAS P required for Clb2 and Ase1 degradation YGL003C|HCT1 gene taxon:4932 20010118 SGD
+SGD S000002971 CDH1 GO:0007092 SGD_REF:S000052656|PMID:9334304 IMP P required for Clb2 and Ase1 degradation YGL003C|HCT1 gene taxon:4932 20050404 SGD
+SGD S000002971 CDH1 GO:0008361 SGD_REF:S000070190|PMID:12089449 IDA P required for Clb2 and Ase1 degradation YGL003C|HCT1 gene taxon:4932 20020730 SGD
+SGD S000002971 CDH1 GO:0016567 SGD_REF:S000044570|PMID:9469814 IPI P required for Clb2 and Ase1 degradation YGL003C|HCT1 gene taxon:4932 20050408 SGD
+SGD S000000233 CDS1 GO:0005739 SGD_REF:S000058496 TAS C phosphatidate cytidylyltransferase YBR029C|CDG1 gene taxon:4932 20010119 SGD
+SGD S000000233 CDS1 GO:0005783 SGD_REF:S000058496 TAS C phosphatidate cytidylyltransferase YBR029C|CDG1 gene taxon:4932 20010119 SGD
+SGD S000000233 CDS1 GO:0004605 SGD_REF:S000051564|PMID:8557688 IDA F phosphatidate cytidylyltransferase YBR029C|CDG1 gene taxon:4932 20010118 SGD
+SGD S000000233 CDS1 GO:0006655 SGD_REF:S000058496 TAS P phosphatidate cytidylyltransferase YBR029C|CDG1 gene taxon:4932 20010119 SGD
+SGD S000000233 CDS1 GO:0006658 SGD_REF:S000058496 TAS P phosphatidate cytidylyltransferase YBR029C|CDG1 gene taxon:4932 20010119 SGD
+SGD S000004826 CEF1 GO:0005681 SGD_REF:S000040831|PMID:10092627 IDA C protein complex component associated with the splicing factor Prp19p YMR213W|NTC85 gene taxon:4932 20010118 SGD
+SGD S000004826 CEF1 GO:0031202 SGD_REF:S000040831|PMID:10092627 IDA F protein complex component associated with the splicing factor Prp19p YMR213W|NTC85 gene taxon:4932 20030128 SGD
+SGD S000004826 CEF1 GO:0000398 SGD_REF:S000040831|PMID:10092627 IMP P protein complex component associated with the splicing factor Prp19p YMR213W|NTC85 gene taxon:4932 20010118 SGD
+SGD S000004826 CEF1 GO:0000398 SGD_REF:S000040831|PMID:10092627 IPI P protein complex component associated with the splicing factor Prp19p YMR213W|NTC85 gene taxon:4932 20010118 SGD
+SGD S000003098 CEG1 GO:0005634 SGD_REF:S000043131|PMID:9832501 IPI C mRNA capping enzyme alpha subunit, mRNA guanylyltransferase YGL130W gene taxon:4932 20021008 SGD
+SGD S000003098 CEG1 GO:0004484 SGD_REF:S000043131|PMID:9832501 TAS F mRNA capping enzyme alpha subunit, mRNA guanylyltransferase YGL130W gene taxon:4932 20020927 SGD
+SGD S000003098 CEG1 GO:0004484 SGD_REF:S000076762|PMID:15226422 TAS F mRNA capping enzyme alpha subunit, mRNA guanylyltransferase YGL130W gene taxon:4932 20041213 SGD
+SGD S000003098 CEG1 GO:0006370 SGD_REF:S000043131|PMID:9832501 TAS P mRNA capping enzyme alpha subunit, mRNA guanylyltransferase YGL130W gene taxon:4932 20020927 SGD
+SGD S000003098 CEG1 GO:0006370 SGD_REF:S000076762|PMID:15226422 TAS P mRNA capping enzyme alpha subunit, mRNA guanylyltransferase YGL130W gene taxon:4932 20041213 SGD
+SGD S000003098 CEG1 GO:0045944 SGD_REF:S000076762|PMID:15226422 IGI P mRNA capping enzyme alpha subunit, mRNA guanylyltransferase YGL130W gene taxon:4932 20041213 SGD
+SGD S000003098 CEG1 GO:0045944 SGD_REF:S000076762|PMID:15226422 IMP P mRNA capping enzyme alpha subunit, mRNA guanylyltransferase YGL130W gene taxon:4932 20041213 SGD
+SGD S000000863 CEM1 GO:0005739 SGD_REF:S000041617|PMID:7988550 TAS C beta-keto-acyl synthase homolog YER061C gene taxon:4932 20010118 SGD
+SGD S000000863 CEM1 GO:0004312 SGD_REF:S000042110|PMID:8412701 ISS F beta-keto-acyl synthase homolog YER061C gene taxon:4932 20050714 SGD
+SGD S000000863 CEM1 GO:0006633 SGD_REF:S000042110|PMID:8412701 ISS P beta-keto-acyl synthase homolog YER061C gene taxon:4932 20050714 SGD
+SGD S000004778 CEP3 GO:0000778 SGD_REF:S000046254|PMID:10097110 TAS C Cbf3 kinetochore protein complex subunit b YMR168C|CBF3|CBF3B|CSL1 gene taxon:4932 20021017 SGD
+SGD S000004778 CEP3 GO:0000778 SGD_REF:S000040580|PMID:10352012 IDA C Cbf3 kinetochore protein complex subunit b YMR168C|CBF3|CBF3B|CSL1 gene taxon:4932 20030403 SGD
+SGD S000004778 CEP3 GO:0031518 SGD_REF:S000056114|PMID:8682209 TAS C Cbf3 kinetochore protein complex subunit b YMR168C|CBF3|CBF3B|CSL1 gene taxon:4932 20050722 SGD
+SGD S000004778 CEP3 GO:0008301 SGD_REF:S000046254|PMID:10097110 IDA F Cbf3 kinetochore protein complex subunit b YMR168C|CBF3|CBF3B|CSL1 gene taxon:4932 20021017 SGD
+SGD S000004778 CEP3 GO:0019237 SGD_REF:S000040580|PMID:10352012 IDA F Cbf3 kinetochore protein complex subunit b YMR168C|CBF3|CBF3B|CSL1 gene taxon:4932 20021017 SGD
+SGD S000004778 CEP3 GO:0007094 SGD_REF:S000060211|PMID:11290706 IMP P Cbf3 kinetochore protein complex subunit b YMR168C|CBF3|CBF3B|CSL1 gene taxon:4932 20030109 SGD
+SGD S000006149 CET1 GO:0005634 SGD_REF:S000043131|PMID:9832501 IPI C RNA 5'-triphosphatase, mRNA capping enzyme beta subunit (80 kDa) YPL228W|CES5 gene taxon:4932 20021008 SGD
+SGD S000006149 CET1 GO:0004651 SGD_REF:S000065933|PMID:11463793 TAS F RNA 5'-triphosphatase, mRNA capping enzyme beta subunit (80 kDa) YPL228W|CES5 gene taxon:4932 20020927 SGD
+SGD S000006149 CET1 GO:0006370 SGD_REF:S000065933|PMID:11463793 TAS P RNA 5'-triphosphatase, mRNA capping enzyme beta subunit (80 kDa) YPL228W|CES5 gene taxon:4932 20020927 SGD
+SGD S000001265 CFD1 GO:0005737 SGD_REF:S000073993|PMID:12970194 IDA C YIL003W|DRE3 gene taxon:4932 20031017 SGD
+SGD S000001265 CFD1 GO:0016887 SGD_REF:S000073993|PMID:12970194 TAS F YIL003W|DRE3 gene taxon:4932 20031229 SGD
+SGD S000001265 CFD1 GO:0016226 SGD_REF:S000073993|PMID:12970194 IMP P YIL003W|DRE3 gene taxon:4932 20031017 SGD
+SGD S000002709 CFT1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C 150 kDa protein associated with polyadenylation factor 1 (PF I), cleavage factor II (CF II) component YDR301W|YHH1 gene taxon:4932 20040928 SGD
+SGD S000002709 CFT1 GO:0005847 SGD_REF:S000046866|PMID:10523662 IPI C 150 kDa protein associated with polyadenylation factor 1 (PF I), cleavage factor II (CF II) component YDR301W|YHH1 gene taxon:4932 20040928 SGD
+SGD S000002709 CFT1 GO:0005847 SGD_REF:S000049364|PMID:9099738 IPI C 150 kDa protein associated with polyadenylation factor 1 (PF I), cleavage factor II (CF II) component YDR301W|YHH1 gene taxon:4932 20040928 SGD
+SGD S000002709 CFT1 GO:0005849 SGD_REF:S000049364|PMID:9099738 IPI C 150 kDa protein associated with polyadenylation factor 1 (PF I), cleavage factor II (CF II) component YDR301W|YHH1 gene taxon:4932 20020410 SGD
+SGD S000002709 CFT1 GO:0003723 SGD_REF:S000049364|PMID:9099738 IDA F 150 kDa protein associated with polyadenylation factor 1 (PF I), cleavage factor II (CF II) component YDR301W|YHH1 gene taxon:4932 20050216 SGD
+SGD S000002709 CFT1 GO:0006369 SGD_REF:S000071175|PMID:12145212 IMP P 150 kDa protein associated with polyadenylation factor 1 (PF I), cleavage factor II (CF II) component YDR301W|YHH1 gene taxon:4932 20030203 SGD
+SGD S000002709 CFT1 GO:0006378 SGD_REF:S000060315|PMID:11344258 IDA P 150 kDa protein associated with polyadenylation factor 1 (PF I), cleavage factor II (CF II) component YDR301W|YHH1 gene taxon:4932 20020410 SGD
+SGD S000002709 CFT1 GO:0006378 SGD_REF:S000060315|PMID:11344258 TAS P 150 kDa protein associated with polyadenylation factor 1 (PF I), cleavage factor II (CF II) component YDR301W|YHH1 gene taxon:4932 20020410 SGD
+SGD S000002709 CFT1 GO:0006379 SGD_REF:S000060315|PMID:11344258 IDA P 150 kDa protein associated with polyadenylation factor 1 (PF I), cleavage factor II (CF II) component YDR301W|YHH1 gene taxon:4932 20020410 SGD
+SGD S000002709 CFT1 GO:0006379 SGD_REF:S000060315|PMID:11344258 TAS P 150 kDa protein associated with polyadenylation factor 1 (PF I), cleavage factor II (CF II) component YDR301W|YHH1 gene taxon:4932 20020410 SGD
+SGD S000004105 CFT2 GO:0005847 SGD_REF:S000046866|PMID:10523662 IPI C 105 kDa protein associated with polyadenylation factor 1 (PF I), cleavage factor II (CF II) component YLR115W|YDH1 gene taxon:4932 20040928 SGD
+SGD S000004105 CFT2 GO:0005847 SGD_REF:S000049364|PMID:9099738 IPI C 105 kDa protein associated with polyadenylation factor 1 (PF I), cleavage factor II (CF II) component YLR115W|YDH1 gene taxon:4932 20040928 SGD
+SGD S000004105 CFT2 GO:0005849 SGD_REF:S000049364|PMID:9099738 IPI C 105 kDa protein associated with polyadenylation factor 1 (PF I), cleavage factor II (CF II) component YLR115W|YDH1 gene taxon:4932 20020410 SGD
+SGD S000004105 CFT2 GO:0003723 SGD_REF:S000049364|PMID:9099738 IPI F 105 kDa protein associated with polyadenylation factor 1 (PF I), cleavage factor II (CF II) component YLR115W|YDH1 gene taxon:4932 20050216 SGD
+SGD S000004105 CFT2 GO:0006378 SGD_REF:S000060315|PMID:11344258 IDA P 105 kDa protein associated with polyadenylation factor 1 (PF I), cleavage factor II (CF II) component YLR115W|YDH1 gene taxon:4932 20020410 SGD
+SGD S000004105 CFT2 GO:0006378 SGD_REF:S000060315|PMID:11344258 TAS P 105 kDa protein associated with polyadenylation factor 1 (PF I), cleavage factor II (CF II) component YLR115W|YDH1 gene taxon:4932 20020410 SGD
+SGD S000004105 CFT2 GO:0006379 SGD_REF:S000060315|PMID:11344258 IDA P 105 kDa protein associated with polyadenylation factor 1 (PF I), cleavage factor II (CF II) component YLR115W|YDH1 gene taxon:4932 20020410 SGD
+SGD S000004105 CFT2 GO:0006379 SGD_REF:S000060315|PMID:11344258 TAS P 105 kDa protein associated with polyadenylation factor 1 (PF I), cleavage factor II (CF II) component YLR115W|YDH1 gene taxon:4932 20020410 SGD
+SGD S000004500 CGI121 GO:0008372 SGD_REF:S000069584 ND C YML036W gene taxon:4932 20021126 SGD
+SGD S000004500 CGI121 GO:0005554 SGD_REF:S000069584 ND F YML036W gene taxon:4932 20021126 SGD
+SGD S000004500 CGI121 GO:0000004 SGD_REF:S000069584 ND P YML036W gene taxon:4932 20021126 SGD
+SGD S000002997 CGR1 GO:0005730 SGD_REF:S000059385|PMID:11116400 IDA C coiled-coil protein YGL029W gene taxon:4932 20010208 SGD
+SGD S000002997 CGR1 GO:0005554 SGD_REF:S000069584 ND F coiled-coil protein YGL029W gene taxon:4932 20010208 SGD
+SGD S000002997 CGR1 GO:0006364 SGD_REF:S000069775|PMID:11932453 IDA P coiled-coil protein YGL029W gene taxon:4932 20020828 SGD
+SGD S000002997 CGR1 GO:0007046 SGD_REF:S000059385|PMID:11116400 IMP P coiled-coil protein YGL029W gene taxon:4932 20010208 SGD
+SGD S000000569 CHA1 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C catabolic serine (threonine) dehydratase YCL064C gene taxon:4932 20031028 SGD
+SGD S000000569 CHA1 GO:0042645 SGD_REF:S000080741|PMID:15692048 IDA C catabolic serine (threonine) dehydratase YCL064C gene taxon:4932 20050401 SGD
+SGD S000000569 CHA1 GO:0003941 SGD_REF:S000044188|PMID:1628804 IMP F catabolic serine (threonine) dehydratase YCL064C gene taxon:4932 20030115 SGD
+SGD S000000569 CHA1 GO:0003941 SGD_REF:S000044188|PMID:1628804 ISS F catabolic serine (threonine) dehydratase YCL064C gene taxon:4932 20030115 SGD
+SGD S000000569 CHA1 GO:0004794 SGD_REF:S000044188|PMID:1628804 IMP F catabolic serine (threonine) dehydratase YCL064C gene taxon:4932 20030115 SGD
+SGD S000000569 CHA1 GO:0004794 SGD_REF:S000044188|PMID:1628804 ISS F catabolic serine (threonine) dehydratase YCL064C gene taxon:4932 20030115 SGD
+SGD S000000569 CHA1 GO:0006567 SGD_REF:S000044188|PMID:1628804 IMP P catabolic serine (threonine) dehydratase YCL064C gene taxon:4932 20030418 SGD
+SGD S000000569 CHA1 GO:0009071 SGD_REF:S000044188|PMID:1628804 IMP P catabolic serine (threonine) dehydratase YCL064C gene taxon:4932 20030418 SGD
+SGD S000004088 CHA4 GO:0005634 SGD_REF:S000045876|PMID:8889513 IPI C DNA binding transcriptional activator of CHA1 YLR098C|SIL2|SIL3 gene taxon:4932 20020715 SGD
+SGD S000004088 CHA4 GO:0003700 SGD_REF:S000045876|PMID:8889513 IPI F DNA binding transcriptional activator of CHA1 YLR098C|SIL2|SIL3 gene taxon:4932 20030402 SGD
+SGD S000004088 CHA4 GO:0003700 SGD_REF:S000045876|PMID:8889513 IDA F DNA binding transcriptional activator of CHA1 YLR098C|SIL2|SIL3 gene taxon:4932 20030402 SGD
+SGD S000004088 CHA4 GO:0003700 SGD_REF:S000045876|PMID:8889513 ISS F DNA binding transcriptional activator of CHA1 YLR098C|SIL2|SIL3 gene taxon:4932 20030402 SGD
+SGD S000004088 CHA4 GO:0006355 SGD_REF:S000045876|PMID:8889513 IMP P DNA binding transcriptional activator of CHA1 YLR098C|SIL2|SIL3 gene taxon:4932 20020715 SGD
+SGD S000004088 CHA4 GO:0009063 SGD_REF:S000045876|PMID:8889513 IGI P DNA binding transcriptional activator of CHA1 YLR098C|SIL2|SIL3 gene taxon:4932 20020715 SGD
+SGD S000004088 CHA4 GO:0009063 SGD_REF:S000045876|PMID:8889513 IMP P DNA binding transcriptional activator of CHA1 YLR098C|SIL2|SIL3 gene taxon:4932 20020715 SGD
+SGD S000003174 CHC1 GO:0030125 SGD_REF:S000049871|PMID:9171338 TAS C Clathrin heavy chain YGL206C|SWA5 gene taxon:4932 20020715 SGD
+SGD S000003174 CHC1 GO:0005198 SGD_REF:S000049871|PMID:9171338 TAS F Clathrin heavy chain YGL206C|SWA5 gene taxon:4932 20020715 SGD
+SGD S000003174 CHC1 GO:0006897 SGD_REF:S000061172|PMID:11252894 TAS P Clathrin heavy chain YGL206C|SWA5 gene taxon:4932 20050509 SGD
+SGD S000003174 CHC1 GO:0016192 SGD_REF:S000049871|PMID:9171338 TAS P Clathrin heavy chain YGL206C|SWA5 gene taxon:4932 20020715 SGD
+SGD S000000966 CHD1 GO:0000124 SGD_REF:S000080442|PMID:15647753 IDA C transcriptional regulator YER164W gene taxon:4932 20050804 SGD
+SGD S000000966 CHD1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C transcriptional regulator YER164W gene taxon:4932 20040928 SGD
+SGD S000000966 CHD1 GO:0008023 SGD_REF:S000071357|PMID:12242279 IPI C transcriptional regulator YER164W gene taxon:4932 20021004 SGD
+SGD S000000966 CHD1 GO:0046695 SGD_REF:S000080442|PMID:15647753 IDA C transcriptional regulator YER164W gene taxon:4932 20050804 SGD
+SGD S000000966 CHD1 GO:0016887 SGD_REF:S000039644|PMID:10811623 IDA F transcriptional regulator YER164W gene taxon:4932 20021004 SGD
+SGD S000000966 CHD1 GO:0016944 SGD_REF:S000071357|PMID:12242279 IPI F transcriptional regulator YER164W gene taxon:4932 20021004 SGD
+SGD S000000966 CHD1 GO:0006338 SGD_REF:S000039644|PMID:10811623 IDA P transcriptional regulator YER164W gene taxon:4932 20021004 SGD
+SGD S000000966 CHD1 GO:0006368 SGD_REF:S000071357|PMID:12242279 IPI P transcriptional regulator YER164W gene taxon:4932 20021004 SGD
+SGD S000000478 CHK1 GO:0005634 SGD_REF:S000060449|PMID:11390356 IPI C protein kinase YBR274W gene taxon:4932 20021104 SGD
+SGD S000000478 CHK1 GO:0004672 SGD_REF:S000039903|PMID:10660074 IMP F protein kinase YBR274W gene taxon:4932 20030110 SGD
+SGD S000000478 CHK1 GO:0004672 SGD_REF:S000039903|PMID:10660074 ISS F protein kinase YBR274W gene taxon:4932 20030110 SGD
+SGD S000000478 CHK1 GO:0000077 SGD_REF:S000039903|PMID:10660074 IMP P protein kinase YBR274W gene taxon:4932 20030110 SGD
+SGD S000000478 CHK1 GO:0006468 SGD_REF:S000039903|PMID:10660074 IMP P protein kinase YBR274W gene taxon:4932 20030110 SGD
+SGD S000000478 CHK1 GO:0006468 SGD_REF:S000039903|PMID:10660074 ISS P protein kinase YBR274W gene taxon:4932 20030110 SGD
+SGD S000005929 CHL1 GO:0005634 SGD_REF:S000053296|PMID:10931920 IDA C deah box protein, kinetochore protein YPL008W|CTF1|LPA9 gene taxon:4932 20020904 SGD
+SGD S000005929 CHL1 GO:0005634 SGD_REF:S000076406|PMID:15020404 IDA C deah box protein, kinetochore protein YPL008W|CTF1|LPA9 gene taxon:4932 20040610 SGD
+SGD S000005929 CHL1 GO:0003678 SGD_REF:S000053296|PMID:10931920 ISS F deah box protein, kinetochore protein YPL008W|CTF1|LPA9 gene taxon:4932 20020904 SGD
+SGD S000005929 CHL1 GO:0003678 SGD_REF:S000053296|PMID:10931920 IMP F deah box protein, kinetochore protein YPL008W|CTF1|LPA9 gene taxon:4932 20020904 SGD
+SGD S000005929 CHL1 GO:0007059 SGD_REF:S000053296|PMID:10931920 IDA P deah box protein, kinetochore protein YPL008W|CTF1|LPA9 gene taxon:4932 20020904 SGD
+SGD S000005929 CHL1 GO:0007064 SGD_REF:S000076406|PMID:15020404 IMP P deah box protein, kinetochore protein YPL008W|CTF1|LPA9 gene taxon:4932 20040610 SGD
+SGD S000005929 CHL1 GO:0007064 SGD_REF:S000076127|PMID:14742714 IMP P deah box protein, kinetochore protein YPL008W|CTF1|LPA9 gene taxon:4932 20050513 SGD
+SGD S000005929 CHL1 GO:0007064 SGD_REF:S000076127|PMID:14742714 IGI SGD:S000001234 P deah box protein, kinetochore protein YPL008W|CTF1|LPA9 gene taxon:4932 20050513 SGD
+SGD S000002662 CHL4 GO:0000942 SGD_REF:S000074151|PMID:12589047 IDA C YDR254W|CTF17|MCM17 gene taxon:4932 20040910 SGD
+SGD S000002662 CHL4 GO:0003677 SGD_REF:S000041140|PMID:10563386 IDA F YDR254W|CTF17|MCM17 gene taxon:4932 20021209 SGD
+SGD S000002662 CHL4 GO:0007059 SGD_REF:S000044107|PMID:8243998 IMP P YDR254W|CTF17|MCM17 gene taxon:4932 20020927 SGD
+SGD S000002662 CHL4 GO:0007059 SGD_REF:S000058222|PMID:9339342 IMP P YDR254W|CTF17|MCM17 gene taxon:4932 20020927 SGD
+SGD S000000828 CHO1 GO:0005783 SGD_REF:S000058496 TAS C phosphatidylserine synthase YER026C|PSS1 gene taxon:4932 20010119 SGD
+SGD S000000828 CHO1 GO:0003882 SGD_REF:S000058496 TAS F phosphatidylserine synthase YER026C|PSS1 gene taxon:4932 20010119 SGD
+SGD S000000828 CHO1 GO:0003882 SGD_REF:S000062220|PMID:6088519 IDA F phosphatidylserine synthase YER026C|PSS1 gene taxon:4932 20050803 SGD
+SGD S000000828 CHO1 GO:0003882 SGD_REF:S000049696|PMID:6988386 IMP F phosphatidylserine synthase YER026C|PSS1 gene taxon:4932 20050803 SGD
+SGD S000000828 CHO1 GO:0006659 SGD_REF:S000058496 TAS P phosphatidylserine synthase YER026C|PSS1 gene taxon:4932 20010119 SGD
+SGD S000000828 CHO1 GO:0006659 SGD_REF:S000049696|PMID:6988386 IMP P phosphatidylserine synthase YER026C|PSS1 gene taxon:4932 20050803 SGD
+SGD S000000828 CHO1 GO:0006659 SGD_REF:S000062220|PMID:6088519 IDA P phosphatidylserine synthase YER026C|PSS1 gene taxon:4932 20050803 SGD
+SGD S000003389 CHO2 GO:0005783 SGD_REF:S000058496 TAS C phosphatidyl-ethanolamine N-methyltransferase YGR157W|PEM1 gene taxon:4932 20010119 SGD
+SGD S000003389 CHO2 GO:0004608 SGD_REF:S000058496 TAS F phosphatidyl-ethanolamine N-methyltransferase YGR157W|PEM1 gene taxon:4932 20030114 SGD
+SGD S000003389 CHO2 GO:0004608 SGD_REF:S000053915|PMID:3066687 IMP F phosphatidyl-ethanolamine N-methyltransferase YGR157W|PEM1 gene taxon:4932 20050804 SGD
+SGD S000003389 CHO2 GO:0004608 SGD_REF:S000042469|PMID:2445736 IDA F phosphatidyl-ethanolamine N-methyltransferase YGR157W|PEM1 gene taxon:4932 20050804 SGD
+SGD S000003389 CHO2 GO:0006656 SGD_REF:S000058496 TAS P phosphatidyl-ethanolamine N-methyltransferase YGR157W|PEM1 gene taxon:4932 20010119 SGD
+SGD S000003389 CHO2 GO:0006656 SGD_REF:S000042469|PMID:2445736 IDA P phosphatidyl-ethanolamine N-methyltransferase YGR157W|PEM1 gene taxon:4932 20050804 SGD
+SGD S000003389 CHO2 GO:0006656 SGD_REF:S000053915|PMID:3066687 IMP P phosphatidyl-ethanolamine N-methyltransferase YGR157W|PEM1 gene taxon:4932 20050804 SGD
+SGD S000005136 CHS1 GO:0005886 SGD_REF:S000048163|PMID:8970154 IDA C chitin synthase 1 YNL192W|USA4 gene taxon:4932 20041014 SGD
+SGD S000005136 CHS1 GO:0045009 SGD_REF:S000048163|PMID:8970154 IDA C chitin synthase 1 YNL192W|USA4 gene taxon:4932 20041014 SGD
+SGD S000005136 CHS1 GO:0004100 SGD_REF:S000054070|PMID:7952171 IDA F chitin synthase 1 YNL192W|USA4 gene taxon:4932 20021218 SGD
+SGD S000005136 CHS1 GO:0007109 SGD_REF:S000055946|PMID:2523889 IMP P chitin synthase 1 YNL192W|USA4 gene taxon:4932 20041014 SGD
+SGD S000005136 CHS1 GO:0007114 SGD_REF:S000049326|PMID:8257107 TAS P chitin synthase 1 YNL192W|USA4 gene taxon:4932 20021218 SGD
+SGD S000000242 CHS2 GO:0005935 SGD_REF:S000042309|PMID:8909536 IDA C chitin synthase 2 YBR038W gene taxon:4932 20041013 SGD
+SGD S000000242 CHS2 GO:0004100 SGD_REF:S000046745|PMID:9990311 IDA F chitin synthase 2 YBR038W gene taxon:4932 20010118 SGD
+SGD S000000242 CHS2 GO:0000910 SGD_REF:S000069165|PMID:11839781 IMP P chitin synthase 2 YBR038W gene taxon:4932 20041013 SGD
+SGD S000000227 CHS3 GO:0000131 SGD_REF:S000052547|PMID:9008706 IDA C chitin synthase 3 YBR023C|CAL1|CSD2|DIT101|KTI2 gene taxon:4932 20041014 SGD
+SGD S000000227 CHS3 GO:0000131 SGD_REF:S000077520|PMID:15470103 IDA C chitin synthase 3 YBR023C|CAL1|CSD2|DIT101|KTI2 gene taxon:4932 20050531 SGD
+SGD S000000227 CHS3 GO:0005628 SGD_REF:S000081076|PMID:15755916 IDA C chitin synthase 3 YBR023C|CAL1|CSD2|DIT101|KTI2 gene taxon:4932 20050324 SGD
+SGD S000000227 CHS3 GO:0005737 SGD_REF:S000052547|PMID:9008706 IDA C chitin synthase 3 YBR023C|CAL1|CSD2|DIT101|KTI2 gene taxon:4932 20041014 SGD
+SGD S000000227 CHS3 GO:0005935 SGD_REF:S000042309|PMID:8909536 IDA C chitin synthase 3 YBR023C|CAL1|CSD2|DIT101|KTI2 gene taxon:4932 20041013 SGD
+SGD S000000227 CHS3 GO:0005935 SGD_REF:S000077520|PMID:15470103 IDA C chitin synthase 3 YBR023C|CAL1|CSD2|DIT101|KTI2 gene taxon:4932 20050531 SGD
+SGD S000000227 CHS3 GO:0045009 SGD_REF:S000048163|PMID:8970154 IDA C chitin synthase 3 YBR023C|CAL1|CSD2|DIT101|KTI2 gene taxon:4932 20041014 SGD
+SGD S000000227 CHS3 GO:0004100 SGD_REF:S000042088|PMID:9760183 IMP F chitin synthase 3 YBR023C|CAL1|CSD2|DIT101|KTI2 gene taxon:4932 20041014 SGD
+SGD S000000227 CHS3 GO:0000910 SGD_REF:S000057374|PMID:7565410 TAS P chitin synthase 3 YBR023C|CAL1|CSD2|DIT101|KTI2 gene taxon:4932 20041014 SGD
+SGD S000000227 CHS3 GO:0006038 SGD_REF:S000057374|PMID:7565410 TAS P chitin synthase 3 YBR023C|CAL1|CSD2|DIT101|KTI2 gene taxon:4932 20041014 SGD
+SGD S000000227 CHS3 GO:0030476 SGD_REF:S000054562|PMID:1293886 IMP P chitin synthase 3 YBR023C|CAL1|CSD2|DIT101|KTI2 gene taxon:4932 20041013 SGD
+SGD S000004322 CHS5 GO:0005737 SGD_REF:S000052547|PMID:9008706 IDA C YLR330W|CAL3 gene taxon:4932 20010118 SGD
+SGD S000004322 CHS5 GO:0005554 SGD_REF:S000069584 ND F YLR330W|CAL3 gene taxon:4932 20021201 SGD
+SGD S000004322 CHS5 GO:0000282 SGD_REF:S000114540|PMID:16498409 IMP P YLR330W|CAL3 gene taxon:4932 20060531 SGD
+SGD S000004322 CHS5 GO:0000747 SGD_REF:S000047270|PMID:9111317 IMP P YLR330W|CAL3 gene taxon:4932 20020614 SGD
+SGD S000004322 CHS5 GO:0006039 SGD_REF:S000047270|PMID:9111317 IMP P YLR330W|CAL3 gene taxon:4932 20010118 SGD
+SGD S000004322 CHS5 GO:0006893 SGD_REF:S000069556|PMID:11879634 IMP P YLR330W|CAL3 gene taxon:4932 20020807 SGD
+SGD S000004322 CHS5 GO:0006893 SGD_REF:S000114540|PMID:16498409 IGI SGD:S000002351 P YLR330W|CAL3 gene taxon:4932 20060531 SGD
+SGD S000004322 CHS5 GO:0006893 SGD_REF:S000114540|PMID:16498409 IMP P YLR330W|CAL3 gene taxon:4932 20060531 SGD
+SGD S000004322 CHS5 GO:0030476 SGD_REF:S000047270|PMID:9111317 IMP P YLR330W|CAL3 gene taxon:4932 20010118 SGD
+SGD S000003635 CHS6 colocalizes_with GO:0030136 SGD_REF:S000074185|PMID:14562095 IDA C YJL099W|CSD3 gene taxon:4932 20031028 SGD
+SGD S000003635 CHS6 colocalizes_with GO:0030140 SGD_REF:S000114540|PMID:16498409 IDA C YJL099W|CSD3 gene taxon:4932 20060531 SGD
+SGD S000003635 CHS6 GO:0005554 SGD_REF:S000069584 ND F YJL099W|CSD3 gene taxon:4932 20020807 SGD
+SGD S000003635 CHS6 GO:0006038 SGD_REF:S000044113|PMID:9614194 IMP P YJL099W|CSD3 gene taxon:4932 20020807 SGD
+SGD S000003635 CHS6 GO:0006893 SGD_REF:S000069556|PMID:11879634 IMP P YJL099W|CSD3 gene taxon:4932 20020807 SGD
+SGD S000003635 CHS6 GO:0006893 SGD_REF:S000114540|PMID:16498409 IGI SGD:S000002351 P YJL099W|CSD3 gene taxon:4932 20060531 SGD
+SGD S000003635 CHS6 GO:0006893 SGD_REF:S000044113|PMID:9614194 IMP P YJL099W|CSD3 gene taxon:4932 20020807 SGD
+SGD S000001184 CHS7 GO:0005789 SGD_REF:S000053720|PMID:10366589 IDA C YHR142W gene taxon:4932 20020807 SGD
+SGD S000001184 CHS7 GO:0005554 SGD_REF:S000069584 ND F YHR142W gene taxon:4932 20020807 SGD
+SGD S000001184 CHS7 GO:0006038 SGD_REF:S000053720|PMID:10366589 IMP P YHR142W gene taxon:4932 20020807 SGD
+SGD S000001184 CHS7 GO:0006457 SGD_REF:S000080152|PMID:15623581 IMP P YHR142W gene taxon:4932 20050708 SGD
+SGD S000001184 CHS7 GO:0006888 SGD_REF:S000053720|PMID:10366589 IDA P YHR142W gene taxon:4932 20020807 SGD
+SGD S000000832 CHZ1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C chaperone YER030W gene taxon:4932 20031028 SGD
+SGD S000000832 CHZ1 GO:0005554 SGD_REF:S000069584 ND F chaperone YER030W gene taxon:4932 20021126 SGD
+SGD S000000832 CHZ1 GO:0000004 SGD_REF:S000069584 ND P chaperone YER030W gene taxon:4932 20021126 SGD
+SGD S000002675 CIA1 GO:0005634 SGD_REF:S000075214|PMID:14690591 IDA C YDR267C gene taxon:4932 20040105 SGD
+SGD S000002675 CIA1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDR267C gene taxon:4932 20031028 SGD
+SGD S000002675 CIA1 GO:0005737 SGD_REF:S000075214|PMID:14690591 IDA C YDR267C gene taxon:4932 20040105 SGD
+SGD S000002675 CIA1 GO:0005554 SGD_REF:S000069584 ND F YDR267C gene taxon:4932 20030203 SGD
+SGD S000002675 CIA1 GO:0000004 SGD_REF:S000069584 ND P YDR267C gene taxon:4932 20030203 SGD
+SGD S000001094 CIC1 GO:0000502 SGD_REF:S000061356|PMID:11500370 IDA C YHR052W|NSA3 gene taxon:4932 20030520 SGD
+SGD S000001094 CIC1 GO:0000502 SGD_REF:S000061356|PMID:11500370 IPI C YHR052W|NSA3 gene taxon:4932 20030520 SGD
+SGD S000001094 CIC1 GO:0005730 SGD_REF:S000061356|PMID:11500370 IDA C YHR052W|NSA3 gene taxon:4932 20030409 SGD
+SGD S000001094 CIC1 GO:0030674 SGD_REF:S000061356|PMID:11500370 IMP F YHR052W|NSA3 gene taxon:4932 20030417 SGD
+SGD S000001094 CIC1 GO:0030674 SGD_REF:S000061356|PMID:11500370 IPI F YHR052W|NSA3 gene taxon:4932 20030417 SGD
+SGD S000001094 CIC1 GO:0030163 SGD_REF:S000061356|PMID:11500370 IMP P YHR052W|NSA3 gene taxon:4932 20011026 SGD
+SGD S000001094 CIC1 GO:0030163 SGD_REF:S000061356|PMID:11500370 IDA P YHR052W|NSA3 gene taxon:4932 20011026 SGD
+SGD S000001094 CIC1 GO:0030163 SGD_REF:S000061356|PMID:11500370 IPI P YHR052W|NSA3 gene taxon:4932 20011026 SGD
+SGD S000001094 CIC1 GO:0042273 SGD_REF:S000076470|PMID:15100437 IPI P YHR052W|NSA3 gene taxon:4932 20050407 SGD
+SGD S000004811 CIK1 GO:0005816 SGD_REF:S000066252|PMID:11729143 IDA C Kar3-binding protein YMR198W gene taxon:4932 20020208 SGD
+SGD S000004811 CIK1 GO:0005816 SGD_REF:S000040753|PMID:1644287 IDA C Kar3-binding protein YMR198W gene taxon:4932 20020208 SGD
+SGD S000004811 CIK1 GO:0005819 SGD_REF:S000066252|PMID:11729143 IDA C Kar3-binding protein YMR198W gene taxon:4932 20020208 SGD
+SGD S000004811 CIK1 GO:0005871 SGD_REF:S000043673|PMID:10087265 IDA C Kar3-binding protein YMR198W gene taxon:4932 20020208 SGD
+SGD S000004811 CIK1 GO:0005881 SGD_REF:S000058447|PMID:9153752 TAS C Kar3-binding protein YMR198W gene taxon:4932 20010118 SGD
+SGD S000004811 CIK1 GO:0003777 SGD_REF:S000043673|PMID:10087265 IMP F Kar3-binding protein YMR198W gene taxon:4932 20020208 SGD
+SGD S000004811 CIK1 GO:0003777 SGD_REF:S000043673|PMID:10087265 ISS F Kar3-binding protein YMR198W gene taxon:4932 20020208 SGD
+SGD S000004811 CIK1 GO:0000070 SGD_REF:S000043673|PMID:10087265 TAS P Kar3-binding protein YMR198W gene taxon:4932 20010118 SGD
+SGD S000004811 CIK1 GO:0000132 SGD_REF:S000049652|PMID:10525539 TAS P Kar3-binding protein YMR198W gene taxon:4932 20040128 SGD
+SGD S000004811 CIK1 GO:0007126 SGD_REF:S000066252|PMID:11729143 IMP P Kar3-binding protein YMR198W gene taxon:4932 20020208 SGD
+SGD S000004811 CIK1 GO:0007126 SGD_REF:S000066252|PMID:11729143 IDA P Kar3-binding protein YMR198W gene taxon:4932 20020208 SGD
+SGD S000004811 CIK1 GO:0030472 SGD_REF:S000043673|PMID:10087265 TAS P Kar3-binding protein YMR198W gene taxon:4932 20010118 SGD
+SGD S000005876 CIN1 GO:0008372 SGD_REF:S000069584 ND C tubulin folding cofactor D YOR349W gene taxon:4932 20040720 SGD
+SGD S000005876 CIN1 GO:0048487 SGD_REF:S000058454|PMID:9885248 NAS F tubulin folding cofactor D YOR349W gene taxon:4932 20040721 SGD
+SGD S000005876 CIN1 GO:0007023 SGD_REF:S000058454|PMID:9885248 TAS P tubulin folding cofactor D YOR349W gene taxon:4932 20010118 SGD
+SGD S000005876 CIN1 GO:0007025 SGD_REF:S000058454|PMID:9885248 TAS P tubulin folding cofactor D YOR349W gene taxon:4932 20010118 SGD
+SGD S000006162 CIN2 GO:0008372 SGD_REF:S000069584 ND C tubulin folding cofactor C YPL241C gene taxon:4932 20021204 SGD
+SGD S000006162 CIN2 GO:0005554 SGD_REF:S000045032|PMID:9215891 TAS F tubulin folding cofactor C YPL241C gene taxon:4932 20010118 SGD
+SGD S000006162 CIN2 GO:0007017 SGD_REF:S000045032|PMID:9215891 TAS P tubulin folding cofactor C YPL241C gene taxon:4932 20010118 SGD
+SGD S000004746 CIN4 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C GTP-binding protein YMR138W|GTP1|UGX1 gene taxon:4932 20031028 SGD
+SGD S000004746 CIN4 GO:0005525 SGD_REF:S000045032|PMID:9215891 TAS F GTP-binding protein YMR138W|GTP1|UGX1 gene taxon:4932 20010118 SGD
+SGD S000004746 CIN4 GO:0007017 SGD_REF:S000045032|PMID:9215891 TAS P GTP-binding protein YMR138W|GTP1|UGX1 gene taxon:4932 20010118 SGD
+SGD S000005554 CIN5 GO:0005634 SGD_REF:S000060008|PMID:11179441 IDA C bZIP (basic-leucine zipper) protein, can activate transcription from a promoter containing a Yap recognition site YOR028C|HAL6|YAP4 gene taxon:4932 20020708 SGD
+SGD S000005554 CIN5 GO:0003677 SGD_REF:S000048602|PMID:9372930 IDA F bZIP (basic-leucine zipper) protein, can activate transcription from a promoter containing a Yap recognition site YOR028C|HAL6|YAP4 gene taxon:4932 20050117 SGD
+SGD S000005554 CIN5 GO:0003702 SGD_REF:S000060008|PMID:11179441 ISS F bZIP (basic-leucine zipper) protein, can activate transcription from a promoter containing a Yap recognition site YOR028C|HAL6|YAP4 gene taxon:4932 20020708 SGD
+SGD S000005554 CIN5 GO:0006357 SGD_REF:S000060008|PMID:11179441 ISS P bZIP (basic-leucine zipper) protein, can activate transcription from a promoter containing a Yap recognition site YOR028C|HAL6|YAP4 gene taxon:4932 20020708 SGD
+SGD S000005554 CIN5 GO:0009651 SGD_REF:S000045640|PMID:9559673 IMP P bZIP (basic-leucine zipper) protein, can activate transcription from a promoter containing a Yap recognition site YOR028C|HAL6|YAP4 gene taxon:4932 20020708 SGD
+SGD S000005554 CIN5 GO:0042493 SGD_REF:S000060008|PMID:11179441 IGI P bZIP (basic-leucine zipper) protein, can activate transcription from a promoter containing a Yap recognition site YOR028C|HAL6|YAP4 gene taxon:4932 20021111 SGD
+SGD S000000787 CIN8 GO:0000778 SGD_REF:S000080960|PMID:11511347 IDA C YEL061C|KSL2|SDS15 gene taxon:4932 20050307 SGD
+SGD S000000787 CIN8 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YEL061C|KSL2|SDS15 gene taxon:4932 20041203 SGD
+SGD S000000787 CIN8 GO:0005871 SGD_REF:S000058447|PMID:9153752 TAS C YEL061C|KSL2|SDS15 gene taxon:4932 20010118 SGD
+SGD S000000787 CIN8 GO:0005876 SGD_REF:S000058447|PMID:9153752 TAS C YEL061C|KSL2|SDS15 gene taxon:4932 20010118 SGD
+SGD S000000787 CIN8 GO:0005876 SGD_REF:S000080960|PMID:11511347 IDA C YEL061C|KSL2|SDS15 gene taxon:4932 20050307 SGD
+SGD S000000787 CIN8 GO:0003777 SGD_REF:S000058447|PMID:9153752 TAS F YEL061C|KSL2|SDS15 gene taxon:4932 20010118 SGD
+SGD S000000787 CIN8 GO:0000070 SGD_REF:S000058447|PMID:9153752 TAS P YEL061C|KSL2|SDS15 gene taxon:4932 20010118 SGD
+SGD S000000787 CIN8 GO:0000092 SGD_REF:S000058448|PMID:9813090 IMP P YEL061C|KSL2|SDS15 gene taxon:4932 20010118 SGD
+SGD S000000787 CIN8 GO:0030472 SGD_REF:S000058447|PMID:9153752 TAS P YEL061C|KSL2|SDS15 gene taxon:4932 20010118 SGD
+SGD S000002429 CIS1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDR022C gene taxon:4932 20031028 SGD
+SGD S000002429 CIS1 GO:0005554 SGD_REF:S000069584 ND F YDR022C gene taxon:4932 20050713 SGD
+SGD S000002429 CIS1 GO:0000226 SGD_REF:S000046368|PMID:9348527 IGI SGD:S000004811 P YDR022C gene taxon:4932 20050713 SGD
+SGD S000003694 CIS3 GO:0005576 SGD_REF:S000073012|PMID:12702350 IDA C released from SDS-extracted cell walls by laminarinase, similar to Hsp150p and Pir1p, Pir2p, and Pir3p YJL158C|CCW11|CCW5|PIR4 gene taxon:4932 20030921 SGD
+SGD S000003694 CIS3 GO:0005783 SGD_REF:S000069459|PMID:11914276 IDA C released from SDS-extracted cell walls by laminarinase, similar to Hsp150p and Pir1p, Pir2p, and Pir3p YJL158C|CCW11|CCW5|PIR4 gene taxon:4932 20020507 SGD
+SGD S000003694 CIS3 GO:0005886 SGD_REF:S000069459|PMID:11914276 IDA C released from SDS-extracted cell walls by laminarinase, similar to Hsp150p and Pir1p, Pir2p, and Pir3p YJL158C|CCW11|CCW5|PIR4 gene taxon:4932 20020508 SGD
+SGD S000003694 CIS3 GO:0005934 SGD_REF:S000053685|PMID:10438739 IDA C released from SDS-extracted cell walls by laminarinase, similar to Hsp150p and Pir1p, Pir2p, and Pir3p YJL158C|CCW11|CCW5|PIR4 gene taxon:4932 20010118 SGD
+SGD S000003694 CIS3 GO:0009277 SGD_REF:S000053685|PMID:10438739 IDA C released from SDS-extracted cell walls by laminarinase, similar to Hsp150p and Pir1p, Pir2p, and Pir3p YJL158C|CCW11|CCW5|PIR4 gene taxon:4932 20010118 SGD
+SGD S000003694 CIS3 GO:0009277 SGD_REF:S000081097|PMID:15781460 IDA C released from SDS-extracted cell walls by laminarinase, similar to Hsp150p and Pir1p, Pir2p, and Pir3p YJL158C|CCW11|CCW5|PIR4 gene taxon:4932 20050601 SGD
+SGD S000003694 CIS3 GO:0005199 SGD_REF:S000053685|PMID:10438739 ISS F released from SDS-extracted cell walls by laminarinase, similar to Hsp150p and Pir1p, Pir2p, and Pir3p YJL158C|CCW11|CCW5|PIR4 gene taxon:4932 20010118 SGD
+SGD S000003694 CIS3 GO:0007047 SGD_REF:S000039809|PMID:10407261 IMP P released from SDS-extracted cell walls by laminarinase, similar to Hsp150p and Pir1p, Pir2p, and Pir3p YJL158C|CCW11|CCW5|PIR4 gene taxon:4932 20010118 SGD
+SGD S000005284 CIT1 GO:0005739 SGD_REF:S000069459|PMID:11914276 IDA C citrate synthase YNR001C|CS1|LYS6 gene taxon:4932 20020507 SGD
+SGD S000005284 CIT1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C citrate synthase YNR001C|CS1|LYS6 gene taxon:4932 20040924 SGD
+SGD S000005284 CIT1 GO:0005759 SGD_REF:S000058126|PMID:9175438 TAS C citrate synthase YNR001C|CS1|LYS6 gene taxon:4932 20010118 SGD
+SGD S000005284 CIT1 GO:0004108 SGD_REF:S000058126|PMID:9175438 TAS F citrate synthase YNR001C|CS1|LYS6 gene taxon:4932 20010118 SGD
+SGD S000005284 CIT1 GO:0006099 SGD_REF:S000058126|PMID:9175438 TAS P citrate synthase YNR001C|CS1|LYS6 gene taxon:4932 20010118 SGD
+SGD S000005284 CIT1 GO:0006101 SGD_REF:S000058126|PMID:9175438 TAS P citrate synthase YNR001C|CS1|LYS6 gene taxon:4932 20010118 SGD
+SGD S000005284 CIT1 GO:0006537 SGD_REF:S000058126|PMID:9175438 TAS P citrate synthase YNR001C|CS1|LYS6 gene taxon:4932 20010118 SGD
+SGD S000000598 CIT2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C citrate synthase YCR005C gene taxon:4932 20040928 SGD
+SGD S000000598 CIT2 GO:0004108 SGD_REF:S000058126|PMID:9175438 TAS F citrate synthase YCR005C gene taxon:4932 20010118 SGD
+SGD S000000598 CIT2 GO:0006097 SGD_REF:S000058126|PMID:9175438 TAS P citrate synthase YCR005C gene taxon:4932 20010118 SGD
+SGD S000000598 CIT2 GO:0006101 SGD_REF:S000058126|PMID:9175438 TAS P citrate synthase YCR005C gene taxon:4932 20010118 SGD
+SGD S000000598 CIT2 GO:0006537 SGD_REF:S000058126|PMID:9175438 TAS P citrate synthase YCR005C gene taxon:4932 20010118 SGD
+SGD S000006205 CIT3 GO:0005759 SGD_REF:S000058491 NAS C citrate synthase YPR001W gene taxon:4932 20010119 SGD
+SGD S000006205 CIT3 GO:0005759 SGD_REF:S000058126|PMID:9175438 NAS C citrate synthase YPR001W gene taxon:4932 20010118 SGD
+SGD S000006205 CIT3 GO:0004108 SGD_REF:S000058126|PMID:9175438 TAS F citrate synthase YPR001W gene taxon:4932 20010118 SGD
+SGD S000006205 CIT3 GO:0006099 SGD_REF:S000058126|PMID:9175438 TAS P citrate synthase YPR001W gene taxon:4932 20010118 SGD
+SGD S000006205 CIT3 GO:0006101 SGD_REF:S000058126|PMID:9175438 TAS P citrate synthase YPR001W gene taxon:4932 20010118 SGD
+SGD S000006205 CIT3 GO:0019541 SGD_REF:S000059712|PMID:11179416 IEP P citrate synthase YPR001W gene taxon:4932 20011023 SGD
+SGD S000001297 CKA1 GO:0005956 SGD_REF:S000045293|PMID:9427841 IDA C protein kinase CK2 alpha subunit YIL035C gene taxon:4932 20010118 SGD
+SGD S000001297 CKA1 GO:0004682 SGD_REF:S000045293|PMID:9427841 IDA F protein kinase CK2 alpha subunit YIL035C gene taxon:4932 20010118 SGD
+SGD S000001297 CKA1 GO:0000082 SGD_REF:S000045293|PMID:9427841 IPI P protein kinase CK2 alpha subunit YIL035C gene taxon:4932 20010118 SGD
+SGD S000001297 CKA1 GO:0000086 SGD_REF:S000045293|PMID:9427841 IPI P protein kinase CK2 alpha subunit YIL035C gene taxon:4932 20010118 SGD
+SGD S000001297 CKA1 GO:0000501 SGD_REF:S000045293|PMID:9427841 IMP P protein kinase CK2 alpha subunit YIL035C gene taxon:4932 20010118 SGD
+SGD S000001297 CKA1 GO:0006356 SGD_REF:S000070263|PMID:11551505 IDA P protein kinase CK2 alpha subunit YIL035C gene taxon:4932 20021022 SGD
+SGD S000001297 CKA1 GO:0006359 SGD_REF:S000070263|PMID:11551505 IDA P protein kinase CK2 alpha subunit YIL035C gene taxon:4932 20021022 SGD
+SGD S000001297 CKA1 GO:0006468 SGD_REF:S000045293|PMID:9427841 IDA P protein kinase CK2 alpha subunit YIL035C gene taxon:4932 20010118 SGD
+SGD S000001297 CKA1 GO:0006873 SGD_REF:S000045293|PMID:9427841 IPI P protein kinase CK2 alpha subunit YIL035C gene taxon:4932 20010118 SGD
+SGD S000001297 CKA1 GO:0006974 SGD_REF:S000070263|PMID:11551505 IDA P protein kinase CK2 alpha subunit YIL035C gene taxon:4932 20021022 SGD
+SGD S000001297 CKA1 GO:0030468 SGD_REF:S000045293|PMID:9427841 IMP P protein kinase CK2 alpha subunit YIL035C gene taxon:4932 20010302 SGD
+SGD S000005587 CKA2 GO:0005956 SGD_REF:S000045293|PMID:9427841 IDA C protein kinase CK2 alpha' subunit YOR061W|YOR29-12 gene taxon:4932 20010118 SGD
+SGD S000005587 CKA2 GO:0004682 SGD_REF:S000045293|PMID:9427841 IDA F protein kinase CK2 alpha' subunit YOR061W|YOR29-12 gene taxon:4932 20010118 SGD
+SGD S000005587 CKA2 GO:0000082 SGD_REF:S000045293|PMID:9427841 IMP P protein kinase CK2 alpha' subunit YOR061W|YOR29-12 gene taxon:4932 20010118 SGD
+SGD S000005587 CKA2 GO:0000086 SGD_REF:S000045293|PMID:9427841 IMP P protein kinase CK2 alpha' subunit YOR061W|YOR29-12 gene taxon:4932 20010118 SGD
+SGD S000005587 CKA2 GO:0000501 SGD_REF:S000045293|PMID:9427841 IMP P protein kinase CK2 alpha' subunit YOR061W|YOR29-12 gene taxon:4932 20010118 SGD
+SGD S000005587 CKA2 GO:0006356 SGD_REF:S000070263|PMID:11551505 IDA P protein kinase CK2 alpha' subunit YOR061W|YOR29-12 gene taxon:4932 20021022 SGD
+SGD S000005587 CKA2 GO:0006359 SGD_REF:S000070263|PMID:11551505 IDA P protein kinase CK2 alpha' subunit YOR061W|YOR29-12 gene taxon:4932 20021022 SGD
+SGD S000005587 CKA2 GO:0006468 SGD_REF:S000045293|PMID:9427841 IDA P protein kinase CK2 alpha' subunit YOR061W|YOR29-12 gene taxon:4932 20010118 SGD
+SGD S000005587 CKA2 GO:0006873 SGD_REF:S000045293|PMID:9427841 IPI P protein kinase CK2 alpha' subunit YOR061W|YOR29-12 gene taxon:4932 20010118 SGD
+SGD S000005587 CKA2 GO:0006974 SGD_REF:S000070263|PMID:11551505 IDA P protein kinase CK2 alpha' subunit YOR061W|YOR29-12 gene taxon:4932 20021022 SGD
+SGD S000005587 CKA2 GO:0030468 SGD_REF:S000045293|PMID:9427841 IPI P protein kinase CK2 alpha' subunit YOR061W|YOR29-12 gene taxon:4932 20010302 SGD
+SGD S000002987 CKB1 GO:0005956 SGD_REF:S000045293|PMID:9427841 IDA C protein kinase CK2 beta subunit YGL019W gene taxon:4932 20010118 SGD
+SGD S000002987 CKB1 GO:0008605 SGD_REF:S000062271|PMID:8135547 IPI SGD:S000001297|SGD:S000005587 F protein kinase CK2 beta subunit YGL019W gene taxon:4932 20050803 SGD
+SGD S000002987 CKB1 GO:0008605 SGD_REF:S000069123|PMID:11827175 IMP F protein kinase CK2 beta subunit YGL019W gene taxon:4932 20050803 SGD
+SGD S000002987 CKB1 GO:0000082 SGD_REF:S000045293|PMID:9427841 IPI P protein kinase CK2 beta subunit YGL019W gene taxon:4932 20010118 SGD
+SGD S000002987 CKB1 GO:0000086 SGD_REF:S000045293|PMID:9427841 IPI P protein kinase CK2 beta subunit YGL019W gene taxon:4932 20010118 SGD
+SGD S000002987 CKB1 GO:0000501 SGD_REF:S000045293|PMID:9427841 IMP P protein kinase CK2 beta subunit YGL019W gene taxon:4932 20010118 SGD
+SGD S000002987 CKB1 GO:0006356 SGD_REF:S000070263|PMID:11551505 IDA P protein kinase CK2 beta subunit YGL019W gene taxon:4932 20021022 SGD
+SGD S000002987 CKB1 GO:0006359 SGD_REF:S000070263|PMID:11551505 IDA P protein kinase CK2 beta subunit YGL019W gene taxon:4932 20021022 SGD
+SGD S000002987 CKB1 GO:0006468 SGD_REF:S000045293|PMID:9427841 IDA P protein kinase CK2 beta subunit YGL019W gene taxon:4932 20010118 SGD
+SGD S000002987 CKB1 GO:0006873 SGD_REF:S000045293|PMID:9427841 IMP P protein kinase CK2 beta subunit YGL019W gene taxon:4932 20010118 SGD
+SGD S000002987 CKB1 GO:0006974 SGD_REF:S000070263|PMID:11551505 IDA P protein kinase CK2 beta subunit YGL019W gene taxon:4932 20021022 SGD
+SGD S000002987 CKB1 GO:0030468 SGD_REF:S000045293|PMID:9427841 IPI P protein kinase CK2 beta subunit YGL019W gene taxon:4932 20010302 SGD
+SGD S000005565 CKB2 GO:0005956 SGD_REF:S000045293|PMID:9427841 IDA C protein kinase CK2, beta' subunit YOR039W gene taxon:4932 20010118 SGD
+SGD S000005565 CKB2 GO:0008605 SGD_REF:S000069123|PMID:11827175 IMP F protein kinase CK2, beta' subunit YOR039W gene taxon:4932 20050803 SGD
+SGD S000005565 CKB2 GO:0008605 SGD_REF:S000062271|PMID:8135547 IPI F protein kinase CK2, beta' subunit YOR039W gene taxon:4932 20050803 SGD
+SGD S000005565 CKB2 GO:0000082 SGD_REF:S000045293|PMID:9427841 IPI P protein kinase CK2, beta' subunit YOR039W gene taxon:4932 20010118 SGD
+SGD S000005565 CKB2 GO:0000086 SGD_REF:S000045293|PMID:9427841 IPI P protein kinase CK2, beta' subunit YOR039W gene taxon:4932 20010118 SGD
+SGD S000005565 CKB2 GO:0000501 SGD_REF:S000045293|PMID:9427841 IMP P protein kinase CK2, beta' subunit YOR039W gene taxon:4932 20010118 SGD
+SGD S000005565 CKB2 GO:0006356 SGD_REF:S000070263|PMID:11551505 IDA P protein kinase CK2, beta' subunit YOR039W gene taxon:4932 20021022 SGD
+SGD S000005565 CKB2 GO:0006359 SGD_REF:S000070263|PMID:11551505 IDA P protein kinase CK2, beta' subunit YOR039W gene taxon:4932 20021022 SGD
+SGD S000005565 CKB2 GO:0006468 SGD_REF:S000045293|PMID:9427841 IDA P protein kinase CK2, beta' subunit YOR039W gene taxon:4932 20010118 SGD
+SGD S000005565 CKB2 GO:0006873 SGD_REF:S000045293|PMID:9427841 IMP P protein kinase CK2, beta' subunit YOR039W gene taxon:4932 20010118 SGD
+SGD S000005565 CKB2 GO:0006974 SGD_REF:S000070263|PMID:11551505 IDA P protein kinase CK2, beta' subunit YOR039W gene taxon:4932 20021022 SGD
+SGD S000005565 CKB2 GO:0030468 SGD_REF:S000045293|PMID:9427841 IPI P protein kinase CK2, beta' subunit YOR039W gene taxon:4932 20010302 SGD
+SGD S000004123 CKI1 GO:0005829 SGD_REF:S000058496 TAS C choline kinase YLR133W gene taxon:4932 20010119 SGD
+SGD S000004123 CKI1 GO:0004103 SGD_REF:S000058496 TAS F choline kinase YLR133W gene taxon:4932 20010119 SGD
+SGD S000004123 CKI1 GO:0004103 SGD_REF:S000056873|PMID:2536698 IDA F choline kinase YLR133W gene taxon:4932 20050718 SGD
+SGD S000004123 CKI1 GO:0006656 SGD_REF:S000058496 TAS P choline kinase YLR133W gene taxon:4932 20010119 SGD
+SGD S000000339 CKS1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C Cdc28 protein kinase subunit YBR135W gene taxon:4932 20031028 SGD
+SGD S000000339 CKS1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C Cdc28 protein kinase subunit YBR135W gene taxon:4932 20031028 SGD
+SGD S000000339 CKS1 GO:0030295 SGD_REF:S000062128|PMID:10913169 IDA F Cdc28 protein kinase subunit YBR135W gene taxon:4932 20030829 SGD
+SGD S000000339 CKS1 GO:0000074 SGD_REF:S000058495 TAS P Cdc28 protein kinase subunit YBR135W gene taxon:4932 20010119 SGD
+SGD S000000339 CKS1 GO:0006350 SGD_REF:S000080329|PMID:15629725 IMP P Cdc28 protein kinase subunit YBR135W gene taxon:4932 20050125 SGD
+SGD S000005242 CLA4 GO:0030478 SGD_REF:S000041005|PMID:10652251 IDA C Ste20p homolog, protein kinase YNL298W|ERC10 gene taxon:4932 20010118 SGD
+SGD S000005242 CLA4 GO:0004674 SGD_REF:S000041005|PMID:10652251 TAS F Ste20p homolog, protein kinase YNL298W|ERC10 gene taxon:4932 20010118 SGD
+SGD S000005242 CLA4 GO:0000910 SGD_REF:S000041005|PMID:10652251 IMP P Ste20p homolog, protein kinase YNL298W|ERC10 gene taxon:4932 20010119 SGD
+SGD S000005242 CLA4 GO:0006468 SGD_REF:S000041005|PMID:10652251 TAS P Ste20p homolog, protein kinase YNL298W|ERC10 gene taxon:4932 20010118 SGD
+SGD S000005242 CLA4 GO:0007096 SGD_REF:S000071653|PMID:12234925 IMP P Ste20p homolog, protein kinase YNL298W|ERC10 gene taxon:4932 20050324 SGD
+SGD S000005242 CLA4 GO:0007118 SGD_REF:S000041005|PMID:10652251 IMP P Ste20p homolog, protein kinase YNL298W|ERC10 gene taxon:4932 20010118 SGD
+SGD S000005242 CLA4 GO:0007266 SGD_REF:S000041005|PMID:10652251 TAS P Ste20p homolog, protein kinase YNL298W|ERC10 gene taxon:4932 20010118 SGD
+SGD S000005242 CLA4 GO:0030468 SGD_REF:S000041005|PMID:10652251 IMP P Ste20p homolog, protein kinase YNL298W|ERC10 gene taxon:4932 20010302 SGD
+SGD S000003340 CLB1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C B-type cyclin YGR108W|SCB1 gene taxon:4932 20031028 SGD
+SGD S000003340 CLB1 GO:0005634 SGD_REF:S000074146|PMID:12972503 IDA C B-type cyclin YGR108W|SCB1 gene taxon:4932 20050602 SGD
+SGD S000003340 CLB1 GO:0005737 SGD_REF:S000074146|PMID:12972503 IDA C B-type cyclin YGR108W|SCB1 gene taxon:4932 20050602 SGD
+SGD S000003340 CLB1 GO:0016538 SGD_REF:S000058495 TAS F B-type cyclin YGR108W|SCB1 gene taxon:4932 20020208 SGD
+SGD S000003340 CLB1 GO:0000079 SGD_REF:S000058495 TAS P B-type cyclin YGR108W|SCB1 gene taxon:4932 20010119 SGD
+SGD S000003340 CLB1 GO:0000086 SGD_REF:S000044336|PMID:1427070 IGI P B-type cyclin YGR108W|SCB1 gene taxon:4932 20020705 SGD
+SGD S000003340 CLB1 GO:0000086 SGD_REF:S000044336|PMID:1427070 IMP P B-type cyclin YGR108W|SCB1 gene taxon:4932 20020705 SGD
+SGD S000003340 CLB1 GO:0000086 SGD_REF:S000044336|PMID:1427070 ISS P B-type cyclin YGR108W|SCB1 gene taxon:4932 20020705 SGD
+SGD S000003340 CLB1 GO:0008315 SGD_REF:S000042501|PMID:8455600 IMP P B-type cyclin YGR108W|SCB1 gene taxon:4932 20010118 SGD
+SGD S000003340 CLB1 GO:0008315 SGD_REF:S000042501|PMID:8455600 IEP P B-type cyclin YGR108W|SCB1 gene taxon:4932 20010118 SGD
+SGD S000003340 CLB1 GO:0030472 SGD_REF:S000044336|PMID:1427070 IMP P B-type cyclin YGR108W|SCB1 gene taxon:4932 20020705 SGD
+SGD S000003340 CLB1 GO:0030472 SGD_REF:S000044336|PMID:1427070 IGI P B-type cyclin YGR108W|SCB1 gene taxon:4932 20020705 SGD
+SGD S000006323 CLB2 GO:0005634 SGD_REF:S000059675|PMID:11171327 IDA C B-type cyclin YPR119W gene taxon:4932 20020705 SGD
+SGD S000006323 CLB2 GO:0005634 SGD_REF:S000074146|PMID:12972503 IDA C B-type cyclin YPR119W gene taxon:4932 20050602 SGD
+SGD S000006323 CLB2 GO:0005737 SGD_REF:S000059675|PMID:11171327 ISS C B-type cyclin YPR119W gene taxon:4932 20020705 SGD
+SGD S000006323 CLB2 GO:0005737 SGD_REF:S000059675|PMID:11171327 IMP C B-type cyclin YPR119W gene taxon:4932 20020705 SGD
+SGD S000006323 CLB2 GO:0005737 SGD_REF:S000074146|PMID:12972503 IDA C B-type cyclin YPR119W gene taxon:4932 20050602 SGD
+SGD S000006323 CLB2 GO:0005816 SGD_REF:S000074146|PMID:12972503 IDA C B-type cyclin YPR119W gene taxon:4932 20050602 SGD
+SGD S000006323 CLB2 GO:0005819 SGD_REF:S000074146|PMID:12972503 IDA C B-type cyclin YPR119W gene taxon:4932 20050602 SGD
+SGD S000006323 CLB2 GO:0005935 SGD_REF:S000074146|PMID:12972503 IDA C B-type cyclin YPR119W gene taxon:4932 20050602 SGD
+SGD S000006323 CLB2 GO:0016538 SGD_REF:S000058495 TAS F B-type cyclin YPR119W gene taxon:4932 20020208 SGD
+SGD S000006323 CLB2 GO:0000079 SGD_REF:S000058495 TAS P B-type cyclin YPR119W gene taxon:4932 20010119 SGD
+SGD S000006323 CLB2 GO:0000086 SGD_REF:S000042501|PMID:8455600 IMP P B-type cyclin YPR119W gene taxon:4932 20010118 SGD
+SGD S000006323 CLB2 GO:0000086 SGD_REF:S000042501|PMID:8455600 IEP P B-type cyclin YPR119W gene taxon:4932 20010118 SGD
+SGD S000002314 CLB3 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C B-type cyclin YDL155W gene taxon:4932 20031028 SGD
+SGD S000002314 CLB3 GO:0005634 SGD_REF:S000074146|PMID:12972503 IDA C B-type cyclin YDL155W gene taxon:4932 20050602 SGD
+SGD S000002314 CLB3 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C B-type cyclin YDL155W gene taxon:4932 20031028 SGD
+SGD S000002314 CLB3 GO:0005737 SGD_REF:S000074146|PMID:12972503 IDA C B-type cyclin YDL155W gene taxon:4932 20050602 SGD
+SGD S000002314 CLB3 GO:0016538 SGD_REF:S000058495 TAS F B-type cyclin YDL155W gene taxon:4932 20020208 SGD
+SGD S000002314 CLB3 GO:0000079 SGD_REF:S000058495 TAS P B-type cyclin YDL155W gene taxon:4932 20010119 SGD
+SGD S000002314 CLB3 GO:0000084 SGD_REF:S000044336|PMID:1427070 IGI P B-type cyclin YDL155W gene taxon:4932 20040726 SGD
+SGD S000002314 CLB3 GO:0000084 SGD_REF:S000044336|PMID:1427070 IMP P B-type cyclin YDL155W gene taxon:4932 20040726 SGD
+SGD S000002314 CLB3 GO:0000086 SGD_REF:S000044336|PMID:1427070 IGI P B-type cyclin YDL155W gene taxon:4932 20010118 SGD
+SGD S000002314 CLB3 GO:0000086 SGD_REF:S000044336|PMID:1427070 IMP P B-type cyclin YDL155W gene taxon:4932 20010118 SGD
+SGD S000004200 CLB4 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C B-type cyclin YLR210W gene taxon:4932 20031028 SGD
+SGD S000004200 CLB4 GO:0005634 SGD_REF:S000074146|PMID:12972503 IDA C B-type cyclin YLR210W gene taxon:4932 20050602 SGD
+SGD S000004200 CLB4 GO:0005737 SGD_REF:S000074146|PMID:12972503 IDA C B-type cyclin YLR210W gene taxon:4932 20050602 SGD
+SGD S000004200 CLB4 colocalizes_with GO:0005816 SGD_REF:S000074185|PMID:14562095 IDA C B-type cyclin YLR210W gene taxon:4932 20031028 SGD
+SGD S000004200 CLB4 GO:0016538 SGD_REF:S000058495 TAS F B-type cyclin YLR210W gene taxon:4932 20020208 SGD
+SGD S000004200 CLB4 GO:0000079 SGD_REF:S000058495 TAS P B-type cyclin YLR210W gene taxon:4932 20010119 SGD
+SGD S000004200 CLB4 GO:0000084 SGD_REF:S000044336|PMID:1427070 IGI P B-type cyclin YLR210W gene taxon:4932 20040726 SGD
+SGD S000004200 CLB4 GO:0000084 SGD_REF:S000044336|PMID:1427070 IMP P B-type cyclin YLR210W gene taxon:4932 20040726 SGD
+SGD S000004200 CLB4 GO:0000086 SGD_REF:S000044336|PMID:1427070 IMP P B-type cyclin YLR210W gene taxon:4932 20010118 SGD
+SGD S000004200 CLB4 GO:0000086 SGD_REF:S000044336|PMID:1427070 IGI P B-type cyclin YLR210W gene taxon:4932 20010118 SGD
+SGD S000006324 CLB5 GO:0005634 SGD_REF:S000062289|PMID:10848575 IDA C B-type cyclin YPR120C gene taxon:4932 20020710 SGD
+SGD S000006324 CLB5 GO:0016538 SGD_REF:S000058495 TAS F B-type cyclin YPR120C gene taxon:4932 20020208 SGD
+SGD S000006324 CLB5 GO:0000079 SGD_REF:S000058495 TAS P B-type cyclin YPR120C gene taxon:4932 20010119 SGD
+SGD S000006324 CLB5 GO:0000082 SGD_REF:S000049552|PMID:8319908 IMP P B-type cyclin YPR120C gene taxon:4932 20010118 SGD
+SGD S000006324 CLB5 GO:0000082 SGD_REF:S000049552|PMID:8319908 IEP P B-type cyclin YPR120C gene taxon:4932 20010118 SGD
+SGD S000006324 CLB5 GO:0000086 SGD_REF:S000049552|PMID:8319908 IMP P B-type cyclin YPR120C gene taxon:4932 20020710 SGD
+SGD S000006324 CLB5 GO:0000086 SGD_REF:S000049552|PMID:8319908 IEP P B-type cyclin YPR120C gene taxon:4932 20020710 SGD
+SGD S000006324 CLB5 GO:0006279 SGD_REF:S000053528|PMID:9732268 IGI P B-type cyclin YPR120C gene taxon:4932 20020710 SGD
+SGD S000006324 CLB5 GO:0006279 SGD_REF:S000053528|PMID:9732268 IMP P B-type cyclin YPR120C gene taxon:4932 20020710 SGD
+SGD S000003341 CLB6 GO:0008372 SGD_REF:S000069584 ND C B-type cyclin YGR109C gene taxon:4932 20010119 SGD
+SGD S000003341 CLB6 GO:0016538 SGD_REF:S000049552|PMID:8319908 IEP F B-type cyclin YGR109C gene taxon:4932 20020208 SGD
+SGD S000003341 CLB6 GO:0016538 SGD_REF:S000049552|PMID:8319908 IMP F B-type cyclin YGR109C gene taxon:4932 20020208 SGD
+SGD S000003341 CLB6 GO:0000079 SGD_REF:S000058495 TAS P B-type cyclin YGR109C gene taxon:4932 20010119 SGD
+SGD S000003341 CLB6 GO:0000082 SGD_REF:S000049552|PMID:8319908 IGI P B-type cyclin YGR109C gene taxon:4932 20010118 SGD
+SGD S000003341 CLB6 GO:0006279 SGD_REF:S000053528|PMID:9732268 IGI P B-type cyclin YGR109C gene taxon:4932 20020710 SGD
+SGD S000003341 CLB6 GO:0006279 SGD_REF:S000053528|PMID:9732268 IMP P B-type cyclin YGR109C gene taxon:4932 20020710 SGD
+SGD S000003399 CLC1 GO:0030125 SGD_REF:S000049871|PMID:9171338 TAS C clathrin light chain YGR167W|SCD4 gene taxon:4932 20020715 SGD
+SGD S000003399 CLC1 GO:0005198 SGD_REF:S000049871|PMID:9171338 TAS F clathrin light chain YGR167W|SCD4 gene taxon:4932 20020715 SGD
+SGD S000003399 CLC1 GO:0006897 SGD_REF:S000061172|PMID:11252894 TAS P clathrin light chain YGR167W|SCD4 gene taxon:4932 20050509 SGD
+SGD S000003399 CLC1 GO:0016192 SGD_REF:S000049871|PMID:9171338 TAS P clathrin light chain YGR167W|SCD4 gene taxon:4932 20020715 SGD
+SGD S000004107 CLF1 GO:0000785 SGD_REF:S000069705|PMID:11973290 IDA C pre-mRNA splicing factor YLR117C|NTC77|SYF3 gene taxon:4932 20040409 SGD
+SGD S000004107 CLF1 GO:0005515 SGD_REF:S000052652|PMID:10445879 IPI SGD:S000001495|SGD:S000001557 F pre-mRNA splicing factor YLR117C|NTC77|SYF3 gene taxon:4932 20051103 SGD
+SGD S000004107 CLF1 GO:0000354 SGD_REF:S000052652|PMID:10445879 IMP P pre-mRNA splicing factor YLR117C|NTC77|SYF3 gene taxon:4932 20051103 SGD
+SGD S000004107 CLF1 GO:0000398 SGD_REF:S000059130|PMID:11105756 IMP P pre-mRNA splicing factor YLR117C|NTC77|SYF3 gene taxon:4932 20030213 SGD
+SGD S000004107 CLF1 GO:0006260 SGD_REF:S000069705|PMID:11973290 IMP P pre-mRNA splicing factor YLR117C|NTC77|SYF3 gene taxon:4932 20040409 SGD
+SGD S000004107 CLF1 GO:0007049 SGD_REF:S000059451|PMID:11102353 TAS P pre-mRNA splicing factor YLR117C|NTC77|SYF3 gene taxon:4932 20010209 SGD
+SGD S000003183 CLG1 GO:0000307 SGD_REF:S000068989|PMID:11602261 TAS C YGL215W gene taxon:4932 20020212 SGD
+SGD S000003183 CLG1 GO:0016538 SGD_REF:S000068989|PMID:11602261 TAS F YGL215W gene taxon:4932 20020211 SGD
+SGD S000003183 CLG1 GO:0007049 SGD_REF:S000068989|PMID:11602261 TAS P YGL215W gene taxon:4932 20020211 SGD
+SGD S000004812 CLN1 GO:0005634 SGD_REF:S000059560|PMID:11080155 IDA C G1 cyclin YMR199W gene taxon:4932 20030619 SGD
+SGD S000004812 CLN1 GO:0005737 SGD_REF:S000059560|PMID:11080155 IDA C G1 cyclin YMR199W gene taxon:4932 20030619 SGD
+SGD S000004812 CLN1 GO:0016538 SGD_REF:S000058495 TAS F G1 cyclin YMR199W gene taxon:4932 20020208 SGD
+SGD S000004812 CLN1 GO:0000079 SGD_REF:S000058495 TAS P G1 cyclin YMR199W gene taxon:4932 20010119 SGD
+SGD S000006177 CLN2 GO:0005634 SGD_REF:S000069008|PMID:11792824 IDA C G1 cyclin YPL256C gene taxon:4932 20030213 SGD
+SGD S000006177 CLN2 GO:0005634 SGD_REF:S000059560|PMID:11080155 IDA C G1 cyclin YPL256C gene taxon:4932 20030619 SGD
+SGD S000006177 CLN2 GO:0005634 SGD_REF:S000043377|PMID:10611233 IDA C G1 cyclin YPL256C gene taxon:4932 20030505 SGD
+SGD S000006177 CLN2 GO:0005737 SGD_REF:S000069008|PMID:11792824 IDA C G1 cyclin YPL256C gene taxon:4932 20030213 SGD
+SGD S000006177 CLN2 GO:0005737 SGD_REF:S000074959|PMID:11509671 IMP C G1 cyclin YPL256C gene taxon:4932 20040617 SGD
+SGD S000006177 CLN2 GO:0005737 SGD_REF:S000043377|PMID:10611233 IDA C G1 cyclin YPL256C gene taxon:4932 20030505 SGD
+SGD S000006177 CLN2 GO:0005737 SGD_REF:S000074959|PMID:11509671 IDA C G1 cyclin YPL256C gene taxon:4932 20040617 SGD
+SGD S000006177 CLN2 GO:0005737 SGD_REF:S000059560|PMID:11080155 IDA C G1 cyclin YPL256C gene taxon:4932 20030619 SGD
+SGD S000006177 CLN2 GO:0016538 SGD_REF:S000058495 TAS F G1 cyclin YPL256C gene taxon:4932 20020208 SGD
+SGD S000006177 CLN2 GO:0000079 SGD_REF:S000058495 TAS P G1 cyclin YPL256C gene taxon:4932 20010119 SGD
+SGD S000006177 CLN2 GO:0000321 SGD_REF:S000053376|PMID:9927449 IGI P G1 cyclin YPL256C gene taxon:4932 20020529 SGD
+SGD S000000038 CLN3 GO:0005634 SGD_REF:S000043377|PMID:10611233 IDA C G1 cyclin YAL040C|DAF1|FUN10|WHI1 gene taxon:4932 20030505 SGD
+SGD S000000038 CLN3 GO:0005634 SGD_REF:S000069008|PMID:11792824 IDA C G1 cyclin YAL040C|DAF1|FUN10|WHI1 gene taxon:4932 20021125 SGD
+SGD S000000038 CLN3 GO:0005634 SGD_REF:S000074959|PMID:11509671 IMP C G1 cyclin YAL040C|DAF1|FUN10|WHI1 gene taxon:4932 20040617 SGD
+SGD S000000038 CLN3 GO:0005634 SGD_REF:S000074959|PMID:11509671 IDA C G1 cyclin YAL040C|DAF1|FUN10|WHI1 gene taxon:4932 20040617 SGD
+SGD S000000038 CLN3 GO:0016538 SGD_REF:S000058495 TAS F G1 cyclin YAL040C|DAF1|FUN10|WHI1 gene taxon:4932 20020208 SGD
+SGD S000000038 CLN3 GO:0000079 SGD_REF:S000058495 TAS P G1 cyclin YAL040C|DAF1|FUN10|WHI1 gene taxon:4932 20010119 SGD
+SGD S000000038 CLN3 GO:0000082 SGD_REF:S000070100|PMID:12024050 TAS P G1 cyclin YAL040C|DAF1|FUN10|WHI1 gene taxon:4932 20021125 SGD
+SGD S000000038 CLN3 GO:0007033 SGD_REF:S000074300|PMID:14573462 IMP P G1 cyclin YAL040C|DAF1|FUN10|WHI1 gene taxon:4932 20040614 SGD
+SGD S000000038 CLN3 GO:0042144 SGD_REF:S000074300|PMID:14573462 IDA P G1 cyclin YAL040C|DAF1|FUN10|WHI1 gene taxon:4932 20040614 SGD
+SGD S000000038 CLN3 GO:0042144 SGD_REF:S000074300|PMID:14573462 IMP P G1 cyclin YAL040C|DAF1|FUN10|WHI1 gene taxon:4932 20040614 SGD
+SGD S000005776 CLP1 GO:0005849 SGD_REF:S000060315|PMID:11344258 IPI C cleavage and polyadenylation factor CF I component involved in pre-mRNA 3'-end processing YOR250C gene taxon:4932 20020409 SGD
+SGD S000005776 CLP1 contributes_to GO:0003723 SGD_REF:S000060315|PMID:11344258 IDA F cleavage and polyadenylation factor CF I component involved in pre-mRNA 3'-end processing YOR250C gene taxon:4932 20050218 SGD
+SGD S000005776 CLP1 GO:0006378 SGD_REF:S000060315|PMID:11344258 IDA P cleavage and polyadenylation factor CF I component involved in pre-mRNA 3'-end processing YOR250C gene taxon:4932 20020410 SGD
+SGD S000005776 CLP1 GO:0006379 SGD_REF:S000060315|PMID:11344258 IDA P cleavage and polyadenylation factor CF I component involved in pre-mRNA 3'-end processing YOR250C gene taxon:4932 20020409 SGD
+SGD S000005776 CLP1 GO:0031124 SGD_REF:S000060315|PMID:11344258 IDA P cleavage and polyadenylation factor CF I component involved in pre-mRNA 3'-end processing YOR250C gene taxon:4932 20050513 SGD
+SGD S000004614 CLU1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C Sometimes copurifies with translation initiation factor eIF3, but apparently not required for translation initiation YMR012W|TIF31 gene taxon:4932 20020507 SGD
+SGD S000004614 CLU1 GO:0005852 SGD_REF:S000050729|PMID:10358023 IPI C Sometimes copurifies with translation initiation factor eIF3, but apparently not required for translation initiation YMR012W|TIF31 gene taxon:4932 20030423 SGD
+SGD S000004614 CLU1 GO:0005554 SGD_REF:S000069584 ND F Sometimes copurifies with translation initiation factor eIF3, but apparently not required for translation initiation YMR012W|TIF31 gene taxon:4932 20050502 SGD
+SGD S000004614 CLU1 GO:0006413 SGD_REF:S000050729|PMID:10358023 IPI P Sometimes copurifies with translation initiation factor eIF3, but apparently not required for translation initiation YMR012W|TIF31 gene taxon:4932 20030423 SGD
+SGD S000004614 CLU1 GO:0007005 SGD_REF:S000053038|PMID:9601101 IMP P Sometimes copurifies with translation initiation factor eIF3, but apparently not required for translation initiation YMR012W|TIF31 gene taxon:4932 20030423 SGD
+SGD S000000313 CMD1 GO:0000131 SGD_REF:S000049233|PMID:1639847 IDA C calmodulin YBR109C gene taxon:4932 20010118 SGD
+SGD S000000313 CMD1 GO:0005737 SGD_REF:S000047941|PMID:8310294 TAS C calmodulin YBR109C gene taxon:4932 20010118 SGD
+SGD S000000313 CMD1 GO:0005823 SGD_REF:S000047587|PMID:8601600 IDA C calmodulin YBR109C gene taxon:4932 20010118 SGD
+SGD S000000313 CMD1 GO:0005934 SGD_REF:S000049233|PMID:1639847 IDA C calmodulin YBR109C gene taxon:4932 20010118 SGD
+SGD S000000313 CMD1 GO:0005935 SGD_REF:S000049233|PMID:1639847 IDA C calmodulin YBR109C gene taxon:4932 20010118 SGD
+SGD S000000313 CMD1 GO:0043332 SGD_REF:S000049233|PMID:1639847 IDA C calmodulin YBR109C gene taxon:4932 20010118 SGD
+SGD S000000313 CMD1 GO:0005509 SGD_REF:S000062307|PMID:8461293 IDA F calmodulin YBR109C gene taxon:4932 20050503 SGD
+SGD S000000313 CMD1 GO:0005515 SGD_REF:S000066251|PMID:11700296 TAS F calmodulin YBR109C gene taxon:4932 20050503 SGD
+SGD S000000313 CMD1 GO:0048306 SGD_REF:S000066251|PMID:11700296 TAS F calmodulin YBR109C gene taxon:4932 20050503 SGD
+SGD S000000313 CMD1 GO:0006897 SGD_REF:S000041618|PMID:7988551 IMP P calmodulin YBR109C gene taxon:4932 20050503 SGD
+SGD S000000313 CMD1 GO:0007010 SGD_REF:S000047941|PMID:8310294 IMP P calmodulin YBR109C gene taxon:4932 20010118 SGD
+SGD S000000313 CMD1 GO:0007067 SGD_REF:S000056540|PMID:1505006 TAS P calmodulin YBR109C gene taxon:4932 20010118 SGD
+SGD S000000313 CMD1 GO:0007114 SGD_REF:S000047941|PMID:8310294 IMP P calmodulin YBR109C gene taxon:4932 20010118 SGD
+SGD S000000313 CMD1 GO:0042144 SGD_REF:S000062321|PMID:9859992 IMP P calmodulin YBR109C gene taxon:4932 20050503 SGD
+SGD S000000313 CMD1 GO:0042144 SGD_REF:S000080958|PMID:15737991 IMP P calmodulin YBR109C gene taxon:4932 20050503 SGD
+SGD S000001910 CMK1 GO:0005737 SGD_REF:S000062320|PMID:9756868 IPI C calmodulin-dependent protein kinase YFR014C gene taxon:4932 20021122 SGD
+SGD S000001910 CMK1 GO:0004684 SGD_REF:S000052932|PMID:2061341 IDA F calmodulin-dependent protein kinase YFR014C gene taxon:4932 20010118 SGD
+SGD S000001910 CMK1 GO:0006468 SGD_REF:S000052932|PMID:2061341 IDA P calmodulin-dependent protein kinase YFR014C gene taxon:4932 20010118 SGD
+SGD S000001910 CMK1 GO:0007165 SGD_REF:S000069069|PMID:11743609 IMP P calmodulin-dependent protein kinase YFR014C gene taxon:4932 20021122 SGD
+SGD S000005376 CMK2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C calmodulin-dependent protein kinase YOL016C gene taxon:4932 20031028 SGD
+SGD S000005376 CMK2 GO:0004685 SGD_REF:S000052932|PMID:2061341 IDA F calmodulin-dependent protein kinase YOL016C gene taxon:4932 20010118 SGD
+SGD S000005376 CMK2 GO:0006468 SGD_REF:S000052932|PMID:2061341 IDA P calmodulin-dependent protein kinase YOL016C gene taxon:4932 20010118 SGD
+SGD S000005376 CMK2 GO:0007165 SGD_REF:S000052932|PMID:2061341 NAS P calmodulin-dependent protein kinase YOL016C gene taxon:4932 20010118 SGD
+SGD S000004521 CMP2 GO:0005737 SGD_REF:S000040143|PMID:9123967 TAS C calcineurin subunit A YML057W|CNA2 gene taxon:4932 20010118 SGD
+SGD S000004521 CMP2 GO:0005955 SGD_REF:S000040630|PMID:1651503 ISS C calcineurin subunit A YML057W|CNA2 gene taxon:4932 20031215 SGD
+SGD S000004521 CMP2 GO:0005955 SGD_REF:S000062324|PMID:10887154 IPI C calcineurin subunit A YML057W|CNA2 gene taxon:4932 20031215 SGD
+SGD S000004521 CMP2 GO:0005955 SGD_REF:S000047822|PMID:1321337 IPI C calcineurin subunit A YML057W|CNA2 gene taxon:4932 20031215 SGD
+SGD S000004521 CMP2 GO:0004723 SGD_REF:S000040630|PMID:1651503 ISS F calcineurin subunit A YML057W|CNA2 gene taxon:4932 20010118 SGD
+SGD S000004521 CMP2 GO:0000754 SGD_REF:S000040630|PMID:1651503 IMP P calcineurin subunit A YML057W|CNA2 gene taxon:4932 20021206 SGD
+SGD S000004521 CMP2 GO:0006873 SGD_REF:S000041651|PMID:8798496 IMP P calcineurin subunit A YML057W|CNA2 gene taxon:4932 20010118 SGD
+SGD S000004425 CNA1 GO:0005737 SGD_REF:S000040143|PMID:9123967 TAS C calcineurin subunit A YLR433C|CMP1 gene taxon:4932 20010118 SGD
+SGD S000004425 CNA1 GO:0005955 SGD_REF:S000040630|PMID:1651503 ISS C calcineurin subunit A YLR433C|CMP1 gene taxon:4932 20031215 SGD
+SGD S000004425 CNA1 GO:0005955 SGD_REF:S000062324|PMID:10887154 IPI C calcineurin subunit A YLR433C|CMP1 gene taxon:4932 20031215 SGD
+SGD S000004425 CNA1 GO:0005955 SGD_REF:S000047822|PMID:1321337 IPI C calcineurin subunit A YLR433C|CMP1 gene taxon:4932 20031215 SGD
+SGD S000004425 CNA1 GO:0004723 SGD_REF:S000040630|PMID:1651503 ISS F calcineurin subunit A YLR433C|CMP1 gene taxon:4932 20010118 SGD
+SGD S000004425 CNA1 GO:0000754 SGD_REF:S000040630|PMID:1651503 IMP P calcineurin subunit A YLR433C|CMP1 gene taxon:4932 20021206 SGD
+SGD S000004425 CNA1 GO:0006873 SGD_REF:S000041651|PMID:8798496 IMP P calcineurin subunit A YLR433C|CMP1 gene taxon:4932 20010118 SGD
+SGD S000004425 CNA1 GO:0007047 SGD_REF:S000039119|PMID:7530227 IMP P calcineurin subunit A YLR433C|CMP1 gene taxon:4932 20010118 SGD
+SGD S000004425 CNA1 GO:0007047 SGD_REF:S000039119|PMID:7530227 IGI P calcineurin subunit A YLR433C|CMP1 gene taxon:4932 20010118 SGD
+SGD S000001673 CNB1 GO:0005737 SGD_REF:S000047822|PMID:1321337 ISS C calcineurin regulatory B subunit, type 2B protein phosphatase YKL190W|CRV1|YCN2 gene taxon:4932 20010118 SGD
+SGD S000001673 CNB1 GO:0005955 SGD_REF:S000062324|PMID:10887154 IPI C calcineurin regulatory B subunit, type 2B protein phosphatase YKL190W|CRV1|YCN2 gene taxon:4932 20031215 SGD
+SGD S000001673 CNB1 GO:0005955 SGD_REF:S000047822|PMID:1321337 IPI C calcineurin regulatory B subunit, type 2B protein phosphatase YKL190W|CRV1|YCN2 gene taxon:4932 20031215 SGD
+SGD S000001673 CNB1 contributes_to GO:0004723 SGD_REF:S000047822|PMID:1321337 IPI F calcineurin regulatory B subunit, type 2B protein phosphatase YKL190W|CRV1|YCN2 gene taxon:4932 20050505 SGD
+SGD S000001673 CNB1 contributes_to GO:0004723 SGD_REF:S000047822|PMID:1321337 ISS F calcineurin regulatory B subunit, type 2B protein phosphatase YKL190W|CRV1|YCN2 gene taxon:4932 20050505 SGD
+SGD S000001673 CNB1 GO:0005509 SGD_REF:S000081513|PMID:11015619 ISS F calcineurin regulatory B subunit, type 2B protein phosphatase YKL190W|CRV1|YCN2 gene taxon:4932 20050505 SGD
+SGD S000001673 CNB1 GO:0000754 SGD_REF:S000047822|PMID:1321337 IMP P calcineurin regulatory B subunit, type 2B protein phosphatase YKL190W|CRV1|YCN2 gene taxon:4932 20021206 SGD
+SGD S000001673 CNB1 GO:0006873 SGD_REF:S000041651|PMID:8798496 IMP P calcineurin regulatory B subunit, type 2B protein phosphatase YKL190W|CRV1|YCN2 gene taxon:4932 20010118 SGD
+SGD S000001673 CNB1 GO:0007047 SGD_REF:S000039119|PMID:7530227 IMP P calcineurin regulatory B subunit, type 2B protein phosphatase YKL190W|CRV1|YCN2 gene taxon:4932 20010118 SGD
+SGD S000001673 CNB1 GO:0007047 SGD_REF:S000039119|PMID:7530227 IGI P calcineurin regulatory B subunit, type 2B protein phosphatase YKL190W|CRV1|YCN2 gene taxon:4932 20010118 SGD
+SGD S000000054 CNE1 GO:0030176 SGD_REF:S000039200|PMID:7814381 IDA C calnexin and calreticulin homolog YAL058W|FUN48 gene taxon:4932 20020717 SGD
+SGD S000000054 CNE1 GO:0051082 SGD_REF:S000076464|PMID:15173200 IMP F calnexin and calreticulin homolog YAL058W|FUN48 gene taxon:4932 20050503 SGD
+SGD S000000054 CNE1 GO:0051082 SGD_REF:S000039200|PMID:7814381 ISS F calnexin and calreticulin homolog YAL058W|FUN48 gene taxon:4932 20050503 SGD
+SGD S000000054 CNE1 GO:0006457 SGD_REF:S000076464|PMID:15173200 IMP P calnexin and calreticulin homolog YAL058W|FUN48 gene taxon:4932 20050503 SGD
+SGD S000000054 CNE1 GO:0030433 SGD_REF:S000039200|PMID:7814381 IMP P calnexin and calreticulin homolog YAL058W|FUN48 gene taxon:4932 20020717 SGD
+SGD S000005169 CNM67 GO:0005816 SGD_REF:S000047788|PMID:9585415 IDA C YNL225C gene taxon:4932 20010118 SGD
+SGD S000005169 CNM67 GO:0005824 SGD_REF:S000061265|PMID:11514632 IDA C YNL225C gene taxon:4932 20030321 SGD
+SGD S000005169 CNM67 GO:0005200 SGD_REF:S000047788|PMID:9585415 IPI F YNL225C gene taxon:4932 20010118 SGD
+SGD S000005169 CNM67 GO:0007020 SGD_REF:S000058447|PMID:9153752 IPI P YNL225C gene taxon:4932 20010118 SGD
+SGD S000005169 CNM67 GO:0007052 SGD_REF:S000053982|PMID:9571234 IMP P YNL225C gene taxon:4932 20050509 SGD
+SGD S000005169 CNM67 GO:0007052 SGD_REF:S000041561|PMID:10749924 IMP P YNL225C gene taxon:4932 20050509 SGD
+SGD S000001942 CNN1 GO:0000776 SGD_REF:S000075142|PMID:14633972 IDA C kinetochore protein YFR046C gene taxon:4932 20050502 SGD
+SGD S000001942 CNN1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C kinetochore protein YFR046C gene taxon:4932 20031028 SGD
+SGD S000001942 CNN1 GO:0005554 SGD_REF:S000069584 ND F kinetochore protein YFR046C gene taxon:4932 20050502 SGD
+SGD S000001942 CNN1 GO:0007059 SGD_REF:S000075142|PMID:14633972 IPI SGD:S000003873 P kinetochore protein YFR046C gene taxon:4932 20050502 SGD
+SGD S000001942 CNN1 GO:0007059 SGD_REF:S000061559|PMID:9520439 IPI SGD:S000004723 P kinetochore protein YFR046C gene taxon:4932 20050502 SGD
+SGD S000000359 CNS1 GO:0005737 SGD_REF:S000047779|PMID:9819421 IPI C YBR155W gene taxon:4932 20021009 SGD
+SGD S000000359 CNS1 GO:0051082 SGD_REF:S000047779|PMID:9819421 IPI F YBR155W gene taxon:4932 20021009 SGD
+SGD S000000359 CNS1 GO:0006457 SGD_REF:S000047779|PMID:9819421 IGI P YBR155W gene taxon:4932 20021009 SGD
+SGD S000000359 CNS1 GO:0006457 SGD_REF:S000076436|PMID:15044454 IPI SGD:S000000004|SGD:S000006161 P YBR155W gene taxon:4932 20050509 SGD
+SGD S000007270 COB GO:0005750 SGD_REF:S000050433|PMID:391561 IDA C cytochrome b Q0105|COB1|CYTB gene taxon:4932 20020906 SGD
+SGD S000007270 COB GO:0005750 SGD_REF:S000046403|PMID:10873857 IDA C cytochrome b Q0105|COB1|CYTB gene taxon:4932 20020906 SGD
+SGD S000007270 COB GO:0008121 SGD_REF:S000050433|PMID:391561 IDA F cytochrome b Q0105|COB1|CYTB gene taxon:4932 20020906 SGD
+SGD S000007270 COB GO:0006122 SGD_REF:S000050433|PMID:391561 IMP P cytochrome b Q0105|COB1|CYTB gene taxon:4932 20020906 SGD
+SGD S000007270 COB GO:0009060 SGD_REF:S000050433|PMID:391561 IMP P cytochrome b Q0105|COB1|CYTB gene taxon:4932 20020906 SGD
+SGD S000003973 COF1 GO:0030479 SGD_REF:S000041005|PMID:10652251 IDA C actin binding and severing protein, cofilin YLL050C gene taxon:4932 20010118 SGD
+SGD S000003973 COF1 GO:0005515 SGD_REF:S000075674|PMID:14680631 IDA F actin binding and severing protein, cofilin YLL050C gene taxon:4932 20040403 SGD
+SGD S000003973 COF1 GO:0007015 SGD_REF:S000041005|PMID:10652251 IPI P actin binding and severing protein, cofilin YLL050C gene taxon:4932 20010118 SGD
+SGD S000003973 COF1 GO:0007015 SGD_REF:S000058447|PMID:9153752 IMP P actin binding and severing protein, cofilin YLL050C gene taxon:4932 20010118 SGD
+SGD S000003973 COF1 GO:0030042 SGD_REF:S000047128|PMID:8440472 IDA P actin binding and severing protein, cofilin YLL050C gene taxon:4932 20010621 SGD
+SGD S000003973 COF1 GO:0030042 SGD_REF:S000039142|PMID:8421056 IDA P actin binding and severing protein, cofilin YLL050C gene taxon:4932 20010621 SGD
+SGD S000003973 COF1 GO:0051014 SGD_REF:S000075674|PMID:14680631 IDA P actin binding and severing protein, cofilin YLL050C gene taxon:4932 20040403 SGD
+SGD S000003191 COG1 GO:0017119 SGD_REF:S000066187|PMID:11703943 IPI C YGL223C|COD3|LDB11|SEC36 gene taxon:4932 20011128 SGD
+SGD S000003191 COG1 GO:0005554 SGD_REF:S000069584 ND F YGL223C|COD3|LDB11|SEC36 gene taxon:4932 20011128 SGD
+SGD S000003191 COG1 GO:0000301 SGD_REF:S000066187|PMID:11703943 IMP P YGL223C|COD3|LDB11|SEC36 gene taxon:4932 20011128 SGD
+SGD S000003191 COG1 GO:0006891 SGD_REF:S000066187|PMID:11703943 IPI P YGL223C|COD3|LDB11|SEC36 gene taxon:4932 20011128 SGD
+SGD S000003191 COG1 GO:0006891 SGD_REF:S000066187|PMID:11703943 IGI P YGL223C|COD3|LDB11|SEC36 gene taxon:4932 20011128 SGD
+SGD S000003352 COG2 GO:0000300 SGD_REF:S000056398|PMID:10512869 IDA C YGR120C|SEC35 gene taxon:4932 20011105 SGD
+SGD S000003352 COG2 GO:0005625 SGD_REF:S000056398|PMID:10512869 IDA C YGR120C|SEC35 gene taxon:4932 20011105 SGD
+SGD S000003352 COG2 GO:0017119 SGD_REF:S000066187|PMID:11703943 IPI C YGR120C|SEC35 gene taxon:4932 20011128 SGD
+SGD S000003352 COG2 GO:0005515 SGD_REF:S000070001|PMID:12011112 IPI F YGR120C|SEC35 gene taxon:4932 20021113 SGD
+SGD S000003352 COG2 GO:0000301 SGD_REF:S000066187|PMID:11703943 IMP P YGR120C|SEC35 gene taxon:4932 20011128 SGD
+SGD S000003352 COG2 GO:0000301 SGD_REF:S000066187|PMID:11703943 TAS P YGR120C|SEC35 gene taxon:4932 20011128 SGD
+SGD S000003352 COG2 GO:0006888 SGD_REF:S000056398|PMID:10512869 IGI P YGR120C|SEC35 gene taxon:4932 20011105 SGD
+SGD S000003352 COG2 GO:0006891 SGD_REF:S000066187|PMID:11703943 IPI P YGR120C|SEC35 gene taxon:4932 20011128 SGD
+SGD S000003352 COG2 GO:0006891 SGD_REF:S000066187|PMID:11703943 IGI P YGR120C|SEC35 gene taxon:4932 20011128 SGD
+SGD S000000959 COG3 GO:0000300 SGD_REF:S000056398|PMID:10512869 IDA C YER157W|GRD20|SEC34 gene taxon:4932 20011105 SGD
+SGD S000000959 COG3 GO:0005625 SGD_REF:S000056398|PMID:10512869 IDA C YER157W|GRD20|SEC34 gene taxon:4932 20011105 SGD
+SGD S000000959 COG3 GO:0017119 SGD_REF:S000066187|PMID:11703943 IPI C YER157W|GRD20|SEC34 gene taxon:4932 20011128 SGD
+SGD S000000959 COG3 GO:0008565 SGD_REF:S000071361|PMID:12077121 TAS F YER157W|GRD20|SEC34 gene taxon:4932 20021002 SGD
+SGD S000000959 COG3 GO:0000301 SGD_REF:S000066187|PMID:11703943 IMP P YER157W|GRD20|SEC34 gene taxon:4932 20011128 SGD
+SGD S000000959 COG3 GO:0000301 SGD_REF:S000066187|PMID:11703943 TAS P YER157W|GRD20|SEC34 gene taxon:4932 20011128 SGD
+SGD S000000959 COG3 GO:0006888 SGD_REF:S000056398|PMID:10512869 IGI P YER157W|GRD20|SEC34 gene taxon:4932 20011105 SGD
+SGD S000000959 COG3 GO:0006891 SGD_REF:S000066187|PMID:11703943 IPI P YER157W|GRD20|SEC34 gene taxon:4932 20011128 SGD
+SGD S000000959 COG3 GO:0006891 SGD_REF:S000066187|PMID:11703943 IGI P YER157W|GRD20|SEC34 gene taxon:4932 20011128 SGD
+SGD S000006309 COG4 GO:0017119 SGD_REF:S000066187|PMID:11703943 IPI C YPR105C|COD1|SEC38|SGF1 gene taxon:4932 20011128 SGD
+SGD S000006309 COG4 GO:0005554 SGD_REF:S000069584 ND F YPR105C|COD1|SEC38|SGF1 gene taxon:4932 20011128 SGD
+SGD S000006309 COG4 GO:0000301 SGD_REF:S000066187|PMID:11703943 IMP P YPR105C|COD1|SEC38|SGF1 gene taxon:4932 20011128 SGD
+SGD S000006309 COG4 GO:0006891 SGD_REF:S000066187|PMID:11703943 IPI P YPR105C|COD1|SEC38|SGF1 gene taxon:4932 20011128 SGD
+SGD S000006309 COG4 GO:0006891 SGD_REF:S000066187|PMID:11703943 IGI P YPR105C|COD1|SEC38|SGF1 gene taxon:4932 20011128 SGD
+SGD S000004996 COG5 GO:0017119 SGD_REF:S000066187|PMID:11703943 IPI C YNL051W|API4|COD4 gene taxon:4932 20011128 SGD
+SGD S000004996 COG5 GO:0005554 SGD_REF:S000069584 ND F YNL051W|API4|COD4 gene taxon:4932 20011128 SGD
+SGD S000004996 COG5 GO:0006891 SGD_REF:S000066187|PMID:11703943 IPI P YNL051W|API4|COD4 gene taxon:4932 20011128 SGD
+SGD S000004996 COG5 GO:0006891 SGD_REF:S000066187|PMID:11703943 IGI P YNL051W|API4|COD4 gene taxon:4932 20011128 SGD
+SGD S000004986 COG6 GO:0017119 SGD_REF:S000066187|PMID:11703943 IPI C YNL041C|COD2|SEC37 gene taxon:4932 20011128 SGD
+SGD S000004986 COG6 GO:0005554 SGD_REF:S000069584 ND F YNL041C|COD2|SEC37 gene taxon:4932 20011128 SGD
+SGD S000004986 COG6 GO:0006891 SGD_REF:S000066187|PMID:11703943 IPI P YNL041C|COD2|SEC37 gene taxon:4932 20011128 SGD
+SGD S000004986 COG6 GO:0006891 SGD_REF:S000066187|PMID:11703943 IGI P YNL041C|COD2|SEC37 gene taxon:4932 20011128 SGD
+SGD S000002973 COG7 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YGL005C|COD5 gene taxon:4932 20040928 SGD
+SGD S000002973 COG7 GO:0017119 SGD_REF:S000066187|PMID:11703943 IPI C YGL005C|COD5 gene taxon:4932 20011128 SGD
+SGD S000002973 COG7 GO:0005554 SGD_REF:S000069584 ND F YGL005C|COD5 gene taxon:4932 20011128 SGD
+SGD S000002973 COG7 GO:0006891 SGD_REF:S000066187|PMID:11703943 IPI P YGL005C|COD5 gene taxon:4932 20011128 SGD
+SGD S000002973 COG7 GO:0006891 SGD_REF:S000066187|PMID:11703943 IGI P YGL005C|COD5 gene taxon:4932 20011128 SGD
+SGD S000004536 COG8 GO:0017119 SGD_REF:S000066187|PMID:11703943 IPI C YML071C|DOR1 gene taxon:4932 20011128 SGD
+SGD S000004536 COG8 GO:0005554 SGD_REF:S000069584 ND F YML071C|DOR1 gene taxon:4932 20011128 SGD
+SGD S000004536 COG8 GO:0006891 SGD_REF:S000066187|PMID:11703943 IPI P YML071C|DOR1 gene taxon:4932 20011128 SGD
+SGD S000004536 COG8 GO:0006891 SGD_REF:S000066187|PMID:11703943 IGI P YML071C|DOR1 gene taxon:4932 20011128 SGD
+SGD S000002304 COP1 GO:0030126 SGD_REF:S000046381|PMID:8001155 ISS C coatomer complex gamma-alpha-COP alpha subunit YDL145C|RET1|SEC33|SOO1 gene taxon:4932 20020807 SGD
+SGD S000002304 COP1 GO:0030126 SGD_REF:S000046381|PMID:8001155 IMP C coatomer complex gamma-alpha-COP alpha subunit YDL145C|RET1|SEC33|SOO1 gene taxon:4932 20020807 SGD
+SGD S000002304 COP1 GO:0005554 SGD_REF:S000069584 ND F coatomer complex gamma-alpha-COP alpha subunit YDL145C|RET1|SEC33|SOO1 gene taxon:4932 20020807 SGD
+SGD S000002304 COP1 GO:0006888 SGD_REF:S000042560|PMID:9427388 IMP P coatomer complex gamma-alpha-COP alpha subunit YDL145C|RET1|SEC33|SOO1 gene taxon:4932 20020807 SGD
+SGD S000002304 COP1 GO:0006890 SGD_REF:S000046381|PMID:8001155 IMP P coatomer complex gamma-alpha-COP alpha subunit YDL145C|RET1|SEC33|SOO1 gene taxon:4932 20020807 SGD
+SGD S000000207 COQ1 GO:0005739 SGD_REF:S000047703|PMID:10760477 IMP C hexaprenyl pyrophosphate synthetase YBR003W gene taxon:4932 20021118 SGD
+SGD S000000207 COQ1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C hexaprenyl pyrophosphate synthetase YBR003W gene taxon:4932 20040928 SGD
+SGD S000000207 COQ1 GO:0000010 SGD_REF:S000040139|PMID:9708911 IMP F hexaprenyl pyrophosphate synthetase YBR003W gene taxon:4932 20010118 SGD
+SGD S000000207 COQ1 GO:0006743 SGD_REF:S000040139|PMID:9708911 IMP P hexaprenyl pyrophosphate synthetase YBR003W gene taxon:4932 20010118 SGD
+SGD S000005368 COQ10 GO:0005743 SGD_REF:S000086908|PMID:16230336 IDA C YOL008W gene taxon:4932 20051019 SGD
+SGD S000005368 COQ10 GO:0048039 SGD_REF:S000086908|PMID:16230336 IDA F YOL008W gene taxon:4932 20051019 SGD
+SGD S000005368 COQ10 GO:0045333 SGD_REF:S000086909|PMID:50596 IMP P YOL008W gene taxon:4932 20051020 SGD
+SGD S000005324 COQ2 GO:0005743 SGD_REF:S000047441|PMID:10469659 TAS C para hydroxybenzoate: polyprenyl transferase YNR041C gene taxon:4932 20021030 SGD
+SGD S000005324 COQ2 GO:0004659 SGD_REF:S000040651|PMID:1740455 IMP F para hydroxybenzoate: polyprenyl transferase YNR041C gene taxon:4932 20030314 SGD
+SGD S000005324 COQ2 GO:0005386 SGD_REF:S000047441|PMID:10469659 TAS F para hydroxybenzoate: polyprenyl transferase YNR041C gene taxon:4932 20021030 SGD
+SGD S000005324 COQ2 GO:0019840 SGD_REF:S000040139|PMID:9708911 TAS F para hydroxybenzoate: polyprenyl transferase YNR041C gene taxon:4932 20021029 SGD
+SGD S000005324 COQ2 GO:0006743 SGD_REF:S000040651|PMID:1740455 IMP P para hydroxybenzoate: polyprenyl transferase YNR041C gene taxon:4932 20010118 SGD
+SGD S000005456 COQ3 GO:0005739 SGD_REF:S000047703|PMID:10760477 IDA C 3,4-dihydroxy-5-hexaprenylbenzoate methyltransferase YOL096C gene taxon:4932 20021004 SGD
+SGD S000005456 COQ3 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C 3,4-dihydroxy-5-hexaprenylbenzoate methyltransferase YOL096C gene taxon:4932 20040924 SGD
+SGD S000005456 COQ3 GO:0005743 SGD_REF:S000046983|PMID:10419476 IDA C 3,4-dihydroxy-5-hexaprenylbenzoate methyltransferase YOL096C gene taxon:4932 20030314 SGD
+SGD S000005456 COQ3 GO:0019898 SGD_REF:S000046983|PMID:10419476 IDA C 3,4-dihydroxy-5-hexaprenylbenzoate methyltransferase YOL096C gene taxon:4932 20030314 SGD
+SGD S000005456 COQ3 GO:0004395 SGD_REF:S000051191|PMID:1885593 IMP F 3,4-dihydroxy-5-hexaprenylbenzoate methyltransferase YOL096C gene taxon:4932 20010118 SGD
+SGD S000005456 COQ3 GO:0006743 SGD_REF:S000051191|PMID:1885593 IMP P 3,4-dihydroxy-5-hexaprenylbenzoate methyltransferase YOL096C gene taxon:4932 20010118 SGD
+SGD S000005456 COQ3 GO:0006744 SGD_REF:S000046983|PMID:10419476 IDA P 3,4-dihydroxy-5-hexaprenylbenzoate methyltransferase YOL096C gene taxon:4932 20030314 SGD
+SGD S000002612 COQ4 GO:0005743 SGD_REF:S000061389|PMID:11469793 IDA C encodes component of the coenzyme Q biosynthetic pathway YDR204W gene taxon:4932 20020709 SGD
+SGD S000002612 COQ4 GO:0005554 SGD_REF:S000069584 ND F encodes component of the coenzyme Q biosynthetic pathway YDR204W gene taxon:4932 20021105 SGD
+SGD S000002612 COQ4 GO:0006743 SGD_REF:S000044198|PMID:9266513 IMP P encodes component of the coenzyme Q biosynthetic pathway YDR204W gene taxon:4932 20010118 SGD
+SGD S000004578 COQ5 GO:0005739 SGD_REF:S000049292|PMID:9083048 TAS C C-methyltransferase (putative) YML110C|DBI56 gene taxon:4932 20010118 SGD
+SGD S000004578 COQ5 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C C-methyltransferase (putative) YML110C|DBI56 gene taxon:4932 20040928 SGD
+SGD S000004578 COQ5 GO:0043334 SGD_REF:S000049294|PMID:9083049 ISS F C-methyltransferase (putative) YML110C|DBI56 gene taxon:4932 20020913 SGD
+SGD S000004578 COQ5 GO:0043334 SGD_REF:S000049294|PMID:9083049 IMP F C-methyltransferase (putative) YML110C|DBI56 gene taxon:4932 20020913 SGD
+SGD S000004578 COQ5 GO:0006743 SGD_REF:S000049292|PMID:9083048 IMP P C-methyltransferase (putative) YML110C|DBI56 gene taxon:4932 20010118 SGD
+SGD S000004578 COQ5 GO:0009060 SGD_REF:S000049294|PMID:9083049 IMP P C-methyltransferase (putative) YML110C|DBI56 gene taxon:4932 20020913 SGD
+SGD S000003487 COQ6 GO:0005739 SGD_REF:S000047703|PMID:10760477 TAS C monooxygenase YGR255C gene taxon:4932 20030314 SGD
+SGD S000003487 COQ6 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C monooxygenase YGR255C gene taxon:4932 20040928 SGD
+SGD S000003487 COQ6 GO:0005743 SGD_REF:S000073496|PMID:12721307 IDA C monooxygenase YGR255C gene taxon:4932 20030916 SGD
+SGD S000003487 COQ6 GO:0015997 SGD_REF:S000072241|PMID:11583838 ISS F monooxygenase YGR255C gene taxon:4932 20030314 SGD
+SGD S000003487 COQ6 GO:0006743 SGD_REF:S000044198|PMID:9266513 IMP P monooxygenase YGR255C gene taxon:4932 20010118 SGD
+SGD S000004191 COQ9 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YLR201C|FMP53 gene taxon:4932 20031028 SGD
+SGD S000004191 COQ9 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YLR201C|FMP53 gene taxon:4932 20040924 SGD
+SGD S000004191 COQ9 GO:0005743 SGD_REF:S000082316|PMID:16027161 IDA C YLR201C|FMP53 gene taxon:4932 20050906 SGD
+SGD S000004191 COQ9 GO:0005554 SGD_REF:S000069584 ND F YLR201C|FMP53 gene taxon:4932 20050906 SGD
+SGD S000004191 COQ9 GO:0006744 SGD_REF:S000082316|PMID:16027161 IMP P YLR201C|FMP53 gene taxon:4932 20050906 SGD
+SGD S000004191 COQ9 GO:0009060 SGD_REF:S000082316|PMID:16027161 IMP P YLR201C|FMP53 gene taxon:4932 20050906 SGD
+SGD S000000141 COR1 GO:0005750 SGD_REF:S000051199|PMID:3023384 IDA C coenzyme QH2 cytochrome c reductase 44 kDa core protein subunit YBL045C|QCR1 gene taxon:4932 20020906 SGD
+SGD S000000141 COR1 GO:0005750 SGD_REF:S000046403|PMID:10873857 IDA C coenzyme QH2 cytochrome c reductase 44 kDa core protein subunit YBL045C|QCR1 gene taxon:4932 20020906 SGD
+SGD S000000141 COR1 GO:0008121 SGD_REF:S000051199|PMID:3023384 IDA F coenzyme QH2 cytochrome c reductase 44 kDa core protein subunit YBL045C|QCR1 gene taxon:4932 20020906 SGD
+SGD S000000141 COR1 GO:0009060 SGD_REF:S000052322|PMID:2174874 IMP P coenzyme QH2 cytochrome c reductase 44 kDa core protein subunit YBL045C|QCR1 gene taxon:4932 20020906 SGD
+SGD S000005280 COS1 GO:0000324 SGD_REF:S000074185|PMID:14562095 IDA C YNL336W gene taxon:4932 20031028 SGD
+SGD S000005280 COS1 GO:0005554 SGD_REF:S000069584 ND F YNL336W gene taxon:4932 20021003 SGD
+SGD S000005280 COS1 GO:0000004 SGD_REF:S000069584 ND P YNL336W gene taxon:4932 20021003 SGD
+SGD S000005358 COS10 GO:0005635 SGD_REF:S000069459|PMID:11914276 IDA C YNR075W gene taxon:4932 20020507 SGD
+SGD S000005358 COS10 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YNR075W gene taxon:4932 20020507 SGD
+SGD S000005358 COS10 GO:0005783 SGD_REF:S000069459|PMID:11914276 IDA C YNR075W gene taxon:4932 20020507 SGD
+SGD S000005358 COS10 GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YNR075W gene taxon:4932 20031028 SGD
+SGD S000005358 COS10 GO:0005554 SGD_REF:S000069584 ND F YNR075W gene taxon:4932 20021003 SGD
+SGD S000005358 COS10 GO:0006897 SGD_REF:S000060817|PMID:11378903 IMP P YNR075W gene taxon:4932 20021004 SGD
+SGD S000000407 COS111 GO:0008372 SGD_REF:S000069584 ND C YBR203W gene taxon:4932 20030410 SGD
+SGD S000000407 COS111 GO:0005554 SGD_REF:S000069584 ND F YBR203W gene taxon:4932 20030410 SGD
+SGD S000000407 COS111 GO:0007165 SGD_REF:S000072861|PMID:12661761 IMP P YBR203W gene taxon:4932 20030410 SGD
+SGD S000003232 COS12 GO:0008372 SGD_REF:S000069584 ND C YGL263W gene taxon:4932 20021003 SGD
+SGD S000003232 COS12 GO:0005554 SGD_REF:S000069584 ND F YGL263W gene taxon:4932 20021003 SGD
+SGD S000003232 COS12 GO:0000004 SGD_REF:S000069584 ND P YGL263W gene taxon:4932 20021003 SGD
+SGD S000000506 COS2 GO:0000324 SGD_REF:S000074185|PMID:14562095 IDA C YBR302C gene taxon:4932 20031028 SGD
+SGD S000000506 COS2 GO:0005554 SGD_REF:S000069584 ND F YBR302C gene taxon:4932 20021003 SGD
+SGD S000000506 COS2 GO:0000004 SGD_REF:S000069584 ND P YBR302C gene taxon:4932 20021003 SGD
+SGD S000004601 COS3 GO:0000324 SGD_REF:S000074185|PMID:14562095 IDA C YML132W gene taxon:4932 20031028 SGD
+SGD S000004601 COS3 GO:0005624 SGD_REF:S000075716|PMID:14718542 IDA C YML132W gene taxon:4932 20040917 SGD
+SGD S000004601 COS3 GO:0005515 SGD_REF:S000075716|PMID:14718542 IMP F YML132W gene taxon:4932 20041123 SGD
+SGD S000004601 COS3 GO:0006883 SGD_REF:S000075716|PMID:14718542 IMP P YML132W gene taxon:4932 20040917 SGD
+SGD S000001832 COS4 GO:0000324 SGD_REF:S000074185|PMID:14562095 IDA C YFL062W gene taxon:4932 20031028 SGD
+SGD S000001832 COS4 GO:0005554 SGD_REF:S000069584 ND F YFL062W gene taxon:4932 20021003 SGD
+SGD S000001832 COS4 GO:0000004 SGD_REF:S000069584 ND P YFL062W gene taxon:4932 20021003 SGD
+SGD S000003922 COS5 GO:0000324 SGD_REF:S000074185|PMID:14562095 IDA C YJR161C gene taxon:4932 20031028 SGD
+SGD S000003922 COS5 GO:0005554 SGD_REF:S000069584 ND F YJR161C gene taxon:4932 20021003 SGD
+SGD S000003922 COS5 GO:0000004 SGD_REF:S000069584 ND P YJR161C gene taxon:4932 20021003 SGD
+SGD S000003527 COS6 GO:0000324 SGD_REF:S000074185|PMID:14562095 IDA C YGR295C gene taxon:4932 20031028 SGD
+SGD S000003527 COS6 GO:0005554 SGD_REF:S000069584 ND F YGR295C gene taxon:4932 20021003 SGD
+SGD S000003527 COS6 GO:0000004 SGD_REF:S000069584 ND P YGR295C gene taxon:4932 20021003 SGD
+SGD S000002407 COS7 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YDL248W gene taxon:4932 20040813 SGD
+SGD S000002407 COS7 GO:0004872 SGD_REF:S000049663|PMID:9560393 IMP F YDL248W gene taxon:4932 20021112 SGD
+SGD S000002407 COS7 GO:0000004 SGD_REF:S000069584 ND P YDL248W gene taxon:4932 20030514 SGD
+SGD S000001040 COS8 GO:0005635 SGD_REF:S000069972|PMID:12051917 IDA C YHL048W gene taxon:4932 20020920 SGD
+SGD S000001040 COS8 GO:0005554 SGD_REF:S000069584 ND F YHL048W gene taxon:4932 20020920 SGD
+SGD S000001040 COS8 GO:0006986 SGD_REF:S000069972|PMID:12051917 IEP P YHL048W gene taxon:4932 20020920 SGD
+SGD S000001702 COS9 GO:0008372 SGD_REF:S000069584 ND C YKL219W gene taxon:4932 20021003 SGD
+SGD S000001702 COS9 GO:0005554 SGD_REF:S000069584 ND F YKL219W gene taxon:4932 20021003 SGD
+SGD S000001702 COS9 GO:0000004 SGD_REF:S000069584 ND P YKL219W gene taxon:4932 20021003 SGD
+SGD S000005843 COT1 GO:0000324 SGD_REF:S000050176|PMID:9712830 IDA C YOR316C gene taxon:4932 20010302 SGD
+SGD S000005843 COT1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YOR316C gene taxon:4932 20040928 SGD
+SGD S000005843 COT1 GO:0005385 SGD_REF:S000039447|PMID:8058041 IGI F YOR316C gene taxon:4932 20010118 SGD
+SGD S000005843 COT1 GO:0015082 SGD_REF:S000058475|PMID:9075641 ISS F YOR316C gene taxon:4932 20010118 SGD
+SGD S000005843 COT1 GO:0015087 SGD_REF:S000045379|PMID:1508175 IMP F YOR316C gene taxon:4932 20010118 SGD
+SGD S000005843 COT1 GO:0006824 SGD_REF:S000045379|PMID:1508175 IMP P YOR316C gene taxon:4932 20010118 SGD
+SGD S000005843 COT1 GO:0006829 SGD_REF:S000039447|PMID:8058041 IGI P YOR316C gene taxon:4932 20010118 SGD
+SGD S000005843 COT1 GO:0006882 SGD_REF:S000041386|PMID:10856230 IMP P YOR316C gene taxon:4932 20010118 SGD
+SGD S000007260 COX1 GO:0005751 SGD_REF:S000056478|PMID:1331058 IPI C cytochrome c oxidase subunit I Q0045|OXI3 gene taxon:4932 20020606 SGD
+SGD S000007260 COX1 GO:0004129 SGD_REF:S000056478|PMID:1331058 IDA F cytochrome c oxidase subunit I Q0045|OXI3 gene taxon:4932 20020603 SGD
+SGD S000007260 COX1 GO:0006123 SGD_REF:S000056478|PMID:1331058 IDA P cytochrome c oxidase subunit I Q0045|OXI3 gene taxon:4932 20050207 SGD
+SGD S000007260 COX1 GO:0009060 SGD_REF:S000054591|PMID:9724417 IMP P cytochrome c oxidase subunit I Q0045|OXI3 gene taxon:4932 20020603 SGD
+SGD S000006093 COX10 GO:0005743 SGD_REF:S000057943|PMID:8811190 TAS C farnesyl transferase (putative) YPL172C gene taxon:4932 20010118 SGD
+SGD S000006093 COX10 GO:0008495 SGD_REF:S000051391|PMID:8118433 ISS F farnesyl transferase (putative) YPL172C gene taxon:4932 20010118 SGD
+SGD S000006093 COX10 GO:0006461 SGD_REF:S000053923|PMID:2167832 IMP P farnesyl transferase (putative) YPL172C gene taxon:4932 20040206 SGD
+SGD S000006093 COX10 GO:0006784 SGD_REF:S000057943|PMID:8811190 TAS P farnesyl transferase (putative) YPL172C gene taxon:4932 20010118 SGD
+SGD S000006053 COX11 GO:0005740 SGD_REF:S000053923|PMID:2167832 IDA C YPL132W|LPI13|PSO7 gene taxon:4932 20040206 SGD
+SGD S000006053 COX11 GO:0005743 SGD_REF:S000055856|PMID:10501934 IDA C YPL132W|LPI13|PSO7 gene taxon:4932 20010118 SGD
+SGD S000006053 COX11 GO:0005743 SGD_REF:S000081153|PMID:15776235 IDA C YPL132W|LPI13|PSO7 gene taxon:4932 20050415 SGD
+SGD S000006053 COX11 GO:0005761 SGD_REF:S000081153|PMID:15776235 IDA C YPL132W|LPI13|PSO7 gene taxon:4932 20050415 SGD
+SGD S000006053 COX11 GO:0005507 SGD_REF:S000076608|PMID:12063264 IDA F YPL132W|LPI13|PSO7 gene taxon:4932 20040716 SGD
+SGD S000006053 COX11 GO:0006461 SGD_REF:S000053923|PMID:2167832 IMP P YPL132W|LPI13|PSO7 gene taxon:4932 20040206 SGD
+SGD S000006053 COX11 GO:0009060 SGD_REF:S000056412|PMID:10617659 IMP P YPL132W|LPI13|PSO7 gene taxon:4932 20020604 SGD
+SGD S000006053 COX11 GO:0015680 SGD_REF:S000076608|PMID:12063264 IDA P YPL132W|LPI13|PSO7 gene taxon:4932 20050415 SGD
+SGD S000004028 COX12 GO:0005751 SGD_REF:S000056478|PMID:1331058 IPI C cytochrome c oxidase subunit VIb YLR038C gene taxon:4932 20020603 SGD
+SGD S000004028 COX12 GO:0004129 SGD_REF:S000056478|PMID:1331058 IDA F cytochrome c oxidase subunit VIb YLR038C gene taxon:4932 20020603 SGD
+SGD S000004028 COX12 GO:0008535 SGD_REF:S000056478|PMID:1331058 IMP P cytochrome c oxidase subunit VIb YLR038C gene taxon:4932 20030115 SGD
+SGD S000003159 COX13 GO:0005751 SGD_REF:S000056478|PMID:1331058 IPI C cytochrome c oxidase subunit VIa, may specifically interact with ATP YGL191W gene taxon:4932 20020603 SGD
+SGD S000003159 COX13 GO:0004129 SGD_REF:S000056478|PMID:1331058 IDA F cytochrome c oxidase subunit VIa, may specifically interact with ATP YGL191W gene taxon:4932 20020603 SGD
+SGD S000003159 COX13 GO:0030234 SGD_REF:S000062382|PMID:10429195 IDA F cytochrome c oxidase subunit VIa, may specifically interact with ATP YGL191W gene taxon:4932 20020614 SGD
+SGD S000003159 COX13 GO:0009060 SGD_REF:S000049791|PMID:8395517 IMP P cytochrome c oxidase subunit VIa, may specifically interact with ATP YGL191W gene taxon:4932 20020614 SGD
+SGD S000004598 COX14 GO:0005740 SGD_REF:S000049651|PMID:7797555 IDA C mitochondrial membrane protein YML129C gene taxon:4932 20010118 SGD
+SGD S000004598 COX14 GO:0005743 SGD_REF:S000077016|PMID:15306853 IDA C mitochondrial membrane protein YML129C gene taxon:4932 20050301 SGD
+SGD S000004598 COX14 GO:0005759 SGD_REF:S000077016|PMID:15306853 IDA C mitochondrial membrane protein YML129C gene taxon:4932 20050301 SGD
+SGD S000004598 COX14 GO:0016021 SGD_REF:S000049651|PMID:7797555 IDA C mitochondrial membrane protein YML129C gene taxon:4932 20020607 SGD
+SGD S000004598 COX14 GO:0019898 SGD_REF:S000077016|PMID:15306853 IDA C mitochondrial membrane protein YML129C gene taxon:4932 20050301 SGD
+SGD S000004598 COX14 GO:0005554 SGD_REF:S000069584 ND F mitochondrial membrane protein YML129C gene taxon:4932 20010119 SGD
+SGD S000004598 COX14 GO:0009060 SGD_REF:S000049651|PMID:7797555 IMP P mitochondrial membrane protein YML129C gene taxon:4932 20020604 SGD
+SGD S000004598 COX14 GO:0016478 SGD_REF:S000077016|PMID:15306853 IPI SGD:S000004193 P mitochondrial membrane protein YML129C gene taxon:4932 20050301 SGD
+SGD S000004598 COX14 GO:0016478 SGD_REF:S000077016|PMID:15306853 IGI P mitochondrial membrane protein YML129C gene taxon:4932 20050301 SGD
+SGD S000000943 COX15 GO:0005743 SGD_REF:S000048816|PMID:9228094 IDA C cytochrome oxidase assembly factor YER141W gene taxon:4932 20010118 SGD
+SGD S000000943 COX15 contributes_to GO:0016653 SGD_REF:S000059902|PMID:11248251 IMP F cytochrome oxidase assembly factor YER141W gene taxon:4932 20041208 SGD
+SGD S000000943 COX15 GO:0006784 SGD_REF:S000069465|PMID:11788607 IGI P cytochrome oxidase assembly factor YER141W gene taxon:4932 20020903 SGD
+SGD S000000943 COX15 GO:0006784 SGD_REF:S000069465|PMID:11788607 IMP P cytochrome oxidase assembly factor YER141W gene taxon:4932 20020903 SGD
+SGD S000000943 COX15 GO:0008535 SGD_REF:S000048816|PMID:9228094 IMP P cytochrome oxidase assembly factor YER141W gene taxon:4932 20010118 SGD
+SGD S000003540 COX16 GO:0005743 SGD_REF:S000072538|PMID:12446688 IDA C Required for assembly of cytochrome oxidase YJL003W gene taxon:4932 20030217 SGD
+SGD S000003540 COX16 GO:0005554 SGD_REF:S000069584 ND F Required for assembly of cytochrome oxidase YJL003W gene taxon:4932 20021121 SGD
+SGD S000003540 COX16 GO:0006461 SGD_REF:S000072538|PMID:12446688 IMP P Required for assembly of cytochrome oxidase YJL003W gene taxon:4932 20030217 SGD
+SGD S000003540 COX16 GO:0009060 SGD_REF:S000072538|PMID:12446688 IMP P Required for assembly of cytochrome oxidase YJL003W gene taxon:4932 20030217 SGD
+SGD S000003932 COX17 GO:0005758 SGD_REF:S000052017|PMID:9407107 IDA C copper chaperone YLL009C gene taxon:4932 20010118 SGD
+SGD S000003932 COX17 GO:0005829 SGD_REF:S000052017|PMID:9407107 IDA C copper chaperone YLL009C gene taxon:4932 20010118 SGD
+SGD S000003932 COX17 GO:0008379 SGD_REF:S000078936|PMID:10954195 ISS F copper chaperone YLL009C gene taxon:4932 20050121 SGD
+SGD S000003932 COX17 GO:0016531 SGD_REF:S000048412|PMID:9585572 IMP F copper chaperone YLL009C gene taxon:4932 20040115 SGD
+SGD S000003932 COX17 GO:0016531 SGD_REF:S000048412|PMID:9585572 IPI F copper chaperone YLL009C gene taxon:4932 20040115 SGD
+SGD S000003932 COX17 GO:0016531 SGD_REF:S000080787|PMID:15199057 IDA F copper chaperone YLL009C gene taxon:4932 20050304 SGD
+SGD S000003932 COX17 GO:0008535 SGD_REF:S000053671|PMID:8662933 IMP P copper chaperone YLL009C gene taxon:4932 20010118 SGD
+SGD S000003932 COX17 GO:0008535 SGD_REF:S000080787|PMID:15199057 IDA P copper chaperone YLL009C gene taxon:4932 20050304 SGD
+SGD S000003932 COX17 GO:0015680 SGD_REF:S000053671|PMID:8662933 IMP P copper chaperone YLL009C gene taxon:4932 20010118 SGD
+SGD S000003932 COX17 GO:0015680 SGD_REF:S000048412|PMID:9585572 IPI P copper chaperone YLL009C gene taxon:4932 20010118 SGD
+SGD S000003932 COX17 GO:0015680 SGD_REF:S000080787|PMID:15199057 IDA P copper chaperone YLL009C gene taxon:4932 20050304 SGD
+SGD S000003294 COX18 GO:0005743 SGD_REF:S000069749|PMID:11950926 IDA C YGR062C|OXA2 gene taxon:4932 20020606 SGD
+SGD S000003294 COX18 GO:0016021 SGD_REF:S000050027|PMID:10809734 IDA C YGR062C|OXA2 gene taxon:4932 20020605 SGD
+SGD S000003294 COX18 GO:0008565 SGD_REF:S000069749|PMID:11950926 IMP F YGR062C|OXA2 gene taxon:4932 20041217 SGD
+SGD S000003294 COX18 GO:0008535 SGD_REF:S000050027|PMID:10809734 IMP P YGR062C|OXA2 gene taxon:4932 20010118 SGD
+SGD S000007245 COX19 GO:0005758 SGD_REF:S000071532|PMID:12171940 IDA C YLL018C-A gene taxon:4932 20030415 SGD
+SGD S000007245 COX19 GO:0005829 SGD_REF:S000071532|PMID:12171940 IDA C YLL018C-A gene taxon:4932 20030415 SGD
+SGD S000007245 COX19 GO:0046873 SGD_REF:S000071532|PMID:12171940 ISS F YLL018C-A gene taxon:4932 20030415 SGD
+SGD S000007245 COX19 GO:0008535 SGD_REF:S000071532|PMID:12171940 IDA P YLL018C-A gene taxon:4932 20030415 SGD
+SGD S000007245 COX19 GO:0008535 SGD_REF:S000071532|PMID:12171940 ISS P YLL018C-A gene taxon:4932 20030415 SGD
+SGD S000007245 COX19 GO:0030001 SGD_REF:S000071532|PMID:12171940 IDA P YLL018C-A gene taxon:4932 20030415 SGD
+SGD S000007245 COX19 GO:0030001 SGD_REF:S000071532|PMID:12171940 ISS P YLL018C-A gene taxon:4932 20030415 SGD
+SGD S000007281 COX2 GO:0005751 SGD_REF:S000056478|PMID:1331058 IPI C cytochrome c oxidase subunit II Q0250|OXI1|OXII gene taxon:4932 20020603 SGD
+SGD S000007281 COX2 GO:0004129 SGD_REF:S000056478|PMID:1331058 IDA F cytochrome c oxidase subunit II Q0250|OXI1|OXII gene taxon:4932 20020603 SGD
+SGD S000007281 COX2 GO:0006123 SGD_REF:S000056478|PMID:1331058 IDA P cytochrome c oxidase subunit II Q0250|OXI1|OXII gene taxon:4932 20050207 SGD
+SGD S000007281 COX2 GO:0009060 SGD_REF:S000062390|PMID:224191 IMP P cytochrome c oxidase subunit II Q0250|OXI1|OXII gene taxon:4932 20020905 SGD
+SGD S000002639 COX20 GO:0005743 SGD_REF:S000062376|PMID:10671482 IDA C required for maturation and assembly of cytochrome oxidase subunit II YDR231C gene taxon:4932 20020604 SGD
+SGD S000002639 COX20 GO:0051082 SGD_REF:S000062376|PMID:10671482 IDA F required for maturation and assembly of cytochrome oxidase subunit II YDR231C gene taxon:4932 20020610 SGD
+SGD S000002639 COX20 GO:0008535 SGD_REF:S000062376|PMID:10671482 IMP P required for maturation and assembly of cytochrome oxidase subunit II YDR231C gene taxon:4932 20020605 SGD
+SGD S000002639 COX20 GO:0009060 SGD_REF:S000062376|PMID:10671482 IMP P required for maturation and assembly of cytochrome oxidase subunit II YDR231C gene taxon:4932 20020604 SGD
+SGD S000002639 COX20 GO:0016485 SGD_REF:S000062376|PMID:10671482 IMP P required for maturation and assembly of cytochrome oxidase subunit II YDR231C gene taxon:4932 20020604 SGD
+SGD S000001158 COX23 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YHR116W gene taxon:4932 20031028 SGD
+SGD S000001158 COX23 GO:0005737 SGD_REF:S000076717|PMID:15145942 IDA C YHR116W gene taxon:4932 20040927 SGD
+SGD S000001158 COX23 GO:0005739 SGD_REF:S000076717|PMID:15145942 IDA C YHR116W gene taxon:4932 20040927 SGD
+SGD S000001158 COX23 GO:0005554 SGD_REF:S000069584 ND F YHR116W gene taxon:4932 20020806 SGD
+SGD S000001158 COX23 GO:0009060 SGD_REF:S000060148|PMID:10929718 IEP P YHR116W gene taxon:4932 20020806 SGD
+SGD S000001158 COX23 GO:0009060 SGD_REF:S000060148|PMID:10929718 IMP P YHR116W gene taxon:4932 20020806 SGD
+SGD S000007283 COX3 GO:0005751 SGD_REF:S000056478|PMID:1331058 IPI C cytochrome c oxidase subunit III Q0275|OXI2 gene taxon:4932 20020603 SGD
+SGD S000007283 COX3 GO:0004129 SGD_REF:S000056478|PMID:1331058 IDA F cytochrome c oxidase subunit III Q0275|OXI2 gene taxon:4932 20020603 SGD
+SGD S000007283 COX3 GO:0006123 SGD_REF:S000056478|PMID:1331058 IDA P cytochrome c oxidase subunit III Q0275|OXI2 gene taxon:4932 20050207 SGD
+SGD S000007283 COX3 GO:0009060 SGD_REF:S000062378|PMID:11171120 IMP P cytochrome c oxidase subunit III Q0275|OXI2 gene taxon:4932 20020604 SGD
+SGD S000003155 COX4 GO:0005751 SGD_REF:S000056478|PMID:1331058 IPI C cytochrome c oxidase subunit IV YGL187C gene taxon:4932 20020603 SGD
+SGD S000003155 COX4 GO:0004129 SGD_REF:S000056478|PMID:1331058 IDA F cytochrome c oxidase subunit IV YGL187C gene taxon:4932 20020603 SGD
+SGD S000003155 COX4 GO:0006123 SGD_REF:S000056478|PMID:1331058 IDA P cytochrome c oxidase subunit IV YGL187C gene taxon:4932 20050207 SGD
+SGD S000003155 COX4 GO:0009060 SGD_REF:S000062372|PMID:163235 IPI P cytochrome c oxidase subunit IV YGL187C gene taxon:4932 20020916 SGD
+SGD S000004997 COX5A GO:0005751 SGD_REF:S000056478|PMID:1331058 IPI C cytochrome c oxidase subunit Va YNL052W gene taxon:4932 20020603 SGD
+SGD S000004997 COX5A GO:0004129 SGD_REF:S000043404|PMID:1847916 IDA F cytochrome c oxidase subunit Va YNL052W gene taxon:4932 20030115 SGD
+SGD S000004997 COX5A GO:0006123 SGD_REF:S000056478|PMID:1331058 IDA P cytochrome c oxidase subunit Va YNL052W gene taxon:4932 20050207 SGD
+SGD S000004997 COX5A GO:0009060 SGD_REF:S000057499|PMID:7814361 TAS P cytochrome c oxidase subunit Va YNL052W gene taxon:4932 20020930 SGD
+SGD S000001373 COX5B GO:0005751 SGD_REF:S000046724|PMID:2986105 IDA C cytochrome c oxidase subunit Vb YIL111W gene taxon:4932 20020905 SGD
+SGD S000001373 COX5B GO:0004129 SGD_REF:S000046724|PMID:2986105 IDA F cytochrome c oxidase subunit Vb YIL111W gene taxon:4932 20020905 SGD
+SGD S000001373 COX5B GO:0006123 SGD_REF:S000056478|PMID:1331058 IDA P cytochrome c oxidase subunit Vb YIL111W gene taxon:4932 20050207 SGD
+SGD S000001373 COX5B GO:0009061 SGD_REF:S000057499|PMID:7814361 TAS P cytochrome c oxidase subunit Vb YIL111W gene taxon:4932 20020930 SGD
+SGD S000001093 COX6 GO:0005751 SGD_REF:S000056478|PMID:1331058 IPI C cytochrome c oxidase subunit YHR051W gene taxon:4932 20020603 SGD
+SGD S000001093 COX6 GO:0004129 SGD_REF:S000056478|PMID:1331058 IDA F cytochrome c oxidase subunit YHR051W gene taxon:4932 20020603 SGD
+SGD S000001093 COX6 GO:0006123 SGD_REF:S000056478|PMID:1331058 IDA P cytochrome c oxidase subunit YHR051W gene taxon:4932 20050207 SGD
+SGD S000001093 COX6 GO:0009060 SGD_REF:S000061156|PMID:10385027 TAS P cytochrome c oxidase subunit YHR051W gene taxon:4932 20020930 SGD
+SGD S000004869 COX7 GO:0005751 SGD_REF:S000056478|PMID:1331058 IPI C cytochrome c oxidase subunit VII YMR256C gene taxon:4932 20020603 SGD
+SGD S000004869 COX7 GO:0004129 SGD_REF:S000056478|PMID:1331058 IDA F cytochrome c oxidase subunit VII YMR256C gene taxon:4932 20020603 SGD
+SGD S000004869 COX7 GO:0006123 SGD_REF:S000056478|PMID:1331058 IDA P cytochrome c oxidase subunit VII YMR256C gene taxon:4932 20050207 SGD
+SGD S000004869 COX7 GO:0009060 SGD_REF:S000061156|PMID:10385027 TAS P cytochrome c oxidase subunit VII YMR256C gene taxon:4932 20020930 SGD
+SGD S000004387 COX8 GO:0005751 SGD_REF:S000056478|PMID:1331058 IPI C cytochrome c oxidase subunit VIII YLR395C gene taxon:4932 20020603 SGD
+SGD S000004387 COX8 GO:0004129 SGD_REF:S000056478|PMID:1331058 IDA F cytochrome c oxidase subunit VIII YLR395C gene taxon:4932 20020603 SGD
+SGD S000004387 COX8 GO:0006123 SGD_REF:S000056478|PMID:1331058 IDA P cytochrome c oxidase subunit VIII YLR395C gene taxon:4932 20050207 SGD
+SGD S000004387 COX8 GO:0009060 SGD_REF:S000061156|PMID:10385027 TAS P cytochrome c oxidase subunit VIII YLR395C gene taxon:4932 20020930 SGD
+SGD S000002225 COX9 GO:0005751 SGD_REF:S000056478|PMID:1331058 IPI C cytochrome c oxidase subunit VIIa YDL067C gene taxon:4932 20020603 SGD
+SGD S000002225 COX9 GO:0004129 SGD_REF:S000056478|PMID:1331058 IDA F cytochrome c oxidase subunit VIIa YDL067C gene taxon:4932 20020603 SGD
+SGD S000002225 COX9 GO:0006123 SGD_REF:S000056478|PMID:1331058 IDA P cytochrome c oxidase subunit VIIa YDL067C gene taxon:4932 20050207 SGD
+SGD S000002225 COX9 GO:0009060 SGD_REF:S000061156|PMID:10385027 TAS P cytochrome c oxidase subunit VIIa YDL067C gene taxon:4932 20020930 SGD
+SGD S000001662 COY1 GO:0000139 SGD_REF:S000071755|PMID:12429822 IGI C YKL179C gene taxon:4932 20021209 SGD
+SGD S000001662 COY1 GO:0005554 SGD_REF:S000069584 ND F YKL179C gene taxon:4932 20021121 SGD
+SGD S000001662 COY1 GO:0048193 SGD_REF:S000071755|PMID:12429822 IGI P YKL179C gene taxon:4932 20030919 SGD
+SGD S000005829 CPA1 GO:0005951 SGD_REF:S000050480|PMID:6086650 ISS C arginine specific, carbamoyl phosphate synthetase YOR303W gene taxon:4932 20050126 SGD
+SGD S000005829 CPA1 GO:0004088 SGD_REF:S000050480|PMID:6086650 ISS F arginine specific, carbamoyl phosphate synthetase YOR303W gene taxon:4932 20010118 SGD
+SGD S000005829 CPA1 GO:0004088 SGD_REF:S000050480|PMID:6086650 IMP F arginine specific, carbamoyl phosphate synthetase YOR303W gene taxon:4932 20010118 SGD
+SGD S000005829 CPA1 GO:0006526 SGD_REF:S000056736|PMID:205532 TAS P arginine specific, carbamoyl phosphate synthetase YOR303W gene taxon:4932 20010118 SGD
+SGD S000003870 CPA2 GO:0005951 SGD_REF:S000057270|PMID:6358221 ISS C carbamyl phosphate synthetase YJR109C gene taxon:4932 20050126 SGD
+SGD S000003870 CPA2 GO:0004088 SGD_REF:S000057270|PMID:6358221 ISS F carbamyl phosphate synthetase YJR109C gene taxon:4932 20010118 SGD
+SGD S000003870 CPA2 GO:0004088 SGD_REF:S000057270|PMID:6358221 IMP F carbamyl phosphate synthetase YJR109C gene taxon:4932 20010118 SGD
+SGD S000003870 CPA2 GO:0006526 SGD_REF:S000056736|PMID:205532 TAS P carbamyl phosphate synthetase YJR109C gene taxon:4932 20010118 SGD
+SGD S000003479 CPD1 colocalizes_with GO:0030136 SGD_REF:S000074185|PMID:14562095 IDA C 2',3'-cyclic nucleotide 3'-phosphodiesterase YGR247W gene taxon:4932 20031028 SGD
+SGD S000003479 CPD1 GO:0004113 SGD_REF:S000056346|PMID:10734185 IDA F 2',3'-cyclic nucleotide 3'-phosphodiesterase YGR247W gene taxon:4932 20011227 SGD
+SGD S000003479 CPD1 GO:0004113 SGD_REF:S000056346|PMID:10734185 IMP F 2',3'-cyclic nucleotide 3'-phosphodiesterase YGR247W gene taxon:4932 20011227 SGD
+SGD S000003479 CPD1 GO:0006259 SGD_REF:S000043176|PMID:10051619 IGI P 2',3'-cyclic nucleotide 3'-phosphodiesterase YGR247W gene taxon:4932 20021004 SGD
+SGD S000003479 CPD1 GO:0007126 SGD_REF:S000043176|PMID:10051619 IEP P 2',3'-cyclic nucleotide 3'-phosphodiesterase YGR247W gene taxon:4932 20021004 SGD
+SGD S000002562 CPR1 GO:0000118 SGD_REF:S000066205|PMID:11711434 IPI C cyclophilin, peptidyl-prolyl cis-trans isomerase (PPIase) YDR155C|CPH1|CYP1 gene taxon:4932 20021010 SGD
+SGD S000002562 CPR1 GO:0000118 SGD_REF:S000080443|PMID:15643056 IPI C cyclophilin, peptidyl-prolyl cis-trans isomerase (PPIase) YDR155C|CPH1|CYP1 gene taxon:4932 20050415 SGD
+SGD S000002562 CPR1 GO:0005634 SGD_REF:S000080443|PMID:15643056 IDA C cyclophilin, peptidyl-prolyl cis-trans isomerase (PPIase) YDR155C|CPH1|CYP1 gene taxon:4932 20050415 SGD
+SGD S000002562 CPR1 GO:0003755 SGD_REF:S000056928|PMID:2687115 IDA F cyclophilin, peptidyl-prolyl cis-trans isomerase (PPIase) YDR155C|CPH1|CYP1 gene taxon:4932 20021010 SGD
+SGD S000002562 CPR1 GO:0019538 SGD_REF:S000069107|PMID:11641409 IMP P cyclophilin, peptidyl-prolyl cis-trans isomerase (PPIase) YDR155C|CPH1|CYP1 gene taxon:4932 20021212 SGD
+SGD S000002562 CPR1 GO:0019538 SGD_REF:S000071560|PMID:12242280 IMP P cyclophilin, peptidyl-prolyl cis-trans isomerase (PPIase) YDR155C|CPH1|CYP1 gene taxon:4932 20021212 SGD
+SGD S000002562 CPR1 GO:0030437 SGD_REF:S000080443|PMID:15643056 IMP P cyclophilin, peptidyl-prolyl cis-trans isomerase (PPIase) YDR155C|CPH1|CYP1 gene taxon:4932 20050415 SGD
+SGD S000001099 CPR2 GO:0008372 SGD_REF:S000069584 ND C cyclophilin, peptidyl-prolyl cis-trans isomerase (PPIase) YHR057C|CYP2 gene taxon:4932 20021201 SGD
+SGD S000001099 CPR2 GO:0003755 SGD_REF:S000047852|PMID:1761234 IDA F cyclophilin, peptidyl-prolyl cis-trans isomerase (PPIase) YHR057C|CYP2 gene taxon:4932 20021201 SGD
+SGD S000001099 CPR2 GO:0000004 SGD_REF:S000069584 ND P cyclophilin, peptidyl-prolyl cis-trans isomerase (PPIase) YHR057C|CYP2 gene taxon:4932 20021201 SGD
+SGD S000004543 CPR3 GO:0005739 SGD_REF:S000044539|PMID:7603990 IDA C cyclophilin, peptidyl-prolyl cis-trans isomerase (PPIase) YML078W|CYP3 gene taxon:4932 20021202 SGD
+SGD S000004543 CPR3 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C cyclophilin, peptidyl-prolyl cis-trans isomerase (PPIase) YML078W|CYP3 gene taxon:4932 20040924 SGD
+SGD S000004543 CPR3 GO:0003755 SGD_REF:S000044539|PMID:7603990 IDA F cyclophilin, peptidyl-prolyl cis-trans isomerase (PPIase) YML078W|CYP3 gene taxon:4932 20021202 SGD
+SGD S000004543 CPR3 GO:0006457 SGD_REF:S000044539|PMID:7603990 IDA P cyclophilin, peptidyl-prolyl cis-trans isomerase (PPIase) YML078W|CYP3 gene taxon:4932 20021202 SGD
+SGD S000000665 CPR4 GO:0016020 SGD_REF:S000040196|PMID:1803821 ISS C cyclophilin, peptidyl-prolyl cis-trans isomerase (PPIase) YCR069W|CYP4|SCC3|YCR070W gene taxon:4932 20021209 SGD
+SGD S000000665 CPR4 GO:0003755 SGD_REF:S000040196|PMID:1803821 ISS F cyclophilin, peptidyl-prolyl cis-trans isomerase (PPIase) YCR069W|CYP4|SCC3|YCR070W gene taxon:4932 20021202 SGD
+SGD S000000665 CPR4 GO:0000004 SGD_REF:S000069584 ND P cyclophilin, peptidyl-prolyl cis-trans isomerase (PPIase) YCR069W|CYP4|SCC3|YCR070W gene taxon:4932 20021202 SGD
+SGD S000002712 CPR5 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C cyclophilin D, peptidyl-prolyl cis-trans isomerase (PPIase) YDR304C|CYP5 gene taxon:4932 20020507 SGD
+SGD S000002712 CPR5 GO:0005783 SGD_REF:S000069459|PMID:11914276 IDA C cyclophilin D, peptidyl-prolyl cis-trans isomerase (PPIase) YDR304C|CYP5 gene taxon:4932 20020507 SGD
+SGD S000002712 CPR5 GO:0005783 SGD_REF:S000057713|PMID:8377189 IDA C cyclophilin D, peptidyl-prolyl cis-trans isomerase (PPIase) YDR304C|CYP5 gene taxon:4932 20021202 SGD
+SGD S000002712 CPR5 GO:0003755 SGD_REF:S000057713|PMID:8377189 ISS F cyclophilin D, peptidyl-prolyl cis-trans isomerase (PPIase) YDR304C|CYP5 gene taxon:4932 20021202 SGD
+SGD S000002712 CPR5 GO:0000004 SGD_REF:S000069584 ND P cyclophilin D, peptidyl-prolyl cis-trans isomerase (PPIase) YDR304C|CYP5 gene taxon:4932 20021202 SGD
+SGD S000004206 CPR6 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C cyclophilin 40, peptidyl-prolyl cis-trans isomerase (PPIase) YLR216C gene taxon:4932 20020507 SGD
+SGD S000004206 CPR6 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C cyclophilin 40, peptidyl-prolyl cis-trans isomerase (PPIase) YLR216C gene taxon:4932 20031028 SGD
+SGD S000004206 CPR6 GO:0003755 SGD_REF:S000059358|PMID:10942767 IDA F cyclophilin 40, peptidyl-prolyl cis-trans isomerase (PPIase) YLR216C gene taxon:4932 20021126 SGD
+SGD S000004206 CPR6 GO:0051082 SGD_REF:S000059358|PMID:10942767 IDA F cyclophilin 40, peptidyl-prolyl cis-trans isomerase (PPIase) YLR216C gene taxon:4932 20021126 SGD
+SGD S000004206 CPR6 GO:0006457 SGD_REF:S000053355|PMID:9927435 IPI P cyclophilin 40, peptidyl-prolyl cis-trans isomerase (PPIase) YLR216C gene taxon:4932 20010118 SGD
+SGD S000004206 CPR6 GO:0006457 SGD_REF:S000053355|PMID:9927435 IDA P cyclophilin 40, peptidyl-prolyl cis-trans isomerase (PPIase) YLR216C gene taxon:4932 20010118 SGD
+SGD S000003793 CPR7 GO:0005829 SGD_REF:S000059358|PMID:10942767 IPI C cyclophilin 40, peptidyl-prolyl cis-trans isomerase (PPIase) YJR032W gene taxon:4932 20021126 SGD
+SGD S000003793 CPR7 GO:0003755 SGD_REF:S000059358|PMID:10942767 IDA F cyclophilin 40, peptidyl-prolyl cis-trans isomerase (PPIase) YJR032W gene taxon:4932 20021126 SGD
+SGD S000003793 CPR7 GO:0051082 SGD_REF:S000059358|PMID:10942767 IDA F cyclophilin 40, peptidyl-prolyl cis-trans isomerase (PPIase) YJR032W gene taxon:4932 20021126 SGD
+SGD S000003793 CPR7 GO:0006950 SGD_REF:S000049475|PMID:9668076 IGI P cyclophilin 40, peptidyl-prolyl cis-trans isomerase (PPIase) YJR032W gene taxon:4932 20030122 SGD
+SGD S000003793 CPR7 GO:0006950 SGD_REF:S000049475|PMID:9668076 IMP P cyclophilin 40, peptidyl-prolyl cis-trans isomerase (PPIase) YJR032W gene taxon:4932 20030122 SGD
+SGD S000005311 CPR8 GO:0000324 SGD_REF:S000074185|PMID:14562095 IDA C cyclophilin, peptidyl-prolyl cis-trans isomerase (PPIase) YNR028W gene taxon:4932 20031028 SGD
+SGD S000005311 CPR8 GO:0003755 SGD_REF:S000046250|PMID:9371805 ISS F cyclophilin, peptidyl-prolyl cis-trans isomerase (PPIase) YNR028W gene taxon:4932 20021202 SGD
+SGD S000005311 CPR8 GO:0000004 SGD_REF:S000069584 ND P cyclophilin, peptidyl-prolyl cis-trans isomerase (PPIase) YNR028W gene taxon:4932 20021202 SGD
+SGD S000003708 CPS1 GO:0000324 SGD_REF:S000046737|PMID:2026161 TAS C carboxypeptidase yscS YJL172W gene taxon:4932 20011213 SGD
+SGD S000003708 CPS1 GO:0004226 SGD_REF:S000046737|PMID:2026161 IMP F carboxypeptidase yscS YJL172W gene taxon:4932 20011213 SGD
+SGD S000003708 CPS1 GO:0004226 SGD_REF:S000046737|PMID:2026161 TAS F carboxypeptidase yscS YJL172W gene taxon:4932 20011213 SGD
+SGD S000003708 CPS1 GO:0006508 SGD_REF:S000046737|PMID:2026161 IMP P carboxypeptidase yscS YJL172W gene taxon:4932 20011213 SGD
+SGD S000003708 CPS1 GO:0006508 SGD_REF:S000046737|PMID:2026161 TAS P carboxypeptidase yscS YJL172W gene taxon:4932 20011213 SGD
+SGD S000003708 CPS1 GO:0006807 SGD_REF:S000046737|PMID:2026161 IMP P carboxypeptidase yscS YJL172W gene taxon:4932 20011213 SGD
+SGD S000005074 CPT1 GO:0005783 SGD_REF:S000058496 TAS C sn-1,2-diacylglycerol cholinephosphotransferase YNL130C gene taxon:4932 20010119 SGD
+SGD S000005074 CPT1 GO:0004142 SGD_REF:S000058496 TAS F sn-1,2-diacylglycerol cholinephosphotransferase YNL130C gene taxon:4932 20010119 SGD
+SGD S000005074 CPT1 GO:0006656 SGD_REF:S000058496 TAS P sn-1,2-diacylglycerol cholinephosphotransferase YNL130C gene taxon:4932 20010119 SGD
+SGD S000005626 CRC1 GO:0005739 SGD_REF:S000069459|PMID:11914276 IDA C carnitine transporter YOR100C gene taxon:4932 20020507 SGD
+SGD S000005626 CRC1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C carnitine transporter YOR100C gene taxon:4932 20040924 SGD
+SGD S000005626 CRC1 GO:0005743 SGD_REF:S000053576|PMID:10545096 IDA C carnitine transporter YOR100C gene taxon:4932 20010118 SGD
+SGD S000005626 CRC1 GO:0005476 SGD_REF:S000053576|PMID:10545096 IDA F carnitine transporter YOR100C gene taxon:4932 20010118 SGD
+SGD S000005626 CRC1 GO:0006631 SGD_REF:S000053576|PMID:10545096 IDA P carnitine transporter YOR100C gene taxon:4932 20010118 SGD
+SGD S000002301 CRD1 GO:0005740 SGD_REF:S000043519|PMID:9614098 IDA C cardiolipin synthase YDL142C|CLS1 gene taxon:4932 20010703 SGD
+SGD S000002301 CRD1 GO:0008808 SGD_REF:S000043519|PMID:9614098 IMP F cardiolipin synthase YDL142C|CLS1 gene taxon:4932 20010703 SGD
+SGD S000002301 CRD1 GO:0008808 SGD_REF:S000060761|PMID:7564918 IDA F cardiolipin synthase YDL142C|CLS1 gene taxon:4932 20010703 SGD
+SGD S000002301 CRD1 GO:0007006 SGD_REF:S000045719|PMID:10777514 IMP P cardiolipin synthase YDL142C|CLS1 gene taxon:4932 20010703 SGD
+SGD S000002301 CRD1 GO:0008610 SGD_REF:S000043519|PMID:9614098 IMP P cardiolipin synthase YDL142C|CLS1 gene taxon:4932 20010703 SGD
+SGD S000002301 CRD1 GO:0008610 SGD_REF:S000060761|PMID:7564918 IDA P cardiolipin synthase YDL142C|CLS1 gene taxon:4932 20010703 SGD
+SGD S000002631 CRF1 GO:0005634 SGD_REF:S000080060|PMID:15620355 IDA C YDR223W gene taxon:4932 20050105 SGD
+SGD S000002631 CRF1 GO:0005737 SGD_REF:S000080060|PMID:15620355 IDA C YDR223W gene taxon:4932 20050105 SGD
+SGD S000002631 CRF1 GO:0016564 SGD_REF:S000080060|PMID:15620355 IDA F YDR223W gene taxon:4932 20050105 SGD
+SGD S000002631 CRF1 GO:0016481 SGD_REF:S000080060|PMID:15620355 IDA P YDR223W gene taxon:4932 20050105 SGD
+SGD S000003421 CRH1 GO:0000131 SGD_REF:S000040902|PMID:10757808 IDA C cell wall protein YGR189C gene taxon:4932 20021201 SGD
+SGD S000003421 CRH1 GO:0009277 SGD_REF:S000040902|PMID:10757808 IDA C cell wall protein YGR189C gene taxon:4932 20021201 SGD
+SGD S000003421 CRH1 GO:0009277 SGD_REF:S000081097|PMID:15781460 IDA C cell wall protein YGR189C gene taxon:4932 20050601 SGD
+SGD S000003421 CRH1 GO:0005554 SGD_REF:S000069584 ND F cell wall protein YGR189C gene taxon:4932 20010119 SGD
+SGD S000003421 CRH1 GO:0000004 SGD_REF:S000069584 ND P cell wall protein YGR189C gene taxon:4932 20010119 SGD
+SGD S000003450 CRM1 GO:0005634 SGD_REF:S000041387|PMID:9891088 IDA C chromosome region maintenance protein YGR218W|KAP124|XPO1 gene taxon:4932 20020807 SGD
+SGD S000003450 CRM1 GO:0008320 SGD_REF:S000046404|PMID:9323132 IDA F chromosome region maintenance protein YGR218W|KAP124|XPO1 gene taxon:4932 20020816 SGD
+SGD S000003450 CRM1 GO:0000055 SGD_REF:S000060446|PMID:11313466 IMP P chromosome region maintenance protein YGR218W|KAP124|XPO1 gene taxon:4932 20020807 SGD
+SGD S000003450 CRM1 GO:0006406 SGD_REF:S000046404|PMID:9323132 IMP P chromosome region maintenance protein YGR218W|KAP124|XPO1 gene taxon:4932 20020807 SGD
+SGD S000003450 CRM1 GO:0006611 SGD_REF:S000046404|PMID:9323132 IMP P chromosome region maintenance protein YGR218W|KAP124|XPO1 gene taxon:4932 20020807 SGD
+SGD S000004421 CRN1 GO:0030479 SGD_REF:S000041005|PMID:10652251 IDA C Dictyostelium and human actin-binding protein coronin homolog YLR429W gene taxon:4932 20010118 SGD
+SGD S000004421 CRN1 GO:0008017 SGD_REF:S000045693|PMID:9885246 IDA F Dictyostelium and human actin-binding protein coronin homolog YLR429W gene taxon:4932 20010118 SGD
+SGD S000004421 CRN1 GO:0030674 SGD_REF:S000045693|PMID:9885246 IDA F Dictyostelium and human actin-binding protein coronin homolog YLR429W gene taxon:4932 20040409 SGD
+SGD S000004421 CRN1 GO:0051015 SGD_REF:S000045693|PMID:9885246 IDA F Dictyostelium and human actin-binding protein coronin homolog YLR429W gene taxon:4932 20040409 SGD
+SGD S000004421 CRN1 GO:0007015 SGD_REF:S000045693|PMID:9885246 IMP P Dictyostelium and human actin-binding protein coronin homolog YLR429W gene taxon:4932 20010118 SGD
+SGD S000004421 CRN1 GO:0007015 SGD_REF:S000045693|PMID:9885246 IPI P Dictyostelium and human actin-binding protein coronin homolog YLR429W gene taxon:4932 20010118 SGD
+SGD S000004421 CRN1 GO:0007017 SGD_REF:S000045693|PMID:9885246 IPI P Dictyostelium and human actin-binding protein coronin homolog YLR429W gene taxon:4932 20010118 SGD
+SGD S000001189 CRP1 GO:0005634 SGD_REF:S000071592|PMID:12419258 IC GO:0003677 C Cruciform DNA binding protein YHR146W gene taxon:4932 20030113 SGD
+SGD S000001189 CRP1 GO:0003677 SGD_REF:S000071592|PMID:12419258 IDA F Cruciform DNA binding protein YHR146W gene taxon:4932 20021112 SGD
+SGD S000001189 CRP1 GO:0000004 SGD_REF:S000069584 ND P Cruciform DNA binding protein YHR146W gene taxon:4932 20030113 SGD
+SGD S000004203 CRR1 GO:0005619 SGD_REF:S000077523|PMID:15470107 IDA C YLR213C gene taxon:4932 20050914 SGD
+SGD S000004203 CRR1 GO:0016810 SGD_REF:S000077523|PMID:15470107 ISS F YLR213C gene taxon:4932 20050914 SGD
+SGD S000004203 CRR1 GO:0030476 SGD_REF:S000077523|PMID:15470107 IMP P YLR213C gene taxon:4932 20050914 SGD
+SGD S000005557 CRS5 GO:0005737 SGD_REF:S000056259|PMID:7929222 ISS C metallothionein-like protein YOR031W gene taxon:4932 20020712 SGD
+SGD S000005557 CRS5 GO:0005507 SGD_REF:S000056259|PMID:7929222 ISS F metallothionein-like protein YOR031W gene taxon:4932 20020712 SGD
+SGD S000005557 CRS5 GO:0005507 SGD_REF:S000056259|PMID:7929222 IMP F metallothionein-like protein YOR031W gene taxon:4932 20020712 SGD
+SGD S000005557 CRS5 GO:0010038 SGD_REF:S000056259|PMID:7929222 IMP P metallothionein-like protein YOR031W gene taxon:4932 20030416 SGD
+SGD S000005424 CRT10 GO:0008372 SGD_REF:S000069584 ND C YOL063C|HUS1 gene taxon:4932 20021125 SGD
+SGD S000005424 CRT10 GO:0005554 SGD_REF:S000069584 ND F YOL063C|HUS1 gene taxon:4932 20021125 SGD
+SGD S000005424 CRT10 GO:0006358 SGD_REF:S000114801|PMID:16600900 IMP P YOL063C|HUS1 gene taxon:4932 20060613 SGD
+SGD S000005424 CRT10 GO:0006974 SGD_REF:S000114801|PMID:16600900 IEA P YOL063C|HUS1 gene taxon:4932 20060613 SGD
+SGD S000004972 CRZ1 GO:0005634 SGD_REF:S000039735|PMID:10197980 IDA C transcription factor YNL027W|HAL8|TCN1 gene taxon:4932 20020715 SGD
+SGD S000004972 CRZ1 GO:0005737 SGD_REF:S000039735|PMID:10197980 IDA C transcription factor YNL027W|HAL8|TCN1 gene taxon:4932 20020715 SGD
+SGD S000004972 CRZ1 GO:0003700 SGD_REF:S000051482|PMID:9407035 IDA F transcription factor YNL027W|HAL8|TCN1 gene taxon:4932 20020715 SGD
+SGD S000004972 CRZ1 GO:0003700 SGD_REF:S000051482|PMID:9407035 ISS F transcription factor YNL027W|HAL8|TCN1 gene taxon:4932 20020715 SGD
+SGD S000004972 CRZ1 GO:0003700 SGD_REF:S000051482|PMID:9407035 IPI F transcription factor YNL027W|HAL8|TCN1 gene taxon:4932 20020715 SGD
+SGD S000004972 CRZ1 GO:0006355 SGD_REF:S000051482|PMID:9407035 IMP P transcription factor YNL027W|HAL8|TCN1 gene taxon:4932 20020715 SGD
+SGD S000004972 CRZ1 GO:0019722 SGD_REF:S000051482|PMID:9407035 IGI P transcription factor YNL027W|HAL8|TCN1 gene taxon:4932 20020715 SGD
+SGD S000004972 CRZ1 GO:0019722 SGD_REF:S000051482|PMID:9407035 IPI P transcription factor YNL027W|HAL8|TCN1 gene taxon:4932 20020715 SGD
+SGD S000004972 CRZ1 GO:0019722 SGD_REF:S000051482|PMID:9407035 IMP P transcription factor YNL027W|HAL8|TCN1 gene taxon:4932 20020715 SGD
+SGD S000003207 CSE1 GO:0005635 SGD_REF:S000055400|PMID:9857050 IDA C YGL238W|KAP109 gene taxon:4932 20020807 SGD
+SGD S000003207 CSE1 GO:0008262 SGD_REF:S000055400|PMID:9857050 IGI F YGL238W|KAP109 gene taxon:4932 20020807 SGD
+SGD S000003207 CSE1 GO:0008262 SGD_REF:S000055400|PMID:9857050 ISS F YGL238W|KAP109 gene taxon:4932 20020807 SGD
+SGD S000003207 CSE1 GO:0008262 SGD_REF:S000055400|PMID:9857050 IPI F YGL238W|KAP109 gene taxon:4932 20020807 SGD
+SGD S000003207 CSE1 GO:0006611 SGD_REF:S000055400|PMID:9857050 IGI P YGL238W|KAP109 gene taxon:4932 20020807 SGD
+SGD S000003207 CSE1 GO:0006611 SGD_REF:S000055400|PMID:9857050 IPI P YGL238W|KAP109 gene taxon:4932 20020807 SGD
+SGD S000005293 CSE2 GO:0000119 SGD_REF:S000056289|PMID:9812975 IDA C RNA polymerase II mediator subcomplex component YNR010W|MED9 gene taxon:4932 20010118 SGD
+SGD S000005293 CSE2 GO:0016455 SGD_REF:S000056289|PMID:9812975 IPI F RNA polymerase II mediator subcomplex component YNR010W|MED9 gene taxon:4932 20010302 SGD
+SGD S000005293 CSE2 GO:0000070 SGD_REF:S000049997|PMID:8336709 IMP P RNA polymerase II mediator subcomplex component YNR010W|MED9 gene taxon:4932 20010118 SGD
+SGD S000005293 CSE2 GO:0006366 SGD_REF:S000056289|PMID:9812975 IPI P RNA polymerase II mediator subcomplex component YNR010W|MED9 gene taxon:4932 20010118 SGD
+SGD S000001532 CSE4 GO:0000776 SGD_REF:S000052739|PMID:10958698 IGI C similar to histone H3 and to human centromere protein CENP-A YKL049C|CSL2 gene taxon:4932 20040924 SGD
+SGD S000001532 CSE4 GO:0000780 SGD_REF:S000059419|PMID:11063678 IGI C similar to histone H3 and to human centromere protein CENP-A YKL049C|CSL2 gene taxon:4932 20030403 SGD
+SGD S000001532 CSE4 GO:0000788 SGD_REF:S000059419|PMID:11063678 IDA C similar to histone H3 and to human centromere protein CENP-A YKL049C|CSL2 gene taxon:4932 20020604 SGD
+SGD S000001532 CSE4 GO:0019237 SGD_REF:S000059419|PMID:11063678 IDA F similar to histone H3 and to human centromere protein CENP-A YKL049C|CSL2 gene taxon:4932 20020604 SGD
+SGD S000001532 CSE4 GO:0000070 SGD_REF:S000046262|PMID:7698647 IMP P similar to histone H3 and to human centromere protein CENP-A YKL049C|CSL2 gene taxon:4932 20020926 SGD
+SGD S000004077 CSF1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YLR087C gene taxon:4932 20040813 SGD
+SGD S000004077 CSF1 GO:0005554 SGD_REF:S000069584 ND F YLR087C gene taxon:4932 20021002 SGD
+SGD S000004077 CSF1 GO:0006113 SGD_REF:S000056347|PMID:10781556 IMP P YLR087C gene taxon:4932 20021002 SGD
+SGD S000000240 CSG2 GO:0030176 SGD_REF:S000053042|PMID:7854312 IDA C YBR036C|CLS2 gene taxon:4932 20020906 SGD
+SGD S000000240 CSG2 GO:0030234 SGD_REF:S000075191|PMID:12954640 IPI F YBR036C|CLS2 gene taxon:4932 20040102 SGD
+SGD S000000240 CSG2 GO:0030234 SGD_REF:S000075191|PMID:12954640 IMP F YBR036C|CLS2 gene taxon:4932 20040102 SGD
+SGD S000000240 CSG2 GO:0006688 SGD_REF:S000055817|PMID:8063782 ISS P YBR036C|CLS2 gene taxon:4932 20050301 SGD
+SGD S000000240 CSG2 GO:0006874 SGD_REF:S000053042|PMID:7854312 IMP P YBR036C|CLS2 gene taxon:4932 20020906 SGD
+SGD S000000365 CSH1 GO:0000324 SGD_REF:S000074185|PMID:14562095 IDA C YBR161W gene taxon:4932 20031028 SGD
+SGD S000000365 CSH1 GO:0000030 SGD_REF:S000075191|PMID:12954640 IGI F YBR161W gene taxon:4932 20040102 SGD
+SGD S000000365 CSH1 GO:0000030 SGD_REF:S000075191|PMID:12954640 IMP F YBR161W gene taxon:4932 20040102 SGD
+SGD S000000365 CSH1 GO:0016757 SGD_REF:S000055539|PMID:9653120 ISS F YBR161W gene taxon:4932 20021204 SGD
+SGD S000000365 CSH1 GO:0006688 SGD_REF:S000075191|PMID:12954640 IMP P YBR161W gene taxon:4932 20050301 SGD
+SGD S000000365 CSH1 GO:0006688 SGD_REF:S000075191|PMID:12954640 ISS P YBR161W gene taxon:4932 20050301 SGD
+SGD S000000365 CSH1 GO:0030148 SGD_REF:S000075191|PMID:12954640 IMP P YBR161W gene taxon:4932 20040102 SGD
+SGD S000004627 CSI1 GO:0008180 SGD_REF:S000071602|PMID:12186635 TAS C Interactor with COP9 signalosome (CSN) complex YMR025W gene taxon:4932 20021115 SGD
+SGD S000004627 CSI1 GO:0008180 SGD_REF:S000071980|PMID:12446563 IDA C Interactor with COP9 signalosome (CSN) complex YMR025W gene taxon:4932 20030325 SGD
+SGD S000004627 CSI1 GO:0005554 SGD_REF:S000069584 ND F Interactor with COP9 signalosome (CSN) complex YMR025W gene taxon:4932 20030325 SGD
+SGD S000004627 CSI1 GO:0000338 SGD_REF:S000071980|PMID:12446563 IMP P Interactor with COP9 signalosome (CSN) complex YMR025W gene taxon:4932 20030325 SGD
+SGD S000004627 CSI1 GO:0000338 SGD_REF:S000071602|PMID:12186635 IMP P Interactor with COP9 signalosome (CSN) complex YMR025W gene taxon:4932 20021115 SGD
+SGD S000004627 CSI1 GO:0000754 SGD_REF:S000071980|PMID:12446563 IMP P Interactor with COP9 signalosome (CSN) complex YMR025W gene taxon:4932 20030325 SGD
+SGD S000005176 CSL4 GO:0000176 SGD_REF:S000041327|PMID:10465791 IDA C YNL232W|SKI4 gene taxon:4932 20010118 SGD
+SGD S000005176 CSL4 GO:0000177 SGD_REF:S000041327|PMID:10465791 IDA C YNL232W|SKI4 gene taxon:4932 20010118 SGD
+SGD S000005176 CSL4 GO:0000175 SGD_REF:S000058443|PMID:10690410 TAS F YNL232W|SKI4 gene taxon:4932 20010118 SGD
+SGD S000005176 CSL4 GO:0006365 SGD_REF:S000058443|PMID:10690410 TAS P YNL232W|SKI4 gene taxon:4932 20010118 SGD
+SGD S000005176 CSL4 GO:0006402 SGD_REF:S000041327|PMID:10465791 IPI P YNL232W|SKI4 gene taxon:4932 20010118 SGD
+SGD S000005176 CSL4 GO:0043330 SGD_REF:S000044399|PMID:363683 IMP P YNL232W|SKI4 gene taxon:4932 20050505 SGD
+SGD S000000682 CSM1 GO:0000778 SGD_REF:S000073065|PMID:12689592 IDA C YCR086W gene taxon:4932 20050310 SGD
+SGD S000000682 CSM1 GO:0005635 SGD_REF:S000061434|PMID:11489916 IDA C YCR086W gene taxon:4932 20030512 SGD
+SGD S000000682 CSM1 GO:0005730 SGD_REF:S000073065|PMID:12689592 IDA C YCR086W gene taxon:4932 20031001 SGD
+SGD S000000682 CSM1 GO:0005554 SGD_REF:S000069584 ND F YCR086W gene taxon:4932 20021002 SGD
+SGD S000000682 CSM1 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P YCR086W gene taxon:4932 20060202 SGD
+SGD S000000682 CSM1 GO:0006260 SGD_REF:S000075698|PMID:15023545 IMP P YCR086W gene taxon:4932 20040408 SGD
+SGD S000000682 CSM1 GO:0006260 SGD_REF:S000075698|PMID:15023545 IPI P YCR086W gene taxon:4932 20040408 SGD
+SGD S000000682 CSM1 GO:0045132 SGD_REF:S000060989|PMID:11470404 IMP P YCR086W gene taxon:4932 20021002 SGD
+SGD S000000682 CSM1 GO:0045143 SGD_REF:S000073065|PMID:12689592 IMP P YCR086W gene taxon:4932 20031001 SGD
+SGD S000000682 CSM1 GO:0045143 SGD_REF:S000073065|PMID:12689592 IPI P YCR086W gene taxon:4932 20031001 SGD
+SGD S000001394 CSM2 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YIL132C gene taxon:4932 20031028 SGD
+SGD S000001394 CSM2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YIL132C gene taxon:4932 20031028 SGD
+SGD S000001394 CSM2 GO:0005554 SGD_REF:S000069584 ND F YIL132C gene taxon:4932 20021002 SGD
+SGD S000001394 CSM2 GO:0045021 SGD_REF:S000080406|PMID:15654096 IMP P YIL132C gene taxon:4932 20050324 SGD
+SGD S000001394 CSM2 GO:0045132 SGD_REF:S000060989|PMID:11470404 IMP P YIL132C gene taxon:4932 20021002 SGD
+SGD S000004651 CSM3 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YMR048W gene taxon:4932 20031028 SGD
+SGD S000004651 CSM3 GO:0005554 SGD_REF:S000069584 ND F YMR048W gene taxon:4932 20021002 SGD
+SGD S000004651 CSM3 GO:0000076 SGD_REF:S000074658|PMID:14764870 IGI P YMR048W gene taxon:4932 20040210 SGD
+SGD S000004651 CSM3 GO:0007064 SGD_REF:S000076127|PMID:14742714 IGI SGD:S000001234 P YMR048W gene taxon:4932 20050513 SGD
+SGD S000004651 CSM3 GO:0007064 SGD_REF:S000076127|PMID:14742714 IMP P YMR048W gene taxon:4932 20050513 SGD
+SGD S000004651 CSM3 GO:0045132 SGD_REF:S000060989|PMID:11470404 IMP P YMR048W gene taxon:4932 20021002 SGD
+SGD S000006121 CSM4 GO:0005789 SGD_REF:S000072636|PMID:12514182 IDA C YPL200W gene taxon:4932 20031014 SGD
+SGD S000006121 CSM4 GO:0005554 SGD_REF:S000069584 ND F YPL200W gene taxon:4932 20021002 SGD
+SGD S000006121 CSM4 GO:0045132 SGD_REF:S000060989|PMID:11470404 IMP P YPL200W gene taxon:4932 20021002 SGD
+SGD S000003844 CSN12 GO:0008180 SGD_REF:S000071980|PMID:12446563 IDA C COP9 signalosome (CSN) subunit YJR084W gene taxon:4932 20030325 SGD
+SGD S000003844 CSN12 GO:0005554 SGD_REF:S000069584 ND F COP9 signalosome (CSN) subunit YJR084W gene taxon:4932 20030325 SGD
+SGD S000003844 CSN12 GO:0000754 SGD_REF:S000071980|PMID:12446563 IMP P COP9 signalosome (CSN) subunit YJR084W gene taxon:4932 20030325 SGD
+SGD S000002586 CSN9 GO:0008180 SGD_REF:S000071602|PMID:12186635 TAS C COP9 signalosome (CSN) subunit YDR179C gene taxon:4932 20021115 SGD
+SGD S000002586 CSN9 GO:0008180 SGD_REF:S000071980|PMID:12446563 IDA C COP9 signalosome (CSN) subunit YDR179C gene taxon:4932 20030325 SGD
+SGD S000002586 CSN9 GO:0005554 SGD_REF:S000069584 ND F COP9 signalosome (CSN) subunit YDR179C gene taxon:4932 20030325 SGD
+SGD S000002586 CSN9 GO:0000338 SGD_REF:S000071980|PMID:12446563 IMP P COP9 signalosome (CSN) subunit YDR179C gene taxon:4932 20030325 SGD
+SGD S000002586 CSN9 GO:0000338 SGD_REF:S000071602|PMID:12186635 IMP P COP9 signalosome (CSN) subunit YDR179C gene taxon:4932 20021115 SGD
+SGD S000002586 CSN9 GO:0000754 SGD_REF:S000071980|PMID:12446563 IMP P COP9 signalosome (CSN) subunit YDR179C gene taxon:4932 20030325 SGD
+SGD S000002586 CSN9 GO:0000754 SGD_REF:S000071980|PMID:12446563 IGI P COP9 signalosome (CSN) subunit YDR179C gene taxon:4932 20030325 SGD
+SGD S000004372 CSR1 GO:0005737 SGD_REF:S000043659|PMID:10848624 IDA C YLR380W|SFH2 gene taxon:4932 20030422 SGD
+SGD S000004372 CSR1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YLR380W|SFH2 gene taxon:4932 20040813 SGD
+SGD S000004372 CSR1 GO:0005792 SGD_REF:S000073885|PMID:12869188 IDA C YLR380W|SFH2 gene taxon:4932 20031001 SGD
+SGD S000004372 CSR1 GO:0005829 SGD_REF:S000073885|PMID:12869188 IDA C YLR380W|SFH2 gene taxon:4932 20031001 SGD
+SGD S000004372 CSR1 GO:0008526 SGD_REF:S000043659|PMID:10848624 IDA F YLR380W|SFH2 gene taxon:4932 20021029 SGD
+SGD S000004372 CSR1 GO:0007047 SGD_REF:S000040781|PMID:10679005 IGI P YLR380W|SFH2 gene taxon:4932 20010118 SGD
+SGD S000004372 CSR1 GO:0015914 SGD_REF:S000043659|PMID:10848624 IDA P YLR380W|SFH2 gene taxon:4932 20021029 SGD
+SGD S000004372 CSR1 GO:0030433 SGD_REF:S000115312|PMID:12711700 IMP P YLR380W|SFH2 gene taxon:4932 20060511 SGD
+SGD S000006234 CSR2 GO:0005634 SGD_REF:S000071990|PMID:12444972 IDA C YPR030W|MRG19 gene taxon:4932 20030107 SGD
+SGD S000006234 CSR2 GO:0005554 SGD_REF:S000069584 ND F YPR030W|MRG19 gene taxon:4932 20010119 SGD
+SGD S000006234 CSR2 GO:0006357 SGD_REF:S000071990|PMID:12444972 IGI P YPR030W|MRG19 gene taxon:4932 20030107 SGD
+SGD S000006234 CSR2 GO:0006357 SGD_REF:S000071990|PMID:12444972 IMP P YPR030W|MRG19 gene taxon:4932 20030107 SGD
+SGD S000006234 CSR2 GO:0007047 SGD_REF:S000040781|PMID:10679005 IGI P YPR030W|MRG19 gene taxon:4932 20010118 SGD
+SGD S000001298 CST6 GO:0005634 SGD_REF:S000046567|PMID:10825197 IPI C basic leucine zipper (bZIP) transcription factor YIL036W|ACA2|SHF1 gene taxon:4932 20021011 SGD
+SGD S000001298 CST6 GO:0003704 SGD_REF:S000046567|PMID:10825197 IDA F basic leucine zipper (bZIP) transcription factor YIL036W|ACA2|SHF1 gene taxon:4932 20021011 SGD
+SGD S000001298 CST6 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P basic leucine zipper (bZIP) transcription factor YIL036W|ACA2|SHF1 gene taxon:4932 20060203 SGD
+SGD S000001298 CST6 GO:0006259 SGD_REF:S000052609|PMID:10454593 IGI P basic leucine zipper (bZIP) transcription factor YIL036W|ACA2|SHF1 gene taxon:4932 20010118 SGD
+SGD S000001298 CST6 GO:0006367 SGD_REF:S000046567|PMID:10825197 IDA P basic leucine zipper (bZIP) transcription factor YIL036W|ACA2|SHF1 gene taxon:4932 20021011 SGD
+SGD S000004386 CST9 GO:0000228 SGD_REF:S000041926|PMID:10943844 IDA C YLR394W|ZIP3 gene taxon:4932 20031001 SGD
+SGD S000004386 CST9 GO:0003677 SGD_REF:S000052609|PMID:10454593 ISS F YLR394W|ZIP3 gene taxon:4932 20010118 SGD
+SGD S000004386 CST9 GO:0007129 SGD_REF:S000081371|PMID:15805472 IGI P YLR394W|ZIP3 gene taxon:4932 20050802 SGD
+SGD S000004386 CST9 GO:0007129 SGD_REF:S000081371|PMID:15805472 IMP P YLR394W|ZIP3 gene taxon:4932 20050802 SGD
+SGD S000004386 CST9 GO:0007130 SGD_REF:S000041926|PMID:10943844 IMP P YLR394W|ZIP3 gene taxon:4932 20031001 SGD
+SGD S000004386 CST9 GO:0007130 SGD_REF:S000041926|PMID:10943844 IPI P YLR394W|ZIP3 gene taxon:4932 20031001 SGD
+SGD S000002664 CTA1 GO:0005739 SGD_REF:S000077411|PMID:14998369 IDA C catalase A YDR256C gene taxon:4932 20041028 SGD
+SGD S000002664 CTA1 GO:0005782 SGD_REF:S000058494 TAS C catalase A YDR256C gene taxon:4932 20030204 SGD
+SGD S000002664 CTA1 GO:0004096 SGD_REF:S000058494 TAS F catalase A YDR256C gene taxon:4932 20010119 SGD
+SGD S000002664 CTA1 GO:0006800 SGD_REF:S000058494 TAS P catalase A YDR256C gene taxon:4932 20010119 SGD
+SGD S000004700 CTF13 GO:0000778 SGD_REF:S000059407|PMID:11070082 TAS C YMR094W|CBF3C gene taxon:4932 20021015 SGD
+SGD S000004700 CTF13 GO:0031518 SGD_REF:S000056114|PMID:8682209 TAS C YMR094W|CBF3C gene taxon:4932 20050722 SGD
+SGD S000004700 CTF13 GO:0008301 SGD_REF:S000046254|PMID:10097110 IDA F YMR094W|CBF3C gene taxon:4932 20021017 SGD
+SGD S000004700 CTF13 GO:0019237 SGD_REF:S000059407|PMID:11070082 TAS F YMR094W|CBF3C gene taxon:4932 20021015 SGD
+SGD S000004700 CTF13 GO:0051382 SGD_REF:S000070182|PMID:12084919 IDA P YMR094W|CBF3C gene taxon:4932 20050720 SGD
+SGD S000004683 CTF18 GO:0005663 SGD_REF:S000060777|PMID:11389843 IPI C YMR078C|CHL12 gene taxon:4932 20020811 SGD
+SGD S000004683 CTF18 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YMR078C|CHL12 gene taxon:4932 20040928 SGD
+SGD S000004683 CTF18 GO:0005554 SGD_REF:S000069584 ND F YMR078C|CHL12 gene taxon:4932 20020811 SGD
+SGD S000004683 CTF18 GO:0007064 SGD_REF:S000060372|PMID:11287619 IMP P YMR078C|CHL12 gene taxon:4932 20040610 SGD
+SGD S000004683 CTF18 GO:0007064 SGD_REF:S000060777|PMID:11389843 IMP P YMR078C|CHL12 gene taxon:4932 20040610 SGD
+SGD S000005939 CTF19 GO:0000778 SGD_REF:S000053236|PMID:10189365 IGI C kinetochore protein YPL018W|MCM18 gene taxon:4932 20020617 SGD
+SGD S000005939 CTF19 GO:0000778 SGD_REF:S000053236|PMID:10189365 IDA C kinetochore protein YPL018W|MCM18 gene taxon:4932 20020617 SGD
+SGD S000005939 CTF19 GO:0000817 SGD_REF:S000075142|PMID:14633972 IDA C kinetochore protein YPL018W|MCM18 gene taxon:4932 20040618 SGD
+SGD S000005939 CTF19 GO:0005634 SGD_REF:S000053236|PMID:10189365 IDA C kinetochore protein YPL018W|MCM18 gene taxon:4932 20020617 SGD
+SGD S000005939 CTF19 GO:0005515 SGD_REF:S000053236|PMID:10189365 TAS F kinetochore protein YPL018W|MCM18 gene taxon:4932 20020617 SGD
+SGD S000005939 CTF19 GO:0007059 SGD_REF:S000053236|PMID:10189365 IGI P kinetochore protein YPL018W|MCM18 gene taxon:4932 20020617 SGD
+SGD S000005939 CTF19 GO:0007059 SGD_REF:S000053236|PMID:10189365 IMP P kinetochore protein YPL018W|MCM18 gene taxon:4932 20020617 SGD
+SGD S000005939 CTF19 GO:0008608 SGD_REF:S000053236|PMID:10189365 IDA P kinetochore protein YPL018W|MCM18 gene taxon:4932 20020617 SGD
+SGD S000005939 CTF19 GO:0008608 SGD_REF:S000053236|PMID:10189365 IMP P kinetochore protein YPL018W|MCM18 gene taxon:4932 20020617 SGD
+SGD S000005939 CTF19 GO:0008608 SGD_REF:S000053236|PMID:10189365 IGI P kinetochore protein YPL018W|MCM18 gene taxon:4932 20020617 SGD
+SGD S000004373 CTF3 GO:0000778 SGD_REF:S000069067|PMID:11782448 IDA C YLR381W|CHL3 gene taxon:4932 20020905 SGD
+SGD S000004373 CTF3 GO:0005515 SGD_REF:S000069067|PMID:11782448 IDA F YLR381W|CHL3 gene taxon:4932 20020905 SGD
+SGD S000004373 CTF3 GO:0007059 SGD_REF:S000069067|PMID:11782448 IPI P YLR381W|CHL3 gene taxon:4932 20020905 SGD
+SGD S000006339 CTF4 GO:0000228 SGD_REF:S000060372|PMID:11287619 IDA C DNA polymerase alpha binding protein YPR135W|CHL15|POB1 gene taxon:4932 20031001 SGD
+SGD S000006339 CTF4 GO:0005634 SGD_REF:S000053212|PMID:1448101 IPI C DNA polymerase alpha binding protein YPR135W|CHL15|POB1 gene taxon:4932 20010118 SGD
+SGD S000006339 CTF4 GO:0003677 SGD_REF:S000053471|PMID:1341195 ISS F DNA polymerase alpha binding protein YPR135W|CHL15|POB1 gene taxon:4932 20010118 SGD
+SGD S000006339 CTF4 GO:0001302 SGD_REF:S000074686|PMID:12024027 IMP P DNA polymerase alpha binding protein YPR135W|CHL15|POB1 gene taxon:4932 20031217 SGD
+SGD S000006339 CTF4 GO:0006261 SGD_REF:S000053212|PMID:1448101 IPI P DNA polymerase alpha binding protein YPR135W|CHL15|POB1 gene taxon:4932 20010118 SGD
+SGD S000006339 CTF4 GO:0006261 SGD_REF:S000053212|PMID:1448101 IMP P DNA polymerase alpha binding protein YPR135W|CHL15|POB1 gene taxon:4932 20010118 SGD
+SGD S000006339 CTF4 GO:0006281 SGD_REF:S000053471|PMID:1341195 IMP P DNA polymerase alpha binding protein YPR135W|CHL15|POB1 gene taxon:4932 20010118 SGD
+SGD S000006339 CTF4 GO:0006281 SGD_REF:S000053471|PMID:1341195 IGI P DNA polymerase alpha binding protein YPR135W|CHL15|POB1 gene taxon:4932 20010118 SGD
+SGD S000006339 CTF4 GO:0006281 SGD_REF:S000053212|PMID:1448101 IMP P DNA polymerase alpha binding protein YPR135W|CHL15|POB1 gene taxon:4932 20010118 SGD
+SGD S000006339 CTF4 GO:0006281 SGD_REF:S000053212|PMID:1448101 IGI P DNA polymerase alpha binding protein YPR135W|CHL15|POB1 gene taxon:4932 20010118 SGD
+SGD S000006339 CTF4 GO:0007064 SGD_REF:S000060372|PMID:11287619 IMP P DNA polymerase alpha binding protein YPR135W|CHL15|POB1 gene taxon:4932 20040610 SGD
+SGD S000006339 CTF4 GO:0007064 SGD_REF:S000076127|PMID:14742714 IGI SGD:S000001234 P DNA polymerase alpha binding protein YPR135W|CHL15|POB1 gene taxon:4932 20050513 SGD
+SGD S000001234 CTF8 GO:0005663 SGD_REF:S000060777|PMID:11389843 IPI C YHR191C gene taxon:4932 20020811 SGD
+SGD S000001234 CTF8 GO:0005554 SGD_REF:S000069584 ND F YHR191C gene taxon:4932 20021003 SGD
+SGD S000001234 CTF8 GO:0006974 SGD_REF:S000076175|PMID:12482937 IMP P YHR191C gene taxon:4932 20060406 SGD
+SGD S000001234 CTF8 GO:0007064 SGD_REF:S000060777|PMID:11389843 IMP P YHR191C gene taxon:4932 20040610 SGD
+SGD S000001234 CTF8 GO:0007064 SGD_REF:S000060777|PMID:11389843 IGI SGD:S000002161|SGD:S000003610|SGD:S000001923|SGD:S000001886|SGD:S000002588 P YHR191C gene taxon:4932 20040610 SGD
+SGD S000002558 CTH1 GO:0005634 SGD_REF:S000052862|PMID:8890739 IC GO:0003700 C CCCH zinc finger protein family that has two or more repeats of a novel zinc finger motif consisting of Cys and His residues in the form Cx8Cx5Cx3H [where x is a variable amino acid (aa)] YDR151C gene taxon:4932 20031002 SGD
+SGD S000002558 CTH1 GO:0003700 SGD_REF:S000052862|PMID:8890739 ISS F CCCH zinc finger protein family that has two or more repeats of a novel zinc finger motif consisting of Cys and His residues in the form Cx8Cx5Cx3H [where x is a variable amino acid (aa)] YDR151C gene taxon:4932 20031002 SGD
+SGD S000002558 CTH1 GO:0006350 SGD_REF:S000052862|PMID:8890739 ISS P CCCH zinc finger protein family that has two or more repeats of a novel zinc finger motif consisting of Cys and His residues in the form Cx8Cx5Cx3H [where x is a variable amino acid (aa)] YDR151C gene taxon:4932 20031002 SGD
+SGD S000002558 CTH1 GO:0006879 SGD_REF:S000080432|PMID:15652485 IGI SGD:S000004126 P CCCH zinc finger protein family that has two or more repeats of a novel zinc finger motif consisting of Cys and His residues in the form Cx8Cx5Cx3H [where x is a variable amino acid (aa)] YDR151C gene taxon:4932 20050217 SGD
+SGD S000006102 CTI6 GO:0005634 SGD_REF:S000070288|PMID:12086626 IC GO:0008134 C YPL181W|RXT1 gene taxon:4932 20031002 SGD
+SGD S000006102 CTI6 GO:0008134 SGD_REF:S000070288|PMID:12086626 IDA F YPL181W|RXT1 gene taxon:4932 20030314 SGD
+SGD S000006102 CTI6 GO:0045941 SGD_REF:S000070288|PMID:12086626 IMP P YPL181W|RXT1 gene taxon:4932 20030314 SGD
+SGD S000001622 CTK1 GO:0005634 SGD_REF:S000058079|PMID:9110987 IDA C kinase subunit of RNA polymerase II carboxy-terminal domain kinase I YKL139W gene taxon:4932 20020919 SGD
+SGD S000001622 CTK1 GO:0004672 SGD_REF:S000055627|PMID:1820212 TAS F kinase subunit of RNA polymerase II carboxy-terminal domain kinase I YKL139W gene taxon:4932 20010118 SGD
+SGD S000001622 CTK1 GO:0004693 SGD_REF:S000043725|PMID:7565723 IDA F kinase subunit of RNA polymerase II carboxy-terminal domain kinase I YKL139W gene taxon:4932 20020919 SGD
+SGD S000001622 CTK1 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P kinase subunit of RNA polymerase II carboxy-terminal domain kinase I YKL139W gene taxon:4932 20060203 SGD
+SGD S000001622 CTK1 GO:0006357 SGD_REF:S000058079|PMID:9110987 TAS P kinase subunit of RNA polymerase II carboxy-terminal domain kinase I YKL139W gene taxon:4932 20010118 SGD
+SGD S000001622 CTK1 GO:0006468 SGD_REF:S000055627|PMID:1820212 TAS P kinase subunit of RNA polymerase II carboxy-terminal domain kinase I YKL139W gene taxon:4932 20010118 SGD
+SGD S000003543 CTK2 GO:0005634 SGD_REF:S000043725|PMID:7565723 IPI C RNA polymerase II C-terminal domain kinase beta subunit, similar to cyclin YJL006C gene taxon:4932 20020919 SGD
+SGD S000003543 CTK2 GO:0016538 SGD_REF:S000055627|PMID:1820212 TAS F RNA polymerase II C-terminal domain kinase beta subunit, similar to cyclin YJL006C gene taxon:4932 20020208 SGD
+SGD S000003543 CTK2 GO:0006357 SGD_REF:S000058079|PMID:9110987 TAS P RNA polymerase II C-terminal domain kinase beta subunit, similar to cyclin YJL006C gene taxon:4932 20010118 SGD
+SGD S000003543 CTK2 GO:0006468 SGD_REF:S000055627|PMID:1820212 TAS P RNA polymerase II C-terminal domain kinase beta subunit, similar to cyclin YJL006C gene taxon:4932 20010118 SGD
+SGD S000004580 CTK3 GO:0005634 SGD_REF:S000043725|PMID:7565723 IPI C RNA polymerase II C-terminal domain kinase gamma subunit, similar to cyclin-dependent kinase YML112W gene taxon:4932 20020919 SGD
+SGD S000004580 CTK3 GO:0004693 SGD_REF:S000043725|PMID:7565723 IDA F RNA polymerase II C-terminal domain kinase gamma subunit, similar to cyclin-dependent kinase YML112W gene taxon:4932 20020919 SGD
+SGD S000004580 CTK3 GO:0006357 SGD_REF:S000058079|PMID:9110987 TAS P RNA polymerase II C-terminal domain kinase gamma subunit, similar to cyclin-dependent kinase YML112W gene taxon:4932 20010118 SGD
+SGD S000004580 CTK3 GO:0006468 SGD_REF:S000058079|PMID:9110987 TAS P RNA polymerase II C-terminal domain kinase gamma subunit, similar to cyclin-dependent kinase YML112W gene taxon:4932 20010118 SGD
+SGD S000004792 CTL1 GO:0005634 SGD_REF:S000051065|PMID:10219091 IDA C RNA triphosphatase YMR180C|CTH1 gene taxon:4932 20020913 SGD
+SGD S000004792 CTL1 GO:0005737 SGD_REF:S000051065|PMID:10219091 IDA C RNA triphosphatase YMR180C|CTH1 gene taxon:4932 20020913 SGD
+SGD S000004792 CTL1 GO:0004651 SGD_REF:S000051065|PMID:10219091 IDA F RNA triphosphatase YMR180C|CTH1 gene taxon:4932 20020913 SGD
+SGD S000004792 CTL1 GO:0006396 SGD_REF:S000051065|PMID:10219091 ISS P RNA triphosphatase YMR180C|CTH1 gene taxon:4932 20020913 SGD
+SGD S000001151 CTM1 GO:0005829 SGD_REF:S000044761|PMID:10791961 IDA C cytochrome c methyltransferase YHR109W gene taxon:4932 20010118 SGD
+SGD S000001151 CTM1 GO:0000277 SGD_REF:S000044761|PMID:10791961 IMP F cytochrome c methyltransferase YHR109W gene taxon:4932 20010118 SGD
+SGD S000001151 CTM1 GO:0000277 SGD_REF:S000044761|PMID:10791961 IDA F cytochrome c methyltransferase YHR109W gene taxon:4932 20010118 SGD
+SGD S000001151 CTM1 GO:0006464 SGD_REF:S000044761|PMID:10791961 IDA P cytochrome c methyltransferase YHR109W gene taxon:4932 20010118 SGD
+SGD S000000495 CTP1 GO:0005743 SGD_REF:S000057523|PMID:7876161 ISS C citrate tranporter YBR291C gene taxon:4932 20010118 SGD
+SGD S000000495 CTP1 GO:0005371 SGD_REF:S000057523|PMID:7876161 IDA F citrate tranporter YBR291C gene taxon:4932 20010118 SGD
+SGD S000000495 CTP1 GO:0006843 SGD_REF:S000057523|PMID:7876161 IDA P citrate tranporter YBR291C gene taxon:4932 20010118 SGD
+SGD S000000495 CTP1 GO:0006843 SGD_REF:S000057523|PMID:7876161 ISS P citrate tranporter YBR291C gene taxon:4932 20010118 SGD
+SGD S000006328 CTR1 GO:0005886 SGD_REF:S000039849|PMID:7929270 IDA C copper transport protein YPR124W gene taxon:4932 20020919 SGD
+SGD S000006328 CTR1 GO:0015088 SGD_REF:S000039849|PMID:7929270 IMP F copper transport protein YPR124W gene taxon:4932 20020919 SGD
+SGD S000006328 CTR1 GO:0015677 SGD_REF:S000039849|PMID:7929270 IMP P copper transport protein YPR124W gene taxon:4932 20020919 SGD
+SGD S000001218 CTR2 GO:0000329 SGD_REF:S000061304|PMID:11523804 IDA C YHR175W gene taxon:4932 20020919 SGD
+SGD S000001218 CTR2 GO:0005375 SGD_REF:S000061304|PMID:11523804 IMP F YHR175W gene taxon:4932 20030224 SGD
+SGD S000001218 CTR2 GO:0015088 SGD_REF:S000052761|PMID:7499355 IGI F YHR175W gene taxon:4932 20020919 SGD
+SGD S000001218 CTR2 GO:0015088 SGD_REF:S000052761|PMID:7499355 ISS F YHR175W gene taxon:4932 20020919 SGD
+SGD S000001218 CTR2 GO:0015677 SGD_REF:S000052761|PMID:7499355 IGI P YHR175W gene taxon:4932 20020919 SGD
+SGD S000001218 CTR2 GO:0015680 SGD_REF:S000061304|PMID:11523804 IMP P YHR175W gene taxon:4932 20020919 SGD
+SGD S000004403 CTR3 GO:0005887 SGD_REF:S000059123|PMID:10924521 IDA C copper transporter YLR411W gene taxon:4932 20020919 SGD
+SGD S000004403 CTR3 GO:0015088 SGD_REF:S000059123|PMID:10924521 IDA F copper transporter YLR411W gene taxon:4932 20020919 SGD
+SGD S000004403 CTR3 GO:0015677 SGD_REF:S000059123|PMID:10924521 IDA P copper transporter YLR411W gene taxon:4932 20020919 SGD
+SGD S000000650 CTR86 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YCR054C gene taxon:4932 20031028 SGD
+SGD S000000650 CTR86 GO:0005554 SGD_REF:S000069584 ND F YCR054C gene taxon:4932 20021002 SGD
+SGD S000000650 CTR86 GO:0000004 SGD_REF:S000069584 ND P YCR054C gene taxon:4932 20021002 SGD
+SGD S000005505 CTR9 GO:0005634 SGD_REF:S000056415|PMID:10684247 IDA C YOL145C|CDP1 gene taxon:4932 20020620 SGD
+SGD S000005505 CTR9 GO:0005634 SGD_REF:S000080456|PMID:15643076 IDA C YOL145C|CDP1 gene taxon:4932 20050228 SGD
+SGD S000005505 CTR9 GO:0008023 SGD_REF:S000071357|PMID:12242279 IPI C YOL145C|CDP1 gene taxon:4932 20021004 SGD
+SGD S000005505 CTR9 GO:0016593 SGD_REF:S000069696|PMID:11884586 IPI C YOL145C|CDP1 gene taxon:4932 20020927 SGD
+SGD S000005505 CTR9 GO:0016593 SGD_REF:S000073599|PMID:12773564 TAS C YOL145C|CDP1 gene taxon:4932 20040129 SGD
+SGD S000005505 CTR9 GO:0016944 SGD_REF:S000071357|PMID:12242279 IPI F YOL145C|CDP1 gene taxon:4932 20021004 SGD
+SGD S000005505 CTR9 GO:0045142 SGD_REF:S000059277|PMID:11058104 IDA F YOL145C|CDP1 gene taxon:4932 20020927 SGD
+SGD S000005505 CTR9 GO:0006366 SGD_REF:S000069696|PMID:11884586 IPI P YOL145C|CDP1 gene taxon:4932 20020927 SGD
+SGD S000005505 CTR9 GO:0006368 SGD_REF:S000071357|PMID:12242279 IPI P YOL145C|CDP1 gene taxon:4932 20021004 SGD
+SGD S000005505 CTR9 GO:0007059 SGD_REF:S000059277|PMID:11058104 IMP P YOL145C|CDP1 gene taxon:4932 20020927 SGD
+SGD S000005505 CTR9 GO:0016571 SGD_REF:S000073147|PMID:12667454 IMP P YOL145C|CDP1 gene taxon:4932 20050503 SGD
+SGD S000004276 CTS1 GO:0005576 SGD_REF:S000053014|PMID:1918080 IDA C endochitinase YLR286C gene taxon:4932 20020927 SGD
+SGD S000004276 CTS1 GO:0005635 SGD_REF:S000069459|PMID:11914276 IDA C endochitinase YLR286C gene taxon:4932 20020507 SGD
+SGD S000004276 CTS1 GO:0005783 SGD_REF:S000069459|PMID:11914276 IDA C endochitinase YLR286C gene taxon:4932 20020507 SGD
+SGD S000004276 CTS1 GO:0009277 SGD_REF:S000050571|PMID:9748433 TAS C endochitinase YLR286C gene taxon:4932 20020913 SGD
+SGD S000004276 CTS1 GO:0008843 SGD_REF:S000057303|PMID:6799506 IDA F endochitinase YLR286C gene taxon:4932 20050418 SGD
+SGD S000004276 CTS1 GO:0006032 SGD_REF:S000056102|PMID:3033651 IC GO:0004568 P endochitinase YLR286C gene taxon:4932 20050418 SGD
+SGD S000004276 CTS1 GO:0007109 SGD_REF:S000053014|PMID:1918080 IMP P endochitinase YLR286C gene taxon:4932 20020927 SGD
+SGD S000002779 CTS2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C Sporulation-specific chitinase YDR371W gene taxon:4932 20031028 SGD
+SGD S000002779 CTS2 GO:0005554 SGD_REF:S000069584 ND F Sporulation-specific chitinase YDR371W gene taxon:4932 20021003 SGD
+SGD S000002779 CTS2 GO:0000004 SGD_REF:S000069584 ND P Sporulation-specific chitinase YDR371W gene taxon:4932 20021003 SGD
+SGD S000003320 CTT1 GO:0005737 SGD_REF:S000042983|PMID:2542766 TAS C catalase T YGR088W gene taxon:4932 20030212 SGD
+SGD S000003320 CTT1 GO:0004096 SGD_REF:S000053472|PMID:3536508 ISS F catalase T YGR088W gene taxon:4932 20010118 SGD
+SGD S000003320 CTT1 GO:0006950 SGD_REF:S000052868|PMID:2061315 IDA P catalase T YGR088W gene taxon:4932 20010118 SGD
+SGD S000004877 CUE1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C Ubc7p binding and recruitment protein YMR264W gene taxon:4932 20040929 SGD
+SGD S000004877 CUE1 GO:0030176 SGD_REF:S000058243|PMID:9388185 IDA C Ubc7p binding and recruitment protein YMR264W gene taxon:4932 20020715 SGD
+SGD S000004877 CUE1 GO:0005515 SGD_REF:S000058243|PMID:9388185 IDA F Ubc7p binding and recruitment protein YMR264W gene taxon:4932 20020715 SGD
+SGD S000004877 CUE1 GO:0030433 SGD_REF:S000058243|PMID:9388185 IMP P Ubc7p binding and recruitment protein YMR264W gene taxon:4932 20020715 SGD
+SGD S000004877 CUE1 GO:0045184 SGD_REF:S000058243|PMID:9388185 IMP P Ubc7p binding and recruitment protein YMR264W gene taxon:4932 20020715 SGD
+SGD S000001573 CUE2 GO:0008372 SGD_REF:S000069584 ND C YKL090W gene taxon:4932 20021121 SGD
+SGD S000001573 CUE2 GO:0005515 SGD_REF:S000073491|PMID:12787503 IDA F YKL090W gene taxon:4932 20030723 SGD
+SGD S000001573 CUE2 GO:0000004 SGD_REF:S000069584 ND P YKL090W gene taxon:4932 20021121 SGD
+SGD S000003078 CUE3 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YGL110C gene taxon:4932 20031028 SGD
+SGD S000003078 CUE3 GO:0005554 SGD_REF:S000069584 ND F YGL110C gene taxon:4932 20021121 SGD
+SGD S000003078 CUE3 GO:0000004 SGD_REF:S000069584 ND P YGL110C gene taxon:4932 20021121 SGD
+SGD S000004568 CUE4 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YML101C gene taxon:4932 20020507 SGD
+SGD S000004568 CUE4 GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YML101C gene taxon:4932 20031028 SGD
+SGD S000004568 CUE4 GO:0005554 SGD_REF:S000069584 ND F YML101C gene taxon:4932 20021209 SGD
+SGD S000004568 CUE4 GO:0000004 SGD_REF:S000069584 ND P YML101C gene taxon:4932 20021209 SGD
+SGD S000005568 CUE5 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YOR042W gene taxon:4932 20031028 SGD
+SGD S000005568 CUE5 GO:0005554 SGD_REF:S000069584 ND F YOR042W gene taxon:4932 20021121 SGD
+SGD S000005568 CUE5 GO:0000004 SGD_REF:S000069584 ND P YOR042W gene taxon:4932 20021121 SGD
+SGD S000003235 CUL3 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YGR003W|CULB|CULLIN B gene taxon:4932 20031028 SGD
+SGD S000003235 CUL3 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YGR003W|CULB|CULLIN B gene taxon:4932 20031028 SGD
+SGD S000003235 CUL3 GO:0004842 SGD_REF:S000073416|PMID:12676951 IDA F YGR003W|CULB|CULLIN B gene taxon:4932 20030708 SGD
+SGD S000003235 CUL3 GO:0005515 SGD_REF:S000044681|PMID:10230407 IPI SGD:S000005493 F YGR003W|CULB|CULLIN B gene taxon:4932 20030708 SGD
+SGD S000003235 CUL3 GO:0006511 SGD_REF:S000042395|PMID:9531531 ISS P YGR003W|CULB|CULLIN B gene taxon:4932 20031006 SGD
+SGD S000003235 CUL3 GO:0006511 SGD_REF:S000073416|PMID:12676951 IC GO:0004842 P YGR003W|CULB|CULLIN B gene taxon:4932 20031006 SGD
+SGD S000001095 CUP1-1 GO:0005829 SGD_REF:S000054957|PMID:3308865 IDA C copper binding metallothionein YHR053C|CUP1 gene taxon:4932 20020722 SGD
+SGD S000001095 CUP1-1 GO:0005507 SGD_REF:S000043106|PMID:3902832 IDA F copper binding metallothionein YHR053C|CUP1 gene taxon:4932 20020720 SGD
+SGD S000001095 CUP1-1 GO:0046688 SGD_REF:S000062486|PMID:6370791 IMP P copper binding metallothionein YHR053C|CUP1 gene taxon:4932 20021107 SGD
+SGD S000001097 CUP1-2 GO:0005829 SGD_REF:S000054957|PMID:3308865 IDA C copper binding metallothionein YHR055C|CUP1 gene taxon:4932 20020722 SGD
+SGD S000001097 CUP1-2 GO:0005507 SGD_REF:S000043106|PMID:3902832 IDA F copper binding metallothionein YHR055C|CUP1 gene taxon:4932 20020720 SGD
+SGD S000001097 CUP1-2 GO:0046688 SGD_REF:S000062486|PMID:6370791 IMP P copper binding metallothionein YHR055C|CUP1 gene taxon:4932 20021107 SGD
+SGD S000003134 CUP2 GO:0005634 SGD_REF:S000050806|PMID:2651899 IDA C transcriptional activator YGL166W|ACE1 gene taxon:4932 20020722 SGD
+SGD S000003134 CUP2 GO:0003706 SGD_REF:S000043999|PMID:2674688 ISS F transcriptional activator YGL166W|ACE1 gene taxon:4932 20020722 SGD
+SGD S000003134 CUP2 GO:0003706 SGD_REF:S000043999|PMID:2674688 IMP F transcriptional activator YGL166W|ACE1 gene taxon:4932 20020722 SGD
+SGD S000003134 CUP2 GO:0006367 SGD_REF:S000043999|PMID:2674688 ISS P transcriptional activator YGL166W|ACE1 gene taxon:4932 20020722 SGD
+SGD S000003134 CUP2 GO:0006367 SGD_REF:S000043999|PMID:2674688 IMP P transcriptional activator YGL166W|ACE1 gene taxon:4932 20020722 SGD
+SGD S000003134 CUP2 GO:0046688 SGD_REF:S000039653|PMID:3043194 IMP P transcriptional activator YGL166W|ACE1 gene taxon:4932 20021107 SGD
+SGD S000000753 CUP5 GO:0000220 SGD_REF:S000056362|PMID:10224039 TAS C 17 kDa, VO sector subunit, dicyclohexylcarbodiimide binding subunit, proteolipid, vacuolar ATP synthase proteolipid C, vacuolar ATPase V0 domain subunit c (dicyclohexylcarbodiimide binding subunit) (17 kDa) YEL027W|CLS7|GEF2|VMA3 gene taxon:4932 20010118 SGD
+SGD S000000753 CUP5 GO:0000220 SGD_REF:S000058276|PMID:9442887 TAS C 17 kDa, VO sector subunit, dicyclohexylcarbodiimide binding subunit, proteolipid, vacuolar ATP synthase proteolipid C, vacuolar ATPase V0 domain subunit c (dicyclohexylcarbodiimide binding subunit) (17 kDa) YEL027W|CLS7|GEF2|VMA3 gene taxon:4932 20010118 SGD
+SGD S000000753 CUP5 GO:0016021 SGD_REF:S000077169|PMID:15252052 IDA C 17 kDa, VO sector subunit, dicyclohexylcarbodiimide binding subunit, proteolipid, vacuolar ATP synthase proteolipid C, vacuolar ATPase V0 domain subunit c (dicyclohexylcarbodiimide binding subunit) (17 kDa) YEL027W|CLS7|GEF2|VMA3 gene taxon:4932 20040929 SGD
+SGD S000000753 CUP5 GO:0015078 SGD_REF:S000073046|PMID:12482875 TAS F 17 kDa, VO sector subunit, dicyclohexylcarbodiimide binding subunit, proteolipid, vacuolar ATP synthase proteolipid C, vacuolar ATPase V0 domain subunit c (dicyclohexylcarbodiimide binding subunit) (17 kDa) YEL027W|CLS7|GEF2|VMA3 gene taxon:4932 20030711 SGD
+SGD S000000753 CUP5 GO:0006623 SGD_REF:S000040485|PMID:2145283 IMP P 17 kDa, VO sector subunit, dicyclohexylcarbodiimide binding subunit, proteolipid, vacuolar ATP synthase proteolipid C, vacuolar ATPase V0 domain subunit c (dicyclohexylcarbodiimide binding subunit) (17 kDa) YEL027W|CLS7|GEF2|VMA3 gene taxon:4932 20010118 SGD
+SGD S000000753 CUP5 GO:0006878 SGD_REF:S000040756|PMID:9434348 IMP P 17 kDa, VO sector subunit, dicyclohexylcarbodiimide binding subunit, proteolipid, vacuolar ATP synthase proteolipid C, vacuolar ATPase V0 domain subunit c (dicyclohexylcarbodiimide binding subunit) (17 kDa) YEL027W|CLS7|GEF2|VMA3 gene taxon:4932 20010118 SGD
+SGD S000000753 CUP5 GO:0006879 SGD_REF:S000040756|PMID:9434348 IMP P 17 kDa, VO sector subunit, dicyclohexylcarbodiimide binding subunit, proteolipid, vacuolar ATP synthase proteolipid C, vacuolar ATPase V0 domain subunit c (dicyclohexylcarbodiimide binding subunit) (17 kDa) YEL027W|CLS7|GEF2|VMA3 gene taxon:4932 20010118 SGD
+SGD S000000753 CUP5 GO:0006897 SGD_REF:S000040485|PMID:2145283 IMP P 17 kDa, VO sector subunit, dicyclohexylcarbodiimide binding subunit, proteolipid, vacuolar ATP synthase proteolipid C, vacuolar ATPase V0 domain subunit c (dicyclohexylcarbodiimide binding subunit) (17 kDa) YEL027W|CLS7|GEF2|VMA3 gene taxon:4932 20010118 SGD
+SGD S000000753 CUP5 GO:0007033 SGD_REF:S000040485|PMID:2145283 IMP P 17 kDa, VO sector subunit, dicyclohexylcarbodiimide binding subunit, proteolipid, vacuolar ATP synthase proteolipid C, vacuolar ATPase V0 domain subunit c (dicyclohexylcarbodiimide binding subunit) (17 kDa) YEL027W|CLS7|GEF2|VMA3 gene taxon:4932 20010118 SGD
+SGD S000000753 CUP5 GO:0007035 SGD_REF:S000056362|PMID:10224039 TAS P 17 kDa, VO sector subunit, dicyclohexylcarbodiimide binding subunit, proteolipid, vacuolar ATP synthase proteolipid C, vacuolar ATPase V0 domain subunit c (dicyclohexylcarbodiimide binding subunit) (17 kDa) YEL027W|CLS7|GEF2|VMA3 gene taxon:4932 20010118 SGD
+SGD S000000753 CUP5 GO:0007035 SGD_REF:S000058276|PMID:9442887 TAS P 17 kDa, VO sector subunit, dicyclohexylcarbodiimide binding subunit, proteolipid, vacuolar ATP synthase proteolipid C, vacuolar ATPase V0 domain subunit c (dicyclohexylcarbodiimide binding subunit) (17 kDa) YEL027W|CLS7|GEF2|VMA3 gene taxon:4932 20010118 SGD
+SGD S000000753 CUP5 GO:0015992 SGD_REF:S000073046|PMID:12482875 TAS P 17 kDa, VO sector subunit, dicyclohexylcarbodiimide binding subunit, proteolipid, vacuolar ATP synthase proteolipid C, vacuolar ATPase V0 domain subunit c (dicyclohexylcarbodiimide binding subunit) (17 kDa) YEL027W|CLS7|GEF2|VMA3 gene taxon:4932 20030711 SGD
+SGD S000006098 CUP9 GO:0005634 SGD_REF:S000051683|PMID:7969120 ISS C DNA binding protein (putative) YPL177C gene taxon:4932 20020708 SGD
+SGD S000006098 CUP9 GO:0003704 SGD_REF:S000051683|PMID:7969120 ISS F DNA binding protein (putative) YPL177C gene taxon:4932 20020708 SGD
+SGD S000006098 CUP9 GO:0006367 SGD_REF:S000051683|PMID:7969120 ISS P DNA binding protein (putative) YPL177C gene taxon:4932 20020708 SGD
+SGD S000006098 CUP9 GO:0006878 SGD_REF:S000051683|PMID:7969120 IMP P DNA binding protein (putative) YPL177C gene taxon:4932 20020708 SGD
+SGD S000004853 CUS1 GO:0005686 SGD_REF:S000069986|PMID:11804584 IDA C U2 snRNP protein YMR240C gene taxon:4932 20020621 SGD
+SGD S000004853 CUS1 colocalizes_with GO:0005686 SGD_REF:S000080993|PMID:15565172 IDA C U2 snRNP protein YMR240C gene taxon:4932 20051006 SGD
+SGD S000004853 CUS1 GO:0003723 SGD_REF:S000045918|PMID:10688664 IDA F U2 snRNP protein YMR240C gene taxon:4932 20021108 SGD
+SGD S000004853 CUS1 GO:0005515 SGD_REF:S000045918|PMID:10688664 IDA F U2 snRNP protein YMR240C gene taxon:4932 20021108 SGD
+SGD S000004853 CUS1 GO:0000245 SGD_REF:S000053771|PMID:8566755 IDA P U2 snRNP protein YMR240C gene taxon:4932 20020826 SGD
+SGD S000005230 CUS2 GO:0005686 SGD_REF:S000069986|PMID:11804584 IDA C YNL286W gene taxon:4932 20020621 SGD
+SGD S000005230 CUS2 GO:0003723 SGD_REF:S000045097|PMID:9710584 ISS F YNL286W gene taxon:4932 20020926 SGD
+SGD S000005230 CUS2 GO:0003723 SGD_REF:S000045097|PMID:9710584 IMP F YNL286W gene taxon:4932 20020926 SGD
+SGD S000005230 CUS2 GO:0000398 SGD_REF:S000045097|PMID:9710584 IGI P YNL286W gene taxon:4932 20020926 SGD
+SGD S000005230 CUS2 GO:0000398 SGD_REF:S000045097|PMID:9710584 IPI P YNL286W gene taxon:4932 20020926 SGD
+SGD S000002570 CWC15 GO:0005681 SGD_REF:S000069712|PMID:11884590 IPI C YDR163W gene taxon:4932 20030320 SGD
+SGD S000002570 CWC15 GO:0005554 SGD_REF:S000069584 ND F YDR163W gene taxon:4932 20021121 SGD
+SGD S000002570 CWC15 GO:0000398 SGD_REF:S000069712|PMID:11884590 IGI SGD:S000003959 P YDR163W gene taxon:4932 20040429 SGD
+SGD S000002368 CWC2 GO:0005681 SGD_REF:S000070110|PMID:12088152 IDA C YDL209C|NTC40 gene taxon:4932 20020905 SGD
+SGD S000002368 CWC2 GO:0005554 SGD_REF:S000069584 ND F YDL209C|NTC40 gene taxon:4932 20020905 SGD
+SGD S000002368 CWC2 GO:0000398 SGD_REF:S000070110|PMID:12088152 IMP P YDL209C|NTC40 gene taxon:4932 20020905 SGD
+SGD S000002368 CWC2 GO:0000398 SGD_REF:S000070110|PMID:12088152 IPI P YDL209C|NTC40 gene taxon:4932 20020905 SGD
+SGD S000002890 CWC21 GO:0005681 SGD_REF:S000069712|PMID:11884590 IPI C YDR482C gene taxon:4932 20030320 SGD
+SGD S000002890 CWC21 GO:0005554 SGD_REF:S000069584 ND F YDR482C gene taxon:4932 20021121 SGD
+SGD S000002890 CWC21 GO:0000004 SGD_REF:S000069584 ND P YDR482C gene taxon:4932 20021121 SGD
+SGD S000003510 CWC22 GO:0005681 SGD_REF:S000069712|PMID:11884590 IPI C YGR278W gene taxon:4932 20030320 SGD
+SGD S000003510 CWC22 GO:0005554 SGD_REF:S000069584 ND F YGR278W gene taxon:4932 20021003 SGD
+SGD S000003510 CWC22 GO:0000398 SGD_REF:S000069712|PMID:11884590 IPI P YGR278W gene taxon:4932 20031103 SGD
+SGD S000003096 CWC23 GO:0005681 SGD_REF:S000069712|PMID:11884590 IPI C YGL128C gene taxon:4932 20030320 SGD
+SGD S000003096 CWC23 GO:0005554 SGD_REF:S000069584 ND F YGL128C gene taxon:4932 20021002 SGD
+SGD S000003096 CWC23 GO:0000004 SGD_REF:S000069584 ND P YGL128C gene taxon:4932 20021002 SGD
+SGD S000004315 CWC24 GO:0005681 SGD_REF:S000069712|PMID:11884590 IPI C YLR323C gene taxon:4932 20030320 SGD
+SGD S000004315 CWC24 GO:0005554 SGD_REF:S000069584 ND F YLR323C gene taxon:4932 20021121 SGD
+SGD S000004315 CWC24 GO:0000004 SGD_REF:S000069584 ND P YLR323C gene taxon:4932 20021121 SGD
+SGD S000005189 CWC25 GO:0005681 SGD_REF:S000069712|PMID:11884590 IPI C YNL245C gene taxon:4932 20030320 SGD
+SGD S000005189 CWC25 GO:0005554 SGD_REF:S000069584 ND F YNL245C gene taxon:4932 20021121 SGD
+SGD S000005189 CWC25 GO:0000398 SGD_REF:S000069712|PMID:11884590 IPI SGD:S000003959 P YNL245C gene taxon:4932 20031231 SGD
+SGD S000005189 CWC25 GO:0000398 SGD_REF:S000075214|PMID:14690591 IPI SGD:S000003959 P YNL245C gene taxon:4932 20031231 SGD
+SGD S000005985 CWC27 GO:0005681 SGD_REF:S000069712|PMID:11884590 IPI C YPL064C gene taxon:4932 20030320 SGD
+SGD S000005985 CWC27 GO:0005554 SGD_REF:S000069584 ND F YPL064C gene taxon:4932 20021121 SGD
+SGD S000005985 CWC27 GO:0000004 SGD_REF:S000069584 ND P YPL064C gene taxon:4932 20021121 SGD
+SGD S000002995 CWH41 GO:0005789 SGD_REF:S000053091|PMID:8576053 IDA C glucosidase I YGL027C|DER7|GLS1 gene taxon:4932 20010118 SGD
+SGD S000002995 CWH41 GO:0004573 SGD_REF:S000053239|PMID:9430631 IMP F glucosidase I YGL027C|DER7|GLS1 gene taxon:4932 20010118 SGD
+SGD S000002995 CWH41 GO:0004573 SGD_REF:S000074936|PMID:14680956 IDA F glucosidase I YGL027C|DER7|GLS1 gene taxon:4932 20041007 SGD
+SGD S000002995 CWH41 GO:0004573 SGD_REF:S000053239|PMID:9430631 ISS F glucosidase I YGL027C|DER7|GLS1 gene taxon:4932 20010118 SGD
+SGD S000002995 CWH41 GO:0007047 SGD_REF:S000053239|PMID:9430631 IMP P glucosidase I YGL027C|DER7|GLS1 gene taxon:4932 20010118 SGD
+SGD S000002995 CWH41 GO:0007047 SGD_REF:S000053239|PMID:9430631 ISS P glucosidase I YGL027C|DER7|GLS1 gene taxon:4932 20010118 SGD
+SGD S000000610 CWH43 GO:0005887 SGD_REF:S000060769|PMID:11427965 IDA C YCR017C gene taxon:4932 20020906 SGD
+SGD S000000610 CWH43 GO:0005934 SGD_REF:S000060769|PMID:11427965 IDA C YCR017C gene taxon:4932 20020906 SGD
+SGD S000000610 CWH43 GO:0005935 SGD_REF:S000060769|PMID:11427965 IDA C YCR017C gene taxon:4932 20020906 SGD
+SGD S000000610 CWH43 GO:0005554 SGD_REF:S000069584 ND F YCR017C gene taxon:4932 20020906 SGD
+SGD S000000610 CWH43 GO:0007047 SGD_REF:S000060769|PMID:11427965 IGI P YCR017C gene taxon:4932 20020906 SGD
+SGD S000000610 CWH43 GO:0007165 SGD_REF:S000060769|PMID:11427965 IGI P YCR017C gene taxon:4932 20020906 SGD
+SGD S000001579 CWP1 GO:0009277 SGD_REF:S000053854|PMID:9335273 IDA C cell wall mannoprotein YKL096W|YJU1 gene taxon:4932 20020726 SGD
+SGD S000001579 CWP1 GO:0009277 SGD_REF:S000081097|PMID:15781460 IDA C cell wall mannoprotein YKL096W|YJU1 gene taxon:4932 20050601 SGD
+SGD S000001579 CWP1 GO:0005199 SGD_REF:S000042960|PMID:7768807 IDA F cell wall mannoprotein YKL096W|YJU1 gene taxon:4932 20020726 SGD
+SGD S000001579 CWP1 GO:0007047 SGD_REF:S000042960|PMID:7768807 IDA P cell wall mannoprotein YKL096W|YJU1 gene taxon:4932 20020726 SGD
+SGD S000001579 CWP1 GO:0007047 SGD_REF:S000042960|PMID:7768807 IMP P cell wall mannoprotein YKL096W|YJU1 gene taxon:4932 20020726 SGD
+SGD S000001956 CWP2 GO:0009277 SGD_REF:S000069752|PMID:11956747 IDA C cell wall mannoprotein YKL096W-A|LPR1|YKL097W-A gene taxon:4932 20020613 SGD
+SGD S000001956 CWP2 GO:0005199 SGD_REF:S000042960|PMID:7768807 IDA F cell wall mannoprotein YKL096W-A|LPR1|YKL097W-A gene taxon:4932 20020726 SGD
+SGD S000001956 CWP2 GO:0006885 SGD_REF:S000059420|PMID:11126778 IGI P cell wall mannoprotein YKL096W-A|LPR1|YKL097W-A gene taxon:4932 20030124 SGD
+SGD S000001956 CWP2 GO:0007047 SGD_REF:S000042960|PMID:7768807 IDA P cell wall mannoprotein YKL096W-A|LPR1|YKL097W-A gene taxon:4932 20020726 SGD
+SGD S000001956 CWP2 GO:0007047 SGD_REF:S000042960|PMID:7768807 IMP P cell wall mannoprotein YKL096W-A|LPR1|YKL097W-A gene taxon:4932 20020726 SGD
+SGD S000004518 CYB2 GO:0005758 SGD_REF:S000056979|PMID:3004948 IDA C L-lactate cytochrome c oxidoreductase, cytochrome b2 YML054C gene taxon:4932 20020927 SGD
+SGD S000004518 CYB2 GO:0005758 SGD_REF:S000062048|PMID:6290489 IDA C L-lactate cytochrome c oxidoreductase, cytochrome b2 YML054C gene taxon:4932 20041005 SGD
+SGD S000004518 CYB2 GO:0004460 SGD_REF:S000056979|PMID:3004948 IDA F L-lactate cytochrome c oxidoreductase, cytochrome b2 YML054C gene taxon:4932 20020927 SGD
+SGD S000004518 CYB2 GO:0006118 SGD_REF:S000068875|PMID:11502169 TAS P L-lactate cytochrome c oxidoreductase, cytochrome b2 YML054C gene taxon:4932 20020927 SGD
+SGD S000005055 CYB5 GO:0005789 SGD_REF:S000072636|PMID:12514182 IDA C cytochrome b5 YNL111C gene taxon:4932 20031014 SGD
+SGD S000005055 CYB5 GO:0005792 SGD_REF:S000062024|PMID:10622712 IDA C cytochrome b5 YNL111C gene taxon:4932 20020425 SGD
+SGD S000005055 CYB5 GO:0009055 SGD_REF:S000062024|PMID:10622712 IDA F cytochrome b5 YNL111C gene taxon:4932 20060324 SGD
+SGD S000005055 CYB5 GO:0006118 SGD_REF:S000062024|PMID:10622712 IDA P cytochrome b5 YNL111C gene taxon:4932 20060324 SGD
+SGD S000005055 CYB5 GO:0016126 SGD_REF:S000062024|PMID:10622712 IDA P cytochrome b5 YNL111C gene taxon:4932 20020425 SGD
+SGD S000005055 CYB5 GO:0016126 SGD_REF:S000062024|PMID:10622712 TAS P cytochrome b5 YNL111C gene taxon:4932 20020425 SGD
+SGD S000003809 CYC1 GO:0005758 SGD_REF:S000062053|PMID:9866716 IDA C iso-1-cytochrome c YJR048W gene taxon:4932 20021002 SGD
+SGD S000003809 CYC1 GO:0009055 SGD_REF:S000053336|PMID:8621494 TAS F iso-1-cytochrome c YJR048W gene taxon:4932 20021002 SGD
+SGD S000003809 CYC1 GO:0006118 SGD_REF:S000053336|PMID:8621494 TAS P iso-1-cytochrome c YJR048W gene taxon:4932 20021002 SGD
+SGD S000005563 CYC2 GO:0005739 SGD_REF:S000069459|PMID:11914276 IDA C YOR037W gene taxon:4932 20020507 SGD
+SGD S000005563 CYC2 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YOR037W gene taxon:4932 20031028 SGD
+SGD S000005563 CYC2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YOR037W gene taxon:4932 20040924 SGD
+SGD S000005563 CYC2 GO:0031314 SGD_REF:S000086902|PMID:16207709 IDA C YOR037W gene taxon:4932 20060502 SGD
+SGD S000005563 CYC2 GO:0016491 SGD_REF:S000086902|PMID:16207709 IDA F YOR037W gene taxon:4932 20060502 SGD
+SGD S000005563 CYC2 GO:0007006 SGD_REF:S000061363|PMID:11488609 IMP P YOR037W gene taxon:4932 20020927 SGD
+SGD S000005563 CYC2 GO:0018063 SGD_REF:S000075319|PMID:14514677 IGI P YOR037W gene taxon:4932 20040119 SGD
+SGD S000005563 CYC2 GO:0018063 SGD_REF:S000086902|PMID:16207709 IGI P YOR037W gene taxon:4932 20060502 SGD
+SGD S000000037 CYC3 GO:0005758 SGD_REF:S000062525|PMID:1656231 IDA C cytochrome c heme lyase (CCHL) YAL039C gene taxon:4932 20020927 SGD
+SGD S000000037 CYC3 GO:0004408 SGD_REF:S000039981|PMID:3034577 IDA F cytochrome c heme lyase (CCHL) YAL039C gene taxon:4932 20020927 SGD
+SGD S000000037 CYC3 GO:0018063 SGD_REF:S000039981|PMID:3034577 IDA P cytochrome c heme lyase (CCHL) YAL039C gene taxon:4932 20020927 SGD
+SGD S000000765 CYC7 GO:0005758 SGD_REF:S000045157|PMID:8636074 IDA C iso-2-cytochrome c YEL039C gene taxon:4932 20020906 SGD
+SGD S000000765 CYC7 GO:0009055 SGD_REF:S000062594|PMID:6244566 IDA F iso-2-cytochrome c YEL039C gene taxon:4932 20020927 SGD
+SGD S000000765 CYC7 GO:0006118 SGD_REF:S000062594|PMID:6244566 IDA P iso-2-cytochrome c YEL039C gene taxon:4932 20020927 SGD
+SGD S000000316 CYC8 GO:0005634 SGD_REF:S000055359|PMID:1739976 IPI C YBR112C|CRT8|SSN6 gene taxon:4932 20020410 SGD
+SGD S000000316 CYC8 GO:0003713 SGD_REF:S000062263|PMID:9867831 IDA F YBR112C|CRT8|SSN6 gene taxon:4932 20020410 SGD
+SGD S000000316 CYC8 GO:0003713 SGD_REF:S000062263|PMID:9867831 IGI F YBR112C|CRT8|SSN6 gene taxon:4932 20020410 SGD
+SGD S000000316 CYC8 GO:0003713 SGD_REF:S000062263|PMID:9867831 IPI F YBR112C|CRT8|SSN6 gene taxon:4932 20020410 SGD
+SGD S000000316 CYC8 GO:0003713 SGD_REF:S000062263|PMID:9867831 IMP F YBR112C|CRT8|SSN6 gene taxon:4932 20020410 SGD
+SGD S000000316 CYC8 GO:0016565 SGD_REF:S000055359|PMID:1739976 IMP F YBR112C|CRT8|SSN6 gene taxon:4932 20020410 SGD
+SGD S000000316 CYC8 GO:0016565 SGD_REF:S000055359|PMID:1739976 IDA F YBR112C|CRT8|SSN6 gene taxon:4932 20020410 SGD
+SGD S000000316 CYC8 GO:0016565 SGD_REF:S000055359|PMID:1739976 IPI F YBR112C|CRT8|SSN6 gene taxon:4932 20020410 SGD
+SGD S000000316 CYC8 GO:0006338 SGD_REF:S000076895|PMID:14739928 IMP P YBR112C|CRT8|SSN6 gene taxon:4932 20041214 SGD
+SGD S000000316 CYC8 GO:0016481 SGD_REF:S000055359|PMID:1739976 IMP P YBR112C|CRT8|SSN6 gene taxon:4932 20020410 SGD
+SGD S000000316 CYC8 GO:0016481 SGD_REF:S000055359|PMID:1739976 IDA P YBR112C|CRT8|SSN6 gene taxon:4932 20020410 SGD
+SGD S000000316 CYC8 GO:0016481 SGD_REF:S000055359|PMID:1739976 IPI P YBR112C|CRT8|SSN6 gene taxon:4932 20020410 SGD
+SGD S000000316 CYC8 GO:0016584 SGD_REF:S000076511|PMID:15116071 IDA P YBR112C|CRT8|SSN6 gene taxon:4932 20041025 SGD
+SGD S000002275 CYK3 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDL117W gene taxon:4932 20031028 SGD
+SGD S000002275 CYK3 GO:0005935 SGD_REF:S000074185|PMID:14562095 IDA C YDL117W gene taxon:4932 20031028 SGD
+SGD S000002275 CYK3 GO:0005554 SGD_REF:S000069584 ND F YDL117W gene taxon:4932 20010212 SGD
+SGD S000002275 CYK3 GO:0000910 SGD_REF:S000059205|PMID:10959846 IGI P YDL117W gene taxon:4932 20010212 SGD
+SGD S000002838 CYM1 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C Metalloprotease YDR430C|MOP112 gene taxon:4932 20031028 SGD
+SGD S000002838 CYM1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C Metalloprotease YDR430C|MOP112 gene taxon:4932 20040924 SGD
+SGD S000002838 CYM1 GO:0005739 SGD_REF:S000080056|PMID:15606766 IDA C Metalloprotease YDR430C|MOP112 gene taxon:4932 20050415 SGD
+SGD S000002838 CYM1 GO:0005758 SGD_REF:S000081142|PMID:15772085 IDA C Metalloprotease YDR430C|MOP112 gene taxon:4932 20050418 SGD
+SGD S000002838 CYM1 GO:0004222 SGD_REF:S000080056|PMID:15606766 IDA F Metalloprotease YDR430C|MOP112 gene taxon:4932 20050415 SGD
+SGD S000002838 CYM1 GO:0004222 SGD_REF:S000081142|PMID:15772085 IMP F Metalloprotease YDR430C|MOP112 gene taxon:4932 20050418 SGD
+SGD S000002838 CYM1 GO:0006508 SGD_REF:S000080056|PMID:15606766 IDA P Metalloprotease YDR430C|MOP112 gene taxon:4932 20050415 SGD
+SGD S000002838 CYM1 GO:0006508 SGD_REF:S000081142|PMID:15772085 IMP P Metalloprotease YDR430C|MOP112 gene taxon:4932 20050418 SGD
+SGD S000003542 CYR1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C adenylate cyclase YJL005W|CDC35|FIL1|HSR1|SRA4|TSM0185 gene taxon:4932 20040928 SGD
+SGD S000003542 CYR1 GO:0005886 SGD_REF:S000042496|PMID:2196438 IDA C adenylate cyclase YJL005W|CDC35|FIL1|HSR1|SRA4|TSM0185 gene taxon:4932 20010118 SGD
+SGD S000003542 CYR1 GO:0004016 SGD_REF:S000042496|PMID:2196438 TAS F adenylate cyclase YJL005W|CDC35|FIL1|HSR1|SRA4|TSM0185 gene taxon:4932 20010118 SGD
+SGD S000003542 CYR1 GO:0000074 SGD_REF:S000043717|PMID:2844421 IMP P adenylate cyclase YJL005W|CDC35|FIL1|HSR1|SRA4|TSM0185 gene taxon:4932 20010118 SGD
+SGD S000003542 CYR1 GO:0001324 SGD_REF:S000060129|PMID:11292860 IMP P adenylate cyclase YJL005W|CDC35|FIL1|HSR1|SRA4|TSM0185 gene taxon:4932 20041025 SGD
+SGD S000003542 CYR1 GO:0007126 SGD_REF:S000055747|PMID:2581976 IMP P adenylate cyclase YJL005W|CDC35|FIL1|HSR1|SRA4|TSM0185 gene taxon:4932 20010118 SGD
+SGD S000003542 CYR1 GO:0007188 SGD_REF:S000050069|PMID:1875942 TAS P adenylate cyclase YJL005W|CDC35|FIL1|HSR1|SRA4|TSM0185 gene taxon:4932 20010118 SGD
+SGD S000003542 CYR1 GO:0007265 SGD_REF:S000050069|PMID:1875942 TAS P adenylate cyclase YJL005W|CDC35|FIL1|HSR1|SRA4|TSM0185 gene taxon:4932 20010118 SGD
+SGD S000029140 CYS1 GO:0008372 SGD_REF:S000069584 ND C serine o-acetyltransferase (EC 2.3.1.30) (putative) gene taxon:4932 20020617 SGD
+SGD S000029140 CYS1 GO:0009001 SGD_REF:S000047826|PMID:8335636 IMP F serine o-acetyltransferase (EC 2.3.1.30) (putative) gene taxon:4932 20020617 SGD
+SGD S000029140 CYS1 GO:0000004 SGD_REF:S000069584 ND P serine o-acetyltransferase (EC 2.3.1.30) (putative) gene taxon:4932 20020617 SGD
+SGD S000000010 CYS3 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C cystathionine gamma-lyase YAL012W|CYI1|FUN35|STR1 gene taxon:4932 20031028 SGD
+SGD S000000010 CYS3 GO:0004123 SGD_REF:S000052707|PMID:1577698 IDA F cystathionine gamma-lyase YAL012W|CYI1|FUN35|STR1 gene taxon:4932 20021113 SGD
+SGD S000000010 CYS3 GO:0000096 SGD_REF:S000056312|PMID:1732168 TAS P cystathionine gamma-lyase YAL012W|CYI1|FUN35|STR1 gene taxon:4932 20020617 SGD
+SGD S000000010 CYS3 GO:0006534 SGD_REF:S000056312|PMID:1732168 TAS P cystathionine gamma-lyase YAL012W|CYI1|FUN35|STR1 gene taxon:4932 20020617 SGD
+SGD S000000010 CYS3 GO:0019346 SGD_REF:S000056312|PMID:1732168 TAS P cystathionine gamma-lyase YAL012W|CYI1|FUN35|STR1 gene taxon:4932 20020617 SGD
+SGD S000003387 CYS4 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C cystathionine beta-synthase YGR155W|NHS5|STR4|VMA41 gene taxon:4932 20020507 SGD
+SGD S000003387 CYS4 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C cystathionine beta-synthase YGR155W|NHS5|STR4|VMA41 gene taxon:4932 20031028 SGD
+SGD S000003387 CYS4 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C cystathionine beta-synthase YGR155W|NHS5|STR4|VMA41 gene taxon:4932 20040813 SGD
+SGD S000003387 CYS4 GO:0004122 SGD_REF:S000062632|PMID:10766767 IDA F cystathionine beta-synthase YGR155W|NHS5|STR4|VMA41 gene taxon:4932 20020927 SGD
+SGD S000003387 CYS4 GO:0019344 SGD_REF:S000055880|PMID:8366024 IMP P cystathionine beta-synthase YGR155W|NHS5|STR4|VMA41 gene taxon:4932 20020927 SGD
+SGD S000005591 CYT1 GO:0005743 SGD_REF:S000060394|PMID:11279090 TAS C cytochrome c1 YOR065W|CTC1|YOR29-16 gene taxon:4932 20020425 SGD
+SGD S000005591 CYT1 GO:0005746 SGD_REF:S000060394|PMID:11279090 TAS C cytochrome c1 YOR065W|CTC1|YOR29-16 gene taxon:4932 20020425 SGD
+SGD S000005591 CYT1 GO:0005750 SGD_REF:S000046403|PMID:10873857 IDA C cytochrome c1 YOR065W|CTC1|YOR29-16 gene taxon:4932 20020906 SGD
+SGD S000005591 CYT1 GO:0045153 SGD_REF:S000060394|PMID:11279090 IMP F cytochrome c1 YOR065W|CTC1|YOR29-16 gene taxon:4932 20020425 SGD
+SGD S000005591 CYT1 GO:0045153 SGD_REF:S000060394|PMID:11279090 TAS F cytochrome c1 YOR065W|CTC1|YOR29-16 gene taxon:4932 20020425 SGD
+SGD S000005591 CYT1 GO:0006119 SGD_REF:S000060394|PMID:11279090 TAS P cytochrome c1 YOR065W|CTC1|YOR29-16 gene taxon:4932 20020425 SGD
+SGD S000005591 CYT1 GO:0006122 SGD_REF:S000060394|PMID:11279090 IMP P cytochrome c1 YOR065W|CTC1|YOR29-16 gene taxon:4932 20020425 SGD
+SGD S000005591 CYT1 GO:0006122 SGD_REF:S000060394|PMID:11279090 TAS P cytochrome c1 YOR065W|CTC1|YOR29-16 gene taxon:4932 20020425 SGD
+SGD S000001570 CYT2 GO:0005758 SGD_REF:S000045294|PMID:7559417 IDA C cytochrome c1 heme lyase (CC1HL) YKL087C gene taxon:4932 20030120 SGD
+SGD S000001570 CYT2 GO:0004408 SGD_REF:S000039886|PMID:1499554 ISS F cytochrome c1 heme lyase (CC1HL) YKL087C gene taxon:4932 20020619 SGD
+SGD S000001570 CYT2 GO:0004408 SGD_REF:S000039886|PMID:1499554 IMP F cytochrome c1 heme lyase (CC1HL) YKL087C gene taxon:4932 20020619 SGD
+SGD S000001570 CYT2 GO:0018063 SGD_REF:S000039886|PMID:1499554 ISS P cytochrome c1 heme lyase (CC1HL) YKL087C gene taxon:4932 20020619 SGD
+SGD S000001570 CYT2 GO:0018063 SGD_REF:S000039886|PMID:1499554 IMP P cytochrome c1 heme lyase (CC1HL) YKL087C gene taxon:4932 20020619 SGD
+SGD S000002423 DAD1 GO:0000778 SGD_REF:S000069091|PMID:11756468 IPI C YDR016C gene taxon:4932 20021008 SGD
+SGD S000002423 DAD1 GO:0005819 SGD_REF:S000069091|PMID:11756468 IPI C YDR016C gene taxon:4932 20021008 SGD
+SGD S000002423 DAD1 GO:0042729 SGD_REF:S000069220|PMID:11782438 IDA C YDR016C gene taxon:4932 20040122 SGD
+SGD S000002423 DAD1 GO:0042729 SGD_REF:S000080444|PMID:15640796 IDA C YDR016C gene taxon:4932 20050328 SGD
+SGD S000002423 DAD1 GO:0042729 SGD_REF:S000069220|PMID:11782438 IPI C YDR016C gene taxon:4932 20040122 SGD
+SGD S000002423 DAD1 GO:0042729 SGD_REF:S000080444|PMID:15640796 IPI C YDR016C gene taxon:4932 20050328 SGD
+SGD S000002423 DAD1 GO:0042729 SGD_REF:S000080667|PMID:15664196 IPI C YDR016C gene taxon:4932 20050328 SGD
+SGD S000002423 DAD1 GO:0042729 SGD_REF:S000080667|PMID:15664196 IDA C YDR016C gene taxon:4932 20050328 SGD
+SGD S000002423 DAD1 GO:0005200 SGD_REF:S000069091|PMID:11756468 IPI F YDR016C gene taxon:4932 20021008 SGD
+SGD S000002423 DAD1 GO:0030472 SGD_REF:S000069091|PMID:11756468 IPI P YDR016C gene taxon:4932 20021008 SGD
+SGD S000002423 DAD1 GO:0031110 SGD_REF:S000080667|PMID:15664196 IPI P YDR016C gene taxon:4932 20050328 SGD
+SGD S000002423 DAD1 GO:0031110 SGD_REF:S000080667|PMID:15664196 IDA P YDR016C gene taxon:4932 20050328 SGD
+SGD S000001791 DAD2 GO:0000778 SGD_REF:S000069091|PMID:11756468 IDA C YKR083C|HSK1 gene taxon:4932 20021008 SGD
+SGD S000001791 DAD2 GO:0005819 SGD_REF:S000069091|PMID:11756468 IDA C YKR083C|HSK1 gene taxon:4932 20021008 SGD
+SGD S000001791 DAD2 GO:0042729 SGD_REF:S000069052|PMID:11799062 IDA C YKR083C|HSK1 gene taxon:4932 20040122 SGD
+SGD S000001791 DAD2 GO:0042729 SGD_REF:S000080444|PMID:15640796 IPI C YKR083C|HSK1 gene taxon:4932 20050328 SGD
+SGD S000001791 DAD2 GO:0042729 SGD_REF:S000080444|PMID:15640796 IDA C YKR083C|HSK1 gene taxon:4932 20050328 SGD
+SGD S000001791 DAD2 GO:0042729 SGD_REF:S000069052|PMID:11799062 IPI C YKR083C|HSK1 gene taxon:4932 20040122 SGD
+SGD S000001791 DAD2 GO:0042729 SGD_REF:S000080667|PMID:15664196 IDA C YKR083C|HSK1 gene taxon:4932 20050328 SGD
+SGD S000001791 DAD2 GO:0042729 SGD_REF:S000080667|PMID:15664196 IPI C YKR083C|HSK1 gene taxon:4932 20050328 SGD
+SGD S000001791 DAD2 GO:0005200 SGD_REF:S000069091|PMID:11756468 IDA F YKR083C|HSK1 gene taxon:4932 20021008 SGD
+SGD S000001791 DAD2 GO:0030472 SGD_REF:S000069091|PMID:11756468 IMP P YKR083C|HSK1 gene taxon:4932 20021008 SGD
+SGD S000001791 DAD2 GO:0031110 SGD_REF:S000080667|PMID:15664196 IPI P YKR083C|HSK1 gene taxon:4932 20050328 SGD
+SGD S000001791 DAD2 GO:0031110 SGD_REF:S000080667|PMID:15664196 IDA P YKR083C|HSK1 gene taxon:4932 20050328 SGD
+SGD S000007595 DAD3 GO:0000776 SGD_REF:S000071581|PMID:12408861 IDA C YBR233W-A gene taxon:4932 20030423 SGD
+SGD S000007595 DAD3 GO:0005819 SGD_REF:S000071581|PMID:12408861 IDA C YBR233W-A gene taxon:4932 20030423 SGD
+SGD S000007595 DAD3 GO:0042729 SGD_REF:S000080667|PMID:15664196 IDA C YBR233W-A gene taxon:4932 20050328 SGD
+SGD S000007595 DAD3 GO:0042729 SGD_REF:S000080667|PMID:15664196 IPI C YBR233W-A gene taxon:4932 20050328 SGD
+SGD S000007595 DAD3 GO:0042729 SGD_REF:S000080444|PMID:15640796 IPI C YBR233W-A gene taxon:4932 20050328 SGD
+SGD S000007595 DAD3 GO:0042729 SGD_REF:S000080444|PMID:15640796 IDA C YBR233W-A gene taxon:4932 20050328 SGD
+SGD S000007595 DAD3 GO:0005515 SGD_REF:S000071581|PMID:12408861 IDA F YBR233W-A gene taxon:4932 20030423 SGD
+SGD S000007595 DAD3 GO:0007067 SGD_REF:S000071581|PMID:12408861 IMP P YBR233W-A gene taxon:4932 20030423 SGD
+SGD S000007595 DAD3 GO:0030472 SGD_REF:S000080667|PMID:15664196 IPI P YBR233W-A gene taxon:4932 20050425 SGD
+SGD S000007595 DAD3 GO:0030472 SGD_REF:S000080444|PMID:15640796 IPI P YBR233W-A gene taxon:4932 20050425 SGD
+SGD S000007595 DAD3 GO:0031110 SGD_REF:S000080667|PMID:15664196 IPI P YBR233W-A gene taxon:4932 20050328 SGD
+SGD S000007595 DAD3 GO:0031110 SGD_REF:S000080667|PMID:15664196 IDA P YBR233W-A gene taxon:4932 20050328 SGD
+SGD S000007604 DAD4 GO:0000776 SGD_REF:S000071581|PMID:12408861 IDA C YDR320C-A|HSK2 gene taxon:4932 20030423 SGD
+SGD S000007604 DAD4 GO:0000776 SGD_REF:S000081123|PMID:15632076 IPI C YDR320C-A|HSK2 gene taxon:4932 20050328 SGD
+SGD S000007604 DAD4 GO:0005819 SGD_REF:S000071581|PMID:12408861 IDA C YDR320C-A|HSK2 gene taxon:4932 20030423 SGD
+SGD S000007604 DAD4 GO:0005819 SGD_REF:S000081123|PMID:15632076 IDA C YDR320C-A|HSK2 gene taxon:4932 20050328 SGD
+SGD S000007604 DAD4 GO:0042729 SGD_REF:S000080667|PMID:15664196 IDA C YDR320C-A|HSK2 gene taxon:4932 20050328 SGD
+SGD S000007604 DAD4 GO:0042729 SGD_REF:S000080667|PMID:15664196 IPI C YDR320C-A|HSK2 gene taxon:4932 20050328 SGD
+SGD S000007604 DAD4 GO:0042729 SGD_REF:S000080444|PMID:15640796 IPI C YDR320C-A|HSK2 gene taxon:4932 20050328 SGD
+SGD S000007604 DAD4 GO:0042729 SGD_REF:S000080444|PMID:15640796 IDA C YDR320C-A|HSK2 gene taxon:4932 20050328 SGD
+SGD S000007604 DAD4 GO:0005515 SGD_REF:S000071581|PMID:12408861 IDA F YDR320C-A|HSK2 gene taxon:4932 20030423 SGD
+SGD S000007604 DAD4 GO:0007067 SGD_REF:S000071581|PMID:12408861 IMP P YDR320C-A|HSK2 gene taxon:4932 20030423 SGD
+SGD S000007604 DAD4 GO:0030472 SGD_REF:S000080667|PMID:15664196 IPI P YDR320C-A|HSK2 gene taxon:4932 20050425 SGD
+SGD S000007604 DAD4 GO:0030472 SGD_REF:S000080444|PMID:15640796 IPI P YDR320C-A|HSK2 gene taxon:4932 20050425 SGD
+SGD S000007604 DAD4 GO:0031110 SGD_REF:S000080667|PMID:15664196 IPI P YDR320C-A|HSK2 gene taxon:4932 20050328 SGD
+SGD S000007604 DAD4 GO:0031110 SGD_REF:S000080667|PMID:15664196 IDA P YDR320C-A|HSK2 gene taxon:4932 20050328 SGD
+SGD S000004535 DAK1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C dihydroxyacetone kinase YML070W gene taxon:4932 20031028 SGD
+SGD S000004535 DAK1 GO:0004371 SGD_REF:S000072321|PMID:12401799 IDA F dihydroxyacetone kinase YML070W gene taxon:4932 20030127 SGD
+SGD S000004535 DAK1 GO:0004371 SGD_REF:S000041661|PMID:9038161 ISS F dihydroxyacetone kinase YML070W gene taxon:4932 20020927 SGD
+SGD S000004535 DAK1 GO:0006950 SGD_REF:S000072321|PMID:12401799 IMP P dihydroxyacetone kinase YML070W gene taxon:4932 20030127 SGD
+SGD S000004535 DAK1 GO:0019563 SGD_REF:S000041661|PMID:9038161 ISS P dihydroxyacetone kinase YML070W gene taxon:4932 20020927 SGD
+SGD S000001841 DAK2 GO:0008372 SGD_REF:S000069584 ND C dihydroxyacetone kinase YFL053W gene taxon:4932 20020927 SGD
+SGD S000001841 DAK2 GO:0004371 SGD_REF:S000072321|PMID:12401799 IDA F dihydroxyacetone kinase YFL053W gene taxon:4932 20030127 SGD
+SGD S000001841 DAK2 GO:0004371 SGD_REF:S000041661|PMID:9038161 ISS F dihydroxyacetone kinase YFL053W gene taxon:4932 20020927 SGD
+SGD S000001841 DAK2 GO:0006950 SGD_REF:S000072321|PMID:12401799 IMP P dihydroxyacetone kinase YFL053W gene taxon:4932 20030127 SGD
+SGD S000001841 DAK2 GO:0019563 SGD_REF:S000041661|PMID:9038161 ISS P dihydroxyacetone kinase YFL053W gene taxon:4932 20020927 SGD
+SGD S000001466 DAL1 GO:0005622 SGD_REF:S000060229|PMID:11244074 IC GO:0000256 C allantoinase YIR027C gene taxon:4932 20021122 SGD
+SGD S000001466 DAL1 GO:0004038 SGD_REF:S000040181|PMID:1803816 ISS F allantoinase YIR027C gene taxon:4932 20020927 SGD
+SGD S000001466 DAL1 GO:0004038 SGD_REF:S000040181|PMID:1803816 IMP F allantoinase YIR027C gene taxon:4932 20020927 SGD
+SGD S000001466 DAL1 GO:0000256 SGD_REF:S000040181|PMID:1803816 IGI P allantoinase YIR027C gene taxon:4932 20020927 SGD
+SGD S000001466 DAL1 GO:0000256 SGD_REF:S000040181|PMID:1803816 ISS P allantoinase YIR027C gene taxon:4932 20020927 SGD
+SGD S000001466 DAL1 GO:0000256 SGD_REF:S000040181|PMID:1803816 IMP P allantoinase YIR027C gene taxon:4932 20020927 SGD
+SGD S000001468 DAL2 GO:0008372 SGD_REF:S000069584 ND C allantoicase YIR029W|ALC1 gene taxon:4932 20020927 SGD
+SGD S000001468 DAL2 GO:0004037 SGD_REF:S000050699|PMID:1916277 ISS F allantoicase YIR029W|ALC1 gene taxon:4932 20020927 SGD
+SGD S000001468 DAL2 GO:0000256 SGD_REF:S000050699|PMID:1916277 IMP P allantoicase YIR029W|ALC1 gene taxon:4932 20020927 SGD
+SGD S000001471 DAL3 GO:0016020 SGD_REF:S000042814|PMID:1776360 ISS C ureidoglycolate hydrolase YIR032C gene taxon:4932 20020927 SGD
+SGD S000001471 DAL3 GO:0004848 SGD_REF:S000042814|PMID:1776360 TAS F ureidoglycolate hydrolase YIR032C gene taxon:4932 20020927 SGD
+SGD S000001471 DAL3 GO:0000256 SGD_REF:S000049816|PMID:3915539 TAS P ureidoglycolate hydrolase YIR032C gene taxon:4932 20020927 SGD
+SGD S000001467 DAL4 GO:0016020 SGD_REF:S000054570|PMID:1293888 ISS C allantoin permease YIR028W gene taxon:4932 20020927 SGD
+SGD S000001467 DAL4 GO:0005274 SGD_REF:S000054570|PMID:1293888 ISS F allantoin permease YIR028W gene taxon:4932 20020927 SGD
+SGD S000001467 DAL4 GO:0005274 SGD_REF:S000054570|PMID:1293888 TAS F allantoin permease YIR028W gene taxon:4932 20020927 SGD
+SGD S000001467 DAL4 GO:0015720 SGD_REF:S000045430|PMID:3028908 TAS P allantoin permease YIR028W gene taxon:4932 20020927 SGD
+SGD S000003913 DAL5 GO:0005886 SGD_REF:S000049030|PMID:3275614 ISS C allantoate permease YJR152W|UREP1 gene taxon:4932 20020919 SGD
+SGD S000003913 DAL5 GO:0005886 SGD_REF:S000049030|PMID:3275614 IMP C allantoate permease YJR152W|UREP1 gene taxon:4932 20020919 SGD
+SGD S000003913 DAL5 GO:0015124 SGD_REF:S000049030|PMID:3275614 ISS F allantoate permease YJR152W|UREP1 gene taxon:4932 20020801 SGD
+SGD S000003913 DAL5 GO:0015124 SGD_REF:S000049030|PMID:3275614 IMP F allantoate permease YJR152W|UREP1 gene taxon:4932 20020801 SGD
+SGD S000003913 DAL5 GO:0015719 SGD_REF:S000049030|PMID:3275614 IMP P allantoate permease YJR152W|UREP1 gene taxon:4932 20020801 SGD
+SGD S000001470 DAL7 GO:0008372 SGD_REF:S000069584 ND C malate synthase 2 YIR031C|MLS2|MSL2 gene taxon:4932 20051214 SGD
+SGD S000001470 DAL7 GO:0004474 SGD_REF:S000058494 TAS F malate synthase 2 YIR031C|MLS2|MSL2 gene taxon:4932 20010119 SGD
+SGD S000001470 DAL7 GO:0000256 SGD_REF:S000058494 TAS P malate synthase 2 YIR031C|MLS2|MSL2 gene taxon:4932 20010119 SGD
+SGD S000001742 DAL80 GO:0005634 SGD_REF:S000061171|PMID:11443099 IDA C GATA family transcriptional repressor YKR034W|UGA43 gene taxon:4932 20020930 SGD
+SGD S000001742 DAL80 GO:0003700 SGD_REF:S000061171|PMID:11443099 TAS F GATA family transcriptional repressor YKR034W|UGA43 gene taxon:4932 20020930 SGD
+SGD S000001742 DAL80 GO:0003700 SGD_REF:S000053664|PMID:8045902 IDA F GATA family transcriptional repressor YKR034W|UGA43 gene taxon:4932 20050117 SGD
+SGD S000001742 DAL80 GO:0006350 SGD_REF:S000061171|PMID:11443099 TAS P GATA family transcriptional repressor YKR034W|UGA43 gene taxon:4932 20020930 SGD
+SGD S000001742 DAL80 GO:0006350 SGD_REF:S000053664|PMID:8045902 IDA P GATA family transcriptional repressor YKR034W|UGA43 gene taxon:4932 20050117 SGD
+SGD S000001742 DAL80 GO:0006808 SGD_REF:S000072524|PMID:12489124 IGI P GATA family transcriptional repressor YKR034W|UGA43 gene taxon:4932 20030214 SGD
+SGD S000001742 DAL80 GO:0006808 SGD_REF:S000072524|PMID:12489124 IMP P GATA family transcriptional repressor YKR034W|UGA43 gene taxon:4932 20030214 SGD
+SGD S000001462 DAL81 GO:0005634 SGD_REF:S000055594|PMID:7899074 IC GO:0003704 C transcriptional activator for allantoin and GABA catabolic genes, contains a Zn[2]-Cys[6] fungal-type binuclear cluster domain in the N-terminal region YIR023W|UGA35 gene taxon:4932 20021111 SGD
+SGD S000001462 DAL81 GO:0003704 SGD_REF:S000055594|PMID:7899074 IMP F transcriptional activator for allantoin and GABA catabolic genes, contains a Zn[2]-Cys[6] fungal-type binuclear cluster domain in the N-terminal region YIR023W|UGA35 gene taxon:4932 20021111 SGD
+SGD S000001462 DAL81 GO:0003704 SGD_REF:S000055594|PMID:7899074 ISS F transcriptional activator for allantoin and GABA catabolic genes, contains a Zn[2]-Cys[6] fungal-type binuclear cluster domain in the N-terminal region YIR023W|UGA35 gene taxon:4932 20021111 SGD
+SGD S000001462 DAL81 GO:0006357 SGD_REF:S000055594|PMID:7899074 IMP P transcriptional activator for allantoin and GABA catabolic genes, contains a Zn[2]-Cys[6] fungal-type binuclear cluster domain in the N-terminal region YIR023W|UGA35 gene taxon:4932 20021111 SGD
+SGD S000001462 DAL81 GO:0006357 SGD_REF:S000055594|PMID:7899074 ISS P transcriptional activator for allantoin and GABA catabolic genes, contains a Zn[2]-Cys[6] fungal-type binuclear cluster domain in the N-terminal region YIR023W|UGA35 gene taxon:4932 20021111 SGD
+SGD S000001462 DAL81 GO:0019740 SGD_REF:S000055594|PMID:7899074 IMP P transcriptional activator for allantoin and GABA catabolic genes, contains a Zn[2]-Cys[6] fungal-type binuclear cluster domain in the N-terminal region YIR023W|UGA35 gene taxon:4932 20021111 SGD
+SGD S000005258 DAL82 GO:0005634 SGD_REF:S000047398|PMID:10702289 IDA C positive transcriptional regulator YNL314W gene taxon:4932 20020920 SGD
+SGD S000005258 DAL82 GO:0016563 SGD_REF:S000047398|PMID:10702289 IDA F positive transcriptional regulator YNL314W gene taxon:4932 20020920 SGD
+SGD S000005258 DAL82 GO:0000256 SGD_REF:S000044349|PMID:1898922 IMP P positive transcriptional regulator YNL314W gene taxon:4932 20020920 SGD
+SGD S000005258 DAL82 GO:0006367 SGD_REF:S000047398|PMID:10702289 IDA P positive transcriptional regulator YNL314W gene taxon:4932 20020920 SGD
+SGD S000003345 DAM1 GO:0000778 SGD_REF:S000069091|PMID:11756468 IPI C YGR113W gene taxon:4932 20021008 SGD
+SGD S000003345 DAM1 GO:0000778 SGD_REF:S000080960|PMID:11511347 IDA C YGR113W gene taxon:4932 20050307 SGD
+SGD S000003345 DAM1 GO:0005819 SGD_REF:S000069091|PMID:11756468 IPI C YGR113W gene taxon:4932 20021008 SGD
+SGD S000003345 DAM1 GO:0005828 SGD_REF:S000066223|PMID:11724818 IDA C YGR113W gene taxon:4932 20020602 SGD
+SGD S000003345 DAM1 GO:0042729 SGD_REF:S000069052|PMID:11799062 IDA C YGR113W gene taxon:4932 20040122 SGD
+SGD S000003345 DAM1 GO:0042729 SGD_REF:S000080444|PMID:15640796 IDA C YGR113W gene taxon:4932 20050328 SGD
+SGD S000003345 DAM1 GO:0042729 SGD_REF:S000069052|PMID:11799062 IPI C YGR113W gene taxon:4932 20040122 SGD
+SGD S000003345 DAM1 GO:0042729 SGD_REF:S000080444|PMID:15640796 IPI C YGR113W gene taxon:4932 20050328 SGD
+SGD S000003345 DAM1 GO:0042729 SGD_REF:S000080667|PMID:15664196 IPI C YGR113W gene taxon:4932 20050328 SGD
+SGD S000003345 DAM1 GO:0042729 SGD_REF:S000080667|PMID:15664196 IDA C YGR113W gene taxon:4932 20050328 SGD
+SGD S000003345 DAM1 GO:0051233 SGD_REF:S000078515|PMID:12566427 IDA C YGR113W gene taxon:4932 20050407 SGD
+SGD S000003345 DAM1 GO:0005200 SGD_REF:S000069091|PMID:11756468 IPI F YGR113W gene taxon:4932 20021008 SGD
+SGD S000003345 DAM1 GO:0030472 SGD_REF:S000069091|PMID:11756468 IGI P YGR113W gene taxon:4932 20021008 SGD
+SGD S000003345 DAM1 GO:0031110 SGD_REF:S000080667|PMID:15664196 IPI P YGR113W gene taxon:4932 20050328 SGD
+SGD S000003345 DAM1 GO:0031110 SGD_REF:S000080667|PMID:15664196 IDA P YGR113W gene taxon:4932 20050328 SGD
+SGD S000003911 DAN1 GO:0009277 SGD_REF:S000048008|PMID:10322008 IDA C cell wall mannoprotein, induced during anaerobic growth YJR150C|CCW13 gene taxon:4932 20020918 SGD
+SGD S000003911 DAN1 GO:0005554 SGD_REF:S000069584 ND F cell wall mannoprotein, induced during anaerobic growth YJR150C|CCW13 gene taxon:4932 20020918 SGD
+SGD S000003911 DAN1 GO:0015918 SGD_REF:S000071132|PMID:12077145 IMP P cell wall mannoprotein, induced during anaerobic growth YJR150C|CCW13 gene taxon:4932 20020918 SGD
+SGD S000004027 DAN2 GO:0009277 SGD_REF:S000060147|PMID:11292809 ISS C putative cell wall protein YLR037C gene taxon:4932 20021011 SGD
+SGD S000004027 DAN2 GO:0005554 SGD_REF:S000069584 ND F putative cell wall protein YLR037C gene taxon:4932 20021011 SGD
+SGD S000004027 DAN2 GO:0000004 SGD_REF:S000069584 ND P putative cell wall protein YLR037C gene taxon:4932 20021011 SGD
+SGD S000000505 DAN3 GO:0009277 SGD_REF:S000060147|PMID:11292809 ISS C putative cell wall protein YBR301W gene taxon:4932 20021011 SGD
+SGD S000000505 DAN3 GO:0005554 SGD_REF:S000069584 ND F putative cell wall protein YBR301W gene taxon:4932 20021011 SGD
+SGD S000000505 DAN3 GO:0000004 SGD_REF:S000069584 ND P putative cell wall protein YBR301W gene taxon:4932 20021011 SGD
+SGD S000003912 DAN4 GO:0009277 SGD_REF:S000040179|PMID:10383953 IDA C cell wall mannoprotein YJR151C gene taxon:4932 20020617 SGD
+SGD S000003912 DAN4 GO:0005554 SGD_REF:S000069584 ND F cell wall mannoprotein YJR151C gene taxon:4932 20021011 SGD
+SGD S000003912 DAN4 GO:0000004 SGD_REF:S000069584 ND P cell wall mannoprotein YJR151C gene taxon:4932 20021011 SGD
+SGD S000006091 DAP1 GO:0016020 SGD_REF:S000072913|PMID:12684380 ISS C YPL170W gene taxon:4932 20030415 SGD
+SGD S000006091 DAP1 GO:0020037 SGD_REF:S000080892|PMID:15713626 IDA F YPL170W gene taxon:4932 20050302 SGD
+SGD S000006091 DAP1 GO:0016125 SGD_REF:S000072913|PMID:12684380 IMP P YPL170W gene taxon:4932 20030415 SGD
+SGD S000006091 DAP1 GO:0016125 SGD_REF:S000080892|PMID:15713626 IMP P YPL170W gene taxon:4932 20050302 SGD
+SGD S000006091 DAP1 GO:0016125 SGD_REF:S000080892|PMID:15713626 IGI SGD:S000001049 P YPL170W gene taxon:4932 20050302 SGD
+SGD S000001070 DAP2 GO:0000329 SGD_REF:S000039425|PMID:2647766 IDA C dipeptidyl aminopeptidase B (DPAP B), dipeptidyl aminopeptidase yscV YHR028C|DPP2 gene taxon:4932 20020711 SGD
+SGD S000001070 DAP2 GO:0016806 SGD_REF:S000039425|PMID:2647766 IDA F dipeptidyl aminopeptidase B (DPAP B), dipeptidyl aminopeptidase yscV YHR028C|DPP2 gene taxon:4932 20020711 SGD
+SGD S000001070 DAP2 GO:0016485 SGD_REF:S000047644|PMID:3305478 ISS P dipeptidyl aminopeptidase B (DPAP B), dipeptidyl aminopeptidase yscV YHR028C|DPP2 gene taxon:4932 20020711 SGD
+SGD S000004581 DAT1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C datin, oligo(dA).oligo(dT)-binding protein YML113W gene taxon:4932 20031028 SGD
+SGD S000004581 DAT1 GO:0003680 SGD_REF:S000056902|PMID:2670564 IDA F datin, oligo(dA).oligo(dT)-binding protein YML113W gene taxon:4932 20020617 SGD
+SGD S000004581 DAT1 GO:0000122 SGD_REF:S000048338|PMID:8248247 IMP P datin, oligo(dA).oligo(dT)-binding protein YML113W gene taxon:4932 20020617 SGD
+SGD S000029142 DBF1 GO:0008372 SGD_REF:S000069584 ND C kinase required for late nuclear division gene taxon:4932 20020528 SGD
+SGD S000029142 DBF1 GO:0005554 SGD_REF:S000069584 ND F kinase required for late nuclear division gene taxon:4932 20020528 SGD
+SGD S000029142 DBF1 GO:0000004 SGD_REF:S000069584 ND P kinase required for late nuclear division gene taxon:4932 20020528 SGD
+SGD S000003324 DBF2 GO:0005816 SGD_REF:S000060813|PMID:11434459 IDA C Ser/Thr Kinase YGR092W gene taxon:4932 20050223 SGD
+SGD S000003324 DBF2 GO:0005816 SGD_REF:S000059285|PMID:10984431 IDA C Ser/Thr Kinase YGR092W gene taxon:4932 20050223 SGD
+SGD S000003324 DBF2 GO:0005935 SGD_REF:S000060813|PMID:11434459 IDA C Ser/Thr Kinase YGR092W gene taxon:4932 20050223 SGD
+SGD S000003324 DBF2 GO:0005935 SGD_REF:S000059285|PMID:10984431 IDA C Ser/Thr Kinase YGR092W gene taxon:4932 20050223 SGD
+SGD S000003324 DBF2 GO:0004674 SGD_REF:S000048013|PMID:8131744 IDA F Ser/Thr Kinase YGR092W gene taxon:4932 20040806 SGD
+SGD S000003324 DBF2 GO:0000280 SGD_REF:S000047050|PMID:2181271 IMP P Ser/Thr Kinase YGR092W gene taxon:4932 20030113 SGD
+SGD S000003324 DBF2 GO:0006468 SGD_REF:S000061406|PMID:11404483 IDA P Ser/Thr Kinase YGR092W gene taxon:4932 20030204 SGD
+SGD S000006315 DBF20 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C Ser/Thr Kinase YPR111W gene taxon:4932 20031028 SGD
+SGD S000006315 DBF20 GO:0004674 SGD_REF:S000048013|PMID:8131744 IDA F Ser/Thr Kinase YPR111W gene taxon:4932 20021118 SGD
+SGD S000006315 DBF20 GO:0006468 SGD_REF:S000048013|PMID:8131744 IDA P Ser/Thr Kinase YPR111W gene taxon:4932 20021118 SGD
+SGD S000006315 DBF20 GO:0007049 SGD_REF:S000048013|PMID:8131744 IGI P Ser/Thr Kinase YPR111W gene taxon:4932 20021118 SGD
+SGD S000006315 DBF20 GO:0007049 SGD_REF:S000048013|PMID:8131744 IEP P Ser/Thr Kinase YPR111W gene taxon:4932 20021118 SGD
+SGD S000002459 DBF4 GO:0005654 SGD_REF:S000058400|PMID:9914182 TAS C Cdc7p-Dbf4p kinase complex regulatory subunit YDR052C|DNA52|LSD7 gene taxon:4932 20010118 SGD
+SGD S000002459 DBF4 GO:0004674 SGD_REF:S000058275|PMID:9442876 TAS F Cdc7p-Dbf4p kinase complex regulatory subunit YDR052C|DNA52|LSD7 gene taxon:4932 20010118 SGD
+SGD S000002459 DBF4 GO:0006270 SGD_REF:S000058275|PMID:9442876 TAS P Cdc7p-Dbf4p kinase complex regulatory subunit YDR052C|DNA52|LSD7 gene taxon:4932 20010118 SGD
+SGD S000002459 DBF4 GO:0006275 SGD_REF:S000058275|PMID:9442876 TAS P Cdc7p-Dbf4p kinase complex regulatory subunit YDR052C|DNA52|LSD7 gene taxon:4932 20010118 SGD
+SGD S000002459 DBF4 GO:0006468 SGD_REF:S000058275|PMID:9442876 TAS P Cdc7p-Dbf4p kinase complex regulatory subunit YDR052C|DNA52|LSD7 gene taxon:4932 20010118 SGD
+SGD S000006040 DBP1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C ATP dependent RNA helicase (putative), dead box protein (putative) YPL119C|LPH8 gene taxon:4932 20031028 SGD
+SGD S000006040 DBP1 GO:0003724 SGD_REF:S000052382|PMID:8144024 ISS F ATP dependent RNA helicase (putative), dead box protein (putative) YPL119C|LPH8 gene taxon:4932 20021002 SGD
+SGD S000006040 DBP1 GO:0003724 SGD_REF:S000042690|PMID:1857205 ISS F ATP dependent RNA helicase (putative), dead box protein (putative) YPL119C|LPH8 gene taxon:4932 20021002 SGD
+SGD S000006040 DBP1 GO:0006397 SGD_REF:S000042690|PMID:1857205 IGI P ATP dependent RNA helicase (putative), dead box protein (putative) YPL119C|LPH8 gene taxon:4932 20021002 SGD
+SGD S000006040 DBP1 GO:0006397 SGD_REF:S000042690|PMID:1857205 ISS P ATP dependent RNA helicase (putative), dead box protein (putative) YPL119C|LPH8 gene taxon:4932 20021002 SGD
+SGD S000006040 DBP1 GO:0006413 SGD_REF:S000074893|PMID:14763975 IMP P ATP dependent RNA helicase (putative), dead box protein (putative) YPL119C|LPH8 gene taxon:4932 20040811 SGD
+SGD S000002189 DBP10 GO:0005730 SGD_REF:S000040231|PMID:10871363 IDA C YDL031W gene taxon:4932 20030922 SGD
+SGD S000002189 DBP10 GO:0004004 SGD_REF:S000058443|PMID:10690410 TAS F YDL031W gene taxon:4932 20010118 SGD
+SGD S000002189 DBP10 GO:0000027 SGD_REF:S000040231|PMID:10871363 IMP P YDL031W gene taxon:4932 20030922 SGD
+SGD S000002189 DBP10 GO:0006365 SGD_REF:S000058443|PMID:10690410 TAS P YDL031W gene taxon:4932 20010118 SGD
+SGD S000005056 DBP2 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C ATP dependent RNA helicase, dead box protein YNL112W gene taxon:4932 20031028 SGD
+SGD S000005056 DBP2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C ATP dependent RNA helicase, dead box protein YNL112W gene taxon:4932 20031028 SGD
+SGD S000005056 DBP2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C ATP dependent RNA helicase, dead box protein YNL112W gene taxon:4932 20040813 SGD
+SGD S000005056 DBP2 GO:0003724 SGD_REF:S000052928|PMID:7641698 ISS F ATP dependent RNA helicase, dead box protein YNL112W gene taxon:4932 20020930 SGD
+SGD S000005056 DBP2 GO:0000184 SGD_REF:S000042824|PMID:7883168 IPI SGD:S000004685 P ATP dependent RNA helicase, dead box protein YNL112W gene taxon:4932 20030922 SGD
+SGD S000003046 DBP3 GO:0005730 SGD_REF:S000049581|PMID:9032262 IDA C ATP dependent RNA helicase, dead/deah box protein CA3 YGL078C gene taxon:4932 20030922 SGD
+SGD S000003046 DBP3 GO:0004004 SGD_REF:S000058443|PMID:10690410 TAS F ATP dependent RNA helicase, dead/deah box protein CA3 YGL078C gene taxon:4932 20010118 SGD
+SGD S000003046 DBP3 GO:0000027 SGD_REF:S000049581|PMID:9032262 IMP P ATP dependent RNA helicase, dead/deah box protein CA3 YGL078C gene taxon:4932 20030922 SGD
+SGD S000003046 DBP3 GO:0006365 SGD_REF:S000049581|PMID:9032262 IMP P ATP dependent RNA helicase, dead/deah box protein CA3 YGL078C gene taxon:4932 20030922 SGD
+SGD S000005572 DBP5 GO:0005634 SGD_REF:S000076881|PMID:15280434 IDA C RNA helicase YOR046C|RAT8 gene taxon:4932 20050421 SGD
+SGD S000005572 DBP5 GO:0005643 SGD_REF:S000062657|PMID:10428971 IPI C RNA helicase YOR046C|RAT8 gene taxon:4932 20020930 SGD
+SGD S000005572 DBP5 GO:0005737 SGD_REF:S000054626|PMID:9564048 IDA C RNA helicase YOR046C|RAT8 gene taxon:4932 20020930 SGD
+SGD S000005572 DBP5 GO:0005737 SGD_REF:S000076881|PMID:15280434 IDA C RNA helicase YOR046C|RAT8 gene taxon:4932 20050421 SGD
+SGD S000005572 DBP5 GO:0003724 SGD_REF:S000054622|PMID:9564047 IDA F RNA helicase YOR046C|RAT8 gene taxon:4932 20020930 SGD
+SGD S000005572 DBP5 GO:0003724 SGD_REF:S000054622|PMID:9564047 ISS F RNA helicase YOR046C|RAT8 gene taxon:4932 20020930 SGD
+SGD S000005572 DBP5 GO:0006406 SGD_REF:S000054626|PMID:9564048 IGI P RNA helicase YOR046C|RAT8 gene taxon:4932 20020930 SGD
+SGD S000005572 DBP5 GO:0006406 SGD_REF:S000054626|PMID:9564048 IMP P RNA helicase YOR046C|RAT8 gene taxon:4932 20020930 SGD
+SGD S000005321 DBP6 GO:0005730 SGD_REF:S000052052|PMID:9528757 IDA C RNA helicase (putative) YNR038W gene taxon:4932 20030922 SGD
+SGD S000005321 DBP6 GO:0030687 SGD_REF:S000076168|PMID:15126390 IDA C RNA helicase (putative) YNR038W gene taxon:4932 20040526 SGD
+SGD S000005321 DBP6 GO:0004004 SGD_REF:S000058443|PMID:10690410 TAS F RNA helicase (putative) YNR038W gene taxon:4932 20010118 SGD
+SGD S000005321 DBP6 GO:0000027 SGD_REF:S000052052|PMID:9528757 IMP P RNA helicase (putative) YNR038W gene taxon:4932 20030922 SGD
+SGD S000005321 DBP6 GO:0006365 SGD_REF:S000052052|PMID:9528757 IMP P RNA helicase (putative) YNR038W gene taxon:4932 20030922 SGD
+SGD S000001732 DBP7 GO:0005730 SGD_REF:S000040523|PMID:9582098 IDA C RNA helicase (putative) YKR024C gene taxon:4932 20030922 SGD
+SGD S000001732 DBP7 GO:0004004 SGD_REF:S000058443|PMID:10690410 TAS F RNA helicase (putative) YKR024C gene taxon:4932 20010118 SGD
+SGD S000001732 DBP7 GO:0000027 SGD_REF:S000040523|PMID:9582098 IMP P RNA helicase (putative) YKR024C gene taxon:4932 20030922 SGD
+SGD S000001732 DBP7 GO:0006365 SGD_REF:S000040523|PMID:9582098 IMP P RNA helicase (putative) YKR024C gene taxon:4932 20030922 SGD
+SGD S000001212 DBP8 GO:0005730 SGD_REF:S000058443|PMID:10690410 TAS C dead box protein YHR169W gene taxon:4932 20010118 SGD
+SGD S000001212 DBP8 GO:0005730 SGD_REF:S000060313|PMID:11222764 IDA C dead box protein YHR169W gene taxon:4932 20010628 SGD
+SGD S000001212 DBP8 GO:0004004 SGD_REF:S000058443|PMID:10690410 TAS F dead box protein YHR169W gene taxon:4932 20010118 SGD
+SGD S000001212 DBP8 GO:0004004 SGD_REF:S000060313|PMID:11222764 IMP F dead box protein YHR169W gene taxon:4932 20010628 SGD
+SGD S000001212 DBP8 GO:0006365 SGD_REF:S000058443|PMID:10690410 TAS P dead box protein YHR169W gene taxon:4932 20010118 SGD
+SGD S000001212 DBP8 GO:0006365 SGD_REF:S000060313|PMID:11222764 IMP P dead box protein YHR169W gene taxon:4932 20010628 SGD
+SGD S000004266 DBP9 GO:0005730 SGD_REF:S000058443|PMID:10690410 TAS C YLR276C gene taxon:4932 20030922 SGD
+SGD S000004266 DBP9 GO:0004004 SGD_REF:S000058443|PMID:10690410 TAS F YLR276C gene taxon:4932 20010118 SGD
+SGD S000004266 DBP9 GO:0000027 SGD_REF:S000065909|PMID:11565753 IMP P YLR276C gene taxon:4932 20030922 SGD
+SGD S000004266 DBP9 GO:0006365 SGD_REF:S000058443|PMID:10690410 TAS P YLR276C gene taxon:4932 20010118 SGD
+SGD S000004266 DBP9 GO:0006365 SGD_REF:S000065909|PMID:11565753 IMP P YLR276C gene taxon:4932 20030922 SGD
+SGD S000004266 DBP9 GO:0006365 SGD_REF:S000065909|PMID:11565753 IPI SGD:S000005321 P YLR276C gene taxon:4932 20030922 SGD
+SGD S000001632 DBR1 GO:0005634 SGD_REF:S000048825|PMID:1850323 IC GO:0008419 C RNA lariat debranching enzyme YKL149C|PRP26 gene taxon:4932 20021118 SGD
+SGD S000001632 DBR1 GO:0008419 SGD_REF:S000048825|PMID:1850323 IMP F RNA lariat debranching enzyme YKL149C|PRP26 gene taxon:4932 20010529 SGD
+SGD S000001632 DBR1 GO:0008419 SGD_REF:S000048825|PMID:1850323 IDA F RNA lariat debranching enzyme YKL149C|PRP26 gene taxon:4932 20010529 SGD
+SGD S000001632 DBR1 GO:0006320 SGD_REF:S000040936|PMID:10652222 IMP P RNA lariat debranching enzyme YKL149C|PRP26 gene taxon:4932 20040519 SGD
+SGD S000001632 DBR1 GO:0006322 SGD_REF:S000040936|PMID:10652222 IMP P RNA lariat debranching enzyme YKL149C|PRP26 gene taxon:4932 20040519 SGD
+SGD S000001632 DBR1 GO:0006401 SGD_REF:S000048825|PMID:1850323 IMP P RNA lariat debranching enzyme YKL149C|PRP26 gene taxon:4932 20010529 SGD
+SGD S000001632 DBR1 GO:0006401 SGD_REF:S000048825|PMID:1850323 IDA P RNA lariat debranching enzyme YKL149C|PRP26 gene taxon:4932 20010529 SGD
+SGD S000001632 DBR1 GO:0016074 SGD_REF:S000052852|PMID:9740128 IMP P RNA lariat debranching enzyme YKL149C|PRP26 gene taxon:4932 20030508 SGD
+SGD S000000521 DCC1 GO:0005663 SGD_REF:S000060777|PMID:11389843 IPI C YCL016C gene taxon:4932 20020811 SGD
+SGD S000000521 DCC1 GO:0005554 SGD_REF:S000069584 ND F YCL016C gene taxon:4932 20020811 SGD
+SGD S000000521 DCC1 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P YCL016C gene taxon:4932 20060202 SGD
+SGD S000000521 DCC1 GO:0006974 SGD_REF:S000076175|PMID:12482937 IMP P YCL016C gene taxon:4932 20060406 SGD
+SGD S000000521 DCC1 GO:0007064 SGD_REF:S000060777|PMID:11389843 IMP P YCL016C gene taxon:4932 20040610 SGD
+SGD S000001187 DCD1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C dCMP deaminase YHR144C gene taxon:4932 20031028 SGD
+SGD S000001187 DCD1 GO:0004132 SGD_REF:S000054551|PMID:3023902 IGI F dCMP deaminase YHR144C gene taxon:4932 20020930 SGD
+SGD S000001187 DCD1 GO:0004132 SGD_REF:S000054551|PMID:3023902 ISS F dCMP deaminase YHR144C gene taxon:4932 20020930 SGD
+SGD S000001187 DCD1 GO:0004132 SGD_REF:S000054551|PMID:3023902 IMP F dCMP deaminase YHR144C gene taxon:4932 20020930 SGD
+SGD S000001187 DCD1 GO:0006220 SGD_REF:S000041785|PMID:6373725 IGI P dCMP deaminase YHR144C gene taxon:4932 20020930 SGD
+SGD S000001187 DCD1 GO:0006220 SGD_REF:S000041785|PMID:6373725 IMP P dCMP deaminase YHR144C gene taxon:4932 20020930 SGD
+SGD S000001469 DCG1 GO:0008372 SGD_REF:S000069584 ND C YIR030C gene taxon:4932 20021011 SGD
+SGD S000001469 DCG1 GO:0005554 SGD_REF:S000069584 ND F YIR030C gene taxon:4932 20021011 SGD
+SGD S000001469 DCG1 GO:0006807 SGD_REF:S000050699|PMID:1916277 IEP P YIR030C gene taxon:4932 20021011 SGD
+SGD S000005706 DCI1 GO:0005782 SGD_REF:S000050692|PMID:10381339 IDA C delta(3,5)-delta(2,4)-dienoyl-CoA isomerase YOR180C|ECI2 gene taxon:4932 20010118 SGD
+SGD S000005706 DCI1 GO:0004165 SGD_REF:S000051780|PMID:10455114 IDA F delta(3,5)-delta(2,4)-dienoyl-CoA isomerase YOR180C|ECI2 gene taxon:4932 20010118 SGD
+SGD S000005706 DCI1 GO:0006635 SGD_REF:S000051780|PMID:10455114 TAS P delta(3,5)-delta(2,4)-dienoyl-CoA isomerase YOR180C|ECI2 gene taxon:4932 20010118 SGD
+SGD S000004118 DCN1 GO:0008372 SGD_REF:S000069584 ND C YLR128W gene taxon:4932 20050705 SGD
+SGD S000004118 DCN1 GO:0008047 SGD_REF:S000082188|PMID:15988528 IMP F YLR128W gene taxon:4932 20050706 SGD
+SGD S000004118 DCN1 GO:0045116 SGD_REF:S000082188|PMID:15988528 IDA P YLR128W gene taxon:4932 20050705 SGD
+SGD S000004118 DCN1 GO:0045116 SGD_REF:S000082188|PMID:15988528 IMP P YLR128W gene taxon:4932 20050705 SGD
+SGD S000004118 DCN1 GO:0051443 SGD_REF:S000082188|PMID:15988528 IMP P YLR128W gene taxon:4932 20050706 SGD
+SGD S000004118 DCN1 GO:0051443 SGD_REF:S000082188|PMID:15988528 IPI SGD:S000002290 P YLR128W gene taxon:4932 20050706 SGD
+SGD S000005509 DCP1 GO:0000932 SGD_REF:S000073211|PMID:12730603 IDA C YOL149W gene taxon:4932 20030718 SGD
+SGD S000005509 DCP1 GO:0000932 SGD_REF:S000073211|PMID:12730603 IMP C YOL149W gene taxon:4932 20030718 SGD
+SGD S000005509 DCP1 GO:0003729 SGD_REF:S000059255|PMID:11139489 IPI F YOL149W gene taxon:4932 20021003 SGD
+SGD S000005509 DCP1 GO:0008047 SGD_REF:S000113839|PMID:16341225 IDA F YOL149W gene taxon:4932 20060123 SGD
+SGD S000005509 DCP1 contributes_to GO:0050072 SGD_REF:S000113839|PMID:16341225 IDA F YOL149W gene taxon:4932 20060123 SGD
+SGD S000005509 DCP1 GO:0000290 SGD_REF:S000059255|PMID:11139489 IDA P YOL149W gene taxon:4932 20021003 SGD
+SGD S000005509 DCP1 GO:0006402 SGD_REF:S000058753|PMID:9841679 TAS P YOL149W gene taxon:4932 20010124 SGD
+SGD S000005062 DCP2 GO:0000932 SGD_REF:S000073211|PMID:12730603 IDA C YNL118C|PSU1 gene taxon:4932 20030718 SGD
+SGD S000005062 DCP2 GO:0005634 SGD_REF:S000069459|PMID:11914276 IDA C YNL118C|PSU1 gene taxon:4932 20020507 SGD
+SGD S000005062 DCP2 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YNL118C|PSU1 gene taxon:4932 20020507 SGD
+SGD S000005062 DCP2 GO:0003729 SGD_REF:S000059255|PMID:11139489 IPI F YNL118C|PSU1 gene taxon:4932 20021003 SGD
+SGD S000005062 DCP2 GO:0016787 SGD_REF:S000073817|PMID:12486012 IDA F YNL118C|PSU1 gene taxon:4932 20030818 SGD
+SGD S000005062 DCP2 GO:0050072 SGD_REF:S000113839|PMID:16341225 IDA F YNL118C|PSU1 gene taxon:4932 20060123 SGD
+SGD S000005062 DCP2 GO:0000290 SGD_REF:S000059255|PMID:11139489 IDA P YNL118C|PSU1 gene taxon:4932 20021003 SGD
+SGD S000005062 DCP2 GO:0000290 SGD_REF:S000045655|PMID:10508173 IDA P YNL118C|PSU1 gene taxon:4932 20030310 SGD
+SGD S000005062 DCP2 GO:0000290 SGD_REF:S000045655|PMID:10508173 IMP P YNL118C|PSU1 gene taxon:4932 20030310 SGD
+SGD S000005062 DCP2 GO:0006402 SGD_REF:S000058753|PMID:9841679 TAS P YNL118C|PSU1 gene taxon:4932 20010124 SGD
+SGD S000005062 DCP2 GO:0031087 SGD_REF:S000076605|PMID:15225544 IMP P YNL118C|PSU1 gene taxon:4932 20050103 SGD
+SGD S000004353 DCR2 GO:0008372 SGD_REF:S000069584 ND C YLR361C gene taxon:4932 20021121 SGD
+SGD S000004353 DCR2 GO:0016788 SGD_REF:S000079972|PMID:15590836 IMP F YLR361C gene taxon:4932 20050810 SGD
+SGD S000004353 DCR2 GO:0016788 SGD_REF:S000079972|PMID:15590836 ISS F YLR361C gene taxon:4932 20050810 SGD
+SGD S000004353 DCR2 GO:0007089 SGD_REF:S000079972|PMID:15590836 IMP P YLR361C gene taxon:4932 20050810 SGD
+SGD S000004260 DCS1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YLR270W|DcpS gene taxon:4932 20031028 SGD
+SGD S000004260 DCS1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YLR270W|DcpS gene taxon:4932 20031028 SGD
+SGD S000004260 DCS1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YLR270W|DcpS gene taxon:4932 20040928 SGD
+SGD S000004260 DCS1 GO:0016818 SGD_REF:S000071470|PMID:12198172 IDA F YLR270W|DcpS gene taxon:4932 20021017 SGD
+SGD S000004260 DCS1 GO:0016818 SGD_REF:S000071470|PMID:12198172 IMP F YLR270W|DcpS gene taxon:4932 20021017 SGD
+SGD S000004260 DCS1 GO:0016818 SGD_REF:S000071470|PMID:12198172 ISS F YLR270W|DcpS gene taxon:4932 20021017 SGD
+SGD S000004260 DCS1 GO:0000290 SGD_REF:S000071470|PMID:12198172 IDA P YLR270W|DcpS gene taxon:4932 20021016 SGD
+SGD S000004260 DCS1 GO:0000290 SGD_REF:S000071470|PMID:12198172 ISS P YLR270W|DcpS gene taxon:4932 20021016 SGD
+SGD S000004260 DCS1 GO:0000290 SGD_REF:S000071470|PMID:12198172 IMP P YLR270W|DcpS gene taxon:4932 20021016 SGD
+SGD S000005699 DCS2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YOR173W gene taxon:4932 20031028 SGD
+SGD S000005699 DCS2 GO:0005554 SGD_REF:S000069584 ND F YOR173W gene taxon:4932 20021004 SGD
+SGD S000005699 DCS2 GO:0000004 SGD_REF:S000069584 ND P YOR173W gene taxon:4932 20021004 SGD
+SGD S000001529 DCW1 GO:0005624 SGD_REF:S000071815|PMID:12421307 IDA C YKL046C gene taxon:4932 20021209 SGD
+SGD S000001529 DCW1 GO:0046658 SGD_REF:S000071815|PMID:12421307 IDA C YKL046C gene taxon:4932 20021209 SGD
+SGD S000001529 DCW1 GO:0015923 SGD_REF:S000071815|PMID:12421307 ISS protein_id:AB024331 F YKL046C gene taxon:4932 20051012 SGD
+SGD S000001529 DCW1 GO:0007117 SGD_REF:S000077534|PMID:15470258 IGI SGD:S000004851 P YKL046C gene taxon:4932 20051012 SGD
+SGD S000001529 DCW1 GO:0009272 SGD_REF:S000071815|PMID:12421307 IDA P YKL046C gene taxon:4932 20021209 SGD
+SGD S000006115 DDC1 GO:0000794 SGD_REF:S000069127|PMID:11825877 IDA C YPL194W gene taxon:4932 20030403 SGD
+SGD S000006115 DDC1 GO:0005554 SGD_REF:S000069584 ND F YPL194W gene taxon:4932 20020920 SGD
+SGD S000006115 DDC1 GO:0000075 SGD_REF:S000069127|PMID:11825877 IMP P YPL194W gene taxon:4932 20020920 SGD
+SGD S000006115 DDC1 GO:0007126 SGD_REF:S000069127|PMID:11825877 IMP P YPL194W gene taxon:4932 20030403 SGD
+SGD S000000945 DDI1 GO:0005886 SGD_REF:S000048628|PMID:10330187 IDA C YER143W|VSM1 gene taxon:4932 20021007 SGD
+SGD S000000945 DDI1 GO:0000149 SGD_REF:S000048628|PMID:10330187 IDA F YER143W|VSM1 gene taxon:4932 20021007 SGD
+SGD S000000945 DDI1 GO:0006511 SGD_REF:S000070040|PMID:12051757 IMP P YER143W|VSM1 gene taxon:4932 20021007 SGD
+SGD S000000945 DDI1 GO:0016192 SGD_REF:S000048628|PMID:10330187 IGI P YER143W|VSM1 gene taxon:4932 20021007 SGD
+SGD S000000945 DDI1 GO:0016192 SGD_REF:S000048628|PMID:10330187 IMP P YER143W|VSM1 gene taxon:4932 20021007 SGD
+SGD S000001833 DDI2 GO:0008372 SGD_REF:S000069584 ND C YFL061W gene taxon:4932 20021223 SGD
+SGD S000001833 DDI2 GO:0005554 SGD_REF:S000069584 ND F YFL061W gene taxon:4932 20021223 SGD
+SGD S000001833 DDI2 GO:0000004 SGD_REF:S000069584 ND P YFL061W gene taxon:4932 20021223 SGD
+SGD S000005279 DDI3 GO:0008372 SGD_REF:S000069584 ND C YNL335W gene taxon:4932 20030203 SGD
+SGD S000005279 DDI3 GO:0005554 SGD_REF:S000069584 ND F YNL335W gene taxon:4932 20030203 SGD
+SGD S000005279 DDI3 GO:0000004 SGD_REF:S000069584 ND P YNL335W gene taxon:4932 20030203 SGD
+SGD S000005689 DDP1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C diadenosine and diphosphoinositol polyphosphate phosphohydrolase YOR163W gene taxon:4932 20031028 SGD
+SGD S000005689 DDP1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C diadenosine and diphosphoinositol polyphosphate phosphohydrolase YOR163W gene taxon:4932 20031028 SGD
+SGD S000005689 DDP1 GO:0008486 SGD_REF:S000046998|PMID:10419486 IDA F diadenosine and diphosphoinositol polyphosphate phosphohydrolase YOR163W gene taxon:4932 20020529 SGD
+SGD S000005689 DDP1 GO:0015959 SGD_REF:S000039733|PMID:10085096 IDA P diadenosine and diphosphoinositol polyphosphate phosphohydrolase YOR163W gene taxon:4932 20020529 SGD
+SGD S000005413 DDR2 GO:0000324 SGD_REF:S000074185|PMID:14562095 IDA C YOL052C-A|DDRA2|YOL053C-A gene taxon:4932 20031028 SGD
+SGD S000005413 DDR2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YOL052C-A|DDRA2|YOL053C-A gene taxon:4932 20031028 SGD
+SGD S000005413 DDR2 GO:0005554 SGD_REF:S000069584 ND F YOL052C-A|DDRA2|YOL053C-A gene taxon:4932 20031028 SGD
+SGD S000005413 DDR2 GO:0006950 SGD_REF:S000053119|PMID:9473471 IDA P YOL052C-A|DDRA2|YOL053C-A gene taxon:4932 20010118 SGD
+SGD S000004784 DDR48 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C flocculent specific protein YMR173W|FSP gene taxon:4932 20031028 SGD
+SGD S000004784 DDR48 GO:0003924 SGD_REF:S000056059|PMID:8444852 IDA F flocculent specific protein YMR173W|FSP gene taxon:4932 20040419 SGD
+SGD S000004784 DDR48 GO:0016887 SGD_REF:S000056059|PMID:8444852 IDA F flocculent specific protein YMR173W|FSP gene taxon:4932 20040419 SGD
+SGD S000004784 DDR48 GO:0006281 SGD_REF:S000042288|PMID:2111448 IMP P flocculent specific protein YMR173W|FSP gene taxon:4932 20010118 SGD
+SGD S000004784 DDR48 GO:0006281 SGD_REF:S000042288|PMID:2111448 IDA P flocculent specific protein YMR173W|FSP gene taxon:4932 20010118 SGD
+SGD S000005730 DED1 GO:0005737 SGD_REF:S000042785|PMID:9045610 IC GO:0006413 C YOR204W|SPP81 gene taxon:4932 20021112 SGD
+SGD S000005730 DED1 GO:0003724 SGD_REF:S000048410|PMID:10364207 IDA F YOR204W|SPP81 gene taxon:4932 20021112 SGD
+SGD S000005730 DED1 GO:0006413 SGD_REF:S000042785|PMID:9045610 IMP P YOR204W|SPP81 gene taxon:4932 20021112 SGD
+SGD S000005730 DED1 GO:0006413 SGD_REF:S000074893|PMID:14763975 IMP P YOR204W|SPP81 gene taxon:4932 20040811 SGD
+SGD S000001061 DED81 GO:0005737 SGD_REF:S000044548|PMID:9605503 TAS C asparaginyl-tRNA synthetase YHR019C gene taxon:4932 20020930 SGD
+SGD S000001061 DED81 GO:0004816 SGD_REF:S000044548|PMID:9605503 IDA F asparaginyl-tRNA synthetase YHR019C gene taxon:4932 20020930 SGD
+SGD S000001061 DED81 GO:0004816 SGD_REF:S000044548|PMID:9605503 ISS F asparaginyl-tRNA synthetase YHR019C gene taxon:4932 20020930 SGD
+SGD S000001061 DED81 GO:0005524 SGD_REF:S000044548|PMID:9605503 TAS F asparaginyl-tRNA synthetase YHR019C gene taxon:4932 20020930 SGD
+SGD S000001061 DED81 GO:0006421 SGD_REF:S000044548|PMID:9605503 IDA P asparaginyl-tRNA synthetase YHR019C gene taxon:4932 20020930 SGD
+SGD S000001061 DED81 GO:0006421 SGD_REF:S000044548|PMID:9605503 ISS P asparaginyl-tRNA synthetase YHR019C gene taxon:4932 20020930 SGD
+SGD S000001061 DED81 GO:0006421 SGD_REF:S000044548|PMID:9605503 IGI P asparaginyl-tRNA synthetase YHR019C gene taxon:4932 20020930 SGD
+SGD S000001537 DEF1 GO:0005634 SGD_REF:S000069590|PMID:11859374 IMP C Rad26-interacting protein YKL054C|VID31 gene taxon:4932 20020716 SGD
+SGD S000001537 DEF1 GO:0005554 SGD_REF:S000069584 ND F Rad26-interacting protein YKL054C|VID31 gene taxon:4932 20020716 SGD
+SGD S000001537 DEF1 GO:0000723 SGD_REF:S000081940|PMID:15863512 IMP P Rad26-interacting protein YKL054C|VID31 gene taxon:4932 20050714 SGD
+SGD S000001537 DEF1 GO:0006511 SGD_REF:S000069590|PMID:11859374 IDA P Rad26-interacting protein YKL054C|VID31 gene taxon:4932 20020719 SGD
+SGD S000001537 DEF1 GO:0006511 SGD_REF:S000069590|PMID:11859374 IMP P Rad26-interacting protein YKL054C|VID31 gene taxon:4932 20020719 SGD
+SGD S000001537 DEF1 GO:0006974 SGD_REF:S000069590|PMID:11859374 IMP P Rad26-interacting protein YKL054C|VID31 gene taxon:4932 20020716 SGD
+SGD S000001895 DEG1 GO:0005634 SGD_REF:S000053287|PMID:9430663 IDA C YFL001W|PUS3 gene taxon:4932 20010118 SGD
+SGD S000001895 DEG1 GO:0005737 SGD_REF:S000053287|PMID:9430663 IDA C YFL001W|PUS3 gene taxon:4932 20010118 SGD
+SGD S000001895 DEG1 GO:0004730 SGD_REF:S000053287|PMID:9430663 IDA F YFL001W|PUS3 gene taxon:4932 20010118 SGD
+SGD S000001895 DEG1 GO:0004730 SGD_REF:S000053287|PMID:9430663 IMP F YFL001W|PUS3 gene taxon:4932 20010118 SGD
+SGD S000001895 DEG1 GO:0006396 SGD_REF:S000053287|PMID:9430663 IDA P YFL001W|PUS3 gene taxon:4932 20010118 SGD
+SGD S000000367 DEM1 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YBR163W gene taxon:4932 20031028 SGD
+SGD S000000367 DEM1 GO:0005554 SGD_REF:S000069584 ND F YBR163W gene taxon:4932 20010215 SGD
+SGD S000000367 DEM1 GO:0000004 SGD_REF:S000069584 ND P YBR163W gene taxon:4932 20010215 SGD
+SGD S000000011 DEP1 GO:0005634 SGD_REF:S000055164|PMID:8056324 IC GO:0006357 C YAL013W|FUN54 gene taxon:4932 20060209 SGD
+SGD S000000011 DEP1 GO:0030528 SGD_REF:S000055164|PMID:8056324 IMP F YAL013W|FUN54 gene taxon:4932 20060209 SGD
+SGD S000000011 DEP1 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P YAL013W|FUN54 gene taxon:4932 20060203 SGD
+SGD S000000011 DEP1 GO:0006357 SGD_REF:S000055164|PMID:8056324 IMP P YAL013W|FUN54 gene taxon:4932 20021101 SGD
+SGD S000000011 DEP1 GO:0006644 SGD_REF:S000055164|PMID:8056324 IMP P YAL013W|FUN54 gene taxon:4932 20021101 SGD
+SGD S000000405 DER1 GO:0005789 SGD_REF:S000055370|PMID:8631297 IDA C YBR201W gene taxon:4932 20011213 SGD
+SGD S000000405 DER1 GO:0005554 SGD_REF:S000069584 ND F YBR201W gene taxon:4932 20021209 SGD
+SGD S000000405 DER1 GO:0030433 SGD_REF:S000055370|PMID:8631297 IMP P YBR201W gene taxon:4932 20011214 SGD
+SGD S000001311 DFG10 GO:0008372 SGD_REF:S000069584 ND C YIL049W gene taxon:4932 20020927 SGD
+SGD S000001311 DFG10 GO:0005554 SGD_REF:S000069584 ND F YIL049W gene taxon:4932 20020927 SGD
+SGD S000001311 DFG10 GO:0007124 SGD_REF:S000042772|PMID:9055077 IMP P YIL049W gene taxon:4932 20020927 SGD
+SGD S000005556 DFG16 GO:0008372 SGD_REF:S000069584 ND C YOR030W|ECM41|ZRG11 gene taxon:4932 20050606 SGD
+SGD S000005556 DFG16 GO:0005554 SGD_REF:S000069584 ND F YOR030W|ECM41|ZRG11 gene taxon:4932 20050606 SGD
+SGD S000005556 DFG16 GO:0001403 SGD_REF:S000042772|PMID:9055077 IMP P YOR030W|ECM41|ZRG11 gene taxon:4932 20021101 SGD
+SGD S000005556 DFG16 GO:0016485 SGD_REF:S000081820|PMID:15879523 IMP P YOR030W|ECM41|ZRG11 gene taxon:4932 20050606 SGD
+SGD S000004851 DFG5 GO:0046658 SGD_REF:S000071815|PMID:12421307 IDA C YMR238W gene taxon:4932 20021209 SGD
+SGD S000004851 DFG5 GO:0015923 SGD_REF:S000071815|PMID:12421307 ISS protein_id:AB024331 F YMR238W gene taxon:4932 20051012 SGD
+SGD S000004851 DFG5 GO:0007117 SGD_REF:S000077534|PMID:15470258 IGI SGD:S000001529 P YMR238W gene taxon:4932 20051012 SGD
+SGD S000004851 DFG5 GO:0007124 SGD_REF:S000042772|PMID:9055077 IMP P YMR238W gene taxon:4932 20021003 SGD
+SGD S000004851 DFG5 GO:0009272 SGD_REF:S000071815|PMID:12421307 IDA P YMR238W gene taxon:4932 20021209 SGD
+SGD S000002819 DFM1 GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YDR411C gene taxon:4932 20031028 SGD
+SGD S000002819 DFM1 GO:0005783 SGD_REF:S000076178|PMID:15093775 IDA C YDR411C gene taxon:4932 20050607 SGD
+SGD S000002819 DFM1 GO:0005554 SGD_REF:S000069584 ND F YDR411C gene taxon:4932 20030203 SGD
+SGD S000002819 DFM1 GO:0000004 SGD_REF:S000069584 ND P YDR411C gene taxon:4932 20030203 SGD
+SGD S000002819 DFM1 NOT GO:0030433 SGD_REF:S000076178|PMID:15093775 IMP P YDR411C gene taxon:4932 20050607 SGD
+SGD S000005762 DFR1 GO:0005829 SGD_REF:S000044176|PMID:7913473 TAS C dihydrofolate reductase YOR236W gene taxon:4932 20020927 SGD
+SGD S000005762 DFR1 GO:0004146 SGD_REF:S000044368|PMID:1427091 IMP F dihydrofolate reductase YOR236W gene taxon:4932 20020927 SGD
+SGD S000005762 DFR1 GO:0006760 SGD_REF:S000044368|PMID:1427091 IMP P dihydrofolate reductase YOR236W gene taxon:4932 20020927 SGD
+SGD S000005771 DGA1 GO:0005811 SGD_REF:S000069030|PMID:11751830 IDA C Acyl-CoA : diacylglycerol acyltransferase YOR245C gene taxon:4932 20020816 SGD
+SGD S000005771 DGA1 GO:0004144 SGD_REF:S000069030|PMID:11751830 ISS F Acyl-CoA : diacylglycerol acyltransferase YOR245C gene taxon:4932 20020816 SGD
+SGD S000005771 DGA1 GO:0004144 SGD_REF:S000069030|PMID:11751830 IMP F Acyl-CoA : diacylglycerol acyltransferase YOR245C gene taxon:4932 20020816 SGD
+SGD S000005771 DGA1 GO:0019432 SGD_REF:S000069030|PMID:11751830 IDA P Acyl-CoA : diacylglycerol acyltransferase YOR245C gene taxon:4932 20020816 SGD
+SGD S000005771 DGA1 GO:0019432 SGD_REF:S000069030|PMID:11751830 IMP P Acyl-CoA : diacylglycerol acyltransferase YOR245C gene taxon:4932 20020816 SGD
+SGD S000005771 DGA1 GO:0019915 SGD_REF:S000069030|PMID:11751830 IMP P Acyl-CoA : diacylglycerol acyltransferase YOR245C gene taxon:4932 20020816 SGD
+SGD S000002319 DHH1 GO:0000932 SGD_REF:S000073211|PMID:12730603 IDA C YDL160C gene taxon:4932 20030718 SGD
+SGD S000002319 DHH1 GO:0005737 SGD_REF:S000069919|PMID:12032091 IDA C YDL160C gene taxon:4932 20020906 SGD
+SGD S000002319 DHH1 GO:0003724 SGD_REF:S000057782|PMID:8511971 ISS F YDL160C gene taxon:4932 20050806 SGD
+SGD S000002319 DHH1 GO:0005515 SGD_REF:S000069111|PMID:11780629 IPI SGD:S000000673|SGD:S000003660|SGD:S000005509 F YDL160C gene taxon:4932 20021108 SGD
+SGD S000002319 DHH1 NOT GO:0000184 SGD_REF:S000069111|PMID:11780629 IMP P YDL160C gene taxon:4932 20020906 SGD
+SGD S000002319 DHH1 GO:0000290 SGD_REF:S000069111|PMID:11780629 IMP P YDL160C gene taxon:4932 20020906 SGD
+SGD S000001561 DHR2 GO:0005730 SGD_REF:S000062679|PMID:10982841 IDA C Required for 18S ribosomal RNA synthesis YKL078W gene taxon:4932 20020319 SGD
+SGD S000001561 DHR2 GO:0003724 SGD_REF:S000062679|PMID:10982841 IDA F Required for 18S ribosomal RNA synthesis YKL078W gene taxon:4932 20020319 SGD
+SGD S000001561 DHR2 GO:0007046 SGD_REF:S000062679|PMID:10982841 IDA P Required for 18S ribosomal RNA synthesis YKL078W gene taxon:4932 20020319 SGD
+SGD S000001561 DHR2 GO:0007046 SGD_REF:S000062679|PMID:10982841 TAS P Required for 18S ribosomal RNA synthesis YKL078W gene taxon:4932 20020319 SGD
+SGD S000004935 DIA1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YMR316W gene taxon:4932 20020507 SGD
+SGD S000004935 DIA1 GO:0005554 SGD_REF:S000069584 ND F YMR316W gene taxon:4932 20021209 SGD
+SGD S000004935 DIA1 GO:0001403 SGD_REF:S000059438|PMID:11063681 IGI P YMR316W gene taxon:4932 20010206 SGD
+SGD S000004935 DIA1 GO:0007124 SGD_REF:S000059438|PMID:11063681 IMP P YMR316W gene taxon:4932 20010206 SGD
+SGD S000005606 DIA2 GO:0019005 SGD_REF:S000075480|PMID:14747994 IDA C YOR080W|YOR29-31 gene taxon:4932 20050218 SGD
+SGD S000005606 DIA2 GO:0019005 SGD_REF:S000114165|PMID:16421250 IPI C YOR080W|YOR29-31 gene taxon:4932 20060123 SGD
+SGD S000005606 DIA2 GO:0003688 SGD_REF:S000114165|PMID:16421250 IPI F YOR080W|YOR29-31 gene taxon:4932 20060123 SGD
+SGD S000005606 DIA2 GO:0001403 SGD_REF:S000059438|PMID:11063681 IGI P YOR080W|YOR29-31 gene taxon:4932 20010206 SGD
+SGD S000005606 DIA2 GO:0006260 SGD_REF:S000114165|PMID:16421250 IMP P YOR080W|YOR29-31 gene taxon:4932 20060123 SGD
+SGD S000005606 DIA2 GO:0016567 SGD_REF:S000080086|PMID:15620357 IMP P YOR080W|YOR29-31 gene taxon:4932 20050218 SGD
+SGD S000002182 DIA3 GO:0009277 SGD_REF:S000075303|PMID:11935221 IDA C YDL024C gene taxon:4932 20040114 SGD
+SGD S000002182 DIA3 GO:0003993 SGD_REF:S000059438|PMID:11063681 ISS F YDL024C gene taxon:4932 20010206 SGD
+SGD S000002182 DIA3 GO:0001403 SGD_REF:S000059438|PMID:11063681 IGI P YDL024C gene taxon:4932 20010206 SGD
+SGD S000002182 DIA3 GO:0007124 SGD_REF:S000059438|PMID:11063681 IMP P YDL024C gene taxon:4932 20010206 SGD
+SGD S000001053 DIA4 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YHR011W gene taxon:4932 20031028 SGD
+SGD S000001053 DIA4 GO:0005739 SGD_REF:S000075186|PMID:11747308 IGI C YHR011W gene taxon:4932 20031222 SGD
+SGD S000001053 DIA4 GO:0005739 SGD_REF:S000075186|PMID:11747308 IMP C YHR011W gene taxon:4932 20031222 SGD
+SGD S000001053 DIA4 GO:0004828 SGD_REF:S000059438|PMID:11063681 ISS F YHR011W gene taxon:4932 20010206 SGD
+SGD S000001053 DIA4 GO:0004828 SGD_REF:S000075186|PMID:11747308 IGI F YHR011W gene taxon:4932 20031222 SGD
+SGD S000001053 DIA4 GO:0004828 SGD_REF:S000075186|PMID:11747308 IMP F YHR011W gene taxon:4932 20031222 SGD
+SGD S000001053 DIA4 GO:0001403 SGD_REF:S000059438|PMID:11063681 IGI P YHR011W gene taxon:4932 20010206 SGD
+SGD S000001053 DIA4 GO:0006434 SGD_REF:S000075186|PMID:11747308 IGI P YHR011W gene taxon:4932 20031222 SGD
+SGD S000001053 DIA4 GO:0007124 SGD_REF:S000059438|PMID:11063681 IMP P YHR011W gene taxon:4932 20010206 SGD
+SGD S000001053 DIA4 GO:0009060 SGD_REF:S000060148|PMID:10929718 IMP P YHR011W gene taxon:4932 20020806 SGD
+SGD S000001053 DIA4 GO:0009060 SGD_REF:S000060148|PMID:10929718 IEP P YHR011W gene taxon:4932 20020806 SGD
+SGD S000006286 DIB1 GO:0005682 SGD_REF:S000066234|PMID:11720284 IPI C 17 kDa U4/U6.U5 associated protein YPR082C|SNU16 gene taxon:4932 20051003 SGD
+SGD S000006286 DIB1 GO:0046540 SGD_REF:S000056376|PMID:10377396 IPI C 17 kDa U4/U6.U5 associated protein YPR082C|SNU16 gene taxon:4932 20050219 SGD
+SGD S000006286 DIB1 GO:0046540 SGD_REF:S000039461|PMID:10449419 IDA C 17 kDa U4/U6.U5 associated protein YPR082C|SNU16 gene taxon:4932 20050926 SGD
+SGD S000006286 DIB1 contributes_to GO:0031202 SGD_REF:S000056376|PMID:10377396 IPI F 17 kDa U4/U6.U5 associated protein YPR082C|SNU16 gene taxon:4932 20020620 SGD
+SGD S000006286 DIB1 contributes_to GO:0031202 SGD_REF:S000039461|PMID:10449419 IDA F 17 kDa U4/U6.U5 associated protein YPR082C|SNU16 gene taxon:4932 20051003 SGD
+SGD S000006286 DIB1 GO:0000398 SGD_REF:S000044581|PMID:10610776 IMP P 17 kDa U4/U6.U5 associated protein YPR082C|SNU16 gene taxon:4932 20030129 SGD
+SGD S000006286 DIB1 GO:0000398 SGD_REF:S000056376|PMID:10377396 IPI P 17 kDa U4/U6.U5 associated protein YPR082C|SNU16 gene taxon:4932 20020620 SGD
+SGD S000006286 DIB1 GO:0000398 SGD_REF:S000066234|PMID:11720284 IMP P 17 kDa U4/U6.U5 associated protein YPR082C|SNU16 gene taxon:4932 20051004 SGD
+SGD S000004340 DIC1 GO:0005740 SGD_REF:S000058029|PMID:9020177 ISS C dicarboxylate transport protein YLR348C gene taxon:4932 20010118 SGD
+SGD S000004340 DIC1 GO:0005740 SGD_REF:S000061777|PMID:9559855 ISS C dicarboxylate transport protein YLR348C gene taxon:4932 20040209 SGD
+SGD S000004340 DIC1 GO:0005740 SGD_REF:S000081426|PMID:15591051 IDA C dicarboxylate transport protein YLR348C gene taxon:4932 20050427 SGD
+SGD S000004340 DIC1 GO:0005310 SGD_REF:S000058029|PMID:9020177 ISS F dicarboxylate transport protein YLR348C gene taxon:4932 20010118 SGD
+SGD S000004340 DIC1 GO:0005310 SGD_REF:S000058029|PMID:9020177 IDA F dicarboxylate transport protein YLR348C gene taxon:4932 20010118 SGD
+SGD S000004340 DIC1 GO:0005310 SGD_REF:S000061777|PMID:9559855 IDA F dicarboxylate transport protein YLR348C gene taxon:4932 20040209 SGD
+SGD S000004340 DIC1 GO:0006835 SGD_REF:S000058029|PMID:9020177 IDA P dicarboxylate transport protein YLR348C gene taxon:4932 20010213 SGD
+SGD S000004340 DIC1 GO:0006835 SGD_REF:S000061777|PMID:9559855 IDA P dicarboxylate transport protein YLR348C gene taxon:4932 20040209 SGD
+SGD S000004340 DIC1 GO:0006835 SGD_REF:S000058029|PMID:9020177 ISS P dicarboxylate transport protein YLR348C gene taxon:4932 20010213 SGD
+SGD S000006435 DID2 GO:0005737 SGD_REF:S000059113|PMID:11029042 IDA C class E vacuolar-protein sorting and endocytosis factor YKR035W-A|CHM1|FTI1|VPS46 gene taxon:4932 20020528 SGD
+SGD S000006435 DID2 GO:0005770 SGD_REF:S000059113|PMID:11029042 IDA C class E vacuolar-protein sorting and endocytosis factor YKR035W-A|CHM1|FTI1|VPS46 gene taxon:4932 20050126 SGD
+SGD S000006435 DID2 GO:0005554 SGD_REF:S000069584 ND F class E vacuolar-protein sorting and endocytosis factor YKR035W-A|CHM1|FTI1|VPS46 gene taxon:4932 20050126 SGD
+SGD S000006435 DID2 GO:0006623 SGD_REF:S000059113|PMID:11029042 IMP P class E vacuolar-protein sorting and endocytosis factor YKR035W-A|CHM1|FTI1|VPS46 gene taxon:4932 20020528 SGD
+SGD S000006435 DID2 GO:0045324 SGD_REF:S000071351|PMID:12194857 IMP P class E vacuolar-protein sorting and endocytosis factor YKR035W-A|CHM1|FTI1|VPS46 gene taxon:4932 20050125 SGD
+SGD S000001485 DID4 GO:0000815 SGD_REF:S000071351|PMID:12194857 IDA C class E vacuolar-protein sorting and endocytosis factor YKL002W|CHM2|GRD7|REN1|VPL2|VPS2|VPT14 gene taxon:4932 20040701 SGD
+SGD S000001485 DID4 GO:0005737 SGD_REF:S000071351|PMID:12194857 IDA C class E vacuolar-protein sorting and endocytosis factor YKL002W|CHM2|GRD7|REN1|VPL2|VPS2|VPT14 gene taxon:4932 20021021 SGD
+SGD S000001485 DID4 GO:0005515 SGD_REF:S000071351|PMID:12194857 TAS F class E vacuolar-protein sorting and endocytosis factor YKL002W|CHM2|GRD7|REN1|VPL2|VPS2|VPT14 gene taxon:4932 20021029 SGD
+SGD S000001485 DID4 GO:0043162 SGD_REF:S000075969|PMID:15086794 IC GO:0000815 P class E vacuolar-protein sorting and endocytosis factor YKL002W|CHM2|GRD7|REN1|VPL2|VPS2|VPT14 gene taxon:4932 20050125 SGD
+SGD S000001485 DID4 GO:0045053 SGD_REF:S000057861|PMID:8649377 IMP P class E vacuolar-protein sorting and endocytosis factor YKL002W|CHM2|GRD7|REN1|VPL2|VPS2|VPT14 gene taxon:4932 20020716 SGD
+SGD S000001485 DID4 GO:0045324 SGD_REF:S000071351|PMID:12194857 IPI P class E vacuolar-protein sorting and endocytosis factor YKL002W|CHM2|GRD7|REN1|VPL2|VPS2|VPT14 gene taxon:4932 20021021 SGD
+SGD S000003459 DIE2 GO:0005789 SGD_REF:S000055074|PMID:9597543 IMP C glucosyltransferase YGR227W|ALG10 gene taxon:4932 20020708 SGD
+SGD S000003459 DIE2 GO:0004583 SGD_REF:S000055074|PMID:9597543 IDA F glucosyltransferase YGR227W|ALG10 gene taxon:4932 20020708 SGD
+SGD S000003459 DIE2 GO:0006487 SGD_REF:S000055074|PMID:9597543 IMP P glucosyltransferase YGR227W|ALG10 gene taxon:4932 20020708 SGD
+SGD S000003459 DIE2 GO:0006488 SGD_REF:S000070115|PMID:10336995 TAS P glucosyltransferase YGR227W|ALG10 gene taxon:4932 20021220 SGD
+SGD S000005970 DIG1 GO:0005634 SGD_REF:S000052329|PMID:9860980 TAS C MAP kinase-associated protein YPL049C|RST1 gene taxon:4932 20021017 SGD
+SGD S000005970 DIG1 GO:0005634 SGD_REF:S000081155|PMID:15343339 IC GO:0003677 C MAP kinase-associated protein YPL049C|RST1 gene taxon:4932 20050331 SGD
+SGD S000005970 DIG1 GO:0003677 SGD_REF:S000081155|PMID:15343339 IPI F MAP kinase-associated protein YPL049C|RST1 gene taxon:4932 20050331 SGD
+SGD S000005970 DIG1 GO:0008134 SGD_REF:S000046547|PMID:10825185 IDA F MAP kinase-associated protein YPL049C|RST1 gene taxon:4932 20021017 SGD
+SGD S000005970 DIG1 GO:0001403 SGD_REF:S000045641|PMID:8918885 IGI P MAP kinase-associated protein YPL049C|RST1 gene taxon:4932 20021218 SGD
+SGD S000002888 DIG2 GO:0005634 SGD_REF:S000052329|PMID:9860980 TAS C MAP kinase-associated protein YDR480W|RST2 gene taxon:4932 20021017 SGD
+SGD S000002888 DIG2 GO:0008134 SGD_REF:S000046547|PMID:10825185 IDA F MAP kinase-associated protein YDR480W|RST2 gene taxon:4932 20021017 SGD
+SGD S000002888 DIG2 GO:0001403 SGD_REF:S000045641|PMID:8918885 IGI P MAP kinase-associated protein YDR480W|RST2 gene taxon:4932 20021218 SGD
+SGD S000006187 DIM1 GO:0005730 SGD_REF:S000058443|PMID:10690410 TAS C dimethyladenosine transferase YPL266W|CDH1 gene taxon:4932 20010118 SGD
+SGD S000006187 DIM1 GO:0000179 SGD_REF:S000058443|PMID:10690410 TAS F dimethyladenosine transferase YPL266W|CDH1 gene taxon:4932 20010118 SGD
+SGD S000006187 DIM1 GO:0000154 SGD_REF:S000058443|PMID:10690410 TAS P dimethyladenosine transferase YPL266W|CDH1 gene taxon:4932 20010118 SGD
+SGD S000006187 DIM1 GO:0006365 SGD_REF:S000058443|PMID:10690410 TAS P dimethyladenosine transferase YPL266W|CDH1 gene taxon:4932 20010118 SGD
+SGD S000002671 DIN7 GO:0005739 SGD_REF:S000045102|PMID:10628970 IDA C YDR263C|DIN3 gene taxon:4932 20020212 SGD
+SGD S000002671 DIN7 GO:0004518 SGD_REF:S000043383|PMID:9079876 ISS F YDR263C|DIN3 gene taxon:4932 20010118 SGD
+SGD S000002671 DIN7 GO:0006281 SGD_REF:S000043383|PMID:9079876 ISS P YDR263C|DIN3 gene taxon:4932 20010118 SGD
+SGD S000002671 DIN7 GO:0006281 SGD_REF:S000043383|PMID:9079876 IDA P YDR263C|DIN3 gene taxon:4932 20010118 SGD
+SGD S000004119 DIP2 GO:0005732 SGD_REF:S000070145|PMID:12068309 IPI C U3 snoRNP protein YLR129W|UTP12 gene taxon:4932 20030224 SGD
+SGD S000004119 DIP2 GO:0030515 SGD_REF:S000070145|PMID:12068309 IPI F U3 snoRNP protein YLR129W|UTP12 gene taxon:4932 20030224 SGD
+SGD S000004119 DIP2 GO:0030490 SGD_REF:S000070145|PMID:12068309 IMP P U3 snoRNP protein YLR129W|UTP12 gene taxon:4932 20020906 SGD
+SGD S000004119 DIP2 GO:0030490 SGD_REF:S000070145|PMID:12068309 IPI P U3 snoRNP protein YLR129W|UTP12 gene taxon:4932 20020906 SGD
+SGD S000006186 DIP5 GO:0005886 SGD_REF:S000043244|PMID:10654085 ISS C dicarboxylic amino acid permease YPL265W gene taxon:4932 20020806 SGD
+SGD S000006186 DIP5 GO:0015171 SGD_REF:S000043244|PMID:10654085 IDA F dicarboxylic amino acid permease YPL265W gene taxon:4932 20020806 SGD
+SGD S000006186 DIP5 GO:0015359 SGD_REF:S000070031|PMID:12073087 IDA F dicarboxylic amino acid permease YPL265W gene taxon:4932 20020801 SGD
+SGD S000006186 DIP5 GO:0006865 SGD_REF:S000043244|PMID:10654085 IDA P dicarboxylic amino acid permease YPL265W gene taxon:4932 20020806 SGD
+SGD S000005381 DIS3 GO:0000176 SGD_REF:S000041327|PMID:10465791 IDA C 3'-5' exoribonuclease complex subunit YOL021C|RRP44 gene taxon:4932 20010118 SGD
+SGD S000005381 DIS3 GO:0000177 SGD_REF:S000041327|PMID:10465791 IDA C 3'-5' exoribonuclease complex subunit YOL021C|RRP44 gene taxon:4932 20010118 SGD
+SGD S000005381 DIS3 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C 3'-5' exoribonuclease complex subunit YOL021C|RRP44 gene taxon:4932 20040928 SGD
+SGD S000005381 DIS3 GO:0000175 SGD_REF:S000058443|PMID:10690410 TAS F 3'-5' exoribonuclease complex subunit YOL021C|RRP44 gene taxon:4932 20010118 SGD
+SGD S000005381 DIS3 GO:0006365 SGD_REF:S000058443|PMID:10690410 TAS P 3'-5' exoribonuclease complex subunit YOL021C|RRP44 gene taxon:4932 20010118 SGD
+SGD S000005381 DIS3 GO:0006402 SGD_REF:S000041327|PMID:10465791 IPI P 3'-5' exoribonuclease complex subunit YOL021C|RRP44 gene taxon:4932 20010118 SGD
+SGD S000002811 DIT1 GO:0008372 SGD_REF:S000069584 ND C first enzyme in dityrosine synthesis in the outer layer of the spore wall pathway, converting L-tyrosine to N-formyl-L-tyrosine YDR403W gene taxon:4932 20020716 SGD
+SGD S000002811 DIT1 GO:0003824 SGD_REF:S000051816|PMID:8183942 IDA F first enzyme in dityrosine synthesis in the outer layer of the spore wall pathway, converting L-tyrosine to N-formyl-L-tyrosine YDR403W gene taxon:4932 20020716 SGD
+SGD S000002811 DIT1 GO:0030476 SGD_REF:S000051816|PMID:8183942 IDA P first enzyme in dityrosine synthesis in the outer layer of the spore wall pathway, converting L-tyrosine to N-formyl-L-tyrosine YDR403W gene taxon:4932 20020716 SGD
+SGD S000002811 DIT1 GO:0030476 SGD_REF:S000051816|PMID:8183942 IMP P first enzyme in dityrosine synthesis in the outer layer of the spore wall pathway, converting L-tyrosine to N-formyl-L-tyrosine YDR403W gene taxon:4932 20020716 SGD
+SGD S000002810 DIT2 GO:0008372 SGD_REF:S000069584 ND C catalyzes oxidation of N-formyl tyrosine to N,N-bisformyl dityrosine in vitro, cytochrome P450 56 YDR402C|CYP56 gene taxon:4932 20050601 SGD
+SGD S000002810 DIT2 GO:0016491 SGD_REF:S000051816|PMID:8183942 ISS F catalyzes oxidation of N-formyl tyrosine to N,N-bisformyl dityrosine in vitro, cytochrome P450 56 YDR402C|CYP56 gene taxon:4932 20050601 SGD
+SGD S000002810 DIT2 GO:0030476 SGD_REF:S000051816|PMID:8183942 IDA P catalyzes oxidation of N-formyl tyrosine to N,N-bisformyl dityrosine in vitro, cytochrome P450 56 YDR402C|CYP56 gene taxon:4932 20020716 SGD
+SGD S000002810 DIT2 GO:0030476 SGD_REF:S000051816|PMID:8183942 IMP P catalyzes oxidation of N-formyl tyrosine to N,N-bisformyl dityrosine in vitro, cytochrome P450 56 YDR402C|CYP56 gene taxon:4932 20020716 SGD
+SGD S000001443 DJP1 GO:0005829 SGD_REF:S000055000|PMID:9679141 IDA C YIR004W|ICS1|PAS22 gene taxon:4932 20020927 SGD
+SGD S000001443 DJP1 GO:0051087 SGD_REF:S000055000|PMID:9679141 ISS SGD:S000000850|CGSC:DnaJ|SGD:S000005008|SGD:S000001878|SGD:S000004827|SGD:S000004952 F YIR004W|ICS1|PAS22 gene taxon:4932 20040720 SGD
+SGD S000001443 DJP1 GO:0016558 SGD_REF:S000055000|PMID:9679141 IMP P YIR004W|ICS1|PAS22 gene taxon:4932 20020927 SGD
+SGD S000002333 DLD1 GO:0005743 SGD_REF:S000048042|PMID:9525904 IDA C D-lactate ferricytochrome c oxidoreductase YDL174C gene taxon:4932 20010118 SGD
+SGD S000002333 DLD1 GO:0004458 SGD_REF:S000051546|PMID:8492799 ISS F D-lactate ferricytochrome c oxidoreductase YDL174C gene taxon:4932 20010118 SGD
+SGD S000002333 DLD1 GO:0004458 SGD_REF:S000051546|PMID:8492799 IMP F D-lactate ferricytochrome c oxidoreductase YDL174C gene taxon:4932 20010118 SGD
+SGD S000002333 DLD1 GO:0005975 SGD_REF:S000051546|PMID:8492799 IMP P D-lactate ferricytochrome c oxidoreductase YDL174C gene taxon:4932 20010118 SGD
+SGD S000002333 DLD1 GO:0009060 SGD_REF:S000051546|PMID:8492799 IMP P D-lactate ferricytochrome c oxidoreductase YDL174C gene taxon:4932 20020605 SGD
+SGD S000002337 DLD2 GO:0005759 SGD_REF:S000046734|PMID:10509019 IDA C YDL178W|AIP2 gene taxon:4932 20010510 SGD
+SGD S000002337 DLD2 GO:0003779 SGD_REF:S000057444|PMID:7719850 IPI F YDL178W|AIP2 gene taxon:4932 20040923 SGD
+SGD S000002337 DLD2 GO:0003779 SGD_REF:S000076317|PMID:15158445 IMP F YDL178W|AIP2 gene taxon:4932 20040923 SGD
+SGD S000002337 DLD2 GO:0003779 SGD_REF:S000076317|PMID:15158445 IPI F YDL178W|AIP2 gene taxon:4932 20040923 SGD
+SGD S000002337 DLD2 GO:0004458 SGD_REF:S000046734|PMID:10509019 IDA F YDL178W|AIP2 gene taxon:4932 20010510 SGD
+SGD S000002337 DLD2 GO:0006089 SGD_REF:S000046734|PMID:10509019 TAS P YDL178W|AIP2 gene taxon:4932 20040924 SGD
+SGD S000000797 DLD3 GO:0005625 SGD_REF:S000046734|PMID:10509019 IDA C D-lactate dehydrogenase YEL071W gene taxon:4932 20010118 SGD
+SGD S000000797 DLD3 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C D-lactate dehydrogenase YEL071W gene taxon:4932 20020507 SGD
+SGD S000000797 DLD3 GO:0004458 SGD_REF:S000046734|PMID:10509019 IDA F D-lactate dehydrogenase YEL071W gene taxon:4932 20010118 SGD
+SGD S000000797 DLD3 GO:0006089 SGD_REF:S000046734|PMID:10509019 ISS P D-lactate dehydrogenase YEL071W gene taxon:4932 20010118 SGD
+SGD S000003601 DLS1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YJL065C gene taxon:4932 20031028 SGD
+SGD S000003601 DLS1 GO:0008623 SGD_REF:S000075426|PMID:14673157 IPI C YJL065C gene taxon:4932 20041031 SGD
+SGD S000003601 DLS1 GO:0005554 SGD_REF:S000069584 ND F YJL065C gene taxon:4932 20021223 SGD
+SGD S000003601 DLS1 GO:0006348 SGD_REF:S000075426|PMID:14673157 IMP P YJL065C gene taxon:4932 20040210 SGD
+SGD S000004733 DLT1 GO:0008372 SGD_REF:S000069584 ND C YMR126C gene taxon:4932 20021126 SGD
+SGD S000004733 DLT1 GO:0005554 SGD_REF:S000069584 ND F YMR126C gene taxon:4932 20021126 SGD
+SGD S000004733 DLT1 GO:0000004 SGD_REF:S000069584 ND P YMR126C gene taxon:4932 20021126 SGD
+SGD S000001157 DMA1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YHR115C|CHF1 gene taxon:4932 20020507 SGD
+SGD S000001157 DMA1 GO:0005554 SGD_REF:S000069584 ND F YHR115C|CHF1 gene taxon:4932 20040921 SGD
+SGD S000001157 DMA1 GO:0000132 SGD_REF:S000077036|PMID:15146058 IGI SGD:S000005060 P YHR115C|CHF1 gene taxon:4932 20040921 SGD
+SGD S000001157 DMA1 GO:0000921 SGD_REF:S000077036|PMID:15146058 IGI P YHR115C|CHF1 gene taxon:4932 20040921 SGD
+SGD S000001157 DMA1 GO:0007094 SGD_REF:S000077036|PMID:15146058 IGI P YHR115C|CHF1 gene taxon:4932 20040921 SGD
+SGD S000005060 DMA2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YNL116W|CHF2 gene taxon:4932 20031028 SGD
+SGD S000005060 DMA2 GO:0005554 SGD_REF:S000069584 ND F YNL116W|CHF2 gene taxon:4932 20040921 SGD
+SGD S000005060 DMA2 GO:0000132 SGD_REF:S000077036|PMID:15146058 IGI SGD:S000001157 P YNL116W|CHF2 gene taxon:4932 20040921 SGD
+SGD S000005060 DMA2 GO:0000921 SGD_REF:S000077036|PMID:15146058 IGI P YNL116W|CHF2 gene taxon:4932 20040921 SGD
+SGD S000005060 DMA2 GO:0007094 SGD_REF:S000077036|PMID:15146058 IGI SGD:S000004659 P YNL116W|CHF2 gene taxon:4932 20040921 SGD
+SGD S000000981 DMC1 GO:0000794 SGD_REF:S000047546|PMID:1581960 IDA C meiosis-specific protein related to RecA and Rad51p. Dmc1p colocalizes with Rad51p to discrete subnuclear sites in nuclear spreads during mid prophase, briefly colocalizes with Zip1p, and then disappears by pachytene YER179W|ISC2 gene taxon:4932 20030403 SGD
+SGD S000000981 DMC1 GO:0005634 SGD_REF:S000049325|PMID:7528104 IDA C meiosis-specific protein related to RecA and Rad51p. Dmc1p colocalizes with Rad51p to discrete subnuclear sites in nuclear spreads during mid prophase, briefly colocalizes with Zip1p, and then disappears by pachytene YER179W|ISC2 gene taxon:4932 20010118 SGD
+SGD S000000981 DMC1 GO:0003690 SGD_REF:S000066194|PMID:11551925 IDA F meiosis-specific protein related to RecA and Rad51p. Dmc1p colocalizes with Rad51p to discrete subnuclear sites in nuclear spreads during mid prophase, briefly colocalizes with Zip1p, and then disappears by pachytene YER179W|ISC2 gene taxon:4932 20020521 SGD
+SGD S000000981 DMC1 GO:0003697 SGD_REF:S000066194|PMID:11551925 IDA F meiosis-specific protein related to RecA and Rad51p. Dmc1p colocalizes with Rad51p to discrete subnuclear sites in nuclear spreads during mid prophase, briefly colocalizes with Zip1p, and then disappears by pachytene YER179W|ISC2 gene taxon:4932 20020521 SGD
+SGD S000000981 DMC1 GO:0000709 SGD_REF:S000046433|PMID:9323140 IMP P meiosis-specific protein related to RecA and Rad51p. Dmc1p colocalizes with Rad51p to discrete subnuclear sites in nuclear spreads during mid prophase, briefly colocalizes with Zip1p, and then disappears by pachytene YER179W|ISC2 gene taxon:4932 20020814 SGD
+SGD S000000981 DMC1 GO:0007126 SGD_REF:S000047546|PMID:1581960 IMP P meiosis-specific protein related to RecA and Rad51p. Dmc1p colocalizes with Rad51p to discrete subnuclear sites in nuclear spreads during mid prophase, briefly colocalizes with Zip1p, and then disappears by pachytene YER179W|ISC2 gene taxon:4932 20010118 SGD
+SGD S000000981 DMC1 GO:0007131 SGD_REF:S000047546|PMID:1581960 IMP P meiosis-specific protein related to RecA and Rad51p. Dmc1p colocalizes with Rad51p to discrete subnuclear sites in nuclear spreads during mid prophase, briefly colocalizes with Zip1p, and then disappears by pachytene YER179W|ISC2 gene taxon:4932 20020618 SGD
+SGD S000004824 DML1 GO:0005737 SGD_REF:S000075214|PMID:14690591 IDA C Protein required for cell viability YMR211W gene taxon:4932 20040105 SGD
+SGD S000004824 DML1 GO:0005739 SGD_REF:S000075214|PMID:14690591 IDA C Protein required for cell viability YMR211W gene taxon:4932 20040105 SGD
+SGD S000004824 DML1 GO:0005198 SGD_REF:S000075214|PMID:14690591 ISS F Protein required for cell viability YMR211W gene taxon:4932 20040105 SGD
+SGD S000004824 DML1 GO:0000002 SGD_REF:S000073023|PMID:12702300 IMP P Protein required for cell viability YMR211W gene taxon:4932 20030429 SGD
+SGD S000004824 DML1 GO:0006276 SGD_REF:S000073023|PMID:12702300 IMP P Protein required for cell viability YMR211W gene taxon:4932 20030429 SGD
+SGD S000001207 DNA2 GO:0000784 SGD_REF:S000074691|PMID:12024033 IDA C DNA replication helicase YHR164C|WEB2 gene taxon:4932 20041107 SGD
+SGD S000001207 DNA2 GO:0005634 SGD_REF:S000039689|PMID:7644470 TAS C DNA replication helicase YHR164C|WEB2 gene taxon:4932 20010118 SGD
+SGD S000001207 DNA2 GO:0000014 SGD_REF:S000053505|PMID:9756935 IDA F DNA replication helicase YHR164C|WEB2 gene taxon:4932 20010118 SGD
+SGD S000001207 DNA2 GO:0004003 SGD_REF:S000039689|PMID:7644470 IDA F DNA replication helicase YHR164C|WEB2 gene taxon:4932 20010118 SGD
+SGD S000001207 DNA2 GO:0017108 SGD_REF:S000080373|PMID:15448135 IDA F DNA replication helicase YHR164C|WEB2 gene taxon:4932 20050119 SGD
+SGD S000001207 DNA2 GO:0000723 SGD_REF:S000074691|PMID:12024033 IMP P DNA replication helicase YHR164C|WEB2 gene taxon:4932 20041107 SGD
+SGD S000001207 DNA2 GO:0001302 SGD_REF:S000074686|PMID:12024027 IMP P DNA replication helicase YHR164C|WEB2 gene taxon:4932 20031217 SGD
+SGD S000001207 DNA2 GO:0006261 SGD_REF:S000044982|PMID:9710536 IDA P DNA replication helicase YHR164C|WEB2 gene taxon:4932 20010118 SGD
+SGD S000001207 DNA2 GO:0006261 SGD_REF:S000049830|PMID:7592912 IMP P DNA replication helicase YHR164C|WEB2 gene taxon:4932 20010118 SGD
+SGD S000001207 DNA2 GO:0006273 SGD_REF:S000046654|PMID:10101169 IGI P DNA replication helicase YHR164C|WEB2 gene taxon:4932 20010118 SGD
+SGD S000001207 DNA2 GO:0006273 SGD_REF:S000048574|PMID:10330154 IGI P DNA replication helicase YHR164C|WEB2 gene taxon:4932 20010118 SGD
+SGD S000001207 DNA2 GO:0006273 SGD_REF:S000046654|PMID:10101169 IMP P DNA replication helicase YHR164C|WEB2 gene taxon:4932 20010118 SGD
+SGD S000001207 DNA2 GO:0006273 SGD_REF:S000048574|PMID:10330154 IMP P DNA replication helicase YHR164C|WEB2 gene taxon:4932 20010118 SGD
+SGD S000001207 DNA2 GO:0006281 SGD_REF:S000046654|PMID:10101169 IMP P DNA replication helicase YHR164C|WEB2 gene taxon:4932 20010118 SGD
+SGD S000001207 DNA2 GO:0006281 SGD_REF:S000046654|PMID:10101169 IGI P DNA replication helicase YHR164C|WEB2 gene taxon:4932 20010118 SGD
+SGD S000000968 DNF1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C Potential aminophospholipid translocase YER166W gene taxon:4932 20040928 SGD
+SGD S000000968 DNF1 GO:0005886 SGD_REF:S000071441|PMID:12221123 IDA C Potential aminophospholipid translocase YER166W gene taxon:4932 20021007 SGD
+SGD S000000968 DNF1 GO:0005886 SGD_REF:S000075362|PMID:12631737 IDA C Potential aminophospholipid translocase YER166W gene taxon:4932 20050421 SGD
+SGD S000000968 DNF1 GO:0004012 SGD_REF:S000071441|PMID:12221123 ISS F Potential aminophospholipid translocase YER166W gene taxon:4932 20021007 SGD
+SGD S000000968 DNF1 GO:0006886 SGD_REF:S000071441|PMID:12221123 IGI P Potential aminophospholipid translocase YER166W gene taxon:4932 20021007 SGD
+SGD S000000968 DNF1 GO:0006897 SGD_REF:S000075362|PMID:12631737 IMP P Potential aminophospholipid translocase YER166W gene taxon:4932 20050421 SGD
+SGD S000000968 DNF1 GO:0045332 SGD_REF:S000075362|PMID:12631737 IMP P Potential aminophospholipid translocase YER166W gene taxon:4932 20050421 SGD
+SGD S000002500 DNF2 GO:0005886 SGD_REF:S000071441|PMID:12221123 IDA C Potential aminophospholipid translocase YDR093W gene taxon:4932 20021007 SGD
+SGD S000002500 DNF2 GO:0005886 SGD_REF:S000075362|PMID:12631737 IDA C Potential aminophospholipid translocase YDR093W gene taxon:4932 20050421 SGD
+SGD S000002500 DNF2 GO:0004012 SGD_REF:S000071441|PMID:12221123 ISS F Potential aminophospholipid translocase YDR093W gene taxon:4932 20021007 SGD
+SGD S000002500 DNF2 GO:0006886 SGD_REF:S000071441|PMID:12221123 IGI P Potential aminophospholipid translocase YDR093W gene taxon:4932 20021007 SGD
+SGD S000002500 DNF2 GO:0006897 SGD_REF:S000075362|PMID:12631737 IMP P Potential aminophospholipid translocase YDR093W gene taxon:4932 20050421 SGD
+SGD S000002500 DNF2 GO:0045332 SGD_REF:S000075362|PMID:12631737 IMP P Potential aminophospholipid translocase YDR093W gene taxon:4932 20050421 SGD
+SGD S000004772 DNF3 GO:0030140 SGD_REF:S000071441|PMID:12221123 IDA C Potential aminophospholipid translocase YMR162C gene taxon:4932 20021007 SGD
+SGD S000004772 DNF3 GO:0004012 SGD_REF:S000071441|PMID:12221123 ISS F Potential aminophospholipid translocase YMR162C gene taxon:4932 20021007 SGD
+SGD S000004772 DNF3 GO:0006886 SGD_REF:S000071441|PMID:12221123 IGI P Potential aminophospholipid translocase YMR162C gene taxon:4932 20021007 SGD
+SGD S000004772 DNF3 GO:0045332 SGD_REF:S000114386|PMID:16452632 IMP P Potential aminophospholipid translocase YMR162C gene taxon:4932 20060216 SGD
+SGD S000005531 DNL4 GO:0005634 SGD_REF:S000047633|PMID:9242411 TAS C ATP dependent DNA ligase YOR005C|LIG4 gene taxon:4932 20010118 SGD
+SGD S000005531 DNL4 GO:0003910 SGD_REF:S000054228|PMID:9271115 IDA F ATP dependent DNA ligase YOR005C|LIG4 gene taxon:4932 20010118 SGD
+SGD S000005531 DNL4 GO:0006303 SGD_REF:S000047633|PMID:9242411 IMP P ATP dependent DNA ligase YOR005C|LIG4 gene taxon:4932 20010118 SGD
+SGD S000005531 DNL4 GO:0006303 SGD_REF:S000079665|PMID:15342630 IDA P ATP dependent DNA ligase YOR005C|LIG4 gene taxon:4932 20041122 SGD
+SGD S000003924 DNM1 GO:0005741 SGD_REF:S000056450|PMID:11038182 IDA C similar to dynamin GTPase YLL001W gene taxon:4932 20030120 SGD
+SGD S000003924 DNM1 GO:0003924 SGD_REF:S000058450|PMID:9891785 TAS F similar to dynamin GTPase YLL001W gene taxon:4932 20010118 SGD
+SGD S000003924 DNM1 GO:0000266 SGD_REF:S000051306|PMID:10559943 IGI SGD:S000000383 P similar to dynamin GTPase YLL001W gene taxon:4932 20030205 SGD
+SGD S000003924 DNM1 GO:0000266 SGD_REF:S000051306|PMID:10559943 IMP P similar to dynamin GTPase YLL001W gene taxon:4932 20030205 SGD
+SGD S000003924 DNM1 GO:0007005 SGD_REF:S000045930|PMID:9786946 IMP P similar to dynamin GTPase YLL001W gene taxon:4932 20050426 SGD
+SGD S000001696 DOA1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C regulatory component of the proteasome pathway YKL213C|UFD3|ZZZ4 gene taxon:4932 20031028 SGD
+SGD S000001696 DOA1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C regulatory component of the proteasome pathway YKL213C|UFD3|ZZZ4 gene taxon:4932 20031028 SGD
+SGD S000001696 DOA1 GO:0043130 SGD_REF:S000114237|PMID:16428438 IDA F regulatory component of the proteasome pathway YKL213C|UFD3|ZZZ4 gene taxon:4932 20060202 SGD
+SGD S000001696 DOA1 GO:0043130 SGD_REF:S000114237|PMID:16428438 IMP F regulatory component of the proteasome pathway YKL213C|UFD3|ZZZ4 gene taxon:4932 20060202 SGD
+SGD S000001696 DOA1 GO:0006303 SGD_REF:S000073203|PMID:12399380 IMP P regulatory component of the proteasome pathway YKL213C|UFD3|ZZZ4 gene taxon:4932 20030528 SGD
+SGD S000001696 DOA1 GO:0006511 SGD_REF:S000056750|PMID:2111732 IMP P regulatory component of the proteasome pathway YKL213C|UFD3|ZZZ4 gene taxon:4932 20010118 SGD
+SGD S000001696 DOA1 GO:0006512 SGD_REF:S000114196|PMID:16427015 IGI P regulatory component of the proteasome pathway YKL213C|UFD3|ZZZ4 gene taxon:4932 20060203 SGD
+SGD S000001696 DOA1 GO:0006512 SGD_REF:S000114196|PMID:16427015 IMP P regulatory component of the proteasome pathway YKL213C|UFD3|ZZZ4 gene taxon:4932 20060203 SGD
+SGD S000001696 DOA1 GO:0006512 SGD_REF:S000114196|PMID:16427015 IPI P regulatory component of the proteasome pathway YKL213C|UFD3|ZZZ4 gene taxon:4932 20060203 SGD
+SGD S000002476 DOA4 GO:0000502 SGD_REF:S000043787|PMID:10069815 IPI C ubiquitin isopeptidase YDR069C|DOS1|MUT4|NPI2|SSV7|UBP4 gene taxon:4932 20030520 SGD
+SGD S000002476 DOA4 GO:0005624 SGD_REF:S000076958|PMID:15326198 IDA C ubiquitin isopeptidase YDR069C|DOS1|MUT4|NPI2|SSV7|UBP4 gene taxon:4932 20050107 SGD
+SGD S000002476 DOA4 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C ubiquitin isopeptidase YDR069C|DOS1|MUT4|NPI2|SSV7|UBP4 gene taxon:4932 20040928 SGD
+SGD S000002476 DOA4 GO:0004175 SGD_REF:S000043787|PMID:10069815 IGI F ubiquitin isopeptidase YDR069C|DOS1|MUT4|NPI2|SSV7|UBP4 gene taxon:4932 20030520 SGD
+SGD S000002476 DOA4 GO:0004175 SGD_REF:S000043787|PMID:10069815 IPI F ubiquitin isopeptidase YDR069C|DOS1|MUT4|NPI2|SSV7|UBP4 gene taxon:4932 20030520 SGD
+SGD S000002476 DOA4 GO:0004221 SGD_REF:S000045956|PMID:8247125 IDA F ubiquitin isopeptidase YDR069C|DOS1|MUT4|NPI2|SSV7|UBP4 gene taxon:4932 20050926 SGD
+SGD S000002476 DOA4 GO:0004221 SGD_REF:S000045956|PMID:8247125 IMP F ubiquitin isopeptidase YDR069C|DOS1|MUT4|NPI2|SSV7|UBP4 gene taxon:4932 20050926 SGD
+SGD S000002476 DOA4 GO:0004843 SGD_REF:S000054052|PMID:8657109 TAS F ubiquitin isopeptidase YDR069C|DOS1|MUT4|NPI2|SSV7|UBP4 gene taxon:4932 20010118 SGD
+SGD S000002476 DOA4 GO:0016787 SGD_REF:S000042743|PMID:9119204 TAS F ubiquitin isopeptidase YDR069C|DOS1|MUT4|NPI2|SSV7|UBP4 gene taxon:4932 20031021 SGD
+SGD S000002476 DOA4 GO:0016787 SGD_REF:S000054052|PMID:8657109 TAS F ubiquitin isopeptidase YDR069C|DOS1|MUT4|NPI2|SSV7|UBP4 gene taxon:4932 20031021 SGD
+SGD S000002476 DOA4 GO:0006275 SGD_REF:S000054052|PMID:8657109 IMP P ubiquitin isopeptidase YDR069C|DOS1|MUT4|NPI2|SSV7|UBP4 gene taxon:4932 20010118 SGD
+SGD S000002476 DOA4 GO:0006897 SGD_REF:S000042743|PMID:9119204 IMP P ubiquitin isopeptidase YDR069C|DOS1|MUT4|NPI2|SSV7|UBP4 gene taxon:4932 20031021 SGD
+SGD S000002476 DOA4 GO:0016579 SGD_REF:S000045956|PMID:8247125 TAS P ubiquitin isopeptidase YDR069C|DOS1|MUT4|NPI2|SSV7|UBP4 gene taxon:4932 20010118 SGD
+SGD S000003209 DOC1 GO:0005680 SGD_REF:S000058476|PMID:10465783 TAS C YGL240W|APC10 gene taxon:4932 20010118 SGD
+SGD S000003209 DOC1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YGL240W|APC10 gene taxon:4932 20040928 SGD
+SGD S000003209 DOC1 GO:0030234 SGD_REF:S000071780|PMID:12402045 IDA F YGL240W|APC10 gene taxon:4932 20021213 SGD
+SGD S000003209 DOC1 GO:0000022 SGD_REF:S000058476|PMID:10465783 TAS P YGL240W|APC10 gene taxon:4932 20010118 SGD
+SGD S000003209 DOC1 GO:0000070 SGD_REF:S000058476|PMID:10465783 TAS P YGL240W|APC10 gene taxon:4932 20010118 SGD
+SGD S000003209 DOC1 GO:0007091 SGD_REF:S000058476|PMID:10465783 TAS P YGL240W|APC10 gene taxon:4932 20010118 SGD
+SGD S000003209 DOC1 GO:0008054 SGD_REF:S000058476|PMID:10465783 TAS P YGL240W|APC10 gene taxon:4932 20010118 SGD
+SGD S000003209 DOC1 GO:0031145 SGD_REF:S000071780|PMID:12402045 IDA P YGL240W|APC10 gene taxon:4932 20050404 SGD
+SGD S000003209 DOC1 GO:0031145 SGD_REF:S000071780|PMID:12402045 IMP P YGL240W|APC10 gene taxon:4932 20050404 SGD
+SGD S000003209 DOC1 GO:0031145 SGD_REF:S000044570|PMID:9469814 IPI P YGL240W|APC10 gene taxon:4932 20050404 SGD
+SGD S000001086 DOG1 GO:0008372 SGD_REF:S000069584 ND C 2-deoxyglucose-6-phosphate phosphatase YHR044C gene taxon:4932 20020930 SGD
+SGD S000001086 DOG1 GO:0003850 SGD_REF:S000057804|PMID:8553694 IDA F 2-deoxyglucose-6-phosphate phosphatase YHR044C gene taxon:4932 20020930 SGD
+SGD S000001086 DOG1 GO:0006006 SGD_REF:S000057804|PMID:8553694 ISS P 2-deoxyglucose-6-phosphate phosphatase YHR044C gene taxon:4932 20020930 SGD
+SGD S000001085 DOG2 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C 2-deoxyglucose-6-phosphate phosphatase YHR043C gene taxon:4932 20031028 SGD
+SGD S000001085 DOG2 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C 2-deoxyglucose-6-phosphate phosphatase YHR043C gene taxon:4932 20020507 SGD
+SGD S000001085 DOG2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C 2-deoxyglucose-6-phosphate phosphatase YHR043C gene taxon:4932 20031028 SGD
+SGD S000001085 DOG2 GO:0003850 SGD_REF:S000057804|PMID:8553694 IDA F 2-deoxyglucose-6-phosphate phosphatase YHR043C gene taxon:4932 20020930 SGD
+SGD S000001085 DOG2 GO:0006006 SGD_REF:S000057804|PMID:8553694 ISS P 2-deoxyglucose-6-phosphate phosphatase YHR043C gene taxon:4932 20020930 SGD
+SGD S000001085 DOG2 GO:0006950 SGD_REF:S000039870|PMID:10960096 IEP P 2-deoxyglucose-6-phosphate phosphatase YHR043C gene taxon:4932 20020930 SGD
+SGD S000001085 DOG2 GO:0030433 SGD_REF:S000115312|PMID:12711700 IMP P 2-deoxyglucose-6-phosphate phosphatase YHR043C gene taxon:4932 20060511 SGD
+SGD S000004946 DOM34 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YNL001W gene taxon:4932 20031028 SGD
+SGD S000004946 DOM34 GO:0005554 SGD_REF:S000069584 ND F YNL001W gene taxon:4932 20020926 SGD
+SGD S000004946 DOM34 GO:0006412 SGD_REF:S000043929|PMID:9584085 IMP P YNL001W gene taxon:4932 20020926 SGD
+SGD S000004946 DOM34 GO:0007126 SGD_REF:S000041663|PMID:8900058 TAS P YNL001W gene taxon:4932 20031030 SGD
+SGD S000002681 DON1 GO:0005628 SGD_REF:S000069721|PMID:11973299 IDA C YDR273W gene taxon:4932 20020920 SGD
+SGD S000002681 DON1 GO:0005628 SGD_REF:S000069149|PMID:11742972 IDA C YDR273W gene taxon:4932 20020920 SGD
+SGD S000002681 DON1 GO:0005819 SGD_REF:S000069721|PMID:11973299 IDA C YDR273W gene taxon:4932 20020920 SGD
+SGD S000002681 DON1 GO:0005554 SGD_REF:S000069584 ND F YDR273W gene taxon:4932 20020920 SGD
+SGD S000002681 DON1 GO:0007126 SGD_REF:S000061397|PMID:10899120 IEP P YDR273W gene taxon:4932 20020920 SGD
+SGD S000002681 DON1 GO:0030476 SGD_REF:S000069721|PMID:11973299 IPI P YDR273W gene taxon:4932 20020920 SGD
+SGD S000002548 DOP1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDR141C gene taxon:4932 20031028 SGD
+SGD S000002548 DOP1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YDR141C gene taxon:4932 20040813 SGD
+SGD S000002548 DOP1 GO:0005554 SGD_REF:S000069584 ND F YDR141C gene taxon:4932 20010212 SGD
+SGD S000002548 DOP1 GO:0000902 SGD_REF:S000059354|PMID:10931277 IMP P YDR141C gene taxon:4932 20021107 SGD
+SGD S000002548 DOP1 GO:0000902 SGD_REF:S000059354|PMID:10931277 ISS P YDR141C gene taxon:4932 20021107 SGD
+SGD S000002475 DOS2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDR068W gene taxon:4932 20031028 SGD
+SGD S000002475 DOS2 GO:0005554 SGD_REF:S000069584 ND F YDR068W gene taxon:4932 20021122 SGD
+SGD S000002475 DOS2 GO:0000004 SGD_REF:S000069584 ND P YDR068W gene taxon:4932 20021122 SGD
+SGD S000002848 DOT1 GO:0005634 SGD_REF:S000059155|PMID:11029058 IDA C YDR440W|PCH1 gene taxon:4932 20020918 SGD
+SGD S000002848 DOT1 GO:0016279 SGD_REF:S000070056|PMID:12080090 IDA F YDR440W|PCH1 gene taxon:4932 20020918 SGD
+SGD S000002848 DOT1 GO:0006348 SGD_REF:S000059155|PMID:11029058 IMP P YDR440W|PCH1 gene taxon:4932 20020918 SGD
+SGD S000002848 DOT1 GO:0016571 SGD_REF:S000070056|PMID:12080090 IDA P YDR440W|PCH1 gene taxon:4932 20020918 SGD
+SGD S000002848 DOT1 GO:0040020 SGD_REF:S000059155|PMID:11029058 IMP P YDR440W|PCH1 gene taxon:4932 20020918 SGD
+SGD S000001272 DOT5 GO:0005634 SGD_REF:S000061961|PMID:2408019 IDA C YIL010W|nTPx gene taxon:4932 20020411 SGD
+SGD S000001272 DOT5 GO:0005634 SGD_REF:S000061563|PMID:10681558 IDA C YIL010W|nTPx gene taxon:4932 20050624 SGD
+SGD S000001272 DOT5 GO:0005634 SGD_REF:S000061961|PMID:2408019 ISS C YIL010W|nTPx gene taxon:4932 20020411 SGD
+SGD S000001272 DOT5 GO:0008379 SGD_REF:S000061563|PMID:10681558 IMP F YIL010W|nTPx gene taxon:4932 20020411 SGD
+SGD S000001272 DOT5 GO:0008379 SGD_REF:S000061563|PMID:10681558 IDA F YIL010W|nTPx gene taxon:4932 20020411 SGD
+SGD S000001272 DOT5 GO:0008379 SGD_REF:S000061563|PMID:10681558 ISS F YIL010W|nTPx gene taxon:4932 20020411 SGD
+SGD S000001272 DOT5 GO:0030503 SGD_REF:S000061563|PMID:10681558 IMP P YIL010W|nTPx gene taxon:4932 20020411 SGD
+SGD S000001272 DOT5 GO:0030503 SGD_REF:S000061563|PMID:10681558 IDA P YIL010W|nTPx gene taxon:4932 20020411 SGD
+SGD S000000890 DOT6 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YER088C gene taxon:4932 20031028 SGD
+SGD S000000890 DOT6 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YER088C gene taxon:4932 20031028 SGD
+SGD S000000890 DOT6 GO:0005554 SGD_REF:S000069584 ND F YER088C gene taxon:4932 20020808 SGD
+SGD S000000890 DOT6 GO:0000183 SGD_REF:S000047238|PMID:9755194 IGI P YER088C gene taxon:4932 20020808 SGD
+SGD S000000890 DOT6 GO:0006348 SGD_REF:S000047238|PMID:9755194 IGI P YER088C gene taxon:4932 20020808 SGD
+SGD S000000890 DOT6 GO:0006357 SGD_REF:S000043169|PMID:9832522 IGI P YER088C gene taxon:4932 20020808 SGD
+SGD S000000890 DOT6 GO:0009826 SGD_REF:S000043169|PMID:9832522 IMP P YER088C gene taxon:4932 20020808 SGD
+SGD S000000890 DOT6 GO:0030447 SGD_REF:S000043169|PMID:9832522 IGI P YER088C gene taxon:4932 20020808 SGD
+SGD S000003626 DPB11 GO:0005657 SGD_REF:S000058372|PMID:9745046 TAS C DNA polymerase II complex YJL090C gene taxon:4932 20010118 SGD
+SGD S000003626 DPB11 GO:0005657 SGD_REF:S000043352|PMID:10733584 IDA C DNA polymerase II complex YJL090C gene taxon:4932 20040928 SGD
+SGD S000003626 DPB11 GO:0005515 SGD_REF:S000043352|PMID:10733584 IPI SGD:S000005206 F DNA polymerase II complex YJL090C gene taxon:4932 20040928 SGD
+SGD S000003626 DPB11 GO:0000076 SGD_REF:S000046281|PMID:10097122 IMP P DNA polymerase II complex YJL090C gene taxon:4932 20040928 SGD
+SGD S000003626 DPB11 GO:0006270 SGD_REF:S000073092|PMID:12730134 TAS P DNA polymerase II complex YJL090C gene taxon:4932 20030508 SGD
+SGD S000003626 DPB11 GO:0006272 SGD_REF:S000058372|PMID:9745046 TAS P DNA polymerase II complex YJL090C gene taxon:4932 20010118 SGD
+SGD S000003626 DPB11 GO:0006273 SGD_REF:S000058372|PMID:9745046 TAS P DNA polymerase II complex YJL090C gene taxon:4932 20010118 SGD
+SGD S000003626 DPB11 GO:0006289 SGD_REF:S000058372|PMID:9745046 TAS P DNA polymerase II complex YJL090C gene taxon:4932 20010118 SGD
+SGD S000003626 DPB11 GO:0006298 SGD_REF:S000058456|PMID:10072354 NAS P DNA polymerase II complex YJL090C gene taxon:4932 20010118 SGD
+SGD S000006379 DPB2 GO:0005634 SGD_REF:S000077144|PMID:15282802 IDA C DNA polymerase epsilon subunit B YPR175W gene taxon:4932 20041008 SGD
+SGD S000006379 DPB2 GO:0005657 SGD_REF:S000058372|PMID:9745046 TAS C DNA polymerase epsilon subunit B YPR175W gene taxon:4932 20010118 SGD
+SGD S000006379 DPB2 GO:0005737 SGD_REF:S000077144|PMID:15282802 IDA C DNA polymerase epsilon subunit B YPR175W gene taxon:4932 20041008 SGD
+SGD S000006379 DPB2 GO:0008622 SGD_REF:S000062082|PMID:2406268 IDA C DNA polymerase epsilon subunit B YPR175W gene taxon:4932 20031216 SGD
+SGD S000006379 DPB2 GO:0003893 SGD_REF:S000058372|PMID:9745046 TAS F DNA polymerase epsilon subunit B YPR175W gene taxon:4932 20010118 SGD
+SGD S000006379 DPB2 GO:0006272 SGD_REF:S000058372|PMID:9745046 TAS P DNA polymerase epsilon subunit B YPR175W gene taxon:4932 20010118 SGD
+SGD S000006379 DPB2 GO:0006273 SGD_REF:S000058372|PMID:9745046 TAS P DNA polymerase epsilon subunit B YPR175W gene taxon:4932 20010118 SGD
+SGD S000006379 DPB2 GO:0006289 SGD_REF:S000058372|PMID:9745046 TAS P DNA polymerase epsilon subunit B YPR175W gene taxon:4932 20010118 SGD
+SGD S000006379 DPB2 GO:0006298 SGD_REF:S000058456|PMID:10072354 TAS P DNA polymerase epsilon subunit B YPR175W gene taxon:4932 20010118 SGD
+SGD S000000482 DPB3 GO:0005657 SGD_REF:S000058372|PMID:9745046 TAS C DNA polymerase II C and C' subunits YBR278W gene taxon:4932 20010118 SGD
+SGD S000000482 DPB3 GO:0008622 SGD_REF:S000062082|PMID:2406268 IDA C DNA polymerase II C and C' subunits YBR278W gene taxon:4932 20031216 SGD
+SGD S000000482 DPB3 GO:0003893 SGD_REF:S000058372|PMID:9745046 TAS F DNA polymerase II C and C' subunits YBR278W gene taxon:4932 20010118 SGD
+SGD S000000482 DPB3 GO:0006272 SGD_REF:S000058372|PMID:9745046 TAS P DNA polymerase II C and C' subunits YBR278W gene taxon:4932 20010118 SGD
+SGD S000000482 DPB3 GO:0006273 SGD_REF:S000058372|PMID:9745046 TAS P DNA polymerase II C and C' subunits YBR278W gene taxon:4932 20010118 SGD
+SGD S000000482 DPB3 GO:0006289 SGD_REF:S000058372|PMID:9745046 TAS P DNA polymerase II C and C' subunits YBR278W gene taxon:4932 20010118 SGD
+SGD S000000482 DPB3 GO:0006298 SGD_REF:S000058456|PMID:10072354 TAS P DNA polymerase II C and C' subunits YBR278W gene taxon:4932 20010118 SGD
+SGD S000000482 DPB3 GO:0006348 SGD_REF:S000075426|PMID:14673157 IMP P DNA polymerase II C and C' subunits YBR278W gene taxon:4932 20040210 SGD
+SGD S000002528 DPB4 GO:0008622 SGD_REF:S000056444|PMID:11024162 IDA C DNA polymerase II (epsilon) 4th subunit YDR121W gene taxon:4932 20010118 SGD
+SGD S000002528 DPB4 GO:0008623 SGD_REF:S000075426|PMID:14673157 IPI C DNA polymerase II (epsilon) 4th subunit YDR121W gene taxon:4932 20041031 SGD
+SGD S000002528 DPB4 GO:0003893 SGD_REF:S000056444|PMID:11024162 IMP F DNA polymerase II (epsilon) 4th subunit YDR121W gene taxon:4932 20010118 SGD
+SGD S000002528 DPB4 GO:0003893 SGD_REF:S000056444|PMID:11024162 IPI F DNA polymerase II (epsilon) 4th subunit YDR121W gene taxon:4932 20010118 SGD
+SGD S000002528 DPB4 GO:0006272 SGD_REF:S000056444|PMID:11024162 IMP P DNA polymerase II (epsilon) 4th subunit YDR121W gene taxon:4932 20010118 SGD
+SGD S000002528 DPB4 GO:0006272 SGD_REF:S000056444|PMID:11024162 IGI P DNA polymerase II (epsilon) 4th subunit YDR121W gene taxon:4932 20010118 SGD
+SGD S000002528 DPB4 GO:0006272 SGD_REF:S000056444|PMID:11024162 IPI P DNA polymerase II (epsilon) 4th subunit YDR121W gene taxon:4932 20010118 SGD
+SGD S000002528 DPB4 GO:0006273 SGD_REF:S000056444|PMID:11024162 IMP P DNA polymerase II (epsilon) 4th subunit YDR121W gene taxon:4932 20010118 SGD
+SGD S000002528 DPB4 GO:0006273 SGD_REF:S000056444|PMID:11024162 IPI P DNA polymerase II (epsilon) 4th subunit YDR121W gene taxon:4932 20010118 SGD
+SGD S000002528 DPB4 GO:0006273 SGD_REF:S000056444|PMID:11024162 IGI P DNA polymerase II (epsilon) 4th subunit YDR121W gene taxon:4932 20010118 SGD
+SGD S000002528 DPB4 GO:0006348 SGD_REF:S000075426|PMID:14673157 IMP P DNA polymerase II (epsilon) 4th subunit YDR121W gene taxon:4932 20040210 SGD
+SGD S000001365 DPH1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YIL103W|KIF48 gene taxon:4932 20020507 SGD
+SGD S000001365 DPH1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YIL103W|KIF48 gene taxon:4932 20031028 SGD
+SGD S000001365 DPH1 GO:0005554 SGD_REF:S000069584 ND F YIL103W|KIF48 gene taxon:4932 20030203 SGD
+SGD S000001365 DPH1 GO:0017183 SGD_REF:S000079857|PMID:15485916 IMP P YIL103W|KIF48 gene taxon:4932 20050303 SGD
+SGD S000001674 DPH2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YKL191W gene taxon:4932 20031028 SGD
+SGD S000001674 DPH2 GO:0005554 SGD_REF:S000069584 ND F YKL191W gene taxon:4932 20020926 SGD
+SGD S000001674 DPH2 GO:0017183 SGD_REF:S000041529|PMID:8406038 IMP P YKL191W gene taxon:4932 20020926 SGD
+SGD S000001674 DPH2 GO:0017183 SGD_REF:S000079857|PMID:15485916 IMP P YKL191W gene taxon:4932 20050303 SGD
+SGD S000004162 DPH5 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YLR172C gene taxon:4932 20031028 SGD
+SGD S000004162 DPH5 GO:0004164 SGD_REF:S000041081|PMID:3042777 IDA F YLR172C gene taxon:4932 20020926 SGD
+SGD S000004162 DPH5 GO:0017183 SGD_REF:S000041081|PMID:3042777 IDA P YLR172C gene taxon:4932 20020926 SGD
+SGD S000004162 DPH5 GO:0017183 SGD_REF:S000079857|PMID:15485916 IMP P YLR172C gene taxon:4932 20050303 SGD
+SGD S000002702 DPL1 GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C dihydrosphingosine phosphate lyase (also known as sphingosine phosphate lyase) YDR294C|BST1 gene taxon:4932 20031028 SGD
+SGD S000002702 DPL1 GO:0008117 SGD_REF:S000058214|PMID:9334171 IDA F dihydrosphingosine phosphate lyase (also known as sphingosine phosphate lyase) YDR294C|BST1 gene taxon:4932 20021113 SGD
+SGD S000002702 DPL1 GO:0006665 SGD_REF:S000058214|PMID:9334171 IGI P dihydrosphingosine phosphate lyase (also known as sphingosine phosphate lyase) YDR294C|BST1 gene taxon:4932 20020925 SGD
+SGD S000002702 DPL1 GO:0006665 SGD_REF:S000058214|PMID:9334171 IMP P dihydrosphingosine phosphate lyase (also known as sphingosine phosphate lyase) YDR294C|BST1 gene taxon:4932 20020925 SGD
+SGD S000002702 DPL1 GO:0009267 SGD_REF:S000044759|PMID:10329480 IMP P dihydrosphingosine phosphate lyase (also known as sphingosine phosphate lyase) YDR294C|BST1 gene taxon:4932 20020925 SGD
+SGD S000002702 DPL1 GO:0019722 SGD_REF:S000060106|PMID:11278643 IMP P dihydrosphingosine phosphate lyase (also known as sphingosine phosphate lyase) YDR294C|BST1 gene taxon:4932 20020925 SGD
+SGD S000006387 DPM1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C dolichol phosphate mannose synthase YPR183W|SED3 gene taxon:4932 20040928 SGD
+SGD S000006387 DPM1 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C dolichol phosphate mannose synthase YPR183W|SED3 gene taxon:4932 20060317 SGD
+SGD S000006387 DPM1 GO:0005783 SGD_REF:S000056641|PMID:1803815 IDA C dolichol phosphate mannose synthase YPR183W|SED3 gene taxon:4932 20020926 SGD
+SGD S000006387 DPM1 GO:0042175 SGD_REF:S000047509|PMID:10419517 IDA C dolichol phosphate mannose synthase YPR183W|SED3 gene taxon:4932 20030207 SGD
+SGD S000006387 DPM1 GO:0004582 SGD_REF:S000045860|PMID:3053713 IDA F dolichol phosphate mannose synthase YPR183W|SED3 gene taxon:4932 20020926 SGD
+SGD S000006387 DPM1 GO:0016757 SGD_REF:S000055539|PMID:9653120 ISS F dolichol phosphate mannose synthase YPR183W|SED3 gene taxon:4932 20021204 SGD
+SGD S000006387 DPM1 GO:0006487 SGD_REF:S000053920|PMID:1333231 IMP P dolichol phosphate mannose synthase YPR183W|SED3 gene taxon:4932 20020926 SGD
+SGD S000006387 DPM1 GO:0006493 SGD_REF:S000053920|PMID:1333231 IMP P dolichol phosphate mannose synthase YPR183W|SED3 gene taxon:4932 20020926 SGD
+SGD S000006387 DPM1 GO:0006506 SGD_REF:S000053920|PMID:1333231 IMP P dolichol phosphate mannose synthase YPR183W|SED3 gene taxon:4932 20020926 SGD
+SGD S000002692 DPP1 GO:0000329 SGD_REF:S000060003|PMID:11139591 IDA C diacylglycerol pyrophosphate phosphatase YDR284C|ZRG1 gene taxon:4932 20030404 SGD
+SGD S000002692 DPP1 GO:0000329 SGD_REF:S000060003|PMID:11139591 TAS C diacylglycerol pyrophosphate phosphatase YDR284C|ZRG1 gene taxon:4932 20030404 SGD
+SGD S000002692 DPP1 GO:0000810 SGD_REF:S000044587|PMID:9452443 IMP F diacylglycerol pyrophosphate phosphatase YDR284C|ZRG1 gene taxon:4932 20030415 SGD
+SGD S000002692 DPP1 GO:0000810 SGD_REF:S000057811|PMID:8567632 IDA F diacylglycerol pyrophosphate phosphatase YDR284C|ZRG1 gene taxon:4932 20030415 SGD
+SGD S000002692 DPP1 GO:0008195 SGD_REF:S000045881|PMID:10329682 IDA F diacylglycerol pyrophosphate phosphatase YDR284C|ZRG1 gene taxon:4932 20020925 SGD
+SGD S000002692 DPP1 GO:0006644 SGD_REF:S000045881|PMID:10329682 IMP P diacylglycerol pyrophosphate phosphatase YDR284C|ZRG1 gene taxon:4932 20020925 SGD
+SGD S000002692 DPP1 GO:0007165 SGD_REF:S000054080|PMID:10545184 TAS P diacylglycerol pyrophosphate phosphatase YDR284C|ZRG1 gene taxon:4932 20031203 SGD
+SGD S000003941 DPS1 GO:0005737 SGD_REF:S000057152|PMID:3902099 ISS C aspartyl-tRNA synthetase YLL018C|AspRS gene taxon:4932 20010118 SGD
+SGD S000003941 DPS1 GO:0003723 SGD_REF:S000076273|PMID:12888345 IDA F aspartyl-tRNA synthetase YLL018C|AspRS gene taxon:4932 20050304 SGD
+SGD S000003941 DPS1 GO:0004815 SGD_REF:S000057152|PMID:3902099 ISS F aspartyl-tRNA synthetase YLL018C|AspRS gene taxon:4932 20010118 SGD
+SGD S000003941 DPS1 GO:0004815 SGD_REF:S000076285|PMID:8263943 IDA F aspartyl-tRNA synthetase YLL018C|AspRS gene taxon:4932 20050304 SGD
+SGD S000003941 DPS1 GO:0006412 SGD_REF:S000057152|PMID:3902099 ISS P aspartyl-tRNA synthetase YLL018C|AspRS gene taxon:4932 20010118 SGD
+SGD S000001779 DRE2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YKR071C gene taxon:4932 20031028 SGD
+SGD S000001779 DRE2 GO:0005554 SGD_REF:S000069584 ND F YKR071C gene taxon:4932 20021122 SGD
+SGD S000001779 DRE2 GO:0000004 SGD_REF:S000069584 ND P YKR071C gene taxon:4932 20021122 SGD
+SGD S000003931 DRS1 GO:0005730 SGD_REF:S000058443|PMID:10690410 TAS C ATP dependent RNA helicase (putative) YLL008W gene taxon:4932 20010118 SGD
+SGD S000003931 DRS1 GO:0004004 SGD_REF:S000058443|PMID:10690410 TAS F ATP dependent RNA helicase (putative) YLL008W gene taxon:4932 20010118 SGD
+SGD S000003931 DRS1 GO:0000027 SGD_REF:S000058443|PMID:10690410 TAS P ATP dependent RNA helicase (putative) YLL008W gene taxon:4932 20010118 SGD
+SGD S000003931 DRS1 GO:0006365 SGD_REF:S000058443|PMID:10690410 TAS P ATP dependent RNA helicase (putative) YLL008W gene taxon:4932 20010118 SGD
+SGD S000000024 DRS2 GO:0000139 SGD_REF:S000040586|PMID:10601336 IDA C P-type ATPase, potential aminophospholipid translocase YAL026C|FUN38|SWA3 gene taxon:4932 20010118 SGD
+SGD S000000024 DRS2 GO:0005802 SGD_REF:S000076777|PMID:15090616 IDA C P-type ATPase, potential aminophospholipid translocase YAL026C|FUN38|SWA3 gene taxon:4932 20051208 SGD
+SGD S000000024 DRS2 GO:0005886 SGD_REF:S000047547|PMID:9852106 TAS C P-type ATPase, potential aminophospholipid translocase YAL026C|FUN38|SWA3 gene taxon:4932 20031229 SGD
+SGD S000000024 DRS2 GO:0030140 SGD_REF:S000071441|PMID:12221123 IDA C P-type ATPase, potential aminophospholipid translocase YAL026C|FUN38|SWA3 gene taxon:4932 20021007 SGD
+SGD S000000024 DRS2 GO:0004012 SGD_REF:S000059994|PMID:8633245 TAS F P-type ATPase, potential aminophospholipid translocase YAL026C|FUN38|SWA3 gene taxon:4932 20010926 SGD
+SGD S000000024 DRS2 GO:0016887 SGD_REF:S000040586|PMID:10601336 TAS F P-type ATPase, potential aminophospholipid translocase YAL026C|FUN38|SWA3 gene taxon:4932 20010118 SGD
+SGD S000000024 DRS2 GO:0006886 SGD_REF:S000071441|PMID:12221123 IGI P P-type ATPase, potential aminophospholipid translocase YAL026C|FUN38|SWA3 gene taxon:4932 20021007 SGD
+SGD S000000024 DRS2 GO:0006892 SGD_REF:S000040586|PMID:10601336 IMP P P-type ATPase, potential aminophospholipid translocase YAL026C|FUN38|SWA3 gene taxon:4932 20010118 SGD
+SGD S000000024 DRS2 GO:0006892 SGD_REF:S000040586|PMID:10601336 IGI P P-type ATPase, potential aminophospholipid translocase YAL026C|FUN38|SWA3 gene taxon:4932 20010118 SGD
+SGD S000000024 DRS2 GO:0006897 SGD_REF:S000086880|PMID:16195350 IGI SGD:S000004046 P P-type ATPase, potential aminophospholipid translocase YAL026C|FUN38|SWA3 gene taxon:4932 20051208 SGD
+SGD S000000024 DRS2 GO:0030490 SGD_REF:S000074158|PMID:11560931 TAS P P-type ATPase, potential aminophospholipid translocase YAL026C|FUN38|SWA3 gene taxon:4932 20031229 SGD
+SGD S000000024 DRS2 GO:0045332 SGD_REF:S000076777|PMID:15090616 IGI SGD:S000005267 P P-type ATPase, potential aminophospholipid translocase YAL026C|FUN38|SWA3 gene taxon:4932 20051212 SGD
+SGD S000000024 DRS2 GO:0045332 SGD_REF:S000114386|PMID:16452632 IMP P P-type ATPase, potential aminophospholipid translocase YAL026C|FUN38|SWA3 gene taxon:4932 20060216 SGD
+SGD S000000926 DSE1 GO:0005935 SGD_REF:S000074185|PMID:14562095 IDA C YER124C gene taxon:4932 20031028 SGD
+SGD S000000926 DSE1 GO:0005554 SGD_REF:S000069584 ND F YER124C gene taxon:4932 20021002 SGD
+SGD S000000926 DSE1 GO:0007047 SGD_REF:S000066216|PMID:11309124 IMP P YER124C gene taxon:4932 20021002 SGD
+SGD S000001186 DSE2 GO:0005576 SGD_REF:S000068760|PMID:11747810 ISS C YHR143W gene taxon:4932 20020918 SGD
+SGD S000001186 DSE2 GO:0005576 SGD_REF:S000075303|PMID:11935221 IDA C YHR143W gene taxon:4932 20040114 SGD
+SGD S000001186 DSE2 GO:0009277 SGD_REF:S000066216|PMID:11309124 IDA C YHR143W gene taxon:4932 20021002 SGD
+SGD S000001186 DSE2 GO:0004338 SGD_REF:S000068760|PMID:11747810 ISS F YHR143W gene taxon:4932 20020918 SGD
+SGD S000001186 DSE2 GO:0007047 SGD_REF:S000066216|PMID:11309124 IMP P YHR143W gene taxon:4932 20021002 SGD
+SGD S000001186 DSE2 GO:0007109 SGD_REF:S000068760|PMID:11747810 ISS P YHR143W gene taxon:4932 20020918 SGD
+SGD S000001186 DSE2 GO:0007109 SGD_REF:S000068760|PMID:11747810 IEP P YHR143W gene taxon:4932 20020918 SGD
+SGD S000005790 DSE3 GO:0005935 SGD_REF:S000074185|PMID:14562095 IDA C YOR264W gene taxon:4932 20031028 SGD
+SGD S000005790 DSE3 GO:0005554 SGD_REF:S000069584 ND F YOR264W gene taxon:4932 20021002 SGD
+SGD S000005790 DSE3 GO:0000004 SGD_REF:S000069584 ND P YOR264W gene taxon:4932 20021002 SGD
+SGD S000005350 DSE4 GO:0005576 SGD_REF:S000068760|PMID:11747810 ISS C YNR067C|ENG1 gene taxon:4932 20020918 SGD
+SGD S000005350 DSE4 GO:0009277 SGD_REF:S000075303|PMID:11935221 IDA C YNR067C|ENG1 gene taxon:4932 20040114 SGD
+SGD S000005350 DSE4 GO:0030428 SGD_REF:S000071737|PMID:12455695 IDA C YNR067C|ENG1 gene taxon:4932 20021206 SGD
+SGD S000005350 DSE4 GO:0004338 SGD_REF:S000068760|PMID:11747810 ISS F YNR067C|ENG1 gene taxon:4932 20020918 SGD
+SGD S000005350 DSE4 GO:0004338 SGD_REF:S000113719|PMID:16328626 ISS F YNR067C|ENG1 gene taxon:4932 20060124 SGD
+SGD S000005350 DSE4 GO:0007109 SGD_REF:S000068760|PMID:11747810 ISS P YNR067C|ENG1 gene taxon:4932 20020918 SGD
+SGD S000005350 DSE4 GO:0007109 SGD_REF:S000113719|PMID:16328626 IMP P YNR067C|ENG1 gene taxon:4932 20060124 SGD
+SGD S000005350 DSE4 GO:0007109 SGD_REF:S000068760|PMID:11747810 IEP P YNR067C|ENG1 gene taxon:4932 20020918 SGD
+SGD S000000796 DSF1 GO:0008372 SGD_REF:S000069584 ND C YEL070W gene taxon:4932 20030203 SGD
+SGD S000000796 DSF1 GO:0005554 SGD_REF:S000069584 ND F YEL070W gene taxon:4932 20030203 SGD
+SGD S000000796 DSF1 GO:0000004 SGD_REF:S000069584 ND P YEL070W gene taxon:4932 20030203 SGD
+SGD S000000211 DSF2 GO:0008372 SGD_REF:S000069584 ND C YBR007C gene taxon:4932 20021126 SGD
+SGD S000000211 DSF2 GO:0005554 SGD_REF:S000069584 ND F YBR007C gene taxon:4932 20021126 SGD
+SGD S000000211 DSF2 GO:0000004 SGD_REF:S000069584 ND P YBR007C gene taxon:4932 20021126 SGD
+SGD S000004889 DSK2 GO:0005634 SGD_REF:S000058447|PMID:9153752 TAS C ubiquitin-like protein YMR276W gene taxon:4932 20010118 SGD
+SGD S000004889 DSK2 GO:0030674 SGD_REF:S000069044|PMID:11805328 IMP F ubiquitin-like protein YMR276W gene taxon:4932 20040123 SGD
+SGD S000004889 DSK2 GO:0030674 SGD_REF:S000069044|PMID:11805328 IPI F ubiquitin-like protein YMR276W gene taxon:4932 20040123 SGD
+SGD S000004889 DSK2 GO:0007103 SGD_REF:S000058447|PMID:9153752 TAS P ubiquitin-like protein YMR276W gene taxon:4932 20010118 SGD
+SGD S000004889 DSK2 GO:0030433 SGD_REF:S000080877|PMID:15167887 IMP P ubiquitin-like protein YMR276W gene taxon:4932 20050310 SGD
+SGD S000005202 DSL1 GO:0005783 SGD_REF:S000069880|PMID:11739780 IDA C YNL258C gene taxon:4932 20020814 SGD
+SGD S000005202 DSL1 GO:0005554 SGD_REF:S000069584 ND F YNL258C gene taxon:4932 20021209 SGD
+SGD S000005202 DSL1 GO:0006890 SGD_REF:S000069880|PMID:11739780 IMP P YNL258C gene taxon:4932 20021209 SGD
+SGD S000001449 DSN1 GO:0000776 SGD_REF:S000075180|PMID:14657030 IDA C Protein required for cell viability YIR010W gene taxon:4932 20031230 SGD
+SGD S000001449 DSN1 GO:0000818 SGD_REF:S000075142|PMID:14633972 IDA C Protein required for cell viability YIR010W gene taxon:4932 20040618 SGD
+SGD S000001449 DSN1 GO:0000922 SGD_REF:S000071701|PMID:12455957 IDA C Protein required for cell viability YIR010W gene taxon:4932 20030522 SGD
+SGD S000001449 DSN1 GO:0005554 SGD_REF:S000069584 ND F Protein required for cell viability YIR010W gene taxon:4932 20021209 SGD
+SGD S000001449 DSN1 GO:0007059 SGD_REF:S000071701|PMID:12455957 IDA P Protein required for cell viability YIR010W gene taxon:4932 20021209 SGD
+SGD S000006221 DSS4 GO:0005624 SGD_REF:S000047841|PMID:9218467 IDA C GDP dissociation factor for Sec4p YPR017C gene taxon:4932 20020717 SGD
+SGD S000006221 DSS4 GO:0005625 SGD_REF:S000047841|PMID:9218467 IDA C GDP dissociation factor for Sec4p YPR017C gene taxon:4932 20020717 SGD
+SGD S000006221 DSS4 GO:0005085 SGD_REF:S000047841|PMID:9218467 IDA F GDP dissociation factor for Sec4p YPR017C gene taxon:4932 20030528 SGD
+SGD S000006221 DSS4 GO:0008270 SGD_REF:S000047841|PMID:9218467 IDA F GDP dissociation factor for Sec4p YPR017C gene taxon:4932 20020717 SGD
+SGD S000006221 DSS4 GO:0045045 SGD_REF:S000047841|PMID:9218467 IGI P GDP dissociation factor for Sec4p YPR017C gene taxon:4932 20020717 SGD
+SGD S000006221 DSS4 GO:0045045 SGD_REF:S000047841|PMID:9218467 IPI P GDP dissociation factor for Sec4p YPR017C gene taxon:4932 20020717 SGD
+SGD S000003011 DST1 GO:0005654 SGD_REF:S000058480|PMID:9334234 IPI C RNA polymerase II elongation factor, Transcription elongation factor S-II (TFIIS), transcription elongation factor YGL043W|P37|PPR2|S-II|SII|TFIIS gene taxon:4932 20010118 SGD
+SGD S000003011 DST1 GO:0008159 SGD_REF:S000058480|PMID:9334234 IDA F RNA polymerase II elongation factor, Transcription elongation factor S-II (TFIIS), transcription elongation factor YGL043W|P37|PPR2|S-II|SII|TFIIS gene taxon:4932 20010118 SGD
+SGD S000003011 DST1 GO:0008159 SGD_REF:S000073612|PMID:8288647 IDA F RNA polymerase II elongation factor, Transcription elongation factor S-II (TFIIS), transcription elongation factor YGL043W|P37|PPR2|S-II|SII|TFIIS gene taxon:4932 20060418 SGD
+SGD S000003011 DST1 GO:0006368 SGD_REF:S000058480|PMID:9334234 IDA P RNA polymerase II elongation factor, Transcription elongation factor S-II (TFIIS), transcription elongation factor YGL043W|P37|PPR2|S-II|SII|TFIIS gene taxon:4932 20010118 SGD
+SGD S000003011 DST1 GO:0006379 SGD_REF:S000077423|PMID:15359273 TAS P RNA polymerase II elongation factor, Transcription elongation factor S-II (TFIIS), transcription elongation factor YGL043W|P37|PPR2|S-II|SII|TFIIS gene taxon:4932 20041101 SGD
+SGD S000003011 DST1 GO:0006379 SGD_REF:S000076264|PMID:12692127 IDA P RNA polymerase II elongation factor, Transcription elongation factor S-II (TFIIS), transcription elongation factor YGL043W|P37|PPR2|S-II|SII|TFIIS gene taxon:4932 20041101 SGD
+SGD S000003011 DST1 GO:0007131 SGD_REF:S000047341|PMID:1850099 IMP P RNA polymerase II elongation factor, Transcription elongation factor S-II (TFIIS), transcription elongation factor YGL043W|P37|PPR2|S-II|SII|TFIIS gene taxon:4932 20010118 SGD
+SGD S000002378 DTD1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C D-Tyr-tRNA(Tyr) deacylase YDL219W gene taxon:4932 20031028 SGD
+SGD S000002378 DTD1 GO:0016788 SGD_REF:S000056337|PMID:10766779 IDA F D-Tyr-tRNA(Tyr) deacylase YDL219W gene taxon:4932 20021011 SGD
+SGD S000002378 DTD1 GO:0019478 SGD_REF:S000056337|PMID:10766779 IDA P D-Tyr-tRNA(Tyr) deacylase YDL219W gene taxon:4932 20021011 SGD
+SGD S000002378 DTD1 GO:0043037 SGD_REF:S000055708|PMID:10618371 TAS P D-Tyr-tRNA(Tyr) deacylase YDL219W gene taxon:4932 20031231 SGD
+SGD S000000384 DTR1 GO:0005628 SGD_REF:S000071740|PMID:12455697 IDA C dityrosine transporter MFS-MDR YBR180W gene taxon:4932 20021202 SGD
+SGD S000000384 DTR1 GO:0005275 SGD_REF:S000071740|PMID:12455697 IMP F dityrosine transporter MFS-MDR YBR180W gene taxon:4932 20021202 SGD
+SGD S000000384 DTR1 GO:0015239 SGD_REF:S000071740|PMID:12455697 IMP F dityrosine transporter MFS-MDR YBR180W gene taxon:4932 20021202 SGD
+SGD S000000384 DTR1 GO:0015239 SGD_REF:S000071740|PMID:12455697 ISS F dityrosine transporter MFS-MDR YBR180W gene taxon:4932 20021202 SGD
+SGD S000000384 DTR1 GO:0015837 SGD_REF:S000071740|PMID:12455697 IMP P dityrosine transporter MFS-MDR YBR180W gene taxon:4932 20021202 SGD
+SGD S000000384 DTR1 GO:0030476 SGD_REF:S000071740|PMID:12455697 IMP P dityrosine transporter MFS-MDR YBR180W gene taxon:4932 20021202 SGD
+SGD S000002259 DUN1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C protein kinase YDL101C gene taxon:4932 20031028 SGD
+SGD S000002259 DUN1 GO:0004672 SGD_REF:S000069725|PMID:11904430 IDA F protein kinase YDL101C gene taxon:4932 20021112 SGD
+SGD S000002259 DUN1 GO:0000075 SGD_REF:S000069725|PMID:11904430 IMP P protein kinase YDL101C gene taxon:4932 20021112 SGD
+SGD S000002259 DUN1 GO:0000077 SGD_REF:S000069725|PMID:11904430 IMP P protein kinase YDL101C gene taxon:4932 20021112 SGD
+SGD S000002259 DUN1 GO:0006468 SGD_REF:S000069725|PMID:11904430 IDA P protein kinase YDL101C gene taxon:4932 20021112 SGD
+SGD S000003029 DUO1 GO:0000778 SGD_REF:S000069091|PMID:11756468 IPI C YGL061C gene taxon:4932 20021008 SGD
+SGD S000003029 DUO1 GO:0005816 SGD_REF:S000046073|PMID:9817759 IDA C YGL061C gene taxon:4932 20040120 SGD
+SGD S000003029 DUO1 GO:0005819 SGD_REF:S000069091|PMID:11756468 IPI C YGL061C gene taxon:4932 20021008 SGD
+SGD S000003029 DUO1 GO:0005876 SGD_REF:S000046073|PMID:9817759 IDA C YGL061C gene taxon:4932 20040120 SGD
+SGD S000003029 DUO1 GO:0042729 SGD_REF:S000069052|PMID:11799062 IDA C YGL061C gene taxon:4932 20040122 SGD
+SGD S000003029 DUO1 GO:0042729 SGD_REF:S000080667|PMID:15664196 IPI C YGL061C gene taxon:4932 20050328 SGD
+SGD S000003029 DUO1 GO:0042729 SGD_REF:S000080667|PMID:15664196 IDA C YGL061C gene taxon:4932 20050328 SGD
+SGD S000003029 DUO1 GO:0042729 SGD_REF:S000080444|PMID:15640796 IPI C YGL061C gene taxon:4932 20050328 SGD
+SGD S000003029 DUO1 GO:0042729 SGD_REF:S000069052|PMID:11799062 IPI C YGL061C gene taxon:4932 20040122 SGD
+SGD S000003029 DUO1 GO:0042729 SGD_REF:S000080444|PMID:15640796 IDA C YGL061C gene taxon:4932 20050328 SGD
+SGD S000003029 DUO1 GO:0005200 SGD_REF:S000069091|PMID:11756468 IPI F YGL061C gene taxon:4932 20021008 SGD
+SGD S000003029 DUO1 GO:0030472 SGD_REF:S000069091|PMID:11756468 IPI P YGL061C gene taxon:4932 20021008 SGD
+SGD S000003029 DUO1 GO:0031110 SGD_REF:S000080667|PMID:15664196 IPI P YGL061C gene taxon:4932 20050328 SGD
+SGD S000003029 DUO1 GO:0031110 SGD_REF:S000080667|PMID:15664196 IDA P YGL061C gene taxon:4932 20050328 SGD
+SGD S000000412 DUR1,2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C urea amidolyase (contains urea carboxylase and allophanate hydrolase) YBR208C|DUR80 gene taxon:4932 20031028 SGD
+SGD S000000412 DUR1,2 GO:0004039 SGD_REF:S000042072|PMID:6105114 IMP F urea amidolyase (contains urea carboxylase and allophanate hydrolase) YBR208C|DUR80 gene taxon:4932 20020926 SGD
+SGD S000000412 DUR1,2 GO:0004847 SGD_REF:S000042072|PMID:6105114 IMP F urea amidolyase (contains urea carboxylase and allophanate hydrolase) YBR208C|DUR80 gene taxon:4932 20020926 SGD
+SGD S000000412 DUR1,2 GO:0000256 SGD_REF:S000047314|PMID:1938916 TAS P urea amidolyase (contains urea carboxylase and allophanate hydrolase) YBR208C|DUR80 gene taxon:4932 20040122 SGD
+SGD S000000412 DUR1,2 GO:0019627 SGD_REF:S000042072|PMID:6105114 IMP P urea amidolyase (contains urea carboxylase and allophanate hydrolase) YBR208C|DUR80 gene taxon:4932 20020926 SGD
+SGD S000001008 DUR3 GO:0005886 SGD_REF:S000047807|PMID:8335627 ISS C YHL016C gene taxon:4932 20021003 SGD
+SGD S000001008 DUR3 GO:0005886 SGD_REF:S000047807|PMID:8335627 IMP C YHL016C gene taxon:4932 20021003 SGD
+SGD S000001008 DUR3 GO:0015204 SGD_REF:S000047807|PMID:8335627 ISS F YHL016C gene taxon:4932 20021003 SGD
+SGD S000001008 DUR3 GO:0015204 SGD_REF:S000047807|PMID:8335627 IMP F YHL016C gene taxon:4932 20021003 SGD
+SGD S000001008 DUR3 GO:0015840 SGD_REF:S000047807|PMID:8335627 ISS P YHL016C gene taxon:4932 20021003 SGD
+SGD S000001008 DUR3 GO:0015840 SGD_REF:S000047807|PMID:8335627 IMP P YHL016C gene taxon:4932 20021003 SGD
+SGD S000004545 DUS1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C tRNA dihydrouridine synthase YML080W gene taxon:4932 20031028 SGD
+SGD S000004545 DUS1 GO:0017150 SGD_REF:S000072844|PMID:12003496 IDA F tRNA dihydrouridine synthase YML080W gene taxon:4932 20011002 SGD
+SGD S000004545 DUS1 GO:0006400 SGD_REF:S000072844|PMID:12003496 IDA P tRNA dihydrouridine synthase YML080W gene taxon:4932 20011002 SGD
+SGD S000004393 DUS3 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C dihydrouridine synthase 3 YLR401C gene taxon:4932 20031028 SGD
+SGD S000004393 DUS3 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C dihydrouridine synthase 3 YLR401C gene taxon:4932 20031028 SGD
+SGD S000004393 DUS3 GO:0017150 SGD_REF:S000072844|PMID:12003496 ISS F dihydrouridine synthase 3 YLR401C gene taxon:4932 20021001 SGD
+SGD S000004393 DUS3 GO:0006400 SGD_REF:S000072844|PMID:12003496 ISS P dihydrouridine synthase 3 YLR401C gene taxon:4932 20021001 SGD
+SGD S000004397 DUS4 GO:0008372 SGD_REF:S000069584 ND C dihydrouridine synthase 4 YLR405W gene taxon:4932 20021001 SGD
+SGD S000004397 DUS4 GO:0017150 SGD_REF:S000072844|PMID:12003496 ISS F dihydrouridine synthase 4 YLR405W gene taxon:4932 20021001 SGD
+SGD S000004397 DUS4 GO:0006400 SGD_REF:S000072844|PMID:12003496 ISS P dihydrouridine synthase 4 YLR405W gene taxon:4932 20021001 SGD
+SGD S000000456 DUT1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C dUTP pyrophosphatase YBR252W gene taxon:4932 20031028 SGD
+SGD S000000456 DUT1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C dUTP pyrophosphatase YBR252W gene taxon:4932 20031028 SGD
+SGD S000000456 DUT1 GO:0004170 SGD_REF:S000051873|PMID:8223452 IMP F dUTP pyrophosphatase YBR252W gene taxon:4932 20020926 SGD
+SGD S000000456 DUT1 GO:0009213 SGD_REF:S000051873|PMID:8223452 IMP P dUTP pyrophosphatase YBR252W gene taxon:4932 20020926 SGD
+SGD S000001762 DYN1 GO:0005868 SGD_REF:S000080445|PMID:15642746 TAS C heavy chain of cytoplasmic dynein YKR054C|DHC1|PAC6 gene taxon:4932 20050224 SGD
+SGD S000001762 DYN1 GO:0005881 SGD_REF:S000058447|PMID:9153752 TAS C heavy chain of cytoplasmic dynein YKR054C|DHC1|PAC6 gene taxon:4932 20010118 SGD
+SGD S000001762 DYN1 GO:0005881 SGD_REF:S000072477|PMID:12566428 IDA C heavy chain of cytoplasmic dynein YKR054C|DHC1|PAC6 gene taxon:4932 20030211 SGD
+SGD S000001762 DYN1 GO:0003774 SGD_REF:S000058447|PMID:9153752 TAS F heavy chain of cytoplasmic dynein YKR054C|DHC1|PAC6 gene taxon:4932 20010118 SGD
+SGD S000001762 DYN1 GO:0000022 SGD_REF:S000058447|PMID:9153752 TAS P heavy chain of cytoplasmic dynein YKR054C|DHC1|PAC6 gene taxon:4932 20010118 SGD
+SGD S000001762 DYN1 GO:0000070 SGD_REF:S000058447|PMID:9153752 TAS P heavy chain of cytoplasmic dynein YKR054C|DHC1|PAC6 gene taxon:4932 20010118 SGD
+SGD S000001762 DYN1 GO:0000132 SGD_REF:S000042553|PMID:9281582 IMP P heavy chain of cytoplasmic dynein YKR054C|DHC1|PAC6 gene taxon:4932 20040128 SGD
+SGD S000001762 DYN1 GO:0000132 SGD_REF:S000042553|PMID:9281582 IGI P heavy chain of cytoplasmic dynein YKR054C|DHC1|PAC6 gene taxon:4932 20040128 SGD
+SGD S000001762 DYN1 GO:0030473 SGD_REF:S000058447|PMID:9153752 TAS P heavy chain of cytoplasmic dynein YKR054C|DHC1|PAC6 gene taxon:4932 20010118 SGD
+SGD S000002832 DYN2 GO:0005868 SGD_REF:S000046295|PMID:8628245 ISS C dynein light chain (putative) YDR424C|SLC1 gene taxon:4932 20050224 SGD
+SGD S000002832 DYN2 GO:0005881 SGD_REF:S000058447|PMID:9153752 TAS C dynein light chain (putative) YDR424C|SLC1 gene taxon:4932 20041203 SGD
+SGD S000002832 DYN2 GO:0003777 SGD_REF:S000046295|PMID:8628245 ISS F dynein light chain (putative) YDR424C|SLC1 gene taxon:4932 20010118 SGD
+SGD S000002832 DYN2 GO:0007017 SGD_REF:S000046295|PMID:8628245 IGI P dynein light chain (putative) YDR424C|SLC1 gene taxon:4932 20010118 SGD
+SGD S000002832 DYN2 GO:0030029 SGD_REF:S000043301|PMID:8293974 IGI P dynein light chain (putative) YDR424C|SLC1 gene taxon:4932 20010620 SGD
+SGD S000004914 DYN3 GO:0005868 SGD_REF:S000080445|PMID:15642746 IPI SGD:S000001762 C Light intermediate chain of dynein YMR299C gene taxon:4932 20050125 SGD
+SGD S000004914 DYN3 GO:0005881 SGD_REF:S000080445|PMID:15642746 IDA C Light intermediate chain of dynein YMR299C gene taxon:4932 20050125 SGD
+SGD S000004914 DYN3 GO:0005881 SGD_REF:S000074658|PMID:14764870 IDA C Light intermediate chain of dynein YMR299C gene taxon:4932 20050125 SGD
+SGD S000004914 DYN3 contributes_to GO:0003774 SGD_REF:S000080445|PMID:15642746 IMP F Light intermediate chain of dynein YMR299C gene taxon:4932 20050125 SGD
+SGD S000004914 DYN3 contributes_to GO:0003774 SGD_REF:S000074658|PMID:14764870 ISS F Light intermediate chain of dynein YMR299C gene taxon:4932 20050125 SGD
+SGD S000004914 DYN3 GO:0030473 SGD_REF:S000080445|PMID:15642746 IMP P Light intermediate chain of dynein YMR299C gene taxon:4932 20050125 SGD
+SGD S000004914 DYN3 GO:0030473 SGD_REF:S000074658|PMID:14764870 IMP P Light intermediate chain of dynein YMR299C gene taxon:4932 20050125 SGD
+SGD S000001110 DYS1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C deoxyhypusine synthase YHR068W gene taxon:4932 20031028 SGD
+SGD S000001110 DYS1 GO:0016765 SGD_REF:S000039694|PMID:7629166 IDA F deoxyhypusine synthase YHR068W gene taxon:4932 20040310 SGD
+SGD S000001110 DYS1 GO:0008612 SGD_REF:S000039694|PMID:7629166 IDA P deoxyhypusine synthase YHR068W gene taxon:4932 20020926 SGD
+SGD S000006227 EAF3 GO:0000123 SGD_REF:S000060726|PMID:11036083 IDA C YPR023C gene taxon:4932 20020918 SGD
+SGD S000006227 EAF3 GO:0043189 SGD_REF:S000079775|PMID:15485911 IPI C YPR023C gene taxon:4932 20050207 SGD
+SGD S000006227 EAF3 GO:0004402 SGD_REF:S000060726|PMID:11036083 IDA F YPR023C gene taxon:4932 20020918 SGD
+SGD S000006227 EAF3 GO:0006357 SGD_REF:S000060726|PMID:11036083 IMP P YPR023C gene taxon:4932 20020918 SGD
+SGD S000006227 EAF3 GO:0016573 SGD_REF:S000060726|PMID:11036083 IDA P YPR023C gene taxon:4932 20020918 SGD
+SGD S000000744 EAF5 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YEL018W gene taxon:4932 20031028 SGD
+SGD S000000744 EAF5 GO:0043189 SGD_REF:S000079775|PMID:15485911 IPI C YEL018W gene taxon:4932 20050207 SGD
+SGD S000000744 EAF5 GO:0005554 SGD_REF:S000069584 ND F YEL018W gene taxon:4932 20021122 SGD
+SGD S000000744 EAF5 GO:0000004 SGD_REF:S000069584 ND P YEL018W gene taxon:4932 20021122 SGD
+SGD S000003842 EAF6 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YJR082C gene taxon:4932 20031028 SGD
+SGD S000003842 EAF6 GO:0043189 SGD_REF:S000079775|PMID:15485911 IPI C YJR082C gene taxon:4932 20050207 SGD
+SGD S000003842 EAF6 GO:0005554 SGD_REF:S000069584 ND F YJR082C gene taxon:4932 20021122 SGD
+SGD S000003842 EAF6 GO:0000004 SGD_REF:S000069584 ND P YJR082C gene taxon:4932 20021122 SGD
+SGD S000005080 EAF7 GO:0000123 SGD_REF:S000077129|PMID:15353583 IDA C YNL136W gene taxon:4932 20040922 SGD
+SGD S000005080 EAF7 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YNL136W gene taxon:4932 20031028 SGD
+SGD S000005080 EAF7 GO:0043189 SGD_REF:S000077129|PMID:15353583 IPI C YNL136W gene taxon:4932 20050207 SGD
+SGD S000005080 EAF7 GO:0005554 SGD_REF:S000069584 ND F YNL136W gene taxon:4932 20030203 SGD
+SGD S000005080 EAF7 GO:0006357 SGD_REF:S000077129|PMID:15353583 IMP P YNL136W gene taxon:4932 20040922 SGD
+SGD S000005080 EAF7 GO:0006357 SGD_REF:S000077129|PMID:15353583 IPI SGD:S000005080 P YNL136W gene taxon:4932 20040922 SGD
+SGD S000005080 EAF7 GO:0016573 SGD_REF:S000077129|PMID:15353583 IPI SGD:S000005080 P YNL136W gene taxon:4932 20040922 SGD
+SGD S000001687 EAP1 GO:0005845 SGD_REF:S000043142|PMID:10848587 IPI C YKL204W gene taxon:4932 20020724 SGD
+SGD S000001687 EAP1 GO:0008190 SGD_REF:S000074429|PMID:14530432 TAS F YKL204W gene taxon:4932 20050330 SGD
+SGD S000001687 EAP1 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P YKL204W gene taxon:4932 20060227 SGD
+SGD S000001687 EAP1 GO:0016478 SGD_REF:S000043142|PMID:10848587 IDA P YKL204W gene taxon:4932 20020724 SGD
+SGD S000001687 EAP1 GO:0016478 SGD_REF:S000043142|PMID:10848587 IMP P YKL204W gene taxon:4932 20020724 SGD
+SGD S000001655 EBP2 GO:0005730 SGD_REF:S000044206|PMID:10849420 IDA C nucleolar protein YKL172W gene taxon:4932 20010118 SGD
+SGD S000001655 EBP2 GO:0005554 SGD_REF:S000069584 ND F nucleolar protein YKL172W gene taxon:4932 20051026 SGD
+SGD S000001655 EBP2 GO:0000280 SGD_REF:S000080298|PMID:15515129 IMP P nucleolar protein YKL172W gene taxon:4932 20051026 SGD
+SGD S000001655 EBP2 GO:0006364 SGD_REF:S000044206|PMID:10849420 IMP P nucleolar protein YKL172W gene taxon:4932 20010118 SGD
+SGD S000002614 EBS1 GO:0005737 SGD_REF:S000114339|PMID:16467471 IDA C YDR206W gene taxon:4932 20060608 SGD
+SGD S000002614 EBS1 GO:0005554 SGD_REF:S000069584 ND F YDR206W gene taxon:4932 20010119 SGD
+SGD S000002614 EBS1 GO:0007004 SGD_REF:S000045887|PMID:10688642 IMP P YDR206W gene taxon:4932 20010118 SGD
+SGD S000002614 EBS1 GO:0007004 SGD_REF:S000045887|PMID:10688642 IGI P YDR206W gene taxon:4932 20010118 SGD
+SGD S000002614 EBS1 GO:0016478 SGD_REF:S000114339|PMID:16467471 IMP P YDR206W gene taxon:4932 20060608 SGD
+SGD S000004274 ECI1 GO:0005777 SGD_REF:S000053557|PMID:9837886 IDA C d3,d2-Enoyl-CoA Isomerase YLR284C gene taxon:4932 20010118 SGD
+SGD S000004274 ECI1 GO:0005777 SGD_REF:S000052895|PMID:9813046 IDA C d3,d2-Enoyl-CoA Isomerase YLR284C gene taxon:4932 20021024 SGD
+SGD S000004274 ECI1 GO:0004165 SGD_REF:S000053557|PMID:9837886 IMP F d3,d2-Enoyl-CoA Isomerase YLR284C gene taxon:4932 20011005 SGD
+SGD S000004274 ECI1 GO:0004165 SGD_REF:S000052895|PMID:9813046 IDA F d3,d2-Enoyl-CoA Isomerase YLR284C gene taxon:4932 20021024 SGD
+SGD S000004274 ECI1 GO:0004165 SGD_REF:S000052895|PMID:9813046 IMP F d3,d2-Enoyl-CoA Isomerase YLR284C gene taxon:4932 20021024 SGD
+SGD S000004274 ECI1 GO:0004165 SGD_REF:S000053557|PMID:9837886 IDA F d3,d2-Enoyl-CoA Isomerase YLR284C gene taxon:4932 20011005 SGD
+SGD S000004274 ECI1 GO:0006635 SGD_REF:S000053557|PMID:9837886 IDA P d3,d2-Enoyl-CoA Isomerase YLR284C gene taxon:4932 20010118 SGD
+SGD S000004274 ECI1 GO:0006635 SGD_REF:S000052895|PMID:9813046 IDA P d3,d2-Enoyl-CoA Isomerase YLR284C gene taxon:4932 20021024 SGD
+SGD S000000055 ECM1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YAL059W gene taxon:4932 20031028 SGD
+SGD S000000055 ECM1 GO:0005654 SGD_REF:S000066162|PMID:11583615 IDA C YAL059W gene taxon:4932 20040127 SGD
+SGD S000000055 ECM1 GO:0005730 SGD_REF:S000066162|PMID:11583615 IDA C YAL059W gene taxon:4932 20040127 SGD
+SGD S000000055 ECM1 GO:0005554 SGD_REF:S000069584 ND F YAL059W gene taxon:4932 20020927 SGD
+SGD S000000055 ECM1 GO:0000055 SGD_REF:S000066162|PMID:11583615 IGI SGD:S000001669 P YAL059W gene taxon:4932 20040127 SGD
+SGD S000000055 ECM1 GO:0000055 SGD_REF:S000072298|PMID:12486219 TAS P YAL059W gene taxon:4932 20040127 SGD
+SGD S000000055 ECM1 GO:0007047 SGD_REF:S000058218|PMID:9335584 IMP P YAL059W gene taxon:4932 20020927 SGD
+SGD S000000756 ECM10 GO:0005739 SGD_REF:S000058437|PMID:11150530 IDA C YEL030W|SSC3 gene taxon:4932 20020808 SGD
+SGD S000000756 ECM10 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YEL030W|SSC3 gene taxon:4932 20040924 SGD
+SGD S000000756 ECM10 GO:0042645 SGD_REF:S000074142|PMID:12943685 IDA C YEL030W|SSC3 gene taxon:4932 20031018 SGD
+SGD S000000756 ECM10 GO:0005554 SGD_REF:S000069584 ND F YEL030W|SSC3 gene taxon:4932 20040715 SGD
+SGD S000000756 ECM10 GO:0006626 SGD_REF:S000058437|PMID:11150530 IGI P YEL030W|SSC3 gene taxon:4932 20020808 SGD
+SGD S000000756 ECM10 GO:0042026 SGD_REF:S000058437|PMID:11150530 IGI P YEL030W|SSC3 gene taxon:4932 20040715 SGD
+SGD S000002854 ECM11 GO:0005634 SGD_REF:S000069464|PMID:11678331 IDA C YDR446W gene taxon:4932 20020819 SGD
+SGD S000002854 ECM11 GO:0005554 SGD_REF:S000069584 ND F YDR446W gene taxon:4932 20051104 SGD
+SGD S000002854 ECM11 GO:0007047 SGD_REF:S000058218|PMID:9335584 IMP P YDR446W gene taxon:4932 20020927 SGD
+SGD S000002854 ECM11 GO:0007131 SGD_REF:S000079868|PMID:15598532 IMP P YDR446W gene taxon:4932 20051104 SGD
+SGD S000003531 ECM12 GO:0008372 SGD_REF:S000069584 ND C YHR021W-A gene taxon:4932 20020927 SGD
+SGD S000003531 ECM12 GO:0005554 SGD_REF:S000069584 ND F YHR021W-A gene taxon:4932 20020927 SGD
+SGD S000003531 ECM12 GO:0007047 SGD_REF:S000058218|PMID:9335584 IMP P YHR021W-A gene taxon:4932 20020927 SGD
+SGD S000000139 ECM13 GO:0008372 SGD_REF:S000069584 ND C YBL043W gene taxon:4932 20020927 SGD
+SGD S000000139 ECM13 GO:0005554 SGD_REF:S000069584 ND F YBL043W gene taxon:4932 20020927 SGD
+SGD S000000139 ECM13 GO:0007047 SGD_REF:S000058218|PMID:9335584 IMP P YBL043W gene taxon:4932 20020927 SGD
+SGD S000001174 ECM14 GO:0000324 SGD_REF:S000074185|PMID:14562095 IDA C YHR132C gene taxon:4932 20031028 SGD
+SGD S000001174 ECM14 GO:0004222 SGD_REF:S000080056|PMID:15606766 ISS F YHR132C gene taxon:4932 20050415 SGD
+SGD S000001174 ECM14 GO:0006508 SGD_REF:S000080056|PMID:15606766 ISS P YHR132C gene taxon:4932 20050415 SGD
+SGD S000001174 ECM14 GO:0007047 SGD_REF:S000058218|PMID:9335584 IMP P YHR132C gene taxon:4932 20020927 SGD
+SGD S000000097 ECM15 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YBL001C gene taxon:4932 20031028 SGD
+SGD S000000097 ECM15 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YBL001C gene taxon:4932 20031028 SGD
+SGD S000000097 ECM15 GO:0005554 SGD_REF:S000069584 ND F YBL001C gene taxon:4932 20020927 SGD
+SGD S000000097 ECM15 GO:0007047 SGD_REF:S000058218|PMID:9335584 IMP P YBL001C gene taxon:4932 20020927 SGD
+SGD S000004735 ECM16 GO:0005730 SGD_REF:S000062679|PMID:10982841 IDA C U3 snoRNP protein YMR128W|DHR1 gene taxon:4932 20020319 SGD
+SGD S000004735 ECM16 GO:0005732 SGD_REF:S000070145|PMID:12068309 IPI C U3 snoRNP protein YMR128W|DHR1 gene taxon:4932 20030224 SGD
+SGD S000004735 ECM16 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C U3 snoRNP protein YMR128W|DHR1 gene taxon:4932 20040928 SGD
+SGD S000004735 ECM16 GO:0003724 SGD_REF:S000062679|PMID:10982841 IDA F U3 snoRNP protein YMR128W|DHR1 gene taxon:4932 20020319 SGD
+SGD S000004735 ECM16 GO:0007046 SGD_REF:S000062679|PMID:10982841 IDA P U3 snoRNP protein YMR128W|DHR1 gene taxon:4932 20020319 SGD
+SGD S000004735 ECM16 GO:0007046 SGD_REF:S000062679|PMID:10982841 TAS P U3 snoRNP protein YMR128W|DHR1 gene taxon:4932 20020319 SGD
+SGD S000004735 ECM16 GO:0030490 SGD_REF:S000070145|PMID:12068309 IPI P U3 snoRNP protein YMR128W|DHR1 gene taxon:4932 20020905 SGD
+SGD S000003898 ECM17 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C sulfite reductase beta subunit YJR137C|MET5 gene taxon:4932 20031028 SGD
+SGD S000003898 ECM17 GO:0005737 SGD_REF:S000069744|PMID:11921096 TAS C sulfite reductase beta subunit YJR137C|MET5 gene taxon:4932 20050130 SGD
+SGD S000003898 ECM17 GO:0009337 SGD_REF:S000044218|PMID:9003798 IDA C sulfite reductase beta subunit YJR137C|MET5 gene taxon:4932 20031215 SGD
+SGD S000003898 ECM17 GO:0009337 SGD_REF:S000044218|PMID:9003798 ISS C sulfite reductase beta subunit YJR137C|MET5 gene taxon:4932 20031215 SGD
+SGD S000003898 ECM17 GO:0004783 SGD_REF:S000048584|PMID:1479340 NAS F sulfite reductase beta subunit YJR137C|MET5 gene taxon:4932 20010118 SGD
+SGD S000003898 ECM17 GO:0000103 SGD_REF:S000048584|PMID:1479340 NAS P sulfite reductase beta subunit YJR137C|MET5 gene taxon:4932 20010118 SGD
+SGD S000003898 ECM17 GO:0007047 SGD_REF:S000058218|PMID:9335584 IMP P sulfite reductase beta subunit YJR137C|MET5 gene taxon:4932 20010118 SGD
+SGD S000003898 ECM17 GO:0008652 SGD_REF:S000049309|PMID:1789001 TAS P sulfite reductase beta subunit YJR137C|MET5 gene taxon:4932 20040217 SGD
+SGD S000002532 ECM18 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YDR125C gene taxon:4932 20031028 SGD
+SGD S000002532 ECM18 GO:0005554 SGD_REF:S000069584 ND F YDR125C gene taxon:4932 20020927 SGD
+SGD S000002532 ECM18 GO:0007047 SGD_REF:S000058218|PMID:9335584 IMP P YDR125C gene taxon:4932 20020927 SGD
+SGD S000004382 ECM19 GO:0008372 SGD_REF:S000069584 ND C YLR390W gene taxon:4932 20020927 SGD
+SGD S000004382 ECM19 GO:0005554 SGD_REF:S000069584 ND F YLR390W gene taxon:4932 20020927 SGD
+SGD S000004382 ECM19 GO:0007047 SGD_REF:S000058218|PMID:9335584 IMP P YLR390W gene taxon:4932 20020927 SGD
+SGD S000000269 ECM2 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YBR065C|SLT11 gene taxon:4932 20031028 SGD
+SGD S000000269 ECM2 GO:0005554 SGD_REF:S000069584 ND F YBR065C|SLT11 gene taxon:4932 20020927 SGD
+SGD S000000269 ECM2 GO:0000398 SGD_REF:S000052102|PMID:9528778 IGI SGD:S000006478 P YBR065C|SLT11 gene taxon:4932 20040217 SGD
+SGD S000000269 ECM2 GO:0007047 SGD_REF:S000058218|PMID:9335584 IMP P YBR065C|SLT11 gene taxon:4932 20020927 SGD
+SGD S000000197 ECM21 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YBL101C gene taxon:4932 20031028 SGD
+SGD S000000197 ECM21 GO:0005554 SGD_REF:S000069584 ND F YBL101C gene taxon:4932 20020927 SGD
+SGD S000000197 ECM21 GO:0007047 SGD_REF:S000058218|PMID:9335584 IMP P YBL101C gene taxon:4932 20020927 SGD
+SGD S000004218 ECM22 GO:0005634 SGD_REF:S000066114|PMID:11533229 IPI C YLR228C gene taxon:4932 20020918 SGD
+SGD S000004218 ECM22 GO:0003702 SGD_REF:S000066114|PMID:11533229 IDA F YLR228C gene taxon:4932 20020918 SGD
+SGD S000004218 ECM22 GO:0016126 SGD_REF:S000066114|PMID:11533229 IMP P YLR228C gene taxon:4932 20020918 SGD
+SGD S000005942 ECM23 GO:0008372 SGD_REF:S000069584 ND C YPL021W|SRD2 gene taxon:4932 20020927 SGD
+SGD S000005942 ECM23 GO:0005554 SGD_REF:S000069584 ND F YPL021W|SRD2 gene taxon:4932 20020927 SGD
+SGD S000005942 ECM23 GO:0007124 SGD_REF:S000070197|PMID:11889490 IMP P YPL021W|SRD2 gene taxon:4932 20020927 SGD
+SGD S000003737 ECM25 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YJL201W gene taxon:4932 20031028 SGD
+SGD S000003737 ECM25 GO:0005554 SGD_REF:S000069584 ND F YJL201W gene taxon:4932 20020927 SGD
+SGD S000003737 ECM25 GO:0007047 SGD_REF:S000058218|PMID:9335584 IMP P YJL201W gene taxon:4932 20020927 SGD
+SGD S000003737 ECM25 GO:0030447 SGD_REF:S000080384|PMID:15645503 IMP P YJL201W gene taxon:4932 20050621 SGD
+SGD S000003867 ECM27 GO:0008372 SGD_REF:S000069584 ND C YJR106W gene taxon:4932 20020927 SGD
+SGD S000003867 ECM27 GO:0005554 SGD_REF:S000069584 ND F YJR106W gene taxon:4932 20020927 SGD
+SGD S000003867 ECM27 GO:0007047 SGD_REF:S000058218|PMID:9335584 IMP P YJR106W gene taxon:4932 20020927 SGD
+SGD S000001022 ECM29 GO:0000502 SGD_REF:S000071808|PMID:12408819 IDA C YHL030W gene taxon:4932 20040314 SGD
+SGD S000001022 ECM29 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YHL030W gene taxon:4932 20031028 SGD
+SGD S000001022 ECM29 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YHL030W gene taxon:4932 20031028 SGD
+SGD S000001022 ECM29 GO:0005515 SGD_REF:S000075596|PMID:35488 IDA F YHL030W gene taxon:4932 20040314 SGD
+SGD S000001022 ECM29 GO:0005515 SGD_REF:S000075596|PMID:35488 IMP F YHL030W gene taxon:4932 20040314 SGD
+SGD S000001022 ECM29 GO:0030163 SGD_REF:S000075596|PMID:35488 IC GO:0000502 P YHL030W gene taxon:4932 20040314 SGD
+SGD S000005618 ECM3 GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YOR092W|YOR3165W gene taxon:4932 20031028 SGD
+SGD S000005618 ECM3 GO:0016887 SGD_REF:S000050653|PMID:9200815 ISS F YOR092W|YOR3165W gene taxon:4932 20030206 SGD
+SGD S000005618 ECM3 GO:0007047 SGD_REF:S000058218|PMID:9335584 IMP P YOR092W|YOR3165W gene taxon:4932 20020927 SGD
+SGD S000004428 ECM30 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YLR436C gene taxon:4932 20031028 SGD
+SGD S000004428 ECM30 GO:0005554 SGD_REF:S000069584 ND F YLR436C gene taxon:4932 20020927 SGD
+SGD S000004428 ECM30 GO:0007047 SGD_REF:S000058218|PMID:9335584 IMP P YLR436C gene taxon:4932 20020927 SGD
+SGD S000000380 ECM31 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YBR176W gene taxon:4932 20031028 SGD
+SGD S000000380 ECM31 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YBR176W gene taxon:4932 20040924 SGD
+SGD S000000380 ECM31 GO:0003864 SGD_REF:S000060103|PMID:11154694 IMP F YBR176W gene taxon:4932 20021218 SGD
+SGD S000000380 ECM31 GO:0003864 SGD_REF:S000060103|PMID:11154694 ISS F YBR176W gene taxon:4932 20021218 SGD
+SGD S000000380 ECM31 GO:0015940 SGD_REF:S000060103|PMID:11154694 IMP P YBR176W gene taxon:4932 20020801 SGD
+SGD S000000978 ECM32 GO:0005844 SGD_REF:S000055065|PMID:10836794 IDA C DNA helicase I YER176W|HEL1|MTT1 gene taxon:4932 20020711 SGD
+SGD S000000978 ECM32 GO:0003678 SGD_REF:S000040773|PMID:9434351 IDA F DNA helicase I YER176W|HEL1|MTT1 gene taxon:4932 20020711 SGD
+SGD S000000978 ECM32 GO:0003724 SGD_REF:S000055065|PMID:10836794 ISS F DNA helicase I YER176W|HEL1|MTT1 gene taxon:4932 20020711 SGD
+SGD S000000978 ECM32 GO:0006449 SGD_REF:S000055065|PMID:10836794 IMP P DNA helicase I YER176W|HEL1|MTT1 gene taxon:4932 20020711 SGD
+SGD S000000282 ECM33 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YBR078W gene taxon:4932 20040928 SGD
+SGD S000000282 ECM33 GO:0005886 SGD_REF:S000072533|PMID:12583915 IDA C YBR078W gene taxon:4932 20030217 SGD
+SGD S000000282 ECM33 GO:0009277 SGD_REF:S000081097|PMID:15781460 IDA C YBR078W gene taxon:4932 20050601 SGD
+SGD S000000282 ECM33 GO:0005554 SGD_REF:S000069584 ND F YBR078W gene taxon:4932 20020927 SGD
+SGD S000000282 ECM33 GO:0007047 SGD_REF:S000058218|PMID:9335584 IMP P YBR078W gene taxon:4932 20020927 SGD
+SGD S000001035 ECM34 GO:0008372 SGD_REF:S000069584 ND C YHL043W gene taxon:4932 20020927 SGD
+SGD S000001035 ECM34 GO:0005554 SGD_REF:S000069584 ND F YHL043W gene taxon:4932 20020927 SGD
+SGD S000001035 ECM34 GO:0007047 SGD_REF:S000058218|PMID:9335584 IMP P YHL043W gene taxon:4932 20020927 SGD
+SGD S000001408 ECM37 GO:0008372 SGD_REF:S000069584 ND C YIL146C gene taxon:4932 20020927 SGD
+SGD S000001408 ECM37 GO:0005554 SGD_REF:S000069584 ND F YIL146C gene taxon:4932 20020927 SGD
+SGD S000001408 ECM37 GO:0007047 SGD_REF:S000058218|PMID:9335584 IMP P YIL146C gene taxon:4932 20020927 SGD
+SGD S000004290 ECM38 GO:0005622 SGD_REF:S000071568|PMID:12406228 TAS C gamma-glutamyltransferase homolog YLR299W|CIS2 gene taxon:4932 20021122 SGD
+SGD S000004290 ECM38 GO:0003810 SGD_REF:S000046368|PMID:9348527 ISS F gamma-glutamyltransferase homolog YLR299W|CIS2 gene taxon:4932 20021003 SGD
+SGD S000004290 ECM38 GO:0006751 SGD_REF:S000072676|PMID:12620619 TAS P gamma-glutamyltransferase homolog YLR299W|CIS2 gene taxon:4932 20030311 SGD
+SGD S000001784 ECM4 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YKR076W|GTO2 gene taxon:4932 20031028 SGD
+SGD S000001784 ECM4 GO:0005554 SGD_REF:S000069584 ND F YKR076W|GTO2 gene taxon:4932 20020927 SGD
+SGD S000001784 ECM4 GO:0007047 SGD_REF:S000058218|PMID:9335584 IMP P YKR076W|GTO2 gene taxon:4932 20020927 SGD
+SGD S000004666 ECM40 GO:0005759 SGD_REF:S000059541|PMID:9847139 NAS C acetylornithine acetyltransferase YMR062C|ARG7 gene taxon:4932 20010302 SGD
+SGD S000004666 ECM40 GO:0004042 SGD_REF:S000045831|PMID:9428669 IGI F acetylornithine acetyltransferase YMR062C|ARG7 gene taxon:4932 20030618 SGD
+SGD S000004666 ECM40 GO:0004042 SGD_REF:S000045831|PMID:9428669 IDA F acetylornithine acetyltransferase YMR062C|ARG7 gene taxon:4932 20030618 SGD
+SGD S000004666 ECM40 GO:0004358 SGD_REF:S000045831|PMID:9428669 IDA F acetylornithine acetyltransferase YMR062C|ARG7 gene taxon:4932 20010118 SGD
+SGD S000004666 ECM40 GO:0006526 SGD_REF:S000073096|PMID:12603335 TAS P acetylornithine acetyltransferase YMR062C|ARG7 gene taxon:4932 20030508 SGD
+SGD S000004666 ECM40 GO:0006592 SGD_REF:S000058497 TAS P acetylornithine acetyltransferase YMR062C|ARG7 gene taxon:4932 20010119 SGD
+SGD S000004666 ECM40 GO:0007047 SGD_REF:S000058218|PMID:9335584 IMP P acetylornithine acetyltransferase YMR062C|ARG7 gene taxon:4932 20010118 SGD
+SGD S000004788 ECM5 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YMR176W gene taxon:4932 20031028 SGD
+SGD S000004788 ECM5 GO:0005554 SGD_REF:S000069584 ND F YMR176W gene taxon:4932 20020927 SGD
+SGD S000004788 ECM5 GO:0007047 SGD_REF:S000058218|PMID:9335584 IMP P YMR176W gene taxon:4932 20020927 SGD
+SGD S000004435 ECM7 GO:0016021 SGD_REF:S000072825|PMID:12524434 ISS C YLR443W|ZRG15 gene taxon:4932 20030409 SGD
+SGD S000004435 ECM7 GO:0005554 SGD_REF:S000069584 ND F YLR443W|ZRG15 gene taxon:4932 20020927 SGD
+SGD S000004435 ECM7 GO:0007047 SGD_REF:S000058218|PMID:9335584 IMP P YLR443W|ZRG15 gene taxon:4932 20020927 SGD
+SGD S000000280 ECM8 GO:0008372 SGD_REF:S000069584 ND C YBR076W gene taxon:4932 20020927 SGD
+SGD S000000280 ECM8 GO:0005554 SGD_REF:S000069584 ND F YBR076W gene taxon:4932 20020927 SGD
+SGD S000000280 ECM8 GO:0007047 SGD_REF:S000058218|PMID:9335584 IMP P YBR076W gene taxon:4932 20020927 SGD
+SGD S000001712 ECM9 GO:0008372 SGD_REF:S000069584 ND C YKR004C|YKR004C-A gene taxon:4932 20020927 SGD
+SGD S000001712 ECM9 GO:0005554 SGD_REF:S000069584 ND F YKR004C|YKR004C-A gene taxon:4932 20020927 SGD
+SGD S000001712 ECM9 GO:0007047 SGD_REF:S000058218|PMID:9335584 IMP P YKR004C|YKR004C-A gene taxon:4932 20020927 SGD
+SGD S000001923 ECO1 GO:0000790 SGD_REF:S000049776|PMID:9990856 IPI C YFR027W|CTF7 gene taxon:4932 20030403 SGD
+SGD S000001923 ECO1 GO:0016407 SGD_REF:S000069235|PMID:11864574 IDA F YFR027W|CTF7 gene taxon:4932 20021203 SGD
+SGD S000001923 ECO1 GO:0006260 SGD_REF:S000049776|PMID:9990856 IMP P YFR027W|CTF7 gene taxon:4932 20021203 SGD
+SGD S000001923 ECO1 GO:0006281 SGD_REF:S000060869|PMID:11448778 IDA P YFR027W|CTF7 gene taxon:4932 20021203 SGD
+SGD S000001923 ECO1 GO:0007064 SGD_REF:S000049775|PMID:9990855 IMP P YFR027W|CTF7 gene taxon:4932 20040610 SGD
+SGD S000003190 EDC1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YGL222C gene taxon:4932 20031028 SGD
+SGD S000003190 EDC1 GO:0003729 SGD_REF:S000059255|PMID:11139489 IPI F YGL222C gene taxon:4932 20021003 SGD
+SGD S000003190 EDC1 GO:0000290 SGD_REF:S000059255|PMID:11139489 IGI P YGL222C gene taxon:4932 20021003 SGD
+SGD S000003190 EDC1 GO:0000290 SGD_REF:S000059255|PMID:11139489 IPI P YGL222C gene taxon:4932 20021003 SGD
+SGD S000000837 EDC2 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YER035W gene taxon:4932 20031028 SGD
+SGD S000000837 EDC2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YER035W gene taxon:4932 20031028 SGD
+SGD S000000837 EDC2 GO:0003723 SGD_REF:S000072968|PMID:12554866 TAS F YER035W gene taxon:4932 20030422 SGD
+SGD S000000837 EDC2 GO:0000290 SGD_REF:S000059255|PMID:11139489 IGI P YER035W gene taxon:4932 20021003 SGD
+SGD S000000741 EDC3 GO:0000932 SGD_REF:S000075618|PMID:15020463 IDA C YEL015W|DCP3|LSM16 gene taxon:4932 20040322 SGD
+SGD S000000741 EDC3 GO:0005554 SGD_REF:S000069584 ND F YEL015W|DCP3|LSM16 gene taxon:4932 20040322 SGD
+SGD S000000741 EDC3 GO:0031087 SGD_REF:S000076605|PMID:15225544 IMP P YEL015W|DCP3|LSM16 gene taxon:4932 20050103 SGD
+SGD S000000143 EDE1 GO:0005934 SGD_REF:S000061390|PMID:11452010 IDA C YBL047C|BUD15 gene taxon:4932 20021010 SGD
+SGD S000000143 EDE1 GO:0005935 SGD_REF:S000061390|PMID:11452010 IDA C YBL047C|BUD15 gene taxon:4932 20021010 SGD
+SGD S000000143 EDE1 GO:0030479 SGD_REF:S000059089|PMID:10954428 IDA C YBL047C|BUD15 gene taxon:4932 20010206 SGD
+SGD S000000143 EDE1 GO:0043130 SGD_REF:S000114965|PMID:16563434 IDA F YBL047C|BUD15 gene taxon:4932 20060608 SGD
+SGD S000000143 EDE1 GO:0006897 SGD_REF:S000059089|PMID:10954428 IMP P YBL047C|BUD15 gene taxon:4932 20010206 SGD
+SGD S000000237 EDS1 GO:0008372 SGD_REF:S000069584 ND C YBR033W gene taxon:4932 20021122 SGD
+SGD S000000237 EDS1 GO:0005554 SGD_REF:S000069584 ND F YBR033W gene taxon:4932 20021122 SGD
+SGD S000000237 EDS1 GO:0000004 SGD_REF:S000069584 ND P YBR033W gene taxon:4932 20021122 SGD
+SGD S000006016 EEB1 GO:0008372 SGD_REF:S000069584 ND C Acyl-coenzymeA:ethanol O-acyltransferase YPL095C gene taxon:4932 20030205 SGD
+SGD S000006016 EEB1 GO:0005554 SGD_REF:S000069584 ND F Acyl-coenzymeA:ethanol O-acyltransferase YPL095C gene taxon:4932 20030205 SGD
+SGD S000006016 EEB1 GO:0000004 SGD_REF:S000069584 ND P Acyl-coenzymeA:ethanol O-acyltransferase YPL095C gene taxon:4932 20030205 SGD
+SGD S000000003 EFB1 GO:0005840 SGD_REF:S000058753|PMID:9841679 TAS C translation elongation factor EF-1beta YAL003W|EF-1 beta|TEF5 gene taxon:4932 20010124 SGD
+SGD S000000003 EFB1 GO:0005853 SGD_REF:S000057741|PMID:8420802 IMP C translation elongation factor EF-1beta YAL003W|EF-1 beta|TEF5 gene taxon:4932 20050105 SGD
+SGD S000000003 EFB1 GO:0005853 SGD_REF:S000057741|PMID:8420802 ISS C translation elongation factor EF-1beta YAL003W|EF-1 beta|TEF5 gene taxon:4932 20050105 SGD
+SGD S000000003 EFB1 GO:0003746 SGD_REF:S000058753|PMID:9841679 TAS F translation elongation factor EF-1beta YAL003W|EF-1 beta|TEF5 gene taxon:4932 20010124 SGD
+SGD S000000003 EFB1 GO:0006414 SGD_REF:S000058753|PMID:9841679 TAS P translation elongation factor EF-1beta YAL003W|EF-1 beta|TEF5 gene taxon:4932 20010124 SGD
+SGD S000004825 EFR3 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YMR212C gene taxon:4932 20040813 SGD
+SGD S000004825 EFR3 GO:0005554 SGD_REF:S000069584 ND F YMR212C gene taxon:4932 20010213 SGD
+SGD S000004825 EFR3 GO:0000902 SGD_REF:S000059267|PMID:11139490 IGI P YMR212C gene taxon:4932 20021108 SGD
+SGD S000005659 EFT1 GO:0005840 SGD_REF:S000058753|PMID:9841679 TAS C translation elongation factor 2 (EF-2) YOR133W gene taxon:4932 20010124 SGD
+SGD S000005659 EFT1 GO:0003746 SGD_REF:S000058753|PMID:9841679 TAS F translation elongation factor 2 (EF-2) YOR133W gene taxon:4932 20010125 SGD
+SGD S000005659 EFT1 GO:0006414 SGD_REF:S000058753|PMID:9841679 TAS P translation elongation factor 2 (EF-2) YOR133W gene taxon:4932 20010125 SGD
+SGD S000002793 EFT2 GO:0005840 SGD_REF:S000058753|PMID:9841679 TAS C translation elongation factor 2 (EF-2) YDR385W gene taxon:4932 20010124 SGD
+SGD S000002793 EFT2 GO:0003746 SGD_REF:S000058753|PMID:9841679 TAS F translation elongation factor 2 (EF-2) YDR385W gene taxon:4932 20010125 SGD
+SGD S000002793 EFT2 GO:0006414 SGD_REF:S000058753|PMID:9841679 TAS P translation elongation factor 2 (EF-2) YDR385W gene taxon:4932 20010125 SGD
+SGD S000005958 EGD1 GO:0005830 SGD_REF:S000039338|PMID:9482879 TAS C pol II transcribed genes regulator YPL037C gene taxon:4932 20040408 SGD
+SGD S000005958 EGD1 GO:0005854 SGD_REF:S000056211|PMID:10219998 IDA C pol II transcribed genes regulator YPL037C gene taxon:4932 20010118 SGD
+SGD S000005958 EGD1 GO:0051082 SGD_REF:S000039338|PMID:9482879 IMP F pol II transcribed genes regulator YPL037C gene taxon:4932 20010118 SGD
+SGD S000005958 EGD1 GO:0051083 SGD_REF:S000056211|PMID:10219998 IPI P pol II transcribed genes regulator YPL037C gene taxon:4932 20010118 SGD
+SGD S000001236 EGD2 GO:0005854 SGD_REF:S000056211|PMID:10219998 IDA C GAL4 enhancer protein, nascent-polypeptide-associated complex human alpha NAC subunit homolog YHR193C gene taxon:4932 20010118 SGD
+SGD S000001236 EGD2 GO:0051082 SGD_REF:S000039338|PMID:9482879 IMP F GAL4 enhancer protein, nascent-polypeptide-associated complex human alpha NAC subunit homolog YHR193C gene taxon:4932 20010118 SGD
+SGD S000001236 EGD2 GO:0051083 SGD_REF:S000056211|PMID:10219998 IPI P GAL4 enhancer protein, nascent-polypeptide-associated complex human alpha NAC subunit homolog YHR193C gene taxon:4932 20010118 SGD
+SGD S000005271 EGT2 GO:0009277 SGD_REF:S000040179|PMID:10383953 IDA C YNL327W gene taxon:4932 20020617 SGD
+SGD S000005271 EGT2 GO:0008810 SGD_REF:S000059111|PMID:11046133 TAS F YNL327W gene taxon:4932 20021209 SGD
+SGD S000005271 EGT2 GO:0000910 SGD_REF:S000041715|PMID:8668141 IMP P YNL327W gene taxon:4932 20021209 SGD
+SGD S000002443 EHD3 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YDR036C|MRP5 gene taxon:4932 20031028 SGD
+SGD S000002443 EHD3 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YDR036C|MRP5 gene taxon:4932 20040929 SGD
+SGD S000002443 EHD3 GO:0003860 SGD_REF:S000072949|PMID:12697341 IDA F YDR036C|MRP5 gene taxon:4932 20030506 SGD
+SGD S000002443 EHD3 GO:0006635 SGD_REF:S000072949|PMID:12697341 ISS P YDR036C|MRP5 gene taxon:4932 20030506 SGD
+SGD S000002443 EHD3 GO:0006897 SGD_REF:S000060817|PMID:11378903 IMP P YDR036C|MRP5 gene taxon:4932 20030506 SGD
+SGD S000000381 EHT1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C alcohol acyl transferase YBR177C gene taxon:4932 20040928 SGD
+SGD S000000381 EHT1 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C alcohol acyl transferase YBR177C gene taxon:4932 20060317 SGD
+SGD S000000381 EHT1 GO:0005811 SGD_REF:S000048561|PMID:10515935 IDA C alcohol acyl transferase YBR177C gene taxon:4932 20010118 SGD
+SGD S000000381 EHT1 GO:0017171 SGD_REF:S000076484|PMID:14645503 IDA F alcohol acyl transferase YBR177C gene taxon:4932 20040604 SGD
+SGD S000000381 EHT1 GO:0017171 SGD_REF:S000076484|PMID:14645503 RCA F alcohol acyl transferase YBR177C gene taxon:4932 20060421 SGD
+SGD S000000381 EHT1 GO:0006629 SGD_REF:S000048561|PMID:10515935 IMP P alcohol acyl transferase YBR177C gene taxon:4932 20010118 SGD
+SGD S000002554 EKI1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C ethanolamine kinase YDR147W gene taxon:4932 20031028 SGD
+SGD S000002554 EKI1 GO:0004103 SGD_REF:S000045886|PMID:10329685 IDA F ethanolamine kinase YDR147W gene taxon:4932 20021003 SGD
+SGD S000002554 EKI1 GO:0004305 SGD_REF:S000045886|PMID:10329685 IDA F ethanolamine kinase YDR147W gene taxon:4932 20021003 SGD
+SGD S000002554 EKI1 GO:0006646 SGD_REF:S000045886|PMID:10329685 IMP P ethanolamine kinase YDR147W gene taxon:4932 20021003 SGD
+SGD S000005174 ELA1 GO:0008023 SGD_REF:S000040848|PMID:10430890 ISS C elongin A transcription elongation factor YNL230C gene taxon:4932 20010118 SGD
+SGD S000005174 ELA1 GO:0003711 SGD_REF:S000040848|PMID:10430890 ISS F elongin A transcription elongation factor YNL230C gene taxon:4932 20010118 SGD
+SGD S000005174 ELA1 GO:0006368 SGD_REF:S000040848|PMID:10430890 ISS P elongin A transcription elongation factor YNL230C gene taxon:4932 20010118 SGD
+SGD S000005967 ELC1 GO:0000113 SGD_REF:S000076778|PMID:15226437 IDA C elongin C transcription elongation factor YPL046C gene taxon:4932 20041007 SGD
+SGD S000005967 ELC1 GO:0008023 SGD_REF:S000040848|PMID:10430890 ISS C elongin C transcription elongation factor YPL046C gene taxon:4932 20010118 SGD
+SGD S000005967 ELC1 GO:0003711 SGD_REF:S000040848|PMID:10430890 ISS F elongin C transcription elongation factor YPL046C gene taxon:4932 20010118 SGD
+SGD S000005967 ELC1 GO:0000715 SGD_REF:S000076778|PMID:15226437 IMP P elongin C transcription elongation factor YPL046C gene taxon:4932 20041007 SGD
+SGD S000005967 ELC1 GO:0006368 SGD_REF:S000040848|PMID:10430890 ISS P elongin C transcription elongation factor YPL046C gene taxon:4932 20010118 SGD
+SGD S000005967 ELC1 GO:0042787 SGD_REF:S000115816|PMID:16705154 IMP P elongin C transcription elongation factor YPL046C gene taxon:4932 20060523 SGD
+SGD S000001643 ELF1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YKL160W gene taxon:4932 20031028 SGD
+SGD S000001643 ELF1 GO:0016944 SGD_REF:S000087062|PMID:16260625 IGI SGD:S000000483|SGD:S000003295|SGD:S000003348|SGD:S000003213|SGD:S000004410|SGD:S000005505|SGD:S000005677|SGD:S000005649|SGD:S000004470|SGD:S000003676|SGD:S000002299|SGD:S000003011 F YKL160W gene taxon:4932 20051108 SGD
+SGD S000001643 ELF1 GO:0016944 SGD_REF:S000087062|PMID:16260625 IMP F YKL160W gene taxon:4932 20051108 SGD
+SGD S000001643 ELF1 GO:0006325 SGD_REF:S000087062|PMID:16260625 IGI SGD:S000000104 P YKL160W gene taxon:4932 20051108 SGD
+SGD S000001643 ELF1 GO:0006325 SGD_REF:S000087062|PMID:16260625 IMP P YKL160W gene taxon:4932 20051108 SGD
+SGD S000001643 ELF1 GO:0006368 SGD_REF:S000087062|PMID:16260625 IGI SGD:S000000483|SGD:S000003213|SGD:S000005677|SGD:S000005649|SGD:S000005505|SGD:S000004470|SGD:S000004410|SGD:S000003676|SGD:S000003348|SGD:S000003295|SGD:S000002299|SGD:S000003011 P YKL160W gene taxon:4932 20051108 SGD
+SGD S000001643 ELF1 GO:0006368 SGD_REF:S000087062|PMID:16260625 IMP P YKL160W gene taxon:4932 20051108 SGD
+SGD S000005670 ELG1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YOR144C|RTT110 gene taxon:4932 20031028 SGD
+SGD S000005670 ELG1 GO:0005663 SGD_REF:S000074131|PMID:12912927 TAS C YOR144C|RTT110 gene taxon:4932 20040415 SGD
+SGD S000005670 ELG1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YOR144C|RTT110 gene taxon:4932 20031028 SGD
+SGD S000005670 ELG1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YOR144C|RTT110 gene taxon:4932 20040928 SGD
+SGD S000005670 ELG1 GO:0005554 SGD_REF:S000069584 ND F YOR144C|RTT110 gene taxon:4932 20020927 SGD
+SGD S000005670 ELG1 GO:0000335 SGD_REF:S000068874|PMID:11779788 IMP P YOR144C|RTT110 gene taxon:4932 20020927 SGD
+SGD S000005670 ELG1 GO:0000723 SGD_REF:S000074132|PMID:13678589 TAS P YOR144C|RTT110 gene taxon:4932 20040415 SGD
+SGD S000005670 ELG1 GO:0006260 SGD_REF:S000074131|PMID:12912927 TAS P YOR144C|RTT110 gene taxon:4932 20040415 SGD
+SGD S000005670 ELG1 GO:0045910 SGD_REF:S000068874|PMID:11779788 NAS P YOR144C|RTT110 gene taxon:4932 20020927 SGD
+SGD S000001531 ELM1 GO:0000142 SGD_REF:S000041005|PMID:10652251 IDA C protein kinase YKL048C|LDB9 gene taxon:4932 20010118 SGD
+SGD S000001531 ELM1 GO:0004674 SGD_REF:S000050997|PMID:9180279 IDA F protein kinase YKL048C|LDB9 gene taxon:4932 20030508 SGD
+SGD S000001531 ELM1 GO:0000135 SGD_REF:S000041518|PMID:10725226 TAS P protein kinase YKL048C|LDB9 gene taxon:4932 20040415 SGD
+SGD S000001531 ELM1 GO:0000902 SGD_REF:S000042994|PMID:9427410 TAS P protein kinase YKL048C|LDB9 gene taxon:4932 20040415 SGD
+SGD S000001531 ELM1 GO:0000910 SGD_REF:S000041005|PMID:10652251 IMP P protein kinase YKL048C|LDB9 gene taxon:4932 20010119 SGD
+SGD S000001531 ELM1 GO:0006006 SGD_REF:S000077210|PMID:15340085 IMP P protein kinase YKL048C|LDB9 gene taxon:4932 20050512 SGD
+SGD S000001531 ELM1 GO:0006006 SGD_REF:S000077210|PMID:15340085 IGI P protein kinase YKL048C|LDB9 gene taxon:4932 20050512 SGD
+SGD S000001531 ELM1 GO:0006468 SGD_REF:S000046823|PMID:8395007 TAS P protein kinase YKL048C|LDB9 gene taxon:4932 20010118 SGD
+SGD S000001531 ELM1 GO:0006970 SGD_REF:S000041005|PMID:10652251 IMP P protein kinase YKL048C|LDB9 gene taxon:4932 20010118 SGD
+SGD S000001531 ELM1 GO:0007117 SGD_REF:S000053441|PMID:10234786 IMP P protein kinase YKL048C|LDB9 gene taxon:4932 20010118 SGD
+SGD S000001531 ELM1 GO:0007120 SGD_REF:S000041005|PMID:10652251 IMP P protein kinase YKL048C|LDB9 gene taxon:4932 20010118 SGD
+SGD S000001531 ELM1 GO:0007124 SGD_REF:S000041353|PMID:9891070 IMP P protein kinase YKL048C|LDB9 gene taxon:4932 20010118 SGD
+SGD S000003732 ELO1 GO:0016020 SGD_REF:S000053821|PMID:8702485 ISS C elongase YJL196C gene taxon:4932 20020923 SGD
+SGD S000003732 ELO1 GO:0009922 SGD_REF:S000073534|PMID:12684876 IMP F elongase YJL196C gene taxon:4932 20030708 SGD
+SGD S000003732 ELO1 GO:0009922 SGD_REF:S000073534|PMID:12684876 TAS F elongase YJL196C gene taxon:4932 20030708 SGD
+SGD S000003732 ELO1 GO:0019368 SGD_REF:S000052872|PMID:10850979 IMP P elongase YJL196C gene taxon:4932 20020923 SGD
+SGD S000003432 ELP2 GO:0008023 SGD_REF:S000068795|PMID:11689709 IDA C RNA polymerase II Elongator subunit YGR200C|TOT2 gene taxon:4932 20020918 SGD
+SGD S000003432 ELP2 GO:0016944 SGD_REF:S000068795|PMID:11689709 IMP F RNA polymerase II Elongator subunit YGR200C|TOT2 gene taxon:4932 20020918 SGD
+SGD S000003432 ELP2 GO:0016944 SGD_REF:S000068795|PMID:11689709 IPI F RNA polymerase II Elongator subunit YGR200C|TOT2 gene taxon:4932 20020918 SGD
+SGD S000003432 ELP2 GO:0006357 SGD_REF:S000068795|PMID:11689709 IMP P RNA polymerase II Elongator subunit YGR200C|TOT2 gene taxon:4932 20020918 SGD
+SGD S000006007 ELP3 GO:0008023 SGD_REF:S000068795|PMID:11689709 IDA C RNA polymerase II Elongator subunit, histone acetyltransferase YPL086C|HPA1|TOT3 gene taxon:4932 20020918 SGD
+SGD S000006007 ELP3 GO:0016591 SGD_REF:S000060112|PMID:11296232 IDA C RNA polymerase II Elongator subunit, histone acetyltransferase YPL086C|HPA1|TOT3 gene taxon:4932 20020616 SGD
+SGD S000006007 ELP3 GO:0004402 SGD_REF:S000069896|PMID:11994165 TAS F RNA polymerase II Elongator subunit, histone acetyltransferase YPL086C|HPA1|TOT3 gene taxon:4932 20020616 SGD
+SGD S000006007 ELP3 GO:0016944 SGD_REF:S000068795|PMID:11689709 IMP F RNA polymerase II Elongator subunit, histone acetyltransferase YPL086C|HPA1|TOT3 gene taxon:4932 20020918 SGD
+SGD S000006007 ELP3 GO:0016944 SGD_REF:S000068795|PMID:11689709 IPI F RNA polymerase II Elongator subunit, histone acetyltransferase YPL086C|HPA1|TOT3 gene taxon:4932 20020918 SGD
+SGD S000006007 ELP3 GO:0006357 SGD_REF:S000068795|PMID:11689709 IMP P RNA polymerase II Elongator subunit, histone acetyltransferase YPL086C|HPA1|TOT3 gene taxon:4932 20020918 SGD
+SGD S000006022 ELP4 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C RNA polymerase II Elongator protein subunit YPL101W|HAP1|TOT7 gene taxon:4932 20020507 SGD
+SGD S000006022 ELP4 GO:0008023 SGD_REF:S000068795|PMID:11689709 IDA C RNA polymerase II Elongator protein subunit YPL101W|HAP1|TOT7 gene taxon:4932 20020918 SGD
+SGD S000006022 ELP4 GO:0016944 SGD_REF:S000068795|PMID:11689709 IMP F RNA polymerase II Elongator protein subunit YPL101W|HAP1|TOT7 gene taxon:4932 20020918 SGD
+SGD S000006022 ELP4 GO:0016944 SGD_REF:S000068795|PMID:11689709 IPI F RNA polymerase II Elongator protein subunit YPL101W|HAP1|TOT7 gene taxon:4932 20020918 SGD
+SGD S000006022 ELP4 GO:0006357 SGD_REF:S000068795|PMID:11689709 IMP P RNA polymerase II Elongator protein subunit YPL101W|HAP1|TOT7 gene taxon:4932 20020918 SGD
+SGD S000004929 ELP6 GO:0008023 SGD_REF:S000068795|PMID:11689709 IDA C RNA polymerase II Elongator protein subunit YMR312W|HAP3|TOT6 gene taxon:4932 20020918 SGD
+SGD S000004929 ELP6 GO:0016944 SGD_REF:S000068795|PMID:11689709 IMP F RNA polymerase II Elongator protein subunit YMR312W|HAP3|TOT6 gene taxon:4932 20020918 SGD
+SGD S000004929 ELP6 GO:0016944 SGD_REF:S000068795|PMID:11689709 IPI F RNA polymerase II Elongator protein subunit YMR312W|HAP3|TOT6 gene taxon:4932 20020918 SGD
+SGD S000004929 ELP6 GO:0006357 SGD_REF:S000068795|PMID:11689709 IMP P RNA polymerase II Elongator protein subunit YMR312W|HAP3|TOT6 gene taxon:4932 20020918 SGD
+SGD S000004176 EMG1 GO:0005634 SGD_REF:S000069531|PMID:11935223 IDA C ribosome biogenesis YLR186W|NEP1 gene taxon:4932 20021209 SGD
+SGD S000004176 EMG1 GO:0005634 SGD_REF:S000066272|PMID:11694595 IDA C ribosome biogenesis YLR186W|NEP1 gene taxon:4932 20021209 SGD
+SGD S000004176 EMG1 GO:0005730 SGD_REF:S000079989|PMID:15590835 IDA C ribosome biogenesis YLR186W|NEP1 gene taxon:4932 20060315 SGD
+SGD S000004176 EMG1 GO:0005732 SGD_REF:S000079989|PMID:15590835 IPI SGD:S000003762 C ribosome biogenesis YLR186W|NEP1 gene taxon:4932 20050124 SGD
+SGD S000004176 EMG1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C ribosome biogenesis YLR186W|NEP1 gene taxon:4932 20020507 SGD
+SGD S000004176 EMG1 GO:0005737 SGD_REF:S000066272|PMID:11694595 IDA C ribosome biogenesis YLR186W|NEP1 gene taxon:4932 20021209 SGD
+SGD S000004176 EMG1 GO:0005880 SGD_REF:S000069531|PMID:11935223 IDA C ribosome biogenesis YLR186W|NEP1 gene taxon:4932 20050615 SGD
+SGD S000004176 EMG1 GO:0005554 SGD_REF:S000069584 ND F ribosome biogenesis YLR186W|NEP1 gene taxon:4932 20060315 SGD
+SGD S000004176 EMG1 GO:0006365 SGD_REF:S000066272|PMID:11694595 IMP P ribosome biogenesis YLR186W|NEP1 gene taxon:4932 20050518 SGD
+SGD S000004176 EMG1 GO:0006365 SGD_REF:S000079989|PMID:15590835 IPI SGD:S000003762|SGD:S000007294|SGD:S000007441 P ribosome biogenesis YLR186W|NEP1 gene taxon:4932 20050518 SGD
+SGD S000004176 EMG1 GO:0006365 SGD_REF:S000079989|PMID:15590835 IMP P ribosome biogenesis YLR186W|NEP1 gene taxon:4932 20050518 SGD
+SGD S000004176 EMG1 GO:0042274 SGD_REF:S000066272|PMID:11694595 IMP P ribosome biogenesis YLR186W|NEP1 gene taxon:4932 20021209 SGD
+SGD S000002920 EMI1 GO:0008372 SGD_REF:S000069584 ND C YDR512C gene taxon:4932 20021122 SGD
+SGD S000002920 EMI1 GO:0005554 SGD_REF:S000069584 ND F YDR512C gene taxon:4932 20021122 SGD
+SGD S000002920 EMI1 GO:0030437 SGD_REF:S000072583|PMID:12586695 IMP P YDR512C gene taxon:4932 20040512 SGD
+SGD S000002924 EMI2 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YDR516C gene taxon:4932 20020507 SGD
+SGD S000002924 EMI2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDR516C gene taxon:4932 20031028 SGD
+SGD S000002924 EMI2 GO:0005554 SGD_REF:S000069584 ND F YDR516C gene taxon:4932 20021209 SGD
+SGD S000002924 EMI2 GO:0030437 SGD_REF:S000072583|PMID:12586695 IMP P YDR516C gene taxon:4932 20040512 SGD
+SGD S000005432 EMI5 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YOL071W gene taxon:4932 20031028 SGD
+SGD S000005432 EMI5 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YOL071W gene taxon:4932 20031210 SGD
+SGD S000005432 EMI5 GO:0005554 SGD_REF:S000069584 ND F YOL071W gene taxon:4932 20021122 SGD
+SGD S000005432 EMI5 GO:0030437 SGD_REF:S000072583|PMID:12586695 IMP P YOL071W gene taxon:4932 20040512 SGD
+SGD S000003168 EMP24 GO:0005783 SGD_REF:S000044848|PMID:8862519 IDA C type I transmembrane protein YGL200C|BST2 gene taxon:4932 20010626 SGD
+SGD S000003168 EMP24 GO:0016021 SGD_REF:S000044848|PMID:8862519 ISS C type I transmembrane protein YGL200C|BST2 gene taxon:4932 20010626 SGD
+SGD S000003168 EMP24 GO:0030134 SGD_REF:S000061877|PMID:11157978 IDA C type I transmembrane protein YGL200C|BST2 gene taxon:4932 20020716 SGD
+SGD S000003168 EMP24 GO:0005554 SGD_REF:S000069584 ND F type I transmembrane protein YGL200C|BST2 gene taxon:4932 20010626 SGD
+SGD S000003168 EMP24 GO:0006621 SGD_REF:S000044848|PMID:8862519 IMP P type I transmembrane protein YGL200C|BST2 gene taxon:4932 20050425 SGD
+SGD S000003168 EMP24 GO:0006888 SGD_REF:S000061877|PMID:11157978 IPI P type I transmembrane protein YGL200C|BST2 gene taxon:4932 20020716 SGD
+SGD S000003168 EMP24 GO:0006888 SGD_REF:S000044848|PMID:8862519 IMP P type I transmembrane protein YGL200C|BST2 gene taxon:4932 20050425 SGD
+SGD S000003168 EMP24 GO:0016050 SGD_REF:S000044848|PMID:8862519 IMP P type I transmembrane protein YGL200C|BST2 gene taxon:4932 20010626 SGD
+SGD S000003168 EMP24 GO:0016050 SGD_REF:S000044848|PMID:8862519 IGI P type I transmembrane protein YGL200C|BST2 gene taxon:4932 20010626 SGD
+SGD S000004070 EMP46 GO:0000139 SGD_REF:S000070266|PMID:12134087 IDA C homolog of the Golgi protein Emp47p YLR080W gene taxon:4932 20020804 SGD
+SGD S000004070 EMP46 GO:0030134 SGD_REF:S000075963|PMID:12857885 IPI C homolog of the Golgi protein Emp47p YLR080W gene taxon:4932 20050105 SGD
+SGD S000004070 EMP46 GO:0001948 SGD_REF:S000114286|PMID:16439369 IDA F homolog of the Golgi protein Emp47p YLR080W gene taxon:4932 20060210 SGD
+SGD S000004070 EMP46 GO:0006888 SGD_REF:S000070266|PMID:12134087 IGI P homolog of the Golgi protein Emp47p YLR080W gene taxon:4932 20021209 SGD
+SGD S000004070 EMP46 GO:0006888 SGD_REF:S000070266|PMID:12134087 ISS P homolog of the Golgi protein Emp47p YLR080W gene taxon:4932 20021209 SGD
+SGD S000001846 EMP47 GO:0005794 SGD_REF:S000066243|PMID:11713678 TAS C 47 kDa type I transmembrane protein localized to the Golgi YFL048C gene taxon:4932 20020617 SGD
+SGD S000001846 EMP47 GO:0030134 SGD_REF:S000061877|PMID:11157978 IDA C 47 kDa type I transmembrane protein localized to the Golgi YFL048C gene taxon:4932 20020716 SGD
+SGD S000001846 EMP47 GO:0005554 SGD_REF:S000069584 ND F 47 kDa type I transmembrane protein localized to the Golgi YFL048C gene taxon:4932 20020716 SGD
+SGD S000001846 EMP47 GO:0006888 SGD_REF:S000061877|PMID:11157978 IPI P 47 kDa type I transmembrane protein localized to the Golgi YFL048C gene taxon:4932 20020716 SGD
+SGD S000004073 EMP70 GO:0005624 SGD_REF:S000045474|PMID:9729438 TAS C YLR083C gene taxon:4932 20020819 SGD
+SGD S000004073 EMP70 GO:0005768 SGD_REF:S000045474|PMID:9729438 TAS C YLR083C gene taxon:4932 20020819 SGD
+SGD S000004073 EMP70 GO:0005215 SGD_REF:S000045474|PMID:9729438 ISS F YLR083C gene taxon:4932 20020819 SGD
+SGD S000004073 EMP70 GO:0006810 SGD_REF:S000045474|PMID:9729438 ISS P YLR083C gene taxon:4932 20020819 SGD
+SGD S000006659 EMT1 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tRNA-Met tM(CAU)D gene taxon:4932 20030507 SGD
+SGD S000006659 EMT1 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tRNA-Met tM(CAU)D gene taxon:4932 20030507 SGD
+SGD S000006659 EMT1 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tRNA-Met tM(CAU)D gene taxon:4932 20030507 SGD
+SGD S000006666 EMT2 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tRNA-Met tM(CAU)O2 gene taxon:4932 20030507 SGD
+SGD S000006666 EMT2 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tRNA-Met tM(CAU)O2 gene taxon:4932 20030507 SGD
+SGD S000006666 EMT2 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tRNA-Met tM(CAU)O2 gene taxon:4932 20030507 SGD
+SGD S000006662 EMT3 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tRNA-Met tM(CAU)J2 gene taxon:4932 20030507 SGD
+SGD S000006662 EMT3 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tRNA-Met tM(CAU)J2 gene taxon:4932 20030507 SGD
+SGD S000006662 EMT3 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tRNA-Met tM(CAU)J2 gene taxon:4932 20030507 SGD
+SGD S000006664 EMT4 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tRNA-Met tM(CAU)M gene taxon:4932 20030507 SGD
+SGD S000006664 EMT4 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tRNA-Met tM(CAU)M gene taxon:4932 20030507 SGD
+SGD S000006664 EMT4 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tRNA-Met tM(CAU)M gene taxon:4932 20030507 SGD
+SGD S000006661 EMT5 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tRNA-Met tM(CAU)J1 gene taxon:4932 20030507 SGD
+SGD S000006661 EMT5 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tRNA-Met tM(CAU)J1 gene taxon:4932 20030507 SGD
+SGD S000006661 EMT5 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tRNA-Met tM(CAU)J1 gene taxon:4932 20030507 SGD
+SGD S000002447 ENA1 GO:0005886 SGD_REF:S000047583|PMID:7664728 IDA C P-type ATPase Na+ pump, plasma membrane ATPase YDR040C|HOR6|PMR2 gene taxon:4932 20020920 SGD
+SGD S000002447 ENA1 GO:0015662 SGD_REF:S000051416|PMID:1657642 IGI F P-type ATPase Na+ pump, plasma membrane ATPase YDR040C|HOR6|PMR2 gene taxon:4932 20020920 SGD
+SGD S000002447 ENA1 GO:0015662 SGD_REF:S000051416|PMID:1657642 IMP F P-type ATPase Na+ pump, plasma membrane ATPase YDR040C|HOR6|PMR2 gene taxon:4932 20020920 SGD
+SGD S000002447 ENA1 GO:0006814 SGD_REF:S000051416|PMID:1657642 IMP P P-type ATPase Na+ pump, plasma membrane ATPase YDR040C|HOR6|PMR2 gene taxon:4932 20020920 SGD
+SGD S000002446 ENA2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C P-type ATPase Na+ pump, plasma membrane ATPase, plasma membrane protein YDR039C gene taxon:4932 20040928 SGD
+SGD S000002446 ENA2 GO:0005886 SGD_REF:S000047583|PMID:7664728 IDA C P-type ATPase Na+ pump, plasma membrane ATPase, plasma membrane protein YDR039C gene taxon:4932 20020920 SGD
+SGD S000002446 ENA2 GO:0015662 SGD_REF:S000056092|PMID:8437581 ISS F P-type ATPase Na+ pump, plasma membrane ATPase, plasma membrane protein YDR039C gene taxon:4932 20020920 SGD
+SGD S000002446 ENA2 GO:0006814 SGD_REF:S000052882|PMID:10073572 IGI P P-type ATPase Na+ pump, plasma membrane ATPase, plasma membrane protein YDR039C gene taxon:4932 20020920 SGD
+SGD S000002445 ENA5 GO:0005886 SGD_REF:S000047583|PMID:7664728 ISS C Na+ ATPase YDR038C gene taxon:4932 20020920 SGD
+SGD S000002445 ENA5 GO:0015662 SGD_REF:S000047583|PMID:7664728 ISS F Na+ ATPase YDR038C gene taxon:4932 20020920 SGD
+SGD S000002445 ENA5 GO:0006814 SGD_REF:S000047583|PMID:7664728 ISS P Na+ ATPase YDR038C gene taxon:4932 20020920 SGD
+SGD S000005518 ENB1 GO:0005768 SGD_REF:S000070405|PMID:12196168 TAS C enterobactin transporter YOL158C|ARN4 gene taxon:4932 20020912 SGD
+SGD S000005518 ENB1 GO:0016021 SGD_REF:S000058352|PMID:9678606 ISS C enterobactin transporter YOL158C|ARN4 gene taxon:4932 20010118 SGD
+SGD S000005518 ENB1 GO:0016023 SGD_REF:S000070405|PMID:12196168 TAS C enterobactin transporter YOL158C|ARN4 gene taxon:4932 20020912 SGD
+SGD S000005518 ENB1 GO:0015620 SGD_REF:S000043642|PMID:10831226 IMP F enterobactin transporter YOL158C|ARN4 gene taxon:4932 20010118 SGD
+SGD S000005518 ENB1 GO:0015685 SGD_REF:S000043642|PMID:10831226 IMP P enterobactin transporter YOL158C|ARN4 gene taxon:4932 20010118 SGD
+SGD S000005028 END3 GO:0030479 SGD_REF:S000041005|PMID:10652251 TAS C YNL084C gene taxon:4932 20010118 SGD
+SGD S000005028 END3 GO:0030674 SGD_REF:S000050915|PMID:10594004 IPI SGD:S000000103|SGD:S000001445 F YNL084C gene taxon:4932 20040107 SGD
+SGD S000005028 END3 GO:0000147 SGD_REF:S000041005|PMID:10652251 TAS P YNL084C gene taxon:4932 20010118 SGD
+SGD S000005028 END3 GO:0000910 SGD_REF:S000041005|PMID:10652251 IMP P YNL084C gene taxon:4932 20010119 SGD
+SGD S000005028 END3 GO:0006897 SGD_REF:S000041005|PMID:10652251 IMP P YNL084C gene taxon:4932 20010118 SGD
+SGD S000005028 END3 GO:0007015 SGD_REF:S000041005|PMID:10652251 IPI P YNL084C gene taxon:4932 20010118 SGD
+SGD S000005028 END3 GO:0007121 SGD_REF:S000041005|PMID:10652251 IMP P YNL084C gene taxon:4932 20010118 SGD
+SGD S000005028 END3 GO:0030476 SGD_REF:S000081858|PMID:15944351 IMP P YNL084C gene taxon:4932 20050822 SGD
+SGD S000003486 ENO1 GO:0000015 SGD_REF:S000055816|PMID:6282834 IDA C enolase I YGR254W|HSP48 gene taxon:4932 20010118 SGD
+SGD S000003486 ENO1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C enolase I YGR254W|HSP48 gene taxon:4932 20020507 SGD
+SGD S000003486 ENO1 GO:0004634 SGD_REF:S000055816|PMID:6282834 IMP F enolase I YGR254W|HSP48 gene taxon:4932 20010118 SGD
+SGD S000003486 ENO1 GO:0006094 SGD_REF:S000045067|PMID:3313003 IEP P enolase I YGR254W|HSP48 gene taxon:4932 20050607 SGD
+SGD S000003486 ENO1 GO:0006096 SGD_REF:S000055816|PMID:6282834 IMP P enolase I YGR254W|HSP48 gene taxon:4932 20050606 SGD
+SGD S000001217 ENO2 GO:0000015 SGD_REF:S000055816|PMID:6282834 IDA C enolase YHR174W gene taxon:4932 20010118 SGD
+SGD S000001217 ENO2 GO:0005625 SGD_REF:S000068747|PMID:11746603 IDA C enolase YHR174W gene taxon:4932 20030130 SGD
+SGD S000001217 ENO2 GO:0004634 SGD_REF:S000055816|PMID:6282834 IMP F enolase YHR174W gene taxon:4932 20010118 SGD
+SGD S000001217 ENO2 GO:0006094 SGD_REF:S000056179|PMID:3537717 IEP P enolase YHR174W gene taxon:4932 20050607 SGD
+SGD S000001217 ENO2 GO:0006096 SGD_REF:S000055816|PMID:6282834 IMP P enolase YHR174W gene taxon:4932 20050606 SGD
+SGD S000000451 ENP1 GO:0005634 SGD_REF:S000053537|PMID:9034325 IDA C 57 kDa protein with an apparent MW of 70 kDa by SDS-PAGE (putative) YBR247C|MEG1 gene taxon:4932 20020920 SGD
+SGD S000000451 ENP1 GO:0005730 SGD_REF:S000072306|PMID:12527778 TAS C 57 kDa protein with an apparent MW of 70 kDa by SDS-PAGE (putative) YBR247C|MEG1 gene taxon:4932 20030130 SGD
+SGD S000000451 ENP1 GO:0030515 SGD_REF:S000072306|PMID:12527778 IDA F 57 kDa protein with an apparent MW of 70 kDa by SDS-PAGE (putative) YBR247C|MEG1 gene taxon:4932 20030130 SGD
+SGD S000000451 ENP1 GO:0006364 SGD_REF:S000072306|PMID:12527778 IPI SGD:S000002172 P 57 kDa protein with an apparent MW of 70 kDa by SDS-PAGE (putative) YBR247C|MEG1 gene taxon:4932 20030130 SGD
+SGD S000000451 ENP1 GO:0006365 SGD_REF:S000072306|PMID:12527778 IMP P 57 kDa protein with an apparent MW of 70 kDa by SDS-PAGE (putative) YBR247C|MEG1 gene taxon:4932 20050518 SGD
+SGD S000003377 ENP2 GO:0005730 SGD_REF:S000075214|PMID:14690591 IDA C YGR145W gene taxon:4932 20031231 SGD
+SGD S000003377 ENP2 GO:0005554 SGD_REF:S000069584 ND F YGR145W gene taxon:4932 20021122 SGD
+SGD S000003377 ENP2 GO:0006364 SGD_REF:S000075214|PMID:14690591 IPI SGD:S000001239 P YGR145W gene taxon:4932 20031231 SGD
+SGD S000029698 ENS2 GO:0005739 SGD_REF:S000043690|PMID:1988456 IDA C endonuclease SceI small subunit Endo.SceI|RF3 gene taxon:4932 20030304 SGD
+SGD S000029698 ENS2 GO:0004520 SGD_REF:S000054598|PMID:10464305 IDA F endonuclease SceI small subunit Endo.SceI|RF3 gene taxon:4932 20030304 SGD
+SGD S000029698 ENS2 GO:0006310 SGD_REF:S000043023|PMID:1628629 IMP P endonuclease SceI small subunit Endo.SceI|RF3 gene taxon:4932 20030304 SGD
+SGD S000002320 ENT1 GO:0030479 SGD_REF:S000041005|PMID:10652251 IPI C YDL161W gene taxon:4932 20010118 SGD
+SGD S000002320 ENT1 GO:0030276 SGD_REF:S000075278|PMID:12461563 TAS F YDL161W gene taxon:4932 20040107 SGD
+SGD S000002320 ENT1 GO:0000147 SGD_REF:S000039475|PMID:10449404 IMP P YDL161W gene taxon:4932 20010118 SGD
+SGD S000002320 ENT1 GO:0006897 SGD_REF:S000039475|PMID:10449404 IMP P YDL161W gene taxon:4932 20010118 SGD
+SGD S000002320 ENT1 GO:0007015 SGD_REF:S000039475|PMID:10449404 IMP P YDL161W gene taxon:4932 20010118 SGD
+SGD S000004196 ENT2 GO:0030479 SGD_REF:S000041005|PMID:10652251 IPI C YLR206W gene taxon:4932 20010118 SGD
+SGD S000004196 ENT2 GO:0030276 SGD_REF:S000075278|PMID:12461563 TAS F YLR206W gene taxon:4932 20040107 SGD
+SGD S000004196 ENT2 GO:0000147 SGD_REF:S000039475|PMID:10449404 IMP P YLR206W gene taxon:4932 20010118 SGD
+SGD S000004196 ENT2 GO:0006897 SGD_REF:S000039475|PMID:10449404 IMP P YLR206W gene taxon:4932 20010118 SGD
+SGD S000004196 ENT2 GO:0007015 SGD_REF:S000039475|PMID:10449404 IMP P YLR206W gene taxon:4932 20010118 SGD
+SGD S000003886 ENT3 GO:0030125 SGD_REF:S000072030|PMID:12483220 IDA C YJR125C gene taxon:4932 20030110 SGD
+SGD S000003886 ENT3 GO:0030479 SGD_REF:S000041005|PMID:10652251 IPI C YJR125C gene taxon:4932 20010118 SGD
+SGD S000003886 ENT3 GO:0005515 SGD_REF:S000072030|PMID:12483220 IPI SGD:S000001150 F YJR125C gene taxon:4932 20040107 SGD
+SGD S000003886 ENT3 GO:0000147 SGD_REF:S000039475|PMID:10449404 ISS P YJR125C gene taxon:4932 20010118 SGD
+SGD S000003886 ENT3 GO:0006605 SGD_REF:S000080625|PMID:15107463 IMP P YJR125C gene taxon:4932 20050620 SGD
+SGD S000003886 ENT3 GO:0006895 SGD_REF:S000072030|PMID:12483220 IMP P YJR125C gene taxon:4932 20030110 SGD
+SGD S000003886 ENT3 GO:0006897 SGD_REF:S000039475|PMID:10449404 ISS P YJR125C gene taxon:4932 20010118 SGD
+SGD S000003886 ENT3 GO:0007015 SGD_REF:S000039475|PMID:10449404 ISS P YJR125C gene taxon:4932 20010118 SGD
+SGD S000003961 ENT4 GO:0030479 SGD_REF:S000041005|PMID:10652251 IPI C YLL038C gene taxon:4932 20010118 SGD
+SGD S000003961 ENT4 GO:0030276 SGD_REF:S000039475|PMID:10449404 ISS F YLL038C gene taxon:4932 20040107 SGD
+SGD S000003961 ENT4 GO:0000147 SGD_REF:S000039475|PMID:10449404 ISS P YLL038C gene taxon:4932 20010118 SGD
+SGD S000003961 ENT4 GO:0006897 SGD_REF:S000039475|PMID:10449404 ISS P YLL038C gene taxon:4932 20010118 SGD
+SGD S000003961 ENT4 GO:0007015 SGD_REF:S000039475|PMID:10449404 ISS P YLL038C gene taxon:4932 20010118 SGD
+SGD S000002560 ENT5 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YDR153C gene taxon:4932 20020507 SGD
+SGD S000002560 ENT5 GO:0005768 SGD_REF:S000080625|PMID:15107463 IDA C YDR153C gene taxon:4932 20050620 SGD
+SGD S000002560 ENT5 GO:0030125 SGD_REF:S000072030|PMID:12483220 IDA C YDR153C gene taxon:4932 20030110 SGD
+SGD S000002560 ENT5 GO:0030276 SGD_REF:S000072030|PMID:12483220 IPI F YDR153C gene taxon:4932 20030110 SGD
+SGD S000002560 ENT5 GO:0006605 SGD_REF:S000080625|PMID:15107463 IMP P YDR153C gene taxon:4932 20050620 SGD
+SGD S000002560 ENT5 GO:0006895 SGD_REF:S000072030|PMID:12483220 IMP P YDR153C gene taxon:4932 20030110 SGD
+SGD S000001870 EPL1 GO:0000123 SGD_REF:S000046619|PMID:10911987 IDA C NuA4 histone acetyltransferase complex component YFL024C gene taxon:4932 20020918 SGD
+SGD S000001870 EPL1 GO:0043189 SGD_REF:S000079775|PMID:15485911 IPI C NuA4 histone acetyltransferase complex component YFL024C gene taxon:4932 20050207 SGD
+SGD S000001870 EPL1 GO:0004402 SGD_REF:S000046619|PMID:10911987 IDA F NuA4 histone acetyltransferase complex component YFL024C gene taxon:4932 20020918 SGD
+SGD S000001870 EPL1 GO:0006357 SGD_REF:S000046619|PMID:10911987 IDA P NuA4 histone acetyltransferase complex component YFL024C gene taxon:4932 20020918 SGD
+SGD S000001870 EPL1 GO:0016573 SGD_REF:S000046619|PMID:10911987 IDA P NuA4 histone acetyltransferase complex component YFL024C gene taxon:4932 20020918 SGD
+SGD S000001267 EPS1 GO:0005789 SGD_REF:S000053951|PMID:10545109 IDA C YIL005W gene taxon:4932 20020920 SGD
+SGD S000001267 EPS1 GO:0003756 SGD_REF:S000059478|PMID:11157982 IMP F YIL005W gene taxon:4932 20020606 SGD
+SGD S000001267 EPS1 GO:0003756 SGD_REF:S000059478|PMID:11157982 TAS F YIL005W gene taxon:4932 20020606 SGD
+SGD S000001267 EPS1 GO:0006621 SGD_REF:S000053951|PMID:10545109 IMP P YIL005W gene taxon:4932 20020920 SGD
+SGD S000001165 EPT1 GO:0005783 SGD_REF:S000058496 TAS C sn-1,2-diacylglycerol ethanolamine- and cholinephosphotranferase YHR123W gene taxon:4932 20010119 SGD
+SGD S000001165 EPT1 GO:0004307 SGD_REF:S000058496 TAS F sn-1,2-diacylglycerol ethanolamine- and cholinephosphotranferase YHR123W gene taxon:4932 20010119 SGD
+SGD S000001165 EPT1 GO:0006646 SGD_REF:S000058496 TAS P sn-1,2-diacylglycerol ethanolamine- and cholinephosphotranferase YHR123W gene taxon:4932 20010119 SGD
+SGD S000004652 ERB1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YMR049C gene taxon:4932 20031028 SGD
+SGD S000004652 ERB1 GO:0005730 SGD_REF:S000074185|PMID:14562095 IDA C YMR049C gene taxon:4932 20031028 SGD
+SGD S000004652 ERB1 GO:0005554 SGD_REF:S000069584 ND F YMR049C gene taxon:4932 20021209 SGD
+SGD S000004652 ERB1 GO:0006364 SGD_REF:S000061187|PMID:11522832 IMP P YMR049C gene taxon:4932 20021209 SGD
+SGD S000002822 ERD1 GO:0016020 SGD_REF:S000042029|PMID:2178921 IDA C YDR414C|LDB2 gene taxon:4932 20020819 SGD
+SGD S000002822 ERD1 GO:0005554 SGD_REF:S000069584 ND F YDR414C|LDB2 gene taxon:4932 20020819 SGD
+SGD S000002822 ERD1 GO:0006621 SGD_REF:S000042029|PMID:2178921 IMP P YDR414C|LDB2 gene taxon:4932 20020819 SGD
+SGD S000000136 ERD2 GO:0030176 SGD_REF:S000040353|PMID:2194670 IDA C HDEL receptor YBL040C gene taxon:4932 20020802 SGD
+SGD S000000136 ERD2 GO:0045015 SGD_REF:S000040353|PMID:2194670 IGI F HDEL receptor YBL040C gene taxon:4932 20020802 SGD
+SGD S000000136 ERD2 GO:0045015 SGD_REF:S000040353|PMID:2194670 IMP F HDEL receptor YBL040C gene taxon:4932 20020802 SGD
+SGD S000000136 ERD2 GO:0045015 SGD_REF:S000040353|PMID:2194670 IPI F HDEL receptor YBL040C gene taxon:4932 20020802 SGD
+SGD S000000136 ERD2 GO:0006621 SGD_REF:S000040356|PMID:2194671 IGI P HDEL receptor YBL040C gene taxon:4932 20020802 SGD
+SGD S000004236 ERF2 GO:0030176 SGD_REF:S000042150|PMID:10490616 IDA C YLR246W gene taxon:4932 20020923 SGD
+SGD S000004236 ERF2 GO:0031211 SGD_REF:S000071573|PMID:12193598 IPI C YLR246W gene taxon:4932 20050217 SGD
+SGD S000004236 ERF2 GO:0019706 SGD_REF:S000074072|PMID:12944483 IMP F YLR246W gene taxon:4932 20050304 SGD
+SGD S000004236 ERF2 GO:0006612 SGD_REF:S000042150|PMID:10490616 IMP P YLR246W gene taxon:4932 20020923 SGD
+SGD S000004236 ERF2 GO:0018318 SGD_REF:S000071573|PMID:12193598 IDA P YLR246W gene taxon:4932 20030123 SGD
+SGD S000003407 ERG1 GO:0005783 SGD_REF:S000058496 TAS C squalene monooxygenase YGR175C gene taxon:4932 20010119 SGD
+SGD S000003407 ERG1 GO:0005811 SGD_REF:S000044217|PMID:9450962 IDA C squalene monooxygenase YGR175C gene taxon:4932 20010118 SGD
+SGD S000003407 ERG1 GO:0004506 SGD_REF:S000058496 TAS F squalene monooxygenase YGR175C gene taxon:4932 20010119 SGD
+SGD S000003407 ERG1 GO:0008144 SGD_REF:S000075218|PMID:14638499 IMP F squalene monooxygenase YGR175C gene taxon:4932 20040813 SGD
+SGD S000003407 ERG1 GO:0006696 SGD_REF:S000058496 TAS P squalene monooxygenase YGR175C gene taxon:4932 20010119 SGD
+SGD S000005949 ERG10 GO:0005829 SGD_REF:S000058496 TAS C acetoacetyl CoA thiolase YPL028W|LPB3|TSM0115 gene taxon:4932 20010119 SGD
+SGD S000005949 ERG10 GO:0003985 SGD_REF:S000042016|PMID:7989303 IDA F acetoacetyl CoA thiolase YPL028W|LPB3|TSM0115 gene taxon:4932 20010118 SGD
+SGD S000005949 ERG10 GO:0006696 SGD_REF:S000058496 TAS P acetoacetyl CoA thiolase YPL028W|LPB3|TSM0115 gene taxon:4932 20010119 SGD
+SGD S000001049 ERG11 GO:0005783 SGD_REF:S000058496 TAS C cytochrome P450 lanosterol 14a-demethylase YHR007C|CYP51 gene taxon:4932 20010119 SGD
+SGD S000001049 ERG11 GO:0005783 SGD_REF:S000069459|PMID:11914276 IDA C cytochrome P450 lanosterol 14a-demethylase YHR007C|CYP51 gene taxon:4932 20020507 SGD
+SGD S000001049 ERG11 GO:0008398 SGD_REF:S000058496 TAS F cytochrome P450 lanosterol 14a-demethylase YHR007C|CYP51 gene taxon:4932 20010119 SGD
+SGD S000001049 ERG11 GO:0006696 SGD_REF:S000058496 TAS P cytochrome P450 lanosterol 14a-demethylase YHR007C|CYP51 gene taxon:4932 20010119 SGD
+SGD S000004821 ERG12 GO:0005829 SGD_REF:S000058496 TAS C mevalonate kinase YMR208W|RAR1 gene taxon:4932 20010119 SGD
+SGD S000004821 ERG12 GO:0004496 SGD_REF:S000058496 TAS F mevalonate kinase YMR208W|RAR1 gene taxon:4932 20010119 SGD
+SGD S000004821 ERG12 GO:0006696 SGD_REF:S000058496 TAS P mevalonate kinase YMR208W|RAR1 gene taxon:4932 20010119 SGD
+SGD S000004595 ERG13 GO:0005739 SGD_REF:S000058496 TAS C 3-hydroxy-3-methylglutaryl coenzyme A synthase YML126C|HMGS gene taxon:4932 20010119 SGD
+SGD S000004595 ERG13 GO:0005783 SGD_REF:S000058496 TAS C 3-hydroxy-3-methylglutaryl coenzyme A synthase YML126C|HMGS gene taxon:4932 20010119 SGD
+SGD S000004595 ERG13 GO:0004421 SGD_REF:S000062859|PMID:6148937 IMP F 3-hydroxy-3-methylglutaryl coenzyme A synthase YML126C|HMGS gene taxon:4932 20060605 SGD
+SGD S000004595 ERG13 GO:0006696 SGD_REF:S000062859|PMID:6148937 IMP P 3-hydroxy-3-methylglutaryl coenzyme A synthase YML126C|HMGS gene taxon:4932 20060605 SGD
+SGD S000004815 ERG2 GO:0005783 SGD_REF:S000058496 TAS C C-8 sterol isomerase YMR202W|END11 gene taxon:4932 20010119 SGD
+SGD S000004815 ERG2 GO:0000247 SGD_REF:S000058496 TAS F C-8 sterol isomerase YMR202W|END11 gene taxon:4932 20010119 SGD
+SGD S000004815 ERG2 GO:0006696 SGD_REF:S000058496 TAS P C-8 sterol isomerase YMR202W|END11 gene taxon:4932 20010119 SGD
+SGD S000003703 ERG20 GO:0005829 SGD_REF:S000058496 TAS C farnesyl diphosphate synthetase (FPP synthetase) YJL167W|BOT3|FDS1|FPP1 gene taxon:4932 20010119 SGD
+SGD S000003703 ERG20 GO:0004161 SGD_REF:S000058496 TAS F farnesyl diphosphate synthetase (FPP synthetase) YJL167W|BOT3|FDS1|FPP1 gene taxon:4932 20010119 SGD
+SGD S000003703 ERG20 GO:0004161 SGD_REF:S000056919|PMID:2681213 IDA F farnesyl diphosphate synthetase (FPP synthetase) YJL167W|BOT3|FDS1|FPP1 gene taxon:4932 20030318 SGD
+SGD S000003703 ERG20 GO:0004337 SGD_REF:S000058496 TAS F farnesyl diphosphate synthetase (FPP synthetase) YJL167W|BOT3|FDS1|FPP1 gene taxon:4932 20010119 SGD
+SGD S000003703 ERG20 GO:0004337 SGD_REF:S000056919|PMID:2681213 IDA F farnesyl diphosphate synthetase (FPP synthetase) YJL167W|BOT3|FDS1|FPP1 gene taxon:4932 20030318 SGD
+SGD S000003703 ERG20 GO:0006696 SGD_REF:S000058496 TAS P farnesyl diphosphate synthetase (FPP synthetase) YJL167W|BOT3|FDS1|FPP1 gene taxon:4932 20010119 SGD
+SGD S000003703 ERG20 GO:0008299 SGD_REF:S000056919|PMID:2681213 IDA P farnesyl diphosphate synthetase (FPP synthetase) YJL167W|BOT3|FDS1|FPP1 gene taxon:4932 20030318 SGD
+SGD S000003703 ERG20 GO:0045337 SGD_REF:S000056919|PMID:2681213 IDA P farnesyl diphosphate synthetase (FPP synthetase) YJL167W|BOT3|FDS1|FPP1 gene taxon:4932 20030318 SGD
+SGD S000005224 ERG24 GO:0005783 SGD_REF:S000058496 TAS C sterol C-14 reductase YNL280C gene taxon:4932 20010119 SGD
+SGD S000005224 ERG24 GO:0050613 SGD_REF:S000058496 TAS F sterol C-14 reductase YNL280C gene taxon:4932 20010119 SGD
+SGD S000005224 ERG24 GO:0006696 SGD_REF:S000058496 TAS P sterol C-14 reductase YNL280C gene taxon:4932 20010119 SGD
+SGD S000003292 ERG25 GO:0005789 SGD_REF:S000051918|PMID:8663358 IDA C C-4 sterol methyl oxidase YGR060W gene taxon:4932 20010118 SGD
+SGD S000003292 ERG25 GO:0005886 SGD_REF:S000051918|PMID:8663358 IDA C C-4 sterol methyl oxidase YGR060W gene taxon:4932 20010118 SGD
+SGD S000003292 ERG25 GO:0000254 SGD_REF:S000051918|PMID:8663358 IDA F C-4 sterol methyl oxidase YGR060W gene taxon:4932 20010118 SGD
+SGD S000003292 ERG25 GO:0006696 SGD_REF:S000051918|PMID:8663358 IDA P C-4 sterol methyl oxidase YGR060W gene taxon:4932 20010118 SGD
+SGD S000002969 ERG26 GO:0005783 SGD_REF:S000060167|PMID:11279045 IDA C C-3 sterol dehydrogenase YGL001C gene taxon:4932 20020630 SGD
+SGD S000002969 ERG26 GO:0005789 SGD_REF:S000070201|PMID:12119386 IDA C C-3 sterol dehydrogenase YGL001C gene taxon:4932 20020819 SGD
+SGD S000002969 ERG26 GO:0000252 SGD_REF:S000054146|PMID:9811880 IDA F C-3 sterol dehydrogenase YGL001C gene taxon:4932 20010118 SGD
+SGD S000002969 ERG26 GO:0006696 SGD_REF:S000054146|PMID:9811880 IDA P C-3 sterol dehydrogenase YGL001C gene taxon:4932 20010118 SGD
+SGD S000004090 ERG27 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C 3-keto sterol reductase YLR100W gene taxon:4932 20060317 SGD
+SGD S000004090 ERG27 GO:0005783 SGD_REF:S000060167|PMID:11279045 IDA C 3-keto sterol reductase YLR100W gene taxon:4932 20020630 SGD
+SGD S000004090 ERG27 GO:0005789 SGD_REF:S000070201|PMID:12119386 IDA C 3-keto sterol reductase YLR100W gene taxon:4932 20020819 SGD
+SGD S000004090 ERG27 GO:0000253 SGD_REF:S000055295|PMID:10535978 IMP F 3-keto sterol reductase YLR100W gene taxon:4932 20010118 SGD
+SGD S000004090 ERG27 GO:0006696 SGD_REF:S000055295|PMID:10535978 IMP P 3-keto sterol reductase YLR100W gene taxon:4932 20010118 SGD
+SGD S000000846 ERG28 GO:0005789 SGD_REF:S000070201|PMID:12119386 IDA C YER044C|BUD18 gene taxon:4932 20020819 SGD
+SGD S000000846 ERG28 GO:0030674 SGD_REF:S000079663|PMID:15522820 IPI SGD:S000004467 F YER044C|BUD18 gene taxon:4932 20041129 SGD
+SGD S000000846 ERG28 GO:0030674 SGD_REF:S000070201|PMID:12119386 IPI SGD:S000004090 F YER044C|BUD18 gene taxon:4932 20041129 SGD
+SGD S000000846 ERG28 GO:0006696 SGD_REF:S000060148|PMID:10929718 IMP P YER044C|BUD18 gene taxon:4932 20010426 SGD
+SGD S000000846 ERG28 GO:0006696 SGD_REF:S000082245|PMID:15995173 IPI P YER044C|BUD18 gene taxon:4932 20050711 SGD
+SGD S000000846 ERG28 GO:0006696 SGD_REF:S000059518|PMID:11160377 IDA P YER044C|BUD18 gene taxon:4932 20010426 SGD
+SGD S000004046 ERG3 GO:0005783 SGD_REF:S000058496 TAS C C-5 sterol desaturase YLR056W|PSO6|SYR1 gene taxon:4932 20010119 SGD
+SGD S000004046 ERG3 GO:0000248 SGD_REF:S000058496 TAS F C-5 sterol desaturase YLR056W|PSO6|SYR1 gene taxon:4932 20010119 SGD
+SGD S000004046 ERG3 GO:0006696 SGD_REF:S000058496 TAS P C-5 sterol desaturase YLR056W|PSO6|SYR1 gene taxon:4932 20010119 SGD
+SGD S000004046 ERG3 GO:0006897 SGD_REF:S000086880|PMID:16195350 IGI SGD:S000000024|SGD:S000000690 P C-5 sterol desaturase YLR056W|PSO6|SYR1 gene taxon:4932 20051208 SGD
+SGD S000002980 ERG4 GO:0005783 SGD_REF:S000040029|PMID:10722850 IDA C sterol C-24 reductase YGL012W gene taxon:4932 20010118 SGD
+SGD S000002980 ERG4 GO:0000246 SGD_REF:S000040029|PMID:10722850 TAS F sterol C-24 reductase YGL012W gene taxon:4932 20010118 SGD
+SGD S000002980 ERG4 GO:0006696 SGD_REF:S000040029|PMID:10722850 TAS P sterol C-24 reductase YGL012W gene taxon:4932 20010118 SGD
+SGD S000004617 ERG5 GO:0005783 SGD_REF:S000058496 TAS C cytochrome P450, involved in C-22 denaturation of the ergosterol side-chain YMR015C|CYP61 gene taxon:4932 20010119 SGD
+SGD S000004617 ERG5 GO:0000249 SGD_REF:S000058496 TAS F cytochrome P450, involved in C-22 denaturation of the ergosterol side-chain YMR015C|CYP61 gene taxon:4932 20010119 SGD
+SGD S000004617 ERG5 GO:0006696 SGD_REF:S000058496 TAS P cytochrome P450, involved in C-22 denaturation of the ergosterol side-chain YMR015C|CYP61 gene taxon:4932 20010119 SGD
+SGD S000004467 ERG6 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YML008C|ISE1|LIS1|SED6 gene taxon:4932 20040928 SGD
+SGD S000004467 ERG6 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C YML008C|ISE1|LIS1|SED6 gene taxon:4932 20060317 SGD
+SGD S000004467 ERG6 GO:0005783 SGD_REF:S000058496 TAS C YML008C|ISE1|LIS1|SED6 gene taxon:4932 20010119 SGD
+SGD S000004467 ERG6 GO:0005811 SGD_REF:S000048561|PMID:10515935 IDA C YML008C|ISE1|LIS1|SED6 gene taxon:4932 20010118 SGD
+SGD S000004467 ERG6 GO:0003838 SGD_REF:S000058496 TAS F YML008C|ISE1|LIS1|SED6 gene taxon:4932 20010119 SGD
+SGD S000004467 ERG6 GO:0006696 SGD_REF:S000058496 TAS P YML008C|ISE1|LIS1|SED6 gene taxon:4932 20010119 SGD
+SGD S000001114 ERG7 GO:0005783 SGD_REF:S000058496 TAS C 2,3-oxidosqualene-lanosterol cyclase YHR072W gene taxon:4932 20010119 SGD
+SGD S000001114 ERG7 GO:0005811 SGD_REF:S000048561|PMID:10515935 IDA C 2,3-oxidosqualene-lanosterol cyclase YHR072W gene taxon:4932 20020917 SGD
+SGD S000001114 ERG7 GO:0005886 SGD_REF:S000048561|PMID:10515935 TAS C 2,3-oxidosqualene-lanosterol cyclase YHR072W gene taxon:4932 20010118 SGD
+SGD S000001114 ERG7 GO:0000250 SGD_REF:S000058496 TAS F 2,3-oxidosqualene-lanosterol cyclase YHR072W gene taxon:4932 20010119 SGD
+SGD S000001114 ERG7 GO:0006696 SGD_REF:S000058496 TAS P 2,3-oxidosqualene-lanosterol cyclase YHR072W gene taxon:4932 20010119 SGD
+SGD S000004833 ERG8 GO:0005829 SGD_REF:S000058496 TAS C 48 kDa phosphomevalonate kinase YMR220W gene taxon:4932 20010119 SGD
+SGD S000004833 ERG8 GO:0004631 SGD_REF:S000058496 TAS F 48 kDa phosphomevalonate kinase YMR220W gene taxon:4932 20010119 SGD
+SGD S000004833 ERG8 GO:0006696 SGD_REF:S000058496 TAS P 48 kDa phosphomevalonate kinase YMR220W gene taxon:4932 20010119 SGD
+SGD S000004833 ERG8 GO:0008299 SGD_REF:S000040103|PMID:1846667 TAS P 48 kDa phosphomevalonate kinase YMR220W gene taxon:4932 20010118 SGD
+SGD S000001233 ERG9 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C squalene synthetase YHR190W gene taxon:4932 20060317 SGD
+SGD S000001233 ERG9 GO:0005783 SGD_REF:S000058496 TAS C squalene synthetase YHR190W gene taxon:4932 20010119 SGD
+SGD S000001233 ERG9 GO:0004310 SGD_REF:S000058496 TAS F squalene synthetase YHR190W gene taxon:4932 20010119 SGD
+SGD S000001233 ERG9 GO:0006696 SGD_REF:S000058496 TAS P squalene synthetase YHR190W gene taxon:4932 20010119 SGD
+SGD S000028423 ERI1 GO:0000506 SGD_REF:S000076482|PMID:15163411 IPI SGD:S000005997 C YPL096C-A|RIN1 gene taxon:4932 20050713 SGD
+SGD S000028423 ERI1 GO:0005789 SGD_REF:S000073610|PMID:12832483 IDA C YPL096C-A|RIN1 gene taxon:4932 20050712 SGD
+SGD S000028423 ERI1 GO:0005095 SGD_REF:S000073610|PMID:12832483 IPI SGD:S000005042 F YPL096C-A|RIN1 gene taxon:4932 20051122 SGD
+SGD S000028423 ERI1 GO:0006506 SGD_REF:S000076482|PMID:15163411 IMP P YPL096C-A|RIN1 gene taxon:4932 20050713 SGD
+SGD S000028423 ERI1 GO:0007265 SGD_REF:S000073610|PMID:12832483 IMP P YPL096C-A|RIN1 gene taxon:4932 20051122 SGD
+SGD S000001937 ERJ5 GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YFR041C gene taxon:4932 20031028 SGD
+SGD S000001937 ERJ5 GO:0005554 SGD_REF:S000069584 ND F YFR041C gene taxon:4932 20030203 SGD
+SGD S000001937 ERJ5 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P YFR041C gene taxon:4932 20060210 SGD
+SGD S000004599 ERO1 GO:0005783 SGD_REF:S000053010|PMID:9659914 IDA C YML130C gene taxon:4932 20021017 SGD
+SGD S000004599 ERO1 GO:0009055 SGD_REF:S000059661|PMID:10982384 IMP F YML130C gene taxon:4932 20030224 SGD
+SGD S000004599 ERO1 GO:0009055 SGD_REF:S000059661|PMID:10982384 ISS F YML130C gene taxon:4932 20030224 SGD
+SGD S000004599 ERO1 GO:0006457 SGD_REF:S000053009|PMID:9659913 IMP P YML130C gene taxon:4932 20021017 SGD
+SGD S000004599 ERO1 GO:0006467 SGD_REF:S000059661|PMID:10982384 IMP P YML130C gene taxon:4932 20021017 SGD
+SGD S000002129 ERP1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C p24 protein involved in membrane trafficking YAR002C-A gene taxon:4932 20040928 SGD
+SGD S000002129 ERP1 GO:0030134 SGD_REF:S000061877|PMID:11157978 IDA C p24 protein involved in membrane trafficking YAR002C-A gene taxon:4932 20020716 SGD
+SGD S000002129 ERP1 GO:0005554 SGD_REF:S000069584 ND F p24 protein involved in membrane trafficking YAR002C-A gene taxon:4932 20020716 SGD
+SGD S000002129 ERP1 GO:0006888 SGD_REF:S000061877|PMID:11157978 IPI P p24 protein involved in membrane trafficking YAR002C-A gene taxon:4932 20020716 SGD
+SGD S000000005 ERP2 GO:0030134 SGD_REF:S000061877|PMID:11157978 IDA C p24 protein involved in membrane trafficking YAL007C gene taxon:4932 20020716 SGD
+SGD S000000005 ERP2 GO:0005554 SGD_REF:S000069584 ND F p24 protein involved in membrane trafficking YAL007C gene taxon:4932 20020716 SGD
+SGD S000000005 ERP2 GO:0006888 SGD_REF:S000061877|PMID:11157978 IPI P p24 protein involved in membrane trafficking YAL007C gene taxon:4932 20020716 SGD
+SGD S000002176 ERP3 GO:0016021 SGD_REF:S000056373|PMID:10359606 ISS C p24 protein involved in membrane trafficking YDL018C gene taxon:4932 20020930 SGD
+SGD S000002176 ERP3 GO:0005554 SGD_REF:S000069584 ND F p24 protein involved in membrane trafficking YDL018C gene taxon:4932 20020930 SGD
+SGD S000002176 ERP3 GO:0045045 SGD_REF:S000056373|PMID:10359606 IMP P p24 protein involved in membrane trafficking YDL018C gene taxon:4932 20020930 SGD
+SGD S000005542 ERP4 GO:0016021 SGD_REF:S000056373|PMID:10359606 ISS C p24 protein involved in membrane trafficking YOR016C gene taxon:4932 20020930 SGD
+SGD S000005542 ERP4 GO:0005554 SGD_REF:S000069584 ND F p24 protein involved in membrane trafficking YOR016C gene taxon:4932 20020930 SGD
+SGD S000005542 ERP4 GO:0045045 SGD_REF:S000056373|PMID:10359606 IMP P p24 protein involved in membrane trafficking YOR016C gene taxon:4932 20020930 SGD
+SGD S000005542 ERP4 GO:0045045 SGD_REF:S000056373|PMID:10359606 IGI SGD:S000000005 P p24 protein involved in membrane trafficking YOR016C gene taxon:4932 20020930 SGD
+SGD S000001152 ERP5 GO:0016021 SGD_REF:S000056373|PMID:10359606 ISS C p24 protein involved in membrane trafficking YHR110W gene taxon:4932 20020930 SGD
+SGD S000001152 ERP5 GO:0005554 SGD_REF:S000069584 ND F p24 protein involved in membrane trafficking YHR110W gene taxon:4932 20020930 SGD
+SGD S000001152 ERP5 GO:0045045 SGD_REF:S000056373|PMID:10359606 IMP P p24 protein involved in membrane trafficking YHR110W gene taxon:4932 20020930 SGD
+SGD S000002970 ERP6 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C p24 protein involved in membrane trafficking YGL002W gene taxon:4932 20040928 SGD
+SGD S000002970 ERP6 GO:0016021 SGD_REF:S000056373|PMID:10359606 ISS C p24 protein involved in membrane trafficking YGL002W gene taxon:4932 20020930 SGD
+SGD S000002970 ERP6 GO:0005554 SGD_REF:S000069584 ND F p24 protein involved in membrane trafficking YGL002W gene taxon:4932 20020930 SGD
+SGD S000002970 ERP6 GO:0045045 SGD_REF:S000056373|PMID:10359606 IMP P p24 protein involved in membrane trafficking YGL002W gene taxon:4932 20020930 SGD
+SGD S000002970 ERP6 GO:0045045 SGD_REF:S000056373|PMID:10359606 IGI SGD:S000002129 P p24 protein involved in membrane trafficking YGL002W gene taxon:4932 20020930 SGD
+SGD S000005920 ERR1 GO:0008372 SGD_REF:S000069584 ND C enolase homolog YOR393W gene taxon:4932 20021002 SGD
+SGD S000005920 ERR1 GO:0004634 SGD_REF:S000057489|PMID:7785338 ISS F enolase homolog YOR393W gene taxon:4932 20021002 SGD
+SGD S000005920 ERR1 GO:0000004 SGD_REF:S000069584 ND P enolase homolog YOR393W gene taxon:4932 20021002 SGD
+SGD S000006202 ERR2 GO:0008372 SGD_REF:S000069584 ND C YPL281C gene taxon:4932 20021002 SGD
+SGD S000006202 ERR2 GO:0004634 SGD_REF:S000057489|PMID:7785338 ISS F YPL281C gene taxon:4932 20021002 SGD
+SGD S000006202 ERR2 GO:0000004 SGD_REF:S000069584 ND P YPL281C gene taxon:4932 20021002 SGD
+SGD S000004942 ERR3 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YMR323W gene taxon:4932 20020507 SGD
+SGD S000004942 ERR3 GO:0004634 SGD_REF:S000072463|PMID:10592175 ISS F YMR323W gene taxon:4932 20030213 SGD
+SGD S000004942 ERR3 GO:0004634 SGD_REF:S000057489|PMID:7785338 ISS F YMR323W gene taxon:4932 20041209 SGD
+SGD S000004942 ERR3 GO:0000004 SGD_REF:S000069584 ND P YMR323W gene taxon:4932 20021002 SGD
+SGD S000000671 ERS1 GO:0005768 SGD_REF:S000081946|PMID:15885099 IDA C YCR075C gene taxon:4932 20050630 SGD
+SGD S000000671 ERS1 GO:0005773 SGD_REF:S000081946|PMID:15885099 IDA C YCR075C gene taxon:4932 20050630 SGD
+SGD S000000671 ERS1 GO:0016021 SGD_REF:S000066123|PMID:11689434 ISS C YCR075C gene taxon:4932 20020923 SGD
+SGD S000000671 ERS1 GO:0015184 SGD_REF:S000066123|PMID:11689434 ISS F YCR075C gene taxon:4932 20020923 SGD
+SGD S000000671 ERS1 GO:0015811 SGD_REF:S000066123|PMID:11689434 ISS P YCR075C gene taxon:4932 20020923 SGD
+SGD S000003261 ERV1 GO:0005739 SGD_REF:S000060826|PMID:11313344 TAS C sulfhydryl oxidase YGR029W gene taxon:4932 20020903 SGD
+SGD S000003261 ERV1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C sulfhydryl oxidase YGR029W gene taxon:4932 20040928 SGD
+SGD S000003261 ERV1 GO:0005758 SGD_REF:S000068968|PMID:11493598 IDA C sulfhydryl oxidase YGR029W gene taxon:4932 20030512 SGD
+SGD S000003261 ERV1 GO:0016972 SGD_REF:S000060826|PMID:11313344 TAS F sulfhydryl oxidase YGR029W gene taxon:4932 20020903 SGD
+SGD S000003261 ERV1 GO:0006879 SGD_REF:S000068968|PMID:11493598 IDA P sulfhydryl oxidase YGR029W gene taxon:4932 20020904 SGD
+SGD S000003261 ERV1 GO:0007005 SGD_REF:S000060826|PMID:11313344 TAS P sulfhydryl oxidase YGR029W gene taxon:4932 20020903 SGD
+SGD S000003022 ERV14 GO:0005789 SGD_REF:S000053551|PMID:9732282 IDA C 14 kDa protein found on ER-derived vesicles YGL054C gene taxon:4932 20010118 SGD
+SGD S000003022 ERV14 GO:0030134 SGD_REF:S000061877|PMID:11157978 IDA C 14 kDa protein found on ER-derived vesicles YGL054C gene taxon:4932 20020716 SGD
+SGD S000003022 ERV14 GO:0005554 SGD_REF:S000069584 ND F 14 kDa protein found on ER-derived vesicles YGL054C gene taxon:4932 20020716 SGD
+SGD S000003022 ERV14 GO:0006888 SGD_REF:S000053551|PMID:9732282 IMP P 14 kDa protein found on ER-derived vesicles YGL054C gene taxon:4932 20010118 SGD
+SGD S000003022 ERV14 GO:0006888 SGD_REF:S000061877|PMID:11157978 IPI P 14 kDa protein found on ER-derived vesicles YGL054C gene taxon:4932 20020716 SGD
+SGD S000003022 ERV14 GO:0006888 SGD_REF:S000053551|PMID:9732282 IPI P 14 kDa protein found on ER-derived vesicles YGL054C gene taxon:4932 20010118 SGD
+SGD S000003022 ERV14 GO:0007120 SGD_REF:S000053551|PMID:9732282 IMP P 14 kDa protein found on ER-derived vesicles YGL054C gene taxon:4932 20010118 SGD
+SGD S000003022 ERV14 GO:0030437 SGD_REF:S000053551|PMID:9732282 IMP P 14 kDa protein found on ER-derived vesicles YGL054C gene taxon:4932 20010118 SGD
+SGD S000000414 ERV15 GO:0016021 SGD_REF:S000072825|PMID:12524434 ISS C YBR210W gene taxon:4932 20030409 SGD
+SGD S000000414 ERV15 GO:0005554 SGD_REF:S000069584 ND F YBR210W gene taxon:4932 20030409 SGD
+SGD S000000414 ERV15 GO:0007120 SGD_REF:S000053551|PMID:9732282 ISS P YBR210W gene taxon:4932 20030409 SGD
+SGD S000006241 ERV2 GO:0005792 SGD_REF:S000060826|PMID:11313344 IDA C YPR037C gene taxon:4932 20020903 SGD
+SGD S000006241 ERV2 GO:0016972 SGD_REF:S000060826|PMID:11313344 IDA F YPR037C gene taxon:4932 20020903 SGD
+SGD S000006241 ERV2 GO:0006467 SGD_REF:S000066106|PMID:11584268 IGI P YPR037C gene taxon:4932 20021223 SGD
+SGD S000004473 ERV25 GO:0030134 SGD_REF:S000061877|PMID:11157978 IDA C vesicle coat component YML012W gene taxon:4932 20020716 SGD
+SGD S000004473 ERV25 GO:0005554 SGD_REF:S000069584 ND F vesicle coat component YML012W gene taxon:4932 20020716 SGD
+SGD S000004473 ERV25 GO:0006888 SGD_REF:S000061877|PMID:11157978 IPI P vesicle coat component YML012W gene taxon:4932 20020716 SGD
+SGD S000003516 ERV29 GO:0030134 SGD_REF:S000061877|PMID:11157978 IDA C ER-Golgi transport vesicle protein YGR284C gene taxon:4932 20020716 SGD
+SGD S000003516 ERV29 GO:0005554 SGD_REF:S000069584 ND F ER-Golgi transport vesicle protein YGR284C gene taxon:4932 20020716 SGD
+SGD S000003516 ERV29 GO:0006888 SGD_REF:S000061877|PMID:11157978 IPI P ER-Golgi transport vesicle protein YGR284C gene taxon:4932 20020716 SGD
+SGD S000004532 ERV41 GO:0030134 SGD_REF:S000061877|PMID:11157978 IDA C YML067C gene taxon:4932 20020716 SGD
+SGD S000004532 ERV41 GO:0030173 SGD_REF:S000061877|PMID:11157978 IDA C YML067C gene taxon:4932 20020716 SGD
+SGD S000004532 ERV41 GO:0030176 SGD_REF:S000061877|PMID:11157978 IDA C YML067C gene taxon:4932 20020716 SGD
+SGD S000004532 ERV41 GO:0005554 SGD_REF:S000069584 ND F YML067C gene taxon:4932 20020716 SGD
+SGD S000004532 ERV41 GO:0006888 SGD_REF:S000061877|PMID:11157978 IPI P YML067C gene taxon:4932 20020716 SGD
+SGD S000000040 ERV46 GO:0030134 SGD_REF:S000061877|PMID:11157978 IDA C ER-Golgi transport vesicle protein YAL042W|FUN9 gene taxon:4932 20020716 SGD
+SGD S000000040 ERV46 GO:0030173 SGD_REF:S000061877|PMID:11157978 IDA C ER-Golgi transport vesicle protein YAL042W|FUN9 gene taxon:4932 20020716 SGD
+SGD S000000040 ERV46 GO:0030176 SGD_REF:S000061877|PMID:11157978 IDA C ER-Golgi transport vesicle protein YAL042W|FUN9 gene taxon:4932 20020716 SGD
+SGD S000000040 ERV46 GO:0005554 SGD_REF:S000069584 ND F ER-Golgi transport vesicle protein YAL042W|FUN9 gene taxon:4932 20020716 SGD
+SGD S000000040 ERV46 GO:0006888 SGD_REF:S000061877|PMID:11157978 IPI P ER-Golgi transport vesicle protein YAL042W|FUN9 gene taxon:4932 20020716 SGD
+SGD S000005770 ESA1 GO:0000123 SGD_REF:S000054358|PMID:10082517 TAS C NuA4 complex component, acetyltransferase in the SAS gene family YOR244W|TAS1 gene taxon:4932 20020731 SGD
+SGD S000005770 ESA1 GO:0000123 SGD_REF:S000060726|PMID:11036083 IDA C NuA4 complex component, acetyltransferase in the SAS gene family YOR244W|TAS1 gene taxon:4932 20020918 SGD
+SGD S000005770 ESA1 GO:0043189 SGD_REF:S000079775|PMID:15485911 IPI C NuA4 complex component, acetyltransferase in the SAS gene family YOR244W|TAS1 gene taxon:4932 20050207 SGD
+SGD S000005770 ESA1 GO:0043189 SGD_REF:S000051286|PMID:10487762 IPI C NuA4 complex component, acetyltransferase in the SAS gene family YOR244W|TAS1 gene taxon:4932 20050207 SGD
+SGD S000005770 ESA1 GO:0004402 SGD_REF:S000054358|PMID:10082517 IDA F NuA4 complex component, acetyltransferase in the SAS gene family YOR244W|TAS1 gene taxon:4932 20020731 SGD
+SGD S000005770 ESA1 GO:0000074 SGD_REF:S000054358|PMID:10082517 IMP P NuA4 complex component, acetyltransferase in the SAS gene family YOR244W|TAS1 gene taxon:4932 20020731 SGD
+SGD S000005770 ESA1 GO:0006354 SGD_REF:S000082344|PMID:15949446 IDA P NuA4 complex component, acetyltransferase in the SAS gene family YOR244W|TAS1 gene taxon:4932 20051107 SGD
+SGD S000005770 ESA1 GO:0006354 SGD_REF:S000082344|PMID:15949446 IMP P NuA4 complex component, acetyltransferase in the SAS gene family YOR244W|TAS1 gene taxon:4932 20051107 SGD
+SGD S000005770 ESA1 GO:0006357 SGD_REF:S000060726|PMID:11036083 IMP P NuA4 complex component, acetyltransferase in the SAS gene family YOR244W|TAS1 gene taxon:4932 20020918 SGD
+SGD S000005770 ESA1 GO:0016573 SGD_REF:S000054358|PMID:10082517 IDA P NuA4 complex component, acetyltransferase in the SAS gene family YOR244W|TAS1 gene taxon:4932 20020731 SGD
+SGD S000005069 ESBP6 GO:0005739 SGD_REF:S000065864|PMID:11536335 IDA C monocarboxylate permease (putative) YNL125C|MCH3 gene taxon:4932 20020918 SGD
+SGD S000005069 ESBP6 GO:0016020 SGD_REF:S000065864|PMID:11536335 ISS C monocarboxylate permease (putative) YNL125C|MCH3 gene taxon:4932 20020918 SGD
+SGD S000005069 ESBP6 GO:0005215 SGD_REF:S000065864|PMID:11536335 ISS F monocarboxylate permease (putative) YNL125C|MCH3 gene taxon:4932 20020918 SGD
+SGD S000005069 ESBP6 NOT GO:0008028 SGD_REF:S000065864|PMID:11536335 IGI F monocarboxylate permease (putative) YNL125C|MCH3 gene taxon:4932 20020918 SGD
+SGD S000005069 ESBP6 NOT GO:0008028 SGD_REF:S000065864|PMID:11536335 IMP F monocarboxylate permease (putative) YNL125C|MCH3 gene taxon:4932 20020918 SGD
+SGD S000005069 ESBP6 GO:0006810 SGD_REF:S000065864|PMID:11536335 ISS P monocarboxylate permease (putative) YNL125C|MCH3 gene taxon:4932 20020918 SGD
+SGD S000004832 ESC1 GO:0005634 SGD_REF:S000072020|PMID:12417731 IDA C YMR219W gene taxon:4932 20030113 SGD
+SGD S000004832 ESC1 GO:0005554 SGD_REF:S000069584 ND F YMR219W gene taxon:4932 20021002 SGD
+SGD S000004832 ESC1 GO:0006348 SGD_REF:S000072020|PMID:12417731 IMP P YMR219W gene taxon:4932 20030113 SGD
+SGD S000002771 ESC2 GO:0005634 SGD_REF:S000056456|PMID:11090616 IDA C YDR363W gene taxon:4932 20020930 SGD
+SGD S000002771 ESC2 GO:0005554 SGD_REF:S000069584 ND F YDR363W gene taxon:4932 20020930 SGD
+SGD S000002771 ESC2 GO:0030466 SGD_REF:S000056456|PMID:11090616 IMP P YDR363W gene taxon:4932 20020930 SGD
+SGD S000029160 ESC3 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20030521 SGD
+SGD S000029160 ESC3 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20030521 SGD
+SGD S000029160 ESC3 GO:0007584 SGD_REF:S000073033|PMID:12702249 IMP P gene taxon:4932 20030521 SGD
+SGD S000005377 ESC8 GO:0005634 SGD_REF:S000071547|PMID:12399377 IPI C YOL017W gene taxon:4932 20021114 SGD
+SGD S000005377 ESC8 GO:0005554 SGD_REF:S000069584 ND F YOL017W gene taxon:4932 20021114 SGD
+SGD S000005377 ESC8 GO:0006342 SGD_REF:S000071547|PMID:12399377 IMP P YOL017W gene taxon:4932 20021114 SGD
+SGD S000002773 ESF1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YDR365C gene taxon:4932 20031028 SGD
+SGD S000002773 ESF1 GO:0005730 SGD_REF:S000074185|PMID:14562095 IDA C YDR365C gene taxon:4932 20031028 SGD
+SGD S000002773 ESF1 GO:0003723 SGD_REF:S000076107|PMID:15056729 IDA F YDR365C gene taxon:4932 20040525 SGD
+SGD S000002773 ESF1 GO:0006364 SGD_REF:S000075214|PMID:14690591 IPI P YDR365C gene taxon:4932 20031231 SGD
+SGD S000002773 ESF1 GO:0006364 SGD_REF:S000076107|PMID:15056729 IPI P YDR365C gene taxon:4932 20040525 SGD
+SGD S000002773 ESF1 GO:0006364 SGD_REF:S000076107|PMID:15056729 IMP P YDR365C gene taxon:4932 20040525 SGD
+SGD S000005337 ESF2 GO:0005730 SGD_REF:S000074185|PMID:14562095 IDA C YNR054C|ABT1 gene taxon:4932 20031028 SGD
+SGD S000005337 ESF2 GO:0005730 SGD_REF:S000082384|PMID:15964808 IDA C YNR054C|ABT1 gene taxon:4932 20050815 SGD
+SGD S000005337 ESF2 GO:0005732 SGD_REF:S000082384|PMID:15964808 IPI SGD:S000000653|SGD:S000004842|SGD:S000002172|SGD:S000003322|SGD:S000000929 C YNR054C|ABT1 gene taxon:4932 20050816 SGD
+SGD S000005337 ESF2 GO:0005732 SGD_REF:S000082384|PMID:15964808 IDA C YNR054C|ABT1 gene taxon:4932 20050815 SGD
+SGD S000005337 ESF2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YNR054C|ABT1 gene taxon:4932 20031028 SGD
+SGD S000005337 ESF2 NOT GO:0005737 SGD_REF:S000082384|PMID:15964808 IDA C YNR054C|ABT1 gene taxon:4932 20050815 SGD
+SGD S000005337 ESF2 GO:0030528 SGD_REF:S000065772|PMID:10648625 ISS F YNR054C|ABT1 gene taxon:4932 20030311 SGD
+SGD S000005337 ESF2 GO:0006365 SGD_REF:S000082384|PMID:15964808 IMP P YNR054C|ABT1 gene taxon:4932 20050817 SGD
+SGD S000003330 ESP1 GO:0005634 SGD_REF:S000058435|PMID:11149918 IDA C separase YGR098C|separin gene taxon:4932 20020808 SGD
+SGD S000003330 ESP1 GO:0005737 SGD_REF:S000058435|PMID:11149918 IDA C separase YGR098C|separin gene taxon:4932 20020808 SGD
+SGD S000003330 ESP1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C separase YGR098C|separin gene taxon:4932 20041203 SGD
+SGD S000003330 ESP1 GO:0005819 SGD_REF:S000058435|PMID:11149918 IDA C separase YGR098C|separin gene taxon:4932 20020808 SGD
+SGD S000003330 ESP1 GO:0004197 SGD_REF:S000062956|PMID:11081625 IDA F separase YGR098C|separin gene taxon:4932 20020811 SGD
+SGD S000003330 ESP1 GO:0000070 SGD_REF:S000054076|PMID:9635435 IMP P separase YGR098C|separin gene taxon:4932 20020808 SGD
+SGD S000003330 ESP1 GO:0000070 SGD_REF:S000054076|PMID:9635435 IPI P separase YGR098C|separin gene taxon:4932 20020808 SGD
+SGD S000003330 ESP1 GO:0007096 SGD_REF:S000073006|PMID:12598903 IGI P separase YGR098C|separin gene taxon:4932 20030430 SGD
+SGD S000003330 ESP1 GO:0007096 SGD_REF:S000073006|PMID:12598903 IPI P separase YGR098C|separin gene taxon:4932 20030430 SGD
+SGD S000003778 ESS1 GO:0005634 SGD_REF:S000045037|PMID:10531363 IPI SGD:S000002299 C peptidyl-prolyl cis-trans isomerase (PPIase) YJR017C|PIN1|PTF1 gene taxon:4932 20030508 SGD
+SGD S000003778 ESS1 GO:0003711 SGD_REF:S000075289|PMID:14704159 IGI F peptidyl-prolyl cis-trans isomerase (PPIase) YJR017C|PIN1|PTF1 gene taxon:4932 20040113 SGD
+SGD S000003778 ESS1 GO:0003755 SGD_REF:S000054808|PMID:7781779 ISS F peptidyl-prolyl cis-trans isomerase (PPIase) YJR017C|PIN1|PTF1 gene taxon:4932 20010118 SGD
+SGD S000003778 ESS1 GO:0003755 SGD_REF:S000045834|PMID:9867817 IDA F peptidyl-prolyl cis-trans isomerase (PPIase) YJR017C|PIN1|PTF1 gene taxon:4932 20030508 SGD
+SGD S000003778 ESS1 GO:0000122 SGD_REF:S000075289|PMID:14704159 IGI P peptidyl-prolyl cis-trans isomerase (PPIase) YJR017C|PIN1|PTF1 gene taxon:4932 20040113 SGD
+SGD S000003778 ESS1 GO:0006369 SGD_REF:S000075289|PMID:14704159 IMP P peptidyl-prolyl cis-trans isomerase (PPIase) YJR017C|PIN1|PTF1 gene taxon:4932 20040113 SGD
+SGD S000003778 ESS1 GO:0006397 SGD_REF:S000045834|PMID:9867817 IMP P peptidyl-prolyl cis-trans isomerase (PPIase) YJR017C|PIN1|PTF1 gene taxon:4932 20010118 SGD
+SGD S000003778 ESS1 GO:0042326 SGD_REF:S000069575|PMID:11904169 IDA P peptidyl-prolyl cis-trans isomerase (PPIase) YJR017C|PIN1|PTF1 gene taxon:4932 20030508 SGD
+SGD S000004223 EST1 GO:0005634 SGD_REF:S000070205|PMID:12101098 IDA C Telomere elongation protein YLR233C gene taxon:4932 20020828 SGD
+SGD S000004223 EST1 GO:0005697 SGD_REF:S000069751|PMID:11884619 TAS C Telomere elongation protein YLR233C gene taxon:4932 20020625 SGD
+SGD S000004223 EST1 GO:0005697 SGD_REF:S000044698|PMID:10898986 IPI C Telomere elongation protein YLR233C gene taxon:4932 20030619 SGD
+SGD S000004223 EST1 GO:0005697 SGD_REF:S000044698|PMID:10898986 IDA C Telomere elongation protein YLR233C gene taxon:4932 20030619 SGD
+SGD S000004223 EST1 GO:0005730 SGD_REF:S000070205|PMID:12101098 IDA C Telomere elongation protein YLR233C gene taxon:4932 20020828 SGD
+SGD S000004223 EST1 GO:0003697 SGD_REF:S000069751|PMID:11884619 TAS F Telomere elongation protein YLR233C gene taxon:4932 20020625 SGD
+SGD S000004223 EST1 GO:0003720 SGD_REF:S000044698|PMID:10898986 IDA F Telomere elongation protein YLR233C gene taxon:4932 20030619 SGD
+SGD S000004223 EST1 GO:0003720 SGD_REF:S000044698|PMID:10898986 IPI F Telomere elongation protein YLR233C gene taxon:4932 20030619 SGD
+SGD S000004223 EST1 GO:0003723 SGD_REF:S000071610|PMID:12414733 IPI F Telomere elongation protein YLR233C gene taxon:4932 20030226 SGD
+SGD S000004223 EST1 GO:0007004 SGD_REF:S000069751|PMID:11884619 TAS P Telomere elongation protein YLR233C gene taxon:4932 20020625 SGD
+SGD S000004310 EST2 GO:0000333 SGD_REF:S000069751|PMID:11884619 TAS C telomerase reverse transcriptase YLR318W|TERT gene taxon:4932 20020625 SGD
+SGD S000004310 EST2 GO:0000333 SGD_REF:S000081300|PMID:15813705 IDA C telomerase reverse transcriptase YLR318W|TERT gene taxon:4932 20050421 SGD
+SGD S000004310 EST2 GO:0000333 SGD_REF:S000081300|PMID:15813705 IPI C telomerase reverse transcriptase YLR318W|TERT gene taxon:4932 20050421 SGD
+SGD S000004310 EST2 GO:0005634 SGD_REF:S000070205|PMID:12101098 IDA C telomerase reverse transcriptase YLR318W|TERT gene taxon:4932 20020828 SGD
+SGD S000004310 EST2 GO:0005697 SGD_REF:S000044698|PMID:10898986 IDA C telomerase reverse transcriptase YLR318W|TERT gene taxon:4932 20030619 SGD
+SGD S000004310 EST2 GO:0005697 SGD_REF:S000044698|PMID:10898986 IPI C telomerase reverse transcriptase YLR318W|TERT gene taxon:4932 20030619 SGD
+SGD S000004310 EST2 GO:0005730 SGD_REF:S000070205|PMID:12101098 IDA C telomerase reverse transcriptase YLR318W|TERT gene taxon:4932 20020828 SGD
+SGD S000004310 EST2 contributes_to GO:0003720 SGD_REF:S000081300|PMID:15813705 IDA F telomerase reverse transcriptase YLR318W|TERT gene taxon:4932 20050421 SGD
+SGD S000004310 EST2 GO:0003721 SGD_REF:S000069751|PMID:11884619 TAS F telomerase reverse transcriptase YLR318W|TERT gene taxon:4932 20020625 SGD
+SGD S000004310 EST2 GO:0007004 SGD_REF:S000069751|PMID:11884619 TAS P telomerase reverse transcriptase YLR318W|TERT gene taxon:4932 20020625 SGD
+SGD S000004310 EST2 GO:0007004 SGD_REF:S000081300|PMID:15813705 IMP P telomerase reverse transcriptase YLR318W|TERT gene taxon:4932 20050421 SGD
+SGD S000004310 EST2 GO:0007004 SGD_REF:S000081300|PMID:15813705 IDA P telomerase reverse transcriptase YLR318W|TERT gene taxon:4932 20050421 SGD
+SGD S000006432 EST3 GO:0005634 SGD_REF:S000070205|PMID:12101098 IDA C 20.5 kDa 181aa protein YIL009C-A gene taxon:4932 20020828 SGD
+SGD S000006432 EST3 GO:0005697 SGD_REF:S000069751|PMID:11884619 TAS C 20.5 kDa 181aa protein YIL009C-A gene taxon:4932 20020625 SGD
+SGD S000006432 EST3 GO:0005697 SGD_REF:S000044698|PMID:10898986 IPI C 20.5 kDa 181aa protein YIL009C-A gene taxon:4932 20030619 SGD
+SGD S000006432 EST3 GO:0005697 SGD_REF:S000044698|PMID:10898986 IDA C 20.5 kDa 181aa protein YIL009C-A gene taxon:4932 20030619 SGD
+SGD S000006432 EST3 GO:0003720 SGD_REF:S000044698|PMID:10898986 IDA F 20.5 kDa 181aa protein YIL009C-A gene taxon:4932 20030619 SGD
+SGD S000006432 EST3 GO:0003720 SGD_REF:S000044698|PMID:10898986 IPI F 20.5 kDa 181aa protein YIL009C-A gene taxon:4932 20030619 SGD
+SGD S000006432 EST3 GO:0007004 SGD_REF:S000069751|PMID:11884619 TAS P 20.5 kDa 181aa protein YIL009C-A gene taxon:4932 20020625 SGD
+SGD S000077072 ETC1 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20040920 SGD
+SGD S000077072 ETC1 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20040920 SGD
+SGD S000077072 ETC1 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20040920 SGD
+SGD S000077073 ETC2 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20040920 SGD
+SGD S000077073 ETC2 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20040920 SGD
+SGD S000077073 ETC2 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20040920 SGD
+SGD S000077074 ETC3 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20040920 SGD
+SGD S000077074 ETC3 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20040920 SGD
+SGD S000077074 ETC3 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20040920 SGD
+SGD S000077075 ETC4 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20040920 SGD
+SGD S000077075 ETC4 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20040920 SGD
+SGD S000077075 ETC4 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20040920 SGD
+SGD S000077076 ETC5 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20040920 SGD
+SGD S000077076 ETC5 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20040920 SGD
+SGD S000077076 ETC5 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20040920 SGD
+SGD S000077077 ETC6 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20040920 SGD
+SGD S000077077 ETC6 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20040920 SGD
+SGD S000077077 ETC6 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20040920 SGD
+SGD S000077078 ETC7 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20040920 SGD
+SGD S000077078 ETC7 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20040920 SGD
+SGD S000077078 ETC7 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20040920 SGD
+SGD S000077079 ETC8 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20040920 SGD
+SGD S000077079 ETC8 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20040920 SGD
+SGD S000077079 ETC8 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20040920 SGD
+SGD S000000230 ETR1 GO:0005739 SGD_REF:S000065945|PMID:11509667 IDA C 2-enoyl thioester reductase, E.C. 1.3.1.- YBR026C|MRF1|MRF1' gene taxon:4932 20021030 SGD
+SGD S000000230 ETR1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C 2-enoyl thioester reductase, E.C. 1.3.1.- YBR026C|MRF1|MRF1' gene taxon:4932 20040924 SGD
+SGD S000000230 ETR1 GO:0016631 SGD_REF:S000065945|PMID:11509667 IDA F 2-enoyl thioester reductase, E.C. 1.3.1.- YBR026C|MRF1|MRF1' gene taxon:4932 20021030 SGD
+SGD S000000230 ETR1 GO:0006633 SGD_REF:S000065945|PMID:11509667 IMP P 2-enoyl thioester reductase, E.C. 1.3.1.- YBR026C|MRF1|MRF1' gene taxon:4932 20021030 SGD
+SGD S000000230 ETR1 GO:0009060 SGD_REF:S000065945|PMID:11509667 IMP P 2-enoyl thioester reductase, E.C. 1.3.1.- YBR026C|MRF1|MRF1' gene taxon:4932 20021030 SGD
+SGD S000029717 ETS1-1 GO:0006364 SGD_REF:S000075517|PMID:7800512 IMP P 5' ETS gene taxon:4932 20040308 SGD
+SGD S000029717 ETS1-1 GO:0006364 SGD_REF:S000075517|PMID:7800512 TAS P 5' ETS gene taxon:4932 20040308 SGD
+SGD S000029707 ETS1-2 GO:0006364 SGD_REF:S000075517|PMID:7800512 IMP P 5' ETS gene taxon:4932 20040308 SGD
+SGD S000029707 ETS1-2 GO:0006364 SGD_REF:S000075517|PMID:7800512 TAS P 5' ETS gene taxon:4932 20040308 SGD
+SGD S000002926 EUG1 GO:0005783 SGD_REF:S000069459|PMID:11914276 IDA C protein disulfide isomerase homolog YDR518W gene taxon:4932 20020507 SGD
+SGD S000002926 EUG1 GO:0003756 SGD_REF:S000059478|PMID:11157982 IMP F protein disulfide isomerase homolog YDR518W gene taxon:4932 20020606 SGD
+SGD S000002926 EUG1 GO:0003756 SGD_REF:S000059478|PMID:11157982 TAS F protein disulfide isomerase homolog YDR518W gene taxon:4932 20020606 SGD
+SGD S000002926 EUG1 GO:0006457 SGD_REF:S000059478|PMID:11157982 IGI SGD:S000000548 P protein disulfide isomerase homolog YDR518W gene taxon:4932 20021108 SGD
+SGD S000004291 EXG1 GO:0009277 SGD_REF:S000050571|PMID:9748433 IDA C exo-1,3-beta-glucanase YLR300W|BGL1 gene taxon:4932 20010801 SGD
+SGD S000004291 EXG1 GO:0004338 SGD_REF:S000050571|PMID:9748433 ISS F exo-1,3-beta-glucanase YLR300W|BGL1 gene taxon:4932 20010801 SGD
+SGD S000004291 EXG1 GO:0006073 SGD_REF:S000042711|PMID:7565587 IMP P exo-1,3-beta-glucanase YLR300W|BGL1 gene taxon:4932 20010801 SGD
+SGD S000004291 EXG1 GO:0006073 SGD_REF:S000042711|PMID:7565587 IGI P exo-1,3-beta-glucanase YLR300W|BGL1 gene taxon:4932 20010801 SGD
+SGD S000004291 EXG1 GO:0007047 SGD_REF:S000050571|PMID:9748433 ISS P exo-1,3-beta-glucanase YLR300W|BGL1 gene taxon:4932 20010801 SGD
+SGD S000002669 EXG2 GO:0009277 SGD_REF:S000045045|PMID:7875558 IDA C exo-1,3-beta-glucanase YDR261C gene taxon:4932 20020924 SGD
+SGD S000002669 EXG2 GO:0004338 SGD_REF:S000045045|PMID:7875558 IDA F exo-1,3-beta-glucanase YDR261C gene taxon:4932 20020924 SGD
+SGD S000002669 EXG2 GO:0007047 SGD_REF:S000045045|PMID:7875558 IC GO:0004338 P exo-1,3-beta-glucanase YDR261C gene taxon:4932 20031016 SGD
+SGD S000005559 EXO1 GO:0005634 SGD_REF:S000061193|PMID:11438669 IPI C exonuclease YOR033C|DHS1 gene taxon:4932 20021022 SGD
+SGD S000005559 EXO1 GO:0004527 SGD_REF:S000061193|PMID:11438669 TAS F exonuclease YOR033C|DHS1 gene taxon:4932 20021022 SGD
+SGD S000005559 EXO1 GO:0008409 SGD_REF:S000072317|PMID:12531018 IDA F exonuclease YOR033C|DHS1 gene taxon:4932 20030702 SGD
+SGD S000005559 EXO1 GO:0017108 SGD_REF:S000072317|PMID:12531018 IDA F exonuclease YOR033C|DHS1 gene taxon:4932 20030702 SGD
+SGD S000005559 EXO1 GO:0000723 SGD_REF:S000076151|PMID:15126387 IGI P exonuclease YOR033C|DHS1 gene taxon:4932 20051010 SGD
+SGD S000005559 EXO1 GO:0006298 SGD_REF:S000061193|PMID:11438669 IMP P exonuclease YOR033C|DHS1 gene taxon:4932 20021022 SGD
+SGD S000003621 EXO70 GO:0000145 SGD_REF:S000047160|PMID:8978675 IPI C exocyst complex component YJL085W gene taxon:4932 20040706 SGD
+SGD S000003621 EXO70 GO:0005515 SGD_REF:S000047160|PMID:8978675 IPI F exocyst complex component YJL085W gene taxon:4932 20040727 SGD
+SGD S000003621 EXO70 GO:0000910 SGD_REF:S000041005|PMID:10652251 IMP P exocyst complex component YJL085W gene taxon:4932 20010119 SGD
+SGD S000003621 EXO70 GO:0006893 SGD_REF:S000039481|PMID:9700152 TAS P exocyst complex component YJL085W gene taxon:4932 20010118 SGD
+SGD S000003621 EXO70 GO:0006904 SGD_REF:S000039481|PMID:9700152 TAS P exocyst complex component YJL085W gene taxon:4932 20010118 SGD
+SGD S000003621 EXO70 GO:0006906 SGD_REF:S000039481|PMID:9700152 TAS P exocyst complex component YJL085W gene taxon:4932 20010118 SGD
+SGD S000003621 EXO70 GO:0007121 SGD_REF:S000041005|PMID:10652251 IMP P exocyst complex component YJL085W gene taxon:4932 20010118 SGD
+SGD S000000306 EXO84 GO:0000131 SGD_REF:S000052580|PMID:10438536 IDA C exocyst complex component, spliceosome assembly protein YBR102C|USA3 gene taxon:4932 20040730 SGD
+SGD S000000306 EXO84 GO:0000145 SGD_REF:S000052580|PMID:10438536 IPI C exocyst complex component, spliceosome assembly protein YBR102C|USA3 gene taxon:4932 20010118 SGD
+SGD S000000306 EXO84 GO:0005934 SGD_REF:S000052580|PMID:10438536 IDA C exocyst complex component, spliceosome assembly protein YBR102C|USA3 gene taxon:4932 20040730 SGD
+SGD S000000306 EXO84 GO:0005935 SGD_REF:S000052580|PMID:10438536 IDA C exocyst complex component, spliceosome assembly protein YBR102C|USA3 gene taxon:4932 20040730 SGD
+SGD S000000306 EXO84 GO:0005515 SGD_REF:S000052580|PMID:10438536 IPI F exocyst complex component, spliceosome assembly protein YBR102C|USA3 gene taxon:4932 20040728 SGD
+SGD S000000306 EXO84 GO:0000245 SGD_REF:S000069169|PMID:11425851 IGI P exocyst complex component, spliceosome assembly protein YBR102C|USA3 gene taxon:4932 20040730 SGD
+SGD S000000306 EXO84 GO:0000245 SGD_REF:S000069169|PMID:11425851 IPI P exocyst complex component, spliceosome assembly protein YBR102C|USA3 gene taxon:4932 20040730 SGD
+SGD S000000306 EXO84 GO:0000245 SGD_REF:S000069169|PMID:11425851 IMP P exocyst complex component, spliceosome assembly protein YBR102C|USA3 gene taxon:4932 20040730 SGD
+SGD S000000306 EXO84 GO:0006887 SGD_REF:S000052580|PMID:10438536 IGI P exocyst complex component, spliceosome assembly protein YBR102C|USA3 gene taxon:4932 20040730 SGD
+SGD S000000306 EXO84 GO:0006887 SGD_REF:S000052580|PMID:10438536 IPI P exocyst complex component, spliceosome assembly protein YBR102C|USA3 gene taxon:4932 20040730 SGD
+SGD S000000306 EXO84 GO:0006887 SGD_REF:S000052580|PMID:10438536 IMP P exocyst complex component, spliceosome assembly protein YBR102C|USA3 gene taxon:4932 20040730 SGD
+SGD S000005844 FAA1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C long chain fatty acyl:CoA synthetase YOR317W gene taxon:4932 20040928 SGD
+SGD S000005844 FAA1 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C long chain fatty acyl:CoA synthetase YOR317W gene taxon:4932 20060317 SGD
+SGD S000005844 FAA1 GO:0005811 SGD_REF:S000048561|PMID:10515935 IDA C long chain fatty acyl:CoA synthetase YOR317W gene taxon:4932 20020917 SGD
+SGD S000005844 FAA1 GO:0004467 SGD_REF:S000053182|PMID:8206942 IDA F long chain fatty acyl:CoA synthetase YOR317W gene taxon:4932 20020917 SGD
+SGD S000005844 FAA1 GO:0006499 SGD_REF:S000039598|PMID:7962057 IGI P long chain fatty acyl:CoA synthetase YOR317W gene taxon:4932 20020917 SGD
+SGD S000005844 FAA1 GO:0006499 SGD_REF:S000039598|PMID:7962057 IMP P long chain fatty acyl:CoA synthetase YOR317W gene taxon:4932 20020917 SGD
+SGD S000005844 FAA1 GO:0006629 SGD_REF:S000039598|PMID:7962057 IGI P long chain fatty acyl:CoA synthetase YOR317W gene taxon:4932 20020917 SGD
+SGD S000005844 FAA1 GO:0006629 SGD_REF:S000039598|PMID:7962057 IMP P long chain fatty acyl:CoA synthetase YOR317W gene taxon:4932 20020917 SGD
+SGD S000005844 FAA1 GO:0006869 SGD_REF:S000073135|PMID:12601005 IGI P long chain fatty acyl:CoA synthetase YOR317W gene taxon:4932 20030512 SGD
+SGD S000005844 FAA1 GO:0006869 SGD_REF:S000073135|PMID:12601005 IPI P long chain fatty acyl:CoA synthetase YOR317W gene taxon:4932 20030512 SGD
+SGD S000000817 FAA2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C acyl-CoA synthetase (fatty acid activator 2) YER015W|FAM1 gene taxon:4932 20040928 SGD
+SGD S000000817 FAA2 GO:0005777 SGD_REF:S000053188|PMID:8670886 IDA C acyl-CoA synthetase (fatty acid activator 2) YER015W|FAM1 gene taxon:4932 20020917 SGD
+SGD S000000817 FAA2 GO:0004467 SGD_REF:S000053182|PMID:8206942 IDA F acyl-CoA synthetase (fatty acid activator 2) YER015W|FAM1 gene taxon:4932 20020917 SGD
+SGD S000000817 FAA2 GO:0006499 SGD_REF:S000039598|PMID:7962057 IGI P acyl-CoA synthetase (fatty acid activator 2) YER015W|FAM1 gene taxon:4932 20020917 SGD
+SGD S000000817 FAA2 GO:0006499 SGD_REF:S000039598|PMID:7962057 IMP P acyl-CoA synthetase (fatty acid activator 2) YER015W|FAM1 gene taxon:4932 20020917 SGD
+SGD S000000817 FAA2 GO:0006629 SGD_REF:S000039598|PMID:7962057 IGI P acyl-CoA synthetase (fatty acid activator 2) YER015W|FAM1 gene taxon:4932 20020917 SGD
+SGD S000000817 FAA2 GO:0006629 SGD_REF:S000039598|PMID:7962057 IMP P acyl-CoA synthetase (fatty acid activator 2) YER015W|FAM1 gene taxon:4932 20020917 SGD
+SGD S000001271 FAA3 GO:0008372 SGD_REF:S000069584 ND C acyl-CoA synthase YIL009W gene taxon:4932 20020917 SGD
+SGD S000001271 FAA3 GO:0004467 SGD_REF:S000053182|PMID:8206942 IDA F acyl-CoA synthase YIL009W gene taxon:4932 20020917 SGD
+SGD S000001271 FAA3 GO:0006499 SGD_REF:S000039598|PMID:7962057 IGI P acyl-CoA synthase YIL009W gene taxon:4932 20020917 SGD
+SGD S000001271 FAA3 GO:0006499 SGD_REF:S000039598|PMID:7962057 IMP P acyl-CoA synthase YIL009W gene taxon:4932 20020917 SGD
+SGD S000001271 FAA3 GO:0006629 SGD_REF:S000039598|PMID:7962057 IGI P acyl-CoA synthase YIL009W gene taxon:4932 20020917 SGD
+SGD S000001271 FAA3 GO:0006629 SGD_REF:S000039598|PMID:7962057 IMP P acyl-CoA synthase YIL009W gene taxon:4932 20020917 SGD
+SGD S000004860 FAA4 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C long chain fatty acyl:CoA synthetase, long-chain fatty acid:CoA ligase YMR246W gene taxon:4932 20020507 SGD
+SGD S000004860 FAA4 GO:0005811 SGD_REF:S000048561|PMID:10515935 IDA C long chain fatty acyl:CoA synthetase, long-chain fatty acid:CoA ligase YMR246W gene taxon:4932 20020917 SGD
+SGD S000004860 FAA4 GO:0004467 SGD_REF:S000050862|PMID:7650027 IDA F long chain fatty acyl:CoA synthetase, long-chain fatty acid:CoA ligase YMR246W gene taxon:4932 20020917 SGD
+SGD S000004860 FAA4 GO:0006499 SGD_REF:S000039598|PMID:7962057 IGI P long chain fatty acyl:CoA synthetase, long-chain fatty acid:CoA ligase YMR246W gene taxon:4932 20020917 SGD
+SGD S000004860 FAA4 GO:0006499 SGD_REF:S000039598|PMID:7962057 IMP P long chain fatty acyl:CoA synthetase, long-chain fatty acid:CoA ligase YMR246W gene taxon:4932 20020917 SGD
+SGD S000004860 FAA4 GO:0006629 SGD_REF:S000039598|PMID:7962057 IGI P long chain fatty acyl:CoA synthetase, long-chain fatty acid:CoA ligase YMR246W gene taxon:4932 20020917 SGD
+SGD S000004860 FAA4 GO:0006629 SGD_REF:S000039598|PMID:7962057 IMP P long chain fatty acyl:CoA synthetase, long-chain fatty acid:CoA ligase YMR246W gene taxon:4932 20020917 SGD
+SGD S000004860 FAA4 GO:0006869 SGD_REF:S000073135|PMID:12601005 IGI P long chain fatty acyl:CoA synthetase, long-chain fatty acid:CoA ligase YMR246W gene taxon:4932 20030512 SGD
+SGD S000004860 FAA4 GO:0006869 SGD_REF:S000073135|PMID:12601005 IPI P long chain fatty acyl:CoA synthetase, long-chain fatty acid:CoA ligase YMR246W gene taxon:4932 20030512 SGD
+SGD S000001915 FAB1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C 1-phosphatidylinositol-3-phosphate 5-kinase YFR019W|SVL7 gene taxon:4932 20040928 SGD
+SGD S000001915 FAB1 GO:0005774 SGD_REF:S000047458|PMID:9624177 TAS C 1-phosphatidylinositol-3-phosphate 5-kinase YFR019W|SVL7 gene taxon:4932 20010216 SGD
+SGD S000001915 FAB1 GO:0000285 SGD_REF:S000052938|PMID:9811604 IDA F 1-phosphatidylinositol-3-phosphate 5-kinase YFR019W|SVL7 gene taxon:4932 20010216 SGD
+SGD S000001915 FAB1 GO:0006644 SGD_REF:S000048576|PMID:9372916 IMP P 1-phosphatidylinositol-3-phosphate 5-kinase YFR019W|SVL7 gene taxon:4932 20020312 SGD
+SGD S000001915 FAB1 GO:0006644 SGD_REF:S000048576|PMID:9372916 IGI P 1-phosphatidylinositol-3-phosphate 5-kinase YFR019W|SVL7 gene taxon:4932 20020312 SGD
+SGD S000001915 FAB1 GO:0006950 SGD_REF:S000072273|PMID:12176349 TAS P 1-phosphatidylinositol-3-phosphate 5-kinase YFR019W|SVL7 gene taxon:4932 20030222 SGD
+SGD S000001915 FAB1 GO:0007033 SGD_REF:S000052938|PMID:9811604 IMP P 1-phosphatidylinositol-3-phosphate 5-kinase YFR019W|SVL7 gene taxon:4932 20010214 SGD
+SGD S000001915 FAB1 GO:0007033 SGD_REF:S000048738|PMID:9763421 IMP P 1-phosphatidylinositol-3-phosphate 5-kinase YFR019W|SVL7 gene taxon:4932 20010214 SGD
+SGD S000002203 FAD1 GO:0005737 SGD_REF:S000055239|PMID:7799934 IDA C FAD synthetase YDL045C gene taxon:4932 20020930 SGD
+SGD S000002203 FAD1 GO:0003919 SGD_REF:S000055239|PMID:7799934 IDA F FAD synthetase YDL045C gene taxon:4932 20020930 SGD
+SGD S000002203 FAD1 GO:0003919 SGD_REF:S000055239|PMID:7799934 ISS F FAD synthetase YDL045C gene taxon:4932 20020930 SGD
+SGD S000002203 FAD1 GO:0006747 SGD_REF:S000055239|PMID:7799934 IDA P FAD synthetase YDL045C gene taxon:4932 20020930 SGD
+SGD S000002203 FAD1 GO:0006747 SGD_REF:S000055239|PMID:7799934 IMP P FAD synthetase YDL045C gene taxon:4932 20020930 SGD
+SGD S000001281 FAF1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YIL019W gene taxon:4932 20031028 SGD
+SGD S000001281 FAF1 GO:0005730 SGD_REF:S000058897|PMID:15078877 IDA C YIL019W gene taxon:4932 20040709 SGD
+SGD S000001281 FAF1 GO:0005730 SGD_REF:S000059059|PMID:15178413 IDA C YIL019W gene taxon:4932 20040709 SGD
+SGD S000001281 FAF1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YIL019W gene taxon:4932 20031028 SGD
+SGD S000001281 FAF1 GO:0005737 SGD_REF:S000058897|PMID:15078877 IDA C YIL019W gene taxon:4932 20040709 SGD
+SGD S000001281 FAF1 GO:0005554 SGD_REF:S000069584 ND F YIL019W gene taxon:4932 20040709 SGD
+SGD S000001281 FAF1 GO:0030490 SGD_REF:S000058897|PMID:15078877 IMP P YIL019W gene taxon:4932 20040709 SGD
+SGD S000001281 FAF1 GO:0030490 SGD_REF:S000059059|PMID:15178413 IMP P YIL019W gene taxon:4932 20040709 SGD
+SGD S000002428 FAL1 GO:0005730 SGD_REF:S000058443|PMID:10690410 TAS C RNA helicase (putative), dead box protein YDR021W gene taxon:4932 20010118 SGD
+SGD S000002428 FAL1 GO:0004004 SGD_REF:S000058443|PMID:10690410 TAS F RNA helicase (putative), dead box protein YDR021W gene taxon:4932 20010118 SGD
+SGD S000002428 FAL1 GO:0006365 SGD_REF:S000058443|PMID:10690410 TAS P RNA helicase (putative), dead box protein YDR021W gene taxon:4932 20010118 SGD
+SGD S000004968 FAP1 GO:0008372 SGD_REF:S000069584 ND C transcription factor homolog; similarity to Drosophila melanogaster shuttle craft protein; similarity to human NFX1 protein; similarity to human DNA-binding protein tenascin YNL023C gene taxon:4932 20020529 SGD
+SGD S000004968 FAP1 GO:0003700 SGD_REF:S000065999|PMID:10998178 ISS F transcription factor homolog; similarity to Drosophila melanogaster shuttle craft protein; similarity to human NFX1 protein; similarity to human DNA-binding protein tenascin YNL023C gene taxon:4932 20020529 SGD
+SGD S000004968 FAP1 GO:0000004 SGD_REF:S000069584 ND P transcription factor homolog; similarity to Drosophila melanogaster shuttle craft protein; similarity to human NFX1 protein; similarity to human DNA-binding protein tenascin YNL023C gene taxon:4932 20020529 SGD
+SGD S000002325 FAP7 GO:0005634 SGD_REF:S000053814|PMID:10692169 IDA C YDL166C gene taxon:4932 20010626 SGD
+SGD S000002325 FAP7 GO:0005737 SGD_REF:S000114485|PMID:16287850 IMP C YDL166C gene taxon:4932 20060301 SGD
+SGD S000002325 FAP7 NOT GO:0030684 SGD_REF:S000114485|PMID:16287850 IPI C YDL166C gene taxon:4932 20060301 SGD
+SGD S000002325 FAP7 GO:0017111 SGD_REF:S000114485|PMID:16287850 IMP F YDL166C gene taxon:4932 20060301 SGD
+SGD S000002325 FAP7 GO:0017111 SGD_REF:S000114485|PMID:16287850 ISS F YDL166C gene taxon:4932 20060301 SGD
+SGD S000002325 FAP7 NOT GO:0000056 SGD_REF:S000114485|PMID:16287850 IMP P YDL166C gene taxon:4932 20060301 SGD
+SGD S000002325 FAP7 GO:0006979 SGD_REF:S000053814|PMID:10692169 IMP P YDL166C gene taxon:4932 20010626 SGD
+SGD S000002325 FAP7 GO:0030490 SGD_REF:S000073750|PMID:12837249 IMP P YDL166C gene taxon:4932 20030805 SGD
+SGD S000002325 FAP7 GO:0030490 SGD_REF:S000114485|PMID:16287850 IMP P YDL166C gene taxon:4932 20060301 SGD
+SGD S000002325 FAP7 GO:0030490 SGD_REF:S000114485|PMID:16287850 IPI P YDL166C gene taxon:4932 20060301 SGD
+SGD S000003693 FAR1 GO:0005634 SGD_REF:S000056151|PMID:9822386 IDA C Cdc28p kinase inhibitor YJL157C gene taxon:4932 20021126 SGD
+SGD S000003693 FAR1 GO:0005737 SGD_REF:S000056151|PMID:9822386 IDA C Cdc28p kinase inhibitor YJL157C gene taxon:4932 20021126 SGD
+SGD S000003693 FAR1 GO:0016020 SGD_REF:S000082147|PMID:14988725 IDA C Cdc28p kinase inhibitor YJL157C gene taxon:4932 20051012 SGD
+SGD S000003693 FAR1 GO:0043332 SGD_REF:S000082147|PMID:14988725 IDA C Cdc28p kinase inhibitor YJL157C gene taxon:4932 20051012 SGD
+SGD S000003693 FAR1 GO:0004861 SGD_REF:S000041783|PMID:8066461 IDA F Cdc28p kinase inhibitor YJL157C gene taxon:4932 20021126 SGD
+SGD S000003693 FAR1 GO:0000750 SGD_REF:S000043671|PMID:10087263 IGI P Cdc28p kinase inhibitor YJL157C gene taxon:4932 20021206 SGD
+SGD S000003693 FAR1 GO:0000750 SGD_REF:S000043671|PMID:10087263 IPI P Cdc28p kinase inhibitor YJL157C gene taxon:4932 20021206 SGD
+SGD S000003693 FAR1 GO:0000750 SGD_REF:S000043671|PMID:10087263 TAS P Cdc28p kinase inhibitor YJL157C gene taxon:4932 20021206 SGD
+SGD S000003693 FAR1 GO:0007050 SGD_REF:S000054989|PMID:8500168 IMP P Cdc28p kinase inhibitor YJL157C gene taxon:4932 20021126 SGD
+SGD S000004228 FAR10 GO:0005783 SGD_REF:S000072636|PMID:12514182 IDA C YLR238W gene taxon:4932 20031014 SGD
+SGD S000004228 FAR10 GO:0005554 SGD_REF:S000069584 ND F YLR238W gene taxon:4932 20030313 SGD
+SGD S000004228 FAR10 GO:0000751 SGD_REF:S000072607|PMID:12588993 IMP P YLR238W gene taxon:4932 20030314 SGD
+SGD S000004228 FAR10 GO:0000751 SGD_REF:S000072607|PMID:12588993 IPI P YLR238W gene taxon:4932 20030314 SGD
+SGD S000005071 FAR11 GO:0008372 SGD_REF:S000069584 ND C YNL127W gene taxon:4932 20030203 SGD
+SGD S000005071 FAR11 GO:0005554 SGD_REF:S000069584 ND F YNL127W gene taxon:4932 20030313 SGD
+SGD S000005071 FAR11 GO:0000751 SGD_REF:S000072607|PMID:12588993 IMP P YNL127W gene taxon:4932 20030314 SGD
+SGD S000005071 FAR11 GO:0000751 SGD_REF:S000072607|PMID:12588993 IPI P YNL127W gene taxon:4932 20030314 SGD
+SGD S000004656 FAR3 GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YMR052W gene taxon:4932 20031028 SGD
+SGD S000004656 FAR3 GO:0005554 SGD_REF:S000069584 ND F YMR052W gene taxon:4932 20010119 SGD
+SGD S000004656 FAR3 GO:0000751 SGD_REF:S000072607|PMID:12588993 IMP P YMR052W gene taxon:4932 20030314 SGD
+SGD S000004656 FAR3 GO:0000751 SGD_REF:S000072607|PMID:12588993 IPI P YMR052W gene taxon:4932 20030314 SGD
+SGD S000001904 FAR7 GO:0008372 SGD_REF:S000069584 ND C YFR008W gene taxon:4932 20021126 SGD
+SGD S000001904 FAR7 GO:0005554 SGD_REF:S000069584 ND F YFR008W gene taxon:4932 20030313 SGD
+SGD S000001904 FAR7 GO:0000751 SGD_REF:S000072607|PMID:12588993 IMP P YFR008W gene taxon:4932 20030314 SGD
+SGD S000001904 FAR7 GO:0000751 SGD_REF:S000072607|PMID:12588993 IPI P YFR008W gene taxon:4932 20030314 SGD
+SGD S000004631 FAR8 GO:0008372 SGD_REF:S000069584 ND C YMR029C gene taxon:4932 20021126 SGD
+SGD S000004631 FAR8 GO:0005554 SGD_REF:S000069584 ND F YMR029C gene taxon:4932 20030313 SGD
+SGD S000004631 FAR8 GO:0000751 SGD_REF:S000072607|PMID:12588993 IMP P YMR029C gene taxon:4932 20030314 SGD
+SGD S000004631 FAR8 GO:0000751 SGD_REF:S000072607|PMID:12588993 IPI P YMR029C gene taxon:4932 20030314 SGD
+SGD S000001665 FAS1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C acetyl transferase, dehydratase, enoyl reductase, malonyl/palmityl transferase, pentafunctional enzyme YKL182W gene taxon:4932 20040928 SGD
+SGD S000001665 FAS1 GO:0005829 SGD_REF:S000058499 TAS C acetyl transferase, dehydratase, enoyl reductase, malonyl/palmityl transferase, pentafunctional enzyme YKL182W gene taxon:4932 20010119 SGD
+SGD S000001665 FAS1 GO:0005835 SGD_REF:S000048878|PMID:2900835 IDA C acetyl transferase, dehydratase, enoyl reductase, malonyl/palmityl transferase, pentafunctional enzyme YKL182W gene taxon:4932 20010118 SGD
+SGD S000001665 FAS1 GO:0004313 SGD_REF:S000054714|PMID:3528750 IMP F acetyl transferase, dehydratase, enoyl reductase, malonyl/palmityl transferase, pentafunctional enzyme YKL182W gene taxon:4932 20010118 SGD
+SGD S000001665 FAS1 GO:0004314 SGD_REF:S000054714|PMID:3528750 IMP F acetyl transferase, dehydratase, enoyl reductase, malonyl/palmityl transferase, pentafunctional enzyme YKL182W gene taxon:4932 20010118 SGD
+SGD S000001665 FAS1 GO:0004317 SGD_REF:S000054714|PMID:3528750 IMP F acetyl transferase, dehydratase, enoyl reductase, malonyl/palmityl transferase, pentafunctional enzyme YKL182W gene taxon:4932 20010118 SGD
+SGD S000001665 FAS1 GO:0004318 SGD_REF:S000054714|PMID:3528750 IMP F acetyl transferase, dehydratase, enoyl reductase, malonyl/palmityl transferase, pentafunctional enzyme YKL182W gene taxon:4932 20010118 SGD
+SGD S000001665 FAS1 GO:0006633 SGD_REF:S000058499 TAS P acetyl transferase, dehydratase, enoyl reductase, malonyl/palmityl transferase, pentafunctional enzyme YKL182W gene taxon:4932 20010119 SGD
+SGD S000006152 FAS2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C fatty acid synthase alpha subunit YPL231W gene taxon:4932 20040928 SGD
+SGD S000006152 FAS2 GO:0005835 SGD_REF:S000058499 TAS C fatty acid synthase alpha subunit YPL231W gene taxon:4932 20010119 SGD
+SGD S000006152 FAS2 GO:0004315 SGD_REF:S000048878|PMID:2900835 ISS F fatty acid synthase alpha subunit YPL231W gene taxon:4932 20010118 SGD
+SGD S000006152 FAS2 GO:0004316 SGD_REF:S000048878|PMID:2900835 ISS F fatty acid synthase alpha subunit YPL231W gene taxon:4932 20010118 SGD
+SGD S000006152 FAS2 GO:0008897 SGD_REF:S000050216|PMID:9712852 TAS F fatty acid synthase alpha subunit YPL231W gene taxon:4932 20030411 SGD
+SGD S000006152 FAS2 GO:0006633 SGD_REF:S000058499 TAS P fatty acid synthase alpha subunit YPL231W gene taxon:4932 20010119 SGD
+SGD S000006152 FAS2 GO:0018065 SGD_REF:S000050216|PMID:9712852 TAS P fatty acid synthase alpha subunit YPL231W gene taxon:4932 20030411 SGD
+SGD S000000245 FAT1 GO:0005777 SGD_REF:S000040108|PMID:9660783 IDA C fatty acid transporter YBR041W gene taxon:4932 20010118 SGD
+SGD S000000245 FAT1 GO:0005792 SGD_REF:S000040108|PMID:9660783 IDA C fatty acid transporter YBR041W gene taxon:4932 20010118 SGD
+SGD S000000245 FAT1 GO:0005811 SGD_REF:S000048561|PMID:10515935 IDA C fatty acid transporter YBR041W gene taxon:4932 20010118 SGD
+SGD S000000245 FAT1 GO:0005886 SGD_REF:S000042249|PMID:9079682 ISS C fatty acid transporter YBR041W gene taxon:4932 20010118 SGD
+SGD S000000245 FAT1 GO:0005886 SGD_REF:S000042249|PMID:9079682 IMP C fatty acid transporter YBR041W gene taxon:4932 20010118 SGD
+SGD S000000245 FAT1 GO:0004467 SGD_REF:S000040108|PMID:9660783 IMP F fatty acid transporter YBR041W gene taxon:4932 20010118 SGD
+SGD S000000245 FAT1 GO:0004467 SGD_REF:S000040108|PMID:9660783 ISS F fatty acid transporter YBR041W gene taxon:4932 20010118 SGD
+SGD S000000245 FAT1 GO:0005324 SGD_REF:S000042249|PMID:9079682 IMP F fatty acid transporter YBR041W gene taxon:4932 20030224 SGD
+SGD S000000245 FAT1 GO:0005324 SGD_REF:S000042249|PMID:9079682 ISS F fatty acid transporter YBR041W gene taxon:4932 20030224 SGD
+SGD S000000245 FAT1 GO:0000038 SGD_REF:S000041813|PMID:9988704 IMP P fatty acid transporter YBR041W gene taxon:4932 20010118 SGD
+SGD S000000245 FAT1 GO:0006869 SGD_REF:S000042249|PMID:9079682 IMP P fatty acid transporter YBR041W gene taxon:4932 20010118 SGD
+SGD S000000245 FAT1 GO:0006869 SGD_REF:S000042249|PMID:9079682 ISS P fatty acid transporter YBR041W gene taxon:4932 20010118 SGD
+SGD S000000985 FAU1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C 5,10-methenyltetrahydrofolate synthetase YER183C gene taxon:4932 20040813 SGD
+SGD S000000985 FAU1 GO:0030272 SGD_REF:S000069955|PMID:11923304 IDA F 5,10-methenyltetrahydrofolate synthetase YER183C gene taxon:4932 20021003 SGD
+SGD S000000985 FAU1 GO:0009396 SGD_REF:S000069955|PMID:11923304 IDA P 5,10-methenyltetrahydrofolate synthetase YER183C gene taxon:4932 20020616 SGD
+SGD S000001543 FBA1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C aldolase YKL060C|LOT1 gene taxon:4932 20020507 SGD
+SGD S000001543 FBA1 GO:0004332 SGD_REF:S000055210|PMID:2647491 IDA F aldolase YKL060C|LOT1 gene taxon:4932 20010118 SGD
+SGD S000001543 FBA1 GO:0004332 SGD_REF:S000055210|PMID:2647491 IMP F aldolase YKL060C|LOT1 gene taxon:4932 20010118 SGD
+SGD S000001543 FBA1 GO:0006094 SGD_REF:S000063028|PMID:6384192 IMP P aldolase YKL060C|LOT1 gene taxon:4932 20050525 SGD
+SGD S000001543 FBA1 GO:0006096 SGD_REF:S000063028|PMID:6384192 IMP P aldolase YKL060C|LOT1 gene taxon:4932 20050525 SGD
+SGD S000004369 FBP1 GO:0005829 SGD_REF:S000056699|PMID:196563 IDA C fructose-1,6-bisphosphatase YLR377C|ACN8|FBPase gene taxon:4932 20050608 SGD
+SGD S000004369 FBP1 GO:0042132 SGD_REF:S000054460|PMID:2841162 IMP F fructose-1,6-bisphosphatase YLR377C|ACN8|FBPase gene taxon:4932 20020222 SGD
+SGD S000004369 FBP1 GO:0006094 SGD_REF:S000045266|PMID:10328823 TAS P fructose-1,6-bisphosphatase YLR377C|ACN8|FBPase gene taxon:4932 20010118 SGD
+SGD S000004369 FBP1 GO:0006094 SGD_REF:S000063043|PMID:6321183 IMP P fructose-1,6-bisphosphatase YLR377C|ACN8|FBPase gene taxon:4932 20050525 SGD
+SGD S000003691 FBP26 GO:0005829 SGD_REF:S000058500 TAS C fructose-2,6-bisphosphatase YJL155C|FBPase-2 gene taxon:4932 20020222 SGD
+SGD S000003691 FBP26 NOT GO:0003873 SGD_REF:S000069170|PMID:9032446 ISS F fructose-2,6-bisphosphatase YJL155C|FBPase-2 gene taxon:4932 20020506 SGD
+SGD S000003691 FBP26 NOT GO:0003873 SGD_REF:S000069170|PMID:9032446 NAS F fructose-2,6-bisphosphatase YJL155C|FBPase-2 gene taxon:4932 20020506 SGD
+SGD S000003691 FBP26 GO:0004331 SGD_REF:S000051318|PMID:1322693 IMP F fructose-2,6-bisphosphatase YJL155C|FBPase-2 gene taxon:4932 20020222 SGD
+SGD S000003691 FBP26 GO:0006006 SGD_REF:S000051318|PMID:1322693 IMP P fructose-2,6-bisphosphatase YJL155C|FBPase-2 gene taxon:4932 20050512 SGD
+SGD S000002747 FCF1 GO:0008372 SGD_REF:S000069584 ND C YDR339C gene taxon:4932 20021126 SGD
+SGD S000002747 FCF1 GO:0005554 SGD_REF:S000069584 ND F YDR339C gene taxon:4932 20021126 SGD
+SGD S000002747 FCF1 GO:0000004 SGD_REF:S000069584 ND P YDR339C gene taxon:4932 20021126 SGD
+SGD S000002747 FCF1 GO:0007005 SGD_REF:S000086425|PMID:16135527 IMP P YDR339C gene taxon:4932 20051111 SGD
+SGD S000004041 FCF2 GO:0005634 SGD_REF:S000075214|PMID:14690591 IDA C YLR051C gene taxon:4932 20040105 SGD
+SGD S000004041 FCF2 GO:0005730 SGD_REF:S000074185|PMID:14562095 IDA C YLR051C gene taxon:4932 20031028 SGD
+SGD S000004041 FCF2 GO:0005730 SGD_REF:S000075214|PMID:14690591 IDA C YLR051C gene taxon:4932 20040105 SGD
+SGD S000004041 FCF2 GO:0005554 SGD_REF:S000069584 ND F YLR051C gene taxon:4932 20021126 SGD
+SGD S000004041 FCF2 GO:0000004 SGD_REF:S000069584 ND P YLR051C gene taxon:4932 20021126 SGD
+SGD S000004890 FCP1 GO:0005634 SGD_REF:S000059167|PMID:11003641 IPI C TFIIF interacting component of CTD phosphatase YMR277W gene taxon:4932 20021115 SGD
+SGD S000004890 FCP1 GO:0004721 SGD_REF:S000069575|PMID:11904169 IDA F TFIIF interacting component of CTD phosphatase YMR277W gene taxon:4932 20021115 SGD
+SGD S000004890 FCP1 GO:0016791 SGD_REF:S000066118|PMID:11606527 TAS F TFIIF interacting component of CTD phosphatase YMR277W gene taxon:4932 20030121 SGD
+SGD S000004890 FCP1 GO:0006350 SGD_REF:S000047897|PMID:10445027 IMP P TFIIF interacting component of CTD phosphatase YMR277W gene taxon:4932 20021115 SGD
+SGD S000004890 FCP1 GO:0006470 SGD_REF:S000069575|PMID:11904169 IDA P TFIIF interacting component of CTD phosphatase YMR277W gene taxon:4932 20021115 SGD
+SGD S000006266 FCY1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C cytosine deaminase YPR062W|yCD gene taxon:4932 20031028 SGD
+SGD S000006266 FCY1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C cytosine deaminase YPR062W|yCD gene taxon:4932 20031028 SGD
+SGD S000006266 FCY1 GO:0004131 SGD_REF:S000054250|PMID:9000374 IDA F cytosine deaminase YPR062W|yCD gene taxon:4932 20020930 SGD
+SGD S000006266 FCY1 GO:0008655 SGD_REF:S000054250|PMID:9000374 IMP P cytosine deaminase YPR062W|yCD gene taxon:4932 20050425 SGD
+SGD S000006266 FCY1 GO:0019858 SGD_REF:S000054250|PMID:9000374 IMP P cytosine deaminase YPR062W|yCD gene taxon:4932 20020930 SGD
+SGD S000006266 FCY1 GO:0046087 SGD_REF:S000055858|PMID:10501935 IMP P cytosine deaminase YPR062W|yCD gene taxon:4932 20051111 SGD
+SGD S000000858 FCY2 GO:0005886 SGD_REF:S000055095|PMID:8267570 IDA C purine-cytosine permease YER056C|BRA7 gene taxon:4932 20020919 SGD
+SGD S000000858 FCY2 GO:0015212 SGD_REF:S000055858|PMID:10501935 IDA F purine-cytosine permease YER056C|BRA7 gene taxon:4932 20051115 SGD
+SGD S000000858 FCY2 GO:0015212 SGD_REF:S000055858|PMID:10501935 IMP F purine-cytosine permease YER056C|BRA7 gene taxon:4932 20051115 SGD
+SGD S000000858 FCY2 GO:0015392 SGD_REF:S000058070|PMID:9092500 IDA F purine-cytosine permease YER056C|BRA7 gene taxon:4932 20020919 SGD
+SGD S000000858 FCY2 GO:0006863 SGD_REF:S000058070|PMID:9092500 IDA P purine-cytosine permease YER056C|BRA7 gene taxon:4932 20020919 SGD
+SGD S000000858 FCY2 GO:0015856 SGD_REF:S000058070|PMID:9092500 IDA P purine-cytosine permease YER056C|BRA7 gene taxon:4932 20020919 SGD
+SGD S000000858 FCY2 GO:0015861 SGD_REF:S000055858|PMID:10501935 IDA P purine-cytosine permease YER056C|BRA7 gene taxon:4932 20051115 SGD
+SGD S000000858 FCY2 GO:0015861 SGD_REF:S000055858|PMID:10501935 IMP P purine-cytosine permease YER056C|BRA7 gene taxon:4932 20051115 SGD
+SGD S000000862 FCY21 GO:0016021 SGD_REF:S000061430|PMID:11418581 ISS C purine-cytosine permease YER060W gene taxon:4932 20021119 SGD
+SGD S000000862 FCY21 GO:0015392 SGD_REF:S000061430|PMID:11418581 ISS F purine-cytosine permease YER060W gene taxon:4932 20021119 SGD
+SGD S000000862 FCY21 GO:0000004 SGD_REF:S000069584 ND P purine-cytosine permease YER060W gene taxon:4932 20021119 SGD
+SGD S000002958 FCY22 GO:0016021 SGD_REF:S000061430|PMID:11418581 ISS C purine-cytosine permease YER060W-A gene taxon:4932 20021119 SGD
+SGD S000002958 FCY22 GO:0015392 SGD_REF:S000061430|PMID:11418581 ISS F purine-cytosine permease YER060W-A gene taxon:4932 20021119 SGD
+SGD S000002958 FCY22 GO:0000004 SGD_REF:S000069584 ND P purine-cytosine permease YER060W-A gene taxon:4932 20021119 SGD
+SGD S000005915 FDH1 GO:0005829 SGD_REF:S000069478|PMID:11921099 IDA C YOR388C gene taxon:4932 20030129 SGD
+SGD S000005915 FDH1 GO:0008863 SGD_REF:S000069478|PMID:11921099 IGI F YOR388C gene taxon:4932 20021002 SGD
+SGD S000005915 FDH1 GO:0008863 SGD_REF:S000069478|PMID:11921099 ISS F YOR388C gene taxon:4932 20021002 SGD
+SGD S000005915 FDH1 GO:0006735 SGD_REF:S000069478|PMID:11921099 TAS P YOR388C gene taxon:4932 20021002 SGD
+SGD S000005915 FDH1 GO:0042183 SGD_REF:S000069478|PMID:11921099 IGI P YOR388C gene taxon:4932 20021002 SGD
+SGD S000005915 FDH1 GO:0042183 SGD_REF:S000069478|PMID:11921099 TAS P YOR388C gene taxon:4932 20021002 SGD
+SGD S000006196 FDH2 GO:0008372 SGD_REF:S000069584 ND C YPL275W gene taxon:4932 20021002 SGD
+SGD S000006196 FDH2 GO:0008863 SGD_REF:S000069478|PMID:11921099 IGI F YPL275W gene taxon:4932 20021002 SGD
+SGD S000006196 FDH2 GO:0008863 SGD_REF:S000069478|PMID:11921099 ISS F YPL275W gene taxon:4932 20021002 SGD
+SGD S000006196 FDH2 GO:0042183 SGD_REF:S000069478|PMID:11921099 IGI P YPL275W gene taxon:4932 20021002 SGD
+SGD S000006196 FDH2 GO:0042183 SGD_REF:S000069478|PMID:11921099 TAS P YPL275W gene taxon:4932 20021002 SGD
+SGD S000000630 FEN1 GO:0005783 SGD_REF:S000071362|PMID:12087109 IDA C YCR034W|ELO2|GNS1|VBM2 gene taxon:4932 20021120 SGD
+SGD S000000630 FEN1 GO:0005789 SGD_REF:S000041813|PMID:9988704 TAS C YCR034W|ELO2|GNS1|VBM2 gene taxon:4932 20010118 SGD
+SGD S000000630 FEN1 GO:0009922 SGD_REF:S000073534|PMID:12684876 IMP F YCR034W|ELO2|GNS1|VBM2 gene taxon:4932 20030708 SGD
+SGD S000000630 FEN1 GO:0009922 SGD_REF:S000073534|PMID:12684876 TAS F YCR034W|ELO2|GNS1|VBM2 gene taxon:4932 20030708 SGD
+SGD S000000630 FEN1 GO:0016192 SGD_REF:S000043234|PMID:9832547 IMP P YCR034W|ELO2|GNS1|VBM2 gene taxon:4932 20010118 SGD
+SGD S000000630 FEN1 GO:0030148 SGD_REF:S000055688|PMID:9211877 IMP P YCR034W|ELO2|GNS1|VBM2 gene taxon:4932 20020923 SGD
+SGD S000000630 FEN1 GO:0030497 SGD_REF:S000055688|PMID:9211877 IMP P YCR034W|ELO2|GNS1|VBM2 gene taxon:4932 20020923 SGD
+SGD S000000623 FEN2 GO:0005886 SGD_REF:S000051423|PMID:10373490 IGI C Plasma Membrane H+-Pantothenate Symporter YCR028C gene taxon:4932 20020919 SGD
+SGD S000000623 FEN2 GO:0005886 SGD_REF:S000051423|PMID:10373490 ISS C Plasma Membrane H+-Pantothenate Symporter YCR028C gene taxon:4932 20020919 SGD
+SGD S000000623 FEN2 GO:0015233 SGD_REF:S000051423|PMID:10373490 IGI F Plasma Membrane H+-Pantothenate Symporter YCR028C gene taxon:4932 20020919 SGD
+SGD S000000623 FEN2 GO:0015233 SGD_REF:S000051423|PMID:10373490 IMP F Plasma Membrane H+-Pantothenate Symporter YCR028C gene taxon:4932 20020919 SGD
+SGD S000000623 FEN2 GO:0006897 SGD_REF:S000075617|PMID:15020461 IMP P Plasma Membrane H+-Pantothenate Symporter YCR028C gene taxon:4932 20040712 SGD
+SGD S000000623 FEN2 GO:0015887 SGD_REF:S000051423|PMID:10373490 IGI P Plasma Membrane H+-Pantothenate Symporter YCR028C gene taxon:4932 20020919 SGD
+SGD S000000623 FEN2 GO:0015887 SGD_REF:S000051423|PMID:10373490 IMP P Plasma Membrane H+-Pantothenate Symporter YCR028C gene taxon:4932 20020919 SGD
+SGD S000000305 FES1 GO:0005829 SGD_REF:S000072758|PMID:12052876 IDA C Hsp70 nucleotide exchange factor YBR101C gene taxon:4932 20030321 SGD
+SGD S000000305 FES1 GO:0005830 SGD_REF:S000072758|PMID:12052876 IPI C Hsp70 nucleotide exchange factor YBR101C gene taxon:4932 20030321 SGD
+SGD S000000305 FES1 GO:0000774 SGD_REF:S000072758|PMID:12052876 IDA F Hsp70 nucleotide exchange factor YBR101C gene taxon:4932 20030331 SGD
+SGD S000000305 FES1 GO:0000774 SGD_REF:S000072758|PMID:12052876 IPI F Hsp70 nucleotide exchange factor YBR101C gene taxon:4932 20030331 SGD
+SGD S000000305 FES1 GO:0006412 SGD_REF:S000072758|PMID:12052876 IPI P Hsp70 nucleotide exchange factor YBR101C gene taxon:4932 20030321 SGD
+SGD S000000305 FES1 GO:0006412 SGD_REF:S000072758|PMID:12052876 IMP P Hsp70 nucleotide exchange factor YBR101C gene taxon:4932 20030321 SGD
+SGD S000004662 FET3 GO:0005886 SGD_REF:S000046469|PMID:9162052 IDA C multicopper oxidase YMR058W gene taxon:4932 20010118 SGD
+SGD S000004662 FET3 GO:0004322 SGD_REF:S000051845|PMID:9722559 IDA F multicopper oxidase YMR058W gene taxon:4932 20031117 SGD
+SGD S000004662 FET3 GO:0006827 SGD_REF:S000040392|PMID:8293473 IMP P multicopper oxidase YMR058W gene taxon:4932 20010118 SGD
+SGD S000004662 FET3 GO:0046688 SGD_REF:S000075152|PMID:12954629 IGI P multicopper oxidase YMR058W gene taxon:4932 20031215 SGD
+SGD S000004662 FET3 GO:0046688 SGD_REF:S000075152|PMID:12954629 IMP P multicopper oxidase YMR058W gene taxon:4932 20031215 SGD
+SGD S000004938 FET4 GO:0005887 SGD_REF:S000053513|PMID:9115232 IDA C low affinity Fe2+ transport protein YMR319C gene taxon:4932 20010118 SGD
+SGD S000004938 FET4 GO:0005381 SGD_REF:S000039427|PMID:7929320 IMP F low affinity Fe2+ transport protein YMR319C gene taxon:4932 20010118 SGD
+SGD S000004938 FET4 GO:0000040 SGD_REF:S000039427|PMID:7929320 IMP P low affinity Fe2+ transport protein YMR319C gene taxon:4932 20010118 SGD
+SGD S000004938 FET4 GO:0015680 SGD_REF:S000061304|PMID:11523804 IMP P low affinity Fe2+ transport protein YMR319C gene taxon:4932 20020919 SGD
+SGD S000001853 FET5 GO:0000329 SGD_REF:S000063062|PMID:10608875 IDA C multicopper oxidase, type 1 integral membrane protein YFL041W gene taxon:4932 20040407 SGD
+SGD S000001853 FET5 GO:0004322 SGD_REF:S000050386|PMID:9413439 IGI F multicopper oxidase, type 1 integral membrane protein YFL041W gene taxon:4932 20031117 SGD
+SGD S000001853 FET5 GO:0004322 SGD_REF:S000050386|PMID:9413439 ISS SGD:S000004662 F multicopper oxidase, type 1 integral membrane protein YFL041W gene taxon:4932 20031117 SGD
+SGD S000001853 FET5 GO:0006826 SGD_REF:S000050386|PMID:9413439 IMP P multicopper oxidase, type 1 integral membrane protein YFL041W gene taxon:4932 20010118 SGD
+SGD S000006308 FHL1 GO:0005634 SGD_REF:S000077407|PMID:15466158 IDA C domain similar to the fork head DNA-binding domain found in the developmental fork head protein of Drosophila melanogaster and in the HNF-3 family of hepatocyte mammalian transcription factors., forkhead protein YPR104C gene taxon:4932 20041029 SGD
+SGD S000006308 FHL1 GO:0005730 SGD_REF:S000077407|PMID:15466158 IDA C domain similar to the fork head DNA-binding domain found in the developmental fork head protein of Drosophila melanogaster and in the HNF-3 family of hepatocyte mammalian transcription factors., forkhead protein YPR104C gene taxon:4932 20041029 SGD
+SGD S000006308 FHL1 GO:0003700 SGD_REF:S000044983|PMID:8164651 IMP F domain similar to the fork head DNA-binding domain found in the developmental fork head protein of Drosophila melanogaster and in the HNF-3 family of hepatocyte mammalian transcription factors., forkhead protein YPR104C gene taxon:4932 20021204 SGD
+SGD S000006308 FHL1 GO:0003700 SGD_REF:S000044983|PMID:8164651 ISS F domain similar to the fork head DNA-binding domain found in the developmental fork head protein of Drosophila melanogaster and in the HNF-3 family of hepatocyte mammalian transcription factors., forkhead protein YPR104C gene taxon:4932 20021204 SGD
+SGD S000006308 FHL1 GO:0006364 SGD_REF:S000044983|PMID:8164651 IMP P domain similar to the fork head DNA-binding domain found in the developmental fork head protein of Drosophila melanogaster and in the HNF-3 family of hepatocyte mammalian transcription factors., forkhead protein YPR104C gene taxon:4932 20010118 SGD
+SGD S000006308 FHL1 GO:0006383 SGD_REF:S000044983|PMID:8164651 IGI P domain similar to the fork head DNA-binding domain found in the developmental fork head protein of Drosophila melanogaster and in the HNF-3 family of hepatocyte mammalian transcription factors., forkhead protein YPR104C gene taxon:4932 20010118 SGD
+SGD S000000244 FIG1 GO:0009277 SGD_REF:S000050758|PMID:9456310 IDA C integral membrane protein YBR040W gene taxon:4932 20020924 SGD
+SGD S000000244 FIG1 GO:0043332 SGD_REF:S000071843|PMID:12374868 IDA C integral membrane protein YBR040W gene taxon:4932 20030129 SGD
+SGD S000000244 FIG1 GO:0005554 SGD_REF:S000069584 ND F integral membrane protein YBR040W gene taxon:4932 20020924 SGD
+SGD S000000244 FIG1 GO:0000753 SGD_REF:S000050758|PMID:9456310 IMP P integral membrane protein YBR040W gene taxon:4932 20021206 SGD
+SGD S000000244 FIG1 GO:0000755 SGD_REF:S000050758|PMID:9456310 IMP P integral membrane protein YBR040W gene taxon:4932 20021206 SGD
+SGD S000000685 FIG2 GO:0009277 SGD_REF:S000050758|PMID:9456310 IDA C GPI-anchored cell wall protein (putative) YCR089W gene taxon:4932 20020924 SGD
+SGD S000000685 FIG2 GO:0005554 SGD_REF:S000069584 ND F GPI-anchored cell wall protein (putative) YCR089W gene taxon:4932 20020924 SGD
+SGD S000000685 FIG2 GO:0000753 SGD_REF:S000050758|PMID:9456310 IMP P GPI-anchored cell wall protein (putative) YCR089W gene taxon:4932 20021206 SGD
+SGD S000000685 FIG2 GO:0000755 SGD_REF:S000050758|PMID:9456310 IMP P GPI-anchored cell wall protein (putative) YCR089W gene taxon:4932 20021206 SGD
+SGD S000005269 FIG4 GO:0000329 SGD_REF:S000074437|PMID:14528018 IDA C YNL325C gene taxon:4932 20041004 SGD
+SGD S000005269 FIG4 GO:0019898 SGD_REF:S000069689|PMID:11950935 IDA C YNL325C gene taxon:4932 20020924 SGD
+SGD S000005269 FIG4 GO:0017120 SGD_REF:S000069689|PMID:11950935 IDA F YNL325C gene taxon:4932 20020802 SGD
+SGD S000005269 FIG4 GO:0000753 SGD_REF:S000050758|PMID:9456310 IMP P YNL325C gene taxon:4932 20021206 SGD
+SGD S000002537 FIN1 GO:0005634 SGD_REF:S000069577|PMID:11929974 IDA C YDR130C gene taxon:4932 20020528 SGD
+SGD S000002537 FIN1 GO:0005882 SGD_REF:S000069577|PMID:11929974 IDA C YDR130C gene taxon:4932 20060118 SGD
+SGD S000002537 FIN1 GO:0005554 SGD_REF:S000069584 ND F YDR130C gene taxon:4932 20060118 SGD
+SGD S000002537 FIN1 GO:0045103 SGD_REF:S000073072|PMID:12551942 IDA P YDR130C gene taxon:4932 20051007 SGD
+SGD S000003853 FIP1 GO:0005847 SGD_REF:S000060315|PMID:11344258 TAS C polyadenylation factor I (PF I) YJR093C gene taxon:4932 20020410 SGD
+SGD S000003853 FIP1 GO:0005847 SGD_REF:S000074089|PMID:12819204 IPI C polyadenylation factor I (PF I) YJR093C gene taxon:4932 20031013 SGD
+SGD S000003853 FIP1 contributes_to GO:0003723 SGD_REF:S000059904|PMID:11238938 IMP F polyadenylation factor I (PF I) YJR093C gene taxon:4932 20050218 SGD
+SGD S000003853 FIP1 GO:0005515 SGD_REF:S000059904|PMID:11238938 IPI SGD:S000001710 F polyadenylation factor I (PF I) YJR093C gene taxon:4932 20050218 SGD
+SGD S000003853 FIP1 GO:0006378 SGD_REF:S000060315|PMID:11344258 IDA P polyadenylation factor I (PF I) YJR093C gene taxon:4932 20020410 SGD
+SGD S000003853 FIP1 GO:0006378 SGD_REF:S000060315|PMID:11344258 TAS P polyadenylation factor I (PF I) YJR093C gene taxon:4932 20020410 SGD
+SGD S000003853 FIP1 GO:0006379 SGD_REF:S000060315|PMID:11344258 IDA P polyadenylation factor I (PF I) YJR093C gene taxon:4932 20020410 SGD
+SGD S000003853 FIP1 GO:0006379 SGD_REF:S000060315|PMID:11344258 TAS P polyadenylation factor I (PF I) YJR093C gene taxon:4932 20020410 SGD
+SGD S000000834 FIR1 GO:0005935 SGD_REF:S000074185|PMID:14562095 IDA C participant in 3' mRNA processing (putative) YER032W|PIP1 gene taxon:4932 20031028 SGD
+SGD S000000834 FIR1 GO:0005554 SGD_REF:S000069584 ND F participant in 3' mRNA processing (putative) YER032W|PIP1 gene taxon:4932 20010119 SGD
+SGD S000000834 FIR1 GO:0006378 SGD_REF:S000045741|PMID:9196079 IMP P participant in 3' mRNA processing (putative) YER032W|PIP1 gene taxon:4932 20010118 SGD
+SGD S000000834 FIR1 GO:0006378 SGD_REF:S000045741|PMID:9196079 IGI P participant in 3' mRNA processing (putative) YER032W|PIP1 gene taxon:4932 20010118 SGD
+SGD S000001327 FIS1 GO:0005741 SGD_REF:S000056451|PMID:11038183 IDA C YIL065C|MDV2 gene taxon:4932 20010118 SGD
+SGD S000001327 FIS1 GO:0005741 SGD_REF:S000081243|PMID:15809300 IDA C YIL065C|MDV2 gene taxon:4932 20050415 SGD
+SGD S000001327 FIS1 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C YIL065C|MDV2 gene taxon:4932 20060317 SGD
+SGD S000001327 FIS1 GO:0005554 SGD_REF:S000069584 ND F YIL065C|MDV2 gene taxon:4932 20010119 SGD
+SGD S000001327 FIS1 GO:0000266 SGD_REF:S000056451|PMID:11038183 IMP P YIL065C|MDV2 gene taxon:4932 20010118 SGD
+SGD S000001327 FIS1 GO:0000266 SGD_REF:S000056450|PMID:11038182 IGI P YIL065C|MDV2 gene taxon:4932 20010118 SGD
+SGD S000001327 FIS1 GO:0000266 SGD_REF:S000056450|PMID:11038182 IMP P YIL065C|MDV2 gene taxon:4932 20010118 SGD
+SGD S000001327 FIS1 GO:0000266 SGD_REF:S000056451|PMID:11038183 IGI P YIL065C|MDV2 gene taxon:4932 20010118 SGD
+SGD S000002942 FIT1 GO:0009277 SGD_REF:S000040179|PMID:10383953 IDA C Cell wall protein involved in iron uptake YDR534C gene taxon:4932 20020617 SGD
+SGD S000002942 FIT1 GO:0005554 SGD_REF:S000069584 ND F Cell wall protein involved in iron uptake YDR534C gene taxon:4932 20021211 SGD
+SGD S000002942 FIT1 GO:0015891 SGD_REF:S000070405|PMID:12196168 IDA P Cell wall protein involved in iron uptake YDR534C gene taxon:4932 20021211 SGD
+SGD S000005909 FIT2 GO:0009277 SGD_REF:S000040179|PMID:10383953 IDA C YOR382W gene taxon:4932 20020617 SGD
+SGD S000005909 FIT2 GO:0005554 SGD_REF:S000069584 ND F YOR382W gene taxon:4932 20021211 SGD
+SGD S000005909 FIT2 GO:0015891 SGD_REF:S000070405|PMID:12196168 IDA P YOR382W gene taxon:4932 20021211 SGD
+SGD S000005910 FIT3 GO:0009277 SGD_REF:S000040179|PMID:10383953 IDA C Cell wall protein involved in iron transport YOR383C gene taxon:4932 20020617 SGD
+SGD S000005910 FIT3 GO:0005554 SGD_REF:S000069584 ND F Cell wall protein involved in iron transport YOR383C gene taxon:4932 20021211 SGD
+SGD S000005910 FIT3 GO:0015891 SGD_REF:S000070405|PMID:12196168 IDA P Cell wall protein involved in iron transport YOR383C gene taxon:4932 20021211 SGD
+SGD S000001393 FKH1 GO:0005634 SGD_REF:S000050457|PMID:10747051 IDA C forkhead protein YIL131C gene taxon:4932 20020305 SGD
+SGD S000001393 FKH1 GO:0003700 SGD_REF:S000050457|PMID:10747051 ISS F forkhead protein YIL131C gene taxon:4932 20020305 SGD
+SGD S000001393 FKH1 GO:0000074 SGD_REF:S000053136|PMID:10894548 IMP P forkhead protein YIL131C gene taxon:4932 20020305 SGD
+SGD S000001393 FKH1 GO:0000074 SGD_REF:S000053136|PMID:10894548 IGI P forkhead protein YIL131C gene taxon:4932 20020305 SGD
+SGD S000001393 FKH1 GO:0007124 SGD_REF:S000050457|PMID:10747051 IGI P forkhead protein YIL131C gene taxon:4932 20020305 SGD
+SGD S000001393 FKH1 GO:0007124 SGD_REF:S000053136|PMID:10894548 IGI P forkhead protein YIL131C gene taxon:4932 20020305 SGD
+SGD S000001393 FKH1 GO:0030466 SGD_REF:S000050457|PMID:10747051 IMP P forkhead protein YIL131C gene taxon:4932 20020305 SGD
+SGD S000001393 FKH1 GO:0030466 SGD_REF:S000050457|PMID:10747051 IGI P forkhead protein YIL131C gene taxon:4932 20020306 SGD
+SGD S000005012 FKH2 GO:0005634 SGD_REF:S000041709|PMID:10899128 IDA C forkhead protein YNL068C gene taxon:4932 20020306 SGD
+SGD S000005012 FKH2 GO:0003700 SGD_REF:S000053136|PMID:10894548 IPI F forkhead protein YNL068C gene taxon:4932 20020306 SGD
+SGD S000005012 FKH2 GO:0003700 SGD_REF:S000053136|PMID:10894548 IGI F forkhead protein YNL068C gene taxon:4932 20020306 SGD
+SGD S000005012 FKH2 GO:0000074 SGD_REF:S000053136|PMID:10894548 IMP P forkhead protein YNL068C gene taxon:4932 20020305 SGD
+SGD S000005012 FKH2 GO:0000074 SGD_REF:S000053136|PMID:10894548 IGI P forkhead protein YNL068C gene taxon:4932 20020305 SGD
+SGD S000005012 FKH2 GO:0000074 SGD_REF:S000050457|PMID:10747051 IMP P forkhead protein YNL068C gene taxon:4932 20020306 SGD
+SGD S000005012 FKH2 GO:0000074 SGD_REF:S000050457|PMID:10747051 IGI P forkhead protein YNL068C gene taxon:4932 20020306 SGD
+SGD S000005012 FKH2 GO:0000116 SGD_REF:S000041709|PMID:10899128 IPI P forkhead protein YNL068C gene taxon:4932 20020306 SGD
+SGD S000005012 FKH2 GO:0000116 SGD_REF:S000041709|PMID:10899128 IMP P forkhead protein YNL068C gene taxon:4932 20020306 SGD
+SGD S000005012 FKH2 GO:0007124 SGD_REF:S000053136|PMID:10894548 IGI P forkhead protein YNL068C gene taxon:4932 20020305 SGD
+SGD S000005012 FKH2 GO:0007124 SGD_REF:S000050457|PMID:10747051 IGI P forkhead protein YNL068C gene taxon:4932 20020306 SGD
+SGD S000004334 FKS1 GO:0000148 SGD_REF:S000048652|PMID:8602515 TAS C 1,3-beta-D-glucan synthase YLR342W|CND1|CWH53|ETG1|GSC1|PBR1 gene taxon:4932 20010118 SGD
+SGD S000004334 FKS1 GO:0030478 SGD_REF:S000041005|PMID:10652251 IDA C 1,3-beta-D-glucan synthase YLR342W|CND1|CWH53|ETG1|GSC1|PBR1 gene taxon:4932 20010118 SGD
+SGD S000004334 FKS1 GO:0030479 SGD_REF:S000075555|PMID:11856368 IDA C 1,3-beta-D-glucan synthase YLR342W|CND1|CWH53|ETG1|GSC1|PBR1 gene taxon:4932 20050216 SGD
+SGD S000004334 FKS1 GO:0003843 SGD_REF:S000045853|PMID:7649185 IDA F 1,3-beta-D-glucan synthase YLR342W|CND1|CWH53|ETG1|GSC1|PBR1 gene taxon:4932 20010118 SGD
+SGD S000004334 FKS1 GO:0006075 SGD_REF:S000048652|PMID:8602515 TAS P 1,3-beta-D-glucan synthase YLR342W|CND1|CWH53|ETG1|GSC1|PBR1 gene taxon:4932 20010118 SGD
+SGD S000004334 FKS1 GO:0006897 SGD_REF:S000075861|PMID:14593073 IMP P 1,3-beta-D-glucan synthase YLR342W|CND1|CWH53|ETG1|GSC1|PBR1 gene taxon:4932 20050505 SGD
+SGD S000004334 FKS1 GO:0007047 SGD_REF:S000048652|PMID:8602515 TAS P 1,3-beta-D-glucan synthase YLR342W|CND1|CWH53|ETG1|GSC1|PBR1 gene taxon:4932 20010118 SGD
+SGD S000004923 FKS3 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YMR306W gene taxon:4932 20040813 SGD
+SGD S000004923 FKS3 GO:0003843 SGD_REF:S000043702|PMID:7565718 ISS F YMR306W gene taxon:4932 20021223 SGD
+SGD S000004923 FKS3 GO:0000004 SGD_REF:S000069584 ND P YMR306W gene taxon:4932 20021001 SGD
+SGD S000006142 FLC1 GO:0000324 SGD_REF:S000074185|PMID:14562095 IDA C YPL221W|BOP1|HUF1 gene taxon:4932 20031028 SGD
+SGD S000006142 FLC1 GO:0005935 SGD_REF:S000074185|PMID:14562095 IDA C YPL221W|BOP1|HUF1 gene taxon:4932 20031028 SGD
+SGD S000006142 FLC1 GO:0005554 SGD_REF:S000069584 ND F YPL221W|BOP1|HUF1 gene taxon:4932 20021121 SGD
+SGD S000006142 FLC1 GO:0000004 SGD_REF:S000069584 ND P YPL221W|BOP1|HUF1 gene taxon:4932 20021121 SGD
+SGD S000000049 FLC2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YAL053W|HUF2 gene taxon:4932 20031028 SGD
+SGD S000000049 FLC2 GO:0005554 SGD_REF:S000069584 ND F YAL053W|HUF2 gene taxon:4932 20021126 SGD
+SGD S000000049 FLC2 GO:0000004 SGD_REF:S000069584 ND P YAL053W|HUF2 gene taxon:4932 20021126 SGD
+SGD S000003107 FLC3 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YGL139W|HUF3 gene taxon:4932 20040928 SGD
+SGD S000003107 FLC3 GO:0016021 SGD_REF:S000041156|PMID:9046099 ISS C YGL139W|HUF3 gene taxon:4932 20030410 SGD
+SGD S000003107 FLC3 GO:0005554 SGD_REF:S000069584 ND F YGL139W|HUF3 gene taxon:4932 20030410 SGD
+SGD S000003107 FLC3 GO:0000004 SGD_REF:S000069584 ND P YGL139W|HUF3 gene taxon:4932 20030410 SGD
+SGD S000000084 FLO1 GO:0009277 SGD_REF:S000069752|PMID:11956747 IDA C YAR050W|FLO2|FLO4 gene taxon:4932 20020613 SGD
+SGD S000000084 FLO1 GO:0009277 SGD_REF:S000040714|PMID:9483793 IDA C YAR050W|FLO2|FLO4 gene taxon:4932 20040130 SGD
+SGD S000000084 FLO1 GO:0005537 SGD_REF:S000050643|PMID:9851992 IMP F YAR050W|FLO2|FLO4 gene taxon:4932 20040130 SGD
+SGD S000000084 FLO1 GO:0000501 SGD_REF:S000042099|PMID:7483845 IMP P YAR050W|FLO2|FLO4 gene taxon:4932 20021125 SGD
+SGD S000001810 FLO10 GO:0009277 SGD_REF:S000052500|PMID:7502576 ISS SGD:S000000084 C YKR102W gene taxon:4932 20040204 SGD
+SGD S000001810 FLO10 GO:0005537 SGD_REF:S000052500|PMID:7502576 ISS SGD:S000000084 F YKR102W gene taxon:4932 20040204 SGD
+SGD S000001810 FLO10 GO:0000501 SGD_REF:S000052500|PMID:7502576 ISS SGD:S000000084 P YKR102W gene taxon:4932 20040204 SGD
+SGD S000001254 FLO5 GO:0009277 SGD_REF:S000048796|PMID:9219336 TAS C flocculin, similar to flocculation protein Flo1p YHR211W gene taxon:4932 20021017 SGD
+SGD S000001254 FLO5 GO:0009277 SGD_REF:S000040714|PMID:9483793 IDA C flocculin, similar to flocculation protein Flo1p YHR211W gene taxon:4932 20040130 SGD
+SGD S000001254 FLO5 GO:0005537 SGD_REF:S000050283|PMID:7668043 ISS SGD:S000000084 F flocculin, similar to flocculation protein Flo1p YHR211W gene taxon:4932 20040203 SGD
+SGD S000001254 FLO5 GO:0005537 SGD_REF:S000063074|PMID:2665372 IMP F flocculin, similar to flocculation protein Flo1p YHR211W gene taxon:4932 20040203 SGD
+SGD S000001254 FLO5 GO:0000501 SGD_REF:S000047428|PMID:7923404 IGI P flocculin, similar to flocculation protein Flo1p YHR211W gene taxon:4932 20021219 SGD
+SGD S000000911 FLO8 GO:0005634 SGD_REF:S000051172|PMID:10064592 TAS C transcriptional activator of FLO1 (putative) YER109C|PHD5|YER108C gene taxon:4932 20010118 SGD
+SGD S000000911 FLO8 GO:0005634 SGD_REF:S000069459|PMID:11914276 IDA C transcriptional activator of FLO1 (putative) YER109C|PHD5|YER108C gene taxon:4932 20020507 SGD
+SGD S000000911 FLO8 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C transcriptional activator of FLO1 (putative) YER109C|PHD5|YER108C gene taxon:4932 20020507 SGD
+SGD S000000911 FLO8 GO:0003704 SGD_REF:S000051172|PMID:10064592 TAS F transcriptional activator of FLO1 (putative) YER109C|PHD5|YER108C gene taxon:4932 20010118 SGD
+SGD S000000911 FLO8 GO:0000501 SGD_REF:S000056409|PMID:10591965 IMP P transcriptional activator of FLO1 (putative) YER109C|PHD5|YER108C gene taxon:4932 20040130 SGD
+SGD S000000911 FLO8 GO:0001403 SGD_REF:S000051172|PMID:10064592 TAS P transcriptional activator of FLO1 (putative) YER109C|PHD5|YER108C gene taxon:4932 20010118 SGD
+SGD S000000911 FLO8 GO:0007124 SGD_REF:S000051172|PMID:10064592 TAS P transcriptional activator of FLO1 (putative) YER109C|PHD5|YER108C gene taxon:4932 20010118 SGD
+SGD S000000059 FLO9 GO:0009277 SGD_REF:S000052500|PMID:7502576 ISS SGD:S000000084 C similar to FLO1 YAL063C gene taxon:4932 20040204 SGD
+SGD S000000059 FLO9 GO:0005537 SGD_REF:S000052500|PMID:7502576 ISS SGD:S000000084 F similar to FLO1 YAL063C gene taxon:4932 20040204 SGD
+SGD S000000059 FLO9 GO:0000501 SGD_REF:S000052500|PMID:7502576 IEP P similar to FLO1 YAL063C gene taxon:4932 20040204 SGD
+SGD S000000059 FLO9 GO:0000501 SGD_REF:S000052500|PMID:7502576 ISS SGD:S000000084 P similar to FLO1 YAL063C gene taxon:4932 20040204 SGD
+SGD S000029654 FLP1 GO:0008372 SGD_REF:S000069584 ND C 2-micron circle recombinase gene taxon:4932 20010119 SGD
+SGD S000029654 FLP1 GO:0009009 SGD_REF:S000057423|PMID:7659779 TAS F 2-micron circle recombinase gene taxon:4932 20020828 SGD
+SGD S000029654 FLP1 GO:0006310 SGD_REF:S000057423|PMID:7659779 TAS P 2-micron circle recombinase gene taxon:4932 20010118 SGD
+SGD S000000212 FLR1 GO:0005887 SGD_REF:S000044268|PMID:10903515 IDA C major facilitator transporter YBR008C gene taxon:4932 20021001 SGD
+SGD S000000212 FLR1 GO:0015239 SGD_REF:S000052308|PMID:9235926 IGI F major facilitator transporter YBR008C gene taxon:4932 20021001 SGD
+SGD S000000212 FLR1 GO:0015239 SGD_REF:S000066144|PMID:9046086 ISS F major facilitator transporter YBR008C gene taxon:4932 20021001 SGD
+SGD S000000212 FLR1 GO:0015239 SGD_REF:S000052308|PMID:9235926 IMP F major facilitator transporter YBR008C gene taxon:4932 20021001 SGD
+SGD S000000212 FLR1 GO:0009636 SGD_REF:S000052308|PMID:9235926 IGI P major facilitator transporter YBR008C gene taxon:4932 20021001 SGD
+SGD S000000212 FLR1 GO:0009636 SGD_REF:S000052308|PMID:9235926 IMP P major facilitator transporter YBR008C gene taxon:4932 20021001 SGD
+SGD S000001396 FLX1 GO:0005739 SGD_REF:S000040843|PMID:8631763 ISS C FAD carrier protein YIL134W gene taxon:4932 20010118 SGD
+SGD S000001396 FLX1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C FAD carrier protein YIL134W gene taxon:4932 20040928 SGD
+SGD S000001396 FLX1 GO:0015230 SGD_REF:S000040843|PMID:8631763 IMP F FAD carrier protein YIL134W gene taxon:4932 20010118 SGD
+SGD S000001396 FLX1 GO:0015230 SGD_REF:S000075300|PMID:14555654 IMP F FAD carrier protein YIL134W gene taxon:4932 20040113 SGD
+SGD S000001396 FLX1 GO:0015230 SGD_REF:S000040843|PMID:8631763 ISS F FAD carrier protein YIL134W gene taxon:4932 20010118 SGD
+SGD S000001396 FLX1 GO:0015883 SGD_REF:S000075300|PMID:14555654 IMP P FAD carrier protein YIL134W gene taxon:4932 20040113 SGD
+SGD S000001360 FMC1 GO:0005739 SGD_REF:S000060013|PMID:11096112 IDA C Assembly factor of ATP synthase in heat stress YIL098C gene taxon:4932 20020528 SGD
+SGD S000001360 FMC1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C Assembly factor of ATP synthase in heat stress YIL098C gene taxon:4932 20040924 SGD
+SGD S000001360 FMC1 GO:0005554 SGD_REF:S000069584 ND F Assembly factor of ATP synthase in heat stress YIL098C gene taxon:4932 20020528 SGD
+SGD S000001360 FMC1 GO:0006461 SGD_REF:S000060013|PMID:11096112 IGI P Assembly factor of ATP synthase in heat stress YIL098C gene taxon:4932 20020528 SGD
+SGD S000001360 FMC1 GO:0006461 SGD_REF:S000060013|PMID:11096112 IMP P Assembly factor of ATP synthase in heat stress YIL098C gene taxon:4932 20020528 SGD
+SGD S000002644 FMN1 GO:0005743 SGD_REF:S000052635|PMID:10887197 IDA C riboflavin kinase YDR236C gene taxon:4932 20021001 SGD
+SGD S000002644 FMN1 GO:0005792 SGD_REF:S000052635|PMID:10887197 IDA C riboflavin kinase YDR236C gene taxon:4932 20021001 SGD
+SGD S000002644 FMN1 NOT GO:0003919 SGD_REF:S000052635|PMID:10887197 IDA F riboflavin kinase YDR236C gene taxon:4932 20030212 SGD
+SGD S000002644 FMN1 GO:0008531 SGD_REF:S000052635|PMID:10887197 IDA F riboflavin kinase YDR236C gene taxon:4932 20021001 SGD
+SGD S000002644 FMN1 GO:0008531 SGD_REF:S000052635|PMID:10887197 IMP F riboflavin kinase YDR236C gene taxon:4932 20021001 SGD
+SGD S000002644 FMN1 GO:0009398 SGD_REF:S000052635|PMID:10887197 IDA P riboflavin kinase YDR236C gene taxon:4932 20021001 SGD
+SGD S000002644 FMN1 GO:0009398 SGD_REF:S000052635|PMID:10887197 IMP P riboflavin kinase YDR236C gene taxon:4932 20021001 SGD
+SGD S000001219 FMO1 GO:0005789 SGD_REF:S000065744|PMID:10077572 IDA C flavin-containing monooxygenase YHR176W|FMO gene taxon:4932 20021124 SGD
+SGD S000001219 FMO1 GO:0004497 SGD_REF:S000065744|PMID:10077572 TAS F flavin-containing monooxygenase YHR176W|FMO gene taxon:4932 20021124 SGD
+SGD S000001219 FMO1 GO:0006457 SGD_REF:S000065744|PMID:10077572 IDA P flavin-containing monooxygenase YHR176W|FMO gene taxon:4932 20021124 SGD
+SGD S000000984 FMP10 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YER182W gene taxon:4932 20031028 SGD
+SGD S000000984 FMP10 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YER182W gene taxon:4932 20031210 SGD
+SGD S000000984 FMP10 GO:0005554 SGD_REF:S000069584 ND F YER182W gene taxon:4932 20021126 SGD
+SGD S000000984 FMP10 GO:0000004 SGD_REF:S000069584 ND P YER182W gene taxon:4932 20021126 SGD
+SGD S000001013 FMP12 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YHL021C gene taxon:4932 20031028 SGD
+SGD S000001013 FMP12 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YHL021C gene taxon:4932 20031210 SGD
+SGD S000001013 FMP12 GO:0005554 SGD_REF:S000069584 ND F YHL021C gene taxon:4932 20030421 SGD
+SGD S000001013 FMP12 GO:0000004 SGD_REF:S000069584 ND P YHL021C gene taxon:4932 20030421 SGD
+SGD S000001724 FMP13 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YKR016W gene taxon:4932 20031028 SGD
+SGD S000001724 FMP13 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YKR016W gene taxon:4932 20031210 SGD
+SGD S000001724 FMP13 GO:0005554 SGD_REF:S000069584 ND F YKR016W gene taxon:4932 20030421 SGD
+SGD S000001724 FMP13 GO:0000004 SGD_REF:S000069584 ND P YKR016W gene taxon:4932 20030421 SGD
+SGD S000006020 FMP14 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YPL099C gene taxon:4932 20040923 SGD
+SGD S000006020 FMP14 GO:0005554 SGD_REF:S000069584 ND F YPL099C gene taxon:4932 20021126 SGD
+SGD S000006020 FMP14 GO:0000004 SGD_REF:S000069584 ND P YPL099C gene taxon:4932 20021126 SGD
+SGD S000002477 FMP16 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YDR070C gene taxon:4932 20031028 SGD
+SGD S000002477 FMP16 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YDR070C gene taxon:4932 20040924 SGD
+SGD S000002477 FMP16 GO:0005554 SGD_REF:S000069584 ND F YDR070C gene taxon:4932 20030203 SGD
+SGD S000002477 FMP16 GO:0000004 SGD_REF:S000069584 ND P YDR070C gene taxon:4932 20030203 SGD
+SGD S000000473 FMP21 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YBR269C gene taxon:4932 20031028 SGD
+SGD S000000473 FMP21 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YBR269C gene taxon:4932 20040924 SGD
+SGD S000000473 FMP21 GO:0005554 SGD_REF:S000069584 ND F YBR269C gene taxon:4932 20021126 SGD
+SGD S000000473 FMP21 GO:0000004 SGD_REF:S000069584 ND P YBR269C gene taxon:4932 20021126 SGD
+SGD S000001241 FMP22 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YHR198C gene taxon:4932 20031028 SGD
+SGD S000001241 FMP22 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YHR198C gene taxon:4932 20040924 SGD
+SGD S000001241 FMP22 GO:0005554 SGD_REF:S000069584 ND F YHR198C gene taxon:4932 20030922 SGD
+SGD S000001241 FMP22 GO:0000004 SGD_REF:S000069584 ND P YHR198C gene taxon:4932 20021126 SGD
+SGD S000000251 FMP23 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YBR047W gene taxon:4932 20031028 SGD
+SGD S000000251 FMP23 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YBR047W gene taxon:4932 20040924 SGD
+SGD S000000251 FMP23 GO:0005554 SGD_REF:S000069584 ND F YBR047W gene taxon:4932 20030203 SGD
+SGD S000000251 FMP23 GO:0000004 SGD_REF:S000069584 ND P YBR047W gene taxon:4932 20030203 SGD
+SGD S000004721 FMP24 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YMR115W gene taxon:4932 20031028 SGD
+SGD S000004721 FMP24 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YMR115W gene taxon:4932 20040924 SGD
+SGD S000004721 FMP24 GO:0005554 SGD_REF:S000069584 ND F YMR115W gene taxon:4932 20021126 SGD
+SGD S000004721 FMP24 GO:0000004 SGD_REF:S000069584 ND P YMR115W gene taxon:4932 20021126 SGD
+SGD S000004067 FMP25 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YLR077W gene taxon:4932 20040923 SGD
+SGD S000004067 FMP25 GO:0005554 SGD_REF:S000069584 ND F YLR077W gene taxon:4932 20030203 SGD
+SGD S000004067 FMP25 GO:0000004 SGD_REF:S000069584 ND P YLR077W gene taxon:4932 20030203 SGD
+SGD S000003841 FMP26 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YJR080C gene taxon:4932 20031028 SGD
+SGD S000003841 FMP26 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YJR080C gene taxon:4932 20040924 SGD
+SGD S000003841 FMP26 GO:0005554 SGD_REF:S000069584 ND F YJR080C gene taxon:4932 20030203 SGD
+SGD S000003841 FMP26 GO:0000004 SGD_REF:S000069584 ND P YJR080C gene taxon:4932 20030203 SGD
+SGD S000004446 FMP27 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YLR454W gene taxon:4932 20040923 SGD
+SGD S000004446 FMP27 GO:0005554 SGD_REF:S000069584 ND F YLR454W gene taxon:4932 20021126 SGD
+SGD S000004446 FMP27 GO:0000004 SGD_REF:S000069584 ND P YLR454W gene taxon:4932 20021126 SGD
+SGD S000000882 FMP29 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YER080W gene taxon:4932 20031028 SGD
+SGD S000000882 FMP29 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YER080W gene taxon:4932 20031210 SGD
+SGD S000000882 FMP29 GO:0005554 SGD_REF:S000069584 ND F YER080W gene taxon:4932 20021126 SGD
+SGD S000000882 FMP29 GO:0000004 SGD_REF:S000069584 ND P YER080W gene taxon:4932 20021126 SGD
+SGD S000006024 FMP30 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YPL103C gene taxon:4932 20040923 SGD
+SGD S000006024 FMP30 GO:0005554 SGD_REF:S000069584 ND F YPL103C gene taxon:4932 20021126 SGD
+SGD S000006024 FMP30 GO:0000004 SGD_REF:S000069584 ND P YPL103C gene taxon:4932 20021126 SGD
+SGD S000005812 FMP31 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YOR286W gene taxon:4932 20031028 SGD
+SGD S000005812 FMP31 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YOR286W gene taxon:4932 20040924 SGD
+SGD S000005812 FMP31 GO:0005554 SGD_REF:S000069584 ND F YOR286W gene taxon:4932 20030203 SGD
+SGD S000005812 FMP31 GO:0000004 SGD_REF:S000069584 ND P YOR286W gene taxon:4932 20030203 SGD
+SGD S000001848 FMP32 GO:0005739 SGD_REF:S000072636|PMID:12514182 IDA C YFL046W gene taxon:4932 20031014 SGD
+SGD S000001848 FMP32 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YFL046W gene taxon:4932 20040924 SGD
+SGD S000001848 FMP32 GO:0005554 SGD_REF:S000069584 ND F YFL046W gene taxon:4932 20030203 SGD
+SGD S000001848 FMP32 GO:0000004 SGD_REF:S000069584 ND P YFL046W gene taxon:4932 20030203 SGD
+SGD S000003697 FMP33 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YJL161W gene taxon:4932 20031028 SGD
+SGD S000003697 FMP33 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YJL161W gene taxon:4932 20040924 SGD
+SGD S000003697 FMP33 GO:0005554 SGD_REF:S000069584 ND F YJL161W gene taxon:4932 20021126 SGD
+SGD S000003697 FMP33 GO:0000004 SGD_REF:S000069584 ND P YJL161W gene taxon:4932 20021126 SGD
+SGD S000001242 FMP34 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YHR199C gene taxon:4932 20031028 SGD
+SGD S000001242 FMP34 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YHR199C gene taxon:4932 20040924 SGD
+SGD S000001242 FMP34 GO:0005554 SGD_REF:S000069584 ND F YHR199C gene taxon:4932 20021126 SGD
+SGD S000001242 FMP34 GO:0000004 SGD_REF:S000069584 ND P YHR199C gene taxon:4932 20021126 SGD
+SGD S000001419 FMP35 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YIL157C gene taxon:4932 20031028 SGD
+SGD S000001419 FMP35 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YIL157C gene taxon:4932 20040924 SGD
+SGD S000001419 FMP35 GO:0005554 SGD_REF:S000069584 ND F YIL157C gene taxon:4932 20021126 SGD
+SGD S000001419 FMP35 GO:0000004 SGD_REF:S000069584 ND P YIL157C gene taxon:4932 20021126 SGD
+SGD S000002901 FMP36 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YDR493W gene taxon:4932 20031028 SGD
+SGD S000002901 FMP36 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YDR493W gene taxon:4932 20040924 SGD
+SGD S000002901 FMP36 GO:0005554 SGD_REF:S000069584 ND F YDR493W gene taxon:4932 20021126 SGD
+SGD S000002901 FMP36 GO:0000004 SGD_REF:S000069584 ND P YDR493W gene taxon:4932 20021126 SGD
+SGD S000003048 FMP37 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YGL080W gene taxon:4932 20031028 SGD
+SGD S000003048 FMP37 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YGL080W gene taxon:4932 20040924 SGD
+SGD S000003048 FMP37 GO:0005554 SGD_REF:S000069584 ND F YGL080W gene taxon:4932 20021126 SGD
+SGD S000003048 FMP37 GO:0000004 SGD_REF:S000069584 ND P YGL080W gene taxon:4932 20021126 SGD
+SGD S000005731 FMP38 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YOR205C gene taxon:4932 20031028 SGD
+SGD S000005731 FMP38 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YOR205C gene taxon:4932 20040924 SGD
+SGD S000005731 FMP38 GO:0005554 SGD_REF:S000069584 ND F YOR205C gene taxon:4932 20021126 SGD
+SGD S000005731 FMP38 GO:0000004 SGD_REF:S000069584 ND P YOR205C gene taxon:4932 20021126 SGD
+SGD S000004766 FMP39 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YMR157C gene taxon:4932 20031030 SGD
+SGD S000004766 FMP39 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YMR157C gene taxon:4932 20040924 SGD
+SGD S000004766 FMP39 GO:0005554 SGD_REF:S000069584 ND F YMR157C gene taxon:4932 20021126 SGD
+SGD S000004766 FMP39 GO:0000004 SGD_REF:S000069584 ND P YMR157C gene taxon:4932 20021126 SGD
+SGD S000006143 FMP40 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YPL222W gene taxon:4932 20031028 SGD
+SGD S000006143 FMP40 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YPL222W gene taxon:4932 20040924 SGD
+SGD S000006143 FMP40 GO:0005554 SGD_REF:S000069584 ND F YPL222W gene taxon:4932 20021126 SGD
+SGD S000006143 FMP40 GO:0000004 SGD_REF:S000069584 ND P YPL222W gene taxon:4932 20021126 SGD
+SGD S000005112 FMP41 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YNL168C gene taxon:4932 20031028 SGD
+SGD S000005112 FMP41 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YNL168C gene taxon:4932 20040924 SGD
+SGD S000005112 FMP41 GO:0005554 SGD_REF:S000069584 ND F YNL168C gene taxon:4932 20030428 SGD
+SGD S000005112 FMP41 GO:0000004 SGD_REF:S000069584 ND P YNL168C gene taxon:4932 20030428 SGD
+SGD S000004834 FMP42 GO:0000324 SGD_REF:S000074185|PMID:14562095 IDA C YMR221C gene taxon:4932 20031028 SGD
+SGD S000004834 FMP42 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YMR221C gene taxon:4932 20040928 SGD
+SGD S000004834 FMP42 GO:0005554 SGD_REF:S000069584 ND F YMR221C gene taxon:4932 20021120 SGD
+SGD S000004834 FMP42 GO:0000004 SGD_REF:S000069584 ND P YMR221C gene taxon:4932 20021120 SGD
+SGD S000003475 FMP43 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YGR243W gene taxon:4932 20031028 SGD
+SGD S000003475 FMP43 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YGR243W gene taxon:4932 20040924 SGD
+SGD S000003475 FMP43 GO:0005554 SGD_REF:S000069584 ND F YGR243W gene taxon:4932 20030421 SGD
+SGD S000003475 FMP43 GO:0000004 SGD_REF:S000069584 ND P YGR243W gene taxon:4932 20030421 SGD
+SGD S000002381 FMP45 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C integral membrane protein YDL222C gene taxon:4932 20040928 SGD
+SGD S000002381 FMP45 GO:0005938 SGD_REF:S000069238|PMID:11784867 IDA C integral membrane protein YDL222C gene taxon:4932 20020612 SGD
+SGD S000002381 FMP45 GO:0016021 SGD_REF:S000048799|PMID:9219339 ISS C integral membrane protein YDL222C gene taxon:4932 20020612 SGD
+SGD S000002381 FMP45 GO:0005554 SGD_REF:S000069584 ND F integral membrane protein YDL222C gene taxon:4932 20020612 SGD
+SGD S000002381 FMP45 GO:0007047 SGD_REF:S000069238|PMID:11784867 IMP P integral membrane protein YDL222C gene taxon:4932 20020612 SGD
+SGD S000002381 FMP45 GO:0030437 SGD_REF:S000069238|PMID:11784867 IGI P integral membrane protein YDL222C gene taxon:4932 20060306 SGD
+SGD S000002381 FMP45 GO:0030437 SGD_REF:S000069238|PMID:11784867 IMP P integral membrane protein YDL222C gene taxon:4932 20060306 SGD
+SGD S000001757 FMP46 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YKR049C gene taxon:4932 20031028 SGD
+SGD S000001757 FMP46 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YKR049C gene taxon:4932 20040924 SGD
+SGD S000001757 FMP46 GO:0016491 SGD_REF:S000086797|PMID:16202234 ISS UniProt:Q6FJI9|UniProt:Q6CN57|UniProt:Q755M5 F YKR049C gene taxon:4932 20051013 SGD
+SGD S000001757 FMP46 GO:0000004 SGD_REF:S000069584 ND P YKR049C gene taxon:4932 20030421 SGD
+SGD S000003284 FMP48 GO:0005739 SGD_REF:S000063829|PMID:10974565 ISS C YGR052W gene taxon:4932 20030130 SGD
+SGD S000003284 FMP48 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YGR052W gene taxon:4932 20040928 SGD
+SGD S000003284 FMP48 GO:0016301 SGD_REF:S000063829|PMID:10974565 ISS F YGR052W gene taxon:4932 20030130 SGD
+SGD S000003284 FMP48 GO:0000004 SGD_REF:S000069584 ND P YGR052W gene taxon:4932 20030130 SGD
+SGD S000000466 FMP51 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YBR262C gene taxon:4932 20031028 SGD
+SGD S000000466 FMP51 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YBR262C gene taxon:4932 20040924 SGD
+SGD S000000466 FMP51 GO:0005554 SGD_REF:S000069584 ND F YBR262C gene taxon:4932 20030423 SGD
+SGD S000000466 FMP51 GO:0000004 SGD_REF:S000069584 ND P YBR262C gene taxon:4932 20030423 SGD
+SGD S000000806 FMP52 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YER004W gene taxon:4932 20040928 SGD
+SGD S000000806 FMP52 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C YER004W gene taxon:4932 20060317 SGD
+SGD S000000806 FMP52 GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YER004W gene taxon:4932 20031028 SGD
+SGD S000000806 FMP52 GO:0005554 SGD_REF:S000069584 ND F YER004W gene taxon:4932 20021126 SGD
+SGD S000000806 FMP52 GO:0000004 SGD_REF:S000069584 ND P YER004W gene taxon:4932 20021126 SGD
+SGD S000004622 FMS1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C putatitive amine oxidase YMR020W gene taxon:4932 20020507 SGD
+SGD S000004622 FMS1 GO:0008131 SGD_REF:S000060103|PMID:11154694 IGI F putatitive amine oxidase YMR020W gene taxon:4932 20021211 SGD
+SGD S000004622 FMS1 GO:0008131 SGD_REF:S000060103|PMID:11154694 ISS F putatitive amine oxidase YMR020W gene taxon:4932 20021211 SGD
+SGD S000004622 FMS1 GO:0008131 SGD_REF:S000072966|PMID:12670477 IDA F putatitive amine oxidase YMR020W gene taxon:4932 20040430 SGD
+SGD S000004622 FMS1 GO:0006598 SGD_REF:S000072585|PMID:12586697 IGI P putatitive amine oxidase YMR020W gene taxon:4932 20030619 SGD
+SGD S000004622 FMS1 GO:0006598 SGD_REF:S000072585|PMID:12586697 IMP P putatitive amine oxidase YMR020W gene taxon:4932 20030619 SGD
+SGD S000004622 FMS1 GO:0015940 SGD_REF:S000060103|PMID:11154694 IMP P putatitive amine oxidase YMR020W gene taxon:4932 20020801 SGD
+SGD S000000109 FMT1 GO:0005739 SGD_REF:S000039777|PMID:10781559 TAS C methionyl-tRNA transformylase YBL013W gene taxon:4932 20010118 SGD
+SGD S000000109 FMT1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C methionyl-tRNA transformylase YBL013W gene taxon:4932 20040928 SGD
+SGD S000000109 FMT1 GO:0004479 SGD_REF:S000039777|PMID:10781559 IDA F methionyl-tRNA transformylase YBL013W gene taxon:4932 20010118 SGD
+SGD S000000109 FMT1 GO:0006413 SGD_REF:S000039777|PMID:10781559 IDA P methionyl-tRNA transformylase YBL013W gene taxon:4932 20010118 SGD
+SGD S000000109 FMT1 GO:0006431 SGD_REF:S000039777|PMID:10781559 IDA P methionyl-tRNA transformylase YBL013W gene taxon:4932 20010118 SGD
+SGD S000002517 FOB1 GO:0005730 SGD_REF:S000044333|PMID:10230397 IDA C DNA replication fork blocking protein YDR110W|HRM1 gene taxon:4932 20010118 SGD
+SGD S000002517 FOB1 GO:0000182 SGD_REF:S000071705|PMID:12374750 TAS F DNA replication fork blocking protein YDR110W|HRM1 gene taxon:4932 20021206 SGD
+SGD S000002517 FOB1 GO:0000182 SGD_REF:S000075098|PMID:14645529 IDA F DNA replication fork blocking protein YDR110W|HRM1 gene taxon:4932 20031216 SGD
+SGD S000002517 FOB1 GO:0000183 SGD_REF:S000074057|PMID:12923057 IDA P DNA replication fork blocking protein YDR110W|HRM1 gene taxon:4932 20031010 SGD
+SGD S000002517 FOB1 GO:0001302 SGD_REF:S000080970|PMID:15722108 IMP P DNA replication fork blocking protein YDR110W|HRM1 gene taxon:4932 20050314 SGD
+SGD S000002517 FOB1 GO:0006310 SGD_REF:S000056096|PMID:9078378 IMP P DNA replication fork blocking protein YDR110W|HRM1 gene taxon:4932 20010118 SGD
+SGD S000002517 FOB1 GO:0007580 SGD_REF:S000044333|PMID:10230397 IMP P DNA replication fork blocking protein YDR110W|HRM1 gene taxon:4932 20010118 SGD
+SGD S000002517 FOB1 GO:0008156 SGD_REF:S000075098|PMID:14645529 IDA P DNA replication fork blocking protein YDR110W|HRM1 gene taxon:4932 20031216 SGD
+SGD S000005200 FOL1 GO:0005737 SGD_REF:S000071582|PMID:8813764 IDA C dihydro-6-hydroxymethylpterin pyrophosphokinase, dihydroneopterin aldolase, dihydropteroate synthetase YNL256W gene taxon:4932 20021106 SGD
+SGD S000005200 FOL1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C dihydro-6-hydroxymethylpterin pyrophosphokinase, dihydroneopterin aldolase, dihydropteroate synthetase YNL256W gene taxon:4932 20040813 SGD
+SGD S000005200 FOL1 GO:0005740 SGD_REF:S000077028|PMID:15169867 IDA C dihydro-6-hydroxymethylpterin pyrophosphokinase, dihydroneopterin aldolase, dihydropteroate synthetase YNL256W gene taxon:4932 20050617 SGD
+SGD S000005200 FOL1 GO:0003848 SGD_REF:S000048854|PMID:9234673 ISS F dihydro-6-hydroxymethylpterin pyrophosphokinase, dihydroneopterin aldolase, dihydropteroate synthetase YNL256W gene taxon:4932 20021106 SGD
+SGD S000005200 FOL1 GO:0003848 SGD_REF:S000077028|PMID:15169867 IDA F dihydro-6-hydroxymethylpterin pyrophosphokinase, dihydroneopterin aldolase, dihydropteroate synthetase YNL256W gene taxon:4932 20050617 SGD
+SGD S000005200 FOL1 GO:0004150 SGD_REF:S000071379|PMID:11752249 ISS F dihydro-6-hydroxymethylpterin pyrophosphokinase, dihydroneopterin aldolase, dihydropteroate synthetase YNL256W gene taxon:4932 20021106 SGD
+SGD S000005200 FOL1 GO:0004150 SGD_REF:S000077028|PMID:15169867 IDA F dihydro-6-hydroxymethylpterin pyrophosphokinase, dihydroneopterin aldolase, dihydropteroate synthetase YNL256W gene taxon:4932 20050617 SGD
+SGD S000005200 FOL1 GO:0004156 SGD_REF:S000066263|PMID:11731153 IMP F dihydro-6-hydroxymethylpterin pyrophosphokinase, dihydroneopterin aldolase, dihydropteroate synthetase YNL256W gene taxon:4932 20021001 SGD
+SGD S000005200 FOL1 GO:0004156 SGD_REF:S000077028|PMID:15169867 IDA F dihydro-6-hydroxymethylpterin pyrophosphokinase, dihydroneopterin aldolase, dihydropteroate synthetase YNL256W gene taxon:4932 20050617 SGD
+SGD S000005200 FOL1 GO:0009396 SGD_REF:S000066263|PMID:11731153 IMP P dihydro-6-hydroxymethylpterin pyrophosphokinase, dihydroneopterin aldolase, dihydropteroate synthetase YNL256W gene taxon:4932 20021001 SGD
+SGD S000005200 FOL1 GO:0009396 SGD_REF:S000077028|PMID:15169867 IMP P dihydro-6-hydroxymethylpterin pyrophosphokinase, dihydroneopterin aldolase, dihydropteroate synthetase YNL256W gene taxon:4932 20050617 SGD
+SGD S000003499 FOL2 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C GTP-cyclohydrolase I YGR267C gene taxon:4932 20031028 SGD
+SGD S000003499 FOL2 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C GTP-cyclohydrolase I YGR267C gene taxon:4932 20020507 SGD
+SGD S000003499 FOL2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C GTP-cyclohydrolase I YGR267C gene taxon:4932 20031028 SGD
+SGD S000003499 FOL2 GO:0003934 SGD_REF:S000048485|PMID:8573145 IMP F GTP-cyclohydrolase I YGR267C gene taxon:4932 20021001 SGD
+SGD S000003499 FOL2 GO:0009396 SGD_REF:S000048485|PMID:8573145 IMP P GTP-cyclohydrolase I YGR267C gene taxon:4932 20021001 SGD
+SGD S000004719 FOL3 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C dihydrofolate synthetase YMR113W gene taxon:4932 20031028 SGD
+SGD S000004719 FOL3 GO:0008841 SGD_REF:S000066263|PMID:11731153 IMP F dihydrofolate synthetase YMR113W gene taxon:4932 20021001 SGD
+SGD S000004719 FOL3 GO:0009396 SGD_REF:S000066263|PMID:11731153 IMP P dihydrofolate synthetase YMR113W gene taxon:4932 20021001 SGD
+SGD S000001717 FOX2 GO:0005782 SGD_REF:S000058494 TAS C multifunctional beta-oxidation protein YKR009C|POX2 gene taxon:4932 20030204 SGD
+SGD S000001717 FOX2 GO:0003857 SGD_REF:S000058496 TAS F multifunctional beta-oxidation protein YKR009C|POX2 gene taxon:4932 20010119 SGD
+SGD S000001717 FOX2 GO:0004300 SGD_REF:S000058496 TAS F multifunctional beta-oxidation protein YKR009C|POX2 gene taxon:4932 20010119 SGD
+SGD S000001717 FOX2 GO:0006635 SGD_REF:S000058496 TAS P multifunctional beta-oxidation protein YKR009C|POX2 gene taxon:4932 20010119 SGD
+SGD S000005079 FPR1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C peptidyl-prolyl cis-trans isomerase (PPIase) YNL135C|FKB1|FKBP12|RBP1 gene taxon:4932 20031028 SGD
+SGD S000005079 FPR1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C peptidyl-prolyl cis-trans isomerase (PPIase) YNL135C|FKB1|FKBP12|RBP1 gene taxon:4932 20031028 SGD
+SGD S000005079 FPR1 GO:0003755 SGD_REF:S000054822|PMID:1705713 ISS F peptidyl-prolyl cis-trans isomerase (PPIase) YNL135C|FKB1|FKBP12|RBP1 gene taxon:4932 20021209 SGD
+SGD S000005079 FPR1 GO:0003755 SGD_REF:S000041838|PMID:1996117 IDA F peptidyl-prolyl cis-trans isomerase (PPIase) YNL135C|FKB1|FKBP12|RBP1 gene taxon:4932 20021209 SGD
+SGD S000005079 FPR1 GO:0006325 SGD_REF:S000063091|PMID:10049913 IGI SGD:S000002581 P peptidyl-prolyl cis-trans isomerase (PPIase) YNL135C|FKB1|FKBP12|RBP1 gene taxon:4932 20060315 SGD
+SGD S000005079 FPR1 GO:0009092 SGD_REF:S000077533|PMID:15470257 IGI SGD:S000005079 P peptidyl-prolyl cis-trans isomerase (PPIase) YNL135C|FKB1|FKBP12|RBP1 gene taxon:4932 20060315 SGD
+SGD S000002927 FPR2 GO:0005789 SGD_REF:S000039323|PMID:7685904 IEP C peptidyl-prolyl cis-trans isomerase (PPIase) YDR519W|FKB2|FKBP13 gene taxon:4932 20021202 SGD
+SGD S000002927 FPR2 GO:0005789 SGD_REF:S000039323|PMID:7685904 ISS C peptidyl-prolyl cis-trans isomerase (PPIase) YDR519W|FKB2|FKBP13 gene taxon:4932 20021202 SGD
+SGD S000002927 FPR2 GO:0003755 SGD_REF:S000039323|PMID:7685904 ISS F peptidyl-prolyl cis-trans isomerase (PPIase) YDR519W|FKB2|FKBP13 gene taxon:4932 20021202 SGD
+SGD S000002927 FPR2 GO:0000004 SGD_REF:S000069584 ND P peptidyl-prolyl cis-trans isomerase (PPIase) YDR519W|FKB2|FKBP13 gene taxon:4932 20021202 SGD
+SGD S000004539 FPR3 GO:0005730 SGD_REF:S000046730|PMID:7525596 IDA C peptidyl-prolyl cis-trans isomerase (PPIase) YML074C|NPI46 gene taxon:4932 20021002 SGD
+SGD S000004539 FPR3 GO:0005730 SGD_REF:S000046096|PMID:8051210 IDA C peptidyl-prolyl cis-trans isomerase (PPIase) YML074C|NPI46 gene taxon:4932 20021002 SGD
+SGD S000004539 FPR3 GO:0003755 SGD_REF:S000046730|PMID:7525596 IDA F peptidyl-prolyl cis-trans isomerase (PPIase) YML074C|NPI46 gene taxon:4932 20021002 SGD
+SGD S000004539 FPR3 GO:0003755 SGD_REF:S000053747|PMID:7925954 IDA F peptidyl-prolyl cis-trans isomerase (PPIase) YML074C|NPI46 gene taxon:4932 20021002 SGD
+SGD S000004539 FPR3 GO:0003755 SGD_REF:S000046096|PMID:8051210 IDA F peptidyl-prolyl cis-trans isomerase (PPIase) YML074C|NPI46 gene taxon:4932 20021002 SGD
+SGD S000004539 FPR3 GO:0000004 SGD_REF:S000069584 ND P peptidyl-prolyl cis-trans isomerase (PPIase) YML074C|NPI46 gene taxon:4932 20021002 SGD
+SGD S000004441 FPR4 GO:0005634 SGD_REF:S000046250|PMID:9371805 IDA C peptidyl-prolyl cis-trans isomerase (PPIase) YLR449W gene taxon:4932 20021209 SGD
+SGD S000004441 FPR4 GO:0003755 SGD_REF:S000061678|PMID:10821187 ISS F peptidyl-prolyl cis-trans isomerase (PPIase) YLR449W gene taxon:4932 20021201 SGD
+SGD S000004441 FPR4 GO:0000004 SGD_REF:S000069584 ND P peptidyl-prolyl cis-trans isomerase (PPIase) YLR449W gene taxon:4932 20021201 SGD
+SGD S000003966 FPS1 GO:0000324 SGD_REF:S000074185|PMID:14562095 IDA C glycerol channel protein YLL043W gene taxon:4932 20031028 SGD
+SGD S000003966 FPS1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C glycerol channel protein YLL043W gene taxon:4932 20020507 SGD
+SGD S000003966 FPS1 GO:0005886 SGD_REF:S000069459|PMID:11914276 IDA C glycerol channel protein YLL043W gene taxon:4932 20020508 SGD
+SGD S000003966 FPS1 GO:0005215 SGD_REF:S000053631|PMID:8550015 IMP F glycerol channel protein YLL043W gene taxon:4932 20010118 SGD
+SGD S000003966 FPS1 GO:0005215 SGD_REF:S000046364|PMID:7729414 IMP F glycerol channel protein YLL043W gene taxon:4932 20010118 SGD
+SGD S000003966 FPS1 GO:0005215 SGD_REF:S000053631|PMID:8550015 IDA F glycerol channel protein YLL043W gene taxon:4932 20010118 SGD
+SGD S000003966 FPS1 GO:0005215 SGD_REF:S000046364|PMID:7729414 IDA F glycerol channel protein YLL043W gene taxon:4932 20010118 SGD
+SGD S000003966 FPS1 GO:0005215 SGD_REF:S000058352|PMID:9678606 ISS F glycerol channel protein YLL043W gene taxon:4932 20010118 SGD
+SGD S000003966 FPS1 GO:0015168 SGD_REF:S000072644|PMID:12486125 IDA F glycerol channel protein YLL043W gene taxon:4932 20030304 SGD
+SGD S000003966 FPS1 GO:0000747 SGD_REF:S000042533|PMID:9281576 IMP P glycerol channel protein YLL043W gene taxon:4932 20020614 SGD
+SGD S000003966 FPS1 GO:0006810 SGD_REF:S000058352|PMID:9678606 ISS P glycerol channel protein YLL043W gene taxon:4932 20010118 SGD
+SGD S000003966 FPS1 GO:0015793 SGD_REF:S000072644|PMID:12486125 IDA P glycerol channel protein YLL043W gene taxon:4932 20030304 SGD
+SGD S000004204 FRE1 GO:0005886 SGD_REF:S000044999|PMID:8164662 IDA C cupric reductase, ferric reductase YLR214W gene taxon:4932 20020919 SGD
+SGD S000004204 FRE1 GO:0000293 SGD_REF:S000044999|PMID:8164662 IDA F cupric reductase, ferric reductase YLR214W gene taxon:4932 20020919 SGD
+SGD S000004204 FRE1 GO:0006826 SGD_REF:S000044999|PMID:8164662 IDA P cupric reductase, ferric reductase YLR214W gene taxon:4932 20020919 SGD
+SGD S000004204 FRE1 GO:0015677 SGD_REF:S000039247|PMID:7814363 IDA P cupric reductase, ferric reductase YLR214W gene taxon:4932 20020919 SGD
+SGD S000001703 FRE2 GO:0005886 SGD_REF:S000044999|PMID:8164662 IDA C ferric reductase YKL220C gene taxon:4932 20020919 SGD
+SGD S000001703 FRE2 GO:0000293 SGD_REF:S000044999|PMID:8164662 IDA F ferric reductase YKL220C gene taxon:4932 20020919 SGD
+SGD S000001703 FRE2 GO:0006826 SGD_REF:S000044999|PMID:8164662 IDA P ferric reductase YKL220C gene taxon:4932 20020919 SGD
+SGD S000001703 FRE2 GO:0015677 SGD_REF:S000045890|PMID:9153234 IDA P ferric reductase YKL220C gene taxon:4932 20020919 SGD
+SGD S000005908 FRE3 GO:0005886 SGD_REF:S000059998|PMID:11120744 IDA C ferric reductase transmembrane component YOR381W gene taxon:4932 20020314 SGD
+SGD S000005908 FRE3 GO:0016021 SGD_REF:S000043516|PMID:9726978 ISS C ferric reductase transmembrane component YOR381W gene taxon:4932 20020314 SGD
+SGD S000005908 FRE3 GO:0000293 SGD_REF:S000053347|PMID:3139452 ISS F ferric reductase transmembrane component YOR381W gene taxon:4932 20020326 SGD
+SGD S000005908 FRE3 GO:0006879 SGD_REF:S000043516|PMID:9726978 IMP P ferric reductase transmembrane component YOR381W gene taxon:4932 20020314 SGD
+SGD S000005908 FRE3 GO:0006879 SGD_REF:S000043516|PMID:9726978 IEP P ferric reductase transmembrane component YOR381W gene taxon:4932 20020314 SGD
+SGD S000005908 FRE3 GO:0006879 SGD_REF:S000055262|PMID:10341420 IEP P ferric reductase transmembrane component YOR381W gene taxon:4932 20020314 SGD
+SGD S000005908 FRE3 GO:0006879 SGD_REF:S000055262|PMID:10341420 IMP P ferric reductase transmembrane component YOR381W gene taxon:4932 20020314 SGD
+SGD S000005908 FRE3 GO:0015892 SGD_REF:S000043516|PMID:9726978 IMP P ferric reductase transmembrane component YOR381W gene taxon:4932 20020314 SGD
+SGD S000005343 FRE4 GO:0005886 SGD_REF:S000059998|PMID:11120744 ISS C YNR060W gene taxon:4932 20020919 SGD
+SGD S000005343 FRE4 GO:0005886 SGD_REF:S000059998|PMID:11120744 IMP C YNR060W gene taxon:4932 20020919 SGD
+SGD S000005343 FRE4 GO:0000293 SGD_REF:S000059998|PMID:11120744 ISS F YNR060W gene taxon:4932 20020919 SGD
+SGD S000005343 FRE4 GO:0000293 SGD_REF:S000059998|PMID:11120744 IMP F YNR060W gene taxon:4932 20020919 SGD
+SGD S000005343 FRE4 GO:0015892 SGD_REF:S000059998|PMID:11120744 IMP P YNR060W gene taxon:4932 20020919 SGD
+SGD S000005911 FRE5 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YOR384W gene taxon:4932 20040813 SGD
+SGD S000005911 FRE5 GO:0000293 SGD_REF:S000059998|PMID:11120744 ISS F YOR384W gene taxon:4932 20020919 SGD
+SGD S000005911 FRE5 GO:0000004 SGD_REF:S000069584 ND P YOR384W gene taxon:4932 20020919 SGD
+SGD S000003974 FRE6 GO:0000324 SGD_REF:S000074185|PMID:14562095 IDA C YLL051C gene taxon:4932 20031028 SGD
+SGD S000003974 FRE6 GO:0000293 SGD_REF:S000059998|PMID:11120744 ISS F YLL051C gene taxon:4932 20020919 SGD
+SGD S000003974 FRE6 GO:0000004 SGD_REF:S000069584 ND P YLL051C gene taxon:4932 20020919 SGD
+SGD S000005512 FRE7 GO:0008372 SGD_REF:S000069584 ND C YOL152W gene taxon:4932 20020919 SGD
+SGD S000005512 FRE7 GO:0000293 SGD_REF:S000059998|PMID:11120744 ISS F YOL152W gene taxon:4932 20020919 SGD
+SGD S000005512 FRE7 GO:0000004 SGD_REF:S000069584 ND P YOL152W gene taxon:4932 20020919 SGD
+SGD S000004037 FRE8 GO:0016020 SGD_REF:S000055262|PMID:10341420 ISS C YLR047C gene taxon:4932 20050812 SGD
+SGD S000004037 FRE8 GO:0016722 SGD_REF:S000055262|PMID:10341420 ISS F YLR047C gene taxon:4932 20050812 SGD
+SGD S000004037 FRE8 GO:0016722 SGD_REF:S000074663|PMID:14534306 IMP F YLR047C gene taxon:4932 20050812 SGD
+SGD S000004037 FRE8 GO:0006875 SGD_REF:S000074663|PMID:14534306 IMP P YLR047C gene taxon:4932 20050812 SGD
+SGD S000000589 FRM2 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YCL026C-A|YCLX08C gene taxon:4932 20031028 SGD
+SGD S000000589 FRM2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YCL026C-A|YCLX08C gene taxon:4932 20031028 SGD
+SGD S000000589 FRM2 GO:0005554 SGD_REF:S000069584 ND F YCL026C-A|YCLX08C gene taxon:4932 20021211 SGD
+SGD S000000589 FRM2 GO:0045922 SGD_REF:S000053179|PMID:8701605 IMP P YCL026C-A|YCLX08C gene taxon:4932 20021001 SGD
+SGD S000002781 FRQ1 GO:0016020 SGD_REF:S000051269|PMID:10559922 ISS C YDR373W gene taxon:4932 20010118 SGD
+SGD S000002781 FRQ1 GO:0005509 SGD_REF:S000051269|PMID:10559922 ISS F YDR373W gene taxon:4932 20010118 SGD
+SGD S000002781 FRQ1 GO:0008047 SGD_REF:S000051269|PMID:10559922 IDA F YDR373W gene taxon:4932 20040227 SGD
+SGD S000002781 FRQ1 GO:0009966 SGD_REF:S000073125|PMID:12477731 IMP P YDR373W gene taxon:4932 20040227 SGD
+SGD S000002781 FRQ1 GO:0009966 SGD_REF:S000073125|PMID:12477731 IPI P YDR373W gene taxon:4932 20040227 SGD
+SGD S000004050 FRS1 GO:0005737 SGD_REF:S000052199|PMID:3049607 TAS C phenylalanine-tRNA ligase subunit YLR060W gene taxon:4932 20041007 SGD
+SGD S000004050 FRS1 GO:0009328 SGD_REF:S000052199|PMID:3049607 TAS C phenylalanine-tRNA ligase subunit YLR060W gene taxon:4932 20021002 SGD
+SGD S000004050 FRS1 GO:0004826 SGD_REF:S000052199|PMID:3049607 ISS F phenylalanine-tRNA ligase subunit YLR060W gene taxon:4932 20021002 SGD
+SGD S000004050 FRS1 GO:0004826 SGD_REF:S000052199|PMID:3049607 IMP F phenylalanine-tRNA ligase subunit YLR060W gene taxon:4932 20021002 SGD
+SGD S000004050 FRS1 GO:0006432 SGD_REF:S000052199|PMID:3049607 TAS P phenylalanine-tRNA ligase subunit YLR060W gene taxon:4932 20021002 SGD
+SGD S000001872 FRS2 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C phenylalanine-tRNA ligase subunit YFL022C gene taxon:4932 20020507 SGD
+SGD S000001872 FRS2 GO:0005737 SGD_REF:S000052199|PMID:3049607 TAS C phenylalanine-tRNA ligase subunit YFL022C gene taxon:4932 20041007 SGD
+SGD S000001872 FRS2 GO:0009328 SGD_REF:S000052199|PMID:3049607 TAS C phenylalanine-tRNA ligase subunit YFL022C gene taxon:4932 20021002 SGD
+SGD S000001872 FRS2 GO:0004826 SGD_REF:S000052199|PMID:3049607 ISS F phenylalanine-tRNA ligase subunit YFL022C gene taxon:4932 20021002 SGD
+SGD S000001872 FRS2 GO:0004826 SGD_REF:S000052199|PMID:3049607 IMP F phenylalanine-tRNA ligase subunit YFL022C gene taxon:4932 20021002 SGD
+SGD S000001872 FRS2 GO:0006432 SGD_REF:S000052199|PMID:3049607 TAS P phenylalanine-tRNA ligase subunit YFL022C gene taxon:4932 20021002 SGD
+SGD S000005851 FRT1 GO:0005783 SGD_REF:S000072636|PMID:12514182 IDA C YOR324C|HPH1 gene taxon:4932 20031014 SGD
+SGD S000005851 FRT1 GO:0005783 SGD_REF:S000059083|PMID:15189990 IDA C YOR324C|HPH1 gene taxon:4932 20040706 SGD
+SGD S000005851 FRT1 GO:0005554 SGD_REF:S000069584 ND F YOR324C|HPH1 gene taxon:4932 20030203 SGD
+SGD S000005851 FRT1 GO:0006950 SGD_REF:S000059083|PMID:15189990 IMP P YOR324C|HPH1 gene taxon:4932 20040706 SGD
+SGD S000000026 FRT2 GO:0005783 SGD_REF:S000059083|PMID:15189990 IDA C YAL028W|HPH2 gene taxon:4932 20040706 SGD
+SGD S000000026 FRT2 GO:0005554 SGD_REF:S000069584 ND F YAL028W|HPH2 gene taxon:4932 20020425 SGD
+SGD S000000026 FRT2 GO:0006950 SGD_REF:S000059083|PMID:15189990 IMP P YAL028W|HPH2 gene taxon:4932 20040706 SGD
+SGD S000001091 FSH1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YHR049W gene taxon:4932 20031205 SGD
+SGD S000001091 FSH1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YHR049W gene taxon:4932 20031205 SGD
+SGD S000001091 FSH1 GO:0017171 SGD_REF:S000076484|PMID:14645503 IDA F YHR049W gene taxon:4932 20040604 SGD
+SGD S000001091 FSH1 GO:0017171 SGD_REF:S000076484|PMID:14645503 RCA F YHR049W gene taxon:4932 20060421 SGD
+SGD S000001091 FSH1 GO:0000004 SGD_REF:S000069584 ND P YHR049W gene taxon:4932 20030609 SGD
+SGD S000004835 FSH2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YMR222C gene taxon:4932 20031028 SGD
+SGD S000004835 FSH2 GO:0017171 SGD_REF:S000076484|PMID:14645503 IDA F YMR222C gene taxon:4932 20040604 SGD
+SGD S000004835 FSH2 GO:0017171 SGD_REF:S000076484|PMID:14645503 RCA F YMR222C gene taxon:4932 20060421 SGD
+SGD S000004835 FSH2 GO:0000004 SGD_REF:S000069584 ND P YMR222C gene taxon:4932 20030617 SGD
+SGD S000005806 FSH3 GO:0008372 SGD_REF:S000069584 ND C YOR280C gene taxon:4932 20060421 SGD
+SGD S000005806 FSH3 GO:0017171 SGD_REF:S000076484|PMID:14645503 IDA F YOR280C gene taxon:4932 20040604 SGD
+SGD S000005806 FSH3 GO:0017171 SGD_REF:S000076484|PMID:14645503 RCA F YOR280C gene taxon:4932 20060421 SGD
+SGD S000005806 FSH3 GO:0000004 SGD_REF:S000069584 ND P YOR280C gene taxon:4932 20060421 SGD
+SGD S000003757 FSP2 GO:0008372 SGD_REF:S000069584 ND C similar to maltase (alpha-D-glucosidase) YJL221C gene taxon:4932 20021001 SGD
+SGD S000003757 FSP2 GO:0004558 SGD_REF:S000041946|PMID:7725802 ISS F similar to maltase (alpha-D-glucosidase) YJL221C gene taxon:4932 20021126 SGD
+SGD S000003757 FSP2 GO:0000004 SGD_REF:S000069584 ND P similar to maltase (alpha-D-glucosidase) YJL221C gene taxon:4932 20021001 SGD
+SGD S000000411 FTH1 GO:0000329 SGD_REF:S000074185|PMID:14562095 IDA C YBR207W gene taxon:4932 20031028 SGD
+SGD S000000411 FTH1 GO:0000329 SGD_REF:S000063062|PMID:10608875 IDA C YBR207W gene taxon:4932 20040407 SGD
+SGD S000000411 FTH1 GO:0005381 SGD_REF:S000063062|PMID:10608875 TAS F YBR207W gene taxon:4932 20040407 SGD
+SGD S000000411 FTH1 GO:0006827 SGD_REF:S000063062|PMID:10608875 IPI P YBR207W gene taxon:4932 20040407 SGD
+SGD S000000411 FTH1 GO:0006897 SGD_REF:S000060817|PMID:11378903 IMP P YBR207W gene taxon:4932 20021004 SGD
+SGD S000000947 FTR1 GO:0005886 SGD_REF:S000052120|PMID:10748025 IDA C iron permease YER145C gene taxon:4932 20020314 SGD
+SGD S000000947 FTR1 GO:0005381 SGD_REF:S000047857|PMID:8599111 IDA F iron permease YER145C gene taxon:4932 20021223 SGD
+SGD S000000947 FTR1 GO:0006827 SGD_REF:S000047857|PMID:8599111 IMP P iron permease YER145C gene taxon:4932 20021223 SGD
+SGD S000000138 FUI1 GO:0005886 SGD_REF:S000049911|PMID:10827169 IGI C uridine permease YBL042C gene taxon:4932 20020919 SGD
+SGD S000000138 FUI1 GO:0005886 SGD_REF:S000049911|PMID:10827169 IMP C uridine permease YBL042C gene taxon:4932 20020919 SGD
+SGD S000000138 FUI1 GO:0015213 SGD_REF:S000049911|PMID:10827169 IGI F uridine permease YBL042C gene taxon:4932 20020919 SGD
+SGD S000000138 FUI1 GO:0015213 SGD_REF:S000049911|PMID:10827169 IMP F uridine permease YBL042C gene taxon:4932 20020919 SGD
+SGD S000000138 FUI1 GO:0015862 SGD_REF:S000049911|PMID:10827169 IGI P uridine permease YBL042C gene taxon:4932 20020919 SGD
+SGD S000000138 FUI1 GO:0015862 SGD_REF:S000049911|PMID:10827169 IMP P uridine permease YBL042C gene taxon:4932 20020919 SGD
+SGD S000006183 FUM1 GO:0005759 SGD_REF:S000067483|PMID:11585823 IDA C fumarase (fumarate hydralase) YPL262W gene taxon:4932 20021202 SGD
+SGD S000006183 FUM1 GO:0005829 SGD_REF:S000067483|PMID:11585823 IDA C fumarase (fumarate hydralase) YPL262W gene taxon:4932 20021202 SGD
+SGD S000006183 FUM1 GO:0004333 SGD_REF:S000058126|PMID:9175438 TAS F fumarase (fumarate hydralase) YPL262W gene taxon:4932 20010118 SGD
+SGD S000006183 FUM1 GO:0006099 SGD_REF:S000058126|PMID:9175438 TAS P fumarase (fumarate hydralase) YPL262W gene taxon:4932 20010118 SGD
+SGD S000006183 FUM1 GO:0006106 SGD_REF:S000058126|PMID:9175438 TAS P fumarase (fumarate hydralase) YPL262W gene taxon:4932 20010118 SGD
+SGD S000000033 FUN12 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C 97 kDa protein YAL035W|eIF5B|yIF2 gene taxon:4932 20040928 SGD
+SGD S000000033 FUN12 GO:0005843 SGD_REF:S000063204|PMID:9624054 IDA C 97 kDa protein YAL035W|eIF5B|yIF2 gene taxon:4932 20021113 SGD
+SGD S000000033 FUN12 GO:0003743 SGD_REF:S000063204|PMID:9624054 IDA F 97 kDa protein YAL035W|eIF5B|yIF2 gene taxon:4932 20021113 SGD
+SGD S000000033 FUN12 GO:0003924 SGD_REF:S000072459|PMID:12471154 IMP F 97 kDa protein YAL035W|eIF5B|yIF2 gene taxon:4932 20030423 SGD
+SGD S000000033 FUN12 GO:0003924 SGD_REF:S000072459|PMID:12471154 ISS F 97 kDa protein YAL035W|eIF5B|yIF2 gene taxon:4932 20030423 SGD
+SGD S000000033 FUN12 GO:0006413 SGD_REF:S000063204|PMID:9624054 IDA P 97 kDa protein YAL035W|eIF5B|yIF2 gene taxon:4932 20020802 SGD
+SGD S000000006 FUN14 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YAL008W gene taxon:4932 20031028 SGD
+SGD S000000006 FUN14 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YAL008W gene taxon:4932 20040924 SGD
+SGD S000000006 FUN14 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C YAL008W gene taxon:4932 20060317 SGD
+SGD S000000006 FUN14 GO:0005554 SGD_REF:S000069584 ND F YAL008W gene taxon:4932 20010119 SGD
+SGD S000000006 FUN14 GO:0000004 SGD_REF:S000069584 ND P YAL008W gene taxon:4932 20010119 SGD
+SGD S000002134 FUN19 GO:0008372 SGD_REF:S000069584 ND C YAL034C gene taxon:4932 20010119 SGD
+SGD S000002134 FUN19 GO:0005554 SGD_REF:S000069584 ND F YAL034C gene taxon:4932 20010119 SGD
+SGD S000002134 FUN19 GO:0000004 SGD_REF:S000069584 ND P YAL034C gene taxon:4932 20010119 SGD
+SGD S000000020 FUN26 GO:0005622 SGD_REF:S000049911|PMID:10827169 IDA C YAL022C gene taxon:4932 20020919 SGD
+SGD S000000020 FUN26 GO:0016020 SGD_REF:S000049911|PMID:10827169 IDA C YAL022C gene taxon:4932 20020919 SGD
+SGD S000000020 FUN26 GO:0005337 SGD_REF:S000049911|PMID:10827169 IDA F YAL022C gene taxon:4932 20020919 SGD
+SGD S000000020 FUN26 GO:0015858 SGD_REF:S000049911|PMID:10827169 IDA P YAL022C gene taxon:4932 20020919 SGD
+SGD S000000017 FUN30 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YAL019W gene taxon:4932 20031028 SGD
+SGD S000000017 FUN30 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YAL019W gene taxon:4932 20040928 SGD
+SGD S000000017 FUN30 GO:0005554 SGD_REF:S000069584 ND F YAL019W gene taxon:4932 20021011 SGD
+SGD S000000017 FUN30 GO:0007001 SGD_REF:S000052609|PMID:10454593 IGI P YAL019W gene taxon:4932 20021011 SGD
+SGD S000001170 FUR1 GO:0005622 SGD_REF:S000045945|PMID:2189783 IC GO:0008655 C UPRTase YHR128W gene taxon:4932 20051125 SGD
+SGD S000001170 FUR1 GO:0004845 SGD_REF:S000045945|PMID:2189783 IDA F UPRTase YHR128W gene taxon:4932 20010703 SGD
+SGD S000001170 FUR1 GO:0008655 SGD_REF:S000045945|PMID:2189783 IDA P UPRTase YHR128W gene taxon:4932 20010703 SGD
+SGD S000000225 FUR4 GO:0005886 SGD_REF:S000053454|PMID:8948441 IDA C uracil permease YBR021W gene taxon:4932 20020920 SGD
+SGD S000000225 FUR4 GO:0045121 SGD_REF:S000079755|PMID:15536122 IDA C uracil permease YBR021W gene taxon:4932 20041215 SGD
+SGD S000000225 FUR4 GO:0015505 SGD_REF:S000053454|PMID:8948441 IDA F uracil permease YBR021W gene taxon:4932 20020920 SGD
+SGD S000000225 FUR4 GO:0015857 SGD_REF:S000053454|PMID:8948441 IDA P uracil permease YBR021W gene taxon:4932 20020920 SGD
+SGD S000000532 FUS1 GO:0005886 SGD_REF:S000040376|PMID:2690078 IDA C YCL027W gene taxon:4932 20010118 SGD
+SGD S000000532 FUS1 GO:0043332 SGD_REF:S000071843|PMID:12374868 IDA C YCL027W gene taxon:4932 20030129 SGD
+SGD S000000532 FUS1 GO:0005554 SGD_REF:S000069584 ND F YCL027W gene taxon:4932 20021209 SGD
+SGD S000000532 FUS1 GO:0000747 SGD_REF:S000045065|PMID:3313002 IMP P YCL027W gene taxon:4932 20020614 SGD
+SGD S000000532 FUS1 GO:0031385 SGD_REF:S000077102|PMID:14734532 IMP P YCL027W gene taxon:4932 20050719 SGD
+SGD S000004845 FUS2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YMR232W gene taxon:4932 20041203 SGD
+SGD S000004845 FUS2 GO:0043332 SGD_REF:S000047183|PMID:7559752 IDA C YMR232W gene taxon:4932 20020819 SGD
+SGD S000004845 FUS2 GO:0005554 SGD_REF:S000069584 ND F YMR232W gene taxon:4932 20020819 SGD
+SGD S000004845 FUS2 GO:0031385 SGD_REF:S000077102|PMID:14734532 IMP P YMR232W gene taxon:4932 20050719 SGD
+SGD S000004845 FUS2 GO:0045026 SGD_REF:S000047183|PMID:7559752 IMP P YMR232W gene taxon:4932 20020819 SGD
+SGD S000000112 FUS3 GO:0005634 SGD_REF:S000048143|PMID:10233162 IDA C CDC28/cdc2 related protein kinase YBL016W|DAC2 gene taxon:4932 20010118 SGD
+SGD S000000112 FUS3 GO:0005737 SGD_REF:S000048143|PMID:10233162 IDA C CDC28/cdc2 related protein kinase YBL016W|DAC2 gene taxon:4932 20010118 SGD
+SGD S000000112 FUS3 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C CDC28/cdc2 related protein kinase YBL016W|DAC2 gene taxon:4932 20041203 SGD
+SGD S000000112 FUS3 GO:0043332 SGD_REF:S000069153|PMID:11781566 IDA C CDC28/cdc2 related protein kinase YBL016W|DAC2 gene taxon:4932 20020829 SGD
+SGD S000000112 FUS3 GO:0004707 SGD_REF:S000045748|PMID:8384702 TAS F CDC28/cdc2 related protein kinase YBL016W|DAC2 gene taxon:4932 20010118 SGD
+SGD S000000112 FUS3 GO:0004707 SGD_REF:S000080086|PMID:15620357 IDA F CDC28/cdc2 related protein kinase YBL016W|DAC2 gene taxon:4932 20050218 SGD
+SGD S000000112 FUS3 GO:0000750 SGD_REF:S000045748|PMID:8384702 IDA P CDC28/cdc2 related protein kinase YBL016W|DAC2 gene taxon:4932 20021206 SGD
+SGD S000000112 FUS3 GO:0001402 SGD_REF:S000039888|PMID:9393860 IMP P CDC28/cdc2 related protein kinase YBL016W|DAC2 gene taxon:4932 20050218 SGD
+SGD S000000112 FUS3 GO:0001403 SGD_REF:S000050425|PMID:8001818 IMP P CDC28/cdc2 related protein kinase YBL016W|DAC2 gene taxon:4932 20050218 SGD
+SGD S000000112 FUS3 GO:0001403 SGD_REF:S000080086|PMID:15620357 IMP P CDC28/cdc2 related protein kinase YBL016W|DAC2 gene taxon:4932 20050218 SGD
+SGD S000000112 FUS3 GO:0001403 SGD_REF:S000062980|PMID:10652102 IMP P CDC28/cdc2 related protein kinase YBL016W|DAC2 gene taxon:4932 20050218 SGD
+SGD S000000112 FUS3 GO:0006468 SGD_REF:S000045748|PMID:8384702 TAS P CDC28/cdc2 related protein kinase YBL016W|DAC2 gene taxon:4932 20010118 SGD
+SGD S000000112 FUS3 GO:0007050 SGD_REF:S000055079|PMID:10049917 TAS P CDC28/cdc2 related protein kinase YBL016W|DAC2 gene taxon:4932 20010118 SGD
+SGD S000001359 FYV10 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YIL097W|GID9 gene taxon:4932 20031028 SGD
+SGD S000001359 FYV10 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YIL097W|GID9 gene taxon:4932 20031028 SGD
+SGD S000001359 FYV10 GO:0005554 SGD_REF:S000069584 ND F YIL097W|GID9 gene taxon:4932 20021211 SGD
+SGD S000001359 FYV10 GO:0045721 SGD_REF:S000072993|PMID:12686616 IMP P YIL097W|GID9 gene taxon:4932 20030708 SGD
+SGD S000005709 FYV12 GO:0008372 SGD_REF:S000069584 ND C YOR183W gene taxon:4932 20010314 SGD
+SGD S000005709 FYV12 GO:0005554 SGD_REF:S000069584 ND F YOR183W gene taxon:4932 20021211 SGD
+SGD S000005709 FYV12 GO:0000004 SGD_REF:S000069584 ND P YOR183W gene taxon:4932 20021211 SGD
+SGD S000001101 FYV4 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YHR059W gene taxon:4932 20031028 SGD
+SGD S000001101 FYV4 GO:0005554 SGD_REF:S000069584 ND F YHR059W gene taxon:4932 20021211 SGD
+SGD S000001101 FYV4 GO:0000004 SGD_REF:S000069584 ND P YHR059W gene taxon:4932 20021211 SGD
+SGD S000005077 FYV6 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YNL133C gene taxon:4932 20031028 SGD
+SGD S000005077 FYV6 GO:0005554 SGD_REF:S000069584 ND F YNL133C gene taxon:4932 20021216 SGD
+SGD S000005077 FYV6 GO:0006303 SGD_REF:S000073203|PMID:12399380 IMP P YNL133C gene taxon:4932 20030528 SGD
+SGD S000004058 FYV7 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YLR068W gene taxon:4932 20031028 SGD
+SGD S000004058 FYV7 GO:0005730 SGD_REF:S000074185|PMID:14562095 IDA C YLR068W gene taxon:4932 20031028 SGD
+SGD S000004058 FYV7 GO:0005554 SGD_REF:S000069584 ND F YLR068W gene taxon:4932 20021216 SGD
+SGD S000004058 FYV7 GO:0030490 SGD_REF:S000073750|PMID:12837249 IMP P YLR068W gene taxon:4932 20030804 SGD
+SGD S000003428 FYV8 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YGR196C gene taxon:4932 20020507 SGD
+SGD S000003428 FYV8 GO:0005554 SGD_REF:S000069584 ND F YGR196C gene taxon:4932 20021216 SGD
+SGD S000003428 FYV8 GO:0000004 SGD_REF:S000069584 ND P YGR196C gene taxon:4932 20021216 SGD
+SGD S000003223 FZF1 GO:0005634 SGD_REF:S000053440|PMID:10234785 IC GO:0003700 C contains five zinc fingers, transcription factor YGL254W|NRC299|RSU1|SUL1 gene taxon:4932 20030410 SGD
+SGD S000003223 FZF1 GO:0003700 SGD_REF:S000053440|PMID:10234785 IDA F contains five zinc fingers, transcription factor YGL254W|NRC299|RSU1|SUL1 gene taxon:4932 20020403 SGD
+SGD S000003223 FZF1 GO:0000316 SGD_REF:S000053440|PMID:10234785 TAS P contains five zinc fingers, transcription factor YGL254W|NRC299|RSU1|SUL1 gene taxon:4932 20020404 SGD
+SGD S000003223 FZF1 GO:0045944 SGD_REF:S000053440|PMID:10234785 IDA P contains five zinc fingers, transcription factor YGL254W|NRC299|RSU1|SUL1 gene taxon:4932 20030410 SGD
+SGD S000000383 FZO1 GO:0005741 SGD_REF:S000058450|PMID:9891785 TAS C Drosophila melanogaster fuzzy onions gene homolog, integral protein of the mitochondrial outer membrane; can be isolated as part of a high molecular weight complex YBR179C gene taxon:4932 20010118 SGD
+SGD S000000383 FZO1 colocalizes_with GO:0005741 SGD_REF:S000081570|PMID:11266460 IDA C Drosophila melanogaster fuzzy onions gene homolog, integral protein of the mitochondrial outer membrane; can be isolated as part of a high molecular weight complex YBR179C gene taxon:4932 20050510 SGD
+SGD S000000383 FZO1 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C Drosophila melanogaster fuzzy onions gene homolog, integral protein of the mitochondrial outer membrane; can be isolated as part of a high molecular weight complex YBR179C gene taxon:4932 20060317 SGD
+SGD S000000383 FZO1 colocalizes_with GO:0005743 SGD_REF:S000081570|PMID:11266460 IDA C Drosophila melanogaster fuzzy onions gene homolog, integral protein of the mitochondrial outer membrane; can be isolated as part of a high molecular weight complex YBR179C gene taxon:4932 20050510 SGD
+SGD S000000383 FZO1 GO:0003924 SGD_REF:S000058450|PMID:9891785 TAS F Drosophila melanogaster fuzzy onions gene homolog, integral protein of the mitochondrial outer membrane; can be isolated as part of a high molecular weight complex YBR179C gene taxon:4932 20010118 SGD
+SGD S000000383 FZO1 GO:0007005 SGD_REF:S000058450|PMID:9891785 TAS P Drosophila melanogaster fuzzy onions gene homolog, integral protein of the mitochondrial outer membrane; can be isolated as part of a high molecular weight complex YBR179C gene taxon:4932 20010118 SGD
+SGD S000000383 FZO1 GO:0008053 SGD_REF:S000073565|PMID:12808034 IMP P Drosophila melanogaster fuzzy onions gene homolog, integral protein of the mitochondrial outer membrane; can be isolated as part of a high molecular weight complex YBR179C gene taxon:4932 20030710 SGD
+SGD S000000383 FZO1 GO:0008053 SGD_REF:S000073565|PMID:12808034 IPI P Drosophila melanogaster fuzzy onions gene homolog, integral protein of the mitochondrial outer membrane; can be isolated as part of a high molecular weight complex YBR179C gene taxon:4932 20030710 SGD
+SGD S000004078 GAA1 GO:0042765 SGD_REF:S000066151|PMID:11598210 IPI C GPI:protein transamidase component (putative) YLR088W|END2 gene taxon:4932 20050209 SGD
+SGD S000004078 GAA1 GO:0003923 SGD_REF:S000066151|PMID:11598210 IMP F GPI:protein transamidase component (putative) YLR088W|END2 gene taxon:4932 20020724 SGD
+SGD S000004078 GAA1 GO:0003923 SGD_REF:S000066151|PMID:11598210 IPI F GPI:protein transamidase component (putative) YLR088W|END2 gene taxon:4932 20020724 SGD
+SGD S000004078 GAA1 GO:0016255 SGD_REF:S000066151|PMID:11598210 IMP P GPI:protein transamidase component (putative) YLR088W|END2 gene taxon:4932 20020724 SGD
+SGD S000004451 GAB1 GO:0042765 SGD_REF:S000076654|PMID:15075373 IPI C YLR459W|CDC91 gene taxon:4932 20050209 SGD
+SGD S000004451 GAB1 GO:0042765 SGD_REF:S000076654|PMID:15075373 IMP C YLR459W|CDC91 gene taxon:4932 20050209 SGD
+SGD S000004451 GAB1 GO:0003923 SGD_REF:S000073230|PMID:12802054 ISS HUGO:CDC91L1 F YLR459W|CDC91 gene taxon:4932 20030618 SGD
+SGD S000004451 GAB1 GO:0016255 SGD_REF:S000073230|PMID:12802054 ISS HUGO:CDC91L1 P YLR459W|CDC91 gene taxon:4932 20030618 SGD
+SGD S000005704 GAC1 GO:0000164 SGD_REF:S000049387|PMID:8289829 IDA C Glc7p regulatory subunit YOR178C gene taxon:4932 20010118 SGD
+SGD S000005704 GAC1 GO:0005198 SGD_REF:S000069720|PMID:11973298 TAS F Glc7p regulatory subunit YOR178C gene taxon:4932 20051007 SGD
+SGD S000005704 GAC1 GO:0008599 SGD_REF:S000065824|PMID:11412094 TAS F Glc7p regulatory subunit YOR178C gene taxon:4932 20030130 SGD
+SGD S000005704 GAC1 GO:0031072 SGD_REF:S000044300|PMID:10207049 IDA F Glc7p regulatory subunit YOR178C gene taxon:4932 20051007 SGD
+SGD S000005704 GAC1 GO:0000122 SGD_REF:S000046186|PMID:8846786 TAS P Glc7p regulatory subunit YOR178C gene taxon:4932 20010118 SGD
+SGD S000005704 GAC1 GO:0005977 SGD_REF:S000049387|PMID:8289829 IPI P Glc7p regulatory subunit YOR178C gene taxon:4932 20010118 SGD
+SGD S000005704 GAC1 GO:0007094 SGD_REF:S000049952|PMID:10072380 IMP P Glc7p regulatory subunit YOR178C gene taxon:4932 20010118 SGD
+SGD S000005704 GAC1 GO:0007126 SGD_REF:S000041210|PMID:8754819 IPI P Glc7p regulatory subunit YOR178C gene taxon:4932 20010118 SGD
+SGD S000005704 GAC1 GO:0009408 SGD_REF:S000044300|PMID:10207049 IPI P Glc7p regulatory subunit YOR178C gene taxon:4932 20010118 SGD
+SGD S000005704 GAC1 GO:0009408 SGD_REF:S000044300|PMID:10207049 IMP P Glc7p regulatory subunit YOR178C gene taxon:4932 20010118 SGD
+SGD S000004862 GAD1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C glutamate decarboxylase YMR250W gene taxon:4932 20020507 SGD
+SGD S000004862 GAD1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C glutamate decarboxylase YMR250W gene taxon:4932 20031028 SGD
+SGD S000004862 GAD1 GO:0004351 SGD_REF:S000042602|PMID:11031268 IPI F glutamate decarboxylase YMR250W gene taxon:4932 20021204 SGD
+SGD S000004862 GAD1 GO:0004351 SGD_REF:S000042602|PMID:11031268 ISS F glutamate decarboxylase YMR250W gene taxon:4932 20021204 SGD
+SGD S000004862 GAD1 GO:0006538 SGD_REF:S000042602|PMID:11031268 IPI P glutamate decarboxylase YMR250W gene taxon:4932 20021204 SGD
+SGD S000004862 GAD1 GO:0006538 SGD_REF:S000042602|PMID:11031268 ISS P glutamate decarboxylase YMR250W gene taxon:4932 20021204 SGD
+SGD S000004862 GAD1 GO:0006979 SGD_REF:S000042602|PMID:11031268 IMP P glutamate decarboxylase YMR250W gene taxon:4932 20021204 SGD
+SGD S000000224 GAL1 GO:0008372 SGD_REF:S000069584 ND C galactokinase YBR020W gene taxon:4932 20030514 SGD
+SGD S000000224 GAL1 GO:0004335 SGD_REF:S000055057|PMID:7601342 TAS F galactokinase YBR020W gene taxon:4932 20010118 SGD
+SGD S000000224 GAL1 GO:0006012 SGD_REF:S000055057|PMID:7601342 TAS P galactokinase YBR020W gene taxon:4932 20010118 SGD
+SGD S000000223 GAL10 GO:0008372 SGD_REF:S000069584 ND C UDP-glucose 4-epimerase YBR019C gene taxon:4932 20030131 SGD
+SGD S000000223 GAL10 GO:0003978 SGD_REF:S000075515|PMID:14764091 IDA F UDP-glucose 4-epimerase YBR019C gene taxon:4932 20040310 SGD
+SGD S000000223 GAL10 GO:0006012 SGD_REF:S000054945|PMID:3082856 NAS P UDP-glucose 4-epimerase YBR019C gene taxon:4932 20010118 SGD
+SGD S000005411 GAL11 GO:0000119 SGD_REF:S000048078|PMID:9420330 IDA C RNA polymerase II holoenzyme complex component, positive and negative transcriptional regulator of genes involved in mating-type specialization YOL051W|ABE1|MED15|RAR3|SDS4|SPT13 gene taxon:4932 20010118 SGD
+SGD S000005411 GAL11 GO:0016455 SGD_REF:S000048078|PMID:9420330 IDA F RNA polymerase II holoenzyme complex component, positive and negative transcriptional regulator of genes involved in mating-type specialization YOL051W|ABE1|MED15|RAR3|SDS4|SPT13 gene taxon:4932 20010302 SGD
+SGD S000005411 GAL11 GO:0006366 SGD_REF:S000048078|PMID:9420330 IDA P RNA polymerase II holoenzyme complex component, positive and negative transcriptional regulator of genes involved in mating-type specialization YOL051W|ABE1|MED15|RAR3|SDS4|SPT13 gene taxon:4932 20010118 SGD
+SGD S000004071 GAL2 GO:0005886 SGD_REF:S000054945|PMID:3082856 NAS C galactose permease YLR081W gene taxon:4932 20010118 SGD
+SGD S000004071 GAL2 GO:0005354 SGD_REF:S000055057|PMID:7601342 TAS F galactose permease YLR081W gene taxon:4932 20010118 SGD
+SGD S000004071 GAL2 GO:0005355 SGD_REF:S000073003|PMID:12702270 IDA F galactose permease YLR081W gene taxon:4932 20030502 SGD
+SGD S000004071 GAL2 GO:0006012 SGD_REF:S000055057|PMID:7601342 TAS P galactose permease YLR081W gene taxon:4932 20010118 SGD
+SGD S000004071 GAL2 GO:0006859 SGD_REF:S000055057|PMID:7601342 TAS P galactose permease YLR081W gene taxon:4932 20010118 SGD
+SGD S000002416 GAL3 GO:0005737 SGD_REF:S000047032|PMID:10866670 IDA C YDR009W gene taxon:4932 20030421 SGD
+SGD S000002416 GAL3 GO:0005515 SGD_REF:S000046883|PMID:8628318 IDA F YDR009W gene taxon:4932 20030425 SGD
+SGD S000002416 GAL3 GO:0006012 SGD_REF:S000055057|PMID:7601342 TAS P YDR009W gene taxon:4932 20010118 SGD
+SGD S000002416 GAL3 GO:0006355 SGD_REF:S000055057|PMID:7601342 TAS P YDR009W gene taxon:4932 20010118 SGD
+SGD S000006169 GAL4 GO:0005634 SGD_REF:S000055057|PMID:7601342 TAS C zinc finger transcription factor of the Zn(2)-Cys(6) binuclear cluster domain type YPL248C|GAL81 gene taxon:4932 20010118 SGD
+SGD S000006169 GAL4 GO:0016563 SGD_REF:S000055057|PMID:7601342 TAS F zinc finger transcription factor of the Zn(2)-Cys(6) binuclear cluster domain type YPL248C|GAL81 gene taxon:4932 20010926 SGD
+SGD S000006169 GAL4 GO:0006012 SGD_REF:S000055057|PMID:7601342 TAS P zinc finger transcription factor of the Zn(2)-Cys(6) binuclear cluster domain type YPL248C|GAL81 gene taxon:4932 20010118 SGD
+SGD S000006169 GAL4 GO:0006355 SGD_REF:S000055057|PMID:7601342 TAS P zinc finger transcription factor of the Zn(2)-Cys(6) binuclear cluster domain type YPL248C|GAL81 gene taxon:4932 20010118 SGD
+SGD S000000222 GAL7 GO:0005737 SGD_REF:S000059401|PMID:10993714 IDA C galactose-1-phosphate uridyl transferase YBR018C gene taxon:4932 20021202 SGD
+SGD S000000222 GAL7 GO:0017103 SGD_REF:S000044791|PMID:2851900 ISS F galactose-1-phosphate uridyl transferase YBR018C gene taxon:4932 20021202 SGD
+SGD S000000222 GAL7 GO:0006012 SGD_REF:S000071144 TAS P galactose-1-phosphate uridyl transferase YBR018C gene taxon:4932 20021202 SGD
+SGD S000004515 GAL80 GO:0005634 SGD_REF:S000047032|PMID:10866670 IDA C transcriptional regulator YML051W gene taxon:4932 20030421 SGD
+SGD S000004515 GAL80 GO:0005737 SGD_REF:S000047032|PMID:10866670 IDA C transcriptional regulator YML051W gene taxon:4932 20030421 SGD
+SGD S000004515 GAL80 GO:0003714 SGD_REF:S000055057|PMID:7601342 TAS F transcriptional regulator YML051W gene taxon:4932 20010118 SGD
+SGD S000004515 GAL80 GO:0006012 SGD_REF:S000055057|PMID:7601342 TAS P transcriptional regulator YML051W gene taxon:4932 20010118 SGD
+SGD S000004515 GAL80 GO:0006355 SGD_REF:S000055057|PMID:7601342 TAS P transcriptional regulator YML051W gene taxon:4932 20010118 SGD
+SGD S000000829 GAL83 GO:0005634 SGD_REF:S000060188|PMID:11331606 IDA C YER027C|SPM1 gene taxon:4932 20021009 SGD
+SGD S000000829 GAL83 GO:0004679 SGD_REF:S000059161|PMID:10990457 IMP F YER027C|SPM1 gene taxon:4932 20050416 SGD
+SGD S000000829 GAL83 GO:0006468 SGD_REF:S000059161|PMID:10990457 IMP P YER027C|SPM1 gene taxon:4932 20020819 SGD
+SGD S000000829 GAL83 GO:0007155 SGD_REF:S000072732|PMID:12556493 IMP P YER027C|SPM1 gene taxon:4932 20030313 SGD
+SGD S000000829 GAL83 GO:0007165 SGD_REF:S000059161|PMID:10990457 IMP P YER027C|SPM1 gene taxon:4932 20020819 SGD
+SGD S000000829 GAL83 GO:0030447 SGD_REF:S000072732|PMID:12556493 IMP P YER027C|SPM1 gene taxon:4932 20030313 SGD
+SGD S000001747 GAP1 GO:0000328 SGD_REF:S000076009|PMID:15039776 IDA C general amino acid permease YKR039W gene taxon:4932 20051026 SGD
+SGD S000001747 GAP1 GO:0005768 SGD_REF:S000076009|PMID:15039776 IDA C general amino acid permease YKR039W gene taxon:4932 20051024 SGD
+SGD S000001747 GAP1 GO:0005771 SGD_REF:S000075331|PMID:14523026 IMP C general amino acid permease YKR039W gene taxon:4932 20051025 SGD
+SGD S000001747 GAP1 GO:0005886 SGD_REF:S000080893|PMID:15707981 IDA C general amino acid permease YKR039W gene taxon:4932 20050318 SGD
+SGD S000001747 GAP1 GO:0005886 SGD_REF:S000080152|PMID:15623581 IDA C general amino acid permease YKR039W gene taxon:4932 20050708 SGD
+SGD S000001747 GAP1 GO:0005887 SGD_REF:S000051490|PMID:9199164 IDA C general amino acid permease YKR039W gene taxon:4932 20010118 SGD
+SGD S000001747 GAP1 GO:0030134 SGD_REF:S000071912|PMID:12499351 IDA C general amino acid permease YKR039W gene taxon:4932 20051024 SGD
+SGD S000001747 GAP1 GO:0005296 SGD_REF:S000074897|PMID:14968425 IGI SGD:S000000530|SGD:S000005875|SGD:S000002916 F general amino acid permease YKR039W gene taxon:4932 20050428 SGD
+SGD S000001747 GAP1 GO:0015203 SGD_REF:S000080893|PMID:15707981 IMP F general amino acid permease YKR039W gene taxon:4932 20050318 SGD
+SGD S000001747 GAP1 GO:0015359 SGD_REF:S000050599|PMID:6759873 IMP F general amino acid permease YKR039W gene taxon:4932 20040907 SGD
+SGD S000001747 GAP1 GO:0006865 SGD_REF:S000050599|PMID:6759873 IMP P general amino acid permease YKR039W gene taxon:4932 20010213 SGD
+SGD S000001747 GAP1 GO:0015846 SGD_REF:S000080893|PMID:15707981 IMP P general amino acid permease YKR039W gene taxon:4932 20050318 SGD
+SGD S000001131 GAR1 GO:0005730 SGD_REF:S000046451|PMID:1531632 IDA C small nucleolar RNP protein YHR089C gene taxon:4932 20021105 SGD
+SGD S000001131 GAR1 GO:0005732 SGD_REF:S000046451|PMID:1531632 IPI C small nucleolar RNP protein YHR089C gene taxon:4932 20021203 SGD
+SGD S000001131 GAR1 GO:0003723 SGD_REF:S000040164|PMID:9556561 IDA F small nucleolar RNP protein YHR089C gene taxon:4932 20021105 SGD
+SGD S000001131 GAR1 GO:0000154 SGD_REF:S000058443|PMID:10690410 TAS P small nucleolar RNP protein YHR089C gene taxon:4932 20010118 SGD
+SGD S000001131 GAR1 GO:0006365 SGD_REF:S000058443|PMID:10690410 TAS P small nucleolar RNP protein YHR089C gene taxon:4932 20010118 SGD
+SGD S000004924 GAS1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C cell surface glycoprotein 115-120 kDa YMR307W|CWH52|GGP1 gene taxon:4932 20041203 SGD
+SGD S000004924 GAS1 GO:0005886 SGD_REF:S000047955|PMID:1824714 IDA C cell surface glycoprotein 115-120 kDa YMR307W|CWH52|GGP1 gene taxon:4932 20020904 SGD
+SGD S000004924 GAS1 GO:0009277 SGD_REF:S000081097|PMID:15781460 IDA C cell surface glycoprotein 115-120 kDa YMR307W|CWH52|GGP1 gene taxon:4932 20050601 SGD
+SGD S000004924 GAS1 GO:0042124 SGD_REF:S000050023|PMID:10809732 IDA F cell surface glycoprotein 115-120 kDa YMR307W|CWH52|GGP1 gene taxon:4932 20020904 SGD
+SGD S000004924 GAS1 GO:0042124 SGD_REF:S000077188|PMID:15355340 IDA F cell surface glycoprotein 115-120 kDa YMR307W|CWH52|GGP1 gene taxon:4932 20050915 SGD
+SGD S000004924 GAS1 GO:0007047 SGD_REF:S000044652|PMID:9515908 IMP P cell surface glycoprotein 115-120 kDa YMR307W|CWH52|GGP1 gene taxon:4932 20020904 SGD
+SGD S000004924 GAS1 GO:0030447 SGD_REF:S000080384|PMID:15645503 IMP P cell surface glycoprotein 115-120 kDa YMR307W|CWH52|GGP1 gene taxon:4932 20050621 SGD
+SGD S000004335 GAS2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YLR343W gene taxon:4932 20031028 SGD
+SGD S000004335 GAS2 GO:0042124 SGD_REF:S000063190|PMID:10769178 ISS SGD:S000004924 F YLR343W gene taxon:4932 20040701 SGD
+SGD S000004335 GAS2 GO:0000004 SGD_REF:S000069584 ND P YLR343W gene taxon:4932 20040701 SGD
+SGD S000004828 GAS3 GO:0009277 SGD_REF:S000040179|PMID:10383953 IDA C YMR215W gene taxon:4932 20020617 SGD
+SGD S000004828 GAS3 GO:0009277 SGD_REF:S000081097|PMID:15781460 IDA C YMR215W gene taxon:4932 20050601 SGD
+SGD S000004828 GAS3 GO:0042124 SGD_REF:S000063190|PMID:10769178 ISS SGD:S000004924 F YMR215W gene taxon:4932 20040701 SGD
+SGD S000004828 GAS3 GO:0000004 SGD_REF:S000069584 ND P YMR215W gene taxon:4932 20040701 SGD
+SGD S000005492 GAS4 GO:0009277 SGD_REF:S000040179|PMID:10383953 IDA C YOL132W gene taxon:4932 20020617 SGD
+SGD S000005492 GAS4 GO:0042124 SGD_REF:S000063190|PMID:10769178 ISS SGD:S000004924 F YOL132W gene taxon:4932 20040701 SGD
+SGD S000005492 GAS4 GO:0000004 SGD_REF:S000069584 ND P YOL132W gene taxon:4932 20040701 SGD
+SGD S000005390 GAS5 GO:0009277 SGD_REF:S000040179|PMID:10383953 IDA C YOL030W gene taxon:4932 20020617 SGD
+SGD S000005390 GAS5 GO:0009277 SGD_REF:S000081097|PMID:15781460 IDA C YOL030W gene taxon:4932 20050601 SGD
+SGD S000005390 GAS5 GO:0042124 SGD_REF:S000063190|PMID:10769178 ISS SGD:S000004924 F YOL030W gene taxon:4932 20040701 SGD
+SGD S000005390 GAS5 GO:0000004 SGD_REF:S000069584 ND P YOL030W gene taxon:4932 20040701 SGD
+SGD S000001873 GAT1 GO:0005634 SGD_REF:S000069962|PMID:12062797 TAS C transcriptional activator with GATA-1-type Zn finger DNA-binding motif YFL021W|MEP80|NIL1 gene taxon:4932 20020819 SGD
+SGD S000001873 GAT1 GO:0005634 SGD_REF:S000055810|PMID:10799523 IDA C transcriptional activator with GATA-1-type Zn finger DNA-binding motif YFL021W|MEP80|NIL1 gene taxon:4932 20050926 SGD
+SGD S000001873 GAT1 GO:0005829 SGD_REF:S000055810|PMID:10799523 IDA C transcriptional activator with GATA-1-type Zn finger DNA-binding motif YFL021W|MEP80|NIL1 gene taxon:4932 20050926 SGD
+SGD S000001873 GAT1 GO:0003704 SGD_REF:S000055992|PMID:8622686 IDA F transcriptional activator with GATA-1-type Zn finger DNA-binding motif YFL021W|MEP80|NIL1 gene taxon:4932 20020927 SGD
+SGD S000001873 GAT1 GO:0016563 SGD_REF:S000059392|PMID:11133970 TAS F transcriptional activator with GATA-1-type Zn finger DNA-binding motif YFL021W|MEP80|NIL1 gene taxon:4932 20021202 SGD
+SGD S000001873 GAT1 GO:0016563 SGD_REF:S000060713|PMID:11409177 IDA F transcriptional activator with GATA-1-type Zn finger DNA-binding motif YFL021W|MEP80|NIL1 gene taxon:4932 20050117 SGD
+SGD S000001873 GAT1 GO:0006367 SGD_REF:S000055992|PMID:8622686 IDA P transcriptional activator with GATA-1-type Zn finger DNA-binding motif YFL021W|MEP80|NIL1 gene taxon:4932 20020927 SGD
+SGD S000001873 GAT1 GO:0006808 SGD_REF:S000055992|PMID:8622686 IMP P transcriptional activator with GATA-1-type Zn finger DNA-binding motif YFL021W|MEP80|NIL1 gene taxon:4932 20020927 SGD
+SGD S000001873 GAT1 GO:0045941 SGD_REF:S000060713|PMID:11409177 IDA P transcriptional activator with GATA-1-type Zn finger DNA-binding motif YFL021W|MEP80|NIL1 gene taxon:4932 20050117 SGD
+SGD S000004744 GAT2 GO:0005634 SGD_REF:S000056382|PMID:10392447 ISS C YMR136W gene taxon:4932 20020215 SGD
+SGD S000004744 GAT2 GO:0003700 SGD_REF:S000056382|PMID:10392447 ISS F YMR136W gene taxon:4932 20020215 SGD
+SGD S000004744 GAT2 GO:0006350 SGD_REF:S000056382|PMID:10392447 ISS P YMR136W gene taxon:4932 20020215 SGD
+SGD S000004003 GAT3 GO:0005634 SGD_REF:S000056382|PMID:10392447 ISS C YLR013W gene taxon:4932 20020215 SGD
+SGD S000004003 GAT3 GO:0003700 SGD_REF:S000056382|PMID:10392447 ISS F YLR013W gene taxon:4932 20020215 SGD
+SGD S000004003 GAT3 GO:0006350 SGD_REF:S000056382|PMID:10392447 ISS P YLR013W gene taxon:4932 20020215 SGD
+SGD S000001452 GAT4 GO:0005634 SGD_REF:S000056382|PMID:10392447 ISS C YIR013C gene taxon:4932 20020215 SGD
+SGD S000001452 GAT4 GO:0003700 SGD_REF:S000056382|PMID:10392447 ISS F YIR013C gene taxon:4932 20020215 SGD
+SGD S000001452 GAT4 GO:0006350 SGD_REF:S000056382|PMID:10392447 ISS P YIR013C gene taxon:4932 20020215 SGD
+SGD S000000517 GBP2 GO:0005634 SGD_REF:S000042934|PMID:7777547 IPI C contains RNA recognition motifs YCL011C|RLF6 gene taxon:4932 20021002 SGD
+SGD S000000517 GBP2 GO:0005634 SGD_REF:S000072869|PMID:12634846 IDA C contains RNA recognition motifs YCL011C|RLF6 gene taxon:4932 20030424 SGD
+SGD S000000517 GBP2 GO:0003723 SGD_REF:S000072869|PMID:12634846 IDA F contains RNA recognition motifs YCL011C|RLF6 gene taxon:4932 20030424 SGD
+SGD S000000517 GBP2 GO:0042162 SGD_REF:S000042934|PMID:7777547 IPI F contains RNA recognition motifs YCL011C|RLF6 gene taxon:4932 20021002 SGD
+SGD S000000517 GBP2 GO:0042162 SGD_REF:S000042934|PMID:7777547 IMP F contains RNA recognition motifs YCL011C|RLF6 gene taxon:4932 20021002 SGD
+SGD S000000517 GBP2 GO:0000723 SGD_REF:S000072779|PMID:12519786 IGI SGD:S000002379 P contains RNA recognition motifs YCL011C|RLF6 gene taxon:4932 20030324 SGD
+SGD S000000517 GBP2 GO:0000723 SGD_REF:S000072779|PMID:12519786 IMP P contains RNA recognition motifs YCL011C|RLF6 gene taxon:4932 20030324 SGD
+SGD S000000517 GBP2 GO:0000723 SGD_REF:S000072779|PMID:12519786 IDA P contains RNA recognition motifs YCL011C|RLF6 gene taxon:4932 20030324 SGD
+SGD S000000517 GBP2 GO:0016973 SGD_REF:S000072869|PMID:12634846 IGI P contains RNA recognition motifs YCL011C|RLF6 gene taxon:4932 20030424 SGD
+SGD S000000517 GBP2 GO:0016973 SGD_REF:S000072869|PMID:12634846 IPI P contains RNA recognition motifs YCL011C|RLF6 gene taxon:4932 20030424 SGD
+SGD S000005786 GCD1 GO:0005840 SGD_REF:S000058753|PMID:9841679 TAS C gamma subunit, negative regulator in the general control of amino acid biosynthesis, translation initiation factor eIF2B subunit YOR260W|TRA3 gene taxon:4932 20010124 SGD
+SGD S000005786 GCD1 GO:0005851 SGD_REF:S000049992|PMID:8336705 IDA C gamma subunit, negative regulator in the general control of amino acid biosynthesis, translation initiation factor eIF2B subunit YOR260W|TRA3 gene taxon:4932 20020802 SGD
+SGD S000005786 GCD1 GO:0003743 SGD_REF:S000058753|PMID:9841679 TAS F gamma subunit, negative regulator in the general control of amino acid biosynthesis, translation initiation factor eIF2B subunit YOR260W|TRA3 gene taxon:4932 20010124 SGD
+SGD S000005786 GCD1 contributes_to GO:0005085 SGD_REF:S000048920|PMID:9472020 IDA F gamma subunit, negative regulator in the general control of amino acid biosynthesis, translation initiation factor eIF2B subunit YOR260W|TRA3 gene taxon:4932 20050722 SGD
+SGD S000005786 GCD1 contributes_to GO:0005085 SGD_REF:S000048920|PMID:9472020 IPI SGD:S000002619 F gamma subunit, negative regulator in the general control of amino acid biosynthesis, translation initiation factor eIF2B subunit YOR260W|TRA3 gene taxon:4932 20050722 SGD
+SGD S000005786 GCD1 GO:0006413 SGD_REF:S000058753|PMID:9841679 TAS P gamma subunit, negative regulator in the general control of amino acid biosynthesis, translation initiation factor eIF2B subunit YOR260W|TRA3 gene taxon:4932 20010124 SGD
+SGD S000005006 GCD10 GO:0005634 SGD_REF:S000050613|PMID:9851972 IDA C RNA-binding protein, subunit of tRNA(1-methyladenosine) methyltransferase, along with Gcd14p YNL062C|TRM6 gene taxon:4932 20020717 SGD
+SGD S000005006 GCD10 GO:0000049 SGD_REF:S000049268|PMID:10779558 IDA F RNA-binding protein, subunit of tRNA(1-methyladenosine) methyltransferase, along with Gcd14p YNL062C|TRM6 gene taxon:4932 20050701 SGD
+SGD S000005006 GCD10 contributes_to GO:0016429 SGD_REF:S000049268|PMID:10779558 IDA F RNA-binding protein, subunit of tRNA(1-methyladenosine) methyltransferase, along with Gcd14p YNL062C|TRM6 gene taxon:4932 20050701 SGD
+SGD S000005006 GCD10 contributes_to GO:0016429 SGD_REF:S000049268|PMID:10779558 IPI SGD:S000003661 F RNA-binding protein, subunit of tRNA(1-methyladenosine) methyltransferase, along with Gcd14p YNL062C|TRM6 gene taxon:4932 20050701 SGD
+SGD S000005006 GCD10 GO:0006413 SGD_REF:S000058753|PMID:9841679 TAS P RNA-binding protein, subunit of tRNA(1-methyladenosine) methyltransferase, along with Gcd14p YNL062C|TRM6 gene taxon:4932 20010124 SGD
+SGD S000005006 GCD10 GO:0030488 SGD_REF:S000049268|PMID:10779558 IDA P RNA-binding protein, subunit of tRNA(1-methyladenosine) methyltransferase, along with Gcd14p YNL062C|TRM6 gene taxon:4932 20020717 SGD
+SGD S000000827 GCD11 GO:0005840 SGD_REF:S000058753|PMID:9841679 TAS C translational initiation factor eIF-2 gamma subunit YER025W|SUI4|eIF2 gamma gene taxon:4932 20010124 SGD
+SGD S000000827 GCD11 GO:0005850 SGD_REF:S000048270|PMID:8417348 IMP C translational initiation factor eIF-2 gamma subunit YER025W|SUI4|eIF2 gamma gene taxon:4932 20050105 SGD
+SGD S000000827 GCD11 GO:0005850 SGD_REF:S000048270|PMID:8417348 ISS C translational initiation factor eIF-2 gamma subunit YER025W|SUI4|eIF2 gamma gene taxon:4932 20050105 SGD
+SGD S000000827 GCD11 GO:0043614 SGD_REF:S000082127|PMID:11018020 IDA C translational initiation factor eIF-2 gamma subunit YER025W|SUI4|eIF2 gamma gene taxon:4932 20060427 SGD
+SGD S000000827 GCD11 GO:0003743 SGD_REF:S000058753|PMID:9841679 TAS F translational initiation factor eIF-2 gamma subunit YER025W|SUI4|eIF2 gamma gene taxon:4932 20010124 SGD
+SGD S000000827 GCD11 GO:0006413 SGD_REF:S000058753|PMID:9841679 TAS P translational initiation factor eIF-2 gamma subunit YER025W|SUI4|eIF2 gamma gene taxon:4932 20010124 SGD
+SGD S000003661 GCD14 GO:0005634 SGD_REF:S000050613|PMID:9851972 IDA C subunit of tRNA(1-methyladenosine) methyltransferase, along with Gcd10p YJL125C|TRM61 gene taxon:4932 20020717 SGD
+SGD S000003661 GCD14 contributes_to GO:0016429 SGD_REF:S000049268|PMID:10779558 IDA F subunit of tRNA(1-methyladenosine) methyltransferase, along with Gcd10p YJL125C|TRM61 gene taxon:4932 20050701 SGD
+SGD S000003661 GCD14 contributes_to GO:0016429 SGD_REF:S000049268|PMID:10779558 IPI SGD:S000005006 F subunit of tRNA(1-methyladenosine) methyltransferase, along with Gcd10p YJL125C|TRM61 gene taxon:4932 20050701 SGD
+SGD S000003661 GCD14 contributes_to GO:0016429 SGD_REF:S000049268|PMID:10779558 IMP F subunit of tRNA(1-methyladenosine) methyltransferase, along with Gcd10p YJL125C|TRM61 gene taxon:4932 20050701 SGD
+SGD S000003661 GCD14 GO:0030488 SGD_REF:S000049268|PMID:10779558 IDA P subunit of tRNA(1-methyladenosine) methyltransferase, along with Gcd10p YJL125C|TRM61 gene taxon:4932 20020717 SGD
+SGD S000003315 GCD2 GO:0005840 SGD_REF:S000058753|PMID:9841679 TAS C 71 kDa subunit (delta), translation initiation factor eIF2B subunit, translational repressor of GCN4 protein YGR083C|GCD12 gene taxon:4932 20010124 SGD
+SGD S000003315 GCD2 GO:0005851 SGD_REF:S000049992|PMID:8336705 IDA C 71 kDa subunit (delta), translation initiation factor eIF2B subunit, translational repressor of GCN4 protein YGR083C|GCD12 gene taxon:4932 20020802 SGD
+SGD S000003315 GCD2 GO:0003743 SGD_REF:S000058753|PMID:9841679 TAS F 71 kDa subunit (delta), translation initiation factor eIF2B subunit, translational repressor of GCN4 protein YGR083C|GCD12 gene taxon:4932 20010124 SGD
+SGD S000003315 GCD2 GO:0030234 SGD_REF:S000043342|PMID:8887689 IGI SGD:S000003315|SGD:S000001734 F 71 kDa subunit (delta), translation initiation factor eIF2B subunit, translational repressor of GCN4 protein YGR083C|GCD12 gene taxon:4932 20050722 SGD
+SGD S000003315 GCD2 GO:0030234 SGD_REF:S000043342|PMID:8887689 IMP F 71 kDa subunit (delta), translation initiation factor eIF2B subunit, translational repressor of GCN4 protein YGR083C|GCD12 gene taxon:4932 20050722 SGD
+SGD S000003315 GCD2 GO:0006413 SGD_REF:S000058753|PMID:9841679 TAS P 71 kDa subunit (delta), translation initiation factor eIF2B subunit, translational repressor of GCN4 protein YGR083C|GCD12 gene taxon:4932 20010124 SGD
+SGD S000029174 GCD3 GO:0005840 SGD_REF:S000058753|PMID:9841679 TAS C gene taxon:4932 20010124 SGD
+SGD S000029174 GCD3 GO:0003743 SGD_REF:S000058753|PMID:9841679 TAS F gene taxon:4932 20010124 SGD
+SGD S000029174 GCD3 GO:0006413 SGD_REF:S000058753|PMID:9841679 TAS P gene taxon:4932 20010124 SGD
+SGD S000002619 GCD6 GO:0005840 SGD_REF:S000058753|PMID:9841679 TAS C translation initiation factor eIF-2B epsilon subunit YDR211W gene taxon:4932 20010124 SGD
+SGD S000002619 GCD6 GO:0005851 SGD_REF:S000049992|PMID:8336705 IDA C translation initiation factor eIF-2B epsilon subunit YDR211W gene taxon:4932 20020802 SGD
+SGD S000002619 GCD6 GO:0043614 SGD_REF:S000082127|PMID:11018020 IDA C translation initiation factor eIF-2B epsilon subunit YDR211W gene taxon:4932 20060427 SGD
+SGD S000002619 GCD6 GO:0003743 SGD_REF:S000058753|PMID:9841679 TAS F translation initiation factor eIF-2B epsilon subunit YDR211W gene taxon:4932 20010124 SGD
+SGD S000002619 GCD6 GO:0005085 SGD_REF:S000048920|PMID:9472020 IDA F translation initiation factor eIF-2B epsilon subunit YDR211W gene taxon:4932 20050722 SGD
+SGD S000002619 GCD6 GO:0006413 SGD_REF:S000058753|PMID:9841679 TAS P translation initiation factor eIF-2B epsilon subunit YDR211W gene taxon:4932 20010124 SGD
+SGD S000004282 GCD7 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C negative regulator of GCN4 expression, translation initiation factor eIF2B subunit YLR291C gene taxon:4932 20040928 SGD
+SGD S000004282 GCD7 GO:0005840 SGD_REF:S000058753|PMID:9841679 TAS C negative regulator of GCN4 expression, translation initiation factor eIF2B subunit YLR291C gene taxon:4932 20010124 SGD
+SGD S000004282 GCD7 GO:0005851 SGD_REF:S000049992|PMID:8336705 IDA C negative regulator of GCN4 expression, translation initiation factor eIF2B subunit YLR291C gene taxon:4932 20020802 SGD
+SGD S000004282 GCD7 GO:0003743 SGD_REF:S000058753|PMID:9841679 TAS F negative regulator of GCN4 expression, translation initiation factor eIF2B subunit YLR291C gene taxon:4932 20010124 SGD
+SGD S000004282 GCD7 GO:0030234 SGD_REF:S000043342|PMID:8887689 IGI SGD:S000003315|SGD:S000001734 F negative regulator of GCN4 expression, translation initiation factor eIF2B subunit YLR291C gene taxon:4932 20050722 SGD
+SGD S000004282 GCD7 GO:0030234 SGD_REF:S000043342|PMID:8887689 IMP F negative regulator of GCN4 expression, translation initiation factor eIF2B subunit YLR291C gene taxon:4932 20050722 SGD
+SGD S000004282 GCD7 GO:0006413 SGD_REF:S000058753|PMID:9841679 TAS P negative regulator of GCN4 expression, translation initiation factor eIF2B subunit YLR291C gene taxon:4932 20010124 SGD
+SGD S000003163 GCN1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C translational activator of GCN4 through activation of GCN2 in response to starvation YGL195W gene taxon:4932 20040928 SGD
+SGD S000003163 GCN1 GO:0005829 SGD_REF:S000049352|PMID:9234705 IDA C translational activator of GCN4 through activation of GCN2 in response to starvation YGL195W gene taxon:4932 20020802 SGD
+SGD S000003163 GCN1 GO:0005830 SGD_REF:S000049352|PMID:9234705 IDA C translational activator of GCN4 through activation of GCN2 in response to starvation YGL195W gene taxon:4932 20020802 SGD
+SGD S000003163 GCN1 GO:0005554 SGD_REF:S000069584 ND F translational activator of GCN4 through activation of GCN2 in response to starvation YGL195W gene taxon:4932 20020802 SGD
+SGD S000003163 GCN1 GO:0006448 SGD_REF:S000049352|PMID:9234705 IMP P translational activator of GCN4 through activation of GCN2 in response to starvation YGL195W gene taxon:4932 20020802 SGD
+SGD S000003163 GCN1 GO:0006448 SGD_REF:S000049352|PMID:9234705 IPI P translational activator of GCN4 through activation of GCN2 in response to starvation YGL195W gene taxon:4932 20020802 SGD
+SGD S000002691 GCN2 GO:0005830 SGD_REF:S000054605|PMID:2038314 IDA C eukaryotic initiation factor 2 alpha (eIF2-alpha) kinase YDR283C|AAS1 gene taxon:4932 20020802 SGD
+SGD S000002691 GCN2 GO:0004672 SGD_REF:S000040728|PMID:2188100 IDA F eukaryotic initiation factor 2 alpha (eIF2-alpha) kinase YDR283C|AAS1 gene taxon:4932 20020802 SGD
+SGD S000002691 GCN2 GO:0004694 SGD_REF:S000043396|PMID:8798780 IDA F eukaryotic initiation factor 2 alpha (eIF2-alpha) kinase YDR283C|AAS1 gene taxon:4932 20050105 SGD
+SGD S000002691 GCN2 GO:0006446 SGD_REF:S000054749|PMID:7934812 IDA P eukaryotic initiation factor 2 alpha (eIF2-alpha) kinase YDR283C|AAS1 gene taxon:4932 20020802 SGD
+SGD S000002691 GCN2 GO:0006468 SGD_REF:S000040728|PMID:2188100 IDA P eukaryotic initiation factor 2 alpha (eIF2-alpha) kinase YDR283C|AAS1 gene taxon:4932 20020802 SGD
+SGD S000002691 GCN2 GO:0008652 SGD_REF:S000045094|PMID:6351059 IMP P eukaryotic initiation factor 2 alpha (eIF2-alpha) kinase YDR283C|AAS1 gene taxon:4932 20020802 SGD
+SGD S000001905 GCN20 GO:0005829 SGD_REF:S000049352|PMID:9234705 IPI C ATP-binding cassette (ABC) family YFR009W gene taxon:4932 20020711 SGD
+SGD S000001905 GCN20 GO:0005830 SGD_REF:S000049352|PMID:9234705 IDA C ATP-binding cassette (ABC) family YFR009W gene taxon:4932 20020711 SGD
+SGD S000001905 GCN20 GO:0016887 SGD_REF:S000047195|PMID:7621831 ISS F ATP-binding cassette (ABC) family YFR009W gene taxon:4932 20050310 SGD
+SGD S000001905 GCN20 GO:0006448 SGD_REF:S000049352|PMID:9234705 IMP P ATP-binding cassette (ABC) family YFR009W gene taxon:4932 20020711 SGD
+SGD S000001905 GCN20 GO:0006448 SGD_REF:S000049352|PMID:9234705 IPI P ATP-binding cassette (ABC) family YFR009W gene taxon:4932 20020711 SGD
+SGD S000001734 GCN3 GO:0005851 SGD_REF:S000049992|PMID:8336705 IDA C eIF2B 34 kDa alpha subunit YKR026C|AAS2 gene taxon:4932 20020802 SGD
+SGD S000001734 GCN3 GO:0043614 SGD_REF:S000082127|PMID:11018020 IDA C eIF2B 34 kDa alpha subunit YKR026C|AAS2 gene taxon:4932 20060427 SGD
+SGD S000001734 GCN3 GO:0003743 SGD_REF:S000049992|PMID:8336705 IDA F eIF2B 34 kDa alpha subunit YKR026C|AAS2 gene taxon:4932 20020802 SGD
+SGD S000001734 GCN3 GO:0030234 SGD_REF:S000043342|PMID:8887689 IGI SGD:S000003315|SGD:S000001734 F eIF2B 34 kDa alpha subunit YKR026C|AAS2 gene taxon:4932 20050722 SGD
+SGD S000001734 GCN3 GO:0030234 SGD_REF:S000043342|PMID:8887689 IMP F eIF2B 34 kDa alpha subunit YKR026C|AAS2 gene taxon:4932 20050722 SGD
+SGD S000001734 GCN3 GO:0006413 SGD_REF:S000049992|PMID:8336705 IDA P eIF2B 34 kDa alpha subunit YKR026C|AAS2 gene taxon:4932 20020802 SGD
+SGD S000000735 GCN4 GO:0005634 SGD_REF:S000043528|PMID:2649888 IPI C transcriptional activator of amino acid biosynthetic genes YEL009C|AAS3|ARG9 gene taxon:4932 20020213 SGD
+SGD S000000735 GCN4 GO:0003677 SGD_REF:S000045435|PMID:3532321 IDA F transcriptional activator of amino acid biosynthetic genes YEL009C|AAS3|ARG9 gene taxon:4932 20020402 SGD
+SGD S000000735 GCN4 GO:0016563 SGD_REF:S000045832|PMID:9268289 TAS F transcriptional activator of amino acid biosynthetic genes YEL009C|AAS3|ARG9 gene taxon:4932 20020213 SGD
+SGD S000000735 GCN4 GO:0006357 SGD_REF:S000061212|PMID:11390663 IMP P transcriptional activator of amino acid biosynthetic genes YEL009C|AAS3|ARG9 gene taxon:4932 20020402 SGD
+SGD S000000735 GCN4 GO:0008652 SGD_REF:S000045832|PMID:9268289 TAS P transcriptional activator of amino acid biosynthetic genes YEL009C|AAS3|ARG9 gene taxon:4932 20020213 SGD
+SGD S000003484 GCN5 GO:0000124 SGD_REF:S000048255|PMID:9674426 IDA C histone acetyltransferase YGR252W|ADA4|SWI9 gene taxon:4932 20010221 SGD
+SGD S000003484 GCN5 GO:0005671 SGD_REF:S000042121|PMID:10490601 IPI C histone acetyltransferase YGR252W|ADA4|SWI9 gene taxon:4932 20031215 SGD
+SGD S000003484 GCN5 GO:0046695 SGD_REF:S000071997|PMID:12446794 IPI C histone acetyltransferase YGR252W|ADA4|SWI9 gene taxon:4932 20041024 SGD
+SGD S000003484 GCN5 GO:0003713 SGD_REF:S000079937|PMID:15075257 TAS F histone acetyltransferase YGR252W|ADA4|SWI9 gene taxon:4932 20050128 SGD
+SGD S000003484 GCN5 GO:0004402 SGD_REF:S000040759|PMID:10430845 TAS F histone acetyltransferase YGR252W|ADA4|SWI9 gene taxon:4932 20030115 SGD
+SGD S000003484 GCN5 GO:0016568 SGD_REF:S000061032|PMID:10839822 TAS P histone acetyltransferase YGR252W|ADA4|SWI9 gene taxon:4932 20020426 SGD
+SGD S000003484 GCN5 GO:0016573 SGD_REF:S000061032|PMID:10839822 TAS P histone acetyltransferase YGR252W|ADA4|SWI9 gene taxon:4932 20020426 SGD
+SGD S000005996 GCR1 GO:0005634 SGD_REF:S000052432|PMID:10455229 IC GO:0045944 C trans-acting positive regulator of the enolase and glyceraldehyde-3-phosphate dehydrogenase gene families YPL075W|LPF10 gene taxon:4932 20050721 SGD
+SGD S000005996 GCR1 GO:0005634 SGD_REF:S000055586|PMID:3547083 IC GO:0016563 C trans-acting positive regulator of the enolase and glyceraldehyde-3-phosphate dehydrogenase gene families YPL075W|LPF10 gene taxon:4932 20050721 SGD
+SGD S000005996 GCR1 GO:0003677 SGD_REF:S000043871|PMID:1946357 IDA F trans-acting positive regulator of the enolase and glyceraldehyde-3-phosphate dehydrogenase gene families YPL075W|LPF10 gene taxon:4932 20030402 SGD
+SGD S000005996 GCR1 GO:0016563 SGD_REF:S000055586|PMID:3547083 IMP F trans-acting positive regulator of the enolase and glyceraldehyde-3-phosphate dehydrogenase gene families YPL075W|LPF10 gene taxon:4932 20050721 SGD
+SGD S000005996 GCR1 GO:0045821 SGD_REF:S000055586|PMID:3547083 IMP P trans-acting positive regulator of the enolase and glyceraldehyde-3-phosphate dehydrogenase gene families YPL075W|LPF10 gene taxon:4932 20020826 SGD
+SGD S000005996 GCR1 GO:0045944 SGD_REF:S000052432|PMID:10455229 IMP P trans-acting positive regulator of the enolase and glyceraldehyde-3-phosphate dehydrogenase gene families YPL075W|LPF10 gene taxon:4932 20030402 SGD
+SGD S000005143 GCR2 GO:0005634 SGD_REF:S000052432|PMID:10455229 IC GO:0045944 C transcription factor YNL199C gene taxon:4932 20050721 SGD
+SGD S000005143 GCR2 GO:0005634 SGD_REF:S000045389|PMID:1508187 IC GO:0016563 C transcription factor YNL199C gene taxon:4932 20050721 SGD
+SGD S000005143 GCR2 GO:0016563 SGD_REF:S000045389|PMID:1508187 IDA F transcription factor YNL199C gene taxon:4932 20020823 SGD
+SGD S000005143 GCR2 GO:0045821 SGD_REF:S000048173|PMID:2247062 IMP P transcription factor YNL199C gene taxon:4932 20020826 SGD
+SGD S000005143 GCR2 GO:0045944 SGD_REF:S000052432|PMID:10455229 IMP P transcription factor YNL199C gene taxon:4932 20030402 SGD
+SGD S000002385 GCS1 GO:0005793 SGD_REF:S000053308|PMID:9927415 IPI C ADP-ribosylation factor GTPase-activating protein (ARF GAP) YDL226C gene taxon:4932 20010118 SGD
+SGD S000002385 GCS1 GO:0005856 SGD_REF:S000043756|PMID:10069805 IPI C ADP-ribosylation factor GTPase-activating protein (ARF GAP) YDL226C gene taxon:4932 20010118 SGD
+SGD S000002385 GCS1 GO:0005856 SGD_REF:S000043756|PMID:10069805 IMP C ADP-ribosylation factor GTPase-activating protein (ARF GAP) YDL226C gene taxon:4932 20010118 SGD
+SGD S000002385 GCS1 GO:0003779 SGD_REF:S000043756|PMID:10069805 IDA F ADP-ribosylation factor GTPase-activating protein (ARF GAP) YDL226C gene taxon:4932 20030509 SGD
+SGD S000002385 GCS1 GO:0008060 SGD_REF:S000053673|PMID:8816753 IDA F ADP-ribosylation factor GTPase-activating protein (ARF GAP) YDL226C gene taxon:4932 20010118 SGD
+SGD S000002385 GCS1 GO:0008060 SGD_REF:S000053673|PMID:8816753 ISS F ADP-ribosylation factor GTPase-activating protein (ARF GAP) YDL226C gene taxon:4932 20010118 SGD
+SGD S000002385 GCS1 GO:0006888 SGD_REF:S000053308|PMID:9927415 IMP P ADP-ribosylation factor GTPase-activating protein (ARF GAP) YDL226C gene taxon:4932 20010118 SGD
+SGD S000002385 GCS1 GO:0006888 SGD_REF:S000053308|PMID:9927415 IGI P ADP-ribosylation factor GTPase-activating protein (ARF GAP) YDL226C gene taxon:4932 20010118 SGD
+SGD S000002385 GCS1 GO:0006890 SGD_REF:S000053308|PMID:9927415 IMP P ADP-ribosylation factor GTPase-activating protein (ARF GAP) YDL226C gene taxon:4932 20010118 SGD
+SGD S000002385 GCS1 GO:0006890 SGD_REF:S000053308|PMID:9927415 IDA P ADP-ribosylation factor GTPase-activating protein (ARF GAP) YDL226C gene taxon:4932 20010118 SGD
+SGD S000002385 GCS1 GO:0006890 SGD_REF:S000053308|PMID:9927415 IGI P ADP-ribosylation factor GTPase-activating protein (ARF GAP) YDL226C gene taxon:4932 20010118 SGD
+SGD S000002385 GCS1 GO:0030037 SGD_REF:S000043756|PMID:10069805 IMP P ADP-ribosylation factor GTPase-activating protein (ARF GAP) YDL226C gene taxon:4932 20010705 SGD
+SGD S000002385 GCS1 GO:0030037 SGD_REF:S000043756|PMID:10069805 IGI P ADP-ribosylation factor GTPase-activating protein (ARF GAP) YDL226C gene taxon:4932 20010705 SGD
+SGD S000002385 GCS1 GO:0030037 SGD_REF:S000043756|PMID:10069805 IPI P ADP-ribosylation factor GTPase-activating protein (ARF GAP) YDL226C gene taxon:4932 20010705 SGD
+SGD S000002426 GCV1 GO:0005739 SGD_REF:S000043392|PMID:8852837 TAS C glycine decarboxylase complex T subunit YDR019C|GSD1 gene taxon:4932 20020930 SGD
+SGD S000002426 GCV1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C glycine decarboxylase complex T subunit YDR019C|GSD1 gene taxon:4932 20040928 SGD
+SGD S000002426 GCV1 GO:0005960 SGD_REF:S000052730|PMID:10187845 TAS C glycine decarboxylase complex T subunit YDR019C|GSD1 gene taxon:4932 20050104 SGD
+SGD S000002426 GCV1 contributes_to GO:0004375 SGD_REF:S000044427|PMID:9047339 ISS F glycine decarboxylase complex T subunit YDR019C|GSD1 gene taxon:4932 20020930 SGD
+SGD S000002426 GCV1 contributes_to GO:0004375 SGD_REF:S000044427|PMID:9047339 IMP F glycine decarboxylase complex T subunit YDR019C|GSD1 gene taxon:4932 20020930 SGD
+SGD S000002426 GCV1 GO:0006544 SGD_REF:S000044427|PMID:9047339 IMP P glycine decarboxylase complex T subunit YDR019C|GSD1 gene taxon:4932 20020927 SGD
+SGD S000002426 GCV1 GO:0006546 SGD_REF:S000044427|PMID:9047339 IC GO:0005960 P glycine decarboxylase complex T subunit YDR019C|GSD1 gene taxon:4932 20050211 SGD
+SGD S000002426 GCV1 GO:0006730 SGD_REF:S000056431|PMID:10871621 IGI P glycine decarboxylase complex T subunit YDR019C|GSD1 gene taxon:4932 20020930 SGD
+SGD S000002426 GCV1 GO:0006730 SGD_REF:S000056431|PMID:10871621 IMP P glycine decarboxylase complex T subunit YDR019C|GSD1 gene taxon:4932 20020930 SGD
+SGD S000004801 GCV2 GO:0005739 SGD_REF:S000070200 TAS C glycine cleavage system P subunit, glycine decarboxylase complex P subunit, glycine synthase P subunit YMR189W|GSD2 gene taxon:4932 20021101 SGD
+SGD S000004801 GCV2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C glycine cleavage system P subunit, glycine decarboxylase complex P subunit, glycine synthase P subunit YMR189W|GSD2 gene taxon:4932 20040928 SGD
+SGD S000004801 GCV2 GO:0005960 SGD_REF:S000052730|PMID:10187845 TAS C glycine cleavage system P subunit, glycine decarboxylase complex P subunit, glycine synthase P subunit YMR189W|GSD2 gene taxon:4932 20050104 SGD
+SGD S000004801 GCV2 contributes_to GO:0004375 SGD_REF:S000047381|PMID:8830251 IMP F glycine cleavage system P subunit, glycine decarboxylase complex P subunit, glycine synthase P subunit YMR189W|GSD2 gene taxon:4932 20020930 SGD
+SGD S000004801 GCV2 contributes_to GO:0004375 SGD_REF:S000047381|PMID:8830251 IEP F glycine cleavage system P subunit, glycine decarboxylase complex P subunit, glycine synthase P subunit YMR189W|GSD2 gene taxon:4932 20020930 SGD
+SGD S000004801 GCV2 GO:0006546 SGD_REF:S000052730|PMID:10187845 IC GO:0005960 P glycine cleavage system P subunit, glycine decarboxylase complex P subunit, glycine synthase P subunit YMR189W|GSD2 gene taxon:4932 20050214 SGD
+SGD S000004801 GCV2 GO:0006730 SGD_REF:S000056431|PMID:10871621 IGI P glycine cleavage system P subunit, glycine decarboxylase complex P subunit, glycine synthase P subunit YMR189W|GSD2 gene taxon:4932 20020930 SGD
+SGD S000004801 GCV2 GO:0006730 SGD_REF:S000056431|PMID:10871621 IMP P glycine cleavage system P subunit, glycine decarboxylase complex P subunit, glycine synthase P subunit YMR189W|GSD2 gene taxon:4932 20020930 SGD
+SGD S000000042 GCV3 GO:0005739 SGD_REF:S000070200 TAS C glycine cleavage system H-protein subunit YAL044C gene taxon:4932 20021101 SGD
+SGD S000000042 GCV3 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C glycine cleavage system H-protein subunit YAL044C gene taxon:4932 20040928 SGD
+SGD S000000042 GCV3 GO:0005960 SGD_REF:S000052730|PMID:10187845 TAS C glycine cleavage system H-protein subunit YAL044C gene taxon:4932 20050104 SGD
+SGD S000000042 GCV3 contributes_to GO:0004375 SGD_REF:S000042313|PMID:9020168 IMP F glycine cleavage system H-protein subunit YAL044C gene taxon:4932 20021101 SGD
+SGD S000000042 GCV3 contributes_to GO:0004375 SGD_REF:S000042313|PMID:9020168 ISS F glycine cleavage system H-protein subunit YAL044C gene taxon:4932 20021101 SGD
+SGD S000000042 GCV3 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P glycine cleavage system H-protein subunit YAL044C gene taxon:4932 20060227 SGD
+SGD S000000042 GCV3 GO:0006546 SGD_REF:S000052730|PMID:10187845 IC GO:0005960 P glycine cleavage system H-protein subunit YAL044C gene taxon:4932 20050214 SGD
+SGD S000000042 GCV3 GO:0006730 SGD_REF:S000056431|PMID:10871621 IGI P glycine cleavage system H-protein subunit YAL044C gene taxon:4932 20020930 SGD
+SGD S000000042 GCV3 GO:0006730 SGD_REF:S000056431|PMID:10871621 IMP P glycine cleavage system H-protein subunit YAL044C gene taxon:4932 20020930 SGD
+SGD S000005646 GCY1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YOR120W|GCY gene taxon:4932 20031028 SGD
+SGD S000005646 GCY1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YOR120W|GCY gene taxon:4932 20031028 SGD
+SGD S000005646 GCY1 GO:0004033 SGD_REF:S000049389|PMID:10818358 IDA F YOR120W|GCY gene taxon:4932 20021007 SGD
+SGD S000005646 GCY1 GO:0004033 SGD_REF:S000060122|PMID:11306085 ISS F YOR120W|GCY gene taxon:4932 20030912 SGD
+SGD S000005646 GCY1 GO:0009651 SGD_REF:S000041661|PMID:9038161 IEP P YOR120W|GCY gene taxon:4932 20021007 SGD
+SGD S000005646 GCY1 GO:0019568 SGD_REF:S000071519|PMID:12271459 IDA P YOR120W|GCY gene taxon:4932 20050131 SGD
+SGD S000005646 GCY1 GO:0042843 SGD_REF:S000071519|PMID:12271459 IDA P YOR120W|GCY gene taxon:4932 20050131 SGD
+SGD S000000768 GDA1 GO:0005794 SGD_REF:S000060740|PMID:11425802 TAS C guanosine diphosphatase of Golgi membrane YEL042W|GDPase gene taxon:4932 20020828 SGD
+SGD S000000768 GDA1 GO:0004382 SGD_REF:S000040023|PMID:7506254 IDA F guanosine diphosphatase of Golgi membrane YEL042W|GDPase gene taxon:4932 20030115 SGD
+SGD S000000768 GDA1 GO:0045134 SGD_REF:S000060740|PMID:11425802 IDA F guanosine diphosphatase of Golgi membrane YEL042W|GDPase gene taxon:4932 20020828 SGD
+SGD S000000768 GDA1 GO:0006486 SGD_REF:S000068842|PMID:11713596 TAS P guanosine diphosphatase of Golgi membrane YEL042W|GDPase gene taxon:4932 20020828 SGD
+SGD S000006388 GDB1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YPR184W gene taxon:4932 20031028 SGD
+SGD S000006388 GDB1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YPR184W gene taxon:4932 20040813 SGD
+SGD S000006388 GDB1 GO:0004134 SGD_REF:S000059249|PMID:11094287 IDA F YPR184W gene taxon:4932 20020813 SGD
+SGD S000006388 GDB1 GO:0004134 SGD_REF:S000059249|PMID:11094287 ISS F YPR184W gene taxon:4932 20020813 SGD
+SGD S000006388 GDB1 GO:0004134 SGD_REF:S000059249|PMID:11094287 IMP F YPR184W gene taxon:4932 20020813 SGD
+SGD S000006388 GDB1 GO:0004135 SGD_REF:S000059249|PMID:11094287 IDA F YPR184W gene taxon:4932 20020813 SGD
+SGD S000006388 GDB1 GO:0004135 SGD_REF:S000059249|PMID:11094287 ISS F YPR184W gene taxon:4932 20020813 SGD
+SGD S000006388 GDB1 GO:0004135 SGD_REF:S000059249|PMID:11094287 IMP F YPR184W gene taxon:4932 20020813 SGD
+SGD S000006388 GDB1 GO:0005980 SGD_REF:S000059249|PMID:11094287 IMP P YPR184W gene taxon:4932 20020813 SGD
+SGD S000006031 GDE1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YPL110C gene taxon:4932 20031028 SGD
+SGD S000006031 GDE1 GO:0047389 SGD_REF:S000086509|PMID:16141200 IMP F YPL110C gene taxon:4932 20050923 SGD
+SGD S000006031 GDE1 GO:0047389 SGD_REF:S000086509|PMID:16141200 ISS F YPL110C gene taxon:4932 20050923 SGD
+SGD S000006031 GDE1 GO:0046475 SGD_REF:S000086509|PMID:16141200 IMP P YPL110C gene taxon:4932 20050923 SGD
+SGD S000006031 GDE1 GO:0046475 SGD_REF:S000086509|PMID:16141200 ISS P YPL110C gene taxon:4932 20050923 SGD
+SGD S000005902 GDH1 GO:0005634 SGD_REF:S000063234|PMID:4126 IDA C NADP-specific glutamate dehydrogenase YOR375C|GDH-A|GDHA|URE1 gene taxon:4932 20021129 SGD
+SGD S000005902 GDH1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C NADP-specific glutamate dehydrogenase YOR375C|GDH-A|GDHA|URE1 gene taxon:4932 20020507 SGD
+SGD S000005902 GDH1 GO:0004354 SGD_REF:S000052640|PMID:2989290 IDA F NADP-specific glutamate dehydrogenase YOR375C|GDH-A|GDHA|URE1 gene taxon:4932 20020930 SGD
+SGD S000005902 GDH1 GO:0006537 SGD_REF:S000052640|PMID:2989290 IGI P NADP-specific glutamate dehydrogenase YOR375C|GDH-A|GDHA|URE1 gene taxon:4932 20031117 SGD
+SGD S000002374 GDH2 GO:0005625 SGD_REF:S000066220|PMID:11562373 IDA C NAD-dependent glutamate dehydrogenase YDL215C|GDH-B|GDHB gene taxon:4932 20021114 SGD
+SGD S000002374 GDH2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C NAD-dependent glutamate dehydrogenase YDL215C|GDH-B|GDHB gene taxon:4932 20040928 SGD
+SGD S000002374 GDH2 GO:0004352 SGD_REF:S000053418|PMID:1975578 ISS F NAD-dependent glutamate dehydrogenase YDL215C|GDH-B|GDHB gene taxon:4932 20020930 SGD
+SGD S000002374 GDH2 GO:0004352 SGD_REF:S000053418|PMID:1975578 IMP F NAD-dependent glutamate dehydrogenase YDL215C|GDH-B|GDHB gene taxon:4932 20020930 SGD
+SGD S000002374 GDH2 GO:0006807 SGD_REF:S000053418|PMID:1975578 IMP P NAD-dependent glutamate dehydrogenase YDL215C|GDH-B|GDHB gene taxon:4932 20020930 SGD
+SGD S000000058 GDH3 GO:0005625 SGD_REF:S000066220|PMID:11562373 IDA C NADP-linked glutamate dehydrogenase YAL062W|FUN51 gene taxon:4932 20021114 SGD
+SGD S000000058 GDH3 GO:0005634 SGD_REF:S000063234|PMID:4126 IDA C NADP-linked glutamate dehydrogenase YAL062W|FUN51 gene taxon:4932 20021129 SGD
+SGD S000000058 GDH3 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C NADP-linked glutamate dehydrogenase YAL062W|FUN51 gene taxon:4932 20040928 SGD
+SGD S000000058 GDH3 GO:0004352 SGD_REF:S000049665|PMID:9287019 ISS F NADP-linked glutamate dehydrogenase YAL062W|FUN51 gene taxon:4932 20020930 SGD
+SGD S000000058 GDH3 GO:0004352 SGD_REF:S000049665|PMID:9287019 IMP F NADP-linked glutamate dehydrogenase YAL062W|FUN51 gene taxon:4932 20020930 SGD
+SGD S000000058 GDH3 GO:0006537 SGD_REF:S000049665|PMID:9287019 IGI P NADP-linked glutamate dehydrogenase YAL062W|FUN51 gene taxon:4932 20020930 SGD
+SGD S000000058 GDH3 GO:0006537 SGD_REF:S000049665|PMID:9287019 IMP P NADP-linked glutamate dehydrogenase YAL062W|FUN51 gene taxon:4932 20020930 SGD
+SGD S000000938 GDI1 GO:0005624 SGD_REF:S000045858|PMID:10329679 IDA C GDP dissociation inhibitor YER136W|SEC19 gene taxon:4932 20020731 SGD
+SGD S000000938 GDI1 GO:0005625 SGD_REF:S000045858|PMID:10329679 IDA C GDP dissociation inhibitor YER136W|SEC19 gene taxon:4932 20020731 SGD
+SGD S000000938 GDI1 GO:0005093 SGD_REF:S000043249|PMID:8157010 IDA F GDP dissociation inhibitor YER136W|SEC19 gene taxon:4932 20020731 SGD
+SGD S000000938 GDI1 GO:0016192 SGD_REF:S000043249|PMID:8157010 IMP P GDP dissociation inhibitor YER136W|SEC19 gene taxon:4932 20020731 SGD
+SGD S000005882 GDS1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YOR355W gene taxon:4932 20031028 SGD
+SGD S000005882 GDS1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YOR355W gene taxon:4932 20031028 SGD
+SGD S000005882 GDS1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YOR355W gene taxon:4932 20040813 SGD
+SGD S000005882 GDS1 GO:0005554 SGD_REF:S000069584 ND F YOR355W gene taxon:4932 20020930 SGD
+SGD S000005882 GDS1 GO:0009060 SGD_REF:S000048397|PMID:8750239 IGI P YOR355W gene taxon:4932 20020930 SGD
+SGD S000005882 GDS1 GO:0009060 SGD_REF:S000048397|PMID:8750239 IMP P YOR355W gene taxon:4932 20020930 SGD
+SGD S000003792 GEA1 GO:0000137 SGD_REF:S000060854|PMID:11294905 IDA C GDP/GTP exchange factor YJR031C gene taxon:4932 20050104 SGD
+SGD S000003792 GEA1 GO:0005798 SGD_REF:S000048358|PMID:8945477 IPI C GDP/GTP exchange factor YJR031C gene taxon:4932 20010118 SGD
+SGD S000003792 GEA1 GO:0005086 SGD_REF:S000048358|PMID:8945477 TAS F GDP/GTP exchange factor YJR031C gene taxon:4932 20020808 SGD
+SGD S000003792 GEA1 GO:0006888 SGD_REF:S000048358|PMID:8945477 IMP P GDP/GTP exchange factor YJR031C gene taxon:4932 20010118 SGD
+SGD S000003792 GEA1 GO:0006890 SGD_REF:S000060854|PMID:11294905 IGI SGD:S000000748 P GDP/GTP exchange factor YJR031C gene taxon:4932 20050104 SGD
+SGD S000003792 GEA1 GO:0006891 SGD_REF:S000048358|PMID:8945477 IPI P GDP/GTP exchange factor YJR031C gene taxon:4932 20010118 SGD
+SGD S000003792 GEA1 GO:0030036 SGD_REF:S000075147|PMID:14668359 IGI SGD:S000005648 P GDP/GTP exchange factor YJR031C gene taxon:4932 20050103 SGD
+SGD S000000748 GEA2 GO:0000137 SGD_REF:S000060854|PMID:11294905 IDA C ARF GTP/GDP exchange factor YEL022W gene taxon:4932 20050104 SGD
+SGD S000000748 GEA2 GO:0005798 SGD_REF:S000048358|PMID:8945477 TAS C ARF GTP/GDP exchange factor YEL022W gene taxon:4932 20010118 SGD
+SGD S000000748 GEA2 GO:0005086 SGD_REF:S000048358|PMID:8945477 TAS F ARF GTP/GDP exchange factor YEL022W gene taxon:4932 20020808 SGD
+SGD S000000748 GEA2 GO:0006888 SGD_REF:S000048358|PMID:8945477 TAS P ARF GTP/GDP exchange factor YEL022W gene taxon:4932 20010118 SGD
+SGD S000000748 GEA2 GO:0006890 SGD_REF:S000060854|PMID:11294905 IGI SGD:S000005231 P ARF GTP/GDP exchange factor YEL022W gene taxon:4932 20050104 SGD
+SGD S000000748 GEA2 GO:0006891 SGD_REF:S000048358|PMID:8945477 TAS P ARF GTP/GDP exchange factor YEL022W gene taxon:4932 20010118 SGD
+SGD S000000748 GEA2 GO:0030036 SGD_REF:S000075147|PMID:14668359 IGI SGD:S000005648 P ARF GTP/GDP exchange factor YEL022W gene taxon:4932 20050103 SGD
+SGD S000003801 GEF1 GO:0005768 SGD_REF:S000080895|PMID:15710404 IDA C transport protein involved in intracellular iron metabolism (putative) YJR040W|CLC gene taxon:4932 20050318 SGD
+SGD S000003801 GEF1 GO:0005794 SGD_REF:S000080895|PMID:15710404 IDA C transport protein involved in intracellular iron metabolism (putative) YJR040W|CLC gene taxon:4932 20050318 SGD
+SGD S000003801 GEF1 GO:0005798 SGD_REF:S000054326|PMID:9520490 TAS C transport protein involved in intracellular iron metabolism (putative) YJR040W|CLC gene taxon:4932 20020913 SGD
+SGD S000003801 GEF1 GO:0005247 SGD_REF:S000070078|PMID:12074596 IDA F transport protein involved in intracellular iron metabolism (putative) YJR040W|CLC gene taxon:4932 20021003 SGD
+SGD S000003801 GEF1 GO:0006878 SGD_REF:S000044014|PMID:9614122 IMP P transport protein involved in intracellular iron metabolism (putative) YJR040W|CLC gene taxon:4932 20050319 SGD
+SGD S000003801 GEF1 GO:0006879 SGD_REF:S000054326|PMID:9520490 IMP P transport protein involved in intracellular iron metabolism (putative) YJR040W|CLC gene taxon:4932 20050319 SGD
+SGD S000003801 GEF1 GO:0030003 SGD_REF:S000054326|PMID:9520490 TAS P transport protein involved in intracellular iron metabolism (putative) YJR040W|CLC gene taxon:4932 20020913 SGD
+SGD S000000046 GEM1 GO:0005741 SGD_REF:S000079817|PMID:15479738 IDA C YAL048C|GON1 gene taxon:4932 20050210 SGD
+SGD S000000046 GEM1 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C YAL048C|GON1 gene taxon:4932 20060317 SGD
+SGD S000000046 GEM1 GO:0003924 SGD_REF:S000079817|PMID:15479738 IDA F YAL048C|GON1 gene taxon:4932 20050210 SGD
+SGD S000000046 GEM1 GO:0016192 SGD_REF:S000039821|PMID:10220001 IGI P YAL048C|GON1 gene taxon:4932 20040604 SGD
+SGD S000000046 GEM1 GO:0016192 SGD_REF:S000039821|PMID:10220001 IMP P YAL048C|GON1 gene taxon:4932 20040604 SGD
+SGD S000002988 GET1 GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YGL020C|MDM39 gene taxon:4932 20031028 SGD
+SGD S000002988 GET1 GO:0043529 SGD_REF:S000087084|PMID:16269340 IMP C YGL020C|MDM39 gene taxon:4932 20051109 SGD
+SGD S000002988 GET1 GO:0005554 SGD_REF:S000069584 ND F YGL020C|MDM39 gene taxon:4932 20021114 SGD
+SGD S000002988 GET1 GO:0006486 SGD_REF:S000081776|PMID:15909163 IMP P YGL020C|MDM39 gene taxon:4932 20051110 SGD
+SGD S000002988 GET1 GO:0006874 SGD_REF:S000081776|PMID:15909163 IMP P YGL020C|MDM39 gene taxon:4932 20051110 SGD
+SGD S000002988 GET1 GO:0006890 SGD_REF:S000087084|PMID:16269340 IDA P YGL020C|MDM39 gene taxon:4932 20051110 SGD
+SGD S000002988 GET1 GO:0006890 SGD_REF:S000087084|PMID:16269340 IGI SGD:S000000136 P YGL020C|MDM39 gene taxon:4932 20051110 SGD
+SGD S000002988 GET1 GO:0006890 SGD_REF:S000087084|PMID:16269340 IMP P YGL020C|MDM39 gene taxon:4932 20051110 SGD
+SGD S000002988 GET1 GO:0007005 SGD_REF:S000071517|PMID:11907266 IMP P YGL020C|MDM39 gene taxon:4932 20021114 SGD
+SGD S000002988 GET1 GO:0030968 SGD_REF:S000081776|PMID:15909163 IMP P YGL020C|MDM39 gene taxon:4932 20051110 SGD
+SGD S000000885 GET2 GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YER083C|HUR2|RMD7 gene taxon:4932 20031028 SGD
+SGD S000000885 GET2 GO:0043529 SGD_REF:S000087084|PMID:16269340 IMP C YER083C|HUR2|RMD7 gene taxon:4932 20051109 SGD
+SGD S000000885 GET2 GO:0005554 SGD_REF:S000069584 ND F YER083C|HUR2|RMD7 gene taxon:4932 20020806 SGD
+SGD S000000885 GET2 GO:0006890 SGD_REF:S000087084|PMID:16269340 IGI SGD:S000000136 P YER083C|HUR2|RMD7 gene taxon:4932 20051110 SGD
+SGD S000000885 GET2 GO:0006890 SGD_REF:S000087084|PMID:16269340 IDA P YER083C|HUR2|RMD7 gene taxon:4932 20051110 SGD
+SGD S000000885 GET2 GO:0006890 SGD_REF:S000087084|PMID:16269340 IMP P YER083C|HUR2|RMD7 gene taxon:4932 20051110 SGD
+SGD S000000885 GET2 GO:0007047 SGD_REF:S000060148|PMID:10929718 IEP P YER083C|HUR2|RMD7 gene taxon:4932 20020806 SGD
+SGD S000000885 GET2 GO:0007047 SGD_REF:S000060148|PMID:10929718 IMP P YER083C|HUR2|RMD7 gene taxon:4932 20020806 SGD
+SGD S000002258 GET3 GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YDL100C|ARR4 gene taxon:4932 20031028 SGD
+SGD S000002258 GET3 GO:0043529 SGD_REF:S000087084|PMID:16269340 IMP C YDL100C|ARR4 gene taxon:4932 20051109 SGD
+SGD S000002258 GET3 GO:0016887 SGD_REF:S000074088|PMID:12680698 IDA F YDL100C|ARR4 gene taxon:4932 20040107 SGD
+SGD S000002258 GET3 GO:0006890 SGD_REF:S000087084|PMID:16269340 IGI SGD:S000000136 P YDL100C|ARR4 gene taxon:4932 20051110 SGD
+SGD S000002258 GET3 GO:0006890 SGD_REF:S000087084|PMID:16269340 IDA P YDL100C|ARR4 gene taxon:4932 20051110 SGD
+SGD S000002258 GET3 GO:0006890 SGD_REF:S000087084|PMID:16269340 IMP P YDL100C|ARR4 gene taxon:4932 20051110 SGD
+SGD S000002258 GET3 GO:0009408 SGD_REF:S000074088|PMID:12680698 IMP P YDL100C|ARR4 gene taxon:4932 20040107 SGD
+SGD S000002258 GET3 GO:0010038 SGD_REF:S000074088|PMID:12680698 IMP P YDL100C|ARR4 gene taxon:4932 20040107 SGD
+SGD S000001587 GFA1 GO:0008372 SGD_REF:S000069584 ND C glucoseamine-6-phosphate synthase, glutamine_fructose-6-phosphate amidotransferase YKL104C gene taxon:4932 20020928 SGD
+SGD S000001587 GFA1 GO:0004360 SGD_REF:S000040621|PMID:2656689 IDA F glucoseamine-6-phosphate synthase, glutamine_fructose-6-phosphate amidotransferase YKL104C gene taxon:4932 20020928 SGD
+SGD S000001587 GFA1 GO:0006038 SGD_REF:S000069499|PMID:11895440 IGI P glucoseamine-6-phosphate synthase, glutamine_fructose-6-phosphate amidotransferase YKL104C gene taxon:4932 20020928 SGD
+SGD S000004868 GFD1 GO:0005643 SGD_REF:S000044974|PMID:10523319 IDA C YMR255W gene taxon:4932 20010118 SGD
+SGD S000004868 GFD1 GO:0005643 SGD_REF:S000042260|PMID:10610322 IDA C YMR255W gene taxon:4932 20010118 SGD
+SGD S000004868 GFD1 GO:0005737 SGD_REF:S000044974|PMID:10523319 IDA C YMR255W gene taxon:4932 20010118 SGD
+SGD S000004868 GFD1 GO:0005554 SGD_REF:S000069584 ND F YMR255W gene taxon:4932 20010119 SGD
+SGD S000004868 GFD1 GO:0006406 SGD_REF:S000044974|PMID:10523319 IGI P YMR255W gene taxon:4932 20010118 SGD
+SGD S000004868 GFD1 GO:0006406 SGD_REF:S000042260|PMID:10610322 IGI P YMR255W gene taxon:4932 20010118 SGD
+SGD S000000541 GFD2 GO:0008372 SGD_REF:S000069584 ND C YCL036W gene taxon:4932 20021122 SGD
+SGD S000000541 GFD2 GO:0005554 SGD_REF:S000069584 ND F YCL036W gene taxon:4932 20021122 SGD
+SGD S000000541 GFD2 GO:0000004 SGD_REF:S000069584 ND P YCL036W gene taxon:4932 20021122 SGD
+SGD S000002766 GGA1 GO:0005802 SGD_REF:S000050497|PMID:10747088 IDA C ARF-binding protein YDR358W gene taxon:4932 20010118 SGD
+SGD S000002766 GGA1 GO:0043130 SGD_REF:S000076009|PMID:15039776 IDA F ARF-binding protein YDR358W gene taxon:4932 20051024 SGD
+SGD S000002766 GGA1 GO:0006895 SGD_REF:S000076009|PMID:15039776 IMP P ARF-binding protein YDR358W gene taxon:4932 20051024 SGD
+SGD S000002766 GGA1 GO:0006896 SGD_REF:S000050497|PMID:10747088 IMP P ARF-binding protein YDR358W gene taxon:4932 20010118 SGD
+SGD S000002766 GGA1 GO:0006896 SGD_REF:S000050497|PMID:10747088 IPI P ARF-binding protein YDR358W gene taxon:4932 20010118 SGD
+SGD S000002766 GGA1 GO:0043328 SGD_REF:S000076009|PMID:15039776 IMP P ARF-binding protein YDR358W gene taxon:4932 20051024 SGD
+SGD S000001150 GGA2 GO:0005802 SGD_REF:S000050497|PMID:10747088 IDA C ARF-binding protein YHR108W gene taxon:4932 20010118 SGD
+SGD S000001150 GGA2 GO:0043130 SGD_REF:S000076009|PMID:15039776 IDA F ARF-binding protein YHR108W gene taxon:4932 20051024 SGD
+SGD S000001150 GGA2 GO:0006895 SGD_REF:S000076009|PMID:15039776 IMP P ARF-binding protein YHR108W gene taxon:4932 20051024 SGD
+SGD S000001150 GGA2 GO:0006896 SGD_REF:S000050497|PMID:10747088 IMP P ARF-binding protein YHR108W gene taxon:4932 20010118 SGD
+SGD S000001150 GGA2 GO:0006896 SGD_REF:S000050497|PMID:10747088 IPI P ARF-binding protein YHR108W gene taxon:4932 20010118 SGD
+SGD S000001150 GGA2 GO:0043328 SGD_REF:S000076009|PMID:15039776 IMP P ARF-binding protein YHR108W gene taxon:4932 20051024 SGD
+SGD S000002357 GGC1 GO:0005743 SGD_REF:S000049213|PMID:10930523 ISS C YDL198C|YHM1 gene taxon:4932 20021017 SGD
+SGD S000002357 GGC1 GO:0001409 SGD_REF:S000076177|PMID:14998997 IDA F YDL198C|YHM1 gene taxon:4932 20040629 SGD
+SGD S000002357 GGC1 GO:0000002 SGD_REF:S000055217|PMID:8905928 IGI P YDL198C|YHM1 gene taxon:4932 20021002 SGD
+SGD S000002357 GGC1 GO:0000002 SGD_REF:S000076177|PMID:14998997 IMP P YDL198C|YHM1 gene taxon:4932 20040512 SGD
+SGD S000002357 GGC1 GO:0001408 SGD_REF:S000076177|PMID:14998997 IDA P YDL198C|YHM1 gene taxon:4932 20040629 SGD
+SGD S000002357 GGC1 GO:0006879 SGD_REF:S000074561|PMID:14629196 IMP P YDL198C|YHM1 gene taxon:4932 20040323 SGD
+SGD S000001103 GIC1 GO:0000131 SGD_REF:S000053861|PMID:9367979 IDA C YHR061C gene taxon:4932 20020906 SGD
+SGD S000001103 GIC1 GO:0005934 SGD_REF:S000053861|PMID:9367979 IDA C YHR061C gene taxon:4932 20020906 SGD
+SGD S000001103 GIC1 GO:0005935 SGD_REF:S000053861|PMID:9367979 IDA C YHR061C gene taxon:4932 20020906 SGD
+SGD S000001103 GIC1 GO:0030478 SGD_REF:S000041005|PMID:10652251 IDA C YHR061C gene taxon:4932 20010118 SGD
+SGD S000001103 GIC1 GO:0043332 SGD_REF:S000053873|PMID:9367980 IDA C YHR061C gene taxon:4932 20050218 SGD
+SGD S000001103 GIC1 GO:0005083 SGD_REF:S000041005|PMID:10652251 TAS F YHR061C gene taxon:4932 20010118 SGD
+SGD S000001103 GIC1 GO:0007096 SGD_REF:S000077103|PMID:14734533 IMP P YHR061C gene taxon:4932 20050330 SGD
+SGD S000001103 GIC1 GO:0007096 SGD_REF:S000077103|PMID:14734533 IPI P YHR061C gene taxon:4932 20050330 SGD
+SGD S000001103 GIC1 GO:0007120 SGD_REF:S000041005|PMID:10652251 IMP P YHR061C gene taxon:4932 20010118 SGD
+SGD S000001103 GIC1 GO:0007266 SGD_REF:S000041005|PMID:10652251 IPI P YHR061C gene taxon:4932 20010118 SGD
+SGD S000001103 GIC1 GO:0030468 SGD_REF:S000041005|PMID:10652251 TAS P YHR061C gene taxon:4932 20010302 SGD
+SGD S000002717 GIC2 GO:0000131 SGD_REF:S000053873|PMID:9367980 IDA C YDR309C gene taxon:4932 20020906 SGD
+SGD S000002717 GIC2 GO:0005934 SGD_REF:S000053873|PMID:9367980 IDA C YDR309C gene taxon:4932 20020906 SGD
+SGD S000002717 GIC2 GO:0030478 SGD_REF:S000041005|PMID:10652251 IDA C YDR309C gene taxon:4932 20010118 SGD
+SGD S000002717 GIC2 GO:0043332 SGD_REF:S000053873|PMID:9367980 IDA C YDR309C gene taxon:4932 20020906 SGD
+SGD S000002717 GIC2 GO:0005083 SGD_REF:S000041005|PMID:10652251 TAS F YDR309C gene taxon:4932 20010118 SGD
+SGD S000002717 GIC2 GO:0007096 SGD_REF:S000077103|PMID:14734533 IMP P YDR309C gene taxon:4932 20050330 SGD
+SGD S000002717 GIC2 GO:0007096 SGD_REF:S000077103|PMID:14734533 IPI P YDR309C gene taxon:4932 20050330 SGD
+SGD S000002717 GIC2 GO:0007120 SGD_REF:S000041005|PMID:10652251 IMP P YDR309C gene taxon:4932 20010118 SGD
+SGD S000002717 GIC2 GO:0007266 SGD_REF:S000041005|PMID:10652251 IPI P YDR309C gene taxon:4932 20010118 SGD
+SGD S000002717 GIC2 GO:0030468 SGD_REF:S000041005|PMID:10652251 TAS P YDR309C gene taxon:4932 20010302 SGD
+SGD S000000544 GID7 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YCL039W|MOH2 gene taxon:4932 20031028 SGD
+SGD S000000544 GID7 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YCL039W|MOH2 gene taxon:4932 20031028 SGD
+SGD S000000544 GID7 GO:0005554 SGD_REF:S000069584 ND F YCL039W|MOH2 gene taxon:4932 20030114 SGD
+SGD S000000544 GID7 GO:0045721 SGD_REF:S000072993|PMID:12686616 IMP P YCL039W|MOH2 gene taxon:4932 20030708 SGD
+SGD S000004742 GID8 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YMR135C|DCR1 gene taxon:4932 20031028 SGD
+SGD S000004742 GID8 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YMR135C|DCR1 gene taxon:4932 20031028 SGD
+SGD S000004742 GID8 GO:0005554 SGD_REF:S000069584 ND F YMR135C|DCR1 gene taxon:4932 20021121 SGD
+SGD S000004742 GID8 GO:0007089 SGD_REF:S000079972|PMID:15590836 IMP P YMR135C|DCR1 gene taxon:4932 20050810 SGD
+SGD S000004742 GID8 GO:0045721 SGD_REF:S000072993|PMID:12686616 IMP P YMR135C|DCR1 gene taxon:4932 20030708 SGD
+SGD S000005097 GIM3 GO:0005737 SGD_REF:S000049112|PMID:9463374 IDA C bovine prefoldin subunit 4 homolog (putative) YNL153C|PFD4 gene taxon:4932 20020617 SGD
+SGD S000005097 GIM3 GO:0016272 SGD_REF:S000058336|PMID:9630229 ISS C bovine prefoldin subunit 4 homolog (putative) YNL153C|PFD4 gene taxon:4932 20031215 SGD
+SGD S000005097 GIM3 GO:0016272 SGD_REF:S000049112|PMID:9463374 IPI SGD:S000003310|SGD:S000004559 C bovine prefoldin subunit 4 homolog (putative) YNL153C|PFD4 gene taxon:4932 20031215 SGD
+SGD S000005097 GIM3 GO:0015631 SGD_REF:S000049112|PMID:9463374 IDA F bovine prefoldin subunit 4 homolog (putative) YNL153C|PFD4 gene taxon:4932 20021101 SGD
+SGD S000005097 GIM3 GO:0007021 SGD_REF:S000049112|PMID:9463374 IMP P bovine prefoldin subunit 4 homolog (putative) YNL153C|PFD4 gene taxon:4932 20021101 SGD
+SGD S000005097 GIM3 GO:0007021 SGD_REF:S000049112|PMID:9463374 ISS P bovine prefoldin subunit 4 homolog (putative) YNL153C|PFD4 gene taxon:4932 20021101 SGD
+SGD S000000729 GIM4 GO:0005737 SGD_REF:S000049112|PMID:9463374 IDA C bovine prefoldin subunit 2 homolog (putative) YEL003W|PFD2 gene taxon:4932 20020617 SGD
+SGD S000000729 GIM4 GO:0016272 SGD_REF:S000058336|PMID:9630229 ISS C bovine prefoldin subunit 2 homolog (putative) YEL003W|PFD2 gene taxon:4932 20031215 SGD
+SGD S000000729 GIM4 GO:0016272 SGD_REF:S000049112|PMID:9463374 IPI SGD:S000003310|SGD:S000004559 C bovine prefoldin subunit 2 homolog (putative) YEL003W|PFD2 gene taxon:4932 20031215 SGD
+SGD S000000729 GIM4 GO:0015631 SGD_REF:S000049112|PMID:9463374 IDA F bovine prefoldin subunit 2 homolog (putative) YEL003W|PFD2 gene taxon:4932 20021101 SGD
+SGD S000000729 GIM4 GO:0007021 SGD_REF:S000049112|PMID:9463374 IMP P bovine prefoldin subunit 2 homolog (putative) YEL003W|PFD2 gene taxon:4932 20021101 SGD
+SGD S000000729 GIM4 GO:0007021 SGD_REF:S000049112|PMID:9463374 ISS P bovine prefoldin subunit 2 homolog (putative) YEL003W|PFD2 gene taxon:4932 20021101 SGD
+SGD S000004559 GIM5 GO:0005737 SGD_REF:S000049112|PMID:9463374 IDA C bovine prefoldin subunit 5 homolog (putative) YML094W|PFD5 gene taxon:4932 20020617 SGD
+SGD S000004559 GIM5 GO:0016272 SGD_REF:S000058336|PMID:9630229 ISS C bovine prefoldin subunit 5 homolog (putative) YML094W|PFD5 gene taxon:4932 20031215 SGD
+SGD S000004559 GIM5 GO:0016272 SGD_REF:S000049112|PMID:9463374 IPI SGD:S000000729|SGD:S000003310|SGD:S000005097|SGD:S000004190 C bovine prefoldin subunit 5 homolog (putative) YML094W|PFD5 gene taxon:4932 20031215 SGD
+SGD S000004559 GIM5 GO:0015631 SGD_REF:S000049112|PMID:9463374 IDA F bovine prefoldin subunit 5 homolog (putative) YML094W|PFD5 gene taxon:4932 20021101 SGD
+SGD S000004559 GIM5 GO:0007021 SGD_REF:S000049112|PMID:9463374 IMP P bovine prefoldin subunit 5 homolog (putative) YML094W|PFD5 gene taxon:4932 20021101 SGD
+SGD S000004559 GIM5 GO:0007021 SGD_REF:S000049112|PMID:9463374 ISS P bovine prefoldin subunit 5 homolog (putative) YML094W|PFD5 gene taxon:4932 20021101 SGD
+SGD S000002915 GIN4 GO:0005935 SGD_REF:S000052982|PMID:9813093 IDA C serine/threonine kinase (putative) YDR507C|ERC47 gene taxon:4932 20010118 SGD
+SGD S000002915 GIN4 GO:0004672 SGD_REF:S000052982|PMID:9813093 ISS F serine/threonine kinase (putative) YDR507C|ERC47 gene taxon:4932 20010118 SGD
+SGD S000002915 GIN4 GO:0000135 SGD_REF:S000051063|PMID:9925642 IMP P serine/threonine kinase (putative) YDR507C|ERC47 gene taxon:4932 20010118 SGD
+SGD S000002915 GIN4 GO:0000135 SGD_REF:S000051063|PMID:9925642 IGI P serine/threonine kinase (putative) YDR507C|ERC47 gene taxon:4932 20010118 SGD
+SGD S000002915 GIN4 GO:0000921 SGD_REF:S000052982|PMID:9813093 IGI P serine/threonine kinase (putative) YDR507C|ERC47 gene taxon:4932 20030321 SGD
+SGD S000002915 GIN4 GO:0000921 SGD_REF:S000052982|PMID:9813093 IMP P serine/threonine kinase (putative) YDR507C|ERC47 gene taxon:4932 20030321 SGD
+SGD S000002915 GIN4 GO:0006468 SGD_REF:S000052982|PMID:9813093 ISS P serine/threonine kinase (putative) YDR507C|ERC47 gene taxon:4932 20010118 SGD
+SGD S000002915 GIN4 GO:0007117 SGD_REF:S000051063|PMID:9925642 IMP P serine/threonine kinase (putative) YDR507C|ERC47 gene taxon:4932 20010118 SGD
+SGD S000002915 GIN4 GO:0007117 SGD_REF:S000051063|PMID:9925642 IGI P serine/threonine kinase (putative) YDR507C|ERC47 gene taxon:4932 20010118 SGD
+SGD S000002915 GIN4 GO:0007117 SGD_REF:S000076016|PMID:15107529 IGI SGD:S000000471 P serine/threonine kinase (putative) YDR507C|ERC47 gene taxon:4932 20040624 SGD
+SGD S000002915 GIN4 GO:0007120 SGD_REF:S000041005|PMID:10652251 TAS P serine/threonine kinase (putative) YDR507C|ERC47 gene taxon:4932 20010118 SGD
+SGD S000000249 GIP1 GO:0000164 SGD_REF:S000043932|PMID:9584086 IPI C Glc7p regulatory subunit YBR045C gene taxon:4932 20020813 SGD
+SGD S000000249 GIP1 GO:0005628 SGD_REF:S000066224|PMID:11724821 IDA C Glc7p regulatory subunit YBR045C gene taxon:4932 20020813 SGD
+SGD S000000249 GIP1 GO:0008157 SGD_REF:S000043932|PMID:9584086 IMP F Glc7p regulatory subunit YBR045C gene taxon:4932 20020813 SGD
+SGD S000000249 GIP1 GO:0008157 SGD_REF:S000043932|PMID:9584086 IPI F Glc7p regulatory subunit YBR045C gene taxon:4932 20020813 SGD
+SGD S000000249 GIP1 GO:0008599 SGD_REF:S000066224|PMID:11724821 IDA F Glc7p regulatory subunit YBR045C gene taxon:4932 20051010 SGD
+SGD S000000249 GIP1 GO:0030476 SGD_REF:S000066224|PMID:11724821 IMP P Glc7p regulatory subunit YBR045C gene taxon:4932 20020813 SGD
+SGD S000000856 GIP2 GO:0000164 SGD_REF:S000041210|PMID:8754819 IPI C YER054C gene taxon:4932 20020523 SGD
+SGD S000000856 GIP2 GO:0019888 SGD_REF:S000041126|PMID:9046081 ISS F YER054C gene taxon:4932 20020523 SGD
+SGD S000000856 GIP2 GO:0019888 SGD_REF:S000041210|PMID:8754819 IPI F YER054C gene taxon:4932 20020523 SGD
+SGD S000000856 GIP2 GO:0005977 SGD_REF:S000069720|PMID:11973298 IMP P YER054C gene taxon:4932 20051013 SGD
+SGD S000000856 GIP2 GO:0005977 SGD_REF:S000041210|PMID:8754819 ISS P YER054C gene taxon:4932 20051013 SGD
+SGD S000000856 GIP2 GO:0006470 SGD_REF:S000041210|PMID:8754819 IPI P YER054C gene taxon:4932 20030416 SGD
+SGD S000006058 GIP3 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C Glc7 interacting protein 3 YPL137C gene taxon:4932 20031028 SGD
+SGD S000006058 GIP3 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C Glc7 interacting protein 3 YPL137C gene taxon:4932 20040928 SGD
+SGD S000006058 GIP3 GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C Glc7 interacting protein 3 YPL137C gene taxon:4932 20031028 SGD
+SGD S000006058 GIP3 GO:0005554 SGD_REF:S000069584 ND F Glc7 interacting protein 3 YPL137C gene taxon:4932 20021126 SGD
+SGD S000006058 GIP3 GO:0000004 SGD_REF:S000069584 ND P Glc7 interacting protein 3 YPL137C gene taxon:4932 20021126 SGD
+SGD S000000029 GIP4 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YAL031C|FUN21 gene taxon:4932 20031028 SGD
+SGD S000000029 GIP4 GO:0005554 SGD_REF:S000069584 ND F YAL031C|FUN21 gene taxon:4932 20010119 SGD
+SGD S000000029 GIP4 GO:0000004 SGD_REF:S000069584 ND P YAL031C|FUN21 gene taxon:4932 20010119 SGD
+SGD S000002559 GIR2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDR152W gene taxon:4932 20031028 SGD
+SGD S000002559 GIR2 GO:0005554 SGD_REF:S000069584 ND F YDR152W gene taxon:4932 20040113 SGD
+SGD S000002559 GIR2 GO:0000004 SGD_REF:S000069584 ND P YDR152W gene taxon:4932 20040113 SGD
+SGD S000002503 GIS1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C zinc finger protein (putative) YDR096W gene taxon:4932 20031028 SGD
+SGD S000002503 GIS1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C zinc finger protein (putative) YDR096W gene taxon:4932 20040928 SGD
+SGD S000002503 GIS1 GO:0003700 SGD_REF:S000062114|PMID:10628841 IMP F zinc finger protein (putative) YDR096W gene taxon:4932 20011026 SGD
+SGD S000002503 GIS1 GO:0003700 SGD_REF:S000062114|PMID:10628841 ISS F zinc finger protein (putative) YDR096W gene taxon:4932 20011026 SGD
+SGD S000002503 GIS1 GO:0006644 SGD_REF:S000073858|PMID:12799368 IMP P zinc finger protein (putative) YDR096W gene taxon:4932 20040707 SGD
+SGD S000002503 GIS1 GO:0030476 SGD_REF:S000079982|PMID:15590821 IMP P zinc finger protein (putative) YDR096W gene taxon:4932 20050127 SGD
+SGD S000005199 GIS2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YNL255C gene taxon:4932 20031028 SGD
+SGD S000005199 GIS2 GO:0005554 SGD_REF:S000073348 ND F YNL255C gene taxon:4932 20060419 SGD
+SGD S000005199 GIS2 GO:0007242 SGD_REF:S000062114|PMID:10628841 IGI SGD:S000004301 P YNL255C gene taxon:4932 20060419 SGD
+SGD S000004084 GIS3 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YLR094C gene taxon:4932 20031028 SGD
+SGD S000004084 GIS3 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YLR094C gene taxon:4932 20031028 SGD
+SGD S000004084 GIS3 GO:0005554 SGD_REF:S000069584 ND F YLR094C gene taxon:4932 20021011 SGD
+SGD S000004084 GIS3 GO:0007242 SGD_REF:S000062114|PMID:10628841 IGI P YLR094C gene taxon:4932 20021011 SGD
+SGD S000004465 GIS4 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C CAAX box containing protein YML006C gene taxon:4932 20031028 SGD
+SGD S000004465 GIS4 GO:0005554 SGD_REF:S000062114|PMID:10628841 ISS F CAAX box containing protein YML006C gene taxon:4932 20011026 SGD
+SGD S000004465 GIS4 GO:0007242 SGD_REF:S000062114|PMID:10628841 IGI P CAAX box containing protein YML006C gene taxon:4932 20020930 SGD
+SGD S000000695 GIT1 GO:0005886 SGD_REF:S000047612|PMID:9691030 ISS C permease involved in the uptake of glycerophosphoinositol (GroPIns) YCR098C gene taxon:4932 20021011 SGD
+SGD S000000695 GIT1 GO:0005886 SGD_REF:S000047612|PMID:9691030 IMP C permease involved in the uptake of glycerophosphoinositol (GroPIns) YCR098C gene taxon:4932 20021011 SGD
+SGD S000000695 GIT1 GO:0001406 SGD_REF:S000047612|PMID:9691030 IMP F permease involved in the uptake of glycerophosphoinositol (GroPIns) YCR098C gene taxon:4932 20040629 SGD
+SGD S000000695 GIT1 GO:0001407 SGD_REF:S000047612|PMID:9691030 IMP P permease involved in the uptake of glycerophosphoinositol (GroPIns) YCR098C gene taxon:4932 20040629 SGD
+SGD S000000695 GIT1 GO:0001407 SGD_REF:S000086509|PMID:16141200 IMP P permease involved in the uptake of glycerophosphoinositol (GroPIns) YCR098C gene taxon:4932 20050923 SGD
+SGD S000000737 GLC3 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C 1,4-glucan-6-(1,4-glucano)-transferase YEL011W|GHA1 gene taxon:4932 20031028 SGD
+SGD S000000737 GLC3 GO:0003844 SGD_REF:S000050212|PMID:1729600 IGI F 1,4-glucan-6-(1,4-glucano)-transferase YEL011W|GHA1 gene taxon:4932 20020930 SGD
+SGD S000000737 GLC3 GO:0003844 SGD_REF:S000050212|PMID:1729600 IMP F 1,4-glucan-6-(1,4-glucano)-transferase YEL011W|GHA1 gene taxon:4932 20020930 SGD
+SGD S000000737 GLC3 GO:0005978 SGD_REF:S000050212|PMID:1729600 IMP P 1,4-glucan-6-(1,4-glucano)-transferase YEL011W|GHA1 gene taxon:4932 20050830 SGD
+SGD S000000935 GLC7 GO:0000164 SGD_REF:S000049387|PMID:8289829 IDA C protein phosphatase type I YER133W|CID1|DIS2|DIS2S1|PP1 gene taxon:4932 20010118 SGD
+SGD S000000935 GLC7 GO:0001400 SGD_REF:S000050512|PMID:10747092 IDA C protein phosphatase type I YER133W|CID1|DIS2|DIS2S1|PP1 gene taxon:4932 20051101 SGD
+SGD S000000935 GLC7 GO:0005730 SGD_REF:S000065824|PMID:11412094 IDA C protein phosphatase type I YER133W|CID1|DIS2|DIS2S1|PP1 gene taxon:4932 20030130 SGD
+SGD S000000935 GLC7 GO:0005816 SGD_REF:S000050512|PMID:10747092 IDA C protein phosphatase type I YER133W|CID1|DIS2|DIS2S1|PP1 gene taxon:4932 20051101 SGD
+SGD S000000935 GLC7 GO:0005847 SGD_REF:S000074089|PMID:12819204 IPI C protein phosphatase type I YER133W|CID1|DIS2|DIS2S1|PP1 gene taxon:4932 20031013 SGD
+SGD S000000935 GLC7 GO:0005935 SGD_REF:S000065824|PMID:11412094 IDA C protein phosphatase type I YER133W|CID1|DIS2|DIS2S1|PP1 gene taxon:4932 20030130 SGD
+SGD S000000935 GLC7 GO:0000163 SGD_REF:S000044191|PMID:1660885 IDA F protein phosphatase type I YER133W|CID1|DIS2|DIS2S1|PP1 gene taxon:4932 20010118 SGD
+SGD S000000935 GLC7 GO:0000163 SGD_REF:S000065824|PMID:11412094 TAS F protein phosphatase type I YER133W|CID1|DIS2|DIS2S1|PP1 gene taxon:4932 20030130 SGD
+SGD S000000935 GLC7 GO:0000074 SGD_REF:S000043932|PMID:9584086 IMP P protein phosphatase type I YER133W|CID1|DIS2|DIS2S1|PP1 gene taxon:4932 20051101 SGD
+SGD S000000935 GLC7 GO:0000074 SGD_REF:S000049952|PMID:10072380 IMP P protein phosphatase type I YER133W|CID1|DIS2|DIS2S1|PP1 gene taxon:4932 20051101 SGD
+SGD S000000935 GLC7 GO:0000074 SGD_REF:S000045029|PMID:8164671 IMP P protein phosphatase type I YER133W|CID1|DIS2|DIS2S1|PP1 gene taxon:4932 20051101 SGD
+SGD S000000935 GLC7 GO:0000074 SGD_REF:S000045597|PMID:7891699 IMP P protein phosphatase type I YER133W|CID1|DIS2|DIS2S1|PP1 gene taxon:4932 20051101 SGD
+SGD S000000935 GLC7 GO:0000903 SGD_REF:S000071946|PMID:12477789 IGI P protein phosphatase type I YER133W|CID1|DIS2|DIS2S1|PP1 gene taxon:4932 20030721 SGD
+SGD S000000935 GLC7 GO:0005977 SGD_REF:S000044191|PMID:1660885 IMP P protein phosphatase type I YER133W|CID1|DIS2|DIS2S1|PP1 gene taxon:4932 20010118 SGD
+SGD S000000935 GLC7 GO:0006109 SGD_REF:S000071682|PMID:12167649 IGI P protein phosphatase type I YER133W|CID1|DIS2|DIS2S1|PP1 gene taxon:4932 20030402 SGD
+SGD S000000935 GLC7 GO:0006109 SGD_REF:S000071682|PMID:12167649 IPI P protein phosphatase type I YER133W|CID1|DIS2|DIS2S1|PP1 gene taxon:4932 20030402 SGD
+SGD S000000935 GLC7 GO:0006109 SGD_REF:S000071682|PMID:12167649 TAS P protein phosphatase type I YER133W|CID1|DIS2|DIS2S1|PP1 gene taxon:4932 20030402 SGD
+SGD S000000935 GLC7 GO:0006365 SGD_REF:S000073750|PMID:12837249 IMP P protein phosphatase type I YER133W|CID1|DIS2|DIS2S1|PP1 gene taxon:4932 20030805 SGD
+SGD S000000935 GLC7 GO:0006470 SGD_REF:S000044191|PMID:1660885 IDA P protein phosphatase type I YER133W|CID1|DIS2|DIS2S1|PP1 gene taxon:4932 20051101 SGD
+SGD S000000935 GLC7 GO:0006873 SGD_REF:S000069720|PMID:11973298 IMP P protein phosphatase type I YER133W|CID1|DIS2|DIS2S1|PP1 gene taxon:4932 20051101 SGD
+SGD S000000935 GLC7 GO:0007059 SGD_REF:S000049957|PMID:10072383 IMP P protein phosphatase type I YER133W|CID1|DIS2|DIS2S1|PP1 gene taxon:4932 20051101 SGD
+SGD S000000935 GLC7 GO:0007094 SGD_REF:S000049952|PMID:10072380 IMP P protein phosphatase type I YER133W|CID1|DIS2|DIS2S1|PP1 gene taxon:4932 20010118 SGD
+SGD S000000935 GLC7 GO:0007114 SGD_REF:S000046613|PMID:10639337 IMP P protein phosphatase type I YER133W|CID1|DIS2|DIS2S1|PP1 gene taxon:4932 20051101 SGD
+SGD S000000935 GLC7 GO:0007126 SGD_REF:S000041210|PMID:8754819 IPI P protein phosphatase type I YER133W|CID1|DIS2|DIS2S1|PP1 gene taxon:4932 20010118 SGD
+SGD S000000935 GLC7 GO:0009408 SGD_REF:S000044300|PMID:10207049 IPI P protein phosphatase type I YER133W|CID1|DIS2|DIS2S1|PP1 gene taxon:4932 20010118 SGD
+SGD S000000935 GLC7 GO:0009408 SGD_REF:S000044300|PMID:10207049 IMP P protein phosphatase type I YER133W|CID1|DIS2|DIS2S1|PP1 gene taxon:4932 20010118 SGD
+SGD S000000935 GLC7 GO:0016576 SGD_REF:S000053597|PMID:10975519 IMP P protein phosphatase type I YER133W|CID1|DIS2|DIS2S1|PP1 gene taxon:4932 20051101 SGD
+SGD S000000935 GLC7 GO:0030437 SGD_REF:S000043932|PMID:9584086 IMP P protein phosphatase type I YER133W|CID1|DIS2|DIS2S1|PP1 gene taxon:4932 20051101 SGD
+SGD S000000935 GLC7 GO:0030846 SGD_REF:S000074089|PMID:12819204 IPI P protein phosphatase type I YER133W|CID1|DIS2|DIS2S1|PP1 gene taxon:4932 20031013 SGD
+SGD S000000935 GLC7 GO:0030847 SGD_REF:S000074089|PMID:12819204 IPI P protein phosphatase type I YER133W|CID1|DIS2|DIS2S1|PP1 gene taxon:4932 20031013 SGD
+SGD S000004928 GLC8 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C protein phosphatase 1 (Glc7p) regulator YMR311C gene taxon:4932 20031028 SGD
+SGD S000004928 GLC8 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C protein phosphatase 1 (Glc7p) regulator YMR311C gene taxon:4932 20020507 SGD
+SGD S000004928 GLC8 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C protein phosphatase 1 (Glc7p) regulator YMR311C gene taxon:4932 20031028 SGD
+SGD S000004928 GLC8 GO:0008047 SGD_REF:S000071137|PMID:12127071 IDA F protein phosphatase 1 (Glc7p) regulator YMR311C gene taxon:4932 20020919 SGD
+SGD S000004928 GLC8 GO:0005978 SGD_REF:S000043932|PMID:9584086 TAS P protein phosphatase 1 (Glc7p) regulator YMR311C gene taxon:4932 20020919 SGD
+SGD S000004928 GLC8 GO:0007059 SGD_REF:S000043811|PMID:7565759 IMP P protein phosphatase 1 (Glc7p) regulator YMR311C gene taxon:4932 20050920 SGD
+SGD S000002366 GLE1 GO:0005643 SGD_REF:S000069412|PMID:11343909 TAS C nuclear pore complex subunit, nuclear-export-signal (NES)-containing protein YDL207W|BRR3|RSS1 gene taxon:4932 20020313 SGD
+SGD S000002366 GLE1 GO:0005643 SGD_REF:S000079791|PMID:15459192 IDA C nuclear pore complex subunit, nuclear-export-signal (NES)-containing protein YDL207W|BRR3|RSS1 gene taxon:4932 20041215 SGD
+SGD S000002366 GLE1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C nuclear pore complex subunit, nuclear-export-signal (NES)-containing protein YDL207W|BRR3|RSS1 gene taxon:4932 20040928 SGD
+SGD S000002366 GLE1 GO:0005554 SGD_REF:S000069584 ND F nuclear pore complex subunit, nuclear-export-signal (NES)-containing protein YDL207W|BRR3|RSS1 gene taxon:4932 20020930 SGD
+SGD S000002366 GLE1 GO:0016973 SGD_REF:S000046531|PMID:8898365 IMP P nuclear pore complex subunit, nuclear-export-signal (NES)-containing protein YDL207W|BRR3|RSS1 gene taxon:4932 20020930 SGD
+SGD S000000909 GLE2 GO:0005643 SGD_REF:S000058277|PMID:9442897 IDA C nuclear pore complex subunit, rae1 S. pombe homolog YER107C|RAE1 gene taxon:4932 20010118 SGD
+SGD S000000909 GLE2 GO:0005198 SGD_REF:S000058277|PMID:9442897 TAS F nuclear pore complex subunit, rae1 S. pombe homolog YER107C|RAE1 gene taxon:4932 20010118 SGD
+SGD S000000909 GLE2 GO:0006406 SGD_REF:S000058277|PMID:9442897 IMP P nuclear pore complex subunit, rae1 S. pombe homolog YER107C|RAE1 gene taxon:4932 20010118 SGD
+SGD S000000909 GLE2 GO:0006407 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit, rae1 S. pombe homolog YER107C|RAE1 gene taxon:4932 20010118 SGD
+SGD S000000909 GLE2 GO:0006408 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit, rae1 S. pombe homolog YER107C|RAE1 gene taxon:4932 20010118 SGD
+SGD S000000909 GLE2 GO:0006409 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit, rae1 S. pombe homolog YER107C|RAE1 gene taxon:4932 20010118 SGD
+SGD S000000909 GLE2 GO:0006606 SGD_REF:S000058277|PMID:9442897 IMP P nuclear pore complex subunit, rae1 S. pombe homolog YER107C|RAE1 gene taxon:4932 20010118 SGD
+SGD S000000909 GLE2 GO:0006607 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit, rae1 S. pombe homolog YER107C|RAE1 gene taxon:4932 20010118 SGD
+SGD S000000909 GLE2 GO:0006608 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit, rae1 S. pombe homolog YER107C|RAE1 gene taxon:4932 20010118 SGD
+SGD S000000909 GLE2 GO:0006609 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit, rae1 S. pombe homolog YER107C|RAE1 gene taxon:4932 20010118 SGD
+SGD S000000909 GLE2 GO:0006610 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit, rae1 S. pombe homolog YER107C|RAE1 gene taxon:4932 20010118 SGD
+SGD S000000909 GLE2 GO:0006611 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit, rae1 S. pombe homolog YER107C|RAE1 gene taxon:4932 20010118 SGD
+SGD S000000909 GLE2 GO:0006998 SGD_REF:S000058277|PMID:9442897 IMP P nuclear pore complex subunit, rae1 S. pombe homolog YER107C|RAE1 gene taxon:4932 20010118 SGD
+SGD S000000909 GLE2 GO:0006999 SGD_REF:S000058277|PMID:9442897 IMP P nuclear pore complex subunit, rae1 S. pombe homolog YER107C|RAE1 gene taxon:4932 20010118 SGD
+SGD S000001766 GLG1 GO:0008372 SGD_REF:S000069584 ND C glycogen synthesis initiator YKR058W gene taxon:4932 20021002 SGD
+SGD S000001766 GLG1 GO:0008466 SGD_REF:S000051500|PMID:8524228 IGI F glycogen synthesis initiator YKR058W gene taxon:4932 20021002 SGD
+SGD S000001766 GLG1 GO:0008466 SGD_REF:S000051500|PMID:8524228 ISS F glycogen synthesis initiator YKR058W gene taxon:4932 20021002 SGD
+SGD S000001766 GLG1 GO:0005978 SGD_REF:S000051500|PMID:8524228 IGI P glycogen synthesis initiator YKR058W gene taxon:4932 20021002 SGD
+SGD S000003673 GLG2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C glycogen synthesis initiator YJL137C gene taxon:4932 20031028 SGD
+SGD S000003673 GLG2 GO:0008466 SGD_REF:S000051500|PMID:8524228 IGI F glycogen synthesis initiator YJL137C gene taxon:4932 20021002 SGD
+SGD S000003673 GLG2 GO:0008466 SGD_REF:S000051500|PMID:8524228 ISS F glycogen synthesis initiator YJL137C gene taxon:4932 20021002 SGD
+SGD S000003673 GLG2 GO:0005978 SGD_REF:S000051500|PMID:8524228 IGI P glycogen synthesis initiator YJL137C gene taxon:4932 20021002 SGD
+SGD S000000545 GLK1 GO:0005829 SGD_REF:S000058491 TAS C glucokinase YCL040W|HOR3 gene taxon:4932 20010119 SGD
+SGD S000000545 GLK1 GO:0004340 SGD_REF:S000043583|PMID:6341351 IMP F glucokinase YCL040W|HOR3 gene taxon:4932 20010118 SGD
+SGD S000000545 GLK1 GO:0004340 SGD_REF:S000081841|PMID:8501032 IDA F glucokinase YCL040W|HOR3 gene taxon:4932 20050609 SGD
+SGD S000000545 GLK1 GO:0005975 SGD_REF:S000043025|PMID:6357942 IMP P glucokinase YCL040W|HOR3 gene taxon:4932 20020930 SGD
+SGD S000000545 GLK1 GO:0006006 SGD_REF:S000048827|PMID:6300872 IMP P glucokinase YCL040W|HOR3 gene taxon:4932 20050609 SGD
+SGD S000006239 GLN1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C glutamine synthetase YPR035W gene taxon:4932 20020507 SGD
+SGD S000006239 GLN1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C glutamine synthetase YPR035W gene taxon:4932 20031028 SGD
+SGD S000006239 GLN1 GO:0004356 SGD_REF:S000049506|PMID:1347768 ISS F glutamine synthetase YPR035W gene taxon:4932 20020930 SGD
+SGD S000006239 GLN1 GO:0004356 SGD_REF:S000049506|PMID:1347768 IMP F glutamine synthetase YPR035W gene taxon:4932 20020930 SGD
+SGD S000006239 GLN1 GO:0006542 SGD_REF:S000070200 TAS P glutamine synthetase YPR035W gene taxon:4932 20030512 SGD
+SGD S000006239 GLN1 GO:0006807 SGD_REF:S000049506|PMID:1347768 ISS P glutamine synthetase YPR035W gene taxon:4932 20020930 SGD
+SGD S000006239 GLN1 GO:0006807 SGD_REF:S000049506|PMID:1347768 IEP P glutamine synthetase YPR035W gene taxon:4932 20020930 SGD
+SGD S000000842 GLN3 GO:0005634 SGD_REF:S000069962|PMID:12062797 TAS C transcriptional activator of nitrogen-regulated genes YER040W gene taxon:4932 20020819 SGD
+SGD S000000842 GLN3 GO:0005634 SGD_REF:S000046200|PMID:10604478 IDA C transcriptional activator of nitrogen-regulated genes YER040W gene taxon:4932 20050926 SGD
+SGD S000000842 GLN3 GO:0005829 SGD_REF:S000071472|PMID:12140287 IDA C transcriptional activator of nitrogen-regulated genes YER040W gene taxon:4932 20021202 SGD
+SGD S000000842 GLN3 GO:0003700 SGD_REF:S000053142|PMID:8655543 IDA F transcriptional activator of nitrogen-regulated genes YER040W gene taxon:4932 20020930 SGD
+SGD S000000842 GLN3 GO:0003700 SGD_REF:S000050428|PMID:9171427 IDA F transcriptional activator of nitrogen-regulated genes YER040W gene taxon:4932 20050117 SGD
+SGD S000000842 GLN3 GO:0016563 SGD_REF:S000071472|PMID:12140287 TAS F transcriptional activator of nitrogen-regulated genes YER040W gene taxon:4932 20021202 SGD
+SGD S000000842 GLN3 GO:0016563 SGD_REF:S000050428|PMID:9171427 IDA F transcriptional activator of nitrogen-regulated genes YER040W gene taxon:4932 20050117 SGD
+SGD S000000842 GLN3 GO:0006807 SGD_REF:S000053142|PMID:8655543 IPI P transcriptional activator of nitrogen-regulated genes YER040W gene taxon:4932 20020930 SGD
+SGD S000000842 GLN3 GO:0006808 SGD_REF:S000072524|PMID:12489124 IGI P transcriptional activator of nitrogen-regulated genes YER040W gene taxon:4932 20030214 SGD
+SGD S000000842 GLN3 GO:0006808 SGD_REF:S000072524|PMID:12489124 IMP P transcriptional activator of nitrogen-regulated genes YER040W gene taxon:4932 20030214 SGD
+SGD S000000842 GLN3 GO:0045941 SGD_REF:S000050428|PMID:9171427 IDA P transcriptional activator of nitrogen-regulated genes YER040W gene taxon:4932 20050117 SGD
+SGD S000000842 GLN3 GO:0045944 SGD_REF:S000053142|PMID:8655543 IDA P transcriptional activator of nitrogen-regulated genes YER040W gene taxon:4932 20030911 SGD
+SGD S000005694 GLN4 GO:0005737 SGD_REF:S000042289|PMID:2991203 IC GO:0004819 C glutamine-tRNA ligase YOR168W gene taxon:4932 20021108 SGD
+SGD S000005694 GLN4 GO:0004819 SGD_REF:S000042289|PMID:2991203 IDA F glutamine-tRNA ligase YOR168W gene taxon:4932 20020930 SGD
+SGD S000005694 GLN4 GO:0006425 SGD_REF:S000042289|PMID:2991203 IMP P glutamine-tRNA ligase YOR168W gene taxon:4932 20031217 SGD
+SGD S000005694 GLN4 GO:0006425 SGD_REF:S000042289|PMID:2991203 ISS P glutamine-tRNA ligase YOR168W gene taxon:4932 20031217 SGD
+SGD S000004463 GLO1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C lactoylglutathione lyase (glyoxalase I) YML004C gene taxon:4932 20031028 SGD
+SGD S000004463 GLO1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C lactoylglutathione lyase (glyoxalase I) YML004C gene taxon:4932 20031028 SGD
+SGD S000004463 GLO1 GO:0004462 SGD_REF:S000050684|PMID:8824231 IGI F lactoylglutathione lyase (glyoxalase I) YML004C gene taxon:4932 20020928 SGD
+SGD S000004463 GLO1 GO:0006749 SGD_REF:S000050684|PMID:8824231 IGI P lactoylglutathione lyase (glyoxalase I) YML004C gene taxon:4932 20020928 SGD
+SGD S000004463 GLO1 GO:0019243 SGD_REF:S000050684|PMID:8824231 IDA P lactoylglutathione lyase (glyoxalase I) YML004C gene taxon:4932 20050715 SGD
+SGD S000002680 GLO2 GO:0005737 SGD_REF:S000050952|PMID:9261170 IDA C glyoxylase-II YDR272W gene taxon:4932 20010118 SGD
+SGD S000002680 GLO2 GO:0004416 SGD_REF:S000050952|PMID:9261170 IMP F glyoxylase-II YDR272W gene taxon:4932 20010118 SGD
+SGD S000002680 GLO2 GO:0005975 SGD_REF:S000050952|PMID:9261170 IMP P glyoxylase-II YDR272W gene taxon:4932 20010118 SGD
+SGD S000002680 GLO2 GO:0019243 SGD_REF:S000050952|PMID:9261170 IDA P glyoxylase-II YDR272W gene taxon:4932 20050720 SGD
+SGD S000000924 GLO3 GO:0005793 SGD_REF:S000053308|PMID:9927415 IPI C similar to Gcs1p and Sps18p, zinc finger protein YER122C gene taxon:4932 20010118 SGD
+SGD S000000924 GLO3 GO:0030126 SGD_REF:S000080878|PMID:15254269 IPI SGD:S000005231 C similar to Gcs1p and Sps18p, zinc finger protein YER122C gene taxon:4932 20050711 SGD
+SGD S000000924 GLO3 GO:0030137 SGD_REF:S000080878|PMID:15254269 IDA C similar to Gcs1p and Sps18p, zinc finger protein YER122C gene taxon:4932 20050711 SGD
+SGD S000000924 GLO3 GO:0008060 SGD_REF:S000053308|PMID:9927415 IDA F similar to Gcs1p and Sps18p, zinc finger protein YER122C gene taxon:4932 20010118 SGD
+SGD S000000924 GLO3 GO:0006888 SGD_REF:S000053308|PMID:9927415 IGI P similar to Gcs1p and Sps18p, zinc finger protein YER122C gene taxon:4932 20010118 SGD
+SGD S000000924 GLO3 GO:0006888 SGD_REF:S000053308|PMID:9927415 IMP P similar to Gcs1p and Sps18p, zinc finger protein YER122C gene taxon:4932 20010118 SGD
+SGD S000000924 GLO3 GO:0006890 SGD_REF:S000053308|PMID:9927415 IGI P similar to Gcs1p and Sps18p, zinc finger protein YER122C gene taxon:4932 20010118 SGD
+SGD S000000924 GLO3 GO:0006890 SGD_REF:S000053308|PMID:9927415 IMP P similar to Gcs1p and Sps18p, zinc finger protein YER122C gene taxon:4932 20010118 SGD
+SGD S000000924 GLO3 GO:0006890 SGD_REF:S000053308|PMID:9927415 IDA P similar to Gcs1p and Sps18p, zinc finger protein YER122C gene taxon:4932 20010118 SGD
+SGD S000000924 GLO3 GO:0048205 SGD_REF:S000080878|PMID:15254269 IDA P similar to Gcs1p and Sps18p, zinc finger protein YER122C gene taxon:4932 20050711 SGD
+SGD S000000924 GLO3 GO:0048205 SGD_REF:S000080878|PMID:15254269 IMP P similar to Gcs1p and Sps18p, zinc finger protein YER122C gene taxon:4932 20050711 SGD
+SGD S000005566 GLO4 GO:0005739 SGD_REF:S000050952|PMID:9261170 IDA C glyoxylase-II YOR040W gene taxon:4932 20010118 SGD
+SGD S000005566 GLO4 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C glyoxylase-II YOR040W gene taxon:4932 20040924 SGD
+SGD S000005566 GLO4 GO:0005759 SGD_REF:S000050952|PMID:9261170 IDA C glyoxylase-II YOR040W gene taxon:4932 20010118 SGD
+SGD S000005566 GLO4 GO:0004416 SGD_REF:S000050952|PMID:9261170 IMP F glyoxylase-II YOR040W gene taxon:4932 20010118 SGD
+SGD S000005566 GLO4 GO:0004416 SGD_REF:S000050952|PMID:9261170 IDA F glyoxylase-II YOR040W gene taxon:4932 20010118 SGD
+SGD S000005566 GLO4 GO:0005975 SGD_REF:S000050952|PMID:9261170 IMP P glyoxylase-II YOR040W gene taxon:4932 20010118 SGD
+SGD S000005566 GLO4 GO:0019243 SGD_REF:S000050952|PMID:9261170 IDA P glyoxylase-II YOR040W gene taxon:4932 20050720 SGD
+SGD S000006012 GLR1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C EC 1.6.4.2, glutathione oxidoreductase YPL091W|LPG17 gene taxon:4932 20031028 SGD
+SGD S000006012 GLR1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C EC 1.6.4.2, glutathione oxidoreductase YPL091W|LPG17 gene taxon:4932 20031028 SGD
+SGD S000006012 GLR1 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C EC 1.6.4.2, glutathione oxidoreductase YPL091W|LPG17 gene taxon:4932 20031028 SGD
+SGD S000006012 GLR1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C EC 1.6.4.2, glutathione oxidoreductase YPL091W|LPG17 gene taxon:4932 20040813 SGD
+SGD S000006012 GLR1 GO:0004362 SGD_REF:S000046931|PMID:7737505 IDA F EC 1.6.4.2, glutathione oxidoreductase YPL091W|LPG17 gene taxon:4932 20020930 SGD
+SGD S000006012 GLR1 GO:0006979 SGD_REF:S000047197|PMID:8951820 IMP P EC 1.6.4.2, glutathione oxidoreductase YPL091W|LPG17 gene taxon:4932 20020930 SGD
+SGD S000002330 GLT1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C glutamate synthase (NADH) YDL171C gene taxon:4932 20040928 SGD
+SGD S000002330 GLT1 GO:0031026 SGD_REF:S000057503|PMID:7836314 IPI C glutamate synthase (NADH) YDL171C gene taxon:4932 20041105 SGD
+SGD S000002330 GLT1 GO:0016040 SGD_REF:S000040073|PMID:8923741 ISS F glutamate synthase (NADH) YDL171C gene taxon:4932 20010723 SGD
+SGD S000002330 GLT1 GO:0006537 SGD_REF:S000049710|PMID:9657994 IEP P glutamate synthase (NADH) YDL171C gene taxon:4932 20020930 SGD
+SGD S000000772 GLY1 GO:0005829 SGD_REF:S000073087|PMID:12676688 IDA C threonine aldolase YEL046C gene taxon:4932 20030506 SGD
+SGD S000000772 GLY1 GO:0004793 SGD_REF:S000053396|PMID:9163906 IDA F threonine aldolase YEL046C gene taxon:4932 20021118 SGD
+SGD S000000772 GLY1 GO:0006545 SGD_REF:S000063295|PMID:3086094 IDA P threonine aldolase YEL046C gene taxon:4932 20020702 SGD
+SGD S000000772 GLY1 GO:0006567 SGD_REF:S000063295|PMID:3086094 IDA P threonine aldolase YEL046C gene taxon:4932 20020702 SGD
+SGD S000001738 GMH1 GO:0030173 SGD_REF:S000073774|PMID:12808035 IDA C YKR030W|MSG1 gene taxon:4932 20031229 SGD
+SGD S000001738 GMH1 GO:0005554 SGD_REF:S000069584 ND F YKR030W|MSG1 gene taxon:4932 20021125 SGD
+SGD S000001738 GMH1 GO:0006810 SGD_REF:S000073774|PMID:12808035 IPI SGD:S000000748|SGD:S000003792 P YKR030W|MSG1 gene taxon:4932 20031229 SGD
+SGD S000001877 GNA1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C glucosamine-phosphate N-acetyltransferase YFL017C|PAT1 gene taxon:4932 20031028 SGD
+SGD S000001877 GNA1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C glucosamine-phosphate N-acetyltransferase YFL017C|PAT1 gene taxon:4932 20031028 SGD
+SGD S000001877 GNA1 GO:0004343 SGD_REF:S000045927|PMID:9867860 IDA F glucosamine-phosphate N-acetyltransferase YFL017C|PAT1 gene taxon:4932 20021002 SGD
+SGD S000001877 GNA1 GO:0006048 SGD_REF:S000045927|PMID:9867860 IMP P glucosamine-phosphate N-acetyltransferase YFL017C|PAT1 gene taxon:4932 20021002 SGD
+SGD S000001877 GNA1 GO:0006048 SGD_REF:S000045927|PMID:9867860 IDA P glucosamine-phosphate N-acetyltransferase YFL017C|PAT1 gene taxon:4932 20021002 SGD
+SGD S000001226 GND1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C 6-phosphogluconate dehydrogenase YHR183W gene taxon:4932 20020507 SGD
+SGD S000001226 GND1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C 6-phosphogluconate dehydrogenase YHR183W gene taxon:4932 20040813 SGD
+SGD S000001226 GND1 GO:0004616 SGD_REF:S000042828|PMID:1328471 IMP F 6-phosphogluconate dehydrogenase YHR183W gene taxon:4932 20020930 SGD
+SGD S000001226 GND1 GO:0006979 SGD_REF:S000061566|PMID:9480895 IMP P 6-phosphogluconate dehydrogenase YHR183W gene taxon:4932 20050105 SGD
+SGD S000001226 GND1 GO:0009051 SGD_REF:S000042828|PMID:1328471 IGI P 6-phosphogluconate dehydrogenase YHR183W gene taxon:4932 20060125 SGD
+SGD S000001226 GND1 GO:0009051 SGD_REF:S000042828|PMID:1328471 IMP P 6-phosphogluconate dehydrogenase YHR183W gene taxon:4932 20060125 SGD
+SGD S000003488 GND2 GO:0005829 SGD_REF:S000071518|PMID:11298766 TAS C 6-phosphogluconate dehydrogenase YGR256W gene taxon:4932 20021101 SGD
+SGD S000003488 GND2 GO:0004616 SGD_REF:S000042828|PMID:1328471 IMP F 6-phosphogluconate dehydrogenase YGR256W gene taxon:4932 20020930 SGD
+SGD S000003488 GND2 GO:0009051 SGD_REF:S000042828|PMID:1328471 IGI P 6-phosphogluconate dehydrogenase YGR256W gene taxon:4932 20060125 SGD
+SGD S000003488 GND2 GO:0009051 SGD_REF:S000042828|PMID:1328471 IMP P 6-phosphogluconate dehydrogenase YGR256W gene taxon:4932 20060125 SGD
+SGD S000002916 GNP1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C high affinity glutamine permease YDR508C gene taxon:4932 20040928 SGD
+SGD S000002916 GNP1 GO:0005886 SGD_REF:S000043244|PMID:10654085 ISS C high affinity glutamine permease YDR508C gene taxon:4932 20020806 SGD
+SGD S000002916 GNP1 GO:0005296 SGD_REF:S000074897|PMID:14968425 IGI SGD:S000000530|SGD:S000005875|SGD:S000001747 F high affinity glutamine permease YDR508C gene taxon:4932 20050428 SGD
+SGD S000002916 GNP1 GO:0015171 SGD_REF:S000043244|PMID:10654085 IDA F high affinity glutamine permease YDR508C gene taxon:4932 20020806 SGD
+SGD S000002916 GNP1 GO:0015359 SGD_REF:S000070031|PMID:12073087 IDA F high affinity glutamine permease YDR508C gene taxon:4932 20020801 SGD
+SGD S000002916 GNP1 GO:0006865 SGD_REF:S000043244|PMID:10654085 IDA P high affinity glutamine permease YDR508C gene taxon:4932 20020806 SGD
+SGD S000005847 GNT1 GO:0005797 SGD_REF:S000073611|PMID:12651885 IDA C N-acetylglucosaminyltransferase YOR320C gene taxon:4932 20030708 SGD
+SGD S000005847 GNT1 GO:0008375 SGD_REF:S000073611|PMID:12651885 IDA F N-acetylglucosaminyltransferase YOR320C gene taxon:4932 20030708 SGD
+SGD S000005847 GNT1 GO:0006487 SGD_REF:S000073611|PMID:12651885 IMP P N-acetylglucosaminyltransferase YOR320C gene taxon:4932 20030708 SGD
+SGD S000003720 GON7 GO:0008372 SGD_REF:S000069584 ND C YJL184W|LDB6 gene taxon:4932 20030203 SGD
+SGD S000003720 GON7 GO:0005554 SGD_REF:S000069584 ND F YJL184W|LDB6 gene taxon:4932 20030203 SGD
+SGD S000003720 GON7 GO:0000032 SGD_REF:S000075422|PMID:14734024 IMP P YJL184W|LDB6 gene taxon:4932 20040202 SGD
+SGD S000003720 GON7 GO:0009269 SGD_REF:S000063137|PMID:10681550 IEP P YJL184W|LDB6 gene taxon:4932 20030210 SGD
+SGD S000001023 GOS1 GO:0016021 SGD_REF:S000051227|PMID:9755865 NAS C YHL031C gene taxon:4932 20020827 SGD
+SGD S000001023 GOS1 GO:0016021 SGD_REF:S000051227|PMID:9755865 ISS C YHL031C gene taxon:4932 20020827 SGD
+SGD S000001023 GOS1 GO:0005485 SGD_REF:S000058453|PMID:10047442 TAS F YHL031C gene taxon:4932 20010118 SGD
+SGD S000001023 GOS1 GO:0006891 SGD_REF:S000058453|PMID:10047442 TAS P YHL031C gene taxon:4932 20010118 SGD
+SGD S000001023 GOS1 GO:0006906 SGD_REF:S000058453|PMID:10047442 TAS P YHL031C gene taxon:4932 20010118 SGD
+SGD S000004906 GOT1 GO:0000139 SGD_REF:S000040382|PMID:10406798 IDA C membrane protein YMR292W gene taxon:4932 20020921 SGD
+SGD S000004906 GOT1 GO:0005554 SGD_REF:S000069584 ND F membrane protein YMR292W gene taxon:4932 20021204 SGD
+SGD S000004906 GOT1 GO:0006888 SGD_REF:S000040382|PMID:10406798 IMP P membrane protein YMR292W gene taxon:4932 20020921 SGD
+SGD S000004906 GOT1 GO:0006895 SGD_REF:S000040382|PMID:10406798 IMP P membrane protein YMR292W gene taxon:4932 20020921 SGD
+SGD S000001047 GPA1 GO:0005834 SGD_REF:S000058498 TAS C G protein alpha subunit, coupled to mating factor receptor YHR005C|CDC70|DAC1|SCG1 gene taxon:4932 20010119 SGD
+SGD S000001047 GPA1 GO:0005886 SGD_REF:S000043515|PMID:8756677 IDA C G protein alpha subunit, coupled to mating factor receptor YHR005C|CDC70|DAC1|SCG1 gene taxon:4932 20010118 SGD
+SGD S000001047 GPA1 GO:0003924 SGD_REF:S000058498 TAS F G protein alpha subunit, coupled to mating factor receptor YHR005C|CDC70|DAC1|SCG1 gene taxon:4932 20010119 SGD
+SGD S000001047 GPA1 GO:0000750 SGD_REF:S000055540|PMID:3113739 IMP P G protein alpha subunit, coupled to mating factor receptor YHR005C|CDC70|DAC1|SCG1 gene taxon:4932 20021206 SGD
+SGD S000000822 GPA2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C nucleotide binding regulatory protein YER020W|SSP101 gene taxon:4932 20040813 SGD
+SGD S000000822 GPA2 GO:0005886 SGD_REF:S000082330|PMID:16030250 IDA C nucleotide binding regulatory protein YER020W|SSP101 gene taxon:4932 20050725 SGD
+SGD S000000822 GPA2 GO:0003924 SGD_REF:S000053546|PMID:1317171 TAS F nucleotide binding regulatory protein YER020W|SSP101 gene taxon:4932 20010118 SGD
+SGD S000000822 GPA2 GO:0001302 SGD_REF:S000080970|PMID:15722108 IMP P nucleotide binding regulatory protein YER020W|SSP101 gene taxon:4932 20050314 SGD
+SGD S000000822 GPA2 GO:0007124 SGD_REF:S000052540|PMID:10454558 IMP P nucleotide binding regulatory protein YER020W|SSP101 gene taxon:4932 20010118 SGD
+SGD S000000822 GPA2 GO:0007165 SGD_REF:S000052540|PMID:10454558 IMP P nucleotide binding regulatory protein YER020W|SSP101 gene taxon:4932 20010118 SGD
+SGD S000000822 GPA2 GO:0030437 SGD_REF:S000052540|PMID:10454558 IMP P nucleotide binding regulatory protein YER020W|SSP101 gene taxon:4932 20010118 SGD
+SGD S000005898 GPB1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YOR371C|KRH2 gene taxon:4932 20031028 SGD
+SGD S000005898 GPB1 GO:0005886 SGD_REF:S000082330|PMID:16030250 IGI C YOR371C|KRH2 gene taxon:4932 20050725 SGD
+SGD S000005898 GPB1 GO:0004871 SGD_REF:S000070204|PMID:12150916 IPI F YOR371C|KRH2 gene taxon:4932 20020903 SGD
+SGD S000005898 GPB1 GO:0007165 SGD_REF:S000070204|PMID:12150916 IPI P YOR371C|KRH2 gene taxon:4932 20020903 SGD
+SGD S000000052 GPB2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YAL056W|KRH1 gene taxon:4932 20031028 SGD
+SGD S000000052 GPB2 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YAL056W|KRH1 gene taxon:4932 20031028 SGD
+SGD S000000052 GPB2 GO:0005886 SGD_REF:S000082330|PMID:16030250 IDA C YAL056W|KRH1 gene taxon:4932 20050725 SGD
+SGD S000000052 GPB2 GO:0004871 SGD_REF:S000070204|PMID:12150916 IPI F YAL056W|KRH1 gene taxon:4932 20020903 SGD
+SGD S000000052 GPB2 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P YAL056W|KRH1 gene taxon:4932 20060214 SGD
+SGD S000000052 GPB2 GO:0007165 SGD_REF:S000070204|PMID:12150916 IPI P YAL056W|KRH1 gene taxon:4932 20020903 SGD
+SGD S000002180 GPD1 GO:0005777 SGD_REF:S000077160|PMID:15210723 IDA C glycerol-3-phosphate dehydrogenase YDL022W|DAR1|HOR1|OSG1|OSR5 gene taxon:4932 20050210 SGD
+SGD S000002180 GPD1 GO:0005829 SGD_REF:S000077160|PMID:15210723 IDA C glycerol-3-phosphate dehydrogenase YDL022W|DAR1|HOR1|OSG1|OSR5 gene taxon:4932 20050210 SGD
+SGD S000002180 GPD1 GO:0004367 SGD_REF:S000041064|PMID:8196651 IMP F glycerol-3-phosphate dehydrogenase YDL022W|DAR1|HOR1|OSG1|OSR5 gene taxon:4932 20010118 SGD
+SGD S000002180 GPD1 GO:0006973 SGD_REF:S000041064|PMID:8196651 IMP P glycerol-3-phosphate dehydrogenase YDL022W|DAR1|HOR1|OSG1|OSR5 gene taxon:4932 20010118 SGD
+SGD S000005420 GPD2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C glycerol-3-phosphate dehydrogenase (NAD+) YOL059W|GPD3 gene taxon:4932 20040928 SGD
+SGD S000005420 GPD2 GO:0005829 SGD_REF:S000039774|PMID:10781551 TAS C glycerol-3-phosphate dehydrogenase (NAD+) YOL059W|GPD3 gene taxon:4932 20020930 SGD
+SGD S000005420 GPD2 GO:0004367 SGD_REF:S000049860|PMID:9171333 IMP F glycerol-3-phosphate dehydrogenase (NAD+) YOL059W|GPD3 gene taxon:4932 20020723 SGD
+SGD S000005420 GPD2 GO:0006071 SGD_REF:S000049860|PMID:9171333 IMP P glycerol-3-phosphate dehydrogenase (NAD+) YOL059W|GPD3 gene taxon:4932 20020930 SGD
+SGD S000003089 GPG1 GO:0008372 SGD_REF:S000069584 ND C Heterotrimeric G protein gamma subunit mimic YGL121C gene taxon:4932 20020903 SGD
+SGD S000003089 GPG1 GO:0004871 SGD_REF:S000070204|PMID:12150916 IPI F Heterotrimeric G protein gamma subunit mimic YGL121C gene taxon:4932 20020903 SGD
+SGD S000003089 GPG1 GO:0007165 SGD_REF:S000070204|PMID:12150916 IPI P Heterotrimeric G protein gamma subunit mimic YGL121C gene taxon:4932 20020903 SGD
+SGD S000006364 GPH1 GO:0005737 SGD_REF:S000041043|PMID:2657401 IC GO:0008184 C glycogen phosphorylase YPR160W gene taxon:4932 20021118 SGD
+SGD S000006364 GPH1 GO:0008184 SGD_REF:S000041043|PMID:2657401 IMP F glycogen phosphorylase YPR160W gene taxon:4932 20020930 SGD
+SGD S000006364 GPH1 GO:0005980 SGD_REF:S000041043|PMID:2657401 IMP P glycogen phosphorylase YPR160W gene taxon:4932 20020930 SGD
+SGD S000003448 GPI1 GO:0000506 SGD_REF:S000062716|PMID:11102867 TAS C YGR216C gene taxon:4932 20050713 SGD
+SGD S000003448 GPI1 GO:0000506 SGD_REF:S000058280|PMID:9463366 ISS C YGR216C gene taxon:4932 20050713 SGD
+SGD S000003448 GPI1 GO:0016020 SGD_REF:S000046763|PMID:8910381 ISS C YGR216C gene taxon:4932 20020813 SGD
+SGD S000003448 GPI1 GO:0016020 SGD_REF:S000046763|PMID:8910381 TAS C YGR216C gene taxon:4932 20020813 SGD
+SGD S000003448 GPI1 contributes_to GO:0008194 SGD_REF:S000058280|PMID:9463366 IC GO:0000506 F YGR216C gene taxon:4932 20050713 SGD
+SGD S000003448 GPI1 GO:0006506 SGD_REF:S000046763|PMID:8910381 IDA P YGR216C gene taxon:4932 20020813 SGD
+SGD S000003448 GPI1 GO:0006506 SGD_REF:S000046763|PMID:8910381 IMP P YGR216C gene taxon:4932 20020813 SGD
+SGD S000003110 GPI10 GO:0016021 SGD_REF:S000044026|PMID:9639537 ISS C alpha 1,2 mannosyltransferase (putative) YGL142C gene taxon:4932 20020903 SGD
+SGD S000003110 GPI10 GO:0000030 SGD_REF:S000048475|PMID:9576863 IMP F alpha 1,2 mannosyltransferase (putative) YGL142C gene taxon:4932 20050103 SGD
+SGD S000003110 GPI10 GO:0006506 SGD_REF:S000039933|PMID:9759715 IMP P alpha 1,2 mannosyltransferase (putative) YGL142C gene taxon:4932 20020903 SGD
+SGD S000002710 GPI11 GO:0005783 SGD_REF:S000043532|PMID:10793139 ISS C YDR302W gene taxon:4932 20010118 SGD
+SGD S000002710 GPI11 GO:0005789 SGD_REF:S000043532|PMID:10793139 IC GO:0006506 C YDR302W gene taxon:4932 20050416 SGD
+SGD S000002710 GPI11 GO:0000234 SGD_REF:S000043532|PMID:10793139 IMP F YDR302W gene taxon:4932 20010118 SGD
+SGD S000002710 GPI11 GO:0006506 SGD_REF:S000043532|PMID:10793139 IMP P YDR302W gene taxon:4932 20010118 SGD
+SGD S000004894 GPI12 GO:0005789 SGD_REF:S000040287|PMID:10085243 ISS C N-acetylglucosaminylphosphatidylinositol de-N-acetylase YMR281W gene taxon:4932 20010118 SGD
+SGD S000004894 GPI12 GO:0000225 SGD_REF:S000040287|PMID:10085243 ISS F N-acetylglucosaminylphosphatidylinositol de-N-acetylase YMR281W gene taxon:4932 20010118 SGD
+SGD S000004894 GPI12 GO:0006506 SGD_REF:S000040287|PMID:10085243 ISS P N-acetylglucosaminylphosphatidylinositol de-N-acetylase YMR281W gene taxon:4932 20010118 SGD
+SGD S000003954 GPI13 GO:0005783 SGD_REF:S000043532|PMID:10793139 ISS C YLL031C|MPC1 gene taxon:4932 20010118 SGD
+SGD S000003954 GPI13 GO:0016772 SGD_REF:S000043532|PMID:10793139 IMP F YLL031C|MPC1 gene taxon:4932 20050328 SGD
+SGD S000003954 GPI13 GO:0006506 SGD_REF:S000043532|PMID:10793139 IMP P YLL031C|MPC1 gene taxon:4932 20010118 SGD
+SGD S000003774 GPI14 GO:0005789 SGD_REF:S000065751|PMID:11226175 ISS C YJR013W|PMH1 gene taxon:4932 20030210 SGD
+SGD S000003774 GPI14 GO:0000030 SGD_REF:S000065751|PMID:11226175 ISS F YJR013W|PMH1 gene taxon:4932 20030210 SGD
+SGD S000003774 GPI14 GO:0006506 SGD_REF:S000065751|PMID:11226175 ISS P YJR013W|PMH1 gene taxon:4932 20030210 SGD
+SGD S000003774 GPI14 GO:0006506 SGD_REF:S000086448|PMID:16134120 IMP P YJR013W|PMH1 gene taxon:4932 20051118 SGD
+SGD S000003774 GPI14 GO:0031505 SGD_REF:S000086448|PMID:16134120 IMP P YJR013W|PMH1 gene taxon:4932 20051118 SGD
+SGD S000004983 GPI15 GO:0000506 SGD_REF:S000062716|PMID:11102867 TAS C human Pig-H homolog (functional and sequence homolog) YNL038W gene taxon:4932 20050713 SGD
+SGD S000004983 GPI15 GO:0000506 SGD_REF:S000068758|PMID:11746600 ISS C human Pig-H homolog (functional and sequence homolog) YNL038W gene taxon:4932 20050713 SGD
+SGD S000004983 GPI15 contributes_to GO:0008194 SGD_REF:S000068758|PMID:11746600 IC GO:0000506 F human Pig-H homolog (functional and sequence homolog) YNL038W gene taxon:4932 20050713 SGD
+SGD S000004983 GPI15 GO:0006506 SGD_REF:S000068758|PMID:11746600 IMP P human Pig-H homolog (functional and sequence homolog) YNL038W gene taxon:4932 20021211 SGD
+SGD S000004983 GPI15 GO:0006506 SGD_REF:S000068758|PMID:11746600 ISS P human Pig-H homolog (functional and sequence homolog) YNL038W gene taxon:4932 20021211 SGD
+SGD S000001231 GPI16 GO:0042765 SGD_REF:S000066151|PMID:11598210 IPI C GPI transamidase component, human PIG-T homologue YHR188C gene taxon:4932 20050209 SGD
+SGD S000001231 GPI16 GO:0003923 SGD_REF:S000066151|PMID:11598210 IMP F GPI transamidase component, human PIG-T homologue YHR188C gene taxon:4932 20020724 SGD
+SGD S000001231 GPI16 GO:0003923 SGD_REF:S000066151|PMID:11598210 IPI F GPI transamidase component, human PIG-T homologue YHR188C gene taxon:4932 20020724 SGD
+SGD S000001231 GPI16 GO:0016255 SGD_REF:S000066151|PMID:11598210 IMP P GPI transamidase component, human PIG-T homologue YHR188C gene taxon:4932 20020724 SGD
+SGD S000002842 GPI17 GO:0042765 SGD_REF:S000061405|PMID:11483512 IMP C GPI transamidase component, human PIG-S homologue YDR434W gene taxon:4932 20050209 SGD
+SGD S000002842 GPI17 GO:0042765 SGD_REF:S000061405|PMID:11483512 ISS C GPI transamidase component, human PIG-S homologue YDR434W gene taxon:4932 20050209 SGD
+SGD S000002842 GPI17 GO:0003923 SGD_REF:S000061405|PMID:11483512 ISS F GPI transamidase component, human PIG-S homologue YDR434W gene taxon:4932 20021003 SGD
+SGD S000002842 GPI17 GO:0003923 SGD_REF:S000061405|PMID:11483512 IMP F GPI transamidase component, human PIG-S homologue YDR434W gene taxon:4932 20021003 SGD
+SGD S000002842 GPI17 GO:0016255 SGD_REF:S000061405|PMID:11483512 ISS P GPI transamidase component, human PIG-S homologue YDR434W gene taxon:4932 20021003 SGD
+SGD S000002842 GPI17 GO:0016255 SGD_REF:S000061405|PMID:11483512 IMP P GPI transamidase component, human PIG-S homologue YDR434W gene taxon:4932 20021003 SGD
+SGD S000000208 GPI18 GO:0005783 SGD_REF:S000080153|PMID:15623507 ISS protein_id:BAA91196 C mannosyltransferase YBR004C|FMP44 gene taxon:4932 20050103 SGD
+SGD S000000208 GPI18 GO:0000030 SGD_REF:S000080153|PMID:15623507 IGI protein_id:BAA91196 F mannosyltransferase YBR004C|FMP44 gene taxon:4932 20050103 SGD
+SGD S000000208 GPI18 GO:0000030 SGD_REF:S000080153|PMID:15623507 ISS protein_id:BAA91196 F mannosyltransferase YBR004C|FMP44 gene taxon:4932 20050103 SGD
+SGD S000000208 GPI18 GO:0000030 SGD_REF:S000080971|PMID:15720390 IGI F mannosyltransferase YBR004C|FMP44 gene taxon:4932 20050317 SGD
+SGD S000000208 GPI18 GO:0000030 SGD_REF:S000080971|PMID:15720390 ISS F mannosyltransferase YBR004C|FMP44 gene taxon:4932 20050317 SGD
+SGD S000000208 GPI18 GO:0000030 SGD_REF:S000080971|PMID:15720390 IMP F mannosyltransferase YBR004C|FMP44 gene taxon:4932 20050317 SGD
+SGD S000000208 GPI18 GO:0006506 SGD_REF:S000080153|PMID:15623507 IGI protein_id:BAA91196 P mannosyltransferase YBR004C|FMP44 gene taxon:4932 20050103 SGD
+SGD S000000208 GPI18 GO:0006506 SGD_REF:S000080971|PMID:15720390 IGI P mannosyltransferase YBR004C|FMP44 gene taxon:4932 20050317 SGD
+SGD S000000208 GPI18 GO:0006506 SGD_REF:S000080971|PMID:15720390 IMP P mannosyltransferase YBR004C|FMP44 gene taxon:4932 20050317 SGD
+SGD S000002845 GPI19 GO:0000506 SGD_REF:S000082258|PMID:10944123 ISS C subunit of the GPI-GlcNAc transferase YDR437W gene taxon:4932 20050712 SGD
+SGD S000002845 GPI19 GO:0000506 SGD_REF:S000087158|PMID:16278447 IPI SGD:S000005997 C subunit of the GPI-GlcNAc transferase YDR437W gene taxon:4932 20051110 SGD
+SGD S000002845 GPI19 GO:0005635 SGD_REF:S000075214|PMID:14690591 IDA C subunit of the GPI-GlcNAc transferase YDR437W gene taxon:4932 20040105 SGD
+SGD S000002845 GPI19 GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C subunit of the GPI-GlcNAc transferase YDR437W gene taxon:4932 20031028 SGD
+SGD S000002845 GPI19 GO:0005783 SGD_REF:S000075214|PMID:14690591 IDA C subunit of the GPI-GlcNAc transferase YDR437W gene taxon:4932 20040105 SGD
+SGD S000002845 GPI19 GO:0030176 SGD_REF:S000087158|PMID:16278447 IDA C subunit of the GPI-GlcNAc transferase YDR437W gene taxon:4932 20051110 SGD
+SGD S000002845 GPI19 contributes_to GO:0008194 SGD_REF:S000082258|PMID:10944123 IC GO:0000506 F subunit of the GPI-GlcNAc transferase YDR437W gene taxon:4932 20050712 SGD
+SGD S000002845 GPI19 contributes_to GO:0008194 SGD_REF:S000087158|PMID:16278447 IMP F subunit of the GPI-GlcNAc transferase YDR437W gene taxon:4932 20051110 SGD
+SGD S000002845 GPI19 GO:0006506 SGD_REF:S000082258|PMID:10944123 IC GO:0000506 P subunit of the GPI-GlcNAc transferase YDR437W gene taxon:4932 20050712 SGD
+SGD S000002845 GPI19 GO:0006506 SGD_REF:S000087158|PMID:16278447 IMP P subunit of the GPI-GlcNAc transferase YDR437W gene taxon:4932 20051110 SGD
+SGD S000005997 GPI2 GO:0000506 SGD_REF:S000076482|PMID:15163411 IPI SGD:S000028423 C YPL076W|GCR4 gene taxon:4932 20040727 SGD
+SGD S000005997 GPI2 GO:0000506 SGD_REF:S000062716|PMID:11102867 TAS C YPL076W|GCR4 gene taxon:4932 20050713 SGD
+SGD S000005997 GPI2 GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YPL076W|GCR4 gene taxon:4932 20031028 SGD
+SGD S000005997 GPI2 contributes_to GO:0008194 SGD_REF:S000076482|PMID:15163411 IC GO:0000506 F YPL076W|GCR4 gene taxon:4932 20050713 SGD
+SGD S000005997 GPI2 GO:0006506 SGD_REF:S000043079|PMID:7768896 IDA P YPL076W|GCR4 gene taxon:4932 20020813 SGD
+SGD S000005997 GPI2 GO:0006506 SGD_REF:S000043079|PMID:7768896 IMP P YPL076W|GCR4 gene taxon:4932 20020813 SGD
+SGD S000005997 GPI2 GO:0006506 SGD_REF:S000043079|PMID:7768896 IGI P YPL076W|GCR4 gene taxon:4932 20020813 SGD
+SGD S000002739 GPI8 GO:0042765 SGD_REF:S000066151|PMID:11598210 IPI C YDR331W gene taxon:4932 20050209 SGD
+SGD S000002739 GPI8 GO:0003923 SGD_REF:S000066151|PMID:11598210 IMP F YDR331W gene taxon:4932 20020724 SGD
+SGD S000002739 GPI8 GO:0003923 SGD_REF:S000066151|PMID:11598210 IPI F YDR331W gene taxon:4932 20020724 SGD
+SGD S000002739 GPI8 GO:0016255 SGD_REF:S000066151|PMID:11598210 IMP P YDR331W gene taxon:4932 20020724 SGD
+SGD S000001635 GPM1 GO:0005829 SGD_REF:S000061087|PMID:3332961 IDA C phosphoglycerate mutase YKL152C gene taxon:4932 20050606 SGD
+SGD S000001635 GPM1 GO:0004619 SGD_REF:S000056991|PMID:3033435 IMP F phosphoglycerate mutase YKL152C gene taxon:4932 20010118 SGD
+SGD S000001635 GPM1 GO:0006094 SGD_REF:S000056991|PMID:3033435 IMP P phosphoglycerate mutase YKL152C gene taxon:4932 20050606 SGD
+SGD S000001635 GPM1 GO:0006096 SGD_REF:S000061500|PMID:11015729 IMP P phosphoglycerate mutase YKL152C gene taxon:4932 20050606 SGD
+SGD S000002179 GPM2 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YDL021W gene taxon:4932 20020507 SGD
+SGD S000002179 GPM2 GO:0005829 SGD_REF:S000058491 TAS C YDL021W gene taxon:4932 20010119 SGD
+SGD S000002179 GPM2 NOT GO:0004619 SGD_REF:S000049007|PMID:9544241 IMP F YDL021W gene taxon:4932 20030911 SGD
+SGD S000002179 GPM2 GO:0005554 SGD_REF:S000069584 ND F YDL021W gene taxon:4932 20040929 SGD
+SGD S000002179 GPM2 GO:0000004 SGD_REF:S000069584 ND P YDL021W gene taxon:4932 20050510 SGD
+SGD S000005417 GPM3 GO:0005829 SGD_REF:S000058491 TAS C phosphoglycerate mutase YOL056W gene taxon:4932 20010119 SGD
+SGD S000005417 GPM3 NOT GO:0004619 SGD_REF:S000049007|PMID:9544241 IMP F phosphoglycerate mutase YOL056W gene taxon:4932 20030911 SGD
+SGD S000005417 GPM3 GO:0005554 SGD_REF:S000069584 ND F phosphoglycerate mutase YOL056W gene taxon:4932 20041206 SGD
+SGD S000005417 GPM3 GO:0000004 SGD_REF:S000069584 ND P phosphoglycerate mutase YOL056W gene taxon:4932 20050510 SGD
+SGD S000002193 GPR1 GO:0005886 SGD_REF:S000045873|PMID:10655215 IDA C G protein coupled receptor (GPCR) YDL035C gene taxon:4932 20010702 SGD
+SGD S000002193 GPR1 GO:0005886 SGD_REF:S000041767|PMID:9524122 IDA C G protein coupled receptor (GPCR) YDL035C gene taxon:4932 20010702 SGD
+SGD S000002193 GPR1 GO:0004930 SGD_REF:S000041767|PMID:9524122 IMP F G protein coupled receptor (GPCR) YDL035C gene taxon:4932 20010702 SGD
+SGD S000002193 GPR1 GO:0004930 SGD_REF:S000041767|PMID:9524122 IPI F G protein coupled receptor (GPCR) YDL035C gene taxon:4932 20010702 SGD
+SGD S000002193 GPR1 GO:0004930 SGD_REF:S000041767|PMID:9524122 ISS F G protein coupled receptor (GPCR) YDL035C gene taxon:4932 20010702 SGD
+SGD S000002193 GPR1 GO:0001302 SGD_REF:S000080970|PMID:15722108 IMP P G protein coupled receptor (GPCR) YDL035C gene taxon:4932 20050314 SGD
+SGD S000002193 GPR1 GO:0007124 SGD_REF:S000045873|PMID:10655215 IMP P G protein coupled receptor (GPCR) YDL035C gene taxon:4932 20010702 SGD
+SGD S000002193 GPR1 GO:0007186 SGD_REF:S000041767|PMID:9524122 IMP P G protein coupled receptor (GPCR) YDL035C gene taxon:4932 20010702 SGD
+SGD S000002193 GPR1 GO:0007186 SGD_REF:S000041767|PMID:9524122 IPI P G protein coupled receptor (GPCR) YDL035C gene taxon:4932 20010702 SGD
+SGD S000001775 GPT2 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C glycerol 3-phosphate/dihydroxyacetone phosphate dual substrate-specific sn-1 acyltransferase YKR067W|GAT1 gene taxon:4932 20020507 SGD
+SGD S000001775 GPT2 GO:0005783 SGD_REF:S000069459|PMID:11914276 IDA C glycerol 3-phosphate/dihydroxyacetone phosphate dual substrate-specific sn-1 acyltransferase YKR067W|GAT1 gene taxon:4932 20020507 SGD
+SGD S000001775 GPT2 GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C glycerol 3-phosphate/dihydroxyacetone phosphate dual substrate-specific sn-1 acyltransferase YKR067W|GAT1 gene taxon:4932 20031028 SGD
+SGD S000001775 GPT2 GO:0004366 SGD_REF:S000066203|PMID:11544256 IGI F glycerol 3-phosphate/dihydroxyacetone phosphate dual substrate-specific sn-1 acyltransferase YKR067W|GAT1 gene taxon:4932 20021028 SGD
+SGD S000001775 GPT2 GO:0004366 SGD_REF:S000066203|PMID:11544256 IDA F glycerol 3-phosphate/dihydroxyacetone phosphate dual substrate-specific sn-1 acyltransferase YKR067W|GAT1 gene taxon:4932 20021028 SGD
+SGD S000001775 GPT2 GO:0004366 SGD_REF:S000066203|PMID:11544256 IMP F glycerol 3-phosphate/dihydroxyacetone phosphate dual substrate-specific sn-1 acyltransferase YKR067W|GAT1 gene taxon:4932 20021028 SGD
+SGD S000001775 GPT2 GO:0008654 SGD_REF:S000066203|PMID:11544256 IGI P glycerol 3-phosphate/dihydroxyacetone phosphate dual substrate-specific sn-1 acyltransferase YKR067W|GAT1 gene taxon:4932 20021028 SGD
+SGD S000001775 GPT2 GO:0008654 SGD_REF:S000066203|PMID:11544256 IMP P glycerol 3-phosphate/dihydroxyacetone phosphate dual substrate-specific sn-1 acyltransferase YKR067W|GAT1 gene taxon:4932 20021028 SGD
+SGD S000001775 GPT2 GO:0008654 SGD_REF:S000066203|PMID:11544256 IDA P glycerol 3-phosphate/dihydroxyacetone phosphate dual substrate-specific sn-1 acyltransferase YKR067W|GAT1 gene taxon:4932 20021028 SGD
+SGD S000001509 GPX1 GO:0008372 SGD_REF:S000069584 ND C YKL026C gene taxon:4932 20020928 SGD
+SGD S000001509 GPX1 GO:0004602 SGD_REF:S000040535|PMID:10480913 IMP F YKL026C gene taxon:4932 20060601 SGD
+SGD S000001509 GPX1 GO:0004602 SGD_REF:S000040535|PMID:10480913 ISS F YKL026C gene taxon:4932 20060601 SGD
+SGD S000001509 GPX1 GO:0047066 SGD_REF:S000065852|PMID:11445588 IDA F YKL026C gene taxon:4932 20060601 SGD
+SGD S000001509 GPX1 GO:0047066 SGD_REF:S000065852|PMID:11445588 IMP F YKL026C gene taxon:4932 20060601 SGD
+SGD S000001509 GPX1 GO:0006979 SGD_REF:S000065852|PMID:11445588 IMP P YKL026C gene taxon:4932 20020928 SGD
+SGD S000000448 GPX2 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YBR244W|AMI1 gene taxon:4932 20031028 SGD
+SGD S000000448 GPX2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YBR244W|AMI1 gene taxon:4932 20031028 SGD
+SGD S000000448 GPX2 GO:0004602 SGD_REF:S000065852|PMID:11445588 IDA F YBR244W|AMI1 gene taxon:4932 20020928 SGD
+SGD S000000448 GPX2 GO:0004602 SGD_REF:S000040535|PMID:10480913 ISS F YBR244W|AMI1 gene taxon:4932 20060601 SGD
+SGD S000000448 GPX2 GO:0004602 SGD_REF:S000040535|PMID:10480913 IMP F YBR244W|AMI1 gene taxon:4932 20060601 SGD
+SGD S000000448 GPX2 GO:0047066 SGD_REF:S000065852|PMID:11445588 IDA F YBR244W|AMI1 gene taxon:4932 20060601 SGD
+SGD S000000448 GPX2 GO:0047066 SGD_REF:S000065852|PMID:11445588 IMP F YBR244W|AMI1 gene taxon:4932 20060601 SGD
+SGD S000000448 GPX2 GO:0006979 SGD_REF:S000065852|PMID:11445588 IMP P YBR244W|AMI1 gene taxon:4932 20020928 SGD
+SGD S000003958 GRC3 GO:0008372 SGD_REF:S000069584 ND C YLL035W gene taxon:4932 20021004 SGD
+SGD S000003958 GRC3 GO:0005554 SGD_REF:S000069584 ND F YLL035W gene taxon:4932 20021004 SGD
+SGD S000003958 GRC3 GO:0006364 SGD_REF:S000073750|PMID:12837249 IMP P YLL035W gene taxon:4932 20030805 SGD
+SGD S000029189 GRD10 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20050722 SGD
+SGD S000029189 GRD10 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20050722 SGD
+SGD S000029189 GRD10 GO:0045053 SGD_REF:S000057861|PMID:8649377 IMP P gene taxon:4932 20020716 SGD
+SGD S000029190 GRD14 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20050722 SGD
+SGD S000029190 GRD14 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20050722 SGD
+SGD S000029190 GRD14 GO:0045053 SGD_REF:S000057861|PMID:8649377 IMP P gene taxon:4932 20020716 SGD
+SGD S000029191 GRD15 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20050722 SGD
+SGD S000029191 GRD15 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20050722 SGD
+SGD S000029191 GRD15 GO:0045053 SGD_REF:S000057861|PMID:8649377 IMP P gene taxon:4932 20020716 SGD
+SGD S000029192 GRD16 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20050722 SGD
+SGD S000029192 GRD16 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20050722 SGD
+SGD S000029192 GRD16 GO:0045053 SGD_REF:S000057861|PMID:8649377 IMP P gene taxon:4932 20020716 SGD
+SGD S000029193 GRD17 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20050722 SGD
+SGD S000029193 GRD17 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20050722 SGD
+SGD S000029193 GRD17 GO:0045053 SGD_REF:S000057861|PMID:8649377 IMP P gene taxon:4932 20020716 SGD
+SGD S000029194 GRD18 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20050722 SGD
+SGD S000029194 GRD18 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20050722 SGD
+SGD S000029194 GRD18 GO:0045053 SGD_REF:S000057861|PMID:8649377 IMP P gene taxon:4932 20020716 SGD
+SGD S000029195 GRD3 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20050722 SGD
+SGD S000029195 GRD3 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20050722 SGD
+SGD S000029195 GRD3 GO:0045053 SGD_REF:S000057861|PMID:8649377 IMP P gene taxon:4932 20020716 SGD
+SGD S000029196 GRD4 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20050722 SGD
+SGD S000029196 GRD4 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20050722 SGD
+SGD S000029196 GRD4 GO:0045053 SGD_REF:S000057861|PMID:8649377 IMP P gene taxon:4932 20020716 SGD
+SGD S000029197 GRD5 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20050722 SGD
+SGD S000029197 GRD5 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20050722 SGD
+SGD S000029197 GRD5 GO:0045053 SGD_REF:S000057861|PMID:8649377 IMP P gene taxon:4932 20020716 SGD
+SGD S000006144 GRE1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YPL223C gene taxon:4932 20020507 SGD
+SGD S000006144 GRE1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YPL223C gene taxon:4932 20031028 SGD
+SGD S000006144 GRE1 GO:0005554 SGD_REF:S000069584 ND F YPL223C gene taxon:4932 20021211 SGD
+SGD S000006144 GRE1 GO:0006950 SGD_REF:S000039816|PMID:10407268 IEP P YPL223C gene taxon:4932 20021211 SGD
+SGD S000006144 GRE1 GO:0009269 SGD_REF:S000063137|PMID:10681550 IEP P YPL223C gene taxon:4932 20030210 SGD
+SGD S000005511 GRE2 GO:0005634 SGD_REF:S000071811|PMID:12206772 IDA C YOL151W gene taxon:4932 20030509 SGD
+SGD S000005511 GRE2 GO:0005737 SGD_REF:S000071811|PMID:12206772 IDA C YOL151W gene taxon:4932 20030509 SGD
+SGD S000005511 GRE2 GO:0016491 SGD_REF:S000060971|PMID:11456752 IDA F YOL151W gene taxon:4932 20021009 SGD
+SGD S000005511 GRE2 GO:0019170 SGD_REF:S000072946|PMID:12722185 IDA F YOL151W gene taxon:4932 20030505 SGD
+SGD S000005511 GRE2 GO:0006950 SGD_REF:S000039816|PMID:10407268 IEP P YOL151W gene taxon:4932 20021211 SGD
+SGD S000001146 GRE3 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C aldose reductase YHR104W gene taxon:4932 20031028 SGD
+SGD S000001146 GRE3 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C aldose reductase YHR104W gene taxon:4932 20031028 SGD
+SGD S000001146 GRE3 GO:0004032 SGD_REF:S000061291|PMID:11525399 IDA F aldose reductase YHR104W gene taxon:4932 20020819 SGD
+SGD S000001146 GRE3 GO:0004032 SGD_REF:S000060122|PMID:11306085 IDA F aldose reductase YHR104W gene taxon:4932 20030912 SGD
+SGD S000001146 GRE3 GO:0004033 SGD_REF:S000060122|PMID:11306085 ISS F aldose reductase YHR104W gene taxon:4932 20030912 SGD
+SGD S000001146 GRE3 GO:0006950 SGD_REF:S000061291|PMID:11525399 IDA P aldose reductase YHR104W gene taxon:4932 20020819 SGD
+SGD S000001146 GRE3 GO:0019568 SGD_REF:S000071519|PMID:12271459 IDA P aldose reductase YHR104W gene taxon:4932 20050131 SGD
+SGD S000001146 GRE3 GO:0019568 SGD_REF:S000071519|PMID:12271459 IMP P aldose reductase YHR104W gene taxon:4932 20050131 SGD
+SGD S000001146 GRE3 GO:0042843 SGD_REF:S000071519|PMID:12271459 IDA P aldose reductase YHR104W gene taxon:4932 20050131 SGD
+SGD S000001146 GRE3 GO:0042843 SGD_REF:S000071519|PMID:12271459 IMP P aldose reductase YHR104W gene taxon:4932 20050131 SGD
+SGD S000002925 GRH1 GO:0005737 SGD_REF:S000072519|PMID:10417390 IDA C mammalian GRASP protein homolog YDR517W gene taxon:4932 20030507 SGD
+SGD S000002925 GRH1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C mammalian GRASP protein homolog YDR517W gene taxon:4932 20020507 SGD
+SGD S000002925 GRH1 GO:0005554 SGD_REF:S000069584 ND F mammalian GRASP protein homolog YDR517W gene taxon:4932 20021209 SGD
+SGD S000002925 GRH1 GO:0007030 SGD_REF:S000072519|PMID:10417390 ISS P mammalian GRASP protein homolog YDR517W gene taxon:4932 20051111 SGD
+SGD S000002925 GRH1 GO:0007094 SGD_REF:S000072519|PMID:10417390 IMP P mammalian GRASP protein homolog YDR517W gene taxon:4932 20030507 SGD
+SGD S000003850 GRR1 GO:0000142 SGD_REF:S000059560|PMID:11080155 IDA C YJR090C|CAT80|COT2|SDC1|SSU2 gene taxon:4932 20030619 SGD
+SGD S000003850 GRR1 GO:0000142 SGD_REF:S000081151|PMID:15775961 IDA C YJR090C|CAT80|COT2|SDC1|SSU2 gene taxon:4932 20050330 SGD
+SGD S000003850 GRR1 GO:0000152 SGD_REF:S000045265|PMID:10409741 TAS C YJR090C|CAT80|COT2|SDC1|SSU2 gene taxon:4932 20010118 SGD
+SGD S000003850 GRR1 GO:0005634 SGD_REF:S000059560|PMID:11080155 IDA C YJR090C|CAT80|COT2|SDC1|SSU2 gene taxon:4932 20030619 SGD
+SGD S000003850 GRR1 GO:0005737 SGD_REF:S000059560|PMID:11080155 IDA C YJR090C|CAT80|COT2|SDC1|SSU2 gene taxon:4932 20030619 SGD
+SGD S000003850 GRR1 GO:0019005 SGD_REF:S000058369|PMID:9736614 IMP C YJR090C|CAT80|COT2|SDC1|SSU2 gene taxon:4932 20050408 SGD
+SGD S000003850 GRR1 GO:0004842 SGD_REF:S000045265|PMID:10409741 TAS F YJR090C|CAT80|COT2|SDC1|SSU2 gene taxon:4932 20010118 SGD
+SGD S000003850 GRR1 GO:0005515 SGD_REF:S000045265|PMID:10409741 TAS F YJR090C|CAT80|COT2|SDC1|SSU2 gene taxon:4932 20010118 SGD
+SGD S000003850 GRR1 GO:0000082 SGD_REF:S000058469|PMID:9346231 TAS P YJR090C|CAT80|COT2|SDC1|SSU2 gene taxon:4932 20010118 SGD
+SGD S000003850 GRR1 GO:0000751 SGD_REF:S000081860|PMID:15942932 IMP P YJR090C|CAT80|COT2|SDC1|SSU2 gene taxon:4932 20050714 SGD
+SGD S000003850 GRR1 GO:0006974 SGD_REF:S000076175|PMID:12482937 IMP P YJR090C|CAT80|COT2|SDC1|SSU2 gene taxon:4932 20060406 SGD
+SGD S000003850 GRR1 GO:0016567 SGD_REF:S000058289|PMID:9499404 IGI P YJR090C|CAT80|COT2|SDC1|SSU2 gene taxon:4932 20050408 SGD
+SGD S000003850 GRR1 GO:0016567 SGD_REF:S000058289|PMID:9499404 IPI P YJR090C|CAT80|COT2|SDC1|SSU2 gene taxon:4932 20050408 SGD
+SGD S000003850 GRR1 GO:0031146 SGD_REF:S000044434|PMID:10213692 IDA P YJR090C|CAT80|COT2|SDC1|SSU2 gene taxon:4932 20050404 SGD
+SGD S000000325 GRS1 GO:0005737 SGD_REF:S000043498|PMID:10874035 IMP C glycine-tRNA ligase YBR121C gene taxon:4932 20020918 SGD
+SGD S000000325 GRS1 GO:0005739 SGD_REF:S000043498|PMID:10874035 IMP C glycine-tRNA ligase YBR121C gene taxon:4932 20020918 SGD
+SGD S000000325 GRS1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C glycine-tRNA ligase YBR121C gene taxon:4932 20040813 SGD
+SGD S000000325 GRS1 GO:0004820 SGD_REF:S000043498|PMID:10874035 ISS F glycine-tRNA ligase YBR121C gene taxon:4932 20020918 SGD
+SGD S000000325 GRS1 GO:0004820 SGD_REF:S000043498|PMID:10874035 IMP F glycine-tRNA ligase YBR121C gene taxon:4932 20020918 SGD
+SGD S000000325 GRS1 GO:0006353 SGD_REF:S000047043|PMID:10224248 IMP P glycine-tRNA ligase YBR121C gene taxon:4932 20020918 SGD
+SGD S000000325 GRS1 GO:0006426 SGD_REF:S000043498|PMID:10874035 ISS P glycine-tRNA ligase YBR121C gene taxon:4932 20020918 SGD
+SGD S000000325 GRS1 GO:0006426 SGD_REF:S000043498|PMID:10874035 IMP P glycine-tRNA ligase YBR121C gene taxon:4932 20020918 SGD
+SGD S000006285 GRS2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YPR081C gene taxon:4932 20031028 SGD
+SGD S000006285 GRS2 GO:0004820 SGD_REF:S000043498|PMID:10874035 ISS F YPR081C gene taxon:4932 20020918 SGD
+SGD S000006285 GRS2 GO:0006426 SGD_REF:S000043498|PMID:10874035 ISS P YPR081C gene taxon:4932 20020918 SGD
+SGD S000000540 GRX1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C EC 1.20.4.1, glutaredoxin YCL035C gene taxon:4932 20031028 SGD
+SGD S000000540 GRX1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C EC 1.20.4.1, glutaredoxin YCL035C gene taxon:4932 20020507 SGD
+SGD S000000540 GRX1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C EC 1.20.4.1, glutaredoxin YCL035C gene taxon:4932 20031028 SGD
+SGD S000000540 GRX1 GO:0004364 SGD_REF:S000073390|PMID:12684511 IDA F EC 1.20.4.1, glutaredoxin YCL035C gene taxon:4932 20030702 SGD
+SGD S000000540 GRX1 GO:0004602 SGD_REF:S000073390|PMID:12684511 IDA F EC 1.20.4.1, glutaredoxin YCL035C gene taxon:4932 20030702 SGD
+SGD S000000540 GRX1 GO:0030508 SGD_REF:S000053996|PMID:9571241 ISS F EC 1.20.4.1, glutaredoxin YCL035C gene taxon:4932 20020416 SGD
+SGD S000000540 GRX1 GO:0006979 SGD_REF:S000053996|PMID:9571241 IMP P EC 1.20.4.1, glutaredoxin YCL035C gene taxon:4932 20010118 SGD
+SGD S000000540 GRX1 GO:0030503 SGD_REF:S000053996|PMID:9571241 IMP P EC 1.20.4.1, glutaredoxin YCL035C gene taxon:4932 20020411 SGD
+SGD S000000540 GRX1 GO:0030503 SGD_REF:S000053996|PMID:9571241 IDA P EC 1.20.4.1, glutaredoxin YCL035C gene taxon:4932 20020411 SGD
+SGD S000000540 GRX1 GO:0030503 SGD_REF:S000061564|PMID:11169096 TAS P EC 1.20.4.1, glutaredoxin YCL035C gene taxon:4932 20020411 SGD
+SGD S000002921 GRX2 GO:0005739 SGD_REF:S000070017|PMID:11958675 IDA C EC 1.20.4.1, glutaredoxin, thioltransferase/glutathione reductase YDR513W|TTR1 gene taxon:4932 20030221 SGD
+SGD S000002921 GRX2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C EC 1.20.4.1, glutaredoxin, thioltransferase/glutathione reductase YDR513W|TTR1 gene taxon:4932 20040924 SGD
+SGD S000002921 GRX2 GO:0005829 SGD_REF:S000070017|PMID:11958675 IDA C EC 1.20.4.1, glutaredoxin, thioltransferase/glutathione reductase YDR513W|TTR1 gene taxon:4932 20030221 SGD
+SGD S000002921 GRX2 GO:0004364 SGD_REF:S000073390|PMID:12684511 IDA F EC 1.20.4.1, glutaredoxin, thioltransferase/glutathione reductase YDR513W|TTR1 gene taxon:4932 20030702 SGD
+SGD S000002921 GRX2 GO:0004602 SGD_REF:S000073390|PMID:12684511 IDA F EC 1.20.4.1, glutaredoxin, thioltransferase/glutathione reductase YDR513W|TTR1 gene taxon:4932 20030702 SGD
+SGD S000002921 GRX2 GO:0030508 SGD_REF:S000053996|PMID:9571241 IMP F EC 1.20.4.1, glutaredoxin, thioltransferase/glutathione reductase YDR513W|TTR1 gene taxon:4932 20020416 SGD
+SGD S000002921 GRX2 GO:0030508 SGD_REF:S000053996|PMID:9571241 ISS F EC 1.20.4.1, glutaredoxin, thioltransferase/glutathione reductase YDR513W|TTR1 gene taxon:4932 20020416 SGD
+SGD S000002921 GRX2 GO:0006979 SGD_REF:S000053996|PMID:9571241 IMP P EC 1.20.4.1, glutaredoxin, thioltransferase/glutathione reductase YDR513W|TTR1 gene taxon:4932 20010118 SGD
+SGD S000002921 GRX2 GO:0030503 SGD_REF:S000053996|PMID:9571241 IMP P EC 1.20.4.1, glutaredoxin, thioltransferase/glutathione reductase YDR513W|TTR1 gene taxon:4932 20020411 SGD
+SGD S000002921 GRX2 GO:0030503 SGD_REF:S000053996|PMID:9571241 IDA P EC 1.20.4.1, glutaredoxin, thioltransferase/glutathione reductase YDR513W|TTR1 gene taxon:4932 20020411 SGD
+SGD S000002505 GRX3 GO:0005622 SGD_REF:S000071410|PMID:11950925 TAS C glutaredoxin YDR098C gene taxon:4932 20021007 SGD
+SGD S000002505 GRX3 GO:0005634 SGD_REF:S000079909|PMID:15456753 IDA C glutaredoxin YDR098C gene taxon:4932 20050126 SGD
+SGD S000002505 GRX3 GO:0030508 SGD_REF:S000048888|PMID:10567543 IMP F glutaredoxin YDR098C gene taxon:4932 20020416 SGD
+SGD S000002505 GRX3 GO:0030508 SGD_REF:S000048888|PMID:10567543 IGI F glutaredoxin YDR098C gene taxon:4932 20020416 SGD
+SGD S000002505 GRX3 GO:0030508 SGD_REF:S000048888|PMID:10567543 ISS F glutaredoxin YDR098C gene taxon:4932 20020416 SGD
+SGD S000002505 GRX3 GO:0006979 SGD_REF:S000048888|PMID:10567543 IMP P glutaredoxin YDR098C gene taxon:4932 20010118 SGD
+SGD S000002505 GRX3 GO:0006979 SGD_REF:S000048888|PMID:10567543 IGI P glutaredoxin YDR098C gene taxon:4932 20010118 SGD
+SGD S000000976 GRX4 GO:0005622 SGD_REF:S000071410|PMID:11950925 TAS C glutaredoxin YER174C gene taxon:4932 20021007 SGD
+SGD S000000976 GRX4 GO:0030508 SGD_REF:S000048888|PMID:10567543 IMP F glutaredoxin YER174C gene taxon:4932 20020416 SGD
+SGD S000000976 GRX4 GO:0030508 SGD_REF:S000048888|PMID:10567543 IGI F glutaredoxin YER174C gene taxon:4932 20020416 SGD
+SGD S000000976 GRX4 GO:0030508 SGD_REF:S000048888|PMID:10567543 ISS F glutaredoxin YER174C gene taxon:4932 20020416 SGD
+SGD S000000976 GRX4 GO:0006979 SGD_REF:S000048888|PMID:10567543 IMP P glutaredoxin YER174C gene taxon:4932 20010118 SGD
+SGD S000000976 GRX4 GO:0006979 SGD_REF:S000048888|PMID:10567543 IGI P glutaredoxin YER174C gene taxon:4932 20010118 SGD
+SGD S000005980 GRX5 GO:0005759 SGD_REF:S000071410|PMID:11950925 TAS C glutaredoxin YPL059W gene taxon:4932 20021007 SGD
+SGD S000005980 GRX5 GO:0005759 SGD_REF:S000079909|PMID:15456753 IDA C glutaredoxin YPL059W gene taxon:4932 20050126 SGD
+SGD S000005980 GRX5 GO:0030508 SGD_REF:S000048888|PMID:10567543 IMP F glutaredoxin YPL059W gene taxon:4932 20020416 SGD
+SGD S000005980 GRX5 GO:0030508 SGD_REF:S000073786|PMID:12730244 IDA F glutaredoxin YPL059W gene taxon:4932 20030821 SGD
+SGD S000005980 GRX5 GO:0030508 SGD_REF:S000048888|PMID:10567543 ISS F glutaredoxin YPL059W gene taxon:4932 20020416 SGD
+SGD S000005980 GRX5 GO:0030508 SGD_REF:S000048888|PMID:10567543 IGI F glutaredoxin YPL059W gene taxon:4932 20020416 SGD
+SGD S000005980 GRX5 GO:0006970 SGD_REF:S000048888|PMID:10567543 IMP P glutaredoxin YPL059W gene taxon:4932 20010118 SGD
+SGD S000005980 GRX5 GO:0006979 SGD_REF:S000048888|PMID:10567543 IMP P glutaredoxin YPL059W gene taxon:4932 20010118 SGD
+SGD S000005980 GRX5 GO:0006979 SGD_REF:S000048888|PMID:10567543 IGI P glutaredoxin YPL059W gene taxon:4932 20010118 SGD
+SGD S000005980 GRX5 GO:0016226 SGD_REF:S000079660|PMID:15382238 TAS P glutaredoxin YPL059W gene taxon:4932 20050328 SGD
+SGD S000003264 GSC2 GO:0000148 SGD_REF:S000045853|PMID:7649185 TAS C 1,3-beta-D-glucan synthase YGR032W|FKS2 gene taxon:4932 20010118 SGD
+SGD S000003264 GSC2 GO:0005628 SGD_REF:S000081076|PMID:15755916 IDA C 1,3-beta-D-glucan synthase YGR032W|FKS2 gene taxon:4932 20050324 SGD
+SGD S000003264 GSC2 GO:0030478 SGD_REF:S000041005|PMID:10652251 IDA C 1,3-beta-D-glucan synthase YGR032W|FKS2 gene taxon:4932 20010118 SGD
+SGD S000003264 GSC2 GO:0003843 SGD_REF:S000045853|PMID:7649185 IDA F 1,3-beta-D-glucan synthase YGR032W|FKS2 gene taxon:4932 20010118 SGD
+SGD S000003264 GSC2 GO:0003843 SGD_REF:S000043702|PMID:7565718 IDA F 1,3-beta-D-glucan synthase YGR032W|FKS2 gene taxon:4932 20010118 SGD
+SGD S000003264 GSC2 GO:0006075 SGD_REF:S000043702|PMID:7565718 TAS P 1,3-beta-D-glucan synthase YGR032W|FKS2 gene taxon:4932 20010118 SGD
+SGD S000003264 GSC2 GO:0007047 SGD_REF:S000043702|PMID:7565718 TAS P 1,3-beta-D-glucan synthase YGR032W|FKS2 gene taxon:4932 20010118 SGD
+SGD S000004511 GSF2 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YML048W|ECM6 gene taxon:4932 20020507 SGD
+SGD S000004511 GSF2 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C YML048W|ECM6 gene taxon:4932 20060317 SGD
+SGD S000004511 GSF2 GO:0030176 SGD_REF:S000040599|PMID:10377429 IDA C YML048W|ECM6 gene taxon:4932 20020920 SGD
+SGD S000004511 GSF2 GO:0005554 SGD_REF:S000069584 ND F YML048W|ECM6 gene taxon:4932 20020920 SGD
+SGD S000004511 GSF2 GO:0006457 SGD_REF:S000080152|PMID:15623581 IMP P YML048W|ECM6 gene taxon:4932 20050708 SGD
+SGD S000004511 GSF2 GO:0045045 SGD_REF:S000040599|PMID:10377429 IGI P YML048W|ECM6 gene taxon:4932 20020920 SGD
+SGD S000004511 GSF2 GO:0045045 SGD_REF:S000040599|PMID:10377429 IPI P YML048W|ECM6 gene taxon:4932 20020920 SGD
+SGD S000004511 GSF2 GO:0045045 SGD_REF:S000040599|PMID:10377429 IMP P YML048W|ECM6 gene taxon:4932 20020920 SGD
+SGD S000002515 GSG1 GO:0030008 SGD_REF:S000043703|PMID:10727015 IDA C YDR108W|MUM1|TRS85 gene taxon:4932 20020716 SGD
+SGD S000002515 GSG1 GO:0005554 SGD_REF:S000069584 ND F YDR108W|MUM1|TRS85 gene taxon:4932 20020716 SGD
+SGD S000002515 GSG1 GO:0006888 SGD_REF:S000043703|PMID:10727015 IMP P YDR108W|MUM1|TRS85 gene taxon:4932 20020716 SGD
+SGD S000002515 GSG1 GO:0006914 SGD_REF:S000086066|PMID:16079147 IMP P YDR108W|MUM1|TRS85 gene taxon:4932 20050808 SGD
+SGD S000002515 GSG1 GO:0007126 SGD_REF:S000045171|PMID:8619313 IMP P YDR108W|MUM1|TRS85 gene taxon:4932 20030115 SGD
+SGD S000002515 GSG1 GO:0016050 SGD_REF:S000086066|PMID:16079147 IMP P YDR108W|MUM1|TRS85 gene taxon:4932 20051018 SGD
+SGD S000002515 GSG1 GO:0030242 SGD_REF:S000086066|PMID:16079147 IMP P YDR108W|MUM1|TRS85 gene taxon:4932 20051018 SGD
+SGD S000003637 GSH1 GO:0005622 SGD_REF:S000071568|PMID:12406228 TAS C gamma-glutamylcysteine synthetase YJL101C gene taxon:4932 20021122 SGD
+SGD S000003637 GSH1 GO:0004357 SGD_REF:S000040589|PMID:1687097 IDA F gamma-glutamylcysteine synthetase YJL101C gene taxon:4932 20030115 SGD
+SGD S000003637 GSH1 GO:0006750 SGD_REF:S000070228|PMID:12011041 TAS P gamma-glutamylcysteine synthetase YJL101C gene taxon:4932 20020927 SGD
+SGD S000003637 GSH1 GO:0046686 SGD_REF:S000059727|PMID:10921921 IDA P gamma-glutamylcysteine synthetase YJL101C gene taxon:4932 20030527 SGD
+SGD S000005409 GSH2 GO:0005622 SGD_REF:S000071568|PMID:12406228 TAS C glutathione synthetase YOL049W gene taxon:4932 20021122 SGD
+SGD S000005409 GSH2 GO:0004363 SGD_REF:S000055388|PMID:9512666 IDA F glutathione synthetase YOL049W gene taxon:4932 20030115 SGD
+SGD S000005409 GSH2 GO:0006750 SGD_REF:S000055388|PMID:9512666 TAS P glutathione synthetase YOL049W gene taxon:4932 20020927 SGD
+SGD S000004284 GSP1 GO:0005634 SGD_REF:S000042505|PMID:8455603 IDA C GTP-binding protein YLR293C|CNR1|CST17 gene taxon:4932 20020724 SGD
+SGD S000004284 GSP1 GO:0005737 SGD_REF:S000071750|PMID:11591812 TAS C GTP-binding protein YLR293C|CNR1|CST17 gene taxon:4932 20021204 SGD
+SGD S000004284 GSP1 GO:0003924 SGD_REF:S000042505|PMID:8455603 IGI F GTP-binding protein YLR293C|CNR1|CST17 gene taxon:4932 20020724 SGD
+SGD S000004284 GSP1 GO:0003924 SGD_REF:S000042505|PMID:8455603 ISS F GTP-binding protein YLR293C|CNR1|CST17 gene taxon:4932 20020724 SGD
+SGD S000004284 GSP1 GO:0006364 SGD_REF:S000060797|PMID:11404326 IMP P GTP-binding protein YLR293C|CNR1|CST17 gene taxon:4932 20020724 SGD
+SGD S000004284 GSP1 GO:0006913 SGD_REF:S000071750|PMID:11591812 TAS P GTP-binding protein YLR293C|CNR1|CST17 gene taxon:4932 20021204 SGD
+SGD S000004284 GSP1 GO:0006997 SGD_REF:S000042505|PMID:8455603 IGI P GTP-binding protein YLR293C|CNR1|CST17 gene taxon:4932 20020724 SGD
+SGD S000004284 GSP1 GO:0006997 SGD_REF:S000042505|PMID:8455603 ISS P GTP-binding protein YLR293C|CNR1|CST17 gene taxon:4932 20020724 SGD
+SGD S000005711 GSP2 GO:0005634 SGD_REF:S000042505|PMID:8455603 IGI C GTP-binding protein, Gsp1p homolog YOR185C|CNR2 gene taxon:4932 20020724 SGD
+SGD S000005711 GSP2 GO:0005634 SGD_REF:S000042505|PMID:8455603 ISS C GTP-binding protein, Gsp1p homolog YOR185C|CNR2 gene taxon:4932 20020724 SGD
+SGD S000005711 GSP2 GO:0003924 SGD_REF:S000042505|PMID:8455603 IGI F GTP-binding protein, Gsp1p homolog YOR185C|CNR2 gene taxon:4932 20020724 SGD
+SGD S000005711 GSP2 GO:0003924 SGD_REF:S000042505|PMID:8455603 ISS F GTP-binding protein, Gsp1p homolog YOR185C|CNR2 gene taxon:4932 20020724 SGD
+SGD S000005711 GSP2 GO:0006997 SGD_REF:S000042505|PMID:8455603 IGI P GTP-binding protein, Gsp1p homolog YOR185C|CNR2 gene taxon:4932 20020724 SGD
+SGD S000005711 GSP2 GO:0006997 SGD_REF:S000042505|PMID:8455603 ISS P GTP-binding protein, Gsp1p homolog YOR185C|CNR2 gene taxon:4932 20020724 SGD
+SGD S000001911 GSY1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C glycogen synthase (UDP-glucose-starch glucosyltransferase) YFR015C gene taxon:4932 20031028 SGD
+SGD S000001911 GSY1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C glycogen synthase (UDP-glucose-starch glucosyltransferase) YFR015C gene taxon:4932 20040813 SGD
+SGD S000001911 GSY1 GO:0004373 SGD_REF:S000048993|PMID:2123485 IDA F glycogen synthase (UDP-glucose-starch glucosyltransferase) YFR015C gene taxon:4932 20021122 SGD
+SGD S000001911 GSY1 GO:0005978 SGD_REF:S000051885|PMID:1908457 IGI P glycogen synthase (UDP-glucose-starch glucosyltransferase) YFR015C gene taxon:4932 20050830 SGD
+SGD S000001911 GSY1 GO:0005978 SGD_REF:S000051885|PMID:1908457 IMP P glycogen synthase (UDP-glucose-starch glucosyltransferase) YFR015C gene taxon:4932 20050830 SGD
+SGD S000001911 GSY1 GO:0005978 SGD_REF:S000051885|PMID:1908457 ISS P glycogen synthase (UDP-glucose-starch glucosyltransferase) YFR015C gene taxon:4932 20050830 SGD
+SGD S000004248 GSY2 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C glycogen synthase (UDP-glucose-starch glucosyltransferase) YLR258W gene taxon:4932 20020507 SGD
+SGD S000004248 GSY2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C glycogen synthase (UDP-glucose-starch glucosyltransferase) YLR258W gene taxon:4932 20031028 SGD
+SGD S000004248 GSY2 GO:0004373 SGD_REF:S000051885|PMID:1908457 IMP F glycogen synthase (UDP-glucose-starch glucosyltransferase) YLR258W gene taxon:4932 20010306 SGD
+SGD S000004248 GSY2 GO:0004373 SGD_REF:S000051885|PMID:1908457 IGI F glycogen synthase (UDP-glucose-starch glucosyltransferase) YLR258W gene taxon:4932 20010306 SGD
+SGD S000004248 GSY2 GO:0004373 SGD_REF:S000051885|PMID:1908457 ISS F glycogen synthase (UDP-glucose-starch glucosyltransferase) YLR258W gene taxon:4932 20010306 SGD
+SGD S000004248 GSY2 GO:0005978 SGD_REF:S000051885|PMID:1908457 IGI P glycogen synthase (UDP-glucose-starch glucosyltransferase) YLR258W gene taxon:4932 20050830 SGD
+SGD S000004248 GSY2 GO:0005978 SGD_REF:S000051885|PMID:1908457 IMP P glycogen synthase (UDP-glucose-starch glucosyltransferase) YLR258W gene taxon:4932 20050830 SGD
+SGD S000004248 GSY2 GO:0005978 SGD_REF:S000051885|PMID:1908457 ISS P glycogen synthase (UDP-glucose-starch glucosyltransferase) YLR258W gene taxon:4932 20050830 SGD
+SGD S000002629 GTB1 GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YDR221W gene taxon:4932 20031028 SGD
+SGD S000002629 GTB1 GO:0005788 SGD_REF:S000113928|PMID:16373354 IDA C YDR221W gene taxon:4932 20060119 SGD
+SGD S000002629 GTB1 contributes_to GO:0004558 SGD_REF:S000113928|PMID:16373354 IMP F YDR221W gene taxon:4932 20060119 SGD
+SGD S000002629 GTB1 contributes_to GO:0004558 SGD_REF:S000113928|PMID:16373354 IPI SGD:S000000433 F YDR221W gene taxon:4932 20060119 SGD
+SGD S000002629 GTB1 GO:0000271 SGD_REF:S000113928|PMID:16373354 IMP P YDR221W gene taxon:4932 20060119 SGD
+SGD S000002629 GTB1 GO:0006487 SGD_REF:S000113928|PMID:16373354 IMP P YDR221W gene taxon:4932 20060119 SGD
+SGD S000003386 GTO1 GO:0008372 SGD_REF:S000069584 ND C Omega-class glutathione transferase YGR154C gene taxon:4932 20051214 SGD
+SGD S000003386 GTO1 GO:0005554 SGD_REF:S000069584 ND F Omega-class glutathione transferase YGR154C gene taxon:4932 20030203 SGD
+SGD S000003386 GTO1 GO:0000004 SGD_REF:S000069584 ND P Omega-class glutathione transferase YGR154C gene taxon:4932 20030203 SGD
+SGD S000004863 GTO3 GO:0008372 SGD_REF:S000069584 ND C Omega class glutathione transferase YMR251W gene taxon:4932 20030203 SGD
+SGD S000004863 GTO3 GO:0005554 SGD_REF:S000069584 ND F Omega class glutathione transferase YMR251W gene taxon:4932 20030203 SGD
+SGD S000004863 GTO3 GO:0000004 SGD_REF:S000069584 ND P Omega class glutathione transferase YMR251W gene taxon:4932 20030203 SGD
+SGD S000004590 GTR1 GO:0005634 SGD_REF:S000047937|PMID:10388807 IDA C small GTPase (putative) YML121W gene taxon:4932 20020529 SGD
+SGD S000004590 GTR1 GO:0005737 SGD_REF:S000047937|PMID:10388807 IDA C small GTPase (putative) YML121W gene taxon:4932 20020529 SGD
+SGD S000004590 GTR1 GO:0005774 SGD_REF:S000081946|PMID:15885099 IDA C small GTPase (putative) YML121W gene taxon:4932 20050719 SGD
+SGD S000004590 GTR1 GO:0003924 SGD_REF:S000047937|PMID:10388807 IPI F small GTPase (putative) YML121W gene taxon:4932 20020529 SGD
+SGD S000004590 GTR1 GO:0003924 SGD_REF:S000047937|PMID:10388807 ISS F small GTPase (putative) YML121W gene taxon:4932 20020529 SGD
+SGD S000004590 GTR1 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P small GTPase (putative) YML121W gene taxon:4932 20060227 SGD
+SGD S000004590 GTR1 GO:0006360 SGD_REF:S000081846|PMID:15937128 IMP P small GTPase (putative) YML121W gene taxon:4932 20060612 SGD
+SGD S000004590 GTR1 GO:0006360 SGD_REF:S000081846|PMID:15937128 IPI SGD:S000005057 P small GTPase (putative) YML121W gene taxon:4932 20060612 SGD
+SGD S000004590 GTR1 GO:0006383 SGD_REF:S000081846|PMID:15937128 IMP P small GTPase (putative) YML121W gene taxon:4932 20060612 SGD
+SGD S000004590 GTR1 GO:0006383 SGD_REF:S000081846|PMID:15937128 IPI SGD:S000005057 P small GTPase (putative) YML121W gene taxon:4932 20060612 SGD
+SGD S000004590 GTR1 GO:0006817 SGD_REF:S000044095|PMID:1620108 IMP P small GTPase (putative) YML121W gene taxon:4932 20020529 SGD
+SGD S000003395 GTR2 GO:0005634 SGD_REF:S000047937|PMID:10388807 IDA C similar to Gtr1, small GTPase (putative) YGR163W gene taxon:4932 20020529 SGD
+SGD S000003395 GTR2 GO:0005634 SGD_REF:S000060307|PMID:11073942 IDA C similar to Gtr1, small GTPase (putative) YGR163W gene taxon:4932 20020529 SGD
+SGD S000003395 GTR2 GO:0005737 SGD_REF:S000047937|PMID:10388807 IDA C similar to Gtr1, small GTPase (putative) YGR163W gene taxon:4932 20020529 SGD
+SGD S000003395 GTR2 GO:0005737 SGD_REF:S000060307|PMID:11073942 IDA C similar to Gtr1, small GTPase (putative) YGR163W gene taxon:4932 20020529 SGD
+SGD S000003395 GTR2 GO:0005774 SGD_REF:S000082228|PMID:15989961 IDA C similar to Gtr1, small GTPase (putative) YGR163W gene taxon:4932 20050718 SGD
+SGD S000003395 GTR2 GO:0003924 SGD_REF:S000047937|PMID:10388807 ISS F similar to Gtr1, small GTPase (putative) YGR163W gene taxon:4932 20020529 SGD
+SGD S000003395 GTR2 GO:0016237 SGD_REF:S000082228|PMID:15989961 IMP P similar to Gtr1, small GTPase (putative) YGR163W gene taxon:4932 20050718 SGD
+SGD S000003149 GTS1 GO:0005634 SGD_REF:S000066000|PMID:11549884 IDA C YGL181W|FHT1|LSR1 gene taxon:4932 20011030 SGD
+SGD S000003149 GTS1 GO:0005737 SGD_REF:S000044875|PMID:9914482 IPI C YGL181W|FHT1|LSR1 gene taxon:4932 20010118 SGD
+SGD S000003149 GTS1 GO:0005554 SGD_REF:S000069584 ND F YGL181W|FHT1|LSR1 gene taxon:4932 20050801 SGD
+SGD S000003149 GTS1 GO:0000074 SGD_REF:S000049798|PMID:8035831 IMP P YGL181W|FHT1|LSR1 gene taxon:4932 20010118 SGD
+SGD S000003149 GTS1 GO:0000902 SGD_REF:S000049798|PMID:8035831 IMP P YGL181W|FHT1|LSR1 gene taxon:4932 20021108 SGD
+SGD S000003149 GTS1 GO:0001300 SGD_REF:S000048465|PMID:8573138 IMP P YGL181W|FHT1|LSR1 gene taxon:4932 20030814 SGD
+SGD S000003149 GTS1 GO:0006855 SGD_REF:S000044875|PMID:9914482 IPI P YGL181W|FHT1|LSR1 gene taxon:4932 20010118 SGD
+SGD S000003149 GTS1 GO:0006855 SGD_REF:S000044875|PMID:9914482 IMP P YGL181W|FHT1|LSR1 gene taxon:4932 20010118 SGD
+SGD S000003149 GTS1 GO:0007624 SGD_REF:S000071796|PMID:12070147 IMP P YGL181W|FHT1|LSR1 gene taxon:4932 20021212 SGD
+SGD S000003149 GTS1 GO:0007624 SGD_REF:S000059805|PMID:11231018 IMP P YGL181W|FHT1|LSR1 gene taxon:4932 20040713 SGD
+SGD S000003149 GTS1 GO:0007624 SGD_REF:S000042554|PMID:9514863 IMP P YGL181W|FHT1|LSR1 gene taxon:4932 20040713 SGD
+SGD S000003149 GTS1 GO:0030437 SGD_REF:S000048465|PMID:8573138 IMP P YGL181W|FHT1|LSR1 gene taxon:4932 20010118 SGD
+SGD S000003149 GTS1 GO:0045449 SGD_REF:S000074013|PMID:12782635 IMP P YGL181W|FHT1|LSR1 gene taxon:4932 20050729 SGD
+SGD S000001477 GTT1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C glutathione transferase YIR038C gene taxon:4932 20040928 SGD
+SGD S000001477 GTT1 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C glutathione transferase YIR038C gene taxon:4932 20060317 SGD
+SGD S000001477 GTT1 GO:0005783 SGD_REF:S000041437|PMID:9792709 IDA C glutathione transferase YIR038C gene taxon:4932 20021003 SGD
+SGD S000001477 GTT1 GO:0004364 SGD_REF:S000041437|PMID:9792709 IDA F glutathione transferase YIR038C gene taxon:4932 20021003 SGD
+SGD S000001477 GTT1 GO:0004364 SGD_REF:S000041437|PMID:9792709 ISS F glutathione transferase YIR038C gene taxon:4932 20021003 SGD
+SGD S000001477 GTT1 GO:0006749 SGD_REF:S000041437|PMID:9792709 IDA P glutathione transferase YIR038C gene taxon:4932 20021003 SGD
+SGD S000003983 GTT2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C glutathione transferase YLL060C gene taxon:4932 20040928 SGD
+SGD S000003983 GTT2 GO:0004364 SGD_REF:S000041437|PMID:9792709 IDA F glutathione transferase YLL060C gene taxon:4932 20021003 SGD
+SGD S000003983 GTT2 GO:0004364 SGD_REF:S000041437|PMID:9792709 ISS F glutathione transferase YLL060C gene taxon:4932 20021003 SGD
+SGD S000003983 GTT2 GO:0006749 SGD_REF:S000041437|PMID:9792709 IDA P glutathione transferase YLL060C gene taxon:4932 20021003 SGD
+SGD S000000743 GTT3 GO:0008372 SGD_REF:S000069584 ND C YEL017W gene taxon:4932 20060315 SGD
+SGD S000000743 GTT3 GO:0005554 SGD_REF:S000069584 ND F YEL017W gene taxon:4932 20060315 SGD
+SGD S000000743 GTT3 GO:0006749 SGD_REF:S000074191|PMID:14566057 RCA P YEL017W gene taxon:4932 20050608 SGD
+SGD S000004830 GUA1 GO:0008372 SGD_REF:S000069584 ND C GMP synthase YMR217W gene taxon:4932 20020927 SGD
+SGD S000004830 GUA1 GO:0003922 SGD_REF:S000041905|PMID:8112582 IMP F GMP synthase YMR217W gene taxon:4932 20030115 SGD
+SGD S000004830 GUA1 GO:0003922 SGD_REF:S000041905|PMID:8112582 ISS F GMP synthase YMR217W gene taxon:4932 20030115 SGD
+SGD S000004830 GUA1 GO:0046037 SGD_REF:S000060059|PMID:11035032 TAS P GMP synthase YMR217W gene taxon:4932 20020927 SGD
+SGD S000002397 GUD1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C guanine deaminase YDL238C gene taxon:4932 20031028 SGD
+SGD S000002397 GUD1 GO:0008892 SGD_REF:S000080256|PMID:15565584 IDA F guanine deaminase YDL238C gene taxon:4932 20050110 SGD
+SGD S000002397 GUD1 GO:0016811 SGD_REF:S000065706|PMID:10542258 ISS F guanine deaminase YDL238C gene taxon:4932 20030422 SGD
+SGD S000002397 GUD1 GO:0046098 SGD_REF:S000065706|PMID:10542258 ISS P guanine deaminase YDL238C gene taxon:4932 20030422 SGD
+SGD S000004280 GUF1 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C GTPase YLR289W gene taxon:4932 20031028 SGD
+SGD S000004280 GUF1 GO:0003924 SGD_REF:S000045172|PMID:8553703 ISS F GTPase YLR289W gene taxon:4932 20021007 SGD
+SGD S000004280 GUF1 GO:0003924 SGD_REF:S000114261|PMID:16415861 IDA F GTPase YLR289W gene taxon:4932 20060203 SGD
+SGD S000004280 GUF1 GO:0000004 SGD_REF:S000069584 ND P GTPase YLR289W gene taxon:4932 20021007 SGD
+SGD S000002862 GUK1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C guanylate kinase YDR454C|PUR5 gene taxon:4932 20031028 SGD
+SGD S000002862 GUK1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C guanylate kinase YDR454C|PUR5 gene taxon:4932 20031028 SGD
+SGD S000002862 GUK1 GO:0004385 SGD_REF:S000039537|PMID:1334480 IDA F guanylate kinase YDR454C|PUR5 gene taxon:4932 20030115 SGD
+SGD S000002862 GUK1 GO:0046037 SGD_REF:S000060059|PMID:11035032 TAS P guanylate kinase YDR454C|PUR5 gene taxon:4932 20020927 SGD
+SGD S000003052 GUP1 GO:0005783 SGD_REF:S000081296|PMID:15813700 IDA C YGL084C gene taxon:4932 20050419 SGD
+SGD S000003052 GUP1 GO:0005886 SGD_REF:S000081296|PMID:15813700 IDA C YGL084C gene taxon:4932 20050419 SGD
+SGD S000003052 GUP1 GO:0016020 SGD_REF:S000049737|PMID:10931309 IDA C YGL084C gene taxon:4932 20020528 SGD
+SGD S000003052 GUP1 GO:0016020 SGD_REF:S000049737|PMID:10931309 ISS C YGL084C gene taxon:4932 20020528 SGD
+SGD S000003052 GUP1 GO:0008374 SGD_REF:S000081341|PMID:10694878 ISS F YGL084C gene taxon:4932 20050419 SGD
+SGD S000003052 GUP1 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P YGL084C gene taxon:4932 20060227 SGD
+SGD S000003052 GUP1 GO:0015793 SGD_REF:S000049737|PMID:10931309 IGI P YGL084C gene taxon:4932 20020528 SGD
+SGD S000003052 GUP1 GO:0015793 SGD_REF:S000049737|PMID:10931309 IMP P YGL084C gene taxon:4932 20020528 SGD
+SGD S000003052 GUP1 GO:0019563 SGD_REF:S000055066|PMID:10747858 IGI P YGL084C gene taxon:4932 20020528 SGD
+SGD S000003052 GUP1 GO:0019563 SGD_REF:S000055066|PMID:10747858 IMP P YGL084C gene taxon:4932 20020528 SGD
+SGD S000006110 GUP2 GO:0016020 SGD_REF:S000049737|PMID:10931309 ISS C YPL189W gene taxon:4932 20020528 SGD
+SGD S000006110 GUP2 GO:0008374 SGD_REF:S000081341|PMID:10694878 ISS F YPL189W gene taxon:4932 20050419 SGD
+SGD S000006110 GUP2 GO:0015793 SGD_REF:S000049737|PMID:10931309 IGI P YPL189W gene taxon:4932 20050419 SGD
+SGD S000003214 GUS1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YGL245W|GSN1|GluRS gene taxon:4932 20031028 SGD
+SGD S000003214 GUS1 GO:0017102 SGD_REF:S000074747|PMID:11069915 IDA C YGL245W|GSN1|GluRS gene taxon:4932 20031217 SGD
+SGD S000003214 GUS1 GO:0004818 SGD_REF:S000074747|PMID:11069915 IDA F YGL245W|GSN1|GluRS gene taxon:4932 20031217 SGD
+SGD S000003214 GUS1 GO:0006424 SGD_REF:S000074747|PMID:11069915 IDA P YGL245W|GSN1|GluRS gene taxon:4932 20031217 SGD
+SGD S000001024 GUT1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C converts glycerol to glycerol-3-phosphate, glycerol kinase YHL032C gene taxon:4932 20031028 SGD
+SGD S000001024 GUT1 GO:0004370 SGD_REF:S000043209|PMID:8358828 IMP F converts glycerol to glycerol-3-phosphate, glycerol kinase YHL032C gene taxon:4932 20030115 SGD
+SGD S000001024 GUT1 GO:0004370 SGD_REF:S000043209|PMID:8358828 ISS F converts glycerol to glycerol-3-phosphate, glycerol kinase YHL032C gene taxon:4932 20030115 SGD
+SGD S000001024 GUT1 GO:0006071 SGD_REF:S000043209|PMID:8358828 TAS P converts glycerol to glycerol-3-phosphate, glycerol kinase YHL032C gene taxon:4932 20020927 SGD
+SGD S000001417 GUT2 GO:0005739 SGD_REF:S000050007|PMID:8256521 IMP C glycerol-3-phosphate dehydrogenase YIL155C gene taxon:4932 20010118 SGD
+SGD S000001417 GUT2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C glycerol-3-phosphate dehydrogenase YIL155C gene taxon:4932 20040928 SGD
+SGD S000001417 GUT2 GO:0005739 SGD_REF:S000050007|PMID:8256521 ISS C glycerol-3-phosphate dehydrogenase YIL155C gene taxon:4932 20010118 SGD
+SGD S000001417 GUT2 GO:0031307 SGD_REF:S000115559|PMID:16689936 IDA C glycerol-3-phosphate dehydrogenase YIL155C gene taxon:4932 20060515 SGD
+SGD S000001417 GUT2 GO:0004368 SGD_REF:S000050007|PMID:8256521 ISS F glycerol-3-phosphate dehydrogenase YIL155C gene taxon:4932 20010118 SGD
+SGD S000001417 GUT2 GO:0004368 SGD_REF:S000070271|PMID:12032156 IDA F glycerol-3-phosphate dehydrogenase YIL155C gene taxon:4932 20030307 SGD
+SGD S000001417 GUT2 GO:0004368 SGD_REF:S000050007|PMID:8256521 IMP F glycerol-3-phosphate dehydrogenase YIL155C gene taxon:4932 20010118 SGD
+SGD S000001417 GUT2 GO:0005975 SGD_REF:S000050007|PMID:8256521 IMP P glycerol-3-phosphate dehydrogenase YIL155C gene taxon:4932 20010118 SGD
+SGD S000001417 GUT2 GO:0006116 SGD_REF:S000070271|PMID:12032156 IDA P glycerol-3-phosphate dehydrogenase YIL155C gene taxon:4932 20030307 SGD
+SGD S000001303 GVP36 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C peripheral membrane protein YIL041W gene taxon:4932 20031028 SGD
+SGD S000001303 GVP36 GO:0030173 SGD_REF:S000086147|PMID:16107716 IDA C peripheral membrane protein YIL041W gene taxon:4932 20050823 SGD
+SGD S000001303 GVP36 GO:0005554 SGD_REF:S000069584 ND F peripheral membrane protein YIL041W gene taxon:4932 20030203 SGD
+SGD S000001303 GVP36 GO:0000004 SGD_REF:S000069584 ND P peripheral membrane protein YIL041W gene taxon:4932 20030203 SGD
+SGD S000003627 GWT1 GO:0016020 SGD_REF:S000042090|PMID:7483841 ISS C YJL091C gene taxon:4932 20030421 SGD
+SGD S000003627 GWT1 GO:0042175 SGD_REF:S000075214|PMID:14690591 IDA C YJL091C gene taxon:4932 20031231 SGD
+SGD S000003627 GWT1 GO:0005554 SGD_REF:S000069584 ND F YJL091C gene taxon:4932 20030421 SGD
+SGD S000003627 GWT1 GO:0006506 SGD_REF:S000073558|PMID:12714589 IDA P YJL091C gene taxon:4932 20030710 SGD
+SGD S000004804 GYL1 GO:0000131 SGD_REF:S000077112|PMID:15331637 IDA C YMR192W|APP2 gene taxon:4932 20050414 SGD
+SGD S000004804 GYL1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YMR192W|APP2 gene taxon:4932 20031028 SGD
+SGD S000004804 GYL1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YMR192W|APP2 gene taxon:4932 20040813 SGD
+SGD S000004804 GYL1 GO:0005798 SGD_REF:S000077112|PMID:15331637 IDA C YMR192W|APP2 gene taxon:4932 20050414 SGD
+SGD S000004804 GYL1 GO:0005886 SGD_REF:S000077112|PMID:15331637 IDA C YMR192W|APP2 gene taxon:4932 20050414 SGD
+SGD S000004804 GYL1 GO:0005933 SGD_REF:S000074185|PMID:14562095 IDA C YMR192W|APP2 gene taxon:4932 20031028 SGD
+SGD S000004804 GYL1 GO:0005934 SGD_REF:S000077112|PMID:15331637 IDA C YMR192W|APP2 gene taxon:4932 20050414 SGD
+SGD S000004804 GYL1 GO:0005935 SGD_REF:S000074185|PMID:14562095 IDA C YMR192W|APP2 gene taxon:4932 20031028 SGD
+SGD S000004804 GYL1 GO:0005935 SGD_REF:S000077112|PMID:15331637 IDA C YMR192W|APP2 gene taxon:4932 20050414 SGD
+SGD S000004804 GYL1 GO:0005515 SGD_REF:S000081252|PMID:15802519 IPI F YMR192W|APP2 gene taxon:4932 20050414 SGD
+SGD S000004804 GYL1 GO:0005515 SGD_REF:S000081252|PMID:15802519 ISS F YMR192W|APP2 gene taxon:4932 20050414 SGD
+SGD S000004804 GYL1 GO:0006888 SGD_REF:S000081252|PMID:15802519 IGI P YMR192W|APP2 gene taxon:4932 20050414 SGD
+SGD S000004804 GYL1 GO:0006888 SGD_REF:S000081252|PMID:15802519 IPI P YMR192W|APP2 gene taxon:4932 20050414 SGD
+SGD S000004804 GYL1 GO:0017157 SGD_REF:S000077112|PMID:15331637 IGI SGD:S000006170 P YMR192W|APP2 gene taxon:4932 20060315 SGD
+SGD S000004804 GYL1 GO:0017157 SGD_REF:S000077112|PMID:15331637 IPI SGD:S000001889 P YMR192W|APP2 gene taxon:4932 20060315 SGD
+SGD S000005596 GYP1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C GTPase activating protein (GAP) YOR070C|YOR29-21 gene taxon:4932 20040928 SGD
+SGD S000005596 GYP1 GO:0005794 SGD_REF:S000060384|PMID:11359917 IDA C GTPase activating protein (GAP) YOR070C|YOR29-21 gene taxon:4932 20020708 SGD
+SGD S000005596 GYP1 GO:0005097 SGD_REF:S000045626|PMID:10508155 IMP F GTPase activating protein (GAP) YOR070C|YOR29-21 gene taxon:4932 20020708 SGD
+SGD S000005596 GYP1 GO:0005097 SGD_REF:S000045626|PMID:10508155 ISS F GTPase activating protein (GAP) YOR070C|YOR29-21 gene taxon:4932 20020708 SGD
+SGD S000005596 GYP1 GO:0005097 SGD_REF:S000045626|PMID:10508155 IPI F GTPase activating protein (GAP) YOR070C|YOR29-21 gene taxon:4932 20020708 SGD
+SGD S000005596 GYP1 GO:0005097 SGD_REF:S000045626|PMID:10508155 IDA F GTPase activating protein (GAP) YOR070C|YOR29-21 gene taxon:4932 20020708 SGD
+SGD S000005596 GYP1 GO:0016192 SGD_REF:S000059867|PMID:11118206 IDA P GTPase activating protein (GAP) YOR070C|YOR29-21 gene taxon:4932 20020708 SGD
+SGD S000006170 GYP5 GO:0000131 SGD_REF:S000077112|PMID:15331637 IDA C GTPase-activating protein YPL249C gene taxon:4932 20050414 SGD
+SGD S000006170 GYP5 GO:0005625 SGD_REF:S000071827|PMID:12189143 IDA C GTPase-activating protein YPL249C gene taxon:4932 20021210 SGD
+SGD S000006170 GYP5 GO:0005798 SGD_REF:S000077112|PMID:15331637 IDA C GTPase-activating protein YPL249C gene taxon:4932 20050414 SGD
+SGD S000006170 GYP5 GO:0005829 SGD_REF:S000071827|PMID:12189143 IDA C GTPase-activating protein YPL249C gene taxon:4932 20021210 SGD
+SGD S000006170 GYP5 GO:0005886 SGD_REF:S000077112|PMID:15331637 IDA C GTPase-activating protein YPL249C gene taxon:4932 20050414 SGD
+SGD S000006170 GYP5 GO:0005934 SGD_REF:S000077112|PMID:15331637 IDA C GTPase-activating protein YPL249C gene taxon:4932 20050414 SGD
+SGD S000006170 GYP5 GO:0005935 SGD_REF:S000077112|PMID:15331637 IDA C GTPase-activating protein YPL249C gene taxon:4932 20050414 SGD
+SGD S000006170 GYP5 GO:0005097 SGD_REF:S000071827|PMID:12189143 IGI F GTPase-activating protein YPL249C gene taxon:4932 20021210 SGD
+SGD S000006170 GYP5 GO:0005097 SGD_REF:S000081252|PMID:15802519 IPI F GTPase-activating protein YPL249C gene taxon:4932 20050414 SGD
+SGD S000006170 GYP5 GO:0005097 SGD_REF:S000081252|PMID:15802519 IGI F GTPase-activating protein YPL249C gene taxon:4932 20050414 SGD
+SGD S000006170 GYP5 GO:0005097 SGD_REF:S000071827|PMID:12189143 ISS SGD:S000005596 F GTPase-activating protein YPL249C gene taxon:4932 20021210 SGD
+SGD S000006170 GYP5 GO:0005097 SGD_REF:S000071827|PMID:12189143 IPI F GTPase-activating protein YPL249C gene taxon:4932 20021210 SGD
+SGD S000006170 GYP5 GO:0006888 SGD_REF:S000081252|PMID:15802519 IGI P GTPase-activating protein YPL249C gene taxon:4932 20050414 SGD
+SGD S000006170 GYP5 GO:0006888 SGD_REF:S000081252|PMID:15802519 IPI P GTPase-activating protein YPL249C gene taxon:4932 20050414 SGD
+SGD S000006170 GYP5 GO:0016192 SGD_REF:S000071827|PMID:12189143 IGI P GTPase-activating protein YPL249C gene taxon:4932 20021210 SGD
+SGD S000003580 GYP6 GO:0005768 SGD_REF:S000075800|PMID:14610088 IDA C GTPase activating protein (GAP) for Ypt6 YJL044C gene taxon:4932 20041004 SGD
+SGD S000003580 GYP6 colocalizes_with GO:0030136 SGD_REF:S000074185|PMID:14562095 IDA C GTPase activating protein (GAP) for Ypt6 YJL044C gene taxon:4932 20031028 SGD
+SGD S000003580 GYP6 GO:0005096 SGD_REF:S000048755|PMID:8441469 IDA F GTPase activating protein (GAP) for Ypt6 YJL044C gene taxon:4932 20020620 SGD
+SGD S000003580 GYP6 GO:0006886 SGD_REF:S000048755|PMID:8441469 ISS P GTPase activating protein (GAP) for Ypt6 YJL044C gene taxon:4932 20020620 SGD
+SGD S000002393 GYP7 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C GTPase activating protein (GAP) YDL234C gene taxon:4932 20031028 SGD
+SGD S000002393 GYP7 GO:0005097 SGD_REF:S000045626|PMID:10508155 IDA F GTPase activating protein (GAP) YDL234C gene taxon:4932 20020708 SGD
+SGD S000002393 GYP7 GO:0005097 SGD_REF:S000045626|PMID:10508155 IPI F GTPase activating protein (GAP) YDL234C gene taxon:4932 20020708 SGD
+SGD S000002393 GYP7 GO:0005097 SGD_REF:S000045626|PMID:10508155 ISS F GTPase activating protein (GAP) YDL234C gene taxon:4932 20020708 SGD
+SGD S000002393 GYP7 GO:0005097 SGD_REF:S000045626|PMID:10508155 IMP F GTPase activating protein (GAP) YDL234C gene taxon:4932 20020708 SGD
+SGD S000002393 GYP7 GO:0016192 SGD_REF:S000059867|PMID:11118206 IDA P GTPase activating protein (GAP) YDL234C gene taxon:4932 20020708 SGD
+SGD S000001867 GYP8 GO:0005622 SGD_REF:S000071827|PMID:12189143 IDA C GTPase-activating protein YFL027C gene taxon:4932 20021210 SGD
+SGD S000001867 GYP8 GO:0005097 SGD_REF:S000071827|PMID:12189143 IGI F GTPase-activating protein YFL027C gene taxon:4932 20021210 SGD
+SGD S000001867 GYP8 GO:0005097 SGD_REF:S000071827|PMID:12189143 IPI F GTPase-activating protein YFL027C gene taxon:4932 20021210 SGD
+SGD S000001867 GYP8 GO:0005097 SGD_REF:S000071827|PMID:12189143 ISS SGD:S000005596 F GTPase-activating protein YFL027C gene taxon:4932 20021210 SGD
+SGD S000001867 GYP8 GO:0016192 SGD_REF:S000071827|PMID:12189143 IGI P GTPase-activating protein YFL027C gene taxon:4932 20021210 SGD
+SGD S000003646 GZF3 GO:0005634 SGD_REF:S000051743|PMID:9106207 IC GO:0003704 C GATA zinc finger protein 3 homologous to Dal80 in structure and function YJL110C|DEH1|NIL2 gene taxon:4932 20030115 SGD
+SGD S000003646 GZF3 GO:0003700 SGD_REF:S000050428|PMID:9171427 IDA F GATA zinc finger protein 3 homologous to Dal80 in structure and function YJL110C|DEH1|NIL2 gene taxon:4932 20050117 SGD
+SGD S000003646 GZF3 GO:0003704 SGD_REF:S000051743|PMID:9106207 IMP F GATA zinc finger protein 3 homologous to Dal80 in structure and function YJL110C|DEH1|NIL2 gene taxon:4932 20030115 SGD
+SGD S000003646 GZF3 GO:0003704 SGD_REF:S000051743|PMID:9106207 ISS F GATA zinc finger protein 3 homologous to Dal80 in structure and function YJL110C|DEH1|NIL2 gene taxon:4932 20030115 SGD
+SGD S000003646 GZF3 GO:0000122 SGD_REF:S000051743|PMID:9106207 ISS P GATA zinc finger protein 3 homologous to Dal80 in structure and function YJL110C|DEH1|NIL2 gene taxon:4932 20030115 SGD
+SGD S000003646 GZF3 GO:0000122 SGD_REF:S000051743|PMID:9106207 IMP P GATA zinc finger protein 3 homologous to Dal80 in structure and function YJL110C|DEH1|NIL2 gene taxon:4932 20030115 SGD
+SGD S000003646 GZF3 GO:0006807 SGD_REF:S000048198|PMID:10048020 TAS P GATA zinc finger protein 3 homologous to Dal80 in structure and function YJL110C|DEH1|NIL2 gene taxon:4932 20021203 SGD
+SGD S000003646 GZF3 GO:0006808 SGD_REF:S000072524|PMID:12489124 IGI P GATA zinc finger protein 3 homologous to Dal80 in structure and function YJL110C|DEH1|NIL2 gene taxon:4932 20030214 SGD
+SGD S000003646 GZF3 GO:0006808 SGD_REF:S000072524|PMID:12489124 IMP P GATA zinc finger protein 3 homologous to Dal80 in structure and function YJL110C|DEH1|NIL2 gene taxon:4932 20030214 SGD
+SGD S000003646 GZF3 GO:0016481 SGD_REF:S000050428|PMID:9171427 IDA P GATA zinc finger protein 3 homologous to Dal80 in structure and function YJL110C|DEH1|NIL2 gene taxon:4932 20050117 SGD
+SGD S000006212 HAA1 GO:0005634 SGD_REF:S000066091|PMID:11504737 IDA C YPR008W gene taxon:4932 20020923 SGD
+SGD S000006212 HAA1 GO:0003704 SGD_REF:S000066091|PMID:11504737 IDA F YPR008W gene taxon:4932 20020923 SGD
+SGD S000006212 HAA1 GO:0006367 SGD_REF:S000066091|PMID:11504737 IDA P YPR008W gene taxon:4932 20020923 SGD
+SGD S000001863 HAC1 GO:0005634 SGD_REF:S000048580|PMID:10346810 TAS C bZIP (basic-leucine zipper) protein YFL031W|ERN4|IRE15 gene taxon:4932 20010118 SGD
+SGD S000001863 HAC1 GO:0003700 SGD_REF:S000055018|PMID:9077435 IDA F bZIP (basic-leucine zipper) protein YFL031W|ERN4|IRE15 gene taxon:4932 20050119 SGD
+SGD S000001863 HAC1 GO:0003704 SGD_REF:S000048580|PMID:10346810 TAS F bZIP (basic-leucine zipper) protein YFL031W|ERN4|IRE15 gene taxon:4932 20010118 SGD
+SGD S000001863 HAC1 GO:0006357 SGD_REF:S000048580|PMID:10346810 TAS P bZIP (basic-leucine zipper) protein YFL031W|ERN4|IRE15 gene taxon:4932 20010118 SGD
+SGD S000001863 HAC1 GO:0006644 SGD_REF:S000048580|PMID:10346810 TAS P bZIP (basic-leucine zipper) protein YFL031W|ERN4|IRE15 gene taxon:4932 20010118 SGD
+SGD S000001863 HAC1 GO:0006990 SGD_REF:S000048580|PMID:10346810 TAS P bZIP (basic-leucine zipper) protein YFL031W|ERN4|IRE15 gene taxon:4932 20010118 SGD
+SGD S000001863 HAC1 GO:0045893 SGD_REF:S000055018|PMID:9077435 IDA P bZIP (basic-leucine zipper) protein YFL031W|ERN4|IRE15 gene taxon:4932 20050119 SGD
+SGD S000006209 HAL1 GO:0005737 SGD_REF:S000042636|PMID:1505513 IDA C polar 32 kDa cytoplasmic protein YPR005C gene taxon:4932 20020926 SGD
+SGD S000006209 HAL1 GO:0005554 SGD_REF:S000069584 ND F polar 32 kDa cytoplasmic protein YPR005C gene taxon:4932 20020926 SGD
+SGD S000006209 HAL1 GO:0009651 SGD_REF:S000042636|PMID:1505513 IGI P polar 32 kDa cytoplasmic protein YPR005C gene taxon:4932 20020926 SGD
+SGD S000006209 HAL1 GO:0009651 SGD_REF:S000042636|PMID:1505513 IMP P polar 32 kDa cytoplasmic protein YPR005C gene taxon:4932 20020926 SGD
+SGD S000006209 HAL1 GO:0045944 SGD_REF:S000042636|PMID:1505513 IMP P polar 32 kDa cytoplasmic protein YPR005C gene taxon:4932 20031013 SGD
+SGD S000003701 HAL5 GO:0008372 SGD_REF:S000069584 ND C YJL165C gene taxon:4932 20020814 SGD
+SGD S000003701 HAL5 GO:0004672 SGD_REF:S000044312|PMID:10207057 ISS F YJL165C gene taxon:4932 20020814 SGD
+SGD S000003701 HAL5 GO:0030003 SGD_REF:S000044312|PMID:10207057 IGI P YJL165C gene taxon:4932 20020814 SGD
+SGD S000003701 HAL5 GO:0030003 SGD_REF:S000044312|PMID:10207057 IMP P YJL165C gene taxon:4932 20020814 SGD
+SGD S000005449 HAL9 GO:0005634 SGD_REF:S000045640|PMID:9559673 ISS C contains zinc finger, transcription factor (putative) YOL089C gene taxon:4932 20020614 SGD
+SGD S000005449 HAL9 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C contains zinc finger, transcription factor (putative) YOL089C gene taxon:4932 20040928 SGD
+SGD S000005449 HAL9 GO:0003704 SGD_REF:S000045640|PMID:9559673 IMP F contains zinc finger, transcription factor (putative) YOL089C gene taxon:4932 20020614 SGD
+SGD S000005449 HAL9 GO:0006367 SGD_REF:S000045640|PMID:9559673 IMP P contains zinc finger, transcription factor (putative) YOL089C gene taxon:4932 20020614 SGD
+SGD S000005449 HAL9 GO:0009651 SGD_REF:S000045640|PMID:9559673 IMP P contains zinc finger, transcription factor (putative) YOL089C gene taxon:4932 20020614 SGD
+SGD S000003830 HAM1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YJR069C gene taxon:4932 20031028 SGD
+SGD S000003830 HAM1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YJR069C gene taxon:4932 20031028 SGD
+SGD S000003830 HAM1 GO:0005554 SGD_REF:S000069584 ND F YJR069C gene taxon:4932 20021211 SGD
+SGD S000003830 HAM1 GO:0006281 SGD_REF:S000056098|PMID:8789257 IMP P YJR069C gene taxon:4932 20021211 SGD
+SGD S000004246 HAP1 GO:0005634 SGD_REF:S000044853|PMID:8182072 IDA C zinc finger transcription factor of the Zn(2)-Cys(6) binuclear cluster domain type YLR256W|CYP1 gene taxon:4932 20021002 SGD
+SGD S000004246 HAP1 GO:0003704 SGD_REF:S000050602|PMID:3030565 IDA F zinc finger transcription factor of the Zn(2)-Cys(6) binuclear cluster domain type YLR256W|CYP1 gene taxon:4932 20021002 SGD
+SGD S000004246 HAP1 GO:0009060 SGD_REF:S000043170|PMID:2851658 IMP P zinc finger transcription factor of the Zn(2)-Cys(6) binuclear cluster domain type YLR256W|CYP1 gene taxon:4932 20021002 SGD
+SGD S000004246 HAP1 GO:0045944 SGD_REF:S000043170|PMID:2851658 IMP P zinc finger transcription factor of the Zn(2)-Cys(6) binuclear cluster domain type YLR256W|CYP1 gene taxon:4932 20021002 SGD
+SGD S000003206 HAP2 GO:0005634 SGD_REF:S000069459|PMID:11914276 IDA C transcriptional activator protein of CYC1 (component of HAP2/HAP3 heteromer) YGL237C gene taxon:4932 20020507 SGD
+SGD S000003206 HAP2 GO:0016602 SGD_REF:S000058334|PMID:9618445 TAS C transcriptional activator protein of CYC1 (component of HAP2/HAP3 heteromer) YGL237C gene taxon:4932 20021001 SGD
+SGD S000003206 HAP2 GO:0016563 SGD_REF:S000058334|PMID:9618445 TAS F transcriptional activator protein of CYC1 (component of HAP2/HAP3 heteromer) YGL237C gene taxon:4932 20021001 SGD
+SGD S000003206 HAP2 GO:0006109 SGD_REF:S000058334|PMID:9618445 TAS P transcriptional activator protein of CYC1 (component of HAP2/HAP3 heteromer) YGL237C gene taxon:4932 20021001 SGD
+SGD S000003206 HAP2 GO:0006350 SGD_REF:S000058334|PMID:9618445 TAS P transcriptional activator protein of CYC1 (component of HAP2/HAP3 heteromer) YGL237C gene taxon:4932 20021001 SGD
+SGD S000000117 HAP3 GO:0005634 SGD_REF:S000052744|PMID:7828851 IC GO:0006350 C transcriptional activator protein of CYC1 (component of HAP2/HAP3 heteromer) YBL021C gene taxon:4932 20050117 SGD
+SGD S000000117 HAP3 GO:0016602 SGD_REF:S000058334|PMID:9618445 TAS C transcriptional activator protein of CYC1 (component of HAP2/HAP3 heteromer) YBL021C gene taxon:4932 20021001 SGD
+SGD S000000117 HAP3 GO:0016563 SGD_REF:S000058334|PMID:9618445 TAS F transcriptional activator protein of CYC1 (component of HAP2/HAP3 heteromer) YBL021C gene taxon:4932 20021001 SGD
+SGD S000000117 HAP3 GO:0006109 SGD_REF:S000058334|PMID:9618445 TAS P transcriptional activator protein of CYC1 (component of HAP2/HAP3 heteromer) YBL021C gene taxon:4932 20021001 SGD
+SGD S000000117 HAP3 GO:0006350 SGD_REF:S000058334|PMID:9618445 TAS P transcriptional activator protein of CYC1 (component of HAP2/HAP3 heteromer) YBL021C gene taxon:4932 20021001 SGD
+SGD S000001592 HAP4 GO:0016602 SGD_REF:S000058334|PMID:9618445 TAS C transcriptional activator protein of CYC1 (component of HAP2/HAP3 heteromer) YKL109W gene taxon:4932 20021001 SGD
+SGD S000001592 HAP4 GO:0016563 SGD_REF:S000058334|PMID:9618445 TAS F transcriptional activator protein of CYC1 (component of HAP2/HAP3 heteromer) YKL109W gene taxon:4932 20021001 SGD
+SGD S000001592 HAP4 GO:0006109 SGD_REF:S000058334|PMID:9618445 TAS P transcriptional activator protein of CYC1 (component of HAP2/HAP3 heteromer) YKL109W gene taxon:4932 20021001 SGD
+SGD S000001592 HAP4 GO:0006350 SGD_REF:S000058334|PMID:9618445 TAS P transcriptional activator protein of CYC1 (component of HAP2/HAP3 heteromer) YKL109W gene taxon:4932 20021001 SGD
+SGD S000005885 HAP5 GO:0005634 SGD_REF:S000052744|PMID:7828851 IC GO:0006350 C CCAAT-binding transcription factor component (along with Hap2p and Hap3p) YOR358W gene taxon:4932 20050117 SGD
+SGD S000005885 HAP5 GO:0016602 SGD_REF:S000058334|PMID:9618445 TAS C CCAAT-binding transcription factor component (along with Hap2p and Hap3p) YOR358W gene taxon:4932 20021001 SGD
+SGD S000005885 HAP5 GO:0003677 SGD_REF:S000081155|PMID:15343339 IPI F CCAAT-binding transcription factor component (along with Hap2p and Hap3p) YOR358W gene taxon:4932 20050331 SGD
+SGD S000005885 HAP5 GO:0016563 SGD_REF:S000058334|PMID:9618445 TAS F CCAAT-binding transcription factor component (along with Hap2p and Hap3p) YOR358W gene taxon:4932 20021001 SGD
+SGD S000005885 HAP5 GO:0006109 SGD_REF:S000058334|PMID:9618445 TAS P CCAAT-binding transcription factor component (along with Hap2p and Hap3p) YOR358W gene taxon:4932 20021001 SGD
+SGD S000005885 HAP5 GO:0006350 SGD_REF:S000058334|PMID:9618445 TAS P CCAAT-binding transcription factor component (along with Hap2p and Hap3p) YOR358W gene taxon:4932 20021001 SGD
+SGD S000004903 HAS1 GO:0005635 SGD_REF:S000056415|PMID:10684247 IDA C RNA-dependent helicase (putative) YMR290C gene taxon:4932 20020620 SGD
+SGD S000004903 HAS1 GO:0005730 SGD_REF:S000076145|PMID:15049817 IDA C RNA-dependent helicase (putative) YMR290C gene taxon:4932 20040721 SGD
+SGD S000004903 HAS1 GO:0005730 SGD_REF:S000056415|PMID:10684247 IDA C RNA-dependent helicase (putative) YMR290C gene taxon:4932 20020620 SGD
+SGD S000004903 HAS1 GO:0003723 SGD_REF:S000080896|PMID:15718299 IDA F RNA-dependent helicase (putative) YMR290C gene taxon:4932 20050304 SGD
+SGD S000004903 HAS1 GO:0004004 SGD_REF:S000080896|PMID:15718299 IDA F RNA-dependent helicase (putative) YMR290C gene taxon:4932 20050304 SGD
+SGD S000004903 HAS1 GO:0008186 SGD_REF:S000080896|PMID:15718299 IDA F RNA-dependent helicase (putative) YMR290C gene taxon:4932 20050304 SGD
+SGD S000004903 HAS1 GO:0006364 SGD_REF:S000076145|PMID:15049817 IMP P RNA-dependent helicase (putative) YMR290C gene taxon:4932 20040721 SGD
+SGD S000004903 HAS1 GO:0006364 SGD_REF:S000076598|PMID:15242642 IMP P RNA-dependent helicase (putative) YMR290C gene taxon:4932 20040713 SGD
+SGD S000005922 HAT1 GO:0000123 SGD_REF:S000076003|PMID:14761951 IPI C histone acetyltransferase YPL001W gene taxon:4932 20040427 SGD
+SGD S000005922 HAT1 GO:0005634 SGD_REF:S000043287|PMID:9575221 IDA C histone acetyltransferase YPL001W gene taxon:4932 20020731 SGD
+SGD S000005922 HAT1 GO:0005737 SGD_REF:S000043287|PMID:9575221 IDA C histone acetyltransferase YPL001W gene taxon:4932 20020731 SGD
+SGD S000005922 HAT1 GO:0004406 SGD_REF:S000043287|PMID:9575221 IMP F histone acetyltransferase YPL001W gene taxon:4932 20020731 SGD
+SGD S000005922 HAT1 GO:0006348 SGD_REF:S000053627|PMID:10982821 IMP P histone acetyltransferase YPL001W gene taxon:4932 20020731 SGD
+SGD S000005922 HAT1 GO:0016573 SGD_REF:S000043287|PMID:9575221 IDA P histone acetyltransferase YPL001W gene taxon:4932 20020731 SGD
+SGD S000000782 HAT2 GO:0000123 SGD_REF:S000076003|PMID:14761951 IPI C histone acetyltransferase subunit YEL056W gene taxon:4932 20040427 SGD
+SGD S000000782 HAT2 GO:0005634 SGD_REF:S000043287|PMID:9575221 IDA C histone acetyltransferase subunit YEL056W gene taxon:4932 20020731 SGD
+SGD S000000782 HAT2 GO:0005737 SGD_REF:S000049470|PMID:8858151 IDA C histone acetyltransferase subunit YEL056W gene taxon:4932 20010118 SGD
+SGD S000000782 HAT2 GO:0005737 SGD_REF:S000043287|PMID:9575221 IDA C histone acetyltransferase subunit YEL056W gene taxon:4932 20020731 SGD
+SGD S000000782 HAT2 GO:0004406 SGD_REF:S000049470|PMID:8858151 IDA F histone acetyltransferase subunit YEL056W gene taxon:4932 20010118 SGD
+SGD S000000782 HAT2 GO:0006333 SGD_REF:S000049470|PMID:8858151 IDA P histone acetyltransferase subunit YEL056W gene taxon:4932 20010118 SGD
+SGD S000000782 HAT2 GO:0006348 SGD_REF:S000053627|PMID:10982821 IMP P histone acetyltransferase subunit YEL056W gene taxon:4932 20020731 SGD
+SGD S000001792 HBS1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YKR084C gene taxon:4932 20031028 SGD
+SGD S000001792 HBS1 GO:0005554 SGD_REF:S000069584 ND F YKR084C gene taxon:4932 20021030 SGD
+SGD S000001792 HBS1 GO:0043037 SGD_REF:S000069709|PMID:11909951 IMP P YKR084C gene taxon:4932 20060413 SGD
+SGD S000001792 HBS1 GO:0043037 SGD_REF:S000069709|PMID:11909951 IPI P YKR084C gene taxon:4932 20060413 SGD
+SGD S000002382 HBT1 GO:0005937 SGD_REF:S000069496|PMID:11923536 IDA C YDL223C gene taxon:4932 20030624 SGD
+SGD S000002382 HBT1 GO:0005554 SGD_REF:S000069584 ND F YDL223C gene taxon:4932 20020923 SGD
+SGD S000002382 HBT1 GO:0000753 SGD_REF:S000069496|PMID:11923536 IMP P YDL223C gene taxon:4932 20021206 SGD
+SGD S000003570 HCA4 GO:0005730 SGD_REF:S000058443|PMID:10690410 TAS C RNA helicase (putative) YJL033W|DBP4|ECM24 gene taxon:4932 20010118 SGD
+SGD S000003570 HCA4 GO:0004004 SGD_REF:S000058443|PMID:10690410 TAS F RNA helicase (putative) YJL033W|DBP4|ECM24 gene taxon:4932 20010118 SGD
+SGD S000003570 HCA4 GO:0006365 SGD_REF:S000058443|PMID:10690410 TAS P RNA helicase (putative) YJL033W|DBP4|ECM24 gene taxon:4932 20010118 SGD
+SGD S000005225 HCH1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YNL281W gene taxon:4932 20031028 SGD
+SGD S000005225 HCH1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YNL281W gene taxon:4932 20031028 SGD
+SGD S000005225 HCH1 GO:0030189 SGD_REF:S000072028|PMID:12504007 IDA F YNL281W gene taxon:4932 20030107 SGD
+SGD S000005225 HCH1 GO:0030189 SGD_REF:S000072028|PMID:12504007 IPI SGD:S000006161 F YNL281W gene taxon:4932 20030107 SGD
+SGD S000005225 HCH1 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P YNL281W gene taxon:4932 20060221 SGD
+SGD S000005225 HCH1 GO:0006457 SGD_REF:S000044986|PMID:9990037 IGI P YNL281W gene taxon:4932 20010118 SGD
+SGD S000005225 HCH1 GO:0006457 SGD_REF:S000072028|PMID:12504007 IPI SGD:S000006161 P YNL281W gene taxon:4932 20030107 SGD
+SGD S000005225 HCH1 GO:0006457 SGD_REF:S000072028|PMID:12504007 IMP P YNL281W gene taxon:4932 20030107 SGD
+SGD S000005225 HCH1 GO:0006950 SGD_REF:S000072028|PMID:12504007 IMP P YNL281W gene taxon:4932 20030107 SGD
+SGD S000005225 HCH1 GO:0006950 SGD_REF:S000072028|PMID:12504007 IPI SGD:S000006161 P YNL281W gene taxon:4932 20030107 SGD
+SGD S000005225 HCH1 GO:0006950 SGD_REF:S000072028|PMID:12504007 IEP P YNL281W gene taxon:4932 20030107 SGD
+SGD S000000661 HCM1 GO:0005634 SGD_REF:S000062141|PMID:9920414 IPI C forkhead protein YCR065W gene taxon:4932 20020621 SGD
+SGD S000000661 HCM1 GO:0003704 SGD_REF:S000062141|PMID:9920414 IDA F forkhead protein YCR065W gene taxon:4932 20020621 SGD
+SGD S000000661 HCM1 GO:0000083 SGD_REF:S000071810|PMID:12464632 IPI P forkhead protein YCR065W gene taxon:4932 20050603 SGD
+SGD S000000661 HCM1 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P forkhead protein YCR065W gene taxon:4932 20060203 SGD
+SGD S000000661 HCM1 GO:0006367 SGD_REF:S000062141|PMID:9920414 IDA P forkhead protein YCR065W gene taxon:4932 20020621 SGD
+SGD S000000661 HCM1 GO:0007051 SGD_REF:S000062141|PMID:9920414 IGI P forkhead protein YCR065W gene taxon:4932 20020621 SGD
+SGD S000004182 HCR1 GO:0005852 SGD_REF:S000059525|PMID:11179233 IPI C Substoichiometric component of eukaryotic translation initiation factor 3 (eIF3) YLR192C gene taxon:4932 20021030 SGD
+SGD S000004182 HCR1 GO:0003743 SGD_REF:S000059525|PMID:11179233 IPI F Substoichiometric component of eukaryotic translation initiation factor 3 (eIF3) YLR192C gene taxon:4932 20021030 SGD
+SGD S000004182 HCR1 GO:0003743 SGD_REF:S000059525|PMID:11179233 ISS F Substoichiometric component of eukaryotic translation initiation factor 3 (eIF3) YLR192C gene taxon:4932 20021030 SGD
+SGD S000004182 HCR1 GO:0019843 SGD_REF:S000074158|PMID:11560931 IDA F Substoichiometric component of eukaryotic translation initiation factor 3 (eIF3) YLR192C gene taxon:4932 20031021 SGD
+SGD S000004182 HCR1 GO:0006412 SGD_REF:S000059525|PMID:11179233 IPI P Substoichiometric component of eukaryotic translation initiation factor 3 (eIF3) YLR192C gene taxon:4932 20021030 SGD
+SGD S000004182 HCR1 GO:0006412 SGD_REF:S000059525|PMID:11179233 ISS P Substoichiometric component of eukaryotic translation initiation factor 3 (eIF3) YLR192C gene taxon:4932 20021030 SGD
+SGD S000004182 HCR1 GO:0030490 SGD_REF:S000074158|PMID:11560931 IMP P Substoichiometric component of eukaryotic translation initiation factor 3 (eIF3) YLR192C gene taxon:4932 20031021 SGD
+SGD S000001500 HCS1 GO:0005658 SGD_REF:S000058490|PMID:8257676 IPI C DNA helicase A YKL017C|DIP1 gene taxon:4932 20010118 SGD
+SGD S000001500 HCS1 GO:0003678 SGD_REF:S000050304|PMID:9341217 IDA F DNA helicase A YKL017C|DIP1 gene taxon:4932 20010118 SGD
+SGD S000001500 HCS1 GO:0006273 SGD_REF:S000058490|PMID:8257676 IPI P DNA helicase A YKL017C|DIP1 gene taxon:4932 20010118 SGD
+SGD S000004966 HDA1 GO:0000118 SGD_REF:S000047708|PMID:8962081 IDA C histone deacetylase, shares sequence similarity with Rpd3p, Hos1p, Hos2p, and Hos3p YNL021W gene taxon:4932 20010118 SGD
+SGD S000004966 HDA1 GO:0004407 SGD_REF:S000047708|PMID:8962081 IDA F histone deacetylase, shares sequence similarity with Rpd3p, Hos1p, Hos2p, and Hos3p YNL021W gene taxon:4932 20010118 SGD
+SGD S000004966 HDA1 GO:0004407 SGD_REF:S000047708|PMID:8962081 IMP F histone deacetylase, shares sequence similarity with Rpd3p, Hos1p, Hos2p, and Hos3p YNL021W gene taxon:4932 20010118 SGD
+SGD S000004966 HDA1 GO:0004407 SGD_REF:S000059710|PMID:11095743 TAS F histone deacetylase, shares sequence similarity with Rpd3p, Hos1p, Hos2p, and Hos3p YNL021W gene taxon:4932 20010405 SGD
+SGD S000004966 HDA1 GO:0001308 SGD_REF:S000043004|PMID:10512855 IMP P histone deacetylase, shares sequence similarity with Rpd3p, Hos1p, Hos2p, and Hos3p YNL021W gene taxon:4932 20030820 SGD
+SGD S000004966 HDA1 GO:0006325 SGD_REF:S000056379|PMID:10384311 TAS P histone deacetylase, shares sequence similarity with Rpd3p, Hos1p, Hos2p, and Hos3p YNL021W gene taxon:4932 20010118 SGD
+SGD S000004966 HDA1 GO:0006325 SGD_REF:S000055604|PMID:10384304 TAS P histone deacetylase, shares sequence similarity with Rpd3p, Hos1p, Hos2p, and Hos3p YNL021W gene taxon:4932 20010118 SGD
+SGD S000004966 HDA1 GO:0006355 SGD_REF:S000056379|PMID:10384311 TAS P histone deacetylase, shares sequence similarity with Rpd3p, Hos1p, Hos2p, and Hos3p YNL021W gene taxon:4932 20010118 SGD
+SGD S000004966 HDA1 GO:0006355 SGD_REF:S000055604|PMID:10384304 TAS P histone deacetylase, shares sequence similarity with Rpd3p, Hos1p, Hos2p, and Hos3p YNL021W gene taxon:4932 20010118 SGD
+SGD S000004966 HDA1 GO:0006476 SGD_REF:S000047708|PMID:8962081 IDA P histone deacetylase, shares sequence similarity with Rpd3p, Hos1p, Hos2p, and Hos3p YNL021W gene taxon:4932 20010118 SGD
+SGD S000004966 HDA1 GO:0006476 SGD_REF:S000055604|PMID:10384304 IDA P histone deacetylase, shares sequence similarity with Rpd3p, Hos1p, Hos2p, and Hos3p YNL021W gene taxon:4932 20010118 SGD
+SGD S000002703 HDA2 GO:0000118 SGD_REF:S000060263|PMID:11287668 IMP C YDR295C|PLO2 gene taxon:4932 20031106 SGD
+SGD S000002703 HDA2 GO:0000118 SGD_REF:S000060263|PMID:11287668 IPI C YDR295C|PLO2 gene taxon:4932 20031106 SGD
+SGD S000002703 HDA2 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YDR295C|PLO2 gene taxon:4932 20031028 SGD
+SGD S000002703 HDA2 GO:0004407 SGD_REF:S000060263|PMID:11287668 IMP F YDR295C|PLO2 gene taxon:4932 20031106 SGD
+SGD S000002703 HDA2 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P YDR295C|PLO2 gene taxon:4932 20060203 SGD
+SGD S000002703 HDA2 GO:0006355 SGD_REF:S000060263|PMID:11287668 IDA P YDR295C|PLO2 gene taxon:4932 20031106 SGD
+SGD S000002703 HDA2 GO:0016575 SGD_REF:S000060263|PMID:11287668 IDA P YDR295C|PLO2 gene taxon:4932 20031106 SGD
+SGD S000006383 HDA3 GO:0000118 SGD_REF:S000060263|PMID:11287668 IPI C YPR179C|PLO1 gene taxon:4932 20031106 SGD
+SGD S000006383 HDA3 GO:0000118 SGD_REF:S000050126|PMID:8663039 IPI C YPR179C|PLO1 gene taxon:4932 20031106 SGD
+SGD S000006383 HDA3 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YPR179C|PLO1 gene taxon:4932 20031028 SGD
+SGD S000006383 HDA3 GO:0004407 SGD_REF:S000060263|PMID:11287668 IMP F YPR179C|PLO1 gene taxon:4932 20031106 SGD
+SGD S000006383 HDA3 GO:0004407 SGD_REF:S000050126|PMID:8663039 IMP F YPR179C|PLO1 gene taxon:4932 20031106 SGD
+SGD S000006383 HDA3 GO:0004407 SGD_REF:S000050126|PMID:8663039 IDA F YPR179C|PLO1 gene taxon:4932 20031106 SGD
+SGD S000006383 HDA3 GO:0006355 SGD_REF:S000060263|PMID:11287668 IDA P YPR179C|PLO1 gene taxon:4932 20031106 SGD
+SGD S000006383 HDA3 GO:0016575 SGD_REF:S000060263|PMID:11287668 IDA P YPR179C|PLO1 gene taxon:4932 20031106 SGD
+SGD S000113613 HED1 GO:0008372 SGD_REF:S000073348 ND C YDR014W-A gene taxon:4932 20060417 SGD
+SGD S000113613 HED1 GO:0005554 SGD_REF:S000073348 ND F YDR014W-A gene taxon:4932 20060417 SGD
+SGD S000113613 HED1 GO:0000004 SGD_REF:S000073348 ND P YDR014W-A gene taxon:4932 20060417 SGD
+SGD S000004959 HEF3 GO:0005830 SGD_REF:S000049016|PMID:9544245 IPI C Translation elongation factor 3 (EF-3) YNL014W|EF-3|ZRG7 gene taxon:4932 20021009 SGD
+SGD S000004959 HEF3 GO:0003746 SGD_REF:S000049016|PMID:9544245 IGI F Translation elongation factor 3 (EF-3) YNL014W|EF-3|ZRG7 gene taxon:4932 20021009 SGD
+SGD S000004959 HEF3 GO:0003746 SGD_REF:S000049016|PMID:9544245 ISS F Translation elongation factor 3 (EF-3) YNL014W|EF-3|ZRG7 gene taxon:4932 20021009 SGD
+SGD S000004959 HEF3 GO:0016887 SGD_REF:S000049016|PMID:9544245 IDA F Translation elongation factor 3 (EF-3) YNL014W|EF-3|ZRG7 gene taxon:4932 20021009 SGD
+SGD S000004959 HEF3 GO:0006414 SGD_REF:S000049016|PMID:9544245 IGI P Translation elongation factor 3 (EF-3) YNL014W|EF-3|ZRG7 gene taxon:4932 20021009 SGD
+SGD S000000128 HEK2 GO:0000784 SGD_REF:S000069066|PMID:11739741 IDA C YBL032W|KHD1 gene taxon:4932 20030403 SGD
+SGD S000000128 HEK2 GO:0005737 SGD_REF:S000069530|PMID:11867544 IDA C YBL032W|KHD1 gene taxon:4932 20021009 SGD
+SGD S000000128 HEK2 GO:0003729 SGD_REF:S000069530|PMID:11867544 IDA F YBL032W|KHD1 gene taxon:4932 20021009 SGD
+SGD S000000128 HEK2 GO:0007004 SGD_REF:S000069066|PMID:11739741 IMP P YBL032W|KHD1 gene taxon:4932 20021009 SGD
+SGD S000000128 HEK2 GO:0007004 SGD_REF:S000069066|PMID:11739741 IPI P YBL032W|KHD1 gene taxon:4932 20021009 SGD
+SGD S000000128 HEK2 GO:0008298 SGD_REF:S000069530|PMID:11867544 IMP P YBL032W|KHD1 gene taxon:4932 20021009 SGD
+SGD S000000128 HEK2 GO:0008298 SGD_REF:S000069530|PMID:11867544 IPI P YBL032W|KHD1 gene taxon:4932 20021009 SGD
+SGD S000002640 HEM1 GO:0005759 SGD_REF:S000054004|PMID:3023841 IDA C 5-aminolevulinate synthase YDR232W|CYD1 gene taxon:4932 20020926 SGD
+SGD S000002640 HEM1 GO:0003870 SGD_REF:S000057328|PMID:7035824 IDA F 5-aminolevulinate synthase YDR232W|CYD1 gene taxon:4932 20021218 SGD
+SGD S000002640 HEM1 GO:0006783 SGD_REF:S000057328|PMID:7035824 IMP P 5-aminolevulinate synthase YDR232W|CYD1 gene taxon:4932 20020926 SGD
+SGD S000002454 HEM12 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C uroporphyrinogen decarboxylase YDR047W|HEM6 gene taxon:4932 20031028 SGD
+SGD S000002454 HEM12 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C uroporphyrinogen decarboxylase YDR047W|HEM6 gene taxon:4932 20031028 SGD
+SGD S000002454 HEM12 GO:0004853 SGD_REF:S000052991|PMID:8346678 ISS F uroporphyrinogen decarboxylase YDR047W|HEM6 gene taxon:4932 20020927 SGD
+SGD S000002454 HEM12 GO:0004853 SGD_REF:S000052991|PMID:8346678 IMP F uroporphyrinogen decarboxylase YDR047W|HEM6 gene taxon:4932 20020927 SGD
+SGD S000002454 HEM12 GO:0006783 SGD_REF:S000057328|PMID:7035824 IMP P uroporphyrinogen decarboxylase YDR047W|HEM6 gene taxon:4932 20020927 SGD
+SGD S000002451 HEM13 GO:0005743 SGD_REF:S000063438|PMID:31872 ISS C coproporphyrinogen III oxidase YDR044W gene taxon:4932 20020927 SGD
+SGD S000002451 HEM13 GO:0004109 SGD_REF:S000047239|PMID:2838478 ISS F coproporphyrinogen III oxidase YDR044W gene taxon:4932 20020927 SGD
+SGD S000002451 HEM13 GO:0004109 SGD_REF:S000047239|PMID:2838478 TAS F coproporphyrinogen III oxidase YDR044W gene taxon:4932 20020927 SGD
+SGD S000002451 HEM13 GO:0006783 SGD_REF:S000047239|PMID:2838478 TAS P coproporphyrinogen III oxidase YDR044W gene taxon:4932 20020927 SGD
+SGD S000000816 HEM14 GO:0005739 SGD_REF:S000051153|PMID:8948097 ISS C protoporphyrinogen oxidase YER014W gene taxon:4932 20020927 SGD
+SGD S000000816 HEM14 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C protoporphyrinogen oxidase YER014W gene taxon:4932 20040928 SGD
+SGD S000000816 HEM14 GO:0004729 SGD_REF:S000051153|PMID:8948097 ISS F protoporphyrinogen oxidase YER014W gene taxon:4932 20020927 SGD
+SGD S000000816 HEM14 GO:0004729 SGD_REF:S000051153|PMID:8948097 IMP F protoporphyrinogen oxidase YER014W gene taxon:4932 20020927 SGD
+SGD S000000816 HEM14 GO:0006783 SGD_REF:S000051153|PMID:8948097 IMP P protoporphyrinogen oxidase YER014W gene taxon:4932 20020927 SGD
+SGD S000005702 HEM15 GO:0005743 SGD_REF:S000053796|PMID:2185242 ISS C ferrochelatase (protoheme ferrolyase) YOR176W gene taxon:4932 20020927 SGD
+SGD S000005702 HEM15 GO:0005743 SGD_REF:S000053796|PMID:2185242 TAS C ferrochelatase (protoheme ferrolyase) YOR176W gene taxon:4932 20020927 SGD
+SGD S000005702 HEM15 GO:0004325 SGD_REF:S000053796|PMID:2185242 ISS F ferrochelatase (protoheme ferrolyase) YOR176W gene taxon:4932 20020927 SGD
+SGD S000005702 HEM15 GO:0004325 SGD_REF:S000053796|PMID:2185242 IMP F ferrochelatase (protoheme ferrolyase) YOR176W gene taxon:4932 20020927 SGD
+SGD S000005702 HEM15 GO:0006783 SGD_REF:S000053796|PMID:2185242 TAS P ferrochelatase (protoheme ferrolyase) YOR176W gene taxon:4932 20020927 SGD
+SGD S000003008 HEM2 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C delta-aminolevulinate dehydratase (porphobilinogen synthase) YGL040C|SLU1 gene taxon:4932 20031028 SGD
+SGD S000003008 HEM2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C delta-aminolevulinate dehydratase (porphobilinogen synthase) YGL040C|SLU1 gene taxon:4932 20031028 SGD
+SGD S000003008 HEM2 GO:0004655 SGD_REF:S000046021|PMID:323256 IMP F delta-aminolevulinate dehydratase (porphobilinogen synthase) YGL040C|SLU1 gene taxon:4932 20020927 SGD
+SGD S000003008 HEM2 GO:0006783 SGD_REF:S000046021|PMID:323256 IMP P delta-aminolevulinate dehydratase (porphobilinogen synthase) YGL040C|SLU1 gene taxon:4932 20020927 SGD
+SGD S000002364 HEM3 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C phorphobilinogen deaminase (uroporphyrinogen synthase) YDL205C gene taxon:4932 20031028 SGD
+SGD S000002364 HEM3 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C phorphobilinogen deaminase (uroporphyrinogen synthase) YDL205C gene taxon:4932 20031028 SGD
+SGD S000002364 HEM3 GO:0004418 SGD_REF:S000046021|PMID:323256 IMP F phorphobilinogen deaminase (uroporphyrinogen synthase) YDL205C gene taxon:4932 20020927 SGD
+SGD S000002364 HEM3 GO:0004418 SGD_REF:S000045327|PMID:1508149 IEP F phorphobilinogen deaminase (uroporphyrinogen synthase) YDL205C gene taxon:4932 20020927 SGD
+SGD S000002364 HEM3 GO:0004418 SGD_REF:S000045327|PMID:1508149 ISS F phorphobilinogen deaminase (uroporphyrinogen synthase) YDL205C gene taxon:4932 20020927 SGD
+SGD S000002364 HEM3 GO:0004418 SGD_REF:S000045327|PMID:1508149 IMP F phorphobilinogen deaminase (uroporphyrinogen synthase) YDL205C gene taxon:4932 20020927 SGD
+SGD S000002364 HEM3 GO:0006783 SGD_REF:S000046021|PMID:323256 IMP P phorphobilinogen deaminase (uroporphyrinogen synthase) YDL205C gene taxon:4932 20020927 SGD
+SGD S000005804 HEM4 GO:0008372 SGD_REF:S000069584 ND C uroporphyrinogen III synthase YOR278W|SLU2 gene taxon:4932 20020927 SGD
+SGD S000005804 HEM4 GO:0004852 SGD_REF:S000040301|PMID:7597845 IMP F uroporphyrinogen III synthase YOR278W|SLU2 gene taxon:4932 20021218 SGD
+SGD S000005804 HEM4 GO:0004852 SGD_REF:S000040301|PMID:7597845 ISS F uroporphyrinogen III synthase YOR278W|SLU2 gene taxon:4932 20021218 SGD
+SGD S000005804 HEM4 GO:0006783 SGD_REF:S000046021|PMID:323256 IMP P uroporphyrinogen III synthase YOR278W|SLU2 gene taxon:4932 20020927 SGD
+SGD S000005763 HES1 GO:0008372 SGD_REF:S000069584 ND C similar to human oxysterol binding protein YOR237W|OSH5 gene taxon:4932 20020926 SGD
+SGD S000005763 HES1 GO:0008142 SGD_REF:S000059993|PMID:11238399 ISS F similar to human oxysterol binding protein YOR237W|OSH5 gene taxon:4932 20020926 SGD
+SGD S000005763 HES1 GO:0006694 SGD_REF:S000059993|PMID:11238399 IGI P similar to human oxysterol binding protein YOR237W|OSH5 gene taxon:4932 20020926 SGD
+SGD S000005763 HES1 GO:0006694 SGD_REF:S000059993|PMID:11238399 IMP P similar to human oxysterol binding protein YOR237W|OSH5 gene taxon:4932 20020926 SGD
+SGD S000002171 HEX3 GO:0005634 SGD_REF:S000059086|PMID:11139495 ISS C YDL013W|SLX5 gene taxon:4932 20021001 SGD
+SGD S000002171 HEX3 GO:0003677 SGD_REF:S000059086|PMID:11139495 ISS F YDL013W|SLX5 gene taxon:4932 20021001 SGD
+SGD S000002171 HEX3 GO:0006310 SGD_REF:S000059086|PMID:11139495 IGI P YDL013W|SLX5 gene taxon:4932 20021001 SGD
+SGD S000002171 HEX3 GO:0006310 SGD_REF:S000059086|PMID:11139495 IMP P YDL013W|SLX5 gene taxon:4932 20021001 SGD
+SGD S000002171 HEX3 GO:0006974 SGD_REF:S000071761|PMID:12402242 TAS P YDL013W|SLX5 gene taxon:4932 20021209 SGD
+SGD S000002171 HEX3 GO:0030437 SGD_REF:S000071761|PMID:12402242 TAS P YDL013W|SLX5 gene taxon:4932 20021209 SGD
+SGD S000004820 HFA1 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YMR207C gene taxon:4932 20031028 SGD
+SGD S000004820 HFA1 GO:0005739 SGD_REF:S000076361|PMID:14761959 IDA C YMR207C gene taxon:4932 20040707 SGD
+SGD S000004820 HFA1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YMR207C gene taxon:4932 20040924 SGD
+SGD S000004820 HFA1 GO:0003989 SGD_REF:S000044127|PMID:7906156 ISS F YMR207C gene taxon:4932 20021004 SGD
+SGD S000004820 HFA1 GO:0003989 SGD_REF:S000076361|PMID:14761959 IGI F YMR207C gene taxon:4932 20040707 SGD
+SGD S000004820 HFA1 GO:0006633 SGD_REF:S000076361|PMID:14761959 IGI P YMR207C gene taxon:4932 20040707 SGD
+SGD S000004716 HFD1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YMR110C gene taxon:4932 20040928 SGD
+SGD S000004716 HFD1 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C YMR110C gene taxon:4932 20060317 SGD
+SGD S000004716 HFD1 GO:0005768 SGD_REF:S000074185|PMID:14562095 IDA C YMR110C gene taxon:4932 20031028 SGD
+SGD S000004716 HFD1 GO:0005811 SGD_REF:S000074185|PMID:14562095 IDA C YMR110C gene taxon:4932 20031028 SGD
+SGD S000004716 HFD1 GO:0031307 SGD_REF:S000115559|PMID:16689936 IDA C YMR110C gene taxon:4932 20060515 SGD
+SGD S000004716 HFD1 GO:0004028 SGD_REF:S000114057|PMID:16407407 ISS F YMR110C gene taxon:4932 20060127 SGD
+SGD S000004716 HFD1 GO:0006081 SGD_REF:S000114057|PMID:16407407 IC GO:0004028 P YMR110C gene taxon:4932 20060313 SGD
+SGD S000006175 HFI1 GO:0000124 SGD_REF:S000048255|PMID:9674426 IDA C Ada/Gcn5 protein complex member, transcription factor YPL254W|ADA1|GAN1|SRM12|SUP110 gene taxon:4932 20010221 SGD
+SGD S000006175 HFI1 GO:0005671 SGD_REF:S000051113|PMID:9154821 IPI C Ada/Gcn5 protein complex member, transcription factor YPL254W|ADA1|GAN1|SRM12|SUP110 gene taxon:4932 20051011 SGD
+SGD S000006175 HFI1 GO:0005671 SGD_REF:S000051113|PMID:9154821 IDA C Ada/Gcn5 protein complex member, transcription factor YPL254W|ADA1|GAN1|SRM12|SUP110 gene taxon:4932 20051011 SGD
+SGD S000006175 HFI1 GO:0046695 SGD_REF:S000071997|PMID:12446794 IPI C Ada/Gcn5 protein complex member, transcription factor YPL254W|ADA1|GAN1|SRM12|SUP110 gene taxon:4932 20041024 SGD
+SGD S000006175 HFI1 GO:0003712 SGD_REF:S000051113|PMID:9154821 IMP F Ada/Gcn5 protein complex member, transcription factor YPL254W|ADA1|GAN1|SRM12|SUP110 gene taxon:4932 20021114 SGD
+SGD S000006175 HFI1 GO:0003712 SGD_REF:S000051113|PMID:9154821 IPI F Ada/Gcn5 protein complex member, transcription factor YPL254W|ADA1|GAN1|SRM12|SUP110 gene taxon:4932 20021114 SGD
+SGD S000006175 HFI1 GO:0003713 SGD_REF:S000048198|PMID:10048020 IMP F Ada/Gcn5 protein complex member, transcription factor YPL254W|ADA1|GAN1|SRM12|SUP110 gene taxon:4932 20051010 SGD
+SGD S000006175 HFI1 GO:0006366 SGD_REF:S000051113|PMID:9154821 IMP P Ada/Gcn5 protein complex member, transcription factor YPL254W|ADA1|GAN1|SRM12|SUP110 gene taxon:4932 20021114 SGD
+SGD S000006175 HFI1 GO:0016568 SGD_REF:S000061032|PMID:10839822 TAS P Ada/Gcn5 protein complex member, transcription factor YPL254W|ADA1|GAN1|SRM12|SUP110 gene taxon:4932 20020426 SGD
+SGD S000006175 HFI1 GO:0016573 SGD_REF:S000061032|PMID:10839822 TAS P Ada/Gcn5 protein complex member, transcription factor YPL254W|ADA1|GAN1|SRM12|SUP110 gene taxon:4932 20020426 SGD
+SGD S000003220 HFM1 GO:0005634 SGD_REF:S000069901|PMID:11971962 IDA C C4 zinc finger DNA-binding protein of low sequence specificity in vitro; Probable 119 kDa DNA/RNA helicase family member YGL251C|MER3 gene taxon:4932 20020731 SGD
+SGD S000003220 HFM1 GO:0003678 SGD_REF:S000069901|PMID:11971962 IDA F C4 zinc finger DNA-binding protein of low sequence specificity in vitro; Probable 119 kDa DNA/RNA helicase family member YGL251C|MER3 gene taxon:4932 20020731 SGD
+SGD S000003220 HFM1 GO:0006268 SGD_REF:S000070274|PMID:12039965 IDA P C4 zinc finger DNA-binding protein of low sequence specificity in vitro; Probable 119 kDa DNA/RNA helicase family member YGL251C|MER3 gene taxon:4932 20030424 SGD
+SGD S000003220 HFM1 GO:0007126 SGD_REF:S000069901|PMID:11971962 IDA P C4 zinc finger DNA-binding protein of low sequence specificity in vitro; Probable 119 kDa DNA/RNA helicase family member YGL251C|MER3 gene taxon:4932 20020731 SGD
+SGD S000003220 HFM1 GO:0007129 SGD_REF:S000081371|PMID:15805472 IGI P C4 zinc finger DNA-binding protein of low sequence specificity in vitro; Probable 119 kDa DNA/RNA helicase family member YGL251C|MER3 gene taxon:4932 20050802 SGD
+SGD S000003220 HFM1 GO:0007129 SGD_REF:S000081371|PMID:15805472 IMP P C4 zinc finger DNA-binding protein of low sequence specificity in vitro; Probable 119 kDa DNA/RNA helicase family member YGL251C|MER3 gene taxon:4932 20050802 SGD
+SGD S000003419 HGH1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YGR187C gene taxon:4932 20031028 SGD
+SGD S000003419 HGH1 GO:0005554 SGD_REF:S000069584 ND F YGR187C gene taxon:4932 20021008 SGD
+SGD S000003419 HGH1 GO:0000004 SGD_REF:S000069584 ND P YGR187C gene taxon:4932 20021008 SGD
+SGD S000000213 HHF1 GO:0000788 SGD_REF:S000060984|PMID:2275823 TAS C histone H4 (HHF1 and HHF2 code for identical proteins) YBR009C gene taxon:4932 20010726 SGD
+SGD S000000213 HHF1 GO:0003677 SGD_REF:S000060984|PMID:2275823 TAS F histone H4 (HHF1 and HHF2 code for identical proteins) YBR009C gene taxon:4932 20020204 SGD
+SGD S000000213 HHF1 GO:0006333 SGD_REF:S000060984|PMID:2275823 TAS P histone H4 (HHF1 and HHF2 code for identical proteins) YBR009C gene taxon:4932 20020204 SGD
+SGD S000004975 HHF2 GO:0000788 SGD_REF:S000060984|PMID:2275823 TAS C histone H4 (HHF1 and HHF2 code for identical proteins) YNL030W gene taxon:4932 20010726 SGD
+SGD S000004975 HHF2 GO:0003677 SGD_REF:S000060984|PMID:2275823 TAS F histone H4 (HHF1 and HHF2 code for identical proteins) YNL030W gene taxon:4932 20020204 SGD
+SGD S000004975 HHF2 GO:0006333 SGD_REF:S000060984|PMID:2275823 TAS P histone H4 (HHF1 and HHF2 code for identical proteins) YNL030W gene taxon:4932 20020204 SGD
+SGD S000006048 HHO1 GO:0000788 SGD_REF:S000065991|PMID:11574687 IPI C histone H1 YPL127C gene taxon:4932 20020213 SGD
+SGD S000006048 HHO1 GO:0005634 SGD_REF:S000069459|PMID:11914276 IDA C histone H1 YPL127C gene taxon:4932 20020507 SGD
+SGD S000006048 HHO1 GO:0005634 SGD_REF:S000041152|PMID:9046096 IDA C histone H1 YPL127C gene taxon:4932 20031113 SGD
+SGD S000006048 HHO1 GO:0003677 SGD_REF:S000065991|PMID:11574687 IPI F histone H1 YPL127C gene taxon:4932 20020213 SGD
+SGD S000006048 HHO1 GO:0006355 SGD_REF:S000065991|PMID:11574687 IMP P histone H1 YPL127C gene taxon:4932 20020213 SGD
+SGD S000006048 HHO1 GO:0045910 SGD_REF:S000073592|PMID:12820979 IMP P histone H1 YPL127C gene taxon:4932 20031114 SGD
+SGD S000006048 HHO1 GO:0045910 SGD_REF:S000073592|PMID:12820979 IGI P histone H1 YPL127C gene taxon:4932 20031114 SGD
+SGD S000000214 HHT1 GO:0000788 SGD_REF:S000060984|PMID:2275823 TAS C histone H3 (HHT1 and HHT2 code for identical proteins) YBR010W|BUR5|SIN2 gene taxon:4932 20010726 SGD
+SGD S000000214 HHT1 GO:0005634 SGD_REF:S000069459|PMID:11914276 IDA C histone H3 (HHT1 and HHT2 code for identical proteins) YBR010W|BUR5|SIN2 gene taxon:4932 20020507 SGD
+SGD S000000214 HHT1 GO:0003677 SGD_REF:S000060984|PMID:2275823 TAS F histone H3 (HHT1 and HHT2 code for identical proteins) YBR010W|BUR5|SIN2 gene taxon:4932 20020204 SGD
+SGD S000000214 HHT1 GO:0006333 SGD_REF:S000060984|PMID:2275823 TAS P histone H3 (HHT1 and HHT2 code for identical proteins) YBR010W|BUR5|SIN2 gene taxon:4932 20020204 SGD
+SGD S000004976 HHT2 GO:0000788 SGD_REF:S000060984|PMID:2275823 TAS C histone H3 (HHT1 and HHT2 code for identical proteins) YNL031C gene taxon:4932 20010726 SGD
+SGD S000004976 HHT2 GO:0003677 SGD_REF:S000060984|PMID:2275823 TAS F histone H3 (HHT1 and HHT2 code for identical proteins) YNL031C gene taxon:4932 20020204 SGD
+SGD S000004976 HHT2 GO:0006333 SGD_REF:S000060984|PMID:2275823 TAS P histone H3 (HHT1 and HHT2 code for identical proteins) YNL031C gene taxon:4932 20020204 SGD
+SGD S000003945 HIF1 GO:0000123 SGD_REF:S000076003|PMID:14761951 IPI C YLL022C gene taxon:4932 20040427 SGD
+SGD S000003945 HIF1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YLL022C gene taxon:4932 20031028 SGD
+SGD S000003945 HIF1 GO:0005634 SGD_REF:S000076003|PMID:14761951 IDA C YLL022C gene taxon:4932 20040427 SGD
+SGD S000003945 HIF1 GO:0005554 SGD_REF:S000069584 ND F YLL022C gene taxon:4932 20020814 SGD
+SGD S000003945 HIF1 GO:0006348 SGD_REF:S000076003|PMID:14761951 IMP P YLL022C gene taxon:4932 20040427 SGD
+SGD S000002725 HIM1 GO:0008372 SGD_REF:S000069584 ND C YDR317W gene taxon:4932 20050609 SGD
+SGD S000002725 HIM1 GO:0005554 SGD_REF:S000069584 ND F YDR317W gene taxon:4932 20050609 SGD
+SGD S000002725 HIM1 GO:0006281 SGD_REF:S000081696|PMID:15885712 IGI SGD:S000001597|SGD:S000005026 P YDR317W gene taxon:4932 20050609 SGD
+SGD S000003423 HIP1 GO:0005886 SGD_REF:S000046358|PMID:3905514 ISS C histidine permease YGR191W gene taxon:4932 20021002 SGD
+SGD S000003423 HIP1 GO:0005886 SGD_REF:S000046358|PMID:3905514 IMP C histidine permease YGR191W gene taxon:4932 20021002 SGD
+SGD S000003423 HIP1 GO:0005290 SGD_REF:S000046358|PMID:3905514 ISS F histidine permease YGR191W gene taxon:4932 20021002 SGD
+SGD S000003423 HIP1 GO:0005290 SGD_REF:S000046358|PMID:3905514 IMP F histidine permease YGR191W gene taxon:4932 20021002 SGD
+SGD S000003423 HIP1 GO:0006828 SGD_REF:S000054469|PMID:9790586 IMP P histidine permease YGR191W gene taxon:4932 20021002 SGD
+SGD S000003423 HIP1 GO:0015817 SGD_REF:S000046358|PMID:3905514 IMP P histidine permease YGR191W gene taxon:4932 20021002 SGD
+SGD S000000104 HIR1 GO:0000775 SGD_REF:S000069112|PMID:11782447 IDA C contains nuclear targeting signal, repressor protein (putative), similar to Tup1p and mammalian retinal transducin YBL008W gene taxon:4932 20030410 SGD
+SGD S000000104 HIR1 GO:0005634 SGD_REF:S000039248|PMID:9504914 IPI C contains nuclear targeting signal, repressor protein (putative), similar to Tup1p and mammalian retinal transducin YBL008W gene taxon:4932 20021121 SGD
+SGD S000000104 HIR1 GO:0003714 SGD_REF:S000055143|PMID:9001207 IDA F contains nuclear targeting signal, repressor protein (putative), similar to Tup1p and mammalian retinal transducin YBL008W gene taxon:4932 20021121 SGD
+SGD S000000104 HIR1 GO:0006357 SGD_REF:S000055143|PMID:9001207 IDA P contains nuclear targeting signal, repressor protein (putative), similar to Tup1p and mammalian retinal transducin YBL008W gene taxon:4932 20021121 SGD
+SGD S000005564 HIR2 GO:0005634 SGD_REF:S000048249|PMID:8417331 IDA C contains nuclear targeting signal, repressor protein (putative) YOR038C|SPT1 gene taxon:4932 20021121 SGD
+SGD S000005564 HIR2 GO:0003714 SGD_REF:S000055143|PMID:9001207 IDA F contains nuclear targeting signal, repressor protein (putative) YOR038C|SPT1 gene taxon:4932 20021121 SGD
+SGD S000005564 HIR2 GO:0006357 SGD_REF:S000055143|PMID:9001207 IDA P contains nuclear targeting signal, repressor protein (putative) YOR038C|SPT1 gene taxon:4932 20021121 SGD
+SGD S000003901 HIR3 GO:0005634 SGD_REF:S000055143|PMID:9001207 IDA C YJR140C|HPC1 gene taxon:4932 20020828 SGD
+SGD S000003901 HIR3 GO:0003714 SGD_REF:S000055143|PMID:9001207 IMP F YJR140C|HPC1 gene taxon:4932 20021004 SGD
+SGD S000003901 HIR3 GO:0000083 SGD_REF:S000039430|PMID:1406694 IMP P YJR140C|HPC1 gene taxon:4932 20021004 SGD
+SGD S000029211 HIR4 GO:0008372 SGD_REF:S000069584 ND C transcriptional activator (putative) gene taxon:4932 20020530 SGD
+SGD S000029211 HIR4 GO:0005554 SGD_REF:S000069584 ND F transcriptional activator (putative) gene taxon:4932 20020530 SGD
+SGD S000029211 HIR4 GO:0006355 SGD_REF:S000055718|PMID:8224824 IMP P transcriptional activator (putative) gene taxon:4932 20020530 SGD
+SGD S000000857 HIS1 GO:0005622 SGD_REF:S000057959|PMID:8852895 TAS C ATP phosphoribosyltransferase YER055C gene taxon:4932 20041206 SGD
+SGD S000000857 HIS1 GO:0003879 SGD_REF:S000057959|PMID:8852895 TAS F ATP phosphoribosyltransferase YER055C gene taxon:4932 20010118 SGD
+SGD S000000857 HIS1 GO:0000105 SGD_REF:S000057959|PMID:8852895 TAS P ATP phosphoribosyltransferase YER055C gene taxon:4932 20010118 SGD
+SGD S000001921 HIS2 GO:0005622 SGD_REF:S000057959|PMID:8852895 TAS C histidinolphosphatase YFR025C gene taxon:4932 20041206 SGD
+SGD S000001921 HIS2 GO:0004401 SGD_REF:S000057959|PMID:8852895 TAS F histidinolphosphatase YFR025C gene taxon:4932 20010118 SGD
+SGD S000001921 HIS2 GO:0000105 SGD_REF:S000057959|PMID:8852895 TAS P histidinolphosphatase YFR025C gene taxon:4932 20010118 SGD
+SGD S000005728 HIS3 GO:0005622 SGD_REF:S000057959|PMID:8852895 TAS C imidazoleglycerol-phosphate dehydratase YOR202W|HIS10 gene taxon:4932 20041206 SGD
+SGD S000005728 HIS3 GO:0004424 SGD_REF:S000057959|PMID:8852895 TAS F imidazoleglycerol-phosphate dehydratase YOR202W|HIS10 gene taxon:4932 20010118 SGD
+SGD S000005728 HIS3 GO:0000105 SGD_REF:S000057959|PMID:8852895 TAS P imidazoleglycerol-phosphate dehydratase YOR202W|HIS10 gene taxon:4932 20010118 SGD
+SGD S000000535 HIS4 GO:0005622 SGD_REF:S000079788|PMID:19214 TAS C histidinol dehydrogenase YCL030C gene taxon:4932 20041206 SGD
+SGD S000000535 HIS4 GO:0004399 SGD_REF:S000057959|PMID:8852895 TAS F histidinol dehydrogenase YCL030C gene taxon:4932 20010118 SGD
+SGD S000000535 HIS4 GO:0004635 SGD_REF:S000057959|PMID:8852895 TAS F histidinol dehydrogenase YCL030C gene taxon:4932 20010118 SGD
+SGD S000000535 HIS4 GO:0004636 SGD_REF:S000057959|PMID:8852895 TAS F histidinol dehydrogenase YCL030C gene taxon:4932 20010118 SGD
+SGD S000000535 HIS4 GO:0000105 SGD_REF:S000057959|PMID:8852895 TAS P histidinol dehydrogenase YCL030C gene taxon:4932 20010118 SGD
+SGD S000001378 HIS5 GO:0005622 SGD_REF:S000057959|PMID:8852895 TAS C histidinol-phosphate aminotransferase YIL116W gene taxon:4932 20041206 SGD
+SGD S000001378 HIS5 GO:0004400 SGD_REF:S000057959|PMID:8852895 TAS F histidinol-phosphate aminotransferase YIL116W gene taxon:4932 20010118 SGD
+SGD S000001378 HIS5 GO:0000105 SGD_REF:S000057959|PMID:8852895 TAS P histidinol-phosphate aminotransferase YIL116W gene taxon:4932 20010118 SGD
+SGD S000001282 HIS6 GO:0005622 SGD_REF:S000057959|PMID:8852895 TAS C phosphoribosyl-5-amino-1-phosphoribosyl-4-imidazolecarboxiamide isomerase YIL020C gene taxon:4932 20041206 SGD
+SGD S000001282 HIS6 GO:0003949 SGD_REF:S000057959|PMID:8852895 TAS F phosphoribosyl-5-amino-1-phosphoribosyl-4-imidazolecarboxiamide isomerase YIL020C gene taxon:4932 20010118 SGD
+SGD S000001282 HIS6 GO:0000105 SGD_REF:S000057959|PMID:8852895 TAS P phosphoribosyl-5-amino-1-phosphoribosyl-4-imidazolecarboxiamide isomerase YIL020C gene taxon:4932 20010118 SGD
+SGD S000000452 HIS7 GO:0005622 SGD_REF:S000057959|PMID:8852895 TAS C imidazole glycerol phosphate synthase YBR248C gene taxon:4932 20031022 SGD
+SGD S000000452 HIS7 GO:0000107 SGD_REF:S000057959|PMID:8852895 TAS F imidazole glycerol phosphate synthase YBR248C gene taxon:4932 20010118 SGD
+SGD S000000452 HIS7 GO:0000107 SGD_REF:S000044976|PMID:10733892 IDA F imidazole glycerol phosphate synthase YBR248C gene taxon:4932 20030331 SGD
+SGD S000000452 HIS7 GO:0000105 SGD_REF:S000057959|PMID:8852895 TAS P imidazole glycerol phosphate synthase YBR248C gene taxon:4932 20010118 SGD
+SGD S000000452 HIS7 GO:0009127 SGD_REF:S000054163|PMID:8939895 TAS P imidazole glycerol phosphate synthase YBR248C gene taxon:4932 20031022 SGD
+SGD S000003816 HIT1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YJR055W gene taxon:4932 20031028 SGD
+SGD S000003816 HIT1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YJR055W gene taxon:4932 20031028 SGD
+SGD S000003816 HIT1 GO:0005554 SGD_REF:S000069584 ND F YJR055W gene taxon:4932 20021011 SGD
+SGD S000003816 HIT1 GO:0000004 SGD_REF:S000069584 ND P YJR055W gene taxon:4932 20031126 SGD
+SGD S000002828 HKR1 GO:0005886 SGD_REF:S000055885|PMID:8550469 IDA C contains EF hand motif, type I transmembrane protein YDR420W gene taxon:4932 20020405 SGD
+SGD S000002828 HKR1 GO:0005886 SGD_REF:S000055885|PMID:8550469 ISS C contains EF hand motif, type I transmembrane protein YDR420W gene taxon:4932 20020405 SGD
+SGD S000002828 HKR1 GO:0005554 SGD_REF:S000069584 ND F contains EF hand motif, type I transmembrane protein YDR420W gene taxon:4932 20021211 SGD
+SGD S000002828 HKR1 GO:0000282 SGD_REF:S000055885|PMID:8550469 IMP P contains EF hand motif, type I transmembrane protein YDR420W gene taxon:4932 20020405 SGD
+SGD S000002828 HKR1 GO:0006075 SGD_REF:S000055885|PMID:8550469 IMP P contains EF hand motif, type I transmembrane protein YDR420W gene taxon:4932 20020405 SGD
+SGD S000002828 HKR1 GO:0007047 SGD_REF:S000055885|PMID:8550469 IMP P contains EF hand motif, type I transmembrane protein YDR420W gene taxon:4932 20020405 SGD
+SGD S000004771 HLJ1 GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YMR161W gene taxon:4932 20031028 SGD
+SGD S000004771 HLJ1 GO:0005789 SGD_REF:S000072636|PMID:12514182 IDA C YMR161W gene taxon:4932 20031014 SGD
+SGD S000004771 HLJ1 GO:0005789 SGD_REF:S000072636|PMID:12514182 ISS C YMR161W gene taxon:4932 20041101 SGD
+SGD S000004771 HLJ1 GO:0001671 SGD_REF:S000077458|PMID:15342786 IDA F YMR161W gene taxon:4932 20041102 SGD
+SGD S000004771 HLJ1 GO:0030188 SGD_REF:S000076441|PMID:15170475 ISS F YMR161W gene taxon:4932 20041101 SGD
+SGD S000004771 HLJ1 GO:0006457 SGD_REF:S000076441|PMID:15170475 IC GO:0030188 P YMR161W gene taxon:4932 20041101 SGD
+SGD S000004771 HLJ1 GO:0030433 SGD_REF:S000077133|PMID:15252059 IMP P YMR161W gene taxon:4932 20041102 SGD
+SGD S000004771 HLJ1 GO:0030433 SGD_REF:S000077458|PMID:15342786 IGI P YMR161W gene taxon:4932 20041102 SGD
+SGD S000004771 HLJ1 GO:0030433 SGD_REF:S000077458|PMID:15342786 IMP P YMR161W gene taxon:4932 20041102 SGD
+SGD S000002936 HLR1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDR528W gene taxon:4932 20031028 SGD
+SGD S000002936 HLR1 GO:0005554 SGD_REF:S000069584 ND F YDR528W gene taxon:4932 20021001 SGD
+SGD S000002936 HLR1 GO:0007047 SGD_REF:S000061266|PMID:11532139 IGI P YDR528W gene taxon:4932 20021001 SGD
+SGD S000000859 HMF1 GO:0005634 SGD_REF:S000060859|PMID:11442631 IDA C YER057C|HIG1 gene taxon:4932 20030414 SGD
+SGD S000000859 HMF1 GO:0005737 SGD_REF:S000060859|PMID:11442631 IDA C YER057C|HIG1 gene taxon:4932 20030414 SGD
+SGD S000000859 HMF1 GO:0005829 SGD_REF:S000060983|PMID:11003673 IDA C YER057C|HIG1 gene taxon:4932 20020926 SGD
+SGD S000000859 HMF1 GO:0005554 SGD_REF:S000069584 ND F YER057C|HIG1 gene taxon:4932 20020926 SGD
+SGD S000000859 HMF1 GO:0000004 SGD_REF:S000069584 ND P YER057C|HIG1 gene taxon:4932 20020926 SGD
+SGD S000004540 HMG1 GO:0005635 SGD_REF:S000055806|PMID:8744950 IDA C 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA) reductase isozyme YML075C gene taxon:4932 20010118 SGD
+SGD S000004540 HMG1 GO:0005759 SGD_REF:S000058496 TAS C 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA) reductase isozyme YML075C gene taxon:4932 20010119 SGD
+SGD S000004540 HMG1 GO:0005789 SGD_REF:S000055806|PMID:8744950 IDA C 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA) reductase isozyme YML075C gene taxon:4932 20010118 SGD
+SGD S000004540 HMG1 GO:0004420 SGD_REF:S000058496 TAS F 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA) reductase isozyme YML075C gene taxon:4932 20010119 SGD
+SGD S000004540 HMG1 GO:0006696 SGD_REF:S000058496 TAS P 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA) reductase isozyme YML075C gene taxon:4932 20010119 SGD
+SGD S000004442 HMG2 GO:0005635 SGD_REF:S000055806|PMID:8744950 TAS C 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA) reductase isozyme YLR450W gene taxon:4932 20010118 SGD
+SGD S000004442 HMG2 GO:0005759 SGD_REF:S000058496 TAS C 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA) reductase isozyme YLR450W gene taxon:4932 20010119 SGD
+SGD S000004442 HMG2 GO:0005789 SGD_REF:S000055806|PMID:8744950 TAS C 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA) reductase isozyme YLR450W gene taxon:4932 20010118 SGD
+SGD S000004442 HMG2 GO:0004420 SGD_REF:S000058496 TAS F 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA) reductase isozyme YLR450W gene taxon:4932 20010119 SGD
+SGD S000004442 HMG2 GO:0006696 SGD_REF:S000058496 TAS P 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA) reductase isozyme YLR450W gene taxon:4932 20010119 SGD
+SGD S000005455 HMI1 GO:0005759 SGD_REF:S000044690|PMID:10409639 IDA C YOL095C gene taxon:4932 20020921 SGD
+SGD S000005455 HMI1 GO:0004003 SGD_REF:S000041593|PMID:10669756 IDA F YOL095C gene taxon:4932 20020921 SGD
+SGD S000005455 HMI1 GO:0000002 SGD_REF:S000041593|PMID:10669756 IMP P YOL095C gene taxon:4932 20020921 SGD
+SGD S000000571 HMLALPHA1 GO:0005634 SGD_REF:S000058493 TAS C involved in the regulation of alpha-specific genes, transcription factor YCL066W|ALPHA1 gene taxon:4932 20010119 SGD
+SGD S000000571 HMLALPHA1 GO:0003713 SGD_REF:S000058493 TAS F involved in the regulation of alpha-specific genes, transcription factor YCL066W|ALPHA1 gene taxon:4932 20010119 SGD
+SGD S000000571 HMLALPHA1 GO:0006357 SGD_REF:S000058493 TAS P involved in the regulation of alpha-specific genes, transcription factor YCL066W|ALPHA1 gene taxon:4932 20010119 SGD
+SGD S000000571 HMLALPHA1 GO:0007532 SGD_REF:S000058493 TAS P involved in the regulation of alpha-specific genes, transcription factor YCL066W|ALPHA1 gene taxon:4932 20010119 SGD
+SGD S000000572 HMLALPHA2 GO:0005634 SGD_REF:S000058493 TAS C YCL067C|ALPHA2 gene taxon:4932 20010119 SGD
+SGD S000000572 HMLALPHA2 GO:0003714 SGD_REF:S000058493 TAS F YCL067C|ALPHA2 gene taxon:4932 20010119 SGD
+SGD S000000572 HMLALPHA2 GO:0006357 SGD_REF:S000058493 TAS P YCL067C|ALPHA2 gene taxon:4932 20010119 SGD
+SGD S000000572 HMLALPHA2 GO:0007532 SGD_REF:S000058493 TAS P YCL067C|ALPHA2 gene taxon:4932 20010119 SGD
+SGD S000000572 HMLALPHA2 GO:0007535 SGD_REF:S000055054|PMID:9928492 TAS P YCL067C|ALPHA2 gene taxon:4932 20010118 SGD
+SGD S000002581 HMO1 GO:0000790 SGD_REF:S000043098|PMID:8969238 ISS C high mobility group (HMG) family YDR174W|HSM2 gene taxon:4932 20011207 SGD
+SGD S000002581 HMO1 GO:0005634 SGD_REF:S000043098|PMID:8969238 IDA C high mobility group (HMG) family YDR174W|HSM2 gene taxon:4932 20011207 SGD
+SGD S000002581 HMO1 GO:0005730 SGD_REF:S000071705|PMID:12374750 IDA C high mobility group (HMG) family YDR174W|HSM2 gene taxon:4932 20040113 SGD
+SGD S000002581 HMO1 GO:0005737 SGD_REF:S000043098|PMID:8969238 IDA C high mobility group (HMG) family YDR174W|HSM2 gene taxon:4932 20011207 SGD
+SGD S000002581 HMO1 GO:0003697 SGD_REF:S000043098|PMID:8969238 IDA F high mobility group (HMG) family YDR174W|HSM2 gene taxon:4932 20011207 SGD
+SGD S000002581 HMO1 GO:0003701 SGD_REF:S000071705|PMID:12374750 IDA F high mobility group (HMG) family YDR174W|HSM2 gene taxon:4932 20021206 SGD
+SGD S000002581 HMO1 GO:0006276 SGD_REF:S000043098|PMID:8969238 IMP P high mobility group (HMG) family YDR174W|HSM2 gene taxon:4932 20011207 SGD
+SGD S000000694 HMRA1 GO:0005634 SGD_REF:S000054505|PMID:8411150 IDA C homeobox transcription factor YCR097W|YCR097WB gene taxon:4932 20030211 SGD
+SGD S000000694 HMRA1 GO:0003714 SGD_REF:S000053871|PMID:1977088 IDA F homeobox transcription factor YCR097W|YCR097WB gene taxon:4932 20010118 SGD
+SGD S000000694 HMRA1 GO:0007532 SGD_REF:S000053871|PMID:1977088 IDA P homeobox transcription factor YCR097W|YCR097WB gene taxon:4932 20030226 SGD
+SGD S000000692 HMRA2 GO:0008372 SGD_REF:S000069584 ND C YCR096C|A2 gene taxon:4932 20010119 SGD
+SGD S000000692 HMRA2 GO:0005554 SGD_REF:S000069584 ND F YCR096C|A2 gene taxon:4932 20010119 SGD
+SGD S000000692 HMRA2 GO:0000004 SGD_REF:S000069584 ND P YCR096C|A2 gene taxon:4932 20030203 SGD
+SGD S000005558 HMS1 GO:0008372 SGD_REF:S000069584 ND C myc-family transcription factor homolog YOR032C gene taxon:4932 20021007 SGD
+SGD S000005558 HMS1 GO:0003700 SGD_REF:S000048296|PMID:10710415 ISS F myc-family transcription factor homolog YOR032C gene taxon:4932 20051108 SGD
+SGD S000005558 HMS1 GO:0007124 SGD_REF:S000043169|PMID:9832522 IGI P myc-family transcription factor homolog YOR032C gene taxon:4932 20021007 SGD
+SGD S000003908 HMS2 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C heat shock transcription factor homolog YJR147W gene taxon:4932 20031028 SGD
+SGD S000003908 HMS2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C heat shock transcription factor homolog YJR147W gene taxon:4932 20031028 SGD
+SGD S000003908 HMS2 GO:0005554 SGD_REF:S000069584 ND F heat shock transcription factor homolog YJR147W gene taxon:4932 20040202 SGD
+SGD S000003908 HMS2 GO:0007124 SGD_REF:S000043169|PMID:9832522 IGI P heat shock transcription factor homolog YJR147W gene taxon:4932 20021007 SGD
+SGD S000000238 HMT1 GO:0005634 SGD_REF:S000041792|PMID:8668183 IDA C arginine methyltransferase, mono- and asymmetrically dimethylating enzyme YBR034C|HCP1|ODP1|RMT1 gene taxon:4932 20020726 SGD
+SGD S000000238 HMT1 GO:0016274 SGD_REF:S000041792|PMID:8668183 IDA F arginine methyltransferase, mono- and asymmetrically dimethylating enzyme YBR034C|HCP1|ODP1|RMT1 gene taxon:4932 20020726 SGD
+SGD S000000238 HMT1 GO:0016274 SGD_REF:S000041792|PMID:8668183 IPI F arginine methyltransferase, mono- and asymmetrically dimethylating enzyme YBR034C|HCP1|ODP1|RMT1 gene taxon:4932 20020726 SGD
+SGD S000000238 HMT1 GO:0016274 SGD_REF:S000041792|PMID:8668183 ISS F arginine methyltransferase, mono- and asymmetrically dimethylating enzyme YBR034C|HCP1|ODP1|RMT1 gene taxon:4932 20020726 SGD
+SGD S000000238 HMT1 GO:0006406 SGD_REF:S000041792|PMID:8668183 IGI P arginine methyltransferase, mono- and asymmetrically dimethylating enzyme YBR034C|HCP1|ODP1|RMT1 gene taxon:4932 20020726 SGD
+SGD S000000238 HMT1 GO:0006406 SGD_REF:S000044295|PMID:10952997 IGI P arginine methyltransferase, mono- and asymmetrically dimethylating enzyme YBR034C|HCP1|ODP1|RMT1 gene taxon:4932 20020726 SGD
+SGD S000000238 HMT1 GO:0018195 SGD_REF:S000041792|PMID:8668183 IDA P arginine methyltransferase, mono- and asymmetrically dimethylating enzyme YBR034C|HCP1|ODP1|RMT1 gene taxon:4932 20020726 SGD
+SGD S000000238 HMT1 GO:0018195 SGD_REF:S000041792|PMID:8668183 ISS P arginine methyltransferase, mono- and asymmetrically dimethylating enzyme YBR034C|HCP1|ODP1|RMT1 gene taxon:4932 20020726 SGD
+SGD S000004195 HMX1 GO:0005783 SGD_REF:S000074012|PMID:12840010 IDA C YLR205C gene taxon:4932 20040219 SGD
+SGD S000004195 HMX1 GO:0016020 SGD_REF:S000065939|PMID:11566881 IDA C YLR205C gene taxon:4932 20020921 SGD
+SGD S000004195 HMX1 GO:0004392 SGD_REF:S000060699|PMID:11112771 ISS F YLR205C gene taxon:4932 20020923 SGD
+SGD S000004195 HMX1 NOT GO:0004392 SGD_REF:S000073085|PMID:12699699 IDA F YLR205C gene taxon:4932 20030625 SGD
+SGD S000004195 HMX1 GO:0004392 SGD_REF:S000060699|PMID:11112771 IEP F YLR205C gene taxon:4932 20020923 SGD
+SGD S000004195 HMX1 GO:0004601 SGD_REF:S000073085|PMID:12699699 IDA F YLR205C gene taxon:4932 20030505 SGD
+SGD S000004195 HMX1 GO:0020037 SGD_REF:S000073085|PMID:12699699 IDA F YLR205C gene taxon:4932 20030505 SGD
+SGD S000004195 HMX1 GO:0006879 SGD_REF:S000060699|PMID:11112771 ISS P YLR205C gene taxon:4932 20020923 SGD
+SGD S000004195 HMX1 GO:0006879 SGD_REF:S000060699|PMID:11112771 IEP P YLR205C gene taxon:4932 20020923 SGD
+SGD S000004195 HMX1 GO:0042167 SGD_REF:S000074012|PMID:12840010 IMP P YLR205C gene taxon:4932 20040219 SGD
+SGD S000004195 HMX1 GO:0042167 SGD_REF:S000074012|PMID:12840010 IGI P YLR205C gene taxon:4932 20040219 SGD
+SGD S000003045 HNM1 GO:0005886 SGD_REF:S000056806|PMID:2203793 ISS C transporter (permease) for choline and nitrogen mustard; share homology with UGA4 YGL077C gene taxon:4932 20021003 SGD
+SGD S000003045 HNM1 GO:0005886 SGD_REF:S000056806|PMID:2203793 IMP C transporter (permease) for choline and nitrogen mustard; share homology with UGA4 YGL077C gene taxon:4932 20021003 SGD
+SGD S000003045 HNM1 GO:0015220 SGD_REF:S000056806|PMID:2203793 ISS F transporter (permease) for choline and nitrogen mustard; share homology with UGA4 YGL077C gene taxon:4932 20021003 SGD
+SGD S000003045 HNM1 GO:0015220 SGD_REF:S000056806|PMID:2203793 IMP F transporter (permease) for choline and nitrogen mustard; share homology with UGA4 YGL077C gene taxon:4932 20021003 SGD
+SGD S000003045 HNM1 GO:0015871 SGD_REF:S000056806|PMID:2203793 ISS P transporter (permease) for choline and nitrogen mustard; share homology with UGA4 YGL077C gene taxon:4932 20021003 SGD
+SGD S000003045 HNM1 GO:0015871 SGD_REF:S000056806|PMID:2203793 IMP P transporter (permease) for choline and nitrogen mustard; share homology with UGA4 YGL077C gene taxon:4932 20021003 SGD
+SGD S000002283 HNT1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YDL125C gene taxon:4932 20031028 SGD
+SGD S000002283 HNT1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YDL125C gene taxon:4932 20020507 SGD
+SGD S000002283 HNT1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDL125C gene taxon:4932 20031028 SGD
+SGD S000002283 HNT1 GO:0000166 SGD_REF:S000058119|PMID:9164465 ISS F YDL125C gene taxon:4932 20010118 SGD
+SGD S000002283 HNT1 GO:0016787 SGD_REF:S000069835|PMID:11805111 IDA F YDL125C gene taxon:4932 20021205 SGD
+SGD S000002283 HNT1 GO:0009117 SGD_REF:S000069835|PMID:11805111 IDA P YDL125C gene taxon:4932 20021205 SGD
+SGD S000002713 HNT2 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YDR305C|APH1 gene taxon:4932 20031028 SGD
+SGD S000002713 HNT2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDR305C|APH1 gene taxon:4932 20031028 SGD
+SGD S000002713 HNT2 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YDR305C|APH1 gene taxon:4932 20031028 SGD
+SGD S000002713 HNT2 GO:0016787 SGD_REF:S000069891|PMID:12028594 IDA F YDR305C|APH1 gene taxon:4932 20020602 SGD
+SGD S000002713 HNT2 GO:0017111 SGD_REF:S000063528|PMID:1653209 IDA F YDR305C|APH1 gene taxon:4932 20020602 SGD
+SGD S000002713 HNT2 GO:0009164 SGD_REF:S000063530|PMID:9573184 IMP P YDR305C|APH1 gene taxon:4932 20021007 SGD
+SGD S000005784 HNT3 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YOR258W gene taxon:4932 20031028 SGD
+SGD S000005784 HNT3 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YOR258W gene taxon:4932 20031028 SGD
+SGD S000005784 HNT3 GO:0005554 SGD_REF:S000069584 ND F YOR258W gene taxon:4932 20021123 SGD
+SGD S000005784 HNT3 GO:0000004 SGD_REF:S000069584 ND P YOR258W gene taxon:4932 20021123 SGD
+SGD S000002386 HO GO:0005634 SGD_REF:S000052889|PMID:10915865 TAS C homothallic switching endonuclease YDL227C gene taxon:4932 20020724 SGD
+SGD S000002386 HO GO:0004519 SGD_REF:S000053754|PMID:6313222 IDA F homothallic switching endonuclease YDL227C gene taxon:4932 20020724 SGD
+SGD S000002386 HO GO:0000728 SGD_REF:S000053754|PMID:6313222 IDA P homothallic switching endonuclease YDL227C gene taxon:4932 20051213 SGD
+SGD S000002386 HO GO:0007533 SGD_REF:S000049724|PMID:6297747 IMP P homothallic switching endonuclease YDL227C gene taxon:4932 20020724 SGD
+SGD S000002386 HO GO:0007534 SGD_REF:S000052889|PMID:10915865 TAS P homothallic switching endonuclease YDL227C gene taxon:4932 20020724 SGD
+SGD S000003836 HOC1 GO:0000136 SGD_REF:S000047367|PMID:10037752 IDA C mannosyltransferase (putative) YJR075W gene taxon:4932 20010118 SGD
+SGD S000003836 HOC1 GO:0000136 SGD_REF:S000053242|PMID:9430634 IPI C mannosyltransferase (putative) YJR075W gene taxon:4932 20020213 SGD
+SGD S000003836 HOC1 contributes_to GO:0000009 SGD_REF:S000047367|PMID:10037752 IDA F mannosyltransferase (putative) YJR075W gene taxon:4932 20050428 SGD
+SGD S000003836 HOC1 GO:0016757 SGD_REF:S000055539|PMID:9653120 ISS F mannosyltransferase (putative) YJR075W gene taxon:4932 20021204 SGD
+SGD S000003836 HOC1 GO:0000032 SGD_REF:S000047367|PMID:10037752 TAS P mannosyltransferase (putative) YJR075W gene taxon:4932 20010118 SGD
+SGD S000003836 HOC1 GO:0006080 SGD_REF:S000047367|PMID:10037752 TAS P mannosyltransferase (putative) YJR075W gene taxon:4932 20010118 SGD
+SGD S000004635 HOF1 GO:0000142 SGD_REF:S000041005|PMID:10652251 IDA C YMR032W|CYK2 gene taxon:4932 20010118 SGD
+SGD S000004635 HOF1 GO:0000142 SGD_REF:S000081151|PMID:15775961 IDA C YMR032W|CYK2 gene taxon:4932 20050330 SGD
+SGD S000004635 HOF1 GO:0008092 SGD_REF:S000055446|PMID:9864366 IPI F YMR032W|CYK2 gene taxon:4932 20010118 SGD
+SGD S000004635 HOF1 GO:0000910 SGD_REF:S000041005|PMID:10652251 IMP P YMR032W|CYK2 gene taxon:4932 20010119 SGD
+SGD S000004635 HOF1 GO:0006974 SGD_REF:S000076175|PMID:12482937 IMP P YMR032W|CYK2 gene taxon:4932 20060406 SGD
+SGD S000004103 HOG1 GO:0005634 SGD_REF:S000050031|PMID:10817757 IDA C MAP kinase YLR113W|SSK3 gene taxon:4932 20021001 SGD
+SGD S000004103 HOG1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C MAP kinase YLR113W|SSK3 gene taxon:4932 20020507 SGD
+SGD S000004103 HOG1 GO:0005737 SGD_REF:S000050031|PMID:10817757 IDA C MAP kinase YLR113W|SSK3 gene taxon:4932 20021001 SGD
+SGD S000004103 HOG1 GO:0004707 SGD_REF:S000046072|PMID:9744858 TAS F MAP kinase YLR113W|SSK3 gene taxon:4932 20021001 SGD
+SGD S000004103 HOG1 GO:0006468 SGD_REF:S000060317|PMID:11283616 TAS P MAP kinase YLR113W|SSK3 gene taxon:4932 20030204 SGD
+SGD S000004103 HOG1 GO:0006972 SGD_REF:S000046072|PMID:9744858 TAS P MAP kinase YLR113W|SSK3 gene taxon:4932 20021001 SGD
+SGD S000004103 HOG1 GO:0045944 SGD_REF:S000068841|PMID:12743037 IDA P MAP kinase YLR113W|SSK3 gene taxon:4932 20030731 SGD
+SGD S000005338 HOL1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C similar to the major facilitator superfamily of transporters YNR055C gene taxon:4932 20040928 SGD
+SGD S000005338 HOL1 GO:0005886 SGD_REF:S000051592|PMID:8955402 ISS C similar to the major facilitator superfamily of transporters YNR055C gene taxon:4932 20021003 SGD
+SGD S000005338 HOL1 GO:0005886 SGD_REF:S000051592|PMID:8955402 IMP C similar to the major facilitator superfamily of transporters YNR055C gene taxon:4932 20021003 SGD
+SGD S000005338 HOL1 GO:0005215 SGD_REF:S000051592|PMID:8955402 ISS F similar to the major facilitator superfamily of transporters YNR055C gene taxon:4932 20021003 SGD
+SGD S000005338 HOL1 GO:0005215 SGD_REF:S000051592|PMID:8955402 IMP F similar to the major facilitator superfamily of transporters YNR055C gene taxon:4932 20021003 SGD
+SGD S000005338 HOL1 GO:0006810 SGD_REF:S000051592|PMID:8955402 ISS P similar to the major facilitator superfamily of transporters YNR055C gene taxon:4932 20021003 SGD
+SGD S000005338 HOL1 GO:0006810 SGD_REF:S000051592|PMID:8955402 IMP P similar to the major facilitator superfamily of transporters YNR055C gene taxon:4932 20021003 SGD
+SGD S000002565 HOM2 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C aspartic beta semi-aldehyde dehydrogenase YDR158W gene taxon:4932 20031028 SGD
+SGD S000002565 HOM2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C aspartic beta semi-aldehyde dehydrogenase YDR158W gene taxon:4932 20031028 SGD
+SGD S000002565 HOM2 GO:0004073 SGD_REF:S000047335|PMID:2570346 TAS F aspartic beta semi-aldehyde dehydrogenase YDR158W gene taxon:4932 20021001 SGD
+SGD S000002565 HOM2 GO:0006555 SGD_REF:S000047335|PMID:2570346 TAS P aspartic beta semi-aldehyde dehydrogenase YDR158W gene taxon:4932 20021001 SGD
+SGD S000002565 HOM2 GO:0006566 SGD_REF:S000047335|PMID:2570346 TAS P aspartic beta semi-aldehyde dehydrogenase YDR158W gene taxon:4932 20021001 SGD
+SGD S000002565 HOM2 GO:0009090 SGD_REF:S000070200 TAS P aspartic beta semi-aldehyde dehydrogenase YDR158W gene taxon:4932 20030528 SGD
+SGD S000000854 HOM3 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C aspartate kinase (L-aspartate 4-P-transferase) (EC 2.7.2.4) YER052C|BOR1|SIL4 gene taxon:4932 20031028 SGD
+SGD S000000854 HOM3 GO:0004072 SGD_REF:S000049419|PMID:9315655 TAS F aspartate kinase (L-aspartate 4-P-transferase) (EC 2.7.2.4) YER052C|BOR1|SIL4 gene taxon:4932 20021001 SGD
+SGD S000000854 HOM3 GO:0006555 SGD_REF:S000049419|PMID:9315655 TAS P aspartate kinase (L-aspartate 4-P-transferase) (EC 2.7.2.4) YER052C|BOR1|SIL4 gene taxon:4932 20021001 SGD
+SGD S000000854 HOM3 GO:0006566 SGD_REF:S000049419|PMID:9315655 TAS P aspartate kinase (L-aspartate 4-P-transferase) (EC 2.7.2.4) YER052C|BOR1|SIL4 gene taxon:4932 20021001 SGD
+SGD S000000854 HOM3 GO:0009090 SGD_REF:S000070200 TAS P aspartate kinase (L-aspartate 4-P-transferase) (EC 2.7.2.4) YER052C|BOR1|SIL4 gene taxon:4932 20030528 SGD
+SGD S000003900 HOM6 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C L-homoserine:NADP oxidoreductase, homoserine dehydrogenase YJR139C gene taxon:4932 20031028 SGD
+SGD S000003900 HOM6 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C L-homoserine:NADP oxidoreductase, homoserine dehydrogenase YJR139C gene taxon:4932 20031028 SGD
+SGD S000003900 HOM6 GO:0004412 SGD_REF:S000040395|PMID:8500624 ISS F L-homoserine:NADP oxidoreductase, homoserine dehydrogenase YJR139C gene taxon:4932 20030102 SGD
+SGD S000003900 HOM6 GO:0004412 SGD_REF:S000063547|PMID:11341915 IDA F L-homoserine:NADP oxidoreductase, homoserine dehydrogenase YJR139C gene taxon:4932 20030425 SGD
+SGD S000003900 HOM6 GO:0006555 SGD_REF:S000049309|PMID:1789001 TAS P L-homoserine:NADP oxidoreductase, homoserine dehydrogenase YJR139C gene taxon:4932 20021001 SGD
+SGD S000003900 HOM6 GO:0006566 SGD_REF:S000049309|PMID:1789001 TAS P L-homoserine:NADP oxidoreductase, homoserine dehydrogenase YJR139C gene taxon:4932 20021001 SGD
+SGD S000003900 HOM6 GO:0009090 SGD_REF:S000070200 TAS P L-homoserine:NADP oxidoreductase, homoserine dehydrogenase YJR139C gene taxon:4932 20030528 SGD
+SGD S000001334 HOP1 GO:0000794 SGD_REF:S000052002|PMID:2107981 IDA C DNA binding protein YIL072W gene taxon:4932 20030403 SGD
+SGD S000001334 HOP1 GO:0000795 SGD_REF:S000051328|PMID:7860625 TAS C DNA binding protein YIL072W gene taxon:4932 20021228 SGD
+SGD S000001334 HOP1 GO:0003677 SGD_REF:S000052002|PMID:2107981 IDA F DNA binding protein YIL072W gene taxon:4932 20010118 SGD
+SGD S000001334 HOP1 GO:0007126 SGD_REF:S000052002|PMID:2107981 IMP P DNA binding protein YIL072W gene taxon:4932 20010118 SGD
+SGD S000001334 HOP1 GO:0007130 SGD_REF:S000051328|PMID:7860625 IC GO:0000795 P DNA binding protein YIL072W gene taxon:4932 20021228 SGD
+SGD S000003001 HOP2 GO:0000794 SGD_REF:S000056309|PMID:9708739 IDA C meiosis-specific gene required for the pairing of similar chromosomes YGL033W gene taxon:4932 20030403 SGD
+SGD S000003001 HOP2 GO:0003690 SGD_REF:S000076683|PMID:15249670 IDA F meiosis-specific gene required for the pairing of similar chromosomes YGL033W gene taxon:4932 20041008 SGD
+SGD S000003001 HOP2 GO:0003690 SGD_REF:S000076683|PMID:15249670 IPI F meiosis-specific gene required for the pairing of similar chromosomes YGL033W gene taxon:4932 20041008 SGD
+SGD S000003001 HOP2 GO:0005515 SGD_REF:S000076683|PMID:15249670 IPI SGD:S000003151 F meiosis-specific gene required for the pairing of similar chromosomes YGL033W gene taxon:4932 20041008 SGD
+SGD S000003001 HOP2 GO:0007129 SGD_REF:S000056309|PMID:9708739 IMP P meiosis-specific gene required for the pairing of similar chromosomes YGL033W gene taxon:4932 20021001 SGD
+SGD S000000864 HOR2 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C DL-glycerol-3-phosphatase YER062C|GPP2 gene taxon:4932 20031028 SGD
+SGD S000000864 HOR2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C DL-glycerol-3-phosphatase YER062C|GPP2 gene taxon:4932 20031028 SGD
+SGD S000000864 HOR2 GO:0000121 SGD_REF:S000052527|PMID:8662716 IDA F DL-glycerol-3-phosphatase YER062C|GPP2 gene taxon:4932 20010118 SGD
+SGD S000000864 HOR2 GO:0005975 SGD_REF:S000052527|PMID:8662716 IDA P DL-glycerol-3-phosphatase YER062C|GPP2 gene taxon:4932 20010118 SGD
+SGD S000000864 HOR2 GO:0006114 SGD_REF:S000060704|PMID:11058591 IMP P DL-glycerol-3-phosphatase YER062C|GPP2 gene taxon:4932 20021115 SGD
+SGD S000000864 HOR2 GO:0006970 SGD_REF:S000052527|PMID:8662716 IDA P DL-glycerol-3-phosphatase YER062C|GPP2 gene taxon:4932 20010118 SGD
+SGD S000004864 HOR7 GO:0005624 SGD_REF:S000048835|PMID:9234669 IDA C YMR251W-A gene taxon:4932 20010118 SGD
+SGD S000004864 HOR7 GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YMR251W-A gene taxon:4932 20031028 SGD
+SGD S000004864 HOR7 GO:0005886 SGD_REF:S000077339|PMID:15208314 IDA C YMR251W-A gene taxon:4932 20041013 SGD
+SGD S000004864 HOR7 GO:0009277 SGD_REF:S000071368|PMID:11136466 TAS C YMR251W-A gene taxon:4932 20021002 SGD
+SGD S000004864 HOR7 GO:0005554 SGD_REF:S000069584 ND F YMR251W-A gene taxon:4932 20021209 SGD
+SGD S000004864 HOR7 GO:0006950 SGD_REF:S000051319|PMID:7500933 IDA P YMR251W-A gene taxon:4932 20010118 SGD
+SGD S000006272 HOS1 GO:0000118 SGD_REF:S000055604|PMID:10384304 TAS C YPR068C gene taxon:4932 20010118 SGD
+SGD S000006272 HOS1 GO:0004407 SGD_REF:S000047708|PMID:8962081 ISS F YPR068C gene taxon:4932 20010118 SGD
+SGD S000006272 HOS1 GO:0004407 SGD_REF:S000055604|PMID:10384304 ISS F YPR068C gene taxon:4932 20010118 SGD
+SGD S000006272 HOS1 GO:0004407 SGD_REF:S000059710|PMID:11095743 TAS F YPR068C gene taxon:4932 20010405 SGD
+SGD S000006272 HOS1 GO:0006325 SGD_REF:S000047708|PMID:8962081 ISS P YPR068C gene taxon:4932 20010118 SGD
+SGD S000006272 HOS1 GO:0006325 SGD_REF:S000055604|PMID:10384304 ISS P YPR068C gene taxon:4932 20010118 SGD
+SGD S000006272 HOS1 GO:0006355 SGD_REF:S000047708|PMID:8962081 ISS P YPR068C gene taxon:4932 20010118 SGD
+SGD S000006272 HOS1 GO:0006355 SGD_REF:S000055604|PMID:10384304 ISS P YPR068C gene taxon:4932 20010118 SGD
+SGD S000006272 HOS1 GO:0006476 SGD_REF:S000047708|PMID:8962081 ISS P YPR068C gene taxon:4932 20010118 SGD
+SGD S000006272 HOS1 GO:0006476 SGD_REF:S000055604|PMID:10384304 ISS P YPR068C gene taxon:4932 20010118 SGD
+SGD S000003162 HOS2 GO:0000118 SGD_REF:S000055604|PMID:10384304 TAS C YGL194C|RTL1 gene taxon:4932 20010118 SGD
+SGD S000003162 HOS2 GO:0000118 SGD_REF:S000066205|PMID:11711434 IPI C YGL194C|RTL1 gene taxon:4932 20021010 SGD
+SGD S000003162 HOS2 GO:0017136 SGD_REF:S000066205|PMID:11711434 IDA F YGL194C|RTL1 gene taxon:4932 20021010 SGD
+SGD S000003162 HOS2 GO:0017136 SGD_REF:S000066205|PMID:11711434 IPI F YGL194C|RTL1 gene taxon:4932 20021010 SGD
+SGD S000003162 HOS2 GO:0045129 SGD_REF:S000066205|PMID:11711434 IDA F YGL194C|RTL1 gene taxon:4932 20021010 SGD
+SGD S000003162 HOS2 GO:0045129 SGD_REF:S000066205|PMID:11711434 IPI F YGL194C|RTL1 gene taxon:4932 20021010 SGD
+SGD S000003162 HOS2 GO:0006325 SGD_REF:S000047708|PMID:8962081 ISS P YGL194C|RTL1 gene taxon:4932 20010118 SGD
+SGD S000003162 HOS2 GO:0006325 SGD_REF:S000055604|PMID:10384304 ISS P YGL194C|RTL1 gene taxon:4932 20010118 SGD
+SGD S000003162 HOS2 GO:0006355 SGD_REF:S000047708|PMID:8962081 ISS P YGL194C|RTL1 gene taxon:4932 20010118 SGD
+SGD S000003162 HOS2 GO:0006355 SGD_REF:S000055604|PMID:10384304 ISS P YGL194C|RTL1 gene taxon:4932 20010118 SGD
+SGD S000003162 HOS2 GO:0016575 SGD_REF:S000066205|PMID:11711434 IDA P YGL194C|RTL1 gene taxon:4932 20021010 SGD
+SGD S000003162 HOS2 GO:0016575 SGD_REF:S000066205|PMID:11711434 IPI P YGL194C|RTL1 gene taxon:4932 20021010 SGD
+SGD S000003162 HOS2 GO:0045835 SGD_REF:S000066205|PMID:11711434 IMP P YGL194C|RTL1 gene taxon:4932 20021010 SGD
+SGD S000006037 HOS3 GO:0005634 SGD_REF:S000069459|PMID:11914276 IDA C YPL116W gene taxon:4932 20020507 SGD
+SGD S000006037 HOS3 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YPL116W gene taxon:4932 20020507 SGD
+SGD S000006037 HOS3 GO:0005935 SGD_REF:S000074185|PMID:14562095 IDA C YPL116W gene taxon:4932 20031028 SGD
+SGD S000006037 HOS3 GO:0004407 SGD_REF:S000055221|PMID:10535926 IDA F YPL116W gene taxon:4932 20021218 SGD
+SGD S000006037 HOS3 GO:0016575 SGD_REF:S000055221|PMID:10535926 IDA P YPL116W gene taxon:4932 20021218 SGD
+SGD S000001374 HOS4 GO:0000118 SGD_REF:S000066205|PMID:11711434 IPI C YIL112W gene taxon:4932 20021010 SGD
+SGD S000001374 HOS4 GO:0017136 SGD_REF:S000066205|PMID:11711434 IPI F YIL112W gene taxon:4932 20021010 SGD
+SGD S000001374 HOS4 GO:0017136 SGD_REF:S000066205|PMID:11711434 IDA F YIL112W gene taxon:4932 20021010 SGD
+SGD S000001374 HOS4 GO:0045129 SGD_REF:S000066205|PMID:11711434 IPI F YIL112W gene taxon:4932 20021010 SGD
+SGD S000001374 HOS4 GO:0045129 SGD_REF:S000066205|PMID:11711434 IDA F YIL112W gene taxon:4932 20021010 SGD
+SGD S000001374 HOS4 GO:0016575 SGD_REF:S000066205|PMID:11711434 IPI P YIL112W gene taxon:4932 20021010 SGD
+SGD S000001374 HOS4 GO:0016575 SGD_REF:S000066205|PMID:11711434 IDA P YIL112W gene taxon:4932 20021010 SGD
+SGD S000001374 HOS4 GO:0045835 SGD_REF:S000066205|PMID:11711434 IPI P YIL112W gene taxon:4932 20021010 SGD
+SGD S000004783 HOT1 GO:0000228 SGD_REF:S000045247|PMID:10409737 IDA C nuclear protein YMR172W gene taxon:4932 20020730 SGD
+SGD S000004783 HOT1 GO:0003704 SGD_REF:S000056162|PMID:10722658 TAS F nuclear protein YMR172W gene taxon:4932 20021211 SGD
+SGD S000004783 HOT1 GO:0006357 SGD_REF:S000056162|PMID:10722658 TAS P nuclear protein YMR172W gene taxon:4932 20021211 SGD
+SGD S000004783 HOT1 GO:0006972 SGD_REF:S000045247|PMID:10409737 IGI P nuclear protein YMR172W gene taxon:4932 20020730 SGD
+SGD S000004783 HOT1 GO:0006972 SGD_REF:S000045247|PMID:10409737 IMP P nuclear protein YMR172W gene taxon:4932 20020730 SGD
+SGD S000001567 HOT13 GO:0005758 SGD_REF:S000077347|PMID:15294910 IDA C Assembly factor for the Translocase of the Inner Membrane complexes YKL084W gene taxon:4932 20041014 SGD
+SGD S000001567 HOT13 GO:0005554 SGD_REF:S000069584 ND F Assembly factor for the Translocase of the Inner Membrane complexes YKL084W gene taxon:4932 20021126 SGD
+SGD S000001567 HOT13 GO:0045041 SGD_REF:S000077347|PMID:15294910 IMP P Assembly factor for the Translocase of the Inner Membrane complexes YKL084W gene taxon:4932 20041014 SGD
+SGD S000001567 HOT13 GO:0045041 SGD_REF:S000077347|PMID:15294910 IPI P Assembly factor for the Translocase of the Inner Membrane complexes YKL084W gene taxon:4932 20041014 SGD
+SGD S000006397 HPA2 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C histone acetyltransferase YPR193C gene taxon:4932 20020507 SGD
+SGD S000006397 HPA2 GO:0004402 SGD_REF:S000056329|PMID:10600387 ISS F histone acetyltransferase YPR193C gene taxon:4932 20020814 SGD
+SGD S000006397 HPA2 GO:0004402 SGD_REF:S000056329|PMID:10600387 IPI F histone acetyltransferase YPR193C gene taxon:4932 20020814 SGD
+SGD S000006397 HPA2 GO:0004402 SGD_REF:S000056329|PMID:10600387 NAS F histone acetyltransferase YPR193C gene taxon:4932 20020814 SGD
+SGD S000006397 HPA2 GO:0016573 SGD_REF:S000056329|PMID:10600387 NAS P histone acetyltransferase YPR193C gene taxon:4932 20020814 SGD
+SGD S000000792 HPA3 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C D-Amino acid N-acetyltransferase YEL066W gene taxon:4932 20031028 SGD
+SGD S000000792 HPA3 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C D-Amino acid N-acetyltransferase YEL066W gene taxon:4932 20031028 SGD
+SGD S000000792 HPA3 GO:0004402 SGD_REF:S000056329|PMID:10600387 ISS F D-Amino acid N-acetyltransferase YEL066W gene taxon:4932 20020814 SGD
+SGD S000000792 HPA3 GO:0004402 SGD_REF:S000056329|PMID:10600387 NAS F D-Amino acid N-acetyltransferase YEL066W gene taxon:4932 20020814 SGD
+SGD S000000792 HPA3 GO:0016573 SGD_REF:S000056329|PMID:10600387 NAS P D-Amino acid N-acetyltransferase YEL066W gene taxon:4932 20020814 SGD
+SGD S000000419 HPC2 GO:0005634 SGD_REF:S000072261|PMID:12524332 IC GO:0003700 C highly charged basic protein YBR215W gene taxon:4932 20030120 SGD
+SGD S000000419 HPC2 GO:0030528 SGD_REF:S000072261|PMID:12524332 TAS F highly charged basic protein YBR215W gene taxon:4932 20030325 SGD
+SGD S000000419 HPC2 GO:0000083 SGD_REF:S000039430|PMID:1406694 IMP P highly charged basic protein YBR215W gene taxon:4932 20021004 SGD
+SGD S000002545 HPR1 GO:0000347 SGD_REF:S000059208|PMID:11060033 IMP C YDR138W|TRF1 gene taxon:4932 20030221 SGD
+SGD S000002545 HPR1 GO:0000347 SGD_REF:S000059208|PMID:11060033 IPI C YDR138W|TRF1 gene taxon:4932 20030221 SGD
+SGD S000002545 HPR1 GO:0016593 SGD_REF:S000041293|PMID:9891041 IPI SGD:S000000019|SGD:S000004410|SGD:S000000483 C YDR138W|TRF1 gene taxon:4932 20051108 SGD
+SGD S000002545 HPR1 GO:0003676 SGD_REF:S000070300|PMID:12093753 IDA F YDR138W|TRF1 gene taxon:4932 20021118 SGD
+SGD S000002545 HPR1 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P YDR138W|TRF1 gene taxon:4932 20060203 SGD
+SGD S000002545 HPR1 GO:0006310 SGD_REF:S000059208|PMID:11060033 IMP P YDR138W|TRF1 gene taxon:4932 20030221 SGD
+SGD S000002545 HPR1 GO:0006310 SGD_REF:S000045399|PMID:3044923 IMP P YDR138W|TRF1 gene taxon:4932 20010118 SGD
+SGD S000002545 HPR1 GO:0006368 SGD_REF:S000070300|PMID:12093753 IMP P YDR138W|TRF1 gene taxon:4932 20021118 SGD
+SGD S000002545 HPR1 GO:0006406 SGD_REF:S000072002|PMID:12417727 IGI P YDR138W|TRF1 gene taxon:4932 20030107 SGD
+SGD S000002545 HPR1 GO:0006406 SGD_REF:S000069956|PMID:11979277 IMP P YDR138W|TRF1 gene taxon:4932 20030214 SGD
+SGD S000002545 HPR1 GO:0006974 SGD_REF:S000076175|PMID:12482937 IMP P YDR138W|TRF1 gene taxon:4932 20060406 SGD
+SGD S000003628 HPR5 GO:0005634 SGD_REF:S000051638|PMID:8419328 ISS C DNA helicase YJL092W|RADH|RADH1|SRS2 gene taxon:4932 20010118 SGD
+SGD S000003628 HPR5 GO:0003678 SGD_REF:S000044473|PMID:2552405 ISS F DNA helicase YJL092W|RADH|RADH1|SRS2 gene taxon:4932 20010118 SGD
+SGD S000003628 HPR5 GO:0003678 SGD_REF:S000051638|PMID:8419328 IDA F DNA helicase YJL092W|RADH|RADH1|SRS2 gene taxon:4932 20010118 SGD
+SGD S000003628 HPR5 GO:0006281 SGD_REF:S000040682|PMID:7768432 IGI P DNA helicase YJL092W|RADH|RADH1|SRS2 gene taxon:4932 20010118 SGD
+SGD S000003628 HPR5 GO:0006303 SGD_REF:S000051563|PMID:10908335 IDA P DNA helicase YJL092W|RADH|RADH1|SRS2 gene taxon:4932 20021101 SGD
+SGD S000002807 HPT1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C hypoxanthine guanine phosphoribosyltransferase YDR399W|BRA6|HGPRTase|HPRT gene taxon:4932 20031028 SGD
+SGD S000002807 HPT1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C hypoxanthine guanine phosphoribosyltransferase YDR399W|BRA6|HGPRTase|HPRT gene taxon:4932 20031028 SGD
+SGD S000002807 HPT1 GO:0004422 SGD_REF:S000055486|PMID:9335580 IMP F hypoxanthine guanine phosphoribosyltransferase YDR399W|BRA6|HGPRTase|HPRT gene taxon:4932 20020321 SGD
+SGD S000002807 HPT1 GO:0004422 SGD_REF:S000055486|PMID:9335580 IGI F hypoxanthine guanine phosphoribosyltransferase YDR399W|BRA6|HGPRTase|HPRT gene taxon:4932 20020321 SGD
+SGD S000002807 HPT1 GO:0004422 SGD_REF:S000055486|PMID:9335580 ISS F hypoxanthine guanine phosphoribosyltransferase YDR399W|BRA6|HGPRTase|HPRT gene taxon:4932 20020321 SGD
+SGD S000002807 HPT1 GO:0006164 SGD_REF:S000055486|PMID:9335580 TAS P hypoxanthine guanine phosphoribosyltransferase YDR399W|BRA6|HGPRTase|HPRT gene taxon:4932 20020321 SGD
+SGD S000004949 HRB1 GO:0005634 SGD_REF:S000052349|PMID:9499403 IDA C hypothetical RNA-binding protein YNL004W|TOM34 gene taxon:4932 20010118 SGD
+SGD S000004949 HRB1 GO:0005737 SGD_REF:S000052349|PMID:9499403 IDA C hypothetical RNA-binding protein YNL004W|TOM34 gene taxon:4932 20010118 SGD
+SGD S000004949 HRB1 GO:0030530 SGD_REF:S000052349|PMID:9499403 ISS C hypothetical RNA-binding protein YNL004W|TOM34 gene taxon:4932 20020219 SGD
+SGD S000004949 HRB1 GO:0030530 SGD_REF:S000052349|PMID:9499403 NAS C hypothetical RNA-binding protein YNL004W|TOM34 gene taxon:4932 20020219 SGD
+SGD S000004949 HRB1 GO:0003723 SGD_REF:S000075936|PMID:76199 IDA F hypothetical RNA-binding protein YNL004W|TOM34 gene taxon:4932 20040416 SGD
+SGD S000004949 HRB1 GO:0016973 SGD_REF:S000075619|PMID:14769921 IPI P hypothetical RNA-binding protein YNL004W|TOM34 gene taxon:4932 20040416 SGD
+SGD S000005373 HRD1 GO:0005789 SGD_REF:S000060383|PMID:11139575 IDA C YOL013C|DER3 gene taxon:4932 20011121 SGD
+SGD S000005373 HRD1 GO:0005789 SGD_REF:S000044060|PMID:9437001 IDA C YOL013C|DER3 gene taxon:4932 20011121 SGD
+SGD S000005373 HRD1 GO:0004842 SGD_REF:S000060764|PMID:11146622 IMP F YOL013C|DER3 gene taxon:4932 20010705 SGD
+SGD S000005373 HRD1 GO:0004842 SGD_REF:S000060764|PMID:11146622 IDA F YOL013C|DER3 gene taxon:4932 20010705 SGD
+SGD S000005373 HRD1 GO:0004842 SGD_REF:S000060383|PMID:11139575 IDA F YOL013C|DER3 gene taxon:4932 20011114 SGD
+SGD S000005373 HRD1 GO:0004842 SGD_REF:S000060383|PMID:11139575 IPI F YOL013C|DER3 gene taxon:4932 20011114 SGD
+SGD S000005373 HRD1 GO:0004842 SGD_REF:S000060764|PMID:11146622 IPI F YOL013C|DER3 gene taxon:4932 20010705 SGD
+SGD S000005373 HRD1 GO:0030433 SGD_REF:S000060764|PMID:11146622 IMP P YOL013C|DER3 gene taxon:4932 20011212 SGD
+SGD S000005373 HRD1 GO:0030433 SGD_REF:S000060764|PMID:11146622 TAS P YOL013C|DER3 gene taxon:4932 20011212 SGD
+SGD S000005373 HRD1 GO:0030433 SGD_REF:S000060383|PMID:11139575 TAS P YOL013C|DER3 gene taxon:4932 20011212 SGD
+SGD S000005373 HRD1 GO:0030433 SGD_REF:S000060764|PMID:11146622 IPI P YOL013C|DER3 gene taxon:4932 20011212 SGD
+SGD S000004197 HRD3 GO:0005783 SGD_REF:S000061261|PMID:11516167 TAS C YLR207W gene taxon:4932 20021004 SGD
+SGD S000004197 HRD3 GO:0004842 SGD_REF:S000061453|PMID:11390656 IDA F YLR207W gene taxon:4932 20021004 SGD
+SGD S000004197 HRD3 GO:0030433 SGD_REF:S000070133|PMID:12105183 IDA P YLR207W gene taxon:4932 20020801 SGD
+SGD S000005793 HRK1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C protein kinase similar to Npr1 YOR267C gene taxon:4932 20031028 SGD
+SGD S000005793 HRK1 GO:0004672 SGD_REF:S000059090|PMID:11003661 ISS F protein kinase similar to Npr1 YOR267C gene taxon:4932 20020814 SGD
+SGD S000005793 HRK1 GO:0006873 SGD_REF:S000059090|PMID:11003661 IGI P protein kinase similar to Npr1 YOR267C gene taxon:4932 20020814 SGD
+SGD S000005793 HRK1 GO:0006873 SGD_REF:S000059090|PMID:11003661 IMP P protein kinase similar to Npr1 YOR267C gene taxon:4932 20020814 SGD
+SGD S000005483 HRP1 GO:0005634 SGD_REF:S000069459|PMID:11914276 IDA C cleavage and polyadenylation factor CF I component involved in pre-mRNA 3'-end processing YOL123W|NAB4|NAB5 gene taxon:4932 20020507 SGD
+SGD S000005483 HRP1 GO:0005634 SGD_REF:S000080288|PMID:15572678 IDA C cleavage and polyadenylation factor CF I component involved in pre-mRNA 3'-end processing YOL123W|NAB4|NAB5 gene taxon:4932 20050222 SGD
+SGD S000005483 HRP1 GO:0005634 SGD_REF:S000052680|PMID:9334319 IDA C cleavage and polyadenylation factor CF I component involved in pre-mRNA 3'-end processing YOL123W|NAB4|NAB5 gene taxon:4932 20040427 SGD
+SGD S000005483 HRP1 GO:0005737 SGD_REF:S000052680|PMID:9334319 IDA C cleavage and polyadenylation factor CF I component involved in pre-mRNA 3'-end processing YOL123W|NAB4|NAB5 gene taxon:4932 20040427 SGD
+SGD S000005483 HRP1 GO:0005849 SGD_REF:S000060315|PMID:11344258 IPI C cleavage and polyadenylation factor CF I component involved in pre-mRNA 3'-end processing YOL123W|NAB4|NAB5 gene taxon:4932 20020409 SGD
+SGD S000005483 HRP1 GO:0003723 SGD_REF:S000052680|PMID:9334319 IDA F cleavage and polyadenylation factor CF I component involved in pre-mRNA 3'-end processing YOL123W|NAB4|NAB5 gene taxon:4932 20040427 SGD
+SGD S000005483 HRP1 GO:0006378 SGD_REF:S000060315|PMID:11344258 IDA P cleavage and polyadenylation factor CF I component involved in pre-mRNA 3'-end processing YOL123W|NAB4|NAB5 gene taxon:4932 20020410 SGD
+SGD S000005483 HRP1 GO:0006378 SGD_REF:S000052680|PMID:9334319 IMP P cleavage and polyadenylation factor CF I component involved in pre-mRNA 3'-end processing YOL123W|NAB4|NAB5 gene taxon:4932 20040427 SGD
+SGD S000005483 HRP1 GO:0006379 SGD_REF:S000060315|PMID:11344258 IDA P cleavage and polyadenylation factor CF I component involved in pre-mRNA 3'-end processing YOL123W|NAB4|NAB5 gene taxon:4932 20020409 SGD
+SGD S000002699 HRQ1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C DNA helicase YDR291W gene taxon:4932 20031028 SGD
+SGD S000002699 HRQ1 GO:0004386 SGD_REF:S000039134|PMID:10077188 ISS F DNA helicase YDR291W gene taxon:4932 20011205 SGD
+SGD S000002699 HRQ1 GO:0000004 SGD_REF:S000069584 ND P DNA helicase YDR291W gene taxon:4932 20011205 SGD
+SGD S000006125 HRR25 GO:0005634 SGD_REF:S000047008|PMID:8034689 IDA C casein kinase I isoform YPL204W gene taxon:4932 20050504 SGD
+SGD S000006125 HRR25 GO:0005886 SGD_REF:S000047008|PMID:8034689 IDA C casein kinase I isoform YPL204W gene taxon:4932 20050504 SGD
+SGD S000006125 HRR25 GO:0004680 SGD_REF:S000044463|PMID:1409656 ISS F casein kinase I isoform YPL204W gene taxon:4932 20020828 SGD
+SGD S000006125 HRR25 GO:0004680 SGD_REF:S000052192|PMID:1495994 IDA F casein kinase I isoform YPL204W gene taxon:4932 20050506 SGD
+SGD S000006125 HRR25 GO:0000280 SGD_REF:S000044463|PMID:1409656 TAS P casein kinase I isoform YPL204W gene taxon:4932 20020828 SGD
+SGD S000006125 HRR25 GO:0006281 SGD_REF:S000046209|PMID:9012827 IMP P casein kinase I isoform YPL204W gene taxon:4932 20021218 SGD
+SGD S000006125 HRR25 GO:0006281 SGD_REF:S000052757|PMID:1887218 IMP P casein kinase I isoform YPL204W gene taxon:4932 20050506 SGD
+SGD S000006125 HRR25 GO:0007059 SGD_REF:S000044463|PMID:1409656 TAS P casein kinase I isoform YPL204W gene taxon:4932 20020828 SGD
+SGD S000006125 HRR25 GO:0007067 SGD_REF:S000052757|PMID:1887218 IMP P casein kinase I isoform YPL204W gene taxon:4932 20050506 SGD
+SGD S000006125 HRR25 GO:0007126 SGD_REF:S000052757|PMID:1887218 IMP P casein kinase I isoform YPL204W gene taxon:4932 20050506 SGD
+SGD S000005493 HRT1 GO:0000152 SGD_REF:S000058476|PMID:10465783 TAS C Skp1-Cullin-F-box ubiquitin protein ligase (SCF) subunit YOL133W|HRT2|RBX1|ROC1 gene taxon:4932 20010118 SGD
+SGD S000005493 HRT1 GO:0005634 SGD_REF:S000059560|PMID:11080155 IDA C Skp1-Cullin-F-box ubiquitin protein ligase (SCF) subunit YOL133W|HRT2|RBX1|ROC1 gene taxon:4932 20030619 SGD
+SGD S000005493 HRT1 GO:0005737 SGD_REF:S000059560|PMID:11080155 IDA C Skp1-Cullin-F-box ubiquitin protein ligase (SCF) subunit YOL133W|HRT2|RBX1|ROC1 gene taxon:4932 20030619 SGD
+SGD S000005493 HRT1 GO:0019005 SGD_REF:S000056381|PMID:10385629 IDA C Skp1-Cullin-F-box ubiquitin protein ligase (SCF) subunit YOL133W|HRT2|RBX1|ROC1 gene taxon:4932 20050408 SGD
+SGD S000005493 HRT1 GO:0019005 SGD_REF:S000056381|PMID:10385629 IPI C Skp1-Cullin-F-box ubiquitin protein ligase (SCF) subunit YOL133W|HRT2|RBX1|ROC1 gene taxon:4932 20050408 SGD
+SGD S000005493 HRT1 GO:0004842 SGD_REF:S000058476|PMID:10465783 TAS F Skp1-Cullin-F-box ubiquitin protein ligase (SCF) subunit YOL133W|HRT2|RBX1|ROC1 gene taxon:4932 20010118 SGD
+SGD S000005493 HRT1 GO:0004842 SGD_REF:S000044681|PMID:10230407 IDA F Skp1-Cullin-F-box ubiquitin protein ligase (SCF) subunit YOL133W|HRT2|RBX1|ROC1 gene taxon:4932 20030708 SGD
+SGD S000005493 HRT1 GO:0005515 SGD_REF:S000058476|PMID:10465783 TAS F Skp1-Cullin-F-box ubiquitin protein ligase (SCF) subunit YOL133W|HRT2|RBX1|ROC1 gene taxon:4932 20010118 SGD
+SGD S000005493 HRT1 GO:0005515 SGD_REF:S000044681|PMID:10230407 IPI SGD:S000002290|SGD:S000003235|SGD:S000004117|SGD:S000003583 F Skp1-Cullin-F-box ubiquitin protein ligase (SCF) subunit YOL133W|HRT2|RBX1|ROC1 gene taxon:4932 20030708 SGD
+SGD S000005493 HRT1 GO:0000082 SGD_REF:S000058476|PMID:10465783 TAS P Skp1-Cullin-F-box ubiquitin protein ligase (SCF) subunit YOL133W|HRT2|RBX1|ROC1 gene taxon:4932 20010118 SGD
+SGD S000005493 HRT1 GO:0000086 SGD_REF:S000058476|PMID:10465783 TAS P Skp1-Cullin-F-box ubiquitin protein ligase (SCF) subunit YOL133W|HRT2|RBX1|ROC1 gene taxon:4932 20010118 SGD
+SGD S000005493 HRT1 GO:0016567 SGD_REF:S000056381|PMID:10385629 IPI P Skp1-Cullin-F-box ubiquitin protein ligase (SCF) subunit YOL133W|HRT2|RBX1|ROC1 gene taxon:4932 20050408 SGD
+SGD S000005493 HRT1 GO:0031146 SGD_REF:S000056381|PMID:10385629 IDA P Skp1-Cullin-F-box ubiquitin protein ligase (SCF) subunit YOL133W|HRT2|RBX1|ROC1 gene taxon:4932 20050404 SGD
+SGD S000004087 HRT3 GO:0000151 SGD_REF:S000058340|PMID:9635407 ISS C YLR097C gene taxon:4932 20060321 SGD
+SGD S000004087 HRT3 GO:0005515 SGD_REF:S000058340|PMID:9635407 ISS F YLR097C gene taxon:4932 20060321 SGD
+SGD S000004087 HRT3 GO:0006511 SGD_REF:S000058340|PMID:9635407 ISS P YLR097C gene taxon:4932 20060321 SGD
+SGD S000004798 HSC82 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C chaperonin YMR186W gene taxon:4932 20031028 SGD
+SGD S000004798 HSC82 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C chaperonin YMR186W gene taxon:4932 20031210 SGD
+SGD S000004798 HSC82 GO:0042623 SGD_REF:S000043994|PMID:2674684 ISS SGD:S000006161 F chaperonin YMR186W gene taxon:4932 20060613 SGD
+SGD S000004798 HSC82 GO:0051082 SGD_REF:S000050722|PMID:9465043 IDA F chaperonin YMR186W gene taxon:4932 20060613 SGD
+SGD S000004798 HSC82 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P chaperonin YMR186W gene taxon:4932 20060221 SGD
+SGD S000004798 HSC82 GO:0006457 SGD_REF:S000040744|PMID:7791797 IMP P chaperonin YMR186W gene taxon:4932 20010118 SGD
+SGD S000004798 HSC82 GO:0006458 SGD_REF:S000043994|PMID:2674684 ISS SGD:S000006161 P chaperonin YMR186W gene taxon:4932 20060613 SGD
+SGD S000004798 HSC82 GO:0006950 SGD_REF:S000043994|PMID:2674684 IMP P chaperonin YMR186W gene taxon:4932 20010118 SGD
+SGD S000004798 HSC82 GO:0042026 SGD_REF:S000043994|PMID:2674684 ISS SGD:S000006161 P chaperonin YMR186W gene taxon:4932 20060613 SGD
+SGD S000004798 HSC82 GO:0043248 SGD_REF:S000074028|PMID:12853471 IMP P chaperonin YMR186W gene taxon:4932 20050111 SGD
+SGD S000004798 HSC82 GO:0043248 SGD_REF:S000074028|PMID:12853471 IPI P chaperonin YMR186W gene taxon:4932 20050111 SGD
+SGD S000005838 HSD1 GO:0016021 SGD_REF:S000061288|PMID:11481671 ISS C ER membrane protein YOR311C gene taxon:4932 20010905 SGD
+SGD S000005838 HSD1 GO:0030176 SGD_REF:S000061288|PMID:11481671 IDA C ER membrane protein YOR311C gene taxon:4932 20010905 SGD
+SGD S000005838 HSD1 GO:0005554 SGD_REF:S000069584 ND F ER membrane protein YOR311C gene taxon:4932 20010905 SGD
+SGD S000005838 HSD1 GO:0000004 SGD_REF:S000069584 ND P ER membrane protein YOR311C gene taxon:4932 20010905 SGD
+SGD S000000994 HSE1 GO:0005768 SGD_REF:S000070211|PMID:12055639 IDA C YHL002W gene taxon:4932 20020804 SGD
+SGD S000000994 HSE1 GO:0005515 SGD_REF:S000070211|PMID:12055639 IDA F YHL002W gene taxon:4932 20021211 SGD
+SGD S000000994 HSE1 GO:0006623 SGD_REF:S000070211|PMID:12055639 IMP P YHL002W gene taxon:4932 20021211 SGD
+SGD S000000994 HSE1 GO:0006623 SGD_REF:S000070211|PMID:12055639 IPI P YHL002W gene taxon:4932 20021211 SGD
+SGD S000003041 HSF1 GO:0005634 SGD_REF:S000039280|PMID:10888672 NAS C heat shock transcription factor YGL073W|EXA3|MAS3 gene taxon:4932 20030212 SGD
+SGD S000003041 HSF1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C heat shock transcription factor YGL073W|EXA3|MAS3 gene taxon:4932 20040928 SGD
+SGD S000003041 HSF1 GO:0003700 SGD_REF:S000043737|PMID:3044612 IDA F heat shock transcription factor YGL073W|EXA3|MAS3 gene taxon:4932 20010118 SGD
+SGD S000003041 HSF1 GO:0006357 SGD_REF:S000043737|PMID:3044612 IDA P heat shock transcription factor YGL073W|EXA3|MAS3 gene taxon:4932 20030321 SGD
+SGD S000003041 HSF1 GO:0006950 SGD_REF:S000042518|PMID:8985158 IMP P heat shock transcription factor YGL073W|EXA3|MAS3 gene taxon:4932 20010118 SGD
+SGD S000003041 HSF1 GO:0006950 SGD_REF:S000043737|PMID:3044612 IMP P heat shock transcription factor YGL073W|EXA3|MAS3 gene taxon:4932 20010118 SGD
+SGD S000003041 HSF1 GO:0006950 SGD_REF:S000045072|PMID:2017170 IMP P heat shock transcription factor YGL073W|EXA3|MAS3 gene taxon:4932 20010118 SGD
+SGD S000003041 HSF1 GO:0009408 SGD_REF:S000042518|PMID:8985158 IMP P heat shock transcription factor YGL073W|EXA3|MAS3 gene taxon:4932 20010118 SGD
+SGD S000003041 HSF1 GO:0009408 SGD_REF:S000043737|PMID:3044612 IMP P heat shock transcription factor YGL073W|EXA3|MAS3 gene taxon:4932 20010118 SGD
+SGD S000003041 HSF1 GO:0009408 SGD_REF:S000045072|PMID:2017170 IMP P heat shock transcription factor YGL073W|EXA3|MAS3 gene taxon:4932 20010118 SGD
+SGD S000003041 HSF1 GO:0030474 SGD_REF:S000070234|PMID:11935220 IMP P heat shock transcription factor YGL073W|EXA3|MAS3 gene taxon:4932 20050120 SGD
+SGD S000004901 HSH155 GO:0005686 SGD_REF:S000069986|PMID:11804584 IDA C YMR288W gene taxon:4932 20020621 SGD
+SGD S000004901 HSH155 colocalizes_with GO:0005686 SGD_REF:S000080993|PMID:15565172 IDA C YMR288W gene taxon:4932 20051006 SGD
+SGD S000004901 HSH155 GO:0003729 SGD_REF:S000073597|PMID:12773561 IDA F YMR288W gene taxon:4932 20030708 SGD
+SGD S000004901 HSH155 GO:0000245 SGD_REF:S000045918|PMID:10688664 IPI P YMR288W gene taxon:4932 20021211 SGD
+SGD S000004901 HSH155 GO:0000245 SGD_REF:S000045918|PMID:10688664 ISS P YMR288W gene taxon:4932 20021211 SGD
+SGD S000005846 HSH49 GO:0005686 SGD_REF:S000069986|PMID:11804584 IDA C mammalian splicing factor/U2 snRNP protein homolog YOR319W gene taxon:4932 20020621 SGD
+SGD S000005846 HSH49 colocalizes_with GO:0005686 SGD_REF:S000080993|PMID:15565172 IDA C mammalian splicing factor/U2 snRNP protein homolog YOR319W gene taxon:4932 20051006 SGD
+SGD S000005846 HSH49 GO:0003723 SGD_REF:S000047550|PMID:9436903 IDA F mammalian splicing factor/U2 snRNP protein homolog YOR319W gene taxon:4932 20021105 SGD
+SGD S000005846 HSH49 GO:0000398 SGD_REF:S000047550|PMID:9436903 IMP P mammalian splicing factor/U2 snRNP protein homolog YOR319W gene taxon:4932 20021105 SGD
+SGD S000005846 HSH49 GO:0000398 SGD_REF:S000047550|PMID:9436903 IPI P mammalian splicing factor/U2 snRNP protein homolog YOR319W gene taxon:4932 20021105 SGD
+SGD S000028421 HSK3 GO:0000776 SGD_REF:S000081123|PMID:15632076 IPI C YKL138C-A gene taxon:4932 20050328 SGD
+SGD S000028421 HSK3 GO:0005819 SGD_REF:S000081123|PMID:15632076 IDA C YKL138C-A gene taxon:4932 20050328 SGD
+SGD S000028421 HSK3 GO:0042729 SGD_REF:S000080667|PMID:15664196 IDA C YKL138C-A gene taxon:4932 20050328 SGD
+SGD S000028421 HSK3 GO:0042729 SGD_REF:S000080667|PMID:15664196 IPI C YKL138C-A gene taxon:4932 20050328 SGD
+SGD S000028421 HSK3 GO:0042729 SGD_REF:S000080444|PMID:15640796 IPI C YKL138C-A gene taxon:4932 20050328 SGD
+SGD S000028421 HSK3 GO:0042729 SGD_REF:S000081123|PMID:15632076 IPI C YKL138C-A gene taxon:4932 20050328 SGD
+SGD S000028421 HSK3 GO:0042729 SGD_REF:S000080444|PMID:15640796 IDA C YKL138C-A gene taxon:4932 20050328 SGD
+SGD S000028421 HSK3 GO:0005515 SGD_REF:S000080667|PMID:15664196 IDA F YKL138C-A gene taxon:4932 20050328 SGD
+SGD S000028421 HSK3 GO:0030472 SGD_REF:S000081123|PMID:15632076 IMP P YKL138C-A gene taxon:4932 20050328 SGD
+SGD S000028421 HSK3 GO:0031110 SGD_REF:S000080667|PMID:15664196 IPI P YKL138C-A gene taxon:4932 20050328 SGD
+SGD S000028421 HSK3 GO:0031110 SGD_REF:S000080667|PMID:15664196 IDA P YKL138C-A gene taxon:4932 20050328 SGD
+SGD S000001584 HSL1 GO:0005935 SGD_REF:S000043338|PMID:10805747 IDA C serine-threonine kinase YKL101W|NIK1 gene taxon:4932 20020618 SGD
+SGD S000001584 HSL1 GO:0005935 SGD_REF:S000077144|PMID:15282802 IDA C serine-threonine kinase YKL101W|NIK1 gene taxon:4932 20041008 SGD
+SGD S000001584 HSL1 GO:0005940 SGD_REF:S000051063|PMID:9925642 IDA C serine-threonine kinase YKL101W|NIK1 gene taxon:4932 20010118 SGD
+SGD S000001584 HSL1 GO:0005940 SGD_REF:S000051063|PMID:9925642 IPI C serine-threonine kinase YKL101W|NIK1 gene taxon:4932 20010118 SGD
+SGD S000001584 HSL1 GO:0004672 SGD_REF:S000051063|PMID:9925642 IDA F serine-threonine kinase YKL101W|NIK1 gene taxon:4932 20010118 SGD
+SGD S000001584 HSL1 GO:0000074 SGD_REF:S000052589|PMID:8647431 IMP P serine-threonine kinase YKL101W|NIK1 gene taxon:4932 20020618 SGD
+SGD S000001584 HSL1 GO:0000078 SGD_REF:S000042717|PMID:10679396 TAS P serine-threonine kinase YKL101W|NIK1 gene taxon:4932 20020618 SGD
+SGD S000001584 HSL1 GO:0000086 SGD_REF:S000042191|PMID:10490630 IGI P serine-threonine kinase YKL101W|NIK1 gene taxon:4932 20020618 SGD
+SGD S000001584 HSL1 GO:0000086 SGD_REF:S000042191|PMID:10490630 IMP P serine-threonine kinase YKL101W|NIK1 gene taxon:4932 20020618 SGD
+SGD S000001584 HSL1 GO:0000135 SGD_REF:S000051063|PMID:9925642 IGI P serine-threonine kinase YKL101W|NIK1 gene taxon:4932 20010118 SGD
+SGD S000001584 HSL1 GO:0000135 SGD_REF:S000051063|PMID:9925642 IMP P serine-threonine kinase YKL101W|NIK1 gene taxon:4932 20010118 SGD
+SGD S000001584 HSL1 GO:0006468 SGD_REF:S000051063|PMID:9925642 IDA P serine-threonine kinase YKL101W|NIK1 gene taxon:4932 20010118 SGD
+SGD S000000337 HSL7 GO:0005935 SGD_REF:S000043338|PMID:10805747 IDA C Has homology to arginine methyltransferases YBR133C gene taxon:4932 20020618 SGD
+SGD S000000337 HSL7 GO:0005935 SGD_REF:S000042219|PMID:10490648 IDA C Has homology to arginine methyltransferases YBR133C gene taxon:4932 20020618 SGD
+SGD S000000337 HSL7 GO:0016274 SGD_REF:S000046525|PMID:10903903 IDA F Has homology to arginine methyltransferases YBR133C gene taxon:4932 20020618 SGD
+SGD S000000337 HSL7 GO:0016274 SGD_REF:S000046525|PMID:10903903 ISS F Has homology to arginine methyltransferases YBR133C gene taxon:4932 20020618 SGD
+SGD S000000337 HSL7 GO:0016274 SGD_REF:S000046525|PMID:10903903 IGI F Has homology to arginine methyltransferases YBR133C gene taxon:4932 20020618 SGD
+SGD S000000337 HSL7 GO:0016274 SGD_REF:S000046525|PMID:10903903 IPI F Has homology to arginine methyltransferases YBR133C gene taxon:4932 20020618 SGD
+SGD S000000337 HSL7 GO:0016274 SGD_REF:S000046525|PMID:10903903 IMP F Has homology to arginine methyltransferases YBR133C gene taxon:4932 20020618 SGD
+SGD S000000337 HSL7 GO:0000074 SGD_REF:S000052589|PMID:8647431 IMP P Has homology to arginine methyltransferases YBR133C gene taxon:4932 20020618 SGD
+SGD S000000337 HSL7 GO:0000086 SGD_REF:S000042191|PMID:10490630 IGI P Has homology to arginine methyltransferases YBR133C gene taxon:4932 20020618 SGD
+SGD S000000337 HSL7 GO:0000086 SGD_REF:S000042191|PMID:10490630 IMP P Has homology to arginine methyltransferases YBR133C gene taxon:4932 20020618 SGD
+SGD S000000476 HSM3 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YBR272C gene taxon:4932 20031028 SGD
+SGD S000000476 HSM3 GO:0005554 SGD_REF:S000069584 ND F YBR272C gene taxon:4932 20021115 SGD
+SGD S000000476 HSM3 GO:0006298 SGD_REF:S000048731|PMID:10681183 IMP P YBR272C gene taxon:4932 20021115 SGD
+SGD S000005546 HSP10 GO:0005759 SGD_REF:S000039320|PMID:7903252 IDA C heat shock protein 10 YOR020C|CPN10 gene taxon:4932 20010118 SGD
+SGD S000005546 HSP10 GO:0051082 SGD_REF:S000039213|PMID:7902576 IDA F heat shock protein 10 YOR020C|CPN10 gene taxon:4932 20010118 SGD
+SGD S000005546 HSP10 GO:0006457 SGD_REF:S000039213|PMID:7902576 IDA P heat shock protein 10 YOR020C|CPN10 gene taxon:4932 20010118 SGD
+SGD S000003949 HSP104 GO:0005634 SGD_REF:S000041055|PMID:10467108 IDA C heat shock protein 104 YLL026W gene taxon:4932 20030325 SGD
+SGD S000003949 HSP104 GO:0005737 SGD_REF:S000041055|PMID:10467108 IDA C heat shock protein 104 YLL026W gene taxon:4932 20030325 SGD
+SGD S000003949 HSP104 GO:0042623 SGD_REF:S000060128|PMID:11158570 IDA F heat shock protein 104 YLL026W gene taxon:4932 20030325 SGD
+SGD S000003949 HSP104 GO:0051087 SGD_REF:S000048256|PMID:9674429 IDA F heat shock protein 104 YLL026W gene taxon:4932 20040721 SGD
+SGD S000003949 HSP104 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P heat shock protein 104 YLL026W gene taxon:4932 20060221 SGD
+SGD S000003949 HSP104 GO:0006950 SGD_REF:S000048256|PMID:9674429 IDA P heat shock protein 104 YLL026W gene taxon:4932 20010118 SGD
+SGD S000003949 HSP104 GO:0051085 SGD_REF:S000048256|PMID:9674429 IDA P heat shock protein 104 YLL026W gene taxon:4932 20040721 SGD
+SGD S000001880 HSP12 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C heat shock protein 12 YFL014W|GLP1|HOR5 gene taxon:4932 20031028 SGD
+SGD S000001880 HSP12 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C heat shock protein 12 YFL014W|GLP1|HOR5 gene taxon:4932 20031028 SGD
+SGD S000001880 HSP12 GO:0005886 SGD_REF:S000076245|PMID:10675505 IDA C heat shock protein 12 YFL014W|GLP1|HOR5 gene taxon:4932 20040702 SGD
+SGD S000001880 HSP12 GO:0005554 SGD_REF:S000069584 ND F heat shock protein 12 YFL014W|GLP1|HOR5 gene taxon:4932 20040715 SGD
+SGD S000001880 HSP12 GO:0006972 SGD_REF:S000043864|PMID:7565776 TAS P heat shock protein 12 YFL014W|GLP1|HOR5 gene taxon:4932 20010118 SGD
+SGD S000001880 HSP12 GO:0006979 SGD_REF:S000043864|PMID:7565776 TAS P heat shock protein 12 YFL014W|GLP1|HOR5 gene taxon:4932 20010118 SGD
+SGD S000001880 HSP12 GO:0007155 SGD_REF:S000069457|PMID:11816034 IDA P heat shock protein 12 YFL014W|GLP1|HOR5 gene taxon:4932 20020403 SGD
+SGD S000001880 HSP12 GO:0009269 SGD_REF:S000063137|PMID:10681550 IEP P heat shock protein 12 YFL014W|GLP1|HOR5 gene taxon:4932 20030210 SGD
+SGD S000001880 HSP12 GO:0009269 SGD_REF:S000076245|PMID:10675505 IDA P heat shock protein 12 YFL014W|GLP1|HOR5 gene taxon:4932 20040702 SGD
+SGD S000001880 HSP12 GO:0009408 SGD_REF:S000043864|PMID:7565776 TAS P heat shock protein 12 YFL014W|GLP1|HOR5 gene taxon:4932 20010118 SGD
+SGD S000003695 HSP150 GO:0009277 SGD_REF:S000051733|PMID:10209754 IDA C heat shock protein, secretory glycoprotein YJL159W|CCW7|ORE1|PIR2 gene taxon:4932 20010118 SGD
+SGD S000003695 HSP150 GO:0009277 SGD_REF:S000058137|PMID:9192695 IDA C heat shock protein, secretory glycoprotein YJL159W|CCW7|ORE1|PIR2 gene taxon:4932 20050317 SGD
+SGD S000003695 HSP150 GO:0009277 SGD_REF:S000081097|PMID:15781460 IDA C heat shock protein, secretory glycoprotein YJL159W|CCW7|ORE1|PIR2 gene taxon:4932 20050601 SGD
+SGD S000003695 HSP150 GO:0005199 SGD_REF:S000051733|PMID:10209754 IPI F heat shock protein, secretory glycoprotein YJL159W|CCW7|ORE1|PIR2 gene taxon:4932 20010118 SGD
+SGD S000003695 HSP150 GO:0007047 SGD_REF:S000039809|PMID:10407261 IMP P heat shock protein, secretory glycoprotein YJL159W|CCW7|ORE1|PIR2 gene taxon:4932 20010118 SGD
+SGD S000000276 HSP26 GO:0005634 SGD_REF:S000050750|PMID:2645298 IDA C heat shock protein 26 YBR072W gene taxon:4932 20010118 SGD
+SGD S000000276 HSP26 GO:0005737 SGD_REF:S000050750|PMID:2645298 IDA C heat shock protein 26 YBR072W gene taxon:4932 20010118 SGD
+SGD S000000276 HSP26 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C heat shock protein 26 YBR072W gene taxon:4932 20020507 SGD
+SGD S000000276 HSP26 GO:0051082 SGD_REF:S000043785|PMID:10581247 IDA F heat shock protein 26 YBR072W gene taxon:4932 20030327 SGD
+SGD S000000276 HSP26 GO:0006457 SGD_REF:S000043785|PMID:10581247 IDA P heat shock protein 26 YBR072W gene taxon:4932 20010118 SGD
+SGD S000000276 HSP26 GO:0006950 SGD_REF:S000043785|PMID:10581247 IDA P heat shock protein 26 YBR072W gene taxon:4932 20010118 SGD
+SGD S000000615 HSP30 GO:0005886 SGD_REF:S000045972|PMID:8319300 ISS C YCR021C|YRO1 gene taxon:4932 20010118 SGD
+SGD S000000615 HSP30 GO:0005886 SGD_REF:S000049795|PMID:1535043 IDA C YCR021C|YRO1 gene taxon:4932 20010118 SGD
+SGD S000000615 HSP30 GO:0005554 SGD_REF:S000069584 ND F YCR021C|YRO1 gene taxon:4932 20040716 SGD
+SGD S000000615 HSP30 GO:0006950 SGD_REF:S000046556|PMID:10206703 IDA P YCR021C|YRO1 gene taxon:4932 20010118 SGD
+SGD S000002941 HSP31 GO:0005625 SGD_REF:S000068747|PMID:11746603 IDA C YDR533C gene taxon:4932 20030130 SGD
+SGD S000002941 HSP31 GO:0008234 SGD_REF:S000074850|PMID:14745011 ISS F YDR533C gene taxon:4932 20040215 SGD
+SGD S000002941 HSP31 GO:0051082 SGD_REF:S000074850|PMID:14745011 ISS F YDR533C gene taxon:4932 20040215 SGD
+SGD S000002941 HSP31 GO:0000004 SGD_REF:S000069584 ND P YDR533C gene taxon:4932 20030130 SGD
+SGD S000006201 HSP32 GO:0008372 SGD_REF:S000069584 ND C YPL280W gene taxon:4932 20021126 SGD
+SGD S000006201 HSP32 GO:0008234 SGD_REF:S000074850|PMID:14745011 ISS F YPL280W gene taxon:4932 20040215 SGD
+SGD S000006201 HSP32 GO:0051082 SGD_REF:S000074850|PMID:14745011 ISS F YPL280W gene taxon:4932 20040215 SGD
+SGD S000006201 HSP32 GO:0000004 SGD_REF:S000069584 ND P YPL280W gene taxon:4932 20021126 SGD
+SGD S000005918 HSP33 GO:0008372 SGD_REF:S000069584 ND C YOR391C gene taxon:4932 20021126 SGD
+SGD S000005918 HSP33 GO:0008234 SGD_REF:S000074850|PMID:14745011 ISS F YOR391C gene taxon:4932 20040215 SGD
+SGD S000005918 HSP33 GO:0051082 SGD_REF:S000074850|PMID:14745011 ISS F YOR391C gene taxon:4932 20040215 SGD
+SGD S000005918 HSP33 GO:0000004 SGD_REF:S000069584 ND P YOR391C gene taxon:4932 20021126 SGD
+SGD S000002578 HSP42 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YDR171W gene taxon:4932 20020507 SGD
+SGD S000002578 HSP42 GO:0005832 SGD_REF:S000080727|PMID:15704212 IPI SGD:S000002596 C YDR171W gene taxon:4932 20050307 SGD
+SGD S000002578 HSP42 GO:0005856 SGD_REF:S000054192|PMID:8576246 IPI C YDR171W gene taxon:4932 20010118 SGD
+SGD S000002578 HSP42 GO:0051082 SGD_REF:S000052667|PMID:9199338 TAS F YDR171W gene taxon:4932 20010118 SGD
+SGD S000002578 HSP42 GO:0006950 SGD_REF:S000054192|PMID:8576246 IEP P YDR171W gene taxon:4932 20010118 SGD
+SGD S000002578 HSP42 GO:0007010 SGD_REF:S000052667|PMID:9199338 IGI P YDR171W gene taxon:4932 20010118 SGD
+SGD S000002578 HSP42 GO:0007010 SGD_REF:S000052667|PMID:9199338 IMP P YDR171W gene taxon:4932 20010118 SGD
+SGD S000004249 HSP60 GO:0005739 SGD_REF:S000052405|PMID:8097278 IDA C chaperonin, groEL homolog YLR259C|CPN60|MIF4 gene taxon:4932 20010118 SGD
+SGD S000004249 HSP60 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C chaperonin, groEL homolog YLR259C|CPN60|MIF4 gene taxon:4932 20040924 SGD
+SGD S000004249 HSP60 GO:0042645 SGD_REF:S000050870|PMID:10869431 IDA C chaperonin, groEL homolog YLR259C|CPN60|MIF4 gene taxon:4932 20050401 SGD
+SGD S000004249 HSP60 GO:0003697 SGD_REF:S000050870|PMID:10869431 IDA F chaperonin, groEL homolog YLR259C|CPN60|MIF4 gene taxon:4932 20040716 SGD
+SGD S000004249 HSP60 GO:0006457 SGD_REF:S000049549|PMID:8336673 TAS P chaperonin, groEL homolog YLR259C|CPN60|MIF4 gene taxon:4932 20010118 SGD
+SGD S000004249 HSP60 GO:0030150 SGD_REF:S000049549|PMID:8336673 TAS P chaperonin, groEL homolog YLR259C|CPN60|MIF4 gene taxon:4932 20031119 SGD
+SGD S000002666 HSP78 GO:0005759 SGD_REF:S000040952|PMID:8413229 IDA C heat shock protein 78 YDR258C gene taxon:4932 20010118 SGD
+SGD S000002666 HSP78 GO:0016887 SGD_REF:S000040952|PMID:8413229 ISS F heat shock protein 78 YDR258C gene taxon:4932 20040721 SGD
+SGD S000002666 HSP78 GO:0051082 SGD_REF:S000070276|PMID:12023279 IDA F heat shock protein 78 YDR258C gene taxon:4932 20021205 SGD
+SGD S000002666 HSP78 GO:0000002 SGD_REF:S000070276|PMID:12023279 IDA P heat shock protein 78 YDR258C gene taxon:4932 20021205 SGD
+SGD S000002666 HSP78 GO:0006457 SGD_REF:S000050221|PMID:8830768 IDA P heat shock protein 78 YDR258C gene taxon:4932 20010118 SGD
+SGD S000002666 HSP78 GO:0006950 SGD_REF:S000050221|PMID:8830768 IDA P heat shock protein 78 YDR258C gene taxon:4932 20010118 SGD
+SGD S000002666 HSP78 GO:0030150 SGD_REF:S000047871|PMID:7500331 IDA P heat shock protein 78 YDR258C gene taxon:4932 20031119 SGD
+SGD S000006161 HSP82 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C heat shock protein 90, mammalian Hsp90 homolog YPL240C|HSP83|HSP90 gene taxon:4932 20020507 SGD
+SGD S000006161 HSP82 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C heat shock protein 90, mammalian Hsp90 homolog YPL240C|HSP83|HSP90 gene taxon:4932 20031028 SGD
+SGD S000006161 HSP82 GO:0042623 SGD_REF:S000072038|PMID:12235160 IDA F heat shock protein 90, mammalian Hsp90 homolog YPL240C|HSP83|HSP90 gene taxon:4932 20030318 SGD
+SGD S000006161 HSP82 GO:0051082 SGD_REF:S000043873|PMID:10564510 IDA F heat shock protein 90, mammalian Hsp90 homolog YPL240C|HSP83|HSP90 gene taxon:4932 20060613 SGD
+SGD S000006161 HSP82 GO:0006458 SGD_REF:S000045779|PMID:9371781 IMP P heat shock protein 90, mammalian Hsp90 homolog YPL240C|HSP83|HSP90 gene taxon:4932 20060613 SGD
+SGD S000006161 HSP82 GO:0006458 SGD_REF:S000043873|PMID:10564510 IDA P heat shock protein 90, mammalian Hsp90 homolog YPL240C|HSP83|HSP90 gene taxon:4932 20060613 SGD
+SGD S000006161 HSP82 GO:0006950 SGD_REF:S000043994|PMID:2674684 IMP P heat shock protein 90, mammalian Hsp90 homolog YPL240C|HSP83|HSP90 gene taxon:4932 20010118 SGD
+SGD S000006161 HSP82 GO:0006970 SGD_REF:S000114463|PMID:16487343 IMP P heat shock protein 90, mammalian Hsp90 homolog YPL240C|HSP83|HSP90 gene taxon:4932 20060512 SGD
+SGD S000006161 HSP82 GO:0042026 SGD_REF:S000045779|PMID:9371781 IMP P heat shock protein 90, mammalian Hsp90 homolog YPL240C|HSP83|HSP90 gene taxon:4932 20060613 SGD
+SGD S000006161 HSP82 GO:0043248 SGD_REF:S000074028|PMID:12853471 IGI P heat shock protein 90, mammalian Hsp90 homolog YPL240C|HSP83|HSP90 gene taxon:4932 20050111 SGD
+SGD S000006161 HSP82 GO:0043248 SGD_REF:S000074028|PMID:12853471 IDA P heat shock protein 90, mammalian Hsp90 homolog YPL240C|HSP83|HSP90 gene taxon:4932 20050111 SGD
+SGD S000006161 HSP82 GO:0043248 SGD_REF:S000074028|PMID:12853471 IMP P heat shock protein 90, mammalian Hsp90 homolog YPL240C|HSP83|HSP90 gene taxon:4932 20050111 SGD
+SGD S000005429 HST1 GO:0000118 SGD_REF:S000066205|PMID:11711434 IDA C YOL068C gene taxon:4932 20020814 SGD
+SGD S000005429 HST1 GO:0000118 SGD_REF:S000066205|PMID:11711434 IPI C YOL068C gene taxon:4932 20020814 SGD
+SGD S000005429 HST1 GO:0005634 SGD_REF:S000060139|PMID:11226170 TAS C YOL068C gene taxon:4932 20030107 SGD
+SGD S000005429 HST1 GO:0017136 SGD_REF:S000066205|PMID:11711434 IDA F YOL068C gene taxon:4932 20021203 SGD
+SGD S000005429 HST1 GO:0045129 SGD_REF:S000066205|PMID:11711434 IDA F YOL068C gene taxon:4932 20020814 SGD
+SGD S000005429 HST1 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P YOL068C gene taxon:4932 20060203 SGD
+SGD S000005429 HST1 GO:0006342 SGD_REF:S000060275|PMID:11313477 IMP P YOL068C gene taxon:4932 20020814 SGD
+SGD S000005429 HST1 GO:0006342 SGD_REF:S000060275|PMID:11313477 IGI P YOL068C gene taxon:4932 20020814 SGD
+SGD S000005936 HST2 GO:0005737 SGD_REF:S000060139|PMID:11226170 IDA C YPL015C gene taxon:4932 20021009 SGD
+SGD S000005936 HST2 GO:0017136 SGD_REF:S000048730|PMID:10841563 IDA F YPL015C gene taxon:4932 20021009 SGD
+SGD S000005936 HST2 GO:0006348 SGD_REF:S000060139|PMID:11226170 IGI P YPL015C gene taxon:4932 20021009 SGD
+SGD S000005936 HST2 GO:0006348 SGD_REF:S000060139|PMID:11226170 IMP P YPL015C gene taxon:4932 20021009 SGD
+SGD S000005551 HST3 GO:0005634 SGD_REF:S000071400|PMID:12242223 IC GO:0006348 C YOR025W gene taxon:4932 20030107 SGD
+SGD S000005551 HST3 GO:0003677 SGD_REF:S000053443|PMID:7498786 ISS F YOR025W gene taxon:4932 20021001 SGD
+SGD S000005551 HST3 GO:0006348 SGD_REF:S000053443|PMID:7498786 IGI P YOR025W gene taxon:4932 20021001 SGD
+SGD S000005551 HST3 GO:0046459 SGD_REF:S000072730|PMID:12618394 IMP P YOR025W gene taxon:4932 20030311 SGD
+SGD S000002599 HST4 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YDR191W gene taxon:4932 20031028 SGD
+SGD S000002599 HST4 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDR191W gene taxon:4932 20031028 SGD
+SGD S000002599 HST4 GO:0003677 SGD_REF:S000053443|PMID:7498786 ISS F YDR191W gene taxon:4932 20021001 SGD
+SGD S000002599 HST4 GO:0006348 SGD_REF:S000053443|PMID:7498786 IGI P YDR191W gene taxon:4932 20021001 SGD
+SGD S000002599 HST4 GO:0046459 SGD_REF:S000072730|PMID:12618394 IMP P YDR191W gene taxon:4932 20030311 SGD
+SGD S000003455 HSV2 GO:0000324 SGD_REF:S000080872|PMID:15155809 IDA C YGR223C gene taxon:4932 20050228 SGD
+SGD S000003455 HSV2 GO:0005737 SGD_REF:S000076078|PMID:15103325 IDA C YGR223C gene taxon:4932 20040511 SGD
+SGD S000003455 HSV2 GO:0035091 SGD_REF:S000076078|PMID:15103325 IDA F YGR223C gene taxon:4932 20040511 SGD
+SGD S000003455 HSV2 GO:0000004 SGD_REF:S000069584 ND P YGR223C gene taxon:4932 20021223 SGD
+SGD S000006707 HSX1 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tRNA-Arg tR(CCU)J gene taxon:4932 20030507 SGD
+SGD S000006707 HSX1 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tRNA-Arg tR(CCU)J gene taxon:4932 20030507 SGD
+SGD S000006707 HSX1 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tRNA-Arg tR(CCU)J gene taxon:4932 20030507 SGD
+SGD S000002633 HTA1 GO:0000788 SGD_REF:S000060984|PMID:2275823 TAS C histone H2A (HTA1 and HTA2 code for nearly identical proteins) YDR225W|H2A1|SPT11 gene taxon:4932 20010726 SGD
+SGD S000002633 HTA1 GO:0003677 SGD_REF:S000060984|PMID:2275823 TAS F histone H2A (HTA1 and HTA2 code for nearly identical proteins) YDR225W|H2A1|SPT11 gene taxon:4932 20020204 SGD
+SGD S000002633 HTA1 GO:0006281 SGD_REF:S000081111|PMID:15781691 IMP P histone H2A (HTA1 and HTA2 code for nearly identical proteins) YDR225W|H2A1|SPT11 gene taxon:4932 20050620 SGD
+SGD S000002633 HTA1 GO:0006333 SGD_REF:S000060984|PMID:2275823 TAS P histone H2A (HTA1 and HTA2 code for nearly identical proteins) YDR225W|H2A1|SPT11 gene taxon:4932 20020204 SGD
+SGD S000000099 HTA2 GO:0000788 SGD_REF:S000060984|PMID:2275823 TAS C histone H2A (HTA1 and HTA2 code for nearly identical proteins) YBL003C|H2A2 gene taxon:4932 20010726 SGD
+SGD S000000099 HTA2 GO:0003677 SGD_REF:S000060984|PMID:2275823 TAS F histone H2A (HTA1 and HTA2 code for nearly identical proteins) YBL003C|H2A2 gene taxon:4932 20020204 SGD
+SGD S000000099 HTA2 GO:0006281 SGD_REF:S000081111|PMID:15781691 IMP P histone H2A (HTA1 and HTA2 code for nearly identical proteins) YBL003C|H2A2 gene taxon:4932 20050620 SGD
+SGD S000000099 HTA2 GO:0006333 SGD_REF:S000060984|PMID:2275823 TAS P histone H2A (HTA1 and HTA2 code for nearly identical proteins) YBL003C|H2A2 gene taxon:4932 20020204 SGD
+SGD S000002632 HTB1 GO:0000788 SGD_REF:S000058171|PMID:9256430 IDA C histone H2B (HTB1 and HTB2 code for nearly identical proteins) YDR224C|SPT12 gene taxon:4932 20010118 SGD
+SGD S000002632 HTB1 GO:0000788 SGD_REF:S000060984|PMID:2275823 TAS C histone H2B (HTB1 and HTB2 code for nearly identical proteins) YDR224C|SPT12 gene taxon:4932 20010726 SGD
+SGD S000002632 HTB1 GO:0003677 SGD_REF:S000057567|PMID:8017102 IDA F histone H2B (HTB1 and HTB2 code for nearly identical proteins) YDR224C|SPT12 gene taxon:4932 20010118 SGD
+SGD S000002632 HTB1 GO:0003677 SGD_REF:S000060984|PMID:2275823 TAS F histone H2B (HTB1 and HTB2 code for nearly identical proteins) YDR224C|SPT12 gene taxon:4932 20020204 SGD
+SGD S000002632 HTB1 GO:0006301 SGD_REF:S000069711|PMID:11973294 IGI P histone H2B (HTB1 and HTB2 code for nearly identical proteins) YDR224C|SPT12 gene taxon:4932 20050328 SGD
+SGD S000002632 HTB1 GO:0006333 SGD_REF:S000057567|PMID:8017102 IDA P histone H2B (HTB1 and HTB2 code for nearly identical proteins) YDR224C|SPT12 gene taxon:4932 20010118 SGD
+SGD S000002632 HTB1 GO:0006333 SGD_REF:S000060984|PMID:2275823 TAS P histone H2B (HTB1 and HTB2 code for nearly identical proteins) YDR224C|SPT12 gene taxon:4932 20020204 SGD
+SGD S000002632 HTB1 GO:0006333 SGD_REF:S000058171|PMID:9256430 IDA P histone H2B (HTB1 and HTB2 code for nearly identical proteins) YDR224C|SPT12 gene taxon:4932 20010118 SGD
+SGD S000000098 HTB2 GO:0000788 SGD_REF:S000060984|PMID:2275823 TAS C histone H2B (HTB1 and HTB2 code for nearly identical proteins) YBL002W gene taxon:4932 20010726 SGD
+SGD S000000098 HTB2 GO:0003677 SGD_REF:S000060984|PMID:2275823 TAS F histone H2B (HTB1 and HTB2 code for nearly identical proteins) YBL002W gene taxon:4932 20020204 SGD
+SGD S000000098 HTB2 GO:0006333 SGD_REF:S000060984|PMID:2275823 TAS P histone H2B (HTB1 and HTB2 code for nearly identical proteins) YBL002W gene taxon:4932 20020204 SGD
+SGD S000001109 HTD2 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YHR067W|RMD12 gene taxon:4932 20031028 SGD
+SGD S000001109 HTD2 GO:0005739 SGD_REF:S000077170|PMID:15387819 IDA C YHR067W|RMD12 gene taxon:4932 20040927 SGD
+SGD S000001109 HTD2 GO:0019171 SGD_REF:S000077170|PMID:15387819 IDA F YHR067W|RMD12 gene taxon:4932 20040927 SGD
+SGD S000001109 HTD2 GO:0006633 SGD_REF:S000077170|PMID:15387819 IGI P YHR067W|RMD12 gene taxon:4932 20040927 SGD
+SGD S000001109 HTD2 GO:0006633 SGD_REF:S000077170|PMID:15387819 ISS P YHR067W|RMD12 gene taxon:4932 20040927 SGD
+SGD S000006439 HTL1 GO:0016586 SGD_REF:S000071998|PMID:12417720 IDA C YCR020W-B gene taxon:4932 20030108 SGD
+SGD S000006439 HTL1 contributes_to GO:0003682 SGD_REF:S000071998|PMID:12417720 IC GO:0016586 F YCR020W-B gene taxon:4932 20060130 SGD
+SGD S000006439 HTL1 GO:0000074 SGD_REF:S000071998|PMID:12417720 IGI P YCR020W-B gene taxon:4932 20030108 SGD
+SGD S000006439 HTL1 GO:0000074 SGD_REF:S000071998|PMID:12417720 IPI P YCR020W-B gene taxon:4932 20030108 SGD
+SGD S000006439 HTL1 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P YCR020W-B gene taxon:4932 20060203 SGD
+SGD S000006439 HTL1 GO:0006338 SGD_REF:S000071998|PMID:12417720 IC GO:0016586 P YCR020W-B gene taxon:4932 20060130 SGD
+SGD S000006439 HTL1 GO:0006974 SGD_REF:S000076175|PMID:12482937 IMP P YCR020W-B gene taxon:4932 20060406 SGD
+SGD S000006237 HTS1 GO:0005737 SGD_REF:S000043557|PMID:3521891 IMP C histidine-tRNA ligase YPR033C|TSM4572 gene taxon:4932 20021001 SGD
+SGD S000006237 HTS1 GO:0005739 SGD_REF:S000043557|PMID:3521891 IMP C histidine-tRNA ligase YPR033C|TSM4572 gene taxon:4932 20021001 SGD
+SGD S000006237 HTS1 GO:0004821 SGD_REF:S000042552|PMID:1459448 TAS F histidine-tRNA ligase YPR033C|TSM4572 gene taxon:4932 20021001 SGD
+SGD S000006237 HTS1 GO:0006427 SGD_REF:S000042552|PMID:1459448 IMP P histidine-tRNA ligase YPR033C|TSM4572 gene taxon:4932 20021001 SGD
+SGD S000006237 HTS1 GO:0006427 SGD_REF:S000042552|PMID:1459448 TAS P histidine-tRNA ligase YPR033C|TSM4572 gene taxon:4932 20021001 SGD
+SGD S000005372 HTZ1 GO:0000790 SGD_REF:S000056456|PMID:11090616 IPI C evolutionarily conserved member of the histone H2A F/Z family of histone variants YOL012C|H2A.F/Z|H2AZ|HTA3 gene taxon:4932 20010118 SGD
+SGD S000005372 HTZ1 GO:0000790 SGD_REF:S000056455|PMID:11081628 IDA C evolutionarily conserved member of the histone H2A F/Z family of histone variants YOL012C|H2A.F/Z|H2AZ|HTA3 gene taxon:4932 20010118 SGD
+SGD S000005372 HTZ1 GO:0000790 SGD_REF:S000056456|PMID:11090616 IDA C evolutionarily conserved member of the histone H2A F/Z family of histone variants YOL012C|H2A.F/Z|H2AZ|HTA3 gene taxon:4932 20010118 SGD
+SGD S000005372 HTZ1 GO:0000790 SGD_REF:S000056455|PMID:11081628 IPI C evolutionarily conserved member of the histone H2A F/Z family of histone variants YOL012C|H2A.F/Z|H2AZ|HTA3 gene taxon:4932 20010118 SGD
+SGD S000005372 HTZ1 GO:0005678 SGD_REF:S000056456|PMID:11090616 IPI C evolutionarily conserved member of the histone H2A F/Z family of histone variants YOL012C|H2A.F/Z|H2AZ|HTA3 gene taxon:4932 20010118 SGD
+SGD S000005372 HTZ1 GO:0003682 SGD_REF:S000056455|PMID:11081628 IDA F evolutionarily conserved member of the histone H2A F/Z family of histone variants YOL012C|H2A.F/Z|H2AZ|HTA3 gene taxon:4932 20010118 SGD
+SGD S000005372 HTZ1 GO:0003682 SGD_REF:S000056442|PMID:11000274 IGI F evolutionarily conserved member of the histone H2A F/Z family of histone variants YOL012C|H2A.F/Z|H2AZ|HTA3 gene taxon:4932 20010118 SGD
+SGD S000005372 HTZ1 GO:0003682 SGD_REF:S000056442|PMID:11000274 ISS F evolutionarily conserved member of the histone H2A F/Z family of histone variants YOL012C|H2A.F/Z|H2AZ|HTA3 gene taxon:4932 20010118 SGD
+SGD S000005372 HTZ1 GO:0006357 SGD_REF:S000056455|PMID:11081628 IMP P evolutionarily conserved member of the histone H2A F/Z family of histone variants YOL012C|H2A.F/Z|H2AZ|HTA3 gene taxon:4932 20010118 SGD
+SGD S000005372 HTZ1 GO:0006357 SGD_REF:S000056455|PMID:11081628 IGI P evolutionarily conserved member of the histone H2A F/Z family of histone variants YOL012C|H2A.F/Z|H2AZ|HTA3 gene taxon:4932 20010118 SGD
+SGD S000005372 HTZ1 GO:0030466 SGD_REF:S000056456|PMID:11090616 IGI P evolutionarily conserved member of the histone H2A F/Z family of histone variants YOL012C|H2A.F/Z|H2AZ|HTA3 gene taxon:4932 20010118 SGD
+SGD S000005372 HTZ1 GO:0030466 SGD_REF:S000056456|PMID:11090616 IPI P evolutionarily conserved member of the histone H2A F/Z family of histone variants YOL012C|H2A.F/Z|H2AZ|HTA3 gene taxon:4932 20010118 SGD
+SGD S000003500 HUA1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YGR268C gene taxon:4932 20020507 SGD
+SGD S000003500 HUA1 GO:0005737 SGD_REF:S000061434|PMID:11489916 IDA C YGR268C gene taxon:4932 20030512 SGD
+SGD S000003500 HUA1 GO:0005554 SGD_REF:S000069584 ND F YGR268C gene taxon:4932 20030117 SGD
+SGD S000003500 HUA1 GO:0000147 SGD_REF:S000074191|PMID:14566057 RCA P YGR268C gene taxon:4932 20050608 SGD
+SGD S000005810 HUA2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YOR284W gene taxon:4932 20031028 SGD
+SGD S000005810 HUA2 GO:0005554 SGD_REF:S000069584 ND F YOR284W gene taxon:4932 20030117 SGD
+SGD S000005810 HUA2 GO:0000147 SGD_REF:S000074191|PMID:14566057 RCA P YOR284W gene taxon:4932 20050608 SGD
+SGD S000007251 HUB1 GO:0005937 SGD_REF:S000069496|PMID:11923536 IPI C ubiquitin-like modifier YNR032C-A gene taxon:4932 20031002 SGD
+SGD S000007251 HUB1 GO:0031386 SGD_REF:S000069496|PMID:11923536 IDA F ubiquitin-like modifier YNR032C-A gene taxon:4932 20050525 SGD
+SGD S000007251 HUB1 GO:0031386 SGD_REF:S000069496|PMID:11923536 ISS F ubiquitin-like modifier YNR032C-A gene taxon:4932 20050525 SGD
+SGD S000007251 HUB1 GO:0000398 SGD_REF:S000080039|PMID:15620657 ISS UniProt:O94650 P ubiquitin-like modifier YNR032C-A gene taxon:4932 20051021 SGD
+SGD S000007251 HUB1 GO:0000398 SGD_REF:S000080039|PMID:15620657 IPI SGD:S000005835 P ubiquitin-like modifier YNR032C-A gene taxon:4932 20051021 SGD
+SGD S000007251 HUB1 GO:0000753 SGD_REF:S000069496|PMID:11923536 IMP P ubiquitin-like modifier YNR032C-A gene taxon:4932 20021206 SGD
+SGD S000007251 HUB1 GO:0006464 SGD_REF:S000069496|PMID:11923536 IDA P ubiquitin-like modifier YNR032C-A gene taxon:4932 20020923 SGD
+SGD S000007472 HUG1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YML058W-A gene taxon:4932 20031028 SGD
+SGD S000007472 HUG1 GO:0005554 SGD_REF:S000069584 ND F YML058W-A gene taxon:4932 20021211 SGD
+SGD S000007472 HUG1 GO:0000075 SGD_REF:S000042214|PMID:10490641 IMP P YML058W-A gene taxon:4932 20021001 SGD
+SGD S000007472 HUG1 GO:0000075 SGD_REF:S000042214|PMID:10490641 IEP P YML058W-A gene taxon:4932 20021001 SGD
+SGD S000007472 HUG1 GO:0006974 SGD_REF:S000042214|PMID:10490641 IMP P YML058W-A gene taxon:4932 20021001 SGD
+SGD S000007472 HUG1 GO:0006974 SGD_REF:S000042214|PMID:10490641 IEP P YML058W-A gene taxon:4932 20021001 SGD
+SGD S000007472 HUG1 GO:0007050 SGD_REF:S000042214|PMID:10490641 IMP P YML058W-A gene taxon:4932 20021001 SGD
+SGD S000007472 HUG1 GO:0007050 SGD_REF:S000042214|PMID:10490641 IEP P YML058W-A gene taxon:4932 20021001 SGD
+SGD S000003797 HUL4 GO:0008372 SGD_REF:S000069584 ND C ubiquitin ligase (E3) YJR036C gene taxon:4932 20010119 SGD
+SGD S000003797 HUL4 GO:0004842 SGD_REF:S000042659|PMID:9858558 TAS F ubiquitin ligase (E3) YJR036C gene taxon:4932 20010118 SGD
+SGD S000003797 HUL4 GO:0000209 SGD_REF:S000042659|PMID:9858558 TAS P ubiquitin ligase (E3) YJR036C gene taxon:4932 20010118 SGD
+SGD S000003797 HUL4 GO:0006513 SGD_REF:S000042659|PMID:9858558 TAS P ubiquitin ligase (E3) YJR036C gene taxon:4932 20010118 SGD
+SGD S000003109 HUL5 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C ubiquitin ligase (E3) YGL141W gene taxon:4932 20031028 SGD
+SGD S000003109 HUL5 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C ubiquitin ligase (E3) YGL141W gene taxon:4932 20031028 SGD
+SGD S000003109 HUL5 GO:0004842 SGD_REF:S000042659|PMID:9858558 TAS F ubiquitin ligase (E3) YGL141W gene taxon:4932 20010118 SGD
+SGD S000003109 HUL5 GO:0000209 SGD_REF:S000042659|PMID:9858558 TAS P ubiquitin ligase (E3) YGL141W gene taxon:4932 20010118 SGD
+SGD S000003109 HUL5 GO:0006513 SGD_REF:S000042659|PMID:9858558 TAS P ubiquitin ligase (E3) YGL141W gene taxon:4932 20010118 SGD
+SGD S000003136 HUR1 GO:0005634 SGD_REF:S000114270|PMID:15161972 IC GO:0000723 C YGL168W gene taxon:4932 20060202 SGD
+SGD S000003136 HUR1 GO:0005554 SGD_REF:S000069584 ND F YGL168W gene taxon:4932 20060202 SGD
+SGD S000003136 HUR1 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P YGL168W gene taxon:4932 20060202 SGD
+SGD S000003136 HUR1 GO:0006260 SGD_REF:S000074308|PMID:12615994 IMP P YGL168W gene taxon:4932 20031114 SGD
+SGD S000006165 HUT1 GO:0008372 SGD_REF:S000069584 ND C YPL244C gene taxon:4932 20020814 SGD
+SGD S000006165 HUT1 GO:0005459 SGD_REF:S000060171|PMID:11284010 ISS F YPL244C gene taxon:4932 20020814 SGD
+SGD S000006165 HUT1 GO:0015785 SGD_REF:S000060240|PMID:11284009 IMP P YPL244C gene taxon:4932 20020814 SGD
+SGD S000000841 HVG1 GO:0008372 SGD_REF:S000069584 ND C nucleotide sugar transporter (putative) YER039C|YEM9 gene taxon:4932 20020528 SGD
+SGD S000000841 HVG1 GO:0005554 SGD_REF:S000069584 ND F nucleotide sugar transporter (putative) YER039C|YEM9 gene taxon:4932 20020528 SGD
+SGD S000000841 HVG1 GO:0000004 SGD_REF:S000069584 ND P nucleotide sugar transporter (putative) YER039C|YEM9 gene taxon:4932 20020528 SGD
+SGD S000001949 HXK1 GO:0005829 SGD_REF:S000058491 TAS C hexokinase I (PI) (also called hexokinase A) YFR053C gene taxon:4932 20010119 SGD
+SGD S000001949 HXK1 GO:0004396 SGD_REF:S000043583|PMID:6341351 IMP F hexokinase I (PI) (also called hexokinase A) YFR053C gene taxon:4932 20010118 SGD
+SGD S000001949 HXK1 GO:0004396 SGD_REF:S000073626|PMID:12611889 IDA F hexokinase I (PI) (also called hexokinase A) YFR053C gene taxon:4932 20030731 SGD
+SGD S000001949 HXK1 GO:0006000 SGD_REF:S000048827|PMID:6300872 IMP P hexokinase I (PI) (also called hexokinase A) YFR053C gene taxon:4932 20010118 SGD
+SGD S000001949 HXK1 GO:0006006 SGD_REF:S000048827|PMID:6300872 IMP P hexokinase I (PI) (also called hexokinase A) YFR053C gene taxon:4932 20050609 SGD
+SGD S000003222 HXK2 GO:0005634 SGD_REF:S000055634|PMID:9563516 IDA C hexokinase II (PII) (also called hexokinase B) YGL253W|HEX1|HKB|SCI2 gene taxon:4932 20050609 SGD
+SGD S000003222 HXK2 GO:0005634 SGD_REF:S000060187|PMID:11311123 IDA C hexokinase II (PII) (also called hexokinase B) YGL253W|HEX1|HKB|SCI2 gene taxon:4932 20050609 SGD
+SGD S000003222 HXK2 GO:0005829 SGD_REF:S000055634|PMID:9563516 IDA C hexokinase II (PII) (also called hexokinase B) YGL253W|HEX1|HKB|SCI2 gene taxon:4932 20050609 SGD
+SGD S000003222 HXK2 GO:0005829 SGD_REF:S000060187|PMID:11311123 IDA C hexokinase II (PII) (also called hexokinase B) YGL253W|HEX1|HKB|SCI2 gene taxon:4932 20050609 SGD
+SGD S000003222 HXK2 GO:0004396 SGD_REF:S000043583|PMID:6341351 IMP F hexokinase II (PII) (also called hexokinase B) YGL253W|HEX1|HKB|SCI2 gene taxon:4932 20010118 SGD
+SGD S000003222 HXK2 GO:0004396 SGD_REF:S000073626|PMID:12611889 IDA F hexokinase II (PII) (also called hexokinase B) YGL253W|HEX1|HKB|SCI2 gene taxon:4932 20030731 SGD
+SGD S000003222 HXK2 GO:0001302 SGD_REF:S000080970|PMID:15722108 IMP P hexokinase II (PII) (also called hexokinase B) YGL253W|HEX1|HKB|SCI2 gene taxon:4932 20050314 SGD
+SGD S000003222 HXK2 GO:0006000 SGD_REF:S000048827|PMID:6300872 IMP P hexokinase II (PII) (also called hexokinase B) YGL253W|HEX1|HKB|SCI2 gene taxon:4932 20010118 SGD
+SGD S000003222 HXK2 GO:0006006 SGD_REF:S000048827|PMID:6300872 IMP P hexokinase II (PII) (also called hexokinase B) YGL253W|HEX1|HKB|SCI2 gene taxon:4932 20050609 SGD
+SGD S000003222 HXK2 GO:0006096 SGD_REF:S000041726|PMID:8917466 IDA P hexokinase II (PII) (also called hexokinase B) YGL253W|HEX1|HKB|SCI2 gene taxon:4932 20050609 SGD
+SGD S000003222 HXK2 GO:0006096 SGD_REF:S000041726|PMID:8917466 IMP P hexokinase II (PII) (also called hexokinase B) YGL253W|HEX1|HKB|SCI2 gene taxon:4932 20050609 SGD
+SGD S000003222 HXK2 GO:0046015 SGD_REF:S000060187|PMID:11311123 IDA P hexokinase II (PII) (also called hexokinase B) YGL253W|HEX1|HKB|SCI2 gene taxon:4932 20050609 SGD
+SGD S000001136 HXT1 GO:0005886 SGD_REF:S000040599|PMID:10377429 IDA C hexose transporter YHR094C|HOR4 gene taxon:4932 20020920 SGD
+SGD S000001136 HXT1 GO:0005353 SGD_REF:S000053220|PMID:7651133 IMP F hexose transporter YHR094C|HOR4 gene taxon:4932 20030206 SGD
+SGD S000001136 HXT1 GO:0005354 SGD_REF:S000056317|PMID:10618490 TAS F hexose transporter YHR094C|HOR4 gene taxon:4932 20011016 SGD
+SGD S000001136 HXT1 GO:0005355 SGD_REF:S000056317|PMID:10618490 TAS F hexose transporter YHR094C|HOR4 gene taxon:4932 20011016 SGD
+SGD S000001136 HXT1 GO:0015578 SGD_REF:S000056317|PMID:10618490 TAS F hexose transporter YHR094C|HOR4 gene taxon:4932 20011016 SGD
+SGD S000001136 HXT1 GO:0008645 SGD_REF:S000056317|PMID:10618490 TAS P hexose transporter YHR094C|HOR4 gene taxon:4932 20011016 SGD
+SGD S000001883 HXT10 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C high affinity hexose transporter YFL011W gene taxon:4932 20040928 SGD
+SGD S000001883 HXT10 GO:0005886 SGD_REF:S000063161|PMID:8929273 ISS C high affinity hexose transporter YFL011W gene taxon:4932 20021003 SGD
+SGD S000001883 HXT10 GO:0005353 SGD_REF:S000056317|PMID:10618490 IGI F high affinity hexose transporter YFL011W gene taxon:4932 20011016 SGD
+SGD S000001883 HXT10 GO:0005354 SGD_REF:S000056317|PMID:10618490 IGI F high affinity hexose transporter YFL011W gene taxon:4932 20011016 SGD
+SGD S000001883 HXT10 GO:0005355 SGD_REF:S000056317|PMID:10618490 IGI F high affinity hexose transporter YFL011W gene taxon:4932 20011016 SGD
+SGD S000001883 HXT10 GO:0015578 SGD_REF:S000056317|PMID:10618490 IGI F high affinity hexose transporter YFL011W gene taxon:4932 20011016 SGD
+SGD S000001883 HXT10 GO:0008645 SGD_REF:S000056317|PMID:10618490 IGI P high affinity hexose transporter YFL011W gene taxon:4932 20011016 SGD
+SGD S000005516 HXT11 GO:0005886 SGD_REF:S000063161|PMID:8929273 ISS C glucose permease YOL156W|LGT3 gene taxon:4932 20021003 SGD
+SGD S000005516 HXT11 GO:0005353 SGD_REF:S000056317|PMID:10618490 IGI F glucose permease YOL156W|LGT3 gene taxon:4932 20011016 SGD
+SGD S000005516 HXT11 GO:0005354 SGD_REF:S000056317|PMID:10618490 IGI F glucose permease YOL156W|LGT3 gene taxon:4932 20011016 SGD
+SGD S000005516 HXT11 GO:0005355 SGD_REF:S000056317|PMID:10618490 IGI F glucose permease YOL156W|LGT3 gene taxon:4932 20011016 SGD
+SGD S000005516 HXT11 GO:0015578 SGD_REF:S000056317|PMID:10618490 IGI F glucose permease YOL156W|LGT3 gene taxon:4932 20011016 SGD
+SGD S000005516 HXT11 GO:0008645 SGD_REF:S000056317|PMID:10618490 IGI P glucose permease YOL156W|LGT3 gene taxon:4932 20011016 SGD
+SGD S000001432 HXT12 GO:0008372 SGD_REF:S000069584 ND C putative hexose permease YIL170W gene taxon:4932 20011228 SGD
+SGD S000001432 HXT12 GO:0005554 SGD_REF:S000069584 ND F putative hexose permease YIL170W gene taxon:4932 20041207 SGD
+SGD S000001432 HXT12 NOT GO:0015149 SGD_REF:S000056317|PMID:10618490 IGI F putative hexose permease YIL170W gene taxon:4932 20041207 SGD
+SGD S000001432 HXT12 GO:0000004 SGD_REF:S000069584 ND P putative hexose permease YIL170W gene taxon:4932 20041207 SGD
+SGD S000001432 HXT12 NOT GO:0008645 SGD_REF:S000056317|PMID:10618490 IGI P putative hexose permease YIL170W gene taxon:4932 20041207 SGD
+SGD S000000795 HXT13 GO:0005886 SGD_REF:S000063161|PMID:8929273 ISS C high affinity hexose transporter YEL069C gene taxon:4932 20021003 SGD
+SGD S000000795 HXT13 GO:0005353 SGD_REF:S000056317|PMID:10618490 IGI F high affinity hexose transporter YEL069C gene taxon:4932 20011016 SGD
+SGD S000000795 HXT13 GO:0005355 SGD_REF:S000056317|PMID:10618490 IGI F high affinity hexose transporter YEL069C gene taxon:4932 20011016 SGD
+SGD S000000795 HXT13 GO:0015578 SGD_REF:S000056317|PMID:10618490 IGI F high affinity hexose transporter YEL069C gene taxon:4932 20011016 SGD
+SGD S000000795 HXT13 GO:0008645 SGD_REF:S000056317|PMID:10618490 IGI P high affinity hexose transporter YEL069C gene taxon:4932 20011016 SGD
+SGD S000005262 HXT14 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C hexose transporter YNL318C gene taxon:4932 20040928 SGD
+SGD S000005262 HXT14 GO:0005886 SGD_REF:S000063161|PMID:8929273 ISS C hexose transporter YNL318C gene taxon:4932 20021003 SGD
+SGD S000005262 HXT14 GO:0005354 SGD_REF:S000056317|PMID:10618490 IGI F hexose transporter YNL318C gene taxon:4932 20011016 SGD
+SGD S000005262 HXT14 GO:0008645 SGD_REF:S000056317|PMID:10618490 IGI P hexose transporter YNL318C gene taxon:4932 20011016 SGD
+SGD S000002404 HXT15 GO:0005886 SGD_REF:S000063161|PMID:8929273 ISS C hexose transporter YDL245C gene taxon:4932 20021003 SGD
+SGD S000002404 HXT15 GO:0005353 SGD_REF:S000056317|PMID:10618490 IGI F hexose transporter YDL245C gene taxon:4932 20011016 SGD
+SGD S000002404 HXT15 GO:0005355 SGD_REF:S000056317|PMID:10618490 IGI F hexose transporter YDL245C gene taxon:4932 20011016 SGD
+SGD S000002404 HXT15 GO:0015578 SGD_REF:S000056317|PMID:10618490 IGI F hexose transporter YDL245C gene taxon:4932 20011016 SGD
+SGD S000002404 HXT15 GO:0008645 SGD_REF:S000056317|PMID:10618490 IGI P hexose transporter YDL245C gene taxon:4932 20011016 SGD
+SGD S000003919 HXT16 GO:0005886 SGD_REF:S000063161|PMID:8929273 ISS C hexose permease YJR158W gene taxon:4932 20021003 SGD
+SGD S000003919 HXT16 GO:0005353 SGD_REF:S000056317|PMID:10618490 IGI F hexose permease YJR158W gene taxon:4932 20011016 SGD
+SGD S000003919 HXT16 GO:0005355 SGD_REF:S000056317|PMID:10618490 IGI F hexose permease YJR158W gene taxon:4932 20011016 SGD
+SGD S000003919 HXT16 GO:0015578 SGD_REF:S000056317|PMID:10618490 IGI F hexose permease YJR158W gene taxon:4932 20011016 SGD
+SGD S000003919 HXT16 GO:0008645 SGD_REF:S000056317|PMID:10618490 IGI P hexose permease YJR158W gene taxon:4932 20011016 SGD
+SGD S000005355 HXT17 GO:0005886 SGD_REF:S000063161|PMID:8929273 ISS C hexose transporter YNR072W gene taxon:4932 20021003 SGD
+SGD S000005355 HXT17 GO:0005353 SGD_REF:S000056317|PMID:10618490 IGI F hexose transporter YNR072W gene taxon:4932 20011016 SGD
+SGD S000005355 HXT17 GO:0005355 SGD_REF:S000056317|PMID:10618490 IGI F hexose transporter YNR072W gene taxon:4932 20011016 SGD
+SGD S000005355 HXT17 GO:0015578 SGD_REF:S000056317|PMID:10618490 IGI F hexose transporter YNR072W gene taxon:4932 20011016 SGD
+SGD S000005355 HXT17 GO:0008645 SGD_REF:S000056317|PMID:10618490 IGI P hexose transporter YNR072W gene taxon:4932 20011016 SGD
+SGD S000004613 HXT2 GO:0005886 SGD_REF:S000042437|PMID:10191260 IDA C high affinity hexose transporter-2 YMR011W gene taxon:4932 20020920 SGD
+SGD S000004613 HXT2 GO:0005353 SGD_REF:S000056317|PMID:10618490 TAS F high affinity hexose transporter-2 YMR011W gene taxon:4932 20011016 SGD
+SGD S000004613 HXT2 GO:0005355 SGD_REF:S000056317|PMID:10618490 TAS F high affinity hexose transporter-2 YMR011W gene taxon:4932 20011016 SGD
+SGD S000004613 HXT2 GO:0005355 SGD_REF:S000073003|PMID:12702270 IDA F high affinity hexose transporter-2 YMR011W gene taxon:4932 20030502 SGD
+SGD S000004613 HXT2 GO:0015578 SGD_REF:S000056317|PMID:10618490 TAS F high affinity hexose transporter-2 YMR011W gene taxon:4932 20011016 SGD
+SGD S000004613 HXT2 GO:0008645 SGD_REF:S000056317|PMID:10618490 TAS P high affinity hexose transporter-2 YMR011W gene taxon:4932 20011016 SGD
+SGD S000002753 HXT3 GO:0005886 SGD_REF:S000063161|PMID:8929273 ISS C low affinity glucose transporter YDR345C gene taxon:4932 20021003 SGD
+SGD S000002753 HXT3 GO:0005353 SGD_REF:S000056317|PMID:10618490 TAS F low affinity glucose transporter YDR345C gene taxon:4932 20011016 SGD
+SGD S000002753 HXT3 GO:0005355 SGD_REF:S000056317|PMID:10618490 TAS F low affinity glucose transporter YDR345C gene taxon:4932 20011016 SGD
+SGD S000002753 HXT3 GO:0005355 SGD_REF:S000073003|PMID:12702270 IDA F low affinity glucose transporter YDR345C gene taxon:4932 20030502 SGD
+SGD S000002753 HXT3 GO:0015578 SGD_REF:S000056317|PMID:10618490 TAS F low affinity glucose transporter YDR345C gene taxon:4932 20011016 SGD
+SGD S000002753 HXT3 GO:0008645 SGD_REF:S000056317|PMID:10618490 TAS P low affinity glucose transporter YDR345C gene taxon:4932 20011016 SGD
+SGD S000001134 HXT4 GO:0005886 SGD_REF:S000063161|PMID:8929273 ISS C high affinity glucose transporter YHR092C|LGT1|RAG1 gene taxon:4932 20021003 SGD
+SGD S000001134 HXT4 GO:0005353 SGD_REF:S000056317|PMID:10618490 TAS F high affinity glucose transporter YHR092C|LGT1|RAG1 gene taxon:4932 20011016 SGD
+SGD S000001134 HXT4 GO:0005355 SGD_REF:S000056317|PMID:10618490 TAS F high affinity glucose transporter YHR092C|LGT1|RAG1 gene taxon:4932 20011016 SGD
+SGD S000001134 HXT4 GO:0005355 SGD_REF:S000073003|PMID:12702270 IDA F high affinity glucose transporter YHR092C|LGT1|RAG1 gene taxon:4932 20030502 SGD
+SGD S000001134 HXT4 GO:0015578 SGD_REF:S000056317|PMID:10618490 TAS F high affinity glucose transporter YHR092C|LGT1|RAG1 gene taxon:4932 20011016 SGD
+SGD S000001134 HXT4 GO:0008645 SGD_REF:S000056317|PMID:10618490 TAS P high affinity glucose transporter YHR092C|LGT1|RAG1 gene taxon:4932 20011016 SGD
+SGD S000001138 HXT5 GO:0005886 SGD_REF:S000063161|PMID:8929273 ISS C hexose transporter YHR096C gene taxon:4932 20021003 SGD
+SGD S000001138 HXT5 GO:0005353 SGD_REF:S000056317|PMID:10618490 IGI F hexose transporter YHR096C gene taxon:4932 20011016 SGD
+SGD S000001138 HXT5 GO:0005355 SGD_REF:S000056317|PMID:10618490 IGI F hexose transporter YHR096C gene taxon:4932 20011016 SGD
+SGD S000001138 HXT5 GO:0005355 SGD_REF:S000073003|PMID:12702270 IDA F hexose transporter YHR096C gene taxon:4932 20030502 SGD
+SGD S000001138 HXT5 GO:0015578 SGD_REF:S000056317|PMID:10618490 IGI F hexose transporter YHR096C gene taxon:4932 20011016 SGD
+SGD S000001138 HXT5 GO:0008645 SGD_REF:S000056317|PMID:10618490 IGI P hexose transporter YHR096C gene taxon:4932 20011016 SGD
+SGD S000002751 HXT6 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C hexose transporter YDR343C gene taxon:4932 20041210 SGD
+SGD S000002751 HXT6 GO:0005886 SGD_REF:S000069562|PMID:11904149 ISS C hexose transporter YDR343C gene taxon:4932 20020920 SGD
+SGD S000002751 HXT6 GO:0005353 SGD_REF:S000056317|PMID:10618490 TAS F hexose transporter YDR343C gene taxon:4932 20011016 SGD
+SGD S000002751 HXT6 GO:0005355 SGD_REF:S000056317|PMID:10618490 TAS F hexose transporter YDR343C gene taxon:4932 20011016 SGD
+SGD S000002751 HXT6 GO:0005355 SGD_REF:S000073003|PMID:12702270 IDA F hexose transporter YDR343C gene taxon:4932 20030502 SGD
+SGD S000002751 HXT6 GO:0015578 SGD_REF:S000056317|PMID:10618490 TAS F hexose transporter YDR343C gene taxon:4932 20011016 SGD
+SGD S000002751 HXT6 GO:0008645 SGD_REF:S000056317|PMID:10618490 TAS P hexose transporter YDR343C gene taxon:4932 20011016 SGD
+SGD S000002750 HXT7 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C hexose transporter YDR342C gene taxon:4932 20041210 SGD
+SGD S000002750 HXT7 GO:0005886 SGD_REF:S000069562|PMID:11904149 IDA C hexose transporter YDR342C gene taxon:4932 20020920 SGD
+SGD S000002750 HXT7 GO:0005353 SGD_REF:S000056317|PMID:10618490 TAS F hexose transporter YDR342C gene taxon:4932 20011016 SGD
+SGD S000002750 HXT7 GO:0005355 SGD_REF:S000056317|PMID:10618490 TAS F hexose transporter YDR342C gene taxon:4932 20011016 SGD
+SGD S000002750 HXT7 GO:0005355 SGD_REF:S000073003|PMID:12702270 IDA F hexose transporter YDR342C gene taxon:4932 20030502 SGD
+SGD S000002750 HXT7 GO:0015578 SGD_REF:S000056317|PMID:10618490 TAS F hexose transporter YDR342C gene taxon:4932 20011016 SGD
+SGD S000002750 HXT7 GO:0008645 SGD_REF:S000056317|PMID:10618490 TAS P hexose transporter YDR342C gene taxon:4932 20011016 SGD
+SGD S000003750 HXT8 GO:0005886 SGD_REF:S000063161|PMID:8929273 ISS C hexose permease YJL214W gene taxon:4932 20021003 SGD
+SGD S000003750 HXT8 GO:0005353 SGD_REF:S000056317|PMID:10618490 IGI F hexose permease YJL214W gene taxon:4932 20011016 SGD
+SGD S000003750 HXT8 GO:0005355 SGD_REF:S000056317|PMID:10618490 IGI F hexose permease YJL214W gene taxon:4932 20011016 SGD
+SGD S000003750 HXT8 GO:0015578 SGD_REF:S000056317|PMID:10618490 IGI F hexose permease YJL214W gene taxon:4932 20011016 SGD
+SGD S000003750 HXT8 GO:0008645 SGD_REF:S000056317|PMID:10618490 IGI P hexose permease YJL214W gene taxon:4932 20011016 SGD
+SGD S000003755 HXT9 GO:0005886 SGD_REF:S000063161|PMID:8929273 ISS C hexose permease YJL219W gene taxon:4932 20021003 SGD
+SGD S000003755 HXT9 GO:0005353 SGD_REF:S000056317|PMID:10618490 IGI F hexose permease YJL219W gene taxon:4932 20011016 SGD
+SGD S000003755 HXT9 GO:0005354 SGD_REF:S000056317|PMID:10618490 IGI F hexose permease YJL219W gene taxon:4932 20011016 SGD
+SGD S000003755 HXT9 GO:0005355 SGD_REF:S000056317|PMID:10618490 IGI F hexose permease YJL219W gene taxon:4932 20011016 SGD
+SGD S000003755 HXT9 GO:0015578 SGD_REF:S000056317|PMID:10618490 IGI F hexose permease YJL219W gene taxon:4932 20011016 SGD
+SGD S000003755 HXT9 GO:0008645 SGD_REF:S000056317|PMID:10618490 IGI P hexose permease YJL219W gene taxon:4932 20011016 SGD
+SGD S000001672 HYM1 GO:0000131 SGD_REF:S000074101|PMID:12972564 IDA C YKL189W gene taxon:4932 20031016 SGD
+SGD S000001672 HYM1 GO:0005622 SGD_REF:S000060221|PMID:11259593 IDA C YKL189W gene taxon:4932 20030110 SGD
+SGD S000001672 HYM1 GO:0005933 SGD_REF:S000074101|PMID:12972564 IDA C YKL189W gene taxon:4932 20031016 SGD
+SGD S000001672 HYM1 GO:0043332 SGD_REF:S000074101|PMID:12972564 IDA C YKL189W gene taxon:4932 20031016 SGD
+SGD S000001672 HYM1 GO:0005554 SGD_REF:S000069584 ND F YKL189W gene taxon:4932 20050708 SGD
+SGD S000001672 HYM1 GO:0000903 SGD_REF:S000074101|PMID:12972564 IGI P YKL189W gene taxon:4932 20050420 SGD
+SGD S000001672 HYM1 GO:0007109 SGD_REF:S000060221|PMID:11259593 IMP P YKL189W gene taxon:4932 20021011 SGD
+SGD S000001672 HYM1 GO:0008360 SGD_REF:S000060221|PMID:11259593 IGI P YKL189W gene taxon:4932 20021011 SGD
+SGD S000001672 HYM1 GO:0045449 SGD_REF:S000074101|PMID:12972564 IMP P YKL189W gene taxon:4932 20050708 SGD
+SGD S000000760 HYP2 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C translation initiation factor eIF-5A YEL034W|TIF51A gene taxon:4932 20020507 SGD
+SGD S000000760 HYP2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C translation initiation factor eIF-5A YEL034W|TIF51A gene taxon:4932 20040813 SGD
+SGD S000000760 HYP2 GO:0005840 SGD_REF:S000058753|PMID:9841679 TAS C translation initiation factor eIF-5A YEL034W|TIF51A gene taxon:4932 20010124 SGD
+SGD S000000760 HYP2 GO:0003743 SGD_REF:S000058753|PMID:9841679 TAS F translation initiation factor eIF-5A YEL034W|TIF51A gene taxon:4932 20010124 SGD
+SGD S000000760 HYP2 GO:0005515 SGD_REF:S000075161|PMID:14675757 IPI SGD:S000001110|SGD:S000003831 F translation initiation factor eIF-5A YEL034W|TIF51A gene taxon:4932 20031218 SGD
+SGD S000000760 HYP2 GO:0006413 SGD_REF:S000058753|PMID:9841679 TAS P translation initiation factor eIF-5A YEL034W|TIF51A gene taxon:4932 20010124 SGD
+SGD S000001476 HYR1 GO:0005622 SGD_REF:S000071903|PMID:12437921 IPI SGD:S000004466 C glutathione-peroxidase (putative) YIR037W|GPX3|ORP1 gene taxon:4932 20030110 SGD
+SGD S000001476 HYR1 GO:0004602 SGD_REF:S000040535|PMID:10480913 ISS F glutathione-peroxidase (putative) YIR037W|GPX3|ORP1 gene taxon:4932 20010118 SGD
+SGD S000001476 HYR1 NOT GO:0004602 SGD_REF:S000071903|PMID:12437921 IGI F glutathione-peroxidase (putative) YIR037W|GPX3|ORP1 gene taxon:4932 20030919 SGD
+SGD S000001476 HYR1 GO:0004602 SGD_REF:S000040535|PMID:10480913 IMP F glutathione-peroxidase (putative) YIR037W|GPX3|ORP1 gene taxon:4932 20010118 SGD
+SGD S000001476 HYR1 GO:0008379 SGD_REF:S000073844|PMID:12743123 TAS F glutathione-peroxidase (putative) YIR037W|GPX3|ORP1 gene taxon:4932 20030904 SGD
+SGD S000001476 HYR1 GO:0047066 SGD_REF:S000065852|PMID:11445588 IDA F glutathione-peroxidase (putative) YIR037W|GPX3|ORP1 gene taxon:4932 20060601 SGD
+SGD S000001476 HYR1 GO:0047066 SGD_REF:S000065852|PMID:11445588 IMP F glutathione-peroxidase (putative) YIR037W|GPX3|ORP1 gene taxon:4932 20060601 SGD
+SGD S000001476 HYR1 GO:0006979 SGD_REF:S000065852|PMID:11445588 IMP P glutathione-peroxidase (putative) YIR037W|GPX3|ORP1 gene taxon:4932 20020928 SGD
+SGD S000003766 HYS2 GO:0043625 SGD_REF:S000058372|PMID:9745046 TAS C DNA polymerase delta subunit YJR006W|HUS2|POL31|SDP5 gene taxon:4932 20010118 SGD
+SGD S000003766 HYS2 contributes_to GO:0003891 SGD_REF:S000058372|PMID:9745046 TAS F DNA polymerase delta subunit YJR006W|HUS2|POL31|SDP5 gene taxon:4932 20010118 SGD
+SGD S000003766 HYS2 contributes_to GO:0008310 SGD_REF:S000058372|PMID:9745046 TAS F DNA polymerase delta subunit YJR006W|HUS2|POL31|SDP5 gene taxon:4932 20060309 SGD
+SGD S000003766 HYS2 GO:0006272 SGD_REF:S000058372|PMID:9745046 TAS P DNA polymerase delta subunit YJR006W|HUS2|POL31|SDP5 gene taxon:4932 20010118 SGD
+SGD S000003766 HYS2 GO:0006273 SGD_REF:S000058372|PMID:9745046 TAS P DNA polymerase delta subunit YJR006W|HUS2|POL31|SDP5 gene taxon:4932 20010118 SGD
+SGD S000003766 HYS2 GO:0006280 SGD_REF:S000058372|PMID:9745046 TAS P DNA polymerase delta subunit YJR006W|HUS2|POL31|SDP5 gene taxon:4932 20010118 SGD
+SGD S000003766 HYS2 GO:0006284 SGD_REF:S000058372|PMID:9745046 TAS P DNA polymerase delta subunit YJR006W|HUS2|POL31|SDP5 gene taxon:4932 20010118 SGD
+SGD S000003766 HYS2 GO:0006289 SGD_REF:S000058372|PMID:9745046 TAS P DNA polymerase delta subunit YJR006W|HUS2|POL31|SDP5 gene taxon:4932 20010118 SGD
+SGD S000003766 HYS2 GO:0006298 SGD_REF:S000058456|PMID:10072354 TAS P DNA polymerase delta subunit YJR006W|HUS2|POL31|SDP5 gene taxon:4932 20021126 SGD
+SGD S000003766 HYS2 GO:0006301 SGD_REF:S000058372|PMID:9745046 TAS P DNA polymerase delta subunit YJR006W|HUS2|POL31|SDP5 gene taxon:4932 20010118 SGD
+SGD S000005652 IAH1 GO:0008372 SGD_REF:S000069584 ND C isoamyl acetate-hydrolyzing esterase YOR126C gene taxon:4932 20021009 SGD
+SGD S000005652 IAH1 GO:0016788 SGD_REF:S000056429|PMID:10855721 IDA F isoamyl acetate-hydrolyzing esterase YOR126C gene taxon:4932 20021009 SGD
+SGD S000005652 IAH1 GO:0006083 SGD_REF:S000056429|PMID:10855721 IDA P isoamyl acetate-hydrolyzing esterase YOR126C gene taxon:4932 20021009 SGD
+SGD S000005108 IBD2 GO:0005634 SGD_REF:S000070089|PMID:12072457 NAS C YNL164C gene taxon:4932 20020708 SGD
+SGD S000005108 IBD2 GO:0005554 SGD_REF:S000069584 ND F YNL164C gene taxon:4932 20020708 SGD
+SGD S000005108 IBD2 GO:0007094 SGD_REF:S000070089|PMID:12072457 IGI P YNL164C gene taxon:4932 20020708 SGD
+SGD S000005108 IBD2 GO:0007094 SGD_REF:S000070089|PMID:12072457 IMP P YNL164C gene taxon:4932 20020708 SGD
+SGD S000001352 ICE2 GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YIL090W gene taxon:4932 20031028 SGD
+SGD S000001352 ICE2 GO:0005783 SGD_REF:S000080474|PMID:15585575 IDA C YIL090W gene taxon:4932 20050126 SGD
+SGD S000001352 ICE2 GO:0005554 SGD_REF:S000069584 ND F YIL090W gene taxon:4932 20050126 SGD
+SGD S000001352 ICE2 GO:0007029 SGD_REF:S000080474|PMID:15585575 IMP P YIL090W gene taxon:4932 20050126 SGD
+SGD S000000867 ICL1 GO:0008372 SGD_REF:S000069584 ND C isocitrate lyase YER065C gene taxon:4932 20020930 SGD
+SGD S000000867 ICL1 GO:0004451 SGD_REF:S000051533|PMID:1551398 IMP F isocitrate lyase YER065C gene taxon:4932 20030117 SGD
+SGD S000000867 ICL1 GO:0004451 SGD_REF:S000051533|PMID:1551398 ISS F isocitrate lyase YER065C gene taxon:4932 20030117 SGD
+SGD S000000867 ICL1 GO:0006097 SGD_REF:S000059330|PMID:11092862 TAS P isocitrate lyase YER065C gene taxon:4932 20020930 SGD
+SGD S000006210 ICL2 GO:0005759 SGD_REF:S000059330|PMID:11092862 IDA C 2-methylisocitrate lyase YPR006C gene taxon:4932 20020921 SGD
+SGD S000006210 ICL2 GO:0046421 SGD_REF:S000059330|PMID:11092862 IDA F 2-methylisocitrate lyase YPR006C gene taxon:4932 20020925 SGD
+SGD S000006210 ICL2 GO:0006567 SGD_REF:S000059330|PMID:11092862 IEP P 2-methylisocitrate lyase YPR006C gene taxon:4932 20020922 SGD
+SGD S000006210 ICL2 GO:0019541 SGD_REF:S000059712|PMID:11179416 IEP P 2-methylisocitrate lyase YPR006C gene taxon:4932 20011023 SGD
+SGD S000006210 ICL2 GO:0019541 SGD_REF:S000059330|PMID:11092862 IDA P 2-methylisocitrate lyase YPR006C gene taxon:4932 20020922 SGD
+SGD S000000361 ICS2 GO:0008372 SGD_REF:S000069584 ND C YBR157C gene taxon:4932 20020930 SGD
+SGD S000000361 ICS2 GO:0005554 SGD_REF:S000069584 ND F YBR157C gene taxon:4932 20021211 SGD
+SGD S000000361 ICS2 GO:0000004 SGD_REF:S000069584 ND P YBR157C gene taxon:4932 20020930 SGD
+SGD S000003613 ICS3 GO:0008372 SGD_REF:S000069584 ND C YJL077C gene taxon:4932 20020930 SGD
+SGD S000003613 ICS3 GO:0005554 SGD_REF:S000069584 ND F YJL077C gene taxon:4932 20021126 SGD
+SGD S000003613 ICS3 GO:0000004 SGD_REF:S000069584 ND P YJL077C gene taxon:4932 20020930 SGD
+SGD S000004089 ICT1 GO:0008372 SGD_REF:S000069584 ND C YLR099C gene taxon:4932 20021001 SGD
+SGD S000004089 ICT1 GO:0005554 SGD_REF:S000069584 ND F YLR099C gene taxon:4932 20021211 SGD
+SGD S000004089 ICT1 GO:0000004 SGD_REF:S000069584 ND P YLR099C gene taxon:4932 20021001 SGD
+SGD S000004808 ICY1 GO:0000329 SGD_REF:S000074185|PMID:14562095 IDA C YMR195W gene taxon:4932 20031028 SGD
+SGD S000004808 ICY1 GO:0005554 SGD_REF:S000069584 ND F YMR195W gene taxon:4932 20021211 SGD
+SGD S000004808 ICY1 GO:0000004 SGD_REF:S000069584 ND P YMR195W gene taxon:4932 20020930 SGD
+SGD S000006171 ICY2 GO:0008372 SGD_REF:S000069584 ND C YPL250C gene taxon:4932 20020930 SGD
+SGD S000006171 ICY2 GO:0005554 SGD_REF:S000069584 ND F YPL250C gene taxon:4932 20021211 SGD
+SGD S000006171 ICY2 GO:0000004 SGD_REF:S000069584 ND P YPL250C gene taxon:4932 20020930 SGD
+SGD S000004982 IDH1 GO:0005759 SGD_REF:S000045174|PMID:8626605 IDA C isocitrate dehydrogenase 1 alpha-4-beta-4 subunit YNL037C gene taxon:4932 20021202 SGD
+SGD S000004982 IDH1 GO:0042645 SGD_REF:S000080741|PMID:15692048 IDA C isocitrate dehydrogenase 1 alpha-4-beta-4 subunit YNL037C gene taxon:4932 20050401 SGD
+SGD S000004982 IDH1 GO:0004449 SGD_REF:S000058126|PMID:9175438 TAS F isocitrate dehydrogenase 1 alpha-4-beta-4 subunit YNL037C gene taxon:4932 20010118 SGD
+SGD S000004982 IDH1 GO:0006099 SGD_REF:S000058126|PMID:9175438 TAS P isocitrate dehydrogenase 1 alpha-4-beta-4 subunit YNL037C gene taxon:4932 20010118 SGD
+SGD S000004982 IDH1 GO:0006102 SGD_REF:S000058126|PMID:9175438 TAS P isocitrate dehydrogenase 1 alpha-4-beta-4 subunit YNL037C gene taxon:4932 20010118 SGD
+SGD S000004982 IDH1 GO:0006537 SGD_REF:S000058126|PMID:9175438 TAS P isocitrate dehydrogenase 1 alpha-4-beta-4 subunit YNL037C gene taxon:4932 20010118 SGD
+SGD S000005662 IDH2 GO:0005739 SGD_REF:S000069459|PMID:11914276 IDA C NAD-dependent isocitrate dehydrogenase YOR136W gene taxon:4932 20020507 SGD
+SGD S000005662 IDH2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C NAD-dependent isocitrate dehydrogenase YOR136W gene taxon:4932 20040924 SGD
+SGD S000005662 IDH2 GO:0005759 SGD_REF:S000058491 NAS C NAD-dependent isocitrate dehydrogenase YOR136W gene taxon:4932 20010119 SGD
+SGD S000005662 IDH2 GO:0005759 SGD_REF:S000058126|PMID:9175438 NAS C NAD-dependent isocitrate dehydrogenase YOR136W gene taxon:4932 20010118 SGD
+SGD S000005662 IDH2 GO:0004449 SGD_REF:S000058126|PMID:9175438 TAS F NAD-dependent isocitrate dehydrogenase YOR136W gene taxon:4932 20010118 SGD
+SGD S000005662 IDH2 GO:0006099 SGD_REF:S000058126|PMID:9175438 TAS P NAD-dependent isocitrate dehydrogenase YOR136W gene taxon:4932 20010118 SGD
+SGD S000005662 IDH2 GO:0006102 SGD_REF:S000058126|PMID:9175438 TAS P NAD-dependent isocitrate dehydrogenase YOR136W gene taxon:4932 20010118 SGD
+SGD S000005662 IDH2 GO:0006537 SGD_REF:S000058126|PMID:9175438 TAS P NAD-dependent isocitrate dehydrogenase YOR136W gene taxon:4932 20010118 SGD
+SGD S000006038 IDI1 GO:0005829 SGD_REF:S000058496 TAS C isopentenyl diphosphate:dimethylallyl diphosphate isomerase (IPP isomerase) YPL117C|BOT2|LPH10 gene taxon:4932 20010119 SGD
+SGD S000006038 IDI1 GO:0004452 SGD_REF:S000058496 TAS F isopentenyl diphosphate:dimethylallyl diphosphate isomerase (IPP isomerase) YPL117C|BOT2|LPH10 gene taxon:4932 20010119 SGD
+SGD S000006038 IDI1 GO:0006696 SGD_REF:S000058496 TAS P isopentenyl diphosphate:dimethylallyl diphosphate isomerase (IPP isomerase) YPL117C|BOT2|LPH10 gene taxon:4932 20010119 SGD
+SGD S000002224 IDP1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C NADP-dependent isocitrate dehydrogenase YDL066W gene taxon:4932 20040928 SGD
+SGD S000002224 IDP1 GO:0005739 SGD_REF:S000075624|PMID:15001388 IDA C NADP-dependent isocitrate dehydrogenase YDL066W gene taxon:4932 20050708 SGD
+SGD S000002224 IDP1 GO:0042645 SGD_REF:S000080741|PMID:15692048 IDA C NADP-dependent isocitrate dehydrogenase YDL066W gene taxon:4932 20050401 SGD
+SGD S000002224 IDP1 GO:0004450 SGD_REF:S000058126|PMID:9175438 TAS F NADP-dependent isocitrate dehydrogenase YDL066W gene taxon:4932 20010118 SGD
+SGD S000002224 IDP1 GO:0006102 SGD_REF:S000058126|PMID:9175438 TAS P NADP-dependent isocitrate dehydrogenase YDL066W gene taxon:4932 20010118 SGD
+SGD S000002224 IDP1 GO:0006537 SGD_REF:S000058126|PMID:9175438 TAS P NADP-dependent isocitrate dehydrogenase YDL066W gene taxon:4932 20010118 SGD
+SGD S000004164 IDP2 GO:0005829 SGD_REF:S000075624|PMID:15001388 IDA C NADP-dependent isocitrate dehydrogenase YLR174W gene taxon:4932 20050708 SGD
+SGD S000004164 IDP2 GO:0004450 SGD_REF:S000058126|PMID:9175438 TAS F NADP-dependent isocitrate dehydrogenase YLR174W gene taxon:4932 20010118 SGD
+SGD S000004164 IDP2 GO:0006102 SGD_REF:S000058126|PMID:9175438 TAS P NADP-dependent isocitrate dehydrogenase YLR174W gene taxon:4932 20010118 SGD
+SGD S000004164 IDP2 GO:0006537 SGD_REF:S000058126|PMID:9175438 TAS P NADP-dependent isocitrate dehydrogenase YLR174W gene taxon:4932 20010118 SGD
+SGD S000004954 IDP3 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C NADP-dependent isocitrate dehydrogenase YNL009W gene taxon:4932 20020507 SGD
+SGD S000004954 IDP3 GO:0005737 SGD_REF:S000075624|PMID:15001388 IDA C NADP-dependent isocitrate dehydrogenase YNL009W gene taxon:4932 20050708 SGD
+SGD S000004954 IDP3 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C NADP-dependent isocitrate dehydrogenase YNL009W gene taxon:4932 20040813 SGD
+SGD S000004954 IDP3 GO:0005777 SGD_REF:S000045074|PMID:9452501 TAS C NADP-dependent isocitrate dehydrogenase YNL009W gene taxon:4932 20050708 SGD
+SGD S000004954 IDP3 GO:0005777 SGD_REF:S000045074|PMID:9452501 IDA C NADP-dependent isocitrate dehydrogenase YNL009W gene taxon:4932 20050708 SGD
+SGD S000004954 IDP3 GO:0004450 SGD_REF:S000058126|PMID:9175438 TAS F NADP-dependent isocitrate dehydrogenase YNL009W gene taxon:4932 20010118 SGD
+SGD S000004954 IDP3 GO:0006102 SGD_REF:S000058126|PMID:9175438 TAS P NADP-dependent isocitrate dehydrogenase YNL009W gene taxon:4932 20010118 SGD
+SGD S000004954 IDP3 GO:0006635 SGD_REF:S000045074|PMID:9452501 IMP P NADP-dependent isocitrate dehydrogenase YNL009W gene taxon:4932 20021202 SGD
+SGD S000004954 IDP3 GO:0006740 SGD_REF:S000045074|PMID:9452501 TAS P NADP-dependent isocitrate dehydrogenase YNL009W gene taxon:4932 20021202 SGD
+SGD S000003682 IDS2 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YJL146W gene taxon:4932 20031028 SGD
+SGD S000003682 IDS2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YJL146W gene taxon:4932 20031028 SGD
+SGD S000003682 IDS2 GO:0005554 SGD_REF:S000069584 ND F YJL146W gene taxon:4932 20021209 SGD
+SGD S000003682 IDS2 GO:0007126 SGD_REF:S000043211|PMID:7565676 IMP P YJL146W gene taxon:4932 20010118 SGD
+SGD S000001881 IES1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YFL013C gene taxon:4932 20031028 SGD
+SGD S000001881 IES1 GO:0031011 SGD_REF:S000073963|PMID:12887900 IPI C YFL013C gene taxon:4932 20041004 SGD
+SGD S000001881 IES1 GO:0005554 SGD_REF:S000069584 ND F YFL013C gene taxon:4932 20021123 SGD
+SGD S000001881 IES1 GO:0006338 SGD_REF:S000073963|PMID:12887900 IPI P YFL013C gene taxon:4932 20031023 SGD
+SGD S000005159 IES2 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YNL215W gene taxon:4932 20031028 SGD
+SGD S000005159 IES2 GO:0005554 SGD_REF:S000069584 ND F YNL215W gene taxon:4932 20021007 SGD
+SGD S000005159 IES2 GO:0000004 SGD_REF:S000069584 ND P YNL215W gene taxon:4932 20021007 SGD
+SGD S000004042 IES3 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YLR052W gene taxon:4932 20031028 SGD
+SGD S000004042 IES3 GO:0031011 SGD_REF:S000073963|PMID:12887900 IPI C YLR052W gene taxon:4932 20041004 SGD
+SGD S000004042 IES3 GO:0005554 SGD_REF:S000069584 ND F YLR052W gene taxon:4932 20021123 SGD
+SGD S000004042 IES3 GO:0006338 SGD_REF:S000073963|PMID:12887900 IPI P YLR052W gene taxon:4932 20031023 SGD
+SGD S000005715 IES4 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YOR189W gene taxon:4932 20031028 SGD
+SGD S000005715 IES4 GO:0005554 SGD_REF:S000069584 ND F YOR189W gene taxon:4932 20021123 SGD
+SGD S000005715 IES4 GO:0000004 SGD_REF:S000069584 ND P YOR189W gene taxon:4932 20021123 SGD
+SGD S000000894 IES5 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YER092W gene taxon:4932 20031028 SGD
+SGD S000000894 IES5 GO:0005554 SGD_REF:S000069584 ND F YER092W gene taxon:4932 20021123 SGD
+SGD S000000894 IES5 GO:0000004 SGD_REF:S000069584 ND P YER092W gene taxon:4932 20021123 SGD
+SGD S000000770 IES6 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YEL044W gene taxon:4932 20031028 SGD
+SGD S000000770 IES6 GO:0005554 SGD_REF:S000069584 ND F YEL044W gene taxon:4932 20021123 SGD
+SGD S000000770 IES6 GO:0008152 SGD_REF:S000075216|PMID:14656964 TAS P YEL044W gene taxon:4932 20040315 SGD
+SGD S000000363 IFA38 GO:0005783 SGD_REF:S000071362|PMID:12087109 IDA C YBR159W gene taxon:4932 20021120 SGD
+SGD S000000363 IFA38 GO:0016021 SGD_REF:S000069482|PMID:11792704 ISS C YBR159W gene taxon:4932 20021120 SGD
+SGD S000000363 IFA38 GO:0045703 SGD_REF:S000069482|PMID:11792704 ISS F YBR159W gene taxon:4932 20021120 SGD
+SGD S000000363 IFA38 GO:0045703 SGD_REF:S000071362|PMID:12087109 IPI F YBR159W gene taxon:4932 20021120 SGD
+SGD S000000363 IFA38 GO:0045703 SGD_REF:S000071362|PMID:12087109 IMP F YBR159W gene taxon:4932 20021120 SGD
+SGD S000000363 IFA38 GO:0045703 SGD_REF:S000071362|PMID:12087109 IGI F YBR159W gene taxon:4932 20021120 SGD
+SGD S000000363 IFA38 GO:0030497 SGD_REF:S000071362|PMID:12087109 IGI P YBR159W gene taxon:4932 20021120 SGD
+SGD S000000363 IFA38 GO:0030497 SGD_REF:S000071362|PMID:12087109 IMP P YBR159W gene taxon:4932 20021120 SGD
+SGD S000000363 IFA38 GO:0030497 SGD_REF:S000071362|PMID:12087109 ISS P YBR159W gene taxon:4932 20021120 SGD
+SGD S000000363 IFA38 GO:0030497 SGD_REF:S000071362|PMID:12087109 IPI P YBR159W gene taxon:4932 20021120 SGD
+SGD S000004213 IFH1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YLR223C gene taxon:4932 20031028 SGD
+SGD S000004213 IFH1 GO:0005634 SGD_REF:S000077407|PMID:15466158 IDA C YLR223C gene taxon:4932 20041029 SGD
+SGD S000004213 IFH1 GO:0005730 SGD_REF:S000077407|PMID:15466158 IDA C YLR223C gene taxon:4932 20041029 SGD
+SGD S000004213 IFH1 GO:0003700 SGD_REF:S000077407|PMID:15466158 IGI F YLR223C gene taxon:4932 20041029 SGD
+SGD S000004213 IFH1 GO:0003700 SGD_REF:S000077407|PMID:15466158 IPI F YLR223C gene taxon:4932 20041029 SGD
+SGD S000004213 IFH1 GO:0006348 SGD_REF:S000047238|PMID:9755194 IMP P YLR223C gene taxon:4932 20010118 SGD
+SGD S000004213 IFH1 GO:0006364 SGD_REF:S000041723|PMID:7785326 IMP P YLR223C gene taxon:4932 20010118 SGD
+SGD S000004213 IFH1 GO:0006364 SGD_REF:S000041723|PMID:7785326 IGI P YLR223C gene taxon:4932 20010118 SGD
+SGD S000004213 IFH1 GO:0006383 SGD_REF:S000077407|PMID:15466158 IGI P YLR223C gene taxon:4932 20041029 SGD
+SGD S000004213 IFH1 GO:0006383 SGD_REF:S000077407|PMID:15466158 IPI P YLR223C gene taxon:4932 20041029 SGD
+SGD S000005383 IFM1 GO:0005739 SGD_REF:S000042316|PMID:1935960 IMP C mitochondrial initiation factor 2 YOL023W gene taxon:4932 20010118 SGD
+SGD S000005383 IFM1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C mitochondrial initiation factor 2 YOL023W gene taxon:4932 20040924 SGD
+SGD S000005383 IFM1 GO:0005739 SGD_REF:S000069459|PMID:11914276 IDA C mitochondrial initiation factor 2 YOL023W gene taxon:4932 20020507 SGD
+SGD S000005383 IFM1 GO:0003723 SGD_REF:S000073334|PMID:12729623 IDA F mitochondrial initiation factor 2 YOL023W gene taxon:4932 20030619 SGD
+SGD S000005383 IFM1 GO:0003743 SGD_REF:S000042316|PMID:1935960 ISS F mitochondrial initiation factor 2 YOL023W gene taxon:4932 20010118 SGD
+SGD S000005383 IFM1 GO:0003743 SGD_REF:S000042316|PMID:1935960 IMP F mitochondrial initiation factor 2 YOL023W gene taxon:4932 20010118 SGD
+SGD S000005383 IFM1 GO:0003924 SGD_REF:S000073334|PMID:12729623 IDA F mitochondrial initiation factor 2 YOL023W gene taxon:4932 20030619 SGD
+SGD S000005383 IFM1 GO:0006413 SGD_REF:S000042316|PMID:1935960 IMP P mitochondrial initiation factor 2 YOL023W gene taxon:4932 20010118 SGD
+SGD S000005383 IFM1 GO:0006413 SGD_REF:S000042316|PMID:1935960 ISS P mitochondrial initiation factor 2 YOL023W gene taxon:4932 20010118 SGD
+SGD S000005101 IGO1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YNL157W gene taxon:4932 20031028 SGD
+SGD S000005101 IGO1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YNL157W gene taxon:4932 20031028 SGD
+SGD S000005101 IGO1 GO:0005554 SGD_REF:S000069584 ND F YNL157W gene taxon:4932 20030203 SGD
+SGD S000005101 IGO1 GO:0000004 SGD_REF:S000069584 ND P YNL157W gene taxon:4932 20030203 SGD
+SGD S000007496 IGO2 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YHR132W-A gene taxon:4932 20031028 SGD
+SGD S000007496 IGO2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YHR132W-A gene taxon:4932 20031028 SGD
+SGD S000007496 IGO2 GO:0005554 SGD_REF:S000069584 ND F YHR132W-A gene taxon:4932 20030203 SGD
+SGD S000007496 IGO2 GO:0000004 SGD_REF:S000069584 ND P YHR132W-A gene taxon:4932 20030203 SGD
+SGD S000001230 IKI1 GO:0008023 SGD_REF:S000068795|PMID:11689709 IDA C YHR187W|ELP5|HAP2|TOT5 gene taxon:4932 20020918 SGD
+SGD S000001230 IKI1 GO:0016591 SGD_REF:S000069518|PMID:11929532 TAS C YHR187W|ELP5|HAP2|TOT5 gene taxon:4932 20020616 SGD
+SGD S000001230 IKI1 GO:0016944 SGD_REF:S000068795|PMID:11689709 IMP F YHR187W|ELP5|HAP2|TOT5 gene taxon:4932 20020918 SGD
+SGD S000001230 IKI1 GO:0016944 SGD_REF:S000068795|PMID:11689709 IPI F YHR187W|ELP5|HAP2|TOT5 gene taxon:4932 20020918 SGD
+SGD S000001230 IKI1 GO:0006357 SGD_REF:S000068795|PMID:11689709 IMP P YHR187W|ELP5|HAP2|TOT5 gene taxon:4932 20020918 SGD
+SGD S000004376 IKI3 GO:0008023 SGD_REF:S000068795|PMID:11689709 IDA C YLR384C|ELP1|TOT1 gene taxon:4932 20020918 SGD
+SGD S000004376 IKI3 GO:0016591 SGD_REF:S000060112|PMID:11296232 IDA C YLR384C|ELP1|TOT1 gene taxon:4932 20020616 SGD
+SGD S000004376 IKI3 GO:0004402 SGD_REF:S000069896|PMID:11994165 TAS F YLR384C|ELP1|TOT1 gene taxon:4932 20020616 SGD
+SGD S000004376 IKI3 GO:0016944 SGD_REF:S000068795|PMID:11689709 IMP F YLR384C|ELP1|TOT1 gene taxon:4932 20020918 SGD
+SGD S000004376 IKI3 GO:0016944 SGD_REF:S000068795|PMID:11689709 IPI F YLR384C|ELP1|TOT1 gene taxon:4932 20020918 SGD
+SGD S000004376 IKI3 GO:0006357 SGD_REF:S000068795|PMID:11689709 IMP P YLR384C|ELP1|TOT1 gene taxon:4932 20020918 SGD
+SGD S000003593 IKS1 GO:0008372 SGD_REF:S000069584 ND C YJL057C gene taxon:4932 20020930 SGD
+SGD S000003593 IKS1 GO:0005554 SGD_REF:S000069584 ND F YJL057C gene taxon:4932 20021126 SGD
+SGD S000003593 IKS1 GO:0000004 SGD_REF:S000069584 ND P YJL057C gene taxon:4932 20020930 SGD
+SGD S000003879 ILM1 GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YJR118C gene taxon:4932 20031028 SGD
+SGD S000003879 ILM1 GO:0005554 SGD_REF:S000069584 ND F YJR118C gene taxon:4932 20021211 SGD
+SGD S000003879 ILM1 GO:0000002 SGD_REF:S000056413|PMID:10628851 IMP P YJR118C gene taxon:4932 20050621 SGD
+SGD S000003879 ILM1 GO:0030447 SGD_REF:S000080384|PMID:15645503 IMP P YJR118C gene taxon:4932 20050621 SGD
+SGD S000000172 ILS1 GO:0005829 SGD_REF:S000063704|PMID:7619074 IDA C isoleucine-tRNA synthetase YBL076C gene taxon:4932 20030117 SGD
+SGD S000000172 ILS1 GO:0004822 SGD_REF:S000063704|PMID:7619074 IDA F isoleucine-tRNA synthetase YBL076C gene taxon:4932 20030117 SGD
+SGD S000000172 ILS1 GO:0006412 SGD_REF:S000063705|PMID:10588711 TAS P isoleucine-tRNA synthetase YBL076C gene taxon:4932 20021001 SGD
+SGD S000000888 ILV1 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C threonine deaminase YER086W|ISO1 gene taxon:4932 20031028 SGD
+SGD S000000888 ILV1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C threonine deaminase YER086W|ISO1 gene taxon:4932 20040924 SGD
+SGD S000000888 ILV1 GO:0004794 SGD_REF:S000042400|PMID:3289762 TAS F threonine deaminase YER086W|ISO1 gene taxon:4932 20030117 SGD
+SGD S000000888 ILV1 GO:0009082 SGD_REF:S000042400|PMID:3289762 TAS P threonine deaminase YER086W|ISO1 gene taxon:4932 20030117 SGD
+SGD S000004714 ILV2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C acetolactate synthase YMR108W|SMR1|THI1 gene taxon:4932 20040928 SGD
+SGD S000004714 ILV2 GO:0005948 SGD_REF:S000055379|PMID:2989783 ISS C acetolactate synthase YMR108W|SMR1|THI1 gene taxon:4932 20050125 SGD
+SGD S000004714 ILV2 GO:0005948 SGD_REF:S000044345|PMID:10213630 IDA C acetolactate synthase YMR108W|SMR1|THI1 gene taxon:4932 20050125 SGD
+SGD S000004714 ILV2 GO:0003984 SGD_REF:S000055379|PMID:2989783 ISS F acetolactate synthase YMR108W|SMR1|THI1 gene taxon:4932 20020211 SGD
+SGD S000004714 ILV2 GO:0003984 SGD_REF:S000044345|PMID:10213630 IDA F acetolactate synthase YMR108W|SMR1|THI1 gene taxon:4932 20030306 SGD
+SGD S000004714 ILV2 GO:0050660 SGD_REF:S000080897|PMID:15709745 IDA F acetolactate synthase YMR108W|SMR1|THI1 gene taxon:4932 20050307 SGD
+SGD S000004714 ILV2 GO:0009082 SGD_REF:S000048191|PMID:2406721 IDA P acetolactate synthase YMR108W|SMR1|THI1 gene taxon:4932 20020211 SGD
+SGD S000004714 ILV2 GO:0009082 SGD_REF:S000048191|PMID:2406721 IMP P acetolactate synthase YMR108W|SMR1|THI1 gene taxon:4932 20020211 SGD
+SGD S000003777 ILV3 GO:0005739 SGD_REF:S000072868|PMID:12626680 TAS C dihydroxyacid dehydratase YJR016C gene taxon:4932 20030415 SGD
+SGD S000003777 ILV3 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C dihydroxyacid dehydratase YJR016C gene taxon:4932 20040929 SGD
+SGD S000003777 ILV3 GO:0004160 SGD_REF:S000053423|PMID:8299945 TAS F dihydroxyacid dehydratase YJR016C gene taxon:4932 20020930 SGD
+SGD S000003777 ILV3 GO:0009082 SGD_REF:S000053423|PMID:8299945 TAS P dihydroxyacid dehydratase YJR016C gene taxon:4932 20020930 SGD
+SGD S000004347 ILV5 GO:0005739 SGD_REF:S000053359|PMID:10675346 TAS C acetohydroxyacid reductoisomerase YLR355C gene taxon:4932 20020819 SGD
+SGD S000004347 ILV5 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C acetohydroxyacid reductoisomerase YLR355C gene taxon:4932 20040928 SGD
+SGD S000004347 ILV5 GO:0042645 SGD_REF:S000050870|PMID:10869431 IDA C acetohydroxyacid reductoisomerase YLR355C gene taxon:4932 20050401 SGD
+SGD S000004347 ILV5 GO:0004455 SGD_REF:S000047200|PMID:7621838 TAS F acetohydroxyacid reductoisomerase YLR355C gene taxon:4932 20030113 SGD
+SGD S000004347 ILV5 GO:0000002 SGD_REF:S000047200|PMID:7621838 IMP P acetohydroxyacid reductoisomerase YLR355C gene taxon:4932 20030113 SGD
+SGD S000004347 ILV5 GO:0009082 SGD_REF:S000053359|PMID:10675346 TAS P acetohydroxyacid reductoisomerase YLR355C gene taxon:4932 20020819 SGD
+SGD S000000515 ILV6 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YCL009C gene taxon:4932 20040924 SGD
+SGD S000000515 ILV6 GO:0005948 SGD_REF:S000044345|PMID:10213630 IDA C YCL009C gene taxon:4932 20050125 SGD
+SGD S000000515 ILV6 GO:0042645 SGD_REF:S000080741|PMID:15692048 IDA C YCL009C gene taxon:4932 20050401 SGD
+SGD S000000515 ILV6 GO:0003984 SGD_REF:S000058005|PMID:8972574 IDA F YCL009C gene taxon:4932 20030117 SGD
+SGD S000000515 ILV6 GO:0030234 SGD_REF:S000058005|PMID:8972574 IDA F YCL009C gene taxon:4932 20030117 SGD
+SGD S000000515 ILV6 GO:0009082 SGD_REF:S000058005|PMID:8972574 IDA P YCL009C gene taxon:4932 20020211 SGD
+SGD S000000515 ILV6 GO:0009082 SGD_REF:S000058005|PMID:8972574 ISS P YCL009C gene taxon:4932 20020211 SGD
+SGD S000001259 IMD2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C IMP dehydrogenase homolog YHR216W|PUR5 gene taxon:4932 20031028 SGD
+SGD S000001259 IMD2 GO:0003938 SGD_REF:S000066045|PMID:11441018 TAS F IMP dehydrogenase homolog YHR216W|PUR5 gene taxon:4932 20020930 SGD
+SGD S000001259 IMD2 GO:0006183 SGD_REF:S000066045|PMID:11441018 TAS P IMP dehydrogenase homolog YHR216W|PUR5 gene taxon:4932 20020930 SGD
+SGD S000004424 IMD3 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C IMP dehydrogenase homolog YLR432W gene taxon:4932 20020507 SGD
+SGD S000004424 IMD3 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C IMP dehydrogenase homolog YLR432W gene taxon:4932 20031028 SGD
+SGD S000004424 IMD3 GO:0003938 SGD_REF:S000066045|PMID:11441018 TAS F IMP dehydrogenase homolog YLR432W gene taxon:4932 20020930 SGD
+SGD S000004424 IMD3 GO:0006183 SGD_REF:S000066045|PMID:11441018 TAS P IMP dehydrogenase homolog YLR432W gene taxon:4932 20020930 SGD
+SGD S000004520 IMD4 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C IMP dehydrogenase homolog YML056C gene taxon:4932 20031028 SGD
+SGD S000004520 IMD4 GO:0003938 SGD_REF:S000059166|PMID:11003640 ISS F IMP dehydrogenase homolog YML056C gene taxon:4932 20021203 SGD
+SGD S000004520 IMD4 GO:0000004 SGD_REF:S000069584 ND P IMP dehydrogenase homolog YML056C gene taxon:4932 20010301 SGD
+SGD S000003854 IME1 GO:0005634 SGD_REF:S000041975|PMID:8462841 IDA C YJR094C gene taxon:4932 20010118 SGD
+SGD S000003854 IME1 GO:0030528 SGD_REF:S000050626|PMID:8177171 TAS F YJR094C gene taxon:4932 20030311 SGD
+SGD S000003854 IME1 GO:0007126 SGD_REF:S000050626|PMID:8177171 TAS P YJR094C gene taxon:4932 20010118 SGD
+SGD S000003642 IME2 GO:0005634 SGD_REF:S000050275|PMID:7764269 IDA C YJL106W|SME1 gene taxon:4932 20020814 SGD
+SGD S000003642 IME2 GO:0004672 SGD_REF:S000050275|PMID:7764269 IDA F YJL106W|SME1 gene taxon:4932 20020814 SGD
+SGD S000003642 IME2 GO:0006468 SGD_REF:S000042283|PMID:9743499 TAS P YJL106W|SME1 gene taxon:4932 20030204 SGD
+SGD S000003642 IME2 GO:0040020 SGD_REF:S000041750|PMID:9003314 IMP P YJL106W|SME1 gene taxon:4932 20020814 SGD
+SGD S000003160 IME4 GO:0008372 SGD_REF:S000069584 ND C methyltransferase YGL192W|SPO8 gene taxon:4932 20021111 SGD
+SGD S000003160 IME4 GO:0008174 SGD_REF:S000071493|PMID:12384598 IDA F methyltransferase YGL192W|SPO8 gene taxon:4932 20021023 SGD
+SGD S000003160 IME4 GO:0008174 SGD_REF:S000071493|PMID:12384598 ISS F methyltransferase YGL192W|SPO8 gene taxon:4932 20021023 SGD
+SGD S000003160 IME4 GO:0008174 SGD_REF:S000071493|PMID:12384598 IMP F methyltransferase YGL192W|SPO8 gene taxon:4932 20021023 SGD
+SGD S000003160 IME4 GO:0007126 SGD_REF:S000039122|PMID:1545790 IMP P methyltransferase YGL192W|SPO8 gene taxon:4932 20021111 SGD
+SGD S000003160 IME4 GO:0016556 SGD_REF:S000071493|PMID:12384598 IMP P methyltransferase YGL192W|SPO8 gene taxon:4932 20021111 SGD
+SGD S000003160 IME4 GO:0016556 SGD_REF:S000071493|PMID:12384598 ISS P methyltransferase YGL192W|SPO8 gene taxon:4932 20021111 SGD
+SGD S000000642 IMG1 GO:0005762 SGD_REF:S000071753|PMID:12392552 IPI C mitochondrial ribosomal protein YCR046C gene taxon:4932 20040202 SGD
+SGD S000000642 IMG1 GO:0003735 SGD_REF:S000071753|PMID:12392552 IPI F mitochondrial ribosomal protein YCR046C gene taxon:4932 20040202 SGD
+SGD S000000642 IMG1 GO:0003735 SGD_REF:S000071753|PMID:12392552 ISS F mitochondrial ribosomal protein YCR046C gene taxon:4932 20040202 SGD
+SGD S000000642 IMG1 GO:0043037 SGD_REF:S000071753|PMID:12392552 IPI P mitochondrial ribosomal protein YCR046C gene taxon:4932 20040202 SGD
+SGD S000000642 IMG1 GO:0043037 SGD_REF:S000057913|PMID:8771712 IMP P mitochondrial ribosomal protein YCR046C gene taxon:4932 20040202 SGD
+SGD S000000667 IMG2 GO:0005762 SGD_REF:S000071753|PMID:12392552 IPI C YCR071C gene taxon:4932 20021209 SGD
+SGD S000000667 IMG2 GO:0003735 SGD_REF:S000071753|PMID:12392552 IPI F YCR071C gene taxon:4932 20021209 SGD
+SGD S000000667 IMG2 GO:0003735 SGD_REF:S000071753|PMID:12392552 ISS F YCR071C gene taxon:4932 20021209 SGD
+SGD S000000667 IMG2 GO:0043037 SGD_REF:S000071753|PMID:12392552 IC GO:0003735|GO:0005762 P YCR071C gene taxon:4932 20021209 SGD
+SGD S000004300 IMH1 GO:0005794 SGD_REF:S000076519|PMID:15077113 IDA C YLR309C|SYS3 gene taxon:4932 20050523 SGD
+SGD S000004300 IMH1 GO:0005829 SGD_REF:S000055301|PMID:9880327 IDA C YLR309C|SYS3 gene taxon:4932 20020926 SGD
+SGD S000004300 IMH1 GO:0005554 SGD_REF:S000069584 ND F YLR309C|SYS3 gene taxon:4932 20020926 SGD
+SGD S000004300 IMH1 GO:0016192 SGD_REF:S000055301|PMID:9880327 IMP P YLR309C|SYS3 gene taxon:4932 20020926 SGD
+SGD S000003899 IML1 GO:0000329 SGD_REF:S000074185|PMID:14562095 IDA C YJR138W gene taxon:4932 20031028 SGD
+SGD S000003899 IML1 GO:0005554 SGD_REF:S000069584 ND F YJR138W gene taxon:4932 20021211 SGD
+SGD S000003899 IML1 GO:0000004 SGD_REF:S000069584 ND P YJR138W gene taxon:4932 20020930 SGD
+SGD S000003618 IML2 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YJL082W gene taxon:4932 20031028 SGD
+SGD S000003618 IML2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YJL082W gene taxon:4932 20031028 SGD
+SGD S000003618 IML2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YJL082W gene taxon:4932 20040813 SGD
+SGD S000003618 IML2 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C YJL082W gene taxon:4932 20060317 SGD
+SGD S000003618 IML2 GO:0005554 SGD_REF:S000069584 ND F YJL082W gene taxon:4932 20021126 SGD
+SGD S000003618 IML2 GO:0000004 SGD_REF:S000069584 ND P YJL082W gene taxon:4932 20020930 SGD
+SGD S000000311 IML3 GO:0000942 SGD_REF:S000074151|PMID:12589047 IDA C YBR107C|MCM19 gene taxon:4932 20040910 SGD
+SGD S000000311 IML3 GO:0005554 SGD_REF:S000069584 ND F YBR107C|MCM19 gene taxon:4932 20051123 SGD
+SGD S000000311 IML3 GO:0007059 SGD_REF:S000060304|PMID:11361335 TAS P YBR107C|MCM19 gene taxon:4932 20020930 SGD
+SGD S000000311 IML3 GO:0030437 SGD_REF:S000080932|PMID:15241623 IMP P YBR107C|MCM19 gene taxon:4932 20051123 SGD
+SGD S000000311 IML3 GO:0045144 SGD_REF:S000080932|PMID:15241623 IMP P YBR107C|MCM19 gene taxon:4932 20051123 SGD
+SGD S000004758 IMP1 GO:0042720 SGD_REF:S000050587|PMID:8266095 IDA C inner membrane protease YMR150C|PET-TS2858 gene taxon:4932 20030430 SGD
+SGD S000004758 IMP1 GO:0004244 SGD_REF:S000056705|PMID:1991446 IDA F inner membrane protease YMR150C|PET-TS2858 gene taxon:4932 20050207 SGD
+SGD S000004758 IMP1 GO:0008233 SGD_REF:S000056705|PMID:1991446 IDA F inner membrane protease YMR150C|PET-TS2858 gene taxon:4932 20010118 SGD
+SGD S000004758 IMP1 GO:0006627 SGD_REF:S000056705|PMID:1991446 IDA P inner membrane protease YMR150C|PET-TS2858 gene taxon:4932 20010118 SGD
+SGD S000004638 IMP2 GO:0042720 SGD_REF:S000050587|PMID:8266095 IDA C protease YMR035W gene taxon:4932 20030430 SGD
+SGD S000004638 IMP2 GO:0004244 SGD_REF:S000056705|PMID:1991446 IDA F protease YMR035W gene taxon:4932 20050207 SGD
+SGD S000004638 IMP2 GO:0008233 SGD_REF:S000056705|PMID:1991446 IDA F protease YMR035W gene taxon:4932 20010118 SGD
+SGD S000004638 IMP2 GO:0006627 SGD_REF:S000056705|PMID:1991446 IDA P protease YMR035W gene taxon:4932 20010118 SGD
+SGD S000001416 IMP2' GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C transcription factor YIL154C|IMP2 gene taxon:4932 20031028 SGD
+SGD S000001416 IMP2' GO:0003713 SGD_REF:S000046369|PMID:8628275 IDA F transcription factor YIL154C|IMP2 gene taxon:4932 20030311 SGD
+SGD S000001416 IMP2' GO:0005975 SGD_REF:S000040254|PMID:1561839 IMP P transcription factor YIL154C|IMP2 gene taxon:4932 20010118 SGD
+SGD S000001416 IMP2' GO:0006281 SGD_REF:S000046369|PMID:8628275 IMP P transcription factor YIL154C|IMP2 gene taxon:4932 20010118 SGD
+SGD S000001191 IMP3 GO:0005732 SGD_REF:S000058443|PMID:10690410 TAS C U3 snoRNP protein YHR148W gene taxon:4932 20010118 SGD
+SGD S000001191 IMP3 GO:0005732 SGD_REF:S000070145|PMID:12068309 IDA C U3 snoRNP protein YHR148W gene taxon:4932 20020905 SGD
+SGD S000001191 IMP3 GO:0030532 SGD_REF:S000058443|PMID:10690410 TAS C U3 snoRNP protein YHR148W gene taxon:4932 20020219 SGD
+SGD S000001191 IMP3 GO:0030515 SGD_REF:S000045246|PMID:10409734 ISS F U3 snoRNP protein YHR148W gene taxon:4932 20030221 SGD
+SGD S000001191 IMP3 GO:0000154 SGD_REF:S000058443|PMID:10690410 TAS P U3 snoRNP protein YHR148W gene taxon:4932 20010118 SGD
+SGD S000001191 IMP3 GO:0006365 SGD_REF:S000058443|PMID:10690410 TAS P U3 snoRNP protein YHR148W gene taxon:4932 20010118 SGD
+SGD S000001191 IMP3 GO:0007046 SGD_REF:S000059203|PMID:11087857 TAS P U3 snoRNP protein YHR148W gene taxon:4932 20030116 SGD
+SGD S000001191 IMP3 GO:0030490 SGD_REF:S000070145|PMID:12068309 IPI P U3 snoRNP protein YHR148W gene taxon:4932 20020905 SGD
+SGD S000005019 IMP4 GO:0005732 SGD_REF:S000058443|PMID:10690410 TAS C U3 snoRNP protein YNL075W gene taxon:4932 20010118 SGD
+SGD S000005019 IMP4 GO:0005732 SGD_REF:S000070145|PMID:12068309 IPI C U3 snoRNP protein YNL075W gene taxon:4932 20030224 SGD
+SGD S000005019 IMP4 GO:0030532 SGD_REF:S000058443|PMID:10690410 TAS C U3 snoRNP protein YNL075W gene taxon:4932 20020219 SGD
+SGD S000005019 IMP4 GO:0042134 SGD_REF:S000069545|PMID:11864606 IPI F U3 snoRNP protein YNL075W gene taxon:4932 20030219 SGD
+SGD S000005019 IMP4 GO:0000154 SGD_REF:S000058443|PMID:10690410 TAS P U3 snoRNP protein YNL075W gene taxon:4932 20010118 SGD
+SGD S000005019 IMP4 GO:0006365 SGD_REF:S000058443|PMID:10690410 TAS P U3 snoRNP protein YNL075W gene taxon:4932 20010118 SGD
+SGD S000005019 IMP4 GO:0030490 SGD_REF:S000070145|PMID:12068309 IPI P U3 snoRNP protein YNL075W gene taxon:4932 20020905 SGD
+SGD S000006665 IMT1 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tM(CAU)O1 gene taxon:4932 20030507 SGD
+SGD S000006665 IMT1 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tM(CAU)O1 gene taxon:4932 20030507 SGD
+SGD S000006665 IMT1 GO:0006413 SGD_REF:S000073094|PMID:9159473 NAS P tM(CAU)O1 gene taxon:4932 20030507 SGD
+SGD S000006667 IMT2 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tM(CAU)P gene taxon:4932 20030507 SGD
+SGD S000006667 IMT2 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tM(CAU)P gene taxon:4932 20030507 SGD
+SGD S000006667 IMT2 GO:0006413 SGD_REF:S000073094|PMID:9159473 NAS P tM(CAU)P gene taxon:4932 20030507 SGD
+SGD S000006663 IMT3 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tM(CAU)J3 gene taxon:4932 20030507 SGD
+SGD S000006663 IMT3 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tM(CAU)J3 gene taxon:4932 20030507 SGD
+SGD S000006663 IMT3 GO:0006413 SGD_REF:S000073094|PMID:9159473 NAS P tM(CAU)J3 gene taxon:4932 20030507 SGD
+SGD S000006660 IMT4 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tM(CAU)E gene taxon:4932 20030507 SGD
+SGD S000006660 IMT4 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tM(CAU)E gene taxon:4932 20030507 SGD
+SGD S000006660 IMT4 GO:0006413 SGD_REF:S000073094|PMID:9159473 NAS P tM(CAU)E gene taxon:4932 20030507 SGD
+SGD S000002340 INH1 GO:0005753 SGD_REF:S000058444|PMID:10838056 TAS C ATPase inhibitor YDL181W gene taxon:4932 20010118 SGD
+SGD S000002340 INH1 GO:0004857 SGD_REF:S000071876|PMID:12167646 IDA F ATPase inhibitor YDL181W gene taxon:4932 20030730 SGD
+SGD S000002340 INH1 GO:0015986 SGD_REF:S000058444|PMID:10838056 TAS P ATPase inhibitor YDL181W gene taxon:4932 20010118 SGD
+SGD S000001088 INM1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YHR046C gene taxon:4932 20031028 SGD
+SGD S000001088 INM1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YHR046C gene taxon:4932 20031028 SGD
+SGD S000001088 INM1 GO:0008934 SGD_REF:S000044239|PMID:10096091 IDA F YHR046C gene taxon:4932 20030325 SGD
+SGD S000001088 INM1 GO:0008934 SGD_REF:S000044239|PMID:10096091 ISS F YHR046C gene taxon:4932 20030325 SGD
+SGD S000001088 INM1 GO:0046855 SGD_REF:S000054433|PMID:10844654 IDA P YHR046C gene taxon:4932 20050331 SGD
+SGD S000003689 INO1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C L-myo-inositol-1-phosphate synthase YJL153C|APR1 gene taxon:4932 20031028 SGD
+SGD S000003689 INO1 GO:0004512 SGD_REF:S000054021|PMID:7016881 IMP F L-myo-inositol-1-phosphate synthase YJL153C|APR1 gene taxon:4932 20021002 SGD
+SGD S000003689 INO1 GO:0006020 SGD_REF:S000041819|PMID:9370339 TAS P L-myo-inositol-1-phosphate synthase YJL153C|APR1 gene taxon:4932 20021001 SGD
+SGD S000002530 INO2 GO:0005634 SGD_REF:S000053264|PMID:8012448 IDA C helix-loop-helix protein YDR123C|DIE1|SCS1 gene taxon:4932 20021003 SGD
+SGD S000002530 INO2 GO:0003704 SGD_REF:S000052663|PMID:8125958 IMP F helix-loop-helix protein YDR123C|DIE1|SCS1 gene taxon:4932 20021003 SGD
+SGD S000002530 INO2 GO:0003704 SGD_REF:S000052663|PMID:8125958 IPI F helix-loop-helix protein YDR123C|DIE1|SCS1 gene taxon:4932 20021003 SGD
+SGD S000002530 INO2 GO:0008654 SGD_REF:S000052663|PMID:8125958 IMP P helix-loop-helix protein YDR123C|DIE1|SCS1 gene taxon:4932 20021003 SGD
+SGD S000002530 INO2 GO:0045944 SGD_REF:S000052663|PMID:8125958 IMP P helix-loop-helix protein YDR123C|DIE1|SCS1 gene taxon:4932 20021003 SGD
+SGD S000002530 INO2 GO:0045944 SGD_REF:S000052663|PMID:8125958 IPI P helix-loop-helix protein YDR123C|DIE1|SCS1 gene taxon:4932 20021003 SGD
+SGD S000005468 INO4 GO:0005634 SGD_REF:S000053926|PMID:8195172 IC GO:0003704 C basic helix-loop-helix (bHLH) protein YOL108C gene taxon:4932 20021105 SGD
+SGD S000005468 INO4 GO:0003677 SGD_REF:S000046557|PMID:7559640 IDA F basic helix-loop-helix (bHLH) protein YOL108C gene taxon:4932 20050117 SGD
+SGD S000005468 INO4 GO:0003704 SGD_REF:S000053926|PMID:8195172 IMP F basic helix-loop-helix (bHLH) protein YOL108C gene taxon:4932 20021105 SGD
+SGD S000005468 INO4 GO:0003704 SGD_REF:S000053926|PMID:8195172 IPI F basic helix-loop-helix (bHLH) protein YOL108C gene taxon:4932 20021105 SGD
+SGD S000005468 INO4 GO:0003704 SGD_REF:S000053926|PMID:8195172 ISS F basic helix-loop-helix (bHLH) protein YOL108C gene taxon:4932 20021105 SGD
+SGD S000005468 INO4 GO:0008654 SGD_REF:S000055942|PMID:2834106 IMP P basic helix-loop-helix (bHLH) protein YOL108C gene taxon:4932 20021105 SGD
+SGD S000005468 INO4 GO:0045944 SGD_REF:S000053926|PMID:8195172 IMP P basic helix-loop-helix (bHLH) protein YOL108C gene taxon:4932 20021105 SGD
+SGD S000005468 INO4 GO:0045944 SGD_REF:S000053926|PMID:8195172 ISS P basic helix-loop-helix (bHLH) protein YOL108C gene taxon:4932 20021105 SGD
+SGD S000005468 INO4 GO:0045944 SGD_REF:S000053926|PMID:8195172 IPI P basic helix-loop-helix (bHLH) protein YOL108C gene taxon:4932 20021105 SGD
+SGD S000003118 INO80 GO:0031011 SGD_REF:S000043526|PMID:10361278 IDA C YGL150C gene taxon:4932 20041004 SGD
+SGD S000003118 INO80 GO:0016887 SGD_REF:S000040657|PMID:10952318 IDA F YGL150C gene taxon:4932 20021011 SGD
+SGD S000003118 INO80 contributes_to GO:0043141 SGD_REF:S000040657|PMID:10952318 IDA F YGL150C gene taxon:4932 20060320 SGD
+SGD S000003118 INO80 GO:0006281 SGD_REF:S000040657|PMID:10952318 IDA P YGL150C gene taxon:4932 20021011 SGD
+SGD S000003118 INO80 GO:0006281 SGD_REF:S000040657|PMID:10952318 IMP P YGL150C gene taxon:4932 20021011 SGD
+SGD S000003118 INO80 GO:0006338 SGD_REF:S000040657|PMID:10952318 IDA P YGL150C gene taxon:4932 20021011 SGD
+SGD S000003118 INO80 GO:0006366 SGD_REF:S000040657|PMID:10952318 IDA P YGL150C gene taxon:4932 20021011 SGD
+SGD S000003118 INO80 GO:0006366 SGD_REF:S000040657|PMID:10952318 IMP P YGL150C gene taxon:4932 20021011 SGD
+SGD S000004817 INP1 GO:0005777 SGD_REF:S000074185|PMID:14562095 IDA C YMR204C gene taxon:4932 20031028 SGD
+SGD S000004817 INP1 GO:0005780 SGD_REF:S000081801|PMID:15928207 IDA C YMR204C gene taxon:4932 20050606 SGD
+SGD S000004817 INP1 GO:0005554 SGD_REF:S000069584 ND F YMR204C gene taxon:4932 20021126 SGD
+SGD S000004817 INP1 GO:0045033 SGD_REF:S000081801|PMID:15928207 IMP P YMR204C gene taxon:4932 20050606 SGD
+SGD S000004817 INP1 GO:0045033 SGD_REF:S000081801|PMID:15928207 IPI P YMR204C gene taxon:4932 20050606 SGD
+SGD S000001264 INP51 GO:0005624 SGD_REF:S000049648|PMID:9560389 IDA C phosphatidylinositol 4,5-bisphosphate 5-phosphatase YIL002C|SJL1 gene taxon:4932 20020730 SGD
+SGD S000001264 INP51 GO:0004445 SGD_REF:S000042276|PMID:9565610 IDA F phosphatidylinositol 4,5-bisphosphate 5-phosphatase YIL002C|SJL1 gene taxon:4932 20020730 SGD
+SGD S000001264 INP51 GO:0006897 SGD_REF:S000048805|PMID:9788876 IGI P phosphatidylinositol 4,5-bisphosphate 5-phosphatase YIL002C|SJL1 gene taxon:4932 20030424 SGD
+SGD S000001264 INP51 GO:0007047 SGD_REF:S000049648|PMID:9560389 IGI P phosphatidylinositol 4,5-bisphosphate 5-phosphatase YIL002C|SJL1 gene taxon:4932 20020730 SGD
+SGD S000001264 INP51 GO:0016311 SGD_REF:S000042276|PMID:9565610 IDA P phosphatidylinositol 4,5-bisphosphate 5-phosphatase YIL002C|SJL1 gene taxon:4932 20020730 SGD
+SGD S000001264 INP51 GO:0046856 SGD_REF:S000049648|PMID:9560389 IDA P phosphatidylinositol 4,5-bisphosphate 5-phosphatase YIL002C|SJL1 gene taxon:4932 20050331 SGD
+SGD S000001264 INP51 GO:0048017 SGD_REF:S000049648|PMID:9560389 TAS P phosphatidylinositol 4,5-bisphosphate 5-phosphatase YIL002C|SJL1 gene taxon:4932 20050524 SGD
+SGD S000005050 INP52 GO:0005624 SGD_REF:S000049648|PMID:9560389 IDA C inositol polyphosphate 5-phosphatase YNL106C|SJL2 gene taxon:4932 20020730 SGD
+SGD S000005050 INP52 GO:0030479 SGD_REF:S000059158|PMID:11094088 IDA C inositol polyphosphate 5-phosphatase YNL106C|SJL2 gene taxon:4932 20030424 SGD
+SGD S000005050 INP52 colocalizes_with GO:0030479 SGD_REF:S000081277|PMID:15798181 IDA C inositol polyphosphate 5-phosphatase YNL106C|SJL2 gene taxon:4932 20050415 SGD
+SGD S000005050 INP52 GO:0004445 SGD_REF:S000049648|PMID:9560389 ISS F inositol polyphosphate 5-phosphatase YNL106C|SJL2 gene taxon:4932 20020730 SGD
+SGD S000005050 INP52 GO:0006897 SGD_REF:S000048805|PMID:9788876 IGI P inositol polyphosphate 5-phosphatase YNL106C|SJL2 gene taxon:4932 20030424 SGD
+SGD S000005050 INP52 GO:0007047 SGD_REF:S000049648|PMID:9560389 IGI P inositol polyphosphate 5-phosphatase YNL106C|SJL2 gene taxon:4932 20020730 SGD
+SGD S000005050 INP52 GO:0046856 SGD_REF:S000049648|PMID:9560389 ISS P inositol polyphosphate 5-phosphatase YNL106C|SJL2 gene taxon:4932 20050331 SGD
+SGD S000005050 INP52 GO:0048017 SGD_REF:S000049648|PMID:9560389 TAS P inositol polyphosphate 5-phosphatase YNL106C|SJL2 gene taxon:4932 20050524 SGD
+SGD S000005635 INP53 GO:0005624 SGD_REF:S000049648|PMID:9560389 IDA C inositol polyphosphate 5-phosphatase YOR109W|SJL3|SOP2 gene taxon:4932 20020730 SGD
+SGD S000005635 INP53 GO:0030479 SGD_REF:S000059158|PMID:11094088 IDA C inositol polyphosphate 5-phosphatase YOR109W|SJL3|SOP2 gene taxon:4932 20030424 SGD
+SGD S000005635 INP53 GO:0004445 SGD_REF:S000049648|PMID:9560389 ISS F inositol polyphosphate 5-phosphatase YOR109W|SJL3|SOP2 gene taxon:4932 20020730 SGD
+SGD S000005635 INP53 GO:0006897 SGD_REF:S000048805|PMID:9788876 IGI P inositol polyphosphate 5-phosphatase YOR109W|SJL3|SOP2 gene taxon:4932 20030424 SGD
+SGD S000005635 INP53 GO:0007047 SGD_REF:S000049648|PMID:9560389 IMP P inositol polyphosphate 5-phosphatase YOR109W|SJL3|SOP2 gene taxon:4932 20020730 SGD
+SGD S000005635 INP53 GO:0046856 SGD_REF:S000049648|PMID:9560389 ISS P inositol polyphosphate 5-phosphatase YOR109W|SJL3|SOP2 gene taxon:4932 20050331 SGD
+SGD S000005635 INP53 GO:0048017 SGD_REF:S000049648|PMID:9560389 TAS P inositol polyphosphate 5-phosphatase YOR109W|SJL3|SOP2 gene taxon:4932 20050524 SGD
+SGD S000005426 INP54 GO:0005783 SGD_REF:S000060340|PMID:11116155 IDA C inositol polyphosphate 5-phosphatase YOL065C gene taxon:4932 20021001 SGD
+SGD S000005426 INP54 GO:0004445 SGD_REF:S000060340|PMID:11116155 TAS F inositol polyphosphate 5-phosphatase YOL065C gene taxon:4932 20030122 SGD
+SGD S000005426 INP54 GO:0006887 SGD_REF:S000060340|PMID:11116155 TAS P inositol polyphosphate 5-phosphatase YOL065C gene taxon:4932 20021001 SGD
+SGD S000005426 INP54 GO:0046856 SGD_REF:S000060340|PMID:11116155 TAS P inositol polyphosphate 5-phosphatase YOL065C gene taxon:4932 20050331 SGD
+SGD S000005426 INP54 GO:0048017 SGD_REF:S000060340|PMID:11116155 TAS P inositol polyphosphate 5-phosphatase YOL065C gene taxon:4932 20050524 SGD
+SGD S000004085 IOC2 GO:0016587 SGD_REF:S000072478|PMID:12482963 IPI SGD:S000000449 C YLR095C gene taxon:4932 20041020 SGD
+SGD S000004085 IOC2 GO:0005515 SGD_REF:S000072478|PMID:12482963 IDA F YLR095C gene taxon:4932 20030213 SGD
+SGD S000004085 IOC2 GO:0006338 SGD_REF:S000072478|PMID:12482963 IPI SGD:S000000449 P YLR095C gene taxon:4932 20030213 SGD
+SGD S000001909 IOC3 GO:0016587 SGD_REF:S000072478|PMID:12482963 IPI SGD:S000000449 C YFR013W gene taxon:4932 20041020 SGD
+SGD S000001909 IOC3 GO:0005515 SGD_REF:S000072478|PMID:12482963 IDA F YFR013W gene taxon:4932 20030213 SGD
+SGD S000001909 IOC3 GO:0006338 SGD_REF:S000071601|PMID:11805826 IPI P YFR013W gene taxon:4932 20021115 SGD
+SGD S000004647 IOC4 GO:0016587 SGD_REF:S000072478|PMID:12482963 IPI SGD:S000000449 C YMR044W gene taxon:4932 20041020 SGD
+SGD S000004647 IOC4 GO:0005515 SGD_REF:S000072478|PMID:12482963 IDA F YMR044W gene taxon:4932 20030213 SGD
+SGD S000004647 IOC4 GO:0006338 SGD_REF:S000072478|PMID:12482963 IPI SGD:S000000449 P YMR044W gene taxon:4932 20030213 SGD
+SGD S000001127 IPI1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YHR085W gene taxon:4932 20031028 SGD
+SGD S000001127 IPI1 GO:0005634 SGD_REF:S000075214|PMID:14690591 IDA C YHR085W gene taxon:4932 20040105 SGD
+SGD S000001127 IPI1 GO:0005654 SGD_REF:S000080956|PMID:15528184 IDA C YHR085W gene taxon:4932 20050310 SGD
+SGD S000001127 IPI1 GO:0005554 SGD_REF:S000069584 ND F YHR085W gene taxon:4932 20021025 SGD
+SGD S000001127 IPI1 GO:0000027 SGD_REF:S000080956|PMID:15528184 IMP P YHR085W gene taxon:4932 20050310 SGD
+SGD S000001127 IPI1 GO:0006364 SGD_REF:S000073209|PMID:12089522 IMP P YHR085W gene taxon:4932 20030530 SGD
+SGD S000001127 IPI1 GO:0006365 SGD_REF:S000074504|PMID:14759368 IMP P YHR085W gene taxon:4932 20040803 SGD
+SGD S000005126 IPI3 GO:0005634 SGD_REF:S000075214|PMID:14690591 IDA C YNL182C gene taxon:4932 20040105 SGD
+SGD S000005126 IPI3 GO:0005654 SGD_REF:S000080956|PMID:15528184 IDA C YNL182C gene taxon:4932 20050310 SGD
+SGD S000005126 IPI3 GO:0005554 SGD_REF:S000069584 ND F YNL182C gene taxon:4932 20021025 SGD
+SGD S000005126 IPI3 GO:0000027 SGD_REF:S000080956|PMID:15528184 IMP P YNL182C gene taxon:4932 20050310 SGD
+SGD S000005126 IPI3 GO:0006365 SGD_REF:S000074504|PMID:14759368 IMP P YNL182C gene taxon:4932 20040803 SGD
+SGD S000002723 IPK1 GO:0005634 SGD_REF:S000052483|PMID:10390371 IDA C inositol 1,3,4,5,6-pentakisphosphate 2-kinase YDR315C|GSL1 gene taxon:4932 20030213 SGD
+SGD S000002723 IPK1 GO:0004428 SGD_REF:S000052483|PMID:10390371 IDA F inositol 1,3,4,5,6-pentakisphosphate 2-kinase YDR315C|GSL1 gene taxon:4932 20020530 SGD
+SGD S000002723 IPK1 GO:0004428 SGD_REF:S000052483|PMID:10390371 IMP F inositol 1,3,4,5,6-pentakisphosphate 2-kinase YDR315C|GSL1 gene taxon:4932 20020530 SGD
+SGD S000002723 IPK1 GO:0006020 SGD_REF:S000052483|PMID:10390371 IDA P inositol 1,3,4,5,6-pentakisphosphate 2-kinase YDR315C|GSL1 gene taxon:4932 20020530 SGD
+SGD S000002723 IPK1 GO:0006020 SGD_REF:S000052483|PMID:10390371 IGI P inositol 1,3,4,5,6-pentakisphosphate 2-kinase YDR315C|GSL1 gene taxon:4932 20020530 SGD
+SGD S000002723 IPK1 GO:0006020 SGD_REF:S000052483|PMID:10390371 IMP P inositol 1,3,4,5,6-pentakisphosphate 2-kinase YDR315C|GSL1 gene taxon:4932 20020530 SGD
+SGD S000006130 IPL1 GO:0000778 SGD_REF:S000080960|PMID:11511347 IDA C protein kinase YPL209C|PAC15 gene taxon:4932 20050307 SGD
+SGD S000006130 IPL1 GO:0000778 SGD_REF:S000078515|PMID:12566427 IDA C protein kinase YPL209C|PAC15 gene taxon:4932 20050407 SGD
+SGD S000006130 IPL1 GO:0005819 SGD_REF:S000078515|PMID:12566427 IDA C protein kinase YPL209C|PAC15 gene taxon:4932 20050407 SGD
+SGD S000006130 IPL1 GO:0005828 SGD_REF:S000066223|PMID:11724818 IDA C protein kinase YPL209C|PAC15 gene taxon:4932 20020602 SGD
+SGD S000006130 IPL1 GO:0005876 SGD_REF:S000066223|PMID:11724818 IDA C protein kinase YPL209C|PAC15 gene taxon:4932 20020602 SGD
+SGD S000006130 IPL1 GO:0005876 SGD_REF:S000080960|PMID:11511347 IDA C protein kinase YPL209C|PAC15 gene taxon:4932 20050307 SGD
+SGD S000006130 IPL1 GO:0051233 SGD_REF:S000078515|PMID:12566427 IDA C protein kinase YPL209C|PAC15 gene taxon:4932 20050407 SGD
+SGD S000006130 IPL1 GO:0004672 SGD_REF:S000041165|PMID:10385519 TAS F protein kinase YPL209C|PAC15 gene taxon:4932 20030110 SGD
+SGD S000006130 IPL1 GO:0004672 SGD_REF:S000062008|PMID:10072382 IDA F protein kinase YPL209C|PAC15 gene taxon:4932 20040713 SGD
+SGD S000006130 IPL1 GO:0004672 SGD_REF:S000086680|PMID:16143104 IDA F protein kinase YPL209C|PAC15 gene taxon:4932 20051013 SGD
+SGD S000006130 IPL1 GO:0007059 SGD_REF:S000066223|PMID:11724818 TAS P protein kinase YPL209C|PAC15 gene taxon:4932 20020602 SGD
+SGD S000006130 IPL1 GO:0008608 SGD_REF:S000062008|PMID:10072382 IMP P protein kinase YPL209C|PAC15 gene taxon:4932 20040713 SGD
+SGD S000006130 IPL1 GO:0051228 SGD_REF:S000078515|PMID:12566427 IMP P protein kinase YPL209C|PAC15 gene taxon:4932 20050407 SGD
+SGD S000000215 IPP1 GO:0005829 SGD_REF:S000071851|PMID:12451180 TAS C inorganic pyrophosphatase YBR011C|PPA1 gene taxon:4932 20021215 SGD
+SGD S000000215 IPP1 GO:0004427 SGD_REF:S000057649|PMID:8224193 IDA F inorganic pyrophosphatase YBR011C|PPA1 gene taxon:4932 20030117 SGD
+SGD S000000215 IPP1 GO:0006796 SGD_REF:S000057649|PMID:8224193 IC GO:0004427 P inorganic pyrophosphatase YBR011C|PPA1 gene taxon:4932 20030117 SGD
+SGD S000002479 IPT1 GO:0005624 SGD_REF:S000050200|PMID:9368028 IDA C inositolphosphotransferase 1 YDR072C|KTI6|SYR4 gene taxon:4932 20020711 SGD
+SGD S000002479 IPT1 GO:0016772 SGD_REF:S000050200|PMID:9368028 IDA F inositolphosphotransferase 1 YDR072C|KTI6|SYR4 gene taxon:4932 20020711 SGD
+SGD S000002479 IPT1 GO:0006676 SGD_REF:S000050200|PMID:9368028 IDA P inositolphosphotransferase 1 YDR072C|KTI6|SYR4 gene taxon:4932 20020711 SGD
+SGD S000002479 IPT1 GO:0030148 SGD_REF:S000081208|PMID:15792805 IGI SGD:S000003375 P inositolphosphotransferase 1 YDR072C|KTI6|SYR4 gene taxon:4932 20050422 SGD
+SGD S000006163 IQG1 GO:0000142 SGD_REF:S000041005|PMID:10652251 IDA C YPL242C|CYK1 gene taxon:4932 20010118 SGD
+SGD S000006163 IQG1 GO:0008092 SGD_REF:S000052795|PMID:9950677 IPI F YPL242C|CYK1 gene taxon:4932 20010118 SGD
+SGD S000006163 IQG1 GO:0000910 SGD_REF:S000039417|PMID:9442111 IMP P YPL242C|CYK1 gene taxon:4932 20030507 SGD
+SGD S000006163 IQG1 GO:0006970 SGD_REF:S000041005|PMID:10652251 IMP P YPL242C|CYK1 gene taxon:4932 20010118 SGD
+SGD S000006163 IQG1 GO:0007015 SGD_REF:S000052795|PMID:9950677 IPI P YPL242C|CYK1 gene taxon:4932 20010118 SGD
+SGD S000000344 IRA1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C GTPase activating protein (GAP) YBR140C|GLC1|PPD1 gene taxon:4932 20040928 SGD
+SGD S000000344 IRA1 GO:0016020 SGD_REF:S000050069|PMID:1875942 IMP C GTPase activating protein (GAP) YBR140C|GLC1|PPD1 gene taxon:4932 20021112 SGD
+SGD S000000344 IRA1 GO:0016020 SGD_REF:S000050069|PMID:1875942 IPI C GTPase activating protein (GAP) YBR140C|GLC1|PPD1 gene taxon:4932 20021112 SGD
+SGD S000000344 IRA1 GO:0005099 SGD_REF:S000050069|PMID:1875942 TAS F GTPase activating protein (GAP) YBR140C|GLC1|PPD1 gene taxon:4932 20010118 SGD
+SGD S000000344 IRA1 GO:0007265 SGD_REF:S000055180|PMID:2540426 IMP P GTPase activating protein (GAP) YBR140C|GLC1|PPD1 gene taxon:4932 20010118 SGD
+SGD S000000344 IRA1 GO:0030437 SGD_REF:S000055180|PMID:2540426 IMP P GTPase activating protein (GAP) YBR140C|GLC1|PPD1 gene taxon:4932 20010118 SGD
+SGD S000005441 IRA2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C GTPase activating protein, highly homologous to Ira1p, neurofibromin homolog YOL081W|CCS1|GLC4 gene taxon:4932 20031028 SGD
+SGD S000005441 IRA2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C GTPase activating protein, highly homologous to Ira1p, neurofibromin homolog YOL081W|CCS1|GLC4 gene taxon:4932 20040813 SGD
+SGD S000005441 IRA2 GO:0005099 SGD_REF:S000051668|PMID:7577970 IDA F GTPase activating protein, highly homologous to Ira1p, neurofibromin homolog YOL081W|CCS1|GLC4 gene taxon:4932 20020807 SGD
+SGD S000005441 IRA2 GO:0007265 SGD_REF:S000047724|PMID:2164637 IMP P GTPase activating protein, highly homologous to Ira1p, neurofibromin homolog YOL081W|CCS1|GLC4 gene taxon:4932 20020807 SGD
+SGD S000005375 IRC10 GO:0008372 SGD_REF:S000069584 ND C YOL015W gene taxon:4932 20021126 SGD
+SGD S000005375 IRC10 GO:0005554 SGD_REF:S000069584 ND F YOL015W gene taxon:4932 20021126 SGD
+SGD S000005375 IRC10 GO:0000004 SGD_REF:S000069584 ND P YOL015W gene taxon:4932 20021126 SGD
+SGD S000002740 IRC3 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YDR332W gene taxon:4932 20031028 SGD
+SGD S000002740 IRC3 GO:0004386 SGD_REF:S000039134|PMID:10077188 ISS F YDR332W gene taxon:4932 20011205 SGD
+SGD S000002740 IRC3 GO:0000004 SGD_REF:S000069584 ND P YDR332W gene taxon:4932 20011205 SGD
+SGD S000002948 IRC4 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YDR540C gene taxon:4932 20031028 SGD
+SGD S000002948 IRC4 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDR540C gene taxon:4932 20031028 SGD
+SGD S000002948 IRC4 GO:0005554 SGD_REF:S000069584 ND F YDR540C gene taxon:4932 20021126 SGD
+SGD S000002948 IRC4 GO:0000004 SGD_REF:S000069584 ND P YDR540C gene taxon:4932 20021126 SGD
+SGD S000001934 IRC5 GO:0008372 SGD_REF:S000069584 ND C YFR038W gene taxon:4932 20011205 SGD
+SGD S000001934 IRC5 GO:0004386 SGD_REF:S000039134|PMID:10077188 ISS F YFR038W gene taxon:4932 20011205 SGD
+SGD S000001934 IRC5 GO:0000004 SGD_REF:S000069584 ND P YFR038W gene taxon:4932 20011205 SGD
+SGD S000001939 IRC6 GO:0008372 SGD_REF:S000069584 ND C YFR043C gene taxon:4932 20021126 SGD
+SGD S000001939 IRC6 GO:0005554 SGD_REF:S000069584 ND F YFR043C gene taxon:4932 20021126 SGD
+SGD S000001939 IRC6 GO:0000004 SGD_REF:S000069584 ND P YFR043C gene taxon:4932 20021126 SGD
+SGD S000001952 IRC7 GO:0008372 SGD_REF:S000069584 ND C YFR055W gene taxon:4932 20021119 SGD
+SGD S000001952 IRC7 GO:0004121 SGD_REF:S000059097|PMID:10922376 ISS F YFR055W gene taxon:4932 20030207 SGD
+SGD S000001952 IRC7 GO:0006790 SGD_REF:S000039910|PMID:10821189 ISS P YFR055W gene taxon:4932 20030530 SGD
+SGD S000001952 IRC7 GO:0006878 SGD_REF:S000059097|PMID:10922376 IEP P YFR055W gene taxon:4932 20021002 SGD
+SGD S000003587 IRC8 GO:0005934 SGD_REF:S000074060|PMID:13679573 IDA C YJL051W gene taxon:4932 20040115 SGD
+SGD S000003587 IRC8 GO:0005554 SGD_REF:S000069584 ND F YJL051W gene taxon:4932 20030421 SGD
+SGD S000003587 IRC8 GO:0000004 SGD_REF:S000069584 ND P YJL051W gene taxon:4932 20030421 SGD
+SGD S000001121 IRE1 GO:0005635 SGD_REF:S000048580|PMID:10346810 TAS C endoribonuclease, serine-threonine kinase, transmembrane protein YHR079C|ERN1 gene taxon:4932 20010118 SGD
+SGD S000001121 IRE1 GO:0005789 SGD_REF:S000048580|PMID:10346810 TAS C endoribonuclease, serine-threonine kinase, transmembrane protein YHR079C|ERN1 gene taxon:4932 20010118 SGD
+SGD S000001121 IRE1 GO:0004521 SGD_REF:S000048580|PMID:10346810 TAS F endoribonuclease, serine-threonine kinase, transmembrane protein YHR079C|ERN1 gene taxon:4932 20010118 SGD
+SGD S000001121 IRE1 GO:0004674 SGD_REF:S000057870|PMID:8663458 IDA F endoribonuclease, serine-threonine kinase, transmembrane protein YHR079C|ERN1 gene taxon:4932 20030213 SGD
+SGD S000001121 IRE1 GO:0006020 SGD_REF:S000048580|PMID:10346810 TAS P endoribonuclease, serine-threonine kinase, transmembrane protein YHR079C|ERN1 gene taxon:4932 20010118 SGD
+SGD S000001121 IRE1 GO:0006468 SGD_REF:S000057870|PMID:8663458 IDA P endoribonuclease, serine-threonine kinase, transmembrane protein YHR079C|ERN1 gene taxon:4932 20030213 SGD
+SGD S000001121 IRE1 GO:0006987 SGD_REF:S000048580|PMID:10346810 TAS P endoribonuclease, serine-threonine kinase, transmembrane protein YHR079C|ERN1 gene taxon:4932 20010118 SGD
+SGD S000001121 IRE1 GO:0030969 SGD_REF:S000048580|PMID:10346810 TAS P endoribonuclease, serine-threonine kinase, transmembrane protein YHR079C|ERN1 gene taxon:4932 20040722 SGD
+SGD S000001288 IRR1 GO:0000798 SGD_REF:S000049776|PMID:9990856 IPI C cohesin complex subunit YIL026C|SCC3 gene taxon:4932 20010118 SGD
+SGD S000001288 IRR1 GO:0000798 SGD_REF:S000049776|PMID:9990856 IDA C cohesin complex subunit YIL026C|SCC3 gene taxon:4932 20010118 SGD
+SGD S000001288 IRR1 GO:0005634 SGD_REF:S000042266|PMID:10028182 IDA C cohesin complex subunit YIL026C|SCC3 gene taxon:4932 20051024 SGD
+SGD S000001288 IRR1 GO:0005515 SGD_REF:S000070010|PMID:11983169 IDA F cohesin complex subunit YIL026C|SCC3 gene taxon:4932 20021205 SGD
+SGD S000001288 IRR1 GO:0000755 SGD_REF:S000042266|PMID:10028182 IMP P cohesin complex subunit YIL026C|SCC3 gene taxon:4932 20021206 SGD
+SGD S000001288 IRR1 GO:0007064 SGD_REF:S000049776|PMID:9990856 IMP P cohesin complex subunit YIL026C|SCC3 gene taxon:4932 20010118 SGD
+SGD S000001288 IRR1 GO:0009847 SGD_REF:S000042266|PMID:10028182 IMP P cohesin complex subunit YIL026C|SCC3 gene taxon:4932 20010118 SGD
+SGD S000001727 IRS4 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YKR019C gene taxon:4932 20040813 SGD
+SGD S000001727 IRS4 GO:0005554 SGD_REF:S000069584 ND F YKR019C gene taxon:4932 20021211 SGD
+SGD S000001727 IRS4 GO:0000183 SGD_REF:S000054483|PMID:10082585 IMP P YKR019C gene taxon:4932 20021211 SGD
+SGD S000001727 IRS4 GO:0007047 SGD_REF:S000077163|PMID:15265867 IGI P YKR019C gene taxon:4932 20041004 SGD
+SGD S000001727 IRS4 GO:0048017 SGD_REF:S000077163|PMID:15265867 IGI P YKR019C gene taxon:4932 20050524 SGD
+SGD S000003950 ISA1 GO:0005759 SGD_REF:S000043306|PMID:10805735 IDA C YLL027W gene taxon:4932 20010118 SGD
+SGD S000003950 ISA1 GO:0005554 SGD_REF:S000069584 ND F YLL027W gene taxon:4932 20010119 SGD
+SGD S000003950 ISA1 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P YLL027W gene taxon:4932 20060227 SGD
+SGD S000003950 ISA1 GO:0006826 SGD_REF:S000043306|PMID:10805735 IGI P YLL027W gene taxon:4932 20010118 SGD
+SGD S000003950 ISA1 GO:0006826 SGD_REF:S000043306|PMID:10805735 ISS P YLL027W gene taxon:4932 20010118 SGD
+SGD S000006271 ISA2 GO:0005758 SGD_REF:S000043306|PMID:10805735 IDA C YPR067W gene taxon:4932 20010118 SGD
+SGD S000006271 ISA2 GO:0005554 SGD_REF:S000069584 ND F YPR067W gene taxon:4932 20010119 SGD
+SGD S000006271 ISA2 GO:0006826 SGD_REF:S000043306|PMID:10805735 IGI P YPR067W gene taxon:4932 20010118 SGD
+SGD S000006271 ISA2 GO:0006826 SGD_REF:S000043306|PMID:10805735 ISS P YPR067W gene taxon:4932 20010118 SGD
+SGD S000000821 ISC1 GO:0005739 SGD_REF:S000075684|PMID:14699160 IDA C ISC1 encodes phospholipase C type enzyme which hydrolyzes inositolphosphosphingolipids (IPC, MIPC, M(IP)2C) as well as sphingomyelin. YER019W gene taxon:4932 20041027 SGD
+SGD S000000821 ISC1 GO:0005783 SGD_REF:S000075684|PMID:14699160 IDA C ISC1 encodes phospholipase C type enzyme which hydrolyzes inositolphosphosphingolipids (IPC, MIPC, M(IP)2C) as well as sphingomyelin. YER019W gene taxon:4932 20041027 SGD
+SGD S000000821 ISC1 GO:0004629 SGD_REF:S000059300|PMID:11006294 IDA F ISC1 encodes phospholipase C type enzyme which hydrolyzes inositolphosphosphingolipids (IPC, MIPC, M(IP)2C) as well as sphingomyelin. YER019W gene taxon:4932 20021108 SGD
+SGD S000000821 ISC1 GO:0009651 SGD_REF:S000070403|PMID:12180980 IMP P ISC1 encodes phospholipase C type enzyme which hydrolyzes inositolphosphosphingolipids (IPC, MIPC, M(IP)2C) as well as sphingomyelin. YER019W gene taxon:4932 20021108 SGD
+SGD S000000821 ISC1 GO:0030149 SGD_REF:S000059300|PMID:11006294 IDA P ISC1 encodes phospholipase C type enzyme which hydrolyzes inositolphosphosphingolipids (IPC, MIPC, M(IP)2C) as well as sphingomyelin. YER019W gene taxon:4932 20021108 SGD
+SGD S000000982 ISC10 GO:0008372 SGD_REF:S000069584 ND C YER180C gene taxon:4932 20021001 SGD
+SGD S000000982 ISC10 GO:0005554 SGD_REF:S000069584 ND F YER180C gene taxon:4932 20021211 SGD
+SGD S000000982 ISC10 GO:0030435 SGD_REF:S000041986|PMID:8455558 IMP P YER180C gene taxon:4932 20050620 SGD
+SGD S000007237 ISD11 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YER048W-A gene taxon:4932 20031028 SGD
+SGD S000007237 ISD11 GO:0005759 SGD_REF:S000113860|PMID:16341090 IDA C YER048W-A gene taxon:4932 20060119 SGD
+SGD S000007237 ISD11 GO:0031314 SGD_REF:S000113860|PMID:16341090 IDA C YER048W-A gene taxon:4932 20060119 SGD
+SGD S000007237 ISD11 GO:0005554 SGD_REF:S000069584 ND F YER048W-A gene taxon:4932 20060119 SGD
+SGD S000007237 ISD11 GO:0016226 SGD_REF:S000113860|PMID:16341090 IMP P YER048W-A gene taxon:4932 20060119 SGD
+SGD S000007237 ISD11 GO:0016226 SGD_REF:S000113860|PMID:16341090 IPI SGD:S000000522 P YER048W-A gene taxon:4932 20060119 SGD
+SGD S000004686 ISF1 GO:0008372 SGD_REF:S000069584 ND C YMR081C|MBR3 gene taxon:4932 20020815 SGD
+SGD S000004686 ISF1 GO:0005554 SGD_REF:S000069584 ND F YMR081C|MBR3 gene taxon:4932 20020815 SGD
+SGD S000004686 ISF1 GO:0009060 SGD_REF:S000052499|PMID:8208248 IGI P YMR081C|MBR3 gene taxon:4932 20020930 SGD
+SGD S000005961 ISM1 GO:0005739 SGD_REF:S000047144|PMID:7607232 IMP C isoleucine-tRNA ligase YPL040C gene taxon:4932 20021028 SGD
+SGD S000005961 ISM1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C isoleucine-tRNA ligase YPL040C gene taxon:4932 20040928 SGD
+SGD S000005961 ISM1 GO:0004822 SGD_REF:S000047144|PMID:7607232 ISS F isoleucine-tRNA ligase YPL040C gene taxon:4932 20021001 SGD
+SGD S000005961 ISM1 GO:0004822 SGD_REF:S000047144|PMID:7607232 IMP F isoleucine-tRNA ligase YPL040C gene taxon:4932 20021001 SGD
+SGD S000005961 ISM1 GO:0006412 SGD_REF:S000047144|PMID:7607232 IMP P isoleucine-tRNA ligase YPL040C gene taxon:4932 20021028 SGD
+SGD S000005961 ISM1 GO:0006412 SGD_REF:S000047144|PMID:7607232 ISS P isoleucine-tRNA ligase YPL040C gene taxon:4932 20021028 SGD
+SGD S000005961 ISM1 GO:0006428 SGD_REF:S000047144|PMID:7607232 IMP P isoleucine-tRNA ligase YPL040C gene taxon:4932 20021028 SGD
+SGD S000005961 ISM1 GO:0006428 SGD_REF:S000047144|PMID:7607232 ISS P isoleucine-tRNA ligase YPL040C gene taxon:4932 20021028 SGD
+SGD S000005681 ISN1 GO:0008372 SGD_REF:S000069584 ND C IMP 5'-Nucleotidase YOR155C gene taxon:4932 20030205 SGD
+SGD S000005681 ISN1 GO:0050483 SGD_REF:S000073207|PMID:12735798 IDA F IMP 5'-Nucleotidase YOR155C gene taxon:4932 20040401 SGD
+SGD S000005681 ISN1 GO:0006190 SGD_REF:S000073207|PMID:12735798 IMP P IMP 5'-Nucleotidase YOR155C gene taxon:4932 20040401 SGD
+SGD S000006310 ISR1 GO:0008372 SGD_REF:S000069584 ND C protein kinase YPR106W gene taxon:4932 20021001 SGD
+SGD S000006310 ISR1 GO:0004672 SGD_REF:S000046620|PMID:9720220 ISS F protein kinase YPR106W gene taxon:4932 20021001 SGD
+SGD S000006310 ISR1 GO:0000004 SGD_REF:S000069584 ND P protein kinase YPR106W gene taxon:4932 20021001 SGD
+SGD S000005209 IST1 GO:0005768 SGD_REF:S000074185|PMID:14562095 IDA C YNL265C gene taxon:4932 20031028 SGD
+SGD S000005209 IST1 GO:0005554 SGD_REF:S000069584 ND F YNL265C gene taxon:4932 20060317 SGD
+SGD S000005209 IST1 GO:0006412 SGD_REF:S000074191|PMID:14566057 RCA P YNL265C gene taxon:4932 20050608 SGD
+SGD S000000290 IST2 GO:0005886 SGD_REF:S000059701|PMID:11030653 IDA C YBR086C gene taxon:4932 20031030 SGD
+SGD S000000290 IST2 GO:0005933 SGD_REF:S000059701|PMID:11030653 IDA C YBR086C gene taxon:4932 20031030 SGD
+SGD S000000290 IST2 GO:0005554 SGD_REF:S000069584 ND F YBR086C gene taxon:4932 20010215 SGD
+SGD S000000290 IST2 GO:0006970 SGD_REF:S000071522|PMID:12362983 TAS P YBR086C gene taxon:4932 20021114 SGD
+SGD S000001444 IST3 GO:0005686 SGD_REF:S000069986|PMID:11804584 IDA C YIR005W|SNU17 gene taxon:4932 20020621 SGD
+SGD S000001444 IST3 GO:0031202 SGD_REF:S000060357|PMID:11287609 IDA F YIR005W|SNU17 gene taxon:4932 20021003 SGD
+SGD S000001444 IST3 GO:0000245 SGD_REF:S000060357|PMID:11287609 IMP P YIR005W|SNU17 gene taxon:4932 20020930 SGD
+SGD S000001444 IST3 GO:0000398 SGD_REF:S000080993|PMID:15565172 IDA P YIR005W|SNU17 gene taxon:4932 20051006 SGD
+SGD S000001444 IST3 GO:0006406 SGD_REF:S000080993|PMID:15565172 IMP P YIR005W|SNU17 gene taxon:4932 20051006 SGD
+SGD S000006056 ISU1 GO:0005739 SGD_REF:S000069459|PMID:11914276 IDA C YPL135W|NUA1 gene taxon:4932 20020507 SGD
+SGD S000006056 ISU1 GO:0005759 SGD_REF:S000045090|PMID:10468587 IDA C YPL135W|NUA1 gene taxon:4932 20010118 SGD
+SGD S000006056 ISU1 GO:0005759 SGD_REF:S000059064|PMID:15143178 IDA C YPL135W|NUA1 gene taxon:4932 20050422 SGD
+SGD S000006056 ISU1 GO:0005515 SGD_REF:S000068798|PMID:12970193 IDA F YPL135W|NUA1 gene taxon:4932 20040414 SGD
+SGD S000006056 ISU1 GO:0006879 SGD_REF:S000045090|PMID:10468587 IMP P YPL135W|NUA1 gene taxon:4932 20010118 SGD
+SGD S000006056 ISU1 GO:0006879 SGD_REF:S000045090|PMID:10468587 ISS P YPL135W|NUA1 gene taxon:4932 20010118 SGD
+SGD S000006056 ISU1 GO:0016226 SGD_REF:S000041686|PMID:10588895 IMP P YPL135W|NUA1 gene taxon:4932 20021209 SGD
+SGD S000006056 ISU1 GO:0016226 SGD_REF:S000041686|PMID:10588895 ISS P YPL135W|NUA1 gene taxon:4932 20021209 SGD
+SGD S000006056 ISU1 GO:0016226 SGD_REF:S000059064|PMID:15143178 IMP P YPL135W|NUA1 gene taxon:4932 20050422 SGD
+SGD S000005752 ISU2 GO:0005759 SGD_REF:S000045090|PMID:10468587 IDA C YOR226C|NUA2 gene taxon:4932 20010118 SGD
+SGD S000005752 ISU2 GO:0005759 SGD_REF:S000059064|PMID:15143178 IDA C YOR226C|NUA2 gene taxon:4932 20050422 SGD
+SGD S000005752 ISU2 GO:0005554 SGD_REF:S000069584 ND F YOR226C|NUA2 gene taxon:4932 20021209 SGD
+SGD S000005752 ISU2 GO:0006879 SGD_REF:S000045090|PMID:10468587 IMP P YOR226C|NUA2 gene taxon:4932 20010118 SGD
+SGD S000005752 ISU2 GO:0006879 SGD_REF:S000045090|PMID:10468587 ISS P YOR226C|NUA2 gene taxon:4932 20010118 SGD
+SGD S000005752 ISU2 GO:0016226 SGD_REF:S000041686|PMID:10588895 IMP P YOR226C|NUA2 gene taxon:4932 20021209 SGD
+SGD S000005752 ISU2 GO:0016226 SGD_REF:S000059064|PMID:15143178 IMP P YOR226C|NUA2 gene taxon:4932 20050422 SGD
+SGD S000005752 ISU2 GO:0016226 SGD_REF:S000041686|PMID:10588895 ISS P YOR226C|NUA2 gene taxon:4932 20021209 SGD
+SGD S000000449 ISW1 GO:0016587 SGD_REF:S000072478|PMID:12482963 IPI C ATPase component of a four subunit chromatin remodeling complex YBR245C|SGN2 gene taxon:4932 20041020 SGD
+SGD S000000449 ISW1 GO:0016887 SGD_REF:S000060136|PMID:11238381 ISS F ATPase component of a four subunit chromatin remodeling complex YBR245C|SGN2 gene taxon:4932 20021001 SGD
+SGD S000000449 ISW1 GO:0016887 SGD_REF:S000060136|PMID:11238381 TAS F ATPase component of a four subunit chromatin remodeling complex YBR245C|SGN2 gene taxon:4932 20021001 SGD
+SGD S000000449 ISW1 GO:0006338 SGD_REF:S000060136|PMID:11238381 IGI P ATPase component of a four subunit chromatin remodeling complex YBR245C|SGN2 gene taxon:4932 20021001 SGD
+SGD S000000449 ISW1 GO:0006338 SGD_REF:S000060136|PMID:11238381 IPI P ATPase component of a four subunit chromatin remodeling complex YBR245C|SGN2 gene taxon:4932 20021001 SGD
+SGD S000000449 ISW1 GO:0006338 SGD_REF:S000060136|PMID:11238381 IMP P ATPase component of a four subunit chromatin remodeling complex YBR245C|SGN2 gene taxon:4932 20021001 SGD
+SGD S000000449 ISW1 GO:0006354 SGD_REF:S000082344|PMID:15949446 IDA P ATPase component of a four subunit chromatin remodeling complex YBR245C|SGN2 gene taxon:4932 20051107 SGD
+SGD S000000449 ISW1 GO:0006354 SGD_REF:S000082344|PMID:15949446 IMP P ATPase component of a four subunit chromatin remodeling complex YBR245C|SGN2 gene taxon:4932 20051107 SGD
+SGD S000005831 ISW2 GO:0005634 SGD_REF:S000060136|PMID:11238381 IPI C ATPase component of a two subunit chromatin remodeling complex YOR304W gene taxon:4932 20021001 SGD
+SGD S000005831 ISW2 GO:0008623 SGD_REF:S000075426|PMID:14673157 IPI C ATPase component of a two subunit chromatin remodeling complex YOR304W gene taxon:4932 20041031 SGD
+SGD S000005831 ISW2 GO:0008623 SGD_REF:S000075426|PMID:14673157 ISS C ATPase component of a two subunit chromatin remodeling complex YOR304W gene taxon:4932 20041031 SGD
+SGD S000005831 ISW2 GO:0016887 SGD_REF:S000060136|PMID:11238381 ISS F ATPase component of a two subunit chromatin remodeling complex YOR304W gene taxon:4932 20021001 SGD
+SGD S000005831 ISW2 GO:0016887 SGD_REF:S000060136|PMID:11238381 TAS F ATPase component of a two subunit chromatin remodeling complex YOR304W gene taxon:4932 20021001 SGD
+SGD S000005831 ISW2 GO:0006338 SGD_REF:S000060136|PMID:11238381 IGI P ATPase component of a two subunit chromatin remodeling complex YOR304W gene taxon:4932 20021001 SGD
+SGD S000005831 ISW2 GO:0006338 SGD_REF:S000060136|PMID:11238381 IPI P ATPase component of a two subunit chromatin remodeling complex YOR304W gene taxon:4932 20021001 SGD
+SGD S000005831 ISW2 GO:0006338 SGD_REF:S000060136|PMID:11238381 IMP P ATPase component of a two subunit chromatin remodeling complex YOR304W gene taxon:4932 20021001 SGD
+SGD S000005831 ISW2 GO:0006348 SGD_REF:S000075426|PMID:14673157 IMP P ATPase component of a two subunit chromatin remodeling complex YOR304W gene taxon:4932 20040210 SGD
+SGD S000005831 ISW2 GO:0016584 SGD_REF:S000076511|PMID:15116071 IDA P ATPase component of a two subunit chromatin remodeling complex YOR304W gene taxon:4932 20041025 SGD
+SGD S000005831 ISW2 GO:0046020 SGD_REF:S000072612|PMID:12624196 IMP P ATPase component of a two subunit chromatin remodeling complex YOR304W gene taxon:4932 20030314 SGD
+SGD S000003811 ISY1 GO:0005681 SGD_REF:S000046470|PMID:11018040 IDA C YJR050W|NTC30|UTR3 gene taxon:4932 20010118 SGD
+SGD S000003811 ISY1 GO:0005681 SGD_REF:S000046470|PMID:11018040 IGI C YJR050W|NTC30|UTR3 gene taxon:4932 20010118 SGD
+SGD S000003811 ISY1 GO:0031202 SGD_REF:S000071476|PMID:12384582 IMP F YJR050W|NTC30|UTR3 gene taxon:4932 20030128 SGD
+SGD S000003811 ISY1 GO:0000398 SGD_REF:S000046470|PMID:11018040 IGI P YJR050W|NTC30|UTR3 gene taxon:4932 20010118 SGD
+SGD S000003811 ISY1 GO:0000398 SGD_REF:S000046470|PMID:11018040 IDA P YJR050W|NTC30|UTR3 gene taxon:4932 20010118 SGD
+SGD S000003101 ITC1 GO:0008623 SGD_REF:S000075426|PMID:14673157 IPI C YGL133W gene taxon:4932 20041031 SGD
+SGD S000003101 ITC1 GO:0005554 SGD_REF:S000069584 ND F YGL133W gene taxon:4932 20010119 SGD
+SGD S000003101 ITC1 GO:0006338 SGD_REF:S000071770|PMID:12370299 TAS P YGL133W gene taxon:4932 20030128 SGD
+SGD S000003101 ITC1 GO:0006348 SGD_REF:S000075426|PMID:14673157 IMP P YGL133W gene taxon:4932 20040210 SGD
+SGD S000003101 ITC1 GO:0046020 SGD_REF:S000072612|PMID:12624196 IMP P YGL133W gene taxon:4932 20030314 SGD
+SGD S000002905 ITR1 GO:0005886 SGD_REF:S000086966|PMID:16233524 IDA C myo-inositol transporter YDR497C gene taxon:4932 20051118 SGD
+SGD S000002905 ITR1 GO:0016020 SGD_REF:S000046064|PMID:2040626 ISS C myo-inositol transporter YDR497C gene taxon:4932 20020926 SGD
+SGD S000002905 ITR1 GO:0005365 SGD_REF:S000046064|PMID:2040626 ISS F myo-inositol transporter YDR497C gene taxon:4932 20020926 SGD
+SGD S000002905 ITR1 GO:0005365 SGD_REF:S000046064|PMID:2040626 IMP F myo-inositol transporter YDR497C gene taxon:4932 20020926 SGD
+SGD S000002905 ITR1 GO:0015798 SGD_REF:S000046064|PMID:2040626 IMP P myo-inositol transporter YDR497C gene taxon:4932 20020926 SGD
+SGD S000005463 ITR2 GO:0005886 SGD_REF:S000086966|PMID:16233524 IDA C myo-inositol transporter YOL103W|HRB612 gene taxon:4932 20051118 SGD
+SGD S000005463 ITR2 GO:0016020 SGD_REF:S000046064|PMID:2040626 ISS C myo-inositol transporter YOL103W|HRB612 gene taxon:4932 20020926 SGD
+SGD S000005463 ITR2 GO:0005365 SGD_REF:S000046064|PMID:2040626 ISS F myo-inositol transporter YOL103W|HRB612 gene taxon:4932 20020926 SGD
+SGD S000005463 ITR2 GO:0005365 SGD_REF:S000046064|PMID:2040626 IMP F myo-inositol transporter YOL103W|HRB612 gene taxon:4932 20020926 SGD
+SGD S000005463 ITR2 GO:0015798 SGD_REF:S000046064|PMID:2040626 IMP P myo-inositol transporter YOL103W|HRB612 gene taxon:4932 20020926 SGD
+SGD S000029715 ITS1-1 GO:0006364 SGD_REF:S000074505|PMID:2249660 IMP P ITS1 gene taxon:4932 20040308 SGD
+SGD S000029715 ITS1-1 GO:0006364 SGD_REF:S000074505|PMID:2249660 TAS P ITS1 gene taxon:4932 20040308 SGD
+SGD S000029709 ITS1-2 GO:0006364 SGD_REF:S000074505|PMID:2249660 IMP P ITS1 gene taxon:4932 20040308 SGD
+SGD S000029709 ITS1-2 GO:0006364 SGD_REF:S000074505|PMID:2249660 TAS P ITS1 gene taxon:4932 20040308 SGD
+SGD S000029716 ITS2-1 GO:0006364 SGD_REF:S000075538|PMID:7602595 IMP P ITS2 gene taxon:4932 20040308 SGD
+SGD S000029712 ITS2-2 GO:0006364 SGD_REF:S000075538|PMID:7602595 IMP P ITS2 gene taxon:4932 20040308 SGD
+SGD S000004533 ITT1 GO:0008372 SGD_REF:S000069584 ND C YML068W gene taxon:4932 20020927 SGD
+SGD S000004533 ITT1 GO:0005554 SGD_REF:S000069584 ND F YML068W gene taxon:4932 20020927 SGD
+SGD S000004533 ITT1 GO:0006449 SGD_REF:S000071358|PMID:11570975 IMP P YML068W gene taxon:4932 20020927 SGD
+SGD S000002637 IVY1 GO:0000329 SGD_REF:S000072328|PMID:12553664 IDA C YDR229W gene taxon:4932 20030213 SGD
+SGD S000002637 IVY1 GO:0005543 SGD_REF:S000072328|PMID:12553664 IDA F YDR229W gene taxon:4932 20030213 SGD
+SGD S000002637 IVY1 GO:0045045 SGD_REF:S000072328|PMID:12553664 IGI P YDR229W gene taxon:4932 20030213 SGD
+SGD S000002637 IVY1 GO:0045045 SGD_REF:S000072328|PMID:12553664 IPI P YDR229W gene taxon:4932 20030213 SGD
+SGD S000002273 IWR1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YDL115C gene taxon:4932 20031028 SGD
+SGD S000002273 IWR1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDL115C gene taxon:4932 20031028 SGD
+SGD S000002273 IWR1 GO:0016591 SGD_REF:S000114782|PMID:16554755 IPI SGD:S000000358|SGD:S000005677|SGD:S000003011|SGD:S000003676|SGD:S000001283|SGD:S000002299|SGD:S000002812 C YDL115C gene taxon:4932 20060410 SGD
+SGD S000002273 IWR1 GO:0005554 SGD_REF:S000069584 ND F YDL115C gene taxon:4932 20021211 SGD
+SGD S000002273 IWR1 GO:0006366 SGD_REF:S000114782|PMID:16554755 IC GO:0016591 P YDL115C gene taxon:4932 20060410 SGD
+SGD S000002273 IWR1 GO:0006366 SGD_REF:S000114782|PMID:16554755 IGI SGD:S000003011 P YDL115C gene taxon:4932 20060410 SGD
+SGD S000002273 IWR1 GO:0007126 SGD_REF:S000042737|PMID:10734188 TAS P YDL115C gene taxon:4932 20031104 SGD
+SGD S000001515 IXR1 GO:0000228 SGD_REF:S000042982|PMID:8634251 IPI C intrastrand crosslink recognition protein YKL032C|ORD1 gene taxon:4932 20020715 SGD
+SGD S000001515 IXR1 GO:0003677 SGD_REF:S000042982|PMID:8634251 IDA F intrastrand crosslink recognition protein YKL032C|ORD1 gene taxon:4932 20020715 SGD
+SGD S000001515 IXR1 GO:0006281 SGD_REF:S000046473|PMID:8538651 IMP P intrastrand crosslink recognition protein YKL032C|ORD1 gene taxon:4932 20020715 SGD
+SGD S000002900 IZH1 GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YDR492W gene taxon:4932 20031028 SGD
+SGD S000002900 IZH1 GO:0016020 SGD_REF:S000076221|PMID:15060275 TAS C YDR492W gene taxon:4932 20040527 SGD
+SGD S000002900 IZH1 GO:0016020 SGD_REF:S000076221|PMID:15060275 ISS C YDR492W gene taxon:4932 20040527 SGD
+SGD S000002900 IZH1 GO:0046872 SGD_REF:S000076221|PMID:15060275 ISS F YDR492W gene taxon:4932 20040527 SGD
+SGD S000002900 IZH1 GO:0006629 SGD_REF:S000076221|PMID:15060275 TAS P YDR492W gene taxon:4932 20040527 SGD
+SGD S000002900 IZH1 GO:0006882 SGD_REF:S000076221|PMID:15060275 IMP P YDR492W gene taxon:4932 20040527 SGD
+SGD S000002900 IZH1 GO:0006882 SGD_REF:S000076221|PMID:15060275 ISS P YDR492W gene taxon:4932 20040527 SGD
+SGD S000002900 IZH1 GO:0010043 SGD_REF:S000076221|PMID:15060275 ISS P YDR492W gene taxon:4932 20040527 SGD
+SGD S000005362 IZH2 GO:0016020 SGD_REF:S000076221|PMID:15060275 TAS C YOL002C|PHO36 gene taxon:4932 20040527 SGD
+SGD S000005362 IZH2 GO:0016020 SGD_REF:S000076221|PMID:15060275 ISS C YOL002C|PHO36 gene taxon:4932 20040527 SGD
+SGD S000005362 IZH2 GO:0016021 SGD_REF:S000055053|PMID:9774671 ISS C YOL002C|PHO36 gene taxon:4932 20040122 SGD
+SGD S000005362 IZH2 GO:0046872 SGD_REF:S000076221|PMID:15060275 ISS F YOL002C|PHO36 gene taxon:4932 20040527 SGD
+SGD S000005362 IZH2 GO:0006629 SGD_REF:S000076221|PMID:15060275 TAS P YOL002C|PHO36 gene taxon:4932 20040527 SGD
+SGD S000005362 IZH2 GO:0006882 SGD_REF:S000076221|PMID:15060275 IMP P YOL002C|PHO36 gene taxon:4932 20040527 SGD
+SGD S000005362 IZH2 GO:0006882 SGD_REF:S000076221|PMID:15060275 ISS P YOL002C|PHO36 gene taxon:4932 20040527 SGD
+SGD S000005362 IZH2 GO:0010043 SGD_REF:S000076221|PMID:15060275 ISS P YOL002C|PHO36 gene taxon:4932 20040527 SGD
+SGD S000004013 IZH3 GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YLR023C gene taxon:4932 20031028 SGD
+SGD S000004013 IZH3 GO:0016020 SGD_REF:S000076221|PMID:15060275 TAS C YLR023C gene taxon:4932 20040527 SGD
+SGD S000004013 IZH3 GO:0016020 SGD_REF:S000076221|PMID:15060275 ISS C YLR023C gene taxon:4932 20040527 SGD
+SGD S000004013 IZH3 GO:0046872 SGD_REF:S000076221|PMID:15060275 ISS F YLR023C gene taxon:4932 20040527 SGD
+SGD S000004013 IZH3 GO:0006629 SGD_REF:S000076221|PMID:15060275 TAS P YLR023C gene taxon:4932 20040527 SGD
+SGD S000004013 IZH3 GO:0006882 SGD_REF:S000076221|PMID:15060275 IMP P YLR023C gene taxon:4932 20040527 SGD
+SGD S000004013 IZH3 GO:0006882 SGD_REF:S000076221|PMID:15060275 ISS P YLR023C gene taxon:4932 20040527 SGD
+SGD S000005461 IZH4 GO:0016020 SGD_REF:S000076221|PMID:15060275 TAS C YOL101C gene taxon:4932 20040527 SGD
+SGD S000005461 IZH4 GO:0016020 SGD_REF:S000076221|PMID:15060275 ISS C YOL101C gene taxon:4932 20040527 SGD
+SGD S000005461 IZH4 GO:0016021 SGD_REF:S000072825|PMID:12524434 ISS C YOL101C gene taxon:4932 20030409 SGD
+SGD S000005461 IZH4 GO:0046872 SGD_REF:S000076221|PMID:15060275 ISS F YOL101C gene taxon:4932 20040527 SGD
+SGD S000005461 IZH4 GO:0006629 SGD_REF:S000076221|PMID:15060275 TAS P YOL101C gene taxon:4932 20040527 SGD
+SGD S000005461 IZH4 GO:0006882 SGD_REF:S000076221|PMID:15060275 IMP P YOL101C gene taxon:4932 20040527 SGD
+SGD S000005461 IZH4 GO:0006882 SGD_REF:S000076221|PMID:15060275 ISS P YOL101C gene taxon:4932 20040527 SGD
+SGD S000002986 JAC1 GO:0005739 SGD_REF:S000060776|PMID:11278728 IDA C E. coli Hsc20 co-chaperone protein homolog, J-protein co-chaperone family 20 kDa YGL018C gene taxon:4932 20020828 SGD
+SGD S000002986 JAC1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C E. coli Hsc20 co-chaperone protein homolog, J-protein co-chaperone family 20 kDa YGL018C gene taxon:4932 20040924 SGD
+SGD S000002986 JAC1 GO:0051087 SGD_REF:S000052831|PMID:9813017 ISS F E. coli Hsc20 co-chaperone protein homolog, J-protein co-chaperone family 20 kDa YGL018C gene taxon:4932 20040722 SGD
+SGD S000002986 JAC1 GO:0051087 SGD_REF:S000060776|PMID:11278728 IMP F E. coli Hsc20 co-chaperone protein homolog, J-protein co-chaperone family 20 kDa YGL018C gene taxon:4932 20040722 SGD
+SGD S000002986 JAC1 GO:0009060 SGD_REF:S000052831|PMID:9813017 IMP P E. coli Hsc20 co-chaperone protein homolog, J-protein co-chaperone family 20 kDa YGL018C gene taxon:4932 20010118 SGD
+SGD S000002986 JAC1 GO:0016226 SGD_REF:S000060776|PMID:11278728 IMP P E. coli Hsc20 co-chaperone protein homolog, J-protein co-chaperone family 20 kDa YGL018C gene taxon:4932 20020828 SGD
+SGD S000003609 JEM1 GO:0000300 SGD_REF:S000054696|PMID:9148890 IDA C YJL073W|KAR8 gene taxon:4932 20020816 SGD
+SGD S000003609 JEM1 GO:0005783 SGD_REF:S000054696|PMID:9148890 IDA C YJL073W|KAR8 gene taxon:4932 20020816 SGD
+SGD S000003609 JEM1 GO:0042175 SGD_REF:S000077144|PMID:15282802 IDA C YJL073W|KAR8 gene taxon:4932 20041008 SGD
+SGD S000003609 JEM1 GO:0051082 SGD_REF:S000054696|PMID:9148890 ISS F YJL073W|KAR8 gene taxon:4932 20040722 SGD
+SGD S000003609 JEM1 GO:0051087 SGD_REF:S000054696|PMID:9148890 ISS F YJL073W|KAR8 gene taxon:4932 20040722 SGD
+SGD S000003609 JEM1 GO:0000742 SGD_REF:S000043757|PMID:10069807 IGI P YJL073W|KAR8 gene taxon:4932 20021206 SGD
+SGD S000003609 JEM1 GO:0000742 SGD_REF:S000043757|PMID:10069807 IMP P YJL073W|KAR8 gene taxon:4932 20021206 SGD
+SGD S000003609 JEM1 GO:0006457 SGD_REF:S000063756|PMID:9817751 IGI P YJL073W|KAR8 gene taxon:4932 20020816 SGD
+SGD S000003609 JEM1 GO:0030433 SGD_REF:S000074517|PMID:11381090 IMP P YJL073W|KAR8 gene taxon:4932 20060201 SGD
+SGD S000001700 JEN1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C carboxylic acid transporter protein homolog YKL217W gene taxon:4932 20040928 SGD
+SGD S000001700 JEN1 GO:0005886 SGD_REF:S000053081|PMID:10198029 ISS C carboxylic acid transporter protein homolog YKL217W gene taxon:4932 20020918 SGD
+SGD S000001700 JEN1 GO:0005886 SGD_REF:S000053081|PMID:10198029 IMP C carboxylic acid transporter protein homolog YKL217W gene taxon:4932 20020918 SGD
+SGD S000001700 JEN1 GO:0015129 SGD_REF:S000053081|PMID:10198029 IMP F carboxylic acid transporter protein homolog YKL217W gene taxon:4932 20020918 SGD
+SGD S000001700 JEN1 GO:0015129 SGD_REF:S000075172|PMID:12962538 IDA F carboxylic acid transporter protein homolog YKL217W gene taxon:4932 20031222 SGD
+SGD S000001700 JEN1 GO:0015727 SGD_REF:S000053081|PMID:10198029 IMP P carboxylic acid transporter protein homolog YKL217W gene taxon:4932 20020918 SGD
+SGD S000001700 JEN1 GO:0015727 SGD_REF:S000075172|PMID:12962538 IDA P carboxylic acid transporter protein homolog YKL217W gene taxon:4932 20031222 SGD
+SGD S000000853 JHD1 GO:0008372 SGD_REF:S000069584 ND C histone H3-K36 demethylase YER051W|JHDM1 gene taxon:4932 20060119 SGD
+SGD S000000853 JHD1 GO:0051864 SGD_REF:S000114094|PMID:16362057 IDA F histone H3-K36 demethylase YER051W|JHDM1 gene taxon:4932 20060126 SGD
+SGD S000000853 JHD1 GO:0016577 SGD_REF:S000114094|PMID:16362057 IDA P histone H3-K36 demethylase YER051W|JHDM1 gene taxon:4932 20060119 SGD
+SGD S000006265 JID1 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YPR061C gene taxon:4932 20031028 SGD
+SGD S000006265 JID1 GO:0005554 SGD_REF:S000069584 ND F YPR061C gene taxon:4932 20030203 SGD
+SGD S000006265 JID1 GO:0000004 SGD_REF:S000069584 ND P YPR061C gene taxon:4932 20030203 SGD
+SGD S000002883 JIP4 GO:0008372 SGD_REF:S000069584 ND C YDR475C|YDR474C gene taxon:4932 20021125 SGD
+SGD S000002883 JIP4 GO:0005554 SGD_REF:S000069584 ND F YDR475C|YDR474C gene taxon:4932 20021125 SGD
+SGD S000002883 JIP4 GO:0000004 SGD_REF:S000069584 ND P YDR475C|YDR474C gene taxon:4932 20021125 SGD
+SGD S000006373 JIP5 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YPR169W gene taxon:4932 20031028 SGD
+SGD S000006373 JIP5 GO:0005634 SGD_REF:S000075214|PMID:14690591 IDA C YPR169W gene taxon:4932 20031231 SGD
+SGD S000006373 JIP5 GO:0005730 SGD_REF:S000074185|PMID:14562095 IDA C YPR169W gene taxon:4932 20031028 SGD
+SGD S000006373 JIP5 GO:0005730 SGD_REF:S000075214|PMID:14690591 IDA C YPR169W gene taxon:4932 20031231 SGD
+SGD S000006373 JIP5 GO:0005554 SGD_REF:S000069584 ND F YPR169W gene taxon:4932 20021029 SGD
+SGD S000006373 JIP5 GO:0006513 SGD_REF:S000075214|PMID:14690591 IPI SGD:S000002232 P YPR169W gene taxon:4932 20031231 SGD
+SGD S000005171 JJJ1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YNL227C gene taxon:4932 20031028 SGD
+SGD S000005171 JJJ1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YNL227C gene taxon:4932 20040928 SGD
+SGD S000005171 JJJ1 GO:0005554 SGD_REF:S000069584 ND F YNL227C gene taxon:4932 20021004 SGD
+SGD S000005171 JJJ1 GO:0006897 SGD_REF:S000060817|PMID:11378903 IMP P YNL227C gene taxon:4932 20021004 SGD
+SGD S000003698 JJJ2 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YJL162C gene taxon:4932 20031028 SGD
+SGD S000003698 JJJ2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YJL162C gene taxon:4932 20031028 SGD
+SGD S000003698 JJJ2 GO:0005554 SGD_REF:S000069584 ND F YJL162C gene taxon:4932 20021126 SGD
+SGD S000003698 JJJ2 GO:0000004 SGD_REF:S000069584 ND P YJL162C gene taxon:4932 20021126 SGD
+SGD S000003858 JJJ3 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YJR097W|DPH4 gene taxon:4932 20031028 SGD
+SGD S000003858 JJJ3 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YJR097W|DPH4 gene taxon:4932 20031028 SGD
+SGD S000003858 JJJ3 GO:0005554 SGD_REF:S000069584 ND F YJR097W|DPH4 gene taxon:4932 20021126 SGD
+SGD S000003858 JJJ3 GO:0017183 SGD_REF:S000079857|PMID:15485916 IMP P YJR097W|DPH4 gene taxon:4932 20050303 SGD
+SGD S000003980 JLP1 GO:0008372 SGD_REF:S000069584 ND C YLL057C gene taxon:4932 20030115 SGD
+SGD S000003980 JLP1 GO:0000907 SGD_REF:S000056345|PMID:10482536 IDA F YLL057C gene taxon:4932 20030214 SGD
+SGD S000003980 JLP1 GO:0006790 SGD_REF:S000056345|PMID:10482536 IDA P YLL057C gene taxon:4932 20030115 SGD
+SGD S000003980 JLP1 GO:0006790 SGD_REF:S000056345|PMID:10482536 IMP P YLL057C gene taxon:4932 20030115 SGD
+SGD S000004739 JLP2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YMR132C gene taxon:4932 20031028 SGD
+SGD S000004739 JLP2 GO:0005554 SGD_REF:S000069584 ND F YMR132C gene taxon:4932 20021126 SGD
+SGD S000004739 JLP2 GO:0000004 SGD_REF:S000069584 ND P YMR132C gene taxon:4932 20021126 SGD
+SGD S000004908 JNM1 GO:0005869 SGD_REF:S000046660|PMID:9658168 IDA C YMR294W|INS1|PAC3 gene taxon:4932 20010118 SGD
+SGD S000004908 JNM1 GO:0005200 SGD_REF:S000046660|PMID:9658168 IPI F YMR294W|INS1|PAC3 gene taxon:4932 20010118 SGD
+SGD S000004908 JNM1 GO:0007097 SGD_REF:S000041294|PMID:8138567 IMP P YMR294W|INS1|PAC3 gene taxon:4932 20050412 SGD
+SGD S000003851 JSN1 GO:0008372 SGD_REF:S000069584 ND C YJR091C|PUF1 gene taxon:4932 20020924 SGD
+SGD S000003851 JSN1 GO:0003729 SGD_REF:S000059700|PMID:11101532 ISS F YJR091C|PUF1 gene taxon:4932 20020924 SGD
+SGD S000003851 JSN1 GO:0000288 SGD_REF:S000059700|PMID:11101532 IGI P YJR091C|PUF1 gene taxon:4932 20020924 SGD
+SGD S000001746 KAE1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C Putative O-sialo-glycoprotein-endopeptidase A1 YKR038C gene taxon:4932 20031028 SGD
+SGD S000001746 KAE1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C Putative O-sialo-glycoprotein-endopeptidase A1 YKR038C gene taxon:4932 20031028 SGD
+SGD S000001746 KAE1 GO:0004222 SGD_REF:S000080056|PMID:15606766 ISS F Putative O-sialo-glycoprotein-endopeptidase A1 YKR038C gene taxon:4932 20050415 SGD
+SGD S000001746 KAE1 GO:0008450 SGD_REF:S000075281|PMID:14519092 ISS F Putative O-sialo-glycoprotein-endopeptidase A1 YKR038C gene taxon:4932 20040109 SGD
+SGD S000001746 KAE1 GO:0006508 SGD_REF:S000075281|PMID:14519092 ISS P Putative O-sialo-glycoprotein-endopeptidase A1 YKR038C gene taxon:4932 20050415 SGD
+SGD S000001746 KAE1 GO:0006508 SGD_REF:S000080056|PMID:15606766 ISS P Putative O-sialo-glycoprotein-endopeptidase A1 YKR038C gene taxon:4932 20050415 SGD
+SGD S000000221 KAP104 GO:0005829 SGD_REF:S000049555|PMID:8849456 IDA C karyopherin beta 2 YBR017C gene taxon:4932 20020125 SGD
+SGD S000000221 KAP104 GO:0008139 SGD_REF:S000047435|PMID:9488461 IPI F karyopherin beta 2 YBR017C gene taxon:4932 20020125 SGD
+SGD S000000221 KAP104 GO:0006606 SGD_REF:S000049555|PMID:8849456 IMP P karyopherin beta 2 YBR017C gene taxon:4932 20020125 SGD
+SGD S000000221 KAP104 GO:0006606 SGD_REF:S000049555|PMID:8849456 IPI P karyopherin beta 2 YBR017C gene taxon:4932 20020125 SGD
+SGD S000000221 KAP104 GO:0006606 SGD_REF:S000047435|PMID:9488461 IDA P karyopherin beta 2 YBR017C gene taxon:4932 20020125 SGD
+SGD S000000221 KAP104 GO:0006606 SGD_REF:S000049555|PMID:8849456 ISS P karyopherin beta 2 YBR017C gene taxon:4932 20020125 SGD
+SGD S000000221 KAP104 GO:0006609 SGD_REF:S000047435|PMID:9488461 IDA P karyopherin beta 2 YBR017C gene taxon:4932 20020125 SGD
+SGD S000000221 KAP104 GO:0006609 SGD_REF:S000049555|PMID:8849456 ISS P karyopherin beta 2 YBR017C gene taxon:4932 20020125 SGD
+SGD S000000221 KAP104 GO:0006609 SGD_REF:S000049555|PMID:8849456 IPI P karyopherin beta 2 YBR017C gene taxon:4932 20020125 SGD
+SGD S000000221 KAP104 GO:0006609 SGD_REF:S000049555|PMID:8849456 IMP P karyopherin beta 2 YBR017C gene taxon:4932 20020125 SGD
+SGD S000000221 KAP104 GO:0007049 SGD_REF:S000072260|PMID:12524331 IMP P karyopherin beta 2 YBR017C gene taxon:4932 20030424 SGD
+SGD S000003210 KAP114 GO:0005634 SGD_REF:S000041178|PMID:10385521 IDA C YGL241W gene taxon:4932 20020816 SGD
+SGD S000003210 KAP114 GO:0005737 SGD_REF:S000041178|PMID:10385521 IDA C YGL241W gene taxon:4932 20020816 SGD
+SGD S000003210 KAP114 GO:0008320 SGD_REF:S000041178|PMID:10385521 ISS F YGL241W gene taxon:4932 20020816 SGD
+SGD S000003210 KAP114 GO:0008320 SGD_REF:S000041178|PMID:10385521 IPI F YGL241W gene taxon:4932 20020816 SGD
+SGD S000003210 KAP114 GO:0006606 SGD_REF:S000041178|PMID:10385521 ISS P YGL241W gene taxon:4932 20020816 SGD
+SGD S000003210 KAP114 GO:0006606 SGD_REF:S000041178|PMID:10385521 IMP P YGL241W gene taxon:4932 20020816 SGD
+SGD S000006046 KAP120 GO:0005643 SGD_REF:S000056415|PMID:10684247 IDA C karyopherin YPL125W gene taxon:4932 20020620 SGD
+SGD S000006046 KAP120 GO:0005737 SGD_REF:S000056415|PMID:10684247 IDA C karyopherin YPL125W gene taxon:4932 20020620 SGD
+SGD S000006046 KAP120 GO:0017056 SGD_REF:S000056415|PMID:10684247 IPI F karyopherin YPL125W gene taxon:4932 20020801 SGD
+SGD S000006046 KAP120 GO:0006606 SGD_REF:S000056415|PMID:10684247 IPI P karyopherin YPL125W gene taxon:4932 20020801 SGD
+SGD S000002984 KAP122 GO:0005643 SGD_REF:S000056415|PMID:10684247 IDA C karyopherin beta family member YGL016W|PDR6 gene taxon:4932 20020620 SGD
+SGD S000002984 KAP122 GO:0005737 SGD_REF:S000056415|PMID:10684247 IDA C karyopherin beta family member YGL016W|PDR6 gene taxon:4932 20020620 SGD
+SGD S000002984 KAP122 GO:0008320 SGD_REF:S000049646|PMID:10525531 TAS F karyopherin beta family member YGL016W|PDR6 gene taxon:4932 20020927 SGD
+SGD S000002984 KAP122 GO:0006606 SGD_REF:S000049646|PMID:10525531 IDA P karyopherin beta family member YGL016W|PDR6 gene taxon:4932 20020926 SGD
+SGD S000002984 KAP122 GO:0042493 SGD_REF:S000045962|PMID:1882553 TAS P karyopherin beta family member YGL016W|PDR6 gene taxon:4932 20021111 SGD
+SGD S000000912 KAP123 GO:0005634 SGD_REF:S000052126|PMID:9238021 IDA C karyopherin beta 4 YER110C|YRB4 gene taxon:4932 20020624 SGD
+SGD S000000912 KAP123 GO:0005643 SGD_REF:S000056415|PMID:10684247 IDA C karyopherin beta 4 YER110C|YRB4 gene taxon:4932 20020620 SGD
+SGD S000000912 KAP123 GO:0005737 SGD_REF:S000056415|PMID:10684247 IDA C karyopherin beta 4 YER110C|YRB4 gene taxon:4932 20020620 SGD
+SGD S000000912 KAP123 GO:0005737 SGD_REF:S000052126|PMID:9238021 IDA C karyopherin beta 4 YER110C|YRB4 gene taxon:4932 20020624 SGD
+SGD S000000912 KAP123 GO:0008320 SGD_REF:S000060938|PMID:11274141 TAS F karyopherin beta 4 YER110C|YRB4 gene taxon:4932 20020926 SGD
+SGD S000000912 KAP123 GO:0006606 SGD_REF:S000060938|PMID:11274141 TAS P karyopherin beta 4 YER110C|YRB4 gene taxon:4932 20020926 SGD
+SGD S000004339 KAP95 GO:0005643 SGD_REF:S000056415|PMID:10684247 IDA C karyopherin beta (importin 90) homolog (95 kDa) YLR347C|RSL1 gene taxon:4932 20020620 SGD
+SGD S000004339 KAP95 GO:0005737 SGD_REF:S000056415|PMID:10684247 IDA C karyopherin beta (importin 90) homolog (95 kDa) YLR347C|RSL1 gene taxon:4932 20020620 SGD
+SGD S000004339 KAP95 GO:0008320 SGD_REF:S000059675|PMID:11171327 IDA F karyopherin beta (importin 90) homolog (95 kDa) YLR347C|RSL1 gene taxon:4932 20020926 SGD
+SGD S000004339 KAP95 GO:0006606 SGD_REF:S000044920|PMID:9151683 TAS P karyopherin beta (importin 90) homolog (95 kDa) YLR347C|RSL1 gene taxon:4932 20020926 SGD
+SGD S000005132 KAR1 GO:0005825 SGD_REF:S000051509|PMID:10428957 IDA C YNL188W gene taxon:4932 20021202 SGD
+SGD S000005132 KAR1 GO:0005515 SGD_REF:S000051509|PMID:10428957 IDA F YNL188W gene taxon:4932 20021202 SGD
+SGD S000005132 KAR1 GO:0000742 SGD_REF:S000056581|PMID:1607389 IGI P YNL188W gene taxon:4932 20021206 SGD
+SGD S000005132 KAR1 GO:0000742 SGD_REF:S000056581|PMID:1607389 IMP P YNL188W gene taxon:4932 20021206 SGD
+SGD S000005132 KAR1 GO:0007103 SGD_REF:S000050579|PMID:3030557 IMP P YNL188W gene taxon:4932 20021202 SGD
+SGD S000003571 KAR2 GO:0005783 SGD_REF:S000049344|PMID:2661018 IDA C HSP70 family, mammalian BiP (GRP78 or HSPA5) homolog YJL034W|BIP|GRP78 gene taxon:4932 20060201 SGD
+SGD S000003571 KAR2 GO:0016887 SGD_REF:S000055090|PMID:1325440 IDA F HSP70 family, mammalian BiP (GRP78 or HSPA5) homolog YJL034W|BIP|GRP78 gene taxon:4932 20021126 SGD
+SGD S000003571 KAR2 GO:0051082 SGD_REF:S000075490|PMID:12808051 IMP F HSP70 family, mammalian BiP (GRP78 or HSPA5) homolog YJL034W|BIP|GRP78 gene taxon:4932 20060201 SGD
+SGD S000003571 KAR2 GO:0000742 SGD_REF:S000043757|PMID:10069807 IGI P HSP70 family, mammalian BiP (GRP78 or HSPA5) homolog YJL034W|BIP|GRP78 gene taxon:4932 20021206 SGD
+SGD S000003571 KAR2 GO:0000742 SGD_REF:S000043757|PMID:10069807 IMP P HSP70 family, mammalian BiP (GRP78 or HSPA5) homolog YJL034W|BIP|GRP78 gene taxon:4932 20021206 SGD
+SGD S000003571 KAR2 GO:0006616 SGD_REF:S000045340|PMID:7568189 IMP P HSP70 family, mammalian BiP (GRP78 or HSPA5) homolog YJL034W|BIP|GRP78 gene taxon:4932 20060613 SGD
+SGD S000003571 KAR2 GO:0006986 SGD_REF:S000075490|PMID:12808051 IMP P HSP70 family, mammalian BiP (GRP78 or HSPA5) homolog YJL034W|BIP|GRP78 gene taxon:4932 20060201 SGD
+SGD S000003571 KAR2 GO:0030433 SGD_REF:S000074517|PMID:11381090 IMP P HSP70 family, mammalian BiP (GRP78 or HSPA5) homolog YJL034W|BIP|GRP78 gene taxon:4932 20060201 SGD
+SGD S000003571 KAR2 GO:0031204 SGD_REF:S000039256|PMID:10367885 IDA P HSP70 family, mammalian BiP (GRP78 or HSPA5) homolog YJL034W|BIP|GRP78 gene taxon:4932 20060613 SGD
+SGD S000003571 KAR2 GO:0031204 SGD_REF:S000045340|PMID:7568189 IMP P HSP70 family, mammalian BiP (GRP78 or HSPA5) homolog YJL034W|BIP|GRP78 gene taxon:4932 20060613 SGD
+SGD S000006345 KAR3 GO:0005816 SGD_REF:S000066252|PMID:11729143 IDA C kinesin-like nuclear fusion protein YPR141C|OSR11 gene taxon:4932 20020208 SGD
+SGD S000006345 KAR3 GO:0005816 SGD_REF:S000043866|PMID:2138512 IDA C kinesin-like nuclear fusion protein YPR141C|OSR11 gene taxon:4932 20020208 SGD
+SGD S000006345 KAR3 GO:0005816 SGD_REF:S000045191|PMID:8106549 IDA C kinesin-like nuclear fusion protein YPR141C|OSR11 gene taxon:4932 20020208 SGD
+SGD S000006345 KAR3 GO:0005874 SGD_REF:S000046665|PMID:9859995 TAS C kinesin-like nuclear fusion protein YPR141C|OSR11 gene taxon:4932 20021227 SGD
+SGD S000006345 KAR3 GO:0003774 SGD_REF:S000045728|PMID:8041770 IDA F kinesin-like nuclear fusion protein YPR141C|OSR11 gene taxon:4932 20021202 SGD
+SGD S000006345 KAR3 GO:0003777 SGD_REF:S000046665|PMID:9859995 TAS F kinesin-like nuclear fusion protein YPR141C|OSR11 gene taxon:4932 20021227 SGD
+SGD S000006345 KAR3 GO:0000742 SGD_REF:S000043866|PMID:2138512 IMP P kinesin-like nuclear fusion protein YPR141C|OSR11 gene taxon:4932 20021206 SGD
+SGD S000006345 KAR3 GO:0007064 SGD_REF:S000076127|PMID:14742714 IGI SGD:S000001234 P kinesin-like nuclear fusion protein YPR141C|OSR11 gene taxon:4932 20050513 SGD
+SGD S000006345 KAR3 GO:0007064 SGD_REF:S000076127|PMID:14742714 IMP P kinesin-like nuclear fusion protein YPR141C|OSR11 gene taxon:4932 20050513 SGD
+SGD S000006345 KAR3 GO:0007067 SGD_REF:S000051764|PMID:9201713 IGI P kinesin-like nuclear fusion protein YPR141C|OSR11 gene taxon:4932 20021202 SGD
+SGD S000006345 KAR3 GO:0007126 SGD_REF:S000066252|PMID:11729143 IMP P kinesin-like nuclear fusion protein YPR141C|OSR11 gene taxon:4932 20020208 SGD
+SGD S000006345 KAR3 GO:0007126 SGD_REF:S000066252|PMID:11729143 IDA P kinesin-like nuclear fusion protein YPR141C|OSR11 gene taxon:4932 20020208 SGD
+SGD S000000560 KAR4 GO:0005634 SGD_REF:S000040721|PMID:8754797 IC GO:0030528 C involved in karyogamy, transcription factor YCL055W gene taxon:4932 20030325 SGD
+SGD S000000560 KAR4 GO:0030528 SGD_REF:S000040721|PMID:8754797 IGI F involved in karyogamy, transcription factor YCL055W gene taxon:4932 20030325 SGD
+SGD S000000560 KAR4 GO:0030528 SGD_REF:S000040721|PMID:8754797 IMP F involved in karyogamy, transcription factor YCL055W gene taxon:4932 20030325 SGD
+SGD S000000560 KAR4 GO:0000742 SGD_REF:S000040721|PMID:8754797 IMP P involved in karyogamy, transcription factor YCL055W gene taxon:4932 20021206 SGD
+SGD S000000560 KAR4 GO:0007067 SGD_REF:S000043073|PMID:9858604 TAS P involved in karyogamy, transcription factor YCL055W gene taxon:4932 20021202 SGD
+SGD S000000560 KAR4 GO:0007126 SGD_REF:S000040721|PMID:8754797 IMP P involved in karyogamy, transcription factor YCL055W gene taxon:4932 20021202 SGD
+SGD S000000560 KAR4 GO:0045944 SGD_REF:S000043073|PMID:9858604 TAS P involved in karyogamy, transcription factor YCL055W gene taxon:4932 20021202 SGD
+SGD S000004669 KAR5 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C coiled-coil membrane protein YMR065W|FIG3 gene taxon:4932 20040928 SGD
+SGD S000004669 KAR5 GO:0005789 SGD_REF:S000051459|PMID:9382856 IDA C coiled-coil membrane protein YMR065W|FIG3 gene taxon:4932 20020924 SGD
+SGD S000004669 KAR5 GO:0005554 SGD_REF:S000069584 ND F coiled-coil membrane protein YMR065W|FIG3 gene taxon:4932 20010119 SGD
+SGD S000004669 KAR5 GO:0000742 SGD_REF:S000043757|PMID:10069807 IGI P coiled-coil membrane protein YMR065W|FIG3 gene taxon:4932 20021206 SGD
+SGD S000004669 KAR5 GO:0000742 SGD_REF:S000043757|PMID:10069807 IMP P coiled-coil membrane protein YMR065W|FIG3 gene taxon:4932 20021206 SGD
+SGD S000006190 KAR9 GO:0005938 SGD_REF:S000039418|PMID:9442113 IDA C YPL269W gene taxon:4932 20021202 SGD
+SGD S000006190 KAR9 GO:0043332 SGD_REF:S000039418|PMID:9442113 IDA C YPL269W gene taxon:4932 20021202 SGD
+SGD S000006190 KAR9 GO:0005554 SGD_REF:S000069584 ND F YPL269W gene taxon:4932 20010119 SGD
+SGD S000006190 KAR9 GO:0030473 SGD_REF:S000039418|PMID:9442113 IMP P YPL269W gene taxon:4932 20021202 SGD
+SGD S000000529 KCC4 GO:0005935 SGD_REF:S000051063|PMID:9925642 IDA C S. pombe Nim1 homolog, protein kinase YCL024W gene taxon:4932 20010118 SGD
+SGD S000000529 KCC4 GO:0005935 SGD_REF:S000077144|PMID:15282802 IDA C S. pombe Nim1 homolog, protein kinase YCL024W gene taxon:4932 20041008 SGD
+SGD S000000529 KCC4 GO:0004672 SGD_REF:S000052982|PMID:9813093 ISS F S. pombe Nim1 homolog, protein kinase YCL024W gene taxon:4932 20010118 SGD
+SGD S000000529 KCC4 GO:0000135 SGD_REF:S000051063|PMID:9925642 IGI P S. pombe Nim1 homolog, protein kinase YCL024W gene taxon:4932 20010118 SGD
+SGD S000000529 KCC4 GO:0000135 SGD_REF:S000051063|PMID:9925642 IMP P S. pombe Nim1 homolog, protein kinase YCL024W gene taxon:4932 20010118 SGD
+SGD S000000529 KCC4 GO:0000921 SGD_REF:S000051063|PMID:9925642 IGI P S. pombe Nim1 homolog, protein kinase YCL024W gene taxon:4932 20030321 SGD
+SGD S000000529 KCC4 GO:0000921 SGD_REF:S000051063|PMID:9925642 IMP P S. pombe Nim1 homolog, protein kinase YCL024W gene taxon:4932 20030321 SGD
+SGD S000000529 KCC4 GO:0006468 SGD_REF:S000052982|PMID:9813093 ISS P S. pombe Nim1 homolog, protein kinase YCL024W gene taxon:4932 20010118 SGD
+SGD S000000529 KCC4 GO:0007117 SGD_REF:S000051063|PMID:9925642 IMP P S. pombe Nim1 homolog, protein kinase YCL024W gene taxon:4932 20010118 SGD
+SGD S000000529 KCC4 GO:0007117 SGD_REF:S000051063|PMID:9925642 IGI P S. pombe Nim1 homolog, protein kinase YCL024W gene taxon:4932 20010118 SGD
+SGD S000000529 KCC4 GO:0007120 SGD_REF:S000041005|PMID:10652251 TAS P S. pombe Nim1 homolog, protein kinase YCL024W gene taxon:4932 20010118 SGD
+SGD S000002424 KCS1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C Inositol polyphosphate kinase YDR017C gene taxon:4932 20031028 SGD
+SGD S000002424 KCS1 GO:0004428 SGD_REF:S000049940|PMID:10827188 IDA F Inositol polyphosphate kinase YDR017C gene taxon:4932 20021105 SGD
+SGD S000002424 KCS1 GO:0006950 SGD_REF:S000070103|PMID:11956213 IMP P Inositol polyphosphate kinase YDR017C gene taxon:4932 20021105 SGD
+SGD S000002424 KCS1 GO:0007033 SGD_REF:S000049940|PMID:10827188 IMP P Inositol polyphosphate kinase YDR017C gene taxon:4932 20021105 SGD
+SGD S000002424 KCS1 GO:0019220 SGD_REF:S000081537|PMID:15866881 IMP P Inositol polyphosphate kinase YDR017C gene taxon:4932 20060425 SGD
+SGD S000001201 KEL1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YHR158C gene taxon:4932 20020507 SGD
+SGD S000001201 KEL1 GO:0005934 SGD_REF:S000045932|PMID:9786949 IDA C YHR158C gene taxon:4932 20020924 SGD
+SGD S000001201 KEL1 GO:0005935 SGD_REF:S000045932|PMID:9786949 IDA C YHR158C gene taxon:4932 20020924 SGD
+SGD S000001201 KEL1 GO:0043332 SGD_REF:S000045932|PMID:9786949 IDA C YHR158C gene taxon:4932 20020924 SGD
+SGD S000001201 KEL1 GO:0005554 SGD_REF:S000069584 ND F YHR158C gene taxon:4932 20020924 SGD
+SGD S000001201 KEL1 GO:0000755 SGD_REF:S000045932|PMID:9786949 IGI P YHR158C gene taxon:4932 20021206 SGD
+SGD S000001201 KEL1 GO:0000755 SGD_REF:S000045932|PMID:9786949 IMP P YHR158C gene taxon:4932 20021206 SGD
+SGD S000001201 KEL1 GO:0000755 SGD_REF:S000045932|PMID:9786949 IPI P YHR158C gene taxon:4932 20021206 SGD
+SGD S000001201 KEL1 GO:0000902 SGD_REF:S000061503|PMID:11079560 TAS P YHR158C gene taxon:4932 20021204 SGD
+SGD S000001201 KEL1 GO:0001100 SGD_REF:S000071653|PMID:12234925 IMP P YHR158C gene taxon:4932 20050324 SGD
+SGD S000001201 KEL1 GO:0001100 SGD_REF:S000071653|PMID:12234925 IPI P YHR158C gene taxon:4932 20050324 SGD
+SGD S000001201 KEL1 GO:0008360 SGD_REF:S000045932|PMID:9786949 IMP P YHR158C gene taxon:4932 20020924 SGD
+SGD S000001201 KEL1 GO:0045026 SGD_REF:S000061503|PMID:11079560 TAS P YHR158C gene taxon:4932 20021204 SGD
+SGD S000003470 KEL2 GO:0005934 SGD_REF:S000045932|PMID:9786949 IDA C YGR238C gene taxon:4932 20020924 SGD
+SGD S000003470 KEL2 GO:0005935 SGD_REF:S000045932|PMID:9786949 IDA C YGR238C gene taxon:4932 20020924 SGD
+SGD S000003470 KEL2 GO:0043332 SGD_REF:S000045932|PMID:9786949 IDA C YGR238C gene taxon:4932 20020924 SGD
+SGD S000003470 KEL2 GO:0005554 SGD_REF:S000069584 ND F YGR238C gene taxon:4932 20020924 SGD
+SGD S000003470 KEL2 GO:0000747 SGD_REF:S000045932|PMID:9786949 IGI P YGR238C gene taxon:4932 20020924 SGD
+SGD S000003470 KEL2 GO:0001100 SGD_REF:S000071653|PMID:12234925 IMP P YGR238C gene taxon:4932 20050324 SGD
+SGD S000003470 KEL2 GO:0001100 SGD_REF:S000071653|PMID:12234925 IPI P YGR238C gene taxon:4932 20050324 SGD
+SGD S000006184 KEL3 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C kelch-repeat protein, similar to Kel1 and Kel2 YPL263C gene taxon:4932 20031028 SGD
+SGD S000006184 KEL3 GO:0005554 SGD_REF:S000069584 ND F kelch-repeat protein, similar to Kel1 and Kel2 YPL263C gene taxon:4932 20021125 SGD
+SGD S000006184 KEL3 GO:0000004 SGD_REF:S000069584 ND P kelch-repeat protein, similar to Kel1 and Kel2 YPL263C gene taxon:4932 20021125 SGD
+SGD S000003141 KEM1 GO:0000932 SGD_REF:S000073211|PMID:12730603 IDA C 5'-3' exonuclease YGL173C|DST2|RAR5|SEP1|SKI1|XRN1 gene taxon:4932 20030718 SGD
+SGD S000003141 KEM1 GO:0000932 SGD_REF:S000073211|PMID:12730603 IMP C 5'-3' exonuclease YGL173C|DST2|RAR5|SEP1|SKI1|XRN1 gene taxon:4932 20030718 SGD
+SGD S000003141 KEM1 GO:0005737 SGD_REF:S000058443|PMID:10690410 TAS C 5'-3' exonuclease YGL173C|DST2|RAR5|SEP1|SKI1|XRN1 gene taxon:4932 20010118 SGD
+SGD S000003141 KEM1 GO:0000150 SGD_REF:S000058004|PMID:8970740 TAS F 5'-3' exonuclease YGL173C|DST2|RAR5|SEP1|SKI1|XRN1 gene taxon:4932 20030327 SGD
+SGD S000003141 KEM1 GO:0004534 SGD_REF:S000058443|PMID:10690410 TAS F 5'-3' exonuclease YGL173C|DST2|RAR5|SEP1|SKI1|XRN1 gene taxon:4932 20010118 SGD
+SGD S000003141 KEM1 GO:0004536 SGD_REF:S000058004|PMID:8970740 TAS F 5'-3' exonuclease YGL173C|DST2|RAR5|SEP1|SKI1|XRN1 gene taxon:4932 20030327 SGD
+SGD S000003141 KEM1 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P 5'-3' exonuclease YGL173C|DST2|RAR5|SEP1|SKI1|XRN1 gene taxon:4932 20060203 SGD
+SGD S000003141 KEM1 GO:0006365 SGD_REF:S000058443|PMID:10690410 TAS P 5'-3' exonuclease YGL173C|DST2|RAR5|SEP1|SKI1|XRN1 gene taxon:4932 20010118 SGD
+SGD S000003141 KEM1 GO:0006402 SGD_REF:S000058443|PMID:10690410 TAS P 5'-3' exonuclease YGL173C|DST2|RAR5|SEP1|SKI1|XRN1 gene taxon:4932 20010118 SGD
+SGD S000003141 KEM1 GO:0007089 SGD_REF:S000087024|PMID:16240118 IMP P 5'-3' exonuclease YGL173C|DST2|RAR5|SEP1|SKI1|XRN1 gene taxon:4932 20051031 SGD
+SGD S000003141 KEM1 GO:0030447 SGD_REF:S000071615|PMID:12423748 IMP P 5'-3' exonuclease YGL173C|DST2|RAR5|SEP1|SKI1|XRN1 gene taxon:4932 20030223 SGD
+SGD S000003141 KEM1 GO:0043330 SGD_REF:S000044399|PMID:363683 IMP P 5'-3' exonuclease YGL173C|DST2|RAR5|SEP1|SKI1|XRN1 gene taxon:4932 20050505 SGD
+SGD S000006066 KES1 GO:0000139 SGD_REF:S000074786|PMID:11916983 IDA C YPL145C|LPI3|OSH4 gene taxon:4932 20040326 SGD
+SGD S000006066 KES1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YPL145C|LPI3|OSH4 gene taxon:4932 20031028 SGD
+SGD S000006066 KES1 GO:0019898 SGD_REF:S000074786|PMID:11916983 IDA C YPL145C|LPI3|OSH4 gene taxon:4932 20040326 SGD
+SGD S000006066 KES1 GO:0008142 SGD_REF:S000059993|PMID:11238399 ISS F YPL145C|LPI3|OSH4 gene taxon:4932 20020926 SGD
+SGD S000006066 KES1 GO:0006694 SGD_REF:S000059993|PMID:11238399 IMP P YPL145C|LPI3|OSH4 gene taxon:4932 20020328 SGD
+SGD S000006066 KES1 GO:0006694 SGD_REF:S000059993|PMID:11238399 IGI P YPL145C|LPI3|OSH4 gene taxon:4932 20020328 SGD
+SGD S000006066 KES1 GO:0016192 SGD_REF:S000047157|PMID:8978672 IGI P YPL145C|LPI3|OSH4 gene taxon:4932 20020926 SGD
+SGD S000003171 KEX1 GO:0005802 SGD_REF:S000039541|PMID:8308064 IDA C protease, similar to carboxypeptidase B YGL203C gene taxon:4932 20020904 SGD
+SGD S000003171 KEX1 GO:0004187 SGD_REF:S000039541|PMID:8308064 TAS F protease, similar to carboxypeptidase B YGL203C gene taxon:4932 20030122 SGD
+SGD S000003171 KEX1 GO:0016485 SGD_REF:S000039730|PMID:8982451 TAS P protease, similar to carboxypeptidase B YGL203C gene taxon:4932 20020927 SGD
+SGD S000005182 KEX2 GO:0005802 SGD_REF:S000039541|PMID:8308064 IDA C Ca2+-dependent serine protease YNL238W|QDS1|SRB1|VMA45|kexin|yscF gene taxon:4932 20020904 SGD
+SGD S000005182 KEX2 GO:0004252 SGD_REF:S000054681|PMID:2646633 IDA F Ca2+-dependent serine protease YNL238W|QDS1|SRB1|VMA45|kexin|yscF gene taxon:4932 20030127 SGD
+SGD S000005182 KEX2 GO:0007323 SGD_REF:S000045169|PMID:6430565 IMP P Ca2+-dependent serine protease YNL238W|QDS1|SRB1|VMA45|kexin|yscF gene taxon:4932 20020904 SGD
+SGD S000001387 KGD1 GO:0005759 SGD_REF:S000058126|PMID:9175438 TAS C alpha-ketoglutarate dehydrogenase YIL125W|OGD1 gene taxon:4932 20010118 SGD
+SGD S000001387 KGD1 GO:0009353 SGD_REF:S000043865|PMID:2072900 IDA C alpha-ketoglutarate dehydrogenase YIL125W|OGD1 gene taxon:4932 20041207 SGD
+SGD S000001387 KGD1 GO:0042645 SGD_REF:S000069519|PMID:11926067 IDA C alpha-ketoglutarate dehydrogenase YIL125W|OGD1 gene taxon:4932 20031218 SGD
+SGD S000001387 KGD1 GO:0042645 SGD_REF:S000080741|PMID:15692048 IDA C alpha-ketoglutarate dehydrogenase YIL125W|OGD1 gene taxon:4932 20050401 SGD
+SGD S000001387 KGD1 GO:0004591 SGD_REF:S000058126|PMID:9175438 TAS F alpha-ketoglutarate dehydrogenase YIL125W|OGD1 gene taxon:4932 20010118 SGD
+SGD S000001387 KGD1 GO:0006099 SGD_REF:S000058126|PMID:9175438 TAS P alpha-ketoglutarate dehydrogenase YIL125W|OGD1 gene taxon:4932 20010118 SGD
+SGD S000001387 KGD1 GO:0006103 SGD_REF:S000058126|PMID:9175438 TAS P alpha-ketoglutarate dehydrogenase YIL125W|OGD1 gene taxon:4932 20010118 SGD
+SGD S000002555 KGD2 GO:0005759 SGD_REF:S000058126|PMID:9175438 NAS C alpha-ketoglutarate dehydrogenase complex dihydrolipoyl transsuccinylase component YDR148C gene taxon:4932 20010118 SGD
+SGD S000002555 KGD2 GO:0009353 SGD_REF:S000043865|PMID:2072900 IDA C alpha-ketoglutarate dehydrogenase complex dihydrolipoyl transsuccinylase component YDR148C gene taxon:4932 20041207 SGD
+SGD S000002555 KGD2 GO:0042645 SGD_REF:S000069519|PMID:11926067 IDA C alpha-ketoglutarate dehydrogenase complex dihydrolipoyl transsuccinylase component YDR148C gene taxon:4932 20031218 SGD
+SGD S000002555 KGD2 GO:0042645 SGD_REF:S000050870|PMID:10869431 IDA C alpha-ketoglutarate dehydrogenase complex dihydrolipoyl transsuccinylase component YDR148C gene taxon:4932 20050401 SGD
+SGD S000002555 KGD2 GO:0004149 SGD_REF:S000047243|PMID:2115121 IMP F alpha-ketoglutarate dehydrogenase complex dihydrolipoyl transsuccinylase component YDR148C gene taxon:4932 20050214 SGD
+SGD S000002555 KGD2 GO:0004149 SGD_REF:S000047243|PMID:2115121 ISS F alpha-ketoglutarate dehydrogenase complex dihydrolipoyl transsuccinylase component YDR148C gene taxon:4932 20050214 SGD
+SGD S000002555 KGD2 GO:0006099 SGD_REF:S000058126|PMID:9175438 TAS P alpha-ketoglutarate dehydrogenase complex dihydrolipoyl transsuccinylase component YDR148C gene taxon:4932 20010118 SGD
+SGD S000002555 KGD2 GO:0006103 SGD_REF:S000058126|PMID:9175438 TAS P alpha-ketoglutarate dehydrogenase complex dihydrolipoyl transsuccinylase component YDR148C gene taxon:4932 20010118 SGD
+SGD S000003630 KHA1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YJL094C gene taxon:4932 20040928 SGD
+SGD S000003630 KHA1 GO:0016020 SGD_REF:S000056339|PMID:9811642 ISS C YJL094C gene taxon:4932 20021003 SGD
+SGD S000003630 KHA1 GO:0015386 SGD_REF:S000056339|PMID:9811642 ISS F YJL094C gene taxon:4932 20021003 SGD
+SGD S000003630 KHA1 GO:0015386 SGD_REF:S000056339|PMID:9811642 IMP F YJL094C gene taxon:4932 20021003 SGD
+SGD S000003630 KHA1 GO:0015672 SGD_REF:S000056339|PMID:9811642 ISS P YJL094C gene taxon:4932 20021003 SGD
+SGD S000003630 KHA1 GO:0015672 SGD_REF:S000056339|PMID:9811642 IMP P YJL094C gene taxon:4932 20021003 SGD
+SGD S000001144 KIC1 GO:0000131 SGD_REF:S000074101|PMID:12972564 IDA C YHR102W|NRK1 gene taxon:4932 20031016 SGD
+SGD S000001144 KIC1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YHR102W|NRK1 gene taxon:4932 20031028 SGD
+SGD S000001144 KIC1 GO:0005933 SGD_REF:S000074101|PMID:12972564 IDA C YHR102W|NRK1 gene taxon:4932 20031016 SGD
+SGD S000001144 KIC1 GO:0043332 SGD_REF:S000074101|PMID:12972564 IDA C YHR102W|NRK1 gene taxon:4932 20031016 SGD
+SGD S000001144 KIC1 GO:0016301 SGD_REF:S000058385|PMID:9813095 IDA F YHR102W|NRK1 gene taxon:4932 20020816 SGD
+SGD S000001144 KIC1 GO:0016301 SGD_REF:S000058385|PMID:9813095 ISS F YHR102W|NRK1 gene taxon:4932 20020816 SGD
+SGD S000001144 KIC1 GO:0000902 SGD_REF:S000058385|PMID:9813095 IGI P YHR102W|NRK1 gene taxon:4932 20021108 SGD
+SGD S000001144 KIC1 GO:0000902 SGD_REF:S000058385|PMID:9813095 IMP P YHR102W|NRK1 gene taxon:4932 20021108 SGD
+SGD S000001144 KIC1 GO:0000903 SGD_REF:S000074101|PMID:12972564 IGI P YHR102W|NRK1 gene taxon:4932 20050420 SGD
+SGD S000001144 KIC1 GO:0007047 SGD_REF:S000072008|PMID:12480907 IGI P YHR102W|NRK1 gene taxon:4932 20030129 SGD
+SGD S000001144 KIC1 GO:0007047 SGD_REF:S000072008|PMID:12480907 IMP P YHR102W|NRK1 gene taxon:4932 20030129 SGD
+SGD S000002529 KIN1 GO:0005624 SGD_REF:S000054277|PMID:8020610 IDA C YDR122W gene taxon:4932 20020816 SGD
+SGD S000002529 KIN1 GO:0005886 SGD_REF:S000080224|PMID:15563607 IPI SGD:S000006236 C YDR122W gene taxon:4932 20050216 SGD
+SGD S000002529 KIN1 GO:0004672 SGD_REF:S000043444|PMID:8203145 IDA F YDR122W gene taxon:4932 20020816 SGD
+SGD S000002529 KIN1 GO:0004672 SGD_REF:S000043444|PMID:8203145 ISS F YDR122W gene taxon:4932 20020816 SGD
+SGD S000002529 KIN1 GO:0006887 SGD_REF:S000080224|PMID:15563607 IGI P YDR122W gene taxon:4932 20050216 SGD
+SGD S000002529 KIN1 GO:0006887 SGD_REF:S000080224|PMID:15563607 IPI P YDR122W gene taxon:4932 20050216 SGD
+SGD S000004086 KIN2 GO:0005624 SGD_REF:S000054277|PMID:8020610 IDA C YLR096W gene taxon:4932 20020816 SGD
+SGD S000004086 KIN2 GO:0005886 SGD_REF:S000080224|PMID:15563607 IPI SGD:S000006236 C YLR096W gene taxon:4932 20050216 SGD
+SGD S000004086 KIN2 GO:0004672 SGD_REF:S000043444|PMID:8203145 IDA F YLR096W gene taxon:4932 20020816 SGD
+SGD S000004086 KIN2 GO:0004672 SGD_REF:S000043444|PMID:8203145 ISS F YLR096W gene taxon:4932 20020816 SGD
+SGD S000004086 KIN2 GO:0006887 SGD_REF:S000080224|PMID:15563607 IGI P YLR096W gene taxon:4932 20050216 SGD
+SGD S000004086 KIN2 GO:0006887 SGD_REF:S000080224|PMID:15563607 IPI P YLR096W gene taxon:4932 20050216 SGD
+SGD S000002266 KIN28 GO:0005675 SGD_REF:S000057565|PMID:8001136 IDA C YDL108W gene taxon:4932 20051102 SGD
+SGD S000002266 KIN28 GO:0005675 SGD_REF:S000057565|PMID:8001136 IPI SGD:S000002719 C YDL108W gene taxon:4932 20051102 SGD
+SGD S000002266 KIN28 GO:0004693 SGD_REF:S000058446|PMID:9774381 TAS F YDL108W gene taxon:4932 20010118 SGD
+SGD S000002266 KIN28 GO:0008353 SGD_REF:S000063826|PMID:2657724 IDA F YDL108W gene taxon:4932 20051102 SGD
+SGD S000002266 KIN28 GO:0008353 SGD_REF:S000055122|PMID:7783209 IMP F YDL108W gene taxon:4932 20051102 SGD
+SGD S000002266 KIN28 GO:0008353 SGD_REF:S000046450|PMID:7760796 IDA F YDL108W gene taxon:4932 20051102 SGD
+SGD S000002266 KIN28 GO:0008353 SGD_REF:S000057565|PMID:8001136 ISS F YDL108W gene taxon:4932 20051102 SGD
+SGD S000002266 KIN28 GO:0016251 SGD_REF:S000058446|PMID:9774381 TAS F YDL108W gene taxon:4932 20010119 SGD
+SGD S000002266 KIN28 NOT GO:0019912 SGD_REF:S000046450|PMID:7760796 IDA F YDL108W gene taxon:4932 20051102 SGD
+SGD S000002266 KIN28 NOT GO:0019912 SGD_REF:S000046450|PMID:7760796 IMP F YDL108W gene taxon:4932 20051102 SGD
+SGD S000002266 KIN28 GO:0006367 SGD_REF:S000056378|PMID:10384286 TAS P YDL108W gene taxon:4932 20010118 SGD
+SGD S000002266 KIN28 GO:0006367 SGD_REF:S000056377|PMID:10384273 TAS P YDL108W gene taxon:4932 20010118 SGD
+SGD S000002266 KIN28 GO:0006468 SGD_REF:S000046450|PMID:7760796 IDA P YDL108W gene taxon:4932 20051102 SGD
+SGD S000002266 KIN28 GO:0006468 SGD_REF:S000063826|PMID:2657724 IDA P YDL108W gene taxon:4932 20051102 SGD
+SGD S000002266 KIN28 GO:0006468 SGD_REF:S000055122|PMID:7783209 IMP P YDL108W gene taxon:4932 20051102 SGD
+SGD S000002266 KIN28 GO:0045944 SGD_REF:S000046450|PMID:7760796 IMP P YDL108W gene taxon:4932 20051102 SGD
+SGD S000002266 KIN28 GO:0045944 SGD_REF:S000055122|PMID:7783209 IMP P YDL108W gene taxon:4932 20051102 SGD
+SGD S000000071 KIN3 GO:0008372 SGD_REF:S000069584 ND C protein kinase YAR018C|FUN52|NPK1 gene taxon:4932 20021009 SGD
+SGD S000000071 KIN3 GO:0004672 SGD_REF:S000046944|PMID:2199332 ISS F protein kinase YAR018C|FUN52|NPK1 gene taxon:4932 20021009 SGD
+SGD S000000071 KIN3 GO:0007059 SGD_REF:S000072536|PMID:12386167 IMP P protein kinase YAR018C|FUN52|NPK1 gene taxon:4932 20030217 SGD
+SGD S000005759 KIN4 GO:0005816 SGD_REF:S000086184|PMID:16039590 IDA C protein kinase YOR233W|KIN3|KIN31 gene taxon:4932 20060216 SGD
+SGD S000005759 KIN4 GO:0005935 SGD_REF:S000086185|PMID:16039591 IDA C protein kinase YOR233W|KIN3|KIN31 gene taxon:4932 20060216 SGD
+SGD S000005759 KIN4 GO:0005938 SGD_REF:S000086185|PMID:16039591 IDA C protein kinase YOR233W|KIN3|KIN31 gene taxon:4932 20060216 SGD
+SGD S000005759 KIN4 GO:0004672 SGD_REF:S000045705|PMID:8465601 ISS F protein kinase YOR233W|KIN3|KIN31 gene taxon:4932 20030122 SGD
+SGD S000005759 KIN4 GO:0004672 SGD_REF:S000086185|PMID:16039591 IMP F protein kinase YOR233W|KIN3|KIN31 gene taxon:4932 20060216 SGD
+SGD S000005759 KIN4 GO:0031578 SGD_REF:S000086185|PMID:16039591 IGI P protein kinase YOR233W|KIN3|KIN31 gene taxon:4932 20060313 SGD
+SGD S000005759 KIN4 GO:0031578 SGD_REF:S000086185|PMID:16039591 IMP P protein kinase YOR233W|KIN3|KIN31 gene taxon:4932 20060313 SGD
+SGD S000005759 KIN4 GO:0031578 SGD_REF:S000086184|PMID:16039590 IGI P protein kinase YOR233W|KIN3|KIN31 gene taxon:4932 20060313 SGD
+SGD S000005759 KIN4 GO:0031578 SGD_REF:S000086184|PMID:16039590 IMP P protein kinase YOR233W|KIN3|KIN31 gene taxon:4932 20060313 SGD
+SGD S000000687 KIN82 GO:0008372 SGD_REF:S000069584 ND C serine/threonine kinase (putative), similar to cyclic nucleotide-dependent protein kinase subfamily and the protein kinase C subfamily YCR091W gene taxon:4932 20020925 SGD
+SGD S000000687 KIN82 GO:0004672 SGD_REF:S000041142|PMID:1580103 ISS F serine/threonine kinase (putative), similar to cyclic nucleotide-dependent protein kinase subfamily and the protein kinase C subfamily YCR091W gene taxon:4932 20020925 SGD
+SGD S000000687 KIN82 GO:0006468 SGD_REF:S000041142|PMID:1580103 ISS P serine/threonine kinase (putative), similar to cyclic nucleotide-dependent protein kinase subfamily and the protein kinase C subfamily YCR091W gene taxon:4932 20030930 SGD
+SGD S000000687 KIN82 GO:0019236 SGD_REF:S000061243|PMID:11337509 IGI P serine/threonine kinase (putative), similar to cyclic nucleotide-dependent protein kinase subfamily and the protein kinase C subfamily YCR091W gene taxon:4932 20030930 SGD
+SGD S000000159 KIP1 GO:0005816 SGD_REF:S000047788|PMID:9585415 IDA C kinesin related protein YBL063W|CIN9 gene taxon:4932 20010118 SGD
+SGD S000000159 KIP1 GO:0005871 SGD_REF:S000058447|PMID:9153752 TAS C kinesin related protein YBL063W|CIN9 gene taxon:4932 20010118 SGD
+SGD S000000159 KIP1 GO:0005876 SGD_REF:S000058447|PMID:9153752 TAS C kinesin related protein YBL063W|CIN9 gene taxon:4932 20010118 SGD
+SGD S000000159 KIP1 GO:0003777 SGD_REF:S000058447|PMID:9153752 TAS F kinesin related protein YBL063W|CIN9 gene taxon:4932 20010118 SGD
+SGD S000000159 KIP1 GO:0005200 SGD_REF:S000047788|PMID:9585415 IPI F kinesin related protein YBL063W|CIN9 gene taxon:4932 20010118 SGD
+SGD S000000159 KIP1 GO:0000092 SGD_REF:S000058448|PMID:9813090 IMP P kinesin related protein YBL063W|CIN9 gene taxon:4932 20010118 SGD
+SGD S000000159 KIP1 GO:0007020 SGD_REF:S000058447|PMID:9153752 IPI P kinesin related protein YBL063W|CIN9 gene taxon:4932 20010118 SGD
+SGD S000006076 KIP2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C kinesin related protein YPL155C gene taxon:4932 20040928 SGD
+SGD S000006076 KIP2 GO:0005871 SGD_REF:S000058447|PMID:9153752 TAS C kinesin related protein YPL155C gene taxon:4932 20010118 SGD
+SGD S000006076 KIP2 GO:0005881 SGD_REF:S000052859|PMID:9693366 IDA C kinesin related protein YPL155C gene taxon:4932 20010118 SGD
+SGD S000006076 KIP2 GO:0003777 SGD_REF:S000058447|PMID:9153752 TAS F kinesin related protein YPL155C gene taxon:4932 20010118 SGD
+SGD S000006076 KIP2 GO:0000092 SGD_REF:S000058448|PMID:9813090 IMP P kinesin related protein YPL155C gene taxon:4932 20010118 SGD
+SGD S000006076 KIP2 GO:0007026 SGD_REF:S000052859|PMID:9693366 IMP P kinesin related protein YPL155C gene taxon:4932 20010118 SGD
+SGD S000006076 KIP2 GO:0030473 SGD_REF:S000052859|PMID:9693366 IMP P kinesin related protein YPL155C gene taxon:4932 20010118 SGD
+SGD S000003184 KIP3 GO:0005871 SGD_REF:S000058447|PMID:9153752 TAS C YGL216W gene taxon:4932 20010118 SGD
+SGD S000003184 KIP3 GO:0005880 SGD_REF:S000052859|PMID:9693366 IDA C YGL216W gene taxon:4932 20010118 SGD
+SGD S000003184 KIP3 GO:0005881 SGD_REF:S000052859|PMID:9693366 IDA C YGL216W gene taxon:4932 20010118 SGD
+SGD S000003184 KIP3 GO:0003777 SGD_REF:S000058447|PMID:9153752 TAS F YGL216W gene taxon:4932 20010118 SGD
+SGD S000003184 KIP3 GO:0000132 SGD_REF:S000042553|PMID:9281582 IMP P YGL216W gene taxon:4932 20040128 SGD
+SGD S000003184 KIP3 GO:0000132 SGD_REF:S000042553|PMID:9281582 IGI P YGL216W gene taxon:4932 20040128 SGD
+SGD S000003184 KIP3 GO:0007019 SGD_REF:S000052859|PMID:9693366 IMP P YGL216W gene taxon:4932 20010118 SGD
+SGD S000003184 KIP3 GO:0030472 SGD_REF:S000049652|PMID:10525539 IMP P YGL216W gene taxon:4932 20010118 SGD
+SGD S000003184 KIP3 GO:0030472 SGD_REF:S000049652|PMID:10525539 IGI P YGL216W gene taxon:4932 20010118 SGD
+SGD S000003184 KIP3 GO:0030473 SGD_REF:S000052859|PMID:9693366 IMP P YGL216W gene taxon:4932 20010118 SGD
+SGD S000003184 KIP3 GO:0051228 SGD_REF:S000058448|PMID:9813090 IMP P YGL216W gene taxon:4932 20050407 SGD
+SGD S000001651 KKQ8 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YKL168C gene taxon:4932 20031028 SGD
+SGD S000001651 KKQ8 GO:0004672 SGD_REF:S000058030|PMID:9020587 ISS F YKL168C gene taxon:4932 20030204 SGD
+SGD S000001651 KKQ8 GO:0000004 SGD_REF:S000069584 ND P YKL168C gene taxon:4932 20021004 SGD
+SGD S000002207 KNH1 GO:0005576 SGD_REF:S000039479|PMID:8810042 IDA C KRE9 homolog YDL049C gene taxon:4932 20020531 SGD
+SGD S000002207 KNH1 GO:0009277 SGD_REF:S000061549|PMID:10672173 NAS C KRE9 homolog YDL049C gene taxon:4932 20020531 SGD
+SGD S000002207 KNH1 GO:0005554 SGD_REF:S000069584 ND F KRE9 homolog YDL049C gene taxon:4932 20020531 SGD
+SGD S000002207 KNH1 GO:0006078 SGD_REF:S000039479|PMID:8810042 IGI P KRE9 homolog YDL049C gene taxon:4932 20020531 SGD
+SGD S000002207 KNH1 GO:0006078 SGD_REF:S000039479|PMID:8810042 IMP P KRE9 homolog YDL049C gene taxon:4932 20020531 SGD
+SGD S000003942 KNS1 GO:0008372 SGD_REF:S000069584 ND C protein kinase homolog YLL019C|L124 gene taxon:4932 20021105 SGD
+SGD S000003942 KNS1 GO:0004674 SGD_REF:S000046621|PMID:8910305 IDA F protein kinase homolog YLL019C|L124 gene taxon:4932 20020703 SGD
+SGD S000003942 KNS1 GO:0004674 SGD_REF:S000046621|PMID:8910305 IMP F protein kinase homolog YLL019C|L124 gene taxon:4932 20020703 SGD
+SGD S000003942 KNS1 GO:0004713 SGD_REF:S000046621|PMID:8910305 IDA F protein kinase homolog YLL019C|L124 gene taxon:4932 20020703 SGD
+SGD S000003942 KNS1 GO:0004713 SGD_REF:S000046621|PMID:8910305 IMP F protein kinase homolog YLL019C|L124 gene taxon:4932 20020703 SGD
+SGD S000003942 KNS1 GO:0006468 SGD_REF:S000046621|PMID:8910305 IDA P protein kinase homolog YLL019C|L124 gene taxon:4932 20020703 SGD
+SGD S000001229 KOG1 GO:0000329 SGD_REF:S000074185|PMID:14562095 IDA C YHR186C|LAS24 gene taxon:4932 20031028 SGD
+SGD S000001229 KOG1 GO:0000329 SGD_REF:S000114144|PMID:16394584 IDA C YHR186C|LAS24 gene taxon:4932 20060118 SGD
+SGD S000001229 KOG1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YHR186C|LAS24 gene taxon:4932 20040928 SGD
+SGD S000001229 KOG1 GO:0005886 SGD_REF:S000114144|PMID:16394584 IDA C YHR186C|LAS24 gene taxon:4932 20060118 SGD
+SGD S000001229 KOG1 GO:0031931 SGD_REF:S000071528|PMID:12408816 IPI C YHR186C|LAS24 gene taxon:4932 20051130 SGD
+SGD S000001229 KOG1 GO:0005554 SGD_REF:S000069584 ND F YHR186C|LAS24 gene taxon:4932 20040528 SGD
+SGD S000001229 KOG1 GO:0001558 SGD_REF:S000071528|PMID:12408816 IPI SGD:S000003827|SGD:S000001686 P YHR186C|LAS24 gene taxon:4932 20051104 SGD
+SGD S000001229 KOG1 GO:0009267 SGD_REF:S000071528|PMID:12408816 IMP P YHR186C|LAS24 gene taxon:4932 20051104 SGD
+SGD S000005266 KRE1 GO:0009277 SGD_REF:S000069752|PMID:11956747 IDA C YNL322C gene taxon:4932 20020613 SGD
+SGD S000005266 KRE1 GO:0005199 SGD_REF:S000069182|PMID:11853673 TAS F YNL322C gene taxon:4932 20020927 SGD
+SGD S000005266 KRE1 GO:0007047 SGD_REF:S000040428|PMID:9791887 TAS P YNL322C gene taxon:4932 20020927 SGD
+SGD S000003398 KRE11 GO:0030008 SGD_REF:S000043703|PMID:10727015 IDA C YGR166W|TRS65 gene taxon:4932 20020716 SGD
+SGD S000003398 KRE11 GO:0005554 SGD_REF:S000069584 ND F YGR166W|TRS65 gene taxon:4932 20020716 SGD
+SGD S000003398 KRE11 GO:0006888 SGD_REF:S000043703|PMID:10727015 IMP P YGR166W|TRS65 gene taxon:4932 20020716 SGD
+SGD S000002891 KRE2 GO:0005794 SGD_REF:S000053395|PMID:1550992 ISS C alpha-1,2-mannosyltransferase YDR483W|MNT1 gene taxon:4932 20010118 SGD
+SGD S000002891 KRE2 GO:0000026 SGD_REF:S000053395|PMID:1550992 ISS F alpha-1,2-mannosyltransferase YDR483W|MNT1 gene taxon:4932 20010118 SGD
+SGD S000002891 KRE2 GO:0000026 SGD_REF:S000053395|PMID:1550992 IDA F alpha-1,2-mannosyltransferase YDR483W|MNT1 gene taxon:4932 20010118 SGD
+SGD S000002891 KRE2 GO:0000032 SGD_REF:S000048175|PMID:1541391 IMP P alpha-1,2-mannosyltransferase YDR483W|MNT1 gene taxon:4932 20010118 SGD
+SGD S000002891 KRE2 GO:0006491 SGD_REF:S000052134|PMID:1495972 IMP P alpha-1,2-mannosyltransferase YDR483W|MNT1 gene taxon:4932 20010118 SGD
+SGD S000002891 KRE2 GO:0006493 SGD_REF:S000052134|PMID:1495972 IMP P alpha-1,2-mannosyltransferase YDR483W|MNT1 gene taxon:4932 20010118 SGD
+SGD S000001289 KRE27 GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YIL027C gene taxon:4932 20031028 SGD
+SGD S000001289 KRE27 GO:0005554 SGD_REF:S000069584 ND F YIL027C gene taxon:4932 20021122 SGD
+SGD S000001289 KRE27 GO:0000004 SGD_REF:S000069584 ND P YIL027C gene taxon:4932 20021122 SGD
+SGD S000000840 KRE29 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YER038C gene taxon:4932 20031028 SGD
+SGD S000000840 KRE29 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YER038C gene taxon:4932 20031028 SGD
+SGD S000000840 KRE29 GO:0030915 SGD_REF:S000080949|PMID:15738391 IPI SGD:S000000745|SGD:S000005394|SGD:S000004375 C YER038C gene taxon:4932 20060309 SGD
+SGD S000000840 KRE29 GO:0005554 SGD_REF:S000069584 ND F YER038C gene taxon:4932 20021122 SGD
+SGD S000000840 KRE29 GO:0006281 SGD_REF:S000080949|PMID:15738391 IMP P YER038C gene taxon:4932 20060309 SGD
+SGD S000005076 KRE33 GO:0005730 SGD_REF:S000074185|PMID:14562095 IDA C YNL132W gene taxon:4932 20031028 SGD
+SGD S000005076 KRE33 GO:0005554 SGD_REF:S000069584 ND F YNL132W gene taxon:4932 20021122 SGD
+SGD S000005076 KRE33 GO:0000004 SGD_REF:S000069584 ND P YNL132W gene taxon:4932 20021122 SGD
+SGD S000005863 KRE5 GO:0005783 SGD_REF:S000039409|PMID:10601196 TAS C YOR336W gene taxon:4932 20020927 SGD
+SGD S000005863 KRE5 GO:0003980 SGD_REF:S000039862|PMID:9611196 IDA F YOR336W gene taxon:4932 20020927 SGD
+SGD S000005863 KRE5 GO:0006078 SGD_REF:S000055885|PMID:8550469 TAS P YOR336W gene taxon:4932 20020927 SGD
+SGD S000006363 KRE6 GO:0000137 SGD_REF:S000071556|PMID:12237851 IDA C beta-glucan synthase (putative) YPR159W|CWH48 gene taxon:4932 20030123 SGD
+SGD S000006363 KRE6 GO:0016021 SGD_REF:S000040783|PMID:7929594 IDA C beta-glucan synthase (putative) YPR159W|CWH48 gene taxon:4932 20020718 SGD
+SGD S000006363 KRE6 GO:0015926 SGD_REF:S000039409|PMID:10601196 IMP F beta-glucan synthase (putative) YPR159W|CWH48 gene taxon:4932 20021111 SGD
+SGD S000006363 KRE6 GO:0015926 SGD_REF:S000039409|PMID:10601196 ISS F beta-glucan synthase (putative) YPR159W|CWH48 gene taxon:4932 20021111 SGD
+SGD S000006363 KRE6 GO:0006078 SGD_REF:S000040783|PMID:7929594 ISS P beta-glucan synthase (putative) YPR159W|CWH48 gene taxon:4932 20020718 SGD
+SGD S000006363 KRE6 GO:0006078 SGD_REF:S000040783|PMID:7929594 IMP P beta-glucan synthase (putative) YPR159W|CWH48 gene taxon:4932 20020718 SGD
+SGD S000006363 KRE6 GO:0007047 SGD_REF:S000040783|PMID:7929594 IMP P beta-glucan synthase (putative) YPR159W|CWH48 gene taxon:4932 20020718 SGD
+SGD S000003710 KRE9 GO:0005576 SGD_REF:S000040973|PMID:8413233 IDA C YJL174W gene taxon:4932 20010118 SGD
+SGD S000003710 KRE9 GO:0005554 SGD_REF:S000069584 ND F YJL174W gene taxon:4932 20021205 SGD
+SGD S000003710 KRE9 GO:0006077 SGD_REF:S000040973|PMID:8413233 IMP P YJL174W gene taxon:4932 20010118 SGD
+SGD S000003710 KRE9 GO:0007047 SGD_REF:S000040973|PMID:8413233 IMP P YJL174W gene taxon:4932 20010118 SGD
+SGD S000005252 KRI1 GO:0005730 SGD_REF:S000059129|PMID:11027267 IDA C Krr1p binding protein YNL308C gene taxon:4932 20010212 SGD
+SGD S000005252 KRI1 GO:0005554 SGD_REF:S000069584 ND F Krr1p binding protein YNL308C gene taxon:4932 20010212 SGD
+SGD S000005252 KRI1 GO:0007046 SGD_REF:S000059129|PMID:11027267 IDA P Krr1p binding protein YNL308C gene taxon:4932 20010212 SGD
+SGD S000000564 KRR1 GO:0005730 SGD_REF:S000059129|PMID:11027267 IDA C YCL059C gene taxon:4932 20010212 SGD
+SGD S000000564 KRR1 GO:0005732 SGD_REF:S000079989|PMID:15590835 IPI SGD:S000003762 C YCL059C gene taxon:4932 20050124 SGD
+SGD S000000564 KRR1 GO:0005554 SGD_REF:S000069584 ND F YCL059C gene taxon:4932 20010212 SGD
+SGD S000000564 KRR1 GO:0006364 SGD_REF:S000069769|PMID:11996121 IMP P YCL059C gene taxon:4932 20030424 SGD
+SGD S000000564 KRR1 GO:0006365 SGD_REF:S000079989|PMID:15590835 IPI SGD:S000003762|SGD:S000007441|SGD:S000007294 P YCL059C gene taxon:4932 20060315 SGD
+SGD S000000564 KRR1 GO:0007046 SGD_REF:S000059129|PMID:11027267 IMP P YCL059C gene taxon:4932 20010212 SGD
+SGD S000002444 KRS1 GO:0005737 SGD_REF:S000048983|PMID:2668951 TAS C lysine-tRNA ligase YDR037W|GCD5 gene taxon:4932 20020927 SGD
+SGD S000002444 KRS1 GO:0004824 SGD_REF:S000054019|PMID:2903861 IDA F lysine-tRNA ligase YDR037W|GCD5 gene taxon:4932 20030114 SGD
+SGD S000002444 KRS1 GO:0006430 SGD_REF:S000063840|PMID:7628447 IDA P lysine-tRNA ligase YDR037W|GCD5 gene taxon:4932 20020927 SGD
+SGD S000001124 KSP1 GO:0005634 SGD_REF:S000045656|PMID:8676864 IDA C YHR082C gene taxon:4932 20020926 SGD
+SGD S000001124 KSP1 GO:0004674 SGD_REF:S000045656|PMID:8676864 IDA F YHR082C gene taxon:4932 20020926 SGD
+SGD S000001124 KSP1 GO:0006468 SGD_REF:S000045656|PMID:8676864 IDA P YHR082C gene taxon:4932 20020926 SGD
+SGD S000003272 KSS1 GO:0005634 SGD_REF:S000053804|PMID:7579701 IDA C MAP kinase YGR040W gene taxon:4932 20010118 SGD
+SGD S000003272 KSS1 GO:0004707 SGD_REF:S000041791|PMID:8668180 ISS F MAP kinase YGR040W gene taxon:4932 20010118 SGD
+SGD S000003272 KSS1 GO:0001402 SGD_REF:S000039888|PMID:9393860 IGI P MAP kinase YGR040W gene taxon:4932 20040921 SGD
+SGD S000003272 KSS1 GO:0001402 SGD_REF:S000039888|PMID:9393860 IMP P MAP kinase YGR040W gene taxon:4932 20040921 SGD
+SGD S000003272 KSS1 GO:0001403 SGD_REF:S000050425|PMID:8001818 IMP P MAP kinase YGR040W gene taxon:4932 20050218 SGD
+SGD S000007587 KTI11 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YBL071W-A|DPH3 gene taxon:4932 20031028 SGD
+SGD S000007587 KTI11 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YBL071W-A|DPH3 gene taxon:4932 20031028 SGD
+SGD S000007587 KTI11 GO:0005554 SGD_REF:S000069584 ND F YBL071W-A|DPH3 gene taxon:4932 20020425 SGD
+SGD S000007587 KTI11 GO:0000080 SGD_REF:S000069896|PMID:11994165 IDA P YBL071W-A|DPH3 gene taxon:4932 20020616 SGD
+SGD S000007587 KTI11 GO:0017183 SGD_REF:S000079857|PMID:15485916 IMP P YBL071W-A|DPH3 gene taxon:4932 20050303 SGD
+SGD S000001593 KTI12 GO:0016591 SGD_REF:S000069518|PMID:11929532 TAS C Elongator associated protein YKL110C|TOT4 gene taxon:4932 20020616 SGD
+SGD S000001593 KTI12 GO:0030234 SGD_REF:S000069518|PMID:11929532 IDA F Elongator associated protein YKL110C|TOT4 gene taxon:4932 20020927 SGD
+SGD S000001593 KTI12 GO:0015976 SGD_REF:S000070415|PMID:12139626 IPI P Elongator associated protein YKL110C|TOT4 gene taxon:4932 20020927 SGD
+SGD S000005625 KTR1 GO:0005794 SGD_REF:S000041908|PMID:8631921 IDA C type II transmembrane protein YOR099W gene taxon:4932 20010118 SGD
+SGD S000005625 KTR1 GO:0000026 SGD_REF:S000046227|PMID:9020857 IDA F type II transmembrane protein YOR099W gene taxon:4932 20010118 SGD
+SGD S000005625 KTR1 GO:0000026 SGD_REF:S000056042|PMID:9182588 IMP F type II transmembrane protein YOR099W gene taxon:4932 20010118 SGD
+SGD S000005625 KTR1 GO:0000032 SGD_REF:S000041908|PMID:8631921 IMP P type II transmembrane protein YOR099W gene taxon:4932 20010118 SGD
+SGD S000005625 KTR1 GO:0006491 SGD_REF:S000056042|PMID:9182588 IMP P type II transmembrane protein YOR099W gene taxon:4932 20010118 SGD
+SGD S000005625 KTR1 GO:0006493 SGD_REF:S000056042|PMID:9182588 IMP P type II transmembrane protein YOR099W gene taxon:4932 20010118 SGD
+SGD S000001769 KTR2 GO:0005794 SGD_REF:S000041908|PMID:8631921 IDA C mannosyltransferase (putative), type 2 membrane protein YKR061W gene taxon:4932 20010118 SGD
+SGD S000001769 KTR2 GO:0000030 SGD_REF:S000041908|PMID:8631921 IDA F mannosyltransferase (putative), type 2 membrane protein YKR061W gene taxon:4932 20010118 SGD
+SGD S000001769 KTR2 GO:0000032 SGD_REF:S000041908|PMID:8631921 IMP P mannosyltransferase (putative), type 2 membrane protein YKR061W gene taxon:4932 20010118 SGD
+SGD S000001769 KTR2 GO:0006487 SGD_REF:S000041908|PMID:8631921 IMP P mannosyltransferase (putative), type 2 membrane protein YKR061W gene taxon:4932 20010118 SGD
+SGD S000000409 KTR3 GO:0005624 SGD_REF:S000056042|PMID:9182588 ISS C alpha-1,2-mannosyltransferase (putative) YBR205W gene taxon:4932 20010118 SGD
+SGD S000000409 KTR3 GO:0000030 SGD_REF:S000056042|PMID:9182588 IMP F alpha-1,2-mannosyltransferase (putative) YBR205W gene taxon:4932 20010118 SGD
+SGD S000000409 KTR3 GO:0000030 SGD_REF:S000056042|PMID:9182588 ISS F alpha-1,2-mannosyltransferase (putative) YBR205W gene taxon:4932 20010118 SGD
+SGD S000000409 KTR3 GO:0006487 SGD_REF:S000056042|PMID:9182588 IMP P alpha-1,2-mannosyltransferase (putative) YBR205W gene taxon:4932 20010118 SGD
+SGD S000000409 KTR3 GO:0006493 SGD_REF:S000056042|PMID:9182588 IMP P alpha-1,2-mannosyltransferase (putative) YBR205W gene taxon:4932 20010118 SGD
+SGD S000000409 KTR3 GO:0007047 SGD_REF:S000050932|PMID:9878809 IMP P alpha-1,2-mannosyltransferase (putative) YBR205W gene taxon:4932 20010118 SGD
+SGD S000000403 KTR4 GO:0005794 SGD_REF:S000050932|PMID:9878809 ISS C alpha-1,2-mannosyltransferase (putative) YBR199W gene taxon:4932 20010118 SGD
+SGD S000000403 KTR4 GO:0000030 SGD_REF:S000050932|PMID:9878809 ISS F alpha-1,2-mannosyltransferase (putative) YBR199W gene taxon:4932 20010118 SGD
+SGD S000000403 KTR4 GO:0006487 SGD_REF:S000050932|PMID:9878809 ISS P alpha-1,2-mannosyltransferase (putative) YBR199W gene taxon:4932 20010118 SGD
+SGD S000004974 KTR5 GO:0005794 SGD_REF:S000050932|PMID:9878809 ISS C mannosyltransferase (putative) YNL029C gene taxon:4932 20010118 SGD
+SGD S000004974 KTR5 GO:0000030 SGD_REF:S000050932|PMID:9878809 ISS F mannosyltransferase (putative) YNL029C gene taxon:4932 20010118 SGD
+SGD S000004974 KTR5 GO:0006487 SGD_REF:S000050932|PMID:9878809 ISS P mannosyltransferase (putative) YNL029C gene taxon:4932 20010118 SGD
+SGD S000004974 KTR5 GO:0007047 SGD_REF:S000047641|PMID:9090056 IMP P mannosyltransferase (putative) YNL029C gene taxon:4932 20010118 SGD
+SGD S000005974 KTR6 GO:0005624 SGD_REF:S000047803|PMID:9218445 ISS C mannosylphosphate transferase YPL053C|MNN6 gene taxon:4932 20010118 SGD
+SGD S000005974 KTR6 GO:0000031 SGD_REF:S000047803|PMID:9218445 ISS F mannosylphosphate transferase YPL053C|MNN6 gene taxon:4932 20010118 SGD
+SGD S000005974 KTR6 GO:0000031 SGD_REF:S000047803|PMID:9218445 IMP F mannosylphosphate transferase YPL053C|MNN6 gene taxon:4932 20010118 SGD
+SGD S000005974 KTR6 GO:0006487 SGD_REF:S000047803|PMID:9218445 IMP P mannosylphosphate transferase YPL053C|MNN6 gene taxon:4932 20010118 SGD
+SGD S000005974 KTR6 GO:0007047 SGD_REF:S000047641|PMID:9090056 IMP P mannosylphosphate transferase YPL053C|MNN6 gene taxon:4932 20010118 SGD
+SGD S000001347 KTR7 GO:0005794 SGD_REF:S000050932|PMID:9878809 ISS C YIL085C gene taxon:4932 20010118 SGD
+SGD S000001347 KTR7 GO:0000030 SGD_REF:S000050932|PMID:9878809 ISS F YIL085C gene taxon:4932 20010118 SGD
+SGD S000001347 KTR7 GO:0006487 SGD_REF:S000050932|PMID:9878809 ISS P YIL085C gene taxon:4932 20010118 SGD
+SGD S000001347 KTR7 GO:0007047 SGD_REF:S000047641|PMID:9090056 IMP P YIL085C gene taxon:4932 20010118 SGD
+SGD S000003743 LAA1 colocalizes_with GO:0030136 SGD_REF:S000074185|PMID:14562095 IDA C YJL207C gene taxon:4932 20031028 SGD
+SGD S000003743 LAA1 GO:0005554 SGD_REF:S000069584 ND F YJL207C gene taxon:4932 20021119 SGD
+SGD S000003743 LAA1 GO:0000004 SGD_REF:S000069584 ND P YJL207C gene taxon:4932 20021119 SGD
+SGD S000001491 LAC1 GO:0005783 SGD_REF:S000062191|PMID:11074293 TAS C LAG1 longevity gene homolog YKL008C|DGT1 gene taxon:4932 20020930 SGD
+SGD S000001491 LAC1 GO:0050291 SGD_REF:S000066247|PMID:11694577 IMP F LAG1 longevity gene homolog YKL008C|DGT1 gene taxon:4932 20040206 SGD
+SGD S000001491 LAC1 GO:0050291 SGD_REF:S000060433|PMID:11387200 IMP F LAG1 longevity gene homolog YKL008C|DGT1 gene taxon:4932 20040206 SGD
+SGD S000001491 LAC1 GO:0050291 SGD_REF:S000081342|PMID:15692566 IDA F LAG1 longevity gene homolog YKL008C|DGT1 gene taxon:4932 20050419 SGD
+SGD S000001491 LAC1 GO:0007568 SGD_REF:S000062191|PMID:11074293 TAS P LAG1 longevity gene homolog YKL008C|DGT1 gene taxon:4932 20020930 SGD
+SGD S000001491 LAC1 GO:0046513 SGD_REF:S000066247|PMID:11694577 IMP P LAG1 longevity gene homolog YKL008C|DGT1 gene taxon:4932 20030130 SGD
+SGD S000001491 LAC1 GO:0046513 SGD_REF:S000081342|PMID:15692566 IDA P LAG1 longevity gene homolog YKL008C|DGT1 gene taxon:4932 20050419 SGD
+SGD S000000995 LAG1 GO:0005783 SGD_REF:S000069459|PMID:11914276 IDA C YHL003C gene taxon:4932 20020507 SGD
+SGD S000000995 LAG1 GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YHL003C gene taxon:4932 20031028 SGD
+SGD S000000995 LAG1 GO:0050291 SGD_REF:S000060433|PMID:11387200 IMP F YHL003C gene taxon:4932 20040206 SGD
+SGD S000000995 LAG1 GO:0050291 SGD_REF:S000081342|PMID:15692566 IDA F YHL003C gene taxon:4932 20050419 SGD
+SGD S000000995 LAG1 GO:0050291 SGD_REF:S000066247|PMID:11694577 IMP F YHL003C gene taxon:4932 20040206 SGD
+SGD S000000995 LAG1 GO:0001302 SGD_REF:S000053949|PMID:8195187 IMP P YHL003C gene taxon:4932 20030814 SGD
+SGD S000000995 LAG1 GO:0001302 SGD_REF:S000053949|PMID:8195187 IEP P YHL003C gene taxon:4932 20030814 SGD
+SGD S000000995 LAG1 GO:0046513 SGD_REF:S000066247|PMID:11694577 IMP P YHL003C gene taxon:4932 20030130 SGD
+SGD S000000995 LAG1 GO:0046513 SGD_REF:S000081342|PMID:15692566 IDA P YHL003C gene taxon:4932 20050419 SGD
+SGD S000005385 LAG2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YOL025W|ECM36 gene taxon:4932 20040813 SGD
+SGD S000005385 LAG2 GO:0005554 SGD_REF:S000069584 ND F YOL025W|ECM36 gene taxon:4932 20021111 SGD
+SGD S000005385 LAG2 GO:0001302 SGD_REF:S000055741|PMID:8760941 IMP P YOL025W|ECM36 gene taxon:4932 20030820 SGD
+SGD S000005183 LAP3 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C aminopeptidase of cysteine protease family YNL239W|BLH1|GAL6|YCP1 gene taxon:4932 20020507 SGD
+SGD S000005183 LAP3 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C aminopeptidase of cysteine protease family YNL239W|BLH1|GAL6|YCP1 gene taxon:4932 20031028 SGD
+SGD S000005183 LAP3 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C aminopeptidase of cysteine protease family YNL239W|BLH1|GAL6|YCP1 gene taxon:4932 20031028 SGD
+SGD S000005183 LAP3 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C aminopeptidase of cysteine protease family YNL239W|BLH1|GAL6|YCP1 gene taxon:4932 20031210 SGD
+SGD S000005183 LAP3 GO:0003676 SGD_REF:S000063844|PMID:9374524 TAS F aminopeptidase of cysteine protease family YNL239W|BLH1|GAL6|YCP1 gene taxon:4932 20020930 SGD
+SGD S000005183 LAP3 GO:0008234 SGD_REF:S000063843|PMID:8063738 IDA F aminopeptidase of cysteine protease family YNL239W|BLH1|GAL6|YCP1 gene taxon:4932 20020930 SGD
+SGD S000005183 LAP3 GO:0030528 SGD_REF:S000063844|PMID:9374524 IDA F aminopeptidase of cysteine protease family YNL239W|BLH1|GAL6|YCP1 gene taxon:4932 20020930 SGD
+SGD S000005183 LAP3 GO:0046677 SGD_REF:S000063843|PMID:8063738 IDA P aminopeptidase of cysteine protease family YNL239W|BLH1|GAL6|YCP1 gene taxon:4932 20021106 SGD
+SGD S000001586 LAP4 GO:0000324 SGD_REF:S000046077|PMID:1400574 IDA C vacuolar aminopeptidase ysc1 YKL103C|APE1|API|YSC1 gene taxon:4932 20010306 SGD
+SGD S000001586 LAP4 GO:0004250 SGD_REF:S000046077|PMID:1400574 IDA F vacuolar aminopeptidase ysc1 YKL103C|APE1|API|YSC1 gene taxon:4932 20030109 SGD
+SGD S000001586 LAP4 GO:0007039 SGD_REF:S000048366|PMID:2651436 ISS P vacuolar aminopeptidase ysc1 YKL103C|APE1|API|YSC1 gene taxon:4932 20010306 SGD
+SGD S000001586 LAP4 GO:0007039 SGD_REF:S000053351|PMID:2689224 ISS P vacuolar aminopeptidase ysc1 YKL103C|APE1|API|YSC1 gene taxon:4932 20010306 SGD
+SGD S000001771 LAS1 GO:0005634 SGD_REF:S000053118|PMID:8582632 TAS C YKR063C gene taxon:4932 20010118 SGD
+SGD S000001771 LAS1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YKR063C gene taxon:4932 20040928 SGD
+SGD S000001771 LAS1 GO:0005554 SGD_REF:S000069584 ND F YKR063C gene taxon:4932 20021205 SGD
+SGD S000001771 LAS1 GO:0007117 SGD_REF:S000053118|PMID:8582632 IMP P YKR063C gene taxon:4932 20010118 SGD
+SGD S000001771 LAS1 GO:0030468 SGD_REF:S000053118|PMID:8582632 IMP P YKR063C gene taxon:4932 20010302 SGD
+SGD S000005707 LAS17 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C actin assembly factor YOR181W|BEE1 gene taxon:4932 20020507 SGD
+SGD S000005707 LAS17 GO:0030479 SGD_REF:S000041005|PMID:10652251 IDA C actin assembly factor YOR181W|BEE1 gene taxon:4932 20010118 SGD
+SGD S000005707 LAS17 GO:0030479 SGD_REF:S000043043|PMID:10512884 IDA C actin assembly factor YOR181W|BEE1 gene taxon:4932 20040405 SGD
+SGD S000005707 LAS17 GO:0008092 SGD_REF:S000040513|PMID:9214384 IDA F actin assembly factor YOR181W|BEE1 gene taxon:4932 20010118 SGD
+SGD S000005707 LAS17 GO:0000910 SGD_REF:S000041005|PMID:10652251 IMP P actin assembly factor YOR181W|BEE1 gene taxon:4932 20010119 SGD
+SGD S000005707 LAS17 GO:0006897 SGD_REF:S000041005|PMID:10652251 IMP P actin assembly factor YOR181W|BEE1 gene taxon:4932 20010118 SGD
+SGD S000005707 LAS17 GO:0006970 SGD_REF:S000041005|PMID:10652251 IMP P actin assembly factor YOR181W|BEE1 gene taxon:4932 20010118 SGD
+SGD S000005707 LAS17 GO:0007015 SGD_REF:S000040513|PMID:9214384 IDA P actin assembly factor YOR181W|BEE1 gene taxon:4932 20010118 SGD
+SGD S000005707 LAS17 GO:0007121 SGD_REF:S000041005|PMID:10652251 IMP P actin assembly factor YOR181W|BEE1 gene taxon:4932 20010118 SGD
+SGD S000005707 LAS17 GO:0008154 SGD_REF:S000040513|PMID:9214384 IDA P actin assembly factor YOR181W|BEE1 gene taxon:4932 20010118 SGD
+SGD S000003598 LAS21 GO:0005887 SGD_REF:S000046429|PMID:10329735 IDA C major facilitator superfamily (putative), membrane protein (putative) YJL062W|GPI7 gene taxon:4932 20020925 SGD
+SGD S000003598 LAS21 GO:0030176 SGD_REF:S000046429|PMID:10329735 IDA C major facilitator superfamily (putative), membrane protein (putative) YJL062W|GPI7 gene taxon:4932 20020925 SGD
+SGD S000003598 LAS21 GO:0016740 SGD_REF:S000046429|PMID:10329735 IMP F major facilitator superfamily (putative), membrane protein (putative) YJL062W|GPI7 gene taxon:4932 20020925 SGD
+SGD S000003598 LAS21 GO:0006506 SGD_REF:S000046429|PMID:10329735 IMP P major facilitator superfamily (putative), membrane protein (putative) YJL062W|GPI7 gene taxon:4932 20020925 SGD
+SGD S000005015 LAT1 GO:0005739 SGD_REF:S000069459|PMID:11914276 IDA C pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase component (E2) YNL071W|ODP2|PDA2 gene taxon:4932 20020507 SGD
+SGD S000005015 LAT1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase component (E2) YNL071W|ODP2|PDA2 gene taxon:4932 20040929 SGD
+SGD S000005015 LAT1 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase component (E2) YNL071W|ODP2|PDA2 gene taxon:4932 20031028 SGD
+SGD S000005015 LAT1 GO:0005967 SGD_REF:S000058092|PMID:9123965 TAS C pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase component (E2) YNL071W|ODP2|PDA2 gene taxon:4932 20040127 SGD
+SGD S000005015 LAT1 GO:0004742 SGD_REF:S000056831|PMID:2271545 IDA F pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase component (E2) YNL071W|ODP2|PDA2 gene taxon:4932 20030114 SGD
+SGD S000005015 LAT1 GO:0006090 SGD_REF:S000058092|PMID:9123965 TAS P pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase component (E2) YNL071W|ODP2|PDA2 gene taxon:4932 20020930 SGD
+SGD S000004911 LCB1 GO:0005624 SGD_REF:S000051148|PMID:10713067 IDA C serine palmitoyltransferase component YMR296C|END8|TSC2 gene taxon:4932 20020925 SGD
+SGD S000004911 LCB1 GO:0005792 SGD_REF:S000051148|PMID:10713067 IPI C serine palmitoyltransferase component YMR296C|END8|TSC2 gene taxon:4932 20020925 SGD
+SGD S000004911 LCB1 GO:0017059 SGD_REF:S000040752|PMID:1556076 IMP C serine palmitoyltransferase component YMR296C|END8|TSC2 gene taxon:4932 20020925 SGD
+SGD S000004911 LCB1 GO:0004758 SGD_REF:S000040752|PMID:1556076 IDA F serine palmitoyltransferase component YMR296C|END8|TSC2 gene taxon:4932 20020925 SGD
+SGD S000004911 LCB1 GO:0030148 SGD_REF:S000070324|PMID:12185836 TAS P serine palmitoyltransferase component YMR296C|END8|TSC2 gene taxon:4932 20020826 SGD
+SGD S000002469 LCB2 GO:0005624 SGD_REF:S000051148|PMID:10713067 IDA C serine palmitoyltransferase component YDR062W|SCS1|TSC1 gene taxon:4932 20020925 SGD
+SGD S000002469 LCB2 GO:0005792 SGD_REF:S000051148|PMID:10713067 IPI C serine palmitoyltransferase component YDR062W|SCS1|TSC1 gene taxon:4932 20020925 SGD
+SGD S000002469 LCB2 GO:0017059 SGD_REF:S000040752|PMID:1556076 IMP C serine palmitoyltransferase component YDR062W|SCS1|TSC1 gene taxon:4932 20020925 SGD
+SGD S000002469 LCB2 GO:0004758 SGD_REF:S000040752|PMID:1556076 IDA F serine palmitoyltransferase component YDR062W|SCS1|TSC1 gene taxon:4932 20020925 SGD
+SGD S000002469 LCB2 GO:0030148 SGD_REF:S000070324|PMID:12185836 TAS P serine palmitoyltransferase component YDR062W|SCS1|TSC1 gene taxon:4932 20020826 SGD
+SGD S000003670 LCB3 GO:0005783 SGD_REF:S000044959|PMID:10477278 IDA C dihydrosphingosine-1-phosphate phophatase YJL134W|LBP1|YSR2 gene taxon:4932 20020925 SGD
+SGD S000003670 LCB3 GO:0042392 SGD_REF:S000060106|PMID:11278643 TAS F dihydrosphingosine-1-phosphate phophatase YJL134W|LBP1|YSR2 gene taxon:4932 20020830 SGD
+SGD S000003670 LCB3 GO:0042392 SGD_REF:S000040227|PMID:9353337 IDA F dihydrosphingosine-1-phosphate phophatase YJL134W|LBP1|YSR2 gene taxon:4932 20030312 SGD
+SGD S000003670 LCB3 GO:0019722 SGD_REF:S000060106|PMID:11278643 IMP P dihydrosphingosine-1-phosphate phophatase YJL134W|LBP1|YSR2 gene taxon:4932 20020925 SGD
+SGD S000003670 LCB3 GO:0030148 SGD_REF:S000041039|PMID:10563329 TAS P dihydrosphingosine-1-phosphate phophatase YJL134W|LBP1|YSR2 gene taxon:4932 20020821 SGD
+SGD S000005697 LCB4 GO:0005624 SGD_REF:S000052946|PMID:9677363 IDA C sphingoid long chain base (LCB) kinase YOR171C gene taxon:4932 20020925 SGD
+SGD S000005697 LCB4 GO:0005625 SGD_REF:S000052946|PMID:9677363 IDA C sphingoid long chain base (LCB) kinase YOR171C gene taxon:4932 20020925 SGD
+SGD S000005697 LCB4 GO:0005783 SGD_REF:S000072710|PMID:12493772 IDA C sphingoid long chain base (LCB) kinase YOR171C gene taxon:4932 20030312 SGD
+SGD S000005697 LCB4 GO:0005794 SGD_REF:S000071822|PMID:12459470 IDA C sphingoid long chain base (LCB) kinase YOR171C gene taxon:4932 20021209 SGD
+SGD S000005697 LCB4 GO:0017050 SGD_REF:S000052946|PMID:9677363 IDA F sphingoid long chain base (LCB) kinase YOR171C gene taxon:4932 20020925 SGD
+SGD S000005697 LCB4 GO:0006665 SGD_REF:S000052946|PMID:9677363 IDA P sphingoid long chain base (LCB) kinase YOR171C gene taxon:4932 20020925 SGD
+SGD S000005697 LCB4 GO:0019722 SGD_REF:S000060106|PMID:11278643 IMP P sphingoid long chain base (LCB) kinase YOR171C gene taxon:4932 20020925 SGD
+SGD S000004250 LCB5 GO:0005624 SGD_REF:S000052946|PMID:9677363 IDA C sphingoid long chain base (LCB) kinase YLR260W gene taxon:4932 20020925 SGD
+SGD S000004250 LCB5 GO:0005625 SGD_REF:S000052946|PMID:9677363 IDA C sphingoid long chain base (LCB) kinase YLR260W gene taxon:4932 20020925 SGD
+SGD S000004250 LCB5 GO:0017050 SGD_REF:S000052946|PMID:9677363 IDA F sphingoid long chain base (LCB) kinase YLR260W gene taxon:4932 20020925 SGD
+SGD S000004250 LCB5 GO:0006665 SGD_REF:S000052946|PMID:9677363 IDA P sphingoid long chain base (LCB) kinase YLR260W gene taxon:4932 20020925 SGD
+SGD S000004250 LCB5 GO:0009408 SGD_REF:S000069943|PMID:11967828 IDA P sphingoid long chain base (LCB) kinase YLR260W gene taxon:4932 20020830 SGD
+SGD S000004250 LCB5 GO:0019722 SGD_REF:S000060106|PMID:11278643 IMP P sphingoid long chain base (LCB) kinase YLR260W gene taxon:4932 20020925 SGD
+SGD S000002907 LCD1 GO:0000228 SGD_REF:S000070022|PMID:11983176 IDA C YDR499W|DDC2|PIE1 gene taxon:4932 20021008 SGD
+SGD S000002907 LCD1 GO:0003684 SGD_REF:S000070022|PMID:11983176 IDA F YDR499W|DDC2|PIE1 gene taxon:4932 20021008 SGD
+SGD S000002907 LCD1 GO:0005515 SGD_REF:S000070022|PMID:11983176 IDA F YDR499W|DDC2|PIE1 gene taxon:4932 20021008 SGD
+SGD S000002907 LCD1 GO:0000077 SGD_REF:S000056452|PMID:11060031 IMP P YDR499W|DDC2|PIE1 gene taxon:4932 20021008 SGD
+SGD S000002907 LCD1 GO:0000077 SGD_REF:S000056452|PMID:11060031 IPI P YDR499W|DDC2|PIE1 gene taxon:4932 20021008 SGD
+SGD S000002907 LCD1 GO:0007004 SGD_REF:S000070385|PMID:12181334 IMP P YDR499W|DDC2|PIE1 gene taxon:4932 20021008 SGD
+SGD S000002907 LCD1 GO:0045184 SGD_REF:S000070022|PMID:11983176 IDA P YDR499W|DDC2|PIE1 gene taxon:4932 20021008 SGD
+SGD S000002907 LCD1 GO:0045184 SGD_REF:S000070022|PMID:11983176 IMP P YDR499W|DDC2|PIE1 gene taxon:4932 20021008 SGD
+SGD S000000929 LCP5 GO:0005732 SGD_REF:S000058443|PMID:10690410 TAS C YER127W gene taxon:4932 20010118 SGD
+SGD S000000929 LCP5 GO:0030532 SGD_REF:S000058443|PMID:10690410 TAS C YER127W gene taxon:4932 20020219 SGD
+SGD S000000929 LCP5 GO:0003723 SGD_REF:S000041158|PMID:9814757 IDA F YER127W gene taxon:4932 20021101 SGD
+SGD S000000929 LCP5 GO:0000154 SGD_REF:S000058443|PMID:10690410 TAS P YER127W gene taxon:4932 20010118 SGD
+SGD S000000929 LCP5 GO:0006365 SGD_REF:S000058443|PMID:10690410 TAS P YER127W gene taxon:4932 20010118 SGD
+SGD S000000511 LDB16 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YCL005W gene taxon:4932 20040928 SGD
+SGD S000000511 LDB16 GO:0005811 SGD_REF:S000074185|PMID:14562095 IDA C YCL005W gene taxon:4932 20031028 SGD
+SGD S000000511 LDB16 GO:0005554 SGD_REF:S000069584 ND F YCL005W gene taxon:4932 20021126 SGD
+SGD S000000511 LDB16 GO:0000004 SGD_REF:S000069584 ND P YCL005W gene taxon:4932 20021126 SGD
+SGD S000002305 LDB17 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDL146W gene taxon:4932 20031028 SGD
+SGD S000002305 LDB17 GO:0005933 SGD_REF:S000074185|PMID:14562095 IDA C YDL146W gene taxon:4932 20031028 SGD
+SGD S000002305 LDB17 GO:0005935 SGD_REF:S000074185|PMID:14562095 IDA C YDL146W gene taxon:4932 20031028 SGD
+SGD S000002305 LDB17 GO:0005554 SGD_REF:S000069584 ND F YDL146W gene taxon:4932 20030203 SGD
+SGD S000002305 LDB17 GO:0000004 SGD_REF:S000069584 ND P YDL146W gene taxon:4932 20030203 SGD
+SGD S000003972 LDB18 GO:0008372 SGD_REF:S000069584 ND C YLL049W gene taxon:4932 20030424 SGD
+SGD S000003972 LDB18 GO:0005554 SGD_REF:S000069584 ND F YLL049W gene taxon:4932 20030424 SGD
+SGD S000003972 LDB18 GO:0000004 SGD_REF:S000069584 ND P YLL049W gene taxon:4932 20030424 SGD
+SGD S000005849 LDB19 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YOR322C gene taxon:4932 20031028 SGD
+SGD S000005849 LDB19 colocalizes_with GO:0030136 SGD_REF:S000074185|PMID:14562095 IDA C YOR322C gene taxon:4932 20031028 SGD
+SGD S000005849 LDB19 GO:0005554 SGD_REF:S000069584 ND F YOR322C gene taxon:4932 20021204 SGD
+SGD S000005849 LDB19 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P YOR322C gene taxon:4932 20060202 SGD
+SGD S000000102 LDB7 GO:0016586 SGD_REF:S000086800|PMID:16204215 IGI SGD:S000002711 C YBL006C|RSC14 gene taxon:4932 20060328 SGD
+SGD S000000102 LDB7 GO:0016586 SGD_REF:S000086800|PMID:16204215 IPI SGD:S000002711|SGD:S000001388 C YBL006C|RSC14 gene taxon:4932 20060328 SGD
+SGD S000000102 LDB7 GO:0016586 SGD_REF:S000086800|PMID:16204215 IMP C YBL006C|RSC14 gene taxon:4932 20060328 SGD
+SGD S000000102 LDB7 GO:0005554 SGD_REF:S000069584 ND F YBL006C|RSC14 gene taxon:4932 20060328 SGD
+SGD S000000102 LDB7 GO:0000032 SGD_REF:S000075144|PMID:14587103 IMP P YBL006C|RSC14 gene taxon:4932 20031229 SGD
+SGD S000000102 LDB7 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P YBL006C|RSC14 gene taxon:4932 20060214 SGD
+SGD S000006134 LEA1 GO:0005686 SGD_REF:S000069986|PMID:11804584 IDA C YPL213W gene taxon:4932 20020621 SGD
+SGD S000006134 LEA1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YPL213W gene taxon:4932 20020507 SGD
+SGD S000006134 LEA1 GO:0031202 SGD_REF:S000069986|PMID:11804584 IPI F YPL213W gene taxon:4932 20020801 SGD
+SGD S000006134 LEA1 GO:0000398 SGD_REF:S000069986|PMID:11804584 IPI P YPL213W gene taxon:4932 20020801 SGD
+SGD S000006134 LEA1 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P YPL213W gene taxon:4932 20060203 SGD
+SGD S000005975 LEE1 GO:0008372 SGD_REF:S000069584 ND C YPL054W gene taxon:4932 20021125 SGD
+SGD S000005975 LEE1 GO:0005554 SGD_REF:S000069584 ND F YPL054W gene taxon:4932 20021125 SGD
+SGD S000005975 LEE1 GO:0000004 SGD_REF:S000069584 ND P YPL054W gene taxon:4932 20021125 SGD
+SGD S000005267 LEM3 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C membrane glycoprotein YNL323W|BRE3|ROS3 gene taxon:4932 20020507 SGD
+SGD S000005267 LEM3 GO:0005783 SGD_REF:S000071454|PMID:12133835 IDA C membrane glycoprotein YNL323W|BRE3|ROS3 gene taxon:4932 20021014 SGD
+SGD S000005267 LEM3 GO:0005886 SGD_REF:S000071454|PMID:12133835 IDA C membrane glycoprotein YNL323W|BRE3|ROS3 gene taxon:4932 20021014 SGD
+SGD S000005267 LEM3 GO:0016021 SGD_REF:S000056454|PMID:11063677 ISS C membrane glycoprotein YNL323W|BRE3|ROS3 gene taxon:4932 20010118 SGD
+SGD S000005267 LEM3 contributes_to GO:0004012 SGD_REF:S000076777|PMID:15090616 IPI SGD:S000000968 F membrane glycoprotein YNL323W|BRE3|ROS3 gene taxon:4932 20051212 SGD
+SGD S000005267 LEM3 GO:0007166 SGD_REF:S000056454|PMID:11063677 IMP P membrane glycoprotein YNL323W|BRE3|ROS3 gene taxon:4932 20010118 SGD
+SGD S000005267 LEM3 GO:0045332 SGD_REF:S000074019|PMID:12842877 IMP P membrane glycoprotein YNL323W|BRE3|ROS3 gene taxon:4932 20051212 SGD
+SGD S000005649 LEO1 GO:0005634 SGD_REF:S000080456|PMID:15643076 IDA C YOR123C gene taxon:4932 20050228 SGD
+SGD S000005649 LEO1 GO:0008023 SGD_REF:S000071357|PMID:12242279 IPI C YOR123C gene taxon:4932 20021004 SGD
+SGD S000005649 LEO1 GO:0016593 SGD_REF:S000069696|PMID:11884586 IPI C YOR123C gene taxon:4932 20020927 SGD
+SGD S000005649 LEO1 GO:0016593 SGD_REF:S000073599|PMID:12773564 TAS C YOR123C gene taxon:4932 20040129 SGD
+SGD S000005649 LEO1 GO:0016944 SGD_REF:S000071357|PMID:12242279 IPI F YOR123C gene taxon:4932 20021004 SGD
+SGD S000005649 LEO1 GO:0006366 SGD_REF:S000069696|PMID:11884586 IMP P YOR123C gene taxon:4932 20020927 SGD
+SGD S000005649 LEO1 GO:0006368 SGD_REF:S000071357|PMID:12242279 IPI P YOR123C gene taxon:4932 20021004 SGD
+SGD S000005649 LEO1 GO:0016571 SGD_REF:S000073147|PMID:12667454 IMP P YOR123C gene taxon:4932 20050503 SGD
+SGD S000002977 LEU1 GO:0005829 SGD_REF:S000070200 TAS C isopropylmalate isomerase YGL009C gene taxon:4932 20030121 SGD
+SGD S000002977 LEU1 GO:0003861 SGD_REF:S000070200 TAS F isopropylmalate isomerase YGL009C gene taxon:4932 20030121 SGD
+SGD S000002977 LEU1 GO:0009098 SGD_REF:S000056457|PMID:1126953 TAS P isopropylmalate isomerase YGL009C gene taxon:4932 20020930 SGD
+SGD S000000523 LEU2 GO:0005829 SGD_REF:S000070200 TAS C beta-IPM (isopropylmalate) dehydrogenase YCL018W gene taxon:4932 20020801 SGD
+SGD S000000523 LEU2 GO:0005829 SGD_REF:S000061835|PMID:4355481 IDA C beta-IPM (isopropylmalate) dehydrogenase YCL018W gene taxon:4932 20051012 SGD
+SGD S000000523 LEU2 GO:0003862 SGD_REF:S000049738|PMID:6297759 ISS F beta-IPM (isopropylmalate) dehydrogenase YCL018W gene taxon:4932 20020801 SGD
+SGD S000000523 LEU2 GO:0003862 SGD_REF:S000049738|PMID:6297759 IMP F beta-IPM (isopropylmalate) dehydrogenase YCL018W gene taxon:4932 20020801 SGD
+SGD S000000523 LEU2 GO:0003862 SGD_REF:S000057024|PMID:3071718 IDA F beta-IPM (isopropylmalate) dehydrogenase YCL018W gene taxon:4932 20051012 SGD
+SGD S000000523 LEU2 GO:0009098 SGD_REF:S000049738|PMID:6297759 IMP P beta-IPM (isopropylmalate) dehydrogenase YCL018W gene taxon:4932 20020801 SGD
+SGD S000004443 LEU3 GO:0005634 SGD_REF:S000050091|PMID:7623798 IDA C zinc finger transcription factor of the Zn(2)-Cys(6) binuclear cluster domain type YLR451W gene taxon:4932 20020212 SGD
+SGD S000004443 LEU3 GO:0003704 SGD_REF:S000048873|PMID:2211632 IDA F zinc finger transcription factor of the Zn(2)-Cys(6) binuclear cluster domain type YLR451W gene taxon:4932 20030121 SGD
+SGD S000004443 LEU3 GO:0006357 SGD_REF:S000048873|PMID:2211632 IDA P zinc finger transcription factor of the Zn(2)-Cys(6) binuclear cluster domain type YLR451W gene taxon:4932 20030121 SGD
+SGD S000004443 LEU3 GO:0009098 SGD_REF:S000051008|PMID:2823102 IMP P zinc finger transcription factor of the Zn(2)-Cys(6) binuclear cluster domain type YLR451W gene taxon:4932 20030121 SGD
+SGD S000005048 LEU4 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C alpha-isopropylmalate synthase (2-isopropylmalate synthase) YNL104C gene taxon:4932 20020507 SGD
+SGD S000005048 LEU4 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C alpha-isopropylmalate synthase (2-isopropylmalate synthase) YNL104C gene taxon:4932 20031028 SGD
+SGD S000005048 LEU4 GO:0005739 SGD_REF:S000069459|PMID:11914276 IDA C alpha-isopropylmalate synthase (2-isopropylmalate synthase) YNL104C gene taxon:4932 20020507 SGD
+SGD S000005048 LEU4 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C alpha-isopropylmalate synthase (2-isopropylmalate synthase) YNL104C gene taxon:4932 20031028 SGD
+SGD S000005048 LEU4 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C alpha-isopropylmalate synthase (2-isopropylmalate synthase) YNL104C gene taxon:4932 20040813 SGD
+SGD S000005048 LEU4 GO:0003852 SGD_REF:S000049092|PMID:3275644 IDA F alpha-isopropylmalate synthase (2-isopropylmalate synthase) YNL104C gene taxon:4932 20030121 SGD
+SGD S000005048 LEU4 GO:0009098 SGD_REF:S000054549|PMID:9765846 TAS P alpha-isopropylmalate synthase (2-isopropylmalate synthase) YNL104C gene taxon:4932 20020903 SGD
+SGD S000001044 LEU5 GO:0005743 SGD_REF:S000059488|PMID:11158296 IDA C YHR002W gene taxon:4932 20021009 SGD
+SGD S000001044 LEU5 GO:0015228 SGD_REF:S000059488|PMID:11158296 ISS F YHR002W gene taxon:4932 20021009 SGD
+SGD S000001044 LEU5 GO:0015228 SGD_REF:S000059488|PMID:11158296 IMP F YHR002W gene taxon:4932 20021009 SGD
+SGD S000001044 LEU5 GO:0015880 SGD_REF:S000059488|PMID:11158296 IMP P YHR002W gene taxon:4932 20021009 SGD
+SGD S000029255 LEU6 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20020523 SGD
+SGD S000029255 LEU6 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20020523 SGD
+SGD S000029255 LEU6 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20020523 SGD
+SGD S000029256 LEU7 GO:0008372 SGD_REF:S000069584 ND C alpha-isopropylmalate synthase (putative) gene taxon:4932 20020523 SGD
+SGD S000029256 LEU7 GO:0005554 SGD_REF:S000069584 ND F alpha-isopropylmalate synthase (putative) gene taxon:4932 20020523 SGD
+SGD S000029256 LEU7 GO:0000004 SGD_REF:S000069584 ND P alpha-isopropylmalate synthase (putative) gene taxon:4932 20020523 SGD
+SGD S000029257 LEU8 GO:0008372 SGD_REF:S000069584 ND C alpha-isopropylmalate synthase (putative) gene taxon:4932 20020523 SGD
+SGD S000029257 LEU8 GO:0005554 SGD_REF:S000069584 ND F alpha-isopropylmalate synthase (putative) gene taxon:4932 20020523 SGD
+SGD S000029257 LEU8 GO:0000004 SGD_REF:S000069584 ND P alpha-isopropylmalate synthase (putative) gene taxon:4932 20020523 SGD
+SGD S000005634 LEU9 GO:0005739 SGD_REF:S000059488|PMID:11158296 IDA C alpha-isopropylmalate synthase (2-isopropylmalate synthase) YOR108W gene taxon:4932 20030414 SGD
+SGD S000005634 LEU9 GO:0003852 SGD_REF:S000041472|PMID:10790691 IGI F alpha-isopropylmalate synthase (2-isopropylmalate synthase) YOR108W gene taxon:4932 20030220 SGD
+SGD S000005634 LEU9 GO:0003852 SGD_REF:S000059488|PMID:11158296 IDA F alpha-isopropylmalate synthase (2-isopropylmalate synthase) YOR108W gene taxon:4932 20030414 SGD
+SGD S000005634 LEU9 GO:0003852 SGD_REF:S000041472|PMID:10790691 ISS F alpha-isopropylmalate synthase (2-isopropylmalate synthase) YOR108W gene taxon:4932 20030220 SGD
+SGD S000005634 LEU9 GO:0009098 SGD_REF:S000041472|PMID:10790691 IGI P alpha-isopropylmalate synthase (2-isopropylmalate synthase) YOR108W gene taxon:4932 20030220 SGD
+SGD S000005976 LGE1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YPL055C gene taxon:4932 20031028 SGD
+SGD S000005976 LGE1 GO:0005634 SGD_REF:S000080207|PMID:15528187 IDA C YPL055C gene taxon:4932 20050210 SGD
+SGD S000005976 LGE1 GO:0005554 SGD_REF:S000069584 ND F YPL055C gene taxon:4932 20021004 SGD
+SGD S000005976 LGE1 GO:0006513 SGD_REF:S000072664|PMID:12535538 IMP P YPL055C gene taxon:4932 20030307 SGD
+SGD S000005976 LGE1 GO:0007126 SGD_REF:S000043176|PMID:10051619 IEP P YPL055C gene taxon:4932 20030307 SGD
+SGD S000005976 LGE1 GO:0008361 SGD_REF:S000070190|PMID:12089449 IGI P YPL055C gene taxon:4932 20030307 SGD
+SGD S000005976 LGE1 GO:0016571 SGD_REF:S000072664|PMID:12535538 IMP P YPL055C gene taxon:4932 20030307 SGD
+SGD S000005976 LGE1 GO:0016574 SGD_REF:S000072664|PMID:12535538 IMP P YPL055C gene taxon:4932 20030307 SGD
+SGD S000002209 LHP1 GO:0005634 SGD_REF:S000042217|PMID:10564276 IDA C YDL051W|LAH1|La protein|YLA1 gene taxon:4932 20010118 SGD
+SGD S000002209 LHP1 GO:0005654 SGD_REF:S000066240|PMID:11720288 IDA C YDL051W|LAH1|La protein|YLA1 gene taxon:4932 20030424 SGD
+SGD S000002209 LHP1 GO:0005730 SGD_REF:S000066240|PMID:11720288 IDA C YDL051W|LAH1|La protein|YLA1 gene taxon:4932 20030424 SGD
+SGD S000002209 LHP1 GO:0003723 SGD_REF:S000052473|PMID:7799435 IDA F YDL051W|LAH1|La protein|YLA1 gene taxon:4932 20010118 SGD
+SGD S000002209 LHP1 GO:0008033 SGD_REF:S000040352|PMID:9150139 IMP P YDL051W|LAH1|La protein|YLA1 gene taxon:4932 20010118 SGD
+SGD S000001556 LHS1 GO:0005788 SGD_REF:S000050250|PMID:8654361 IDA C Hsp70 family YKL073W|CER1|SSI1 gene taxon:4932 20030730 SGD
+SGD S000001556 LHS1 GO:0005788 SGD_REF:S000050250|PMID:8654361 ISS C Hsp70 family YKL073W|CER1|SSI1 gene taxon:4932 20030730 SGD
+SGD S000001556 LHS1 GO:0005788 SGD_REF:S000073525|PMID:11101517 TAS C Hsp70 family YKL073W|CER1|SSI1 gene taxon:4932 20030730 SGD
+SGD S000001556 LHS1 GO:0051082 SGD_REF:S000043311|PMID:8887673 IMP F Hsp70 family YKL073W|CER1|SSI1 gene taxon:4932 20020618 SGD
+SGD S000001556 LHS1 GO:0051082 SGD_REF:S000043311|PMID:8887673 IGI F Hsp70 family YKL073W|CER1|SSI1 gene taxon:4932 20020618 SGD
+SGD S000001556 LHS1 GO:0051082 SGD_REF:S000045221|PMID:10409721 IPI F Hsp70 family YKL073W|CER1|SSI1 gene taxon:4932 20020618 SGD
+SGD S000001556 LHS1 GO:0051082 SGD_REF:S000045221|PMID:10409721 ISS F Hsp70 family YKL073W|CER1|SSI1 gene taxon:4932 20020618 SGD
+SGD S000001556 LHS1 GO:0051082 SGD_REF:S000050250|PMID:8654361 ISS F Hsp70 family YKL073W|CER1|SSI1 gene taxon:4932 20020618 SGD
+SGD S000001556 LHS1 GO:0051082 SGD_REF:S000043311|PMID:8887673 ISS F Hsp70 family YKL073W|CER1|SSI1 gene taxon:4932 20020618 SGD
+SGD S000001556 LHS1 GO:0051082 SGD_REF:S000050250|PMID:8654361 IGI F Hsp70 family YKL073W|CER1|SSI1 gene taxon:4932 20020618 SGD
+SGD S000001556 LHS1 GO:0051082 SGD_REF:S000050250|PMID:8654361 IMP F Hsp70 family YKL073W|CER1|SSI1 gene taxon:4932 20020618 SGD
+SGD S000001556 LHS1 GO:0051082 SGD_REF:S000045221|PMID:10409721 IMP F Hsp70 family YKL073W|CER1|SSI1 gene taxon:4932 20020618 SGD
+SGD S000001556 LHS1 GO:0006986 SGD_REF:S000043311|PMID:8887673 IGI P Hsp70 family YKL073W|CER1|SSI1 gene taxon:4932 20020618 SGD
+SGD S000001556 LHS1 GO:0006986 SGD_REF:S000050250|PMID:8654361 IGI P Hsp70 family YKL073W|CER1|SSI1 gene taxon:4932 20020618 SGD
+SGD S000001556 LHS1 GO:0006986 SGD_REF:S000050250|PMID:8654361 IMP P Hsp70 family YKL073W|CER1|SSI1 gene taxon:4932 20020618 SGD
+SGD S000001556 LHS1 GO:0006986 SGD_REF:S000043311|PMID:8887673 IMP P Hsp70 family YKL073W|CER1|SSI1 gene taxon:4932 20020618 SGD
+SGD S000001556 LHS1 GO:0015031 SGD_REF:S000054967|PMID:8940034 IGI P Hsp70 family YKL073W|CER1|SSI1 gene taxon:4932 20020618 SGD
+SGD S000001556 LHS1 GO:0015031 SGD_REF:S000054967|PMID:8940034 IMP P Hsp70 family YKL073W|CER1|SSI1 gene taxon:4932 20020618 SGD
+SGD S000003831 LIA1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YJR070C|MMD1 gene taxon:4932 20031028 SGD
+SGD S000003831 LIA1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YJR070C|MMD1 gene taxon:4932 20031028 SGD
+SGD S000003831 LIA1 GO:0005515 SGD_REF:S000075161|PMID:14675757 IPI SGD:S000000760 F YJR070C|MMD1 gene taxon:4932 20031218 SGD
+SGD S000003831 LIA1 GO:0019135 SGD_REF:S000113927|PMID:16371467 IDA F YJR070C|MMD1 gene taxon:4932 20060106 SGD
+SGD S000003831 LIA1 GO:0019135 SGD_REF:S000113927|PMID:16371467 IMP F YJR070C|MMD1 gene taxon:4932 20060106 SGD
+SGD S000003831 LIA1 GO:0000226 SGD_REF:S000076064|PMID:14767070 IGI P YJR070C|MMD1 gene taxon:4932 20050324 SGD
+SGD S000003831 LIA1 GO:0000226 SGD_REF:S000076064|PMID:14767070 IMP P YJR070C|MMD1 gene taxon:4932 20050324 SGD
+SGD S000003831 LIA1 GO:0046515 SGD_REF:S000113927|PMID:16371467 IDA P YJR070C|MMD1 gene taxon:4932 20060106 SGD
+SGD S000003831 LIA1 GO:0046515 SGD_REF:S000113927|PMID:16371467 IMP P YJR070C|MMD1 gene taxon:4932 20060106 SGD
+SGD S000003058 LIF1 GO:0005634 SGD_REF:S000039687|PMID:9670033 TAS C YGL090W gene taxon:4932 20010118 SGD
+SGD S000003058 LIF1 GO:0005198 SGD_REF:S000073203|PMID:12399380 TAS F YGL090W gene taxon:4932 20030528 SGD
+SGD S000003058 LIF1 GO:0006303 SGD_REF:S000039687|PMID:9670033 IPI P YGL090W gene taxon:4932 20010118 SGD
+SGD S000003058 LIF1 GO:0006303 SGD_REF:S000079665|PMID:15342630 IDA P YGL090W gene taxon:4932 20041122 SGD
+SGD S000001199 LIN1 GO:0000785 SGD_REF:S000071761|PMID:12402242 IDA C YHR156C|SNU40 gene taxon:4932 20030528 SGD
+SGD S000001199 LIN1 GO:0005634 SGD_REF:S000071761|PMID:12402242 IDA C YHR156C|SNU40 gene taxon:4932 20030528 SGD
+SGD S000001199 LIN1 GO:0005682 SGD_REF:S000066234|PMID:11720284 IPI C YHR156C|SNU40 gene taxon:4932 20051003 SGD
+SGD S000001199 LIN1 GO:0005515 SGD_REF:S000071761|PMID:12402242 IPI SGD:S000002171|SGD:S000001208|SGD:S000001288|SGD:S000005743|SGD:S000005682|SGD:S000003685|SGD:S000001176 F YHR156C|SNU40 gene taxon:4932 20030528 SGD
+SGD S000001199 LIN1 GO:0000004 SGD_REF:S000069584 ND P YHR156C|SNU40 gene taxon:4932 20051003 SGD
+SGD S000004913 LIP1 GO:0005635 SGD_REF:S000075214|PMID:14690591 IDA C YMR298W gene taxon:4932 20040105 SGD
+SGD S000004913 LIP1 GO:0005783 SGD_REF:S000075214|PMID:14690591 IDA C YMR298W gene taxon:4932 20040105 SGD
+SGD S000004913 LIP1 GO:0005789 SGD_REF:S000081342|PMID:15692566 IDA C YMR298W gene taxon:4932 20050419 SGD
+SGD S000004913 LIP1 contributes_to GO:0050291 SGD_REF:S000081342|PMID:15692566 IMP F YMR298W gene taxon:4932 20050419 SGD
+SGD S000004913 LIP1 contributes_to GO:0050291 SGD_REF:S000081342|PMID:15692566 IPI SGD:S000000995|SGD:S000001491 F YMR298W gene taxon:4932 20050419 SGD
+SGD S000004913 LIP1 GO:0046513 SGD_REF:S000081342|PMID:15692566 IMP P YMR298W gene taxon:4932 20050419 SGD
+SGD S000004913 LIP1 GO:0046513 SGD_REF:S000081342|PMID:15692566 IPI SGD:S000000995|SGD:S000001491 P YMR298W gene taxon:4932 20050419 SGD
+SGD S000004229 LIP2 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C Lipoyl ligase YLR239C gene taxon:4932 20031028 SGD
+SGD S000004229 LIP2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C Lipoyl ligase YLR239C gene taxon:4932 20040924 SGD
+SGD S000004229 LIP2 GO:0016874 SGD_REF:S000060276|PMID:11356580 ISS F Lipoyl ligase YLR239C gene taxon:4932 20021011 SGD
+SGD S000004229 LIP2 GO:0016874 SGD_REF:S000060276|PMID:11356580 IMP F Lipoyl ligase YLR239C gene taxon:4932 20021011 SGD
+SGD S000004229 LIP2 GO:0009249 SGD_REF:S000060276|PMID:11356580 ISS P Lipoyl ligase YLR239C gene taxon:4932 20021011 SGD
+SGD S000004229 LIP2 GO:0009249 SGD_REF:S000060276|PMID:11356580 IMP P Lipoyl ligase YLR239C gene taxon:4932 20021011 SGD
+SGD S000005722 LIP5 GO:0005739 SGD_REF:S000069459|PMID:11914276 IDA C lipoic acid synthase YOR196C gene taxon:4932 20020507 SGD
+SGD S000005722 LIP5 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C lipoic acid synthase YOR196C gene taxon:4932 20040924 SGD
+SGD S000005722 LIP5 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C lipoic acid synthase YOR196C gene taxon:4932 20031028 SGD
+SGD S000005722 LIP5 GO:0017140 SGD_REF:S000040454|PMID:8349643 ISS F lipoic acid synthase YOR196C gene taxon:4932 20040708 SGD
+SGD S000005722 LIP5 GO:0009105 SGD_REF:S000040454|PMID:8349643 IMP P lipoic acid synthase YOR196C gene taxon:4932 20040708 SGD
+SGD S000001897 LOC1 GO:0005634 SGD_REF:S000060131|PMID:11309412 IDA C YFR001W gene taxon:4932 20020816 SGD
+SGD S000001897 LOC1 GO:0003729 SGD_REF:S000060131|PMID:11309412 IDA F YFR001W gene taxon:4932 20020816 SGD
+SGD S000001897 LOC1 GO:0003729 SGD_REF:S000060131|PMID:11309412 IPI F YFR001W gene taxon:4932 20020816 SGD
+SGD S000001897 LOC1 GO:0008298 SGD_REF:S000060131|PMID:11309412 IMP P YFR001W gene taxon:4932 20040708 SGD
+SGD S000001897 LOC1 GO:0042273 SGD_REF:S000066002|PMID:11583614 IMP P YFR001W gene taxon:4932 20020927 SGD
+SGD S000001897 LOC1 GO:0042273 SGD_REF:S000066002|PMID:11583614 IPI P YFR001W gene taxon:4932 20020927 SGD
+SGD S000001688 LOS1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C exportin-t YKL205W gene taxon:4932 20040928 SGD
+SGD S000001688 LOS1 GO:0016363 SGD_REF:S000056025|PMID:8366091 IDA C exportin-t YKL205W gene taxon:4932 20020917 SGD
+SGD S000001688 LOS1 GO:0000049 SGD_REF:S000069567|PMID:11959996 TAS F exportin-t YKL205W gene taxon:4932 20020917 SGD
+SGD S000001688 LOS1 GO:0008536 SGD_REF:S000055025|PMID:9774653 IDA F exportin-t YKL205W gene taxon:4932 20020917 SGD
+SGD S000001688 LOS1 GO:0006388 SGD_REF:S000056025|PMID:8366091 IMP P exportin-t YKL205W gene taxon:4932 20020917 SGD
+SGD S000001688 LOS1 GO:0006409 SGD_REF:S000052576|PMID:9802895 IMP P exportin-t YKL205W gene taxon:4932 20020917 SGD
+SGD S000001666 LOT5 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YKL183W gene taxon:4932 20031028 SGD
+SGD S000001666 LOT5 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YKL183W gene taxon:4932 20031028 SGD
+SGD S000001666 LOT5 GO:0005554 SGD_REF:S000069584 ND F YKL183W gene taxon:4932 20021011 SGD
+SGD S000001666 LOT5 GO:0000004 SGD_REF:S000069584 ND P YKL183W gene taxon:4932 20021011 SGD
+SGD S000004001 LOT6 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YLR011W gene taxon:4932 20031028 SGD
+SGD S000004001 LOT6 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YLR011W gene taxon:4932 20031028 SGD
+SGD S000004001 LOT6 GO:0008752 SGD_REF:S000076907|PMID:15184374 IDA F YLR011W gene taxon:4932 20040917 SGD
+SGD S000004001 LOT6 GO:0008752 SGD_REF:S000076907|PMID:15184374 ISS F YLR011W gene taxon:4932 20040917 SGD
+SGD S000004001 LOT6 GO:0000004 SGD_REF:S000069584 ND P YLR011W gene taxon:4932 20021011 SGD
+SGD S000001876 LPD1 GO:0005960 SGD_REF:S000052730|PMID:10187845 TAS C dihydrolipoamide dehydrogenase precursor (mature protein is the E3 component of alpha-ketoacid dehydrogenase complexes) YFL018C|HPD1 gene taxon:4932 20050104 SGD
+SGD S000001876 LPD1 GO:0005967 SGD_REF:S000058500 TAS C dihydrolipoamide dehydrogenase precursor (mature protein is the E3 component of alpha-ketoacid dehydrogenase complexes) YFL018C|HPD1 gene taxon:4932 20010119 SGD
+SGD S000001876 LPD1 GO:0009353 SGD_REF:S000043865|PMID:2072900 IDA C dihydrolipoamide dehydrogenase precursor (mature protein is the E3 component of alpha-ketoacid dehydrogenase complexes) YFL018C|HPD1 gene taxon:4932 20041207 SGD
+SGD S000001876 LPD1 GO:0042645 SGD_REF:S000069519|PMID:11926067 IDA C dihydrolipoamide dehydrogenase precursor (mature protein is the E3 component of alpha-ketoacid dehydrogenase complexes) YFL018C|HPD1 gene taxon:4932 20031218 SGD
+SGD S000001876 LPD1 GO:0042645 SGD_REF:S000050870|PMID:10869431 IDA C dihydrolipoamide dehydrogenase precursor (mature protein is the E3 component of alpha-ketoacid dehydrogenase complexes) YFL018C|HPD1 gene taxon:4932 20050401 SGD
+SGD S000001876 LPD1 GO:0004148 SGD_REF:S000047776|PMID:2821168 IDA F dihydrolipoamide dehydrogenase precursor (mature protein is the E3 component of alpha-ketoacid dehydrogenase complexes) YFL018C|HPD1 gene taxon:4932 20010118 SGD
+SGD S000001876 LPD1 contributes_to GO:0004375 SGD_REF:S000052730|PMID:10187845 TAS F dihydrolipoamide dehydrogenase precursor (mature protein is the E3 component of alpha-ketoacid dehydrogenase complexes) YFL018C|HPD1 gene taxon:4932 20050104 SGD
+SGD S000001876 LPD1 contributes_to GO:0004591 SGD_REF:S000043865|PMID:2072900 IC GO:0009353 F dihydrolipoamide dehydrogenase precursor (mature protein is the E3 component of alpha-ketoacid dehydrogenase complexes) YFL018C|HPD1 gene taxon:4932 20050419 SGD
+SGD S000001876 LPD1 contributes_to GO:0004739 SGD_REF:S000058500 IC GO:0005967 F dihydrolipoamide dehydrogenase precursor (mature protein is the E3 component of alpha-ketoacid dehydrogenase complexes) YFL018C|HPD1 gene taxon:4932 20050214 SGD
+SGD S000001876 LPD1 GO:0006086 SGD_REF:S000058500 TAS P dihydrolipoamide dehydrogenase precursor (mature protein is the E3 component of alpha-ketoacid dehydrogenase complexes) YFL018C|HPD1 gene taxon:4932 20010119 SGD
+SGD S000001876 LPD1 GO:0006546 SGD_REF:S000053400|PMID:7498764 IMP P dihydrolipoamide dehydrogenase precursor (mature protein is the E3 component of alpha-ketoacid dehydrogenase complexes) YFL018C|HPD1 gene taxon:4932 20010118 SGD
+SGD S000001876 LPD1 GO:0006550 SGD_REF:S000048586|PMID:1479341 IMP P dihydrolipoamide dehydrogenase precursor (mature protein is the E3 component of alpha-ketoacid dehydrogenase complexes) YFL018C|HPD1 gene taxon:4932 20010118 SGD
+SGD S000001876 LPD1 GO:0006552 SGD_REF:S000048586|PMID:1479341 IMP P dihydrolipoamide dehydrogenase precursor (mature protein is the E3 component of alpha-ketoacid dehydrogenase complexes) YFL018C|HPD1 gene taxon:4932 20010118 SGD
+SGD S000001876 LPD1 GO:0006564 SGD_REF:S000053400|PMID:7498764 IMP P dihydrolipoamide dehydrogenase precursor (mature protein is the E3 component of alpha-ketoacid dehydrogenase complexes) YFL018C|HPD1 gene taxon:4932 20010118 SGD
+SGD S000001876 LPD1 GO:0006574 SGD_REF:S000048586|PMID:1479341 IMP P dihydrolipoamide dehydrogenase precursor (mature protein is the E3 component of alpha-ketoacid dehydrogenase complexes) YFL018C|HPD1 gene taxon:4932 20010118 SGD
+SGD S000005981 LPE10 GO:0005743 SGD_REF:S000060104|PMID:11254124 IDA C YPL060W gene taxon:4932 20020920 SGD
+SGD S000005981 LPE10 GO:0015095 SGD_REF:S000060104|PMID:11254124 IGI F YPL060W gene taxon:4932 20020920 SGD
+SGD S000005981 LPE10 GO:0015095 SGD_REF:S000060104|PMID:11254124 ISS F YPL060W gene taxon:4932 20020920 SGD
+SGD S000005981 LPE10 GO:0015095 SGD_REF:S000060104|PMID:11254124 IMP F YPL060W gene taxon:4932 20020920 SGD
+SGD S000005981 LPE10 GO:0045016 SGD_REF:S000060104|PMID:11254124 IGI P YPL060W gene taxon:4932 20020920 SGD
+SGD S000005981 LPE10 GO:0045016 SGD_REF:S000060104|PMID:11254124 ISS P YPL060W gene taxon:4932 20020920 SGD
+SGD S000005981 LPE10 GO:0045016 SGD_REF:S000060104|PMID:11254124 IMP P YPL060W gene taxon:4932 20020920 SGD
+SGD S000002911 LPP1 GO:0016020 SGD_REF:S000054861|PMID:10685032 IDA C lipid phosphate phosphatase YDR503C gene taxon:4932 20020925 SGD
+SGD S000002911 LPP1 GO:0008195 SGD_REF:S000054861|PMID:10685032 IDA F lipid phosphate phosphatase YDR503C gene taxon:4932 20020925 SGD
+SGD S000002911 LPP1 GO:0006644 SGD_REF:S000045881|PMID:10329682 IMP P lipid phosphate phosphatase YDR503C gene taxon:4932 20020925 SGD
+SGD S000000556 LRE1 GO:0009277 SGD_REF:S000061266|PMID:11532139 TAS C YCL051W gene taxon:4932 20021001 SGD
+SGD S000000556 LRE1 GO:0004860 SGD_REF:S000065971|PMID:11580836 IDA F YCL051W gene taxon:4932 20021001 SGD
+SGD S000000556 LRE1 GO:0030528 SGD_REF:S000065971|PMID:11580836 IDA F YCL051W gene taxon:4932 20021001 SGD
+SGD S000000556 LRE1 GO:0007047 SGD_REF:S000061266|PMID:11532139 IGI P YCL051W gene taxon:4932 20021001 SGD
+SGD S000000556 LRE1 GO:0009408 SGD_REF:S000065971|PMID:11580836 IDA P YCL051W gene taxon:4932 20021001 SGD
+SGD S000002399 LRG1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C similar to LIM-domain proteins and to rho/rac GTPase-activating family of proteins YDL240W gene taxon:4932 20031028 SGD
+SGD S000002399 LRG1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C similar to LIM-domain proteins and to rho/rac GTPase-activating family of proteins YDL240W gene taxon:4932 20040813 SGD
+SGD S000002399 LRG1 GO:0005935 SGD_REF:S000074185|PMID:14562095 IDA C similar to LIM-domain proteins and to rho/rac GTPase-activating family of proteins YDL240W gene taxon:4932 20031028 SGD
+SGD S000002399 LRG1 GO:0005100 SGD_REF:S000066007|PMID:11591390 IDA F similar to LIM-domain proteins and to rho/rac GTPase-activating family of proteins YDL240W gene taxon:4932 20021029 SGD
+SGD S000002399 LRG1 GO:0007264 SGD_REF:S000066007|PMID:11591390 IC GO:0005100 P similar to LIM-domain proteins and to rho/rac GTPase-activating family of proteins YDL240W gene taxon:4932 20021029 SGD
+SGD S000002399 LRG1 GO:0007264 SGD_REF:S000066007|PMID:11591390 IPI P similar to LIM-domain proteins and to rho/rac GTPase-activating family of proteins YDL240W gene taxon:4932 20021029 SGD
+SGD S000002399 LRG1 GO:0009272 SGD_REF:S000061282|PMID:11447600 IGI P similar to LIM-domain proteins and to rho/rac GTPase-activating family of proteins YDL240W gene taxon:4932 20020711 SGD
+SGD S000005291 LRO1 GO:0005783 SGD_REF:S000069030|PMID:11751830 TAS C phospholipid:diacylglycerol acyltransferase YNR008W gene taxon:4932 20020816 SGD
+SGD S000005291 LRO1 GO:0046027 SGD_REF:S000055066|PMID:10747858 IDA F phospholipid:diacylglycerol acyltransferase YNR008W gene taxon:4932 20020820 SGD
+SGD S000005291 LRO1 GO:0019432 SGD_REF:S000055066|PMID:10747858 IDA P phospholipid:diacylglycerol acyltransferase YNR008W gene taxon:4932 20020816 SGD
+SGD S000005291 LRO1 GO:0019432 SGD_REF:S000055066|PMID:10747858 IMP P phospholipid:diacylglycerol acyltransferase YNR008W gene taxon:4932 20020816 SGD
+SGD S000005291 LRO1 GO:0019915 SGD_REF:S000055066|PMID:10747858 IMP P phospholipid:diacylglycerol acyltransferase YNR008W gene taxon:4932 20020816 SGD
+SGD S000005291 LRO1 GO:0019915 SGD_REF:S000055066|PMID:10747858 IDA P phospholipid:diacylglycerol acyltransferase YNR008W gene taxon:4932 20020816 SGD
+SGD S000001123 LRP1 GO:0000176 SGD_REF:S000073750|PMID:12837249 IPI SGD:S000005527 C YHR081W|RRP47|YC1D gene taxon:4932 20030804 SGD
+SGD S000001123 LRP1 GO:0005554 SGD_REF:S000069584 ND F YHR081W|RRP47|YC1D gene taxon:4932 20021025 SGD
+SGD S000001123 LRP1 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P YHR081W|RRP47|YC1D gene taxon:4932 20060202 SGD
+SGD S000001123 LRP1 GO:0000724 SGD_REF:S000072912|PMID:12421302 IDA P YHR081W|RRP47|YC1D gene taxon:4932 20030408 SGD
+SGD S000001123 LRP1 GO:0006281 SGD_REF:S000077467|PMID:15489286 IDA P YHR081W|RRP47|YC1D gene taxon:4932 20050110 SGD
+SGD S000001123 LRP1 GO:0006303 SGD_REF:S000072912|PMID:12421302 IDA P YHR081W|RRP47|YC1D gene taxon:4932 20030408 SGD
+SGD S000001123 LRP1 GO:0006402 SGD_REF:S000077467|PMID:15489286 IDA P YHR081W|RRP47|YC1D gene taxon:4932 20050110 SGD
+SGD S000001123 LRP1 GO:0016180 SGD_REF:S000074272|PMID:12972615 IDA P YHR081W|RRP47|YC1D gene taxon:4932 20050110 SGD
+SGD S000001123 LRP1 GO:0030489 SGD_REF:S000073750|PMID:12837249 IMP P YHR081W|RRP47|YC1D gene taxon:4932 20030804 SGD
+SGD S000001123 LRP1 GO:0043144 SGD_REF:S000074272|PMID:12972615 IDA P YHR081W|RRP47|YC1D gene taxon:4932 20050110 SGD
+SGD S000002847 LRS4 GO:0000778 SGD_REF:S000073065|PMID:12689592 IDA C YDR439W gene taxon:4932 20050310 SGD
+SGD S000002847 LRS4 GO:0005634 SGD_REF:S000054483|PMID:10082585 IDA C YDR439W gene taxon:4932 20021001 SGD
+SGD S000002847 LRS4 GO:0005730 SGD_REF:S000073065|PMID:12689592 IDA C YDR439W gene taxon:4932 20031001 SGD
+SGD S000002847 LRS4 GO:0005554 SGD_REF:S000069584 ND F YDR439W gene taxon:4932 20021211 SGD
+SGD S000002847 LRS4 GO:0000183 SGD_REF:S000054483|PMID:10082585 IDA P YDR439W gene taxon:4932 20021001 SGD
+SGD S000002847 LRS4 GO:0045143 SGD_REF:S000073065|PMID:12689592 IMP P YDR439W gene taxon:4932 20031001 SGD
+SGD S000002847 LRS4 GO:0045143 SGD_REF:S000073065|PMID:12689592 IPI P YDR439W gene taxon:4932 20031001 SGD
+SGD S000003368 LSB1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YGR136W gene taxon:4932 20031028 SGD
+SGD S000003368 LSB1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YGR136W gene taxon:4932 20020507 SGD
+SGD S000003368 LSB1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YGR136W gene taxon:4932 20031028 SGD
+SGD S000003368 LSB1 GO:0005554 SGD_REF:S000069584 ND F YGR136W gene taxon:4932 20001002 SGD
+SGD S000003368 LSB1 GO:0000004 SGD_REF:S000069584 ND P YGR136W gene taxon:4932 20001002 SGD
+SGD S000002968 LSB3 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YFR024C-A|YFR024C gene taxon:4932 20031028 SGD
+SGD S000002968 LSB3 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YFR024C-A|YFR024C gene taxon:4932 20031028 SGD
+SGD S000002968 LSB3 GO:0005935 SGD_REF:S000074185|PMID:14562095 IDA C YFR024C-A|YFR024C gene taxon:4932 20031028 SGD
+SGD S000002968 LSB3 GO:0005554 SGD_REF:S000069584 ND F YFR024C-A|YFR024C gene taxon:4932 20021007 SGD
+SGD S000002968 LSB3 GO:0007015 SGD_REF:S000074191|PMID:14566057 RCA P YFR024C-A|YFR024C gene taxon:4932 20050608 SGD
+SGD S000000539 LSB5 GO:0005938 SGD_REF:S000071530|PMID:12388763 IDA C YCL034W gene taxon:4932 20021114 SGD
+SGD S000000539 LSB5 GO:0005554 SGD_REF:S000069584 ND F YCL034W gene taxon:4932 20021011 SGD
+SGD S000000539 LSB5 GO:0006897 SGD_REF:S000071530|PMID:12388763 IMP P YCL034W gene taxon:4932 20021114 SGD
+SGD S000000539 LSB5 GO:0007015 SGD_REF:S000043043|PMID:10512884 IPI P YCL034W gene taxon:4932 20021011 SGD
+SGD S000003636 LSB6 GO:0005624 SGD_REF:S000071857|PMID:12361950 IDA C YJL100W gene taxon:4932 20021215 SGD
+SGD S000003636 LSB6 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YJL100W gene taxon:4932 20020507 SGD
+SGD S000003636 LSB6 GO:0005774 SGD_REF:S000072987|PMID:12523934 IDA C YJL100W gene taxon:4932 20030421 SGD
+SGD S000003636 LSB6 GO:0005886 SGD_REF:S000072987|PMID:12523934 IDA C YJL100W gene taxon:4932 20030421 SGD
+SGD S000003636 LSB6 GO:0004430 SGD_REF:S000071857|PMID:12361950 IMP F YJL100W gene taxon:4932 20021215 SGD
+SGD S000003636 LSB6 GO:0004430 SGD_REF:S000072987|PMID:12523934 IDA F YJL100W gene taxon:4932 20030421 SGD
+SGD S000003636 LSB6 GO:0007015 SGD_REF:S000043043|PMID:10512884 IPI P YJL100W gene taxon:4932 20021011 SGD
+SGD S000003636 LSB6 GO:0046854 SGD_REF:S000071857|PMID:12361950 IDA P YJL100W gene taxon:4932 20050420 SGD
+SGD S000003636 LSB6 GO:0048017 SGD_REF:S000071857|PMID:12361950 TAS P YJL100W gene taxon:4932 20050524 SGD
+SGD S000005668 LSC1 GO:0005739 SGD_REF:S000040792|PMID:9874242 IDA C YOR142W gene taxon:4932 20030211 SGD
+SGD S000005668 LSC1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YOR142W gene taxon:4932 20040924 SGD
+SGD S000005668 LSC1 GO:0042645 SGD_REF:S000080741|PMID:15692048 IDA C YOR142W gene taxon:4932 20050401 SGD
+SGD S000005668 LSC1 GO:0004775 SGD_REF:S000040792|PMID:9874242 IDA F YOR142W gene taxon:4932 20030211 SGD
+SGD S000005668 LSC1 GO:0004775 SGD_REF:S000040792|PMID:9874242 ISS F YOR142W gene taxon:4932 20030211 SGD
+SGD S000005668 LSC1 GO:0004775 SGD_REF:S000040792|PMID:9874242 IMP F YOR142W gene taxon:4932 20030211 SGD
+SGD S000005668 LSC1 GO:0006099 SGD_REF:S000058126|PMID:9175438 TAS P YOR142W gene taxon:4932 20010118 SGD
+SGD S000005668 LSC1 GO:0006104 SGD_REF:S000058126|PMID:9175438 TAS P YOR142W gene taxon:4932 20010118 SGD
+SGD S000005668 LSC1 GO:0006104 SGD_REF:S000040792|PMID:9874242 IDA P YOR142W gene taxon:4932 20030211 SGD
+SGD S000003476 LSC2 GO:0005739 SGD_REF:S000040792|PMID:9874242 IDA C YGR244C gene taxon:4932 20030211 SGD
+SGD S000003476 LSC2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YGR244C gene taxon:4932 20040924 SGD
+SGD S000003476 LSC2 GO:0004775 SGD_REF:S000040792|PMID:9874242 IDA F YGR244C gene taxon:4932 20030204 SGD
+SGD S000003476 LSC2 GO:0004775 SGD_REF:S000040792|PMID:9874242 IMP F YGR244C gene taxon:4932 20030204 SGD
+SGD S000003476 LSC2 GO:0004775 SGD_REF:S000040792|PMID:9874242 ISS F YGR244C gene taxon:4932 20030204 SGD
+SGD S000003476 LSC2 GO:0006099 SGD_REF:S000058126|PMID:9175438 TAS P YGR244C gene taxon:4932 20010118 SGD
+SGD S000003476 LSC2 GO:0006104 SGD_REF:S000058126|PMID:9175438 TAS P YGR244C gene taxon:4932 20010118 SGD
+SGD S000003476 LSC2 GO:0006104 SGD_REF:S000040792|PMID:9874242 IDA P YGR244C gene taxon:4932 20030204 SGD
+SGD S000003067 LSG1 GO:0005737 SGD_REF:S000073608|PMID:12773575 IDA C YGL099W|KRE35 gene taxon:4932 20030706 SGD
+SGD S000003067 LSG1 GO:0003924 SGD_REF:S000073608|PMID:12773575 ISS F YGL099W|KRE35 gene taxon:4932 20030706 SGD
+SGD S000003067 LSG1 GO:0000054 SGD_REF:S000073608|PMID:12773575 IMP P YGL099W|KRE35 gene taxon:4932 20030706 SGD
+SGD S000003067 LSG1 GO:0000054 SGD_REF:S000073608|PMID:12773575 IPI P YGL099W|KRE35 gene taxon:4932 20030706 SGD
+SGD S000003067 LSG1 GO:0000747 SGD_REF:S000042229|PMID:10669874 IMP P YGL099W|KRE35 gene taxon:4932 20021011 SGD
+SGD S000003067 LSG1 GO:0030437 SGD_REF:S000042229|PMID:10669874 IMP P YGL099W|KRE35 gene taxon:4932 20021011 SGD
+SGD S000003660 LSM1 GO:0000932 SGD_REF:S000073211|PMID:12730603 IDA C YJL124C|SPB8 gene taxon:4932 20030718 SGD
+SGD S000003660 LSM1 GO:0000932 SGD_REF:S000073211|PMID:12730603 IMP C YJL124C|SPB8 gene taxon:4932 20030718 SGD
+SGD S000003660 LSM1 GO:0005845 SGD_REF:S000069047|PMID:11741542 IPI C YJL124C|SPB8 gene taxon:4932 20030410 SGD
+SGD S000003660 LSM1 GO:0005845 SGD_REF:S000069047|PMID:11741542 TAS C YJL124C|SPB8 gene taxon:4932 20030410 SGD
+SGD S000003660 LSM1 GO:0000339 SGD_REF:S000069047|PMID:11741542 IGI F YJL124C|SPB8 gene taxon:4932 20030410 SGD
+SGD S000003660 LSM1 GO:0000339 SGD_REF:S000069047|PMID:11741542 IMP F YJL124C|SPB8 gene taxon:4932 20030410 SGD
+SGD S000003660 LSM1 GO:0000339 SGD_REF:S000069047|PMID:11741542 IPI F YJL124C|SPB8 gene taxon:4932 20030410 SGD
+SGD S000003660 LSM1 GO:0000339 SGD_REF:S000069047|PMID:11741542 TAS F YJL124C|SPB8 gene taxon:4932 20030410 SGD
+SGD S000003660 LSM1 GO:0003723 SGD_REF:S000058981|PMID:15075370 TAS F YJL124C|SPB8 gene taxon:4932 20050222 SGD
+SGD S000003660 LSM1 GO:0000288 SGD_REF:S000050418|PMID:10747033 IGI P YJL124C|SPB8 gene taxon:4932 20020819 SGD
+SGD S000003660 LSM1 GO:0000288 SGD_REF:S000050418|PMID:10747033 IMP P YJL124C|SPB8 gene taxon:4932 20020819 SGD
+SGD S000003660 LSM1 GO:0000290 SGD_REF:S000052220|PMID:10761922 IGI P YJL124C|SPB8 gene taxon:4932 20020819 SGD
+SGD S000003660 LSM1 GO:0000290 SGD_REF:S000052220|PMID:10761922 IMP P YJL124C|SPB8 gene taxon:4932 20020819 SGD
+SGD S000003660 LSM1 GO:0000290 SGD_REF:S000052220|PMID:10761922 IPI P YJL124C|SPB8 gene taxon:4932 20020819 SGD
+SGD S000003660 LSM1 GO:0006402 SGD_REF:S000058981|PMID:15075370 TAS P YJL124C|SPB8 gene taxon:4932 20050222 SGD
+SGD S000001163 LSM12 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YHR121W gene taxon:4932 20031028 SGD
+SGD S000001163 LSM12 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YHR121W gene taxon:4932 20031028 SGD
+SGD S000001163 LSM12 GO:0003723 SGD_REF:S000076596|PMID:15225602 ISS F YHR121W gene taxon:4932 20040712 SGD
+SGD S000001163 LSM12 GO:0016070 SGD_REF:S000076596|PMID:15225602 ISS P YHR121W gene taxon:4932 20040712 SGD
+SGD S000001163 LSM12 GO:0016070 SGD_REF:S000115662|PMID:16702403 IPI SGD:S000002211|SGD:S000003410 P YHR121W gene taxon:4932 20060521 SGD
+SGD S000000122 LSM2 GO:0005688 SGD_REF:S000043309|PMID:10580475 TAS C snRNA-associated protein, Sm class YBL026W|SMX5|SNP3 gene taxon:4932 20050219 SGD
+SGD S000000122 LSM2 GO:0005688 SGD_REF:S000056374|PMID:10369684 IDA C snRNA-associated protein, Sm class YBL026W|SMX5|SNP3 gene taxon:4932 20051129 SGD
+SGD S000000122 LSM2 GO:0005688 SGD_REF:S000066234|PMID:11720284 IDA C snRNA-associated protein, Sm class YBL026W|SMX5|SNP3 gene taxon:4932 20051003 SGD
+SGD S000000122 LSM2 GO:0005730 SGD_REF:S000058981|PMID:15075370 IDA C snRNA-associated protein, Sm class YBL026W|SMX5|SNP3 gene taxon:4932 20050222 SGD
+SGD S000000122 LSM2 GO:0005732 SGD_REF:S000058981|PMID:15075370 IPI C snRNA-associated protein, Sm class YBL026W|SMX5|SNP3 gene taxon:4932 20050222 SGD
+SGD S000000122 LSM2 GO:0046540 SGD_REF:S000056376|PMID:10377396 IPI C snRNA-associated protein, Sm class YBL026W|SMX5|SNP3 gene taxon:4932 20050219 SGD
+SGD S000000122 LSM2 GO:0046540 SGD_REF:S000039461|PMID:10449419 IDA C snRNA-associated protein, Sm class YBL026W|SMX5|SNP3 gene taxon:4932 20050926 SGD
+SGD S000000122 LSM2 contributes_to GO:0003723 SGD_REF:S000058981|PMID:15075370 IDA F snRNA-associated protein, Sm class YBL026W|SMX5|SNP3 gene taxon:4932 20051129 SGD
+SGD S000000122 LSM2 contributes_to GO:0003723 SGD_REF:S000056374|PMID:10369684 IPI F snRNA-associated protein, Sm class YBL026W|SMX5|SNP3 gene taxon:4932 20051129 SGD
+SGD S000000122 LSM2 contributes_to GO:0031202 SGD_REF:S000039461|PMID:10449419 IDA F snRNA-associated protein, Sm class YBL026W|SMX5|SNP3 gene taxon:4932 20051003 SGD
+SGD S000000122 LSM2 contributes_to GO:0031202 SGD_REF:S000056376|PMID:10377396 IPI F snRNA-associated protein, Sm class YBL026W|SMX5|SNP3 gene taxon:4932 20051003 SGD
+SGD S000000122 LSM2 GO:0000398 SGD_REF:S000056376|PMID:10377396 IPI P snRNA-associated protein, Sm class YBL026W|SMX5|SNP3 gene taxon:4932 20020620 SGD
+SGD S000000122 LSM2 GO:0006402 SGD_REF:S000058981|PMID:15075370 TAS P snRNA-associated protein, Sm class YBL026W|SMX5|SNP3 gene taxon:4932 20050222 SGD
+SGD S000006434 LSM3 GO:0005688 SGD_REF:S000052072|PMID:9528767 TAS C snRNP protein YLR438C-A|SMX4|USS2 gene taxon:4932 20021023 SGD
+SGD S000006434 LSM3 GO:0005688 SGD_REF:S000043309|PMID:10580475 TAS C snRNP protein YLR438C-A|SMX4|USS2 gene taxon:4932 20050219 SGD
+SGD S000006434 LSM3 GO:0005688 SGD_REF:S000056374|PMID:10369684 IDA C snRNP protein YLR438C-A|SMX4|USS2 gene taxon:4932 20051129 SGD
+SGD S000006434 LSM3 GO:0005688 SGD_REF:S000066234|PMID:11720284 IDA C snRNP protein YLR438C-A|SMX4|USS2 gene taxon:4932 20051003 SGD
+SGD S000006434 LSM3 GO:0005730 SGD_REF:S000058981|PMID:15075370 IDA C snRNP protein YLR438C-A|SMX4|USS2 gene taxon:4932 20050222 SGD
+SGD S000006434 LSM3 GO:0005732 SGD_REF:S000058981|PMID:15075370 IPI C snRNP protein YLR438C-A|SMX4|USS2 gene taxon:4932 20050222 SGD
+SGD S000006434 LSM3 GO:0046540 SGD_REF:S000056376|PMID:10377396 NAS C snRNP protein YLR438C-A|SMX4|USS2 gene taxon:4932 20050219 SGD
+SGD S000006434 LSM3 GO:0046540 SGD_REF:S000039461|PMID:10449419 IDA C snRNP protein YLR438C-A|SMX4|USS2 gene taxon:4932 20050926 SGD
+SGD S000006434 LSM3 GO:0003723 SGD_REF:S000058981|PMID:15075370 TAS F snRNP protein YLR438C-A|SMX4|USS2 gene taxon:4932 20050222 SGD
+SGD S000006434 LSM3 contributes_to GO:0003723 SGD_REF:S000056374|PMID:10369684 IPI F snRNP protein YLR438C-A|SMX4|USS2 gene taxon:4932 20051129 SGD
+SGD S000006434 LSM3 GO:0000398 SGD_REF:S000056376|PMID:10377396 IPI P snRNP protein YLR438C-A|SMX4|USS2 gene taxon:4932 20030113 SGD
+SGD S000006434 LSM3 GO:0000398 SGD_REF:S000058981|PMID:15075370 TAS P snRNP protein YLR438C-A|SMX4|USS2 gene taxon:4932 20050222 SGD
+SGD S000006434 LSM3 GO:0006402 SGD_REF:S000058981|PMID:15075370 TAS P snRNP protein YLR438C-A|SMX4|USS2 gene taxon:4932 20050222 SGD
+SGD S000000914 LSM4 GO:0005688 SGD_REF:S000043309|PMID:10580475 TAS C U6 snRNA associated protein YER112W|SDB23|USS1 gene taxon:4932 20050219 SGD
+SGD S000000914 LSM4 GO:0005688 SGD_REF:S000066234|PMID:11720284 IDA C U6 snRNA associated protein YER112W|SDB23|USS1 gene taxon:4932 20051003 SGD
+SGD S000000914 LSM4 GO:0005688 SGD_REF:S000056374|PMID:10369684 IDA C U6 snRNA associated protein YER112W|SDB23|USS1 gene taxon:4932 20051129 SGD
+SGD S000000914 LSM4 GO:0005730 SGD_REF:S000058981|PMID:15075370 IDA C U6 snRNA associated protein YER112W|SDB23|USS1 gene taxon:4932 20050222 SGD
+SGD S000000914 LSM4 GO:0005732 SGD_REF:S000058981|PMID:15075370 IPI C U6 snRNA associated protein YER112W|SDB23|USS1 gene taxon:4932 20050222 SGD
+SGD S000000914 LSM4 GO:0046540 SGD_REF:S000056376|PMID:10377396 IPI C U6 snRNA associated protein YER112W|SDB23|USS1 gene taxon:4932 20050219 SGD
+SGD S000000914 LSM4 GO:0046540 SGD_REF:S000039461|PMID:10449419 IDA C U6 snRNA associated protein YER112W|SDB23|USS1 gene taxon:4932 20050926 SGD
+SGD S000000914 LSM4 GO:0003723 SGD_REF:S000058981|PMID:15075370 TAS F U6 snRNA associated protein YER112W|SDB23|USS1 gene taxon:4932 20050222 SGD
+SGD S000000914 LSM4 contributes_to GO:0003723 SGD_REF:S000056374|PMID:10369684 IPI F U6 snRNA associated protein YER112W|SDB23|USS1 gene taxon:4932 20051129 SGD
+SGD S000000914 LSM4 contributes_to GO:0031202 SGD_REF:S000039461|PMID:10449419 IDA F U6 snRNA associated protein YER112W|SDB23|USS1 gene taxon:4932 20051003 SGD
+SGD S000000914 LSM4 contributes_to GO:0031202 SGD_REF:S000056376|PMID:10377396 IPI F U6 snRNA associated protein YER112W|SDB23|USS1 gene taxon:4932 20051003 SGD
+SGD S000000914 LSM4 GO:0000398 SGD_REF:S000056376|PMID:10377396 IPI P U6 snRNA associated protein YER112W|SDB23|USS1 gene taxon:4932 20020620 SGD
+SGD S000000914 LSM4 GO:0000398 SGD_REF:S000058981|PMID:15075370 TAS P U6 snRNA associated protein YER112W|SDB23|USS1 gene taxon:4932 20050222 SGD
+SGD S000000914 LSM4 GO:0006402 SGD_REF:S000058981|PMID:15075370 TAS P U6 snRNA associated protein YER112W|SDB23|USS1 gene taxon:4932 20050222 SGD
+SGD S000000948 LSM5 GO:0005688 SGD_REF:S000043309|PMID:10580475 TAS C snRNP protein YER146W gene taxon:4932 20050219 SGD
+SGD S000000948 LSM5 GO:0005688 SGD_REF:S000066234|PMID:11720284 IDA C snRNP protein YER146W gene taxon:4932 20051003 SGD
+SGD S000000948 LSM5 GO:0005688 SGD_REF:S000056374|PMID:10369684 IDA C snRNP protein YER146W gene taxon:4932 20051129 SGD
+SGD S000000948 LSM5 GO:0005730 SGD_REF:S000058981|PMID:15075370 IDA C snRNP protein YER146W gene taxon:4932 20050222 SGD
+SGD S000000948 LSM5 GO:0005732 SGD_REF:S000058981|PMID:15075370 IPI C snRNP protein YER146W gene taxon:4932 20050222 SGD
+SGD S000000948 LSM5 GO:0046540 SGD_REF:S000056376|PMID:10377396 IPI C snRNP protein YER146W gene taxon:4932 20050219 SGD
+SGD S000000948 LSM5 GO:0046540 SGD_REF:S000039461|PMID:10449419 IDA C snRNP protein YER146W gene taxon:4932 20050926 SGD
+SGD S000000948 LSM5 contributes_to GO:0003723 SGD_REF:S000058981|PMID:15075370 IDA F snRNP protein YER146W gene taxon:4932 20051129 SGD
+SGD S000000948 LSM5 contributes_to GO:0003723 SGD_REF:S000056374|PMID:10369684 IPI F snRNP protein YER146W gene taxon:4932 20051129 SGD
+SGD S000000948 LSM5 contributes_to GO:0031202 SGD_REF:S000039461|PMID:10449419 IDA F snRNP protein YER146W gene taxon:4932 20051003 SGD
+SGD S000000948 LSM5 contributes_to GO:0031202 SGD_REF:S000056376|PMID:10377396 IPI F snRNP protein YER146W gene taxon:4932 20051003 SGD
+SGD S000000948 LSM5 GO:0000398 SGD_REF:S000056376|PMID:10377396 IPI P snRNP protein YER146W gene taxon:4932 20020620 SGD
+SGD S000000948 LSM5 GO:0006402 SGD_REF:S000058981|PMID:15075370 TAS P snRNP protein YER146W gene taxon:4932 20050222 SGD
+SGD S000002786 LSM6 GO:0005688 SGD_REF:S000043309|PMID:10580475 TAS C snRNP protein YDR378C gene taxon:4932 20050219 SGD
+SGD S000002786 LSM6 GO:0005688 SGD_REF:S000056374|PMID:10369684 IDA C snRNP protein YDR378C gene taxon:4932 20051129 SGD
+SGD S000002786 LSM6 GO:0005688 SGD_REF:S000066234|PMID:11720284 IDA C snRNP protein YDR378C gene taxon:4932 20051003 SGD
+SGD S000002786 LSM6 GO:0005730 SGD_REF:S000058981|PMID:15075370 IDA C snRNP protein YDR378C gene taxon:4932 20050222 SGD
+SGD S000002786 LSM6 GO:0005732 SGD_REF:S000058981|PMID:15075370 IPI C snRNP protein YDR378C gene taxon:4932 20050222 SGD
+SGD S000002786 LSM6 GO:0046540 SGD_REF:S000056376|PMID:10377396 IPI C snRNP protein YDR378C gene taxon:4932 20050219 SGD
+SGD S000002786 LSM6 GO:0046540 SGD_REF:S000039461|PMID:10449419 IDA C snRNP protein YDR378C gene taxon:4932 20050926 SGD
+SGD S000002786 LSM6 contributes_to GO:0003723 SGD_REF:S000058981|PMID:15075370 IDA F snRNP protein YDR378C gene taxon:4932 20051129 SGD
+SGD S000002786 LSM6 contributes_to GO:0003723 SGD_REF:S000056374|PMID:10369684 IPI F snRNP protein YDR378C gene taxon:4932 20051129 SGD
+SGD S000002786 LSM6 contributes_to GO:0031202 SGD_REF:S000039461|PMID:10449419 IDA F snRNP protein YDR378C gene taxon:4932 20051003 SGD
+SGD S000002786 LSM6 contributes_to GO:0031202 SGD_REF:S000056376|PMID:10377396 IPI F snRNP protein YDR378C gene taxon:4932 20051003 SGD
+SGD S000002786 LSM6 GO:0000398 SGD_REF:S000056376|PMID:10377396 IPI P snRNP protein YDR378C gene taxon:4932 20020620 SGD
+SGD S000002786 LSM6 GO:0006402 SGD_REF:S000058981|PMID:15075370 TAS P snRNP protein YDR378C gene taxon:4932 20050222 SGD
+SGD S000005091 LSM7 GO:0005688 SGD_REF:S000050418|PMID:10747033 IDA C snRNP protein YNL147W gene taxon:4932 20020715 SGD
+SGD S000005091 LSM7 GO:0005688 SGD_REF:S000066234|PMID:11720284 IDA C snRNP protein YNL147W gene taxon:4932 20051003 SGD
+SGD S000005091 LSM7 GO:0005688 SGD_REF:S000043309|PMID:10580475 TAS C snRNP protein YNL147W gene taxon:4932 20050219 SGD
+SGD S000005091 LSM7 GO:0005688 SGD_REF:S000056374|PMID:10369684 IDA C snRNP protein YNL147W gene taxon:4932 20051129 SGD
+SGD S000005091 LSM7 GO:0005730 SGD_REF:S000058981|PMID:15075370 IDA C snRNP protein YNL147W gene taxon:4932 20050222 SGD
+SGD S000005091 LSM7 GO:0005732 SGD_REF:S000058981|PMID:15075370 IPI C snRNP protein YNL147W gene taxon:4932 20050222 SGD
+SGD S000005091 LSM7 GO:0046540 SGD_REF:S000056376|PMID:10377396 NAS C snRNP protein YNL147W gene taxon:4932 20050219 SGD
+SGD S000005091 LSM7 GO:0046540 SGD_REF:S000039461|PMID:10449419 IDA C snRNP protein YNL147W gene taxon:4932 20050926 SGD
+SGD S000005091 LSM7 GO:0003723 SGD_REF:S000058981|PMID:15075370 TAS F snRNP protein YNL147W gene taxon:4932 20050222 SGD
+SGD S000005091 LSM7 contributes_to GO:0003723 SGD_REF:S000056374|PMID:10369684 IPI F snRNP protein YNL147W gene taxon:4932 20051129 SGD
+SGD S000005091 LSM7 contributes_to GO:0031202 SGD_REF:S000039461|PMID:10449419 IDA F snRNP protein YNL147W gene taxon:4932 20051003 SGD
+SGD S000005091 LSM7 GO:0000398 SGD_REF:S000060393|PMID:11333229 IMP P snRNP protein YNL147W gene taxon:4932 20020715 SGD
+SGD S000005091 LSM7 GO:0000398 SGD_REF:S000058981|PMID:15075370 TAS P snRNP protein YNL147W gene taxon:4932 20050222 SGD
+SGD S000005091 LSM7 GO:0006402 SGD_REF:S000050418|PMID:10747033 IMP P snRNP protein YNL147W gene taxon:4932 20020715 SGD
+SGD S000005091 LSM7 GO:0006402 SGD_REF:S000058981|PMID:15075370 TAS P snRNP protein YNL147W gene taxon:4932 20050222 SGD
+SGD S000005091 LSM7 GO:0006402 SGD_REF:S000050418|PMID:10747033 IPI P snRNP protein YNL147W gene taxon:4932 20020715 SGD
+SGD S000003783 LSM8 GO:0005634 SGD_REF:S000073211|PMID:12730603 IDA C snRNP protein YJR022W gene taxon:4932 20030718 SGD
+SGD S000003783 LSM8 GO:0005688 SGD_REF:S000043309|PMID:10580475 TAS C snRNP protein YJR022W gene taxon:4932 20050219 SGD
+SGD S000003783 LSM8 GO:0005688 SGD_REF:S000056374|PMID:10369684 IDA C snRNP protein YJR022W gene taxon:4932 20051129 SGD
+SGD S000003783 LSM8 GO:0005688 SGD_REF:S000066234|PMID:11720284 IDA C snRNP protein YJR022W gene taxon:4932 20051003 SGD
+SGD S000003783 LSM8 GO:0046540 SGD_REF:S000056376|PMID:10377396 IPI C snRNP protein YJR022W gene taxon:4932 20050219 SGD
+SGD S000003783 LSM8 GO:0046540 SGD_REF:S000039461|PMID:10449419 IDA C snRNP protein YJR022W gene taxon:4932 20050926 SGD
+SGD S000003783 LSM8 contributes_to GO:0003723 SGD_REF:S000058981|PMID:15075370 IDA F snRNP protein YJR022W gene taxon:4932 20051129 SGD
+SGD S000003783 LSM8 contributes_to GO:0003723 SGD_REF:S000056374|PMID:10369684 IPI F snRNP protein YJR022W gene taxon:4932 20051129 SGD
+SGD S000003783 LSM8 contributes_to GO:0031202 SGD_REF:S000039461|PMID:10449419 IDA F snRNP protein YJR022W gene taxon:4932 20051003 SGD
+SGD S000003783 LSM8 contributes_to GO:0031202 SGD_REF:S000056376|PMID:10377396 IPI F snRNP protein YJR022W gene taxon:4932 20051003 SGD
+SGD S000003783 LSM8 GO:0000398 SGD_REF:S000056376|PMID:10377396 IPI P snRNP protein YJR022W gene taxon:4932 20020620 SGD
+SGD S000005925 LSP1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YPL004C gene taxon:4932 20020507 SGD
+SGD S000005925 LSP1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YPL004C gene taxon:4932 20031028 SGD
+SGD S000005925 LSP1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YPL004C gene taxon:4932 20031210 SGD
+SGD S000005925 LSP1 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C YPL004C gene taxon:4932 20060317 SGD
+SGD S000005925 LSP1 GO:0004860 SGD_REF:S000076362|PMID:15016821 IMP F YPL004C gene taxon:4932 20040630 SGD
+SGD S000005925 LSP1 GO:0006897 SGD_REF:S000114479|PMID:16496001 IGI P YPL004C gene taxon:4932 20060303 SGD
+SGD S000005925 LSP1 GO:0006897 SGD_REF:S000114479|PMID:16496001 IMP P YPL004C gene taxon:4932 20060303 SGD
+SGD S000005925 LSP1 GO:0009408 SGD_REF:S000076362|PMID:15016821 IMP P YPL004C gene taxon:4932 20040630 SGD
+SGD S000006478 LSR1 GO:0005686 SGD_REF:S000069987|PMID:2977088 TAS C U2 snRNA snR20 gene taxon:4932 20020621 SGD
+SGD S000006478 LSR1 GO:0003723 SGD_REF:S000059987|PMID:11158289 TAS F U2 snRNA snR20 gene taxon:4932 20021118 SGD
+SGD S000006478 LSR1 GO:0000398 SGD_REF:S000059987|PMID:11158289 IPI P U2 snRNA snR20 gene taxon:4932 20021118 SGD
+SGD S000001659 LST4 GO:0030120 SGD_REF:S000041998|PMID:9409822 IDA C YKL176C gene taxon:4932 20021001 SGD
+SGD S000001659 LST4 GO:0008565 SGD_REF:S000041998|PMID:9409822 IDA F YKL176C gene taxon:4932 20021001 SGD
+SGD S000001659 LST4 GO:0006886 SGD_REF:S000041998|PMID:9409822 IDA P YKL176C gene taxon:4932 20021001 SGD
+SGD S000001659 LST4 GO:0006893 SGD_REF:S000041998|PMID:9409822 IDA P YKL176C gene taxon:4932 20021001 SGD
+SGD S000001659 LST4 GO:0015031 SGD_REF:S000041998|PMID:9409822 IDA P YKL176C gene taxon:4932 20021001 SGD
+SGD S000001659 LST4 GO:0016192 SGD_REF:S000041998|PMID:9409822 IDA P YKL176C gene taxon:4932 20021001 SGD
+SGD S000003289 LST7 GO:0030120 SGD_REF:S000041998|PMID:9409822 IDA C YGR057C gene taxon:4932 20021001 SGD
+SGD S000003289 LST7 GO:0008565 SGD_REF:S000041998|PMID:9409822 IDA F YGR057C gene taxon:4932 20021001 SGD
+SGD S000003289 LST7 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P YGR057C gene taxon:4932 20060210 SGD
+SGD S000003289 LST7 GO:0006886 SGD_REF:S000041998|PMID:9409822 IDA P YGR057C gene taxon:4932 20021001 SGD
+SGD S000003289 LST7 GO:0006893 SGD_REF:S000041998|PMID:9409822 IDA P YGR057C gene taxon:4932 20021001 SGD
+SGD S000003289 LST7 GO:0015031 SGD_REF:S000041998|PMID:9409822 IDA P YGR057C gene taxon:4932 20021001 SGD
+SGD S000003289 LST7 GO:0016192 SGD_REF:S000041998|PMID:9409822 IDA P YGR057C gene taxon:4932 20021001 SGD
+SGD S000004951 LST8 GO:0000139 SGD_REF:S000072954|PMID:12719473 IDA C YNL006W gene taxon:4932 20030507 SGD
+SGD S000004951 LST8 GO:0000300 SGD_REF:S000072954|PMID:12719473 IDA C YNL006W gene taxon:4932 20030507 SGD
+SGD S000004951 LST8 GO:0010008 SGD_REF:S000072954|PMID:12719473 IDA C YNL006W gene taxon:4932 20030507 SGD
+SGD S000004951 LST8 GO:0031234 SGD_REF:S000072891|PMID:12631735 IDA C YNL006W gene taxon:4932 20051104 SGD
+SGD S000004951 LST8 GO:0031931 SGD_REF:S000071528|PMID:12408816 IPI C YNL006W gene taxon:4932 20051130 SGD
+SGD S000004951 LST8 GO:0031932 SGD_REF:S000071528|PMID:12408816 IPI C YNL006W gene taxon:4932 20051130 SGD
+SGD S000004951 LST8 GO:0005515 SGD_REF:S000072891|PMID:12631735 IPI SGD:S000003827|SGD:S000001686 F YNL006W gene taxon:4932 20030604 SGD
+SGD S000004951 LST8 GO:0030295 SGD_REF:S000082468|PMID:16002396 IMP F YNL006W gene taxon:4932 20051104 SGD
+SGD S000004951 LST8 GO:0001558 SGD_REF:S000071528|PMID:12408816 IPI SGD:S000003827|SGD:S000001686 P YNL006W gene taxon:4932 20051104 SGD
+SGD S000004951 LST8 GO:0006810 SGD_REF:S000041998|PMID:9409822 IMP P YNL006W gene taxon:4932 20010118 SGD
+SGD S000004951 LST8 GO:0007165 SGD_REF:S000072954|PMID:12719473 IMP P YNL006W gene taxon:4932 20030507 SGD
+SGD S000004951 LST8 GO:0030950 SGD_REF:S000071528|PMID:12408816 IMP P YNL006W gene taxon:4932 20051104 SGD
+SGD S000004951 LST8 GO:0031505 SGD_REF:S000072954|PMID:12719473 IMP P YNL006W gene taxon:4932 20051108 SGD
+SGD S000004951 LST8 GO:0031930 SGD_REF:S000074991|PMID:11742997 IMP P YNL006W gene taxon:4932 20051130 SGD
+SGD S000000022 LTE1 GO:0005933 SGD_REF:S000060286|PMID:11148127 TAS C YAL024C|MSI2 gene taxon:4932 20021016 SGD
+SGD S000000022 LTE1 GO:0005085 SGD_REF:S000053431|PMID:7985422 ISS F YAL024C|MSI2 gene taxon:4932 20021015 SGD
+SGD S000000022 LTE1 GO:0007096 SGD_REF:S000056360|PMID:10219244 TAS P YAL024C|MSI2 gene taxon:4932 20021016 SGD
+SGD S000000022 LTE1 GO:0007096 SGD_REF:S000086185|PMID:16039591 TAS P YAL024C|MSI2 gene taxon:4932 20060314 SGD
+SGD S000000022 LTE1 GO:0031578 SGD_REF:S000086185|PMID:16039591 TAS P YAL024C|MSI2 gene taxon:4932 20060314 SGD
+SGD S000006277 LTP1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C 18 kDa phosphotyrosine phosphatase YPR073C gene taxon:4932 20031028 SGD
+SGD S000006277 LTP1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C 18 kDa phosphotyrosine phosphatase YPR073C gene taxon:4932 20031028 SGD
+SGD S000006277 LTP1 GO:0004725 SGD_REF:S000039669|PMID:7629177 IDA F 18 kDa phosphotyrosine phosphatase YPR073C gene taxon:4932 20020708 SGD
+SGD S000006277 LTP1 GO:0004725 SGD_REF:S000077098|PMID:15358193 IDA F 18 kDa phosphotyrosine phosphatase YPR073C gene taxon:4932 20051005 SGD
+SGD S000006277 LTP1 GO:0004725 SGD_REF:S000039669|PMID:7629177 IMP F 18 kDa phosphotyrosine phosphatase YPR073C gene taxon:4932 20020708 SGD
+SGD S000006277 LTP1 GO:0006470 SGD_REF:S000039669|PMID:7629177 IDA P 18 kDa phosphotyrosine phosphatase YPR073C gene taxon:4932 20020925 SGD
+SGD S000001626 LTV1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YKL143W|YKL2 gene taxon:4932 20031028 SGD
+SGD S000001626 LTV1 GO:0005554 SGD_REF:S000069584 ND F YKL143W|YKL2 gene taxon:4932 20010119 SGD
+SGD S000001626 LTV1 GO:0006970 SGD_REF:S000080092|PMID:15611164 IMP P YKL143W|YKL2 gene taxon:4932 20050503 SGD
+SGD S000001626 LTV1 GO:0006979 SGD_REF:S000080092|PMID:15611164 IMP P YKL143W|YKL2 gene taxon:4932 20050503 SGD
+SGD S000001626 LTV1 GO:0042274 SGD_REF:S000080092|PMID:15611164 IMP P YKL143W|YKL2 gene taxon:4932 20050503 SGD
+SGD S000002245 LUC7 GO:0005685 SGD_REF:S000069986|PMID:11804584 IDA C YDL087C|EPE1|EXM2 gene taxon:4932 20020621 SGD
+SGD S000002245 LUC7 GO:0005685 SGD_REF:S000049155|PMID:10500099 ISS C YDL087C|EPE1|EXM2 gene taxon:4932 20020219 SGD
+SGD S000002245 LUC7 GO:0005685 SGD_REF:S000049155|PMID:10500099 IGI C YDL087C|EPE1|EXM2 gene taxon:4932 20020219 SGD
+SGD S000002245 LUC7 GO:0005685 SGD_REF:S000049155|PMID:10500099 IMP C YDL087C|EPE1|EXM2 gene taxon:4932 20020219 SGD
+SGD S000002245 LUC7 GO:0003729 SGD_REF:S000049155|PMID:10500099 ISS F YDL087C|EPE1|EXM2 gene taxon:4932 20021007 SGD
+SGD S000002245 LUC7 GO:0006376 SGD_REF:S000049155|PMID:10500099 IMP P YDL087C|EPE1|EXM2 gene taxon:4932 20010118 SGD
+SGD S000002245 LUC7 GO:0006376 SGD_REF:S000049155|PMID:10500099 IGI P YDL087C|EPE1|EXM2 gene taxon:4932 20010118 SGD
+SGD S000005212 LYP1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C lysine permease YNL268W gene taxon:4932 20040928 SGD
+SGD S000005212 LYP1 GO:0005886 SGD_REF:S000043244|PMID:10654085 ISS C lysine permease YNL268W gene taxon:4932 20020806 SGD
+SGD S000005212 LYP1 GO:0015174 SGD_REF:S000043244|PMID:10654085 IDA F lysine permease YNL268W gene taxon:4932 20020806 SGD
+SGD S000005212 LYP1 GO:0015802 SGD_REF:S000043244|PMID:10654085 IDA P lysine permease YNL268W gene taxon:4932 20020806 SGD
+SGD S000001473 LYS1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YIR034C gene taxon:4932 20020507 SGD
+SGD S000001473 LYS1 GO:0004754 SGD_REF:S000039895|PMID:3928261 TAS F YIR034C gene taxon:4932 20030122 SGD
+SGD S000001473 LYS1 GO:0019878 SGD_REF:S000039895|PMID:3928261 TAS P YIR034C gene taxon:4932 20030122 SGD
+SGD S000001473 LYS1 GO:0019878 SGD_REF:S000071379|PMID:11752249 NAS P YIR034C gene taxon:4932 20020930 SGD
+SGD S000001356 LYS12 GO:0005739 SGD_REF:S000069459|PMID:11914276 IDA C homo-isocitrate dehydrogenase YIL094C|LYS10|LYS11 gene taxon:4932 20020507 SGD
+SGD S000001356 LYS12 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C homo-isocitrate dehydrogenase YIL094C|LYS10|LYS11 gene taxon:4932 20040813 SGD
+SGD S000001356 LYS12 GO:0047046 SGD_REF:S000066074 TAS F homo-isocitrate dehydrogenase YIL094C|LYS10|LYS11 gene taxon:4932 20040408 SGD
+SGD S000001356 LYS12 GO:0047046 SGD_REF:S000075849|PMID:10714900 TAS F homo-isocitrate dehydrogenase YIL094C|LYS10|LYS11 gene taxon:4932 20040408 SGD
+SGD S000001356 LYS12 GO:0009085 SGD_REF:S000070200 TAS P homo-isocitrate dehydrogenase YIL094C|LYS10|LYS11 gene taxon:4932 20021111 SGD
+SGD S000002441 LYS14 GO:0005634 SGD_REF:S000059225|PMID:10975256 IDA C YDR034C gene taxon:4932 20020930 SGD
+SGD S000002441 LYS14 GO:0016563 SGD_REF:S000053639|PMID:7935367 IMP F YDR034C gene taxon:4932 20030122 SGD
+SGD S000002441 LYS14 GO:0016563 SGD_REF:S000053639|PMID:7935367 TAS F YDR034C gene taxon:4932 20030122 SGD
+SGD S000002441 LYS14 GO:0019878 SGD_REF:S000039895|PMID:3928261 TAS P YDR034C gene taxon:4932 20020930 SGD
+SGD S000000319 LYS2 GO:0005737 SGD_REF:S000039895|PMID:3928261 TAS C alpha aminoadipate reductase YBR115C gene taxon:4932 20010118 SGD
+SGD S000000319 LYS2 GO:0004043 SGD_REF:S000039895|PMID:3928261 TAS F alpha aminoadipate reductase YBR115C gene taxon:4932 20010118 SGD
+SGD S000000319 LYS2 GO:0019878 SGD_REF:S000039895|PMID:3928261 TAS P alpha aminoadipate reductase YBR115C gene taxon:4932 20020930 SGD
+SGD S000002341 LYS20 GO:0005634 SGD_REF:S000069459|PMID:11914276 IDA C YDL131W (LYS21) homolog, homocitrate synthase YDL182W gene taxon:4932 20020507 SGD
+SGD S000002341 LYS20 GO:0005634 SGD_REF:S000049366|PMID:9099739 IDA C YDL131W (LYS21) homolog, homocitrate synthase YDL182W gene taxon:4932 20020930 SGD
+SGD S000002341 LYS20 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YDL131W (LYS21) homolog, homocitrate synthase YDL182W gene taxon:4932 20040928 SGD
+SGD S000002341 LYS20 GO:0004410 SGD_REF:S000040054|PMID:8923736 IGI F YDL131W (LYS21) homolog, homocitrate synthase YDL182W gene taxon:4932 20020930 SGD
+SGD S000002341 LYS20 GO:0004410 SGD_REF:S000040054|PMID:8923736 ISS F YDL131W (LYS21) homolog, homocitrate synthase YDL182W gene taxon:4932 20020930 SGD
+SGD S000002341 LYS20 GO:0004410 SGD_REF:S000040054|PMID:8923736 IMP F YDL131W (LYS21) homolog, homocitrate synthase YDL182W gene taxon:4932 20020930 SGD
+SGD S000002341 LYS20 GO:0004410 SGD_REF:S000040054|PMID:8923736 IEP F YDL131W (LYS21) homolog, homocitrate synthase YDL182W gene taxon:4932 20020930 SGD
+SGD S000002341 LYS20 GO:0004410 SGD_REF:S000049366|PMID:9099739 ISS F YDL131W (LYS21) homolog, homocitrate synthase YDL182W gene taxon:4932 20020930 SGD
+SGD S000002341 LYS20 GO:0019878 SGD_REF:S000049445|PMID:10103047 TAS P YDL131W (LYS21) homolog, homocitrate synthase YDL182W gene taxon:4932 20020930 SGD
+SGD S000002289 LYS21 GO:0005634 SGD_REF:S000069459|PMID:11914276 IDA C YDL182W (LYS20) homolog, homocitrate synthase YDL131W gene taxon:4932 20020507 SGD
+SGD S000002289 LYS21 GO:0005634 SGD_REF:S000049366|PMID:9099739 IDA C YDL182W (LYS20) homolog, homocitrate synthase YDL131W gene taxon:4932 20020930 SGD
+SGD S000002289 LYS21 GO:0004410 SGD_REF:S000049366|PMID:9099739 ISS F YDL182W (LYS20) homolog, homocitrate synthase YDL131W gene taxon:4932 20020930 SGD
+SGD S000002289 LYS21 GO:0019878 SGD_REF:S000049445|PMID:10103047 TAS P YDL182W (LYS20) homolog, homocitrate synthase YDL131W gene taxon:4932 20020930 SGD
+SGD S000002642 LYS4 GO:0005739 SGD_REF:S000070200 TAS C homoaconitase YDR234W|LYS3 gene taxon:4932 20021111 SGD
+SGD S000002642 LYS4 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C homoaconitase YDR234W|LYS3 gene taxon:4932 20040928 SGD
+SGD S000002642 LYS4 GO:0004409 SGD_REF:S000070200 TAS F homoaconitase YDR234W|LYS3 gene taxon:4932 20021111 SGD
+SGD S000002642 LYS4 GO:0019878 SGD_REF:S000071379|PMID:11752249 NAS P homoaconitase YDR234W|LYS3 gene taxon:4932 20020930 SGD
+SGD S000003122 LYS5 GO:0005737 SGD_REF:S000039895|PMID:3928261 TAS C alpha aminoadipate reductase phosphopantetheinyl transferase YGL154C gene taxon:4932 20010118 SGD
+SGD S000003122 LYS5 GO:0008897 SGD_REF:S000046365|PMID:10320345 IDA F alpha aminoadipate reductase phosphopantetheinyl transferase YGL154C gene taxon:4932 20041207 SGD
+SGD S000003122 LYS5 GO:0018065 SGD_REF:S000060241|PMID:11286508 IDA P alpha aminoadipate reductase phosphopantetheinyl transferase YGL154C gene taxon:4932 20030411 SGD
+SGD S000003122 LYS5 GO:0019878 SGD_REF:S000039895|PMID:3928261 TAS P alpha aminoadipate reductase phosphopantetheinyl transferase YGL154C gene taxon:4932 20020930 SGD
+SGD S000005333 LYS9 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YNR050C|LYS13 gene taxon:4932 20020507 SGD
+SGD S000005333 LYS9 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YNR050C|LYS13 gene taxon:4932 20031028 SGD
+SGD S000005333 LYS9 GO:0004755 SGD_REF:S000055949|PMID:3123231 TAS F YNR050C|LYS13 gene taxon:4932 20030117 SGD
+SGD S000005333 LYS9 GO:0019878 SGD_REF:S000039895|PMID:3928261 TAS P YNR050C|LYS13 gene taxon:4932 20020930 SGD
+SGD S000004623 MAC1 GO:0005634 SGD_REF:S000043766|PMID:8262047 IDA C metal-binding transcriptional activator YMR021C|CUA1 gene taxon:4932 20020930 SGD
+SGD S000004623 MAC1 GO:0003704 SGD_REF:S000043547|PMID:9726991 IDA F metal-binding transcriptional activator YMR021C|CUA1 gene taxon:4932 20020930 SGD
+SGD S000004623 MAC1 GO:0006876 SGD_REF:S000048227|PMID:9188496 IMP P metal-binding transcriptional activator YMR021C|CUA1 gene taxon:4932 20020930 SGD
+SGD S000004623 MAC1 GO:0042176 SGD_REF:S000070359|PMID:12011036 IMP P metal-binding transcriptional activator YMR021C|CUA1 gene taxon:4932 20031002 SGD
+SGD S000004623 MAC1 GO:0045944 SGD_REF:S000043547|PMID:9726991 IDA P metal-binding transcriptional activator YMR021C|CUA1 gene taxon:4932 20020930 SGD
+SGD S000003054 MAD1 GO:0005634 SGD_REF:S000057390|PMID:7593191 IDA C YGL086W gene taxon:4932 20010118 SGD
+SGD S000003054 MAD1 GO:0005643 SGD_REF:S000071853|PMID:12473689 IDA C YGL086W gene taxon:4932 20030203 SGD
+SGD S000003054 MAD1 GO:0005554 SGD_REF:S000069584 ND F YGL086W gene taxon:4932 20021205 SGD
+SGD S000003054 MAD1 GO:0006913 SGD_REF:S000071853|PMID:12473689 IGI P YGL086W gene taxon:4932 20030203 SGD
+SGD S000003054 MAD1 GO:0006913 SGD_REF:S000071853|PMID:12473689 IPI P YGL086W gene taxon:4932 20030203 SGD
+SGD S000003054 MAD1 GO:0007094 SGD_REF:S000056419|PMID:10704439 IMP P YGL086W gene taxon:4932 20010118 SGD
+SGD S000003054 MAD1 GO:0007094 SGD_REF:S000056419|PMID:10704439 IGI P YGL086W gene taxon:4932 20010118 SGD
+SGD S000003567 MAD2 GO:0000778 SGD_REF:S000071853|PMID:12473689 IDA C spindle checkpoint complex subunit YJL030W gene taxon:4932 20030203 SGD
+SGD S000003567 MAD2 GO:0005643 SGD_REF:S000071853|PMID:12473689 IDA C spindle checkpoint complex subunit YJL030W gene taxon:4932 20030203 SGD
+SGD S000003567 MAD2 GO:0005554 SGD_REF:S000069584 ND F spindle checkpoint complex subunit YJL030W gene taxon:4932 20021205 SGD
+SGD S000003567 MAD2 GO:0007094 SGD_REF:S000056419|PMID:10704439 IMP P spindle checkpoint complex subunit YJL030W gene taxon:4932 20010118 SGD
+SGD S000003567 MAD2 GO:0007094 SGD_REF:S000056419|PMID:10704439 IGI P spindle checkpoint complex subunit YJL030W gene taxon:4932 20010118 SGD
+SGD S000003550 MAD3 GO:0005634 SGD_REF:S000056419|PMID:10704439 IDA C spindle checkpoint complex subunit YJL013C gene taxon:4932 20010118 SGD
+SGD S000003550 MAD3 GO:0005554 SGD_REF:S000069584 ND F spindle checkpoint complex subunit YJL013C gene taxon:4932 20021209 SGD
+SGD S000003550 MAD3 GO:0007094 SGD_REF:S000056419|PMID:10704439 IMP P spindle checkpoint complex subunit YJL013C gene taxon:4932 20010118 SGD
+SGD S000003550 MAD3 GO:0007094 SGD_REF:S000056419|PMID:10704439 IGI P spindle checkpoint complex subunit YJL013C gene taxon:4932 20010118 SGD
+SGD S000001512 MAE1 GO:0005739 SGD_REF:S000043053|PMID:9603875 IDA C malic enzyme YKL029C gene taxon:4932 20010118 SGD
+SGD S000001512 MAE1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C malic enzyme YKL029C gene taxon:4932 20040924 SGD
+SGD S000001512 MAE1 GO:0004470 SGD_REF:S000043053|PMID:9603875 IDA F malic enzyme YKL029C gene taxon:4932 20050727 SGD
+SGD S000001512 MAE1 GO:0004470 SGD_REF:S000043053|PMID:9603875 ISS F malic enzyme YKL029C gene taxon:4932 20050727 SGD
+SGD S000001512 MAE1 GO:0006090 SGD_REF:S000043053|PMID:9603875 IMP P malic enzyme YKL029C gene taxon:4932 20010118 SGD
+SGD S000001512 MAE1 GO:0006520 SGD_REF:S000043053|PMID:9603875 IMP P malic enzyme YKL029C gene taxon:4932 20010118 SGD
+SGD S000002412 MAF1 GO:0005634 SGD_REF:S000061185|PMID:11438659 IDA C YDR005C gene taxon:4932 20020805 SGD
+SGD S000002412 MAF1 GO:0005554 SGD_REF:S000069584 ND F YDR005C gene taxon:4932 20020930 SGD
+SGD S000002412 MAF1 GO:0016480 SGD_REF:S000061185|PMID:11438659 IMP P YDR005C gene taxon:4932 20020930 SGD
+SGD S000002412 MAF1 GO:0016480 SGD_REF:S000061185|PMID:11438659 IPI P YDR005C gene taxon:4932 20020930 SGD
+SGD S000000944 MAG1 GO:0005634 SGD_REF:S000056826|PMID:2265619 IC GO:0003905 C 3-methyladenine DNA glycosylase YER142C|MMS5 gene taxon:4932 20021114 SGD
+SGD S000000944 MAG1 GO:0003905 SGD_REF:S000056826|PMID:2265619 IDA F 3-methyladenine DNA glycosylase YER142C|MMS5 gene taxon:4932 20020930 SGD
+SGD S000000944 MAG1 GO:0003905 SGD_REF:S000063934|PMID:2682633 IDA F 3-methyladenine DNA glycosylase YER142C|MMS5 gene taxon:4932 20040521 SGD
+SGD S000000944 MAG1 GO:0006307 SGD_REF:S000056827|PMID:2265620 IGI P 3-methyladenine DNA glycosylase YER142C|MMS5 gene taxon:4932 20020930 SGD
+SGD S000000944 MAG1 GO:0006307 SGD_REF:S000056827|PMID:2265620 ISS P 3-methyladenine DNA glycosylase YER142C|MMS5 gene taxon:4932 20020930 SGD
+SGD S000000944 MAG1 GO:0006307 SGD_REF:S000056827|PMID:2265620 IEP P 3-methyladenine DNA glycosylase YER142C|MMS5 gene taxon:4932 20020930 SGD
+SGD S000004419 MAG2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YLR427W gene taxon:4932 20031028 SGD
+SGD S000004419 MAG2 GO:0005554 SGD_REF:S000069584 ND F YLR427W gene taxon:4932 20060315 SGD
+SGD S000004419 MAG2 GO:0006307 SGD_REF:S000074191|PMID:14566057 RCA P YLR427W gene taxon:4932 20050608 SGD
+SGD S000000779 MAK10 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YEL053C gene taxon:4932 20031028 SGD
+SGD S000000779 MAK10 GO:0031417 SGD_REF:S000062002|PMID:10504710 IDA C YEL053C gene taxon:4932 20060119 SGD
+SGD S000000779 MAK10 contributes_to GO:0004596 SGD_REF:S000060692|PMID:11274203 IMP F YEL053C gene taxon:4932 20060119 SGD
+SGD S000000779 MAK10 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P YEL053C gene taxon:4932 20060221 SGD
+SGD S000000779 MAK10 GO:0006474 SGD_REF:S000060692|PMID:11274203 IMP P YEL053C gene taxon:4932 20060119 SGD
+SGD S000001504 MAK11 GO:0005624 SGD_REF:S000040504|PMID:2826479 IDA C YKL021C gene taxon:4932 20020925 SGD
+SGD S000001504 MAK11 GO:0005554 SGD_REF:S000069584 ND F YKL021C gene taxon:4932 20020925 SGD
+SGD S000001504 MAK11 GO:0042273 SGD_REF:S000050422|PMID:7739558 IMP P YKL021C gene taxon:4932 20020925 SGD
+SGD S000000023 MAK16 GO:0005730 SGD_REF:S000055378|PMID:10838225 IDA C nuclear protein (putative) YAL025C gene taxon:4932 20020925 SGD
+SGD S000000023 MAK16 GO:0005554 SGD_REF:S000069584 ND F nuclear protein (putative) YAL025C gene taxon:4932 20020925 SGD
+SGD S000000023 MAK16 GO:0042273 SGD_REF:S000050422|PMID:7739558 IMP P nuclear protein (putative) YAL025C gene taxon:4932 20020925 SGD
+SGD S000002467 MAK21 GO:0030690 SGD_REF:S000061344|PMID:11371346 IPI C YDR060W|NOC1 gene taxon:4932 20041024 SGD
+SGD S000002467 MAK21 GO:0005554 SGD_REF:S000069584 ND F YDR060W|NOC1 gene taxon:4932 20010703 SGD
+SGD S000002467 MAK21 GO:0000027 SGD_REF:S000045436|PMID:9786894 IMP P YDR060W|NOC1 gene taxon:4932 20010703 SGD
+SGD S000006255 MAK3 GO:0031417 SGD_REF:S000062002|PMID:10504710 IDA C N-acetyltransferase YPR051W gene taxon:4932 20060119 SGD
+SGD S000006255 MAK3 GO:0004596 SGD_REF:S000060692|PMID:11274203 IMP F N-acetyltransferase YPR051W gene taxon:4932 20060119 SGD
+SGD S000006255 MAK3 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P N-acetyltransferase YPR051W gene taxon:4932 20060221 SGD
+SGD S000006255 MAK3 GO:0006474 SGD_REF:S000060692|PMID:11274203 IMP P N-acetyltransferase YPR051W gene taxon:4932 20060119 SGD
+SGD S000000614 MAK31 GO:0031417 SGD_REF:S000062002|PMID:10504710 IDA C YCR020C-A|LSM9|SMX1 gene taxon:4932 20060119 SGD
+SGD S000000614 MAK31 contributes_to GO:0004596 SGD_REF:S000060692|PMID:11274203 IMP F YCR020C-A|LSM9|SMX1 gene taxon:4932 20060119 SGD
+SGD S000000614 MAK31 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P YCR020C-A|LSM9|SMX1 gene taxon:4932 20060221 SGD
+SGD S000000614 MAK31 GO:0006474 SGD_REF:S000060692|PMID:11274203 IMP P YCR020C-A|LSM9|SMX1 gene taxon:4932 20060119 SGD
+SGD S000000612 MAK32 GO:0008372 SGD_REF:S000069584 ND C YCR019W gene taxon:4932 20051114 SGD
+SGD S000000612 MAK32 GO:0005554 SGD_REF:S000069584 ND F YCR019W gene taxon:4932 20051114 SGD
+SGD S000000612 MAK32 GO:0044419 SGD_REF:S000053976|PMID:3551911 IMP P YCR019W gene taxon:4932 20051114 SGD
+SGD S000000346 MAK5 GO:0005730 SGD_REF:S000074465|PMID:13680366 IDA C YBR142W gene taxon:4932 20040325 SGD
+SGD S000000346 MAK5 GO:0004004 SGD_REF:S000058443|PMID:10690410 TAS F YBR142W gene taxon:4932 20010118 SGD
+SGD S000000346 MAK5 GO:0000027 SGD_REF:S000058443|PMID:10690410 TAS P YBR142W gene taxon:4932 20010118 SGD
+SGD S000000346 MAK5 GO:0006364 SGD_REF:S000058443|PMID:10690410 TAS P YBR142W gene taxon:4932 20010118 SGD
+SGD S000003521 MAL11 GO:0005624 SGD_REF:S000040568|PMID:8594329 TAS C alpha-glucoside transporter, hexose transporter, maltose permease YGR289C|AGT1 gene taxon:4932 20010118 SGD
+SGD S000003521 MAL11 GO:0005352 SGD_REF:S000040568|PMID:8594329 TAS F alpha-glucoside transporter, hexose transporter, maltose permease YGR289C|AGT1 gene taxon:4932 20010118 SGD
+SGD S000003521 MAL11 GO:0005352 SGD_REF:S000073038|PMID:12702465 IDA F alpha-glucoside transporter, hexose transporter, maltose permease YGR289C|AGT1 gene taxon:4932 20030429 SGD
+SGD S000003521 MAL11 GO:0005364 SGD_REF:S000048189|PMID:1999393 IMP F alpha-glucoside transporter, hexose transporter, maltose permease YGR289C|AGT1 gene taxon:4932 20020531 SGD
+SGD S000003521 MAL11 GO:0015574 SGD_REF:S000073038|PMID:12702465 IDA F alpha-glucoside transporter, hexose transporter, maltose permease YGR289C|AGT1 gene taxon:4932 20030429 SGD
+SGD S000003521 MAL11 GO:0000017 SGD_REF:S000040568|PMID:8594329 TAS P alpha-glucoside transporter, hexose transporter, maltose permease YGR289C|AGT1 gene taxon:4932 20010118 SGD
+SGD S000003521 MAL11 GO:0015771 SGD_REF:S000073038|PMID:12702465 IDA P alpha-glucoside transporter, hexose transporter, maltose permease YGR289C|AGT1 gene taxon:4932 20030429 SGD
+SGD S000003524 MAL12 GO:0008372 SGD_REF:S000069584 ND C maltase YGR292W gene taxon:4932 20020531 SGD
+SGD S000003524 MAL12 GO:0004558 SGD_REF:S000056071|PMID:3025617 TAS F maltase YGR292W gene taxon:4932 20010118 SGD
+SGD S000003524 MAL12 GO:0000025 SGD_REF:S000058499 TAS P maltase YGR292W gene taxon:4932 20010119 SGD
+SGD S000003520 MAL13 GO:0005634 SGD_REF:S000054266|PMID:10447589 ISS C MAL-activator protein YGR288W gene taxon:4932 20020605 SGD
+SGD S000003520 MAL13 GO:0003700 SGD_REF:S000054266|PMID:10447589 ISS F MAL-activator protein YGR288W gene taxon:4932 20020605 SGD
+SGD S000003520 MAL13 GO:0005975 SGD_REF:S000056071|PMID:3025617 IGI P MAL-activator protein YGR288W gene taxon:4932 20020605 SGD
+SGD S000003520 MAL13 GO:0006355 SGD_REF:S000054266|PMID:10447589 ISS P MAL-activator protein YGR288W gene taxon:4932 20020605 SGD
+SGD S000029681 MAL21 GO:0005624 SGD_REF:S000052562|PMID:2549370 ISS C maltose permease gene taxon:4932 20020531 SGD
+SGD S000029681 MAL21 GO:0005352 SGD_REF:S000052562|PMID:2549370 ISS F maltose permease gene taxon:4932 20020531 SGD
+SGD S000029681 MAL21 GO:0005352 SGD_REF:S000073038|PMID:12702465 IDA F maltose permease gene taxon:4932 20030429 SGD
+SGD S000029681 MAL21 GO:0005363 SGD_REF:S000073038|PMID:12702465 IDA F maltose permease gene taxon:4932 20030429 SGD
+SGD S000029681 MAL21 GO:0000017 SGD_REF:S000052562|PMID:2549370 ISS P maltose permease gene taxon:4932 20020531 SGD
+SGD S000029681 MAL21 GO:0015768 SGD_REF:S000073038|PMID:12702465 IDA P maltose permease gene taxon:4932 20030429 SGD
+SGD S000029682 MAL22 GO:0008372 SGD_REF:S000069584 ND C maltase gene taxon:4932 20020531 SGD
+SGD S000029682 MAL22 GO:0004558 SGD_REF:S000052562|PMID:2549370 ISS F maltase gene taxon:4932 20020531 SGD
+SGD S000029682 MAL22 GO:0000025 SGD_REF:S000052562|PMID:2549370 ISS P maltase gene taxon:4932 20020531 SGD
+SGD S000029657 MAL23 GO:0005634 SGD_REF:S000054266|PMID:10447589 ISS C MAL-activator protein gene taxon:4932 20020605 SGD
+SGD S000029657 MAL23 GO:0003677 SGD_REF:S000054266|PMID:10447589 ISS F MAL-activator protein gene taxon:4932 20020605 SGD
+SGD S000029657 MAL23 GO:0003700 SGD_REF:S000054266|PMID:10447589 ISS F MAL-activator protein gene taxon:4932 20020605 SGD
+SGD S000029657 MAL23 GO:0005975 SGD_REF:S000052562|PMID:2549370 ISS P MAL-activator protein gene taxon:4932 20020531 SGD
+SGD S000029657 MAL23 GO:0006355 SGD_REF:S000054266|PMID:10447589 ISS P MAL-activator protein gene taxon:4932 20020605 SGD
+SGD S000000502 MAL31 GO:0005624 SGD_REF:S000052562|PMID:2549370 ISS C maltose permease YBR298C|MAL3T gene taxon:4932 20020531 SGD
+SGD S000000502 MAL31 GO:0005352 SGD_REF:S000052562|PMID:2549370 ISS F maltose permease YBR298C|MAL3T gene taxon:4932 20020531 SGD
+SGD S000000502 MAL31 GO:0000017 SGD_REF:S000052562|PMID:2549370 ISS P maltose permease YBR298C|MAL3T gene taxon:4932 20020531 SGD
+SGD S000000503 MAL32 GO:0008372 SGD_REF:S000069584 ND C maltase YBR299W|MAL3S gene taxon:4932 20020531 SGD
+SGD S000000503 MAL32 GO:0004558 SGD_REF:S000052562|PMID:2549370 ISS F maltase YBR299W|MAL3S gene taxon:4932 20020531 SGD
+SGD S000000503 MAL32 GO:0000025 SGD_REF:S000052562|PMID:2549370 ISS P maltase YBR299W|MAL3S gene taxon:4932 20020531 SGD
+SGD S000000501 MAL33 GO:0005634 SGD_REF:S000054266|PMID:10447589 ISS C MAL-activator protein YBR297W|MAL3R gene taxon:4932 20020605 SGD
+SGD S000000501 MAL33 GO:0003700 SGD_REF:S000054266|PMID:10447589 ISS F MAL-activator protein YBR297W|MAL3R gene taxon:4932 20020605 SGD
+SGD S000000501 MAL33 GO:0005975 SGD_REF:S000052562|PMID:2549370 ISS P MAL-activator protein YBR297W|MAL3R gene taxon:4932 20020531 SGD
+SGD S000000501 MAL33 GO:0006355 SGD_REF:S000054266|PMID:10447589 ISS P MAL-activator protein YBR297W|MAL3R gene taxon:4932 20020605 SGD
+SGD S000029686 MAL41 GO:0005624 SGD_REF:S000052562|PMID:2549370 ISS C maltose permease gene taxon:4932 20020531 SGD
+SGD S000029686 MAL41 GO:0005352 SGD_REF:S000052562|PMID:2549370 ISS F maltose permease gene taxon:4932 20020531 SGD
+SGD S000029686 MAL41 GO:0000017 SGD_REF:S000052562|PMID:2549370 ISS P maltose permease gene taxon:4932 20020531 SGD
+SGD S000029687 MAL42 GO:0008372 SGD_REF:S000069584 ND C maltase gene taxon:4932 20020531 SGD
+SGD S000029687 MAL42 GO:0004558 SGD_REF:S000052562|PMID:2549370 ISS F maltase gene taxon:4932 20020531 SGD
+SGD S000029687 MAL42 GO:0000025 SGD_REF:S000052562|PMID:2549370 ISS P maltase gene taxon:4932 20020531 SGD
+SGD S000029688 MAL43 GO:0005634 SGD_REF:S000054266|PMID:10447589 ISS C MAL-activator protein gene taxon:4932 20020605 SGD
+SGD S000029688 MAL43 GO:0003700 SGD_REF:S000054266|PMID:10447589 ISS F MAL-activator protein gene taxon:4932 20020605 SGD
+SGD S000029688 MAL43 GO:0005975 SGD_REF:S000052562|PMID:2549370 ISS P MAL-activator protein gene taxon:4932 20020531 SGD
+SGD S000029688 MAL43 GO:0006355 SGD_REF:S000054266|PMID:10447589 ISS P MAL-activator protein gene taxon:4932 20020605 SGD
+SGD S000029658 MAL61 GO:0005624 SGD_REF:S000052562|PMID:2549370 ISS C maltose permease gene taxon:4932 20020531 SGD
+SGD S000029658 MAL61 GO:0005352 SGD_REF:S000052562|PMID:2549370 ISS F maltose permease gene taxon:4932 20020531 SGD
+SGD S000029658 MAL61 GO:0005364 SGD_REF:S000048189|PMID:1999393 IMP F maltose permease gene taxon:4932 20020531 SGD
+SGD S000029658 MAL61 GO:0000017 SGD_REF:S000052562|PMID:2549370 ISS P maltose permease gene taxon:4932 20020531 SGD
+SGD S000029658 MAL61 GO:0000017 SGD_REF:S000048189|PMID:1999393 IMP P maltose permease gene taxon:4932 20020531 SGD
+SGD S000029690 MAL62 GO:0008372 SGD_REF:S000069584 ND C alpha-glucosidase, maltase gene taxon:4932 20020531 SGD
+SGD S000029690 MAL62 GO:0004558 SGD_REF:S000064884|PMID:8636115 IDA F alpha-glucosidase, maltase gene taxon:4932 20030317 SGD
+SGD S000029690 MAL62 GO:0000025 SGD_REF:S000052562|PMID:2549370 ISS P alpha-glucosidase, maltase gene taxon:4932 20020531 SGD
+SGD S000029659 MAL63 GO:0005634 SGD_REF:S000054266|PMID:10447589 IPI C MAL-activator protein, zinc finger transcription factor, Zn(2)-Cys(6) binuclear cluster domain gene taxon:4932 20020605 SGD
+SGD S000029659 MAL63 GO:0003677 SGD_REF:S000054266|PMID:10447589 IDA F MAL-activator protein, zinc finger transcription factor, Zn(2)-Cys(6) binuclear cluster domain gene taxon:4932 20020605 SGD
+SGD S000029659 MAL63 GO:0003677 SGD_REF:S000054266|PMID:10447589 ISS F MAL-activator protein, zinc finger transcription factor, Zn(2)-Cys(6) binuclear cluster domain gene taxon:4932 20020605 SGD
+SGD S000029659 MAL63 GO:0003700 SGD_REF:S000054266|PMID:10447589 TAS F MAL-activator protein, zinc finger transcription factor, Zn(2)-Cys(6) binuclear cluster domain gene taxon:4932 20020605 SGD
+SGD S000029659 MAL63 GO:0005975 SGD_REF:S000052562|PMID:2549370 ISS P MAL-activator protein, zinc finger transcription factor, Zn(2)-Cys(6) binuclear cluster domain gene taxon:4932 20020531 SGD
+SGD S000029659 MAL63 GO:0006355 SGD_REF:S000054266|PMID:10447589 IDA P MAL-activator protein, zinc finger transcription factor, Zn(2)-Cys(6) binuclear cluster domain gene taxon:4932 20020605 SGD
+SGD S000029659 MAL63 GO:0006355 SGD_REF:S000054266|PMID:10447589 IMP P MAL-activator protein, zinc finger transcription factor, Zn(2)-Cys(6) binuclear cluster domain gene taxon:4932 20020605 SGD
+SGD S000000908 MAM1 GO:0000778 SGD_REF:S000072986|PMID:12663816 IDA C Monopolin YER106W gene taxon:4932 20030421 SGD
+SGD S000000908 MAM1 GO:0005554 SGD_REF:S000069584 ND F Monopolin YER106W gene taxon:4932 20021028 SGD
+SGD S000000908 MAM1 GO:0045132 SGD_REF:S000060989|PMID:11470404 IMP P Monopolin YER106W gene taxon:4932 20021028 SGD
+SGD S000000908 MAM1 GO:0045132 SGD_REF:S000059510|PMID:11163190 IMP P Monopolin YER106W gene taxon:4932 20021028 SGD
+SGD S000005421 MAM3 GO:0000329 SGD_REF:S000074185|PMID:14562095 IDA C YOL060C gene taxon:4932 20031028 SGD
+SGD S000005421 MAM3 GO:0005554 SGD_REF:S000069584 ND F YOL060C gene taxon:4932 20050511 SGD
+SGD S000005421 MAM3 GO:0007005 SGD_REF:S000056413|PMID:10628851 IMP P YOL060C gene taxon:4932 20020930 SGD
+SGD S000005421 MAM3 GO:0030026 SGD_REF:S000080173|PMID:15498024 IMP P YOL060C gene taxon:4932 20050511 SGD
+SGD S000001332 MAM33 GO:0005759 SGD_REF:S000058204|PMID:9305894 IDA C YIL070C gene taxon:4932 20020605 SGD
+SGD S000001332 MAM33 GO:0005554 SGD_REF:S000069584 ND F YIL070C gene taxon:4932 20020605 SGD
+SGD S000001332 MAM33 GO:0009060 SGD_REF:S000058204|PMID:9305894 IMP P YIL070C gene taxon:4932 20020605 SGD
+SGD S000004234 MAP1 GO:0005830 SGD_REF:S000071468|PMID:11968008 IDA C methionine aminopeptidase YLR244C gene taxon:4932 20021114 SGD
+SGD S000004234 MAP1 GO:0004239 SGD_REF:S000069146|PMID:11811952 IDA F methionine aminopeptidase YLR244C gene taxon:4932 20020930 SGD
+SGD S000004234 MAP1 GO:0006508 SGD_REF:S000069146|PMID:11811952 IDA P methionine aminopeptidase YLR244C gene taxon:4932 20020930 SGD
+SGD S000000187 MAP2 GO:0005737 SGD_REF:S000069146|PMID:11811952 TAS C methionine aminopeptidase 2 YBL091C gene taxon:4932 20021108 SGD
+SGD S000000187 MAP2 GO:0004239 SGD_REF:S000069146|PMID:11811952 IDA F methionine aminopeptidase 2 YBL091C gene taxon:4932 20020930 SGD
+SGD S000000187 MAP2 GO:0006508 SGD_REF:S000069146|PMID:11811952 IDA P methionine aminopeptidase 2 YBL091C gene taxon:4932 20020930 SGD
+SGD S000004153 MAS1 GO:0017087 SGD_REF:S000053941|PMID:2905264 IDA C mitochondrial processing protease subunit YLR163C|MIF1 gene taxon:4932 20030417 SGD
+SGD S000004153 MAS1 GO:0004240 SGD_REF:S000044414|PMID:3044780 IDA F mitochondrial processing protease subunit YLR163C|MIF1 gene taxon:4932 20030224 SGD
+SGD S000004153 MAS1 GO:0004240 SGD_REF:S000053941|PMID:2905264 IDA F mitochondrial processing protease subunit YLR163C|MIF1 gene taxon:4932 20030224 SGD
+SGD S000004153 MAS1 GO:0006627 SGD_REF:S000044187|PMID:2007593 IDA P mitochondrial processing protease subunit YLR163C|MIF1 gene taxon:4932 20010118 SGD
+SGD S000001066 MAS2 GO:0017087 SGD_REF:S000053941|PMID:2905264 IDA C mitochondrial processing protease 53 kDa subunit YHR024C|MIF2 gene taxon:4932 20030417 SGD
+SGD S000001066 MAS2 GO:0004240 SGD_REF:S000046455|PMID:3061808 IDA F mitochondrial processing protease 53 kDa subunit YHR024C|MIF2 gene taxon:4932 20030224 SGD
+SGD S000001066 MAS2 GO:0006627 SGD_REF:S000046455|PMID:3061808 IMP P mitochondrial processing protease 53 kDa subunit YHR024C|MIF2 gene taxon:4932 20020916 SGD
+SGD S000005300 MAS6 GO:0005739 SGD_REF:S000069459|PMID:11914276 IDA C 23 kDa mitochondrial inner membrane protein YNR017W|MIM23|MPI3|TIM23 gene taxon:4932 20020507 SGD
+SGD S000005300 MAS6 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C 23 kDa mitochondrial inner membrane protein YNR017W|MIM23|MPI3|TIM23 gene taxon:4932 20040924 SGD
+SGD S000005300 MAS6 GO:0005744 SGD_REF:S000058449|PMID:10744987 TAS C 23 kDa mitochondrial inner membrane protein YNR017W|MIM23|MPI3|TIM23 gene taxon:4932 20010118 SGD
+SGD S000005300 MAS6 GO:0008565 SGD_REF:S000058449|PMID:10744987 TAS F 23 kDa mitochondrial inner membrane protein YNR017W|MIM23|MPI3|TIM23 gene taxon:4932 20010118 SGD
+SGD S000005300 MAS6 GO:0030150 SGD_REF:S000058449|PMID:10744987 TAS P 23 kDa mitochondrial inner membrane protein YNR017W|MIM23|MPI3|TIM23 gene taxon:4932 20031119 SGD
+SGD S000029660 MATA1 GO:0005634 SGD_REF:S000054505|PMID:8411150 IDA C homeobox transcription factor A1 gene taxon:4932 20030211 SGD
+SGD S000029660 MATA1 GO:0003714 SGD_REF:S000053871|PMID:1977088 IDA F homeobox transcription factor A1 gene taxon:4932 20010118 SGD
+SGD S000029660 MATA1 GO:0007532 SGD_REF:S000053871|PMID:1977088 NAS P homeobox transcription factor A1 gene taxon:4932 20010118 SGD
+SGD S000029661 MATA2 GO:0008372 SGD_REF:S000069584 ND C A2 gene taxon:4932 20010119 SGD
+SGD S000029661 MATA2 GO:0005554 SGD_REF:S000058493 NAS F A2 gene taxon:4932 20040420 SGD
+SGD S000029661 MATA2 GO:0000004 SGD_REF:S000058493 NAS P A2 gene taxon:4932 20040420 SGD
+SGD S000000636 MATALPHA1 GO:0005634 SGD_REF:S000058493 TAS C involved in the regulation of alpha-specific genes, transcription factor YCR040W|ALPHA1 gene taxon:4932 20010119 SGD
+SGD S000000636 MATALPHA1 GO:0003713 SGD_REF:S000058493 TAS F involved in the regulation of alpha-specific genes, transcription factor YCR040W|ALPHA1 gene taxon:4932 20010119 SGD
+SGD S000000636 MATALPHA1 GO:0006357 SGD_REF:S000058493 TAS P involved in the regulation of alpha-specific genes, transcription factor YCR040W|ALPHA1 gene taxon:4932 20010119 SGD
+SGD S000000636 MATALPHA1 GO:0007532 SGD_REF:S000058493 TAS P involved in the regulation of alpha-specific genes, transcription factor YCR040W|ALPHA1 gene taxon:4932 20010119 SGD
+SGD S000000635 MATALPHA2 GO:0005634 SGD_REF:S000058493 TAS C YCR039C|ALPHA2 gene taxon:4932 20010119 SGD
+SGD S000000635 MATALPHA2 GO:0003714 SGD_REF:S000058493 TAS F YCR039C|ALPHA2 gene taxon:4932 20010119 SGD
+SGD S000000635 MATALPHA2 GO:0006357 SGD_REF:S000058493 TAS P YCR039C|ALPHA2 gene taxon:4932 20010119 SGD
+SGD S000000635 MATALPHA2 GO:0007532 SGD_REF:S000058493 TAS P YCR039C|ALPHA2 gene taxon:4932 20010119 SGD
+SGD S000000635 MATALPHA2 GO:0007535 SGD_REF:S000055054|PMID:9928492 TAS P YCR039C|ALPHA2 gene taxon:4932 20010118 SGD
+SGD S000000389 MBA1 GO:0005743 SGD_REF:S000060351|PMID:11381092 IDA C YBR185C gene taxon:4932 20020606 SGD
+SGD S000000389 MBA1 GO:0005554 SGD_REF:S000069584 ND F YBR185C gene taxon:4932 20020606 SGD
+SGD S000000389 MBA1 GO:0007007 SGD_REF:S000060351|PMID:11381092 IDA P YBR185C gene taxon:4932 20020606 SGD
+SGD S000000389 MBA1 GO:0009060 SGD_REF:S000055120|PMID:8690083 IMP P YBR185C gene taxon:4932 20020606 SGD
+SGD S000007253 MBF1 GO:0005634 SGD_REF:S000045096|PMID:9710580 IC GO:0003713 C multiprotein bridging factor YOR298C-A|SUF13 gene taxon:4932 20021105 SGD
+SGD S000007253 MBF1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C multiprotein bridging factor YOR298C-A|SUF13 gene taxon:4932 20041203 SGD
+SGD S000007253 MBF1 GO:0003713 SGD_REF:S000045096|PMID:9710580 IDA F multiprotein bridging factor YOR298C-A|SUF13 gene taxon:4932 20021105 SGD
+SGD S000007253 MBF1 GO:0045944 SGD_REF:S000045096|PMID:9710580 IDA P multiprotein bridging factor YOR298C-A|SUF13 gene taxon:4932 20021105 SGD
+SGD S000002214 MBP1 GO:0005634 SGD_REF:S000054389|PMID:8372350 IPI C transcription factor YDL056W gene taxon:4932 20010118 SGD
+SGD S000002214 MBP1 GO:0005634 SGD_REF:S000069459|PMID:11914276 IDA C transcription factor YDL056W gene taxon:4932 20020507 SGD
+SGD S000002214 MBP1 GO:0003677 SGD_REF:S000072548|PMID:12564929 IDA F transcription factor YDL056W gene taxon:4932 20030218 SGD
+SGD S000002214 MBP1 GO:0003700 SGD_REF:S000054389|PMID:8372350 IPI F transcription factor YDL056W gene taxon:4932 20010118 SGD
+SGD S000002214 MBP1 GO:0003700 SGD_REF:S000054389|PMID:8372350 IMP F transcription factor YDL056W gene taxon:4932 20010118 SGD
+SGD S000002214 MBP1 GO:0000074 SGD_REF:S000054389|PMID:8372350 IMP P transcription factor YDL056W gene taxon:4932 20010118 SGD
+SGD S000002214 MBP1 GO:0000074 SGD_REF:S000054389|PMID:8372350 IGI P transcription factor YDL056W gene taxon:4932 20010118 SGD
+SGD S000002214 MBP1 GO:0006260 SGD_REF:S000054389|PMID:8372350 IPI P transcription factor YDL056W gene taxon:4932 20010118 SGD
+SGD S000002214 MBP1 GO:0006260 SGD_REF:S000054389|PMID:8372350 IMP P transcription factor YDL056W gene taxon:4932 20010118 SGD
+SGD S000001576 MBR1 GO:0008372 SGD_REF:S000069584 ND C YKL093W gene taxon:4932 20021113 SGD
+SGD S000001576 MBR1 GO:0005554 SGD_REF:S000069584 ND F YKL093W gene taxon:4932 20021113 SGD
+SGD S000001576 MBR1 GO:0009060 SGD_REF:S000052499|PMID:8208248 IMP P YKL093W gene taxon:4932 20020930 SGD
+SGD S000005723 MCA1 GO:0005634 SGD_REF:S000069959|PMID:12062425 IDA C putative cysteine protease YOR197W|YCA1 gene taxon:4932 20021009 SGD
+SGD S000005723 MCA1 GO:0030693 SGD_REF:S000070033|PMID:11983181 IDA F putative cysteine protease YOR197W|YCA1 gene taxon:4932 20030530 SGD
+SGD S000005723 MCA1 GO:0006915 SGD_REF:S000070033|PMID:11983181 IDA P putative cysteine protease YOR197W|YCA1 gene taxon:4932 20020808 SGD
+SGD S000002161 MCD1 GO:0000798 SGD_REF:S000058398|PMID:9887095 TAS C YDL003W|PDS3|RHC21|SCC1 gene taxon:4932 20010118 SGD
+SGD S000002161 MCD1 GO:0005634 SGD_REF:S000077144|PMID:15282802 IDA C YDL003W|PDS3|RHC21|SCC1 gene taxon:4932 20041008 SGD
+SGD S000002161 MCD1 GO:0005554 SGD_REF:S000069584 ND F YDL003W|PDS3|RHC21|SCC1 gene taxon:4932 20010119 SGD
+SGD S000002161 MCD1 GO:0007064 SGD_REF:S000054347|PMID:9335334 IMP P YDL003W|PDS3|RHC21|SCC1 gene taxon:4932 20010118 SGD
+SGD S000002161 MCD1 GO:0007064 SGD_REF:S000058398|PMID:9887095 TAS P YDL003W|PDS3|RHC21|SCC1 gene taxon:4932 20010118 SGD
+SGD S000002161 MCD1 GO:0007064 SGD_REF:S000054345|PMID:9335333 IMP P YDL003W|PDS3|RHC21|SCC1 gene taxon:4932 20040610 SGD
+SGD S000002161 MCD1 GO:0007076 SGD_REF:S000054347|PMID:9335334 IMP P YDL003W|PDS3|RHC21|SCC1 gene taxon:4932 20010118 SGD
+SGD S000001648 MCD4 GO:0000324 SGD_REF:S000044617|PMID:10514566 IDA C YKL165C|FSR2|SSU21|ZRG16 gene taxon:4932 20030227 SGD
+SGD S000001648 MCD4 GO:0005783 SGD_REF:S000043758|PMID:10069808 IDA C YKL165C|FSR2|SSU21|ZRG16 gene taxon:4932 20050705 SGD
+SGD S000001648 MCD4 GO:0009277 SGD_REF:S000069846|PMID:12023081 IDA C YKL165C|FSR2|SSU21|ZRG16 gene taxon:4932 20020816 SGD
+SGD S000001648 MCD4 GO:0005554 SGD_REF:S000069584 ND F YKL165C|FSR2|SSU21|ZRG16 gene taxon:4932 20021118 SGD
+SGD S000001648 MCD4 GO:0006506 SGD_REF:S000069846|PMID:12023081 IDA P YKL165C|FSR2|SSU21|ZRG16 gene taxon:4932 20020816 SGD
+SGD S000001648 MCD4 GO:0015867 SGD_REF:S000073890|PMID:12807869 IDA P YKL165C|FSR2|SSU21|ZRG16 gene taxon:4932 20030909 SGD
+SGD S000002212 MCH1 GO:0016020 SGD_REF:S000065864|PMID:11536335 ISS C YDL054C gene taxon:4932 20020918 SGD
+SGD S000002212 MCH1 GO:0005215 SGD_REF:S000065864|PMID:11536335 ISS F YDL054C gene taxon:4932 20020918 SGD
+SGD S000002212 MCH1 NOT GO:0008028 SGD_REF:S000065864|PMID:11536335 IGI F YDL054C gene taxon:4932 20020918 SGD
+SGD S000002212 MCH1 NOT GO:0008028 SGD_REF:S000065864|PMID:11536335 IMP F YDL054C gene taxon:4932 20020918 SGD
+SGD S000002212 MCH1 GO:0006810 SGD_REF:S000065864|PMID:11536335 ISS P YDL054C gene taxon:4932 20020918 SGD
+SGD S000001704 MCH2 GO:0016020 SGD_REF:S000065864|PMID:11536335 ISS C YKL221W gene taxon:4932 20020918 SGD
+SGD S000001704 MCH2 GO:0005215 SGD_REF:S000065864|PMID:11536335 ISS F YKL221W gene taxon:4932 20020918 SGD
+SGD S000001704 MCH2 NOT GO:0008028 SGD_REF:S000065864|PMID:11536335 IGI F YKL221W gene taxon:4932 20020918 SGD
+SGD S000001704 MCH2 NOT GO:0008028 SGD_REF:S000065864|PMID:11536335 IMP F YKL221W gene taxon:4932 20020918 SGD
+SGD S000001704 MCH2 GO:0006810 SGD_REF:S000065864|PMID:11536335 ISS P YKL221W gene taxon:4932 20020918 SGD
+SGD S000005479 MCH4 GO:0000329 SGD_REF:S000065864|PMID:11536335 IDA C YOL119C gene taxon:4932 20020918 SGD
+SGD S000005479 MCH4 GO:0005215 SGD_REF:S000065864|PMID:11536335 ISS F YOL119C gene taxon:4932 20020918 SGD
+SGD S000005479 MCH4 NOT GO:0008028 SGD_REF:S000065864|PMID:11536335 IGI F YOL119C gene taxon:4932 20020918 SGD
+SGD S000005479 MCH4 NOT GO:0008028 SGD_REF:S000065864|PMID:11536335 IMP F YOL119C gene taxon:4932 20020918 SGD
+SGD S000005479 MCH4 GO:0006810 SGD_REF:S000065864|PMID:11536335 ISS P YOL119C gene taxon:4932 20020918 SGD
+SGD S000005833 MCH5 GO:0016020 SGD_REF:S000065864|PMID:11536335 ISS C YOR306C gene taxon:4932 20020918 SGD
+SGD S000005833 MCH5 GO:0005215 SGD_REF:S000065864|PMID:11536335 ISS F YOR306C gene taxon:4932 20020918 SGD
+SGD S000005833 MCH5 NOT GO:0008028 SGD_REF:S000065864|PMID:11536335 IGI F YOR306C gene taxon:4932 20020918 SGD
+SGD S000005833 MCH5 NOT GO:0008028 SGD_REF:S000065864|PMID:11536335 IMP F YOR306C gene taxon:4932 20020918 SGD
+SGD S000005833 MCH5 GO:0006810 SGD_REF:S000065864|PMID:11536335 ISS P YOR306C gene taxon:4932 20020918 SGD
+SGD S000005251 MCK1 GO:0005625 SGD_REF:S000044085|PMID:1701015 IDA C 43.1 kDa serine/threonine/tyrosine protein kinase YNL307C|YPK1 gene taxon:4932 20010118 SGD
+SGD S000005251 MCK1 GO:0004696 SGD_REF:S000072503|PMID:12529445 ISS F 43.1 kDa serine/threonine/tyrosine protein kinase YNL307C|YPK1 gene taxon:4932 20030219 SGD
+SGD S000005251 MCK1 GO:0004712 SGD_REF:S000048421|PMID:8407952 IDA F 43.1 kDa serine/threonine/tyrosine protein kinase YNL307C|YPK1 gene taxon:4932 20010118 SGD
+SGD S000005251 MCK1 GO:0000070 SGD_REF:S000050205|PMID:2010084 IMP P 43.1 kDa serine/threonine/tyrosine protein kinase YNL307C|YPK1 gene taxon:4932 20010118 SGD
+SGD S000005251 MCK1 GO:0000070 SGD_REF:S000050205|PMID:2010084 IGI P 43.1 kDa serine/threonine/tyrosine protein kinase YNL307C|YPK1 gene taxon:4932 20010118 SGD
+SGD S000005251 MCK1 GO:0006303 SGD_REF:S000073203|PMID:12399380 IMP P 43.1 kDa serine/threonine/tyrosine protein kinase YNL307C|YPK1 gene taxon:4932 20030528 SGD
+SGD S000005251 MCK1 GO:0006468 SGD_REF:S000048421|PMID:8407952 IDA P 43.1 kDa serine/threonine/tyrosine protein kinase YNL307C|YPK1 gene taxon:4932 20010118 SGD
+SGD S000005251 MCK1 GO:0006950 SGD_REF:S000072503|PMID:12529445 IGI P 43.1 kDa serine/threonine/tyrosine protein kinase YNL307C|YPK1 gene taxon:4932 20030219 SGD
+SGD S000005251 MCK1 GO:0006950 SGD_REF:S000072503|PMID:12529445 IMP P 43.1 kDa serine/threonine/tyrosine protein kinase YNL307C|YPK1 gene taxon:4932 20030219 SGD
+SGD S000005251 MCK1 GO:0007126 SGD_REF:S000050204|PMID:2010083 IMP P 43.1 kDa serine/threonine/tyrosine protein kinase YNL307C|YPK1 gene taxon:4932 20010118 SGD
+SGD S000005251 MCK1 GO:0030437 SGD_REF:S000050204|PMID:2010083 IMP P 43.1 kDa serine/threonine/tyrosine protein kinase YNL307C|YPK1 gene taxon:4932 20010118 SGD
+SGD S000004646 MCM1 GO:0000790 SGD_REF:S000072646|PMID:12473677 IDA C contains the 56 amino-acid MADS (MCM1, AG, DEFAm SRF)-box motif within its DNA binding domain, plays a central role in the formation of both repressor and activator complexes, transcription factor YMR043W|FUN80 gene taxon:4932 20030304 SGD
+SGD S000004646 MCM1 GO:0005634 SGD_REF:S000042373|PMID:7744019 TAS C contains the 56 amino-acid MADS (MCM1, AG, DEFAm SRF)-box motif within its DNA binding domain, plays a central role in the formation of both repressor and activator complexes, transcription factor YMR043W|FUN80 gene taxon:4932 20021002 SGD
+SGD S000004646 MCM1 GO:0005634 SGD_REF:S000042373|PMID:7744019 IPI C contains the 56 amino-acid MADS (MCM1, AG, DEFAm SRF)-box motif within its DNA binding domain, plays a central role in the formation of both repressor and activator complexes, transcription factor YMR043W|FUN80 gene taxon:4932 20021002 SGD
+SGD S000004646 MCM1 GO:0003677 SGD_REF:S000070419|PMID:12138185 TAS F contains the 56 amino-acid MADS (MCM1, AG, DEFAm SRF)-box motif within its DNA binding domain, plays a central role in the formation of both repressor and activator complexes, transcription factor YMR043W|FUN80 gene taxon:4932 20021203 SGD
+SGD S000004646 MCM1 GO:0003688 SGD_REF:S000072646|PMID:12473677 IDA F contains the 56 amino-acid MADS (MCM1, AG, DEFAm SRF)-box motif within its DNA binding domain, plays a central role in the formation of both repressor and activator complexes, transcription factor YMR043W|FUN80 gene taxon:4932 20030304 SGD
+SGD S000004646 MCM1 GO:0003702 SGD_REF:S000042373|PMID:7744019 TAS F contains the 56 amino-acid MADS (MCM1, AG, DEFAm SRF)-box motif within its DNA binding domain, plays a central role in the formation of both repressor and activator complexes, transcription factor YMR043W|FUN80 gene taxon:4932 20021002 SGD
+SGD S000004646 MCM1 GO:0006270 SGD_REF:S000072646|PMID:12473677 TAS P contains the 56 amino-acid MADS (MCM1, AG, DEFAm SRF)-box motif within its DNA binding domain, plays a central role in the formation of both repressor and activator complexes, transcription factor YMR043W|FUN80 gene taxon:4932 20030304 SGD
+SGD S000004646 MCM1 GO:0006357 SGD_REF:S000042373|PMID:7744019 TAS P contains the 56 amino-acid MADS (MCM1, AG, DEFAm SRF)-box motif within its DNA binding domain, plays a central role in the formation of both repressor and activator complexes, transcription factor YMR043W|FUN80 gene taxon:4932 20021002 SGD
+SGD S000001412 MCM10 GO:0005634 SGD_REF:S000051117|PMID:9154825 IDA C YIL150C|DNA43 gene taxon:4932 20010118 SGD
+SGD S000001412 MCM10 GO:0005634 SGD_REF:S000076850|PMID:13680157 IDA C YIL150C|DNA43 gene taxon:4932 20050708 SGD
+SGD S000001412 MCM10 GO:0003682 SGD_REF:S000040243|PMID:10783164 IDA F YIL150C|DNA43 gene taxon:4932 20010118 SGD
+SGD S000001412 MCM10 GO:0006270 SGD_REF:S000051117|PMID:9154825 IPI P YIL150C|DNA43 gene taxon:4932 20010118 SGD
+SGD S000001412 MCM10 GO:0006270 SGD_REF:S000051117|PMID:9154825 IMP P YIL150C|DNA43 gene taxon:4932 20010118 SGD
+SGD S000001412 MCM10 GO:0006271 SGD_REF:S000051117|PMID:9154825 IMP P YIL150C|DNA43 gene taxon:4932 20010118 SGD
+SGD S000001412 MCM10 GO:0006348 SGD_REF:S000086101|PMID:16085704 IMP P YIL150C|DNA43 gene taxon:4932 20050926 SGD
+SGD S000001412 MCM10 GO:0006348 SGD_REF:S000086101|PMID:16085704 IPI SGD:S000002200|SGD:S000004434 P YIL150C|DNA43 gene taxon:4932 20050926 SGD
+SGD S000001412 MCM10 GO:0030466 SGD_REF:S000086101|PMID:16085704 IMP P YIL150C|DNA43 gene taxon:4932 20050926 SGD
+SGD S000001412 MCM10 GO:0030466 SGD_REF:S000086101|PMID:16085704 IPI SGD:S000002200|SGD:S000004434 P YIL150C|DNA43 gene taxon:4932 20050926 SGD
+SGD S000001412 MCM10 GO:0030466 SGD_REF:S000113950|PMID:16328881 IPI SGD:S000002200|SGD:S000004434 P YIL150C|DNA43 gene taxon:4932 20060106 SGD
+SGD S000001412 MCM10 GO:0030466 SGD_REF:S000113950|PMID:16328881 IMP P YIL150C|DNA43 gene taxon:4932 20060106 SGD
+SGD S000006250 MCM16 GO:0000778 SGD_REF:S000069067|PMID:11782448 IDA C YPR046W gene taxon:4932 20020905 SGD
+SGD S000006250 MCM16 GO:0005515 SGD_REF:S000069067|PMID:11782448 IDA F YPR046W gene taxon:4932 20020905 SGD
+SGD S000006250 MCM16 GO:0007059 SGD_REF:S000069067|PMID:11782448 IPI P YPR046W gene taxon:4932 20020905 SGD
+SGD S000000119 MCM2 GO:0005634 SGD_REF:S000051716|PMID:10704410 IDA C YBL023C gene taxon:4932 20020625 SGD
+SGD S000000119 MCM2 GO:0005656 SGD_REF:S000054350|PMID:9335335 IDA C YBL023C gene taxon:4932 20021202 SGD
+SGD S000000119 MCM2 GO:0005737 SGD_REF:S000058275|PMID:9442876 TAS C YBL023C gene taxon:4932 20010118 SGD
+SGD S000000119 MCM2 GO:0005737 SGD_REF:S000051716|PMID:10704410 IDA C YBL023C gene taxon:4932 20020625 SGD
+SGD S000000119 MCM2 GO:0042555 SGD_REF:S000072578|PMID:12480933 IDA C YBL023C gene taxon:4932 20041024 SGD
+SGD S000000119 MCM2 GO:0003682 SGD_REF:S000058275|PMID:9442876 TAS F YBL023C gene taxon:4932 20010118 SGD
+SGD S000000119 MCM2 GO:0004003 SGD_REF:S000058400|PMID:9914182 TAS F YBL023C gene taxon:4932 20010118 SGD
+SGD S000000119 MCM2 GO:0006267 SGD_REF:S000054350|PMID:9335335 IPI P YBL023C gene taxon:4932 20021202 SGD
+SGD S000000119 MCM2 GO:0006268 SGD_REF:S000058400|PMID:9914182 TAS P YBL023C gene taxon:4932 20010118 SGD
+SGD S000000119 MCM2 GO:0006270 SGD_REF:S000058275|PMID:9442876 TAS P YBL023C gene taxon:4932 20010118 SGD
+SGD S000002726 MCM21 GO:0000778 SGD_REF:S000054451|PMID:10323865 IDA C YDR318W|CTF5 gene taxon:4932 20030403 SGD
+SGD S000002726 MCM21 GO:0000817 SGD_REF:S000075142|PMID:14633972 IDA C YDR318W|CTF5 gene taxon:4932 20040618 SGD
+SGD S000002726 MCM21 GO:0005515 SGD_REF:S000054451|PMID:10323865 IDA F YDR318W|CTF5 gene taxon:4932 20020920 SGD
+SGD S000002726 MCM21 GO:0007059 SGD_REF:S000054451|PMID:10323865 IPI P YDR318W|CTF5 gene taxon:4932 20020920 SGD
+SGD S000003896 MCM22 GO:0000778 SGD_REF:S000069067|PMID:11782448 IDA C YJR135C gene taxon:4932 20020905 SGD
+SGD S000003896 MCM22 GO:0005515 SGD_REF:S000069067|PMID:11782448 IDA F YJR135C gene taxon:4932 20020905 SGD
+SGD S000003896 MCM22 GO:0007059 SGD_REF:S000069067|PMID:11782448 IPI P YJR135C gene taxon:4932 20020905 SGD
+SGD S000000758 MCM3 GO:0005634 SGD_REF:S000051716|PMID:10704410 IDA C YEL032W gene taxon:4932 20020625 SGD
+SGD S000000758 MCM3 GO:0005656 SGD_REF:S000054350|PMID:9335335 IDA C YEL032W gene taxon:4932 20021202 SGD
+SGD S000000758 MCM3 GO:0005737 SGD_REF:S000058275|PMID:9442876 TAS C YEL032W gene taxon:4932 20010118 SGD
+SGD S000000758 MCM3 GO:0005737 SGD_REF:S000051716|PMID:10704410 IDA C YEL032W gene taxon:4932 20020625 SGD
+SGD S000000758 MCM3 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YEL032W gene taxon:4932 20020507 SGD
+SGD S000000758 MCM3 GO:0042555 SGD_REF:S000072578|PMID:12480933 IDA C YEL032W gene taxon:4932 20041024 SGD
+SGD S000000758 MCM3 GO:0003682 SGD_REF:S000058275|PMID:9442876 TAS F YEL032W gene taxon:4932 20010118 SGD
+SGD S000000758 MCM3 GO:0004003 SGD_REF:S000058400|PMID:9914182 TAS F YEL032W gene taxon:4932 20010118 SGD
+SGD S000000758 MCM3 GO:0006267 SGD_REF:S000054350|PMID:9335335 IPI P YEL032W gene taxon:4932 20021202 SGD
+SGD S000000758 MCM3 GO:0006268 SGD_REF:S000058400|PMID:9914182 TAS P YEL032W gene taxon:4932 20010118 SGD
+SGD S000000758 MCM3 GO:0006270 SGD_REF:S000058275|PMID:9442876 TAS P YEL032W gene taxon:4932 20010118 SGD
+SGD S000003169 MCM6 GO:0005634 SGD_REF:S000051716|PMID:10704410 IDA C YGL201C gene taxon:4932 20020625 SGD
+SGD S000003169 MCM6 GO:0005656 SGD_REF:S000054350|PMID:9335335 IDA C YGL201C gene taxon:4932 20021202 SGD
+SGD S000003169 MCM6 GO:0005737 SGD_REF:S000058275|PMID:9442876 TAS C YGL201C gene taxon:4932 20010118 SGD
+SGD S000003169 MCM6 GO:0005737 SGD_REF:S000051716|PMID:10704410 IDA C YGL201C gene taxon:4932 20020625 SGD
+SGD S000003169 MCM6 GO:0042555 SGD_REF:S000072578|PMID:12480933 IDA C YGL201C gene taxon:4932 20041024 SGD
+SGD S000003169 MCM6 GO:0003682 SGD_REF:S000058275|PMID:9442876 TAS F YGL201C gene taxon:4932 20010118 SGD
+SGD S000003169 MCM6 GO:0004003 SGD_REF:S000058400|PMID:9914182 TAS F YGL201C gene taxon:4932 20010118 SGD
+SGD S000003169 MCM6 GO:0006268 SGD_REF:S000058400|PMID:9914182 TAS P YGL201C gene taxon:4932 20010118 SGD
+SGD S000003169 MCM6 GO:0006270 SGD_REF:S000058275|PMID:9442876 TAS P YGL201C gene taxon:4932 20010118 SGD
+SGD S000003169 MCM6 GO:0006270 SGD_REF:S000054350|PMID:9335335 IPI P YGL201C gene taxon:4932 20021202 SGD
+SGD S000001633 MCR1 GO:0005741 SGD_REF:S000046304|PMID:8001120 IDA C NADH-cytochrome b5 reductase YKL150W gene taxon:4932 20020926 SGD
+SGD S000001633 MCR1 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C NADH-cytochrome b5 reductase YKL150W gene taxon:4932 20060317 SGD
+SGD S000001633 MCR1 GO:0005758 SGD_REF:S000046304|PMID:8001120 IDA C NADH-cytochrome b5 reductase YKL150W gene taxon:4932 20020926 SGD
+SGD S000001633 MCR1 GO:0031307 SGD_REF:S000115559|PMID:16689936 IDA C NADH-cytochrome b5 reductase YKL150W gene taxon:4932 20060515 SGD
+SGD S000001633 MCR1 GO:0004128 SGD_REF:S000046304|PMID:8001120 IDA F NADH-cytochrome b5 reductase YKL150W gene taxon:4932 20020926 SGD
+SGD S000001633 MCR1 GO:0006118 SGD_REF:S000062024|PMID:10622712 IDA P NADH-cytochrome b5 reductase YKL150W gene taxon:4932 20020926 SGD
+SGD S000001633 MCR1 GO:0006696 SGD_REF:S000062024|PMID:10622712 IDA P NADH-cytochrome b5 reductase YKL150W gene taxon:4932 20020926 SGD
+SGD S000001633 MCR1 GO:0006979 SGD_REF:S000060822|PMID:11420140 IMP P NADH-cytochrome b5 reductase YKL150W gene taxon:4932 20020926 SGD
+SGD S000005747 MCT1 GO:0005739 SGD_REF:S000040710|PMID:9388293 ISS C malonyl-CoA:ACP transferase YOR221C gene taxon:4932 20021021 SGD
+SGD S000005747 MCT1 GO:0005739 SGD_REF:S000040710|PMID:9388293 IMP C malonyl-CoA:ACP transferase YOR221C gene taxon:4932 20021021 SGD
+SGD S000005747 MCT1 GO:0004314 SGD_REF:S000040710|PMID:9388293 ISS F malonyl-CoA:ACP transferase YOR221C gene taxon:4932 20021021 SGD
+SGD S000005747 MCT1 GO:0004314 SGD_REF:S000040710|PMID:9388293 IMP F malonyl-CoA:ACP transferase YOR221C gene taxon:4932 20021021 SGD
+SGD S000005747 MCT1 GO:0006631 SGD_REF:S000040710|PMID:9388293 ISS P malonyl-CoA:ACP transferase YOR221C gene taxon:4932 20021021 SGD
+SGD S000005747 MCT1 GO:0006631 SGD_REF:S000040710|PMID:9388293 IMP P malonyl-CoA:ACP transferase YOR221C gene taxon:4932 20021021 SGD
+SGD S000005747 MCT1 GO:0009060 SGD_REF:S000040710|PMID:9388293 IMP P malonyl-CoA:ACP transferase YOR221C gene taxon:4932 20021028 SGD
+SGD S000000431 MCX1 GO:0005759 SGD_REF:S000048344|PMID:9827555 IDA C ATP-binding protein, similar to ClpX YBR227C gene taxon:4932 20010118 SGD
+SGD S000000431 MCX1 GO:0005524 SGD_REF:S000048344|PMID:9827555 ISS F ATP-binding protein, similar to ClpX YBR227C gene taxon:4932 20010118 SGD
+SGD S000000431 MCX1 GO:0051082 SGD_REF:S000048344|PMID:9827555 TAS F ATP-binding protein, similar to ClpX YBR227C gene taxon:4932 20010118 SGD
+SGD S000000431 MCX1 GO:0000004 SGD_REF:S000069584 ND P ATP-binding protein, similar to ClpX YBR227C gene taxon:4932 20010119 SGD
+SGD S000005117 MDG1 GO:0005886 SGD_REF:S000054662|PMID:8914522 IDA C YNL173C gene taxon:4932 20010118 SGD
+SGD S000005117 MDG1 GO:0005554 SGD_REF:S000069584 ND F YNL173C gene taxon:4932 20021210 SGD
+SGD S000005117 MDG1 GO:0000750 SGD_REF:S000054662|PMID:8914522 IMP P YNL173C gene taxon:4932 20021206 SGD
+SGD S000001568 MDH1 GO:0005759 SGD_REF:S000058126|PMID:9175438 TAS C malate dehydrogenase YKL085W gene taxon:4932 20010118 SGD
+SGD S000001568 MDH1 GO:0030060 SGD_REF:S000040049|PMID:2663847 TAS F malate dehydrogenase YKL085W gene taxon:4932 20030618 SGD
+SGD S000001568 MDH1 GO:0006099 SGD_REF:S000058126|PMID:9175438 TAS P malate dehydrogenase YKL085W gene taxon:4932 20010118 SGD
+SGD S000001568 MDH1 GO:0006108 SGD_REF:S000058126|PMID:9175438 TAS P malate dehydrogenase YKL085W gene taxon:4932 20010118 SGD
+SGD S000005486 MDH2 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C malate dehydrogenase YOL126C gene taxon:4932 20020507 SGD
+SGD S000005486 MDH2 GO:0005829 SGD_REF:S000058126|PMID:9175438 TAS C malate dehydrogenase YOL126C gene taxon:4932 20010118 SGD
+SGD S000005486 MDH2 GO:0030060 SGD_REF:S000039783|PMID:1986231 IMP F malate dehydrogenase YOL126C gene taxon:4932 20050429 SGD
+SGD S000005486 MDH2 GO:0030060 SGD_REF:S000045671|PMID:7673155 TAS F malate dehydrogenase YOL126C gene taxon:4932 20050429 SGD
+SGD S000005486 MDH2 GO:0006094 SGD_REF:S000058126|PMID:9175438 TAS P malate dehydrogenase YOL126C gene taxon:4932 20010118 SGD
+SGD S000005486 MDH2 GO:0006094 SGD_REF:S000080362|PMID:15358789 IEP P malate dehydrogenase YOL126C gene taxon:4932 20050608 SGD
+SGD S000005486 MDH2 GO:0006108 SGD_REF:S000058126|PMID:9175438 TAS P malate dehydrogenase YOL126C gene taxon:4932 20010118 SGD
+SGD S000002236 MDH3 GO:0005777 SGD_REF:S000052076|PMID:1447211 IDA C malate dehydrogenase YDL078C gene taxon:4932 20050516 SGD
+SGD S000002236 MDH3 GO:0005782 SGD_REF:S000058494 TAS C malate dehydrogenase YDL078C gene taxon:4932 20010119 SGD
+SGD S000002236 MDH3 GO:0030060 SGD_REF:S000045671|PMID:7673155 TAS F malate dehydrogenase YDL078C gene taxon:4932 20050429 SGD
+SGD S000002236 MDH3 GO:0030060 SGD_REF:S000039783|PMID:1986231 IMP F malate dehydrogenase YDL078C gene taxon:4932 20050429 SGD
+SGD S000002236 MDH3 GO:0006097 SGD_REF:S000058126|PMID:9175438 TAS P malate dehydrogenase YDL078C gene taxon:4932 20010118 SGD
+SGD S000002236 MDH3 GO:0006108 SGD_REF:S000058126|PMID:9175438 TAS P malate dehydrogenase YDL078C gene taxon:4932 20010118 SGD
+SGD S000002236 MDH3 GO:0006635 SGD_REF:S000058126|PMID:9175438 TAS P malate dehydrogenase YDL078C gene taxon:4932 20010118 SGD
+SGD S000002236 MDH3 GO:0006735 SGD_REF:S000058126|PMID:9175438 TAS P malate dehydrogenase YDL078C gene taxon:4932 20010118 SGD
+SGD S000001878 MDJ1 GO:0005743 SGD_REF:S000048831|PMID:8168133 IDA C DnaJ homolog, involved in mitochondrial biogenesis and protein folding YFL016C gene taxon:4932 20010118 SGD
+SGD S000001878 MDJ1 GO:0051082 SGD_REF:S000044393|PMID:8943361 IMP F DnaJ homolog, involved in mitochondrial biogenesis and protein folding YFL016C gene taxon:4932 20040722 SGD
+SGD S000001878 MDJ1 GO:0051087 SGD_REF:S000044393|PMID:8943361 IMP F DnaJ homolog, involved in mitochondrial biogenesis and protein folding YFL016C gene taxon:4932 20040722 SGD
+SGD S000001878 MDJ1 GO:0006457 SGD_REF:S000048831|PMID:8168133 IDA P DnaJ homolog, involved in mitochondrial biogenesis and protein folding YFL016C gene taxon:4932 20010118 SGD
+SGD S000001878 MDJ1 GO:0006508 SGD_REF:S000044484|PMID:7957078 IMP P DnaJ homolog, involved in mitochondrial biogenesis and protein folding YFL016C gene taxon:4932 20010118 SGD
+SGD S000005272 MDJ2 GO:0001405 SGD_REF:S000082529|PMID:16027163 IPI C chaperonin YNL328C gene taxon:4932 20060302 SGD
+SGD S000005272 MDJ2 GO:0005743 SGD_REF:S000049796|PMID:9325105 IDA C chaperonin YNL328C gene taxon:4932 20010118 SGD
+SGD S000005272 MDJ2 GO:0001671 SGD_REF:S000082529|PMID:16027163 IDA F chaperonin YNL328C gene taxon:4932 20060302 SGD
+SGD S000005272 MDJ2 contributes_to GO:0008565 SGD_REF:S000082529|PMID:16027163 IGI F chaperonin YNL328C gene taxon:4932 20060302 SGD
+SGD S000005272 MDJ2 contributes_to GO:0008565 SGD_REF:S000082529|PMID:16027163 IPI F chaperonin YNL328C gene taxon:4932 20060302 SGD
+SGD S000005272 MDJ2 GO:0030150 SGD_REF:S000082529|PMID:16027163 IGI P chaperonin YNL328C gene taxon:4932 20060302 SGD
+SGD S000005272 MDJ2 GO:0030150 SGD_REF:S000082529|PMID:16027163 IPI P chaperonin YNL328C gene taxon:4932 20060302 SGD
+SGD S000004178 MDL1 GO:0005743 SGD_REF:S000060200|PMID:11251115 IDA C YLR188W gene taxon:4932 20020920 SGD
+SGD S000004178 MDL1 GO:0015440 SGD_REF:S000060200|PMID:11251115 IMP F YLR188W gene taxon:4932 20020920 SGD
+SGD S000004178 MDL1 GO:0016887 SGD_REF:S000073656|PMID:12746444 IDA F YLR188W gene taxon:4932 20030730 SGD
+SGD S000004178 MDL1 GO:0042626 SGD_REF:S000060200|PMID:11251115 IMP F YLR188W gene taxon:4932 20020920 SGD
+SGD S000004178 MDL1 GO:0042626 SGD_REF:S000060200|PMID:11251115 ISS F YLR188W gene taxon:4932 20020920 SGD
+SGD S000004178 MDL1 GO:0006857 SGD_REF:S000060200|PMID:11251115 ISS P YLR188W gene taxon:4932 20020920 SGD
+SGD S000004178 MDL1 GO:0006857 SGD_REF:S000060200|PMID:11251115 IMP P YLR188W gene taxon:4932 20020920 SGD
+SGD S000006191 MDL2 GO:0005743 SGD_REF:S000060200|PMID:11251115 IDA C YPL270W gene taxon:4932 20020920 SGD
+SGD S000006191 MDL2 GO:0042626 SGD_REF:S000060200|PMID:11251115 ISS F YPL270W gene taxon:4932 20020920 SGD
+SGD S000006191 MDL2 GO:0009060 SGD_REF:S000060200|PMID:11251115 IMP P YPL270W gene taxon:4932 20020920 SGD
+SGD S000004572 MDM1 GO:0005737 SGD_REF:S000054560|PMID:9245780 TAS C intermediate filament protein YML104C gene taxon:4932 20020806 SGD
+SGD S000004572 MDM1 GO:0005882 SGD_REF:S000058450|PMID:9891785 TAS C intermediate filament protein YML104C gene taxon:4932 20010118 SGD
+SGD S000004572 MDM1 GO:0005200 SGD_REF:S000058450|PMID:9891785 TAS F intermediate filament protein YML104C gene taxon:4932 20010118 SGD
+SGD S000004572 MDM1 GO:0000001 SGD_REF:S000054560|PMID:9245780 IDA P intermediate filament protein YML104C gene taxon:4932 20020806 SGD
+SGD S000004572 MDM1 GO:0007005 SGD_REF:S000058450|PMID:9891785 TAS P intermediate filament protein YML104C gene taxon:4932 20010118 SGD
+SGD S000004572 MDM1 GO:0007097 SGD_REF:S000058450|PMID:9891785 TAS P intermediate filament protein YML104C gene taxon:4932 20010118 SGD
+SGD S000000008 MDM10 GO:0001401 SGD_REF:S000076734|PMID:15239954 IPI C mitochondrial outer membrane protein YAL010C|FUN37 gene taxon:4932 20040928 SGD
+SGD S000000008 MDM10 GO:0005741 SGD_REF:S000058450|PMID:9891785 TAS C mitochondrial outer membrane protein YAL010C|FUN37 gene taxon:4932 20010118 SGD
+SGD S000000008 MDM10 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C mitochondrial outer membrane protein YAL010C|FUN37 gene taxon:4932 20060317 SGD
+SGD S000000008 MDM10 GO:0005554 SGD_REF:S000069584 ND F mitochondrial outer membrane protein YAL010C|FUN37 gene taxon:4932 20021119 SGD
+SGD S000000008 MDM10 GO:0000001 SGD_REF:S000058450|PMID:9891785 TAS P mitochondrial outer membrane protein YAL010C|FUN37 gene taxon:4932 20010118 SGD
+SGD S000000008 MDM10 GO:0000002 SGD_REF:S000058450|PMID:9891785 TAS P mitochondrial outer membrane protein YAL010C|FUN37 gene taxon:4932 20010118 SGD
+SGD S000000008 MDM10 GO:0006461 SGD_REF:S000076734|PMID:15239954 IMP P mitochondrial outer membrane protein YAL010C|FUN37 gene taxon:4932 20040928 SGD
+SGD S000000008 MDM10 GO:0007005 SGD_REF:S000058450|PMID:9891785 TAS P mitochondrial outer membrane protein YAL010C|FUN37 gene taxon:4932 20010118 SGD
+SGD S000005369 MDM12 GO:0005741 SGD_REF:S000058450|PMID:9891785 TAS C YOL009C gene taxon:4932 20010118 SGD
+SGD S000005369 MDM12 GO:0005554 SGD_REF:S000058450|PMID:9891785 TAS F YOL009C gene taxon:4932 20010118 SGD
+SGD S000005369 MDM12 GO:0000001 SGD_REF:S000058450|PMID:9891785 TAS P YOL009C gene taxon:4932 20010118 SGD
+SGD S000005369 MDM12 GO:0007005 SGD_REF:S000058450|PMID:9891785 TAS P YOL009C gene taxon:4932 20010118 SGD
+SGD S000005436 MDM20 GO:0031416 SGD_REF:S000073836|PMID:12890471 TAS C YOL076W|DEC1 gene taxon:4932 20060119 SGD
+SGD S000005436 MDM20 contributes_to GO:0004596 SGD_REF:S000073825|PMID:12783868 IMP F YOL076W|DEC1 gene taxon:4932 20050512 SGD
+SGD S000005436 MDM20 contributes_to GO:0004596 SGD_REF:S000073825|PMID:12783868 IPI F YOL076W|DEC1 gene taxon:4932 20050512 SGD
+SGD S000005436 MDM20 GO:0000001 SGD_REF:S000048916|PMID:9105043 IGI P YOL076W|DEC1 gene taxon:4932 20020517 SGD
+SGD S000005436 MDM20 GO:0000001 SGD_REF:S000048916|PMID:9105043 IMP P YOL076W|DEC1 gene taxon:4932 20020517 SGD
+SGD S000005436 MDM20 GO:0007010 SGD_REF:S000048916|PMID:9105043 IMP P YOL076W|DEC1 gene taxon:4932 20020517 SGD
+SGD S000005436 MDM20 GO:0017196 SGD_REF:S000073825|PMID:12783868 IGI P YOL076W|DEC1 gene taxon:4932 20030826 SGD
+SGD S000005436 MDM20 GO:0017196 SGD_REF:S000073825|PMID:12783868 IMP P YOL076W|DEC1 gene taxon:4932 20030826 SGD
+SGD S000004360 MDM30 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YLR368W|DSG1 gene taxon:4932 20040813 SGD
+SGD S000004360 MDM30 GO:0005554 SGD_REF:S000069584 ND F YLR368W|DSG1 gene taxon:4932 20021114 SGD
+SGD S000004360 MDM30 GO:0007005 SGD_REF:S000071517|PMID:11907266 IMP P YLR368W|DSG1 gene taxon:4932 20021114 SGD
+SGD S000004360 MDM30 GO:0008053 SGD_REF:S000075479|PMID:12808031 IMP P YLR368W|DSG1 gene taxon:4932 20050415 SGD
+SGD S000001237 MDM31 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YHR194W gene taxon:4932 20031028 SGD
+SGD S000001237 MDM31 GO:0005743 SGD_REF:S000080209|PMID:15631992 IDA C YHR194W gene taxon:4932 20050208 SGD
+SGD S000001237 MDM31 GO:0005554 SGD_REF:S000069584 ND F YHR194W gene taxon:4932 20021114 SGD
+SGD S000001237 MDM31 GO:0000001 SGD_REF:S000080209|PMID:15631992 IMP P YHR194W gene taxon:4932 20050208 SGD
+SGD S000001237 MDM31 GO:0006873 SGD_REF:S000082328|PMID:16020778 IMP P YHR194W gene taxon:4932 20051221 SGD
+SGD S000001237 MDM31 GO:0007005 SGD_REF:S000071517|PMID:11907266 IMP P YHR194W gene taxon:4932 20021114 SGD
+SGD S000001237 MDM31 GO:0007005 SGD_REF:S000082328|PMID:16020778 IMP P YHR194W gene taxon:4932 20051221 SGD
+SGD S000005673 MDM32 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YOR147W gene taxon:4932 20031028 SGD
+SGD S000005673 MDM32 GO:0005743 SGD_REF:S000080209|PMID:15631992 IDA C YOR147W gene taxon:4932 20050208 SGD
+SGD S000005673 MDM32 GO:0005554 SGD_REF:S000069584 ND F YOR147W gene taxon:4932 20021114 SGD
+SGD S000005673 MDM32 GO:0000001 SGD_REF:S000080209|PMID:15631992 IMP P YOR147W gene taxon:4932 20050208 SGD
+SGD S000005673 MDM32 GO:0006873 SGD_REF:S000082328|PMID:16020778 IMP P YOR147W gene taxon:4932 20051221 SGD
+SGD S000005673 MDM32 GO:0007005 SGD_REF:S000071517|PMID:11907266 IMP P YOR147W gene taxon:4932 20021114 SGD
+SGD S000005673 MDM32 GO:0007005 SGD_REF:S000082328|PMID:16020778 IMP P YOR147W gene taxon:4932 20051221 SGD
+SGD S000003187 MDM34 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YGL219C|MMM2 gene taxon:4932 20031028 SGD
+SGD S000003187 MDM34 GO:0005741 SGD_REF:S000076174|PMID:14981098 IDA C YGL219C|MMM2 gene taxon:4932 20040923 SGD
+SGD S000003187 MDM34 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C YGL219C|MMM2 gene taxon:4932 20060317 SGD
+SGD S000003187 MDM34 GO:0005554 SGD_REF:S000069584 ND F YGL219C|MMM2 gene taxon:4932 20010611 SGD
+SGD S000003187 MDM34 GO:0007005 SGD_REF:S000071517|PMID:11907266 IMP P YGL219C|MMM2 gene taxon:4932 20021114 SGD
+SGD S000007243 MDM35 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YKL053C-A gene taxon:4932 20031028 SGD
+SGD S000007243 MDM35 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YKL053C-A gene taxon:4932 20031028 SGD
+SGD S000007243 MDM35 GO:0005554 SGD_REF:S000069584 ND F YKL053C-A gene taxon:4932 20021114 SGD
+SGD S000007243 MDM35 GO:0007005 SGD_REF:S000071517|PMID:11907266 IMP P YKL053C-A gene taxon:4932 20021114 SGD
+SGD S000006287 MDM36 GO:0008372 SGD_REF:S000069584 ND C YPR083W gene taxon:4932 20021114 SGD
+SGD S000006287 MDM36 GO:0005554 SGD_REF:S000069584 ND F YPR083W gene taxon:4932 20021114 SGD
+SGD S000006287 MDM36 GO:0007005 SGD_REF:S000071517|PMID:11907266 IMP P YPR083W gene taxon:4932 20021114 SGD
+SGD S000005387 MDM38 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YOL027C|MKH1 gene taxon:4932 20031028 SGD
+SGD S000005387 MDM38 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YOL027C|MKH1 gene taxon:4932 20040929 SGD
+SGD S000005387 MDM38 GO:0005743 SGD_REF:S000076911|PMID:15138253 IDA C YOL027C|MKH1 gene taxon:4932 20040923 SGD
+SGD S000005387 MDM38 GO:0005743 SGD_REF:S000114395|PMID:16476776 IDA C YOL027C|MKH1 gene taxon:4932 20060410 SGD
+SGD S000005387 MDM38 GO:0005554 SGD_REF:S000069584 ND F YOL027C|MKH1 gene taxon:4932 20050915 SGD
+SGD S000005387 MDM38 GO:0006813 SGD_REF:S000082022|PMID:15904662 IMP P YOL027C|MKH1 gene taxon:4932 20050915 SGD
+SGD S000005387 MDM38 GO:0007005 SGD_REF:S000071517|PMID:11907266 IMP P YOL027C|MKH1 gene taxon:4932 20021114 SGD
+SGD S000005387 MDM38 GO:0030007 SGD_REF:S000076911|PMID:15138253 IMP P YOL027C|MKH1 gene taxon:4932 20040923 SGD
+SGD S000005387 MDM38 GO:0051204 SGD_REF:S000114395|PMID:16476776 IMP P YOL027C|MKH1 gene taxon:4932 20060410 SGD
+SGD S000004096 MDN1 GO:0005634 SGD_REF:S000070139|PMID:12102729 IDA C midasin YLR106C|REA1 gene taxon:4932 20020715 SGD
+SGD S000004096 MDN1 GO:0005654 SGD_REF:S000080956|PMID:15528184 IDA C midasin YLR106C|REA1 gene taxon:4932 20050310 SGD
+SGD S000004096 MDN1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C midasin YLR106C|REA1 gene taxon:4932 20040928 SGD
+SGD S000004096 MDN1 GO:0016887 SGD_REF:S000070139|PMID:12102729 ISS F midasin YLR106C|REA1 gene taxon:4932 20020715 SGD
+SGD S000004096 MDN1 GO:0000027 SGD_REF:S000071707|PMID:12374754 IPI P midasin YLR106C|REA1 gene taxon:4932 20031103 SGD
+SGD S000004096 MDN1 GO:0000027 SGD_REF:S000066162|PMID:11583615 IPI P midasin YLR106C|REA1 gene taxon:4932 20031103 SGD
+SGD S000004096 MDN1 GO:0000027 SGD_REF:S000080956|PMID:15528184 IMP P midasin YLR106C|REA1 gene taxon:4932 20050310 SGD
+SGD S000004096 MDN1 GO:0006364 SGD_REF:S000073750|PMID:12837249 IMP P midasin YLR106C|REA1 gene taxon:4932 20030805 SGD
+SGD S000004096 MDN1 GO:0006461 SGD_REF:S000070139|PMID:12102729 ISS P midasin YLR106C|REA1 gene taxon:4932 20021126 SGD
+SGD S000003332 MDR1 GO:0005625 SGD_REF:S000056405|PMID:10559187 TAS C GTPase activating protein (GAP) for Ypt6 YGR100W|GYP2|MIC1 gene taxon:4932 20010118 SGD
+SGD S000003332 MDR1 GO:0005737 SGD_REF:S000075633|PMID:12807768 IDA C GTPase activating protein (GAP) for Ypt6 YGR100W|GYP2|MIC1 gene taxon:4932 20040630 SGD
+SGD S000003332 MDR1 GO:0005097 SGD_REF:S000056405|PMID:10559187 IDA F GTPase activating protein (GAP) for Ypt6 YGR100W|GYP2|MIC1 gene taxon:4932 20010118 SGD
+SGD S000003332 MDR1 GO:0005097 SGD_REF:S000056405|PMID:10559187 ISS F GTPase activating protein (GAP) for Ypt6 YGR100W|GYP2|MIC1 gene taxon:4932 20010118 SGD
+SGD S000003332 MDR1 GO:0006886 SGD_REF:S000080187|PMID:15574876 IGI P GTPase activating protein (GAP) for Ypt6 YGR100W|GYP2|MIC1 gene taxon:4932 20060309 SGD
+SGD S000003165 MDS3 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YGL197W gene taxon:4932 20020507 SGD
+SGD S000003165 MDS3 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YGL197W gene taxon:4932 20031028 SGD
+SGD S000003165 MDS3 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YGL197W gene taxon:4932 20040813 SGD
+SGD S000003165 MDS3 GO:0005554 SGD_REF:S000069584 ND F YGL197W gene taxon:4932 20021028 SGD
+SGD S000003165 MDS3 GO:0042174 SGD_REF:S000048503|PMID:9383076 IGI P YGL197W gene taxon:4932 20050225 SGD
+SGD S000003165 MDS3 GO:0042174 SGD_REF:S000048503|PMID:9383076 IMP P YGL197W gene taxon:4932 20050225 SGD
+SGD S000003648 MDV1 GO:0005741 SGD_REF:S000056449|PMID:11038180 IDA C YJL112W|FIS2|GAG3|NET2 gene taxon:4932 20010118 SGD
+SGD S000003648 MDV1 GO:0005741 SGD_REF:S000056450|PMID:11038182 IDA C YJL112W|FIS2|GAG3|NET2 gene taxon:4932 20010118 SGD
+SGD S000003648 MDV1 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C YJL112W|FIS2|GAG3|NET2 gene taxon:4932 20060317 SGD
+SGD S000003648 MDV1 GO:0005554 SGD_REF:S000069584 ND F YJL112W|FIS2|GAG3|NET2 gene taxon:4932 20010119 SGD
+SGD S000003648 MDV1 GO:0000002 SGD_REF:S000056450|PMID:11038182 IMP P YJL112W|FIS2|GAG3|NET2 gene taxon:4932 20010118 SGD
+SGD S000003648 MDV1 GO:0000002 SGD_REF:S000056450|PMID:11038182 IGI P YJL112W|FIS2|GAG3|NET2 gene taxon:4932 20010118 SGD
+SGD S000003648 MDV1 GO:0000266 SGD_REF:S000056449|PMID:11038180 IMP P YJL112W|FIS2|GAG3|NET2 gene taxon:4932 20010118 SGD
+SGD S000003648 MDV1 GO:0000266 SGD_REF:S000056449|PMID:11038180 IGI P YJL112W|FIS2|GAG3|NET2 gene taxon:4932 20010118 SGD
+SGD S000003648 MDV1 GO:0000266 SGD_REF:S000056450|PMID:11038182 IGI P YJL112W|FIS2|GAG3|NET2 gene taxon:4932 20010118 SGD
+SGD S000003648 MDV1 GO:0000266 SGD_REF:S000060697|PMID:11179417 IGI SGD:S000000383 P YJL112W|FIS2|GAG3|NET2 gene taxon:4932 20030205 SGD
+SGD S000003648 MDV1 GO:0000266 SGD_REF:S000056451|PMID:11038183 IGI P YJL112W|FIS2|GAG3|NET2 gene taxon:4932 20010118 SGD
+SGD S000003648 MDV1 GO:0000266 SGD_REF:S000060697|PMID:11179417 IPI SGD:S000003924 P YJL112W|FIS2|GAG3|NET2 gene taxon:4932 20030205 SGD
+SGD S000003648 MDV1 GO:0000266 SGD_REF:S000056450|PMID:11038182 IMP P YJL112W|FIS2|GAG3|NET2 gene taxon:4932 20010118 SGD
+SGD S000003648 MDV1 GO:0000266 SGD_REF:S000060697|PMID:11179417 IMP P YJL112W|FIS2|GAG3|NET2 gene taxon:4932 20030205 SGD
+SGD S000003648 MDV1 GO:0000266 SGD_REF:S000056450|PMID:11038182 IPI P YJL112W|FIS2|GAG3|NET2 gene taxon:4932 20010118 SGD
+SGD S000003648 MDV1 GO:0000266 SGD_REF:S000056451|PMID:11038183 IMP P YJL112W|FIS2|GAG3|NET2 gene taxon:4932 20010118 SGD
+SGD S000005471 MDY2 GO:0005634 SGD_REF:S000113970|PMID:16390866 IDA C YOL111C|TMA24 gene taxon:4932 20060106 SGD
+SGD S000005471 MDY2 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YOL111C|TMA24 gene taxon:4932 20020507 SGD
+SGD S000005471 MDY2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YOL111C|TMA24 gene taxon:4932 20031028 SGD
+SGD S000005471 MDY2 GO:0005554 SGD_REF:S000069584 ND F YOL111C|TMA24 gene taxon:4932 20030429 SGD
+SGD S000005471 MDY2 GO:0000753 SGD_REF:S000113970|PMID:16390866 IMP P YOL111C|TMA24 gene taxon:4932 20060106 SGD
+SGD S000000340 MEC1 GO:0005634 SGD_REF:S000072000|PMID:12417725 IC GO:0000077 C YBR136W|ESR1|SAD3 gene taxon:4932 20030131 SGD
+SGD S000000340 MEC1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YBR136W|ESR1|SAD3 gene taxon:4932 20040928 SGD
+SGD S000000340 MEC1 GO:0004672 SGD_REF:S000059421|PMID:11095737 IDA F YBR136W|ESR1|SAD3 gene taxon:4932 20040311 SGD
+SGD S000000340 MEC1 GO:0000076 SGD_REF:S000039353|PMID:10511542 IMP P YBR136W|ESR1|SAD3 gene taxon:4932 20010118 SGD
+SGD S000000340 MEC1 GO:0000077 SGD_REF:S000058330|PMID:9610409 TAS P YBR136W|ESR1|SAD3 gene taxon:4932 20010118 SGD
+SGD S000000340 MEC1 GO:0000723 SGD_REF:S000080865|PMID:15721260 IDA P YBR136W|ESR1|SAD3 gene taxon:4932 20050712 SGD
+SGD S000000340 MEC1 GO:0006139 SGD_REF:S000046108|PMID:9744871 IGI P YBR136W|ESR1|SAD3 gene taxon:4932 20011101 SGD
+SGD S000000340 MEC1 GO:0006310 SGD_REF:S000039357|PMID:10511543 IMP P YBR136W|ESR1|SAD3 gene taxon:4932 20010118 SGD
+SGD S000000340 MEC1 GO:0007131 SGD_REF:S000039357|PMID:10511543 IMP P YBR136W|ESR1|SAD3 gene taxon:4932 20020806 SGD
+SGD S000004279 MEC3 GO:0005634 SGD_REF:S000061928|PMID:10723032 TAS C YLR288C|PIP3 gene taxon:4932 20021104 SGD
+SGD S000004279 MEC3 GO:0003677 SGD_REF:S000062131|PMID:10915872 IDA F YLR288C|PIP3 gene taxon:4932 20021103 SGD
+SGD S000004279 MEC3 GO:0000077 SGD_REF:S000041189|PMID:9725831 IMP P YLR288C|PIP3 gene taxon:4932 20020821 SGD
+SGD S000004279 MEC3 GO:0006259 SGD_REF:S000062668|PMID:10924458 TAS P YLR288C|PIP3 gene taxon:4932 20021103 SGD
+SGD S000004279 MEC3 GO:0006348 SGD_REF:S000039871|PMID:9988274 IMP P YLR288C|PIP3 gene taxon:4932 20020821 SGD
+SGD S000006274 MED1 GO:0000119 SGD_REF:S000048078|PMID:9420330 IDA C essential for transcriptional regulation, mediator complex subunit 1 YPR070W gene taxon:4932 20010118 SGD
+SGD S000006274 MED1 GO:0016455 SGD_REF:S000048078|PMID:9420330 IDA F essential for transcriptional regulation, mediator complex subunit 1 YPR070W gene taxon:4932 20010302 SGD
+SGD S000006274 MED1 GO:0006366 SGD_REF:S000048078|PMID:9420330 IDA P essential for transcriptional regulation, mediator complex subunit 1 YPR070W gene taxon:4932 20010118 SGD
+SGD S000004718 MED11 GO:0000119 SGD_REF:S000056289|PMID:9812975 IDA C RNA polymerase II holoenzyme/mediator subunit 14 kDa YMR112C gene taxon:4932 20010118 SGD
+SGD S000004718 MED11 GO:0016455 SGD_REF:S000056289|PMID:9812975 IPI F RNA polymerase II holoenzyme/mediator subunit 14 kDa YMR112C gene taxon:4932 20010302 SGD
+SGD S000004718 MED11 GO:0006366 SGD_REF:S000056289|PMID:9812975 IPI P RNA polymerase II holoenzyme/mediator subunit 14 kDa YMR112C gene taxon:4932 20010118 SGD
+SGD S000002163 MED2 GO:0000119 SGD_REF:S000048078|PMID:9420330 IDA C RNA polymerase II holoenzyme/mediator subunit YDL005C gene taxon:4932 20010118 SGD
+SGD S000002163 MED2 GO:0016455 SGD_REF:S000048078|PMID:9420330 IDA F RNA polymerase II holoenzyme/mediator subunit YDL005C gene taxon:4932 20010302 SGD
+SGD S000002163 MED2 GO:0006366 SGD_REF:S000048078|PMID:9420330 IDA P RNA polymerase II holoenzyme/mediator subunit YDL005C gene taxon:4932 20010118 SGD
+SGD S000005700 MED4 GO:0000119 SGD_REF:S000048078|PMID:9420330 IDA C RNA polymerase II holoenzyme/mediator subunit YOR174W gene taxon:4932 20010118 SGD
+SGD S000005700 MED4 GO:0016455 SGD_REF:S000048078|PMID:9420330 IDA F RNA polymerase II holoenzyme/mediator subunit YOR174W gene taxon:4932 20010302 SGD
+SGD S000005700 MED4 GO:0006366 SGD_REF:S000048078|PMID:9420330 IDA P RNA polymerase II holoenzyme/mediator subunit YOR174W gene taxon:4932 20010118 SGD
+SGD S000001100 MED6 GO:0000119 SGD_REF:S000058446|PMID:9774381 TAS C YHR058C gene taxon:4932 20010118 SGD
+SGD S000001100 MED6 GO:0000119 SGD_REF:S000048078|PMID:9420330 IDA C YHR058C gene taxon:4932 20010118 SGD
+SGD S000001100 MED6 GO:0016455 SGD_REF:S000048078|PMID:9420330 IDA F YHR058C gene taxon:4932 20010302 SGD
+SGD S000001100 MED6 GO:0016455 SGD_REF:S000058446|PMID:9774381 TAS F YHR058C gene taxon:4932 20010302 SGD
+SGD S000001100 MED6 GO:0006366 SGD_REF:S000058446|PMID:9774381 TAS P YHR058C gene taxon:4932 20010118 SGD
+SGD S000001100 MED6 GO:0006366 SGD_REF:S000048078|PMID:9420330 IDA P YHR058C gene taxon:4932 20010118 SGD
+SGD S000005495 MED7 GO:0000119 SGD_REF:S000048078|PMID:9420330 IDA C RNA polymerase II holoenzyme/mediator subunit YOL135C gene taxon:4932 20010118 SGD
+SGD S000005495 MED7 GO:0016455 SGD_REF:S000048078|PMID:9420330 IDA F RNA polymerase II holoenzyme/mediator subunit YOL135C gene taxon:4932 20010302 SGD
+SGD S000005495 MED7 GO:0006366 SGD_REF:S000048078|PMID:9420330 IDA P RNA polymerase II holoenzyme/mediator subunit YOL135C gene taxon:4932 20010118 SGD
+SGD S000000397 MED8 GO:0000119 SGD_REF:S000048078|PMID:9420330 IDA C RNA polymerase II holoenzyme/mediator subunit YBR193C gene taxon:4932 20010118 SGD
+SGD S000000397 MED8 GO:0016455 SGD_REF:S000048078|PMID:9420330 IDA F RNA polymerase II holoenzyme/mediator subunit YBR193C gene taxon:4932 20010302 SGD
+SGD S000000397 MED8 GO:0006366 SGD_REF:S000048078|PMID:9420330 IDA P RNA polymerase II holoenzyme/mediator subunit YBR193C gene taxon:4932 20010118 SGD
+SGD S000004059 MEF1 GO:0005739 SGD_REF:S000042316|PMID:1935960 IMP C mitochondrial elongation factor G-like protein YLR069C gene taxon:4932 20010118 SGD
+SGD S000004059 MEF1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C mitochondrial elongation factor G-like protein YLR069C gene taxon:4932 20040928 SGD
+SGD S000004059 MEF1 GO:0003746 SGD_REF:S000042316|PMID:1935960 ISS F mitochondrial elongation factor G-like protein YLR069C gene taxon:4932 20010118 SGD
+SGD S000004059 MEF1 GO:0003746 SGD_REF:S000042316|PMID:1935960 IMP F mitochondrial elongation factor G-like protein YLR069C gene taxon:4932 20010118 SGD
+SGD S000004059 MEF1 GO:0006414 SGD_REF:S000042316|PMID:1935960 IMP P mitochondrial elongation factor G-like protein YLR069C gene taxon:4932 20010118 SGD
+SGD S000004059 MEF1 GO:0006414 SGD_REF:S000042316|PMID:1935960 ISS P mitochondrial elongation factor G-like protein YLR069C gene taxon:4932 20010118 SGD
+SGD S000003638 MEF2 GO:0005739 SGD_REF:S000042119|PMID:7483851 ISS C mitochondrial elongation factor G-like protein YJL102W gene taxon:4932 20010118 SGD
+SGD S000003638 MEF2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C mitochondrial elongation factor G-like protein YJL102W gene taxon:4932 20040928 SGD
+SGD S000003638 MEF2 GO:0003746 SGD_REF:S000042119|PMID:7483851 ISS F mitochondrial elongation factor G-like protein YJL102W gene taxon:4932 20010118 SGD
+SGD S000003638 MEF2 GO:0006414 SGD_REF:S000042119|PMID:7483851 ISS P mitochondrial elongation factor G-like protein YJL102W gene taxon:4932 20010118 SGD
+SGD S000001715 MEH1 GO:0000329 SGD_REF:S000074185|PMID:14562095 IDA C YKR007W|EGO1 gene taxon:4932 20031028 SGD
+SGD S000001715 MEH1 GO:0000329 SGD_REF:S000081946|PMID:15885099 IDA C YKR007W|EGO1 gene taxon:4932 20050630 SGD
+SGD S000001715 MEH1 GO:0005774 SGD_REF:S000082228|PMID:15989961 IDA C YKR007W|EGO1 gene taxon:4932 20050718 SGD
+SGD S000001715 MEH1 GO:0005774 SGD_REF:S000081946|PMID:15885099 IDA C YKR007W|EGO1 gene taxon:4932 20050719 SGD
+SGD S000001715 MEH1 GO:0005554 SGD_REF:S000069584 ND F YKR007W|EGO1 gene taxon:4932 20030410 SGD
+SGD S000001715 MEH1 GO:0007035 SGD_REF:S000081946|PMID:15885099 IMP P YKR007W|EGO1 gene taxon:4932 20050630 SGD
+SGD S000001715 MEH1 GO:0016237 SGD_REF:S000082228|PMID:15989961 IMP P YKR007W|EGO1 gene taxon:4932 20050718 SGD
+SGD S000001954 MEI4 GO:0008372 SGD_REF:S000069584 ND C 88 bp intron at 5' end spliced independently of MER1, meiosis-specific protein YER044C-A gene taxon:4932 20021118 SGD
+SGD S000001954 MEI4 GO:0005554 SGD_REF:S000069584 ND F 88 bp intron at 5' end spliced independently of MER1, meiosis-specific protein YER044C-A gene taxon:4932 20021118 SGD
+SGD S000001954 MEI4 GO:0007131 SGD_REF:S000044006|PMID:9039264 TAS P 88 bp intron at 5' end spliced independently of MER1, meiosis-specific protein YER044C-A gene taxon:4932 20020919 SGD
+SGD S000001954 MEI4 GO:0030437 SGD_REF:S000045497|PMID:8598049 TAS P 88 bp intron at 5' end spliced independently of MER1, meiosis-specific protein YER044C-A gene taxon:4932 20020919 SGD
+SGD S000001954 MEI4 GO:0042138 SGD_REF:S000044006|PMID:9039264 TAS P 88 bp intron at 5' end spliced independently of MER1, meiosis-specific protein YER044C-A gene taxon:4932 20020919 SGD
+SGD S000006042 MEI5 GO:0000794 SGD_REF:S000080355|PMID:15620352 IDA C YPL121C|LPH6 gene taxon:4932 20050119 SGD
+SGD S000006042 MEI5 GO:0000794 SGD_REF:S000080356|PMID:15579681 IDA C YPL121C|LPH6 gene taxon:4932 20050119 SGD
+SGD S000006042 MEI5 GO:0005554 SGD_REF:S000069584 ND F YPL121C|LPH6 gene taxon:4932 20050119 SGD
+SGD S000006042 MEI5 GO:0000707 SGD_REF:S000080355|PMID:15620352 IMP P YPL121C|LPH6 gene taxon:4932 20050119 SGD
+SGD S000006042 MEI5 GO:0000707 SGD_REF:S000080356|PMID:15579681 IMP P YPL121C|LPH6 gene taxon:4932 20050119 SGD
+SGD S000006042 MEI5 GO:0007131 SGD_REF:S000080356|PMID:15579681 IMP P YPL121C|LPH6 gene taxon:4932 20050119 SGD
+SGD S000006042 MEI5 GO:0007131 SGD_REF:S000080355|PMID:15620352 IMP P YPL121C|LPH6 gene taxon:4932 20050119 SGD
+SGD S000005878 MEK1 GO:0005634 SGD_REF:S000054320|PMID:7926789 IDA C meiosis-specific serine/threonine protein kinase YOR351C|MRE4 gene taxon:4932 20010118 SGD
+SGD S000005878 MEK1 GO:0004674 SGD_REF:S000043136|PMID:9832507 IDA F meiosis-specific serine/threonine protein kinase YOR351C|MRE4 gene taxon:4932 20010118 SGD
+SGD S000005878 MEK1 GO:0004674 SGD_REF:S000049251|PMID:10786836 IMP F meiosis-specific serine/threonine protein kinase YOR351C|MRE4 gene taxon:4932 20020708 SGD
+SGD S000005878 MEK1 GO:0006468 SGD_REF:S000043136|PMID:9832507 IDA P meiosis-specific serine/threonine protein kinase YOR351C|MRE4 gene taxon:4932 20010118 SGD
+SGD S000005878 MEK1 GO:0006468 SGD_REF:S000039745|PMID:9880561 IDA P meiosis-specific serine/threonine protein kinase YOR351C|MRE4 gene taxon:4932 20010118 SGD
+SGD S000005878 MEK1 GO:0007126 SGD_REF:S000047404|PMID:1752435 IMP P meiosis-specific serine/threonine protein kinase YOR351C|MRE4 gene taxon:4932 20010118 SGD
+SGD S000029662 MEL1 GO:0005576 SGD_REF:S000055271|PMID:2997745 IDA C alpha-galactosidase gene taxon:4932 20020708 SGD
+SGD S000029662 MEL1 GO:0004557 SGD_REF:S000055271|PMID:2997745 IDA F alpha-galactosidase gene taxon:4932 20020708 SGD
+SGD S000029662 MEL1 GO:0005995 SGD_REF:S000055271|PMID:2997745 IMP P alpha-galactosidase gene taxon:4932 20020708 SGD
+SGD S000029692 MEL10 GO:0008372 SGD_REF:S000069584 ND C alpha-galactosidase gene taxon:4932 20021204 SGD
+SGD S000029692 MEL10 GO:0004557 SGD_REF:S000050182|PMID:1657419 ISS F alpha-galactosidase gene taxon:4932 20020621 SGD
+SGD S000029692 MEL10 GO:0005995 SGD_REF:S000040322|PMID:7597853 IMP P alpha-galactosidase gene taxon:4932 20020621 SGD
+SGD S000029663 MEL2 GO:0008372 SGD_REF:S000069584 ND C alpha-galactosidase gene taxon:4932 20020621 SGD
+SGD S000029663 MEL2 GO:0004557 SGD_REF:S000041566|PMID:7725791 ISS F alpha-galactosidase gene taxon:4932 20020621 SGD
+SGD S000029663 MEL2 GO:0005995 SGD_REF:S000040322|PMID:7597853 IMP P alpha-galactosidase gene taxon:4932 20020621 SGD
+SGD S000029693 MEL3 GO:0008372 SGD_REF:S000069584 ND C alpha-galactosidase gene taxon:4932 20020708 SGD
+SGD S000029693 MEL3 GO:0004557 SGD_REF:S000048138|PMID:1980522 ISS F alpha-galactosidase gene taxon:4932 20020708 SGD
+SGD S000029693 MEL3 GO:0005995 SGD_REF:S000040322|PMID:7597853 IMP P alpha-galactosidase gene taxon:4932 20020708 SGD
+SGD S000029694 MEL4 GO:0008372 SGD_REF:S000069584 ND C alpha-galactosidase gene taxon:4932 20020708 SGD
+SGD S000029694 MEL4 GO:0004557 SGD_REF:S000048138|PMID:1980522 ISS F alpha-galactosidase gene taxon:4932 20020708 SGD
+SGD S000029694 MEL4 GO:0005995 SGD_REF:S000040322|PMID:7597853 IMP P alpha-galactosidase gene taxon:4932 20020708 SGD
+SGD S000029664 MEL5 GO:0008372 SGD_REF:S000069584 ND C alpha-galactosidase gene taxon:4932 20020708 SGD
+SGD S000029664 MEL5 GO:0004557 SGD_REF:S000048138|PMID:1980522 ISS F alpha-galactosidase gene taxon:4932 20021204 SGD
+SGD S000029664 MEL5 GO:0005995 SGD_REF:S000040322|PMID:7597853 IMP P alpha-galactosidase gene taxon:4932 20020708 SGD
+SGD S000029665 MEL6 GO:0008372 SGD_REF:S000069584 ND C alpha-galactosidase gene taxon:4932 20020708 SGD
+SGD S000029665 MEL6 GO:0004557 SGD_REF:S000048138|PMID:1980522 ISS F alpha-galactosidase gene taxon:4932 20020708 SGD
+SGD S000029665 MEL6 GO:0005995 SGD_REF:S000040322|PMID:7597853 IMP P alpha-galactosidase gene taxon:4932 20020708 SGD
+SGD S000029695 MEL7 GO:0008372 SGD_REF:S000069584 ND C alpha-galactosidase gene taxon:4932 20020708 SGD
+SGD S000029695 MEL7 GO:0004557 SGD_REF:S000048138|PMID:1980522 ISS F alpha-galactosidase gene taxon:4932 20020708 SGD
+SGD S000029695 MEL7 GO:0005995 SGD_REF:S000040322|PMID:7597853 IMP P alpha-galactosidase gene taxon:4932 20020708 SGD
+SGD S000029696 MEL8 GO:0008372 SGD_REF:S000069584 ND C alpha-galactosidase gene taxon:4932 20020621 SGD
+SGD S000029696 MEL8 GO:0004557 SGD_REF:S000050182|PMID:1657419 ISS F alpha-galactosidase gene taxon:4932 20020621 SGD
+SGD S000029696 MEL8 GO:0005995 SGD_REF:S000050182|PMID:1657419 ISS P alpha-galactosidase gene taxon:4932 20020621 SGD
+SGD S000029697 MEL9 GO:0008372 SGD_REF:S000069584 ND C alpha-galactosidase gene taxon:4932 20020620 SGD
+SGD S000029697 MEL9 GO:0004557 SGD_REF:S000050182|PMID:1657419 ISS F alpha-galactosidase gene taxon:4932 20020620 SGD
+SGD S000029697 MEL9 GO:0004557 SGD_REF:S000050182|PMID:1657419 IMP F alpha-galactosidase gene taxon:4932 20020620 SGD
+SGD S000029697 MEL9 GO:0005995 SGD_REF:S000050182|PMID:1657419 ISS P alpha-galactosidase gene taxon:4932 20020620 SGD
+SGD S000029697 MEL9 GO:0005995 SGD_REF:S000050182|PMID:1657419 IMP P alpha-galactosidase gene taxon:4932 20020620 SGD
+SGD S000003353 MEP1 GO:0005886 SGD_REF:S000064003|PMID:11486013 TAS C ammonia permease YGR121C|AMT1 gene taxon:4932 20020706 SGD
+SGD S000003353 MEP1 GO:0005886 SGD_REF:S000048883|PMID:9234685 ISS C ammonia permease YGR121C|AMT1 gene taxon:4932 20021003 SGD
+SGD S000003353 MEP1 GO:0005886 SGD_REF:S000048883|PMID:9234685 IMP C ammonia permease YGR121C|AMT1 gene taxon:4932 20021003 SGD
+SGD S000003353 MEP1 GO:0008519 SGD_REF:S000048883|PMID:9234685 ISS F ammonia permease YGR121C|AMT1 gene taxon:4932 20021003 SGD
+SGD S000003353 MEP1 GO:0008519 SGD_REF:S000048883|PMID:9234685 IMP F ammonia permease YGR121C|AMT1 gene taxon:4932 20021003 SGD
+SGD S000003353 MEP1 GO:0015696 SGD_REF:S000048883|PMID:9234685 ISS P ammonia permease YGR121C|AMT1 gene taxon:4932 20021003 SGD
+SGD S000003353 MEP1 GO:0015696 SGD_REF:S000048883|PMID:9234685 IMP P ammonia permease YGR121C|AMT1 gene taxon:4932 20021003 SGD
+SGD S000005086 MEP2 GO:0005886 SGD_REF:S000059104|PMID:11069679 IDA C ammonia transport protein YNL142W gene taxon:4932 20010629 SGD
+SGD S000005086 MEP2 GO:0008519 SGD_REF:S000048883|PMID:9234685 IMP F ammonia transport protein YNL142W gene taxon:4932 20010629 SGD
+SGD S000005086 MEP2 GO:0007124 SGD_REF:S000056260|PMID:9482721 IMP P ammonia transport protein YNL142W gene taxon:4932 20010629 SGD
+SGD S000005086 MEP2 GO:0015696 SGD_REF:S000048883|PMID:9234685 IMP P ammonia transport protein YNL142W gene taxon:4932 20010629 SGD
+SGD S000006342 MEP3 GO:0005886 SGD_REF:S000064003|PMID:11486013 TAS C NH4+ transporter YPR138C gene taxon:4932 20020706 SGD
+SGD S000006342 MEP3 GO:0005886 SGD_REF:S000048883|PMID:9234685 IMP C NH4+ transporter YPR138C gene taxon:4932 20021003 SGD
+SGD S000006342 MEP3 GO:0005886 SGD_REF:S000048883|PMID:9234685 ISS C NH4+ transporter YPR138C gene taxon:4932 20021003 SGD
+SGD S000006342 MEP3 GO:0008519 SGD_REF:S000048883|PMID:9234685 ISS F NH4+ transporter YPR138C gene taxon:4932 20021003 SGD
+SGD S000006342 MEP3 GO:0008519 SGD_REF:S000048883|PMID:9234685 IMP F NH4+ transporter YPR138C gene taxon:4932 20021003 SGD
+SGD S000006342 MEP3 GO:0015696 SGD_REF:S000048883|PMID:9234685 ISS P NH4+ transporter YPR138C gene taxon:4932 20021003 SGD
+SGD S000006342 MEP3 GO:0015696 SGD_REF:S000048883|PMID:9234685 IMP P NH4+ transporter YPR138C gene taxon:4932 20021003 SGD
+SGD S000005154 MER1 GO:0005634 SGD_REF:S000045583|PMID:7891689 IDA C RNA-binding motif protein required for MRE2-dependent mRNA splicing YNL210W gene taxon:4932 20010118 SGD
+SGD S000005154 MER1 GO:0031202 SGD_REF:S000075527|PMID:14973223 IDA F RNA-binding motif protein required for MRE2-dependent mRNA splicing YNL210W gene taxon:4932 20050223 SGD
+SGD S000005154 MER1 GO:0007126 SGD_REF:S000050626|PMID:8177171 TAS P RNA-binding motif protein required for MRE2-dependent mRNA splicing YNL210W gene taxon:4932 20010118 SGD
+SGD S000005154 MER1 GO:0048026 SGD_REF:S000075527|PMID:14973223 TAS P RNA-binding motif protein required for MRE2-dependent mRNA splicing YNL210W gene taxon:4932 20040329 SGD
+SGD S000003496 MES1 GO:0005737 SGD_REF:S000047746|PMID:3905796 IDA C methionine-tRNA ligase YGR264C|MESI|MetRS gene taxon:4932 20020930 SGD
+SGD S000003496 MES1 GO:0017102 SGD_REF:S000074747|PMID:11069915 IDA C methionine-tRNA ligase YGR264C|MESI|MetRS gene taxon:4932 20031217 SGD
+SGD S000003496 MES1 GO:0004825 SGD_REF:S000044209|PMID:3312199 IDA F methionine-tRNA ligase YGR264C|MESI|MetRS gene taxon:4932 20020930 SGD
+SGD S000003496 MES1 GO:0006431 SGD_REF:S000044209|PMID:3312199 IDA P methionine-tRNA ligase YGR264C|MESI|MetRS gene taxon:4932 20031217 SGD
+SGD S000001777 MET1 GO:0008372 SGD_REF:S000069584 ND C YKR069W|MET20 gene taxon:4932 20010119 SGD
+SGD S000001777 MET1 GO:0004851 SGD_REF:S000042087|PMID:10051442 IDA F YKR069W|MET20 gene taxon:4932 20010118 SGD
+SGD S000001777 MET1 GO:0004851 SGD_REF:S000042087|PMID:10051442 ISS CGSC:CysG F YKR069W|MET20 gene taxon:4932 20040225 SGD
+SGD S000001777 MET1 GO:0000103 SGD_REF:S000044218|PMID:9003798 NAS P YKR069W|MET20 gene taxon:4932 20010118 SGD
+SGD S000001777 MET1 GO:0006555 SGD_REF:S000045625|PMID:1101032 IMP P YKR069W|MET20 gene taxon:4932 20010118 SGD
+SGD S000001777 MET1 GO:0006780 SGD_REF:S000044218|PMID:9003798 NAS P YKR069W|MET20 gene taxon:4932 20010118 SGD
+SGD S000001777 MET1 GO:0019354 SGD_REF:S000044218|PMID:9003798 IGI P YKR069W|MET20 gene taxon:4932 20030922 SGD
+SGD S000001777 MET1 GO:0019354 SGD_REF:S000044218|PMID:9003798 ISS P YKR069W|MET20 gene taxon:4932 20030922 SGD
+SGD S000001926 MET10 GO:0005737 SGD_REF:S000069744|PMID:11921096 TAS C sulfite reductase alpha subunit YFR030W gene taxon:4932 20050130 SGD
+SGD S000001926 MET10 GO:0009337 SGD_REF:S000041414|PMID:7928966 IDA C sulfite reductase alpha subunit YFR030W gene taxon:4932 20030922 SGD
+SGD S000001926 MET10 GO:0009337 SGD_REF:S000041414|PMID:7928966 ISS C sulfite reductase alpha subunit YFR030W gene taxon:4932 20030922 SGD
+SGD S000001926 MET10 GO:0004783 SGD_REF:S000041414|PMID:7928966 ISS F sulfite reductase alpha subunit YFR030W gene taxon:4932 20010118 SGD
+SGD S000001926 MET10 GO:0000103 SGD_REF:S000041414|PMID:7928966 TAS P sulfite reductase alpha subunit YFR030W gene taxon:4932 20010118 SGD
+SGD S000005944 MET12 GO:0005737 SGD_REF:S000055171|PMID:10600168 IDA C methylenetetrahydrofolate reductase (mthfr) (putative) YPL023C gene taxon:4932 20041206 SGD
+SGD S000005944 MET12 GO:0004489 SGD_REF:S000055171|PMID:10600168 IDA F methylenetetrahydrofolate reductase (mthfr) (putative) YPL023C gene taxon:4932 20010118 SGD
+SGD S000005944 MET12 GO:0006555 SGD_REF:S000058500 TAS P methylenetetrahydrofolate reductase (mthfr) (putative) YPL023C gene taxon:4932 20010119 SGD
+SGD S000005944 MET12 GO:0006555 SGD_REF:S000055171|PMID:10600168 TAS P methylenetetrahydrofolate reductase (mthfr) (putative) YPL023C gene taxon:4932 20010118 SGD
+SGD S000003093 MET13 GO:0005737 SGD_REF:S000055171|PMID:10600168 IDA C methylenetetrahydrofolate reductase (mthfr) (putative) YGL125W|MET11|MRPL45 gene taxon:4932 20041206 SGD
+SGD S000003093 MET13 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C methylenetetrahydrofolate reductase (mthfr) (putative) YGL125W|MET11|MRPL45 gene taxon:4932 20040928 SGD
+SGD S000003093 MET13 GO:0003735 SGD_REF:S000058278|PMID:9445368 TAS F methylenetetrahydrofolate reductase (mthfr) (putative) YGL125W|MET11|MRPL45 gene taxon:4932 20010118 SGD
+SGD S000003093 MET13 GO:0004489 SGD_REF:S000042632|PMID:8896269 ISS F methylenetetrahydrofolate reductase (mthfr) (putative) YGL125W|MET11|MRPL45 gene taxon:4932 20010118 SGD
+SGD S000003093 MET13 GO:0004489 SGD_REF:S000055171|PMID:10600168 IDA F methylenetetrahydrofolate reductase (mthfr) (putative) YGL125W|MET11|MRPL45 gene taxon:4932 20010118 SGD
+SGD S000003093 MET13 GO:0000097 SGD_REF:S000058500 TAS P methylenetetrahydrofolate reductase (mthfr) (putative) YGL125W|MET11|MRPL45 gene taxon:4932 20010119 SGD
+SGD S000003093 MET13 GO:0000097 SGD_REF:S000055171|PMID:10600168 TAS P methylenetetrahydrofolate reductase (mthfr) (putative) YGL125W|MET11|MRPL45 gene taxon:4932 20010118 SGD
+SGD S000003093 MET13 GO:0006555 SGD_REF:S000048523|PMID:10029993 IMP P methylenetetrahydrofolate reductase (mthfr) (putative) YGL125W|MET11|MRPL45 gene taxon:4932 20010118 SGD
+SGD S000003093 MET13 GO:0006555 SGD_REF:S000058500 TAS P methylenetetrahydrofolate reductase (mthfr) (putative) YGL125W|MET11|MRPL45 gene taxon:4932 20010119 SGD
+SGD S000003093 MET13 GO:0006555 SGD_REF:S000055171|PMID:10600168 TAS P methylenetetrahydrofolate reductase (mthfr) (putative) YGL125W|MET11|MRPL45 gene taxon:4932 20010118 SGD
+SGD S000001484 MET14 GO:0005622 SGD_REF:S000064015|PMID:3019265 IDA C adenylylsulfate kinase YKL001C gene taxon:4932 20041206 SGD
+SGD S000001484 MET14 GO:0005737 SGD_REF:S000069744|PMID:11921096 TAS C adenylylsulfate kinase YKL001C gene taxon:4932 20050130 SGD
+SGD S000001484 MET14 GO:0004020 SGD_REF:S000045586|PMID:1654509 TAS F adenylylsulfate kinase YKL001C gene taxon:4932 20010118 SGD
+SGD S000001484 MET14 GO:0000103 SGD_REF:S000045586|PMID:1654509 NAS P adenylylsulfate kinase YKL001C gene taxon:4932 20010118 SGD
+SGD S000001484 MET14 GO:0006555 SGD_REF:S000045625|PMID:1101032 IMP P adenylylsulfate kinase YKL001C gene taxon:4932 20010118 SGD
+SGD S000006371 MET16 GO:0005622 SGD_REF:S000071568|PMID:12406228 TAS C 3'phosphoadenylylsulfate reductase YPR167C gene taxon:4932 20021122 SGD
+SGD S000006371 MET16 GO:0005737 SGD_REF:S000069744|PMID:11921096 TAS C 3'phosphoadenylylsulfate reductase YPR167C gene taxon:4932 20050130 SGD
+SGD S000006371 MET16 GO:0004604 SGD_REF:S000049622|PMID:2203779 IDA F 3'phosphoadenylylsulfate reductase YPR167C gene taxon:4932 20010118 SGD
+SGD S000006371 MET16 GO:0000103 SGD_REF:S000049622|PMID:2203779 TAS P 3'phosphoadenylylsulfate reductase YPR167C gene taxon:4932 20010118 SGD
+SGD S000006371 MET16 GO:0006555 SGD_REF:S000045625|PMID:1101032 IMP P 3'phosphoadenylylsulfate reductase YPR167C gene taxon:4932 20010118 SGD
+SGD S000004294 MET17 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C O-acetylhomoserine (thiol)-lyase YLR303W|MET15|MET25 gene taxon:4932 20020507 SGD
+SGD S000004294 MET17 GO:0003961 SGD_REF:S000057063|PMID:3299001 TAS F O-acetylhomoserine (thiol)-lyase YLR303W|MET15|MET25 gene taxon:4932 20010118 SGD
+SGD S000004294 MET17 GO:0003961 SGD_REF:S000055307|PMID:7765825 IDA F O-acetylhomoserine (thiol)-lyase YLR303W|MET15|MET25 gene taxon:4932 20030528 SGD
+SGD S000004294 MET17 GO:0004124 SGD_REF:S000055307|PMID:7765825 IDA F O-acetylhomoserine (thiol)-lyase YLR303W|MET15|MET25 gene taxon:4932 20030528 SGD
+SGD S000004294 MET17 GO:0006555 SGD_REF:S000045625|PMID:1101032 IMP P O-acetylhomoserine (thiol)-lyase YLR303W|MET15|MET25 gene taxon:4932 20010118 SGD
+SGD S000004294 MET17 GO:0019344 SGD_REF:S000075748|PMID:15042590 TAS P O-acetylhomoserine (thiol)-lyase YLR303W|MET15|MET25 gene taxon:4932 20040403 SGD
+SGD S000001390 MET18 GO:0005654 SGD_REF:S000044358|PMID:8943333 IMP C TFIIH regulator YIL128W|MMS19 gene taxon:4932 20010118 SGD
+SGD S000001390 MET18 GO:0003702 SGD_REF:S000044358|PMID:8943333 IMP F TFIIH regulator YIL128W|MMS19 gene taxon:4932 20010118 SGD
+SGD S000001390 MET18 GO:0003702 SGD_REF:S000044358|PMID:8943333 IGI F TFIIH regulator YIL128W|MMS19 gene taxon:4932 20010118 SGD
+SGD S000001390 MET18 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P TFIIH regulator YIL128W|MMS19 gene taxon:4932 20060203 SGD
+SGD S000001390 MET18 GO:0006289 SGD_REF:S000044358|PMID:8943333 IMP P TFIIH regulator YIL128W|MMS19 gene taxon:4932 20010118 SGD
+SGD S000001390 MET18 GO:0006366 SGD_REF:S000044358|PMID:8943333 IMP P TFIIH regulator YIL128W|MMS19 gene taxon:4932 20010118 SGD
+SGD S000001390 MET18 GO:0006366 SGD_REF:S000044358|PMID:8943333 IGI P TFIIH regulator YIL128W|MMS19 gene taxon:4932 20010118 SGD
+SGD S000001390 MET18 GO:0006555 SGD_REF:S000044358|PMID:8943333 IMP P TFIIH regulator YIL128W|MMS19 gene taxon:4932 20010118 SGD
+SGD S000005221 MET2 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C homoserine O-trans-acetylase YNL277W gene taxon:4932 20020507 SGD
+SGD S000005221 MET2 GO:0004414 SGD_REF:S000051183|PMID:3542717 IDA F homoserine O-trans-acetylase YNL277W gene taxon:4932 20030113 SGD
+SGD S000005221 MET2 GO:0009086 SGD_REF:S000049925|PMID:8987848 TAS P homoserine O-trans-acetylase YNL277W gene taxon:4932 20020618 SGD
+SGD S000005221 MET2 GO:0009092 SGD_REF:S000049925|PMID:8987848 TAS P homoserine O-trans-acetylase YNL277W gene taxon:4932 20020618 SGD
+SGD S000005425 MET22 GO:0005737 SGD_REF:S000051103|PMID:10656801 IDA C 3'(2')5'-bisphosphate nucleotidase YOL064C|HAL2 gene taxon:4932 20010628 SGD
+SGD S000005425 MET22 GO:0008441 SGD_REF:S000046424|PMID:7809627 TAS F 3'(2')5'-bisphosphate nucleotidase YOL064C|HAL2 gene taxon:4932 20010628 SGD
+SGD S000005425 MET22 GO:0000103 SGD_REF:S000047943|PMID:8910555 TAS P 3'(2')5'-bisphosphate nucleotidase YOL064C|HAL2 gene taxon:4932 20010628 SGD
+SGD S000005425 MET22 GO:0009086 SGD_REF:S000047697|PMID:8393782 TAS P 3'(2')5'-bisphosphate nucleotidase YOL064C|HAL2 gene taxon:4932 20010628 SGD
+SGD S000005425 MET22 GO:0042538 SGD_REF:S000047943|PMID:8910555 TAS P 3'(2')5'-bisphosphate nucleotidase YOL064C|HAL2 gene taxon:4932 20030922 SGD
+SGD S000001456 MET28 GO:0005634 SGD_REF:S000040724|PMID:8665859 TAS C transcriptional activator in the Cbf1p-Met4p-Met28p complex YIR017C gene taxon:4932 20010118 SGD
+SGD S000001456 MET28 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C transcriptional activator in the Cbf1p-Met4p-Met28p complex YIR017C gene taxon:4932 20031028 SGD
+SGD S000001456 MET28 GO:0003677 SGD_REF:S000040724|PMID:8665859 IDA F transcriptional activator in the Cbf1p-Met4p-Met28p complex YIR017C gene taxon:4932 20030530 SGD
+SGD S000001456 MET28 GO:0003704 SGD_REF:S000040724|PMID:8665859 TAS F transcriptional activator in the Cbf1p-Met4p-Met28p complex YIR017C gene taxon:4932 20010118 SGD
+SGD S000001456 MET28 GO:0016563 SGD_REF:S000042750|PMID:10637232 TAS F transcriptional activator in the Cbf1p-Met4p-Met28p complex YIR017C gene taxon:4932 20021203 SGD
+SGD S000001456 MET28 GO:0000097 SGD_REF:S000055397|PMID:9409150 TAS P transcriptional activator in the Cbf1p-Met4p-Met28p complex YIR017C gene taxon:4932 20010118 SGD
+SGD S000001456 MET28 GO:0006357 SGD_REF:S000040724|PMID:8665859 TAS P transcriptional activator in the Cbf1p-Met4p-Met28p complex YIR017C gene taxon:4932 20010118 SGD
+SGD S000001456 MET28 GO:0042762 SGD_REF:S000040724|PMID:8665859 IDA P transcriptional activator in the Cbf1p-Met4p-Met28p complex YIR017C gene taxon:4932 20030616 SGD
+SGD S000003771 MET3 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C ATP sulfurylase YJR010W gene taxon:4932 20031028 SGD
+SGD S000003771 MET3 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C ATP sulfurylase YJR010W gene taxon:4932 20040813 SGD
+SGD S000003771 MET3 GO:0004781 SGD_REF:S000058418|PMID:197388 TAS F ATP sulfurylase YJR010W gene taxon:4932 20010118 SGD
+SGD S000003771 MET3 GO:0000103 SGD_REF:S000058418|PMID:197388 TAS P ATP sulfurylase YJR010W gene taxon:4932 20010118 SGD
+SGD S000003771 MET3 GO:0006555 SGD_REF:S000058418|PMID:197388 IMP P ATP sulfurylase YJR010W gene taxon:4932 20010118 SGD
+SGD S000001308 MET30 GO:0019005 SGD_REF:S000054644|PMID:9716410 IPI SGD:S000002290|SGD:S000002736 C F-box protein YIL046W|ZRG11 gene taxon:4932 20030523 SGD
+SGD S000001308 MET30 GO:0043224 SGD_REF:S000042750|PMID:10637232 IDA C F-box protein YIL046W|ZRG11 gene taxon:4932 20050421 SGD
+SGD S000001308 MET30 GO:0005515 SGD_REF:S000045265|PMID:10409741 TAS F F-box protein YIL046W|ZRG11 gene taxon:4932 20010118 SGD
+SGD S000001308 MET30 GO:0007049 SGD_REF:S000045265|PMID:10409741 TAS P F-box protein YIL046W|ZRG11 gene taxon:4932 20010118 SGD
+SGD S000001308 MET30 GO:0016567 SGD_REF:S000058289|PMID:9499404 IGI P F-box protein YIL046W|ZRG11 gene taxon:4932 20050408 SGD
+SGD S000001308 MET30 GO:0016567 SGD_REF:S000058289|PMID:9499404 IPI P F-box protein YIL046W|ZRG11 gene taxon:4932 20050408 SGD
+SGD S000001308 MET30 GO:0031146 SGD_REF:S000054644|PMID:9716410 IDA P F-box protein YIL046W|ZRG11 gene taxon:4932 20050404 SGD
+SGD S000001308 MET30 GO:0046685 SGD_REF:S000080759|PMID:15689486 IDA P F-box protein YIL046W|ZRG11 gene taxon:4932 20050321 SGD
+SGD S000001308 MET30 GO:0046686 SGD_REF:S000080759|PMID:15689486 IDA P F-box protein YIL046W|ZRG11 gene taxon:4932 20050321 SGD
+SGD S000005959 MET31 GO:0005634 SGD_REF:S000069459|PMID:11914276 IDA C highly homologous to Met32p, transcriptional regulator of sulfur amino acid metabolism, zinc finger protein YPL038W gene taxon:4932 20020507 SGD
+SGD S000005959 MET31 GO:0005634 SGD_REF:S000050356|PMID:9799240 IPI C highly homologous to Met32p, transcriptional regulator of sulfur amino acid metabolism, zinc finger protein YPL038W gene taxon:4932 20020930 SGD
+SGD S000005959 MET31 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C highly homologous to Met32p, transcriptional regulator of sulfur amino acid metabolism, zinc finger protein YPL038W gene taxon:4932 20020507 SGD
+SGD S000005959 MET31 GO:0003677 SGD_REF:S000050356|PMID:9799240 IDA F highly homologous to Met32p, transcriptional regulator of sulfur amino acid metabolism, zinc finger protein YPL038W gene taxon:4932 20030529 SGD
+SGD S000005959 MET31 GO:0003704 SGD_REF:S000052183|PMID:9199298 IDA F highly homologous to Met32p, transcriptional regulator of sulfur amino acid metabolism, zinc finger protein YPL038W gene taxon:4932 20020930 SGD
+SGD S000005959 MET31 GO:0000096 SGD_REF:S000052183|PMID:9199298 IDA P highly homologous to Met32p, transcriptional regulator of sulfur amino acid metabolism, zinc finger protein YPL038W gene taxon:4932 20020930 SGD
+SGD S000005959 MET31 GO:0045449 SGD_REF:S000052183|PMID:9199298 IDA P highly homologous to Met32p, transcriptional regulator of sulfur amino acid metabolism, zinc finger protein YPL038W gene taxon:4932 20030527 SGD
+SGD S000005959 MET31 GO:0045449 SGD_REF:S000042750|PMID:10637232 TAS P highly homologous to Met32p, transcriptional regulator of sulfur amino acid metabolism, zinc finger protein YPL038W gene taxon:4932 20030527 SGD
+SGD S000005959 MET31 GO:0045449 SGD_REF:S000050396|PMID:10747029 TAS P highly homologous to Met32p, transcriptional regulator of sulfur amino acid metabolism, zinc finger protein YPL038W gene taxon:4932 20030527 SGD
+SGD S000002661 MET32 GO:0005634 SGD_REF:S000050356|PMID:9799240 IPI C highly homologous to Met31p, transcriptional regulator of sulfur amino acid metabolism, zinc finger protein YDR253C gene taxon:4932 20020930 SGD
+SGD S000002661 MET32 GO:0003677 SGD_REF:S000050396|PMID:10747029 TAS F highly homologous to Met31p, transcriptional regulator of sulfur amino acid metabolism, zinc finger protein YDR253C gene taxon:4932 20030530 SGD
+SGD S000002661 MET32 GO:0003704 SGD_REF:S000052183|PMID:9199298 IDA F highly homologous to Met31p, transcriptional regulator of sulfur amino acid metabolism, zinc finger protein YDR253C gene taxon:4932 20020930 SGD
+SGD S000002661 MET32 GO:0000096 SGD_REF:S000052183|PMID:9199298 IDA P highly homologous to Met31p, transcriptional regulator of sulfur amino acid metabolism, zinc finger protein YDR253C gene taxon:4932 20020930 SGD
+SGD S000005047 MET4 GO:0005634 SGD_REF:S000050356|PMID:9799240 IPI C leucine zipper family, transcriptional activator YNL103W gene taxon:4932 20021112 SGD
+SGD S000005047 MET4 GO:0003713 SGD_REF:S000050356|PMID:9799240 IDA F leucine zipper family, transcriptional activator YNL103W gene taxon:4932 20021112 SGD
+SGD S000005047 MET4 GO:0000096 SGD_REF:S000042966|PMID:1549123 IMP P leucine zipper family, transcriptional activator YNL103W gene taxon:4932 20021112 SGD
+SGD S000005047 MET4 GO:0045944 SGD_REF:S000050356|PMID:9799240 IDA P leucine zipper family, transcriptional activator YNL103W gene taxon:4932 20021112 SGD
+SGD S000005047 MET4 GO:0046685 SGD_REF:S000080759|PMID:15689486 IDA P leucine zipper family, transcriptional activator YNL103W gene taxon:4932 20050321 SGD
+SGD S000005047 MET4 GO:0046686 SGD_REF:S000080759|PMID:15689486 IDA P leucine zipper family, transcriptional activator YNL103W gene taxon:4932 20050321 SGD
+SGD S000000893 MET6 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C 5-methyltetrahydropteroyl triglutamate homocysteine methyltransferase, N5-methyltetrahydrofolate homocysteine methyltransferase, vitamin B12-(cobalamin)-independent methionine synthase YER091C gene taxon:4932 20031028 SGD
+SGD S000000893 MET6 GO:0003871 SGD_REF:S000051200|PMID:3542720 IMP F 5-methyltetrahydropteroyl triglutamate homocysteine methyltransferase, N5-methyltetrahydrofolate homocysteine methyltransferase, vitamin B12-(cobalamin)-independent methionine synthase YER091C gene taxon:4932 20030204 SGD
+SGD S000000893 MET6 GO:0009086 SGD_REF:S000045625|PMID:1101032 IMP P 5-methyltetrahydropteroyl triglutamate homocysteine methyltransferase, N5-methyltetrahydrofolate homocysteine methyltransferase, vitamin B12-(cobalamin)-independent methionine synthase YER091C gene taxon:4932 20030528 SGD
+SGD S000005767 MET7 GO:0005737 SGD_REF:S000041882|PMID:10775416 IDA C folylpolyglutamate synthetase YOR241W|MET23 gene taxon:4932 20020930 SGD
+SGD S000005767 MET7 GO:0005739 SGD_REF:S000041882|PMID:10775416 IDA C folylpolyglutamate synthetase YOR241W|MET23 gene taxon:4932 20020930 SGD
+SGD S000005767 MET7 GO:0004326 SGD_REF:S000041882|PMID:10775416 IDA F folylpolyglutamate synthetase YOR241W|MET23 gene taxon:4932 20020930 SGD
+SGD S000005767 MET7 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P folylpolyglutamate synthetase YOR241W|MET23 gene taxon:4932 20060227 SGD
+SGD S000005767 MET7 GO:0006730 SGD_REF:S000041882|PMID:10775416 IMP P folylpolyglutamate synthetase YOR241W|MET23 gene taxon:4932 20020930 SGD
+SGD S000000417 MET8 GO:0008372 SGD_REF:S000069584 ND C YBR213W gene taxon:4932 20021114 SGD
+SGD S000000417 MET8 GO:0004325 SGD_REF:S000069702|PMID:11980703 IDA F YBR213W gene taxon:4932 20021130 SGD
+SGD S000000417 MET8 GO:0043115 SGD_REF:S000042087|PMID:10051442 IDA F YBR213W gene taxon:4932 20040225 SGD
+SGD S000000417 MET8 GO:0000103 SGD_REF:S000042087|PMID:10051442 IMP P YBR213W gene taxon:4932 20021114 SGD
+SGD S000000417 MET8 GO:0019354 SGD_REF:S000044218|PMID:9003798 IMP P YBR213W gene taxon:4932 20021114 SGD
+SGD S000004007 MEU1 GO:0005737 SGD_REF:S000049135|PMID:8807288 IDA C YLR017W gene taxon:4932 20020820 SGD
+SGD S000004007 MEU1 GO:0017061 SGD_REF:S000075168|PMID:14506228 IDA F YLR017W gene taxon:4932 20040927 SGD
+SGD S000004007 MEU1 GO:0017061 SGD_REF:S000075168|PMID:14506228 IMP F YLR017W gene taxon:4932 20040927 SGD
+SGD S000004007 MEU1 GO:0006537 SGD_REF:S000049135|PMID:8807288 IMP P YLR017W gene taxon:4932 20020820 SGD
+SGD S000004007 MEU1 GO:0019509 SGD_REF:S000075168|PMID:14506228 IDA P YLR017W gene taxon:4932 20040927 SGD
+SGD S000004007 MEU1 GO:0019509 SGD_REF:S000075168|PMID:14506228 IMP P YLR017W gene taxon:4932 20040927 SGD
+SGD S000006090 MEX67 GO:0005643 SGD_REF:S000056415|PMID:10684247 IDA C a poly(A)+RNA binding protein YPL169C gene taxon:4932 20020620 SGD
+SGD S000006090 MEX67 GO:0005737 SGD_REF:S000056415|PMID:10684247 IDA C a poly(A)+RNA binding protein YPL169C gene taxon:4932 20020620 SGD
+SGD S000006090 MEX67 GO:0003723 SGD_REF:S000072688|PMID:12524544 IDA F a poly(A)+RNA binding protein YPL169C gene taxon:4932 20030311 SGD
+SGD S000006090 MEX67 GO:0005515 SGD_REF:S000071844|PMID:12411502 IPI SGD:S000002566 F a poly(A)+RNA binding protein YPL169C gene taxon:4932 20030605 SGD
+SGD S000006090 MEX67 GO:0017056 SGD_REF:S000056415|PMID:10684247 IDA F a poly(A)+RNA binding protein YPL169C gene taxon:4932 20020930 SGD
+SGD S000006090 MEX67 GO:0006406 SGD_REF:S000056189|PMID:10722667 IMP P a poly(A)+RNA binding protein YPL169C gene taxon:4932 20020930 SGD
+SGD S000006108 MF(ALPHA)1 GO:0005576 SGD_REF:S000057300|PMID:6754095 TAS C mating factor alpha YPL187W gene taxon:4932 20010118 SGD
+SGD S000006108 MF(ALPHA)1 GO:0005576 SGD_REF:S000052020|PMID:6339075 TAS C mating factor alpha YPL187W gene taxon:4932 20050216 SGD
+SGD S000006108 MF(ALPHA)1 GO:0000772 SGD_REF:S000057245|PMID:6306574 IDA F mating factor alpha YPL187W gene taxon:4932 20050216 SGD
+SGD S000006108 MF(ALPHA)1 GO:0000772 SGD_REF:S000060099|PMID:3887136 IMP F mating factor alpha YPL187W gene taxon:4932 20050216 SGD
+SGD S000006108 MF(ALPHA)1 GO:0000749 SGD_REF:S000060099|PMID:3887136 IMP P mating factor alpha YPL187W gene taxon:4932 20050216 SGD
+SGD S000003057 MF(ALPHA)2 GO:0005576 SGD_REF:S000052020|PMID:6339075 TAS C alpha mating factor YGL089C gene taxon:4932 20050216 SGD
+SGD S000003057 MF(ALPHA)2 GO:0000772 SGD_REF:S000057245|PMID:6306574 IDA F alpha mating factor YGL089C gene taxon:4932 20050216 SGD
+SGD S000003057 MF(ALPHA)2 GO:0000772 SGD_REF:S000060099|PMID:3887136 IMP F alpha mating factor YGL089C gene taxon:4932 20050216 SGD
+SGD S000003057 MF(ALPHA)2 GO:0000749 SGD_REF:S000060099|PMID:3887136 IMP P alpha mating factor YGL089C gene taxon:4932 20050216 SGD
+SGD S000002869 MFA1 GO:0005576 SGD_REF:S000054127|PMID:10022942 IDA C a-factor mating pheromone precursor YDR461W gene taxon:4932 20010118 SGD
+SGD S000002869 MFA1 GO:0005625 SGD_REF:S000068747|PMID:11746603 IDA C a-factor mating pheromone precursor YDR461W gene taxon:4932 20030130 SGD
+SGD S000002869 MFA1 GO:0000772 SGD_REF:S000049639|PMID:3285180 IMP F a-factor mating pheromone precursor YDR461W gene taxon:4932 20050216 SGD
+SGD S000002869 MFA1 GO:0000750 SGD_REF:S000049639|PMID:3285180 IGI P a-factor mating pheromone precursor YDR461W gene taxon:4932 20021206 SGD
+SGD S000002869 MFA1 GO:0000750 SGD_REF:S000049639|PMID:3285180 IMP P a-factor mating pheromone precursor YDR461W gene taxon:4932 20021206 SGD
+SGD S000005089 MFA2 GO:0005576 SGD_REF:S000056270|PMID:2046670 IDA C a-factor mating pheromone precursor YNL145W gene taxon:4932 20021023 SGD
+SGD S000005089 MFA2 GO:0000772 SGD_REF:S000049639|PMID:3285180 IMP F a-factor mating pheromone precursor YNL145W gene taxon:4932 20050216 SGD
+SGD S000005089 MFA2 GO:0000750 SGD_REF:S000049639|PMID:3285180 IGI P a-factor mating pheromone precursor YNL145W gene taxon:4932 20021206 SGD
+SGD S000005089 MFA2 GO:0000750 SGD_REF:S000049639|PMID:3285180 IMP P a-factor mating pheromone precursor YNL145W gene taxon:4932 20021206 SGD
+SGD S000002627 MFB1 GO:0000151 SGD_REF:S000058340|PMID:9635407 ISS C YDR219C gene taxon:4932 20030205 SGD
+SGD S000002627 MFB1 GO:0005515 SGD_REF:S000058340|PMID:9635407 ISS F YDR219C gene taxon:4932 20030205 SGD
+SGD S000002627 MFB1 GO:0006511 SGD_REF:S000058340|PMID:9635407 ISS P YDR219C gene taxon:4932 20030205 SGD
+SGD S000004527 MFT1 GO:0000347 SGD_REF:S000059208|PMID:11060033 IMP C mitochondrial targeting protein YML062C|MFT52 gene taxon:4932 20030221 SGD
+SGD S000004527 MFT1 GO:0000347 SGD_REF:S000059208|PMID:11060033 IPI C mitochondrial targeting protein YML062C|MFT52 gene taxon:4932 20030221 SGD
+SGD S000004527 MFT1 GO:0003676 SGD_REF:S000070300|PMID:12093753 IDA F mitochondrial targeting protein YML062C|MFT52 gene taxon:4932 20021118 SGD
+SGD S000004527 MFT1 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P mitochondrial targeting protein YML062C|MFT52 gene taxon:4932 20060203 SGD
+SGD S000004527 MFT1 GO:0006310 SGD_REF:S000059208|PMID:11060033 IMP P mitochondrial targeting protein YML062C|MFT52 gene taxon:4932 20030221 SGD
+SGD S000004527 MFT1 GO:0006368 SGD_REF:S000070300|PMID:12093753 IMP P mitochondrial targeting protein YML062C|MFT52 gene taxon:4932 20021118 SGD
+SGD S000004527 MFT1 GO:0006406 SGD_REF:S000069956|PMID:11979277 IMP P mitochondrial targeting protein YML062C|MFT52 gene taxon:4932 20030214 SGD
+SGD S000003481 MGA1 GO:0008372 SGD_REF:S000069584 ND C similar to heat shock transcription factor YGR249W gene taxon:4932 20020930 SGD
+SGD S000003481 MGA1 GO:0005554 SGD_REF:S000069584 ND F similar to heat shock transcription factor YGR249W gene taxon:4932 20020930 SGD
+SGD S000003481 MGA1 GO:0030447 SGD_REF:S000043169|PMID:9832522 IGI P similar to heat shock transcription factor YGR249W gene taxon:4932 20020930 SGD
+SGD S000001472 MGA2 GO:0005789 SGD_REF:S000066217|PMID:11557770 IDA C YIR033W gene taxon:4932 20021023 SGD
+SGD S000001472 MGA2 GO:0016563 SGD_REF:S000066217|PMID:11557770 IMP F YIR033W gene taxon:4932 20021023 SGD
+SGD S000001472 MGA2 GO:0006631 SGD_REF:S000066217|PMID:11557770 IMP P YIR033W gene taxon:4932 20021023 SGD
+SGD S000001472 MGA2 GO:0009409 SGD_REF:S000069399|PMID:11855848 IEP P YIR033W gene taxon:4932 20021023 SGD
+SGD S000001472 MGA2 GO:0009409 SGD_REF:S000069399|PMID:11855848 IMP P YIR033W gene taxon:4932 20021023 SGD
+SGD S000001472 MGA2 GO:0045944 SGD_REF:S000066217|PMID:11557770 IMP P YIR033W gene taxon:4932 20021023 SGD
+SGD S000005758 MGE1 GO:0001405 SGD_REF:S000074354|PMID:14638855 IPI C GrpE homolog YOR232W|GRPE|YGE1 gene taxon:4932 20031218 SGD
+SGD S000005758 MGE1 GO:0001405 SGD_REF:S000074353|PMID:14517234 IPI C GrpE homolog YOR232W|GRPE|YGE1 gene taxon:4932 20031218 SGD
+SGD S000005758 MGE1 GO:0005739 SGD_REF:S000069459|PMID:11914276 IDA C GrpE homolog YOR232W|GRPE|YGE1 gene taxon:4932 20020507 SGD
+SGD S000005758 MGE1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C GrpE homolog YOR232W|GRPE|YGE1 gene taxon:4932 20040924 SGD
+SGD S000005758 MGE1 GO:0005759 SGD_REF:S000041394|PMID:8022808 IDA C GrpE homolog YOR232W|GRPE|YGE1 gene taxon:4932 20010118 SGD
+SGD S000005758 MGE1 GO:0051082 SGD_REF:S000042738|PMID:8798629 IDA F GrpE homolog YOR232W|GRPE|YGE1 gene taxon:4932 20010118 SGD
+SGD S000005758 MGE1 GO:0030150 SGD_REF:S000041394|PMID:8022808 IMP P GrpE homolog YOR232W|GRPE|YGE1 gene taxon:4932 20031119 SGD
+SGD S000005737 MGM1 GO:0005758 SGD_REF:S000059280|PMID:11038181 IDA C GTP-binding domain protein related to dynamin YOR211C|MNA1 gene taxon:4932 20021202 SGD
+SGD S000005737 MGM1 GO:0003924 SGD_REF:S000058450|PMID:9891785 TAS F GTP-binding domain protein related to dynamin YOR211C|MNA1 gene taxon:4932 20020709 SGD
+SGD S000005737 MGM1 GO:0000002 SGD_REF:S000045229|PMID:1532158 IMP P GTP-binding domain protein related to dynamin YOR211C|MNA1 gene taxon:4932 20021202 SGD
+SGD S000005737 MGM1 GO:0007005 SGD_REF:S000058450|PMID:9891785 TAS P GTP-binding domain protein related to dynamin YOR211C|MNA1 gene taxon:4932 20010118 SGD
+SGD S000005737 MGM1 GO:0007005 SGD_REF:S000058923|PMID:15125685 IMP P GTP-binding domain protein related to dynamin YOR211C|MNA1 gene taxon:4932 20041215 SGD
+SGD S000005737 MGM1 GO:0008053 SGD_REF:S000073565|PMID:12808034 IMP P GTP-binding domain protein related to dynamin YOR211C|MNA1 gene taxon:4932 20030710 SGD
+SGD S000005737 MGM1 GO:0008053 SGD_REF:S000073565|PMID:12808034 IPI P GTP-binding domain protein related to dynamin YOR211C|MNA1 gene taxon:4932 20030710 SGD
+SGD S000003905 MGM101 GO:0000262 SGD_REF:S000047653|PMID:10209025 IDA C mitochondrial nucleoid protein YJR144W|MGM9 gene taxon:4932 20021108 SGD
+SGD S000003905 MGM101 GO:0042645 SGD_REF:S000050870|PMID:10869431 IDA C mitochondrial nucleoid protein YJR144W|MGM9 gene taxon:4932 20050401 SGD
+SGD S000003905 MGM101 GO:0003677 SGD_REF:S000047653|PMID:10209025 IDA F mitochondrial nucleoid protein YJR144W|MGM9 gene taxon:4932 20021108 SGD
+SGD S000003905 MGM101 GO:0000002 SGD_REF:S000069714|PMID:11973295 IMP P mitochondrial nucleoid protein YJR144W|MGM9 gene taxon:4932 20021108 SGD
+SGD S000003905 MGM101 GO:0006281 SGD_REF:S000047653|PMID:10209025 IMP P mitochondrial nucleoid protein YJR144W|MGM9 gene taxon:4932 20021108 SGD
+SGD S000000549 MGR1 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YCL044C gene taxon:4932 20031028 SGD
+SGD S000000549 MGR1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YCL044C gene taxon:4932 20040924 SGD
+SGD S000000549 MGR1 GO:0031942 SGD_REF:S000113568|PMID:16267274 IDA C YCL044C gene taxon:4932 20051129 SGD
+SGD S000000549 MGR1 GO:0005554 SGD_REF:S000069584 ND F YCL044C gene taxon:4932 20051119 SGD
+SGD S000000549 MGR1 GO:0000002 SGD_REF:S000113568|PMID:16267274 IGI P YCL044C gene taxon:4932 20051119 SGD
+SGD S000000549 MGR1 GO:0000002 SGD_REF:S000113568|PMID:16267274 IMP P YCL044C gene taxon:4932 20051119 SGD
+SGD S000006019 MGR2 GO:0008372 SGD_REF:S000069584 ND C YPL098C gene taxon:4932 20051119 SGD
+SGD S000006019 MGR2 GO:0005554 SGD_REF:S000069584 ND F YPL098C gene taxon:4932 20051119 SGD
+SGD S000006019 MGR2 GO:0000002 SGD_REF:S000113568|PMID:16267274 IGI P YPL098C gene taxon:4932 20051119 SGD
+SGD S000006019 MGR2 GO:0000002 SGD_REF:S000113568|PMID:16267274 IMP P YPL098C gene taxon:4932 20051119 SGD
+SGD S000005162 MGS1 GO:0005634 SGD_REF:S000071762|PMID:12436259 IC GO:0006275 C YNL218W gene taxon:4932 20030225 SGD
+SGD S000005162 MGS1 GO:0004386 SGD_REF:S000039134|PMID:10077188 ISS F YNL218W gene taxon:4932 20011205 SGD
+SGD S000005162 MGS1 GO:0016887 SGD_REF:S000060955|PMID:11459965 IDA F YNL218W gene taxon:4932 20011205 SGD
+SGD S000005162 MGS1 GO:0006260 SGD_REF:S000060955|PMID:11459965 IMP P YNL218W gene taxon:4932 20011205 SGD
+SGD S000005162 MGS1 GO:0006260 SGD_REF:S000060955|PMID:11459965 IGI P YNL218W gene taxon:4932 20011205 SGD
+SGD S000005162 MGS1 GO:0006275 SGD_REF:S000071762|PMID:12436259 IGI P YNL218W gene taxon:4932 20030225 SGD
+SGD S000005162 MGS1 GO:0006275 SGD_REF:S000071762|PMID:12436259 ISS P YNL218W gene taxon:4932 20030225 SGD
+SGD S000002359 MGT1 GO:0005634 SGD_REF:S000053642|PMID:1641326 IC GO:0006307 C 6-O-methylguanine-DNA methylase YDL200C|MGMT gene taxon:4932 20021114 SGD
+SGD S000002359 MGT1 GO:0003908 SGD_REF:S000043946|PMID:2065659 IDA F 6-O-methylguanine-DNA methylase YDL200C|MGMT gene taxon:4932 20020930 SGD
+SGD S000002359 MGT1 GO:0003908 SGD_REF:S000064085|PMID:2403555 IDA F 6-O-methylguanine-DNA methylase YDL200C|MGMT gene taxon:4932 20040525 SGD
+SGD S000002359 MGT1 GO:0006307 SGD_REF:S000053642|PMID:1641326 IMP P 6-O-methylguanine-DNA methylase YDL200C|MGMT gene taxon:4932 20020930 SGD
+SGD S000003578 MHP1 GO:0005874 SGD_REF:S000052352|PMID:8947554 IDA C microtubule-associated protein (MAP) (putative) YJL042W gene taxon:4932 20010118 SGD
+SGD S000003578 MHP1 GO:0005200 SGD_REF:S000052682|PMID:9855114 IDA F microtubule-associated protein (MAP) (putative) YJL042W gene taxon:4932 20021126 SGD
+SGD S000003578 MHP1 GO:0007026 SGD_REF:S000052682|PMID:9855114 IMP P microtubule-associated protein (MAP) (putative) YJL042W gene taxon:4932 20010118 SGD
+SGD S000003578 MHP1 GO:0007047 SGD_REF:S000047618|PMID:9090049 IMP P microtubule-associated protein (MAP) (putative) YJL042W gene taxon:4932 20010118 SGD
+SGD S000002704 MHR1 GO:0005634 SGD_REF:S000069969|PMID:12034822 IDA C YDR296W|XTC1 gene taxon:4932 20020806 SGD
+SGD S000002704 MHR1 GO:0005739 SGD_REF:S000069969|PMID:12034822 IDA C YDR296W|XTC1 gene taxon:4932 20020806 SGD
+SGD S000002704 MHR1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YDR296W|XTC1 gene taxon:4932 20040924 SGD
+SGD S000002704 MHR1 GO:0030528 SGD_REF:S000069969|PMID:12034822 TAS F YDR296W|XTC1 gene taxon:4932 20020806 SGD
+SGD S000002704 MHR1 GO:0000002 SGD_REF:S000069969|PMID:12034822 IDA P YDR296W|XTC1 gene taxon:4932 20020806 SGD
+SGD S000003985 MHT1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C S-Methylmethionine Homocysteine methylTransferase YLL062C gene taxon:4932 20031028 SGD
+SGD S000003985 MHT1 GO:0008898 SGD_REF:S000066027|PMID:11013242 IDA F S-Methylmethionine Homocysteine methylTransferase YLL062C gene taxon:4932 20020801 SGD
+SGD S000003985 MHT1 GO:0000096 SGD_REF:S000066027|PMID:11013242 IMP P S-Methylmethionine Homocysteine methylTransferase YLL062C gene taxon:4932 20020801 SGD
+SGD S000001678 MIA40 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YKL195W|FMP15|TIM40 gene taxon:4932 20031028 SGD
+SGD S000001678 MIA40 GO:0005739 SGD_REF:S000075214|PMID:14690591 IDA C YKL195W|FMP15|TIM40 gene taxon:4932 20031231 SGD
+SGD S000001678 MIA40 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YKL195W|FMP15|TIM40 gene taxon:4932 20040924 SGD
+SGD S000001678 MIA40 GO:0005743 SGD_REF:S000080487|PMID:15364952 IDA C YKL195W|FMP15|TIM40 gene taxon:4932 20050208 SGD
+SGD S000001678 MIA40 GO:0005758 SGD_REF:S000077205|PMID:15359280 IDA C YKL195W|FMP15|TIM40 gene taxon:4932 20060515 SGD
+SGD S000001678 MIA40 GO:0005554 SGD_REF:S000069584 ND F YKL195W|FMP15|TIM40 gene taxon:4932 20021126 SGD
+SGD S000001678 MIA40 GO:0006605 SGD_REF:S000075214|PMID:14690591 IPI SGD:S000000912|SGD:S000004816 P YKL195W|FMP15|TIM40 gene taxon:4932 20031231 SGD
+SGD S000001678 MIA40 GO:0045041 SGD_REF:S000077205|PMID:15359280 IMP P YKL195W|FMP15|TIM40 gene taxon:4932 20041004 SGD
+SGD S000001678 MIA40 GO:0045041 SGD_REF:S000080487|PMID:15364952 IMP P YKL195W|FMP15|TIM40 gene taxon:4932 20050208 SGD
+SGD S000005235 MID1 GO:0005783 SGD_REF:S000075534|PMID:14729456 IDA C N-glycosylated integral plasma membrane protein YNL291C gene taxon:4932 20041007 SGD
+SGD S000005235 MID1 GO:0005886 SGD_REF:S000052677|PMID:10958666 IDA C N-glycosylated integral plasma membrane protein YNL291C gene taxon:4932 20021003 SGD
+SGD S000005235 MID1 contributes_to GO:0005262 SGD_REF:S000052677|PMID:10958666 IMP F N-glycosylated integral plasma membrane protein YNL291C gene taxon:4932 20050128 SGD
+SGD S000005235 MID1 contributes_to GO:0015275 SGD_REF:S000046805|PMID:10436155 IDA F N-glycosylated integral plasma membrane protein YNL291C gene taxon:4932 20050128 SGD
+SGD S000005235 MID1 GO:0006816 SGD_REF:S000052677|PMID:10958666 IDA P N-glycosylated integral plasma membrane protein YNL291C gene taxon:4932 20021003 SGD
+SGD S000004324 MID2 GO:0005887 SGD_REF:S000052074|PMID:10348843 IDA C YLR332W|KAI1 gene taxon:4932 20020618 SGD
+SGD S000004324 MID2 GO:0004888 SGD_REF:S000048543|PMID:10330137 IGI F YLR332W|KAI1 gene taxon:4932 20030708 SGD
+SGD S000004324 MID2 GO:0004888 SGD_REF:S000048543|PMID:10330137 ISS F YLR332W|KAI1 gene taxon:4932 20030708 SGD
+SGD S000004324 MID2 GO:0004888 SGD_REF:S000048543|PMID:10330137 IMP F YLR332W|KAI1 gene taxon:4932 20030708 SGD
+SGD S000004324 MID2 GO:0000767 SGD_REF:S000048543|PMID:10330137 IGI P YLR332W|KAI1 gene taxon:4932 20030708 SGD
+SGD S000004324 MID2 GO:0000767 SGD_REF:S000048543|PMID:10330137 IMP P YLR332W|KAI1 gene taxon:4932 20030708 SGD
+SGD S000004324 MID2 GO:0006970 SGD_REF:S000074629|PMID:14871941 IGI SGD:S000004478 P YLR332W|KAI1 gene taxon:4932 20050505 SGD
+SGD S000004324 MID2 GO:0007047 SGD_REF:S000059326|PMID:11014808 IMP P YLR332W|KAI1 gene taxon:4932 20020618 SGD
+SGD S000004324 MID2 GO:0007047 SGD_REF:S000052074|PMID:10348843 IGI SGD:S000000201|SGD:S000006369|SGD:S000005534 P YLR332W|KAI1 gene taxon:4932 20021108 SGD
+SGD S000001572 MIF2 GO:0000778 SGD_REF:S000053236|PMID:10189365 TAS C YKL089W gene taxon:4932 20021015 SGD
+SGD S000001572 MIF2 GO:0005634 SGD_REF:S000053236|PMID:10189365 TAS C YKL089W gene taxon:4932 20021015 SGD
+SGD S000001572 MIF2 GO:0019237 SGD_REF:S000059407|PMID:11070082 TAS F YKL089W gene taxon:4932 20021015 SGD
+SGD S000001572 MIF2 GO:0007059 SGD_REF:S000045933|PMID:8408221 IMP P YKL089W gene taxon:4932 20050329 SGD
+SGD S000001572 MIF2 GO:0030472 SGD_REF:S000045933|PMID:8408221 IMP P YKL089W gene taxon:4932 20030113 SGD
+SGD S000003003 MIG1 GO:0005634 SGD_REF:S000069459|PMID:11914276 IDA C C2H2 zinc finger protein that resembles the mammalian Egr and Wilms tumour proteins YGL035C|CAT4|SSN1|TDS22 gene taxon:4932 20020507 SGD
+SGD S000003003 MIG1 GO:0005634 SGD_REF:S000050919|PMID:9285828 IDA C C2H2 zinc finger protein that resembles the mammalian Egr and Wilms tumour proteins YGL035C|CAT4|SSN1|TDS22 gene taxon:4932 20021202 SGD
+SGD S000003003 MIG1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C C2H2 zinc finger protein that resembles the mammalian Egr and Wilms tumour proteins YGL035C|CAT4|SSN1|TDS22 gene taxon:4932 20020507 SGD
+SGD S000003003 MIG1 GO:0005737 SGD_REF:S000050919|PMID:9285828 IDA C C2H2 zinc finger protein that resembles the mammalian Egr and Wilms tumour proteins YGL035C|CAT4|SSN1|TDS22 gene taxon:4932 20021202 SGD
+SGD S000003003 MIG1 GO:0003704 SGD_REF:S000043150|PMID:9832517 TAS F C2H2 zinc finger protein that resembles the mammalian Egr and Wilms tumour proteins YGL035C|CAT4|SSN1|TDS22 gene taxon:4932 20021202 SGD
+SGD S000003003 MIG1 GO:0006006 SGD_REF:S000043150|PMID:9832517 TAS P C2H2 zinc finger protein that resembles the mammalian Egr and Wilms tumour proteins YGL035C|CAT4|SSN1|TDS22 gene taxon:4932 20021202 SGD
+SGD S000003003 MIG1 GO:0006357 SGD_REF:S000043150|PMID:9832517 TAS P C2H2 zinc finger protein that resembles the mammalian Egr and Wilms tumour proteins YGL035C|CAT4|SSN1|TDS22 gene taxon:4932 20021202 SGD
+SGD S000003177 MIG2 GO:0005634 SGD_REF:S000043150|PMID:9832517 TAS C contains zinc fingers very similar to zinc fingers in Mig1p YGL209W|MLZ1 gene taxon:4932 20021202 SGD
+SGD S000003177 MIG2 GO:0003704 SGD_REF:S000043150|PMID:9832517 TAS F contains zinc fingers very similar to zinc fingers in Mig1p YGL209W|MLZ1 gene taxon:4932 20021202 SGD
+SGD S000003177 MIG2 GO:0006006 SGD_REF:S000043150|PMID:9832517 TAS P contains zinc fingers very similar to zinc fingers in Mig1p YGL209W|MLZ1 gene taxon:4932 20021202 SGD
+SGD S000003177 MIG2 GO:0006357 SGD_REF:S000043150|PMID:9832517 TAS P contains zinc fingers very similar to zinc fingers in Mig1p YGL209W|MLZ1 gene taxon:4932 20021202 SGD
+SGD S000000830 MIG3 GO:0005634 SGD_REF:S000071146|PMID:12239282 IDA C DNA binding transcription co-repressor YER028C gene taxon:4932 20021122 SGD
+SGD S000000830 MIG3 GO:0003677 SGD_REF:S000071146|PMID:12239282 IDA F DNA binding transcription co-repressor YER028C gene taxon:4932 20021122 SGD
+SGD S000000830 MIG3 GO:0003700 SGD_REF:S000071146|PMID:12239282 TAS F DNA binding transcription co-repressor YER028C gene taxon:4932 20021122 SGD
+SGD S000000830 MIG3 GO:0016566 SGD_REF:S000043150|PMID:9832517 IPI F DNA binding transcription co-repressor YER028C gene taxon:4932 20040311 SGD
+SGD S000000830 MIG3 GO:0016566 SGD_REF:S000075549|PMID:14993292 IGI F DNA binding transcription co-repressor YER028C gene taxon:4932 20040311 SGD
+SGD S000000830 MIG3 GO:0016566 SGD_REF:S000075549|PMID:14993292 ISS F DNA binding transcription co-repressor YER028C gene taxon:4932 20040311 SGD
+SGD S000000830 MIG3 GO:0000122 SGD_REF:S000075549|PMID:14993292 IGI P DNA binding transcription co-repressor YER028C gene taxon:4932 20040311 SGD
+SGD S000000830 MIG3 GO:0006352 SGD_REF:S000071146|PMID:12239282 TAS P DNA binding transcription co-repressor YER028C gene taxon:4932 20021122 SGD
+SGD S000000830 MIG3 GO:0006974 SGD_REF:S000075549|PMID:14993292 IGI P DNA binding transcription co-repressor YER028C gene taxon:4932 20040311 SGD
+SGD S000004639 MIH1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C protein phosphatase YMR036C gene taxon:4932 20031028 SGD
+SGD S000004639 MIH1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C protein phosphatase YMR036C gene taxon:4932 20031028 SGD
+SGD S000004639 MIH1 GO:0004725 SGD_REF:S000040024|PMID:2649252 ISS F protein phosphatase YMR036C gene taxon:4932 20020820 SGD
+SGD S000004639 MIH1 GO:0000079 SGD_REF:S000040024|PMID:2649252 IMP P protein phosphatase YMR036C gene taxon:4932 20020321 SGD
+SGD S000004639 MIH1 GO:0000079 SGD_REF:S000040024|PMID:2649252 IGI P protein phosphatase YMR036C gene taxon:4932 20020321 SGD
+SGD S000004639 MIH1 GO:0000086 SGD_REF:S000040024|PMID:2649252 IGI P protein phosphatase YMR036C gene taxon:4932 20050902 SGD
+SGD S000004639 MIH1 GO:0000086 SGD_REF:S000040024|PMID:2649252 ISS P protein phosphatase YMR036C gene taxon:4932 20050902 SGD
+SGD S000004639 MIH1 GO:0000086 SGD_REF:S000040024|PMID:2649252 IMP P protein phosphatase YMR036C gene taxon:4932 20050902 SGD
+SGD S000005386 MIM1 GO:0005741 SGD_REF:S000077462|PMID:15326197 IDA C YOL026C|TOM13 gene taxon:4932 20050214 SGD
+SGD S000005386 MIM1 GO:0031307 SGD_REF:S000081337|PMID:15608614 IDA C YOL026C|TOM13 gene taxon:4932 20050419 SGD
+SGD S000005386 MIM1 GO:0005554 SGD_REF:S000069584 ND F YOL026C|TOM13 gene taxon:4932 20030203 SGD
+SGD S000005386 MIM1 GO:0006461 SGD_REF:S000081337|PMID:15608614 IMP P YOL026C|TOM13 gene taxon:4932 20050419 SGD
+SGD S000005386 MIM1 GO:0006626 SGD_REF:S000076598|PMID:15242642 IMP P YOL026C|TOM13 gene taxon:4932 20040713 SGD
+SGD S000005386 MIM1 GO:0006626 SGD_REF:S000081337|PMID:15608614 IMP P YOL026C|TOM13 gene taxon:4932 20050419 SGD
+SGD S000005857 MIP1 GO:0005739 SGD_REF:S000048890|PMID:10567545 IDA C mitochondrial DNA polymerase catalytic subunit YOR330C gene taxon:4932 20030213 SGD
+SGD S000005857 MIP1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C mitochondrial DNA polymerase catalytic subunit YOR330C gene taxon:4932 20040924 SGD
+SGD S000005857 MIP1 GO:0003895 SGD_REF:S000058372|PMID:9745046 TAS F mitochondrial DNA polymerase catalytic subunit YOR330C gene taxon:4932 20010118 SGD
+SGD S000005857 MIP1 GO:0006261 SGD_REF:S000048961|PMID:2684980 IMP P mitochondrial DNA polymerase catalytic subunit YOR330C gene taxon:4932 20030213 SGD
+SGD S000005857 MIP1 GO:0006261 SGD_REF:S000070276|PMID:12023279 IDA P mitochondrial DNA polymerase catalytic subunit YOR330C gene taxon:4932 20030213 SGD
+SGD S000005857 MIP1 GO:0006264 SGD_REF:S000070276|PMID:12023279 IDA P mitochondrial DNA polymerase catalytic subunit YOR330C gene taxon:4932 20050207 SGD
+SGD S000001057 MIP6 GO:0005643 SGD_REF:S000042202|PMID:9214641 IPI C YHR015W gene taxon:4932 20020820 SGD
+SGD S000001057 MIP6 GO:0003723 SGD_REF:S000042202|PMID:9214641 ISS F YHR015W gene taxon:4932 20020820 SGD
+SGD S000001057 MIP6 GO:0006406 SGD_REF:S000042202|PMID:9214641 IPI P YHR015W gene taxon:4932 20020820 SGD
+SGD S000003838 MIR1 GO:0005739 SGD_REF:S000069459|PMID:11914276 IDA C YJR077C gene taxon:4932 20020507 SGD
+SGD S000003838 MIR1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YJR077C gene taxon:4932 20040924 SGD
+SGD S000003838 MIR1 GO:0005740 SGD_REF:S000042082|PMID:8245029 IDA C YJR077C gene taxon:4932 20010118 SGD
+SGD S000003838 MIR1 GO:0005740 SGD_REF:S000045388|PMID:2170848 IDA C YJR077C gene taxon:4932 20010118 SGD
+SGD S000003838 MIR1 GO:0005315 SGD_REF:S000058074|PMID:9099701 IDA F YJR077C gene taxon:4932 20010118 SGD
+SGD S000003838 MIR1 GO:0006817 SGD_REF:S000058074|PMID:9099701 IDA P YJR077C gene taxon:4932 20010118 SGD
+SGD S000000288 MIS1 GO:0005739 SGD_REF:S000051219|PMID:3528153 IDA C C1-tetrahydrofolate synthase YBR084W gene taxon:4932 20010118 SGD
+SGD S000000288 MIS1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C C1-tetrahydrofolate synthase YBR084W gene taxon:4932 20040924 SGD
+SGD S000000288 MIS1 GO:0004329 SGD_REF:S000051219|PMID:3528153 IDA F C1-tetrahydrofolate synthase YBR084W gene taxon:4932 20010118 SGD
+SGD S000000288 MIS1 GO:0004477 SGD_REF:S000051219|PMID:3528153 IDA F C1-tetrahydrofolate synthase YBR084W gene taxon:4932 20010118 SGD
+SGD S000000288 MIS1 GO:0004488 SGD_REF:S000051219|PMID:3528153 IDA F C1-tetrahydrofolate synthase YBR084W gene taxon:4932 20010118 SGD
+SGD S000000288 MIS1 GO:0001718 SGD_REF:S000039777|PMID:10781559 IMP P C1-tetrahydrofolate synthase YBR084W gene taxon:4932 20021205 SGD
+SGD S000000288 MIS1 GO:0006139 SGD_REF:S000039777|PMID:10781559 IMP P C1-tetrahydrofolate synthase YBR084W gene taxon:4932 20021205 SGD
+SGD S000000288 MIS1 GO:0019415 SGD_REF:S000051219|PMID:3528153 IDA P C1-tetrahydrofolate synthase YBR084W gene taxon:4932 20040409 SGD
+SGD S000000288 MIS1 GO:0019653 SGD_REF:S000051219|PMID:3528153 IDA P C1-tetrahydrofolate synthase YBR084W gene taxon:4932 20040409 SGD
+SGD S000000288 MIS1 GO:0046656 SGD_REF:S000051219|PMID:3528153 IDA P C1-tetrahydrofolate synthase YBR084W gene taxon:4932 20040409 SGD
+SGD S000002551 MKC7 GO:0009277 SGD_REF:S000040179|PMID:10383953 IDA C aspartyl protease, related to Yap3p, yapsin 2 YDR144C|YPS2 gene taxon:4932 20020617 SGD
+SGD S000002551 MKC7 GO:0009049 SGD_REF:S000050704|PMID:10446224 IDA F aspartyl protease, related to Yap3p, yapsin 2 YDR144C|YPS2 gene taxon:4932 20020930 SGD
+SGD S000002551 MKC7 GO:0006508 SGD_REF:S000048889|PMID:7479877 IMP P aspartyl protease, related to Yap3p, yapsin 2 YDR144C|YPS2 gene taxon:4932 20020930 SGD
+SGD S000005757 MKK1 GO:0005934 SGD_REF:S000073832|PMID:12361575 IDA C MAP kinase kinase (MEK) YOR231W|SSP32 gene taxon:4932 20030827 SGD
+SGD S000005757 MKK1 GO:0004708 SGD_REF:S000046946|PMID:8386320 ISS F MAP kinase kinase (MEK) YOR231W|SSP32 gene taxon:4932 20010118 SGD
+SGD S000005757 MKK1 GO:0006468 SGD_REF:S000046946|PMID:8386320 ISS P MAP kinase kinase (MEK) YOR231W|SSP32 gene taxon:4932 20010118 SGD
+SGD S000005757 MKK1 GO:0007165 SGD_REF:S000046946|PMID:8386320 IMP P MAP kinase kinase (MEK) YOR231W|SSP32 gene taxon:4932 20010118 SGD
+SGD S000006061 MKK2 GO:0005622 SGD_REF:S000043521|PMID:10361272 TAS C protein kinase YPL140C|LPI6|SSP33 gene taxon:4932 20030327 SGD
+SGD S000006061 MKK2 GO:0004708 SGD_REF:S000046946|PMID:8386320 ISS F protein kinase YPL140C|LPI6|SSP33 gene taxon:4932 20010118 SGD
+SGD S000006061 MKK2 GO:0006468 SGD_REF:S000046946|PMID:8386320 ISS P protein kinase YPL140C|LPI6|SSP33 gene taxon:4932 20010118 SGD
+SGD S000006061 MKK2 GO:0007165 SGD_REF:S000046946|PMID:8386320 IMP P protein kinase YPL140C|LPI6|SSP33 gene taxon:4932 20010118 SGD
+SGD S000005020 MKS1 GO:0005622 SGD_REF:S000070242|PMID:11882290 IC GO:0016564 C negative transcriptional regulator YNL076W|LYS80 gene taxon:4932 20030508 SGD
+SGD S000005020 MKS1 GO:0016564 SGD_REF:S000070242|PMID:11882290 IDA F negative transcriptional regulator YNL076W|LYS80 gene taxon:4932 20030508 SGD
+SGD S000005020 MKS1 GO:0006808 SGD_REF:S000039352|PMID:10511541 IMP P negative transcriptional regulator YNL076W|LYS80 gene taxon:4932 20020725 SGD
+SGD S000005020 MKS1 GO:0031930 SGD_REF:S000074762|PMID:14536080 IPI SGD:S000003221 P negative transcriptional regulator YNL076W|LYS80 gene taxon:4932 20051130 SGD
+SGD S000005029 MKT1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C retroviral protease signature protein YNL085W gene taxon:4932 20031028 SGD
+SGD S000005029 MKT1 GO:0005844 SGD_REF:S000076382|PMID:15082763 IDA C retroviral protease signature protein YNL085W gene taxon:4932 20040903 SGD
+SGD S000005029 MKT1 GO:0004518 SGD_REF:S000076382|PMID:15082763 ISS F retroviral protease signature protein YNL085W gene taxon:4932 20040903 SGD
+SGD S000005029 MKT1 GO:0044419 SGD_REF:S000046750|PMID:7532890 IMP P retroviral protease signature protein YNL085W gene taxon:4932 20051114 SGD
+SGD S000005029 MKT1 GO:0045946 SGD_REF:S000076382|PMID:15082763 IMP P retroviral protease signature protein YNL085W gene taxon:4932 20051114 SGD
+SGD S000005029 MKT1 GO:0045946 SGD_REF:S000076382|PMID:15082763 IPI P retroviral protease signature protein YNL085W gene taxon:4932 20051114 SGD
+SGD S000003074 MLC1 GO:0030478 SGD_REF:S000041005|PMID:10652251 IPI C myosin Myo2p light chain YGL106W gene taxon:4932 20010118 SGD
+SGD S000003074 MLC1 GO:0000146 SGD_REF:S000039464|PMID:9700160 IPI F myosin Myo2p light chain YGL106W gene taxon:4932 20010118 SGD
+SGD S000003074 MLC1 GO:0000001 SGD_REF:S000041005|PMID:10652251 TAS P myosin Myo2p light chain YGL106W gene taxon:4932 20010118 SGD
+SGD S000003074 MLC1 GO:0000011 SGD_REF:S000041005|PMID:10652251 TAS P myosin Myo2p light chain YGL106W gene taxon:4932 20010118 SGD
+SGD S000003074 MLC1 GO:0000910 SGD_REF:S000041005|PMID:10652251 IMP P myosin Myo2p light chain YGL106W gene taxon:4932 20010119 SGD
+SGD S000003074 MLC1 GO:0006897 SGD_REF:S000041005|PMID:10652251 IPI P myosin Myo2p light chain YGL106W gene taxon:4932 20010118 SGD
+SGD S000003074 MLC1 GO:0007118 SGD_REF:S000041005|PMID:10652251 IPI P myosin Myo2p light chain YGL106W gene taxon:4932 20010118 SGD
+SGD S000003074 MLC1 GO:0007119 SGD_REF:S000041005|PMID:10652251 IPI P myosin Myo2p light chain YGL106W gene taxon:4932 20010118 SGD
+SGD S000003074 MLC1 GO:0016192 SGD_REF:S000041005|PMID:10652251 IPI P myosin Myo2p light chain YGL106W gene taxon:4932 20010118 SGD
+SGD S000003074 MLC1 GO:0030468 SGD_REF:S000041005|PMID:10652251 IPI P myosin Myo2p light chain YGL106W gene taxon:4932 20010302 SGD
+SGD S000006392 MLC2 GO:0000142 SGD_REF:S000076268|PMID:15210731 IDA C light chain for Myo1p YPR188C gene taxon:4932 20040629 SGD
+SGD S000006392 MLC2 GO:0045159 SGD_REF:S000076268|PMID:15210731 IPI SGD:S000001065 F light chain for Myo1p YPR188C gene taxon:4932 20040722 SGD
+SGD S000006392 MLC2 GO:0000916 SGD_REF:S000076268|PMID:15210731 IMP P light chain for Myo1p YPR188C gene taxon:4932 20040722 SGD
+SGD S000005018 MLF3 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YNL074C|YMK1 gene taxon:4932 20031028 SGD
+SGD S000005018 MLF3 GO:0005554 SGD_REF:S000069584 ND F YNL074C|YMK1 gene taxon:4932 20021011 SGD
+SGD S000005018 MLF3 GO:0042493 SGD_REF:S000052849|PMID:9805003 IMP P YNL074C|YMK1 gene taxon:4932 20021106 SGD
+SGD S000004777 MLH1 GO:0005634 SGD_REF:S000068890|PMID:11689704 IMP C mutL homolog YMR167W|PMS2 gene taxon:4932 20021028 SGD
+SGD S000004777 MLH1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C mutL homolog YMR167W|PMS2 gene taxon:4932 20040928 SGD
+SGD S000004777 MLH1 GO:0003677 SGD_REF:S000065918|PMID:11575920 IDA F mutL homolog YMR167W|PMS2 gene taxon:4932 20021029 SGD
+SGD S000004777 MLH1 GO:0005524 SGD_REF:S000054482|PMID:10082584 ISS F mutL homolog YMR167W|PMS2 gene taxon:4932 20021029 SGD
+SGD S000004777 MLH1 GO:0016887 SGD_REF:S000054482|PMID:10082584 ISS F mutL homolog YMR167W|PMS2 gene taxon:4932 20021029 SGD
+SGD S000004777 MLH1 GO:0007131 SGD_REF:S000069490|PMID:11901110 TAS P mutL homolog YMR167W|PMS2 gene taxon:4932 20021029 SGD
+SGD S000004025 MLH2 GO:0005634 SGD_REF:S000071499|PMID:12200140 IPI SGD:S000004777 C YLR035C gene taxon:4932 20021029 SGD
+SGD S000004025 MLH2 GO:0005554 SGD_REF:S000042567|PMID:10679328 TAS F YLR035C gene taxon:4932 20021029 SGD
+SGD S000004025 MLH2 GO:0006281 SGD_REF:S000042567|PMID:10679328 IDA P YLR035C gene taxon:4932 20030122 SGD
+SGD S000006085 MLH3 GO:0005634 SGD_REF:S000055563|PMID:10570173 IPI SGD:S000004777|SGD:S000005026 C YPL164C gene taxon:4932 20021029 SGD
+SGD S000006085 MLH3 GO:0005554 SGD_REF:S000069584 ND F YPL164C gene taxon:4932 20020822 SGD
+SGD S000006085 MLH3 GO:0006298 SGD_REF:S000047209|PMID:9770499 IMP P YPL164C gene taxon:4932 20020822 SGD
+SGD S000006085 MLH3 GO:0007131 SGD_REF:S000069490|PMID:11901110 TAS P YPL164C gene taxon:4932 20021029 SGD
+SGD S000001803 MLP1 GO:0005635 SGD_REF:S000040348|PMID:10085285 IDA C colied-coil protein (putative), similar to myosin and TPR YKR095W|MPL1 gene taxon:4932 20010118 SGD
+SGD S000001803 MLP1 GO:0005654 SGD_REF:S000040348|PMID:10085285 IDA C colied-coil protein (putative), similar to myosin and TPR YKR095W|MPL1 gene taxon:4932 20010118 SGD
+SGD S000001803 MLP1 colocalizes_with GO:0030529 SGD_REF:S000081415|PMID:15692572 IPI SGD:S000002789|SGD:S000003090 C colied-coil protein (putative), similar to myosin and TPR YKR095W|MPL1 gene taxon:4932 20051102 SGD
+SGD S000001803 MLP1 GO:0043021 SGD_REF:S000081415|PMID:15692572 IGI F colied-coil protein (putative), similar to myosin and TPR YKR095W|MPL1 gene taxon:4932 20050427 SGD
+SGD S000001803 MLP1 GO:0043021 SGD_REF:S000081415|PMID:15692572 IPI F colied-coil protein (putative), similar to myosin and TPR YKR095W|MPL1 gene taxon:4932 20050427 SGD
+SGD S000001803 MLP1 GO:0006406 SGD_REF:S000081415|PMID:15692572 IGI P colied-coil protein (putative), similar to myosin and TPR YKR095W|MPL1 gene taxon:4932 20050427 SGD
+SGD S000001803 MLP1 GO:0006406 SGD_REF:S000086641|PMID:16162818 IGI P colied-coil protein (putative), similar to myosin and TPR YKR095W|MPL1 gene taxon:4932 20050923 SGD
+SGD S000001803 MLP1 GO:0006406 SGD_REF:S000086641|PMID:16162818 IMP P colied-coil protein (putative), similar to myosin and TPR YKR095W|MPL1 gene taxon:4932 20050923 SGD
+SGD S000001803 MLP1 GO:0006406 SGD_REF:S000081415|PMID:15692572 IPI P colied-coil protein (putative), similar to myosin and TPR YKR095W|MPL1 gene taxon:4932 20050427 SGD
+SGD S000001803 MLP1 GO:0006606 SGD_REF:S000040348|PMID:10085285 IGI P colied-coil protein (putative), similar to myosin and TPR YKR095W|MPL1 gene taxon:4932 20050427 SGD
+SGD S000001803 MLP1 GO:0045449 SGD_REF:S000081415|PMID:15692572 IGI P colied-coil protein (putative), similar to myosin and TPR YKR095W|MPL1 gene taxon:4932 20050427 SGD
+SGD S000001803 MLP1 GO:0045449 SGD_REF:S000081415|PMID:15692572 IEP P colied-coil protein (putative), similar to myosin and TPR YKR095W|MPL1 gene taxon:4932 20050427 SGD
+SGD S000001411 MLP2 GO:0005635 SGD_REF:S000040348|PMID:10085285 IDA C coiled-coil protein (putative), similar to myosin and TPR YIL149C gene taxon:4932 20010118 SGD
+SGD S000001411 MLP2 GO:0005654 SGD_REF:S000040348|PMID:10085285 IDA C coiled-coil protein (putative), similar to myosin and TPR YIL149C gene taxon:4932 20010118 SGD
+SGD S000001411 MLP2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C coiled-coil protein (putative), similar to myosin and TPR YIL149C gene taxon:4932 20040928 SGD
+SGD S000001411 MLP2 colocalizes_with GO:0030529 SGD_REF:S000081415|PMID:15692572 IPI SGD:S000002789|SGD:S000003090 C coiled-coil protein (putative), similar to myosin and TPR YIL149C gene taxon:4932 20051102 SGD
+SGD S000001411 MLP2 GO:0043021 SGD_REF:S000081415|PMID:15692572 IGI F coiled-coil protein (putative), similar to myosin and TPR YIL149C gene taxon:4932 20050427 SGD
+SGD S000001411 MLP2 GO:0043021 SGD_REF:S000081415|PMID:15692572 IPI F coiled-coil protein (putative), similar to myosin and TPR YIL149C gene taxon:4932 20050427 SGD
+SGD S000001411 MLP2 GO:0006406 SGD_REF:S000081415|PMID:15692572 IGI P coiled-coil protein (putative), similar to myosin and TPR YIL149C gene taxon:4932 20050427 SGD
+SGD S000001411 MLP2 GO:0006406 SGD_REF:S000081415|PMID:15692572 IPI P coiled-coil protein (putative), similar to myosin and TPR YIL149C gene taxon:4932 20050427 SGD
+SGD S000001411 MLP2 GO:0006606 SGD_REF:S000040348|PMID:10085285 IGI P coiled-coil protein (putative), similar to myosin and TPR YIL149C gene taxon:4932 20050427 SGD
+SGD S000001411 MLP2 GO:0045449 SGD_REF:S000081415|PMID:15692572 IGI P coiled-coil protein (putative), similar to myosin and TPR YIL149C gene taxon:4932 20050427 SGD
+SGD S000001411 MLP2 GO:0045449 SGD_REF:S000081415|PMID:15692572 IEP P coiled-coil protein (putative), similar to myosin and TPR YIL149C gene taxon:4932 20050427 SGD
+SGD S000005061 MLS1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C carbon-catabolite sensitive malate synthase YNL117W gene taxon:4932 20020507 SGD
+SGD S000005061 MLS1 GO:0005782 SGD_REF:S000058494 TAS C carbon-catabolite sensitive malate synthase YNL117W gene taxon:4932 20010119 SGD
+SGD S000005061 MLS1 GO:0004474 SGD_REF:S000058494 TAS F carbon-catabolite sensitive malate synthase YNL117W gene taxon:4932 20010119 SGD
+SGD S000005061 MLS1 GO:0006097 SGD_REF:S000058494 TAS P carbon-catabolite sensitive malate synthase YNL117W gene taxon:4932 20010119 SGD
+SGD S000001313 MMF1 GO:0005739 SGD_REF:S000070333|PMID:12185840 TAS C YIL051C|IBM1 gene taxon:4932 20020829 SGD
+SGD S000001313 MMF1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YIL051C|IBM1 gene taxon:4932 20040928 SGD
+SGD S000001313 MMF1 GO:0005759 SGD_REF:S000060983|PMID:11003673 IDA C YIL051C|IBM1 gene taxon:4932 20020926 SGD
+SGD S000001313 MMF1 GO:0005554 SGD_REF:S000069584 ND F YIL051C|IBM1 gene taxon:4932 20020926 SGD
+SGD S000001313 MMF1 GO:0000002 SGD_REF:S000060983|PMID:11003673 IMP P YIL051C|IBM1 gene taxon:4932 20020926 SGD
+SGD S000001313 MMF1 GO:0009097 SGD_REF:S000060859|PMID:11442631 IMP P YIL051C|IBM1 gene taxon:4932 20020926 SGD
+SGD S000003929 MMM1 GO:0005741 SGD_REF:S000059964|PMID:11266455 IDA C mitochondrial outer membrane protein YLL006W|YME6 gene taxon:4932 20021121 SGD
+SGD S000003929 MMM1 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C mitochondrial outer membrane protein YLL006W|YME6 gene taxon:4932 20060317 SGD
+SGD S000003929 MMM1 GO:0005554 SGD_REF:S000069584 ND F mitochondrial outer membrane protein YLL006W|YME6 gene taxon:4932 20021121 SGD
+SGD S000003929 MMM1 GO:0000002 SGD_REF:S000059964|PMID:11266455 IMP P mitochondrial outer membrane protein YLL006W|YME6 gene taxon:4932 20021121 SGD
+SGD S000003929 MMM1 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P mitochondrial outer membrane protein YLL006W|YME6 gene taxon:4932 20060227 SGD
+SGD S000003929 MMM1 GO:0007005 SGD_REF:S000051815|PMID:8089172 IMP P mitochondrial outer membrane protein YLL006W|YME6 gene taxon:4932 20021121 SGD
+SGD S000003984 MMP1 GO:0005886 SGD_REF:S000051126|PMID:10497160 ISS C high affinity S-methylmethionine permease YLL061W gene taxon:4932 20021002 SGD
+SGD S000003984 MMP1 GO:0005886 SGD_REF:S000051126|PMID:10497160 IMP C high affinity S-methylmethionine permease YLL061W gene taxon:4932 20021002 SGD
+SGD S000003984 MMP1 GO:0000100 SGD_REF:S000051126|PMID:10497160 ISS F high affinity S-methylmethionine permease YLL061W gene taxon:4932 20021002 SGD
+SGD S000003984 MMP1 GO:0000100 SGD_REF:S000051126|PMID:10497160 IMP F high affinity S-methylmethionine permease YLL061W gene taxon:4932 20021002 SGD
+SGD S000003984 MMP1 GO:0015806 SGD_REF:S000051126|PMID:10497160 IMP P high affinity S-methylmethionine permease YLL061W gene taxon:4932 20021002 SGD
+SGD S000004180 MMR1 GO:0000131 SGD_REF:S000074060|PMID:13679573 IDA C YLR190W gene taxon:4932 20040115 SGD
+SGD S000004180 MMR1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YLR190W gene taxon:4932 20040928 SGD
+SGD S000004180 MMR1 GO:0005741 SGD_REF:S000080659|PMID:15201867 IDA C YLR190W gene taxon:4932 20050208 SGD
+SGD S000004180 MMR1 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C YLR190W gene taxon:4932 20060317 SGD
+SGD S000004180 MMR1 GO:0005933 SGD_REF:S000074060|PMID:13679573 IDA C YLR190W gene taxon:4932 20040115 SGD
+SGD S000004180 MMR1 GO:0005935 SGD_REF:S000074060|PMID:13679573 IDA C YLR190W gene taxon:4932 20040115 SGD
+SGD S000004180 MMR1 GO:0005554 SGD_REF:S000069584 ND F YLR190W gene taxon:4932 20030418 SGD
+SGD S000004180 MMR1 GO:0000001 SGD_REF:S000080659|PMID:15201867 IMP P YLR190W gene taxon:4932 20050208 SGD
+SGD S000006368 MMS1 GO:0008372 SGD_REF:S000069584 ND C YPR164W|RTT108|SLM6 gene taxon:4932 20021028 SGD
+SGD S000006368 MMS1 GO:0005554 SGD_REF:S000069584 ND F YPR164W|RTT108|SLM6 gene taxon:4932 20021028 SGD
+SGD S000006368 MMS1 GO:0000335 SGD_REF:S000068874|PMID:11779788 IMP P YPR164W|RTT108|SLM6 gene taxon:4932 20020927 SGD
+SGD S000006368 MMS1 GO:0006281 SGD_REF:S000069116|PMID:11810260 IGI P YPR164W|RTT108|SLM6 gene taxon:4932 20030107 SGD
+SGD S000006368 MMS1 GO:0006281 SGD_REF:S000069116|PMID:11810260 IMP P YPR164W|RTT108|SLM6 gene taxon:4932 20030107 SGD
+SGD S000003055 MMS2 GO:0005634 SGD_REF:S000042429|PMID:10880451 IDA C YGL087C gene taxon:4932 20020806 SGD
+SGD S000003055 MMS2 GO:0005737 SGD_REF:S000042429|PMID:10880451 IDA C YGL087C gene taxon:4932 20020806 SGD
+SGD S000003055 MMS2 GO:0031371 SGD_REF:S000050556|PMID:10089880 IPI SGD:S000002499 C YGL087C gene taxon:4932 20051028 SGD
+SGD S000003055 MMS2 contributes_to GO:0004840 SGD_REF:S000050556|PMID:10089880 IDA F YGL087C gene taxon:4932 20051028 SGD
+SGD S000003055 MMS2 GO:0004840 SGD_REF:S000050556|PMID:10089880 ISS F YGL087C gene taxon:4932 20051028 SGD
+SGD S000003055 MMS2 GO:0004840 SGD_REF:S000049026|PMID:9576943 ISS SGD:S000000286|SGD:S000003026 F YGL087C gene taxon:4932 20051028 SGD
+SGD S000003055 MMS2 GO:0000209 SGD_REF:S000050556|PMID:10089880 IDA P YGL087C gene taxon:4932 20051026 SGD
+SGD S000003055 MMS2 GO:0000209 SGD_REF:S000050556|PMID:10089880 IPI P YGL087C gene taxon:4932 20051026 SGD
+SGD S000003055 MMS2 GO:0006301 SGD_REF:S000050556|PMID:10089880 IGI SGD:S000002499 P YGL087C gene taxon:4932 20051028 SGD
+SGD S000003055 MMS2 GO:0006301 SGD_REF:S000049026|PMID:9576943 IGI SGD:S000000662|SGD:S000003026|SGD:S000006088 P YGL087C gene taxon:4932 20051028 SGD
+SGD S000003055 MMS2 GO:0006301 SGD_REF:S000050556|PMID:10089880 IMP P YGL087C gene taxon:4932 20051028 SGD
+SGD S000003055 MMS2 GO:0006301 SGD_REF:S000049026|PMID:9576943 IMP P YGL087C gene taxon:4932 20051028 SGD
+SGD S000003055 MMS2 GO:0006974 SGD_REF:S000076175|PMID:12482937 IMP P YGL087C gene taxon:4932 20060406 SGD
+SGD S000000745 MMS21 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YEL019C gene taxon:4932 20031028 SGD
+SGD S000000745 MMS21 GO:0005635 SGD_REF:S000080949|PMID:15738391 IDA C YEL019C gene taxon:4932 20050321 SGD
+SGD S000000745 MMS21 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YEL019C gene taxon:4932 20031028 SGD
+SGD S000000745 MMS21 GO:0030915 SGD_REF:S000080949|PMID:15738391 IPI SGD:S000000745|SGD:S000005394|SGD:S000004375 C YEL019C gene taxon:4932 20060309 SGD
+SGD S000000745 MMS21 GO:0019789 SGD_REF:S000080949|PMID:15738391 IDA F YEL019C gene taxon:4932 20050321 SGD
+SGD S000000745 MMS21 GO:0019789 SGD_REF:S000080949|PMID:15738391 IMP F YEL019C gene taxon:4932 20050321 SGD
+SGD S000000745 MMS21 GO:0006281 SGD_REF:S000049039|PMID:7788712 IMP P YEL019C gene taxon:4932 20021105 SGD
+SGD S000000745 MMS21 GO:0006281 SGD_REF:S000080949|PMID:15738391 IMP P YEL019C gene taxon:4932 20060309 SGD
+SGD S000004312 MMS22 GO:0005634 SGD_REF:S000080900|PMID:15718301 IDA C YLR320W|SLM2 gene taxon:4932 20050318 SGD
+SGD S000004312 MMS22 GO:0005554 SGD_REF:S000069584 ND F YLR320W|SLM2 gene taxon:4932 20020329 SGD
+SGD S000004312 MMS22 GO:0006302 SGD_REF:S000069458|PMID:11726929 IMP P YLR320W|SLM2 gene taxon:4932 20020927 SGD
+SGD S000000302 MMS4 GO:0005634 SGD_REF:S000044724|PMID:9604884 ISS C YBR098W|SLX2|YBR100W gene taxon:4932 20010118 SGD
+SGD S000000302 MMS4 GO:0003713 SGD_REF:S000044724|PMID:9604884 IDA F YBR098W|SLX2|YBR100W gene taxon:4932 20010118 SGD
+SGD S000000302 MMS4 GO:0004519 SGD_REF:S000068964|PMID:11641278 IDA F YBR098W|SLX2|YBR100W gene taxon:4932 20021001 SGD
+SGD S000000302 MMS4 GO:0006281 SGD_REF:S000044724|PMID:9604884 IMP P YBR098W|SLX2|YBR100W gene taxon:4932 20010118 SGD
+SGD S000000302 MMS4 GO:0007131 SGD_REF:S000068964|PMID:11641278 IGI P YBR098W|SLX2|YBR100W gene taxon:4932 20021001 SGD
+SGD S000004789 MMT1 GO:0005739 SGD_REF:S000040184|PMID:9353309 IDA C mitochondrial metal transporter (putative) YMR177W gene taxon:4932 20020604 SGD
+SGD S000004789 MMT1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C mitochondrial metal transporter (putative) YMR177W gene taxon:4932 20040924 SGD
+SGD S000004789 MMT1 GO:0016021 SGD_REF:S000040184|PMID:9353309 ISS C mitochondrial metal transporter (putative) YMR177W gene taxon:4932 20020604 SGD
+SGD S000004789 MMT1 GO:0005554 SGD_REF:S000069584 ND F mitochondrial metal transporter (putative) YMR177W gene taxon:4932 20020604 SGD
+SGD S000004789 MMT1 GO:0006879 SGD_REF:S000040184|PMID:9353309 IGI P mitochondrial metal transporter (putative) YMR177W gene taxon:4932 20020604 SGD
+SGD S000004789 MMT1 GO:0006879 SGD_REF:S000040184|PMID:9353309 IMP P mitochondrial metal transporter (putative) YMR177W gene taxon:4932 20020604 SGD
+SGD S000006145 MMT2 GO:0005739 SGD_REF:S000040184|PMID:9353309 IDA C YPL224C|MFT2 gene taxon:4932 20020604 SGD
+SGD S000006145 MMT2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YPL224C|MFT2 gene taxon:4932 20040924 SGD
+SGD S000006145 MMT2 GO:0016021 SGD_REF:S000040184|PMID:9353309 ISS C YPL224C|MFT2 gene taxon:4932 20020604 SGD
+SGD S000006145 MMT2 GO:0005554 SGD_REF:S000069584 ND F YPL224C|MFT2 gene taxon:4932 20020604 SGD
+SGD S000006145 MMT2 GO:0006879 SGD_REF:S000040184|PMID:9353309 IGI P YPL224C|MFT2 gene taxon:4932 20020604 SGD
+SGD S000006145 MMT2 GO:0006879 SGD_REF:S000040184|PMID:9353309 IMP P YPL224C|MFT2 gene taxon:4932 20020604 SGD
+SGD S000003151 MND1 GO:0000794 SGD_REF:S000069966|PMID:11940665 IDA C YGL183C gene taxon:4932 20030403 SGD
+SGD S000003151 MND1 GO:0003690 SGD_REF:S000076683|PMID:15249670 IDA F YGL183C gene taxon:4932 20041008 SGD
+SGD S000003151 MND1 GO:0003690 SGD_REF:S000076683|PMID:15249670 IPI F YGL183C gene taxon:4932 20041008 SGD
+SGD S000003151 MND1 GO:0005515 SGD_REF:S000076683|PMID:15249670 IPI SGD:S000003001 F YGL183C gene taxon:4932 20041008 SGD
+SGD S000003151 MND1 GO:0007131 SGD_REF:S000060989|PMID:11470404 IMP P YGL183C gene taxon:4932 20010730 SGD
+SGD S000001464 MND2 GO:0005634 SGD_REF:S000081746|PMID:15797380 IDA C YIR025W gene taxon:4932 20050812 SGD
+SGD S000001464 MND2 GO:0005680 SGD_REF:S000072817|PMID:12574115 IDA C YIR025W gene taxon:4932 20030402 SGD
+SGD S000001464 MND2 GO:0005680 SGD_REF:S000081274|PMID:15797379 IPI C YIR025W gene taxon:4932 20050419 SGD
+SGD S000001464 MND2 GO:0005554 SGD_REF:S000069584 ND F YIR025W gene taxon:4932 20010730 SGD
+SGD S000001464 MND2 GO:0000070 SGD_REF:S000081274|PMID:15797379 IMP P YIR025W gene taxon:4932 20050419 SGD
+SGD S000001464 MND2 GO:0007131 SGD_REF:S000060989|PMID:11470404 IMP P YIR025W gene taxon:4932 20010730 SGD
+SGD S000001464 MND2 GO:0016567 SGD_REF:S000073158|PMID:12609981 IPI P YIR025W gene taxon:4932 20050407 SGD
+SGD S000001464 MND2 GO:0030071 SGD_REF:S000073158|PMID:12609981 IMP P YIR025W gene taxon:4932 20030611 SGD
+SGD S000001464 MND2 GO:0031145 SGD_REF:S000073158|PMID:12609981 IPI P YIR025W gene taxon:4932 20050407 SGD
+SGD S000005877 MNE1 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YOR350C gene taxon:4932 20031028 SGD
+SGD S000005877 MNE1 GO:0005554 SGD_REF:S000069584 ND F YOR350C gene taxon:4932 20021125 SGD
+SGD S000005877 MNE1 GO:0000004 SGD_REF:S000069584 ND P YOR350C gene taxon:4932 20021125 SGD
+SGD S000001247 MNL1 GO:0005783 SGD_REF:S000059976|PMID:11254655 IDA C YHR204W|HTM1 gene taxon:4932 20020820 SGD
+SGD S000001247 MNL1 GO:0030246 SGD_REF:S000060356|PMID:11375935 ISS F YHR204W|HTM1 gene taxon:4932 20020820 SGD
+SGD S000001247 MNL1 GO:0030246 SGD_REF:S000060356|PMID:11375935 IMP F YHR204W|HTM1 gene taxon:4932 20020820 SGD
+SGD S000001247 MNL1 GO:0030433 SGD_REF:S000060356|PMID:11375935 IMP P YHR204W|HTM1 gene taxon:4932 20020820 SGD
+SGD S000001247 MNL1 GO:0030433 SGD_REF:S000059976|PMID:11254655 IMP P YHR204W|HTM1 gene taxon:4932 20020820 SGD
+SGD S000000803 MNN1 GO:0005794 SGD_REF:S000039589|PMID:7962051 IDA C alpha-1,3-mannosyltransferase YER001W gene taxon:4932 20010118 SGD
+SGD S000000803 MNN1 GO:0000033 SGD_REF:S000056275|PMID:8146181 IMP F alpha-1,3-mannosyltransferase YER001W gene taxon:4932 20010118 SGD
+SGD S000000803 MNN1 GO:0006491 SGD_REF:S000056275|PMID:8146181 IMP P alpha-1,3-mannosyltransferase YER001W gene taxon:4932 20010118 SGD
+SGD S000000803 MNN1 GO:0006493 SGD_REF:S000039589|PMID:7962051 IDA P alpha-1,3-mannosyltransferase YER001W gene taxon:4932 20010118 SGD
+SGD S000002653 MNN10 GO:0000136 SGD_REF:S000047367|PMID:10037752 IDA C galactosyltransferase YDR245W|BED1|REC41|SLC2 gene taxon:4932 20010118 SGD
+SGD S000002653 MNN10 GO:0000009 SGD_REF:S000047367|PMID:10037752 IDA F galactosyltransferase YDR245W|BED1|REC41|SLC2 gene taxon:4932 20010118 SGD
+SGD S000002653 MNN10 GO:0000032 SGD_REF:S000047367|PMID:10037752 TAS P galactosyltransferase YDR245W|BED1|REC41|SLC2 gene taxon:4932 20010118 SGD
+SGD S000002653 MNN10 GO:0006080 SGD_REF:S000047367|PMID:10037752 TAS P galactosyltransferase YDR245W|BED1|REC41|SLC2 gene taxon:4932 20010118 SGD
+SGD S000002653 MNN10 GO:0006491 SGD_REF:S000047367|PMID:10037752 TAS P galactosyltransferase YDR245W|BED1|REC41|SLC2 gene taxon:4932 20010118 SGD
+SGD S000002653 MNN10 GO:0007015 SGD_REF:S000058447|PMID:9153752 IMP P galactosyltransferase YDR245W|BED1|REC41|SLC2 gene taxon:4932 20010118 SGD
+SGD S000003719 MNN11 GO:0000136 SGD_REF:S000053242|PMID:9430634 IPI C mannosyltransferase complex component YJL183W gene taxon:4932 20020213 SGD
+SGD S000003719 MNN11 GO:0000009 SGD_REF:S000041162|PMID:10635561 IDA F mannosyltransferase complex component YJL183W gene taxon:4932 20021010 SGD
+SGD S000003719 MNN11 GO:0006486 SGD_REF:S000041162|PMID:10635561 IDA P mannosyltransferase complex component YJL183W gene taxon:4932 20021010 SGD
+SGD S000003719 MNN11 GO:0006486 SGD_REF:S000041162|PMID:10635561 IMP P mannosyltransferase complex component YJL183W gene taxon:4932 20021010 SGD
+SGD S000000219 MNN2 GO:0005794 SGD_REF:S000053482|PMID:9756928 IDA C golgi alpha-1,2-mannosyltransferase (putative) YBR015C|CRV4|LDB8|TTP1 gene taxon:4932 20020925 SGD
+SGD S000000219 MNN2 GO:0000026 SGD_REF:S000053482|PMID:9756928 IMP F golgi alpha-1,2-mannosyltransferase (putative) YBR015C|CRV4|LDB8|TTP1 gene taxon:4932 20020925 SGD
+SGD S000000219 MNN2 GO:0000026 SGD_REF:S000041385|PMID:10929130 TAS F golgi alpha-1,2-mannosyltransferase (putative) YBR015C|CRV4|LDB8|TTP1 gene taxon:4932 20020903 SGD
+SGD S000000219 MNN2 GO:0006486 SGD_REF:S000053482|PMID:9756928 IMP P golgi alpha-1,2-mannosyltransferase (putative) YBR015C|CRV4|LDB8|TTP1 gene taxon:4932 20020925 SGD
+SGD S000001684 MNN4 GO:0016020 SGD_REF:S000049636|PMID:9023541 ISS C YKL201C gene taxon:4932 20040506 SGD
+SGD S000001684 MNN4 GO:0005554 SGD_REF:S000069584 ND F YKL201C gene taxon:4932 20021113 SGD
+SGD S000001684 MNN4 GO:0006487 SGD_REF:S000049636|PMID:9023541 IMP P YKL201C gene taxon:4932 20021113 SGD
+SGD S000001684 MNN4 GO:0006493 SGD_REF:S000054589|PMID:9813355 IMP P YKL201C gene taxon:4932 20021113 SGD
+SGD S000001684 MNN4 GO:0006950 SGD_REF:S000055704|PMID:9459307 IDA P YKL201C gene taxon:4932 20020903 SGD
+SGD S000003722 MNN5 GO:0005794 SGD_REF:S000053482|PMID:9756928 IDA C golgi alpha-1,2-mannosyltransferase (putative) YJL186W gene taxon:4932 20020925 SGD
+SGD S000003722 MNN5 GO:0000026 SGD_REF:S000053482|PMID:9756928 IMP F golgi alpha-1,2-mannosyltransferase (putative) YJL186W gene taxon:4932 20020925 SGD
+SGD S000003722 MNN5 GO:0006486 SGD_REF:S000053482|PMID:9756928 IMP P golgi alpha-1,2-mannosyltransferase (putative) YJL186W gene taxon:4932 20020925 SGD
+SGD S000005971 MNN9 GO:0000136 SGD_REF:S000053242|PMID:9430634 IPI C required for complex glycosylation YPL050C gene taxon:4932 20020213 SGD
+SGD S000005971 MNN9 GO:0005801 SGD_REF:S000049702|PMID:10500155 TAS C required for complex glycosylation YPL050C gene taxon:4932 20030224 SGD
+SGD S000005971 MNN9 GO:0016020 SGD_REF:S000049702|PMID:10500155 TAS C required for complex glycosylation YPL050C gene taxon:4932 20030224 SGD
+SGD S000005971 MNN9 GO:0000030 SGD_REF:S000053242|PMID:9430634 IMP F required for complex glycosylation YPL050C gene taxon:4932 20020213 SGD
+SGD S000005971 MNN9 GO:0000030 SGD_REF:S000053242|PMID:9430634 IDA F required for complex glycosylation YPL050C gene taxon:4932 20020213 SGD
+SGD S000005971 MNN9 GO:0000030 SGD_REF:S000043074|PMID:9434768 ISS F required for complex glycosylation YPL050C gene taxon:4932 20020213 SGD
+SGD S000005971 MNN9 GO:0006487 SGD_REF:S000053242|PMID:9430634 IMP P required for complex glycosylation YPL050C gene taxon:4932 20020213 SGD
+SGD S000005971 MNN9 GO:0006487 SGD_REF:S000053242|PMID:9430634 IDA P required for complex glycosylation YPL050C gene taxon:4932 20020213 SGD
+SGD S000003036 MNP1 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YGL068W gene taxon:4932 20031028 SGD
+SGD S000003036 MNP1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YGL068W gene taxon:4932 20040924 SGD
+SGD S000003036 MNP1 GO:0005761 SGD_REF:S000058278|PMID:9445368 ISS C YGL068W gene taxon:4932 20050217 SGD
+SGD S000003036 MNP1 GO:0003735 SGD_REF:S000058278|PMID:9445368 ISS F YGL068W gene taxon:4932 20050217 SGD
+SGD S000003036 MNP1 GO:0005554 SGD_REF:S000069584 ND F YGL068W gene taxon:4932 20021126 SGD
+SGD S000003036 MNP1 GO:0009060 SGD_REF:S000076248|PMID:15221522 IMP P YGL068W gene taxon:4932 20050215 SGD
+SGD S000003036 MNP1 GO:0043037 SGD_REF:S000058278|PMID:9445368 ISS P YGL068W gene taxon:4932 20050217 SGD
+SGD S000001547 MNR2 GO:0016020 SGD_REF:S000053741|PMID:9430719 ISS C YKL064W gene taxon:4932 20020930 SGD
+SGD S000001547 MNR2 GO:0015095 SGD_REF:S000053741|PMID:9430719 ISS F YKL064W gene taxon:4932 20020930 SGD
+SGD S000001547 MNR2 GO:0015693 SGD_REF:S000053741|PMID:9430719 ISS P YKL064W gene taxon:4932 20020930 SGD
+SGD S000003892 MNS1 GO:0005783 SGD_REF:S000048905|PMID:8864657 IDA C alpha-mannosidase YJR131W gene taxon:4932 20020930 SGD
+SGD S000003892 MNS1 GO:0004571 SGD_REF:S000054810|PMID:1714453 IDA F alpha-mannosidase YJR131W gene taxon:4932 20020930 SGD
+SGD S000003892 MNS1 GO:0006487 SGD_REF:S000040422|PMID:8439291 IMP P alpha-mannosidase YJR131W gene taxon:4932 20020930 SGD
+SGD S000003892 MNS1 GO:0030433 SGD_REF:S000055216|PMID:8905927 IMP P alpha-mannosidase YJR131W gene taxon:4932 20050728 SGD
+SGD S000003226 MNT2 GO:0008372 SGD_REF:S000069584 ND C alpha-1,3-mannosyltransferase YGL257C gene taxon:4932 20010119 SGD
+SGD S000003226 MNT2 GO:0000033 SGD_REF:S000042908|PMID:10521541 IDA F alpha-1,3-mannosyltransferase YGL257C gene taxon:4932 20010118 SGD
+SGD S000003226 MNT2 GO:0006493 SGD_REF:S000042908|PMID:10521541 IDA P alpha-1,3-mannosyltransferase YGL257C gene taxon:4932 20010118 SGD
+SGD S000001276 MNT3 GO:0008372 SGD_REF:S000069584 ND C alpha-1,3-mannosyltransferase YIL014W gene taxon:4932 20010119 SGD
+SGD S000001276 MNT3 GO:0000033 SGD_REF:S000042908|PMID:10521541 IDA F alpha-1,3-mannosyltransferase YIL014W gene taxon:4932 20010118 SGD
+SGD S000001276 MNT3 GO:0006493 SGD_REF:S000042908|PMID:10521541 IDA P alpha-1,3-mannosyltransferase YIL014W gene taxon:4932 20010118 SGD
+SGD S000005342 MNT4 GO:0008372 SGD_REF:S000069584 ND C mannosyltransferase (putative) YNR059W gene taxon:4932 20010119 SGD
+SGD S000005342 MNT4 GO:0000033 SGD_REF:S000042908|PMID:10521541 IDA F mannosyltransferase (putative) YNR059W gene taxon:4932 20010118 SGD
+SGD S000005342 MNT4 GO:0006493 SGD_REF:S000042908|PMID:10521541 IDA P mannosyltransferase (putative) YNR059W gene taxon:4932 20010118 SGD
+SGD S000001368 MOB1 GO:0005816 SGD_REF:S000060813|PMID:11434459 IDA C YIL106W gene taxon:4932 20050223 SGD
+SGD S000001368 MOB1 GO:0005935 SGD_REF:S000060813|PMID:11434459 IDA C YIL106W gene taxon:4932 20050223 SGD
+SGD S000001368 MOB1 GO:0019207 SGD_REF:S000061406|PMID:11404483 IDA F YIL106W gene taxon:4932 20021211 SGD
+SGD S000001368 MOB1 GO:0006468 SGD_REF:S000061406|PMID:11404483 IDA P YIL106W gene taxon:4932 20021211 SGD
+SGD S000001368 MOB1 GO:0007096 SGD_REF:S000061406|PMID:11404483 TAS P YIL106W gene taxon:4932 20021211 SGD
+SGD S000001859 MOB2 GO:0005634 SGD_REF:S000070382|PMID:12196508 IDA C Mob1p-like protein YFL034C-B|YFL035C|YFL035C-A gene taxon:4932 20020930 SGD
+SGD S000001859 MOB2 GO:0005933 SGD_REF:S000070382|PMID:12196508 IDA C Mob1p-like protein YFL034C-B|YFL035C|YFL035C-A gene taxon:4932 20020930 SGD
+SGD S000001859 MOB2 GO:0005935 SGD_REF:S000070382|PMID:12196508 IDA C Mob1p-like protein YFL034C-B|YFL035C|YFL035C-A gene taxon:4932 20020930 SGD
+SGD S000001859 MOB2 GO:0043332 SGD_REF:S000074101|PMID:12972564 TAS C Mob1p-like protein YFL034C-B|YFL035C|YFL035C-A gene taxon:4932 20031016 SGD
+SGD S000001859 MOB2 GO:0030295 SGD_REF:S000070382|PMID:12196508 IDA F Mob1p-like protein YFL034C-B|YFL035C|YFL035C-A gene taxon:4932 20020930 SGD
+SGD S000001859 MOB2 GO:0000903 SGD_REF:S000074101|PMID:12972564 IGI P Mob1p-like protein YFL034C-B|YFL035C|YFL035C-A gene taxon:4932 20050420 SGD
+SGD S000001859 MOB2 GO:0006468 SGD_REF:S000070382|PMID:12196508 IDA P Mob1p-like protein YFL034C-B|YFL035C|YFL035C-A gene taxon:4932 20020930 SGD
+SGD S000001859 MOB2 GO:0007096 SGD_REF:S000070382|PMID:12196508 IMP P Mob1p-like protein YFL034C-B|YFL035C|YFL035C-A gene taxon:4932 20020930 SGD
+SGD S000001859 MOB2 GO:0030467 SGD_REF:S000070382|PMID:12196508 IMP P Mob1p-like protein YFL034C-B|YFL035C|YFL035C-A gene taxon:4932 20020930 SGD
+SGD S000005800 MOD5 GO:0005634 SGD_REF:S000041492|PMID:9872948 IDA C transfer RNA isopentenyl transferase YOR274W gene taxon:4932 20020903 SGD
+SGD S000005800 MOD5 GO:0005730 SGD_REF:S000041492|PMID:9872948 IDA C transfer RNA isopentenyl transferase YOR274W gene taxon:4932 20020903 SGD
+SGD S000005800 MOD5 GO:0005739 SGD_REF:S000041492|PMID:9872948 IDA C transfer RNA isopentenyl transferase YOR274W gene taxon:4932 20020903 SGD
+SGD S000005800 MOD5 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C transfer RNA isopentenyl transferase YOR274W gene taxon:4932 20040924 SGD
+SGD S000005800 MOD5 GO:0005829 SGD_REF:S000041492|PMID:9872948 IDA C transfer RNA isopentenyl transferase YOR274W gene taxon:4932 20020903 SGD
+SGD S000005800 MOD5 GO:0004811 SGD_REF:S000051677|PMID:3031456 IDA F transfer RNA isopentenyl transferase YOR274W gene taxon:4932 20020903 SGD
+SGD S000005800 MOD5 GO:0006400 SGD_REF:S000051677|PMID:3031456 IMP P transfer RNA isopentenyl transferase YOR274W gene taxon:4932 20020903 SGD
+SGD S000003835 MOG1 GO:0005634 SGD_REF:S000052316|PMID:9860978 IDA C nuclear protein that interacts with GTP-Gsp1p YJR074W gene taxon:4932 20021203 SGD
+SGD S000003835 MOG1 GO:0008536 SGD_REF:S000066175|PMID:11509570 IPI F nuclear protein that interacts with GTP-Gsp1p YJR074W gene taxon:4932 20020924 SGD
+SGD S000003835 MOG1 GO:0006606 SGD_REF:S000052316|PMID:9860978 IMP P nuclear protein that interacts with GTP-Gsp1p YJR074W gene taxon:4932 20020924 SGD
+SGD S000000145 MOH1 GO:0008372 SGD_REF:S000069584 ND C YBL049W gene taxon:4932 20030114 SGD
+SGD S000000145 MOH1 GO:0005554 SGD_REF:S000069584 ND F YBL049W gene taxon:4932 20030114 SGD
+SGD S000000145 MOH1 GO:0000004 SGD_REF:S000069584 ND P YBL049W gene taxon:4932 20030114 SGD
+SGD S000003092 MON1 GO:0000329 SGD_REF:S000072494|PMID:12364329 IDA C YGL124C|AUT12 gene taxon:4932 20030226 SGD
+SGD S000003092 MON1 GO:0005829 SGD_REF:S000071831|PMID:12387888 IDA C YGL124C|AUT12 gene taxon:4932 20030331 SGD
+SGD S000003092 MON1 GO:0005554 SGD_REF:S000069584 ND F YGL124C|AUT12 gene taxon:4932 20021001 SGD
+SGD S000003092 MON1 GO:0006623 SGD_REF:S000070264|PMID:12134085 IMP P YGL124C|AUT12 gene taxon:4932 20021001 SGD
+SGD S000003092 MON1 GO:0006914 SGD_REF:S000071831|PMID:12387888 IMP P YGL124C|AUT12 gene taxon:4932 20030331 SGD
+SGD S000003092 MON1 GO:0048278 SGD_REF:S000074698|PMID:14662743 IMP P YGL124C|AUT12 gene taxon:4932 20051003 SGD
+SGD S000005241 MON2 GO:0005768 SGD_REF:S000071747|PMID:12052896 IDA C YNL297C|YSL2 gene taxon:4932 20021202 SGD
+SGD S000005241 MON2 GO:0005829 SGD_REF:S000071747|PMID:12052896 TAS C YNL297C|YSL2 gene taxon:4932 20031226 SGD
+SGD S000005241 MON2 GO:0019898 SGD_REF:S000071747|PMID:12052896 IDA C YNL297C|YSL2 gene taxon:4932 20031226 SGD
+SGD S000005241 MON2 GO:0005085 SGD_REF:S000071747|PMID:12052896 IGI F YNL297C|YSL2 gene taxon:4932 20050429 SGD
+SGD S000005241 MON2 GO:0005085 SGD_REF:S000071747|PMID:12052896 IPI F YNL297C|YSL2 gene taxon:4932 20050429 SGD
+SGD S000005241 MON2 GO:0005085 SGD_REF:S000071747|PMID:12052896 ISS F YNL297C|YSL2 gene taxon:4932 20050429 SGD
+SGD S000005241 MON2 GO:0006623 SGD_REF:S000070264|PMID:12134085 IMP P YNL297C|YSL2 gene taxon:4932 20021001 SGD
+SGD S000005241 MON2 GO:0006810 SGD_REF:S000061289|PMID:11169758 IMP P YNL297C|YSL2 gene taxon:4932 20011018 SGD
+SGD S000005241 MON2 GO:0006810 SGD_REF:S000061289|PMID:11169758 ISS P YNL297C|YSL2 gene taxon:4932 20011018 SGD
+SGD S000005241 MON2 GO:0006897 SGD_REF:S000071747|PMID:12052896 IMP P YNL297C|YSL2 gene taxon:4932 20050429 SGD
+SGD S000006003 MOT1 GO:0000228 SGD_REF:S000069758|PMID:11880621 IDA C helicase (putative) YPL082C|BTAF1|BUR3|LPF4 gene taxon:4932 20021003 SGD
+SGD S000006003 MOT1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C helicase (putative) YPL082C|BTAF1|BUR3|LPF4 gene taxon:4932 20040928 SGD
+SGD S000006003 MOT1 GO:0016887 SGD_REF:S000049440|PMID:9234740 IDA F helicase (putative) YPL082C|BTAF1|BUR3|LPF4 gene taxon:4932 20021003 SGD
+SGD S000006003 MOT1 GO:0006357 SGD_REF:S000049440|PMID:9234740 IDA P helicase (putative) YPL082C|BTAF1|BUR3|LPF4 gene taxon:4932 20021003 SGD
+SGD S000006003 MOT1 GO:0045898 SGD_REF:S000082219|PMID:15861138 IMP P helicase (putative) YPL082C|BTAF1|BUR3|LPF4 gene taxon:4932 20051114 SGD
+SGD S000000870 MOT2 GO:0005737 SGD_REF:S000069437|PMID:11889048 IDA C zinc finger protein (putative) YER068W|NOT4|SIG1 gene taxon:4932 20020802 SGD
+SGD S000000870 MOT2 GO:0030015 SGD_REF:S000042122|PMID:10490603 IPI C zinc finger protein (putative) YER068W|NOT4|SIG1 gene taxon:4932 20020802 SGD
+SGD S000000870 MOT2 GO:0000175 SGD_REF:S000069437|PMID:11889048 IDA F zinc finger protein (putative) YER068W|NOT4|SIG1 gene taxon:4932 20020802 SGD
+SGD S000000870 MOT2 GO:0016564 SGD_REF:S000071517|PMID:11907266 TAS F zinc finger protein (putative) YER068W|NOT4|SIG1 gene taxon:4932 20021115 SGD
+SGD S000000870 MOT2 GO:0000289 SGD_REF:S000069437|PMID:11889048 IDA P zinc finger protein (putative) YER068W|NOT4|SIG1 gene taxon:4932 20020802 SGD
+SGD S000000870 MOT2 GO:0000747 SGD_REF:S000045027|PMID:8164670 IMP P zinc finger protein (putative) YER068W|NOT4|SIG1 gene taxon:4932 20020802 SGD
+SGD S000000870 MOT2 GO:0006357 SGD_REF:S000042122|PMID:10490603 IPI P zinc finger protein (putative) YER068W|NOT4|SIG1 gene taxon:4932 20020802 SGD
+SGD S000004674 MOT3 GO:0005634 SGD_REF:S000069459|PMID:11914276 IDA C 2 Cys2-His2 zinc fingers at c-terminus, glutamine and asparagine rich YMR070W|ROX7 gene taxon:4932 20020507 SGD
+SGD S000004674 MOT3 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C 2 Cys2-His2 zinc fingers at c-terminus, glutamine and asparagine rich YMR070W|ROX7 gene taxon:4932 20031028 SGD
+SGD S000004674 MOT3 GO:0003677 SGD_REF:S000070244|PMID:12145211 IPI F 2 Cys2-His2 zinc fingers at c-terminus, glutamine and asparagine rich YMR070W|ROX7 gene taxon:4932 20030122 SGD
+SGD S000004674 MOT3 GO:0016563 SGD_REF:S000070244|PMID:12145211 TAS F 2 Cys2-His2 zinc fingers at c-terminus, glutamine and asparagine rich YMR070W|ROX7 gene taxon:4932 20030122 SGD
+SGD S000004674 MOT3 GO:0016564 SGD_REF:S000070244|PMID:12145211 IDA F 2 Cys2-His2 zinc fingers at c-terminus, glutamine and asparagine rich YMR070W|ROX7 gene taxon:4932 20020823 SGD
+SGD S000004674 MOT3 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P 2 Cys2-His2 zinc fingers at c-terminus, glutamine and asparagine rich YMR070W|ROX7 gene taxon:4932 20060210 SGD
+SGD S000004674 MOT3 GO:0006350 SGD_REF:S000070244|PMID:12145211 IPI P 2 Cys2-His2 zinc fingers at c-terminus, glutamine and asparagine rich YMR070W|ROX7 gene taxon:4932 20030122 SGD
+SGD S000004674 MOT3 GO:0006350 SGD_REF:S000070244|PMID:12145211 IGI P 2 Cys2-His2 zinc fingers at c-terminus, glutamine and asparagine rich YMR070W|ROX7 gene taxon:4932 20030122 SGD
+SGD S000004674 MOT3 GO:0006350 SGD_REF:S000070244|PMID:12145211 IMP P 2 Cys2-His2 zinc fingers at c-terminus, glutamine and asparagine rich YMR070W|ROX7 gene taxon:4932 20030122 SGD
+SGD S000005193 MPA43 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YNL249C gene taxon:4932 20040813 SGD
+SGD S000005193 MPA43 GO:0005554 SGD_REF:S000069584 ND F YNL249C gene taxon:4932 20021009 SGD
+SGD S000005193 MPA43 GO:0000004 SGD_REF:S000069584 ND P YNL249C gene taxon:4932 20021009 SGD
+SGD S000005703 MPC54 GO:0005816 SGD_REF:S000061397|PMID:10899120 IDA C YOR177C gene taxon:4932 20020920 SGD
+SGD S000005703 MPC54 GO:0005198 SGD_REF:S000073593|PMID:12796288 IDA F YOR177C gene taxon:4932 20030708 SGD
+SGD S000005703 MPC54 GO:0005198 SGD_REF:S000073593|PMID:12796288 IMP F YOR177C gene taxon:4932 20030708 SGD
+SGD S000005703 MPC54 GO:0030476 SGD_REF:S000061397|PMID:10899120 IMP P YOR177C gene taxon:4932 20020920 SGD
+SGD S000005814 MPD1 GO:0000324 SGD_REF:S000074185|PMID:14562095 IDA C disulfide isomerase related protein YOR288C gene taxon:4932 20031028 SGD
+SGD S000005814 MPD1 GO:0003756 SGD_REF:S000059478|PMID:11157982 IMP F disulfide isomerase related protein YOR288C gene taxon:4932 20020606 SGD
+SGD S000005814 MPD1 GO:0003756 SGD_REF:S000059478|PMID:11157982 TAS F disulfide isomerase related protein YOR288C gene taxon:4932 20020606 SGD
+SGD S000005814 MPD1 GO:0006457 SGD_REF:S000059478|PMID:11157982 IGI SGD:S000000548 P disulfide isomerase related protein YOR288C gene taxon:4932 20021108 SGD
+SGD S000005448 MPD2 GO:0005783 SGD_REF:S000044010|PMID:10549279 TAS C protein disulfide isomerase related protein YOL088C gene taxon:4932 20021113 SGD
+SGD S000005448 MPD2 GO:0003756 SGD_REF:S000059478|PMID:11157982 IMP F protein disulfide isomerase related protein YOL088C gene taxon:4932 20020606 SGD
+SGD S000005448 MPD2 GO:0003756 SGD_REF:S000059478|PMID:11157982 TAS F protein disulfide isomerase related protein YOL088C gene taxon:4932 20020606 SGD
+SGD S000005448 MPD2 GO:0006457 SGD_REF:S000059478|PMID:11157982 IGI SGD:S000000548 P protein disulfide isomerase related protein YOL088C gene taxon:4932 20021108 SGD
+SGD S000001542 MPE1 GO:0005847 SGD_REF:S000068779|PMID:11713271 IPI C YKL059C gene taxon:4932 20021202 SGD
+SGD S000001542 MPE1 contributes_to GO:0003723 SGD_REF:S000068779|PMID:11713271 IC GO:0005847 F YKL059C gene taxon:4932 20050222 SGD
+SGD S000001542 MPE1 GO:0006378 SGD_REF:S000068779|PMID:11713271 IGI P YKL059C gene taxon:4932 20021202 SGD
+SGD S000001542 MPE1 GO:0006378 SGD_REF:S000068779|PMID:11713271 IMP P YKL059C gene taxon:4932 20021202 SGD
+SGD S000001542 MPE1 GO:0006378 SGD_REF:S000068779|PMID:11713271 IDA P YKL059C gene taxon:4932 20021202 SGD
+SGD S000001542 MPE1 GO:0006378 SGD_REF:S000068779|PMID:11713271 IPI P YKL059C gene taxon:4932 20021202 SGD
+SGD S000001542 MPE1 GO:0006379 SGD_REF:S000068779|PMID:11713271 IGI P YKL059C gene taxon:4932 20021202 SGD
+SGD S000001542 MPE1 GO:0006379 SGD_REF:S000068779|PMID:11713271 IPI P YKL059C gene taxon:4932 20021202 SGD
+SGD S000001542 MPE1 GO:0006379 SGD_REF:S000068779|PMID:11713271 IMP P YKL059C gene taxon:4932 20021202 SGD
+SGD S000001542 MPE1 GO:0006379 SGD_REF:S000068779|PMID:11713271 IDA P YKL059C gene taxon:4932 20021202 SGD
+SGD S000001441 MPH1 GO:0005634 SGD_REF:S000042465|PMID:10880470 IDA C YIR002C gene taxon:4932 20011205 SGD
+SGD S000001441 MPH1 GO:0003724 SGD_REF:S000042465|PMID:10880470 ISS F YIR002C gene taxon:4932 20011205 SGD
+SGD S000001441 MPH1 GO:0003724 SGD_REF:S000042465|PMID:10880470 IMP F YIR002C gene taxon:4932 20011205 SGD
+SGD S000001441 MPH1 GO:0043138 SGD_REF:S000080196|PMID:15634678 IDA F YIR002C gene taxon:4932 20050119 SGD
+SGD S000001441 MPH1 GO:0006281 SGD_REF:S000042465|PMID:10880470 IMP P YIR002C gene taxon:4932 20011205 SGD
+SGD S000002406 MPH2 GO:0005886 SGD_REF:S000071147|PMID:12210897 ISS C alpha-glucoside permease YDL247W gene taxon:4932 20021028 SGD
+SGD S000002406 MPH2 GO:0015144 SGD_REF:S000071147|PMID:12210897 ISS F alpha-glucoside permease YDL247W gene taxon:4932 20021028 SGD
+SGD S000002406 MPH2 GO:0015581 SGD_REF:S000071147|PMID:12210897 IDA F alpha-glucoside permease YDL247W gene taxon:4932 20021028 SGD
+SGD S000002406 MPH2 GO:0015581 SGD_REF:S000071147|PMID:12210897 ISS F alpha-glucoside permease YDL247W gene taxon:4932 20021028 SGD
+SGD S000002406 MPH2 GO:0008643 SGD_REF:S000071147|PMID:12210897 IDA P alpha-glucoside permease YDL247W gene taxon:4932 20021028 SGD
+SGD S000002406 MPH2 GO:0008643 SGD_REF:S000071147|PMID:12210897 ISS P alpha-glucoside permease YDL247W gene taxon:4932 20021028 SGD
+SGD S000003921 MPH3 GO:0005886 SGD_REF:S000071147|PMID:12210897 ISS C alpha-glucoside permease YJR160C gene taxon:4932 20021028 SGD
+SGD S000003921 MPH3 GO:0015144 SGD_REF:S000071147|PMID:12210897 ISS F alpha-glucoside permease YJR160C gene taxon:4932 20021028 SGD
+SGD S000003921 MPH3 GO:0015581 SGD_REF:S000071147|PMID:12210897 ISS F alpha-glucoside permease YJR160C gene taxon:4932 20020924 SGD
+SGD S000003921 MPH3 GO:0008643 SGD_REF:S000071147|PMID:12210897 IDA P alpha-glucoside permease YJR160C gene taxon:4932 20021028 SGD
+SGD S000003921 MPH3 GO:0008643 SGD_REF:S000071147|PMID:12210897 ISS P alpha-glucoside permease YJR160C gene taxon:4932 20021028 SGD
+SGD S000003602 MPM1 GO:0005624 SGD_REF:S000069017|PMID:11791739 IDA C YJL066C gene taxon:4932 20051006 SGD
+SGD S000003602 MPM1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YJL066C gene taxon:4932 20040924 SGD
+SGD S000003602 MPM1 GO:0005739 SGD_REF:S000069017|PMID:11791739 IDA C YJL066C gene taxon:4932 20051006 SGD
+SGD S000003602 MPM1 GO:0005554 SGD_REF:S000069584 ND F YJL066C gene taxon:4932 20020103 SGD
+SGD S000003602 MPM1 GO:0000004 SGD_REF:S000069584 ND P YJL066C gene taxon:4932 20020103 SGD
+SGD S000003762 MPP10 GO:0005634 SGD_REF:S000069459|PMID:11914276 IDA C U3 snoRNP protein YJR002W gene taxon:4932 20020507 SGD
+SGD S000003762 MPP10 GO:0005730 SGD_REF:S000069459|PMID:11914276 IDA C U3 snoRNP protein YJR002W gene taxon:4932 20020507 SGD
+SGD S000003762 MPP10 GO:0005732 SGD_REF:S000058443|PMID:10690410 TAS C U3 snoRNP protein YJR002W gene taxon:4932 20010118 SGD
+SGD S000003762 MPP10 GO:0005732 SGD_REF:S000070145|PMID:12068309 IPI C U3 snoRNP protein YJR002W gene taxon:4932 20030224 SGD
+SGD S000003762 MPP10 GO:0030532 SGD_REF:S000058443|PMID:10690410 TAS C U3 snoRNP protein YJR002W gene taxon:4932 20020219 SGD
+SGD S000003762 MPP10 GO:0005554 SGD_REF:S000069584 ND F U3 snoRNP protein YJR002W gene taxon:4932 20030224 SGD
+SGD S000003762 MPP10 GO:0000154 SGD_REF:S000058443|PMID:10690410 TAS P U3 snoRNP protein YJR002W gene taxon:4932 20010118 SGD
+SGD S000003762 MPP10 GO:0006365 SGD_REF:S000058443|PMID:10690410 TAS P U3 snoRNP protein YJR002W gene taxon:4932 20010118 SGD
+SGD S000003762 MPP10 GO:0030490 SGD_REF:S000070145|PMID:12068309 IPI P U3 snoRNP protein YJR002W gene taxon:4932 20020905 SGD
+SGD S000029666 MPR1 GO:0008372 SGD_REF:S000069584 ND C N-acetyltransferase gene taxon:4932 20020605 SGD
+SGD S000029666 MPR1 GO:0008080 SGD_REF:S000054221|PMID:10894734 ISS F N-acetyltransferase gene taxon:4932 20020604 SGD
+SGD S000029666 MPR1 GO:0008080 SGD_REF:S000066190|PMID:11555637 IPI F N-acetyltransferase gene taxon:4932 20020604 SGD
+SGD S000029666 MPR1 GO:0008080 SGD_REF:S000066190|PMID:11555637 IDA F N-acetyltransferase gene taxon:4932 20020604 SGD
+SGD S000029666 MPR1 GO:0008080 SGD_REF:S000066190|PMID:11555637 IMP F N-acetyltransferase gene taxon:4932 20020604 SGD
+SGD S000029666 MPR1 GO:0006979 SGD_REF:S000076932|PMID:15308773 IDA P N-acetyltransferase gene taxon:4932 20050323 SGD
+SGD S000029666 MPR1 GO:0006979 SGD_REF:S000076932|PMID:15308773 IMP P N-acetyltransferase gene taxon:4932 20050323 SGD
+SGD S000002186 MPS1 GO:0000778 SGD_REF:S000069129|PMID:11827982 IDA C YDL028C|RPK1 gene taxon:4932 20020214 SGD
+SGD S000002186 MPS1 GO:0005816 SGD_REF:S000069129|PMID:11827982 IDA C YDL028C|RPK1 gene taxon:4932 20020214 SGD
+SGD S000002186 MPS1 GO:0004712 SGD_REF:S000044607|PMID:7737118 IDA F YDL028C|RPK1 gene taxon:4932 20010118 SGD
+SGD S000002186 MPS1 GO:0004712 SGD_REF:S000080481|PMID:15668173 ISS F YDL028C|RPK1 gene taxon:4932 20051221 SGD
+SGD S000002186 MPS1 GO:0004712 SGD_REF:S000080481|PMID:15668173 IMP F YDL028C|RPK1 gene taxon:4932 20051221 SGD
+SGD S000002186 MPS1 GO:0007094 SGD_REF:S000044607|PMID:7737118 TAS P YDL028C|RPK1 gene taxon:4932 20010118 SGD
+SGD S000002186 MPS1 GO:0007103 SGD_REF:S000058447|PMID:9153752 TAS P YDL028C|RPK1 gene taxon:4932 20010118 SGD
+SGD S000002186 MPS1 GO:0051227 SGD_REF:S000080481|PMID:15668173 IMP P YDL028C|RPK1 gene taxon:4932 20051221 SGD
+SGD S000003043 MPS2 GO:0005635 SGD_REF:S000049069|PMID:10397772 IDA C YGL075C|MMC1 gene taxon:4932 20010118 SGD
+SGD S000003043 MPS2 GO:0005816 SGD_REF:S000049069|PMID:10397772 IDA C YGL075C|MMC1 gene taxon:4932 20010118 SGD
+SGD S000003043 MPS2 GO:0005200 SGD_REF:S000049069|PMID:10397772 IMP F YGL075C|MMC1 gene taxon:4932 20010118 SGD
+SGD S000003043 MPS2 GO:0000090 SGD_REF:S000049069|PMID:10397772 TAS P YGL075C|MMC1 gene taxon:4932 20010118 SGD
+SGD S000003043 MPS2 GO:0007103 SGD_REF:S000058447|PMID:9153752 TAS P YGL075C|MMC1 gene taxon:4932 20010118 SGD
+SGD S000003556 MPS3 GO:0005825 SGD_REF:S000071915|PMID:12486115 IDA C nuclear envelope protein YJL019W|NEP98|YJL018W gene taxon:4932 20041008 SGD
+SGD S000003556 MPS3 GO:0016021 SGD_REF:S000072782|PMID:12493774 IDA C nuclear envelope protein YJL019W|NEP98|YJL018W gene taxon:4932 20030325 SGD
+SGD S000003556 MPS3 GO:0016021 SGD_REF:S000071915|PMID:12486115 IDA C nuclear envelope protein YJL019W|NEP98|YJL018W gene taxon:4932 20041008 SGD
+SGD S000003556 MPS3 GO:0005554 SGD_REF:S000069584 ND F nuclear envelope protein YJL019W|NEP98|YJL018W gene taxon:4932 20021125 SGD
+SGD S000003556 MPS3 GO:0000743 SGD_REF:S000072782|PMID:12493774 IMP P nuclear envelope protein YJL019W|NEP98|YJL018W gene taxon:4932 20030325 SGD
+SGD S000003556 MPS3 GO:0007064 SGD_REF:S000080389|PMID:15355977 IMP P nuclear envelope protein YJL019W|NEP98|YJL018W gene taxon:4932 20050119 SGD
+SGD S000003556 MPS3 GO:0007103 SGD_REF:S000071915|PMID:12486115 IMP P nuclear envelope protein YJL019W|NEP98|YJL018W gene taxon:4932 20021228 SGD
+SGD S000003146 MPT5 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YGL178W|HTR1|PUF5|UTH4 gene taxon:4932 20031028 SGD
+SGD S000003146 MPT5 GO:0003729 SGD_REF:S000059468|PMID:11157761 IDA F YGL178W|HTR1|PUF5|UTH4 gene taxon:4932 20020924 SGD
+SGD S000003146 MPT5 GO:0000288 SGD_REF:S000059700|PMID:11101532 IGI P YGL178W|HTR1|PUF5|UTH4 gene taxon:4932 20020924 SGD
+SGD S000003146 MPT5 GO:0000321 SGD_REF:S000051164|PMID:9154842 IMP P YGL178W|HTR1|PUF5|UTH4 gene taxon:4932 20020924 SGD
+SGD S000003146 MPT5 GO:0001302 SGD_REF:S000080970|PMID:15722108 IMP P YGL178W|HTR1|PUF5|UTH4 gene taxon:4932 20050314 SGD
+SGD S000003146 MPT5 GO:0001308 SGD_REF:S000040351|PMID:9150138 IGI P YGL178W|HTR1|PUF5|UTH4 gene taxon:4932 20030814 SGD
+SGD S000003146 MPT5 GO:0001308 SGD_REF:S000040351|PMID:9150138 IEP P YGL178W|HTR1|PUF5|UTH4 gene taxon:4932 20030814 SGD
+SGD S000003146 MPT5 GO:0001308 SGD_REF:S000040351|PMID:9150138 IMP P YGL178W|HTR1|PUF5|UTH4 gene taxon:4932 20030814 SGD
+SGD S000003146 MPT5 GO:0006605 SGD_REF:S000040351|PMID:9150138 IMP P YGL178W|HTR1|PUF5|UTH4 gene taxon:4932 20020924 SGD
+SGD S000003146 MPT5 GO:0007047 SGD_REF:S000069081|PMID:11805047 IMP P YGL178W|HTR1|PUF5|UTH4 gene taxon:4932 20020924 SGD
+SGD S000000566 MRC1 GO:0000228 SGD_REF:S000073860|PMID:12944972 IPI C YCL061C|YCL060C gene taxon:4932 20040210 SGD
+SGD S000000566 MRC1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YCL061C|YCL060C gene taxon:4932 20031028 SGD
+SGD S000000566 MRC1 GO:0005657 SGD_REF:S000073790|PMID:12865299 IDA C YCL061C|YCL060C gene taxon:4932 20040514 SGD
+SGD S000000566 MRC1 GO:0005554 SGD_REF:S000069584 ND F YCL061C|YCL060C gene taxon:4932 20010814 SGD
+SGD S000000566 MRC1 GO:0000076 SGD_REF:S000061242|PMID:11331602 IMP P YCL061C|YCL060C gene taxon:4932 20010814 SGD
+SGD S000000566 MRC1 GO:0000076 SGD_REF:S000073860|PMID:12944972 IMP P YCL061C|YCL060C gene taxon:4932 20040210 SGD
+SGD S000000566 MRC1 GO:0000076 SGD_REF:S000073860|PMID:12944972 IPI P YCL061C|YCL060C gene taxon:4932 20040210 SGD
+SGD S000000566 MRC1 GO:0000076 SGD_REF:S000061242|PMID:11331602 IGI P YCL061C|YCL060C gene taxon:4932 20010814 SGD
+SGD S000000566 MRC1 GO:0006348 SGD_REF:S000061242|PMID:11331602 IMP P YCL061C|YCL060C gene taxon:4932 20010814 SGD
+SGD S000000566 MRC1 GO:0006348 SGD_REF:S000061242|PMID:11331602 IGI P YCL061C|YCL060C gene taxon:4932 20010814 SGD
+SGD S000000566 MRC1 GO:0030466 SGD_REF:S000061242|PMID:11331602 IMP P YCL061C|YCL060C gene taxon:4932 20010814 SGD
+SGD S000000566 MRC1 GO:0030466 SGD_REF:S000061242|PMID:11331602 IGI P YCL061C|YCL060C gene taxon:4932 20010814 SGD
+SGD S000006316 MRD1 GO:0005730 SGD_REF:S000069866|PMID:11884397 IDA C YPR112C gene taxon:4932 20020925 SGD
+SGD S000006316 MRD1 GO:0030515 SGD_REF:S000069866|PMID:11884397 IDA F YPR112C gene taxon:4932 20020925 SGD
+SGD S000006316 MRD1 GO:0042134 SGD_REF:S000069866|PMID:11884397 IDA F YPR112C gene taxon:4932 20020925 SGD
+SGD S000006316 MRD1 GO:0006365 SGD_REF:S000069866|PMID:11884397 IMP P YPR112C gene taxon:4932 20020925 SGD
+SGD S000004837 MRE11 GO:0005634 SGD_REF:S000050527|PMID:9845372 IDA C YMR224C|NGS1|RAD58|XRS4 gene taxon:4932 20030403 SGD
+SGD S000004837 MRE11 GO:0005634 SGD_REF:S000082253|PMID:15548595 IDA C YMR224C|NGS1|RAD58|XRS4 gene taxon:4932 20050808 SGD
+SGD S000004837 MRE11 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YMR224C|NGS1|RAD58|XRS4 gene taxon:4932 20040928 SGD
+SGD S000004837 MRE11 GO:0030870 SGD_REF:S000050527|PMID:9845372 IPI C YMR224C|NGS1|RAD58|XRS4 gene taxon:4932 20041024 SGD
+SGD S000004837 MRE11 GO:0004519 SGD_REF:S000042701|PMID:9858579 IDA F YMR224C|NGS1|RAD58|XRS4 gene taxon:4932 20010118 SGD
+SGD S000004837 MRE11 GO:0004520 SGD_REF:S000086451|PMID:16116037 IDA F YMR224C|NGS1|RAD58|XRS4 gene taxon:4932 20050919 SGD
+SGD S000004837 MRE11 GO:0005515 SGD_REF:S000050527|PMID:9845372 IPI F YMR224C|NGS1|RAD58|XRS4 gene taxon:4932 20020925 SGD
+SGD S000004837 MRE11 GO:0008408 SGD_REF:S000065930|PMID:11454871 IDA F YMR224C|NGS1|RAD58|XRS4 gene taxon:4932 20020906 SGD
+SGD S000004837 MRE11 GO:0042162 SGD_REF:S000080865|PMID:15721260 IDA F YMR224C|NGS1|RAD58|XRS4 gene taxon:4932 20050712 SGD
+SGD S000004837 MRE11 GO:0042162 SGD_REF:S000086451|PMID:16116037 IDA F YMR224C|NGS1|RAD58|XRS4 gene taxon:4932 20050919 SGD
+SGD S000004837 MRE11 GO:0000706 SGD_REF:S000069981|PMID:9334324 TAS P YMR224C|NGS1|RAD58|XRS4 gene taxon:4932 20020708 SGD
+SGD S000004837 MRE11 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P YMR224C|NGS1|RAD58|XRS4 gene taxon:4932 20060202 SGD
+SGD S000004837 MRE11 GO:0000727 SGD_REF:S000060952|PMID:11459961 TAS P YMR224C|NGS1|RAD58|XRS4 gene taxon:4932 20020925 SGD
+SGD S000004837 MRE11 GO:0006281 SGD_REF:S000050826|PMID:7789757 IMP P YMR224C|NGS1|RAD58|XRS4 gene taxon:4932 20010118 SGD
+SGD S000004837 MRE11 GO:0006303 SGD_REF:S000073203|PMID:12399380 IMP P YMR224C|NGS1|RAD58|XRS4 gene taxon:4932 20030528 SGD
+SGD S000004837 MRE11 GO:0042138 SGD_REF:S000069981|PMID:9334324 TAS P YMR224C|NGS1|RAD58|XRS4 gene taxon:4932 20020708 SGD
+SGD S000003111 MRF1 GO:0005739 SGD_REF:S000040823|PMID:1475194 IMP C mitochondrial polypeptide chain release factor YGL143C gene taxon:4932 20010118 SGD
+SGD S000003111 MRF1 GO:0005739 SGD_REF:S000050535|PMID:8265342 IDA C mitochondrial polypeptide chain release factor YGL143C gene taxon:4932 20010118 SGD
+SGD S000003111 MRF1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C mitochondrial polypeptide chain release factor YGL143C gene taxon:4932 20040924 SGD
+SGD S000003111 MRF1 GO:0003747 SGD_REF:S000040823|PMID:1475194 IMP F mitochondrial polypeptide chain release factor YGL143C gene taxon:4932 20010118 SGD
+SGD S000003111 MRF1 GO:0003747 SGD_REF:S000040823|PMID:1475194 ISS F mitochondrial polypeptide chain release factor YGL143C gene taxon:4932 20010118 SGD
+SGD S000003111 MRF1 GO:0006412 SGD_REF:S000040823|PMID:1475194 IMP P mitochondrial polypeptide chain release factor YGL143C gene taxon:4932 20010118 SGD
+SGD S000003111 MRF1 GO:0006412 SGD_REF:S000040823|PMID:1475194 ISS P mitochondrial polypeptide chain release factor YGL143C gene taxon:4932 20010118 SGD
+SGD S000003111 MRF1 GO:0006415 SGD_REF:S000040823|PMID:1475194 IMP P mitochondrial polypeptide chain release factor YGL143C gene taxon:4932 20010118 SGD
+SGD S000003111 MRF1 GO:0006415 SGD_REF:S000040823|PMID:1475194 ISS P mitochondrial polypeptide chain release factor YGL143C gene taxon:4932 20010118 SGD
+SGD S000002440 MRH1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YDR033W gene taxon:4932 20040929 SGD
+SGD S000002440 MRH1 GO:0005886 SGD_REF:S000054431|PMID:10675524 IDA C YDR033W gene taxon:4932 20010118 SGD
+SGD S000002440 MRH1 GO:0005554 SGD_REF:S000069584 ND F YDR033W gene taxon:4932 20010119 SGD
+SGD S000002440 MRH1 GO:0000004 SGD_REF:S000069584 ND P YDR033W gene taxon:4932 20010119 SGD
+SGD S000003032 MRH4 GO:0005739 SGD_REF:S000073008|PMID:12702275 IDA C mitochondrial DEAD box RNA helicase YGL064C gene taxon:4932 20030710 SGD
+SGD S000003032 MRH4 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C mitochondrial DEAD box RNA helicase YGL064C gene taxon:4932 20040924 SGD
+SGD S000003032 MRH4 GO:0003724 SGD_REF:S000073008|PMID:12702275 IDA F mitochondrial DEAD box RNA helicase YGL064C gene taxon:4932 20030710 SGD
+SGD S000003032 MRH4 GO:0007046 SGD_REF:S000073008|PMID:12702275 TAS P mitochondrial DEAD box RNA helicase YGL064C gene taxon:4932 20030710 SGD
+SGD S000002237 MRK1 GO:0008372 SGD_REF:S000069584 ND C MDS1 related protein kinase YDL079C gene taxon:4932 20021009 SGD
+SGD S000002237 MRK1 GO:0004696 SGD_REF:S000052678|PMID:10958669 IGI F MDS1 related protein kinase YDL079C gene taxon:4932 20021009 SGD
+SGD S000002237 MRK1 GO:0004696 SGD_REF:S000052678|PMID:10958669 ISS F MDS1 related protein kinase YDL079C gene taxon:4932 20021009 SGD
+SGD S000002237 MRK1 GO:0006468 SGD_REF:S000052678|PMID:10958669 IGI P MDS1 related protein kinase YDL079C gene taxon:4932 20021009 SGD
+SGD S000002237 MRK1 GO:0006468 SGD_REF:S000052678|PMID:10958669 ISS P MDS1 related protein kinase YDL079C gene taxon:4932 20021009 SGD
+SGD S000002237 MRK1 GO:0006950 SGD_REF:S000072503|PMID:12529445 IGI P MDS1 related protein kinase YDL079C gene taxon:4932 20030219 SGD
+SGD S000002237 MRK1 GO:0006950 SGD_REF:S000072503|PMID:12529445 IMP P MDS1 related protein kinase YDL079C gene taxon:4932 20030219 SGD
+SGD S000002237 MRK1 GO:0042176 SGD_REF:S000052678|PMID:10958669 IGI P MDS1 related protein kinase YDL079C gene taxon:4932 20050629 SGD
+SGD S000006283 MRL1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YPR079W gene taxon:4932 20020507 SGD
+SGD S000006283 MRL1 GO:0005770 SGD_REF:S000060994|PMID:11470415 IDA C YPR079W gene taxon:4932 20010730 SGD
+SGD S000006283 MRL1 GO:0005048 SGD_REF:S000060994|PMID:11470415 IGI SGD:S000000113 F YPR079W gene taxon:4932 20050124 SGD
+SGD S000006283 MRL1 GO:0005048 SGD_REF:S000060994|PMID:11470415 ISS F YPR079W gene taxon:4932 20050124 SGD
+SGD S000006283 MRL1 GO:0007034 SGD_REF:S000060994|PMID:11470415 IGI P YPR079W gene taxon:4932 20010730 SGD
+SGD S000006283 MRL1 GO:0007034 SGD_REF:S000060994|PMID:11470415 ISS P YPR079W gene taxon:4932 20010730 SGD
+SGD S000005727 MRM1 GO:0005739 SGD_REF:S000045600|PMID:8643404 IDA C ribose methyltransferase for mitochondrial 21S rRNA YOR201C|PET56 gene taxon:4932 20030130 SGD
+SGD S000005727 MRM1 GO:0008989 SGD_REF:S000045600|PMID:8643404 IDA F ribose methyltransferase for mitochondrial 21S rRNA YOR201C|PET56 gene taxon:4932 20030130 SGD
+SGD S000005727 MRM1 GO:0000154 SGD_REF:S000045600|PMID:8643404 IDA P ribose methyltransferase for mitochondrial 21S rRNA YOR201C|PET56 gene taxon:4932 20030130 SGD
+SGD S000003104 MRM2 GO:0005739 SGD_REF:S000069245|PMID:11867542 IDA C 2'O-ribose methyltransferase YGL136C gene taxon:4932 20020313 SGD
+SGD S000003104 MRM2 GO:0008650 SGD_REF:S000069245|PMID:11867542 IMP F 2'O-ribose methyltransferase YGL136C gene taxon:4932 20020313 SGD
+SGD S000003104 MRM2 GO:0008650 SGD_REF:S000075306|PMID:14636587 IMP F 2'O-ribose methyltransferase YGL136C gene taxon:4932 20060512 SGD
+SGD S000003104 MRM2 GO:0008650 SGD_REF:S000069245|PMID:11867542 IDA F 2'O-ribose methyltransferase YGL136C gene taxon:4932 20020313 SGD
+SGD S000003104 MRM2 GO:0031167 SGD_REF:S000075306|PMID:14636587 IMP P 2'O-ribose methyltransferase YGL136C gene taxon:4932 20060512 SGD
+SGD S000003104 MRM2 GO:0031167 SGD_REF:S000069245|PMID:11867542 IDA P 2'O-ribose methyltransferase YGL136C gene taxon:4932 20060512 SGD
+SGD S000003104 MRM2 GO:0031167 SGD_REF:S000069245|PMID:11867542 IMP P 2'O-ribose methyltransferase YGL136C gene taxon:4932 20060512 SGD
+SGD S000002755 MRP1 GO:0005763 SGD_REF:S000058278|PMID:9445368 TAS C 37 kDa mitochondrial ribosomal protein YDR347W gene taxon:4932 20010118 SGD
+SGD S000002755 MRP1 GO:0005763 SGD_REF:S000060645|PMID:11278769 IDA C 37 kDa mitochondrial ribosomal protein YDR347W gene taxon:4932 20010918 SGD
+SGD S000002755 MRP1 GO:0003735 SGD_REF:S000058278|PMID:9445368 TAS F 37 kDa mitochondrial ribosomal protein YDR347W gene taxon:4932 20010118 SGD
+SGD S000002755 MRP1 GO:0003735 SGD_REF:S000060645|PMID:11278769 IDA F 37 kDa mitochondrial ribosomal protein YDR347W gene taxon:4932 20010918 SGD
+SGD S000002755 MRP1 GO:0043037 SGD_REF:S000058278|PMID:9445368 TAS P 37 kDa mitochondrial ribosomal protein YDR347W gene taxon:4932 20010118 SGD
+SGD S000002755 MRP1 GO:0043037 SGD_REF:S000060645|PMID:11278769 IDA P 37 kDa mitochondrial ribosomal protein YDR347W gene taxon:4932 20010918 SGD
+SGD S000006430 MRP10 GO:0005763 SGD_REF:S000058278|PMID:9445368 IDA C mitochondrial ribosome 37 S subunit component YDL045W-A gene taxon:4932 20010118 SGD
+SGD S000006430 MRP10 GO:0005763 SGD_REF:S000047859|PMID:9065385 IDA C mitochondrial ribosome 37 S subunit component YDL045W-A gene taxon:4932 20010118 SGD
+SGD S000006430 MRP10 GO:0003735 SGD_REF:S000058278|PMID:9445368 IDA F mitochondrial ribosome 37 S subunit component YDL045W-A gene taxon:4932 20010118 SGD
+SGD S000006430 MRP10 GO:0003735 SGD_REF:S000047859|PMID:9065385 IDA F mitochondrial ribosome 37 S subunit component YDL045W-A gene taxon:4932 20010118 SGD
+SGD S000006430 MRP10 GO:0043037 SGD_REF:S000058278|PMID:9445368 IDA P mitochondrial ribosome 37 S subunit component YDL045W-A gene taxon:4932 20010118 SGD
+SGD S000006430 MRP10 GO:0043037 SGD_REF:S000047859|PMID:9065385 IDA P mitochondrial ribosome 37 S subunit component YDL045W-A gene taxon:4932 20010118 SGD
+SGD S000003316 MRP13 GO:0005763 SGD_REF:S000058278|PMID:9445368 TAS C 35 kDa mitochondrial ribosomal small subunit protein YGR084C gene taxon:4932 20010118 SGD
+SGD S000003316 MRP13 GO:0005763 SGD_REF:S000071753|PMID:12392552 IDA C 35 kDa mitochondrial ribosomal small subunit protein YGR084C gene taxon:4932 20040203 SGD
+SGD S000003316 MRP13 GO:0003735 SGD_REF:S000058278|PMID:9445368 TAS F 35 kDa mitochondrial ribosomal small subunit protein YGR084C gene taxon:4932 20010118 SGD
+SGD S000003316 MRP13 GO:0043037 SGD_REF:S000058278|PMID:9445368 TAS P 35 kDa mitochondrial ribosomal small subunit protein YGR084C gene taxon:4932 20010118 SGD
+SGD S000001486 MRP17 GO:0005763 SGD_REF:S000058278|PMID:9445368 TAS C ribosomal protein MRP17 YKL003C gene taxon:4932 20010118 SGD
+SGD S000001486 MRP17 GO:0005763 SGD_REF:S000071753|PMID:12392552 IDA C ribosomal protein MRP17 YKL003C gene taxon:4932 20040203 SGD
+SGD S000001486 MRP17 GO:0003735 SGD_REF:S000058278|PMID:9445368 TAS F ribosomal protein MRP17 YKL003C gene taxon:4932 20010118 SGD
+SGD S000001486 MRP17 GO:0043037 SGD_REF:S000058278|PMID:9445368 TAS P ribosomal protein MRP17 YKL003C gene taxon:4932 20010118 SGD
+SGD S000006370 MRP2 GO:0005763 SGD_REF:S000058278|PMID:9445368 TAS C 14 kDa mitochondrial ribosomal protein, similar to E. coli S14 protein YPR166C gene taxon:4932 20010118 SGD
+SGD S000006370 MRP2 GO:0005763 SGD_REF:S000060645|PMID:11278769 IDA C 14 kDa mitochondrial ribosomal protein, similar to E. coli S14 protein YPR166C gene taxon:4932 20010918 SGD
+SGD S000006370 MRP2 GO:0003735 SGD_REF:S000058278|PMID:9445368 TAS F 14 kDa mitochondrial ribosomal protein, similar to E. coli S14 protein YPR166C gene taxon:4932 20010118 SGD
+SGD S000006370 MRP2 GO:0003735 SGD_REF:S000060645|PMID:11278769 IDA F 14 kDa mitochondrial ribosomal protein, similar to E. coli S14 protein YPR166C gene taxon:4932 20010918 SGD
+SGD S000006370 MRP2 GO:0043037 SGD_REF:S000058278|PMID:9445368 TAS P 14 kDa mitochondrial ribosomal protein, similar to E. coli S14 protein YPR166C gene taxon:4932 20010118 SGD
+SGD S000006370 MRP2 GO:0043037 SGD_REF:S000060645|PMID:11278769 IDA P 14 kDa mitochondrial ribosomal protein, similar to E. coli S14 protein YPR166C gene taxon:4932 20010918 SGD
+SGD S000002813 MRP20 GO:0005762 SGD_REF:S000058278|PMID:9445368 TAS C YDR405W|MRPL41|YmL41 gene taxon:4932 20010118 SGD
+SGD S000002813 MRP20 GO:0003735 SGD_REF:S000058278|PMID:9445368 TAS F YDR405W|MRPL41|YmL41 gene taxon:4932 20010118 SGD
+SGD S000002813 MRP20 GO:0043037 SGD_REF:S000058278|PMID:9445368 TAS P YDR405W|MRPL41|YmL41 gene taxon:4932 20010118 SGD
+SGD S000000186 MRP21 GO:0005763 SGD_REF:S000052047|PMID:9528754 IDA C mitochondrial ribosome small subunit component YBL090W|MRP50 gene taxon:4932 20010118 SGD
+SGD S000000186 MRP21 GO:0003735 SGD_REF:S000052047|PMID:9528754 IDA F mitochondrial ribosome small subunit component YBL090W|MRP50 gene taxon:4932 20010118 SGD
+SGD S000000186 MRP21 GO:0006413 SGD_REF:S000052047|PMID:9528754 IMP P mitochondrial ribosome small subunit component YBL090W|MRP50 gene taxon:4932 20010118 SGD
+SGD S000000186 MRP21 GO:0043037 SGD_REF:S000052047|PMID:9528754 IDA P mitochondrial ribosome small subunit component YBL090W|MRP50 gene taxon:4932 20010118 SGD
+SGD S000000996 MRP4 GO:0005763 SGD_REF:S000058278|PMID:9445368 TAS C mitochondrial ribosomal protein, mitochondrial ribosome 37 S subunit component, similar to E. coli ribosomal protein S2 YHL004W gene taxon:4932 20010118 SGD
+SGD S000000996 MRP4 GO:0005763 SGD_REF:S000060645|PMID:11278769 IDA C mitochondrial ribosomal protein, mitochondrial ribosome 37 S subunit component, similar to E. coli ribosomal protein S2 YHL004W gene taxon:4932 20010918 SGD
+SGD S000000996 MRP4 GO:0000049 SGD_REF:S000058278|PMID:9445368 ISS F mitochondrial ribosomal protein, mitochondrial ribosome 37 S subunit component, similar to E. coli ribosomal protein S2 YHL004W gene taxon:4932 20010118 SGD
+SGD S000000996 MRP4 GO:0003735 SGD_REF:S000058278|PMID:9445368 TAS F mitochondrial ribosomal protein, mitochondrial ribosome 37 S subunit component, similar to E. coli ribosomal protein S2 YHL004W gene taxon:4932 20010118 SGD
+SGD S000000996 MRP4 GO:0003735 SGD_REF:S000060645|PMID:11278769 IDA F mitochondrial ribosomal protein, mitochondrial ribosome 37 S subunit component, similar to E. coli ribosomal protein S2 YHL004W gene taxon:4932 20010918 SGD
+SGD S000000996 MRP4 GO:0043037 SGD_REF:S000058278|PMID:9445368 TAS P mitochondrial ribosomal protein, mitochondrial ribosome 37 S subunit component, similar to E. coli ribosomal protein S2 YHL004W gene taxon:4932 20010118 SGD
+SGD S000000996 MRP4 GO:0043037 SGD_REF:S000060645|PMID:11278769 IDA P mitochondrial ribosomal protein, mitochondrial ribosome 37 S subunit component, similar to E. coli ribosomal protein S2 YHL004W gene taxon:4932 20010918 SGD
+SGD S000001650 MRP49 GO:0005762 SGD_REF:S000058278|PMID:9445368 TAS C 16 kDa mitochondrial ribosomal large subunit protein YKL167C gene taxon:4932 20010118 SGD
+SGD S000001650 MRP49 GO:0003735 SGD_REF:S000058278|PMID:9445368 TAS F 16 kDa mitochondrial ribosomal large subunit protein YKL167C gene taxon:4932 20010118 SGD
+SGD S000001650 MRP49 GO:0043037 SGD_REF:S000058278|PMID:9445368 TAS P 16 kDa mitochondrial ribosomal large subunit protein YKL167C gene taxon:4932 20010118 SGD
+SGD S000006039 MRP51 GO:0005763 SGD_REF:S000052047|PMID:9528754 IDA C mitochondrial ribosome small subunit component YPL118W gene taxon:4932 20010118 SGD
+SGD S000006039 MRP51 GO:0005763 SGD_REF:S000060645|PMID:11278769 IDA C mitochondrial ribosome small subunit component YPL118W gene taxon:4932 20010918 SGD
+SGD S000006039 MRP51 GO:0003735 SGD_REF:S000052047|PMID:9528754 IDA F mitochondrial ribosome small subunit component YPL118W gene taxon:4932 20010118 SGD
+SGD S000006039 MRP51 GO:0003735 SGD_REF:S000060645|PMID:11278769 IDA F mitochondrial ribosome small subunit component YPL118W gene taxon:4932 20010918 SGD
+SGD S000006039 MRP51 GO:0006413 SGD_REF:S000052047|PMID:9528754 IMP P mitochondrial ribosome small subunit component YPL118W gene taxon:4932 20010118 SGD
+SGD S000006039 MRP51 GO:0043037 SGD_REF:S000052047|PMID:9528754 IDA P mitochondrial ribosome small subunit component YPL118W gene taxon:4932 20010118 SGD
+SGD S000006039 MRP51 GO:0043037 SGD_REF:S000060645|PMID:11278769 IDA P mitochondrial ribosome small subunit component YPL118W gene taxon:4932 20010918 SGD
+SGD S000004950 MRP7 GO:0005762 SGD_REF:S000071753|PMID:12392552 IPI C YNL005C|MRPL2|YmL2 gene taxon:4932 20040203 SGD
+SGD S000004950 MRP7 GO:0000048 SGD_REF:S000058278|PMID:9445368 ISS F YNL005C|MRPL2|YmL2 gene taxon:4932 20010118 SGD
+SGD S000004950 MRP7 GO:0003735 SGD_REF:S000058278|PMID:9445368 TAS F YNL005C|MRPL2|YmL2 gene taxon:4932 20010118 SGD
+SGD S000004950 MRP7 GO:0043037 SGD_REF:S000058278|PMID:9445368 TAS P YNL005C|MRPL2|YmL2 gene taxon:4932 20010118 SGD
+SGD S000001625 MRP8 GO:0005761 SGD_REF:S000049173|PMID:1574929 ISS C ribosomal protein YKL142W|YKL3 gene taxon:4932 20010118 SGD
+SGD S000001625 MRP8 GO:0003735 SGD_REF:S000049173|PMID:1574929 ISS F ribosomal protein YKL142W|YKL3 gene taxon:4932 20010118 SGD
+SGD S000001625 MRP8 GO:0043037 SGD_REF:S000049173|PMID:1574929 ISS P ribosomal protein YKL142W|YKL3 gene taxon:4932 20010118 SGD
+SGD S000002523 MRPL1 GO:0005762 SGD_REF:S000060148|PMID:10929718 ISS C YDR116C gene taxon:4932 20020806 SGD
+SGD S000002523 MRPL1 GO:0005762 SGD_REF:S000071753|PMID:12392552 IPI C YDR116C gene taxon:4932 20021213 SGD
+SGD S000002523 MRPL1 GO:0003735 SGD_REF:S000060148|PMID:10929718 ISS F YDR116C gene taxon:4932 20020806 SGD
+SGD S000002523 MRPL1 GO:0003735 SGD_REF:S000071753|PMID:12392552 IPI F YDR116C gene taxon:4932 20021213 SGD
+SGD S000002523 MRPL1 GO:0009060 SGD_REF:S000060148|PMID:10929718 IEP P YDR116C gene taxon:4932 20020806 SGD
+SGD S000002523 MRPL1 GO:0009060 SGD_REF:S000060148|PMID:10929718 IMP P YDR116C gene taxon:4932 20020806 SGD
+SGD S000002523 MRPL1 GO:0043037 SGD_REF:S000071753|PMID:12392552 IC GO:0003735|GO:0005762 P YDR116C gene taxon:4932 20021213 SGD
+SGD S000005228 MRPL10 GO:0005762 SGD_REF:S000058278|PMID:9445368 TAS C YNL284C|MRPL18|YmL10|YmL18 gene taxon:4932 20010118 SGD
+SGD S000005228 MRPL10 GO:0003735 SGD_REF:S000058278|PMID:9445368 TAS F YNL284C|MRPL18|YmL10|YmL18 gene taxon:4932 20010118 SGD
+SGD S000005228 MRPL10 GO:0043037 SGD_REF:S000058278|PMID:9445368 TAS P YNL284C|MRPL18|YmL10|YmL18 gene taxon:4932 20010118 SGD
+SGD S000002361 MRPL11 GO:0005762 SGD_REF:S000058278|PMID:9445368 TAS C YDL202W|YmL11 gene taxon:4932 20010118 SGD
+SGD S000002361 MRPL11 GO:0003735 SGD_REF:S000058278|PMID:9445368 TAS F YDL202W|YmL11 gene taxon:4932 20010118 SGD
+SGD S000002361 MRPL11 GO:0043037 SGD_REF:S000058278|PMID:9445368 TAS P YDL202W|YmL11 gene taxon:4932 20010118 SGD
+SGD S000001714 MRPL13 GO:0005762 SGD_REF:S000058278|PMID:9445368 TAS C YKR006C|YK105|YmL13 gene taxon:4932 20010118 SGD
+SGD S000001714 MRPL13 GO:0003735 SGD_REF:S000058278|PMID:9445368 TAS F YKR006C|YK105|YmL13 gene taxon:4932 20010118 SGD
+SGD S000001714 MRPL13 GO:0043037 SGD_REF:S000058278|PMID:9445368 TAS P YKR006C|YK105|YmL13 gene taxon:4932 20010118 SGD
+SGD S000004304 MRPL15 GO:0005762 SGD_REF:S000058278|PMID:9445368 TAS C YLR312W-A|YmL15 gene taxon:4932 20010118 SGD
+SGD S000004304 MRPL15 GO:0005762 SGD_REF:S000071753|PMID:12392552 IPI C YLR312W-A|YmL15 gene taxon:4932 20040203 SGD
+SGD S000004304 MRPL15 GO:0003735 SGD_REF:S000058278|PMID:9445368 TAS F YLR312W-A|YmL15 gene taxon:4932 20010118 SGD
+SGD S000004304 MRPL15 GO:0043037 SGD_REF:S000058278|PMID:9445368 TAS P YLR312W-A|YmL15 gene taxon:4932 20010118 SGD
+SGD S000000134 MRPL16 GO:0005762 SGD_REF:S000058278|PMID:9445368 TAS C ribosomal protein YBL038W gene taxon:4932 20010118 SGD
+SGD S000000134 MRPL16 GO:0000048 SGD_REF:S000058278|PMID:9445368 ISS F ribosomal protein YBL038W gene taxon:4932 20010118 SGD
+SGD S000000134 MRPL16 GO:0003735 SGD_REF:S000058278|PMID:9445368 TAS F ribosomal protein YBL038W gene taxon:4932 20010118 SGD
+SGD S000000134 MRPL16 GO:0043037 SGD_REF:S000058278|PMID:9445368 TAS P ribosomal protein YBL038W gene taxon:4932 20010118 SGD
+SGD S000005196 MRPL17 GO:0005762 SGD_REF:S000058278|PMID:9445368 TAS C YNL252C|MRPL30|YmL30 gene taxon:4932 20010118 SGD
+SGD S000005196 MRPL17 GO:0005762 SGD_REF:S000071753|PMID:12392552 IPI C YNL252C|MRPL30|YmL30 gene taxon:4932 20040203 SGD
+SGD S000005196 MRPL17 GO:0003735 SGD_REF:S000058278|PMID:9445368 TAS F YNL252C|MRPL30|YmL30 gene taxon:4932 20010118 SGD
+SGD S000005196 MRPL17 GO:0043037 SGD_REF:S000058278|PMID:9445368 TAS P YNL252C|MRPL30|YmL30 gene taxon:4932 20010118 SGD
+SGD S000005129 MRPL19 GO:0005762 SGD_REF:S000058278|PMID:9445368 TAS C YNL185C|YmL19 gene taxon:4932 20010118 SGD
+SGD S000005129 MRPL19 GO:0003735 SGD_REF:S000058278|PMID:9445368 TAS F YNL185C|YmL19 gene taxon:4932 20010118 SGD
+SGD S000005129 MRPL19 GO:0043037 SGD_REF:S000058278|PMID:9445368 TAS P YNL185C|YmL19 gene taxon:4932 20010118 SGD
+SGD S000001793 MRPL20 GO:0005762 SGD_REF:S000058278|PMID:9445368 TAS C YKR085C|YmL20 gene taxon:4932 20010118 SGD
+SGD S000001793 MRPL20 GO:0005762 SGD_REF:S000071753|PMID:12392552 IPI C YKR085C|YmL20 gene taxon:4932 20040203 SGD
+SGD S000001793 MRPL20 GO:0003735 SGD_REF:S000058278|PMID:9445368 TAS F YKR085C|YmL20 gene taxon:4932 20010118 SGD
+SGD S000001793 MRPL20 GO:0000002 SGD_REF:S000049904|PMID:2183197 IMP P YKR085C|YmL20 gene taxon:4932 20010118 SGD
+SGD S000001793 MRPL20 GO:0043037 SGD_REF:S000058278|PMID:9445368 TAS P YKR085C|YmL20 gene taxon:4932 20010118 SGD
+SGD S000005121 MRPL22 GO:0005762 SGD_REF:S000071753|PMID:12392552 IPI C YNL177C gene taxon:4932 20021209 SGD
+SGD S000005121 MRPL22 GO:0005762 SGD_REF:S000060148|PMID:10929718 ISS C YNL177C gene taxon:4932 20020806 SGD
+SGD S000005121 MRPL22 GO:0003735 SGD_REF:S000071753|PMID:12392552 IPI F YNL177C gene taxon:4932 20021209 SGD
+SGD S000005121 MRPL22 GO:0003735 SGD_REF:S000060148|PMID:10929718 ISS F YNL177C gene taxon:4932 20020806 SGD
+SGD S000005121 MRPL22 GO:0009060 SGD_REF:S000060148|PMID:10929718 IEP P YNL177C gene taxon:4932 20020806 SGD
+SGD S000005121 MRPL22 GO:0009060 SGD_REF:S000060148|PMID:10929718 IMP P YNL177C gene taxon:4932 20020806 SGD
+SGD S000005121 MRPL22 GO:0043037 SGD_REF:S000071753|PMID:12392552 IC GO:0003735|GO:0005762 P YNL177C gene taxon:4932 20021213 SGD
+SGD S000005676 MRPL23 GO:0005762 SGD_REF:S000058278|PMID:9445368 TAS C YOR150W|YmL23 gene taxon:4932 20010118 SGD
+SGD S000005676 MRPL23 GO:0005762 SGD_REF:S000071753|PMID:12392552 IPI C YOR150W|YmL23 gene taxon:4932 20040203 SGD
+SGD S000005676 MRPL23 GO:0003735 SGD_REF:S000058278|PMID:9445368 TAS F YOR150W|YmL23 gene taxon:4932 20010118 SGD
+SGD S000005676 MRPL23 GO:0000027 SGD_REF:S000058278|PMID:9445368 ISS P YOR150W|YmL23 gene taxon:4932 20010118 SGD
+SGD S000005676 MRPL23 GO:0043037 SGD_REF:S000058278|PMID:9445368 TAS P YOR150W|YmL23 gene taxon:4932 20010118 SGD
+SGD S000004806 MRPL24 GO:0005762 SGD_REF:S000058278|PMID:9445368 TAS C YMR193W|MRPL14|YmL14|YmL24 gene taxon:4932 20010118 SGD
+SGD S000004806 MRPL24 GO:0003735 SGD_REF:S000058278|PMID:9445368 TAS F YMR193W|MRPL14|YmL14|YmL24 gene taxon:4932 20010118 SGD
+SGD S000004806 MRPL24 GO:0043037 SGD_REF:S000058278|PMID:9445368 TAS P YMR193W|MRPL14|YmL14|YmL24 gene taxon:4932 20010118 SGD
+SGD S000003308 MRPL25 GO:0005762 SGD_REF:S000058278|PMID:9445368 TAS C YGR076C|YMR26|YmL25 gene taxon:4932 20010118 SGD
+SGD S000003308 MRPL25 GO:0005762 SGD_REF:S000071753|PMID:12392552 IPI C YGR076C|YMR26|YmL25 gene taxon:4932 20040203 SGD
+SGD S000003308 MRPL25 GO:0003735 SGD_REF:S000058278|PMID:9445368 TAS F YGR076C|YMR26|YmL25 gene taxon:4932 20010118 SGD
+SGD S000003308 MRPL25 GO:0043037 SGD_REF:S000058278|PMID:9445368 TAS P YGR076C|YMR26|YmL25 gene taxon:4932 20010118 SGD
+SGD S000000486 MRPL27 GO:0005762 SGD_REF:S000058278|PMID:9445368 TAS C YBR282W|YmL27 gene taxon:4932 20010118 SGD
+SGD S000000486 MRPL27 GO:0005762 SGD_REF:S000071753|PMID:12392552 IPI C YBR282W|YmL27 gene taxon:4932 20040203 SGD
+SGD S000000486 MRPL27 GO:0003735 SGD_REF:S000058278|PMID:9445368 TAS F YBR282W|YmL27 gene taxon:4932 20010118 SGD
+SGD S000000486 MRPL27 GO:0043037 SGD_REF:S000058278|PMID:9445368 TAS P YBR282W|YmL27 gene taxon:4932 20010118 SGD
+SGD S000002870 MRPL28 GO:0005762 SGD_REF:S000058278|PMID:9445368 TAS C YDR462W|YmL28 gene taxon:4932 20010118 SGD
+SGD S000002870 MRPL28 GO:0003735 SGD_REF:S000058278|PMID:9445368 TAS F YDR462W|YmL28 gene taxon:4932 20010118 SGD
+SGD S000002870 MRPL28 GO:0043037 SGD_REF:S000058278|PMID:9445368 TAS P YDR462W|YmL28 gene taxon:4932 20010118 SGD
+SGD S000004626 MRPL3 GO:0005762 SGD_REF:S000058278|PMID:9445368 TAS C YMR024W|YmL3 gene taxon:4932 20010118 SGD
+SGD S000004626 MRPL3 GO:0005762 SGD_REF:S000071753|PMID:12392552 IPI C YMR024W|YmL3 gene taxon:4932 20040203 SGD
+SGD S000004626 MRPL3 GO:0003735 SGD_REF:S000058278|PMID:9445368 TAS F YMR024W|YmL3 gene taxon:4932 20010118 SGD
+SGD S000004626 MRPL3 GO:0043037 SGD_REF:S000058278|PMID:9445368 TAS P YMR024W|YmL3 gene taxon:4932 20010118 SGD
+SGD S000001621 MRPL31 GO:0005762 SGD_REF:S000058278|PMID:9445368 TAS C YKL138C|YmL31 gene taxon:4932 20010118 SGD
+SGD S000001621 MRPL31 GO:0005762 SGD_REF:S000071753|PMID:12392552 IPI C YKL138C|YmL31 gene taxon:4932 20040203 SGD
+SGD S000001621 MRPL31 GO:0003735 SGD_REF:S000058278|PMID:9445368 TAS F YKL138C|YmL31 gene taxon:4932 20010118 SGD
+SGD S000001621 MRPL31 GO:0043037 SGD_REF:S000058278|PMID:9445368 TAS P YKL138C|YmL31 gene taxon:4932 20010118 SGD
+SGD S000000596 MRPL32 GO:0005762 SGD_REF:S000058278|PMID:9445368 TAS C ribosomal protein (YmL32) YCR003W|YmL32 gene taxon:4932 20010118 SGD
+SGD S000000596 MRPL32 GO:0003735 SGD_REF:S000058278|PMID:9445368 TAS F ribosomal protein (YmL32) YCR003W|YmL32 gene taxon:4932 20010118 SGD
+SGD S000000596 MRPL32 GO:0043037 SGD_REF:S000058278|PMID:9445368 TAS P ribosomal protein (YmL32) YCR003W|YmL32 gene taxon:4932 20010118 SGD
+SGD S000004899 MRPL33 GO:0005762 SGD_REF:S000058278|PMID:9445368 TAS C YMR286W|YmL33 gene taxon:4932 20010118 SGD
+SGD S000004899 MRPL33 GO:0003735 SGD_REF:S000058278|PMID:9445368 TAS F YMR286W|YmL33 gene taxon:4932 20010118 SGD
+SGD S000004899 MRPL33 GO:0043037 SGD_REF:S000058278|PMID:9445368 TAS P YMR286W|YmL33 gene taxon:4932 20010118 SGD
+SGD S000002730 MRPL35 GO:0005762 SGD_REF:S000058278|PMID:9445368 TAS C YDR322W|YmL35 gene taxon:4932 20010118 SGD
+SGD S000002730 MRPL35 GO:0005762 SGD_REF:S000071753|PMID:12392552 IPI C YDR322W|YmL35 gene taxon:4932 20040203 SGD
+SGD S000002730 MRPL35 GO:0003735 SGD_REF:S000058278|PMID:9445368 TAS F YDR322W|YmL35 gene taxon:4932 20010118 SGD
+SGD S000002730 MRPL35 GO:0043037 SGD_REF:S000058278|PMID:9445368 TAS P YDR322W|YmL35 gene taxon:4932 20010118 SGD
+SGD S000000326 MRPL36 GO:0005762 SGD_REF:S000058278|PMID:9445368 TAS C YBR122C|YmL36 gene taxon:4932 20010118 SGD
+SGD S000000326 MRPL36 GO:0005762 SGD_REF:S000071753|PMID:12392552 IPI C YBR122C|YmL36 gene taxon:4932 20040203 SGD
+SGD S000000326 MRPL36 GO:0003735 SGD_REF:S000058278|PMID:9445368 TAS F YBR122C|YmL36 gene taxon:4932 20010118 SGD
+SGD S000000326 MRPL36 GO:0043037 SGD_REF:S000058278|PMID:9445368 TAS P YBR122C|YmL36 gene taxon:4932 20010118 SGD
+SGD S000000472 MRPL37 GO:0005762 SGD_REF:S000058278|PMID:9445368 TAS C YBR268W|YmL37 gene taxon:4932 20010118 SGD
+SGD S000000472 MRPL37 GO:0003735 SGD_REF:S000058278|PMID:9445368 TAS F YBR268W|YmL37 gene taxon:4932 20010118 SGD
+SGD S000000472 MRPL37 GO:0043037 SGD_REF:S000058278|PMID:9445368 TAS P YBR268W|YmL37 gene taxon:4932 20010118 SGD
+SGD S000001653 MRPL38 GO:0005762 SGD_REF:S000058278|PMID:9445368 TAS C YKL170W|MRPL34|YmL34|YmL38 gene taxon:4932 20010118 SGD
+SGD S000001653 MRPL38 GO:0005762 SGD_REF:S000071753|PMID:12392552 IPI C YKL170W|MRPL34|YmL34|YmL38 gene taxon:4932 20040203 SGD
+SGD S000001653 MRPL38 GO:0003735 SGD_REF:S000058278|PMID:9445368 TAS F YKL170W|MRPL34|YmL34|YmL38 gene taxon:4932 20010118 SGD
+SGD S000001653 MRPL38 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P YKL170W|MRPL34|YmL34|YmL38 gene taxon:4932 20060227 SGD
+SGD S000001653 MRPL38 GO:0043037 SGD_REF:S000058278|PMID:9445368 TAS P YKL170W|MRPL34|YmL34|YmL38 gene taxon:4932 20010118 SGD
+SGD S000004468 MRPL39 GO:0005762 SGD_REF:S000058278|PMID:9445368 TAS C YML009C|YmL39 gene taxon:4932 20010118 SGD
+SGD S000004468 MRPL39 GO:0003735 SGD_REF:S000058278|PMID:9445368 TAS F YML009C|YmL39 gene taxon:4932 20010118 SGD
+SGD S000004468 MRPL39 GO:0043037 SGD_REF:S000058278|PMID:9445368 TAS P YML009C|YmL39 gene taxon:4932 20010118 SGD
+SGD S000004431 MRPL4 GO:0005762 SGD_REF:S000058278|PMID:9445368 TAS C YLR439W|YmL4 gene taxon:4932 20010118 SGD
+SGD S000004431 MRPL4 GO:0003735 SGD_REF:S000058278|PMID:9445368 TAS F YLR439W|YmL4 gene taxon:4932 20010118 SGD
+SGD S000004431 MRPL4 GO:0043037 SGD_REF:S000058278|PMID:9445368 TAS P YLR439W|YmL4 gene taxon:4932 20010118 SGD
+SGD S000006094 MRPL40 GO:0005762 SGD_REF:S000058278|PMID:9445368 TAS C YPL173W|YmL40 gene taxon:4932 20010118 SGD
+SGD S000006094 MRPL40 GO:0005762 SGD_REF:S000071753|PMID:12392552 IPI C YPL173W|YmL40 gene taxon:4932 20040203 SGD
+SGD S000006094 MRPL40 GO:0003735 SGD_REF:S000058278|PMID:9445368 TAS F YPL173W|YmL40 gene taxon:4932 20010118 SGD
+SGD S000006094 MRPL40 GO:0043037 SGD_REF:S000058278|PMID:9445368 TAS P YPL173W|YmL40 gene taxon:4932 20010118 SGD
+SGD S000004838 MRPL44 GO:0005762 SGD_REF:S000058278|PMID:9445368 TAS C YMR225C|YMR44|YmL44 gene taxon:4932 20010118 SGD
+SGD S000004838 MRPL44 GO:0003735 SGD_REF:S000058278|PMID:9445368 TAS F YMR225C|YMR44|YmL44 gene taxon:4932 20010118 SGD
+SGD S000004838 MRPL44 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P YMR225C|YMR44|YmL44 gene taxon:4932 20060227 SGD
+SGD S000004838 MRPL44 GO:0043037 SGD_REF:S000058278|PMID:9445368 TAS P YMR225C|YMR44|YmL44 gene taxon:4932 20010118 SGD
+SGD S000003632 MRPL49 GO:0005762 SGD_REF:S000058278|PMID:9445368 TAS C YJL096W|YmL49 gene taxon:4932 20010118 SGD
+SGD S000003632 MRPL49 GO:0005762 SGD_REF:S000071753|PMID:12392552 IPI C YJL096W|YmL49 gene taxon:4932 20040203 SGD
+SGD S000003632 MRPL49 GO:0003735 SGD_REF:S000058278|PMID:9445368 TAS F YJL096W|YmL49 gene taxon:4932 20010118 SGD
+SGD S000003632 MRPL49 GO:0043037 SGD_REF:S000058278|PMID:9445368 TAS P YJL096W|YmL49 gene taxon:4932 20010118 SGD
+SGD S000005305 MRPL50 GO:0005762 SGD_REF:S000071753|PMID:12392552 IPI C YNR022C gene taxon:4932 20021209 SGD
+SGD S000005305 MRPL50 GO:0003735 SGD_REF:S000071753|PMID:12392552 IPI F YNR022C gene taxon:4932 20021209 SGD
+SGD S000005305 MRPL50 GO:0043037 SGD_REF:S000071753|PMID:12392552 IC GO:0003735|GO:0005762 P YNR022C gene taxon:4932 20021212 SGD
+SGD S000006304 MRPL51 GO:0005762 SGD_REF:S000071753|PMID:12392552 IPI C YPR100W gene taxon:4932 20021209 SGD
+SGD S000006304 MRPL51 GO:0003735 SGD_REF:S000071753|PMID:12392552 IPI F YPR100W gene taxon:4932 20021209 SGD
+SGD S000006304 MRPL51 GO:0009060 SGD_REF:S000071753|PMID:12392552 IMP P YPR100W gene taxon:4932 20021209 SGD
+SGD S000006304 MRPL51 GO:0043037 SGD_REF:S000071753|PMID:12392552 IC GO:0003735|GO:0005762 P YPR100W gene taxon:4932 20021212 SGD
+SGD S000001190 MRPL6 GO:0005762 SGD_REF:S000058278|PMID:9445368 TAS C YHR147C|YmL16 gene taxon:4932 20010118 SGD
+SGD S000001190 MRPL6 GO:0005762 SGD_REF:S000071753|PMID:12392552 IPI C YHR147C|YmL16 gene taxon:4932 20040203 SGD
+SGD S000001190 MRPL6 GO:0003735 SGD_REF:S000058278|PMID:9445368 TAS F YHR147C|YmL16 gene taxon:4932 20010118 SGD
+SGD S000001190 MRPL6 GO:0043037 SGD_REF:S000058278|PMID:9445368 TAS P YHR147C|YmL16 gene taxon:4932 20010118 SGD
+SGD S000002645 MRPL7 GO:0005762 SGD_REF:S000058278|PMID:9445368 TAS C YDR237W|YmL5/7 gene taxon:4932 20010118 SGD
+SGD S000002645 MRPL7 GO:0003735 SGD_REF:S000058278|PMID:9445368 TAS F YDR237W|YmL5/7 gene taxon:4932 20010118 SGD
+SGD S000002645 MRPL7 GO:0043037 SGD_REF:S000058278|PMID:9445368 TAS P YDR237W|YmL5/7 gene taxon:4932 20010118 SGD
+SGD S000003599 MRPL8 GO:0005762 SGD_REF:S000058278|PMID:9445368 TAS C YJL063C|HRD238|YmL8 gene taxon:4932 20010118 SGD
+SGD S000003599 MRPL8 GO:0005762 SGD_REF:S000071753|PMID:12392552 IPI C YJL063C|HRD238|YmL8 gene taxon:4932 20040203 SGD
+SGD S000003599 MRPL8 GO:0003735 SGD_REF:S000058278|PMID:9445368 TAS F YJL063C|HRD238|YmL8 gene taxon:4932 20010118 SGD
+SGD S000003599 MRPL8 GO:0000002 SGD_REF:S000049904|PMID:2183197 IMP P YJL063C|HRD238|YmL8 gene taxon:4932 20010118 SGD
+SGD S000003599 MRPL8 GO:0043037 SGD_REF:S000058278|PMID:9445368 TAS P YJL063C|HRD238|YmL8 gene taxon:4932 20010118 SGD
+SGD S000003452 MRPL9 GO:0005762 SGD_REF:S000058278|PMID:9445368 TAS C YGR220C|YmL9 gene taxon:4932 20010118 SGD
+SGD S000003452 MRPL9 GO:0000048 SGD_REF:S000058278|PMID:9445368 ISS F YGR220C|YmL9 gene taxon:4932 20010118 SGD
+SGD S000003452 MRPL9 GO:0003735 SGD_REF:S000058278|PMID:9445368 TAS F YGR220C|YmL9 gene taxon:4932 20010118 SGD
+SGD S000003452 MRPL9 GO:0000027 SGD_REF:S000058278|PMID:9445368 ISS P YGR220C|YmL9 gene taxon:4932 20010118 SGD
+SGD S000003452 MRPL9 GO:0043037 SGD_REF:S000058278|PMID:9445368 TAS P YGR220C|YmL9 gene taxon:4932 20010118 SGD
+SGD S000005934 MRPS16 GO:0005763 SGD_REF:S000071753|PMID:12392552 IPI C YPL013C gene taxon:4932 20021213 SGD
+SGD S000005934 MRPS16 GO:0005763 SGD_REF:S000071753|PMID:12392552 ISS C YPL013C gene taxon:4932 20021213 SGD
+SGD S000005934 MRPS16 GO:0003735 SGD_REF:S000071753|PMID:12392552 ISS F YPL013C gene taxon:4932 20021209 SGD
+SGD S000005934 MRPS16 GO:0003735 SGD_REF:S000071753|PMID:12392552 IPI F YPL013C gene taxon:4932 20021209 SGD
+SGD S000005934 MRPS16 GO:0043037 SGD_REF:S000071753|PMID:12392552 IC GO:0003735|GO:0005763 P YPL013C gene taxon:4932 20021213 SGD
+SGD S000004800 MRPS17 GO:0005763 SGD_REF:S000071753|PMID:12392552 IPI C YMR188C gene taxon:4932 20021212 SGD
+SGD S000004800 MRPS17 GO:0005763 SGD_REF:S000060148|PMID:10929718 ISS C YMR188C gene taxon:4932 20020806 SGD
+SGD S000004800 MRPS17 GO:0003735 SGD_REF:S000071753|PMID:12392552 IPI F YMR188C gene taxon:4932 20021209 SGD
+SGD S000004800 MRPS17 GO:0003735 SGD_REF:S000060148|PMID:10929718 ISS F YMR188C gene taxon:4932 20020806 SGD
+SGD S000004800 MRPS17 GO:0009060 SGD_REF:S000060148|PMID:10929718 IEP P YMR188C gene taxon:4932 20020806 SGD
+SGD S000004800 MRPS17 GO:0009060 SGD_REF:S000060148|PMID:10929718 IMP P YMR188C gene taxon:4932 20020806 SGD
+SGD S000004800 MRPS17 GO:0043037 SGD_REF:S000071753|PMID:12392552 IC GO:0003735|GO:0005763 P YMR188C gene taxon:4932 20021213 SGD
+SGD S000005250 MRPS18 GO:0005763 SGD_REF:S000058441|PMID:9151978 IPI C YNL306W|YmS18 gene taxon:4932 20010918 SGD
+SGD S000005250 MRPS18 GO:0003735 SGD_REF:S000058441|PMID:9151978 ISS F YNL306W|YmS18 gene taxon:4932 20010105 SGD
+SGD S000005250 MRPS18 GO:0003735 SGD_REF:S000058441|PMID:9151978 IPI F YNL306W|YmS18 gene taxon:4932 20010105 SGD
+SGD S000005250 MRPS18 GO:0043037 SGD_REF:S000058441|PMID:9151978 IPI P YNL306W|YmS18 gene taxon:4932 20010105 SGD
+SGD S000002745 MRPS28 GO:0005763 SGD_REF:S000058278|PMID:9445368 TAS C ribosomal protein (E. coli S15) YDR337W gene taxon:4932 20010118 SGD
+SGD S000002745 MRPS28 GO:0005763 SGD_REF:S000060645|PMID:11278769 IDA C ribosomal protein (E. coli S15) YDR337W gene taxon:4932 20010918 SGD
+SGD S000002745 MRPS28 GO:0003723 SGD_REF:S000058278|PMID:9445368 ISS F ribosomal protein (E. coli S15) YDR337W gene taxon:4932 20010118 SGD
+SGD S000002745 MRPS28 GO:0003735 SGD_REF:S000058278|PMID:9445368 TAS F ribosomal protein (E. coli S15) YDR337W gene taxon:4932 20010118 SGD
+SGD S000002745 MRPS28 GO:0003735 SGD_REF:S000060645|PMID:11278769 IDA F ribosomal protein (E. coli S15) YDR337W gene taxon:4932 20010918 SGD
+SGD S000002745 MRPS28 GO:0000028 SGD_REF:S000058278|PMID:9445368 ISS P ribosomal protein (E. coli S15) YDR337W gene taxon:4932 20010118 SGD
+SGD S000002745 MRPS28 GO:0043037 SGD_REF:S000058278|PMID:9445368 TAS P ribosomal protein (E. coli S15) YDR337W gene taxon:4932 20010118 SGD
+SGD S000002745 MRPS28 GO:0043037 SGD_REF:S000060645|PMID:11278769 IDA P ribosomal protein (E. coli S15) YDR337W gene taxon:4932 20010918 SGD
+SGD S000003397 MRPS35 GO:0005763 SGD_REF:S000071753|PMID:12392552 IPI C YGR165W gene taxon:4932 20021209 SGD
+SGD S000003397 MRPS35 GO:0003735 SGD_REF:S000071753|PMID:12392552 IPI F YGR165W gene taxon:4932 20021209 SGD
+SGD S000003397 MRPS35 GO:0009060 SGD_REF:S000060148|PMID:10929718 IEP P YGR165W gene taxon:4932 20020806 SGD
+SGD S000003397 MRPS35 GO:0009060 SGD_REF:S000060148|PMID:10929718 IMP P YGR165W gene taxon:4932 20020806 SGD
+SGD S000003397 MRPS35 GO:0043037 SGD_REF:S000071753|PMID:12392552 IC GO:0003735|GO:0005763 P YGR165W gene taxon:4932 20021212 SGD
+SGD S000000455 MRPS5 GO:0005763 SGD_REF:S000060645|PMID:11278769 IDA C ribosomal protein S5 (putative) YBR251W gene taxon:4932 20010918 SGD
+SGD S000000455 MRPS5 GO:0003735 SGD_REF:S000060645|PMID:11278769 IDA F ribosomal protein S5 (putative) YBR251W gene taxon:4932 20010918 SGD
+SGD S000000455 MRPS5 GO:0043037 SGD_REF:S000060645|PMID:11278769 IDA P ribosomal protein S5 (putative) YBR251W gene taxon:4932 20010918 SGD
+SGD S000004767 MRPS8 GO:0005763 SGD_REF:S000071753|PMID:12392552 IPI C YMR158W gene taxon:4932 20021209 SGD
+SGD S000004767 MRPS8 GO:0003735 SGD_REF:S000071753|PMID:12392552 ISS F YMR158W gene taxon:4932 20021209 SGD
+SGD S000004767 MRPS8 GO:0003735 SGD_REF:S000071753|PMID:12392552 IPI F YMR158W gene taxon:4932 20021209 SGD
+SGD S000004767 MRPS8 GO:0043037 SGD_REF:S000071753|PMID:12392552 IC GO:0003735|GO:0005763 P YMR158W gene taxon:4932 20021213 SGD
+SGD S000000350 MRPS9 GO:0005763 SGD_REF:S000058278|PMID:9445368 TAS C ribosomal protein S9 (putative) YBR146W gene taxon:4932 20010118 SGD
+SGD S000000350 MRPS9 GO:0005763 SGD_REF:S000060645|PMID:11278769 IDA C ribosomal protein S9 (putative) YBR146W gene taxon:4932 20010918 SGD
+SGD S000000350 MRPS9 GO:0003735 SGD_REF:S000058278|PMID:9445368 TAS F ribosomal protein S9 (putative) YBR146W gene taxon:4932 20010118 SGD
+SGD S000000350 MRPS9 GO:0003735 SGD_REF:S000060645|PMID:11278769 IDA F ribosomal protein S9 (putative) YBR146W gene taxon:4932 20010918 SGD
+SGD S000000350 MRPS9 GO:0043037 SGD_REF:S000058278|PMID:9445368 TAS P ribosomal protein S9 (putative) YBR146W gene taxon:4932 20010118 SGD
+SGD S000000350 MRPS9 GO:0043037 SGD_REF:S000060645|PMID:11278769 IDA P ribosomal protein S9 (putative) YBR146W gene taxon:4932 20010918 SGD
+SGD S000001460 MRS1 GO:0005739 SGD_REF:S000068996|PMID:11773622 TAS C YIR021W|PET157 gene taxon:4932 20030821 SGD
+SGD S000001460 MRS1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YIR021W|PET157 gene taxon:4932 20040928 SGD
+SGD S000001460 MRS1 GO:0003723 SGD_REF:S000068996|PMID:11773622 IDA F YIR021W|PET157 gene taxon:4932 20030821 SGD
+SGD S000001460 MRS1 NOT GO:0004520 SGD_REF:S000068996|PMID:11773622 IDA F YIR021W|PET157 gene taxon:4932 20030821 SGD
+SGD S000001460 MRS1 NOT GO:0004520 SGD_REF:S000068996|PMID:11773622 ISS SGD:S000001494 F YIR021W|PET157 gene taxon:4932 20030821 SGD
+SGD S000001460 MRS1 GO:0000372 SGD_REF:S000068996|PMID:11773622 IDA P YIR021W|PET157 gene taxon:4932 20030821 SGD
+SGD S000003530 MRS11 GO:0005758 SGD_REF:S000044939|PMID:9495346 TAS C YHR005C-A|TIM10 gene taxon:4932 20010118 SGD
+SGD S000003530 MRS11 GO:0042719 SGD_REF:S000040056|PMID:9822593 IDA C YHR005C-A|TIM10 gene taxon:4932 20030430 SGD
+SGD S000003530 MRS11 GO:0008565 SGD_REF:S000052756|PMID:9430585 IMP F YHR005C-A|TIM10 gene taxon:4932 20010118 SGD
+SGD S000003530 MRS11 GO:0008565 SGD_REF:S000044939|PMID:9495346 IPI F YHR005C-A|TIM10 gene taxon:4932 20010118 SGD
+SGD S000003530 MRS11 GO:0051082 SGD_REF:S000071708|PMID:12138093 IDA F YHR005C-A|TIM10 gene taxon:4932 20030121 SGD
+SGD S000003530 MRS11 GO:0045039 SGD_REF:S000044939|PMID:9495346 IPI P YHR005C-A|TIM10 gene taxon:4932 20031119 SGD
+SGD S000003530 MRS11 GO:0045039 SGD_REF:S000052756|PMID:9430585 IMP P YHR005C-A|TIM10 gene taxon:4932 20031119 SGD
+SGD S000005861 MRS2 GO:0005743 SGD_REF:S000047067|PMID:10400670 IDA C magnesium ion transporter YOR334W gene taxon:4932 20010118 SGD
+SGD S000005861 MRS2 GO:0015095 SGD_REF:S000047067|PMID:10400670 IMP F magnesium ion transporter YOR334W gene taxon:4932 20010118 SGD
+SGD S000005861 MRS2 GO:0015095 SGD_REF:S000047067|PMID:10400670 ISS F magnesium ion transporter YOR334W gene taxon:4932 20010118 SGD
+SGD S000005861 MRS2 GO:0015095 SGD_REF:S000047067|PMID:10400670 IGI F magnesium ion transporter YOR334W gene taxon:4932 20010118 SGD
+SGD S000005861 MRS2 GO:0015095 SGD_REF:S000073152|PMID:12628916 IDA F magnesium ion transporter YOR334W gene taxon:4932 20030519 SGD
+SGD S000005861 MRS2 GO:0000373 SGD_REF:S000054851|PMID:1551905 IMP P magnesium ion transporter YOR334W gene taxon:4932 20010118 SGD
+SGD S000005861 MRS2 GO:0045016 SGD_REF:S000047067|PMID:10400670 IGI P magnesium ion transporter YOR334W gene taxon:4932 20020920 SGD
+SGD S000005861 MRS2 GO:0045016 SGD_REF:S000047067|PMID:10400670 ISS P magnesium ion transporter YOR334W gene taxon:4932 20020920 SGD
+SGD S000005861 MRS2 GO:0045016 SGD_REF:S000047067|PMID:10400670 IMP P magnesium ion transporter YOR334W gene taxon:4932 20020920 SGD
+SGD S000005861 MRS2 GO:0045016 SGD_REF:S000073152|PMID:12628916 IDA P magnesium ion transporter YOR334W gene taxon:4932 20030519 SGD
+SGD S000003669 MRS3 GO:0005739 SGD_REF:S000048548|PMID:1703236 IDA C carrier protein YJL133W gene taxon:4932 20010118 SGD
+SGD S000003669 MRS3 GO:0005381 SGD_REF:S000075094|PMID:12902335 IMP F carrier protein YJL133W gene taxon:4932 20040415 SGD
+SGD S000003669 MRS3 GO:0005386 SGD_REF:S000048548|PMID:1703236 ISS F carrier protein YJL133W gene taxon:4932 20010118 SGD
+SGD S000003669 MRS3 GO:0006839 SGD_REF:S000048548|PMID:1703236 ISS P carrier protein YJL133W gene taxon:4932 20050207 SGD
+SGD S000003669 MRS3 GO:0008380 SGD_REF:S000046397|PMID:2448588 IGI P carrier protein YJL133W gene taxon:4932 20010118 SGD
+SGD S000003669 MRS3 GO:0048250 SGD_REF:S000075094|PMID:12902335 IDA P carrier protein YJL133W gene taxon:4932 20050207 SGD
+SGD S000001760 MRS4 GO:0005739 SGD_REF:S000048548|PMID:1703236 IDA C carrier protein YKR052C gene taxon:4932 20010118 SGD
+SGD S000001760 MRS4 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C carrier protein YKR052C gene taxon:4932 20040924 SGD
+SGD S000001760 MRS4 GO:0005381 SGD_REF:S000075094|PMID:12902335 IMP F carrier protein YKR052C gene taxon:4932 20040415 SGD
+SGD S000001760 MRS4 GO:0005386 SGD_REF:S000048548|PMID:1703236 ISS F carrier protein YKR052C gene taxon:4932 20010118 SGD
+SGD S000001760 MRS4 GO:0006839 SGD_REF:S000048548|PMID:1703236 ISS P carrier protein YKR052C gene taxon:4932 20050207 SGD
+SGD S000001760 MRS4 GO:0008380 SGD_REF:S000043922|PMID:8252639 IGI P carrier protein YKR052C gene taxon:4932 20010118 SGD
+SGD S000001760 MRS4 GO:0048250 SGD_REF:S000075094|PMID:12902335 IDA P carrier protein YKR052C gene taxon:4932 20050207 SGD
+SGD S000000295 MRS5 GO:0005758 SGD_REF:S000044939|PMID:9495346 TAS C YBR091C|TIM12 gene taxon:4932 20010118 SGD
+SGD S000000295 MRS5 GO:0042721 SGD_REF:S000073048|PMID:12581629 TAS C YBR091C|TIM12 gene taxon:4932 20030430 SGD
+SGD S000000295 MRS5 GO:0008565 SGD_REF:S000052756|PMID:9430585 IMP F YBR091C|TIM12 gene taxon:4932 20010118 SGD
+SGD S000000295 MRS5 GO:0008565 SGD_REF:S000044939|PMID:9495346 IPI F YBR091C|TIM12 gene taxon:4932 20010118 SGD
+SGD S000000295 MRS5 GO:0045039 SGD_REF:S000044939|PMID:9495346 IPI P YBR091C|TIM12 gene taxon:4932 20031119 SGD
+SGD S000000295 MRS5 GO:0045039 SGD_REF:S000052756|PMID:9430585 IMP P YBR091C|TIM12 gene taxon:4932 20031119 SGD
+SGD S000005897 MRS6 GO:0005737 SGD_REF:S000049341|PMID:9202009 IDA C rab geranylgeranyltransferase regulatory subunit YOR370C|MSI4 gene taxon:4932 20010118 SGD
+SGD S000005897 MRS6 GO:0016020 SGD_REF:S000049341|PMID:9202009 IDA C rab geranylgeranyltransferase regulatory subunit YOR370C|MSI4 gene taxon:4932 20010118 SGD
+SGD S000005897 MRS6 GO:0005084 SGD_REF:S000049341|PMID:9202009 TAS F rab geranylgeranyltransferase regulatory subunit YOR370C|MSI4 gene taxon:4932 20010118 SGD
+SGD S000005897 MRS6 GO:0006886 SGD_REF:S000049341|PMID:9202009 TAS P rab geranylgeranyltransferase regulatory subunit YOR370C|MSI4 gene taxon:4932 20010118 SGD
+SGD S000001492 MRT4 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YKL009W gene taxon:4932 20031028 SGD
+SGD S000001492 MRT4 GO:0005730 SGD_REF:S000074185|PMID:14562095 IDA C YKL009W gene taxon:4932 20031028 SGD
+SGD S000001492 MRT4 GO:0005554 SGD_REF:S000069584 ND F YKL009W gene taxon:4932 20020927 SGD
+SGD S000001492 MRT4 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P YKL009W gene taxon:4932 20060227 SGD
+SGD S000001492 MRT4 GO:0006364 SGD_REF:S000073750|PMID:12837249 IMP P YKL009W gene taxon:4932 20030805 SGD
+SGD S000001492 MRT4 GO:0006402 SGD_REF:S000054755|PMID:10471698 IMP P YKL009W gene taxon:4932 20040617 SGD
+SGD S000001492 MRT4 GO:0042273 SGD_REF:S000066002|PMID:11583614 IMP P YKL009W gene taxon:4932 20020927 SGD
+SGD S000001492 MRT4 GO:0042273 SGD_REF:S000066002|PMID:11583614 IPI P YKL009W gene taxon:4932 20020927 SGD
+SGD S000005714 MSB1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YOR188W gene taxon:4932 20040928 SGD
+SGD S000005714 MSB1 GO:0005934 SGD_REF:S000040830|PMID:10679030 TAS C YOR188W gene taxon:4932 20021101 SGD
+SGD S000005714 MSB1 GO:0005935 SGD_REF:S000040830|PMID:10679030 TAS C YOR188W gene taxon:4932 20021101 SGD
+SGD S000005714 MSB1 GO:0005554 SGD_REF:S000069584 ND F YOR188W gene taxon:4932 20021101 SGD
+SGD S000005714 MSB1 GO:0030468 SGD_REF:S000040830|PMID:10679030 IGI P YOR188W gene taxon:4932 20021101 SGD
+SGD S000003246 MSB2 GO:0005887 SGD_REF:S000070226|PMID:12052881 IMP C integral membrane protein (putative) YGR014W gene taxon:4932 20021205 SGD
+SGD S000003246 MSB2 GO:0005887 SGD_REF:S000070226|PMID:12052881 ISS C integral membrane protein (putative) YGR014W gene taxon:4932 20021205 SGD
+SGD S000003246 MSB2 GO:0030427 SGD_REF:S000077085|PMID:15256499 IDA C integral membrane protein (putative) YGR014W gene taxon:4932 20041012 SGD
+SGD S000003246 MSB2 GO:0005034 SGD_REF:S000070226|PMID:12052881 IMP F integral membrane protein (putative) YGR014W gene taxon:4932 20021205 SGD
+SGD S000003246 MSB2 GO:0001402 SGD_REF:S000077085|PMID:15256499 IGI P integral membrane protein (putative) YGR014W gene taxon:4932 20041012 SGD
+SGD S000003246 MSB2 GO:0001402 SGD_REF:S000077085|PMID:15256499 IMP P integral membrane protein (putative) YGR014W gene taxon:4932 20041012 SGD
+SGD S000003246 MSB2 GO:0001402 SGD_REF:S000077085|PMID:15256499 IEP P integral membrane protein (putative) YGR014W gene taxon:4932 20041012 SGD
+SGD S000003246 MSB2 GO:0006970 SGD_REF:S000070226|PMID:12052881 IMP P integral membrane protein (putative) YGR014W gene taxon:4932 20021205 SGD
+SGD S000003246 MSB2 GO:0030468 SGD_REF:S000043084|PMID:1514328 IGI P integral membrane protein (putative) YGR014W gene taxon:4932 20010302 SGD
+SGD S000005237 MSB3 GO:0000131 SGD_REF:S000040830|PMID:10679030 IDA C GTPase activating protein (GAP) for Ypt6 YNL293W|GYP3 gene taxon:4932 20010118 SGD
+SGD S000005237 MSB3 GO:0005934 SGD_REF:S000040830|PMID:10679030 IDA C GTPase activating protein (GAP) for Ypt6 YNL293W|GYP3 gene taxon:4932 20010118 SGD
+SGD S000005237 MSB3 GO:0005097 SGD_REF:S000056405|PMID:10559187 ISS F GTPase activating protein (GAP) for Ypt6 YNL293W|GYP3 gene taxon:4932 20010118 SGD
+SGD S000005237 MSB3 GO:0005097 SGD_REF:S000056405|PMID:10559187 IDA F GTPase activating protein (GAP) for Ypt6 YNL293W|GYP3 gene taxon:4932 20010118 SGD
+SGD S000005237 MSB3 GO:0006887 SGD_REF:S000056405|PMID:10559187 TAS P GTPase activating protein (GAP) for Ypt6 YNL293W|GYP3 gene taxon:4932 20010118 SGD
+SGD S000005237 MSB3 GO:0007015 SGD_REF:S000040830|PMID:10679030 TAS P GTPase activating protein (GAP) for Ypt6 YNL293W|GYP3 gene taxon:4932 20010118 SGD
+SGD S000005472 MSB4 GO:0000131 SGD_REF:S000040830|PMID:10679030 IDA C YOL112W gene taxon:4932 20010118 SGD
+SGD S000005472 MSB4 GO:0005934 SGD_REF:S000040830|PMID:10679030 IDA C YOL112W gene taxon:4932 20010118 SGD
+SGD S000005472 MSB4 GO:0005097 SGD_REF:S000062162|PMID:10937877 IDA F YOL112W gene taxon:4932 20021001 SGD
+SGD S000005472 MSB4 GO:0007015 SGD_REF:S000040830|PMID:10679030 TAS P YOL112W gene taxon:4932 20010118 SGD
+SGD S000004597 MSC1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YML128C gene taxon:4932 20040928 SGD
+SGD S000004597 MSC1 GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YML128C gene taxon:4932 20031028 SGD
+SGD S000004597 MSC1 GO:0005554 SGD_REF:S000069584 ND F YML128C gene taxon:4932 20021011 SGD
+SGD S000004597 MSC1 GO:0007131 SGD_REF:S000039358|PMID:10511544 IMP P YML128C gene taxon:4932 20021011 SGD
+SGD S000002613 MSC2 GO:0005634 SGD_REF:S000060746|PMID:11058603 IDA C YDR205W gene taxon:4932 20020925 SGD
+SGD S000002613 MSC2 GO:0005783 SGD_REF:S000060746|PMID:11058603 IDA C YDR205W gene taxon:4932 20020925 SGD
+SGD S000002613 MSC2 GO:0016020 SGD_REF:S000060746|PMID:11058603 ISS C YDR205W gene taxon:4932 20020925 SGD
+SGD S000002613 MSC2 GO:0015491 SGD_REF:S000060746|PMID:11058603 ISS F YDR205W gene taxon:4932 20020925 SGD
+SGD S000002613 MSC2 GO:0015491 SGD_REF:S000060746|PMID:11058603 IMP F YDR205W gene taxon:4932 20020925 SGD
+SGD S000002613 MSC2 GO:0006882 SGD_REF:S000060746|PMID:11058603 IMP P YDR205W gene taxon:4932 20020925 SGD
+SGD S000004209 MSC3 GO:0008372 SGD_REF:S000069584 ND C YLR219W gene taxon:4932 20021011 SGD
+SGD S000004209 MSC3 GO:0005554 SGD_REF:S000069584 ND F YLR219W gene taxon:4932 20021011 SGD
+SGD S000004209 MSC3 GO:0007131 SGD_REF:S000039358|PMID:10511544 IMP P YLR219W gene taxon:4932 20021011 SGD
+SGD S000005881 MSC6 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YOR354C gene taxon:4932 20031028 SGD
+SGD S000005881 MSC6 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YOR354C gene taxon:4932 20040924 SGD
+SGD S000005881 MSC6 GO:0005554 SGD_REF:S000069584 ND F YOR354C gene taxon:4932 20021011 SGD
+SGD S000005881 MSC6 GO:0007131 SGD_REF:S000039358|PMID:10511544 IMP P YOR354C gene taxon:4932 20021011 SGD
+SGD S000001081 MSC7 GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YHR039C gene taxon:4932 20031028 SGD
+SGD S000001081 MSC7 GO:0005554 SGD_REF:S000069584 ND F YHR039C gene taxon:4932 20021011 SGD
+SGD S000001081 MSC7 GO:0007131 SGD_REF:S000039358|PMID:10511544 IMP P YHR039C gene taxon:4932 20021011 SGD
+SGD S000006025 MSD1 GO:0005739 SGD_REF:S000048983|PMID:2668951 ISS C aspartyl-tRNA synthetase YPL104W|LPG5 gene taxon:4932 20010118 SGD
+SGD S000006025 MSD1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C aspartyl-tRNA synthetase YPL104W|LPG5 gene taxon:4932 20040928 SGD
+SGD S000006025 MSD1 GO:0005739 SGD_REF:S000048983|PMID:2668951 IMP C aspartyl-tRNA synthetase YPL104W|LPG5 gene taxon:4932 20010118 SGD
+SGD S000006025 MSD1 GO:0004815 SGD_REF:S000048983|PMID:2668951 ISS F aspartyl-tRNA synthetase YPL104W|LPG5 gene taxon:4932 20010118 SGD
+SGD S000006025 MSD1 GO:0004815 SGD_REF:S000048983|PMID:2668951 IMP F aspartyl-tRNA synthetase YPL104W|LPG5 gene taxon:4932 20010118 SGD
+SGD S000006025 MSD1 GO:0006412 SGD_REF:S000048983|PMID:2668951 IMP P aspartyl-tRNA synthetase YPL104W|LPG5 gene taxon:4932 20010118 SGD
+SGD S000006025 MSD1 GO:0006412 SGD_REF:S000048983|PMID:2668951 ISS P aspartyl-tRNA synthetase YPL104W|LPG5 gene taxon:4932 20010118 SGD
+SGD S000005393 MSE1 GO:0005739 SGD_REF:S000047144|PMID:7607232 IDA C glutamine-tRNA ligase YOL033W gene taxon:4932 20021009 SGD
+SGD S000005393 MSE1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C glutamine-tRNA ligase YOL033W gene taxon:4932 20040924 SGD
+SGD S000005393 MSE1 GO:0004818 SGD_REF:S000047144|PMID:7607232 ISS F glutamine-tRNA ligase YOL033W gene taxon:4932 20020930 SGD
+SGD S000005393 MSE1 GO:0004818 SGD_REF:S000047144|PMID:7607232 IMP F glutamine-tRNA ligase YOL033W gene taxon:4932 20020930 SGD
+SGD S000005393 MSE1 GO:0006412 SGD_REF:S000047144|PMID:7607232 IMP P glutamine-tRNA ligase YOL033W gene taxon:4932 20021028 SGD
+SGD S000005393 MSE1 GO:0006412 SGD_REF:S000047144|PMID:7607232 ISS P glutamine-tRNA ligase YOL033W gene taxon:4932 20021028 SGD
+SGD S000005393 MSE1 GO:0006424 SGD_REF:S000047144|PMID:7607232 IMP P glutamine-tRNA ligase YOL033W gene taxon:4932 20020930 SGD
+SGD S000006251 MSF1 GO:0005739 SGD_REF:S000042633|PMID:3029120 IMP C phenylalanyl-tRNA synthetase alpha subunit YPR047W gene taxon:4932 20010118 SGD
+SGD S000006251 MSF1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C phenylalanyl-tRNA synthetase alpha subunit YPR047W gene taxon:4932 20040928 SGD
+SGD S000006251 MSF1 GO:0004826 SGD_REF:S000042633|PMID:3029120 IMP F phenylalanyl-tRNA synthetase alpha subunit YPR047W gene taxon:4932 20010118 SGD
+SGD S000006251 MSF1 GO:0004826 SGD_REF:S000042633|PMID:3029120 ISS F phenylalanyl-tRNA synthetase alpha subunit YPR047W gene taxon:4932 20010118 SGD
+SGD S000006251 MSF1 GO:0006412 SGD_REF:S000042633|PMID:3029120 IMP P phenylalanyl-tRNA synthetase alpha subunit YPR047W gene taxon:4932 20010118 SGD
+SGD S000004998 MSG5 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C protein tyrosine phosphatase YNL053W gene taxon:4932 20031028 SGD
+SGD S000004998 MSG5 GO:0004727 SGD_REF:S000041317|PMID:8306972 IMP F protein tyrosine phosphatase YNL053W gene taxon:4932 20010118 SGD
+SGD S000004998 MSG5 GO:0000754 SGD_REF:S000041317|PMID:8306972 IMP P protein tyrosine phosphatase YNL053W gene taxon:4932 20021206 SGD
+SGD S000004998 MSG5 GO:0006470 SGD_REF:S000075679|PMID:14703512 IDA P protein tyrosine phosphatase YNL053W gene taxon:4932 20040617 SGD
+SGD S000001162 MSH1 GO:0005739 SGD_REF:S000069205|PMID:11862493 IDA C mutS homolog YHR120W gene taxon:4932 20021022 SGD
+SGD S000001162 MSH1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C mutS homolog YHR120W gene taxon:4932 20040924 SGD
+SGD S000001162 MSH1 GO:0005524 SGD_REF:S000069205|PMID:11862493 ISS F mutS homolog YHR120W gene taxon:4932 20021022 SGD
+SGD S000001162 MSH1 GO:0006281 SGD_REF:S000054454|PMID:1334021 IMP P mutS homolog YHR120W gene taxon:4932 20030123 SGD
+SGD S000005450 MSH2 GO:0000228 SGD_REF:S000044043|PMID:10882115 IDA C mutS homolog YOL090W|PMS5 gene taxon:4932 20020806 SGD
+SGD S000005450 MSH2 GO:0003684 SGD_REF:S000057936|PMID:8805366 IDA F mutS homolog YOL090W|PMS5 gene taxon:4932 20020925 SGD
+SGD S000005450 MSH2 GO:0005524 SGD_REF:S000051290|PMID:9545323 IDA F mutS homolog YOL090W|PMS5 gene taxon:4932 20021021 SGD
+SGD S000005450 MSH2 GO:0016887 SGD_REF:S000047828|PMID:9819445 IDA F mutS homolog YOL090W|PMS5 gene taxon:4932 20021021 SGD
+SGD S000005450 MSH2 GO:0000735 SGD_REF:S000053753|PMID:10357855 TAS P mutS homolog YOL090W|PMS5 gene taxon:4932 20020925 SGD
+SGD S000005450 MSH2 GO:0006298 SGD_REF:S000055135|PMID:8056309 IMP P mutS homolog YOL090W|PMS5 gene taxon:4932 20020806 SGD
+SGD S000005450 MSH2 GO:0006310 SGD_REF:S000040358|PMID:9256462 IMP P mutS homolog YOL090W|PMS5 gene taxon:4932 20020806 SGD
+SGD S000005450 MSH2 GO:0006310 SGD_REF:S000081889|PMID:15920474 IMP P mutS homolog YOL090W|PMS5 gene taxon:4932 20050714 SGD
+SGD S000005450 MSH2 GO:0006312 SGD_REF:S000051942|PMID:8849883 IMP P mutS homolog YOL090W|PMS5 gene taxon:4932 20020806 SGD
+SGD S000000688 MSH3 GO:0000228 SGD_REF:S000044043|PMID:10882115 IPI C forms a complex with Msh2p to repair insertion-deletion mispairs; redundant with Pms3/Msh6p in repair of insertion-deletion mispairs, mutS homolog YCR092C gene taxon:4932 20020806 SGD
+SGD S000000688 MSH3 GO:0003684 SGD_REF:S000057936|PMID:8805366 IDA F forms a complex with Msh2p to repair insertion-deletion mispairs; redundant with Pms3/Msh6p in repair of insertion-deletion mispairs, mutS homolog YCR092C gene taxon:4932 20020925 SGD
+SGD S000000688 MSH3 GO:0000735 SGD_REF:S000053753|PMID:10357855 TAS P forms a complex with Msh2p to repair insertion-deletion mispairs; redundant with Pms3/Msh6p in repair of insertion-deletion mispairs, mutS homolog YCR092C gene taxon:4932 20020925 SGD
+SGD S000000688 MSH3 GO:0006298 SGD_REF:S000043851|PMID:8510668 IMP P forms a complex with Msh2p to repair insertion-deletion mispairs; redundant with Pms3/Msh6p in repair of insertion-deletion mispairs, mutS homolog YCR092C gene taxon:4932 20020806 SGD
+SGD S000000688 MSH3 GO:0006310 SGD_REF:S000040358|PMID:9256462 IMP P forms a complex with Msh2p to repair insertion-deletion mispairs; redundant with Pms3/Msh6p in repair of insertion-deletion mispairs, mutS homolog YCR092C gene taxon:4932 20020806 SGD
+SGD S000000688 MSH3 GO:0006310 SGD_REF:S000081889|PMID:15920474 IMP P forms a complex with Msh2p to repair insertion-deletion mispairs; redundant with Pms3/Msh6p in repair of insertion-deletion mispairs, mutS homolog YCR092C gene taxon:4932 20050714 SGD
+SGD S000000688 MSH3 GO:0006312 SGD_REF:S000051942|PMID:8849883 IMP P forms a complex with Msh2p to repair insertion-deletion mispairs; redundant with Pms3/Msh6p in repair of insertion-deletion mispairs, mutS homolog YCR092C gene taxon:4932 20020806 SGD
+SGD S000001891 MSH4 GO:0000228 SGD_REF:S000066161|PMID:11454751 IDA C meiosis specific protein, E.coli MutS protein, localizes to discrete sites on meiotic chromosomes YFL003C gene taxon:4932 20020806 SGD
+SGD S000001891 MSH4 GO:0003677 SGD_REF:S000066161|PMID:11454751 IPI F meiosis specific protein, E.coli MutS protein, localizes to discrete sites on meiotic chromosomes YFL003C gene taxon:4932 20020806 SGD
+SGD S000001891 MSH4 GO:0007131 SGD_REF:S000066161|PMID:11454751 IMP P meiosis specific protein, E.coli MutS protein, localizes to discrete sites on meiotic chromosomes YFL003C gene taxon:4932 20020806 SGD
+SGD S000002313 MSH5 GO:0005634 SGD_REF:S000069459|PMID:11914276 IDA C mutS homolog YDL154W gene taxon:4932 20020507 SGD
+SGD S000002313 MSH5 GO:0005554 SGD_REF:S000069584 ND F mutS homolog YDL154W gene taxon:4932 20021115 SGD
+SGD S000002313 MSH5 GO:0007131 SGD_REF:S000049715|PMID:9374523 IMP P mutS homolog YDL154W gene taxon:4932 20021115 SGD
+SGD S000002504 MSH6 GO:0005634 SGD_REF:S000051290|PMID:9545323 IPI C human GTBP protein homolog YDR097C|PMS3 gene taxon:4932 20021021 SGD
+SGD S000002504 MSH6 GO:0003677 SGD_REF:S000068895|PMID:11641390 IDA F human GTBP protein homolog YDR097C|PMS3 gene taxon:4932 20021022 SGD
+SGD S000002504 MSH6 GO:0005524 SGD_REF:S000051290|PMID:9545323 IDA F human GTBP protein homolog YDR097C|PMS3 gene taxon:4932 20021021 SGD
+SGD S000002504 MSH6 GO:0016887 SGD_REF:S000047828|PMID:9819445 IDA F human GTBP protein homolog YDR097C|PMS3 gene taxon:4932 20021021 SGD
+SGD S000002504 MSH6 GO:0006298 SGD_REF:S000059906|PMID:11237611 IDA P human GTBP protein homolog YDR097C|PMS3 gene taxon:4932 20021022 SGD
+SGD S000000399 MSI1 GO:0005677 SGD_REF:S000047698|PMID:9436982 IMP C chromatin assembly factor-I (CAF-I) p50 subunit, negative regulator of ras-mediated cAMP induction, similar to GTP-binding protein beta subunit YBR195C|CAC3 gene taxon:4932 20010118 SGD
+SGD S000000399 MSI1 GO:0005678 SGD_REF:S000047698|PMID:9436982 TAS C chromatin assembly factor-I (CAF-I) p50 subunit, negative regulator of ras-mediated cAMP induction, similar to GTP-binding protein beta subunit YBR195C|CAC3 gene taxon:4932 20010118 SGD
+SGD S000000399 MSI1 GO:0005678 SGD_REF:S000048516|PMID:9030687 IDA C chromatin assembly factor-I (CAF-I) p50 subunit, negative regulator of ras-mediated cAMP induction, similar to GTP-binding protein beta subunit YBR195C|CAC3 gene taxon:4932 20020716 SGD
+SGD S000000399 MSI1 GO:0030528 SGD_REF:S000080322|PMID:15632066 IMP F chromatin assembly factor-I (CAF-I) p50 subunit, negative regulator of ras-mediated cAMP induction, similar to GTP-binding protein beta subunit YBR195C|CAC3 gene taxon:4932 20050216 SGD
+SGD S000000399 MSI1 GO:0006281 SGD_REF:S000053371|PMID:9927445 IMP P chromatin assembly factor-I (CAF-I) p50 subunit, negative regulator of ras-mediated cAMP induction, similar to GTP-binding protein beta subunit YBR195C|CAC3 gene taxon:4932 20010118 SGD
+SGD S000000399 MSI1 GO:0006334 SGD_REF:S000048516|PMID:9030687 IMP P chromatin assembly factor-I (CAF-I) p50 subunit, negative regulator of ras-mediated cAMP induction, similar to GTP-binding protein beta subunit YBR195C|CAC3 gene taxon:4932 20010118 SGD
+SGD S000000399 MSI1 GO:0006342 SGD_REF:S000047698|PMID:9436982 IMP P chromatin assembly factor-I (CAF-I) p50 subunit, negative regulator of ras-mediated cAMP induction, similar to GTP-binding protein beta subunit YBR195C|CAC3 gene taxon:4932 20010118 SGD
+SGD S000000399 MSI1 GO:0007265 SGD_REF:S000047778|PMID:8350924 TAS P chromatin assembly factor-I (CAF-I) p50 subunit, negative regulator of ras-mediated cAMP induction, similar to GTP-binding protein beta subunit YBR195C|CAC3 gene taxon:4932 20010118 SGD
+SGD S000005017 MSK1 GO:0005739 SGD_REF:S000046853|PMID:2016746 ISS C lysine-tRNA ligase YNL073W gene taxon:4932 20021009 SGD
+SGD S000005017 MSK1 GO:0005739 SGD_REF:S000046853|PMID:2016746 IMP C lysine-tRNA ligase YNL073W gene taxon:4932 20021009 SGD
+SGD S000005017 MSK1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C lysine-tRNA ligase YNL073W gene taxon:4932 20040928 SGD
+SGD S000005017 MSK1 GO:0004824 SGD_REF:S000046853|PMID:2016746 ISS F lysine-tRNA ligase YNL073W gene taxon:4932 20030115 SGD
+SGD S000005017 MSK1 GO:0006430 SGD_REF:S000046853|PMID:2016746 IMP P lysine-tRNA ligase YNL073W gene taxon:4932 20030115 SGD
+SGD S000005017 MSK1 GO:0006430 SGD_REF:S000046853|PMID:2016746 ISS P lysine-tRNA ligase YNL073W gene taxon:4932 20030115 SGD
+SGD S000001448 MSL1 GO:0005686 SGD_REF:S000069986|PMID:11804584 IDA C U2 snRNP component, YU2B'' YIR009W|YIB9|YIB9w gene taxon:4932 20020621 SGD
+SGD S000001448 MSL1 GO:0003723 SGD_REF:S000055331|PMID:8649387 IDA F U2 snRNP component, YU2B'' YIR009W|YIB9|YIB9w gene taxon:4932 20021101 SGD
+SGD S000001448 MSL1 GO:0000398 SGD_REF:S000055331|PMID:8649387 IPI P U2 snRNP component, YU2B'' YIR009W|YIB9|YIB9w gene taxon:4932 20021101 SGD
+SGD S000001448 MSL1 GO:0000398 SGD_REF:S000055331|PMID:8649387 ISS P U2 snRNP component, YU2B'' YIR009W|YIB9|YIB9w gene taxon:4932 20021101 SGD
+SGD S000004106 MSL5 GO:0000243 SGD_REF:S000041389|PMID:10376880 IDA C YLR116W|BBP gene taxon:4932 20021118 SGD
+SGD S000004106 MSL5 GO:0000243 SGD_REF:S000040368|PMID:9150140 IDA C YLR116W|BBP gene taxon:4932 20051103 SGD
+SGD S000004106 MSL5 GO:0003723 SGD_REF:S000039901|PMID:9182766 IDA F YLR116W|BBP gene taxon:4932 20021118 SGD
+SGD S000004106 MSL5 GO:0000398 SGD_REF:S000039901|PMID:9182766 IPI P YLR116W|BBP gene taxon:4932 20021118 SGD
+SGD S000003403 MSM1 GO:0005739 SGD_REF:S000050047|PMID:2645139 IDA C methionine-tRNA ligase YGR171C gene taxon:4932 20020930 SGD
+SGD S000003403 MSM1 GO:0005739 SGD_REF:S000050047|PMID:2645139 IMP C methionine-tRNA ligase YGR171C gene taxon:4932 20020930 SGD
+SGD S000003403 MSM1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C methionine-tRNA ligase YGR171C gene taxon:4932 20040924 SGD
+SGD S000003403 MSM1 GO:0004825 SGD_REF:S000050047|PMID:2645139 ISS F methionine-tRNA ligase YGR171C gene taxon:4932 20020930 SGD
+SGD S000003403 MSM1 GO:0004825 SGD_REF:S000050047|PMID:2645139 IMP F methionine-tRNA ligase YGR171C gene taxon:4932 20020930 SGD
+SGD S000003403 MSM1 GO:0006431 SGD_REF:S000050047|PMID:2645139 ISS P methionine-tRNA ligase YGR171C gene taxon:4932 20020930 SGD
+SGD S000003403 MSM1 GO:0006431 SGD_REF:S000050047|PMID:2645139 IMP P methionine-tRNA ligase YGR171C gene taxon:4932 20020930 SGD
+SGD S000005476 MSN1 GO:0005634 SGD_REF:S000050427|PMID:2263457 IDA C transcriptional activator YOL116W|FUP1|HRB382|MSS10|PHD2 gene taxon:4932 20020730 SGD
+SGD S000005476 MSN1 GO:0016563 SGD_REF:S000075227|PMID:14523573 TAS F transcriptional activator YOL116W|FUP1|HRB382|MSS10|PHD2 gene taxon:4932 20040322 SGD
+SGD S000005476 MSN1 GO:0016563 SGD_REF:S000050427|PMID:2263457 IDA F transcriptional activator YOL116W|FUP1|HRB382|MSS10|PHD2 gene taxon:4932 20040708 SGD
+SGD S000005476 MSN1 GO:0001403 SGD_REF:S000055959|PMID:8710886 IMP P transcriptional activator YOL116W|FUP1|HRB382|MSS10|PHD2 gene taxon:4932 20040708 SGD
+SGD S000005476 MSN1 GO:0006972 SGD_REF:S000045247|PMID:10409737 IGI P transcriptional activator YOL116W|FUP1|HRB382|MSS10|PHD2 gene taxon:4932 20020730 SGD
+SGD S000005476 MSN1 GO:0006972 SGD_REF:S000045247|PMID:10409737 IMP P transcriptional activator YOL116W|FUP1|HRB382|MSS10|PHD2 gene taxon:4932 20020730 SGD
+SGD S000004640 MSN2 GO:0005634 SGD_REF:S000048927|PMID:9472026 IDA C zinc finger protein YMR037C gene taxon:4932 20021014 SGD
+SGD S000004640 MSN2 GO:0005829 SGD_REF:S000071579|PMID:12093809 IDA C zinc finger protein YMR037C gene taxon:4932 20030130 SGD
+SGD S000004640 MSN2 GO:0003677 SGD_REF:S000071531|PMID:12395196 TAS F zinc finger protein YMR037C gene taxon:4932 20021114 SGD
+SGD S000004640 MSN2 GO:0003677 SGD_REF:S000057352|PMID:7492309 IDA F zinc finger protein YMR037C gene taxon:4932 20050119 SGD
+SGD S000004640 MSN2 GO:0003700 SGD_REF:S000060704|PMID:11058591 TAS F zinc finger protein YMR037C gene taxon:4932 20030325 SGD
+SGD S000004640 MSN2 GO:0001302 SGD_REF:S000075416|PMID:14741356 IMP P zinc finger protein YMR037C gene taxon:4932 20041025 SGD
+SGD S000004640 MSN2 GO:0001324 SGD_REF:S000060129|PMID:11292860 IMP P zinc finger protein YMR037C gene taxon:4932 20041025 SGD
+SGD S000004640 MSN2 GO:0006355 SGD_REF:S000070097|PMID:12090248 TAS P zinc finger protein YMR037C gene taxon:4932 20020728 SGD
+SGD S000004640 MSN2 GO:0006950 SGD_REF:S000059106|PMID:11102521 IMP P zinc finger protein YMR037C gene taxon:4932 20030122 SGD
+SGD S000004640 MSN2 GO:0006950 SGD_REF:S000059106|PMID:11102521 TAS P zinc finger protein YMR037C gene taxon:4932 20030122 SGD
+SGD S000001545 MSN4 GO:0005634 SGD_REF:S000048927|PMID:9472026 IDA C zinc finger protein YKL062W gene taxon:4932 20021014 SGD
+SGD S000001545 MSN4 GO:0005737 SGD_REF:S000061818|PMID:10366774 TAS C zinc finger protein YKL062W gene taxon:4932 20030311 SGD
+SGD S000001545 MSN4 GO:0003677 SGD_REF:S000071531|PMID:12395196 TAS F zinc finger protein YKL062W gene taxon:4932 20021114 SGD
+SGD S000001545 MSN4 GO:0003700 SGD_REF:S000060704|PMID:11058591 TAS F zinc finger protein YKL062W gene taxon:4932 20030325 SGD
+SGD S000001545 MSN4 GO:0001302 SGD_REF:S000075416|PMID:14741356 IMP P zinc finger protein YKL062W gene taxon:4932 20041025 SGD
+SGD S000001545 MSN4 GO:0001324 SGD_REF:S000060129|PMID:11292860 IMP P zinc finger protein YKL062W gene taxon:4932 20041025 SGD
+SGD S000001545 MSN4 GO:0006355 SGD_REF:S000070097|PMID:12090248 TAS P zinc finger protein YKL062W gene taxon:4932 20020728 SGD
+SGD S000001545 MSN4 GO:0006950 SGD_REF:S000070097|PMID:12090248 TAS P zinc finger protein YKL062W gene taxon:4932 20020728 SGD
+SGD S000002743 MSN5 GO:0005634 SGD_REF:S000055677|PMID:10545454 IDA C YDR335W|KAP142|STE21 gene taxon:4932 20010118 SGD
+SGD S000002743 MSN5 GO:0005634 SGD_REF:S000048425|PMID:10485850 IDA C YDR335W|KAP142|STE21 gene taxon:4932 20010118 SGD
+SGD S000002743 MSN5 GO:0005515 SGD_REF:S000073233|PMID:12697814 IPI SGD:S000004172 F YDR335W|KAP142|STE21 gene taxon:4932 20030618 SGD
+SGD S000002743 MSN5 GO:0008262 SGD_REF:S000040511|PMID:9214382 ISS F YDR335W|KAP142|STE21 gene taxon:4932 20010118 SGD
+SGD S000002743 MSN5 GO:0008262 SGD_REF:S000040511|PMID:9214382 IDA F YDR335W|KAP142|STE21 gene taxon:4932 20010118 SGD
+SGD S000002743 MSN5 GO:0006611 SGD_REF:S000052885|PMID:9853758 IDA P YDR335W|KAP142|STE21 gene taxon:4932 20010118 SGD
+SGD S000002743 MSN5 GO:0006611 SGD_REF:S000073233|PMID:12697814 IDA P YDR335W|KAP142|STE21 gene taxon:4932 20030618 SGD
+SGD S000005332 MSO1 GO:0005792 SGD_REF:S000040510|PMID:9207091 IDA C YNR049C gene taxon:4932 20020930 SGD
+SGD S000005332 MSO1 GO:0005554 SGD_REF:S000069584 ND F YNR049C gene taxon:4932 20021211 SGD
+SGD S000005332 MSO1 GO:0006904 SGD_REF:S000040510|PMID:9207091 IDA P YNR049C gene taxon:4932 20020930 SGD
+SGD S000005332 MSO1 GO:0006904 SGD_REF:S000040510|PMID:9207091 IMP P YNR049C gene taxon:4932 20020930 SGD
+SGD S000005332 MSO1 GO:0006904 SGD_REF:S000040510|PMID:9207091 IPI P YNR049C gene taxon:4932 20020930 SGD
+SGD S000005332 MSO1 GO:0030437 SGD_REF:S000069693|PMID:11839791 IGI P YNR049C gene taxon:4932 20020930 SGD
+SGD S000005332 MSO1 GO:0030437 SGD_REF:S000069693|PMID:11839791 IMP P YNR049C gene taxon:4932 20020930 SGD
+SGD S000005332 MSO1 GO:0030437 SGD_REF:S000069693|PMID:11839791 IPI P YNR049C gene taxon:4932 20020930 SGD
+SGD S000003260 MSP1 GO:0005741 SGD_REF:S000042427|PMID:8226973 IDA C 40 kDa membrane-spanning ATPase YGR028W|YTA4 gene taxon:4932 20010118 SGD
+SGD S000003260 MSP1 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C 40 kDa membrane-spanning ATPase YGR028W|YTA4 gene taxon:4932 20060317 SGD
+SGD S000003260 MSP1 GO:0016887 SGD_REF:S000042427|PMID:8226973 ISS F 40 kDa membrane-spanning ATPase YGR028W|YTA4 gene taxon:4932 20010118 SGD
+SGD S000003260 MSP1 GO:0006626 SGD_REF:S000042427|PMID:8226973 IGI P 40 kDa membrane-spanning ATPase YGR028W|YTA4 gene taxon:4932 20031119 SGD
+SGD S000001133 MSR1 GO:0005739 SGD_REF:S000047144|PMID:7607232 IMP C arginyl-tRNA synthetase YHR091C gene taxon:4932 20021028 SGD
+SGD S000001133 MSR1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C arginyl-tRNA synthetase YHR091C gene taxon:4932 20040928 SGD
+SGD S000001133 MSR1 GO:0004814 SGD_REF:S000047144|PMID:7607232 IMP F arginyl-tRNA synthetase YHR091C gene taxon:4932 20021028 SGD
+SGD S000001133 MSR1 GO:0006412 SGD_REF:S000047144|PMID:7607232 IMP P arginyl-tRNA synthetase YHR091C gene taxon:4932 20021028 SGD
+SGD S000001133 MSR1 GO:0006412 SGD_REF:S000047144|PMID:7607232 ISS P arginyl-tRNA synthetase YHR091C gene taxon:4932 20021028 SGD
+SGD S000001133 MSR1 GO:0006420 SGD_REF:S000047144|PMID:7607232 IMP P arginyl-tRNA synthetase YHR091C gene taxon:4932 20020930 SGD
+SGD S000004625 MSS1 GO:0005743 SGD_REF:S000066248|PMID:11604502 IDA C GTPase (putative) YMR023C|PET53 gene taxon:4932 20021003 SGD
+SGD S000004625 MSS1 GO:0005525 SGD_REF:S000044773|PMID:8392589 ISS F GTPase (putative) YMR023C|PET53 gene taxon:4932 20010118 SGD
+SGD S000004625 MSS1 GO:0006400 SGD_REF:S000080941|PMID:15509579 IMP P GTPase (putative) YMR023C|PET53 gene taxon:4932 20050407 SGD
+SGD S000004625 MSS1 GO:0006412 SGD_REF:S000044773|PMID:8392589 IMP P GTPase (putative) YMR023C|PET53 gene taxon:4932 20010118 SGD
+SGD S000004625 MSS1 GO:0006412 SGD_REF:S000080941|PMID:15509579 IMP P GTPase (putative) YMR023C|PET53 gene taxon:4932 20050407 SGD
+SGD S000004774 MSS11 GO:0005634 SGD_REF:S000072527|PMID:12492858 IC GO:0003704 C 758 amino acid polypeptide with poly-glutamine and poly-asparagine domains YMR164C gene taxon:4932 20030213 SGD
+SGD S000004774 MSS11 GO:0003704 SGD_REF:S000072527|PMID:12492858 IDA F 758 amino acid polypeptide with poly-glutamine and poly-asparagine domains YMR164C gene taxon:4932 20030213 SGD
+SGD S000004774 MSS11 GO:0005983 SGD_REF:S000053194|PMID:9342405 IMP P 758 amino acid polypeptide with poly-glutamine and poly-asparagine domains YMR164C gene taxon:4932 20030213 SGD
+SGD S000004774 MSS11 GO:0007124 SGD_REF:S000043169|PMID:9832522 IGI P 758 amino acid polypeptide with poly-glutamine and poly-asparagine domains YMR164C gene taxon:4932 20030213 SGD
+SGD S000004774 MSS11 GO:0045944 SGD_REF:S000072527|PMID:12492858 IDA P 758 amino acid polypeptide with poly-glutamine and poly-asparagine domains YMR164C gene taxon:4932 20030213 SGD
+SGD S000002602 MSS116 GO:0005759 SGD_REF:S000056872|PMID:2535893 IMP C RNA helicase DEAD box YDR194C gene taxon:4932 20010118 SGD
+SGD S000002602 MSS116 GO:0003724 SGD_REF:S000056872|PMID:2535893 ISS F RNA helicase DEAD box YDR194C gene taxon:4932 20010118 SGD
+SGD S000002602 MSS116 GO:0031202 SGD_REF:S000080136|PMID:15618406 IMP F RNA helicase DEAD box YDR194C gene taxon:4932 20050213 SGD
+SGD S000002602 MSS116 GO:0008380 SGD_REF:S000056872|PMID:2535893 ISS P RNA helicase DEAD box YDR194C gene taxon:4932 20010118 SGD
+SGD S000002602 MSS116 GO:0008380 SGD_REF:S000080136|PMID:15618406 IMP P RNA helicase DEAD box YDR194C gene taxon:4932 20050213 SGD
+SGD S000006338 MSS18 GO:0005739 SGD_REF:S000055996|PMID:2842150 IC GO:0000372 C YPR134W gene taxon:4932 20030821 SGD
+SGD S000006338 MSS18 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YPR134W gene taxon:4932 20040928 SGD
+SGD S000006338 MSS18 GO:0005554 SGD_REF:S000069584 ND F YPR134W gene taxon:4932 20050301 SGD
+SGD S000006338 MSS18 GO:0000372 SGD_REF:S000055996|PMID:2842150 IDA P YPR134W gene taxon:4932 20020930 SGD
+SGD S000006338 MSS18 GO:0000372 SGD_REF:S000055996|PMID:2842150 IMP P YPR134W gene taxon:4932 20020930 SGD
+SGD S000002265 MSS2 GO:0005743 SGD_REF:S000066248|PMID:11604502 IDA C cox2 pre-mRNA splicing factor YDL107W gene taxon:4932 20021001 SGD
+SGD S000002265 MSS2 GO:0015450 SGD_REF:S000066248|PMID:11604502 IGI F cox2 pre-mRNA splicing factor YDL107W gene taxon:4932 20040123 SGD
+SGD S000002265 MSS2 GO:0015450 SGD_REF:S000066248|PMID:11604502 IMP F cox2 pre-mRNA splicing factor YDL107W gene taxon:4932 20040123 SGD
+SGD S000002265 MSS2 GO:0006461 SGD_REF:S000066248|PMID:11604502 IDA P cox2 pre-mRNA splicing factor YDL107W gene taxon:4932 20021001 SGD
+SGD S000002265 MSS2 GO:0006461 SGD_REF:S000066248|PMID:11604502 IPI P cox2 pre-mRNA splicing factor YDL107W gene taxon:4932 20021001 SGD
+SGD S000002265 MSS2 GO:0006461 SGD_REF:S000066248|PMID:11604502 IMP P cox2 pre-mRNA splicing factor YDL107W gene taxon:4932 20021001 SGD
+SGD S000002265 MSS2 GO:0050821 SGD_REF:S000066248|PMID:11604502 IMP P cox2 pre-mRNA splicing factor YDL107W gene taxon:4932 20021001 SGD
+SGD S000002265 MSS2 GO:0050821 SGD_REF:S000066248|PMID:11604502 IDA P cox2 pre-mRNA splicing factor YDL107W gene taxon:4932 20021001 SGD
+SGD S000002616 MSS4 GO:0005886 SGD_REF:S000047458|PMID:9624177 IDA C phosphatidylinositol 4-phosphate kinase YDR208W gene taxon:4932 20010214 SGD
+SGD S000002616 MSS4 GO:0016308 SGD_REF:S000047458|PMID:9624177 IDA F phosphatidylinositol 4-phosphate kinase YDR208W gene taxon:4932 20010214 SGD
+SGD S000002616 MSS4 GO:0030036 SGD_REF:S000047459|PMID:9624178 IMP P phosphatidylinositol 4-phosphate kinase YDR208W gene taxon:4932 20021001 SGD
+SGD S000002616 MSS4 GO:0030437 SGD_REF:S000075947|PMID:14528019 IGI P phosphatidylinositol 4-phosphate kinase YDR208W gene taxon:4932 20040816 SGD
+SGD S000002616 MSS4 GO:0030437 SGD_REF:S000075947|PMID:14528019 IMP P phosphatidylinositol 4-phosphate kinase YDR208W gene taxon:4932 20040816 SGD
+SGD S000002616 MSS4 GO:0045011 SGD_REF:S000047459|PMID:9624178 IMP P phosphatidylinositol 4-phosphate kinase YDR208W gene taxon:4932 20021001 SGD
+SGD S000004193 MSS51 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YLR203C gene taxon:4932 20031028 SGD
+SGD S000004193 MSS51 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YLR203C gene taxon:4932 20040924 SGD
+SGD S000004193 MSS51 GO:0005743 SGD_REF:S000077016|PMID:15306853 IDA C YLR203C gene taxon:4932 20050301 SGD
+SGD S000004193 MSS51 GO:0005759 SGD_REF:S000077016|PMID:15306853 IDA C YLR203C gene taxon:4932 20050301 SGD
+SGD S000004193 MSS51 GO:0019898 SGD_REF:S000077016|PMID:15306853 IDA C YLR203C gene taxon:4932 20050301 SGD
+SGD S000004193 MSS51 GO:0005554 SGD_REF:S000057943|PMID:8811190 TAS F YLR203C gene taxon:4932 20010118 SGD
+SGD S000004193 MSS51 GO:0006412 SGD_REF:S000057943|PMID:8811190 TAS P YLR203C gene taxon:4932 20010118 SGD
+SGD S000004193 MSS51 GO:0045946 SGD_REF:S000077016|PMID:15306853 IGI SGD:S000003344 P YLR203C gene taxon:4932 20050301 SGD
+SGD S000004193 MSS51 GO:0045946 SGD_REF:S000077016|PMID:15306853 IMP P YLR203C gene taxon:4932 20050301 SGD
+SGD S000004193 MSS51 GO:0045946 SGD_REF:S000077016|PMID:15306853 IPI SGD:S000004598|SGD:S000007260 P YLR203C gene taxon:4932 20050301 SGD
+SGD S000001677 MST1 GO:0005739 SGD_REF:S000055130|PMID:2999113 TAS C YKL194C gene taxon:4932 20021001 SGD
+SGD S000001677 MST1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YKL194C gene taxon:4932 20040928 SGD
+SGD S000001677 MST1 GO:0004829 SGD_REF:S000055130|PMID:2999113 ISS F YKL194C gene taxon:4932 20021001 SGD
+SGD S000001677 MST1 GO:0004829 SGD_REF:S000055130|PMID:2999113 IMP F YKL194C gene taxon:4932 20021001 SGD
+SGD S000001677 MST1 GO:0006435 SGD_REF:S000055130|PMID:2999113 IMP P YKL194C gene taxon:4932 20021001 SGD
+SGD S000001677 MST1 GO:0006435 SGD_REF:S000055130|PMID:2999113 TAS P YKL194C gene taxon:4932 20021001 SGD
+SGD S000003019 MST27 GO:0005783 SGD_REF:S000073907|PMID:12925749 IDA C protein with COPI and COPII bindng motifs YGL051W gene taxon:4932 20030918 SGD
+SGD S000003019 MST27 GO:0005794 SGD_REF:S000073907|PMID:12925749 IDA C protein with COPI and COPII bindng motifs YGL051W gene taxon:4932 20030918 SGD
+SGD S000003019 MST27 GO:0016021 SGD_REF:S000073907|PMID:12925749 IDA C protein with COPI and COPII bindng motifs YGL051W gene taxon:4932 20030918 SGD
+SGD S000003019 MST27 GO:0005515 SGD_REF:S000073907|PMID:12925749 IDA F protein with COPI and COPII bindng motifs YGL051W gene taxon:4932 20030918 SGD
+SGD S000003019 MST27 GO:0016050 SGD_REF:S000073907|PMID:12925749 IGI P protein with COPI and COPII bindng motifs YGL051W gene taxon:4932 20030918 SGD
+SGD S000003019 MST27 GO:0016050 SGD_REF:S000073907|PMID:12925749 IPI P protein with COPI and COPII bindng motifs YGL051W gene taxon:4932 20030918 SGD
+SGD S000000079 MST28 GO:0005783 SGD_REF:S000073907|PMID:12925749 IPI C YAR033W gene taxon:4932 20030918 SGD
+SGD S000000079 MST28 GO:0005794 SGD_REF:S000073907|PMID:12925749 IPI C YAR033W gene taxon:4932 20030918 SGD
+SGD S000000079 MST28 GO:0016021 SGD_REF:S000073907|PMID:12925749 IDA C YAR033W gene taxon:4932 20030918 SGD
+SGD S000000079 MST28 GO:0005515 SGD_REF:S000073907|PMID:12925749 IDA F YAR033W gene taxon:4932 20030918 SGD
+SGD S000000079 MST28 GO:0016050 SGD_REF:S000073907|PMID:12925749 IGI P YAR033W gene taxon:4932 20030918 SGD
+SGD S000000079 MST28 GO:0016050 SGD_REF:S000073907|PMID:12925749 IPI P YAR033W gene taxon:4932 20030918 SGD
+SGD S000004900 MSU1 GO:0005739 SGD_REF:S000053502|PMID:9829834 IDA C 3'-5' exonuclease complex component YMR287C|DSS1 gene taxon:4932 20020715 SGD
+SGD S000004900 MSU1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C 3'-5' exonuclease complex component YMR287C|DSS1 gene taxon:4932 20040924 SGD
+SGD S000004900 MSU1 GO:0005759 SGD_REF:S000072589|PMID:12426313 IDA C 3'-5' exonuclease complex component YMR287C|DSS1 gene taxon:4932 20030225 SGD
+SGD S000004900 MSU1 GO:0008859 SGD_REF:S000072589|PMID:12426313 IDA F 3'-5' exonuclease complex component YMR287C|DSS1 gene taxon:4932 20030225 SGD
+SGD S000004900 MSU1 GO:0006401 SGD_REF:S000072589|PMID:12426313 IDA P 3'-5' exonuclease complex component YMR287C|DSS1 gene taxon:4932 20030225 SGD
+SGD S000004900 MSU1 GO:0006401 SGD_REF:S000072589|PMID:12426313 IMP P 3'-5' exonuclease complex component YMR287C|DSS1 gene taxon:4932 20030225 SGD
+SGD S000004900 MSU1 GO:0006401 SGD_REF:S000053502|PMID:9829834 IMP P 3'-5' exonuclease complex component YMR287C|DSS1 gene taxon:4932 20020715 SGD
+SGD S000002676 MSW1 GO:0005739 SGD_REF:S000056978|PMID:2999114 TAS C tryptophan-tRNA ligase YDR268W gene taxon:4932 20021001 SGD
+SGD S000002676 MSW1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C tryptophan-tRNA ligase YDR268W gene taxon:4932 20040928 SGD
+SGD S000002676 MSW1 GO:0004830 SGD_REF:S000056978|PMID:2999114 ISS F tryptophan-tRNA ligase YDR268W gene taxon:4932 20021001 SGD
+SGD S000002676 MSW1 GO:0004830 SGD_REF:S000056978|PMID:2999114 IMP F tryptophan-tRNA ligase YDR268W gene taxon:4932 20021001 SGD
+SGD S000002676 MSW1 GO:0006436 SGD_REF:S000056978|PMID:2999114 IMP P tryptophan-tRNA ligase YDR268W gene taxon:4932 20021001 SGD
+SGD S000006018 MSY1 GO:0005739 SGD_REF:S000064160|PMID:3315228 TAS C tyrosine-tRNA ligase YPL097W gene taxon:4932 20021125 SGD
+SGD S000006018 MSY1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C tyrosine-tRNA ligase YPL097W gene taxon:4932 20040928 SGD
+SGD S000006018 MSY1 GO:0004831 SGD_REF:S000064160|PMID:3315228 TAS F tyrosine-tRNA ligase YPL097W gene taxon:4932 20021125 SGD
+SGD S000006018 MSY1 GO:0006437 SGD_REF:S000064160|PMID:3315228 TAS P tyrosine-tRNA ligase YPL097W gene taxon:4932 20031217 SGD
+SGD S000001788 MTD1 GO:0005829 SGD_REF:S000039764|PMID:8608153 IDA C NAD-dependent 5,10-methylenetetrahydrafolate dehydrogenase YKR080W gene taxon:4932 20021104 SGD
+SGD S000001788 MTD1 GO:0004487 SGD_REF:S000050049|PMID:8416923 IMP F NAD-dependent 5,10-methylenetetrahydrafolate dehydrogenase YKR080W gene taxon:4932 20030116 SGD
+SGD S000001788 MTD1 GO:0004487 SGD_REF:S000050049|PMID:8416923 ISS F NAD-dependent 5,10-methylenetetrahydrafolate dehydrogenase YKR080W gene taxon:4932 20030116 SGD
+SGD S000001788 MTD1 GO:0006730 SGD_REF:S000039764|PMID:8608153 IDA P NAD-dependent 5,10-methylenetetrahydrafolate dehydrogenase YKR080W gene taxon:4932 20021001 SGD
+SGD S000001788 MTD1 GO:0006730 SGD_REF:S000039764|PMID:8608153 IMP P NAD-dependent 5,10-methylenetetrahydrafolate dehydrogenase YKR080W gene taxon:4932 20021001 SGD
+SGD S000001788 MTD1 GO:0009113 SGD_REF:S000039764|PMID:8608153 IDA P NAD-dependent 5,10-methylenetetrahydrafolate dehydrogenase YKR080W gene taxon:4932 20021001 SGD
+SGD S000001788 MTD1 GO:0009113 SGD_REF:S000039764|PMID:8608153 IMP P NAD-dependent 5,10-methylenetetrahydrafolate dehydrogenase YKR080W gene taxon:4932 20021001 SGD
+SGD S000004841 MTF1 GO:0005759 SGD_REF:S000054279|PMID:10447593 TAS C mitochondrial RNA polymerase specificity factor YMR228W gene taxon:4932 20010118 SGD
+SGD S000004841 MTF1 GO:0003712 SGD_REF:S000071170|PMID:12021282 IGI F mitochondrial RNA polymerase specificity factor YMR228W gene taxon:4932 20030311 SGD
+SGD S000004841 MTF1 GO:0003712 SGD_REF:S000071170|PMID:12021282 IMP F mitochondrial RNA polymerase specificity factor YMR228W gene taxon:4932 20030311 SGD
+SGD S000004841 MTF1 GO:0003712 SGD_REF:S000071170|PMID:12021282 TAS F mitochondrial RNA polymerase specificity factor YMR228W gene taxon:4932 20030311 SGD
+SGD S000004841 MTF1 GO:0008757 SGD_REF:S000074033|PMID:12872006 ISS F mitochondrial RNA polymerase specificity factor YMR228W gene taxon:4932 20031001 SGD
+SGD S000004841 MTF1 GO:0006390 SGD_REF:S000054279|PMID:10447593 TAS P mitochondrial RNA polymerase specificity factor YMR228W gene taxon:4932 20010118 SGD
+SGD S000002202 MTF2 GO:0005739 SGD_REF:S000039394|PMID:8200349 IDA C YDL044C|NAM1 gene taxon:4932 20010118 SGD
+SGD S000002202 MTF2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YDL044C|NAM1 gene taxon:4932 20040924 SGD
+SGD S000002202 MTF2 GO:0003723 SGD_REF:S000040489|PMID:8413192 IMP F YDL044C|NAM1 gene taxon:4932 20010118 SGD
+SGD S000002202 MTF2 GO:0006397 SGD_REF:S000040489|PMID:8413192 IMP P YDL044C|NAM1 gene taxon:4932 20010118 SGD
+SGD S000002202 MTF2 GO:0006412 SGD_REF:S000073179|PMID:12637560 IMP P YDL044C|NAM1 gene taxon:4932 20030616 SGD
+SGD S000004703 MTG1 GO:0005743 SGD_REF:S000073563|PMID:12808030 IDA C GTPase YMR097C gene taxon:4932 20030707 SGD
+SGD S000004703 MTG1 GO:0003924 SGD_REF:S000073563|PMID:12808030 ISS F GTPase YMR097C gene taxon:4932 20030707 SGD
+SGD S000004703 MTG1 GO:0006412 SGD_REF:S000073563|PMID:12808030 IDA P GTPase YMR097C gene taxon:4932 20030707 SGD
+SGD S000004703 MTG1 GO:0042255 SGD_REF:S000073563|PMID:12808030 IMP P GTPase YMR097C gene taxon:4932 20030707 SGD
+SGD S000001211 MTG2 GO:0005743 SGD_REF:S000080105|PMID:15591131 IDA C GTPase YHR168W gene taxon:4932 20050104 SGD
+SGD S000001211 MTG2 GO:0019898 SGD_REF:S000080105|PMID:15591131 IDA C GTPase YHR168W gene taxon:4932 20050104 SGD
+SGD S000001211 MTG2 GO:0003924 SGD_REF:S000080105|PMID:15591131 ISS F GTPase YHR168W gene taxon:4932 20050104 SGD
+SGD S000001211 MTG2 GO:0043022 SGD_REF:S000080105|PMID:15591131 IDA F GTPase YHR168W gene taxon:4932 20050104 SGD
+SGD S000001211 MTG2 GO:0006412 SGD_REF:S000080105|PMID:15591131 IMP P GTPase YHR168W gene taxon:4932 20050104 SGD
+SGD S000002685 MTH1 GO:0008372 SGD_REF:S000069584 ND C Msn3p homolog (61% identical) YDR277C|BPC1|DGT1|HTR1 gene taxon:4932 20021003 SGD
+SGD S000002685 MTH1 GO:0005554 SGD_REF:S000069584 ND F Msn3p homolog (61% identical) YDR277C|BPC1|DGT1|HTR1 gene taxon:4932 20021003 SGD
+SGD S000002685 MTH1 GO:0007165 SGD_REF:S000042733|PMID:10629208 IGI P Msn3p homolog (61% identical) YDR277C|BPC1|DGT1|HTR1 gene taxon:4932 20021003 SGD
+SGD S000002685 MTH1 GO:0007165 SGD_REF:S000042733|PMID:10629208 IMP P Msn3p homolog (61% identical) YDR277C|BPC1|DGT1|HTR1 gene taxon:4932 20021003 SGD
+SGD S000002685 MTH1 GO:0015758 SGD_REF:S000042733|PMID:10629208 IMP P Msn3p homolog (61% identical) YDR277C|BPC1|DGT1|HTR1 gene taxon:4932 20020408 SGD
+SGD S000003255 MTL1 GO:0005887 SGD_REF:S000048543|PMID:10330137 ISS C acts in concert with Mid2p to transduce cell wall stress signals YGR023W gene taxon:4932 20021001 SGD
+SGD S000003255 MTL1 GO:0005554 SGD_REF:S000069584 ND F acts in concert with Mid2p to transduce cell wall stress signals YGR023W gene taxon:4932 20021211 SGD
+SGD S000003255 MTL1 GO:0007047 SGD_REF:S000048543|PMID:10330137 IGI P acts in concert with Mid2p to transduce cell wall stress signals YGR023W gene taxon:4932 20021001 SGD
+SGD S000003255 MTL1 GO:0007047 SGD_REF:S000048543|PMID:10330137 IMP P acts in concert with Mid2p to transduce cell wall stress signals YGR023W gene taxon:4932 20021001 SGD
+SGD S000003489 MTM1 GO:0005739 SGD_REF:S000073895|PMID:12890866 IDA C putative mitochondrial carrier protein YGR257C gene taxon:4932 20030911 SGD
+SGD S000003489 MTM1 GO:0005743 SGD_REF:S000049213|PMID:10930523 ISS C putative mitochondrial carrier protein YGR257C gene taxon:4932 20021017 SGD
+SGD S000003489 MTM1 GO:0005215 SGD_REF:S000049213|PMID:10930523 ISS F putative mitochondrial carrier protein YGR257C gene taxon:4932 20021017 SGD
+SGD S000003489 MTM1 GO:0016530 SGD_REF:S000073895|PMID:12890866 IMP F putative mitochondrial carrier protein YGR257C gene taxon:4932 20030911 SGD
+SGD S000003489 MTM1 GO:0006810 SGD_REF:S000049213|PMID:10930523 ISS P putative mitochondrial carrier protein YGR257C gene taxon:4932 20021017 SGD
+SGD S000003489 MTM1 GO:0006828 SGD_REF:S000073895|PMID:12890866 IMP P putative mitochondrial carrier protein YGR257C gene taxon:4932 20030911 SGD
+SGD S000003205 MTO1 GO:0005739 SGD_REF:S000053827|PMID:9774408 IDA C YGL236C|IPS1 gene taxon:4932 20010118 SGD
+SGD S000003205 MTO1 GO:0005554 SGD_REF:S000069584 ND F YGL236C|IPS1 gene taxon:4932 20041217 SGD
+SGD S000003205 MTO1 GO:0006400 SGD_REF:S000080941|PMID:15509579 IMP P YGL236C|IPS1 gene taxon:4932 20050407 SGD
+SGD S000003205 MTO1 GO:0006412 SGD_REF:S000053827|PMID:9774408 IMP P YGL236C|IPS1 gene taxon:4932 20010118 SGD
+SGD S000003205 MTO1 GO:0006412 SGD_REF:S000080941|PMID:15509579 IMP P YGL236C|IPS1 gene taxon:4932 20050407 SGD
+SGD S000005007 MTQ1 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YNL063W gene taxon:4932 20031028 SGD
+SGD S000005007 MTQ1 GO:0008757 SGD_REF:S000056343|PMID:10220893 ISS F YNL063W gene taxon:4932 20030120 SGD
+SGD S000005007 MTQ1 GO:0008757 SGD_REF:S000113699|PMID:16321977 IMP F YNL063W gene taxon:4932 20051212 SGD
+SGD S000005007 MTQ1 GO:0008757 SGD_REF:S000113699|PMID:16321977 ISS F YNL063W gene taxon:4932 20051212 SGD
+SGD S000005007 MTQ1 GO:0008757 SGD_REF:S000113699|PMID:16321977 IDA F YNL063W gene taxon:4932 20051212 SGD
+SGD S000005007 MTQ1 GO:0000004 SGD_REF:S000069584 ND P YNL063W gene taxon:4932 20030120 SGD
+SGD S000002547 MTQ2 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YDR140W gene taxon:4932 20031028 SGD
+SGD S000002547 MTQ2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDR140W gene taxon:4932 20031028 SGD
+SGD S000002547 MTQ2 GO:0008276 SGD_REF:S000080294|PMID:15509572 IDA F YDR140W gene taxon:4932 20050225 SGD
+SGD S000002547 MTQ2 GO:0008757 SGD_REF:S000073093|PMID:9873020 ISS F YDR140W gene taxon:4932 20030507 SGD
+SGD S000002547 MTQ2 GO:0008757 SGD_REF:S000113699|PMID:16321977 ISS F YDR140W gene taxon:4932 20051212 SGD
+SGD S000002547 MTQ2 GO:0008757 SGD_REF:S000113699|PMID:16321977 IMP F YDR140W gene taxon:4932 20051212 SGD
+SGD S000002547 MTQ2 GO:0008757 SGD_REF:S000113699|PMID:16321977 IDA F YDR140W gene taxon:4932 20051212 SGD
+SGD S000002547 MTQ2 GO:0018364 SGD_REF:S000080294|PMID:15509572 IDA P YDR140W gene taxon:4932 20050225 SGD
+SGD S000005686 MTR10 GO:0005634 SGD_REF:S000063400|PMID:9545233 IDA C YOR160W|KAP111 gene taxon:4932 20020125 SGD
+SGD S000005686 MTR10 GO:0005737 SGD_REF:S000048708|PMID:9412460 IDA C YOR160W|KAP111 gene taxon:4932 20020125 SGD
+SGD S000005686 MTR10 GO:0008139 SGD_REF:S000063400|PMID:9545233 IPI F YOR160W|KAP111 gene taxon:4932 20020125 SGD
+SGD S000005686 MTR10 GO:0008139 SGD_REF:S000063400|PMID:9545233 TAS F YOR160W|KAP111 gene taxon:4932 20020125 SGD
+SGD S000005686 MTR10 GO:0006403 SGD_REF:S000071397|PMID:12167699 IMP P YOR160W|KAP111 gene taxon:4932 20030203 SGD
+SGD S000005686 MTR10 GO:0006606 SGD_REF:S000048708|PMID:9412460 IMP P YOR160W|KAP111 gene taxon:4932 20020125 SGD
+SGD S000005686 MTR10 GO:0006606 SGD_REF:S000063400|PMID:9545233 IPI P YOR160W|KAP111 gene taxon:4932 20020125 SGD
+SGD S000005686 MTR10 GO:0006606 SGD_REF:S000048708|PMID:9412460 ISS P YOR160W|KAP111 gene taxon:4932 20020125 SGD
+SGD S000005686 MTR10 GO:0006606 SGD_REF:S000048708|PMID:9412460 IPI P YOR160W|KAP111 gene taxon:4932 20020125 SGD
+SGD S000005686 MTR10 GO:0006606 SGD_REF:S000063400|PMID:9545233 IMP P YOR160W|KAP111 gene taxon:4932 20020125 SGD
+SGD S000005686 MTR10 GO:0006606 SGD_REF:S000063400|PMID:9545233 ISS P YOR160W|KAP111 gene taxon:4932 20020125 SGD
+SGD S000005686 MTR10 GO:0006609 SGD_REF:S000048708|PMID:9412460 IMP P YOR160W|KAP111 gene taxon:4932 20020125 SGD
+SGD S000005686 MTR10 GO:0006609 SGD_REF:S000063400|PMID:9545233 IPI P YOR160W|KAP111 gene taxon:4932 20020125 SGD
+SGD S000005686 MTR10 GO:0006609 SGD_REF:S000048708|PMID:9412460 ISS P YOR160W|KAP111 gene taxon:4932 20020125 SGD
+SGD S000005686 MTR10 GO:0006609 SGD_REF:S000048708|PMID:9412460 IPI P YOR160W|KAP111 gene taxon:4932 20020125 SGD
+SGD S000005686 MTR10 GO:0006609 SGD_REF:S000063400|PMID:9545233 IMP P YOR160W|KAP111 gene taxon:4932 20020125 SGD
+SGD S000005686 MTR10 GO:0006609 SGD_REF:S000063400|PMID:9545233 ISS P YOR160W|KAP111 gene taxon:4932 20020125 SGD
+SGD S000001669 MTR2 GO:0005643 SGD_REF:S000055080|PMID:9774696 IDA C mRNA transport regulator YKL186C gene taxon:4932 20020916 SGD
+SGD S000001669 MTR2 GO:0005515 SGD_REF:S000044294|PMID:10952996 IDA F mRNA transport regulator YKL186C gene taxon:4932 20020916 SGD
+SGD S000001669 MTR2 GO:0016973 SGD_REF:S000043592|PMID:7865887 IMP P mRNA transport regulator YKL186C gene taxon:4932 20020916 SGD
+SGD S000001669 MTR2 GO:0016973 SGD_REF:S000055080|PMID:9774696 IMP P mRNA transport regulator YKL186C gene taxon:4932 20020916 SGD
+SGD S000001669 MTR2 GO:0016973 SGD_REF:S000055080|PMID:9774696 IPI P mRNA transport regulator YKL186C gene taxon:4932 20020916 SGD
+SGD S000003390 MTR3 GO:0000176 SGD_REF:S000041327|PMID:10465791 IDA C YGR158C gene taxon:4932 20010118 SGD
+SGD S000003390 MTR3 GO:0000177 SGD_REF:S000041327|PMID:10465791 IDA C YGR158C gene taxon:4932 20010118 SGD
+SGD S000003390 MTR3 GO:0000175 SGD_REF:S000058443|PMID:10690410 TAS F YGR158C gene taxon:4932 20010118 SGD
+SGD S000003390 MTR3 GO:0006365 SGD_REF:S000058443|PMID:10690410 TAS P YGR158C gene taxon:4932 20010118 SGD
+SGD S000003390 MTR3 GO:0006402 SGD_REF:S000041327|PMID:10465791 IPI P YGR158C gene taxon:4932 20010118 SGD
+SGD S000003586 MTR4 GO:0005634 SGD_REF:S000043511|PMID:8756671 IDA C RNA helicase YJL050W|DOB1 gene taxon:4932 20050415 SGD
+SGD S000003586 MTR4 GO:0005730 SGD_REF:S000058443|PMID:10690410 TAS C RNA helicase YJL050W|DOB1 gene taxon:4932 20010118 SGD
+SGD S000003586 MTR4 GO:0031499 SGD_REF:S000081843|PMID:15935758 IDA C RNA helicase YJL050W|DOB1 gene taxon:4932 20050621 SGD
+SGD S000003586 MTR4 GO:0031499 SGD_REF:S000081843|PMID:15935758 IPI SGD:S000002334|SGD:S000005475 C RNA helicase YJL050W|DOB1 gene taxon:4932 20050621 SGD
+SGD S000003586 MTR4 GO:0031499 SGD_REF:S000081438|PMID:15828860 IDA C RNA helicase YJL050W|DOB1 gene taxon:4932 20050621 SGD
+SGD S000003586 MTR4 GO:0004004 SGD_REF:S000043511|PMID:8756671 ISS SGD:S000004390 F RNA helicase YJL050W|DOB1 gene taxon:4932 20050415 SGD
+SGD S000003586 MTR4 GO:0006365 SGD_REF:S000058443|PMID:10690410 TAS P RNA helicase YJL050W|DOB1 gene taxon:4932 20010118 SGD
+SGD S000003586 MTR4 GO:0006406 SGD_REF:S000043511|PMID:8756671 IMP P RNA helicase YJL050W|DOB1 gene taxon:4932 20050415 SGD
+SGD S000003586 MTR4 GO:0016075 SGD_REF:S000114120|PMID:16374505 IMP P RNA helicase YJL050W|DOB1 gene taxon:4932 20060120 SGD
+SGD S000003586 MTR4 GO:0016078 SGD_REF:S000081438|PMID:15828860 IDA P RNA helicase YJL050W|DOB1 gene taxon:4932 20050610 SGD
+SGD S000003586 MTR4 GO:0016078 SGD_REF:S000081843|PMID:15935758 IDA P RNA helicase YJL050W|DOB1 gene taxon:4932 20050610 SGD
+SGD S000000032 MTW1 GO:0000818 SGD_REF:S000075142|PMID:14633972 IDA C YAL034W-A|DSN3|NSL2 gene taxon:4932 20040618 SGD
+SGD S000000032 MTW1 GO:0000922 SGD_REF:S000071701|PMID:12455957 IDA C YAL034W-A|DSN3|NSL2 gene taxon:4932 20030522 SGD
+SGD S000000032 MTW1 GO:0005554 SGD_REF:S000069584 ND F YAL034W-A|DSN3|NSL2 gene taxon:4932 20021125 SGD
+SGD S000000032 MTW1 GO:0007059 SGD_REF:S000071701|PMID:12455957 IDA P YAL034W-A|DSN3|NSL2 gene taxon:4932 20021209 SGD
+SGD S000004706 MUB1 GO:0008372 SGD_REF:S000069584 ND C YMR100W gene taxon:4932 20021029 SGD
+SGD S000004706 MUB1 GO:0005554 SGD_REF:S000069584 ND F YMR100W gene taxon:4932 20021029 SGD
+SGD S000004706 MUB1 GO:0007116 SGD_REF:S000044755|PMID:9427754 ISS P YMR100W gene taxon:4932 20021001 SGD
+SGD S000004706 MUB1 GO:0007116 SGD_REF:S000044755|PMID:9427754 IMP P YMR100W gene taxon:4932 20021001 SGD
+SGD S000001458 MUC1 GO:0005886 SGD_REF:S000061547|PMID:11027318 IDA C cell surface flocculin with structure similar to serine/threonine-rich GPI-anchored cell wall proteins YIR019C|FLO11|STA4 gene taxon:4932 20020408 SGD
+SGD S000001458 MUC1 GO:0005554 SGD_REF:S000069584 ND F cell surface flocculin with structure similar to serine/threonine-rich GPI-anchored cell wall proteins YIR019C|FLO11|STA4 gene taxon:4932 20040422 SGD
+SGD S000001458 MUC1 GO:0001403 SGD_REF:S000055959|PMID:8710886 IMP P cell surface flocculin with structure similar to serine/threonine-rich GPI-anchored cell wall proteins YIR019C|FLO11|STA4 gene taxon:4932 20020408 SGD
+SGD S000001458 MUC1 GO:0007124 SGD_REF:S000055959|PMID:8710886 IMP P cell surface flocculin with structure similar to serine/threonine-rich GPI-anchored cell wall proteins YIR019C|FLO11|STA4 gene taxon:4932 20020408 SGD
+SGD S000001458 MUC1 GO:0016337 SGD_REF:S000069739|PMID:11967069 TAS P cell surface flocculin with structure similar to serine/threonine-rich GPI-anchored cell wall proteins YIR019C|FLO11|STA4 gene taxon:4932 20021101 SGD
+SGD S000001458 MUC1 GO:0030447 SGD_REF:S000070081|PMID:12072450 IDA P cell surface flocculin with structure similar to serine/threonine-rich GPI-anchored cell wall proteins YIR019C|FLO11|STA4 gene taxon:4932 20021101 SGD
+SGD S000000323 MUD1 GO:0005685 SGD_REF:S000069986|PMID:11804584 IDA C U1 snRNP A protein YBR119W|U1-A|U1A gene taxon:4932 20020621 SGD
+SGD S000000323 MUD1 GO:0005685 SGD_REF:S000044485|PMID:9630245 IDA C U1 snRNP A protein YBR119W|U1-A|U1A gene taxon:4932 20050929 SGD
+SGD S000000323 MUD1 GO:0003723 SGD_REF:S000057758|PMID:8449403 IGI F U1 snRNP A protein YBR119W|U1-A|U1A gene taxon:4932 20021115 SGD
+SGD S000000323 MUD1 GO:0003723 SGD_REF:S000057758|PMID:8449403 ISS F U1 snRNP A protein YBR119W|U1-A|U1A gene taxon:4932 20021115 SGD
+SGD S000000323 MUD1 GO:0000398 SGD_REF:S000057758|PMID:8449403 IGI P U1 snRNP A protein YBR119W|U1-A|U1A gene taxon:4932 20021115 SGD
+SGD S000001557 MUD2 GO:0000243 SGD_REF:S000040368|PMID:9150140 IPI C YKL074C gene taxon:4932 20010118 SGD
+SGD S000001557 MUD2 GO:0003729 SGD_REF:S000054302|PMID:7926772 IDA F YKL074C gene taxon:4932 20010118 SGD
+SGD S000001557 MUD2 GO:0031202 SGD_REF:S000058281|PMID:9476892 TAS F YKL074C gene taxon:4932 20010118 SGD
+SGD S000001557 MUD2 GO:0000370 SGD_REF:S000040368|PMID:9150140 TAS P YKL074C gene taxon:4932 20030825 SGD
+SGD S000005991 MUK1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YPL070W gene taxon:4932 20031028 SGD
+SGD S000005991 MUK1 GO:0005554 SGD_REF:S000069584 ND F YPL070W gene taxon:4932 20030114 SGD
+SGD S000005991 MUK1 GO:0045449 SGD_REF:S000074191|PMID:14566057 RCA P YPL070W gene taxon:4932 20050608 SGD
+SGD S000000261 MUM2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YBR057C|SPOT8 gene taxon:4932 20031028 SGD
+SGD S000000261 MUM2 GO:0005554 SGD_REF:S000069584 ND F YBR057C|SPOT8 gene taxon:4932 20021104 SGD
+SGD S000000261 MUM2 GO:0006279 SGD_REF:S000039264|PMID:9504908 IMP P YBR057C|SPOT8 gene taxon:4932 20020419 SGD
+SGD S000000261 MUM2 GO:0006279 SGD_REF:S000060063|PMID:11238403 IGI P YBR057C|SPOT8 gene taxon:4932 20020419 SGD
+SGD S000005824 MUM3 GO:0008372 SGD_REF:S000069584 ND C YOR298W gene taxon:4932 20021120 SGD
+SGD S000005824 MUM3 GO:0008415 SGD_REF:S000065692|PMID:9259571 ISS F YOR298W gene taxon:4932 20030423 SGD
+SGD S000005824 MUM3 GO:0008654 SGD_REF:S000065692|PMID:9259571 ISS P YOR298W gene taxon:4932 20030423 SGD
+SGD S000005824 MUM3 GO:0030476 SGD_REF:S000079982|PMID:15590821 IMP P YOR298W gene taxon:4932 20050127 SGD
+SGD S000003287 MUP1 GO:0005887 SGD_REF:S000041040|PMID:8893857 ISS C high affinity methionine permease YGR055W gene taxon:4932 20010118 SGD
+SGD S000003287 MUP1 GO:0000102 SGD_REF:S000041040|PMID:8893857 IDA F high affinity methionine permease YGR055W gene taxon:4932 20010118 SGD
+SGD S000003287 MUP1 GO:0000101 SGD_REF:S000041040|PMID:8893857 IMP P high affinity methionine permease YGR055W gene taxon:4932 20010118 SGD
+SGD S000029316 MUP2 GO:0008372 SGD_REF:S000069584 ND C low affinity methionine permease gene taxon:4932 20020523 SGD
+SGD S000029316 MUP2 GO:0005554 SGD_REF:S000069584 ND F low affinity methionine permease gene taxon:4932 20020523 SGD
+SGD S000029316 MUP2 GO:0006865 SGD_REF:S000041040|PMID:8893857 NAS P low affinity methionine permease gene taxon:4932 20020523 SGD
+SGD S000001028 MUP3 GO:0016020 SGD_REF:S000041040|PMID:8893857 ISS C very low affinity methionine permease YHL036W gene taxon:4932 20020523 SGD
+SGD S000001028 MUP3 GO:0015191 SGD_REF:S000041040|PMID:8893857 IGI F very low affinity methionine permease YHL036W gene taxon:4932 20020523 SGD
+SGD S000001028 MUP3 GO:0015191 SGD_REF:S000041040|PMID:8893857 ISS F very low affinity methionine permease YHL036W gene taxon:4932 20020523 SGD
+SGD S000001028 MUP3 GO:0015191 SGD_REF:S000041040|PMID:8893857 IMP F very low affinity methionine permease YHL036W gene taxon:4932 20020523 SGD
+SGD S000001028 MUP3 GO:0006865 SGD_REF:S000041040|PMID:8893857 IGI P very low affinity methionine permease YHL036W gene taxon:4932 20020523 SGD
+SGD S000001028 MUP3 GO:0006865 SGD_REF:S000041040|PMID:8893857 IMP P very low affinity methionine permease YHL036W gene taxon:4932 20020523 SGD
+SGD S000003239 MUQ1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C choline phosphate cytidylyltransferase (also called phosphoethanolamine cytidylyltransferase or phosphocholine cytidylyltransferase) YGR007W|ECT1 gene taxon:4932 20031028 SGD
+SGD S000003239 MUQ1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C choline phosphate cytidylyltransferase (also called phosphoethanolamine cytidylyltransferase or phosphocholine cytidylyltransferase) YGR007W|ECT1 gene taxon:4932 20031028 SGD
+SGD S000003239 MUQ1 GO:0004306 SGD_REF:S000041558|PMID:8982874 IDA F choline phosphate cytidylyltransferase (also called phosphoethanolamine cytidylyltransferase or phosphocholine cytidylyltransferase) YGR007W|ECT1 gene taxon:4932 20030103 SGD
+SGD S000003239 MUQ1 GO:0004306 SGD_REF:S000041558|PMID:8982874 ISS F choline phosphate cytidylyltransferase (also called phosphoethanolamine cytidylyltransferase or phosphocholine cytidylyltransferase) YGR007W|ECT1 gene taxon:4932 20030103 SGD
+SGD S000003239 MUQ1 GO:0004306 SGD_REF:S000041558|PMID:8982874 IMP F choline phosphate cytidylyltransferase (also called phosphoethanolamine cytidylyltransferase or phosphocholine cytidylyltransferase) YGR007W|ECT1 gene taxon:4932 20030103 SGD
+SGD S000003239 MUQ1 GO:0006646 SGD_REF:S000041558|PMID:8982874 IMP P choline phosphate cytidylyltransferase (also called phosphoethanolamine cytidylyltransferase or phosphocholine cytidylyltransferase) YGR007W|ECT1 gene taxon:4932 20021001 SGD
+SGD S000003239 MUQ1 GO:0006646 SGD_REF:S000041558|PMID:8982874 TAS P choline phosphate cytidylyltransferase (also called phosphoethanolamine cytidylyltransferase or phosphocholine cytidylyltransferase) YGR007W|ECT1 gene taxon:4932 20021001 SGD
+SGD S000002794 MUS81 GO:0005634 SGD_REF:S000046484|PMID:10905349 IMP C YDR386W|SLX3 gene taxon:4932 20030713 SGD
+SGD S000002794 MUS81 GO:0005634 SGD_REF:S000046484|PMID:10905349 IPI C YDR386W|SLX3 gene taxon:4932 20030713 SGD
+SGD S000002794 MUS81 GO:0004519 SGD_REF:S000068964|PMID:11641278 IDA F YDR386W|SLX3 gene taxon:4932 20021001 SGD
+SGD S000002794 MUS81 GO:0006281 SGD_REF:S000069922|PMID:12032096 IGI P YDR386W|SLX3 gene taxon:4932 20021001 SGD
+SGD S000002794 MUS81 GO:0007131 SGD_REF:S000068964|PMID:11641278 IGI P YDR386W|SLX3 gene taxon:4932 20021001 SGD
+SGD S000005326 MVD1 GO:0005829 SGD_REF:S000058496 TAS C mevalonate pyrophosphate decarboxylase YNR043W|ERG19 gene taxon:4932 20010119 SGD
+SGD S000005326 MVD1 GO:0004163 SGD_REF:S000058496 TAS F mevalonate pyrophosphate decarboxylase YNR043W|ERG19 gene taxon:4932 20010119 SGD
+SGD S000005326 MVD1 GO:0006696 SGD_REF:S000058496 TAS P mevalonate pyrophosphate decarboxylase YNR043W|ERG19 gene taxon:4932 20010119 SGD
+SGD S000005326 MVD1 GO:0008299 SGD_REF:S000049898|PMID:9244250 TAS P mevalonate pyrophosphate decarboxylase YNR043W|ERG19 gene taxon:4932 20010118 SGD
+SGD S000004606 MVP1 GO:0005737 SGD_REF:S000051863|PMID:7862158 IDA C YMR004W gene taxon:4932 20020820 SGD
+SGD S000004606 MVP1 GO:0005554 SGD_REF:S000069584 ND F YMR004W gene taxon:4932 20020820 SGD
+SGD S000004606 MVP1 GO:0006623 SGD_REF:S000051863|PMID:7862158 IMP P YMR004W gene taxon:4932 20020820 SGD
+SGD S000000844 MXR1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C peptide methionine sulfoxide reductase YER042W|MSRA gene taxon:4932 20031028 SGD
+SGD S000000844 MXR1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C peptide methionine sulfoxide reductase YER042W|MSRA gene taxon:4932 20031028 SGD
+SGD S000000844 MXR1 GO:0008113 SGD_REF:S000043611|PMID:9275166 ISS F peptide methionine sulfoxide reductase YER042W|MSRA gene taxon:4932 20010118 SGD
+SGD S000000844 MXR1 GO:0006979 SGD_REF:S000043611|PMID:9275166 IMP P peptide methionine sulfoxide reductase YER042W|MSRA gene taxon:4932 20010118 SGD
+SGD S000000844 MXR1 GO:0006979 SGD_REF:S000069481|PMID:11929995 IGI P peptide methionine sulfoxide reductase YER042W|MSRA gene taxon:4932 20020405 SGD
+SGD S000000844 MXR1 GO:0006979 SGD_REF:S000069481|PMID:11929995 IMP P peptide methionine sulfoxide reductase YER042W|MSRA gene taxon:4932 20020405 SGD
+SGD S000001065 MYO1 GO:0000142 SGD_REF:S000041005|PMID:10652251 IDA C class II myosin YHR023W gene taxon:4932 20010118 SGD
+SGD S000001065 MYO1 GO:0000146 SGD_REF:S000058447|PMID:9153752 TAS F class II myosin YHR023W gene taxon:4932 20010118 SGD
+SGD S000001065 MYO1 GO:0000910 SGD_REF:S000041005|PMID:10652251 IMP P class II myosin YHR023W gene taxon:4932 20010119 SGD
+SGD S000001065 MYO1 GO:0006970 SGD_REF:S000041005|PMID:10652251 IMP P class II myosin YHR023W gene taxon:4932 20010118 SGD
+SGD S000001065 MYO1 GO:0007120 SGD_REF:S000041005|PMID:10652251 IMP P class II myosin YHR023W gene taxon:4932 20010118 SGD
+SGD S000005853 MYO2 GO:0030478 SGD_REF:S000041005|PMID:10652251 IDA C class V myosin YOR326W|CDC66 gene taxon:4932 20010118 SGD
+SGD S000005853 MYO2 GO:0030482 SGD_REF:S000041005|PMID:10652251 IDA C class V myosin YOR326W|CDC66 gene taxon:4932 20010118 SGD
+SGD S000005853 MYO2 GO:0000146 SGD_REF:S000058447|PMID:9153752 TAS F class V myosin YOR326W|CDC66 gene taxon:4932 20010118 SGD
+SGD S000005853 MYO2 GO:0000001 SGD_REF:S000041005|PMID:10652251 TAS P class V myosin YOR326W|CDC66 gene taxon:4932 20010118 SGD
+SGD S000005853 MYO2 GO:0000011 SGD_REF:S000041005|PMID:10652251 TAS P class V myosin YOR326W|CDC66 gene taxon:4932 20010118 SGD
+SGD S000005853 MYO2 GO:0006897 SGD_REF:S000041005|PMID:10652251 IMP P class V myosin YOR326W|CDC66 gene taxon:4932 20010118 SGD
+SGD S000005853 MYO2 GO:0006897 SGD_REF:S000041005|PMID:10652251 IPI P class V myosin YOR326W|CDC66 gene taxon:4932 20010118 SGD
+SGD S000005853 MYO2 GO:0007118 SGD_REF:S000041005|PMID:10652251 IPI P class V myosin YOR326W|CDC66 gene taxon:4932 20010118 SGD
+SGD S000005853 MYO2 GO:0007118 SGD_REF:S000041005|PMID:10652251 IMP P class V myosin YOR326W|CDC66 gene taxon:4932 20010118 SGD
+SGD S000005853 MYO2 GO:0007119 SGD_REF:S000041005|PMID:10652251 IMP P class V myosin YOR326W|CDC66 gene taxon:4932 20010118 SGD
+SGD S000005853 MYO2 GO:0007119 SGD_REF:S000041005|PMID:10652251 IPI P class V myosin YOR326W|CDC66 gene taxon:4932 20010118 SGD
+SGD S000005853 MYO2 GO:0016192 SGD_REF:S000041005|PMID:10652251 IMP P class V myosin YOR326W|CDC66 gene taxon:4932 20010118 SGD
+SGD S000005853 MYO2 GO:0016192 SGD_REF:S000041005|PMID:10652251 IPI P class V myosin YOR326W|CDC66 gene taxon:4932 20010118 SGD
+SGD S000005853 MYO2 GO:0030468 SGD_REF:S000041005|PMID:10652251 IMP P class V myosin YOR326W|CDC66 gene taxon:4932 20010302 SGD
+SGD S000005853 MYO2 GO:0030468 SGD_REF:S000041005|PMID:10652251 IGI P class V myosin YOR326W|CDC66 gene taxon:4932 20010302 SGD
+SGD S000005853 MYO2 GO:0030468 SGD_REF:S000041005|PMID:10652251 IPI P class V myosin YOR326W|CDC66 gene taxon:4932 20010302 SGD
+SGD S000001612 MYO3 GO:0030479 SGD_REF:S000041005|PMID:10652251 IPI C myosin I YKL129C gene taxon:4932 20010118 SGD
+SGD S000001612 MYO3 GO:0000146 SGD_REF:S000058447|PMID:9153752 TAS F myosin I YKL129C gene taxon:4932 20010118 SGD
+SGD S000001612 MYO3 GO:0006887 SGD_REF:S000041005|PMID:10652251 IMP P myosin I YKL129C gene taxon:4932 20010118 SGD
+SGD S000001612 MYO3 GO:0006897 SGD_REF:S000041005|PMID:10652251 IMP P myosin I YKL129C gene taxon:4932 20010118 SGD
+SGD S000001612 MYO3 GO:0006970 SGD_REF:S000041005|PMID:10652251 IMP P myosin I YKL129C gene taxon:4932 20010118 SGD
+SGD S000001612 MYO3 GO:0007047 SGD_REF:S000041005|PMID:10652251 IMP P myosin I YKL129C gene taxon:4932 20010118 SGD
+SGD S000001612 MYO3 GO:0007121 SGD_REF:S000041005|PMID:10652251 IMP P myosin I YKL129C gene taxon:4932 20010118 SGD
+SGD S000000027 MYO4 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C myosin V heavy chain YAL029C|FUN22|SHE1 gene taxon:4932 20040928 SGD
+SGD S000000027 MYO4 GO:0030478 SGD_REF:S000041005|PMID:10652251 IDA C myosin V heavy chain YAL029C|FUN22|SHE1 gene taxon:4932 20010118 SGD
+SGD S000000027 MYO4 GO:0000146 SGD_REF:S000058447|PMID:9153752 TAS F myosin V heavy chain YAL029C|FUN22|SHE1 gene taxon:4932 20010118 SGD
+SGD S000000027 MYO4 GO:0008298 SGD_REF:S000041005|PMID:10652251 TAS P myosin V heavy chain YAL029C|FUN22|SHE1 gene taxon:4932 20010118 SGD
+SGD S000000027 MYO4 GO:0048309 SGD_REF:S000075200|PMID:14691136 IMP P myosin V heavy chain YAL029C|FUN22|SHE1 gene taxon:4932 20040318 SGD
+SGD S000004715 MYO5 GO:0030479 SGD_REF:S000041005|PMID:10652251 IDA C myosin I YMR109W gene taxon:4932 20010118 SGD
+SGD S000004715 MYO5 GO:0000146 SGD_REF:S000058447|PMID:9153752 TAS F myosin I YMR109W gene taxon:4932 20010118 SGD
+SGD S000004715 MYO5 GO:0006887 SGD_REF:S000041005|PMID:10652251 IMP P myosin I YMR109W gene taxon:4932 20010118 SGD
+SGD S000004715 MYO5 GO:0006897 SGD_REF:S000041005|PMID:10652251 IMP P myosin I YMR109W gene taxon:4932 20010118 SGD
+SGD S000004715 MYO5 GO:0006970 SGD_REF:S000041005|PMID:10652251 IMP P myosin I YMR109W gene taxon:4932 20010118 SGD
+SGD S000004715 MYO5 GO:0007047 SGD_REF:S000041005|PMID:10652251 IMP P myosin I YMR109W gene taxon:4932 20010118 SGD
+SGD S000004715 MYO5 GO:0007121 SGD_REF:S000041005|PMID:10652251 IMP P myosin I YMR109W gene taxon:4932 20010118 SGD
+SGD S000004715 MYO5 GO:0009651 SGD_REF:S000071805|PMID:12391157 IGI SGD:S000001156 P myosin I YMR109W gene taxon:4932 20021218 SGD
+SGD S000004715 MYO5 GO:0009651 SGD_REF:S000071805|PMID:12391157 IPI SGD:S000001156 P myosin I YMR109W gene taxon:4932 20021218 SGD
+SGD S000003090 NAB2 GO:0005634 SGD_REF:S000069418|PMID:11779864 IDA C polyadenylated RNA binding protein YGL122C gene taxon:4932 20020419 SGD
+SGD S000003090 NAB2 GO:0005634 SGD_REF:S000069418|PMID:11779864 TAS C polyadenylated RNA binding protein YGL122C gene taxon:4932 20020419 SGD
+SGD S000003090 NAB2 GO:0005634 SGD_REF:S000039514|PMID:7962083 IDA C polyadenylated RNA binding protein YGL122C gene taxon:4932 20040430 SGD
+SGD S000003090 NAB2 GO:0005737 SGD_REF:S000069418|PMID:11779864 TAS C polyadenylated RNA binding protein YGL122C gene taxon:4932 20020419 SGD
+SGD S000003090 NAB2 GO:0008143 SGD_REF:S000069418|PMID:11779864 TAS F polyadenylated RNA binding protein YGL122C gene taxon:4932 20020419 SGD
+SGD S000003090 NAB2 GO:0006378 SGD_REF:S000069963|PMID:11927564 IDA P polyadenylated RNA binding protein YGL122C gene taxon:4932 20030312 SGD
+SGD S000003090 NAB2 GO:0016973 SGD_REF:S000069418|PMID:11779864 IMP P polyadenylated RNA binding protein YGL122C gene taxon:4932 20020419 SGD
+SGD S000006111 NAB3 GO:0005634 SGD_REF:S000039514|PMID:7962083 IDA C polyadenylated RNA binding protein, polyadenylated single strand DNA-binding protein YPL190C|HMD1 gene taxon:4932 20040430 SGD
+SGD S000006111 NAB3 GO:0008143 SGD_REF:S000039514|PMID:7962083 IDA F polyadenylated RNA binding protein, polyadenylated single strand DNA-binding protein YPL190C|HMD1 gene taxon:4932 20021021 SGD
+SGD S000006111 NAB3 GO:0006357 SGD_REF:S000045868|PMID:10655211 IPI P polyadenylated RNA binding protein, polyadenylated single strand DNA-binding protein YPL190C|HMD1 gene taxon:4932 20021021 SGD
+SGD S000006111 NAB3 GO:0006357 SGD_REF:S000045868|PMID:10655211 IGI P polyadenylated RNA binding protein, polyadenylated single strand DNA-binding protein YPL190C|HMD1 gene taxon:4932 20021021 SGD
+SGD S000004585 NAB6 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YML117W gene taxon:4932 20031028 SGD
+SGD S000004585 NAB6 GO:0005554 SGD_REF:S000069584 ND F YML117W gene taxon:4932 20060315 SGD
+SGD S000004585 NAB6 GO:0016070 SGD_REF:S000074191|PMID:14566057 RCA P YML117W gene taxon:4932 20060315 SGD
+SGD S000005068 NAF1 GO:0005654 SGD_REF:S000071570|PMID:12242285 TAS C YNL124W gene taxon:4932 20021114 SGD
+SGD S000005068 NAF1 GO:0003723 SGD_REF:S000072364|PMID:12515383 IDA F YNL124W gene taxon:4932 20030207 SGD
+SGD S000005068 NAF1 GO:0006461 SGD_REF:S000081782|PMID:15798213 IPI P YNL124W gene taxon:4932 20060518 SGD
+SGD S000005068 NAF1 GO:0016074 SGD_REF:S000072364|PMID:12515383 IMP P YNL124W gene taxon:4932 20030207 SGD
+SGD S000004374 NAM2 GO:0005739 SGD_REF:S000048527|PMID:1990003 IDA C LeuRS, leucine-tRNA ligase YLR382C|MSL1 gene taxon:4932 20021001 SGD
+SGD S000004374 NAM2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C LeuRS, leucine-tRNA ligase YLR382C|MSL1 gene taxon:4932 20040924 SGD
+SGD S000004374 NAM2 GO:0003729 SGD_REF:S000059609|PMID:11142386 IPI F LeuRS, leucine-tRNA ligase YLR382C|MSL1 gene taxon:4932 20021001 SGD
+SGD S000004374 NAM2 GO:0004823 SGD_REF:S000048527|PMID:1990003 IDA F LeuRS, leucine-tRNA ligase YLR382C|MSL1 gene taxon:4932 20021001 SGD
+SGD S000004374 NAM2 GO:0000372 SGD_REF:S000044227|PMID:2277640 IMP P LeuRS, leucine-tRNA ligase YLR382C|MSL1 gene taxon:4932 20021001 SGD
+SGD S000004374 NAM2 GO:0006429 SGD_REF:S000048527|PMID:1990003 IDA P LeuRS, leucine-tRNA ligase YLR382C|MSL1 gene taxon:4932 20021001 SGD
+SGD S000004685 NAM7 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C helicase (putative) YMR080C|IFS2|MOF4|UPF1 gene taxon:4932 20020507 SGD
+SGD S000004685 NAM7 NOT GO:0005739 SGD_REF:S000076002|PMID:14763985 IDA C helicase (putative) YMR080C|IFS2|MOF4|UPF1 gene taxon:4932 20050301 SGD
+SGD S000004685 NAM7 GO:0005844 SGD_REF:S000049793|PMID:10098411 TAS C helicase (putative) YMR080C|IFS2|MOF4|UPF1 gene taxon:4932 20020127 SGD
+SGD S000004685 NAM7 GO:0003676 SGD_REF:S000049793|PMID:10098411 TAS F helicase (putative) YMR080C|IFS2|MOF4|UPF1 gene taxon:4932 20020127 SGD
+SGD S000004685 NAM7 GO:0004004 SGD_REF:S000061923|PMID:10322435 TAS F helicase (putative) YMR080C|IFS2|MOF4|UPF1 gene taxon:4932 20050416 SGD
+SGD S000004685 NAM7 GO:0008186 SGD_REF:S000061923|PMID:10322435 TAS F helicase (putative) YMR080C|IFS2|MOF4|UPF1 gene taxon:4932 20050416 SGD
+SGD S000004685 NAM7 GO:0000184 SGD_REF:S000049793|PMID:10098411 TAS P helicase (putative) YMR080C|IFS2|MOF4|UPF1 gene taxon:4932 20020127 SGD
+SGD S000004685 NAM7 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P helicase (putative) YMR080C|IFS2|MOF4|UPF1 gene taxon:4932 20060203 SGD
+SGD S000004685 NAM7 GO:0006402 SGD_REF:S000058753|PMID:9841679 TAS P helicase (putative) YMR080C|IFS2|MOF4|UPF1 gene taxon:4932 20010124 SGD
+SGD S000004685 NAM7 GO:0006449 SGD_REF:S000049793|PMID:10098411 TAS P helicase (putative) YMR080C|IFS2|MOF4|UPF1 gene taxon:4932 20020127 SGD
+SGD S000004685 NAM7 NOT GO:0006452 SGD_REF:S000079922|PMID:15388879 IMP P helicase (putative) YMR080C|IFS2|MOF4|UPF1 gene taxon:4932 20050301 SGD
+SGD S000001128 NAM8 GO:0000243 SGD_REF:S000064189|PMID:10072386 IPI C RNA-binding protein, U1 snRNP protein YHR086W|MRE2|MUD15 gene taxon:4932 20020405 SGD
+SGD S000001128 NAM8 GO:0005685 SGD_REF:S000069986|PMID:11804584 IDA C RNA-binding protein, U1 snRNP protein YHR086W|MRE2|MUD15 gene taxon:4932 20020621 SGD
+SGD S000001128 NAM8 GO:0005685 SGD_REF:S000044485|PMID:9630245 IDA C RNA-binding protein, U1 snRNP protein YHR086W|MRE2|MUD15 gene taxon:4932 20050929 SGD
+SGD S000001128 NAM8 GO:0003723 SGD_REF:S000049958|PMID:10072385 IPI F RNA-binding protein, U1 snRNP protein YHR086W|MRE2|MUD15 gene taxon:4932 20020405 SGD
+SGD S000001128 NAM8 GO:0003729 SGD_REF:S000064189|PMID:10072386 IPI F RNA-binding protein, U1 snRNP protein YHR086W|MRE2|MUD15 gene taxon:4932 20020729 SGD
+SGD S000001128 NAM8 GO:0000398 SGD_REF:S000064189|PMID:10072386 IPI P RNA-binding protein, U1 snRNP protein YHR086W|MRE2|MUD15 gene taxon:4932 20020729 SGD
+SGD S000001128 NAM8 GO:0006376 SGD_REF:S000049958|PMID:10072385 IMP P RNA-binding protein, U1 snRNP protein YHR086W|MRE2|MUD15 gene taxon:4932 20020405 SGD
+SGD S000005081 NAM9 GO:0005763 SGD_REF:S000058278|PMID:9445368 TAS C mitochondrial S4 ribosomal protein (putative) YNL137C|MNA6 gene taxon:4932 20010118 SGD
+SGD S000005081 NAM9 GO:0005763 SGD_REF:S000060645|PMID:11278769 IDA C mitochondrial S4 ribosomal protein (putative) YNL137C|MNA6 gene taxon:4932 20010918 SGD
+SGD S000005081 NAM9 GO:0003735 SGD_REF:S000058278|PMID:9445368 TAS F mitochondrial S4 ribosomal protein (putative) YNL137C|MNA6 gene taxon:4932 20010118 SGD
+SGD S000005081 NAM9 GO:0003735 SGD_REF:S000060645|PMID:11278769 IDA F mitochondrial S4 ribosomal protein (putative) YNL137C|MNA6 gene taxon:4932 20010918 SGD
+SGD S000005081 NAM9 GO:0043037 SGD_REF:S000058278|PMID:9445368 TAS P mitochondrial S4 ribosomal protein (putative) YNL137C|MNA6 gene taxon:4932 20010118 SGD
+SGD S000005081 NAM9 GO:0043037 SGD_REF:S000060645|PMID:11278769 IDA P mitochondrial S4 ribosomal protein (putative) YNL137C|MNA6 gene taxon:4932 20010918 SGD
+SGD S000006047 NAN1 GO:0005732 SGD_REF:S000070145|PMID:12068309 IPI C U3 snoRNP protein YPL126W|UTP17 gene taxon:4932 20030224 SGD
+SGD S000006047 NAN1 colocalizes_with GO:0030869 SGD_REF:S000056360|PMID:10219244 IPI SGD:S000003612 C U3 snoRNP protein YPL126W|UTP17 gene taxon:4932 20041112 SGD
+SGD S000006047 NAN1 GO:0030515 SGD_REF:S000070145|PMID:12068309 IPI F U3 snoRNP protein YPL126W|UTP17 gene taxon:4932 20030224 SGD
+SGD S000006047 NAN1 GO:0030490 SGD_REF:S000070145|PMID:12068309 IMP P U3 snoRNP protein YPL126W|UTP17 gene taxon:4932 20020906 SGD
+SGD S000006047 NAN1 GO:0030490 SGD_REF:S000070145|PMID:12068309 IPI P U3 snoRNP protein YPL126W|UTP17 gene taxon:4932 20020906 SGD
+SGD S000001756 NAP1 GO:0005634 SGD_REF:S000042635|PMID:10767562 IPI C nucleosome assembly protein I YKR048C gene taxon:4932 20021014 SGD
+SGD S000001756 NAP1 GO:0005737 SGD_REF:S000075265|PMID:13680156 TAS C nucleosome assembly protein I YKR048C gene taxon:4932 20040115 SGD
+SGD S000001756 NAP1 GO:0005515 SGD_REF:S000062287|PMID:8743889 TAS F nucleosome assembly protein I YKR048C gene taxon:4932 20020130 SGD
+SGD S000001756 NAP1 GO:0000087 SGD_REF:S000062287|PMID:8743889 TAS P nucleosome assembly protein I YKR048C gene taxon:4932 20020130 SGD
+SGD S000001756 NAP1 GO:0006334 SGD_REF:S000056718|PMID:2016313 IDA P nucleosome assembly protein I YKR048C gene taxon:4932 20020130 SGD
+SGD S000001756 NAP1 GO:0006334 SGD_REF:S000056718|PMID:2016313 ISS P nucleosome assembly protein I YKR048C gene taxon:4932 20020130 SGD
+SGD S000001756 NAP1 GO:0007117 SGD_REF:S000075265|PMID:13680156 IMP P nucleosome assembly protein I YKR048C gene taxon:4932 20040115 SGD
+SGD S000001756 NAP1 GO:0007117 SGD_REF:S000075265|PMID:13680156 IGI P nucleosome assembly protein I YKR048C gene taxon:4932 20040115 SGD
+SGD S000005184 NAR1 GO:0005829 SGD_REF:S000076226|PMID:15103330 IDA C YNL240C gene taxon:4932 20041208 SGD
+SGD S000005184 NAR1 GO:0016020 SGD_REF:S000076226|PMID:15103330 IDA C YNL240C gene taxon:4932 20041208 SGD
+SGD S000005184 NAR1 GO:0016948 SGD_REF:S000056399|PMID:10514485 ISS F YNL240C gene taxon:4932 20021001 SGD
+SGD S000005184 NAR1 GO:0016226 SGD_REF:S000076226|PMID:15103330 IMP P YNL240C gene taxon:4932 20041208 SGD
+SGD S000001269 NAS2 GO:0005737 SGD_REF:S000061434|PMID:11489916 IDA C YIL007C gene taxon:4932 20030512 SGD
+SGD S000001269 NAS2 GO:0005554 SGD_REF:S000069584 ND F YIL007C gene taxon:4932 20030203 SGD
+SGD S000001269 NAS2 GO:0006511 SGD_REF:S000047509|PMID:10419517 ISS P YIL007C gene taxon:4932 20030207 SGD
+SGD S000003464 NAS6 GO:0005838 SGD_REF:S000056447|PMID:11029046 IDA C 26S proteasome interacting protein YGR232W gene taxon:4932 20010118 SGD
+SGD S000003464 NAS6 GO:0005554 SGD_REF:S000069584 ND F 26S proteasome interacting protein YGR232W gene taxon:4932 20010119 SGD
+SGD S000003464 NAS6 GO:0006508 SGD_REF:S000056447|PMID:11029046 IPI P 26S proteasome interacting protein YGR232W gene taxon:4932 20010118 SGD
+SGD S000003464 NAS6 GO:0006508 SGD_REF:S000056447|PMID:11029046 ISS P 26S proteasome interacting protein YGR232W gene taxon:4932 20010118 SGD
+SGD S000002198 NAT1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C N-terminal acetyltransferase YDL040C|AAA1 gene taxon:4932 20040813 SGD
+SGD S000002198 NAT1 colocalizes_with GO:0005830 SGD_REF:S000074487|PMID:14517307 IDA C N-terminal acetyltransferase YDL040C|AAA1 gene taxon:4932 20041201 SGD
+SGD S000002198 NAT1 GO:0031415 SGD_REF:S000073836|PMID:12890471 TAS C N-terminal acetyltransferase YDL040C|AAA1 gene taxon:4932 20051205 SGD
+SGD S000002198 NAT1 GO:0031415 SGD_REF:S000074487|PMID:14517307 IDA C N-terminal acetyltransferase YDL040C|AAA1 gene taxon:4932 20060119 SGD
+SGD S000002198 NAT1 contributes_to GO:0004596 SGD_REF:S000073836|PMID:12890471 TAS F N-terminal acetyltransferase YDL040C|AAA1 gene taxon:4932 20051205 SGD
+SGD S000002198 NAT1 contributes_to GO:0004596 SGD_REF:S000044111|PMID:2551674 IDA F N-terminal acetyltransferase YDL040C|AAA1 gene taxon:4932 20060120 SGD
+SGD S000002198 NAT1 contributes_to GO:0004596 SGD_REF:S000044111|PMID:2551674 IMP F N-terminal acetyltransferase YDL040C|AAA1 gene taxon:4932 20060120 SGD
+SGD S000002198 NAT1 GO:0006474 SGD_REF:S000044111|PMID:2551674 IDA P N-terminal acetyltransferase YDL040C|AAA1 gene taxon:4932 20060120 SGD
+SGD S000002198 NAT1 GO:0006474 SGD_REF:S000044111|PMID:2551674 IMP P N-terminal acetyltransferase YDL040C|AAA1 gene taxon:4932 20060120 SGD
+SGD S000003379 NAT2 GO:0005737 SGD_REF:S000050676|PMID:8175741 IC GO:0004596 C N alpha-acetyltransferase YGR147C gene taxon:4932 20021115 SGD
+SGD S000003379 NAT2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C N alpha-acetyltransferase YGR147C gene taxon:4932 20031210 SGD
+SGD S000003379 NAT2 GO:0004596 SGD_REF:S000050676|PMID:8175741 IMP F N alpha-acetyltransferase YGR147C gene taxon:4932 20020424 SGD
+SGD S000003379 NAT2 GO:0004596 SGD_REF:S000050676|PMID:8175741 ISS F N alpha-acetyltransferase YGR147C gene taxon:4932 20020424 SGD
+SGD S000003379 NAT2 GO:0017196 SGD_REF:S000050676|PMID:8175741 IMP P N alpha-acetyltransferase YGR147C gene taxon:4932 20020424 SGD
+SGD S000006335 NAT3 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C N-terminal acetyltransferase YPR131C gene taxon:4932 20031028 SGD
+SGD S000006335 NAT3 GO:0031416 SGD_REF:S000073836|PMID:12890471 TAS C N-terminal acetyltransferase YPR131C gene taxon:4932 20060119 SGD
+SGD S000006335 NAT3 GO:0004596 SGD_REF:S000053967|PMID:10545125 IMP F N-terminal acetyltransferase YPR131C gene taxon:4932 20030128 SGD
+SGD S000006335 NAT3 GO:0004596 SGD_REF:S000053967|PMID:10545125 ISS F N-terminal acetyltransferase YPR131C gene taxon:4932 20030128 SGD
+SGD S000006335 NAT3 GO:0000001 SGD_REF:S000073773|PMID:12808144 IMP P N-terminal acetyltransferase YPR131C gene taxon:4932 20050615 SGD
+SGD S000006335 NAT3 GO:0000001 SGD_REF:S000073773|PMID:12808144 IGI SGD:S000005436 P N-terminal acetyltransferase YPR131C gene taxon:4932 20050615 SGD
+SGD S000006335 NAT3 GO:0007010 SGD_REF:S000073773|PMID:12808144 IMP P N-terminal acetyltransferase YPR131C gene taxon:4932 20050615 SGD
+SGD S000006335 NAT3 GO:0007010 SGD_REF:S000073773|PMID:12808144 IGI SGD:S000005436 P N-terminal acetyltransferase YPR131C gene taxon:4932 20050615 SGD
+SGD S000006335 NAT3 GO:0017196 SGD_REF:S000053967|PMID:10545125 IMP P N-terminal acetyltransferase YPR131C gene taxon:4932 20020711 SGD
+SGD S000004673 NAT4 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C N-alpha acetyltransferase YMR069W gene taxon:4932 20031028 SGD
+SGD S000004673 NAT4 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C N-alpha acetyltransferase YMR069W gene taxon:4932 20031028 SGD
+SGD S000004673 NAT4 GO:0004596 SGD_REF:S000074259|PMID:12915400 IDA F N-alpha acetyltransferase YMR069W gene taxon:4932 20040723 SGD
+SGD S000004673 NAT4 GO:0006473 SGD_REF:S000074259|PMID:12915400 IMP P N-alpha acetyltransferase YMR069W gene taxon:4932 20040723 SGD
+SGD S000005779 NAT5 colocalizes_with GO:0005830 SGD_REF:S000074487|PMID:14517307 IDA C N-acetyltransferase YOR253W|ARD2|ROG2 gene taxon:4932 20041201 SGD
+SGD S000005779 NAT5 GO:0031415 SGD_REF:S000074487|PMID:14517307 IDA C N-acetyltransferase YOR253W|ARD2|ROG2 gene taxon:4932 20060119 SGD
+SGD S000005779 NAT5 GO:0004596 SGD_REF:S000072048|PMID:12507466 ISS protein_id:HsBAB14397|protein_id:AtCAB96669|protein_id:SpCAA20373|protein_id:AtCAC01844|protein_id:DmAA50213|protein_id:HsBAB14853|protein_id:CeT16306|protein_id:DmAAF34715 F N-acetyltransferase YOR253W|ARD2|ROG2 gene taxon:4932 20030116 SGD
+SGD S000005779 NAT5 GO:0006474 SGD_REF:S000072048|PMID:12507466 ISS protein_id:HsBAB14397|protein_id:SpCAA20373|protein_id:DmAA50213|protein_id:DmAAF34715|protein_id:AtCAC01844|protein_id:HsBAB14853|protein_id:CeT16306|protein_id:AtCAB96669 P N-acetyltransferase YOR253W|ARD2|ROG2 gene taxon:4932 20060119 SGD
+SGD S000005779 NAT5 GO:0006474 SGD_REF:S000074487|PMID:14517307 IC GO:0031415 P N-acetyltransferase YOR253W|ARD2|ROG2 gene taxon:4932 20060119 SGD
+SGD S000004449 NBP1 GO:0005634 SGD_REF:S000042635|PMID:10767562 IDA C YLR457C gene taxon:4932 20021002 SGD
+SGD S000004449 NBP1 GO:0005816 SGD_REF:S000114231|PMID:16436507 IDA C YLR457C gene taxon:4932 20060203 SGD
+SGD S000004449 NBP1 GO:0005823 SGD_REF:S000114231|PMID:16436507 IDA C YLR457C gene taxon:4932 20060203 SGD
+SGD S000004449 NBP1 GO:0005554 SGD_REF:S000069584 ND F YLR457C gene taxon:4932 20021002 SGD
+SGD S000004449 NBP1 GO:0007103 SGD_REF:S000114231|PMID:16436507 IGI SGD:S000002186|SGD:S000003043|SGD:S000003556|SGD:S000001525|SGD:S000004493|SGD:S000005783 P YLR457C gene taxon:4932 20060203 SGD
+SGD S000004449 NBP1 GO:0007103 SGD_REF:S000114231|PMID:16436507 IPI SGD:S000003043|SGD:S000004493 P YLR457C gene taxon:4932 20060203 SGD
+SGD S000004449 NBP1 GO:0007103 SGD_REF:S000114231|PMID:16436507 IMP P YLR457C gene taxon:4932 20060203 SGD
+SGD S000002569 NBP2 GO:0005634 SGD_REF:S000076220|PMID:14685261 TAS C YDR162C gene taxon:4932 20041014 SGD
+SGD S000002569 NBP2 GO:0005737 SGD_REF:S000076220|PMID:14685261 TAS C YDR162C gene taxon:4932 20041014 SGD
+SGD S000002569 NBP2 GO:0005737 SGD_REF:S000074302|PMID:14573466 IDA C YDR162C gene taxon:4932 20041014 SGD
+SGD S000002569 NBP2 GO:0005554 SGD_REF:S000069584 ND F YDR162C gene taxon:4932 20021002 SGD
+SGD S000002569 NBP2 GO:0006469 SGD_REF:S000076220|PMID:14685261 IDA P YDR162C gene taxon:4932 20041014 SGD
+SGD S000002569 NBP2 GO:0006972 SGD_REF:S000076220|PMID:14685261 IMP P YDR162C gene taxon:4932 20041014 SGD
+SGD S000002569 NBP2 GO:0006972 SGD_REF:S000076220|PMID:14685261 IPI P YDR162C gene taxon:4932 20041014 SGD
+SGD S000002569 NBP2 GO:0009408 SGD_REF:S000074302|PMID:14573466 IMP P YDR162C gene taxon:4932 20041014 SGD
+SGD S000003059 NBP35 GO:0005634 SGD_REF:S000054766|PMID:8921898 IDA C 35 kDa nucleotide binding protein YGL091C gene taxon:4932 20021002 SGD
+SGD S000003059 NBP35 GO:0016887 SGD_REF:S000054766|PMID:8921898 ISS F 35 kDa nucleotide binding protein YGL091C gene taxon:4932 20021002 SGD
+SGD S000003059 NBP35 GO:0016887 SGD_REF:S000054766|PMID:8921898 IMP F 35 kDa nucleotide binding protein YGL091C gene taxon:4932 20021002 SGD
+SGD S000003059 NBP35 GO:0000004 SGD_REF:S000069584 ND P 35 kDa nucleotide binding protein YGL091C gene taxon:4932 20021002 SGD
+SGD S000006359 NCA2 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YPR155C gene taxon:4932 20031028 SGD
+SGD S000006359 NCA2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YPR155C gene taxon:4932 20040924 SGD
+SGD S000006359 NCA2 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C YPR155C gene taxon:4932 20060317 SGD
+SGD S000006359 NCA2 GO:0005554 SGD_REF:S000069584 ND F YPR155C gene taxon:4932 20020821 SGD
+SGD S000006359 NCA2 GO:0009060 SGD_REF:S000051437|PMID:7723016 IMP P YPR155C gene taxon:4932 20020821 SGD
+SGD S000006359 NCA2 GO:0016071 SGD_REF:S000051437|PMID:7723016 IMP P YPR155C gene taxon:4932 20020821 SGD
+SGD S000003652 NCA3 GO:0008372 SGD_REF:S000069584 ND C YJL116C gene taxon:4932 20020821 SGD
+SGD S000003652 NCA3 GO:0005554 SGD_REF:S000069584 ND F YJL116C gene taxon:4932 20020821 SGD
+SGD S000003652 NCA3 GO:0007005 SGD_REF:S000048030|PMID:7586026 IGI P YJL116C gene taxon:4932 20020821 SGD
+SGD S000002805 NCB2 GO:0005634 SGD_REF:S000051732|PMID:10713169 IPI C YDR397C|YDR1 gene taxon:4932 20020918 SGD
+SGD S000002805 NCB2 GO:0003714 SGD_REF:S000051732|PMID:10713169 IGI F YDR397C|YDR1 gene taxon:4932 20020918 SGD
+SGD S000002805 NCB2 GO:0003714 SGD_REF:S000051732|PMID:10713169 IMP F YDR397C|YDR1 gene taxon:4932 20020918 SGD
+SGD S000002805 NCB2 GO:0000122 SGD_REF:S000051732|PMID:10713169 IGI P YDR397C|YDR1 gene taxon:4932 20020918 SGD
+SGD S000002805 NCB2 GO:0000122 SGD_REF:S000051732|PMID:10713169 IMP P YDR397C|YDR1 gene taxon:4932 20020918 SGD
+SGD S000003742 NCE101 GO:0008372 SGD_REF:S000069584 ND C YJL205C|NCE1|YJL205C-A|YJL206C-A gene taxon:4932 20020927 SGD
+SGD S000003742 NCE101 GO:0005554 SGD_REF:S000069584 ND F YJL205C|NCE1|YJL205C-A|YJL206C-A gene taxon:4932 20020927 SGD
+SGD S000003742 NCE101 GO:0009306 SGD_REF:S000053186|PMID:8655575 IGI P YJL205C|NCE1|YJL205C-A|YJL206C-A gene taxon:4932 20020927 SGD
+SGD S000006353 NCE102 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YPR149W|NCE2 gene taxon:4932 20020507 SGD
+SGD S000006353 NCE102 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YPR149W|NCE2 gene taxon:4932 20040813 SGD
+SGD S000006353 NCE102 GO:0005783 SGD_REF:S000069459|PMID:11914276 IDA C YPR149W|NCE2 gene taxon:4932 20020507 SGD
+SGD S000006353 NCE102 GO:0016021 SGD_REF:S000053186|PMID:8655575 ISS C YPR149W|NCE2 gene taxon:4932 20020927 SGD
+SGD S000006353 NCE102 GO:0005554 SGD_REF:S000069584 ND F YPR149W|NCE2 gene taxon:4932 20020927 SGD
+SGD S000006353 NCE102 GO:0009306 SGD_REF:S000053186|PMID:8655575 IGI P YPR149W|NCE2 gene taxon:4932 20020927 SGD
+SGD S000006353 NCE102 GO:0009306 SGD_REF:S000053186|PMID:8655575 IMP P YPR149W|NCE2 gene taxon:4932 20020927 SGD
+SGD S000004981 NCE103 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C carbonic anhydrase-like protein YNL036W|NCE3 gene taxon:4932 20031028 SGD
+SGD S000004981 NCE103 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C carbonic anhydrase-like protein YNL036W|NCE3 gene taxon:4932 20020507 SGD
+SGD S000004981 NCE103 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C carbonic anhydrase-like protein YNL036W|NCE3 gene taxon:4932 20031028 SGD
+SGD S000004981 NCE103 GO:0004089 SGD_REF:S000077065|PMID:15096093 IDA F carbonic anhydrase-like protein YNL036W|NCE3 gene taxon:4932 20041006 SGD
+SGD S000004981 NCE103 GO:0004089 SGD_REF:S000081355|PMID:15813743 IDA F carbonic anhydrase-like protein YNL036W|NCE3 gene taxon:4932 20050510 SGD
+SGD S000004981 NCE103 GO:0006979 SGD_REF:S000077065|PMID:15096093 IMP P carbonic anhydrase-like protein YNL036W|NCE3 gene taxon:4932 20041006 SGD
+SGD S000000120 NCL1 GO:0005634 SGD_REF:S000053868|PMID:9767141 IDA C tRNA:m5C-methyltransferase YBL024W|TRM4 gene taxon:4932 20021009 SGD
+SGD S000000120 NCL1 GO:0016428 SGD_REF:S000052672|PMID:10445884 IDA F tRNA:m5C-methyltransferase YBL024W|TRM4 gene taxon:4932 20021009 SGD
+SGD S000000120 NCL1 GO:0030488 SGD_REF:S000052672|PMID:10445884 IDA P tRNA:m5C-methyltransferase YBL024W|TRM4 gene taxon:4932 20021009 SGD
+SGD S000001084 NCP1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C NADP-cytochrome P450 reductase YHR042W|CPR1 gene taxon:4932 20040928 SGD
+SGD S000001084 NCP1 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C NADP-cytochrome P450 reductase YHR042W|CPR1 gene taxon:4932 20060317 SGD
+SGD S000001084 NCP1 GO:0005792 SGD_REF:S000041204|PMID:9468503 IDA C NADP-cytochrome P450 reductase YHR042W|CPR1 gene taxon:4932 20020419 SGD
+SGD S000001084 NCP1 GO:0009055 SGD_REF:S000114664|PMID:11485306 IDA F NADP-cytochrome P450 reductase YHR042W|CPR1 gene taxon:4932 20060324 SGD
+SGD S000001084 NCP1 GO:0006118 SGD_REF:S000062024|PMID:10622712 IDA P NADP-cytochrome P450 reductase YHR042W|CPR1 gene taxon:4932 20060324 SGD
+SGD S000001084 NCP1 GO:0006696 SGD_REF:S000041204|PMID:9468503 IMP P NADP-cytochrome P450 reductase YHR042W|CPR1 gene taxon:4932 20020419 SGD
+SGD S000005927 NCR1 GO:0000329 SGD_REF:S000074185|PMID:14562095 IDA C transmembrane protein (putative) YPL006W gene taxon:4932 20031028 SGD
+SGD S000005927 NCR1 GO:0000329 SGD_REF:S000086645|PMID:16138904 IDA C transmembrane protein (putative) YPL006W gene taxon:4932 20051118 SGD
+SGD S000005927 NCR1 GO:0046624 SGD_REF:S000075552|PMID:14970192 IMP F transmembrane protein (putative) YPL006W gene taxon:4932 20040311 SGD
+SGD S000005927 NCR1 GO:0006665 SGD_REF:S000075552|PMID:14970192 IMP P transmembrane protein (putative) YPL006W gene taxon:4932 20040311 SGD
+SGD S000005063 NCS2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YNL119W gene taxon:4932 20031028 SGD
+SGD S000005063 NCS2 GO:0005554 SGD_REF:S000069584 ND F YNL119W gene taxon:4932 20030423 SGD
+SGD S000005063 NCS2 GO:0001403 SGD_REF:S000075061|PMID:14551258 IMP P YNL119W gene taxon:4932 20040811 SGD
+SGD S000005063 NCS2 GO:0006464 SGD_REF:S000075061|PMID:14551258 IMP P YNL119W gene taxon:4932 20040811 SGD
+SGD S000005063 NCS2 GO:0007124 SGD_REF:S000075061|PMID:14551258 IMP P YNL119W gene taxon:4932 20040811 SGD
+SGD S000003179 NCS6 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YGL211W|YGL210W-A gene taxon:4932 20031028 SGD
+SGD S000003179 NCS6 GO:0005554 SGD_REF:S000069584 ND F YGL211W|YGL210W-A gene taxon:4932 20030203 SGD
+SGD S000003179 NCS6 GO:0000004 SGD_REF:S000069584 ND P YGL211W|YGL210W-A gene taxon:4932 20030203 SGD
+SGD S000004493 NDC1 GO:0005643 SGD_REF:S000056415|PMID:10684247 IDA C multiple transmembrane domains (putative), nuclear envelope protein, nuclear pore complex subunit YML031W gene taxon:4932 20020617 SGD
+SGD S000004493 NDC1 GO:0005643 SGD_REF:S000055427|PMID:9864355 IDA C multiple transmembrane domains (putative), nuclear envelope protein, nuclear pore complex subunit YML031W gene taxon:4932 20010118 SGD
+SGD S000004493 NDC1 GO:0005816 SGD_REF:S000055427|PMID:9864355 IDA C multiple transmembrane domains (putative), nuclear envelope protein, nuclear pore complex subunit YML031W gene taxon:4932 20010118 SGD
+SGD S000004493 NDC1 GO:0005200 SGD_REF:S000055427|PMID:9864355 IPI F multiple transmembrane domains (putative), nuclear envelope protein, nuclear pore complex subunit YML031W gene taxon:4932 20010118 SGD
+SGD S000004493 NDC1 GO:0006405 SGD_REF:S000055427|PMID:9864355 IPI P multiple transmembrane domains (putative), nuclear envelope protein, nuclear pore complex subunit YML031W gene taxon:4932 20010118 SGD
+SGD S000004493 NDC1 GO:0006405 SGD_REF:S000058277|PMID:9442897 IPI P multiple transmembrane domains (putative), nuclear envelope protein, nuclear pore complex subunit YML031W gene taxon:4932 20010118 SGD
+SGD S000004493 NDC1 GO:0006606 SGD_REF:S000055427|PMID:9864355 IPI P multiple transmembrane domains (putative), nuclear envelope protein, nuclear pore complex subunit YML031W gene taxon:4932 20010118 SGD
+SGD S000004493 NDC1 GO:0006606 SGD_REF:S000058277|PMID:9442897 IPI P multiple transmembrane domains (putative), nuclear envelope protein, nuclear pore complex subunit YML031W gene taxon:4932 20010118 SGD
+SGD S000004493 NDC1 GO:0007020 SGD_REF:S000055427|PMID:9864355 IPI P multiple transmembrane domains (putative), nuclear envelope protein, nuclear pore complex subunit YML031W gene taxon:4932 20010118 SGD
+SGD S000004493 NDC1 GO:0007020 SGD_REF:S000058447|PMID:9153752 IPI P multiple transmembrane domains (putative), nuclear envelope protein, nuclear pore complex subunit YML031W gene taxon:4932 20010118 SGD
+SGD S000004493 NDC1 GO:0007103 SGD_REF:S000055427|PMID:9864355 IMP P multiple transmembrane domains (putative), nuclear envelope protein, nuclear pore complex subunit YML031W gene taxon:4932 20010118 SGD
+SGD S000005899 NDD1 GO:0005634 SGD_REF:S000044311|PMID:10207056 IDA C YOR372C gene taxon:4932 20020201 SGD
+SGD S000005899 NDD1 GO:0016563 SGD_REF:S000044311|PMID:10207056 IDA F YOR372C gene taxon:4932 20020204 SGD
+SGD S000005899 NDD1 GO:0016563 SGD_REF:S000044311|PMID:10207056 IMP F YOR372C gene taxon:4932 20020204 SGD
+SGD S000005899 NDD1 GO:0000117 SGD_REF:S000044311|PMID:10207056 IMP P YOR372C gene taxon:4932 20020204 SGD
+SGD S000004753 NDE1 GO:0005739 SGD_REF:S000040550|PMID:9733747 IMP C NADH:ubiquinone oxidoreductase, Type II NAD(P)H:quinone oxidoreductase YMR145C|NDH1 gene taxon:4932 20020109 SGD
+SGD S000004753 NDE1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C NADH:ubiquinone oxidoreductase, Type II NAD(P)H:quinone oxidoreductase YMR145C|NDH1 gene taxon:4932 20040924 SGD
+SGD S000004753 NDE1 GO:0005739 SGD_REF:S000042730|PMID:9696750 IMP C NADH:ubiquinone oxidoreductase, Type II NAD(P)H:quinone oxidoreductase YMR145C|NDH1 gene taxon:4932 20020109 SGD
+SGD S000004753 NDE1 GO:0005739 SGD_REF:S000042730|PMID:9696750 IDA C NADH:ubiquinone oxidoreductase, Type II NAD(P)H:quinone oxidoreductase YMR145C|NDH1 gene taxon:4932 20020109 SGD
+SGD S000004753 NDE1 GO:0005739 SGD_REF:S000040550|PMID:9733747 IDA C NADH:ubiquinone oxidoreductase, Type II NAD(P)H:quinone oxidoreductase YMR145C|NDH1 gene taxon:4932 20020109 SGD
+SGD S000004753 NDE1 GO:0003954 SGD_REF:S000040550|PMID:9733747 IDA F NADH:ubiquinone oxidoreductase, Type II NAD(P)H:quinone oxidoreductase YMR145C|NDH1 gene taxon:4932 20020109 SGD
+SGD S000004753 NDE1 GO:0003954 SGD_REF:S000042730|PMID:9696750 IDA F NADH:ubiquinone oxidoreductase, Type II NAD(P)H:quinone oxidoreductase YMR145C|NDH1 gene taxon:4932 20020109 SGD
+SGD S000004753 NDE1 GO:0003954 SGD_REF:S000042730|PMID:9696750 ISS F NADH:ubiquinone oxidoreductase, Type II NAD(P)H:quinone oxidoreductase YMR145C|NDH1 gene taxon:4932 20020109 SGD
+SGD S000004753 NDE1 GO:0003954 SGD_REF:S000040550|PMID:9733747 ISS F NADH:ubiquinone oxidoreductase, Type II NAD(P)H:quinone oxidoreductase YMR145C|NDH1 gene taxon:4932 20020109 SGD
+SGD S000004753 NDE1 GO:0001300 SGD_REF:S000114324|PMID:16436509 IMP P NADH:ubiquinone oxidoreductase, Type II NAD(P)H:quinone oxidoreductase YMR145C|NDH1 gene taxon:4932 20060302 SGD
+SGD S000004753 NDE1 GO:0006116 SGD_REF:S000070271|PMID:12032156 IDA P NADH:ubiquinone oxidoreductase, Type II NAD(P)H:quinone oxidoreductase YMR145C|NDH1 gene taxon:4932 20030307 SGD
+SGD S000004753 NDE1 GO:0019655 SGD_REF:S000042730|PMID:9696750 IMP P NADH:ubiquinone oxidoreductase, Type II NAD(P)H:quinone oxidoreductase YMR145C|NDH1 gene taxon:4932 20020109 SGD
+SGD S000004753 NDE1 GO:0019655 SGD_REF:S000040550|PMID:9733747 IMP P NADH:ubiquinone oxidoreductase, Type II NAD(P)H:quinone oxidoreductase YMR145C|NDH1 gene taxon:4932 20020109 SGD
+SGD S000002243 NDE2 GO:0005739 SGD_REF:S000040550|PMID:9733747 ISS C Type II NAD(P)H:quinone oxidoreductase YDL085W|NDH2 gene taxon:4932 20021007 SGD
+SGD S000002243 NDE2 GO:0005739 SGD_REF:S000040550|PMID:9733747 IMP C Type II NAD(P)H:quinone oxidoreductase YDL085W|NDH2 gene taxon:4932 20021007 SGD
+SGD S000002243 NDE2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C Type II NAD(P)H:quinone oxidoreductase YDL085W|NDH2 gene taxon:4932 20040929 SGD
+SGD S000002243 NDE2 GO:0003954 SGD_REF:S000040550|PMID:9733747 ISS F Type II NAD(P)H:quinone oxidoreductase YDL085W|NDH2 gene taxon:4932 20020109 SGD
+SGD S000002243 NDE2 GO:0003954 SGD_REF:S000042730|PMID:9696750 ISS F Type II NAD(P)H:quinone oxidoreductase YDL085W|NDH2 gene taxon:4932 20020109 SGD
+SGD S000002243 NDE2 GO:0006116 SGD_REF:S000070271|PMID:12032156 IDA P Type II NAD(P)H:quinone oxidoreductase YDL085W|NDH2 gene taxon:4932 20030307 SGD
+SGD S000002243 NDE2 GO:0019655 SGD_REF:S000040550|PMID:9733747 IGI P Type II NAD(P)H:quinone oxidoreductase YDL085W|NDH2 gene taxon:4932 20021007 SGD
+SGD S000002243 NDE2 GO:0019655 SGD_REF:S000040550|PMID:9733747 ISS P Type II NAD(P)H:quinone oxidoreductase YDL085W|NDH2 gene taxon:4932 20021007 SGD
+SGD S000002243 NDE2 GO:0019655 SGD_REF:S000040550|PMID:9733747 IMP P Type II NAD(P)H:quinone oxidoreductase YDL085W|NDH2 gene taxon:4932 20021007 SGD
+SGD S000004589 NDI1 GO:0005759 SGD_REF:S000058452|PMID:1900238 IDA C NADH:ubiquinone oxidoreductase, Type II NAD(P)H:quinone oxidoreductase YML120C gene taxon:4932 20060302 SGD
+SGD S000004589 NDI1 GO:0005759 SGD_REF:S000058452|PMID:1900238 IMP C NADH:ubiquinone oxidoreductase, Type II NAD(P)H:quinone oxidoreductase YML120C gene taxon:4932 20060302 SGD
+SGD S000004589 NDI1 GO:0008137 SGD_REF:S000064203|PMID:3138118 IDA F NADH:ubiquinone oxidoreductase, Type II NAD(P)H:quinone oxidoreductase YML120C gene taxon:4932 20060302 SGD
+SGD S000004589 NDI1 GO:0001300 SGD_REF:S000114324|PMID:16436509 IMP P NADH:ubiquinone oxidoreductase, Type II NAD(P)H:quinone oxidoreductase YML120C gene taxon:4932 20060302 SGD
+SGD S000004589 NDI1 GO:0006120 SGD_REF:S000058452|PMID:1900238 IDA P NADH:ubiquinone oxidoreductase, Type II NAD(P)H:quinone oxidoreductase YML120C gene taxon:4932 20010118 SGD
+SGD S000004589 NDI1 GO:0043065 SGD_REF:S000114324|PMID:16436509 IMP P NADH:ubiquinone oxidoreductase, Type II NAD(P)H:quinone oxidoreductase YML120C gene taxon:4932 20060302 SGD
+SGD S000005464 NDJ1 GO:0000784 SGD_REF:S000056202|PMID:9157883 IDA C YOL104C|TAM1 gene taxon:4932 20030403 SGD
+SGD S000005464 NDJ1 GO:0042162 SGD_REF:S000073275|PMID:12734403 TAS F YOL104C|TAM1 gene taxon:4932 20030630 SGD
+SGD S000005464 NDJ1 GO:0007129 SGD_REF:S000056202|PMID:9157883 IMP P YOL104C|TAM1 gene taxon:4932 20020204 SGD
+SGD S000005464 NDJ1 GO:0007129 SGD_REF:S000056202|PMID:9157883 IDA P YOL104C|TAM1 gene taxon:4932 20020204 SGD
+SGD S000005464 NDJ1 GO:0045141 SGD_REF:S000073275|PMID:12734403 IDA P YOL104C|TAM1 gene taxon:4932 20030630 SGD
+SGD S000005464 NDJ1 GO:0045141 SGD_REF:S000073275|PMID:12734403 TAS P YOL104C|TAM1 gene taxon:4932 20030630 SGD
+SGD S000004244 NDL1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YLR254C gene taxon:4932 20031028 SGD
+SGD S000004244 NDL1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YLR254C gene taxon:4932 20031028 SGD
+SGD S000004244 NDL1 GO:0005881 SGD_REF:S000082291|PMID:15965467 IDA C YLR254C gene taxon:4932 20050718 SGD
+SGD S000004244 NDL1 GO:0005554 SGD_REF:S000069584 ND F YLR254C gene taxon:4932 20050718 SGD
+SGD S000004244 NDL1 GO:0030473 SGD_REF:S000082291|PMID:15965467 IMP P YLR254C gene taxon:4932 20050718 SGD
+SGD S000004244 NDL1 GO:0030473 SGD_REF:S000082291|PMID:15965467 IPI SGD:S000005795 P YLR254C gene taxon:4932 20050718 SGD
+SGD S000001166 NDT80 GO:0000228 SGD_REF:S000059676|PMID:11035815 IDA C DNA binding transcription factor that activates middle sporulation genes YHR124W gene taxon:4932 20030403 SGD
+SGD S000001166 NDT80 GO:0003700 SGD_REF:S000041194|PMID:9660952 IPI F DNA binding transcription factor that activates middle sporulation genes YHR124W gene taxon:4932 20020307 SGD
+SGD S000001166 NDT80 GO:0003700 SGD_REF:S000041194|PMID:9660952 IMP F DNA binding transcription factor that activates middle sporulation genes YHR124W gene taxon:4932 20020307 SGD
+SGD S000001166 NDT80 GO:0003700 SGD_REF:S000041194|PMID:9660952 IDA F DNA binding transcription factor that activates middle sporulation genes YHR124W gene taxon:4932 20020307 SGD
+SGD S000001166 NDT80 GO:0006350 SGD_REF:S000041194|PMID:9660952 IGI P DNA binding transcription factor that activates middle sporulation genes YHR124W gene taxon:4932 20030402 SGD
+SGD S000001166 NDT80 GO:0006350 SGD_REF:S000041194|PMID:9660952 IMP P DNA binding transcription factor that activates middle sporulation genes YHR124W gene taxon:4932 20030402 SGD
+SGD S000001166 NDT80 GO:0006350 SGD_REF:S000041194|PMID:9660952 IPI P DNA binding transcription factor that activates middle sporulation genes YHR124W gene taxon:4932 20030402 SGD
+SGD S000001166 NDT80 GO:0006350 SGD_REF:S000041194|PMID:9660952 TAS P DNA binding transcription factor that activates middle sporulation genes YHR124W gene taxon:4932 20030402 SGD
+SGD S000001166 NDT80 GO:0007126 SGD_REF:S000041194|PMID:9660952 IMP P DNA binding transcription factor that activates middle sporulation genes YHR124W gene taxon:4932 20020307 SGD
+SGD S000001166 NDT80 GO:0007126 SGD_REF:S000041194|PMID:9660952 IEP P DNA binding transcription factor that activates middle sporulation genes YHR124W gene taxon:4932 20020307 SGD
+SGD S000001166 NDT80 GO:0007126 SGD_REF:S000051499|PMID:8524222 IMP P DNA binding transcription factor that activates middle sporulation genes YHR124W gene taxon:4932 20020307 SGD
+SGD S000001166 NDT80 GO:0007126 SGD_REF:S000041194|PMID:9660952 IGI P DNA binding transcription factor that activates middle sporulation genes YHR124W gene taxon:4932 20020307 SGD
+SGD S000004255 NEJ1 GO:0005634 SGD_REF:S000069053|PMID:11676923 IDA C Mating-type regulated component of NHEJ YLR265C|LIF2 gene taxon:4932 20020904 SGD
+SGD S000004255 NEJ1 GO:0005554 SGD_REF:S000069584 ND F Mating-type regulated component of NHEJ YLR265C|LIF2 gene taxon:4932 20021216 SGD
+SGD S000004255 NEJ1 GO:0006281 SGD_REF:S000069053|PMID:11676923 IDA P Mating-type regulated component of NHEJ YLR265C|LIF2 gene taxon:4932 20020904 SGD
+SGD S000004255 NEJ1 GO:0006302 SGD_REF:S000069053|PMID:11676923 IDA P Mating-type regulated component of NHEJ YLR265C|LIF2 gene taxon:4932 20020904 SGD
+SGD S000001046 NEM1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YHR004C gene taxon:4932 20040928 SGD
+SGD S000001046 NEM1 GO:0016021 SGD_REF:S000040050|PMID:9822591 IDA C YHR004C gene taxon:4932 20021002 SGD
+SGD S000001046 NEM1 GO:0016021 SGD_REF:S000040050|PMID:9822591 ISS C YHR004C gene taxon:4932 20021002 SGD
+SGD S000001046 NEM1 GO:0042175 SGD_REF:S000040050|PMID:9822591 IDA C YHR004C gene taxon:4932 20021002 SGD
+SGD S000001046 NEM1 GO:0005554 SGD_REF:S000069584 ND F YHR004C gene taxon:4932 20021002 SGD
+SGD S000001046 NEM1 GO:0006997 SGD_REF:S000040050|PMID:9822591 IGI P YHR004C gene taxon:4932 20021002 SGD
+SGD S000001046 NEM1 GO:0006997 SGD_REF:S000040050|PMID:9822591 IMP P YHR004C gene taxon:4932 20021002 SGD
+SGD S000001046 NEM1 GO:0030437 SGD_REF:S000040050|PMID:9822591 IMP P YHR004C gene taxon:4932 20021002 SGD
+SGD S000001310 NEO1 GO:0000139 SGD_REF:S000075219|PMID:12960419 IDA C P-type ATPase YIL048W gene taxon:4932 20041001 SGD
+SGD S000001310 NEO1 GO:0005768 SGD_REF:S000077336|PMID:15314152 IDA C P-type ATPase YIL048W gene taxon:4932 20050223 SGD
+SGD S000001310 NEO1 GO:0005789 SGD_REF:S000075219|PMID:12960419 IDA C P-type ATPase YIL048W gene taxon:4932 20041001 SGD
+SGD S000001310 NEO1 GO:0005794 SGD_REF:S000077336|PMID:15314152 IDA C P-type ATPase YIL048W gene taxon:4932 20050223 SGD
+SGD S000001310 NEO1 colocalizes_with GO:0030137 SGD_REF:S000074185|PMID:14562095 IDA C P-type ATPase YIL048W gene taxon:4932 20031028 SGD
+SGD S000001310 NEO1 GO:0004012 SGD_REF:S000071441|PMID:12221123 ISS F P-type ATPase YIL048W gene taxon:4932 20021007 SGD
+SGD S000001310 NEO1 GO:0005388 SGD_REF:S000062336|PMID:8790914 ISS F P-type ATPase YIL048W gene taxon:4932 20020523 SGD
+SGD S000001310 NEO1 GO:0006886 SGD_REF:S000071441|PMID:12221123 TAS P P-type ATPase YIL048W gene taxon:4932 20021007 SGD
+SGD S000001310 NEO1 GO:0006890 SGD_REF:S000075219|PMID:12960419 IMP P P-type ATPase YIL048W gene taxon:4932 20041001 SGD
+SGD S000001310 NEO1 GO:0006895 SGD_REF:S000077336|PMID:15314152 IMP P P-type ATPase YIL048W gene taxon:4932 20050223 SGD
+SGD S000001310 NEO1 GO:0006895 SGD_REF:S000077336|PMID:15314152 IPI P P-type ATPase YIL048W gene taxon:4932 20050223 SGD
+SGD S000001310 NEO1 GO:0006895 SGD_REF:S000077336|PMID:15314152 IGI P P-type ATPase YIL048W gene taxon:4932 20050223 SGD
+SGD S000003612 NET1 GO:0005730 SGD_REF:S000058443|PMID:10690410 TAS C YJL076W|CFI1|ESC5|SRM8 gene taxon:4932 20010118 SGD
+SGD S000003612 NET1 GO:0030869 SGD_REF:S000056360|PMID:10219244 IDA C YJL076W|CFI1|ESC5|SRM8 gene taxon:4932 20040906 SGD
+SGD S000003612 NET1 GO:0000182 SGD_REF:S000052205|PMID:10219245 IDA F YJL076W|CFI1|ESC5|SRM8 gene taxon:4932 20010118 SGD
+SGD S000003612 NET1 GO:0000183 SGD_REF:S000052205|PMID:10219245 IPI P YJL076W|CFI1|ESC5|SRM8 gene taxon:4932 20010118 SGD
+SGD S000003612 NET1 GO:0000183 SGD_REF:S000052205|PMID:10219245 IMP P YJL076W|CFI1|ESC5|SRM8 gene taxon:4932 20010118 SGD
+SGD S000003612 NET1 GO:0007000 SGD_REF:S000052205|PMID:10219245 IMP P YJL076W|CFI1|ESC5|SRM8 gene taxon:4932 20010118 SGD
+SGD S000003612 NET1 GO:0007096 SGD_REF:S000056360|PMID:10219244 IMP P YJL076W|CFI1|ESC5|SRM8 gene taxon:4932 20010118 SGD
+SGD S000003612 NET1 GO:0007096 SGD_REF:S000052205|PMID:10219245 IPI P YJL076W|CFI1|ESC5|SRM8 gene taxon:4932 20010118 SGD
+SGD S000003612 NET1 GO:0007096 SGD_REF:S000056360|PMID:10219244 IPI P YJL076W|CFI1|ESC5|SRM8 gene taxon:4932 20010118 SGD
+SGD S000006147 NEW1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YPL226W gene taxon:4932 20031028 SGD
+SGD S000006147 NEW1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YPL226W gene taxon:4932 20040813 SGD
+SGD S000006147 NEW1 GO:0005524 SGD_REF:S000045454|PMID:9720054 ISS F YPL226W gene taxon:4932 20040929 SGD
+SGD S000006147 NEW1 GO:0016887 SGD_REF:S000045454|PMID:9720054 ISS F YPL226W gene taxon:4932 20040929 SGD
+SGD S000006147 NEW1 GO:0000004 SGD_REF:S000069584 ND P YPL226W gene taxon:4932 20021009 SGD
+SGD S000005682 NFI1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C chromatin protein YOR156C|SIZ2 gene taxon:4932 20031028 SGD
+SGD S000005682 NFI1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C chromatin protein YOR156C|SIZ2 gene taxon:4932 20031028 SGD
+SGD S000005682 NFI1 GO:0019789 SGD_REF:S000075867|PMID:12761287 IDA F chromatin protein YOR156C|SIZ2 gene taxon:4932 20040806 SGD
+SGD S000005682 NFI1 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P chromatin protein YOR156C|SIZ2 gene taxon:4932 20060202 SGD
+SGD S000005682 NFI1 GO:0016925 SGD_REF:S000075867|PMID:12761287 IDA P chromatin protein YOR156C|SIZ2 gene taxon:4932 20040806 SGD
+SGD S000005682 NFI1 GO:0030261 SGD_REF:S000071761|PMID:12402242 TAS P chromatin protein YOR156C|SIZ2 gene taxon:4932 20021209 SGD
+SGD S000000522 NFS1 GO:0005634 SGD_REF:S000060314|PMID:11110795 IMP C YCL017C|SPL1 gene taxon:4932 20060308 SGD
+SGD S000000522 NFS1 GO:0005634 SGD_REF:S000060314|PMID:11110795 ISS C YCL017C|SPL1 gene taxon:4932 20060308 SGD
+SGD S000000522 NFS1 GO:0005739 SGD_REF:S000040793|PMID:10406803 TAS C YCL017C|SPL1 gene taxon:4932 20020207 SGD
+SGD S000000522 NFS1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YCL017C|SPL1 gene taxon:4932 20040928 SGD
+SGD S000000522 NFS1 GO:0004123 SGD_REF:S000070337|PMID:12065597 ISS F YCL017C|SPL1 gene taxon:4932 20021216 SGD
+SGD S000000522 NFS1 GO:0016227 SGD_REF:S000076996|PMID:15220327 IMP F YCL017C|SPL1 gene taxon:4932 20060308 SGD
+SGD S000000522 NFS1 GO:0031071 SGD_REF:S000076996|PMID:15220327 IDA F YCL017C|SPL1 gene taxon:4932 20060308 SGD
+SGD S000000522 NFS1 GO:0006879 SGD_REF:S000054740|PMID:10551871 IMP P YCL017C|SPL1 gene taxon:4932 20020207 SGD
+SGD S000000522 NFS1 GO:0016226 SGD_REF:S000052831|PMID:9813017 TAS P YCL017C|SPL1 gene taxon:4932 20020207 SGD
+SGD S000000522 NFS1 GO:0016226 SGD_REF:S000076996|PMID:15220327 IDA P YCL017C|SPL1 gene taxon:4932 20060308 SGD
+SGD S000000522 NFS1 GO:0016226 SGD_REF:S000052831|PMID:9813017 ISS P YCL017C|SPL1 gene taxon:4932 20020207 SGD
+SGD S000001811 NFT1 GO:0016020 SGD_REF:S000058031|PMID:9020838 ISS C Putative MRP-type ABC transporter YKR103W gene taxon:4932 20021120 SGD
+SGD S000001811 NFT1 GO:0042626 SGD_REF:S000058031|PMID:9020838 ISS F Putative MRP-type ABC transporter YKR103W gene taxon:4932 20021120 SGD
+SGD S000001811 NFT1 GO:0042626 SGD_REF:S000073529|PMID:12796304 ISS F Putative MRP-type ABC transporter YKR103W gene taxon:4932 20030630 SGD
+SGD S000001811 NFT1 GO:0006810 SGD_REF:S000058031|PMID:9020838 ISS P Putative MRP-type ABC transporter YKR103W gene taxon:4932 20021120 SGD
+SGD S000001523 NFU1 GO:0005759 SGD_REF:S000045090|PMID:10468587 IDA C YKL040C|NUB1 gene taxon:4932 20010118 SGD
+SGD S000001523 NFU1 GO:0005554 SGD_REF:S000069584 ND F YKL040C|NUB1 gene taxon:4932 20021206 SGD
+SGD S000001523 NFU1 GO:0006879 SGD_REF:S000045090|PMID:10468587 IMP P YKL040C|NUB1 gene taxon:4932 20010118 SGD
+SGD S000001523 NFU1 GO:0006879 SGD_REF:S000045090|PMID:10468587 ISS P YKL040C|NUB1 gene taxon:4932 20010118 SGD
+SGD S000002583 NGG1 GO:0000124 SGD_REF:S000048255|PMID:9674426 IDA C genetic and mutant analyses suggest that Ngg1p (Ada3p) is part of two transcriptional adaptor/HAT (histone acetyltransferase complexes, the 0.8 MD ADA complex and the 1.8 MD SAGA complex, transcription factor YDR176W|ADA3|SWI7 gene taxon:4932 20010221 SGD
+SGD S000002583 NGG1 GO:0005671 SGD_REF:S000042121|PMID:10490601 IPI C genetic and mutant analyses suggest that Ngg1p (Ada3p) is part of two transcriptional adaptor/HAT (histone acetyltransferase complexes, the 0.8 MD ADA complex and the 1.8 MD SAGA complex, transcription factor YDR176W|ADA3|SWI7 gene taxon:4932 20031215 SGD
+SGD S000002583 NGG1 GO:0046695 SGD_REF:S000071997|PMID:12446794 IPI C genetic and mutant analyses suggest that Ngg1p (Ada3p) is part of two transcriptional adaptor/HAT (histone acetyltransferase complexes, the 0.8 MD ADA complex and the 1.8 MD SAGA complex, transcription factor YDR176W|ADA3|SWI7 gene taxon:4932 20041024 SGD
+SGD S000002583 NGG1 GO:0003712 SGD_REF:S000041664|PMID:9038164 TAS F genetic and mutant analyses suggest that Ngg1p (Ada3p) is part of two transcriptional adaptor/HAT (histone acetyltransferase complexes, the 0.8 MD ADA complex and the 1.8 MD SAGA complex, transcription factor YDR176W|ADA3|SWI7 gene taxon:4932 20021101 SGD
+SGD S000002583 NGG1 GO:0016568 SGD_REF:S000061032|PMID:10839822 TAS P genetic and mutant analyses suggest that Ngg1p (Ada3p) is part of two transcriptional adaptor/HAT (histone acetyltransferase complexes, the 0.8 MD ADA complex and the 1.8 MD SAGA complex, transcription factor YDR176W|ADA3|SWI7 gene taxon:4932 20020426 SGD
+SGD S000002583 NGG1 GO:0016573 SGD_REF:S000061032|PMID:10839822 TAS P genetic and mutant analyses suggest that Ngg1p (Ada3p) is part of two transcriptional adaptor/HAT (histone acetyltransferase complexes, the 0.8 MD ADA complex and the 1.8 MD SAGA complex, transcription factor YDR176W|ADA3|SWI7 gene taxon:4932 20020426 SGD
+SGD S000005402 NGL1 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C DNase (putative), RNase (putative) YOL042W gene taxon:4932 20031028 SGD
+SGD S000005402 NGL1 GO:0004519 SGD_REF:S000071405|PMID:12358428 ISS F DNase (putative), RNase (putative) YOL042W gene taxon:4932 20021216 SGD
+SGD S000005402 NGL1 GO:0000004 SGD_REF:S000069584 ND P DNase (putative), RNase (putative) YOL042W gene taxon:4932 20021216 SGD
+SGD S000004898 NGL2 GO:0005622 SGD_REF:S000071405|PMID:12358428 IDA C RNase YMR285C gene taxon:4932 20021008 SGD
+SGD S000004898 NGL2 GO:0004521 SGD_REF:S000071405|PMID:12358428 IMP F RNase YMR285C gene taxon:4932 20021216 SGD
+SGD S000004898 NGL2 GO:0004521 SGD_REF:S000071405|PMID:12358428 ISS F RNase YMR285C gene taxon:4932 20021216 SGD
+SGD S000004898 NGL2 GO:0006364 SGD_REF:S000071405|PMID:12358428 IMP P RNase YMR285C gene taxon:4932 20021008 SGD
+SGD S000004587 NGL3 GO:0008372 SGD_REF:S000069584 ND C DNase (putative), RNase (putative) YML118W gene taxon:4932 20010208 SGD
+SGD S000004587 NGL3 GO:0004519 SGD_REF:S000071405|PMID:12358428 ISS F DNase (putative), RNase (putative) YML118W gene taxon:4932 20021216 SGD
+SGD S000004587 NGL3 GO:0000004 SGD_REF:S000069584 ND P DNase (putative), RNase (putative) YML118W gene taxon:4932 20021216 SGD
+SGD S000000416 NGR1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C glucose-repressible RNA binding protein YBR212W|RBP1 gene taxon:4932 20020507 SGD
+SGD S000000416 NGR1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C glucose-repressible RNA binding protein YBR212W|RBP1 gene taxon:4932 20031028 SGD
+SGD S000000416 NGR1 GO:0048471 SGD_REF:S000075288|PMID:14570877 IDA C glucose-repressible RNA binding protein YBR212W|RBP1 gene taxon:4932 20040915 SGD
+SGD S000000416 NGR1 GO:0003697 SGD_REF:S000057697|PMID:8325883 IDA F glucose-repressible RNA binding protein YBR212W|RBP1 gene taxon:4932 20021009 SGD
+SGD S000000416 NGR1 GO:0003723 SGD_REF:S000057697|PMID:8325883 IDA F glucose-repressible RNA binding protein YBR212W|RBP1 gene taxon:4932 20021009 SGD
+SGD S000000416 NGR1 GO:0045182 SGD_REF:S000075288|PMID:14570877 IMP F glucose-repressible RNA binding protein YBR212W|RBP1 gene taxon:4932 20040915 SGD
+SGD S000000416 NGR1 GO:0007005 SGD_REF:S000075288|PMID:14570877 IMP P glucose-repressible RNA binding protein YBR212W|RBP1 gene taxon:4932 20040915 SGD
+SGD S000000416 NGR1 GO:0040008 SGD_REF:S000057697|PMID:8325883 IMP P glucose-repressible RNA binding protein YBR212W|RBP1 gene taxon:4932 20021009 SGD
+SGD S000004128 NHA1 GO:0005886 SGD_REF:S000047735|PMID:9802016 IDA C YLR138W gene taxon:4932 20020206 SGD
+SGD S000004128 NHA1 GO:0005886 SGD_REF:S000082239|PMID:15950597 IDA C YLR138W gene taxon:4932 20050711 SGD
+SGD S000004128 NHA1 GO:0015385 SGD_REF:S000082239|PMID:15950597 IDA F YLR138W gene taxon:4932 20050711 SGD
+SGD S000004128 NHA1 GO:0015491 SGD_REF:S000051446|PMID:8654575 ISS F YLR138W gene taxon:4932 20020206 SGD
+SGD S000004128 NHA1 GO:0015491 SGD_REF:S000047735|PMID:9802016 IMP F YLR138W gene taxon:4932 20020206 SGD
+SGD S000004128 NHA1 GO:0006970 SGD_REF:S000114072|PMID:16402204 IMP P YLR138W gene taxon:4932 20060403 SGD
+SGD S000004128 NHA1 GO:0030004 SGD_REF:S000047735|PMID:9802016 IMP P YLR138W gene taxon:4932 20020206 SGD
+SGD S000004128 NHA1 GO:0030007 SGD_REF:S000114072|PMID:16402204 IMP P YLR138W gene taxon:4932 20060403 SGD
+SGD S000002160 NHP10 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C HMG1-box containing protein YDL002C|HMO2 gene taxon:4932 20031028 SGD
+SGD S000002160 NHP10 GO:0031011 SGD_REF:S000073963|PMID:12887900 IPI C HMG1-box containing protein YDL002C|HMO2 gene taxon:4932 20041007 SGD
+SGD S000002160 NHP10 GO:0005554 SGD_REF:S000069584 ND F HMG1-box containing protein YDL002C|HMO2 gene taxon:4932 20020523 SGD
+SGD S000002160 NHP10 GO:0006338 SGD_REF:S000073963|PMID:12887900 IPI P HMG1-box containing protein YDL002C|HMO2 gene taxon:4932 20031023 SGD
+SGD S000002367 NHP2 GO:0005732 SGD_REF:S000048199|PMID:9843512 IPI C HMG-like protein YDL208W gene taxon:4932 20050218 SGD
+SGD S000002367 NHP2 GO:0003723 SGD_REF:S000061428|PMID:11433018 IDA F HMG-like protein YDL208W gene taxon:4932 20021114 SGD
+SGD S000002367 NHP2 GO:0000154 SGD_REF:S000058443|PMID:10690410 TAS P HMG-like protein YDL208W gene taxon:4932 20010118 SGD
+SGD S000002367 NHP2 GO:0006365 SGD_REF:S000058443|PMID:10690410 TAS P HMG-like protein YDL208W gene taxon:4932 20010118 SGD
+SGD S000002367 NHP2 GO:0031118 SGD_REF:S000048199|PMID:9843512 IMP P HMG-like protein YDL208W gene taxon:4932 20050416 SGD
+SGD S000006256 NHP6A GO:0000790 SGD_REF:S000053344|PMID:10228169 IPI C 11 kDa nonhistone chromosomal protein YPR052C gene taxon:4932 20010118 SGD
+SGD S000006256 NHP6A GO:0035101 SGD_REF:S000061420|PMID:11432837 IGI C 11 kDa nonhistone chromosomal protein YPR052C gene taxon:4932 20041021 SGD
+SGD S000006256 NHP6A GO:0035101 SGD_REF:S000061420|PMID:11432837 IPI C 11 kDa nonhistone chromosomal protein YPR052C gene taxon:4932 20041021 SGD
+SGD S000006256 NHP6A GO:0003682 SGD_REF:S000053344|PMID:10228169 IDA F 11 kDa nonhistone chromosomal protein YPR052C gene taxon:4932 20010118 SGD
+SGD S000006256 NHP6A GO:0003682 SGD_REF:S000076895|PMID:14739928 IDA F 11 kDa nonhistone chromosomal protein YPR052C gene taxon:4932 20041214 SGD
+SGD S000006256 NHP6A GO:0003682 SGD_REF:S000053344|PMID:10228169 IPI F 11 kDa nonhistone chromosomal protein YPR052C gene taxon:4932 20010118 SGD
+SGD S000006256 NHP6A GO:0006325 SGD_REF:S000053344|PMID:10228169 IPI P 11 kDa nonhistone chromosomal protein YPR052C gene taxon:4932 20010118 SGD
+SGD S000006256 NHP6A GO:0006338 SGD_REF:S000076895|PMID:14739928 IMP P 11 kDa nonhistone chromosomal protein YPR052C gene taxon:4932 20041214 SGD
+SGD S000006256 NHP6A GO:0006357 SGD_REF:S000041491|PMID:9872947 IGI P 11 kDa nonhistone chromosomal protein YPR052C gene taxon:4932 20010118 SGD
+SGD S000006256 NHP6A GO:0006357 SGD_REF:S000041491|PMID:9872947 ISS P 11 kDa nonhistone chromosomal protein YPR052C gene taxon:4932 20010118 SGD
+SGD S000006256 NHP6A GO:0006359 SGD_REF:S000060111|PMID:11239460 IMP P 11 kDa nonhistone chromosomal protein YPR052C gene taxon:4932 20020207 SGD
+SGD S000006256 NHP6A GO:0006359 SGD_REF:S000060111|PMID:11239460 IGI P 11 kDa nonhistone chromosomal protein YPR052C gene taxon:4932 20020207 SGD
+SGD S000006256 NHP6A GO:0006359 SGD_REF:S000060111|PMID:11239460 IDA P 11 kDa nonhistone chromosomal protein YPR052C gene taxon:4932 20020207 SGD
+SGD S000006256 NHP6A GO:0045944 SGD_REF:S000076895|PMID:14739928 IMP P 11 kDa nonhistone chromosomal protein YPR052C gene taxon:4932 20041214 SGD
+SGD S000006256 NHP6A GO:0045944 SGD_REF:S000076895|PMID:14739928 IPI P 11 kDa nonhistone chromosomal protein YPR052C gene taxon:4932 20041214 SGD
+SGD S000002157 NHP6B GO:0000790 SGD_REF:S000053344|PMID:10228169 ISS C 11 kDa nonhistone chromosomal protein YBR089C-A|YBR090C-A gene taxon:4932 20010118 SGD
+SGD S000002157 NHP6B GO:0035101 SGD_REF:S000061420|PMID:11432837 IGI C 11 kDa nonhistone chromosomal protein YBR089C-A|YBR090C-A gene taxon:4932 20041021 SGD
+SGD S000002157 NHP6B GO:0035101 SGD_REF:S000061420|PMID:11432837 IPI C 11 kDa nonhistone chromosomal protein YBR089C-A|YBR090C-A gene taxon:4932 20041021 SGD
+SGD S000002157 NHP6B GO:0003682 SGD_REF:S000053344|PMID:10228169 ISS F 11 kDa nonhistone chromosomal protein YBR089C-A|YBR090C-A gene taxon:4932 20010118 SGD
+SGD S000002157 NHP6B GO:0003682 SGD_REF:S000076895|PMID:14739928 IDA F 11 kDa nonhistone chromosomal protein YBR089C-A|YBR090C-A gene taxon:4932 20041214 SGD
+SGD S000002157 NHP6B GO:0006325 SGD_REF:S000053344|PMID:10228169 ISS P 11 kDa nonhistone chromosomal protein YBR089C-A|YBR090C-A gene taxon:4932 20010118 SGD
+SGD S000002157 NHP6B GO:0006338 SGD_REF:S000076895|PMID:14739928 IMP P 11 kDa nonhistone chromosomal protein YBR089C-A|YBR090C-A gene taxon:4932 20041214 SGD
+SGD S000002157 NHP6B GO:0006357 SGD_REF:S000041491|PMID:9872947 ISS P 11 kDa nonhistone chromosomal protein YBR089C-A|YBR090C-A gene taxon:4932 20010118 SGD
+SGD S000002157 NHP6B GO:0006359 SGD_REF:S000060111|PMID:11239460 IMP P 11 kDa nonhistone chromosomal protein YBR089C-A|YBR090C-A gene taxon:4932 20020207 SGD
+SGD S000002157 NHP6B GO:0006359 SGD_REF:S000060111|PMID:11239460 IGI P 11 kDa nonhistone chromosomal protein YBR089C-A|YBR090C-A gene taxon:4932 20020207 SGD
+SGD S000002157 NHP6B GO:0006359 SGD_REF:S000060366|PMID:11287614 IDA P 11 kDa nonhistone chromosomal protein YBR089C-A|YBR090C-A gene taxon:4932 20020207 SGD
+SGD S000002157 NHP6B GO:0045944 SGD_REF:S000076895|PMID:14739928 IMP P 11 kDa nonhistone chromosomal protein YBR089C-A|YBR090C-A gene taxon:4932 20041214 SGD
+SGD S000002157 NHP6B GO:0045944 SGD_REF:S000076895|PMID:14739928 IPI P 11 kDa nonhistone chromosomal protein YBR089C-A|YBR090C-A gene taxon:4932 20041214 SGD
+SGD S000002864 NHX1 GO:0005770 SGD_REF:S000039966|PMID:9694857 IDA C Na+/H+ exchanger YDR456W|NHA2|VPS44 gene taxon:4932 20010626 SGD
+SGD S000002864 NHX1 GO:0015077 SGD_REF:S000051567|PMID:9334180 IMP F Na+/H+ exchanger YDR456W|NHA2|VPS44 gene taxon:4932 20010626 SGD
+SGD S000002864 NHX1 GO:0015077 SGD_REF:S000051567|PMID:9334180 ISS F Na+/H+ exchanger YDR456W|NHA2|VPS44 gene taxon:4932 20010626 SGD
+SGD S000002864 NHX1 GO:0015077 SGD_REF:S000046741|PMID:10998367 IDA F Na+/H+ exchanger YDR456W|NHA2|VPS44 gene taxon:4932 20010626 SGD
+SGD S000002864 NHX1 GO:0007035 SGD_REF:S000042739|PMID:10589731 IMP P Na+/H+ exchanger YDR456W|NHA2|VPS44 gene taxon:4932 20010626 SGD
+SGD S000002864 NHX1 GO:0015672 SGD_REF:S000051567|PMID:9334180 IMP P Na+/H+ exchanger YDR456W|NHA2|VPS44 gene taxon:4932 20010626 SGD
+SGD S000002864 NHX1 GO:0015672 SGD_REF:S000051567|PMID:9334180 ISS P Na+/H+ exchanger YDR456W|NHA2|VPS44 gene taxon:4932 20010626 SGD
+SGD S000002864 NHX1 GO:0016197 SGD_REF:S000060733|PMID:20757 IMP P Na+/H+ exchanger YDR456W|NHA2|VPS44 gene taxon:4932 20010626 SGD
+SGD S000002864 NHX1 GO:0030004 SGD_REF:S000042739|PMID:10589731 IMP P Na+/H+ exchanger YDR456W|NHA2|VPS44 gene taxon:4932 20010626 SGD
+SGD S000001898 NIC96 GO:0005643 SGD_REF:S000058277|PMID:9442897 IDA C 96 kDa nucleoporin-interacting component, nuclear pore complex subunit YFR002W gene taxon:4932 20010118 SGD
+SGD S000001898 NIC96 GO:0005198 SGD_REF:S000058277|PMID:9442897 TAS F 96 kDa nucleoporin-interacting component, nuclear pore complex subunit YFR002W gene taxon:4932 20010118 SGD
+SGD S000001898 NIC96 GO:0006406 SGD_REF:S000058277|PMID:9442897 TAS P 96 kDa nucleoporin-interacting component, nuclear pore complex subunit YFR002W gene taxon:4932 20010118 SGD
+SGD S000001898 NIC96 GO:0006407 SGD_REF:S000058277|PMID:9442897 TAS P 96 kDa nucleoporin-interacting component, nuclear pore complex subunit YFR002W gene taxon:4932 20010118 SGD
+SGD S000001898 NIC96 GO:0006408 SGD_REF:S000058277|PMID:9442897 TAS P 96 kDa nucleoporin-interacting component, nuclear pore complex subunit YFR002W gene taxon:4932 20010118 SGD
+SGD S000001898 NIC96 GO:0006409 SGD_REF:S000058277|PMID:9442897 TAS P 96 kDa nucleoporin-interacting component, nuclear pore complex subunit YFR002W gene taxon:4932 20010118 SGD
+SGD S000001898 NIC96 GO:0006606 SGD_REF:S000058277|PMID:9442897 IMP P 96 kDa nucleoporin-interacting component, nuclear pore complex subunit YFR002W gene taxon:4932 20010118 SGD
+SGD S000001898 NIC96 GO:0006607 SGD_REF:S000058277|PMID:9442897 TAS P 96 kDa nucleoporin-interacting component, nuclear pore complex subunit YFR002W gene taxon:4932 20010118 SGD
+SGD S000001898 NIC96 GO:0006608 SGD_REF:S000058277|PMID:9442897 TAS P 96 kDa nucleoporin-interacting component, nuclear pore complex subunit YFR002W gene taxon:4932 20010118 SGD
+SGD S000001898 NIC96 GO:0006609 SGD_REF:S000058277|PMID:9442897 TAS P 96 kDa nucleoporin-interacting component, nuclear pore complex subunit YFR002W gene taxon:4932 20010118 SGD
+SGD S000001898 NIC96 GO:0006610 SGD_REF:S000058277|PMID:9442897 TAS P 96 kDa nucleoporin-interacting component, nuclear pore complex subunit YFR002W gene taxon:4932 20010118 SGD
+SGD S000001898 NIC96 GO:0006611 SGD_REF:S000058277|PMID:9442897 TAS P 96 kDa nucleoporin-interacting component, nuclear pore complex subunit YFR002W gene taxon:4932 20010118 SGD
+SGD S000001898 NIC96 GO:0006999 SGD_REF:S000058277|PMID:9442897 IMP P 96 kDa nucleoporin-interacting component, nuclear pore complex subunit YFR002W gene taxon:4932 20010118 SGD
+SGD S000003189 NIF3 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YGL221C gene taxon:4932 20031028 SGD
+SGD S000003189 NIF3 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YGL221C gene taxon:4932 20031028 SGD
+SGD S000003189 NIF3 GO:0005554 SGD_REF:S000069584 ND F YGL221C gene taxon:4932 20021125 SGD
+SGD S000003189 NIF3 GO:0000004 SGD_REF:S000069584 ND P YGL221C gene taxon:4932 20021125 SGD
+SGD S000004926 NIP1 GO:0005737 SGD_REF:S000051068|PMID:1332047 IDA C translation initiation factor eIF3 subunit YMR309C gene taxon:4932 20020116 SGD
+SGD S000004926 NIP1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C translation initiation factor eIF3 subunit YMR309C gene taxon:4932 20020507 SGD
+SGD S000004926 NIP1 GO:0005852 SGD_REF:S000043795|PMID:9671501 IPI C translation initiation factor eIF3 subunit YMR309C gene taxon:4932 20020116 SGD
+SGD S000004926 NIP1 GO:0005852 SGD_REF:S000040522|PMID:9660829 IDA C translation initiation factor eIF3 subunit YMR309C gene taxon:4932 20060118 SGD
+SGD S000004926 NIP1 GO:0005852 SGD_REF:S000043795|PMID:9671501 IDA C translation initiation factor eIF3 subunit YMR309C gene taxon:4932 20020116 SGD
+SGD S000004926 NIP1 GO:0043614 SGD_REF:S000082127|PMID:11018020 IDA C translation initiation factor eIF3 subunit YMR309C gene taxon:4932 20060427 SGD
+SGD S000004926 NIP1 GO:0003743 SGD_REF:S000043795|PMID:9671501 IDA F translation initiation factor eIF3 subunit YMR309C gene taxon:4932 20020116 SGD
+SGD S000004926 NIP1 GO:0006413 SGD_REF:S000051901|PMID:9722586 IMP P translation initiation factor eIF3 subunit YMR309C gene taxon:4932 20020116 SGD
+SGD S000004926 NIP1 GO:0006413 SGD_REF:S000051901|PMID:9722586 IGI P translation initiation factor eIF3 subunit YMR309C gene taxon:4932 20020116 SGD
+SGD S000004926 NIP1 GO:0006413 SGD_REF:S000043795|PMID:9671501 IDA P translation initiation factor eIF3 subunit YMR309C gene taxon:4932 20020116 SGD
+SGD S000006095 NIP100 colocalizes_with GO:0005816 SGD_REF:S000046660|PMID:9658168 IDA C large subunit of dynactin complex (putative) YPL174C|PAC13 gene taxon:4932 20050512 SGD
+SGD S000006095 NIP100 GO:0005869 SGD_REF:S000046660|PMID:9658168 IDA C large subunit of dynactin complex (putative) YPL174C|PAC13 gene taxon:4932 20010118 SGD
+SGD S000006095 NIP100 GO:0005515 SGD_REF:S000046660|PMID:9658168 ISS F large subunit of dynactin complex (putative) YPL174C|PAC13 gene taxon:4932 20020624 SGD
+SGD S000006095 NIP100 GO:0008017 SGD_REF:S000046660|PMID:9658168 ISS F large subunit of dynactin complex (putative) YPL174C|PAC13 gene taxon:4932 20020624 SGD
+SGD S000006095 NIP100 GO:0000132 SGD_REF:S000046660|PMID:9658168 IMP P large subunit of dynactin complex (putative) YPL174C|PAC13 gene taxon:4932 20050512 SGD
+SGD S000006132 NIP7 GO:0005730 SGD_REF:S000041383|PMID:9891085 TAS C YPL211W gene taxon:4932 20010118 SGD
+SGD S000006132 NIP7 GO:0005842 SGD_REF:S000041383|PMID:9891085 TAS C YPL211W gene taxon:4932 20010118 SGD
+SGD S000006132 NIP7 GO:0005554 SGD_REF:S000069584 ND F YPL211W gene taxon:4932 20021205 SGD
+SGD S000006132 NIP7 GO:0000027 SGD_REF:S000058443|PMID:10690410 TAS P YPL211W gene taxon:4932 20010118 SGD
+SGD S000006132 NIP7 GO:0006364 SGD_REF:S000058443|PMID:10690410 TAS P YPL211W gene taxon:4932 20010118 SGD
+SGD S000006132 NIP7 GO:0042273 SGD_REF:S000076470|PMID:15100437 IPI P YPL211W gene taxon:4932 20050407 SGD
+SGD S000005022 NIS1 GO:0005634 SGD_REF:S000069114|PMID:11817649 IDA C YNL078W|JIP1 gene taxon:4932 20021010 SGD
+SGD S000005022 NIS1 GO:0005935 SGD_REF:S000069114|PMID:11817649 IDA C YNL078W|JIP1 gene taxon:4932 20021010 SGD
+SGD S000005022 NIS1 GO:0005554 SGD_REF:S000069584 ND F YNL078W|JIP1 gene taxon:4932 20021010 SGD
+SGD S000005022 NIS1 GO:0007088 SGD_REF:S000069114|PMID:11817649 IPI P YNL078W|JIP1 gene taxon:4932 20021010 SGD
+SGD S000001426 NIT1 GO:0008372 SGD_REF:S000069584 ND C nitrilase YIL164C gene taxon:4932 20010119 SGD
+SGD S000001426 NIT1 GO:0000257 SGD_REF:S000069984|PMID:11380987 ISS F nitrilase YIL164C gene taxon:4932 20040326 SGD
+SGD S000001426 NIT1 GO:0000004 SGD_REF:S000069584 ND P nitrilase YIL164C gene taxon:4932 20020425 SGD
+SGD S000003662 NIT2 GO:0008372 SGD_REF:S000069584 ND C YJL126W gene taxon:4932 20010119 SGD
+SGD S000003662 NIT2 GO:0016810 SGD_REF:S000069984|PMID:11380987 ISS F YJL126W gene taxon:4932 20030822 SGD
+SGD S000003662 NIT2 GO:0000004 SGD_REF:S000069584 ND P YJL126W gene taxon:4932 20010119 SGD
+SGD S000004343 NIT3 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YLR351C gene taxon:4932 20031028 SGD
+SGD S000004343 NIT3 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YLR351C gene taxon:4932 20031028 SGD
+SGD S000004343 NIT3 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YLR351C gene taxon:4932 20040813 SGD
+SGD S000004343 NIT3 GO:0016810 SGD_REF:S000069984|PMID:11380987 ISS F YLR351C gene taxon:4932 20030822 SGD
+SGD S000004343 NIT3 GO:0000004 SGD_REF:S000069584 ND P YLR351C gene taxon:4932 20010119 SGD
+SGD S000002791 NKP1 GO:0000776 SGD_REF:S000071581|PMID:12408861 IDA C YDR383C gene taxon:4932 20031105 SGD
+SGD S000002791 NKP1 GO:0005554 SGD_REF:S000069584 ND F YDR383C gene taxon:4932 20031105 SGD
+SGD S000002791 NKP1 GO:0000004 SGD_REF:S000069584 ND P YDR383C gene taxon:4932 20021121 SGD
+SGD S000004307 NKP2 GO:0000776 SGD_REF:S000071581|PMID:12408861 IDA C YLR315W gene taxon:4932 20031105 SGD
+SGD S000004307 NKP2 colocalizes_with GO:0005816 SGD_REF:S000074185|PMID:14562095 IDA C YLR315W gene taxon:4932 20031028 SGD
+SGD S000004307 NKP2 GO:0005554 SGD_REF:S000069584 ND F YLR315W gene taxon:4932 20021125 SGD
+SGD S000004307 NKP2 GO:0000004 SGD_REF:S000069584 ND P YLR315W gene taxon:4932 20021125 SGD
+SGD S000004320 NMA1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C nicotinamide/nicotinic acid mononucleotide adenylyltransferase YLR328W gene taxon:4932 20031028 SGD
+SGD S000004320 NMA1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C nicotinamide/nicotinic acid mononucleotide adenylyltransferase YLR328W gene taxon:4932 20031028 SGD
+SGD S000004320 NMA1 GO:0000309 SGD_REF:S000056352|PMID:10428462 IDA F nicotinamide/nicotinic acid mononucleotide adenylyltransferase YLR328W gene taxon:4932 20020708 SGD
+SGD S000004320 NMA1 GO:0019674 SGD_REF:S000070049|PMID:11884393 TAS P nicotinamide/nicotinic acid mononucleotide adenylyltransferase YLR328W gene taxon:4932 20020629 SGD
+SGD S000005067 NMA111 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YNL123W|YNM3 gene taxon:4932 20031028 SGD
+SGD S000005067 NMA111 GO:0005634 SGD_REF:S000114563|PMID:14657274 IDA C YNL123W|YNM3 gene taxon:4932 20060313 SGD
+SGD S000005067 NMA111 GO:0008236 SGD_REF:S000074355|PMID:14534547 ISS MGI:1928676 F YNL123W|YNM3 gene taxon:4932 20031126 SGD
+SGD S000005067 NMA111 GO:0006629 SGD_REF:S000114421|PMID:16470384 IMP P YNL123W|YNM3 gene taxon:4932 20060313 SGD
+SGD S000005067 NMA111 GO:0006629 SGD_REF:S000114421|PMID:16470384 IPI SGD:S000005844 P YNL123W|YNM3 gene taxon:4932 20060313 SGD
+SGD S000005067 NMA111 GO:0006915 SGD_REF:S000114421|PMID:16470384 IMP P YNL123W|YNM3 gene taxon:4932 20060313 SGD
+SGD S000005067 NMA111 GO:0006915 SGD_REF:S000114563|PMID:14657274 ISS P YNL123W|YNM3 gene taxon:4932 20060313 SGD
+SGD S000005067 NMA111 GO:0006915 SGD_REF:S000114563|PMID:14657274 IMP P YNL123W|YNM3 gene taxon:4932 20060313 SGD
+SGD S000005067 NMA111 GO:0006915 SGD_REF:S000114421|PMID:16470384 ISS UniProt:O43464 P YNL123W|YNM3 gene taxon:4932 20060313 SGD
+SGD S000003242 NMA2 GO:0005634 SGD_REF:S000070049|PMID:11884393 IDA C nicotinamide/nicotinic acid mononucleotide adenylyltransferase YGR010W gene taxon:4932 20020629 SGD
+SGD S000003242 NMA2 GO:0004515 SGD_REF:S000070049|PMID:11884393 IGI F nicotinamide/nicotinic acid mononucleotide adenylyltransferase YGR010W gene taxon:4932 20030106 SGD
+SGD S000003242 NMA2 GO:0004515 SGD_REF:S000070049|PMID:11884393 ISS F nicotinamide/nicotinic acid mononucleotide adenylyltransferase YGR010W gene taxon:4932 20030106 SGD
+SGD S000003242 NMA2 GO:0019674 SGD_REF:S000070049|PMID:11884393 TAS P nicotinamide/nicotinic acid mononucleotide adenylyltransferase YGR010W gene taxon:4932 20020629 SGD
+SGD S000001119 NMD2 GO:0005737 SGD_REF:S000059900|PMID:11238889 TAS C YHR077C|IFS1|SUA1|UPF2 gene taxon:4932 20020528 SGD
+SGD S000001119 NMD2 GO:0005844 SGD_REF:S000046443|PMID:9268361 IDA C YHR077C|IFS1|SUA1|UPF2 gene taxon:4932 20020528 SGD
+SGD S000001119 NMD2 GO:0005515 SGD_REF:S000059900|PMID:11238889 TAS F YHR077C|IFS1|SUA1|UPF2 gene taxon:4932 20020528 SGD
+SGD S000001119 NMD2 GO:0000184 SGD_REF:S000049793|PMID:10098411 TAS P YHR077C|IFS1|SUA1|UPF2 gene taxon:4932 20020528 SGD
+SGD S000001119 NMD2 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P YHR077C|IFS1|SUA1|UPF2 gene taxon:4932 20060203 SGD
+SGD S000001119 NMD2 GO:0006402 SGD_REF:S000058753|PMID:9841679 TAS P YHR077C|IFS1|SUA1|UPF2 gene taxon:4932 20010124 SGD
+SGD S000001119 NMD2 NOT GO:0006452 SGD_REF:S000079922|PMID:15388879 IMP P YHR077C|IFS1|SUA1|UPF2 gene taxon:4932 20050301 SGD
+SGD S000001213 NMD3 GO:0005829 SGD_REF:S000054078|PMID:10022925 IDA C factor required for a late assembly step of the 60S subunit YHR170W|SRC5 gene taxon:4932 20010118 SGD
+SGD S000001213 NMD3 GO:0005842 SGD_REF:S000054078|PMID:10022925 IDA C factor required for a late assembly step of the 60S subunit YHR170W|SRC5 gene taxon:4932 20010118 SGD
+SGD S000001213 NMD3 GO:0003723 SGD_REF:S000054078|PMID:10022925 ISS F factor required for a late assembly step of the 60S subunit YHR170W|SRC5 gene taxon:4932 20010118 SGD
+SGD S000001213 NMD3 GO:0005515 SGD_REF:S000054078|PMID:10022925 ISS F factor required for a late assembly step of the 60S subunit YHR170W|SRC5 gene taxon:4932 20010118 SGD
+SGD S000001213 NMD3 GO:0000027 SGD_REF:S000054078|PMID:10022925 IMP P factor required for a late assembly step of the 60S subunit YHR170W|SRC5 gene taxon:4932 20010118 SGD
+SGD S000001213 NMD3 GO:0000055 SGD_REF:S000059624|PMID:11086007 IMP P factor required for a late assembly step of the 60S subunit YHR170W|SRC5 gene taxon:4932 20050416 SGD
+SGD S000004355 NMD4 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YLR363C gene taxon:4932 20031028 SGD
+SGD S000004355 NMD4 GO:0005554 SGD_REF:S000069584 ND F YLR363C gene taxon:4932 20021119 SGD
+SGD S000004355 NMD4 GO:0000184 SGD_REF:S000042824|PMID:7883168 IPI P YLR363C gene taxon:4932 20021119 SGD
+SGD S000003893 NMD5 GO:0005634 SGD_REF:S000047619|PMID:9852143 IDA C Upf1p interacting protein, importin beta homolog Kap119p YJR132W|KAP119 gene taxon:4932 20021007 SGD
+SGD S000003893 NMD5 GO:0005737 SGD_REF:S000047619|PMID:9852143 IDA C Upf1p interacting protein, importin beta homolog Kap119p YJR132W|KAP119 gene taxon:4932 20021007 SGD
+SGD S000003893 NMD5 GO:0008320 SGD_REF:S000058374|PMID:9755161 ISS F Upf1p interacting protein, importin beta homolog Kap119p YJR132W|KAP119 gene taxon:4932 20021007 SGD
+SGD S000003893 NMD5 GO:0008320 SGD_REF:S000058374|PMID:9755161 IMP F Upf1p interacting protein, importin beta homolog Kap119p YJR132W|KAP119 gene taxon:4932 20021007 SGD
+SGD S000003893 NMD5 GO:0006606 SGD_REF:S000058374|PMID:9755161 ISS P Upf1p interacting protein, importin beta homolog Kap119p YJR132W|KAP119 gene taxon:4932 20021007 SGD
+SGD S000003893 NMD5 GO:0006606 SGD_REF:S000058374|PMID:9755161 IMP P Upf1p interacting protein, importin beta homolog Kap119p YJR132W|KAP119 gene taxon:4932 20021007 SGD
+SGD S000007436 NME1 GO:0000172 SGD_REF:S000061290|PMID:11241345 TAS C RNase MRP subunit RRP2 gene taxon:4932 20010906 SGD
+SGD S000007436 NME1 GO:0000171 SGD_REF:S000061290|PMID:11241345 TAS F RNase MRP subunit RRP2 gene taxon:4932 20010906 SGD
+SGD S000007436 NME1 GO:0006364 SGD_REF:S000061290|PMID:11241345 TAS P RNase MRP subunit RRP2 gene taxon:4932 20010906 SGD
+SGD S000004185 NMT1 GO:0005829 SGD_REF:S000039761|PMID:1544917 IDA C N-myristoyl transferase YLR195C|CDC72 gene taxon:4932 20020528 SGD
+SGD S000004185 NMT1 GO:0004379 SGD_REF:S000049951|PMID:8955162 IMP F N-myristoyl transferase YLR195C|CDC72 gene taxon:4932 20020528 SGD
+SGD S000004185 NMT1 GO:0004379 SGD_REF:S000049951|PMID:8955162 TAS F N-myristoyl transferase YLR195C|CDC72 gene taxon:4932 20020528 SGD
+SGD S000004185 NMT1 GO:0018008 SGD_REF:S000056061|PMID:10570244 TAS P N-myristoyl transferase YLR195C|CDC72 gene taxon:4932 20020528 SGD
+SGD S000003873 NNF1 GO:0000776 SGD_REF:S000075180|PMID:14657030 IDA C YJR112W gene taxon:4932 20031230 SGD
+SGD S000003873 NNF1 GO:0000818 SGD_REF:S000075142|PMID:14633972 IDA C YJR112W gene taxon:4932 20040618 SGD
+SGD S000003873 NNF1 GO:0000922 SGD_REF:S000071701|PMID:12455957 IDA C YJR112W gene taxon:4932 20030522 SGD
+SGD S000003873 NNF1 GO:0005554 SGD_REF:S000069584 ND F YJR112W gene taxon:4932 20021104 SGD
+SGD S000003873 NNF1 GO:0007059 SGD_REF:S000071701|PMID:12455957 IDA P YJR112W gene taxon:4932 20021209 SGD
+SGD S000003321 NNF2 GO:0005624 SGD_REF:S000065940|PMID:11486042 IDA C YGR089W gene taxon:4932 20030122 SGD
+SGD S000003321 NNF2 GO:0005554 SGD_REF:S000069584 ND F YGR089W gene taxon:4932 20030122 SGD
+SGD S000003321 NNF2 GO:0007059 SGD_REF:S000074191|PMID:14566057 RCA P YGR089W gene taxon:4932 20050608 SGD
+SGD S000004275 NNT1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C Putative nicotinamide N-methyltransferase YLR285W gene taxon:4932 20031028 SGD
+SGD S000004275 NNT1 GO:0008112 SGD_REF:S000073098|PMID:12736687 ISS F Putative nicotinamide N-methyltransferase YLR285W gene taxon:4932 20030509 SGD
+SGD S000004275 NNT1 GO:0000183 SGD_REF:S000073098|PMID:12736687 IMP P Putative nicotinamide N-methyltransferase YLR285W gene taxon:4932 20030509 SGD
+SGD S000004275 NNT1 GO:0006769 SGD_REF:S000073098|PMID:12736687 ISS P Putative nicotinamide N-methyltransferase YLR285W gene taxon:4932 20030509 SGD
+SGD S000005582 NOB1 GO:0005634 SGD_REF:S000071991|PMID:12502737 IDA C Associated with the 26S proteasome YOR056C|YOR29-07 gene taxon:4932 20030331 SGD
+SGD S000005582 NOB1 GO:0030684 SGD_REF:S000071991|PMID:12502737 IDA C Associated with the 26S proteasome YOR056C|YOR29-07 gene taxon:4932 20041115 SGD
+SGD S000005582 NOB1 GO:0030684 SGD_REF:S000071991|PMID:12502737 IPI C Associated with the 26S proteasome YOR056C|YOR29-07 gene taxon:4932 20041115 SGD
+SGD S000005582 NOB1 GO:0030684 SGD_REF:S000071991|PMID:12502737 IEP C Associated with the 26S proteasome YOR056C|YOR29-07 gene taxon:4932 20041115 SGD
+SGD S000005582 NOB1 GO:0003723 SGD_REF:S000071991|PMID:12502737 IDA F Associated with the 26S proteasome YOR056C|YOR29-07 gene taxon:4932 20041115 SGD
+SGD S000005582 NOB1 GO:0003723 SGD_REF:S000071991|PMID:12502737 ISS F Associated with the 26S proteasome YOR056C|YOR29-07 gene taxon:4932 20041115 SGD
+SGD S000005582 NOB1 GO:0005515 SGD_REF:S000071991|PMID:12502737 IDA F Associated with the 26S proteasome YOR056C|YOR29-07 gene taxon:4932 20041115 SGD
+SGD S000005582 NOB1 GO:0005515 SGD_REF:S000071991|PMID:12502737 IMP F Associated with the 26S proteasome YOR056C|YOR29-07 gene taxon:4932 20041115 SGD
+SGD S000005582 NOB1 GO:0030490 SGD_REF:S000077867|PMID:12588997 IMP P Associated with the 26S proteasome YOR056C|YOR29-07 gene taxon:4932 20041115 SGD
+SGD S000005582 NOB1 GO:0030490 SGD_REF:S000077867|PMID:12588997 IEP P Associated with the 26S proteasome YOR056C|YOR29-07 gene taxon:4932 20041115 SGD
+SGD S000005582 NOB1 GO:0030490 SGD_REF:S000079921|PMID:15388878 IMP P Associated with the 26S proteasome YOR056C|YOR29-07 gene taxon:4932 20050511 SGD
+SGD S000005582 NOB1 GO:0042274 SGD_REF:S000073159|PMID:12628929 IPI P Associated with the 26S proteasome YOR056C|YOR29-07 gene taxon:4932 20050511 SGD
+SGD S000005582 NOB1 GO:0043248 SGD_REF:S000071991|PMID:12502737 IMP P Associated with the 26S proteasome YOR056C|YOR29-07 gene taxon:4932 20041115 SGD
+SGD S000005582 NOB1 GO:0043248 SGD_REF:S000071991|PMID:12502737 IPI P Associated with the 26S proteasome YOR056C|YOR29-07 gene taxon:4932 20041115 SGD
+SGD S000005732 NOC2 GO:0005634 SGD_REF:S000056415|PMID:10684247 IDA C YOR206W gene taxon:4932 20001207 SGD
+SGD S000005732 NOC2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YOR206W gene taxon:4932 20040928 SGD
+SGD S000005732 NOC2 GO:0030690 SGD_REF:S000061344|PMID:11371346 IPI C YOR206W gene taxon:4932 20041024 SGD
+SGD S000005732 NOC2 GO:0030691 SGD_REF:S000061344|PMID:11371346 IPI C YOR206W gene taxon:4932 20041024 SGD
+SGD S000005732 NOC2 GO:0005554 SGD_REF:S000069584 ND F YOR206W gene taxon:4932 20001207 SGD
+SGD S000005732 NOC2 GO:0000054 SGD_REF:S000072821|PMID:12446671 TAS P YOR206W gene taxon:4932 20030402 SGD
+SGD S000005732 NOC2 GO:0042255 SGD_REF:S000072821|PMID:12446671 TAS P YOR206W gene taxon:4932 20030402 SGD
+SGD S000003992 NOC3 GO:0005634 SGD_REF:S000070305|PMID:12110182 IDA C YLR002C gene taxon:4932 20020820 SGD
+SGD S000003992 NOC3 GO:0005730 SGD_REF:S000070305|PMID:12110182 TAS C YLR002C gene taxon:4932 20020820 SGD
+SGD S000003992 NOC3 GO:0030691 SGD_REF:S000061344|PMID:11371346 IPI C YLR002C gene taxon:4932 20041024 SGD
+SGD S000003992 NOC3 GO:0003682 SGD_REF:S000070305|PMID:12110182 IDA F YLR002C gene taxon:4932 20021104 SGD
+SGD S000003992 NOC3 GO:0005515 SGD_REF:S000070305|PMID:12110182 IDA F YLR002C gene taxon:4932 20021104 SGD
+SGD S000003992 NOC3 GO:0006270 SGD_REF:S000070305|PMID:12110182 IDA P YLR002C gene taxon:4932 20020820 SGD
+SGD S000003992 NOC3 GO:0006364 SGD_REF:S000070305|PMID:12110182 IDA P YLR002C gene taxon:4932 20020820 SGD
+SGD S000006348 NOC4 GO:0005634 SGD_REF:S000056415|PMID:10684247 IDA C U3 snoRNP protein YPR144C|UTP19 gene taxon:4932 20001207 SGD
+SGD S000006348 NOC4 GO:0005730 SGD_REF:S000072821|PMID:12446671 IDA C U3 snoRNP protein YPR144C|UTP19 gene taxon:4932 20060315 SGD
+SGD S000006348 NOC4 GO:0005730 SGD_REF:S000079989|PMID:15590835 IDA C U3 snoRNP protein YPR144C|UTP19 gene taxon:4932 20060315 SGD
+SGD S000006348 NOC4 GO:0005732 SGD_REF:S000079989|PMID:15590835 IPI SGD:S000003762 C U3 snoRNP protein YPR144C|UTP19 gene taxon:4932 20050124 SGD
+SGD S000006348 NOC4 GO:0030692 SGD_REF:S000072821|PMID:12446671 IPI SGD:S000002307 C U3 snoRNP protein YPR144C|UTP19 gene taxon:4932 20060315 SGD
+SGD S000006348 NOC4 GO:0005554 SGD_REF:S000069584 ND F U3 snoRNP protein YPR144C|UTP19 gene taxon:4932 20060315 SGD
+SGD S000006348 NOC4 GO:0006365 SGD_REF:S000072821|PMID:12446671 IMP P U3 snoRNP protein YPR144C|UTP19 gene taxon:4932 20060315 SGD
+SGD S000006348 NOC4 GO:0006365 SGD_REF:S000079989|PMID:15590835 IMP P U3 snoRNP protein YPR144C|UTP19 gene taxon:4932 20060315 SGD
+SGD S000006348 NOC4 GO:0006365 SGD_REF:S000079989|PMID:15590835 IPI SGD:S000003762|SGD:S000007294|SGD:S000007441 P U3 snoRNP protein YPR144C|UTP19 gene taxon:4932 20060315 SGD
+SGD S000006348 NOC4 GO:0042274 SGD_REF:S000072821|PMID:12446671 IMP P U3 snoRNP protein YPR144C|UTP19 gene taxon:4932 20060315 SGD
+SGD S000006014 NOG1 GO:0005730 SGD_REF:S000059087|PMID:11112701 IDA C homologs identified in human and Trypanosoma brucei, nucleolar G-protein (putative) YPL093W gene taxon:4932 20010125 SGD
+SGD S000006014 NOG1 GO:0005525 SGD_REF:S000059087|PMID:11112701 ISS F homologs identified in human and Trypanosoma brucei, nucleolar G-protein (putative) YPL093W gene taxon:4932 20051213 SGD
+SGD S000006014 NOG1 GO:0000054 SGD_REF:S000073608|PMID:12773575 IMP P homologs identified in human and Trypanosoma brucei, nucleolar G-protein (putative) YPL093W gene taxon:4932 20030706 SGD
+SGD S000006014 NOG1 GO:0000054 SGD_REF:S000073608|PMID:12773575 IPI P homologs identified in human and Trypanosoma brucei, nucleolar G-protein (putative) YPL093W gene taxon:4932 20030706 SGD
+SGD S000005336 NOG2 GO:0005634 SGD_REF:S000056415|PMID:10684247 IDA C part of a pre-60S complex YNR053C gene taxon:4932 20001207 SGD
+SGD S000005336 NOG2 GO:0005654 SGD_REF:S000070114|PMID:11707418 IDA C part of a pre-60S complex YNR053C gene taxon:4932 20030514 SGD
+SGD S000005336 NOG2 GO:0005730 SGD_REF:S000070114|PMID:11707418 IDA C part of a pre-60S complex YNR053C gene taxon:4932 20030514 SGD
+SGD S000005336 NOG2 GO:0003924 SGD_REF:S000071522|PMID:12362983 TAS F part of a pre-60S complex YNR053C gene taxon:4932 20021114 SGD
+SGD S000005336 NOG2 GO:0000055 SGD_REF:S000070114|PMID:11707418 IMP P part of a pre-60S complex YNR053C gene taxon:4932 20030822 SGD
+SGD S000005336 NOG2 GO:0000055 SGD_REF:S000070114|PMID:11707418 IPI P part of a pre-60S complex YNR053C gene taxon:4932 20030822 SGD
+SGD S000005336 NOG2 GO:0042255 SGD_REF:S000076076|PMID:15116429 TAS P part of a pre-60S complex YNR053C gene taxon:4932 20040618 SGD
+SGD S000002172 NOP1 GO:0005730 SGD_REF:S000069775|PMID:11932453 IDA C U3 snoRNP protein, similar to mammalian fibrillarin YDL014W|LOT3 gene taxon:4932 20020828 SGD
+SGD S000002172 NOP1 GO:0005732 SGD_REF:S000070145|PMID:12068309 IPI C U3 snoRNP protein, similar to mammalian fibrillarin YDL014W|LOT3 gene taxon:4932 20030224 SGD
+SGD S000002172 NOP1 GO:0030532 SGD_REF:S000058443|PMID:10690410 TAS C U3 snoRNP protein, similar to mammalian fibrillarin YDL014W|LOT3 gene taxon:4932 20020219 SGD
+SGD S000002172 NOP1 GO:0008168 SGD_REF:S000071539|PMID:12215523 IPI F U3 snoRNP protein, similar to mammalian fibrillarin YDL014W|LOT3 gene taxon:4932 20030224 SGD
+SGD S000002172 NOP1 GO:0008168 SGD_REF:S000071539|PMID:12215523 ISS F U3 snoRNP protein, similar to mammalian fibrillarin YDL014W|LOT3 gene taxon:4932 20030224 SGD
+SGD S000002172 NOP1 GO:0008168 SGD_REF:S000071539|PMID:12215523 IMP F U3 snoRNP protein, similar to mammalian fibrillarin YDL014W|LOT3 gene taxon:4932 20030224 SGD
+SGD S000002172 NOP1 GO:0000027 SGD_REF:S000058443|PMID:10690410 TAS P U3 snoRNP protein, similar to mammalian fibrillarin YDL014W|LOT3 gene taxon:4932 20010118 SGD
+SGD S000002172 NOP1 GO:0000154 SGD_REF:S000058443|PMID:10690410 TAS P U3 snoRNP protein, similar to mammalian fibrillarin YDL014W|LOT3 gene taxon:4932 20010118 SGD
+SGD S000002172 NOP1 GO:0001510 SGD_REF:S000071539|PMID:12215523 IMP P U3 snoRNP protein, similar to mammalian fibrillarin YDL014W|LOT3 gene taxon:4932 20030224 SGD
+SGD S000002172 NOP1 GO:0001510 SGD_REF:S000071539|PMID:12215523 ISS P U3 snoRNP protein, similar to mammalian fibrillarin YDL014W|LOT3 gene taxon:4932 20030224 SGD
+SGD S000002172 NOP1 GO:0001510 SGD_REF:S000071539|PMID:12215523 IPI P U3 snoRNP protein, similar to mammalian fibrillarin YDL014W|LOT3 gene taxon:4932 20030224 SGD
+SGD S000002172 NOP1 GO:0006365 SGD_REF:S000058443|PMID:10690410 TAS P U3 snoRNP protein, similar to mammalian fibrillarin YDL014W|LOT3 gene taxon:4932 20010118 SGD
+SGD S000002172 NOP1 GO:0030490 SGD_REF:S000070145|PMID:12068309 IPI P U3 snoRNP protein, similar to mammalian fibrillarin YDL014W|LOT3 gene taxon:4932 20020905 SGD
+SGD S000007455 NOP10 GO:0005732 SGD_REF:S000048199|PMID:9843512 IPI C H/ACA-box snoRNPs component YHR072W-A gene taxon:4932 20050218 SGD
+SGD S000007455 NOP10 GO:0003723 SGD_REF:S000048199|PMID:9843512 IDA F H/ACA-box snoRNPs component YHR072W-A gene taxon:4932 20021114 SGD
+SGD S000007455 NOP10 GO:0000154 SGD_REF:S000058443|PMID:10690410 TAS P H/ACA-box snoRNPs component YHR072W-A gene taxon:4932 20010118 SGD
+SGD S000007455 NOP10 GO:0006365 SGD_REF:S000058443|PMID:10690410 TAS P H/ACA-box snoRNPs component YHR072W-A gene taxon:4932 20010118 SGD
+SGD S000007455 NOP10 GO:0031118 SGD_REF:S000048199|PMID:9843512 IMP P H/ACA-box snoRNPs component YHR072W-A gene taxon:4932 20050416 SGD
+SGD S000005401 NOP12 GO:0005730 SGD_REF:S000060934|PMID:11452019 IDA C YOL041C gene taxon:4932 20020926 SGD
+SGD S000005401 NOP12 GO:0003723 SGD_REF:S000060934|PMID:11452019 ISS F YOL041C gene taxon:4932 20020926 SGD
+SGD S000005401 NOP12 GO:0016072 SGD_REF:S000060934|PMID:11452019 IMP P YOL041C gene taxon:4932 20020926 SGD
+SGD S000005119 NOP13 GO:0005654 SGD_REF:S000060934|PMID:11452019 IDA C YNL175C gene taxon:4932 20020926 SGD
+SGD S000005119 NOP13 GO:0005730 SGD_REF:S000060934|PMID:11452019 IDA C YNL175C gene taxon:4932 20020926 SGD
+SGD S000005119 NOP13 GO:0003723 SGD_REF:S000060934|PMID:11452019 ISS F YNL175C gene taxon:4932 20020926 SGD
+SGD S000005119 NOP13 GO:0000004 SGD_REF:S000069584 ND P YNL175C gene taxon:4932 20020926 SGD
+SGD S000002307 NOP14 GO:0005730 SGD_REF:S000056415|PMID:10684247 IDA C U3 snoRNP protein YDL148C|UTP2 gene taxon:4932 20001207 SGD
+SGD S000002307 NOP14 GO:0005732 SGD_REF:S000070145|PMID:12068309 IPI C U3 snoRNP protein YDL148C|UTP2 gene taxon:4932 20030224 SGD
+SGD S000002307 NOP14 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C U3 snoRNP protein YDL148C|UTP2 gene taxon:4932 20040928 SGD
+SGD S000002307 NOP14 GO:0030692 SGD_REF:S000072821|PMID:12446671 IPI SGD:S000006348 C U3 snoRNP protein YDL148C|UTP2 gene taxon:4932 20060315 SGD
+SGD S000002307 NOP14 GO:0030515 SGD_REF:S000070145|PMID:12068309 IPI F U3 snoRNP protein YDL148C|UTP2 gene taxon:4932 20030224 SGD
+SGD S000002307 NOP14 GO:0006365 SGD_REF:S000066272|PMID:11694595 IMP P U3 snoRNP protein YDL148C|UTP2 gene taxon:4932 20060315 SGD
+SGD S000002307 NOP14 GO:0030490 SGD_REF:S000070145|PMID:12068309 IMP P U3 snoRNP protein YDL148C|UTP2 gene taxon:4932 20020906 SGD
+SGD S000002307 NOP14 GO:0030490 SGD_REF:S000070145|PMID:12068309 IPI P U3 snoRNP protein YDL148C|UTP2 gene taxon:4932 20020906 SGD
+SGD S000002307 NOP14 GO:0042274 SGD_REF:S000066272|PMID:11694595 IMP P U3 snoRNP protein YDL148C|UTP2 gene taxon:4932 20060315 SGD
+SGD S000005054 NOP15 GO:0005634 SGD_REF:S000059544|PMID:10953080 IDA C ribosome biogenesis YNL110C gene taxon:4932 20010626 SGD
+SGD S000005054 NOP15 GO:0005730 SGD_REF:S000066002|PMID:11583614 IDA C ribosome biogenesis YNL110C gene taxon:4932 20020927 SGD
+SGD S000005054 NOP15 GO:0005554 SGD_REF:S000069584 ND F ribosome biogenesis YNL110C gene taxon:4932 20010626 SGD
+SGD S000005054 NOP15 GO:0000915 SGD_REF:S000075486|PMID:14657029 IMP P ribosome biogenesis YNL110C gene taxon:4932 20040521 SGD
+SGD S000005054 NOP15 GO:0042255 SGD_REF:S000076076|PMID:15116429 TAS P ribosome biogenesis YNL110C gene taxon:4932 20040618 SGD
+SGD S000005054 NOP15 GO:0042273 SGD_REF:S000066002|PMID:11583614 IMP P ribosome biogenesis YNL110C gene taxon:4932 20020927 SGD
+SGD S000005054 NOP15 GO:0042273 SGD_REF:S000066002|PMID:11583614 IPI P ribosome biogenesis YNL110C gene taxon:4932 20020927 SGD
+SGD S000000804 NOP16 GO:0005634 SGD_REF:S000056415|PMID:10684247 IDA C ribosome biogenesis YER002W gene taxon:4932 20001207 SGD
+SGD S000000804 NOP16 GO:0005634 SGD_REF:S000069459|PMID:11914276 IDA C ribosome biogenesis YER002W gene taxon:4932 20020507 SGD
+SGD S000000804 NOP16 GO:0005730 SGD_REF:S000056415|PMID:10684247 IDA C ribosome biogenesis YER002W gene taxon:4932 20001207 SGD
+SGD S000000804 NOP16 GO:0005554 SGD_REF:S000069584 ND F ribosome biogenesis YER002W gene taxon:4932 20001207 SGD
+SGD S000000804 NOP16 GO:0042273 SGD_REF:S000066002|PMID:11583614 IMP P ribosome biogenesis YER002W gene taxon:4932 20020927 SGD
+SGD S000000804 NOP16 GO:0042273 SGD_REF:S000066002|PMID:11583614 IPI P ribosome biogenesis YER002W gene taxon:4932 20020927 SGD
+SGD S000005005 NOP2 GO:0005730 SGD_REF:S000058443|PMID:10690410 TAS C 90 kDa protein homologous to a human proliferation-associated nucleolar protein, p120 YNL061W|YNA1 gene taxon:4932 20010118 SGD
+SGD S000005005 NOP2 GO:0008173 SGD_REF:S000058443|PMID:10690410 TAS F 90 kDa protein homologous to a human proliferation-associated nucleolar protein, p120 YNL061W|YNA1 gene taxon:4932 20010118 SGD
+SGD S000005005 NOP2 GO:0008757 SGD_REF:S000074033|PMID:12872006 ISS F 90 kDa protein homologous to a human proliferation-associated nucleolar protein, p120 YNL061W|YNA1 gene taxon:4932 20031001 SGD
+SGD S000005005 NOP2 GO:0006364 SGD_REF:S000058443|PMID:10690410 TAS P 90 kDa protein homologous to a human proliferation-associated nucleolar protein, p120 YNL061W|YNA1 gene taxon:4932 20010118 SGD
+SGD S000005964 NOP4 GO:0005730 SGD_REF:S000058443|PMID:10690410 TAS C RNA binding protein (putative) YPL043W|NOP77 gene taxon:4932 20010118 SGD
+SGD S000005964 NOP4 GO:0003723 SGD_REF:S000041483|PMID:9312154 ISS F RNA binding protein (putative) YPL043W|NOP77 gene taxon:4932 20010118 SGD
+SGD S000005964 NOP4 GO:0006364 SGD_REF:S000058443|PMID:10690410 TAS P RNA binding protein (putative) YPL043W|NOP77 gene taxon:4932 20010118 SGD
+SGD S000006067 NOP53 GO:0005634 SGD_REF:S000056415|PMID:10684247 IDA C YPL146C|RRP16 gene taxon:4932 20010301 SGD
+SGD S000006067 NOP53 GO:0005634 SGD_REF:S000086196|PMID:16043506 IDA C YPL146C|RRP16 gene taxon:4932 20060313 SGD
+SGD S000006067 NOP53 GO:0005634 SGD_REF:S000069459|PMID:11914276 IDA C YPL146C|RRP16 gene taxon:4932 20020507 SGD
+SGD S000006067 NOP53 GO:0005730 SGD_REF:S000056415|PMID:10684247 IDA C YPL146C|RRP16 gene taxon:4932 20010301 SGD
+SGD S000006067 NOP53 GO:0005730 SGD_REF:S000086196|PMID:16043506 IDA C YPL146C|RRP16 gene taxon:4932 20060313 SGD
+SGD S000006067 NOP53 GO:0019843 SGD_REF:S000086545|PMID:16128814 IDA F YPL146C|RRP16 gene taxon:4932 20060313 SGD
+SGD S000006067 NOP53 GO:0000055 SGD_REF:S000086196|PMID:16043506 IMP P YPL146C|RRP16 gene taxon:4932 20060313 SGD
+SGD S000006067 NOP53 GO:0030489 SGD_REF:S000080643|PMID:15686447 IMP P YPL146C|RRP16 gene taxon:4932 20050208 SGD
+SGD S000005837 NOP58 GO:0005732 SGD_REF:S000070145|PMID:12068309 IPI C U3 snoRNP protein YOR310C|NOP5 gene taxon:4932 20030224 SGD
+SGD S000005837 NOP58 GO:0030532 SGD_REF:S000058443|PMID:10690410 TAS C U3 snoRNP protein YOR310C|NOP5 gene taxon:4932 20020219 SGD
+SGD S000005837 NOP58 GO:0005554 SGD_REF:S000069584 ND F U3 snoRNP protein YOR310C|NOP5 gene taxon:4932 20030224 SGD
+SGD S000005837 NOP58 GO:0000154 SGD_REF:S000058443|PMID:10690410 TAS P U3 snoRNP protein YOR310C|NOP5 gene taxon:4932 20010118 SGD
+SGD S000005837 NOP58 GO:0006365 SGD_REF:S000058443|PMID:10690410 TAS P U3 snoRNP protein YOR310C|NOP5 gene taxon:4932 20010118 SGD
+SGD S000005837 NOP58 GO:0030490 SGD_REF:S000070145|PMID:12068309 IPI P U3 snoRNP protein YOR310C|NOP5 gene taxon:4932 20020905 SGD
+SGD S000002372 NOP6 GO:0005730 SGD_REF:S000074185|PMID:14562095 IDA C YDL213C gene taxon:4932 20031028 SGD
+SGD S000002372 NOP6 GO:0005554 SGD_REF:S000069584 ND F YDL213C gene taxon:4932 20030114 SGD
+SGD S000002372 NOP6 GO:0006364 SGD_REF:S000074191|PMID:14566057 RCA P YDL213C gene taxon:4932 20050608 SGD
+SGD S000003335 NOP7 GO:0005634 SGD_REF:S000056415|PMID:10684247 IDA C YGR103W|YPH1 gene taxon:4932 20001207 SGD
+SGD S000003335 NOP7 GO:0005730 SGD_REF:S000056415|PMID:10684247 IDA C YGR103W|YPH1 gene taxon:4932 20001207 SGD
+SGD S000003335 NOP7 GO:0005554 SGD_REF:S000069584 ND F YGR103W|YPH1 gene taxon:4932 20001207 SGD
+SGD S000003335 NOP7 GO:0030490 SGD_REF:S000073750|PMID:12837249 IMP P YGR103W|YPH1 gene taxon:4932 20030805 SGD
+SGD S000003335 NOP7 GO:0042273 SGD_REF:S000069466|PMID:11911362 IDA P YGR103W|YPH1 gene taxon:4932 20020927 SGD
+SGD S000005504 NOP8 GO:0005730 SGD_REF:S000058443|PMID:10690410 TAS C YOL144W gene taxon:4932 20010118 SGD
+SGD S000005504 NOP8 GO:0005554 SGD_REF:S000069584 ND F YOL144W gene taxon:4932 20021205 SGD
+SGD S000005504 NOP8 GO:0000027 SGD_REF:S000058443|PMID:10690410 TAS P YOL144W gene taxon:4932 20010118 SGD
+SGD S000005504 NOP8 GO:0006364 SGD_REF:S000058443|PMID:10690410 TAS P YOL144W gene taxon:4932 20010118 SGD
+SGD S000003547 NOP9 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YJL010C gene taxon:4932 20031028 SGD
+SGD S000003547 NOP9 GO:0005634 SGD_REF:S000075214|PMID:14690591 IDA C YJL010C gene taxon:4932 20031231 SGD
+SGD S000003547 NOP9 GO:0005730 SGD_REF:S000074185|PMID:14562095 IDA C YJL010C gene taxon:4932 20031028 SGD
+SGD S000003547 NOP9 GO:0005730 SGD_REF:S000075214|PMID:14690591 IDA C YJL010C gene taxon:4932 20031231 SGD
+SGD S000003547 NOP9 GO:0003723 SGD_REF:S000075214|PMID:14690591 ISS F YJL010C gene taxon:4932 20031231 SGD
+SGD S000003547 NOP9 GO:0006364 SGD_REF:S000075214|PMID:14690591 IPI P YJL010C gene taxon:4932 20031231 SGD
+SGD S000001300 NOT3 GO:0005737 SGD_REF:S000069437|PMID:11889048 IDA C CCR4 transcriptional complex component YIL038C gene taxon:4932 20020802 SGD
+SGD S000001300 NOT3 GO:0030015 SGD_REF:S000042122|PMID:10490603 IPI C CCR4 transcriptional complex component YIL038C gene taxon:4932 20020802 SGD
+SGD S000001300 NOT3 GO:0000175 SGD_REF:S000069437|PMID:11889048 IDA F CCR4 transcriptional complex component YIL038C gene taxon:4932 20020802 SGD
+SGD S000001300 NOT3 GO:0000289 SGD_REF:S000069437|PMID:11889048 IDA P CCR4 transcriptional complex component YIL038C gene taxon:4932 20020802 SGD
+SGD S000001300 NOT3 GO:0006357 SGD_REF:S000042122|PMID:10490603 IPI P CCR4 transcriptional complex component YIL038C gene taxon:4932 20020802 SGD
+SGD S000006276 NOT5 GO:0005737 SGD_REF:S000069437|PMID:11889048 IDA C NOT complex member, a global negative regulator of transcription YPR072W gene taxon:4932 20020802 SGD
+SGD S000006276 NOT5 GO:0030015 SGD_REF:S000042122|PMID:10490603 IPI C NOT complex member, a global negative regulator of transcription YPR072W gene taxon:4932 20020802 SGD
+SGD S000006276 NOT5 GO:0000175 SGD_REF:S000069437|PMID:11889048 IDA F NOT complex member, a global negative regulator of transcription YPR072W gene taxon:4932 20020802 SGD
+SGD S000006276 NOT5 GO:0000289 SGD_REF:S000069437|PMID:11889048 IDA P NOT complex member, a global negative regulator of transcription YPR072W gene taxon:4932 20020802 SGD
+SGD S000006276 NOT5 GO:0006357 SGD_REF:S000042122|PMID:10490603 IPI P NOT complex member, a global negative regulator of transcription YPR072W gene taxon:4932 20020802 SGD
+SGD S000003833 NPA3 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YJR072C|EPA1 gene taxon:4932 20031028 SGD
+SGD S000003833 NPA3 GO:0016887 SGD_REF:S000081511|PMID:15082539 IDA F YJR072C|EPA1 gene taxon:4932 20060510 SGD
+SGD S000003833 NPA3 GO:0000004 SGD_REF:S000069584 ND P YJR072C|EPA1 gene taxon:4932 20060510 SGD
+SGD S000002204 NPC2 GO:0000324 SGD_REF:S000074185|PMID:14562095 IDA C Functional homologue of human NPC2/He1 YDL046W gene taxon:4932 20031028 SGD
+SGD S000002204 NPC2 GO:0000328 SGD_REF:S000087177|PMID:16278452 IDA C Functional homologue of human NPC2/He1 YDL046W gene taxon:4932 20051118 SGD
+SGD S000002204 NPC2 GO:0005554 SGD_REF:S000069584 ND F Functional homologue of human NPC2/He1 YDL046W gene taxon:4932 20030122 SGD
+SGD S000002204 NPC2 GO:0015918 SGD_REF:S000087177|PMID:16278452 IGI protein_id:P61916 P Functional homologue of human NPC2/He1 YDL046W gene taxon:4932 20051118 SGD
+SGD S000002204 NPC2 GO:0015918 SGD_REF:S000087177|PMID:16278452 ISS protein_id:P61916|protein_id:P79345 P Functional homologue of human NPC2/He1 YDL046W gene taxon:4932 20051118 SGD
+SGD S000002840 NPL3 GO:0005634 SGD_REF:S000039584|PMID:8675010 IMP C contains RNA recognition motif, nuclear shuttling protein YDR432W|MTR13|MTS1|NAB1|NOP3 gene taxon:4932 20020304 SGD
+SGD S000002840 NPL3 GO:0005634 SGD_REF:S000069459|PMID:11914276 IDA C contains RNA recognition motif, nuclear shuttling protein YDR432W|MTR13|MTS1|NAB1|NOP3 gene taxon:4932 20020507 SGD
+SGD S000002840 NPL3 GO:0005634 SGD_REF:S000080288|PMID:15572678 IDA C contains RNA recognition motif, nuclear shuttling protein YDR432W|MTR13|MTS1|NAB1|NOP3 gene taxon:4932 20050222 SGD
+SGD S000002840 NPL3 GO:0005634 SGD_REF:S000039514|PMID:7962083 IDA C contains RNA recognition motif, nuclear shuttling protein YDR432W|MTR13|MTS1|NAB1|NOP3 gene taxon:4932 20040430 SGD
+SGD S000002840 NPL3 GO:0005737 SGD_REF:S000039584|PMID:8675010 IMP C contains RNA recognition motif, nuclear shuttling protein YDR432W|MTR13|MTS1|NAB1|NOP3 gene taxon:4932 20020304 SGD
+SGD S000002840 NPL3 GO:0003729 SGD_REF:S000055760|PMID:7774613 IDA F contains RNA recognition motif, nuclear shuttling protein YDR432W|MTR13|MTS1|NAB1|NOP3 gene taxon:4932 20020304 SGD
+SGD S000002840 NPL3 GO:0008143 SGD_REF:S000039514|PMID:7962083 IDA F contains RNA recognition motif, nuclear shuttling protein YDR432W|MTR13|MTS1|NAB1|NOP3 gene taxon:4932 20040430 SGD
+SGD S000002840 NPL3 GO:0006406 SGD_REF:S000060975|PMID:11459827 TAS P contains RNA recognition motif, nuclear shuttling protein YDR432W|MTR13|MTS1|NAB1|NOP3 gene taxon:4932 20020304 SGD
+SGD S000002840 NPL3 GO:0006406 SGD_REF:S000060975|PMID:11459827 IGI P contains RNA recognition motif, nuclear shuttling protein YDR432W|MTR13|MTS1|NAB1|NOP3 gene taxon:4932 20020304 SGD
+SGD S000000374 NPL4 GO:0005783 SGD_REF:S000069082|PMID:11740563 IDA C YBR170C|HRD4 gene taxon:4932 20020906 SGD
+SGD S000000374 NPL4 GO:0042175 SGD_REF:S000066133|PMID:11598205 IDA C YBR170C|HRD4 gene taxon:4932 20031010 SGD
+SGD S000000374 NPL4 GO:0005554 SGD_REF:S000069584 ND F YBR170C|HRD4 gene taxon:4932 20031010 SGD
+SGD S000000374 NPL4 GO:0030433 SGD_REF:S000069870|PMID:11739805 IMP P YBR170C|HRD4 gene taxon:4932 20031010 SGD
+SGD S000004697 NPL6 GO:0005634 SGD_REF:S000069459|PMID:11914276 IDA C YMR091C|RSC7 gene taxon:4932 20031010 SGD
+SGD S000004697 NPL6 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YMR091C|RSC7 gene taxon:4932 20031028 SGD
+SGD S000004697 NPL6 GO:0016586 SGD_REF:S000075541|PMID:14729968 IPI C YMR091C|RSC7 gene taxon:4932 20040714 SGD
+SGD S000004697 NPL6 GO:0005554 SGD_REF:S000069584 ND F YMR091C|RSC7 gene taxon:4932 20021001 SGD
+SGD S000004697 NPL6 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P YMR091C|RSC7 gene taxon:4932 20060202 SGD
+SGD S000004697 NPL6 GO:0006606 SGD_REF:S000051237|PMID:2556404 IMP P YMR091C|RSC7 gene taxon:4932 20031010 SGD
+SGD S000004697 NPL6 GO:0006974 SGD_REF:S000076175|PMID:12482937 IMP P YMR091C|RSC7 gene taxon:4932 20060406 SGD
+SGD S000000621 NPP1 GO:0008372 SGD_REF:S000069584 ND C nucleotide phosphatase YCR026C gene taxon:4932 20030203 SGD
+SGD S000000621 NPP1 GO:0004528 SGD_REF:S000087166|PMID:16278456 ISS protein_id:AAF36094|protein_id:BAA08260|protein_id:AAF44374|protein_id:BAA06333|protein_id:AF320054|protein_id:CAB56566|protein_id:BAA74902|protein_id:AAC51813 F nucleotide phosphatase YCR026C gene taxon:4932 20051111 SGD
+SGD S000000621 NPP1 GO:0004551 SGD_REF:S000087166|PMID:16278456 ISS protein_id:AAF36094|protein_id:BAA08260|protein_id:AAC51813|protein_id:BAA74902|protein_id:CAB56566|protein_id:AF320054|protein_id:AAF44374|protein_id:BAA06333 F nucleotide phosphatase YCR026C gene taxon:4932 20051111 SGD
+SGD S000000621 NPP1 GO:0017111 SGD_REF:S000087166|PMID:16278456 IMP F nucleotide phosphatase YCR026C gene taxon:4932 20051111 SGD
+SGD S000000621 NPP1 GO:0017111 SGD_REF:S000087166|PMID:16278456 IGI SGD:S000000297|SGD:S000000742 F nucleotide phosphatase YCR026C gene taxon:4932 20051111 SGD
+SGD S000000621 NPP1 GO:0047429 SGD_REF:S000087166|PMID:16278456 IDA F nucleotide phosphatase YCR026C gene taxon:4932 20051111 SGD
+SGD S000000621 NPP1 GO:0047429 SGD_REF:S000087166|PMID:16278456 IMP F nucleotide phosphatase YCR026C gene taxon:4932 20051111 SGD
+SGD S000000621 NPP1 GO:0047429 SGD_REF:S000087166|PMID:16278456 IGI SGD:S000000297|SGD:S000000742 F nucleotide phosphatase YCR026C gene taxon:4932 20051111 SGD
+SGD S000000621 NPP1 GO:0006796 SGD_REF:S000087166|PMID:16278456 IMP P nucleotide phosphatase YCR026C gene taxon:4932 20051111 SGD
+SGD S000000621 NPP1 GO:0006796 SGD_REF:S000087166|PMID:16278456 ISS protein_id:AAF36094|protein_id:BAA08260|protein_id:AAF44374|protein_id:BAA06333|protein_id:AF320054|protein_id:CAB56566|protein_id:BAA74902|protein_id:AAC51813 P nucleotide phosphatase YCR026C gene taxon:4932 20051111 SGD
+SGD S000000621 NPP1 GO:0016036 SGD_REF:S000087166|PMID:16278456 IMP P nucleotide phosphatase YCR026C gene taxon:4932 20051111 SGD
+SGD S000000621 NPP1 GO:0016036 SGD_REF:S000087166|PMID:16278456 IEP P nucleotide phosphatase YCR026C gene taxon:4932 20051111 SGD
+SGD S000000742 NPP2 GO:0008372 SGD_REF:S000069584 ND C nucleotide phosphatase YEL016C gene taxon:4932 20021126 SGD
+SGD S000000742 NPP2 GO:0004528 SGD_REF:S000087166|PMID:16278456 ISS protein_id:AAF36094|protein_id:BAA08260|protein_id:AAF44374|protein_id:BAA06333|protein_id:AF320054|protein_id:CAB56566|protein_id:BAA74902|protein_id:AAC51813 F nucleotide phosphatase YEL016C gene taxon:4932 20051111 SGD
+SGD S000000742 NPP2 GO:0004551 SGD_REF:S000087166|PMID:16278456 ISS protein_id:AAF36094|protein_id:BAA08260|protein_id:AAC51813|protein_id:CAB56566|protein_id:AAF44374|protein_id:BAA06333|protein_id:AF320054|protein_id:BAA74902 F nucleotide phosphatase YEL016C gene taxon:4932 20051111 SGD
+SGD S000000742 NPP2 GO:0017111 SGD_REF:S000087166|PMID:16278456 IMP F nucleotide phosphatase YEL016C gene taxon:4932 20051111 SGD
+SGD S000000742 NPP2 GO:0017111 SGD_REF:S000087166|PMID:16278456 IGI SGD:S000000297|SGD:S000000621 F nucleotide phosphatase YEL016C gene taxon:4932 20051111 SGD
+SGD S000000742 NPP2 GO:0047429 SGD_REF:S000087166|PMID:16278456 IDA F nucleotide phosphatase YEL016C gene taxon:4932 20051111 SGD
+SGD S000000742 NPP2 GO:0047429 SGD_REF:S000087166|PMID:16278456 IMP F nucleotide phosphatase YEL016C gene taxon:4932 20051111 SGD
+SGD S000000742 NPP2 GO:0047429 SGD_REF:S000087166|PMID:16278456 IGI SGD:S000000297|SGD:S000000621 F nucleotide phosphatase YEL016C gene taxon:4932 20051111 SGD
+SGD S000000742 NPP2 GO:0006796 SGD_REF:S000087166|PMID:16278456 IMP P nucleotide phosphatase YEL016C gene taxon:4932 20051111 SGD
+SGD S000000742 NPP2 GO:0006796 SGD_REF:S000087166|PMID:16278456 ISS protein_id:AAF36094|protein_id:BAA08260|protein_id:AAF44374|protein_id:BAA06333|protein_id:AF320054|protein_id:CAB56566|protein_id:BAA74902|protein_id:AAC51813 P nucleotide phosphatase YEL016C gene taxon:4932 20051111 SGD
+SGD S000005127 NPR1 GO:0005737 SGD_REF:S000059919|PMID:11238915 TAS C protein kinase homolog YNL183C gene taxon:4932 20021021 SGD
+SGD S000005127 NPR1 GO:0016301 SGD_REF:S000059919|PMID:11238915 TAS F protein kinase homolog YNL183C gene taxon:4932 20021021 SGD
+SGD S000005127 NPR1 GO:0016301 SGD_REF:S000053618|PMID:2125693 ISS F protein kinase homolog YNL183C gene taxon:4932 20050921 SGD
+SGD S000005127 NPR1 GO:0006808 SGD_REF:S000066226|PMID:11500493 IMP P protein kinase homolog YNL183C gene taxon:4932 20020304 SGD
+SGD S000000788 NPR2 GO:0008372 SGD_REF:S000069584 ND C YEL062W gene taxon:4932 20021001 SGD
+SGD S000000788 NPR2 GO:0016247 SGD_REF:S000046769|PMID:7867803 IMP F YEL062W gene taxon:4932 20040409 SGD
+SGD S000000788 NPR2 GO:0016247 SGD_REF:S000046769|PMID:7867803 ISS F YEL062W gene taxon:4932 20040409 SGD
+SGD S000000788 NPR2 GO:0015824 SGD_REF:S000046769|PMID:7867803 IMP P YEL062W gene taxon:4932 20021001 SGD
+SGD S000000788 NPR2 GO:0015840 SGD_REF:S000046769|PMID:7867803 IMP P YEL062W gene taxon:4932 20021001 SGD
+SGD S000005735 NPT1 GO:0005634 SGD_REF:S000070049|PMID:11884393 IDA C nicotinate phosphoribosyltransferase YOR209C gene taxon:4932 20020629 SGD
+SGD S000005735 NPT1 GO:0004516 SGD_REF:S000064246|PMID:9521740 IDA F nicotinate phosphoribosyltransferase YOR209C gene taxon:4932 20020708 SGD
+SGD S000005735 NPT1 GO:0000183 SGD_REF:S000069524|PMID:11901108 IMP P nicotinate phosphoribosyltransferase YOR209C gene taxon:4932 20020708 SGD
+SGD S000005735 NPT1 GO:0001302 SGD_REF:S000047674|PMID:11000115 IMP P nicotinate phosphoribosyltransferase YOR209C gene taxon:4932 20050323 SGD
+SGD S000005735 NPT1 GO:0006348 SGD_REF:S000069524|PMID:11901108 IMP P nicotinate phosphoribosyltransferase YOR209C gene taxon:4932 20020708 SGD
+SGD S000005735 NPT1 GO:0019358 SGD_REF:S000070049|PMID:11884393 IDA P nicotinate phosphoribosyltransferase YOR209C gene taxon:4932 20020708 SGD
+SGD S000003035 NPY1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C NADH pyrophosphatase 1 YGL067W gene taxon:4932 20020507 SGD
+SGD S000003035 NPY1 GO:0005777 SGD_REF:S000060303|PMID:11361135 IDA C NADH pyrophosphatase 1 YGL067W gene taxon:4932 20020801 SGD
+SGD S000003035 NPY1 GO:0000210 SGD_REF:S000060303|PMID:11361135 IDA F NADH pyrophosphatase 1 YGL067W gene taxon:4932 20020801 SGD
+SGD S000003035 NPY1 GO:0006734 SGD_REF:S000060303|PMID:11361135 IDA P NADH pyrophosphatase 1 YGL067W gene taxon:4932 20020801 SGD
+SGD S000005195 NRD1 GO:0005634 SGD_REF:S000045868|PMID:10655211 IPI C YNL251C gene taxon:4932 20021113 SGD
+SGD S000005195 NRD1 GO:0003723 SGD_REF:S000052606|PMID:9618475 IDA F YNL251C gene taxon:4932 20020304 SGD
+SGD S000005195 NRD1 GO:0030847 SGD_REF:S000045868|PMID:10655211 IGI P YNL251C gene taxon:4932 20031010 SGD
+SGD S000005195 NRD1 GO:0030847 SGD_REF:S000045868|PMID:10655211 IMP P YNL251C gene taxon:4932 20031010 SGD
+SGD S000005195 NRD1 GO:0030847 SGD_REF:S000045868|PMID:10655211 IPI P YNL251C gene taxon:4932 20031010 SGD
+SGD S000002450 NRG1 GO:0005634 SGD_REF:S000060795|PMID:11404322 IDA C binds to UAS-1 in the STA1 promoter and can interact with Ssn6p, transcriptional repressor YDR043C gene taxon:4932 20020305 SGD
+SGD S000002450 NRG1 GO:0003677 SGD_REF:S000053650|PMID:10022891 IDA F binds to UAS-1 in the STA1 promoter and can interact with Ssn6p, transcriptional repressor YDR043C gene taxon:4932 20020305 SGD
+SGD S000002450 NRG1 GO:0016564 SGD_REF:S000053650|PMID:10022891 IDA F binds to UAS-1 in the STA1 promoter and can interact with Ssn6p, transcriptional repressor YDR043C gene taxon:4932 20020305 SGD
+SGD S000002450 NRG1 GO:0001403 SGD_REF:S000070028|PMID:12024013 IDA P binds to UAS-1 in the STA1 promoter and can interact with Ssn6p, transcriptional repressor YDR043C gene taxon:4932 20020815 SGD
+SGD S000002450 NRG1 GO:0006006 SGD_REF:S000053650|PMID:10022891 IMP P binds to UAS-1 in the STA1 promoter and can interact with Ssn6p, transcriptional repressor YDR043C gene taxon:4932 20020305 SGD
+SGD S000002450 NRG1 GO:0006357 SGD_REF:S000053650|PMID:10022891 IMP P binds to UAS-1 in the STA1 promoter and can interact with Ssn6p, transcriptional repressor YDR043C gene taxon:4932 20020305 SGD
+SGD S000002450 NRG1 GO:0009268 SGD_REF:S000072488|PMID:12509465 IDA P binds to UAS-1 in the STA1 promoter and can interact with Ssn6p, transcriptional repressor YDR043C gene taxon:4932 20030218 SGD
+SGD S000000270 NRG2 GO:0005634 SGD_REF:S000060795|PMID:11404322 IC GO:0016564 C NRG1 homolog YBR066C gene taxon:4932 20021104 SGD
+SGD S000000270 NRG2 GO:0016564 SGD_REF:S000060795|PMID:11404322 IDA F NRG1 homolog YBR066C gene taxon:4932 20020305 SGD
+SGD S000000270 NRG2 GO:0001403 SGD_REF:S000070028|PMID:12024013 IDA P NRG1 homolog YBR066C gene taxon:4932 20020815 SGD
+SGD S000005073 NRK1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C nicotinamide riboside kinase YNL129W gene taxon:4932 20031028 SGD
+SGD S000005073 NRK1 GO:0000816 SGD_REF:S000076181|PMID:15137942 IDA F nicotinamide riboside kinase YNL129W gene taxon:4932 20040624 SGD
+SGD S000005073 NRK1 GO:0046495 SGD_REF:S000076181|PMID:15137942 IGI SGD:S000001116 P nicotinamide riboside kinase YNL129W gene taxon:4932 20040518 SGD
+SGD S000005073 NRK1 GO:0046495 SGD_REF:S000076181|PMID:15137942 IDA P nicotinamide riboside kinase YNL129W gene taxon:4932 20040518 SGD
+SGD S000005292 NRM1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YNR009W gene taxon:4932 20031028 SGD
+SGD S000005292 NRM1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YNR009W gene taxon:4932 20031028 SGD
+SGD S000005292 NRM1 GO:0005554 SGD_REF:S000069584 ND F YNR009W gene taxon:4932 20030203 SGD
+SGD S000005292 NRM1 GO:0000004 SGD_REF:S000069584 ND P YNR009W gene taxon:4932 20030203 SGD
+SGD S000002326 NRP1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDL167C gene taxon:4932 20031028 SGD
+SGD S000002326 NRP1 GO:0005554 SGD_REF:S000069584 ND F YDL167C gene taxon:4932 20010703 SGD
+SGD S000002326 NRP1 GO:0000004 SGD_REF:S000069584 ND P YDL167C gene taxon:4932 20010703 SGD
+SGD S000003079 NSA1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C ribosome biogenesis YGL111W gene taxon:4932 20031028 SGD
+SGD S000003079 NSA1 GO:0005730 SGD_REF:S000074185|PMID:14562095 IDA C ribosome biogenesis YGL111W gene taxon:4932 20031028 SGD
+SGD S000003079 NSA1 GO:0005554 SGD_REF:S000069584 ND F ribosome biogenesis YGL111W gene taxon:4932 20020927 SGD
+SGD S000003079 NSA1 GO:0042273 SGD_REF:S000066002|PMID:11583614 IMP P ribosome biogenesis YGL111W gene taxon:4932 20020927 SGD
+SGD S000003079 NSA1 GO:0042273 SGD_REF:S000066002|PMID:11583614 IPI P ribosome biogenesis YGL111W gene taxon:4932 20020927 SGD
+SGD S000000928 NSA2 GO:0005634 SGD_REF:S000056415|PMID:10684247 IDA C ribosome biogenesis YER126C gene taxon:4932 20001207 SGD
+SGD S000000928 NSA2 GO:0005554 SGD_REF:S000069584 ND F ribosome biogenesis YER126C gene taxon:4932 20001207 SGD
+SGD S000000928 NSA2 GO:0042273 SGD_REF:S000066002|PMID:11583614 IMP P ribosome biogenesis YER126C gene taxon:4932 20020927 SGD
+SGD S000000928 NSA2 GO:0042273 SGD_REF:S000066002|PMID:11583614 IPI P ribosome biogenesis YER126C gene taxon:4932 20020927 SGD
+SGD S000003997 NSE1 GO:0005634 SGD_REF:S000069988|PMID:11927594 IDA C YLR007W gene taxon:4932 20020622 SGD
+SGD S000003997 NSE1 GO:0030915 SGD_REF:S000069988|PMID:11927594 IPI C YLR007W gene taxon:4932 20041025 SGD
+SGD S000003997 NSE1 GO:0030915 SGD_REF:S000080949|PMID:15738391 IPI SGD:S000000745|SGD:S000005394|SGD:S000004375 C YLR007W gene taxon:4932 20060309 SGD
+SGD S000003997 NSE1 GO:0005554 SGD_REF:S000069584 ND F YLR007W gene taxon:4932 20021216 SGD
+SGD S000003997 NSE1 GO:0006281 SGD_REF:S000069988|PMID:11927594 IDA P YLR007W gene taxon:4932 20020622 SGD
+SGD S000003997 NSE1 GO:0006281 SGD_REF:S000080949|PMID:15738391 IMP P YLR007W gene taxon:4932 20060309 SGD
+SGD S000003997 NSE1 GO:0008283 SGD_REF:S000069988|PMID:11927594 IDA P YLR007W gene taxon:4932 20020622 SGD
+SGD S000002696 NSE3 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YDR288W gene taxon:4932 20031028 SGD
+SGD S000002696 NSE3 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDR288W gene taxon:4932 20031028 SGD
+SGD S000002696 NSE3 GO:0030915 SGD_REF:S000080949|PMID:15738391 IPI SGD:S000000745|SGD:S000005394|SGD:S000004375 C YDR288W gene taxon:4932 20060309 SGD
+SGD S000002696 NSE3 GO:0003677 SGD_REF:S000075214|PMID:14690591 ISS F YDR288W gene taxon:4932 20031230 SGD
+SGD S000002696 NSE3 GO:0006281 SGD_REF:S000075214|PMID:14690591 IPI P YDR288W gene taxon:4932 20031230 SGD
+SGD S000002696 NSE3 GO:0006281 SGD_REF:S000080949|PMID:15738391 IMP P YDR288W gene taxon:4932 20060309 SGD
+SGD S000002263 NSE4 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YDL105W|QRI2 gene taxon:4932 20031028 SGD
+SGD S000002263 NSE4 GO:0030915 SGD_REF:S000081063|PMID:15752197 IPI C YDL105W|QRI2 gene taxon:4932 20050328 SGD
+SGD S000002263 NSE4 GO:0030915 SGD_REF:S000080949|PMID:15738391 IPI SGD:S000000745|SGD:S000005394|SGD:S000004375 C YDL105W|QRI2 gene taxon:4932 20060309 SGD
+SGD S000002263 NSE4 GO:0005554 SGD_REF:S000069584 ND F YDL105W|QRI2 gene taxon:4932 20021001 SGD
+SGD S000002263 NSE4 GO:0006281 SGD_REF:S000081063|PMID:15752197 IMP P YDL105W|QRI2 gene taxon:4932 20050328 SGD
+SGD S000002263 NSE4 GO:0006281 SGD_REF:S000081063|PMID:15752197 IPI P YDL105W|QRI2 gene taxon:4932 20050328 SGD
+SGD S000002263 NSE4 GO:0006281 SGD_REF:S000080949|PMID:15738391 IMP P YDL105W|QRI2 gene taxon:4932 20060309 SGD
+SGD S000004485 NSE5 GO:0005634 SGD_REF:S000075214|PMID:14690591 IDA C non-SMC element of the Smc5-Smc6 complex YML023C gene taxon:4932 20031230 SGD
+SGD S000004485 NSE5 GO:0030915 SGD_REF:S000080949|PMID:15738391 IPI SGD:S000000745|SGD:S000005394|SGD:S000004375 C non-SMC element of the Smc5-Smc6 complex YML023C gene taxon:4932 20060309 SGD
+SGD S000004485 NSE5 GO:0005554 SGD_REF:S000069584 ND F non-SMC element of the Smc5-Smc6 complex YML023C gene taxon:4932 20021126 SGD
+SGD S000004485 NSE5 GO:0006281 SGD_REF:S000075214|PMID:14690591 IPI SGD:S000004375|SGD:S000005394 P non-SMC element of the Smc5-Smc6 complex YML023C gene taxon:4932 20031230 SGD
+SGD S000004485 NSE5 GO:0006281 SGD_REF:S000080949|PMID:15738391 IMP P non-SMC element of the Smc5-Smc6 complex YML023C gene taxon:4932 20060309 SGD
+SGD S000001175 NSG1 GO:0008372 SGD_REF:S000069584 ND C YHR133C gene taxon:4932 20060221 SGD
+SGD S000001175 NSG1 GO:0005515 SGD_REF:S000113649|PMID:16270032 IPI SGD:S000004540 F YHR133C gene taxon:4932 20060221 SGD
+SGD S000001175 NSG1 GO:0016126 SGD_REF:S000113649|PMID:16270032 IMP P YHR133C gene taxon:4932 20060221 SGD
+SGD S000001175 NSG1 GO:0016126 SGD_REF:S000113649|PMID:16270032 IPI SGD:S000004540 P YHR133C gene taxon:4932 20060221 SGD
+SGD S000005100 NSG2 GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YNL156C gene taxon:4932 20031028 SGD
+SGD S000005100 NSG2 GO:0005554 SGD_REF:S000069584 ND F YNL156C gene taxon:4932 20030203 SGD
+SGD S000005100 NSG2 GO:0016126 SGD_REF:S000113649|PMID:16270032 IMP P YNL156C gene taxon:4932 20060221 SGD
+SGD S000006154 NSL1 GO:0000776 SGD_REF:S000075180|PMID:14657030 IDA C Protein required for cell viability YPL233W gene taxon:4932 20031230 SGD
+SGD S000006154 NSL1 GO:0000818 SGD_REF:S000075142|PMID:14633972 IDA C Protein required for cell viability YPL233W gene taxon:4932 20040618 SGD
+SGD S000006154 NSL1 GO:0000922 SGD_REF:S000071701|PMID:12455957 IDA C Protein required for cell viability YPL233W gene taxon:4932 20030522 SGD
+SGD S000006154 NSL1 GO:0005554 SGD_REF:S000069584 ND F Protein required for cell viability YPL233W gene taxon:4932 20021209 SGD
+SGD S000006154 NSL1 GO:0007059 SGD_REF:S000071701|PMID:12455957 IDA P Protein required for cell viability YPL233W gene taxon:4932 20021209 SGD
+SGD S000003577 NSP1 GO:0005643 SGD_REF:S000058277|PMID:9442897 IDA C nuclear pore complex subunit YJL041W gene taxon:4932 20010118 SGD
+SGD S000003577 NSP1 GO:0005198 SGD_REF:S000058277|PMID:9442897 TAS F nuclear pore complex subunit YJL041W gene taxon:4932 20010118 SGD
+SGD S000003577 NSP1 GO:0000055 SGD_REF:S000044179|PMID:9971735 IMP P nuclear pore complex subunit YJL041W gene taxon:4932 20010118 SGD
+SGD S000003577 NSP1 GO:0006405 SGD_REF:S000058277|PMID:9442897 IGI P nuclear pore complex subunit YJL041W gene taxon:4932 20010118 SGD
+SGD S000003577 NSP1 GO:0006405 SGD_REF:S000058277|PMID:9442897 IPI P nuclear pore complex subunit YJL041W gene taxon:4932 20010118 SGD
+SGD S000003577 NSP1 GO:0006406 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YJL041W gene taxon:4932 20010118 SGD
+SGD S000003577 NSP1 GO:0006407 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YJL041W gene taxon:4932 20010118 SGD
+SGD S000003577 NSP1 GO:0006408 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YJL041W gene taxon:4932 20010118 SGD
+SGD S000003577 NSP1 GO:0006409 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YJL041W gene taxon:4932 20010118 SGD
+SGD S000003577 NSP1 GO:0006606 SGD_REF:S000058277|PMID:9442897 IMP P nuclear pore complex subunit YJL041W gene taxon:4932 20010118 SGD
+SGD S000003577 NSP1 GO:0006607 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YJL041W gene taxon:4932 20010118 SGD
+SGD S000003577 NSP1 GO:0006608 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YJL041W gene taxon:4932 20010118 SGD
+SGD S000003577 NSP1 GO:0006609 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YJL041W gene taxon:4932 20010118 SGD
+SGD S000003577 NSP1 GO:0006610 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YJL041W gene taxon:4932 20010118 SGD
+SGD S000003577 NSP1 GO:0006611 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YJL041W gene taxon:4932 20010118 SGD
+SGD S000003577 NSP1 GO:0006999 SGD_REF:S000058277|PMID:9442897 IMP P nuclear pore complex subunit YJL041W gene taxon:4932 20010118 SGD
+SGD S000003577 NSP1 GO:0006999 SGD_REF:S000058277|PMID:9442897 IGI P nuclear pore complex subunit YJL041W gene taxon:4932 20010118 SGD
+SGD S000003577 NSP1 GO:0006999 SGD_REF:S000058277|PMID:9442897 IPI P nuclear pore complex subunit YJL041W gene taxon:4932 20010118 SGD
+SGD S000003391 NSR1 GO:0005634 SGD_REF:S000069459|PMID:11914276 IDA C nuclear localization sequence binding protein YGR159C|SHE5 gene taxon:4932 20020507 SGD
+SGD S000003391 NSR1 GO:0005730 SGD_REF:S000058443|PMID:10690410 TAS C nuclear localization sequence binding protein YGR159C|SHE5 gene taxon:4932 20010118 SGD
+SGD S000003391 NSR1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C nuclear localization sequence binding protein YGR159C|SHE5 gene taxon:4932 20040928 SGD
+SGD S000003391 NSR1 GO:0003697 SGD_REF:S000047678|PMID:7800479 IDA F nuclear localization sequence binding protein YGR159C|SHE5 gene taxon:4932 20021205 SGD
+SGD S000003391 NSR1 GO:0003723 SGD_REF:S000039838|PMID:1706724 ISS F nuclear localization sequence binding protein YGR159C|SHE5 gene taxon:4932 20021205 SGD
+SGD S000003391 NSR1 GO:0000028 SGD_REF:S000058443|PMID:10690410 TAS P nuclear localization sequence binding protein YGR159C|SHE5 gene taxon:4932 20010118 SGD
+SGD S000003391 NSR1 GO:0006364 SGD_REF:S000058443|PMID:10690410 TAS P nuclear localization sequence binding protein YGR159C|SHE5 gene taxon:4932 20010118 SGD
+SGD S000005035 NST1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YNL091W gene taxon:4932 20031028 SGD
+SGD S000005035 NST1 GO:0005554 SGD_REF:S000069584 ND F YNL091W gene taxon:4932 20021010 SGD
+SGD S000005035 NST1 GO:0009651 SGD_REF:S000069195|PMID:11816027 IMP P YNL091W gene taxon:4932 20021010 SGD
+SGD S000003823 NTA1 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C 52 kDa amidase specific for N-terminal asparagine and glutamine YJR062C|DEA1 gene taxon:4932 20031028 SGD
+SGD S000003823 NTA1 GO:0008418 SGD_REF:S000047045|PMID:7744855 IDA F 52 kDa amidase specific for N-terminal asparagine and glutamine YJR062C|DEA1 gene taxon:4932 20020605 SGD
+SGD S000003823 NTA1 GO:0008418 SGD_REF:S000047045|PMID:7744855 ISS F 52 kDa amidase specific for N-terminal asparagine and glutamine YJR062C|DEA1 gene taxon:4932 20020605 SGD
+SGD S000003823 NTA1 GO:0008418 SGD_REF:S000047045|PMID:7744855 IMP F 52 kDa amidase specific for N-terminal asparagine and glutamine YJR062C|DEA1 gene taxon:4932 20020605 SGD
+SGD S000003823 NTA1 GO:0006464 SGD_REF:S000047045|PMID:7744855 IMP P 52 kDa amidase specific for N-terminal asparagine and glutamine YJR062C|DEA1 gene taxon:4932 20020605 SGD
+SGD S000003823 NTA1 GO:0030163 SGD_REF:S000047045|PMID:7744855 IMP P 52 kDa amidase specific for N-terminal asparagine and glutamine YJR062C|DEA1 gene taxon:4932 20020605 SGD
+SGD S000000392 NTC20 GO:0005681 SGD_REF:S000046470|PMID:11018040 IDA C splicing factor YBR188C gene taxon:4932 20010118 SGD
+SGD S000000392 NTC20 GO:0005681 SGD_REF:S000046470|PMID:11018040 IGI C splicing factor YBR188C gene taxon:4932 20010118 SGD
+SGD S000000392 NTC20 GO:0031202 SGD_REF:S000071476|PMID:12384582 IMP F splicing factor YBR188C gene taxon:4932 20030128 SGD
+SGD S000000392 NTC20 GO:0000398 SGD_REF:S000046470|PMID:11018040 IGI P splicing factor YBR188C gene taxon:4932 20010118 SGD
+SGD S000000392 NTC20 GO:0000398 SGD_REF:S000046470|PMID:11018040 IDA P splicing factor YBR188C gene taxon:4932 20010118 SGD
+SGD S000004524 NTE1 GO:0005783 SGD_REF:S000076411|PMID:15044461 IDA C phosphatidylcholine and lysophosphatidylcholine phospholipase YML059C gene taxon:4932 20040722 SGD
+SGD S000004524 NTE1 GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C phosphatidylcholine and lysophosphatidylcholine phospholipase YML059C gene taxon:4932 20031028 SGD
+SGD S000004524 NTE1 GO:0004622 SGD_REF:S000076411|PMID:15044461 IDA F phosphatidylcholine and lysophosphatidylcholine phospholipase YML059C gene taxon:4932 20040722 SGD
+SGD S000004524 NTE1 GO:0004759 SGD_REF:S000076411|PMID:15044461 IDA F phosphatidylcholine and lysophosphatidylcholine phospholipase YML059C gene taxon:4932 20040722 SGD
+SGD S000004524 NTE1 GO:0016787 SGD_REF:S000065765|PMID:10816586 ISS F phosphatidylcholine and lysophosphatidylcholine phospholipase YML059C gene taxon:4932 20030204 SGD
+SGD S000004524 NTE1 GO:0046470 SGD_REF:S000076411|PMID:15044461 IMP P phosphatidylcholine and lysophosphatidylcholine phospholipase YML059C gene taxon:4932 20040722 SGD
+SGD S000000811 NTF2 GO:0005635 SGD_REF:S000053836|PMID:8702493 IDA C nuclear transport factor, similar to mammalian cytosolic nuclear import factor NTF2 YER009W gene taxon:4932 20020307 SGD
+SGD S000000811 NTF2 GO:0008536 SGD_REF:S000056252|PMID:10889207 IPI F nuclear transport factor, similar to mammalian cytosolic nuclear import factor NTF2 YER009W gene taxon:4932 20020307 SGD
+SGD S000000811 NTF2 GO:0006606 SGD_REF:S000053836|PMID:8702493 IMP P nuclear transport factor, similar to mammalian cytosolic nuclear import factor NTF2 YER009W gene taxon:4932 20020307 SGD
+SGD S000000811 NTF2 GO:0006913 SGD_REF:S000053836|PMID:8702493 IMP P nuclear transport factor, similar to mammalian cytosolic nuclear import factor NTF2 YER009W gene taxon:4932 20020307 SGD
+SGD S000000013 NTG1 GO:0005634 SGD_REF:S000044732|PMID:10207101 IDA C DNA glycosylase YAL015C|FUN33|SCR1 gene taxon:4932 20010118 SGD
+SGD S000000013 NTG1 GO:0005739 SGD_REF:S000044732|PMID:10207101 IDA C DNA glycosylase YAL015C|FUN33|SCR1 gene taxon:4932 20010118 SGD
+SGD S000000013 NTG1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C DNA glycosylase YAL015C|FUN33|SCR1 gene taxon:4932 20040924 SGD
+SGD S000000013 NTG1 GO:0000703 SGD_REF:S000045646|PMID:9020769 IDA F DNA glycosylase YAL015C|FUN33|SCR1 gene taxon:4932 20020517 SGD
+SGD S000000013 NTG1 GO:0000703 SGD_REF:S000045646|PMID:9020769 ISS F DNA glycosylase YAL015C|FUN33|SCR1 gene taxon:4932 20020517 SGD
+SGD S000000013 NTG1 GO:0003906 SGD_REF:S000074087|PMID:14500818 IDA F DNA glycosylase YAL015C|FUN33|SCR1 gene taxon:4932 20031017 SGD
+SGD S000000013 NTG1 GO:0008534 SGD_REF:S000044880|PMID:8855249 IDA F DNA glycosylase YAL015C|FUN33|SCR1 gene taxon:4932 20020517 SGD
+SGD S000000013 NTG1 GO:0006281 SGD_REF:S000044880|PMID:8855249 IDA P DNA glycosylase YAL015C|FUN33|SCR1 gene taxon:4932 20010118 SGD
+SGD S000000013 NTG1 GO:0006284 SGD_REF:S000074087|PMID:14500818 IDA P DNA glycosylase YAL015C|FUN33|SCR1 gene taxon:4932 20031017 SGD
+SGD S000000013 NTG1 GO:0006285 SGD_REF:S000047847|PMID:9826748 IDA P DNA glycosylase YAL015C|FUN33|SCR1 gene taxon:4932 20020307 SGD
+SGD S000005403 NTG2 GO:0005634 SGD_REF:S000052463|PMID:10471279 IDA C endonuclease III DNA base excision repair N-glycosylase YOL043C|SCR2 gene taxon:4932 20020308 SGD
+SGD S000005403 NTG2 GO:0000703 SGD_REF:S000045646|PMID:9020769 IDA F endonuclease III DNA base excision repair N-glycosylase YOL043C|SCR2 gene taxon:4932 20020517 SGD
+SGD S000005403 NTG2 GO:0000703 SGD_REF:S000045646|PMID:9020769 ISS F endonuclease III DNA base excision repair N-glycosylase YOL043C|SCR2 gene taxon:4932 20020517 SGD
+SGD S000005403 NTG2 GO:0003906 SGD_REF:S000074087|PMID:14500818 IDA F endonuclease III DNA base excision repair N-glycosylase YOL043C|SCR2 gene taxon:4932 20031017 SGD
+SGD S000005403 NTG2 GO:0006284 SGD_REF:S000074087|PMID:14500818 IDA P endonuclease III DNA base excision repair N-glycosylase YOL043C|SCR2 gene taxon:4932 20031017 SGD
+SGD S000005403 NTG2 GO:0006285 SGD_REF:S000047847|PMID:9826748 IDA P endonuclease III DNA base excision repair N-glycosylase YOL043C|SCR2 gene taxon:4932 20020307 SGD
+SGD S000002408 NTH1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C neutral trehalase YDR001C gene taxon:4932 20031028 SGD
+SGD S000002408 NTH1 GO:0005829 SGD_REF:S000049422|PMID:9308367 TAS C neutral trehalase YDR001C gene taxon:4932 20031017 SGD
+SGD S000002408 NTH1 GO:0004555 SGD_REF:S000049422|PMID:9308367 TAS F neutral trehalase YDR001C gene taxon:4932 20010306 SGD
+SGD S000002408 NTH1 GO:0005993 SGD_REF:S000049422|PMID:9308367 TAS P neutral trehalase YDR001C gene taxon:4932 20010306 SGD
+SGD S000002408 NTH1 GO:0006950 SGD_REF:S000049422|PMID:9308367 TAS P neutral trehalase YDR001C gene taxon:4932 20010306 SGD
+SGD S000000205 NTH2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C neutral trehalase YBR001C gene taxon:4932 20031028 SGD
+SGD S000000205 NTH2 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C neutral trehalase YBR001C gene taxon:4932 20031028 SGD
+SGD S000000205 NTH2 GO:0004555 SGD_REF:S000049422|PMID:9308367 TAS F neutral trehalase YBR001C gene taxon:4932 20010306 SGD
+SGD S000000205 NTH2 GO:0005993 SGD_REF:S000049422|PMID:9308367 TAS P neutral trehalase YBR001C gene taxon:4932 20010306 SGD
+SGD S000000205 NTH2 GO:0006950 SGD_REF:S000049422|PMID:9308367 TAS P neutral trehalase YBR001C gene taxon:4932 20010306 SGD
+SGD S000006235 NTO1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C HAT complex component YPR031W gene taxon:4932 20031028 SGD
+SGD S000006235 NTO1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C HAT complex component YPR031W gene taxon:4932 20031028 SGD
+SGD S000006235 NTO1 GO:0005554 SGD_REF:S000069584 ND F HAT complex component YPR031W gene taxon:4932 20021125 SGD
+SGD S000006235 NTO1 GO:0000004 SGD_REF:S000069584 ND P HAT complex component YPR031W gene taxon:4932 20021125 SGD
+SGD S000001730 NTR2 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YKR022C gene taxon:4932 20031028 SGD
+SGD S000001730 NTR2 GO:0005634 SGD_REF:S000075214|PMID:14690591 IDA C YKR022C gene taxon:4932 20031230 SGD
+SGD S000001730 NTR2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YKR022C gene taxon:4932 20031028 SGD
+SGD S000001730 NTR2 GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YKR022C gene taxon:4932 20031028 SGD
+SGD S000001730 NTR2 GO:0005554 SGD_REF:S000069584 ND F YKR022C gene taxon:4932 20030421 SGD
+SGD S000001730 NTR2 GO:0000391 SGD_REF:S000113869|PMID:16357217 IDA P YKR022C gene taxon:4932 20051222 SGD
+SGD S000001730 NTR2 GO:0000398 SGD_REF:S000075214|PMID:14690591 IPI SGD:S000002368|SGD:S000001208 P YKR022C gene taxon:4932 20031230 SGD
+SGD S000003744 NUC1 GO:0005743 SGD_REF:S000057053|PMID:3286639 IDA C nuclease YJL208C gene taxon:4932 20010118 SGD
+SGD S000003744 NUC1 GO:0004520 SGD_REF:S000057053|PMID:3286639 IDA F nuclease YJL208C gene taxon:4932 20010118 SGD
+SGD S000003744 NUC1 GO:0004529 SGD_REF:S000057053|PMID:3286639 IDA F nuclease YJL208C gene taxon:4932 20010118 SGD
+SGD S000003744 NUC1 GO:0004540 SGD_REF:S000057053|PMID:3286639 IDA F nuclease YJL208C gene taxon:4932 20010118 SGD
+SGD S000003744 NUC1 GO:0006308 SGD_REF:S000057053|PMID:3286639 IDA P nuclease YJL208C gene taxon:4932 20030721 SGD
+SGD S000003744 NUC1 GO:0006310 SGD_REF:S000052577|PMID:8087883 IMP P nuclease YJL208C gene taxon:4932 20010118 SGD
+SGD S000003744 NUC1 GO:0006401 SGD_REF:S000057053|PMID:3286639 IDA P nuclease YJL208C gene taxon:4932 20030721 SGD
+SGD S000005900 NUD1 GO:0005816 SGD_REF:S000047788|PMID:9585415 IDA C YOR373W gene taxon:4932 20010118 SGD
+SGD S000005900 NUD1 GO:0005200 SGD_REF:S000047788|PMID:9585415 IPI F YOR373W gene taxon:4932 20010118 SGD
+SGD S000005900 NUD1 GO:0007020 SGD_REF:S000058447|PMID:9153752 IPI P YOR373W gene taxon:4932 20010118 SGD
+SGD S000005430 NUF2 GO:0000778 SGD_REF:S000062011|PMID:11179222 IPI C YOL069W gene taxon:4932 20030404 SGD
+SGD S000005430 NUF2 GO:0000778 SGD_REF:S000062011|PMID:11179222 IDA C YOL069W gene taxon:4932 20030404 SGD
+SGD S000005430 NUF2 GO:0000778 SGD_REF:S000080960|PMID:11511347 IDA C YOL069W gene taxon:4932 20050307 SGD
+SGD S000005430 NUF2 GO:0000778 SGD_REF:S000062011|PMID:11179222 IMP C YOL069W gene taxon:4932 20030404 SGD
+SGD S000005430 NUF2 GO:0000780 SGD_REF:S000059963|PMID:11266451 IDA C YOL069W gene taxon:4932 20030404 SGD
+SGD S000005430 NUF2 GO:0000780 SGD_REF:S000059963|PMID:11266451 IPI C YOL069W gene taxon:4932 20030404 SGD
+SGD S000005430 NUF2 GO:0000780 SGD_REF:S000059963|PMID:11266451 IGI C YOL069W gene taxon:4932 20030404 SGD
+SGD S000005430 NUF2 colocalizes_with GO:0005816 SGD_REF:S000041647|PMID:8188751 IDA C YOL069W gene taxon:4932 20050303 SGD
+SGD S000005430 NUF2 GO:0005876 SGD_REF:S000059963|PMID:11266451 IDA C YOL069W gene taxon:4932 20050303 SGD
+SGD S000005430 NUF2 GO:0031262 SGD_REF:S000059963|PMID:11266451 IDA C YOL069W gene taxon:4932 20050303 SGD
+SGD S000005430 NUF2 GO:0031262 SGD_REF:S000062011|PMID:11179222 IPI SGD:S000004723 C YOL069W gene taxon:4932 20050303 SGD
+SGD S000005430 NUF2 GO:0005200 SGD_REF:S000047788|PMID:9585415 IPI F YOL069W gene taxon:4932 20010118 SGD
+SGD S000005430 NUF2 GO:0007020 SGD_REF:S000058447|PMID:9153752 IPI P YOL069W gene taxon:4932 20010118 SGD
+SGD S000005430 NUF2 GO:0007059 SGD_REF:S000059963|PMID:11266451 IGI P YOL069W gene taxon:4932 20020214 SGD
+SGD S000000808 NUG1 GO:0005634 SGD_REF:S000056415|PMID:10684247 IDA C Nuclear GTPase involved in Ribosome biogenesis YER006W gene taxon:4932 20001207 SGD
+SGD S000000808 NUG1 GO:0005730 SGD_REF:S000056415|PMID:10684247 IDA C Nuclear GTPase involved in Ribosome biogenesis YER006W gene taxon:4932 20001207 SGD
+SGD S000000808 NUG1 GO:0003924 SGD_REF:S000066162|PMID:11583615 TAS F Nuclear GTPase involved in Ribosome biogenesis YER006W gene taxon:4932 20031125 SGD
+SGD S000000808 NUG1 GO:0006364 SGD_REF:S000073209|PMID:12089522 IMP P Nuclear GTPase involved in Ribosome biogenesis YER006W gene taxon:4932 20030530 SGD
+SGD S000002557 NUM1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YDR150W|PAC12 gene taxon:4932 20041203 SGD
+SGD S000002557 NUM1 GO:0005934 SGD_REF:S000061741|PMID:11121446 IDA C YDR150W|PAC12 gene taxon:4932 20020312 SGD
+SGD S000002557 NUM1 GO:0005938 SGD_REF:S000061741|PMID:11121446 IDA C YDR150W|PAC12 gene taxon:4932 20020312 SGD
+SGD S000002557 NUM1 GO:0015631 SGD_REF:S000060284|PMID:11266443 IPI F YDR150W|PAC12 gene taxon:4932 20020312 SGD
+SGD S000002557 NUM1 GO:0000226 SGD_REF:S000061741|PMID:11121446 IMP P YDR150W|PAC12 gene taxon:4932 20020312 SGD
+SGD S000002557 NUM1 GO:0030473 SGD_REF:S000061741|PMID:11121446 IMP P YDR150W|PAC12 gene taxon:4932 20020312 SGD
+SGD S000005624 NUP1 GO:0005643 SGD_REF:S000051060|PMID:2190694 IDA C nuclear pore complex subunit YOR098C gene taxon:4932 20030929 SGD
+SGD S000005624 NUP1 GO:0005198 SGD_REF:S000058277|PMID:9442897 TAS F nuclear pore complex subunit YOR098C gene taxon:4932 20010118 SGD
+SGD S000005624 NUP1 GO:0005515 SGD_REF:S000071844|PMID:12411502 IPI SGD:S000002566 F nuclear pore complex subunit YOR098C gene taxon:4932 20030605 SGD
+SGD S000005624 NUP1 GO:0006405 SGD_REF:S000058277|PMID:9442897 IMP P nuclear pore complex subunit YOR098C gene taxon:4932 20010118 SGD
+SGD S000005624 NUP1 GO:0006406 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YOR098C gene taxon:4932 20010118 SGD
+SGD S000005624 NUP1 GO:0006407 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YOR098C gene taxon:4932 20010118 SGD
+SGD S000005624 NUP1 GO:0006408 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YOR098C gene taxon:4932 20010118 SGD
+SGD S000005624 NUP1 GO:0006409 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YOR098C gene taxon:4932 20010118 SGD
+SGD S000005624 NUP1 GO:0006606 SGD_REF:S000058277|PMID:9442897 IMP P nuclear pore complex subunit YOR098C gene taxon:4932 20010118 SGD
+SGD S000005624 NUP1 GO:0006607 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YOR098C gene taxon:4932 20010118 SGD
+SGD S000005624 NUP1 GO:0006608 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YOR098C gene taxon:4932 20010118 SGD
+SGD S000005624 NUP1 GO:0006609 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YOR098C gene taxon:4932 20010118 SGD
+SGD S000005624 NUP1 GO:0006610 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YOR098C gene taxon:4932 20010118 SGD
+SGD S000005624 NUP1 GO:0006611 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YOR098C gene taxon:4932 20010118 SGD
+SGD S000005624 NUP1 GO:0006998 SGD_REF:S000058277|PMID:9442897 IMP P nuclear pore complex subunit YOR098C gene taxon:4932 20010118 SGD
+SGD S000005624 NUP1 GO:0006999 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YOR098C gene taxon:4932 20010118 SGD
+SGD S000001551 NUP100 GO:0005643 SGD_REF:S000058277|PMID:9442897 IDA C nuclear pore complex subunit YKL068W|NSP100 gene taxon:4932 20010118 SGD
+SGD S000001551 NUP100 GO:0005198 SGD_REF:S000058277|PMID:9442897 TAS F nuclear pore complex subunit YKL068W|NSP100 gene taxon:4932 20010118 SGD
+SGD S000001551 NUP100 GO:0006406 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YKL068W|NSP100 gene taxon:4932 20010118 SGD
+SGD S000001551 NUP100 GO:0006407 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YKL068W|NSP100 gene taxon:4932 20010118 SGD
+SGD S000001551 NUP100 GO:0006408 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YKL068W|NSP100 gene taxon:4932 20010118 SGD
+SGD S000001551 NUP100 GO:0006409 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YKL068W|NSP100 gene taxon:4932 20010118 SGD
+SGD S000001551 NUP100 GO:0006607 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YKL068W|NSP100 gene taxon:4932 20010118 SGD
+SGD S000001551 NUP100 GO:0006608 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YKL068W|NSP100 gene taxon:4932 20010118 SGD
+SGD S000001551 NUP100 GO:0006609 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YKL068W|NSP100 gene taxon:4932 20010118 SGD
+SGD S000001551 NUP100 GO:0006610 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YKL068W|NSP100 gene taxon:4932 20010118 SGD
+SGD S000001551 NUP100 GO:0006611 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YKL068W|NSP100 gene taxon:4932 20010118 SGD
+SGD S000001551 NUP100 GO:0006999 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YKL068W|NSP100 gene taxon:4932 20010118 SGD
+SGD S000004650 NUP116 GO:0005643 SGD_REF:S000058277|PMID:9442897 IDA C nuclear pore complex subunit YMR047C|NSP116 gene taxon:4932 20010118 SGD
+SGD S000004650 NUP116 GO:0005198 SGD_REF:S000058277|PMID:9442897 TAS F nuclear pore complex subunit YMR047C|NSP116 gene taxon:4932 20010118 SGD
+SGD S000004650 NUP116 GO:0006388 SGD_REF:S000052060|PMID:8524308 IMP P nuclear pore complex subunit YMR047C|NSP116 gene taxon:4932 20010118 SGD
+SGD S000004650 NUP116 GO:0006406 SGD_REF:S000058277|PMID:9442897 IMP P nuclear pore complex subunit YMR047C|NSP116 gene taxon:4932 20010118 SGD
+SGD S000004650 NUP116 GO:0006407 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YMR047C|NSP116 gene taxon:4932 20010118 SGD
+SGD S000004650 NUP116 GO:0006408 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YMR047C|NSP116 gene taxon:4932 20010118 SGD
+SGD S000004650 NUP116 GO:0006409 SGD_REF:S000058277|PMID:9442897 IMP P nuclear pore complex subunit YMR047C|NSP116 gene taxon:4932 20010118 SGD
+SGD S000004650 NUP116 GO:0006409 SGD_REF:S000052576|PMID:9802895 IMP P nuclear pore complex subunit YMR047C|NSP116 gene taxon:4932 20010118 SGD
+SGD S000004650 NUP116 GO:0006606 SGD_REF:S000058277|PMID:9442897 IMP P nuclear pore complex subunit YMR047C|NSP116 gene taxon:4932 20010118 SGD
+SGD S000004650 NUP116 GO:0006607 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YMR047C|NSP116 gene taxon:4932 20010118 SGD
+SGD S000004650 NUP116 GO:0006608 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YMR047C|NSP116 gene taxon:4932 20010118 SGD
+SGD S000004650 NUP116 GO:0006609 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YMR047C|NSP116 gene taxon:4932 20010118 SGD
+SGD S000004650 NUP116 GO:0006610 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YMR047C|NSP116 gene taxon:4932 20010118 SGD
+SGD S000004650 NUP116 GO:0006611 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YMR047C|NSP116 gene taxon:4932 20010118 SGD
+SGD S000004650 NUP116 GO:0006999 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YMR047C|NSP116 gene taxon:4932 20010118 SGD
+SGD S000001540 NUP120 GO:0005643 SGD_REF:S000058277|PMID:9442897 IDA C 100 kDa protein (predicted molecular weight is 120 kDa) with two leucine zipper motifs, coiled-coil region, and some homology to Nup133p, nuclear pore complex subunit YKL057C|RAT2 gene taxon:4932 20010118 SGD
+SGD S000001540 NUP120 GO:0005198 SGD_REF:S000058277|PMID:9442897 TAS F 100 kDa protein (predicted molecular weight is 120 kDa) with two leucine zipper motifs, coiled-coil region, and some homology to Nup133p, nuclear pore complex subunit YKL057C|RAT2 gene taxon:4932 20010118 SGD
+SGD S000001540 NUP120 GO:0006259 SGD_REF:S000080974|PMID:15725626 IGI P 100 kDa protein (predicted molecular weight is 120 kDa) with two leucine zipper motifs, coiled-coil region, and some homology to Nup133p, nuclear pore complex subunit YKL057C|RAT2 gene taxon:4932 20050317 SGD
+SGD S000001540 NUP120 GO:0006406 SGD_REF:S000058277|PMID:9442897 IMP P 100 kDa protein (predicted molecular weight is 120 kDa) with two leucine zipper motifs, coiled-coil region, and some homology to Nup133p, nuclear pore complex subunit YKL057C|RAT2 gene taxon:4932 20010118 SGD
+SGD S000001540 NUP120 GO:0006407 SGD_REF:S000058277|PMID:9442897 TAS P 100 kDa protein (predicted molecular weight is 120 kDa) with two leucine zipper motifs, coiled-coil region, and some homology to Nup133p, nuclear pore complex subunit YKL057C|RAT2 gene taxon:4932 20010118 SGD
+SGD S000001540 NUP120 GO:0006408 SGD_REF:S000058277|PMID:9442897 TAS P 100 kDa protein (predicted molecular weight is 120 kDa) with two leucine zipper motifs, coiled-coil region, and some homology to Nup133p, nuclear pore complex subunit YKL057C|RAT2 gene taxon:4932 20010118 SGD
+SGD S000001540 NUP120 GO:0006409 SGD_REF:S000058277|PMID:9442897 TAS P 100 kDa protein (predicted molecular weight is 120 kDa) with two leucine zipper motifs, coiled-coil region, and some homology to Nup133p, nuclear pore complex subunit YKL057C|RAT2 gene taxon:4932 20010118 SGD
+SGD S000001540 NUP120 GO:0006607 SGD_REF:S000058277|PMID:9442897 TAS P 100 kDa protein (predicted molecular weight is 120 kDa) with two leucine zipper motifs, coiled-coil region, and some homology to Nup133p, nuclear pore complex subunit YKL057C|RAT2 gene taxon:4932 20010118 SGD
+SGD S000001540 NUP120 GO:0006608 SGD_REF:S000058277|PMID:9442897 TAS P 100 kDa protein (predicted molecular weight is 120 kDa) with two leucine zipper motifs, coiled-coil region, and some homology to Nup133p, nuclear pore complex subunit YKL057C|RAT2 gene taxon:4932 20010118 SGD
+SGD S000001540 NUP120 GO:0006609 SGD_REF:S000058277|PMID:9442897 TAS P 100 kDa protein (predicted molecular weight is 120 kDa) with two leucine zipper motifs, coiled-coil region, and some homology to Nup133p, nuclear pore complex subunit YKL057C|RAT2 gene taxon:4932 20010118 SGD
+SGD S000001540 NUP120 GO:0006610 SGD_REF:S000058277|PMID:9442897 TAS P 100 kDa protein (predicted molecular weight is 120 kDa) with two leucine zipper motifs, coiled-coil region, and some homology to Nup133p, nuclear pore complex subunit YKL057C|RAT2 gene taxon:4932 20010118 SGD
+SGD S000001540 NUP120 GO:0006611 SGD_REF:S000058277|PMID:9442897 TAS P 100 kDa protein (predicted molecular weight is 120 kDa) with two leucine zipper motifs, coiled-coil region, and some homology to Nup133p, nuclear pore complex subunit YKL057C|RAT2 gene taxon:4932 20010118 SGD
+SGD S000001540 NUP120 GO:0006999 SGD_REF:S000058277|PMID:9442897 IMP P 100 kDa protein (predicted molecular weight is 120 kDa) with two leucine zipper motifs, coiled-coil region, and some homology to Nup133p, nuclear pore complex subunit YKL057C|RAT2 gene taxon:4932 20010118 SGD
+SGD S000001540 NUP120 GO:0050000 SGD_REF:S000114163|PMID:16418532 IMP P 100 kDa protein (predicted molecular weight is 120 kDa) with two leucine zipper motifs, coiled-coil region, and some homology to Nup133p, nuclear pore complex subunit YKL057C|RAT2 gene taxon:4932 20060222 SGD
+SGD S000001790 NUP133 GO:0005643 SGD_REF:S000058277|PMID:9442897 IDA C nuclear pore complex subunit YKR082W|RAT3 gene taxon:4932 20010118 SGD
+SGD S000001790 NUP133 GO:0005198 SGD_REF:S000058277|PMID:9442897 TAS F nuclear pore complex subunit YKR082W|RAT3 gene taxon:4932 20010118 SGD
+SGD S000001790 NUP133 GO:0006259 SGD_REF:S000080974|PMID:15725626 IGI P nuclear pore complex subunit YKR082W|RAT3 gene taxon:4932 20050317 SGD
+SGD S000001790 NUP133 GO:0006406 SGD_REF:S000058277|PMID:9442897 IMP P nuclear pore complex subunit YKR082W|RAT3 gene taxon:4932 20010118 SGD
+SGD S000001790 NUP133 GO:0006407 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YKR082W|RAT3 gene taxon:4932 20010118 SGD
+SGD S000001790 NUP133 GO:0006408 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YKR082W|RAT3 gene taxon:4932 20010118 SGD
+SGD S000001790 NUP133 GO:0006409 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YKR082W|RAT3 gene taxon:4932 20010118 SGD
+SGD S000001790 NUP133 GO:0006607 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YKR082W|RAT3 gene taxon:4932 20010118 SGD
+SGD S000001790 NUP133 GO:0006608 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YKR082W|RAT3 gene taxon:4932 20010118 SGD
+SGD S000001790 NUP133 GO:0006609 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YKR082W|RAT3 gene taxon:4932 20010118 SGD
+SGD S000001790 NUP133 GO:0006610 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YKR082W|RAT3 gene taxon:4932 20010118 SGD
+SGD S000001790 NUP133 GO:0006611 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YKR082W|RAT3 gene taxon:4932 20010118 SGD
+SGD S000001790 NUP133 GO:0006999 SGD_REF:S000058277|PMID:9442897 IMP P nuclear pore complex subunit YKR082W|RAT3 gene taxon:4932 20010118 SGD
+SGD S000001790 NUP133 GO:0050000 SGD_REF:S000114163|PMID:16418532 IMP P nuclear pore complex subunit YKR082W|RAT3 gene taxon:4932 20060222 SGD
+SGD S000003060 NUP145 GO:0005643 SGD_REF:S000058277|PMID:9442897 IDA C nuclear pore complex subunit YGL092W|RAT10 gene taxon:4932 20010118 SGD
+SGD S000003060 NUP145 GO:0005198 SGD_REF:S000058277|PMID:9442897 TAS F nuclear pore complex subunit YGL092W|RAT10 gene taxon:4932 20010118 SGD
+SGD S000003060 NUP145 GO:0006388 SGD_REF:S000052060|PMID:8524308 IMP P nuclear pore complex subunit YGL092W|RAT10 gene taxon:4932 20010118 SGD
+SGD S000003060 NUP145 GO:0006406 SGD_REF:S000058277|PMID:9442897 IMP P nuclear pore complex subunit YGL092W|RAT10 gene taxon:4932 20010118 SGD
+SGD S000003060 NUP145 GO:0006407 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YGL092W|RAT10 gene taxon:4932 20010118 SGD
+SGD S000003060 NUP145 GO:0006408 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YGL092W|RAT10 gene taxon:4932 20010118 SGD
+SGD S000003060 NUP145 GO:0006409 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YGL092W|RAT10 gene taxon:4932 20010118 SGD
+SGD S000003060 NUP145 GO:0006606 SGD_REF:S000058277|PMID:9442897 IMP P nuclear pore complex subunit YGL092W|RAT10 gene taxon:4932 20010118 SGD
+SGD S000003060 NUP145 GO:0006607 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YGL092W|RAT10 gene taxon:4932 20010118 SGD
+SGD S000003060 NUP145 GO:0006608 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YGL092W|RAT10 gene taxon:4932 20010118 SGD
+SGD S000003060 NUP145 GO:0006609 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YGL092W|RAT10 gene taxon:4932 20010118 SGD
+SGD S000003060 NUP145 GO:0006610 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YGL092W|RAT10 gene taxon:4932 20010118 SGD
+SGD S000003060 NUP145 GO:0006611 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YGL092W|RAT10 gene taxon:4932 20010118 SGD
+SGD S000003060 NUP145 GO:0006999 SGD_REF:S000058277|PMID:9442897 IMP P nuclear pore complex subunit YGL092W|RAT10 gene taxon:4932 20010118 SGD
+SGD S000003060 NUP145 GO:0050000 SGD_REF:S000114163|PMID:16418532 IMP P nuclear pore complex subunit YGL092W|RAT10 gene taxon:4932 20060222 SGD
+SGD S000000907 NUP157 GO:0005643 SGD_REF:S000058277|PMID:9442897 IDA C nuclear pore complex subunit YER105C gene taxon:4932 20010118 SGD
+SGD S000000907 NUP157 GO:0005198 SGD_REF:S000058277|PMID:9442897 TAS F nuclear pore complex subunit YER105C gene taxon:4932 20010118 SGD
+SGD S000000907 NUP157 GO:0006406 SGD_REF:S000058277|PMID:9442897 IMP P nuclear pore complex subunit YER105C gene taxon:4932 20010118 SGD
+SGD S000000907 NUP157 GO:0006406 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YER105C gene taxon:4932 20010118 SGD
+SGD S000000907 NUP157 GO:0006407 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YER105C gene taxon:4932 20010118 SGD
+SGD S000000907 NUP157 GO:0006408 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YER105C gene taxon:4932 20010118 SGD
+SGD S000000907 NUP157 GO:0006409 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YER105C gene taxon:4932 20010118 SGD
+SGD S000000907 NUP157 GO:0006607 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YER105C gene taxon:4932 20010118 SGD
+SGD S000000907 NUP157 GO:0006608 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YER105C gene taxon:4932 20010118 SGD
+SGD S000000907 NUP157 GO:0006609 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YER105C gene taxon:4932 20010118 SGD
+SGD S000000907 NUP157 GO:0006610 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YER105C gene taxon:4932 20010118 SGD
+SGD S000000907 NUP157 GO:0006611 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YER105C gene taxon:4932 20010118 SGD
+SGD S000000907 NUP157 GO:0006999 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YER105C gene taxon:4932 20010118 SGD
+SGD S000001377 NUP159 GO:0005643 SGD_REF:S000069412|PMID:11343909 TAS C nucleoporin YIL115C|NUP158|RAT7 gene taxon:4932 20020313 SGD
+SGD S000001377 NUP159 GO:0005198 SGD_REF:S000069412|PMID:11343909 TAS F nucleoporin YIL115C|NUP158|RAT7 gene taxon:4932 20020313 SGD
+SGD S000001377 NUP159 GO:0000054 SGD_REF:S000067496|PMID:11739405 IMP P nucleoporin YIL115C|NUP158|RAT7 gene taxon:4932 20020313 SGD
+SGD S000001377 NUP159 GO:0006406 SGD_REF:S000053379|PMID:9359887 IMP P nucleoporin YIL115C|NUP158|RAT7 gene taxon:4932 20020313 SGD
+SGD S000001377 NUP159 GO:0006407 SGD_REF:S000067496|PMID:11739405 IMP P nucleoporin YIL115C|NUP158|RAT7 gene taxon:4932 20020313 SGD
+SGD S000001377 NUP159 GO:0006999 SGD_REF:S000053379|PMID:9359887 IMP P nucleoporin YIL115C|NUP158|RAT7 gene taxon:4932 20020313 SGD
+SGD S000000175 NUP170 GO:0005643 SGD_REF:S000058277|PMID:9442897 IDA C nuclear pore complex subunit YBL079W|NLE3 gene taxon:4932 20010118 SGD
+SGD S000000175 NUP170 GO:0005198 SGD_REF:S000058277|PMID:9442897 TAS F nuclear pore complex subunit YBL079W|NLE3 gene taxon:4932 20010118 SGD
+SGD S000000175 NUP170 GO:0000059 SGD_REF:S000055428|PMID:9864357 IPI P nuclear pore complex subunit YBL079W|NLE3 gene taxon:4932 20010118 SGD
+SGD S000000175 NUP170 GO:0006406 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YBL079W|NLE3 gene taxon:4932 20010118 SGD
+SGD S000000175 NUP170 GO:0006407 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YBL079W|NLE3 gene taxon:4932 20010118 SGD
+SGD S000000175 NUP170 GO:0006408 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YBL079W|NLE3 gene taxon:4932 20010118 SGD
+SGD S000000175 NUP170 GO:0006409 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YBL079W|NLE3 gene taxon:4932 20010118 SGD
+SGD S000000175 NUP170 GO:0006607 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YBL079W|NLE3 gene taxon:4932 20010118 SGD
+SGD S000000175 NUP170 GO:0006608 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YBL079W|NLE3 gene taxon:4932 20010118 SGD
+SGD S000000175 NUP170 GO:0006609 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YBL079W|NLE3 gene taxon:4932 20010118 SGD
+SGD S000000175 NUP170 GO:0006610 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YBL079W|NLE3 gene taxon:4932 20010118 SGD
+SGD S000000175 NUP170 GO:0006611 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YBL079W|NLE3 gene taxon:4932 20010118 SGD
+SGD S000000175 NUP170 GO:0006999 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YBL079W|NLE3 gene taxon:4932 20010118 SGD
+SGD S000000175 NUP170 GO:0007059 SGD_REF:S000060228|PMID:11290711 IMP P nuclear pore complex subunit YBL079W|NLE3 gene taxon:4932 20030721 SGD
+SGD S000004571 NUP188 GO:0005643 SGD_REF:S000058277|PMID:9442897 IDA C nuclear pore complex subunit YML103C gene taxon:4932 20010118 SGD
+SGD S000004571 NUP188 GO:0005198 SGD_REF:S000058277|PMID:9442897 TAS F nuclear pore complex subunit YML103C gene taxon:4932 20010118 SGD
+SGD S000004571 NUP188 GO:0006406 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YML103C gene taxon:4932 20010118 SGD
+SGD S000004571 NUP188 GO:0006407 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YML103C gene taxon:4932 20010118 SGD
+SGD S000004571 NUP188 GO:0006408 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YML103C gene taxon:4932 20010118 SGD
+SGD S000004571 NUP188 GO:0006409 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YML103C gene taxon:4932 20010118 SGD
+SGD S000004571 NUP188 GO:0006607 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YML103C gene taxon:4932 20010118 SGD
+SGD S000004571 NUP188 GO:0006608 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YML103C gene taxon:4932 20010118 SGD
+SGD S000004571 NUP188 GO:0006609 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YML103C gene taxon:4932 20010118 SGD
+SGD S000004571 NUP188 GO:0006610 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YML103C gene taxon:4932 20010118 SGD
+SGD S000004571 NUP188 GO:0006611 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YML103C gene taxon:4932 20010118 SGD
+SGD S000004571 NUP188 GO:0006999 SGD_REF:S000058277|PMID:9442897 IMP P nuclear pore complex subunit YML103C gene taxon:4932 20010118 SGD
+SGD S000003576 NUP192 GO:0005643 SGD_REF:S000069412|PMID:11343909 TAS C nuclear pore complex subunit YJL039C gene taxon:4932 20020313 SGD
+SGD S000003576 NUP192 GO:0017056 SGD_REF:S000050902|PMID:10428845 IMP F nuclear pore complex subunit YJL039C gene taxon:4932 20021001 SGD
+SGD S000003576 NUP192 GO:0017056 SGD_REF:S000050902|PMID:10428845 IPI F nuclear pore complex subunit YJL039C gene taxon:4932 20021001 SGD
+SGD S000003576 NUP192 GO:0006999 SGD_REF:S000050902|PMID:10428845 IMP P nuclear pore complex subunit YJL039C gene taxon:4932 20021001 SGD
+SGD S000003576 NUP192 GO:0006999 SGD_REF:S000050902|PMID:10428845 IPI P nuclear pore complex subunit YJL039C gene taxon:4932 20021001 SGD
+SGD S000004327 NUP2 GO:0000790 SGD_REF:S000114102|PMID:16365162 IDA C nucleoporin YLR335W gene taxon:4932 20060210 SGD
+SGD S000004327 NUP2 GO:0005643 SGD_REF:S000058277|PMID:9442897 IDA C nucleoporin YLR335W gene taxon:4932 20010118 SGD
+SGD S000004327 NUP2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C nucleoporin YLR335W gene taxon:4932 20040928 SGD
+SGD S000004327 NUP2 GO:0005198 SGD_REF:S000058277|PMID:9442897 TAS F nucleoporin YLR335W gene taxon:4932 20010118 SGD
+SGD S000004327 NUP2 GO:0006342 SGD_REF:S000069953|PMID:12062099 IMP P nucleoporin YLR335W gene taxon:4932 20041101 SGD
+SGD S000004327 NUP2 GO:0006348 SGD_REF:S000114102|PMID:16365162 IMP P nucleoporin YLR335W gene taxon:4932 20060210 SGD
+SGD S000004327 NUP2 GO:0006406 SGD_REF:S000058277|PMID:9442897 TAS P nucleoporin YLR335W gene taxon:4932 20010118 SGD
+SGD S000004327 NUP2 GO:0006407 SGD_REF:S000058277|PMID:9442897 TAS P nucleoporin YLR335W gene taxon:4932 20010118 SGD
+SGD S000004327 NUP2 GO:0006408 SGD_REF:S000058277|PMID:9442897 TAS P nucleoporin YLR335W gene taxon:4932 20010118 SGD
+SGD S000004327 NUP2 GO:0006409 SGD_REF:S000058277|PMID:9442897 TAS P nucleoporin YLR335W gene taxon:4932 20010118 SGD
+SGD S000004327 NUP2 GO:0006607 SGD_REF:S000058277|PMID:9442897 TAS P nucleoporin YLR335W gene taxon:4932 20010118 SGD
+SGD S000004327 NUP2 GO:0006608 SGD_REF:S000058277|PMID:9442897 TAS P nucleoporin YLR335W gene taxon:4932 20010118 SGD
+SGD S000004327 NUP2 GO:0006609 SGD_REF:S000058277|PMID:9442897 TAS P nucleoporin YLR335W gene taxon:4932 20010118 SGD
+SGD S000004327 NUP2 GO:0006610 SGD_REF:S000058277|PMID:9442897 TAS P nucleoporin YLR335W gene taxon:4932 20010118 SGD
+SGD S000004327 NUP2 GO:0006611 SGD_REF:S000058277|PMID:9442897 TAS P nucleoporin YLR335W gene taxon:4932 20010118 SGD
+SGD S000004327 NUP2 GO:0006999 SGD_REF:S000058277|PMID:9442897 TAS P nucleoporin YLR335W gene taxon:4932 20010118 SGD
+SGD S000002600 NUP42 GO:0005643 SGD_REF:S000058277|PMID:9442897 IDA C 42 kDa protein associated with nuclear pore complexes; structurally related to the FG-nucleoporin family of pore proteins, nuclear pore complex subunit YDR192C|RIP1|UIP1 gene taxon:4932 20010118 SGD
+SGD S000002600 NUP42 GO:0005198 SGD_REF:S000058277|PMID:9442897 TAS F 42 kDa protein associated with nuclear pore complexes; structurally related to the FG-nucleoporin family of pore proteins, nuclear pore complex subunit YDR192C|RIP1|UIP1 gene taxon:4932 20010118 SGD
+SGD S000002600 NUP42 GO:0006406 SGD_REF:S000058277|PMID:9442897 TAS P 42 kDa protein associated with nuclear pore complexes; structurally related to the FG-nucleoporin family of pore proteins, nuclear pore complex subunit YDR192C|RIP1|UIP1 gene taxon:4932 20010118 SGD
+SGD S000002600 NUP42 GO:0006407 SGD_REF:S000058277|PMID:9442897 TAS P 42 kDa protein associated with nuclear pore complexes; structurally related to the FG-nucleoporin family of pore proteins, nuclear pore complex subunit YDR192C|RIP1|UIP1 gene taxon:4932 20010118 SGD
+SGD S000002600 NUP42 GO:0006408 SGD_REF:S000058277|PMID:9442897 TAS P 42 kDa protein associated with nuclear pore complexes; structurally related to the FG-nucleoporin family of pore proteins, nuclear pore complex subunit YDR192C|RIP1|UIP1 gene taxon:4932 20010118 SGD
+SGD S000002600 NUP42 GO:0006409 SGD_REF:S000058277|PMID:9442897 TAS P 42 kDa protein associated with nuclear pore complexes; structurally related to the FG-nucleoporin family of pore proteins, nuclear pore complex subunit YDR192C|RIP1|UIP1 gene taxon:4932 20010118 SGD
+SGD S000002600 NUP42 GO:0006607 SGD_REF:S000058277|PMID:9442897 TAS P 42 kDa protein associated with nuclear pore complexes; structurally related to the FG-nucleoporin family of pore proteins, nuclear pore complex subunit YDR192C|RIP1|UIP1 gene taxon:4932 20010118 SGD
+SGD S000002600 NUP42 GO:0006608 SGD_REF:S000058277|PMID:9442897 TAS P 42 kDa protein associated with nuclear pore complexes; structurally related to the FG-nucleoporin family of pore proteins, nuclear pore complex subunit YDR192C|RIP1|UIP1 gene taxon:4932 20010118 SGD
+SGD S000002600 NUP42 GO:0006609 SGD_REF:S000058277|PMID:9442897 TAS P 42 kDa protein associated with nuclear pore complexes; structurally related to the FG-nucleoporin family of pore proteins, nuclear pore complex subunit YDR192C|RIP1|UIP1 gene taxon:4932 20010118 SGD
+SGD S000002600 NUP42 GO:0006610 SGD_REF:S000058277|PMID:9442897 TAS P 42 kDa protein associated with nuclear pore complexes; structurally related to the FG-nucleoporin family of pore proteins, nuclear pore complex subunit YDR192C|RIP1|UIP1 gene taxon:4932 20010118 SGD
+SGD S000002600 NUP42 GO:0006611 SGD_REF:S000058277|PMID:9442897 TAS P 42 kDa protein associated with nuclear pore complexes; structurally related to the FG-nucleoporin family of pore proteins, nuclear pore complex subunit YDR192C|RIP1|UIP1 gene taxon:4932 20010118 SGD
+SGD S000002600 NUP42 GO:0006999 SGD_REF:S000058277|PMID:9442897 TAS P 42 kDa protein associated with nuclear pore complexes; structurally related to the FG-nucleoporin family of pore proteins, nuclear pore complex subunit YDR192C|RIP1|UIP1 gene taxon:4932 20010118 SGD
+SGD S000003140 NUP49 GO:0005635 SGD_REF:S000069459|PMID:11914276 IDA C nuclear pore complex subunit YGL172W|NSP49 gene taxon:4932 20020507 SGD
+SGD S000003140 NUP49 GO:0005643 SGD_REF:S000058277|PMID:9442897 IDA C nuclear pore complex subunit YGL172W|NSP49 gene taxon:4932 20010118 SGD
+SGD S000003140 NUP49 GO:0005198 SGD_REF:S000058277|PMID:9442897 TAS F nuclear pore complex subunit YGL172W|NSP49 gene taxon:4932 20010118 SGD
+SGD S000003140 NUP49 GO:0000055 SGD_REF:S000044179|PMID:9971735 IMP P nuclear pore complex subunit YGL172W|NSP49 gene taxon:4932 20010118 SGD
+SGD S000003140 NUP49 GO:0006388 SGD_REF:S000052060|PMID:8524308 IMP P nuclear pore complex subunit YGL172W|NSP49 gene taxon:4932 20010118 SGD
+SGD S000003140 NUP49 GO:0006406 SGD_REF:S000058277|PMID:9442897 IMP P nuclear pore complex subunit YGL172W|NSP49 gene taxon:4932 20010118 SGD
+SGD S000003140 NUP49 GO:0006407 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YGL172W|NSP49 gene taxon:4932 20010118 SGD
+SGD S000003140 NUP49 GO:0006408 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YGL172W|NSP49 gene taxon:4932 20010118 SGD
+SGD S000003140 NUP49 GO:0006409 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YGL172W|NSP49 gene taxon:4932 20010118 SGD
+SGD S000003140 NUP49 GO:0006606 SGD_REF:S000058277|PMID:9442897 IMP P nuclear pore complex subunit YGL172W|NSP49 gene taxon:4932 20010118 SGD
+SGD S000003140 NUP49 GO:0006607 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YGL172W|NSP49 gene taxon:4932 20010118 SGD
+SGD S000003140 NUP49 GO:0006608 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YGL172W|NSP49 gene taxon:4932 20010118 SGD
+SGD S000003140 NUP49 GO:0006609 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YGL172W|NSP49 gene taxon:4932 20010118 SGD
+SGD S000003140 NUP49 GO:0006610 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YGL172W|NSP49 gene taxon:4932 20010118 SGD
+SGD S000003140 NUP49 GO:0006611 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YGL172W|NSP49 gene taxon:4932 20010118 SGD
+SGD S000003140 NUP49 GO:0006999 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YGL172W|NSP49 gene taxon:4932 20010118 SGD
+SGD S000004762 NUP53 GO:0005643 SGD_REF:S000058277|PMID:9442897 IDA C karyopherin docking complex component of the nuclear pore complex, nuclear pore complex subunit YMR153W gene taxon:4932 20010118 SGD
+SGD S000004762 NUP53 GO:0005198 SGD_REF:S000058277|PMID:9442897 TAS F karyopherin docking complex component of the nuclear pore complex, nuclear pore complex subunit YMR153W gene taxon:4932 20010118 SGD
+SGD S000004762 NUP53 GO:0000059 SGD_REF:S000055428|PMID:9864357 IPI P karyopherin docking complex component of the nuclear pore complex, nuclear pore complex subunit YMR153W gene taxon:4932 20010118 SGD
+SGD S000004762 NUP53 GO:0006406 SGD_REF:S000058277|PMID:9442897 TAS P karyopherin docking complex component of the nuclear pore complex, nuclear pore complex subunit YMR153W gene taxon:4932 20010118 SGD
+SGD S000004762 NUP53 GO:0006407 SGD_REF:S000058277|PMID:9442897 TAS P karyopherin docking complex component of the nuclear pore complex, nuclear pore complex subunit YMR153W gene taxon:4932 20010118 SGD
+SGD S000004762 NUP53 GO:0006408 SGD_REF:S000058277|PMID:9442897 TAS P karyopherin docking complex component of the nuclear pore complex, nuclear pore complex subunit YMR153W gene taxon:4932 20010118 SGD
+SGD S000004762 NUP53 GO:0006409 SGD_REF:S000058277|PMID:9442897 TAS P karyopherin docking complex component of the nuclear pore complex, nuclear pore complex subunit YMR153W gene taxon:4932 20010118 SGD
+SGD S000004762 NUP53 GO:0006607 SGD_REF:S000058277|PMID:9442897 TAS P karyopherin docking complex component of the nuclear pore complex, nuclear pore complex subunit YMR153W gene taxon:4932 20010118 SGD
+SGD S000004762 NUP53 GO:0006608 SGD_REF:S000058277|PMID:9442897 TAS P karyopherin docking complex component of the nuclear pore complex, nuclear pore complex subunit YMR153W gene taxon:4932 20010118 SGD
+SGD S000004762 NUP53 GO:0006609 SGD_REF:S000058277|PMID:9442897 TAS P karyopherin docking complex component of the nuclear pore complex, nuclear pore complex subunit YMR153W gene taxon:4932 20010118 SGD
+SGD S000004762 NUP53 GO:0006610 SGD_REF:S000058277|PMID:9442897 TAS P karyopherin docking complex component of the nuclear pore complex, nuclear pore complex subunit YMR153W gene taxon:4932 20010118 SGD
+SGD S000004762 NUP53 GO:0006611 SGD_REF:S000058277|PMID:9442897 TAS P karyopherin docking complex component of the nuclear pore complex, nuclear pore complex subunit YMR153W gene taxon:4932 20010118 SGD
+SGD S000004762 NUP53 GO:0006999 SGD_REF:S000058277|PMID:9442897 TAS P karyopherin docking complex component of the nuclear pore complex, nuclear pore complex subunit YMR153W gene taxon:4932 20010118 SGD
+SGD S000003351 NUP57 GO:0005643 SGD_REF:S000058277|PMID:9442897 IDA C nucleoporin YGR119C gene taxon:4932 20010118 SGD
+SGD S000003351 NUP57 GO:0005198 SGD_REF:S000058277|PMID:9442897 TAS F nucleoporin YGR119C gene taxon:4932 20010118 SGD
+SGD S000003351 NUP57 GO:0006406 SGD_REF:S000058277|PMID:9442897 IMP P nucleoporin YGR119C gene taxon:4932 20010118 SGD
+SGD S000003351 NUP57 GO:0006407 SGD_REF:S000058277|PMID:9442897 TAS P nucleoporin YGR119C gene taxon:4932 20010118 SGD
+SGD S000003351 NUP57 GO:0006408 SGD_REF:S000058277|PMID:9442897 TAS P nucleoporin YGR119C gene taxon:4932 20010118 SGD
+SGD S000003351 NUP57 GO:0006409 SGD_REF:S000058277|PMID:9442897 TAS P nucleoporin YGR119C gene taxon:4932 20010118 SGD
+SGD S000003351 NUP57 GO:0006606 SGD_REF:S000058277|PMID:9442897 IMP P nucleoporin YGR119C gene taxon:4932 20010118 SGD
+SGD S000003351 NUP57 GO:0006607 SGD_REF:S000058277|PMID:9442897 TAS P nucleoporin YGR119C gene taxon:4932 20010118 SGD
+SGD S000003351 NUP57 GO:0006608 SGD_REF:S000058277|PMID:9442897 TAS P nucleoporin YGR119C gene taxon:4932 20010118 SGD
+SGD S000003351 NUP57 GO:0006609 SGD_REF:S000058277|PMID:9442897 TAS P nucleoporin YGR119C gene taxon:4932 20010118 SGD
+SGD S000003351 NUP57 GO:0006610 SGD_REF:S000058277|PMID:9442897 TAS P nucleoporin YGR119C gene taxon:4932 20010118 SGD
+SGD S000003351 NUP57 GO:0006611 SGD_REF:S000058277|PMID:9442897 TAS P nucleoporin YGR119C gene taxon:4932 20010118 SGD
+SGD S000003351 NUP57 GO:0006999 SGD_REF:S000058277|PMID:9442897 TAS P nucleoporin YGR119C gene taxon:4932 20010118 SGD
+SGD S000000063 NUP60 GO:0005643 SGD_REF:S000069412|PMID:11343909 TAS C nuclear pore complex subunit YAR002W gene taxon:4932 20020313 SGD
+SGD S000000063 NUP60 GO:0017056 SGD_REF:S000061235|PMID:11535617 TAS F nuclear pore complex subunit YAR002W gene taxon:4932 20021001 SGD
+SGD S000000063 NUP60 GO:0000059 SGD_REF:S000061235|PMID:11535617 IMP P nuclear pore complex subunit YAR002W gene taxon:4932 20021001 SGD
+SGD S000000063 NUP60 GO:0000059 SGD_REF:S000061235|PMID:11535617 IPI P nuclear pore complex subunit YAR002W gene taxon:4932 20021001 SGD
+SGD S000000063 NUP60 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P nuclear pore complex subunit YAR002W gene taxon:4932 20060203 SGD
+SGD S000000063 NUP60 GO:0006913 SGD_REF:S000061235|PMID:11535617 IMP P nuclear pore complex subunit YAR002W gene taxon:4932 20021001 SGD
+SGD S000029330 NUP63 GO:0005643 SGD_REF:S000058489|PMID:8227139 IDA C gene taxon:4932 20021206 SGD
+SGD S000029330 NUP63 GO:0017056 SGD_REF:S000058489|PMID:8227139 IPI F gene taxon:4932 20021206 SGD
+SGD S000029330 NUP63 GO:0006404 SGD_REF:S000058489|PMID:8227139 IPI P gene taxon:4932 20021206 SGD
+SGD S000029330 NUP63 GO:0006405 SGD_REF:S000058489|PMID:8227139 IPI P gene taxon:4932 20021206 SGD
+SGD S000029330 NUP63 GO:0006606 SGD_REF:S000058489|PMID:8227139 IPI P gene taxon:4932 20021206 SGD
+SGD S000029330 NUP63 GO:0006611 SGD_REF:S000058489|PMID:8227139 IPI P gene taxon:4932 20021206 SGD
+SGD S000003597 NUP82 GO:0005643 SGD_REF:S000058277|PMID:9442897 IDA C 82 kDa protein, with putative coiled-coil domain, has carboxy-terminal domain, containing heptad repeats, that binds Nsp1p, nuclear pore complex subunit, nucleoporin YJL061W|HRB187 gene taxon:4932 20010118 SGD
+SGD S000003597 NUP82 GO:0005198 SGD_REF:S000058277|PMID:9442897 TAS F 82 kDa protein, with putative coiled-coil domain, has carboxy-terminal domain, containing heptad repeats, that binds Nsp1p, nuclear pore complex subunit, nucleoporin YJL061W|HRB187 gene taxon:4932 20010118 SGD
+SGD S000003597 NUP82 GO:0006406 SGD_REF:S000058277|PMID:9442897 IMP P 82 kDa protein, with putative coiled-coil domain, has carboxy-terminal domain, containing heptad repeats, that binds Nsp1p, nuclear pore complex subunit, nucleoporin YJL061W|HRB187 gene taxon:4932 20010118 SGD
+SGD S000003597 NUP82 GO:0006407 SGD_REF:S000058277|PMID:9442897 TAS P 82 kDa protein, with putative coiled-coil domain, has carboxy-terminal domain, containing heptad repeats, that binds Nsp1p, nuclear pore complex subunit, nucleoporin YJL061W|HRB187 gene taxon:4932 20010118 SGD
+SGD S000003597 NUP82 GO:0006408 SGD_REF:S000058277|PMID:9442897 TAS P 82 kDa protein, with putative coiled-coil domain, has carboxy-terminal domain, containing heptad repeats, that binds Nsp1p, nuclear pore complex subunit, nucleoporin YJL061W|HRB187 gene taxon:4932 20010118 SGD
+SGD S000003597 NUP82 GO:0006409 SGD_REF:S000058277|PMID:9442897 TAS P 82 kDa protein, with putative coiled-coil domain, has carboxy-terminal domain, containing heptad repeats, that binds Nsp1p, nuclear pore complex subunit, nucleoporin YJL061W|HRB187 gene taxon:4932 20010118 SGD
+SGD S000003597 NUP82 GO:0006607 SGD_REF:S000058277|PMID:9442897 TAS P 82 kDa protein, with putative coiled-coil domain, has carboxy-terminal domain, containing heptad repeats, that binds Nsp1p, nuclear pore complex subunit, nucleoporin YJL061W|HRB187 gene taxon:4932 20010118 SGD
+SGD S000003597 NUP82 GO:0006608 SGD_REF:S000058277|PMID:9442897 TAS P 82 kDa protein, with putative coiled-coil domain, has carboxy-terminal domain, containing heptad repeats, that binds Nsp1p, nuclear pore complex subunit, nucleoporin YJL061W|HRB187 gene taxon:4932 20010118 SGD
+SGD S000003597 NUP82 GO:0006609 SGD_REF:S000058277|PMID:9442897 TAS P 82 kDa protein, with putative coiled-coil domain, has carboxy-terminal domain, containing heptad repeats, that binds Nsp1p, nuclear pore complex subunit, nucleoporin YJL061W|HRB187 gene taxon:4932 20010118 SGD
+SGD S000003597 NUP82 GO:0006610 SGD_REF:S000058277|PMID:9442897 TAS P 82 kDa protein, with putative coiled-coil domain, has carboxy-terminal domain, containing heptad repeats, that binds Nsp1p, nuclear pore complex subunit, nucleoporin YJL061W|HRB187 gene taxon:4932 20010118 SGD
+SGD S000003597 NUP82 GO:0006611 SGD_REF:S000058277|PMID:9442897 TAS P 82 kDa protein, with putative coiled-coil domain, has carboxy-terminal domain, containing heptad repeats, that binds Nsp1p, nuclear pore complex subunit, nucleoporin YJL061W|HRB187 gene taxon:4932 20010118 SGD
+SGD S000003597 NUP82 GO:0006999 SGD_REF:S000058277|PMID:9442897 TAS P 82 kDa protein, with putative coiled-coil domain, has carboxy-terminal domain, containing heptad repeats, that binds Nsp1p, nuclear pore complex subunit, nucleoporin YJL061W|HRB187 gene taxon:4932 20010118 SGD
+SGD S000002274 NUP84 GO:0005643 SGD_REF:S000058277|PMID:9442897 IDA C nuclear pore complex subunit, similar to mammalian Nup107p YDL116W gene taxon:4932 20010118 SGD
+SGD S000002274 NUP84 GO:0005198 SGD_REF:S000058277|PMID:9442897 TAS F nuclear pore complex subunit, similar to mammalian Nup107p YDL116W gene taxon:4932 20010118 SGD
+SGD S000002274 NUP84 GO:0006259 SGD_REF:S000080974|PMID:15725626 IGI P nuclear pore complex subunit, similar to mammalian Nup107p YDL116W gene taxon:4932 20050317 SGD
+SGD S000002274 NUP84 GO:0006406 SGD_REF:S000058277|PMID:9442897 IMP P nuclear pore complex subunit, similar to mammalian Nup107p YDL116W gene taxon:4932 20010118 SGD
+SGD S000002274 NUP84 GO:0006407 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit, similar to mammalian Nup107p YDL116W gene taxon:4932 20010118 SGD
+SGD S000002274 NUP84 GO:0006408 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit, similar to mammalian Nup107p YDL116W gene taxon:4932 20010118 SGD
+SGD S000002274 NUP84 GO:0006409 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit, similar to mammalian Nup107p YDL116W gene taxon:4932 20010118 SGD
+SGD S000002274 NUP84 GO:0006607 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit, similar to mammalian Nup107p YDL116W gene taxon:4932 20010118 SGD
+SGD S000002274 NUP84 GO:0006608 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit, similar to mammalian Nup107p YDL116W gene taxon:4932 20010118 SGD
+SGD S000002274 NUP84 GO:0006609 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit, similar to mammalian Nup107p YDL116W gene taxon:4932 20010118 SGD
+SGD S000002274 NUP84 GO:0006610 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit, similar to mammalian Nup107p YDL116W gene taxon:4932 20010118 SGD
+SGD S000002274 NUP84 GO:0006611 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit, similar to mammalian Nup107p YDL116W gene taxon:4932 20010118 SGD
+SGD S000002274 NUP84 GO:0006974 SGD_REF:S000076175|PMID:12482937 IMP P nuclear pore complex subunit, similar to mammalian Nup107p YDL116W gene taxon:4932 20060406 SGD
+SGD S000002274 NUP84 GO:0006998 SGD_REF:S000057810|PMID:8565072 IMP P nuclear pore complex subunit, similar to mammalian Nup107p YDL116W gene taxon:4932 20010118 SGD
+SGD S000002274 NUP84 GO:0006999 SGD_REF:S000058277|PMID:9442897 IMP P nuclear pore complex subunit, similar to mammalian Nup107p YDL116W gene taxon:4932 20010118 SGD
+SGD S000002274 NUP84 GO:0050000 SGD_REF:S000114163|PMID:16418532 IMP P nuclear pore complex subunit, similar to mammalian Nup107p YDL116W gene taxon:4932 20060222 SGD
+SGD S000003803 NUP85 GO:0005643 SGD_REF:S000058277|PMID:9442897 IDA C nuclear pore complex subunit YJR042W|RAT9 gene taxon:4932 20010118 SGD
+SGD S000003803 NUP85 GO:0005198 SGD_REF:S000058277|PMID:9442897 TAS F nuclear pore complex subunit YJR042W|RAT9 gene taxon:4932 20010118 SGD
+SGD S000003803 NUP85 GO:0006406 SGD_REF:S000058277|PMID:9442897 IMP P nuclear pore complex subunit YJR042W|RAT9 gene taxon:4932 20010118 SGD
+SGD S000003803 NUP85 GO:0006407 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YJR042W|RAT9 gene taxon:4932 20010118 SGD
+SGD S000003803 NUP85 GO:0006408 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YJR042W|RAT9 gene taxon:4932 20010118 SGD
+SGD S000003803 NUP85 GO:0006409 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YJR042W|RAT9 gene taxon:4932 20010118 SGD
+SGD S000003803 NUP85 GO:0006607 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YJR042W|RAT9 gene taxon:4932 20010118 SGD
+SGD S000003803 NUP85 GO:0006608 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YJR042W|RAT9 gene taxon:4932 20010118 SGD
+SGD S000003803 NUP85 GO:0006609 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YJR042W|RAT9 gene taxon:4932 20010118 SGD
+SGD S000003803 NUP85 GO:0006610 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YJR042W|RAT9 gene taxon:4932 20010118 SGD
+SGD S000003803 NUP85 GO:0006611 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YJR042W|RAT9 gene taxon:4932 20010118 SGD
+SGD S000003803 NUP85 GO:0006998 SGD_REF:S000058277|PMID:9442897 IMP P nuclear pore complex subunit YJR042W|RAT9 gene taxon:4932 20010118 SGD
+SGD S000003803 NUP85 GO:0006999 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YJR042W|RAT9 gene taxon:4932 20010118 SGD
+SGD S000002352 NUS1 GO:0005635 SGD_REF:S000075214|PMID:14690591 IDA C prenyltransferase YDL193W gene taxon:4932 20040105 SGD
+SGD S000002352 NUS1 GO:0005783 SGD_REF:S000059093|PMID:11086160 IDA C prenyltransferase YDL193W gene taxon:4932 20010626 SGD
+SGD S000002352 NUS1 GO:0005811 SGD_REF:S000048561|PMID:10515935 IDA C prenyltransferase YDL193W gene taxon:4932 20010626 SGD
+SGD S000002352 NUS1 GO:0005811 SGD_REF:S000075214|PMID:14690591 IDA C prenyltransferase YDL193W gene taxon:4932 20040105 SGD
+SGD S000002352 NUS1 GO:0004659 SGD_REF:S000075214|PMID:14690591 ISS F prenyltransferase YDL193W gene taxon:4932 20040105 SGD
+SGD S000002352 NUS1 GO:0000004 SGD_REF:S000069584 ND P prenyltransferase YDL193W gene taxon:4932 20010626 SGD
+SGD S000003119 NUT1 GO:0005634 SGD_REF:S000043365|PMID:9671481 IDA C YGL151W|MED5 gene taxon:4932 20020822 SGD
+SGD S000003119 NUT1 GO:0005554 SGD_REF:S000069584 ND F YGL151W|MED5 gene taxon:4932 20020822 SGD
+SGD S000003119 NUT1 GO:0006357 SGD_REF:S000043365|PMID:9671481 IMP P YGL151W|MED5 gene taxon:4932 20020822 SGD
+SGD S000006372 NUT2 GO:0000119 SGD_REF:S000056289|PMID:9812975 IDA C RNA polymerase II holoenzyme 21 kDa mediator subunit YPR168W|MED10 gene taxon:4932 20010118 SGD
+SGD S000006372 NUT2 GO:0016455 SGD_REF:S000056289|PMID:9812975 IPI F RNA polymerase II holoenzyme 21 kDa mediator subunit YPR168W|MED10 gene taxon:4932 20010302 SGD
+SGD S000006372 NUT2 GO:0006366 SGD_REF:S000056289|PMID:9812975 IPI P RNA polymerase II holoenzyme 21 kDa mediator subunit YPR168W|MED10 gene taxon:4932 20010118 SGD
+SGD S000001238 NVJ1 GO:0005635 SGD_REF:S000039257|PMID:10888680 IDA C YHR195W|VAB36 gene taxon:4932 20020927 SGD
+SGD S000001238 NVJ1 GO:0005515 SGD_REF:S000039257|PMID:10888680 IPI F YHR195W|VAB36 gene taxon:4932 20020927 SGD
+SGD S000001238 NVJ1 GO:0016237 SGD_REF:S000072498|PMID:12529432 IMP P YHR195W|VAB36 gene taxon:4932 20030213 SGD
+SGD S000004083 NYV1 GO:0005774 SGD_REF:S000058453|PMID:10047442 TAS C vacuolar v-SNARE YLR093C|MAM2 gene taxon:4932 20010118 SGD
+SGD S000004083 NYV1 GO:0005485 SGD_REF:S000058453|PMID:10047442 TAS F vacuolar v-SNARE YLR093C|MAM2 gene taxon:4932 20010118 SGD
+SGD S000004083 NYV1 GO:0006906 SGD_REF:S000058453|PMID:10047442 TAS P vacuolar v-SNARE YLR093C|MAM2 gene taxon:4932 20010118 SGD
+SGD S000001603 OAC1 GO:0005743 SGD_REF:S000056389|PMID:10428783 IDA C oxaloacetate transport protein YKL120W gene taxon:4932 20010118 SGD
+SGD S000001603 OAC1 GO:0000227 SGD_REF:S000056389|PMID:10428783 IDA F oxaloacetate transport protein YKL120W gene taxon:4932 20010118 SGD
+SGD S000001603 OAC1 GO:0008271 SGD_REF:S000056389|PMID:10428783 IDA F oxaloacetate transport protein YKL120W gene taxon:4932 20010118 SGD
+SGD S000001603 OAC1 GO:0008272 SGD_REF:S000056389|PMID:10428783 IDA P oxaloacetate transport protein YKL120W gene taxon:4932 20010118 SGD
+SGD S000001603 OAC1 GO:0015729 SGD_REF:S000056389|PMID:10428783 IDA P oxaloacetate transport protein YKL120W gene taxon:4932 20010118 SGD
+SGD S000000048 OAF1 GO:0005634 SGD_REF:S000051452|PMID:8662598 IPI C transcription factor YAL051W|YAF1 gene taxon:4932 20010118 SGD
+SGD S000000048 OAF1 GO:0003677 SGD_REF:S000051452|PMID:8662598 IDA F transcription factor YAL051W|YAF1 gene taxon:4932 20030225 SGD
+SGD S000000048 OAF1 GO:0003677 SGD_REF:S000051452|PMID:8662598 ISS F transcription factor YAL051W|YAF1 gene taxon:4932 20030225 SGD
+SGD S000000048 OAF1 GO:0003677 SGD_REF:S000051452|PMID:8662598 IPI F transcription factor YAL051W|YAF1 gene taxon:4932 20030225 SGD
+SGD S000000048 OAF1 GO:0016563 SGD_REF:S000051452|PMID:8662598 IMP F transcription factor YAL051W|YAF1 gene taxon:4932 20030225 SGD
+SGD S000000048 OAF1 GO:0016563 SGD_REF:S000051452|PMID:8662598 ISS F transcription factor YAL051W|YAF1 gene taxon:4932 20030225 SGD
+SGD S000000048 OAF1 GO:0016563 SGD_REF:S000051452|PMID:8662598 IPI F transcription factor YAL051W|YAF1 gene taxon:4932 20030225 SGD
+SGD S000000048 OAF1 GO:0006631 SGD_REF:S000051452|PMID:8662598 IGI P transcription factor YAL051W|YAF1 gene taxon:4932 20030225 SGD
+SGD S000000048 OAF1 GO:0006631 SGD_REF:S000051452|PMID:8662598 IMP P transcription factor YAL051W|YAF1 gene taxon:4932 20030225 SGD
+SGD S000000048 OAF1 GO:0007031 SGD_REF:S000055053|PMID:9774671 IGI P transcription factor YAL051W|YAF1 gene taxon:4932 20030225 SGD
+SGD S000000048 OAF1 GO:0007031 SGD_REF:S000055053|PMID:9774671 IMP P transcription factor YAL051W|YAF1 gene taxon:4932 20030225 SGD
+SGD S000000048 OAF1 GO:0045941 SGD_REF:S000051452|PMID:8662598 IMP P transcription factor YAL051W|YAF1 gene taxon:4932 20030225 SGD
+SGD S000000048 OAF1 GO:0045941 SGD_REF:S000051452|PMID:8662598 IGI P transcription factor YAL051W|YAF1 gene taxon:4932 20030225 SGD
+SGD S000000048 OAF1 GO:0045941 SGD_REF:S000051452|PMID:8662598 IPI P transcription factor YAL051W|YAF1 gene taxon:4932 20030225 SGD
+SGD S000001538 OAR1 GO:0005739 SGD_REF:S000040710|PMID:9388293 IMP C 3-oxoacyl-[acyl-carrier-protein] reductase YKL055C gene taxon:4932 20021028 SGD
+SGD S000001538 OAR1 GO:0005739 SGD_REF:S000040710|PMID:9388293 ISS C 3-oxoacyl-[acyl-carrier-protein] reductase YKL055C gene taxon:4932 20021028 SGD
+SGD S000001538 OAR1 GO:0004316 SGD_REF:S000040710|PMID:9388293 IMP F 3-oxoacyl-[acyl-carrier-protein] reductase YKL055C gene taxon:4932 20021028 SGD
+SGD S000001538 OAR1 GO:0004316 SGD_REF:S000040710|PMID:9388293 ISS F 3-oxoacyl-[acyl-carrier-protein] reductase YKL055C gene taxon:4932 20021028 SGD
+SGD S000001538 OAR1 GO:0006631 SGD_REF:S000040710|PMID:9388293 IMP P 3-oxoacyl-[acyl-carrier-protein] reductase YKL055C gene taxon:4932 20021028 SGD
+SGD S000001538 OAR1 GO:0006631 SGD_REF:S000040710|PMID:9388293 ISS P 3-oxoacyl-[acyl-carrier-protein] reductase YKL055C gene taxon:4932 20021028 SGD
+SGD S000001538 OAR1 GO:0009060 SGD_REF:S000040710|PMID:9388293 IMP P 3-oxoacyl-[acyl-carrier-protein] reductase YKL055C gene taxon:4932 20021028 SGD
+SGD S000005973 OAZ1 GO:0005623 SGD_REF:S000079797|PMID:15538383 IC GO:0004857|GO:0030163 C YPL052W|YPL052W-A gene taxon:4932 20041213 SGD
+SGD S000005973 OAZ1 GO:0004857 SGD_REF:S000079797|PMID:15538383 IDA F YPL052W|YPL052W-A gene taxon:4932 20041213 SGD
+SGD S000005973 OAZ1 GO:0030163 SGD_REF:S000079797|PMID:15538383 IDA P YPL052W|YPL052W-A gene taxon:4932 20041213 SGD
+SGD S000005043 OCA1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YNL099C gene taxon:4932 20031028 SGD
+SGD S000005043 OCA1 GO:0004725 SGD_REF:S000060767|PMID:11408586 ISS F YNL099C gene taxon:4932 20021010 SGD
+SGD S000005043 OCA1 GO:0006979 SGD_REF:S000060767|PMID:11408586 IMP P YNL099C gene taxon:4932 20021010 SGD
+SGD S000005001 OCA2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YNL056W gene taxon:4932 20031028 SGD
+SGD S000005001 OCA2 GO:0005554 SGD_REF:S000069584 ND F YNL056W gene taxon:4932 20030115 SGD
+SGD S000005001 OCA2 GO:0000004 SGD_REF:S000069584 ND P YNL056W gene taxon:4932 20030115 SGD
+SGD S000000691 OCA4 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YCR095C gene taxon:4932 20031028 SGD
+SGD S000000691 OCA4 GO:0005554 SGD_REF:S000069584 ND F YCR095C gene taxon:4932 20030203 SGD
+SGD S000000691 OCA4 GO:0000004 SGD_REF:S000069584 ND P YCR095C gene taxon:4932 20030203 SGD
+SGD S000001021 OCA5 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YHL029C gene taxon:4932 20031028 SGD
+SGD S000001021 OCA5 GO:0005554 SGD_REF:S000069584 ND F YHL029C gene taxon:4932 20021126 SGD
+SGD S000001021 OCA5 GO:0008152 SGD_REF:S000075216|PMID:14656964 TAS P YHL029C gene taxon:4932 20040315 SGD
+SGD S000002474 OCA6 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDR067C gene taxon:4932 20031028 SGD
+SGD S000002474 OCA6 GO:0005554 SGD_REF:S000069584 ND F YDR067C gene taxon:4932 20021126 SGD
+SGD S000002474 OCA6 GO:0000004 SGD_REF:S000069584 ND P YDR067C gene taxon:4932 20021126 SGD
+SGD S000003006 OCH1 GO:0000137 SGD_REF:S000043008|PMID:1628616 IDA C alpha-1,6-mannosyltransferase YGL038C|LDB12|NGD29 gene taxon:4932 20020213 SGD
+SGD S000003006 OCH1 GO:0000137 SGD_REF:S000053238|PMID:10189369 IDA C alpha-1,6-mannosyltransferase YGL038C|LDB12|NGD29 gene taxon:4932 20050714 SGD
+SGD S000003006 OCH1 GO:0000009 SGD_REF:S000046070|PMID:8253757 IMP F alpha-1,6-mannosyltransferase YGL038C|LDB12|NGD29 gene taxon:4932 20010118 SGD
+SGD S000003006 OCH1 GO:0000009 SGD_REF:S000047009|PMID:9276464 IDA F alpha-1,6-mannosyltransferase YGL038C|LDB12|NGD29 gene taxon:4932 20050228 SGD
+SGD S000003006 OCH1 GO:0016757 SGD_REF:S000055539|PMID:9653120 ISS F alpha-1,6-mannosyltransferase YGL038C|LDB12|NGD29 gene taxon:4932 20021204 SGD
+SGD S000003006 OCH1 GO:0006487 SGD_REF:S000046948|PMID:7649302 IMP P alpha-1,6-mannosyltransferase YGL038C|LDB12|NGD29 gene taxon:4932 20050511 SGD
+SGD S000001617 OCT1 GO:0005739 SGD_REF:S000051417|PMID:10332043 IGI C intermediate peptidase, possesses octapeptidyl amino-peptidase activity YKL134C gene taxon:4932 20010118 SGD
+SGD S000001617 OCT1 GO:0005739 SGD_REF:S000051417|PMID:10332043 IMP C intermediate peptidase, possesses octapeptidyl amino-peptidase activity YKL134C gene taxon:4932 20010118 SGD
+SGD S000001617 OCT1 GO:0004243 SGD_REF:S000057953|PMID:8831696 IDA F intermediate peptidase, possesses octapeptidyl amino-peptidase activity YKL134C gene taxon:4932 20050207 SGD
+SGD S000001617 OCT1 GO:0004243 SGD_REF:S000057953|PMID:8831696 IMP F intermediate peptidase, possesses octapeptidyl amino-peptidase activity YKL134C gene taxon:4932 20050207 SGD
+SGD S000001617 OCT1 GO:0008237 SGD_REF:S000057953|PMID:8831696 IMP F intermediate peptidase, possesses octapeptidyl amino-peptidase activity YKL134C gene taxon:4932 20010118 SGD
+SGD S000001617 OCT1 GO:0008237 SGD_REF:S000057953|PMID:8831696 IDA F intermediate peptidase, possesses octapeptidyl amino-peptidase activity YKL134C gene taxon:4932 20010118 SGD
+SGD S000001617 OCT1 GO:0006627 SGD_REF:S000057577|PMID:8035833 IMP P intermediate peptidase, possesses octapeptidyl amino-peptidase activity YKL134C gene taxon:4932 20010118 SGD
+SGD S000001617 OCT1 GO:0006879 SGD_REF:S000051417|PMID:10332043 IMP P intermediate peptidase, possesses octapeptidyl amino-peptidase activity YKL134C gene taxon:4932 20010118 SGD
+SGD S000001617 OCT1 GO:0006879 SGD_REF:S000051417|PMID:10332043 IGI P intermediate peptidase, possesses octapeptidyl amino-peptidase activity YKL134C gene taxon:4932 20010118 SGD
+SGD S000006055 ODC1 GO:0005739 SGD_REF:S000061149|PMID:9178508 IDA C mitochondrial 2-oxodicarboxylate transport protein YPL134C gene taxon:4932 20020813 SGD
+SGD S000006055 ODC1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C mitochondrial 2-oxodicarboxylate transport protein YPL134C gene taxon:4932 20040924 SGD
+SGD S000006055 ODC1 GO:0005743 SGD_REF:S000059531|PMID:11013234 IDA C mitochondrial 2-oxodicarboxylate transport protein YPL134C gene taxon:4932 20020920 SGD
+SGD S000006055 ODC1 GO:0005342 SGD_REF:S000059531|PMID:11013234 IDA F mitochondrial 2-oxodicarboxylate transport protein YPL134C gene taxon:4932 20020920 SGD
+SGD S000006055 ODC1 GO:0005478 SGD_REF:S000059531|PMID:11013234 IDA F mitochondrial 2-oxodicarboxylate transport protein YPL134C gene taxon:4932 20020920 SGD
+SGD S000006055 ODC1 GO:0006839 SGD_REF:S000059531|PMID:11013234 IDA P mitochondrial 2-oxodicarboxylate transport protein YPL134C gene taxon:4932 20020920 SGD
+SGD S000005748 ODC2 GO:0005743 SGD_REF:S000059531|PMID:11013234 IDA C mitochondrial 2-oxodicarboxylate transport protein YOR222W gene taxon:4932 20020920 SGD
+SGD S000005748 ODC2 GO:0005342 SGD_REF:S000059531|PMID:11013234 IDA F mitochondrial 2-oxodicarboxylate transport protein YOR222W gene taxon:4932 20020920 SGD
+SGD S000005748 ODC2 GO:0005478 SGD_REF:S000059531|PMID:11013234 IDA F mitochondrial 2-oxodicarboxylate transport protein YOR222W gene taxon:4932 20020920 SGD
+SGD S000005748 ODC2 GO:0006839 SGD_REF:S000059531|PMID:11013234 IDA P mitochondrial 2-oxodicarboxylate transport protein YOR222W gene taxon:4932 20020920 SGD
+SGD S000004525 OGG1 GO:0005739 SGD_REF:S000059916|PMID:11239005 IDA C 43 kDa 8-oxo-guanine DNA glycosylase YML060W gene taxon:4932 20020307 SGD
+SGD S000004525 OGG1 GO:0008534 SGD_REF:S000046294|PMID:8643552 IDA F 43 kDa 8-oxo-guanine DNA glycosylase YML060W gene taxon:4932 20020318 SGD
+SGD S000004525 OGG1 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P 43 kDa 8-oxo-guanine DNA glycosylase YML060W gene taxon:4932 20060202 SGD
+SGD S000004525 OGG1 GO:0006281 SGD_REF:S000059916|PMID:11239005 IMP P 43 kDa 8-oxo-guanine DNA glycosylase YML060W gene taxon:4932 20020318 SGD
+SGD S000004525 OGG1 GO:0006285 SGD_REF:S000046294|PMID:8643552 IDA P 43 kDa 8-oxo-guanine DNA glycosylase YML060W gene taxon:4932 20020318 SGD
+SGD S000003411 OKP1 GO:0000778 SGD_REF:S000054451|PMID:10323865 IDA C YGR179C gene taxon:4932 20030403 SGD
+SGD S000003411 OKP1 GO:0000817 SGD_REF:S000075142|PMID:14633972 IDA C YGR179C gene taxon:4932 20040618 SGD
+SGD S000003411 OKP1 GO:0005515 SGD_REF:S000054451|PMID:10323865 IDA F YGR179C gene taxon:4932 20020920 SGD
+SGD S000003411 OKP1 GO:0007059 SGD_REF:S000054451|PMID:10323865 IPI P YGR179C gene taxon:4932 20020920 SGD
+SGD S000003023 OLE1 GO:0005789 SGD_REF:S000048690|PMID:8530368 TAS C delta-9-fatty acid desaturase YGL055W|MDM2 gene taxon:4932 20021202 SGD
+SGD S000003023 OLE1 GO:0004768 SGD_REF:S000041996|PMID:1978720 IMP F delta-9-fatty acid desaturase YGL055W|MDM2 gene taxon:4932 20021202 SGD
+SGD S000003023 OLE1 GO:0004768 SGD_REF:S000041996|PMID:1978720 ISS F delta-9-fatty acid desaturase YGL055W|MDM2 gene taxon:4932 20021202 SGD
+SGD S000003023 OLE1 GO:0000001 SGD_REF:S000058450|PMID:9891785 TAS P delta-9-fatty acid desaturase YGL055W|MDM2 gene taxon:4932 20010118 SGD
+SGD S000003023 OLE1 GO:0006636 SGD_REF:S000041996|PMID:1978720 IMP P delta-9-fatty acid desaturase YGL055W|MDM2 gene taxon:4932 20021202 SGD
+SGD S000003023 OLE1 GO:0006636 SGD_REF:S000041996|PMID:1978720 ISS P delta-9-fatty acid desaturase YGL055W|MDM2 gene taxon:4932 20021202 SGD
+SGD S000007274 OLI1 GO:0000276 SGD_REF:S000058444|PMID:10838056 TAS C ATPase-associated proteolipid, F0-ATP synthase subunit 9 Q0130|ATP9|OLI3 gene taxon:4932 20010118 SGD
+SGD S000007274 OLI1 GO:0005198 SGD_REF:S000058444|PMID:10838056 TAS F ATPase-associated proteolipid, F0-ATP synthase subunit 9 Q0130|ATP9|OLI3 gene taxon:4932 20030711 SGD
+SGD S000007274 OLI1 GO:0015078 SGD_REF:S000058444|PMID:10838056 TAS F ATPase-associated proteolipid, F0-ATP synthase subunit 9 Q0130|ATP9|OLI3 gene taxon:4932 20030711 SGD
+SGD S000007274 OLI1 GO:0046933 SGD_REF:S000058444|PMID:10838056 TAS F ATPase-associated proteolipid, F0-ATP synthase subunit 9 Q0130|ATP9|OLI3 gene taxon:4932 20030714 SGD
+SGD S000007274 OLI1 GO:0006461 SGD_REF:S000058444|PMID:10838056 TAS P ATPase-associated proteolipid, F0-ATP synthase subunit 9 Q0130|ATP9|OLI3 gene taxon:4932 20030711 SGD
+SGD S000007274 OLI1 GO:0015986 SGD_REF:S000058444|PMID:10838056 TAS P ATPase-associated proteolipid, F0-ATP synthase subunit 9 Q0130|ATP9|OLI3 gene taxon:4932 20010118 SGD
+SGD S000000434 OM14 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C major outer membrane protein of yeast mitochondria YBR230C gene taxon:4932 20031028 SGD
+SGD S000000434 OM14 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C major outer membrane protein of yeast mitochondria YBR230C gene taxon:4932 20040924 SGD
+SGD S000000434 OM14 GO:0031307 SGD_REF:S000115559|PMID:16689936 IDA C major outer membrane protein of yeast mitochondria YBR230C gene taxon:4932 20060515 SGD
+SGD S000000434 OM14 GO:0005554 SGD_REF:S000069584 ND F major outer membrane protein of yeast mitochondria YBR230C gene taxon:4932 20030422 SGD
+SGD S000000434 OM14 GO:0000004 SGD_REF:S000069584 ND P major outer membrane protein of yeast mitochondria YBR230C gene taxon:4932 20030422 SGD
+SGD S000001398 OM45 GO:0005741 SGD_REF:S000069842|PMID:1039 TAS C 45 kDa mitochondrial outer membrane protein YIL136W gene taxon:4932 20020523 SGD
+SGD S000001398 OM45 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C 45 kDa mitochondrial outer membrane protein YIL136W gene taxon:4932 20060317 SGD
+SGD S000001398 OM45 GO:0005741 SGD_REF:S000060697|PMID:11179417 IDA C 45 kDa mitochondrial outer membrane protein YIL136W gene taxon:4932 20020523 SGD
+SGD S000001398 OM45 GO:0031307 SGD_REF:S000115559|PMID:16689936 IDA C 45 kDa mitochondrial outer membrane protein YIL136W gene taxon:4932 20060515 SGD
+SGD S000001398 OM45 GO:0005554 SGD_REF:S000069584 ND F 45 kDa mitochondrial outer membrane protein YIL136W gene taxon:4932 20020523 SGD
+SGD S000001398 OM45 GO:0000004 SGD_REF:S000069584 ND P 45 kDa mitochondrial outer membrane protein YIL136W gene taxon:4932 20020523 SGD
+SGD S000001795 OMA1 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YKR087C gene taxon:4932 20031028 SGD
+SGD S000001795 OMA1 GO:0005743 SGD_REF:S000074704|PMID:12963738 IDA C YKR087C gene taxon:4932 20040209 SGD
+SGD S000001795 OMA1 GO:0004222 SGD_REF:S000074704|PMID:12963738 IMP F YKR087C gene taxon:4932 20040209 SGD
+SGD S000001795 OMA1 GO:0004222 SGD_REF:S000074704|PMID:12963738 ISS F YKR087C gene taxon:4932 20040209 SGD
+SGD S000001795 OMA1 GO:0006515 SGD_REF:S000074704|PMID:12963738 IMP P YKR087C gene taxon:4932 20040209 SGD
+SGD S000002724 OMS1 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YDR316W gene taxon:4932 20031028 SGD
+SGD S000002724 OMS1 GO:0005740 SGD_REF:S000080496|PMID:15355998 IDA C YDR316W gene taxon:4932 20050207 SGD
+SGD S000002724 OMS1 GO:0008757 SGD_REF:S000073093|PMID:9873020 ISS F YDR316W gene taxon:4932 20030317 SGD
+SGD S000002724 OMS1 GO:0000004 SGD_REF:S000069584 ND P YDR316W gene taxon:4932 20030203 SGD
+SGD S000001012 OPI1 GO:0005634 SGD_REF:S000061407|PMID:11454208 IC GO:0003714 C YHL020C gene taxon:4932 20021105 SGD
+SGD S000001012 OPI1 GO:0003714 SGD_REF:S000061407|PMID:11454208 IPI F YHL020C gene taxon:4932 20020321 SGD
+SGD S000001012 OPI1 GO:0000122 SGD_REF:S000041557|PMID:1985968 IMP P YHL020C gene taxon:4932 20020321 SGD
+SGD S000001012 OPI1 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P YHL020C gene taxon:4932 20060203 SGD
+SGD S000001012 OPI1 GO:0008654 SGD_REF:S000041557|PMID:1985968 IMP P YHL020C gene taxon:4932 20020321 SGD
+SGD S000001012 OPI1 GO:0045944 SGD_REF:S000074120|PMID:12871953 IMP P YHL020C gene taxon:4932 20031014 SGD
+SGD S000005392 OPI10 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YOL032W gene taxon:4932 20031028 SGD
+SGD S000005392 OPI10 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YOL032W gene taxon:4932 20031028 SGD
+SGD S000005392 OPI10 GO:0005554 SGD_REF:S000069584 ND F YOL032W gene taxon:4932 20010119 SGD
+SGD S000005392 OPI10 GO:0000004 SGD_REF:S000069584 ND P YOL032W gene taxon:4932 20010119 SGD
+SGD S000003834 OPI3 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C unsaturated phospholipid N-methyltransferase YJR073C|PEM2 gene taxon:4932 20040928 SGD
+SGD S000003834 OPI3 GO:0005783 SGD_REF:S000058496 TAS C unsaturated phospholipid N-methyltransferase YJR073C|PEM2 gene taxon:4932 20010119 SGD
+SGD S000003834 OPI3 GO:0000773 SGD_REF:S000058496 TAS F unsaturated phospholipid N-methyltransferase YJR073C|PEM2 gene taxon:4932 20030114 SGD
+SGD S000003834 OPI3 GO:0006656 SGD_REF:S000058496 TAS P unsaturated phospholipid N-methyltransferase YJR073C|PEM2 gene taxon:4932 20010119 SGD
+SGD S000003748 OPT1 GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C glutathione transporter, peptide transporter YJL212C|GSH11|HGT1 gene taxon:4932 20031028 SGD
+SGD S000003748 OPT1 GO:0005887 SGD_REF:S000050331|PMID:10788431 IMP C glutathione transporter, peptide transporter YJL212C|GSH11|HGT1 gene taxon:4932 20031014 SGD
+SGD S000003748 OPT1 GO:0005887 SGD_REF:S000050331|PMID:10788431 ISS C glutathione transporter, peptide transporter YJL212C|GSH11|HGT1 gene taxon:4932 20031014 SGD
+SGD S000003748 OPT1 GO:0015198 SGD_REF:S000041069|PMID:10652283 IMP F glutathione transporter, peptide transporter YJL212C|GSH11|HGT1 gene taxon:4932 20020605 SGD
+SGD S000003748 OPT1 GO:0006790 SGD_REF:S000069207|PMID:11862495 IEP P glutathione transporter, peptide transporter YJL212C|GSH11|HGT1 gene taxon:4932 20020605 SGD
+SGD S000006398 OPT2 GO:0005887 SGD_REF:S000054683|PMID:9643541 IC GO:0015198 C peptide transporter YPR194C gene taxon:4932 20031014 SGD
+SGD S000006398 OPT2 GO:0015198 SGD_REF:S000054683|PMID:9643541 ISS F peptide transporter YPR194C gene taxon:4932 20010118 SGD
+SGD S000006398 OPT2 GO:0015198 SGD_REF:S000054683|PMID:9643541 IDA F peptide transporter YPR194C gene taxon:4932 20031014 SGD
+SGD S000006398 OPT2 GO:0006857 SGD_REF:S000054683|PMID:9643541 ISS P peptide transporter YPR194C gene taxon:4932 20010118 SGD
+SGD S000006398 OPT2 GO:0006857 SGD_REF:S000054683|PMID:9643541 IDA P peptide transporter YPR194C gene taxon:4932 20031014 SGD
+SGD S000000333 OPY1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YBR129C gene taxon:4932 20031028 SGD
+SGD S000000333 OPY1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YBR129C gene taxon:4932 20040813 SGD
+SGD S000000333 OPY1 GO:0005554 SGD_REF:S000069584 ND F YBR129C gene taxon:4932 20021028 SGD
+SGD S000000333 OPY1 GO:0000747 SGD_REF:S000048463|PMID:9383053 IGI P YBR129C gene taxon:4932 20021028 SGD
+SGD S000006279 OPY2 GO:0000324 SGD_REF:S000074185|PMID:14562095 IDA C YPR075C gene taxon:4932 20031028 SGD
+SGD S000006279 OPY2 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YPR075C gene taxon:4932 20020507 SGD
+SGD S000006279 OPY2 GO:0005886 SGD_REF:S000114997|PMID:16543225 IDA C YPR075C gene taxon:4932 20060424 SGD
+SGD S000006279 OPY2 GO:0016021 SGD_REF:S000114997|PMID:16543225 IDA C YPR075C gene taxon:4932 20060424 SGD
+SGD S000006279 OPY2 GO:0005554 SGD_REF:S000069584 ND F YPR075C gene taxon:4932 20021001 SGD
+SGD S000006279 OPY2 GO:0000751 SGD_REF:S000048463|PMID:9383053 IGI P YPR075C gene taxon:4932 20021206 SGD
+SGD S000006279 OPY2 GO:0007231 SGD_REF:S000114997|PMID:16543225 IGI SGD:S000003996 P YPR075C gene taxon:4932 20060424 SGD
+SGD S000006279 OPY2 GO:0007231 SGD_REF:S000114997|PMID:16543225 IPI SGD:S000000537 P YPR075C gene taxon:4932 20060424 SGD
+SGD S000004530 ORC1 GO:0005656 SGD_REF:S000074972|PMID:12045100 TAS C origin recognition complex (ORC) 120 kDa (largest) subunit, similar to Cdc6p, Cdc18p, and Sir3p and to proteins from K. lactis, S. pombe, and humans YML065W gene taxon:4932 20041117 SGD
+SGD S000004530 ORC1 GO:0005664 SGD_REF:S000058275|PMID:9442876 TAS C origin recognition complex (ORC) 120 kDa (largest) subunit, similar to Cdc6p, Cdc18p, and Sir3p and to proteins from K. lactis, S. pombe, and humans YML065W gene taxon:4932 20010118 SGD
+SGD S000004530 ORC1 GO:0003688 SGD_REF:S000058275|PMID:9442876 TAS F origin recognition complex (ORC) 120 kDa (largest) subunit, similar to Cdc6p, Cdc18p, and Sir3p and to proteins from K. lactis, S. pombe, and humans YML065W gene taxon:4932 20010118 SGD
+SGD S000004530 ORC1 GO:0016887 SGD_REF:S000058275|PMID:9442876 TAS F origin recognition complex (ORC) 120 kDa (largest) subunit, similar to Cdc6p, Cdc18p, and Sir3p and to proteins from K. lactis, S. pombe, and humans YML065W gene taxon:4932 20010118 SGD
+SGD S000004530 ORC1 GO:0006267 SGD_REF:S000058275|PMID:9442876 TAS P origin recognition complex (ORC) 120 kDa (largest) subunit, similar to Cdc6p, Cdc18p, and Sir3p and to proteins from K. lactis, S. pombe, and humans YML065W gene taxon:4932 20010118 SGD
+SGD S000004530 ORC1 GO:0006270 SGD_REF:S000058275|PMID:9442876 TAS P origin recognition complex (ORC) 120 kDa (largest) subunit, similar to Cdc6p, Cdc18p, and Sir3p and to proteins from K. lactis, S. pombe, and humans YML065W gene taxon:4932 20010118 SGD
+SGD S000004530 ORC1 GO:0030466 SGD_REF:S000058275|PMID:9442876 TAS P origin recognition complex (ORC) 120 kDa (largest) subunit, similar to Cdc6p, Cdc18p, and Sir3p and to proteins from K. lactis, S. pombe, and humans YML065W gene taxon:4932 20010118 SGD
+SGD S000000264 ORC2 GO:0005656 SGD_REF:S000074972|PMID:12045100 TAS C origin recognition complex subunit 2 YBR060C|RRR1|SIR5 gene taxon:4932 20041117 SGD
+SGD S000000264 ORC2 GO:0005664 SGD_REF:S000058275|PMID:9442876 TAS C origin recognition complex subunit 2 YBR060C|RRR1|SIR5 gene taxon:4932 20010118 SGD
+SGD S000000264 ORC2 GO:0003688 SGD_REF:S000058275|PMID:9442876 TAS F origin recognition complex subunit 2 YBR060C|RRR1|SIR5 gene taxon:4932 20010118 SGD
+SGD S000000264 ORC2 GO:0006267 SGD_REF:S000058275|PMID:9442876 TAS P origin recognition complex subunit 2 YBR060C|RRR1|SIR5 gene taxon:4932 20010118 SGD
+SGD S000000264 ORC2 GO:0006270 SGD_REF:S000058275|PMID:9442876 TAS P origin recognition complex subunit 2 YBR060C|RRR1|SIR5 gene taxon:4932 20010118 SGD
+SGD S000000264 ORC2 GO:0030466 SGD_REF:S000058275|PMID:9442876 TAS P origin recognition complex subunit 2 YBR060C|RRR1|SIR5 gene taxon:4932 20010118 SGD
+SGD S000003927 ORC3 GO:0005656 SGD_REF:S000074972|PMID:12045100 TAS C origin recognition complex subunit YLL004W gene taxon:4932 20041117 SGD
+SGD S000003927 ORC3 GO:0005664 SGD_REF:S000058275|PMID:9442876 TAS C origin recognition complex subunit YLL004W gene taxon:4932 20010118 SGD
+SGD S000003927 ORC3 GO:0003688 SGD_REF:S000058275|PMID:9442876 TAS F origin recognition complex subunit YLL004W gene taxon:4932 20010118 SGD
+SGD S000003927 ORC3 GO:0006267 SGD_REF:S000058275|PMID:9442876 TAS P origin recognition complex subunit YLL004W gene taxon:4932 20010118 SGD
+SGD S000003927 ORC3 GO:0006270 SGD_REF:S000058275|PMID:9442876 TAS P origin recognition complex subunit YLL004W gene taxon:4932 20010118 SGD
+SGD S000003927 ORC3 GO:0030466 SGD_REF:S000058275|PMID:9442876 TAS P origin recognition complex subunit YLL004W gene taxon:4932 20010118 SGD
+SGD S000006366 ORC4 GO:0005656 SGD_REF:S000074972|PMID:12045100 TAS C origin recognition complex (ORC) 56 kDa subunit YPR162C gene taxon:4932 20041117 SGD
+SGD S000006366 ORC4 GO:0005664 SGD_REF:S000058275|PMID:9442876 TAS C origin recognition complex (ORC) 56 kDa subunit YPR162C gene taxon:4932 20010118 SGD
+SGD S000006366 ORC4 GO:0003688 SGD_REF:S000058275|PMID:9442876 TAS F origin recognition complex (ORC) 56 kDa subunit YPR162C gene taxon:4932 20010118 SGD
+SGD S000006366 ORC4 GO:0006267 SGD_REF:S000058275|PMID:9442876 TAS P origin recognition complex (ORC) 56 kDa subunit YPR162C gene taxon:4932 20010118 SGD
+SGD S000006366 ORC4 GO:0006270 SGD_REF:S000058275|PMID:9442876 TAS P origin recognition complex (ORC) 56 kDa subunit YPR162C gene taxon:4932 20010118 SGD
+SGD S000006366 ORC4 GO:0030466 SGD_REF:S000058275|PMID:9442876 TAS P origin recognition complex (ORC) 56 kDa subunit YPR162C gene taxon:4932 20010118 SGD
+SGD S000005205 ORC5 GO:0005656 SGD_REF:S000074972|PMID:12045100 TAS C ATP-binding site (putative), origin recognition complex fifth largest subunit YNL261W gene taxon:4932 20041117 SGD
+SGD S000005205 ORC5 GO:0005664 SGD_REF:S000058275|PMID:9442876 TAS C ATP-binding site (putative), origin recognition complex fifth largest subunit YNL261W gene taxon:4932 20010118 SGD
+SGD S000005205 ORC5 GO:0003688 SGD_REF:S000058275|PMID:9442876 TAS F ATP-binding site (putative), origin recognition complex fifth largest subunit YNL261W gene taxon:4932 20010118 SGD
+SGD S000005205 ORC5 GO:0016887 SGD_REF:S000058275|PMID:9442876 TAS F ATP-binding site (putative), origin recognition complex fifth largest subunit YNL261W gene taxon:4932 20010118 SGD
+SGD S000005205 ORC5 GO:0006267 SGD_REF:S000058275|PMID:9442876 TAS P ATP-binding site (putative), origin recognition complex fifth largest subunit YNL261W gene taxon:4932 20010118 SGD
+SGD S000005205 ORC5 GO:0006270 SGD_REF:S000058275|PMID:9442876 TAS P ATP-binding site (putative), origin recognition complex fifth largest subunit YNL261W gene taxon:4932 20010118 SGD
+SGD S000005205 ORC5 GO:0030466 SGD_REF:S000058275|PMID:9442876 TAS P ATP-binding site (putative), origin recognition complex fifth largest subunit YNL261W gene taxon:4932 20010118 SGD
+SGD S000001160 ORC6 GO:0005656 SGD_REF:S000074972|PMID:12045100 TAS C ORC 50 kDa subunit YHR118C gene taxon:4932 20041117 SGD
+SGD S000001160 ORC6 GO:0005664 SGD_REF:S000058275|PMID:9442876 TAS C ORC 50 kDa subunit YHR118C gene taxon:4932 20010118 SGD
+SGD S000001160 ORC6 GO:0003688 SGD_REF:S000058275|PMID:9442876 TAS F ORC 50 kDa subunit YHR118C gene taxon:4932 20010118 SGD
+SGD S000001160 ORC6 GO:0006267 SGD_REF:S000058275|PMID:9442876 TAS P ORC 50 kDa subunit YHR118C gene taxon:4932 20010118 SGD
+SGD S000001160 ORC6 GO:0006270 SGD_REF:S000058275|PMID:9442876 TAS P ORC 50 kDa subunit YHR118C gene taxon:4932 20010118 SGD
+SGD S000001160 ORC6 GO:0030466 SGD_REF:S000058275|PMID:9442876 TAS P ORC 50 kDa subunit YHR118C gene taxon:4932 20010118 SGD
+SGD S000003270 ORM1 GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YGR038W gene taxon:4932 20031028 SGD
+SGD S000003270 ORM1 GO:0005554 SGD_REF:S000069584 ND F YGR038W gene taxon:4932 20021125 SGD
+SGD S000003270 ORM1 GO:0006986 SGD_REF:S000074113|PMID:12093374 IMP P YGR038W gene taxon:4932 20031007 SGD
+SGD S000003270 ORM1 GO:0006986 SGD_REF:S000074113|PMID:12093374 ISS P YGR038W gene taxon:4932 20031007 SGD
+SGD S000004342 ORM2 GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C Endoplasmic reticulum membrane-anchored protein YLR350W gene taxon:4932 20031028 SGD
+SGD S000004342 ORM2 GO:0005554 SGD_REF:S000069584 ND F Endoplasmic reticulum membrane-anchored protein YLR350W gene taxon:4932 20021201 SGD
+SGD S000004342 ORM2 GO:0006986 SGD_REF:S000074113|PMID:12093374 IMP P Endoplasmic reticulum membrane-anchored protein YLR350W gene taxon:4932 20031007 SGD
+SGD S000004342 ORM2 GO:0006986 SGD_REF:S000074113|PMID:12093374 ISS P Endoplasmic reticulum membrane-anchored protein YLR350W gene taxon:4932 20031007 SGD
+SGD S000005656 ORT1 GO:0005740 SGD_REF:S000043399|PMID:8798783 IDA C YOR130C|ARG11 gene taxon:4932 20010118 SGD
+SGD S000005656 ORT1 GO:0000064 SGD_REF:S000053985|PMID:9237680 IDA F YOR130C|ARG11 gene taxon:4932 20010118 SGD
+SGD S000005656 ORT1 GO:0000066 SGD_REF:S000053985|PMID:9237680 IDA P YOR130C|ARG11 gene taxon:4932 20031008 SGD
+SGD S000005656 ORT1 GO:0006526 SGD_REF:S000043399|PMID:8798783 IMP P YOR130C|ARG11 gene taxon:4932 20010118 SGD
+SGD S000002177 OSH2 GO:0005886 SGD_REF:S000060812|PMID:11408574 IDA C YDL019C gene taxon:4932 20020328 SGD
+SGD S000002177 OSH2 GO:0005935 SGD_REF:S000060812|PMID:11408574 IDA C YDL019C gene taxon:4932 20020328 SGD
+SGD S000002177 OSH2 GO:0008142 SGD_REF:S000059993|PMID:11238399 ISS F YDL019C gene taxon:4932 20020926 SGD
+SGD S000002177 OSH2 GO:0006694 SGD_REF:S000059993|PMID:11238399 IMP P YDL019C gene taxon:4932 20020328 SGD
+SGD S000002177 OSH2 GO:0006694 SGD_REF:S000059993|PMID:11238399 IGI P YDL019C gene taxon:4932 20020328 SGD
+SGD S000001115 OSH3 GO:0005737 SGD_REF:S000060812|PMID:11408574 IDA C YHR073W gene taxon:4932 20020328 SGD
+SGD S000001115 OSH3 GO:0008142 SGD_REF:S000059993|PMID:11238399 ISS F YHR073W gene taxon:4932 20020926 SGD
+SGD S000001115 OSH3 GO:0006694 SGD_REF:S000059993|PMID:11238399 IMP P YHR073W gene taxon:4932 20020328 SGD
+SGD S000001115 OSH3 GO:0006694 SGD_REF:S000059993|PMID:11238399 IGI P YHR073W gene taxon:4932 20020328 SGD
+SGD S000001711 OSH6 GO:0008372 SGD_REF:S000069584 ND C YKR003W gene taxon:4932 20020926 SGD
+SGD S000001711 OSH6 GO:0008142 SGD_REF:S000059993|PMID:11238399 ISS F YKR003W gene taxon:4932 20020926 SGD
+SGD S000001711 OSH6 GO:0006694 SGD_REF:S000059993|PMID:11238399 IMP P YKR003W gene taxon:4932 20020328 SGD
+SGD S000001711 OSH6 GO:0006694 SGD_REF:S000059993|PMID:11238399 IGI P YKR003W gene taxon:4932 20020328 SGD
+SGD S000001043 OSH7 GO:0008372 SGD_REF:S000069584 ND C YHR001W gene taxon:4932 20020926 SGD
+SGD S000001043 OSH7 GO:0008142 SGD_REF:S000059993|PMID:11238399 ISS F YHR001W gene taxon:4932 20020926 SGD
+SGD S000001043 OSH7 GO:0006694 SGD_REF:S000059993|PMID:11238399 IMP P YHR001W gene taxon:4932 20020328 SGD
+SGD S000001043 OSH7 GO:0006694 SGD_REF:S000059993|PMID:11238399 IGI P YHR001W gene taxon:4932 20020328 SGD
+SGD S000003812 OSM1 GO:0005739 SGD_REF:S000051098|PMID:9587404 IDA C osmotic growth protein YJR051W gene taxon:4932 20040812 SGD
+SGD S000003812 OSM1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C osmotic growth protein YJR051W gene taxon:4932 20040924 SGD
+SGD S000003812 OSM1 GO:0016156 SGD_REF:S000051098|PMID:9587404 IDA F osmotic growth protein YJR051W gene taxon:4932 20010625 SGD
+SGD S000003812 OSM1 GO:0008152 SGD_REF:S000051098|PMID:9587404 TAS P osmotic growth protein YJR051W gene taxon:4932 20010625 SGD
+SGD S000029332 OSR10 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20010119 SGD
+SGD S000029332 OSR10 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20010119 SGD
+SGD S000029332 OSR10 GO:0006970 SGD_REF:S000051125|PMID:9683646 IMP P gene taxon:4932 20010118 SGD
+SGD S000029333 OSR2 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20010119 SGD
+SGD S000029333 OSR2 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20010119 SGD
+SGD S000029333 OSR2 GO:0006970 SGD_REF:S000051125|PMID:9683646 IMP P gene taxon:4932 20010118 SGD
+SGD S000029334 OSR3 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20010119 SGD
+SGD S000029334 OSR3 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20010119 SGD
+SGD S000029334 OSR3 GO:0006970 SGD_REF:S000051125|PMID:9683646 IMP P gene taxon:4932 20010118 SGD
+SGD S000029335 OSR4 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20010119 SGD
+SGD S000029335 OSR4 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20010119 SGD
+SGD S000029335 OSR4 GO:0006970 SGD_REF:S000051125|PMID:9683646 IMP P gene taxon:4932 20010118 SGD
+SGD S000029336 OSR6 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20010119 SGD
+SGD S000029336 OSR6 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20010119 SGD
+SGD S000029336 OSR6 GO:0006970 SGD_REF:S000051125|PMID:9683646 IMP P gene taxon:4932 20010118 SGD
+SGD S000029337 OSR7 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20040419 SGD
+SGD S000029337 OSR7 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20040419 SGD
+SGD S000029337 OSR7 GO:0006970 SGD_REF:S000051125|PMID:9683646 IMP P gene taxon:4932 20010118 SGD
+SGD S000029338 OSR8 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20010119 SGD
+SGD S000029338 OSR8 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20010119 SGD
+SGD S000029338 OSR8 GO:0006970 SGD_REF:S000051125|PMID:9683646 IMP P gene taxon:4932 20010118 SGD
+SGD S000029339 OSR9 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20010119 SGD
+SGD S000029339 OSR9 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20010119 SGD
+SGD S000029339 OSR9 GO:0006970 SGD_REF:S000051125|PMID:9683646 IMP P gene taxon:4932 20010118 SGD
+SGD S000003539 OST1 GO:0008250 SGD_REF:S000050823|PMID:10358084 IPI C 64 kDa, alpha subunit of oligosaccharyltransferase complex; homologous to mammalian ribophorin I YJL002C|NLT1 gene taxon:4932 20020328 SGD
+SGD S000003539 OST1 GO:0008250 SGD_REF:S000050479|PMID:9405463 IPI C 64 kDa, alpha subunit of oligosaccharyltransferase complex; homologous to mammalian ribophorin I YJL002C|NLT1 gene taxon:4932 20050504 SGD
+SGD S000003539 OST1 GO:0008250 SGD_REF:S000113605|PMID:16297388 IPI C 64 kDa, alpha subunit of oligosaccharyltransferase complex; homologous to mammalian ribophorin I YJL002C|NLT1 gene taxon:4932 20060203 SGD
+SGD S000003539 OST1 GO:0004579 SGD_REF:S000048528|PMID:9015380 IDA F 64 kDa, alpha subunit of oligosaccharyltransferase complex; homologous to mammalian ribophorin I YJL002C|NLT1 gene taxon:4932 20010118 SGD
+SGD S000003539 OST1 GO:0006487 SGD_REF:S000048528|PMID:9015380 IDA P 64 kDa, alpha subunit of oligosaccharyltransferase complex; homologous to mammalian ribophorin I YJL002C|NLT1 gene taxon:4932 20010118 SGD
+SGD S000003539 OST1 GO:0018279 SGD_REF:S000041850|PMID:9988747 IPI P 64 kDa, alpha subunit of oligosaccharyltransferase complex; homologous to mammalian ribophorin I YJL002C|NLT1 gene taxon:4932 20020328 SGD
+SGD S000005629 OST2 GO:0008250 SGD_REF:S000050823|PMID:10358084 IPI C 40% identical to vertebrate DAD1 protein, oligosaccharyltransferase complex 16 kDa epsilon subunit YOR103C gene taxon:4932 20020328 SGD
+SGD S000005629 OST2 GO:0008250 SGD_REF:S000050479|PMID:9405463 IPI C 40% identical to vertebrate DAD1 protein, oligosaccharyltransferase complex 16 kDa epsilon subunit YOR103C gene taxon:4932 20050504 SGD
+SGD S000005629 OST2 GO:0008250 SGD_REF:S000113605|PMID:16297388 IPI C 40% identical to vertebrate DAD1 protein, oligosaccharyltransferase complex 16 kDa epsilon subunit YOR103C gene taxon:4932 20060203 SGD
+SGD S000005629 OST2 GO:0004579 SGD_REF:S000042079|PMID:9135133 TAS F 40% identical to vertebrate DAD1 protein, oligosaccharyltransferase complex 16 kDa epsilon subunit YOR103C gene taxon:4932 20021001 SGD
+SGD S000005629 OST2 GO:0004579 SGD_REF:S000050479|PMID:9405463 IPI F 40% identical to vertebrate DAD1 protein, oligosaccharyltransferase complex 16 kDa epsilon subunit YOR103C gene taxon:4932 20021001 SGD
+SGD S000005629 OST2 GO:0006487 SGD_REF:S000042079|PMID:9135133 TAS P 40% identical to vertebrate DAD1 protein, oligosaccharyltransferase complex 16 kDa epsilon subunit YOR103C gene taxon:4932 20021001 SGD
+SGD S000005629 OST2 GO:0006487 SGD_REF:S000050479|PMID:9405463 IPI P 40% identical to vertebrate DAD1 protein, oligosaccharyltransferase complex 16 kDa epsilon subunit YOR103C gene taxon:4932 20021001 SGD
+SGD S000005611 OST3 GO:0008250 SGD_REF:S000050823|PMID:10358084 IPI C oligosaccharyl transferase glycoprotein complex 34 kDa gamma subunit YOR085W gene taxon:4932 20020328 SGD
+SGD S000005611 OST3 GO:0008250 SGD_REF:S000113605|PMID:16297388 IPI C oligosaccharyl transferase glycoprotein complex 34 kDa gamma subunit YOR085W gene taxon:4932 20060203 SGD
+SGD S000005611 OST3 GO:0008250 SGD_REF:S000050479|PMID:9405463 IPI C oligosaccharyl transferase glycoprotein complex 34 kDa gamma subunit YOR085W gene taxon:4932 20050504 SGD
+SGD S000005611 OST3 GO:0016021 SGD_REF:S000047177|PMID:7622558 IMP C oligosaccharyl transferase glycoprotein complex 34 kDa gamma subunit YOR085W gene taxon:4932 20010118 SGD
+SGD S000005611 OST3 GO:0004579 SGD_REF:S000047177|PMID:7622558 IMP F oligosaccharyl transferase glycoprotein complex 34 kDa gamma subunit YOR085W gene taxon:4932 20010118 SGD
+SGD S000005611 OST3 GO:0004579 SGD_REF:S000050479|PMID:9405463 IPI F oligosaccharyl transferase glycoprotein complex 34 kDa gamma subunit YOR085W gene taxon:4932 20021001 SGD
+SGD S000005611 OST3 GO:0006461 SGD_REF:S000050823|PMID:10358084 IMP P oligosaccharyl transferase glycoprotein complex 34 kDa gamma subunit YOR085W gene taxon:4932 20021104 SGD
+SGD S000005611 OST3 GO:0006486 SGD_REF:S000047177|PMID:7622558 IMP P oligosaccharyl transferase glycoprotein complex 34 kDa gamma subunit YOR085W gene taxon:4932 20010118 SGD
+SGD S000005611 OST3 GO:0006487 SGD_REF:S000050479|PMID:9405463 IPI P oligosaccharyl transferase glycoprotein complex 34 kDa gamma subunit YOR085W gene taxon:4932 20021001 SGD
+SGD S000002391 OST4 GO:0005789 SGD_REF:S000039944|PMID:10677492 IMP C 3.6 kDa protein YDL232W gene taxon:4932 20021008 SGD
+SGD S000002391 OST4 GO:0008250 SGD_REF:S000050479|PMID:9405463 IPI C 3.6 kDa protein YDL232W gene taxon:4932 20050325 SGD
+SGD S000002391 OST4 GO:0008250 SGD_REF:S000113605|PMID:16297388 IPI C 3.6 kDa protein YDL232W gene taxon:4932 20060203 SGD
+SGD S000002391 OST4 GO:0004579 SGD_REF:S000050479|PMID:9405463 IPI F 3.6 kDa protein YDL232W gene taxon:4932 20021001 SGD
+SGD S000002391 OST4 GO:0030674 SGD_REF:S000073368|PMID:12810948 IDA F 3.6 kDa protein YDL232W gene taxon:4932 20030702 SGD
+SGD S000002391 OST4 GO:0006487 SGD_REF:S000042079|PMID:9135133 TAS P 3.6 kDa protein YDL232W gene taxon:4932 20021001 SGD
+SGD S000002391 OST4 GO:0006487 SGD_REF:S000050479|PMID:9405463 IPI P 3.6 kDa protein YDL232W gene taxon:4932 20021001 SGD
+SGD S000003194 OST5 GO:0008250 SGD_REF:S000050823|PMID:10358084 IPI C oligosaccharyltransferase complex 9.5 kDa zeta subunit YGL226C-A gene taxon:4932 20020328 SGD
+SGD S000003194 OST5 GO:0008250 SGD_REF:S000113605|PMID:16297388 IPI C oligosaccharyltransferase complex 9.5 kDa zeta subunit YGL226C-A gene taxon:4932 20060203 SGD
+SGD S000003194 OST5 GO:0008250 SGD_REF:S000050479|PMID:9405463 IPI C oligosaccharyltransferase complex 9.5 kDa zeta subunit YGL226C-A gene taxon:4932 20050504 SGD
+SGD S000003194 OST5 GO:0004579 SGD_REF:S000050479|PMID:9405463 IPI F oligosaccharyltransferase complex 9.5 kDa zeta subunit YGL226C-A gene taxon:4932 20021001 SGD
+SGD S000003194 OST5 GO:0006487 SGD_REF:S000050479|PMID:9405463 IPI P oligosaccharyltransferase complex 9.5 kDa zeta subunit YGL226C-A gene taxon:4932 20021001 SGD
+SGD S000004481 OST6 GO:0008250 SGD_REF:S000050823|PMID:10358084 IPI C N-oligosaccharyltransferase complex 37kDa subunit (putative) YML019W gene taxon:4932 20020328 SGD
+SGD S000004481 OST6 GO:0008250 SGD_REF:S000113605|PMID:16297388 IPI C N-oligosaccharyltransferase complex 37kDa subunit (putative) YML019W gene taxon:4932 20060203 SGD
+SGD S000004481 OST6 GO:0004579 SGD_REF:S000050823|PMID:10358084 IPI F N-oligosaccharyltransferase complex 37kDa subunit (putative) YML019W gene taxon:4932 20021104 SGD
+SGD S000004481 OST6 GO:0006461 SGD_REF:S000050823|PMID:10358084 IMP P N-oligosaccharyltransferase complex 37kDa subunit (putative) YML019W gene taxon:4932 20021104 SGD
+SGD S000004481 OST6 GO:0018279 SGD_REF:S000050823|PMID:10358084 IGI P N-oligosaccharyltransferase complex 37kDa subunit (putative) YML019W gene taxon:4932 20020328 SGD
+SGD S000004481 OST6 GO:0018279 SGD_REF:S000050823|PMID:10358084 IMP P N-oligosaccharyltransferase complex 37kDa subunit (putative) YML019W gene taxon:4932 20020328 SGD
+SGD S000005781 OSW1 GO:0005628 SGD_REF:S000079982|PMID:15590821 IDA C YOR255W gene taxon:4932 20050127 SGD
+SGD S000005781 OSW1 GO:0005554 SGD_REF:S000069584 ND F YOR255W gene taxon:4932 20050127 SGD
+SGD S000005781 OSW1 GO:0030476 SGD_REF:S000079982|PMID:15590821 IMP P YOR255W gene taxon:4932 20050127 SGD
+SGD S000004044 OSW2 GO:0005628 SGD_REF:S000079982|PMID:15590821 IDA C YLR054C gene taxon:4932 20050127 SGD
+SGD S000004044 OSW2 GO:0005737 SGD_REF:S000079982|PMID:15590821 IDA C YLR054C gene taxon:4932 20050127 SGD
+SGD S000004044 OSW2 GO:0005554 SGD_REF:S000069584 ND F YLR054C gene taxon:4932 20050127 SGD
+SGD S000004044 OSW2 GO:0030476 SGD_REF:S000079982|PMID:15590821 IMP P YLR054C gene taxon:4932 20050127 SGD
+SGD S000001850 OTU1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C De-ubiquitylation enzyme (DUB) of the OTU (ovarian tumor) family YFL044C|YOD1 gene taxon:4932 20031028 SGD
+SGD S000001850 OTU1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C De-ubiquitylation enzyme (DUB) of the OTU (ovarian tumor) family YFL044C|YOD1 gene taxon:4932 20031028 SGD
+SGD S000001850 OTU1 GO:0004843 SGD_REF:S000114196|PMID:16427015 IDA F De-ubiquitylation enzyme (DUB) of the OTU (ovarian tumor) family YFL044C|YOD1 gene taxon:4932 20060203 SGD
+SGD S000001850 OTU1 GO:0006512 SGD_REF:S000114196|PMID:16427015 IGI P De-ubiquitylation enzyme (DUB) of the OTU (ovarian tumor) family YFL044C|YOD1 gene taxon:4932 20060203 SGD
+SGD S000001850 OTU1 GO:0006512 SGD_REF:S000114196|PMID:16427015 IPI P De-ubiquitylation enzyme (DUB) of the OTU (ovarian tumor) family YFL044C|YOD1 gene taxon:4932 20060203 SGD
+SGD S000001850 OTU1 GO:0016579 SGD_REF:S000114196|PMID:16427015 IDA P De-ubiquitylation enzyme (DUB) of the OTU (ovarian tumor) family YFL044C|YOD1 gene taxon:4932 20060203 SGD
+SGD S000001850 OTU1 GO:0045449 SGD_REF:S000081066|PMID:15755922 IMP P De-ubiquitylation enzyme (DUB) of the OTU (ovarian tumor) family YFL044C|YOD1 gene taxon:4932 20050420 SGD
+SGD S000001005 OTU2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YHL013C gene taxon:4932 20031028 SGD
+SGD S000001005 OTU2 GO:0005554 SGD_REF:S000069584 ND F YHL013C gene taxon:4932 20060203 SGD
+SGD S000001005 OTU2 GO:0000004 SGD_REF:S000069584 ND P YHL013C gene taxon:4932 20060203 SGD
+SGD S000000956 OXA1 GO:0005743 SGD_REF:S000058124|PMID:9171337 IDA C YER154W|PET1402 gene taxon:4932 20010118 SGD
+SGD S000000956 OXA1 GO:0008565 SGD_REF:S000039335|PMID:9482871 IMP F YER154W|PET1402 gene taxon:4932 20010118 SGD
+SGD S000000956 OXA1 GO:0008565 SGD_REF:S000039335|PMID:9482871 IPI F YER154W|PET1402 gene taxon:4932 20010118 SGD
+SGD S000000956 OXA1 GO:0045039 SGD_REF:S000039335|PMID:9482871 IMP P YER154W|PET1402 gene taxon:4932 20031203 SGD
+SGD S000000956 OXA1 GO:0045039 SGD_REF:S000039335|PMID:9482871 IPI P YER154W|PET1402 gene taxon:4932 20031203 SGD
+SGD S000006117 OXR1 GO:0005739 SGD_REF:S000076223|PMID:15060142 IDA C YPL196W gene taxon:4932 20040927 SGD
+SGD S000006117 OXR1 GO:0005554 SGD_REF:S000069584 ND F YPL196W gene taxon:4932 20040927 SGD
+SGD S000006117 OXR1 GO:0006979 SGD_REF:S000061002|PMID:11114193 IMP P YPL196W gene taxon:4932 20021011 SGD
+SGD S000001222 OYE2 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C NAPDH dehydrogenase (old yellow enzyme), isoform 2 YHR179W|Old Yellow Enzyme gene taxon:4932 20031028 SGD
+SGD S000001222 OYE2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C NAPDH dehydrogenase (old yellow enzyme), isoform 2 YHR179W|Old Yellow Enzyme gene taxon:4932 20031028 SGD
+SGD S000001222 OYE2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C NAPDH dehydrogenase (old yellow enzyme), isoform 2 YHR179W|Old Yellow Enzyme gene taxon:4932 20040813 SGD
+SGD S000001222 OYE2 GO:0003959 SGD_REF:S000057760|PMID:8454584 IDA F NAPDH dehydrogenase (old yellow enzyme), isoform 2 YHR179W|Old Yellow Enzyme gene taxon:4932 20021001 SGD
+SGD S000001222 OYE2 GO:0003959 SGD_REF:S000057760|PMID:8454584 ISS F NAPDH dehydrogenase (old yellow enzyme), isoform 2 YHR179W|Old Yellow Enzyme gene taxon:4932 20021001 SGD
+SGD S000001222 OYE2 GO:0000004 SGD_REF:S000069584 ND P NAPDH dehydrogenase (old yellow enzyme), isoform 2 YHR179W|Old Yellow Enzyme gene taxon:4932 20021009 SGD
+SGD S000006092 OYE3 GO:0008372 SGD_REF:S000069584 ND C NADPH dehydrogenase YPL171C|Old Yellow Enzyme|ZRG6 gene taxon:4932 20021007 SGD
+SGD S000006092 OYE3 GO:0003959 SGD_REF:S000050253|PMID:7836424 IDA F NADPH dehydrogenase YPL171C|Old Yellow Enzyme|ZRG6 gene taxon:4932 20021001 SGD
+SGD S000006092 OYE3 GO:0003959 SGD_REF:S000050253|PMID:7836424 ISS F NADPH dehydrogenase YPL171C|Old Yellow Enzyme|ZRG6 gene taxon:4932 20021001 SGD
+SGD S000006092 OYE3 GO:0000004 SGD_REF:S000050253|PMID:7836424 NAS P NADPH dehydrogenase YPL171C|Old Yellow Enzyme|ZRG6 gene taxon:4932 20021001 SGD
+SGD S000002478 PAA1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C polyamine acetyltransferase YDR071C gene taxon:4932 20031028 SGD
+SGD S000002478 PAA1 GO:0004059 SGD_REF:S000077173|PMID:11559708 IDA F polyamine acetyltransferase YDR071C gene taxon:4932 20041001 SGD
+SGD S000002478 PAA1 GO:0004145 SGD_REF:S000080964|PMID:15723835 IDA F polyamine acetyltransferase YDR071C gene taxon:4932 20050323 SGD
+SGD S000002478 PAA1 GO:0006325 SGD_REF:S000080964|PMID:15723835 IMP P polyamine acetyltransferase YDR071C gene taxon:4932 20050323 SGD
+SGD S000000967 PAB1 GO:0005634 SGD_REF:S000069459|PMID:11914276 IDA C poly(A) binding protein YER165W gene taxon:4932 20020507 SGD
+SGD S000000967 PAB1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C poly(A) binding protein YER165W gene taxon:4932 20020507 SGD
+SGD S000000967 PAB1 GO:0005840 SGD_REF:S000041867|PMID:8631901 IDA C poly(A) binding protein YER165W gene taxon:4932 20020402 SGD
+SGD S000000967 PAB1 GO:0008143 SGD_REF:S000069475|PMID:9193001 IMP F poly(A) binding protein YER165W gene taxon:4932 20020402 SGD
+SGD S000000967 PAB1 GO:0008143 SGD_REF:S000069475|PMID:9193001 IDA F poly(A) binding protein YER165W gene taxon:4932 20020402 SGD
+SGD S000000967 PAB1 GO:0006446 SGD_REF:S000053705|PMID:10357826 IMP P poly(A) binding protein YER165W gene taxon:4932 20020402 SGD
+SGD S000000967 PAB1 GO:0006446 SGD_REF:S000053705|PMID:10357826 IDA P poly(A) binding protein YER165W gene taxon:4932 20020402 SGD
+SGD S000005795 PAC1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YOR269W gene taxon:4932 20020507 SGD
+SGD S000005795 PAC1 GO:0005881 SGD_REF:S000072477|PMID:12566428 IDA C YOR269W gene taxon:4932 20030211 SGD
+SGD S000005795 PAC1 GO:0005554 SGD_REF:S000069584 ND F YOR269W gene taxon:4932 20021104 SGD
+SGD S000005795 PAC1 GO:0030473 SGD_REF:S000072477|PMID:12566428 IMP P YOR269W gene taxon:4932 20030211 SGD
+SGD S000003310 PAC10 GO:0005737 SGD_REF:S000049112|PMID:9463374 IDA C bovine NABC complex component homolog, non-native actin binding complex polypeptide 3, prefoldin complex subunit YGR078C|GIM2|PFD3|RKS2 gene taxon:4932 20020617 SGD
+SGD S000003310 PAC10 GO:0016272 SGD_REF:S000058336|PMID:9630229 ISS C bovine NABC complex component homolog, non-native actin binding complex polypeptide 3, prefoldin complex subunit YGR078C|GIM2|PFD3|RKS2 gene taxon:4932 20031215 SGD
+SGD S000003310 PAC10 GO:0016272 SGD_REF:S000049112|PMID:9463374 IPI SGD:S000004190|SGD:S000004559 C bovine NABC complex component homolog, non-native actin binding complex polypeptide 3, prefoldin complex subunit YGR078C|GIM2|PFD3|RKS2 gene taxon:4932 20031215 SGD
+SGD S000003310 PAC10 GO:0015631 SGD_REF:S000049112|PMID:9463374 IDA F bovine NABC complex component homolog, non-native actin binding complex polypeptide 3, prefoldin complex subunit YGR078C|GIM2|PFD3|RKS2 gene taxon:4932 20021101 SGD
+SGD S000003310 PAC10 GO:0007021 SGD_REF:S000039864|PMID:9611197 IMP P bovine NABC complex component homolog, non-native actin binding complex polypeptide 3, prefoldin complex subunit YGR078C|GIM2|PFD3|RKS2 gene taxon:4932 20010118 SGD
+SGD S000003310 PAC10 GO:0007021 SGD_REF:S000039864|PMID:9611197 IGI P bovine NABC complex component homolog, non-native actin binding complex polypeptide 3, prefoldin complex subunit YGR078C|GIM2|PFD3|RKS2 gene taxon:4932 20010118 SGD
+SGD S000002896 PAC11 GO:0005868 SGD_REF:S000080445|PMID:15642746 TAS C YDR488C gene taxon:4932 20050224 SGD
+SGD S000002896 PAC11 GO:0005881 SGD_REF:S000046660|PMID:9658168 IPI C YDR488C gene taxon:4932 20041203 SGD
+SGD S000002896 PAC11 GO:0005881 SGD_REF:S000080445|PMID:15642746 IDA C YDR488C gene taxon:4932 20050125 SGD
+SGD S000002896 PAC11 GO:0003777 SGD_REF:S000051765|PMID:9201714 ISS F YDR488C gene taxon:4932 20010118 SGD
+SGD S000002896 PAC11 contributes_to GO:0008574 SGD_REF:S000080445|PMID:15642746 IMP F YDR488C gene taxon:4932 20050125 SGD
+SGD S000002896 PAC11 GO:0007017 SGD_REF:S000051765|PMID:9201714 IGI P YDR488C gene taxon:4932 20010118 SGD
+SGD S000002896 PAC11 GO:0030473 SGD_REF:S000080445|PMID:15642746 IMP P YDR488C gene taxon:4932 20050125 SGD
+SGD S000000809 PAC2 GO:0008372 SGD_REF:S000069584 ND C tubulin folding cofactor E YER007W gene taxon:4932 20030203 SGD
+SGD S000000809 PAC2 GO:0043014 SGD_REF:S000058454|PMID:9885248 IPI SGD:S000004550 F tubulin folding cofactor E YER007W gene taxon:4932 20040722 SGD
+SGD S000000809 PAC2 GO:0007023 SGD_REF:S000058454|PMID:9885248 TAS P tubulin folding cofactor E YER007W gene taxon:4932 20010118 SGD
+SGD S000000809 PAC2 GO:0007024 SGD_REF:S000058454|PMID:9885248 TAS P tubulin folding cofactor E YER007W gene taxon:4932 20010118 SGD
+SGD S000002946 PAD1 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C phenylacrylic acid decarboxylase YDR538W|POF1 gene taxon:4932 20031028 SGD
+SGD S000002946 PAD1 GO:0016831 SGD_REF:S000066157|PMID:11693915 IDA F phenylacrylic acid decarboxylase YDR538W|POF1 gene taxon:4932 20020711 SGD
+SGD S000002946 PAD1 GO:0019439 SGD_REF:S000066157|PMID:11693915 IDA P phenylacrylic acid decarboxylase YDR538W|POF1 gene taxon:4932 20020711 SGD
+SGD S000000483 PAF1 GO:0005634 SGD_REF:S000076633|PMID:15149594 IDA C YBR279W gene taxon:4932 20040804 SGD
+SGD S000000483 PAF1 GO:0005634 SGD_REF:S000080456|PMID:15643076 IDA C YBR279W gene taxon:4932 20050228 SGD
+SGD S000000483 PAF1 GO:0008023 SGD_REF:S000071357|PMID:12242279 IPI C YBR279W gene taxon:4932 20021004 SGD
+SGD S000000483 PAF1 GO:0016593 SGD_REF:S000073599|PMID:12773564 TAS C YBR279W gene taxon:4932 20040129 SGD
+SGD S000000483 PAF1 GO:0016593 SGD_REF:S000058039|PMID:9032243 IPI SGD:S000004410 C YBR279W gene taxon:4932 20051108 SGD
+SGD S000000483 PAF1 GO:0016944 SGD_REF:S000071357|PMID:12242279 IPI F YBR279W gene taxon:4932 20021004 SGD
+SGD S000000483 PAF1 GO:0006310 SGD_REF:S000041293|PMID:9891041 IMP P YBR279W gene taxon:4932 20051108 SGD
+SGD S000000483 PAF1 GO:0006368 SGD_REF:S000071357|PMID:12242279 IPI P YBR279W gene taxon:4932 20021004 SGD
+SGD S000000483 PAF1 GO:0016571 SGD_REF:S000073147|PMID:12667454 IMP P YBR279W gene taxon:4932 20050503 SGD
+SGD S000004775 PAH1 GO:0005624 SGD_REF:S000114345|PMID:16467296 IDA C phosphatidate phosphohydrolase YMR165C|SMP2 gene taxon:4932 20060215 SGD
+SGD S000004775 PAH1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C phosphatidate phosphohydrolase YMR165C|SMP2 gene taxon:4932 20031028 SGD
+SGD S000004775 PAH1 GO:0008195 SGD_REF:S000114345|PMID:16467296 IMP F phosphatidate phosphohydrolase YMR165C|SMP2 gene taxon:4932 20060215 SGD
+SGD S000004775 PAH1 GO:0008195 SGD_REF:S000114345|PMID:16467296 IDA F phosphatidate phosphohydrolase YMR165C|SMP2 gene taxon:4932 20060215 SGD
+SGD S000004775 PAH1 GO:0006276 SGD_REF:S000056077|PMID:8437575 IMP P phosphatidate phosphohydrolase YMR165C|SMP2 gene taxon:4932 20021001 SGD
+SGD S000004775 PAH1 GO:0008610 SGD_REF:S000114345|PMID:16467296 IMP P phosphatidate phosphohydrolase YMR165C|SMP2 gene taxon:4932 20060215 SGD
+SGD S000004775 PAH1 GO:0009060 SGD_REF:S000056077|PMID:8437575 IMP P phosphatidate phosphohydrolase YMR165C|SMP2 gene taxon:4932 20021001 SGD
+SGD S000004786 PAI3 GO:0005737 SGD_REF:S000051253|PMID:2037077 TAS C inhibitor of proteinase Pep4p YMR174C gene taxon:4932 20010118 SGD
+SGD S000004786 PAI3 GO:0004866 SGD_REF:S000051253|PMID:2037077 IMP F inhibitor of proteinase Pep4p YMR174C gene taxon:4932 20010118 SGD
+SGD S000004786 PAI3 GO:0007039 SGD_REF:S000051253|PMID:2037077 IMP P inhibitor of proteinase Pep4p YMR174C gene taxon:4932 20010118 SGD
+SGD S000002659 PAM1 GO:0005933 SGD_REF:S000074185|PMID:14562095 IDA C YDR251W gene taxon:4932 20031028 SGD
+SGD S000002659 PAM1 GO:0005935 SGD_REF:S000074185|PMID:14562095 IDA C YDR251W gene taxon:4932 20031028 SGD
+SGD S000002659 PAM1 GO:0005554 SGD_REF:S000069584 ND F YDR251W gene taxon:4932 20021206 SGD
+SGD S000002659 PAM1 GO:0007124 SGD_REF:S000044195|PMID:8106383 IMP P YDR251W gene taxon:4932 20010118 SGD
+SGD S000003640 PAM16 GO:0001405 SGD_REF:S000075545|PMID:14981507 IDA C YJL104W|MIA1|TIM16 gene taxon:4932 20040308 SGD
+SGD S000003640 PAM16 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YJL104W|MIA1|TIM16 gene taxon:4932 20031028 SGD
+SGD S000003640 PAM16 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YJL104W|MIA1|TIM16 gene taxon:4932 20040924 SGD
+SGD S000003640 PAM16 GO:0005744 SGD_REF:S000075546|PMID:14981506 IDA C YJL104W|MIA1|TIM16 gene taxon:4932 20040713 SGD
+SGD S000003640 PAM16 GO:0005515 SGD_REF:S000075545|PMID:14981507 IDA F YJL104W|MIA1|TIM16 gene taxon:4932 20040308 SGD
+SGD S000003640 PAM16 GO:0005515 SGD_REF:S000075546|PMID:14981506 IDA F YJL104W|MIA1|TIM16 gene taxon:4932 20040713 SGD
+SGD S000003640 PAM16 GO:0008565 SGD_REF:S000075545|PMID:14981507 IMP F YJL104W|MIA1|TIM16 gene taxon:4932 20040308 SGD
+SGD S000003640 PAM16 GO:0008565 SGD_REF:S000075546|PMID:14981506 IPI F YJL104W|MIA1|TIM16 gene taxon:4932 20040713 SGD
+SGD S000003640 PAM16 GO:0008565 SGD_REF:S000075546|PMID:14981506 IMP F YJL104W|MIA1|TIM16 gene taxon:4932 20040713 SGD
+SGD S000003640 PAM16 GO:0030150 SGD_REF:S000075545|PMID:14981507 IMP P YJL104W|MIA1|TIM16 gene taxon:4932 20040308 SGD
+SGD S000003640 PAM16 GO:0030150 SGD_REF:S000075546|PMID:14981506 IPI P YJL104W|MIA1|TIM16 gene taxon:4932 20040713 SGD
+SGD S000003640 PAM16 GO:0030150 SGD_REF:S000075545|PMID:14981507 IPI P YJL104W|MIA1|TIM16 gene taxon:4932 20040713 SGD
+SGD S000003640 PAM16 GO:0030150 SGD_REF:S000075546|PMID:14981506 IMP P YJL104W|MIA1|TIM16 gene taxon:4932 20040713 SGD
+SGD S000001773 PAM17 GO:0001405 SGD_REF:S000086111 IPI C YKR065C|FMP18 gene taxon:4932 20050815 SGD
+SGD S000001773 PAM17 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YKR065C|FMP18 gene taxon:4932 20040928 SGD
+SGD S000001773 PAM17 GO:0016021 SGD_REF:S000072825|PMID:12524434 ISS C YKR065C|FMP18 gene taxon:4932 20030409 SGD
+SGD S000001773 PAM17 GO:0005554 SGD_REF:S000069584 ND F YKR065C|FMP18 gene taxon:4932 20021126 SGD
+SGD S000001773 PAM17 GO:0030150 SGD_REF:S000086111 IMP P YKR065C|FMP18 gene taxon:4932 20050815 SGD
+SGD S000003998 PAM18 GO:0001405 SGD_REF:S000074354|PMID:14638855 IPI C DnaJ-like protein, cochaperone YLR008C|TIM14 gene taxon:4932 20031218 SGD
+SGD S000003998 PAM18 GO:0001405 SGD_REF:S000074353|PMID:14517234 IPI C DnaJ-like protein, cochaperone YLR008C|TIM14 gene taxon:4932 20031218 SGD
+SGD S000003998 PAM18 GO:0005744 SGD_REF:S000074353|PMID:14517234 IPI C DnaJ-like protein, cochaperone YLR008C|TIM14 gene taxon:4932 20031126 SGD
+SGD S000003998 PAM18 GO:0005744 SGD_REF:S000074354|PMID:14638855 IPI C DnaJ-like protein, cochaperone YLR008C|TIM14 gene taxon:4932 20031210 SGD
+SGD S000003998 PAM18 GO:0001671 SGD_REF:S000074354|PMID:14638855 IDA F DnaJ-like protein, cochaperone YLR008C|TIM14 gene taxon:4932 20031210 SGD
+SGD S000003998 PAM18 GO:0001671 SGD_REF:S000075099|PMID:14605210 IDA F DnaJ-like protein, cochaperone YLR008C|TIM14 gene taxon:4932 20031210 SGD
+SGD S000003998 PAM18 GO:0008565 SGD_REF:S000074353|PMID:14517234 IMP F DnaJ-like protein, cochaperone YLR008C|TIM14 gene taxon:4932 20031126 SGD
+SGD S000003998 PAM18 GO:0008565 SGD_REF:S000074353|PMID:14517234 IPI F DnaJ-like protein, cochaperone YLR008C|TIM14 gene taxon:4932 20031126 SGD
+SGD S000003998 PAM18 GO:0051082 SGD_REF:S000075214|PMID:14690591 ISS F DnaJ-like protein, cochaperone YLR008C|TIM14 gene taxon:4932 20040105 SGD
+SGD S000003998 PAM18 GO:0030150 SGD_REF:S000074353|PMID:14517234 IPI P DnaJ-like protein, cochaperone YLR008C|TIM14 gene taxon:4932 20031126 SGD
+SGD S000003998 PAM18 GO:0030150 SGD_REF:S000075099|PMID:14605210 IMP P DnaJ-like protein, cochaperone YLR008C|TIM14 gene taxon:4932 20031210 SGD
+SGD S000003998 PAM18 GO:0030150 SGD_REF:S000074354|PMID:14638855 IMP P DnaJ-like protein, cochaperone YLR008C|TIM14 gene taxon:4932 20031210 SGD
+SGD S000003998 PAM18 GO:0030150 SGD_REF:S000075099|PMID:14605210 IPI P DnaJ-like protein, cochaperone YLR008C|TIM14 gene taxon:4932 20031210 SGD
+SGD S000003998 PAM18 GO:0030150 SGD_REF:S000074354|PMID:14638855 IPI P DnaJ-like protein, cochaperone YLR008C|TIM14 gene taxon:4932 20031210 SGD
+SGD S000003998 PAM18 GO:0030150 SGD_REF:S000074353|PMID:14517234 IMP P DnaJ-like protein, cochaperone YLR008C|TIM14 gene taxon:4932 20031126 SGD
+SGD S000001445 PAN1 GO:0005886 SGD_REF:S000069459|PMID:11914276 IDA C YIR006C|DIM2|MDP3|MIP3 gene taxon:4932 20020508 SGD
+SGD S000001445 PAN1 GO:0030479 SGD_REF:S000041005|PMID:10652251 IDA C YIR006C|DIM2|MDP3|MIP3 gene taxon:4932 20010118 SGD
+SGD S000001445 PAN1 GO:0030674 SGD_REF:S000074352|PMID:11792548 IPI F YIR006C|DIM2|MDP3|MIP3 gene taxon:4932 20040107 SGD
+SGD S000001445 PAN1 GO:0000147 SGD_REF:S000041005|PMID:10652251 TAS P YIR006C|DIM2|MDP3|MIP3 gene taxon:4932 20010118 SGD
+SGD S000001445 PAN1 GO:0000910 SGD_REF:S000041005|PMID:10652251 IMP P YIR006C|DIM2|MDP3|MIP3 gene taxon:4932 20010119 SGD
+SGD S000001445 PAN1 GO:0006897 SGD_REF:S000041005|PMID:10652251 IMP P YIR006C|DIM2|MDP3|MIP3 gene taxon:4932 20010118 SGD
+SGD S000001445 PAN1 GO:0007120 SGD_REF:S000041005|PMID:10652251 IMP P YIR006C|DIM2|MDP3|MIP3 gene taxon:4932 20010118 SGD
+SGD S000001445 PAN1 GO:0007121 SGD_REF:S000041005|PMID:10652251 IMP P YIR006C|DIM2|MDP3|MIP3 gene taxon:4932 20010118 SGD
+SGD S000003062 PAN2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C poly(A) ribonuclease 135 kDa subunit YGL094C gene taxon:4932 20031028 SGD
+SGD S000003062 PAN2 GO:0031251 SGD_REF:S000051984|PMID:8816488 IDA C poly(A) ribonuclease 135 kDa subunit YGL094C gene taxon:4932 20050302 SGD
+SGD S000003062 PAN2 GO:0004535 SGD_REF:S000070046|PMID:11953437 TAS F poly(A) ribonuclease 135 kDa subunit YGL094C gene taxon:4932 20021001 SGD
+SGD S000003062 PAN2 GO:0004535 SGD_REF:S000051984|PMID:8816488 IDA F poly(A) ribonuclease 135 kDa subunit YGL094C gene taxon:4932 20021118 SGD
+SGD S000003062 PAN2 GO:0006301 SGD_REF:S000070046|PMID:11953437 IGI P poly(A) ribonuclease 135 kDa subunit YGL094C gene taxon:4932 20021118 SGD
+SGD S000003062 PAN2 GO:0006301 SGD_REF:S000070046|PMID:11953437 IPI P poly(A) ribonuclease 135 kDa subunit YGL094C gene taxon:4932 20021118 SGD
+SGD S000003062 PAN2 GO:0006397 SGD_REF:S000039732|PMID:8550599 IMP P poly(A) ribonuclease 135 kDa subunit YGL094C gene taxon:4932 20010118 SGD
+SGD S000003062 PAN2 GO:0006397 SGD_REF:S000039732|PMID:8550599 IPI P poly(A) ribonuclease 135 kDa subunit YGL094C gene taxon:4932 20010118 SGD
+SGD S000003062 PAN2 GO:0031124 SGD_REF:S000039732|PMID:8550599 IMP P poly(A) ribonuclease 135 kDa subunit YGL094C gene taxon:4932 20050512 SGD
+SGD S000003062 PAN2 GO:0031124 SGD_REF:S000039732|PMID:8550599 IPI P poly(A) ribonuclease 135 kDa subunit YGL094C gene taxon:4932 20050512 SGD
+SGD S000001508 PAN3 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C Pab1p-dependent poly(A) ribonuclease (PAN) 76 kDa subunit YKL025C|ECM35 gene taxon:4932 20031028 SGD
+SGD S000001508 PAN3 GO:0031251 SGD_REF:S000051984|PMID:8816488 IDA C Pab1p-dependent poly(A) ribonuclease (PAN) 76 kDa subunit YKL025C|ECM35 gene taxon:4932 20050302 SGD
+SGD S000001508 PAN3 GO:0004535 SGD_REF:S000051984|PMID:8816488 IDA F Pab1p-dependent poly(A) ribonuclease (PAN) 76 kDa subunit YKL025C|ECM35 gene taxon:4932 20021118 SGD
+SGD S000001508 PAN3 GO:0006281 SGD_REF:S000070046|PMID:11953437 IDA P Pab1p-dependent poly(A) ribonuclease (PAN) 76 kDa subunit YKL025C|ECM35 gene taxon:4932 20021001 SGD
+SGD S000001508 PAN3 GO:0006301 SGD_REF:S000070046|PMID:11953437 IGI P Pab1p-dependent poly(A) ribonuclease (PAN) 76 kDa subunit YKL025C|ECM35 gene taxon:4932 20021118 SGD
+SGD S000001508 PAN3 GO:0006301 SGD_REF:S000070046|PMID:11953437 IPI P Pab1p-dependent poly(A) ribonuclease (PAN) 76 kDa subunit YKL025C|ECM35 gene taxon:4932 20021118 SGD
+SGD S000001508 PAN3 GO:0031124 SGD_REF:S000051984|PMID:8816488 IMP P Pab1p-dependent poly(A) ribonuclease (PAN) 76 kDa subunit YKL025C|ECM35 gene taxon:4932 20050512 SGD
+SGD S000001508 PAN3 GO:0031124 SGD_REF:S000051984|PMID:8816488 IPI P Pab1p-dependent poly(A) ribonuclease (PAN) 76 kDa subunit YKL025C|ECM35 gene taxon:4932 20050512 SGD
+SGD S000001105 PAN5 GO:0005625 SGD_REF:S000075303|PMID:11935221 IDA C YHR063C gene taxon:4932 20040114 SGD
+SGD S000001105 PAN5 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YHR063C gene taxon:4932 20031028 SGD
+SGD S000001105 PAN5 GO:0008677 SGD_REF:S000060103|PMID:11154694 ISS F YHR063C gene taxon:4932 20031006 SGD
+SGD S000001105 PAN5 GO:0015940 SGD_REF:S000060103|PMID:11154694 ISS P YHR063C gene taxon:4932 20031006 SGD
+SGD S000001407 PAN6 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C pantothenate synthase YIL145C gene taxon:4932 20031028 SGD
+SGD S000001407 PAN6 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C pantothenate synthase YIL145C gene taxon:4932 20031028 SGD
+SGD S000001407 PAN6 GO:0004592 SGD_REF:S000070199|PMID:10417331 IDA F pantothenate synthase YIL145C gene taxon:4932 20020801 SGD
+SGD S000001407 PAN6 GO:0004592 SGD_REF:S000070199|PMID:10417331 ISS F pantothenate synthase YIL145C gene taxon:4932 20020801 SGD
+SGD S000001407 PAN6 GO:0015940 SGD_REF:S000060103|PMID:11154694 IMP P pantothenate synthase YIL145C gene taxon:4932 20020801 SGD
+SGD S000001710 PAP1 GO:0005654 SGD_REF:S000041867|PMID:8631901 IPI C poly(A) polymerase YKR002W gene taxon:4932 20020404 SGD
+SGD S000001710 PAP1 GO:0005847 SGD_REF:S000074089|PMID:12819204 IPI C poly(A) polymerase YKR002W gene taxon:4932 20031013 SGD
+SGD S000001710 PAP1 GO:0004652 SGD_REF:S000056654|PMID:1840648 IDA F poly(A) polymerase YKR002W gene taxon:4932 20020404 SGD
+SGD S000001710 PAP1 GO:0006378 SGD_REF:S000051576|PMID:8524265 IMP P poly(A) polymerase YKR002W gene taxon:4932 20020404 SGD
+SGD S000001710 PAP1 GO:0006378 SGD_REF:S000056654|PMID:1840648 IDA P poly(A) polymerase YKR002W gene taxon:4932 20020404 SGD
+SGD S000001710 PAP1 GO:0006406 SGD_REF:S000059583|PMID:11142374 IMP P poly(A) polymerase YKR002W gene taxon:4932 20050415 SGD
+SGD S000005475 PAP2 GO:0005634 SGD_REF:S000055612|PMID:10066793 IDA C DNA polymerase sigma, poly(A) polymerase YOL115W|TRF4 gene taxon:4932 20010118 SGD
+SGD S000005475 PAP2 GO:0031499 SGD_REF:S000081843|PMID:15935758 IDA C DNA polymerase sigma, poly(A) polymerase YOL115W|TRF4 gene taxon:4932 20050621 SGD
+SGD S000005475 PAP2 GO:0031499 SGD_REF:S000081438|PMID:15828860 IPI SGD:S000002334|SGD:S000001341 C DNA polymerase sigma, poly(A) polymerase YOL115W|TRF4 gene taxon:4932 20050621 SGD
+SGD S000005475 PAP2 GO:0031499 SGD_REF:S000081438|PMID:15828860 IDA C DNA polymerase sigma, poly(A) polymerase YOL115W|TRF4 gene taxon:4932 20050621 SGD
+SGD S000005475 PAP2 GO:0031499 SGD_REF:S000081843|PMID:15935758 IPI SGD:S000002334|SGD:S000003586 C DNA polymerase sigma, poly(A) polymerase YOL115W|TRF4 gene taxon:4932 20050621 SGD
+SGD S000005475 PAP2 GO:0003887 SGD_REF:S000055910|PMID:10926539 IDA F DNA polymerase sigma, poly(A) polymerase YOL115W|TRF4 gene taxon:4932 20010118 SGD
+SGD S000005475 PAP2 NOT GO:0003887 SGD_REF:S000087060|PMID:16260630 IDA F DNA polymerase sigma, poly(A) polymerase YOL115W|TRF4 gene taxon:4932 20051108 SGD
+SGD S000005475 PAP2 NOT GO:0003887 SGD_REF:S000081293|PMID:12062100 IDA F DNA polymerase sigma, poly(A) polymerase YOL115W|TRF4 gene taxon:4932 20050610 SGD
+SGD S000005475 PAP2 NOT GO:0003887 SGD_REF:S000081438|PMID:15828860 NAS F DNA polymerase sigma, poly(A) polymerase YOL115W|TRF4 gene taxon:4932 20050610 SGD
+SGD S000005475 PAP2 GO:0004652 SGD_REF:S000081293|PMID:12062100 IDA F DNA polymerase sigma, poly(A) polymerase YOL115W|TRF4 gene taxon:4932 20050414 SGD
+SGD S000005475 PAP2 GO:0004652 SGD_REF:S000087060|PMID:16260630 IDA F DNA polymerase sigma, poly(A) polymerase YOL115W|TRF4 gene taxon:4932 20051108 SGD
+SGD S000005475 PAP2 GO:0004652 SGD_REF:S000114120|PMID:16374505 IGI SGD:S000005527 F DNA polymerase sigma, poly(A) polymerase YOL115W|TRF4 gene taxon:4932 20060120 SGD
+SGD S000005475 PAP2 GO:0004652 SGD_REF:S000114120|PMID:16374505 IDA F DNA polymerase sigma, poly(A) polymerase YOL115W|TRF4 gene taxon:4932 20060120 SGD
+SGD S000005475 PAP2 GO:0004652 SGD_REF:S000087060|PMID:16260630 IMP F DNA polymerase sigma, poly(A) polymerase YOL115W|TRF4 gene taxon:4932 20051108 SGD
+SGD S000005475 PAP2 GO:0004652 SGD_REF:S000081843|PMID:15935758 IDA F DNA polymerase sigma, poly(A) polymerase YOL115W|TRF4 gene taxon:4932 20050610 SGD
+SGD S000005475 PAP2 GO:0004652 SGD_REF:S000081438|PMID:15828860 IMP F DNA polymerase sigma, poly(A) polymerase YOL115W|TRF4 gene taxon:4932 20050610 SGD
+SGD S000005475 PAP2 GO:0004652 SGD_REF:S000081438|PMID:15828860 IDA F DNA polymerase sigma, poly(A) polymerase YOL115W|TRF4 gene taxon:4932 20050610 SGD
+SGD S000005475 PAP2 GO:0006265 SGD_REF:S000052027|PMID:8647385 IGI P DNA polymerase sigma, poly(A) polymerase YOL115W|TRF4 gene taxon:4932 20010118 SGD
+SGD S000005475 PAP2 GO:0006265 SGD_REF:S000052027|PMID:8647385 IMP P DNA polymerase sigma, poly(A) polymerase YOL115W|TRF4 gene taxon:4932 20010118 SGD
+SGD S000005475 PAP2 GO:0007062 SGD_REF:S000055612|PMID:10066793 TAS P DNA polymerase sigma, poly(A) polymerase YOL115W|TRF4 gene taxon:4932 20010118 SGD
+SGD S000005475 PAP2 GO:0007064 SGD_REF:S000055910|PMID:10926539 IMP P DNA polymerase sigma, poly(A) polymerase YOL115W|TRF4 gene taxon:4932 20040610 SGD
+SGD S000005475 PAP2 GO:0007076 SGD_REF:S000043188|PMID:8895658 IMP P DNA polymerase sigma, poly(A) polymerase YOL115W|TRF4 gene taxon:4932 20010118 SGD
+SGD S000005475 PAP2 GO:0007076 SGD_REF:S000043188|PMID:8895658 IPI P DNA polymerase sigma, poly(A) polymerase YOL115W|TRF4 gene taxon:4932 20010118 SGD
+SGD S000005475 PAP2 GO:0016075 SGD_REF:S000081843|PMID:15935758 IMP P DNA polymerase sigma, poly(A) polymerase YOL115W|TRF4 gene taxon:4932 20050610 SGD
+SGD S000005475 PAP2 GO:0016077 SGD_REF:S000081843|PMID:15935758 IMP P DNA polymerase sigma, poly(A) polymerase YOL115W|TRF4 gene taxon:4932 20050610 SGD
+SGD S000005475 PAP2 GO:0016078 SGD_REF:S000081438|PMID:15828860 IDA P DNA polymerase sigma, poly(A) polymerase YOL115W|TRF4 gene taxon:4932 20050610 SGD
+SGD S000005475 PAP2 GO:0016078 SGD_REF:S000081438|PMID:15828860 IMP P DNA polymerase sigma, poly(A) polymerase YOL115W|TRF4 gene taxon:4932 20050610 SGD
+SGD S000005475 PAP2 GO:0016078 SGD_REF:S000081843|PMID:15935758 IDA P DNA polymerase sigma, poly(A) polymerase YOL115W|TRF4 gene taxon:4932 20050610 SGD
+SGD S000000673 PAT1 GO:0000932 SGD_REF:S000073211|PMID:12730603 IDA C YCR077C|MRT1 gene taxon:4932 20030718 SGD
+SGD S000000673 PAT1 GO:0000932 SGD_REF:S000073211|PMID:12730603 IMP C YCR077C|MRT1 gene taxon:4932 20030718 SGD
+SGD S000000673 PAT1 GO:0005843 SGD_REF:S000048098|PMID:10779343 IDA C YCR077C|MRT1 gene taxon:4932 20020409 SGD
+SGD S000000673 PAT1 GO:0005554 SGD_REF:S000069584 ND F YCR077C|MRT1 gene taxon:4932 20030128 SGD
+SGD S000000673 PAT1 GO:0006446 SGD_REF:S000048098|PMID:10779343 IMP P YCR077C|MRT1 gene taxon:4932 20020409 SGD
+SGD S000000673 PAT1 GO:0006446 SGD_REF:S000048098|PMID:10779343 IGI P YCR077C|MRT1 gene taxon:4932 20020409 SGD
+SGD S000000673 PAT1 GO:0007059 SGD_REF:S000055552|PMID:8972867 IMP P YCR077C|MRT1 gene taxon:4932 20020409 SGD
+SGD S000003759 PAU1 GO:0008372 SGD_REF:S000069584 ND C YJL223C gene taxon:4932 20021002 SGD
+SGD S000003759 PAU1 GO:0005554 SGD_REF:S000069584 ND F YJL223C gene taxon:4932 20021002 SGD
+SGD S000003759 PAU1 GO:0000004 SGD_REF:S000069584 ND P YJL223C gene taxon:4932 20021002 SGD
+SGD S000002950 PAU10 GO:0008372 SGD_REF:S000069584 ND C YDR542W gene taxon:4932 20030203 SGD
+SGD S000002950 PAU10 GO:0005554 SGD_REF:S000069584 ND F YDR542W gene taxon:4932 20030203 SGD
+SGD S000002950 PAU10 GO:0000004 SGD_REF:S000069584 ND P YDR542W gene taxon:4932 20030203 SGD
+SGD S000003230 PAU11 GO:0008372 SGD_REF:S000069584 ND C YGL261C gene taxon:4932 20030203 SGD
+SGD S000003230 PAU11 GO:0005554 SGD_REF:S000069584 ND F YGL261C gene taxon:4932 20030203 SGD
+SGD S000003230 PAU11 GO:0000004 SGD_REF:S000069584 ND P YGL261C gene taxon:4932 20030203 SGD
+SGD S000003526 PAU12 GO:0008372 SGD_REF:S000069584 ND C YGR294W gene taxon:4932 20021120 SGD
+SGD S000003526 PAU12 GO:0005554 SGD_REF:S000069584 ND F YGR294W gene taxon:4932 20021120 SGD
+SGD S000003526 PAU12 GO:0000004 SGD_REF:S000069584 ND P YGR294W gene taxon:4932 20021120 SGD
+SGD S000001038 PAU13 GO:0008372 SGD_REF:S000069584 ND C YHL046C gene taxon:4932 20030203 SGD
+SGD S000001038 PAU13 GO:0005554 SGD_REF:S000069584 ND F YHL046C gene taxon:4932 20030203 SGD
+SGD S000001038 PAU13 GO:0000004 SGD_REF:S000069584 ND P YHL046C gene taxon:4932 20030203 SGD
+SGD S000001438 PAU14 GO:0008372 SGD_REF:S000069584 ND C YIL176C gene taxon:4932 20030203 SGD
+SGD S000001438 PAU14 GO:0005554 SGD_REF:S000069584 ND F YIL176C gene taxon:4932 20030203 SGD
+SGD S000001438 PAU14 GO:0000004 SGD_REF:S000069584 ND P YIL176C gene taxon:4932 20030203 SGD
+SGD S000001480 PAU15 GO:0008372 SGD_REF:S000069584 ND C YIR041W gene taxon:4932 20030203 SGD
+SGD S000001480 PAU15 GO:0005554 SGD_REF:S000069584 ND F YIR041W gene taxon:4932 20030203 SGD
+SGD S000001480 PAU15 GO:0000004 SGD_REF:S000069584 ND P YIR041W gene taxon:4932 20030203 SGD
+SGD S000001707 PAU16 GO:0008372 SGD_REF:S000069584 ND C YKL224C gene taxon:4932 20030203 SGD
+SGD S000001707 PAU16 GO:0005554 SGD_REF:S000069584 ND F YKL224C gene taxon:4932 20030203 SGD
+SGD S000001707 PAU16 GO:0000004 SGD_REF:S000069584 ND P YKL224C gene taxon:4932 20030203 SGD
+SGD S000003948 PAU17 GO:0008372 SGD_REF:S000069584 ND C YLL025W gene taxon:4932 20030424 SGD
+SGD S000003948 PAU17 GO:0005554 SGD_REF:S000069584 ND F YLL025W gene taxon:4932 20030424 SGD
+SGD S000003948 PAU17 GO:0000004 SGD_REF:S000069584 ND P YLL025W gene taxon:4932 20030424 SGD
+SGD S000003987 PAU18 GO:0008372 SGD_REF:S000069584 ND C YLL064C gene taxon:4932 20030203 SGD
+SGD S000003987 PAU18 GO:0005554 SGD_REF:S000069584 ND F YLL064C gene taxon:4932 20030203 SGD
+SGD S000003987 PAU18 GO:0000004 SGD_REF:S000069584 ND P YLL064C gene taxon:4932 20030203 SGD
+SGD S000004944 PAU19 GO:0008372 SGD_REF:S000069584 ND C YMR325W gene taxon:4932 20030203 SGD
+SGD S000004944 PAU19 GO:0005554 SGD_REF:S000069584 ND F YMR325W gene taxon:4932 20030203 SGD
+SGD S000004944 PAU19 GO:0000004 SGD_REF:S000069584 ND P YMR325W gene taxon:4932 20030203 SGD
+SGD S000000775 PAU2 GO:0008372 SGD_REF:S000069584 ND C YEL049W gene taxon:4932 20021002 SGD
+SGD S000000775 PAU2 GO:0005554 SGD_REF:S000069584 ND F YEL049W gene taxon:4932 20021002 SGD
+SGD S000000775 PAU2 GO:0000004 SGD_REF:S000069584 ND P YEL049W gene taxon:4932 20021002 SGD
+SGD S000005521 PAU20 GO:0008372 SGD_REF:S000069584 ND C YOL161C gene taxon:4932 20030203 SGD
+SGD S000005521 PAU20 GO:0005554 SGD_REF:S000069584 ND F YOL161C gene taxon:4932 20030203 SGD
+SGD S000005521 PAU20 GO:0000004 SGD_REF:S000069584 ND P YOL161C gene taxon:4932 20030203 SGD
+SGD S000005921 PAU21 GO:0008372 SGD_REF:S000069584 ND C YOR394W gene taxon:4932 20030203 SGD
+SGD S000005921 PAU21 GO:0005554 SGD_REF:S000069584 ND F YOR394W gene taxon:4932 20030203 SGD
+SGD S000005921 PAU21 GO:0000004 SGD_REF:S000069584 ND P YOR394W gene taxon:4932 20030203 SGD
+SGD S000006203 PAU22 GO:0008372 SGD_REF:S000069584 ND C YPL282C gene taxon:4932 20030203 SGD
+SGD S000006203 PAU22 GO:0005554 SGD_REF:S000069584 ND F YPL282C gene taxon:4932 20030203 SGD
+SGD S000006203 PAU22 GO:0000004 SGD_REF:S000069584 ND P YPL282C gene taxon:4932 20030203 SGD
+SGD S000000701 PAU3 GO:0008372 SGD_REF:S000069584 ND C YCR104W gene taxon:4932 20021002 SGD
+SGD S000000701 PAU3 GO:0005554 SGD_REF:S000069584 ND F YCR104W gene taxon:4932 20021002 SGD
+SGD S000000701 PAU3 GO:0000004 SGD_REF:S000069584 ND P YCR104W gene taxon:4932 20021002 SGD
+SGD S000004453 PAU4 GO:0008372 SGD_REF:S000069584 ND C YLR461W gene taxon:4932 20021002 SGD
+SGD S000004453 PAU4 GO:0005554 SGD_REF:S000069584 ND F YLR461W gene taxon:4932 20021002 SGD
+SGD S000004453 PAU4 GO:0000004 SGD_REF:S000069584 ND P YLR461W gene taxon:4932 20021002 SGD
+SGD S000001874 PAU5 GO:0008372 SGD_REF:S000069584 ND C YFL020C gene taxon:4932 20021002 SGD
+SGD S000001874 PAU5 GO:0005554 SGD_REF:S000069584 ND F YFL020C gene taxon:4932 20021002 SGD
+SGD S000001874 PAU5 GO:0000004 SGD_REF:S000069584 ND P YFL020C gene taxon:4932 20021002 SGD
+SGD S000005359 PAU6 GO:0008372 SGD_REF:S000069584 ND C YNR076W gene taxon:4932 20021002 SGD
+SGD S000005359 PAU6 GO:0005554 SGD_REF:S000069584 ND F YNR076W gene taxon:4932 20021002 SGD
+SGD S000005359 PAU6 GO:0000004 SGD_REF:S000069584 ND P YNR076W gene taxon:4932 20021002 SGD
+SGD S000000073 PAU7 GO:0008372 SGD_REF:S000069584 ND C YAR020C gene taxon:4932 20021002 SGD
+SGD S000000073 PAU7 GO:0005554 SGD_REF:S000069584 ND F YAR020C gene taxon:4932 20021002 SGD
+SGD S000000073 PAU7 GO:0000004 SGD_REF:S000069584 ND P YAR020C gene taxon:4932 20021002 SGD
+SGD S000002142 PAU8 GO:0008372 SGD_REF:S000069584 ND C YAL068C gene taxon:4932 20021126 SGD
+SGD S000002142 PAU8 GO:0005554 SGD_REF:S000069584 ND F YAL068C gene taxon:4932 20021126 SGD
+SGD S000002142 PAU8 GO:0000004 SGD_REF:S000069584 ND P YAL068C gene taxon:4932 20021126 SGD
+SGD S000007592 PAU9 GO:0008372 SGD_REF:S000069584 ND C YBL108C-A gene taxon:4932 20010226 SGD
+SGD S000007592 PAU9 GO:0005554 SGD_REF:S000069584 ND F YBL108C-A gene taxon:4932 20010226 SGD
+SGD S000007592 PAU9 GO:0000004 SGD_REF:S000069584 ND P YBL108C-A gene taxon:4932 20010226 SGD
+SGD S000004960 PBI2 GO:0000324 SGD_REF:S000044876|PMID:9657146 IPI C proteinase inhibitor I2B (PBI2) YNL015W|I2B|IB2|LMA1 gene taxon:4932 20020411 SGD
+SGD S000004960 PBI2 GO:0005737 SGD_REF:S000045610|PMID:2015812 TAS C proteinase inhibitor I2B (PBI2) YNL015W|I2B|IB2|LMA1 gene taxon:4932 20011213 SGD
+SGD S000004960 PBI2 GO:0004866 SGD_REF:S000045610|PMID:2015812 IDA F proteinase inhibitor I2B (PBI2) YNL015W|I2B|IB2|LMA1 gene taxon:4932 20011213 SGD
+SGD S000004960 PBI2 GO:0030162 SGD_REF:S000045610|PMID:2015812 IMP P proteinase inhibitor I2B (PBI2) YNL015W|I2B|IB2|LMA1 gene taxon:4932 20011213 SGD
+SGD S000004960 PBI2 GO:0042144 SGD_REF:S000064306|PMID:9159115 IDA P proteinase inhibitor I2B (PBI2) YNL015W|I2B|IB2|LMA1 gene taxon:4932 20020411 SGD
+SGD S000000557 PBN1 GO:0005783 SGD_REF:S000047343|PMID:9649520 IDA C protease B nonderepressible form YCL052C gene taxon:4932 20020711 SGD
+SGD S000000557 PBN1 contributes_to GO:0000030 SGD_REF:S000080293|PMID:15635094 IMP F protease B nonderepressible form YCL052C gene taxon:4932 20050210 SGD
+SGD S000000557 PBN1 GO:0006506 SGD_REF:S000080293|PMID:15635094 IMP P protease B nonderepressible form YCL052C gene taxon:4932 20050210 SGD
+SGD S000000557 PBN1 GO:0016485 SGD_REF:S000047343|PMID:9649520 IMP P protease B nonderepressible form YCL052C gene taxon:4932 20020711 SGD
+SGD S000003410 PBP1 GO:0005634 SGD_REF:S000069459|PMID:11914276 IDA C YGR178C|MRS16 gene taxon:4932 20020507 SGD
+SGD S000003410 PBP1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YGR178C|MRS16 gene taxon:4932 20031028 SGD
+SGD S000003410 PBP1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YGR178C|MRS16 gene taxon:4932 20020507 SGD
+SGD S000003410 PBP1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YGR178C|MRS16 gene taxon:4932 20031028 SGD
+SGD S000003410 PBP1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YGR178C|MRS16 gene taxon:4932 20040813 SGD
+SGD S000003410 PBP1 GO:0005844 SGD_REF:S000076382|PMID:15082763 IDA C YGR178C|MRS16 gene taxon:4932 20040903 SGD
+SGD S000003410 PBP1 GO:0005554 SGD_REF:S000069584 ND F YGR178C|MRS16 gene taxon:4932 20020801 SGD
+SGD S000003410 PBP1 GO:0006378 SGD_REF:S000047789|PMID:9819425 IGI P YGR178C|MRS16 gene taxon:4932 20020801 SGD
+SGD S000003410 PBP1 GO:0006378 SGD_REF:S000047789|PMID:9819425 IPI P YGR178C|MRS16 gene taxon:4932 20020801 SGD
+SGD S000003410 PBP1 GO:0006378 SGD_REF:S000047789|PMID:9819425 IMP P YGR178C|MRS16 gene taxon:4932 20020801 SGD
+SGD S000003410 PBP1 GO:0045946 SGD_REF:S000076382|PMID:15082763 IMP P YGR178C|MRS16 gene taxon:4932 20051114 SGD
+SGD S000003410 PBP1 GO:0045946 SGD_REF:S000076382|PMID:15082763 IPI P YGR178C|MRS16 gene taxon:4932 20051114 SGD
+SGD S000000437 PBP2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YBR233W|HEK1 gene taxon:4932 20031028 SGD
+SGD S000000437 PBP2 GO:0005554 SGD_REF:S000069584 ND F YBR233W|HEK1 gene taxon:4932 20021001 SGD
+SGD S000000437 PBP2 GO:0000004 SGD_REF:S000069584 ND P YBR233W|HEK1 gene taxon:4932 20021001 SGD
+SGD S000002211 PBP4 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YDL053C gene taxon:4932 20031028 SGD
+SGD S000002211 PBP4 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDL053C gene taxon:4932 20031028 SGD
+SGD S000002211 PBP4 GO:0005554 SGD_REF:S000069584 ND F YDL053C gene taxon:4932 20040504 SGD
+SGD S000002211 PBP4 GO:0000004 SGD_REF:S000069584 ND P YDL053C gene taxon:4932 20040504 SGD
+SGD S000003664 PBS2 GO:0005737 SGD_REF:S000058374|PMID:9755161 IDA C MAP kinase kinase (MEK), may act as a scaffolding protein for Sho1p, Ste11p, and Hog1p YJL128C|HOG4|SFS4|SSK4 gene taxon:4932 20010118 SGD
+SGD S000003664 PBS2 GO:0004708 SGD_REF:S000051778|PMID:7624781 TAS F MAP kinase kinase (MEK), may act as a scaffolding protein for Sho1p, Ste11p, and Hog1p YJL128C|HOG4|SFS4|SSK4 gene taxon:4932 20010118 SGD
+SGD S000003664 PBS2 GO:0005078 SGD_REF:S000049858|PMID:9180081 IPI F MAP kinase kinase (MEK), may act as a scaffolding protein for Sho1p, Ste11p, and Hog1p YJL128C|HOG4|SFS4|SSK4 gene taxon:4932 20010118 SGD
+SGD S000003664 PBS2 GO:0000169 SGD_REF:S000051778|PMID:7624781 TAS P MAP kinase kinase (MEK), may act as a scaffolding protein for Sho1p, Ste11p, and Hog1p YJL128C|HOG4|SFS4|SSK4 gene taxon:4932 20010118 SGD
+SGD S000003664 PBS2 GO:0006468 SGD_REF:S000051778|PMID:7624781 TAS P MAP kinase kinase (MEK), may act as a scaffolding protein for Sho1p, Ste11p, and Hog1p YJL128C|HOG4|SFS4|SSK4 gene taxon:4932 20010118 SGD
+SGD S000003664 PBS2 GO:0007015 SGD_REF:S000052507|PMID:7941729 IMP P MAP kinase kinase (MEK), may act as a scaffolding protein for Sho1p, Ste11p, and Hog1p YJL128C|HOG4|SFS4|SSK4 gene taxon:4932 20030116 SGD
+SGD S000003664 PBS2 GO:0007231 SGD_REF:S000051778|PMID:7624781 IMP P MAP kinase kinase (MEK), may act as a scaffolding protein for Sho1p, Ste11p, and Hog1p YJL128C|HOG4|SFS4|SSK4 gene taxon:4932 20010118 SGD
+SGD S000000499 PCA1 GO:0016020 SGD_REF:S000049758|PMID:7754711 IMP C P-type ATPase Cu(2+)-transporting (putative) YBR295W|CAD2|PAY2 gene taxon:4932 20021111 SGD
+SGD S000000499 PCA1 GO:0016020 SGD_REF:S000049758|PMID:7754711 ISS C P-type ATPase Cu(2+)-transporting (putative) YBR295W|CAD2|PAY2 gene taxon:4932 20021111 SGD
+SGD S000000499 PCA1 GO:0015662 SGD_REF:S000049758|PMID:7754711 IMP F P-type ATPase Cu(2+)-transporting (putative) YBR295W|CAD2|PAY2 gene taxon:4932 20021111 SGD
+SGD S000000499 PCA1 GO:0015662 SGD_REF:S000049758|PMID:7754711 ISS F P-type ATPase Cu(2+)-transporting (putative) YBR295W|CAD2|PAY2 gene taxon:4932 20021111 SGD
+SGD S000000499 PCA1 GO:0006878 SGD_REF:S000049706|PMID:10940034 TAS P P-type ATPase Cu(2+)-transporting (putative) YBR295W|CAD2|PAY2 gene taxon:4932 20021001 SGD
+SGD S000000499 PCA1 GO:0006879 SGD_REF:S000074663|PMID:14534306 IMP P P-type ATPase Cu(2+)-transporting (putative) YBR295W|CAD2|PAY2 gene taxon:4932 20040701 SGD
+SGD S000028512 PCC1 GO:0008372 SGD_REF:S000069584 ND C YKR095W-A gene taxon:4932 20030730 SGD
+SGD S000028512 PCC1 GO:0005554 SGD_REF:S000069584 ND F YKR095W-A gene taxon:4932 20030730 SGD
+SGD S000028512 PCC1 GO:0000004 SGD_REF:S000069584 ND P YKR095W-A gene taxon:4932 20030730 SGD
+SGD S000004141 PCD1 GO:0005777 SGD_REF:S000059371|PMID:10922370 IDA C coenzyme A diphosphatase YLR151C gene taxon:4932 20021010 SGD
+SGD S000004141 PCD1 GO:0016462 SGD_REF:S000059371|PMID:10922370 IDA F coenzyme A diphosphatase YLR151C gene taxon:4932 20021010 SGD
+SGD S000004141 PCD1 GO:0000004 SGD_REF:S000069584 ND P coenzyme A diphosphatase YLR151C gene taxon:4932 20021010 SGD
+SGD S000002636 PCF11 GO:0005849 SGD_REF:S000060315|PMID:11344258 IPI C cleavage and polyadenylation factor CF I component involved in pre-mRNA 3'-end processing YDR228C gene taxon:4932 20020409 SGD
+SGD S000002636 PCF11 GO:0005515 SGD_REF:S000073340|PMID:12727883 IDA F cleavage and polyadenylation factor CF I component involved in pre-mRNA 3'-end processing YDR228C gene taxon:4932 20030623 SGD
+SGD S000002636 PCF11 GO:0006369 SGD_REF:S000073340|PMID:12727883 IDA P cleavage and polyadenylation factor CF I component involved in pre-mRNA 3'-end processing YDR228C gene taxon:4932 20030623 SGD
+SGD S000002636 PCF11 GO:0006378 SGD_REF:S000060315|PMID:11344258 IDA P cleavage and polyadenylation factor CF I component involved in pre-mRNA 3'-end processing YDR228C gene taxon:4932 20020410 SGD
+SGD S000002636 PCF11 GO:0006379 SGD_REF:S000060315|PMID:11344258 IDA P cleavage and polyadenylation factor CF I component involved in pre-mRNA 3'-end processing YDR228C gene taxon:4932 20020409 SGD
+SGD S000000390 PCH2 GO:0005730 SGD_REF:S000059155|PMID:11029058 TAS C ATPase (putative) YBR186W gene taxon:4932 20021001 SGD
+SGD S000000390 PCH2 GO:0005554 SGD_REF:S000069584 ND F ATPase (putative) YBR186W gene taxon:4932 20021001 SGD
+SGD S000000390 PCH2 GO:0040020 SGD_REF:S000059155|PMID:11029058 TAS P ATPase (putative) YBR186W gene taxon:4932 20021001 SGD
+SGD S000001333 PCI8 GO:0008180 SGD_REF:S000071602|PMID:12186635 TAS C COP9 signalosome (CSN) subunit, translational regulator (putative) YIL071C|CSN11|YIH1 gene taxon:4932 20021115 SGD
+SGD S000001333 PCI8 GO:0008180 SGD_REF:S000071980|PMID:12446563 IDA C COP9 signalosome (CSN) subunit, translational regulator (putative) YIL071C|CSN11|YIH1 gene taxon:4932 20030325 SGD
+SGD S000001333 PCI8 GO:0005554 SGD_REF:S000069584 ND F COP9 signalosome (CSN) subunit, translational regulator (putative) YIL071C|CSN11|YIH1 gene taxon:4932 20030325 SGD
+SGD S000001333 PCI8 GO:0000338 SGD_REF:S000071980|PMID:12446563 IMP P COP9 signalosome (CSN) subunit, translational regulator (putative) YIL071C|CSN11|YIH1 gene taxon:4932 20030325 SGD
+SGD S000001333 PCI8 GO:0000338 SGD_REF:S000071602|PMID:12186635 IMP P COP9 signalosome (CSN) subunit, translational regulator (putative) YIL071C|CSN11|YIH1 gene taxon:4932 20021115 SGD
+SGD S000001805 PCK1 GO:0005829 SGD_REF:S000056699|PMID:196563 IDA C phosphoenolpyruvate carboxylkinase YKR097W|JPM2|PPC1 gene taxon:4932 20050608 SGD
+SGD S000001805 PCK1 GO:0004612 SGD_REF:S000053348|PMID:2689220 IMP F phosphoenolpyruvate carboxylkinase YKR097W|JPM2|PPC1 gene taxon:4932 20010118 SGD
+SGD S000001805 PCK1 GO:0006094 SGD_REF:S000053348|PMID:2689220 IEP P phosphoenolpyruvate carboxylkinase YKR097W|JPM2|PPC1 gene taxon:4932 20050608 SGD
+SGD S000005233 PCL1 GO:0000307 SGD_REF:S000068989|PMID:11602261 TAS C G1 cyclin, associates with PHO85 YNL289W|HCS26 gene taxon:4932 20020212 SGD
+SGD S000005233 PCL1 GO:0016538 SGD_REF:S000068989|PMID:11602261 TAS F G1 cyclin, associates with PHO85 YNL289W|HCS26 gene taxon:4932 20020211 SGD
+SGD S000005233 PCL1 GO:0007049 SGD_REF:S000068989|PMID:11602261 TAS P G1 cyclin, associates with PHO85 YNL289W|HCS26 gene taxon:4932 20020211 SGD
+SGD S000003102 PCL10 GO:0000307 SGD_REF:S000068989|PMID:11602261 TAS C YGL134W gene taxon:4932 20020212 SGD
+SGD S000003102 PCL10 GO:0016538 SGD_REF:S000068989|PMID:11602261 TAS F YGL134W gene taxon:4932 20020212 SGD
+SGD S000003102 PCL10 GO:0005979 SGD_REF:S000044412|PMID:9584169 IMP P YGL134W gene taxon:4932 20010907 SGD
+SGD S000003102 PCL10 GO:0005979 SGD_REF:S000044412|PMID:9584169 IGI P YGL134W gene taxon:4932 20010907 SGD
+SGD S000003102 PCL10 GO:0005981 SGD_REF:S000068989|PMID:11602261 IGI SGD:S000002885|SGD:S000000861|SGD:S000001312 P YGL134W gene taxon:4932 20021212 SGD
+SGD S000002285 PCL2 GO:0000307 SGD_REF:S000068989|PMID:11602261 TAS C G1 cyclin YDL127W|CLN4 gene taxon:4932 20020212 SGD
+SGD S000002285 PCL2 GO:0016538 SGD_REF:S000068989|PMID:11602261 TAS F G1 cyclin YDL127W|CLN4 gene taxon:4932 20020211 SGD
+SGD S000002285 PCL2 GO:0007049 SGD_REF:S000068989|PMID:11602261 TAS P G1 cyclin YDL127W|CLN4 gene taxon:4932 20020211 SGD
+SGD S000001113 PCL5 GO:0000307 SGD_REF:S000068989|PMID:11602261 TAS C YHR071W gene taxon:4932 20020212 SGD
+SGD S000001113 PCL5 GO:0016538 SGD_REF:S000068989|PMID:11602261 TAS F YHR071W gene taxon:4932 20020211 SGD
+SGD S000001113 PCL5 GO:0007049 SGD_REF:S000068989|PMID:11602261 TAS P YHR071W gene taxon:4932 20020211 SGD
+SGD S000000861 PCL6 GO:0000307 SGD_REF:S000068989|PMID:11602261 TAS C YER059W gene taxon:4932 20020212 SGD
+SGD S000000861 PCL6 GO:0016538 SGD_REF:S000068989|PMID:11602261 TAS F YER059W gene taxon:4932 20020212 SGD
+SGD S000000861 PCL6 GO:0005979 SGD_REF:S000068989|PMID:11602261 IGI SGD:S000002885|SGD:S000006140|SGD:S000001312|SGD:S000003102 P YER059W gene taxon:4932 20020212 SGD
+SGD S000000861 PCL6 GO:0005981 SGD_REF:S000068989|PMID:11602261 IGI SGD:S000002885|SGD:S000001312|SGD:S000006140|SGD:S000003102 P YER059W gene taxon:4932 20020212 SGD
+SGD S000001312 PCL7 GO:0000307 SGD_REF:S000068989|PMID:11602261 TAS C cyclin YIL050W gene taxon:4932 20020212 SGD
+SGD S000001312 PCL7 GO:0016538 SGD_REF:S000068989|PMID:11602261 TAS F cyclin YIL050W gene taxon:4932 20020212 SGD
+SGD S000001312 PCL7 GO:0005979 SGD_REF:S000068989|PMID:11602261 IGI SGD:S000002885|SGD:S000006140|SGD:S000003102|SGD:S000000861 P cyclin YIL050W gene taxon:4932 20020212 SGD
+SGD S000001312 PCL7 GO:0005981 SGD_REF:S000068989|PMID:11602261 IGI SGD:S000002885|SGD:S000000861|SGD:S000006140|SGD:S000003102 P cyclin YIL050W gene taxon:4932 20020212 SGD
+SGD S000006140 PCL8 GO:0000307 SGD_REF:S000068989|PMID:11602261 TAS C cyclin YPL219W gene taxon:4932 20020212 SGD
+SGD S000006140 PCL8 GO:0016538 SGD_REF:S000044412|PMID:9584169 ISS F cyclin YPL219W gene taxon:4932 20010907 SGD
+SGD S000006140 PCL8 GO:0016538 SGD_REF:S000068989|PMID:11602261 TAS F cyclin YPL219W gene taxon:4932 20020212 SGD
+SGD S000006140 PCL8 GO:0005979 SGD_REF:S000044412|PMID:9584169 IMP P cyclin YPL219W gene taxon:4932 20010907 SGD
+SGD S000006140 PCL8 GO:0005979 SGD_REF:S000044412|PMID:9584169 IGI P cyclin YPL219W gene taxon:4932 20010907 SGD
+SGD S000006140 PCL8 GO:0005981 SGD_REF:S000068989|PMID:11602261 IGI SGD:S000002885|SGD:S000000861|SGD:S000001312 P cyclin YPL219W gene taxon:4932 20021212 SGD
+SGD S000002338 PCL9 GO:0000307 SGD_REF:S000068989|PMID:11602261 TAS C YDL179W gene taxon:4932 20020212 SGD
+SGD S000002338 PCL9 GO:0016538 SGD_REF:S000068989|PMID:11602261 TAS F YDL179W gene taxon:4932 20020211 SGD
+SGD S000002338 PCL9 GO:0007049 SGD_REF:S000068989|PMID:11602261 TAS P YDL179W gene taxon:4932 20020211 SGD
+SGD S000000784 PCM1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C phosphoacetylglucosamine mutase YEL058W|AGM1 gene taxon:4932 20031028 SGD
+SGD S000000784 PCM1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C phosphoacetylglucosamine mutase YEL058W|AGM1 gene taxon:4932 20020507 SGD
+SGD S000000784 PCM1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C phosphoacetylglucosamine mutase YEL058W|AGM1 gene taxon:4932 20031028 SGD
+SGD S000000784 PCM1 GO:0004610 SGD_REF:S000047874|PMID:8174553 IMP F phosphoacetylglucosamine mutase YEL058W|AGM1 gene taxon:4932 20030122 SGD
+SGD S000000784 PCM1 GO:0004610 SGD_REF:S000047874|PMID:8174553 ISS F phosphoacetylglucosamine mutase YEL058W|AGM1 gene taxon:4932 20030122 SGD
+SGD S000000784 PCM1 GO:0006045 SGD_REF:S000045927|PMID:9867860 TAS P phosphoacetylglucosamine mutase YEL058W|AGM1 gene taxon:4932 20021001 SGD
+SGD S000003333 PCP1 GO:0005739 SGD_REF:S000071826|PMID:12417197 TAS C rhomboid protease YGR101W|MDM37|RBD1 gene taxon:4932 20021210 SGD
+SGD S000003333 PCP1 GO:0008233 SGD_REF:S000071826|PMID:12417197 ISS F rhomboid protease YGR101W|MDM37|RBD1 gene taxon:4932 20021210 SGD
+SGD S000003333 PCP1 GO:0008233 SGD_REF:S000071826|PMID:12417197 IMP F rhomboid protease YGR101W|MDM37|RBD1 gene taxon:4932 20021210 SGD
+SGD S000003333 PCP1 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P rhomboid protease YGR101W|MDM37|RBD1 gene taxon:4932 20060227 SGD
+SGD S000003333 PCP1 GO:0006465 SGD_REF:S000071826|PMID:12417197 IMP P rhomboid protease YGR101W|MDM37|RBD1 gene taxon:4932 20050503 SGD
+SGD S000003333 PCP1 GO:0007005 SGD_REF:S000071517|PMID:11907266 IMP P rhomboid protease YGR101W|MDM37|RBD1 gene taxon:4932 20021114 SGD
+SGD S000003333 PCP1 GO:0045041 SGD_REF:S000071826|PMID:12417197 TAS P rhomboid protease YGR101W|MDM37|RBD1 gene taxon:4932 20021212 SGD
+SGD S000000426 PCS60 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YBR222C|FAT2 gene taxon:4932 20020507 SGD
+SGD S000000426 PCS60 GO:0005778 SGD_REF:S000063026|PMID:8841414 IDA C YBR222C|FAT2 gene taxon:4932 20030204 SGD
+SGD S000000426 PCS60 GO:0005782 SGD_REF:S000063026|PMID:8841414 IDA C YBR222C|FAT2 gene taxon:4932 20030204 SGD
+SGD S000000426 PCS60 GO:0016208 SGD_REF:S000063026|PMID:8841414 ISS F YBR222C|FAT2 gene taxon:4932 20030204 SGD
+SGD S000000426 PCS60 GO:0000004 SGD_REF:S000069584 ND P YBR222C|FAT2 gene taxon:4932 20030203 SGD
+SGD S000003434 PCT1 GO:0005634 SGD_REF:S000071641|PMID:12200438 IDA C cholinephosphate cytidylyltransferase, phosphorylcholine transferase YGR202C|BSR2|CCT1 gene taxon:4932 20021125 SGD
+SGD S000003434 PCT1 GO:0005635 SGD_REF:S000071641|PMID:12200438 IDA C cholinephosphate cytidylyltransferase, phosphorylcholine transferase YGR202C|BSR2|CCT1 gene taxon:4932 20021125 SGD
+SGD S000003434 PCT1 GO:0005794 SGD_REF:S000062283|PMID:10397762 TAS C cholinephosphate cytidylyltransferase, phosphorylcholine transferase YGR202C|BSR2|CCT1 gene taxon:4932 20021002 SGD
+SGD S000003434 PCT1 GO:0004105 SGD_REF:S000056938|PMID:2826147 IDA F cholinephosphate cytidylyltransferase, phosphorylcholine transferase YGR202C|BSR2|CCT1 gene taxon:4932 20030113 SGD
+SGD S000003434 PCT1 GO:0006656 SGD_REF:S000062283|PMID:10397762 IDA P cholinephosphate cytidylyltransferase, phosphorylcholine transferase YGR202C|BSR2|CCT1 gene taxon:4932 20021002 SGD
+SGD S000003434 PCT1 GO:0006657 SGD_REF:S000062283|PMID:10397762 IDA P cholinephosphate cytidylyltransferase, phosphorylcholine transferase YGR202C|BSR2|CCT1 gene taxon:4932 20021002 SGD
+SGD S000000980 PDA1 GO:0005739 SGD_REF:S000057382|PMID:7589446 IDA C pyruvate dehydrogenase alpha subunit (E1 alpha) YER178W gene taxon:4932 20021001 SGD
+SGD S000000980 PDA1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C pyruvate dehydrogenase alpha subunit (E1 alpha) YER178W gene taxon:4932 20040924 SGD
+SGD S000000980 PDA1 GO:0005967 SGD_REF:S000058092|PMID:9123965 TAS C pyruvate dehydrogenase alpha subunit (E1 alpha) YER178W gene taxon:4932 20040127 SGD
+SGD S000000980 PDA1 GO:0042645 SGD_REF:S000080741|PMID:15692048 IDA C pyruvate dehydrogenase alpha subunit (E1 alpha) YER178W gene taxon:4932 20050401 SGD
+SGD S000000980 PDA1 GO:0004739 SGD_REF:S000066143|PMID:11589696 IMP F pyruvate dehydrogenase alpha subunit (E1 alpha) YER178W gene taxon:4932 20021001 SGD
+SGD S000000980 PDA1 GO:0004739 SGD_REF:S000066143|PMID:11589696 TAS F pyruvate dehydrogenase alpha subunit (E1 alpha) YER178W gene taxon:4932 20021001 SGD
+SGD S000000980 PDA1 GO:0006090 SGD_REF:S000071379|PMID:11752249 NAS P pyruvate dehydrogenase alpha subunit (E1 alpha) YER178W gene taxon:4932 20021001 SGD
+SGD S000000425 PDB1 GO:0005739 SGD_REF:S000057749|PMID:8433986 IMP C pyruvate dehydrogenase beta subunit (E1 beta) YBR221C gene taxon:4932 20021001 SGD
+SGD S000000425 PDB1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C pyruvate dehydrogenase beta subunit (E1 beta) YBR221C gene taxon:4932 20040928 SGD
+SGD S000000425 PDB1 GO:0005967 SGD_REF:S000058092|PMID:9123965 TAS C pyruvate dehydrogenase beta subunit (E1 beta) YBR221C gene taxon:4932 20040127 SGD
+SGD S000000425 PDB1 GO:0005967 SGD_REF:S000057749|PMID:8433986 TAS C pyruvate dehydrogenase beta subunit (E1 beta) YBR221C gene taxon:4932 20040127 SGD
+SGD S000000425 PDB1 GO:0042645 SGD_REF:S000080741|PMID:15692048 IDA C pyruvate dehydrogenase beta subunit (E1 beta) YBR221C gene taxon:4932 20050401 SGD
+SGD S000000425 PDB1 GO:0004739 SGD_REF:S000057749|PMID:8433986 IMP F pyruvate dehydrogenase beta subunit (E1 beta) YBR221C gene taxon:4932 20021001 SGD
+SGD S000000425 PDB1 GO:0006090 SGD_REF:S000071379|PMID:11752249 NAS P pyruvate dehydrogenase beta subunit (E1 beta) YBR221C gene taxon:4932 20021001 SGD
+SGD S000004034 PDC1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C pyruvate decarboxylase YLR044C gene taxon:4932 20031028 SGD
+SGD S000004034 PDC1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C pyruvate decarboxylase YLR044C gene taxon:4932 20031028 SGD
+SGD S000004034 PDC1 GO:0004737 SGD_REF:S000045894|PMID:10231381 TAS F pyruvate decarboxylase YLR044C gene taxon:4932 20020605 SGD
+SGD S000004034 PDC1 GO:0006090 SGD_REF:S000045894|PMID:10231381 TAS P pyruvate decarboxylase YLR044C gene taxon:4932 20021001 SGD
+SGD S000004034 PDC1 GO:0019655 SGD_REF:S000045894|PMID:10231381 TAS P pyruvate decarboxylase YLR044C gene taxon:4932 20020605 SGD
+SGD S000002488 PDC2 GO:0005634 SGD_REF:S000050008|PMID:8264540 IC GO:0003700 C asparagine and serine-rich protein YDR081C gene taxon:4932 20021111 SGD
+SGD S000002488 PDC2 GO:0030528 SGD_REF:S000050008|PMID:8264540 IMP F asparagine and serine-rich protein YDR081C gene taxon:4932 20030403 SGD
+SGD S000002488 PDC2 GO:0006366 SGD_REF:S000050008|PMID:8264540 IMP P asparagine and serine-rich protein YDR081C gene taxon:4932 20020610 SGD
+SGD S000002488 PDC2 GO:0009228 SGD_REF:S000046055|PMID:9655908 TAS P asparagine and serine-rich protein YDR081C gene taxon:4932 20010118 SGD
+SGD S000002488 PDC2 GO:0019655 SGD_REF:S000050008|PMID:8264540 IMP P asparagine and serine-rich protein YDR081C gene taxon:4932 20020610 SGD
+SGD S000004124 PDC5 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C pyruvate decarboxylase YLR134W gene taxon:4932 20031028 SGD
+SGD S000004124 PDC5 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C pyruvate decarboxylase YLR134W gene taxon:4932 20031028 SGD
+SGD S000004124 PDC5 GO:0004737 SGD_REF:S000045894|PMID:10231381 TAS F pyruvate decarboxylase YLR134W gene taxon:4932 20020605 SGD
+SGD S000004124 PDC5 GO:0006090 SGD_REF:S000045894|PMID:10231381 TAS P pyruvate decarboxylase YLR134W gene taxon:4932 20021001 SGD
+SGD S000004124 PDC5 GO:0019655 SGD_REF:S000045894|PMID:10231381 TAS P pyruvate decarboxylase YLR134W gene taxon:4932 20020605 SGD
+SGD S000003319 PDC6 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C pyruvate decarboxylase isozyme YGR087C gene taxon:4932 20031028 SGD
+SGD S000003319 PDC6 GO:0004737 SGD_REF:S000045894|PMID:10231381 TAS F pyruvate decarboxylase isozyme YGR087C gene taxon:4932 20020605 SGD
+SGD S000003319 PDC6 GO:0006067 SGD_REF:S000044980|PMID:1744053 IMP P pyruvate decarboxylase isozyme YGR087C gene taxon:4932 20021001 SGD
+SGD S000003217 PDE1 GO:0008372 SGD_REF:S000069584 ND C 3',5'-cyclic-nucleotide phosphodiesterase, low affinity YGL248W gene taxon:4932 20020606 SGD
+SGD S000003217 PDE1 GO:0004115 SGD_REF:S000055305|PMID:9880329 TAS F 3',5'-cyclic-nucleotide phosphodiesterase, low affinity YGL248W gene taxon:4932 20020606 SGD
+SGD S000003217 PDE1 GO:0019933 SGD_REF:S000055305|PMID:9880329 IMP P 3',5'-cyclic-nucleotide phosphodiesterase, low affinity YGL248W gene taxon:4932 20020606 SGD
+SGD S000005887 PDE2 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C high affinity cAMP phosphodiesterase YOR360C|SRA5 gene taxon:4932 20031028 SGD
+SGD S000005887 PDE2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C high affinity cAMP phosphodiesterase YOR360C|SRA5 gene taxon:4932 20031028 SGD
+SGD S000005887 PDE2 GO:0004115 SGD_REF:S000055305|PMID:9880329 TAS F high affinity cAMP phosphodiesterase YOR360C|SRA5 gene taxon:4932 20020606 SGD
+SGD S000005887 PDE2 GO:0019933 SGD_REF:S000061752|PMID:9799282 TAS P high affinity cAMP phosphodiesterase YOR360C|SRA5 gene taxon:4932 20020606 SGD
+SGD S000006206 PDH1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YPR002W gene taxon:4932 20031028 SGD
+SGD S000006206 PDH1 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YPR002W gene taxon:4932 20031028 SGD
+SGD S000006206 PDH1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YPR002W gene taxon:4932 20040813 SGD
+SGD S000006206 PDH1 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C YPR002W gene taxon:4932 20060317 SGD
+SGD S000006206 PDH1 GO:0005554 SGD_REF:S000059712|PMID:11179416 TAS F YPR002W gene taxon:4932 20011023 SGD
+SGD S000006206 PDH1 GO:0019541 SGD_REF:S000059712|PMID:11179416 IMP P YPR002W gene taxon:4932 20011023 SGD
+SGD S000000548 PDI1 GO:0005788 SGD_REF:S000069894|PMID:1740407 TAS C protein disulfide isomerase YCL043C|MFP1|TRG1 gene taxon:4932 20020607 SGD
+SGD S000000548 PDI1 GO:0003756 SGD_REF:S000059478|PMID:11157982 IMP F protein disulfide isomerase YCL043C|MFP1|TRG1 gene taxon:4932 20020606 SGD
+SGD S000000548 PDI1 GO:0003756 SGD_REF:S000114255|PMID:16413482 IDA F protein disulfide isomerase YCL043C|MFP1|TRG1 gene taxon:4932 20060210 SGD
+SGD S000000548 PDI1 GO:0006457 SGD_REF:S000059478|PMID:11157982 IMP P protein disulfide isomerase YCL043C|MFP1|TRG1 gene taxon:4932 20020607 SGD
+SGD S000002981 PDR1 GO:0005634 SGD_REF:S000041650|PMID:8798494 IPI C zinc finger transcription factor of the Zn(2)-Cys(6) binuclear cluster domain type YGL013C|AMY1|ANT1|BOR2|CYH3|NRA2|SMR2|TIL1|TPE1|TPE3 gene taxon:4932 20020617 SGD
+SGD S000002981 PDR1 GO:0003677 SGD_REF:S000069766|PMID:11421285 TAS F zinc finger transcription factor of the Zn(2)-Cys(6) binuclear cluster domain type YGL013C|AMY1|ANT1|BOR2|CYH3|NRA2|SMR2|TIL1|TPE1|TPE3 gene taxon:4932 20020607 SGD
+SGD S000002981 PDR1 GO:0003677 SGD_REF:S000041650|PMID:8798494 IPI F zinc finger transcription factor of the Zn(2)-Cys(6) binuclear cluster domain type YGL013C|AMY1|ANT1|BOR2|CYH3|NRA2|SMR2|TIL1|TPE1|TPE3 gene taxon:4932 20020617 SGD
+SGD S000002981 PDR1 GO:0016563 SGD_REF:S000069766|PMID:11421285 TAS F zinc finger transcription factor of the Zn(2)-Cys(6) binuclear cluster domain type YGL013C|AMY1|ANT1|BOR2|CYH3|NRA2|SMR2|TIL1|TPE1|TPE3 gene taxon:4932 20020607 SGD
+SGD S000002981 PDR1 GO:0006357 SGD_REF:S000069766|PMID:11421285 TAS P zinc finger transcription factor of the Zn(2)-Cys(6) binuclear cluster domain type YGL013C|AMY1|ANT1|BOR2|CYH3|NRA2|SMR2|TIL1|TPE1|TPE3 gene taxon:4932 20020607 SGD
+SGD S000002981 PDR1 GO:0042493 SGD_REF:S000069766|PMID:11421285 TAS P zinc finger transcription factor of the Zn(2)-Cys(6) binuclear cluster domain type YGL013C|AMY1|ANT1|BOR2|CYH3|NRA2|SMR2|TIL1|TPE1|TPE3 gene taxon:4932 20021111 SGD
+SGD S000002981 PDR1 GO:0042493 SGD_REF:S000080916|PMID:15713640 IMP P zinc finger transcription factor of the Zn(2)-Cys(6) binuclear cluster domain type YGL013C|AMY1|ANT1|BOR2|CYH3|NRA2|SMR2|TIL1|TPE1|TPE3 gene taxon:4932 20050816 SGD
+SGD S000005855 PDR10 GO:0005886 SGD_REF:S000046396|PMID:9428726 ISS C ABC transporter (putative), highly similar to Pdr5p YOR328W gene taxon:4932 20021003 SGD
+SGD S000005855 PDR10 GO:0042626 SGD_REF:S000046396|PMID:9428726 ISS F ABC transporter (putative), highly similar to Pdr5p YOR328W gene taxon:4932 20021003 SGD
+SGD S000005855 PDR10 GO:0006855 SGD_REF:S000046396|PMID:9428726 ISS P ABC transporter (putative), highly similar to Pdr5p YOR328W gene taxon:4932 20021003 SGD
+SGD S000005855 PDR10 GO:0006855 SGD_REF:S000046396|PMID:9428726 IEP P ABC transporter (putative), highly similar to Pdr5p YOR328W gene taxon:4932 20021003 SGD
+SGD S000001275 PDR11 GO:0016020 SGD_REF:S000060194|PMID:11321575 ISS C ABC transporter (putative) YIL013C gene taxon:4932 20020918 SGD
+SGD S000001275 PDR11 GO:0042626 SGD_REF:S000060194|PMID:11321575 ISS F ABC transporter (putative) YIL013C gene taxon:4932 20020918 SGD
+SGD S000001275 PDR11 GO:0015918 SGD_REF:S000071132|PMID:12077145 IMP P ABC transporter (putative) YIL013C gene taxon:4932 20020918 SGD
+SGD S000005979 PDR12 GO:0005886 SGD_REF:S000039567|PMID:9687494 IDA C multidrug resistance transporter YPL058C gene taxon:4932 20020920 SGD
+SGD S000005979 PDR12 GO:0005342 SGD_REF:S000049881|PMID:10419965 IDA F multidrug resistance transporter YPL058C gene taxon:4932 20030623 SGD
+SGD S000005979 PDR12 GO:0008559 SGD_REF:S000069766|PMID:11421285 TAS F multidrug resistance transporter YPL058C gene taxon:4932 20020607 SGD
+SGD S000005979 PDR12 GO:0006810 SGD_REF:S000069766|PMID:11421285 TAS P multidrug resistance transporter YPL058C gene taxon:4932 20020607 SGD
+SGD S000005979 PDR12 GO:0015849 SGD_REF:S000049881|PMID:10419965 IDA P multidrug resistance transporter YPL058C gene taxon:4932 20030623 SGD
+SGD S000005979 PDR12 GO:0019541 SGD_REF:S000059712|PMID:11179416 IEP P multidrug resistance transporter YPL058C gene taxon:4932 20011023 SGD
+SGD S000002814 PDR15 GO:0016021 SGD_REF:S000058031|PMID:9020838 ISS C multidrug resistance transporter (putative) YDR406W gene taxon:4932 20020711 SGD
+SGD S000002814 PDR15 GO:0042626 SGD_REF:S000058031|PMID:9020838 ISS F multidrug resistance transporter (putative) YDR406W gene taxon:4932 20020711 SGD
+SGD S000002814 PDR15 GO:0006810 SGD_REF:S000058031|PMID:9020838 ISS P multidrug resistance transporter (putative) YDR406W gene taxon:4932 20020711 SGD
+SGD S000005175 PDR16 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C Pdr17p homolog, Sec14p homolog YNL231C|SFH3 gene taxon:4932 20020507 SGD
+SGD S000005175 PDR16 GO:0005792 SGD_REF:S000073885|PMID:12869188 IDA C Pdr17p homolog, Sec14p homolog YNL231C|SFH3 gene taxon:4932 20031001 SGD
+SGD S000005175 PDR16 GO:0005811 SGD_REF:S000073885|PMID:12869188 IDA C Pdr17p homolog, Sec14p homolog YNL231C|SFH3 gene taxon:4932 20031001 SGD
+SGD S000005175 PDR16 GO:0008526 SGD_REF:S000043659|PMID:10848624 IDA F Pdr17p homolog, Sec14p homolog YNL231C|SFH3 gene taxon:4932 20021029 SGD
+SGD S000005175 PDR16 GO:0015914 SGD_REF:S000043659|PMID:10848624 IDA P Pdr17p homolog, Sec14p homolog YNL231C|SFH3 gene taxon:4932 20021029 SGD
+SGD S000005175 PDR16 GO:0016126 SGD_REF:S000044730|PMID:9890948 IMP P Pdr17p homolog, Sec14p homolog YNL231C|SFH3 gene taxon:4932 20020607 SGD
+SGD S000005175 PDR16 GO:0042493 SGD_REF:S000044730|PMID:9890948 IGI P Pdr17p homolog, Sec14p homolog YNL231C|SFH3 gene taxon:4932 20021111 SGD
+SGD S000005208 PDR17 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C Pdr16p homolog, Sec14p homolog YNL264C|ISS1|SFH4 gene taxon:4932 20020507 SGD
+SGD S000005208 PDR17 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C Pdr16p homolog, Sec14p homolog YNL264C|ISS1|SFH4 gene taxon:4932 20031028 SGD
+SGD S000005208 PDR17 GO:0008526 SGD_REF:S000043659|PMID:10848624 IDA F Pdr16p homolog, Sec14p homolog YNL264C|ISS1|SFH4 gene taxon:4932 20021029 SGD
+SGD S000005208 PDR17 GO:0008654 SGD_REF:S000044730|PMID:9890948 IMP P Pdr16p homolog, Sec14p homolog YNL264C|ISS1|SFH4 gene taxon:4932 20020607 SGD
+SGD S000005208 PDR17 GO:0015914 SGD_REF:S000043659|PMID:10848624 IDA P Pdr16p homolog, Sec14p homolog YNL264C|ISS1|SFH4 gene taxon:4932 20021029 SGD
+SGD S000005208 PDR17 GO:0042493 SGD_REF:S000044730|PMID:9890948 IGI P Pdr16p homolog, Sec14p homolog YNL264C|ISS1|SFH4 gene taxon:4932 20021111 SGD
+SGD S000000101 PDR3 GO:0005634 SGD_REF:S000069459|PMID:11914276 IDA C YBL005W|AMY2|TPE2 gene taxon:4932 20020507 SGD
+SGD S000000101 PDR3 GO:0005634 SGD_REF:S000041650|PMID:8798494 IPI C YBL005W|AMY2|TPE2 gene taxon:4932 20020617 SGD
+SGD S000000101 PDR3 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YBL005W|AMY2|TPE2 gene taxon:4932 20020507 SGD
+SGD S000000101 PDR3 GO:0003677 SGD_REF:S000069766|PMID:11421285 TAS F YBL005W|AMY2|TPE2 gene taxon:4932 20020607 SGD
+SGD S000000101 PDR3 GO:0003677 SGD_REF:S000041650|PMID:8798494 IPI F YBL005W|AMY2|TPE2 gene taxon:4932 20020617 SGD
+SGD S000000101 PDR3 GO:0016563 SGD_REF:S000069766|PMID:11421285 TAS F YBL005W|AMY2|TPE2 gene taxon:4932 20020607 SGD
+SGD S000000101 PDR3 GO:0016563 SGD_REF:S000050499|PMID:7623800 IDA F YBL005W|AMY2|TPE2 gene taxon:4932 20050119 SGD
+SGD S000000101 PDR3 GO:0006357 SGD_REF:S000069766|PMID:11421285 TAS P YBL005W|AMY2|TPE2 gene taxon:4932 20020607 SGD
+SGD S000000101 PDR3 GO:0042493 SGD_REF:S000069766|PMID:11421285 TAS P YBL005W|AMY2|TPE2 gene taxon:4932 20021111 SGD
+SGD S000000101 PDR3 GO:0045893 SGD_REF:S000050499|PMID:7623800 IDA P YBL005W|AMY2|TPE2 gene taxon:4932 20050119 SGD
+SGD S000005679 PDR5 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C multidrug resistance transporter YOR153W|LEM1|STS1|YDR1 gene taxon:4932 20040928 SGD
+SGD S000005679 PDR5 GO:0005886 SGD_REF:S000040660|PMID:8810273 IDA C multidrug resistance transporter YOR153W|LEM1|STS1|YDR1 gene taxon:4932 20020919 SGD
+SGD S000005679 PDR5 GO:0008559 SGD_REF:S000069766|PMID:11421285 TAS F multidrug resistance transporter YOR153W|LEM1|STS1|YDR1 gene taxon:4932 20020607 SGD
+SGD S000005679 PDR5 GO:0015893 SGD_REF:S000069766|PMID:11421285 TAS P multidrug resistance transporter YOR153W|LEM1|STS1|YDR1 gene taxon:4932 20020920 SGD
+SGD S000005679 PDR5 GO:0042493 SGD_REF:S000069766|PMID:11421285 TAS P multidrug resistance transporter YOR153W|LEM1|STS1|YDR1 gene taxon:4932 20021111 SGD
+SGD S000029350 PDR7 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20020605 SGD
+SGD S000029350 PDR7 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20020605 SGD
+SGD S000029350 PDR7 GO:0009410 SGD_REF:S000050153|PMID:8150279 IMP P gene taxon:4932 20020605 SGD
+SGD S000004256 PDR8 GO:0005634 SGD_REF:S000072862|PMID:12529331 IPI C zinc finger transcription factor YLR266C gene taxon:4932 20030409 SGD
+SGD S000004256 PDR8 GO:0005634 SGD_REF:S000072862|PMID:12529331 ISS C zinc finger transcription factor YLR266C gene taxon:4932 20030409 SGD
+SGD S000004256 PDR8 GO:0003677 SGD_REF:S000072862|PMID:12529331 IDA F zinc finger transcription factor YLR266C gene taxon:4932 20030409 SGD
+SGD S000004256 PDR8 GO:0003704 SGD_REF:S000072862|PMID:12529331 ISS F zinc finger transcription factor YLR266C gene taxon:4932 20030409 SGD
+SGD S000004256 PDR8 GO:0006950 SGD_REF:S000072862|PMID:12529331 IGI P zinc finger transcription factor YLR266C gene taxon:4932 20030409 SGD
+SGD S000004256 PDR8 GO:0045944 SGD_REF:S000072862|PMID:12529331 IGI P zinc finger transcription factor YLR266C gene taxon:4932 20030409 SGD
+SGD S000004256 PDR8 GO:0045944 SGD_REF:S000072862|PMID:12529331 IPI P zinc finger transcription factor YLR266C gene taxon:4932 20030409 SGD
+SGD S000002520 PDS1 GO:0005634 SGD_REF:S000058435|PMID:11149918 IDA C 42 kDa nuclear securin YDR113C gene taxon:4932 20020808 SGD
+SGD S000002520 PDS1 GO:0005819 SGD_REF:S000058435|PMID:11149918 IDA C 42 kDa nuclear securin YDR113C gene taxon:4932 20020808 SGD
+SGD S000002520 PDS1 GO:0005515 SGD_REF:S000054076|PMID:9635435 IDA F 42 kDa nuclear securin YDR113C gene taxon:4932 20021104 SGD
+SGD S000002520 PDS1 GO:0005515 SGD_REF:S000058435|PMID:11149918 IDA F 42 kDa nuclear securin YDR113C gene taxon:4932 20021104 SGD
+SGD S000002520 PDS1 GO:0000070 SGD_REF:S000054076|PMID:9635435 IMP P 42 kDa nuclear securin YDR113C gene taxon:4932 20020808 SGD
+SGD S000002520 PDS1 GO:0000070 SGD_REF:S000054076|PMID:9635435 IPI P 42 kDa nuclear securin YDR113C gene taxon:4932 20020808 SGD
+SGD S000002520 PDS1 GO:0000725 SGD_REF:S000080276|PMID:15533838 IGI SGD:S000002625|SGD:S000000897 P 42 kDa nuclear securin YDR113C gene taxon:4932 20050613 SGD
+SGD S000002520 PDS1 GO:0000725 SGD_REF:S000080276|PMID:15533838 IMP P 42 kDa nuclear securin YDR113C gene taxon:4932 20050613 SGD
+SGD S000002520 PDS1 GO:0006606 SGD_REF:S000058435|PMID:11149918 IMP P 42 kDa nuclear securin YDR113C gene taxon:4932 20020808 SGD
+SGD S000004681 PDS5 GO:0000794 SGD_REF:S000059143|PMID:11062262 IDA C YMR076C gene taxon:4932 20030403 SGD
+SGD S000004681 PDS5 GO:0005198 SGD_REF:S000060755|PMID:11137006 ISS F YMR076C gene taxon:4932 20021001 SGD
+SGD S000004681 PDS5 GO:0007064 SGD_REF:S000059143|PMID:11062262 IMP P YMR076C gene taxon:4932 20021001 SGD
+SGD S000004681 PDS5 GO:0007064 SGD_REF:S000077724|PMID:14623866 IMP P YMR076C gene taxon:4932 20051005 SGD
+SGD S000004681 PDS5 GO:0007076 SGD_REF:S000059143|PMID:11062262 IMP P YMR076C gene taxon:4932 20021001 SGD
+SGD S000003425 PDX1 GO:0005739 SGD_REF:S000041729|PMID:2007123 TAS C pyruvate dehydrogenase complex protein X component YGR193C gene taxon:4932 20021014 SGD
+SGD S000003425 PDX1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C pyruvate dehydrogenase complex protein X component YGR193C gene taxon:4932 20040928 SGD
+SGD S000003425 PDX1 GO:0005967 SGD_REF:S000041729|PMID:2007123 TAS C pyruvate dehydrogenase complex protein X component YGR193C gene taxon:4932 20021014 SGD
+SGD S000003425 PDX1 GO:0005515 SGD_REF:S000041729|PMID:2007123 IDA F pyruvate dehydrogenase complex protein X component YGR193C gene taxon:4932 20030122 SGD
+SGD S000003425 PDX1 GO:0005515 SGD_REF:S000041729|PMID:2007123 IMP F pyruvate dehydrogenase complex protein X component YGR193C gene taxon:4932 20030122 SGD
+SGD S000003425 PDX1 GO:0006086 SGD_REF:S000058092|PMID:9123965 TAS P pyruvate dehydrogenase complex protein X component YGR193C gene taxon:4932 20020830 SGD
+SGD S000000239 PDX3 GO:0008372 SGD_REF:S000069584 ND C pyridoxine (pyridoxiamine) phosphate oxidase YBR035C gene taxon:4932 20020801 SGD
+SGD S000000239 PDX3 GO:0004733 SGD_REF:S000054601|PMID:7896706 ISS F pyridoxine (pyridoxiamine) phosphate oxidase YBR035C gene taxon:4932 20020801 SGD
+SGD S000000239 PDX3 GO:0004733 SGD_REF:S000054601|PMID:7896706 IMP F pyridoxine (pyridoxiamine) phosphate oxidase YBR035C gene taxon:4932 20020801 SGD
+SGD S000000239 PDX3 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P pyridoxine (pyridoxiamine) phosphate oxidase YBR035C gene taxon:4932 20060210 SGD
+SGD S000000239 PDX3 GO:0006631 SGD_REF:S000054601|PMID:7896706 IMP P pyridoxine (pyridoxiamine) phosphate oxidase YBR035C gene taxon:4932 20020801 SGD
+SGD S000000951 PEA2 GO:0000133 SGD_REF:S000046605|PMID:10639324 TAS C coiled-coil domain YER149C|DFG9|PPF2 gene taxon:4932 20010118 SGD
+SGD S000000951 PEA2 GO:0030478 SGD_REF:S000041005|PMID:10652251 IDA C coiled-coil domain YER149C|DFG9|PPF2 gene taxon:4932 20010118 SGD
+SGD S000000951 PEA2 GO:0005519 SGD_REF:S000046605|PMID:10639324 IPI F coiled-coil domain YER149C|DFG9|PPF2 gene taxon:4932 20010118 SGD
+SGD S000000951 PEA2 GO:0007015 SGD_REF:S000046605|PMID:10639324 IPI P coiled-coil domain YER149C|DFG9|PPF2 gene taxon:4932 20010118 SGD
+SGD S000000951 PEA2 GO:0007121 SGD_REF:S000041005|PMID:10652251 TAS P coiled-coil domain YER149C|DFG9|PPF2 gene taxon:4932 20010118 SGD
+SGD S000000951 PEA2 GO:0007266 SGD_REF:S000046605|PMID:10639324 IPI P coiled-coil domain YER149C|DFG9|PPF2 gene taxon:4932 20010118 SGD
+SGD S000000951 PEA2 GO:0030447 SGD_REF:S000080384|PMID:15645503 IMP P coiled-coil domain YER149C|DFG9|PPF2 gene taxon:4932 20050621 SGD
+SGD S000000951 PEA2 GO:0030468 SGD_REF:S000046605|PMID:10639324 IMP P coiled-coil domain YER149C|DFG9|PPF2 gene taxon:4932 20010302 SGD
+SGD S000000951 PEA2 GO:0030468 SGD_REF:S000046605|PMID:10639324 IPI P coiled-coil domain YER149C|DFG9|PPF2 gene taxon:4932 20010302 SGD
+SGD S000000951 PEA2 GO:0031384 SGD_REF:S000077102|PMID:14734532 IMP P coiled-coil domain YER149C|DFG9|PPF2 gene taxon:4932 20050719 SGD
+SGD S000000951 PEA2 GO:0031385 SGD_REF:S000077102|PMID:14734532 IMP P coiled-coil domain YER149C|DFG9|PPF2 gene taxon:4932 20050719 SGD
+SGD S000000113 PEP1 GO:0005794 SGD_REF:S000053957|PMID:8187177 TAS C Type I integral membrane protein 166aa cytoplasmic tail, 1300 aa lumenal domain YBL017C|VPS10|VPT1 gene taxon:4932 20010118 SGD
+SGD S000000113 PEP1 GO:0005048 SGD_REF:S000053957|PMID:8187177 IMP F Type I integral membrane protein 166aa cytoplasmic tail, 1300 aa lumenal domain YBL017C|VPS10|VPT1 gene taxon:4932 20030527 SGD
+SGD S000000113 PEP1 GO:0005048 SGD_REF:S000053957|PMID:8187177 IPI F Type I integral membrane protein 166aa cytoplasmic tail, 1300 aa lumenal domain YBL017C|VPS10|VPT1 gene taxon:4932 20030527 SGD
+SGD S000000113 PEP1 GO:0006623 SGD_REF:S000053957|PMID:8187177 IMP P Type I integral membrane protein 166aa cytoplasmic tail, 1300 aa lumenal domain YBL017C|VPS10|VPT1 gene taxon:4932 20010118 SGD
+SGD S000000113 PEP1 GO:0006623 SGD_REF:S000053957|PMID:8187177 IPI P Type I integral membrane protein 166aa cytoplasmic tail, 1300 aa lumenal domain YBL017C|VPS10|VPT1 gene taxon:4932 20010118 SGD
+SGD S000000113 PEP1 GO:0007034 SGD_REF:S000053957|PMID:8187177 IMP P Type I integral membrane protein 166aa cytoplasmic tail, 1300 aa lumenal domain YBL017C|VPS10|VPT1 gene taxon:4932 20010118 SGD
+SGD S000000113 PEP1 GO:0007034 SGD_REF:S000053957|PMID:8187177 IPI P Type I integral membrane protein 166aa cytoplasmic tail, 1300 aa lumenal domain YBL017C|VPS10|VPT1 gene taxon:4932 20010118 SGD
+SGD S000005562 PEP12 GO:0005768 SGD_REF:S000041143|PMID:8730101 IMP C c-terminal TMD, integral membrane protein YOR036W|VPL6|VPS6|VPT13 gene taxon:4932 20010118 SGD
+SGD S000005562 PEP12 GO:0005794 SGD_REF:S000041143|PMID:8730101 IMP C c-terminal TMD, integral membrane protein YOR036W|VPL6|VPS6|VPT13 gene taxon:4932 20010118 SGD
+SGD S000005562 PEP12 GO:0005486 SGD_REF:S000041143|PMID:8730101 IMP F c-terminal TMD, integral membrane protein YOR036W|VPL6|VPS6|VPT13 gene taxon:4932 20010118 SGD
+SGD S000005562 PEP12 GO:0005486 SGD_REF:S000041143|PMID:8730101 ISS F c-terminal TMD, integral membrane protein YOR036W|VPL6|VPS6|VPT13 gene taxon:4932 20010118 SGD
+SGD S000005562 PEP12 GO:0005486 SGD_REF:S000076087|PMID:14981247 IDA F c-terminal TMD, integral membrane protein YOR036W|VPL6|VPS6|VPT13 gene taxon:4932 20050614 SGD
+SGD S000005562 PEP12 GO:0006896 SGD_REF:S000041143|PMID:8730101 IMP P c-terminal TMD, integral membrane protein YOR036W|VPL6|VPS6|VPT13 gene taxon:4932 20010118 SGD
+SGD S000004138 PEP3 GO:0000306 SGD_REF:S000039952|PMID:1944264 IDA C vacuolar membrane protein YLR148W|VAM8|VPS18|VPT18 gene taxon:4932 20020802 SGD
+SGD S000004138 PEP3 GO:0000329 SGD_REF:S000040175|PMID:10944212 IDA C vacuolar membrane protein YLR148W|VAM8|VPS18|VPT18 gene taxon:4932 20020827 SGD
+SGD S000004138 PEP3 GO:0030897 SGD_REF:S000040175|PMID:10944212 IPI C vacuolar membrane protein YLR148W|VAM8|VPS18|VPT18 gene taxon:4932 20041024 SGD
+SGD S000004138 PEP3 GO:0005515 SGD_REF:S000039377|PMID:10978279 IMP F vacuolar membrane protein YLR148W|VAM8|VPS18|VPT18 gene taxon:4932 20020802 SGD
+SGD S000004138 PEP3 GO:0005515 SGD_REF:S000039377|PMID:10978279 IPI F vacuolar membrane protein YLR148W|VAM8|VPS18|VPT18 gene taxon:4932 20020802 SGD
+SGD S000004138 PEP3 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P vacuolar membrane protein YLR148W|VAM8|VPS18|VPT18 gene taxon:4932 20060209 SGD
+SGD S000004138 PEP3 GO:0006895 SGD_REF:S000066047|PMID:11422941 IGI P vacuolar membrane protein YLR148W|VAM8|VPS18|VPT18 gene taxon:4932 20020827 SGD
+SGD S000004138 PEP3 GO:0006904 SGD_REF:S000039377|PMID:10978279 IMP P vacuolar membrane protein YLR148W|VAM8|VPS18|VPT18 gene taxon:4932 20020802 SGD
+SGD S000004138 PEP3 GO:0042144 SGD_REF:S000040175|PMID:10944212 IDA P vacuolar membrane protein YLR148W|VAM8|VPS18|VPT18 gene taxon:4932 20020827 SGD
+SGD S000004138 PEP3 GO:0045324 SGD_REF:S000066047|PMID:11422941 IGI P vacuolar membrane protein YLR148W|VAM8|VPS18|VPT18 gene taxon:4932 20020827 SGD
+SGD S000006075 PEP4 GO:0000324 SGD_REF:S000056906|PMID:2674123 TAS C vacuolar proteinase A YPL154C|PHO9|PRA1|yscA gene taxon:4932 20011214 SGD
+SGD S000006075 PEP4 GO:0000328 SGD_REF:S000080163|PMID:9529893 TAS C vacuolar proteinase A YPL154C|PHO9|PRA1|yscA gene taxon:4932 20050107 SGD
+SGD S000006075 PEP4 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C vacuolar proteinase A YPL154C|PHO9|PRA1|yscA gene taxon:4932 20040928 SGD
+SGD S000006075 PEP4 GO:0004175 SGD_REF:S000056906|PMID:2674123 TAS F vacuolar proteinase A YPL154C|PHO9|PRA1|yscA gene taxon:4932 20011214 SGD
+SGD S000006075 PEP4 GO:0004196 SGD_REF:S000056906|PMID:2674123 TAS F vacuolar proteinase A YPL154C|PHO9|PRA1|yscA gene taxon:4932 20011214 SGD
+SGD S000006075 PEP4 GO:0007039 SGD_REF:S000056906|PMID:2674123 IMP P vacuolar proteinase A YPL154C|PHO9|PRA1|yscA gene taxon:4932 20011214 SGD
+SGD S000006075 PEP4 GO:0007039 SGD_REF:S000056906|PMID:2674123 TAS P vacuolar proteinase A YPL154C|PHO9|PRA1|yscA gene taxon:4932 20011214 SGD
+SGD S000006075 PEP4 GO:0009267 SGD_REF:S000056906|PMID:2674123 IMP P vacuolar proteinase A YPL154C|PHO9|PRA1|yscA gene taxon:4932 20011214 SGD
+SGD S000006075 PEP4 GO:0016237 SGD_REF:S000072498|PMID:12529432 IMP P vacuolar proteinase A YPL154C|PHO9|PRA1|yscA gene taxon:4932 20030213 SGD
+SGD S000006075 PEP4 GO:0030435 SGD_REF:S000056906|PMID:2674123 IMP P vacuolar proteinase A YPL154C|PHO9|PRA1|yscA gene taxon:4932 20011214 SGD
+SGD S000004844 PEP5 GO:0000329 SGD_REF:S000040175|PMID:10944212 IDA C Zn-finger protein (putative) YMR231W|END1|VAM1|VPL9|VPS11|VPT11 gene taxon:4932 20020827 SGD
+SGD S000004844 PEP5 GO:0030897 SGD_REF:S000040175|PMID:10944212 IPI C Zn-finger protein (putative) YMR231W|END1|VAM1|VPL9|VPS11|VPT11 gene taxon:4932 20041024 SGD
+SGD S000004844 PEP5 GO:0005554 SGD_REF:S000069584 ND F Zn-finger protein (putative) YMR231W|END1|VAM1|VPL9|VPS11|VPT11 gene taxon:4932 20020827 SGD
+SGD S000004844 PEP5 GO:0006895 SGD_REF:S000066047|PMID:11422941 IGI P Zn-finger protein (putative) YMR231W|END1|VAM1|VPL9|VPS11|VPT11 gene taxon:4932 20020827 SGD
+SGD S000004844 PEP5 GO:0006904 SGD_REF:S000039377|PMID:10978279 IMP P Zn-finger protein (putative) YMR231W|END1|VAM1|VPL9|VPS11|VPT11 gene taxon:4932 20020802 SGD
+SGD S000004844 PEP5 GO:0042144 SGD_REF:S000040175|PMID:10944212 IDA P Zn-finger protein (putative) YMR231W|END1|VAM1|VPL9|VPS11|VPT11 gene taxon:4932 20020827 SGD
+SGD S000004844 PEP5 GO:0045324 SGD_REF:S000066047|PMID:11422941 IGI P Zn-finger protein (putative) YMR231W|END1|VAM1|VPL9|VPS11|VPT11 gene taxon:4932 20020827 SGD
+SGD S000002731 PEP7 GO:0005737 SGD_REF:S000041553|PMID:9168472 IDA C three zinc fingers; cysteine rich regions of amino acids are essential for function YDR323C|VAC1|VPL21|VPS19|VPT19 gene taxon:4932 20010118 SGD
+SGD S000002731 PEP7 GO:0010009 SGD_REF:S000041553|PMID:9168472 IDA C three zinc fingers; cysteine rich regions of amino acids are essential for function YDR323C|VAC1|VPL21|VPS19|VPT19 gene taxon:4932 20040405 SGD
+SGD S000002731 PEP7 GO:0005554 SGD_REF:S000069584 ND F three zinc fingers; cysteine rich regions of amino acids are essential for function YDR323C|VAC1|VPL21|VPS19|VPT19 gene taxon:4932 20021113 SGD
+SGD S000002731 PEP7 GO:0006896 SGD_REF:S000048985|PMID:10021387 IGI P three zinc fingers; cysteine rich regions of amino acids are essential for function YDR323C|VAC1|VPL21|VPS19|VPT19 gene taxon:4932 20010118 SGD
+SGD S000002731 PEP7 GO:0006896 SGD_REF:S000048985|PMID:10021387 IPI P three zinc fingers; cysteine rich regions of amino acids are essential for function YDR323C|VAC1|VPL21|VPS19|VPT19 gene taxon:4932 20010118 SGD
+SGD S000002731 PEP7 GO:0006904 SGD_REF:S000041553|PMID:9168472 IMP P three zinc fingers; cysteine rich regions of amino acids are essential for function YDR323C|VAC1|VPL21|VPS19|VPT19 gene taxon:4932 20010118 SGD
+SGD S000002731 PEP7 GO:0006906 SGD_REF:S000041553|PMID:9168472 IMP P three zinc fingers; cysteine rich regions of amino acids are essential for function YDR323C|VAC1|VPL21|VPS19|VPT19 gene taxon:4932 20010118 SGD
+SGD S000003589 PEP8 GO:0005768 SGD_REF:S000039451|PMID:9700157 IPI C vacuolar protein similar to mouse gene H<beta>58 YJL053W|GRD6|VPS26|VPT4 gene taxon:4932 20020826 SGD
+SGD S000003589 PEP8 GO:0030904 SGD_REF:S000074969|PMID:11598206 TAS C vacuolar protein similar to mouse gene H<beta>58 YJL053W|GRD6|VPS26|VPT4 gene taxon:4932 20040804 SGD
+SGD S000003589 PEP8 GO:0005554 SGD_REF:S000069584 ND F vacuolar protein similar to mouse gene H<beta>58 YJL053W|GRD6|VPS26|VPT4 gene taxon:4932 20020826 SGD
+SGD S000003589 PEP8 contributes_to GO:0008565 SGD_REF:S000039451|PMID:9700157 IMP F vacuolar protein similar to mouse gene H<beta>58 YJL053W|GRD6|VPS26|VPT4 gene taxon:4932 20060426 SGD
+SGD S000003589 PEP8 contributes_to GO:0008565 SGD_REF:S000039451|PMID:9700157 IPI F vacuolar protein similar to mouse gene H<beta>58 YJL053W|GRD6|VPS26|VPT4 gene taxon:4932 20060426 SGD
+SGD S000003589 PEP8 GO:0042147 SGD_REF:S000039451|PMID:9700157 IPI P vacuolar protein similar to mouse gene H<beta>58 YJL053W|GRD6|VPS26|VPT4 gene taxon:4932 20020826 SGD
+SGD S000003589 PEP8 GO:0045053 SGD_REF:S000057861|PMID:8649377 IMP P vacuolar protein similar to mouse gene H<beta>58 YJL053W|GRD6|VPS26|VPT4 gene taxon:4932 20020716 SGD
+SGD S000000640 PER1 GO:0000329 SGD_REF:S000049663|PMID:9560393 IDA C YCR044C|COS16 gene taxon:4932 20030218 SGD
+SGD S000000640 PER1 GO:0005554 SGD_REF:S000069584 ND F YCR044C|COS16 gene taxon:4932 20020930 SGD
+SGD S000000640 PER1 GO:0006986 SGD_REF:S000049671|PMID:10893258 IMP P YCR044C|COS16 gene taxon:4932 20020930 SGD
+SGD S000000640 PER1 GO:0030026 SGD_REF:S000049663|PMID:9560393 IMP P YCR044C|COS16 gene taxon:4932 20030218 SGD
+SGD S000001919 PES4 GO:0008372 SGD_REF:S000069584 ND C poly(A) binding protein YFR023W gene taxon:4932 20030211 SGD
+SGD S000001919 PES4 GO:0005554 SGD_REF:S000069584 ND F poly(A) binding protein YFR023W gene taxon:4932 20010119 SGD
+SGD S000001919 PES4 GO:0000004 SGD_REF:S000069584 ND P poly(A) binding protein YFR023W gene taxon:4932 20040419 SGD
+SGD S000029354 PET1 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20010119 SGD
+SGD S000029354 PET1 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20010119 SGD
+SGD S000029354 PET1 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20010119 SGD
+SGD S000001754 PET10 GO:0005811 SGD_REF:S000048561|PMID:10515935 IDA C YKR046C gene taxon:4932 20020917 SGD
+SGD S000001754 PET10 GO:0005554 SGD_REF:S000069584 ND F YKR046C gene taxon:4932 20030117 SGD
+SGD S000001754 PET10 GO:0009060 SGD_REF:S000061788|PMID:10618406 IEP P YKR046C gene taxon:4932 20030916 SGD
+SGD S000002486 PET100 GO:0005743 SGD_REF:S000061220|PMID:11498004 IDA C cytochrome c oxidase-specific assembly factor YDR079W gene taxon:4932 20020613 SGD
+SGD S000002486 PET100 GO:0051082 SGD_REF:S000061220|PMID:11498004 IDA F cytochrome c oxidase-specific assembly factor YDR079W gene taxon:4932 20020613 SGD
+SGD S000002486 PET100 GO:0008535 SGD_REF:S000061220|PMID:11498004 IDA P cytochrome c oxidase-specific assembly factor YDR079W gene taxon:4932 20020613 SGD
+SGD S000002486 PET100 GO:0009060 SGD_REF:S000053838|PMID:8702496 IMP P cytochrome c oxidase-specific assembly factor YDR079W gene taxon:4932 20020613 SGD
+SGD S000029355 PET11 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20010119 SGD
+SGD S000029355 PET11 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20010119 SGD
+SGD S000029355 PET11 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20010119 SGD
+SGD S000004870 PET111 GO:0005743 SGD_REF:S000059792|PMID:11106667 IDA C translational activator of cytochrome C oxidase subunit II YMR257C gene taxon:4932 20030210 SGD
+SGD S000004870 PET111 GO:0045182 SGD_REF:S000040998|PMID:3034718 IMP F translational activator of cytochrome C oxidase subunit II YMR257C gene taxon:4932 20030210 SGD
+SGD S000004870 PET111 GO:0006412 SGD_REF:S000040998|PMID:3034718 IMP P translational activator of cytochrome C oxidase subunit II YMR257C gene taxon:4932 20030210 SGD
+SGD S000000176 PET112 GO:0005739 SGD_REF:S000049683|PMID:9287027 IGI C 62 kDa protein YBL080C gene taxon:4932 20020619 SGD
+SGD S000000176 PET112 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C 62 kDa protein YBL080C gene taxon:4932 20040928 SGD
+SGD S000000176 PET112 GO:0005554 SGD_REF:S000069584 ND F 62 kDa protein YBL080C gene taxon:4932 20021204 SGD
+SGD S000000176 PET112 GO:0006412 SGD_REF:S000040039|PMID:8082172 IMP P 62 kDa protein YBL080C gene taxon:4932 20020619 SGD
+SGD S000000176 PET112 GO:0007005 SGD_REF:S000040039|PMID:8082172 IMP P 62 kDa protein YBL080C gene taxon:4932 20020619 SGD
+SGD S000000176 PET112 GO:0009060 SGD_REF:S000040039|PMID:8082172 IMP P 62 kDa protein YBL080C gene taxon:4932 20020619 SGD
+SGD S000029356 PET114 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20010119 SGD
+SGD S000029356 PET114 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20010119 SGD
+SGD S000029356 PET114 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20010119 SGD
+SGD S000000860 PET117 GO:0005743 SGD_REF:S000057943|PMID:8811190 TAS C YER058W gene taxon:4932 20010118 SGD
+SGD S000000860 PET117 GO:0005554 SGD_REF:S000057943|PMID:8811190 TAS F YER058W gene taxon:4932 20010118 SGD
+SGD S000000860 PET117 GO:0008535 SGD_REF:S000055882|PMID:8381337 IMP P YER058W gene taxon:4932 20010118 SGD
+SGD S000000955 PET122 GO:0005743 SGD_REF:S000052138|PMID:8389363 IDA C translational activator of cytochrome C oxidase subunit III YER153C gene taxon:4932 20030210 SGD
+SGD S000000955 PET122 GO:0045182 SGD_REF:S000040475|PMID:2833749 IMP F translational activator of cytochrome C oxidase subunit III YER153C gene taxon:4932 20030210 SGD
+SGD S000000955 PET122 GO:0006412 SGD_REF:S000040475|PMID:2833749 IMP P translational activator of cytochrome C oxidase subunit III YER153C gene taxon:4932 20030210 SGD
+SGD S000005684 PET123 GO:0005763 SGD_REF:S000058278|PMID:9445368 TAS C mitochondrial ribosomal protein of small subunit YOR158W gene taxon:4932 20010118 SGD
+SGD S000005684 PET123 GO:0005763 SGD_REF:S000060645|PMID:11278769 IDA C mitochondrial ribosomal protein of small subunit YOR158W gene taxon:4932 20010918 SGD
+SGD S000005684 PET123 GO:0003735 SGD_REF:S000058278|PMID:9445368 TAS F mitochondrial ribosomal protein of small subunit YOR158W gene taxon:4932 20010118 SGD
+SGD S000005684 PET123 GO:0003735 SGD_REF:S000060645|PMID:11278769 IDA F mitochondrial ribosomal protein of small subunit YOR158W gene taxon:4932 20010918 SGD
+SGD S000005684 PET123 GO:0043037 SGD_REF:S000058278|PMID:9445368 TAS P mitochondrial ribosomal protein of small subunit YOR158W gene taxon:4932 20010118 SGD
+SGD S000005684 PET123 GO:0043037 SGD_REF:S000060645|PMID:11278769 IDA P mitochondrial ribosomal protein of small subunit YOR158W gene taxon:4932 20010918 SGD
+SGD S000005543 PET127 GO:0005740 SGD_REF:S000047375|PMID:9111353 IDA C mitochondrial membrane protein YOR017W gene taxon:4932 20010118 SGD
+SGD S000005543 PET127 GO:0005554 SGD_REF:S000069584 ND F mitochondrial membrane protein YOR017W gene taxon:4932 20021206 SGD
+SGD S000005543 PET127 GO:0006396 SGD_REF:S000047375|PMID:9111353 IMP P mitochondrial membrane protein YOR017W gene taxon:4932 20010118 SGD
+SGD S000003560 PET130 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YJL023C gene taxon:4932 20040813 SGD
+SGD S000003560 PET130 GO:0005554 SGD_REF:S000069584 ND F YJL023C gene taxon:4932 20010119 SGD
+SGD S000003560 PET130 GO:0000004 SGD_REF:S000069584 ND P YJL023C gene taxon:4932 20010119 SGD
+SGD S000029357 PET14 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20010119 SGD
+SGD S000029357 PET14 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20010119 SGD
+SGD S000029357 PET14 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20010119 SGD
+SGD S000029358 PET17 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20010119 SGD
+SGD S000029358 PET17 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20010119 SGD
+SGD S000029358 PET17 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20010119 SGD
+SGD S000000613 PET18 GO:0008372 SGD_REF:S000069584 ND C YCR020C|HIT2 gene taxon:4932 20021001 SGD
+SGD S000000613 PET18 GO:0005554 SGD_REF:S000069584 ND F YCR020C|HIT2 gene taxon:4932 20021001 SGD
+SGD S000000613 PET18 GO:0006772 SGD_REF:S000056318|PMID:10383756 IEP P YCR020C|HIT2 gene taxon:4932 20021007 SGD
+SGD S000000613 PET18 GO:0007005 SGD_REF:S000053353|PMID:3916862 IMP P YCR020C|HIT2 gene taxon:4932 20021001 SGD
+SGD S000003795 PET191 GO:0005743 SGD_REF:S000057943|PMID:8811190 TAS C YJR034W gene taxon:4932 20010118 SGD
+SGD S000003795 PET191 GO:0005554 SGD_REF:S000057943|PMID:8811190 TAS F YJR034W gene taxon:4932 20010118 SGD
+SGD S000003795 PET191 GO:0008535 SGD_REF:S000055882|PMID:8381337 IMP P YJR034W gene taxon:4932 20010118 SGD
+SGD S000029359 PET2 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20010119 SGD
+SGD S000029359 PET2 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20010119 SGD
+SGD S000029359 PET2 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20010119 SGD
+SGD S000006080 PET20 GO:0008372 SGD_REF:S000069584 ND C YPL159C gene taxon:4932 20030205 SGD
+SGD S000006080 PET20 GO:0005554 SGD_REF:S000069584 ND F YPL159C gene taxon:4932 20030205 SGD
+SGD S000006080 PET20 GO:0000004 SGD_REF:S000069584 ND P YPL159C gene taxon:4932 20030205 SGD
+SGD S000029360 PET3 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20010119 SGD
+SGD S000029360 PET3 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20010119 SGD
+SGD S000029360 PET3 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20010119 SGD
+SGD S000004057 PET309 GO:0005743 SGD_REF:S000054498|PMID:9692914 IDA C YLR067C gene taxon:4932 20020607 SGD
+SGD S000004057 PET309 GO:0016021 SGD_REF:S000054498|PMID:9692914 IDA C YLR067C gene taxon:4932 20020607 SGD
+SGD S000004057 PET309 GO:0045182 SGD_REF:S000047623|PMID:7664742 IGI F YLR067C gene taxon:4932 20020607 SGD
+SGD S000004057 PET309 GO:0006412 SGD_REF:S000047623|PMID:7664742 IMP P YLR067C gene taxon:4932 20010118 SGD
+SGD S000004057 PET309 GO:0009060 SGD_REF:S000047623|PMID:7664742 IMP P YLR067C gene taxon:4932 20020610 SGD
+SGD S000004057 PET309 GO:0016070 SGD_REF:S000047623|PMID:7664742 IMP P YLR067C gene taxon:4932 20020610 SGD
+SGD S000029361 PET4 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20030724 SGD
+SGD S000029361 PET4 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20030724 SGD
+SGD S000029361 PET4 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20030724 SGD
+SGD S000005328 PET494 GO:0005743 SGD_REF:S000052138|PMID:8389363 IDA C translational activator of cytochrome C oxidase YNR045W gene taxon:4932 20030210 SGD
+SGD S000005328 PET494 GO:0045182 SGD_REF:S000040475|PMID:2833749 IMP F translational activator of cytochrome C oxidase YNR045W gene taxon:4932 20030210 SGD
+SGD S000005328 PET494 GO:0006412 SGD_REF:S000040475|PMID:2833749 IMP P translational activator of cytochrome C oxidase YNR045W gene taxon:4932 20030210 SGD
+SGD S000029362 PET5 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20030724 SGD
+SGD S000029362 PET5 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20030724 SGD
+SGD S000029362 PET5 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20030724 SGD
+SGD S000003454 PET54 GO:0005743 SGD_REF:S000052138|PMID:8389363 IDA C YGR222W gene taxon:4932 20030210 SGD
+SGD S000003454 PET54 GO:0005759 SGD_REF:S000052138|PMID:8389363 IDA C YGR222W gene taxon:4932 20030210 SGD
+SGD S000003454 PET54 GO:0003723 SGD_REF:S000052834|PMID:9341683 NAS F YGR222W gene taxon:4932 20030822 SGD
+SGD S000003454 PET54 GO:0045182 SGD_REF:S000054211|PMID:2548921 IMP F YGR222W gene taxon:4932 20030210 SGD
+SGD S000003454 PET54 GO:0000372 SGD_REF:S000052834|PMID:9341683 IGI P YGR222W gene taxon:4932 20030822 SGD
+SGD S000003454 PET54 GO:0006412 SGD_REF:S000054211|PMID:2548921 IMP P YGR222W gene taxon:4932 20030210 SGD
+SGD S000029363 PET6 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20030724 SGD
+SGD S000029363 PET6 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20030724 SGD
+SGD S000029363 PET6 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20030724 SGD
+SGD S000029364 PET7 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20030724 SGD
+SGD S000029364 PET7 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20030724 SGD
+SGD S000029364 PET7 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20030724 SGD
+SGD S000004948 PET8 GO:0005739 SGD_REF:S000074329|PMID:14609944 IDA C YNL003C|SAM5 gene taxon:4932 20031117 SGD
+SGD S000004948 PET8 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YNL003C|SAM5 gene taxon:4932 20040924 SGD
+SGD S000004948 PET8 GO:0005743 SGD_REF:S000049213|PMID:10930523 ISS C YNL003C|SAM5 gene taxon:4932 20021017 SGD
+SGD S000004948 PET8 GO:0000095 SGD_REF:S000074329|PMID:14609944 IDA F YNL003C|SAM5 gene taxon:4932 20031117 SGD
+SGD S000004948 PET8 GO:0000095 SGD_REF:S000074329|PMID:14609944 IGI SGD:S000004170 F YNL003C|SAM5 gene taxon:4932 20031117 SGD
+SGD S000004948 PET8 GO:0000095 SGD_REF:S000074329|PMID:14609944 IMP F YNL003C|SAM5 gene taxon:4932 20031117 SGD
+SGD S000004948 PET8 GO:0015805 SGD_REF:S000074329|PMID:14609944 IDA P YNL003C|SAM5 gene taxon:4932 20031117 SGD
+SGD S000004948 PET8 GO:0015805 SGD_REF:S000074329|PMID:14609944 IGI SGD:S000004170 P YNL003C|SAM5 gene taxon:4932 20031117 SGD
+SGD S000004948 PET8 GO:0015805 SGD_REF:S000074329|PMID:14609944 IMP P YNL003C|SAM5 gene taxon:4932 20031117 SGD
+SGD S000000126 PET9 GO:0005743 SGD_REF:S000043940|PMID:795470 IDA C ADP/ATP translocator YBL030C|AAC2|ANC2|OP1 gene taxon:4932 20010118 SGD
+SGD S000000126 PET9 GO:0005471 SGD_REF:S000049750|PMID:8476415 IDA F ADP/ATP translocator YBL030C|AAC2|ANC2|OP1 gene taxon:4932 20010213 SGD
+SGD S000000126 PET9 GO:0006839 SGD_REF:S000050955|PMID:2167309 IMP P ADP/ATP translocator YBL030C|AAC2|ANC2|OP1 gene taxon:4932 20040226 SGD
+SGD S000000126 PET9 GO:0009060 SGD_REF:S000050955|PMID:2167309 IMP P ADP/ATP translocator YBL030C|AAC2|ANC2|OP1 gene taxon:4932 20040226 SGD
+SGD S000000126 PET9 GO:0009061 SGD_REF:S000052497|PMID:1915842 IGI SGD:S000000289 P ADP/ATP translocator YBL030C|AAC2|ANC2|OP1 gene taxon:4932 20040226 SGD
+SGD S000029365 PETX GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20010119 SGD
+SGD S000029365 PETX GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20010119 SGD
+SGD S000029365 PETX GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20010119 SGD
+SGD S000001680 PEX1 GO:0005777 SGD_REF:S000074185|PMID:14562095 IDA C AAA ATPase, peroxin YKL197C|PAS1 gene taxon:4932 20031028 SGD
+SGD S000001680 PEX1 GO:0016887 SGD_REF:S000045468|PMID:1825027 ISS F AAA ATPase, peroxin YKL197C|PAS1 gene taxon:4932 20010118 SGD
+SGD S000001680 PEX1 GO:0007031 SGD_REF:S000058494 TAS P AAA ATPase, peroxin YKL197C|PAS1 gene taxon:4932 20010119 SGD
+SGD S000002673 PEX10 GO:0005778 SGD_REF:S000073142|PMID:12667447 TAS C C3HC4 zinc-binding integral peroxisomal membrane protein, peroxin YDR265W|PAS4 gene taxon:4932 20030603 SGD
+SGD S000002673 PEX10 GO:0005515 SGD_REF:S000073142|PMID:12667447 TAS F C3HC4 zinc-binding integral peroxisomal membrane protein, peroxin YDR265W|PAS4 gene taxon:4932 20030603 SGD
+SGD S000002673 PEX10 GO:0007031 SGD_REF:S000058494 TAS P C3HC4 zinc-binding integral peroxisomal membrane protein, peroxin YDR265W|PAS4 gene taxon:4932 20010119 SGD
+SGD S000005507 PEX11 GO:0005778 SGD_REF:S000058494 TAS C peroxin, peroxisomal membrane protein YOL147C|PMP24|PMP27 gene taxon:4932 20010119 SGD
+SGD S000005507 PEX11 GO:0005554 SGD_REF:S000069584 ND F peroxin, peroxisomal membrane protein YOL147C|PMP24|PMP27 gene taxon:4932 20010119 SGD
+SGD S000005507 PEX11 GO:0007031 SGD_REF:S000058494 TAS P peroxin, peroxisomal membrane protein YOL147C|PMP24|PMP27 gene taxon:4932 20010119 SGD
+SGD S000005507 PEX11 GO:0016559 SGD_REF:S000078206|PMID:12417726 TAS P peroxin, peroxisomal membrane protein YOL147C|PMP24|PMP27 gene taxon:4932 20050302 SGD
+SGD S000005507 PEX11 GO:0016559 SGD_REF:S000069445|PMID:11839773 TAS P peroxin, peroxisomal membrane protein YOL147C|PMP24|PMP27 gene taxon:4932 20050302 SGD
+SGD S000005507 PEX11 GO:0019395 SGD_REF:S000052800|PMID:10931862 IMP P peroxin, peroxisomal membrane protein YOL147C|PMP24|PMP27 gene taxon:4932 20050302 SGD
+SGD S000004628 PEX12 GO:0005778 SGD_REF:S000058494 TAS C C3HC4 zinc-binding integral peroxisomal membrane protein YMR026C|PAS11 gene taxon:4932 20010119 SGD
+SGD S000004628 PEX12 GO:0005515 SGD_REF:S000073142|PMID:12667447 TAS F C3HC4 zinc-binding integral peroxisomal membrane protein YMR026C|PAS11 gene taxon:4932 20030603 SGD
+SGD S000004628 PEX12 GO:0007031 SGD_REF:S000058494 TAS P C3HC4 zinc-binding integral peroxisomal membrane protein YMR026C|PAS11 gene taxon:4932 20010119 SGD
+SGD S000004628 PEX12 GO:0016558 SGD_REF:S000058069|PMID:9090384 IMP P C3HC4 zinc-binding integral peroxisomal membrane protein YMR026C|PAS11 gene taxon:4932 20050308 SGD
+SGD S000004181 PEX13 GO:0005778 SGD_REF:S000058494 TAS C contains Src homology 3 (SH3) domain YLR191W|PAS20 gene taxon:4932 20010119 SGD
+SGD S000004181 PEX13 GO:0005515 SGD_REF:S000043668|PMID:10087260 IDA F contains Src homology 3 (SH3) domain YLR191W|PAS20 gene taxon:4932 20010118 SGD
+SGD S000004181 PEX13 GO:0006625 SGD_REF:S000043668|PMID:10087260 IPI P contains Src homology 3 (SH3) domain YLR191W|PAS20 gene taxon:4932 20010118 SGD
+SGD S000004181 PEX13 GO:0006625 SGD_REF:S000043668|PMID:10087260 IGI P contains Src homology 3 (SH3) domain YLR191W|PAS20 gene taxon:4932 20010118 SGD
+SGD S000004181 PEX13 GO:0007031 SGD_REF:S000058494 TAS P contains Src homology 3 (SH3) domain YLR191W|PAS20 gene taxon:4932 20010119 SGD
+SGD S000004181 PEX13 GO:0016558 SGD_REF:S000049491|PMID:8858167 IMP P contains Src homology 3 (SH3) domain YLR191W|PAS20 gene taxon:4932 20050316 SGD
+SGD S000003121 PEX14 GO:0005778 SGD_REF:S000043668|PMID:10087260 IDA C peroxin YGL153W gene taxon:4932 20010118 SGD
+SGD S000003121 PEX14 GO:0005778 SGD_REF:S000043668|PMID:10087260 TAS C peroxin YGL153W gene taxon:4932 20010118 SGD
+SGD S000003121 PEX14 GO:0005515 SGD_REF:S000043668|PMID:10087260 TAS F peroxin YGL153W gene taxon:4932 20010118 SGD
+SGD S000003121 PEX14 GO:0006625 SGD_REF:S000043668|PMID:10087260 IMP P peroxin YGL153W gene taxon:4932 20010118 SGD
+SGD S000003121 PEX14 GO:0006625 SGD_REF:S000043668|PMID:10087260 IPI P peroxin YGL153W gene taxon:4932 20010118 SGD
+SGD S000003121 PEX14 GO:0006625 SGD_REF:S000043668|PMID:10087260 TAS P peroxin YGL153W gene taxon:4932 20010118 SGD
+SGD S000003121 PEX14 GO:0016558 SGD_REF:S000040803|PMID:9312008 IPI SGD:S000002549|SGD:S000002652|SGD:S000004181 P peroxin YGL153W gene taxon:4932 20050316 SGD
+SGD S000005404 PEX15 GO:0005778 SGD_REF:S000049903|PMID:9405362 IDA C 44 kDa phosphorylated integral peroxisomal membrane protein YOL044W|PAS21 gene taxon:4932 20010118 SGD
+SGD S000005404 PEX15 GO:0005554 SGD_REF:S000069584 ND F 44 kDa phosphorylated integral peroxisomal membrane protein YOL044W|PAS21 gene taxon:4932 20010119 SGD
+SGD S000005404 PEX15 GO:0006625 SGD_REF:S000049903|PMID:9405362 IMP P 44 kDa phosphorylated integral peroxisomal membrane protein YOL044W|PAS21 gene taxon:4932 20010118 SGD
+SGD S000005404 PEX15 GO:0007031 SGD_REF:S000049903|PMID:9405362 IMP P 44 kDa phosphorylated integral peroxisomal membrane protein YOL044W|PAS21 gene taxon:4932 20010118 SGD
+SGD S000005158 PEX17 GO:0005778 SGD_REF:S000055336|PMID:9425153 IMP C peroxin YNL214W|PAS9 gene taxon:4932 20010118 SGD
+SGD S000005158 PEX17 GO:0005515 SGD_REF:S000055336|PMID:9425153 IDA F peroxin YNL214W|PAS9 gene taxon:4932 20010118 SGD
+SGD S000005158 PEX17 GO:0007031 SGD_REF:S000058494 TAS P peroxin YNL214W|PAS9 gene taxon:4932 20010119 SGD
+SGD S000001203 PEX18 GO:0005777 SGD_REF:S000055442|PMID:9864360 IDA C peroxin YHR160C gene taxon:4932 20010118 SGD
+SGD S000001203 PEX18 GO:0005829 SGD_REF:S000055442|PMID:9864360 IDA C peroxin YHR160C gene taxon:4932 20010118 SGD
+SGD S000001203 PEX18 GO:0005515 SGD_REF:S000055442|PMID:9864360 IDA F peroxin YHR160C gene taxon:4932 20010118 SGD
+SGD S000001203 PEX18 GO:0006625 SGD_REF:S000055442|PMID:9864360 IMP P peroxin YHR160C gene taxon:4932 20010118 SGD
+SGD S000001203 PEX18 GO:0006625 SGD_REF:S000055442|PMID:9864360 IPI P peroxin YHR160C gene taxon:4932 20010118 SGD
+SGD S000002223 PEX19 GO:0005829 SGD_REF:S000044250|PMID:9418908 IDA C 40 kDa farnesylated protein associated with peroxisomes YDL065C|PAS12 gene taxon:4932 20010118 SGD
+SGD S000002223 PEX19 GO:0005515 SGD_REF:S000077162|PMID:15007061 IDA F 40 kDa farnesylated protein associated with peroxisomes YDL065C|PAS12 gene taxon:4932 20050315 SGD
+SGD S000002223 PEX19 GO:0006457 SGD_REF:S000077162|PMID:15007061 TAS P 40 kDa farnesylated protein associated with peroxisomes YDL065C|PAS12 gene taxon:4932 20050315 SGD
+SGD S000002223 PEX19 GO:0006625 SGD_REF:S000042731|PMID:10637226 IMP P 40 kDa farnesylated protein associated with peroxisomes YDL065C|PAS12 gene taxon:4932 20010118 SGD
+SGD S000002223 PEX19 GO:0007031 SGD_REF:S000044250|PMID:9418908 IMP P 40 kDa farnesylated protein associated with peroxisomes YDL065C|PAS12 gene taxon:4932 20010118 SGD
+SGD S000002223 PEX19 GO:0007031 SGD_REF:S000042731|PMID:10637226 IMP P 40 kDa farnesylated protein associated with peroxisomes YDL065C|PAS12 gene taxon:4932 20010118 SGD
+SGD S000002223 PEX19 GO:0045046 SGD_REF:S000077162|PMID:15007061 TAS P 40 kDa farnesylated protein associated with peroxisomes YDL065C|PAS12 gene taxon:4932 20050315 SGD
+SGD S000003746 PEX2 GO:0005778 SGD_REF:S000073142|PMID:12667447 TAS C CH3HC4 zinc-binding integral peroxisomal membrane protein, peroxin YJL210W|CRT1|PAS5 gene taxon:4932 20030603 SGD
+SGD S000003746 PEX2 GO:0005515 SGD_REF:S000073142|PMID:12667447 TAS F CH3HC4 zinc-binding integral peroxisomal membrane protein, peroxin YJL210W|CRT1|PAS5 gene taxon:4932 20030603 SGD
+SGD S000003746 PEX2 GO:0007031 SGD_REF:S000058494 TAS P CH3HC4 zinc-binding integral peroxisomal membrane protein, peroxin YJL210W|CRT1|PAS5 gene taxon:4932 20010119 SGD
+SGD S000003471 PEX21 GO:0005777 SGD_REF:S000055442|PMID:9864360 IDA C peroxin YGR239C gene taxon:4932 20010118 SGD
+SGD S000003471 PEX21 GO:0005829 SGD_REF:S000055442|PMID:9864360 IDA C peroxin YGR239C gene taxon:4932 20010118 SGD
+SGD S000003471 PEX21 GO:0005515 SGD_REF:S000055442|PMID:9864360 IDA F peroxin YGR239C gene taxon:4932 20010118 SGD
+SGD S000003471 PEX21 GO:0008047 SGD_REF:S000070395|PMID:12204379 IDA F peroxin YGR239C gene taxon:4932 20030414 SGD
+SGD S000003471 PEX21 GO:0006625 SGD_REF:S000055442|PMID:9864360 IMP P peroxin YGR239C gene taxon:4932 20010118 SGD
+SGD S000003471 PEX21 GO:0006625 SGD_REF:S000055442|PMID:9864360 IPI P peroxin YGR239C gene taxon:4932 20010118 SGD
+SGD S000000051 PEX22 GO:0005777 SGD_REF:S000049243|PMID:10402463 ISS C YAL055W|YAF5 gene taxon:4932 20010118 SGD
+SGD S000000051 PEX22 GO:0005554 SGD_REF:S000069584 ND F YAL055W|YAF5 gene taxon:4932 20010119 SGD
+SGD S000000051 PEX22 GO:0006625 SGD_REF:S000049243|PMID:10402463 ISS P YAL055W|YAF5 gene taxon:4932 20010118 SGD
+SGD S000006033 PEX25 GO:0005778 SGD_REF:S000070290|PMID:12135984 IDA C peroxin YPL112C gene taxon:4932 20020820 SGD
+SGD S000006033 PEX25 GO:0005554 SGD_REF:S000069584 ND F peroxin YPL112C gene taxon:4932 20021220 SGD
+SGD S000006033 PEX25 GO:0007031 SGD_REF:S000070290|PMID:12135984 IMP P peroxin YPL112C gene taxon:4932 20021220 SGD
+SGD S000006033 PEX25 GO:0007031 SGD_REF:S000070290|PMID:12135984 ISS P peroxin YPL112C gene taxon:4932 20021220 SGD
+SGD S000006033 PEX25 GO:0007031 SGD_REF:S000070290|PMID:12135984 IEP P peroxin YPL112C gene taxon:4932 20021220 SGD
+SGD S000006033 PEX25 GO:0016558 SGD_REF:S000070290|PMID:12135984 IMP P peroxin YPL112C gene taxon:4932 20050317 SGD
+SGD S000005719 PEX27 GO:0005778 SGD_REF:S000074269|PMID:14517321 IDA C YOR193W gene taxon:4932 20040129 SGD
+SGD S000005719 PEX27 GO:0005554 SGD_REF:S000069584 ND F YOR193W gene taxon:4932 20040129 SGD
+SGD S000005719 PEX27 GO:0007031 SGD_REF:S000074269|PMID:14517321 IMP P YOR193W gene taxon:4932 20040129 SGD
+SGD S000005719 PEX27 GO:0007031 SGD_REF:S000074269|PMID:14517321 ISS P YOR193W gene taxon:4932 20040129 SGD
+SGD S000005719 PEX27 GO:0007031 SGD_REF:S000074269|PMID:14517321 IPI SGD:S000006033 P YOR193W gene taxon:4932 20040129 SGD
+SGD S000001193 PEX28 GO:0005778 SGD_REF:S000073055|PMID:12707309 IDA C peroxin YHR150W gene taxon:4932 20030513 SGD
+SGD S000001193 PEX28 GO:0005554 SGD_REF:S000069584 ND F peroxin YHR150W gene taxon:4932 20030506 SGD
+SGD S000001193 PEX28 GO:0007031 SGD_REF:S000073055|PMID:12707309 IGI P peroxin YHR150W gene taxon:4932 20030506 SGD
+SGD S000001193 PEX28 GO:0007031 SGD_REF:S000073055|PMID:12707309 IDA P peroxin YHR150W gene taxon:4932 20030506 SGD
+SGD S000001193 PEX28 GO:0007031 SGD_REF:S000073055|PMID:12707309 IMP P peroxin YHR150W gene taxon:4932 20030506 SGD
+SGD S000002887 PEX29 GO:0005778 SGD_REF:S000073055|PMID:12707309 IDA C peroxin YDR479C gene taxon:4932 20030513 SGD
+SGD S000002887 PEX29 GO:0005554 SGD_REF:S000069584 ND F peroxin YDR479C gene taxon:4932 20030506 SGD
+SGD S000002887 PEX29 GO:0007031 SGD_REF:S000073055|PMID:12707309 IGI P peroxin YDR479C gene taxon:4932 20030506 SGD
+SGD S000002887 PEX29 GO:0007031 SGD_REF:S000073055|PMID:12707309 IMP P peroxin YDR479C gene taxon:4932 20030506 SGD
+SGD S000002887 PEX29 GO:0007031 SGD_REF:S000073055|PMID:12707309 IDA P peroxin YDR479C gene taxon:4932 20030506 SGD
+SGD S000002737 PEX3 GO:0005778 SGD_REF:S000053475|PMID:1894692 IDA C 48 kDa peroxisomal integral membrane protein YDR329C|PAS3 gene taxon:4932 20010118 SGD
+SGD S000002737 PEX3 GO:0005515 SGD_REF:S000077162|PMID:15007061 IDA F 48 kDa peroxisomal integral membrane protein YDR329C|PAS3 gene taxon:4932 20050315 SGD
+SGD S000002737 PEX3 GO:0006625 SGD_REF:S000042731|PMID:10637226 IMP P 48 kDa peroxisomal integral membrane protein YDR329C|PAS3 gene taxon:4932 20010118 SGD
+SGD S000002737 PEX3 GO:0007031 SGD_REF:S000058494 TAS P 48 kDa peroxisomal integral membrane protein YDR329C|PAS3 gene taxon:4932 20010119 SGD
+SGD S000002737 PEX3 GO:0045046 SGD_REF:S000077162|PMID:15007061 IMP P 48 kDa peroxisomal integral membrane protein YDR329C|PAS3 gene taxon:4932 20050315 SGD
+SGD S000004316 PEX30 GO:0005777 SGD_REF:S000074185|PMID:14562095 IDA C YLR324W gene taxon:4932 20031028 SGD
+SGD S000004316 PEX30 GO:0005779 SGD_REF:S000075501|PMID:14617799 IDA C YLR324W gene taxon:4932 20040310 SGD
+SGD S000004316 PEX30 GO:0005554 SGD_REF:S000069584 ND F YLR324W gene taxon:4932 20021126 SGD
+SGD S000004316 PEX30 GO:0007031 SGD_REF:S000075501|PMID:14617799 IMP P YLR324W gene taxon:4932 20040310 SGD
+SGD S000003236 PEX31 GO:0005779 SGD_REF:S000075501|PMID:14617799 IDA C YGR004W gene taxon:4932 20040310 SGD
+SGD S000003236 PEX31 GO:0005554 SGD_REF:S000069584 ND F YGR004W gene taxon:4932 20021126 SGD
+SGD S000003236 PEX31 GO:0007031 SGD_REF:S000075501|PMID:14617799 IMP P YGR004W gene taxon:4932 20040310 SGD
+SGD S000000372 PEX32 GO:0005779 SGD_REF:S000075501|PMID:14617799 IDA C YBR168W gene taxon:4932 20040310 SGD
+SGD S000000372 PEX32 GO:0005554 SGD_REF:S000069584 ND F YBR168W gene taxon:4932 20030421 SGD
+SGD S000000372 PEX32 GO:0007031 SGD_REF:S000075501|PMID:14617799 IMP P YBR168W gene taxon:4932 20040310 SGD
+SGD S000003365 PEX4 GO:0005777 SGD_REF:S000054606|PMID:1326082 IDA C ubiquitin-conjugating protein family YGR133W|PAS2|UBC10 gene taxon:4932 20051027 SGD
+SGD S000003365 PEX4 GO:0004840 SGD_REF:S000054606|PMID:1326082 ISS SGD:S000000286|SGD:S000002461|SGD:S000003026|SGD:S000000738 F ubiquitin-conjugating protein family YGR133W|PAS2|UBC10 gene taxon:4932 20051027 SGD
+SGD S000003365 PEX4 GO:0000209 SGD_REF:S000058010|PMID:8982460 TAS P ubiquitin-conjugating protein family YGR133W|PAS2|UBC10 gene taxon:4932 20010118 SGD
+SGD S000003365 PEX4 GO:0006513 SGD_REF:S000058010|PMID:8982460 TAS P ubiquitin-conjugating protein family YGR133W|PAS2|UBC10 gene taxon:4932 20010118 SGD
+SGD S000003365 PEX4 GO:0006625 SGD_REF:S000073905|PMID:12876220 IPI SGD:S000002673 P ubiquitin-conjugating protein family YGR133W|PAS2|UBC10 gene taxon:4932 20050322 SGD
+SGD S000003365 PEX4 GO:0007031 SGD_REF:S000058494 TAS P ubiquitin-conjugating protein family YGR133W|PAS2|UBC10 gene taxon:4932 20010119 SGD
+SGD S000003365 PEX4 GO:0007031 SGD_REF:S000058010|PMID:8982460 TAS P ubiquitin-conjugating protein family YGR133W|PAS2|UBC10 gene taxon:4932 20010118 SGD
+SGD S000003365 PEX4 GO:0016558 SGD_REF:S000080208|PMID:15632140 IMP P ubiquitin-conjugating protein family YGR133W|PAS2|UBC10 gene taxon:4932 20050322 SGD
+SGD S000002652 PEX5 GO:0005777 SGD_REF:S000049490|PMID:8858166 IDA C 69 kDa protein containing tetratricopeptide repeat (TPR), peroxin YDR244W|PAS10 gene taxon:4932 20010118 SGD
+SGD S000002652 PEX5 GO:0005777 SGD_REF:S000080208|PMID:15632140 IDA C 69 kDa protein containing tetratricopeptide repeat (TPR), peroxin YDR244W|PAS10 gene taxon:4932 20050126 SGD
+SGD S000002652 PEX5 GO:0005829 SGD_REF:S000049490|PMID:8858166 IDA C 69 kDa protein containing tetratricopeptide repeat (TPR), peroxin YDR244W|PAS10 gene taxon:4932 20010118 SGD
+SGD S000002652 PEX5 GO:0000268 SGD_REF:S000045482|PMID:7980572 IDA F 69 kDa protein containing tetratricopeptide repeat (TPR), peroxin YDR244W|PAS10 gene taxon:4932 20010118 SGD
+SGD S000002652 PEX5 GO:0005052 SGD_REF:S000045482|PMID:7980572 IPI F 69 kDa protein containing tetratricopeptide repeat (TPR), peroxin YDR244W|PAS10 gene taxon:4932 20030319 SGD
+SGD S000002652 PEX5 GO:0006625 SGD_REF:S000045482|PMID:7980572 IPI P 69 kDa protein containing tetratricopeptide repeat (TPR), peroxin YDR244W|PAS10 gene taxon:4932 20010118 SGD
+SGD S000002652 PEX5 GO:0007031 SGD_REF:S000058494 TAS P 69 kDa protein containing tetratricopeptide repeat (TPR), peroxin YDR244W|PAS10 gene taxon:4932 20010119 SGD
+SGD S000005273 PEX6 GO:0005625 SGD_REF:S000073552|PMID:12808025 IDA C AAA ATPase YNL329C|PAS8 gene taxon:4932 20040816 SGD
+SGD S000005273 PEX6 GO:0005737 SGD_REF:S000073552|PMID:12808025 IDA C AAA ATPase YNL329C|PAS8 gene taxon:4932 20040816 SGD
+SGD S000005273 PEX6 GO:0005737 SGD_REF:S000073552|PMID:12808025 IMP C AAA ATPase YNL329C|PAS8 gene taxon:4932 20040816 SGD
+SGD S000005273 PEX6 GO:0005777 SGD_REF:S000064382|PMID:9588209 ISS C AAA ATPase YNL329C|PAS8 gene taxon:4932 20021206 SGD
+SGD S000005273 PEX6 GO:0005777 SGD_REF:S000073552|PMID:12808025 IDA C AAA ATPase YNL329C|PAS8 gene taxon:4932 20040816 SGD
+SGD S000005273 PEX6 GO:0005777 SGD_REF:S000073552|PMID:12808025 IMP C AAA ATPase YNL329C|PAS8 gene taxon:4932 20040816 SGD
+SGD S000005273 PEX6 GO:0016887 SGD_REF:S000054025|PMID:8241279 ISS F AAA ATPase YNL329C|PAS8 gene taxon:4932 20010118 SGD
+SGD S000005273 PEX6 GO:0007031 SGD_REF:S000058494 TAS P AAA ATPase YNL329C|PAS8 gene taxon:4932 20010119 SGD
+SGD S000002549 PEX7 GO:0005782 SGD_REF:S000058494 TAS C beta-transducin-related (WD-40) protein family YDR142C|PAS7|PEB1 gene taxon:4932 20010119 SGD
+SGD S000002549 PEX7 GO:0005782 SGD_REF:S000055442|PMID:9864360 IDA C beta-transducin-related (WD-40) protein family YDR142C|PAS7|PEB1 gene taxon:4932 20030319 SGD
+SGD S000002549 PEX7 GO:0005829 SGD_REF:S000055442|PMID:9864360 IDA C beta-transducin-related (WD-40) protein family YDR142C|PAS7|PEB1 gene taxon:4932 20030319 SGD
+SGD S000002549 PEX7 GO:0000268 SGD_REF:S000044455|PMID:7957058 IGI SGD:S000001422 F beta-transducin-related (WD-40) protein family YDR142C|PAS7|PEB1 gene taxon:4932 20050929 SGD
+SGD S000002549 PEX7 GO:0005053 SGD_REF:S000046192|PMID:8636211 IPI F beta-transducin-related (WD-40) protein family YDR142C|PAS7|PEB1 gene taxon:4932 20030319 SGD
+SGD S000002549 PEX7 GO:0006625 SGD_REF:S000043668|PMID:10087260 TAS P beta-transducin-related (WD-40) protein family YDR142C|PAS7|PEB1 gene taxon:4932 20010118 SGD
+SGD S000002549 PEX7 GO:0006625 SGD_REF:S000064264|PMID:7902359 IMP P beta-transducin-related (WD-40) protein family YDR142C|PAS7|PEB1 gene taxon:4932 20050315 SGD
+SGD S000002549 PEX7 GO:0007031 SGD_REF:S000058494 TAS P beta-transducin-related (WD-40) protein family YDR142C|PAS7|PEB1 gene taxon:4932 20010119 SGD
+SGD S000003309 PEX8 GO:0005778 SGD_REF:S000041571|PMID:10652355 IDA C peroxisome associated protein containing a PTS1 signal YGR077C|PAS6 gene taxon:4932 20010118 SGD
+SGD S000003309 PEX8 GO:0005782 SGD_REF:S000058494 TAS C peroxisome associated protein containing a PTS1 signal YGR077C|PAS6 gene taxon:4932 20010119 SGD
+SGD S000003309 PEX8 GO:0000268 SGD_REF:S000041571|PMID:10652355 NAS F peroxisome associated protein containing a PTS1 signal YGR077C|PAS6 gene taxon:4932 20010118 SGD
+SGD S000003309 PEX8 GO:0006625 SGD_REF:S000041571|PMID:10652355 IMP P peroxisome associated protein containing a PTS1 signal YGR077C|PAS6 gene taxon:4932 20010118 SGD
+SGD S000003309 PEX8 GO:0007031 SGD_REF:S000058494 TAS P peroxisome associated protein containing a PTS1 signal YGR077C|PAS6 gene taxon:4932 20010119 SGD
+SGD S000005270 PFA3 GO:0000324 SGD_REF:S000074185|PMID:14562095 IDA C palmitoyltransferase for Vac8p YNL326C gene taxon:4932 20031028 SGD
+SGD S000005270 PFA3 GO:0000329 SGD_REF:S000086830|PMID:16186255 IDA C palmitoyltransferase for Vac8p YNL326C gene taxon:4932 20051017 SGD
+SGD S000005270 PFA3 GO:0019706 SGD_REF:S000082414|PMID:15973437 ISS F palmitoyltransferase for Vac8p YNL326C gene taxon:4932 20051017 SGD
+SGD S000005270 PFA3 GO:0019706 SGD_REF:S000086830|PMID:16186255 IDA F palmitoyltransferase for Vac8p YNL326C gene taxon:4932 20051017 SGD
+SGD S000005270 PFA3 GO:0018318 SGD_REF:S000082414|PMID:15973437 ISS P palmitoyltransferase for Vac8p YNL326C gene taxon:4932 20051017 SGD
+SGD S000005270 PFA3 GO:0018318 SGD_REF:S000086830|PMID:16186255 IDA P palmitoyltransferase for Vac8p YNL326C gene taxon:4932 20051017 SGD
+SGD S000005270 PFA3 GO:0042144 SGD_REF:S000086830|PMID:16186255 IGI P palmitoyltransferase for Vac8p YNL326C gene taxon:4932 20051017 SGD
+SGD S000005270 PFA3 GO:0042144 SGD_REF:S000086830|PMID:16186255 IMP P palmitoyltransferase for Vac8p YNL326C gene taxon:4932 20051017 SGD
+SGD S000005363 PFA4 GO:0008372 SGD_REF:S000069584 ND C palmitoyltransferase YOL003C gene taxon:4932 20051017 SGD
+SGD S000005363 PFA4 GO:0019706 SGD_REF:S000082414|PMID:15973437 ISS F palmitoyltransferase YOL003C gene taxon:4932 20051017 SGD
+SGD S000005363 PFA4 GO:0019706 SGD_REF:S000086830|PMID:16186255 IDA F palmitoyltransferase YOL003C gene taxon:4932 20051018 SGD
+SGD S000005363 PFA4 GO:0018318 SGD_REF:S000082414|PMID:15973437 ISS P palmitoyltransferase YOL003C gene taxon:4932 20051017 SGD
+SGD S000005363 PFA4 GO:0018318 SGD_REF:S000086830|PMID:16186255 ISS P palmitoyltransferase YOL003C gene taxon:4932 20051017 SGD
+SGD S000002867 PFA5 GO:0008372 SGD_REF:S000069584 ND C palmitoyltransferase YDR459C gene taxon:4932 20051017 SGD
+SGD S000002867 PFA5 GO:0019706 SGD_REF:S000082414|PMID:15973437 ISS F palmitoyltransferase YDR459C gene taxon:4932 20051017 SGD
+SGD S000002867 PFA5 GO:0019706 SGD_REF:S000086830|PMID:16186255 IDA F palmitoyltransferase YDR459C gene taxon:4932 20051018 SGD
+SGD S000002867 PFA5 GO:0018318 SGD_REF:S000082414|PMID:15973437 ISS P palmitoyltransferase YDR459C gene taxon:4932 20051017 SGD
+SGD S000002867 PFA5 GO:0018318 SGD_REF:S000086830|PMID:16186255 ISS P palmitoyltransferase YDR459C gene taxon:4932 20051017 SGD
+SGD S000003715 PFD1 GO:0016272 SGD_REF:S000058336|PMID:9630229 IMP C bovine prefoldin subunit 1 homolog (putative) YJL179W|GIM6 gene taxon:4932 20021028 SGD
+SGD S000003715 PFD1 GO:0016272 SGD_REF:S000058336|PMID:9630229 ISS C bovine prefoldin subunit 1 homolog (putative) YJL179W|GIM6 gene taxon:4932 20021028 SGD
+SGD S000003715 PFD1 GO:0051082 SGD_REF:S000058336|PMID:9630229 IMP F bovine prefoldin subunit 1 homolog (putative) YJL179W|GIM6 gene taxon:4932 20021028 SGD
+SGD S000003715 PFD1 GO:0051082 SGD_REF:S000058336|PMID:9630229 ISS F bovine prefoldin subunit 1 homolog (putative) YJL179W|GIM6 gene taxon:4932 20021028 SGD
+SGD S000003715 PFD1 GO:0006457 SGD_REF:S000058336|PMID:9630229 IMP P bovine prefoldin subunit 1 homolog (putative) YJL179W|GIM6 gene taxon:4932 20021028 SGD
+SGD S000003715 PFD1 GO:0006457 SGD_REF:S000058336|PMID:9630229 ISS P bovine prefoldin subunit 1 homolog (putative) YJL179W|GIM6 gene taxon:4932 20021028 SGD
+SGD S000003715 PFD1 GO:0007010 SGD_REF:S000058336|PMID:9630229 IMP P bovine prefoldin subunit 1 homolog (putative) YJL179W|GIM6 gene taxon:4932 20021028 SGD
+SGD S000003472 PFK1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C phosphofructokinase alpha subunit YGR240C gene taxon:4932 20020507 SGD
+SGD S000003472 PFK1 GO:0005945 SGD_REF:S000054694|PMID:3007939 IMP C phosphofructokinase alpha subunit YGR240C gene taxon:4932 20010118 SGD
+SGD S000003472 PFK1 GO:0003872 SGD_REF:S000054694|PMID:3007939 IMP F phosphofructokinase alpha subunit YGR240C gene taxon:4932 20010118 SGD
+SGD S000003472 PFK1 GO:0006096 SGD_REF:S000058499 TAS P phosphofructokinase alpha subunit YGR240C gene taxon:4932 20010119 SGD
+SGD S000004818 PFK2 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C phosphofructokinase beta subunit YMR205C gene taxon:4932 20020507 SGD
+SGD S000004818 PFK2 GO:0005945 SGD_REF:S000054694|PMID:3007939 IMP C phosphofructokinase beta subunit YMR205C gene taxon:4932 20010118 SGD
+SGD S000004818 PFK2 GO:0003872 SGD_REF:S000054694|PMID:3007939 IMP F phosphofructokinase beta subunit YMR205C gene taxon:4932 20010118 SGD
+SGD S000004818 PFK2 GO:0006096 SGD_REF:S000058499 TAS P phosphofructokinase beta subunit YMR205C gene taxon:4932 20010119 SGD
+SGD S000001369 PFK26 GO:0005737 SGD_REF:S000058500 IC GO:0006110 C 6-phosphofructose-2-kinase YIL107C|PFK-2 gene taxon:4932 20021118 SGD
+SGD S000001369 PFK26 GO:0003873 SGD_REF:S000051318|PMID:1322693 IDA F 6-phosphofructose-2-kinase YIL107C|PFK-2 gene taxon:4932 20021001 SGD
+SGD S000001369 PFK26 GO:0003873 SGD_REF:S000051318|PMID:1322693 ISS F 6-phosphofructose-2-kinase YIL107C|PFK-2 gene taxon:4932 20021001 SGD
+SGD S000001369 PFK26 GO:0006003 SGD_REF:S000058500 NAS P 6-phosphofructose-2-kinase YIL107C|PFK-2 gene taxon:4932 20021001 SGD
+SGD S000001369 PFK26 GO:0006110 SGD_REF:S000058500 NAS P 6-phosphofructose-2-kinase YIL107C|PFK-2 gene taxon:4932 20021001 SGD
+SGD S000005496 PFK27 GO:0005737 SGD_REF:S000058500 IC GO:0006110 C 6-phosphofructo-2-kinase YOL136C|PFK-2 gene taxon:4932 20021118 SGD
+SGD S000005496 PFK27 GO:0003873 SGD_REF:S000041499|PMID:8861205 ISS F 6-phosphofructo-2-kinase YOL136C|PFK-2 gene taxon:4932 20021001 SGD
+SGD S000005496 PFK27 GO:0006003 SGD_REF:S000041499|PMID:8861205 IMP P 6-phosphofructo-2-kinase YOL136C|PFK-2 gene taxon:4932 20050506 SGD
+SGD S000005496 PFK27 GO:0006110 SGD_REF:S000041499|PMID:8861205 IMP P 6-phosphofructo-2-kinase YOL136C|PFK-2 gene taxon:4932 20050506 SGD
+SGD S000029366 PFK4 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20021118 SGD
+SGD S000029366 PFK4 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20021118 SGD
+SGD S000029366 PFK4 GO:0006096 SGD_REF:S000054944|PMID:6241288 IMP P gene taxon:4932 20010118 SGD
+SGD S000029367 PFK5 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20021118 SGD
+SGD S000029367 PFK5 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20021118 SGD
+SGD S000029367 PFK5 GO:0006096 SGD_REF:S000054944|PMID:6241288 IMP P gene taxon:4932 20010118 SGD
+SGD S000001228 PFS1 GO:0008372 SGD_REF:S000069584 ND C YHR185C|ADY1 gene taxon:4932 20020923 SGD
+SGD S000001228 PFS1 GO:0005554 SGD_REF:S000069584 ND F YHR185C|ADY1 gene taxon:4932 20020923 SGD
+SGD S000001228 PFS1 GO:0030476 SGD_REF:S000065968|PMID:11553705 IMP P YHR185C|ADY1 gene taxon:4932 20020923 SGD
+SGD S000005261 PFS2 GO:0005847 SGD_REF:S000060315|PMID:11344258 TAS C polyadenylation factor I (PF I) YNL317W gene taxon:4932 20020410 SGD
+SGD S000005261 PFS2 GO:0005847 SGD_REF:S000074089|PMID:12819204 IPI C polyadenylation factor I (PF I) YNL317W gene taxon:4932 20031013 SGD
+SGD S000005261 PFS2 contributes_to GO:0003723 SGD_REF:S000074089|PMID:12819204 IC GO:0005847 F polyadenylation factor I (PF I) YNL317W gene taxon:4932 20050218 SGD
+SGD S000005261 PFS2 GO:0006378 SGD_REF:S000060315|PMID:11344258 IDA P polyadenylation factor I (PF I) YNL317W gene taxon:4932 20020410 SGD
+SGD S000005261 PFS2 GO:0006378 SGD_REF:S000042899|PMID:10619842 IMP P polyadenylation factor I (PF I) YNL317W gene taxon:4932 20020410 SGD
+SGD S000005261 PFS2 GO:0006378 SGD_REF:S000060315|PMID:11344258 TAS P polyadenylation factor I (PF I) YNL317W gene taxon:4932 20020410 SGD
+SGD S000005261 PFS2 GO:0006379 SGD_REF:S000060315|PMID:11344258 IDA P polyadenylation factor I (PF I) YNL317W gene taxon:4932 20020410 SGD
+SGD S000005261 PFS2 GO:0006379 SGD_REF:S000042899|PMID:10619842 IMP P polyadenylation factor I (PF I) YNL317W gene taxon:4932 20020410 SGD
+SGD S000005261 PFS2 GO:0006379 SGD_REF:S000060315|PMID:11344258 TAS P polyadenylation factor I (PF I) YNL317W gene taxon:4932 20020410 SGD
+SGD S000005648 PFY1 GO:0000142 SGD_REF:S000041005|PMID:10652251 IDA C profilin YOR122C|PRF1 gene taxon:4932 20010118 SGD
+SGD S000005648 PFY1 GO:0030478 SGD_REF:S000041005|PMID:10652251 IPI C profilin YOR122C|PRF1 gene taxon:4932 20010118 SGD
+SGD S000005648 PFY1 GO:0003785 SGD_REF:S000058447|PMID:9153752 TAS F profilin YOR122C|PRF1 gene taxon:4932 20010118 SGD
+SGD S000005648 PFY1 GO:0006970 SGD_REF:S000041005|PMID:10652251 IMP P profilin YOR122C|PRF1 gene taxon:4932 20010118 SGD
+SGD S000005648 PFY1 GO:0007120 SGD_REF:S000041005|PMID:10652251 IMP P profilin YOR122C|PRF1 gene taxon:4932 20010118 SGD
+SGD S000005648 PFY1 GO:0007121 SGD_REF:S000041005|PMID:10652251 IMP P profilin YOR122C|PRF1 gene taxon:4932 20010118 SGD
+SGD S000005648 PFY1 GO:0008154 SGD_REF:S000041005|PMID:10652251 TAS P profilin YOR122C|PRF1 gene taxon:4932 20010118 SGD
+SGD S000005648 PFY1 GO:0045010 SGD_REF:S000070394|PMID:12134165 TAS P profilin YOR122C|PRF1 gene taxon:4932 20041014 SGD
+SGD S000005648 PFY1 GO:0046907 SGD_REF:S000050201|PMID:9720869 IGI SGD:S000000810 P profilin YOR122C|PRF1 gene taxon:4932 20041014 SGD
+SGD S000005102 PGA1 GO:0005635 SGD_REF:S000075214|PMID:14690591 IDA C YNL158W gene taxon:4932 20040105 SGD
+SGD S000005102 PGA1 GO:0005554 SGD_REF:S000069584 ND F YNL158W gene taxon:4932 20051014 SGD
+SGD S000005102 PGA1 GO:0045045 SGD_REF:S000086691|PMID:16155567 IGI P YNL158W gene taxon:4932 20051014 SGD
+SGD S000005102 PGA1 GO:0045045 SGD_REF:S000086691|PMID:16155567 IMP P YNL158W gene taxon:4932 20051014 SGD
+SGD S000005093 PGA2 GO:0005635 SGD_REF:S000075214|PMID:14690591 IDA C YNL149C gene taxon:4932 20040105 SGD
+SGD S000005093 PGA2 GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YNL149C gene taxon:4932 20031028 SGD
+SGD S000005093 PGA2 GO:0005783 SGD_REF:S000075214|PMID:14690591 IDA C YNL149C gene taxon:4932 20040105 SGD
+SGD S000005093 PGA2 GO:0005554 SGD_REF:S000069584 ND F YNL149C gene taxon:4932 20030203 SGD
+SGD S000005093 PGA2 GO:0007005 SGD_REF:S000086425|PMID:16135527 IMP P YNL149C gene taxon:4932 20051111 SGD
+SGD S000004594 PGA3 GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YML125C gene taxon:4932 20031028 SGD
+SGD S000004594 PGA3 GO:0005554 SGD_REF:S000069584 ND F YML125C gene taxon:4932 20021126 SGD
+SGD S000004594 PGA3 GO:0000004 SGD_REF:S000069584 ND P YML125C gene taxon:4932 20021126 SGD
+SGD S000002993 PGD1 GO:0000119 SGD_REF:S000048078|PMID:9420330 IDA C YGL025C|HRS1|MED3 gene taxon:4932 20010118 SGD
+SGD S000002993 PGD1 GO:0016455 SGD_REF:S000048078|PMID:9420330 IDA F YGL025C|HRS1|MED3 gene taxon:4932 20010302 SGD
+SGD S000002993 PGD1 GO:0006366 SGD_REF:S000048078|PMID:9420330 IDA P YGL025C|HRS1|MED3 gene taxon:4932 20010118 SGD
+SGD S000000400 PGI1 GO:0005829 SGD_REF:S000058491 TAS C glucose-6-phosphate isomerase, phosphoglucose isomerase YBR196C|CDC30 gene taxon:4932 20010119 SGD
+SGD S000000400 PGI1 GO:0004347 SGD_REF:S000054701|PMID:3007940 IMP F glucose-6-phosphate isomerase, phosphoglucose isomerase YBR196C|CDC30 gene taxon:4932 20010118 SGD
+SGD S000000400 PGI1 GO:0006094 SGD_REF:S000046006|PMID:3020369 IMP P glucose-6-phosphate isomerase, phosphoglucose isomerase YBR196C|CDC30 gene taxon:4932 20050525 SGD
+SGD S000000400 PGI1 GO:0006096 SGD_REF:S000054701|PMID:3007940 IMP P glucose-6-phosphate isomerase, phosphoglucose isomerase YBR196C|CDC30 gene taxon:4932 20010118 SGD
+SGD S000000400 PGI1 GO:0006098 SGD_REF:S000052495|PMID:7901008 IMP P glucose-6-phosphate isomerase, phosphoglucose isomerase YBR196C|CDC30 gene taxon:4932 20050728 SGD
+SGD S000000605 PGK1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C 3-phosphoglycerate kinase YCR012W gene taxon:4932 20020507 SGD
+SGD S000000605 PGK1 GO:0004618 SGD_REF:S000058483|PMID:6254992 IDA F 3-phosphoglycerate kinase YCR012W gene taxon:4932 20010118 SGD
+SGD S000000605 PGK1 GO:0006094 SGD_REF:S000057166|PMID:400791 IMP P 3-phosphoglycerate kinase YCR012W gene taxon:4932 20050525 SGD
+SGD S000000605 PGK1 GO:0006096 SGD_REF:S000057166|PMID:400791 IMP P 3-phosphoglycerate kinase YCR012W gene taxon:4932 20050525 SGD
+SGD S000001610 PGM1 GO:0005829 SGD_REF:S000058491 TAS C phosphoglucomutase minor isoform YKL127W gene taxon:4932 20010119 SGD
+SGD S000001610 PGM1 GO:0004614 SGD_REF:S000052493|PMID:8119301 IMP F phosphoglucomutase minor isoform YKL127W gene taxon:4932 20010118 SGD
+SGD S000001610 PGM1 GO:0004614 SGD_REF:S000052493|PMID:8119301 ISS F phosphoglucomutase minor isoform YKL127W gene taxon:4932 20010118 SGD
+SGD S000001610 PGM1 GO:0006008 SGD_REF:S000052493|PMID:8119301 IMP P phosphoglucomutase minor isoform YKL127W gene taxon:4932 20010118 SGD
+SGD S000001610 PGM1 GO:0006008 SGD_REF:S000052493|PMID:8119301 ISS P phosphoglucomutase minor isoform YKL127W gene taxon:4932 20010118 SGD
+SGD S000001610 PGM1 GO:0006010 SGD_REF:S000052493|PMID:8119301 ISS P phosphoglucomutase minor isoform YKL127W gene taxon:4932 20010118 SGD
+SGD S000001610 PGM1 GO:0006010 SGD_REF:S000052493|PMID:8119301 IMP P phosphoglucomutase minor isoform YKL127W gene taxon:4932 20010118 SGD
+SGD S000004711 PGM2 GO:0005829 SGD_REF:S000058491 TAS C phosphoglucomutase YMR105C|GAL5 gene taxon:4932 20010119 SGD
+SGD S000004711 PGM2 GO:0004614 SGD_REF:S000052493|PMID:8119301 IMP F phosphoglucomutase YMR105C|GAL5 gene taxon:4932 20010118 SGD
+SGD S000004711 PGM2 GO:0004614 SGD_REF:S000052493|PMID:8119301 ISS F phosphoglucomutase YMR105C|GAL5 gene taxon:4932 20010118 SGD
+SGD S000004711 PGM2 GO:0006008 SGD_REF:S000052493|PMID:8119301 IMP P phosphoglucomutase YMR105C|GAL5 gene taxon:4932 20010118 SGD
+SGD S000004711 PGM2 GO:0006008 SGD_REF:S000052493|PMID:8119301 ISS P phosphoglucomutase YMR105C|GAL5 gene taxon:4932 20010118 SGD
+SGD S000004711 PGM2 GO:0006010 SGD_REF:S000052493|PMID:8119301 ISS P phosphoglucomutase YMR105C|GAL5 gene taxon:4932 20010118 SGD
+SGD S000004711 PGM2 GO:0006010 SGD_REF:S000052493|PMID:8119301 IMP P phosphoglucomutase YMR105C|GAL5 gene taxon:4932 20010118 SGD
+SGD S000000510 PGS1 GO:0005739 SGD_REF:S000050970|PMID:9799363 IDA C 17 kDa phosphatidylglycerolphosphate synthase YCL004W|PEL1|YCL003W gene taxon:4932 20020723 SGD
+SGD S000000510 PGS1 GO:0008444 SGD_REF:S000051289|PMID:9545322 IMP F 17 kDa phosphatidylglycerolphosphate synthase YCL004W|PEL1|YCL003W gene taxon:4932 20020723 SGD
+SGD S000000510 PGS1 GO:0008654 SGD_REF:S000051289|PMID:9545322 IMP P 17 kDa phosphatidylglycerolphosphate synthase YCL004W|PEL1|YCL003W gene taxon:4932 20020723 SGD
+SGD S000003914 PGU1 GO:0005576 SGD_REF:S000042265|PMID:10028181 IDA C endo-polygalacturonase YJR153W|PGL1|PSM1 gene taxon:4932 20021118 SGD
+SGD S000003914 PGU1 GO:0005576 SGD_REF:S000075303|PMID:11935221 IDA C endo-polygalacturonase YJR153W|PGL1|PSM1 gene taxon:4932 20040114 SGD
+SGD S000003914 PGU1 GO:0004650 SGD_REF:S000054958|PMID:10650215 IDA F endo-polygalacturonase YJR153W|PGL1|PSM1 gene taxon:4932 20020930 SGD
+SGD S000003914 PGU1 GO:0007124 SGD_REF:S000060062|PMID:11255250 NAS P endo-polygalacturonase YJR153W|PGL1|PSM1 gene taxon:4932 20020930 SGD
+SGD S000003914 PGU1 GO:0045490 SGD_REF:S000042265|PMID:10028181 IDA P endo-polygalacturonase YJR153W|PGL1|PSM1 gene taxon:4932 20021118 SGD
+SGD S000005260 PHA2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C prephenate dehydratase YNL316C gene taxon:4932 20031028 SGD
+SGD S000005260 PHA2 GO:0004664 SGD_REF:S000052518|PMID:7502583 TAS F prephenate dehydratase YNL316C gene taxon:4932 20020620 SGD
+SGD S000005260 PHA2 GO:0019274 SGD_REF:S000052518|PMID:7502583 TAS P prephenate dehydratase YNL316C gene taxon:4932 20020620 SGD
+SGD S000003364 PHB1 GO:0005739 SGD_REF:S000045872|PMID:9259555 IDA C Phb2p homolog, mitochondrial protein YGR132C gene taxon:4932 20010118 SGD
+SGD S000003364 PHB1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C Phb2p homolog, mitochondrial protein YGR132C gene taxon:4932 20040924 SGD
+SGD S000003364 PHB1 GO:0005743 SGD_REF:S000050987|PMID:10835343 IDA C Phb2p homolog, mitochondrial protein YGR132C gene taxon:4932 20050308 SGD
+SGD S000003364 PHB1 GO:0005743 SGD_REF:S000050840|PMID:9632789 IDA C Phb2p homolog, mitochondrial protein YGR132C gene taxon:4932 20050308 SGD
+SGD S000003364 PHB1 GO:0005554 SGD_REF:S000069584 ND F Phb2p homolog, mitochondrial protein YGR132C gene taxon:4932 20010119 SGD
+SGD S000003364 PHB1 GO:0001302 SGD_REF:S000073674|PMID:12882345 IMP P Phb2p homolog, mitochondrial protein YGR132C gene taxon:4932 20030820 SGD
+SGD S000003364 PHB1 GO:0001302 SGD_REF:S000045872|PMID:9259555 IMP P Phb2p homolog, mitochondrial protein YGR132C gene taxon:4932 20030820 SGD
+SGD S000003364 PHB1 GO:0006457 SGD_REF:S000050987|PMID:10835343 IDA P Phb2p homolog, mitochondrial protein YGR132C gene taxon:4932 20050308 SGD
+SGD S000003364 PHB1 GO:0006457 SGD_REF:S000050987|PMID:10835343 IPI P Phb2p homolog, mitochondrial protein YGR132C gene taxon:4932 20050308 SGD
+SGD S000003364 PHB1 GO:0006457 SGD_REF:S000050987|PMID:10835343 ISS P Phb2p homolog, mitochondrial protein YGR132C gene taxon:4932 20050308 SGD
+SGD S000003364 PHB1 GO:0045861 SGD_REF:S000044332|PMID:10207067 IMP P Phb2p homolog, mitochondrial protein YGR132C gene taxon:4932 20050308 SGD
+SGD S000003364 PHB1 GO:0045861 SGD_REF:S000044332|PMID:10207067 IPI P Phb2p homolog, mitochondrial protein YGR132C gene taxon:4932 20050308 SGD
+SGD S000003463 PHB2 GO:0005739 SGD_REF:S000045872|PMID:9259555 IDA C mammalian BAP37 and S. cerevisiae Phb1p homolog, prohibitin homolog YGR231C gene taxon:4932 20010118 SGD
+SGD S000003463 PHB2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C mammalian BAP37 and S. cerevisiae Phb1p homolog, prohibitin homolog YGR231C gene taxon:4932 20040924 SGD
+SGD S000003463 PHB2 GO:0005743 SGD_REF:S000050987|PMID:10835343 IDA C mammalian BAP37 and S. cerevisiae Phb1p homolog, prohibitin homolog YGR231C gene taxon:4932 20050308 SGD
+SGD S000003463 PHB2 GO:0005743 SGD_REF:S000050840|PMID:9632789 IDA C mammalian BAP37 and S. cerevisiae Phb1p homolog, prohibitin homolog YGR231C gene taxon:4932 20050308 SGD
+SGD S000003463 PHB2 GO:0005554 SGD_REF:S000069584 ND F mammalian BAP37 and S. cerevisiae Phb1p homolog, prohibitin homolog YGR231C gene taxon:4932 20010119 SGD
+SGD S000003463 PHB2 GO:0001302 SGD_REF:S000073674|PMID:12882345 IMP P mammalian BAP37 and S. cerevisiae Phb1p homolog, prohibitin homolog YGR231C gene taxon:4932 20030820 SGD
+SGD S000003463 PHB2 GO:0001302 SGD_REF:S000045872|PMID:9259555 IMP P mammalian BAP37 and S. cerevisiae Phb1p homolog, prohibitin homolog YGR231C gene taxon:4932 20030820 SGD
+SGD S000003463 PHB2 GO:0006457 SGD_REF:S000050987|PMID:10835343 IDA P mammalian BAP37 and S. cerevisiae Phb1p homolog, prohibitin homolog YGR231C gene taxon:4932 20050308 SGD
+SGD S000003463 PHB2 GO:0006457 SGD_REF:S000050987|PMID:10835343 IPI P mammalian BAP37 and S. cerevisiae Phb1p homolog, prohibitin homolog YGR231C gene taxon:4932 20050308 SGD
+SGD S000003463 PHB2 GO:0006457 SGD_REF:S000050987|PMID:10835343 ISS P mammalian BAP37 and S. cerevisiae Phb1p homolog, prohibitin homolog YGR231C gene taxon:4932 20050308 SGD
+SGD S000003463 PHB2 GO:0045861 SGD_REF:S000044332|PMID:10207067 IMP P mammalian BAP37 and S. cerevisiae Phb1p homolog, prohibitin homolog YGR231C gene taxon:4932 20050308 SGD
+SGD S000003463 PHB2 GO:0045861 SGD_REF:S000044332|PMID:10207067 IPI P mammalian BAP37 and S. cerevisiae Phb1p homolog, prohibitin homolog YGR231C gene taxon:4932 20050308 SGD
+SGD S000001526 PHD1 GO:0005634 SGD_REF:S000046309|PMID:8114741 IDA C transcription factor (putative) YKL043W gene taxon:4932 20020215 SGD
+SGD S000001526 PHD1 GO:0003704 SGD_REF:S000050758|PMID:9456310 TAS F transcription factor (putative) YKL043W gene taxon:4932 20010118 SGD
+SGD S000001526 PHD1 GO:0007124 SGD_REF:S000046309|PMID:8114741 IMP P transcription factor (putative) YKL043W gene taxon:4932 20010118 SGD
+SGD S000001526 PHD1 GO:0045944 SGD_REF:S000046309|PMID:8114741 IMP P transcription factor (putative) YKL043W gene taxon:4932 20051211 SGD
+SGD S000001526 PHD1 GO:0045944 SGD_REF:S000046309|PMID:8114741 ISS P transcription factor (putative) YKL043W gene taxon:4932 20051211 SGD
+SGD S000002689 PHM6 GO:0000324 SGD_REF:S000074185|PMID:14562095 IDA C YDR281C gene taxon:4932 20031028 SGD
+SGD S000002689 PHM6 GO:0005554 SGD_REF:S000069584 ND F YDR281C gene taxon:4932 20020905 SGD
+SGD S000002689 PHM6 GO:0000004 SGD_REF:S000069584 ND P YDR281C gene taxon:4932 20020905 SGD
+SGD S000005444 PHM7 GO:0000324 SGD_REF:S000074185|PMID:14562095 IDA C YOL084W gene taxon:4932 20031028 SGD
+SGD S000005444 PHM7 GO:0005554 SGD_REF:S000069584 ND F YOL084W gene taxon:4932 20010119 SGD
+SGD S000005444 PHM7 GO:0000004 SGD_REF:S000069584 ND P YOL084W gene taxon:4932 20010119 SGD
+SGD S000000839 PHM8 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YER037W gene taxon:4932 20031028 SGD
+SGD S000000839 PHM8 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YER037W gene taxon:4932 20031028 SGD
+SGD S000000839 PHM8 GO:0005554 SGD_REF:S000069584 ND F YER037W gene taxon:4932 20010119 SGD
+SGD S000000839 PHM8 GO:0000004 SGD_REF:S000069584 ND P YER037W gene taxon:4932 20010119 SGD
+SGD S000000094 PHO11 GO:0005576 SGD_REF:S000039848|PMID:8817921 IDA C acid phosphatase YAR071W gene taxon:4932 20010118 SGD
+SGD S000000094 PHO11 GO:0003993 SGD_REF:S000039848|PMID:8817921 IDA F acid phosphatase YAR071W gene taxon:4932 20010118 SGD
+SGD S000000094 PHO11 GO:0006796 SGD_REF:S000059109|PMID:11102525 TAS P acid phosphatase YAR071W gene taxon:4932 20021001 SGD
+SGD S000001258 PHO12 GO:0000324 SGD_REF:S000074185|PMID:14562095 IDA C acid phosphatase YHR215W|PHO10 gene taxon:4932 20031028 SGD
+SGD S000001258 PHO12 GO:0003993 SGD_REF:S000055567|PMID:2688928 ISS F acid phosphatase YHR215W|PHO10 gene taxon:4932 20010118 SGD
+SGD S000001258 PHO12 GO:0000004 SGD_REF:S000069584 ND P acid phosphatase YHR215W|PHO10 gene taxon:4932 20010119 SGD
+SGD S000002395 PHO13 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C p-nitrophenyl phosphatase YDL236W gene taxon:4932 20031028 SGD
+SGD S000002395 PHO13 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C p-nitrophenyl phosphatase YDL236W gene taxon:4932 20031028 SGD
+SGD S000002395 PHO13 GO:0003869 SGD_REF:S000053605|PMID:9561742 IDA F p-nitrophenyl phosphatase YDL236W gene taxon:4932 20020930 SGD
+SGD S000002395 PHO13 GO:0004035 SGD_REF:S000053605|PMID:9561742 IDA F p-nitrophenyl phosphatase YDL236W gene taxon:4932 20020930 SGD
+SGD S000002395 PHO13 GO:0006470 SGD_REF:S000053605|PMID:9561742 IDA P p-nitrophenyl phosphatase YDL236W gene taxon:4932 20020930 SGD
+SGD S000002395 PHO13 GO:0016576 SGD_REF:S000053605|PMID:9561742 IDA P p-nitrophenyl phosphatase YDL236W gene taxon:4932 20020930 SGD
+SGD S000002264 PHO2 GO:0005634 SGD_REF:S000047624|PMID:1493793 IDA C homeobox transcription factor, positive regulator of PHO5 and other genes YDL106C|BAS2|GRF10 gene taxon:4932 20030211 SGD
+SGD S000002264 PHO2 GO:0003700 SGD_REF:S000039230|PMID:7902583 ISS F homeobox transcription factor, positive regulator of PHO5 and other genes YDL106C|BAS2|GRF10 gene taxon:4932 20030403 SGD
+SGD S000002264 PHO2 GO:0003700 SGD_REF:S000039230|PMID:7902583 IPI F homeobox transcription factor, positive regulator of PHO5 and other genes YDL106C|BAS2|GRF10 gene taxon:4932 20030403 SGD
+SGD S000002264 PHO2 GO:0003700 SGD_REF:S000049914|PMID:3049251 IGI F homeobox transcription factor, positive regulator of PHO5 and other genes YDL106C|BAS2|GRF10 gene taxon:4932 20030403 SGD
+SGD S000002264 PHO2 GO:0003700 SGD_REF:S000049914|PMID:3049251 TAS F homeobox transcription factor, positive regulator of PHO5 and other genes YDL106C|BAS2|GRF10 gene taxon:4932 20030403 SGD
+SGD S000002264 PHO2 GO:0003700 SGD_REF:S000049914|PMID:3049251 IMP F homeobox transcription factor, positive regulator of PHO5 and other genes YDL106C|BAS2|GRF10 gene taxon:4932 20030403 SGD
+SGD S000002264 PHO2 GO:0000105 SGD_REF:S000052116|PMID:1495962 TAS P homeobox transcription factor, positive regulator of PHO5 and other genes YDL106C|BAS2|GRF10 gene taxon:4932 20011106 SGD
+SGD S000002264 PHO2 GO:0006350 SGD_REF:S000071684|PMID:12145299 IGI P homeobox transcription factor, positive regulator of PHO5 and other genes YDL106C|BAS2|GRF10 gene taxon:4932 20030403 SGD
+SGD S000002264 PHO2 GO:0006350 SGD_REF:S000071684|PMID:12145299 TAS P homeobox transcription factor, positive regulator of PHO5 and other genes YDL106C|BAS2|GRF10 gene taxon:4932 20030403 SGD
+SGD S000002264 PHO2 GO:0009113 SGD_REF:S000052116|PMID:1495962 IDA P homeobox transcription factor, positive regulator of PHO5 and other genes YDL106C|BAS2|GRF10 gene taxon:4932 20011106 SGD
+SGD S000002264 PHO2 GO:0016036 SGD_REF:S000041722|PMID:8918192 TAS P homeobox transcription factor, positive regulator of PHO5 and other genes YDL106C|BAS2|GRF10 gene taxon:4932 20011106 SGD
+SGD S000005041 PHO23 GO:0000118 SGD_REF:S000073630|PMID:12672825 IDA C YNL097C gene taxon:4932 20030718 SGD
+SGD S000005041 PHO23 GO:0005634 SGD_REF:S000069459|PMID:11914276 IDA C YNL097C gene taxon:4932 20020507 SGD
+SGD S000005041 PHO23 GO:0004407 SGD_REF:S000073630|PMID:12672825 IDA F YNL097C gene taxon:4932 20030718 SGD
+SGD S000005041 PHO23 GO:0016568 SGD_REF:S000043268|PMID:10805724 IMP P YNL097C gene taxon:4932 20020321 SGD
+SGD S000005041 PHO23 GO:0016568 SGD_REF:S000043268|PMID:10805724 IPI P YNL097C gene taxon:4932 20020321 SGD
+SGD S000005041 PHO23 GO:0016568 SGD_REF:S000043268|PMID:10805724 ISS P YNL097C gene taxon:4932 20020321 SGD
+SGD S000000296 PHO3 GO:0030287 SGD_REF:S000047763|PMID:2676709 IMP C acid phosphatase YBR092C gene taxon:4932 20010924 SGD
+SGD S000000296 PHO3 GO:0030287 SGD_REF:S000048140|PMID:1965216 NAS C acid phosphatase YBR092C gene taxon:4932 20010926 SGD
+SGD S000000296 PHO3 GO:0003993 SGD_REF:S000047763|PMID:2676709 IMP F acid phosphatase YBR092C gene taxon:4932 20010118 SGD
+SGD S000000296 PHO3 GO:0006796 SGD_REF:S000047115|PMID:2407294 IDA P acid phosphatase YBR092C gene taxon:4932 20041220 SGD
+SGD S000000296 PHO3 GO:0006796 SGD_REF:S000047115|PMID:2407294 TAS P acid phosphatase YBR092C gene taxon:4932 20041220 SGD
+SGD S000000296 PHO3 GO:0042723 SGD_REF:S000047115|PMID:2407294 IDA P acid phosphatase YBR092C gene taxon:4932 20041220 SGD
+SGD S000001930 PHO4 GO:0005634 SGD_REF:S000046458|PMID:10320381 IDA C myc-family transcription factor YFR034C gene taxon:4932 20011101 SGD
+SGD S000001930 PHO4 GO:0005737 SGD_REF:S000046458|PMID:10320381 IDA C myc-family transcription factor YFR034C gene taxon:4932 20011101 SGD
+SGD S000001930 PHO4 GO:0003700 SGD_REF:S000041722|PMID:8918192 TAS F myc-family transcription factor YFR034C gene taxon:4932 20011101 SGD
+SGD S000001930 PHO4 GO:0006796 SGD_REF:S000041722|PMID:8918192 TAS P myc-family transcription factor YFR034C gene taxon:4932 20011101 SGD
+SGD S000001930 PHO4 GO:0016036 SGD_REF:S000046458|PMID:10320381 IMP P myc-family transcription factor YFR034C gene taxon:4932 20011101 SGD
+SGD S000001930 PHO4 GO:0016036 SGD_REF:S000046458|PMID:10320381 IDA P myc-family transcription factor YFR034C gene taxon:4932 20011101 SGD
+SGD S000000297 PHO5 GO:0009277 SGD_REF:S000055744|PMID:3537693 IDA C acid phosphatase YBR093C gene taxon:4932 20010926 SGD
+SGD S000000297 PHO5 GO:0030287 SGD_REF:S000048140|PMID:1965216 NAS C acid phosphatase YBR093C gene taxon:4932 20010926 SGD
+SGD S000000297 PHO5 GO:0003993 SGD_REF:S000041722|PMID:8918192 TAS F acid phosphatase YBR093C gene taxon:4932 20011101 SGD
+SGD S000000297 PHO5 GO:0017111 SGD_REF:S000087166|PMID:16278456 IGI SGD:S000000621|SGD:S000000742 F acid phosphatase YBR093C gene taxon:4932 20051111 SGD
+SGD S000000297 PHO5 GO:0017111 SGD_REF:S000087166|PMID:16278456 IMP F acid phosphatase YBR093C gene taxon:4932 20051111 SGD
+SGD S000000297 PHO5 GO:0047429 SGD_REF:S000087166|PMID:16278456 IGI SGD:S000000621|SGD:S000000742 F acid phosphatase YBR093C gene taxon:4932 20051111 SGD
+SGD S000000297 PHO5 GO:0047429 SGD_REF:S000087166|PMID:16278456 IMP F acid phosphatase YBR093C gene taxon:4932 20051111 SGD
+SGD S000000297 PHO5 GO:0006796 SGD_REF:S000041722|PMID:8918192 TAS P acid phosphatase YBR093C gene taxon:4932 20011101 SGD
+SGD S000000297 PHO5 GO:0006796 SGD_REF:S000087166|PMID:16278456 IMP P acid phosphatase YBR093C gene taxon:4932 20051111 SGD
+SGD S000000297 PHO5 GO:0016036 SGD_REF:S000041722|PMID:8918192 TAS P acid phosphatase YBR093C gene taxon:4932 20011101 SGD
+SGD S000000297 PHO5 GO:0016036 SGD_REF:S000087166|PMID:16278456 IEP P acid phosphatase YBR093C gene taxon:4932 20051111 SGD
+SGD S000000297 PHO5 GO:0016036 SGD_REF:S000087166|PMID:16278456 IMP P acid phosphatase YBR093C gene taxon:4932 20051111 SGD
+SGD S000002889 PHO8 GO:0000329 SGD_REF:S000058260|PMID:9412470 IDA C repressible alkaline phosphatase YDR481C gene taxon:4932 20020930 SGD
+SGD S000002889 PHO8 GO:0004035 SGD_REF:S000058260|PMID:9412470 IDA F repressible alkaline phosphatase YDR481C gene taxon:4932 20020930 SGD
+SGD S000002889 PHO8 GO:0004035 SGD_REF:S000058260|PMID:9412470 ISS F repressible alkaline phosphatase YDR481C gene taxon:4932 20020930 SGD
+SGD S000002889 PHO8 GO:0006470 SGD_REF:S000058260|PMID:9412470 IDA P repressible alkaline phosphatase YDR481C gene taxon:4932 20020930 SGD
+SGD S000002889 PHO8 GO:0016576 SGD_REF:S000058260|PMID:9412470 IDA P repressible alkaline phosphatase YDR481C gene taxon:4932 20020930 SGD
+SGD S000005361 PHO80 GO:0000307 SGD_REF:S000068989|PMID:11602261 TAS C Pho80p cyclin YOL001W|AGS3|TUP7|VAC5 gene taxon:4932 20020212 SGD
+SGD S000005361 PHO80 GO:0016538 SGD_REF:S000068989|PMID:11602261 TAS F Pho80p cyclin YOL001W|AGS3|TUP7|VAC5 gene taxon:4932 20020212 SGD
+SGD S000005361 PHO80 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P Pho80p cyclin YOL001W|AGS3|TUP7|VAC5 gene taxon:4932 20060227 SGD
+SGD S000005361 PHO80 GO:0019220 SGD_REF:S000068989|PMID:11602261 TAS P Pho80p cyclin YOL001W|AGS3|TUP7|VAC5 gene taxon:4932 20020212 SGD
+SGD S000003465 PHO81 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YGR233C gene taxon:4932 20031028 SGD
+SGD S000003465 PHO81 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YGR233C gene taxon:4932 20031028 SGD
+SGD S000003465 PHO81 GO:0004861 SGD_REF:S000059109|PMID:11102525 TAS F YGR233C gene taxon:4932 20021001 SGD
+SGD S000003465 PHO81 GO:0006796 SGD_REF:S000059109|PMID:11102525 TAS P YGR233C gene taxon:4932 20021001 SGD
+SGD S000004592 PHO84 GO:0005887 SGD_REF:S000054641|PMID:2038328 ISS C inorganic phosphate transporter YML123C gene taxon:4932 20010118 SGD
+SGD S000004592 PHO84 GO:0005887 SGD_REF:S000054641|PMID:2038328 IDA C inorganic phosphate transporter YML123C gene taxon:4932 20010118 SGD
+SGD S000004592 PHO84 GO:0005315 SGD_REF:S000054641|PMID:2038328 IMP F inorganic phosphate transporter YML123C gene taxon:4932 20010118 SGD
+SGD S000004592 PHO84 GO:0005315 SGD_REF:S000054641|PMID:2038328 ISS F inorganic phosphate transporter YML123C gene taxon:4932 20010118 SGD
+SGD S000004592 PHO84 GO:0005315 SGD_REF:S000048488|PMID:7851439 IDA F inorganic phosphate transporter YML123C gene taxon:4932 20030324 SGD
+SGD S000004592 PHO84 GO:0005384 SGD_REF:S000074209|PMID:12923174 IMP F inorganic phosphate transporter YML123C gene taxon:4932 20040415 SGD
+SGD S000004592 PHO84 GO:0006817 SGD_REF:S000054641|PMID:2038328 IMP P inorganic phosphate transporter YML123C gene taxon:4932 20010118 SGD
+SGD S000004592 PHO84 GO:0006817 SGD_REF:S000054641|PMID:2038328 ISS P inorganic phosphate transporter YML123C gene taxon:4932 20010118 SGD
+SGD S000004592 PHO84 GO:0006817 SGD_REF:S000048488|PMID:7851439 IDA P inorganic phosphate transporter YML123C gene taxon:4932 20030324 SGD
+SGD S000004592 PHO84 GO:0006828 SGD_REF:S000074209|PMID:12923174 IMP P inorganic phosphate transporter YML123C gene taxon:4932 20040415 SGD
+SGD S000005952 PHO85 GO:0005634 SGD_REF:S000071719|PMID:12455686 IDA C cyclin-dependent protein kinase YPL031C|LDB15 gene taxon:4932 20021203 SGD
+SGD S000005952 PHO85 GO:0004693 SGD_REF:S000044412|PMID:9584169 IMP F cyclin-dependent protein kinase YPL031C|LDB15 gene taxon:4932 20011017 SGD
+SGD S000005952 PHO85 GO:0004693 SGD_REF:S000044412|PMID:9584169 IPI F cyclin-dependent protein kinase YPL031C|LDB15 gene taxon:4932 20011017 SGD
+SGD S000005952 PHO85 GO:0004693 SGD_REF:S000041722|PMID:8918192 TAS F cyclin-dependent protein kinase YPL031C|LDB15 gene taxon:4932 20011017 SGD
+SGD S000005952 PHO85 GO:0004693 SGD_REF:S000044412|PMID:9584169 IDA F cyclin-dependent protein kinase YPL031C|LDB15 gene taxon:4932 20011017 SGD
+SGD S000005952 PHO85 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P cyclin-dependent protein kinase YPL031C|LDB15 gene taxon:4932 20060227 SGD
+SGD S000005952 PHO85 GO:0005977 SGD_REF:S000044660|PMID:8722762 IDA P cyclin-dependent protein kinase YPL031C|LDB15 gene taxon:4932 20011017 SGD
+SGD S000005952 PHO85 GO:0005977 SGD_REF:S000044660|PMID:8722762 IGI P cyclin-dependent protein kinase YPL031C|LDB15 gene taxon:4932 20011017 SGD
+SGD S000005952 PHO85 GO:0005977 SGD_REF:S000041236|PMID:8754836 IDA P cyclin-dependent protein kinase YPL031C|LDB15 gene taxon:4932 20011017 SGD
+SGD S000005952 PHO85 GO:0005977 SGD_REF:S000041236|PMID:8754836 IMP P cyclin-dependent protein kinase YPL031C|LDB15 gene taxon:4932 20011017 SGD
+SGD S000005952 PHO85 GO:0005977 SGD_REF:S000044660|PMID:8722762 IMP P cyclin-dependent protein kinase YPL031C|LDB15 gene taxon:4932 20011017 SGD
+SGD S000005952 PHO85 GO:0005977 SGD_REF:S000041236|PMID:8754836 IGI P cyclin-dependent protein kinase YPL031C|LDB15 gene taxon:4932 20011017 SGD
+SGD S000005952 PHO85 GO:0006468 SGD_REF:S000041722|PMID:8918192 TAS P cyclin-dependent protein kinase YPL031C|LDB15 gene taxon:4932 20011017 SGD
+SGD S000005952 PHO85 GO:0006468 SGD_REF:S000044412|PMID:9584169 IMP P cyclin-dependent protein kinase YPL031C|LDB15 gene taxon:4932 20011017 SGD
+SGD S000005952 PHO85 GO:0006468 SGD_REF:S000044412|PMID:9584169 IDA P cyclin-dependent protein kinase YPL031C|LDB15 gene taxon:4932 20011017 SGD
+SGD S000005952 PHO85 GO:0006796 SGD_REF:S000041722|PMID:8918192 TAS P cyclin-dependent protein kinase YPL031C|LDB15 gene taxon:4932 20011017 SGD
+SGD S000005952 PHO85 GO:0007049 SGD_REF:S000046677|PMID:9593297 IMP P cyclin-dependent protein kinase YPL031C|LDB15 gene taxon:4932 20011017 SGD
+SGD S000005952 PHO85 GO:0007049 SGD_REF:S000046677|PMID:9593297 IGI P cyclin-dependent protein kinase YPL031C|LDB15 gene taxon:4932 20011017 SGD
+SGD S000003653 PHO86 GO:0005783 SGD_REF:S000047328|PMID:10655492 IDA C YJL117W gene taxon:4932 20020920 SGD
+SGD S000003653 PHO86 GO:0005554 SGD_REF:S000069584 ND F YJL117W gene taxon:4932 20020920 SGD
+SGD S000003653 PHO86 GO:0006457 SGD_REF:S000080152|PMID:15623581 IMP P YJL117W gene taxon:4932 20050708 SGD
+SGD S000003653 PHO86 GO:0006817 SGD_REF:S000047328|PMID:10655492 IMP P YJL117W gene taxon:4932 20020920 SGD
+SGD S000003653 PHO86 GO:0045045 SGD_REF:S000047328|PMID:10655492 IMP P YJL117W gene taxon:4932 20020920 SGD
+SGD S000000633 PHO87 GO:0016020 SGD_REF:S000045510|PMID:8598055 ISS C phosphate permease YCR037C gene taxon:4932 20021003 SGD
+SGD S000000633 PHO87 GO:0005315 SGD_REF:S000045510|PMID:8598055 IGI F phosphate permease YCR037C gene taxon:4932 20021003 SGD
+SGD S000000633 PHO87 GO:0005315 SGD_REF:S000045510|PMID:8598055 IMP F phosphate permease YCR037C gene taxon:4932 20021003 SGD
+SGD S000000633 PHO87 GO:0005315 SGD_REF:S000045510|PMID:8598055 ISS F phosphate permease YCR037C gene taxon:4932 20021003 SGD
+SGD S000000633 PHO87 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P phosphate permease YCR037C gene taxon:4932 20060227 SGD
+SGD S000000633 PHO87 GO:0006817 SGD_REF:S000045510|PMID:8598055 IGI P phosphate permease YCR037C gene taxon:4932 20021003 SGD
+SGD S000000633 PHO87 GO:0006817 SGD_REF:S000045510|PMID:8598055 ISS P phosphate permease YCR037C gene taxon:4932 20021003 SGD
+SGD S000000633 PHO87 GO:0006817 SGD_REF:S000045510|PMID:8598055 IMP P phosphate permease YCR037C gene taxon:4932 20021003 SGD
+SGD S000000310 PHO88 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YBR106W gene taxon:4932 20040929 SGD
+SGD S000000310 PHO88 GO:0016020 SGD_REF:S000051002|PMID:8709965 IDA C YBR106W gene taxon:4932 20020920 SGD
+SGD S000000310 PHO88 GO:0015114 SGD_REF:S000051002|PMID:8709965 IGI F YBR106W gene taxon:4932 20020920 SGD
+SGD S000000310 PHO88 GO:0015114 SGD_REF:S000051002|PMID:8709965 ISS F YBR106W gene taxon:4932 20020920 SGD
+SGD S000000310 PHO88 GO:0015114 SGD_REF:S000051002|PMID:8709965 IMP F YBR106W gene taxon:4932 20020920 SGD
+SGD S000000310 PHO88 GO:0006817 SGD_REF:S000051002|PMID:8709965 IGI P YBR106W gene taxon:4932 20020920 SGD
+SGD S000000310 PHO88 GO:0006817 SGD_REF:S000051002|PMID:8709965 ISS P YBR106W gene taxon:4932 20020920 SGD
+SGD S000000310 PHO88 GO:0006817 SGD_REF:S000051002|PMID:8709965 IMP P YBR106W gene taxon:4932 20020920 SGD
+SGD S000000500 PHO89 GO:0005886 SGD_REF:S000040930|PMID:9671031 IMP C Na+/Pi symporter (putative) YBR296C|ITN1 gene taxon:4932 20021104 SGD
+SGD S000000500 PHO89 GO:0005886 SGD_REF:S000040930|PMID:9671031 ISS C Na+/Pi symporter (putative) YBR296C|ITN1 gene taxon:4932 20021104 SGD
+SGD S000000500 PHO89 GO:0015319 SGD_REF:S000040930|PMID:9671031 IMP F Na+/Pi symporter (putative) YBR296C|ITN1 gene taxon:4932 20021104 SGD
+SGD S000000500 PHO89 GO:0015319 SGD_REF:S000040930|PMID:9671031 ISS F Na+/Pi symporter (putative) YBR296C|ITN1 gene taxon:4932 20021104 SGD
+SGD S000000500 PHO89 GO:0006817 SGD_REF:S000040930|PMID:9671031 IMP P Na+/Pi symporter (putative) YBR296C|ITN1 gene taxon:4932 20021104 SGD
+SGD S000003734 PHO90 GO:0016020 SGD_REF:S000068919|PMID:11779791 ISS C YJL198W gene taxon:4932 20021001 SGD
+SGD S000003734 PHO90 GO:0015114 SGD_REF:S000068919|PMID:11779791 IGI F YJL198W gene taxon:4932 20021001 SGD
+SGD S000003734 PHO90 GO:0015114 SGD_REF:S000068919|PMID:11779791 TAS F YJL198W gene taxon:4932 20021001 SGD
+SGD S000003734 PHO90 GO:0006817 SGD_REF:S000068919|PMID:11779791 IGI P YJL198W gene taxon:4932 20021001 SGD
+SGD S000005296 PHO91 GO:0016020 SGD_REF:S000068919|PMID:11779791 ISS C YNR013C gene taxon:4932 20021001 SGD
+SGD S000005296 PHO91 GO:0015114 SGD_REF:S000068919|PMID:11779791 IGI F YNR013C gene taxon:4932 20021001 SGD
+SGD S000005296 PHO91 GO:0015114 SGD_REF:S000068919|PMID:11779791 TAS F YNR013C gene taxon:4932 20021001 SGD
+SGD S000005296 PHO91 GO:0006817 SGD_REF:S000068919|PMID:11779791 IGI P YNR013C gene taxon:4932 20021001 SGD
+SGD S000005913 PHR1 GO:0005634 SGD_REF:S000052887|PMID:10915863 TAS C photolyase YOR386W gene taxon:4932 20020726 SGD
+SGD S000005913 PHR1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C photolyase YOR386W gene taxon:4932 20040928 SGD
+SGD S000005913 PHR1 GO:0003904 SGD_REF:S000052887|PMID:10915863 TAS F photolyase YOR386W gene taxon:4932 20020726 SGD
+SGD S000005913 PHR1 GO:0003904 SGD_REF:S000078535|PMID:2911265 IDA F photolyase YOR386W gene taxon:4932 20050407 SGD
+SGD S000005913 PHR1 GO:0000719 SGD_REF:S000052887|PMID:10915863 TAS P photolyase YOR386W gene taxon:4932 20020726 SGD
+SGD S000003633 PHS1 GO:0000324 SGD_REF:S000074185|PMID:14562095 IDA C YJL097W gene taxon:4932 20031028 SGD
+SGD S000003633 PHS1 GO:0000324 SGD_REF:S000075214|PMID:14690591 IDA C YJL097W gene taxon:4932 20040105 SGD
+SGD S000003633 PHS1 GO:0000329 SGD_REF:S000075214|PMID:14690591 IDA C YJL097W gene taxon:4932 20040105 SGD
+SGD S000003633 PHS1 GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YJL097W gene taxon:4932 20031028 SGD
+SGD S000003633 PHS1 GO:0042175 SGD_REF:S000075214|PMID:14690591 IDA C YJL097W gene taxon:4932 20040105 SGD
+SGD S000003633 PHS1 GO:0005554 SGD_REF:S000069584 ND F YJL097W gene taxon:4932 20021223 SGD
+SGD S000003633 PHS1 GO:0000004 SGD_REF:S000069584 ND P YJL097W gene taxon:4932 20021223 SGD
+SGD S000002721 PIB1 GO:0000329 SGD_REF:S000066182|PMID:11526110 IDA C YDR313C gene taxon:4932 20020822 SGD
+SGD S000002721 PIB1 GO:0005770 SGD_REF:S000066182|PMID:11526110 IDA C YDR313C gene taxon:4932 20020822 SGD
+SGD S000002721 PIB1 GO:0004842 SGD_REF:S000066182|PMID:11526110 IDA F YDR313C gene taxon:4932 20020822 SGD
+SGD S000002721 PIB1 GO:0016567 SGD_REF:S000066182|PMID:11526110 IDA P YDR313C gene taxon:4932 20020822 SGD
+SGD S000002991 PIB2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YGL023C gene taxon:4932 20040928 SGD
+SGD S000002991 PIB2 GO:0005770 SGD_REF:S000043357|PMID:9702203 TAS C YGL023C gene taxon:4932 20020924 SGD
+SGD S000002991 PIB2 GO:0005545 SGD_REF:S000043357|PMID:9702203 ISS F YGL023C gene taxon:4932 20020924 SGD
+SGD S000002991 PIB2 GO:0016192 SGD_REF:S000043357|PMID:9702203 ISS P YGL023C gene taxon:4932 20020924 SGD
+SGD S000000855 PIC2 GO:0005739 SGD_REF:S000075429|PMID:14756774 IDA C YER053C gene taxon:4932 20040427 SGD
+SGD S000000855 PIC2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YER053C gene taxon:4932 20040924 SGD
+SGD S000000855 PIC2 GO:0005315 SGD_REF:S000075429|PMID:14756774 IDA F YER053C gene taxon:4932 20040427 SGD
+SGD S000000855 PIC2 GO:0006817 SGD_REF:S000075429|PMID:14756774 IDA P YER053C gene taxon:4932 20040427 SGD
+SGD S000004526 PIF1 GO:0005634 SGD_REF:S000046034|PMID:8253734 IC GO:0003678 C 5'-3' DNA helicase YML061C|TST1 gene taxon:4932 20030403 SGD
+SGD S000004526 PIF1 GO:0005739 SGD_REF:S000041657|PMID:1849081 IDA C 5'-3' DNA helicase YML061C|TST1 gene taxon:4932 20010118 SGD
+SGD S000004526 PIF1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C 5'-3' DNA helicase YML061C|TST1 gene taxon:4932 20040924 SGD
+SGD S000004526 PIF1 GO:0003678 SGD_REF:S000046034|PMID:8253734 IDA F 5'-3' DNA helicase YML061C|TST1 gene taxon:4932 20010118 SGD
+SGD S000004526 PIF1 GO:0000002 SGD_REF:S000081767|PMID:15907372 IMP P 5'-3' DNA helicase YML061C|TST1 gene taxon:4932 20050620 SGD
+SGD S000004526 PIF1 GO:0000723 SGD_REF:S000055909|PMID:10926538 IMP P 5'-3' DNA helicase YML061C|TST1 gene taxon:4932 20030403 SGD
+SGD S000004526 PIF1 GO:0006310 SGD_REF:S000041657|PMID:1849081 IMP P 5'-3' DNA helicase YML061C|TST1 gene taxon:4932 20010118 SGD
+SGD S000004526 PIF1 GO:0007001 SGD_REF:S000043828|PMID:8287473 IMP P 5'-3' DNA helicase YML061C|TST1 gene taxon:4932 20010118 SGD
+SGD S000004263 PIG1 GO:0000164 SGD_REF:S000039250|PMID:10790385 IPI C type-1 protein phosphatase regulatory subunit YLR273C gene taxon:4932 20020523 SGD
+SGD S000004263 PIG1 GO:0008599 SGD_REF:S000041126|PMID:9046081 IMP F type-1 protein phosphatase regulatory subunit YLR273C gene taxon:4932 20051025 SGD
+SGD S000004263 PIG1 GO:0008599 SGD_REF:S000041126|PMID:9046081 IGI SGD:S000005704 F type-1 protein phosphatase regulatory subunit YLR273C gene taxon:4932 20051025 SGD
+SGD S000004263 PIG1 GO:0005979 SGD_REF:S000041126|PMID:9046081 IGI P type-1 protein phosphatase regulatory subunit YLR273C gene taxon:4932 20020523 SGD
+SGD S000001307 PIG2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C type-1 protein phosphatase regulatory subunit YIL045W gene taxon:4932 20031028 SGD
+SGD S000001307 PIG2 GO:0008599 SGD_REF:S000041126|PMID:9046081 ISS F type-1 protein phosphatase regulatory subunit YIL045W gene taxon:4932 20051025 SGD
+SGD S000001307 PIG2 GO:0005979 SGD_REF:S000069720|PMID:11973298 ISS P type-1 protein phosphatase regulatory subunit YIL045W gene taxon:4932 20051025 SGD
+SGD S000001307 PIG2 GO:0005979 SGD_REF:S000041126|PMID:9046081 IPI SGD:S000004248 P type-1 protein phosphatase regulatory subunit YIL045W gene taxon:4932 20051025 SGD
+SGD S000001076 PIH1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YHR034C|NOP17 gene taxon:4932 20031028 SGD
+SGD S000001076 PIH1 GO:0005732 SGD_REF:S000080660|PMID:15670595 IPI C YHR034C|NOP17 gene taxon:4932 20050216 SGD
+SGD S000001076 PIH1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YHR034C|NOP17 gene taxon:4932 20031028 SGD
+SGD S000001076 PIH1 GO:0005554 SGD_REF:S000069584 ND F YHR034C|NOP17 gene taxon:4932 20050317 SGD
+SGD S000001076 PIH1 GO:0006364 SGD_REF:S000080660|PMID:15670595 IMP P YHR034C|NOP17 gene taxon:4932 20050209 SGD
+SGD S000001076 PIH1 GO:0006364 SGD_REF:S000080660|PMID:15670595 IGI SGD:S000005837 P YHR034C|NOP17 gene taxon:4932 20050216 SGD
+SGD S000001076 PIH1 GO:0006364 SGD_REF:S000080660|PMID:15670595 IPI P YHR034C|NOP17 gene taxon:4932 20050216 SGD
+SGD S000001076 PIH1 GO:0006457 SGD_REF:S000081009|PMID:15766533 IMP P YHR034C|NOP17 gene taxon:4932 20050317 SGD
+SGD S000001076 PIH1 GO:0006457 SGD_REF:S000081009|PMID:15766533 IPI SGD:S000006161 P YHR034C|NOP17 gene taxon:4932 20050317 SGD
+SGD S000001076 PIH1 GO:0006457 SGD_REF:S000081009|PMID:15766533 IGI SGD:S000006161 P YHR034C|NOP17 gene taxon:4932 20050317 SGD
+SGD S000005211 PIK1 GO:0005634 SGD_REF:S000054492|PMID:8194527 IDA C phosphatidylinositol 4-kinase YNL267W|PIK120|PIK41 gene taxon:4932 20010118 SGD
+SGD S000005211 PIK1 GO:0005634 SGD_REF:S000114103|PMID:16365163 IDA C phosphatidylinositol 4-kinase YNL267W|PIK120|PIK41 gene taxon:4932 20060201 SGD
+SGD S000005211 PIK1 GO:0005794 SGD_REF:S000069992|PMID:12015967 TAS C phosphatidylinositol 4-kinase YNL267W|PIK120|PIK41 gene taxon:4932 20020821 SGD
+SGD S000005211 PIK1 GO:0005794 SGD_REF:S000114103|PMID:16365163 IDA C phosphatidylinositol 4-kinase YNL267W|PIK120|PIK41 gene taxon:4932 20060201 SGD
+SGD S000005211 PIK1 GO:0004430 SGD_REF:S000054492|PMID:8194527 TAS F phosphatidylinositol 4-kinase YNL267W|PIK120|PIK41 gene taxon:4932 20010118 SGD
+SGD S000005211 PIK1 GO:0004430 SGD_REF:S000049912|PMID:1331109 IDA F phosphatidylinositol 4-kinase YNL267W|PIK120|PIK41 gene taxon:4932 20050420 SGD
+SGD S000005211 PIK1 GO:0000910 SGD_REF:S000054492|PMID:8194527 IMP P phosphatidylinositol 4-kinase YNL267W|PIK120|PIK41 gene taxon:4932 20010119 SGD
+SGD S000005211 PIK1 GO:0006892 SGD_REF:S000048258|PMID:10567405 IGI P phosphatidylinositol 4-kinase YNL267W|PIK120|PIK41 gene taxon:4932 20010118 SGD
+SGD S000005211 PIK1 GO:0030437 SGD_REF:S000075947|PMID:14528019 IGI P phosphatidylinositol 4-kinase YNL267W|PIK120|PIK41 gene taxon:4932 20040816 SGD
+SGD S000005211 PIK1 GO:0030437 SGD_REF:S000075947|PMID:14528019 IMP P phosphatidylinositol 4-kinase YNL267W|PIK120|PIK41 gene taxon:4932 20040816 SGD
+SGD S000005211 PIK1 GO:0046854 SGD_REF:S000049912|PMID:1331109 IDA P phosphatidylinositol 4-kinase YNL267W|PIK120|PIK41 gene taxon:4932 20050420 SGD
+SGD S000005211 PIK1 GO:0048017 SGD_REF:S000054492|PMID:8194527 TAS P phosphatidylinositol 4-kinase YNL267W|PIK120|PIK41 gene taxon:4932 20050524 SGD
+SGD S000003318 PIL1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YGR086C gene taxon:4932 20031028 SGD
+SGD S000003318 PIL1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YGR086C gene taxon:4932 20031210 SGD
+SGD S000003318 PIL1 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C YGR086C gene taxon:4932 20060317 SGD
+SGD S000003318 PIL1 GO:0004860 SGD_REF:S000076362|PMID:15016821 IMP F YGR086C gene taxon:4932 20040630 SGD
+SGD S000003318 PIL1 GO:0006897 SGD_REF:S000114479|PMID:16496001 IGI P YGR086C gene taxon:4932 20060303 SGD
+SGD S000003318 PIL1 GO:0006897 SGD_REF:S000114479|PMID:16496001 IMP P YGR086C gene taxon:4932 20060303 SGD
+SGD S000003318 PIL1 GO:0009408 SGD_REF:S000076362|PMID:15016821 IMP P YGR086C gene taxon:4932 20040630 SGD
+SGD S000000118 PIM1 GO:0005759 SGD_REF:S000040977|PMID:8276800 ISS C ATP-dependent protease YBL022C|LON1|Lon gene taxon:4932 20010118 SGD
+SGD S000000118 PIM1 GO:0005759 SGD_REF:S000040977|PMID:8276800 IDA C ATP-dependent protease YBL022C|LON1|Lon gene taxon:4932 20010118 SGD
+SGD S000000118 PIM1 GO:0005759 SGD_REF:S000040977|PMID:8276800 IMP C ATP-dependent protease YBL022C|LON1|Lon gene taxon:4932 20010118 SGD
+SGD S000000118 PIM1 GO:0004176 SGD_REF:S000040977|PMID:8276800 IDA F ATP-dependent protease YBL022C|LON1|Lon gene taxon:4932 20010118 SGD
+SGD S000000118 PIM1 GO:0006508 SGD_REF:S000044484|PMID:7957078 IGI P ATP-dependent protease YBL022C|LON1|Lon gene taxon:4932 20010118 SGD
+SGD S000000118 PIM1 GO:0009408 SGD_REF:S000040977|PMID:8276800 IEP P ATP-dependent protease YBL022C|LON1|Lon gene taxon:4932 20010118 SGD
+SGD S000005630 PIN2 GO:0008372 SGD_REF:S000069584 ND C YOR104W gene taxon:4932 20021011 SGD
+SGD S000005630 PIN2 GO:0005554 SGD_REF:S000069584 ND F YOR104W gene taxon:4932 20021011 SGD
+SGD S000005630 PIN2 GO:0000004 SGD_REF:S000069584 ND P YOR104W gene taxon:4932 20021011 SGD
+SGD S000006358 PIN3 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YPR154W|LSB2 gene taxon:4932 20031028 SGD
+SGD S000006358 PIN3 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YPR154W|LSB2 gene taxon:4932 20031028 SGD
+SGD S000006358 PIN3 GO:0005554 SGD_REF:S000069584 ND F YPR154W|LSB2 gene taxon:4932 20021001 SGD
+SGD S000006358 PIN3 GO:0030036 SGD_REF:S000043043|PMID:10512884 IPI P YPR154W|LSB2 gene taxon:4932 20030619 SGD
+SGD S000000147 PIN4 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YBL051C|MDT1 gene taxon:4932 20031028 SGD
+SGD S000000147 PIN4 GO:0005554 SGD_REF:S000069584 ND F YBL051C|MDT1 gene taxon:4932 20021011 SGD
+SGD S000000147 PIN4 GO:0000077 SGD_REF:S000076053|PMID:15024067 IGI P YBL051C|MDT1 gene taxon:4932 20040628 SGD
+SGD S000000147 PIN4 GO:0000077 SGD_REF:S000076053|PMID:15024067 IPI P YBL051C|MDT1 gene taxon:4932 20040628 SGD
+SGD S000000147 PIN4 GO:0000086 SGD_REF:S000076053|PMID:15024067 IMP P YBL051C|MDT1 gene taxon:4932 20040628 SGD
+SGD S000005890 PIP2 GO:0005634 SGD_REF:S000052641|PMID:8670793 IPI C transcription factor YOR363C|OAF2 gene taxon:4932 20010118 SGD
+SGD S000005890 PIP2 GO:0003677 SGD_REF:S000052641|PMID:8670793 IPI F transcription factor YOR363C|OAF2 gene taxon:4932 20030225 SGD
+SGD S000005890 PIP2 GO:0003677 SGD_REF:S000052641|PMID:8670793 ISS F transcription factor YOR363C|OAF2 gene taxon:4932 20030225 SGD
+SGD S000005890 PIP2 GO:0016563 SGD_REF:S000052641|PMID:8670793 IMP F transcription factor YOR363C|OAF2 gene taxon:4932 20030225 SGD
+SGD S000005890 PIP2 GO:0016563 SGD_REF:S000052641|PMID:8670793 IPI F transcription factor YOR363C|OAF2 gene taxon:4932 20030225 SGD
+SGD S000005890 PIP2 GO:0006631 SGD_REF:S000052641|PMID:8670793 IMP P transcription factor YOR363C|OAF2 gene taxon:4932 20030225 SGD
+SGD S000005890 PIP2 GO:0007031 SGD_REF:S000052641|PMID:8670793 IMP P transcription factor YOR363C|OAF2 gene taxon:4932 20030225 SGD
+SGD S000005890 PIP2 GO:0045941 SGD_REF:S000052641|PMID:8670793 IMP P transcription factor YOR363C|OAF2 gene taxon:4932 20030225 SGD
+SGD S000005890 PIP2 GO:0045941 SGD_REF:S000052641|PMID:8670793 IPI P transcription factor YOR363C|OAF2 gene taxon:4932 20030225 SGD
+SGD S000001647 PIR1 GO:0009277 SGD_REF:S000039809|PMID:10407261 TAS C YKL164C|CCW6 gene taxon:4932 20010118 SGD
+SGD S000001647 PIR1 GO:0009277 SGD_REF:S000058137|PMID:9192695 IDA C YKL164C|CCW6 gene taxon:4932 20050317 SGD
+SGD S000001647 PIR1 GO:0009277 SGD_REF:S000081097|PMID:15781460 IDA C YKL164C|CCW6 gene taxon:4932 20050601 SGD
+SGD S000001647 PIR1 GO:0005199 SGD_REF:S000053320|PMID:9301021 IPI F YKL164C|CCW6 gene taxon:4932 20010607 SGD
+SGD S000001647 PIR1 GO:0006886 SGD_REF:S000060116|PMID:11238901 IMP P YKL164C|CCW6 gene taxon:4932 20030213 SGD
+SGD S000001647 PIR1 GO:0006886 SGD_REF:S000060116|PMID:11238901 IPI P YKL164C|CCW6 gene taxon:4932 20030213 SGD
+SGD S000001647 PIR1 GO:0007047 SGD_REF:S000039809|PMID:10407261 IMP P YKL164C|CCW6 gene taxon:4932 20010118 SGD
+SGD S000001646 PIR3 GO:0009277 SGD_REF:S000039809|PMID:10407261 TAS C YKL163W|CCW8 gene taxon:4932 20010118 SGD
+SGD S000001646 PIR3 GO:0009277 SGD_REF:S000058137|PMID:9192695 IDA C YKL163W|CCW8 gene taxon:4932 20050317 SGD
+SGD S000001646 PIR3 GO:0009277 SGD_REF:S000081097|PMID:15781460 IDA C YKL163W|CCW8 gene taxon:4932 20050601 SGD
+SGD S000001646 PIR3 GO:0005199 SGD_REF:S000039809|PMID:10407261 IPI F YKL163W|CCW8 gene taxon:4932 20010118 SGD
+SGD S000001646 PIR3 GO:0007047 SGD_REF:S000039809|PMID:10407261 IMP P YKL163W|CCW8 gene taxon:4932 20010118 SGD
+SGD S000006317 PIS1 GO:0005741 SGD_REF:S000062202|PMID:3005242 IDA C phosphatidylinositol synthase YPR113W gene taxon:4932 20050311 SGD
+SGD S000006317 PIS1 GO:0005783 SGD_REF:S000058496 TAS C phosphatidylinositol synthase YPR113W gene taxon:4932 20010119 SGD
+SGD S000006317 PIS1 GO:0005792 SGD_REF:S000062202|PMID:3005242 IDA C phosphatidylinositol synthase YPR113W gene taxon:4932 20050311 SGD
+SGD S000006317 PIS1 GO:0003881 SGD_REF:S000058496 TAS F phosphatidylinositol synthase YPR113W gene taxon:4932 20010119 SGD
+SGD S000006317 PIS1 GO:0003881 SGD_REF:S000057215|PMID:6088233 IMP F phosphatidylinositol synthase YPR113W gene taxon:4932 20050311 SGD
+SGD S000006317 PIS1 GO:0006661 SGD_REF:S000058496 TAS P phosphatidylinositol synthase YPR113W gene taxon:4932 20010119 SGD
+SGD S000006317 PIS1 GO:0006661 SGD_REF:S000057215|PMID:6088233 IMP P phosphatidylinositol synthase YPR113W gene taxon:4932 20050311 SGD
+SGD S000006317 PIS1 GO:0007049 SGD_REF:S000056989|PMID:3031032 IMP P phosphatidylinositol synthase YPR113W gene taxon:4932 20050311 SGD
+SGD S000000201 PKC1 GO:0005634 SGD_REF:S000077921|PMID:11545731 IDA C YBL105C|CLY15|HPO2|STT1 gene taxon:4932 20050503 SGD
+SGD S000000201 PKC1 GO:0005737 SGD_REF:S000077921|PMID:11545731 IDA C YBL105C|CLY15|HPO2|STT1 gene taxon:4932 20050503 SGD
+SGD S000000201 PKC1 GO:0005856 SGD_REF:S000086063|PMID:15910746 IDA C YBL105C|CLY15|HPO2|STT1 gene taxon:4932 20050808 SGD
+SGD S000000201 PKC1 GO:0030427 SGD_REF:S000049103|PMID:10893184 IDA C YBL105C|CLY15|HPO2|STT1 gene taxon:4932 20030430 SGD
+SGD S000000201 PKC1 GO:0004697 SGD_REF:S000049517|PMID:8207005 IDA F YBL105C|CLY15|HPO2|STT1 gene taxon:4932 20010118 SGD
+SGD S000000201 PKC1 GO:0006468 SGD_REF:S000049517|PMID:8207005 IDA P YBL105C|CLY15|HPO2|STT1 gene taxon:4932 20010118 SGD
+SGD S000000201 PKC1 GO:0007015 SGD_REF:S000073801|PMID:12810699 IGI P YBL105C|CLY15|HPO2|STT1 gene taxon:4932 20030821 SGD
+SGD S000000201 PKC1 GO:0007047 SGD_REF:S000041609|PMID:7874200 IMP P YBL105C|CLY15|HPO2|STT1 gene taxon:4932 20010118 SGD
+SGD S000000201 PKC1 GO:0007165 SGD_REF:S000041609|PMID:7874200 IMP P YBL105C|CLY15|HPO2|STT1 gene taxon:4932 20010118 SGD
+SGD S000000201 PKC1 GO:0007243 SGD_REF:S000041609|PMID:7874200 IMP P YBL105C|CLY15|HPO2|STT1 gene taxon:4932 20010118 SGD
+SGD S000002898 PKH1 GO:0005829 SGD_REF:S000071423|PMID:12221112 IDA C YDR490C gene taxon:4932 20021008 SGD
+SGD S000002898 PKH1 GO:0004672 SGD_REF:S000053842|PMID:10074427 IDA F YDR490C gene taxon:4932 20021008 SGD
+SGD S000002898 PKH1 GO:0000196 SGD_REF:S000048917|PMID:10567559 IGI P YDR490C gene taxon:4932 20021008 SGD
+SGD S000002898 PKH1 GO:0000196 SGD_REF:S000048917|PMID:10567559 IMP P YDR490C gene taxon:4932 20021008 SGD
+SGD S000002898 PKH1 GO:0006468 SGD_REF:S000053842|PMID:10074427 IDA P YDR490C gene taxon:4932 20021008 SGD
+SGD S000002898 PKH1 GO:0006897 SGD_REF:S000069470|PMID:11807089 IMP P YDR490C gene taxon:4932 20021008 SGD
+SGD S000005460 PKH2 GO:0005634 SGD_REF:S000071423|PMID:12221112 IDA C YOL100W gene taxon:4932 20021008 SGD
+SGD S000005460 PKH2 GO:0004672 SGD_REF:S000048917|PMID:10567559 IDA F YOL100W gene taxon:4932 20021008 SGD
+SGD S000005460 PKH2 GO:0000196 SGD_REF:S000048917|PMID:10567559 IGI P YOL100W gene taxon:4932 20021008 SGD
+SGD S000005460 PKH2 GO:0000196 SGD_REF:S000048917|PMID:10567559 IMP P YOL100W gene taxon:4932 20021008 SGD
+SGD S000005460 PKH2 GO:0006468 SGD_REF:S000048917|PMID:10567559 IDA P YOL100W gene taxon:4932 20021008 SGD
+SGD S000002874 PKH3 GO:0008372 SGD_REF:S000069584 ND C YDR466W gene taxon:4932 20030203 SGD
+SGD S000002874 PKH3 GO:0004672 SGD_REF:S000058030|PMID:9020587 ISS F YDR466W gene taxon:4932 20030203 SGD
+SGD S000002874 PKH3 GO:0004672 SGD_REF:S000048917|PMID:10567559 ISS SGD:S000002898|protein_id:O15530|SGD:S000005460 F YDR466W gene taxon:4932 20040126 SGD
+SGD S000002874 PKH3 GO:0000196 SGD_REF:S000048917|PMID:10567559 IGI SGD:S000002898|SGD:S000005460 P YDR466W gene taxon:4932 20040126 SGD
+SGD S000004730 PKR1 GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YMR123W gene taxon:4932 20031028 SGD
+SGD S000004730 PKR1 GO:0005554 SGD_REF:S000069584 ND F YMR123W gene taxon:4932 20020930 SGD
+SGD S000004730 PKR1 GO:0000004 SGD_REF:S000069584 ND P YMR123W gene taxon:4932 20020930 SGD
+SGD S000004610 PLB1 GO:0009277 SGD_REF:S000040179|PMID:10383953 IDA C phospholipase B (lypophospholipase) YMR008C gene taxon:4932 20020617 SGD
+SGD S000004610 PLB1 GO:0004622 SGD_REF:S000045017|PMID:8051052 ISS F phospholipase B (lypophospholipase) YMR008C gene taxon:4932 20020930 SGD
+SGD S000004610 PLB1 GO:0004622 SGD_REF:S000045017|PMID:8051052 IMP F phospholipase B (lypophospholipase) YMR008C gene taxon:4932 20020930 SGD
+SGD S000004610 PLB1 GO:0006650 SGD_REF:S000045017|PMID:8051052 IMP P phospholipase B (lypophospholipase) YMR008C gene taxon:4932 20020930 SGD
+SGD S000004608 PLB2 GO:0005576 SGD_REF:S000051129|PMID:10497163 IDA C lysophospholipase, phospholipase B YMR006C gene taxon:4932 20030921 SGD
+SGD S000004608 PLB2 GO:0009277 SGD_REF:S000040179|PMID:10383953 IDA C lysophospholipase, phospholipase B YMR006C gene taxon:4932 20020617 SGD
+SGD S000004608 PLB2 GO:0009277 SGD_REF:S000081097|PMID:15781460 IDA C lysophospholipase, phospholipase B YMR006C gene taxon:4932 20050601 SGD
+SGD S000004608 PLB2 GO:0004622 SGD_REF:S000051129|PMID:10497163 IDA F lysophospholipase, phospholipase B YMR006C gene taxon:4932 20020930 SGD
+SGD S000004608 PLB2 GO:0004622 SGD_REF:S000051129|PMID:10497163 ISS F lysophospholipase, phospholipase B YMR006C gene taxon:4932 20020930 SGD
+SGD S000004608 PLB2 GO:0004622 SGD_REF:S000051129|PMID:10497163 IMP F lysophospholipase, phospholipase B YMR006C gene taxon:4932 20020930 SGD
+SGD S000004608 PLB2 GO:0006650 SGD_REF:S000051129|PMID:10497163 IDA P lysophospholipase, phospholipase B YMR006C gene taxon:4932 20020930 SGD
+SGD S000004608 PLB2 GO:0006650 SGD_REF:S000051129|PMID:10497163 IGI P lysophospholipase, phospholipase B YMR006C gene taxon:4932 20020930 SGD
+SGD S000004608 PLB2 GO:0006650 SGD_REF:S000051129|PMID:10497163 IMP P lysophospholipase, phospholipase B YMR006C gene taxon:4932 20020930 SGD
+SGD S000005371 PLB3 GO:0005576 SGD_REF:S000051129|PMID:10497163 IDA C phospholipase B (lysophospholipase) YOL011W gene taxon:4932 20030921 SGD
+SGD S000005371 PLB3 GO:0005886 SGD_REF:S000051129|PMID:10497163 ISS C phospholipase B (lysophospholipase) YOL011W gene taxon:4932 20020930 SGD
+SGD S000005371 PLB3 GO:0004622 SGD_REF:S000051129|PMID:10497163 ISS F phospholipase B (lysophospholipase) YOL011W gene taxon:4932 20020930 SGD
+SGD S000005371 PLB3 GO:0004622 SGD_REF:S000051129|PMID:10497163 IMP F phospholipase B (lysophospholipase) YOL011W gene taxon:4932 20020930 SGD
+SGD S000005371 PLB3 GO:0006660 SGD_REF:S000051129|PMID:10497163 IDA P phospholipase B (lysophospholipase) YOL011W gene taxon:4932 20021203 SGD
+SGD S000005371 PLB3 GO:0006660 SGD_REF:S000051129|PMID:10497163 IMP P phospholipase B (lysophospholipase) YOL011W gene taxon:4932 20021203 SGD
+SGD S000005371 PLB3 GO:0030384 SGD_REF:S000051129|PMID:10497163 IDA P phospholipase B (lysophospholipase) YOL011W gene taxon:4932 20020930 SGD
+SGD S000005371 PLB3 GO:0030384 SGD_REF:S000051129|PMID:10497163 IMP P phospholipase B (lysophospholipase) YOL011W gene taxon:4932 20020930 SGD
+SGD S000006189 PLC1 GO:0000778 SGD_REF:S000048102|PMID:10779349 IDA C phosphoinositide-specific phospholipase C YPL268W gene taxon:4932 20021021 SGD
+SGD S000006189 PLC1 GO:0005634 SGD_REF:S000048102|PMID:10779349 IDA C phosphoinositide-specific phospholipase C YPL268W gene taxon:4932 20021021 SGD
+SGD S000006189 PLC1 GO:0004435 SGD_REF:S000046841|PMID:8395015 ISS F phosphoinositide-specific phospholipase C YPL268W gene taxon:4932 20010118 SGD
+SGD S000006189 PLC1 GO:0007124 SGD_REF:S000044165|PMID:10514491 IMP P phosphoinositide-specific phospholipase C YPL268W gene taxon:4932 20010118 SGD
+SGD S000006189 PLC1 GO:0007165 SGD_REF:S000044075|PMID:7753023 IMP P phosphoinositide-specific phospholipase C YPL268W gene taxon:4932 20010118 SGD
+SGD S000006189 PLC1 GO:0019220 SGD_REF:S000081537|PMID:15866881 IMP P phosphoinositide-specific phospholipase C YPL268W gene taxon:4932 20060425 SGD
+SGD S000006189 PLC1 GO:0042144 SGD_REF:S000080027|PMID:15485855 IMP P phosphoinositide-specific phospholipase C YPL268W gene taxon:4932 20050105 SGD
+SGD S000002909 PLM2 GO:0005634 SGD_REF:S000071810|PMID:12464632 IC GO:0003700 C YDR501W gene taxon:4932 20050603 SGD
+SGD S000002909 PLM2 GO:0003700 SGD_REF:S000071810|PMID:12464632 NAS F YDR501W gene taxon:4932 20050603 SGD
+SGD S000002909 PLM2 GO:0003700 SGD_REF:S000071810|PMID:12464632 IPI F YDR501W gene taxon:4932 20050603 SGD
+SGD S000002909 PLM2 GO:0000083 SGD_REF:S000071810|PMID:12464632 IPI P YDR501W gene taxon:4932 20050603 SGD
+SGD S000002591 PLP1 GO:0005737 SGD_REF:S000056422|PMID:10749875 IPI C YDR183W gene taxon:4932 20010118 SGD
+SGD S000002591 PLP1 GO:0005095 SGD_REF:S000056422|PMID:10749875 ISS F YDR183W gene taxon:4932 20010118 SGD
+SGD S000002591 PLP1 GO:0007025 SGD_REF:S000074303|PMID:14573467 IGI P YDR183W gene taxon:4932 20040115 SGD
+SGD S000002591 PLP1 GO:0007329 SGD_REF:S000056422|PMID:10749875 IMP P YDR183W gene taxon:4932 20010118 SGD
+SGD S000002591 PLP1 GO:0007329 SGD_REF:S000056422|PMID:10749875 IPI P YDR183W gene taxon:4932 20010118 SGD
+SGD S000005807 PLP2 GO:0005737 SGD_REF:S000056422|PMID:10749875 IPI C YOR281C gene taxon:4932 20010118 SGD
+SGD S000005807 PLP2 GO:0005095 SGD_REF:S000056422|PMID:10749875 ISS F YOR281C gene taxon:4932 20010118 SGD
+SGD S000005807 PLP2 GO:0007329 SGD_REF:S000056422|PMID:10749875 IPI P YOR281C gene taxon:4932 20010118 SGD
+SGD S000005807 PLP2 GO:0007329 SGD_REF:S000056422|PMID:10749875 IMP P YOR281C gene taxon:4932 20010118 SGD
+SGD S000002976 PMA1 GO:0005886 SGD_REF:S000069871|PMID:11739806 IDA C plasma membrane H+-ATPase YGL008C gene taxon:4932 20041201 SGD
+SGD S000002976 PMA1 GO:0045121 SGD_REF:S000079755|PMID:15536122 IDA C plasma membrane H+-ATPase YGL008C gene taxon:4932 20041215 SGD
+SGD S000002976 PMA1 GO:0008553 SGD_REF:S000071836|PMID:12169695 TAS F plasma membrane H+-ATPase YGL008C gene taxon:4932 20030710 SGD
+SGD S000002976 PMA1 GO:0008553 SGD_REF:S000049175|PMID:8396147 TAS F plasma membrane H+-ATPase YGL008C gene taxon:4932 20030710 SGD
+SGD S000002976 PMA1 GO:0006885 SGD_REF:S000047350|PMID:8929277 IEP P plasma membrane H+-ATPase YGL008C gene taxon:4932 20020801 SGD
+SGD S000002976 PMA1 GO:0015992 SGD_REF:S000049175|PMID:8396147 IDA P plasma membrane H+-ATPase YGL008C gene taxon:4932 20020801 SGD
+SGD S000005957 PMA2 GO:0005886 SGD_REF:S000049175|PMID:8396147 IDA C plasma membrane ATPase YPL036W gene taxon:4932 20020801 SGD
+SGD S000005957 PMA2 GO:0008553 SGD_REF:S000049175|PMID:8396147 IDA F plasma membrane ATPase YPL036W gene taxon:4932 20020801 SGD
+SGD S000005957 PMA2 GO:0006885 SGD_REF:S000047350|PMID:8929277 IEP P plasma membrane ATPase YPL036W gene taxon:4932 20020801 SGD
+SGD S000005957 PMA2 GO:0015992 SGD_REF:S000049175|PMID:8396147 IDA P plasma membrane ATPase YPL036W gene taxon:4932 20020801 SGD
+SGD S000002974 PMC1 GO:0000329 SGD_REF:S000042898|PMID:7507493 IDA C Ca2+ ATPase (putative) YGL006W gene taxon:4932 20020919 SGD
+SGD S000002974 PMC1 GO:0005388 SGD_REF:S000042898|PMID:7507493 ISS F Ca2+ ATPase (putative) YGL006W gene taxon:4932 20020919 SGD
+SGD S000002974 PMC1 GO:0005388 SGD_REF:S000042898|PMID:7507493 IMP F Ca2+ ATPase (putative) YGL006W gene taxon:4932 20020919 SGD
+SGD S000002974 PMC1 GO:0006816 SGD_REF:S000042898|PMID:7507493 ISS P Ca2+ ATPase (putative) YGL006W gene taxon:4932 20020919 SGD
+SGD S000002974 PMC1 GO:0006816 SGD_REF:S000042898|PMID:7507493 IMP P Ca2+ ATPase (putative) YGL006W gene taxon:4932 20020919 SGD
+SGD S000002974 PMC1 GO:0006874 SGD_REF:S000042898|PMID:7507493 IMP P Ca2+ ATPase (putative) YGL006W gene taxon:4932 20020919 SGD
+SGD S000000934 PMD1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YER132C gene taxon:4932 20031028 SGD
+SGD S000000934 PMD1 GO:0005554 SGD_REF:S000069584 ND F YER132C gene taxon:4932 20021028 SGD
+SGD S000000934 PMD1 GO:0030435 SGD_REF:S000048503|PMID:9383076 IGI P YER132C gene taxon:4932 20021028 SGD
+SGD S000000934 PMD1 GO:0030435 SGD_REF:S000048503|PMID:9383076 IMP P YER132C gene taxon:4932 20021028 SGD
+SGD S000000805 PMI40 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C mannose-6-phosphate isomerase YER003C|PMI gene taxon:4932 20031028 SGD
+SGD S000000805 PMI40 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C mannose-6-phosphate isomerase YER003C|PMI gene taxon:4932 20031028 SGD
+SGD S000000805 PMI40 GO:0004476 SGD_REF:S000052711|PMID:8011630 IDA F mannose-6-phosphate isomerase YER003C|PMI gene taxon:4932 20020930 SGD
+SGD S000000805 PMI40 GO:0000032 SGD_REF:S000042091|PMID:1377774 IMP P mannose-6-phosphate isomerase YER003C|PMI gene taxon:4932 20020930 SGD
+SGD S000000805 PMI40 GO:0006486 SGD_REF:S000042091|PMID:1377774 IMP P mannose-6-phosphate isomerase YER003C|PMI gene taxon:4932 20020930 SGD
+SGD S000000805 PMI40 GO:0009298 SGD_REF:S000042091|PMID:1377774 IMP P mannose-6-phosphate isomerase YER003C|PMI gene taxon:4932 20020930 SGD
+SGD S000004006 PML1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YLR016C gene taxon:4932 20031028 SGD
+SGD S000004006 PML1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YLR016C gene taxon:4932 20031028 SGD
+SGD S000004006 PML1 GO:0005554 SGD_REF:S000069584 ND F YLR016C gene taxon:4932 20030203 SGD
+SGD S000004006 PML1 GO:0000398 SGD_REF:S000080993|PMID:15565172 IDA P YLR016C gene taxon:4932 20051006 SGD
+SGD S000004006 PML1 GO:0006406 SGD_REF:S000086641|PMID:16162818 IGI P YLR016C gene taxon:4932 20050923 SGD
+SGD S000004006 PML1 GO:0006406 SGD_REF:S000086641|PMID:16162818 IMP P YLR016C gene taxon:4932 20050923 SGD
+SGD S000004006 PML1 GO:0006406 SGD_REF:S000080993|PMID:15565172 IMP P YLR016C gene taxon:4932 20051006 SGD
+SGD S000004575 PML39 GO:0005643 SGD_REF:S000086641|PMID:16162818 IDA C nuclear pore-associated protein YML107C gene taxon:4932 20050923 SGD
+SGD S000004575 PML39 GO:0005554 SGD_REF:S000069584 ND F nuclear pore-associated protein YML107C gene taxon:4932 20050923 SGD
+SGD S000004575 PML39 GO:0006406 SGD_REF:S000086641|PMID:16162818 IGI P nuclear pore-associated protein YML107C gene taxon:4932 20050923 SGD
+SGD S000004575 PML39 GO:0006406 SGD_REF:S000086641|PMID:16162818 IMP P nuclear pore-associated protein YML107C gene taxon:4932 20050923 SGD
+SGD S000000619 PMP1 GO:0005886 SGD_REF:S000047706|PMID:1532582 IDA C proteolipid associated with plasma membrane H(+)-ATPase (Pma1p) YCR024C-A gene taxon:4932 20030415 SGD
+SGD S000000619 PMP1 GO:0016020 SGD_REF:S000047706|PMID:1532582 IDA C proteolipid associated with plasma membrane H(+)-ATPase (Pma1p) YCR024C-A gene taxon:4932 20020523 SGD
+SGD S000000619 PMP1 GO:0030234 SGD_REF:S000055783|PMID:8063750 IMP F proteolipid associated with plasma membrane H(+)-ATPase (Pma1p) YCR024C-A gene taxon:4932 20030415 SGD
+SGD S000000619 PMP1 GO:0006812 SGD_REF:S000055783|PMID:8063750 IGI P proteolipid associated with plasma membrane H(+)-ATPase (Pma1p) YCR024C-A gene taxon:4932 20020523 SGD
+SGD S000002103 PMP2 GO:0016020 SGD_REF:S000055783|PMID:8063750 IDA C proteolipid associated with plasma membrane H(+)-ATPase (Pma1p) YEL017C-A gene taxon:4932 20020523 SGD
+SGD S000002103 PMP2 GO:0005554 SGD_REF:S000069584 ND F proteolipid associated with plasma membrane H(+)-ATPase (Pma1p) YEL017C-A gene taxon:4932 20020523 SGD
+SGD S000002103 PMP2 GO:0006812 SGD_REF:S000055783|PMID:8063750 IGI P proteolipid associated with plasma membrane H(+)-ATPase (Pma1p) YEL017C-A gene taxon:4932 20020523 SGD
+SGD S000002684 PMP3 GO:0005886 SGD_REF:S000051000|PMID:10835350 IDA C hypothetical transmembrane protein YDR276C|SNA1 gene taxon:4932 20010118 SGD
+SGD S000002684 PMP3 GO:0005554 SGD_REF:S000069584 ND F hypothetical transmembrane protein YDR276C|SNA1 gene taxon:4932 20010119 SGD
+SGD S000002684 PMP3 GO:0006812 SGD_REF:S000051000|PMID:10835350 IMP P hypothetical transmembrane protein YDR276C|SNA1 gene taxon:4932 20010118 SGD
+SGD S000003135 PMR1 GO:0005794 SGD_REF:S000070157|PMID:12058017 TAS C Ca2+ ATPase YGL167C|BSD1|LDB1 gene taxon:4932 20020817 SGD
+SGD S000003135 PMR1 GO:0005388 SGD_REF:S000045924|PMID:1379856 ISS F Ca2+ ATPase YGL167C|BSD1|LDB1 gene taxon:4932 20021002 SGD
+SGD S000003135 PMR1 GO:0005388 SGD_REF:S000045924|PMID:1379856 IMP F Ca2+ ATPase YGL167C|BSD1|LDB1 gene taxon:4932 20021002 SGD
+SGD S000003135 PMR1 GO:0005388 SGD_REF:S000054055|PMID:10545175 IDA F Ca2+ ATPase YGL167C|BSD1|LDB1 gene taxon:4932 20030414 SGD
+SGD S000003135 PMR1 GO:0015410 SGD_REF:S000062338|PMID:10801856 IDA F Ca2+ ATPase YGL167C|BSD1|LDB1 gene taxon:4932 20030415 SGD
+SGD S000003135 PMR1 GO:0006816 SGD_REF:S000054055|PMID:10545175 IDA P Ca2+ ATPase YGL167C|BSD1|LDB1 gene taxon:4932 20030414 SGD
+SGD S000003135 PMR1 GO:0006828 SGD_REF:S000062338|PMID:10801856 IDA P Ca2+ ATPase YGL167C|BSD1|LDB1 gene taxon:4932 20030415 SGD
+SGD S000003135 PMR1 GO:0045045 SGD_REF:S000045924|PMID:1379856 IMP P Ca2+ ATPase YGL167C|BSD1|LDB1 gene taxon:4932 20021002 SGD
+SGD S000005026 PMS1 GO:0000228 SGD_REF:S000042567|PMID:10679328 TAS C mutL homolog, similar to Mlh1p; associates with Mlh1p, forming a heterodimer that then forms a ternary complex with either Msh2p-Msh3p or Msh2p-Msh6p bound to mismatched DNA YNL082W gene taxon:4932 20021004 SGD
+SGD S000005026 PMS1 GO:0003677 SGD_REF:S000065918|PMID:11575920 IDA F mutL homolog, similar to Mlh1p; associates with Mlh1p, forming a heterodimer that then forms a ternary complex with either Msh2p-Msh3p or Msh2p-Msh6p bound to mismatched DNA YNL082W gene taxon:4932 20021029 SGD
+SGD S000005026 PMS1 GO:0005524 SGD_REF:S000042935|PMID:10938116 TAS F mutL homolog, similar to Mlh1p; associates with Mlh1p, forming a heterodimer that then forms a ternary complex with either Msh2p-Msh3p or Msh2p-Msh6p bound to mismatched DNA YNL082W gene taxon:4932 20021029 SGD
+SGD S000005026 PMS1 GO:0016887 SGD_REF:S000069240|PMID:11717305 IDA F mutL homolog, similar to Mlh1p; associates with Mlh1p, forming a heterodimer that then forms a ternary complex with either Msh2p-Msh3p or Msh2p-Msh6p bound to mismatched DNA YNL082W gene taxon:4932 20021004 SGD
+SGD S000005026 PMS1 GO:0006298 SGD_REF:S000058456|PMID:10072354 TAS P mutL homolog, similar to Mlh1p; associates with Mlh1p, forming a heterodimer that then forms a ternary complex with either Msh2p-Msh3p or Msh2p-Msh6p bound to mismatched DNA YNL082W gene taxon:4932 20021004 SGD
+SGD S000005026 PMS1 GO:0007126 SGD_REF:S000062972|PMID:10915869 TAS P mutL homolog, similar to Mlh1p; associates with Mlh1p, forming a heterodimer that then forms a ternary complex with either Msh2p-Msh3p or Msh2p-Msh6p bound to mismatched DNA YNL082W gene taxon:4932 20021004 SGD
+SGD S000002253 PMT1 GO:0005789 SGD_REF:S000042697|PMID:8367478 TAS C dolichyl phosphate-D-mannose:protein O-D-mannosyltransferase YDL095W gene taxon:4932 20010118 SGD
+SGD S000002253 PMT1 GO:0004169 SGD_REF:S000042697|PMID:8367478 IDA F dolichyl phosphate-D-mannose:protein O-D-mannosyltransferase YDL095W gene taxon:4932 20010118 SGD
+SGD S000002253 PMT1 GO:0004169 SGD_REF:S000042697|PMID:8367478 IMP F dolichyl phosphate-D-mannose:protein O-D-mannosyltransferase YDL095W gene taxon:4932 20010118 SGD
+SGD S000002253 PMT1 GO:0006493 SGD_REF:S000042697|PMID:8367478 IMP P dolichyl phosphate-D-mannose:protein O-D-mannosyltransferase YDL095W gene taxon:4932 20010118 SGD
+SGD S000002253 PMT1 GO:0006493 SGD_REF:S000042697|PMID:8367478 IDA P dolichyl phosphate-D-mannose:protein O-D-mannosyltransferase YDL095W gene taxon:4932 20010118 SGD
+SGD S000000021 PMT2 GO:0005783 SGD_REF:S000043405|PMID:8918452 TAS C dolichyl phosphate-D-mannose:protein O-D-mannosyltransferase YAL023C|FUN25 gene taxon:4932 20010118 SGD
+SGD S000000021 PMT2 GO:0004169 SGD_REF:S000049666|PMID:7852348 ISS F dolichyl phosphate-D-mannose:protein O-D-mannosyltransferase YAL023C|FUN25 gene taxon:4932 20010118 SGD
+SGD S000000021 PMT2 GO:0004169 SGD_REF:S000049666|PMID:7852348 IMP F dolichyl phosphate-D-mannose:protein O-D-mannosyltransferase YAL023C|FUN25 gene taxon:4932 20010118 SGD
+SGD S000000021 PMT2 GO:0006493 SGD_REF:S000049666|PMID:7852348 ISS P dolichyl phosphate-D-mannose:protein O-D-mannosyltransferase YAL023C|FUN25 gene taxon:4932 20010118 SGD
+SGD S000000021 PMT2 GO:0006493 SGD_REF:S000049666|PMID:7852348 IMP P dolichyl phosphate-D-mannose:protein O-D-mannosyltransferase YAL023C|FUN25 gene taxon:4932 20010118 SGD
+SGD S000005848 PMT3 GO:0005783 SGD_REF:S000043405|PMID:8918452 TAS C dolichyl phosphate-D-mannose:protein O-D-mannosyltransferase YOR321W gene taxon:4932 20010118 SGD
+SGD S000005848 PMT3 GO:0004169 SGD_REF:S000056249|PMID:8585318 ISS F dolichyl phosphate-D-mannose:protein O-D-mannosyltransferase YOR321W gene taxon:4932 20010118 SGD
+SGD S000005848 PMT3 GO:0004169 SGD_REF:S000056249|PMID:8585318 IMP F dolichyl phosphate-D-mannose:protein O-D-mannosyltransferase YOR321W gene taxon:4932 20010118 SGD
+SGD S000005848 PMT3 GO:0006493 SGD_REF:S000056249|PMID:8585318 IMP P dolichyl phosphate-D-mannose:protein O-D-mannosyltransferase YOR321W gene taxon:4932 20010118 SGD
+SGD S000005848 PMT3 GO:0006493 SGD_REF:S000056249|PMID:8585318 ISS P dolichyl phosphate-D-mannose:protein O-D-mannosyltransferase YOR321W gene taxon:4932 20010118 SGD
+SGD S000003904 PMT4 GO:0005783 SGD_REF:S000043405|PMID:8918452 TAS C dolichyl phosphate-D-mannose:protein O-D-mannosyltransferase YJR143C gene taxon:4932 20010118 SGD
+SGD S000003904 PMT4 GO:0004169 SGD_REF:S000056249|PMID:8585318 IMP F dolichyl phosphate-D-mannose:protein O-D-mannosyltransferase YJR143C gene taxon:4932 20010118 SGD
+SGD S000003904 PMT4 GO:0004169 SGD_REF:S000056249|PMID:8585318 ISS F dolichyl phosphate-D-mannose:protein O-D-mannosyltransferase YJR143C gene taxon:4932 20010118 SGD
+SGD S000003904 PMT4 GO:0006493 SGD_REF:S000056249|PMID:8585318 IMP P dolichyl phosphate-D-mannose:protein O-D-mannosyltransferase YJR143C gene taxon:4932 20010118 SGD
+SGD S000003904 PMT4 GO:0006493 SGD_REF:S000056249|PMID:8585318 ISS P dolichyl phosphate-D-mannose:protein O-D-mannosyltransferase YJR143C gene taxon:4932 20010118 SGD
+SGD S000002251 PMT5 GO:0005783 SGD_REF:S000043405|PMID:8918452 TAS C dolichyl phosphate-D-mannose:protein O-D-mannosyltransferase YDL093W gene taxon:4932 20010118 SGD
+SGD S000002251 PMT5 GO:0004169 SGD_REF:S000043405|PMID:8918452 TAS F dolichyl phosphate-D-mannose:protein O-D-mannosyltransferase YDL093W gene taxon:4932 20010118 SGD
+SGD S000002251 PMT5 GO:0006493 SGD_REF:S000043405|PMID:8918452 TAS P dolichyl phosphate-D-mannose:protein O-D-mannosyltransferase YDL093W gene taxon:4932 20010118 SGD
+SGD S000003431 PMT6 GO:0005783 SGD_REF:S000043405|PMID:8918452 TAS C dolichyl phosphate-D-mannose:protein O-D-mannosyltransferase YGR199W gene taxon:4932 20010118 SGD
+SGD S000003431 PMT6 GO:0004169 SGD_REF:S000043405|PMID:8918452 TAS F dolichyl phosphate-D-mannose:protein O-D-mannosyltransferase YGR199W gene taxon:4932 20010118 SGD
+SGD S000003431 PMT6 GO:0006493 SGD_REF:S000043405|PMID:8918452 TAS P dolichyl phosphate-D-mannose:protein O-D-mannosyltransferase YGR199W gene taxon:4932 20010118 SGD
+SGD S000029378 PMT7 GO:0005783 SGD_REF:S000043405|PMID:8918452 TAS C dolichyl phosphate-D-mannose:protein O-D-mannosyltransferase gene taxon:4932 20010118 SGD
+SGD S000029378 PMT7 GO:0004169 SGD_REF:S000043405|PMID:8918452 TAS F dolichyl phosphate-D-mannose:protein O-D-mannosyltransferase gene taxon:4932 20010118 SGD
+SGD S000029378 PMT7 GO:0006493 SGD_REF:S000043405|PMID:8918452 TAS P dolichyl phosphate-D-mannose:protein O-D-mannosyltransferase gene taxon:4932 20010118 SGD
+SGD S000001611 PMU1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C phosphomutase homolog YKL128C gene taxon:4932 20031028 SGD
+SGD S000001611 PMU1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C phosphomutase homolog YKL128C gene taxon:4932 20031028 SGD
+SGD S000001611 PMU1 GO:0005554 SGD_REF:S000069584 ND F phosphomutase homolog YKL128C gene taxon:4932 20021001 SGD
+SGD S000001611 PMU1 GO:0000004 SGD_REF:S000069584 ND P phosphomutase homolog YKL128C gene taxon:4932 20021001 SGD
+SGD S000003005 PNC1 GO:0005634 SGD_REF:S000073098|PMID:12736687 IDA C nicotinamidase, pyrazinamidase YGL037C gene taxon:4932 20030509 SGD
+SGD S000003005 PNC1 GO:0005737 SGD_REF:S000073098|PMID:12736687 IDA C nicotinamidase, pyrazinamidase YGL037C gene taxon:4932 20030509 SGD
+SGD S000003005 PNC1 GO:0005777 SGD_REF:S000073098|PMID:12736687 IDA C nicotinamidase, pyrazinamidase YGL037C gene taxon:4932 20030509 SGD
+SGD S000003005 PNC1 GO:0008936 SGD_REF:S000069524|PMID:11901108 ISS F nicotinamidase, pyrazinamidase YGL037C gene taxon:4932 20020708 SGD
+SGD S000003005 PNC1 GO:0000183 SGD_REF:S000069524|PMID:11901108 IMP P nicotinamidase, pyrazinamidase YGL037C gene taxon:4932 20020708 SGD
+SGD S000003005 PNC1 GO:0001302 SGD_REF:S000073098|PMID:12736687 IMP P nicotinamidase, pyrazinamidase YGL037C gene taxon:4932 20050323 SGD
+SGD S000003005 PNC1 GO:0001302 SGD_REF:S000073098|PMID:12736687 IEP P nicotinamidase, pyrazinamidase YGL037C gene taxon:4932 20050323 SGD
+SGD S000003005 PNC1 GO:0006348 SGD_REF:S000069524|PMID:11901108 IMP P nicotinamidase, pyrazinamidase YGL037C gene taxon:4932 20020708 SGD
+SGD S000003005 PNC1 GO:0019358 SGD_REF:S000069524|PMID:11901108 ISS P nicotinamidase, pyrazinamidase YGL037C gene taxon:4932 20020708 SGD
+SGD S000006017 PNG1 GO:0005634 SGD_REF:S000045805|PMID:10831608 IDA C peptide:N-glycanase YPL096W|PNGase gene taxon:4932 20010118 SGD
+SGD S000006017 PNG1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C peptide:N-glycanase YPL096W|PNGase gene taxon:4932 20040928 SGD
+SGD S000006017 PNG1 GO:0005829 SGD_REF:S000045805|PMID:10831608 IDA C peptide:N-glycanase YPL096W|PNGase gene taxon:4932 20010118 SGD
+SGD S000006017 PNG1 GO:0005829 SGD_REF:S000086063|PMID:15910746 IDA C peptide:N-glycanase YPL096W|PNGase gene taxon:4932 20050808 SGD
+SGD S000006017 PNG1 GO:0000224 SGD_REF:S000045805|PMID:10831608 IDA F peptide:N-glycanase YPL096W|PNGase gene taxon:4932 20010118 SGD
+SGD S000006017 PNG1 GO:0006515 SGD_REF:S000045805|PMID:10831608 IMP P peptide:N-glycanase YPL096W|PNGase gene taxon:4932 20010118 SGD
+SGD S000006017 PNG1 GO:0006517 SGD_REF:S000045805|PMID:10831608 IDA P peptide:N-glycanase YPL096W|PNGase gene taxon:4932 20010118 SGD
+SGD S000005671 PNO1 GO:0005634 SGD_REF:S000071991|PMID:12502737 IDA C Associated with Nob1 YOR145C|DIM2|RRP20 gene taxon:4932 20030331 SGD
+SGD S000005671 PNO1 GO:0005730 SGD_REF:S000048046|PMID:10923024 IDA C Associated with Nob1 YOR145C|DIM2|RRP20 gene taxon:4932 20030203 SGD
+SGD S000005671 PNO1 GO:0051082 SGD_REF:S000071991|PMID:12502737 IPI F Associated with Nob1 YOR145C|DIM2|RRP20 gene taxon:4932 20030331 SGD
+SGD S000005671 PNO1 GO:0051082 SGD_REF:S000071991|PMID:12502737 IDA F Associated with Nob1 YOR145C|DIM2|RRP20 gene taxon:4932 20030331 SGD
+SGD S000005671 PNO1 GO:0006364 SGD_REF:S000073160|PMID:12736301 IMP P Associated with Nob1 YOR145C|DIM2|RRP20 gene taxon:4932 20030616 SGD
+SGD S000005671 PNO1 GO:0006365 SGD_REF:S000073750|PMID:12837249 IMP P Associated with Nob1 YOR145C|DIM2|RRP20 gene taxon:4932 20030805 SGD
+SGD S000005671 PNO1 GO:0006461 SGD_REF:S000071991|PMID:12502737 IMP P Associated with Nob1 YOR145C|DIM2|RRP20 gene taxon:4932 20030311 SGD
+SGD S000005671 PNO1 GO:0006461 SGD_REF:S000071991|PMID:12502737 IPI P Associated with Nob1 YOR145C|DIM2|RRP20 gene taxon:4932 20030311 SGD
+SGD S000004199 PNP1 GO:0008372 SGD_REF:S000069584 ND C purine nucleoside phosphorylase YLR209C gene taxon:4932 20010803 SGD
+SGD S000004199 PNP1 GO:0004731 SGD_REF:S000061001|PMID:11466296 IMP F purine nucleoside phosphorylase YLR209C gene taxon:4932 20010803 SGD
+SGD S000004199 PNP1 GO:0004731 SGD_REF:S000061001|PMID:11466296 ISS F purine nucleoside phosphorylase YLR209C gene taxon:4932 20010803 SGD
+SGD S000004199 PNP1 GO:0004731 SGD_REF:S000061001|PMID:11466296 IDA F purine nucleoside phosphorylase YLR209C gene taxon:4932 20010803 SGD
+SGD S000004199 PNP1 GO:0006152 SGD_REF:S000061001|PMID:11466296 IMP P purine nucleoside phosphorylase YLR209C gene taxon:4932 20010803 SGD
+SGD S000005687 PNS1 GO:0005887 SGD_REF:S000048046|PMID:10923024 ISS C YOR161C gene taxon:4932 20030205 SGD
+SGD S000005687 PNS1 GO:0005554 SGD_REF:S000069584 ND F YOR161C gene taxon:4932 20030205 SGD
+SGD S000005687 PNS1 NOT GO:0015220 SGD_REF:S000075553|PMID:15002745 IMP F YOR161C gene taxon:4932 20040316 SGD
+SGD S000005687 PNS1 GO:0000004 SGD_REF:S000069584 ND P YOR161C gene taxon:4932 20030205 SGD
+SGD S000005792 PNT1 GO:0005743 SGD_REF:S000041706|PMID:10490599 IDA C YOR266W gene taxon:4932 20010319 SGD
+SGD S000005792 PNT1 GO:0005554 SGD_REF:S000041706|PMID:10490599 TAS F YOR266W gene taxon:4932 20010319 SGD
+SGD S000005792 PNT1 GO:0007007 SGD_REF:S000041706|PMID:10490599 IMP P YOR266W gene taxon:4932 20010319 SGD
+SGD S000000226 POA1 GO:0008372 SGD_REF:S000069584 ND C small molecule phosphatase YBR022W gene taxon:4932 20030203 SGD
+SGD S000000226 POA1 GO:0016791 SGD_REF:S000062464|PMID:10550052 IDA F small molecule phosphatase YBR022W gene taxon:4932 20050310 SGD
+SGD S000000226 POA1 GO:0016791 SGD_REF:S000080601|PMID:15684411 IDA F small molecule phosphatase YBR022W gene taxon:4932 20050310 SGD
+SGD S000000226 POA1 GO:0006388 SGD_REF:S000080601|PMID:15684411 TAS P small molecule phosphatase YBR022W gene taxon:4932 20050310 SGD
+SGD S000004534 POB3 GO:0005634 SGD_REF:S000052704|PMID:9199353 IPI C DNA polymerase delta binding protein YML069W gene taxon:4932 20010118 SGD
+SGD S000004534 POB3 GO:0035101 SGD_REF:S000061420|PMID:11432837 IGI C DNA polymerase delta binding protein YML069W gene taxon:4932 20041021 SGD
+SGD S000004534 POB3 GO:0035101 SGD_REF:S000061420|PMID:11432837 IPI C DNA polymerase delta binding protein YML069W gene taxon:4932 20041021 SGD
+SGD S000004534 POB3 GO:0035101 SGD_REF:S000048981|PMID:9705338 IDA C DNA polymerase delta binding protein YML069W gene taxon:4932 20041115 SGD
+SGD S000004534 POB3 GO:0003682 SGD_REF:S000054316|PMID:10413469 IDA F DNA polymerase delta binding protein YML069W gene taxon:4932 20021206 SGD
+SGD S000004534 POB3 GO:0006261 SGD_REF:S000052704|PMID:9199353 IPI P DNA polymerase delta binding protein YML069W gene taxon:4932 20010118 SGD
+SGD S000004534 POB3 GO:0006333 SGD_REF:S000052704|PMID:9199353 IPI P DNA polymerase delta binding protein YML069W gene taxon:4932 20010118 SGD
+SGD S000004534 POB3 GO:0006338 SGD_REF:S000048981|PMID:9705338 IPI P DNA polymerase delta binding protein YML069W gene taxon:4932 20010118 SGD
+SGD S000004534 POB3 GO:0006367 SGD_REF:S000082428|PMID:15987999 IDA P DNA polymerase delta binding protein YML069W gene taxon:4932 20051114 SGD
+SGD S000004534 POB3 GO:0006367 SGD_REF:S000082428|PMID:15987999 IMP P DNA polymerase delta binding protein YML069W gene taxon:4932 20051114 SGD
+SGD S000004534 POB3 GO:0006368 SGD_REF:S000048981|PMID:9705338 IPI SGD:S000003175 P DNA polymerase delta binding protein YML069W gene taxon:4932 20041115 SGD
+SGD S000001384 POG1 GO:0005634 SGD_REF:S000069459|PMID:11914276 IDA C transcription factor (putative) YIL122W gene taxon:4932 20020507 SGD
+SGD S000001384 POG1 GO:0005634 SGD_REF:S000053376|PMID:9927449 IDA C transcription factor (putative) YIL122W gene taxon:4932 20020529 SGD
+SGD S000001384 POG1 GO:0003704 SGD_REF:S000053376|PMID:9927449 ISS F transcription factor (putative) YIL122W gene taxon:4932 20020529 SGD
+SGD S000001384 POG1 GO:0000083 SGD_REF:S000071810|PMID:12464632 IPI P transcription factor (putative) YIL122W gene taxon:4932 20050603 SGD
+SGD S000001384 POG1 GO:0000321 SGD_REF:S000053376|PMID:9927449 IGI P transcription factor (putative) YIL122W gene taxon:4932 20020529 SGD
+SGD S000001384 POG1 GO:0000321 SGD_REF:S000053376|PMID:9927449 IMP P transcription factor (putative) YIL122W gene taxon:4932 20020529 SGD
+SGD S000005046 POL1 GO:0005657 SGD_REF:S000081149|PMID:15773893 IDA C DNA polymerase I alpha subunit p180 YNL102W|CDC17|CRT5|HPR3 gene taxon:4932 20050708 SGD
+SGD S000005046 POL1 GO:0005658 SGD_REF:S000058372|PMID:9745046 TAS C DNA polymerase I alpha subunit p180 YNL102W|CDC17|CRT5|HPR3 gene taxon:4932 20010118 SGD
+SGD S000005046 POL1 GO:0003889 SGD_REF:S000058372|PMID:9745046 TAS F DNA polymerase I alpha subunit p180 YNL102W|CDC17|CRT5|HPR3 gene taxon:4932 20010118 SGD
+SGD S000005046 POL1 GO:0000731 SGD_REF:S000056091|PMID:10025407 IMP P DNA polymerase I alpha subunit p180 YNL102W|CDC17|CRT5|HPR3 gene taxon:4932 20021101 SGD
+SGD S000005046 POL1 GO:0006269 SGD_REF:S000058372|PMID:9745046 TAS P DNA polymerase I alpha subunit p180 YNL102W|CDC17|CRT5|HPR3 gene taxon:4932 20010118 SGD
+SGD S000005046 POL1 GO:0006270 SGD_REF:S000058372|PMID:9745046 TAS P DNA polymerase I alpha subunit p180 YNL102W|CDC17|CRT5|HPR3 gene taxon:4932 20010118 SGD
+SGD S000005046 POL1 GO:0006273 SGD_REF:S000058372|PMID:9745046 TAS P DNA polymerase I alpha subunit p180 YNL102W|CDC17|CRT5|HPR3 gene taxon:4932 20010118 SGD
+SGD S000000131 POL12 GO:0005634 SGD_REF:S000077144|PMID:15282802 IDA C DNA polymerase alpha-primase complex B subunit YBL035C gene taxon:4932 20041008 SGD
+SGD S000000131 POL12 GO:0005635 SGD_REF:S000077144|PMID:15282802 IDA C DNA polymerase alpha-primase complex B subunit YBL035C gene taxon:4932 20041008 SGD
+SGD S000000131 POL12 GO:0005658 SGD_REF:S000058372|PMID:9745046 TAS C DNA polymerase alpha-primase complex B subunit YBL035C gene taxon:4932 20010118 SGD
+SGD S000000131 POL12 GO:0003889 SGD_REF:S000058372|PMID:9745046 TAS F DNA polymerase alpha-primase complex B subunit YBL035C gene taxon:4932 20010118 SGD
+SGD S000000131 POL12 GO:0006269 SGD_REF:S000058372|PMID:9745046 TAS P DNA polymerase alpha-primase complex B subunit YBL035C gene taxon:4932 20010118 SGD
+SGD S000000131 POL12 GO:0006270 SGD_REF:S000058372|PMID:9745046 TAS P DNA polymerase alpha-primase complex B subunit YBL035C gene taxon:4932 20010118 SGD
+SGD S000000131 POL12 GO:0006273 SGD_REF:S000058372|PMID:9745046 TAS P DNA polymerase alpha-primase complex B subunit YBL035C gene taxon:4932 20010118 SGD
+SGD S000005206 POL2 GO:0005657 SGD_REF:S000081149|PMID:15773893 IDA C DNA polymerase II YNL262W|DUN2 gene taxon:4932 20050708 SGD
+SGD S000005206 POL2 GO:0008622 SGD_REF:S000062082|PMID:2406268 IDA C DNA polymerase II YNL262W|DUN2 gene taxon:4932 20031216 SGD
+SGD S000005206 POL2 GO:0003893 SGD_REF:S000058372|PMID:9745046 TAS F DNA polymerase II YNL262W|DUN2 gene taxon:4932 20010118 SGD
+SGD S000005206 POL2 GO:0000731 SGD_REF:S000056091|PMID:10025407 IMP P DNA polymerase II YNL262W|DUN2 gene taxon:4932 20021101 SGD
+SGD S000005206 POL2 GO:0006272 SGD_REF:S000058372|PMID:9745046 TAS P DNA polymerase II YNL262W|DUN2 gene taxon:4932 20010118 SGD
+SGD S000005206 POL2 GO:0006273 SGD_REF:S000058372|PMID:9745046 TAS P DNA polymerase II YNL262W|DUN2 gene taxon:4932 20010118 SGD
+SGD S000005206 POL2 GO:0006289 SGD_REF:S000058372|PMID:9745046 TAS P DNA polymerase II YNL262W|DUN2 gene taxon:4932 20010118 SGD
+SGD S000005206 POL2 GO:0006298 SGD_REF:S000058456|PMID:10072354 TAS P DNA polymerase II YNL262W|DUN2 gene taxon:4932 20010118 SGD
+SGD S000005206 POL2 GO:0006348 SGD_REF:S000075426|PMID:14673157 IMP P DNA polymerase II YNL262W|DUN2 gene taxon:4932 20040210 SGD
+SGD S000000292 POL30 GO:0005634 SGD_REF:S000077144|PMID:15282802 IDA C Proliferating Cell Nuclear Antigen (PCNA) YBR088C|PCNA gene taxon:4932 20041008 SGD
+SGD S000000292 POL30 GO:0005657 SGD_REF:S000058459|PMID:9759502 TAS C Proliferating Cell Nuclear Antigen (PCNA) YBR088C|PCNA gene taxon:4932 20011005 SGD
+SGD S000000292 POL30 GO:0043626 SGD_REF:S000058372|PMID:9745046 TAS C Proliferating Cell Nuclear Antigen (PCNA) YBR088C|PCNA gene taxon:4932 20060309 SGD
+SGD S000000292 POL30 GO:0030337 SGD_REF:S000072596|PMID:2902631 IDA F Proliferating Cell Nuclear Antigen (PCNA) YBR088C|PCNA gene taxon:4932 20060419 SGD
+SGD S000000292 POL30 GO:0006272 SGD_REF:S000060654|PMID:1682321 IDA P Proliferating Cell Nuclear Antigen (PCNA) YBR088C|PCNA gene taxon:4932 20060419 SGD
+SGD S000000292 POL30 GO:0006273 SGD_REF:S000045718|PMID:7673186 IDA P Proliferating Cell Nuclear Antigen (PCNA) YBR088C|PCNA gene taxon:4932 20060419 SGD
+SGD S000000292 POL30 GO:0006273 SGD_REF:S000045718|PMID:7673186 IPI SGD:S000001596 P Proliferating Cell Nuclear Antigen (PCNA) YBR088C|PCNA gene taxon:4932 20060419 SGD
+SGD S000000292 POL30 GO:0006280 SGD_REF:S000059415|PMID:11126776 IMP P Proliferating Cell Nuclear Antigen (PCNA) YBR088C|PCNA gene taxon:4932 20060419 SGD
+SGD S000000292 POL30 GO:0006280 SGD_REF:S000059415|PMID:11126776 IGI SGD:S000003804 P Proliferating Cell Nuclear Antigen (PCNA) YBR088C|PCNA gene taxon:4932 20060419 SGD
+SGD S000000292 POL30 GO:0006284 SGD_REF:S000058372|PMID:9745046 TAS P Proliferating Cell Nuclear Antigen (PCNA) YBR088C|PCNA gene taxon:4932 20010118 SGD
+SGD S000000292 POL30 GO:0006289 SGD_REF:S000039617|PMID:9806417 IMP P Proliferating Cell Nuclear Antigen (PCNA) YBR088C|PCNA gene taxon:4932 20060419 SGD
+SGD S000000292 POL30 GO:0006298 SGD_REF:S000057962|PMID:8858149 IMP P Proliferating Cell Nuclear Antigen (PCNA) YBR088C|PCNA gene taxon:4932 20060419 SGD
+SGD S000000292 POL30 GO:0006298 SGD_REF:S000057962|PMID:8858149 IPI SGD:S000005450 P Proliferating Cell Nuclear Antigen (PCNA) YBR088C|PCNA gene taxon:4932 20060419 SGD
+SGD S000000292 POL30 GO:0006301 SGD_REF:S000064609|PMID:8790390 IMP P Proliferating Cell Nuclear Antigen (PCNA) YBR088C|PCNA gene taxon:4932 20060419 SGD
+SGD S000003804 POL32 GO:0005634 SGD_REF:S000069459|PMID:11914276 IDA C DNA polymerase delta subunit YJR043C gene taxon:4932 20020507 SGD
+SGD S000003804 POL32 GO:0043625 SGD_REF:S000058372|PMID:9745046 TAS C DNA polymerase delta subunit YJR043C gene taxon:4932 20010118 SGD
+SGD S000003804 POL32 contributes_to GO:0003891 SGD_REF:S000058372|PMID:9745046 TAS F DNA polymerase delta subunit YJR043C gene taxon:4932 20010118 SGD
+SGD S000003804 POL32 contributes_to GO:0008310 SGD_REF:S000058372|PMID:9745046 TAS F DNA polymerase delta subunit YJR043C gene taxon:4932 20060309 SGD
+SGD S000003804 POL32 GO:0006272 SGD_REF:S000058372|PMID:9745046 TAS P DNA polymerase delta subunit YJR043C gene taxon:4932 20010118 SGD
+SGD S000003804 POL32 GO:0006273 SGD_REF:S000058372|PMID:9745046 TAS P DNA polymerase delta subunit YJR043C gene taxon:4932 20010118 SGD
+SGD S000003804 POL32 GO:0006280 SGD_REF:S000058372|PMID:9745046 TAS P DNA polymerase delta subunit YJR043C gene taxon:4932 20010118 SGD
+SGD S000003804 POL32 GO:0006284 SGD_REF:S000058372|PMID:9745046 TAS P DNA polymerase delta subunit YJR043C gene taxon:4932 20010118 SGD
+SGD S000003804 POL32 GO:0006289 SGD_REF:S000058372|PMID:9745046 TAS P DNA polymerase delta subunit YJR043C gene taxon:4932 20010118 SGD
+SGD S000003804 POL32 GO:0006298 SGD_REF:S000058372|PMID:9745046 NAS P DNA polymerase delta subunit YJR043C gene taxon:4932 20010118 SGD
+SGD S000003804 POL32 GO:0006298 SGD_REF:S000058456|PMID:10072354 NAS P DNA polymerase delta subunit YJR043C gene taxon:4932 20010118 SGD
+SGD S000003804 POL32 GO:0006301 SGD_REF:S000058372|PMID:9745046 TAS P DNA polymerase delta subunit YJR043C gene taxon:4932 20010118 SGD
+SGD S000000607 POL4 GO:0005634 SGD_REF:S000058372|PMID:9745046 TAS C DNA polymerase IV YCR014C|POLX gene taxon:4932 20010118 SGD
+SGD S000000607 POL4 GO:0003890 SGD_REF:S000058372|PMID:9745046 TAS F DNA polymerase IV YCR014C|POLX gene taxon:4932 20010118 SGD
+SGD S000000607 POL4 GO:0006287 SGD_REF:S000058372|PMID:9745046 TAS P DNA polymerase IV YCR014C|POLX gene taxon:4932 20010118 SGD
+SGD S000000607 POL4 GO:0006302 SGD_REF:S000071649|PMID:12235149 IDA P DNA polymerase IV YCR014C|POLX gene taxon:4932 20030203 SGD
+SGD S000000607 POL4 GO:0006303 SGD_REF:S000079665|PMID:15342630 IDA P DNA polymerase IV YCR014C|POLX gene taxon:4932 20041122 SGD
+SGD S000000781 POL5 GO:0005730 SGD_REF:S000070138|PMID:12093911 IDA C DNA polymerase phi YEL055C gene taxon:4932 20020713 SGD
+SGD S000000781 POL5 GO:0003887 SGD_REF:S000070138|PMID:12093911 IDA F DNA polymerase phi YEL055C gene taxon:4932 20051130 SGD
+SGD S000000781 POL5 GO:0003887 SGD_REF:S000070138|PMID:12093911 ISS F DNA polymerase phi YEL055C gene taxon:4932 20051130 SGD
+SGD S000000781 POL5 GO:0009303 SGD_REF:S000070138|PMID:12093911 IMP P DNA polymerase phi YEL055C gene taxon:4932 20040701 SGD
+SGD S000004736 POM152 GO:0005643 SGD_REF:S000058277|PMID:9442897 IDA C membrane glycoprotein, nuclear pore complex subunit YMR129W gene taxon:4932 20010118 SGD
+SGD S000004736 POM152 GO:0005643 SGD_REF:S000041899|PMID:9988776 IDA C membrane glycoprotein, nuclear pore complex subunit YMR129W gene taxon:4932 20010118 SGD
+SGD S000004736 POM152 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C membrane glycoprotein, nuclear pore complex subunit YMR129W gene taxon:4932 20040928 SGD
+SGD S000004736 POM152 GO:0005198 SGD_REF:S000058277|PMID:9442897 TAS F membrane glycoprotein, nuclear pore complex subunit YMR129W gene taxon:4932 20010118 SGD
+SGD S000004736 POM152 GO:0006406 SGD_REF:S000058277|PMID:9442897 TAS P membrane glycoprotein, nuclear pore complex subunit YMR129W gene taxon:4932 20010118 SGD
+SGD S000004736 POM152 GO:0006407 SGD_REF:S000058277|PMID:9442897 TAS P membrane glycoprotein, nuclear pore complex subunit YMR129W gene taxon:4932 20010118 SGD
+SGD S000004736 POM152 GO:0006408 SGD_REF:S000058277|PMID:9442897 TAS P membrane glycoprotein, nuclear pore complex subunit YMR129W gene taxon:4932 20010118 SGD
+SGD S000004736 POM152 GO:0006409 SGD_REF:S000058277|PMID:9442897 TAS P membrane glycoprotein, nuclear pore complex subunit YMR129W gene taxon:4932 20010118 SGD
+SGD S000004736 POM152 GO:0006607 SGD_REF:S000058277|PMID:9442897 TAS P membrane glycoprotein, nuclear pore complex subunit YMR129W gene taxon:4932 20010118 SGD
+SGD S000004736 POM152 GO:0006608 SGD_REF:S000058277|PMID:9442897 TAS P membrane glycoprotein, nuclear pore complex subunit YMR129W gene taxon:4932 20010118 SGD
+SGD S000004736 POM152 GO:0006609 SGD_REF:S000058277|PMID:9442897 TAS P membrane glycoprotein, nuclear pore complex subunit YMR129W gene taxon:4932 20010118 SGD
+SGD S000004736 POM152 GO:0006610 SGD_REF:S000058277|PMID:9442897 TAS P membrane glycoprotein, nuclear pore complex subunit YMR129W gene taxon:4932 20010118 SGD
+SGD S000004736 POM152 GO:0006611 SGD_REF:S000058277|PMID:9442897 TAS P membrane glycoprotein, nuclear pore complex subunit YMR129W gene taxon:4932 20010118 SGD
+SGD S000004736 POM152 GO:0006999 SGD_REF:S000058277|PMID:9442897 TAS P membrane glycoprotein, nuclear pore complex subunit YMR129W gene taxon:4932 20010118 SGD
+SGD S000004008 POM34 GO:0005643 SGD_REF:S000069412|PMID:11343909 TAS C integral membrane protein, nuclear pore complex subunit YLR018C gene taxon:4932 20020313 SGD
+SGD S000004008 POM34 GO:0005643 SGD_REF:S000056415|PMID:10684247 IDA C integral membrane protein, nuclear pore complex subunit YLR018C gene taxon:4932 20020617 SGD
+SGD S000004008 POM34 GO:0031301 SGD_REF:S000113875|PMID:16361228 IDA C integral membrane protein, nuclear pore complex subunit YLR018C gene taxon:4932 20060530 SGD
+SGD S000004008 POM34 GO:0005554 SGD_REF:S000069584 ND F integral membrane protein, nuclear pore complex subunit YLR018C gene taxon:4932 20020930 SGD
+SGD S000004008 POM34 GO:0006913 SGD_REF:S000056415|PMID:10684247 IPI P integral membrane protein, nuclear pore complex subunit YLR018C gene taxon:4932 20020930 SGD
+SGD S000004008 POM34 GO:0006913 SGD_REF:S000113875|PMID:16361228 IMP P integral membrane protein, nuclear pore complex subunit YLR018C gene taxon:4932 20060530 SGD
+SGD S000005165 POP1 GO:0000172 SGD_REF:S000044608|PMID:9620854 IDA C Nuclear RNase P subunit, RNase MRP subunit YNL221C gene taxon:4932 20010118 SGD
+SGD S000005165 POP1 GO:0005655 SGD_REF:S000044608|PMID:9620854 IDA C Nuclear RNase P subunit, RNase MRP subunit YNL221C gene taxon:4932 20010118 SGD
+SGD S000005165 POP1 GO:0000171 SGD_REF:S000044608|PMID:9620854 IDA F Nuclear RNase P subunit, RNase MRP subunit YNL221C gene taxon:4932 20010118 SGD
+SGD S000005165 POP1 GO:0004526 SGD_REF:S000044608|PMID:9620854 IDA F Nuclear RNase P subunit, RNase MRP subunit YNL221C gene taxon:4932 20010118 SGD
+SGD S000005165 POP1 GO:0006364 SGD_REF:S000044608|PMID:9620854 TAS P Nuclear RNase P subunit, RNase MRP subunit YNL221C gene taxon:4932 20010118 SGD
+SGD S000005165 POP1 GO:0008033 SGD_REF:S000044608|PMID:9620854 TAS P Nuclear RNase P subunit, RNase MRP subunit YNL221C gene taxon:4932 20010118 SGD
+SGD S000005335 POP2 GO:0005737 SGD_REF:S000069437|PMID:11889048 IDA C transcription factor (putative) YNR052C|CAF1 gene taxon:4932 20020802 SGD
+SGD S000005335 POP2 GO:0030015 SGD_REF:S000042122|PMID:10490603 IPI C transcription factor (putative) YNR052C|CAF1 gene taxon:4932 20020802 SGD
+SGD S000005335 POP2 GO:0000175 SGD_REF:S000069437|PMID:11889048 IDA F transcription factor (putative) YNR052C|CAF1 gene taxon:4932 20020802 SGD
+SGD S000005335 POP2 GO:0000175 SGD_REF:S000073816|PMID:11410650 IDA F transcription factor (putative) YNR052C|CAF1 gene taxon:4932 20030818 SGD
+SGD S000005335 POP2 GO:0000289 SGD_REF:S000069437|PMID:11889048 IDA P transcription factor (putative) YNR052C|CAF1 gene taxon:4932 20020802 SGD
+SGD S000005335 POP2 GO:0000289 SGD_REF:S000073816|PMID:11410650 IMP P transcription factor (putative) YNR052C|CAF1 gene taxon:4932 20030818 SGD
+SGD S000005335 POP2 GO:0000289 SGD_REF:S000073816|PMID:11410650 IDA P transcription factor (putative) YNR052C|CAF1 gene taxon:4932 20030818 SGD
+SGD S000005335 POP2 GO:0006357 SGD_REF:S000042122|PMID:10490603 IPI P transcription factor (putative) YNR052C|CAF1 gene taxon:4932 20020802 SGD
+SGD S000005226 POP3 GO:0000172 SGD_REF:S000044608|PMID:9620854 IDA C Nuclear RNase P subunit, RNase MRP subunit YNL282W gene taxon:4932 20010118 SGD
+SGD S000005226 POP3 GO:0005655 SGD_REF:S000044608|PMID:9620854 IDA C Nuclear RNase P subunit, RNase MRP subunit YNL282W gene taxon:4932 20010118 SGD
+SGD S000005226 POP3 GO:0000171 SGD_REF:S000044608|PMID:9620854 IDA F Nuclear RNase P subunit, RNase MRP subunit YNL282W gene taxon:4932 20010118 SGD
+SGD S000005226 POP3 GO:0004526 SGD_REF:S000044608|PMID:9620854 IDA F Nuclear RNase P subunit, RNase MRP subunit YNL282W gene taxon:4932 20010118 SGD
+SGD S000005226 POP3 GO:0006364 SGD_REF:S000044608|PMID:9620854 TAS P Nuclear RNase P subunit, RNase MRP subunit YNL282W gene taxon:4932 20010118 SGD
+SGD S000005226 POP3 GO:0008033 SGD_REF:S000044608|PMID:9620854 TAS P Nuclear RNase P subunit, RNase MRP subunit YNL282W gene taxon:4932 20010118 SGD
+SGD S000000461 POP4 GO:0000172 SGD_REF:S000044608|PMID:9620854 IDA C Nuclear RNase P subunit, RNase MRP subunit YBR257W gene taxon:4932 20010118 SGD
+SGD S000000461 POP4 GO:0005655 SGD_REF:S000044608|PMID:9620854 IDA C Nuclear RNase P subunit, RNase MRP subunit YBR257W gene taxon:4932 20010118 SGD
+SGD S000000461 POP4 GO:0000171 SGD_REF:S000044608|PMID:9620854 IDA F Nuclear RNase P subunit, RNase MRP subunit YBR257W gene taxon:4932 20010118 SGD
+SGD S000000461 POP4 GO:0004526 SGD_REF:S000044608|PMID:9620854 IDA F Nuclear RNase P subunit, RNase MRP subunit YBR257W gene taxon:4932 20010118 SGD
+SGD S000000461 POP4 GO:0006364 SGD_REF:S000044608|PMID:9620854 TAS P Nuclear RNase P subunit, RNase MRP subunit YBR257W gene taxon:4932 20010118 SGD
+SGD S000000461 POP4 GO:0008033 SGD_REF:S000044608|PMID:9620854 TAS P Nuclear RNase P subunit, RNase MRP subunit YBR257W gene taxon:4932 20010118 SGD
+SGD S000000031 POP5 GO:0000172 SGD_REF:S000044608|PMID:9620854 IDA C Nuclear RNase P subunit, RNase MRP subunit YAL033W|FUN53 gene taxon:4932 20010118 SGD
+SGD S000000031 POP5 GO:0005655 SGD_REF:S000044608|PMID:9620854 IDA C Nuclear RNase P subunit, RNase MRP subunit YAL033W|FUN53 gene taxon:4932 20010118 SGD
+SGD S000000031 POP5 GO:0000171 SGD_REF:S000044608|PMID:9620854 IDA F Nuclear RNase P subunit, RNase MRP subunit YAL033W|FUN53 gene taxon:4932 20010118 SGD
+SGD S000000031 POP5 GO:0004526 SGD_REF:S000044608|PMID:9620854 IDA F Nuclear RNase P subunit, RNase MRP subunit YAL033W|FUN53 gene taxon:4932 20010118 SGD
+SGD S000000031 POP5 GO:0006364 SGD_REF:S000044608|PMID:9620854 TAS P Nuclear RNase P subunit, RNase MRP subunit YAL033W|FUN53 gene taxon:4932 20010118 SGD
+SGD S000000031 POP5 GO:0008033 SGD_REF:S000044608|PMID:9620854 TAS P Nuclear RNase P subunit, RNase MRP subunit YAL033W|FUN53 gene taxon:4932 20010118 SGD
+SGD S000003262 POP6 GO:0000172 SGD_REF:S000044608|PMID:9620854 IDA C Nuclear RNase P subunit, RNase MRP subunit YGR030C gene taxon:4932 20010118 SGD
+SGD S000003262 POP6 GO:0005655 SGD_REF:S000044608|PMID:9620854 IDA C Nuclear RNase P subunit, RNase MRP subunit YGR030C gene taxon:4932 20010118 SGD
+SGD S000003262 POP6 GO:0000171 SGD_REF:S000044608|PMID:9620854 IDA F Nuclear RNase P subunit, RNase MRP subunit YGR030C gene taxon:4932 20010118 SGD
+SGD S000003262 POP6 GO:0004526 SGD_REF:S000044608|PMID:9620854 IDA F Nuclear RNase P subunit, RNase MRP subunit YGR030C gene taxon:4932 20010118 SGD
+SGD S000003262 POP6 GO:0006364 SGD_REF:S000044608|PMID:9620854 TAS P Nuclear RNase P subunit, RNase MRP subunit YGR030C gene taxon:4932 20010118 SGD
+SGD S000003262 POP6 GO:0008033 SGD_REF:S000044608|PMID:9620854 TAS P Nuclear RNase P subunit, RNase MRP subunit YGR030C gene taxon:4932 20010118 SGD
+SGD S000000371 POP7 GO:0000172 SGD_REF:S000044608|PMID:9620854 IDA C Nuclear RNase P subunit, RNase MRP subunit YBR167C|RPP2 gene taxon:4932 20010118 SGD
+SGD S000000371 POP7 GO:0005655 SGD_REF:S000044608|PMID:9620854 IDA C Nuclear RNase P subunit, RNase MRP subunit YBR167C|RPP2 gene taxon:4932 20010118 SGD
+SGD S000000371 POP7 GO:0000171 SGD_REF:S000044608|PMID:9620854 IDA F Nuclear RNase P subunit, RNase MRP subunit YBR167C|RPP2 gene taxon:4932 20010118 SGD
+SGD S000000371 POP7 GO:0004526 SGD_REF:S000044608|PMID:9620854 IDA F Nuclear RNase P subunit, RNase MRP subunit YBR167C|RPP2 gene taxon:4932 20010118 SGD
+SGD S000000371 POP7 GO:0006364 SGD_REF:S000044608|PMID:9620854 TAS P Nuclear RNase P subunit, RNase MRP subunit YBR167C|RPP2 gene taxon:4932 20010118 SGD
+SGD S000000371 POP7 GO:0008033 SGD_REF:S000044608|PMID:9620854 TAS P Nuclear RNase P subunit, RNase MRP subunit YBR167C|RPP2 gene taxon:4932 20010118 SGD
+SGD S000000114 POP8 GO:0000172 SGD_REF:S000044608|PMID:9620854 IDA C Nuclear RNase P subunit, RNase MRP subunit YBL018C gene taxon:4932 20010118 SGD
+SGD S000000114 POP8 GO:0005655 SGD_REF:S000044608|PMID:9620854 IDA C Nuclear RNase P subunit, RNase MRP subunit YBL018C gene taxon:4932 20010118 SGD
+SGD S000000114 POP8 GO:0000171 SGD_REF:S000044608|PMID:9620854 IDA F Nuclear RNase P subunit, RNase MRP subunit YBL018C gene taxon:4932 20010118 SGD
+SGD S000000114 POP8 GO:0004526 SGD_REF:S000044608|PMID:9620854 IDA F Nuclear RNase P subunit, RNase MRP subunit YBL018C gene taxon:4932 20010118 SGD
+SGD S000000114 POP8 GO:0006364 SGD_REF:S000044608|PMID:9620854 TAS P Nuclear RNase P subunit, RNase MRP subunit YBL018C gene taxon:4932 20010118 SGD
+SGD S000000114 POP8 GO:0008033 SGD_REF:S000044608|PMID:9620854 TAS P Nuclear RNase P subunit, RNase MRP subunit YBL018C gene taxon:4932 20010118 SGD
+SGD S000005000 POR1 GO:0005741 SGD_REF:S000057358|PMID:7499333 IDA C porin, voltage-dependent anion channel (VDAC) YNL055C|OMP2|YVDAC1 gene taxon:4932 20020919 SGD
+SGD S000005000 POR1 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C porin, voltage-dependent anion channel (VDAC) YNL055C|OMP2|YVDAC1 gene taxon:4932 20060317 SGD
+SGD S000005000 POR1 GO:0031307 SGD_REF:S000115559|PMID:16689936 IDA C porin, voltage-dependent anion channel (VDAC) YNL055C|OMP2|YVDAC1 gene taxon:4932 20060515 SGD
+SGD S000005000 POR1 GO:0008308 SGD_REF:S000058326|PMID:9593723 IDA F porin, voltage-dependent anion channel (VDAC) YNL055C|OMP2|YVDAC1 gene taxon:4932 20020919 SGD
+SGD S000005000 POR1 GO:0006811 SGD_REF:S000058326|PMID:9593723 IDA P porin, voltage-dependent anion channel (VDAC) YNL055C|OMP2|YVDAC1 gene taxon:4932 20020919 SGD
+SGD S000005000 POR1 GO:0007005 SGD_REF:S000061363|PMID:11488609 IMP P porin, voltage-dependent anion channel (VDAC) YNL055C|OMP2|YVDAC1 gene taxon:4932 20020919 SGD
+SGD S000005000 POR1 GO:0009060 SGD_REF:S000056855|PMID:2438132 IMP P porin, voltage-dependent anion channel (VDAC) YNL055C|OMP2|YVDAC1 gene taxon:4932 20020919 SGD
+SGD S000001376 POR2 GO:0005739 SGD_REF:S000069459|PMID:11914276 IDA C voltage dependent anion channel (YVDAC2) YIL114C|YVDAC2 gene taxon:4932 20020507 SGD
+SGD S000001376 POR2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C voltage dependent anion channel (YVDAC2) YIL114C|YVDAC2 gene taxon:4932 20040924 SGD
+SGD S000001376 POR2 GO:0005741 SGD_REF:S000049372|PMID:9315631 IDA C voltage dependent anion channel (YVDAC2) YIL114C|YVDAC2 gene taxon:4932 20020919 SGD
+SGD S000001376 POR2 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C voltage dependent anion channel (YVDAC2) YIL114C|YVDAC2 gene taxon:4932 20060317 SGD
+SGD S000001376 POR2 GO:0008308 SGD_REF:S000049372|PMID:9315631 IGI F voltage dependent anion channel (YVDAC2) YIL114C|YVDAC2 gene taxon:4932 20020919 SGD
+SGD S000001376 POR2 GO:0008308 SGD_REF:S000049372|PMID:9315631 ISS F voltage dependent anion channel (YVDAC2) YIL114C|YVDAC2 gene taxon:4932 20020919 SGD
+SGD S000001376 POR2 GO:0006811 SGD_REF:S000049372|PMID:9315631 IGI P voltage dependent anion channel (YVDAC2) YIL114C|YVDAC2 gene taxon:4932 20020919 SGD
+SGD S000001376 POR2 GO:0006811 SGD_REF:S000049372|PMID:9315631 ISS P voltage dependent anion channel (YVDAC2) YIL114C|YVDAC2 gene taxon:4932 20020919 SGD
+SGD S000006109 POS5 GO:0005759 SGD_REF:S000073134|PMID:12727869 IDA C YPL188W gene taxon:4932 20030512 SGD
+SGD S000006109 POS5 GO:0042736 SGD_REF:S000073134|PMID:12727869 IDA F YPL188W gene taxon:4932 20030530 SGD
+SGD S000006109 POS5 GO:0006741 SGD_REF:S000073134|PMID:12727869 IDA P YPL188W gene taxon:4932 20030512 SGD
+SGD S000006109 POS5 GO:0006979 SGD_REF:S000048034|PMID:7586028 IMP P YPL188W gene taxon:4932 20021011 SGD
+SGD S000001422 POT1 GO:0005782 SGD_REF:S000058494 TAS C 3-oxoacyl CoA thiolase YIL160C|FOX3|POX3 gene taxon:4932 20010119 SGD
+SGD S000001422 POT1 GO:0003988 SGD_REF:S000058496 TAS F 3-oxoacyl CoA thiolase YIL160C|FOX3|POX3 gene taxon:4932 20010119 SGD
+SGD S000001422 POT1 GO:0006635 SGD_REF:S000058496 TAS P 3-oxoacyl CoA thiolase YIL160C|FOX3|POX3 gene taxon:4932 20010119 SGD
+SGD S000003173 POX1 GO:0005782 SGD_REF:S000058494 TAS C fatty-acyl coenzyme A oxidase YGL205W|FOX1 gene taxon:4932 20010119 SGD
+SGD S000003173 POX1 GO:0003997 SGD_REF:S000058496 TAS F fatty-acyl coenzyme A oxidase YGL205W|FOX1 gene taxon:4932 20010119 SGD
+SGD S000003173 POX1 GO:0006635 SGD_REF:S000058496 TAS P fatty-acyl coenzyme A oxidase YGL205W|FOX1 gene taxon:4932 20010119 SGD
+SGD S000001068 PPA1 GO:0000220 SGD_REF:S000056362|PMID:10224039 TAS C proteolipid, vacuolar ATPase V0 domain subunit c'' YHR026W|VMA16 gene taxon:4932 20010118 SGD
+SGD S000001068 PPA1 GO:0000220 SGD_REF:S000058276|PMID:9442887 TAS C proteolipid, vacuolar ATPase V0 domain subunit c'' YHR026W|VMA16 gene taxon:4932 20010118 SGD
+SGD S000001068 PPA1 GO:0016021 SGD_REF:S000077169|PMID:15252052 IDA C proteolipid, vacuolar ATPase V0 domain subunit c'' YHR026W|VMA16 gene taxon:4932 20040929 SGD
+SGD S000001068 PPA1 GO:0046961 SGD_REF:S000056362|PMID:10224039 TAS F proteolipid, vacuolar ATPase V0 domain subunit c'' YHR026W|VMA16 gene taxon:4932 20030716 SGD
+SGD S000001068 PPA1 GO:0046961 SGD_REF:S000058276|PMID:9442887 TAS F proteolipid, vacuolar ATPase V0 domain subunit c'' YHR026W|VMA16 gene taxon:4932 20030716 SGD
+SGD S000001068 PPA1 GO:0007035 SGD_REF:S000056362|PMID:10224039 TAS P proteolipid, vacuolar ATPase V0 domain subunit c'' YHR026W|VMA16 gene taxon:4932 20010118 SGD
+SGD S000001068 PPA1 GO:0007035 SGD_REF:S000058276|PMID:9442887 TAS P proteolipid, vacuolar ATPase V0 domain subunit c'' YHR026W|VMA16 gene taxon:4932 20010118 SGD
+SGD S000004880 PPA2 GO:0005739 SGD_REF:S000046247|PMID:1648084 IMP C inorganic pyrophosphatase YMR267W|IPP2 gene taxon:4932 20030930 SGD
+SGD S000004880 PPA2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C inorganic pyrophosphatase YMR267W|IPP2 gene taxon:4932 20040928 SGD
+SGD S000004880 PPA2 GO:0004427 SGD_REF:S000046247|PMID:1648084 ISS F inorganic pyrophosphatase YMR267W|IPP2 gene taxon:4932 20030930 SGD
+SGD S000004880 PPA2 GO:0004427 SGD_REF:S000046247|PMID:1648084 IMP F inorganic pyrophosphatase YMR267W|IPP2 gene taxon:4932 20030930 SGD
+SGD S000004880 PPA2 GO:0009060 SGD_REF:S000046247|PMID:1648084 IMP P inorganic pyrophosphatase YMR267W|IPP2 gene taxon:4932 20030930 SGD
+SGD S000001117 PPE1 GO:0005763 SGD_REF:S000058278|PMID:9445368 IPI C YHR075C|MRPS2|YmS2 gene taxon:4932 20040203 SGD
+SGD S000001117 PPE1 GO:0003735 SGD_REF:S000058278|PMID:9445368 IPI F YHR075C|MRPS2|YmS2 gene taxon:4932 20040203 SGD
+SGD S000001117 PPE1 GO:0016789 SGD_REF:S000059601|PMID:11060018 IDA F YHR075C|MRPS2|YmS2 gene taxon:4932 20020821 SGD
+SGD S000001117 PPE1 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P YHR075C|MRPS2|YmS2 gene taxon:4932 20060227 SGD
+SGD S000001117 PPE1 GO:0006464 SGD_REF:S000059601|PMID:11060018 IGI P YHR075C|MRPS2|YmS2 gene taxon:4932 20040203 SGD
+SGD S000001117 PPE1 GO:0043037 SGD_REF:S000058278|PMID:9445368 IPI P YHR075C|MRPS2|YmS2 gene taxon:4932 20040203 SGD
+SGD S000005315 PPG1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YNR032W gene taxon:4932 20031028 SGD
+SGD S000005315 PPG1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YNR032W gene taxon:4932 20031028 SGD
+SGD S000005315 PPG1 GO:0000158 SGD_REF:S000057432|PMID:7678255 ISS F YNR032W gene taxon:4932 20020930 SGD
+SGD S000005315 PPG1 GO:0005977 SGD_REF:S000057432|PMID:7678255 IMP P YNR032W gene taxon:4932 20020930 SGD
+SGD S000005315 PPG1 GO:0006470 SGD_REF:S000057432|PMID:7678255 ISS P YNR032W gene taxon:4932 20020930 SGD
+SGD S000002292 PPH21 GO:0000159 SGD_REF:S000045742|PMID:10329624 TAS C YDL134C|PPH1 gene taxon:4932 20010118 SGD
+SGD S000002292 PPH21 GO:0000158 SGD_REF:S000045742|PMID:10329624 TAS F YDL134C|PPH1 gene taxon:4932 20010118 SGD
+SGD S000002292 PPH21 GO:0000082 SGD_REF:S000072514|PMID:12518319 IGI P YDL134C|PPH1 gene taxon:4932 20030217 SGD
+SGD S000002292 PPH21 GO:0006412 SGD_REF:S000045742|PMID:10329624 IPI P YDL134C|PPH1 gene taxon:4932 20010118 SGD
+SGD S000002292 PPH21 GO:0006470 SGD_REF:S000055155|PMID:9001215 TAS P YDL134C|PPH1 gene taxon:4932 20030430 SGD
+SGD S000002292 PPH21 GO:0007015 SGD_REF:S000055155|PMID:9001215 TAS P YDL134C|PPH1 gene taxon:4932 20010118 SGD
+SGD S000002292 PPH21 GO:0007094 SGD_REF:S000055155|PMID:9001215 IPI P YDL134C|PPH1 gene taxon:4932 20010118 SGD
+SGD S000002292 PPH21 GO:0007117 SGD_REF:S000055155|PMID:9001215 TAS P YDL134C|PPH1 gene taxon:4932 20010118 SGD
+SGD S000002347 PPH22 GO:0000159 SGD_REF:S000045742|PMID:10329624 TAS C protein phosphatase type 2A YDL188C|PPH2 gene taxon:4932 20010118 SGD
+SGD S000002347 PPH22 GO:0000780 SGD_REF:S000115004|PMID:16541024 IDA C protein phosphatase type 2A YDL188C|PPH2 gene taxon:4932 20060525 SGD
+SGD S000002347 PPH22 GO:0000158 SGD_REF:S000045742|PMID:10329624 TAS F protein phosphatase type 2A YDL188C|PPH2 gene taxon:4932 20010118 SGD
+SGD S000002347 PPH22 GO:0000158 SGD_REF:S000070222|PMID:12135475 IDA F protein phosphatase type 2A YDL188C|PPH2 gene taxon:4932 20030414 SGD
+SGD S000002347 PPH22 GO:0000082 SGD_REF:S000072514|PMID:12518319 IGI P protein phosphatase type 2A YDL188C|PPH2 gene taxon:4932 20030217 SGD
+SGD S000002347 PPH22 GO:0006412 SGD_REF:S000045742|PMID:10329624 IPI P protein phosphatase type 2A YDL188C|PPH2 gene taxon:4932 20010118 SGD
+SGD S000002347 PPH22 GO:0006470 SGD_REF:S000070222|PMID:12135475 IDA P protein phosphatase type 2A YDL188C|PPH2 gene taxon:4932 20030414 SGD
+SGD S000002347 PPH22 GO:0007015 SGD_REF:S000055155|PMID:9001215 TAS P protein phosphatase type 2A YDL188C|PPH2 gene taxon:4932 20010118 SGD
+SGD S000002347 PPH22 GO:0007094 SGD_REF:S000055155|PMID:9001215 IPI P protein phosphatase type 2A YDL188C|PPH2 gene taxon:4932 20010118 SGD
+SGD S000002347 PPH22 GO:0007117 SGD_REF:S000055155|PMID:9001215 TAS P protein phosphatase type 2A YDL188C|PPH2 gene taxon:4932 20010118 SGD
+SGD S000002482 PPH3 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C protein phosphatase type 2A YDR075W gene taxon:4932 20031028 SGD
+SGD S000002482 PPH3 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C protein phosphatase type 2A YDR075W gene taxon:4932 20031028 SGD
+SGD S000002482 PPH3 GO:0000158 SGD_REF:S000052551|PMID:7941742 IDA F protein phosphatase type 2A YDR075W gene taxon:4932 20020930 SGD
+SGD S000002482 PPH3 GO:0006470 SGD_REF:S000052551|PMID:7941742 IDA P protein phosphatase type 2A YDR075W gene taxon:4932 20020930 SGD
+SGD S000002482 PPH3 GO:0006807 SGD_REF:S000051382|PMID:10940301 IMP P protein phosphatase type 2A YDR075W gene taxon:4932 20020930 SGD
+SGD S000002843 PPM1 GO:0008372 SGD_REF:S000069584 ND C carboxy methyl transferase for protein phosphatase 2A catalytic subunit YDR435C gene taxon:4932 20020821 SGD
+SGD S000002843 PPM1 GO:0003880 SGD_REF:S000059601|PMID:11060018 IDA F carboxy methyl transferase for protein phosphatase 2A catalytic subunit YDR435C gene taxon:4932 20020821 SGD
+SGD S000002843 PPM1 GO:0006481 SGD_REF:S000059601|PMID:11060018 IDA P carboxy methyl transferase for protein phosphatase 2A catalytic subunit YDR435C gene taxon:4932 20020821 SGD
+SGD S000005501 PPM2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C PPM1 homolog, carboxy methyl transferase YOL141W|TYW4 gene taxon:4932 20031028 SGD
+SGD S000005501 PPM2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C PPM1 homolog, carboxy methyl transferase YOL141W|TYW4 gene taxon:4932 20040813 SGD
+SGD S000005501 PPM2 GO:0003880 SGD_REF:S000066200|PMID:11697862 ISS F PPM1 homolog, carboxy methyl transferase YOL141W|TYW4 gene taxon:4932 20021104 SGD
+SGD S000005501 PPM2 GO:0000004 SGD_REF:S000069584 ND P PPM1 homolog, carboxy methyl transferase YOL141W|TYW4 gene taxon:4932 20021104 SGD
+SGD S000002860 PPN1 GO:0005774 SGD_REF:S000065939|PMID:11566881 IMP C vacuolar endopolyphosphatase YDR452W|PHM5 gene taxon:4932 20011105 SGD
+SGD S000002860 PPN1 GO:0005774 SGD_REF:S000065939|PMID:11566881 IDA C vacuolar endopolyphosphatase YDR452W|PHM5 gene taxon:4932 20011105 SGD
+SGD S000002860 PPN1 GO:0000298 SGD_REF:S000060974|PMID:11447286 IMP F vacuolar endopolyphosphatase YDR452W|PHM5 gene taxon:4932 20011106 SGD
+SGD S000002860 PPN1 GO:0000298 SGD_REF:S000060974|PMID:11447286 IDA F vacuolar endopolyphosphatase YDR452W|PHM5 gene taxon:4932 20011106 SGD
+SGD S000002860 PPN1 GO:0006797 SGD_REF:S000060974|PMID:11447286 IMP P vacuolar endopolyphosphatase YDR452W|PHM5 gene taxon:4932 20011105 SGD
+SGD S000002860 PPN1 GO:0006797 SGD_REF:S000060974|PMID:11447286 IDA P vacuolar endopolyphosphatase YDR452W|PHM5 gene taxon:4932 20011105 SGD
+SGD S000006100 PPQ1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C protein phosphatase Q YPL179W|SAL6 gene taxon:4932 20031028 SGD
+SGD S000006100 PPQ1 GO:0004722 SGD_REF:S000043390|PMID:8269960 ISS F protein phosphatase Q YPL179W|SAL6 gene taxon:4932 20021118 SGD
+SGD S000006100 PPQ1 GO:0006445 SGD_REF:S000043390|PMID:8269960 IMP P protein phosphatase Q YPL179W|SAL6 gene taxon:4932 20021118 SGD
+SGD S000006100 PPQ1 GO:0006470 SGD_REF:S000043390|PMID:8269960 ISS P protein phosphatase Q YPL179W|SAL6 gene taxon:4932 20021118 SGD
+SGD S000004004 PPR1 GO:0005634 SGD_REF:S000042419|PMID:9290251 TAS C zinc finger transcription factor of the Zn(2)-Cys(6) binuclear cluster domain type YLR014C gene taxon:4932 20020930 SGD
+SGD S000004004 PPR1 GO:0003700 SGD_REF:S000042419|PMID:9290251 TAS F zinc finger transcription factor of the Zn(2)-Cys(6) binuclear cluster domain type YLR014C gene taxon:4932 20020930 SGD
+SGD S000004004 PPR1 GO:0006355 SGD_REF:S000042419|PMID:9290251 TAS P zinc finger transcription factor of the Zn(2)-Cys(6) binuclear cluster domain type YLR014C gene taxon:4932 20020930 SGD
+SGD S000004004 PPR1 GO:0046107 SGD_REF:S000042419|PMID:9290251 TAS P zinc finger transcription factor of the Zn(2)-Cys(6) binuclear cluster domain type YLR014C gene taxon:4932 20020930 SGD
+SGD S000000480 PPS1 GO:0008372 SGD_REF:S000069584 ND C dual specificity protein phosphatase YBR276C gene taxon:4932 20020930 SGD
+SGD S000000480 PPS1 GO:0008330 SGD_REF:S000049346|PMID:9083070 IDA F dual specificity protein phosphatase YBR276C gene taxon:4932 20020930 SGD
+SGD S000000480 PPS1 GO:0008330 SGD_REF:S000049346|PMID:9083070 ISS F dual specificity protein phosphatase YBR276C gene taxon:4932 20020930 SGD
+SGD S000000480 PPS1 GO:0006470 SGD_REF:S000049346|PMID:9083070 IDA P dual specificity protein phosphatase YBR276C gene taxon:4932 20040607 SGD
+SGD S000000480 PPS1 GO:0007090 SGD_REF:S000049346|PMID:9083070 IGI P dual specificity protein phosphatase YBR276C gene taxon:4932 20020930 SGD
+SGD S000000480 PPS1 GO:0007090 SGD_REF:S000049346|PMID:9083070 IMP P dual specificity protein phosphatase YBR276C gene taxon:4932 20020930 SGD
+SGD S000003355 PPT1 GO:0005634 SGD_REF:S000072959|PMID:12694636 IDA C YGR123C gene taxon:4932 20030421 SGD
+SGD S000003355 PPT1 GO:0005737 SGD_REF:S000072959|PMID:12694636 IDA C YGR123C gene taxon:4932 20030421 SGD
+SGD S000003355 PPT1 GO:0004722 SGD_REF:S000049716|PMID:7925273 ISS F YGR123C gene taxon:4932 20020930 SGD
+SGD S000003355 PPT1 GO:0004722 SGD_REF:S000072959|PMID:12694636 IDA F YGR123C gene taxon:4932 20030421 SGD
+SGD S000003355 PPT1 GO:0006470 SGD_REF:S000049716|PMID:7925273 IDA P YGR123C gene taxon:4932 20050722 SGD
+SGD S000003355 PPT1 GO:0006470 SGD_REF:S000049716|PMID:7925273 ISS P YGR123C gene taxon:4932 20050722 SGD
+SGD S000006069 PPT2 GO:0005739 SGD_REF:S000050216|PMID:9712852 IMP C phosphopantetheine:protein transferase (PPTase) YPL148C gene taxon:4932 20021002 SGD
+SGD S000006069 PPT2 GO:0008897 SGD_REF:S000050216|PMID:9712852 IDA F phosphopantetheine:protein transferase (PPTase) YPL148C gene taxon:4932 20021002 SGD
+SGD S000006069 PPT2 GO:0018065 SGD_REF:S000050216|PMID:9712852 IDA P phosphopantetheine:protein transferase (PPTase) YPL148C gene taxon:4932 20021002 SGD
+SGD S000001244 PPX1 GO:0005737 SGD_REF:S000050857|PMID:7860598 IDA C exopolyphosphatase YHR201C gene taxon:4932 20010118 SGD
+SGD S000001244 PPX1 GO:0005759 SGD_REF:S000073318|PMID:12689631 TAS C exopolyphosphatase YHR201C gene taxon:4932 20050630 SGD
+SGD S000001244 PPX1 GO:0005829 SGD_REF:S000073318|PMID:12689631 TAS C exopolyphosphatase YHR201C gene taxon:4932 20050630 SGD
+SGD S000001244 PPX1 GO:0005886 SGD_REF:S000073318|PMID:12689631 TAS C exopolyphosphatase YHR201C gene taxon:4932 20050630 SGD
+SGD S000001244 PPX1 GO:0004309 SGD_REF:S000050857|PMID:7860598 IMP F exopolyphosphatase YHR201C gene taxon:4932 20010118 SGD
+SGD S000001244 PPX1 GO:0004309 SGD_REF:S000050857|PMID:7860598 IDA F exopolyphosphatase YHR201C gene taxon:4932 20010118 SGD
+SGD S000001244 PPX1 GO:0006797 SGD_REF:S000057622|PMID:8157625 IDA P exopolyphosphatase YHR201C gene taxon:4932 20030213 SGD
+SGD S000004478 PPZ1 GO:0005634 SGD_REF:S000050776|PMID:8824289 IDA C YML016C gene taxon:4932 20010703 SGD
+SGD S000004478 PPZ1 GO:0005634 SGD_REF:S000069459|PMID:11914276 IDA C YML016C gene taxon:4932 20020507 SGD
+SGD S000004478 PPZ1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YML016C gene taxon:4932 20020507 SGD
+SGD S000004478 PPZ1 GO:0004722 SGD_REF:S000045961|PMID:7615085 IDA F YML016C gene taxon:4932 20010703 SGD
+SGD S000004478 PPZ1 GO:0006883 SGD_REF:S000043080|PMID:7768897 IMP P YML016C gene taxon:4932 20010703 SGD
+SGD S000004478 PPZ1 GO:0006883 SGD_REF:S000043080|PMID:7768897 IGI P YML016C gene taxon:4932 20010703 SGD
+SGD S000002844 PPZ2 GO:0008372 SGD_REF:S000069584 ND C YDR436W gene taxon:4932 20010703 SGD
+SGD S000002844 PPZ2 GO:0004722 SGD_REF:S000043080|PMID:7768897 TAS F YDR436W gene taxon:4932 20030122 SGD
+SGD S000002844 PPZ2 GO:0006883 SGD_REF:S000043080|PMID:7768897 IMP P YDR436W gene taxon:4932 20010703 SGD
+SGD S000002844 PPZ2 GO:0006883 SGD_REF:S000043080|PMID:7768897 IGI P YDR436W gene taxon:4932 20010703 SGD
+SGD S000000786 PRB1 GO:0000324 SGD_REF:S000056906|PMID:2674123 TAS C vacuolar protease B YEL060C|CVT1|yscB gene taxon:4932 20011214 SGD
+SGD S000000786 PRB1 GO:0000328 SGD_REF:S000080163|PMID:9529893 TAS C vacuolar protease B YEL060C|CVT1|yscB gene taxon:4932 20050107 SGD
+SGD S000000786 PRB1 GO:0004252 SGD_REF:S000045026|PMID:1744078 TAS F vacuolar protease B YEL060C|CVT1|yscB gene taxon:4932 20030127 SGD
+SGD S000000786 PRB1 GO:0007039 SGD_REF:S000056906|PMID:2674123 IMP P vacuolar protease B YEL060C|CVT1|yscB gene taxon:4932 20011214 SGD
+SGD S000000786 PRB1 GO:0007039 SGD_REF:S000056906|PMID:2674123 TAS P vacuolar protease B YEL060C|CVT1|yscB gene taxon:4932 20011214 SGD
+SGD S000000786 PRB1 GO:0009267 SGD_REF:S000056906|PMID:2674123 IMP P vacuolar protease B YEL060C|CVT1|yscB gene taxon:4932 20011214 SGD
+SGD S000000786 PRB1 GO:0030435 SGD_REF:S000056906|PMID:2674123 IMP P vacuolar protease B YEL060C|CVT1|yscB gene taxon:4932 20011214 SGD
+SGD S000004912 PRC1 GO:0000324 SGD_REF:S000074185|PMID:14562095 IDA C CPY, carboxypeptidase Y (proteinase C), carboxypeptidase yscY YMR297W|LBC1 gene taxon:4932 20031028 SGD
+SGD S000004912 PRC1 GO:0000328 SGD_REF:S000080163|PMID:9529893 TAS C CPY, carboxypeptidase Y (proteinase C), carboxypeptidase yscY YMR297W|LBC1 gene taxon:4932 20050107 SGD
+SGD S000004912 PRC1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C CPY, carboxypeptidase Y (proteinase C), carboxypeptidase yscY YMR297W|LBC1 gene taxon:4932 20020507 SGD
+SGD S000004912 PRC1 GO:0005783 SGD_REF:S000069459|PMID:11914276 IDA C CPY, carboxypeptidase Y (proteinase C), carboxypeptidase yscY YMR297W|LBC1 gene taxon:4932 20020507 SGD
+SGD S000004912 PRC1 GO:0004186 SGD_REF:S000057916|PMID:8789256 TAS F CPY, carboxypeptidase Y (proteinase C), carboxypeptidase yscY YMR297W|LBC1 gene taxon:4932 20021001 SGD
+SGD S000004912 PRC1 GO:0007039 SGD_REF:S000057916|PMID:8789256 TAS P CPY, carboxypeptidase Y (proteinase C), carboxypeptidase yscY YMR297W|LBC1 gene taxon:4932 20021001 SGD
+SGD S000000562 PRD1 GO:0005737 SGD_REF:S000055068|PMID:8307027 IDA C YCL057W gene taxon:4932 20011214 SGD
+SGD S000000562 PRD1 GO:0005737 SGD_REF:S000055068|PMID:8307027 TAS C YCL057W gene taxon:4932 20011214 SGD
+SGD S000000562 PRD1 GO:0005758 SGD_REF:S000055068|PMID:8307027 IDA C YCL057W gene taxon:4932 20011214 SGD
+SGD S000000562 PRD1 GO:0004222 SGD_REF:S000055068|PMID:8307027 IMP F YCL057W gene taxon:4932 20011213 SGD
+SGD S000000562 PRD1 GO:0004222 SGD_REF:S000055068|PMID:8307027 IDA F YCL057W gene taxon:4932 20011213 SGD
+SGD S000000562 PRD1 GO:0004222 SGD_REF:S000055068|PMID:8307027 ISS F YCL057W gene taxon:4932 20011213 SGD
+SGD S000000562 PRD1 GO:0004247 SGD_REF:S000055068|PMID:8307027 IDA F YCL057W gene taxon:4932 20011214 SGD
+SGD S000000562 PRD1 GO:0006508 SGD_REF:S000055068|PMID:8307027 IMP P YCL057W gene taxon:4932 20011213 SGD
+SGD S000000562 PRD1 GO:0006508 SGD_REF:S000055068|PMID:8307027 IDA P YCL057W gene taxon:4932 20011213 SGD
+SGD S000000814 PRE1 GO:0005634 SGD_REF:S000047509|PMID:10419517 IDA C 22.6 kDa proteasome subunit YER012W gene taxon:4932 20030207 SGD
+SGD S000000814 PRE1 GO:0019774 SGD_REF:S000049615|PMID:10500111 TAS C 22.6 kDa proteasome subunit YER012W gene taxon:4932 20030924 SGD
+SGD S000000814 PRE1 GO:0019774 SGD_REF:S000040877|PMID:9087403 IPI C 22.6 kDa proteasome subunit YER012W gene taxon:4932 20041109 SGD
+SGD S000000814 PRE1 GO:0004175 SGD_REF:S000058010|PMID:8982460 TAS F 22.6 kDa proteasome subunit YER012W gene taxon:4932 20030520 SGD
+SGD S000000814 PRE1 GO:0004175 SGD_REF:S000058457|PMID:10872471 TAS F 22.6 kDa proteasome subunit YER012W gene taxon:4932 20030520 SGD
+SGD S000000814 PRE1 GO:0006511 SGD_REF:S000058010|PMID:8982460 TAS P 22.6 kDa proteasome subunit YER012W gene taxon:4932 20010118 SGD
+SGD S000000814 PRE1 GO:0006511 SGD_REF:S000058457|PMID:10872471 TAS P 22.6 kDa proteasome subunit YER012W gene taxon:4932 20010118 SGD
+SGD S000000814 PRE1 GO:0006950 SGD_REF:S000058010|PMID:8982460 TAS P 22.6 kDa proteasome subunit YER012W gene taxon:4932 20010118 SGD
+SGD S000000814 PRE1 GO:0030437 SGD_REF:S000058010|PMID:8982460 TAS P 22.6 kDa proteasome subunit YER012W gene taxon:4932 20010118 SGD
+SGD S000005889 PRE10 GO:0019773 SGD_REF:S000040877|PMID:9087403 IPI C proteasome component YC1 (protease yscE subunit 1) YOR362C gene taxon:4932 20041109 SGD
+SGD S000005889 PRE10 GO:0004175 SGD_REF:S000058010|PMID:8982460 TAS F proteasome component YC1 (protease yscE subunit 1) YOR362C gene taxon:4932 20010118 SGD
+SGD S000005889 PRE10 GO:0004175 SGD_REF:S000058457|PMID:10872471 TAS F proteasome component YC1 (protease yscE subunit 1) YOR362C gene taxon:4932 20010118 SGD
+SGD S000005889 PRE10 GO:0006511 SGD_REF:S000058010|PMID:8982460 TAS P proteasome component YC1 (protease yscE subunit 1) YOR362C gene taxon:4932 20010118 SGD
+SGD S000005889 PRE10 GO:0006511 SGD_REF:S000058457|PMID:10872471 TAS P proteasome component YC1 (protease yscE subunit 1) YOR362C gene taxon:4932 20010118 SGD
+SGD S000006307 PRE2 GO:0019774 SGD_REF:S000049615|PMID:10500111 TAS C proteasome subunit YPR103W|DOA3|PRG1|SRR2 gene taxon:4932 20030924 SGD
+SGD S000006307 PRE2 GO:0019774 SGD_REF:S000040877|PMID:9087403 IPI C proteasome subunit YPR103W|DOA3|PRG1|SRR2 gene taxon:4932 20041109 SGD
+SGD S000006307 PRE2 GO:0004175 SGD_REF:S000058457|PMID:10872471 TAS F proteasome subunit YPR103W|DOA3|PRG1|SRR2 gene taxon:4932 20030520 SGD
+SGD S000006307 PRE2 GO:0004175 SGD_REF:S000058010|PMID:8982460 TAS F proteasome subunit YPR103W|DOA3|PRG1|SRR2 gene taxon:4932 20030520 SGD
+SGD S000006307 PRE2 GO:0006511 SGD_REF:S000058010|PMID:8982460 TAS P proteasome subunit YPR103W|DOA3|PRG1|SRR2 gene taxon:4932 20010118 SGD
+SGD S000006307 PRE2 GO:0006511 SGD_REF:S000058457|PMID:10872471 TAS P proteasome subunit YPR103W|DOA3|PRG1|SRR2 gene taxon:4932 20010118 SGD
+SGD S000003538 PRE3 GO:0019774 SGD_REF:S000049615|PMID:10500111 TAS C 20S proteasome subunit YJL001W|CRL21 gene taxon:4932 20030924 SGD
+SGD S000003538 PRE3 GO:0019774 SGD_REF:S000040877|PMID:9087403 IPI C 20S proteasome subunit YJL001W|CRL21 gene taxon:4932 20041109 SGD
+SGD S000003538 PRE3 GO:0004175 SGD_REF:S000058010|PMID:8982460 TAS F 20S proteasome subunit YJL001W|CRL21 gene taxon:4932 20030520 SGD
+SGD S000003538 PRE3 GO:0004175 SGD_REF:S000058457|PMID:10872471 TAS F 20S proteasome subunit YJL001W|CRL21 gene taxon:4932 20030520 SGD
+SGD S000003538 PRE3 GO:0006511 SGD_REF:S000058010|PMID:8982460 TAS P 20S proteasome subunit YJL001W|CRL21 gene taxon:4932 20010118 SGD
+SGD S000003538 PRE3 GO:0006511 SGD_REF:S000058457|PMID:10872471 TAS P 20S proteasome subunit YJL001W|CRL21 gene taxon:4932 20010118 SGD
+SGD S000003538 PRE3 GO:0006950 SGD_REF:S000058010|PMID:8982460 TAS P 20S proteasome subunit YJL001W|CRL21 gene taxon:4932 20010118 SGD
+SGD S000003538 PRE3 GO:0030437 SGD_REF:S000058010|PMID:8982460 TAS P 20S proteasome subunit YJL001W|CRL21 gene taxon:4932 20010118 SGD
+SGD S000001946 PRE4 GO:0019774 SGD_REF:S000049615|PMID:10500111 TAS C necessary for peptidyl glutamyl peptide hydrolyzing activity, proteasome subunit YFR050C gene taxon:4932 20030924 SGD
+SGD S000001946 PRE4 GO:0019774 SGD_REF:S000040877|PMID:9087403 IPI C necessary for peptidyl glutamyl peptide hydrolyzing activity, proteasome subunit YFR050C gene taxon:4932 20041109 SGD
+SGD S000001946 PRE4 GO:0004175 SGD_REF:S000058010|PMID:8982460 TAS F necessary for peptidyl glutamyl peptide hydrolyzing activity, proteasome subunit YFR050C gene taxon:4932 20030520 SGD
+SGD S000001946 PRE4 GO:0004175 SGD_REF:S000058457|PMID:10872471 TAS F necessary for peptidyl glutamyl peptide hydrolyzing activity, proteasome subunit YFR050C gene taxon:4932 20030520 SGD
+SGD S000001946 PRE4 GO:0006511 SGD_REF:S000058010|PMID:8982460 TAS P necessary for peptidyl glutamyl peptide hydrolyzing activity, proteasome subunit YFR050C gene taxon:4932 20010118 SGD
+SGD S000001946 PRE4 GO:0006511 SGD_REF:S000058457|PMID:10872471 TAS P necessary for peptidyl glutamyl peptide hydrolyzing activity, proteasome subunit YFR050C gene taxon:4932 20010118 SGD
+SGD S000004931 PRE5 GO:0019773 SGD_REF:S000052602|PMID:7918444 ISS C 20S proteasome alpha-type subunit YMR314W gene taxon:4932 20030924 SGD
+SGD S000004931 PRE5 GO:0019773 SGD_REF:S000040877|PMID:9087403 IPI C 20S proteasome alpha-type subunit YMR314W gene taxon:4932 20041109 SGD
+SGD S000004931 PRE5 GO:0004175 SGD_REF:S000058010|PMID:8982460 TAS F 20S proteasome alpha-type subunit YMR314W gene taxon:4932 20030520 SGD
+SGD S000004931 PRE5 GO:0004175 SGD_REF:S000058457|PMID:10872471 TAS F 20S proteasome alpha-type subunit YMR314W gene taxon:4932 20030520 SGD
+SGD S000004931 PRE5 GO:0006511 SGD_REF:S000058010|PMID:8982460 TAS P 20S proteasome alpha-type subunit YMR314W gene taxon:4932 20010118 SGD
+SGD S000004931 PRE5 GO:0006511 SGD_REF:S000058457|PMID:10872471 TAS P 20S proteasome alpha-type subunit YMR314W gene taxon:4932 20010118 SGD
+SGD S000005398 PRE6 GO:0019773 SGD_REF:S000052602|PMID:7918444 ISS C 20S proteasome alpha-type subunit YOL038W gene taxon:4932 20030924 SGD
+SGD S000005398 PRE6 GO:0019773 SGD_REF:S000040877|PMID:9087403 IPI C 20S proteasome alpha-type subunit YOL038W gene taxon:4932 20041109 SGD
+SGD S000005398 PRE6 GO:0004175 SGD_REF:S000058010|PMID:8982460 TAS F 20S proteasome alpha-type subunit YOL038W gene taxon:4932 20030520 SGD
+SGD S000005398 PRE6 GO:0004175 SGD_REF:S000058457|PMID:10872471 TAS F 20S proteasome alpha-type subunit YOL038W gene taxon:4932 20030520 SGD
+SGD S000005398 PRE6 GO:0006511 SGD_REF:S000058010|PMID:8982460 TAS P 20S proteasome alpha-type subunit YOL038W gene taxon:4932 20010118 SGD
+SGD S000005398 PRE6 GO:0006511 SGD_REF:S000058457|PMID:10872471 TAS P 20S proteasome alpha-type subunit YOL038W gene taxon:4932 20010118 SGD
+SGD S000000137 PRE7 GO:0019774 SGD_REF:S000040877|PMID:9087403 IPI C proteasome subunit YBL041W|PRS3 gene taxon:4932 20041109 SGD
+SGD S000000137 PRE7 GO:0004175 SGD_REF:S000058010|PMID:8982460 TAS F proteasome subunit YBL041W|PRS3 gene taxon:4932 20030520 SGD
+SGD S000000137 PRE7 GO:0004175 SGD_REF:S000058457|PMID:10872471 TAS F proteasome subunit YBL041W|PRS3 gene taxon:4932 20030520 SGD
+SGD S000000137 PRE7 GO:0006511 SGD_REF:S000058010|PMID:8982460 TAS P proteasome subunit YBL041W|PRS3 gene taxon:4932 20010118 SGD
+SGD S000000137 PRE7 GO:0006511 SGD_REF:S000058457|PMID:10872471 TAS P proteasome subunit YBL041W|PRS3 gene taxon:4932 20010118 SGD
+SGD S000004557 PRE8 GO:0019773 SGD_REF:S000049481|PMID:10744762 TAS C proteasome component Y7 YML092C gene taxon:4932 20041109 SGD
+SGD S000004557 PRE8 GO:0019773 SGD_REF:S000040877|PMID:9087403 IPI C proteasome component Y7 YML092C gene taxon:4932 20041109 SGD
+SGD S000004557 PRE8 GO:0004175 SGD_REF:S000058010|PMID:8982460 TAS F proteasome component Y7 YML092C gene taxon:4932 20030520 SGD
+SGD S000004557 PRE8 GO:0004175 SGD_REF:S000058457|PMID:10872471 TAS F proteasome component Y7 YML092C gene taxon:4932 20030520 SGD
+SGD S000004557 PRE8 GO:0006511 SGD_REF:S000058010|PMID:8982460 TAS P proteasome component Y7 YML092C gene taxon:4932 20010118 SGD
+SGD S000004557 PRE8 GO:0006511 SGD_REF:S000058457|PMID:10872471 TAS P proteasome component Y7 YML092C gene taxon:4932 20010118 SGD
+SGD S000003367 PRE9 GO:0019773 SGD_REF:S000040877|PMID:9087403 IPI C proteasome component Y13 YGR135W gene taxon:4932 20041109 SGD
+SGD S000003367 PRE9 GO:0004175 SGD_REF:S000058010|PMID:8982460 TAS F proteasome component Y13 YGR135W gene taxon:4932 20010118 SGD
+SGD S000003367 PRE9 GO:0004175 SGD_REF:S000058457|PMID:10872471 TAS F proteasome component Y13 YGR135W gene taxon:4932 20010118 SGD
+SGD S000003367 PRE9 GO:0006511 SGD_REF:S000058010|PMID:8982460 TAS P proteasome component Y13 YGR135W gene taxon:4932 20010118 SGD
+SGD S000003367 PRE9 GO:0006511 SGD_REF:S000058457|PMID:10872471 TAS P proteasome component Y13 YGR135W gene taxon:4932 20010118 SGD
+SGD S000003367 PRE9 GO:0030447 SGD_REF:S000074064|PMID:12940986 IMP P proteasome component Y13 YGR135W gene taxon:4932 20041012 SGD
+SGD S000001447 PRI1 GO:0005658 SGD_REF:S000058372|PMID:9745046 TAS C DNA primase p48 polypeptide YIR008C gene taxon:4932 20010118 SGD
+SGD S000001447 PRI1 GO:0003889 SGD_REF:S000058372|PMID:9745046 TAS F DNA primase p48 polypeptide YIR008C gene taxon:4932 20010118 SGD
+SGD S000001447 PRI1 GO:0006269 SGD_REF:S000058372|PMID:9745046 TAS P DNA primase p48 polypeptide YIR008C gene taxon:4932 20010118 SGD
+SGD S000001447 PRI1 GO:0006270 SGD_REF:S000058372|PMID:9745046 TAS P DNA primase p48 polypeptide YIR008C gene taxon:4932 20010118 SGD
+SGD S000001447 PRI1 GO:0006273 SGD_REF:S000058372|PMID:9745046 TAS P DNA primase p48 polypeptide YIR008C gene taxon:4932 20010118 SGD
+SGD S000001528 PRI2 GO:0005634 SGD_REF:S000077144|PMID:15282802 IDA C DNA primase p58 polypeptide YKL045W gene taxon:4932 20041008 SGD
+SGD S000001528 PRI2 GO:0005635 SGD_REF:S000077144|PMID:15282802 IDA C DNA primase p58 polypeptide YKL045W gene taxon:4932 20041008 SGD
+SGD S000001528 PRI2 GO:0005658 SGD_REF:S000058372|PMID:9745046 TAS C DNA primase p58 polypeptide YKL045W gene taxon:4932 20010118 SGD
+SGD S000001528 PRI2 GO:0003889 SGD_REF:S000058372|PMID:9745046 TAS F DNA primase p58 polypeptide YKL045W gene taxon:4932 20010118 SGD
+SGD S000001528 PRI2 GO:0000731 SGD_REF:S000056091|PMID:10025407 IMP P DNA primase p58 polypeptide YKL045W gene taxon:4932 20021101 SGD
+SGD S000001528 PRI2 GO:0006269 SGD_REF:S000058372|PMID:9745046 TAS P DNA primase p58 polypeptide YKL045W gene taxon:4932 20010118 SGD
+SGD S000001528 PRI2 GO:0006270 SGD_REF:S000058372|PMID:9745046 TAS P DNA primase p58 polypeptide YKL045W gene taxon:4932 20010118 SGD
+SGD S000001528 PRI2 GO:0006273 SGD_REF:S000058372|PMID:9745046 TAS P DNA primase p58 polypeptide YKL045W gene taxon:4932 20010118 SGD
+SGD S000001357 PRK1 GO:0030479 SGD_REF:S000041005|PMID:10652251 IDA C serine/threonine protein kinase YIL095W|PAK1 gene taxon:4932 20010118 SGD
+SGD S000001357 PRK1 GO:0004674 SGD_REF:S000045692|PMID:9885245 IDA F serine/threonine protein kinase YIL095W|PAK1 gene taxon:4932 20010118 SGD
+SGD S000001357 PRK1 GO:0000147 SGD_REF:S000041005|PMID:10652251 TAS P serine/threonine protein kinase YIL095W|PAK1 gene taxon:4932 20010118 SGD
+SGD S000001357 PRK1 GO:0000910 SGD_REF:S000041005|PMID:10652251 IMP P serine/threonine protein kinase YIL095W|PAK1 gene taxon:4932 20010119 SGD
+SGD S000001357 PRK1 GO:0006468 SGD_REF:S000045692|PMID:9885245 IDA P serine/threonine protein kinase YIL095W|PAK1 gene taxon:4932 20010118 SGD
+SGD S000001357 PRK1 GO:0007015 SGD_REF:S000045692|PMID:9885245 IMP P serine/threonine protein kinase YIL095W|PAK1 gene taxon:4932 20010118 SGD
+SGD S000001357 PRK1 GO:0030100 SGD_REF:S000075418|PMID:12956961 IMP P serine/threonine protein kinase YIL095W|PAK1 gene taxon:4932 20040520 SGD
+SGD S000005223 PRM1 GO:0016021 SGD_REF:S000056453|PMID:11062271 ISS C YNL279W gene taxon:4932 20010118 SGD
+SGD S000005223 PRM1 GO:0043332 SGD_REF:S000056453|PMID:11062271 IDA C YNL279W gene taxon:4932 20010118 SGD
+SGD S000005223 PRM1 GO:0005554 SGD_REF:S000069584 ND F YNL279W gene taxon:4932 20010119 SGD
+SGD S000005223 PRM1 GO:0045026 SGD_REF:S000056453|PMID:11062271 IMP P YNL279W gene taxon:4932 20010118 SGD
+SGD S000005223 PRM1 GO:0045026 SGD_REF:S000056453|PMID:11062271 IEP P YNL279W gene taxon:4932 20010118 SGD
+SGD S000003644 PRM10 GO:0016021 SGD_REF:S000056453|PMID:11062271 ISS C YJL108C gene taxon:4932 20010118 SGD
+SGD S000003644 PRM10 GO:0005554 SGD_REF:S000069584 ND F YJL108C gene taxon:4932 20010119 SGD
+SGD S000003644 PRM10 GO:0000747 SGD_REF:S000056453|PMID:11062271 IEP P YJL108C gene taxon:4932 20010118 SGD
+SGD S000001299 PRM2 GO:0016021 SGD_REF:S000056453|PMID:11062271 ISS C YIL037C gene taxon:4932 20010118 SGD
+SGD S000001299 PRM2 GO:0005554 SGD_REF:S000069584 ND F YIL037C gene taxon:4932 20010119 SGD
+SGD S000001299 PRM2 GO:0000747 SGD_REF:S000056453|PMID:11062271 IEP P YIL037C gene taxon:4932 20010118 SGD
+SGD S000006113 PRM3 GO:0005635 SGD_REF:S000072636|PMID:12514182 IDA C YPL192C gene taxon:4932 20030508 SGD
+SGD S000006113 PRM3 GO:0005635 SGD_REF:S000072636|PMID:12514182 IMP C YPL192C gene taxon:4932 20030508 SGD
+SGD S000006113 PRM3 GO:0005554 SGD_REF:S000069584 ND F YPL192C gene taxon:4932 20010119 SGD
+SGD S000006113 PRM3 GO:0000741 SGD_REF:S000072636|PMID:12514182 IDA P YPL192C gene taxon:4932 20030508 SGD
+SGD S000006113 PRM3 GO:0000741 SGD_REF:S000072636|PMID:12514182 IMP P YPL192C gene taxon:4932 20030508 SGD
+SGD S000006077 PRM4 GO:0016021 SGD_REF:S000056453|PMID:11062271 ISS C YPL156C gene taxon:4932 20010118 SGD
+SGD S000006077 PRM4 GO:0005554 SGD_REF:S000069584 ND F YPL156C gene taxon:4932 20010119 SGD
+SGD S000006077 PRM4 GO:0000747 SGD_REF:S000056453|PMID:11062271 IEP P YPL156C gene taxon:4932 20010118 SGD
+SGD S000001379 PRM5 GO:0016021 SGD_REF:S000056453|PMID:11062271 ISS C YIL117C gene taxon:4932 20010118 SGD
+SGD S000001379 PRM5 GO:0005554 SGD_REF:S000069584 ND F YIL117C gene taxon:4932 20010119 SGD
+SGD S000001379 PRM5 GO:0000747 SGD_REF:S000056453|PMID:11062271 IEP P YIL117C gene taxon:4932 20010118 SGD
+SGD S000004510 PRM6 GO:0016021 SGD_REF:S000056453|PMID:11062271 ISS C YML047C gene taxon:4932 20010118 SGD
+SGD S000004510 PRM6 GO:0005554 SGD_REF:S000069584 ND F YML047C gene taxon:4932 20010119 SGD
+SGD S000004510 PRM6 GO:0000747 SGD_REF:S000056453|PMID:11062271 IEP P YML047C gene taxon:4932 20010118 SGD
+SGD S000002197 PRM7 GO:0016021 SGD_REF:S000056453|PMID:11062271 ISS C YDL039C gene taxon:4932 20010118 SGD
+SGD S000002197 PRM7 GO:0005554 SGD_REF:S000069584 ND F YDL039C gene taxon:4932 20010119 SGD
+SGD S000002197 PRM7 GO:0000747 SGD_REF:S000056453|PMID:11062271 IEP P YDL039C gene taxon:4932 20010118 SGD
+SGD S000003021 PRM8 GO:0005783 SGD_REF:S000073907|PMID:12925749 IDA C YGL053W gene taxon:4932 20030918 SGD
+SGD S000003021 PRM8 GO:0005886 SGD_REF:S000074227|PMID:12101299 IDA C YGL053W gene taxon:4932 20031125 SGD
+SGD S000003021 PRM8 GO:0016021 SGD_REF:S000056453|PMID:11062271 ISS C YGL053W gene taxon:4932 20010118 SGD
+SGD S000003021 PRM8 GO:0005554 SGD_REF:S000069584 ND F YGL053W gene taxon:4932 20010119 SGD
+SGD S000003021 PRM8 GO:0000747 SGD_REF:S000056453|PMID:11062271 IEP P YGL053W gene taxon:4932 20010118 SGD
+SGD S000000078 PRM9 GO:0005783 SGD_REF:S000073907|PMID:12925749 IPI C YAR031W gene taxon:4932 20030918 SGD
+SGD S000000078 PRM9 GO:0005886 SGD_REF:S000074227|PMID:12101299 IDA C YAR031W gene taxon:4932 20031125 SGD
+SGD S000000078 PRM9 GO:0016021 SGD_REF:S000056453|PMID:11062271 ISS C YAR031W gene taxon:4932 20010118 SGD
+SGD S000000078 PRM9 GO:0005554 SGD_REF:S000069584 ND F YAR031W gene taxon:4932 20010119 SGD
+SGD S000000078 PRM9 GO:0016050 SGD_REF:S000073907|PMID:12925749 IPI P YAR031W gene taxon:4932 20040629 SGD
+SGD S000002708 PRO1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C gamma-glutamyl kinase YDR300C gene taxon:4932 20031028 SGD
+SGD S000002708 PRO1 GO:0004349 SGD_REF:S000072492|PMID:12513997 IDA F gamma-glutamyl kinase YDR300C gene taxon:4932 20030210 SGD
+SGD S000002708 PRO1 GO:0004349 SGD_REF:S000041111|PMID:1350780 ISS F gamma-glutamyl kinase YDR300C gene taxon:4932 20020927 SGD
+SGD S000002708 PRO1 GO:0004349 SGD_REF:S000054523|PMID:2824433 IGI F gamma-glutamyl kinase YDR300C gene taxon:4932 20020927 SGD
+SGD S000002708 PRO1 GO:0004349 SGD_REF:S000054523|PMID:2824433 IMP F gamma-glutamyl kinase YDR300C gene taxon:4932 20020927 SGD
+SGD S000002708 PRO1 GO:0006561 SGD_REF:S000072492|PMID:12513997 IDA P gamma-glutamyl kinase YDR300C gene taxon:4932 20030210 SGD
+SGD S000005850 PRO2 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C gamma-glutamyl phosphate reductase YOR323C gene taxon:4932 20031028 SGD
+SGD S000005850 PRO2 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C gamma-glutamyl phosphate reductase YOR323C gene taxon:4932 20020507 SGD
+SGD S000005850 PRO2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C gamma-glutamyl phosphate reductase YOR323C gene taxon:4932 20031028 SGD
+SGD S000005850 PRO2 GO:0004350 SGD_REF:S000072492|PMID:12513997 IDA F gamma-glutamyl phosphate reductase YOR323C gene taxon:4932 20030210 SGD
+SGD S000005850 PRO2 GO:0004350 SGD_REF:S000054523|PMID:2824433 IGI F gamma-glutamyl phosphate reductase YOR323C gene taxon:4932 20030122 SGD
+SGD S000005850 PRO2 GO:0006561 SGD_REF:S000072492|PMID:12513997 IDA P gamma-glutamyl phosphate reductase YOR323C gene taxon:4932 20030210 SGD
+SGD S000005850 PRO2 GO:0006561 SGD_REF:S000060327|PMID:11084050 TAS P gamma-glutamyl phosphate reductase YOR323C gene taxon:4932 20020729 SGD
+SGD S000000825 PRO3 GO:0005737 SGD_REF:S000057314|PMID:7009582 IDA C delta 1-pyrroline-5-carboxylate reductase YER023W|ORE2 gene taxon:4932 20010118 SGD
+SGD S000000825 PRO3 GO:0004735 SGD_REF:S000054523|PMID:2824433 IGI F delta 1-pyrroline-5-carboxylate reductase YER023W|ORE2 gene taxon:4932 20010118 SGD
+SGD S000000825 PRO3 GO:0004735 SGD_REF:S000045323|PMID:1508147 ISS F delta 1-pyrroline-5-carboxylate reductase YER023W|ORE2 gene taxon:4932 20010118 SGD
+SGD S000000825 PRO3 GO:0006561 SGD_REF:S000045323|PMID:1508147 IMP P delta 1-pyrroline-5-carboxylate reductase YER023W|ORE2 gene taxon:4932 20010118 SGD
+SGD S000000825 PRO3 GO:0006561 SGD_REF:S000054523|PMID:2824433 IMP P delta 1-pyrroline-5-carboxylate reductase YER023W|ORE2 gene taxon:4932 20010118 SGD
+SGD S000000825 PRO3 GO:0006561 SGD_REF:S000045323|PMID:1508147 ISS P delta 1-pyrroline-5-carboxylate reductase YER023W|ORE2 gene taxon:4932 20010118 SGD
+SGD S000002201 PRP11 GO:0005686 SGD_REF:S000069986|PMID:11804584 IDA C snRNA-associated protein YDL043C|RNA11 gene taxon:4932 20020621 SGD
+SGD S000002201 PRP11 colocalizes_with GO:0005686 SGD_REF:S000080993|PMID:15565172 IDA C snRNA-associated protein YDL043C|RNA11 gene taxon:4932 20051006 SGD
+SGD S000002201 PRP11 GO:0003723 SGD_REF:S000039421|PMID:8065365 IDA F snRNA-associated protein YDL043C|RNA11 gene taxon:4932 20021112 SGD
+SGD S000002201 PRP11 GO:0000245 SGD_REF:S000042680|PMID:8969185 IDA P snRNA-associated protein YDL043C|RNA11 gene taxon:4932 20021112 SGD
+SGD S000001794 PRP16 GO:0005681 SGD_REF:S000058281|PMID:9476892 TAS C ATP-binding protein (putative) YKR086W gene taxon:4932 20010118 SGD
+SGD S000001794 PRP16 GO:0004004 SGD_REF:S000058281|PMID:9476892 TAS F ATP-binding protein (putative) YKR086W gene taxon:4932 20010118 SGD
+SGD S000001794 PRP16 GO:0031202 SGD_REF:S000058281|PMID:9476892 TAS F ATP-binding protein (putative) YKR086W gene taxon:4932 20010118 SGD
+SGD S000001794 PRP16 GO:0000358 SGD_REF:S000058281|PMID:9476892 TAS P ATP-binding protein (putative) YKR086W gene taxon:4932 20030825 SGD
+SGD S000001794 PRP16 GO:0000358 SGD_REF:S000073846 TAS P ATP-binding protein (putative) YKR086W gene taxon:4932 20030825 SGD
+SGD S000003238 PRP18 GO:0005681 SGD_REF:S000071184|PMID:12212850 IDA C RNA splicing factor, U5 snRNP protein YGR006W gene taxon:4932 20020924 SGD
+SGD S000003238 PRP18 GO:0046540 SGD_REF:S000039461|PMID:10449419 TAS C RNA splicing factor, U5 snRNP protein YGR006W gene taxon:4932 20051004 SGD
+SGD S000003238 PRP18 contributes_to GO:0000386 SGD_REF:S000071184|PMID:12212850 IDA F RNA splicing factor, U5 snRNP protein YGR006W gene taxon:4932 20050921 SGD
+SGD S000003238 PRP18 contributes_to GO:0031202 SGD_REF:S000071184|PMID:12212850 IDA F RNA splicing factor, U5 snRNP protein YGR006W gene taxon:4932 20050921 SGD
+SGD S000003238 PRP18 GO:0000350 SGD_REF:S000071184|PMID:12212850 IDA P RNA splicing factor, U5 snRNP protein YGR006W gene taxon:4932 20050921 SGD
+SGD S000003238 PRP18 GO:0000398 SGD_REF:S000071567|PMID:12403466 IMP P RNA splicing factor, U5 snRNP protein YGR006W gene taxon:4932 20030110 SGD
+SGD S000003959 PRP19 GO:0005634 SGD_REF:S000069459|PMID:11914276 IDA C RNA splicing factor YLL036C|PSO4 gene taxon:4932 20020507 SGD
+SGD S000003959 PRP19 GO:0005681 SGD_REF:S000046470|PMID:11018040 IDA C RNA splicing factor YLL036C|PSO4 gene taxon:4932 20010118 SGD
+SGD S000003959 PRP19 GO:0005681 SGD_REF:S000046470|PMID:11018040 IGI C RNA splicing factor YLL036C|PSO4 gene taxon:4932 20010118 SGD
+SGD S000003959 PRP19 GO:0005681 SGD_REF:S000048670|PMID:8441419 IDA C RNA splicing factor YLL036C|PSO4 gene taxon:4932 20050308 SGD
+SGD S000003959 PRP19 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C RNA splicing factor YLL036C|PSO4 gene taxon:4932 20020507 SGD
+SGD S000003959 PRP19 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C RNA splicing factor YLL036C|PSO4 gene taxon:4932 20040813 SGD
+SGD S000003959 PRP19 contributes_to GO:0031202 SGD_REF:S000040831|PMID:10092627 IDA F RNA splicing factor YLL036C|PSO4 gene taxon:4932 20050308 SGD
+SGD S000003959 PRP19 GO:0031202 SGD_REF:S000048670|PMID:8441419 IMP F RNA splicing factor YLL036C|PSO4 gene taxon:4932 20050315 SGD
+SGD S000003959 PRP19 GO:0000398 SGD_REF:S000046470|PMID:11018040 IGI P RNA splicing factor YLL036C|PSO4 gene taxon:4932 20010118 SGD
+SGD S000003959 PRP19 GO:0000398 SGD_REF:S000048670|PMID:8441419 IMP P RNA splicing factor YLL036C|PSO4 gene taxon:4932 20050315 SGD
+SGD S000003959 PRP19 GO:0000398 SGD_REF:S000046470|PMID:11018040 IDA P RNA splicing factor YLL036C|PSO4 gene taxon:4932 20010118 SGD
+SGD S000003959 PRP19 GO:0006511 SGD_REF:S000080586|PMID:15660529 IPI SGD:S000001946 P RNA splicing factor YLL036C|PSO4 gene taxon:4932 20050316 SGD
+SGD S000005294 PRP2 GO:0005634 SGD_REF:S000058281|PMID:9476892 TAS C RNA splicing factor RNA-dependent NTPase with DEAD-box motif YNR011C|RNA2 gene taxon:4932 20010118 SGD
+SGD S000005294 PRP2 GO:0005681 SGD_REF:S000058281|PMID:9476892 TAS C RNA splicing factor RNA-dependent NTPase with DEAD-box motif YNR011C|RNA2 gene taxon:4932 20010118 SGD
+SGD S000005294 PRP2 GO:0004004 SGD_REF:S000058281|PMID:9476892 TAS F RNA splicing factor RNA-dependent NTPase with DEAD-box motif YNR011C|RNA2 gene taxon:4932 20010118 SGD
+SGD S000005294 PRP2 GO:0031202 SGD_REF:S000058281|PMID:9476892 TAS F RNA splicing factor RNA-dependent NTPase with DEAD-box motif YNR011C|RNA2 gene taxon:4932 20010118 SGD
+SGD S000005294 PRP2 GO:0000356 SGD_REF:S000073846 TAS P RNA splicing factor RNA-dependent NTPase with DEAD-box motif YNR011C|RNA2 gene taxon:4932 20030825 SGD
+SGD S000005294 PRP2 GO:0000356 SGD_REF:S000058281|PMID:9476892 TAS P RNA splicing factor RNA-dependent NTPase with DEAD-box motif YNR011C|RNA2 gene taxon:4932 20030825 SGD
+SGD S000003739 PRP21 GO:0005686 SGD_REF:S000069986|PMID:11804584 IDA C RNA splicing factor YJL203W|SPP91 gene taxon:4932 20020621 SGD
+SGD S000003739 PRP21 colocalizes_with GO:0005686 SGD_REF:S000080993|PMID:15565172 IDA C RNA splicing factor YJL203W|SPP91 gene taxon:4932 20051006 SGD
+SGD S000003739 PRP21 GO:0003723 SGD_REF:S000039421|PMID:8065365 IDA F RNA splicing factor YJL203W|SPP91 gene taxon:4932 20021114 SGD
+SGD S000003739 PRP21 GO:0000398 SGD_REF:S000042680|PMID:8969185 IDA P RNA splicing factor YJL203W|SPP91 gene taxon:4932 20021114 SGD
+SGD S000000815 PRP22 GO:0005681 SGD_REF:S000058281|PMID:9476892 TAS C helicase-like protein YER013W gene taxon:4932 20010118 SGD
+SGD S000000815 PRP22 contributes_to GO:0000386 SGD_REF:S000071184|PMID:12212850 IDA F helicase-like protein YER013W gene taxon:4932 20050921 SGD
+SGD S000000815 PRP22 GO:0004004 SGD_REF:S000058281|PMID:9476892 TAS F helicase-like protein YER013W gene taxon:4932 20010118 SGD
+SGD S000000815 PRP22 GO:0031202 SGD_REF:S000058281|PMID:9476892 TAS F helicase-like protein YER013W gene taxon:4932 20010118 SGD
+SGD S000000815 PRP22 GO:0031202 SGD_REF:S000071184|PMID:12212850 IDA F helicase-like protein YER013W gene taxon:4932 20050921 SGD
+SGD S000000815 PRP22 GO:0000350 SGD_REF:S000071184|PMID:12212850 IDA P helicase-like protein YER013W gene taxon:4932 20050921 SGD
+SGD S000000815 PRP22 GO:0000358 SGD_REF:S000071184|PMID:12212850 IDA P helicase-like protein YER013W gene taxon:4932 20050916 SGD
+SGD S000000815 PRP22 GO:0000391 SGD_REF:S000058281|PMID:9476892 TAS P helicase-like protein YER013W gene taxon:4932 20030825 SGD
+SGD S000000815 PRP22 GO:0000391 SGD_REF:S000073846 TAS P helicase-like protein YER013W gene taxon:4932 20030825 SGD
+SGD S000004881 PRP24 GO:0005688 SGD_REF:S000066234|PMID:11720284 IDA C U4/U6 snRNP-associated protein YMR268C gene taxon:4932 20051003 SGD
+SGD S000004881 PRP24 GO:0031202 SGD_REF:S000058281|PMID:9476892 TAS F U4/U6 snRNP-associated protein YMR268C gene taxon:4932 20010118 SGD
+SGD S000004881 PRP24 GO:0000244 SGD_REF:S000044160|PMID:9452384 IDA P U4/U6 snRNP-associated protein YMR268C gene taxon:4932 20010118 SGD
+SGD S000004881 PRP24 GO:0000245 SGD_REF:S000053641|PMID:10022888 IMP P U4/U6 snRNP-associated protein YMR268C gene taxon:4932 20010118 SGD
+SGD S000002651 PRP28 GO:0005681 SGD_REF:S000058281|PMID:9476892 TAS C RNA helicase YDR243C gene taxon:4932 20010118 SGD
+SGD S000002651 PRP28 GO:0005682 SGD_REF:S000066234|PMID:11720284 IPI C RNA helicase YDR243C gene taxon:4932 20051003 SGD
+SGD S000002651 PRP28 GO:0004004 SGD_REF:S000058281|PMID:9476892 TAS F RNA helicase YDR243C gene taxon:4932 20010118 SGD
+SGD S000002651 PRP28 GO:0031202 SGD_REF:S000058281|PMID:9476892 TAS F RNA helicase YDR243C gene taxon:4932 20010118 SGD
+SGD S000002651 PRP28 GO:0000360 SGD_REF:S000073846 TAS P RNA helicase YDR243C gene taxon:4932 20030825 SGD
+SGD S000002651 PRP28 GO:0000360 SGD_REF:S000058281|PMID:9476892 TAS P RNA helicase YDR243C gene taxon:4932 20030825 SGD
+SGD S000002881 PRP3 GO:0046540 SGD_REF:S000056376|PMID:10377396 IPI C snRNP from U4/U6 and U5 snRNPs YDR473C|RNA3 gene taxon:4932 20050219 SGD
+SGD S000002881 PRP3 GO:0046540 SGD_REF:S000039461|PMID:10449419 IDA C snRNP from U4/U6 and U5 snRNPs YDR473C|RNA3 gene taxon:4932 20050926 SGD
+SGD S000002881 PRP3 contributes_to GO:0031202 SGD_REF:S000056376|PMID:10377396 IPI F snRNP from U4/U6 and U5 snRNPs YDR473C|RNA3 gene taxon:4932 20020620 SGD
+SGD S000002881 PRP3 contributes_to GO:0031202 SGD_REF:S000039461|PMID:10449419 IDA F snRNP from U4/U6 and U5 snRNPs YDR473C|RNA3 gene taxon:4932 20051003 SGD
+SGD S000002881 PRP3 GO:0000398 SGD_REF:S000056376|PMID:10377396 IPI P snRNP from U4/U6 and U5 snRNPs YDR473C|RNA3 gene taxon:4932 20020620 SGD
+SGD S000003323 PRP31 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C pre-mRNA splicing protein YGR091W gene taxon:4932 20040928 SGD
+SGD S000003323 PRP31 GO:0046540 SGD_REF:S000056376|PMID:10377396 IPI C pre-mRNA splicing protein YGR091W gene taxon:4932 20050219 SGD
+SGD S000003323 PRP31 GO:0046540 SGD_REF:S000039461|PMID:10449419 IDA C pre-mRNA splicing protein YGR091W gene taxon:4932 20050926 SGD
+SGD S000003323 PRP31 contributes_to GO:0031202 SGD_REF:S000056376|PMID:10377396 IPI F pre-mRNA splicing protein YGR091W gene taxon:4932 20020620 SGD
+SGD S000003323 PRP31 contributes_to GO:0031202 SGD_REF:S000039461|PMID:10449419 IDA F pre-mRNA splicing protein YGR091W gene taxon:4932 20051003 SGD
+SGD S000003323 PRP31 GO:0000398 SGD_REF:S000056376|PMID:10377396 IPI P pre-mRNA splicing protein YGR091W gene taxon:4932 20020620 SGD
+SGD S000003307 PRP38 GO:0046540 SGD_REF:S000064701|PMID:9582287 IMP C RNA splicing factor YGR075C gene taxon:4932 20040331 SGD
+SGD S000003307 PRP38 GO:0046540 SGD_REF:S000056376|PMID:10377396 IPI C RNA splicing factor YGR075C gene taxon:4932 20050219 SGD
+SGD S000003307 PRP38 GO:0046540 SGD_REF:S000039461|PMID:10449419 IDA C RNA splicing factor YGR075C gene taxon:4932 20050926 SGD
+SGD S000003307 PRP38 contributes_to GO:0031202 SGD_REF:S000056376|PMID:10377396 IPI F RNA splicing factor YGR075C gene taxon:4932 20020620 SGD
+SGD S000003307 PRP38 contributes_to GO:0031202 SGD_REF:S000039461|PMID:10449419 IDA F RNA splicing factor YGR075C gene taxon:4932 20051003 SGD
+SGD S000003307 PRP38 GO:0000398 SGD_REF:S000056376|PMID:10377396 IPI P RNA splicing factor YGR075C gene taxon:4932 20020620 SGD
+SGD S000004509 PRP39 GO:0000243 SGD_REF:S000040958|PMID:8196608 IGI SGD:S000006478 C RNA splicing factor, U1 snRNP protein YML046W gene taxon:4932 20051102 SGD
+SGD S000004509 PRP39 GO:0005685 SGD_REF:S000069986|PMID:11804584 IDA C RNA splicing factor, U1 snRNP protein YML046W gene taxon:4932 20020621 SGD
+SGD S000004509 PRP39 GO:0005685 SGD_REF:S000040958|PMID:8196608 IDA C RNA splicing factor, U1 snRNP protein YML046W gene taxon:4932 20051102 SGD
+SGD S000004509 PRP39 GO:0005685 SGD_REF:S000044485|PMID:9630245 IDA C RNA splicing factor, U1 snRNP protein YML046W gene taxon:4932 20050929 SGD
+SGD S000004509 PRP39 contributes_to GO:0030627 SGD_REF:S000040958|PMID:8196608 IGI SGD:S000006478 F RNA splicing factor, U1 snRNP protein YML046W gene taxon:4932 20051102 SGD
+SGD S000004509 PRP39 contributes_to GO:0031202 SGD_REF:S000040958|PMID:8196608 IMP F RNA splicing factor, U1 snRNP protein YML046W gene taxon:4932 20051102 SGD
+SGD S000004509 PRP39 GO:0000395 SGD_REF:S000040958|PMID:8196608 IGI SGD:S000006478 P RNA splicing factor, U1 snRNP protein YML046W gene taxon:4932 20051102 SGD
+SGD S000006382 PRP4 GO:0046540 SGD_REF:S000056376|PMID:10377396 IPI C associates with the U4/U6 snRNP YPR178W|RNA4 gene taxon:4932 20050219 SGD
+SGD S000006382 PRP4 GO:0046540 SGD_REF:S000039461|PMID:10449419 IDA C associates with the U4/U6 snRNP YPR178W|RNA4 gene taxon:4932 20050926 SGD
+SGD S000006382 PRP4 contributes_to GO:0031202 SGD_REF:S000056376|PMID:10377396 IPI F associates with the U4/U6 snRNP YPR178W|RNA4 gene taxon:4932 20020620 SGD
+SGD S000006382 PRP4 contributes_to GO:0031202 SGD_REF:S000039461|PMID:10449419 IDA F associates with the U4/U6 snRNP YPR178W|RNA4 gene taxon:4932 20051003 SGD
+SGD S000006382 PRP4 GO:0000398 SGD_REF:S000056376|PMID:10377396 IPI P associates with the U4/U6 snRNP YPR178W|RNA4 gene taxon:4932 20020620 SGD
+SGD S000001495 PRP40 GO:0005685 SGD_REF:S000069986|PMID:11804584 IDA C U1 snRNP protein YKL012W gene taxon:4932 20020621 SGD
+SGD S000001495 PRP40 GO:0005685 SGD_REF:S000044485|PMID:9630245 IDA C U1 snRNP protein YKL012W gene taxon:4932 20050929 SGD
+SGD S000001495 PRP40 GO:0003723 SGD_REF:S000056013|PMID:8622699 IDA F U1 snRNP protein YKL012W gene taxon:4932 20021114 SGD
+SGD S000001495 PRP40 GO:0000398 SGD_REF:S000056013|PMID:8622699 IDA P U1 snRNP protein YKL012W gene taxon:4932 20021114 SGD
+SGD S000002643 PRP42 GO:0005685 SGD_REF:S000069986|PMID:11804584 IDA C U1 snRNP protein, shares 50% sequence similarity with Prp39p U1 snRNP protein and has multiple copies of the crn-like TPR motif YDR235W|MUD16|SNU65 gene taxon:4932 20020621 SGD
+SGD S000002643 PRP42 GO:0005685 SGD_REF:S000044485|PMID:9630245 IDA C U1 snRNP protein, shares 50% sequence similarity with Prp39p U1 snRNP protein and has multiple copies of the crn-like TPR motif YDR235W|MUD16|SNU65 gene taxon:4932 20050929 SGD
+SGD S000002643 PRP42 GO:0003723 SGD_REF:S000043832|PMID:9418882 IDA F U1 snRNP protein, shares 50% sequence similarity with Prp39p U1 snRNP protein and has multiple copies of the crn-like TPR motif YDR235W|MUD16|SNU65 gene taxon:4932 20021104 SGD
+SGD S000002643 PRP42 GO:0000398 SGD_REF:S000043832|PMID:9418882 IMP P U1 snRNP protein, shares 50% sequence similarity with Prp39p U1 snRNP protein and has multiple copies of the crn-like TPR motif YDR235W|MUD16|SNU65 gene taxon:4932 20021104 SGD
+SGD S000003088 PRP43 GO:0005681 SGD_REF:S000058281|PMID:9476892 TAS C RNA helicase YGL120C|JA1 gene taxon:4932 20010118 SGD
+SGD S000003088 PRP43 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C RNA helicase YGL120C|JA1 gene taxon:4932 20040928 SGD
+SGD S000003088 PRP43 GO:0004004 SGD_REF:S000058281|PMID:9476892 TAS F RNA helicase YGL120C|JA1 gene taxon:4932 20010118 SGD
+SGD S000003088 PRP43 GO:0031202 SGD_REF:S000058281|PMID:9476892 TAS F RNA helicase YGL120C|JA1 gene taxon:4932 20010118 SGD
+SGD S000003088 PRP43 GO:0000391 SGD_REF:S000058281|PMID:9476892 TAS P RNA helicase YGL120C|JA1 gene taxon:4932 20030825 SGD
+SGD S000003088 PRP43 GO:0000391 SGD_REF:S000073846 TAS P RNA helicase YGL120C|JA1 gene taxon:4932 20030825 SGD
+SGD S000003088 PRP43 GO:0000391 SGD_REF:S000113869|PMID:16357217 IDA P RNA helicase YGL120C|JA1 gene taxon:4932 20051222 SGD
+SGD S000000030 PRP45 GO:0005634 SGD_REF:S000071580|PMID:12359070 IDA C pre-mRNA splicing factor YAL032C|FUN20 gene taxon:4932 20021114 SGD
+SGD S000000030 PRP45 GO:0016563 SGD_REF:S000071580|PMID:12359070 IDA F pre-mRNA splicing factor YAL032C|FUN20 gene taxon:4932 20021114 SGD
+SGD S000000030 PRP45 GO:0045944 SGD_REF:S000071580|PMID:12359070 IDA P pre-mRNA splicing factor YAL032C|FUN20 gene taxon:4932 20021125 SGD
+SGD S000006072 PRP46 GO:0005681 SGD_REF:S000070110|PMID:12088152 IDA C pre-mRNA splicing factor YPL151C|NTC50 gene taxon:4932 20020905 SGD
+SGD S000006072 PRP46 GO:0005554 SGD_REF:S000069584 ND F pre-mRNA splicing factor YPL151C|NTC50 gene taxon:4932 20020905 SGD
+SGD S000006072 PRP46 GO:0000398 SGD_REF:S000070110|PMID:12088152 IPI P pre-mRNA splicing factor YPL151C|NTC50 gene taxon:4932 20020905 SGD
+SGD S000000441 PRP5 GO:0005681 SGD_REF:S000058281|PMID:9476892 TAS C RNA helicase YBR237W|RNA5 gene taxon:4932 20010118 SGD
+SGD S000000441 PRP5 GO:0004004 SGD_REF:S000058281|PMID:9476892 TAS F RNA helicase YBR237W|RNA5 gene taxon:4932 20010118 SGD
+SGD S000000441 PRP5 GO:0031202 SGD_REF:S000058281|PMID:9476892 TAS F RNA helicase YBR237W|RNA5 gene taxon:4932 20010118 SGD
+SGD S000000441 PRP5 GO:0000370 SGD_REF:S000058281|PMID:9476892 TAS P RNA helicase YBR237W|RNA5 gene taxon:4932 20030825 SGD
+SGD S000000441 PRP5 GO:0000370 SGD_REF:S000073846 TAS P RNA helicase YBR237W|RNA5 gene taxon:4932 20030825 SGD
+SGD S000000259 PRP6 GO:0046540 SGD_REF:S000056376|PMID:10377396 IPI C RNA splicing factor YBR055C|RNA6|TSM7269 gene taxon:4932 20050219 SGD
+SGD S000000259 PRP6 GO:0046540 SGD_REF:S000039461|PMID:10449419 IDA C RNA splicing factor YBR055C|RNA6|TSM7269 gene taxon:4932 20050926 SGD
+SGD S000000259 PRP6 contributes_to GO:0031202 SGD_REF:S000056376|PMID:10377396 IPI F RNA splicing factor YBR055C|RNA6|TSM7269 gene taxon:4932 20020620 SGD
+SGD S000000259 PRP6 contributes_to GO:0031202 SGD_REF:S000039461|PMID:10449419 IDA F RNA splicing factor YBR055C|RNA6|TSM7269 gene taxon:4932 20051003 SGD
+SGD S000000259 PRP6 GO:0000398 SGD_REF:S000056376|PMID:10377396 IPI P RNA splicing factor YBR055C|RNA6|TSM7269 gene taxon:4932 20020620 SGD
+SGD S000001208 PRP8 GO:0005682 SGD_REF:S000066236|PMID:11720285 IDA C U5 snRNP and spliceosome component YHR165C|DBF3|DNA39|RNA8|SLT21|USA2 gene taxon:4932 20030408 SGD
+SGD S000001208 PRP8 GO:0005682 SGD_REF:S000066236|PMID:11720285 IPI C U5 snRNP and spliceosome component YHR165C|DBF3|DNA39|RNA8|SLT21|USA2 gene taxon:4932 20030408 SGD
+SGD S000001208 PRP8 GO:0005682 SGD_REF:S000066234|PMID:11720284 IPI C U5 snRNP and spliceosome component YHR165C|DBF3|DNA39|RNA8|SLT21|USA2 gene taxon:4932 20051003 SGD
+SGD S000001208 PRP8 GO:0046540 SGD_REF:S000056376|PMID:10377396 IPI C U5 snRNP and spliceosome component YHR165C|DBF3|DNA39|RNA8|SLT21|USA2 gene taxon:4932 20050219 SGD
+SGD S000001208 PRP8 GO:0046540 SGD_REF:S000039461|PMID:10449419 IDA C U5 snRNP and spliceosome component YHR165C|DBF3|DNA39|RNA8|SLT21|USA2 gene taxon:4932 20050926 SGD
+SGD S000001208 PRP8 GO:0030623 SGD_REF:S000039943|PMID:9848662 IDA F U5 snRNP and spliceosome component YHR165C|DBF3|DNA39|RNA8|SLT21|USA2 gene taxon:4932 20051006 SGD
+SGD S000001208 PRP8 contributes_to GO:0031202 SGD_REF:S000056376|PMID:10377396 IPI F U5 snRNP and spliceosome component YHR165C|DBF3|DNA39|RNA8|SLT21|USA2 gene taxon:4932 20020620 SGD
+SGD S000001208 PRP8 contributes_to GO:0031202 SGD_REF:S000039461|PMID:10449419 IDA F U5 snRNP and spliceosome component YHR165C|DBF3|DNA39|RNA8|SLT21|USA2 gene taxon:4932 20051003 SGD
+SGD S000001208 PRP8 GO:0000398 SGD_REF:S000056376|PMID:10377396 IPI P U5 snRNP and spliceosome component YHR165C|DBF3|DNA39|RNA8|SLT21|USA2 gene taxon:4932 20020620 SGD
+SGD S000002188 PRP9 GO:0005686 SGD_REF:S000069986|PMID:11804584 IDA C RNA splicing factor YDL030W gene taxon:4932 20020621 SGD
+SGD S000002188 PRP9 colocalizes_with GO:0005686 SGD_REF:S000080993|PMID:15565172 IDA C RNA splicing factor YDL030W gene taxon:4932 20051006 SGD
+SGD S000002188 PRP9 GO:0003723 SGD_REF:S000039421|PMID:8065365 IDA F RNA splicing factor YDL030W gene taxon:4932 20021114 SGD
+SGD S000002188 PRP9 GO:0000398 SGD_REF:S000042680|PMID:8969185 IDA P RNA splicing factor YDL030W gene taxon:4932 20021114 SGD
+SGD S000001599 PRR1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C protein kinase YKL116C gene taxon:4932 20031028 SGD
+SGD S000001599 PRR1 GO:0004702 SGD_REF:S000061243|PMID:11337509 IMP F protein kinase YKL116C gene taxon:4932 20010822 SGD
+SGD S000001599 PRR1 GO:0004702 SGD_REF:S000061243|PMID:11337509 ISS F protein kinase YKL116C gene taxon:4932 20010822 SGD
+SGD S000001599 PRR1 GO:0000165 SGD_REF:S000061243|PMID:11337509 IMP P protein kinase YKL116C gene taxon:4932 20010822 SGD
+SGD S000002373 PRR2 GO:0005634 SGD_REF:S000061243|PMID:11337509 ISS C protein kinase YDL214C gene taxon:4932 20050201 SGD
+SGD S000002373 PRR2 GO:0004702 SGD_REF:S000061243|PMID:11337509 IMP F protein kinase YDL214C gene taxon:4932 20010822 SGD
+SGD S000002373 PRR2 GO:0004702 SGD_REF:S000061243|PMID:11337509 ISS F protein kinase YDL214C gene taxon:4932 20010822 SGD
+SGD S000002373 PRR2 GO:0000165 SGD_REF:S000061243|PMID:11337509 IMP P protein kinase YDL214C gene taxon:4932 20010822 SGD
+SGD S000001664 PRS1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C ribose-phosphate pyrophosphokinase YKL181W|PRP1 gene taxon:4932 20031028 SGD
+SGD S000001664 PRS1 GO:0004749 SGD_REF:S000040328|PMID:10212224 TAS F ribose-phosphate pyrophosphokinase YKL181W|PRP1 gene taxon:4932 20010118 SGD
+SGD S000001664 PRS1 GO:0000105 SGD_REF:S000040328|PMID:10212224 TAS P ribose-phosphate pyrophosphokinase YKL181W|PRP1 gene taxon:4932 20010118 SGD
+SGD S000001664 PRS1 GO:0000162 SGD_REF:S000040328|PMID:10212224 TAS P ribose-phosphate pyrophosphokinase YKL181W|PRP1 gene taxon:4932 20010118 SGD
+SGD S000001664 PRS1 GO:0006166 SGD_REF:S000040328|PMID:10212224 TAS P ribose-phosphate pyrophosphokinase YKL181W|PRP1 gene taxon:4932 20010118 SGD
+SGD S000001664 PRS1 GO:0006189 SGD_REF:S000040328|PMID:10212224 TAS P ribose-phosphate pyrophosphokinase YKL181W|PRP1 gene taxon:4932 20010118 SGD
+SGD S000001664 PRS1 GO:0006207 SGD_REF:S000040328|PMID:10212224 TAS P ribose-phosphate pyrophosphokinase YKL181W|PRP1 gene taxon:4932 20010118 SGD
+SGD S000000901 PRS2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C ribose-phosphate pyrophosphokinase YER099C gene taxon:4932 20031028 SGD
+SGD S000000901 PRS2 GO:0004749 SGD_REF:S000040328|PMID:10212224 TAS F ribose-phosphate pyrophosphokinase YER099C gene taxon:4932 20010118 SGD
+SGD S000000901 PRS2 GO:0000105 SGD_REF:S000040328|PMID:10212224 TAS P ribose-phosphate pyrophosphokinase YER099C gene taxon:4932 20010118 SGD
+SGD S000000901 PRS2 GO:0000162 SGD_REF:S000040328|PMID:10212224 TAS P ribose-phosphate pyrophosphokinase YER099C gene taxon:4932 20010118 SGD
+SGD S000000901 PRS2 GO:0006166 SGD_REF:S000040328|PMID:10212224 TAS P ribose-phosphate pyrophosphokinase YER099C gene taxon:4932 20010118 SGD
+SGD S000000901 PRS2 GO:0006189 SGD_REF:S000040328|PMID:10212224 TAS P ribose-phosphate pyrophosphokinase YER099C gene taxon:4932 20010118 SGD
+SGD S000000901 PRS2 GO:0006207 SGD_REF:S000040328|PMID:10212224 TAS P ribose-phosphate pyrophosphokinase YER099C gene taxon:4932 20010118 SGD
+SGD S000001003 PRS3 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C ribose-phosphate pyrophosphokinase YHL011C gene taxon:4932 20031028 SGD
+SGD S000001003 PRS3 GO:0004749 SGD_REF:S000040328|PMID:10212224 TAS F ribose-phosphate pyrophosphokinase YHL011C gene taxon:4932 20010118 SGD
+SGD S000001003 PRS3 GO:0000105 SGD_REF:S000040328|PMID:10212224 TAS P ribose-phosphate pyrophosphokinase YHL011C gene taxon:4932 20010118 SGD
+SGD S000001003 PRS3 GO:0000162 SGD_REF:S000040328|PMID:10212224 TAS P ribose-phosphate pyrophosphokinase YHL011C gene taxon:4932 20010118 SGD
+SGD S000001003 PRS3 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P ribose-phosphate pyrophosphokinase YHL011C gene taxon:4932 20060227 SGD
+SGD S000001003 PRS3 GO:0006166 SGD_REF:S000040328|PMID:10212224 TAS P ribose-phosphate pyrophosphokinase YHL011C gene taxon:4932 20010118 SGD
+SGD S000001003 PRS3 GO:0006189 SGD_REF:S000040328|PMID:10212224 TAS P ribose-phosphate pyrophosphokinase YHL011C gene taxon:4932 20010118 SGD
+SGD S000001003 PRS3 GO:0006207 SGD_REF:S000040328|PMID:10212224 TAS P ribose-phosphate pyrophosphokinase YHL011C gene taxon:4932 20010118 SGD
+SGD S000001003 PRS3 GO:0008361 SGD_REF:S000070190|PMID:12089449 IDA P ribose-phosphate pyrophosphokinase YHL011C gene taxon:4932 20020730 SGD
+SGD S000000164 PRS4 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C ribose-phosphate pyrophosphokinase YBL068W gene taxon:4932 20031028 SGD
+SGD S000000164 PRS4 GO:0004749 SGD_REF:S000040328|PMID:10212224 TAS F ribose-phosphate pyrophosphokinase YBL068W gene taxon:4932 20010118 SGD
+SGD S000000164 PRS4 GO:0000105 SGD_REF:S000040328|PMID:10212224 TAS P ribose-phosphate pyrophosphokinase YBL068W gene taxon:4932 20010118 SGD
+SGD S000000164 PRS4 GO:0000162 SGD_REF:S000040328|PMID:10212224 TAS P ribose-phosphate pyrophosphokinase YBL068W gene taxon:4932 20010118 SGD
+SGD S000000164 PRS4 GO:0006166 SGD_REF:S000040328|PMID:10212224 TAS P ribose-phosphate pyrophosphokinase YBL068W gene taxon:4932 20010118 SGD
+SGD S000000164 PRS4 GO:0006189 SGD_REF:S000040328|PMID:10212224 TAS P ribose-phosphate pyrophosphokinase YBL068W gene taxon:4932 20010118 SGD
+SGD S000000164 PRS4 GO:0006207 SGD_REF:S000040328|PMID:10212224 TAS P ribose-phosphate pyrophosphokinase YBL068W gene taxon:4932 20010118 SGD
+SGD S000005422 PRS5 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C phosphoribosylpyrophosphate synthetase (ribose-phosphate pyrophosphokinase) YOL061W gene taxon:4932 20031028 SGD
+SGD S000005422 PRS5 GO:0004749 SGD_REF:S000040328|PMID:10212224 TAS F phosphoribosylpyrophosphate synthetase (ribose-phosphate pyrophosphokinase) YOL061W gene taxon:4932 20010118 SGD
+SGD S000005422 PRS5 GO:0000105 SGD_REF:S000040328|PMID:10212224 TAS P phosphoribosylpyrophosphate synthetase (ribose-phosphate pyrophosphokinase) YOL061W gene taxon:4932 20010118 SGD
+SGD S000005422 PRS5 GO:0000162 SGD_REF:S000040328|PMID:10212224 TAS P phosphoribosylpyrophosphate synthetase (ribose-phosphate pyrophosphokinase) YOL061W gene taxon:4932 20010118 SGD
+SGD S000005422 PRS5 GO:0006166 SGD_REF:S000040328|PMID:10212224 TAS P phosphoribosylpyrophosphate synthetase (ribose-phosphate pyrophosphokinase) YOL061W gene taxon:4932 20010118 SGD
+SGD S000005422 PRS5 GO:0006189 SGD_REF:S000040328|PMID:10212224 TAS P phosphoribosylpyrophosphate synthetase (ribose-phosphate pyrophosphokinase) YOL061W gene taxon:4932 20010118 SGD
+SGD S000005422 PRS5 GO:0006207 SGD_REF:S000040328|PMID:10212224 TAS P phosphoribosylpyrophosphate synthetase (ribose-phosphate pyrophosphokinase) YOL061W gene taxon:4932 20010118 SGD
+SGD S000005888 PRT1 GO:0005737 SGD_REF:S000051901|PMID:9722586 IPI C translation initiation factor eIF3 subunit YOR361C|CDC63|DNA26 gene taxon:4932 20010118 SGD
+SGD S000005888 PRT1 GO:0005852 SGD_REF:S000043795|PMID:9671501 IPI C translation initiation factor eIF3 subunit YOR361C|CDC63|DNA26 gene taxon:4932 20020116 SGD
+SGD S000005888 PRT1 GO:0005852 SGD_REF:S000043795|PMID:9671501 IDA C translation initiation factor eIF3 subunit YOR361C|CDC63|DNA26 gene taxon:4932 20020116 SGD
+SGD S000005888 PRT1 GO:0005852 SGD_REF:S000040522|PMID:9660829 IPI SGD:S000002837|SGD:S000004754 C translation initiation factor eIF3 subunit YOR361C|CDC63|DNA26 gene taxon:4932 20060118 SGD
+SGD S000005888 PRT1 GO:0005852 SGD_REF:S000040522|PMID:9660829 IDA C translation initiation factor eIF3 subunit YOR361C|CDC63|DNA26 gene taxon:4932 20060118 SGD
+SGD S000005888 PRT1 GO:0043614 SGD_REF:S000082127|PMID:11018020 IDA C translation initiation factor eIF3 subunit YOR361C|CDC63|DNA26 gene taxon:4932 20060427 SGD
+SGD S000005888 PRT1 GO:0003743 SGD_REF:S000044517|PMID:7876188 IPI F translation initiation factor eIF3 subunit YOR361C|CDC63|DNA26 gene taxon:4932 20010118 SGD
+SGD S000005888 PRT1 GO:0003743 SGD_REF:S000044517|PMID:7876188 ISS F translation initiation factor eIF3 subunit YOR361C|CDC63|DNA26 gene taxon:4932 20010118 SGD
+SGD S000005888 PRT1 GO:0003743 SGD_REF:S000044517|PMID:7876188 IDA F translation initiation factor eIF3 subunit YOR361C|CDC63|DNA26 gene taxon:4932 20010118 SGD
+SGD S000005888 PRT1 GO:0003743 SGD_REF:S000043795|PMID:9671501 IDA F translation initiation factor eIF3 subunit YOR361C|CDC63|DNA26 gene taxon:4932 20020116 SGD
+SGD S000005888 PRT1 GO:0006413 SGD_REF:S000042163|PMID:3029094 IMP P translation initiation factor eIF3 subunit YOR361C|CDC63|DNA26 gene taxon:4932 20010118 SGD
+SGD S000005888 PRT1 GO:0006413 SGD_REF:S000043795|PMID:9671501 IDA P translation initiation factor eIF3 subunit YOR361C|CDC63|DNA26 gene taxon:4932 20020116 SGD
+SGD S000000160 PRX1 GO:0005739 SGD_REF:S000061563|PMID:10681558 IDA C peroxiredoxin YBL064C|mTPx gene taxon:4932 20020411 SGD
+SGD S000000160 PRX1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C peroxiredoxin YBL064C|mTPx gene taxon:4932 20040929 SGD
+SGD S000000160 PRX1 GO:0005739 SGD_REF:S000061563|PMID:10681558 ISS C peroxiredoxin YBL064C|mTPx gene taxon:4932 20020411 SGD
+SGD S000000160 PRX1 GO:0008379 SGD_REF:S000061563|PMID:10681558 IMP F peroxiredoxin YBL064C|mTPx gene taxon:4932 20020411 SGD
+SGD S000000160 PRX1 GO:0008379 SGD_REF:S000061563|PMID:10681558 ISS F peroxiredoxin YBL064C|mTPx gene taxon:4932 20020411 SGD
+SGD S000000160 PRX1 GO:0008379 SGD_REF:S000061563|PMID:10681558 IDA F peroxiredoxin YBL064C|mTPx gene taxon:4932 20020411 SGD
+SGD S000000160 PRX1 GO:0030503 SGD_REF:S000061563|PMID:10681558 IMP P peroxiredoxin YBL064C|mTPx gene taxon:4932 20020411 SGD
+SGD S000000160 PRX1 GO:0030503 SGD_REF:S000061563|PMID:10681558 IDA P peroxiredoxin YBL064C|mTPx gene taxon:4932 20020411 SGD
+SGD S000003615 PRY1 GO:0000324 SGD_REF:S000074185|PMID:14562095 IDA C YJL079C gene taxon:4932 20031028 SGD
+SGD S000003615 PRY1 GO:0005576 SGD_REF:S000075303|PMID:11935221 IDA C YJL079C gene taxon:4932 20040114 SGD
+SGD S000003615 PRY1 GO:0005635 SGD_REF:S000069459|PMID:11914276 IDA C YJL079C gene taxon:4932 20020507 SGD
+SGD S000003615 PRY1 GO:0005783 SGD_REF:S000069459|PMID:11914276 IDA C YJL079C gene taxon:4932 20020507 SGD
+SGD S000003615 PRY1 GO:0005554 SGD_REF:S000069584 ND F YJL079C gene taxon:4932 20021126 SGD
+SGD S000003615 PRY1 GO:0000004 SGD_REF:S000069584 ND P YJL079C gene taxon:4932 20021126 SGD
+SGD S000001721 PRY2 GO:0000324 SGD_REF:S000074185|PMID:14562095 IDA C YKR013W|YFW12 gene taxon:4932 20031028 SGD
+SGD S000001721 PRY2 GO:0005576 SGD_REF:S000075303|PMID:11935221 IDA C YKR013W|YFW12 gene taxon:4932 20040114 SGD
+SGD S000001721 PRY2 GO:0005554 SGD_REF:S000069584 ND F YKR013W|YFW12 gene taxon:4932 20021010 SGD
+SGD S000001721 PRY2 GO:0000004 SGD_REF:S000069584 ND P YKR013W|YFW12 gene taxon:4932 20021010 SGD
+SGD S000003614 PRY3 GO:0009277 SGD_REF:S000040179|PMID:10383953 IDA C YJL078C gene taxon:4932 20020617 SGD
+SGD S000003614 PRY3 GO:0009277 SGD_REF:S000081097|PMID:15781460 IDA C YJL078C gene taxon:4932 20050601 SGD
+SGD S000003614 PRY3 GO:0005554 SGD_REF:S000069584 ND F YJL078C gene taxon:4932 20021126 SGD
+SGD S000003614 PRY3 GO:0000004 SGD_REF:S000069584 ND P YJL078C gene taxon:4932 20021126 SGD
+SGD S000002213 PSA1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C GDP-mannose pyrophosphorylase, mannose-1-phosphate guanyltransferase YDL055C|MPG1|SRB1|VIG9 gene taxon:4932 20020507 SGD
+SGD S000002213 PSA1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C GDP-mannose pyrophosphorylase, mannose-1-phosphate guanyltransferase YDL055C|MPG1|SRB1|VIG9 gene taxon:4932 20031028 SGD
+SGD S000002213 PSA1 GO:0004475 SGD_REF:S000049301|PMID:9195935 IDA F GDP-mannose pyrophosphorylase, mannose-1-phosphate guanyltransferase YDL055C|MPG1|SRB1|VIG9 gene taxon:4932 20020927 SGD
+SGD S000002213 PSA1 GO:0004475 SGD_REF:S000049301|PMID:9195935 IMP F GDP-mannose pyrophosphorylase, mannose-1-phosphate guanyltransferase YDL055C|MPG1|SRB1|VIG9 gene taxon:4932 20020927 SGD
+SGD S000002213 PSA1 GO:0000032 SGD_REF:S000059380|PMID:11055399 IMP P GDP-mannose pyrophosphorylase, mannose-1-phosphate guanyltransferase YDL055C|MPG1|SRB1|VIG9 gene taxon:4932 20020927 SGD
+SGD S000002213 PSA1 GO:0006486 SGD_REF:S000049301|PMID:9195935 IMP P GDP-mannose pyrophosphorylase, mannose-1-phosphate guanyltransferase YDL055C|MPG1|SRB1|VIG9 gene taxon:4932 20020927 SGD
+SGD S000002213 PSA1 GO:0009298 SGD_REF:S000049301|PMID:9195935 IDA P GDP-mannose pyrophosphorylase, mannose-1-phosphate guanyltransferase YDL055C|MPG1|SRB1|VIG9 gene taxon:4932 20020927 SGD
+SGD S000002213 PSA1 GO:0009298 SGD_REF:S000049301|PMID:9195935 IMP P GDP-mannose pyrophosphorylase, mannose-1-phosphate guanyltransferase YDL055C|MPG1|SRB1|VIG9 gene taxon:4932 20020927 SGD
+SGD S000005113 PSD1 GO:0005739 SGD_REF:S000068772|PMID:11602607 TAS C phosphatidylserine decarboxylase YNL169C gene taxon:4932 20020827 SGD
+SGD S000005113 PSD1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C phosphatidylserine decarboxylase YNL169C gene taxon:4932 20040928 SGD
+SGD S000005113 PSD1 GO:0005743 SGD_REF:S000072717|PMID:12589040 TAS C phosphatidylserine decarboxylase YNL169C gene taxon:4932 20030310 SGD
+SGD S000005113 PSD1 GO:0004609 SGD_REF:S000068772|PMID:11602607 TAS F phosphatidylserine decarboxylase YNL169C gene taxon:4932 20030122 SGD
+SGD S000005113 PSD1 GO:0006656 SGD_REF:S000064718|PMID:6427211 IDA P phosphatidylserine decarboxylase YNL169C gene taxon:4932 20020827 SGD
+SGD S000003402 PSD2 GO:0000139 SGD_REF:S000064720|PMID:9370338 TAS C phosphatidylserine decarboxylase YGR170W gene taxon:4932 20021004 SGD
+SGD S000003402 PSD2 GO:0000329 SGD_REF:S000064720|PMID:9370338 TAS C phosphatidylserine decarboxylase YGR170W gene taxon:4932 20021004 SGD
+SGD S000003402 PSD2 GO:0004609 SGD_REF:S000068772|PMID:11602607 TAS F phosphatidylserine decarboxylase YGR170W gene taxon:4932 20030122 SGD
+SGD S000003402 PSD2 GO:0006656 SGD_REF:S000064718|PMID:6427211 IDA P phosphatidylserine decarboxylase YGR170W gene taxon:4932 20020827 SGD
+SGD S000004925 PSE1 GO:0005634 SGD_REF:S000052126|PMID:9238021 IDA C karyopherin YMR308C|KAP121 gene taxon:4932 20020624 SGD
+SGD S000004925 PSE1 GO:0005737 SGD_REF:S000052126|PMID:9238021 IDA C karyopherin YMR308C|KAP121 gene taxon:4932 20020624 SGD
+SGD S000004925 PSE1 GO:0008320 SGD_REF:S000052126|PMID:9238021 TAS F karyopherin YMR308C|KAP121 gene taxon:4932 20020624 SGD
+SGD S000004925 PSE1 GO:0006406 SGD_REF:S000052126|PMID:9238021 TAS P karyopherin YMR308C|KAP121 gene taxon:4932 20020624 SGD
+SGD S000004925 PSE1 GO:0006606 SGD_REF:S000115804|PMID:16651379 IMP P karyopherin YMR308C|KAP121 gene taxon:4932 20060522 SGD
+SGD S000002420 PSF1 GO:0000811 SGD_REF:S000073092|PMID:12730134 IPI SGD:S000002897|SGD:S000005506|SGD:S000003608 C subunit of the GINS complex YDR013W|CDC101 gene taxon:4932 20030522 SGD
+SGD S000002420 PSF1 GO:0000811 SGD_REF:S000073501|PMID:12768207 IPI SGD:S000002897|SGD:S000003608|SGD:S000005506 C subunit of the GINS complex YDR013W|CDC101 gene taxon:4932 20051201 SGD
+SGD S000002420 PSF1 GO:0005554 SGD_REF:S000069584 ND F subunit of the GINS complex YDR013W|CDC101 gene taxon:4932 20051201 SGD
+SGD S000002420 PSF1 GO:0006261 SGD_REF:S000073092|PMID:12730134 IMP P subunit of the GINS complex YDR013W|CDC101 gene taxon:4932 20030508 SGD
+SGD S000002420 PSF1 GO:0006261 SGD_REF:S000073501|PMID:12768207 IMP P subunit of the GINS complex YDR013W|CDC101 gene taxon:4932 20051201 SGD
+SGD S000003608 PSF2 GO:0000811 SGD_REF:S000073092|PMID:12730134 IPI SGD:S000002420|SGD:S000002897|SGD:S000005506 C subunit of the GINS complex YJL072C|CDC102 gene taxon:4932 20030522 SGD
+SGD S000003608 PSF2 GO:0000811 SGD_REF:S000073501|PMID:12768207 IPI SGD:S000002420|SGD:S000005506|SGD:S000002897 C subunit of the GINS complex YJL072C|CDC102 gene taxon:4932 20051201 SGD
+SGD S000003608 PSF2 GO:0005634 SGD_REF:S000077144|PMID:15282802 IDA C subunit of the GINS complex YJL072C|CDC102 gene taxon:4932 20041008 SGD
+SGD S000003608 PSF2 GO:0005554 SGD_REF:S000069584 ND F subunit of the GINS complex YJL072C|CDC102 gene taxon:4932 20051201 SGD
+SGD S000003608 PSF2 GO:0006261 SGD_REF:S000073501|PMID:12768207 IMP P subunit of the GINS complex YJL072C|CDC102 gene taxon:4932 20051201 SGD
+SGD S000003608 PSF2 GO:0006261 SGD_REF:S000073092|PMID:12730134 IGI SGD:S000002897 P subunit of the GINS complex YJL072C|CDC102 gene taxon:4932 20051201 SGD
+SGD S000005506 PSF3 GO:0000811 SGD_REF:S000073092|PMID:12730134 IPI SGD:S000002420|SGD:S000002897|SGD:S000003608 C subunit of the GINS complex YOL146W gene taxon:4932 20030522 SGD
+SGD S000005506 PSF3 GO:0000811 SGD_REF:S000073501|PMID:12768207 IPI SGD:S000002420|SGD:S000002897|SGD:S000003608 C subunit of the GINS complex YOL146W gene taxon:4932 20051201 SGD
+SGD S000005506 PSF3 GO:0005554 SGD_REF:S000069584 ND F subunit of the GINS complex YOL146W gene taxon:4932 20051201 SGD
+SGD S000005506 PSF3 GO:0006261 SGD_REF:S000073092|PMID:12730134 IGI SGD:S000002420 P subunit of the GINS complex YOL146W gene taxon:4932 20051201 SGD
+SGD S000005415 PSH1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YOL054W gene taxon:4932 20031028 SGD
+SGD S000005415 PSH1 GO:0005554 SGD_REF:S000069584 ND F YOL054W gene taxon:4932 20021004 SGD
+SGD S000005415 PSH1 GO:0006368 SGD_REF:S000071357|PMID:12242279 IPI P YOL054W gene taxon:4932 20021004 SGD
+SGD S000000015 PSK1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YAL017W|FUN31 gene taxon:4932 20031028 SGD
+SGD S000000015 PSK1 GO:0004674 SGD_REF:S000056110|PMID:8322517 ISS F YAL017W|FUN31 gene taxon:4932 20010208 SGD
+SGD S000000015 PSK1 GO:0004674 SGD_REF:S000072754|PMID:12372297 ISS SGD:S000005405 F YAL017W|FUN31 gene taxon:4932 20030317 SGD
+SGD S000000015 PSK1 GO:0004674 SGD_REF:S000072754|PMID:12372297 IMP F YAL017W|FUN31 gene taxon:4932 20030317 SGD
+SGD S000000015 PSK1 GO:0006468 SGD_REF:S000072754|PMID:12372297 IMP P YAL017W|FUN31 gene taxon:4932 20030317 SGD
+SGD S000000015 PSK1 GO:0006468 SGD_REF:S000072754|PMID:12372297 ISS SGD:S000005405 P YAL017W|FUN31 gene taxon:4932 20030317 SGD
+SGD S000000015 PSK1 GO:0019318 SGD_REF:S000072754|PMID:12372297 IGI P YAL017W|FUN31 gene taxon:4932 20030317 SGD
+SGD S000000015 PSK1 GO:0019318 SGD_REF:S000072754|PMID:12372297 IMP P YAL017W|FUN31 gene taxon:4932 20030317 SGD
+SGD S000005405 PSK2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C PAS kinase YOL045W gene taxon:4932 20031028 SGD
+SGD S000005405 PSK2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C PAS kinase YOL045W gene taxon:4932 20040813 SGD
+SGD S000005405 PSK2 GO:0004674 SGD_REF:S000072754|PMID:12372297 IDA F PAS kinase YOL045W gene taxon:4932 20030317 SGD
+SGD S000005405 PSK2 GO:0004674 SGD_REF:S000072754|PMID:12372297 IMP F PAS kinase YOL045W gene taxon:4932 20030317 SGD
+SGD S000005405 PSK2 GO:0006468 SGD_REF:S000072754|PMID:12372297 IDA P PAS kinase YOL045W gene taxon:4932 20030317 SGD
+SGD S000005405 PSK2 GO:0006468 SGD_REF:S000072754|PMID:12372297 IMP P PAS kinase YOL045W gene taxon:4932 20030317 SGD
+SGD S000005405 PSK2 GO:0019318 SGD_REF:S000072754|PMID:12372297 IGI P PAS kinase YOL045W gene taxon:4932 20030317 SGD
+SGD S000005405 PSK2 GO:0019318 SGD_REF:S000072754|PMID:12372297 IMP P PAS kinase YOL045W gene taxon:4932 20030317 SGD
+SGD S000004745 PSO2 GO:0005634 SGD_REF:S000045114|PMID:1736091 IC GO:0006281 C interstrand crosslink repair protein YMR137C|SNM1 gene taxon:4932 20021112 SGD
+SGD S000004745 PSO2 GO:0003684 SGD_REF:S000042032|PMID:7035927 IMP F interstrand crosslink repair protein YMR137C|SNM1 gene taxon:4932 20021112 SGD
+SGD S000004745 PSO2 GO:0008409 SGD_REF:S000079985|PMID:15590324 IDA F interstrand crosslink repair protein YMR137C|SNM1 gene taxon:4932 20041228 SGD
+SGD S000004745 PSO2 GO:0008409 SGD_REF:S000079985|PMID:15590324 IMP F interstrand crosslink repair protein YMR137C|SNM1 gene taxon:4932 20041228 SGD
+SGD S000004745 PSO2 GO:0006281 SGD_REF:S000045114|PMID:1736091 IMP P interstrand crosslink repair protein YMR137C|SNM1 gene taxon:4932 20021112 SGD
+SGD S000004745 PSO2 GO:0006302 SGD_REF:S000071988|PMID:12509272 TAS P interstrand crosslink repair protein YMR137C|SNM1 gene taxon:4932 20030207 SGD
+SGD S000002913 PSP1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDR505C|GIN5 gene taxon:4932 20031028 SGD
+SGD S000002913 PSP1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YDR505C|GIN5 gene taxon:4932 20040813 SGD
+SGD S000002913 PSP1 GO:0005554 SGD_REF:S000069584 ND F YDR505C|GIN5 gene taxon:4932 20021001 SGD
+SGD S000002913 PSP1 GO:0000004 SGD_REF:S000069584 ND P YDR505C|GIN5 gene taxon:4932 20021001 SGD
+SGD S000004479 PSP2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YML017W|MRS15 gene taxon:4932 20031028 SGD
+SGD S000004479 PSP2 GO:0005554 SGD_REF:S000069584 ND F YML017W|MRS15 gene taxon:4932 20020927 SGD
+SGD S000004479 PSP2 GO:0000004 SGD_REF:S000069584 ND P YML017W|MRS15 gene taxon:4932 20020927 SGD
+SGD S000003933 PSR1 GO:0005886 SGD_REF:S000045346|PMID:10777497 IDA C YLL010C gene taxon:4932 20010118 SGD
+SGD S000003933 PSR1 GO:0004721 SGD_REF:S000045346|PMID:10777497 IDA F YLL010C gene taxon:4932 20010118 SGD
+SGD S000003933 PSR1 GO:0004721 SGD_REF:S000045346|PMID:10777497 ISS F YLL010C gene taxon:4932 20010118 SGD
+SGD S000003933 PSR1 GO:0006950 SGD_REF:S000045346|PMID:10777497 IGI P YLL010C gene taxon:4932 20010118 SGD
+SGD S000004009 PSR2 GO:0005886 SGD_REF:S000045346|PMID:10777497 ISS SGD:S000003933 C YLR019W gene taxon:4932 20040917 SGD
+SGD S000004009 PSR2 GO:0004721 SGD_REF:S000045346|PMID:10777497 ISS F YLR019W gene taxon:4932 20010118 SGD
+SGD S000004009 PSR2 GO:0006950 SGD_REF:S000045346|PMID:10777497 IGI P YLR019W gene taxon:4932 20010118 SGD
+SGD S000002462 PST1 GO:0009277 SGD_REF:S000040179|PMID:10383953 IDA C the gene product has been detected among the proteins secreted by regenerating protoplasts YDR055W gene taxon:4932 20020617 SGD
+SGD S000002462 PST1 GO:0005554 SGD_REF:S000069584 ND F the gene product has been detected among the proteins secreted by regenerating protoplasts YDR055W gene taxon:4932 20021216 SGD
+SGD S000002462 PST1 GO:0007047 SGD_REF:S000061885|PMID:10234784 IGI P the gene product has been detected among the proteins secreted by regenerating protoplasts YDR055W gene taxon:4932 20041109 SGD
+SGD S000002439 PST2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDR032C gene taxon:4932 20031028 SGD
+SGD S000002439 PST2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YDR032C gene taxon:4932 20040813 SGD
+SGD S000002439 PST2 GO:0005554 SGD_REF:S000069584 ND F YDR032C gene taxon:4932 20021001 SGD
+SGD S000002439 PST2 GO:0000004 SGD_REF:S000069584 ND P YDR032C gene taxon:4932 20021001 SGD
+SGD S000005145 PSY2 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YNL201C gene taxon:4932 20031028 SGD
+SGD S000005145 PSY2 GO:0005554 SGD_REF:S000069584 ND F YNL201C gene taxon:4932 20021011 SGD
+SGD S000005145 PSY2 GO:0000004 SGD_REF:S000069584 ND P YNL201C gene taxon:4932 20021011 SGD
+SGD S000004368 PSY3 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YLR376C gene taxon:4932 20031028 SGD
+SGD S000004368 PSY3 GO:0005634 SGD_REF:S000080406|PMID:15654096 IDA C YLR376C gene taxon:4932 20050324 SGD
+SGD S000004368 PSY3 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YLR376C gene taxon:4932 20031028 SGD
+SGD S000004368 PSY3 GO:0005554 SGD_REF:S000069584 ND F YLR376C gene taxon:4932 20021011 SGD
+SGD S000004368 PSY3 GO:0045021 SGD_REF:S000080406|PMID:15654096 IMP P YLR376C gene taxon:4932 20050324 SGD
+SGD S000000142 PSY4 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C Regulatory subunit of Pph3p YBL046W gene taxon:4932 20031028 SGD
+SGD S000000142 PSY4 GO:0005554 SGD_REF:S000069584 ND F Regulatory subunit of Pph3p YBL046W gene taxon:4932 20021223 SGD
+SGD S000000142 PSY4 GO:0000004 SGD_REF:S000069584 ND P Regulatory subunit of Pph3p YBL046W gene taxon:4932 20021223 SGD
+SGD S000000041 PTA1 GO:0005847 SGD_REF:S000046866|PMID:10523662 IPI C cleavage factor II (CF II) component, polyadenylation factor I (PF I) YAL043C|FUN39 gene taxon:4932 20040928 SGD
+SGD S000000041 PTA1 GO:0005849 SGD_REF:S000049364|PMID:9099738 IPI C cleavage factor II (CF II) component, polyadenylation factor I (PF I) YAL043C|FUN39 gene taxon:4932 20020410 SGD
+SGD S000000041 PTA1 contributes_to GO:0003723 SGD_REF:S000046866|PMID:10523662 IC GO:0005847 F cleavage factor II (CF II) component, polyadenylation factor I (PF I) YAL043C|FUN39 gene taxon:4932 20050218 SGD
+SGD S000000041 PTA1 GO:0006378 SGD_REF:S000046866|PMID:10523662 IMP P cleavage factor II (CF II) component, polyadenylation factor I (PF I) YAL043C|FUN39 gene taxon:4932 20040928 SGD
+SGD S000000041 PTA1 GO:0006378 SGD_REF:S000040911|PMID:9303317 IMP P cleavage factor II (CF II) component, polyadenylation factor I (PF I) YAL043C|FUN39 gene taxon:4932 20040928 SGD
+SGD S000000041 PTA1 GO:0006379 SGD_REF:S000046866|PMID:10523662 IMP P cleavage factor II (CF II) component, polyadenylation factor I (PF I) YAL043C|FUN39 gene taxon:4932 20040928 SGD
+SGD S000000041 PTA1 GO:0008033 SGD_REF:S000045390|PMID:1508188 IMP P cleavage factor II (CF II) component, polyadenylation factor I (PF I) YAL043C|FUN39 gene taxon:4932 20021125 SGD
+SGD S000000041 PTA1 GO:0030846 SGD_REF:S000074089|PMID:12819204 IPI P cleavage factor II (CF II) component, polyadenylation factor I (PF I) YAL043C|FUN39 gene taxon:4932 20031013 SGD
+SGD S000000041 PTA1 GO:0030847 SGD_REF:S000074089|PMID:12819204 IPI P cleavage factor II (CF II) component, polyadenylation factor I (PF I) YAL043C|FUN39 gene taxon:4932 20031013 SGD
+SGD S000002164 PTC1 GO:0005634 SGD_REF:S000059233|PMID:11113180 IDA C YDL006W|CWH47|KCS2|TPD1 gene taxon:4932 20021202 SGD
+SGD S000002164 PTC1 GO:0005737 SGD_REF:S000059233|PMID:11113180 IDA C YDL006W|CWH47|KCS2|TPD1 gene taxon:4932 20021202 SGD
+SGD S000002164 PTC1 GO:0015071 SGD_REF:S000040841|PMID:10580002 IDA F YDL006W|CWH47|KCS2|TPD1 gene taxon:4932 20010118 SGD
+SGD S000002164 PTC1 GO:0000001 SGD_REF:S000051463|PMID:9529388 IMP P YDL006W|CWH47|KCS2|TPD1 gene taxon:4932 20021202 SGD
+SGD S000002164 PTC1 GO:0000173 SGD_REF:S000059233|PMID:11113180 IGI P YDL006W|CWH47|KCS2|TPD1 gene taxon:4932 20041019 SGD
+SGD S000002164 PTC1 GO:0000173 SGD_REF:S000059233|PMID:11113180 IMP P YDL006W|CWH47|KCS2|TPD1 gene taxon:4932 20041019 SGD
+SGD S000002164 PTC1 GO:0000173 SGD_REF:S000059233|PMID:11113180 IDA P YDL006W|CWH47|KCS2|TPD1 gene taxon:4932 20041019 SGD
+SGD S000002164 PTC1 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P YDL006W|CWH47|KCS2|TPD1 gene taxon:4932 20060227 SGD
+SGD S000002164 PTC1 GO:0006388 SGD_REF:S000040961|PMID:8196609 IMP P YDL006W|CWH47|KCS2|TPD1 gene taxon:4932 20021202 SGD
+SGD S000002164 PTC1 GO:0006470 SGD_REF:S000040841|PMID:10580002 IDA P YDL006W|CWH47|KCS2|TPD1 gene taxon:4932 20021202 SGD
+SGD S000002164 PTC1 GO:0006470 SGD_REF:S000059233|PMID:11113180 IDA P YDL006W|CWH47|KCS2|TPD1 gene taxon:4932 20041019 SGD
+SGD S000000891 PTC2 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C protein phosphatase type 2C YER089C gene taxon:4932 20031028 SGD
+SGD S000000891 PTC2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C protein phosphatase type 2C YER089C gene taxon:4932 20031028 SGD
+SGD S000000891 PTC2 GO:0015071 SGD_REF:S000040841|PMID:10580002 IDA F protein phosphatase type 2C YER089C gene taxon:4932 20041001 SGD
+SGD S000000891 PTC2 GO:0000077 SGD_REF:S000050455|PMID:10747050 IGI P protein phosphatase type 2C YER089C gene taxon:4932 20020927 SGD
+SGD S000000891 PTC2 GO:0000079 SGD_REF:S000040841|PMID:10580002 IMP P protein phosphatase type 2C YER089C gene taxon:4932 20041001 SGD
+SGD S000000891 PTC2 GO:0000079 SGD_REF:S000040841|PMID:10580002 IPI P protein phosphatase type 2C YER089C gene taxon:4932 20041001 SGD
+SGD S000000891 PTC2 GO:0000082 SGD_REF:S000072514|PMID:12518319 IGI P protein phosphatase type 2C YER089C gene taxon:4932 20030217 SGD
+SGD S000000891 PTC2 GO:0000173 SGD_REF:S000059233|PMID:11113180 IGI P protein phosphatase type 2C YER089C gene taxon:4932 20020927 SGD
+SGD S000000891 PTC2 GO:0000173 SGD_REF:S000071972|PMID:12477803 IMP P protein phosphatase type 2C YER089C gene taxon:4932 20041019 SGD
+SGD S000000891 PTC2 GO:0000173 SGD_REF:S000071972|PMID:12477803 IGI P protein phosphatase type 2C YER089C gene taxon:4932 20041019 SGD
+SGD S000000891 PTC2 GO:0000173 SGD_REF:S000071972|PMID:12477803 IDA P protein phosphatase type 2C YER089C gene taxon:4932 20041019 SGD
+SGD S000000891 PTC2 GO:0006470 SGD_REF:S000040841|PMID:10580002 IDA P protein phosphatase type 2C YER089C gene taxon:4932 20041001 SGD
+SGD S000000891 PTC2 GO:0006470 SGD_REF:S000071972|PMID:12477803 IDA P protein phosphatase type 2C YER089C gene taxon:4932 20041019 SGD
+SGD S000000891 PTC2 GO:0006986 SGD_REF:S000052073|PMID:9528768 IMP P protein phosphatase type 2C YER089C gene taxon:4932 20020927 SGD
+SGD S000000891 PTC2 GO:0006986 SGD_REF:S000052073|PMID:9528768 IPI P protein phosphatase type 2C YER089C gene taxon:4932 20020927 SGD
+SGD S000000152 PTC3 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C protein phosphatase type 2C YBL056W gene taxon:4932 20031028 SGD
+SGD S000000152 PTC3 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C protein phosphatase type 2C YBL056W gene taxon:4932 20031028 SGD
+SGD S000000152 PTC3 GO:0015071 SGD_REF:S000040841|PMID:10580002 IDA F protein phosphatase type 2C YBL056W gene taxon:4932 20020927 SGD
+SGD S000000152 PTC3 GO:0000079 SGD_REF:S000040841|PMID:10580002 IMP P protein phosphatase type 2C YBL056W gene taxon:4932 20020927 SGD
+SGD S000000152 PTC3 GO:0000079 SGD_REF:S000040841|PMID:10580002 IPI P protein phosphatase type 2C YBL056W gene taxon:4932 20020927 SGD
+SGD S000000152 PTC3 GO:0000173 SGD_REF:S000059233|PMID:11113180 IGI P protein phosphatase type 2C YBL056W gene taxon:4932 20020927 SGD
+SGD S000000152 PTC3 GO:0000173 SGD_REF:S000071972|PMID:12477803 IGI P protein phosphatase type 2C YBL056W gene taxon:4932 20041019 SGD
+SGD S000000152 PTC3 GO:0006470 SGD_REF:S000040841|PMID:10580002 IDA P protein phosphatase type 2C YBL056W gene taxon:4932 20020927 SGD
+SGD S000000329 PTC4 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C type 2C protein phosphatase YBR125C|GCT1 gene taxon:4932 20031028 SGD
+SGD S000000329 PTC4 GO:0015071 SGD_REF:S000040841|PMID:10580002 IDA F type 2C protein phosphatase YBR125C|GCT1 gene taxon:4932 20010118 SGD
+SGD S000000329 PTC4 GO:0015071 SGD_REF:S000040841|PMID:10580002 ISS F type 2C protein phosphatase YBR125C|GCT1 gene taxon:4932 20010118 SGD
+SGD S000000329 PTC4 GO:0000004 SGD_REF:S000069584 ND P type 2C protein phosphatase YBR125C|GCT1 gene taxon:4932 20010119 SGD
+SGD S000005616 PTC5 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C type 2C Protein Phosphatase YOR090C gene taxon:4932 20040813 SGD
+SGD S000005616 PTC5 GO:0015071 SGD_REF:S000040841|PMID:10580002 IDA F type 2C Protein Phosphatase YOR090C gene taxon:4932 20010118 SGD
+SGD S000005616 PTC5 GO:0015071 SGD_REF:S000040841|PMID:10580002 ISS F type 2C Protein Phosphatase YOR090C gene taxon:4932 20010118 SGD
+SGD S000005616 PTC5 GO:0000004 SGD_REF:S000069584 ND P type 2C Protein Phosphatase YOR090C gene taxon:4932 20010119 SGD
+SGD S000001118 PTC7 GO:0005739 SGD_REF:S000060170|PMID:11327310 IDA C type 2C Protein Phosphatase YHR076W gene taxon:4932 20010626 SGD
+SGD S000001118 PTC7 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C type 2C Protein Phosphatase YHR076W gene taxon:4932 20040924 SGD
+SGD S000001118 PTC7 GO:0015071 SGD_REF:S000071678|PMID:12220683 IDA F type 2C Protein Phosphatase YHR076W gene taxon:4932 20030701 SGD
+SGD S000001118 PTC7 GO:0000004 SGD_REF:S000069584 ND P type 2C Protein Phosphatase YHR076W gene taxon:4932 20030701 SGD
+SGD S000001232 PTH1 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YHR189W|PTH gene taxon:4932 20031028 SGD
+SGD S000001232 PTH1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YHR189W|PTH gene taxon:4932 20040924 SGD
+SGD S000001232 PTH1 GO:0004045 SGD_REF:S000071900|PMID:12475929 ISS F YHR189W|PTH gene taxon:4932 20021229 SGD
+SGD S000001232 PTH1 GO:0004045 SGD_REF:S000073282|PMID:12799450 IDA F YHR189W|PTH gene taxon:4932 20030623 SGD
+SGD S000001232 PTH1 GO:0006412 SGD_REF:S000071900|PMID:12475929 IC GO:0004045 P YHR189W|PTH gene taxon:4932 20021229 SGD
+SGD S000001232 PTH1 GO:0006412 SGD_REF:S000048070|PMID:8563640 ISS P YHR189W|PTH gene taxon:4932 20020806 SGD
+SGD S000000153 PTH2 GO:0005737 SGD_REF:S000071900|PMID:12475929 IC GO:0004045 C YBL057C gene taxon:4932 20030108 SGD
+SGD S000000153 PTH2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YBL057C gene taxon:4932 20040813 SGD
+SGD S000000153 PTH2 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C YBL057C gene taxon:4932 20060317 SGD
+SGD S000000153 PTH2 GO:0004045 SGD_REF:S000071900|PMID:12475929 IGI F YBL057C gene taxon:4932 20030108 SGD
+SGD S000000153 PTH2 GO:0004045 SGD_REF:S000073282|PMID:12799450 IDA F YBL057C gene taxon:4932 20030623 SGD
+SGD S000000153 PTH2 GO:0004045 SGD_REF:S000071900|PMID:12475929 ISS F YBL057C gene taxon:4932 20021229 SGD
+SGD S000000153 PTH2 GO:0006412 SGD_REF:S000071900|PMID:12475929 IC GO:0004045 P YBL057C gene taxon:4932 20021229 SGD
+SGD S000003388 PTI1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YGR156W gene taxon:4932 20031028 SGD
+SGD S000003388 PTI1 GO:0005847 SGD_REF:S000074089|PMID:12819204 IPI C YGR156W gene taxon:4932 20031013 SGD
+SGD S000003388 PTI1 contributes_to GO:0003723 SGD_REF:S000074089|PMID:12819204 IC GO:0005847 F YGR156W gene taxon:4932 20050218 SGD
+SGD S000003388 PTI1 GO:0006378 SGD_REF:S000071951|PMID:12504017 IMP P YGR156W gene taxon:4932 20030106 SGD
+SGD S000003388 PTI1 GO:0006378 SGD_REF:S000071951|PMID:12504017 IPI SGD:S000000041|SGD:S000002636|SGD:S000004665 P YGR156W gene taxon:4932 20030106 SGD
+SGD S000003388 PTI1 GO:0006379 SGD_REF:S000071951|PMID:12504017 IPI SGD:S000000041|SGD:S000002636|SGD:S000004665 P YGR156W gene taxon:4932 20030106 SGD
+SGD S000003388 PTI1 GO:0006379 SGD_REF:S000071951|PMID:12504017 IMP P YGR156W gene taxon:4932 20030106 SGD
+SGD S000003388 PTI1 GO:0030846 SGD_REF:S000074089|PMID:12819204 IPI P YGR156W gene taxon:4932 20031013 SGD
+SGD S000003388 PTI1 GO:0030847 SGD_REF:S000073502|PMID:12773397 IMP P YGR156W gene taxon:4932 20031010 SGD
+SGD S000003388 PTI1 GO:0030847 SGD_REF:S000074089|PMID:12819204 IPI P YGR156W gene taxon:4932 20031013 SGD
+SGD S000003388 PTI1 GO:0031126 SGD_REF:S000073502|PMID:12773397 IMP P YGR156W gene taxon:4932 20050218 SGD
+SGD S000001681 PTK1 GO:0008372 SGD_REF:S000069584 ND C YKL198C|KKT8|POT1|STK1|YKL199C|YKT9 gene taxon:4932 20020814 SGD
+SGD S000001681 PTK1 GO:0004672 SGD_REF:S000053577|PMID:8920934 ISS F YKL198C|KKT8|POT1|STK1|YKL199C|YKT9 gene taxon:4932 20020814 SGD
+SGD S000001681 PTK1 GO:0015846 SGD_REF:S000057349|PMID:7488221 IGI P YKL198C|KKT8|POT1|STK1|YKL199C|YKT9 gene taxon:4932 20020814 SGD
+SGD S000001681 PTK1 GO:0015846 SGD_REF:S000057349|PMID:7488221 IMP P YKL198C|KKT8|POT1|STK1|YKL199C|YKT9 gene taxon:4932 20020814 SGD
+SGD S000003820 PTK2 GO:0005634 SGD_REF:S000071811|PMID:12206772 IDA C YJR059W|STK2 gene taxon:4932 20030509 SGD
+SGD S000003820 PTK2 GO:0005737 SGD_REF:S000071811|PMID:12206772 IDA C YJR059W|STK2 gene taxon:4932 20030509 SGD
+SGD S000003820 PTK2 GO:0005886 SGD_REF:S000114531|PMID:16510118 IDA C YJR059W|STK2 gene taxon:4932 20060310 SGD
+SGD S000003820 PTK2 GO:0004672 SGD_REF:S000053577|PMID:8920934 ISS F YJR059W|STK2 gene taxon:4932 20020814 SGD
+SGD S000003820 PTK2 GO:0004672 SGD_REF:S000114531|PMID:16510118 IDA F YJR059W|STK2 gene taxon:4932 20060310 SGD
+SGD S000003820 PTK2 GO:0000082 SGD_REF:S000072514|PMID:12518319 IGI P YJR059W|STK2 gene taxon:4932 20030217 SGD
+SGD S000003820 PTK2 GO:0006873 SGD_REF:S000059090|PMID:11003661 IGI P YJR059W|STK2 gene taxon:4932 20020814 SGD
+SGD S000003820 PTK2 GO:0006873 SGD_REF:S000059090|PMID:11003661 IMP P YJR059W|STK2 gene taxon:4932 20020814 SGD
+SGD S000003820 PTK2 GO:0015846 SGD_REF:S000053577|PMID:8920934 IGI P YJR059W|STK2 gene taxon:4932 20020814 SGD
+SGD S000003820 PTK2 GO:0015846 SGD_REF:S000053577|PMID:8920934 IMP P YJR059W|STK2 gene taxon:4932 20020814 SGD
+SGD S000001522 PTM1 GO:0008372 SGD_REF:S000069584 ND C membrane protein (putative) YKL039W gene taxon:4932 20021125 SGD
+SGD S000001522 PTM1 GO:0005554 SGD_REF:S000069584 ND F membrane protein (putative) YKL039W gene taxon:4932 20021125 SGD
+SGD S000001522 PTM1 GO:0000004 SGD_REF:S000069584 ND P membrane protein (putative) YKL039W gene taxon:4932 20021125 SGD
+SGD S000002389 PTP1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C phosphotyrosine-specific protein phosphatase YDL230W gene taxon:4932 20031028 SGD
+SGD S000002389 PTP1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C phosphotyrosine-specific protein phosphatase YDL230W gene taxon:4932 20040813 SGD
+SGD S000002389 PTP1 GO:0004725 SGD_REF:S000048538|PMID:1649172 IDA F phosphotyrosine-specific protein phosphatase YDL230W gene taxon:4932 20020927 SGD
+SGD S000002389 PTP1 GO:0004725 SGD_REF:S000048538|PMID:1649172 ISS F phosphotyrosine-specific protein phosphatase YDL230W gene taxon:4932 20020927 SGD
+SGD S000002389 PTP1 GO:0006470 SGD_REF:S000046580|PMID:7559654 IDA P phosphotyrosine-specific protein phosphatase YDL230W gene taxon:4932 20020927 SGD
+SGD S000002389 PTP1 GO:0006470 SGD_REF:S000046580|PMID:7559654 IMP P phosphotyrosine-specific protein phosphatase YDL230W gene taxon:4932 20020927 SGD
+SGD S000005734 PTP2 GO:0005634 SGD_REF:S000046847|PMID:10523653 IDA C tyrosine phosphatase YOR208W gene taxon:4932 20010118 SGD
+SGD S000005734 PTP2 GO:0004725 SGD_REF:S000046820|PMID:8395005 TAS F tyrosine phosphatase YOR208W gene taxon:4932 20010118 SGD
+SGD S000005734 PTP2 GO:0000173 SGD_REF:S000046847|PMID:10523653 TAS P tyrosine phosphatase YOR208W gene taxon:4932 20010118 SGD
+SGD S000005734 PTP2 GO:0000750 SGD_REF:S000046847|PMID:10523653 TAS P tyrosine phosphatase YOR208W gene taxon:4932 20021206 SGD
+SGD S000005734 PTP2 GO:0006470 SGD_REF:S000046820|PMID:8395005 TAS P tyrosine phosphatase YOR208W gene taxon:4932 20010118 SGD
+SGD S000005734 PTP2 GO:0007231 SGD_REF:S000046847|PMID:10523653 TAS P tyrosine phosphatase YOR208W gene taxon:4932 20010118 SGD
+SGD S000000877 PTP3 GO:0005737 SGD_REF:S000046847|PMID:10523653 IDA C tyrosine phosphatase YER075C gene taxon:4932 20020927 SGD
+SGD S000000877 PTP3 GO:0004725 SGD_REF:S000045964|PMID:9224718 IDA F tyrosine phosphatase YER075C gene taxon:4932 20020927 SGD
+SGD S000000877 PTP3 GO:0000173 SGD_REF:S000056177|PMID:9211927 IMP P tyrosine phosphatase YER075C gene taxon:4932 20020927 SGD
+SGD S000000877 PTP3 GO:0000173 SGD_REF:S000056177|PMID:9211927 IPI P tyrosine phosphatase YER075C gene taxon:4932 20020927 SGD
+SGD S000000877 PTP3 GO:0000750 SGD_REF:S000045964|PMID:9224718 IMP P tyrosine phosphatase YER075C gene taxon:4932 20021206 SGD
+SGD S000000877 PTP3 GO:0000750 SGD_REF:S000045964|PMID:9224718 IPI P tyrosine phosphatase YER075C gene taxon:4932 20021206 SGD
+SGD S000000877 PTP3 GO:0006470 SGD_REF:S000045964|PMID:9224718 IDA P tyrosine phosphatase YER075C gene taxon:4932 20020927 SGD
+SGD S000000877 PTP3 GO:0006470 SGD_REF:S000045964|PMID:9224718 IMP P tyrosine phosphatase YER075C gene taxon:4932 20020927 SGD
+SGD S000001801 PTR2 GO:0005886 SGD_REF:S000050072|PMID:8264579 ISS C peptide transporter YKR093W gene taxon:4932 20020920 SGD
+SGD S000001801 PTR2 GO:0005886 SGD_REF:S000050072|PMID:8264579 IMP C peptide transporter YKR093W gene taxon:4932 20020920 SGD
+SGD S000001801 PTR2 GO:0015197 SGD_REF:S000050072|PMID:8264579 ISS F peptide transporter YKR093W gene taxon:4932 20020920 SGD
+SGD S000001801 PTR2 GO:0015197 SGD_REF:S000050072|PMID:8264579 IMP F peptide transporter YKR093W gene taxon:4932 20020920 SGD
+SGD S000001801 PTR2 GO:0015833 SGD_REF:S000050072|PMID:8264579 IMP P peptide transporter YKR093W gene taxon:4932 20020920 SGD
+SGD S000001925 PTR3 GO:0019897 SGD_REF:S000045243|PMID:10409731 IDA C YFR029W|SSY3 gene taxon:4932 20020920 SGD
+SGD S000001925 PTR3 GO:0016597 SGD_REF:S000045243|PMID:10409731 IGI F YFR029W|SSY3 gene taxon:4932 20020920 SGD
+SGD S000001925 PTR3 GO:0016597 SGD_REF:S000045243|PMID:10409731 IMP F YFR029W|SSY3 gene taxon:4932 20020920 SGD
+SGD S000001925 PTR3 GO:0007606 SGD_REF:S000045243|PMID:10409731 IGI P YFR029W|SSY3 gene taxon:4932 20020920 SGD
+SGD S000001925 PTR3 GO:0007606 SGD_REF:S000045243|PMID:10409731 IMP P YFR029W|SSY3 gene taxon:4932 20020920 SGD
+SGD S000004961 PUB1 GO:0005634 SGD_REF:S000040925|PMID:8413212 IDA C poly(A) binding protein YNL016W|RNP1 gene taxon:4932 20021015 SGD
+SGD S000004961 PUB1 GO:0005737 SGD_REF:S000040925|PMID:8413212 IDA C poly(A) binding protein YNL016W|RNP1 gene taxon:4932 20021015 SGD
+SGD S000004961 PUB1 GO:0030530 SGD_REF:S000040925|PMID:8413212 IDA C poly(A) binding protein YNL016W|RNP1 gene taxon:4932 20021015 SGD
+SGD S000004961 PUB1 GO:0003676 SGD_REF:S000040925|PMID:8413212 TAS F poly(A) binding protein YNL016W|RNP1 gene taxon:4932 20021015 SGD
+SGD S000004961 PUB1 GO:0003729 SGD_REF:S000082383|PMID:15964806 IDA F poly(A) binding protein YNL016W|RNP1 gene taxon:4932 20060530 SGD
+SGD S000004961 PUB1 GO:0000184 SGD_REF:S000050842|PMID:10892745 IDA P poly(A) binding protein YNL016W|RNP1 gene taxon:4932 20030110 SGD
+SGD S000004961 PUB1 GO:0043488 SGD_REF:S000082383|PMID:15964806 IMP P poly(A) binding protein YNL016W|RNP1 gene taxon:4932 20060530 SGD
+SGD S000006246 PUF2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C mRNA binding protein YPR042C gene taxon:4932 20031028 SGD
+SGD S000006246 PUF2 GO:0003729 SGD_REF:S000059700|PMID:11101532 ISS F mRNA binding protein YPR042C gene taxon:4932 20020924 SGD
+SGD S000006246 PUF2 GO:0000288 SGD_REF:S000059700|PMID:11101532 IGI P mRNA binding protein YPR042C gene taxon:4932 20020924 SGD
+SGD S000003936 PUF3 GO:0005737 SGD_REF:S000073211|PMID:12730603 IDA C YLL013C gene taxon:4932 20030606 SGD
+SGD S000003936 PUF3 GO:0003729 SGD_REF:S000059700|PMID:11101532 IDA F YLL013C gene taxon:4932 20020924 SGD
+SGD S000003936 PUF3 GO:0000288 SGD_REF:S000059700|PMID:11101532 IMP P YLL013C gene taxon:4932 20020924 SGD
+SGD S000002982 PUF4 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YGL014W|YGL023 gene taxon:4932 20031028 SGD
+SGD S000002982 PUF4 GO:0003729 SGD_REF:S000059700|PMID:11101532 ISS F YGL014W|YGL023 gene taxon:4932 20020924 SGD
+SGD S000002982 PUF4 GO:0000288 SGD_REF:S000059700|PMID:11101532 IGI P YGL014W|YGL023 gene taxon:4932 20020924 SGD
+SGD S000002982 PUF4 GO:0001308 SGD_REF:S000040351|PMID:9150138 IGI P YGL014W|YGL023 gene taxon:4932 20030814 SGD
+SGD S000002982 PUF4 GO:0001308 SGD_REF:S000040351|PMID:9150138 IMP P YGL014W|YGL023 gene taxon:4932 20030814 SGD
+SGD S000002982 PUF4 GO:0008104 SGD_REF:S000040351|PMID:9150138 IMP P YGL014W|YGL023 gene taxon:4932 20050728 SGD
+SGD S000002904 PUF6 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YDR496C gene taxon:4932 20031028 SGD
+SGD S000002904 PUF6 GO:0005730 SGD_REF:S000074185|PMID:14562095 IDA C YDR496C gene taxon:4932 20031028 SGD
+SGD S000002904 PUF6 GO:0016566 SGD_REF:S000076338|PMID:15198983 IDA F YDR496C gene taxon:4932 20040806 SGD
+SGD S000002904 PUF6 GO:0007532 SGD_REF:S000076338|PMID:15198983 IDA P YDR496C gene taxon:4932 20040806 SGD
+SGD S000002904 PUF6 GO:0007532 SGD_REF:S000076338|PMID:15198983 IMP P YDR496C gene taxon:4932 20040806 SGD
+SGD S000005683 PUP1 GO:0019774 SGD_REF:S000049615|PMID:10500111 TAS C proteasome subunit (putative) YOR157C gene taxon:4932 20030924 SGD
+SGD S000005683 PUP1 GO:0019774 SGD_REF:S000040877|PMID:9087403 IPI C proteasome subunit (putative) YOR157C gene taxon:4932 20041109 SGD
+SGD S000005683 PUP1 GO:0004175 SGD_REF:S000058010|PMID:8982460 TAS F proteasome subunit (putative) YOR157C gene taxon:4932 20010118 SGD
+SGD S000005683 PUP1 GO:0004175 SGD_REF:S000058457|PMID:10872471 TAS F proteasome subunit (putative) YOR157C gene taxon:4932 20010118 SGD
+SGD S000005683 PUP1 GO:0006511 SGD_REF:S000058010|PMID:8982460 TAS P proteasome subunit (putative) YOR157C gene taxon:4932 20010118 SGD
+SGD S000005683 PUP1 GO:0006511 SGD_REF:S000058457|PMID:10872471 TAS P proteasome subunit (putative) YOR157C gene taxon:4932 20010118 SGD
+SGD S000003485 PUP2 GO:0019773 SGD_REF:S000049615|PMID:10500111 TAS C proteasome subunit YGR253C|DOA5 gene taxon:4932 20030924 SGD
+SGD S000003485 PUP2 GO:0019773 SGD_REF:S000040877|PMID:9087403 IPI C proteasome subunit YGR253C|DOA5 gene taxon:4932 20041109 SGD
+SGD S000003485 PUP2 GO:0004175 SGD_REF:S000058010|PMID:8982460 TAS F proteasome subunit YGR253C|DOA5 gene taxon:4932 20010118 SGD
+SGD S000003485 PUP2 GO:0004175 SGD_REF:S000058457|PMID:10872471 TAS F proteasome subunit YGR253C|DOA5 gene taxon:4932 20010118 SGD
+SGD S000003485 PUP2 GO:0006511 SGD_REF:S000058010|PMID:8982460 TAS P proteasome subunit YGR253C|DOA5 gene taxon:4932 20010118 SGD
+SGD S000003485 PUP2 GO:0006511 SGD_REF:S000058457|PMID:10872471 TAS P proteasome subunit YGR253C|DOA5 gene taxon:4932 20010118 SGD
+SGD S000003485 PUP2 GO:0006950 SGD_REF:S000058010|PMID:8982460 TAS P proteasome subunit YGR253C|DOA5 gene taxon:4932 20010118 SGD
+SGD S000003485 PUP2 GO:0030437 SGD_REF:S000058010|PMID:8982460 TAS P proteasome subunit YGR253C|DOA5 gene taxon:4932 20010118 SGD
+SGD S000000896 PUP3 GO:0019774 SGD_REF:S000049615|PMID:10500111 TAS C 20S proteasome subunit beta3_sc YER094C|SCS32 gene taxon:4932 20030924 SGD
+SGD S000000896 PUP3 GO:0019774 SGD_REF:S000040877|PMID:9087403 IPI C 20S proteasome subunit beta3_sc YER094C|SCS32 gene taxon:4932 20041109 SGD
+SGD S000000896 PUP3 GO:0004175 SGD_REF:S000058010|PMID:8982460 TAS F 20S proteasome subunit beta3_sc YER094C|SCS32 gene taxon:4932 20010118 SGD
+SGD S000000896 PUP3 GO:0004175 SGD_REF:S000058457|PMID:10872471 TAS F 20S proteasome subunit beta3_sc YER094C|SCS32 gene taxon:4932 20010118 SGD
+SGD S000000896 PUP3 GO:0006511 SGD_REF:S000058010|PMID:8982460 TAS P 20S proteasome subunit beta3_sc YER094C|SCS32 gene taxon:4932 20010118 SGD
+SGD S000000896 PUP3 GO:0006511 SGD_REF:S000058457|PMID:10872471 TAS P 20S proteasome subunit beta3_sc YER094C|SCS32 gene taxon:4932 20010118 SGD
+SGD S000006133 PUS1 GO:0005634 SGD_REF:S000057854|PMID:8641292 IPI C tRNA pseudouridine synthase YPL212C gene taxon:4932 20021014 SGD
+SGD S000006133 PUS1 GO:0016439 SGD_REF:S000049065|PMID:10356324 IDA F tRNA pseudouridine synthase YPL212C gene taxon:4932 20050721 SGD
+SGD S000006133 PUS1 GO:0006400 SGD_REF:S000049065|PMID:10356324 IDA P tRNA pseudouridine synthase YPL212C gene taxon:4932 20020927 SGD
+SGD S000003031 PUS2 GO:0008372 SGD_REF:S000069584 ND C pseudouridine synthase YGL063W gene taxon:4932 20021104 SGD
+SGD S000003031 PUS2 GO:0016439 SGD_REF:S000049065|PMID:10356324 ISS F pseudouridine synthase YGL063W gene taxon:4932 20050721 SGD
+SGD S000003031 PUS2 GO:0006400 SGD_REF:S000049065|PMID:10356324 ISS P pseudouridine synthase YGL063W gene taxon:4932 20021001 SGD
+SGD S000005236 PUS4 GO:0005634 SGD_REF:S000047525|PMID:9358157 IMP C pseudouridine synthase YNL292W gene taxon:4932 20020927 SGD
+SGD S000005236 PUS4 GO:0005739 SGD_REF:S000047525|PMID:9358157 IMP C pseudouridine synthase YNL292W gene taxon:4932 20020927 SGD
+SGD S000005236 PUS4 GO:0004730 SGD_REF:S000047525|PMID:9358157 IDA F pseudouridine synthase YNL292W gene taxon:4932 20020927 SGD
+SGD S000005236 PUS4 GO:0006400 SGD_REF:S000047525|PMID:9358157 IDA P pseudouridine synthase YNL292W gene taxon:4932 20020927 SGD
+SGD S000004155 PUS5 GO:0005739 SGD_REF:S000056334|PMID:10756195 IMP C YLR165C gene taxon:4932 20021011 SGD
+SGD S000004155 PUS5 GO:0004730 SGD_REF:S000056334|PMID:10756195 ISS F YLR165C gene taxon:4932 20021011 SGD
+SGD S000004155 PUS5 GO:0004730 SGD_REF:S000056334|PMID:10756195 IMP F YLR165C gene taxon:4932 20021011 SGD
+SGD S000004155 PUS5 GO:0000154 SGD_REF:S000056334|PMID:10756195 IMP P YLR165C gene taxon:4932 20021011 SGD
+SGD S000004155 PUS5 GO:0001522 SGD_REF:S000056334|PMID:10756195 IMP P YLR165C gene taxon:4932 20021011 SGD
+SGD S000003401 PUS6 GO:0005737 SGD_REF:S000065863|PMID:11406626 IDA C YGR169C gene taxon:4932 20021014 SGD
+SGD S000003401 PUS6 GO:0005739 SGD_REF:S000065863|PMID:11406626 IDA C YGR169C gene taxon:4932 20021014 SGD
+SGD S000003401 PUS6 GO:0004730 SGD_REF:S000065863|PMID:11406626 IDA F YGR169C gene taxon:4932 20021014 SGD
+SGD S000003401 PUS6 GO:0001522 SGD_REF:S000065863|PMID:11406626 IDA P YGR169C gene taxon:4932 20021014 SGD
+SGD S000003401 PUS6 GO:0006400 SGD_REF:S000065863|PMID:11406626 IDA P YGR169C gene taxon:4932 20021014 SGD
+SGD S000005769 PUS7 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C pseudouridine synthase YOR243C gene taxon:4932 20031028 SGD
+SGD S000005769 PUS7 GO:0009982 SGD_REF:S000072999|PMID:12682021 IDA F pseudouridine synthase YOR243C gene taxon:4932 20030421 SGD
+SGD S000005769 PUS7 GO:0001522 SGD_REF:S000072999|PMID:12682021 IDA P pseudouridine synthase YOR243C gene taxon:4932 20030421 SGD
+SGD S000005769 PUS7 GO:0006400 SGD_REF:S000074539|PMID:14561887 IDA P pseudouridine synthase YOR243C gene taxon:4932 20031228 SGD
+SGD S000005769 PUS7 GO:0040031 SGD_REF:S000074539|PMID:14561887 IDA P pseudouridine synthase YOR243C gene taxon:4932 20031228 SGD
+SGD S000002194 PUS9 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C tRNA pseudouridine synthase YDL036C gene taxon:4932 20031028 SGD
+SGD S000002194 PUS9 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C tRNA pseudouridine synthase YDL036C gene taxon:4932 20031028 SGD
+SGD S000002194 PUS9 GO:0005739 SGD_REF:S000080014|PMID:15466869 ISS C tRNA pseudouridine synthase YDL036C gene taxon:4932 20051108 SGD
+SGD S000002194 PUS9 GO:0005739 SGD_REF:S000080014|PMID:15466869 IMP C tRNA pseudouridine synthase YDL036C gene taxon:4932 20051108 SGD
+SGD S000002194 PUS9 GO:0016439 SGD_REF:S000080014|PMID:15466869 IDA F tRNA pseudouridine synthase YDL036C gene taxon:4932 20051108 SGD
+SGD S000002194 PUS9 GO:0016439 SGD_REF:S000080014|PMID:15466869 IMP F tRNA pseudouridine synthase YDL036C gene taxon:4932 20051108 SGD
+SGD S000002194 PUS9 GO:0031119 SGD_REF:S000080014|PMID:15466869 IDA P tRNA pseudouridine synthase YDL036C gene taxon:4932 20051108 SGD
+SGD S000002194 PUS9 GO:0031119 SGD_REF:S000080014|PMID:15466869 IMP P tRNA pseudouridine synthase YDL036C gene taxon:4932 20051108 SGD
+SGD S000004132 PUT1 GO:0005739 SGD_REF:S000061758|PMID:10640599 TAS C proline oxidase YLR142W gene taxon:4932 20011029 SGD
+SGD S000004132 PUT1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C proline oxidase YLR142W gene taxon:4932 20040928 SGD
+SGD S000004132 PUT1 GO:0004657 SGD_REF:S000061758|PMID:10640599 TAS F proline oxidase YLR142W gene taxon:4932 20011029 SGD
+SGD S000004132 PUT1 GO:0004657 SGD_REF:S000040886|PMID:387737 IMP F proline oxidase YLR142W gene taxon:4932 20050930 SGD
+SGD S000004132 PUT1 GO:0006537 SGD_REF:S000061758|PMID:10640599 TAS P proline oxidase YLR142W gene taxon:4932 20011029 SGD
+SGD S000004132 PUT1 GO:0010133 SGD_REF:S000061758|PMID:10640599 TAS P proline oxidase YLR142W gene taxon:4932 20050921 SGD
+SGD S000004132 PUT1 GO:0010133 SGD_REF:S000040886|PMID:387737 IMP P proline oxidase YLR142W gene taxon:4932 20050930 SGD
+SGD S000001079 PUT2 GO:0005739 SGD_REF:S000061758|PMID:10640599 TAS C delta-1-pyrroline-5-carboxylate dehydrogenase YHR037W gene taxon:4932 20011029 SGD
+SGD S000001079 PUT2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C delta-1-pyrroline-5-carboxylate dehydrogenase YHR037W gene taxon:4932 20040928 SGD
+SGD S000001079 PUT2 GO:0003842 SGD_REF:S000061758|PMID:10640599 TAS F delta-1-pyrroline-5-carboxylate dehydrogenase YHR037W gene taxon:4932 20011029 SGD
+SGD S000001079 PUT2 GO:0003842 SGD_REF:S000040886|PMID:387737 IMP F delta-1-pyrroline-5-carboxylate dehydrogenase YHR037W gene taxon:4932 20050930 SGD
+SGD S000001079 PUT2 GO:0006537 SGD_REF:S000061758|PMID:10640599 TAS P delta-1-pyrroline-5-carboxylate dehydrogenase YHR037W gene taxon:4932 20011029 SGD
+SGD S000001079 PUT2 GO:0006562 SGD_REF:S000061758|PMID:10640599 TAS P delta-1-pyrroline-5-carboxylate dehydrogenase YHR037W gene taxon:4932 20011029 SGD
+SGD S000001079 PUT2 GO:0010133 SGD_REF:S000040886|PMID:387737 IMP P delta-1-pyrroline-5-carboxylate dehydrogenase YHR037W gene taxon:4932 20050930 SGD
+SGD S000001498 PUT3 GO:0005634 SGD_REF:S000039769|PMID:1986247 IC GO:0003704 C zinc finger transcription factor of the Zn(2)-Cys(6) binuclear cluster domain type YKL015W gene taxon:4932 20021112 SGD
+SGD S000001498 PUT3 GO:0003704 SGD_REF:S000039769|PMID:1986247 IDA F zinc finger transcription factor of the Zn(2)-Cys(6) binuclear cluster domain type YKL015W gene taxon:4932 20021112 SGD
+SGD S000001498 PUT3 GO:0016563 SGD_REF:S000046832|PMID:8846888 IDA F zinc finger transcription factor of the Zn(2)-Cys(6) binuclear cluster domain type YKL015W gene taxon:4932 20050906 SGD
+SGD S000001498 PUT3 GO:0016563 SGD_REF:S000046832|PMID:8846888 IMP F zinc finger transcription factor of the Zn(2)-Cys(6) binuclear cluster domain type YKL015W gene taxon:4932 20050906 SGD
+SGD S000001498 PUT3 GO:0006562 SGD_REF:S000046832|PMID:8846888 IMP P zinc finger transcription factor of the Zn(2)-Cys(6) binuclear cluster domain type YKL015W gene taxon:4932 20021112 SGD
+SGD S000001498 PUT3 GO:0045944 SGD_REF:S000039769|PMID:1986247 IDA P zinc finger transcription factor of the Zn(2)-Cys(6) binuclear cluster domain type YKL015W gene taxon:4932 20021112 SGD
+SGD S000005875 PUT4 GO:0005886 SGD_REF:S000043244|PMID:10654085 ISS C proline specific permease YOR348C gene taxon:4932 20020806 SGD
+SGD S000005875 PUT4 GO:0005296 SGD_REF:S000054020|PMID:3552672 IMP F proline specific permease YOR348C gene taxon:4932 20050428 SGD
+SGD S000005875 PUT4 GO:0005296 SGD_REF:S000074897|PMID:14968425 IGI SGD:S000000530|SGD:S000002916|SGD:S000001747 F proline specific permease YOR348C gene taxon:4932 20050428 SGD
+SGD S000005875 PUT4 GO:0015175 SGD_REF:S000043244|PMID:10654085 IDA F proline specific permease YOR348C gene taxon:4932 20020806 SGD
+SGD S000005875 PUT4 GO:0006562 SGD_REF:S000061758|PMID:10640599 TAS P proline specific permease YOR348C gene taxon:4932 20050428 SGD
+SGD S000005875 PUT4 GO:0015804 SGD_REF:S000043244|PMID:10654085 IDA P proline specific permease YOR348C gene taxon:4932 20020806 SGD
+SGD S000004186 PWP1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YLR196W gene taxon:4932 20031028 SGD
+SGD S000004186 PWP1 GO:0005730 SGD_REF:S000074185|PMID:14562095 IDA C YLR196W gene taxon:4932 20031028 SGD
+SGD S000004186 PWP1 GO:0005730 SGD_REF:S000080108|PMID:15588312 IPI C YLR196W gene taxon:4932 20050324 SGD
+SGD S000004186 PWP1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YLR196W gene taxon:4932 20031028 SGD
+SGD S000004186 PWP1 GO:0005554 SGD_REF:S000069584 ND F YLR196W gene taxon:4932 20021001 SGD
+SGD S000004186 PWP1 GO:0006364 SGD_REF:S000080108|PMID:15588312 IMP P YLR196W gene taxon:4932 20050324 SGD
+SGD S000004186 PWP1 GO:0006364 SGD_REF:S000080108|PMID:15588312 ISS P YLR196W gene taxon:4932 20050324 SGD
+SGD S000000653 PWP2 GO:0005732 SGD_REF:S000070145|PMID:12068309 IPI C U3 snoRNP protein YCR057C|UTP1|YCR055C|YCR058C gene taxon:4932 20030224 SGD
+SGD S000000653 PWP2 GO:0005737 SGD_REF:S000045028|PMID:8804409 IDA C U3 snoRNP protein YCR057C|UTP1|YCR055C|YCR058C gene taxon:4932 20010118 SGD
+SGD S000000653 PWP2 GO:0030686 SGD_REF:S000079905|PMID:15231838 IDA C U3 snoRNP protein YCR057C|UTP1|YCR055C|YCR058C gene taxon:4932 20050126 SGD
+SGD S000000653 PWP2 GO:0030515 SGD_REF:S000070145|PMID:12068309 IPI F U3 snoRNP protein YCR057C|UTP1|YCR055C|YCR058C gene taxon:4932 20030224 SGD
+SGD S000000653 PWP2 GO:0000910 SGD_REF:S000045028|PMID:8804409 IMP P U3 snoRNP protein YCR057C|UTP1|YCR055C|YCR058C gene taxon:4932 20010119 SGD
+SGD S000000653 PWP2 GO:0006365 SGD_REF:S000079905|PMID:15231838 IMP P U3 snoRNP protein YCR057C|UTP1|YCR055C|YCR058C gene taxon:4932 20050126 SGD
+SGD S000000653 PWP2 GO:0006365 SGD_REF:S000079905|PMID:15231838 IPI P U3 snoRNP protein YCR057C|UTP1|YCR055C|YCR058C gene taxon:4932 20050126 SGD
+SGD S000000653 PWP2 GO:0006365 SGD_REF:S000079989|PMID:15590835 IMP P U3 snoRNP protein YCR057C|UTP1|YCR055C|YCR058C gene taxon:4932 20060315 SGD
+SGD S000000653 PWP2 GO:0030468 SGD_REF:S000045028|PMID:8804409 IMP P U3 snoRNP protein YCR057C|UTP1|YCR055C|YCR058C gene taxon:4932 20010302 SGD
+SGD S000000653 PWP2 GO:0030490 SGD_REF:S000070145|PMID:12068309 IMP P U3 snoRNP protein YCR057C|UTP1|YCR055C|YCR058C gene taxon:4932 20020906 SGD
+SGD S000000653 PWP2 GO:0030490 SGD_REF:S000070145|PMID:12068309 IPI P U3 snoRNP protein YCR057C|UTP1|YCR055C|YCR058C gene taxon:4932 20020906 SGD
+SGD S000006068 PXA1 GO:0005779 SGD_REF:S000053188|PMID:8670886 IDA C ABC transporter of long-chain fatty acids YPL147W|LPI1|PAL1|PAT2|SSH2 gene taxon:4932 20020919 SGD
+SGD S000006068 PXA1 GO:0042626 SGD_REF:S000053188|PMID:8670886 IMP F ABC transporter of long-chain fatty acids YPL147W|LPI1|PAL1|PAT2|SSH2 gene taxon:4932 20020919 SGD
+SGD S000006068 PXA1 GO:0042626 SGD_REF:S000053188|PMID:8670886 ISS F ABC transporter of long-chain fatty acids YPL147W|LPI1|PAL1|PAT2|SSH2 gene taxon:4932 20020919 SGD
+SGD S000006068 PXA1 GO:0015908 SGD_REF:S000053188|PMID:8670886 IMP P ABC transporter of long-chain fatty acids YPL147W|LPI1|PAL1|PAT2|SSH2 gene taxon:4932 20020919 SGD
+SGD S000001671 PXA2 GO:0005779 SGD_REF:S000039468|PMID:9395310 IDA C ABC transporter 2 YKL188C|PAT1 gene taxon:4932 20020918 SGD
+SGD S000001671 PXA2 GO:0042626 SGD_REF:S000039468|PMID:9395310 IDA F ABC transporter 2 YKL188C|PAT1 gene taxon:4932 20020918 SGD
+SGD S000001671 PXA2 GO:0015908 SGD_REF:S000039468|PMID:9395310 IDA P ABC transporter 2 YKL188C|PAT1 gene taxon:4932 20020918 SGD
+SGD S000001798 PXL1 GO:0000131 SGD_REF:S000076155|PMID:14767053 IDA C YKR090W gene taxon:4932 20040519 SGD
+SGD S000001798 PXL1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YKR090W gene taxon:4932 20031028 SGD
+SGD S000001798 PXL1 GO:0005933 SGD_REF:S000074185|PMID:14562095 IDA C YKR090W gene taxon:4932 20031028 SGD
+SGD S000001798 PXL1 GO:0005934 SGD_REF:S000076155|PMID:14767053 IDA C YKR090W gene taxon:4932 20040519 SGD
+SGD S000001798 PXL1 GO:0005934 SGD_REF:S000077144|PMID:15282802 IDA C YKR090W gene taxon:4932 20041008 SGD
+SGD S000001798 PXL1 GO:0005935 SGD_REF:S000074185|PMID:14562095 IDA C YKR090W gene taxon:4932 20031028 SGD
+SGD S000001798 PXL1 GO:0005935 SGD_REF:S000076155|PMID:14767053 IDA C YKR090W gene taxon:4932 20040519 SGD
+SGD S000001798 PXL1 GO:0005935 SGD_REF:S000077144|PMID:15282802 IDA C YKR090W gene taxon:4932 20041008 SGD
+SGD S000001798 PXL1 GO:0043332 SGD_REF:S000076155|PMID:14767053 IDA C YKR090W gene taxon:4932 20040519 SGD
+SGD S000001798 PXL1 GO:0005515 SGD_REF:S000076155|PMID:14767053 ISS F YKR090W gene taxon:4932 20040519 SGD
+SGD S000001798 PXL1 GO:0030469 SGD_REF:S000076155|PMID:14767053 IMP P YKR090W gene taxon:4932 20040519 SGD
+SGD S000003512 PXR1 GO:0005730 SGD_REF:S000071554|PMID:12107183 IDA C YGR280C|GNO1|PinX1 gene taxon:4932 20060313 SGD
+SGD S000003512 PXR1 GO:0005554 SGD_REF:S000069584 ND F YGR280C|GNO1|PinX1 gene taxon:4932 20060313 SGD
+SGD S000003512 PXR1 GO:0006365 SGD_REF:S000071554|PMID:12107183 IMP P YGR280C|GNO1|PinX1 gene taxon:4932 20030121 SGD
+SGD S000003512 PXR1 GO:0031126 SGD_REF:S000071554|PMID:12107183 IMP P YGR280C|GNO1|PinX1 gene taxon:4932 20060313 SGD
+SGD S000003030 PYC1 GO:0005829 SGD_REF:S000040003|PMID:2039506 IDA C pyruvate carboxylase YGL062W gene taxon:4932 20010118 SGD
+SGD S000003030 PYC1 GO:0005829 SGD_REF:S000056699|PMID:196563 IDA C pyruvate carboxylase YGL062W gene taxon:4932 20050512 SGD
+SGD S000003030 PYC1 GO:0004736 SGD_REF:S000040003|PMID:2039506 IDA F pyruvate carboxylase YGL062W gene taxon:4932 20010118 SGD
+SGD S000003030 PYC1 GO:0004736 SGD_REF:S000040003|PMID:2039506 IMP F pyruvate carboxylase YGL062W gene taxon:4932 20010118 SGD
+SGD S000003030 PYC1 GO:0006094 SGD_REF:S000051649|PMID:8185321 IMP P pyruvate carboxylase YGL062W gene taxon:4932 20050524 SGD
+SGD S000003030 PYC1 GO:0006740 SGD_REF:S000058499 TAS P pyruvate carboxylase YGL062W gene taxon:4932 20010119 SGD
+SGD S000000422 PYC2 GO:0005829 SGD_REF:S000040003|PMID:2039506 IDA C pyruvate carboxylase YBR218C gene taxon:4932 20010118 SGD
+SGD S000000422 PYC2 GO:0005829 SGD_REF:S000056699|PMID:196563 IDA C pyruvate carboxylase YBR218C gene taxon:4932 20050608 SGD
+SGD S000000422 PYC2 GO:0004736 SGD_REF:S000040003|PMID:2039506 IMP F pyruvate carboxylase YBR218C gene taxon:4932 20010118 SGD
+SGD S000000422 PYC2 GO:0004736 SGD_REF:S000040003|PMID:2039506 IDA F pyruvate carboxylase YBR218C gene taxon:4932 20010118 SGD
+SGD S000000422 PYC2 GO:0006094 SGD_REF:S000051649|PMID:8185321 IMP P pyruvate carboxylase YBR218C gene taxon:4932 20050524 SGD
+SGD S000000422 PYC2 GO:0006740 SGD_REF:S000058499 TAS P pyruvate carboxylase YBR218C gene taxon:4932 20010119 SGD
+SGD S000005874 PYK2 GO:0005829 SGD_REF:S000058491 TAS C YOR347C gene taxon:4932 20010119 SGD
+SGD S000005874 PYK2 GO:0004743 SGD_REF:S000053531|PMID:9139918 IMP F YOR347C gene taxon:4932 20010118 SGD
+SGD S000005874 PYK2 GO:0006090 SGD_REF:S000053531|PMID:9139918 IMP P YOR347C gene taxon:4932 20050727 SGD
+SGD S000006390 PZF1 GO:0005667 SGD_REF:S000057773|PMID:8496187 IPI C transcription factor IIIA (putative) YPR186C|TFC2 gene taxon:4932 20010118 SGD
+SGD S000006390 PZF1 GO:0003709 SGD_REF:S000056310|PMID:1570325 IPI F transcription factor IIIA (putative) YPR186C|TFC2 gene taxon:4932 20010118 SGD
+SGD S000006390 PZF1 GO:0003709 SGD_REF:S000056310|PMID:1570325 ISS F transcription factor IIIA (putative) YPR186C|TFC2 gene taxon:4932 20010118 SGD
+SGD S000006390 PZF1 GO:0006384 SGD_REF:S000056310|PMID:1570325 ISS P transcription factor IIIA (putative) YPR186C|TFC2 gene taxon:4932 20010118 SGD
+SGD S000006390 PZF1 GO:0006384 SGD_REF:S000056310|PMID:1570325 IPI P transcription factor IIIA (putative) YPR186C|TFC2 gene taxon:4932 20010118 SGD
+SGD S000003529 QCR10 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C ubiqunol-cytochrome c oxidoreductase complex 8.5 kDa subunit YHR001W-A gene taxon:4932 20031028 SGD
+SGD S000003529 QCR10 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C ubiqunol-cytochrome c oxidoreductase complex 8.5 kDa subunit YHR001W-A gene taxon:4932 20040924 SGD
+SGD S000003529 QCR10 GO:0005750 SGD_REF:S000050624|PMID:8175712 IDA C ubiqunol-cytochrome c oxidoreductase complex 8.5 kDa subunit YHR001W-A gene taxon:4932 20020906 SGD
+SGD S000003529 QCR10 GO:0008121 SGD_REF:S000050624|PMID:8175712 IDA F ubiqunol-cytochrome c oxidoreductase complex 8.5 kDa subunit YHR001W-A gene taxon:4932 20020906 SGD
+SGD S000003529 QCR10 GO:0006122 SGD_REF:S000050624|PMID:8175712 IMP P ubiqunol-cytochrome c oxidoreductase complex 8.5 kDa subunit YHR001W-A gene taxon:4932 20020906 SGD
+SGD S000003529 QCR10 GO:0009060 SGD_REF:S000050624|PMID:8175712 IGI P ubiqunol-cytochrome c oxidoreductase complex 8.5 kDa subunit YHR001W-A gene taxon:4932 20020906 SGD
+SGD S000006395 QCR2 GO:0005739 SGD_REF:S000069459|PMID:11914276 IDA C 40 kDa ubiquinol cytochrome-c reductase core protein 2 YPR191W|COR2|UCR2 gene taxon:4932 20020507 SGD
+SGD S000006395 QCR2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C 40 kDa ubiquinol cytochrome-c reductase core protein 2 YPR191W|COR2|UCR2 gene taxon:4932 20040924 SGD
+SGD S000006395 QCR2 GO:0005750 SGD_REF:S000046403|PMID:10873857 IDA C 40 kDa ubiquinol cytochrome-c reductase core protein 2 YPR191W|COR2|UCR2 gene taxon:4932 20020906 SGD
+SGD S000006395 QCR2 GO:0008121 SGD_REF:S000056985|PMID:3028797 IDA F 40 kDa ubiquinol cytochrome-c reductase core protein 2 YPR191W|COR2|UCR2 gene taxon:4932 20020906 SGD
+SGD S000006395 QCR2 GO:0006122 SGD_REF:S000056985|PMID:3028797 IDA P 40 kDa ubiquinol cytochrome-c reductase core protein 2 YPR191W|COR2|UCR2 gene taxon:4932 20020906 SGD
+SGD S000006395 QCR2 GO:0009060 SGD_REF:S000056985|PMID:3028797 IMP P 40 kDa ubiquinol cytochrome-c reductase core protein 2 YPR191W|COR2|UCR2 gene taxon:4932 20020906 SGD
+SGD S000001929 QCR6 GO:0005739 SGD_REF:S000069459|PMID:11914276 IDA C ubiquinol cytochrome C oxidoreductase subunit 6 (17 kDa) YFR033C|COR3|UCR6 gene taxon:4932 20020507 SGD
+SGD S000001929 QCR6 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C ubiquinol cytochrome C oxidoreductase subunit 6 (17 kDa) YFR033C|COR3|UCR6 gene taxon:4932 20040924 SGD
+SGD S000001929 QCR6 GO:0005750 SGD_REF:S000046403|PMID:10873857 IDA C ubiquinol cytochrome C oxidoreductase subunit 6 (17 kDa) YFR033C|COR3|UCR6 gene taxon:4932 20020906 SGD
+SGD S000001929 QCR6 GO:0008121 SGD_REF:S000045986|PMID:8288589 IMP F ubiquinol cytochrome C oxidoreductase subunit 6 (17 kDa) YFR033C|COR3|UCR6 gene taxon:4932 20020906 SGD
+SGD S000001929 QCR6 GO:0006122 SGD_REF:S000045986|PMID:8288589 IMP P ubiquinol cytochrome C oxidoreductase subunit 6 (17 kDa) YFR033C|COR3|UCR6 gene taxon:4932 20020906 SGD
+SGD S000001929 QCR6 GO:0009060 SGD_REF:S000045986|PMID:8288589 IMP P ubiquinol cytochrome C oxidoreductase subunit 6 (17 kDa) YFR033C|COR3|UCR6 gene taxon:4932 20020906 SGD
+SGD S000002937 QCR7 GO:0005750 SGD_REF:S000046403|PMID:10873857 IDA C ubiquinol cytochrome C oxidoreductase subunit 7 (14 kDa) YDR529C|COR4|CRO1|UCR7 gene taxon:4932 20020906 SGD
+SGD S000002937 QCR7 GO:0008121 SGD_REF:S000056875|PMID:2540976 IMP F ubiquinol cytochrome C oxidoreductase subunit 7 (14 kDa) YDR529C|COR4|CRO1|UCR7 gene taxon:4932 20020906 SGD
+SGD S000002937 QCR7 GO:0006122 SGD_REF:S000056875|PMID:2540976 IMP P ubiquinol cytochrome C oxidoreductase subunit 7 (14 kDa) YDR529C|COR4|CRO1|UCR7 gene taxon:4932 20020906 SGD
+SGD S000002937 QCR7 GO:0009060 SGD_REF:S000056875|PMID:2540976 IMP P ubiquinol cytochrome C oxidoreductase subunit 7 (14 kDa) YDR529C|COR4|CRO1|UCR7 gene taxon:4932 20020906 SGD
+SGD S000002937 QCR7 GO:0017062 SGD_REF:S000066042|PMID:11556808 IMP P ubiquinol cytochrome C oxidoreductase subunit 7 (14 kDa) YDR529C|COR4|CRO1|UCR7 gene taxon:4932 20020906 SGD
+SGD S000003702 QCR8 GO:0005750 SGD_REF:S000046403|PMID:10873857 IDA C ubiquinol cytochrome C reductase subunit 8 (11 kDa) YJL166W|COR5 gene taxon:4932 20020906 SGD
+SGD S000003702 QCR8 GO:0008121 SGD_REF:S000049829|PMID:8394810 IDA F ubiquinol cytochrome C reductase subunit 8 (11 kDa) YJL166W|COR5 gene taxon:4932 20020906 SGD
+SGD S000003702 QCR8 GO:0006122 SGD_REF:S000049829|PMID:8394810 IMP P ubiquinol cytochrome C reductase subunit 8 (11 kDa) YJL166W|COR5 gene taxon:4932 20020906 SGD
+SGD S000003702 QCR8 GO:0009060 SGD_REF:S000049829|PMID:8394810 IMP P ubiquinol cytochrome C reductase subunit 8 (11 kDa) YJL166W|COR5 gene taxon:4932 20020906 SGD
+SGD S000003415 QCR9 GO:0005750 SGD_REF:S000046403|PMID:10873857 IDA C ubiquinol cytochrome c oxidoreductase complex 7.3 kDa subunit 9 YGR183C|UCR9 gene taxon:4932 20020906 SGD
+SGD S000003415 QCR9 GO:0008121 SGD_REF:S000055696|PMID:1332881 IDA F ubiquinol cytochrome c oxidoreductase complex 7.3 kDa subunit 9 YGR183C|UCR9 gene taxon:4932 20020906 SGD
+SGD S000003415 QCR9 GO:0006122 SGD_REF:S000055696|PMID:1332881 IMP P ubiquinol cytochrome c oxidoreductase complex 7.3 kDa subunit 9 YGR183C|UCR9 gene taxon:4932 20020906 SGD
+SGD S000003415 QCR9 GO:0009060 SGD_REF:S000055696|PMID:1332881 IMP P ubiquinol cytochrome c oxidoreductase complex 7.3 kDa subunit 9 YGR183C|UCR9 gene taxon:4932 20020906 SGD
+SGD S000003415 QCR9 GO:0016226 SGD_REF:S000052135|PMID:8389362 IMP P ubiquinol cytochrome c oxidoreductase complex 7.3 kDa subunit 9 YGR183C|UCR9 gene taxon:4932 20020906 SGD
+SGD S000001382 QDR1 GO:0005886 SGD_REF:S000060349|PMID:11302822 IDA C multidrug resistance transporter YIL120W gene taxon:4932 20020930 SGD
+SGD S000001382 QDR1 GO:0005887 SGD_REF:S000060349|PMID:11302822 ISS C multidrug resistance transporter YIL120W gene taxon:4932 20020930 SGD
+SGD S000001382 QDR1 GO:0015239 SGD_REF:S000060349|PMID:11302822 ISS F multidrug resistance transporter YIL120W gene taxon:4932 20020930 SGD
+SGD S000001382 QDR1 GO:0015559 SGD_REF:S000080433|PMID:15649438 IMP F multidrug resistance transporter YIL120W gene taxon:4932 20050201 SGD
+SGD S000001382 QDR1 GO:0006855 SGD_REF:S000060349|PMID:11302822 IMP P multidrug resistance transporter YIL120W gene taxon:4932 20020930 SGD
+SGD S000001383 QDR2 GO:0005887 SGD_REF:S000076810|PMID:15215105 IDA C plasma membrane transporter YIL121W gene taxon:4932 20040811 SGD
+SGD S000001383 QDR2 GO:0015559 SGD_REF:S000076810|PMID:15215105 IMP F plasma membrane transporter YIL121W gene taxon:4932 20040811 SGD
+SGD S000001383 QDR2 GO:0006855 SGD_REF:S000076810|PMID:15215105 IMP P plasma membrane transporter YIL121W gene taxon:4932 20040811 SGD
+SGD S000000247 QDR3 GO:0005886 SGD_REF:S000080433|PMID:15649438 IDA C YBR043C|AQR2 gene taxon:4932 20050201 SGD
+SGD S000000247 QDR3 GO:0005887 SGD_REF:S000066144|PMID:9046086 ISS C YBR043C|AQR2 gene taxon:4932 20050201 SGD
+SGD S000000247 QDR3 GO:0015559 SGD_REF:S000080433|PMID:15649438 IMP F YBR043C|AQR2 gene taxon:4932 20050201 SGD
+SGD S000000247 QDR3 GO:0015559 SGD_REF:S000066144|PMID:9046086 ISS F YBR043C|AQR2 gene taxon:4932 20050201 SGD
+SGD S000000247 QDR3 GO:0006855 SGD_REF:S000080433|PMID:15649438 IMP P YBR043C|AQR2 gene taxon:4932 20050201 SGD
+SGD S000001116 QNS1 GO:0005634 SGD_REF:S000073900|PMID:12898714 IDA C glutamine-dependent NAD synthetase YHR074W gene taxon:4932 20030915 SGD
+SGD S000001116 QNS1 GO:0005737 SGD_REF:S000073900|PMID:12898714 IDA C glutamine-dependent NAD synthetase YHR074W gene taxon:4932 20030915 SGD
+SGD S000001116 QNS1 GO:0003952 SGD_REF:S000069984|PMID:11380987 ISS F glutamine-dependent NAD synthetase YHR074W gene taxon:4932 20020619 SGD
+SGD S000001116 QNS1 GO:0003952 SGD_REF:S000073900|PMID:12898714 IDA F glutamine-dependent NAD synthetase YHR074W gene taxon:4932 20030915 SGD
+SGD S000001116 QNS1 GO:0003952 SGD_REF:S000073884|PMID:12771147 IMP F glutamine-dependent NAD synthetase YHR074W gene taxon:4932 20030902 SGD
+SGD S000001116 QNS1 GO:0003952 SGD_REF:S000073884|PMID:12771147 IDA F glutamine-dependent NAD synthetase YHR074W gene taxon:4932 20030902 SGD
+SGD S000001116 QNS1 GO:0003952 SGD_REF:S000073900|PMID:12898714 IMP F glutamine-dependent NAD synthetase YHR074W gene taxon:4932 20030915 SGD
+SGD S000001116 QNS1 GO:0016811 SGD_REF:S000073884|PMID:12771147 IDA F glutamine-dependent NAD synthetase YHR074W gene taxon:4932 20030902 SGD
+SGD S000001116 QNS1 GO:0016811 SGD_REF:S000073884|PMID:12771147 IMP F glutamine-dependent NAD synthetase YHR074W gene taxon:4932 20030902 SGD
+SGD S000001116 QNS1 GO:0009435 SGD_REF:S000073884|PMID:12771147 IDA P glutamine-dependent NAD synthetase YHR074W gene taxon:4932 20050706 SGD
+SGD S000001116 QNS1 GO:0009435 SGD_REF:S000073884|PMID:12771147 IMP P glutamine-dependent NAD synthetase YHR074W gene taxon:4932 20050706 SGD
+SGD S000001116 QNS1 GO:0009435 SGD_REF:S000073900|PMID:12898714 IMP P glutamine-dependent NAD synthetase YHR074W gene taxon:4932 20050706 SGD
+SGD S000001116 QNS1 GO:0009435 SGD_REF:S000073900|PMID:12898714 IDA P glutamine-dependent NAD synthetase YHR074W gene taxon:4932 20050706 SGD
+SGD S000002261 QRI1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C UDP-N-acetylglucosamine pyrophosphorylase YDL103C|UAP1 gene taxon:4932 20031028 SGD
+SGD S000002261 QRI1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C UDP-N-acetylglucosamine pyrophosphorylase YDL103C|UAP1 gene taxon:4932 20031028 SGD
+SGD S000002261 QRI1 GO:0003977 SGD_REF:S000043624|PMID:9603950 IDA F UDP-N-acetylglucosamine pyrophosphorylase YDL103C|UAP1 gene taxon:4932 20021105 SGD
+SGD S000002261 QRI1 GO:0006048 SGD_REF:S000043624|PMID:9603950 IDA P UDP-N-acetylglucosamine pyrophosphorylase YDL103C|UAP1 gene taxon:4932 20021105 SGD
+SGD S000004194 QRI5 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YLR204W|COX24 gene taxon:4932 20031028 SGD
+SGD S000004194 QRI5 GO:0005554 SGD_REF:S000069584 ND F YLR204W|COX24 gene taxon:4932 20060104 SGD
+SGD S000004194 QRI5 GO:0006396 SGD_REF:S000113797|PMID:16339141 IMP P YLR204W|COX24 gene taxon:4932 20060104 SGD
+SGD S000002262 QRI7 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YDL104C gene taxon:4932 20031028 SGD
+SGD S000002262 QRI7 GO:0004222 SGD_REF:S000080056|PMID:15606766 ISS F YDL104C gene taxon:4932 20050415 SGD
+SGD S000002262 QRI7 GO:0006508 SGD_REF:S000080056|PMID:15606766 ISS P YDL104C gene taxon:4932 20050415 SGD
+SGD S000004624 QRI8 GO:0005783 SGD_REF:S000061261|PMID:11516167 TAS C ubiquitin-conjugating enzyme YMR022W|UBC7 gene taxon:4932 20021004 SGD
+SGD S000004624 QRI8 GO:0004840 SGD_REF:S000053950|PMID:9172777 IDA F ubiquitin-conjugating enzyme YMR022W|UBC7 gene taxon:4932 20051026 SGD
+SGD S000004624 QRI8 GO:0004840 SGD_REF:S000039604|PMID:1327148 ISS SGD:S000000286|SGD:S000003026|SGD:S000002584|SGD:S000002466|SGD:S000002461 F ubiquitin-conjugating enzyme YMR022W|UBC7 gene taxon:4932 20051026 SGD
+SGD S000004624 QRI8 GO:0006333 SGD_REF:S000080436|PMID:15643069 IMP P ubiquitin-conjugating enzyme YMR022W|UBC7 gene taxon:4932 20050204 SGD
+SGD S000004624 QRI8 GO:0030433 SGD_REF:S000070133|PMID:12105183 IDA P ubiquitin-conjugating enzyme YMR022W|UBC7 gene taxon:4932 20020801 SGD
+SGD S000004624 QRI8 GO:0030433 SGD_REF:S000057852|PMID:8641272 IMP P ubiquitin-conjugating enzyme YMR022W|UBC7 gene taxon:4932 20051026 SGD
+SGD S000004624 QRI8 GO:0030433 SGD_REF:S000057852|PMID:8641272 IGI SGD:S000000902|SGD:S000004370 P ubiquitin-conjugating enzyme YMR022W|UBC7 gene taxon:4932 20051026 SGD
+SGD S000005943 RAD1 GO:0000110 SGD_REF:S000070118|PMID:10915862 TAS C UV endonuclease YPL022W|LPB9 gene taxon:4932 20020710 SGD
+SGD S000005943 RAD1 GO:0000110 SGD_REF:S000053761|PMID:8621533 IPI SGD:S000004560|SGD:S000004814 C UV endonuclease YPL022W|LPB9 gene taxon:4932 20060308 SGD
+SGD S000005943 RAD1 GO:0005634 SGD_REF:S000047071|PMID:9852079 IDA C UV endonuclease YPL022W|LPB9 gene taxon:4932 20060308 SGD
+SGD S000005943 RAD1 contributes_to GO:0000014 SGD_REF:S000046088|PMID:8253764 IDA F UV endonuclease YPL022W|LPB9 gene taxon:4932 20060308 SGD
+SGD S000005943 RAD1 GO:0003677 SGD_REF:S000046088|PMID:8253764 IDA F UV endonuclease YPL022W|LPB9 gene taxon:4932 20060308 SGD
+SGD S000005943 RAD1 GO:0000710 SGD_REF:S000061201|PMID:11514439 IMP P UV endonuclease YPL022W|LPB9 gene taxon:4932 20060308 SGD
+SGD S000005943 RAD1 GO:0000735 SGD_REF:S000051157|PMID:1411547 IMP P UV endonuclease YPL022W|LPB9 gene taxon:4932 20060308 SGD
+SGD S000005943 RAD1 GO:0000735 SGD_REF:S000046045|PMID:7891718 IMP P UV endonuclease YPL022W|LPB9 gene taxon:4932 20060308 SGD
+SGD S000005943 RAD1 GO:0000736 SGD_REF:S000051157|PMID:1411547 IMP P UV endonuclease YPL022W|LPB9 gene taxon:4932 20060308 SGD
+SGD S000005943 RAD1 GO:0000736 SGD_REF:S000046045|PMID:7891718 IMP P UV endonuclease YPL022W|LPB9 gene taxon:4932 20060308 SGD
+SGD S000005943 RAD1 GO:0006296 SGD_REF:S000070118|PMID:10915862 TAS P UV endonuclease YPL022W|LPB9 gene taxon:4932 20020726 SGD
+SGD S000005943 RAD1 GO:0006296 SGD_REF:S000045969|PMID:7559571 IDA P UV endonuclease YPL022W|LPB9 gene taxon:4932 20060308 SGD
+SGD S000005943 RAD1 GO:0006312 SGD_REF:S000052152|PMID:3065620 IMP P UV endonuclease YPL022W|LPB9 gene taxon:4932 20060308 SGD
+SGD S000004560 RAD10 GO:0000110 SGD_REF:S000070118|PMID:10915862 TAS C ssDNA endonuclease YML095C gene taxon:4932 20020710 SGD
+SGD S000004560 RAD10 GO:0000110 SGD_REF:S000053761|PMID:8621533 IPI SGD:S000004814|SGD:S000005943 C ssDNA endonuclease YML095C gene taxon:4932 20060308 SGD
+SGD S000004560 RAD10 GO:0005634 SGD_REF:S000047071|PMID:9852079 IDA C ssDNA endonuclease YML095C gene taxon:4932 20060308 SGD
+SGD S000004560 RAD10 contributes_to GO:0000014 SGD_REF:S000046088|PMID:8253764 IDA F ssDNA endonuclease YML095C gene taxon:4932 20060308 SGD
+SGD S000004560 RAD10 GO:0000739 SGD_REF:S000040100|PMID:1741062 IDA F ssDNA endonuclease YML095C gene taxon:4932 20060308 SGD
+SGD S000004560 RAD10 GO:0003697 SGD_REF:S000040100|PMID:1741062 IDA F ssDNA endonuclease YML095C gene taxon:4932 20060308 SGD
+SGD S000004560 RAD10 GO:0000710 SGD_REF:S000061201|PMID:11514439 IMP P ssDNA endonuclease YML095C gene taxon:4932 20060308 SGD
+SGD S000004560 RAD10 GO:0000735 SGD_REF:S000046045|PMID:7891718 IMP P ssDNA endonuclease YML095C gene taxon:4932 20060308 SGD
+SGD S000004560 RAD10 GO:0000736 SGD_REF:S000046045|PMID:7891718 IMP P ssDNA endonuclease YML095C gene taxon:4932 20060308 SGD
+SGD S000004560 RAD10 GO:0006296 SGD_REF:S000070118|PMID:10915862 TAS P ssDNA endonuclease YML095C gene taxon:4932 20020726 SGD
+SGD S000004560 RAD10 GO:0006296 SGD_REF:S000045969|PMID:7559571 IDA P ssDNA endonuclease YML095C gene taxon:4932 20060308 SGD
+SGD S000004560 RAD10 GO:0006312 SGD_REF:S000040325|PMID:2188090 IMP P ssDNA endonuclease YML095C gene taxon:4932 20060308 SGD
+SGD S000004814 RAD14 GO:0000110 SGD_REF:S000070118|PMID:10915862 TAS C human xeroderma pigmentosum group A DNA repair gene homolog YMR201C gene taxon:4932 20020710 SGD
+SGD S000004814 RAD14 GO:0000110 SGD_REF:S000053761|PMID:8621533 IPI SGD:S000004560|SGD:S000005943 C human xeroderma pigmentosum group A DNA repair gene homolog YMR201C gene taxon:4932 20060308 SGD
+SGD S000004814 RAD14 GO:0005634 SGD_REF:S000047071|PMID:9852079 IDA C human xeroderma pigmentosum group A DNA repair gene homolog YMR201C gene taxon:4932 20060308 SGD
+SGD S000004814 RAD14 GO:0003684 SGD_REF:S000070118|PMID:10915862 TAS F human xeroderma pigmentosum group A DNA repair gene homolog YMR201C gene taxon:4932 20020710 SGD
+SGD S000004814 RAD14 GO:0003684 SGD_REF:S000051637|PMID:8516285 IDA F human xeroderma pigmentosum group A DNA repair gene homolog YMR201C gene taxon:4932 20060308 SGD
+SGD S000004814 RAD14 GO:0008270 SGD_REF:S000051637|PMID:8516285 IDA F human xeroderma pigmentosum group A DNA repair gene homolog YMR201C gene taxon:4932 20060308 SGD
+SGD S000004814 RAD14 GO:0000715 SGD_REF:S000070118|PMID:10915862 TAS P human xeroderma pigmentosum group A DNA repair gene homolog YMR201C gene taxon:4932 20020726 SGD
+SGD S000004814 RAD14 GO:0000715 SGD_REF:S000051637|PMID:8516285 IDA P human xeroderma pigmentosum group A DNA repair gene homolog YMR201C gene taxon:4932 20060308 SGD
+SGD S000000318 RAD16 GO:0000108 SGD_REF:S000047071|PMID:9852079 IDA C YBR114W|PSO5 gene taxon:4932 20010118 SGD
+SGD S000000318 RAD16 GO:0000113 SGD_REF:S000048401|PMID:9497356 IDA C YBR114W|PSO5 gene taxon:4932 20010118 SGD
+SGD S000000318 RAD16 GO:0008094 SGD_REF:S000048401|PMID:9497356 IDA F YBR114W|PSO5 gene taxon:4932 20010118 SGD
+SGD S000000318 RAD16 GO:0000715 SGD_REF:S000070118|PMID:10915862 TAS P YBR114W|PSO5 gene taxon:4932 20020726 SGD
+SGD S000000318 RAD16 GO:0000715 SGD_REF:S000077426|PMID:15177043 IMP P YBR114W|PSO5 gene taxon:4932 20051018 SGD
+SGD S000000318 RAD16 GO:0000715 SGD_REF:S000077426|PMID:15177043 IDA P YBR114W|PSO5 gene taxon:4932 20051018 SGD
+SGD S000005895 RAD17 GO:0005634 SGD_REF:S000060948|PMID:11356855 IPI SGD:S000004279|SGD:S000006115 C 3'-5'exonuclease (putative) YOR368W gene taxon:4932 20021104 SGD
+SGD S000005895 RAD17 GO:0003690 SGD_REF:S000072671|PMID:12604797 IDA F 3'-5'exonuclease (putative) YOR368W gene taxon:4932 20040929 SGD
+SGD S000005895 RAD17 GO:0000077 SGD_REF:S000054646|PMID:9564050 IMP P 3'-5'exonuclease (putative) YOR368W gene taxon:4932 20020806 SGD
+SGD S000005895 RAD17 GO:0007131 SGD_REF:S000039357|PMID:10511543 IMP P 3'-5'exonuclease (putative) YOR368W gene taxon:4932 20020806 SGD
+SGD S000000662 RAD18 GO:0000790 SGD_REF:S000042429|PMID:10880451 IDA C ATPase (putative), zinc finger protein YCR066W gene taxon:4932 20020806 SGD
+SGD S000000662 RAD18 GO:0003697 SGD_REF:S000054293|PMID:7926769 IDA F ATPase (putative), zinc finger protein YCR066W gene taxon:4932 20020806 SGD
+SGD S000000662 RAD18 GO:0004840 SGD_REF:S000051450|PMID:9287349 IDA F ATPase (putative), zinc finger protein YCR066W gene taxon:4932 20020806 SGD
+SGD S000000662 RAD18 GO:0008094 SGD_REF:S000051450|PMID:9287349 IDA F ATPase (putative), zinc finger protein YCR066W gene taxon:4932 20020806 SGD
+SGD S000000662 RAD18 GO:0006281 SGD_REF:S000055157|PMID:2540415 IMP P ATPase (putative), zinc finger protein YCR066W gene taxon:4932 20020806 SGD
+SGD S000000662 RAD18 GO:0006301 SGD_REF:S000043802|PMID:7038396 IMP P ATPase (putative), zinc finger protein YCR066W gene taxon:4932 20060508 SGD
+SGD S000003490 RAD2 GO:0000112 SGD_REF:S000070118|PMID:10915862 TAS C xeroderma pigmentosum group G (XPG) protein homolog YGR258C gene taxon:4932 20020710 SGD
+SGD S000003490 RAD2 GO:0000014 SGD_REF:S000070118|PMID:10915862 TAS F xeroderma pigmentosum group G (XPG) protein homolog YGR258C gene taxon:4932 20020710 SGD
+SGD S000003490 RAD2 GO:0006295 SGD_REF:S000070118|PMID:10915862 TAS P xeroderma pigmentosum group G (XPG) protein homolog YGR258C gene taxon:4932 20020726 SGD
+SGD S000000763 RAD23 GO:0000108 SGD_REF:S000047071|PMID:9852079 IDA C ubiquitin-like protein YEL037C gene taxon:4932 20010118 SGD
+SGD S000000763 RAD23 GO:0000111 SGD_REF:S000043066|PMID:7768886 IDA C ubiquitin-like protein YEL037C gene taxon:4932 20010118 SGD
+SGD S000000763 RAD23 GO:0000502 SGD_REF:S000076867|PMID:15117949 IPI C ubiquitin-like protein YEL037C gene taxon:4932 20041011 SGD
+SGD S000000763 RAD23 GO:0000502 SGD_REF:S000076808|PMID:15242647 IMP C ubiquitin-like protein YEL037C gene taxon:4932 20041011 SGD
+SGD S000000763 RAD23 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C ubiquitin-like protein YEL037C gene taxon:4932 20040928 SGD
+SGD S000000763 RAD23 GO:0003684 SGD_REF:S000052945|PMID:9813069 IDA F ubiquitin-like protein YEL037C gene taxon:4932 20010118 SGD
+SGD S000000763 RAD23 GO:0003684 SGD_REF:S000053544|PMID:9837874 IDA F ubiquitin-like protein YEL037C gene taxon:4932 20010118 SGD
+SGD S000000763 RAD23 GO:0030674 SGD_REF:S000080646|PMID:15121879 IPI SGD:S000001069 F ubiquitin-like protein YEL037C gene taxon:4932 20051102 SGD
+SGD S000000763 RAD23 GO:0000715 SGD_REF:S000070118|PMID:10915862 TAS P ubiquitin-like protein YEL037C gene taxon:4932 20020726 SGD
+SGD S000000763 RAD23 GO:0030433 SGD_REF:S000080877|PMID:15167887 IMP P ubiquitin-like protein YEL037C gene taxon:4932 20050310 SGD
+SGD S000000763 RAD23 GO:0042177 SGD_REF:S000069439|PMID:11804604 TAS P ubiquitin-like protein YEL037C gene taxon:4932 20030328 SGD
+SGD S000000975 RAD24 GO:0005634 SGD_REF:S000041463|PMID:10660302 IPI C cell cycle exonuclease (putative) YER173W|RS1 gene taxon:4932 20020806 SGD
+SGD S000000975 RAD24 GO:0005663 SGD_REF:S000074139|PMID:12909721 TAS C cell cycle exonuclease (putative) YER173W|RS1 gene taxon:4932 20040415 SGD
+SGD S000000975 RAD24 contributes_to GO:0003689 SGD_REF:S000072671|PMID:12604797 IDA F cell cycle exonuclease (putative) YER173W|RS1 gene taxon:4932 20030311 SGD
+SGD S000000975 RAD24 GO:0000077 SGD_REF:S000054646|PMID:9564050 IMP P cell cycle exonuclease (putative) YER173W|RS1 gene taxon:4932 20020806 SGD
+SGD S000000975 RAD24 GO:0006289 SGD_REF:S000060020|PMID:11267834 IMP P cell cycle exonuclease (putative) YER173W|RS1 gene taxon:4932 20020806 SGD
+SGD S000000975 RAD24 GO:0007131 SGD_REF:S000039357|PMID:10511543 IMP P cell cycle exonuclease (putative) YER173W|RS1 gene taxon:4932 20020806 SGD
+SGD S000003796 RAD26 GO:0005634 SGD_REF:S000045136|PMID:9566886 NAS C DNA dependent ATPase, human Cockayne syndrome B gene ERCC6 homolog YJR035W gene taxon:4932 20010118 SGD
+SGD S000003796 RAD26 GO:0008094 SGD_REF:S000044855|PMID:7957102 TAS F DNA dependent ATPase, human Cockayne syndrome B gene ERCC6 homolog YJR035W gene taxon:4932 20010118 SGD
+SGD S000003796 RAD26 GO:0006283 SGD_REF:S000044855|PMID:7957102 TAS P DNA dependent ATPase, human Cockayne syndrome B gene ERCC6 homolog YJR035W gene taxon:4932 20010118 SGD
+SGD S000003796 RAD26 GO:0006289 SGD_REF:S000044855|PMID:7957102 TAS P DNA dependent ATPase, human Cockayne syndrome B gene ERCC6 homolog YJR035W gene taxon:4932 20010118 SGD
+SGD S000001596 RAD27 GO:0005634 SGD_REF:S000043331|PMID:9671469 IMP C 42 kDa 5' to 3' exonuclease required for Okazaki fragment processing YKL113C|ERC11|FEN1|RTH1 gene taxon:4932 20021028 SGD
+SGD S000001596 RAD27 GO:0017108 SGD_REF:S000069591|PMID:11825897 IDA F 42 kDa 5' to 3' exonuclease required for Okazaki fragment processing YKL113C|ERC11|FEN1|RTH1 gene taxon:4932 20030226 SGD
+SGD S000001596 RAD27 GO:0017108 SGD_REF:S000053753|PMID:10357855 TAS F 42 kDa 5' to 3' exonuclease required for Okazaki fragment processing YKL113C|ERC11|FEN1|RTH1 gene taxon:4932 20021002 SGD
+SGD S000001596 RAD27 GO:0000731 SGD_REF:S000056091|PMID:10025407 IMP P 42 kDa 5' to 3' exonuclease required for Okazaki fragment processing YKL113C|ERC11|FEN1|RTH1 gene taxon:4932 20021101 SGD
+SGD S000001596 RAD27 GO:0001302 SGD_REF:S000074686|PMID:12024027 IMP P 42 kDa 5' to 3' exonuclease required for Okazaki fragment processing YKL113C|ERC11|FEN1|RTH1 gene taxon:4932 20031217 SGD
+SGD S000001596 RAD27 GO:0006260 SGD_REF:S000053753|PMID:10357855 TAS P 42 kDa 5' to 3' exonuclease required for Okazaki fragment processing YKL113C|ERC11|FEN1|RTH1 gene taxon:4932 20021002 SGD
+SGD S000001596 RAD27 GO:0006281 SGD_REF:S000053753|PMID:10357855 TAS P 42 kDa 5' to 3' exonuclease required for Okazaki fragment processing YKL113C|ERC11|FEN1|RTH1 gene taxon:4932 20021002 SGD
+SGD S000001596 RAD27 GO:0006303 SGD_REF:S000079665|PMID:15342630 IDA P 42 kDa 5' to 3' exonuclease required for Okazaki fragment processing YKL113C|ERC11|FEN1|RTH1 gene taxon:4932 20041122 SGD
+SGD S000002437 RAD28 GO:0005634 SGD_REF:S000049720|PMID:8830695 IC GO:0006281 C YDR030C gene taxon:4932 20021113 SGD
+SGD S000002437 RAD28 GO:0005554 SGD_REF:S000069584 ND F YDR030C gene taxon:4932 20021113 SGD
+SGD S000002437 RAD28 GO:0006281 SGD_REF:S000049720|PMID:8830695 IMP P YDR030C gene taxon:4932 20021113 SGD
+SGD S000000973 RAD3 GO:0000112 SGD_REF:S000070118|PMID:10915862 TAS C YER171W|REM1 gene taxon:4932 20020710 SGD
+SGD S000000973 RAD3 GO:0005675 SGD_REF:S000058446|PMID:9774381 TAS C YER171W|REM1 gene taxon:4932 20010118 SGD
+SGD S000000973 RAD3 GO:0005675 SGD_REF:S000075290|PMID:14500720 IDA C YER171W|REM1 gene taxon:4932 20041013 SGD
+SGD S000000973 RAD3 GO:0003678 SGD_REF:S000058446|PMID:9774381 TAS F YER171W|REM1 gene taxon:4932 20010118 SGD
+SGD S000000973 RAD3 GO:0016251 SGD_REF:S000058446|PMID:9774381 TAS F YER171W|REM1 gene taxon:4932 20010119 SGD
+SGD S000000973 RAD3 GO:0000717 SGD_REF:S000070118|PMID:10915862 TAS P YER171W|REM1 gene taxon:4932 20020726 SGD
+SGD S000000973 RAD3 GO:0006367 SGD_REF:S000056378|PMID:10384286 TAS P YER171W|REM1 gene taxon:4932 20010118 SGD
+SGD S000000973 RAD3 GO:0006367 SGD_REF:S000056377|PMID:10384273 TAS P YER171W|REM1 gene taxon:4932 20010118 SGD
+SGD S000000973 RAD3 GO:0007070 SGD_REF:S000056377|PMID:10384273 TAS P YER171W|REM1 gene taxon:4932 20010118 SGD
+SGD S000002827 RAD30 GO:0005657 SGD_REF:S000046956|PMID:9974380 IDA C DNA polymerase eta YDR419W|DBH1 gene taxon:4932 20030220 SGD
+SGD S000002827 RAD30 GO:0015999 SGD_REF:S000046956|PMID:9974380 IDA F DNA polymerase eta YDR419W|DBH1 gene taxon:4932 20030219 SGD
+SGD S000002827 RAD30 GO:0006260 SGD_REF:S000046956|PMID:9974380 IDA P DNA polymerase eta YDR419W|DBH1 gene taxon:4932 20030219 SGD
+SGD S000002827 RAD30 GO:0006281 SGD_REF:S000042179|PMID:10725365 IDA P DNA polymerase eta YDR419W|DBH1 gene taxon:4932 20030219 SGD
+SGD S000002827 RAD30 GO:0019985 SGD_REF:S000070167|PMID:12110599 IGI P DNA polymerase eta YDR419W|DBH1 gene taxon:4932 20030219 SGD
+SGD S000004472 RAD33 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YML011C gene taxon:4932 20031028 SGD
+SGD S000004472 RAD33 GO:0005554 SGD_REF:S000069584 ND F YML011C gene taxon:4932 20021126 SGD
+SGD S000004472 RAD33 GO:0000004 SGD_REF:S000069584 ND P YML011C gene taxon:4932 20021126 SGD
+SGD S000002722 RAD34 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YDR314C gene taxon:4932 20031028 SGD
+SGD S000002722 RAD34 GO:0005554 SGD_REF:S000069584 ND F YDR314C gene taxon:4932 20021126 SGD
+SGD S000002722 RAD34 GO:0000004 SGD_REF:S000069584 ND P YDR314C gene taxon:4932 20021126 SGD
+SGD S000000964 RAD4 GO:0000108 SGD_REF:S000053653|PMID:7813015 IDA C YER162C gene taxon:4932 20010118 SGD
+SGD S000000964 RAD4 GO:0000111 SGD_REF:S000043066|PMID:7768886 IDA C YER162C gene taxon:4932 20010118 SGD
+SGD S000000964 RAD4 GO:0003684 SGD_REF:S000052945|PMID:9813069 IDA F YER162C gene taxon:4932 20010118 SGD
+SGD S000000964 RAD4 GO:0003684 SGD_REF:S000053544|PMID:9837874 IDA F YER162C gene taxon:4932 20010118 SGD
+SGD S000000964 RAD4 GO:0000715 SGD_REF:S000070118|PMID:10915862 TAS P YER162C gene taxon:4932 20020726 SGD
+SGD S000004022 RAD5 GO:0000790 SGD_REF:S000042429|PMID:10880451 IDA C ATPase (putative), DNA helicase (putative) YLR032W|REV2|SNM2 gene taxon:4932 20020806 SGD
+SGD S000004022 RAD5 GO:0003697 SGD_REF:S000086919|PMID:16224103 IDA F ATPase (putative), DNA helicase (putative) YLR032W|REV2|SNM2 gene taxon:4932 20051028 SGD
+SGD S000004022 RAD5 GO:0016887 SGD_REF:S000069690|PMID:11884624 TAS F ATPase (putative), DNA helicase (putative) YLR032W|REV2|SNM2 gene taxon:4932 20030122 SGD
+SGD S000004022 RAD5 GO:0006281 SGD_REF:S000071643|PMID:12226100 IMP P ATPase (putative), DNA helicase (putative) YLR032W|REV2|SNM2 gene taxon:4932 20030122 SGD
+SGD S000004022 RAD5 GO:0006302 SGD_REF:S000086919|PMID:16224103 IGI SGD:S000002777|SGD:S000005194|SGD:S000004837 P ATPase (putative), DNA helicase (putative) YLR032W|REV2|SNM2 gene taxon:4932 20051028 SGD
+SGD S000004022 RAD5 GO:0006302 SGD_REF:S000086919|PMID:16224103 IMP P ATPase (putative), DNA helicase (putative) YLR032W|REV2|SNM2 gene taxon:4932 20051028 SGD
+SGD S000005194 RAD50 GO:0005634 SGD_REF:S000050527|PMID:9845372 IDA C Mre11-Rad50-Xrs2 protein complex member involved in joining double-stranded breaks and DNA recombination YNL250W gene taxon:4932 20030403 SGD
+SGD S000005194 RAD50 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C Mre11-Rad50-Xrs2 protein complex member involved in joining double-stranded breaks and DNA recombination YNL250W gene taxon:4932 20040928 SGD
+SGD S000005194 RAD50 GO:0030870 SGD_REF:S000050527|PMID:9845372 IPI C Mre11-Rad50-Xrs2 protein complex member involved in joining double-stranded breaks and DNA recombination YNL250W gene taxon:4932 20041024 SGD
+SGD S000005194 RAD50 GO:0003690 SGD_REF:S000041919|PMID:8367302 IDA F Mre11-Rad50-Xrs2 protein complex member involved in joining double-stranded breaks and DNA recombination YNL250W gene taxon:4932 20020925 SGD
+SGD S000005194 RAD50 GO:0003690 SGD_REF:S000041919|PMID:8367302 IPI F Mre11-Rad50-Xrs2 protein complex member involved in joining double-stranded breaks and DNA recombination YNL250W gene taxon:4932 20020925 SGD
+SGD S000005194 RAD50 GO:0005515 SGD_REF:S000050527|PMID:9845372 IPI F Mre11-Rad50-Xrs2 protein complex member involved in joining double-stranded breaks and DNA recombination YNL250W gene taxon:4932 20020925 SGD
+SGD S000005194 RAD50 GO:0016887 SGD_REF:S000071350|PMID:2162963 ISS F Mre11-Rad50-Xrs2 protein complex member involved in joining double-stranded breaks and DNA recombination YNL250W gene taxon:4932 20020925 SGD
+SGD S000005194 RAD50 GO:0016887 SGD_REF:S000080291|PMID:15546877 IDA F Mre11-Rad50-Xrs2 protein complex member involved in joining double-stranded breaks and DNA recombination YNL250W gene taxon:4932 20051014 SGD
+SGD S000005194 RAD50 GO:0042162 SGD_REF:S000080865|PMID:15721260 IDA F Mre11-Rad50-Xrs2 protein complex member involved in joining double-stranded breaks and DNA recombination YNL250W gene taxon:4932 20050712 SGD
+SGD S000005194 RAD50 GO:0000706 SGD_REF:S000069981|PMID:9334324 TAS P Mre11-Rad50-Xrs2 protein complex member involved in joining double-stranded breaks and DNA recombination YNL250W gene taxon:4932 20020708 SGD
+SGD S000005194 RAD50 GO:0000722 SGD_REF:S000060123|PMID:11238918 IMP P Mre11-Rad50-Xrs2 protein complex member involved in joining double-stranded breaks and DNA recombination YNL250W gene taxon:4932 20020925 SGD
+SGD S000005194 RAD50 GO:0000727 SGD_REF:S000060952|PMID:11459961 TAS P Mre11-Rad50-Xrs2 protein complex member involved in joining double-stranded breaks and DNA recombination YNL250W gene taxon:4932 20020925 SGD
+SGD S000005194 RAD50 GO:0006303 SGD_REF:S000073203|PMID:12399380 IMP P Mre11-Rad50-Xrs2 protein complex member involved in joining double-stranded breaks and DNA recombination YNL250W gene taxon:4932 20030528 SGD
+SGD S000005194 RAD50 GO:0042138 SGD_REF:S000069981|PMID:9334324 TAS P Mre11-Rad50-Xrs2 protein complex member involved in joining double-stranded breaks and DNA recombination YNL250W gene taxon:4932 20020708 SGD
+SGD S000000897 RAD51 GO:0000228 SGD_REF:S000060976|PMID:11459983 IDA C Rad51p colocalizes to ~ 65 spots with Dmc1p prior to synapsis (independently of ZIP1 and DMC1), and interacts with Rad52p and Rad55p; human Rad51p homolog interacts with Brca2 protein which has been implicated in causing breast cancer, RecA homolog YER095W|MUT5 gene taxon:4932 20020814 SGD
+SGD S000000897 RAD51 GO:0000228 SGD_REF:S000060976|PMID:11459983 TAS C Rad51p colocalizes to ~ 65 spots with Dmc1p prior to synapsis (independently of ZIP1 and DMC1), and interacts with Rad52p and Rad55p; human Rad51p homolog interacts with Brca2 protein which has been implicated in causing breast cancer, RecA homolog YER095W|MUT5 gene taxon:4932 20020814 SGD
+SGD S000000897 RAD51 GO:0000794 SGD_REF:S000041932|PMID:9427283 IDA C Rad51p colocalizes to ~ 65 spots with Dmc1p prior to synapsis (independently of ZIP1 and DMC1), and interacts with Rad52p and Rad55p; human Rad51p homolog interacts with Brca2 protein which has been implicated in causing breast cancer, RecA homolog YER095W|MUT5 gene taxon:4932 20030403 SGD
+SGD S000000897 RAD51 GO:0000150 SGD_REF:S000041787|PMID:8066464 IDA F Rad51p colocalizes to ~ 65 spots with Dmc1p prior to synapsis (independently of ZIP1 and DMC1), and interacts with Rad52p and Rad55p; human Rad51p homolog interacts with Brca2 protein which has been implicated in causing breast cancer, RecA homolog YER095W|MUT5 gene taxon:4932 20020814 SGD
+SGD S000000897 RAD51 GO:0000709 SGD_REF:S000047548|PMID:1581961 IMP P Rad51p colocalizes to ~ 65 spots with Dmc1p prior to synapsis (independently of ZIP1 and DMC1), and interacts with Rad52p and Rad55p; human Rad51p homolog interacts with Brca2 protein which has been implicated in causing breast cancer, RecA homolog YER095W|MUT5 gene taxon:4932 20020814 SGD
+SGD S000000897 RAD51 GO:0000722 SGD_REF:S000060123|PMID:11238918 IMP P Rad51p colocalizes to ~ 65 spots with Dmc1p prior to synapsis (independently of ZIP1 and DMC1), and interacts with Rad52p and Rad55p; human Rad51p homolog interacts with Brca2 protein which has been implicated in causing breast cancer, RecA homolog YER095W|MUT5 gene taxon:4932 20020925 SGD
+SGD S000000897 RAD51 GO:0030491 SGD_REF:S000042882|PMID:10506208 IDA P Rad51p colocalizes to ~ 65 spots with Dmc1p prior to synapsis (independently of ZIP1 and DMC1), and interacts with Rad52p and Rad55p; human Rad51p homolog interacts with Brca2 protein which has been implicated in causing breast cancer, RecA homolog YER095W|MUT5 gene taxon:4932 20020925 SGD
+SGD S000000897 RAD51 GO:0042148 SGD_REF:S000048467|PMID:9632377 TAS P Rad51p colocalizes to ~ 65 spots with Dmc1p prior to synapsis (independently of ZIP1 and DMC1), and interacts with Rad52p and Rad55p; human Rad51p homolog interacts with Brca2 protein which has been implicated in causing breast cancer, RecA homolog YER095W|MUT5 gene taxon:4932 20020925 SGD
+SGD S000000897 RAD51 NOT GO:0045002 SGD_REF:S000051939|PMID:8849880 IMP P Rad51p colocalizes to ~ 65 spots with Dmc1p prior to synapsis (independently of ZIP1 and DMC1), and interacts with Rad52p and Rad55p; human Rad51p homolog interacts with Brca2 protein which has been implicated in causing breast cancer, RecA homolog YER095W|MUT5 gene taxon:4932 20020925 SGD
+SGD S000000897 RAD51 GO:0045003 SGD_REF:S000053753|PMID:10357855 TAS P Rad51p colocalizes to ~ 65 spots with Dmc1p prior to synapsis (independently of ZIP1 and DMC1), and interacts with Rad52p and Rad55p; human Rad51p homolog interacts with Brca2 protein which has been implicated in causing breast cancer, RecA homolog YER095W|MUT5 gene taxon:4932 20020814 SGD
+SGD S000004494 RAD52 GO:0000228 SGD_REF:S000073586|PMID:12766777 IDA C YML032C gene taxon:4932 20030710 SGD
+SGD S000004494 RAD52 GO:0005634 SGD_REF:S000060954|PMID:11459964 IDA C YML032C gene taxon:4932 20020905 SGD
+SGD S000004494 RAD52 GO:0000150 SGD_REF:S000076544|PMID:15205482 IDA F YML032C gene taxon:4932 20041008 SGD
+SGD S000004494 RAD52 GO:0000739 SGD_REF:S000055236|PMID:9619627 IDA F YML032C gene taxon:4932 20020925 SGD
+SGD S000004494 RAD52 GO:0000707 SGD_REF:S000060976|PMID:11459983 TAS P YML032C gene taxon:4932 20020708 SGD
+SGD S000004494 RAD52 GO:0000722 SGD_REF:S000060123|PMID:11238918 IMP P YML032C gene taxon:4932 20020925 SGD
+SGD S000004494 RAD52 GO:0000727 SGD_REF:S000060952|PMID:11459961 TAS P YML032C gene taxon:4932 20020925 SGD
+SGD S000004494 RAD52 GO:0000730 SGD_REF:S000060976|PMID:11459983 IDA P YML032C gene taxon:4932 20020925 SGD
+SGD S000004494 RAD52 GO:0000730 SGD_REF:S000060976|PMID:11459983 TAS P YML032C gene taxon:4932 20020925 SGD
+SGD S000004494 RAD52 GO:0006301 SGD_REF:S000043802|PMID:7038396 IMP P YML032C gene taxon:4932 20060508 SGD
+SGD S000004494 RAD52 GO:0045002 SGD_REF:S000069022|PMID:11606529 IGI P YML032C gene taxon:4932 20020925 SGD
+SGD S000004494 RAD52 GO:0045003 SGD_REF:S000053753|PMID:10357855 TAS P YML032C gene taxon:4932 20020814 SGD
+SGD S000006074 RAD53 GO:0005634 SGD_REF:S000054998|PMID:8355715 IDA C protein kinase YPL153C|LSD1|MEC2|SPK1 gene taxon:4932 20011101 SGD
+SGD S000006074 RAD53 GO:0004712 SGD_REF:S000054998|PMID:8355715 IDA F protein kinase YPL153C|LSD1|MEC2|SPK1 gene taxon:4932 20011101 SGD
+SGD S000006074 RAD53 GO:0006139 SGD_REF:S000046108|PMID:9744871 IGI P protein kinase YPL153C|LSD1|MEC2|SPK1 gene taxon:4932 20011101 SGD
+SGD S000006074 RAD53 GO:0006281 SGD_REF:S000054998|PMID:8355715 IMP P protein kinase YPL153C|LSD1|MEC2|SPK1 gene taxon:4932 20011101 SGD
+SGD S000003131 RAD54 GO:0005634 SGD_REF:S000071548|PMID:12399378 IMP C YGL163C|XRS1 gene taxon:4932 20021115 SGD
+SGD S000003131 RAD54 GO:0003916 SGD_REF:S000042882|PMID:10506208 IDA F YGL163C|XRS1 gene taxon:4932 20040917 SGD
+SGD S000003131 RAD54 GO:0008094 SGD_REF:S000042882|PMID:10506208 IDA F YGL163C|XRS1 gene taxon:4932 20020814 SGD
+SGD S000003131 RAD54 GO:0000722 SGD_REF:S000060123|PMID:11238918 IMP P YGL163C|XRS1 gene taxon:4932 20020925 SGD
+SGD S000003131 RAD54 GO:0006338 SGD_REF:S000072870|PMID:12577053 IDA P YGL163C|XRS1 gene taxon:4932 20030606 SGD
+SGD S000003131 RAD54 GO:0030491 SGD_REF:S000042882|PMID:10506208 IDA P YGL163C|XRS1 gene taxon:4932 20020925 SGD
+SGD S000003131 RAD54 NOT GO:0045002 SGD_REF:S000051939|PMID:8849880 IMP P YGL163C|XRS1 gene taxon:4932 20020925 SGD
+SGD S000003131 RAD54 GO:0045003 SGD_REF:S000053753|PMID:10357855 TAS P YGL163C|XRS1 gene taxon:4932 20020814 SGD
+SGD S000002483 RAD55 GO:0005634 SGD_REF:S000041926|PMID:10943844 IPI C RecA homolog, interacts with Rad51p and Rad57p by two-hybrid analysis, similar to DMC1, RAD51, RAD57 YDR076W gene taxon:4932 20021002 SGD
+SGD S000002483 RAD55 GO:0005515 SGD_REF:S000039618|PMID:9159392 IPI F RecA homolog, interacts with Rad51p and Rad57p by two-hybrid analysis, similar to DMC1, RAD51, RAD57 YDR076W gene taxon:4932 20020925 SGD
+SGD S000002483 RAD55 GO:0000707 SGD_REF:S000060976|PMID:11459983 TAS P RecA homolog, interacts with Rad51p and Rad57p by two-hybrid analysis, similar to DMC1, RAD51, RAD57 YDR076W gene taxon:4932 20020708 SGD
+SGD S000002483 RAD55 GO:0000730 SGD_REF:S000060976|PMID:11459983 IDA P RecA homolog, interacts with Rad51p and Rad57p by two-hybrid analysis, similar to DMC1, RAD51, RAD57 YDR076W gene taxon:4932 20020925 SGD
+SGD S000002483 RAD55 GO:0000730 SGD_REF:S000060976|PMID:11459983 TAS P RecA homolog, interacts with Rad51p and Rad57p by two-hybrid analysis, similar to DMC1, RAD51, RAD57 YDR076W gene taxon:4932 20020925 SGD
+SGD S000002483 RAD55 NOT GO:0045002 SGD_REF:S000051939|PMID:8849880 IMP P RecA homolog, interacts with Rad51p and Rad57p by two-hybrid analysis, similar to DMC1, RAD51, RAD57 YDR076W gene taxon:4932 20020925 SGD
+SGD S000002483 RAD55 GO:0045003 SGD_REF:S000053753|PMID:10357855 TAS P RecA homolog, interacts with Rad51p and Rad57p by two-hybrid analysis, similar to DMC1, RAD51, RAD57 YDR076W gene taxon:4932 20020925 SGD
+SGD S000002411 RAD57 GO:0005634 SGD_REF:S000041926|PMID:10943844 IPI C RecA homolog, interacts with Rad 55p by two-hybrid analysis, similar to DMC1, RAD51, and RAD55 YDR004W gene taxon:4932 20021002 SGD
+SGD S000002411 RAD57 GO:0005515 SGD_REF:S000039618|PMID:9159392 IPI F RecA homolog, interacts with Rad 55p by two-hybrid analysis, similar to DMC1, RAD51, and RAD55 YDR004W gene taxon:4932 20020925 SGD
+SGD S000002411 RAD57 GO:0000707 SGD_REF:S000060976|PMID:11459983 TAS P RecA homolog, interacts with Rad 55p by two-hybrid analysis, similar to DMC1, RAD51, and RAD55 YDR004W gene taxon:4932 20020708 SGD
+SGD S000002411 RAD57 GO:0000722 SGD_REF:S000060123|PMID:11238918 IMP P RecA homolog, interacts with Rad 55p by two-hybrid analysis, similar to DMC1, RAD51, and RAD55 YDR004W gene taxon:4932 20020925 SGD
+SGD S000002411 RAD57 GO:0000730 SGD_REF:S000060976|PMID:11459983 IDA P RecA homolog, interacts with Rad 55p by two-hybrid analysis, similar to DMC1, RAD51, and RAD55 YDR004W gene taxon:4932 20020925 SGD
+SGD S000002411 RAD57 GO:0000730 SGD_REF:S000060976|PMID:11459983 TAS P RecA homolog, interacts with Rad 55p by two-hybrid analysis, similar to DMC1, RAD51, and RAD55 YDR004W gene taxon:4932 20020925 SGD
+SGD S000002411 RAD57 NOT GO:0045002 SGD_REF:S000051939|PMID:8849880 IMP P RecA homolog, interacts with Rad 55p by two-hybrid analysis, similar to DMC1, RAD51, and RAD55 YDR004W gene taxon:4932 20020925 SGD
+SGD S000002411 RAD57 GO:0045003 SGD_REF:S000053753|PMID:10357855 TAS P RecA homolog, interacts with Rad 55p by two-hybrid analysis, similar to DMC1, RAD51, and RAD55 YDR004W gene taxon:4932 20020814 SGD
+SGD S000002217 RAD59 GO:0005634 SGD_REF:S000071478|PMID:12368472 IGI C the RAD59 gene product has homology to the Rad52 protein YDL059C gene taxon:4932 20021028 SGD
+SGD S000002217 RAD59 GO:0000739 SGD_REF:S000047792|PMID:10567339 IDA F the RAD59 gene product has homology to the Rad52 protein YDL059C gene taxon:4932 20020925 SGD
+SGD S000002217 RAD59 GO:0005515 SGD_REF:S000073225|PMID:10655498 IPI SGD:S000001835 F the RAD59 gene product has homology to the Rad52 protein YDL059C gene taxon:4932 20030602 SGD
+SGD S000002217 RAD59 GO:0000722 SGD_REF:S000060123|PMID:11238918 IMP P the RAD59 gene product has homology to the Rad52 protein YDL059C gene taxon:4932 20020925 SGD
+SGD S000002217 RAD59 GO:0000727 SGD_REF:S000060952|PMID:11459961 TAS P the RAD59 gene product has homology to the Rad52 protein YDL059C gene taxon:4932 20020925 SGD
+SGD S000002217 RAD59 GO:0045002 SGD_REF:S000069022|PMID:11606529 IGI P the RAD59 gene product has homology to the Rad52 protein YDL059C gene taxon:4932 20020925 SGD
+SGD S000003026 RAD6 GO:0000502 SGD_REF:S000064672|PMID:10848595 IPI C ubiquitin-conjugating enzyme YGL058W|UBC2 gene taxon:4932 20030520 SGD
+SGD S000003026 RAD6 GO:0005634 SGD_REF:S000054293|PMID:7926769 IPI C ubiquitin-conjugating enzyme YGL058W|UBC2 gene taxon:4932 20010118 SGD
+SGD S000003026 RAD6 GO:0005634 SGD_REF:S000042429|PMID:10880451 IDA C ubiquitin-conjugating enzyme YGL058W|UBC2 gene taxon:4932 20020806 SGD
+SGD S000003026 RAD6 GO:0005737 SGD_REF:S000042429|PMID:10880451 IDA C ubiquitin-conjugating enzyme YGL058W|UBC2 gene taxon:4932 20020806 SGD
+SGD S000003026 RAD6 GO:0004840 SGD_REF:S000047033|PMID:2157209 IMP F ubiquitin-conjugating enzyme YGL058W|UBC2 gene taxon:4932 20010118 SGD
+SGD S000003026 RAD6 GO:0004840 SGD_REF:S000056659|PMID:1848239 IDA F ubiquitin-conjugating enzyme YGL058W|UBC2 gene taxon:4932 20051028 SGD
+SGD S000003026 RAD6 GO:0004840 SGD_REF:S000049161|PMID:3306404 IDA F ubiquitin-conjugating enzyme YGL058W|UBC2 gene taxon:4932 20051028 SGD
+SGD S000003026 RAD6 GO:0004840 SGD_REF:S000051450|PMID:9287349 IDA F ubiquitin-conjugating enzyme YGL058W|UBC2 gene taxon:4932 20020806 SGD
+SGD S000003026 RAD6 GO:0006281 SGD_REF:S000040155|PMID:8031302 TAS P ubiquitin-conjugating enzyme YGL058W|UBC2 gene taxon:4932 20010118 SGD
+SGD S000003026 RAD6 GO:0006301 SGD_REF:S000043802|PMID:7038396 IMP P ubiquitin-conjugating enzyme YGL058W|UBC2 gene taxon:4932 20060508 SGD
+SGD S000003026 RAD6 GO:0006511 SGD_REF:S000047033|PMID:2157209 IMP P ubiquitin-conjugating enzyme YGL058W|UBC2 gene taxon:4932 20010118 SGD
+SGD S000003026 RAD6 GO:0006513 SGD_REF:S000072664|PMID:12535538 IMP P ubiquitin-conjugating enzyme YGL058W|UBC2 gene taxon:4932 20030307 SGD
+SGD S000003026 RAD6 GO:0016574 SGD_REF:S000072664|PMID:12535538 IMP P ubiquitin-conjugating enzyme YGL058W|UBC2 gene taxon:4932 20030307 SGD
+SGD S000003026 RAD6 GO:0016574 SGD_REF:S000049161|PMID:3306404 IDA P ubiquitin-conjugating enzyme YGL058W|UBC2 gene taxon:4932 20051028 SGD
+SGD S000003026 RAD6 GO:0016574 SGD_REF:S000056659|PMID:1848239 IDA P ubiquitin-conjugating enzyme YGL058W|UBC2 gene taxon:4932 20051028 SGD
+SGD S000002421 RAD61 GO:0005634 SGD_REF:S000073736|PMID:12816519 ISS C YDR014W gene taxon:4932 20030808 SGD
+SGD S000002421 RAD61 GO:0005554 SGD_REF:S000069584 ND F YDR014W gene taxon:4932 20030808 SGD
+SGD S000002421 RAD61 GO:0009314 SGD_REF:S000073736|PMID:12816519 IMP P YDR014W gene taxon:4932 20030808 SGD
+SGD S000003813 RAD7 GO:0000108 SGD_REF:S000047071|PMID:9852079 IDA C nucleotide excision NEF4 component YJR052W gene taxon:4932 20010118 SGD
+SGD S000003813 RAD7 GO:0000113 SGD_REF:S000048401|PMID:9497356 IDA C nucleotide excision NEF4 component YJR052W gene taxon:4932 20010118 SGD
+SGD S000003813 RAD7 GO:0003677 SGD_REF:S000050677|PMID:10446201 IDA F nucleotide excision NEF4 component YJR052W gene taxon:4932 20010118 SGD
+SGD S000003813 RAD7 GO:0008094 SGD_REF:S000048401|PMID:9497356 IDA F nucleotide excision NEF4 component YJR052W gene taxon:4932 20010118 SGD
+SGD S000003813 RAD7 GO:0000715 SGD_REF:S000070118|PMID:10915862 TAS P nucleotide excision NEF4 component YJR052W gene taxon:4932 20020726 SGD
+SGD S000003813 RAD7 GO:0000715 SGD_REF:S000077426|PMID:15177043 IDA P nucleotide excision NEF4 component YJR052W gene taxon:4932 20051018 SGD
+SGD S000003813 RAD7 GO:0000715 SGD_REF:S000077426|PMID:15177043 IMP P nucleotide excision NEF4 component YJR052W gene taxon:4932 20051018 SGD
+SGD S000002625 RAD9 GO:0005634 SGD_REF:S000039557|PMID:2664461 IC GO:0006281 C cell cycle arrest protein YDR217C gene taxon:4932 20021210 SGD
+SGD S000002625 RAD9 GO:0005515 SGD_REF:S000069936|PMID:12049741 IDA F cell cycle arrest protein YDR217C gene taxon:4932 20021210 SGD
+SGD S000002625 RAD9 GO:0000074 SGD_REF:S000039557|PMID:2664461 IMP P cell cycle arrest protein YDR217C gene taxon:4932 20010118 SGD
+SGD S000002625 RAD9 GO:0000074 SGD_REF:S000039557|PMID:2664461 IGI P cell cycle arrest protein YDR217C gene taxon:4932 20010118 SGD
+SGD S000002625 RAD9 GO:0000077 SGD_REF:S000054646|PMID:9564050 IMP P cell cycle arrest protein YDR217C gene taxon:4932 20020806 SGD
+SGD S000002625 RAD9 GO:0006281 SGD_REF:S000039557|PMID:2664461 IMP P cell cycle arrest protein YDR217C gene taxon:4932 20010118 SGD
+SGD S000002625 RAD9 GO:0006281 SGD_REF:S000039557|PMID:2664461 IGI P cell cycle arrest protein YDR217C gene taxon:4932 20010118 SGD
+SGD S000002625 RAD9 GO:0006289 SGD_REF:S000060020|PMID:11267834 IMP P cell cycle arrest protein YDR217C gene taxon:4932 20020806 SGD
+SGD S000002625 RAD9 GO:0045944 SGD_REF:S000053208|PMID:8670896 IMP P cell cycle arrest protein YDR217C gene taxon:4932 20030626 SGD
+SGD S000029674 RAF1 GO:0008372 SGD_REF:S000069584 ND C 2-micron circle protein D gene taxon:4932 20020717 SGD
+SGD S000029674 RAF1 GO:0005554 SGD_REF:S000069584 ND F 2-micron circle protein D gene taxon:4932 20020717 SGD
+SGD S000029674 RAF1 GO:0006276 SGD_REF:S000055748|PMID:9393716 TAS P 2-micron circle protein D gene taxon:4932 20020717 SGD
+SGD S000029406 RAH1 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20020523 SGD
+SGD S000029406 RAH1 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20020523 SGD
+SGD S000029406 RAH1 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20020523 SGD
+SGD S000029407 RAH2 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20020523 SGD
+SGD S000029407 RAH2 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20020523 SGD
+SGD S000029407 RAH2 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20020523 SGD
+SGD S000029408 RAH3 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20020523 SGD
+SGD S000029408 RAH3 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20020523 SGD
+SGD S000029408 RAH3 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20020523 SGD
+SGD S000003215 RAI1 GO:0005634 SGD_REF:S000043334|PMID:10805743 IPI C YGL246C gene taxon:4932 20021018 SGD
+SGD S000003215 RAI1 GO:0005634 SGD_REF:S000072983|PMID:12612077 IDA C YGL246C gene taxon:4932 20030421 SGD
+SGD S000003215 RAI1 GO:0030234 SGD_REF:S000043334|PMID:10805743 IDA F YGL246C gene taxon:4932 20021018 SGD
+SGD S000003215 RAI1 GO:0030489 SGD_REF:S000043334|PMID:10805743 IMP P YGL246C gene taxon:4932 20021018 SGD
+SGD S000003215 RAI1 GO:0030846 SGD_REF:S000080022|PMID:15565157 IMP P YGL246C gene taxon:4932 20050718 SGD
+SGD S000002248 RAM1 GO:0005965 SGD_REF:S000048882|PMID:8424764 IDA C farnesyltransferase beta subunit YDL090C|DPR1|FUS8|SCG2|SGP2|STE16 gene taxon:4932 20020712 SGD
+SGD S000002248 RAM1 GO:0004660 SGD_REF:S000047476|PMID:9380709 IDA F farnesyltransferase beta subunit YDL090C|DPR1|FUS8|SCG2|SGP2|STE16 gene taxon:4932 20020712 SGD
+SGD S000002248 RAM1 GO:0018347 SGD_REF:S000043701|PMID:7565716 IDA P farnesyltransferase beta subunit YDL090C|DPR1|FUS8|SCG2|SGP2|STE16 gene taxon:4932 20030324 SGD
+SGD S000002248 RAM1 GO:0018347 SGD_REF:S000050062|PMID:1763050 IDA P farnesyltransferase beta subunit YDL090C|DPR1|FUS8|SCG2|SGP2|STE16 gene taxon:4932 20020712 SGD
+SGD S000001502 RAM2 GO:0005953 SGD_REF:S000044942|PMID:1400380 IDA C CAAX farnesyltransferase alpha subunit YKL019W gene taxon:4932 20050404 SGD
+SGD S000001502 RAM2 GO:0005965 SGD_REF:S000050062|PMID:1763050 IDA C CAAX farnesyltransferase alpha subunit YKL019W gene taxon:4932 20021210 SGD
+SGD S000001502 RAM2 GO:0004660 SGD_REF:S000050062|PMID:1763050 IDA F CAAX farnesyltransferase alpha subunit YKL019W gene taxon:4932 20010118 SGD
+SGD S000001502 RAM2 GO:0004661 SGD_REF:S000049697|PMID:2034682 IDA F CAAX farnesyltransferase alpha subunit YKL019W gene taxon:4932 20030324 SGD
+SGD S000001502 RAM2 GO:0004662 SGD_REF:S000044942|PMID:1400380 IDA F CAAX farnesyltransferase alpha subunit YKL019W gene taxon:4932 20051228 SGD
+SGD S000001502 RAM2 GO:0007323 SGD_REF:S000050062|PMID:1763050 IDA P CAAX farnesyltransferase alpha subunit YKL019W gene taxon:4932 20010118 SGD
+SGD S000001502 RAM2 GO:0018347 SGD_REF:S000043701|PMID:7565716 IDA P CAAX farnesyltransferase alpha subunit YKL019W gene taxon:4932 20030324 SGD
+SGD S000001502 RAM2 GO:0018348 SGD_REF:S000049697|PMID:2034682 IDA P CAAX farnesyltransferase alpha subunit YKL019W gene taxon:4932 20030324 SGD
+SGD S000005160 RAP1 GO:0000783 SGD_REF:S000045567|PMID:9710643 IDA C repressor activator protein YNL216W|GRF1|TBA1|TUF1 gene taxon:4932 20030403 SGD
+SGD S000005160 RAP1 GO:0005634 SGD_REF:S000048216|PMID:7809947 TAS C repressor activator protein YNL216W|GRF1|TBA1|TUF1 gene taxon:4932 20010118 SGD
+SGD S000005160 RAP1 GO:0005724 SGD_REF:S000070058|PMID:12080091 TAS C repressor activator protein YNL216W|GRF1|TBA1|TUF1 gene taxon:4932 20021101 SGD
+SGD S000005160 RAP1 GO:0003677 SGD_REF:S000061169|PMID:11455386 IDA F repressor activator protein YNL216W|GRF1|TBA1|TUF1 gene taxon:4932 20030117 SGD
+SGD S000005160 RAP1 GO:0003677 SGD_REF:S000050312|PMID:3275867 IDA F repressor activator protein YNL216W|GRF1|TBA1|TUF1 gene taxon:4932 20030117 SGD
+SGD S000005160 RAP1 GO:0003700 SGD_REF:S000048216|PMID:7809947 TAS F repressor activator protein YNL216W|GRF1|TBA1|TUF1 gene taxon:4932 20010118 SGD
+SGD S000005160 RAP1 GO:0006342 SGD_REF:S000046588|PMID:1881914 IMP P repressor activator protein YNL216W|GRF1|TBA1|TUF1 gene taxon:4932 20010118 SGD
+SGD S000005160 RAP1 GO:0006348 SGD_REF:S000072020|PMID:12417731 IMP P repressor activator protein YNL216W|GRF1|TBA1|TUF1 gene taxon:4932 20030113 SGD
+SGD S000005160 RAP1 GO:0006383 SGD_REF:S000050210|PMID:2010087 IMP P repressor activator protein YNL216W|GRF1|TBA1|TUF1 gene taxon:4932 20010118 SGD
+SGD S000005160 RAP1 GO:0007004 SGD_REF:S000046588|PMID:1881914 IMP P repressor activator protein YNL216W|GRF1|TBA1|TUF1 gene taxon:4932 20010118 SGD
+SGD S000005160 RAP1 GO:0031848 SGD_REF:S000086126|PMID:16096640 IMP P repressor activator protein YNL216W|GRF1|TBA1|TUF1 gene taxon:4932 20051020 SGD
+SGD S000005627 RAS1 GO:0005886 SGD_REF:S000039463|PMID:3513173 IDA C ras homolog YOR101W gene taxon:4932 20010118 SGD
+SGD S000005627 RAS1 GO:0003924 SGD_REF:S000045204|PMID:6327067 IMP F ras homolog YOR101W gene taxon:4932 20010118 SGD
+SGD S000005627 RAS1 GO:0007189 SGD_REF:S000044051|PMID:3891097 IDA P ras homolog YOR101W gene taxon:4932 20010118 SGD
+SGD S000005627 RAS1 GO:0007265 SGD_REF:S000044051|PMID:3891097 TAS P ras homolog YOR101W gene taxon:4932 20010118 SGD
+SGD S000005627 RAS1 GO:0008283 SGD_REF:S000045204|PMID:6327067 IMP P ras homolog YOR101W gene taxon:4932 20010118 SGD
+SGD S000005042 RAS2 GO:0005886 SGD_REF:S000058484|PMID:7708760 TAS C small GTP-binding protein YNL098C|CTN5|CYR3|GLC5|TSL7 gene taxon:4932 20010118 SGD
+SGD S000005042 RAS2 GO:0005886 SGD_REF:S000069459|PMID:11914276 IDA C small GTP-binding protein YNL098C|CTN5|CYR3|GLC5|TSL7 gene taxon:4932 20020508 SGD
+SGD S000005042 RAS2 GO:0003924 SGD_REF:S000058484|PMID:7708760 TAS F small GTP-binding protein YNL098C|CTN5|CYR3|GLC5|TSL7 gene taxon:4932 20010118 SGD
+SGD S000005042 RAS2 GO:0001302 SGD_REF:S000073789|PMID:12839995 IMP P small GTP-binding protein YNL098C|CTN5|CYR3|GLC5|TSL7 gene taxon:4932 20030827 SGD
+SGD S000005042 RAS2 GO:0007124 SGD_REF:S000041853|PMID:1547504 IMP P small GTP-binding protein YNL098C|CTN5|CYR3|GLC5|TSL7 gene taxon:4932 20010118 SGD
+SGD S000005042 RAS2 GO:0007190 SGD_REF:S000044051|PMID:3891097 TAS P small GTP-binding protein YNL098C|CTN5|CYR3|GLC5|TSL7 gene taxon:4932 20010118 SGD
+SGD S000005042 RAS2 GO:0007265 SGD_REF:S000044051|PMID:3891097 TAS P small GTP-binding protein YNL098C|CTN5|CYR3|GLC5|TSL7 gene taxon:4932 20010118 SGD
+SGD S000005042 RAS2 GO:0030437 SGD_REF:S000040191|PMID:2558958 IMP P small GTP-binding protein YNL098C|CTN5|CYR3|GLC5|TSL7 gene taxon:4932 20010118 SGD
+SGD S000005574 RAT1 GO:0005634 SGD_REF:S000049466|PMID:9315672 IDA C 5'-3' exoribonuclease YOR048C|HKE1|TAP1|XRN2 gene taxon:4932 20010118 SGD
+SGD S000005574 RAT1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C 5'-3' exoribonuclease YOR048C|HKE1|TAP1|XRN2 gene taxon:4932 20040928 SGD
+SGD S000005574 RAT1 GO:0004534 SGD_REF:S000048250|PMID:8417335 IDA F 5'-3' exoribonuclease YOR048C|HKE1|TAP1|XRN2 gene taxon:4932 20010118 SGD
+SGD S000005574 RAT1 GO:0006365 SGD_REF:S000059142|PMID:11142370 IMP P 5'-3' exoribonuclease YOR048C|HKE1|TAP1|XRN2 gene taxon:4932 20030210 SGD
+SGD S000005574 RAT1 GO:0006396 SGD_REF:S000047392|PMID:9488433 IMP P 5'-3' exoribonuclease YOR048C|HKE1|TAP1|XRN2 gene taxon:4932 20010118 SGD
+SGD S000005574 RAT1 GO:0030846 SGD_REF:S000080022|PMID:15565157 IMP P 5'-3' exoribonuclease YOR048C|HKE1|TAP1|XRN2 gene taxon:4932 20050208 SGD
+SGD S000003794 RAV1 GO:0005737 SGD_REF:S000060747|PMID:11283612 IDA C YJR033C|SOI3 gene taxon:4932 20020930 SGD
+SGD S000003794 RAV1 GO:0019898 SGD_REF:S000079674|PMID:15090613 IDA C YJR033C|SOI3 gene taxon:4932 20041129 SGD
+SGD S000003794 RAV1 GO:0043291 SGD_REF:S000060747|PMID:11283612 IPI SGD:S000002610|SGD:S000002736 C YJR033C|SOI3 gene taxon:4932 20041216 SGD
+SGD S000003794 RAV1 GO:0043291 SGD_REF:S000079675|PMID:11844802 IPI SGD:S000002736 C YJR033C|SOI3 gene taxon:4932 20050103 SGD
+SGD S000003794 RAV1 GO:0005554 SGD_REF:S000069584 ND F YJR033C|SOI3 gene taxon:4932 20041129 SGD
+SGD S000003794 RAV1 GO:0007035 SGD_REF:S000060747|PMID:11283612 IGI SGD:S000002610 P YJR033C|SOI3 gene taxon:4932 20050527 SGD
+SGD S000003794 RAV1 GO:0007035 SGD_REF:S000060747|PMID:11283612 IMP P YJR033C|SOI3 gene taxon:4932 20050527 SGD
+SGD S000003794 RAV1 GO:0007035 SGD_REF:S000079675|PMID:11844802 IGI SGD:S000002610 P YJR033C|SOI3 gene taxon:4932 20050527 SGD
+SGD S000003794 RAV1 GO:0007035 SGD_REF:S000079675|PMID:11844802 IMP P YJR033C|SOI3 gene taxon:4932 20050527 SGD
+SGD S000003794 RAV1 GO:0043254 SGD_REF:S000060747|PMID:11283612 IMP P YJR033C|SOI3 gene taxon:4932 20050527 SGD
+SGD S000003794 RAV1 GO:0043254 SGD_REF:S000079675|PMID:11844802 IMP P YJR033C|SOI3 gene taxon:4932 20050527 SGD
+SGD S000003794 RAV1 GO:0043254 SGD_REF:S000079675|PMID:11844802 IGI SGD:S000002610|SGD:S000006155 P YJR033C|SOI3 gene taxon:4932 20050527 SGD
+SGD S000003794 RAV1 GO:0043254 SGD_REF:S000060747|PMID:11283612 IPI SGD:S000000331|SGD:S000002610|SGD:S000002736|SGD:S000005859|SGD:S000002344 P YJR033C|SOI3 gene taxon:4932 20050527 SGD
+SGD S000003794 RAV1 GO:0045022 SGD_REF:S000079674|PMID:15090613 IGI P YJR033C|SOI3 gene taxon:4932 20041129 SGD
+SGD S000003794 RAV1 GO:0045022 SGD_REF:S000079674|PMID:15090613 IMP P YJR033C|SOI3 gene taxon:4932 20041129 SGD
+SGD S000002610 RAV2 GO:0043291 SGD_REF:S000060747|PMID:11283612 IPI SGD:S000002736|SGD:S000003794 C YDR202C gene taxon:4932 20041216 SGD
+SGD S000002610 RAV2 GO:0005554 SGD_REF:S000069584 ND F YDR202C gene taxon:4932 20020930 SGD
+SGD S000002610 RAV2 GO:0007035 SGD_REF:S000060747|PMID:11283612 IGI SGD:S000003794 P YDR202C gene taxon:4932 20051025 SGD
+SGD S000002610 RAV2 GO:0007035 SGD_REF:S000079675|PMID:11844802 IMP P YDR202C gene taxon:4932 20051025 SGD
+SGD S000002610 RAV2 GO:0007035 SGD_REF:S000060747|PMID:11283612 IMP P YDR202C gene taxon:4932 20051025 SGD
+SGD S000002610 RAV2 GO:0007035 SGD_REF:S000079675|PMID:11844802 IGI SGD:S000003794 P YDR202C gene taxon:4932 20051025 SGD
+SGD S000002610 RAV2 GO:0043254 SGD_REF:S000060747|PMID:11283612 IPI SGD:S000002736|SGD:S000003794 P YDR202C gene taxon:4932 20051025 SGD
+SGD S000002610 RAV2 GO:0043254 SGD_REF:S000079675|PMID:11844802 IMP P YDR202C gene taxon:4932 20051025 SGD
+SGD S000002610 RAV2 GO:0043254 SGD_REF:S000060747|PMID:11283612 IGI SGD:S000003794 P YDR202C gene taxon:4932 20051025 SGD
+SGD S000002610 RAV2 GO:0043254 SGD_REF:S000079675|PMID:11844802 IGI SGD:S000003794 P YDR202C gene taxon:4932 20051025 SGD
+SGD S000005827 RAX1 GO:0005935 SGD_REF:S000075503|PMID:14980713 IDA C YOR301W gene taxon:4932 20040712 SGD
+SGD S000005827 RAX1 GO:0005935 SGD_REF:S000079777|PMID:15356260 IDA C YOR301W gene taxon:4932 20041209 SGD
+SGD S000005827 RAX1 GO:0016021 SGD_REF:S000079777|PMID:15356260 ISS C YOR301W gene taxon:4932 20050208 SGD
+SGD S000005827 RAX1 GO:0005554 SGD_REF:S000069584 ND F YOR301W gene taxon:4932 20020930 SGD
+SGD S000005827 RAX1 GO:0000282 SGD_REF:S000060270|PMID:11110666 IGI P YOR301W gene taxon:4932 20020930 SGD
+SGD S000004074 RAX2 GO:0005621 SGD_REF:S000060270|PMID:11110666 IDA C YLR084C gene taxon:4932 20020930 SGD
+SGD S000004074 RAX2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YLR084C gene taxon:4932 20041203 SGD
+SGD S000004074 RAX2 GO:0005935 SGD_REF:S000060270|PMID:11110666 IDA C YLR084C gene taxon:4932 20010525 SGD
+SGD S000004074 RAX2 GO:0005935 SGD_REF:S000079777|PMID:15356260 IDA C YLR084C gene taxon:4932 20041209 SGD
+SGD S000004074 RAX2 GO:0016020 SGD_REF:S000060270|PMID:11110666 ISS C YLR084C gene taxon:4932 20020930 SGD
+SGD S000004074 RAX2 GO:0005554 SGD_REF:S000069584 ND F YLR084C gene taxon:4932 20021001 SGD
+SGD S000004074 RAX2 GO:0000282 SGD_REF:S000060270|PMID:11110666 IGI P YLR084C gene taxon:4932 20020930 SGD
+SGD S000004074 RAX2 GO:0000282 SGD_REF:S000060270|PMID:11110666 IMP P YLR084C gene taxon:4932 20020930 SGD
+SGD S000002935 RBA50 GO:0005665 SGD_REF:S000075214|PMID:14690591 ISS C YDR527W gene taxon:4932 20040802 SGD
+SGD S000002935 RBA50 GO:0005665 SGD_REF:S000075214|PMID:14690591 IPI C YDR527W gene taxon:4932 20051114 SGD
+SGD S000002935 RBA50 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDR527W gene taxon:4932 20031028 SGD
+SGD S000002935 RBA50 contributes_to GO:0003899 SGD_REF:S000075214|PMID:14690591 IMP F YDR527W gene taxon:4932 20051108 SGD
+SGD S000002935 RBA50 GO:0006366 SGD_REF:S000075214|PMID:14690591 IMP P YDR527W gene taxon:4932 20040802 SGD
+SGD S000002935 RBA50 GO:0006366 SGD_REF:S000076732|PMID:15282305 IMP P YDR527W gene taxon:4932 20050216 SGD
+SGD S000006167 RBD2 GO:0005794 SGD_REF:S000074185|PMID:14562095 IDA C rhomboid protease YPL246C gene taxon:4932 20031028 SGD
+SGD S000006167 RBD2 colocalizes_with GO:0030137 SGD_REF:S000074185|PMID:14562095 IDA C rhomboid protease YPL246C gene taxon:4932 20031028 SGD
+SGD S000006167 RBD2 GO:0005554 SGD_REF:S000069584 ND F rhomboid protease YPL246C gene taxon:4932 20050216 SGD
+SGD S000006167 RBD2 GO:0000004 SGD_REF:S000069584 ND P rhomboid protease YPL246C gene taxon:4932 20050216 SGD
+SGD S000000034 RBG1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YAL036C|FUN11 gene taxon:4932 20031028 SGD
+SGD S000000034 RBG1 GO:0005525 SGD_REF:S000048243|PMID:10760581 ISS F YAL036C|FUN11 gene taxon:4932 20040506 SGD
+SGD S000000034 RBG1 GO:0000004 SGD_REF:S000069584 ND P YAL036C|FUN11 gene taxon:4932 20010119 SGD
+SGD S000003405 RBG2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YGR173W|GIR1 gene taxon:4932 20031028 SGD
+SGD S000003405 RBG2 GO:0005525 SGD_REF:S000048243|PMID:10760581 ISS F YGR173W|GIR1 gene taxon:4932 20040506 SGD
+SGD S000003405 RBG2 GO:0000004 SGD_REF:S000069584 ND P YGR173W|GIR1 gene taxon:4932 20030203 SGD
+SGD S000000632 RBK1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C ribokinase YCR036W gene taxon:4932 20031028 SGD
+SGD S000000632 RBK1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C ribokinase YCR036W gene taxon:4932 20031028 SGD
+SGD S000000632 RBK1 GO:0004747 SGD_REF:S000047093|PMID:1964349 ISS F ribokinase YCR036W gene taxon:4932 20020930 SGD
+SGD S000000632 RBK1 GO:0005524 SGD_REF:S000047093|PMID:1964349 ISS F ribokinase YCR036W gene taxon:4932 20020930 SGD
+SGD S000000632 RBK1 GO:0006014 SGD_REF:S000047093|PMID:1964349 ISS P ribokinase YCR036W gene taxon:4932 20020930 SGD
+SGD S000005791 RBL2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C tubulin folding cofactor A YOR265W gene taxon:4932 20031028 SGD
+SGD S000005791 RBL2 GO:0015631 SGD_REF:S000069075|PMID:11739729 IDA F tubulin folding cofactor A YOR265W gene taxon:4932 20030211 SGD
+SGD S000005791 RBL2 GO:0048487 SGD_REF:S000069075|PMID:11739729 IMP F tubulin folding cofactor A YOR265W gene taxon:4932 20040726 SGD
+SGD S000005791 RBL2 GO:0000226 SGD_REF:S000069075|PMID:11739729 IMP P tubulin folding cofactor A YOR265W gene taxon:4932 20050217 SGD
+SGD S000005791 RBL2 GO:0007023 SGD_REF:S000048424|PMID:10542094 TAS P tubulin folding cofactor A YOR265W gene taxon:4932 20010118 SGD
+SGD S000005791 RBL2 GO:0007025 SGD_REF:S000048424|PMID:10542094 TAS P tubulin folding cofactor A YOR265W gene taxon:4932 20010118 SGD
+SGD S000002348 RBS1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C R3H-domain protein YDL189W gene taxon:4932 20031028 SGD
+SGD S000002348 RBS1 GO:0005554 SGD_REF:S000069584 ND F R3H-domain protein YDL189W gene taxon:4932 20050217 SGD
+SGD S000002348 RBS1 GO:0006012 SGD_REF:S000072754|PMID:12372297 IGI SGD:S000000015|SGD:S000005405 P R3H-domain protein YDL189W gene taxon:4932 20050217 SGD
+SGD S000004887 RCE1 GO:0030176 SGD_REF:S000045444|PMID:9736709 IDA C protease YMR274C gene taxon:4932 20020717 SGD
+SGD S000004887 RCE1 GO:0008487 SGD_REF:S000054985|PMID:10747800 IDA F protease YMR274C gene taxon:4932 20020717 SGD
+SGD S000004887 RCE1 GO:0007323 SGD_REF:S000048235|PMID:9065405 IMP P protease YMR274C gene taxon:4932 20020717 SGD
+SGD S000004887 RCE1 GO:0016485 SGD_REF:S000046992|PMID:10825201 IDA P protease YMR274C gene taxon:4932 20020717 SGD
+SGD S000003126 RCK1 GO:0008372 SGD_REF:S000069584 ND C YGL158W gene taxon:4932 20021008 SGD
+SGD S000003126 RCK1 GO:0004674 SGD_REF:S000048705|PMID:10778743 ISS F YGL158W gene taxon:4932 20021008 SGD
+SGD S000003126 RCK1 GO:0006468 SGD_REF:S000048705|PMID:10778743 ISS P YGL158W gene taxon:4932 20021008 SGD
+SGD S000003126 RCK1 GO:0040020 SGD_REF:S000048705|PMID:10778743 IGI P YGL158W gene taxon:4932 20021008 SGD
+SGD S000003126 RCK1 GO:0040020 SGD_REF:S000048705|PMID:10778743 IMP P YGL158W gene taxon:4932 20021008 SGD
+SGD S000004238 RCK2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YLR248W|CLK1|CMK3 gene taxon:4932 20031028 SGD
+SGD S000004238 RCK2 GO:0004674 SGD_REF:S000048705|PMID:10778743 ISS F YLR248W|CLK1|CMK3 gene taxon:4932 20021008 SGD
+SGD S000004238 RCK2 GO:0004674 SGD_REF:S000082290|PMID:11344302 IDA F YLR248W|CLK1|CMK3 gene taxon:4932 20050720 SGD
+SGD S000004238 RCK2 GO:0006468 SGD_REF:S000048705|PMID:10778743 ISS P YLR248W|CLK1|CMK3 gene taxon:4932 20021008 SGD
+SGD S000004238 RCK2 GO:0006468 SGD_REF:S000082290|PMID:11344302 IDA P YLR248W|CLK1|CMK3 gene taxon:4932 20050720 SGD
+SGD S000004238 RCK2 GO:0007231 SGD_REF:S000082290|PMID:11344302 IGI SGD:S000004103 P YLR248W|CLK1|CMK3 gene taxon:4932 20050720 SGD
+SGD S000004238 RCK2 GO:0007231 SGD_REF:S000082290|PMID:11344302 IPI SGD:S000004103 P YLR248W|CLK1|CMK3 gene taxon:4932 20050720 SGD
+SGD S000004238 RCK2 GO:0007231 SGD_REF:S000082290|PMID:11344302 IMP P YLR248W|CLK1|CMK3 gene taxon:4932 20050720 SGD
+SGD S000004238 RCK2 GO:0040020 SGD_REF:S000048705|PMID:10778743 IGI P YLR248W|CLK1|CMK3 gene taxon:4932 20021008 SGD
+SGD S000004238 RCK2 GO:0040020 SGD_REF:S000048705|PMID:10778743 IMP P YLR248W|CLK1|CMK3 gene taxon:4932 20021008 SGD
+SGD S000005370 RCL1 GO:0005730 SGD_REF:S000039255|PMID:10790377 IDA C YOL010W gene taxon:4932 20010118 SGD
+SGD S000005370 RCL1 NOT GO:0003963 SGD_REF:S000039255|PMID:10790377 ISS protein_id:AW078116|UniProt:P56175|UniProt:Q23400|protein_id:AJ276894|UniProt:O77264|UniProt:Q60335|protein_id:AAB70847|protein_id:AAB86375|protein_id:AAC06852|protein_id:AAB89810|protein_id:BAA30639|UniProt:P46849|UniProt:O00442|UniProt:Q09870|protein_id:AJ276895|protein_id:AW059073 F YOL010W gene taxon:4932 20020530 SGD
+SGD S000005370 RCL1 NOT GO:0003963 SGD_REF:S000039255|PMID:10790377 NAS F YOL010W gene taxon:4932 20020530 SGD
+SGD S000005370 RCL1 GO:0005554 SGD_REF:S000069584 ND F YOL010W gene taxon:4932 20050920 SGD
+SGD S000005370 RCL1 GO:0006365 SGD_REF:S000039255|PMID:10790377 IMP P YOL010W gene taxon:4932 20050920 SGD
+SGD S000001642 RCN1 colocalizes_with GO:0005955 SGD_REF:S000062324|PMID:10887154 IPI C calcineurin inhibitor YKL159C gene taxon:4932 20020930 SGD
+SGD S000001642 RCN1 GO:0008597 SGD_REF:S000062324|PMID:10887154 IGI F calcineurin inhibitor YKL159C gene taxon:4932 20020930 SGD
+SGD S000001642 RCN1 GO:0008597 SGD_REF:S000062324|PMID:10887154 IMP F calcineurin inhibitor YKL159C gene taxon:4932 20020930 SGD
+SGD S000001642 RCN1 GO:0008597 SGD_REF:S000062324|PMID:10887154 IPI F calcineurin inhibitor YKL159C gene taxon:4932 20020930 SGD
+SGD S000001642 RCN1 GO:0019722 SGD_REF:S000062324|PMID:10887154 IPI P calcineurin inhibitor YKL159C gene taxon:4932 20020930 SGD
+SGD S000004680 RCO1 GO:0000118 SGD_REF:S000113735|PMID:16286007 IDA C YMR075W gene taxon:4932 20060509 SGD
+SGD S000004680 RCO1 GO:0000118 SGD_REF:S000113736|PMID:16286008 IDA C YMR075W gene taxon:4932 20060509 SGD
+SGD S000004680 RCO1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YMR075W gene taxon:4932 20031028 SGD
+SGD S000004680 RCO1 GO:0005554 SGD_REF:S000069584 ND F YMR075W gene taxon:4932 20021125 SGD
+SGD S000004680 RCO1 GO:0000004 SGD_REF:S000069584 ND P YMR075W gene taxon:4932 20021125 SGD
+SGD S000000209 RCR1 GO:0030176 SGD_REF:S000080111|PMID:15590673 IDA C ER membrane protein YBR005W gene taxon:4932 20050107 SGD
+SGD S000000209 RCR1 GO:0030176 SGD_REF:S000080111|PMID:15590673 ISS C ER membrane protein YBR005W gene taxon:4932 20050107 SGD
+SGD S000000209 RCR1 GO:0005554 SGD_REF:S000069584 ND F ER membrane protein YBR005W gene taxon:4932 20030203 SGD
+SGD S000000209 RCR1 GO:0007047 SGD_REF:S000080111|PMID:15590673 IMP P ER membrane protein YBR005W gene taxon:4932 20050107 SGD
+SGD S000002410 RCR2 GO:0000324 SGD_REF:S000074185|PMID:14562095 IDA C YDR003W gene taxon:4932 20031028 SGD
+SGD S000002410 RCR2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDR003W gene taxon:4932 20031028 SGD
+SGD S000002410 RCR2 GO:0016021 SGD_REF:S000080111|PMID:15590673 ISS C YDR003W gene taxon:4932 20050107 SGD
+SGD S000002410 RCR2 GO:0005554 SGD_REF:S000069584 ND F YDR003W gene taxon:4932 20021126 SGD
+SGD S000002410 RCR2 GO:0000004 SGD_REF:S000069584 ND P YDR003W gene taxon:4932 20021126 SGD
+SGD S000003039 RCS1 GO:0005634 SGD_REF:S000069867|PMID:11877447 IDA C binds the consensus site PyPuCACCCPu YGL071W|AFT1 gene taxon:4932 20021003 SGD
+SGD S000003039 RCS1 GO:0005737 SGD_REF:S000069867|PMID:11877447 IDA C binds the consensus site PyPuCACCCPu YGL071W|AFT1 gene taxon:4932 20021003 SGD
+SGD S000003039 RCS1 GO:0003700 SGD_REF:S000070405|PMID:12196168 TAS F binds the consensus site PyPuCACCCPu YGL071W|AFT1 gene taxon:4932 20020912 SGD
+SGD S000003039 RCS1 GO:0003700 SGD_REF:S000076895|PMID:14739928 IDA F binds the consensus site PyPuCACCCPu YGL071W|AFT1 gene taxon:4932 20041214 SGD
+SGD S000003039 RCS1 GO:0006827 SGD_REF:S000053105|PMID:8670839 IMP P binds the consensus site PyPuCACCCPu YGL071W|AFT1 gene taxon:4932 20021003 SGD
+SGD S000003039 RCS1 GO:0006827 SGD_REF:S000053105|PMID:8670839 IPI P binds the consensus site PyPuCACCCPu YGL071W|AFT1 gene taxon:4932 20021003 SGD
+SGD S000003039 RCS1 GO:0045944 SGD_REF:S000053105|PMID:8670839 IMP P binds the consensus site PyPuCACCCPu YGL071W|AFT1 gene taxon:4932 20021003 SGD
+SGD S000003039 RCS1 GO:0045944 SGD_REF:S000076895|PMID:14739928 IDA P binds the consensus site PyPuCACCCPu YGL071W|AFT1 gene taxon:4932 20041214 SGD
+SGD S000003039 RCS1 GO:0045944 SGD_REF:S000053105|PMID:8670839 IPI P binds the consensus site PyPuCACCCPu YGL071W|AFT1 gene taxon:4932 20021003 SGD
+SGD S000003740 RCY1 GO:0005768 SGD_REF:S000082256|PMID:15537705 IDA C YJL204C gene taxon:4932 20050711 SGD
+SGD S000003740 RCY1 GO:0005794 SGD_REF:S000082256|PMID:15537705 IDA C YJL204C gene taxon:4932 20050711 SGD
+SGD S000003740 RCY1 GO:0030427 SGD_REF:S000060367|PMID:11287615 IDA C YJL204C gene taxon:4932 20030509 SGD
+SGD S000003740 RCY1 GO:0005515 SGD_REF:S000060367|PMID:11287615 IMP F YJL204C gene taxon:4932 20030509 SGD
+SGD S000003740 RCY1 GO:0005515 SGD_REF:S000060367|PMID:11287615 IPI F YJL204C gene taxon:4932 20030509 SGD
+SGD S000003740 RCY1 GO:0006897 SGD_REF:S000060817|PMID:11378903 IMP P YJL204C gene taxon:4932 20021004 SGD
+SGD S000003740 RCY1 GO:0006897 SGD_REF:S000043012|PMID:10769031 IMP P YJL204C gene taxon:4932 20021004 SGD
+SGD S000000277 RDH54 GO:0005634 SGD_REF:S000041985|PMID:9409819 IC GO:0007131 C helicase (putative), similar to RAD54 YBR073W|TID1 gene taxon:4932 20021105 SGD
+SGD S000000277 RDH54 GO:0003916 SGD_REF:S000046962|PMID:10970884 IDA F helicase (putative), similar to RAD54 YBR073W|TID1 gene taxon:4932 20040917 SGD
+SGD S000000277 RDH54 GO:0008094 SGD_REF:S000046962|PMID:10970884 IDA F helicase (putative), similar to RAD54 YBR073W|TID1 gene taxon:4932 20020814 SGD
+SGD S000000277 RDH54 GO:0000727 SGD_REF:S000060952|PMID:11459961 TAS P helicase (putative), similar to RAD54 YBR073W|TID1 gene taxon:4932 20020925 SGD
+SGD S000000277 RDH54 GO:0007131 SGD_REF:S000041992|PMID:9409820 IMP P helicase (putative), similar to RAD54 YBR073W|TID1 gene taxon:4932 20020109 SGD
+SGD S000000277 RDH54 GO:0007131 SGD_REF:S000041985|PMID:9409819 IGI P helicase (putative), similar to RAD54 YBR073W|TID1 gene taxon:4932 20020109 SGD
+SGD S000000277 RDH54 GO:0007131 SGD_REF:S000041985|PMID:9409819 IMP P helicase (putative), similar to RAD54 YBR073W|TID1 gene taxon:4932 20020109 SGD
+SGD S000000277 RDH54 GO:0007131 SGD_REF:S000041992|PMID:9409820 IGI P helicase (putative), similar to RAD54 YBR073W|TID1 gene taxon:4932 20020109 SGD
+SGD S000000277 RDH54 GO:0030491 SGD_REF:S000046962|PMID:10970884 IDA P helicase (putative), similar to RAD54 YBR073W|TID1 gene taxon:4932 20020925 SGD
+SGD S000000277 RDH54 GO:0045144 SGD_REF:S000086946|PMID:16230461 IMP P helicase (putative), similar to RAD54 YBR073W|TID1 gene taxon:4932 20051222 SGD
+SGD S000002294 RDI1 GO:0005829 SGD_REF:S000056064|PMID:10066831 IDA C YDL135C gene taxon:4932 20010118 SGD
+SGD S000002294 RDI1 GO:0004871 SGD_REF:S000056064|PMID:10066831 IPI F YDL135C gene taxon:4932 20010118 SGD
+SGD S000002294 RDI1 GO:0005094 SGD_REF:S000056064|PMID:10066831 IDA F YDL135C gene taxon:4932 20010118 SGD
+SGD S000002294 RDI1 GO:0007015 SGD_REF:S000047133|PMID:9242378 IDA P YDL135C gene taxon:4932 20030116 SGD
+SGD S000002294 RDI1 GO:0007015 SGD_REF:S000047133|PMID:9242378 IMP P YDL135C gene taxon:4932 20030116 SGD
+SGD S000002294 RDI1 GO:0007264 SGD_REF:S000056064|PMID:10066831 IPI P YDL135C gene taxon:4932 20010118 SGD
+SGD S000006482 RDN18-1 GO:0005843 SGD_REF:S000075494|PMID:11701127 IDA C 18S ribosomal RNA RDN18 gene taxon:4932 20040324 SGD
+SGD S000006482 RDN18-1 GO:0003735 SGD_REF:S000058443|PMID:10690410 TAS F 18S ribosomal RNA RDN18 gene taxon:4932 20020619 SGD
+SGD S000006482 RDN18-1 GO:0006412 SGD_REF:S000058443|PMID:10690410 TAS P 18S ribosomal RNA RDN18 gene taxon:4932 20020619 SGD
+SGD S000006483 RDN18-2 GO:0005843 SGD_REF:S000075494|PMID:11701127 IDA C 18S ribosomal RNA RDN18 gene taxon:4932 20040324 SGD
+SGD S000006483 RDN18-2 GO:0003735 SGD_REF:S000058443|PMID:10690410 TAS F 18S ribosomal RNA RDN18 gene taxon:4932 20020619 SGD
+SGD S000006483 RDN18-2 GO:0006412 SGD_REF:S000058443|PMID:10690410 TAS P 18S ribosomal RNA RDN18 gene taxon:4932 20020619 SGD
+SGD S000006484 RDN25-1 GO:0005842 SGD_REF:S000058443|PMID:10690410 TAS C 25S ribosomal RNA RDN25 gene taxon:4932 20020619 SGD
+SGD S000006484 RDN25-1 GO:0003735 SGD_REF:S000058443|PMID:10690410 TAS F 25S ribosomal RNA RDN25 gene taxon:4932 20020619 SGD
+SGD S000006484 RDN25-1 GO:0006412 SGD_REF:S000058443|PMID:10690410 TAS P 25S ribosomal RNA RDN25 gene taxon:4932 20020619 SGD
+SGD S000006485 RDN25-2 GO:0005842 SGD_REF:S000058443|PMID:10690410 TAS C 25S ribosomal RNA RDN25 gene taxon:4932 20020619 SGD
+SGD S000006485 RDN25-2 GO:0003735 SGD_REF:S000058443|PMID:10690410 TAS F 25S ribosomal RNA RDN25 gene taxon:4932 20020619 SGD
+SGD S000006485 RDN25-2 GO:0006412 SGD_REF:S000058443|PMID:10690410 TAS P 25S ribosomal RNA RDN25 gene taxon:4932 20020619 SGD
+SGD S000006479 RDN5-1 GO:0005842 SGD_REF:S000058443|PMID:10690410 TAS C 5S ribosomal RNA RDN5 gene taxon:4932 20020619 SGD
+SGD S000006479 RDN5-1 GO:0003735 SGD_REF:S000058443|PMID:10690410 TAS F 5S ribosomal RNA RDN5 gene taxon:4932 20020619 SGD
+SGD S000006479 RDN5-1 GO:0006412 SGD_REF:S000058443|PMID:10690410 TAS P 5S ribosomal RNA RDN5 gene taxon:4932 20020619 SGD
+SGD S000006480 RDN5-2 GO:0005842 SGD_REF:S000058443|PMID:10690410 TAS C 5S ribosomal RNA RDN5 gene taxon:4932 20020619 SGD
+SGD S000006480 RDN5-2 GO:0003735 SGD_REF:S000058443|PMID:10690410 TAS F 5S ribosomal RNA RDN5 gene taxon:4932 20020619 SGD
+SGD S000006480 RDN5-2 GO:0006412 SGD_REF:S000058443|PMID:10690410 TAS P 5S ribosomal RNA RDN5 gene taxon:4932 20020619 SGD
+SGD S000006481 RDN5-3 GO:0005842 SGD_REF:S000058443|PMID:10690410 TAS C 5S ribosomal RNA RDN5 gene taxon:4932 20020619 SGD
+SGD S000006481 RDN5-3 GO:0003735 SGD_REF:S000058443|PMID:10690410 TAS F 5S ribosomal RNA RDN5 gene taxon:4932 20020619 SGD
+SGD S000006481 RDN5-3 GO:0006412 SGD_REF:S000058443|PMID:10690410 TAS P 5S ribosomal RNA RDN5 gene taxon:4932 20020619 SGD
+SGD S000029708 RDN5-4 GO:0005842 SGD_REF:S000058443|PMID:10690410 TAS C 5S ribosomal RNA RDN5 gene taxon:4932 20040304 SGD
+SGD S000029708 RDN5-4 GO:0003735 SGD_REF:S000058443|PMID:10690410 TAS F 5S ribosomal RNA RDN5 gene taxon:4932 20040304 SGD
+SGD S000029708 RDN5-4 GO:0006412 SGD_REF:S000058443|PMID:10690410 TAS P 5S ribosomal RNA RDN5 gene taxon:4932 20040304 SGD
+SGD S000029710 RDN5-5 GO:0005842 SGD_REF:S000058443|PMID:10690410 TAS C 5S ribosomal RNA RDN5 gene taxon:4932 20040304 SGD
+SGD S000029710 RDN5-5 GO:0003735 SGD_REF:S000058443|PMID:10690410 TAS F 5S ribosomal RNA RDN5 gene taxon:4932 20040304 SGD
+SGD S000029710 RDN5-5 GO:0006412 SGD_REF:S000058443|PMID:10690410 TAS P 5S ribosomal RNA RDN5 gene taxon:4932 20040304 SGD
+SGD S000029711 RDN5-6 GO:0005842 SGD_REF:S000058443|PMID:10690410 TAS C 5S ribosomal RNA RDN5 gene taxon:4932 20040304 SGD
+SGD S000029711 RDN5-6 GO:0003735 SGD_REF:S000058443|PMID:10690410 TAS F 5S ribosomal RNA RDN5 gene taxon:4932 20040304 SGD
+SGD S000029711 RDN5-6 GO:0006412 SGD_REF:S000058443|PMID:10690410 TAS P 5S ribosomal RNA RDN5 gene taxon:4932 20040304 SGD
+SGD S000006488 RDN58-1 GO:0005842 SGD_REF:S000058443|PMID:10690410 TAS C 5.8S ribosomal RNA RDN58 gene taxon:4932 20020619 SGD
+SGD S000006488 RDN58-1 GO:0003735 SGD_REF:S000058443|PMID:10690410 TAS F 5.8S ribosomal RNA RDN58 gene taxon:4932 20020619 SGD
+SGD S000006488 RDN58-1 GO:0006412 SGD_REF:S000058443|PMID:10690410 TAS P 5.8S ribosomal RNA RDN58 gene taxon:4932 20020619 SGD
+SGD S000006489 RDN58-2 GO:0005842 SGD_REF:S000058443|PMID:10690410 TAS C 5.8S ribosomal RNA RDN58 gene taxon:4932 20020619 SGD
+SGD S000006489 RDN58-2 GO:0003735 SGD_REF:S000058443|PMID:10690410 TAS F 5.8S ribosomal RNA RDN58 gene taxon:4932 20020619 SGD
+SGD S000006489 RDN58-2 GO:0006412 SGD_REF:S000058443|PMID:10690410 TAS P 5.8S ribosomal RNA RDN58 gene taxon:4932 20020619 SGD
+SGD S000005907 RDR1 GO:0005634 SGD_REF:S000069950|PMID:11882665 TAS C YOR380W gene taxon:4932 20020617 SGD
+SGD S000005907 RDR1 GO:0003700 SGD_REF:S000069950|PMID:11882665 IGI F YOR380W gene taxon:4932 20020617 SGD
+SGD S000005907 RDR1 GO:0003700 SGD_REF:S000069950|PMID:11882665 IMP F YOR380W gene taxon:4932 20020617 SGD
+SGD S000005907 RDR1 GO:0003700 SGD_REF:S000069950|PMID:11882665 ISS F YOR380W gene taxon:4932 20020617 SGD
+SGD S000005907 RDR1 GO:0009410 SGD_REF:S000069950|PMID:11882665 IMP P YOR380W gene taxon:4932 20020617 SGD
+SGD S000000703 RDS1 GO:0005634 SGD_REF:S000081155|PMID:15343339 IC GO:0003677 C transcriptional regulator YCR106W gene taxon:4932 20050331 SGD
+SGD S000000703 RDS1 GO:0003677 SGD_REF:S000081155|PMID:15343339 IPI F transcriptional regulator YCR106W gene taxon:4932 20050331 SGD
+SGD S000000703 RDS1 GO:0003700 SGD_REF:S000069947|PMID:11943786 ISS F transcriptional regulator YCR106W gene taxon:4932 20020617 SGD
+SGD S000000703 RDS1 GO:0003700 SGD_REF:S000069947|PMID:11943786 IMP F transcriptional regulator YCR106W gene taxon:4932 20020617 SGD
+SGD S000000703 RDS1 GO:0009410 SGD_REF:S000069947|PMID:11943786 IMP P transcriptional regulator YCR106W gene taxon:4932 20020617 SGD
+SGD S000006054 RDS2 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C transcriptional regulator YPL133C gene taxon:4932 20031028 SGD
+SGD S000006054 RDS2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C transcriptional regulator YPL133C gene taxon:4932 20031028 SGD
+SGD S000006054 RDS2 GO:0003700 SGD_REF:S000069947|PMID:11943786 ISS F transcriptional regulator YPL133C gene taxon:4932 20020617 SGD
+SGD S000006054 RDS2 GO:0003700 SGD_REF:S000069947|PMID:11943786 IMP F transcriptional regulator YPL133C gene taxon:4932 20020617 SGD
+SGD S000006054 RDS2 GO:0009410 SGD_REF:S000069947|PMID:11943786 IMP P transcriptional regulator YPL133C gene taxon:4932 20020617 SGD
+SGD S000006298 RDS3 GO:0005681 SGD_REF:S000074486|PMID:14517302 TAS C YPR094W gene taxon:4932 20040501 SGD
+SGD S000006298 RDS3 colocalizes_with GO:0005686 SGD_REF:S000080993|PMID:15565172 IDA C YPR094W gene taxon:4932 20051006 SGD
+SGD S000006298 RDS3 GO:0005554 SGD_REF:S000073348 ND F YPR094W gene taxon:4932 20060419 SGD
+SGD S000006298 RDS3 GO:0000398 SGD_REF:S000080962|PMID:12871902 IMP P YPR094W gene taxon:4932 20050310 SGD
+SGD S000006298 RDS3 GO:0000398 SGD_REF:S000080962|PMID:12871902 IGI SGD:S000004107 P YPR094W gene taxon:4932 20050310 SGD
+SGD S000006298 RDS3 GO:0009410 SGD_REF:S000069947|PMID:11943786 IMP P YPR094W gene taxon:4932 20020617 SGD
+SGD S000000253 REB1 GO:0005634 SGD_REF:S000051324|PMID:9632820 TAS C RNA polymerase I enhancer binding protein YBR049C|GRF2 gene taxon:4932 20010118 SGD
+SGD S000000253 REB1 GO:0003702 SGD_REF:S000044785|PMID:9435793 IDA F RNA polymerase I enhancer binding protein YBR049C|GRF2 gene taxon:4932 20030318 SGD
+SGD S000000253 REB1 GO:0003716 SGD_REF:S000043778|PMID:7565745 TAS F RNA polymerase I enhancer binding protein YBR049C|GRF2 gene taxon:4932 20010118 SGD
+SGD S000000253 REB1 GO:0006357 SGD_REF:S000051324|PMID:9632820 TAS P RNA polymerase I enhancer binding protein YBR049C|GRF2 gene taxon:4932 20010118 SGD
+SGD S000000253 REB1 GO:0006363 SGD_REF:S000043778|PMID:7565745 TAS P RNA polymerase I enhancer binding protein YBR049C|GRF2 gene taxon:4932 20010118 SGD
+SGD S000029412 REC1 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20040419 SGD
+SGD S000029412 REC1 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20040419 SGD
+SGD S000029412 REC1 GO:0006310 SGD_REF:S000041051|PMID:2178786 IMP P gene taxon:4932 20010118 SGD
+SGD S000004321 REC102 GO:0000794 SGD_REF:S000082211|PMID:15044957 IDA C 23 kDa protein containing a putative leucine zipper, meiosis specific recombination protein YLR329W gene taxon:4932 20060109 SGD
+SGD S000004321 REC102 GO:0005634 SGD_REF:S000073936|PMID:12897161 IPI C 23 kDa protein containing a putative leucine zipper, meiosis specific recombination protein YLR329W gene taxon:4932 20040716 SGD
+SGD S000004321 REC102 GO:0005515 SGD_REF:S000073936|PMID:12897161 IDA F 23 kDa protein containing a putative leucine zipper, meiosis specific recombination protein YLR329W gene taxon:4932 20040716 SGD
+SGD S000004321 REC102 GO:0007131 SGD_REF:S000056314|PMID:1732169 IMP P 23 kDa protein containing a putative leucine zipper, meiosis specific recombination protein YLR329W gene taxon:4932 20010118 SGD
+SGD S000004321 REC102 GO:0042138 SGD_REF:S000069981|PMID:9334324 TAS P 23 kDa protein containing a putative leucine zipper, meiosis specific recombination protein YLR329W gene taxon:4932 20020708 SGD
+SGD S000001200 REC104 GO:0000794 SGD_REF:S000082211|PMID:15044957 IDA C meiosis-specific protein YHR157W gene taxon:4932 20060109 SGD
+SGD S000001200 REC104 GO:0005554 SGD_REF:S000069584 ND F meiosis-specific protein YHR157W gene taxon:4932 20060109 SGD
+SGD S000001200 REC104 GO:0007131 SGD_REF:S000046029|PMID:9177999 IMP P meiosis-specific protein YHR157W gene taxon:4932 20010118 SGD
+SGD S000001200 REC104 GO:0042138 SGD_REF:S000069981|PMID:9334324 TAS P meiosis-specific protein YHR157W gene taxon:4932 20020708 SGD
+SGD S000003782 REC107 GO:0008372 SGD_REF:S000069584 ND C ds break formation complex subunit YJR021C|MER2 gene taxon:4932 20040419 SGD
+SGD S000003782 REC107 GO:0005554 SGD_REF:S000069584 ND F ds break formation complex subunit YJR021C|MER2 gene taxon:4932 20040419 SGD
+SGD S000003782 REC107 GO:0007131 SGD_REF:S000044851|PMID:8536989 IMP P ds break formation complex subunit YJR021C|MER2 gene taxon:4932 20010118 SGD
+SGD S000004740 REC114 GO:0005634 SGD_REF:S000069981|PMID:9334324 IC GO:0042138 C early sporulation protein YMR133W gene taxon:4932 20040419 SGD
+SGD S000004740 REC114 GO:0005554 SGD_REF:S000069584 ND F early sporulation protein YMR133W gene taxon:4932 20040419 SGD
+SGD S000004740 REC114 GO:0007131 SGD_REF:S000051870|PMID:8417989 IMP P early sporulation protein YMR133W gene taxon:4932 20010118 SGD
+SGD S000004740 REC114 GO:0042138 SGD_REF:S000069981|PMID:9334324 TAS P early sporulation protein YMR133W gene taxon:4932 20020708 SGD
+SGD S000006211 REC8 GO:0000780 SGD_REF:S000055468|PMID:10412984 IDA C YPR007C|SPO69 gene taxon:4932 20030404 SGD
+SGD S000006211 REC8 GO:0000798 SGD_REF:S000055468|PMID:10412984 IDA C YPR007C|SPO69 gene taxon:4932 20021113 SGD
+SGD S000006211 REC8 GO:0005488 SGD_REF:S000055468|PMID:10412984 IDA F YPR007C|SPO69 gene taxon:4932 20021113 SGD
+SGD S000006211 REC8 GO:0007062 SGD_REF:S000070004|PMID:11983163 TAS P YPR007C|SPO69 gene taxon:4932 20020930 SGD
+SGD S000006211 REC8 GO:0007126 SGD_REF:S000055468|PMID:10412984 IMP P YPR007C|SPO69 gene taxon:4932 20030404 SGD
+SGD S000004253 RED1 GO:0000795 SGD_REF:S000039988|PMID:9060462 IDA C meiosis-specific component of synaptonemal complex axial element protein core YLR263W gene taxon:4932 20030404 SGD
+SGD S000004253 RED1 GO:0005198 SGD_REF:S000068921|PMID:11779793 IDA F meiosis-specific component of synaptonemal complex axial element protein core YLR263W gene taxon:4932 20051014 SGD
+SGD S000004253 RED1 GO:0005198 SGD_REF:S000068921|PMID:11779793 IPI F meiosis-specific component of synaptonemal complex axial element protein core YLR263W gene taxon:4932 20051014 SGD
+SGD S000004253 RED1 GO:0005515 SGD_REF:S000075943|PMID:14595109 IPI F meiosis-specific component of synaptonemal complex axial element protein core YLR263W gene taxon:4932 20051014 SGD
+SGD S000004253 RED1 GO:0005515 SGD_REF:S000049251|PMID:10786836 IDA F meiosis-specific component of synaptonemal complex axial element protein core YLR263W gene taxon:4932 20051014 SGD
+SGD S000004253 RED1 GO:0005515 SGD_REF:S000075943|PMID:14595109 IDA F meiosis-specific component of synaptonemal complex axial element protein core YLR263W gene taxon:4932 20051014 SGD
+SGD S000004253 RED1 GO:0005515 SGD_REF:S000049251|PMID:10786836 IPI F meiosis-specific component of synaptonemal complex axial element protein core YLR263W gene taxon:4932 20051014 SGD
+SGD S000004253 RED1 GO:0031490 SGD_REF:S000072627|PMID:12526806 IDA F meiosis-specific component of synaptonemal complex axial element protein core YLR263W gene taxon:4932 20051014 SGD
+SGD S000004253 RED1 GO:0031490 SGD_REF:S000072627|PMID:12526806 IPI F meiosis-specific component of synaptonemal complex axial element protein core YLR263W gene taxon:4932 20051014 SGD
+SGD S000004253 RED1 GO:0007130 SGD_REF:S000039745|PMID:9880561 IPI P meiosis-specific component of synaptonemal complex axial element protein core YLR263W gene taxon:4932 20010118 SGD
+SGD S000004253 RED1 GO:0007130 SGD_REF:S000039745|PMID:9880561 IMP P meiosis-specific component of synaptonemal complex axial element protein core YLR263W gene taxon:4932 20010118 SGD
+SGD S000004253 RED1 GO:0007130 SGD_REF:S000042967|PMID:2550770 TAS P meiosis-specific component of synaptonemal complex axial element protein core YLR263W gene taxon:4932 20010118 SGD
+SGD S000004253 RED1 GO:0043085 SGD_REF:S000075943|PMID:14595109 IDA P meiosis-specific component of synaptonemal complex axial element protein core YLR263W gene taxon:4932 20051014 SGD
+SGD S000004253 RED1 GO:0051598 SGD_REF:S000043633|PMID:10848609 IMP P meiosis-specific component of synaptonemal complex axial element protein core YLR263W gene taxon:4932 20051014 SGD
+SGD S000002603 REF2 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C RNA-binding protein YDR195W gene taxon:4932 20031028 SGD
+SGD S000002603 REF2 GO:0005847 SGD_REF:S000074089|PMID:12819204 IPI C RNA-binding protein YDR195W gene taxon:4932 20031013 SGD
+SGD S000002603 REF2 GO:0003677 SGD_REF:S000074089|PMID:12819204 IPI F RNA-binding protein YDR195W gene taxon:4932 20050929 SGD
+SGD S000002603 REF2 GO:0003723 SGD_REF:S000051876|PMID:7862160 IDA F RNA-binding protein YDR195W gene taxon:4932 20050218 SGD
+SGD S000002603 REF2 GO:0006397 SGD_REF:S000051876|PMID:7862160 IGI P RNA-binding protein YDR195W gene taxon:4932 20020930 SGD
+SGD S000002603 REF2 GO:0006397 SGD_REF:S000051876|PMID:7862160 IPI P RNA-binding protein YDR195W gene taxon:4932 20020930 SGD
+SGD S000002603 REF2 GO:0006397 SGD_REF:S000051876|PMID:7862160 IMP P RNA-binding protein YDR195W gene taxon:4932 20020930 SGD
+SGD S000002603 REF2 GO:0030846 SGD_REF:S000074089|PMID:12819204 IPI P RNA-binding protein YDR195W gene taxon:4932 20031013 SGD
+SGD S000002603 REF2 GO:0030847 SGD_REF:S000073502|PMID:12773397 IMP P RNA-binding protein YDR195W gene taxon:4932 20031010 SGD
+SGD S000002603 REF2 GO:0030847 SGD_REF:S000074089|PMID:12819204 IPI P RNA-binding protein YDR195W gene taxon:4932 20031013 SGD
+SGD S000002603 REF2 GO:0031126 SGD_REF:S000073502|PMID:12773397 IMP P RNA-binding protein YDR195W gene taxon:4932 20050218 SGD
+SGD S000002435 REG1 GO:0000164 SGD_REF:S000052535|PMID:10454550 TAS C Glc7p regulatory subunit YDR028C|HEX2|PZF240|SPP43|SRN1 gene taxon:4932 20010118 SGD
+SGD S000002435 REG1 GO:0005737 SGD_REF:S000052535|PMID:10454550 IDA C Glc7p regulatory subunit YDR028C|HEX2|PZF240|SPP43|SRN1 gene taxon:4932 20010118 SGD
+SGD S000002435 REG1 GO:0008599 SGD_REF:S000065824|PMID:11412094 TAS F Glc7p regulatory subunit YDR028C|HEX2|PZF240|SPP43|SRN1 gene taxon:4932 20030130 SGD
+SGD S000002435 REG1 GO:0000122 SGD_REF:S000052535|PMID:10454550 TAS P Glc7p regulatory subunit YDR028C|HEX2|PZF240|SPP43|SRN1 gene taxon:4932 20010118 SGD
+SGD S000002435 REG1 GO:0005977 SGD_REF:S000052535|PMID:10454550 TAS P Glc7p regulatory subunit YDR028C|HEX2|PZF240|SPP43|SRN1 gene taxon:4932 20010118 SGD
+SGD S000002435 REG1 GO:0006109 SGD_REF:S000071682|PMID:12167649 IGI P Glc7p regulatory subunit YDR028C|HEX2|PZF240|SPP43|SRN1 gene taxon:4932 20030402 SGD
+SGD S000002435 REG1 GO:0006109 SGD_REF:S000071682|PMID:12167649 TAS P Glc7p regulatory subunit YDR028C|HEX2|PZF240|SPP43|SRN1 gene taxon:4932 20030402 SGD
+SGD S000002435 REG1 GO:0006109 SGD_REF:S000071682|PMID:12167649 IPI P Glc7p regulatory subunit YDR028C|HEX2|PZF240|SPP43|SRN1 gene taxon:4932 20030402 SGD
+SGD S000002435 REG1 GO:0007039 SGD_REF:S000076235|PMID:14684743 IDA P Glc7p regulatory subunit YDR028C|HEX2|PZF240|SPP43|SRN1 gene taxon:4932 20051025 SGD
+SGD S000002435 REG1 GO:0007039 SGD_REF:S000076235|PMID:14684743 IMP P Glc7p regulatory subunit YDR028C|HEX2|PZF240|SPP43|SRN1 gene taxon:4932 20051025 SGD
+SGD S000000254 REG2 GO:0000164 SGD_REF:S000055740|PMID:8649403 IPI C Glc7p regulatory subunit YBR050C gene taxon:4932 20020822 SGD
+SGD S000000254 REG2 GO:0008599 SGD_REF:S000055740|PMID:8649403 IGI F Glc7p regulatory subunit YBR050C gene taxon:4932 20051005 SGD
+SGD S000000254 REG2 GO:0008599 SGD_REF:S000055740|PMID:8649403 IPI F Glc7p regulatory subunit YBR050C gene taxon:4932 20051005 SGD
+SGD S000000254 REG2 GO:0000122 SGD_REF:S000055740|PMID:8649403 IGI P Glc7p regulatory subunit YBR050C gene taxon:4932 20020822 SGD
+SGD S000004379 REH1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YLR387C gene taxon:4932 20031028 SGD
+SGD S000004379 REH1 GO:0005554 SGD_REF:S000069584 ND F YLR387C gene taxon:4932 20030203 SGD
+SGD S000004379 REH1 GO:0000004 SGD_REF:S000069584 ND P YLR387C gene taxon:4932 20030203 SGD
+SGD S000004379 REH1 NOT GO:0007117 SGD_REF:S000076016|PMID:15107529 IGI SGD:S000001756 P YLR387C gene taxon:4932 20040624 SGD
+SGD S000000471 REI1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YBR267W gene taxon:4932 20031028 SGD
+SGD S000000471 REI1 GO:0005737 SGD_REF:S000076016|PMID:15107529 IDA C YBR267W gene taxon:4932 20040624 SGD
+SGD S000000471 REI1 GO:0005554 SGD_REF:S000069584 ND F YBR267W gene taxon:4932 20040624 SGD
+SGD S000000471 REI1 GO:0000278 SGD_REF:S000076016|PMID:15107529 IGI SGD:S000003723 P YBR267W gene taxon:4932 20040624 SGD
+SGD S000000471 REI1 GO:0006913 SGD_REF:S000115804|PMID:16651379 IMP P YBR267W gene taxon:4932 20060522 SGD
+SGD S000000471 REI1 GO:0007117 SGD_REF:S000076016|PMID:15107529 IGI SGD:S000001756 P YBR267W gene taxon:4932 20040624 SGD
+SGD S000000471 REI1 GO:0042273 SGD_REF:S000115804|PMID:16651379 IMP P YBR267W gene taxon:4932 20060522 SGD
+SGD S000029675 REP1 GO:0005634 SGD_REF:S000055748|PMID:9393716 IDA C 2-micron circle protein B gene taxon:4932 20020717 SGD
+SGD S000029675 REP1 GO:0005554 SGD_REF:S000069584 ND F 2-micron circle protein B gene taxon:4932 20020717 SGD
+SGD S000029675 REP1 GO:0030541 SGD_REF:S000055748|PMID:9393716 IMP P 2-micron circle protein B gene taxon:4932 20020717 SGD
+SGD S000029676 REP2 GO:0005634 SGD_REF:S000055748|PMID:9393716 IDA C 2-micron circle protein C gene taxon:4932 20020717 SGD
+SGD S000029676 REP2 GO:0005554 SGD_REF:S000069584 ND F 2-micron circle protein C gene taxon:4932 20020717 SGD
+SGD S000029676 REP2 GO:0030541 SGD_REF:S000055748|PMID:9393716 IMP P 2-micron circle protein C gene taxon:4932 20020717 SGD
+SGD S000000507 RER1 GO:0030134 SGD_REF:S000061877|PMID:11157978 IDA C YCL001W gene taxon:4932 20020716 SGD
+SGD S000000507 RER1 GO:0030137 SGD_REF:S000060272|PMID:11238450 IDA C YCL001W gene taxon:4932 20040715 SGD
+SGD S000000507 RER1 GO:0030137 SGD_REF:S000060272|PMID:11238450 IMP C YCL001W gene taxon:4932 20040715 SGD
+SGD S000000507 RER1 GO:0005554 SGD_REF:S000069584 ND F YCL001W gene taxon:4932 20020716 SGD
+SGD S000000507 RER1 GO:0006621 SGD_REF:S000046953|PMID:8707815 IMP P YCL001W gene taxon:4932 20050105 SGD
+SGD S000000507 RER1 GO:0006888 SGD_REF:S000061877|PMID:11157978 IPI P YCL001W gene taxon:4932 20020716 SGD
+SGD S000000507 RER1 GO:0006890 SGD_REF:S000060272|PMID:11238450 IDA P YCL001W gene taxon:4932 20040715 SGD
+SGD S000000507 RER1 GO:0006890 SGD_REF:S000060272|PMID:11238450 IMP P YCL001W gene taxon:4932 20040715 SGD
+SGD S000000206 RER2 GO:0005783 SGD_REF:S000042696|PMID:9858571 IDA C cis-prenyltransferase YBR002C gene taxon:4932 20020307 SGD
+SGD S000000206 RER2 GO:0005783 SGD_REF:S000060857|PMID:11442630 IDA C cis-prenyltransferase YBR002C gene taxon:4932 20020307 SGD
+SGD S000000206 RER2 GO:0004659 SGD_REF:S000042696|PMID:9858571 IDA F cis-prenyltransferase YBR002C gene taxon:4932 20020307 SGD
+SGD S000000206 RER2 GO:0045547 SGD_REF:S000060857|PMID:11442630 IDA F cis-prenyltransferase YBR002C gene taxon:4932 20050708 SGD
+SGD S000000206 RER2 GO:0006486 SGD_REF:S000042696|PMID:9858571 IDA P cis-prenyltransferase YBR002C gene taxon:4932 20020307 SGD
+SGD S000000206 RER2 GO:0006486 SGD_REF:S000042696|PMID:9858571 IMP P cis-prenyltransferase YBR002C gene taxon:4932 20020307 SGD
+SGD S000000206 RER2 GO:0006888 SGD_REF:S000076242|PMID:12911815 IMP P cis-prenyltransferase YBR002C gene taxon:4932 20050712 SGD
+SGD S000000206 RER2 GO:0019408 SGD_REF:S000051704|PMID:10217761 IDA P cis-prenyltransferase YBR002C gene taxon:4932 20020827 SGD
+SGD S000005733 RET1 GO:0005666 SGD_REF:S000057661|PMID:8246845 TAS C YOR207C|C128|PDS2|RPC128|RPC2 gene taxon:4932 20010118 SGD
+SGD S000005733 RET1 GO:0003899 SGD_REF:S000057661|PMID:8246845 TAS F YOR207C|C128|PDS2|RPC128|RPC2 gene taxon:4932 20010118 SGD
+SGD S000005733 RET1 GO:0006383 SGD_REF:S000058500 TAS P YOR207C|C128|PDS2|RPC128|RPC2 gene taxon:4932 20010119 SGD
+SGD S000001947 RET2 GO:0030126 SGD_REF:S000041370|PMID:8617224 ISS C YFR051C gene taxon:4932 20020820 SGD
+SGD S000001947 RET2 GO:0030126 SGD_REF:S000041370|PMID:8617224 IMP C YFR051C gene taxon:4932 20020820 SGD
+SGD S000001947 RET2 GO:0005515 SGD_REF:S000052418|PMID:9811561 IMP F YFR051C gene taxon:4932 20020820 SGD
+SGD S000001947 RET2 GO:0006888 SGD_REF:S000041370|PMID:8617224 IMP P YFR051C gene taxon:4932 20020820 SGD
+SGD S000001947 RET2 GO:0006890 SGD_REF:S000041370|PMID:8617224 IMP P YFR051C gene taxon:4932 20020820 SGD
+SGD S000005931 RET3 GO:0030126 SGD_REF:S000041370|PMID:8617224 ISS C vesicle coat component YPL010W gene taxon:4932 20020620 SGD
+SGD S000005931 RET3 GO:0030126 SGD_REF:S000041370|PMID:8617224 IMP C vesicle coat component YPL010W gene taxon:4932 20020620 SGD
+SGD S000005931 RET3 GO:0005515 SGD_REF:S000052418|PMID:9811561 IMP F vesicle coat component YPL010W gene taxon:4932 20020620 SGD
+SGD S000005931 RET3 GO:0006890 SGD_REF:S000041370|PMID:8617224 IMP P vesicle coat component YPL010W gene taxon:4932 20020620 SGD
+SGD S000005873 REV1 GO:0005634 SGD_REF:S000069786|PMID:11850424 IC GO:0003887 C deoxycytidyl transferase YOR346W gene taxon:4932 20021025 SGD
+SGD S000005873 REV1 GO:0005739 SGD_REF:S000114282|PMID:16452144 IDA C deoxycytidyl transferase YOR346W gene taxon:4932 20060314 SGD
+SGD S000005873 REV1 GO:0003887 SGD_REF:S000069786|PMID:11850424 IDA F deoxycytidyl transferase YOR346W gene taxon:4932 20021025 SGD
+SGD S000005873 REV1 GO:0017125 SGD_REF:S000051294|PMID:8751446 IDA F deoxycytidyl transferase YOR346W gene taxon:4932 20041027 SGD
+SGD S000005873 REV1 GO:0006261 SGD_REF:S000069786|PMID:11850424 IDA P deoxycytidyl transferase YOR346W gene taxon:4932 20021025 SGD
+SGD S000005873 REV1 GO:0006281 SGD_REF:S000052530|PMID:2492497 IMP P deoxycytidyl transferase YOR346W gene taxon:4932 20021025 SGD
+SGD S000006088 REV3 GO:0005739 SGD_REF:S000114282|PMID:16452144 IDA C DNA polymerase zeta subunit YPL167C|PSO1 gene taxon:4932 20060314 SGD
+SGD S000006088 REV3 GO:0016035 SGD_REF:S000055705|PMID:8658138 IDA C DNA polymerase zeta subunit YPL167C|PSO1 gene taxon:4932 20041024 SGD
+SGD S000006088 REV3 GO:0003894 SGD_REF:S000055705|PMID:8658138 IDA F DNA polymerase zeta subunit YPL167C|PSO1 gene taxon:4932 20041024 SGD
+SGD S000006088 REV3 GO:0006280 SGD_REF:S000058372|PMID:9745046 TAS P DNA polymerase zeta subunit YPL167C|PSO1 gene taxon:4932 20010118 SGD
+SGD S000006088 REV3 GO:0006281 SGD_REF:S000058372|PMID:9745046 TAS P DNA polymerase zeta subunit YPL167C|PSO1 gene taxon:4932 20010118 SGD
+SGD S000001401 REV7 GO:0005739 SGD_REF:S000114282|PMID:16452144 IDA C DNA polymerase zeta (pol-zeta) subunit YIL139C gene taxon:4932 20060314 SGD
+SGD S000001401 REV7 GO:0016035 SGD_REF:S000055705|PMID:8658138 IDA C DNA polymerase zeta (pol-zeta) subunit YIL139C gene taxon:4932 20041024 SGD
+SGD S000001401 REV7 GO:0003894 SGD_REF:S000055705|PMID:8658138 IDA F DNA polymerase zeta (pol-zeta) subunit YIL139C gene taxon:4932 20041024 SGD
+SGD S000001401 REV7 GO:0006280 SGD_REF:S000058372|PMID:9745046 TAS P DNA polymerase zeta (pol-zeta) subunit YIL139C gene taxon:4932 20010118 SGD
+SGD S000001401 REV7 GO:0006281 SGD_REF:S000058372|PMID:9745046 TAS P DNA polymerase zeta (pol-zeta) subunit YIL139C gene taxon:4932 20010118 SGD
+SGD S000004049 REX2 GO:0005739 SGD_REF:S000049298|PMID:9933355 IMP C RNA exonuclease YLR059C|YNT20 gene taxon:4932 20010118 SGD
+SGD S000004049 REX2 GO:0005739 SGD_REF:S000049298|PMID:9933355 IDA C RNA exonuclease YLR059C|YNT20 gene taxon:4932 20010118 SGD
+SGD S000004049 REX2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C RNA exonuclease YLR059C|YNT20 gene taxon:4932 20040924 SGD
+SGD S000004049 REX2 GO:0008408 SGD_REF:S000044002|PMID:10716935 IMP F RNA exonuclease YLR059C|YNT20 gene taxon:4932 20010118 SGD
+SGD S000004049 REX2 GO:0008408 SGD_REF:S000044002|PMID:10716935 ISS F RNA exonuclease YLR059C|YNT20 gene taxon:4932 20010118 SGD
+SGD S000004049 REX2 GO:0006396 SGD_REF:S000044002|PMID:10716935 IMP P RNA exonuclease YLR059C|YNT20 gene taxon:4932 20010118 SGD
+SGD S000004097 REX3 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YLR107W gene taxon:4932 20031028 SGD
+SGD S000004097 REX3 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YLR107W gene taxon:4932 20031028 SGD
+SGD S000004097 REX3 GO:0008408 SGD_REF:S000044002|PMID:10716935 IMP F YLR107W gene taxon:4932 20010118 SGD
+SGD S000004097 REX3 GO:0008408 SGD_REF:S000044002|PMID:10716935 ISS F YLR107W gene taxon:4932 20010118 SGD
+SGD S000004097 REX3 GO:0006396 SGD_REF:S000044002|PMID:10716935 IMP P YLR107W gene taxon:4932 20010118 SGD
+SGD S000005440 REX4 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YOL080C gene taxon:4932 20031028 SGD
+SGD S000005440 REX4 GO:0005730 SGD_REF:S000074185|PMID:14562095 IDA C YOL080C gene taxon:4932 20031028 SGD
+SGD S000005440 REX4 GO:0008408 SGD_REF:S000044002|PMID:10716935 ISS F YOL080C gene taxon:4932 20010118 SGD
+SGD S000005440 REX4 GO:0008408 SGD_REF:S000044002|PMID:10716935 IMP F YOL080C gene taxon:4932 20010118 SGD
+SGD S000005440 REX4 GO:0006364 SGD_REF:S000071873|PMID:12364601 IGI SGD:S000004842 P YOL080C gene taxon:4932 20021222 SGD
+SGD S000005440 REX4 GO:0042255 SGD_REF:S000071873|PMID:12364601 IMP P YOL080C gene taxon:4932 20021222 SGD
+SGD S000029417 RF2 GO:0005739 SGD_REF:S000055782|PMID:1651178 IDA C gene taxon:4932 20021025 SGD
+SGD S000029417 RF2 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20021025 SGD
+SGD S000029417 RF2 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20021025 SGD
+SGD S000000065 RFA1 GO:0000781 SGD_REF:S000074597|PMID:14702040 IMP C RF-A, heterotrimeric RPA (RF-A) single-stranded DNA binding protein 69 kDa subunit YAR007C|BUF2|FUN3|RPA1 gene taxon:4932 20040327 SGD
+SGD S000000065 RFA1 GO:0005634 SGD_REF:S000077144|PMID:15282802 IDA C RF-A, heterotrimeric RPA (RF-A) single-stranded DNA binding protein 69 kDa subunit YAR007C|BUF2|FUN3|RPA1 gene taxon:4932 20041008 SGD
+SGD S000000065 RFA1 GO:0005662 SGD_REF:S000058458|PMID:9242902 TAS C RF-A, heterotrimeric RPA (RF-A) single-stranded DNA binding protein 69 kDa subunit YAR007C|BUF2|FUN3|RPA1 gene taxon:4932 20010118 SGD
+SGD S000000065 RFA1 GO:0005737 SGD_REF:S000077144|PMID:15282802 IDA C RF-A, heterotrimeric RPA (RF-A) single-stranded DNA binding protein 69 kDa subunit YAR007C|BUF2|FUN3|RPA1 gene taxon:4932 20041008 SGD
+SGD S000000065 RFA1 GO:0003684 SGD_REF:S000058458|PMID:9242902 TAS F RF-A, heterotrimeric RPA (RF-A) single-stranded DNA binding protein 69 kDa subunit YAR007C|BUF2|FUN3|RPA1 gene taxon:4932 20010118 SGD
+SGD S000000065 RFA1 GO:0003697 SGD_REF:S000058458|PMID:9242902 TAS F RF-A, heterotrimeric RPA (RF-A) single-stranded DNA binding protein 69 kDa subunit YAR007C|BUF2|FUN3|RPA1 gene taxon:4932 20010118 SGD
+SGD S000000065 RFA1 GO:0006268 SGD_REF:S000058458|PMID:9242902 TAS P RF-A, heterotrimeric RPA (RF-A) single-stranded DNA binding protein 69 kDa subunit YAR007C|BUF2|FUN3|RPA1 gene taxon:4932 20010118 SGD
+SGD S000000065 RFA1 GO:0006269 SGD_REF:S000058458|PMID:9242902 TAS P RF-A, heterotrimeric RPA (RF-A) single-stranded DNA binding protein 69 kDa subunit YAR007C|BUF2|FUN3|RPA1 gene taxon:4932 20010118 SGD
+SGD S000000065 RFA1 GO:0006271 SGD_REF:S000058458|PMID:9242902 TAS P RF-A, heterotrimeric RPA (RF-A) single-stranded DNA binding protein 69 kDa subunit YAR007C|BUF2|FUN3|RPA1 gene taxon:4932 20010118 SGD
+SGD S000000065 RFA1 GO:0006289 SGD_REF:S000058458|PMID:9242902 TAS P RF-A, heterotrimeric RPA (RF-A) single-stranded DNA binding protein 69 kDa subunit YAR007C|BUF2|FUN3|RPA1 gene taxon:4932 20010118 SGD
+SGD S000000065 RFA1 GO:0006301 SGD_REF:S000058458|PMID:9242902 TAS P RF-A, heterotrimeric RPA (RF-A) single-stranded DNA binding protein 69 kDa subunit YAR007C|BUF2|FUN3|RPA1 gene taxon:4932 20010118 SGD
+SGD S000000065 RFA1 GO:0006302 SGD_REF:S000058458|PMID:9242902 TAS P RF-A, heterotrimeric RPA (RF-A) single-stranded DNA binding protein 69 kDa subunit YAR007C|BUF2|FUN3|RPA1 gene taxon:4932 20010118 SGD
+SGD S000000065 RFA1 GO:0006310 SGD_REF:S000058458|PMID:9242902 TAS P RF-A, heterotrimeric RPA (RF-A) single-stranded DNA binding protein 69 kDa subunit YAR007C|BUF2|FUN3|RPA1 gene taxon:4932 20010118 SGD
+SGD S000005256 RFA2 GO:0000781 SGD_REF:S000074597|PMID:14702040 IMP C 29% identical to the human p34 subunit of RF-A, replication factor RF-A subunit 2 YNL312W|BUF1|RPA2 gene taxon:4932 20040327 SGD
+SGD S000005256 RFA2 GO:0005662 SGD_REF:S000058458|PMID:9242902 TAS C 29% identical to the human p34 subunit of RF-A, replication factor RF-A subunit 2 YNL312W|BUF1|RPA2 gene taxon:4932 20010118 SGD
+SGD S000005256 RFA2 GO:0003677 SGD_REF:S000058458|PMID:9242902 TAS F 29% identical to the human p34 subunit of RF-A, replication factor RF-A subunit 2 YNL312W|BUF1|RPA2 gene taxon:4932 20021107 SGD
+SGD S000005256 RFA2 GO:0006268 SGD_REF:S000058458|PMID:9242902 TAS P 29% identical to the human p34 subunit of RF-A, replication factor RF-A subunit 2 YNL312W|BUF1|RPA2 gene taxon:4932 20010118 SGD
+SGD S000005256 RFA2 GO:0006269 SGD_REF:S000058458|PMID:9242902 TAS P 29% identical to the human p34 subunit of RF-A, replication factor RF-A subunit 2 YNL312W|BUF1|RPA2 gene taxon:4932 20010118 SGD
+SGD S000005256 RFA2 GO:0006271 SGD_REF:S000058458|PMID:9242902 TAS P 29% identical to the human p34 subunit of RF-A, replication factor RF-A subunit 2 YNL312W|BUF1|RPA2 gene taxon:4932 20010118 SGD
+SGD S000005256 RFA2 GO:0006289 SGD_REF:S000058458|PMID:9242902 TAS P 29% identical to the human p34 subunit of RF-A, replication factor RF-A subunit 2 YNL312W|BUF1|RPA2 gene taxon:4932 20010118 SGD
+SGD S000005256 RFA2 GO:0006301 SGD_REF:S000058458|PMID:9242902 TAS P 29% identical to the human p34 subunit of RF-A, replication factor RF-A subunit 2 YNL312W|BUF1|RPA2 gene taxon:4932 20010118 SGD
+SGD S000005256 RFA2 GO:0006302 SGD_REF:S000058458|PMID:9242902 TAS P 29% identical to the human p34 subunit of RF-A, replication factor RF-A subunit 2 YNL312W|BUF1|RPA2 gene taxon:4932 20010118 SGD
+SGD S000005256 RFA2 GO:0006310 SGD_REF:S000058458|PMID:9242902 TAS P 29% identical to the human p34 subunit of RF-A, replication factor RF-A subunit 2 YNL312W|BUF1|RPA2 gene taxon:4932 20010118 SGD
+SGD S000003709 RFA3 GO:0000781 SGD_REF:S000074597|PMID:14702040 IMP C replication factor-A subunit 3 YJL173C gene taxon:4932 20040327 SGD
+SGD S000003709 RFA3 GO:0005662 SGD_REF:S000058458|PMID:9242902 TAS C replication factor-A subunit 3 YJL173C gene taxon:4932 20010118 SGD
+SGD S000003709 RFA3 GO:0003677 SGD_REF:S000058458|PMID:9242902 TAS F replication factor-A subunit 3 YJL173C gene taxon:4932 20021107 SGD
+SGD S000003709 RFA3 GO:0006268 SGD_REF:S000058458|PMID:9242902 TAS P replication factor-A subunit 3 YJL173C gene taxon:4932 20010118 SGD
+SGD S000003709 RFA3 GO:0006269 SGD_REF:S000058458|PMID:9242902 TAS P replication factor-A subunit 3 YJL173C gene taxon:4932 20010118 SGD
+SGD S000003709 RFA3 GO:0006271 SGD_REF:S000058458|PMID:9242902 TAS P replication factor-A subunit 3 YJL173C gene taxon:4932 20010118 SGD
+SGD S000003709 RFA3 GO:0006289 SGD_REF:S000058458|PMID:9242902 TAS P replication factor-A subunit 3 YJL173C gene taxon:4932 20010118 SGD
+SGD S000003709 RFA3 GO:0006301 SGD_REF:S000058458|PMID:9242902 TAS P replication factor-A subunit 3 YJL173C gene taxon:4932 20010118 SGD
+SGD S000003709 RFA3 GO:0006302 SGD_REF:S000058458|PMID:9242902 TAS P replication factor-A subunit 3 YJL173C gene taxon:4932 20010118 SGD
+SGD S000003709 RFA3 GO:0006310 SGD_REF:S000058458|PMID:9242902 TAS P replication factor-A subunit 3 YJL173C gene taxon:4932 20010118 SGD
+SGD S000005743 RFC1 GO:0005663 SGD_REF:S000054418|PMID:7651383 IDA C replication factor C subunit 1, similar to human RFC 140 kDa subunit YOR217W|CDC44 gene taxon:4932 20030205 SGD
+SGD S000005743 RFC1 contributes_to GO:0003689 SGD_REF:S000047559|PMID:8995429 IDA F replication factor C subunit 1, similar to human RFC 140 kDa subunit YOR217W|CDC44 gene taxon:4932 20051017 SGD
+SGD S000005743 RFC1 GO:0006272 SGD_REF:S000056486|PMID:1346062 IDA P replication factor C subunit 1, similar to human RFC 140 kDa subunit YOR217W|CDC44 gene taxon:4932 20030205 SGD
+SGD S000005743 RFC1 GO:0006281 SGD_REF:S000039438|PMID:8770585 IMP P replication factor C subunit 1, similar to human RFC 140 kDa subunit YOR217W|CDC44 gene taxon:4932 20030205 SGD
+SGD S000005743 RFC1 GO:0006298 SGD_REF:S000058456|PMID:10072354 TAS P replication factor C subunit 1, similar to human RFC 140 kDa subunit YOR217W|CDC44 gene taxon:4932 20010118 SGD
+SGD S000003829 RFC2 GO:0005663 SGD_REF:S000042913|PMID:8202350 IDA C replication factor C subunit 2, similar to human RFC 37 kDa subunit YJR068W gene taxon:4932 20030205 SGD
+SGD S000003829 RFC2 contributes_to GO:0003689 SGD_REF:S000072671|PMID:12604797 IDA F replication factor C subunit 2, similar to human RFC 37 kDa subunit YJR068W gene taxon:4932 20030311 SGD
+SGD S000003829 RFC2 contributes_to GO:0003689 SGD_REF:S000047559|PMID:8995429 IDA F replication factor C subunit 2, similar to human RFC 37 kDa subunit YJR068W gene taxon:4932 20051017 SGD
+SGD S000003829 RFC2 GO:0017076 SGD_REF:S000054418|PMID:7651383 ISS F replication factor C subunit 2, similar to human RFC 37 kDa subunit YJR068W gene taxon:4932 20030205 SGD
+SGD S000003829 RFC2 GO:0000075 SGD_REF:S000043382|PMID:9671499 IMP P replication factor C subunit 2, similar to human RFC 37 kDa subunit YJR068W gene taxon:4932 20030205 SGD
+SGD S000003829 RFC2 GO:0006272 SGD_REF:S000056486|PMID:1346062 IDA P replication factor C subunit 2, similar to human RFC 37 kDa subunit YJR068W gene taxon:4932 20030205 SGD
+SGD S000003829 RFC2 GO:0006298 SGD_REF:S000058456|PMID:10072354 TAS P replication factor C subunit 2, similar to human RFC 37 kDa subunit YJR068W gene taxon:4932 20010118 SGD
+SGD S000003829 RFC2 GO:0007062 SGD_REF:S000060777|PMID:11389843 IPI P replication factor C subunit 2, similar to human RFC 37 kDa subunit YJR068W gene taxon:4932 20020811 SGD
+SGD S000005234 RFC3 GO:0005634 SGD_REF:S000069459|PMID:11914276 IDA C replication factor C subunit 3, similar to human RFC 36 kDa subunit YNL290W gene taxon:4932 20020507 SGD
+SGD S000005234 RFC3 GO:0005663 SGD_REF:S000054418|PMID:7651383 IDA C replication factor C subunit 3, similar to human RFC 36 kDa subunit YNL290W gene taxon:4932 20030205 SGD
+SGD S000005234 RFC3 contributes_to GO:0003689 SGD_REF:S000072671|PMID:12604797 IDA F replication factor C subunit 3, similar to human RFC 36 kDa subunit YNL290W gene taxon:4932 20030311 SGD
+SGD S000005234 RFC3 contributes_to GO:0003689 SGD_REF:S000047559|PMID:8995429 IDA F replication factor C subunit 3, similar to human RFC 36 kDa subunit YNL290W gene taxon:4932 20051017 SGD
+SGD S000005234 RFC3 GO:0016887 SGD_REF:S000051370|PMID:8302859 IDA F replication factor C subunit 3, similar to human RFC 36 kDa subunit YNL290W gene taxon:4932 20030205 SGD
+SGD S000005234 RFC3 GO:0006272 SGD_REF:S000056486|PMID:1346062 IDA P replication factor C subunit 3, similar to human RFC 36 kDa subunit YNL290W gene taxon:4932 20030205 SGD
+SGD S000005234 RFC3 GO:0006298 SGD_REF:S000058456|PMID:10072354 TAS P replication factor C subunit 3, similar to human RFC 36 kDa subunit YNL290W gene taxon:4932 20010118 SGD
+SGD S000005234 RFC3 GO:0007062 SGD_REF:S000060777|PMID:11389843 IPI P replication factor C subunit 3, similar to human RFC 36 kDa subunit YNL290W gene taxon:4932 20020811 SGD
+SGD S000005454 RFC4 GO:0005663 SGD_REF:S000056323|PMID:8063832 IDA C replication factor C subunit 4, similar to human RFC 40 kDa subunit YOL094C gene taxon:4932 20030206 SGD
+SGD S000005454 RFC4 GO:0005663 SGD_REF:S000056323|PMID:8063832 ISS C replication factor C subunit 4, similar to human RFC 40 kDa subunit YOL094C gene taxon:4932 20030206 SGD
+SGD S000005454 RFC4 contributes_to GO:0003689 SGD_REF:S000072671|PMID:12604797 IDA F replication factor C subunit 4, similar to human RFC 40 kDa subunit YOL094C gene taxon:4932 20030311 SGD
+SGD S000005454 RFC4 contributes_to GO:0003689 SGD_REF:S000047559|PMID:8995429 IDA F replication factor C subunit 4, similar to human RFC 40 kDa subunit YOL094C gene taxon:4932 20051017 SGD
+SGD S000005454 RFC4 GO:0017076 SGD_REF:S000054418|PMID:7651383 ISS F replication factor C subunit 4, similar to human RFC 40 kDa subunit YOL094C gene taxon:4932 20030206 SGD
+SGD S000005454 RFC4 GO:0006272 SGD_REF:S000056486|PMID:1346062 IDA P replication factor C subunit 4, similar to human RFC 40 kDa subunit YOL094C gene taxon:4932 20030205 SGD
+SGD S000005454 RFC4 GO:0006298 SGD_REF:S000058456|PMID:10072354 TAS P replication factor C subunit 4, similar to human RFC 40 kDa subunit YOL094C gene taxon:4932 20010118 SGD
+SGD S000005454 RFC4 GO:0007062 SGD_REF:S000060777|PMID:11389843 IPI P replication factor C subunit 4, similar to human RFC 40 kDa subunit YOL094C gene taxon:4932 20020811 SGD
+SGD S000000291 RFC5 GO:0005663 SGD_REF:S000054418|PMID:7651383 IDA C replication factor C subunit 5, similar to human RFC 38 kDa subunit YBR087W gene taxon:4932 20030131 SGD
+SGD S000000291 RFC5 GO:0005663 SGD_REF:S000054883|PMID:8559655 IMP C replication factor C subunit 5, similar to human RFC 38 kDa subunit YBR087W gene taxon:4932 20030131 SGD
+SGD S000000291 RFC5 contributes_to GO:0003689 SGD_REF:S000072671|PMID:12604797 IDA F replication factor C subunit 5, similar to human RFC 38 kDa subunit YBR087W gene taxon:4932 20030311 SGD
+SGD S000000291 RFC5 contributes_to GO:0003689 SGD_REF:S000047559|PMID:8995429 IDA F replication factor C subunit 5, similar to human RFC 38 kDa subunit YBR087W gene taxon:4932 20051017 SGD
+SGD S000000291 RFC5 GO:0006272 SGD_REF:S000056486|PMID:1346062 IDA P replication factor C subunit 5, similar to human RFC 38 kDa subunit YBR087W gene taxon:4932 20030205 SGD
+SGD S000000291 RFC5 GO:0006298 SGD_REF:S000058456|PMID:10072354 TAS P replication factor C subunit 5, similar to human RFC 38 kDa subunit YBR087W gene taxon:4932 20010118 SGD
+SGD S000000291 RFC5 GO:0007062 SGD_REF:S000060777|PMID:11389843 IPI P replication factor C subunit 5, similar to human RFC 38 kDa subunit YBR087W gene taxon:4932 20020811 SGD
+SGD S000005805 RFM1 GO:0000118 SGD_REF:S000072806|PMID:12612074 IPI C DNA-binding protein YOR279C gene taxon:4932 20030325 SGD
+SGD S000005805 RFM1 GO:0005634 SGD_REF:S000066205|PMID:11711434 IPI C DNA-binding protein YOR279C gene taxon:4932 20021120 SGD
+SGD S000005805 RFM1 GO:0051082 SGD_REF:S000072806|PMID:12612074 IMP F DNA-binding protein YOR279C gene taxon:4932 20030327 SGD
+SGD S000005805 RFM1 GO:0051082 SGD_REF:S000072806|PMID:12612074 IGI F DNA-binding protein YOR279C gene taxon:4932 20030327 SGD
+SGD S000005805 RFM1 GO:0051082 SGD_REF:S000072806|PMID:12612074 IPI F DNA-binding protein YOR279C gene taxon:4932 20030327 SGD
+SGD S000005805 RFM1 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P DNA-binding protein YOR279C gene taxon:4932 20060203 SGD
+SGD S000005805 RFM1 GO:0006342 SGD_REF:S000072806|PMID:12612074 IMP P DNA-binding protein YOR279C gene taxon:4932 20030325 SGD
+SGD S000005805 RFM1 GO:0006342 SGD_REF:S000072806|PMID:12612074 IGI P DNA-binding protein YOR279C gene taxon:4932 20030325 SGD
+SGD S000005805 RFM1 GO:0006342 SGD_REF:S000072806|PMID:12612074 IPI P DNA-binding protein YOR279C gene taxon:4932 20030325 SGD
+SGD S000000256 RFS1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C member of a flavodoxin-like fold protein family (including also Pst2 and Ycp4). YBR052C gene taxon:4932 20031028 SGD
+SGD S000000256 RFS1 GO:0005554 SGD_REF:S000069584 ND F member of a flavodoxin-like fold protein family (including also Pst2 and Ycp4). YBR052C gene taxon:4932 20030203 SGD
+SGD S000000256 RFS1 GO:0000004 SGD_REF:S000069584 ND P member of a flavodoxin-like fold protein family (including also Pst2 and Ycp4). YBR052C gene taxon:4932 20030203 SGD
+SGD S000000116 RFT1 GO:0005789 SGD_REF:S000069444|PMID:11807558 IDA C 67 kDa integral membrane protein YBL020W gene taxon:4932 20021023 SGD
+SGD S000000116 RFT1 GO:0015157 SGD_REF:S000069444|PMID:11807558 IMP F 67 kDa integral membrane protein YBL020W gene taxon:4932 20021023 SGD
+SGD S000000116 RFT1 GO:0006487 SGD_REF:S000069444|PMID:11807558 IMP P 67 kDa integral membrane protein YBL020W gene taxon:4932 20021023 SGD
+SGD S000000116 RFT1 GO:0015772 SGD_REF:S000069444|PMID:11807558 IMP P 67 kDa integral membrane protein YBL020W gene taxon:4932 20021023 SGD
+SGD S000004166 RFX1 GO:0005634 SGD_REF:S000069459|PMID:11914276 IDA C YLR176C|CRT1 gene taxon:4932 20020507 SGD
+SGD S000004166 RFX1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YLR176C|CRT1 gene taxon:4932 20031028 SGD
+SGD S000004166 RFX1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YLR176C|CRT1 gene taxon:4932 20020507 SGD
+SGD S000004166 RFX1 GO:0016566 SGD_REF:S000039971|PMID:9741624 IDA F YLR176C|CRT1 gene taxon:4932 20021216 SGD
+SGD S000004166 RFX1 GO:0000077 SGD_REF:S000039971|PMID:9741624 TAS P YLR176C|CRT1 gene taxon:4932 20021216 SGD
+SGD S000004166 RFX1 GO:0000122 SGD_REF:S000039971|PMID:9741624 IDA P YLR176C|CRT1 gene taxon:4932 20021216 SGD
+SGD S000005653 RGA1 GO:0005622 SGD_REF:S000058399|PMID:9891811 TAS C rho GTPase activating protein (GAP) YOR127W|DBM1|THE1 gene taxon:4932 20010118 SGD
+SGD S000005653 RGA1 GO:0004871 SGD_REF:S000058399|PMID:9891811 IPI F rho GTPase activating protein (GAP) YOR127W|DBM1|THE1 gene taxon:4932 20010118 SGD
+SGD S000005653 RGA1 GO:0005100 SGD_REF:S000058399|PMID:9891811 IPI F rho GTPase activating protein (GAP) YOR127W|DBM1|THE1 gene taxon:4932 20010118 SGD
+SGD S000005653 RGA1 GO:0005100 SGD_REF:S000058399|PMID:9891811 ISS F rho GTPase activating protein (GAP) YOR127W|DBM1|THE1 gene taxon:4932 20010118 SGD
+SGD S000005653 RGA1 GO:0000750 SGD_REF:S000053458|PMID:7498791 IGI P rho GTPase activating protein (GAP) YOR127W|DBM1|THE1 gene taxon:4932 20021206 SGD
+SGD S000005653 RGA1 GO:0001403 SGD_REF:S000056064|PMID:10066831 IPI P rho GTPase activating protein (GAP) YOR127W|DBM1|THE1 gene taxon:4932 20010118 SGD
+SGD S000005653 RGA1 GO:0007015 SGD_REF:S000054066|PMID:8657111 IMP P rho GTPase activating protein (GAP) YOR127W|DBM1|THE1 gene taxon:4932 20030116 SGD
+SGD S000005653 RGA1 GO:0007118 SGD_REF:S000056064|PMID:10066831 IPI P rho GTPase activating protein (GAP) YOR127W|DBM1|THE1 gene taxon:4932 20010118 SGD
+SGD S000005653 RGA1 GO:0007119 SGD_REF:S000056064|PMID:10066831 IPI P rho GTPase activating protein (GAP) YOR127W|DBM1|THE1 gene taxon:4932 20010118 SGD
+SGD S000005653 RGA1 GO:0007124 SGD_REF:S000056064|PMID:10066831 IPI P rho GTPase activating protein (GAP) YOR127W|DBM1|THE1 gene taxon:4932 20010118 SGD
+SGD S000005653 RGA1 GO:0007264 SGD_REF:S000058399|PMID:9891811 IPI P rho GTPase activating protein (GAP) YOR127W|DBM1|THE1 gene taxon:4932 20010118 SGD
+SGD S000005653 RGA1 GO:0030468 SGD_REF:S000058399|PMID:9891811 IPI P rho GTPase activating protein (GAP) YOR127W|DBM1|THE1 gene taxon:4932 20010302 SGD
+SGD S000002787 RGA2 GO:0005622 SGD_REF:S000058399|PMID:9891811 TAS C Rho-GTPase Activating Protein YDR379W gene taxon:4932 20010118 SGD
+SGD S000002787 RGA2 GO:0004871 SGD_REF:S000058399|PMID:9891811 ISS F Rho-GTPase Activating Protein YDR379W gene taxon:4932 20010118 SGD
+SGD S000002787 RGA2 GO:0005100 SGD_REF:S000058399|PMID:9891811 ISS F Rho-GTPase Activating Protein YDR379W gene taxon:4932 20010118 SGD
+SGD S000002787 RGA2 GO:0000750 SGD_REF:S000056064|PMID:10066831 TAS P Rho-GTPase Activating Protein YDR379W gene taxon:4932 20021206 SGD
+SGD S000002787 RGA2 GO:0001403 SGD_REF:S000056064|PMID:10066831 ISS P Rho-GTPase Activating Protein YDR379W gene taxon:4932 20010118 SGD
+SGD S000002787 RGA2 GO:0007015 SGD_REF:S000053458|PMID:7498791 ISS P Rho-GTPase Activating Protein YDR379W gene taxon:4932 20030116 SGD
+SGD S000002787 RGA2 GO:0007118 SGD_REF:S000056064|PMID:10066831 ISS P Rho-GTPase Activating Protein YDR379W gene taxon:4932 20010118 SGD
+SGD S000002787 RGA2 GO:0007119 SGD_REF:S000056064|PMID:10066831 ISS P Rho-GTPase Activating Protein YDR379W gene taxon:4932 20010118 SGD
+SGD S000002787 RGA2 GO:0007124 SGD_REF:S000056064|PMID:10066831 ISS P Rho-GTPase Activating Protein YDR379W gene taxon:4932 20010118 SGD
+SGD S000002787 RGA2 GO:0007264 SGD_REF:S000058399|PMID:9891811 ISS P Rho-GTPase Activating Protein YDR379W gene taxon:4932 20010118 SGD
+SGD S000002787 RGA2 GO:0030468 SGD_REF:S000058399|PMID:9891811 ISS P Rho-GTPase Activating Protein YDR379W gene taxon:4932 20010302 SGD
+SGD S000000464 RGD1 GO:0005933 SGD_REF:S000059395|PMID:10931290 IDA C GTPase activating protein (GAP) (putative) YBR260C gene taxon:4932 20021007 SGD
+SGD S000000464 RGD1 GO:0030479 SGD_REF:S000059395|PMID:10931290 IDA C GTPase activating protein (GAP) (putative) YBR260C gene taxon:4932 20021007 SGD
+SGD S000000464 RGD1 GO:0005100 SGD_REF:S000049067|PMID:10526184 IDA F GTPase activating protein (GAP) (putative) YBR260C gene taxon:4932 20021007 SGD
+SGD S000000464 RGD1 GO:0007231 SGD_REF:S000046581|PMID:10590461 IGI P GTPase activating protein (GAP) (putative) YBR260C gene taxon:4932 20021007 SGD
+SGD S000001847 RGD2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YFL047W gene taxon:4932 20031028 SGD
+SGD S000001847 RGD2 GO:0005935 SGD_REF:S000074185|PMID:14562095 IDA C YFL047W gene taxon:4932 20031028 SGD
+SGD S000001847 RGD2 GO:0005100 SGD_REF:S000066007|PMID:11591390 IDA F YFL047W gene taxon:4932 20021029 SGD
+SGD S000001847 RGD2 GO:0007264 SGD_REF:S000066007|PMID:11591390 IC GO:0005100 P YFL047W gene taxon:4932 20021029 SGD
+SGD S000001847 RGD2 GO:0007264 SGD_REF:S000066007|PMID:11591390 IPI P YFL047W gene taxon:4932 20021029 SGD
+SGD S000004794 RGM1 GO:0005634 SGD_REF:S000051858|PMID:1923755 IC GO:0003702 C transcriptional repressor with proline-rich zinc fingers (putative) YMR182C gene taxon:4932 20021029 SGD
+SGD S000004794 RGM1 GO:0003702 SGD_REF:S000051858|PMID:1923755 IDA F transcriptional repressor with proline-rich zinc fingers (putative) YMR182C gene taxon:4932 20021029 SGD
+SGD S000004794 RGM1 GO:0003702 SGD_REF:S000051858|PMID:1923755 ISS F transcriptional repressor with proline-rich zinc fingers (putative) YMR182C gene taxon:4932 20021029 SGD
+SGD S000004794 RGM1 GO:0000122 SGD_REF:S000051858|PMID:1923755 IDA P transcriptional repressor with proline-rich zinc fingers (putative) YMR182C gene taxon:4932 20021029 SGD
+SGD S000002544 RGP1 GO:0000139 SGD_REF:S000071749|PMID:10990452 IPI SGD:S000004029 C YDR137W gene taxon:4932 20060413 SGD
+SGD S000002544 RGP1 GO:0005794 SGD_REF:S000071749|PMID:10990452 IDA C YDR137W gene taxon:4932 20060413 SGD
+SGD S000002544 RGP1 GO:0032045 SGD_REF:S000071749|PMID:10990452 IDA C YDR137W gene taxon:4932 20060425 SGD
+SGD S000002544 RGP1 contributes_to GO:0005085 SGD_REF:S000071749|PMID:10990452 IDA F YDR137W gene taxon:4932 20060414 SGD
+SGD S000002544 RGP1 contributes_to GO:0005085 SGD_REF:S000071749|PMID:10990452 IPI SGD:S000004252 F YDR137W gene taxon:4932 20060414 SGD
+SGD S000002544 RGP1 GO:0042147 SGD_REF:S000071749|PMID:10990452 IPI SGD:S000004252 P YDR137W gene taxon:4932 20060414 SGD
+SGD S000002544 RGP1 GO:0042147 SGD_REF:S000059967|PMID:11082047 IMP P YDR137W gene taxon:4932 20060414 SGD
+SGD S000004061 RGR1 GO:0000119 SGD_REF:S000048078|PMID:9420330 IDA C RNA polymerase II holoenzyme/mediator subunit, interacts with Sin4p, Gal11p, and a 50 kDa polypeptide YLR071C|MED14 gene taxon:4932 20010118 SGD
+SGD S000004061 RGR1 GO:0016455 SGD_REF:S000048078|PMID:9420330 IDA F RNA polymerase II holoenzyme/mediator subunit, interacts with Sin4p, Gal11p, and a 50 kDa polypeptide YLR071C|MED14 gene taxon:4932 20010302 SGD
+SGD S000004061 RGR1 GO:0006366 SGD_REF:S000048078|PMID:9420330 IDA P RNA polymerase II holoenzyme/mediator subunit, interacts with Sin4p, Gal11p, and a 50 kDa polypeptide YLR071C|MED14 gene taxon:4932 20010118 SGD
+SGD S000005633 RGS2 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C GTPase activating protein (GAP) YOR107W gene taxon:4932 20031028 SGD
+SGD S000005633 RGS2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C GTPase activating protein (GAP) YOR107W gene taxon:4932 20031028 SGD
+SGD S000005633 RGS2 GO:0005096 SGD_REF:S000044950|PMID:10523302 IDA F GTPase activating protein (GAP) YOR107W gene taxon:4932 20020708 SGD
+SGD S000005633 RGS2 GO:0007188 SGD_REF:S000044950|PMID:10523302 IMP P GTPase activating protein (GAP) YOR107W gene taxon:4932 20020708 SGD
+SGD S000001521 RGT1 GO:0005634 SGD_REF:S000058451|PMID:10087931 IC GO:0003677 C transcriptional activator, transcriptional repressor YKL038W gene taxon:4932 20021114 SGD
+SGD S000001521 RGT1 GO:0003677 SGD_REF:S000058451|PMID:10087931 TAS F transcriptional activator, transcriptional repressor YKL038W gene taxon:4932 20010926 SGD
+SGD S000001521 RGT1 GO:0003677 SGD_REF:S000073901|PMID:12861007 IDA F transcriptional activator, transcriptional repressor YKL038W gene taxon:4932 20050117 SGD
+SGD S000001521 RGT1 GO:0003702 SGD_REF:S000058451|PMID:10087931 TAS F transcriptional activator, transcriptional repressor YKL038W gene taxon:4932 20010926 SGD
+SGD S000001521 RGT1 GO:0003714 SGD_REF:S000058451|PMID:10087931 TAS F transcriptional activator, transcriptional repressor YKL038W gene taxon:4932 20010926 SGD
+SGD S000001521 RGT1 GO:0016563 SGD_REF:S000058451|PMID:10087931 TAS F transcriptional activator, transcriptional repressor YKL038W gene taxon:4932 20010926 SGD
+SGD S000001521 RGT1 GO:0016564 SGD_REF:S000073901|PMID:12861007 IDA F transcriptional activator, transcriptional repressor YKL038W gene taxon:4932 20050117 SGD
+SGD S000001521 RGT1 GO:0006006 SGD_REF:S000058451|PMID:10087931 TAS P transcriptional activator, transcriptional repressor YKL038W gene taxon:4932 20010926 SGD
+SGD S000001521 RGT1 GO:0016481 SGD_REF:S000073901|PMID:12861007 IDA P transcriptional activator, transcriptional repressor YKL038W gene taxon:4932 20050117 SGD
+SGD S000001521 RGT1 GO:0046324 SGD_REF:S000043305|PMID:8887670 IEP P transcriptional activator, transcriptional repressor YKL038W gene taxon:4932 20040710 SGD
+SGD S000002297 RGT2 GO:0005886 SGD_REF:S000046235|PMID:8901598 ISS C glucose receptor YDL138W gene taxon:4932 20021003 SGD
+SGD S000002297 RGT2 GO:0005886 SGD_REF:S000046235|PMID:8901598 IMP C glucose receptor YDL138W gene taxon:4932 20021003 SGD
+SGD S000002297 RGT2 GO:0004872 SGD_REF:S000045421|PMID:10477308 TAS F glucose receptor YDL138W gene taxon:4932 20021204 SGD
+SGD S000002297 RGT2 NOT GO:0005355 SGD_REF:S000045421|PMID:10477308 TAS F glucose receptor YDL138W gene taxon:4932 20021204 SGD
+SGD S000002297 RGT2 GO:0005536 SGD_REF:S000045421|PMID:10477308 TAS F glucose receptor YDL138W gene taxon:4932 20021204 SGD
+SGD S000002297 RGT2 GO:0007165 SGD_REF:S000045421|PMID:10477308 TAS P glucose receptor YDL138W gene taxon:4932 20021204 SGD
+SGD S000002297 RGT2 GO:0009749 SGD_REF:S000046235|PMID:8901598 IMP P glucose receptor YDL138W gene taxon:4932 20021003 SGD
+SGD S000000622 RHB1 GO:0019897 SGD_REF:S000052257|PMID:10753927 IGI C GTP-binding protein, Rheb, ras family YCR027C|RSG1 gene taxon:4932 20020104 SGD
+SGD S000000622 RHB1 GO:0003924 SGD_REF:S000052257|PMID:10753927 ISS F GTP-binding protein, Rheb, ras family YCR027C|RSG1 gene taxon:4932 20011023 SGD
+SGD S000000622 RHB1 GO:0015809 SGD_REF:S000052257|PMID:10753927 IMP P GTP-binding protein, Rheb, ras family YCR027C|RSG1 gene taxon:4932 20011023 SGD
+SGD S000000622 RHB1 GO:0015809 SGD_REF:S000052257|PMID:10753927 IGI P GTP-binding protein, Rheb, ras family YCR027C|RSG1 gene taxon:4932 20011023 SGD
+SGD S000000622 RHB1 GO:0015819 SGD_REF:S000052257|PMID:10753927 IMP P GTP-binding protein, Rheb, ras family YCR027C|RSG1 gene taxon:4932 20011023 SGD
+SGD S000006369 RHO1 GO:0000148 SGD_REF:S000048652|PMID:8602515 IDA C GTP-binding protein, rho subfamily YPR165W gene taxon:4932 20010118 SGD
+SGD S000006369 RHO1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C GTP-binding protein, rho subfamily YPR165W gene taxon:4932 20041203 SGD
+SGD S000006369 RHO1 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C GTP-binding protein, rho subfamily YPR165W gene taxon:4932 20060317 SGD
+SGD S000006369 RHO1 GO:0005777 SGD_REF:S000079988|PMID:15596542 IDA C GTP-binding protein, rho subfamily YPR165W gene taxon:4932 20050224 SGD
+SGD S000006369 RHO1 GO:0005934 SGD_REF:S000058399|PMID:9891811 IDA C GTP-binding protein, rho subfamily YPR165W gene taxon:4932 20010118 SGD
+SGD S000006369 RHO1 GO:0005935 SGD_REF:S000058399|PMID:9891811 IDA C GTP-binding protein, rho subfamily YPR165W gene taxon:4932 20010118 SGD
+SGD S000006369 RHO1 GO:0043332 SGD_REF:S000073335|PMID:12660244 IDA C GTP-binding protein, rho subfamily YPR165W gene taxon:4932 20030622 SGD
+SGD S000006369 RHO1 GO:0003924 SGD_REF:S000058399|PMID:9891811 TAS F GTP-binding protein, rho subfamily YPR165W gene taxon:4932 20010118 SGD
+SGD S000006369 RHO1 GO:0004871 SGD_REF:S000058399|PMID:9891811 IMP F GTP-binding protein, rho subfamily YPR165W gene taxon:4932 20010118 SGD
+SGD S000006369 RHO1 GO:0004871 SGD_REF:S000058399|PMID:9891811 IPI F GTP-binding protein, rho subfamily YPR165W gene taxon:4932 20010118 SGD
+SGD S000006369 RHO1 GO:0006897 SGD_REF:S000075861|PMID:14593073 IMP P GTP-binding protein, rho subfamily YPR165W gene taxon:4932 20050505 SGD
+SGD S000006369 RHO1 GO:0007015 SGD_REF:S000058399|PMID:9891811 TAS P GTP-binding protein, rho subfamily YPR165W gene taxon:4932 20030116 SGD
+SGD S000006369 RHO1 GO:0007047 SGD_REF:S000058399|PMID:9891811 IPI P GTP-binding protein, rho subfamily YPR165W gene taxon:4932 20010118 SGD
+SGD S000006369 RHO1 GO:0007117 SGD_REF:S000058399|PMID:9891811 IMP P GTP-binding protein, rho subfamily YPR165W gene taxon:4932 20010118 SGD
+SGD S000006369 RHO1 GO:0007264 SGD_REF:S000058399|PMID:9891811 IMP P GTP-binding protein, rho subfamily YPR165W gene taxon:4932 20010118 SGD
+SGD S000006369 RHO1 GO:0030468 SGD_REF:S000058399|PMID:9891811 IMP P GTP-binding protein, rho subfamily YPR165W gene taxon:4932 20010302 SGD
+SGD S000005034 RHO2 GO:0005622 SGD_REF:S000058399|PMID:9891811 TAS C GTP-binding protein, rho subfamily YNL090W gene taxon:4932 20010118 SGD
+SGD S000005034 RHO2 GO:0003924 SGD_REF:S000058399|PMID:9891811 ISS F GTP-binding protein, rho subfamily YNL090W gene taxon:4932 20010118 SGD
+SGD S000005034 RHO2 GO:0004871 SGD_REF:S000058399|PMID:9891811 ISS F GTP-binding protein, rho subfamily YNL090W gene taxon:4932 20010118 SGD
+SGD S000005034 RHO2 GO:0007015 SGD_REF:S000058399|PMID:9891811 TAS P GTP-binding protein, rho subfamily YNL090W gene taxon:4932 20030116 SGD
+SGD S000005034 RHO2 GO:0007017 SGD_REF:S000058399|PMID:9891811 IMP P GTP-binding protein, rho subfamily YNL090W gene taxon:4932 20010118 SGD
+SGD S000005034 RHO2 GO:0007047 SGD_REF:S000058399|PMID:9891811 ISS P GTP-binding protein, rho subfamily YNL090W gene taxon:4932 20010118 SGD
+SGD S000005034 RHO2 GO:0007264 SGD_REF:S000058399|PMID:9891811 ISS P GTP-binding protein, rho subfamily YNL090W gene taxon:4932 20010118 SGD
+SGD S000005034 RHO2 GO:0030468 SGD_REF:S000058399|PMID:9891811 ISS P GTP-binding protein, rho subfamily YNL090W gene taxon:4932 20010302 SGD
+SGD S000001380 RHO3 GO:0005622 SGD_REF:S000058399|PMID:9891811 TAS C GTP-binding protein, ras homolog YIL118W gene taxon:4932 20010118 SGD
+SGD S000001380 RHO3 GO:0003924 SGD_REF:S000058399|PMID:9891811 ISS F GTP-binding protein, ras homolog YIL118W gene taxon:4932 20010118 SGD
+SGD S000001380 RHO3 GO:0004871 SGD_REF:S000058399|PMID:9891811 ISS F GTP-binding protein, ras homolog YIL118W gene taxon:4932 20010118 SGD
+SGD S000001380 RHO3 GO:0006887 SGD_REF:S000058399|PMID:9891811 IMP P GTP-binding protein, ras homolog YIL118W gene taxon:4932 20010118 SGD
+SGD S000001380 RHO3 GO:0007015 SGD_REF:S000058399|PMID:9891811 TAS P GTP-binding protein, ras homolog YIL118W gene taxon:4932 20030116 SGD
+SGD S000001380 RHO3 GO:0007264 SGD_REF:S000058399|PMID:9891811 ISS P GTP-binding protein, ras homolog YIL118W gene taxon:4932 20010118 SGD
+SGD S000001380 RHO3 GO:0030468 SGD_REF:S000046605|PMID:10639324 IMP P GTP-binding protein, ras homolog YIL118W gene taxon:4932 20010302 SGD
+SGD S000001380 RHO3 GO:0030468 SGD_REF:S000046605|PMID:10639324 IGI P GTP-binding protein, ras homolog YIL118W gene taxon:4932 20010302 SGD
+SGD S000001380 RHO3 GO:0030468 SGD_REF:S000046605|PMID:10639324 IPI P GTP-binding protein, ras homolog YIL118W gene taxon:4932 20010302 SGD
+SGD S000001763 RHO4 GO:0005622 SGD_REF:S000058399|PMID:9891811 TAS C GTP-binding protein, ras homolog YKR055W gene taxon:4932 20010118 SGD
+SGD S000001763 RHO4 GO:0003924 SGD_REF:S000058399|PMID:9891811 ISS F GTP-binding protein, ras homolog YKR055W gene taxon:4932 20010118 SGD
+SGD S000001763 RHO4 GO:0004871 SGD_REF:S000058399|PMID:9891811 ISS F GTP-binding protein, ras homolog YKR055W gene taxon:4932 20010118 SGD
+SGD S000001763 RHO4 GO:0007015 SGD_REF:S000058399|PMID:9891811 TAS P GTP-binding protein, ras homolog YKR055W gene taxon:4932 20030116 SGD
+SGD S000001763 RHO4 GO:0007264 SGD_REF:S000058399|PMID:9891811 ISS P GTP-binding protein, ras homolog YKR055W gene taxon:4932 20010118 SGD
+SGD S000001763 RHO4 GO:0030468 SGD_REF:S000046605|PMID:10639324 IMP P GTP-binding protein, ras homolog YKR055W gene taxon:4932 20010302 SGD
+SGD S000001763 RHO4 GO:0030468 SGD_REF:S000046605|PMID:10639324 IGI P GTP-binding protein, ras homolog YKR055W gene taxon:4932 20010302 SGD
+SGD S000001763 RHO4 GO:0030468 SGD_REF:S000046605|PMID:10639324 IPI P GTP-binding protein, ras homolog YKR055W gene taxon:4932 20010302 SGD
+SGD S000005124 RHO5 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C rho GTPase YNL180C gene taxon:4932 20031028 SGD
+SGD S000005124 RHO5 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C rho GTPase YNL180C gene taxon:4932 20031028 SGD
+SGD S000005124 RHO5 GO:0003924 SGD_REF:S000066007|PMID:11591390 IDA F rho GTPase YNL180C gene taxon:4932 20020620 SGD
+SGD S000005124 RHO5 GO:0007266 SGD_REF:S000066007|PMID:11591390 ISS P rho GTPase YNL180C gene taxon:4932 20020620 SGD
+SGD S000001315 RHR2 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C DL-glycerol-3-phosphatase YIL053W|GPP1 gene taxon:4932 20031028 SGD
+SGD S000001315 RHR2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C DL-glycerol-3-phosphatase YIL053W|GPP1 gene taxon:4932 20031028 SGD
+SGD S000001315 RHR2 GO:0000121 SGD_REF:S000052527|PMID:8662716 IDA F DL-glycerol-3-phosphatase YIL053W|GPP1 gene taxon:4932 20021115 SGD
+SGD S000001315 RHR2 GO:0006114 SGD_REF:S000060704|PMID:11058591 IMP P DL-glycerol-3-phosphatase YIL053W|GPP1 gene taxon:4932 20021115 SGD
+SGD S000001315 RHR2 GO:0006970 SGD_REF:S000066126|PMID:11676566 TAS P DL-glycerol-3-phosphatase YIL053W|GPP1 gene taxon:4932 20020911 SGD
+SGD S000005107 RIA1 GO:0005737 SGD_REF:S000068872|PMID:11779510 IDA C GTPase YNL163C|EFL1 gene taxon:4932 20020212 SGD
+SGD S000005107 RIA1 GO:0003924 SGD_REF:S000068872|PMID:11779510 IDA F GTPase YNL163C|EFL1 gene taxon:4932 20040929 SGD
+SGD S000005107 RIA1 GO:0030489 SGD_REF:S000068872|PMID:11779510 IMP P GTPase YNL163C|EFL1 gene taxon:4932 20040929 SGD
+SGD S000005107 RIA1 GO:0042273 SGD_REF:S000066242|PMID:11713675 IMP P GTPase YNL163C|EFL1 gene taxon:4932 20040929 SGD
+SGD S000005107 RIA1 GO:0042273 SGD_REF:S000066242|PMID:11713675 ISS SGD:S000002793 P GTPase YNL163C|EFL1 gene taxon:4932 20040929 SGD
+SGD S000005107 RIA1 GO:0042273 SGD_REF:S000066242|PMID:11713675 IPI P GTPase YNL163C|EFL1 gene taxon:4932 20040929 SGD
+SGD S000000129 RIB1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C GTP cyclohydrolase II YBL033C gene taxon:4932 20031028 SGD
+SGD S000000129 RIB1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C GTP cyclohydrolase II YBL033C gene taxon:4932 20031028 SGD
+SGD S000000129 RIB1 GO:0019238 SGD_REF:S000057176|PMID:4555411 IGI F GTP cyclohydrolase II YBL033C gene taxon:4932 20020607 SGD
+SGD S000000129 RIB1 GO:0019238 SGD_REF:S000057176|PMID:4555411 IMP F GTP cyclohydrolase II YBL033C gene taxon:4932 20020607 SGD
+SGD S000000129 RIB1 GO:0009231 SGD_REF:S000057176|PMID:4555411 IMP P GTP cyclohydrolase II YBL033C gene taxon:4932 20020607 SGD
+SGD S000000129 RIB1 GO:0009231 SGD_REF:S000057199|PMID:5366000 IMP P GTP cyclohydrolase II YBL033C gene taxon:4932 20020607 SGD
+SGD S000005427 RIB2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C DRAP deaminase, pseudouridine synthase YOL066C|PUS8 gene taxon:4932 20031028 SGD
+SGD S000005427 RIB2 GO:0005737 SGD_REF:S000080014|PMID:15466869 IMP C DRAP deaminase, pseudouridine synthase YOL066C|PUS8 gene taxon:4932 20051108 SGD
+SGD S000005427 RIB2 GO:0004730 SGD_REF:S000072854|PMID:8710514 ISS F DRAP deaminase, pseudouridine synthase YOL066C|PUS8 gene taxon:4932 20030404 SGD
+SGD S000005427 RIB2 GO:0016439 SGD_REF:S000080014|PMID:15466869 IDA F DRAP deaminase, pseudouridine synthase YOL066C|PUS8 gene taxon:4932 20051108 SGD
+SGD S000005427 RIB2 GO:0016439 SGD_REF:S000080014|PMID:15466869 IMP F DRAP deaminase, pseudouridine synthase YOL066C|PUS8 gene taxon:4932 20051108 SGD
+SGD S000005427 RIB2 GO:0017173 SGD_REF:S000057176|PMID:4555411 IGI F DRAP deaminase, pseudouridine synthase YOL066C|PUS8 gene taxon:4932 20030212 SGD
+SGD S000005427 RIB2 GO:0017173 SGD_REF:S000057176|PMID:4555411 IMP F DRAP deaminase, pseudouridine synthase YOL066C|PUS8 gene taxon:4932 20030212 SGD
+SGD S000005427 RIB2 GO:0009231 SGD_REF:S000057199|PMID:5366000 IMP P DRAP deaminase, pseudouridine synthase YOL066C|PUS8 gene taxon:4932 20020607 SGD
+SGD S000005427 RIB2 GO:0031119 SGD_REF:S000080014|PMID:15466869 IDA P DRAP deaminase, pseudouridine synthase YOL066C|PUS8 gene taxon:4932 20051108 SGD
+SGD S000005427 RIB2 GO:0031119 SGD_REF:S000080014|PMID:15466869 IMP P DRAP deaminase, pseudouridine synthase YOL066C|PUS8 gene taxon:4932 20051108 SGD
+SGD S000002895 RIB3 GO:0005758 SGD_REF:S000072957|PMID:12595523 IDA C 3,4-dihydroxy-2-butanone 4-phosphate synthase YDR487C gene taxon:4932 20030505 SGD
+SGD S000002895 RIB3 GO:0005829 SGD_REF:S000072957|PMID:12595523 IDA C 3,4-dihydroxy-2-butanone 4-phosphate synthase YDR487C gene taxon:4932 20030505 SGD
+SGD S000002895 RIB3 GO:0008686 SGD_REF:S000045926|PMID:7559556 IMP F 3,4-dihydroxy-2-butanone 4-phosphate synthase YDR487C gene taxon:4932 20030213 SGD
+SGD S000002895 RIB3 GO:0009060 SGD_REF:S000072957|PMID:12595523 IMP P 3,4-dihydroxy-2-butanone 4-phosphate synthase YDR487C gene taxon:4932 20030505 SGD
+SGD S000002895 RIB3 GO:0009231 SGD_REF:S000057199|PMID:5366000 IMP P 3,4-dihydroxy-2-butanone 4-phosphate synthase YDR487C gene taxon:4932 20020607 SGD
+SGD S000005503 RIB4 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C 6,7-dimethyl-8-ribityllumazine synthase (DMRL synthase) YOL143C gene taxon:4932 20031028 SGD
+SGD S000005503 RIB4 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C 6,7-dimethyl-8-ribityllumazine synthase (DMRL synthase) YOL143C gene taxon:4932 20031028 SGD
+SGD S000005503 RIB4 GO:0000906 SGD_REF:S000045926|PMID:7559556 IGI F 6,7-dimethyl-8-ribityllumazine synthase (DMRL synthase) YOL143C gene taxon:4932 20030214 SGD
+SGD S000005503 RIB4 GO:0000906 SGD_REF:S000045926|PMID:7559556 ISS F 6,7-dimethyl-8-ribityllumazine synthase (DMRL synthase) YOL143C gene taxon:4932 20030214 SGD
+SGD S000005503 RIB4 GO:0009231 SGD_REF:S000057199|PMID:5366000 IMP P 6,7-dimethyl-8-ribityllumazine synthase (DMRL synthase) YOL143C gene taxon:4932 20020607 SGD
+SGD S000005503 RIB4 GO:0009231 SGD_REF:S000045926|PMID:7559556 IMP P 6,7-dimethyl-8-ribityllumazine synthase (DMRL synthase) YOL143C gene taxon:4932 20020607 SGD
+SGD S000000460 RIB5 GO:0005625 SGD_REF:S000040213|PMID:7814407 IDA C YBR256C gene taxon:4932 20020606 SGD
+SGD S000000460 RIB5 GO:0004746 SGD_REF:S000040213|PMID:7814407 IDA F YBR256C gene taxon:4932 20020606 SGD
+SGD S000000460 RIB5 GO:0004746 SGD_REF:S000040213|PMID:7814407 ISS F YBR256C gene taxon:4932 20020606 SGD
+SGD S000000460 RIB5 GO:0009231 SGD_REF:S000040213|PMID:7814407 IMP P YBR256C gene taxon:4932 20020606 SGD
+SGD S000000357 RIB7 GO:0008372 SGD_REF:S000069584 ND C YBR153W gene taxon:4932 20020607 SGD
+SGD S000000357 RIB7 GO:0008835 SGD_REF:S000057176|PMID:4555411 IGI F YBR153W gene taxon:4932 20030212 SGD
+SGD S000000357 RIB7 GO:0008835 SGD_REF:S000057176|PMID:4555411 IMP F YBR153W gene taxon:4932 20030212 SGD
+SGD S000000357 RIB7 GO:0009231 SGD_REF:S000057199|PMID:5366000 IMP P YBR153W gene taxon:4932 20020607 SGD
+SGD S000004029 RIC1 GO:0000139 SGD_REF:S000071749|PMID:10990452 IDA C YLR039C gene taxon:4932 20060413 SGD
+SGD S000004029 RIC1 GO:0005634 SGD_REF:S000050028|PMID:9099877 ISS C YLR039C gene taxon:4932 20010118 SGD
+SGD S000004029 RIC1 GO:0032045 SGD_REF:S000071749|PMID:10990452 IDA C YLR039C gene taxon:4932 20060425 SGD
+SGD S000004029 RIC1 contributes_to GO:0005085 SGD_REF:S000071749|PMID:10990452 IGI SGD:S000004252 F YLR039C gene taxon:4932 20060414 SGD
+SGD S000004029 RIC1 contributes_to GO:0005085 SGD_REF:S000071749|PMID:10990452 IDA F YLR039C gene taxon:4932 20060414 SGD
+SGD S000004029 RIC1 contributes_to GO:0005085 SGD_REF:S000071749|PMID:10990452 IPI SGD:S000004252 F YLR039C gene taxon:4932 20060414 SGD
+SGD S000004029 RIC1 GO:0006886 SGD_REF:S000059520|PMID:11160819 IMP P YLR039C gene taxon:4932 20050310 SGD
+SGD S000004029 RIC1 GO:0042147 SGD_REF:S000071749|PMID:10990452 IGI SGD:S000004300 P YLR039C gene taxon:4932 20060413 SGD
+SGD S000004029 RIC1 GO:0042147 SGD_REF:S000071749|PMID:10990452 IPI SGD:S000004252 P YLR039C gene taxon:4932 20060413 SGD
+SGD S000004029 RIC1 GO:0042147 SGD_REF:S000071749|PMID:10990452 IMP P YLR039C gene taxon:4932 20060413 SGD
+SGD S000000479 RIF1 GO:0000783 SGD_REF:S000045567|PMID:9710643 IDA C RAP1-interacting factor YBR275C gene taxon:4932 20030403 SGD
+SGD S000000479 RIF1 GO:0005515 SGD_REF:S000040919|PMID:9087429 IGI F RAP1-interacting factor YBR275C gene taxon:4932 20041109 SGD
+SGD S000000479 RIF1 GO:0005515 SGD_REF:S000040919|PMID:9087429 IPI F RAP1-interacting factor YBR275C gene taxon:4932 20041109 SGD
+SGD S000000479 RIF1 GO:0042162 SGD_REF:S000045567|PMID:9710643 IPI F RAP1-interacting factor YBR275C gene taxon:4932 20041109 SGD
+SGD S000000479 RIF1 GO:0006348 SGD_REF:S000050268|PMID:1577274 IMP P RAP1-interacting factor YBR275C gene taxon:4932 20010118 SGD
+SGD S000000479 RIF1 GO:0007004 SGD_REF:S000050268|PMID:1577274 IMP P RAP1-interacting factor YBR275C gene taxon:4932 20010118 SGD
+SGD S000004445 RIF2 GO:0000783 SGD_REF:S000045567|PMID:9710643 IDA C nuclear protein YLR453C gene taxon:4932 20030403 SGD
+SGD S000004445 RIF2 GO:0042162 SGD_REF:S000045567|PMID:9710643 IDA F nuclear protein YLR453C gene taxon:4932 20020717 SGD
+SGD S000004445 RIF2 GO:0007004 SGD_REF:S000040919|PMID:9087429 IMP P nuclear protein YLR453C gene taxon:4932 20020717 SGD
+SGD S000007222 RIM1 GO:0005739 SGD_REF:S000051758|PMID:1324172 IDA C DNA binding protein YCR028C-A gene taxon:4932 20020820 SGD
+SGD S000007222 RIM1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C DNA binding protein YCR028C-A gene taxon:4932 20040924 SGD
+SGD S000007222 RIM1 GO:0042645 SGD_REF:S000050870|PMID:10869431 IDA C DNA binding protein YCR028C-A gene taxon:4932 20050401 SGD
+SGD S000007222 RIM1 GO:0003697 SGD_REF:S000051758|PMID:1324172 ISS F DNA binding protein YCR028C-A gene taxon:4932 20020820 SGD
+SGD S000007222 RIM1 GO:0000002 SGD_REF:S000051758|PMID:1324172 IMP P DNA binding protein YCR028C-A gene taxon:4932 20020820 SGD
+SGD S000001019 RIM101 GO:0005634 SGD_REF:S000072488|PMID:12509465 IC GO:0016566 C YHL027W|RIM1 gene taxon:4932 20030218 SGD
+SGD S000001019 RIM101 GO:0016566 SGD_REF:S000072488|PMID:12509465 IDA F YHL027W|RIM1 gene taxon:4932 20030218 SGD
+SGD S000001019 RIM101 GO:0000122 SGD_REF:S000072488|PMID:12509465 IDA P YHL027W|RIM1 gene taxon:4932 20030218 SGD
+SGD S000001019 RIM101 GO:0007126 SGD_REF:S000041539|PMID:8367297 IMP P YHL027W|RIM1 gene taxon:4932 20020820 SGD
+SGD S000001019 RIM101 GO:0009268 SGD_REF:S000059522|PMID:11050096 IMP P YHL027W|RIM1 gene taxon:4932 20020820 SGD
+SGD S000001019 RIM101 GO:0030437 SGD_REF:S000051887|PMID:8417990 IMP P YHL027W|RIM1 gene taxon:4932 20020820 SGD
+SGD S000004747 RIM11 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YMR139W|GSK3|MDS1 gene taxon:4932 20031028 SGD
+SGD S000004747 RIM11 GO:0004674 SGD_REF:S000048643|PMID:9372955 IDA F YMR139W|GSK3|MDS1 gene taxon:4932 20050214 SGD
+SGD S000004747 RIM11 GO:0004696 SGD_REF:S000052678|PMID:10958669 ISS F YMR139W|GSK3|MDS1 gene taxon:4932 20021009 SGD
+SGD S000004747 RIM11 GO:0006468 SGD_REF:S000052678|PMID:10958669 IGI P YMR139W|GSK3|MDS1 gene taxon:4932 20021009 SGD
+SGD S000004747 RIM11 GO:0006468 SGD_REF:S000052678|PMID:10958669 ISS P YMR139W|GSK3|MDS1 gene taxon:4932 20021009 SGD
+SGD S000004747 RIM11 GO:0006508 SGD_REF:S000052678|PMID:10958669 IGI P YMR139W|GSK3|MDS1 gene taxon:4932 20021009 SGD
+SGD S000004747 RIM11 GO:0006950 SGD_REF:S000072503|PMID:12529445 IGI P YMR139W|GSK3|MDS1 gene taxon:4932 20030219 SGD
+SGD S000004747 RIM11 GO:0006950 SGD_REF:S000072503|PMID:12529445 IMP P YMR139W|GSK3|MDS1 gene taxon:4932 20030219 SGD
+SGD S000004747 RIM11 GO:0030437 SGD_REF:S000040816|PMID:10679022 IMP P YMR139W|GSK3|MDS1 gene taxon:4932 20021113 SGD
+SGD S000004763 RIM13 GO:0008372 SGD_REF:S000069584 ND C cysteine protease YMR154C|CPL1 gene taxon:4932 20020711 SGD
+SGD S000004763 RIM13 GO:0004197 SGD_REF:S000040427|PMID:9928935 IDA F cysteine protease YMR154C|CPL1 gene taxon:4932 20020711 SGD
+SGD S000004763 RIM13 GO:0016485 SGD_REF:S000040427|PMID:9928935 IGI P cysteine protease YMR154C|CPL1 gene taxon:4932 20020711 SGD
+SGD S000004763 RIM13 GO:0016485 SGD_REF:S000040427|PMID:9928935 IMP P cysteine protease YMR154C|CPL1 gene taxon:4932 20020711 SGD
+SGD S000001861 RIM15 GO:0005634 SGD_REF:S000075231|PMID:14690612 IDA C trehalose-associated protein kinase related to S. pombe cek1+ YFL033C|TAK1 gene taxon:4932 20041026 SGD
+SGD S000001861 RIM15 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C trehalose-associated protein kinase related to S. pombe cek1+ YFL033C|TAK1 gene taxon:4932 20031028 SGD
+SGD S000001861 RIM15 GO:0005737 SGD_REF:S000075231|PMID:14690612 IDA C trehalose-associated protein kinase related to S. pombe cek1+ YFL033C|TAK1 gene taxon:4932 20041026 SGD
+SGD S000001861 RIM15 GO:0004672 SGD_REF:S000046107|PMID:9744870 IDA F trehalose-associated protein kinase related to S. pombe cek1+ YFL033C|TAK1 gene taxon:4932 20021118 SGD
+SGD S000001861 RIM15 GO:0001324 SGD_REF:S000060129|PMID:11292860 IMP P trehalose-associated protein kinase related to S. pombe cek1+ YFL033C|TAK1 gene taxon:4932 20041025 SGD
+SGD S000001861 RIM15 GO:0006468 SGD_REF:S000046107|PMID:9744870 IDA P trehalose-associated protein kinase related to S. pombe cek1+ YFL033C|TAK1 gene taxon:4932 20021118 SGD
+SGD S000001861 RIM15 GO:0006950 SGD_REF:S000046107|PMID:9744870 IMP P trehalose-associated protein kinase related to S. pombe cek1+ YFL033C|TAK1 gene taxon:4932 20021118 SGD
+SGD S000001861 RIM15 GO:0040020 SGD_REF:S000047336|PMID:9111339 IMP P trehalose-associated protein kinase related to S. pombe cek1+ YFL033C|TAK1 gene taxon:4932 20021118 SGD
+SGD S000000396 RIM2 GO:0005739 SGD_REF:S000045513|PMID:7891656 IDA C YBR192W gene taxon:4932 20021002 SGD
+SGD S000000396 RIM2 GO:0005215 SGD_REF:S000045513|PMID:7891656 ISS F YBR192W gene taxon:4932 20021002 SGD
+SGD S000000396 RIM2 GO:0015218 SGD_REF:S000086806|PMID:16194150 IDA F YBR192W gene taxon:4932 20051021 SGD
+SGD S000000396 RIM2 GO:0000002 SGD_REF:S000045513|PMID:7891656 IGI P YBR192W gene taxon:4932 20021002 SGD
+SGD S000000396 RIM2 GO:0006864 SGD_REF:S000086806|PMID:16194150 IDA P YBR192W gene taxon:4932 20051021 SGD
+SGD S000005801 RIM20 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YOR275C gene taxon:4932 20031028 SGD
+SGD S000005801 RIM20 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YOR275C gene taxon:4932 20031028 SGD
+SGD S000005801 RIM20 GO:0005554 SGD_REF:S000069584 ND F YOR275C gene taxon:4932 20021028 SGD
+SGD S000005801 RIM20 GO:0001403 SGD_REF:S000068804|PMID:11698381 IMP P YOR275C gene taxon:4932 20021028 SGD
+SGD S000005801 RIM20 GO:0006508 SGD_REF:S000068804|PMID:11698381 IMP P YOR275C gene taxon:4932 20021028 SGD
+SGD S000005801 RIM20 GO:0016485 SGD_REF:S000068804|PMID:11698381 IGI P YOR275C gene taxon:4932 20021028 SGD
+SGD S000005801 RIM20 GO:0016485 SGD_REF:S000068804|PMID:11698381 IDA P YOR275C gene taxon:4932 20021028 SGD
+SGD S000005801 RIM20 GO:0016485 SGD_REF:S000068804|PMID:11698381 IMP P YOR275C gene taxon:4932 20021028 SGD
+SGD S000005801 RIM20 GO:0030435 SGD_REF:S000068804|PMID:11698381 IMP P YOR275C gene taxon:4932 20021028 SGD
+SGD S000005238 RIM21 GO:0008372 SGD_REF:S000069584 ND C YNL294C|PAL2 gene taxon:4932 20021029 SGD
+SGD S000005238 RIM21 GO:0005554 SGD_REF:S000069584 ND F YNL294C|PAL2 gene taxon:4932 20021029 SGD
+SGD S000005238 RIM21 GO:0001403 SGD_REF:S000039908|PMID:10821185 IMP P YNL294C|PAL2 gene taxon:4932 20021029 SGD
+SGD S000005238 RIM21 GO:0030437 SGD_REF:S000039908|PMID:10821185 IMP P YNL294C|PAL2 gene taxon:4932 20021029 SGD
+SGD S000001016 RIM4 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C RNA-binding protein of the RRM class (putative) YHL024W gene taxon:4932 20020507 SGD
+SGD S000001016 RIM4 GO:0003723 SGD_REF:S000043182|PMID:10806425 ISS F RNA-binding protein of the RRM class (putative) YHL024W gene taxon:4932 20020930 SGD
+SGD S000001016 RIM4 GO:0003723 SGD_REF:S000043182|PMID:10806425 IMP F RNA-binding protein of the RRM class (putative) YHL024W gene taxon:4932 20020930 SGD
+SGD S000001016 RIM4 GO:0006279 SGD_REF:S000066244|PMID:11713679 IMP P RNA-binding protein of the RRM class (putative) YHL024W gene taxon:4932 20020930 SGD
+SGD S000001016 RIM4 GO:0007126 SGD_REF:S000043182|PMID:10806425 IEP P RNA-binding protein of the RRM class (putative) YHL024W gene taxon:4932 20020930 SGD
+SGD S000001016 RIM4 GO:0007126 SGD_REF:S000066244|PMID:11713679 IMP P RNA-binding protein of the RRM class (putative) YHL024W gene taxon:4932 20020930 SGD
+SGD S000001016 RIM4 GO:0007131 SGD_REF:S000066244|PMID:11713679 IMP P RNA-binding protein of the RRM class (putative) YHL024W gene taxon:4932 20020930 SGD
+SGD S000001016 RIM4 GO:0030435 SGD_REF:S000043182|PMID:10806425 IGI P RNA-binding protein of the RRM class (putative) YHL024W gene taxon:4932 20020930 SGD
+SGD S000001016 RIM4 GO:0030435 SGD_REF:S000043182|PMID:10806425 IMP P RNA-binding protein of the RRM class (putative) YHL024W gene taxon:4932 20020930 SGD
+SGD S000003013 RIM8 GO:0008372 SGD_REF:S000069584 ND C YGL045W|PAL3|YGL046W gene taxon:4932 20030110 SGD
+SGD S000003013 RIM8 GO:0005554 SGD_REF:S000069584 ND F YGL045W|PAL3|YGL046W gene taxon:4932 20030110 SGD
+SGD S000003013 RIM8 GO:0001403 SGD_REF:S000051973|PMID:9017390 IMP P YGL045W|PAL3|YGL046W gene taxon:4932 20030110 SGD
+SGD S000003013 RIM8 GO:0007126 SGD_REF:S000051973|PMID:9017390 IMP P YGL045W|PAL3|YGL046W gene taxon:4932 20030110 SGD
+SGD S000003013 RIM8 GO:0016485 SGD_REF:S000051973|PMID:9017390 IMP P YGL045W|PAL3|YGL046W gene taxon:4932 20030110 SGD
+SGD S000004667 RIM9 GO:0008372 SGD_REF:S000069584 ND C YMR063W gene taxon:4932 20020820 SGD
+SGD S000004667 RIM9 GO:0005554 SGD_REF:S000069584 ND F YMR063W gene taxon:4932 20020820 SGD
+SGD S000004667 RIM9 GO:0030437 SGD_REF:S000051887|PMID:8417990 IMP P YMR063W gene taxon:4932 20020820 SGD
+SGD S000005645 RIO1 GO:0005634 SGD_REF:S000072808|PMID:12612080 IDA C Protein serine kinase YOR119C|RRP10 gene taxon:4932 20050322 SGD
+SGD S000005645 RIO1 GO:0005737 SGD_REF:S000065921|PMID:11483523 IDA C Protein serine kinase YOR119C|RRP10 gene taxon:4932 20020312 SGD
+SGD S000005645 RIO1 GO:0004672 SGD_REF:S000070331|PMID:11972772 IDA F Protein serine kinase YOR119C|RRP10 gene taxon:4932 20030128 SGD
+SGD S000005645 RIO1 GO:0000084 SGD_REF:S000070331|PMID:11972772 IDA P Protein serine kinase YOR119C|RRP10 gene taxon:4932 20020829 SGD
+SGD S000005645 RIO1 GO:0007096 SGD_REF:S000070331|PMID:11972772 IDA P Protein serine kinase YOR119C|RRP10 gene taxon:4932 20020829 SGD
+SGD S000005645 RIO1 GO:0030490 SGD_REF:S000065921|PMID:11483523 IDA P Protein serine kinase YOR119C|RRP10 gene taxon:4932 20020312 SGD
+SGD S000005645 RIO1 GO:0030490 SGD_REF:S000072808|PMID:12612080 IDA P Protein serine kinase YOR119C|RRP10 gene taxon:4932 20050322 SGD
+SGD S000005151 RIO2 GO:0005634 SGD_REF:S000072808|PMID:12612080 IDA C YNL207W gene taxon:4932 20030325 SGD
+SGD S000005151 RIO2 GO:0005634 SGD_REF:S000073447|PMID:12690111 IDA C YNL207W gene taxon:4932 20050322 SGD
+SGD S000005151 RIO2 GO:0005737 SGD_REF:S000076341|PMID:15167894 IDA C YNL207W gene taxon:4932 20050322 SGD
+SGD S000005151 RIO2 GO:0005829 SGD_REF:S000072808|PMID:12612080 IDA C YNL207W gene taxon:4932 20030325 SGD
+SGD S000005151 RIO2 GO:0004672 SGD_REF:S000073447|PMID:12690111 IDA F YNL207W gene taxon:4932 20030701 SGD
+SGD S000005151 RIO2 GO:0005487 SGD_REF:S000072808|PMID:12612080 IGI F YNL207W gene taxon:4932 20030325 SGD
+SGD S000005151 RIO2 GO:0030490 SGD_REF:S000072808|PMID:12612080 IMP P YNL207W gene taxon:4932 20030325 SGD
+SGD S000005151 RIO2 GO:0030490 SGD_REF:S000073447|PMID:12690111 IMP P YNL207W gene taxon:4932 20050322 SGD
+SGD S000005151 RIO2 GO:0030490 SGD_REF:S000072808|PMID:12612080 ISS SGD:S000005645 P YNL207W gene taxon:4932 20030325 SGD
+SGD S000000750 RIP1 GO:0005750 SGD_REF:S000044869|PMID:3036836 IDA C Rieske iron-sulfur protein of the mitochondrial cytochrome bc1 complex YEL024W gene taxon:4932 20020906 SGD
+SGD S000000750 RIP1 GO:0005750 SGD_REF:S000046403|PMID:10873857 IDA C Rieske iron-sulfur protein of the mitochondrial cytochrome bc1 complex YEL024W gene taxon:4932 20020906 SGD
+SGD S000000750 RIP1 GO:0008121 SGD_REF:S000044869|PMID:3036836 IDA F Rieske iron-sulfur protein of the mitochondrial cytochrome bc1 complex YEL024W gene taxon:4932 20020906 SGD
+SGD S000000750 RIP1 GO:0006122 SGD_REF:S000044869|PMID:3036836 IDA P Rieske iron-sulfur protein of the mitochondrial cytochrome bc1 complex YEL024W gene taxon:4932 20020906 SGD
+SGD S000000750 RIP1 GO:0009060 SGD_REF:S000044869|PMID:3036836 IMP P Rieske iron-sulfur protein of the mitochondrial cytochrome bc1 complex YEL024W gene taxon:4932 20020906 SGD
+SGD S000005717 RIS1 GO:0005634 SGD_REF:S000055850|PMID:9271422 IPI C SWI2/SNF2 DNA-dependent ATPase family member (putative) YOR191W|DIS1 gene taxon:4932 20020522 SGD
+SGD S000005717 RIS1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C SWI2/SNF2 DNA-dependent ATPase family member (putative) YOR191W|DIS1 gene taxon:4932 20040928 SGD
+SGD S000005717 RIS1 GO:0008094 SGD_REF:S000055850|PMID:9271422 ISS F SWI2/SNF2 DNA-dependent ATPase family member (putative) YOR191W|DIS1 gene taxon:4932 20020522 SGD
+SGD S000005717 RIS1 GO:0006333 SGD_REF:S000055850|PMID:9271422 IGI P SWI2/SNF2 DNA-dependent ATPase family member (putative) YOR191W|DIS1 gene taxon:4932 20020522 SGD
+SGD S000005717 RIS1 GO:0006333 SGD_REF:S000055850|PMID:9271422 IPI P SWI2/SNF2 DNA-dependent ATPase family member (putative) YOR191W|DIS1 gene taxon:4932 20020522 SGD
+SGD S000005717 RIS1 GO:0006333 SGD_REF:S000055850|PMID:9271422 IMP P SWI2/SNF2 DNA-dependent ATPase family member (putative) YOR191W|DIS1 gene taxon:4932 20020522 SGD
+SGD S000005717 RIS1 GO:0007533 SGD_REF:S000055850|PMID:9271422 IMP P SWI2/SNF2 DNA-dependent ATPase family member (putative) YOR191W|DIS1 gene taxon:4932 20020522 SGD
+SGD S000004896 RIT1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C initiator methionine tRNA 2'-O-ribosyl phosphate transferase YMR283C gene taxon:4932 20031028 SGD
+SGD S000004896 RIT1 GO:0016763 SGD_REF:S000044027|PMID:7954819 IGI F initiator methionine tRNA 2'-O-ribosyl phosphate transferase YMR283C gene taxon:4932 20021028 SGD
+SGD S000004896 RIT1 GO:0016763 SGD_REF:S000044027|PMID:7954819 IDA F initiator methionine tRNA 2'-O-ribosyl phosphate transferase YMR283C gene taxon:4932 20021028 SGD
+SGD S000004896 RIT1 GO:0016763 SGD_REF:S000044027|PMID:7954819 IMP F initiator methionine tRNA 2'-O-ribosyl phosphate transferase YMR283C gene taxon:4932 20021028 SGD
+SGD S000004896 RIT1 GO:0019988 SGD_REF:S000044027|PMID:7954819 IMP P initiator methionine tRNA 2'-O-ribosyl phosphate transferase YMR283C gene taxon:4932 20021028 SGD
+SGD S000004896 RIT1 GO:0019988 SGD_REF:S000044027|PMID:7954819 IGI P initiator methionine tRNA 2'-O-ribosyl phosphate transferase YMR283C gene taxon:4932 20021028 SGD
+SGD S000001240 RIX1 GO:0005634 SGD_REF:S000075214|PMID:14690591 IDA C YHR197W|IPI2 gene taxon:4932 20040105 SGD
+SGD S000001240 RIX1 GO:0005654 SGD_REF:S000071707|PMID:12374754 IDA C YHR197W|IPI2 gene taxon:4932 20030624 SGD
+SGD S000001240 RIX1 GO:0005654 SGD_REF:S000080956|PMID:15528184 IDA C YHR197W|IPI2 gene taxon:4932 20050310 SGD
+SGD S000001240 RIX1 GO:0005554 SGD_REF:S000069584 ND F YHR197W|IPI2 gene taxon:4932 20030624 SGD
+SGD S000001240 RIX1 GO:0000027 SGD_REF:S000080956|PMID:15528184 IMP P YHR197W|IPI2 gene taxon:4932 20050310 SGD
+SGD S000001240 RIX1 GO:0000054 SGD_REF:S000071707|PMID:12374754 IPI P YHR197W|IPI2 gene taxon:4932 20030624 SGD
+SGD S000001240 RIX1 GO:0000054 SGD_REF:S000060446|PMID:11313466 IMP P YHR197W|IPI2 gene taxon:4932 20030624 SGD
+SGD S000001240 RIX1 GO:0000054 SGD_REF:S000071707|PMID:12374754 TAS P YHR197W|IPI2 gene taxon:4932 20030624 SGD
+SGD S000001240 RIX1 GO:0006365 SGD_REF:S000074504|PMID:14759368 IMP P YHR197W|IPI2 gene taxon:4932 20040803 SGD
+SGD S000003957 RIX7 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YLL034C gene taxon:4932 20031028 SGD
+SGD S000003957 RIX7 GO:0005634 SGD_REF:S000075190|PMID:11447111 IDA C YLL034C gene taxon:4932 20031229 SGD
+SGD S000003957 RIX7 GO:0005730 SGD_REF:S000075190|PMID:11447111 IDA C YLL034C gene taxon:4932 20031229 SGD
+SGD S000003957 RIX7 GO:0005730 SGD_REF:S000074185|PMID:14562095 IDA C YLL034C gene taxon:4932 20031028 SGD
+SGD S000003957 RIX7 GO:0004386 SGD_REF:S000039134|PMID:10077188 ISS F YLL034C gene taxon:4932 20011205 SGD
+SGD S000003957 RIX7 GO:0016887 SGD_REF:S000075190|PMID:11447111 ISS F YLL034C gene taxon:4932 20031229 SGD
+SGD S000003957 RIX7 GO:0000055 SGD_REF:S000075190|PMID:11447111 IMP P YLL034C gene taxon:4932 20031229 SGD
+SGD S000005621 RKI1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C ribose-5-phosphate ketol-isomerase YOR095C gene taxon:4932 20031028 SGD
+SGD S000005621 RKI1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C ribose-5-phosphate ketol-isomerase YOR095C gene taxon:4932 20031028 SGD
+SGD S000005621 RKI1 GO:0004751 SGD_REF:S000047933|PMID:8929392 ISS F ribose-5-phosphate ketol-isomerase YOR095C gene taxon:4932 20020607 SGD
+SGD S000005621 RKI1 GO:0004751 SGD_REF:S000047933|PMID:8929392 IMP F ribose-5-phosphate ketol-isomerase YOR095C gene taxon:4932 20020607 SGD
+SGD S000005621 RKI1 GO:0006098 SGD_REF:S000047933|PMID:8929392 IGI P ribose-5-phosphate ketol-isomerase YOR095C gene taxon:4932 20020607 SGD
+SGD S000005621 RKI1 GO:0008615 SGD_REF:S000076698|PMID:14690456 IMP P ribose-5-phosphate ketol-isomerase YOR095C gene taxon:4932 20051214 SGD
+SGD S000006129 RKM1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C methyltransferase YPL208W gene taxon:4932 20031028 SGD
+SGD S000006129 RKM1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C methyltransferase YPL208W gene taxon:4932 20031028 SGD
+SGD S000006129 RKM1 GO:0016279 SGD_REF:S000086145|PMID:16096273 IDA F methyltransferase YPL208W gene taxon:4932 20051006 SGD
+SGD S000006129 RKM1 GO:0016279 SGD_REF:S000086145|PMID:16096273 IMP F methyltransferase YPL208W gene taxon:4932 20051006 SGD
+SGD S000006129 RKM1 GO:0000004 SGD_REF:S000069584 ND P methyltransferase YPL208W gene taxon:4932 20050812 SGD
+SGD S000002606 RKM2 GO:0008372 SGD_REF:S000069584 ND C lysine methyltransferase YDR198C gene taxon:4932 20021126 SGD
+SGD S000002606 RKM2 GO:0005554 SGD_REF:S000069584 ND F lysine methyltransferase YDR198C gene taxon:4932 20021126 SGD
+SGD S000002606 RKM2 GO:0000004 SGD_REF:S000069584 ND P lysine methyltransferase YDR198C gene taxon:4932 20021126 SGD
+SGD S000004861 RKR1 GO:0008372 SGD_REF:S000069584 ND C YMR247C gene taxon:4932 20030203 SGD
+SGD S000004861 RKR1 GO:0005554 SGD_REF:S000069584 ND F YMR247C gene taxon:4932 20030203 SGD
+SGD S000004861 RKR1 GO:0000004 SGD_REF:S000069584 ND P YMR247C gene taxon:4932 20030203 SGD
+SGD S000006222 RLF2 GO:0000775 SGD_REF:S000069112|PMID:11782447 IDA C chromatin assembly factor-I (CAF-I) p90 subunit YPR018W|CAC1 gene taxon:4932 20030410 SGD
+SGD S000006222 RLF2 GO:0005634 SGD_REF:S000048517|PMID:9030688 IDA C chromatin assembly factor-I (CAF-I) p90 subunit YPR018W|CAC1 gene taxon:4932 20021202 SGD
+SGD S000006222 RLF2 GO:0005678 SGD_REF:S000048516|PMID:9030687 IDA C chromatin assembly factor-I (CAF-I) p90 subunit YPR018W|CAC1 gene taxon:4932 20020716 SGD
+SGD S000006222 RLF2 GO:0030528 SGD_REF:S000080322|PMID:15632066 IMP F chromatin assembly factor-I (CAF-I) p90 subunit YPR018W|CAC1 gene taxon:4932 20050216 SGD
+SGD S000006222 RLF2 GO:0006334 SGD_REF:S000048517|PMID:9030688 IMP P chromatin assembly factor-I (CAF-I) p90 subunit YPR018W|CAC1 gene taxon:4932 20021202 SGD
+SGD S000002498 RLI1 GO:0005634 SGD_REF:S000079736|PMID:15277527 IDA C YDR091C gene taxon:4932 20050217 SGD
+SGD S000002498 RLI1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDR091C gene taxon:4932 20031028 SGD
+SGD S000002498 RLI1 GO:0005737 SGD_REF:S000081201|PMID:15660134 IDA C YDR091C gene taxon:4932 20050404 SGD
+SGD S000002498 RLI1 GO:0005737 SGD_REF:S000079736|PMID:15277527 IDA C YDR091C gene taxon:4932 20050217 SGD
+SGD S000002498 RLI1 GO:0005830 SGD_REF:S000079736|PMID:15277527 IDA C YDR091C gene taxon:4932 20050217 SGD
+SGD S000002498 RLI1 GO:0005830 SGD_REF:S000081201|PMID:15660134 IDA C YDR091C gene taxon:4932 20050404 SGD
+SGD S000002498 RLI1 GO:0005506 SGD_REF:S000081201|PMID:15660134 IDA F YDR091C gene taxon:4932 20050404 SGD
+SGD S000002498 RLI1 GO:0016887 SGD_REF:S000079736|PMID:15277527 ISS F YDR091C gene taxon:4932 20050217 SGD
+SGD S000002498 RLI1 GO:0000054 SGD_REF:S000081201|PMID:15660134 IMP P YDR091C gene taxon:4932 20050404 SGD
+SGD S000002498 RLI1 GO:0006413 SGD_REF:S000079736|PMID:15277527 IMP P YDR091C gene taxon:4932 20050217 SGD
+SGD S000002498 RLI1 GO:0006413 SGD_REF:S000081201|PMID:15660134 IMP P YDR091C gene taxon:4932 20050404 SGD
+SGD S000002498 RLI1 GO:0042273 SGD_REF:S000079736|PMID:15277527 IMP P YDR091C gene taxon:4932 20050217 SGD
+SGD S000006010 RLM1 GO:0005634 SGD_REF:S000047330|PMID:9111331 TAS C YPL089C gene taxon:4932 20010118 SGD
+SGD S000006010 RLM1 GO:0003677 SGD_REF:S000051198|PMID:9121433 IDA F YPL089C gene taxon:4932 20020827 SGD
+SGD S000006010 RLM1 GO:0008301 SGD_REF:S000061714|PMID:10064699 IDA F YPL089C gene taxon:4932 20020827 SGD
+SGD S000006010 RLM1 GO:0016563 SGD_REF:S000071754|PMID:12410835 IMP F YPL089C gene taxon:4932 20030318 SGD
+SGD S000006010 RLM1 GO:0016563 SGD_REF:S000071754|PMID:12410835 IDA F YPL089C gene taxon:4932 20030318 SGD
+SGD S000006010 RLM1 GO:0007047 SGD_REF:S000055516|PMID:10594829 TAS P YPL089C gene taxon:4932 20030708 SGD
+SGD S000006010 RLM1 GO:0007165 SGD_REF:S000043729|PMID:7565726 IMP P YPL089C gene taxon:4932 20010118 SGD
+SGD S000006010 RLM1 GO:0045944 SGD_REF:S000071754|PMID:12410835 IDA P YPL089C gene taxon:4932 20030318 SGD
+SGD S000003999 RLP24 GO:0005730 SGD_REF:S000070114|PMID:11707418 TAS C part of a pre-60S complex YLR009W gene taxon:4932 20030514 SGD
+SGD S000003999 RLP24 GO:0005554 SGD_REF:S000069584 ND F part of a pre-60S complex YLR009W gene taxon:4932 20010105 SGD
+SGD S000003999 RLP24 GO:0042273 SGD_REF:S000066002|PMID:11583614 IMP P part of a pre-60S complex YLR009W gene taxon:4932 20020927 SGD
+SGD S000003999 RLP24 GO:0042273 SGD_REF:S000066002|PMID:11583614 IPI P part of a pre-60S complex YLR009W gene taxon:4932 20020927 SGD
+SGD S000004947 RLP7 GO:0005730 SGD_REF:S000059203|PMID:11087857 IDA C YNL002C|RPL7 gene taxon:4932 20020820 SGD
+SGD S000004947 RLP7 GO:0019843 SGD_REF:S000059203|PMID:11087857 ISS F YNL002C|RPL7 gene taxon:4932 20020820 SGD
+SGD S000004947 RLP7 GO:0030489 SGD_REF:S000059203|PMID:11087857 IMP P YNL002C|RPL7 gene taxon:4932 20020820 SGD
+SGD S000004947 RLP7 GO:0042273 SGD_REF:S000059203|PMID:11087857 IMP P YNL002C|RPL7 gene taxon:4932 20020820 SGD
+SGD S000005083 RLR1 GO:0000347 SGD_REF:S000059208|PMID:11060033 IMP C YNL139C|LDB5|THO2|ZRG13 gene taxon:4932 20030221 SGD
+SGD S000005083 RLR1 GO:0000347 SGD_REF:S000059208|PMID:11060033 IPI C YNL139C|LDB5|THO2|ZRG13 gene taxon:4932 20030221 SGD
+SGD S000005083 RLR1 GO:0005634 SGD_REF:S000081155|PMID:15343339 IC GO:0003677 C YNL139C|LDB5|THO2|ZRG13 gene taxon:4932 20050331 SGD
+SGD S000005083 RLR1 GO:0003676 SGD_REF:S000070300|PMID:12093753 IDA F YNL139C|LDB5|THO2|ZRG13 gene taxon:4932 20021118 SGD
+SGD S000005083 RLR1 GO:0003677 SGD_REF:S000081155|PMID:15343339 IPI F YNL139C|LDB5|THO2|ZRG13 gene taxon:4932 20050331 SGD
+SGD S000005083 RLR1 GO:0006310 SGD_REF:S000059208|PMID:11060033 IMP P YNL139C|LDB5|THO2|ZRG13 gene taxon:4932 20030221 SGD
+SGD S000005083 RLR1 GO:0006368 SGD_REF:S000070300|PMID:12093753 IMP P YNL139C|LDB5|THO2|ZRG13 gene taxon:4932 20021118 SGD
+SGD S000005083 RLR1 GO:0006406 SGD_REF:S000069956|PMID:11979277 IMP P YNL139C|LDB5|THO2|ZRG13 gene taxon:4932 20030214 SGD
+SGD S000001615 RMA1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YKL132C gene taxon:4932 20040813 SGD
+SGD S000001615 RMA1 GO:0004326 SGD_REF:S000055367|PMID:10799479 ISS F YKL132C gene taxon:4932 20021001 SGD
+SGD S000001615 RMA1 GO:0000004 SGD_REF:S000069584 ND P YKL132C gene taxon:4932 20021001 SGD
+SGD S000002159 RMD1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDL001W gene taxon:4932 20031028 SGD
+SGD S000002159 RMD1 GO:0005554 SGD_REF:S000069584 ND F YDL001W gene taxon:4932 20021122 SGD
+SGD S000002159 RMD1 GO:0000004 SGD_REF:S000069584 ND P YDL001W gene taxon:4932 20021122 SGD
+SGD S000001015 RMD11 GO:0008372 SGD_REF:S000069584 ND C YHL023C gene taxon:4932 20021122 SGD
+SGD S000001015 RMD11 GO:0005554 SGD_REF:S000069584 ND F YHL023C gene taxon:4932 20021122 SGD
+SGD S000001015 RMD11 GO:0000004 SGD_REF:S000069584 ND P YHL023C gene taxon:4932 20021122 SGD
+SGD S000002663 RMD5 GO:0005829 SGD_REF:S000072993|PMID:12686616 IDA C YDR255C|GID2 gene taxon:4932 20030708 SGD
+SGD S000002663 RMD5 GO:0005554 SGD_REF:S000069584 ND F YDR255C|GID2 gene taxon:4932 20021122 SGD
+SGD S000002663 RMD5 GO:0045721 SGD_REF:S000072993|PMID:12686616 IMP P YDR255C|GID2 gene taxon:4932 20030708 SGD
+SGD S000000798 RMD6 GO:0008372 SGD_REF:S000069584 ND C YEL072W gene taxon:4932 20021122 SGD
+SGD S000000798 RMD6 GO:0005554 SGD_REF:S000069584 ND F YEL072W gene taxon:4932 20021122 SGD
+SGD S000000798 RMD6 GO:0000004 SGD_REF:S000069584 ND P YEL072W gene taxon:4932 20021122 SGD
+SGD S000001944 RMD8 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YFR048W gene taxon:4932 20020507 SGD
+SGD S000001944 RMD8 GO:0005554 SGD_REF:S000069584 ND F YFR048W gene taxon:4932 20030108 SGD
+SGD S000001944 RMD8 GO:0000004 SGD_REF:S000069584 ND P YFR048W gene taxon:4932 20030108 SGD
+SGD S000003075 RMD9 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YGL107C gene taxon:4932 20031028 SGD
+SGD S000003075 RMD9 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YGL107C gene taxon:4932 20040924 SGD
+SGD S000003075 RMD9 GO:0005554 SGD_REF:S000069584 ND F YGL107C gene taxon:4932 20021122 SGD
+SGD S000003075 RMD9 GO:0000004 SGD_REF:S000069584 ND P YGL107C gene taxon:4932 20021122 SGD
+SGD S000003276 RME1 GO:0005634 SGD_REF:S000040607|PMID:9580682 IDA C negative regulator of meiosis; directly repressed by a1-alpha 2 regulator, zinc finger protein YGR044C|CSP1 gene taxon:4932 20021008 SGD
+SGD S000003276 RME1 GO:0016566 SGD_REF:S000040607|PMID:9580682 IDA F negative regulator of meiosis; directly repressed by a1-alpha 2 regulator, zinc finger protein YGR044C|CSP1 gene taxon:4932 20030109 SGD
+SGD S000003276 RME1 GO:0000122 SGD_REF:S000040607|PMID:9580682 IDA P negative regulator of meiosis; directly repressed by a1-alpha 2 regulator, zinc finger protein YGR044C|CSP1 gene taxon:4932 20030109 SGD
+SGD S000003276 RME1 GO:0007126 SGD_REF:S000040607|PMID:9580682 TAS P negative regulator of meiosis; directly repressed by a1-alpha 2 regulator, zinc finger protein YGR044C|CSP1 gene taxon:4932 20030109 SGD
+SGD S000005945 RMI1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YPL024W|NCE4 gene taxon:4932 20031028 SGD
+SGD S000005945 RMI1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YPL024W|NCE4 gene taxon:4932 20031028 SGD
+SGD S000005945 RMI1 GO:0031422 SGD_REF:S000081006|PMID:15889139 IPI SGD:S000004224|SGD:S000004802 C YPL024W|NCE4 gene taxon:4932 20050606 SGD
+SGD S000005945 RMI1 GO:0005554 SGD_REF:S000069584 ND F YPL024W|NCE4 gene taxon:4932 20050531 SGD
+SGD S000005945 RMI1 GO:0006974 SGD_REF:S000081006|PMID:15889139 IGI SGD:S000000302|SGD:S000002625|SGD:S000002794|SGD:S000000918|SGD:S000003131|SGD:S000001073|SGD:S000004802|SGD:S000004651|SGD:S000004494|SGD:S000004224|SGD:S000004125|SGD:S000003628|SGD:S000000975|SGD:S000000897|SGD:S000002171|SGD:S000000566|SGD:S000000432|SGD:S000006074|SGD:S000005217 P YPL024W|NCE4 gene taxon:4932 20050606 SGD
+SGD S000000776 RML2 GO:0005762 SGD_REF:S000058278|PMID:9445368 TAS C mitochondrial ribosomal protein L2 of the large subunit YEL050C gene taxon:4932 20010118 SGD
+SGD S000000776 RML2 GO:0003735 SGD_REF:S000058278|PMID:9445368 TAS F mitochondrial ribosomal protein L2 of the large subunit YEL050C gene taxon:4932 20010118 SGD
+SGD S000000776 RML2 GO:0006631 SGD_REF:S000049231|PMID:10320805 IMP P mitochondrial ribosomal protein L2 of the large subunit YEL050C gene taxon:4932 20010118 SGD
+SGD S000000776 RML2 GO:0043037 SGD_REF:S000058278|PMID:9445368 TAS P mitochondrial ribosomal protein L2 of the large subunit YEL050C gene taxon:4932 20010118 SGD
+SGD S000004135 RMP1 GO:0000172 SGD_REF:S000080342|PMID:15637077 IDA C Protein component of RNase MRP complex YLR145W gene taxon:4932 20050208 SGD
+SGD S000004135 RMP1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C Protein component of RNase MRP complex YLR145W gene taxon:4932 20031028 SGD
+SGD S000004135 RMP1 GO:0005730 SGD_REF:S000075214|PMID:14690591 IDA C Protein component of RNase MRP complex YLR145W gene taxon:4932 20040105 SGD
+SGD S000004135 RMP1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C Protein component of RNase MRP complex YLR145W gene taxon:4932 20031028 SGD
+SGD S000004135 RMP1 GO:0005554 SGD_REF:S000069584 ND F Protein component of RNase MRP complex YLR145W gene taxon:4932 20030422 SGD
+SGD S000004135 RMP1 GO:0006364 SGD_REF:S000080342|PMID:15637077 IMP P Protein component of RNase MRP complex YLR145W gene taxon:4932 20050208 SGD
+SGD S000004135 RMP1 GO:0008033 SGD_REF:S000075214|PMID:14690591 IDA P Protein component of RNase MRP complex YLR145W gene taxon:4932 20040105 SGD
+SGD S000004135 RMP1 NOT GO:0008033 SGD_REF:S000080342|PMID:15637077 IMP P Protein component of RNase MRP complex YLR145W gene taxon:4932 20050208 SGD
+SGD S000002873 RMT2 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C arginine methyltransferase YDR465C gene taxon:4932 20031028 SGD
+SGD S000002873 RMT2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C arginine methyltransferase YDR465C gene taxon:4932 20031028 SGD
+SGD S000002873 RMT2 GO:0016274 SGD_REF:S000069773|PMID:11856739 ISS F arginine methyltransferase YDR465C gene taxon:4932 20030507 SGD
+SGD S000002873 RMT2 GO:0016274 SGD_REF:S000069773|PMID:11856739 IDA F arginine methyltransferase YDR465C gene taxon:4932 20030507 SGD
+SGD S000002873 RMT2 GO:0018216 SGD_REF:S000069584 IDA P arginine methyltransferase YDR465C gene taxon:4932 20021028 SGD
+SGD S000004848 RNA1 GO:0005634 SGD_REF:S000041191|PMID:8755533 IDA C GTPase activating protein (GAP) for Gsp1p YMR235C gene taxon:4932 20021021 SGD
+SGD S000004848 RNA1 GO:0005829 SGD_REF:S000041191|PMID:8755533 IDA C GTPase activating protein (GAP) for Gsp1p YMR235C gene taxon:4932 20021021 SGD
+SGD S000004848 RNA1 GO:0005098 SGD_REF:S000047837|PMID:9305944 IDA F GTPase activating protein (GAP) for Gsp1p YMR235C gene taxon:4932 20021021 SGD
+SGD S000004848 RNA1 GO:0000054 SGD_REF:S000067496|PMID:11739405 IMP P GTPase activating protein (GAP) for Gsp1p YMR235C gene taxon:4932 20020313 SGD
+SGD S000004848 RNA1 GO:0006407 SGD_REF:S000067496|PMID:11739405 IMP P GTPase activating protein (GAP) for Gsp1p YMR235C gene taxon:4932 20020313 SGD
+SGD S000004848 RNA1 GO:0006606 SGD_REF:S000048758|PMID:7657689 IDA P GTPase activating protein (GAP) for Gsp1p YMR235C gene taxon:4932 20030423 SGD
+SGD S000004848 RNA1 GO:0016072 SGD_REF:S000073750|PMID:12837249 IMP P GTPase activating protein (GAP) for Gsp1p YMR235C gene taxon:4932 20030804 SGD
+SGD S000004665 RNA14 GO:0005634 SGD_REF:S000039127|PMID:10660071 IDA C cleavage and polyadenylation factor CF I component involved in pre-mRNA 3'-end processing YMR061W gene taxon:4932 20030401 SGD
+SGD S000004665 RNA14 GO:0005739 SGD_REF:S000039127|PMID:10660071 IDA C cleavage and polyadenylation factor CF I component involved in pre-mRNA 3'-end processing YMR061W gene taxon:4932 20030401 SGD
+SGD S000004665 RNA14 GO:0005849 SGD_REF:S000060315|PMID:11344258 IPI C cleavage and polyadenylation factor CF I component involved in pre-mRNA 3'-end processing YMR061W gene taxon:4932 20020409 SGD
+SGD S000004665 RNA14 contributes_to GO:0003723 SGD_REF:S000076255|PMID:15215336 IDA F cleavage and polyadenylation factor CF I component involved in pre-mRNA 3'-end processing YMR061W gene taxon:4932 20050218 SGD
+SGD S000004665 RNA14 GO:0046982 SGD_REF:S000076255|PMID:15215336 IPI SGD:S000003012 F cleavage and polyadenylation factor CF I component involved in pre-mRNA 3'-end processing YMR061W gene taxon:4932 20050218 SGD
+SGD S000004665 RNA14 GO:0006378 SGD_REF:S000060315|PMID:11344258 IDA P cleavage and polyadenylation factor CF I component involved in pre-mRNA 3'-end processing YMR061W gene taxon:4932 20020410 SGD
+SGD S000004665 RNA14 GO:0006379 SGD_REF:S000060315|PMID:11344258 IDA P cleavage and polyadenylation factor CF I component involved in pre-mRNA 3'-end processing YMR061W gene taxon:4932 20020409 SGD
+SGD S000003012 RNA15 GO:0005849 SGD_REF:S000060315|PMID:11344258 IPI C cleavage and polyadenylation factor CF I component involved in pre-mRNA 3'-end processing YGL044C gene taxon:4932 20020409 SGD
+SGD S000003012 RNA15 GO:0003723 SGD_REF:S000073613|PMID:12782649 TAS F cleavage and polyadenylation factor CF I component involved in pre-mRNA 3'-end processing YGL044C gene taxon:4932 20050218 SGD
+SGD S000003012 RNA15 GO:0046982 SGD_REF:S000076255|PMID:15215336 IPI SGD:S000004665 F cleavage and polyadenylation factor CF I component involved in pre-mRNA 3'-end processing YGL044C gene taxon:4932 20050218 SGD
+SGD S000003012 RNA15 GO:0006378 SGD_REF:S000060315|PMID:11344258 IDA P cleavage and polyadenylation factor CF I component involved in pre-mRNA 3'-end processing YGL044C gene taxon:4932 20020410 SGD
+SGD S000003012 RNA15 GO:0006379 SGD_REF:S000060315|PMID:11344258 IDA P cleavage and polyadenylation factor CF I component involved in pre-mRNA 3'-end processing YGL044C gene taxon:4932 20020409 SGD
+SGD S000004847 RNH1 GO:0005622 SGD_REF:S000058485|PMID:7489497 TAS C ribonuclease H YMR234W gene taxon:4932 20041206 SGD
+SGD S000004847 RNH1 GO:0005634 SGD_REF:S000058459|PMID:9759502 IC GO:0043137 C ribonuclease H YMR234W gene taxon:4932 20050623 SGD
+SGD S000004847 RNH1 GO:0004523 SGD_REF:S000058485|PMID:7489497 IDA F ribonuclease H YMR234W gene taxon:4932 20010118 SGD
+SGD S000004847 RNH1 GO:0007047 SGD_REF:S000058218|PMID:9335584 IMP P ribonuclease H YMR234W gene taxon:4932 20010118 SGD
+SGD S000004847 RNH1 GO:0043137 SGD_REF:S000058459|PMID:9759502 TAS P ribonuclease H YMR234W gene taxon:4932 20050623 SGD
+SGD S000005016 RNH201 GO:0005634 SGD_REF:S000064878|PMID:11029655 IDA C YNL072W|RNH35|Rnh2A gene taxon:4932 20031002 SGD
+SGD S000005016 RNH201 GO:0004523 SGD_REF:S000050269|PMID:9462832 ISS F YNL072W|RNH35|Rnh2A gene taxon:4932 20010118 SGD
+SGD S000005016 RNH201 GO:0006260 SGD_REF:S000058459|PMID:9759502 TAS P YNL072W|RNH35|Rnh2A gene taxon:4932 20010118 SGD
+SGD S000002687 RNH202 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YDR279W|Rnh2B gene taxon:4932 20031028 SGD
+SGD S000002687 RNH202 GO:0004523 SGD_REF:S000075427|PMID:14734815 IPI SGD:S000005016 F YDR279W|Rnh2B gene taxon:4932 20040206 SGD
+SGD S000002687 RNH202 GO:0006260 SGD_REF:S000075427|PMID:14734815 IPI SGD:S000005016 P YDR279W|Rnh2B gene taxon:4932 20040206 SGD
+SGD S000004144 RNH203 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YLR154C|Rnh2C gene taxon:4932 20031028 SGD
+SGD S000004144 RNH203 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YLR154C|Rnh2C gene taxon:4932 20031028 SGD
+SGD S000004144 RNH203 GO:0004523 SGD_REF:S000075427|PMID:14734815 IPI SGD:S000005016 F YLR154C|Rnh2C gene taxon:4932 20040206 SGD
+SGD S000004144 RNH203 GO:0006260 SGD_REF:S000075427|PMID:14734815 IPI SGD:S000005016 P YLR154C|Rnh2C gene taxon:4932 20040206 SGD
+SGD S000003508 RNH70 GO:0005634 SGD_REF:S000052595|PMID:10359084 IDA C ribonuclease H YGR276C|REX1 gene taxon:4932 20030204 SGD
+SGD S000003508 RNH70 GO:0008408 SGD_REF:S000044002|PMID:10716935 IMP F ribonuclease H YGR276C|REX1 gene taxon:4932 20010118 SGD
+SGD S000003508 RNH70 GO:0008408 SGD_REF:S000044002|PMID:10716935 ISS F ribonuclease H YGR276C|REX1 gene taxon:4932 20010118 SGD
+SGD S000003508 RNH70 GO:0006396 SGD_REF:S000044002|PMID:10716935 IMP P ribonuclease H YGR276C|REX1 gene taxon:4932 20010118 SGD
+SGD S000003969 RNP1 GO:0005737 SGD_REF:S000043974|PMID:8341595 IDA C RNA binding protein (putative) YLL046C gene taxon:4932 20021010 SGD
+SGD S000003969 RNP1 GO:0003723 SGD_REF:S000043974|PMID:8341595 ISS F RNA binding protein (putative) YLL046C gene taxon:4932 20021010 SGD
+SGD S000003969 RNP1 GO:0042254 SGD_REF:S000043974|PMID:8341595 IMP P RNA binding protein (putative) YLL046C gene taxon:4932 20021010 SGD
+SGD S000000533 RNQ1 GO:0005829 SGD_REF:S000061331|PMID:11511345 IDA C transferable epigenetic modifier, forms a prion responsible for the [PIN(+)] phenotype YCL028W|[PIN(+)] gene taxon:4932 20021009 SGD
+SGD S000000533 RNQ1 GO:0005554 SGD_REF:S000069584 ND F transferable epigenetic modifier, forms a prion responsible for the [PIN(+)] phenotype YCL028W|[PIN(+)] gene taxon:4932 20021009 SGD
+SGD S000000533 RNQ1 GO:0000004 SGD_REF:S000069584 ND P transferable epigenetic modifier, forms a prion responsible for the [PIN(+)] phenotype YCL028W|[PIN(+)] gene taxon:4932 20021009 SGD
+SGD S000000872 RNR1 GO:0005737 SGD_REF:S000049463|PMID:9315670 IDA C ribonucleotide reductase, large (R1) subunit YER070W|CRT7|RIR1|SDS12 gene taxon:4932 20030204 SGD
+SGD S000000872 RNR1 GO:0005737 SGD_REF:S000073212|PMID:12732713 IDA C ribonucleotide reductase, large (R1) subunit YER070W|CRT7|RIR1|SDS12 gene taxon:4932 20030606 SGD
+SGD S000000872 RNR1 GO:0005971 SGD_REF:S000064879|PMID:10716984 IDA C ribonucleotide reductase, large (R1) subunit YER070W|CRT7|RIR1|SDS12 gene taxon:4932 20050209 SGD
+SGD S000000872 RNR1 GO:0004748 SGD_REF:S000039376|PMID:8552025 IMP F ribonucleotide reductase, large (R1) subunit YER070W|CRT7|RIR1|SDS12 gene taxon:4932 20030203 SGD
+SGD S000000872 RNR1 GO:0006260 SGD_REF:S000058460|PMID:9759483 TAS P ribonucleotide reductase, large (R1) subunit YER070W|CRT7|RIR1|SDS12 gene taxon:4932 20010118 SGD
+SGD S000003563 RNR2 GO:0005634 SGD_REF:S000073212|PMID:12732713 IDA C ribonucleotide reductase subunit, ribonucleotide reductase, small (R2) subunit YJL026W|CRT6 gene taxon:4932 20030606 SGD
+SGD S000003563 RNR2 GO:0005737 SGD_REF:S000049463|PMID:9315670 IDA C ribonucleotide reductase subunit, ribonucleotide reductase, small (R2) subunit YJL026W|CRT6 gene taxon:4932 20030204 SGD
+SGD S000003563 RNR2 GO:0005737 SGD_REF:S000073212|PMID:12732713 IDA C ribonucleotide reductase subunit, ribonucleotide reductase, small (R2) subunit YJL026W|CRT6 gene taxon:4932 20030606 SGD
+SGD S000003563 RNR2 GO:0005971 SGD_REF:S000064879|PMID:10716984 IDA C ribonucleotide reductase subunit, ribonucleotide reductase, small (R2) subunit YJL026W|CRT6 gene taxon:4932 20050209 SGD
+SGD S000003563 RNR2 GO:0004748 SGD_REF:S000045069|PMID:3313004 IEP F ribonucleotide reductase subunit, ribonucleotide reductase, small (R2) subunit YJL026W|CRT6 gene taxon:4932 20021126 SGD
+SGD S000003563 RNR2 GO:0004748 SGD_REF:S000045069|PMID:3313004 ISS F ribonucleotide reductase subunit, ribonucleotide reductase, small (R2) subunit YJL026W|CRT6 gene taxon:4932 20021126 SGD
+SGD S000003563 RNR2 GO:0006260 SGD_REF:S000058460|PMID:9759483 TAS P ribonucleotide reductase subunit, ribonucleotide reductase, small (R2) subunit YJL026W|CRT6 gene taxon:4932 20010118 SGD
+SGD S000001328 RNR3 GO:0005737 SGD_REF:S000073212|PMID:12732713 IDA C ribonucleotide reductase, large (R1) subunit YIL066C|DIN1|RIR3 gene taxon:4932 20030606 SGD
+SGD S000001328 RNR3 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C ribonucleotide reductase, large (R1) subunit YIL066C|DIN1|RIR3 gene taxon:4932 20040813 SGD
+SGD S000001328 RNR3 GO:0005971 SGD_REF:S000064879|PMID:10716984 IDA C ribonucleotide reductase, large (R1) subunit YIL066C|DIN1|RIR3 gene taxon:4932 20050209 SGD
+SGD S000001328 RNR3 GO:0004748 SGD_REF:S000069883|PMID:11893751 IDA F ribonucleotide reductase, large (R1) subunit YIL066C|DIN1|RIR3 gene taxon:4932 20030204 SGD
+SGD S000001328 RNR3 GO:0006260 SGD_REF:S000058460|PMID:9759483 TAS P ribonucleotide reductase, large (R1) subunit YIL066C|DIN1|RIR3 gene taxon:4932 20010118 SGD
+SGD S000003412 RNR4 GO:0005634 SGD_REF:S000049463|PMID:9315670 IDA C ribonucleotide reductase, small (R2) subunit YGR180C|CRT3 gene taxon:4932 20030204 SGD
+SGD S000003412 RNR4 GO:0005634 SGD_REF:S000073212|PMID:12732713 IDA C ribonucleotide reductase, small (R2) subunit YGR180C|CRT3 gene taxon:4932 20030606 SGD
+SGD S000003412 RNR4 GO:0005737 SGD_REF:S000073212|PMID:12732713 IDA C ribonucleotide reductase, small (R2) subunit YGR180C|CRT3 gene taxon:4932 20030606 SGD
+SGD S000003412 RNR4 GO:0005971 SGD_REF:S000049463|PMID:9315670 IMP C ribonucleotide reductase, small (R2) subunit YGR180C|CRT3 gene taxon:4932 20050209 SGD
+SGD S000003412 RNR4 GO:0005971 SGD_REF:S000049463|PMID:9315670 IPI C ribonucleotide reductase, small (R2) subunit YGR180C|CRT3 gene taxon:4932 20050209 SGD
+SGD S000003412 RNR4 GO:0005971 SGD_REF:S000064879|PMID:10716984 IDA C ribonucleotide reductase, small (R2) subunit YGR180C|CRT3 gene taxon:4932 20050209 SGD
+SGD S000003412 RNR4 GO:0004748 SGD_REF:S000049463|PMID:9315670 IGI F ribonucleotide reductase, small (R2) subunit YGR180C|CRT3 gene taxon:4932 20030204 SGD
+SGD S000003412 RNR4 GO:0004748 SGD_REF:S000049463|PMID:9315670 IPI F ribonucleotide reductase, small (R2) subunit YGR180C|CRT3 gene taxon:4932 20030204 SGD
+SGD S000003412 RNR4 GO:0004748 SGD_REF:S000049463|PMID:9315670 IEP F ribonucleotide reductase, small (R2) subunit YGR180C|CRT3 gene taxon:4932 20030204 SGD
+SGD S000003412 RNR4 GO:0006260 SGD_REF:S000058460|PMID:9759483 TAS P ribonucleotide reductase, small (R2) subunit YGR180C|CRT3 gene taxon:4932 20010118 SGD
+SGD S000004852 RNT1 GO:0005654 SGD_REF:S000076783|PMID:15090619 IDA C ribonuclease III YMR239C gene taxon:4932 20050708 SGD
+SGD S000004852 RNT1 GO:0005730 SGD_REF:S000076783|PMID:15090619 IDA C ribonuclease III YMR239C gene taxon:4932 20050708 SGD
+SGD S000004852 RNT1 GO:0004525 SGD_REF:S000058443|PMID:10690410 TAS F ribonuclease III YMR239C gene taxon:4932 20010118 SGD
+SGD S000004852 RNT1 GO:0006365 SGD_REF:S000058443|PMID:10690410 TAS P ribonuclease III YMR239C gene taxon:4932 20010118 SGD
+SGD S000006044 RNY1 GO:0005576 SGD_REF:S000059474|PMID:11158587 IDA C ribonuclease, T2 family YPL123C gene taxon:4932 20021029 SGD
+SGD S000006044 RNY1 GO:0004521 SGD_REF:S000059474|PMID:11158587 IDA F ribonuclease, T2 family YPL123C gene taxon:4932 20021029 SGD
+SGD S000006044 RNY1 GO:0000902 SGD_REF:S000059474|PMID:11158587 IMP P ribonuclease, T2 family YPL123C gene taxon:4932 20021108 SGD
+SGD S000005544 ROD1 GO:0005886 SGD_REF:S000054414|PMID:8621680 IDA C YOR018W gene taxon:4932 20010525 SGD
+SGD S000005544 ROD1 GO:0005554 SGD_REF:S000069584 ND F YOR018W gene taxon:4932 20021028 SGD
+SGD S000005544 ROD1 GO:0042493 SGD_REF:S000070307|PMID:12163175 IMP P YOR018W gene taxon:4932 20021111 SGD
+SGD S000003112 ROG1 GO:0008372 SGD_REF:S000069584 ND C YGL144C gene taxon:4932 20021203 SGD
+SGD S000003112 ROG1 GO:0016298 SGD_REF:S000062226|PMID:10341423 NAS F YGL144C gene taxon:4932 20021203 SGD
+SGD S000003112 ROG1 GO:0006629 SGD_REF:S000062226|PMID:10341423 IMP P YGL144C gene taxon:4932 20021203 SGD
+SGD S000001918 ROG3 GO:0008372 SGD_REF:S000069584 ND C YFR022W gene taxon:4932 20030424 SGD
+SGD S000001918 ROG3 GO:0005554 SGD_REF:S000069584 ND F YFR022W gene taxon:4932 20030424 SGD
+SGD S000001918 ROG3 GO:0000004 SGD_REF:S000069584 ND P YFR022W gene taxon:4932 20030424 SGD
+SGD S000003139 ROK1 GO:0005730 SGD_REF:S000058443|PMID:10690410 TAS C YGL171W gene taxon:4932 20010118 SGD
+SGD S000003139 ROK1 GO:0004004 SGD_REF:S000058443|PMID:10690410 TAS F YGL171W gene taxon:4932 20010118 SGD
+SGD S000003139 ROK1 GO:0016887 SGD_REF:S000051998|PMID:10373593 IDA F YGL171W gene taxon:4932 20030310 SGD
+SGD S000003139 ROK1 GO:0006365 SGD_REF:S000058443|PMID:10690410 TAS P YGL171W gene taxon:4932 20010118 SGD
+SGD S000003302 ROM1 GO:0005622 SGD_REF:S000058399|PMID:9891811 TAS C YGR070W|SKC1 gene taxon:4932 20010118 SGD
+SGD S000003302 ROM1 GO:0004871 SGD_REF:S000058399|PMID:9891811 IPI F YGR070W|SKC1 gene taxon:4932 20010118 SGD
+SGD S000003302 ROM1 GO:0005089 SGD_REF:S000058399|PMID:9891811 IMP F YGR070W|SKC1 gene taxon:4932 20010118 SGD
+SGD S000003302 ROM1 GO:0007015 SGD_REF:S000058399|PMID:9891811 TAS P YGR070W|SKC1 gene taxon:4932 20030116 SGD
+SGD S000003302 ROM1 GO:0007047 SGD_REF:S000058399|PMID:9891811 IPI P YGR070W|SKC1 gene taxon:4932 20010118 SGD
+SGD S000003302 ROM1 GO:0007117 SGD_REF:S000058399|PMID:9891811 IPI P YGR070W|SKC1 gene taxon:4932 20010118 SGD
+SGD S000003302 ROM1 GO:0007264 SGD_REF:S000058399|PMID:9891811 IPI P YGR070W|SKC1 gene taxon:4932 20010118 SGD
+SGD S000003302 ROM1 GO:0030468 SGD_REF:S000058399|PMID:9891811 IPI P YGR070W|SKC1 gene taxon:4932 20010302 SGD
+SGD S000004363 ROM2 GO:0005934 SGD_REF:S000058399|PMID:9891811 IDA C YLR371W gene taxon:4932 20010118 SGD
+SGD S000004363 ROM2 GO:0004871 SGD_REF:S000058399|PMID:9891811 IPI F YLR371W gene taxon:4932 20010118 SGD
+SGD S000004363 ROM2 GO:0005089 SGD_REF:S000058399|PMID:9891811 IDA F YLR371W gene taxon:4932 20010118 SGD
+SGD S000004363 ROM2 GO:0006897 SGD_REF:S000075861|PMID:14593073 IMP P YLR371W gene taxon:4932 20050505 SGD
+SGD S000004363 ROM2 GO:0006950 SGD_REF:S000080277|PMID:15545276 IMP P YLR371W gene taxon:4932 20050126 SGD
+SGD S000004363 ROM2 GO:0007015 SGD_REF:S000058399|PMID:9891811 TAS P YLR371W gene taxon:4932 20030116 SGD
+SGD S000004363 ROM2 GO:0007047 SGD_REF:S000058399|PMID:9891811 IPI P YLR371W gene taxon:4932 20010118 SGD
+SGD S000004363 ROM2 GO:0007117 SGD_REF:S000058399|PMID:9891811 IPI P YLR371W gene taxon:4932 20010118 SGD
+SGD S000004363 ROM2 GO:0007264 SGD_REF:S000058399|PMID:9891811 IPI P YLR371W gene taxon:4932 20010118 SGD
+SGD S000004363 ROM2 GO:0030468 SGD_REF:S000058399|PMID:9891811 IPI P YLR371W gene taxon:4932 20010302 SGD
+SGD S000004813 ROT1 GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C membrane protein (putative) YMR200W gene taxon:4932 20031028 SGD
+SGD S000004813 ROT1 GO:0005554 SGD_REF:S000069584 ND F membrane protein (putative) YMR200W gene taxon:4932 20021001 SGD
+SGD S000004813 ROT1 GO:0007047 SGD_REF:S000050727|PMID:9545237 IMP P membrane protein (putative) YMR200W gene taxon:4932 20021001 SGD
+SGD S000000433 ROT2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C glucosidase II YBR229C|GLS2 gene taxon:4932 20040928 SGD
+SGD S000000433 ROT2 GO:0005783 SGD_REF:S000064885|PMID:8910335 ISS C glucosidase II YBR229C|GLS2 gene taxon:4932 20020708 SGD
+SGD S000000433 ROT2 GO:0005788 SGD_REF:S000113928|PMID:16373354 IDA C glucosidase II YBR229C|GLS2 gene taxon:4932 20060119 SGD
+SGD S000000433 ROT2 GO:0004558 SGD_REF:S000053239|PMID:9430631 IDA F glucosidase II YBR229C|GLS2 gene taxon:4932 20060119 SGD
+SGD S000000433 ROT2 GO:0009272 SGD_REF:S000053239|PMID:9430631 IMP P glucosidase II YBR229C|GLS2 gene taxon:4932 20020708 SGD
+SGD S000006269 ROX1 GO:0000228 SGD_REF:S000043831|PMID:7565763 IPI C HMG-domain site-specific DNA binding protein. YPR065W|REO1 gene taxon:4932 20020806 SGD
+SGD S000006269 ROX1 GO:0008301 SGD_REF:S000043831|PMID:7565763 IDA F HMG-domain site-specific DNA binding protein. YPR065W|REO1 gene taxon:4932 20020806 SGD
+SGD S000006269 ROX1 GO:0016566 SGD_REF:S000045308|PMID:3062365 IMP F HMG-domain site-specific DNA binding protein. YPR065W|REO1 gene taxon:4932 20020806 SGD
+SGD S000006269 ROX1 GO:0000122 SGD_REF:S000045308|PMID:3062365 IMP P HMG-domain site-specific DNA binding protein. YPR065W|REO1 gene taxon:4932 20020806 SGD
+SGD S000000189 ROX3 GO:0000119 SGD_REF:S000048078|PMID:9420330 IDA C RNA polymerase II holoenzyme/mediator subunit YBL093C|MED19|NUT3|SSN7 gene taxon:4932 20010118 SGD
+SGD S000000189 ROX3 GO:0005634 SGD_REF:S000069459|PMID:11914276 IDA C RNA polymerase II holoenzyme/mediator subunit YBL093C|MED19|NUT3|SSN7 gene taxon:4932 20020507 SGD
+SGD S000000189 ROX3 GO:0016455 SGD_REF:S000048078|PMID:9420330 IDA F RNA polymerase II holoenzyme/mediator subunit YBL093C|MED19|NUT3|SSN7 gene taxon:4932 20010302 SGD
+SGD S000000189 ROX3 GO:0006366 SGD_REF:S000048078|PMID:9420330 IDA P RNA polymerase II holoenzyme/mediator subunit YBL093C|MED19|NUT3|SSN7 gene taxon:4932 20010118 SGD
+SGD S000003824 RPA12 GO:0005736 SGD_REF:S000057661|PMID:8246845 TAS C RNA polymerase I A12.2 subunit YJR063W|A12.2|RRN4 gene taxon:4932 20010118 SGD
+SGD S000003824 RPA12 GO:0003899 SGD_REF:S000057661|PMID:8246845 TAS F RNA polymerase I A12.2 subunit YJR063W|A12.2|RRN4 gene taxon:4932 20010118 SGD
+SGD S000003824 RPA12 GO:0006360 SGD_REF:S000058500 TAS P RNA polymerase I A12.2 subunit YJR063W|A12.2|RRN4 gene taxon:4932 20010119 SGD
+SGD S000006214 RPA135 GO:0005736 SGD_REF:S000057661|PMID:8246845 TAS C RNA polymerase I subunit YPR010C|A135|RPA2|RRN2|SRP3 gene taxon:4932 20010118 SGD
+SGD S000006214 RPA135 GO:0003899 SGD_REF:S000057661|PMID:8246845 TAS F RNA polymerase I subunit YPR010C|A135|RPA2|RRN2|SRP3 gene taxon:4932 20010118 SGD
+SGD S000006214 RPA135 GO:0006360 SGD_REF:S000058500 TAS P RNA polymerase I subunit YPR010C|A135|RPA2|RRN2|SRP3 gene taxon:4932 20010119 SGD
+SGD S000002563 RPA14 GO:0005736 SGD_REF:S000043630|PMID:7768955 IDA C RNA polymerase I subunit YDR156W|A14 gene taxon:4932 20010118 SGD
+SGD S000002563 RPA14 GO:0003899 SGD_REF:S000043630|PMID:7768955 IDA F RNA polymerase I subunit YDR156W|A14 gene taxon:4932 20010118 SGD
+SGD S000002563 RPA14 GO:0006360 SGD_REF:S000058500 TAS P RNA polymerase I subunit YDR156W|A14 gene taxon:4932 20010119 SGD
+SGD S000005868 RPA190 GO:0005736 SGD_REF:S000057661|PMID:8246845 TAS C RNA polymerase I subunit YOR341W|A190|RRN1 gene taxon:4932 20010118 SGD
+SGD S000005868 RPA190 GO:0003899 SGD_REF:S000057661|PMID:8246845 TAS F RNA polymerase I subunit YOR341W|A190|RRN1 gene taxon:4932 20010118 SGD
+SGD S000005868 RPA190 GO:0006360 SGD_REF:S000058500 TAS P RNA polymerase I subunit YOR341W|A190|RRN1 gene taxon:4932 20010119 SGD
+SGD S000003684 RPA34 GO:0005634 SGD_REF:S000071811|PMID:12206772 IDA C YJL148W|A34.5 gene taxon:4932 20021210 SGD
+SGD S000003684 RPA34 GO:0005730 SGD_REF:S000071811|PMID:12206772 IDA C YJL148W|A34.5 gene taxon:4932 20030605 SGD
+SGD S000003684 RPA34 GO:0005736 SGD_REF:S000057661|PMID:8246845 TAS C YJL148W|A34.5 gene taxon:4932 20010118 SGD
+SGD S000003684 RPA34 GO:0003899 SGD_REF:S000057661|PMID:8246845 TAS F YJL148W|A34.5 gene taxon:4932 20010118 SGD
+SGD S000003684 RPA34 GO:0006360 SGD_REF:S000058500 TAS P YJL148W|A34.5 gene taxon:4932 20010119 SGD
+SGD S000005867 RPA43 GO:0005736 SGD_REF:S000057661|PMID:8246845 TAS C DNA dependent RNA polymerase I subunit A43 YOR340C|A43 gene taxon:4932 20010118 SGD
+SGD S000005867 RPA43 GO:0003899 SGD_REF:S000057661|PMID:8246845 TAS F DNA dependent RNA polymerase I subunit A43 YOR340C|A43 gene taxon:4932 20010118 SGD
+SGD S000005867 RPA43 GO:0006360 SGD_REF:S000058500 TAS P DNA dependent RNA polymerase I subunit A43 YOR340C|A43 gene taxon:4932 20010119 SGD
+SGD S000005192 RPA49 GO:0005736 SGD_REF:S000057661|PMID:8246845 TAS C RNA polymerase A 49 kDa alpha subunit YNL248C|A49 gene taxon:4932 20010118 SGD
+SGD S000005192 RPA49 GO:0003899 SGD_REF:S000057661|PMID:8246845 TAS F RNA polymerase A 49 kDa alpha subunit YNL248C|A49 gene taxon:4932 20010118 SGD
+SGD S000005192 RPA49 GO:0006360 SGD_REF:S000058500 TAS P RNA polymerase A 49 kDa alpha subunit YNL248C|A49 gene taxon:4932 20010119 SGD
+SGD S000005736 RPB10 GO:0005665 SGD_REF:S000058446|PMID:9774381 TAS C RNA polymerase II core subunit YOR210W|ABC10-beta gene taxon:4932 20010118 SGD
+SGD S000005736 RPB10 GO:0005666 SGD_REF:S000058446|PMID:9774381 TAS C RNA polymerase II core subunit YOR210W|ABC10-beta gene taxon:4932 20010118 SGD
+SGD S000005736 RPB10 GO:0005736 SGD_REF:S000058446|PMID:9774381 TAS C RNA polymerase II core subunit YOR210W|ABC10-beta gene taxon:4932 20010118 SGD
+SGD S000005736 RPB10 GO:0003899 SGD_REF:S000058446|PMID:9774381 TAS F RNA polymerase II core subunit YOR210W|ABC10-beta gene taxon:4932 20010118 SGD
+SGD S000005736 RPB10 GO:0006360 SGD_REF:S000058500 TAS P RNA polymerase II core subunit YOR210W|ABC10-beta gene taxon:4932 20010119 SGD
+SGD S000005736 RPB10 GO:0006366 SGD_REF:S000058446|PMID:9774381 TAS P RNA polymerase II core subunit YOR210W|ABC10-beta gene taxon:4932 20050920 SGD
+SGD S000005736 RPB10 GO:0006383 SGD_REF:S000058500 TAS P RNA polymerase II core subunit YOR210W|ABC10-beta gene taxon:4932 20010119 SGD
+SGD S000005365 RPB11 GO:0005665 SGD_REF:S000058446|PMID:9774381 TAS C RNA polymerase II core subunit YOL005C|B12.5 gene taxon:4932 20010118 SGD
+SGD S000005365 RPB11 GO:0003899 SGD_REF:S000058446|PMID:9774381 TAS F RNA polymerase II core subunit YOL005C|B12.5 gene taxon:4932 20010118 SGD
+SGD S000005365 RPB11 GO:0006366 SGD_REF:S000058446|PMID:9774381 TAS P RNA polymerase II core subunit YOL005C|B12.5 gene taxon:4932 20050920 SGD
+SGD S000005677 RPB2 GO:0005665 SGD_REF:S000058446|PMID:9774381 TAS C YOR151C|B150|RPB150|RPO22|SIT2|SOH2 gene taxon:4932 20010118 SGD
+SGD S000005677 RPB2 GO:0003899 SGD_REF:S000058446|PMID:9774381 TAS F YOR151C|B150|RPB150|RPO22|SIT2|SOH2 gene taxon:4932 20010118 SGD
+SGD S000005677 RPB2 GO:0006366 SGD_REF:S000058446|PMID:9774381 TAS P YOR151C|B150|RPB150|RPO22|SIT2|SOH2 gene taxon:4932 20050920 SGD
+SGD S000001283 RPB3 GO:0005665 SGD_REF:S000058446|PMID:9774381 TAS C RNA polymerase II 45 kDa subunit YIL021W|B44 gene taxon:4932 20010118 SGD
+SGD S000001283 RPB3 GO:0003899 SGD_REF:S000058446|PMID:9774381 TAS F RNA polymerase II 45 kDa subunit YIL021W|B44 gene taxon:4932 20010118 SGD
+SGD S000001283 RPB3 GO:0006366 SGD_REF:S000058446|PMID:9774381 TAS P RNA polymerase II 45 kDa subunit YIL021W|B44 gene taxon:4932 20050920 SGD
+SGD S000003676 RPB4 GO:0005634 SGD_REF:S000075953|PMID:12857861 IDA C RNA polymerase II fourth largest subunit YJL140W|B32|CTF15 gene taxon:4932 20050227 SGD
+SGD S000003676 RPB4 GO:0005665 SGD_REF:S000058446|PMID:9774381 TAS C RNA polymerase II fourth largest subunit YJL140W|B32|CTF15 gene taxon:4932 20010118 SGD
+SGD S000003676 RPB4 GO:0005737 SGD_REF:S000075953|PMID:12857861 IDA C RNA polymerase II fourth largest subunit YJL140W|B32|CTF15 gene taxon:4932 20050227 SGD
+SGD S000003676 RPB4 GO:0003899 SGD_REF:S000058446|PMID:9774381 TAS F RNA polymerase II fourth largest subunit YJL140W|B32|CTF15 gene taxon:4932 20010118 SGD
+SGD S000003676 RPB4 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P RNA polymerase II fourth largest subunit YJL140W|B32|CTF15 gene taxon:4932 20060203 SGD
+SGD S000003676 RPB4 GO:0006366 SGD_REF:S000058446|PMID:9774381 TAS P RNA polymerase II fourth largest subunit YJL140W|B32|CTF15 gene taxon:4932 20050920 SGD
+SGD S000003676 RPB4 GO:0006406 SGD_REF:S000075953|PMID:12857861 IMP P RNA polymerase II fourth largest subunit YJL140W|B32|CTF15 gene taxon:4932 20050227 SGD
+SGD S000000358 RPB5 GO:0005665 SGD_REF:S000058446|PMID:9774381 TAS C 25 kDa RNA polymerase subunit (common to polymerases I, II and III) YBR154C|ABC27 gene taxon:4932 20010118 SGD
+SGD S000000358 RPB5 GO:0005666 SGD_REF:S000058446|PMID:9774381 TAS C 25 kDa RNA polymerase subunit (common to polymerases I, II and III) YBR154C|ABC27 gene taxon:4932 20010118 SGD
+SGD S000000358 RPB5 GO:0005736 SGD_REF:S000058446|PMID:9774381 TAS C 25 kDa RNA polymerase subunit (common to polymerases I, II and III) YBR154C|ABC27 gene taxon:4932 20010118 SGD
+SGD S000000358 RPB5 GO:0003899 SGD_REF:S000058446|PMID:9774381 TAS F 25 kDa RNA polymerase subunit (common to polymerases I, II and III) YBR154C|ABC27 gene taxon:4932 20010118 SGD
+SGD S000000358 RPB5 GO:0006360 SGD_REF:S000058500 TAS P 25 kDa RNA polymerase subunit (common to polymerases I, II and III) YBR154C|ABC27 gene taxon:4932 20010119 SGD
+SGD S000000358 RPB5 GO:0006366 SGD_REF:S000058446|PMID:9774381 TAS P 25 kDa RNA polymerase subunit (common to polymerases I, II and III) YBR154C|ABC27 gene taxon:4932 20050920 SGD
+SGD S000000358 RPB5 GO:0006383 SGD_REF:S000058500 TAS P 25 kDa RNA polymerase subunit (common to polymerases I, II and III) YBR154C|ABC27 gene taxon:4932 20010119 SGD
+SGD S000002812 RPB7 GO:0005665 SGD_REF:S000058446|PMID:9774381 TAS C RNA polymerase II dissociable subunit YDR404C|B16 gene taxon:4932 20010118 SGD
+SGD S000002812 RPB7 GO:0003899 SGD_REF:S000058446|PMID:9774381 TAS F RNA polymerase II dissociable subunit YDR404C|B16 gene taxon:4932 20010118 SGD
+SGD S000002812 RPB7 GO:0006366 SGD_REF:S000058446|PMID:9774381 TAS P RNA polymerase II dissociable subunit YDR404C|B16 gene taxon:4932 20050920 SGD
+SGD S000005750 RPB8 GO:0005665 SGD_REF:S000058446|PMID:9774381 TAS C 16 kDa RNA polymerase subunit (common to polymerases I, II and III) YOR224C|ABC14.5 gene taxon:4932 20010118 SGD
+SGD S000005750 RPB8 GO:0005666 SGD_REF:S000058446|PMID:9774381 TAS C 16 kDa RNA polymerase subunit (common to polymerases I, II and III) YOR224C|ABC14.5 gene taxon:4932 20010118 SGD
+SGD S000005750 RPB8 GO:0005736 SGD_REF:S000058446|PMID:9774381 TAS C 16 kDa RNA polymerase subunit (common to polymerases I, II and III) YOR224C|ABC14.5 gene taxon:4932 20010118 SGD
+SGD S000005750 RPB8 GO:0003899 SGD_REF:S000058446|PMID:9774381 TAS F 16 kDa RNA polymerase subunit (common to polymerases I, II and III) YOR224C|ABC14.5 gene taxon:4932 20010118 SGD
+SGD S000005750 RPB8 GO:0006360 SGD_REF:S000058500 TAS P 16 kDa RNA polymerase subunit (common to polymerases I, II and III) YOR224C|ABC14.5 gene taxon:4932 20010119 SGD
+SGD S000005750 RPB8 GO:0006366 SGD_REF:S000058446|PMID:9774381 TAS P 16 kDa RNA polymerase subunit (common to polymerases I, II and III) YOR224C|ABC14.5 gene taxon:4932 20050920 SGD
+SGD S000005750 RPB8 GO:0006383 SGD_REF:S000058500 TAS P 16 kDa RNA polymerase subunit (common to polymerases I, II and III) YOR224C|ABC14.5 gene taxon:4932 20010119 SGD
+SGD S000003038 RPB9 GO:0005665 SGD_REF:S000058446|PMID:9774381 TAS C RNA polymerase II core subunit YGL070C|B12.6|SHI1|SSU73 gene taxon:4932 20010118 SGD
+SGD S000003038 RPB9 GO:0003899 SGD_REF:S000058446|PMID:9774381 TAS F RNA polymerase II core subunit YGL070C|B12.6|SHI1|SSU73 gene taxon:4932 20010118 SGD
+SGD S000003038 RPB9 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P RNA polymerase II core subunit YGL070C|B12.6|SHI1|SSU73 gene taxon:4932 20060203 SGD
+SGD S000003038 RPB9 GO:0006366 SGD_REF:S000058446|PMID:9774381 TAS P RNA polymerase II core subunit YGL070C|B12.6|SHI1|SSU73 gene taxon:4932 20050920 SGD
+SGD S000003038 RPB9 GO:0006974 SGD_REF:S000076175|PMID:12482937 IMP P RNA polymerase II core subunit YGL070C|B12.6|SHI1|SSU73 gene taxon:4932 20060406 SGD
+SGD S000001185 RPC10 GO:0005665 SGD_REF:S000058446|PMID:9774381 TAS C RNA polymerase II subunit YHR143W-A|ABC10-alpha|RPB12 gene taxon:4932 20010118 SGD
+SGD S000001185 RPC10 GO:0005666 SGD_REF:S000058446|PMID:9774381 TAS C RNA polymerase II subunit YHR143W-A|ABC10-alpha|RPB12 gene taxon:4932 20010118 SGD
+SGD S000001185 RPC10 GO:0005736 SGD_REF:S000058446|PMID:9774381 TAS C RNA polymerase II subunit YHR143W-A|ABC10-alpha|RPB12 gene taxon:4932 20010118 SGD
+SGD S000001185 RPC10 GO:0003899 SGD_REF:S000058446|PMID:9774381 TAS F RNA polymerase II subunit YHR143W-A|ABC10-alpha|RPB12 gene taxon:4932 20010118 SGD
+SGD S000001185 RPC10 GO:0006360 SGD_REF:S000058500 TAS P RNA polymerase II subunit YHR143W-A|ABC10-alpha|RPB12 gene taxon:4932 20010119 SGD
+SGD S000001185 RPC10 GO:0006366 SGD_REF:S000058446|PMID:9774381 TAS P RNA polymerase II subunit YHR143W-A|ABC10-alpha|RPB12 gene taxon:4932 20050920 SGD
+SGD S000001185 RPC10 GO:0006383 SGD_REF:S000058500 TAS P RNA polymerase II subunit YHR143W-A|ABC10-alpha|RPB12 gene taxon:4932 20010119 SGD
+SGD S000002452 RPC11 GO:0005666 SGD_REF:S000058394|PMID:9869639 IDA C TFIIS-like small Pol III subunit C11 YDR045C|C11 gene taxon:4932 20010118 SGD
+SGD S000002452 RPC11 GO:0003899 SGD_REF:S000058394|PMID:9869639 IDA F TFIIS-like small Pol III subunit C11 YDR045C|C11 gene taxon:4932 20010118 SGD
+SGD S000002452 RPC11 GO:0006383 SGD_REF:S000058500 TAS P TFIIS-like small Pol III subunit C11 YDR045C|C11 gene taxon:4932 20010119 SGD
+SGD S000003548 RPC17 GO:0005666 SGD_REF:S000061911|PMID:10611227 IDA C YJL011C|C17 gene taxon:4932 20020807 SGD
+SGD S000003548 RPC17 GO:0003899 SGD_REF:S000061911|PMID:10611227 IPI F YJL011C|C17 gene taxon:4932 20020925 SGD
+SGD S000003548 RPC17 GO:0003899 SGD_REF:S000061911|PMID:10611227 IDA F YJL011C|C17 gene taxon:4932 20020925 SGD
+SGD S000003548 RPC17 GO:0006384 SGD_REF:S000061911|PMID:10611227 IDA P YJL011C|C17 gene taxon:4932 20020925 SGD
+SGD S000003548 RPC17 GO:0006384 SGD_REF:S000061911|PMID:10611227 IPI P YJL011C|C17 gene taxon:4932 20020925 SGD
+SGD S000005057 RPC19 GO:0005666 SGD_REF:S000057661|PMID:8246845 TAS C RNA polymerases I (A) and III (C) subunit YNL113W|AC19 gene taxon:4932 20010118 SGD
+SGD S000005057 RPC19 GO:0005736 SGD_REF:S000057661|PMID:8246845 TAS C RNA polymerases I (A) and III (C) subunit YNL113W|AC19 gene taxon:4932 20010118 SGD
+SGD S000005057 RPC19 GO:0003899 SGD_REF:S000057661|PMID:8246845 TAS F RNA polymerases I (A) and III (C) subunit YNL113W|AC19 gene taxon:4932 20010118 SGD
+SGD S000005057 RPC19 GO:0006360 SGD_REF:S000058500 TAS P RNA polymerases I (A) and III (C) subunit YNL113W|AC19 gene taxon:4932 20010119 SGD
+SGD S000005057 RPC19 GO:0006383 SGD_REF:S000058500 TAS P RNA polymerases I (A) and III (C) subunit YNL113W|AC19 gene taxon:4932 20010119 SGD
+SGD S000001627 RPC25 GO:0005666 SGD_REF:S000057661|PMID:8246845 TAS C RNA polymerase III subunit YKL144C|C25|YKL1 gene taxon:4932 20010118 SGD
+SGD S000001627 RPC25 GO:0003899 SGD_REF:S000057661|PMID:8246845 TAS F RNA polymerase III subunit YKL144C|C25|YKL1 gene taxon:4932 20010118 SGD
+SGD S000001627 RPC25 GO:0006383 SGD_REF:S000058500 TAS P RNA polymerase III subunit YKL144C|C25|YKL1 gene taxon:4932 20010119 SGD
+SGD S000005095 RPC31 GO:0005666 SGD_REF:S000057661|PMID:8246845 TAS C HMG1-like protein, RNA polymerase III (C) 31 kDa subunit YNL151C|ACP2|C31|RPC8 gene taxon:4932 20010118 SGD
+SGD S000005095 RPC31 GO:0003899 SGD_REF:S000057661|PMID:8246845 TAS F HMG1-like protein, RNA polymerase III (C) 31 kDa subunit YNL151C|ACP2|C31|RPC8 gene taxon:4932 20010118 SGD
+SGD S000005095 RPC31 GO:0006383 SGD_REF:S000058500 TAS P HMG1-like protein, RNA polymerase III (C) 31 kDa subunit YNL151C|ACP2|C31|RPC8 gene taxon:4932 20010119 SGD
+SGD S000005286 RPC34 GO:0005634 SGD_REF:S000069459|PMID:11914276 IDA C RNA polymerase III (C) 34 kDa subunit YNR003C|C34 gene taxon:4932 20020507 SGD
+SGD S000005286 RPC34 GO:0005666 SGD_REF:S000057661|PMID:8246845 TAS C RNA polymerase III (C) 34 kDa subunit YNR003C|C34 gene taxon:4932 20010118 SGD
+SGD S000005286 RPC34 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C RNA polymerase III (C) 34 kDa subunit YNR003C|C34 gene taxon:4932 20020507 SGD
+SGD S000005286 RPC34 GO:0003899 SGD_REF:S000057661|PMID:8246845 TAS F RNA polymerase III (C) 34 kDa subunit YNR003C|C34 gene taxon:4932 20010118 SGD
+SGD S000005286 RPC34 GO:0006383 SGD_REF:S000058500 TAS P RNA polymerase III (C) 34 kDa subunit YNR003C|C34 gene taxon:4932 20010119 SGD
+SGD S000001733 RPC37 GO:0005666 SGD_REF:S000057661|PMID:8246845 TAS C RNA polymerase III subunit YKR025W|C37 gene taxon:4932 20010118 SGD
+SGD S000001733 RPC37 GO:0003899 SGD_REF:S000057661|PMID:8246845 TAS F RNA polymerase III subunit YKR025W|C37 gene taxon:4932 20010118 SGD
+SGD S000001733 RPC37 GO:0006383 SGD_REF:S000058500 TAS P RNA polymerase III subunit YKR025W|C37 gene taxon:4932 20010119 SGD
+SGD S000006314 RPC40 GO:0005666 SGD_REF:S000057661|PMID:8246845 TAS C RNA polymerase III subunit YPR110C|AC40|RPC5 gene taxon:4932 20010118 SGD
+SGD S000006314 RPC40 GO:0005736 SGD_REF:S000057661|PMID:8246845 TAS C RNA polymerase III subunit YPR110C|AC40|RPC5 gene taxon:4932 20010118 SGD
+SGD S000006314 RPC40 GO:0003899 SGD_REF:S000057661|PMID:8246845 TAS F RNA polymerase III subunit YPR110C|AC40|RPC5 gene taxon:4932 20010118 SGD
+SGD S000006314 RPC40 GO:0006360 SGD_REF:S000058500 TAS P RNA polymerase III subunit YPR110C|AC40|RPC5 gene taxon:4932 20010119 SGD
+SGD S000006314 RPC40 GO:0006383 SGD_REF:S000058500 TAS P RNA polymerase III subunit YPR110C|AC40|RPC5 gene taxon:4932 20010119 SGD
+SGD S000002309 RPC53 GO:0005666 SGD_REF:S000057661|PMID:8246845 TAS C RNA polymerase III subunit YDL150W|C53|RPC4 gene taxon:4932 20010118 SGD
+SGD S000002309 RPC53 GO:0003899 SGD_REF:S000057661|PMID:8246845 TAS F RNA polymerase III subunit YDL150W|C53|RPC4 gene taxon:4932 20010118 SGD
+SGD S000002309 RPC53 GO:0006383 SGD_REF:S000058500 TAS P RNA polymerase III subunit YDL150W|C53|RPC4 gene taxon:4932 20010119 SGD
+SGD S000006394 RPC82 GO:0005666 SGD_REF:S000057661|PMID:8246845 TAS C 82 kDa subunit of RNA polymerase III (C) YPR190C|C82|RPC3 gene taxon:4932 20010118 SGD
+SGD S000006394 RPC82 GO:0003899 SGD_REF:S000057661|PMID:8246845 TAS F 82 kDa subunit of RNA polymerase III (C) YPR190C|C82|RPC3 gene taxon:4932 20010118 SGD
+SGD S000006394 RPC82 GO:0006383 SGD_REF:S000058500 TAS P 82 kDa subunit of RNA polymerase III (C) YPR190C|C82|RPC3 gene taxon:4932 20010119 SGD
+SGD S000005274 RPD3 GO:0000118 SGD_REF:S000047708|PMID:8962081 IDA C histone deacetylase YNL330C|MOF6|REC3|SDI2|SDS6 gene taxon:4932 20010118 SGD
+SGD S000005274 RPD3 GO:0004407 SGD_REF:S000047708|PMID:8962081 IMP F histone deacetylase YNL330C|MOF6|REC3|SDI2|SDS6 gene taxon:4932 20010118 SGD
+SGD S000005274 RPD3 GO:0004407 SGD_REF:S000055604|PMID:10384304 IMP F histone deacetylase YNL330C|MOF6|REC3|SDI2|SDS6 gene taxon:4932 20010118 SGD
+SGD S000005274 RPD3 GO:0004407 SGD_REF:S000059710|PMID:11095743 TAS F histone deacetylase YNL330C|MOF6|REC3|SDI2|SDS6 gene taxon:4932 20010405 SGD
+SGD S000005274 RPD3 GO:0004407 SGD_REF:S000055604|PMID:10384304 IDA F histone deacetylase YNL330C|MOF6|REC3|SDI2|SDS6 gene taxon:4932 20010118 SGD
+SGD S000005274 RPD3 GO:0000183 SGD_REF:S000047950|PMID:10388812 IMP P histone deacetylase YNL330C|MOF6|REC3|SDI2|SDS6 gene taxon:4932 20021008 SGD
+SGD S000005274 RPD3 GO:0001308 SGD_REF:S000043004|PMID:10512855 IMP P histone deacetylase YNL330C|MOF6|REC3|SDI2|SDS6 gene taxon:4932 20030820 SGD
+SGD S000005274 RPD3 GO:0006303 SGD_REF:S000074417|PMID:14711989 IMP P histone deacetylase YNL330C|MOF6|REC3|SDI2|SDS6 gene taxon:4932 20050224 SGD
+SGD S000005274 RPD3 GO:0006312 SGD_REF:S000044241|PMID:10079324 IMP P histone deacetylase YNL330C|MOF6|REC3|SDI2|SDS6 gene taxon:4932 20010118 SGD
+SGD S000005274 RPD3 GO:0006325 SGD_REF:S000056379|PMID:10384311 TAS P histone deacetylase YNL330C|MOF6|REC3|SDI2|SDS6 gene taxon:4932 20010118 SGD
+SGD S000005274 RPD3 GO:0006325 SGD_REF:S000055604|PMID:10384304 TAS P histone deacetylase YNL330C|MOF6|REC3|SDI2|SDS6 gene taxon:4932 20010118 SGD
+SGD S000005274 RPD3 GO:0006342 SGD_REF:S000047950|PMID:10388812 IDA P histone deacetylase YNL330C|MOF6|REC3|SDI2|SDS6 gene taxon:4932 20010118 SGD
+SGD S000005274 RPD3 GO:0006348 SGD_REF:S000047950|PMID:10388812 IMP P histone deacetylase YNL330C|MOF6|REC3|SDI2|SDS6 gene taxon:4932 20021008 SGD
+SGD S000005274 RPD3 GO:0006355 SGD_REF:S000056379|PMID:10384311 TAS P histone deacetylase YNL330C|MOF6|REC3|SDI2|SDS6 gene taxon:4932 20010118 SGD
+SGD S000005274 RPD3 GO:0006355 SGD_REF:S000055604|PMID:10384304 TAS P histone deacetylase YNL330C|MOF6|REC3|SDI2|SDS6 gene taxon:4932 20010118 SGD
+SGD S000005274 RPD3 GO:0006476 SGD_REF:S000047708|PMID:8962081 IDA P histone deacetylase YNL330C|MOF6|REC3|SDI2|SDS6 gene taxon:4932 20010118 SGD
+SGD S000005274 RPD3 GO:0006476 SGD_REF:S000055604|PMID:10384304 IDA P histone deacetylase YNL330C|MOF6|REC3|SDI2|SDS6 gene taxon:4932 20010118 SGD
+SGD S000005274 RPD3 GO:0030466 SGD_REF:S000047950|PMID:10388812 IMP P histone deacetylase YNL330C|MOF6|REC3|SDI2|SDS6 gene taxon:4932 20021008 SGD
+SGD S000003657 RPE1 GO:0005829 SGD_REF:S000071518|PMID:11298766 TAS C D-ribulose-5-Phosphate 3-epimerase YJL121C|EPI1|POS18 gene taxon:4932 20021101 SGD
+SGD S000003657 RPE1 GO:0004750 SGD_REF:S000047933|PMID:8929392 IDA F D-ribulose-5-Phosphate 3-epimerase YJL121C|EPI1|POS18 gene taxon:4932 20020607 SGD
+SGD S000003657 RPE1 GO:0004750 SGD_REF:S000047933|PMID:8929392 ISS F D-ribulose-5-Phosphate 3-epimerase YJL121C|EPI1|POS18 gene taxon:4932 20020607 SGD
+SGD S000003657 RPE1 GO:0004750 SGD_REF:S000047933|PMID:8929392 IMP F D-ribulose-5-Phosphate 3-epimerase YJL121C|EPI1|POS18 gene taxon:4932 20020607 SGD
+SGD S000003657 RPE1 GO:0006098 SGD_REF:S000047933|PMID:8929392 IMP P D-ribulose-5-Phosphate 3-epimerase YJL121C|EPI1|POS18 gene taxon:4932 20020607 SGD
+SGD S000001130 RPF1 GO:0005730 SGD_REF:S000069545|PMID:11864606 IDA C YHR088W gene taxon:4932 20030219 SGD
+SGD S000001130 RPF1 GO:0005730 SGD_REF:S000069532|PMID:11864607 IPI C YHR088W gene taxon:4932 20020826 SGD
+SGD S000001130 RPF1 GO:0042134 SGD_REF:S000069545|PMID:11864606 IPI F YHR088W gene taxon:4932 20030219 SGD
+SGD S000001130 RPF1 GO:0000027 SGD_REF:S000069532|PMID:11864607 IPI P YHR088W gene taxon:4932 20020826 SGD
+SGD S000001130 RPF1 GO:0030489 SGD_REF:S000069545|PMID:11864606 IMP P YHR088W gene taxon:4932 20030219 SGD
+SGD S000001789 RPF2 GO:0005730 SGD_REF:S000069545|PMID:11864606 IDA C YKR081C gene taxon:4932 20030219 SGD
+SGD S000001789 RPF2 GO:0005730 SGD_REF:S000069532|PMID:11864607 IPI C YKR081C gene taxon:4932 20020826 SGD
+SGD S000001789 RPF2 GO:0008097 SGD_REF:S000069545|PMID:11864606 IPI F YKR081C gene taxon:4932 20030219 SGD
+SGD S000001789 RPF2 GO:0008312 SGD_REF:S000069545|PMID:11864606 IPI F YKR081C gene taxon:4932 20030219 SGD
+SGD S000001789 RPF2 GO:0019843 SGD_REF:S000069545|PMID:11864606 IPI F YKR081C gene taxon:4932 20030219 SGD
+SGD S000001789 RPF2 GO:0000027 SGD_REF:S000069545|PMID:11864606 IMP P YKR081C gene taxon:4932 20030219 SGD
+SGD S000001789 RPF2 GO:0000027 SGD_REF:S000069532|PMID:11864607 IPI P YKR081C gene taxon:4932 20020826 SGD
+SGD S000001789 RPF2 GO:0030489 SGD_REF:S000069545|PMID:11864606 IMP P YKR081C gene taxon:4932 20030219 SGD
+SGD S000000283 RPG1 GO:0000131 SGD_REF:S000060151|PMID:11302750 IDA C translation initiation factor eIF3 subunit YBR079C|TIF32 gene taxon:4932 20030422 SGD
+SGD S000000283 RPG1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C translation initiation factor eIF3 subunit YBR079C|TIF32 gene taxon:4932 20020507 SGD
+SGD S000000283 RPG1 GO:0005840 SGD_REF:S000058753|PMID:9841679 TAS C translation initiation factor eIF3 subunit YBR079C|TIF32 gene taxon:4932 20010124 SGD
+SGD S000000283 RPG1 GO:0005852 SGD_REF:S000043795|PMID:9671501 IPI C translation initiation factor eIF3 subunit YBR079C|TIF32 gene taxon:4932 20020116 SGD
+SGD S000000283 RPG1 GO:0005852 SGD_REF:S000043795|PMID:9671501 IDA C translation initiation factor eIF3 subunit YBR079C|TIF32 gene taxon:4932 20020116 SGD
+SGD S000000283 RPG1 GO:0005852 SGD_REF:S000040522|PMID:9660829 IPI SGD:S000004926|SGD:S000005888 C translation initiation factor eIF3 subunit YBR079C|TIF32 gene taxon:4932 20060118 SGD
+SGD S000000283 RPG1 GO:0003743 SGD_REF:S000058753|PMID:9841679 TAS F translation initiation factor eIF3 subunit YBR079C|TIF32 gene taxon:4932 20010124 SGD
+SGD S000000283 RPG1 GO:0003743 SGD_REF:S000043795|PMID:9671501 IDA F translation initiation factor eIF3 subunit YBR079C|TIF32 gene taxon:4932 20020116 SGD
+SGD S000000283 RPG1 GO:0006413 SGD_REF:S000058753|PMID:9841679 TAS P translation initiation factor eIF3 subunit YBR079C|TIF32 gene taxon:4932 20010124 SGD
+SGD S000000283 RPG1 GO:0006413 SGD_REF:S000043795|PMID:9671501 IDA P translation initiation factor eIF3 subunit YBR079C|TIF32 gene taxon:4932 20020116 SGD
+SGD S000000971 RPH1 GO:0005634 SGD_REF:S000046845|PMID:10523651 IC GO:0016566 C binds to PHR1 URS, transcriptional repressor YER169W gene taxon:4932 20021104 SGD
+SGD S000000971 RPH1 GO:0016566 SGD_REF:S000046845|PMID:10523651 IDA F binds to PHR1 URS, transcriptional repressor YER169W gene taxon:4932 20021104 SGD
+SGD S000000971 RPH1 GO:0000122 SGD_REF:S000046845|PMID:10523651 IDA P binds to PHR1 URS, transcriptional repressor YER169W gene taxon:4932 20021104 SGD
+SGD S000000971 RPH1 GO:0006281 SGD_REF:S000046845|PMID:10523651 IMP P binds to PHR1 URS, transcriptional repressor YER169W gene taxon:4932 20021104 SGD
+SGD S000001381 RPI1 GO:0005634 SGD_REF:S000071721|PMID:12455971 IDA C ras inhibitor YIL119C gene taxon:4932 20021209 SGD
+SGD S000001381 RPI1 GO:0005083 SGD_REF:S000049786|PMID:1649384 IMP F ras inhibitor YIL119C gene taxon:4932 20010118 SGD
+SGD S000001381 RPI1 GO:0007265 SGD_REF:S000049786|PMID:1649384 IMP P ras inhibitor YIL119C gene taxon:4932 20010118 SGD
+SGD S000001381 RPI1 GO:0009228 SGD_REF:S000046055|PMID:9655908 TAS P ras inhibitor YIL119C gene taxon:4932 20010118 SGD
+SGD S000004065 RPL10 GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L10 YLR075W|GRC5|QSR1 gene taxon:4932 20010118 SGD
+SGD S000004065 RPL10 GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L10 YLR075W|GRC5|QSR1 gene taxon:4932 20010118 SGD
+SGD S000004065 RPL10 GO:0000027 SGD_REF:S000040623|PMID:9580698 IMP P ribosomal protein L10 YLR075W|GRC5|QSR1 gene taxon:4932 20010118 SGD
+SGD S000004065 RPL10 GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L10 YLR075W|GRC5|QSR1 gene taxon:4932 20010119 SGD
+SGD S000004065 RPL10 GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L10 YLR075W|GRC5|QSR1 gene taxon:4932 20010118 SGD
+SGD S000006306 RPL11A GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L11A (L16A) (rp39A) (YL22) YPR102C gene taxon:4932 20010118 SGD
+SGD S000006306 RPL11A GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L11A (L16A) (rp39A) (YL22) YPR102C gene taxon:4932 20010118 SGD
+SGD S000006306 RPL11A GO:0000027 SGD_REF:S000058462|PMID:2277060 IMP P ribosomal protein L11A (L16A) (rp39A) (YL22) YPR102C gene taxon:4932 20010118 SGD
+SGD S000006306 RPL11A GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L11A (L16A) (rp39A) (YL22) YPR102C gene taxon:4932 20010119 SGD
+SGD S000006306 RPL11A GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L11A (L16A) (rp39A) (YL22) YPR102C gene taxon:4932 20010118 SGD
+SGD S000003317 RPL11B GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L11B (L16B) (rp39B) (YL22) YGR085C gene taxon:4932 20010118 SGD
+SGD S000003317 RPL11B GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L11B (L16B) (rp39B) (YL22) YGR085C gene taxon:4932 20010118 SGD
+SGD S000003317 RPL11B GO:0000027 SGD_REF:S000058462|PMID:2277060 IMP P ribosomal protein L11B (L16B) (rp39B) (YL22) YGR085C gene taxon:4932 20010118 SGD
+SGD S000003317 RPL11B GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L11B (L16B) (rp39B) (YL22) YGR085C gene taxon:4932 20010119 SGD
+SGD S000003317 RPL11B GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L11B (L16B) (rp39B) (YL22) YGR085C gene taxon:4932 20010118 SGD
+SGD S000000780 RPL12A GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L12A (L15A) (YL23) YEL054C gene taxon:4932 20010118 SGD
+SGD S000000780 RPL12A GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L12A (L15A) (YL23) YEL054C gene taxon:4932 20010118 SGD
+SGD S000000780 RPL12A GO:0000027 SGD_REF:S000040519|PMID:9822666 IMP P ribosomal protein L12A (L15A) (YL23) YEL054C gene taxon:4932 20010118 SGD
+SGD S000000780 RPL12A GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L12A (L15A) (YL23) YEL054C gene taxon:4932 20010119 SGD
+SGD S000000780 RPL12A GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L12A (L15A) (YL23) YEL054C gene taxon:4932 20010118 SGD
+SGD S000002826 RPL12B GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L12B (L15B) (YL23) YDR418W gene taxon:4932 20010118 SGD
+SGD S000002826 RPL12B GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L12B (L15B) (YL23) YDR418W gene taxon:4932 20010118 SGD
+SGD S000002826 RPL12B GO:0000027 SGD_REF:S000040519|PMID:9822666 IMP P ribosomal protein L12B (L15B) (YL23) YDR418W gene taxon:4932 20010118 SGD
+SGD S000002826 RPL12B GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P ribosomal protein L12B (L15B) (YL23) YDR418W gene taxon:4932 20060227 SGD
+SGD S000002826 RPL12B GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L12B (L15B) (YL23) YDR418W gene taxon:4932 20010119 SGD
+SGD S000002826 RPL12B GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L12B (L15B) (YL23) YDR418W gene taxon:4932 20010118 SGD
+SGD S000002240 RPL13A GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L13A YDL082W gene taxon:4932 20010118 SGD
+SGD S000002240 RPL13A GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L13A YDL082W gene taxon:4932 20010118 SGD
+SGD S000002240 RPL13A GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L13A YDL082W gene taxon:4932 20010119 SGD
+SGD S000002240 RPL13A GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L13A YDL082W gene taxon:4932 20010118 SGD
+SGD S000004750 RPL13B GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L13B YMR142C gene taxon:4932 20010118 SGD
+SGD S000004750 RPL13B GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L13B YMR142C gene taxon:4932 20010118 SGD
+SGD S000004750 RPL13B GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P ribosomal protein L13B YMR142C gene taxon:4932 20060227 SGD
+SGD S000004750 RPL13B GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L13B YMR142C gene taxon:4932 20010119 SGD
+SGD S000004750 RPL13B GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L13B YMR142C gene taxon:4932 20010118 SGD
+SGD S000001489 RPL14A GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L14A YKL006W gene taxon:4932 20010118 SGD
+SGD S000001489 RPL14A GO:0003723 SGD_REF:S000057255|PMID:6337137 IDA F ribosomal protein L14A YKL006W gene taxon:4932 20010118 SGD
+SGD S000001489 RPL14A GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L14A YKL006W gene taxon:4932 20010118 SGD
+SGD S000001489 RPL14A GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L14A YKL006W gene taxon:4932 20010119 SGD
+SGD S000001489 RPL14A GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L14A YKL006W gene taxon:4932 20010118 SGD
+SGD S000000993 RPL14B GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L14B YHL001W gene taxon:4932 20010118 SGD
+SGD S000000993 RPL14B GO:0003723 SGD_REF:S000057255|PMID:6337137 IDA F ribosomal protein L14B YHL001W gene taxon:4932 20010118 SGD
+SGD S000000993 RPL14B GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L14B YHL001W gene taxon:4932 20010118 SGD
+SGD S000000993 RPL14B GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L14B YHL001W gene taxon:4932 20010119 SGD
+SGD S000000993 RPL14B GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L14B YHL001W gene taxon:4932 20010118 SGD
+SGD S000004019 RPL15A GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L15A (YL10) (rp15R) (L13A) YLR029C|RPL10A gene taxon:4932 20010118 SGD
+SGD S000004019 RPL15A GO:0003723 SGD_REF:S000057255|PMID:6337137 IDA F ribosomal protein L15A (YL10) (rp15R) (L13A) YLR029C|RPL10A gene taxon:4932 20010118 SGD
+SGD S000004019 RPL15A GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L15A (YL10) (rp15R) (L13A) YLR029C|RPL10A gene taxon:4932 20010118 SGD
+SGD S000004019 RPL15A GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L15A (YL10) (rp15R) (L13A) YLR029C|RPL10A gene taxon:4932 20010119 SGD
+SGD S000004019 RPL15A GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L15A (YL10) (rp15R) (L13A) YLR029C|RPL10A gene taxon:4932 20010118 SGD
+SGD S000004728 RPL15B GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L15B (YL10) (L13B) (rp15R) YMR121C gene taxon:4932 20010118 SGD
+SGD S000004728 RPL15B GO:0003723 SGD_REF:S000057255|PMID:6337137 IDA F ribosomal protein L15B (YL10) (L13B) (rp15R) YMR121C gene taxon:4932 20010118 SGD
+SGD S000004728 RPL15B GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L15B (YL10) (L13B) (rp15R) YMR121C gene taxon:4932 20010118 SGD
+SGD S000004728 RPL15B GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L15B (YL10) (L13B) (rp15R) YMR121C gene taxon:4932 20010119 SGD
+SGD S000004728 RPL15B GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L15B (YL10) (L13B) (rp15R) YMR121C gene taxon:4932 20010118 SGD
+SGD S000001395 RPL16A GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L16A (L21A) (rp22) (YL15) YIL133C|RPL13 gene taxon:4932 20010118 SGD
+SGD S000001395 RPL16A GO:0003723 SGD_REF:S000057255|PMID:6337137 IDA F ribosomal protein L16A (L21A) (rp22) (YL15) YIL133C|RPL13 gene taxon:4932 20010118 SGD
+SGD S000001395 RPL16A GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L16A (L21A) (rp22) (YL15) YIL133C|RPL13 gene taxon:4932 20010118 SGD
+SGD S000001395 RPL16A GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L16A (L21A) (rp22) (YL15) YIL133C|RPL13 gene taxon:4932 20010119 SGD
+SGD S000001395 RPL16A GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L16A (L21A) (rp22) (YL15) YIL133C|RPL13 gene taxon:4932 20010118 SGD
+SGD S000005013 RPL16B GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L16B (L21B) (rp23) (YL15) YNL069C|RP23 gene taxon:4932 20010118 SGD
+SGD S000005013 RPL16B GO:0003723 SGD_REF:S000057255|PMID:6337137 IDA F ribosomal protein L16B (L21B) (rp23) (YL15) YNL069C|RP23 gene taxon:4932 20010118 SGD
+SGD S000005013 RPL16B GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L16B (L21B) (rp23) (YL15) YNL069C|RP23 gene taxon:4932 20010118 SGD
+SGD S000005013 RPL16B GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L16B (L21B) (rp23) (YL15) YNL069C|RP23 gene taxon:4932 20010119 SGD
+SGD S000005013 RPL16B GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L16B (L21B) (rp23) (YL15) YNL069C|RP23 gene taxon:4932 20010118 SGD
+SGD S000001663 RPL17A GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C ribosomal protein L17A (L20A) (YL17) YKL180W|RPL17 gene taxon:4932 20020507 SGD
+SGD S000001663 RPL17A GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L17A (L20A) (YL17) YKL180W|RPL17 gene taxon:4932 20010118 SGD
+SGD S000001663 RPL17A GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L17A (L20A) (YL17) YKL180W|RPL17 gene taxon:4932 20010118 SGD
+SGD S000001663 RPL17A GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L17A (L20A) (YL17) YKL180W|RPL17 gene taxon:4932 20010119 SGD
+SGD S000001663 RPL17A GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L17A (L20A) (YL17) YKL180W|RPL17 gene taxon:4932 20010118 SGD
+SGD S000003713 RPL17B GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L17B (L20B) (YL17) YJL177W gene taxon:4932 20010118 SGD
+SGD S000003713 RPL17B GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L17B (L20B) (YL17) YJL177W gene taxon:4932 20010118 SGD
+SGD S000003713 RPL17B GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L17B (L20B) (YL17) YJL177W gene taxon:4932 20010119 SGD
+SGD S000003713 RPL17B GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L17B (L20B) (YL17) YJL177W gene taxon:4932 20010118 SGD
+SGD S000005480 RPL18A GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L18A (rp28A) YOL120C|RP28A gene taxon:4932 20010118 SGD
+SGD S000005480 RPL18A GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L18A (rp28A) YOL120C|RP28A gene taxon:4932 20010118 SGD
+SGD S000005480 RPL18A GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L18A (rp28A) YOL120C|RP28A gene taxon:4932 20010119 SGD
+SGD S000005480 RPL18A GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L18A (rp28A) YOL120C|RP28A gene taxon:4932 20010118 SGD
+SGD S000005245 RPL18B GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L18B (rp28B) YNL301C|RP28B gene taxon:4932 20010118 SGD
+SGD S000005245 RPL18B GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L18B (rp28B) YNL301C|RP28B gene taxon:4932 20010118 SGD
+SGD S000005245 RPL18B GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L18B (rp28B) YNL301C|RP28B gene taxon:4932 20010119 SGD
+SGD S000005245 RPL18B GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L18B (rp28B) YNL301C|RP28B gene taxon:4932 20010118 SGD
+SGD S000002156 RPL19A GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L19A (L23A) (rpl5L) (YL14) YBR084C-A gene taxon:4932 20010118 SGD
+SGD S000002156 RPL19A GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L19A (L23A) (rpl5L) (YL14) YBR084C-A gene taxon:4932 20010118 SGD
+SGD S000002156 RPL19A GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L19A (L23A) (rpl5L) (YL14) YBR084C-A gene taxon:4932 20010119 SGD
+SGD S000002156 RPL19A GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L19A (L23A) (rpl5L) (YL14) YBR084C-A gene taxon:4932 20010118 SGD
+SGD S000000123 RPL19B GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L19B (YL14) (L23B) (rpl5L) YBL027W gene taxon:4932 20010118 SGD
+SGD S000000123 RPL19B GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L19B (YL14) (L23B) (rpl5L) YBL027W gene taxon:4932 20010118 SGD
+SGD S000000123 RPL19B GO:0006412 SGD_REF:S000058497 TAS P ribosomal protein L19B (YL14) (L23B) (rpl5L) YBL027W gene taxon:4932 20010119 SGD
+SGD S000000123 RPL19B GO:0006412 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L19B (YL14) (L23B) (rpl5L) YBL027W gene taxon:4932 20010118 SGD
+SGD S000006141 RPL1A GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L1A, forms part of the 60S ribosomal subunit YPL220W|SSM1 gene taxon:4932 20010118 SGD
+SGD S000006141 RPL1A GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L1A, forms part of the 60S ribosomal subunit YPL220W|SSM1 gene taxon:4932 20010118 SGD
+SGD S000006141 RPL1A GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L1A, forms part of the 60S ribosomal subunit YPL220W|SSM1 gene taxon:4932 20010119 SGD
+SGD S000006141 RPL1A GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L1A, forms part of the 60S ribosomal subunit YPL220W|SSM1 gene taxon:4932 20010118 SGD
+SGD S000003103 RPL1B GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L1B YGL135W|SSM2 gene taxon:4932 20010118 SGD
+SGD S000003103 RPL1B GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L1B YGL135W|SSM2 gene taxon:4932 20010118 SGD
+SGD S000003103 RPL1B GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P ribosomal protein L1B YGL135W|SSM2 gene taxon:4932 20060227 SGD
+SGD S000003103 RPL1B GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L1B YGL135W|SSM2 gene taxon:4932 20010119 SGD
+SGD S000003103 RPL1B GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L1B YGL135W|SSM2 gene taxon:4932 20010118 SGD
+SGD S000004855 RPL20A GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L20A (L18A) YMR242C|RPL18A2 gene taxon:4932 20010118 SGD
+SGD S000004855 RPL20A GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L20A (L18A) YMR242C|RPL18A2 gene taxon:4932 20010118 SGD
+SGD S000004855 RPL20A GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L20A (L18A) YMR242C|RPL18A2 gene taxon:4932 20010119 SGD
+SGD S000004855 RPL20A GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L20A (L18A) YMR242C|RPL18A2 gene taxon:4932 20010118 SGD
+SGD S000005839 RPL20B GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L20B (L18B) YOR312C|RPL18A1 gene taxon:4932 20010118 SGD
+SGD S000005839 RPL20B GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L20B (L18B) YOR312C|RPL18A1 gene taxon:4932 20010118 SGD
+SGD S000005839 RPL20B GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L20B (L18B) YOR312C|RPL18A1 gene taxon:4932 20010119 SGD
+SGD S000005839 RPL20B GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L20B (L18B) YOR312C|RPL18A1 gene taxon:4932 20010118 SGD
+SGD S000000395 RPL21A GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L21A YBR191W|URP1 gene taxon:4932 20010118 SGD
+SGD S000000395 RPL21A GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L21A YBR191W|URP1 gene taxon:4932 20010118 SGD
+SGD S000000395 RPL21A GO:0030447 SGD_REF:S000080384|PMID:15645503 IMP P ribosomal protein L21A YBR191W|URP1 gene taxon:4932 20050621 SGD
+SGD S000000395 RPL21A GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L21A YBR191W|URP1 gene taxon:4932 20010119 SGD
+SGD S000000395 RPL21A GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L21A YBR191W|URP1 gene taxon:4932 20010118 SGD
+SGD S000006000 RPL21B GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L21B YPL079W gene taxon:4932 20010118 SGD
+SGD S000006000 RPL21B GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L21B YPL079W gene taxon:4932 20010118 SGD
+SGD S000006000 RPL21B GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L21B YPL079W gene taxon:4932 20010119 SGD
+SGD S000006000 RPL21B GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L21B YPL079W gene taxon:4932 20010118 SGD
+SGD S000004051 RPL22A GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L22A (L1c) (rp4) (YL31) YLR061W gene taxon:4932 20010118 SGD
+SGD S000004051 RPL22A GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L22A (L1c) (rp4) (YL31) YLR061W gene taxon:4932 20010118 SGD
+SGD S000004051 RPL22A GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L22A (L1c) (rp4) (YL31) YLR061W gene taxon:4932 20010119 SGD
+SGD S000004051 RPL22A GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L22A (L1c) (rp4) (YL31) YLR061W gene taxon:4932 20010118 SGD
+SGD S000006436 RPL22B GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L22B (L1c) (rp4) (YL31) YFL034C-A|YFL035C-B gene taxon:4932 20010118 SGD
+SGD S000006436 RPL22B GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L22B (L1c) (rp4) (YL31) YFL034C-A|YFL035C-B gene taxon:4932 20010118 SGD
+SGD S000006436 RPL22B GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L22B (L1c) (rp4) (YL31) YFL034C-A|YFL035C-B gene taxon:4932 20010119 SGD
+SGD S000006436 RPL22B GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L22B (L1c) (rp4) (YL31) YFL034C-A|YFL035C-B gene taxon:4932 20010118 SGD
+SGD S000000183 RPL23A GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L23A (L17aA) (YL32) YBL087C gene taxon:4932 20010118 SGD
+SGD S000000183 RPL23A GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L23A (L17aA) (YL32) YBL087C gene taxon:4932 20010118 SGD
+SGD S000000183 RPL23A GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L23A (L17aA) (YL32) YBL087C gene taxon:4932 20010119 SGD
+SGD S000000183 RPL23A GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L23A (L17aA) (YL32) YBL087C gene taxon:4932 20010118 SGD
+SGD S000000919 RPL23B GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L23B (L17aB) (YL32) YER117W gene taxon:4932 20010118 SGD
+SGD S000000919 RPL23B GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L23B (L17aB) (YL32) YER117W gene taxon:4932 20010118 SGD
+SGD S000000919 RPL23B GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L23B (L17aB) (YL32) YER117W gene taxon:4932 20010119 SGD
+SGD S000000919 RPL23B GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L23B (L17aB) (YL32) YER117W gene taxon:4932 20010118 SGD
+SGD S000002999 RPL24A GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L24A (rp29) (YL21) (L30A) YGL031C|RPL30A gene taxon:4932 20010118 SGD
+SGD S000002999 RPL24A GO:0003723 SGD_REF:S000057255|PMID:6337137 IDA F ribosomal protein L24A (rp29) (YL21) (L30A) YGL031C|RPL30A gene taxon:4932 20010118 SGD
+SGD S000002999 RPL24A GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L24A (rp29) (YL21) (L30A) YGL031C|RPL30A gene taxon:4932 20010118 SGD
+SGD S000002999 RPL24A GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L24A (rp29) (YL21) (L30A) YGL031C|RPL30A gene taxon:4932 20010119 SGD
+SGD S000002999 RPL24A GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L24A (rp29) (YL21) (L30A) YGL031C|RPL30A gene taxon:4932 20010118 SGD
+SGD S000003380 RPL24B GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L24B (rp29) (YL21) (L30B) YGR148C|RPL30B gene taxon:4932 20010118 SGD
+SGD S000003380 RPL24B GO:0003723 SGD_REF:S000057255|PMID:6337137 IDA F ribosomal protein L24B (rp29) (YL21) (L30B) YGR148C|RPL30B gene taxon:4932 20010118 SGD
+SGD S000003380 RPL24B GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L24B (rp29) (YL21) (L30B) YGR148C|RPL30B gene taxon:4932 20010118 SGD
+SGD S000003380 RPL24B GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L24B (rp29) (YL21) (L30B) YGR148C|RPL30B gene taxon:4932 20010119 SGD
+SGD S000003380 RPL24B GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L24B (rp29) (YL21) (L30B) YGR148C|RPL30B gene taxon:4932 20010118 SGD
+SGD S000005487 RPL25 GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L25 (rpl6L) (YL25) YOL127W gene taxon:4932 20010118 SGD
+SGD S000005487 RPL25 GO:0003723 SGD_REF:S000057573|PMID:8028007 IDA F ribosomal protein L25 (rpl6L) (YL25) YOL127W gene taxon:4932 20010118 SGD
+SGD S000005487 RPL25 GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L25 (rpl6L) (YL25) YOL127W gene taxon:4932 20010118 SGD
+SGD S000005487 RPL25 GO:0000027 SGD_REF:S000057573|PMID:8028007 IMP P ribosomal protein L25 (rpl6L) (YL25) YOL127W gene taxon:4932 20010118 SGD
+SGD S000005487 RPL25 GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L25 (rpl6L) (YL25) YOL127W gene taxon:4932 20010119 SGD
+SGD S000005487 RPL25 GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L25 (rpl6L) (YL25) YOL127W gene taxon:4932 20010118 SGD
+SGD S000004336 RPL26A GO:0005842 SGD_REF:S000064949|PMID:9672752 IDA C ribosomal protein L26A (L33A) (YL33) YLR344W gene taxon:4932 20040922 SGD
+SGD S000004336 RPL26A GO:0003723 SGD_REF:S000057255|PMID:6337137 IDA F ribosomal protein L26A (L33A) (YL33) YLR344W gene taxon:4932 20010118 SGD
+SGD S000004336 RPL26A GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L26A (L33A) (YL33) YLR344W gene taxon:4932 20010118 SGD
+SGD S000004336 RPL26A GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L26A (L33A) (YL33) YLR344W gene taxon:4932 20010119 SGD
+SGD S000004336 RPL26A GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L26A (L33A) (YL33) YLR344W gene taxon:4932 20010118 SGD
+SGD S000003266 RPL26B GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L26B (L33B) (YL33) YGR034W gene taxon:4932 20010118 SGD
+SGD S000003266 RPL26B GO:0003723 SGD_REF:S000057255|PMID:6337137 IDA F ribosomal protein L26B (L33B) (YL33) YGR034W gene taxon:4932 20010118 SGD
+SGD S000003266 RPL26B GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L26B (L33B) (YL33) YGR034W gene taxon:4932 20010118 SGD
+SGD S000003266 RPL26B GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L26B (L33B) (YL33) YGR034W gene taxon:4932 20010119 SGD
+SGD S000003266 RPL26B GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L26B (L33B) (YL33) YGR034W gene taxon:4932 20010118 SGD
+SGD S000001052 RPL27A GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L27A YHR010W|RPL27 gene taxon:4932 20010118 SGD
+SGD S000001052 RPL27A GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L27A YHR010W|RPL27 gene taxon:4932 20010118 SGD
+SGD S000001052 RPL27A GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L27A YHR010W|RPL27 gene taxon:4932 20010119 SGD
+SGD S000001052 RPL27A GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L27A YHR010W|RPL27 gene taxon:4932 20010118 SGD
+SGD S000002879 RPL27B GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L27B YDR471W gene taxon:4932 20010118 SGD
+SGD S000002879 RPL27B GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L27B YDR471W gene taxon:4932 20010118 SGD
+SGD S000002879 RPL27B GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L27B YDR471W gene taxon:4932 20010119 SGD
+SGD S000002879 RPL27B GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L27B YDR471W gene taxon:4932 20010118 SGD
+SGD S000003071 RPL28 GO:0005634 SGD_REF:S000064950|PMID:2104804 IMP C ribosomal protein L28 (L29) (rp44) (YL24) YGL103W|CYH2 gene taxon:4932 20030112 SGD
+SGD S000003071 RPL28 GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L28 (L29) (rp44) (YL24) YGL103W|CYH2 gene taxon:4932 20010118 SGD
+SGD S000003071 RPL28 GO:0003723 SGD_REF:S000057255|PMID:6337137 IDA F ribosomal protein L28 (L29) (rp44) (YL24) YGL103W|CYH2 gene taxon:4932 20010118 SGD
+SGD S000003071 RPL28 GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L28 (L29) (rp44) (YL24) YGL103W|CYH2 gene taxon:4932 20010118 SGD
+SGD S000003071 RPL28 GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L28 (L29) (rp44) (YL24) YGL103W|CYH2 gene taxon:4932 20010119 SGD
+SGD S000003071 RPL28 GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L28 (L29) (rp44) (YL24) YGL103W|CYH2 gene taxon:4932 20010118 SGD
+SGD S000006437 RPL29 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C ribosomal protein L29 (YL43) YFR032C-A gene taxon:4932 20031028 SGD
+SGD S000006437 RPL29 GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L29 (YL43) YFR032C-A gene taxon:4932 20010118 SGD
+SGD S000006437 RPL29 GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L29 (YL43) YFR032C-A gene taxon:4932 20010118 SGD
+SGD S000006437 RPL29 GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L29 (YL43) YFR032C-A gene taxon:4932 20010119 SGD
+SGD S000006437 RPL29 GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L29 (YL43) YFR032C-A gene taxon:4932 20010118 SGD
+SGD S000002104 RPL2A GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L2A (L5A) (rp8) (YL6) YFR031C-A|RPL5B gene taxon:4932 20010118 SGD
+SGD S000002104 RPL2A GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L2A (L5A) (rp8) (YL6) YFR031C-A|RPL5B gene taxon:4932 20010118 SGD
+SGD S000002104 RPL2A GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L2A (L5A) (rp8) (YL6) YFR031C-A|RPL5B gene taxon:4932 20010119 SGD
+SGD S000002104 RPL2A GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L2A (L5A) (rp8) (YL6) YFR031C-A|RPL5B gene taxon:4932 20010118 SGD
+SGD S000001280 RPL2B GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L2B (L5B) (rp8) (YL6) YIL018W|LOT2|RPL5A gene taxon:4932 20010118 SGD
+SGD S000001280 RPL2B GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L2B (L5B) (rp8) (YL6) YIL018W|LOT2|RPL5A gene taxon:4932 20010118 SGD
+SGD S000001280 RPL2B GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L2B (L5B) (rp8) (YL6) YIL018W|LOT2|RPL5A gene taxon:4932 20010119 SGD
+SGD S000001280 RPL2B GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L2B (L5B) (rp8) (YL6) YIL018W|LOT2|RPL5A gene taxon:4932 20010118 SGD
+SGD S000005589 RPL3 GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L3 (rp1) (YL1) YOR063W|MAK8|TCM1|YOR29-14 gene taxon:4932 20010118 SGD
+SGD S000005589 RPL3 GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L3 (rp1) (YL1) YOR063W|MAK8|TCM1|YOR29-14 gene taxon:4932 20010118 SGD
+SGD S000005589 RPL3 GO:0000027 SGD_REF:S000056145|PMID:3537704 IMP P ribosomal protein L3 (rp1) (YL1) YOR063W|MAK8|TCM1|YOR29-14 gene taxon:4932 20010118 SGD
+SGD S000005589 RPL3 GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L3 (rp1) (YL1) YOR063W|MAK8|TCM1|YOR29-14 gene taxon:4932 20010119 SGD
+SGD S000005589 RPL3 GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L3 (rp1) (YL1) YOR063W|MAK8|TCM1|YOR29-14 gene taxon:4932 20010118 SGD
+SGD S000002998 RPL30 GO:0005737 SGD_REF:S000059154|PMID:11142377 IDA C ribosomal protein L30 (L32) (rp73) (YL38) large subunit YGL030W gene taxon:4932 20020823 SGD
+SGD S000002998 RPL30 GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L30 (L32) (rp73) (YL38) large subunit YGL030W gene taxon:4932 20010118 SGD
+SGD S000002998 RPL30 GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L30 (L32) (rp73) (YL38) large subunit YGL030W gene taxon:4932 20010118 SGD
+SGD S000002998 RPL30 GO:0003735 SGD_REF:S000058089|PMID:9121443 IDA F ribosomal protein L30 (L32) (rp73) (YL38) large subunit YGL030W gene taxon:4932 20010118 SGD
+SGD S000002998 RPL30 GO:0006364 SGD_REF:S000058089|PMID:9121443 IMP P ribosomal protein L30 (L32) (rp73) (YL38) large subunit YGL030W gene taxon:4932 20010118 SGD
+SGD S000002998 RPL30 GO:0016478 SGD_REF:S000058089|PMID:9121443 TAS P ribosomal protein L30 (L32) (rp73) (YL38) large subunit YGL030W gene taxon:4932 20030822 SGD
+SGD S000002998 RPL30 GO:0016478 SGD_REF:S000057855|PMID:8643676 TAS P ribosomal protein L30 (L32) (rp73) (YL38) large subunit YGL030W gene taxon:4932 20030822 SGD
+SGD S000002998 RPL30 GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L30 (L32) (rp73) (YL38) large subunit YGL030W gene taxon:4932 20010118 SGD
+SGD S000002998 RPL30 GO:0048025 SGD_REF:S000058089|PMID:9121443 IMP P ribosomal protein L30 (L32) (rp73) (YL38) large subunit YGL030W gene taxon:4932 20030822 SGD
+SGD S000002233 RPL31A GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L31A (L34A) (YL28) YDL075W|RPL34 gene taxon:4932 20010118 SGD
+SGD S000002233 RPL31A GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L31A (L34A) (YL28) YDL075W|RPL34 gene taxon:4932 20010118 SGD
+SGD S000002233 RPL31A GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L31A (L34A) (YL28) YDL075W|RPL34 gene taxon:4932 20010119 SGD
+SGD S000002233 RPL31A GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L31A (L34A) (YL28) YDL075W|RPL34 gene taxon:4932 20010118 SGD
+SGD S000004398 RPL31B GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L31B (L34B) (YL28) YLR406C gene taxon:4932 20010118 SGD
+SGD S000004398 RPL31B GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L31B (L34B) (YL28) YLR406C gene taxon:4932 20010118 SGD
+SGD S000004398 RPL31B GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L31B (L34B) (YL28) YLR406C gene taxon:4932 20010119 SGD
+SGD S000004398 RPL31B GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L31B (L34B) (YL28) YLR406C gene taxon:4932 20010118 SGD
+SGD S000000188 RPL32 GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L32 YBL092W gene taxon:4932 20010118 SGD
+SGD S000000188 RPL32 GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L32 YBL092W gene taxon:4932 20010118 SGD
+SGD S000000188 RPL32 GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L32 YBL092W gene taxon:4932 20010119 SGD
+SGD S000000188 RPL32 GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L32 YBL092W gene taxon:4932 20010118 SGD
+SGD S000006064 RPL33A GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L33A (L37A) (YL37) (rp47) YPL143W|RPL37A gene taxon:4932 20010118 SGD
+SGD S000006064 RPL33A GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L33A (L37A) (YL37) (rp47) YPL143W|RPL37A gene taxon:4932 20010118 SGD
+SGD S000006064 RPL33A GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L33A (L37A) (YL37) (rp47) YPL143W|RPL37A gene taxon:4932 20010119 SGD
+SGD S000006064 RPL33A GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L33A (L37A) (YL37) (rp47) YPL143W|RPL37A gene taxon:4932 20010118 SGD
+SGD S000005760 RPL33B GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L33B (L37B) (rp47) (YL37) YOR234C|RPL37B gene taxon:4932 20010118 SGD
+SGD S000005760 RPL33B GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L33B (L37B) (rp47) (YL37) YOR234C|RPL37B gene taxon:4932 20010118 SGD
+SGD S000005760 RPL33B GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L33B (L37B) (rp47) (YL37) YOR234C|RPL37B gene taxon:4932 20010119 SGD
+SGD S000005760 RPL33B GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L33B (L37B) (rp47) (YL37) YOR234C|RPL37B gene taxon:4932 20010118 SGD
+SGD S000002135 RPL34A GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L34A YER056C-A gene taxon:4932 20010118 SGD
+SGD S000002135 RPL34A GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L34A YER056C-A gene taxon:4932 20010118 SGD
+SGD S000002135 RPL34A GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L34A YER056C-A gene taxon:4932 20010119 SGD
+SGD S000002135 RPL34A GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L34A YER056C-A gene taxon:4932 20010118 SGD
+SGD S000001314 RPL34B GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L34B YIL052C gene taxon:4932 20010118 SGD
+SGD S000001314 RPL34B GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L34B YIL052C gene taxon:4932 20010118 SGD
+SGD S000001314 RPL34B GO:0030447 SGD_REF:S000080384|PMID:15645503 IMP P ribosomal protein L34B YIL052C gene taxon:4932 20050621 SGD
+SGD S000001314 RPL34B GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L34B YIL052C gene taxon:4932 20010119 SGD
+SGD S000001314 RPL34B GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L34B YIL052C gene taxon:4932 20010118 SGD
+SGD S000002350 RPL35A GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L35A YDL191W|SOS1 gene taxon:4932 20010118 SGD
+SGD S000002350 RPL35A GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L35A YDL191W|SOS1 gene taxon:4932 20010118 SGD
+SGD S000002350 RPL35A GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L35A YDL191W|SOS1 gene taxon:4932 20010119 SGD
+SGD S000002350 RPL35A GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L35A YDL191W|SOS1 gene taxon:4932 20010118 SGD
+SGD S000002295 RPL35B GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L35B YDL136W|SOS2 gene taxon:4932 20010118 SGD
+SGD S000002295 RPL35B GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L35B YDL136W|SOS2 gene taxon:4932 20010118 SGD
+SGD S000002295 RPL35B GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L35B YDL136W|SOS2 gene taxon:4932 20010119 SGD
+SGD S000002295 RPL35B GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L35B YDL136W|SOS2 gene taxon:4932 20010118 SGD
+SGD S000004807 RPL36A GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L36A (L39) (YL39) YMR194W|RPL39B gene taxon:4932 20010118 SGD
+SGD S000004807 RPL36A GO:0003723 SGD_REF:S000057255|PMID:6337137 IDA F ribosomal protein L36A (L39) (YL39) YMR194W|RPL39B gene taxon:4932 20010118 SGD
+SGD S000004807 RPL36A GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L36A (L39) (YL39) YMR194W|RPL39B gene taxon:4932 20010118 SGD
+SGD S000004807 RPL36A GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L36A (L39) (YL39) YMR194W|RPL39B gene taxon:4932 20010119 SGD
+SGD S000004807 RPL36A GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L36A (L39) (YL39) YMR194W|RPL39B gene taxon:4932 20010118 SGD
+SGD S000006438 RPL36B GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L36B (L39) (YL39) YPL249C-A gene taxon:4932 20010118 SGD
+SGD S000006438 RPL36B GO:0003723 SGD_REF:S000057255|PMID:6337137 IDA F ribosomal protein L36B (L39) (YL39) YPL249C-A gene taxon:4932 20010118 SGD
+SGD S000006438 RPL36B GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L36B (L39) (YL39) YPL249C-A gene taxon:4932 20010118 SGD
+SGD S000006438 RPL36B GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L36B (L39) (YL39) YPL249C-A gene taxon:4932 20010119 SGD
+SGD S000006438 RPL36B GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L36B (L39) (YL39) YPL249C-A gene taxon:4932 20010118 SGD
+SGD S000004175 RPL37A GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L37A (L43) (YL35) YLR185W gene taxon:4932 20010118 SGD
+SGD S000004175 RPL37A GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L37A (L43) (YL35) YLR185W gene taxon:4932 20010118 SGD
+SGD S000004175 RPL37A GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L37A (L43) (YL35) YLR185W gene taxon:4932 20010119 SGD
+SGD S000004175 RPL37A GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L37A (L43) (YL35) YLR185W gene taxon:4932 20010118 SGD
+SGD S000002908 RPL37B GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L37B (L43) (YL35) YDR500C gene taxon:4932 20010118 SGD
+SGD S000002908 RPL37B GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L37B (L43) (YL35) YDR500C gene taxon:4932 20010118 SGD
+SGD S000002908 RPL37B GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L37B (L43) (YL35) YDR500C gene taxon:4932 20010119 SGD
+SGD S000002908 RPL37B GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L37B (L43) (YL35) YDR500C gene taxon:4932 20010118 SGD
+SGD S000004317 RPL38 GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L38 YLR325C gene taxon:4932 20010118 SGD
+SGD S000004317 RPL38 GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L38 YLR325C gene taxon:4932 20010118 SGD
+SGD S000004317 RPL38 GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L38 YLR325C gene taxon:4932 20010119 SGD
+SGD S000004317 RPL38 GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L38 YLR325C gene taxon:4932 20010118 SGD
+SGD S000003725 RPL39 GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L39 (L46) (YL40) YJL189W|PUB2|RPL46|SPB2 gene taxon:4932 20010118 SGD
+SGD S000003725 RPL39 GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L39 (L46) (YL40) YJL189W|PUB2|RPL46|SPB2 gene taxon:4932 20010118 SGD
+SGD S000003725 RPL39 GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L39 (L46) (YL40) YJL189W|PUB2|RPL46|SPB2 gene taxon:4932 20010119 SGD
+SGD S000003725 RPL39 GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L39 (L46) (YL40) YJL189W|PUB2|RPL46|SPB2 gene taxon:4932 20010118 SGD
+SGD S000001410 RPL40A GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C also encodes a ubiquitin protein, ribosomal protein L40A YIL148W|CEP52A|UB11|UBI1 gene taxon:4932 20010118 SGD
+SGD S000001410 RPL40A GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F also encodes a ubiquitin protein, ribosomal protein L40A YIL148W|CEP52A|UB11|UBI1 gene taxon:4932 20010118 SGD
+SGD S000001410 RPL40A GO:0031386 SGD_REF:S000056997|PMID:3038523 ISS F also encodes a ubiquitin protein, ribosomal protein L40A YIL148W|CEP52A|UB11|UBI1 gene taxon:4932 20050525 SGD
+SGD S000001410 RPL40A GO:0016567 SGD_REF:S000049784|PMID:8035826 IMP P also encodes a ubiquitin protein, ribosomal protein L40A YIL148W|CEP52A|UB11|UBI1 gene taxon:4932 20050407 SGD
+SGD S000001410 RPL40A GO:0042254 SGD_REF:S000064966|PMID:2538753 IDA P also encodes a ubiquitin protein, ribosomal protein L40A YIL148W|CEP52A|UB11|UBI1 gene taxon:4932 20040719 SGD
+SGD S000001410 RPL40A GO:0043037 SGD_REF:S000058497 TAS P also encodes a ubiquitin protein, ribosomal protein L40A YIL148W|CEP52A|UB11|UBI1 gene taxon:4932 20010119 SGD
+SGD S000001410 RPL40A GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P also encodes a ubiquitin protein, ribosomal protein L40A YIL148W|CEP52A|UB11|UBI1 gene taxon:4932 20010118 SGD
+SGD S000001802 RPL40B GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C also encodes a ubiquitin protein, ribosomal protein L40B YKR094C|CEP52B|UB12|UBI2 gene taxon:4932 20040928 SGD
+SGD S000001802 RPL40B GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C also encodes a ubiquitin protein, ribosomal protein L40B YKR094C|CEP52B|UB12|UBI2 gene taxon:4932 20010118 SGD
+SGD S000001802 RPL40B GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F also encodes a ubiquitin protein, ribosomal protein L40B YKR094C|CEP52B|UB12|UBI2 gene taxon:4932 20010118 SGD
+SGD S000001802 RPL40B GO:0031386 SGD_REF:S000056997|PMID:3038523 ISS F also encodes a ubiquitin protein, ribosomal protein L40B YKR094C|CEP52B|UB12|UBI2 gene taxon:4932 20050525 SGD
+SGD S000001802 RPL40B GO:0016567 SGD_REF:S000049784|PMID:8035826 IMP P also encodes a ubiquitin protein, ribosomal protein L40B YKR094C|CEP52B|UB12|UBI2 gene taxon:4932 20050407 SGD
+SGD S000001802 RPL40B GO:0042254 SGD_REF:S000064966|PMID:2538753 IDA P also encodes a ubiquitin protein, ribosomal protein L40B YKR094C|CEP52B|UB12|UBI2 gene taxon:4932 20040719 SGD
+SGD S000001802 RPL40B GO:0043037 SGD_REF:S000058497 TAS P also encodes a ubiquitin protein, ribosomal protein L40B YKR094C|CEP52B|UB12|UBI2 gene taxon:4932 20010119 SGD
+SGD S000001802 RPL40B GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P also encodes a ubiquitin protein, ribosomal protein L40B YKR094C|CEP52B|UB12|UBI2 gene taxon:4932 20010118 SGD
+SGD S000002343 RPL41A GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L41A (YL41) (L47A) YDL184C|RPL47A gene taxon:4932 20010118 SGD
+SGD S000002343 RPL41A GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L41A (YL41) (L47A) YDL184C|RPL47A gene taxon:4932 20010118 SGD
+SGD S000002343 RPL41A GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L41A (YL41) (L47A) YDL184C|RPL47A gene taxon:4932 20010119 SGD
+SGD S000002343 RPL41A GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L41A (YL41) (L47A) YDL184C|RPL47A gene taxon:4932 20010118 SGD
+SGD S000002293 RPL41B GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L41B (YL41) (L47B) YDL133C-A|RPL47B gene taxon:4932 20010118 SGD
+SGD S000002293 RPL41B GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L41B (YL41) (L47B) YDL133C-A|RPL47B gene taxon:4932 20010118 SGD
+SGD S000002293 RPL41B GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L41B (YL41) (L47B) YDL133C-A|RPL47B gene taxon:4932 20010119 SGD
+SGD S000002293 RPL41B GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L41B (YL41) (L47B) YDL133C-A|RPL47B gene taxon:4932 20010118 SGD
+SGD S000005106 RPL42A GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L42A (YL27) (L41A) YNL162W gene taxon:4932 20010118 SGD
+SGD S000005106 RPL42A GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L42A (YL27) (L41A) YNL162W gene taxon:4932 20010118 SGD
+SGD S000005106 RPL42A GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L42A (YL27) (L41A) YNL162W gene taxon:4932 20010119 SGD
+SGD S000005106 RPL42A GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L42A (YL27) (L41A) YNL162W gene taxon:4932 20010118 SGD
+SGD S000001183 RPL42B GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L42B (YL27) (L41B) (YP44) YHR141C|MAK18 gene taxon:4932 20010118 SGD
+SGD S000001183 RPL42B GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L42B (YL27) (L41B) (YP44) YHR141C|MAK18 gene taxon:4932 20010118 SGD
+SGD S000001183 RPL42B GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L42B (YL27) (L41B) (YP44) YHR141C|MAK18 gene taxon:4932 20010119 SGD
+SGD S000001183 RPL42B GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L42B (YL27) (L41B) (YP44) YHR141C|MAK18 gene taxon:4932 20010118 SGD
+SGD S000006247 RPL43A GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L43A YPR043W gene taxon:4932 20010118 SGD
+SGD S000006247 RPL43A GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L43A YPR043W gene taxon:4932 20010118 SGD
+SGD S000006247 RPL43A GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L43A YPR043W gene taxon:4932 20010119 SGD
+SGD S000006247 RPL43A GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L43A YPR043W gene taxon:4932 20010118 SGD
+SGD S000003855 RPL43B GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L43B YJR094W-A gene taxon:4932 20010118 SGD
+SGD S000003855 RPL43B GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L43B YJR094W-A gene taxon:4932 20010118 SGD
+SGD S000003855 RPL43B GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L43B YJR094W-A gene taxon:4932 20010119 SGD
+SGD S000003855 RPL43B GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L43B YJR094W-A gene taxon:4932 20010118 SGD
+SGD S000000235 RPL4A GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L4A (L2A) (rp2) (YL2) YBR031W gene taxon:4932 20010118 SGD
+SGD S000000235 RPL4A GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L4A (L2A) (rp2) (YL2) YBR031W gene taxon:4932 20010118 SGD
+SGD S000000235 RPL4A GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L4A (L2A) (rp2) (YL2) YBR031W gene taxon:4932 20010119 SGD
+SGD S000000235 RPL4A GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L4A (L2A) (rp2) (YL2) YBR031W gene taxon:4932 20010118 SGD
+SGD S000002419 RPL4B GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C ribosomal protein L4B (L2B) (rp2) (YL2) YDR012W gene taxon:4932 20020507 SGD
+SGD S000002419 RPL4B GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L4B (L2B) (rp2) (YL2) YDR012W gene taxon:4932 20010118 SGD
+SGD S000002419 RPL4B GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L4B (L2B) (rp2) (YL2) YDR012W gene taxon:4932 20010118 SGD
+SGD S000002419 RPL4B GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L4B (L2B) (rp2) (YL2) YDR012W gene taxon:4932 20010119 SGD
+SGD S000002419 RPL4B GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L4B (L2B) (rp2) (YL2) YDR012W gene taxon:4932 20010118 SGD
+SGD S000006052 RPL5 GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L5 (L1a)(YL3) YPL131W|LPI14|RPL1 gene taxon:4932 20010118 SGD
+SGD S000006052 RPL5 GO:0003723 SGD_REF:S000046340|PMID:8474444 IDA F ribosomal protein L5 (L1a)(YL3) YPL131W|LPI14|RPL1 gene taxon:4932 20010118 SGD
+SGD S000006052 RPL5 GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L5 (L1a)(YL3) YPL131W|LPI14|RPL1 gene taxon:4932 20010118 SGD
+SGD S000006052 RPL5 GO:0000027 SGD_REF:S000046340|PMID:8474444 IMP P ribosomal protein L5 (L1a)(YL3) YPL131W|LPI14|RPL1 gene taxon:4932 20010118 SGD
+SGD S000006052 RPL5 GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L5 (L1a)(YL3) YPL131W|LPI14|RPL1 gene taxon:4932 20010119 SGD
+SGD S000006052 RPL5 GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L5 (L1a)(YL3) YPL131W|LPI14|RPL1 gene taxon:4932 20010118 SGD
+SGD S000004538 RPL6A GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L6A (L17A) (rp18) (YL16) YML073C|YL16A gene taxon:4932 20010118 SGD
+SGD S000004538 RPL6A GO:0003723 SGD_REF:S000057255|PMID:6337137 IDA F ribosomal protein L6A (L17A) (rp18) (YL16) YML073C|YL16A gene taxon:4932 20010118 SGD
+SGD S000004538 RPL6A GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L6A (L17A) (rp18) (YL16) YML073C|YL16A gene taxon:4932 20010118 SGD
+SGD S000004538 RPL6A GO:0000027 SGD_REF:S000057049|PMID:3282992 IMP P ribosomal protein L6A (L17A) (rp18) (YL16) YML073C|YL16A gene taxon:4932 20010118 SGD
+SGD S000004538 RPL6A GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L6A (L17A) (rp18) (YL16) YML073C|YL16A gene taxon:4932 20010119 SGD
+SGD S000004538 RPL6A GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L6A (L17A) (rp18) (YL16) YML073C|YL16A gene taxon:4932 20010118 SGD
+SGD S000004440 RPL6B GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L6B (L17B) (rp18) (YL16) YLR448W gene taxon:4932 20010118 SGD
+SGD S000004440 RPL6B GO:0003723 SGD_REF:S000057255|PMID:6337137 IDA F ribosomal protein L6B (L17B) (rp18) (YL16) YLR448W gene taxon:4932 20010118 SGD
+SGD S000004440 RPL6B GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L6B (L17B) (rp18) (YL16) YLR448W gene taxon:4932 20010118 SGD
+SGD S000004440 RPL6B GO:0000027 SGD_REF:S000057049|PMID:3282992 IMP P ribosomal protein L6B (L17B) (rp18) (YL16) YLR448W gene taxon:4932 20010118 SGD
+SGD S000004440 RPL6B GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L6B (L17B) (rp18) (YL16) YLR448W gene taxon:4932 20010119 SGD
+SGD S000004440 RPL6B GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L6B (L17B) (rp18) (YL16) YLR448W gene taxon:4932 20010118 SGD
+SGD S000003044 RPL7A GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L7A (L6A) (rp11) (YL8) YGL076C gene taxon:4932 20010118 SGD
+SGD S000003044 RPL7A GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L7A (L6A) (rp11) (YL8) YGL076C gene taxon:4932 20010118 SGD
+SGD S000003044 RPL7A GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L7A (L6A) (rp11) (YL8) YGL076C gene taxon:4932 20010119 SGD
+SGD S000003044 RPL7A GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L7A (L6A) (rp11) (YL8) YGL076C gene taxon:4932 20010118 SGD
+SGD S000006119 RPL7B GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L7B (L6B) (rp11) (YL8) YPL198W gene taxon:4932 20010118 SGD
+SGD S000006119 RPL7B GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L7B (L6B) (rp11) (YL8) YPL198W gene taxon:4932 20010118 SGD
+SGD S000006119 RPL7B GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L7B (L6B) (rp11) (YL8) YPL198W gene taxon:4932 20010119 SGD
+SGD S000006119 RPL7B GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L7B (L6B) (rp11) (YL8) YPL198W gene taxon:4932 20010118 SGD
+SGD S000001025 RPL8A GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L8A (rp6) (YL5) (L4A) YHL033C|MAK7 gene taxon:4932 20010118 SGD
+SGD S000001025 RPL8A GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L8A (rp6) (YL5) (L4A) YHL033C|MAK7 gene taxon:4932 20010118 SGD
+SGD S000001025 RPL8A GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L8A (rp6) (YL5) (L4A) YHL033C|MAK7 gene taxon:4932 20010119 SGD
+SGD S000001025 RPL8A GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L8A (rp6) (YL5) (L4A) YHL033C|MAK7 gene taxon:4932 20010118 SGD
+SGD S000003968 RPL8B GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L8B (L4B) (rp6) (YL5) YLL045C|KRB1|SCL41 gene taxon:4932 20010118 SGD
+SGD S000003968 RPL8B GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L8B (L4B) (rp6) (YL5) YLL045C|KRB1|SCL41 gene taxon:4932 20010118 SGD
+SGD S000003968 RPL8B GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L8B (L4B) (rp6) (YL5) YLL045C|KRB1|SCL41 gene taxon:4932 20010119 SGD
+SGD S000003968 RPL8B GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L8B (L4B) (rp6) (YL5) YLL045C|KRB1|SCL41 gene taxon:4932 20010118 SGD
+SGD S000003115 RPL9A GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L9A (L8A) (rp24) (YL11) YGL147C gene taxon:4932 20010118 SGD
+SGD S000003115 RPL9A GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L9A (L8A) (rp24) (YL11) YGL147C gene taxon:4932 20010118 SGD
+SGD S000003115 RPL9A GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L9A (L8A) (rp24) (YL11) YGL147C gene taxon:4932 20010119 SGD
+SGD S000003115 RPL9A GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L9A (L8A) (rp24) (YL11) YGL147C gene taxon:4932 20010118 SGD
+SGD S000005011 RPL9B GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein L9B (L8B) (rp24) (YL11) YNL067W gene taxon:4932 20010118 SGD
+SGD S000005011 RPL9B GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein L9B (L8B) (rp24) (YL11) YNL067W gene taxon:4932 20010118 SGD
+SGD S000005011 RPL9B GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein L9B (L8B) (rp24) (YL11) YNL067W gene taxon:4932 20010119 SGD
+SGD S000005011 RPL9B GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein L9B (L8B) (rp24) (YL11) YNL067W gene taxon:4932 20010118 SGD
+SGD S000029023 RPM1 GO:0005739 SGD_REF:S000061188|PMID:11522833 IDA C gene taxon:4932 20020619 SGD
+SGD S000029023 RPM1 GO:0004526 SGD_REF:S000061188|PMID:11522833 IDA F gene taxon:4932 20020619 SGD
+SGD S000029023 RPM1 GO:0008033 SGD_REF:S000061188|PMID:11522833 IDA P gene taxon:4932 20020619 SGD
+SGD S000004556 RPM2 GO:0005739 SGD_REF:S000039785|PMID:8366116 IDA C mitochondrial RNase P subunit YML091C gene taxon:4932 20020829 SGD
+SGD S000004556 RPM2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C mitochondrial RNase P subunit YML091C gene taxon:4932 20040924 SGD
+SGD S000004556 RPM2 GO:0004526 SGD_REF:S000039785|PMID:8366116 IDA F mitochondrial RNase P subunit YML091C gene taxon:4932 20020829 SGD
+SGD S000004556 RPM2 GO:0001682 SGD_REF:S000039785|PMID:8366116 IDA P mitochondrial RNase P subunit YML091C gene taxon:4932 20020829 SGD
+SGD S000004556 RPM2 GO:0006412 SGD_REF:S000060796|PMID:11404323 IMP P mitochondrial RNase P subunit YML091C gene taxon:4932 20020829 SGD
+SGD S000004556 RPM2 GO:0007005 SGD_REF:S000060796|PMID:11404323 IGI P mitochondrial RNase P subunit YML091C gene taxon:4932 20020207 SGD
+SGD S000001069 RPN1 GO:0005634 SGD_REF:S000079924|PMID:15210724 IDA C 26S proteasome PA700 subunit YHR027C|HRD2|NAS1 gene taxon:4932 20050314 SGD
+SGD S000001069 RPN1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C 26S proteasome PA700 subunit YHR027C|HRD2|NAS1 gene taxon:4932 20020507 SGD
+SGD S000001069 RPN1 GO:0005783 SGD_REF:S000069459|PMID:11914276 IDA C 26S proteasome PA700 subunit YHR027C|HRD2|NAS1 gene taxon:4932 20020507 SGD
+SGD S000001069 RPN1 GO:0008540 SGD_REF:S000039974|PMID:9741626 IPI C 26S proteasome PA700 subunit YHR027C|HRD2|NAS1 gene taxon:4932 20050306 SGD
+SGD S000001069 RPN1 contributes_to GO:0004175 SGD_REF:S000058010|PMID:8982460 TAS F 26S proteasome PA700 subunit YHR027C|HRD2|NAS1 gene taxon:4932 20051102 SGD
+SGD S000001069 RPN1 contributes_to GO:0004175 SGD_REF:S000058463|PMID:9697412 TAS F 26S proteasome PA700 subunit YHR027C|HRD2|NAS1 gene taxon:4932 20051102 SGD
+SGD S000001069 RPN1 GO:0030674 SGD_REF:S000074998|PMID:12198498 IPI SGD:S000000763 F 26S proteasome PA700 subunit YHR027C|HRD2|NAS1 gene taxon:4932 20051102 SGD
+SGD S000001069 RPN1 GO:0006511 SGD_REF:S000058463|PMID:9697412 TAS P 26S proteasome PA700 subunit YHR027C|HRD2|NAS1 gene taxon:4932 20010118 SGD
+SGD S000001069 RPN1 GO:0006511 SGD_REF:S000058010|PMID:8982460 TAS P 26S proteasome PA700 subunit YHR027C|HRD2|NAS1 gene taxon:4932 20010118 SGD
+SGD S000001243 RPN10 GO:0000502 SGD_REF:S000076808|PMID:15242647 IMP C 26S proteasome component, mammalian S5a protein homolog YHR200W|MCB1|SUN1 gene taxon:4932 20041011 SGD
+SGD S000001243 RPN10 GO:0008540 SGD_REF:S000039974|PMID:9741626 IPI C 26S proteasome component, mammalian S5a protein homolog YHR200W|MCB1|SUN1 gene taxon:4932 20050306 SGD
+SGD S000001243 RPN10 GO:0008540 SGD_REF:S000082213|PMID:15907469 IPI C 26S proteasome component, mammalian S5a protein homolog YHR200W|MCB1|SUN1 gene taxon:4932 20050715 SGD
+SGD S000001243 RPN10 GO:0004175 SGD_REF:S000058463|PMID:9697412 TAS F 26S proteasome component, mammalian S5a protein homolog YHR200W|MCB1|SUN1 gene taxon:4932 20010118 SGD
+SGD S000001243 RPN10 GO:0004175 SGD_REF:S000058010|PMID:8982460 TAS F 26S proteasome component, mammalian S5a protein homolog YHR200W|MCB1|SUN1 gene taxon:4932 20010118 SGD
+SGD S000001243 RPN10 GO:0006511 SGD_REF:S000058463|PMID:9697412 TAS P 26S proteasome component, mammalian S5a protein homolog YHR200W|MCB1|SUN1 gene taxon:4932 20010118 SGD
+SGD S000001243 RPN10 GO:0006511 SGD_REF:S000058010|PMID:8982460 TAS P 26S proteasome component, mammalian S5a protein homolog YHR200W|MCB1|SUN1 gene taxon:4932 20010118 SGD
+SGD S000001900 RPN11 GO:0005634 SGD_REF:S000079924|PMID:15210724 IDA C YFR004W|MPR1 gene taxon:4932 20050314 SGD
+SGD S000001900 RPN11 GO:0008541 SGD_REF:S000068750|PMID:11742986 IDA C YFR004W|MPR1 gene taxon:4932 20020823 SGD
+SGD S000001900 RPN11 GO:0008541 SGD_REF:S000039974|PMID:9741626 IPI C YFR004W|MPR1 gene taxon:4932 20050307 SGD
+SGD S000001900 RPN11 GO:0004175 SGD_REF:S000058463|PMID:9697412 TAS F YFR004W|MPR1 gene taxon:4932 20010118 SGD
+SGD S000001900 RPN11 GO:0004175 SGD_REF:S000058010|PMID:8982460 TAS F YFR004W|MPR1 gene taxon:4932 20010118 SGD
+SGD S000001900 RPN11 GO:0006511 SGD_REF:S000058463|PMID:9697412 TAS P YFR004W|MPR1 gene taxon:4932 20010118 SGD
+SGD S000001900 RPN11 GO:0006511 SGD_REF:S000058010|PMID:8982460 TAS P YFR004W|MPR1 gene taxon:4932 20010118 SGD
+SGD S000001948 RPN12 GO:0008541 SGD_REF:S000039974|PMID:9741626 IPI C 32-34 kDa protein YFR052W|NIN1 gene taxon:4932 20050307 SGD
+SGD S000001948 RPN12 GO:0004175 SGD_REF:S000054953|PMID:10675611 NAS F 32-34 kDa protein YFR052W|NIN1 gene taxon:4932 20030206 SGD
+SGD S000001948 RPN12 GO:0006511 SGD_REF:S000042175|PMID:10490625 IMP P 32-34 kDa protein YFR052W|NIN1 gene taxon:4932 20030211 SGD
+SGD S000004413 RPN13 GO:0008541 SGD_REF:S000056447|PMID:11029046 IPI C YLR421C gene taxon:4932 20050307 SGD
+SGD S000004413 RPN13 GO:0004175 SGD_REF:S000056447|PMID:11029046 IPI F YLR421C gene taxon:4932 20030206 SGD
+SGD S000004413 RPN13 GO:0006508 SGD_REF:S000056447|PMID:11029046 IMP P YLR421C gene taxon:4932 20010118 SGD
+SGD S000004413 RPN13 GO:0006508 SGD_REF:S000056447|PMID:11029046 IPI P YLR421C gene taxon:4932 20010118 SGD
+SGD S000002972 RPN14 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YGL004C gene taxon:4932 20031028 SGD
+SGD S000002972 RPN14 GO:0005838 SGD_REF:S000074191|PMID:14566057 RCA C YGL004C gene taxon:4932 20050608 SGD
+SGD S000002972 RPN14 GO:0005554 SGD_REF:S000069584 ND F YGL004C gene taxon:4932 20060106 SGD
+SGD S000002972 RPN14 GO:0006508 SGD_REF:S000074191|PMID:14566057 RCA P YGL004C gene taxon:4932 20050608 SGD
+SGD S000001337 RPN2 GO:0005634 SGD_REF:S000079924|PMID:15210724 IDA C YIL075C|SEN3 gene taxon:4932 20050314 SGD
+SGD S000001337 RPN2 GO:0008540 SGD_REF:S000039974|PMID:9741626 IPI C YIL075C|SEN3 gene taxon:4932 20050306 SGD
+SGD S000001337 RPN2 GO:0004175 SGD_REF:S000043874|PMID:7565784 IPI F YIL075C|SEN3 gene taxon:4932 20030210 SGD
+SGD S000001337 RPN2 GO:0004872 SGD_REF:S000071480|PMID:12200120 IDA F YIL075C|SEN3 gene taxon:4932 20030116 SGD
+SGD S000001337 RPN2 GO:0006511 SGD_REF:S000043874|PMID:7565784 IMP P YIL075C|SEN3 gene taxon:4932 20010118 SGD
+SGD S000001337 RPN2 GO:0006511 SGD_REF:S000043874|PMID:7565784 IPI P YIL075C|SEN3 gene taxon:4932 20010118 SGD
+SGD S000000823 RPN3 GO:0008541 SGD_REF:S000039974|PMID:9741626 IPI C 26S proteasome regulatory module component YER021W|SUN2 gene taxon:4932 20050307 SGD
+SGD S000000823 RPN3 GO:0005554 SGD_REF:S000069584 ND F 26S proteasome regulatory module component YER021W|SUN2 gene taxon:4932 20040706 SGD
+SGD S000000823 RPN3 GO:0006511 SGD_REF:S000058463|PMID:9697412 TAS P 26S proteasome regulatory module component YER021W|SUN2 gene taxon:4932 20010118 SGD
+SGD S000000823 RPN3 GO:0006511 SGD_REF:S000058010|PMID:8982460 TAS P 26S proteasome regulatory module component YER021W|SUN2 gene taxon:4932 20010118 SGD
+SGD S000002178 RPN4 GO:0005838 SGD_REF:S000053714|PMID:9512348 IPI C YDL020C|SON1|UFD5 gene taxon:4932 20040217 SGD
+SGD S000002178 RPN4 GO:0005839 SGD_REF:S000059915|PMID:11248031 IDA C YDL020C|SON1|UFD5 gene taxon:4932 20040217 SGD
+SGD S000002178 RPN4 GO:0005839 SGD_REF:S000059915|PMID:11248031 IPI SGD:S000001337 C YDL020C|SON1|UFD5 gene taxon:4932 20040217 SGD
+SGD S000002178 RPN4 GO:0016563 SGD_REF:S000061866|PMID:10350051 IDA F YDL020C|SON1|UFD5 gene taxon:4932 20040217 SGD
+SGD S000002178 RPN4 GO:0000086 SGD_REF:S000059915|PMID:11248031 IMP P YDL020C|SON1|UFD5 gene taxon:4932 20040217 SGD
+SGD S000002178 RPN4 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P YDL020C|SON1|UFD5 gene taxon:4932 20060210 SGD
+SGD S000002178 RPN4 GO:0006511 SGD_REF:S000058463|PMID:9697412 TAS P YDL020C|SON1|UFD5 gene taxon:4932 20010118 SGD
+SGD S000002178 RPN4 GO:0006511 SGD_REF:S000058010|PMID:8982460 TAS P YDL020C|SON1|UFD5 gene taxon:4932 20010118 SGD
+SGD S000002178 RPN4 GO:0046685 SGD_REF:S000080191|PMID:15575969 IMP P YDL020C|SON1|UFD5 gene taxon:4932 20050331 SGD
+SGD S000002178 RPN4 GO:0046685 SGD_REF:S000080191|PMID:15575969 IEP P YDL020C|SON1|UFD5 gene taxon:4932 20050331 SGD
+SGD S000002306 RPN5 GO:0008541 SGD_REF:S000068750|PMID:11742986 IDA C proteasome regulatory particle subunit YDL147W|NAS5 gene taxon:4932 20020823 SGD
+SGD S000002306 RPN5 GO:0008541 SGD_REF:S000039974|PMID:9741626 IPI C proteasome regulatory particle subunit YDL147W|NAS5 gene taxon:4932 20050307 SGD
+SGD S000002306 RPN5 GO:0005554 SGD_REF:S000069584 ND F proteasome regulatory particle subunit YDL147W|NAS5 gene taxon:4932 20040706 SGD
+SGD S000002306 RPN5 GO:0006511 SGD_REF:S000058463|PMID:9697412 TAS P proteasome regulatory particle subunit YDL147W|NAS5 gene taxon:4932 20010118 SGD
+SGD S000002306 RPN5 GO:0006511 SGD_REF:S000058010|PMID:8982460 TAS P proteasome regulatory particle subunit YDL147W|NAS5 gene taxon:4932 20010118 SGD
+SGD S000002255 RPN6 GO:0008541 SGD_REF:S000039974|PMID:9741626 IPI C proteasome regulatory particle subunit YDL097C|NAS4 gene taxon:4932 20050307 SGD
+SGD S000002255 RPN6 GO:0005198 SGD_REF:S000072728|PMID:12486135 IMP F proteasome regulatory particle subunit YDL097C|NAS4 gene taxon:4932 20030423 SGD
+SGD S000002255 RPN6 GO:0006511 SGD_REF:S000058463|PMID:9697412 TAS P proteasome regulatory particle subunit YDL097C|NAS4 gene taxon:4932 20010118 SGD
+SGD S000002255 RPN6 GO:0006511 SGD_REF:S000058010|PMID:8982460 TAS P proteasome regulatory particle subunit YDL097C|NAS4 gene taxon:4932 20010118 SGD
+SGD S000006312 RPN7 GO:0008541 SGD_REF:S000039974|PMID:9741626 IPI C proteasome regulatory particle subunit YPR108W gene taxon:4932 20050307 SGD
+SGD S000006312 RPN7 GO:0005198 SGD_REF:S000058990|PMID:15102831 IMP F proteasome regulatory particle subunit YPR108W gene taxon:4932 20040706 SGD
+SGD S000006312 RPN7 GO:0006511 SGD_REF:S000058463|PMID:9697412 TAS P proteasome regulatory particle subunit YPR108W gene taxon:4932 20010118 SGD
+SGD S000006312 RPN7 GO:0006511 SGD_REF:S000058010|PMID:8982460 TAS P proteasome regulatory particle subunit YPR108W gene taxon:4932 20010118 SGD
+SGD S000005787 RPN8 GO:0008541 SGD_REF:S000068750|PMID:11742986 IDA C proteasome regulatory particle subunit YOR261C gene taxon:4932 20020823 SGD
+SGD S000005787 RPN8 GO:0008541 SGD_REF:S000039974|PMID:9741626 IPI C proteasome regulatory particle subunit YOR261C gene taxon:4932 20050307 SGD
+SGD S000005787 RPN8 GO:0005554 SGD_REF:S000069584 ND F proteasome regulatory particle subunit YOR261C gene taxon:4932 20040706 SGD
+SGD S000005787 RPN8 GO:0006511 SGD_REF:S000058463|PMID:9697412 TAS P proteasome regulatory particle subunit YOR261C gene taxon:4932 20010118 SGD
+SGD S000005787 RPN8 GO:0006511 SGD_REF:S000058010|PMID:8982460 TAS P proteasome regulatory particle subunit YOR261C gene taxon:4932 20010118 SGD
+SGD S000002835 RPN9 GO:0008541 SGD_REF:S000068750|PMID:11742986 IDA C proteasome regulatory particle subunit YDR427W gene taxon:4932 20020823 SGD
+SGD S000002835 RPN9 GO:0008541 SGD_REF:S000039974|PMID:9741626 IPI C proteasome regulatory particle subunit YDR427W gene taxon:4932 20050307 SGD
+SGD S000002835 RPN9 GO:0005198 SGD_REF:S000041704|PMID:10490597 IMP F proteasome regulatory particle subunit YDR427W gene taxon:4932 20040706 SGD
+SGD S000002835 RPN9 GO:0006511 SGD_REF:S000058463|PMID:9697412 TAS P proteasome regulatory particle subunit YDR427W gene taxon:4932 20010118 SGD
+SGD S000002835 RPN9 GO:0006511 SGD_REF:S000058010|PMID:8982460 TAS P proteasome regulatory particle subunit YDR427W gene taxon:4932 20010118 SGD
+SGD S000002299 RPO21 GO:0005665 SGD_REF:S000058446|PMID:9774381 TAS C RNA polymerase II core subunit YDL140C|B220|RPB1|RPB220|SUA8 gene taxon:4932 20010118 SGD
+SGD S000002299 RPO21 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C RNA polymerase II core subunit YDL140C|B220|RPB1|RPB220|SUA8 gene taxon:4932 20040928 SGD
+SGD S000002299 RPO21 GO:0003899 SGD_REF:S000058446|PMID:9774381 TAS F RNA polymerase II core subunit YDL140C|B220|RPB1|RPB220|SUA8 gene taxon:4932 20010118 SGD
+SGD S000002299 RPO21 GO:0006366 SGD_REF:S000058446|PMID:9774381 TAS P RNA polymerase II core subunit YDL140C|B220|RPB1|RPB220|SUA8 gene taxon:4932 20050920 SGD
+SGD S000006391 RPO26 GO:0005665 SGD_REF:S000058446|PMID:9774381 TAS C RNA polymerases I, II, and III subunit YPR187W|ABC23|RPB6 gene taxon:4932 20010118 SGD
+SGD S000006391 RPO26 GO:0005666 SGD_REF:S000058446|PMID:9774381 TAS C RNA polymerases I, II, and III subunit YPR187W|ABC23|RPB6 gene taxon:4932 20010118 SGD
+SGD S000006391 RPO26 GO:0005736 SGD_REF:S000058446|PMID:9774381 TAS C RNA polymerases I, II, and III subunit YPR187W|ABC23|RPB6 gene taxon:4932 20010118 SGD
+SGD S000006391 RPO26 GO:0003899 SGD_REF:S000058446|PMID:9774381 TAS F RNA polymerases I, II, and III subunit YPR187W|ABC23|RPB6 gene taxon:4932 20010118 SGD
+SGD S000006391 RPO26 GO:0006360 SGD_REF:S000058500 TAS P RNA polymerases I, II, and III subunit YPR187W|ABC23|RPB6 gene taxon:4932 20010119 SGD
+SGD S000006391 RPO26 GO:0006366 SGD_REF:S000058446|PMID:9774381 TAS P RNA polymerases I, II, and III subunit YPR187W|ABC23|RPB6 gene taxon:4932 20050920 SGD
+SGD S000006391 RPO26 GO:0006383 SGD_REF:S000058500 TAS P RNA polymerases I, II, and III subunit YPR187W|ABC23|RPB6 gene taxon:4932 20010119 SGD
+SGD S000005642 RPO31 GO:0005666 SGD_REF:S000057661|PMID:8246845 TAS C RNA polymerase III subunit YOR116C|C160|RPC1|RPC160 gene taxon:4932 20010118 SGD
+SGD S000005642 RPO31 GO:0003899 SGD_REF:S000057661|PMID:8246845 TAS F RNA polymerase III subunit YOR116C|C160|RPC1|RPC160 gene taxon:4932 20010118 SGD
+SGD S000005642 RPO31 GO:0006383 SGD_REF:S000058500 TAS P RNA polymerase III subunit YOR116C|C160|RPC1|RPC160 gene taxon:4932 20010119 SGD
+SGD S000001858 RPO41 GO:0005759 SGD_REF:S000050238|PMID:3517858 IDA C mitochondrial RNA polymerase YFL036W gene taxon:4932 20010118 SGD
+SGD S000001858 RPO41 GO:0005759 SGD_REF:S000056852|PMID:2426263 IDA C mitochondrial RNA polymerase YFL036W gene taxon:4932 20010118 SGD
+SGD S000001858 RPO41 GO:0042645 SGD_REF:S000080741|PMID:15692048 IDA C mitochondrial RNA polymerase YFL036W gene taxon:4932 20050401 SGD
+SGD S000001858 RPO41 GO:0003899 SGD_REF:S000050238|PMID:3517858 IDA F mitochondrial RNA polymerase YFL036W gene taxon:4932 20010118 SGD
+SGD S000001858 RPO41 GO:0003899 SGD_REF:S000056852|PMID:2426263 IDA F mitochondrial RNA polymerase YFL036W gene taxon:4932 20010118 SGD
+SGD S000001858 RPO41 GO:0000002 SGD_REF:S000050238|PMID:3517858 IMP P mitochondrial RNA polymerase YFL036W gene taxon:4932 20010118 SGD
+SGD S000001858 RPO41 GO:0006390 SGD_REF:S000050238|PMID:3517858 IMP P mitochondrial RNA polymerase YFL036W gene taxon:4932 20010118 SGD
+SGD S000004332 RPP0 GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein P0 (A0) (L10E) YLR340W|RPL10E gene taxon:4932 20010118 SGD
+SGD S000004332 RPP0 GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein P0 (A0) (L10E) YLR340W|RPL10E gene taxon:4932 20010118 SGD
+SGD S000004332 RPP0 GO:0000027 SGD_REF:S000057635|PMID:8195220 IMP P ribosomal protein P0 (A0) (L10E) YLR340W|RPL10E gene taxon:4932 20010118 SGD
+SGD S000004332 RPP0 GO:0006414 SGD_REF:S000058464|PMID:9175862 ISS P ribosomal protein P0 (A0) (L10E) YLR340W|RPL10E gene taxon:4932 20010118 SGD
+SGD S000004332 RPP0 GO:0006414 SGD_REF:S000058461|PMID:9559554 ISS P ribosomal protein P0 (A0) (L10E) YLR340W|RPL10E gene taxon:4932 20010118 SGD
+SGD S000004332 RPP0 GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein P0 (A0) (L10E) YLR340W|RPL10E gene taxon:4932 20010118 SGD
+SGD S000001104 RPP1 GO:0000172 SGD_REF:S000061290|PMID:11241345 TAS C Nuclear RNase P subunit, RNase MRP subunit YHR062C gene taxon:4932 20010906 SGD
+SGD S000001104 RPP1 GO:0005655 SGD_REF:S000061290|PMID:11241345 TAS C Nuclear RNase P subunit, RNase MRP subunit YHR062C gene taxon:4932 20010906 SGD
+SGD S000001104 RPP1 GO:0000171 SGD_REF:S000061290|PMID:11241345 TAS F Nuclear RNase P subunit, RNase MRP subunit YHR062C gene taxon:4932 20010906 SGD
+SGD S000001104 RPP1 GO:0004526 SGD_REF:S000061290|PMID:11241345 TAS F Nuclear RNase P subunit, RNase MRP subunit YHR062C gene taxon:4932 20010906 SGD
+SGD S000001104 RPP1 GO:0006364 SGD_REF:S000061290|PMID:11241345 TAS P Nuclear RNase P subunit, RNase MRP subunit YHR062C gene taxon:4932 20010906 SGD
+SGD S000001104 RPP1 GO:0008033 SGD_REF:S000061290|PMID:11241345 TAS P Nuclear RNase P subunit, RNase MRP subunit YHR062C gene taxon:4932 20010906 SGD
+SGD S000002239 RPP1A GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C acidic ribosomal protein P1A (YP1alpha) (A1) YDL081C|RPLA1 gene taxon:4932 20010118 SGD
+SGD S000002239 RPP1A GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F acidic ribosomal protein P1A (YP1alpha) (A1) YDL081C|RPLA1 gene taxon:4932 20010118 SGD
+SGD S000002239 RPP1A GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P acidic ribosomal protein P1A (YP1alpha) (A1) YDL081C|RPLA1 gene taxon:4932 20060227 SGD
+SGD S000002239 RPP1A GO:0006414 SGD_REF:S000058464|PMID:9175862 ISS P acidic ribosomal protein P1A (YP1alpha) (A1) YDL081C|RPLA1 gene taxon:4932 20010118 SGD
+SGD S000002239 RPP1A GO:0006414 SGD_REF:S000058461|PMID:9559554 ISS P acidic ribosomal protein P1A (YP1alpha) (A1) YDL081C|RPLA1 gene taxon:4932 20010118 SGD
+SGD S000002239 RPP1A GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P acidic ribosomal protein P1A (YP1alpha) (A1) YDL081C|RPLA1 gene taxon:4932 20010118 SGD
+SGD S000002288 RPP1B GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein P1B (L44') (YP1beta) (Ax) YDL130W|RPL44'|RPLA3 gene taxon:4932 20010118 SGD
+SGD S000002288 RPP1B GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein P1B (L44') (YP1beta) (Ax) YDL130W|RPL44'|RPLA3 gene taxon:4932 20010118 SGD
+SGD S000002288 RPP1B GO:0006414 SGD_REF:S000058464|PMID:9175862 ISS P ribosomal protein P1B (L44') (YP1beta) (Ax) YDL130W|RPL44'|RPLA3 gene taxon:4932 20010118 SGD
+SGD S000002288 RPP1B GO:0006414 SGD_REF:S000058461|PMID:9559554 ISS P ribosomal protein P1B (L44') (YP1beta) (Ax) YDL130W|RPL44'|RPLA3 gene taxon:4932 20010118 SGD
+SGD S000002288 RPP1B GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein P1B (L44') (YP1beta) (Ax) YDL130W|RPL44'|RPLA3 gene taxon:4932 20010118 SGD
+SGD S000005399 RPP2A GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C 60S acidic ribosomal protein P2A (L44) (A2) (YP2alpha) YOL039W|RPL44|RPLA2 gene taxon:4932 20010118 SGD
+SGD S000005399 RPP2A GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F 60S acidic ribosomal protein P2A (L44) (A2) (YP2alpha) YOL039W|RPL44|RPLA2 gene taxon:4932 20010118 SGD
+SGD S000005399 RPP2A GO:0006414 SGD_REF:S000058464|PMID:9175862 ISS P 60S acidic ribosomal protein P2A (L44) (A2) (YP2alpha) YOL039W|RPL44|RPLA2 gene taxon:4932 20010118 SGD
+SGD S000005399 RPP2A GO:0006414 SGD_REF:S000058461|PMID:9559554 ISS P 60S acidic ribosomal protein P2A (L44) (A2) (YP2alpha) YOL039W|RPL44|RPLA2 gene taxon:4932 20010118 SGD
+SGD S000005399 RPP2A GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P 60S acidic ribosomal protein P2A (L44) (A2) (YP2alpha) YOL039W|RPL44|RPLA2 gene taxon:4932 20010118 SGD
+SGD S000002790 RPP2B GO:0005842 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein P2B (YP2beta) (L45) YDR382W|RPL45|YPA1 gene taxon:4932 20010118 SGD
+SGD S000002790 RPP2B GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein P2B (YP2beta) (L45) YDR382W|RPL45|YPA1 gene taxon:4932 20010118 SGD
+SGD S000002790 RPP2B GO:0006414 SGD_REF:S000058464|PMID:9175862 ISS P ribosomal protein P2B (YP2beta) (L45) YDR382W|RPL45|YPA1 gene taxon:4932 20010118 SGD
+SGD S000002790 RPP2B GO:0006414 SGD_REF:S000058461|PMID:9559554 ISS P ribosomal protein P2B (YP2beta) (L45) YDR382W|RPL45|YPA1 gene taxon:4932 20010118 SGD
+SGD S000002790 RPP2B GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein P2B (YP2beta) (L45) YDR382W|RPL45|YPA1 gene taxon:4932 20010118 SGD
+SGD S000006490 RPR1 GO:0005655 SGD_REF:S000061290|PMID:11241345 TAS C Nuclear RNase P subunit gene taxon:4932 20010906 SGD
+SGD S000006490 RPR1 GO:0004526 SGD_REF:S000061290|PMID:11241345 TAS F Nuclear RNase P subunit gene taxon:4932 20010906 SGD
+SGD S000006490 RPR1 GO:0008033 SGD_REF:S000061290|PMID:11241345 TAS P Nuclear RNase P subunit gene taxon:4932 20010906 SGD
+SGD S000001454 RPR2 GO:0005655 SGD_REF:S000044608|PMID:9620854 IDA C Nuclear RNase P subunit YIR015W gene taxon:4932 20010906 SGD
+SGD S000001454 RPR2 GO:0004526 SGD_REF:S000044608|PMID:9620854 IDA F Nuclear RNase P subunit YIR015W gene taxon:4932 20010906 SGD
+SGD S000001454 RPR2 GO:0008033 SGD_REF:S000044608|PMID:9620854 TAS P Nuclear RNase P subunit YIR015W gene taxon:4932 20010118 SGD
+SGD S000003446 RPS0A GO:0005843 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein S0A YGR214W|NAB1|NAB1A|YST1 gene taxon:4932 20010118 SGD
+SGD S000003446 RPS0A GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein S0A YGR214W|NAB1|NAB1A|YST1 gene taxon:4932 20010118 SGD
+SGD S000003446 RPS0A GO:0000028 SGD_REF:S000045335|PMID:8626693 IMP P ribosomal protein S0A YGR214W|NAB1|NAB1A|YST1 gene taxon:4932 20010118 SGD
+SGD S000003446 RPS0A GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein S0A YGR214W|NAB1|NAB1A|YST1 gene taxon:4932 20010119 SGD
+SGD S000003446 RPS0A GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein S0A YGR214W|NAB1|NAB1A|YST1 gene taxon:4932 20010118 SGD
+SGD S000004038 RPS0B GO:0005843 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein S0B YLR048W|NAB1B|YST2 gene taxon:4932 20010118 SGD
+SGD S000004038 RPS0B GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein S0B YLR048W|NAB1B|YST2 gene taxon:4932 20010118 SGD
+SGD S000004038 RPS0B GO:0000028 SGD_REF:S000045335|PMID:8626693 IMP P ribosomal protein S0B YLR048W|NAB1B|YST2 gene taxon:4932 20010118 SGD
+SGD S000004038 RPS0B GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein S0B YLR048W|NAB1B|YST2 gene taxon:4932 20010119 SGD
+SGD S000004038 RPS0B GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein S0B YLR048W|NAB1B|YST2 gene taxon:4932 20010118 SGD
+SGD S000005819 RPS10A GO:0005843 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein S10A YOR293W gene taxon:4932 20010118 SGD
+SGD S000005819 RPS10A GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein S10A YOR293W gene taxon:4932 20010118 SGD
+SGD S000005819 RPS10A GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein S10A YOR293W gene taxon:4932 20010119 SGD
+SGD S000005819 RPS10A GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein S10A YOR293W gene taxon:4932 20010118 SGD
+SGD S000004843 RPS10B GO:0005843 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein S10B YMR230W gene taxon:4932 20010118 SGD
+SGD S000004843 RPS10B GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein S10B YMR230W gene taxon:4932 20010118 SGD
+SGD S000004843 RPS10B GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein S10B YMR230W gene taxon:4932 20010119 SGD
+SGD S000004843 RPS10B GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein S10B YMR230W gene taxon:4932 20010118 SGD
+SGD S000002432 RPS11A GO:0005843 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein S11A (S18A) (rp41A) (YS12) YDR025W gene taxon:4932 20010118 SGD
+SGD S000002432 RPS11A GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein S11A (S18A) (rp41A) (YS12) YDR025W gene taxon:4932 20010118 SGD
+SGD S000002432 RPS11A GO:0000028 SGD_REF:S000053615|PMID:8070651 IMP P ribosomal protein S11A (S18A) (rp41A) (YS12) YDR025W gene taxon:4932 20010118 SGD
+SGD S000002432 RPS11A GO:0000028 SGD_REF:S000053615|PMID:8070651 ISS P ribosomal protein S11A (S18A) (rp41A) (YS12) YDR025W gene taxon:4932 20010118 SGD
+SGD S000002432 RPS11A GO:0006450 SGD_REF:S000053615|PMID:8070651 IMP P ribosomal protein S11A (S18A) (rp41A) (YS12) YDR025W gene taxon:4932 20001002 SGD
+SGD S000002432 RPS11A GO:0006450 SGD_REF:S000053615|PMID:8070651 ISS P ribosomal protein S11A (S18A) (rp41A) (YS12) YDR025W gene taxon:4932 20001002 SGD
+SGD S000002432 RPS11A GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein S11A (S18A) (rp41A) (YS12) YDR025W gene taxon:4932 20010119 SGD
+SGD S000002432 RPS11A GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein S11A (S18A) (rp41A) (YS12) YDR025W gene taxon:4932 20010118 SGD
+SGD S000000252 RPS11B GO:0005843 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein S11B (S18B) (rp41B) (YS12) YBR048W gene taxon:4932 20010118 SGD
+SGD S000000252 RPS11B GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein S11B (S18B) (rp41B) (YS12) YBR048W gene taxon:4932 20010118 SGD
+SGD S000000252 RPS11B GO:0000028 SGD_REF:S000053615|PMID:8070651 IMP P ribosomal protein S11B (S18B) (rp41B) (YS12) YBR048W gene taxon:4932 20010118 SGD
+SGD S000000252 RPS11B GO:0000028 SGD_REF:S000053615|PMID:8070651 ISS P ribosomal protein S11B (S18B) (rp41B) (YS12) YBR048W gene taxon:4932 20010118 SGD
+SGD S000000252 RPS11B GO:0006450 SGD_REF:S000053615|PMID:8070651 ISS P ribosomal protein S11B (S18B) (rp41B) (YS12) YBR048W gene taxon:4932 20001002 SGD
+SGD S000000252 RPS11B GO:0006450 SGD_REF:S000053615|PMID:8070651 IMP P ribosomal protein S11B (S18B) (rp41B) (YS12) YBR048W gene taxon:4932 20001002 SGD
+SGD S000000252 RPS11B GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein S11B (S18B) (rp41B) (YS12) YBR048W gene taxon:4932 20010119 SGD
+SGD S000000252 RPS11B GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein S11B (S18B) (rp41B) (YS12) YBR048W gene taxon:4932 20010118 SGD
+SGD S000005896 RPS12 GO:0005843 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein S12 YOR369C gene taxon:4932 20010118 SGD
+SGD S000005896 RPS12 GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein S12 YOR369C gene taxon:4932 20010118 SGD
+SGD S000005896 RPS12 GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein S12 YOR369C gene taxon:4932 20010119 SGD
+SGD S000005896 RPS12 GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein S12 YOR369C gene taxon:4932 20010118 SGD
+SGD S000002471 RPS13 GO:0005843 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein S13 (S27a) (YS15) YDR064W|RPS13B|RPS13C gene taxon:4932 20010118 SGD
+SGD S000002471 RPS13 GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein S13 (S27a) (YS15) YDR064W|RPS13B|RPS13C gene taxon:4932 20010118 SGD
+SGD S000002471 RPS13 GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein S13 (S27a) (YS15) YDR064W|RPS13B|RPS13C gene taxon:4932 20010119 SGD
+SGD S000002471 RPS13 GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein S13 (S27a) (YS15) YDR064W|RPS13B|RPS13C gene taxon:4932 20010118 SGD
+SGD S000000627 RPS14A GO:0005732 SGD_REF:S000079989|PMID:15590835 IPI SGD:S000003762 C ribosomal protein S14A (rp59A) YCR031C|CRY1|RPL59 gene taxon:4932 20050124 SGD
+SGD S000000627 RPS14A GO:0005843 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein S14A (rp59A) YCR031C|CRY1|RPL59 gene taxon:4932 20010118 SGD
+SGD S000000627 RPS14A GO:0003723 SGD_REF:S000043075|PMID:9858605 IDA F ribosomal protein S14A (rp59A) YCR031C|CRY1|RPL59 gene taxon:4932 20010118 SGD
+SGD S000000627 RPS14A GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein S14A (rp59A) YCR031C|CRY1|RPL59 gene taxon:4932 20010118 SGD
+SGD S000000627 RPS14A GO:0000028 SGD_REF:S000058462|PMID:2277060 IMP P ribosomal protein S14A (rp59A) YCR031C|CRY1|RPL59 gene taxon:4932 20010118 SGD
+SGD S000000627 RPS14A GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P ribosomal protein S14A (rp59A) YCR031C|CRY1|RPL59 gene taxon:4932 20060227 SGD
+SGD S000000627 RPS14A GO:0030490 SGD_REF:S000076292|PMID:15125836 IMP P ribosomal protein S14A (rp59A) YCR031C|CRY1|RPL59 gene taxon:4932 20050407 SGD
+SGD S000000627 RPS14A GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein S14A (rp59A) YCR031C|CRY1|RPL59 gene taxon:4932 20010119 SGD
+SGD S000000627 RPS14A GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein S14A (rp59A) YCR031C|CRY1|RPL59 gene taxon:4932 20010118 SGD
+SGD S000003727 RPS14B GO:0005732 SGD_REF:S000079989|PMID:15590835 IPI SGD:S000003762 C ribosomal protein S14B (rp59B) YJL191W|CRY2 gene taxon:4932 20050124 SGD
+SGD S000003727 RPS14B GO:0005843 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein S14B (rp59B) YJL191W|CRY2 gene taxon:4932 20010118 SGD
+SGD S000003727 RPS14B GO:0003723 SGD_REF:S000043075|PMID:9858605 IDA F ribosomal protein S14B (rp59B) YJL191W|CRY2 gene taxon:4932 20010118 SGD
+SGD S000003727 RPS14B GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein S14B (rp59B) YJL191W|CRY2 gene taxon:4932 20010118 SGD
+SGD S000003727 RPS14B GO:0000028 SGD_REF:S000058462|PMID:2277060 IMP P ribosomal protein S14B (rp59B) YJL191W|CRY2 gene taxon:4932 20010118 SGD
+SGD S000003727 RPS14B GO:0030490 SGD_REF:S000076292|PMID:15125836 IMP P ribosomal protein S14B (rp59B) YJL191W|CRY2 gene taxon:4932 20050407 SGD
+SGD S000003727 RPS14B GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein S14B (rp59B) YJL191W|CRY2 gene taxon:4932 20010119 SGD
+SGD S000003727 RPS14B GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein S14B (rp59B) YJL191W|CRY2 gene taxon:4932 20010118 SGD
+SGD S000005400 RPS15 GO:0005843 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein S15 (S21) (rp52) (RIG protein) YOL040C|RPS21 gene taxon:4932 20010118 SGD
+SGD S000005400 RPS15 GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein S15 (S21) (rp52) (RIG protein) YOL040C|RPS21 gene taxon:4932 20010118 SGD
+SGD S000005400 RPS15 GO:0000056 SGD_REF:S000076341|PMID:15167894 IMP P ribosomal protein S15 (S21) (rp52) (RIG protein) YOL040C|RPS21 gene taxon:4932 20040922 SGD
+SGD S000005400 RPS15 GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein S15 (S21) (rp52) (RIG protein) YOL040C|RPS21 gene taxon:4932 20010119 SGD
+SGD S000005400 RPS15 GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein S15 (S21) (rp52) (RIG protein) YOL040C|RPS21 gene taxon:4932 20010118 SGD
+SGD S000004751 RPS16A GO:0005843 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein S16A (rp61R) YMR143W gene taxon:4932 20010118 SGD
+SGD S000004751 RPS16A GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein S16A (rp61R) YMR143W gene taxon:4932 20010118 SGD
+SGD S000004751 RPS16A GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein S16A (rp61R) YMR143W gene taxon:4932 20010119 SGD
+SGD S000004751 RPS16A GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein S16A (rp61R) YMR143W gene taxon:4932 20010118 SGD
+SGD S000002241 RPS16B GO:0005843 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein S16B (rp61R) YDL083C gene taxon:4932 20010118 SGD
+SGD S000002241 RPS16B GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein S16B (rp61R) YDL083C gene taxon:4932 20010118 SGD
+SGD S000002241 RPS16B GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein S16B (rp61R) YDL083C gene taxon:4932 20010119 SGD
+SGD S000002241 RPS16B GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein S16B (rp61R) YDL083C gene taxon:4932 20010118 SGD
+SGD S000004486 RPS17A GO:0005843 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein S17A (rp51A) YML024W|RP51A|RPL51A gene taxon:4932 20010118 SGD
+SGD S000004486 RPS17A GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein S17A (rp51A) YML024W|RP51A|RPL51A gene taxon:4932 20010118 SGD
+SGD S000004486 RPS17A GO:0000028 SGD_REF:S000051019|PMID:3915776 IMP P ribosomal protein S17A (rp51A) YML024W|RP51A|RPL51A gene taxon:4932 20010118 SGD
+SGD S000004486 RPS17A GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P ribosomal protein S17A (rp51A) YML024W|RP51A|RPL51A gene taxon:4932 20060227 SGD
+SGD S000004486 RPS17A GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein S17A (rp51A) YML024W|RP51A|RPL51A gene taxon:4932 20010119 SGD
+SGD S000004486 RPS17A GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein S17A (rp51A) YML024W|RP51A|RPL51A gene taxon:4932 20010118 SGD
+SGD S000002855 RPS17B GO:0005843 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein S17B (rp51B) YDR447C|RP51B|RPL51B gene taxon:4932 20010118 SGD
+SGD S000002855 RPS17B GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein S17B (rp51B) YDR447C|RP51B|RPL51B gene taxon:4932 20010118 SGD
+SGD S000002855 RPS17B GO:0000028 SGD_REF:S000051019|PMID:3915776 IMP P ribosomal protein S17B (rp51B) YDR447C|RP51B|RPL51B gene taxon:4932 20010118 SGD
+SGD S000002855 RPS17B GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein S17B (rp51B) YDR447C|RP51B|RPL51B gene taxon:4932 20010119 SGD
+SGD S000002855 RPS17B GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein S17B (rp51B) YDR447C|RP51B|RPL51B gene taxon:4932 20010118 SGD
+SGD S000002858 RPS18A GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C ribosomal protein S18A YDR450W gene taxon:4932 20040928 SGD
+SGD S000002858 RPS18A GO:0005843 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein S18A YDR450W gene taxon:4932 20010118 SGD
+SGD S000002858 RPS18A GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein S18A YDR450W gene taxon:4932 20010118 SGD
+SGD S000002858 RPS18A GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein S18A YDR450W gene taxon:4932 20010119 SGD
+SGD S000002858 RPS18A GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein S18A YDR450W gene taxon:4932 20010118 SGD
+SGD S000004488 RPS18B GO:0005843 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein S18B YML026C gene taxon:4932 20010118 SGD
+SGD S000004488 RPS18B GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein S18B YML026C gene taxon:4932 20010118 SGD
+SGD S000004488 RPS18B GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein S18B YML026C gene taxon:4932 20010119 SGD
+SGD S000004488 RPS18B GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein S18B YML026C gene taxon:4932 20010118 SGD
+SGD S000005481 RPS19A GO:0005843 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein S19A (S16aA) (rp55A) (YS16A) YOL121C gene taxon:4932 20010118 SGD
+SGD S000005481 RPS19A GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein S19A (S16aA) (rp55A) (YS16A) YOL121C gene taxon:4932 20010118 SGD
+SGD S000005481 RPS19A GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein S19A (S16aA) (rp55A) (YS16A) YOL121C gene taxon:4932 20010119 SGD
+SGD S000005481 RPS19A GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein S19A (S16aA) (rp55A) (YS16A) YOL121C gene taxon:4932 20010118 SGD
+SGD S000005246 RPS19B GO:0005843 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein S19B (rp55B) (S16aB) (YS16B) YNL302C|RP55B gene taxon:4932 20010118 SGD
+SGD S000005246 RPS19B GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein S19B (rp55B) (S16aB) (YS16B) YNL302C|RP55B gene taxon:4932 20010118 SGD
+SGD S000005246 RPS19B GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein S19B (rp55B) (S16aB) (YS16B) YNL302C|RP55B gene taxon:4932 20010119 SGD
+SGD S000005246 RPS19B GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein S19B (rp55B) (S16aB) (YS16B) YNL302C|RP55B gene taxon:4932 20010118 SGD
+SGD S000004433 RPS1A GO:0005843 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein S1A (rp10A) YLR441C|RP10A gene taxon:4932 20010118 SGD
+SGD S000004433 RPS1A GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein S1A (rp10A) YLR441C|RP10A gene taxon:4932 20010118 SGD
+SGD S000004433 RPS1A GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein S1A (rp10A) YLR441C|RP10A gene taxon:4932 20010119 SGD
+SGD S000004433 RPS1A GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein S1A (rp10A) YLR441C|RP10A gene taxon:4932 20010118 SGD
+SGD S000004528 RPS1B GO:0005843 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein S1B (rp10B) YML063W|PLC2|RP10B gene taxon:4932 20010118 SGD
+SGD S000004528 RPS1B GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein S1B (rp10B) YML063W|PLC2|RP10B gene taxon:4932 20010118 SGD
+SGD S000004528 RPS1B GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein S1B (rp10B) YML063W|PLC2|RP10B gene taxon:4932 20010119 SGD
+SGD S000004528 RPS1B GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein S1B (rp10B) YML063W|PLC2|RP10B gene taxon:4932 20010118 SGD
+SGD S000003091 RPS2 GO:0005732 SGD_REF:S000079989|PMID:15590835 IPI SGD:S000003762 C ribosomal protein S2 (S4) (rp12) (YS5) YGL123W|RPS4|SUP138|SUP38|SUP44 gene taxon:4932 20050124 SGD
+SGD S000003091 RPS2 GO:0005843 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein S2 (S4) (rp12) (YS5) YGL123W|RPS4|SUP138|SUP38|SUP44 gene taxon:4932 20010118 SGD
+SGD S000003091 RPS2 GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein S2 (S4) (rp12) (YS5) YGL123W|RPS4|SUP138|SUP38|SUP44 gene taxon:4932 20010118 SGD
+SGD S000003091 RPS2 GO:0006450 SGD_REF:S000041585|PMID:8950190 IMP P ribosomal protein S2 (S4) (rp12) (YS5) YGL123W|RPS4|SUP138|SUP38|SUP44 gene taxon:4932 20001002 SGD
+SGD S000003091 RPS2 GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein S2 (S4) (rp12) (YS5) YGL123W|RPS4|SUP138|SUP38|SUP44 gene taxon:4932 20010119 SGD
+SGD S000003091 RPS2 GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein S2 (S4) (rp12) (YS5) YGL123W|RPS4|SUP138|SUP38|SUP44 gene taxon:4932 20010118 SGD
+SGD S000001007 RPS20 GO:0005843 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein S20 YHL015W|URP2 gene taxon:4932 20010118 SGD
+SGD S000001007 RPS20 GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein S20 YHL015W|URP2 gene taxon:4932 20010118 SGD
+SGD S000001007 RPS20 GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein S20 YHL015W|URP2 gene taxon:4932 20010119 SGD
+SGD S000001007 RPS20 GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein S20 YHL015W|URP2 gene taxon:4932 20010118 SGD
+SGD S000001765 RPS21A GO:0005843 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein S21A (S26A) (YS25) YKR057W|RPS25 gene taxon:4932 20010118 SGD
+SGD S000001765 RPS21A GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein S21A (S26A) (YS25) YKR057W|RPS25 gene taxon:4932 20010118 SGD
+SGD S000001765 RPS21A GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein S21A (S26A) (YS25) YKR057W|RPS25 gene taxon:4932 20010119 SGD
+SGD S000001765 RPS21A GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein S21A (S26A) (YS25) YKR057W|RPS25 gene taxon:4932 20010118 SGD
+SGD S000003672 RPS21B GO:0005843 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein S21B (S26B) (YS25) YJL136C gene taxon:4932 20010118 SGD
+SGD S000003672 RPS21B GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein S21B (S26B) (YS25) YJL136C gene taxon:4932 20010118 SGD
+SGD S000003672 RPS21B GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein S21B (S26B) (YS25) YJL136C gene taxon:4932 20010119 SGD
+SGD S000003672 RPS21B GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein S21B (S26B) (YS25) YJL136C gene taxon:4932 20010118 SGD
+SGD S000003726 RPS22A GO:0005843 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein S22A (S24A) (rp50) (YS22) YJL190C|RPS24 gene taxon:4932 20010118 SGD
+SGD S000003726 RPS22A GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein S22A (S24A) (rp50) (YS22) YJL190C|RPS24 gene taxon:4932 20010118 SGD
+SGD S000003726 RPS22A GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein S22A (S24A) (rp50) (YS22) YJL190C|RPS24 gene taxon:4932 20010119 SGD
+SGD S000003726 RPS22A GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein S22A (S24A) (rp50) (YS22) YJL190C|RPS24 gene taxon:4932 20010118 SGD
+SGD S000004359 RPS22B GO:0005843 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein S22B (S24B) (rp50) (YS22) YLR367W gene taxon:4932 20010118 SGD
+SGD S000004359 RPS22B GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein S22B (S24B) (rp50) (YS22) YLR367W gene taxon:4932 20010118 SGD
+SGD S000004359 RPS22B GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein S22B (S24B) (rp50) (YS22) YLR367W gene taxon:4932 20010119 SGD
+SGD S000004359 RPS22B GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein S22B (S24B) (rp50) (YS22) YLR367W gene taxon:4932 20010118 SGD
+SGD S000003350 RPS23A GO:0005843 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein S23A (S28A) (rp37) (YS14) YGR118W gene taxon:4932 20010118 SGD
+SGD S000003350 RPS23A GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein S23A (S28A) (rp37) (YS14) YGR118W gene taxon:4932 20010118 SGD
+SGD S000003350 RPS23A GO:0006450 SGD_REF:S000041585|PMID:8950190 IMP P ribosomal protein S23A (S28A) (rp37) (YS14) YGR118W gene taxon:4932 20001002 SGD
+SGD S000003350 RPS23A GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein S23A (S28A) (rp37) (YS14) YGR118W gene taxon:4932 20010119 SGD
+SGD S000003350 RPS23A GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein S23A (S28A) (rp37) (YS14) YGR118W gene taxon:4932 20010118 SGD
+SGD S000006336 RPS23B GO:0005843 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein S23B (S28B) (rp37) (YS14) YPR132W gene taxon:4932 20010118 SGD
+SGD S000006336 RPS23B GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein S23B (S28B) (rp37) (YS14) YPR132W gene taxon:4932 20010118 SGD
+SGD S000006336 RPS23B GO:0006450 SGD_REF:S000041585|PMID:8950190 IMP P ribosomal protein S23B (S28B) (rp37) (YS14) YPR132W gene taxon:4932 20001002 SGD
+SGD S000006336 RPS23B GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein S23B (S28B) (rp37) (YS14) YPR132W gene taxon:4932 20010119 SGD
+SGD S000006336 RPS23B GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein S23B (S28B) (rp37) (YS14) YPR132W gene taxon:4932 20010118 SGD
+SGD S000000876 RPS24A GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C ribosomal protein S24A YER074W|RPS24EA gene taxon:4932 20040928 SGD
+SGD S000000876 RPS24A GO:0005843 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein S24A YER074W|RPS24EA gene taxon:4932 20010118 SGD
+SGD S000000876 RPS24A GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein S24A YER074W|RPS24EA gene taxon:4932 20010118 SGD
+SGD S000000876 RPS24A GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein S24A YER074W|RPS24EA gene taxon:4932 20010119 SGD
+SGD S000000876 RPS24A GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein S24A YER074W|RPS24EA gene taxon:4932 20010118 SGD
+SGD S000001331 RPS24B GO:0005843 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein S24B YIL069C|RPS24EB gene taxon:4932 20010118 SGD
+SGD S000001331 RPS24B GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein S24B YIL069C|RPS24EB gene taxon:4932 20010118 SGD
+SGD S000001331 RPS24B GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein S24B YIL069C|RPS24EB gene taxon:4932 20010119 SGD
+SGD S000001331 RPS24B GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein S24B YIL069C|RPS24EB gene taxon:4932 20010118 SGD
+SGD S000003259 RPS25A GO:0005843 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein S25A (S31A) (rp45) (YS23) YGR027C|RPS31A gene taxon:4932 20010118 SGD
+SGD S000003259 RPS25A GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein S25A (S31A) (rp45) (YS23) YGR027C|RPS31A gene taxon:4932 20010118 SGD
+SGD S000003259 RPS25A GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein S25A (S31A) (rp45) (YS23) YGR027C|RPS31A gene taxon:4932 20010119 SGD
+SGD S000003259 RPS25A GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein S25A (S31A) (rp45) (YS23) YGR027C|RPS31A gene taxon:4932 20010118 SGD
+SGD S000004325 RPS25B GO:0005843 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein S25B (S31B) (rp45) (YS23) YLR333C gene taxon:4932 20010118 SGD
+SGD S000004325 RPS25B GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein S25B (S31B) (rp45) (YS23) YLR333C gene taxon:4932 20010118 SGD
+SGD S000004325 RPS25B GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein S25B (S31B) (rp45) (YS23) YLR333C gene taxon:4932 20010119 SGD
+SGD S000004325 RPS25B GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein S25B (S31B) (rp45) (YS23) YLR333C gene taxon:4932 20010118 SGD
+SGD S000003157 RPS26A GO:0005843 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein S26A YGL189C|RPS26 gene taxon:4932 20010118 SGD
+SGD S000003157 RPS26A GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein S26A YGL189C|RPS26 gene taxon:4932 20010118 SGD
+SGD S000003157 RPS26A GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein S26A YGL189C|RPS26 gene taxon:4932 20010119 SGD
+SGD S000003157 RPS26A GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein S26A YGL189C|RPS26 gene taxon:4932 20010118 SGD
+SGD S000000933 RPS26B GO:0005843 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein S26B YER131W gene taxon:4932 20010118 SGD
+SGD S000000933 RPS26B GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein S26B YER131W gene taxon:4932 20010118 SGD
+SGD S000000933 RPS26B GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein S26B YER131W gene taxon:4932 20010119 SGD
+SGD S000000933 RPS26B GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein S26B YER131W gene taxon:4932 20010118 SGD
+SGD S000001639 RPS27A GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C ribosomal protein S27A (rp61) (YS20) YKL156W gene taxon:4932 20020507 SGD
+SGD S000001639 RPS27A GO:0005843 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein S27A (rp61) (YS20) YKL156W gene taxon:4932 20010118 SGD
+SGD S000001639 RPS27A GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein S27A (rp61) (YS20) YKL156W gene taxon:4932 20010118 SGD
+SGD S000001639 RPS27A GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein S27A (rp61) (YS20) YKL156W gene taxon:4932 20010119 SGD
+SGD S000001639 RPS27A GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein S27A (rp61) (YS20) YKL156W gene taxon:4932 20010118 SGD
+SGD S000001063 RPS27B GO:0005843 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein S27B (rp61) (YS20) YHR021C gene taxon:4932 20010118 SGD
+SGD S000001063 RPS27B GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein S27B (rp61) (YS20) YHR021C gene taxon:4932 20010118 SGD
+SGD S000001063 RPS27B GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein S27B (rp61) (YS20) YHR021C gene taxon:4932 20010119 SGD
+SGD S000001063 RPS27B GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein S27B (rp61) (YS20) YHR021C gene taxon:4932 20010118 SGD
+SGD S000005693 RPS28A GO:0005843 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein S28A (S33A) (YS27) YOR167C|RPS33A gene taxon:4932 20010118 SGD
+SGD S000005693 RPS28A GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein S28A (S33A) (YS27) YOR167C|RPS33A gene taxon:4932 20010118 SGD
+SGD S000005693 RPS28A GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein S28A (S33A) (YS27) YOR167C|RPS33A gene taxon:4932 20010119 SGD
+SGD S000005693 RPS28A GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein S28A (S33A) (YS27) YOR167C|RPS33A gene taxon:4932 20010118 SGD
+SGD S000004254 RPS28B GO:0005843 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein S28B (S33B) (YS27) YLR264W|RPS33B gene taxon:4932 20010118 SGD
+SGD S000004254 RPS28B GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein S28B (S33B) (YS27) YLR264W|RPS33B gene taxon:4932 20010118 SGD
+SGD S000004254 RPS28B GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein S28B (S33B) (YS27) YLR264W|RPS33B gene taxon:4932 20010119 SGD
+SGD S000004254 RPS28B GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein S28B (S33B) (YS27) YLR264W|RPS33B gene taxon:4932 20010118 SGD
+SGD S000004380 RPS29A GO:0005843 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein S29A (S36A) (YS29) YLR388W gene taxon:4932 20010118 SGD
+SGD S000004380 RPS29A GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein S29A (S36A) (YS29) YLR388W gene taxon:4932 20010118 SGD
+SGD S000004380 RPS29A GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein S29A (S36A) (YS29) YLR388W gene taxon:4932 20010119 SGD
+SGD S000004380 RPS29A GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein S29A (S36A) (YS29) YLR388W gene taxon:4932 20010118 SGD
+SGD S000002219 RPS29B GO:0005843 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein S29B (S36B) (YS29) YDL061C|YS29B gene taxon:4932 20010118 SGD
+SGD S000002219 RPS29B GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein S29B (S36B) (YS29) YDL061C|YS29B gene taxon:4932 20010118 SGD
+SGD S000002219 RPS29B GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein S29B (S36B) (YS29) YDL061C|YS29B gene taxon:4932 20010119 SGD
+SGD S000002219 RPS29B GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein S29B (S36B) (YS29) YDL061C|YS29B gene taxon:4932 20010118 SGD
+SGD S000005122 RPS3 GO:0005843 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein S3 (rp13) (YS3) YNL178W|SUF14 gene taxon:4932 20010118 SGD
+SGD S000005122 RPS3 GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein S3 (rp13) (YS3) YNL178W|SUF14 gene taxon:4932 20010118 SGD
+SGD S000005122 RPS3 GO:0006974 SGD_REF:S000069743|PMID:11561734 IDA P ribosomal protein S3 (rp13) (YS3) YNL178W|SUF14 gene taxon:4932 20020823 SGD
+SGD S000005122 RPS3 GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein S3 (rp13) (YS3) YNL178W|SUF14 gene taxon:4932 20010119 SGD
+SGD S000005122 RPS3 GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein S3 (rp13) (YS3) YNL178W|SUF14 gene taxon:4932 20010118 SGD
+SGD S000004278 RPS30A GO:0005843 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein S30A YLR287C-A gene taxon:4932 20010118 SGD
+SGD S000004278 RPS30A GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein S30A YLR287C-A gene taxon:4932 20010118 SGD
+SGD S000004278 RPS30A GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein S30A YLR287C-A gene taxon:4932 20010119 SGD
+SGD S000004278 RPS30A GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein S30A YLR287C-A gene taxon:4932 20010118 SGD
+SGD S000005708 RPS30B GO:0005843 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein S30B YOR182C gene taxon:4932 20010118 SGD
+SGD S000005708 RPS30B GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein S30B YOR182C gene taxon:4932 20010118 SGD
+SGD S000005708 RPS30B GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein S30B YOR182C gene taxon:4932 20010119 SGD
+SGD S000005708 RPS30B GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein S30B YOR182C gene taxon:4932 20010118 SGD
+SGD S000004157 RPS31 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C also encodes a ubiquitin protein, ribosomal protein S31 (S37) (YS24) YLR167W|RPS37|UBI3 gene taxon:4932 20020507 SGD
+SGD S000004157 RPS31 GO:0005843 SGD_REF:S000058461|PMID:9559554 TAS C also encodes a ubiquitin protein, ribosomal protein S31 (S37) (YS24) YLR167W|RPS37|UBI3 gene taxon:4932 20010118 SGD
+SGD S000004157 RPS31 GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F also encodes a ubiquitin protein, ribosomal protein S31 (S37) (YS24) YLR167W|RPS37|UBI3 gene taxon:4932 20010118 SGD
+SGD S000004157 RPS31 GO:0031386 SGD_REF:S000056997|PMID:3038523 ISS F also encodes a ubiquitin protein, ribosomal protein S31 (S37) (YS24) YLR167W|RPS37|UBI3 gene taxon:4932 20050525 SGD
+SGD S000004157 RPS31 GO:0000028 SGD_REF:S000054410|PMID:9830035 IMP P also encodes a ubiquitin protein, ribosomal protein S31 (S37) (YS24) YLR167W|RPS37|UBI3 gene taxon:4932 20010118 SGD
+SGD S000004157 RPS31 GO:0016567 SGD_REF:S000049784|PMID:8035826 IMP P also encodes a ubiquitin protein, ribosomal protein S31 (S37) (YS24) YLR167W|RPS37|UBI3 gene taxon:4932 20050407 SGD
+SGD S000004157 RPS31 GO:0042254 SGD_REF:S000064966|PMID:2538753 IDA P also encodes a ubiquitin protein, ribosomal protein S31 (S37) (YS24) YLR167W|RPS37|UBI3 gene taxon:4932 20040719 SGD
+SGD S000004157 RPS31 GO:0043037 SGD_REF:S000058497 TAS P also encodes a ubiquitin protein, ribosomal protein S31 (S37) (YS24) YLR167W|RPS37|UBI3 gene taxon:4932 20010119 SGD
+SGD S000004157 RPS31 GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P also encodes a ubiquitin protein, ribosomal protein S31 (S37) (YS24) YLR167W|RPS37|UBI3 gene taxon:4932 20010118 SGD
+SGD S000003906 RPS4A GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C ribosomal protein S4A (YS6) (rp5) (S7A) YJR145C gene taxon:4932 20020507 SGD
+SGD S000003906 RPS4A GO:0005843 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein S4A (YS6) (rp5) (S7A) YJR145C gene taxon:4932 20010118 SGD
+SGD S000003906 RPS4A GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein S4A (YS6) (rp5) (S7A) YJR145C gene taxon:4932 20010118 SGD
+SGD S000003906 RPS4A GO:0030490 SGD_REF:S000073750|PMID:12837249 IMP P ribosomal protein S4A (YS6) (rp5) (S7A) YJR145C gene taxon:4932 20030805 SGD
+SGD S000003906 RPS4A GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein S4A (YS6) (rp5) (S7A) YJR145C gene taxon:4932 20010119 SGD
+SGD S000003906 RPS4A GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein S4A (YS6) (rp5) (S7A) YJR145C gene taxon:4932 20010118 SGD
+SGD S000001246 RPS4B GO:0005843 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein S4B (YS6) (rp5) (S7B) YHR203C gene taxon:4932 20010118 SGD
+SGD S000001246 RPS4B GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein S4B (YS6) (rp5) (S7B) YHR203C gene taxon:4932 20010118 SGD
+SGD S000001246 RPS4B GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P ribosomal protein S4B (YS6) (rp5) (S7B) YHR203C gene taxon:4932 20060227 SGD
+SGD S000001246 RPS4B GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein S4B (YS6) (rp5) (S7B) YHR203C gene taxon:4932 20010119 SGD
+SGD S000001246 RPS4B GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein S4B (YS6) (rp5) (S7B) YHR203C gene taxon:4932 20010118 SGD
+SGD S000003884 RPS5 GO:0005843 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein S5 (S2) (rp14) (YS8) YJR123W gene taxon:4932 20010118 SGD
+SGD S000003884 RPS5 GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein S5 (S2) (rp14) (YS8) YJR123W gene taxon:4932 20010118 SGD
+SGD S000003884 RPS5 GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein S5 (S2) (rp14) (YS8) YJR123W gene taxon:4932 20010119 SGD
+SGD S000003884 RPS5 GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein S5 (S2) (rp14) (YS8) YJR123W gene taxon:4932 20010118 SGD
+SGD S000006011 RPS6A GO:0005732 SGD_REF:S000079989|PMID:15590835 IPI SGD:S000003762 C ribosomal protein S6A (S10A) (rp9) (YS4) YPL090C gene taxon:4932 20050124 SGD
+SGD S000006011 RPS6A GO:0005843 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein S6A (S10A) (rp9) (YS4) YPL090C gene taxon:4932 20010118 SGD
+SGD S000006011 RPS6A GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein S6A (S10A) (rp9) (YS4) YPL090C gene taxon:4932 20010118 SGD
+SGD S000006011 RPS6A GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein S6A (S10A) (rp9) (YS4) YPL090C gene taxon:4932 20010119 SGD
+SGD S000006011 RPS6A GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein S6A (S10A) (rp9) (YS4) YPL090C gene taxon:4932 20010118 SGD
+SGD S000000385 RPS6B GO:0005732 SGD_REF:S000079989|PMID:15590835 IPI SGD:S000003762 C ribosomal gene product S6B (S10B) (rp9) (YS4) YBR181C|LPG18|RPS101|RPS102 gene taxon:4932 20050124 SGD
+SGD S000000385 RPS6B GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C ribosomal gene product S6B (S10B) (rp9) (YS4) YBR181C|LPG18|RPS101|RPS102 gene taxon:4932 20020507 SGD
+SGD S000000385 RPS6B GO:0005843 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal gene product S6B (S10B) (rp9) (YS4) YBR181C|LPG18|RPS101|RPS102 gene taxon:4932 20010118 SGD
+SGD S000000385 RPS6B GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal gene product S6B (S10B) (rp9) (YS4) YBR181C|LPG18|RPS101|RPS102 gene taxon:4932 20010118 SGD
+SGD S000000385 RPS6B GO:0043037 SGD_REF:S000058497 TAS P ribosomal gene product S6B (S10B) (rp9) (YS4) YBR181C|LPG18|RPS101|RPS102 gene taxon:4932 20010119 SGD
+SGD S000000385 RPS6B GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal gene product S6B (S10B) (rp9) (YS4) YBR181C|LPG18|RPS101|RPS102 gene taxon:4932 20010118 SGD
+SGD S000005622 RPS7A GO:0005732 SGD_REF:S000079989|PMID:15590835 IPI SGD:S000003762 C ribosomal protein S7A (rp30) YOR096W|RPS30 gene taxon:4932 20050124 SGD
+SGD S000005622 RPS7A GO:0005843 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein S7A (rp30) YOR096W|RPS30 gene taxon:4932 20010118 SGD
+SGD S000005622 RPS7A GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein S7A (rp30) YOR096W|RPS30 gene taxon:4932 20010118 SGD
+SGD S000005622 RPS7A GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein S7A (rp30) YOR096W|RPS30 gene taxon:4932 20010119 SGD
+SGD S000005622 RPS7A GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein S7A (rp30) YOR096W|RPS30 gene taxon:4932 20010118 SGD
+SGD S000005040 RPS7B GO:0005732 SGD_REF:S000079989|PMID:15590835 IPI SGD:S000003762 C ribosomal protein S7B (rp30) YNL096C gene taxon:4932 20050124 SGD
+SGD S000005040 RPS7B GO:0005843 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein S7B (rp30) YNL096C gene taxon:4932 20010118 SGD
+SGD S000005040 RPS7B GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein S7B (rp30) YNL096C gene taxon:4932 20010118 SGD
+SGD S000005040 RPS7B GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein S7B (rp30) YNL096C gene taxon:4932 20010119 SGD
+SGD S000005040 RPS7B GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein S7B (rp30) YNL096C gene taxon:4932 20010118 SGD
+SGD S000000168 RPS8A GO:0005843 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein S8A (S14A) (rp19) (YS9) YBL072C gene taxon:4932 20010118 SGD
+SGD S000000168 RPS8A GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein S8A (S14A) (rp19) (YS9) YBL072C gene taxon:4932 20010118 SGD
+SGD S000000168 RPS8A GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein S8A (S14A) (rp19) (YS9) YBL072C gene taxon:4932 20010119 SGD
+SGD S000000168 RPS8A GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein S8A (S14A) (rp19) (YS9) YBL072C gene taxon:4932 20010118 SGD
+SGD S000000904 RPS8B GO:0005843 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein S8B (S14B) (rp19) (YS9) YER102W gene taxon:4932 20010118 SGD
+SGD S000000904 RPS8B GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein S8B (S14B) (rp19) (YS9) YER102W gene taxon:4932 20010118 SGD
+SGD S000000904 RPS8B GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein S8B (S14B) (rp19) (YS9) YER102W gene taxon:4932 20010119 SGD
+SGD S000000904 RPS8B GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein S8B (S14B) (rp19) (YS9) YER102W gene taxon:4932 20010118 SGD
+SGD S000006002 RPS9A GO:0005732 SGD_REF:S000079989|PMID:15590835 IPI SGD:S000003762 C ribosomal protein S9A (S13) (rp21) (YS11) YPL081W gene taxon:4932 20050124 SGD
+SGD S000006002 RPS9A GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C ribosomal protein S9A (S13) (rp21) (YS11) YPL081W gene taxon:4932 20020507 SGD
+SGD S000006002 RPS9A GO:0005843 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein S9A (S13) (rp21) (YS11) YPL081W gene taxon:4932 20010118 SGD
+SGD S000006002 RPS9A GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein S9A (S13) (rp21) (YS11) YPL081W gene taxon:4932 20010118 SGD
+SGD S000006002 RPS9A GO:0006450 SGD_REF:S000040015|PMID:9733638 IMP P ribosomal protein S9A (S13) (rp21) (YS11) YPL081W gene taxon:4932 20001002 SGD
+SGD S000006002 RPS9A GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein S9A (S13) (rp21) (YS11) YPL081W gene taxon:4932 20010119 SGD
+SGD S000006002 RPS9A GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein S9A (S13) (rp21) (YS11) YPL081W gene taxon:4932 20010118 SGD
+SGD S000000393 RPS9B GO:0005732 SGD_REF:S000079989|PMID:15590835 IPI SGD:S000003762 C ribosomal protein S9B (S13) (rp21) (YS11) YBR189W|RPS13A|SUP46 gene taxon:4932 20050124 SGD
+SGD S000000393 RPS9B GO:0005843 SGD_REF:S000058461|PMID:9559554 TAS C ribosomal protein S9B (S13) (rp21) (YS11) YBR189W|RPS13A|SUP46 gene taxon:4932 20010118 SGD
+SGD S000000393 RPS9B GO:0003735 SGD_REF:S000058461|PMID:9559554 TAS F ribosomal protein S9B (S13) (rp21) (YS11) YBR189W|RPS13A|SUP46 gene taxon:4932 20010118 SGD
+SGD S000000393 RPS9B GO:0006450 SGD_REF:S000040015|PMID:9733638 IMP P ribosomal protein S9B (S13) (rp21) (YS11) YBR189W|RPS13A|SUP46 gene taxon:4932 20001002 SGD
+SGD S000000393 RPS9B GO:0043037 SGD_REF:S000058497 TAS P ribosomal protein S9B (S13) (rp21) (YS11) YBR189W|RPS13A|SUP46 gene taxon:4932 20010119 SGD
+SGD S000000393 RPS9B GO:0043037 SGD_REF:S000058461|PMID:9559554 TAS P ribosomal protein S9B (S13) (rp21) (YS11) YBR189W|RPS13A|SUP46 gene taxon:4932 20010118 SGD
+SGD S000001628 RPT1 GO:0008540 SGD_REF:S000039974|PMID:9741626 IPI C 26S protease subunit component (putative), ATPase YKL145W|CIM5|YTA3 gene taxon:4932 20050306 SGD
+SGD S000001628 RPT1 GO:0004175 SGD_REF:S000058463|PMID:9697412 TAS F 26S protease subunit component (putative), ATPase YKL145W|CIM5|YTA3 gene taxon:4932 20010118 SGD
+SGD S000001628 RPT1 GO:0004175 SGD_REF:S000058010|PMID:8982460 TAS F 26S protease subunit component (putative), ATPase YKL145W|CIM5|YTA3 gene taxon:4932 20010118 SGD
+SGD S000001628 RPT1 GO:0016887 SGD_REF:S000058463|PMID:9697412 TAS F 26S protease subunit component (putative), ATPase YKL145W|CIM5|YTA3 gene taxon:4932 20010118 SGD
+SGD S000001628 RPT1 GO:0016887 SGD_REF:S000065027|PMID:9724628 IDA F 26S protease subunit component (putative), ATPase YKL145W|CIM5|YTA3 gene taxon:4932 20050310 SGD
+SGD S000001628 RPT1 GO:0006511 SGD_REF:S000058463|PMID:9697412 TAS P 26S protease subunit component (putative), ATPase YKL145W|CIM5|YTA3 gene taxon:4932 20010118 SGD
+SGD S000001628 RPT1 GO:0006511 SGD_REF:S000058010|PMID:8982460 TAS P 26S protease subunit component (putative), ATPase YKL145W|CIM5|YTA3 gene taxon:4932 20010118 SGD
+SGD S000002165 RPT2 GO:0005634 SGD_REF:S000079924|PMID:15210724 IDA C one of the ATPase subunits of the proteasome YDL007W|YHS4|YTA5 gene taxon:4932 20050314 SGD
+SGD S000002165 RPT2 GO:0008540 SGD_REF:S000039974|PMID:9741626 IPI C one of the ATPase subunits of the proteasome YDL007W|YHS4|YTA5 gene taxon:4932 20050306 SGD
+SGD S000002165 RPT2 GO:0004175 SGD_REF:S000058463|PMID:9697412 TAS F one of the ATPase subunits of the proteasome YDL007W|YHS4|YTA5 gene taxon:4932 20010118 SGD
+SGD S000002165 RPT2 GO:0004175 SGD_REF:S000058010|PMID:8982460 TAS F one of the ATPase subunits of the proteasome YDL007W|YHS4|YTA5 gene taxon:4932 20010118 SGD
+SGD S000002165 RPT2 GO:0016887 SGD_REF:S000058463|PMID:9697412 TAS F one of the ATPase subunits of the proteasome YDL007W|YHS4|YTA5 gene taxon:4932 20010118 SGD
+SGD S000002165 RPT2 GO:0016887 SGD_REF:S000052814|PMID:7721833 IDA F one of the ATPase subunits of the proteasome YDL007W|YHS4|YTA5 gene taxon:4932 20050310 SGD
+SGD S000002165 RPT2 GO:0016887 SGD_REF:S000065027|PMID:9724628 IDA F one of the ATPase subunits of the proteasome YDL007W|YHS4|YTA5 gene taxon:4932 20050310 SGD
+SGD S000002165 RPT2 GO:0006511 SGD_REF:S000058463|PMID:9697412 TAS P one of the ATPase subunits of the proteasome YDL007W|YHS4|YTA5 gene taxon:4932 20010118 SGD
+SGD S000002165 RPT2 GO:0006511 SGD_REF:S000058010|PMID:8982460 TAS P one of the ATPase subunits of the proteasome YDL007W|YHS4|YTA5 gene taxon:4932 20010118 SGD
+SGD S000002802 RPT3 GO:0008540 SGD_REF:S000068750|PMID:11742986 IDA C YDR394W|YNT1|YTA2 gene taxon:4932 20020823 SGD
+SGD S000002802 RPT3 GO:0008540 SGD_REF:S000039974|PMID:9741626 IPI C YDR394W|YNT1|YTA2 gene taxon:4932 20050306 SGD
+SGD S000002802 RPT3 GO:0004175 SGD_REF:S000058463|PMID:9697412 TAS F YDR394W|YNT1|YTA2 gene taxon:4932 20010118 SGD
+SGD S000002802 RPT3 GO:0004175 SGD_REF:S000058010|PMID:8982460 TAS F YDR394W|YNT1|YTA2 gene taxon:4932 20010118 SGD
+SGD S000002802 RPT3 GO:0016887 SGD_REF:S000058463|PMID:9697412 TAS F YDR394W|YNT1|YTA2 gene taxon:4932 20010118 SGD
+SGD S000002802 RPT3 GO:0016887 SGD_REF:S000065027|PMID:9724628 IDA F YDR394W|YNT1|YTA2 gene taxon:4932 20050310 SGD
+SGD S000002802 RPT3 GO:0006511 SGD_REF:S000058463|PMID:9697412 TAS P YDR394W|YNT1|YTA2 gene taxon:4932 20010118 SGD
+SGD S000002802 RPT3 GO:0006511 SGD_REF:S000058010|PMID:8982460 TAS P YDR394W|YNT1|YTA2 gene taxon:4932 20010118 SGD
+SGD S000005785 RPT4 GO:0005634 SGD_REF:S000047509|PMID:10419517 IDA C 26S proteasome cap subunit component, ATPase YOR259C|CRL13|PCS1|SUG2 gene taxon:4932 20030207 SGD
+SGD S000005785 RPT4 GO:0008540 SGD_REF:S000068750|PMID:11742986 IDA C 26S proteasome cap subunit component, ATPase YOR259C|CRL13|PCS1|SUG2 gene taxon:4932 20020823 SGD
+SGD S000005785 RPT4 GO:0008540 SGD_REF:S000039974|PMID:9741626 IPI C 26S proteasome cap subunit component, ATPase YOR259C|CRL13|PCS1|SUG2 gene taxon:4932 20050306 SGD
+SGD S000005785 RPT4 GO:0004175 SGD_REF:S000058463|PMID:9697412 TAS F 26S proteasome cap subunit component, ATPase YOR259C|CRL13|PCS1|SUG2 gene taxon:4932 20010118 SGD
+SGD S000005785 RPT4 GO:0004175 SGD_REF:S000058010|PMID:8982460 TAS F 26S proteasome cap subunit component, ATPase YOR259C|CRL13|PCS1|SUG2 gene taxon:4932 20010118 SGD
+SGD S000005785 RPT4 GO:0016887 SGD_REF:S000058463|PMID:9697412 TAS F 26S proteasome cap subunit component, ATPase YOR259C|CRL13|PCS1|SUG2 gene taxon:4932 20010118 SGD
+SGD S000005785 RPT4 GO:0016887 SGD_REF:S000065027|PMID:9724628 IDA F 26S proteasome cap subunit component, ATPase YOR259C|CRL13|PCS1|SUG2 gene taxon:4932 20050310 SGD
+SGD S000005785 RPT4 GO:0006511 SGD_REF:S000058463|PMID:9697412 TAS P 26S proteasome cap subunit component, ATPase YOR259C|CRL13|PCS1|SUG2 gene taxon:4932 20010118 SGD
+SGD S000005785 RPT4 GO:0006511 SGD_REF:S000058010|PMID:8982460 TAS P 26S proteasome cap subunit component, ATPase YOR259C|CRL13|PCS1|SUG2 gene taxon:4932 20010118 SGD
+SGD S000005643 RPT5 GO:0008540 SGD_REF:S000068750|PMID:11742986 IDA C YOR117W|YTA1 gene taxon:4932 20020823 SGD
+SGD S000005643 RPT5 GO:0008540 SGD_REF:S000039974|PMID:9741626 IPI C YOR117W|YTA1 gene taxon:4932 20050306 SGD
+SGD S000005643 RPT5 GO:0004175 SGD_REF:S000058463|PMID:9697412 TAS F YOR117W|YTA1 gene taxon:4932 20010118 SGD
+SGD S000005643 RPT5 GO:0004175 SGD_REF:S000058010|PMID:8982460 TAS F YOR117W|YTA1 gene taxon:4932 20010118 SGD
+SGD S000005643 RPT5 GO:0016887 SGD_REF:S000058463|PMID:9697412 TAS F YOR117W|YTA1 gene taxon:4932 20010118 SGD
+SGD S000005643 RPT5 GO:0016887 SGD_REF:S000065027|PMID:9724628 IDA F YOR117W|YTA1 gene taxon:4932 20050310 SGD
+SGD S000005643 RPT5 GO:0006511 SGD_REF:S000058463|PMID:9697412 TAS P YOR117W|YTA1 gene taxon:4932 20010118 SGD
+SGD S000005643 RPT5 GO:0006511 SGD_REF:S000058010|PMID:8982460 TAS P YOR117W|YTA1 gene taxon:4932 20010118 SGD
+SGD S000003016 RPT6 GO:0005634 SGD_REF:S000047509|PMID:10419517 IDA C ATPase YGL048C|CIM3|CRL3|SCB68|SUG1 gene taxon:4932 20030207 SGD
+SGD S000003016 RPT6 GO:0008540 SGD_REF:S000068750|PMID:11742986 IDA C ATPase YGL048C|CIM3|CRL3|SCB68|SUG1 gene taxon:4932 20020823 SGD
+SGD S000003016 RPT6 GO:0008540 SGD_REF:S000039974|PMID:9741626 IPI C ATPase YGL048C|CIM3|CRL3|SCB68|SUG1 gene taxon:4932 20050306 SGD
+SGD S000003016 RPT6 GO:0004175 SGD_REF:S000058463|PMID:9697412 TAS F ATPase YGL048C|CIM3|CRL3|SCB68|SUG1 gene taxon:4932 20010118 SGD
+SGD S000003016 RPT6 GO:0004175 SGD_REF:S000058010|PMID:8982460 TAS F ATPase YGL048C|CIM3|CRL3|SCB68|SUG1 gene taxon:4932 20010118 SGD
+SGD S000003016 RPT6 GO:0016887 SGD_REF:S000058463|PMID:9697412 TAS F ATPase YGL048C|CIM3|CRL3|SCB68|SUG1 gene taxon:4932 20010118 SGD
+SGD S000003016 RPT6 GO:0016887 SGD_REF:S000065027|PMID:9724628 IDA F ATPase YGL048C|CIM3|CRL3|SCB68|SUG1 gene taxon:4932 20050310 SGD
+SGD S000003016 RPT6 GO:0006511 SGD_REF:S000058463|PMID:9697412 TAS P ATPase YGL048C|CIM3|CRL3|SCB68|SUG1 gene taxon:4932 20010118 SGD
+SGD S000003016 RPT6 GO:0006511 SGD_REF:S000058010|PMID:8982460 TAS P ATPase YGL048C|CIM3|CRL3|SCB68|SUG1 gene taxon:4932 20010118 SGD
+SGD S000004738 RRB1 GO:0005730 SGD_REF:S000056415|PMID:10684247 IDA C YMR131C gene taxon:4932 20020620 SGD
+SGD S000004738 RRB1 GO:0005554 SGD_REF:S000069584 ND F YMR131C gene taxon:4932 20030108 SGD
+SGD S000004738 RRB1 GO:0007046 SGD_REF:S000069167|PMID:11728313 IMP P YMR131C gene taxon:4932 20030108 SGD
+SGD S000004738 RRB1 GO:0007046 SGD_REF:S000069167|PMID:11728313 IPI P YMR131C gene taxon:4932 20030108 SGD
+SGD S000001415 RRD1 GO:0000267 SGD_REF:S000065029|PMID:7813481 IDA C YIL153W|YPA1 gene taxon:4932 20030123 SGD
+SGD S000001415 RRD1 GO:0005634 SGD_REF:S000080935|PMID:15150670 IDA C YIL153W|YPA1 gene taxon:4932 20050309 SGD
+SGD S000001415 RRD1 GO:0005737 SGD_REF:S000080935|PMID:15150670 IDA C YIL153W|YPA1 gene taxon:4932 20050309 SGD
+SGD S000001415 RRD1 GO:0008601 SGD_REF:S000039114|PMID:10660069 IGI F YIL153W|YPA1 gene taxon:4932 20010118 SGD
+SGD S000001415 RRD1 GO:0008601 SGD_REF:S000081883|PMID:12952889 IMP F YIL153W|YPA1 gene taxon:4932 20050616 SGD
+SGD S000001415 RRD1 GO:0008601 SGD_REF:S000039114|PMID:10660069 ISS F YIL153W|YPA1 gene taxon:4932 20010118 SGD
+SGD S000001415 RRD1 GO:0006281 SGD_REF:S000064637|PMID:9705277 IDA P YIL153W|YPA1 gene taxon:4932 20030123 SGD
+SGD S000001415 RRD1 GO:0006281 SGD_REF:S000080935|PMID:15150670 IMP P YIL153W|YPA1 gene taxon:4932 20050309 SGD
+SGD S000001415 RRD1 GO:0006970 SGD_REF:S000039114|PMID:10660069 IMP P YIL153W|YPA1 gene taxon:4932 20010118 SGD
+SGD S000001415 RRD1 GO:0006970 SGD_REF:S000039114|PMID:10660069 IGI P YIL153W|YPA1 gene taxon:4932 20010118 SGD
+SGD S000001415 RRD1 GO:0030472 SGD_REF:S000060029|PMID:11262194 IMP P YIL153W|YPA1 gene taxon:4932 20040128 SGD
+SGD S000006073 RRD2 GO:0000267 SGD_REF:S000065029|PMID:7813481 IDA C YPL152W|YPA2 gene taxon:4932 20030123 SGD
+SGD S000006073 RRD2 GO:0005829 SGD_REF:S000065030|PMID:9737869 TAS C YPL152W|YPA2 gene taxon:4932 20030123 SGD
+SGD S000006073 RRD2 GO:0008601 SGD_REF:S000039114|PMID:10660069 IGI F YPL152W|YPA2 gene taxon:4932 20010118 SGD
+SGD S000006073 RRD2 GO:0008601 SGD_REF:S000039114|PMID:10660069 ISS F YPL152W|YPA2 gene taxon:4932 20010118 SGD
+SGD S000006073 RRD2 GO:0008601 SGD_REF:S000081883|PMID:12952889 IMP F YPL152W|YPA2 gene taxon:4932 20050616 SGD
+SGD S000006073 RRD2 GO:0006970 SGD_REF:S000039114|PMID:10660069 IMP P YPL152W|YPA2 gene taxon:4932 20010118 SGD
+SGD S000006073 RRD2 GO:0006970 SGD_REF:S000039114|PMID:10660069 IGI P YPL152W|YPA2 gene taxon:4932 20010118 SGD
+SGD S000006073 RRD2 GO:0030472 SGD_REF:S000060029|PMID:11262194 IMP P YPL152W|YPA2 gene taxon:4932 20040128 SGD
+SGD S000001080 RRF1 GO:0005739 SGD_REF:S000046633|PMID:9746366 ISS C mitochondrial ribosome recycling factor YHR038W|FIL1|KIM4 gene taxon:4932 20010118 SGD
+SGD S000001080 RRF1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C mitochondrial ribosome recycling factor YHR038W|FIL1|KIM4 gene taxon:4932 20040929 SGD
+SGD S000001080 RRF1 GO:0008079 SGD_REF:S000046633|PMID:9746366 ISS F mitochondrial ribosome recycling factor YHR038W|FIL1|KIM4 gene taxon:4932 20010118 SGD
+SGD S000001080 RRF1 GO:0006412 SGD_REF:S000046633|PMID:9746366 IMP P mitochondrial ribosome recycling factor YHR038W|FIL1|KIM4 gene taxon:4932 20010118 SGD
+SGD S000001080 RRF1 GO:0006412 SGD_REF:S000046633|PMID:9746366 ISS P mitochondrial ribosome recycling factor YHR038W|FIL1|KIM4 gene taxon:4932 20010118 SGD
+SGD S000002375 RRI1 GO:0008180 SGD_REF:S000071602|PMID:12186635 TAS C COP9 signalosome (CSN) subunit YDL216C|CSN5|JAB1 gene taxon:4932 20021115 SGD
+SGD S000002375 RRI1 GO:0008180 SGD_REF:S000071980|PMID:12446563 IDA C COP9 signalosome (CSN) subunit YDL216C|CSN5|JAB1 gene taxon:4932 20030325 SGD
+SGD S000002375 RRI1 GO:0004222 SGD_REF:S000071600|PMID:12183637 IMP F COP9 signalosome (CSN) subunit YDL216C|CSN5|JAB1 gene taxon:4932 20021114 SGD
+SGD S000002375 RRI1 GO:0000338 SGD_REF:S000071980|PMID:12446563 IMP P COP9 signalosome (CSN) subunit YDL216C|CSN5|JAB1 gene taxon:4932 20030325 SGD
+SGD S000002375 RRI1 GO:0000338 SGD_REF:S000071602|PMID:12186635 IMP P COP9 signalosome (CSN) subunit YDL216C|CSN5|JAB1 gene taxon:4932 20021115 SGD
+SGD S000002375 RRI1 GO:0000754 SGD_REF:S000071980|PMID:12446563 IMP P COP9 signalosome (CSN) subunit YDL216C|CSN5|JAB1 gene taxon:4932 20030325 SGD
+SGD S000005477 RRI2 GO:0008180 SGD_REF:S000071602|PMID:12186635 TAS C COP9 signalosome (CSN) subunit YOL117W|CSN10 gene taxon:4932 20021115 SGD
+SGD S000005477 RRI2 GO:0008180 SGD_REF:S000071980|PMID:12446563 IDA C COP9 signalosome (CSN) subunit YOL117W|CSN10 gene taxon:4932 20030325 SGD
+SGD S000005477 RRI2 GO:0005554 SGD_REF:S000069584 ND F COP9 signalosome (CSN) subunit YOL117W|CSN10 gene taxon:4932 20030325 SGD
+SGD S000005477 RRI2 GO:0000338 SGD_REF:S000071980|PMID:12446563 IMP P COP9 signalosome (CSN) subunit YOL117W|CSN10 gene taxon:4932 20030325 SGD
+SGD S000005477 RRI2 GO:0000338 SGD_REF:S000071602|PMID:12186635 IMP P COP9 signalosome (CSN) subunit YOL117W|CSN10 gene taxon:4932 20021115 SGD
+SGD S000005477 RRI2 GO:0000754 SGD_REF:S000071980|PMID:12446563 IGI P COP9 signalosome (CSN) subunit YOL117W|CSN10 gene taxon:4932 20030325 SGD
+SGD S000001073 RRM3 GO:0005724 SGD_REF:S000041506|PMID:10693764 IPI C DNA helicase YHR031C|RTT104 gene taxon:4932 20030403 SGD
+SGD S000001073 RRM3 GO:0003678 SGD_REF:S000041506|PMID:10693764 IMP F DNA helicase YHR031C|RTT104 gene taxon:4932 20011205 SGD
+SGD S000001073 RRM3 GO:0003678 SGD_REF:S000041506|PMID:10693764 ISS F DNA helicase YHR031C|RTT104 gene taxon:4932 20011205 SGD
+SGD S000001073 RRM3 GO:0004003 SGD_REF:S000069903|PMID:12050116 IDA F DNA helicase YHR031C|RTT104 gene taxon:4932 20030226 SGD
+SGD S000001073 RRM3 GO:0000002 SGD_REF:S000081767|PMID:15907372 IGI SGD:S000004526 P DNA helicase YHR031C|RTT104 gene taxon:4932 20050620 SGD
+SGD S000001073 RRM3 GO:0006260 SGD_REF:S000041506|PMID:10693764 IMP P DNA helicase YHR031C|RTT104 gene taxon:4932 20011205 SGD
+SGD S000001073 RRM3 GO:0006260 SGD_REF:S000041506|PMID:10693764 IGI P DNA helicase YHR031C|RTT104 gene taxon:4932 20011205 SGD
+SGD S000001073 RRM3 GO:0006260 SGD_REF:S000041506|PMID:10693764 IPI P DNA helicase YHR031C|RTT104 gene taxon:4932 20011205 SGD
+SGD S000000121 RRN10 GO:0000500 SGD_REF:S000061332|PMID:11500378 TAS C upstream activation factor subunit YBL025W gene taxon:4932 20011212 SGD
+SGD S000000121 RRN10 GO:0000182 SGD_REF:S000061332|PMID:11500378 TAS F upstream activation factor subunit YBL025W gene taxon:4932 20011212 SGD
+SGD S000000121 RRN10 GO:0003701 SGD_REF:S000058402|PMID:9932458 TAS F upstream activation factor subunit YBL025W gene taxon:4932 20010118 SGD
+SGD S000000121 RRN10 GO:0006360 SGD_REF:S000058402|PMID:9932458 TAS P upstream activation factor subunit YBL025W gene taxon:4932 20010118 SGD
+SGD S000004507 RRN11 GO:0000120 SGD_REF:S000058402|PMID:9932458 TAS C rDNA transcription factor component YML043C gene taxon:4932 20010118 SGD
+SGD S000004507 RRN11 GO:0003701 SGD_REF:S000058402|PMID:9932458 TAS F rDNA transcription factor component YML043C gene taxon:4932 20010118 SGD
+SGD S000004507 RRN11 GO:0006360 SGD_REF:S000058402|PMID:9932458 TAS P rDNA transcription factor component YML043C gene taxon:4932 20010118 SGD
+SGD S000001608 RRN3 GO:0000120 SGD_REF:S000058402|PMID:9932458 TAS C DNA independent RNA polymerase I transcription factor YKL125W gene taxon:4932 20010118 SGD
+SGD S000001608 RRN3 GO:0003701 SGD_REF:S000058402|PMID:9932458 TAS F DNA independent RNA polymerase I transcription factor YKL125W gene taxon:4932 20010118 SGD
+SGD S000001608 RRN3 GO:0006360 SGD_REF:S000058402|PMID:9932458 TAS P DNA independent RNA polymerase I transcription factor YKL125W gene taxon:4932 20010118 SGD
+SGD S000004131 RRN5 GO:0000500 SGD_REF:S000061332|PMID:11500378 TAS C UAF member (upstream activation factor) along with Rrn9p and Rrn10p, transcription factor YLR141W gene taxon:4932 20011212 SGD
+SGD S000004131 RRN5 GO:0000182 SGD_REF:S000061332|PMID:11500378 TAS F UAF member (upstream activation factor) along with Rrn9p and Rrn10p, transcription factor YLR141W gene taxon:4932 20011212 SGD
+SGD S000004131 RRN5 GO:0003701 SGD_REF:S000058402|PMID:9932458 TAS F UAF member (upstream activation factor) along with Rrn9p and Rrn10p, transcription factor YLR141W gene taxon:4932 20010118 SGD
+SGD S000004131 RRN5 GO:0006360 SGD_REF:S000058402|PMID:9932458 TAS P UAF member (upstream activation factor) along with Rrn9p and Rrn10p, transcription factor YLR141W gene taxon:4932 20010118 SGD
+SGD S000000110 RRN6 GO:0000120 SGD_REF:S000058402|PMID:9932458 TAS C yeast Pol I core factor (CF) also composed of Rrn11p, Rrn7p and TATA-binding protein YBL014C gene taxon:4932 20010118 SGD
+SGD S000000110 RRN6 GO:0003701 SGD_REF:S000058402|PMID:9932458 TAS F yeast Pol I core factor (CF) also composed of Rrn11p, Rrn7p and TATA-binding protein YBL014C gene taxon:4932 20010118 SGD
+SGD S000000110 RRN6 GO:0006360 SGD_REF:S000058402|PMID:9932458 TAS P yeast Pol I core factor (CF) also composed of Rrn11p, Rrn7p and TATA-binding protein YBL014C gene taxon:4932 20010118 SGD
+SGD S000003562 RRN7 GO:0000120 SGD_REF:S000058402|PMID:9932458 TAS C yeast Pol I core factor (CF) also composed of Rrn11p, Rrn6p and TATA-binding protein YJL025W gene taxon:4932 20010118 SGD
+SGD S000003562 RRN7 GO:0003701 SGD_REF:S000058402|PMID:9932458 TAS F yeast Pol I core factor (CF) also composed of Rrn11p, Rrn6p and TATA-binding protein YJL025W gene taxon:4932 20010118 SGD
+SGD S000003562 RRN7 GO:0006360 SGD_REF:S000058402|PMID:9932458 TAS P yeast Pol I core factor (CF) also composed of Rrn11p, Rrn6p and TATA-binding protein YJL025W gene taxon:4932 20010118 SGD
+SGD S000004883 RRN9 GO:0000500 SGD_REF:S000061332|PMID:11500378 TAS C upstream activation factor subunit YMR270C gene taxon:4932 20011212 SGD
+SGD S000004883 RRN9 GO:0000182 SGD_REF:S000061332|PMID:11500378 TAS F upstream activation factor subunit YMR270C gene taxon:4932 20011212 SGD
+SGD S000004883 RRN9 GO:0003701 SGD_REF:S000058402|PMID:9932458 TAS F upstream activation factor subunit YMR270C gene taxon:4932 20010118 SGD
+SGD S000004883 RRN9 GO:0006360 SGD_REF:S000058402|PMID:9932458 TAS P upstream activation factor subunit YMR270C gene taxon:4932 20010118 SGD
+SGD S000002494 RRP1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YDR087C gene taxon:4932 20031028 SGD
+SGD S000002494 RRP1 GO:0005730 SGD_REF:S000074185|PMID:14562095 IDA C YDR087C gene taxon:4932 20031028 SGD
+SGD S000002494 RRP1 GO:0005554 SGD_REF:S000069584 ND F YDR087C gene taxon:4932 20021206 SGD
+SGD S000002494 RRP1 GO:0006364 SGD_REF:S000045009|PMID:3549696 IMP P YDR087C gene taxon:4932 20010118 SGD
+SGD S000005933 RRP12 GO:0005634 SGD_REF:S000074529|PMID:14729571 IDA C YPL012W gene taxon:4932 20041004 SGD
+SGD S000005933 RRP12 GO:0005840 SGD_REF:S000071346|PMID:12067653 TAS C YPL012W gene taxon:4932 20021002 SGD
+SGD S000005933 RRP12 GO:0005554 SGD_REF:S000069584 ND F YPL012W gene taxon:4932 20030108 SGD
+SGD S000005933 RRP12 GO:0007046 SGD_REF:S000071346|PMID:12067653 TAS P YPL012W gene taxon:4932 20021002 SGD
+SGD S000005933 RRP12 GO:0030490 SGD_REF:S000071346|PMID:12067653 TAS P YPL012W gene taxon:4932 20021002 SGD
+SGD S000001565 RRP14 GO:0005730 SGD_REF:S000061434|PMID:11489916 IDA C YKL082C gene taxon:4932 20030512 SGD
+SGD S000001565 RRP14 GO:0005554 SGD_REF:S000069584 ND F YKL082C gene taxon:4932 20030407 SGD
+SGD S000001565 RRP14 GO:0030468 SGD_REF:S000075214|PMID:14690591 IPI P YKL082C gene taxon:4932 20040105 SGD
+SGD S000001565 RRP14 GO:0042273 SGD_REF:S000076470|PMID:15100437 IPI P YKL082C gene taxon:4932 20050407 SGD
+SGD S000006347 RRP15 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YPR143W gene taxon:4932 20031028 SGD
+SGD S000006347 RRP15 GO:0005730 SGD_REF:S000074185|PMID:14562095 IDA C YPR143W gene taxon:4932 20031028 SGD
+SGD S000006347 RRP15 GO:0005554 SGD_REF:S000069584 ND F YPR143W gene taxon:4932 20021126 SGD
+SGD S000006347 RRP15 GO:0030489 SGD_REF:S000081140|PMID:15769876 IMP P YPR143W gene taxon:4932 20050415 SGD
+SGD S000006347 RRP15 GO:0030489 SGD_REF:S000081140|PMID:15769876 IPI P YPR143W gene taxon:4932 20050415 SGD
+SGD S000002820 RRP17 GO:0005737 SGD_REF:S000056415|PMID:10684247 IDA C YDR412W gene taxon:4932 20010301 SGD
+SGD S000002820 RRP17 GO:0005554 SGD_REF:S000069584 ND F YDR412W gene taxon:4932 20010119 SGD
+SGD S000002820 RRP17 GO:0006364 SGD_REF:S000073750|PMID:12837249 IMP P YDR412W gene taxon:4932 20030805 SGD
+SGD S000001107 RRP3 GO:0005730 SGD_REF:S000058443|PMID:10690410 TAS C weak RNA-dependent ATPase activity which is not specific for rRNA YHR065C gene taxon:4932 20010118 SGD
+SGD S000001107 RRP3 GO:0004004 SGD_REF:S000058443|PMID:10690410 TAS F weak RNA-dependent ATPase activity which is not specific for rRNA YHR065C gene taxon:4932 20010118 SGD
+SGD S000001107 RRP3 GO:0006365 SGD_REF:S000058443|PMID:10690410 TAS P weak RNA-dependent ATPase activity which is not specific for rRNA YHR065C gene taxon:4932 20010118 SGD
+SGD S000001111 RRP4 GO:0000176 SGD_REF:S000041327|PMID:10465791 IDA C 3'-5' exoribonuclease, 3'-5' exoribonuclease complex component with Rrp4p, Rrp41p, Rrp42p and Dis3p (Rrp44p) YHR069C gene taxon:4932 20010118 SGD
+SGD S000001111 RRP4 GO:0000177 SGD_REF:S000041327|PMID:10465791 IDA C 3'-5' exoribonuclease, 3'-5' exoribonuclease complex component with Rrp4p, Rrp41p, Rrp42p and Dis3p (Rrp44p) YHR069C gene taxon:4932 20010118 SGD
+SGD S000001111 RRP4 GO:0000175 SGD_REF:S000058443|PMID:10690410 TAS F 3'-5' exoribonuclease, 3'-5' exoribonuclease complex component with Rrp4p, Rrp41p, Rrp42p and Dis3p (Rrp44p) YHR069C gene taxon:4932 20010118 SGD
+SGD S000001111 RRP4 GO:0006365 SGD_REF:S000058443|PMID:10690410 TAS P 3'-5' exoribonuclease, 3'-5' exoribonuclease complex component with Rrp4p, Rrp41p, Rrp42p and Dis3p (Rrp44p) YHR069C gene taxon:4932 20010118 SGD
+SGD S000001111 RRP4 GO:0006402 SGD_REF:S000058465|PMID:9482746 IMP P 3'-5' exoribonuclease, 3'-5' exoribonuclease complex component with Rrp4p, Rrp41p, Rrp42p and Dis3p (Rrp44p) YHR069C gene taxon:4932 20010118 SGD
+SGD S000005502 RRP40 GO:0000176 SGD_REF:S000041327|PMID:10465791 IDA C 3' -> 5' exoribonuclease YOL142W gene taxon:4932 20010118 SGD
+SGD S000005502 RRP40 GO:0000177 SGD_REF:S000041327|PMID:10465791 IDA C 3' -> 5' exoribonuclease YOL142W gene taxon:4932 20010118 SGD
+SGD S000005502 RRP40 GO:0000175 SGD_REF:S000058443|PMID:10690410 TAS F 3' -> 5' exoribonuclease YOL142W gene taxon:4932 20010118 SGD
+SGD S000005502 RRP40 GO:0006365 SGD_REF:S000058443|PMID:10690410 TAS P 3' -> 5' exoribonuclease YOL142W gene taxon:4932 20010118 SGD
+SGD S000005502 RRP40 GO:0006402 SGD_REF:S000041327|PMID:10465791 IPI P 3' -> 5' exoribonuclease YOL142W gene taxon:4932 20010118 SGD
+SGD S000005502 RRP40 GO:0042255 SGD_REF:S000076076|PMID:15116429 TAS P 3' -> 5' exoribonuclease YOL142W gene taxon:4932 20040618 SGD
+SGD S000002269 RRP42 GO:0000176 SGD_REF:S000041327|PMID:10465791 IDA C exosome 3->5 exoribonuclease complex component with Rrp4p, Rrp41p, Rrp43p and Dis3p (Rrp44p) YDL111C gene taxon:4932 20010118 SGD
+SGD S000002269 RRP42 GO:0000177 SGD_REF:S000041327|PMID:10465791 IDA C exosome 3->5 exoribonuclease complex component with Rrp4p, Rrp41p, Rrp43p and Dis3p (Rrp44p) YDL111C gene taxon:4932 20010118 SGD
+SGD S000002269 RRP42 GO:0000175 SGD_REF:S000058443|PMID:10690410 TAS F exosome 3->5 exoribonuclease complex component with Rrp4p, Rrp41p, Rrp43p and Dis3p (Rrp44p) YDL111C gene taxon:4932 20010118 SGD
+SGD S000002269 RRP42 GO:0006365 SGD_REF:S000058443|PMID:10690410 TAS P exosome 3->5 exoribonuclease complex component with Rrp4p, Rrp41p, Rrp43p and Dis3p (Rrp44p) YDL111C gene taxon:4932 20010118 SGD
+SGD S000002269 RRP42 GO:0006402 SGD_REF:S000041327|PMID:10465791 IPI P exosome 3->5 exoribonuclease complex component with Rrp4p, Rrp41p, Rrp43p and Dis3p (Rrp44p) YDL111C gene taxon:4932 20010118 SGD
+SGD S000000631 RRP43 GO:0000176 SGD_REF:S000041327|PMID:10465791 IDA C exosome 3->5 exoribonuclease complex component with Rrp4p, Rrp41p, Rrp42p and Dis3p (Rrp44p) YCR035C gene taxon:4932 20010118 SGD
+SGD S000000631 RRP43 GO:0000177 SGD_REF:S000041327|PMID:10465791 IDA C exosome 3->5 exoribonuclease complex component with Rrp4p, Rrp41p, Rrp42p and Dis3p (Rrp44p) YCR035C gene taxon:4932 20010118 SGD
+SGD S000000631 RRP43 GO:0000175 SGD_REF:S000058443|PMID:10690410 TAS F exosome 3->5 exoribonuclease complex component with Rrp4p, Rrp41p, Rrp42p and Dis3p (Rrp44p) YCR035C gene taxon:4932 20010118 SGD
+SGD S000000631 RRP43 GO:0006365 SGD_REF:S000058443|PMID:10690410 TAS P exosome 3->5 exoribonuclease complex component with Rrp4p, Rrp41p, Rrp42p and Dis3p (Rrp44p) YCR035C gene taxon:4932 20010118 SGD
+SGD S000000631 RRP43 GO:0006402 SGD_REF:S000041327|PMID:10465791 IPI P exosome 3->5 exoribonuclease complex component with Rrp4p, Rrp41p, Rrp42p and Dis3p (Rrp44p) YCR035C gene taxon:4932 20010118 SGD
+SGD S000002688 RRP45 GO:0000176 SGD_REF:S000041327|PMID:10465791 IDA C 3'->5' exoribonuclease YDR280W gene taxon:4932 20010118 SGD
+SGD S000002688 RRP45 GO:0000177 SGD_REF:S000041327|PMID:10465791 IDA C 3'->5' exoribonuclease YDR280W gene taxon:4932 20010118 SGD
+SGD S000002688 RRP45 GO:0000175 SGD_REF:S000058443|PMID:10690410 TAS F 3'->5' exoribonuclease YDR280W gene taxon:4932 20010118 SGD
+SGD S000002688 RRP45 GO:0006365 SGD_REF:S000058443|PMID:10690410 TAS P 3'->5' exoribonuclease YDR280W gene taxon:4932 20010118 SGD
+SGD S000002688 RRP45 GO:0006402 SGD_REF:S000041327|PMID:10465791 IPI P 3'->5' exoribonuclease YDR280W gene taxon:4932 20010118 SGD
+SGD S000003327 RRP46 GO:0000176 SGD_REF:S000041327|PMID:10465791 IDA C 3'->5' exoribonuclease YGR095C gene taxon:4932 20010118 SGD
+SGD S000003327 RRP46 GO:0000177 SGD_REF:S000041327|PMID:10465791 IDA C 3'->5' exoribonuclease YGR095C gene taxon:4932 20010118 SGD
+SGD S000003327 RRP46 GO:0000175 SGD_REF:S000058443|PMID:10690410 TAS F 3'->5' exoribonuclease YGR095C gene taxon:4932 20010118 SGD
+SGD S000003327 RRP46 GO:0006365 SGD_REF:S000058443|PMID:10690410 TAS P 3'->5' exoribonuclease YGR095C gene taxon:4932 20010118 SGD
+SGD S000003327 RRP46 GO:0006402 SGD_REF:S000041327|PMID:10465791 IPI P 3'->5' exoribonuclease YGR095C gene taxon:4932 20010118 SGD
+SGD S000004842 RRP5 GO:0005730 SGD_REF:S000058443|PMID:10690410 TAS C U3 snoRNP protein YMR229C gene taxon:4932 20010118 SGD
+SGD S000004842 RRP5 GO:0005732 SGD_REF:S000070145|PMID:12068309 IPI C U3 snoRNP protein YMR229C gene taxon:4932 20031215 SGD
+SGD S000004842 RRP5 GO:0003723 SGD_REF:S000058443|PMID:10690410 TAS F U3 snoRNP protein YMR229C gene taxon:4932 20010118 SGD
+SGD S000004842 RRP5 GO:0030515 SGD_REF:S000070145|PMID:12068309 IPI F U3 snoRNP protein YMR229C gene taxon:4932 20030224 SGD
+SGD S000004842 RRP5 GO:0042134 SGD_REF:S000079754|PMID:15523097 IDA F U3 snoRNP protein YMR229C gene taxon:4932 20050526 SGD
+SGD S000004842 RRP5 GO:0006364 SGD_REF:S000058443|PMID:10690410 TAS P U3 snoRNP protein YMR229C gene taxon:4932 20010118 SGD
+SGD S000004842 RRP5 GO:0006365 SGD_REF:S000079754|PMID:15523097 IPI P U3 snoRNP protein YMR229C gene taxon:4932 20050526 SGD
+SGD S000004842 RRP5 GO:0030490 SGD_REF:S000070145|PMID:12068309 IPI P U3 snoRNP protein YMR229C gene taxon:4932 20020905 SGD
+SGD S000005527 RRP6 GO:0000176 SGD_REF:S000041327|PMID:10465791 IDA C YOR001W gene taxon:4932 20010118 SGD
+SGD S000005527 RRP6 GO:0000175 SGD_REF:S000058443|PMID:10690410 TAS F YOR001W gene taxon:4932 20010118 SGD
+SGD S000005527 RRP6 GO:0006365 SGD_REF:S000058443|PMID:10690410 TAS P YOR001W gene taxon:4932 20010118 SGD
+SGD S000005527 RRP6 GO:0006402 SGD_REF:S000081206|PMID:15713618 IMP P YOR001W gene taxon:4932 20050511 SGD
+SGD S000005527 RRP6 GO:0006402 SGD_REF:S000073903|PMID:12897126 IMP P YOR001W gene taxon:4932 20050511 SGD
+SGD S000000536 RRP7 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YCL031C gene taxon:4932 20031028 SGD
+SGD S000000536 RRP7 GO:0005730 SGD_REF:S000074185|PMID:14562095 IDA C YCL031C gene taxon:4932 20031028 SGD
+SGD S000000536 RRP7 GO:0005554 SGD_REF:S000069584 ND F YCL031C gene taxon:4932 20021206 SGD
+SGD S000000536 RRP7 GO:0000028 SGD_REF:S000058443|PMID:10690410 TAS P YCL031C gene taxon:4932 20010118 SGD
+SGD S000000536 RRP7 GO:0006365 SGD_REF:S000058443|PMID:10690410 TAS P YCL031C gene taxon:4932 20010118 SGD
+SGD S000002490 RRP8 GO:0005730 SGD_REF:S000040189|PMID:10864042 IDA C nucleolar protein required for efficient processing of pre-rRNA at site A2; methyltransferase homolog YDR083W gene taxon:4932 20020807 SGD
+SGD S000002490 RRP8 GO:0008168 SGD_REF:S000040189|PMID:10864042 ISS F nucleolar protein required for efficient processing of pre-rRNA at site A2; methyltransferase homolog YDR083W gene taxon:4932 20020807 SGD
+SGD S000002490 RRP8 GO:0008168 SGD_REF:S000040189|PMID:10864042 IMP F nucleolar protein required for efficient processing of pre-rRNA at site A2; methyltransferase homolog YDR083W gene taxon:4932 20020807 SGD
+SGD S000002490 RRP8 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P nucleolar protein required for efficient processing of pre-rRNA at site A2; methyltransferase homolog YDR083W gene taxon:4932 20060203 SGD
+SGD S000002490 RRP8 GO:0006364 SGD_REF:S000040189|PMID:10864042 IGI P nucleolar protein required for efficient processing of pre-rRNA at site A2; methyltransferase homolog YDR083W gene taxon:4932 20020807 SGD
+SGD S000002490 RRP8 GO:0006364 SGD_REF:S000040189|PMID:10864042 IMP P nucleolar protein required for efficient processing of pre-rRNA at site A2; methyltransferase homolog YDR083W gene taxon:4932 20020807 SGD
+SGD S000006341 RRP9 GO:0005732 SGD_REF:S000058443|PMID:10690410 TAS C U3 snoRNP protein YPR137W gene taxon:4932 20010118 SGD
+SGD S000006341 RRP9 GO:0005732 SGD_REF:S000070145|PMID:12068309 IPI C U3 snoRNP protein YPR137W gene taxon:4932 20030224 SGD
+SGD S000006341 RRP9 GO:0030532 SGD_REF:S000058443|PMID:10690410 TAS C U3 snoRNP protein YPR137W gene taxon:4932 20020219 SGD
+SGD S000006341 RRP9 GO:0030515 SGD_REF:S000059590|PMID:11105764 IPI F U3 snoRNP protein YPR137W gene taxon:4932 20030224 SGD
+SGD S000006341 RRP9 GO:0000154 SGD_REF:S000058443|PMID:10690410 TAS P U3 snoRNP protein YPR137W gene taxon:4932 20010118 SGD
+SGD S000006341 RRP9 GO:0006365 SGD_REF:S000058443|PMID:10690410 TAS P U3 snoRNP protein YPR137W gene taxon:4932 20010118 SGD
+SGD S000006341 RRP9 GO:0030490 SGD_REF:S000070145|PMID:12068309 IPI P U3 snoRNP protein YPR137W gene taxon:4932 20020905 SGD
+SGD S000005820 RRS1 GO:0005634 SGD_REF:S000045899|PMID:10688653 IDA C YOR294W gene taxon:4932 20010118 SGD
+SGD S000005820 RRS1 GO:0005554 SGD_REF:S000069584 ND F YOR294W gene taxon:4932 20010119 SGD
+SGD S000005820 RRS1 GO:0006364 SGD_REF:S000070294|PMID:12048200 TAS P YOR294W gene taxon:4932 20030110 SGD
+SGD S000005820 RRS1 GO:0007046 SGD_REF:S000045899|PMID:10688653 IMP P YOR294W gene taxon:4932 20010118 SGD
+SGD S000006114 RSA1 GO:0005654 SGD_REF:S000048972|PMID:10567587 IDA C YPL193W gene taxon:4932 20010118 SGD
+SGD S000006114 RSA1 GO:0005554 SGD_REF:S000069584 ND F YPL193W gene taxon:4932 20021210 SGD
+SGD S000006114 RSA1 GO:0000027 SGD_REF:S000048972|PMID:10567587 IMP P YPL193W gene taxon:4932 20010118 SGD
+SGD S000004211 RSA3 GO:0005730 SGD_REF:S000074185|PMID:14562095 IDA C YLR221C gene taxon:4932 20031028 SGD
+SGD S000004211 RSA3 GO:0030687 SGD_REF:S000076168|PMID:15126390 IDA C YLR221C gene taxon:4932 20040526 SGD
+SGD S000004211 RSA3 GO:0005554 SGD_REF:S000069584 ND F YLR221C gene taxon:4932 20021125 SGD
+SGD S000004211 RSA3 GO:0000027 SGD_REF:S000076168|PMID:15126390 IGI P YLR221C gene taxon:4932 20040526 SGD
+SGD S000004211 RSA3 GO:0000027 SGD_REF:S000076168|PMID:15126390 IMP P YLR221C gene taxon:4932 20040526 SGD
+SGD S000004211 RSA3 GO:0000027 SGD_REF:S000076168|PMID:15126390 IPI P YLR221C gene taxon:4932 20040526 SGD
+SGD S000000668 RSA4 GO:0005730 SGD_REF:S000087089|PMID:16221974 IDA C YCR072C gene taxon:4932 20051108 SGD
+SGD S000000668 RSA4 GO:0005554 SGD_REF:S000069584 ND F YCR072C gene taxon:4932 20051108 SGD
+SGD S000000668 RSA4 GO:0000027 SGD_REF:S000087089|PMID:16221974 IMP P YCR072C gene taxon:4932 20051108 SGD
+SGD S000005575 RSB1 GO:0005783 SGD_REF:S000071185|PMID:12034738 IDA C YOR049C gene taxon:4932 20020923 SGD
+SGD S000005575 RSB1 GO:0005886 SGD_REF:S000071185|PMID:12034738 IDA C YOR049C gene taxon:4932 20020923 SGD
+SGD S000005575 RSB1 GO:0016021 SGD_REF:S000071185|PMID:12034738 IDA C YOR049C gene taxon:4932 20020923 SGD
+SGD S000005575 RSB1 GO:0004012 SGD_REF:S000071185|PMID:12034738 IDA F YOR049C gene taxon:4932 20020923 SGD
+SGD S000005575 RSB1 GO:0004012 SGD_REF:S000071185|PMID:12034738 ISS F YOR049C gene taxon:4932 20020923 SGD
+SGD S000005575 RSB1 GO:0015908 SGD_REF:S000071185|PMID:12034738 IDA P YOR049C gene taxon:4932 20020924 SGD
+SGD S000005575 RSB1 GO:0045332 SGD_REF:S000081314|PMID:15342785 IMP P YOR049C gene taxon:4932 20050420 SGD
+SGD S000003288 RSC1 GO:0016586 SGD_REF:S000055568|PMID:10619019 IPI C RSC complex member YGR056W gene taxon:4932 20041006 SGD
+SGD S000003288 RSC1 GO:0005554 SGD_REF:S000069584 ND F RSC complex member YGR056W gene taxon:4932 20010119 SGD
+SGD S000003288 RSC1 GO:0006303 SGD_REF:S000081821|PMID:15870268 IPI SGD:S000004837 P RSC complex member YGR056W gene taxon:4932 20051020 SGD
+SGD S000003288 RSC1 GO:0006338 SGD_REF:S000058466|PMID:10025404 IDA P RSC complex member YGR056W gene taxon:4932 20010118 SGD
+SGD S000004349 RSC2 GO:0016586 SGD_REF:S000052087|PMID:8980231 IPI C RSC complex member YLR357W gene taxon:4932 20041006 SGD
+SGD S000004349 RSC2 GO:0005554 SGD_REF:S000069584 ND F RSC complex member YLR357W gene taxon:4932 20010119 SGD
+SGD S000004349 RSC2 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P RSC complex member YLR357W gene taxon:4932 20060203 SGD
+SGD S000004349 RSC2 GO:0006303 SGD_REF:S000081821|PMID:15870268 IPI SGD:S000004837 P RSC complex member YLR357W gene taxon:4932 20051020 SGD
+SGD S000004349 RSC2 GO:0006338 SGD_REF:S000058466|PMID:10025404 IDA P RSC complex member YLR357W gene taxon:4932 20010118 SGD
+SGD S000004349 RSC2 GO:0007062 SGD_REF:S000075541|PMID:14729968 IMP P RSC complex member YLR357W gene taxon:4932 20040714 SGD
+SGD S000002711 RSC3 GO:0005634 SGD_REF:S000069459|PMID:11914276 IDA C YDR303C gene taxon:4932 20020507 SGD
+SGD S000002711 RSC3 GO:0016586 SGD_REF:S000060732|PMID:11336698 IPI C YDR303C gene taxon:4932 20010625 SGD
+SGD S000002711 RSC3 GO:0003677 SGD_REF:S000060732|PMID:11336698 ISS F YDR303C gene taxon:4932 20010625 SGD
+SGD S000002711 RSC3 GO:0000074 SGD_REF:S000060732|PMID:11336698 IMP P YDR303C gene taxon:4932 20010625 SGD
+SGD S000002711 RSC3 GO:0000074 SGD_REF:S000060732|PMID:11336698 IGI P YDR303C gene taxon:4932 20010625 SGD
+SGD S000002711 RSC3 GO:0006355 SGD_REF:S000060732|PMID:11336698 IMP P YDR303C gene taxon:4932 20010625 SGD
+SGD S000001098 RSC30 GO:0016586 SGD_REF:S000060732|PMID:11336698 IPI C YHR056C gene taxon:4932 20010625 SGD
+SGD S000001098 RSC30 GO:0003677 SGD_REF:S000060732|PMID:11336698 ISS F YHR056C gene taxon:4932 20010625 SGD
+SGD S000001098 RSC30 GO:0006303 SGD_REF:S000081821|PMID:15870268 IDA P YHR056C gene taxon:4932 20051020 SGD
+SGD S000001098 RSC30 GO:0006303 SGD_REF:S000081821|PMID:15870268 IMP P YHR056C gene taxon:4932 20051020 SGD
+SGD S000001098 RSC30 GO:0006355 SGD_REF:S000060732|PMID:11336698 IMP P YHR056C gene taxon:4932 20010625 SGD
+SGD S000001716 RSC4 GO:0016586 SGD_REF:S000052087|PMID:8980231 IPI C RSC complex member YKR008W gene taxon:4932 20041006 SGD
+SGD S000001716 RSC4 GO:0005554 SGD_REF:S000069584 ND F RSC complex member YKR008W gene taxon:4932 20010119 SGD
+SGD S000001716 RSC4 GO:0006338 SGD_REF:S000058466|PMID:10025404 IDA P RSC complex member YKR008W gene taxon:4932 20010118 SGD
+SGD S000004023 RSC58 GO:0016586 SGD_REF:S000070225|PMID:12052880 IDA C 58KDa Subunit of RSC Chromatin Remodeling Complex YLR033W gene taxon:4932 20020925 SGD
+SGD S000004023 RSC58 GO:0005554 SGD_REF:S000069584 ND F 58KDa Subunit of RSC Chromatin Remodeling Complex YLR033W gene taxon:4932 20021029 SGD
+SGD S000004023 RSC58 GO:0006338 SGD_REF:S000070225|PMID:12052880 IDA P 58KDa Subunit of RSC Chromatin Remodeling Complex YLR033W gene taxon:4932 20020925 SGD
+SGD S000000648 RSC6 GO:0016586 SGD_REF:S000052087|PMID:8980231 IPI C YCR052W gene taxon:4932 20041006 SGD
+SGD S000000648 RSC6 GO:0005554 SGD_REF:S000069584 ND F YCR052W gene taxon:4932 20010119 SGD
+SGD S000000648 RSC6 GO:0006338 SGD_REF:S000052087|PMID:8980231 ISS P YCR052W gene taxon:4932 20010118 SGD
+SGD S000000648 RSC6 GO:0006338 SGD_REF:S000058466|PMID:10025404 IDA P YCR052W gene taxon:4932 20010118 SGD
+SGD S000001933 RSC8 GO:0005634 SGD_REF:S000069459|PMID:11914276 IDA C YFR037C|SWH3 gene taxon:4932 20020507 SGD
+SGD S000001933 RSC8 GO:0016586 SGD_REF:S000052087|PMID:8980231 IPI C YFR037C|SWH3 gene taxon:4932 20041006 SGD
+SGD S000001933 RSC8 GO:0005554 SGD_REF:S000069584 ND F YFR037C|SWH3 gene taxon:4932 20010119 SGD
+SGD S000001933 RSC8 GO:0006303 SGD_REF:S000081821|PMID:15870268 IDA P YFR037C|SWH3 gene taxon:4932 20051020 SGD
+SGD S000001933 RSC8 GO:0006303 SGD_REF:S000081821|PMID:15870268 IMP P YFR037C|SWH3 gene taxon:4932 20051020 SGD
+SGD S000001933 RSC8 GO:0006338 SGD_REF:S000052087|PMID:8980231 ISS P YFR037C|SWH3 gene taxon:4932 20010118 SGD
+SGD S000001933 RSC8 GO:0006338 SGD_REF:S000058466|PMID:10025404 IDA P YFR037C|SWH3 gene taxon:4932 20010118 SGD
+SGD S000004596 RSC9 GO:0016586 SGD_REF:S000069534|PMID:11931764 IDA C YML127W gene taxon:4932 20041006 SGD
+SGD S000004596 RSC9 GO:0003682 SGD_REF:S000069534|PMID:11931764 IPI F YML127W gene taxon:4932 20021018 SGD
+SGD S000004596 RSC9 GO:0006338 SGD_REF:S000069534|PMID:11931764 IPI P YML127W gene taxon:4932 20021018 SGD
+SGD S000004596 RSC9 GO:0006357 SGD_REF:S000069534|PMID:11931764 IMP P YML127W gene taxon:4932 20021018 SGD
+SGD S000004596 RSC9 GO:0009303 SGD_REF:S000069534|PMID:11931764 IMP P YML127W gene taxon:4932 20021018 SGD
+SGD S000004513 RSE1 GO:0005686 SGD_REF:S000041866|PMID:10369685 IPI C YML049C gene taxon:4932 20021001 SGD
+SGD S000004513 RSE1 colocalizes_with GO:0005686 SGD_REF:S000080993|PMID:15565172 IDA C YML049C gene taxon:4932 20051006 SGD
+SGD S000004513 RSE1 GO:0005686 SGD_REF:S000069986|PMID:11804584 IDA C YML049C gene taxon:4932 20020621 SGD
+SGD S000004513 RSE1 GO:0030620 SGD_REF:S000041866|PMID:10369685 IPI F YML049C gene taxon:4932 20021001 SGD
+SGD S000004513 RSE1 GO:0000245 SGD_REF:S000041866|PMID:10369685 IDA P YML049C gene taxon:4932 20021001 SGD
+SGD S000004513 RSE1 GO:0000398 SGD_REF:S000047738|PMID:9819400 IMP P YML049C gene taxon:4932 20021001 SGD
+SGD S000004513 RSE1 GO:0000398 SGD_REF:S000047738|PMID:9819400 IGI P YML049C gene taxon:4932 20021001 SGD
+SGD S000004632 RSF1 GO:0005634 SGD_REF:S000073691|PMID:12734673 IDA C YMR030W gene taxon:4932 20031014 SGD
+SGD S000004632 RSF1 GO:0005739 SGD_REF:S000073691|PMID:12734673 IDA C YMR030W gene taxon:4932 20031014 SGD
+SGD S000004632 RSF1 GO:0005554 SGD_REF:S000069584 ND F YMR030W gene taxon:4932 20031014 SGD
+SGD S000004632 RSF1 GO:0006366 SGD_REF:S000073691|PMID:12734673 IMP P YMR030W gene taxon:4932 20031014 SGD
+SGD S000004632 RSF1 GO:0006390 SGD_REF:S000073691|PMID:12734673 IMP P YMR030W gene taxon:4932 20031014 SGD
+SGD S000004632 RSF1 GO:0009060 SGD_REF:S000073691|PMID:12734673 IMP P YMR030W gene taxon:4932 20031014 SGD
+SGD S000004632 RSF1 GO:0019722 SGD_REF:S000051482|PMID:9407035 IGI P YMR030W gene taxon:4932 20030212 SGD
+SGD S000003888 RSF2 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YJR127C|ZMS1 gene taxon:4932 20031028 SGD
+SGD S000003888 RSF2 GO:0003700 SGD_REF:S000073045|PMID:12584194 ISS SGD:S000002624 F YJR127C|ZMS1 gene taxon:4932 20030428 SGD
+SGD S000003888 RSF2 GO:0045449 SGD_REF:S000086803|PMID:16208474 IMP P YJR127C|ZMS1 gene taxon:4932 20051014 SGD
+SGD S000002448 RSM10 GO:0005763 SGD_REF:S000060645|PMID:11278769 IDA C mitochondrial ribosome small subunit component YDR041W gene taxon:4932 20010918 SGD
+SGD S000002448 RSM10 GO:0003735 SGD_REF:S000060645|PMID:11278769 IDA F mitochondrial ribosome small subunit component YDR041W gene taxon:4932 20010918 SGD
+SGD S000002448 RSM10 GO:0043037 SGD_REF:S000060645|PMID:11278769 IDA P mitochondrial ribosome small subunit component YDR041W gene taxon:4932 20010918 SGD
+SGD S000000852 RSM18 GO:0005763 SGD_REF:S000060645|PMID:11278769 IDA C mitochondrial ribosome small subunit component YER050C gene taxon:4932 20010918 SGD
+SGD S000000852 RSM18 GO:0003735 SGD_REF:S000060645|PMID:11278769 IDA F mitochondrial ribosome small subunit component YER050C gene taxon:4932 20010918 SGD
+SGD S000000852 RSM18 GO:0043037 SGD_REF:S000060645|PMID:11278769 IDA P mitochondrial ribosome small subunit component YER050C gene taxon:4932 20010918 SGD
+SGD S000005320 RSM19 GO:0005763 SGD_REF:S000060645|PMID:11278769 IDA C mitochondrial ribosome small subunit component YNR037C gene taxon:4932 20010918 SGD
+SGD S000005320 RSM19 GO:0003735 SGD_REF:S000060645|PMID:11278769 IDA F mitochondrial ribosome small subunit component YNR037C gene taxon:4932 20010918 SGD
+SGD S000005320 RSM19 GO:0043037 SGD_REF:S000060645|PMID:11278769 IDA P mitochondrial ribosome small subunit component YNR037C gene taxon:4932 20010918 SGD
+SGD S000001638 RSM22 GO:0005763 SGD_REF:S000060645|PMID:11278769 IDA C mitochondrial ribosome small subunit component YKL155C gene taxon:4932 20010918 SGD
+SGD S000001638 RSM22 GO:0003735 SGD_REF:S000060645|PMID:11278769 IDA F mitochondrial ribosome small subunit component YKL155C gene taxon:4932 20010918 SGD
+SGD S000001638 RSM22 GO:0043037 SGD_REF:S000060645|PMID:11278769 IDA P mitochondrial ribosome small subunit component YKL155C gene taxon:4932 20010918 SGD
+SGD S000003097 RSM23 GO:0005763 SGD_REF:S000060645|PMID:11278769 IDA C ATPase (putative), mitochondrial ribosome small subunit component YGL129C gene taxon:4932 20010918 SGD
+SGD S000003097 RSM23 GO:0003735 SGD_REF:S000060645|PMID:11278769 IDA F ATPase (putative), mitochondrial ribosome small subunit component YGL129C gene taxon:4932 20010918 SGD
+SGD S000003097 RSM23 GO:0043037 SGD_REF:S000060645|PMID:11278769 IDA P ATPase (putative), mitochondrial ribosome small subunit component YGL129C gene taxon:4932 20010918 SGD
+SGD S000002582 RSM24 GO:0005763 SGD_REF:S000060645|PMID:11278769 IDA C mitochondrial ribosome small subunit component YDR175C gene taxon:4932 20010918 SGD
+SGD S000002582 RSM24 GO:0003735 SGD_REF:S000060645|PMID:11278769 IDA F mitochondrial ribosome small subunit component YDR175C gene taxon:4932 20010918 SGD
+SGD S000002582 RSM24 GO:0009060 SGD_REF:S000060148|PMID:10929718 IMP P mitochondrial ribosome small subunit component YDR175C gene taxon:4932 20020806 SGD
+SGD S000002582 RSM24 GO:0009060 SGD_REF:S000060148|PMID:10929718 IEP P mitochondrial ribosome small subunit component YDR175C gene taxon:4932 20020806 SGD
+SGD S000002582 RSM24 GO:0043037 SGD_REF:S000060645|PMID:11278769 IDA P mitochondrial ribosome small subunit component YDR175C gene taxon:4932 20010918 SGD
+SGD S000001355 RSM25 GO:0005763 SGD_REF:S000060645|PMID:11278769 IDA C mitochondrial ribosome small subunit component YIL093C gene taxon:4932 20010918 SGD
+SGD S000001355 RSM25 GO:0003735 SGD_REF:S000060645|PMID:11278769 IDA F mitochondrial ribosome small subunit component YIL093C gene taxon:4932 20010918 SGD
+SGD S000001355 RSM25 GO:0043037 SGD_REF:S000060645|PMID:11278769 IDA P mitochondrial ribosome small subunit component YIL093C gene taxon:4932 20010918 SGD
+SGD S000003862 RSM26 GO:0005763 SGD_REF:S000060645|PMID:11278769 IDA C mitochondrial ribosome small subunit component YJR101W gene taxon:4932 20010918 SGD
+SGD S000003862 RSM26 GO:0003735 SGD_REF:S000060645|PMID:11278769 IDA F mitochondrial ribosome small subunit component YJR101W gene taxon:4932 20010918 SGD
+SGD S000003862 RSM26 GO:0043037 SGD_REF:S000060645|PMID:11278769 IDA P mitochondrial ribosome small subunit component YJR101W gene taxon:4932 20010918 SGD
+SGD S000003447 RSM27 GO:0005763 SGD_REF:S000060645|PMID:11278769 IDA C mitochondrial ribosome small subunit component YGR215W gene taxon:4932 20010918 SGD
+SGD S000003447 RSM27 GO:0003735 SGD_REF:S000060645|PMID:11278769 IDA F mitochondrial ribosome small subunit component YGR215W gene taxon:4932 20010918 SGD
+SGD S000003447 RSM27 GO:0043037 SGD_REF:S000060645|PMID:11278769 IDA P mitochondrial ribosome small subunit component YGR215W gene taxon:4932 20010918 SGD
+SGD S000002902 RSM28 GO:0005763 SGD_REF:S000080846|PMID:15701796 IDA C Mitochondrial ribosomal small subunit protein YDR494W gene taxon:4932 20050301 SGD
+SGD S000002902 RSM28 GO:0003735 SGD_REF:S000080846|PMID:15701796 IDA F Mitochondrial ribosomal small subunit protein YDR494W gene taxon:4932 20050301 SGD
+SGD S000002902 RSM28 GO:0006413 SGD_REF:S000080846|PMID:15701796 IGI P Mitochondrial ribosomal small subunit protein YDR494W gene taxon:4932 20050301 SGD
+SGD S000002902 RSM28 GO:0043037 SGD_REF:S000080846|PMID:15701796 IGI P Mitochondrial ribosomal small subunit protein YDR494W gene taxon:4932 20050301 SGD
+SGD S000002902 RSM28 GO:0043037 SGD_REF:S000080846|PMID:15701796 IPI P Mitochondrial ribosomal small subunit protein YDR494W gene taxon:4932 20050301 SGD
+SGD S000003874 RSM7 GO:0005763 SGD_REF:S000060645|PMID:11278769 IDA C mitochondrial ribosome small subunit component YJR113C gene taxon:4932 20010918 SGD
+SGD S000003874 RSM7 GO:0003735 SGD_REF:S000060645|PMID:11278769 IDA F mitochondrial ribosome small subunit component YJR113C gene taxon:4932 20010918 SGD
+SGD S000003874 RSM7 GO:0043037 SGD_REF:S000060645|PMID:11278769 IDA P mitochondrial ribosome small subunit component YJR113C gene taxon:4932 20010918 SGD
+SGD S000004879 RSN1 GO:0008372 SGD_REF:S000069584 ND C YMR266W gene taxon:4932 20021125 SGD
+SGD S000004879 RSN1 GO:0005554 SGD_REF:S000069584 ND F YMR266W gene taxon:4932 20021125 SGD
+SGD S000004879 RSN1 GO:0000004 SGD_REF:S000069584 ND P YMR266W gene taxon:4932 20021125 SGD
+SGD S000000927 RSP5 GO:0000151 SGD_REF:S000053994|PMID:9108033 IDA C YER125W|MDP1|MUT2|NPI1|SMM1|UBY1 gene taxon:4932 20021210 SGD
+SGD S000000927 RSP5 GO:0005737 SGD_REF:S000077431|PMID:14657247 IDA C YER125W|MDP1|MUT2|NPI1|SMM1|UBY1 gene taxon:4932 20050125 SGD
+SGD S000000927 RSP5 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YER125W|MDP1|MUT2|NPI1|SMM1|UBY1 gene taxon:4932 20040928 SGD
+SGD S000000927 RSP5 GO:0005794 SGD_REF:S000077431|PMID:14657247 IDA C YER125W|MDP1|MUT2|NPI1|SMM1|UBY1 gene taxon:4932 20050125 SGD
+SGD S000000927 RSP5 GO:0005886 SGD_REF:S000077431|PMID:14657247 IDA C YER125W|MDP1|MUT2|NPI1|SMM1|UBY1 gene taxon:4932 20050125 SGD
+SGD S000000927 RSP5 GO:0010008 SGD_REF:S000077431|PMID:14657247 IDA C YER125W|MDP1|MUT2|NPI1|SMM1|UBY1 gene taxon:4932 20050125 SGD
+SGD S000000927 RSP5 GO:0004842 SGD_REF:S000053994|PMID:9108033 IDA F YER125W|MDP1|MUT2|NPI1|SMM1|UBY1 gene taxon:4932 20010118 SGD
+SGD S000000927 RSP5 GO:0000209 SGD_REF:S000053994|PMID:9108033 IDA P YER125W|MDP1|MUT2|NPI1|SMM1|UBY1 gene taxon:4932 20010118 SGD
+SGD S000000927 RSP5 GO:0006333 SGD_REF:S000071545|PMID:12399376 IMP P YER125W|MDP1|MUT2|NPI1|SMM1|UBY1 gene taxon:4932 20021115 SGD
+SGD S000000927 RSP5 GO:0006350 SGD_REF:S000073465|PMID:12821147 TAS P YER125W|MDP1|MUT2|NPI1|SMM1|UBY1 gene taxon:4932 20041005 SGD
+SGD S000000927 RSP5 GO:0006406 SGD_REF:S000073904|PMID:12839499 IMP P YER125W|MDP1|MUT2|NPI1|SMM1|UBY1 gene taxon:4932 20050314 SGD
+SGD S000000927 RSP5 GO:0006513 SGD_REF:S000053994|PMID:9108033 IDA P YER125W|MDP1|MUT2|NPI1|SMM1|UBY1 gene taxon:4932 20010118 SGD
+SGD S000000927 RSP5 GO:0006897 SGD_REF:S000073465|PMID:12821147 TAS P YER125W|MDP1|MUT2|NPI1|SMM1|UBY1 gene taxon:4932 20041005 SGD
+SGD S000000927 RSP5 GO:0010142 SGD_REF:S000081445|PMID:15827618 IMP P YER125W|MDP1|MUT2|NPI1|SMM1|UBY1 gene taxon:4932 20050715 SGD
+SGD S000003384 RSR1 GO:0005886 SGD_REF:S000044100|PMID:8723349 IDA C YGR152C|BUD1 gene taxon:4932 20021201 SGD
+SGD S000003384 RSR1 GO:0005935 SGD_REF:S000077144|PMID:15282802 IDA C YGR152C|BUD1 gene taxon:4932 20041008 SGD
+SGD S000003384 RSR1 GO:0003924 SGD_REF:S000039621|PMID:1910037 IDA F YGR152C|BUD1 gene taxon:4932 20021201 SGD
+SGD S000003384 RSR1 GO:0003924 SGD_REF:S000055611|PMID:9759491 TAS F YGR152C|BUD1 gene taxon:4932 20010118 SGD
+SGD S000003384 RSR1 GO:0004871 SGD_REF:S000058399|PMID:9891811 TAS F YGR152C|BUD1 gene taxon:4932 20010118 SGD
+SGD S000003384 RSR1 GO:0000282 SGD_REF:S000055611|PMID:9759491 TAS P YGR152C|BUD1 gene taxon:4932 20010302 SGD
+SGD S000003384 RSR1 GO:0007120 SGD_REF:S000040385|PMID:2690082 TAS P YGR152C|BUD1 gene taxon:4932 20010118 SGD
+SGD S000003384 RSR1 GO:0007120 SGD_REF:S000042162|PMID:2065354 TAS P YGR152C|BUD1 gene taxon:4932 20010118 SGD
+SGD S000003384 RSR1 GO:0007121 SGD_REF:S000040385|PMID:2690082 TAS P YGR152C|BUD1 gene taxon:4932 20010118 SGD
+SGD S000003384 RSR1 GO:0007121 SGD_REF:S000042162|PMID:2065354 TAS P YGR152C|BUD1 gene taxon:4932 20010118 SGD
+SGD S000003384 RSR1 GO:0007264 SGD_REF:S000058399|PMID:9891811 TAS P YGR152C|BUD1 gene taxon:4932 20010118 SGD
+SGD S000003445 RTA1 GO:0016021 SGD_REF:S000072825|PMID:12524434 ISS C YGR213C gene taxon:4932 20030409 SGD
+SGD S000003445 RTA1 GO:0016021 SGD_REF:S000047493|PMID:8660468 ISS C YGR213C gene taxon:4932 20020801 SGD
+SGD S000003445 RTA1 GO:0005554 SGD_REF:S000069584 ND F YGR213C gene taxon:4932 20020801 SGD
+SGD S000003445 RTA1 GO:0000004 SGD_REF:S000069584 ND P YGR213C gene taxon:4932 20020801 SGD
+SGD S000003213 RTF1 GO:0005634 SGD_REF:S000080456|PMID:15643076 IDA C nuclear protein YGL244W|CSL3 gene taxon:4932 20050228 SGD
+SGD S000003213 RTF1 GO:0008023 SGD_REF:S000071357|PMID:12242279 IPI C nuclear protein YGL244W|CSL3 gene taxon:4932 20021004 SGD
+SGD S000003213 RTF1 GO:0016593 SGD_REF:S000069696|PMID:11884586 IPI C nuclear protein YGL244W|CSL3 gene taxon:4932 20020927 SGD
+SGD S000003213 RTF1 GO:0016593 SGD_REF:S000073599|PMID:12773564 TAS C nuclear protein YGL244W|CSL3 gene taxon:4932 20040129 SGD
+SGD S000003213 RTF1 GO:0016944 SGD_REF:S000071357|PMID:12242279 IPI F nuclear protein YGL244W|CSL3 gene taxon:4932 20021004 SGD
+SGD S000003213 RTF1 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P nuclear protein YGL244W|CSL3 gene taxon:4932 20060203 SGD
+SGD S000003213 RTF1 GO:0006366 SGD_REF:S000069696|PMID:11884586 IMP P nuclear protein YGL244W|CSL3 gene taxon:4932 20020927 SGD
+SGD S000003213 RTF1 GO:0006368 SGD_REF:S000071357|PMID:12242279 IPI P nuclear protein YGL244W|CSL3 gene taxon:4932 20021004 SGD
+SGD S000003213 RTF1 GO:0016571 SGD_REF:S000073147|PMID:12667454 IMP P nuclear protein YGL244W|CSL3 gene taxon:4932 20050503 SGD
+SGD S000005428 RTG1 GO:0005634 SGD_REF:S000043674|PMID:10848632 IDA C transcription factor YOL067C gene taxon:4932 20020801 SGD
+SGD S000005428 RTG1 GO:0005737 SGD_REF:S000043674|PMID:10848632 IDA C transcription factor YOL067C gene taxon:4932 20020801 SGD
+SGD S000005428 RTG1 GO:0003713 SGD_REF:S000049522|PMID:9032238 IDA F transcription factor YOL067C gene taxon:4932 20020801 SGD
+SGD S000005428 RTG1 GO:0006367 SGD_REF:S000043674|PMID:10848632 IDA P transcription factor YOL067C gene taxon:4932 20020801 SGD
+SGD S000005428 RTG1 GO:0008104 SGD_REF:S000043674|PMID:10848632 IMP P transcription factor YOL067C gene taxon:4932 20020801 SGD
+SGD S000005428 RTG1 GO:0008104 SGD_REF:S000043674|PMID:10848632 IGI P transcription factor YOL067C gene taxon:4932 20020801 SGD
+SGD S000005428 RTG1 GO:0031930 SGD_REF:S000044921|PMID:8422683 IMP P transcription factor YOL067C gene taxon:4932 20051130 SGD
+SGD S000005428 RTG1 GO:0031930 SGD_REF:S000045999|PMID:7493987 IDA P transcription factor YOL067C gene taxon:4932 20051130 SGD
+SGD S000003221 RTG2 GO:0005737 SGD_REF:S000043674|PMID:10848632 IDA C YGL252C gene taxon:4932 20020801 SGD
+SGD S000003221 RTG2 GO:0005737 SGD_REF:S000050990|PMID:11076970 TAS C YGL252C gene taxon:4932 20030508 SGD
+SGD S000003221 RTG2 GO:0046695 SGD_REF:S000071997|PMID:12446794 IPI C YGL252C gene taxon:4932 20041024 SGD
+SGD S000003221 RTG2 GO:0030528 SGD_REF:S000070242|PMID:11882290 IDA F YGL252C gene taxon:4932 20030508 SGD
+SGD S000003221 RTG2 GO:0030528 SGD_REF:S000050990|PMID:11076970 TAS F YGL252C gene taxon:4932 20030508 SGD
+SGD S000003221 RTG2 GO:0001310 SGD_REF:S000077528|PMID:15020466 IMP P YGL252C gene taxon:4932 20050314 SGD
+SGD S000003221 RTG2 GO:0007242 SGD_REF:S000043674|PMID:10848632 IMP P YGL252C gene taxon:4932 20020801 SGD
+SGD S000003221 RTG2 GO:0031930 SGD_REF:S000044921|PMID:8422683 IMP P YGL252C gene taxon:4932 20051130 SGD
+SGD S000003221 RTG2 GO:0031930 SGD_REF:S000045999|PMID:7493987 IMP P YGL252C gene taxon:4932 20051130 SGD
+SGD S000000199 RTG3 GO:0005634 SGD_REF:S000043674|PMID:10848632 IDA C phosphoprotein YBL103C gene taxon:4932 20020801 SGD
+SGD S000000199 RTG3 GO:0005737 SGD_REF:S000043674|PMID:10848632 IDA C phosphoprotein YBL103C gene taxon:4932 20020801 SGD
+SGD S000000199 RTG3 GO:0003704 SGD_REF:S000049522|PMID:9032238 IDA F phosphoprotein YBL103C gene taxon:4932 20020801 SGD
+SGD S000000199 RTG3 GO:0006367 SGD_REF:S000043674|PMID:10848632 IDA P phosphoprotein YBL103C gene taxon:4932 20020801 SGD
+SGD S000000199 RTG3 GO:0031930 SGD_REF:S000049522|PMID:9032238 IDA P phosphoprotein YBL103C gene taxon:4932 20051130 SGD
+SGD S000002641 RTN1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YDR233C gene taxon:4932 20040928 SGD
+SGD S000002641 RTN1 GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YDR233C gene taxon:4932 20031028 SGD
+SGD S000002641 RTN1 GO:0005783 SGD_REF:S000082473|PMID:16002643 IDA C YDR233C gene taxon:4932 20060426 SGD
+SGD S000002641 RTN1 GO:0005789 SGD_REF:S000115116|PMID:16624861 IDA C YDR233C gene taxon:4932 20060425 SGD
+SGD S000002641 RTN1 GO:0005794 SGD_REF:S000082473|PMID:16002643 IDA C YDR233C gene taxon:4932 20060426 SGD
+SGD S000002641 RTN1 GO:0005554 SGD_REF:S000069584 ND F YDR233C gene taxon:4932 20021125 SGD
+SGD S000002641 RTN1 GO:0000004 SGD_REF:S000069584 ND P YDR233C gene taxon:4932 20021125 SGD
+SGD S000002363 RTN2 GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YDL204W gene taxon:4932 20031028 SGD
+SGD S000002363 RTN2 GO:0005554 SGD_REF:S000069584 ND F YDL204W gene taxon:4932 20021125 SGD
+SGD S000002363 RTN2 GO:0000004 SGD_REF:S000069584 ND P YDL204W gene taxon:4932 20021125 SGD
+SGD S000005540 RTS1 GO:0000159 SGD_REF:S000045742|PMID:10329624 TAS C protein phosphatase 2A (PP2A) B-type regulatory subunit YOR014W|SCS1 gene taxon:4932 20010118 SGD
+SGD S000005540 RTS1 GO:0000780 SGD_REF:S000115004|PMID:16541024 IDA C protein phosphatase 2A (PP2A) B-type regulatory subunit YOR014W|SCS1 gene taxon:4932 20060525 SGD
+SGD S000005540 RTS1 GO:0005634 SGD_REF:S000071578|PMID:12388751 IDA C protein phosphatase 2A (PP2A) B-type regulatory subunit YOR014W|SCS1 gene taxon:4932 20030430 SGD
+SGD S000005540 RTS1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C protein phosphatase 2A (PP2A) B-type regulatory subunit YOR014W|SCS1 gene taxon:4932 20020507 SGD
+SGD S000005540 RTS1 GO:0005816 SGD_REF:S000071578|PMID:12388751 IDA C protein phosphatase 2A (PP2A) B-type regulatory subunit YOR014W|SCS1 gene taxon:4932 20030430 SGD
+SGD S000005540 RTS1 GO:0005935 SGD_REF:S000071578|PMID:12388751 IDA C protein phosphatase 2A (PP2A) B-type regulatory subunit YOR014W|SCS1 gene taxon:4932 20030430 SGD
+SGD S000005540 RTS1 contributes_to GO:0000158 SGD_REF:S000045742|PMID:10329624 TAS F protein phosphatase 2A (PP2A) B-type regulatory subunit YOR014W|SCS1 gene taxon:4932 20060105 SGD
+SGD S000005540 RTS1 GO:0006412 SGD_REF:S000045742|PMID:10329624 ISS P protein phosphatase 2A (PP2A) B-type regulatory subunit YOR014W|SCS1 gene taxon:4932 20010118 SGD
+SGD S000005540 RTS1 GO:0006470 SGD_REF:S000055155|PMID:9001215 TAS P protein phosphatase 2A (PP2A) B-type regulatory subunit YOR014W|SCS1 gene taxon:4932 20030430 SGD
+SGD S000005540 RTS1 GO:0051754 SGD_REF:S000115004|PMID:16541024 IMP P protein phosphatase 2A (PP2A) B-type regulatory subunit YOR014W|SCS1 gene taxon:4932 20060525 SGD
+SGD S000005603 RTS2 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YOR077W|YOR29-28 gene taxon:4932 20031028 SGD
+SGD S000005603 RTS2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YOR077W|YOR29-28 gene taxon:4932 20031028 SGD
+SGD S000005603 RTS2 GO:0005554 SGD_REF:S000069584 ND F YOR077W|YOR29-28 gene taxon:4932 20021029 SGD
+SGD S000005603 RTS2 GO:0000004 SGD_REF:S000069584 ND P YOR077W|YOR29-28 gene taxon:4932 20021029 SGD
+SGD S000003393 RTS3 GO:0000159 SGD_REF:S000074191|PMID:14566057 RCA C YGR161C gene taxon:4932 20050608 SGD
+SGD S000003393 RTS3 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YGR161C gene taxon:4932 20031028 SGD
+SGD S000003393 RTS3 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YGR161C gene taxon:4932 20031028 SGD
+SGD S000003393 RTS3 contributes_to GO:0000158 SGD_REF:S000074191|PMID:14566057 RCA F YGR161C gene taxon:4932 20060105 SGD
+SGD S000003393 RTS3 GO:0006470 SGD_REF:S000074191|PMID:14566057 RCA P YGR161C gene taxon:4932 20050608 SGD
+SGD S000003583 RTT101 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YJL047C|CUL8|CULC|CULLIN 8 gene taxon:4932 20031028 SGD
+SGD S000003583 RTT101 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YJL047C|CUL8|CULC|CULLIN 8 gene taxon:4932 20031028 SGD
+SGD S000003583 RTT101 GO:0004842 SGD_REF:S000073416|PMID:12676951 IDA F YJL047C|CUL8|CULC|CULLIN 8 gene taxon:4932 20030708 SGD
+SGD S000003583 RTT101 GO:0005515 SGD_REF:S000044681|PMID:10230407 IPI SGD:S000005493 F YJL047C|CUL8|CULC|CULLIN 8 gene taxon:4932 20030708 SGD
+SGD S000003583 RTT101 GO:0005515 SGD_REF:S000073416|PMID:12676951 IPI SGD:S000005493 F YJL047C|CUL8|CULC|CULLIN 8 gene taxon:4932 20030708 SGD
+SGD S000003583 RTT101 GO:0000335 SGD_REF:S000068874|PMID:11779788 IMP P YJL047C|CUL8|CULC|CULLIN 8 gene taxon:4932 20020927 SGD
+SGD S000003583 RTT101 GO:0006511 SGD_REF:S000073416|PMID:12676951 IC GO:0004842 P YJL047C|CUL8|CULC|CULLIN 8 gene taxon:4932 20031006 SGD
+SGD S000003583 RTT101 GO:0007088 SGD_REF:S000073416|PMID:12676951 IMP P YJL047C|CUL8|CULC|CULLIN 8 gene taxon:4932 20031006 SGD
+SGD S000003507 RTT102 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YGR275W gene taxon:4932 20031028 SGD
+SGD S000003507 RTT102 GO:0016514 SGD_REF:S000077755|PMID:15506919 IPI SGD:S000001017|SGD:S000003712 C YGR275W gene taxon:4932 20050607 SGD
+SGD S000003507 RTT102 GO:0016586 SGD_REF:S000075541|PMID:14729968 IPI C YGR275W gene taxon:4932 20040714 SGD
+SGD S000003507 RTT102 GO:0016586 SGD_REF:S000077755|PMID:15506919 IPI SGD:S000001388 C YGR275W gene taxon:4932 20050607 SGD
+SGD S000003507 RTT102 GO:0005554 SGD_REF:S000069584 ND F YGR275W gene taxon:4932 20060321 SGD
+SGD S000003507 RTT102 GO:0007059 SGD_REF:S000075541|PMID:14729968 IGI SGD:S000004700 P YGR275W gene taxon:4932 20060321 SGD
+SGD S000002697 RTT103 GO:0008372 SGD_REF:S000069584 ND C YDR289C gene taxon:4932 20020927 SGD
+SGD S000002697 RTT103 GO:0005554 SGD_REF:S000069584 ND F YDR289C gene taxon:4932 20020927 SGD
+SGD S000002697 RTT103 GO:0000335 SGD_REF:S000068874|PMID:11779788 IMP P YDR289C gene taxon:4932 20020927 SGD
+SGD S000002697 RTT103 GO:0030846 SGD_REF:S000080022|PMID:15565157 IPI SGD:S000002299|SGD:S000005574 P YDR289C gene taxon:4932 20050718 SGD
+SGD S000000906 RTT105 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YER104W gene taxon:4932 20031028 SGD
+SGD S000000906 RTT105 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YER104W gene taxon:4932 20031028 SGD
+SGD S000000906 RTT105 GO:0005554 SGD_REF:S000069584 ND F YER104W gene taxon:4932 20020927 SGD
+SGD S000000906 RTT105 GO:0000335 SGD_REF:S000068874|PMID:11779788 IMP P YER104W gene taxon:4932 20020927 SGD
+SGD S000005150 RTT106 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YNL206C gene taxon:4932 20031028 SGD
+SGD S000005150 RTT106 GO:0005554 SGD_REF:S000069584 ND F YNL206C gene taxon:4932 20020927 SGD
+SGD S000005150 RTT106 GO:0000335 SGD_REF:S000068874|PMID:11779788 IMP P YNL206C gene taxon:4932 20020927 SGD
+SGD S000001197 RTT107 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YHR154W|ESC4 gene taxon:4932 20031028 SGD
+SGD S000001197 RTT107 GO:0005554 SGD_REF:S000069584 ND F YHR154W|ESC4 gene taxon:4932 20020927 SGD
+SGD S000001197 RTT107 GO:0000335 SGD_REF:S000068874|PMID:11779788 IMP P YHR154W|ESC4 gene taxon:4932 20020927 SGD
+SGD S000001197 RTT107 GO:0006302 SGD_REF:S000079746|PMID:14988729 IMP P YHR154W|ESC4 gene taxon:4932 20050718 SGD
+SGD S000003925 RTT109 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YLL002W|KIM2|REM50 gene taxon:4932 20031028 SGD
+SGD S000003925 RTT109 GO:0005634 SGD_REF:S000077144|PMID:15282802 IDA C YLL002W|KIM2|REM50 gene taxon:4932 20041008 SGD
+SGD S000003925 RTT109 GO:0005554 SGD_REF:S000069584 ND F YLL002W|KIM2|REM50 gene taxon:4932 20020927 SGD
+SGD S000003925 RTT109 GO:0000335 SGD_REF:S000068874|PMID:11779788 IMP P YLL002W|KIM2|REM50 gene taxon:4932 20020927 SGD
+SGD S000003925 RTT109 GO:0006974 SGD_REF:S000076175|PMID:12482937 IMP P YLL002W|KIM2|REM50 gene taxon:4932 20060406 SGD
+SGD S000002546 RUB1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C ubiquitin-like protein YDR139C gene taxon:4932 20031028 SGD
+SGD S000002546 RUB1 GO:0031386 SGD_REF:S000050724|PMID:9545234 IDA F ubiquitin-like protein YDR139C gene taxon:4932 20050427 SGD
+SGD S000002546 RUB1 GO:0031386 SGD_REF:S000050724|PMID:9545234 ISS SGD:S000002918|SGD:S000003962 F ubiquitin-like protein YDR139C gene taxon:4932 20051018 SGD
+SGD S000002546 RUB1 GO:0031386 SGD_REF:S000042395|PMID:9531531 IDA F ubiquitin-like protein YDR139C gene taxon:4932 20050427 SGD
+SGD S000002546 RUB1 GO:0045116 SGD_REF:S000042395|PMID:9531531 IGI SGD:S000002290|SGD:S000002461 P ubiquitin-like protein YDR139C gene taxon:4932 20050427 SGD
+SGD S000002546 RUB1 GO:0045116 SGD_REF:S000050724|PMID:9545234 IDA P ubiquitin-like protein YDR139C gene taxon:4932 20050427 SGD
+SGD S000002546 RUB1 GO:0045116 SGD_REF:S000042395|PMID:9531531 IDA P ubiquitin-like protein YDR139C gene taxon:4932 20050427 SGD
+SGD S000005742 RUD3 GO:0005794 SGD_REF:S000056398|PMID:10512869 NAS C YOR216C|GRP1 gene taxon:4932 20011105 SGD
+SGD S000005742 RUD3 GO:0005554 SGD_REF:S000069584 ND F YOR216C|GRP1 gene taxon:4932 20011105 SGD
+SGD S000005742 RUD3 GO:0006888 SGD_REF:S000056398|PMID:10512869 IGI P YOR216C|GRP1 gene taxon:4932 20011105 SGD
+SGD S000005742 RUD3 GO:0006888 SGD_REF:S000056160|PMID:10562277 IGI P YOR216C|GRP1 gene taxon:4932 20011105 SGD
+SGD S000028470 RUF5-1 GO:0008372 SGD_REF:S000069584 ND C non-coding RNA RUF5 gene taxon:4932 20040903 SGD
+SGD S000028470 RUF5-1 GO:0005554 SGD_REF:S000069584 ND F non-coding RNA RUF5 gene taxon:4932 20040903 SGD
+SGD S000028470 RUF5-1 GO:0000004 SGD_REF:S000069584 ND P non-coding RNA RUF5 gene taxon:4932 20040903 SGD
+SGD S000028474 RUF5-2 GO:0008372 SGD_REF:S000069584 ND C non-coding RNA RUF5 gene taxon:4932 20040903 SGD
+SGD S000028474 RUF5-2 GO:0005554 SGD_REF:S000069584 ND F non-coding RNA RUF5 gene taxon:4932 20040903 SGD
+SGD S000028474 RUF5-2 GO:0000004 SGD_REF:S000069584 ND P non-coding RNA RUF5 gene taxon:4932 20040903 SGD
+SGD S000005664 RUP1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YOR138C gene taxon:4932 20031028 SGD
+SGD S000005664 RUP1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YOR138C gene taxon:4932 20020507 SGD
+SGD S000005664 RUP1 GO:0005515 SGD_REF:S000081856|PMID:15933713 IDA F YOR138C gene taxon:4932 20050715 SGD
+SGD S000005664 RUP1 GO:0016579 SGD_REF:S000081856|PMID:15933713 IMP P YOR138C gene taxon:4932 20050715 SGD
+SGD S000002598 RVB1 GO:0000812 SGD_REF:S000074662|PMID:14645854 IPI C YDR190C|TIH1|TIP48|TIP49A gene taxon:4932 20040412 SGD
+SGD S000002598 RVB1 GO:0000812 SGD_REF:S000075430|PMID:14690608 IPI C YDR190C|TIH1|TIP48|TIP49A gene taxon:4932 20040412 SGD
+SGD S000002598 RVB1 GO:0005634 SGD_REF:S000056415|PMID:10684247 IDA C YDR190C|TIH1|TIP48|TIP49A gene taxon:4932 20010118 SGD
+SGD S000002598 RVB1 GO:0016585 SGD_REF:S000060643|PMID:11278922 IDA C YDR190C|TIH1|TIP48|TIP49A gene taxon:4932 20020926 SGD
+SGD S000002598 RVB1 GO:0031011 SGD_REF:S000040657|PMID:10952318 IPI SGD:S000003118 C YDR190C|TIH1|TIP48|TIP49A gene taxon:4932 20050411 SGD
+SGD S000002598 RVB1 GO:0016887 SGD_REF:S000060643|PMID:11278922 IMP F YDR190C|TIH1|TIP48|TIP49A gene taxon:4932 20020926 SGD
+SGD S000002598 RVB1 contributes_to GO:0043141 SGD_REF:S000040657|PMID:10952318 IDA F YDR190C|TIH1|TIP48|TIP49A gene taxon:4932 20060320 SGD
+SGD S000002598 RVB1 GO:0006338 SGD_REF:S000074662|PMID:14645854 IDA P YDR190C|TIH1|TIP48|TIP49A gene taxon:4932 20040322 SGD
+SGD S000002598 RVB1 GO:0006338 SGD_REF:S000075430|PMID:14690608 IPI P YDR190C|TIH1|TIP48|TIP49A gene taxon:4932 20040323 SGD
+SGD S000002598 RVB1 GO:0006357 SGD_REF:S000060643|PMID:11278922 IMP P YDR190C|TIH1|TIP48|TIP49A gene taxon:4932 20020926 SGD
+SGD S000006156 RVB2 GO:0000812 SGD_REF:S000074662|PMID:14645854 IPI C transcriptional regulator YPL235W|TIH2|TIP49|TIP49B gene taxon:4932 20040412 SGD
+SGD S000006156 RVB2 GO:0000812 SGD_REF:S000075430|PMID:14690608 IPI C transcriptional regulator YPL235W|TIH2|TIP49|TIP49B gene taxon:4932 20040412 SGD
+SGD S000006156 RVB2 GO:0005634 SGD_REF:S000066250|PMID:11604509 IDA C transcriptional regulator YPL235W|TIH2|TIP49|TIP49B gene taxon:4932 20020926 SGD
+SGD S000006156 RVB2 GO:0016585 SGD_REF:S000060643|PMID:11278922 IDA C transcriptional regulator YPL235W|TIH2|TIP49|TIP49B gene taxon:4932 20020926 SGD
+SGD S000006156 RVB2 GO:0031011 SGD_REF:S000040657|PMID:10952318 IPI SGD:S000003118 C transcriptional regulator YPL235W|TIH2|TIP49|TIP49B gene taxon:4932 20050411 SGD
+SGD S000006156 RVB2 GO:0016887 SGD_REF:S000060643|PMID:11278922 IMP F transcriptional regulator YPL235W|TIH2|TIP49|TIP49B gene taxon:4932 20020926 SGD
+SGD S000006156 RVB2 contributes_to GO:0043141 SGD_REF:S000040657|PMID:10952318 IDA F transcriptional regulator YPL235W|TIH2|TIP49|TIP49B gene taxon:4932 20060320 SGD
+SGD S000006156 RVB2 GO:0006338 SGD_REF:S000074662|PMID:14645854 IDA P transcriptional regulator YPL235W|TIH2|TIP49|TIP49B gene taxon:4932 20040322 SGD
+SGD S000006156 RVB2 GO:0006338 SGD_REF:S000075430|PMID:14690608 IPI P transcriptional regulator YPL235W|TIH2|TIP49|TIP49B gene taxon:4932 20040323 SGD
+SGD S000006156 RVB2 GO:0006357 SGD_REF:S000060643|PMID:11278922 IMP P transcriptional regulator YPL235W|TIH2|TIP49|TIP49B gene taxon:4932 20020926 SGD
+SGD S000006156 RVB2 GO:0006365 SGD_REF:S000066250|PMID:11604509 IMP P transcriptional regulator YPL235W|TIH2|TIP49|TIP49B gene taxon:4932 20020926 SGD
+SGD S000006156 RVB2 GO:0016074 SGD_REF:S000066250|PMID:11604509 IMP P transcriptional regulator YPL235W|TIH2|TIP49|TIP49B gene taxon:4932 20020926 SGD
+SGD S000000602 RVS161 GO:0005937 SGD_REF:S000045636|PMID:9566960 IDA C YCR009C|END6|FUS7|SPE161 gene taxon:4932 20050328 SGD
+SGD S000000602 RVS161 GO:0030479 SGD_REF:S000041005|PMID:10652251 TAS C YCR009C|END6|FUS7|SPE161 gene taxon:4932 20050328 SGD
+SGD S000000602 RVS161 GO:0045121 SGD_REF:S000071971|PMID:12477802 IDA C YCR009C|END6|FUS7|SPE161 gene taxon:4932 20030220 SGD
+SGD S000000602 RVS161 GO:0008092 SGD_REF:S000047939|PMID:10388809 ISS F YCR009C|END6|FUS7|SPE161 gene taxon:4932 20010118 SGD
+SGD S000000602 RVS161 GO:0008092 SGD_REF:S000047939|PMID:10388809 IPI F YCR009C|END6|FUS7|SPE161 gene taxon:4932 20010118 SGD
+SGD S000000602 RVS161 GO:0006897 SGD_REF:S000041005|PMID:10652251 IMP P YCR009C|END6|FUS7|SPE161 gene taxon:4932 20010118 SGD
+SGD S000000602 RVS161 GO:0006970 SGD_REF:S000041005|PMID:10652251 IMP P YCR009C|END6|FUS7|SPE161 gene taxon:4932 20010118 SGD
+SGD S000000602 RVS161 GO:0007121 SGD_REF:S000041005|PMID:10652251 IMP P YCR009C|END6|FUS7|SPE161 gene taxon:4932 20010118 SGD
+SGD S000002796 RVS167 GO:0030479 SGD_REF:S000041005|PMID:10652251 TAS C cytoskeletal protein (putative) YDR388W gene taxon:4932 20050328 SGD
+SGD S000002796 RVS167 colocalizes_with GO:0030479 SGD_REF:S000042845|PMID:10393809 IDA C cytoskeletal protein (putative) YDR388W gene taxon:4932 20050328 SGD
+SGD S000002796 RVS167 GO:0008092 SGD_REF:S000047939|PMID:10388809 ISS F cytoskeletal protein (putative) YDR388W gene taxon:4932 20010118 SGD
+SGD S000002796 RVS167 GO:0008092 SGD_REF:S000047939|PMID:10388809 IPI F cytoskeletal protein (putative) YDR388W gene taxon:4932 20010118 SGD
+SGD S000002796 RVS167 GO:0006897 SGD_REF:S000041005|PMID:10652251 IMP P cytoskeletal protein (putative) YDR388W gene taxon:4932 20010118 SGD
+SGD S000002796 RVS167 GO:0006970 SGD_REF:S000041005|PMID:10652251 IMP P cytoskeletal protein (putative) YDR388W gene taxon:4932 20010118 SGD
+SGD S000002796 RVS167 GO:0007121 SGD_REF:S000041005|PMID:10652251 IMP P cytoskeletal protein (putative) YDR388W gene taxon:4932 20010118 SGD
+SGD S000002796 RVS167 GO:0016192 SGD_REF:S000081252|PMID:15802519 IGI P cytoskeletal protein (putative) YDR388W gene taxon:4932 20050414 SGD
+SGD S000002796 RVS167 GO:0016192 SGD_REF:S000081252|PMID:15802519 IPI P cytoskeletal protein (putative) YDR388W gene taxon:4932 20050414 SGD
+SGD S000000299 RXT2 GO:0000118 SGD_REF:S000113697|PMID:16314178 IDA C YBR095C gene taxon:4932 20060509 SGD
+SGD S000000299 RXT2 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YBR095C gene taxon:4932 20031028 SGD
+SGD S000000299 RXT2 GO:0005554 SGD_REF:S000069584 ND F YBR095C gene taxon:4932 20021029 SGD
+SGD S000000299 RXT2 GO:0000747 SGD_REF:S000056413|PMID:10628851 IMP P YBR095C gene taxon:4932 20021029 SGD
+SGD S000000299 RXT2 GO:0001403 SGD_REF:S000056413|PMID:10628851 IMP P YBR095C gene taxon:4932 20021029 SGD
+SGD S000002234 RXT3 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YDL076C gene taxon:4932 20031028 SGD
+SGD S000002234 RXT3 GO:0005554 SGD_REF:S000069584 ND F YDL076C gene taxon:4932 20051129 SGD
+SGD S000002234 RXT3 GO:0006342 SGD_REF:S000074191|PMID:14566057 RCA P YDL076C gene taxon:4932 20050608 SGD
+SGD S000002234 RXT3 GO:0016575 SGD_REF:S000074191|PMID:14566057 RCA P YDL076C gene taxon:4932 20051129 SGD
+SGD S000029425 RYE4 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20020107 SGD
+SGD S000029425 RYE4 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20020107 SGD
+SGD S000029425 RYE4 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20020107 SGD
+SGD S000029426 RYE6 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20020107 SGD
+SGD S000029426 RYE6 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20020107 SGD
+SGD S000029426 RYE6 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20020107 SGD
+SGD S000029427 RYE7 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20020107 SGD
+SGD S000029427 RYE7 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20020107 SGD
+SGD S000029427 RYE7 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20020107 SGD
+SGD S000029428 RYE8 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20020107 SGD
+SGD S000029428 RYE8 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20020107 SGD
+SGD S000029428 RYE8 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20020107 SGD
+SGD S000001695 SAC1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C phosphoinositide phosphatase YKL212W|RSD1 gene taxon:4932 20040928 SGD
+SGD S000001695 SAC1 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C phosphoinositide phosphatase YKL212W|RSD1 gene taxon:4932 20060317 SGD
+SGD S000001695 SAC1 GO:0030173 SGD_REF:S000040606|PMID:8314848 IDA C phosphoinositide phosphatase YKL212W|RSD1 gene taxon:4932 20020802 SGD
+SGD S000001695 SAC1 GO:0030176 SGD_REF:S000040606|PMID:8314848 IDA C phosphoinositide phosphatase YKL212W|RSD1 gene taxon:4932 20020802 SGD
+SGD S000001695 SAC1 GO:0004437 SGD_REF:S000055623|PMID:10625610 IDA F phosphoinositide phosphatase YKL212W|RSD1 gene taxon:4932 20020802 SGD
+SGD S000001695 SAC1 GO:0006887 SGD_REF:S000069028|PMID:11566100 IMP P phosphoinositide phosphatase YKL212W|RSD1 gene taxon:4932 20050425 SGD
+SGD S000001695 SAC1 GO:0017157 SGD_REF:S000080590|PMID:15657391 IMP P phosphoinositide phosphatase YKL212W|RSD1 gene taxon:4932 20050425 SGD
+SGD S000001695 SAC1 GO:0017157 SGD_REF:S000080590|PMID:15657391 IPI P phosphoinositide phosphatase YKL212W|RSD1 gene taxon:4932 20050425 SGD
+SGD S000001695 SAC1 GO:0046856 SGD_REF:S000055623|PMID:10625610 IDA P phosphoinositide phosphatase YKL212W|RSD1 gene taxon:4932 20050331 SGD
+SGD S000001695 SAC1 GO:0046856 SGD_REF:S000055623|PMID:10625610 IMP P phosphoinositide phosphatase YKL212W|RSD1 gene taxon:4932 20050331 SGD
+SGD S000001695 SAC1 GO:0048017 SGD_REF:S000055623|PMID:10625610 IMP P phosphoinositide phosphatase YKL212W|RSD1 gene taxon:4932 20050524 SGD
+SGD S000002566 SAC3 GO:0005643 SGD_REF:S000072894|PMID:12631707 IDA C YDR159W|LEP1 gene taxon:4932 20031215 SGD
+SGD S000002566 SAC3 GO:0005515 SGD_REF:S000071844|PMID:12411502 IPI SGD:S000002242|SGD:S000006090|SGD:S000005624|SGD:S000005433 F YDR159W|LEP1 gene taxon:4932 20030605 SGD
+SGD S000002566 SAC3 GO:0006406 SGD_REF:S000072894|PMID:12631707 IGI SGD:S000001669|SGD:S000006090 P YDR159W|LEP1 gene taxon:4932 20030709 SGD
+SGD S000002566 SAC3 GO:0006406 SGD_REF:S000072894|PMID:12631707 IMP P YDR159W|LEP1 gene taxon:4932 20030709 SGD
+SGD S000002566 SAC3 GO:0006406 SGD_REF:S000072894|PMID:12631707 IPI SGD:S000003577|SGD:S000005572|SGD:S000006090|SGD:S000004650|SGD:S000001669 P YDR159W|LEP1 gene taxon:4932 20030709 SGD
+SGD S000002566 SAC3 GO:0006611 SGD_REF:S000062095|PMID:10716708 IGI P YDR159W|LEP1 gene taxon:4932 20021211 SGD
+SGD S000002566 SAC3 GO:0006611 SGD_REF:S000062095|PMID:10716708 IMP P YDR159W|LEP1 gene taxon:4932 20021211 SGD
+SGD S000002566 SAC3 GO:0007067 SGD_REF:S000045465|PMID:8799844 IMP P YDR159W|LEP1 gene taxon:4932 20010118 SGD
+SGD S000002566 SAC3 GO:0030029 SGD_REF:S000058447|PMID:9153752 IGI P YDR159W|LEP1 gene taxon:4932 20010620 SGD
+SGD S000002536 SAC6 GO:0030479 SGD_REF:S000041005|PMID:10652251 IDA C actin filament bundling protein, fimbrin homolog YDR129C|ABP67 gene taxon:4932 20010118 SGD
+SGD S000002536 SAC6 GO:0030482 SGD_REF:S000041005|PMID:10652251 IDA C actin filament bundling protein, fimbrin homolog YDR129C|ABP67 gene taxon:4932 20010118 SGD
+SGD S000002536 SAC6 GO:0030674 SGD_REF:S000073708|PMID:12857851 IDA F actin filament bundling protein, fimbrin homolog YDR129C|ABP67 gene taxon:4932 20040409 SGD
+SGD S000002536 SAC6 GO:0051015 SGD_REF:S000046691|PMID:2643162 IDA F actin filament bundling protein, fimbrin homolog YDR129C|ABP67 gene taxon:4932 20040409 SGD
+SGD S000002536 SAC6 GO:0006897 SGD_REF:S000041005|PMID:10652251 IMP P actin filament bundling protein, fimbrin homolog YDR129C|ABP67 gene taxon:4932 20010118 SGD
+SGD S000002536 SAC6 GO:0006970 SGD_REF:S000041005|PMID:10652251 IMP P actin filament bundling protein, fimbrin homolog YDR129C|ABP67 gene taxon:4932 20010118 SGD
+SGD S000002536 SAC6 GO:0007015 SGD_REF:S000050406|PMID:8522605 IMP P actin filament bundling protein, fimbrin homolog YDR129C|ABP67 gene taxon:4932 20030827 SGD
+SGD S000002536 SAC6 GO:0007015 SGD_REF:S000050406|PMID:8522605 IPI P actin filament bundling protein, fimbrin homolog YDR129C|ABP67 gene taxon:4932 20030827 SGD
+SGD S000002536 SAC6 GO:0007121 SGD_REF:S000041005|PMID:10652251 IMP P actin filament bundling protein, fimbrin homolog YDR129C|ABP67 gene taxon:4932 20010118 SGD
+SGD S000002797 SAC7 GO:0005622 SGD_REF:S000058399|PMID:9891811 TAS C GTPase activating protein (GAP) for RHO1 YDR389W gene taxon:4932 20010118 SGD
+SGD S000002797 SAC7 GO:0004871 SGD_REF:S000058399|PMID:9891811 IPI F GTPase activating protein (GAP) for RHO1 YDR389W gene taxon:4932 20010118 SGD
+SGD S000002797 SAC7 GO:0005100 SGD_REF:S000058399|PMID:9891811 IDA F GTPase activating protein (GAP) for RHO1 YDR389W gene taxon:4932 20010118 SGD
+SGD S000002797 SAC7 GO:0007264 SGD_REF:S000058399|PMID:9891811 IPI P GTPase activating protein (GAP) for RHO1 YDR389W gene taxon:4932 20010118 SGD
+SGD S000002797 SAC7 GO:0030037 SGD_REF:S000042831|PMID:9038344 IMP P GTPase activating protein (GAP) for RHO1 YDR389W gene taxon:4932 20011217 SGD
+SGD S000001901 SAD1 GO:0005634 SGD_REF:S000053641|PMID:10022888 IDA C YFR005C gene taxon:4932 20021021 SGD
+SGD S000001901 SAD1 GO:0031202 SGD_REF:S000053641|PMID:10022888 IMP F YFR005C gene taxon:4932 20021030 SGD
+SGD S000001901 SAD1 GO:0000398 SGD_REF:S000053641|PMID:10022888 IDA P YFR005C gene taxon:4932 20020822 SGD
+SGD S000003143 SAE2 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YGL175C|COM1 gene taxon:4932 20031028 SGD
+SGD S000003143 SAE2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YGL175C|COM1 gene taxon:4932 20031028 SGD
+SGD S000003143 SAE2 GO:0005554 SGD_REF:S000069584 ND F YGL175C|COM1 gene taxon:4932 20021118 SGD
+SGD S000003143 SAE2 GO:0000706 SGD_REF:S000069981|PMID:9334324 TAS P YGL175C|COM1 gene taxon:4932 20020708 SGD
+SGD S000001957 SAE3 GO:0000794 SGD_REF:S000080355|PMID:15620352 IDA C YHR079C-A|YHR079BC|YHR079C-B gene taxon:4932 20050119 SGD
+SGD S000001957 SAE3 GO:0000794 SGD_REF:S000080356|PMID:15579681 IDA C YHR079C-A|YHR079BC|YHR079C-B gene taxon:4932 20050119 SGD
+SGD S000001957 SAE3 GO:0005554 SGD_REF:S000069584 ND F YHR079C-A|YHR079BC|YHR079C-B gene taxon:4932 20020927 SGD
+SGD S000001957 SAE3 GO:0000707 SGD_REF:S000080355|PMID:15620352 IMP P YHR079C-A|YHR079BC|YHR079C-B gene taxon:4932 20050119 SGD
+SGD S000001957 SAE3 GO:0000707 SGD_REF:S000080356|PMID:15579681 IMP P YHR079C-A|YHR079BC|YHR079C-B gene taxon:4932 20050119 SGD
+SGD S000001957 SAE3 GO:0006302 SGD_REF:S000069127|PMID:11825877 TAS P YHR079C-A|YHR079BC|YHR079C-B gene taxon:4932 20031104 SGD
+SGD S000001957 SAE3 GO:0007131 SGD_REF:S000045010|PMID:9215889 IMP P YHR079C-A|YHR079BC|YHR079C-B gene taxon:4932 20020927 SGD
+SGD S000003764 SAG1 GO:0009277 SGD_REF:S000040179|PMID:10383953 IDA C alpha-agglutinin YJR004C|AG(ALPHA)1 gene taxon:4932 20020617 SGD
+SGD S000003764 SAG1 GO:0050839 SGD_REF:S000041613|PMID:2673555 IMP F alpha-agglutinin YJR004C|AG(ALPHA)1 gene taxon:4932 20010118 SGD
+SGD S000003764 SAG1 GO:0050839 SGD_REF:S000061548|PMID:11292808 TAS F alpha-agglutinin YJR004C|AG(ALPHA)1 gene taxon:4932 20040130 SGD
+SGD S000003764 SAG1 GO:0050839 SGD_REF:S000056908|PMID:2677666 IMP F alpha-agglutinin YJR004C|AG(ALPHA)1 gene taxon:4932 20010118 SGD
+SGD S000003764 SAG1 GO:0000752 SGD_REF:S000041613|PMID:2673555 IMP P alpha-agglutinin YJR004C|AG(ALPHA)1 gene taxon:4932 20021206 SGD
+SGD S000003764 SAG1 GO:0000752 SGD_REF:S000056908|PMID:2677666 IMP P alpha-agglutinin YJR004C|AG(ALPHA)1 gene taxon:4932 20021206 SGD
+SGD S000000845 SAH1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C S-adenosyl-L-homocysteine hydrolase (putative) YER043C gene taxon:4932 20031028 SGD
+SGD S000000845 SAH1 GO:0004013 SGD_REF:S000061038|PMID:8962070 ISS F S-adenosyl-L-homocysteine hydrolase (putative) YER043C gene taxon:4932 20040211 SGD
+SGD S000000845 SAH1 GO:0006555 SGD_REF:S000071379|PMID:11752249 NAS P S-adenosyl-L-homocysteine hydrolase (putative) YER043C gene taxon:4932 20021001 SGD
+SGD S000000845 SAH1 GO:0016259 SGD_REF:S000071379|PMID:11752249 NAS P S-adenosyl-L-homocysteine hydrolase (putative) YER043C gene taxon:4932 20021001 SGD
+SGD S000000931 SAK1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YER129W|PAK1 gene taxon:4932 20031028 SGD
+SGD S000000931 SAK1 GO:0004672 SGD_REF:S000052819|PMID:9341678 IDA F YER129W|PAK1 gene taxon:4932 20010118 SGD
+SGD S000000931 SAK1 GO:0006006 SGD_REF:S000077210|PMID:15340085 IGI P YER129W|PAK1 gene taxon:4932 20050512 SGD
+SGD S000000931 SAK1 GO:0006006 SGD_REF:S000077210|PMID:15340085 IMP P YER129W|PAK1 gene taxon:4932 20050512 SGD
+SGD S000000931 SAK1 GO:0006261 SGD_REF:S000052819|PMID:9341678 IGI P YER129W|PAK1 gene taxon:4932 20010118 SGD
+SGD S000000931 SAK1 GO:0006468 SGD_REF:S000052819|PMID:9341678 IDA P YER129W|PAK1 gene taxon:4932 20010118 SGD
+SGD S000005027 SAL1 GO:0005743 SGD_REF:S000049213|PMID:10930523 ISS C YNL083W gene taxon:4932 20021017 SGD
+SGD S000005027 SAL1 GO:0005215 SGD_REF:S000049213|PMID:10930523 ISS F YNL083W gene taxon:4932 20021017 SGD
+SGD S000005027 SAL1 GO:0005509 SGD_REF:S000076579|PMID:15238515 IDA F YNL083W gene taxon:4932 20040716 SGD
+SGD S000005027 SAL1 GO:0006810 SGD_REF:S000049213|PMID:10930523 ISS P YNL083W gene taxon:4932 20021017 SGD
+SGD S000004170 SAM1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YLR180W|ETH10 gene taxon:4932 20020507 SGD
+SGD S000004170 SAM1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YLR180W|ETH10 gene taxon:4932 20031028 SGD
+SGD S000004170 SAM1 GO:0004478 SGD_REF:S000051411|PMID:3316224 IGI F YLR180W|ETH10 gene taxon:4932 20010703 SGD
+SGD S000004170 SAM1 GO:0004478 SGD_REF:S000051411|PMID:3316224 ISS F YLR180W|ETH10 gene taxon:4932 20010703 SGD
+SGD S000004170 SAM1 GO:0006555 SGD_REF:S000043985|PMID:1903502 TAS P YLR180W|ETH10 gene taxon:4932 20010703 SGD
+SGD S000002910 SAM2 GO:0008372 SGD_REF:S000069584 ND C YDR502C|ETH2 gene taxon:4932 20021114 SGD
+SGD S000002910 SAM2 GO:0004478 SGD_REF:S000043985|PMID:1903502 TAS F YDR502C|ETH2 gene taxon:4932 20010703 SGD
+SGD S000002910 SAM2 GO:0006555 SGD_REF:S000043985|PMID:1903502 TAS P YDR502C|ETH2 gene taxon:4932 20010703 SGD
+SGD S000006195 SAM3 GO:0005886 SGD_REF:S000051126|PMID:10497160 ISS C high affinity S-adenosylmethionine permease YPL274W gene taxon:4932 20021002 SGD
+SGD S000006195 SAM3 GO:0005886 SGD_REF:S000051126|PMID:10497160 IMP C high affinity S-adenosylmethionine permease YPL274W gene taxon:4932 20021002 SGD
+SGD S000006195 SAM3 GO:0000095 SGD_REF:S000051126|PMID:10497160 ISS F high affinity S-adenosylmethionine permease YPL274W gene taxon:4932 20021002 SGD
+SGD S000006195 SAM3 GO:0000095 SGD_REF:S000051126|PMID:10497160 IMP F high affinity S-adenosylmethionine permease YPL274W gene taxon:4932 20021002 SGD
+SGD S000006195 SAM3 GO:0015805 SGD_REF:S000051126|PMID:10497160 IMP P high affinity S-adenosylmethionine permease YPL274W gene taxon:4932 20021002 SGD
+SGD S000001125 SAM35 GO:0001401 SGD_REF:S000076561|PMID:15205677 IDA C YHR083W|FMP20|TOB38|TOM38 gene taxon:4932 20040707 SGD
+SGD S000001125 SAM35 GO:0001401 SGD_REF:S000076561|PMID:15205677 IMP C YHR083W|FMP20|TOB38|TOM38 gene taxon:4932 20040707 SGD
+SGD S000001125 SAM35 GO:0001401 SGD_REF:S000076328|PMID:15067005 IDA C YHR083W|FMP20|TOB38|TOM38 gene taxon:4932 20040909 SGD
+SGD S000001125 SAM35 GO:0005741 SGD_REF:S000076561|PMID:15205677 IDA C YHR083W|FMP20|TOB38|TOM38 gene taxon:4932 20040707 SGD
+SGD S000001125 SAM35 GO:0005741 SGD_REF:S000076328|PMID:15067005 IDA C YHR083W|FMP20|TOB38|TOM38 gene taxon:4932 20040909 SGD
+SGD S000001125 SAM35 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C YHR083W|FMP20|TOB38|TOM38 gene taxon:4932 20060317 SGD
+SGD S000001125 SAM35 GO:0019898 SGD_REF:S000076328|PMID:15067005 IDA C YHR083W|FMP20|TOB38|TOM38 gene taxon:4932 20040909 SGD
+SGD S000001125 SAM35 GO:0005515 SGD_REF:S000076561|PMID:15205677 IDA F YHR083W|FMP20|TOB38|TOM38 gene taxon:4932 20040707 SGD
+SGD S000001125 SAM35 GO:0045040 SGD_REF:S000076561|PMID:15205677 IC GO:0001401 P YHR083W|FMP20|TOB38|TOM38 gene taxon:4932 20040707 SGD
+SGD S000001125 SAM35 GO:0045040 SGD_REF:S000076328|PMID:15067005 IMP P YHR083W|FMP20|TOB38|TOM38 gene taxon:4932 20040909 SGD
+SGD S000004664 SAM37 GO:0001401 SGD_REF:S000073845|PMID:12891361 IDA C mitochondrial SAM complex constituent YMR060C|MAS37|PET3027|TOM37 gene taxon:4932 20031107 SGD
+SGD S000004664 SAM37 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C mitochondrial SAM complex constituent YMR060C|MAS37|PET3027|TOM37 gene taxon:4932 20060317 SGD
+SGD S000004664 SAM37 GO:0005515 SGD_REF:S000073845|PMID:12891361 IMP F mitochondrial SAM complex constituent YMR060C|MAS37|PET3027|TOM37 gene taxon:4932 20030826 SGD
+SGD S000004664 SAM37 GO:0005515 SGD_REF:S000073845|PMID:12891361 IPI F mitochondrial SAM complex constituent YMR060C|MAS37|PET3027|TOM37 gene taxon:4932 20030826 SGD
+SGD S000004664 SAM37 GO:0007008 SGD_REF:S000073845|PMID:12891361 IDA P mitochondrial SAM complex constituent YMR060C|MAS37|PET3027|TOM37 gene taxon:4932 20030826 SGD
+SGD S000004664 SAM37 GO:0007008 SGD_REF:S000073845|PMID:12891361 IMP P mitochondrial SAM complex constituent YMR060C|MAS37|PET3027|TOM37 gene taxon:4932 20030826 SGD
+SGD S000006194 SAM4 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C AdoMet-homocysteine methyltransferase YPL273W gene taxon:4932 20031028 SGD
+SGD S000006194 SAM4 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C AdoMet-homocysteine methyltransferase YPL273W gene taxon:4932 20031028 SGD
+SGD S000006194 SAM4 GO:0008898 SGD_REF:S000066027|PMID:11013242 IDA F AdoMet-homocysteine methyltransferase YPL273W gene taxon:4932 20020801 SGD
+SGD S000006194 SAM4 GO:0000096 SGD_REF:S000066027|PMID:11013242 IMP P AdoMet-homocysteine methyltransferase YPL273W gene taxon:4932 20020801 SGD
+SGD S000004971 SAM50 GO:0001401 SGD_REF:S000075495|PMID:14570913 IDA C YNL026W|OMP85|TOB55 gene taxon:4932 20040303 SGD
+SGD S000004971 SAM50 GO:0005739 SGD_REF:S000075214|PMID:14690591 IDA C YNL026W|OMP85|TOB55 gene taxon:4932 20040105 SGD
+SGD S000004971 SAM50 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YNL026W|OMP85|TOB55 gene taxon:4932 20040924 SGD
+SGD S000004971 SAM50 GO:0005741 SGD_REF:S000075550|PMID:14685243 IDA C YNL026W|OMP85|TOB55 gene taxon:4932 20040310 SGD
+SGD S000004971 SAM50 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C YNL026W|OMP85|TOB55 gene taxon:4932 20060317 SGD
+SGD S000004971 SAM50 GO:0005554 SGD_REF:S000069584 ND F YNL026W|OMP85|TOB55 gene taxon:4932 20031027 SGD
+SGD S000004971 SAM50 GO:0006461 SGD_REF:S000075495|PMID:14570913 IMP P YNL026W|OMP85|TOB55 gene taxon:4932 20040303 SGD
+SGD S000004971 SAM50 GO:0006461 SGD_REF:S000075550|PMID:14685243 IMP P YNL026W|OMP85|TOB55 gene taxon:4932 20040310 SGD
+SGD S000004971 SAM50 GO:0006461 SGD_REF:S000075550|PMID:14685243 IPI P YNL026W|OMP85|TOB55 gene taxon:4932 20040310 SGD
+SGD S000004971 SAM50 GO:0045040 SGD_REF:S000075495|PMID:14570913 IMP P YNL026W|OMP85|TOB55 gene taxon:4932 20040909 SGD
+SGD S000002550 SAN1 GO:0005634 SGD_REF:S000081200|PMID:15797381 IDA C YDR143C gene taxon:4932 20050414 SGD
+SGD S000002550 SAN1 GO:0004842 SGD_REF:S000058946|PMID:15078868 IDA F YDR143C gene taxon:4932 20040905 SGD
+SGD S000002550 SAN1 GO:0006325 SGD_REF:S000049062|PMID:8246972 IGI P YDR143C gene taxon:4932 20020620 SGD
+SGD S000002550 SAN1 GO:0006511 SGD_REF:S000058946|PMID:15078868 IDA P YDR143C gene taxon:4932 20040905 SGD
+SGD S000002550 SAN1 GO:0006950 SGD_REF:S000081200|PMID:15797381 IMP P YDR143C gene taxon:4932 20050414 SGD
+SGD S000000849 SAP1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C AAA ATPase YER047C gene taxon:4932 20031028 SGD
+SGD S000000849 SAP1 GO:0016887 SGD_REF:S000051461|PMID:8654588 ISS F AAA ATPase YER047C gene taxon:4932 20040211 SGD
+SGD S000000849 SAP1 GO:0000004 SGD_REF:S000069584 ND P AAA ATPase YER047C gene taxon:4932 20020522 SGD
+SGD S000001936 SAP155 GO:0005737 SGD_REF:S000055325|PMID:8649382 IPI C YFR040W gene taxon:4932 20010118 SGD
+SGD S000001936 SAP155 GO:0004722 SGD_REF:S000055325|PMID:8649382 IPI F YFR040W gene taxon:4932 20010118 SGD
+SGD S000001936 SAP155 GO:0000082 SGD_REF:S000055325|PMID:8649382 IMP P YFR040W gene taxon:4932 20010118 SGD
+SGD S000001936 SAP155 GO:0000082 SGD_REF:S000055325|PMID:8649382 IGI P YFR040W gene taxon:4932 20010118 SGD
+SGD S000001936 SAP155 GO:0000082 SGD_REF:S000055325|PMID:8649382 IPI P YFR040W gene taxon:4932 20010118 SGD
+SGD S000003634 SAP185 GO:0005737 SGD_REF:S000055325|PMID:8649382 IPI C YJL098W gene taxon:4932 20010118 SGD
+SGD S000003634 SAP185 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YJL098W gene taxon:4932 20040813 SGD
+SGD S000003634 SAP185 GO:0004722 SGD_REF:S000055325|PMID:8649382 IPI F YJL098W gene taxon:4932 20010118 SGD
+SGD S000003634 SAP185 GO:0000082 SGD_REF:S000055325|PMID:8649382 IMP P YJL098W gene taxon:4932 20010118 SGD
+SGD S000003634 SAP185 GO:0000082 SGD_REF:S000055325|PMID:8649382 IPI P YJL098W gene taxon:4932 20010118 SGD
+SGD S000003634 SAP185 GO:0000082 SGD_REF:S000055325|PMID:8649382 IGI P YJL098W gene taxon:4932 20010118 SGD
+SGD S000001736 SAP190 GO:0005737 SGD_REF:S000055325|PMID:8649382 IPI C type 2A-related protein phosphatase YKR028W gene taxon:4932 20010118 SGD
+SGD S000001736 SAP190 GO:0004722 SGD_REF:S000055325|PMID:8649382 IPI F type 2A-related protein phosphatase YKR028W gene taxon:4932 20010118 SGD
+SGD S000001736 SAP190 GO:0000082 SGD_REF:S000055325|PMID:8649382 IGI P type 2A-related protein phosphatase YKR028W gene taxon:4932 20010118 SGD
+SGD S000001736 SAP190 GO:0000082 SGD_REF:S000055325|PMID:8649382 IMP P type 2A-related protein phosphatase YKR028W gene taxon:4932 20010118 SGD
+SGD S000001736 SAP190 GO:0000082 SGD_REF:S000055325|PMID:8649382 IPI P type 2A-related protein phosphatase YKR028W gene taxon:4932 20010118 SGD
+SGD S000004876 SAP30 GO:0000118 SGD_REF:S000047950|PMID:10388812 IPI C YMR263W gene taxon:4932 20021008 SGD
+SGD S000004876 SAP30 GO:0004407 SGD_REF:S000047950|PMID:10388812 IPI F YMR263W gene taxon:4932 20021008 SGD
+SGD S000004876 SAP30 GO:0000183 SGD_REF:S000047950|PMID:10388812 IMP P YMR263W gene taxon:4932 20021008 SGD
+SGD S000004876 SAP30 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P YMR263W gene taxon:4932 20060203 SGD
+SGD S000004876 SAP30 GO:0006348 SGD_REF:S000047950|PMID:10388812 IMP P YMR263W gene taxon:4932 20021008 SGD
+SGD S000004876 SAP30 GO:0030466 SGD_REF:S000047950|PMID:10388812 IMP P YMR263W gene taxon:4932 20021008 SGD
+SGD S000003198 SAP4 GO:0005737 SGD_REF:S000055325|PMID:8649382 ISS C YGL229C gene taxon:4932 20010118 SGD
+SGD S000003198 SAP4 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YGL229C gene taxon:4932 20040813 SGD
+SGD S000003198 SAP4 GO:0004722 SGD_REF:S000055325|PMID:8649382 ISS F YGL229C gene taxon:4932 20010118 SGD
+SGD S000003198 SAP4 GO:0000082 SGD_REF:S000055325|PMID:8649382 IMP P YGL229C gene taxon:4932 20010118 SGD
+SGD S000003198 SAP4 GO:0000082 SGD_REF:S000055325|PMID:8649382 IGI P YGL229C gene taxon:4932 20010118 SGD
+SGD S000006139 SAR1 GO:0030127 SGD_REF:S000061172|PMID:11252894 TAS C ARF family, GTP-binding protein YPL218W gene taxon:4932 20010912 SGD
+SGD S000006139 SAR1 GO:0003924 SGD_REF:S000061172|PMID:11252894 TAS F ARF family, GTP-binding protein YPL218W gene taxon:4932 20010912 SGD
+SGD S000006139 SAR1 GO:0006888 SGD_REF:S000061172|PMID:11252894 TAS P ARF family, GTP-binding protein YPL218W gene taxon:4932 20010912 SGD
+SGD S000002312 SAS10 GO:0005634 SGD_REF:S000039496|PMID:9611201 IDA C U3 snoRNP protein YDL153C|UTP3 gene taxon:4932 20020617 SGD
+SGD S000002312 SAS10 GO:0005732 SGD_REF:S000070145|PMID:12068309 IPI C U3 snoRNP protein YDL153C|UTP3 gene taxon:4932 20030224 SGD
+SGD S000002312 SAS10 GO:0030515 SGD_REF:S000070145|PMID:12068309 IPI F U3 snoRNP protein YDL153C|UTP3 gene taxon:4932 20030224 SGD
+SGD S000002312 SAS10 GO:0006325 SGD_REF:S000039496|PMID:9611201 IGI P U3 snoRNP protein YDL153C|UTP3 gene taxon:4932 20020617 SGD
+SGD S000002312 SAS10 GO:0006325 SGD_REF:S000039496|PMID:9611201 IMP P U3 snoRNP protein YDL153C|UTP3 gene taxon:4932 20020617 SGD
+SGD S000002312 SAS10 GO:0030490 SGD_REF:S000070145|PMID:12068309 IMP P U3 snoRNP protein YDL153C|UTP3 gene taxon:4932 20020906 SGD
+SGD S000002312 SAS10 GO:0030490 SGD_REF:S000070145|PMID:12068309 IPI P U3 snoRNP protein YDL153C|UTP3 gene taxon:4932 20020906 SGD
+SGD S000002312 SAS10 GO:0030490 SGD_REF:S000073750|PMID:12837249 IMP P U3 snoRNP protein YDL153C|UTP3 gene taxon:4932 20030805 SGD
+SGD S000004734 SAS2 GO:0000784 SGD_REF:S000066269|PMID:11731479 IC GO:0006348 C zinc finger protein YMR127C gene taxon:4932 20030403 SGD
+SGD S000004734 SAS2 GO:0000790 SGD_REF:S000066269|PMID:11731479 IDA C zinc finger protein YMR127C gene taxon:4932 20020601 SGD
+SGD S000004734 SAS2 GO:0004406 SGD_REF:S000073145|PMID:12626510 IDA F zinc finger protein YMR127C gene taxon:4932 20030717 SGD
+SGD S000004734 SAS2 GO:0016407 SGD_REF:S000066269|PMID:11731479 IDA F zinc finger protein YMR127C gene taxon:4932 20020531 SGD
+SGD S000004734 SAS2 GO:0006348 SGD_REF:S000066269|PMID:11731479 IDA P zinc finger protein YMR127C gene taxon:4932 20020601 SGD
+SGD S000000148 SAS3 GO:0000123 SGD_REF:S000050029|PMID:10817755 IPI C YBL052C gene taxon:4932 20041007 SGD
+SGD S000000148 SAS3 GO:0000788 SGD_REF:S000070253|PMID:12077334 TAS C YBL052C gene taxon:4932 20020807 SGD
+SGD S000000148 SAS3 GO:0004402 SGD_REF:S000074032|PMID:11092823 TAS F YBL052C gene taxon:4932 20040702 SGD
+SGD S000000148 SAS3 GO:0016407 SGD_REF:S000066269|PMID:11731479 IDA F YBL052C gene taxon:4932 20020531 SGD
+SGD S000000148 SAS3 GO:0006348 SGD_REF:S000066269|PMID:11731479 IMP P YBL052C gene taxon:4932 20021001 SGD
+SGD S000000148 SAS3 GO:0016568 SGD_REF:S000066268|PMID:11731478 IMP P YBL052C gene taxon:4932 20021001 SGD
+SGD S000000148 SAS3 GO:0030466 SGD_REF:S000066269|PMID:11731479 IMP P YBL052C gene taxon:4932 20021001 SGD
+SGD S000002589 SAS4 GO:0000784 SGD_REF:S000066269|PMID:11731479 IC GO:0006348 C YDR181C gene taxon:4932 20030403 SGD
+SGD S000002589 SAS4 GO:0000790 SGD_REF:S000066269|PMID:11731479 IDA C YDR181C gene taxon:4932 20020601 SGD
+SGD S000002589 SAS4 GO:0004406 SGD_REF:S000073145|PMID:12626510 IDA F YDR181C gene taxon:4932 20030717 SGD
+SGD S000002589 SAS4 GO:0016407 SGD_REF:S000066269|PMID:11731479 IDA F YDR181C gene taxon:4932 20020531 SGD
+SGD S000002589 SAS4 GO:0006348 SGD_REF:S000066269|PMID:11731479 IDA P YDR181C gene taxon:4932 20020601 SGD
+SGD S000005739 SAS5 GO:0000784 SGD_REF:S000066269|PMID:11731479 IC GO:0006348 C YOR213C gene taxon:4932 20030403 SGD
+SGD S000005739 SAS5 GO:0000790 SGD_REF:S000066269|PMID:11731479 IDA C YOR213C gene taxon:4932 20020601 SGD
+SGD S000005739 SAS5 GO:0004406 SGD_REF:S000073145|PMID:12626510 IDA F YOR213C gene taxon:4932 20030717 SGD
+SGD S000005739 SAS5 GO:0016407 SGD_REF:S000066269|PMID:11731479 IDA F YOR213C gene taxon:4932 20020531 SGD
+SGD S000005739 SAS5 GO:0006348 SGD_REF:S000066269|PMID:11731479 IDA P YOR213C gene taxon:4932 20020601 SGD
+SGD S000000601 SAT4 GO:0008372 SGD_REF:S000069584 ND C YCR008W|HAL4 gene taxon:4932 20020814 SGD
+SGD S000000601 SAT4 GO:0004672 SGD_REF:S000044312|PMID:10207057 ISS F YCR008W|HAL4 gene taxon:4932 20020814 SGD
+SGD S000000601 SAT4 GO:0000082 SGD_REF:S000072514|PMID:12518319 IGI P YCR008W|HAL4 gene taxon:4932 20030217 SGD
+SGD S000000601 SAT4 GO:0030003 SGD_REF:S000044312|PMID:10207057 IGI P YCR008W|HAL4 gene taxon:4932 20020814 SGD
+SGD S000000601 SAT4 GO:0030003 SGD_REF:S000044312|PMID:10207057 IMP P YCR008W|HAL4 gene taxon:4932 20020814 SGD
+SGD S000001600 SBA1 GO:0005634 SGD_REF:S000044376|PMID:10207098 IDA C HSP90 associated co-chaperone YKL117W gene taxon:4932 20020822 SGD
+SGD S000001600 SBA1 GO:0005737 SGD_REF:S000044376|PMID:10207098 IDA C HSP90 associated co-chaperone YKL117W gene taxon:4932 20020822 SGD
+SGD S000001600 SBA1 GO:0051087 SGD_REF:S000050786|PMID:9632755 IMP F HSP90 associated co-chaperone YKL117W gene taxon:4932 20040723 SGD
+SGD S000001600 SBA1 GO:0051087 SGD_REF:S000050786|PMID:9632755 ISS F HSP90 associated co-chaperone YKL117W gene taxon:4932 20040723 SGD
+SGD S000001600 SBA1 GO:0051087 SGD_REF:S000050786|PMID:9632755 IPI F HSP90 associated co-chaperone YKL117W gene taxon:4932 20040723 SGD
+SGD S000001600 SBA1 GO:0006457 SGD_REF:S000050786|PMID:9632755 IMP P HSP90 associated co-chaperone YKL117W gene taxon:4932 20021118 SGD
+SGD S000001600 SBA1 GO:0006457 SGD_REF:S000050786|PMID:9632755 ISS P HSP90 associated co-chaperone YKL117W gene taxon:4932 20021118 SGD
+SGD S000001600 SBA1 GO:0006457 SGD_REF:S000050786|PMID:9632755 IPI P HSP90 associated co-chaperone YKL117W gene taxon:4932 20021118 SGD
+SGD S000002759 SBE2 GO:0005794 SGD_REF:S000040781|PMID:10679005 IDA C YDR351W gene taxon:4932 20030130 SGD
+SGD S000002759 SBE2 GO:0005554 SGD_REF:S000069584 ND F YDR351W gene taxon:4932 20010119 SGD
+SGD S000002759 SBE2 GO:0007047 SGD_REF:S000040781|PMID:10679005 IGI P YDR351W gene taxon:4932 20030130 SGD
+SGD S000002759 SBE2 GO:0007047 SGD_REF:S000040781|PMID:10679005 IMP P YDR351W gene taxon:4932 20030130 SGD
+SGD S000001145 SBE22 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YHR103W gene taxon:4932 20031028 SGD
+SGD S000001145 SBE22 GO:0005554 SGD_REF:S000069584 ND F YHR103W gene taxon:4932 20010119 SGD
+SGD S000001145 SBE22 GO:0007047 SGD_REF:S000040781|PMID:10679005 IGI P YHR103W gene taxon:4932 20030130 SGD
+SGD S000001145 SBE22 GO:0007047 SGD_REF:S000040781|PMID:10679005 IMP P YHR103W gene taxon:4932 20030130 SGD
+SGD S000002128 SBH1 GO:0005784 SGD_REF:S000058467|PMID:10921929 TAS C Sbh2p homolog YER087C-B|SEB1|YER087C-A gene taxon:4932 20010118 SGD
+SGD S000002128 SBH1 GO:0005784 SGD_REF:S000073831|PMID:12750387 IDA C Sbh2p homolog YER087C-B|SEB1|YER087C-A gene taxon:4932 20041115 SGD
+SGD S000002128 SBH1 GO:0031206 SGD_REF:S000063769|PMID:9252322 TAS C Sbh2p homolog YER087C-B|SEB1|YER087C-A gene taxon:4932 20050317 SGD
+SGD S000002128 SBH1 GO:0005086 SGD_REF:S000073831|PMID:12750387 IDA F Sbh2p homolog YER087C-B|SEB1|YER087C-A gene taxon:4932 20041115 SGD
+SGD S000002128 SBH1 GO:0008565 SGD_REF:S000058467|PMID:10921929 TAS F Sbh2p homolog YER087C-B|SEB1|YER087C-A gene taxon:4932 20010118 SGD
+SGD S000002128 SBH1 GO:0006613 SGD_REF:S000058467|PMID:10921929 TAS P Sbh2p homolog YER087C-B|SEB1|YER087C-A gene taxon:4932 20010118 SGD
+SGD S000002128 SBH1 GO:0006613 SGD_REF:S000073831|PMID:12750387 IDA P Sbh2p homolog YER087C-B|SEB1|YER087C-A gene taxon:4932 20041115 SGD
+SGD S000002128 SBH1 GO:0006616 SGD_REF:S000080325|PMID:15631991 TAS P Sbh2p homolog YER087C-B|SEB1|YER087C-A gene taxon:4932 20050127 SGD
+SGD S000002128 SBH1 GO:0031204 SGD_REF:S000063769|PMID:9252322 TAS P Sbh2p homolog YER087C-B|SEB1|YER087C-A gene taxon:4932 20050317 SGD
+SGD S000002127 SBH2 GO:0005783 SGD_REF:S000065067|PMID:8939984 TAS C Sbh1p homolog YER019C-A|SEB2 gene taxon:4932 20021223 SGD
+SGD S000002127 SBH2 GO:0005784 SGD_REF:S000058467|PMID:10921929 TAS C Sbh1p homolog YER019C-A|SEB2 gene taxon:4932 20010118 SGD
+SGD S000002127 SBH2 GO:0005086 SGD_REF:S000073831|PMID:12750387 IDA F Sbh1p homolog YER019C-A|SEB2 gene taxon:4932 20041115 SGD
+SGD S000002127 SBH2 GO:0008565 SGD_REF:S000058467|PMID:10921929 TAS F Sbh1p homolog YER019C-A|SEB2 gene taxon:4932 20010118 SGD
+SGD S000002127 SBH2 GO:0006613 SGD_REF:S000058467|PMID:10921929 TAS P Sbh1p homolog YER019C-A|SEB2 gene taxon:4932 20010118 SGD
+SGD S000001026 SBP1 GO:0005730 SGD_REF:S000051014|PMID:2823109 IDA C YHL034C|SSB1|SSBR1 gene taxon:4932 20030307 SGD
+SGD S000001026 SBP1 GO:0003723 SGD_REF:S000051014|PMID:2823109 IDA F YHL034C|SSB1|SSBR1 gene taxon:4932 20021029 SGD
+SGD S000001026 SBP1 GO:0016070 SGD_REF:S000051014|PMID:2823109 IPI P YHL034C|SSB1|SSBR1 gene taxon:4932 20021029 SGD
+SGD S000002588 SCC2 GO:0000798 SGD_REF:S000056390|PMID:10429180 TAS C YDR180W gene taxon:4932 20010118 SGD
+SGD S000002588 SCC2 GO:0005554 SGD_REF:S000069584 ND F YDR180W gene taxon:4932 20060428 SGD
+SGD S000002588 SCC2 GO:0000724 SGD_REF:S000080735|PMID:15610742 IMP P YDR180W gene taxon:4932 20050405 SGD
+SGD S000002588 SCC2 GO:0007064 SGD_REF:S000056390|PMID:10429180 TAS P YDR180W gene taxon:4932 20010118 SGD
+SGD S000002588 SCC2 GO:0007064 SGD_REF:S000054345|PMID:9335333 IMP P YDR180W gene taxon:4932 20040610 SGD
+SGD S000000949 SCC4 GO:0000790 SGD_REF:S000060398|PMID:10882066 IDA C YER147C gene taxon:4932 20021018 SGD
+SGD S000000949 SCC4 GO:0005554 SGD_REF:S000069584 ND F YER147C gene taxon:4932 20021018 SGD
+SGD S000000949 SCC4 GO:0000724 SGD_REF:S000080735|PMID:15610742 IMP P YER147C gene taxon:4932 20050405 SGD
+SGD S000000949 SCC4 GO:0007062 SGD_REF:S000060398|PMID:10882066 IMP P YER147C gene taxon:4932 20021018 SGD
+SGD S000005856 SCD5 GO:0000300 SGD_REF:S000050735|PMID:8688556 IDA C YOR329C|FTB1 gene taxon:4932 20020820 SGD
+SGD S000005856 SCD5 GO:0030479 SGD_REF:S000072915|PMID:12181333 IDA C YOR329C|FTB1 gene taxon:4932 20030416 SGD
+SGD S000005856 SCD5 GO:0005515 SGD_REF:S000072915|PMID:12181333 IDA F YOR329C|FTB1 gene taxon:4932 20030416 SGD
+SGD S000005856 SCD5 GO:0006897 SGD_REF:S000072437|PMID:12356757 TAS P YOR329C|FTB1 gene taxon:4932 20030203 SGD
+SGD S000005856 SCD5 GO:0007015 SGD_REF:S000072437|PMID:12356757 TAS P YOR329C|FTB1 gene taxon:4932 20030203 SGD
+SGD S000005856 SCD5 GO:0009306 SGD_REF:S000050735|PMID:8688556 IGI P YOR329C|FTB1 gene taxon:4932 20020820 SGD
+SGD S000005856 SCD5 GO:0009306 SGD_REF:S000050735|PMID:8688556 IMP P YOR329C|FTB1 gene taxon:4932 20020820 SGD
+SGD S000005856 SCD5 GO:0030866 SGD_REF:S000072915|PMID:12181333 IMP P YOR329C|FTB1 gene taxon:4932 20040520 SGD
+SGD S000006333 SCD6 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YPR129W|LSM13 gene taxon:4932 20031028 SGD
+SGD S000006333 SCD6 GO:0003723 SGD_REF:S000076596|PMID:15225602 ISS F YPR129W|LSM13 gene taxon:4932 20040712 SGD
+SGD S000006333 SCD6 GO:0016070 SGD_REF:S000076596|PMID:15225602 ISS P YPR129W|LSM13 gene taxon:4932 20040712 SGD
+SGD S000007279 SCEI GO:0005739 SGD_REF:S000053753|PMID:10357855 TAS C Q0160|I-SceI|OMEGA gene taxon:4932 20021002 SGD
+SGD S000007279 SCEI GO:0004519 SGD_REF:S000053753|PMID:10357855 TAS F Q0160|I-SceI|OMEGA gene taxon:4932 20021002 SGD
+SGD S000007279 SCEI GO:0006314 SGD_REF:S000053753|PMID:10357855 TAS P Q0160|I-SceI|OMEGA gene taxon:4932 20021002 SGD
+SGD S000029678 SCH1 GO:0008372 SGD_REF:S000069584 ND C chitin synthase regulator gene taxon:4932 20020614 SGD
+SGD S000029678 SCH1 GO:0005554 SGD_REF:S000069584 ND F chitin synthase regulator gene taxon:4932 20020614 SGD
+SGD S000029678 SCH1 GO:0006038 SGD_REF:S000057748|PMID:8431950 IGI P chitin synthase regulator gene taxon:4932 20020614 SGD
+SGD S000001248 SCH9 GO:0000329 SGD_REF:S000077407|PMID:15466158 IDA C cAMP-dependent protein kinase homolog, suppressor of cdc25ts YHR205W|KOM1 gene taxon:4932 20041028 SGD
+SGD S000001248 SCH9 GO:0005634 SGD_REF:S000077407|PMID:15466158 IDA C cAMP-dependent protein kinase homolog, suppressor of cdc25ts YHR205W|KOM1 gene taxon:4932 20041028 SGD
+SGD S000001248 SCH9 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C cAMP-dependent protein kinase homolog, suppressor of cdc25ts YHR205W|KOM1 gene taxon:4932 20031028 SGD
+SGD S000001248 SCH9 GO:0004674 SGD_REF:S000043958|PMID:3290050 IGI F cAMP-dependent protein kinase homolog, suppressor of cdc25ts YHR205W|KOM1 gene taxon:4932 20021111 SGD
+SGD S000001248 SCH9 GO:0004674 SGD_REF:S000043958|PMID:3290050 ISS F cAMP-dependent protein kinase homolog, suppressor of cdc25ts YHR205W|KOM1 gene taxon:4932 20021111 SGD
+SGD S000001248 SCH9 GO:0001302 SGD_REF:S000080970|PMID:15722108 IMP P cAMP-dependent protein kinase homolog, suppressor of cdc25ts YHR205W|KOM1 gene taxon:4932 20050314 SGD
+SGD S000001248 SCH9 GO:0001324 SGD_REF:S000060129|PMID:11292860 IMP P cAMP-dependent protein kinase homolog, suppressor of cdc25ts YHR205W|KOM1 gene taxon:4932 20030814 SGD
+SGD S000001248 SCH9 GO:0006468 SGD_REF:S000043958|PMID:3290050 IGI P cAMP-dependent protein kinase homolog, suppressor of cdc25ts YHR205W|KOM1 gene taxon:4932 20021111 SGD
+SGD S000001248 SCH9 GO:0006468 SGD_REF:S000043958|PMID:3290050 ISS P cAMP-dependent protein kinase homolog, suppressor of cdc25ts YHR205W|KOM1 gene taxon:4932 20021111 SGD
+SGD S000001248 SCH9 GO:0008361 SGD_REF:S000070190|PMID:12089449 IDA P cAMP-dependent protein kinase homolog, suppressor of cdc25ts YHR205W|KOM1 gene taxon:4932 20020730 SGD
+SGD S000004827 SCJ1 GO:0005788 SGD_REF:S000047685|PMID:7744969 IDA C DnaJ homolog YMR214W gene taxon:4932 20020926 SGD
+SGD S000004827 SCJ1 GO:0051087 SGD_REF:S000063756|PMID:9817751 IMP F DnaJ homolog YMR214W gene taxon:4932 20040723 SGD
+SGD S000004827 SCJ1 GO:0051087 SGD_REF:S000063756|PMID:9817751 ISS F DnaJ homolog YMR214W gene taxon:4932 20040723 SGD
+SGD S000004827 SCJ1 GO:0006457 SGD_REF:S000063756|PMID:9817751 IMP P DnaJ homolog YMR214W gene taxon:4932 20020926 SGD
+SGD S000004827 SCJ1 GO:0030433 SGD_REF:S000074517|PMID:11381090 IMP P DnaJ homolog YMR214W gene taxon:4932 20060201 SGD
+SGD S000004827 SCJ1 GO:0030968 SGD_REF:S000063756|PMID:9817751 IMP P DnaJ homolog YMR214W gene taxon:4932 20040723 SGD
+SGD S000002979 SCL1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C proteasome subunit YC7alpha/Y8 (protease yscE subunit 7) YGL011C|PRC2 gene taxon:4932 20040928 SGD
+SGD S000002979 SCL1 GO:0019773 SGD_REF:S000058010|PMID:8982460 TAS C proteasome subunit YC7alpha/Y8 (protease yscE subunit 7) YGL011C|PRC2 gene taxon:4932 20030924 SGD
+SGD S000002979 SCL1 GO:0019773 SGD_REF:S000040877|PMID:9087403 IPI C proteasome subunit YC7alpha/Y8 (protease yscE subunit 7) YGL011C|PRC2 gene taxon:4932 20041109 SGD
+SGD S000002979 SCL1 GO:0004175 SGD_REF:S000058010|PMID:8982460 TAS F proteasome subunit YC7alpha/Y8 (protease yscE subunit 7) YGL011C|PRC2 gene taxon:4932 20010118 SGD
+SGD S000002979 SCL1 GO:0004175 SGD_REF:S000058457|PMID:10872471 TAS F proteasome subunit YC7alpha/Y8 (protease yscE subunit 7) YGL011C|PRC2 gene taxon:4932 20010118 SGD
+SGD S000002979 SCL1 GO:0006511 SGD_REF:S000058010|PMID:8982460 TAS P proteasome subunit YC7alpha/Y8 (protease yscE subunit 7) YGL011C|PRC2 gene taxon:4932 20010118 SGD
+SGD S000002979 SCL1 GO:0006511 SGD_REF:S000058457|PMID:10872471 TAS P proteasome subunit YC7alpha/Y8 (protease yscE subunit 7) YGL011C|PRC2 gene taxon:4932 20010118 SGD
+SGD S000002298 SCM3 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YDL139C gene taxon:4932 20031028 SGD
+SGD S000002298 SCM3 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDL139C gene taxon:4932 20031028 SGD
+SGD S000002298 SCM3 GO:0005554 SGD_REF:S000069584 ND F YDL139C gene taxon:4932 20021001 SGD
+SGD S000002298 SCM3 GO:0000004 SGD_REF:S000069584 ND P YDL139C gene taxon:4932 20021001 SGD
+SGD S000003281 SCM4 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YGR049W gene taxon:4932 20031028 SGD
+SGD S000003281 SCM4 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YGR049W gene taxon:4932 20040924 SGD
+SGD S000003281 SCM4 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C YGR049W gene taxon:4932 20060317 SGD
+SGD S000003281 SCM4 GO:0005554 SGD_REF:S000069584 ND F YGR049W gene taxon:4932 20021030 SGD
+SGD S000003281 SCM4 GO:0007049 SGD_REF:S000054769|PMID:1465103 IGI SGD:S000001885 P YGR049W gene taxon:4932 20021030 SGD
+SGD S000000241 SCO1 GO:0005743 SGD_REF:S000039911|PMID:1944230 IDA C YBR037C|PET161 gene taxon:4932 20010118 SGD
+SGD S000000241 SCO1 GO:0005507 SGD_REF:S000076607|PMID:11546815 IDA F YBR037C|PET161 gene taxon:4932 20040716 SGD
+SGD S000000241 SCO1 GO:0008379 SGD_REF:S000078936|PMID:10954195 ISS F YBR037C|PET161 gene taxon:4932 20050121 SGD
+SGD S000000241 SCO1 GO:0006461 SGD_REF:S000043230|PMID:2835635 IMP P YBR037C|PET161 gene taxon:4932 20010118 SGD
+SGD S000000241 SCO1 GO:0006825 SGD_REF:S000053671|PMID:8662933 IGI P YBR037C|PET161 gene taxon:4932 20010118 SGD
+SGD S000000241 SCO1 GO:0006825 SGD_REF:S000053671|PMID:8662933 ISS P YBR037C|PET161 gene taxon:4932 20010118 SGD
+SGD S000000241 SCO1 GO:0006980 SGD_REF:S000080592|PMID:15659396 ISS P YBR037C|PET161 gene taxon:4932 20050324 SGD
+SGD S000000228 SCO2 GO:0005740 SGD_REF:S000053671|PMID:8662933 IDA C YBR024W gene taxon:4932 20010118 SGD
+SGD S000000228 SCO2 GO:0008379 SGD_REF:S000078936|PMID:10954195 ISS F YBR024W gene taxon:4932 20050121 SGD
+SGD S000000228 SCO2 GO:0006825 SGD_REF:S000053671|PMID:8662933 ISS P YBR024W gene taxon:4932 20010118 SGD
+SGD S000005894 SCP1 GO:0030479 SGD_REF:S000073708|PMID:12857851 IDA C calponin homolog YOR367W gene taxon:4932 20030828 SGD
+SGD S000005894 SCP1 GO:0030674 SGD_REF:S000073708|PMID:12857851 IDA F calponin homolog YOR367W gene taxon:4932 20040409 SGD
+SGD S000005894 SCP1 GO:0051015 SGD_REF:S000073708|PMID:12857851 IDA F calponin homolog YOR367W gene taxon:4932 20040409 SGD
+SGD S000005894 SCP1 GO:0001300 SGD_REF:S000077155|PMID:15024029 IGI P calponin homolog YOR367W gene taxon:4932 20041001 SGD
+SGD S000005894 SCP1 GO:0001300 SGD_REF:S000077155|PMID:15024029 IMP P calponin homolog YOR367W gene taxon:4932 20041001 SGD
+SGD S000005894 SCP1 GO:0007015 SGD_REF:S000073708|PMID:12857851 IDA P calponin homolog YOR367W gene taxon:4932 20030828 SGD
+SGD S000003616 SCP160 GO:0005789 SGD_REF:S000060283|PMID:11278502 IDA C YJL080C gene taxon:4932 20020924 SGD
+SGD S000003616 SCP160 GO:0005844 SGD_REF:S000060283|PMID:11278502 IDA C YJL080C gene taxon:4932 20020924 SGD
+SGD S000003616 SCP160 GO:0042175 SGD_REF:S000054401|PMID:8533468 IDA C YJL080C gene taxon:4932 20020924 SGD
+SGD S000003616 SCP160 GO:0001965 SGD_REF:S000074143|PMID:14536090 IPI SGD:S000001047 F YJL080C gene taxon:4932 20060427 SGD
+SGD S000003616 SCP160 GO:0003723 SGD_REF:S000060283|PMID:11278502 IDA F YJL080C gene taxon:4932 20030226 SGD
+SGD S000003616 SCP160 GO:0000750 SGD_REF:S000074143|PMID:14536090 IGI SGD:S000001047 P YJL080C gene taxon:4932 20060427 SGD
+SGD S000003616 SCP160 GO:0006348 SGD_REF:S000115153|PMID:16632467 IMP P YJL080C gene taxon:4932 20060427 SGD
+SGD S000003616 SCP160 GO:0006348 SGD_REF:S000115153|PMID:16632467 IGI SGD:S000000479|SGD:S000004434|SGD:S000005274|SGD:S000004445 P YJL080C gene taxon:4932 20060427 SGD
+SGD S000003616 SCP160 GO:0007059 SGD_REF:S000054401|PMID:8533468 IMP P YJL080C gene taxon:4932 20020924 SGD
+SGD S000003616 SCP160 GO:0008298 SGD_REF:S000060283|PMID:11278502 IPI P YJL080C gene taxon:4932 20020924 SGD
+SGD S000003616 SCP160 GO:0030466 SGD_REF:S000115153|PMID:16632467 IMP P YJL080C gene taxon:4932 20060427 SGD
+SGD S000003616 SCP160 GO:0045141 SGD_REF:S000115153|PMID:16632467 IMP P YJL080C gene taxon:4932 20060427 SGD
+SGD S000006491 SCR1 GO:0005786 SGD_REF:S000049731|PMID:7925282 IDA C small cytoplasmic RNA gene taxon:4932 20020620 SGD
+SGD S000006491 SCR1 GO:0005048 SGD_REF:S000049731|PMID:7925282 IPI F small cytoplasmic RNA gene taxon:4932 20030527 SGD
+SGD S000006491 SCR1 GO:0006617 SGD_REF:S000049731|PMID:7925282 IC GO:0005786 P small cytoplasmic RNA gene taxon:4932 20050128 SGD
+SGD S000006491 SCR1 GO:0045047 SGD_REF:S000049731|PMID:7925282 IPI P small cytoplasmic RNA gene taxon:4932 20020620 SGD
+SGD S000000922 SCS2 GO:0005783 SGD_REF:S000051398|PMID:9537365 IDA C YER120W gene taxon:4932 20020820 SGD
+SGD S000000922 SCS2 GO:0016021 SGD_REF:S000051398|PMID:9537365 IDA C YER120W gene taxon:4932 20020820 SGD
+SGD S000000922 SCS2 GO:0005515 SGD_REF:S000073325|PMID:12727870 IDA F YER120W gene taxon:4932 20030624 SGD
+SGD S000000922 SCS2 GO:0006020 SGD_REF:S000051398|PMID:9537365 IMP P YER120W gene taxon:4932 20020820 SGD
+SGD S000000922 SCS2 GO:0006348 SGD_REF:S000060389|PMID:11333225 IDA P YER120W gene taxon:4932 20031104 SGD
+SGD S000000922 SCS2 GO:0006348 SGD_REF:S000060389|PMID:11333225 IMP P YER120W gene taxon:4932 20031104 SGD
+SGD S000000922 SCS2 GO:0045047 SGD_REF:S000073325|PMID:12727870 IMP P YER120W gene taxon:4932 20030624 SGD
+SGD S000000922 SCS2 GO:0045047 SGD_REF:S000073325|PMID:12727870 IPI P YER120W gene taxon:4932 20030624 SGD
+SGD S000007228 SCS22 GO:0008372 SGD_REF:S000069584 ND C YBL091C-A gene taxon:4932 20030203 SGD
+SGD S000007228 SCS22 GO:0005554 SGD_REF:S000069584 ND F YBL091C-A gene taxon:4932 20031104 SGD
+SGD S000007228 SCS22 GO:0000004 SGD_REF:S000069584 ND P YBL091C-A gene taxon:4932 20040701 SGD
+SGD S000007228 SCS22 NOT GO:0006348 SGD_REF:S000060389|PMID:11333225 IGI SGD:S000000922 P YBL091C-A gene taxon:4932 20031104 SGD
+SGD S000007228 SCS22 NOT GO:0006348 SGD_REF:S000060389|PMID:11333225 IDA P YBL091C-A gene taxon:4932 20031104 SGD
+SGD S000007228 SCS22 NOT GO:0006348 SGD_REF:S000060389|PMID:11333225 IMP P YBL091C-A gene taxon:4932 20031104 SGD
+SGD S000003094 SCS3 GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YGL126W gene taxon:4932 20031028 SGD
+SGD S000003094 SCS3 GO:0005554 SGD_REF:S000069584 ND F YGL126W gene taxon:4932 20021104 SGD
+SGD S000003094 SCS3 GO:0006644 SGD_REF:S000050979|PMID:7706223 IMP P YGL126W gene taxon:4932 20021104 SGD
+SGD S000004885 SCS7 GO:0005783 SGD_REF:S000045035|PMID:9559540 IMP C desaturase, hydroxylase, sphingolipid alpha-hydroxylase YMR272C|FAH1 gene taxon:4932 20021115 SGD
+SGD S000004885 SCS7 GO:0005783 SGD_REF:S000045035|PMID:9559540 ISS C desaturase, hydroxylase, sphingolipid alpha-hydroxylase YMR272C|FAH1 gene taxon:4932 20021115 SGD
+SGD S000004885 SCS7 GO:0016491 SGD_REF:S000045035|PMID:9559540 IMP F desaturase, hydroxylase, sphingolipid alpha-hydroxylase YMR272C|FAH1 gene taxon:4932 20021115 SGD
+SGD S000004885 SCS7 GO:0016491 SGD_REF:S000045035|PMID:9559540 ISS F desaturase, hydroxylase, sphingolipid alpha-hydroxylase YMR272C|FAH1 gene taxon:4932 20021115 SGD
+SGD S000004885 SCS7 GO:0006631 SGD_REF:S000045035|PMID:9559540 IMP P desaturase, hydroxylase, sphingolipid alpha-hydroxylase YMR272C|FAH1 gene taxon:4932 20021115 SGD
+SGD S000000107 SCT1 GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C glycerol 3-phosphate/dihydroxyacetone phosphate dual substrate-specific sn-1 acyltransferase YBL011W|GAT2 gene taxon:4932 20031028 SGD
+SGD S000000107 SCT1 GO:0004366 SGD_REF:S000066203|PMID:11544256 IGI F glycerol 3-phosphate/dihydroxyacetone phosphate dual substrate-specific sn-1 acyltransferase YBL011W|GAT2 gene taxon:4932 20021028 SGD
+SGD S000000107 SCT1 GO:0004366 SGD_REF:S000066203|PMID:11544256 IDA F glycerol 3-phosphate/dihydroxyacetone phosphate dual substrate-specific sn-1 acyltransferase YBL011W|GAT2 gene taxon:4932 20021028 SGD
+SGD S000000107 SCT1 GO:0004366 SGD_REF:S000066203|PMID:11544256 IMP F glycerol 3-phosphate/dihydroxyacetone phosphate dual substrate-specific sn-1 acyltransferase YBL011W|GAT2 gene taxon:4932 20021028 SGD
+SGD S000000107 SCT1 GO:0008654 SGD_REF:S000066203|PMID:11544256 IGI P glycerol 3-phosphate/dihydroxyacetone phosphate dual substrate-specific sn-1 acyltransferase YBL011W|GAT2 gene taxon:4932 20021028 SGD
+SGD S000000107 SCT1 GO:0008654 SGD_REF:S000066203|PMID:11544256 IMP P glycerol 3-phosphate/dihydroxyacetone phosphate dual substrate-specific sn-1 acyltransferase YBL011W|GAT2 gene taxon:4932 20021028 SGD
+SGD S000029434 SCW1 GO:0009277 SGD_REF:S000053320|PMID:9301021 IDA C gene taxon:4932 20020920 SGD
+SGD S000029434 SCW1 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20020920 SGD
+SGD S000029434 SCW1 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20020920 SGD
+SGD S000004921 SCW10 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C soluble cell wall protein YMR305C gene taxon:4932 20020507 SGD
+SGD S000004921 SCW10 GO:0005783 SGD_REF:S000069459|PMID:11914276 IDA C soluble cell wall protein YMR305C gene taxon:4932 20020507 SGD
+SGD S000004921 SCW10 GO:0009277 SGD_REF:S000050571|PMID:9748433 IDA C soluble cell wall protein YMR305C gene taxon:4932 20010801 SGD
+SGD S000004921 SCW10 GO:0009277 SGD_REF:S000081097|PMID:15781460 IDA C soluble cell wall protein YMR305C gene taxon:4932 20050601 SGD
+SGD S000004921 SCW10 GO:0015926 SGD_REF:S000050571|PMID:9748433 ISS F soluble cell wall protein YMR305C gene taxon:4932 20010801 SGD
+SGD S000004921 SCW10 GO:0000747 SGD_REF:S000050571|PMID:9748433 IGI P soluble cell wall protein YMR305C gene taxon:4932 20010801 SGD
+SGD S000002996 SCW11 GO:0009277 SGD_REF:S000050571|PMID:9748433 IDA C glucanase YGL028C gene taxon:4932 20020619 SGD
+SGD S000002996 SCW11 GO:0004338 SGD_REF:S000050571|PMID:9748433 ISS F glucanase YGL028C gene taxon:4932 20020619 SGD
+SGD S000002996 SCW11 GO:0007109 SGD_REF:S000050571|PMID:9748433 IMP P glucanase YGL028C gene taxon:4932 20020619 SGD
+SGD S000029435 SCW2 GO:0009277 SGD_REF:S000053320|PMID:9301021 IDA C gene taxon:4932 20020920 SGD
+SGD S000029435 SCW2 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20020920 SGD
+SGD S000029435 SCW2 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20020920 SGD
+SGD S000003511 SCW4 GO:0009277 SGD_REF:S000050571|PMID:9748433 IDA C soluble cell wall protein YGR279C gene taxon:4932 20010801 SGD
+SGD S000003511 SCW4 GO:0009277 SGD_REF:S000081097|PMID:15781460 IDA C soluble cell wall protein YGR279C gene taxon:4932 20050601 SGD
+SGD S000003511 SCW4 GO:0015926 SGD_REF:S000050571|PMID:9748433 ISS F soluble cell wall protein YGR279C gene taxon:4932 20010801 SGD
+SGD S000003511 SCW4 GO:0000747 SGD_REF:S000050571|PMID:9748433 IGI P soluble cell wall protein YGR279C gene taxon:4932 20010801 SGD
+SGD S000029436 SCW5 GO:0009277 SGD_REF:S000053320|PMID:9301021 IDA C gene taxon:4932 20020920 SGD
+SGD S000029436 SCW5 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20020920 SGD
+SGD S000029436 SCW5 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20020920 SGD
+SGD S000029437 SCW6 GO:0009277 SGD_REF:S000053320|PMID:9301021 IDA C gene taxon:4932 20020920 SGD
+SGD S000029437 SCW6 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20020920 SGD
+SGD S000029437 SCW6 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20020920 SGD
+SGD S000029438 SCW7 GO:0009277 SGD_REF:S000053320|PMID:9301021 IDA C gene taxon:4932 20020920 SGD
+SGD S000029438 SCW7 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20020920 SGD
+SGD S000029438 SCW7 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20020920 SGD
+SGD S000029439 SCW8 GO:0009277 SGD_REF:S000053320|PMID:9301021 IDA C gene taxon:4932 20020920 SGD
+SGD S000029439 SCW8 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20020920 SGD
+SGD S000029439 SCW8 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20020920 SGD
+SGD S000029440 SCW9 GO:0009277 SGD_REF:S000053320|PMID:9301021 IDA C gene taxon:4932 20020920 SGD
+SGD S000029440 SCW9 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20020920 SGD
+SGD S000029440 SCW9 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20020920 SGD
+SGD S000003051 SCY1 colocalizes_with GO:0030136 SGD_REF:S000074185|PMID:14562095 IDA C YGL083W gene taxon:4932 20031028 SGD
+SGD S000003051 SCY1 GO:0005554 SGD_REF:S000069584 ND F YGL083W gene taxon:4932 20021122 SGD
+SGD S000003051 SCY1 GO:0000004 SGD_REF:S000069584 ND P YGL083W gene taxon:4932 20021122 SGD
+SGD S000003477 SDA1 GO:0005634 SGD_REF:S000051263|PMID:10704371 IDA C YGR245C gene taxon:4932 20021001 SGD
+SGD S000003477 SDA1 GO:0005554 SGD_REF:S000069584 ND F YGR245C gene taxon:4932 20021001 SGD
+SGD S000003477 SDA1 GO:0007089 SGD_REF:S000062301|PMID:11160833 IMP P YGR245C gene taxon:4932 20021001 SGD
+SGD S000003477 SDA1 GO:0030036 SGD_REF:S000051263|PMID:10704371 IMP P YGR245C gene taxon:4932 20021001 SGD
+SGD S000003477 SDA1 GO:0042255 SGD_REF:S000076076|PMID:15116429 TAS P YGR245C gene taxon:4932 20040618 SGD
+SGD S000002877 SDC1 GO:0048188 SGD_REF:S000066156|PMID:11687631 IPI SGD:S000000064|SGD:S000000379|SGD:S000004005|SGD:S000006059|SGD:S000001501|SGD:S000001161 C compass (complex proteins associated with Set1p) component YDR469W|CPS25|SAF19 gene taxon:4932 20050524 SGD
+SGD S000002877 SDC1 GO:0048188 SGD_REF:S000068991|PMID:11752412 IPI SGD:S000000064|SGD:S000006059|SGD:S000004005|SGD:S000001501|SGD:S000001161|SGD:S000000379 C compass (complex proteins associated with Set1p) component YDR469W|CPS25|SAF19 gene taxon:4932 20050524 SGD
+SGD S000002877 SDC1 GO:0048188 SGD_REF:S000068755|PMID:11742990 IPI SGD:S000000064|SGD:S000001161|SGD:S000000379|SGD:S000000462|SGD:S000001501|SGD:S000006059|SGD:S000004005 C compass (complex proteins associated with Set1p) component YDR469W|CPS25|SAF19 gene taxon:4932 20050524 SGD
+SGD S000002877 SDC1 contributes_to GO:0042800 SGD_REF:S000068991|PMID:11752412 IMP F compass (complex proteins associated with Set1p) component YDR469W|CPS25|SAF19 gene taxon:4932 20050524 SGD
+SGD S000002877 SDC1 contributes_to GO:0042800 SGD_REF:S000069538|PMID:11805083 IDA F compass (complex proteins associated with Set1p) component YDR469W|CPS25|SAF19 gene taxon:4932 20050525 SGD
+SGD S000002877 SDC1 contributes_to GO:0042800 SGD_REF:S000068755|PMID:11742990 IDA F compass (complex proteins associated with Set1p) component YDR469W|CPS25|SAF19 gene taxon:4932 20050525 SGD
+SGD S000002877 SDC1 contributes_to GO:0042800 SGD_REF:S000069538|PMID:11805083 IMP F compass (complex proteins associated with Set1p) component YDR469W|CPS25|SAF19 gene taxon:4932 20050525 SGD
+SGD S000002877 SDC1 GO:0006348 SGD_REF:S000066156|PMID:11687631 IMP P compass (complex proteins associated with Set1p) component YDR469W|CPS25|SAF19 gene taxon:4932 20020212 SGD
+SGD S000002877 SDC1 GO:0006348 SGD_REF:S000069538|PMID:11805083 IMP P compass (complex proteins associated with Set1p) component YDR469W|CPS25|SAF19 gene taxon:4932 20050525 SGD
+SGD S000002877 SDC1 GO:0006348 SGD_REF:S000068991|PMID:11752412 IMP P compass (complex proteins associated with Set1p) component YDR469W|CPS25|SAF19 gene taxon:4932 20050524 SGD
+SGD S000002877 SDC1 GO:0016571 SGD_REF:S000068755|PMID:11742990 IDA P compass (complex proteins associated with Set1p) component YDR469W|CPS25|SAF19 gene taxon:4932 20020212 SGD
+SGD S000002877 SDC1 GO:0016571 SGD_REF:S000068991|PMID:11752412 IDA P compass (complex proteins associated with Set1p) component YDR469W|CPS25|SAF19 gene taxon:4932 20050524 SGD
+SGD S000002877 SDC1 GO:0016571 SGD_REF:S000069538|PMID:11805083 IMP P compass (complex proteins associated with Set1p) component YDR469W|CPS25|SAF19 gene taxon:4932 20050525 SGD
+SGD S000002877 SDC1 GO:0016571 SGD_REF:S000069538|PMID:11805083 IDA P compass (complex proteins associated with Set1p) component YDR469W|CPS25|SAF19 gene taxon:4932 20050525 SGD
+SGD S000002877 SDC1 GO:0016571 SGD_REF:S000068991|PMID:11752412 IMP P compass (complex proteins associated with Set1p) component YDR469W|CPS25|SAF19 gene taxon:4932 20050524 SGD
+SGD S000003939 SDC25 GO:0008372 SGD_REF:S000069584 ND C YLL016W gene taxon:4932 20010119 SGD
+SGD S000003939 SDC25 GO:0005088 SGD_REF:S000052520|PMID:7941731 TAS F YLL016W gene taxon:4932 20010118 SGD
+SGD S000003939 SDC25 GO:0007265 SGD_REF:S000052520|PMID:7941731 TAS P YLL016W gene taxon:4932 20010118 SGD
+SGD S000001631 SDH1 GO:0005749 SGD_REF:S000054301|PMID:9929002 TAS C succinate dehydrogenase flavoprotein subunit YKL148C gene taxon:4932 20030722 SGD
+SGD S000001631 SDH1 GO:0008177 SGD_REF:S000054301|PMID:9929002 TAS F succinate dehydrogenase flavoprotein subunit YKL148C gene taxon:4932 20030722 SGD
+SGD S000001631 SDH1 GO:0008177 SGD_REF:S000086932|PMID:16232921 IGI SGD:S000003581 F succinate dehydrogenase flavoprotein subunit YKL148C gene taxon:4932 20051128 SGD
+SGD S000001631 SDH1 GO:0008177 SGD_REF:S000086932|PMID:16232921 IMP F succinate dehydrogenase flavoprotein subunit YKL148C gene taxon:4932 20051128 SGD
+SGD S000001631 SDH1 GO:0006099 SGD_REF:S000058126|PMID:9175438 TAS P succinate dehydrogenase flavoprotein subunit YKL148C gene taxon:4932 20010118 SGD
+SGD S000001631 SDH1 GO:0006121 SGD_REF:S000054301|PMID:9929002 TAS P succinate dehydrogenase flavoprotein subunit YKL148C gene taxon:4932 20030722 SGD
+SGD S000003964 SDH2 GO:0005749 SGD_REF:S000054301|PMID:9929002 TAS C succinate dehydrogenase (ubiquinone) iron-sulfur protein subunit YLL041C|ACN17 gene taxon:4932 20030722 SGD
+SGD S000003964 SDH2 GO:0008177 SGD_REF:S000054301|PMID:9929002 TAS F succinate dehydrogenase (ubiquinone) iron-sulfur protein subunit YLL041C|ACN17 gene taxon:4932 20030722 SGD
+SGD S000003964 SDH2 GO:0006099 SGD_REF:S000058126|PMID:9175438 TAS P succinate dehydrogenase (ubiquinone) iron-sulfur protein subunit YLL041C|ACN17 gene taxon:4932 20010118 SGD
+SGD S000003964 SDH2 GO:0006121 SGD_REF:S000054301|PMID:9929002 TAS P succinate dehydrogenase (ubiquinone) iron-sulfur protein subunit YLL041C|ACN17 gene taxon:4932 20030722 SGD
+SGD S000001624 SDH3 GO:0005749 SGD_REF:S000054301|PMID:9929002 TAS C succinate dehydrogenase cytochrome b YKL141W|CYB3|YKL4 gene taxon:4932 20030722 SGD
+SGD S000001624 SDH3 GO:0008177 SGD_REF:S000054301|PMID:9929002 TAS F succinate dehydrogenase cytochrome b YKL141W|CYB3|YKL4 gene taxon:4932 20030722 SGD
+SGD S000001624 SDH3 GO:0008177 SGD_REF:S000054301|PMID:9929002 IMP F succinate dehydrogenase cytochrome b YKL141W|CYB3|YKL4 gene taxon:4932 20030722 SGD
+SGD S000001624 SDH3 GO:0006099 SGD_REF:S000058126|PMID:9175438 TAS P succinate dehydrogenase cytochrome b YKL141W|CYB3|YKL4 gene taxon:4932 20010118 SGD
+SGD S000001624 SDH3 GO:0006121 SGD_REF:S000054301|PMID:9929002 TAS P succinate dehydrogenase cytochrome b YKL141W|CYB3|YKL4 gene taxon:4932 20030722 SGD
+SGD S000002585 SDH4 GO:0005749 SGD_REF:S000054301|PMID:9929002 TAS C succinate dehydrogenase membrane anchor subunit YDR178W|ACN18 gene taxon:4932 20030722 SGD
+SGD S000002585 SDH4 GO:0008177 SGD_REF:S000054301|PMID:9929002 TAS F succinate dehydrogenase membrane anchor subunit YDR178W|ACN18 gene taxon:4932 20030722 SGD
+SGD S000002585 SDH4 GO:0008177 SGD_REF:S000054301|PMID:9929002 IMP F succinate dehydrogenase membrane anchor subunit YDR178W|ACN18 gene taxon:4932 20030722 SGD
+SGD S000002585 SDH4 GO:0006099 SGD_REF:S000058126|PMID:9175438 TAS P succinate dehydrogenase membrane anchor subunit YDR178W|ACN18 gene taxon:4932 20010118 SGD
+SGD S000002585 SDH4 GO:0006121 SGD_REF:S000054301|PMID:9929002 TAS P succinate dehydrogenase membrane anchor subunit YDR178W|ACN18 gene taxon:4932 20030722 SGD
+SGD S000001429 SDL1 GO:0008372 SGD_REF:S000069584 ND C L-serine dehydratase YIL167W gene taxon:4932 20021001 SGD
+SGD S000001429 SDL1 GO:0003941 SGD_REF:S000065076|PMID:2194168 ISS F L-serine dehydratase YIL167W gene taxon:4932 20051101 SGD
+SGD S000001429 SDL1 GO:0009069 SGD_REF:S000065076|PMID:2194168 ISS P L-serine dehydratase YIL167W gene taxon:4932 20051101 SGD
+SGD S000004012 SDO1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YLR022C gene taxon:4932 20031028 SGD
+SGD S000004012 SDO1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YLR022C gene taxon:4932 20031028 SGD
+SGD S000004012 SDO1 GO:0005737 SGD_REF:S000075214|PMID:14690591 IDA C YLR022C gene taxon:4932 20040105 SGD
+SGD S000004012 SDO1 GO:0005554 SGD_REF:S000069584 ND F YLR022C gene taxon:4932 20021126 SGD
+SGD S000004012 SDO1 GO:0006365 SGD_REF:S000073750|PMID:12837249 IMP P YLR022C gene taxon:4932 20030805 SGD
+SGD S000004012 SDO1 GO:0016070 SGD_REF:S000080732|PMID:15701634 IPI P YLR022C gene taxon:4932 20050405 SGD
+SGD S000001375 SDP1 GO:0005634 SGD_REF:S000070007|PMID:11923319 IDA C YIL113W gene taxon:4932 20020715 SGD
+SGD S000001375 SDP1 GO:0005737 SGD_REF:S000070007|PMID:11923319 IDA C YIL113W gene taxon:4932 20020715 SGD
+SGD S000001375 SDP1 GO:0017017 SGD_REF:S000071142|PMID:12220658 IDA F YIL113W gene taxon:4932 20021001 SGD
+SGD S000001375 SDP1 GO:0000196 SGD_REF:S000070007|PMID:11923319 IGI P YIL113W gene taxon:4932 20021001 SGD
+SGD S000001375 SDP1 GO:0000196 SGD_REF:S000070007|PMID:11923319 IMP P YIL113W gene taxon:4932 20021001 SGD
+SGD S000001676 SDS22 GO:0005634 SGD_REF:S000069459|PMID:11914276 IDA C Glc7p regulatory subunit YKL193C|EGP1 gene taxon:4932 20020507 SGD
+SGD S000001676 SDS22 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C Glc7p regulatory subunit YKL193C|EGP1 gene taxon:4932 20031028 SGD
+SGD S000001676 SDS22 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C Glc7p regulatory subunit YKL193C|EGP1 gene taxon:4932 20020507 SGD
+SGD S000001676 SDS22 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C Glc7p regulatory subunit YKL193C|EGP1 gene taxon:4932 20031028 SGD
+SGD S000001676 SDS22 GO:0008599 SGD_REF:S000065824|PMID:11412094 TAS F Glc7p regulatory subunit YKL193C|EGP1 gene taxon:4932 20030130 SGD
+SGD S000001676 SDS22 GO:0030234 SGD_REF:S000071137|PMID:12127071 TAS F Glc7p regulatory subunit YKL193C|EGP1 gene taxon:4932 20020919 SGD
+SGD S000001676 SDS22 GO:0006605 SGD_REF:S000069049|PMID:11801737 IGI P Glc7p regulatory subunit YKL193C|EGP1 gene taxon:4932 20021001 SGD
+SGD S000001676 SDS22 GO:0006605 SGD_REF:S000069049|PMID:11801737 IMP P Glc7p regulatory subunit YKL193C|EGP1 gene taxon:4932 20021001 SGD
+SGD S000001676 SDS22 GO:0006605 SGD_REF:S000069049|PMID:11801737 IPI P Glc7p regulatory subunit YKL193C|EGP1 gene taxon:4932 20021001 SGD
+SGD S000001676 SDS22 GO:0007059 SGD_REF:S000069049|PMID:11801737 IGI P Glc7p regulatory subunit YKL193C|EGP1 gene taxon:4932 20021001 SGD
+SGD S000001676 SDS22 GO:0007059 SGD_REF:S000069049|PMID:11801737 IMP P Glc7p regulatory subunit YKL193C|EGP1 gene taxon:4932 20021001 SGD
+SGD S000003024 SDS23 GO:0005634 SGD_REF:S000069459|PMID:11914276 IDA C YGL056C gene taxon:4932 20020507 SGD
+SGD S000003024 SDS23 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YGL056C gene taxon:4932 20031028 SGD
+SGD S000003024 SDS23 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YGL056C gene taxon:4932 20020507 SGD
+SGD S000003024 SDS23 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YGL056C gene taxon:4932 20031028 SGD
+SGD S000003024 SDS23 GO:0005554 SGD_REF:S000069584 ND F YGL056C gene taxon:4932 20021216 SGD
+SGD S000003024 SDS23 GO:0000004 SGD_REF:S000069584 ND P YGL056C gene taxon:4932 20021216 SGD
+SGD S000000418 SDS24 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YBR214W gene taxon:4932 20020507 SGD
+SGD S000000418 SDS24 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YBR214W gene taxon:4932 20031028 SGD
+SGD S000000418 SDS24 GO:0005554 SGD_REF:S000069584 ND F YBR214W gene taxon:4932 20021004 SGD
+SGD S000000418 SDS24 GO:0006259 SGD_REF:S000043176|PMID:10051619 IGI P YBR214W gene taxon:4932 20021004 SGD
+SGD S000000418 SDS24 GO:0006897 SGD_REF:S000060817|PMID:11378903 IMP P YBR214W gene taxon:4932 20021004 SGD
+SGD S000000418 SDS24 GO:0007126 SGD_REF:S000043176|PMID:10051619 IEP P YBR214W gene taxon:4932 20021004 SGD
+SGD S000001346 SDS3 GO:0000118 SGD_REF:S000063428|PMID:11024051 IPI C YIL084C gene taxon:4932 20020820 SGD
+SGD S000001346 SDS3 GO:0005515 SGD_REF:S000063428|PMID:11024051 IPI F YIL084C gene taxon:4932 20020820 SGD
+SGD S000001346 SDS3 GO:0006342 SGD_REF:S000063428|PMID:11024051 IMP P YIL084C gene taxon:4932 20020820 SGD
+SGD S000001346 SDS3 GO:0006342 SGD_REF:S000063428|PMID:11024051 IGI P YIL084C gene taxon:4932 20020820 SGD
+SGD S000001346 SDS3 GO:0016575 SGD_REF:S000063428|PMID:11024051 IMP P YIL084C gene taxon:4932 20020820 SGD
+SGD S000001346 SDS3 GO:0016575 SGD_REF:S000063428|PMID:11024051 IPI P YIL084C gene taxon:4932 20020820 SGD
+SGD S000003192 SDT1 GO:0008372 SGD_REF:S000069584 ND C YGL224C|SSM1 gene taxon:4932 20021010 SGD
+SGD S000003192 SDT1 GO:0008252 SGD_REF:S000070009|PMID:11934891 IDA F YGL224C|SSM1 gene taxon:4932 20020808 SGD
+SGD S000003192 SDT1 GO:0006206 SGD_REF:S000070009|PMID:11934891 IMP P YGL224C|SSM1 gene taxon:4932 20021010 SGD
+SGD S000002571 SEC1 GO:0005886 SGD_REF:S000077350|PMID:15466482 IDA C SNARE docking complex subunit (putative) YDR164C gene taxon:4932 20050324 SGD
+SGD S000002571 SEC1 GO:0005934 SGD_REF:S000074785|PMID:11038189 IDA C SNARE docking complex subunit (putative) YDR164C gene taxon:4932 20040518 SGD
+SGD S000002571 SEC1 GO:0005934 SGD_REF:S000044621|PMID:10427089 IDA C SNARE docking complex subunit (putative) YDR164C gene taxon:4932 20040518 SGD
+SGD S000002571 SEC1 GO:0005935 SGD_REF:S000074785|PMID:11038189 IDA C SNARE docking complex subunit (putative) YDR164C gene taxon:4932 20040518 SGD
+SGD S000002571 SEC1 GO:0005935 SGD_REF:S000044621|PMID:10427089 IDA C SNARE docking complex subunit (putative) YDR164C gene taxon:4932 20040518 SGD
+SGD S000002571 SEC1 GO:0000149 SGD_REF:S000044621|PMID:10427089 IDA F SNARE docking complex subunit (putative) YDR164C gene taxon:4932 20010118 SGD
+SGD S000002571 SEC1 GO:0006887 SGD_REF:S000044621|PMID:10427089 IMP P SNARE docking complex subunit (putative) YDR164C gene taxon:4932 20010118 SGD
+SGD S000002571 SEC1 GO:0006887 SGD_REF:S000044621|PMID:10427089 IPI P SNARE docking complex subunit (putative) YDR164C gene taxon:4932 20010118 SGD
+SGD S000002571 SEC1 GO:0006904 SGD_REF:S000044621|PMID:10427089 IPI P SNARE docking complex subunit (putative) YDR164C gene taxon:4932 20010118 SGD
+SGD S000002571 SEC1 GO:0006906 SGD_REF:S000044621|PMID:10427089 IMP P SNARE docking complex subunit (putative) YDR164C gene taxon:4932 20010118 SGD
+SGD S000002571 SEC1 GO:0006906 SGD_REF:S000077350|PMID:15466482 IDA P SNARE docking complex subunit (putative) YDR164C gene taxon:4932 20050324 SGD
+SGD S000004156 SEC10 GO:0000145 SGD_REF:S000039481|PMID:9700152 TAS C exocyst complex component YLR166C gene taxon:4932 20010118 SGD
+SGD S000004156 SEC10 GO:0000145 SGD_REF:S000047160|PMID:8978675 IPI C exocyst complex component YLR166C gene taxon:4932 20040706 SGD
+SGD S000004156 SEC10 GO:0005515 SGD_REF:S000046659|PMID:9658167 IDA F exocyst complex component YLR166C gene taxon:4932 20021105 SGD
+SGD S000004156 SEC10 GO:0005515 SGD_REF:S000049442|PMID:7615633 IGI F exocyst complex component YLR166C gene taxon:4932 20040727 SGD
+SGD S000004156 SEC10 GO:0005515 SGD_REF:S000047160|PMID:8978675 IPI F exocyst complex component YLR166C gene taxon:4932 20040727 SGD
+SGD S000004156 SEC10 GO:0000910 SGD_REF:S000041005|PMID:10652251 IMP P exocyst complex component YLR166C gene taxon:4932 20010119 SGD
+SGD S000004156 SEC10 GO:0006893 SGD_REF:S000039481|PMID:9700152 TAS P exocyst complex component YLR166C gene taxon:4932 20010118 SGD
+SGD S000004156 SEC10 GO:0006904 SGD_REF:S000039481|PMID:9700152 TAS P exocyst complex component YLR166C gene taxon:4932 20010118 SGD
+SGD S000004156 SEC10 GO:0006906 SGD_REF:S000039481|PMID:9700152 TAS P exocyst complex component YLR166C gene taxon:4932 20010118 SGD
+SGD S000004156 SEC10 GO:0007121 SGD_REF:S000041005|PMID:10652251 IMP P exocyst complex component YLR166C gene taxon:4932 20010118 SGD
+SGD S000004156 SEC10 GO:0030468 SGD_REF:S000039481|PMID:9700152 TAS P exocyst complex component YLR166C gene taxon:4932 20010302 SGD
+SGD S000001461 SEC11 GO:0005783 SGD_REF:S000060705|PMID:11058593 IDA C YIR022W gene taxon:4932 20020822 SGD
+SGD S000001461 SEC11 GO:0005787 SGD_REF:S000056198|PMID:1846444 IDA C YIR022W gene taxon:4932 20010118 SGD
+SGD S000001461 SEC11 GO:0009003 SGD_REF:S000058486|PMID:10206957 IMP F YIR022W gene taxon:4932 20010118 SGD
+SGD S000001461 SEC11 GO:0009003 SGD_REF:S000058486|PMID:10206957 ISS F YIR022W gene taxon:4932 20010118 SGD
+SGD S000001461 SEC11 GO:0006465 SGD_REF:S000056198|PMID:1846444 IPI P YIR022W gene taxon:4932 20010118 SGD
+SGD S000001461 SEC11 GO:0006465 SGD_REF:S000058486|PMID:10206957 IMP P YIR022W gene taxon:4932 20010118 SGD
+SGD S000001461 SEC11 GO:0006465 SGD_REF:S000058486|PMID:10206957 IDA P YIR022W gene taxon:4932 20010118 SGD
+SGD S000001461 SEC11 GO:0006465 SGD_REF:S000058486|PMID:10206957 ISS P YIR022W gene taxon:4932 20010118 SGD
+SGD S000001461 SEC11 GO:0006465 SGD_REF:S000046082|PMID:3283143 IMP P YIR022W gene taxon:4932 20010118 SGD
+SGD S000005309 SEC12 GO:0000299 SGD_REF:S000045857|PMID:3047151 IDA C guanine nucleotide exchange factor for Sar1p YNR026C|SED2 gene taxon:4932 20020806 SGD
+SGD S000005309 SEC12 GO:0030176 SGD_REF:S000043640|PMID:9275186 IDA C guanine nucleotide exchange factor for Sar1p YNR026C|SED2 gene taxon:4932 20020806 SGD
+SGD S000005309 SEC12 GO:0005085 SGD_REF:S000048204|PMID:8377826 IDA F guanine nucleotide exchange factor for Sar1p YNR026C|SED2 gene taxon:4932 20020806 SGD
+SGD S000005309 SEC12 GO:0006888 SGD_REF:S000053172|PMID:1907973 IDA P guanine nucleotide exchange factor for Sar1p YNR026C|SED2 gene taxon:4932 20020806 SGD
+SGD S000005309 SEC12 GO:0030433 SGD_REF:S000072312|PMID:12538638 IMP P guanine nucleotide exchange factor for Sar1p YNR026C|SED2 gene taxon:4932 20030128 SGD
+SGD S000004198 SEC13 GO:0005643 SGD_REF:S000069412|PMID:11343909 TAS C nuclear pore complex subunit, protein involved in release of transport vesicles from the ER YLR208W|ANU3 gene taxon:4932 20020313 SGD
+SGD S000004198 SEC13 GO:0005643 SGD_REF:S000050495|PMID:10747086 IGI C nuclear pore complex subunit, protein involved in release of transport vesicles from the ER YLR208W|ANU3 gene taxon:4932 20040929 SGD
+SGD S000004198 SEC13 GO:0005643 SGD_REF:S000050495|PMID:10747086 IPI C nuclear pore complex subunit, protein involved in release of transport vesicles from the ER YLR208W|ANU3 gene taxon:4932 20040929 SGD
+SGD S000004198 SEC13 GO:0005737 SGD_REF:S000048768|PMID:8432727 IDA C nuclear pore complex subunit, protein involved in release of transport vesicles from the ER YLR208W|ANU3 gene taxon:4932 20050926 SGD
+SGD S000004198 SEC13 GO:0019898 SGD_REF:S000065058|PMID:8004676 IDA C nuclear pore complex subunit, protein involved in release of transport vesicles from the ER YLR208W|ANU3 gene taxon:4932 20040929 SGD
+SGD S000004198 SEC13 GO:0030127 SGD_REF:S000061172|PMID:11252894 TAS C nuclear pore complex subunit, protein involved in release of transport vesicles from the ER YLR208W|ANU3 gene taxon:4932 20010912 SGD
+SGD S000004198 SEC13 GO:0030127 SGD_REF:S000048768|PMID:8432727 IDA C nuclear pore complex subunit, protein involved in release of transport vesicles from the ER YLR208W|ANU3 gene taxon:4932 20050926 SGD
+SGD S000004198 SEC13 GO:0005198 SGD_REF:S000050495|PMID:10747086 IGI F nuclear pore complex subunit, protein involved in release of transport vesicles from the ER YLR208W|ANU3 gene taxon:4932 20040929 SGD
+SGD S000004198 SEC13 GO:0005198 SGD_REF:S000050495|PMID:10747086 IPI F nuclear pore complex subunit, protein involved in release of transport vesicles from the ER YLR208W|ANU3 gene taxon:4932 20040929 SGD
+SGD S000004198 SEC13 GO:0005198 SGD_REF:S000065058|PMID:8004676 IDA F nuclear pore complex subunit, protein involved in release of transport vesicles from the ER YLR208W|ANU3 gene taxon:4932 20040929 SGD
+SGD S000004198 SEC13 GO:0006888 SGD_REF:S000061172|PMID:11252894 TAS P nuclear pore complex subunit, protein involved in release of transport vesicles from the ER YLR208W|ANU3 gene taxon:4932 20010912 SGD
+SGD S000004198 SEC13 GO:0006888 SGD_REF:S000048768|PMID:8432727 IDA P nuclear pore complex subunit, protein involved in release of transport vesicles from the ER YLR208W|ANU3 gene taxon:4932 20050926 SGD
+SGD S000004198 SEC13 GO:0006900 SGD_REF:S000048768|PMID:8432727 IMP P nuclear pore complex subunit, protein involved in release of transport vesicles from the ER YLR208W|ANU3 gene taxon:4932 20010118 SGD
+SGD S000004198 SEC13 GO:0006900 SGD_REF:S000048768|PMID:8432727 IDA P nuclear pore complex subunit, protein involved in release of transport vesicles from the ER YLR208W|ANU3 gene taxon:4932 20050926 SGD
+SGD S000004198 SEC13 GO:0006999 SGD_REF:S000050495|PMID:10747086 IC GO:0005198|GO:0005643 P nuclear pore complex subunit, protein involved in release of transport vesicles from the ER YLR208W|ANU3 gene taxon:4932 20040929 SGD
+SGD S000004198 SEC13 GO:0006999 SGD_REF:S000050495|PMID:10747086 TAS P nuclear pore complex subunit, protein involved in release of transport vesicles from the ER YLR208W|ANU3 gene taxon:4932 20040929 SGD
+SGD S000004198 SEC13 GO:0030433 SGD_REF:S000072312|PMID:12538638 IMP P nuclear pore complex subunit, protein involved in release of transport vesicles from the ER YLR208W|ANU3 gene taxon:4932 20040929 SGD
+SGD S000004684 SEC14 GO:0005829 SGD_REF:S000051431|PMID:2466847 IDA C phosphatidylcholine transfer protein, phosphatidylinositol transfer protein YMR079W|PIT1 gene taxon:4932 20020806 SGD
+SGD S000004684 SEC14 GO:0008526 SGD_REF:S000055664|PMID:2215682 IDA F phosphatidylcholine transfer protein, phosphatidylinositol transfer protein YMR079W|PIT1 gene taxon:4932 20020806 SGD
+SGD S000004684 SEC14 GO:0006893 SGD_REF:S000049815|PMID:6094514 IMP P phosphatidylcholine transfer protein, phosphatidylinositol transfer protein YMR079W|PIT1 gene taxon:4932 20020806 SGD
+SGD S000004684 SEC14 GO:0015914 SGD_REF:S000055664|PMID:2215682 IDA P phosphatidylcholine transfer protein, phosphatidylinositol transfer protein YMR079W|PIT1 gene taxon:4932 20020806 SGD
+SGD S000004684 SEC14 GO:0030437 SGD_REF:S000075947|PMID:14528019 IMP P phosphatidylcholine transfer protein, phosphatidylinositol transfer protein YMR079W|PIT1 gene taxon:4932 20040816 SGD
+SGD S000004684 SEC14 GO:0030437 SGD_REF:S000075947|PMID:14528019 IGI P phosphatidylcholine transfer protein, phosphatidylinositol transfer protein YMR079W|PIT1 gene taxon:4932 20040816 SGD
+SGD S000004684 SEC14 GO:0046470 SGD_REF:S000075391|PMID:11208102 TAS P phosphatidylcholine transfer protein, phosphatidylinositol transfer protein YMR079W|PIT1 gene taxon:4932 20050201 SGD
+SGD S000004684 SEC14 GO:0046470 SGD_REF:S000045374|PMID:7816798 IDA P phosphatidylcholine transfer protein, phosphatidylinositol transfer protein YMR079W|PIT1 gene taxon:4932 20050201 SGD
+SGD S000004684 SEC14 GO:0046488 SGD_REF:S000075391|PMID:11208102 TAS P phosphatidylcholine transfer protein, phosphatidylinositol transfer protein YMR079W|PIT1 gene taxon:4932 20050201 SGD
+SGD S000003202 SEC15 GO:0000145 SGD_REF:S000039481|PMID:9700152 TAS C exocyst complex component YGL233W gene taxon:4932 20010118 SGD
+SGD S000003202 SEC15 GO:0000145 SGD_REF:S000047160|PMID:8978675 IPI C exocyst complex component YGL233W gene taxon:4932 20040706 SGD
+SGD S000003202 SEC15 GO:0005934 SGD_REF:S000049442|PMID:7615633 IPI C exocyst complex component YGL233W gene taxon:4932 20040706 SGD
+SGD S000003202 SEC15 GO:0005515 SGD_REF:S000053578|PMID:10022848 IDA F exocyst complex component YGL233W gene taxon:4932 20021105 SGD
+SGD S000003202 SEC15 GO:0000910 SGD_REF:S000041005|PMID:10652251 IMP P exocyst complex component YGL233W gene taxon:4932 20010119 SGD
+SGD S000003202 SEC15 GO:0006893 SGD_REF:S000039481|PMID:9700152 TAS P exocyst complex component YGL233W gene taxon:4932 20010118 SGD
+SGD S000003202 SEC15 GO:0006904 SGD_REF:S000039481|PMID:9700152 TAS P exocyst complex component YGL233W gene taxon:4932 20010118 SGD
+SGD S000003202 SEC15 GO:0006906 SGD_REF:S000039481|PMID:9700152 TAS P exocyst complex component YGL233W gene taxon:4932 20010118 SGD
+SGD S000003202 SEC15 GO:0007121 SGD_REF:S000041005|PMID:10652251 IMP P exocyst complex component YGL233W gene taxon:4932 20010118 SGD
+SGD S000006006 SEC16 GO:0005789 SGD_REF:S000046927|PMID:7593161 IDA C vesicle coat component YPL085W|LPF1 gene taxon:4932 20020731 SGD
+SGD S000006006 SEC16 GO:0019898 SGD_REF:S000071166|PMID:12235121 TAS C vesicle coat component YPL085W|LPF1 gene taxon:4932 20050201 SGD
+SGD S000006006 SEC16 GO:0030127 SGD_REF:S000046927|PMID:7593161 IDA C vesicle coat component YPL085W|LPF1 gene taxon:4932 20020731 SGD
+SGD S000006006 SEC16 GO:0030127 SGD_REF:S000046927|PMID:7593161 IPI C vesicle coat component YPL085W|LPF1 gene taxon:4932 20020731 SGD
+SGD S000006006 SEC16 GO:0005198 SGD_REF:S000046927|PMID:7593161 IPI F vesicle coat component YPL085W|LPF1 gene taxon:4932 20020731 SGD
+SGD S000006006 SEC16 GO:0006901 SGD_REF:S000071166|PMID:12235121 IDA P vesicle coat component YPL085W|LPF1 gene taxon:4932 20050201 SGD
+SGD S000006006 SEC16 GO:0006914 SGD_REF:S000066273|PMID:11694599 IMP P vesicle coat component YPL085W|LPF1 gene taxon:4932 20020731 SGD
+SGD S000006006 SEC16 GO:0016192 SGD_REF:S000046927|PMID:7593161 IDA P vesicle coat component YPL085W|LPF1 gene taxon:4932 20020731 SGD
+SGD S000000146 SEC17 GO:0000300 SGD_REF:S000043228|PMID:1601878 IDA C YBL050W gene taxon:4932 20020827 SGD
+SGD S000000146 SEC17 GO:0005483 SGD_REF:S000043228|PMID:1601878 IDA F YBL050W gene taxon:4932 20020827 SGD
+SGD S000000146 SEC17 GO:0006888 SGD_REF:S000057323|PMID:7026045 IGI P YBL050W gene taxon:4932 20020827 SGD
+SGD S000000146 SEC17 GO:0006888 SGD_REF:S000047231|PMID:2082939 TAS P YBL050W gene taxon:4932 20020827 SGD
+SGD S000000146 SEC17 GO:0006888 SGD_REF:S000057323|PMID:7026045 IMP P YBL050W gene taxon:4932 20020827 SGD
+SGD S000000146 SEC17 GO:0042144 SGD_REF:S000052079|PMID:8620540 IMP P YBL050W gene taxon:4932 20050509 SGD
+SGD S000000284 SEC18 GO:0005737 SGD_REF:S000047466|PMID:9624182 IDA C ATPase, NSF, protein involved in protein transport between ER and Golgi YBR080C|ANU4 gene taxon:4932 20010118 SGD
+SGD S000000284 SEC18 GO:0019897 SGD_REF:S000047466|PMID:9624182 IDA C ATPase, NSF, protein involved in protein transport between ER and Golgi YBR080C|ANU4 gene taxon:4932 20020104 SGD
+SGD S000000284 SEC18 GO:0016887 SGD_REF:S000041605|PMID:10387016 IDA F ATPase, NSF, protein involved in protein transport between ER and Golgi YBR080C|ANU4 gene taxon:4932 20030227 SGD
+SGD S000000284 SEC18 GO:0000011 SGD_REF:S000048402|PMID:9015301 IDA P ATPase, NSF, protein involved in protein transport between ER and Golgi YBR080C|ANU4 gene taxon:4932 20010118 SGD
+SGD S000000284 SEC18 GO:0006888 SGD_REF:S000047231|PMID:2082939 TAS P ATPase, NSF, protein involved in protein transport between ER and Golgi YBR080C|ANU4 gene taxon:4932 20010118 SGD
+SGD S000000284 SEC18 GO:0042144 SGD_REF:S000052079|PMID:8620540 IMP P ATPase, NSF, protein involved in protein transport between ER and Golgi YBR080C|ANU4 gene taxon:4932 20050509 SGD
+SGD S000005216 SEC2 GO:0005829 SGD_REF:S000069949|PMID:12045183 IDA C GDP/GTP exchange factor YNL272C gene taxon:4932 20020729 SGD
+SGD S000005216 SEC2 GO:0016023 SGD_REF:S000069949|PMID:12045183 IDA C GDP/GTP exchange factor YNL272C gene taxon:4932 20020729 SGD
+SGD S000005216 SEC2 GO:0005085 SGD_REF:S000051492|PMID:9199166 IDA F GDP/GTP exchange factor YNL272C gene taxon:4932 20020729 SGD
+SGD S000005216 SEC2 GO:0006887 SGD_REF:S000069949|PMID:12045183 IMP P GDP/GTP exchange factor YNL272C gene taxon:4932 20020729 SGD
+SGD S000002906 SEC20 GO:0005783 SGD_REF:S000069459|PMID:11914276 IDA C v-SNARE YDR498C gene taxon:4932 20020507 SGD
+SGD S000002906 SEC20 GO:0005789 SGD_REF:S000058453|PMID:10047442 TAS C v-SNARE YDR498C gene taxon:4932 20010118 SGD
+SGD S000002906 SEC20 GO:0005485 SGD_REF:S000058453|PMID:10047442 TAS F v-SNARE YDR498C gene taxon:4932 20010118 SGD
+SGD S000002906 SEC20 GO:0006890 SGD_REF:S000058453|PMID:10047442 TAS P v-SNARE YDR498C gene taxon:4932 20010118 SGD
+SGD S000002906 SEC20 GO:0006906 SGD_REF:S000058453|PMID:10047442 TAS P v-SNARE YDR498C gene taxon:4932 20010118 SGD
+SGD S000005231 SEC21 GO:0030126 SGD_REF:S000048685|PMID:1461285 IDA C PEST sequence-containing protein, non-clathrin coat protein YNL287W gene taxon:4932 20020807 SGD
+SGD S000005231 SEC21 GO:0005554 SGD_REF:S000069584 ND F PEST sequence-containing protein, non-clathrin coat protein YNL287W gene taxon:4932 20020807 SGD
+SGD S000005231 SEC21 GO:0006888 SGD_REF:S000048685|PMID:1461285 IMP P PEST sequence-containing protein, non-clathrin coat protein YNL287W gene taxon:4932 20020807 SGD
+SGD S000005231 SEC21 GO:0006890 SGD_REF:S000046381|PMID:8001155 IMP P PEST sequence-containing protein, non-clathrin coat protein YNL287W gene taxon:4932 20020807 SGD
+SGD S000004258 SEC22 GO:0005783 SGD_REF:S000040030|PMID:9580559 IDA C YLR268W|SLY2|TSL26 gene taxon:4932 20020917 SGD
+SGD S000004258 SEC22 GO:0005794 SGD_REF:S000040030|PMID:9580559 IDA C YLR268W|SLY2|TSL26 gene taxon:4932 20020917 SGD
+SGD S000004258 SEC22 GO:0016021 SGD_REF:S000045607|PMID:1903839 IDA C YLR268W|SLY2|TSL26 gene taxon:4932 20021001 SGD
+SGD S000004258 SEC22 GO:0005485 SGD_REF:S000058453|PMID:10047442 TAS F YLR268W|SLY2|TSL26 gene taxon:4932 20010118 SGD
+SGD S000004258 SEC22 GO:0006888 SGD_REF:S000058453|PMID:10047442 TAS P YLR268W|SLY2|TSL26 gene taxon:4932 20010118 SGD
+SGD S000004258 SEC22 GO:0006890 SGD_REF:S000058453|PMID:10047442 TAS P YLR268W|SLY2|TSL26 gene taxon:4932 20010118 SGD
+SGD S000004258 SEC22 GO:0006891 SGD_REF:S000058453|PMID:10047442 TAS P YLR268W|SLY2|TSL26 gene taxon:4932 20010118 SGD
+SGD S000004258 SEC22 GO:0006906 SGD_REF:S000058453|PMID:10047442 TAS P YLR268W|SLY2|TSL26 gene taxon:4932 20010118 SGD
+SGD S000006385 SEC23 GO:0005737 SGD_REF:S000053984|PMID:2670558 IDA C GTPase activating protein (GAP) YPR181C gene taxon:4932 20010118 SGD
+SGD S000006385 SEC23 GO:0030127 SGD_REF:S000061172|PMID:11252894 TAS C GTPase activating protein (GAP) YPR181C gene taxon:4932 20010912 SGD
+SGD S000006385 SEC23 GO:0005096 SGD_REF:S000053350|PMID:8451644 IDA F GTPase activating protein (GAP) YPR181C gene taxon:4932 20010118 SGD
+SGD S000006385 SEC23 GO:0006888 SGD_REF:S000053984|PMID:2670558 IMP P GTPase activating protein (GAP) YPR181C gene taxon:4932 20010118 SGD
+SGD S000006385 SEC23 GO:0006888 SGD_REF:S000061172|PMID:11252894 TAS P GTPase activating protein (GAP) YPR181C gene taxon:4932 20010912 SGD
+SGD S000006385 SEC23 GO:0006914 SGD_REF:S000066273|PMID:11694599 IMP P GTPase activating protein (GAP) YPR181C gene taxon:4932 20020731 SGD
+SGD S000006385 SEC23 GO:0030433 SGD_REF:S000072312|PMID:12538638 IMP P GTPase activating protein (GAP) YPR181C gene taxon:4932 20030128 SGD
+SGD S000001371 SEC24 GO:0030127 SGD_REF:S000061172|PMID:11252894 TAS C vesicle coat component YIL109C|ANU1 gene taxon:4932 20010912 SGD
+SGD S000001371 SEC24 GO:0005515 SGD_REF:S000059360|PMID:11086000 IDA F vesicle coat component YIL109C|ANU1 gene taxon:4932 20021112 SGD
+SGD S000001371 SEC24 GO:0006888 SGD_REF:S000061172|PMID:11252894 TAS P vesicle coat component YIL109C|ANU1 gene taxon:4932 20010912 SGD
+SGD S000001371 SEC24 GO:0006914 SGD_REF:S000066273|PMID:11694599 IMP P vesicle coat component YIL109C|ANU1 gene taxon:4932 20020731 SGD
+SGD S000002646 SEC26 GO:0030126 SGD_REF:S000055669|PMID:7929113 IGI C yeast coatomer subunit YDR238C gene taxon:4932 20020724 SGD
+SGD S000002646 SEC26 GO:0030126 SGD_REF:S000055669|PMID:7929113 ISS C yeast coatomer subunit YDR238C gene taxon:4932 20020724 SGD
+SGD S000002646 SEC26 GO:0030135 SGD_REF:S000055669|PMID:7929113 ISS C yeast coatomer subunit YDR238C gene taxon:4932 20020614 SGD
+SGD S000002646 SEC26 GO:0005554 SGD_REF:S000069584 ND F yeast coatomer subunit YDR238C gene taxon:4932 20020614 SGD
+SGD S000002646 SEC26 GO:0006888 SGD_REF:S000055669|PMID:7929113 IMP P yeast coatomer subunit YDR238C gene taxon:4932 20020614 SGD
+SGD S000003105 SEC27 GO:0030126 SGD_REF:S000055669|PMID:7929113 ISS C yeast coatomer beta'-subunit YGL137W gene taxon:4932 20020724 SGD
+SGD S000003105 SEC27 GO:0030126 SGD_REF:S000055669|PMID:7929113 IGI C yeast coatomer beta'-subunit YGL137W gene taxon:4932 20020724 SGD
+SGD S000003105 SEC27 GO:0005554 SGD_REF:S000069584 ND F yeast coatomer beta'-subunit YGL137W gene taxon:4932 20020724 SGD
+SGD S000003105 SEC27 GO:0006888 SGD_REF:S000055669|PMID:7929113 IMP P yeast coatomer beta'-subunit YGL137W gene taxon:4932 20020724 SGD
+SGD S000003105 SEC27 GO:0006890 SGD_REF:S000046381|PMID:8001155 IMP P yeast coatomer beta'-subunit YGL137W gene taxon:4932 20020807 SGD
+SGD S000001338 SEC28 GO:0030126 SGD_REF:S000049114|PMID:9463377 ISS C epsilon-COP coatomer subunit YIL076W|ANU2 gene taxon:4932 20021021 SGD
+SGD S000001338 SEC28 GO:0030126 SGD_REF:S000049114|PMID:9463377 IMP C epsilon-COP coatomer subunit YIL076W|ANU2 gene taxon:4932 20021021 SGD
+SGD S000001338 SEC28 GO:0005554 SGD_REF:S000069584 ND F epsilon-COP coatomer subunit YIL076W|ANU2 gene taxon:4932 20021021 SGD
+SGD S000001338 SEC28 GO:0006888 SGD_REF:S000046756|PMID:10532354 IMP P epsilon-COP coatomer subunit YIL076W|ANU2 gene taxon:4932 20021021 SGD
+SGD S000001338 SEC28 GO:0006901 SGD_REF:S000049114|PMID:9463377 IMP P epsilon-COP coatomer subunit YIL076W|ANU2 gene taxon:4932 20010118 SGD
+SGD S000001338 SEC28 GO:0006901 SGD_REF:S000049114|PMID:9463377 IGI P epsilon-COP coatomer subunit YIL076W|ANU2 gene taxon:4932 20010118 SGD
+SGD S000000810 SEC3 GO:0000131 SGD_REF:S000068748|PMID:11595741 IDA C exocyst complex component YER008C|PSL1 gene taxon:4932 20050728 SGD
+SGD S000000810 SEC3 GO:0000145 SGD_REF:S000039481|PMID:9700152 TAS C exocyst complex component YER008C|PSL1 gene taxon:4932 20010118 SGD
+SGD S000000810 SEC3 GO:0000145 SGD_REF:S000047160|PMID:8978675 IPI C exocyst complex component YER008C|PSL1 gene taxon:4932 20040706 SGD
+SGD S000000810 SEC3 GO:0005934 SGD_REF:S000068748|PMID:11595741 IDA C exocyst complex component YER008C|PSL1 gene taxon:4932 20050728 SGD
+SGD S000000810 SEC3 GO:0005935 SGD_REF:S000068748|PMID:11595741 IDA C exocyst complex component YER008C|PSL1 gene taxon:4932 20050728 SGD
+SGD S000000810 SEC3 GO:0030427 SGD_REF:S000041326|PMID:9491896 IDA C exocyst complex component YER008C|PSL1 gene taxon:4932 20040706 SGD
+SGD S000000810 SEC3 GO:0005515 SGD_REF:S000047160|PMID:8978675 IPI F exocyst complex component YER008C|PSL1 gene taxon:4932 20040727 SGD
+SGD S000000810 SEC3 GO:0005515 SGD_REF:S000049442|PMID:7615633 IGI F exocyst complex component YER008C|PSL1 gene taxon:4932 20040727 SGD
+SGD S000000810 SEC3 GO:0000910 SGD_REF:S000041005|PMID:10652251 IMP P exocyst complex component YER008C|PSL1 gene taxon:4932 20010119 SGD
+SGD S000000810 SEC3 GO:0006893 SGD_REF:S000039481|PMID:9700152 TAS P exocyst complex component YER008C|PSL1 gene taxon:4932 20010118 SGD
+SGD S000000810 SEC3 GO:0006904 SGD_REF:S000039481|PMID:9700152 TAS P exocyst complex component YER008C|PSL1 gene taxon:4932 20010118 SGD
+SGD S000000810 SEC3 GO:0006906 SGD_REF:S000039481|PMID:9700152 TAS P exocyst complex component YER008C|PSL1 gene taxon:4932 20010118 SGD
+SGD S000000810 SEC3 GO:0007121 SGD_REF:S000041005|PMID:10652251 IMP P exocyst complex component YER008C|PSL1 gene taxon:4932 20010118 SGD
+SGD S000002354 SEC31 GO:0030127 SGD_REF:S000061172|PMID:11252894 TAS C COPII coat of secretory pathway vesicles component (p150) YDL195W|WEB1 gene taxon:4932 20010912 SGD
+SGD S000002354 SEC31 GO:0005198 SGD_REF:S000068883|PMID:11717432 IPI F COPII coat of secretory pathway vesicles component (p150) YDL195W|WEB1 gene taxon:4932 20021114 SGD
+SGD S000002354 SEC31 GO:0006888 SGD_REF:S000061172|PMID:11252894 TAS P COPII coat of secretory pathway vesicles component (p150) YDL195W|WEB1 gene taxon:4932 20010912 SGD
+SGD S000004432 SEC39 GO:0005635 SGD_REF:S000075214|PMID:14690591 IDA C YLR440C gene taxon:4932 20040105 SGD
+SGD S000004432 SEC39 GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YLR440C gene taxon:4932 20031028 SGD
+SGD S000004432 SEC39 GO:0005554 SGD_REF:S000069584 ND F YLR440C gene taxon:4932 20030203 SGD
+SGD S000004432 SEC39 GO:0045045 SGD_REF:S000076598|PMID:15242642 IMP P YLR440C gene taxon:4932 20040713 SGD
+SGD S000001889 SEC4 GO:0000131 SGD_REF:S000044417|PMID:9128251 IDA C ras homolog, small GTP binding protein YFL005W|SRO6 gene taxon:4932 20050314 SGD
+SGD S000001889 SEC4 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C ras homolog, small GTP binding protein YFL005W|SRO6 gene taxon:4932 20040928 SGD
+SGD S000001889 SEC4 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C ras homolog, small GTP binding protein YFL005W|SRO6 gene taxon:4932 20060317 SGD
+SGD S000001889 SEC4 GO:0030133 SGD_REF:S000073320|PMID:12665530 TAS C ras homolog, small GTP binding protein YFL005W|SRO6 gene taxon:4932 20030623 SGD
+SGD S000001889 SEC4 GO:0030478 SGD_REF:S000041005|PMID:10652251 IDA C ras homolog, small GTP binding protein YFL005W|SRO6 gene taxon:4932 20010118 SGD
+SGD S000001889 SEC4 GO:0003924 SGD_REF:S000041005|PMID:10652251 TAS F ras homolog, small GTP binding protein YFL005W|SRO6 gene taxon:4932 20010118 SGD
+SGD S000001889 SEC4 GO:0000910 SGD_REF:S000041005|PMID:10652251 IMP P ras homolog, small GTP binding protein YFL005W|SRO6 gene taxon:4932 20010119 SGD
+SGD S000001889 SEC4 GO:0006887 SGD_REF:S000073320|PMID:12665530 TAS P ras homolog, small GTP binding protein YFL005W|SRO6 gene taxon:4932 20030623 SGD
+SGD S000001889 SEC4 GO:0006893 SGD_REF:S000041005|PMID:10652251 TAS P ras homolog, small GTP binding protein YFL005W|SRO6 gene taxon:4932 20010118 SGD
+SGD S000001889 SEC4 GO:0006906 SGD_REF:S000041005|PMID:10652251 TAS P ras homolog, small GTP binding protein YFL005W|SRO6 gene taxon:4932 20010118 SGD
+SGD S000001889 SEC4 GO:0007121 SGD_REF:S000041005|PMID:10652251 IMP P ras homolog, small GTP binding protein YFL005W|SRO6 gene taxon:4932 20010118 SGD
+SGD S000001889 SEC4 GO:0007264 SGD_REF:S000041005|PMID:10652251 TAS P ras homolog, small GTP binding protein YFL005W|SRO6 gene taxon:4932 20010118 SGD
+SGD S000002573 SEC5 GO:0000131 SGD_REF:S000068748|PMID:11595741 IDA C exocyst complex component YDR166C gene taxon:4932 20050728 SGD
+SGD S000002573 SEC5 GO:0000145 SGD_REF:S000039481|PMID:9700152 TAS C exocyst complex component YDR166C gene taxon:4932 20010118 SGD
+SGD S000002573 SEC5 GO:0000145 SGD_REF:S000047160|PMID:8978675 IPI C exocyst complex component YDR166C gene taxon:4932 20040706 SGD
+SGD S000002573 SEC5 GO:0005934 SGD_REF:S000068748|PMID:11595741 IDA C exocyst complex component YDR166C gene taxon:4932 20050728 SGD
+SGD S000002573 SEC5 GO:0005935 SGD_REF:S000068748|PMID:11595741 IDA C exocyst complex component YDR166C gene taxon:4932 20050728 SGD
+SGD S000002573 SEC5 GO:0005515 SGD_REF:S000047160|PMID:8978675 IPI F exocyst complex component YDR166C gene taxon:4932 20040727 SGD
+SGD S000002573 SEC5 GO:0005515 SGD_REF:S000049442|PMID:7615633 IGI F exocyst complex component YDR166C gene taxon:4932 20040727 SGD
+SGD S000002573 SEC5 GO:0000910 SGD_REF:S000041005|PMID:10652251 IMP P exocyst complex component YDR166C gene taxon:4932 20010119 SGD
+SGD S000002573 SEC5 GO:0006893 SGD_REF:S000039481|PMID:9700152 TAS P exocyst complex component YDR166C gene taxon:4932 20010118 SGD
+SGD S000002573 SEC5 GO:0006904 SGD_REF:S000039481|PMID:9700152 TAS P exocyst complex component YDR166C gene taxon:4932 20010118 SGD
+SGD S000002573 SEC5 GO:0006906 SGD_REF:S000039481|PMID:9700152 TAS P exocyst complex component YDR166C gene taxon:4932 20010118 SGD
+SGD S000002573 SEC5 GO:0007121 SGD_REF:S000041005|PMID:10652251 IMP P exocyst complex component YDR166C gene taxon:4932 20010118 SGD
+SGD S000001849 SEC53 GO:0005829 SGD_REF:S000048162|PMID:3905826 IDA C phosphomannomutase YFL045C|ALG4 gene taxon:4932 20021001 SGD
+SGD S000001849 SEC53 GO:0004615 SGD_REF:S000040118|PMID:3288631 IDA F phosphomannomutase YFL045C|ALG4 gene taxon:4932 20021001 SGD
+SGD S000001849 SEC53 GO:0045047 SGD_REF:S000045674|PMID:6368572 IMP P phosphomannomutase YFL045C|ALG4 gene taxon:4932 20021001 SGD
+SGD S000004615 SEC59 GO:0005789 SGD_REF:S000040566|PMID:2657387 IDA C membrane protein, required for core glycosylation YMR013C gene taxon:4932 20050416 SGD
+SGD S000004615 SEC59 GO:0005789 SGD_REF:S000040566|PMID:2657387 IMP C membrane protein, required for core glycosylation YMR013C gene taxon:4932 20050416 SGD
+SGD S000004615 SEC59 GO:0004168 SGD_REF:S000040566|PMID:2657387 IMP F membrane protein, required for core glycosylation YMR013C gene taxon:4932 20021001 SGD
+SGD S000004615 SEC59 GO:0006486 SGD_REF:S000040566|PMID:2657387 IMP P membrane protein, required for core glycosylation YMR013C gene taxon:4932 20021001 SGD
+SGD S000004615 SEC59 GO:0045047 SGD_REF:S000045674|PMID:6368572 IMP P membrane protein, required for core glycosylation YMR013C gene taxon:4932 20021001 SGD
+SGD S000001330 SEC6 GO:0000145 SGD_REF:S000039481|PMID:9700152 TAS C exocyst complex component YIL068C gene taxon:4932 20010118 SGD
+SGD S000001330 SEC6 GO:0000145 SGD_REF:S000047160|PMID:8978675 IPI C exocyst complex component YIL068C gene taxon:4932 20040706 SGD
+SGD S000001330 SEC6 GO:0005934 SGD_REF:S000049442|PMID:7615633 IPI C exocyst complex component YIL068C gene taxon:4932 20040706 SGD
+SGD S000001330 SEC6 GO:0005515 SGD_REF:S000047160|PMID:8978675 IPI F exocyst complex component YIL068C gene taxon:4932 20040728 SGD
+SGD S000001330 SEC6 GO:0005515 SGD_REF:S000047160|PMID:8978675 TAS F exocyst complex component YIL068C gene taxon:4932 20040728 SGD
+SGD S000001330 SEC6 GO:0000910 SGD_REF:S000041005|PMID:10652251 IMP P exocyst complex component YIL068C gene taxon:4932 20010119 SGD
+SGD S000001330 SEC6 GO:0006893 SGD_REF:S000039481|PMID:9700152 TAS P exocyst complex component YIL068C gene taxon:4932 20010118 SGD
+SGD S000001330 SEC6 GO:0006904 SGD_REF:S000039481|PMID:9700152 TAS P exocyst complex component YIL068C gene taxon:4932 20010118 SGD
+SGD S000001330 SEC6 GO:0006906 SGD_REF:S000039481|PMID:9700152 TAS P exocyst complex component YIL068C gene taxon:4932 20010118 SGD
+SGD S000001330 SEC6 GO:0007121 SGD_REF:S000041005|PMID:10652251 IMP P exocyst complex component YIL068C gene taxon:4932 20010118 SGD
+SGD S000004370 SEC61 GO:0005784 SGD_REF:S000044438|PMID:10564637 TAS C YLR378C gene taxon:4932 20021126 SGD
+SGD S000004370 SEC61 GO:0005788 SGD_REF:S000060855|PMID:11294909 IDA C YLR378C gene taxon:4932 20020826 SGD
+SGD S000004370 SEC61 GO:0030176 SGD_REF:S000053331|PMID:1550957 IDA C YLR378C gene taxon:4932 20031020 SGD
+SGD S000004370 SEC61 GO:0031206 SGD_REF:S000063769|PMID:9252322 TAS C YLR378C gene taxon:4932 20050317 SGD
+SGD S000004370 SEC61 GO:0008565 SGD_REF:S000044438|PMID:10564637 TAS F YLR378C gene taxon:4932 20021126 SGD
+SGD S000004370 SEC61 GO:0006616 SGD_REF:S000044438|PMID:10564637 TAS P YLR378C gene taxon:4932 20021126 SGD
+SGD S000004370 SEC61 GO:0031204 SGD_REF:S000063769|PMID:9252322 TAS P YLR378C gene taxon:4932 20050317 SGD
+SGD S000004370 SEC61 GO:0045047 SGD_REF:S000053331|PMID:1550957 IMP P YLR378C gene taxon:4932 20031020 SGD
+SGD S000006015 SEC62 GO:0005789 SGD_REF:S000044438|PMID:10564637 TAS C ER protein translocation apparatus membrane component YPL094C|LPG14 gene taxon:4932 20021126 SGD
+SGD S000006015 SEC62 GO:0031207 SGD_REF:S000047471|PMID:2000150 IPI SGD:S000005780 C ER protein translocation apparatus membrane component YPL094C|LPG14 gene taxon:4932 20050316 SGD
+SGD S000006015 SEC62 GO:0005515 SGD_REF:S000059366|PMID:11071912 IMP F ER protein translocation apparatus membrane component YPL094C|LPG14 gene taxon:4932 20030521 SGD
+SGD S000006015 SEC62 GO:0005515 SGD_REF:S000059366|PMID:11071912 IPI F ER protein translocation apparatus membrane component YPL094C|LPG14 gene taxon:4932 20030521 SGD
+SGD S000006015 SEC62 GO:0008565 SGD_REF:S000044438|PMID:10564637 TAS F ER protein translocation apparatus membrane component YPL094C|LPG14 gene taxon:4932 20030521 SGD
+SGD S000006015 SEC62 GO:0006620 SGD_REF:S000063769|PMID:9252322 TAS P ER protein translocation apparatus membrane component YPL094C|LPG14 gene taxon:4932 20050126 SGD
+SGD S000005780 SEC63 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YOR254C|PTL1 gene taxon:4932 20040928 SGD
+SGD S000005780 SEC63 GO:0005789 SGD_REF:S000043640|PMID:9275186 TAS C YOR254C|PTL1 gene taxon:4932 20020909 SGD
+SGD S000005780 SEC63 GO:0005789 SGD_REF:S000044438|PMID:10564637 TAS C YOR254C|PTL1 gene taxon:4932 20021126 SGD
+SGD S000005780 SEC63 GO:0031207 SGD_REF:S000047471|PMID:2000150 IPI SGD:S000006015 C YOR254C|PTL1 gene taxon:4932 20050316 SGD
+SGD S000005780 SEC63 GO:0008565 SGD_REF:S000081824|PMID:15671059 IMP F YOR254C|PTL1 gene taxon:4932 20050808 SGD
+SGD S000005780 SEC63 GO:0006614 SGD_REF:S000060140|PMID:11226176 IMP P YOR254C|PTL1 gene taxon:4932 20050207 SGD
+SGD S000005780 SEC63 GO:0006620 SGD_REF:S000081824|PMID:15671059 IMP P YOR254C|PTL1 gene taxon:4932 20050808 SGD
+SGD S000005780 SEC63 GO:0046967 SGD_REF:S000081824|PMID:15671059 IMP P YOR254C|PTL1 gene taxon:4932 20050808 SGD
+SGD S000004573 SEC65 GO:0005786 SGD_REF:S000051321|PMID:1313947 IDA C YML105C gene taxon:4932 20021202 SGD
+SGD S000004573 SEC65 GO:0005786 SGD_REF:S000051322|PMID:1313948 ISS C YML105C gene taxon:4932 20031020 SGD
+SGD S000004573 SEC65 GO:0005786 SGD_REF:S000051322|PMID:1313948 IMP C YML105C gene taxon:4932 20031020 SGD
+SGD S000004573 SEC65 GO:0005554 SGD_REF:S000069584 ND F YML105C gene taxon:4932 20010119 SGD
+SGD S000004573 SEC65 GO:0006617 SGD_REF:S000051321|PMID:1313947 IMP P YML105C gene taxon:4932 20021202 SGD
+SGD S000004573 SEC65 GO:0045047 SGD_REF:S000051322|PMID:1313948 IMP P YML105C gene taxon:4932 20031020 SGD
+SGD S000000375 SEC66 GO:0005789 SGD_REF:S000043640|PMID:9275186 TAS C glycoprotein complexed with Sec62p and Sec63p in the Sec63 complex, an integral endoplasmic reticulum membrane protein complex required for translocation of presecretory proteins YBR171W|HSS1|SEC71 gene taxon:4932 20020909 SGD
+SGD S000000375 SEC66 GO:0005789 SGD_REF:S000044438|PMID:10564637 TAS C glycoprotein complexed with Sec62p and Sec63p in the Sec63 complex, an integral endoplasmic reticulum membrane protein complex required for translocation of presecretory proteins YBR171W|HSS1|SEC71 gene taxon:4932 20021126 SGD
+SGD S000000375 SEC66 GO:0031207 SGD_REF:S000053068|PMID:8257795 IPI SGD:S000005780 C glycoprotein complexed with Sec62p and Sec63p in the Sec63 complex, an integral endoplasmic reticulum membrane protein complex required for translocation of presecretory proteins YBR171W|HSS1|SEC71 gene taxon:4932 20050316 SGD
+SGD S000000375 SEC66 GO:0008565 SGD_REF:S000044438|PMID:10564637 TAS F glycoprotein complexed with Sec62p and Sec63p in the Sec63 complex, an integral endoplasmic reticulum membrane protein complex required for translocation of presecretory proteins YBR171W|HSS1|SEC71 gene taxon:4932 20030521 SGD
+SGD S000000375 SEC66 GO:0006620 SGD_REF:S000063769|PMID:9252322 TAS P glycoprotein complexed with Sec62p and Sec63p in the Sec63 complex, an integral endoplasmic reticulum membrane protein complex required for translocation of presecretory proteins YBR171W|HSS1|SEC71 gene taxon:4932 20050126 SGD
+SGD S000000375 SEC66 GO:0030447 SGD_REF:S000080384|PMID:15645503 IMP P glycoprotein complexed with Sec62p and Sec63p in the Sec63 complex, an integral endoplasmic reticulum membrane protein complex required for translocation of presecretory proteins YBR171W|HSS1|SEC71 gene taxon:4932 20050621 SGD
+SGD S000002577 SEC7 GO:0005770 SGD_REF:S000069841|PMID:12006663 IDA C guanine nucleotide exchange protein for ARF YDR170C gene taxon:4932 20030131 SGD
+SGD S000002577 SEC7 GO:0005798 SGD_REF:S000050306|PMID:1729652 IDA C guanine nucleotide exchange protein for ARF YDR170C gene taxon:4932 20010118 SGD
+SGD S000002577 SEC7 GO:0005829 SGD_REF:S000055279|PMID:1986005 IDA C guanine nucleotide exchange protein for ARF YDR170C gene taxon:4932 20010118 SGD
+SGD S000002577 SEC7 GO:0005086 SGD_REF:S000039382|PMID:9539714 IDA F guanine nucleotide exchange protein for ARF YDR170C gene taxon:4932 20010118 SGD
+SGD S000002577 SEC7 GO:0006888 SGD_REF:S000053572|PMID:9473503 IMP P guanine nucleotide exchange protein for ARF YDR170C gene taxon:4932 20010118 SGD
+SGD S000002577 SEC7 GO:0006891 SGD_REF:S000041083|PMID:3042778 IMP P guanine nucleotide exchange protein for ARF YDR170C gene taxon:4932 20010118 SGD
+SGD S000004283 SEC72 GO:0005789 SGD_REF:S000044438|PMID:10564637 TAS C YLR292C|SEC67|SIM2 gene taxon:4932 20021126 SGD
+SGD S000004283 SEC72 GO:0031207 SGD_REF:S000046098|PMID:8051213 IPI SGD:S000005780 C YLR292C|SEC67|SIM2 gene taxon:4932 20050316 SGD
+SGD S000004283 SEC72 GO:0008565 SGD_REF:S000044438|PMID:10564637 TAS F YLR292C|SEC67|SIM2 gene taxon:4932 20030521 SGD
+SGD S000004283 SEC72 GO:0006620 SGD_REF:S000063769|PMID:9252322 TAS P YLR292C|SEC67|SIM2 gene taxon:4932 20050126 SGD
+SGD S000006259 SEC8 GO:0000131 SGD_REF:S000044417|PMID:9128251 TAS C exocyst complex component YPR055W gene taxon:4932 20021112 SGD
+SGD S000006259 SEC8 GO:0000145 SGD_REF:S000039481|PMID:9700152 TAS C exocyst complex component YPR055W gene taxon:4932 20010118 SGD
+SGD S000006259 SEC8 GO:0000145 SGD_REF:S000047160|PMID:8978675 IPI C exocyst complex component YPR055W gene taxon:4932 20040706 SGD
+SGD S000006259 SEC8 GO:0005934 SGD_REF:S000049442|PMID:7615633 IDA C exocyst complex component YPR055W gene taxon:4932 20040706 SGD
+SGD S000006259 SEC8 GO:0030427 SGD_REF:S000041326|PMID:9491896 IDA C exocyst complex component YPR055W gene taxon:4932 20040706 SGD
+SGD S000006259 SEC8 GO:0005515 SGD_REF:S000073320|PMID:12665530 IDA F exocyst complex component YPR055W gene taxon:4932 20030623 SGD
+SGD S000006259 SEC8 GO:0005515 SGD_REF:S000073320|PMID:12665530 TAS F exocyst complex component YPR055W gene taxon:4932 20030623 SGD
+SGD S000006259 SEC8 GO:0000910 SGD_REF:S000041005|PMID:10652251 IMP P exocyst complex component YPR055W gene taxon:4932 20010119 SGD
+SGD S000006259 SEC8 GO:0006893 SGD_REF:S000039481|PMID:9700152 TAS P exocyst complex component YPR055W gene taxon:4932 20010118 SGD
+SGD S000006259 SEC8 GO:0006904 SGD_REF:S000039481|PMID:9700152 TAS P exocyst complex component YPR055W gene taxon:4932 20010118 SGD
+SGD S000006259 SEC8 GO:0006906 SGD_REF:S000039481|PMID:9700152 TAS P exocyst complex component YPR055W gene taxon:4932 20010118 SGD
+SGD S000006259 SEC8 GO:0007121 SGD_REF:S000041005|PMID:10652251 IMP P exocyst complex component YPR055W gene taxon:4932 20010118 SGD
+SGD S000003241 SEC9 GO:0019897 SGD_REF:S000043550|PMID:7954793 IDA C t-SNARE (putative) YGR009C|HSS7 gene taxon:4932 20060531 SGD
+SGD S000003241 SEC9 GO:0031201 SGD_REF:S000058139|PMID:9195974 IDA C t-SNARE (putative) YGR009C|HSS7 gene taxon:4932 20060531 SGD
+SGD S000003241 SEC9 GO:0005486 SGD_REF:S000075375|PMID:14675424 TAS F t-SNARE (putative) YGR009C|HSS7 gene taxon:4932 20040929 SGD
+SGD S000003241 SEC9 GO:0006893 SGD_REF:S000058453|PMID:10047442 TAS P t-SNARE (putative) YGR009C|HSS7 gene taxon:4932 20010118 SGD
+SGD S000003241 SEC9 GO:0006906 SGD_REF:S000058453|PMID:10047442 TAS P t-SNARE (putative) YGR009C|HSS7 gene taxon:4932 20010118 SGD
+SGD S000002484 SED1 GO:0005739 SGD_REF:S000077189|PMID:15351639 IDA C cell surface glycoprotein (putative) YDR077W gene taxon:4932 20050419 SGD
+SGD S000002484 SED1 GO:0005840 SGD_REF:S000073114|PMID:12627396 IDA C cell surface glycoprotein (putative) YDR077W gene taxon:4932 20030512 SGD
+SGD S000002484 SED1 GO:0009277 SGD_REF:S000059732|PMID:9613572 IDA C cell surface glycoprotein (putative) YDR077W gene taxon:4932 20010306 SGD
+SGD S000002484 SED1 GO:0009277 SGD_REF:S000059732|PMID:9613572 ISS C cell surface glycoprotein (putative) YDR077W gene taxon:4932 20010306 SGD
+SGD S000002484 SED1 GO:0005199 SGD_REF:S000050723|PMID:9642191 IMP F cell surface glycoprotein (putative) YDR077W gene taxon:4932 20010306 SGD
+SGD S000002484 SED1 GO:0005199 SGD_REF:S000050723|PMID:9642191 IEP F cell surface glycoprotein (putative) YDR077W gene taxon:4932 20010306 SGD
+SGD S000002484 SED1 GO:0000002 SGD_REF:S000077189|PMID:15351639 IMP P cell surface glycoprotein (putative) YDR077W gene taxon:4932 20050419 SGD
+SGD S000002484 SED1 GO:0007047 SGD_REF:S000050723|PMID:9642191 IMP P cell surface glycoprotein (putative) YDR077W gene taxon:4932 20010306 SGD
+SGD S000002484 SED1 GO:0007047 SGD_REF:S000050723|PMID:9642191 IEP P cell surface glycoprotein (putative) YDR077W gene taxon:4932 20010306 SGD
+SGD S000000663 SED4 GO:0005783 SGD_REF:S000046929|PMID:7593162 TAS C YCR067C gene taxon:4932 20020827 SGD
+SGD S000000663 SED4 GO:0030176 SGD_REF:S000046929|PMID:7593162 IDA C YCR067C gene taxon:4932 20050419 SGD
+SGD S000000663 SED4 GO:0005554 SGD_REF:S000069584 ND F YCR067C gene taxon:4932 20020827 SGD
+SGD S000000663 SED4 GO:0006888 SGD_REF:S000060010|PMID:11168590 IGI P YCR067C gene taxon:4932 20020827 SGD
+SGD S000000663 SED4 GO:0006888 SGD_REF:S000060010|PMID:11168590 IMP P YCR067C gene taxon:4932 20020827 SGD
+SGD S000004016 SED5 GO:0005801 SGD_REF:S000040760|PMID:7929581 IDA C syntaxin family YLR026C gene taxon:4932 20020917 SGD
+SGD S000004016 SED5 GO:0005486 SGD_REF:S000058453|PMID:10047442 TAS F syntaxin family YLR026C gene taxon:4932 20010118 SGD
+SGD S000004016 SED5 GO:0006888 SGD_REF:S000058453|PMID:10047442 TAS P syntaxin family YLR026C gene taxon:4932 20010118 SGD
+SGD S000004016 SED5 GO:0006890 SGD_REF:S000058453|PMID:10047442 TAS P syntaxin family YLR026C gene taxon:4932 20010118 SGD
+SGD S000004016 SED5 GO:0006891 SGD_REF:S000058453|PMID:10047442 TAS P syntaxin family YLR026C gene taxon:4932 20010118 SGD
+SGD S000004016 SED5 GO:0006906 SGD_REF:S000058453|PMID:10047442 TAS P syntaxin family YLR026C gene taxon:4932 20010118 SGD
+SGD S000000162 SEF1 GO:0008372 SGD_REF:S000069584 ND C transcription factor (putative) YBL066C gene taxon:4932 20021104 SGD
+SGD S000000162 SEF1 GO:0005554 SGD_REF:S000069584 ND F transcription factor (putative) YBL066C gene taxon:4932 20021104 SGD
+SGD S000000162 SEF1 GO:0000004 SGD_REF:S000069584 ND P transcription factor (putative) YBL066C gene taxon:4932 20021104 SGD
+SGD S000003068 SEH1 GO:0005643 SGD_REF:S000058277|PMID:9442897 IDA C nuclear pore complex subunit YGL100W gene taxon:4932 20010118 SGD
+SGD S000003068 SEH1 GO:0005198 SGD_REF:S000058277|PMID:9442897 TAS F nuclear pore complex subunit YGL100W gene taxon:4932 20010118 SGD
+SGD S000003068 SEH1 GO:0006406 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YGL100W gene taxon:4932 20010118 SGD
+SGD S000003068 SEH1 GO:0006407 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YGL100W gene taxon:4932 20010118 SGD
+SGD S000003068 SEH1 GO:0006408 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YGL100W gene taxon:4932 20010118 SGD
+SGD S000003068 SEH1 GO:0006409 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YGL100W gene taxon:4932 20010118 SGD
+SGD S000003068 SEH1 GO:0006607 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YGL100W gene taxon:4932 20010118 SGD
+SGD S000003068 SEH1 GO:0006608 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YGL100W gene taxon:4932 20010118 SGD
+SGD S000003068 SEH1 GO:0006609 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YGL100W gene taxon:4932 20010118 SGD
+SGD S000003068 SEH1 GO:0006610 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YGL100W gene taxon:4932 20010118 SGD
+SGD S000003068 SEH1 GO:0006611 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YGL100W gene taxon:4932 20010118 SGD
+SGD S000003068 SEH1 GO:0006999 SGD_REF:S000058277|PMID:9442897 TAS P nuclear pore complex subunit YGL100W gene taxon:4932 20010118 SGD
+SGD S000004475 SEL1 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C YML013W|UBX2 gene taxon:4932 20060317 SGD
+SGD S000004475 SEL1 GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YML013W|UBX2 gene taxon:4932 20031028 SGD
+SGD S000004475 SEL1 GO:0005554 SGD_REF:S000069584 ND F YML013W|UBX2 gene taxon:4932 20021125 SGD
+SGD S000004475 SEL1 GO:0009306 SGD_REF:S000072522|PMID:12489121 IMP P YML013W|UBX2 gene taxon:4932 20030210 SGD
+SGD S000004475 SEL1 GO:0043161 SGD_REF:S000076733|PMID:15258615 IMP P YML013W|UBX2 gene taxon:4932 20040806 SGD
+SGD S000007235 SEM1 GO:0005634 SGD_REF:S000074074|PMID:12961755 IPI C YDR363W-A|DSS1|HOD1 gene taxon:4932 20040714 SGD
+SGD S000007235 SEM1 GO:0005792 SGD_REF:S000054521|PMID:9927667 IDA C YDR363W-A|DSS1|HOD1 gene taxon:4932 20021216 SGD
+SGD S000007235 SEM1 GO:0005829 SGD_REF:S000054521|PMID:9927667 IDA C YDR363W-A|DSS1|HOD1 gene taxon:4932 20021216 SGD
+SGD S000007235 SEM1 GO:0008541 SGD_REF:S000076568|PMID:15117943 IDA C YDR363W-A|DSS1|HOD1 gene taxon:4932 20040805 SGD
+SGD S000007235 SEM1 GO:0008541 SGD_REF:S000079881|PMID:15572408 IDA C YDR363W-A|DSS1|HOD1 gene taxon:4932 20050211 SGD
+SGD S000007235 SEM1 GO:0005554 SGD_REF:S000069584 ND F YDR363W-A|DSS1|HOD1 gene taxon:4932 20021216 SGD
+SGD S000007235 SEM1 GO:0000074 SGD_REF:S000051865|PMID:10373512 IMP P YDR363W-A|DSS1|HOD1 gene taxon:4932 20020715 SGD
+SGD S000007235 SEM1 GO:0006511 SGD_REF:S000079881|PMID:15572408 IMP P YDR363W-A|DSS1|HOD1 gene taxon:4932 20050421 SGD
+SGD S000007235 SEM1 GO:0006887 SGD_REF:S000054521|PMID:9927667 IGI P YDR363W-A|DSS1|HOD1 gene taxon:4932 20021216 SGD
+SGD S000007235 SEM1 GO:0006887 SGD_REF:S000054521|PMID:9927667 IPI P YDR363W-A|DSS1|HOD1 gene taxon:4932 20021216 SGD
+SGD S000007235 SEM1 GO:0030447 SGD_REF:S000054521|PMID:9927667 IMP P YDR363W-A|DSS1|HOD1 gene taxon:4932 20021216 SGD
+SGD S000007235 SEM1 GO:0043161 SGD_REF:S000076568|PMID:15117943 IDA P YDR363W-A|DSS1|HOD1 gene taxon:4932 20040805 SGD
+SGD S000007235 SEM1 GO:0043161 SGD_REF:S000076568|PMID:15117943 IMP P YDR363W-A|DSS1|HOD1 gene taxon:4932 20040805 SGD
+SGD S000004422 SEN1 GO:0005634 SGD_REF:S000044234|PMID:8544822 IDA C nuclear-localized tRNA splicing complex component YLR430W|CIK3|NRD2 gene taxon:4932 20040212 SGD
+SGD S000004422 SEN1 GO:0004004 SGD_REF:S000058443|PMID:10690410 TAS F nuclear-localized tRNA splicing complex component YLR430W|CIK3|NRD2 gene taxon:4932 20010118 SGD
+SGD S000004422 SEN1 GO:0006365 SGD_REF:S000046278|PMID:9365256 IMP P nuclear-localized tRNA splicing complex component YLR430W|CIK3|NRD2 gene taxon:4932 20030210 SGD
+SGD S000004422 SEN1 GO:0008033 SGD_REF:S000046278|PMID:9365256 IMP P nuclear-localized tRNA splicing complex component YLR430W|CIK3|NRD2 gene taxon:4932 20060522 SGD
+SGD S000004422 SEN1 GO:0016180 SGD_REF:S000046278|PMID:9365256 IMP P nuclear-localized tRNA splicing complex component YLR430W|CIK3|NRD2 gene taxon:4932 20060522 SGD
+SGD S000004422 SEN1 GO:0043144 SGD_REF:S000046278|PMID:9365256 IMP P nuclear-localized tRNA splicing complex component YLR430W|CIK3|NRD2 gene taxon:4932 20060522 SGD
+SGD S000004663 SEN15 GO:0000214 SGD_REF:S000058320|PMID:9582290 TAS C tetrameric tRNA splicing endonuclease 15kDa subunit YMR059W gene taxon:4932 20010118 SGD
+SGD S000004663 SEN15 GO:0005637 SGD_REF:S000058320|PMID:9582290 TAS C tetrameric tRNA splicing endonuclease 15kDa subunit YMR059W gene taxon:4932 20010118 SGD
+SGD S000004663 SEN15 GO:0005741 SGD_REF:S000076331|PMID:12925762 IDA C tetrameric tRNA splicing endonuclease 15kDa subunit YMR059W gene taxon:4932 20040609 SGD
+SGD S000004663 SEN15 GO:0005741 SGD_REF:S000076331|PMID:12925762 IMP C tetrameric tRNA splicing endonuclease 15kDa subunit YMR059W gene taxon:4932 20040609 SGD
+SGD S000004663 SEN15 GO:0005741 SGD_REF:S000076331|PMID:12925762 IPI C tetrameric tRNA splicing endonuclease 15kDa subunit YMR059W gene taxon:4932 20040609 SGD
+SGD S000004663 SEN15 GO:0000213 SGD_REF:S000058320|PMID:9582290 TAS F tetrameric tRNA splicing endonuclease 15kDa subunit YMR059W gene taxon:4932 20010118 SGD
+SGD S000004663 SEN15 GO:0006388 SGD_REF:S000058320|PMID:9582290 TAS P tetrameric tRNA splicing endonuclease 15kDa subunit YMR059W gene taxon:4932 20010118 SGD
+SGD S000004095 SEN2 GO:0000214 SGD_REF:S000058320|PMID:9582290 TAS C tRNA splicing endonuclease subunit YLR105C gene taxon:4932 20010118 SGD
+SGD S000004095 SEN2 GO:0005637 SGD_REF:S000058320|PMID:9582290 TAS C tRNA splicing endonuclease subunit YLR105C gene taxon:4932 20010118 SGD
+SGD S000004095 SEN2 GO:0005741 SGD_REF:S000076331|PMID:12925762 IDA C tRNA splicing endonuclease subunit YLR105C gene taxon:4932 20040609 SGD
+SGD S000004095 SEN2 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C tRNA splicing endonuclease subunit YLR105C gene taxon:4932 20060317 SGD
+SGD S000004095 SEN2 GO:0005741 SGD_REF:S000076331|PMID:12925762 IPI C tRNA splicing endonuclease subunit YLR105C gene taxon:4932 20040609 SGD
+SGD S000004095 SEN2 GO:0005741 SGD_REF:S000076331|PMID:12925762 IMP C tRNA splicing endonuclease subunit YLR105C gene taxon:4932 20040609 SGD
+SGD S000004095 SEN2 GO:0000213 SGD_REF:S000058320|PMID:9582290 TAS F tRNA splicing endonuclease subunit YLR105C gene taxon:4932 20010118 SGD
+SGD S000004095 SEN2 GO:0006388 SGD_REF:S000058320|PMID:9582290 TAS P tRNA splicing endonuclease subunit YLR105C gene taxon:4932 20010118 SGD
+SGD S000000066 SEN34 GO:0000214 SGD_REF:S000058320|PMID:9582290 TAS C tetrameric tRNA splicing endonuclease 34 kDa subunit YAR008W|FUN4 gene taxon:4932 20010118 SGD
+SGD S000000066 SEN34 GO:0005637 SGD_REF:S000058320|PMID:9582290 TAS C tetrameric tRNA splicing endonuclease 34 kDa subunit YAR008W|FUN4 gene taxon:4932 20010118 SGD
+SGD S000000066 SEN34 GO:0005741 SGD_REF:S000076331|PMID:12925762 IDA C tetrameric tRNA splicing endonuclease 34 kDa subunit YAR008W|FUN4 gene taxon:4932 20040609 SGD
+SGD S000000066 SEN34 GO:0005741 SGD_REF:S000076331|PMID:12925762 IMP C tetrameric tRNA splicing endonuclease 34 kDa subunit YAR008W|FUN4 gene taxon:4932 20040609 SGD
+SGD S000000066 SEN34 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C tetrameric tRNA splicing endonuclease 34 kDa subunit YAR008W|FUN4 gene taxon:4932 20060317 SGD
+SGD S000000066 SEN34 GO:0005741 SGD_REF:S000076331|PMID:12925762 IPI C tetrameric tRNA splicing endonuclease 34 kDa subunit YAR008W|FUN4 gene taxon:4932 20040609 SGD
+SGD S000000066 SEN34 GO:0000213 SGD_REF:S000058320|PMID:9582290 TAS F tetrameric tRNA splicing endonuclease 34 kDa subunit YAR008W|FUN4 gene taxon:4932 20010118 SGD
+SGD S000000066 SEN34 GO:0006388 SGD_REF:S000058320|PMID:9582290 TAS P tetrameric tRNA splicing endonuclease 34 kDa subunit YAR008W|FUN4 gene taxon:4932 20010118 SGD
+SGD S000006004 SEN54 GO:0000214 SGD_REF:S000058320|PMID:9582290 TAS C tetrameric tRNA splicing endonuclease 54 kDa subunit YPL083C gene taxon:4932 20010118 SGD
+SGD S000006004 SEN54 GO:0005637 SGD_REF:S000058320|PMID:9582290 TAS C tetrameric tRNA splicing endonuclease 54 kDa subunit YPL083C gene taxon:4932 20010118 SGD
+SGD S000006004 SEN54 GO:0005741 SGD_REF:S000076331|PMID:12925762 IDA C tetrameric tRNA splicing endonuclease 54 kDa subunit YPL083C gene taxon:4932 20040609 SGD
+SGD S000006004 SEN54 GO:0005741 SGD_REF:S000076331|PMID:12925762 IMP C tetrameric tRNA splicing endonuclease 54 kDa subunit YPL083C gene taxon:4932 20040609 SGD
+SGD S000006004 SEN54 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C tetrameric tRNA splicing endonuclease 54 kDa subunit YPL083C gene taxon:4932 20060317 SGD
+SGD S000006004 SEN54 GO:0005741 SGD_REF:S000076331|PMID:12925762 IPI C tetrameric tRNA splicing endonuclease 54 kDa subunit YPL083C gene taxon:4932 20040609 SGD
+SGD S000006004 SEN54 GO:0000213 SGD_REF:S000058320|PMID:9582290 TAS F tetrameric tRNA splicing endonuclease 54 kDa subunit YPL083C gene taxon:4932 20010118 SGD
+SGD S000006004 SEN54 GO:0006388 SGD_REF:S000058320|PMID:9582290 TAS P tetrameric tRNA splicing endonuclease 54 kDa subunit YPL083C gene taxon:4932 20010118 SGD
+SGD S000000062 SEO1 GO:0016020 SGD_REF:S000058231|PMID:9348664 ISS C permease (putative) YAL067C gene taxon:4932 20020614 SGD
+SGD S000000062 SEO1 GO:0005215 SGD_REF:S000058231|PMID:9348664 ISS F permease (putative) YAL067C gene taxon:4932 20020614 SGD
+SGD S000000062 SEO1 GO:0006810 SGD_REF:S000058231|PMID:9348664 ISS P permease (putative) YAL067C gene taxon:4932 20020614 SGD
+SGD S000005710 SER1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C phosphoserine transaminase YOR184W|ADE9 gene taxon:4932 20031028 SGD
+SGD S000005710 SER1 GO:0004648 SGD_REF:S000042391|PMID:8017107 IMP F phosphoserine transaminase YOR184W|ADE9 gene taxon:4932 20021001 SGD
+SGD S000005710 SER1 GO:0004648 SGD_REF:S000042391|PMID:8017107 ISS F phosphoserine transaminase YOR184W|ADE9 gene taxon:4932 20021001 SGD
+SGD S000005710 SER1 GO:0006564 SGD_REF:S000042391|PMID:8017107 ISS P phosphoserine transaminase YOR184W|ADE9 gene taxon:4932 20021001 SGD
+SGD S000005710 SER1 GO:0006564 SGD_REF:S000042391|PMID:8017107 IMP P phosphoserine transaminase YOR184W|ADE9 gene taxon:4932 20021001 SGD
+SGD S000005710 SER1 GO:0009070 SGD_REF:S000039638|PMID:1326413 IMP P phosphoserine transaminase YOR184W|ADE9 gene taxon:4932 20021001 SGD
+SGD S000005710 SER1 GO:0009113 SGD_REF:S000046728|PMID:10509016 IMP P phosphoserine transaminase YOR184W|ADE9 gene taxon:4932 20021111 SGD
+SGD S000003440 SER2 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C phosphoserine phosphatase YGR208W gene taxon:4932 20031028 SGD
+SGD S000003440 SER2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C phosphoserine phosphatase YGR208W gene taxon:4932 20031028 SGD
+SGD S000003440 SER2 GO:0004647 SGD_REF:S000039638|PMID:1326413 IMP F phosphoserine phosphatase YGR208W gene taxon:4932 20021001 SGD
+SGD S000003440 SER2 GO:0009070 SGD_REF:S000039638|PMID:1326413 IMP P phosphoserine phosphatase YGR208W gene taxon:4932 20021001 SGD
+SGD S000000883 SER3 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C 3-phosphoglycerate dehydrogenase YER081W gene taxon:4932 20031028 SGD
+SGD S000000883 SER3 GO:0004617 SGD_REF:S000072828|PMID:12525494 IMP F 3-phosphoglycerate dehydrogenase YER081W gene taxon:4932 20030401 SGD
+SGD S000000883 SER3 GO:0009070 SGD_REF:S000072828|PMID:12525494 IMP P 3-phosphoglycerate dehydrogenase YER081W gene taxon:4932 20030401 SGD
+SGD S000001336 SER33 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C 3-phosphoglycerate dehydrogenase YIL074C gene taxon:4932 20031028 SGD
+SGD S000001336 SER33 GO:0004617 SGD_REF:S000072828|PMID:12525494 IMP F 3-phosphoglycerate dehydrogenase YIL074C gene taxon:4932 20030401 SGD
+SGD S000001336 SER33 GO:0009070 SGD_REF:S000072828|PMID:12525494 IMP P 3-phosphoglycerate dehydrogenase YIL074C gene taxon:4932 20030401 SGD
+SGD S000002430 SES1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C serine-tRNA ligase YDR023W|SerRS gene taxon:4932 20020507 SGD
+SGD S000002430 SES1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C serine-tRNA ligase YDR023W|SerRS gene taxon:4932 20031028 SGD
+SGD S000002430 SES1 GO:0004828 SGD_REF:S000056990|PMID:3031581 IDA F serine-tRNA ligase YDR023W|SerRS gene taxon:4932 20021001 SGD
+SGD S000002430 SES1 GO:0006434 SGD_REF:S000056990|PMID:3031581 IDA P serine-tRNA ligase YDR023W|SerRS gene taxon:4932 20031217 SGD
+SGD S000001161 SET1 GO:0048188 SGD_REF:S000068991|PMID:11752412 IPI SGD:S000000064|SGD:S000001501|SGD:S000004005|SGD:S000006059|SGD:S000002877|SGD:S000000379 C YHR119W|YTX1 gene taxon:4932 20050524 SGD
+SGD S000001161 SET1 GO:0048188 SGD_REF:S000066156|PMID:11687631 IPI SGD:S000000064|SGD:S000006059|SGD:S000004005|SGD:S000001501|SGD:S000002877|SGD:S000000379 C YHR119W|YTX1 gene taxon:4932 20050524 SGD
+SGD S000001161 SET1 GO:0048188 SGD_REF:S000068755|PMID:11742990 IPI SGD:S000000064|SGD:S000000462|SGD:S000006059|SGD:S000004005|SGD:S000001501|SGD:S000002877|SGD:S000000379 C YHR119W|YTX1 gene taxon:4932 20050524 SGD
+SGD S000001161 SET1 GO:0016279 SGD_REF:S000086680|PMID:16143104 IMP F YHR119W|YTX1 gene taxon:4932 20051013 SGD
+SGD S000001161 SET1 GO:0016279 SGD_REF:S000086680|PMID:16143104 IPI SGD:S000003345 F YHR119W|YTX1 gene taxon:4932 20051013 SGD
+SGD S000001161 SET1 GO:0042054 SGD_REF:S000073471|PMID:12845608 ISS F YHR119W|YTX1 gene taxon:4932 20050525 SGD
+SGD S000001161 SET1 contributes_to GO:0042800 SGD_REF:S000068991|PMID:11752412 IMP F YHR119W|YTX1 gene taxon:4932 20050524 SGD
+SGD S000001161 SET1 contributes_to GO:0042800 SGD_REF:S000069538|PMID:11805083 IDA F YHR119W|YTX1 gene taxon:4932 20050525 SGD
+SGD S000001161 SET1 contributes_to GO:0042800 SGD_REF:S000068755|PMID:11742990 IMP F YHR119W|YTX1 gene taxon:4932 20050525 SGD
+SGD S000001161 SET1 contributes_to GO:0042800 SGD_REF:S000068755|PMID:11742990 IDA F YHR119W|YTX1 gene taxon:4932 20050525 SGD
+SGD S000001161 SET1 contributes_to GO:0042800 SGD_REF:S000073471|PMID:12845608 IMP F YHR119W|YTX1 gene taxon:4932 20050525 SGD
+SGD S000001161 SET1 contributes_to GO:0042800 SGD_REF:S000069538|PMID:11805083 IMP F YHR119W|YTX1 gene taxon:4932 20050525 SGD
+SGD S000001161 SET1 GO:0000183 SGD_REF:S000077207|PMID:15340082 TAS P YHR119W|YTX1 gene taxon:4932 20041206 SGD
+SGD S000001161 SET1 GO:0000723 SGD_REF:S000068755|PMID:11742990 IMP P YHR119W|YTX1 gene taxon:4932 20050525 SGD
+SGD S000001161 SET1 GO:0000723 SGD_REF:S000046241|PMID:9398665 IMP P YHR119W|YTX1 gene taxon:4932 20050525 SGD
+SGD S000001161 SET1 GO:0006348 SGD_REF:S000039871|PMID:9988274 IMP P YHR119W|YTX1 gene taxon:4932 20020821 SGD
+SGD S000001161 SET1 GO:0006348 SGD_REF:S000046241|PMID:9398665 IMP P YHR119W|YTX1 gene taxon:4932 20050525 SGD
+SGD S000001161 SET1 GO:0006348 SGD_REF:S000069538|PMID:11805083 IMP P YHR119W|YTX1 gene taxon:4932 20050525 SGD
+SGD S000001161 SET1 GO:0006348 SGD_REF:S000068991|PMID:11752412 IMP P YHR119W|YTX1 gene taxon:4932 20050524 SGD
+SGD S000001161 SET1 GO:0016571 SGD_REF:S000068991|PMID:11752412 IMP P YHR119W|YTX1 gene taxon:4932 20020211 SGD
+SGD S000001161 SET1 GO:0016571 SGD_REF:S000068991|PMID:11752412 IDA P YHR119W|YTX1 gene taxon:4932 20050524 SGD
+SGD S000001161 SET1 GO:0016571 SGD_REF:S000069538|PMID:11805083 IMP P YHR119W|YTX1 gene taxon:4932 20050525 SGD
+SGD S000001161 SET1 GO:0016571 SGD_REF:S000069538|PMID:11805083 IDA P YHR119W|YTX1 gene taxon:4932 20050525 SGD
+SGD S000001161 SET1 GO:0016571 SGD_REF:S000068755|PMID:11742990 IDA P YHR119W|YTX1 gene taxon:4932 20020212 SGD
+SGD S000001161 SET1 GO:0018027 SGD_REF:S000086680|PMID:16143104 IMP P YHR119W|YTX1 gene taxon:4932 20051013 SGD
+SGD S000001161 SET1 GO:0018027 SGD_REF:S000086680|PMID:16143104 IPI SGD:S000003345 P YHR119W|YTX1 gene taxon:4932 20051013 SGD
+SGD S000001161 SET1 GO:0030466 SGD_REF:S000046241|PMID:9398665 IMP P YHR119W|YTX1 gene taxon:4932 20050525 SGD
+SGD S000003704 SET2 GO:0005634 SGD_REF:S000069489|PMID:11839797 IPI C YJL168C|EZL1 gene taxon:4932 20020522 SGD
+SGD S000003704 SET2 GO:0042054 SGD_REF:S000073471|PMID:12845608 ISS F YJL168C|EZL1 gene taxon:4932 20050525 SGD
+SGD S000003704 SET2 GO:0042054 SGD_REF:S000069489|PMID:11839797 ISS F YJL168C|EZL1 gene taxon:4932 20050525 SGD
+SGD S000003704 SET2 GO:0046975 SGD_REF:S000069489|PMID:11839797 IDA F YJL168C|EZL1 gene taxon:4932 20050525 SGD
+SGD S000003704 SET2 GO:0046975 SGD_REF:S000069489|PMID:11839797 IMP F YJL168C|EZL1 gene taxon:4932 20050525 SGD
+SGD S000003704 SET2 GO:0046975 SGD_REF:S000069489|PMID:11839797 IPI F YJL168C|EZL1 gene taxon:4932 20050525 SGD
+SGD S000003704 SET2 GO:0006354 SGD_REF:S000073151|PMID:12736296 IDA P YJL168C|EZL1 gene taxon:4932 20030706 SGD
+SGD S000003704 SET2 GO:0006354 SGD_REF:S000073151|PMID:12736296 IPI P YJL168C|EZL1 gene taxon:4932 20030706 SGD
+SGD S000003704 SET2 GO:0006355 SGD_REF:S000069489|PMID:11839797 IDA P YJL168C|EZL1 gene taxon:4932 20020522 SGD
+SGD S000003704 SET2 GO:0006355 SGD_REF:S000069489|PMID:11839797 IMP P YJL168C|EZL1 gene taxon:4932 20020522 SGD
+SGD S000003704 SET2 GO:0016571 SGD_REF:S000069489|PMID:11839797 IDA P YJL168C|EZL1 gene taxon:4932 20020522 SGD
+SGD S000003704 SET2 GO:0016571 SGD_REF:S000069489|PMID:11839797 IMP P YJL168C|EZL1 gene taxon:4932 20020522 SGD
+SGD S000001737 SET3 GO:0000118 SGD_REF:S000066205|PMID:11711434 IPI C YKR029C gene taxon:4932 20021010 SGD
+SGD S000001737 SET3 contributes_to GO:0017136 SGD_REF:S000066205|PMID:11711434 IPI F YKR029C gene taxon:4932 20050429 SGD
+SGD S000001737 SET3 contributes_to GO:0045129 SGD_REF:S000066205|PMID:11711434 IPI F YKR029C gene taxon:4932 20050429 SGD
+SGD S000001737 SET3 GO:0016575 SGD_REF:S000066205|PMID:11711434 IDA P YKR029C gene taxon:4932 20021010 SGD
+SGD S000001737 SET3 GO:0016575 SGD_REF:S000066205|PMID:11711434 IPI P YKR029C gene taxon:4932 20021010 SGD
+SGD S000001737 SET3 GO:0045835 SGD_REF:S000066205|PMID:11711434 IMP P YKR029C gene taxon:4932 20021010 SGD
+SGD S000003641 SET4 GO:0008372 SGD_REF:S000069584 ND C YJL105W gene taxon:4932 20021125 SGD
+SGD S000003641 SET4 GO:0005554 SGD_REF:S000069584 ND F YJL105W gene taxon:4932 20021125 SGD
+SGD S000003641 SET4 GO:0000004 SGD_REF:S000069584 ND P YJL105W gene taxon:4932 20021125 SGD
+SGD S000001250 SET5 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YHR207C gene taxon:4932 20031028 SGD
+SGD S000001250 SET5 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YHR207C gene taxon:4932 20031028 SGD
+SGD S000001250 SET5 GO:0005554 SGD_REF:S000069584 ND F YHR207C gene taxon:4932 20021125 SGD
+SGD S000001250 SET5 GO:0000004 SGD_REF:S000069584 ND P YHR207C gene taxon:4932 20021125 SGD
+SGD S000006086 SET6 GO:0008372 SGD_REF:S000069584 ND C YPL165C gene taxon:4932 20021029 SGD
+SGD S000006086 SET6 GO:0005554 SGD_REF:S000069584 ND F YPL165C gene taxon:4932 20021029 SGD
+SGD S000006086 SET6 GO:0000004 SGD_REF:S000069584 ND P YPL165C gene taxon:4932 20021029 SGD
+SGD S000002665 SET7 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YDR257C|RMS1 gene taxon:4932 20031028 SGD
+SGD S000002665 SET7 GO:0005554 SGD_REF:S000069584 ND F YDR257C|RMS1 gene taxon:4932 20021120 SGD
+SGD S000002665 SET7 GO:0000004 SGD_REF:S000069584 ND P YDR257C|RMS1 gene taxon:4932 20021120 SGD
+SGD S000005691 SEY1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YOR165W gene taxon:4932 20031028 SGD
+SGD S000005691 SEY1 GO:0005554 SGD_REF:S000069584 ND F YOR165W gene taxon:4932 20021125 SGD
+SGD S000005691 SEY1 GO:0016044 SGD_REF:S000071802|PMID:12427979 IGI SGD:S000006232 P YOR165W gene taxon:4932 20021212 SGD
+SGD S000002327 SFA1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C glutathione-dependent formaldehyde dehydrogenase YDL168W|ADH5 gene taxon:4932 20031028 SGD
+SGD S000002327 SFA1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C glutathione-dependent formaldehyde dehydrogenase YDL168W|ADH5 gene taxon:4932 20040813 SGD
+SGD S000002327 SFA1 GO:0004022 SGD_REF:S000072614|PMID:12499363 IMP F glutathione-dependent formaldehyde dehydrogenase YDL168W|ADH5 gene taxon:4932 20050426 SGD
+SGD S000002327 SFA1 GO:0004327 SGD_REF:S000048065|PMID:8483449 IDA F glutathione-dependent formaldehyde dehydrogenase YDL168W|ADH5 gene taxon:4932 20020917 SGD
+SGD S000002327 SFA1 GO:0046294 SGD_REF:S000048065|PMID:8483449 IDA P glutathione-dependent formaldehyde dehydrogenase YDL168W|ADH5 gene taxon:4932 20050412 SGD
+SGD S000004994 SFB2 GO:0030127 SGD_REF:S000041070|PMID:10749860 IPI C zinc finger protein (putative) YNL049C gene taxon:4932 20020926 SGD
+SGD S000004994 SFB2 GO:0005554 SGD_REF:S000069584 ND F zinc finger protein (putative) YNL049C gene taxon:4932 20020926 SGD
+SGD S000004994 SFB2 GO:0006888 SGD_REF:S000041070|PMID:10749860 IGI P zinc finger protein (putative) YNL049C gene taxon:4932 20020926 SGD
+SGD S000001140 SFB3 GO:0000300 SGD_REF:S000049853|PMID:10330397 IDA C YHR098C|LST1 gene taxon:4932 20020827 SGD
+SGD S000001140 SFB3 GO:0000300 SGD_REF:S000049853|PMID:10330397 IPI C YHR098C|LST1 gene taxon:4932 20020827 SGD
+SGD S000001140 SFB3 GO:0005783 SGD_REF:S000049853|PMID:10330397 IDA C YHR098C|LST1 gene taxon:4932 20020827 SGD
+SGD S000001140 SFB3 GO:0030127 SGD_REF:S000049853|PMID:10330397 IGI C YHR098C|LST1 gene taxon:4932 20020827 SGD
+SGD S000001140 SFB3 GO:0030127 SGD_REF:S000049853|PMID:10330397 ISS C YHR098C|LST1 gene taxon:4932 20020827 SGD
+SGD S000001140 SFB3 GO:0030127 SGD_REF:S000049853|PMID:10330397 IMP C YHR098C|LST1 gene taxon:4932 20020827 SGD
+SGD S000001140 SFB3 GO:0030127 SGD_REF:S000049853|PMID:10330397 IPI C YHR098C|LST1 gene taxon:4932 20020827 SGD
+SGD S000001140 SFB3 GO:0005554 SGD_REF:S000069584 ND F YHR098C|LST1 gene taxon:4932 20021003 SGD
+SGD S000001140 SFB3 GO:0006888 SGD_REF:S000049853|PMID:10330397 IGI P YHR098C|LST1 gene taxon:4932 20020827 SGD
+SGD S000001140 SFB3 GO:0006888 SGD_REF:S000049853|PMID:10330397 IMP P YHR098C|LST1 gene taxon:4932 20020827 SGD
+SGD S000003856 SFC1 GO:0005743 SGD_REF:S000050868|PMID:7908717 ISS C succinate-fumarate transport protein YJR095W|ACR1 gene taxon:4932 20010118 SGD
+SGD S000003856 SFC1 GO:0005469 SGD_REF:S000055218|PMID:9395087 IDA F succinate-fumarate transport protein YJR095W|ACR1 gene taxon:4932 20010118 SGD
+SGD S000003856 SFC1 GO:0015741 SGD_REF:S000055218|PMID:9395087 IDA P succinate-fumarate transport protein YJR095W|ACR1 gene taxon:4932 20010118 SGD
+SGD S000003856 SFC1 GO:0015744 SGD_REF:S000055218|PMID:9395087 IDA P succinate-fumarate transport protein YJR095W|ACR1 gene taxon:4932 20010118 SGD
+SGD S000005842 SFG1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YOR315W gene taxon:4932 20031028 SGD
+SGD S000005842 SFG1 GO:0005634 SGD_REF:S000113722|PMID:16289536 IDA C YOR315W gene taxon:4932 20051211 SGD
+SGD S000005842 SFG1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YOR315W gene taxon:4932 20031028 SGD
+SGD S000005842 SFG1 GO:0003704 SGD_REF:S000113722|PMID:16289536 IMP F YOR315W gene taxon:4932 20051211 SGD
+SGD S000005842 SFG1 GO:0003704 SGD_REF:S000113722|PMID:16289536 ISS F YOR315W gene taxon:4932 20051211 SGD
+SGD S000005842 SFG1 GO:0007124 SGD_REF:S000113722|PMID:16289536 IMP P YOR315W gene taxon:4932 20051211 SGD
+SGD S000005842 SFG1 GO:0045944 SGD_REF:S000113722|PMID:16289536 IMP P YOR315W gene taxon:4932 20051211 SGD
+SGD S000005842 SFG1 GO:0045944 SGD_REF:S000113722|PMID:16289536 ISS P YOR315W gene taxon:4932 20051211 SGD
+SGD S000004313 SFH1 GO:0016586 SGD_REF:S000051142|PMID:9154831 IPI C Snf5p homolog, chromatin remodeling complex member, RSC YLR321C gene taxon:4932 20041020 SGD
+SGD S000004313 SFH1 GO:0005515 SGD_REF:S000073229|PMID:12697820 IDA F Snf5p homolog, chromatin remodeling complex member, RSC YLR321C gene taxon:4932 20030619 SGD
+SGD S000004313 SFH1 GO:0005515 SGD_REF:S000073229|PMID:12697820 TAS F Snf5p homolog, chromatin remodeling complex member, RSC YLR321C gene taxon:4932 20030619 SGD
+SGD S000004313 SFH1 GO:0006338 SGD_REF:S000052087|PMID:8980231 ISS P Snf5p homolog, chromatin remodeling complex member, RSC YLR321C gene taxon:4932 20010118 SGD
+SGD S000004313 SFH1 GO:0006338 SGD_REF:S000058466|PMID:10025404 IDA P Snf5p homolog, chromatin remodeling complex member, RSC YLR321C gene taxon:4932 20010118 SGD
+SGD S000003681 SFH5 GO:0005792 SGD_REF:S000073885|PMID:12869188 IDA C phosphatidylinositol transfer protein YJL145W gene taxon:4932 20031001 SGD
+SGD S000003681 SFH5 GO:0005829 SGD_REF:S000073885|PMID:12869188 IDA C phosphatidylinositol transfer protein YJL145W gene taxon:4932 20031001 SGD
+SGD S000003681 SFH5 GO:0008526 SGD_REF:S000043659|PMID:10848624 IDA F phosphatidylinositol transfer protein YJL145W gene taxon:4932 20021029 SGD
+SGD S000003681 SFH5 GO:0015914 SGD_REF:S000043659|PMID:10848624 IDA P phosphatidylinositol transfer protein YJL145W gene taxon:4932 20021029 SGD
+SGD S000003926 SFI1 GO:0005825 SGD_REF:S000074049|PMID:14504268 IDA C YLL003W gene taxon:4932 20040211 SGD
+SGD S000003926 SFI1 GO:0005554 SGD_REF:S000069584 ND F YLL003W gene taxon:4932 20021029 SGD
+SGD S000003926 SFI1 GO:0000086 SGD_REF:S000052451|PMID:10455233 IMP P YLL003W gene taxon:4932 20021029 SGD
+SGD S000003926 SFI1 GO:0007103 SGD_REF:S000074049|PMID:14504268 IMP P YLL003W gene taxon:4932 20040210 SGD
+SGD S000001534 SFK1 GO:0005886 SGD_REF:S000069992|PMID:12015967 IDA C YKL051W gene taxon:4932 20030505 SGD
+SGD S000001534 SFK1 GO:0005886 SGD_REF:S000069992|PMID:12015967 IMP C YKL051W gene taxon:4932 20030505 SGD
+SGD S000001534 SFK1 GO:0005554 SGD_REF:S000069584 ND F YKL051W gene taxon:4932 20030505 SGD
+SGD S000001534 SFK1 GO:0006646 SGD_REF:S000069992|PMID:12015967 IMP P YKL051W gene taxon:4932 20030505 SGD
+SGD S000001534 SFK1 GO:0007033 SGD_REF:S000069992|PMID:12015967 IMP P YKL051W gene taxon:4932 20030505 SGD
+SGD S000001534 SFK1 GO:0030036 SGD_REF:S000069992|PMID:12015967 IMP P YKL051W gene taxon:4932 20030505 SGD
+SGD S000005666 SFL1 GO:0000228 SGD_REF:S000060868|PMID:11399075 IPI C transcription factor YOR140W gene taxon:4932 20021001 SGD
+SGD S000005666 SFL1 GO:0016566 SGD_REF:S000060868|PMID:11399075 IDA F transcription factor YOR140W gene taxon:4932 20021001 SGD
+SGD S000005666 SFL1 GO:0000122 SGD_REF:S000060868|PMID:11399075 IMP P transcription factor YOR140W gene taxon:4932 20021001 SGD
+SGD S000005666 SFL1 GO:0000122 SGD_REF:S000060868|PMID:11399075 IPI P transcription factor YOR140W gene taxon:4932 20021001 SGD
+SGD S000004395 SFP1 GO:0005634 SGD_REF:S000043166|PMID:9832520 TAS C split zinc finger protein YLR403W gene taxon:4932 20021014 SGD
+SGD S000004395 SFP1 GO:0005634 SGD_REF:S000077407|PMID:15466158 IDA C split zinc finger protein YLR403W gene taxon:4932 20041028 SGD
+SGD S000004395 SFP1 GO:0005737 SGD_REF:S000077407|PMID:15466158 IDA C split zinc finger protein YLR403W gene taxon:4932 20041028 SGD
+SGD S000004395 SFP1 GO:0003700 SGD_REF:S000070190|PMID:12089449 TAS F split zinc finger protein YLR403W gene taxon:4932 20020730 SGD
+SGD S000004395 SFP1 GO:0003700 SGD_REF:S000077407|PMID:15466158 IGI F split zinc finger protein YLR403W gene taxon:4932 20041028 SGD
+SGD S000004395 SFP1 GO:0006383 SGD_REF:S000077407|PMID:15466158 IGI P split zinc finger protein YLR403W gene taxon:4932 20041029 SGD
+SGD S000004395 SFP1 GO:0006383 SGD_REF:S000077407|PMID:15466158 IPI P split zinc finger protein YLR403W gene taxon:4932 20041029 SGD
+SGD S000004395 SFP1 GO:0006383 SGD_REF:S000077407|PMID:15466158 TAS P split zinc finger protein YLR403W gene taxon:4932 20041029 SGD
+SGD S000004395 SFP1 GO:0007046 SGD_REF:S000076617|PMID:14555489 IMP P split zinc finger protein YLR403W gene taxon:4932 20050609 SGD
+SGD S000004395 SFP1 GO:0008361 SGD_REF:S000070190|PMID:12089449 IDA P split zinc finger protein YLR403W gene taxon:4932 20020730 SGD
+SGD S000004395 SFP1 GO:0008361 SGD_REF:S000077407|PMID:15466158 IGI P split zinc finger protein YLR403W gene taxon:4932 20041028 SGD
+SGD S000004395 SFP1 GO:0008361 SGD_REF:S000077407|PMID:15466158 IMP P split zinc finger protein YLR403W gene taxon:4932 20041028 SGD
+SGD S000002101 SFT1 GO:0000139 SGD_REF:S000053696|PMID:7596416 TAS C v-SNARE YKL006C-A gene taxon:4932 20010118 SGD
+SGD S000002101 SFT1 GO:0005485 SGD_REF:S000053696|PMID:7596416 IGI F v-SNARE YKL006C-A gene taxon:4932 20010118 SGD
+SGD S000002101 SFT1 GO:0005485 SGD_REF:S000053696|PMID:7596416 IMP F v-SNARE YKL006C-A gene taxon:4932 20010118 SGD
+SGD S000002101 SFT1 GO:0005485 SGD_REF:S000053696|PMID:7596416 ISS F v-SNARE YKL006C-A gene taxon:4932 20010118 SGD
+SGD S000002101 SFT1 GO:0006891 SGD_REF:S000053696|PMID:7596416 IMP P v-SNARE YKL006C-A gene taxon:4932 20010118 SGD
+SGD S000002101 SFT1 GO:0006891 SGD_REF:S000053696|PMID:7596416 IGI P v-SNARE YKL006C-A gene taxon:4932 20010118 SGD
+SGD S000002101 SFT1 GO:0006891 SGD_REF:S000053696|PMID:7596416 ISS P v-SNARE YKL006C-A gene taxon:4932 20010118 SGD
+SGD S000000198 SFT2 GO:0000139 SGD_REF:S000058468|PMID:9725919 IDA C YBL102W gene taxon:4932 20010118 SGD
+SGD S000000198 SFT2 GO:0005554 SGD_REF:S000069584 ND F YBL102W gene taxon:4932 20010119 SGD
+SGD S000000198 SFT2 GO:0006895 SGD_REF:S000040382|PMID:10406798 IMP P YBL102W gene taxon:4932 20010118 SGD
+SGD S000000198 SFT2 GO:0006895 SGD_REF:S000040382|PMID:10406798 IGI P YBL102W gene taxon:4932 20010118 SGD
+SGD S000001361 SGA1 GO:0000324 SGD_REF:S000056864|PMID:2493265 IDA C glucoamylase YIL099W gene taxon:4932 20010118 SGD
+SGD S000001361 SGA1 GO:0004339 SGD_REF:S000056864|PMID:2493265 IDA F glucoamylase YIL099W gene taxon:4932 20010118 SGD
+SGD S000001361 SGA1 GO:0005980 SGD_REF:S000065951|PMID:11486014 IMP P glucoamylase YIL099W gene taxon:4932 20050211 SGD
+SGD S000001361 SGA1 GO:0030437 SGD_REF:S000057097|PMID:350852 IEP P glucoamylase YIL099W gene taxon:4932 20010118 SGD
+SGD S000004328 SGD1 GO:0005634 SGD_REF:S000059303|PMID:11042259 IDA C YLR336C gene taxon:4932 20020820 SGD
+SGD S000004328 SGD1 GO:0005634 SGD_REF:S000059303|PMID:11042259 ISS C YLR336C gene taxon:4932 20020820 SGD
+SGD S000004328 SGD1 GO:0005730 SGD_REF:S000059303|PMID:11042259 IDA C YLR336C gene taxon:4932 20050324 SGD
+SGD S000004328 SGD1 GO:0005554 SGD_REF:S000069584 ND F YLR336C gene taxon:4932 20020820 SGD
+SGD S000004328 SGD1 GO:0018987 SGD_REF:S000059303|PMID:11042259 IGI P YLR336C gene taxon:4932 20020820 SGD
+SGD S000004328 SGD1 GO:0018987 SGD_REF:S000070006|PMID:12073033 IGI P YLR336C gene taxon:4932 20020820 SGD
+SGD S000004328 SGD1 GO:0018987 SGD_REF:S000070006|PMID:12073033 IMP P YLR336C gene taxon:4932 20020820 SGD
+SGD S000004328 SGD1 GO:0018987 SGD_REF:S000059303|PMID:11042259 IMP P YLR336C gene taxon:4932 20020820 SGD
+SGD S000006402 SGE1 GO:0005887 SGD_REF:S000040717|PMID:9483795 IDA C YPR198W|NOR1 gene taxon:4932 20020920 SGD
+SGD S000006402 SGE1 GO:0008559 SGD_REF:S000040717|PMID:9483795 IMP F YPR198W|NOR1 gene taxon:4932 20020920 SGD
+SGD S000006402 SGE1 GO:0015893 SGD_REF:S000040717|PMID:9483795 IMP P YPR198W|NOR1 gene taxon:4932 20020920 SGD
+SGD S000006402 SGE1 GO:0042493 SGD_REF:S000040717|PMID:9483795 IMP P YPR198W|NOR1 gene taxon:4932 20021111 SGD
+SGD S000005968 SGF11 GO:0000124 SGD_REF:S000077054|PMID:15282323 IDA C YPL047W gene taxon:4932 20040916 SGD
+SGD S000005968 SGF11 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YPL047W gene taxon:4932 20031028 SGD
+SGD S000005968 SGF11 GO:0005554 SGD_REF:S000069584 ND F YPL047W gene taxon:4932 20021126 SGD
+SGD S000005968 SGF11 GO:0006357 SGD_REF:S000077054|PMID:15282323 IMP P YPL047W gene taxon:4932 20050510 SGD
+SGD S000005968 SGF11 GO:0016578 SGD_REF:S000080990|PMID:15657442 IMP P YPL047W gene taxon:4932 20050510 SGD
+SGD S000005968 SGF11 GO:0016578 SGD_REF:S000080598|PMID:15657441 IMP P YPL047W gene taxon:4932 20050510 SGD
+SGD S000000516 SGF29 GO:0000124 SGD_REF:S000070225|PMID:12052880 IDA C Probable 29kKDa Subunit of SAGA histone acetyltransferase complex YCL010C gene taxon:4932 20020925 SGD
+SGD S000000516 SGF29 GO:0005554 SGD_REF:S000069584 ND F Probable 29kKDa Subunit of SAGA histone acetyltransferase complex YCL010C gene taxon:4932 20021216 SGD
+SGD S000000516 SGF29 GO:0016573 SGD_REF:S000070225|PMID:12052880 IPI P Probable 29kKDa Subunit of SAGA histone acetyltransferase complex YCL010C gene taxon:4932 20021216 SGD
+SGD S000003034 SGF73 GO:0000124 SGD_REF:S000070225|PMID:12052880 IDA C Probable 73KkDa Subunit of SAGA histone acetyltransferase complex YGL066W|sca7 gene taxon:4932 20020925 SGD
+SGD S000003034 SGF73 GO:0000124 SGD_REF:S000081847|PMID:15932941 IPI SGD:S000002552|SGD:S000002856 C Probable 73KkDa Subunit of SAGA histone acetyltransferase complex YGL066W|sca7 gene taxon:4932 20060414 SGD
+SGD S000003034 SGF73 GO:0046695 SGD_REF:S000081847|PMID:15932941 IPI SGD:S000002552|SGD:S000002856 C Probable 73KkDa Subunit of SAGA histone acetyltransferase complex YGL066W|sca7 gene taxon:4932 20060414 SGD
+SGD S000003034 SGF73 contributes_to GO:0004402 SGD_REF:S000081847|PMID:15932941 IMP F Probable 73KkDa Subunit of SAGA histone acetyltransferase complex YGL066W|sca7 gene taxon:4932 20060414 SGD
+SGD S000003034 SGF73 GO:0005198 SGD_REF:S000081847|PMID:15932941 IGI HUGO:ATXN7 F Probable 73KkDa Subunit of SAGA histone acetyltransferase complex YGL066W|sca7 gene taxon:4932 20060413 SGD
+SGD S000003034 SGF73 GO:0005198 SGD_REF:S000081847|PMID:15932941 IMP F Probable 73KkDa Subunit of SAGA histone acetyltransferase complex YGL066W|sca7 gene taxon:4932 20060413 SGD
+SGD S000003034 SGF73 GO:0016568 SGD_REF:S000081847|PMID:15932941 IMP P Probable 73KkDa Subunit of SAGA histone acetyltransferase complex YGL066W|sca7 gene taxon:4932 20060414 SGD
+SGD S000003034 SGF73 GO:0016573 SGD_REF:S000070225|PMID:12052880 IPI P Probable 73KkDa Subunit of SAGA histone acetyltransferase complex YGL066W|sca7 gene taxon:4932 20021216 SGD
+SGD S000003034 SGF73 GO:0016573 SGD_REF:S000081847|PMID:15932941 IMP P Probable 73KkDa Subunit of SAGA histone acetyltransferase complex YGL066W|sca7 gene taxon:4932 20060414 SGD
+SGD S000003895 SGM1 GO:0005794 SGD_REF:S000074185|PMID:14562095 IDA C YJR134C gene taxon:4932 20031028 SGD
+SGD S000003895 SGM1 colocalizes_with GO:0030137 SGD_REF:S000074185|PMID:14562095 IDA C YJR134C gene taxon:4932 20031028 SGD
+SGD S000003895 SGM1 GO:0005554 SGD_REF:S000069584 ND F YJR134C gene taxon:4932 20010119 SGD
+SGD S000003895 SGM1 GO:0000004 SGD_REF:S000069584 ND P YJR134C gene taxon:4932 20010119 SGD
+SGD S000001440 SGN1 GO:0005737 SGD_REF:S000056083|PMID:10764794 IDA C YIR001C|RBP1|RBP29 gene taxon:4932 20021010 SGD
+SGD S000001440 SGN1 GO:0008143 SGD_REF:S000056083|PMID:10764794 IDA F YIR001C|RBP1|RBP29 gene taxon:4932 20021010 SGD
+SGD S000001440 SGN1 GO:0016071 SGD_REF:S000056083|PMID:10764794 IGI P YIR001C|RBP1|RBP29 gene taxon:4932 20021010 SGD
+SGD S000005599 SGO1 GO:0000775 SGD_REF:S000074657|PMID:14730319 IDA C YOR073W|YOR29-24 gene taxon:4932 20040209 SGD
+SGD S000005599 SGO1 GO:0000776 SGD_REF:S000076556|PMID:15062096 IDA C YOR073W|YOR29-24 gene taxon:4932 20040804 SGD
+SGD S000005599 SGO1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YOR073W|YOR29-24 gene taxon:4932 20031028 SGD
+SGD S000005599 SGO1 colocalizes_with GO:0005816 SGD_REF:S000074185|PMID:14562095 IDA C YOR073W|YOR29-24 gene taxon:4932 20031028 SGD
+SGD S000005599 SGO1 GO:0005554 SGD_REF:S000069584 ND F YOR073W|YOR29-24 gene taxon:4932 20030203 SGD
+SGD S000005599 SGO1 GO:0000070 SGD_REF:S000074657|PMID:14730319 IMP P YOR073W|YOR29-24 gene taxon:4932 20040209 SGD
+SGD S000005599 SGO1 GO:0000070 SGD_REF:S000080316|PMID:15637284 IGI P YOR073W|YOR29-24 gene taxon:4932 20050225 SGD
+SGD S000005599 SGO1 GO:0000070 SGD_REF:S000080316|PMID:15637284 IMP P YOR073W|YOR29-24 gene taxon:4932 20050225 SGD
+SGD S000005599 SGO1 GO:0007094 SGD_REF:S000080316|PMID:15637284 IMP P YOR073W|YOR29-24 gene taxon:4932 20051114 SGD
+SGD S000005599 SGO1 GO:0007094 SGD_REF:S000080316|PMID:15637284 IGI SGD:S000000364|SGD:S000002161|SGD:S000002186 P YOR073W|YOR29-24 gene taxon:4932 20051114 SGD
+SGD S000005599 SGO1 GO:0045144 SGD_REF:S000074657|PMID:14730319 IMP P YOR073W|YOR29-24 gene taxon:4932 20040209 SGD
+SGD S000005599 SGO1 GO:0045144 SGD_REF:S000080316|PMID:15637284 IMP P YOR073W|YOR29-24 gene taxon:4932 20050225 SGD
+SGD S000005599 SGO1 GO:0045144 SGD_REF:S000080316|PMID:15637284 IGI P YOR073W|YOR29-24 gene taxon:4932 20050225 SGD
+SGD S000004802 SGS1 GO:0005730 SGD_REF:S000055270|PMID:10198430 IDA C YMR190C gene taxon:4932 20020806 SGD
+SGD S000004802 SGS1 GO:0031422 SGD_REF:S000081006|PMID:15889139 IPI SGD:S000004224|SGD:S000005945 C YMR190C gene taxon:4932 20050531 SGD
+SGD S000004802 SGS1 GO:0004003 SGD_REF:S000050822|PMID:9545297 IDA F YMR190C gene taxon:4932 20020806 SGD
+SGD S000004802 SGS1 GO:0000070 SGD_REF:S000045316|PMID:7736577 IMP P YMR190C gene taxon:4932 20020806 SGD
+SGD S000004802 SGS1 GO:0000722 SGD_REF:S000082449|PMID:15994923 IMP P YMR190C gene taxon:4932 20050802 SGD
+SGD S000004802 SGS1 GO:0001302 SGD_REF:S000059901|PMID:11248051 IMP P YMR190C gene taxon:4932 20050323 SGD
+SGD S000004802 SGS1 GO:0006268 SGD_REF:S000053590|PMID:10366502 IDA P YMR190C gene taxon:4932 20020806 SGD
+SGD S000004802 SGS1 GO:0006974 SGD_REF:S000076175|PMID:12482937 IMP P YMR190C gene taxon:4932 20060406 SGD
+SGD S000004802 SGS1 GO:0007001 SGD_REF:S000059189|PMID:11138010 IMP P YMR190C gene taxon:4932 20020806 SGD
+SGD S000004802 SGS1 GO:0045132 SGD_REF:S000045316|PMID:7736577 IMP P YMR190C gene taxon:4932 20020806 SGD
+SGD S000005583 SGT1 GO:0000151 SGD_REF:S000047894|PMID:10445024 IDA C YOR057W|YOR29-08 gene taxon:4932 20020630 SGD
+SGD S000005583 SGT1 GO:0051087 SGD_REF:S000071668|PMID:12456005 ISS F YOR057W|YOR29-08 gene taxon:4932 20040723 SGD
+SGD S000005583 SGT1 GO:0000074 SGD_REF:S000069587|PMID:11847307 TAS P YOR057W|YOR29-08 gene taxon:4932 20020630 SGD
+SGD S000005583 SGT1 GO:0006461 SGD_REF:S000071668|PMID:12456005 IGI P YOR057W|YOR29-08 gene taxon:4932 20030108 SGD
+SGD S000005583 SGT1 GO:0006461 SGD_REF:S000071668|PMID:12456005 ISS P YOR057W|YOR29-08 gene taxon:4932 20030108 SGD
+SGD S000005583 SGT1 GO:0006461 SGD_REF:S000076779|PMID:15090617 IDA P YOR057W|YOR29-08 gene taxon:4932 20040904 SGD
+SGD S000005583 SGT1 GO:0016567 SGD_REF:S000071668|PMID:12456005 TAS P YOR057W|YOR29-08 gene taxon:4932 20030108 SGD
+SGD S000005583 SGT1 GO:0019933 SGD_REF:S000071668|PMID:12456005 IGI P YOR057W|YOR29-08 gene taxon:4932 20030108 SGD
+SGD S000005583 SGT1 GO:0019933 SGD_REF:S000071668|PMID:12456005 IPI P YOR057W|YOR29-08 gene taxon:4932 20030108 SGD
+SGD S000005583 SGT1 GO:0051382 SGD_REF:S000047894|PMID:10445024 IDA P YOR057W|YOR29-08 gene taxon:4932 20050720 SGD
+SGD S000005533 SGT2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YOR007C gene taxon:4932 20031028 SGD
+SGD S000005533 SGT2 GO:0005554 SGD_REF:S000069584 ND F YOR007C gene taxon:4932 20010119 SGD
+SGD S000005533 SGT2 GO:0000004 SGD_REF:S000069584 ND P YOR007C gene taxon:4932 20010119 SGD
+SGD S000006365 SGV1 GO:0005634 SGD_REF:S000061433|PMID:11390638 IPI C CDC28/cdc2 related protein kinase YPR161C|BUR1 gene taxon:4932 20021118 SGD
+SGD S000006365 SGV1 GO:0004693 SGD_REF:S000053628|PMID:10982824 IDA F CDC28/cdc2 related protein kinase YPR161C|BUR1 gene taxon:4932 20020930 SGD
+SGD S000006365 SGV1 GO:0004693 SGD_REF:S000053628|PMID:10982824 IPI F CDC28/cdc2 related protein kinase YPR161C|BUR1 gene taxon:4932 20020930 SGD
+SGD S000006365 SGV1 GO:0006350 SGD_REF:S000053628|PMID:10982824 IDA P CDC28/cdc2 related protein kinase YPR161C|BUR1 gene taxon:4932 20020930 SGD
+SGD S000006365 SGV1 GO:0006350 SGD_REF:S000053628|PMID:10982824 IPI P CDC28/cdc2 related protein kinase YPR161C|BUR1 gene taxon:4932 20020930 SGD
+SGD S000006365 SGV1 GO:0006350 SGD_REF:S000053628|PMID:10982824 IMP P CDC28/cdc2 related protein kinase YPR161C|BUR1 gene taxon:4932 20020930 SGD
+SGD S000006365 SGV1 GO:0006468 SGD_REF:S000053628|PMID:10982824 IDA P CDC28/cdc2 related protein kinase YPR161C|BUR1 gene taxon:4932 20021118 SGD
+SGD S000006365 SGV1 GO:0006468 SGD_REF:S000053628|PMID:10982824 IPI P CDC28/cdc2 related protein kinase YPR161C|BUR1 gene taxon:4932 20021118 SGD
+SGD S000000898 SHC1 GO:0005628 SGD_REF:S000081076|PMID:15755916 IDA C YER096W gene taxon:4932 20050324 SGD
+SGD S000000898 SHC1 GO:0008047 SGD_REF:S000069520|PMID:11918806 IGI F YER096W gene taxon:4932 20021104 SGD
+SGD S000000898 SHC1 GO:0006031 SGD_REF:S000069520|PMID:11918806 IGI P YER096W gene taxon:4932 20021104 SGD
+SGD S000000898 SHC1 GO:0030437 SGD_REF:S000069520|PMID:11918806 IDA P YER096W gene taxon:4932 20020807 SGD
+SGD S000000127 SHE1 GO:0015630 SGD_REF:S000074185|PMID:14562095 IDA C YBL031W gene taxon:4932 20031028 SGD
+SGD S000000127 SHE1 GO:0005554 SGD_REF:S000069584 ND F YBL031W gene taxon:4932 20021008 SGD
+SGD S000000127 SHE1 GO:0000004 SGD_REF:S000069584 ND P YBL031W gene taxon:4932 20021008 SGD
+SGD S000003197 SHE10 GO:0008372 SGD_REF:S000069584 ND C YGL228W gene taxon:4932 20021029 SGD
+SGD S000003197 SHE10 GO:0005554 SGD_REF:S000069584 ND F YGL228W gene taxon:4932 20021029 SGD
+SGD S000003197 SHE10 GO:0000004 SGD_REF:S000069584 ND P YGL228W gene taxon:4932 20021029 SGD
+SGD S000001613 SHE2 GO:0005737 SGD_REF:S000042421|PMID:8625407 IDA C YKL130C gene taxon:4932 20021001 SGD
+SGD S000001613 SHE2 GO:0003729 SGD_REF:S000059427|PMID:11101531 IDA F YKL130C gene taxon:4932 20020804 SGD
+SGD S000001613 SHE2 GO:0008298 SGD_REF:S000059649|PMID:11032818 IDA P YKL130C gene taxon:4932 20020804 SGD
+SGD S000000334 SHE3 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YBR130C gene taxon:4932 20020507 SGD
+SGD S000000334 SHE3 GO:0030478 SGD_REF:S000041005|PMID:10652251 IDA C YBR130C gene taxon:4932 20010118 SGD
+SGD S000000334 SHE3 GO:0003729 SGD_REF:S000039183|PMID:10212145 IDA F YBR130C gene taxon:4932 20010118 SGD
+SGD S000000334 SHE3 GO:0008298 SGD_REF:S000039183|PMID:10212145 IMP P YBR130C gene taxon:4932 20010118 SGD
+SGD S000000334 SHE3 GO:0048309 SGD_REF:S000075200|PMID:14691136 IMP P YBR130C gene taxon:4932 20040318 SGD
+SGD S000005561 SHE4 GO:0005737 SGD_REF:S000042421|PMID:8625407 IDA C YOR035C|DIM1 gene taxon:4932 20021001 SGD
+SGD S000005561 SHE4 GO:0017022 SGD_REF:S000074363|PMID:12725728 IDA F YOR035C|DIM1 gene taxon:4932 20040519 SGD
+SGD S000005561 SHE4 GO:0008298 SGD_REF:S000068954|PMID:11553699 IMP P YOR035C|DIM1 gene taxon:4932 20021001 SGD
+SGD S000005561 SHE4 GO:0030036 SGD_REF:S000041284|PMID:10792032 TAS P YOR035C|DIM1 gene taxon:4932 20030616 SGD
+SGD S000002801 SHE9 GO:0005743 SGD_REF:S000072597|PMID:12591915 IDA C YDR393W|MDM33 gene taxon:4932 20030224 SGD
+SGD S000002801 SHE9 GO:0005554 SGD_REF:S000069584 ND F YDR393W|MDM33 gene taxon:4932 20021009 SGD
+SGD S000002801 SHE9 GO:0007005 SGD_REF:S000071517|PMID:11907266 IMP P YDR393W|MDM33 gene taxon:4932 20021114 SGD
+SGD S000002801 SHE9 GO:0007007 SGD_REF:S000072597|PMID:12591915 IGI P YDR393W|MDM33 gene taxon:4932 20030224 SGD
+SGD S000002801 SHE9 GO:0007007 SGD_REF:S000072597|PMID:12591915 IMP P YDR393W|MDM33 gene taxon:4932 20030224 SGD
+SGD S000000462 SHG1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C compass (complex proteins associated with Set1p) component YBR258C|CPS15 gene taxon:4932 20031028 SGD
+SGD S000000462 SHG1 GO:0048188 SGD_REF:S000068755|PMID:11742990 IPI SGD:S000000064|SGD:S000000379|SGD:S000002877|SGD:S000006059|SGD:S000004005|SGD:S000001501|SGD:S000001161 C compass (complex proteins associated with Set1p) component YBR258C|CPS15 gene taxon:4932 20050524 SGD
+SGD S000000462 SHG1 GO:0048188 SGD_REF:S000069538|PMID:11805083 IPI SGD:S000000064|SGD:S000000379|SGD:S000006059|SGD:S000004005|SGD:S000001501|SGD:S000001161|SGD:S000002877 C compass (complex proteins associated with Set1p) component YBR258C|CPS15 gene taxon:4932 20050524 SGD
+SGD S000000462 SHG1 contributes_to GO:0042800 SGD_REF:S000069538|PMID:11805083 IDA F compass (complex proteins associated with Set1p) component YBR258C|CPS15 gene taxon:4932 20050525 SGD
+SGD S000000462 SHG1 contributes_to GO:0042800 SGD_REF:S000068755|PMID:11742990 IDA F compass (complex proteins associated with Set1p) component YBR258C|CPS15 gene taxon:4932 20050525 SGD
+SGD S000000462 SHG1 GO:0016571 SGD_REF:S000068755|PMID:11742990 IDA P compass (complex proteins associated with Set1p) component YBR258C|CPS15 gene taxon:4932 20020212 SGD
+SGD S000000462 SHG1 GO:0016571 SGD_REF:S000069538|PMID:11805083 IDA P compass (complex proteins associated with Set1p) component YBR258C|CPS15 gene taxon:4932 20050525 SGD
+SGD S000000467 SHM1 GO:0005739 SGD_REF:S000043392|PMID:8852837 TAS C YBR263W|SHMT1|TMP3 gene taxon:4932 20020930 SGD
+SGD S000000467 SHM1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YBR263W|SHMT1|TMP3 gene taxon:4932 20040928 SGD
+SGD S000000467 SHM1 GO:0004372 SGD_REF:S000043392|PMID:8852837 TAS F YBR263W|SHMT1|TMP3 gene taxon:4932 20020930 SGD
+SGD S000000467 SHM1 GO:0006730 SGD_REF:S000043392|PMID:8852837 TAS P YBR263W|SHMT1|TMP3 gene taxon:4932 20020930 SGD
+SGD S000004048 SHM2 GO:0005737 SGD_REF:S000043392|PMID:8852837 TAS C YLR058C|SHMT2 gene taxon:4932 20020930 SGD
+SGD S000004048 SHM2 GO:0004372 SGD_REF:S000043392|PMID:8852837 TAS F YLR058C|SHMT2 gene taxon:4932 20020930 SGD
+SGD S000004048 SHM2 GO:0006730 SGD_REF:S000043392|PMID:8852837 TAS P YLR058C|SHMT2 gene taxon:4932 20020930 SGD
+SGD S000000920 SHO1 GO:0005886 SGD_REF:S000051778|PMID:7624781 ISS C transmembrane osmosensor YER118C|SSU81 gene taxon:4932 20010118 SGD
+SGD S000000920 SHO1 GO:0043332 SGD_REF:S000071843|PMID:12374868 IDA C transmembrane osmosensor YER118C|SSU81 gene taxon:4932 20030129 SGD
+SGD S000000920 SHO1 GO:0005034 SGD_REF:S000049858|PMID:9180081 TAS F transmembrane osmosensor YER118C|SSU81 gene taxon:4932 20010118 SGD
+SGD S000000920 SHO1 GO:0007124 SGD_REF:S000046092|PMID:9744864 IMP P transmembrane osmosensor YER118C|SSU81 gene taxon:4932 20010118 SGD
+SGD S000000920 SHO1 GO:0007232 SGD_REF:S000051778|PMID:7624781 TAS P transmembrane osmosensor YER118C|SSU81 gene taxon:4932 20010118 SGD
+SGD S000000154 SHP1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YBL058W|UBX1 gene taxon:4932 20031028 SGD
+SGD S000000154 SHP1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YBL058W|UBX1 gene taxon:4932 20031028 SGD
+SGD S000000154 SHP1 GO:0008599 SGD_REF:S000045597|PMID:7891699 IMP F YBL058W|UBX1 gene taxon:4932 20051101 SGD
+SGD S000000154 SHP1 GO:0005977 SGD_REF:S000045597|PMID:7891699 IMP P YBL058W|UBX1 gene taxon:4932 20010118 SGD
+SGD S000000154 SHP1 GO:0030437 SGD_REF:S000045597|PMID:7891699 IMP P YBL058W|UBX1 gene taxon:4932 20010118 SGD
+SGD S000000154 SHP1 GO:0043161 SGD_REF:S000076733|PMID:15258615 IMP P YBL058W|UBX1 gene taxon:4932 20040806 SGD
+SGD S000001366 SHQ1 GO:0005654 SGD_REF:S000071691|PMID:12228251 IDA C YIL104C gene taxon:4932 20021202 SGD
+SGD S000001366 SHQ1 GO:0005554 SGD_REF:S000069584 ND F YIL104C gene taxon:4932 20021202 SGD
+SGD S000001366 SHQ1 GO:0016074 SGD_REF:S000071691|PMID:12228251 IMP P YIL104C gene taxon:4932 20021202 SGD
+SGD S000001366 SHQ1 GO:0016074 SGD_REF:S000071691|PMID:12228251 IPI SGD:S000004852 P YIL104C gene taxon:4932 20021202 SGD
+SGD S000002371 SHR3 GO:0030176 SGD_REF:S000040945|PMID:1423607 IDA C YDL212W|APF1 gene taxon:4932 20020726 SGD
+SGD S000002371 SHR3 GO:0030176 SGD_REF:S000080152|PMID:15623581 IDA C YDL212W|APF1 gene taxon:4932 20050708 SGD
+SGD S000002371 SHR3 GO:0030176 SGD_REF:S000040945|PMID:1423607 ISS C YDL212W|APF1 gene taxon:4932 20020726 SGD
+SGD S000002371 SHR3 GO:0051082 SGD_REF:S000042178|PMID:10564255 IMP F YDL212W|APF1 gene taxon:4932 20020726 SGD
+SGD S000002371 SHR3 GO:0051082 SGD_REF:S000042178|PMID:10564255 IPI F YDL212W|APF1 gene taxon:4932 20020726 SGD
+SGD S000002371 SHR3 GO:0006457 SGD_REF:S000080152|PMID:15623581 IMP P YDL212W|APF1 gene taxon:4932 20050708 SGD
+SGD S000002371 SHR3 GO:0006865 SGD_REF:S000040945|PMID:1423607 IMP P YDL212W|APF1 gene taxon:4932 20020726 SGD
+SGD S000002371 SHR3 GO:0006888 SGD_REF:S000042178|PMID:10564255 IGI P YDL212W|APF1 gene taxon:4932 20020726 SGD
+SGD S000002371 SHR3 GO:0006888 SGD_REF:S000042178|PMID:10564255 IPI P YDL212W|APF1 gene taxon:4932 20020726 SGD
+SGD S000005470 SHR5 GO:0031211 SGD_REF:S000071573|PMID:12193598 IPI C YOL110W|ERF4 gene taxon:4932 20050217 SGD
+SGD S000005470 SHR5 GO:0042406 SGD_REF:S000072560|PMID:12379641 IDA C YOL110W|ERF4 gene taxon:4932 20030310 SGD
+SGD S000005470 SHR5 GO:0019706 SGD_REF:S000074072|PMID:12944483 IMP F YOL110W|ERF4 gene taxon:4932 20050304 SGD
+SGD S000005470 SHR5 GO:0007265 SGD_REF:S000043291|PMID:7532279 IMP P YOL110W|ERF4 gene taxon:4932 20010118 SGD
+SGD S000005470 SHR5 GO:0008104 SGD_REF:S000043291|PMID:7532279 IMP P YOL110W|ERF4 gene taxon:4932 20010118 SGD
+SGD S000005470 SHR5 GO:0018318 SGD_REF:S000071573|PMID:12193598 IDA P YOL110W|ERF4 gene taxon:4932 20030123 SGD
+SGD S000002384 SHS1 GO:0005940 SGD_REF:S000056396|PMID:10481176 IDA C septin YDL225W|SEP7 gene taxon:4932 20010118 SGD
+SGD S000002384 SHS1 GO:0005200 SGD_REF:S000056396|PMID:10481176 IPI F septin YDL225W|SEP7 gene taxon:4932 20010118 SGD
+SGD S000002384 SHS1 GO:0005200 SGD_REF:S000056396|PMID:10481176 ISS F septin YDL225W|SEP7 gene taxon:4932 20010118 SGD
+SGD S000002384 SHS1 GO:0000902 SGD_REF:S000056396|PMID:10481176 IMP P septin YDL225W|SEP7 gene taxon:4932 20021107 SGD
+SGD S000002384 SHS1 GO:0000902 SGD_REF:S000056396|PMID:10481176 ISS P septin YDL225W|SEP7 gene taxon:4932 20021107 SGD
+SGD S000002384 SHS1 GO:0000902 SGD_REF:S000056396|PMID:10481176 IPI P septin YDL225W|SEP7 gene taxon:4932 20021107 SGD
+SGD S000002384 SHS1 GO:0000910 SGD_REF:S000056396|PMID:10481176 IMP P septin YDL225W|SEP7 gene taxon:4932 20010119 SGD
+SGD S000002384 SHS1 GO:0000910 SGD_REF:S000056396|PMID:10481176 ISS P septin YDL225W|SEP7 gene taxon:4932 20010119 SGD
+SGD S000002384 SHS1 GO:0000910 SGD_REF:S000056396|PMID:10481176 IPI P septin YDL225W|SEP7 gene taxon:4932 20010119 SGD
+SGD S000002384 SHS1 GO:0030468 SGD_REF:S000056396|PMID:10481176 IMP P septin YDL225W|SEP7 gene taxon:4932 20010302 SGD
+SGD S000002384 SHS1 GO:0030468 SGD_REF:S000056396|PMID:10481176 ISS P septin YDL225W|SEP7 gene taxon:4932 20010302 SGD
+SGD S000002384 SHS1 GO:0030468 SGD_REF:S000056396|PMID:10481176 IPI P septin YDL225W|SEP7 gene taxon:4932 20010302 SGD
+SGD S000000998 SHU1 GO:0005634 SGD_REF:S000080406|PMID:15654096 IDA C YHL006C gene taxon:4932 20050324 SGD
+SGD S000000998 SHU1 GO:0005554 SGD_REF:S000069584 ND F YHL006C gene taxon:4932 20021122 SGD
+SGD S000000998 SHU1 GO:0045021 SGD_REF:S000080406|PMID:15654096 IMP P YHL006C gene taxon:4932 20050324 SGD
+SGD S000002485 SHU2 GO:0008372 SGD_REF:S000069584 ND C YDR078C gene taxon:4932 20021122 SGD
+SGD S000002485 SHU2 GO:0005554 SGD_REF:S000069584 ND F YDR078C gene taxon:4932 20021122 SGD
+SGD S000002485 SHU2 GO:0045021 SGD_REF:S000080406|PMID:15654096 IMP P YDR078C gene taxon:4932 20050324 SGD
+SGD S000003344 SHY1 GO:0005743 SGD_REF:S000046510|PMID:9162072 IDA C similar to the mammalian SURF-1 gene YGR112W gene taxon:4932 20010118 SGD
+SGD S000003344 SHY1 GO:0005743 SGD_REF:S000077016|PMID:15306853 IDA C similar to the mammalian SURF-1 gene YGR112W gene taxon:4932 20050301 SGD
+SGD S000003344 SHY1 GO:0016021 SGD_REF:S000077016|PMID:15306853 IDA C similar to the mammalian SURF-1 gene YGR112W gene taxon:4932 20050301 SGD
+SGD S000003344 SHY1 GO:0051082 SGD_REF:S000060745|PMID:11389896 IMP F similar to the mammalian SURF-1 gene YGR112W gene taxon:4932 20030930 SGD
+SGD S000003344 SHY1 GO:0009060 SGD_REF:S000046510|PMID:9162072 IMP P similar to the mammalian SURF-1 gene YGR112W gene taxon:4932 20030930 SGD
+SGD S000005663 SIA1 GO:0008372 SGD_REF:S000069584 ND C YOR137C gene taxon:4932 20021029 SGD
+SGD S000005663 SIA1 GO:0005554 SGD_REF:S000069584 ND F YOR137C gene taxon:4932 20021029 SGD
+SGD S000005663 SIA1 GO:0015992 SGD_REF:S000041836|PMID:9450541 IMP P YOR137C gene taxon:4932 20021029 SGD
+SGD S000004069 SIC1 GO:0005634 SGD_REF:S000069008|PMID:11792824 IDA C YLR079W|SDB25 gene taxon:4932 20020528 SGD
+SGD S000004069 SIC1 GO:0005634 SGD_REF:S000059560|PMID:11080155 IDA C YLR079W|SDB25 gene taxon:4932 20030619 SGD
+SGD S000004069 SIC1 GO:0005737 SGD_REF:S000069008|PMID:11792824 IDA C YLR079W|SDB25 gene taxon:4932 20020528 SGD
+SGD S000004069 SIC1 GO:0005515 SGD_REF:S000057743|PMID:8421781 IPI F YLR079W|SDB25 gene taxon:4932 20020528 SGD
+SGD S000004069 SIC1 GO:0019210 SGD_REF:S000043548|PMID:7954792 IDA F YLR079W|SDB25 gene taxon:4932 20020321 SGD
+SGD S000004069 SIC1 GO:0000079 SGD_REF:S000043548|PMID:7954792 IMP P YLR079W|SDB25 gene taxon:4932 20020321 SGD
+SGD S000004069 SIC1 GO:0000079 SGD_REF:S000043548|PMID:7954792 IPI P YLR079W|SDB25 gene taxon:4932 20020321 SGD
+SGD S000004069 SIC1 GO:0000079 SGD_REF:S000043548|PMID:7954792 IDA P YLR079W|SDB25 gene taxon:4932 20020321 SGD
+SGD S000004069 SIC1 GO:0000079 SGD_REF:S000043548|PMID:7954792 IEP P YLR079W|SDB25 gene taxon:4932 20020321 SGD
+SGD S000004069 SIC1 GO:0000082 SGD_REF:S000043548|PMID:7954792 TAS P YLR079W|SDB25 gene taxon:4932 20020528 SGD
+SGD S000000307 SIF2 GO:0000118 SGD_REF:S000066205|PMID:11711434 IPI C YBR103W|EMB1 gene taxon:4932 20021010 SGD
+SGD S000000307 SIF2 GO:0005634 SGD_REF:S000055195|PMID:9651685 IPI C YBR103W|EMB1 gene taxon:4932 20021001 SGD
+SGD S000000307 SIF2 contributes_to GO:0003714 SGD_REF:S000066205|PMID:11711434 IDA F YBR103W|EMB1 gene taxon:4932 20050808 SGD
+SGD S000000307 SIF2 contributes_to GO:0017136 SGD_REF:S000066205|PMID:11711434 IPI SGD:S000001737 F YBR103W|EMB1 gene taxon:4932 20050808 SGD
+SGD S000000307 SIF2 contributes_to GO:0045129 SGD_REF:S000066205|PMID:11711434 IPI SGD:S000001737 F YBR103W|EMB1 gene taxon:4932 20050808 SGD
+SGD S000000307 SIF2 GO:0000122 SGD_REF:S000066205|PMID:11711434 IPI P YBR103W|EMB1 gene taxon:4932 20021001 SGD
+SGD S000000307 SIF2 GO:0006348 SGD_REF:S000055195|PMID:9651685 IGI P YBR103W|EMB1 gene taxon:4932 20021001 SGD
+SGD S000000307 SIF2 GO:0006348 SGD_REF:S000055195|PMID:9651685 IPI P YBR103W|EMB1 gene taxon:4932 20021001 SGD
+SGD S000000307 SIF2 GO:0016575 SGD_REF:S000066205|PMID:11711434 IDA P YBR103W|EMB1 gene taxon:4932 20021010 SGD
+SGD S000000307 SIF2 GO:0016575 SGD_REF:S000066205|PMID:11711434 IPI P YBR103W|EMB1 gene taxon:4932 20021010 SGD
+SGD S000000307 SIF2 GO:0045835 SGD_REF:S000066205|PMID:11711434 IPI P YBR103W|EMB1 gene taxon:4932 20021001 SGD
+SGD S000004187 SIK1 GO:0005634 SGD_REF:S000069459|PMID:11914276 IDA C U3 snoRNP protein YLR197W|NOP56 gene taxon:4932 20020507 SGD
+SGD S000004187 SIK1 GO:0005730 SGD_REF:S000069459|PMID:11914276 IDA C U3 snoRNP protein YLR197W|NOP56 gene taxon:4932 20020507 SGD
+SGD S000004187 SIK1 GO:0005732 SGD_REF:S000070145|PMID:12068309 IPI C U3 snoRNP protein YLR197W|NOP56 gene taxon:4932 20030224 SGD
+SGD S000004187 SIK1 GO:0030532 SGD_REF:S000058443|PMID:10690410 TAS C U3 snoRNP protein YLR197W|NOP56 gene taxon:4932 20020219 SGD
+SGD S000004187 SIK1 GO:0031428 SGD_REF:S000043312|PMID:10733567 IDA C U3 snoRNP protein YLR197W|NOP56 gene taxon:4932 20050614 SGD
+SGD S000004187 SIK1 GO:0031428 SGD_REF:S000043312|PMID:10733567 IMP C U3 snoRNP protein YLR197W|NOP56 gene taxon:4932 20050614 SGD
+SGD S000004187 SIK1 GO:0005554 SGD_REF:S000069584 ND F U3 snoRNP protein YLR197W|NOP56 gene taxon:4932 20030224 SGD
+SGD S000004187 SIK1 GO:0000154 SGD_REF:S000058443|PMID:10690410 TAS P U3 snoRNP protein YLR197W|NOP56 gene taxon:4932 20010118 SGD
+SGD S000004187 SIK1 GO:0006365 SGD_REF:S000058443|PMID:10690410 TAS P U3 snoRNP protein YLR197W|NOP56 gene taxon:4932 20010118 SGD
+SGD S000004187 SIK1 GO:0030490 SGD_REF:S000070145|PMID:12068309 IPI P U3 snoRNP protein YLR197W|NOP56 gene taxon:4932 20020905 SGD
+SGD S000005391 SIL1 GO:0005783 SGD_REF:S000052716|PMID:10958688 IPI C Nucleotide exchange factor YOL031C|SLS1 gene taxon:4932 20010626 SGD
+SGD S000005391 SIL1 GO:0005554 SGD_REF:S000069584 ND F Nucleotide exchange factor YOL031C|SLS1 gene taxon:4932 20020425 SGD
+SGD S000005391 SIL1 GO:0006616 SGD_REF:S000052716|PMID:10958688 IMP P Nucleotide exchange factor YOL031C|SLS1 gene taxon:4932 20010626 SGD
+SGD S000005391 SIL1 GO:0006616 SGD_REF:S000052716|PMID:10958688 IGI P Nucleotide exchange factor YOL031C|SLS1 gene taxon:4932 20010626 SGD
+SGD S000001385 SIM1 GO:0009277 SGD_REF:S000069559|PMID:11958935 IDA C YIL123W gene taxon:4932 20020721 SGD
+SGD S000001385 SIM1 GO:0005554 SGD_REF:S000069584 ND F YIL123W gene taxon:4932 20030108 SGD
+SGD S000001385 SIM1 GO:0000226 SGD_REF:S000047973|PMID:10612745 IGI P YIL123W gene taxon:4932 20030108 SGD
+SGD S000005364 SIN3 GO:0000118 SGD_REF:S000047950|PMID:10388812 IPI C DNA binding protein, involved in transcriptional regulation YOL004W|CPE1|GAM2|RPD1|SDI1|SDS16|UME4 gene taxon:4932 20021008 SGD
+SGD S000005364 SIN3 GO:0016580 SGD_REF:S000054148|PMID:9393435 IPI C DNA binding protein, involved in transcriptional regulation YOL004W|CPE1|GAM2|RPD1|SDI1|SDS16|UME4 gene taxon:4932 20040614 SGD
+SGD S000005364 SIN3 GO:0004407 SGD_REF:S000047950|PMID:10388812 IPI F DNA binding protein, involved in transcriptional regulation YOL004W|CPE1|GAM2|RPD1|SDI1|SDS16|UME4 gene taxon:4932 20021008 SGD
+SGD S000005364 SIN3 GO:0000183 SGD_REF:S000047950|PMID:10388812 IMP P DNA binding protein, involved in transcriptional regulation YOL004W|CPE1|GAM2|RPD1|SDI1|SDS16|UME4 gene taxon:4932 20021008 SGD
+SGD S000005364 SIN3 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P DNA binding protein, involved in transcriptional regulation YOL004W|CPE1|GAM2|RPD1|SDI1|SDS16|UME4 gene taxon:4932 20060203 SGD
+SGD S000005364 SIN3 GO:0006303 SGD_REF:S000074417|PMID:14711989 IMP P DNA binding protein, involved in transcriptional regulation YOL004W|CPE1|GAM2|RPD1|SDI1|SDS16|UME4 gene taxon:4932 20050224 SGD
+SGD S000005364 SIN3 GO:0006348 SGD_REF:S000047950|PMID:10388812 IMP P DNA binding protein, involved in transcriptional regulation YOL004W|CPE1|GAM2|RPD1|SDI1|SDS16|UME4 gene taxon:4932 20021008 SGD
+SGD S000005364 SIN3 GO:0006357 SGD_REF:S000051705|PMID:10713159 IGI P DNA binding protein, involved in transcriptional regulation YOL004W|CPE1|GAM2|RPD1|SDI1|SDS16|UME4 gene taxon:4932 20021008 SGD
+SGD S000005364 SIN3 GO:0006357 SGD_REF:S000051705|PMID:10713159 IMP P DNA binding protein, involved in transcriptional regulation YOL004W|CPE1|GAM2|RPD1|SDI1|SDS16|UME4 gene taxon:4932 20021008 SGD
+SGD S000005364 SIN3 GO:0030466 SGD_REF:S000047950|PMID:10388812 IMP P DNA binding protein, involved in transcriptional regulation YOL004W|CPE1|GAM2|RPD1|SDI1|SDS16|UME4 gene taxon:4932 20021008 SGD
+SGD S000005180 SIN4 GO:0000119 SGD_REF:S000048078|PMID:9420330 IDA C RNA polymerase II holoenzyme/mediator subunit YNL236W|BEL2|GAL22|MED16|RYE1|SDI3|SSF5|SSN4|TSF3 gene taxon:4932 20010118 SGD
+SGD S000005180 SIN4 GO:0016455 SGD_REF:S000048078|PMID:9420330 IDA F RNA polymerase II holoenzyme/mediator subunit YNL236W|BEL2|GAL22|MED16|RYE1|SDI3|SSF5|SSN4|TSF3 gene taxon:4932 20021203 SGD
+SGD S000005180 SIN4 GO:0006366 SGD_REF:S000048078|PMID:9420330 IDA P RNA polymerase II holoenzyme/mediator subunit YNL236W|BEL2|GAL22|MED16|RYE1|SDI3|SSF5|SSN4|TSF3 gene taxon:4932 20010118 SGD
+SGD S000002830 SIP1 GO:0005773 SGD_REF:S000060188|PMID:11331606 IDA C protein kinase complex component YDR422C gene taxon:4932 20021009 SGD
+SGD S000002830 SIP1 GO:0004679 SGD_REF:S000059161|PMID:10990457 IMP F protein kinase complex component YDR422C gene taxon:4932 20050416 SGD
+SGD S000002830 SIP1 GO:0006468 SGD_REF:S000059161|PMID:10990457 IMP P protein kinase complex component YDR422C gene taxon:4932 20020819 SGD
+SGD S000002830 SIP1 GO:0007165 SGD_REF:S000059161|PMID:10990457 IMP P protein kinase complex component YDR422C gene taxon:4932 20020819 SGD
+SGD S000004787 SIP18 GO:0005625 SGD_REF:S000068747|PMID:11746603 IDA C YMR175W gene taxon:4932 20030130 SGD
+SGD S000004787 SIP18 GO:0005543 SGD_REF:S000070070|PMID:12082171 IDA F YMR175W gene taxon:4932 20021009 SGD
+SGD S000004787 SIP18 GO:0006970 SGD_REF:S000040158|PMID:8801420 IEP P YMR175W gene taxon:4932 20021009 SGD
+SGD S000004787 SIP18 GO:0009269 SGD_REF:S000063137|PMID:10681550 IEP P YMR175W gene taxon:4932 20030210 SGD
+SGD S000003176 SIP2 GO:0005737 SGD_REF:S000060188|PMID:11331606 IDA C YGL208W|SPM2 gene taxon:4932 20021009 SGD
+SGD S000003176 SIP2 GO:0005886 SGD_REF:S000072977|PMID:12562756 IDA C YGL208W|SPM2 gene taxon:4932 20030425 SGD
+SGD S000003176 SIP2 contributes_to GO:0004679 SGD_REF:S000059161|PMID:10990457 IMP F YGL208W|SPM2 gene taxon:4932 20050416 SGD
+SGD S000003176 SIP2 GO:0001302 SGD_REF:S000049850|PMID:10921902 IMP P YGL208W|SPM2 gene taxon:4932 20050323 SGD
+SGD S000003176 SIP2 GO:0006468 SGD_REF:S000059161|PMID:10990457 IMP P YGL208W|SPM2 gene taxon:4932 20020819 SGD
+SGD S000003176 SIP2 GO:0007165 SGD_REF:S000059161|PMID:10990457 IMP P YGL208W|SPM2 gene taxon:4932 20020819 SGD
+SGD S000003176 SIP2 GO:0007569 SGD_REF:S000072977|PMID:12562756 IMP P YGL208W|SPM2 gene taxon:4932 20030814 SGD
+SGD S000003176 SIP2 GO:0030447 SGD_REF:S000072732|PMID:12556493 IMP P YGL208W|SPM2 gene taxon:4932 20030313 SGD
+SGD S000003176 SIP2 GO:0042149 SGD_REF:S000049850|PMID:10921902 IMP P YGL208W|SPM2 gene taxon:4932 20050416 SGD
+SGD S000005201 SIP3 GO:0005634 SGD_REF:S000054748|PMID:8127709 IPI SGD:S000002885 C transcriptional activator (putative) YNL257C gene taxon:4932 20050609 SGD
+SGD S000005201 SIP3 GO:0003712 SGD_REF:S000054748|PMID:8127709 IDA F transcriptional activator (putative) YNL257C gene taxon:4932 20020614 SGD
+SGD S000005201 SIP3 GO:0006367 SGD_REF:S000054748|PMID:8127709 IGI P transcriptional activator (putative) YNL257C gene taxon:4932 20020614 SGD
+SGD S000003625 SIP4 GO:0005634 SGD_REF:S000048186|PMID:9843506 IDA C YJL089W gene taxon:4932 20021001 SGD
+SGD S000003625 SIP4 GO:0003704 SGD_REF:S000048186|PMID:9843506 IDA F YJL089W gene taxon:4932 20021001 SGD
+SGD S000003625 SIP4 GO:0003704 SGD_REF:S000048186|PMID:9843506 IMP F YJL089W gene taxon:4932 20021001 SGD
+SGD S000003625 SIP4 GO:0006357 SGD_REF:S000048186|PMID:9843506 IMP P YJL089W gene taxon:4932 20021001 SGD
+SGD S000003625 SIP4 GO:0006357 SGD_REF:S000048186|PMID:9843506 IPI P YJL089W gene taxon:4932 20021001 SGD
+SGD S000003625 SIP4 GO:0045722 SGD_REF:S000048186|PMID:9843506 IMP P YJL089W gene taxon:4932 20021001 SGD
+SGD S000003625 SIP4 GO:0045722 SGD_REF:S000048186|PMID:9843506 IPI P YJL089W gene taxon:4932 20021001 SGD
+SGD S000004748 SIP5 GO:0005737 SGD_REF:S000045104|PMID:10628972 IPI C YMR140W gene taxon:4932 20021029 SGD
+SGD S000004748 SIP5 GO:0005554 SGD_REF:S000069584 ND F YMR140W gene taxon:4932 20021029 SGD
+SGD S000004748 SIP5 GO:0042149 SGD_REF:S000045104|PMID:10628972 IMP P YMR140W gene taxon:4932 20021029 SGD
+SGD S000004748 SIP5 GO:0042149 SGD_REF:S000045104|PMID:10628972 IPI P YMR140W gene taxon:4932 20021029 SGD
+SGD S000001809 SIR1 GO:0005677 SGD_REF:S000039704|PMID:8622770 IDA C silent mating loci repressor YKR101W gene taxon:4932 20021121 SGD
+SGD S000001809 SIR1 GO:0003677 SGD_REF:S000060818|PMID:11408576 TAS F silent mating loci repressor YKR101W gene taxon:4932 20021105 SGD
+SGD S000001809 SIR1 GO:0003682 SGD_REF:S000070406|PMID:12198162 IPI F silent mating loci repressor YKR101W gene taxon:4932 20021105 SGD
+SGD S000001809 SIR1 GO:0006343 SGD_REF:S000045892|PMID:2684414 IMP P silent mating loci repressor YKR101W gene taxon:4932 20021121 SGD
+SGD S000001809 SIR1 GO:0030466 SGD_REF:S000045268|PMID:397913 IGI P silent mating loci repressor YKR101W gene taxon:4932 20021121 SGD
+SGD S000002200 SIR2 GO:0000783 SGD_REF:S000045567|PMID:9710643 IDA C nuclear NAD-dependent deacetylase YDL042C|MAR1 gene taxon:4932 20030403 SGD
+SGD S000002200 SIR2 GO:0005677 SGD_REF:S000051211|PMID:9122169 IDA C nuclear NAD-dependent deacetylase YDL042C|MAR1 gene taxon:4932 20040407 SGD
+SGD S000002200 SIR2 GO:0005724 SGD_REF:S000052512|PMID:9000052 IDA C nuclear NAD-dependent deacetylase YDL042C|MAR1 gene taxon:4932 20021202 SGD
+SGD S000002200 SIR2 GO:0005730 SGD_REF:S000042199|PMID:9214640 IDA C nuclear NAD-dependent deacetylase YDL042C|MAR1 gene taxon:4932 20021202 SGD
+SGD S000002200 SIR2 GO:0030869 SGD_REF:S000056360|PMID:10219244 IDA C nuclear NAD-dependent deacetylase YDL042C|MAR1 gene taxon:4932 20040906 SGD
+SGD S000002200 SIR2 GO:0032041 SGD_REF:S000063496|PMID:10693811 IDA F nuclear NAD-dependent deacetylase YDL042C|MAR1 gene taxon:4932 20060421 SGD
+SGD S000002200 SIR2 GO:0032041 SGD_REF:S000063496|PMID:10693811 ISS protein_id:AF214646 F nuclear NAD-dependent deacetylase YDL042C|MAR1 gene taxon:4932 20060421 SGD
+SGD S000002200 SIR2 GO:0046969 SGD_REF:S000063496|PMID:10693811 IDA F nuclear NAD-dependent deacetylase YDL042C|MAR1 gene taxon:4932 20060314 SGD
+SGD S000002200 SIR2 GO:0046969 SGD_REF:S000063496|PMID:10693811 ISS protein_id:AF214646 F nuclear NAD-dependent deacetylase YDL042C|MAR1 gene taxon:4932 20060314 SGD
+SGD S000002200 SIR2 GO:0046970 SGD_REF:S000063496|PMID:10693811 IDA F nuclear NAD-dependent deacetylase YDL042C|MAR1 gene taxon:4932 20060314 SGD
+SGD S000002200 SIR2 GO:0046970 SGD_REF:S000063496|PMID:10693811 ISS protein_id:AF214646 F nuclear NAD-dependent deacetylase YDL042C|MAR1 gene taxon:4932 20060314 SGD
+SGD S000002200 SIR2 GO:0000183 SGD_REF:S000054554|PMID:2647300 IMP P nuclear NAD-dependent deacetylase YDL042C|MAR1 gene taxon:4932 20030814 SGD
+SGD S000002200 SIR2 GO:0001300 SGD_REF:S000113737|PMID:16286010 IMP P nuclear NAD-dependent deacetylase YDL042C|MAR1 gene taxon:4932 20051219 SGD
+SGD S000002200 SIR2 GO:0001302 SGD_REF:S000080970|PMID:15722108 IMP P nuclear NAD-dependent deacetylase YDL042C|MAR1 gene taxon:4932 20050314 SGD
+SGD S000002200 SIR2 GO:0001308 SGD_REF:S000065135|PMID:10809662 TAS P nuclear NAD-dependent deacetylase YDL042C|MAR1 gene taxon:4932 20030814 SGD
+SGD S000002200 SIR2 GO:0006303 SGD_REF:S000051563|PMID:10908335 IDA P nuclear NAD-dependent deacetylase YDL042C|MAR1 gene taxon:4932 20021101 SGD
+SGD S000002200 SIR2 GO:0006333 SGD_REF:S000068980|PMID:11553718 IDA P nuclear NAD-dependent deacetylase YDL042C|MAR1 gene taxon:4932 20021101 SGD
+SGD S000002200 SIR2 GO:0006348 SGD_REF:S000052512|PMID:9000052 IPI P nuclear NAD-dependent deacetylase YDL042C|MAR1 gene taxon:4932 20021202 SGD
+SGD S000002200 SIR2 GO:0006348 SGD_REF:S000069732|PMID:11950950 IMP P nuclear NAD-dependent deacetylase YDL042C|MAR1 gene taxon:4932 20021202 SGD
+SGD S000002200 SIR2 GO:0008156 SGD_REF:S000076193|PMID:15082529 IMP P nuclear NAD-dependent deacetylase YDL042C|MAR1 gene taxon:4932 20040725 SGD
+SGD S000002200 SIR2 GO:0030466 SGD_REF:S000069732|PMID:11950950 IMP P nuclear NAD-dependent deacetylase YDL042C|MAR1 gene taxon:4932 20021202 SGD
+SGD S000004434 SIR3 GO:0000783 SGD_REF:S000045567|PMID:9710643 IDA C silencing regulator at HML, HMR, and telomeres YLR442C|CMT1|MAR2|STE8 gene taxon:4932 20030403 SGD
+SGD S000004434 SIR3 GO:0005677 SGD_REF:S000051211|PMID:9122169 IDA C silencing regulator at HML, HMR, and telomeres YLR442C|CMT1|MAR2|STE8 gene taxon:4932 20040407 SGD
+SGD S000004434 SIR3 GO:0005724 SGD_REF:S000042199|PMID:9214640 IDA C silencing regulator at HML, HMR, and telomeres YLR442C|CMT1|MAR2|STE8 gene taxon:4932 20021202 SGD
+SGD S000004434 SIR3 GO:0005730 SGD_REF:S000040351|PMID:9150138 IDA C silencing regulator at HML, HMR, and telomeres YLR442C|CMT1|MAR2|STE8 gene taxon:4932 20021202 SGD
+SGD S000004434 SIR3 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C silencing regulator at HML, HMR, and telomeres YLR442C|CMT1|MAR2|STE8 gene taxon:4932 20040928 SGD
+SGD S000004434 SIR3 GO:0030527 SGD_REF:S000068792|PMID:11689698 TAS F silencing regulator at HML, HMR, and telomeres YLR442C|CMT1|MAR2|STE8 gene taxon:4932 20021001 SGD
+SGD S000004434 SIR3 GO:0042393 SGD_REF:S000070058|PMID:12080091 TAS F silencing regulator at HML, HMR, and telomeres YLR442C|CMT1|MAR2|STE8 gene taxon:4932 20021101 SGD
+SGD S000004434 SIR3 GO:0001308 SGD_REF:S000040351|PMID:9150138 IDA P silencing regulator at HML, HMR, and telomeres YLR442C|CMT1|MAR2|STE8 gene taxon:4932 20030814 SGD
+SGD S000004434 SIR3 GO:0006303 SGD_REF:S000051563|PMID:10908335 IDA P silencing regulator at HML, HMR, and telomeres YLR442C|CMT1|MAR2|STE8 gene taxon:4932 20021101 SGD
+SGD S000004434 SIR3 GO:0006342 SGD_REF:S000050683|PMID:10744999 TAS P silencing regulator at HML, HMR, and telomeres YLR442C|CMT1|MAR2|STE8 gene taxon:4932 20021202 SGD
+SGD S000002635 SIR4 GO:0000783 SGD_REF:S000045567|PMID:9710643 IDA C silencing regulator at HML, HMR, and telomeres YDR227W|ASD1|STE9|UTH2 gene taxon:4932 20030403 SGD
+SGD S000002635 SIR4 GO:0005677 SGD_REF:S000051211|PMID:9122169 IDA C silencing regulator at HML, HMR, and telomeres YDR227W|ASD1|STE9|UTH2 gene taxon:4932 20040407 SGD
+SGD S000002635 SIR4 GO:0005724 SGD_REF:S000052512|PMID:9000052 IDA C silencing regulator at HML, HMR, and telomeres YDR227W|ASD1|STE9|UTH2 gene taxon:4932 20021202 SGD
+SGD S000002635 SIR4 GO:0030527 SGD_REF:S000068792|PMID:11689698 TAS F silencing regulator at HML, HMR, and telomeres YDR227W|ASD1|STE9|UTH2 gene taxon:4932 20021001 SGD
+SGD S000002635 SIR4 GO:0042393 SGD_REF:S000070058|PMID:12080091 TAS F silencing regulator at HML, HMR, and telomeres YDR227W|ASD1|STE9|UTH2 gene taxon:4932 20021101 SGD
+SGD S000002635 SIR4 GO:0001308 SGD_REF:S000040351|PMID:9150138 IDA P silencing regulator at HML, HMR, and telomeres YDR227W|ASD1|STE9|UTH2 gene taxon:4932 20030814 SGD
+SGD S000002635 SIR4 GO:0006303 SGD_REF:S000051563|PMID:10908335 IDA P silencing regulator at HML, HMR, and telomeres YDR227W|ASD1|STE9|UTH2 gene taxon:4932 20021101 SGD
+SGD S000002635 SIR4 GO:0006342 SGD_REF:S000050683|PMID:10744999 TAS P silencing regulator at HML, HMR, and telomeres YDR227W|ASD1|STE9|UTH2 gene taxon:4932 20021202 SGD
+SGD S000004952 SIS1 GO:0005843 SGD_REF:S000048154|PMID:8513501 IDA C YNL007C gene taxon:4932 20021001 SGD
+SGD S000004952 SIS1 GO:0030188 SGD_REF:S000065137|PMID:9774392 IDA F YNL007C gene taxon:4932 20050418 SGD
+SGD S000004952 SIS1 GO:0051082 SGD_REF:S000070059|PMID:11923285 TAS F YNL007C gene taxon:4932 20020713 SGD
+SGD S000004952 SIS1 GO:0006413 SGD_REF:S000048154|PMID:8513501 IMP P YNL007C gene taxon:4932 20021001 SGD
+SGD S000004952 SIS1 GO:0006457 SGD_REF:S000065137|PMID:9774392 IDA P YNL007C gene taxon:4932 20050418 SGD
+SGD S000004952 SIS1 GO:0006457 SGD_REF:S000077437|PMID:14657253 IMP P YNL007C gene taxon:4932 20050418 SGD
+SGD S000001780 SIS2 GO:0005634 SGD_REF:S000051661|PMID:7705654 IDA C YKR072C|HAL3 gene taxon:4932 20030212 SGD
+SGD S000001780 SIS2 GO:0005634 SGD_REF:S000054046|PMID:9636153 IPI C YKR072C|HAL3 gene taxon:4932 20021113 SGD
+SGD S000001780 SIS2 GO:0005737 SGD_REF:S000054046|PMID:9636153 IC GO:0004864 C YKR072C|HAL3 gene taxon:4932 20021113 SGD
+SGD S000001780 SIS2 GO:0005737 SGD_REF:S000054046|PMID:9636153 IPI C YKR072C|HAL3 gene taxon:4932 20021113 SGD
+SGD S000001780 SIS2 GO:0004633 SGD_REF:S000072463|PMID:10592175 ISS F YKR072C|HAL3 gene taxon:4932 20030619 SGD
+SGD S000001780 SIS2 GO:0004864 SGD_REF:S000054046|PMID:9636153 IDA F YKR072C|HAL3 gene taxon:4932 20021001 SGD
+SGD S000001780 SIS2 GO:0000082 SGD_REF:S000072514|PMID:12518319 IGI P YKR072C|HAL3 gene taxon:4932 20030217 SGD
+SGD S000001780 SIS2 GO:0007346 SGD_REF:S000054079|PMID:10022927 IGI P YKR072C|HAL3 gene taxon:4932 20021001 SGD
+SGD S000001780 SIS2 GO:0009651 SGD_REF:S000054046|PMID:9636153 IGI P YKR072C|HAL3 gene taxon:4932 20021001 SGD
+SGD S000001780 SIS2 GO:0009651 SGD_REF:S000054046|PMID:9636153 IMP P YKR072C|HAL3 gene taxon:4932 20021001 SGD
+SGD S000001780 SIS2 GO:0015937 SGD_REF:S000072463|PMID:10592175 ISS P YKR072C|HAL3 gene taxon:4932 20030619 SGD
+SGD S000000791 SIT1 GO:0005768 SGD_REF:S000070405|PMID:12196168 TAS C ferrioxamine B permease YEL065W|ARN3 gene taxon:4932 20020912 SGD
+SGD S000000791 SIT1 GO:0016023 SGD_REF:S000052120|PMID:10748025 IDA C ferrioxamine B permease YEL065W|ARN3 gene taxon:4932 20020314 SGD
+SGD S000000791 SIT1 GO:0015344 SGD_REF:S000044146|PMID:9884238 IMP F ferrioxamine B permease YEL065W|ARN3 gene taxon:4932 20020314 SGD
+SGD S000000791 SIT1 GO:0015344 SGD_REF:S000044146|PMID:9884238 ISS F ferrioxamine B permease YEL065W|ARN3 gene taxon:4932 20020314 SGD
+SGD S000000791 SIT1 GO:0006879 SGD_REF:S000044146|PMID:9884238 IMP P ferrioxamine B permease YEL065W|ARN3 gene taxon:4932 20020314 SGD
+SGD S000000791 SIT1 GO:0006879 SGD_REF:S000044146|PMID:9884238 IDA P ferrioxamine B permease YEL065W|ARN3 gene taxon:4932 20020314 SGD
+SGD S000000791 SIT1 GO:0015892 SGD_REF:S000044146|PMID:9884238 IMP P ferrioxamine B permease YEL065W|ARN3 gene taxon:4932 20020314 SGD
+SGD S000029447 SIT3 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20020522 SGD
+SGD S000029447 SIT3 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20020522 SGD
+SGD S000029447 SIT3 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20020522 SGD
+SGD S000002205 SIT4 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C similar to catalytic subunit of bovine type 2A protein phosphatase YDL047W|LGN4 gene taxon:4932 20031028 SGD
+SGD S000002205 SIT4 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C similar to catalytic subunit of bovine type 2A protein phosphatase YDL047W|LGN4 gene taxon:4932 20031028 SGD
+SGD S000002205 SIT4 GO:0004722 SGD_REF:S000040143|PMID:9123967 TAS F similar to catalytic subunit of bovine type 2A protein phosphatase YDL047W|LGN4 gene taxon:4932 20010118 SGD
+SGD S000002205 SIT4 GO:0000082 SGD_REF:S000043456|PMID:1848673 IGI P similar to catalytic subunit of bovine type 2A protein phosphatase YDL047W|LGN4 gene taxon:4932 20010118 SGD
+SGD S000002205 SIT4 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P similar to catalytic subunit of bovine type 2A protein phosphatase YDL047W|LGN4 gene taxon:4932 20060227 SGD
+SGD S000002205 SIT4 GO:0001302 SGD_REF:S000081390|PMID:15843932 IMP P similar to catalytic subunit of bovine type 2A protein phosphatase YDL047W|LGN4 gene taxon:4932 20050630 SGD
+SGD S000002205 SIT4 GO:0006281 SGD_REF:S000080935|PMID:15150670 IMP P similar to catalytic subunit of bovine type 2A protein phosphatase YDL047W|LGN4 gene taxon:4932 20050309 SGD
+SGD S000002205 SIT4 GO:0006468 SGD_REF:S000071141|PMID:12080055 TAS P similar to catalytic subunit of bovine type 2A protein phosphatase YDL047W|LGN4 gene taxon:4932 20021211 SGD
+SGD S000002205 SIT4 GO:0007047 SGD_REF:S000071141|PMID:12080055 IMP P similar to catalytic subunit of bovine type 2A protein phosphatase YDL047W|LGN4 gene taxon:4932 20021211 SGD
+SGD S000002205 SIT4 GO:0007243 SGD_REF:S000071141|PMID:12080055 IMP P similar to catalytic subunit of bovine type 2A protein phosphatase YDL047W|LGN4 gene taxon:4932 20021211 SGD
+SGD S000002205 SIT4 GO:0030036 SGD_REF:S000071141|PMID:12080055 IMP P similar to catalytic subunit of bovine type 2A protein phosphatase YDL047W|LGN4 gene taxon:4932 20021211 SGD
+SGD S000004977 SIW14 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C tyrosine phosphatase YNL032W|OCA3 gene taxon:4932 20031028 SGD
+SGD S000004977 SIW14 GO:0004725 SGD_REF:S000069895|PMID:11967829 ISS F tyrosine phosphatase YNL032W|OCA3 gene taxon:4932 20021118 SGD
+SGD S000004977 SIW14 GO:0006470 SGD_REF:S000069895|PMID:11967829 ISS P tyrosine phosphatase YNL032W|OCA3 gene taxon:4932 20021118 SGD
+SGD S000004977 SIW14 GO:0006897 SGD_REF:S000075617|PMID:15020461 IMP P tyrosine phosphatase YNL032W|OCA3 gene taxon:4932 20040712 SGD
+SGD S000004977 SIW14 GO:0006950 SGD_REF:S000044615|PMID:10514564 IGI P tyrosine phosphatase YNL032W|OCA3 gene taxon:4932 20021118 SGD
+SGD S000004977 SIW14 GO:0007015 SGD_REF:S000075617|PMID:15020461 IMP P tyrosine phosphatase YNL032W|OCA3 gene taxon:4932 20040712 SGD
+SGD S000002817 SIZ1 GO:0005940 SGD_REF:S000068942|PMID:11587849 IDA C chromatin protein; SUMO1/Smt3 ligase YDR409W|ULL1 gene taxon:4932 20020404 SGD
+SGD S000002817 SIZ1 GO:0019789 SGD_REF:S000068870|PMID:11577116 IMP F chromatin protein; SUMO1/Smt3 ligase YDR409W|ULL1 gene taxon:4932 20020404 SGD
+SGD S000002817 SIZ1 GO:0019789 SGD_REF:S000068942|PMID:11587849 IMP F chromatin protein; SUMO1/Smt3 ligase YDR409W|ULL1 gene taxon:4932 20020404 SGD
+SGD S000002817 SIZ1 GO:0019789 SGD_REF:S000068942|PMID:11587849 IPI F chromatin protein; SUMO1/Smt3 ligase YDR409W|ULL1 gene taxon:4932 20020404 SGD
+SGD S000002817 SIZ1 GO:0019789 SGD_REF:S000068870|PMID:11577116 IDA F chromatin protein; SUMO1/Smt3 ligase YDR409W|ULL1 gene taxon:4932 20020404 SGD
+SGD S000002817 SIZ1 GO:0016925 SGD_REF:S000068942|PMID:11587849 IMP P chromatin protein; SUMO1/Smt3 ligase YDR409W|ULL1 gene taxon:4932 20020404 SGD
+SGD S000002817 SIZ1 GO:0016925 SGD_REF:S000068942|PMID:11587849 ISS P chromatin protein; SUMO1/Smt3 ligase YDR409W|ULL1 gene taxon:4932 20020404 SGD
+SGD S000001808 SKG1 GO:0000131 SGD_REF:S000080360|PMID:15645486 IDA C YKR100C|YKR099C-A gene taxon:4932 20050321 SGD
+SGD S000001808 SKG1 GO:0005933 SGD_REF:S000074185|PMID:14562095 IDA C YKR100C|YKR099C-A gene taxon:4932 20031028 SGD
+SGD S000001808 SKG1 GO:0005934 SGD_REF:S000080360|PMID:15645486 IDA C YKR100C|YKR099C-A gene taxon:4932 20050321 SGD
+SGD S000001808 SKG1 GO:0005554 SGD_REF:S000069584 ND F YKR100C|YKR099C-A gene taxon:4932 20030203 SGD
+SGD S000001808 SKG1 GO:0007047 SGD_REF:S000080360|PMID:15645486 IMP P YKR100C|YKR099C-A gene taxon:4932 20050321 SGD
+SGD S000004177 SKG3 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YLR187W gene taxon:4932 20031028 SGD
+SGD S000004177 SKG3 GO:0005933 SGD_REF:S000074185|PMID:14562095 IDA C YLR187W gene taxon:4932 20031028 SGD
+SGD S000004177 SKG3 GO:0005935 SGD_REF:S000074185|PMID:14562095 IDA C YLR187W gene taxon:4932 20031028 SGD
+SGD S000004177 SKG3 GO:0005554 SGD_REF:S000069584 ND F YLR187W gene taxon:4932 20021126 SGD
+SGD S000004177 SKG3 GO:0000004 SGD_REF:S000069584 ND P YLR187W gene taxon:4932 20021126 SGD
+SGD S000001192 SKG6 GO:0005934 SGD_REF:S000061434|PMID:11489916 IDA C YHR149C gene taxon:4932 20030512 SGD
+SGD S000001192 SKG6 GO:0005935 SGD_REF:S000061434|PMID:11489916 IDA C YHR149C gene taxon:4932 20030512 SGD
+SGD S000001192 SKG6 GO:0005554 SGD_REF:S000069584 ND F YHR149C gene taxon:4932 20021126 SGD
+SGD S000001192 SKG6 GO:0000004 SGD_REF:S000069584 ND P YHR149C gene taxon:4932 20021126 SGD
+SGD S000004390 SKI2 GO:0005730 SGD_REF:S000057960|PMID:8852903 TAS C antiviral protein, helicase (putative) YLR398C gene taxon:4932 20050419 SGD
+SGD S000004390 SKI2 GO:0005737 SGD_REF:S000045264|PMID:10744028 IDA C antiviral protein, helicase (putative) YLR398C gene taxon:4932 20021018 SGD
+SGD S000004390 SKI2 GO:0003724 SGD_REF:S000052935|PMID:8321235 ISS F antiviral protein, helicase (putative) YLR398C gene taxon:4932 20011205 SGD
+SGD S000004390 SKI2 GO:0030371 SGD_REF:S000050422|PMID:7739558 TAS F antiviral protein, helicase (putative) YLR398C gene taxon:4932 20021030 SGD
+SGD S000004390 SKI2 GO:0006402 SGD_REF:S000058465|PMID:9482746 IMP P antiviral protein, helicase (putative) YLR398C gene taxon:4932 20021018 SGD
+SGD S000004390 SKI2 GO:0006402 SGD_REF:S000058753|PMID:9841679 TAS P antiviral protein, helicase (putative) YLR398C gene taxon:4932 20010124 SGD
+SGD S000004390 SKI2 GO:0006445 SGD_REF:S000046376|PMID:10922069 IMP P antiviral protein, helicase (putative) YLR398C gene taxon:4932 20011205 SGD
+SGD S000004390 SKI2 GO:0006445 SGD_REF:S000061230|PMID:11438647 IGI P antiviral protein, helicase (putative) YLR398C gene taxon:4932 20011205 SGD
+SGD S000004390 SKI2 GO:0006445 SGD_REF:S000046376|PMID:10922069 IGI P antiviral protein, helicase (putative) YLR398C gene taxon:4932 20011205 SGD
+SGD S000004390 SKI2 GO:0006445 SGD_REF:S000061230|PMID:11438647 IMP P antiviral protein, helicase (putative) YLR398C gene taxon:4932 20011205 SGD
+SGD S000004390 SKI2 GO:0043330 SGD_REF:S000044399|PMID:363683 IMP P antiviral protein, helicase (putative) YLR398C gene taxon:4932 20050505 SGD
+SGD S000006393 SKI3 GO:0005634 SGD_REF:S000057960|PMID:8852903 TAS C antiviral protein that blocks translation of un-polyadenylated mRNAs YPR189W|SKI5 gene taxon:4932 20050419 SGD
+SGD S000006393 SKI3 GO:0005737 SGD_REF:S000045264|PMID:10744028 IDA C antiviral protein that blocks translation of un-polyadenylated mRNAs YPR189W|SKI5 gene taxon:4932 20021018 SGD
+SGD S000006393 SKI3 GO:0030371 SGD_REF:S000050422|PMID:7739558 TAS F antiviral protein that blocks translation of un-polyadenylated mRNAs YPR189W|SKI5 gene taxon:4932 20021030 SGD
+SGD S000006393 SKI3 GO:0006402 SGD_REF:S000058465|PMID:9482746 IMP P antiviral protein that blocks translation of un-polyadenylated mRNAs YPR189W|SKI5 gene taxon:4932 20021018 SGD
+SGD S000006393 SKI3 GO:0006402 SGD_REF:S000058753|PMID:9841679 TAS P antiviral protein that blocks translation of un-polyadenylated mRNAs YPR189W|SKI5 gene taxon:4932 20010124 SGD
+SGD S000006393 SKI3 GO:0043330 SGD_REF:S000044399|PMID:363683 IMP P antiviral protein that blocks translation of un-polyadenylated mRNAs YPR189W|SKI5 gene taxon:4932 20050505 SGD
+SGD S000003427 SKI6 GO:0000176 SGD_REF:S000041327|PMID:10465791 IDA C RNAse PH homolog YGR195W|ECM20|RRP41 gene taxon:4932 20010118 SGD
+SGD S000003427 SKI6 GO:0000177 SGD_REF:S000041327|PMID:10465791 IDA C RNAse PH homolog YGR195W|ECM20|RRP41 gene taxon:4932 20010118 SGD
+SGD S000003427 SKI6 GO:0000175 SGD_REF:S000058443|PMID:10690410 TAS F RNAse PH homolog YGR195W|ECM20|RRP41 gene taxon:4932 20010118 SGD
+SGD S000003427 SKI6 GO:0006365 SGD_REF:S000058443|PMID:10690410 TAS P RNAse PH homolog YGR195W|ECM20|RRP41 gene taxon:4932 20010118 SGD
+SGD S000003427 SKI6 GO:0006402 SGD_REF:S000058465|PMID:9482746 IMP P RNAse PH homolog YGR195W|ECM20|RRP41 gene taxon:4932 20010118 SGD
+SGD S000003427 SKI6 GO:0006402 SGD_REF:S000058753|PMID:9841679 TAS P RNAse PH homolog YGR195W|ECM20|RRP41 gene taxon:4932 20010124 SGD
+SGD S000003427 SKI6 GO:0043330 SGD_REF:S000054260|PMID:6371496 IMP P RNAse PH homolog YGR195W|ECM20|RRP41 gene taxon:4932 20050505 SGD
+SGD S000005602 SKI7 GO:0000178 SGD_REF:S000069566|PMID:11910110 IDA C GTPase (putative) YOR076C|YOR29-27 gene taxon:4932 20020905 SGD
+SGD S000005602 SKI7 GO:0005737 SGD_REF:S000073211|PMID:12730603 IDA C GTPase (putative) YOR076C|YOR29-27 gene taxon:4932 20030718 SGD
+SGD S000005602 SKI7 GO:0005515 SGD_REF:S000066048|PMID:11532933 IDA F GTPase (putative) YOR076C|YOR29-27 gene taxon:4932 20041105 SGD
+SGD S000005602 SKI7 GO:0006402 SGD_REF:S000069566|PMID:11910110 IDA P GTPase (putative) YOR076C|YOR29-27 gene taxon:4932 20020905 SGD
+SGD S000005602 SKI7 GO:0043330 SGD_REF:S000054260|PMID:6371496 IMP P GTPase (putative) YOR076C|YOR29-27 gene taxon:4932 20050505 SGD
+SGD S000003181 SKI8 GO:0000228 SGD_REF:S000075846|PMID:14992724 IDA C antiviral protein, mRNA is induced early in meiosis YGL213C|REC103 gene taxon:4932 20040405 SGD
+SGD S000003181 SKI8 GO:0005737 SGD_REF:S000045264|PMID:10744028 IPI C antiviral protein, mRNA is induced early in meiosis YGL213C|REC103 gene taxon:4932 20021018 SGD
+SGD S000003181 SKI8 GO:0030371 SGD_REF:S000050422|PMID:7739558 TAS F antiviral protein, mRNA is induced early in meiosis YGL213C|REC103 gene taxon:4932 20021030 SGD
+SGD S000003181 SKI8 GO:0006402 SGD_REF:S000058465|PMID:9482746 IMP P antiviral protein, mRNA is induced early in meiosis YGL213C|REC103 gene taxon:4932 20021018 SGD
+SGD S000003181 SKI8 GO:0006402 SGD_REF:S000058753|PMID:9841679 TAS P antiviral protein, mRNA is induced early in meiosis YGL213C|REC103 gene taxon:4932 20010124 SGD
+SGD S000003181 SKI8 GO:0006461 SGD_REF:S000075846|PMID:14992724 IMP P antiviral protein, mRNA is induced early in meiosis YGL213C|REC103 gene taxon:4932 20040406 SGD
+SGD S000003181 SKI8 GO:0042138 SGD_REF:S000075846|PMID:14992724 IPI P antiviral protein, mRNA is induced early in meiosis YGL213C|REC103 gene taxon:4932 20040405 SGD
+SGD S000003181 SKI8 GO:0043330 SGD_REF:S000054260|PMID:6371496 IMP P antiviral protein, mRNA is induced early in meiosis YGL213C|REC103 gene taxon:4932 20050505 SGD
+SGD S000005473 SKM1 GO:0008372 SGD_REF:S000069584 ND C YOL113W gene taxon:4932 20030227 SGD
+SGD S000005473 SKM1 GO:0004674 SGD_REF:S000056216|PMID:9044278 ISS F YOL113W gene taxon:4932 20010118 SGD
+SGD S000005473 SKM1 GO:0000074 SGD_REF:S000053834|PMID:9422741 IGI P YOL113W gene taxon:4932 20010118 SGD
+SGD S000005473 SKM1 GO:0000920 SGD_REF:S000056216|PMID:9044278 IMP P YOL113W gene taxon:4932 20050422 SGD
+SGD S000005473 SKM1 GO:0006468 SGD_REF:S000056216|PMID:9044278 ISS P YOL113W gene taxon:4932 20010118 SGD
+SGD S000003375 SKN1 GO:0016021 SGD_REF:S000040783|PMID:7929594 IDA C highly homologous to Kre6p, type II membrane protein (putative) YGR143W gene taxon:4932 20020718 SGD
+SGD S000003375 SKN1 GO:0015926 SGD_REF:S000039409|PMID:10601196 IMP F highly homologous to Kre6p, type II membrane protein (putative) YGR143W gene taxon:4932 20021111 SGD
+SGD S000003375 SKN1 GO:0015926 SGD_REF:S000039409|PMID:10601196 ISS F highly homologous to Kre6p, type II membrane protein (putative) YGR143W gene taxon:4932 20021111 SGD
+SGD S000003375 SKN1 GO:0006078 SGD_REF:S000040783|PMID:7929594 ISS P highly homologous to Kre6p, type II membrane protein (putative) YGR143W gene taxon:4932 20020718 SGD
+SGD S000003375 SKN1 GO:0006078 SGD_REF:S000040783|PMID:7929594 IMP P highly homologous to Kre6p, type II membrane protein (putative) YGR143W gene taxon:4932 20020718 SGD
+SGD S000003375 SKN1 GO:0007047 SGD_REF:S000040783|PMID:7929594 IMP P highly homologous to Kre6p, type II membrane protein (putative) YGR143W gene taxon:4932 20020718 SGD
+SGD S000003375 SKN1 GO:0030148 SGD_REF:S000081208|PMID:15792805 IGI SGD:S000002479 P highly homologous to Kre6p, type II membrane protein (putative) YGR143W gene taxon:4932 20050422 SGD
+SGD S000003375 SKN1 GO:0030148 SGD_REF:S000081208|PMID:15792805 IMP P highly homologous to Kre6p, type II membrane protein (putative) YGR143W gene taxon:4932 20050422 SGD
+SGD S000001249 SKN7 GO:0005634 SGD_REF:S000039280|PMID:10888672 IDA C YHR206W|BRY1|POS9 gene taxon:4932 20030212 SGD
+SGD S000001249 SKN7 GO:0005634 SGD_REF:S000045055|PMID:9118942 IPI C YHR206W|BRY1|POS9 gene taxon:4932 20020726 SGD
+SGD S000001249 SKN7 GO:0000156 SGD_REF:S000059148|PMID:11073911 IDA F YHR206W|BRY1|POS9 gene taxon:4932 20020726 SGD
+SGD S000001249 SKN7 GO:0000156 SGD_REF:S000059148|PMID:11073911 IMP F YHR206W|BRY1|POS9 gene taxon:4932 20020726 SGD
+SGD S000001249 SKN7 GO:0003700 SGD_REF:S000045055|PMID:9118942 IDA F YHR206W|BRY1|POS9 gene taxon:4932 20020726 SGD
+SGD S000001249 SKN7 GO:0003700 SGD_REF:S000045055|PMID:9118942 IPI F YHR206W|BRY1|POS9 gene taxon:4932 20020726 SGD
+SGD S000001249 SKN7 GO:0003700 SGD_REF:S000045055|PMID:9118942 IMP F YHR206W|BRY1|POS9 gene taxon:4932 20020726 SGD
+SGD S000001249 SKN7 GO:0003700 SGD_REF:S000069996|PMID:11854400 IDA F YHR206W|BRY1|POS9 gene taxon:4932 20050117 SGD
+SGD S000001249 SKN7 GO:0006350 SGD_REF:S000045055|PMID:9118942 IDA P YHR206W|BRY1|POS9 gene taxon:4932 20020726 SGD
+SGD S000001249 SKN7 GO:0006350 SGD_REF:S000045055|PMID:9118942 IMP P YHR206W|BRY1|POS9 gene taxon:4932 20020726 SGD
+SGD S000001249 SKN7 GO:0006350 SGD_REF:S000069996|PMID:11854400 IDA P YHR206W|BRY1|POS9 gene taxon:4932 20050117 SGD
+SGD S000001249 SKN7 GO:0006970 SGD_REF:S000069996|PMID:11854400 TAS P YHR206W|BRY1|POS9 gene taxon:4932 20020726 SGD
+SGD S000001249 SKN7 GO:0006979 SGD_REF:S000042360|PMID:10512701 TAS P YHR206W|BRY1|POS9 gene taxon:4932 20020726 SGD
+SGD S000005111 SKO1 GO:0005634 SGD_REF:S000066009|PMID:11500510 IDA C YNL167C|ACR1 gene taxon:4932 20030127 SGD
+SGD S000005111 SKO1 GO:0005829 SGD_REF:S000066009|PMID:11500510 IDA C YNL167C|ACR1 gene taxon:4932 20030127 SGD
+SGD S000005111 SKO1 GO:0003702 SGD_REF:S000050501|PMID:1437546 IMP F YNL167C|ACR1 gene taxon:4932 20021115 SGD
+SGD S000005111 SKO1 GO:0003702 SGD_REF:S000050501|PMID:1437546 IPI F YNL167C|ACR1 gene taxon:4932 20021115 SGD
+SGD S000005111 SKO1 GO:0003702 SGD_REF:S000050501|PMID:1437546 ISS F YNL167C|ACR1 gene taxon:4932 20021115 SGD
+SGD S000005111 SKO1 GO:0000122 SGD_REF:S000050501|PMID:1437546 IMP P YNL167C|ACR1 gene taxon:4932 20021115 SGD
+SGD S000002736 SKP1 GO:0000152 SGD_REF:S000058469|PMID:9346231 TAS C YDR328C|CBF3D|MGO1 gene taxon:4932 20010118 SGD
+SGD S000002736 SKP1 GO:0000776 SGD_REF:S000073469|PMID:12769845 TAS C YDR328C|CBF3D|MGO1 gene taxon:4932 20030725 SGD
+SGD S000002736 SKP1 GO:0005634 SGD_REF:S000059560|PMID:11080155 IDA C YDR328C|CBF3D|MGO1 gene taxon:4932 20030619 SGD
+SGD S000002736 SKP1 GO:0005737 SGD_REF:S000059560|PMID:11080155 IDA C YDR328C|CBF3D|MGO1 gene taxon:4932 20030619 SGD
+SGD S000002736 SKP1 GO:0019005 SGD_REF:S000054644|PMID:9716410 TAS C YDR328C|CBF3D|MGO1 gene taxon:4932 20030523 SGD
+SGD S000002736 SKP1 GO:0019005 SGD_REF:S000041398|PMID:9346239 IDA C YDR328C|CBF3D|MGO1 gene taxon:4932 20050408 SGD
+SGD S000002736 SKP1 GO:0031518 SGD_REF:S000056114|PMID:8682209 TAS C YDR328C|CBF3D|MGO1 gene taxon:4932 20050722 SGD
+SGD S000002736 SKP1 GO:0043291 SGD_REF:S000060747|PMID:11283612 IPI SGD:S000002610|SGD:S000003794 C YDR328C|CBF3D|MGO1 gene taxon:4932 20041216 SGD
+SGD S000002736 SKP1 GO:0043291 SGD_REF:S000079675|PMID:11844802 IPI SGD:S000003794 C YDR328C|CBF3D|MGO1 gene taxon:4932 20050103 SGD
+SGD S000002736 SKP1 GO:0003688 SGD_REF:S000114165|PMID:16421250 IPI F YDR328C|CBF3D|MGO1 gene taxon:4932 20060123 SGD
+SGD S000002736 SKP1 GO:0004842 SGD_REF:S000058469|PMID:9346231 TAS F YDR328C|CBF3D|MGO1 gene taxon:4932 20010118 SGD
+SGD S000002736 SKP1 GO:0005515 SGD_REF:S000073469|PMID:12769845 IPI SGD:S000003420 F YDR328C|CBF3D|MGO1 gene taxon:4932 20030725 SGD
+SGD S000002736 SKP1 GO:0000082 SGD_REF:S000058469|PMID:9346231 TAS P YDR328C|CBF3D|MGO1 gene taxon:4932 20010118 SGD
+SGD S000002736 SKP1 GO:0000086 SGD_REF:S000045265|PMID:10409741 IMP P YDR328C|CBF3D|MGO1 gene taxon:4932 20030619 SGD
+SGD S000002736 SKP1 GO:0006461 SGD_REF:S000076779|PMID:15090617 IDA P YDR328C|CBF3D|MGO1 gene taxon:4932 20040904 SGD
+SGD S000002736 SKP1 GO:0007035 SGD_REF:S000060747|PMID:11283612 IGI SGD:S000002610|SGD:S000003794 P YDR328C|CBF3D|MGO1 gene taxon:4932 20050527 SGD
+SGD S000002736 SKP1 GO:0007035 SGD_REF:S000060747|PMID:11283612 IMP P YDR328C|CBF3D|MGO1 gene taxon:4932 20050527 SGD
+SGD S000002736 SKP1 GO:0016567 SGD_REF:S000058289|PMID:9499404 IGI P YDR328C|CBF3D|MGO1 gene taxon:4932 20050408 SGD
+SGD S000002736 SKP1 GO:0016567 SGD_REF:S000058289|PMID:9499404 IPI P YDR328C|CBF3D|MGO1 gene taxon:4932 20050408 SGD
+SGD S000002736 SKP1 GO:0031146 SGD_REF:S000041398|PMID:9346239 IDA P YDR328C|CBF3D|MGO1 gene taxon:4932 20050404 SGD
+SGD S000002736 SKP1 GO:0043254 SGD_REF:S000060747|PMID:11283612 IPI SGD:S000002610|SGD:S000003794 P YDR328C|CBF3D|MGO1 gene taxon:4932 20050527 SGD
+SGD S000002736 SKP1 GO:0045116 SGD_REF:S000042395|PMID:9531531 IGI SGD:S000005924 P YDR328C|CBF3D|MGO1 gene taxon:4932 20051018 SGD
+SGD S000002736 SKP1 GO:0045116 SGD_REF:S000042395|PMID:9531531 IMP P YDR328C|CBF3D|MGO1 gene taxon:4932 20051018 SGD
+SGD S000002736 SKP1 GO:0051382 SGD_REF:S000070182|PMID:12084919 IDA P YDR328C|CBF3D|MGO1 gene taxon:4932 20050720 SGD
+SGD S000002736 SKP1 GO:0051382 SGD_REF:S000070182|PMID:12084919 IMP P YDR328C|CBF3D|MGO1 gene taxon:4932 20050720 SGD
+SGD S000005255 SKP2 GO:0000151 SGD_REF:S000058340|PMID:9635407 ISS C F-box protein YNL311C gene taxon:4932 20030205 SGD
+SGD S000005255 SKP2 GO:0005515 SGD_REF:S000058340|PMID:9635407 ISS F F-box protein YNL311C gene taxon:4932 20030205 SGD
+SGD S000005255 SKP2 GO:0006511 SGD_REF:S000058340|PMID:9635407 ISS P F-box protein YNL311C gene taxon:4932 20030205 SGD
+SGD S000005947 SKS1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YPL026C|SHA3 gene taxon:4932 20031028 SGD
+SGD S000005947 SKS1 GO:0004674 SGD_REF:S000051152|PMID:8948096 ISS F YPL026C|SHA3 gene taxon:4932 20021001 SGD
+SGD S000005947 SKS1 GO:0006468 SGD_REF:S000051152|PMID:8948096 ISS P YPL026C|SHA3 gene taxon:4932 20021001 SGD
+SGD S000005947 SKS1 GO:0009749 SGD_REF:S000045042|PMID:9559544 IGI SGD:S000002353 P YPL026C|SHA3 gene taxon:4932 20050425 SGD
+SGD S000005947 SKS1 GO:0015758 SGD_REF:S000051152|PMID:8948096 IGI P YPL026C|SHA3 gene taxon:4932 20021001 SGD
+SGD S000005947 SKS1 GO:0045944 SGD_REF:S000051152|PMID:8948096 IGI P YPL026C|SHA3 gene taxon:4932 20021001 SGD
+SGD S000000157 SKT5 GO:0000131 SGD_REF:S000077520|PMID:15470103 IDA C YBL061C|CAL2|CHS4|CSD4 gene taxon:4932 20050531 SGD
+SGD S000000157 SKT5 colocalizes_with GO:0000144 SGD_REF:S000047109|PMID:9314530 IDA C YBL061C|CAL2|CHS4|CSD4 gene taxon:4932 20050303 SGD
+SGD S000000157 SKT5 GO:0005935 SGD_REF:S000047109|PMID:9314530 IDA C YBL061C|CAL2|CHS4|CSD4 gene taxon:4932 20050303 SGD
+SGD S000000157 SKT5 GO:0005935 SGD_REF:S000077520|PMID:15470103 IDA C YBL061C|CAL2|CHS4|CSD4 gene taxon:4932 20050531 SGD
+SGD S000000157 SKT5 GO:0008047 SGD_REF:S000048834|PMID:9234668 IMP F YBL061C|CAL2|CHS4|CSD4 gene taxon:4932 20010118 SGD
+SGD S000000157 SKT5 GO:0000910 SGD_REF:S000041005|PMID:10652251 IMP P YBL061C|CAL2|CHS4|CSD4 gene taxon:4932 20010119 SGD
+SGD S000000157 SKT5 GO:0006038 SGD_REF:S000048834|PMID:9234668 IMP P YBL061C|CAL2|CHS4|CSD4 gene taxon:4932 20010118 SGD
+SGD S000000157 SKT5 GO:0006970 SGD_REF:S000041005|PMID:10652251 IMP P YBL061C|CAL2|CHS4|CSD4 gene taxon:4932 20010118 SGD
+SGD S000004829 SKY1 GO:0005737 SGD_REF:S000059966|PMID:11233987 IDA C YMR216C gene taxon:4932 20020925 SGD
+SGD S000004829 SKY1 GO:0004672 SGD_REF:S000042558|PMID:10318902 IDA F YMR216C gene taxon:4932 20020925 SGD
+SGD S000004829 SKY1 GO:0006376 SGD_REF:S000065954|PMID:11565750 IGI P YMR216C gene taxon:4932 20020925 SGD
+SGD S000004829 SKY1 GO:0006873 SGD_REF:S000059258|PMID:11113192 IMP P YMR216C gene taxon:4932 20020925 SGD
+SGD S000004829 SKY1 GO:0030003 SGD_REF:S000071364|PMID:12225850 IMP P YMR216C gene taxon:4932 20050425 SGD
+SGD S000004829 SKY1 GO:0042307 SGD_REF:S000044295|PMID:10952997 IMP P YMR216C gene taxon:4932 20020925 SGD
+SGD S000004829 SKY1 GO:0042493 SGD_REF:S000065970|PMID:11585720 IMP P YMR216C gene taxon:4932 20021111 SGD
+SGD S000000103 SLA1 GO:0030479 SGD_REF:S000041005|PMID:10652251 IDA C cytoskeletal protein binding protein YBL007C gene taxon:4932 20010118 SGD
+SGD S000000103 SLA1 GO:0008092 SGD_REF:S000041005|PMID:10652251 IMP F cytoskeletal protein binding protein YBL007C gene taxon:4932 20010118 SGD
+SGD S000000103 SLA1 GO:0008092 SGD_REF:S000041005|PMID:10652251 IPI F cytoskeletal protein binding protein YBL007C gene taxon:4932 20010118 SGD
+SGD S000000103 SLA1 GO:0030674 SGD_REF:S000072033|PMID:11950888 IPI F cytoskeletal protein binding protein YBL007C gene taxon:4932 20040107 SGD
+SGD S000000103 SLA1 GO:0000147 SGD_REF:S000041005|PMID:10652251 TAS P cytoskeletal protein binding protein YBL007C gene taxon:4932 20010118 SGD
+SGD S000000103 SLA1 GO:0006897 SGD_REF:S000069574|PMID:11940605 IMP P cytoskeletal protein binding protein YBL007C gene taxon:4932 20030207 SGD
+SGD S000000103 SLA1 GO:0006897 SGD_REF:S000069574|PMID:11940605 IPI P cytoskeletal protein binding protein YBL007C gene taxon:4932 20030207 SGD
+SGD S000000103 SLA1 GO:0007015 SGD_REF:S000041005|PMID:10652251 IPI P cytoskeletal protein binding protein YBL007C gene taxon:4932 20010118 SGD
+SGD S000000103 SLA1 GO:0007015 SGD_REF:S000041005|PMID:10652251 IMP P cytoskeletal protein binding protein YBL007C gene taxon:4932 20010118 SGD
+SGD S000000103 SLA1 GO:0007047 SGD_REF:S000041005|PMID:10652251 IMP P cytoskeletal protein binding protein YBL007C gene taxon:4932 20010118 SGD
+SGD S000000103 SLA1 GO:0007121 SGD_REF:S000041005|PMID:10652251 IMP P cytoskeletal protein binding protein YBL007C gene taxon:4932 20010118 SGD
+SGD S000005187 SLA2 GO:0000131 SGD_REF:S000060151|PMID:11302750 IDA C transmembrane protein YNL243W|END4|MOP2 gene taxon:4932 20030422 SGD
+SGD S000005187 SLA2 GO:0030479 SGD_REF:S000041005|PMID:10652251 IDA C transmembrane protein YNL243W|END4|MOP2 gene taxon:4932 20010118 SGD
+SGD S000005187 SLA2 GO:0030674 SGD_REF:S000075279|PMID:14704157 IGI F transmembrane protein YNL243W|END4|MOP2 gene taxon:4932 20040107 SGD
+SGD S000005187 SLA2 GO:0030674 SGD_REF:S000075279|PMID:14704157 IPI F transmembrane protein YNL243W|END4|MOP2 gene taxon:4932 20040107 SGD
+SGD S000005187 SLA2 GO:0006887 SGD_REF:S000041005|PMID:10652251 IMP P transmembrane protein YNL243W|END4|MOP2 gene taxon:4932 20010118 SGD
+SGD S000005187 SLA2 GO:0006897 SGD_REF:S000041005|PMID:10652251 IMP P transmembrane protein YNL243W|END4|MOP2 gene taxon:4932 20010118 SGD
+SGD S000005187 SLA2 GO:0007015 SGD_REF:S000058470|PMID:10397764 IMP P transmembrane protein YNL243W|END4|MOP2 gene taxon:4932 20010118 SGD
+SGD S000005187 SLA2 GO:0007047 SGD_REF:S000041005|PMID:10652251 IMP P transmembrane protein YNL243W|END4|MOP2 gene taxon:4932 20010118 SGD
+SGD S000005187 SLA2 GO:0007121 SGD_REF:S000041005|PMID:10652251 IMP P transmembrane protein YNL243W|END4|MOP2 gene taxon:4932 20010118 SGD
+SGD S000002210 SLC1 GO:0005811 SGD_REF:S000048561|PMID:10515935 IDA C 1-acyl-sn-gylcerol-3-phosphate acyl transferase (putative) YDL052C gene taxon:4932 20020917 SGD
+SGD S000002210 SLC1 GO:0003841 SGD_REF:S000055092|PMID:9212466 IDA F 1-acyl-sn-gylcerol-3-phosphate acyl transferase (putative) YDL052C gene taxon:4932 20021001 SGD
+SGD S000002210 SLC1 GO:0030148 SGD_REF:S000044872|PMID:8408076 IMP P 1-acyl-sn-gylcerol-3-phosphate acyl transferase (putative) YDL052C gene taxon:4932 20021001 SGD
+SGD S000001591 SLD2 GO:0005657 SGD_REF:S000056038|PMID:9742127 IGI C YKL108W|DRC1 gene taxon:4932 20010118 SGD
+SGD S000001591 SLD2 GO:0005657 SGD_REF:S000056038|PMID:9742127 IPI C YKL108W|DRC1 gene taxon:4932 20010118 SGD
+SGD S000001591 SLD2 GO:0005554 SGD_REF:S000069584 ND F YKL108W|DRC1 gene taxon:4932 20010119 SGD
+SGD S000001591 SLD2 GO:0006271 SGD_REF:S000056038|PMID:9742127 IPI P YKL108W|DRC1 gene taxon:4932 20010118 SGD
+SGD S000001591 SLD2 GO:0006271 SGD_REF:S000056038|PMID:9742127 IGI P YKL108W|DRC1 gene taxon:4932 20010118 SGD
+SGD S000003081 SLD3 GO:0000790 SGD_REF:S000060072|PMID:11296242 IDA C YGL113W gene taxon:4932 20010412 SGD
+SGD S000003081 SLD3 GO:0003682 SGD_REF:S000060072|PMID:11296242 IDA F YGL113W gene taxon:4932 20010412 SGD
+SGD S000003081 SLD3 GO:0006268 SGD_REF:S000060072|PMID:11296242 IMP P YGL113W gene taxon:4932 20010412 SGD
+SGD S000003081 SLD3 GO:0006270 SGD_REF:S000060072|PMID:11296242 IMP P YGL113W gene taxon:4932 20010412 SGD
+SGD S000003081 SLD3 GO:0006270 SGD_REF:S000060072|PMID:11296242 IPI P YGL113W gene taxon:4932 20010412 SGD
+SGD S000002897 SLD5 GO:0000811 SGD_REF:S000073092|PMID:12730134 IPI SGD:S000002420|SGD:S000003608|SGD:S000005506 C subunit of the GINS complex YDR489W|CDC105 gene taxon:4932 20051201 SGD
+SGD S000002897 SLD5 GO:0000811 SGD_REF:S000073501|PMID:12768207 IPI SGD:S000002420|SGD:S000005506|SGD:S000003608 C subunit of the GINS complex YDR489W|CDC105 gene taxon:4932 20051201 SGD
+SGD S000002897 SLD5 GO:0005554 SGD_REF:S000069584 ND F subunit of the GINS complex YDR489W|CDC105 gene taxon:4932 20051201 SGD
+SGD S000002897 SLD5 GO:0006261 SGD_REF:S000073092|PMID:12730134 IMP P subunit of the GINS complex YDR489W|CDC105 gene taxon:4932 20030508 SGD
+SGD S000002897 SLD5 GO:0006261 SGD_REF:S000073501|PMID:12768207 IMP P subunit of the GINS complex YDR489W|CDC105 gene taxon:4932 20051201 SGD
+SGD S000002923 SLF1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YDR515W|SRO99 gene taxon:4932 20020507 SGD
+SGD S000002923 SLF1 GO:0005844 SGD_REF:S000042217|PMID:10564276 IDA C YDR515W|SRO99 gene taxon:4932 20020826 SGD
+SGD S000002923 SLF1 GO:0003723 SGD_REF:S000042217|PMID:10564276 IDA F YDR515W|SRO99 gene taxon:4932 20020826 SGD
+SGD S000002923 SLF1 GO:0006445 SGD_REF:S000042217|PMID:10564276 IGI P YDR515W|SRO99 gene taxon:4932 20021001 SGD
+SGD S000002923 SLF1 GO:0006445 SGD_REF:S000042217|PMID:10564276 IMP P YDR515W|SRO99 gene taxon:4932 20021001 SGD
+SGD S000002923 SLF1 GO:0006445 SGD_REF:S000042217|PMID:10564276 IPI P YDR515W|SRO99 gene taxon:4932 20021001 SGD
+SGD S000002923 SLF1 GO:0006878 SGD_REF:S000046879|PMID:8628314 IMP P YDR515W|SRO99 gene taxon:4932 20021001 SGD
+SGD S000002923 SLF1 GO:0006878 SGD_REF:S000046879|PMID:8628314 IPI P YDR515W|SRO99 gene taxon:4932 20021001 SGD
+SGD S000005534 SLG1 GO:0005624 SGD_REF:S000052074|PMID:10348843 IDA C YOR008C|HCS77|WSC1 gene taxon:4932 20010118 SGD
+SGD S000005534 SLG1 GO:0005886 SGD_REF:S000048928|PMID:9391108 IDA C YOR008C|HCS77|WSC1 gene taxon:4932 20050630 SGD
+SGD S000005534 SLG1 GO:0030478 SGD_REF:S000041005|PMID:10652251 IDA C YOR008C|HCS77|WSC1 gene taxon:4932 20010118 SGD
+SGD S000005534 SLG1 GO:0004888 SGD_REF:S000039898|PMID:10430578 IGI F YOR008C|HCS77|WSC1 gene taxon:4932 20021206 SGD
+SGD S000005534 SLG1 GO:0004888 SGD_REF:S000039898|PMID:10430578 ISS F YOR008C|HCS77|WSC1 gene taxon:4932 20021206 SGD
+SGD S000005534 SLG1 GO:0006897 SGD_REF:S000075861|PMID:14593073 IMP P YOR008C|HCS77|WSC1 gene taxon:4932 20050505 SGD
+SGD S000005534 SLG1 GO:0006970 SGD_REF:S000041005|PMID:10652251 IMP P YOR008C|HCS77|WSC1 gene taxon:4932 20010118 SGD
+SGD S000005534 SLG1 GO:0006970 SGD_REF:S000074629|PMID:14871941 IGI SGD:S000004478 P YOR008C|HCS77|WSC1 gene taxon:4932 20050505 SGD
+SGD S000005534 SLG1 GO:0007047 SGD_REF:S000052074|PMID:10348843 IMP P YOR008C|HCS77|WSC1 gene taxon:4932 20010118 SGD
+SGD S000005534 SLG1 GO:0007266 SGD_REF:S000049820|PMID:10508863 IMP P YOR008C|HCS77|WSC1 gene taxon:4932 20010118 SGD
+SGD S000005534 SLG1 GO:0007266 SGD_REF:S000052074|PMID:10348843 IMP P YOR008C|HCS77|WSC1 gene taxon:4932 20010118 SGD
+SGD S000005534 SLG1 GO:0007266 SGD_REF:S000052074|PMID:10348843 IGI P YOR008C|HCS77|WSC1 gene taxon:4932 20010118 SGD
+SGD S000005534 SLG1 GO:0009408 SGD_REF:S000049820|PMID:10508863 IMP P YOR008C|HCS77|WSC1 gene taxon:4932 20010118 SGD
+SGD S000005534 SLG1 GO:0009408 SGD_REF:S000052074|PMID:10348843 IMP P YOR008C|HCS77|WSC1 gene taxon:4932 20010118 SGD
+SGD S000005534 SLG1 GO:0030036 SGD_REF:S000049820|PMID:10508863 IMP P YOR008C|HCS77|WSC1 gene taxon:4932 20030116 SGD
+SGD S000005534 SLG1 GO:0030468 SGD_REF:S000049820|PMID:10508863 IMP P YOR008C|HCS77|WSC1 gene taxon:4932 20010302 SGD
+SGD S000003503 SLH1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YGR271W gene taxon:4932 20031028 SGD
+SGD S000003503 SLH1 GO:0003724 SGD_REF:S000042257|PMID:9133744 ISS F YGR271W gene taxon:4932 20011205 SGD
+SGD S000003503 SLH1 GO:0006445 SGD_REF:S000046376|PMID:10922069 IMP P YGR271W gene taxon:4932 20011205 SGD
+SGD S000003503 SLH1 GO:0006445 SGD_REF:S000061230|PMID:11438647 IMP P YGR271W gene taxon:4932 20011205 SGD
+SGD S000003503 SLH1 GO:0006445 SGD_REF:S000046376|PMID:10922069 IGI P YGR271W gene taxon:4932 20011205 SGD
+SGD S000003503 SLH1 GO:0006445 SGD_REF:S000061230|PMID:11438647 IGI P YGR271W gene taxon:4932 20011205 SGD
+SGD S000003444 SLI1 colocalizes_with GO:0005635 SGD_REF:S000076247|PMID:15025559 IDA C YGR212W gene taxon:4932 20050505 SGD
+SGD S000003444 SLI1 colocalizes_with GO:0005886 SGD_REF:S000076247|PMID:15025559 IDA C YGR212W gene taxon:4932 20050505 SGD
+SGD S000003444 SLI1 GO:0008080 SGD_REF:S000076247|PMID:15025559 IDA F YGR212W gene taxon:4932 20040712 SGD
+SGD S000003444 SLI1 GO:0008080 SGD_REF:S000076247|PMID:15025559 IMP F YGR212W gene taxon:4932 20040712 SGD
+SGD S000003444 SLI1 GO:0042493 SGD_REF:S000076247|PMID:15025559 IDA P YGR212W gene taxon:4932 20050505 SGD
+SGD S000000360 SLI15 GO:0005828 SGD_REF:S000066223|PMID:11724818 IDA C YBR156C gene taxon:4932 20020602 SGD
+SGD S000000360 SLI15 GO:0005876 SGD_REF:S000066223|PMID:11724818 IDA C YBR156C gene taxon:4932 20020602 SGD
+SGD S000000360 SLI15 GO:0051233 SGD_REF:S000078515|PMID:12566427 IDA C YBR156C gene taxon:4932 20050407 SGD
+SGD S000000360 SLI15 GO:0030295 SGD_REF:S000041165|PMID:10385519 IMP F YBR156C gene taxon:4932 20030110 SGD
+SGD S000000360 SLI15 GO:0030295 SGD_REF:S000041165|PMID:10385519 IPI F YBR156C gene taxon:4932 20030110 SGD
+SGD S000000360 SLI15 GO:0006468 SGD_REF:S000041165|PMID:10385519 IMP P YBR156C gene taxon:4932 20030110 SGD
+SGD S000000360 SLI15 GO:0006468 SGD_REF:S000041165|PMID:10385519 IPI P YBR156C gene taxon:4932 20030110 SGD
+SGD S000000360 SLI15 GO:0007059 SGD_REF:S000066223|PMID:11724818 TAS P YBR156C gene taxon:4932 20020602 SGD
+SGD S000005721 SLK19 GO:0000776 SGD_REF:S000077144|PMID:15282802 IDA C leucine zipper (putative) YOR195W gene taxon:4932 20041008 SGD
+SGD S000005721 SLK19 GO:0000778 SGD_REF:S000044638|PMID:10427094 IDA C leucine zipper (putative) YOR195W gene taxon:4932 20030403 SGD
+SGD S000005721 SLK19 GO:0005819 SGD_REF:S000066036|PMID:11533655 IDA C leucine zipper (putative) YOR195W gene taxon:4932 20030627 SGD
+SGD S000005721 SLK19 GO:0005554 SGD_REF:S000069584 ND F leucine zipper (putative) YOR195W gene taxon:4932 20010119 SGD
+SGD S000005721 SLK19 GO:0007126 SGD_REF:S000051050|PMID:10835382 IMP P leucine zipper (putative) YOR195W gene taxon:4932 20010118 SGD
+SGD S000005721 SLK19 GO:0030472 SGD_REF:S000044638|PMID:10427094 IMP P leucine zipper (putative) YOR195W gene taxon:4932 20010118 SGD
+SGD S000005721 SLK19 GO:0030472 SGD_REF:S000066036|PMID:11533655 IGI P leucine zipper (putative) YOR195W gene taxon:4932 20030627 SGD
+SGD S000005721 SLK19 GO:0030472 SGD_REF:S000066036|PMID:11533655 IMP P leucine zipper (putative) YOR195W gene taxon:4932 20030627 SGD
+SGD S000005721 SLK19 GO:0030472 SGD_REF:S000044638|PMID:10427094 IGI P leucine zipper (putative) YOR195W gene taxon:4932 20010118 SGD
+SGD S000001367 SLM1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YIL105C|LIT2 gene taxon:4932 20031028 SGD
+SGD S000001367 SLM1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YIL105C|LIT2 gene taxon:4932 20040928 SGD
+SGD S000001367 SLM1 GO:0005886 SGD_REF:S000080098|PMID:15372071 IDA C YIL105C|LIT2 gene taxon:4932 20050106 SGD
+SGD S000001367 SLM1 GO:0005886 SGD_REF:S000080639|PMID:15689497 IDA C YIL105C|LIT2 gene taxon:4932 20050418 SGD
+SGD S000001367 SLM1 GO:0031932 SGD_REF:S000080639|PMID:15689497 IPI C YIL105C|LIT2 gene taxon:4932 20051130 SGD
+SGD S000001367 SLM1 GO:0035091 SGD_REF:S000080098|PMID:15372071 TAS F YIL105C|LIT2 gene taxon:4932 20050106 SGD
+SGD S000001367 SLM1 GO:0035091 SGD_REF:S000080639|PMID:15689497 IMP F YIL105C|LIT2 gene taxon:4932 20050418 SGD
+SGD S000001367 SLM1 GO:0035091 SGD_REF:S000080639|PMID:15689497 IPI F YIL105C|LIT2 gene taxon:4932 20050418 SGD
+SGD S000001367 SLM1 GO:0001558 SGD_REF:S000080639|PMID:15689497 IPI SGD:S000003594|SGD:S000004672 P YIL105C|LIT2 gene taxon:4932 20051108 SGD
+SGD S000001367 SLM1 GO:0001558 SGD_REF:S000080639|PMID:15689497 IGI SGD:S000004992 P YIL105C|LIT2 gene taxon:4932 20051108 SGD
+SGD S000001367 SLM1 GO:0030036 SGD_REF:S000080098|PMID:15372071 IGI SGD:S000004992 P YIL105C|LIT2 gene taxon:4932 20050106 SGD
+SGD S000001367 SLM1 GO:0030036 SGD_REF:S000080639|PMID:15689497 IGI SGD:S000004992 P YIL105C|LIT2 gene taxon:4932 20050418 SGD
+SGD S000001367 SLM1 GO:0030950 SGD_REF:S000080639|PMID:15689497 IPI SGD:S000003594|SGD:S000004672 P YIL105C|LIT2 gene taxon:4932 20051108 SGD
+SGD S000001367 SLM1 GO:0045011 SGD_REF:S000080639|PMID:15689497 IGI SGD:S000004992 P YIL105C|LIT2 gene taxon:4932 20050418 SGD
+SGD S000004992 SLM2 GO:0005886 SGD_REF:S000080098|PMID:15372071 IDA C YNL047C|LIT1 gene taxon:4932 20050106 SGD
+SGD S000004992 SLM2 GO:0005886 SGD_REF:S000080639|PMID:15689497 IDA C YNL047C|LIT1 gene taxon:4932 20050418 SGD
+SGD S000004992 SLM2 GO:0031932 SGD_REF:S000080639|PMID:15689497 IPI C YNL047C|LIT1 gene taxon:4932 20051130 SGD
+SGD S000004992 SLM2 GO:0035091 SGD_REF:S000080098|PMID:15372071 TAS F YNL047C|LIT1 gene taxon:4932 20050106 SGD
+SGD S000004992 SLM2 GO:0001558 SGD_REF:S000080639|PMID:15689497 IPI SGD:S000003594|SGD:S000004672 P YNL047C|LIT1 gene taxon:4932 20051108 SGD
+SGD S000004992 SLM2 GO:0001558 SGD_REF:S000080639|PMID:15689497 IGI SGD:S000001367 P YNL047C|LIT1 gene taxon:4932 20051108 SGD
+SGD S000004992 SLM2 GO:0030036 SGD_REF:S000080098|PMID:15372071 IGI SGD:S000001367 P YNL047C|LIT1 gene taxon:4932 20050106 SGD
+SGD S000004992 SLM2 GO:0030036 SGD_REF:S000080639|PMID:15689497 IGI P YNL047C|LIT1 gene taxon:4932 20050418 SGD
+SGD S000004992 SLM2 GO:0030950 SGD_REF:S000080639|PMID:15689497 IPI SGD:S000003594|SGD:S000004672 P YNL047C|LIT1 gene taxon:4932 20051108 SGD
+SGD S000004992 SLM2 GO:0045011 SGD_REF:S000080639|PMID:15689497 IGI SGD:S000001367 P YNL047C|LIT1 gene taxon:4932 20050418 SGD
+SGD S000002191 SLM3 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YDL033C|MTO2|MTU1 gene taxon:4932 20031028 SGD
+SGD S000002191 SLM3 GO:0005739 SGD_REF:S000082099|PMID:15944150 IDA C YDL033C|MTO2|MTU1 gene taxon:4932 20050704 SGD
+SGD S000002191 SLM3 GO:0004808 SGD_REF:S000072463|PMID:10592175 ISS F YDL033C|MTO2|MTU1 gene taxon:4932 20030204 SGD
+SGD S000002191 SLM3 GO:0004808 SGD_REF:S000080941|PMID:15509579 IMP F YDL033C|MTO2|MTU1 gene taxon:4932 20050407 SGD
+SGD S000002191 SLM3 GO:0006400 SGD_REF:S000080941|PMID:15509579 IMP P YDL033C|MTO2|MTU1 gene taxon:4932 20050407 SGD
+SGD S000002191 SLM3 GO:0006412 SGD_REF:S000080941|PMID:15509579 IMP P YDL033C|MTO2|MTU1 gene taxon:4932 20050407 SGD
+SGD S000000281 SLM4 GO:0000329 SGD_REF:S000074185|PMID:14562095 IDA C YBR077C|EGO3|NIR1 gene taxon:4932 20031028 SGD
+SGD S000000281 SLM4 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YBR077C|EGO3|NIR1 gene taxon:4932 20020507 SGD
+SGD S000000281 SLM4 GO:0005774 SGD_REF:S000082228|PMID:15989961 IDA C YBR077C|EGO3|NIR1 gene taxon:4932 20050718 SGD
+SGD S000000281 SLM4 GO:0043325 SGD_REF:S000079695|PMID:15539461 TAS F YBR077C|EGO3|NIR1 gene taxon:4932 20050228 SGD
+SGD S000000281 SLM4 GO:0007165 SGD_REF:S000079695|PMID:15539461 IMP P YBR077C|EGO3|NIR1 gene taxon:4932 20050228 SGD
+SGD S000000281 SLM4 GO:0016237 SGD_REF:S000082228|PMID:15989961 IMP P YBR077C|EGO3|NIR1 gene taxon:4932 20050718 SGD
+SGD S000000618 SLM5 GO:0005739 SGD_REF:S000058439|PMID:9030748 ISS C YCR024C gene taxon:4932 20010301 SGD
+SGD S000000618 SLM5 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YCR024C gene taxon:4932 20040928 SGD
+SGD S000000618 SLM5 GO:0004816 SGD_REF:S000058439|PMID:9030748 IDA F YCR024C gene taxon:4932 20010301 SGD
+SGD S000000618 SLM5 GO:0004816 SGD_REF:S000058439|PMID:9030748 ISS F YCR024C gene taxon:4932 20010301 SGD
+SGD S000000618 SLM5 GO:0006412 SGD_REF:S000058439|PMID:9030748 IDA P YCR024C gene taxon:4932 20010301 SGD
+SGD S000001409 SLN1 GO:0005886 SGD_REF:S000053117|PMID:8808622 ISS C histidine kinase osmosensor that regulates an osmosensing MAP kinase cascade, similar to bacterial two-component regulators YIL147C|YPD2 gene taxon:4932 20010118 SGD
+SGD S000001409 SLN1 GO:0000155 SGD_REF:S000053117|PMID:8808622 TAS F histidine kinase osmosensor that regulates an osmosensing MAP kinase cascade, similar to bacterial two-component regulators YIL147C|YPD2 gene taxon:4932 20010118 SGD
+SGD S000001409 SLN1 GO:0004673 SGD_REF:S000053117|PMID:8808622 IDA F histidine kinase osmosensor that regulates an osmosensing MAP kinase cascade, similar to bacterial two-component regulators YIL147C|YPD2 gene taxon:4932 20030226 SGD
+SGD S000001409 SLN1 GO:0005034 SGD_REF:S000053117|PMID:8808622 TAS F histidine kinase osmosensor that regulates an osmosensing MAP kinase cascade, similar to bacterial two-component regulators YIL147C|YPD2 gene taxon:4932 20010118 SGD
+SGD S000001409 SLN1 GO:0005034 SGD_REF:S000073815|PMID:12821642 IDA F histidine kinase osmosensor that regulates an osmosensing MAP kinase cascade, similar to bacterial two-component regulators YIL147C|YPD2 gene taxon:4932 20040430 SGD
+SGD S000001409 SLN1 GO:0006468 SGD_REF:S000053117|PMID:8808622 TAS P histidine kinase osmosensor that regulates an osmosensing MAP kinase cascade, similar to bacterial two-component regulators YIL147C|YPD2 gene taxon:4932 20010118 SGD
+SGD S000001409 SLN1 GO:0007234 SGD_REF:S000053117|PMID:8808622 IDA P histidine kinase osmosensor that regulates an osmosensing MAP kinase cascade, similar to bacterial two-component regulators YIL147C|YPD2 gene taxon:4932 20030226 SGD
+SGD S000001409 SLN1 GO:0042542 SGD_REF:S000059181|PMID:11084293 IMP P histidine kinase osmosensor that regulates an osmosensing MAP kinase cascade, similar to bacterial two-component regulators YIL147C|YPD2 gene taxon:4932 20030213 SGD
+SGD S000028437 SLO1 GO:0005737 SGD_REF:S000072666|PMID:12620189 NAS C YER180C-A gene taxon:4932 20030307 SGD
+SGD S000028437 SLO1 GO:0005083 SGD_REF:S000072666|PMID:12620189 ISS F YER180C-A gene taxon:4932 20030307 SGD
+SGD S000028437 SLO1 GO:0006623 SGD_REF:S000072666|PMID:12620189 IPI P YER180C-A gene taxon:4932 20030307 SGD
+SGD S000004129 SLS1 GO:0005743 SGD_REF:S000041084|PMID:8917313 IDA C 73 kDa mitochondrial integral membrane protein YLR139C gene taxon:4932 20020617 SGD
+SGD S000004129 SLS1 GO:0016021 SGD_REF:S000041084|PMID:8917313 IDA C 73 kDa mitochondrial integral membrane protein YLR139C gene taxon:4932 20020617 SGD
+SGD S000004129 SLS1 GO:0042645 SGD_REF:S000073179|PMID:12637560 IDA C 73 kDa mitochondrial integral membrane protein YLR139C gene taxon:4932 20030616 SGD
+SGD S000004129 SLS1 GO:0042645 SGD_REF:S000080741|PMID:15692048 IDA C 73 kDa mitochondrial integral membrane protein YLR139C gene taxon:4932 20050401 SGD
+SGD S000004129 SLS1 GO:0005554 SGD_REF:S000069584 ND F 73 kDa mitochondrial integral membrane protein YLR139C gene taxon:4932 20020617 SGD
+SGD S000004129 SLS1 GO:0006412 SGD_REF:S000069068|PMID:11805046 IMP P 73 kDa mitochondrial integral membrane protein YLR139C gene taxon:4932 20020617 SGD
+SGD S000004129 SLS1 GO:0006412 SGD_REF:S000073179|PMID:12637560 IMP P 73 kDa mitochondrial integral membrane protein YLR139C gene taxon:4932 20030616 SGD
+SGD S000004129 SLS1 GO:0009060 SGD_REF:S000041084|PMID:8917313 IMP P 73 kDa mitochondrial integral membrane protein YLR139C gene taxon:4932 20020617 SGD
+SGD S000001072 SLT2 GO:0005634 SGD_REF:S000046847|PMID:10523653 IGI C YHR030C|BYC2|MPK1|SLK2 gene taxon:4932 20010118 SGD
+SGD S000001072 SLT2 GO:0005634 SGD_REF:S000073832|PMID:12361575 IDA C YHR030C|BYC2|MPK1|SLK2 gene taxon:4932 20030827 SGD
+SGD S000001072 SLT2 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YHR030C|BYC2|MPK1|SLK2 gene taxon:4932 20020507 SGD
+SGD S000001072 SLT2 GO:0005934 SGD_REF:S000073832|PMID:12361575 IDA C YHR030C|BYC2|MPK1|SLK2 gene taxon:4932 20030827 SGD
+SGD S000001072 SLT2 GO:0004707 SGD_REF:S000046937|PMID:8386319 ISS F YHR030C|BYC2|MPK1|SLK2 gene taxon:4932 20010118 SGD
+SGD S000001072 SLT2 GO:0006468 SGD_REF:S000046937|PMID:8386319 ISS P YHR030C|BYC2|MPK1|SLK2 gene taxon:4932 20010118 SGD
+SGD S000001072 SLT2 GO:0007047 SGD_REF:S000055516|PMID:10594829 TAS P YHR030C|BYC2|MPK1|SLK2 gene taxon:4932 20030708 SGD
+SGD S000001072 SLT2 GO:0007165 SGD_REF:S000046937|PMID:8386319 IMP P YHR030C|BYC2|MPK1|SLK2 gene taxon:4932 20010118 SGD
+SGD S000002495 SLU7 GO:0005681 SGD_REF:S000071184|PMID:12212850 IDA C YDR088C|SLT17 gene taxon:4932 20020924 SGD
+SGD S000002495 SLU7 contributes_to GO:0000386 SGD_REF:S000071184|PMID:12212850 IDA F YDR088C|SLT17 gene taxon:4932 20050921 SGD
+SGD S000002495 SLU7 GO:0031202 SGD_REF:S000071184|PMID:12212850 IDA F YDR088C|SLT17 gene taxon:4932 20050921 SGD
+SGD S000002495 SLU7 GO:0031202 SGD_REF:S000071184|PMID:12212850 IMP F YDR088C|SLT17 gene taxon:4932 20050921 SGD
+SGD S000002495 SLU7 GO:0000350 SGD_REF:S000071184|PMID:12212850 IDA P YDR088C|SLT17 gene taxon:4932 20050921 SGD
+SGD S000000432 SLX1 GO:0005634 SGD_REF:S000073797|PMID:12832395 IC GO:0006261 C YBR228W gene taxon:4932 20040210 SGD
+SGD S000000432 SLX1 GO:0017108 SGD_REF:S000073797|PMID:12832395 IDA F YBR228W gene taxon:4932 20040210 SGD
+SGD S000000432 SLX1 GO:0006261 SGD_REF:S000073797|PMID:12832395 IGI P YBR228W gene taxon:4932 20040210 SGD
+SGD S000000432 SLX1 GO:0006281 SGD_REF:S000059086|PMID:11139495 IGI P YBR228W gene taxon:4932 20021009 SGD
+SGD S000004125 SLX4 GO:0005634 SGD_REF:S000071416|PMID:12228808 IMP C YLR135W gene taxon:4932 20021008 SGD
+SGD S000004125 SLX4 GO:0005634 SGD_REF:S000073797|PMID:12832395 IC GO:0006261 C YLR135W gene taxon:4932 20040210 SGD
+SGD S000004125 SLX4 GO:0017108 SGD_REF:S000073797|PMID:12832395 IDA F YLR135W gene taxon:4932 20040210 SGD
+SGD S000004125 SLX4 GO:0006260 SGD_REF:S000071416|PMID:12228808 IMP P YLR135W gene taxon:4932 20021008 SGD
+SGD S000004125 SLX4 GO:0006261 SGD_REF:S000073797|PMID:12832395 IGI P YLR135W gene taxon:4932 20040210 SGD
+SGD S000000918 SLX8 GO:0005634 SGD_REF:S000059086|PMID:11139495 ISS C YER116C gene taxon:4932 20021001 SGD
+SGD S000000918 SLX8 GO:0003677 SGD_REF:S000059086|PMID:11139495 ISS F YER116C gene taxon:4932 20021001 SGD
+SGD S000000918 SLX8 GO:0006310 SGD_REF:S000059086|PMID:11139495 IGI P YER116C gene taxon:4932 20021001 SGD
+SGD S000000918 SLX8 GO:0006310 SGD_REF:S000059086|PMID:11139495 IMP P YER116C gene taxon:4932 20021001 SGD
+SGD S000003313 SLX9 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YGR081C gene taxon:4932 20031028 SGD
+SGD S000003313 SLX9 GO:0005730 SGD_REF:S000074185|PMID:14562095 IDA C YGR081C gene taxon:4932 20031028 SGD
+SGD S000003313 SLX9 GO:0005554 SGD_REF:S000069584 ND F YGR081C gene taxon:4932 20021126 SGD
+SGD S000003313 SLX9 GO:0006259 SGD_REF:S000074214|PMID:14566339 IGI P YGR081C gene taxon:4932 20031103 SGD
+SGD S000002597 SLY1 GO:0005783 SGD_REF:S000050496|PMID:10747087 IDA C t-SNARE-interacting protein that functions in ER-to-Golgi traffic YDR189W gene taxon:4932 20020827 SGD
+SGD S000002597 SLY1 GO:0005794 SGD_REF:S000050496|PMID:10747087 IDA C t-SNARE-interacting protein that functions in ER-to-Golgi traffic YDR189W gene taxon:4932 20020827 SGD
+SGD S000002597 SLY1 GO:0030134 SGD_REF:S000050496|PMID:10747087 IDA C t-SNARE-interacting protein that functions in ER-to-Golgi traffic YDR189W gene taxon:4932 20020827 SGD
+SGD S000002597 SLY1 GO:0000149 SGD_REF:S000050496|PMID:10747087 TAS F t-SNARE-interacting protein that functions in ER-to-Golgi traffic YDR189W gene taxon:4932 20020827 SGD
+SGD S000002597 SLY1 GO:0006888 SGD_REF:S000050702|PMID:9545229 IMP P t-SNARE-interacting protein that functions in ER-to-Golgi traffic YDR189W gene taxon:4932 20020827 SGD
+SGD S000005834 SLY41 GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C chloroplast phosphate transporter homolog YOR307C gene taxon:4932 20031028 SGD
+SGD S000005834 SLY41 GO:0005554 SGD_REF:S000069584 ND F chloroplast phosphate transporter homolog YOR307C gene taxon:4932 20060210 SGD
+SGD S000005834 SLY41 GO:0006888 SGD_REF:S000045607|PMID:1903839 IGI P chloroplast phosphate transporter homolog YOR307C gene taxon:4932 20021001 SGD
+SGD S000005948 SMA1 GO:0008372 SGD_REF:S000069584 ND C YPL027W gene taxon:4932 20021029 SGD
+SGD S000005948 SMA1 GO:0005554 SGD_REF:S000069584 ND F YPL027W gene taxon:4932 20021029 SGD
+SGD S000005948 SMA1 GO:0030476 SGD_REF:S000060989|PMID:11470404 IMP P YPL027W gene taxon:4932 20021029 SGD
+SGD S000004531 SMA2 GO:0008372 SGD_REF:S000069584 ND C YML066C gene taxon:4932 20021029 SGD
+SGD S000004531 SMA2 GO:0005554 SGD_REF:S000069584 ND F YML066C gene taxon:4932 20021029 SGD
+SGD S000004531 SMA2 GO:0030476 SGD_REF:S000060989|PMID:11470404 IMP P YML066C gene taxon:4932 20021029 SGD
+SGD S000000831 SMB1 GO:0005682 SGD_REF:S000066234|PMID:11720284 IPI C YER029C|Sm B|SmB gene taxon:4932 20051003 SGD
+SGD S000000831 SMB1 GO:0005685 SGD_REF:S000044485|PMID:9630245 IDA C YER029C|Sm B|SmB gene taxon:4932 20050929 SGD
+SGD S000000831 SMB1 GO:0046540 SGD_REF:S000056376|PMID:10377396 IPI C YER029C|Sm B|SmB gene taxon:4932 20050219 SGD
+SGD S000000831 SMB1 GO:0046540 SGD_REF:S000039461|PMID:10449419 IDA C YER029C|Sm B|SmB gene taxon:4932 20050926 SGD
+SGD S000000831 SMB1 contributes_to GO:0031202 SGD_REF:S000056376|PMID:10377396 IPI F YER029C|Sm B|SmB gene taxon:4932 20020620 SGD
+SGD S000000831 SMB1 contributes_to GO:0031202 SGD_REF:S000039461|PMID:10449419 IDA F YER029C|Sm B|SmB gene taxon:4932 20051003 SGD
+SGD S000000831 SMB1 GO:0000398 SGD_REF:S000056376|PMID:10377396 IPI P YER029C|Sm B|SmB gene taxon:4932 20020620 SGD
+SGD S000001886 SMC1 GO:0000798 SGD_REF:S000046168|PMID:10428036 IDA C SMC chromosomal ATPase family member YFL008W|CHL10 gene taxon:4932 20010118 SGD
+SGD S000001886 SMC1 GO:0000798 SGD_REF:S000041059|PMID:10499801 IDA C SMC chromosomal ATPase family member YFL008W|CHL10 gene taxon:4932 20010118 SGD
+SGD S000001886 SMC1 GO:0000798 SGD_REF:S000049776|PMID:9990856 IDA C SMC chromosomal ATPase family member YFL008W|CHL10 gene taxon:4932 20010118 SGD
+SGD S000001886 SMC1 GO:0000217 SGD_REF:S000039938|PMID:9727028 IDA F SMC chromosomal ATPase family member YFL008W|CHL10 gene taxon:4932 20010118 SGD
+SGD S000001886 SMC1 GO:0003680 SGD_REF:S000039938|PMID:9727028 IDA F SMC chromosomal ATPase family member YFL008W|CHL10 gene taxon:4932 20010118 SGD
+SGD S000001886 SMC1 GO:0003690 SGD_REF:S000039938|PMID:9727028 IDA F SMC chromosomal ATPase family member YFL008W|CHL10 gene taxon:4932 20010118 SGD
+SGD S000001886 SMC1 GO:0016887 SGD_REF:S000040742|PMID:7929577 ISS F SMC chromosomal ATPase family member YFL008W|CHL10 gene taxon:4932 20010118 SGD
+SGD S000001886 SMC1 GO:0000070 SGD_REF:S000041136|PMID:8276886 IMP P SMC chromosomal ATPase family member YFL008W|CHL10 gene taxon:4932 20010118 SGD
+SGD S000001886 SMC1 GO:0006302 SGD_REF:S000076782|PMID:15280507 IMP P SMC chromosomal ATPase family member YFL008W|CHL10 gene taxon:4932 20050121 SGD
+SGD S000001886 SMC1 GO:0007064 SGD_REF:S000054345|PMID:9335333 IMP P SMC chromosomal ATPase family member YFL008W|CHL10 gene taxon:4932 20040610 SGD
+SGD S000001927 SMC2 GO:0000799 SGD_REF:S000046263|PMID:7698648 IPI C SMC chromosomal ATPase family member, similar to ScII (chicken), XCAPE (xenopus), and cut14 (S. pombe) YFR031C gene taxon:4932 20010118 SGD
+SGD S000001927 SMC2 GO:0000799 SGD_REF:S000046263|PMID:7698648 ISS C SMC chromosomal ATPase family member, similar to ScII (chicken), XCAPE (xenopus), and cut14 (S. pombe) YFR031C gene taxon:4932 20010118 SGD
+SGD S000001927 SMC2 GO:0000799 SGD_REF:S000040443|PMID:10811823 TAS C SMC chromosomal ATPase family member, similar to ScII (chicken), XCAPE (xenopus), and cut14 (S. pombe) YFR031C gene taxon:4932 20010118 SGD
+SGD S000001927 SMC2 GO:0000799 SGD_REF:S000058398|PMID:9887095 TAS C SMC chromosomal ATPase family member, similar to ScII (chicken), XCAPE (xenopus), and cut14 (S. pombe) YFR031C gene taxon:4932 20010118 SGD
+SGD S000001927 SMC2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C SMC chromosomal ATPase family member, similar to ScII (chicken), XCAPE (xenopus), and cut14 (S. pombe) YFR031C gene taxon:4932 20040928 SGD
+SGD S000001927 SMC2 GO:0000217 SGD_REF:S000039938|PMID:9727028 IDA F SMC chromosomal ATPase family member, similar to ScII (chicken), XCAPE (xenopus), and cut14 (S. pombe) YFR031C gene taxon:4932 20010118 SGD
+SGD S000001927 SMC2 GO:0003680 SGD_REF:S000039938|PMID:9727028 IDA F SMC chromosomal ATPase family member, similar to ScII (chicken), XCAPE (xenopus), and cut14 (S. pombe) YFR031C gene taxon:4932 20010118 SGD
+SGD S000001927 SMC2 GO:0003690 SGD_REF:S000039938|PMID:9727028 IDA F SMC chromosomal ATPase family member, similar to ScII (chicken), XCAPE (xenopus), and cut14 (S. pombe) YFR031C gene taxon:4932 20010118 SGD
+SGD S000001927 SMC2 GO:0016887 SGD_REF:S000039938|PMID:9727028 IDA F SMC chromosomal ATPase family member, similar to ScII (chicken), XCAPE (xenopus), and cut14 (S. pombe) YFR031C gene taxon:4932 20010118 SGD
+SGD S000001927 SMC2 GO:0000070 SGD_REF:S000058398|PMID:9887095 TAS P SMC chromosomal ATPase family member, similar to ScII (chicken), XCAPE (xenopus), and cut14 (S. pombe) YFR031C gene taxon:4932 20010118 SGD
+SGD S000001927 SMC2 GO:0007076 SGD_REF:S000040443|PMID:10811823 IMP P SMC chromosomal ATPase family member, similar to ScII (chicken), XCAPE (xenopus), and cut14 (S. pombe) YFR031C gene taxon:4932 20010118 SGD
+SGD S000001927 SMC2 GO:0007076 SGD_REF:S000058398|PMID:9887095 TAS P SMC chromosomal ATPase family member, similar to ScII (chicken), XCAPE (xenopus), and cut14 (S. pombe) YFR031C gene taxon:4932 20010118 SGD
+SGD S000001927 SMC2 GO:0007076 SGD_REF:S000046263|PMID:7698648 IMP P SMC chromosomal ATPase family member, similar to ScII (chicken), XCAPE (xenopus), and cut14 (S. pombe) YFR031C gene taxon:4932 20010118 SGD
+SGD S000003610 SMC3 GO:0000798 SGD_REF:S000058398|PMID:9887095 TAS C SMC chromosomal ATPase family member YJL074C gene taxon:4932 20010118 SGD
+SGD S000003610 SMC3 GO:0005634 SGD_REF:S000077144|PMID:15282802 IDA C SMC chromosomal ATPase family member YJL074C gene taxon:4932 20041008 SGD
+SGD S000003610 SMC3 GO:0016887 SGD_REF:S000058398|PMID:9887095 ISS F SMC chromosomal ATPase family member YJL074C gene taxon:4932 20010118 SGD
+SGD S000003610 SMC3 GO:0007064 SGD_REF:S000058398|PMID:9887095 TAS P SMC chromosomal ATPase family member YJL074C gene taxon:4932 20010118 SGD
+SGD S000003610 SMC3 GO:0007064 SGD_REF:S000054345|PMID:9335333 IMP P SMC chromosomal ATPase family member YJL074C gene taxon:4932 20040610 SGD
+SGD S000003610 SMC3 GO:0007130 SGD_REF:S000055468|PMID:10412984 IMP P SMC chromosomal ATPase family member YJL074C gene taxon:4932 20010118 SGD
+SGD S000003610 SMC3 GO:0030437 SGD_REF:S000055468|PMID:10412984 IMP P SMC chromosomal ATPase family member YJL074C gene taxon:4932 20010118 SGD
+SGD S000004076 SMC4 GO:0000799 SGD_REF:S000040443|PMID:10811823 IPI C SMC chromosomal ATPase family member YLR086W gene taxon:4932 20010118 SGD
+SGD S000004076 SMC4 GO:0000799 SGD_REF:S000058398|PMID:9887095 TAS C SMC chromosomal ATPase family member YLR086W gene taxon:4932 20010118 SGD
+SGD S000004076 SMC4 GO:0003682 SGD_REF:S000069542|PMID:11864994 IGI SGD:S000000193|SGD:S000001927|SGD:S000004262|SGD:S000002733 F SMC chromosomal ATPase family member YLR086W gene taxon:4932 20050718 SGD
+SGD S000004076 SMC4 GO:0003682 SGD_REF:S000069542|PMID:11864994 IDA F SMC chromosomal ATPase family member YLR086W gene taxon:4932 20050718 SGD
+SGD S000004076 SMC4 GO:0016887 SGD_REF:S000058398|PMID:9887095 ISS F SMC chromosomal ATPase family member YLR086W gene taxon:4932 20010118 SGD
+SGD S000004076 SMC4 GO:0000070 SGD_REF:S000058398|PMID:9887095 TAS P SMC chromosomal ATPase family member YLR086W gene taxon:4932 20010118 SGD
+SGD S000004076 SMC4 GO:0007076 SGD_REF:S000040443|PMID:10811823 IMP P SMC chromosomal ATPase family member YLR086W gene taxon:4932 20010118 SGD
+SGD S000004076 SMC4 GO:0007076 SGD_REF:S000058398|PMID:9887095 TAS P SMC chromosomal ATPase family member YLR086W gene taxon:4932 20010118 SGD
+SGD S000005394 SMC5 GO:0005634 SGD_REF:S000069988|PMID:11927594 IDA C YOL034W gene taxon:4932 20020622 SGD
+SGD S000005394 SMC5 GO:0030915 SGD_REF:S000069988|PMID:11927594 IPI C YOL034W gene taxon:4932 20041025 SGD
+SGD S000005394 SMC5 GO:0030915 SGD_REF:S000080949|PMID:15738391 IPI SGD:S000000745|SGD:S000005394|SGD:S000004375 C YOL034W gene taxon:4932 20060309 SGD
+SGD S000005394 SMC5 GO:0005554 SGD_REF:S000069584 ND F YOL034W gene taxon:4932 20030108 SGD
+SGD S000005394 SMC5 GO:0006281 SGD_REF:S000069988|PMID:11927594 IDA P YOL034W gene taxon:4932 20020622 SGD
+SGD S000005394 SMC5 GO:0006281 SGD_REF:S000080949|PMID:15738391 IMP P YOL034W gene taxon:4932 20060309 SGD
+SGD S000005394 SMC5 GO:0008283 SGD_REF:S000069988|PMID:11927594 IDA P YOL034W gene taxon:4932 20020622 SGD
+SGD S000004375 SMC6 GO:0005634 SGD_REF:S000069988|PMID:11927594 IDA C YLR383W|RHC18 gene taxon:4932 20020622 SGD
+SGD S000004375 SMC6 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YLR383W|RHC18 gene taxon:4932 20040928 SGD
+SGD S000004375 SMC6 GO:0030915 SGD_REF:S000069988|PMID:11927594 IPI C YLR383W|RHC18 gene taxon:4932 20041025 SGD
+SGD S000004375 SMC6 GO:0030915 SGD_REF:S000080949|PMID:15738391 IPI SGD:S000000745|SGD:S000005394|SGD:S000004375 C YLR383W|RHC18 gene taxon:4932 20060309 SGD
+SGD S000004375 SMC6 GO:0005554 SGD_REF:S000069584 ND F YLR383W|RHC18 gene taxon:4932 20021216 SGD
+SGD S000004375 SMC6 GO:0006281 SGD_REF:S000069988|PMID:11927594 IDA P YLR383W|RHC18 gene taxon:4932 20020622 SGD
+SGD S000004375 SMC6 GO:0006281 SGD_REF:S000080949|PMID:15738391 IMP P YLR383W|RHC18 gene taxon:4932 20060309 SGD
+SGD S000004375 SMC6 GO:0008283 SGD_REF:S000069988|PMID:11927594 IDA P YLR383W|RHC18 gene taxon:4932 20020622 SGD
+SGD S000003306 SMD1 GO:0000243 SGD_REF:S000064189|PMID:10072386 IPI C YGR074W|SPP92|Sm D1 gene taxon:4932 20020729 SGD
+SGD S000003306 SMD1 GO:0005682 SGD_REF:S000066234|PMID:11720284 IPI C YGR074W|SPP92|Sm D1 gene taxon:4932 20051003 SGD
+SGD S000003306 SMD1 GO:0005685 SGD_REF:S000045702|PMID:9012791 IDA C YGR074W|SPP92|Sm D1 gene taxon:4932 20050922 SGD
+SGD S000003306 SMD1 GO:0005685 SGD_REF:S000044485|PMID:9630245 IDA C YGR074W|SPP92|Sm D1 gene taxon:4932 20050929 SGD
+SGD S000003306 SMD1 GO:0046540 SGD_REF:S000056376|PMID:10377396 IPI C YGR074W|SPP92|Sm D1 gene taxon:4932 20050219 SGD
+SGD S000003306 SMD1 GO:0046540 SGD_REF:S000039461|PMID:10449419 IDA C YGR074W|SPP92|Sm D1 gene taxon:4932 20050926 SGD
+SGD S000003306 SMD1 GO:0003729 SGD_REF:S000064189|PMID:10072386 IPI F YGR074W|SPP92|Sm D1 gene taxon:4932 20020729 SGD
+SGD S000003306 SMD1 contributes_to GO:0031202 SGD_REF:S000056376|PMID:10377396 IPI F YGR074W|SPP92|Sm D1 gene taxon:4932 20020620 SGD
+SGD S000003306 SMD1 contributes_to GO:0031202 SGD_REF:S000039461|PMID:10449419 IDA F YGR074W|SPP92|Sm D1 gene taxon:4932 20051003 SGD
+SGD S000003306 SMD1 GO:0000398 SGD_REF:S000056376|PMID:10377396 IPI P YGR074W|SPP92|Sm D1 gene taxon:4932 20020620 SGD
+SGD S000003306 SMD1 GO:0000398 SGD_REF:S000064189|PMID:10072386 IPI P YGR074W|SPP92|Sm D1 gene taxon:4932 20020729 SGD
+SGD S000004265 SMD2 GO:0005682 SGD_REF:S000066234|PMID:11720284 IPI C YLR275W|Sm D2 gene taxon:4932 20051003 SGD
+SGD S000004265 SMD2 GO:0005685 SGD_REF:S000045702|PMID:9012791 IDA C YLR275W|Sm D2 gene taxon:4932 20050922 SGD
+SGD S000004265 SMD2 GO:0005685 SGD_REF:S000044485|PMID:9630245 IDA C YLR275W|Sm D2 gene taxon:4932 20050929 SGD
+SGD S000004265 SMD2 GO:0046540 SGD_REF:S000056376|PMID:10377396 IPI C YLR275W|Sm D2 gene taxon:4932 20050219 SGD
+SGD S000004265 SMD2 GO:0046540 SGD_REF:S000039461|PMID:10449419 IDA C YLR275W|Sm D2 gene taxon:4932 20050926 SGD
+SGD S000004265 SMD2 contributes_to GO:0031202 SGD_REF:S000056376|PMID:10377396 IPI F YLR275W|Sm D2 gene taxon:4932 20020620 SGD
+SGD S000004265 SMD2 contributes_to GO:0031202 SGD_REF:S000039461|PMID:10449419 IDA F YLR275W|Sm D2 gene taxon:4932 20051003 SGD
+SGD S000004265 SMD2 GO:0000398 SGD_REF:S000056376|PMID:10377396 IPI P YLR275W|Sm D2 gene taxon:4932 20020620 SGD
+SGD S000004137 SMD3 GO:0000243 SGD_REF:S000064189|PMID:10072386 IPI C core snRNP protein YLR147C|SLT16|Sm D3 gene taxon:4932 20020729 SGD
+SGD S000004137 SMD3 GO:0005682 SGD_REF:S000066234|PMID:11720284 IPI C core snRNP protein YLR147C|SLT16|Sm D3 gene taxon:4932 20051003 SGD
+SGD S000004137 SMD3 GO:0005685 SGD_REF:S000045702|PMID:9012791 IDA C core snRNP protein YLR147C|SLT16|Sm D3 gene taxon:4932 20050922 SGD
+SGD S000004137 SMD3 GO:0005685 SGD_REF:S000044485|PMID:9630245 IDA C core snRNP protein YLR147C|SLT16|Sm D3 gene taxon:4932 20050929 SGD
+SGD S000004137 SMD3 GO:0046540 SGD_REF:S000056376|PMID:10377396 IPI C core snRNP protein YLR147C|SLT16|Sm D3 gene taxon:4932 20050219 SGD
+SGD S000004137 SMD3 GO:0046540 SGD_REF:S000039461|PMID:10449419 IDA C core snRNP protein YLR147C|SLT16|Sm D3 gene taxon:4932 20050926 SGD
+SGD S000004137 SMD3 GO:0003729 SGD_REF:S000064189|PMID:10072386 IPI F core snRNP protein YLR147C|SLT16|Sm D3 gene taxon:4932 20020729 SGD
+SGD S000004137 SMD3 contributes_to GO:0031202 SGD_REF:S000056376|PMID:10377396 IPI F core snRNP protein YLR147C|SLT16|Sm D3 gene taxon:4932 20020620 SGD
+SGD S000004137 SMD3 contributes_to GO:0031202 SGD_REF:S000039461|PMID:10449419 IDA F core snRNP protein YLR147C|SLT16|Sm D3 gene taxon:4932 20051003 SGD
+SGD S000004137 SMD3 GO:0000398 SGD_REF:S000056376|PMID:10377396 IPI P core snRNP protein YLR147C|SLT16|Sm D3 gene taxon:4932 20020620 SGD
+SGD S000004137 SMD3 GO:0000398 SGD_REF:S000064189|PMID:10072386 IPI P core snRNP protein YLR147C|SLT16|Sm D3 gene taxon:4932 20020729 SGD
+SGD S000005685 SME1 GO:0005682 SGD_REF:S000066234|PMID:11720284 IPI C human E core protein homolog YOR159C|Sm E|SmE gene taxon:4932 20051003 SGD
+SGD S000005685 SME1 GO:0005685 SGD_REF:S000045702|PMID:9012791 IDA C human E core protein homolog YOR159C|Sm E|SmE gene taxon:4932 20050922 SGD
+SGD S000005685 SME1 GO:0005685 SGD_REF:S000044485|PMID:9630245 IDA C human E core protein homolog YOR159C|Sm E|SmE gene taxon:4932 20050929 SGD
+SGD S000005685 SME1 GO:0046540 SGD_REF:S000056376|PMID:10377396 IPI C human E core protein homolog YOR159C|Sm E|SmE gene taxon:4932 20050219 SGD
+SGD S000005685 SME1 GO:0046540 SGD_REF:S000039461|PMID:10449419 IDA C human E core protein homolog YOR159C|Sm E|SmE gene taxon:4932 20050926 SGD
+SGD S000005685 SME1 contributes_to GO:0031202 SGD_REF:S000056376|PMID:10377396 IPI F human E core protein homolog YOR159C|Sm E|SmE gene taxon:4932 20020620 SGD
+SGD S000005685 SME1 contributes_to GO:0031202 SGD_REF:S000039461|PMID:10449419 IDA F human E core protein homolog YOR159C|Sm E|SmE gene taxon:4932 20051003 SGD
+SGD S000005685 SME1 GO:0000398 SGD_REF:S000056376|PMID:10377396 IPI P human E core protein homolog YOR159C|Sm E|SmE gene taxon:4932 20020620 SGD
+SGD S000029458 SME2 GO:0008372 SGD_REF:S000069584 ND C Unknown; stimulates meiosis and sporulation when overexpressed gene taxon:4932 20050722 SGD
+SGD S000029458 SME2 GO:0005554 SGD_REF:S000069584 ND F Unknown; stimulates meiosis and sporulation when overexpressed gene taxon:4932 20050722 SGD
+SGD S000029458 SME2 GO:0040020 SGD_REF:S000072297 IGI P Unknown; stimulates meiosis and sporulation when overexpressed gene taxon:4932 20030128 SGD
+SGD S000029459 SME3 GO:0008372 SGD_REF:S000069584 ND C Unknown; stimulates meiosis and sporulation when overexpressed gene taxon:4932 20050722 SGD
+SGD S000029459 SME3 GO:0005554 SGD_REF:S000069584 ND F Unknown; stimulates meiosis and sporulation when overexpressed gene taxon:4932 20050722 SGD
+SGD S000029459 SME3 GO:0040020 SGD_REF:S000072297 IGI P Unknown; stimulates meiosis and sporulation when overexpressed gene taxon:4932 20030128 SGD
+SGD S000005482 SMF1 GO:0000324 SGD_REF:S000041834|PMID:9988727 IDA C YOL122C|SBS1 gene taxon:4932 20010118 SGD
+SGD S000005482 SMF1 GO:0005886 SGD_REF:S000046253|PMID:8643535 IDA C YOL122C|SBS1 gene taxon:4932 20010118 SGD
+SGD S000005482 SMF1 GO:0005384 SGD_REF:S000046253|PMID:8643535 IMP F YOL122C|SBS1 gene taxon:4932 20010118 SGD
+SGD S000005482 SMF1 GO:0015082 SGD_REF:S000049618|PMID:10574989 IDA F YOL122C|SBS1 gene taxon:4932 20050510 SGD
+SGD S000005482 SMF1 GO:0006828 SGD_REF:S000046253|PMID:8643535 IMP P YOL122C|SBS1 gene taxon:4932 20010118 SGD
+SGD S000001092 SMF2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YHR050W gene taxon:4932 20040928 SGD
+SGD S000001092 SMF2 GO:0016023 SGD_REF:S000068752|PMID:11602606 IDA C YHR050W gene taxon:4932 20030127 SGD
+SGD S000001092 SMF2 GO:0005384 SGD_REF:S000041965|PMID:9360964 ISS F YHR050W gene taxon:4932 20010118 SGD
+SGD S000001092 SMF2 GO:0005384 SGD_REF:S000041965|PMID:9360964 IGI F YHR050W gene taxon:4932 20010118 SGD
+SGD S000001092 SMF2 GO:0015082 SGD_REF:S000049618|PMID:10574989 IDA F YHR050W gene taxon:4932 20050510 SGD
+SGD S000001092 SMF2 GO:0006828 SGD_REF:S000041965|PMID:9360964 IGI P YHR050W gene taxon:4932 20010118 SGD
+SGD S000001092 SMF2 GO:0006828 SGD_REF:S000041965|PMID:9360964 ISS P YHR050W gene taxon:4932 20010118 SGD
+SGD S000004024 SMF3 GO:0000329 SGD_REF:S000056446|PMID:11027260 IDA C Nramp homolog, SMF1 and SMF2 homolog, metal transporter (putative) YLR034C gene taxon:4932 20020708 SGD
+SGD S000004024 SMF3 GO:0005381 SGD_REF:S000069965|PMID:12051835 TAS F Nramp homolog, SMF1 and SMF2 homolog, metal transporter (putative) YLR034C gene taxon:4932 20020709 SGD
+SGD S000004024 SMF3 GO:0006880 SGD_REF:S000056446|PMID:11027260 IMP P Nramp homolog, SMF1 and SMF2 homolog, metal transporter (putative) YLR034C gene taxon:4932 20020708 SGD
+SGD S000003461 SMI1 GO:0005634 SGD_REF:S000046559|PMID:10206705 IDA C 57 kDa nuclear protein YGR229C|KNR4 gene taxon:4932 20020405 SGD
+SGD S000003461 SMI1 GO:0005934 SGD_REF:S000046559|PMID:10206705 TAS C 57 kDa nuclear protein YGR229C|KNR4 gene taxon:4932 20020405 SGD
+SGD S000003461 SMI1 GO:0005554 SGD_REF:S000069584 ND F 57 kDa nuclear protein YGR229C|KNR4 gene taxon:4932 20021113 SGD
+SGD S000003461 SMI1 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P 57 kDa nuclear protein YGR229C|KNR4 gene taxon:4932 20060214 SGD
+SGD S000003461 SMI1 GO:0006075 SGD_REF:S000048868|PMID:8289782 TAS P 57 kDa nuclear protein YGR229C|KNR4 gene taxon:4932 20020405 SGD
+SGD S000003461 SMI1 GO:0007047 SGD_REF:S000048868|PMID:8289782 TAS P 57 kDa nuclear protein YGR229C|KNR4 gene taxon:4932 20020405 SGD
+SGD S000006258 SMK1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C MAP kinase YPR054W gene taxon:4932 20040813 SGD
+SGD S000006258 SMK1 GO:0004707 SGD_REF:S000050827|PMID:7958885 ISS F MAP kinase YPR054W gene taxon:4932 20021001 SGD
+SGD S000006258 SMK1 GO:0006468 SGD_REF:S000050827|PMID:7958885 ISS P MAP kinase YPR054W gene taxon:4932 20021001 SGD
+SGD S000006258 SMK1 GO:0030476 SGD_REF:S000050827|PMID:7958885 IMP P MAP kinase YPR054W gene taxon:4932 20021001 SGD
+SGD S000004523 SML1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YML058W gene taxon:4932 20031028 SGD
+SGD S000004523 SML1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YML058W gene taxon:4932 20031028 SGD
+SGD S000004523 SML1 GO:0004857 SGD_REF:S000070046|PMID:11953437 TAS F YML058W gene taxon:4932 20021001 SGD
+SGD S000004523 SML1 GO:0006974 SGD_REF:S000039565|PMID:9774971 IMP P YML058W gene taxon:4932 20010118 SGD
+SGD S000004523 SML1 GO:0007005 SGD_REF:S000039565|PMID:9774971 IMP P YML058W gene taxon:4932 20010118 SGD
+SGD S000005298 SMM1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C tRNA dihydrouridine synthase YNR015W|DUS2 gene taxon:4932 20031028 SGD
+SGD S000005298 SMM1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C tRNA dihydrouridine synthase YNR015W|DUS2 gene taxon:4932 20031028 SGD
+SGD S000005298 SMM1 GO:0017150 SGD_REF:S000072844|PMID:12003496 IDA F tRNA dihydrouridine synthase YNR015W|DUS2 gene taxon:4932 20021001 SGD
+SGD S000005298 SMM1 GO:0006400 SGD_REF:S000072844|PMID:12003496 IDA P tRNA dihydrouridine synthase YNR015W|DUS2 gene taxon:4932 20021001 SGD
+SGD S000005298 SMM1 GO:0008033 SGD_REF:S000072474|PMID:12559567 IGI P tRNA dihydrouridine synthase YNR015W|DUS2 gene taxon:4932 20030213 SGD
+SGD S000000386 SMP1 GO:0005634 SGD_REF:S000072486|PMID:12482976 IDA C YBR182C gene taxon:4932 20030218 SGD
+SGD S000000386 SMP1 GO:0005737 SGD_REF:S000072486|PMID:12482976 IDA C YBR182C gene taxon:4932 20030218 SGD
+SGD S000000386 SMP1 GO:0003700 SGD_REF:S000051198|PMID:9121433 ISS F YBR182C gene taxon:4932 20020827 SGD
+SGD S000000386 SMP1 GO:0003700 SGD_REF:S000051198|PMID:9121433 IPI F YBR182C gene taxon:4932 20020827 SGD
+SGD S000000386 SMP1 GO:0008301 SGD_REF:S000061714|PMID:10064699 IDA F YBR182C gene taxon:4932 20020827 SGD
+SGD S000000386 SMP1 GO:0045944 SGD_REF:S000072486|PMID:12482976 IGI P YBR182C gene taxon:4932 20030218 SGD
+SGD S000000386 SMP1 GO:0045944 SGD_REF:S000072486|PMID:12482976 ISS P YBR182C gene taxon:4932 20030218 SGD
+SGD S000000386 SMP1 GO:0045944 SGD_REF:S000072486|PMID:12482976 IMP P YBR182C gene taxon:4932 20030218 SGD
+SGD S000000386 SMP1 GO:0047484 SGD_REF:S000072486|PMID:12482976 IMP P YBR182C gene taxon:4932 20050513 SGD
+SGD S000000386 SMP1 GO:0047484 SGD_REF:S000072486|PMID:12482976 IGI SGD:S000004103 P YBR182C gene taxon:4932 20050513 SGD
+SGD S000005675 SMP3 GO:0005783 SGD_REF:S000060996|PMID:11356840 TAS C alpha 1,2 mannosyltransferase YOR149C|LAS2|SAP2 gene taxon:4932 20040419 SGD
+SGD S000005675 SMP3 GO:0000026 SGD_REF:S000060996|PMID:11356840 IMP F alpha 1,2 mannosyltransferase YOR149C|LAS2|SAP2 gene taxon:4932 20040419 SGD
+SGD S000005675 SMP3 GO:0006276 SGD_REF:S000042476|PMID:2005867 IMP P alpha 1,2 mannosyltransferase YOR149C|LAS2|SAP2 gene taxon:4932 20010118 SGD
+SGD S000005675 SMP3 GO:0006506 SGD_REF:S000060996|PMID:11356840 IMP P alpha 1,2 mannosyltransferase YOR149C|LAS2|SAP2 gene taxon:4932 20040419 SGD
+SGD S000002918 SMT3 GO:0005634 SGD_REF:S000049722|PMID:10364461 IDA C YDR510W gene taxon:4932 20020404 SGD
+SGD S000002918 SMT3 GO:0005634 SGD_REF:S000039641|PMID:10579719 IDA C YDR510W gene taxon:4932 20020404 SGD
+SGD S000002918 SMT3 GO:0005940 SGD_REF:S000049722|PMID:10364461 IDA C YDR510W gene taxon:4932 20020404 SGD
+SGD S000002918 SMT3 GO:0005940 SGD_REF:S000039641|PMID:10579719 IDA C YDR510W gene taxon:4932 20020404 SGD
+SGD S000002918 SMT3 GO:0031386 SGD_REF:S000039641|PMID:10579719 IDA F YDR510W gene taxon:4932 20050525 SGD
+SGD S000002918 SMT3 GO:0031386 SGD_REF:S000065162|PMID:9019411 ISS F YDR510W gene taxon:4932 20050525 SGD
+SGD S000002918 SMT3 GO:0031386 SGD_REF:S000049722|PMID:10364461 IDA F YDR510W gene taxon:4932 20050525 SGD
+SGD S000002918 SMT3 GO:0016925 SGD_REF:S000068983|PMID:11595179 TAS P YDR510W gene taxon:4932 20020404 SGD
+SGD S000002965 SMX2 GO:0005682 SGD_REF:S000066234|PMID:11720284 IPI C snRNP G protein (human Sm-G homolog) YFL017W-A|SNP2|Sm G|SmG|YFL018W-A gene taxon:4932 20051003 SGD
+SGD S000002965 SMX2 GO:0005685 SGD_REF:S000045702|PMID:9012791 IDA C snRNP G protein (human Sm-G homolog) YFL017W-A|SNP2|Sm G|SmG|YFL018W-A gene taxon:4932 20050922 SGD
+SGD S000002965 SMX2 GO:0005685 SGD_REF:S000044485|PMID:9630245 IDA C snRNP G protein (human Sm-G homolog) YFL017W-A|SNP2|Sm G|SmG|YFL018W-A gene taxon:4932 20050929 SGD
+SGD S000002965 SMX2 GO:0046540 SGD_REF:S000056376|PMID:10377396 IPI C snRNP G protein (human Sm-G homolog) YFL017W-A|SNP2|Sm G|SmG|YFL018W-A gene taxon:4932 20050219 SGD
+SGD S000002965 SMX2 GO:0046540 SGD_REF:S000039461|PMID:10449419 IDA C snRNP G protein (human Sm-G homolog) YFL017W-A|SNP2|Sm G|SmG|YFL018W-A gene taxon:4932 20050926 SGD
+SGD S000002965 SMX2 contributes_to GO:0031202 SGD_REF:S000056376|PMID:10377396 IPI F snRNP G protein (human Sm-G homolog) YFL017W-A|SNP2|Sm G|SmG|YFL018W-A gene taxon:4932 20020620 SGD
+SGD S000002965 SMX2 contributes_to GO:0031202 SGD_REF:S000039461|PMID:10449419 IDA F snRNP G protein (human Sm-G homolog) YFL017W-A|SNP2|Sm G|SmG|YFL018W-A gene taxon:4932 20051003 SGD
+SGD S000002965 SMX2 GO:0000398 SGD_REF:S000056376|PMID:10377396 IPI P snRNP G protein (human Sm-G homolog) YFL017W-A|SNP2|Sm G|SmG|YFL018W-A gene taxon:4932 20020620 SGD
+SGD S000006386 SMX3 GO:0005682 SGD_REF:S000066234|PMID:11720284 IPI C snRNP protein YPR182W|Sm F|SmF gene taxon:4932 20051003 SGD
+SGD S000006386 SMX3 GO:0005685 SGD_REF:S000045702|PMID:9012791 IDA C snRNP protein YPR182W|Sm F|SmF gene taxon:4932 20050922 SGD
+SGD S000006386 SMX3 GO:0005685 SGD_REF:S000044485|PMID:9630245 IDA C snRNP protein YPR182W|Sm F|SmF gene taxon:4932 20050929 SGD
+SGD S000006386 SMX3 GO:0046540 SGD_REF:S000056376|PMID:10377396 IPI C snRNP protein YPR182W|Sm F|SmF gene taxon:4932 20050219 SGD
+SGD S000006386 SMX3 GO:0046540 SGD_REF:S000039461|PMID:10449419 IDA C snRNP protein YPR182W|Sm F|SmF gene taxon:4932 20050926 SGD
+SGD S000006386 SMX3 contributes_to GO:0031202 SGD_REF:S000056376|PMID:10377396 IPI F snRNP protein YPR182W|Sm F|SmF gene taxon:4932 20020620 SGD
+SGD S000006386 SMX3 contributes_to GO:0031202 SGD_REF:S000039461|PMID:10449419 IDA F snRNP protein YPR182W|Sm F|SmF gene taxon:4932 20051003 SGD
+SGD S000006386 SMX3 GO:0000398 SGD_REF:S000056376|PMID:10377396 IPI P snRNP protein YPR182W|Sm F|SmF gene taxon:4932 20020620 SGD
+SGD S000001562 SMY1 GO:0005934 SGD_REF:S000048949|PMID:9472039 IDA C kinesin heavy chain homolog YKL079W gene taxon:4932 20010118 SGD
+SGD S000001562 SMY1 GO:0005935 SGD_REF:S000058447|PMID:9153752 TAS C kinesin heavy chain homolog YKL079W gene taxon:4932 20010118 SGD
+SGD S000001562 SMY1 GO:0003774 SGD_REF:S000048949|PMID:9472039 ISS F kinesin heavy chain homolog YKL079W gene taxon:4932 20010118 SGD
+SGD S000001562 SMY1 GO:0006887 SGD_REF:S000048949|PMID:9472039 IGI P kinesin heavy chain homolog YKL079W gene taxon:4932 20010118 SGD
+SGD S000000376 SMY2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YBR172C gene taxon:4932 20031028 SGD
+SGD S000000376 SMY2 GO:0005554 SGD_REF:S000069584 ND F YBR172C gene taxon:4932 20010119 SGD
+SGD S000000376 SMY2 GO:0007010 SGD_REF:S000052143|PMID:10924454 TAS P YBR172C gene taxon:4932 20030131 SGD
+SGD S000007236 SNA2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDR525W-A gene taxon:4932 20031028 SGD
+SGD S000007236 SNA2 GO:0016021 SGD_REF:S000072825|PMID:12524434 ISS C YDR525W-A gene taxon:4932 20030409 SGD
+SGD S000007236 SNA2 GO:0005554 SGD_REF:S000069584 ND F YDR525W-A gene taxon:4932 20021018 SGD
+SGD S000007236 SNA2 GO:0000004 SGD_REF:S000069584 ND P YDR525W-A gene taxon:4932 20021018 SGD
+SGD S000003687 SNA3 GO:0000328 SGD_REF:S000072757|PMID:12499386 IDA C YJL151C gene taxon:4932 20030325 SGD
+SGD S000003687 SNA3 GO:0016020 SGD_REF:S000065939|PMID:11566881 IDA C YJL151C gene taxon:4932 20021010 SGD
+SGD S000003687 SNA3 GO:0005554 SGD_REF:S000069584 ND F YJL151C gene taxon:4932 20021010 SGD
+SGD S000003687 SNA3 GO:0000004 SGD_REF:S000069584 ND P YJL151C gene taxon:4932 20021010 SGD
+SGD S000002281 SNA4 GO:0000329 SGD_REF:S000065939|PMID:11566881 IDA C YDL123W gene taxon:4932 20021018 SGD
+SGD S000002281 SNA4 GO:0005554 SGD_REF:S000069584 ND F YDL123W gene taxon:4932 20021018 SGD
+SGD S000002281 SNA4 GO:0000004 SGD_REF:S000069584 ND P YDL123W gene taxon:4932 20021018 SGD
+SGD S000000028 SNC1 GO:0030133 SGD_REF:S000049383|PMID:9195971 IDA C Snc2p homolog, synaptobrevin homolog YAL030W gene taxon:4932 20020823 SGD
+SGD S000000028 SNC1 GO:0031201 SGD_REF:S000058139|PMID:9195974 IDA C Snc2p homolog, synaptobrevin homolog YAL030W gene taxon:4932 20060531 SGD
+SGD S000000028 SNC1 GO:0005485 SGD_REF:S000058453|PMID:10047442 TAS F Snc2p homolog, synaptobrevin homolog YAL030W gene taxon:4932 20010118 SGD
+SGD S000000028 SNC1 GO:0006893 SGD_REF:S000058453|PMID:10047442 TAS P Snc2p homolog, synaptobrevin homolog YAL030W gene taxon:4932 20010118 SGD
+SGD S000000028 SNC1 GO:0006897 SGD_REF:S000058453|PMID:10047442 TAS P Snc2p homolog, synaptobrevin homolog YAL030W gene taxon:4932 20010118 SGD
+SGD S000000028 SNC1 GO:0006897 SGD_REF:S000059602|PMID:11029060 IMP P Snc2p homolog, synaptobrevin homolog YAL030W gene taxon:4932 20050614 SGD
+SGD S000000028 SNC1 GO:0006906 SGD_REF:S000058453|PMID:10047442 TAS P Snc2p homolog, synaptobrevin homolog YAL030W gene taxon:4932 20010118 SGD
+SGD S000005854 SNC2 GO:0030133 SGD_REF:S000049383|PMID:9195971 TAS C vesicle-associated membrane protein (synaptobrevin) homolog YOR327C gene taxon:4932 20020823 SGD
+SGD S000005854 SNC2 GO:0005485 SGD_REF:S000058453|PMID:10047442 TAS F vesicle-associated membrane protein (synaptobrevin) homolog YOR327C gene taxon:4932 20010118 SGD
+SGD S000005854 SNC2 GO:0005485 SGD_REF:S000076087|PMID:14981247 IDA F vesicle-associated membrane protein (synaptobrevin) homolog YOR327C gene taxon:4932 20050614 SGD
+SGD S000005854 SNC2 GO:0006893 SGD_REF:S000058453|PMID:10047442 TAS P vesicle-associated membrane protein (synaptobrevin) homolog YOR327C gene taxon:4932 20010118 SGD
+SGD S000005854 SNC2 GO:0006897 SGD_REF:S000058453|PMID:10047442 TAS P vesicle-associated membrane protein (synaptobrevin) homolog YOR327C gene taxon:4932 20010118 SGD
+SGD S000005854 SNC2 GO:0006906 SGD_REF:S000058453|PMID:10047442 TAS P vesicle-associated membrane protein (synaptobrevin) homolog YOR327C gene taxon:4932 20010118 SGD
+SGD S000002885 SNF1 GO:0000324 SGD_REF:S000060188|PMID:11331606 IPI C serine/threonine kinase YDR477W|CAT1|CCR1|GLC2|HAF3|PAS14 gene taxon:4932 20021202 SGD
+SGD S000002885 SNF1 GO:0005634 SGD_REF:S000060188|PMID:11331606 IPI C serine/threonine kinase YDR477W|CAT1|CCR1|GLC2|HAF3|PAS14 gene taxon:4932 20021202 SGD
+SGD S000002885 SNF1 GO:0005737 SGD_REF:S000060188|PMID:11331606 IPI C serine/threonine kinase YDR477W|CAT1|CCR1|GLC2|HAF3|PAS14 gene taxon:4932 20021202 SGD
+SGD S000002885 SNF1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C serine/threonine kinase YDR477W|CAT1|CCR1|GLC2|HAF3|PAS14 gene taxon:4932 20040813 SGD
+SGD S000002885 SNF1 GO:0004679 SGD_REF:S000066184|PMID:11486005 IDA F serine/threonine kinase YDR477W|CAT1|CCR1|GLC2|HAF3|PAS14 gene taxon:4932 20021202 SGD
+SGD S000002885 SNF1 GO:0001302 SGD_REF:S000049850|PMID:10921902 IDA P serine/threonine kinase YDR477W|CAT1|CCR1|GLC2|HAF3|PAS14 gene taxon:4932 20050323 SGD
+SGD S000002885 SNF1 GO:0006006 SGD_REF:S000048626|PMID:10322167 TAS P serine/threonine kinase YDR477W|CAT1|CCR1|GLC2|HAF3|PAS14 gene taxon:4932 20021202 SGD
+SGD S000002885 SNF1 GO:0006109 SGD_REF:S000071682|PMID:12167649 IGI P serine/threonine kinase YDR477W|CAT1|CCR1|GLC2|HAF3|PAS14 gene taxon:4932 20030402 SGD
+SGD S000002885 SNF1 GO:0006109 SGD_REF:S000071682|PMID:12167649 TAS P serine/threonine kinase YDR477W|CAT1|CCR1|GLC2|HAF3|PAS14 gene taxon:4932 20030402 SGD
+SGD S000002885 SNF1 GO:0006109 SGD_REF:S000071682|PMID:12167649 IPI P serine/threonine kinase YDR477W|CAT1|CCR1|GLC2|HAF3|PAS14 gene taxon:4932 20030402 SGD
+SGD S000002885 SNF1 GO:0006468 SGD_REF:S000066184|PMID:11486005 IDA P serine/threonine kinase YDR477W|CAT1|CCR1|GLC2|HAF3|PAS14 gene taxon:4932 20021202 SGD
+SGD S000002885 SNF1 GO:0006995 SGD_REF:S000070028|PMID:12024013 IDA P serine/threonine kinase YDR477W|CAT1|CCR1|GLC2|HAF3|PAS14 gene taxon:4932 20020815 SGD
+SGD S000002885 SNF1 GO:0007155 SGD_REF:S000072732|PMID:12556493 IMP P serine/threonine kinase YDR477W|CAT1|CCR1|GLC2|HAF3|PAS14 gene taxon:4932 20030313 SGD
+SGD S000002885 SNF1 GO:0007165 SGD_REF:S000048626|PMID:10322167 TAS P serine/threonine kinase YDR477W|CAT1|CCR1|GLC2|HAF3|PAS14 gene taxon:4932 20021202 SGD
+SGD S000002885 SNF1 GO:0030447 SGD_REF:S000072732|PMID:12556493 IMP P serine/threonine kinase YDR477W|CAT1|CCR1|GLC2|HAF3|PAS14 gene taxon:4932 20030313 SGD
+SGD S000002480 SNF11 GO:0016514 SGD_REF:S000043500|PMID:9726966 TAS C SWI/SNF global transcription activator complex component YDR073W gene taxon:4932 20030513 SGD
+SGD S000002480 SNF11 GO:0016585 SGD_REF:S000058455|PMID:9048886 TAS C SWI/SNF global transcription activator complex component YDR073W gene taxon:4932 20010118 SGD
+SGD S000002480 SNF11 GO:0016251 SGD_REF:S000058455|PMID:9048886 TAS F SWI/SNF global transcription activator complex component YDR073W gene taxon:4932 20020528 SGD
+SGD S000002480 SNF11 GO:0006338 SGD_REF:S000058455|PMID:9048886 TAS P SWI/SNF global transcription activator complex component YDR073W gene taxon:4932 20010118 SGD
+SGD S000005306 SNF12 GO:0016514 SGD_REF:S000043500|PMID:9726966 TAS C RSC chromatin remodeling complex Rsc6p subunit homolog, SWI/SNF transcription activation complex 73 kDa subunit YNR023W|SWP73 gene taxon:4932 20030513 SGD
+SGD S000005306 SNF12 GO:0016585 SGD_REF:S000058455|PMID:9048886 TAS C RSC chromatin remodeling complex Rsc6p subunit homolog, SWI/SNF transcription activation complex 73 kDa subunit YNR023W|SWP73 gene taxon:4932 20010118 SGD
+SGD S000005306 SNF12 GO:0016251 SGD_REF:S000058455|PMID:9048886 TAS F RSC chromatin remodeling complex Rsc6p subunit homolog, SWI/SNF transcription activation complex 73 kDa subunit YNR023W|SWP73 gene taxon:4932 20020528 SGD
+SGD S000005306 SNF12 GO:0006338 SGD_REF:S000058455|PMID:9048886 TAS P RSC chromatin remodeling complex Rsc6p subunit homolog, SWI/SNF transcription activation complex 73 kDa subunit YNR023W|SWP73 gene taxon:4932 20010118 SGD
+SGD S000005816 SNF2 GO:0016514 SGD_REF:S000043500|PMID:9726966 TAS C transcriptional regulator YOR290C|GAM1|HAF1|SWI2|TYE3 gene taxon:4932 20030513 SGD
+SGD S000005816 SNF2 GO:0016585 SGD_REF:S000058455|PMID:9048886 TAS C transcriptional regulator YOR290C|GAM1|HAF1|SWI2|TYE3 gene taxon:4932 20010118 SGD
+SGD S000005816 SNF2 GO:0008094 SGD_REF:S000047100|PMID:8458575 IDA F transcriptional regulator YOR290C|GAM1|HAF1|SWI2|TYE3 gene taxon:4932 20060327 SGD
+SGD S000005816 SNF2 GO:0008094 SGD_REF:S000047100|PMID:8458575 IMP F transcriptional regulator YOR290C|GAM1|HAF1|SWI2|TYE3 gene taxon:4932 20060327 SGD
+SGD S000005816 SNF2 GO:0016251 SGD_REF:S000058455|PMID:9048886 TAS F transcriptional regulator YOR290C|GAM1|HAF1|SWI2|TYE3 gene taxon:4932 20020528 SGD
+SGD S000005816 SNF2 GO:0006338 SGD_REF:S000058455|PMID:9048886 TAS P transcriptional regulator YOR290C|GAM1|HAF1|SWI2|TYE3 gene taxon:4932 20010118 SGD
+SGD S000002353 SNF3 GO:0005886 SGD_REF:S000047106|PMID:2406560 IDA C glucose sensor YDL194W gene taxon:4932 20021002 SGD
+SGD S000002353 SNF3 GO:0004872 SGD_REF:S000045421|PMID:10477308 TAS F glucose sensor YDL194W gene taxon:4932 20021204 SGD
+SGD S000002353 SNF3 NOT GO:0005355 SGD_REF:S000045421|PMID:10477308 TAS F glucose sensor YDL194W gene taxon:4932 20021204 SGD
+SGD S000002353 SNF3 GO:0005536 SGD_REF:S000045421|PMID:10477308 TAS F glucose sensor YDL194W gene taxon:4932 20021204 SGD
+SGD S000002353 SNF3 GO:0007165 SGD_REF:S000045421|PMID:10477308 TAS P glucose sensor YDL194W gene taxon:4932 20021204 SGD
+SGD S000002353 SNF3 GO:0009749 SGD_REF:S000046235|PMID:8901598 IMP P glucose sensor YDL194W gene taxon:4932 20021003 SGD
+SGD S000003083 SNF4 GO:0005634 SGD_REF:S000046049|PMID:2481228 IDA C associates with Snf1p YGL115W|CAT3|SCI1 gene taxon:4932 20020806 SGD
+SGD S000003083 SNF4 GO:0005737 SGD_REF:S000046049|PMID:2481228 IDA C associates with Snf1p YGL115W|CAT3|SCI1 gene taxon:4932 20020806 SGD
+SGD S000003083 SNF4 GO:0005886 SGD_REF:S000072977|PMID:12562756 IDA C associates with Snf1p YGL115W|CAT3|SCI1 gene taxon:4932 20030425 SGD
+SGD S000003083 SNF4 GO:0030295 SGD_REF:S000053604|PMID:2557546 IGI F associates with Snf1p YGL115W|CAT3|SCI1 gene taxon:4932 20020806 SGD
+SGD S000003083 SNF4 GO:0006357 SGD_REF:S000053604|PMID:2557546 IGI P associates with Snf1p YGL115W|CAT3|SCI1 gene taxon:4932 20020806 SGD
+SGD S000003083 SNF4 GO:0007031 SGD_REF:S000047076|PMID:1355328 IMP P associates with Snf1p YGL115W|CAT3|SCI1 gene taxon:4932 20020806 SGD
+SGD S000000493 SNF5 GO:0016514 SGD_REF:S000043500|PMID:9726966 TAS C chromatin remodeling Snf/Swi complex subunit YBR289W|HAF4|SWI10|TYE4 gene taxon:4932 20030513 SGD
+SGD S000000493 SNF5 GO:0016585 SGD_REF:S000058455|PMID:9048886 TAS C chromatin remodeling Snf/Swi complex subunit YBR289W|HAF4|SWI10|TYE4 gene taxon:4932 20010118 SGD
+SGD S000000493 SNF5 GO:0016251 SGD_REF:S000058455|PMID:9048886 TAS F chromatin remodeling Snf/Swi complex subunit YBR289W|HAF4|SWI10|TYE4 gene taxon:4932 20020528 SGD
+SGD S000000493 SNF5 GO:0006338 SGD_REF:S000058455|PMID:9048886 TAS P chromatin remodeling Snf/Swi complex subunit YBR289W|HAF4|SWI10|TYE4 gene taxon:4932 20010118 SGD
+SGD S000001017 SNF6 GO:0016514 SGD_REF:S000043500|PMID:9726966 TAS C chromatin remodeling Snf/Swi complex subunit YHL025W gene taxon:4932 20030513 SGD
+SGD S000001017 SNF6 GO:0016585 SGD_REF:S000058455|PMID:9048886 TAS C chromatin remodeling Snf/Swi complex subunit YHL025W gene taxon:4932 20010118 SGD
+SGD S000001017 SNF6 GO:0016251 SGD_REF:S000058455|PMID:9048886 TAS F chromatin remodeling Snf/Swi complex subunit YHL025W gene taxon:4932 20020528 SGD
+SGD S000001017 SNF6 GO:0006338 SGD_REF:S000058455|PMID:9048886 TAS P chromatin remodeling Snf/Swi complex subunit YHL025W gene taxon:4932 20010118 SGD
+SGD S000004015 SNF7 GO:0000815 SGD_REF:S000071351|PMID:12194857 IDA C YLR025W|DID1|VPS32 gene taxon:4932 20040701 SGD
+SGD S000004015 SNF7 GO:0005737 SGD_REF:S000044124|PMID:9606181 IDA C YLR025W|DID1|VPS32 gene taxon:4932 20020826 SGD
+SGD S000004015 SNF7 GO:0005515 SGD_REF:S000071351|PMID:12194857 IDA F YLR025W|DID1|VPS32 gene taxon:4932 20060301 SGD
+SGD S000004015 SNF7 GO:0005515 SGD_REF:S000075969|PMID:15086794 IDA F YLR025W|DID1|VPS32 gene taxon:4932 20060301 SGD
+SGD S000004015 SNF7 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P YLR025W|DID1|VPS32 gene taxon:4932 20060209 SGD
+SGD S000004015 SNF7 GO:0043162 SGD_REF:S000075969|PMID:15086794 IC GO:0000815 P YLR025W|DID1|VPS32 gene taxon:4932 20050125 SGD
+SGD S000004015 SNF7 GO:0045324 SGD_REF:S000044124|PMID:9606181 IMP P YLR025W|DID1|VPS32 gene taxon:4932 20020826 SGD
+SGD S000005923 SNF8 GO:0000814 SGD_REF:S000071345|PMID:12194858 IDA C YPL002C|VPS22 gene taxon:4932 20040701 SGD
+SGD S000005923 SNF8 GO:0005515 SGD_REF:S000075969|PMID:15086794 IDA F YPL002C|VPS22 gene taxon:4932 20060202 SGD
+SGD S000005923 SNF8 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P YPL002C|VPS22 gene taxon:4932 20060209 SGD
+SGD S000005923 SNF8 GO:0006623 SGD_REF:S000071345|PMID:12194858 IMP P YPL002C|VPS22 gene taxon:4932 20021001 SGD
+SGD S000005923 SNF8 GO:0006623 SGD_REF:S000071345|PMID:12194858 IPI P YPL002C|VPS22 gene taxon:4932 20021001 SGD
+SGD S000005923 SNF8 GO:0043162 SGD_REF:S000075969|PMID:15086794 IC GO:0000814 P YPL002C|VPS22 gene taxon:4932 20050125 SGD
+SGD S000005923 SNF8 GO:0045014 SGD_REF:S000041716|PMID:7785322 IMP P YPL002C|VPS22 gene taxon:4932 20021001 SGD
+SGD S000003429 SNG1 GO:0016020 SGD_REF:S000044547|PMID:7753113 ISS C YGR197C gene taxon:4932 20021001 SGD
+SGD S000003429 SNG1 GO:0005554 SGD_REF:S000069584 ND F YGR197C gene taxon:4932 20021001 SGD
+SGD S000003429 SNG1 GO:0042493 SGD_REF:S000044547|PMID:7753113 IMP P YGR197C gene taxon:4932 20021111 SGD
+SGD S000001278 SNL1 GO:0005635 SGD_REF:S000044216|PMID:9450961 IDA C 18.3 kDa integral membrane protein YIL016W gene taxon:4932 20020522 SGD
+SGD S000001278 SNL1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C 18.3 kDa integral membrane protein YIL016W gene taxon:4932 20040929 SGD
+SGD S000001278 SNL1 GO:0005789 SGD_REF:S000044216|PMID:9450961 IDA C 18.3 kDa integral membrane protein YIL016W gene taxon:4932 20020522 SGD
+SGD S000001278 SNL1 GO:0016020 SGD_REF:S000044216|PMID:9450961 ISS C 18.3 kDa integral membrane protein YIL016W gene taxon:4932 20020522 SGD
+SGD S000001278 SNL1 GO:0030188 SGD_REF:S000071139|PMID:12105220 ISS UniProt:Q99933 F 18.3 kDa integral membrane protein YIL016W gene taxon:4932 20050614 SGD
+SGD S000001278 SNL1 GO:0006457 SGD_REF:S000071139|PMID:12105220 IPI SGD:S000000004|SGD:S000002388 P 18.3 kDa integral membrane protein YIL016W gene taxon:4932 20050614 SGD
+SGD S000001278 SNL1 GO:0006999 SGD_REF:S000044216|PMID:9450961 IGI P 18.3 kDa integral membrane protein YIL016W gene taxon:4932 20020522 SGD
+SGD S000002886 SNM1 GO:0000172 SGD_REF:S000058443|PMID:10690410 TAS C RNase MRP subunit YDR478W gene taxon:4932 20010118 SGD
+SGD S000002886 SNM1 GO:0000171 SGD_REF:S000058443|PMID:10690410 TAS F RNase MRP subunit YDR478W gene taxon:4932 20010118 SGD
+SGD S000002886 SNM1 GO:0006364 SGD_REF:S000058443|PMID:10690410 TAS P RNase MRP subunit YDR478W gene taxon:4932 20010118 SGD
+SGD S000004701 SNO1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YMR095C gene taxon:4932 20031028 SGD
+SGD S000004701 SNO1 GO:0005554 SGD_REF:S000069584 ND F YMR095C gene taxon:4932 20031201 SGD
+SGD S000004701 SNO1 GO:0008614 SGD_REF:S000071751|PMID:12271461 IMP P YMR095C gene taxon:4932 20031201 SGD
+SGD S000004701 SNO1 GO:0008614 SGD_REF:S000060055|PMID:11238395 ISS P YMR095C gene taxon:4932 20020524 SGD
+SGD S000004701 SNO1 GO:0008614 SGD_REF:S000065170|PMID:10438537 ISS P YMR095C gene taxon:4932 20020524 SGD
+SGD S000004701 SNO1 NOT GO:0009228 SGD_REF:S000071751|PMID:12271461 IMP P YMR095C gene taxon:4932 20021205 SGD
+SGD S000005278 SNO2 GO:0008372 SGD_REF:S000069584 ND C YNL334C gene taxon:4932 20030602 SGD
+SGD S000005278 SNO2 GO:0005554 SGD_REF:S000069584 ND F YNL334C gene taxon:4932 20031203 SGD
+SGD S000005278 SNO2 GO:0008614 SGD_REF:S000053723|PMID:9791124 IDA P YNL334C gene taxon:4932 20020524 SGD
+SGD S000005278 SNO2 GO:0008614 SGD_REF:S000065170|PMID:10438537 ISS P YNL334C gene taxon:4932 20020524 SGD
+SGD S000005278 SNO2 GO:0008614 SGD_REF:S000060055|PMID:11238395 ISS P YNL334C gene taxon:4932 20020524 SGD
+SGD S000005278 SNO2 GO:0009228 SGD_REF:S000071751|PMID:12271461 IMP P YNL334C gene taxon:4932 20021205 SGD
+SGD S000001834 SNO3 GO:0008372 SGD_REF:S000069584 ND C YFL060C gene taxon:4932 20030602 SGD
+SGD S000001834 SNO3 GO:0005554 SGD_REF:S000069584 ND F YFL060C gene taxon:4932 20031203 SGD
+SGD S000001834 SNO3 GO:0008614 SGD_REF:S000053723|PMID:9791124 IDA P YFL060C gene taxon:4932 20020524 SGD
+SGD S000001834 SNO3 GO:0008614 SGD_REF:S000065170|PMID:10438537 ISS P YFL060C gene taxon:4932 20020524 SGD
+SGD S000001834 SNO3 GO:0008614 SGD_REF:S000060055|PMID:11238395 ISS P YFL060C gene taxon:4932 20020524 SGD
+SGD S000001834 SNO3 GO:0009228 SGD_REF:S000071751|PMID:12271461 IMP P YFL060C gene taxon:4932 20021205 SGD
+SGD S000004941 SNO4 GO:0008372 SGD_REF:S000069584 ND C YMR322C|HSP34 gene taxon:4932 20030122 SGD
+SGD S000004941 SNO4 GO:0008234 SGD_REF:S000074850|PMID:14745011 ISS F YMR322C|HSP34 gene taxon:4932 20040215 SGD
+SGD S000004941 SNO4 GO:0051082 SGD_REF:S000074850|PMID:14745011 ISS F YMR322C|HSP34 gene taxon:4932 20040215 SGD
+SGD S000004941 SNO4 GO:0008614 SGD_REF:S000074191|PMID:14566057 RCA P YMR322C|HSP34 gene taxon:4932 20050608 SGD
+SGD S000001323 SNP1 GO:0000243 SGD_REF:S000064189|PMID:10072386 IPI C U1snRNP 70K protein homolog YIL061C|U1 70K|U1-70K gene taxon:4932 20020729 SGD
+SGD S000001323 SNP1 GO:0005685 SGD_REF:S000069986|PMID:11804584 IDA C U1snRNP 70K protein homolog YIL061C|U1 70K|U1-70K gene taxon:4932 20020621 SGD
+SGD S000001323 SNP1 GO:0005685 SGD_REF:S000044485|PMID:9630245 IDA C U1snRNP 70K protein homolog YIL061C|U1 70K|U1-70K gene taxon:4932 20050929 SGD
+SGD S000001323 SNP1 GO:0003729 SGD_REF:S000064189|PMID:10072386 IPI F U1snRNP 70K protein homolog YIL061C|U1 70K|U1-70K gene taxon:4932 20020729 SGD
+SGD S000001323 SNP1 GO:0030619 SGD_REF:S000056496|PMID:1387202 IPI SGD:S000007295 F U1snRNP 70K protein homolog YIL061C|U1 70K|U1-70K gene taxon:4932 20050922 SGD
+SGD S000001323 SNP1 GO:0000398 SGD_REF:S000064189|PMID:10072386 IPI P U1snRNP 70K protein homolog YIL061C|U1 70K|U1-70K gene taxon:4932 20020729 SGD
+SGD S000002418 SNQ2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C ABC transporter YDR011W gene taxon:4932 20040928 SGD
+SGD S000002418 SNQ2 GO:0005886 SGD_REF:S000060708|PMID:11409174 TAS C ABC transporter YDR011W gene taxon:4932 20011228 SGD
+SGD S000002418 SNQ2 GO:0008559 SGD_REF:S000044365|PMID:10581358 TAS F ABC transporter YDR011W gene taxon:4932 20011228 SGD
+SGD S000002418 SNQ2 GO:0000304 SGD_REF:S000060708|PMID:11409174 IMP P ABC transporter YDR011W gene taxon:4932 20011228 SGD
+SGD S000002418 SNQ2 GO:0042493 SGD_REF:S000069766|PMID:11421285 TAS P ABC transporter YDR011W gene taxon:4932 20021111 SGD
+SGD S000007499 SNR10 GO:0005730 SGD_REF:S000047400|PMID:2121740 IPI C H/ACA box snoRNA snR10 gene taxon:4932 20021118 SGD
+SGD S000007499 SNR10 GO:0005730 SGD_REF:S000058471|PMID:9847166 TAS C H/ACA box snoRNA snR10 gene taxon:4932 20020311 SGD
+SGD S000007499 SNR10 GO:0030559 SGD_REF:S000058471|PMID:9847166 TAS F H/ACA box snoRNA snR10 gene taxon:4932 20020311 SGD
+SGD S000007499 SNR10 GO:0000154 SGD_REF:S000058471|PMID:9847166 TAS P H/ACA box snoRNA snR10 gene taxon:4932 20010118 SGD
+SGD S000007499 SNR10 GO:0006365 SGD_REF:S000058471|PMID:9847166 TAS P H/ACA box snoRNA snR10 gene taxon:4932 20010118 SGD
+SGD S000007293 SNR11 GO:0005730 SGD_REF:S000047400|PMID:2121740 IPI C H/ACA box snoRNA snR11 gene taxon:4932 20021118 SGD
+SGD S000007293 SNR11 GO:0030559 SGD_REF:S000058471|PMID:9847166 ISS F H/ACA box snoRNA snR11 gene taxon:4932 20020311 SGD
+SGD S000007293 SNR11 GO:0000154 SGD_REF:S000058471|PMID:9847166 TAS P H/ACA box snoRNA snR11 gene taxon:4932 20010118 SGD
+SGD S000007293 SNR11 GO:0006365 SGD_REF:S000058471|PMID:9847166 TAS P H/ACA box snoRNA snR11 gene taxon:4932 20010118 SGD
+SGD S000006508 SNR128 GO:0005730 SGD_REF:S000040421|PMID:2850487 IDA C C/D box snoRNA snR128|U14 gene taxon:4932 20060407 SGD
+SGD S000006508 SNR128 GO:0030563 SGD_REF:S000053492|PMID:10024243 ISS F C/D box snoRNA snR128|U14 gene taxon:4932 20020306 SGD
+SGD S000006508 SNR128 GO:0030563 SGD_REF:S000069247|PMID:8674114 ISS F C/D box snoRNA snR128|U14 gene taxon:4932 20060407 SGD
+SGD S000006508 SNR128 GO:0030490 SGD_REF:S000047107|PMID:2406561 IMP P C/D box snoRNA snR128|U14 gene taxon:4932 20060407 SGD
+SGD S000006508 SNR128 GO:0031167 SGD_REF:S000069247|PMID:8674114 IC GO:0030563 P C/D box snoRNA snR128|U14 gene taxon:4932 20060407 SGD
+SGD S000006498 SNR13 GO:0005730 SGD_REF:S000053492|PMID:10024243 TAS C C/D box snoRNA snR13 gene taxon:4932 20020306 SGD
+SGD S000006498 SNR13 GO:0030563 SGD_REF:S000053492|PMID:10024243 IDA F C/D box snoRNA snR13 gene taxon:4932 20020306 SGD
+SGD S000006498 SNR13 GO:0000154 SGD_REF:S000053492|PMID:10024243 IDA P C/D box snoRNA snR13 gene taxon:4932 20010118 SGD
+SGD S000006499 SNR14 GO:0005681 SGD_REF:S000055353|PMID:2962902 IDA C U4 snRNA snR14 gene taxon:4932 20020708 SGD
+SGD S000006499 SNR14 GO:0005687 SGD_REF:S000055353|PMID:2962902 IDA C U4 snRNA snR14 gene taxon:4932 20020708 SGD
+SGD S000006499 SNR14 GO:0046540 SGD_REF:S000056376|PMID:10377396 IPI C U4 snRNA snR14 gene taxon:4932 20050219 SGD
+SGD S000006499 SNR14 GO:0046540 SGD_REF:S000039461|PMID:10449419 IDA C U4 snRNA snR14 gene taxon:4932 20051003 SGD
+SGD S000006499 SNR14 GO:0005554 SGD_REF:S000069584 ND F U4 snRNA snR14 gene taxon:4932 20020708 SGD
+SGD S000006499 SNR14 contributes_to GO:0031202 SGD_REF:S000039461|PMID:10449419 IDA F U4 snRNA snR14 gene taxon:4932 20051003 SGD
+SGD S000006499 SNR14 contributes_to GO:0031202 SGD_REF:S000056376|PMID:10377396 IPI F U4 snRNA snR14 gene taxon:4932 20051003 SGD
+SGD S000006499 SNR14 GO:0000398 SGD_REF:S000051807|PMID:7862121 TAS P U4 snRNA snR14 gene taxon:4932 20020708 SGD
+SGD S000087162 SNR161 GO:0005730 SGD_REF:S000081218|PMID:15306656 IC GO:0000154|GO:0030559 C snR161 gene taxon:4932 20051111 SGD
+SGD S000087162 SNR161 GO:0030559 SGD_REF:S000081218|PMID:15306656 IMP F snR161 gene taxon:4932 20051111 SGD
+SGD S000087162 SNR161 GO:0000154 SGD_REF:S000081218|PMID:15306656 IMP P snR161 gene taxon:4932 20051111 SGD
+SGD S000007294 SNR17A GO:0005730 SGD_REF:S000064237|PMID:7556076 IC GO:0006364 C U3 snoRNA snR17a gene taxon:4932 20021118 SGD
+SGD S000007294 SNR17A GO:0003723 SGD_REF:S000064237|PMID:7556076 IGI F U3 snoRNA snR17a gene taxon:4932 20021118 SGD
+SGD S000007294 SNR17A GO:0003723 SGD_REF:S000064237|PMID:7556076 IMP F U3 snoRNA snR17a gene taxon:4932 20021118 SGD
+SGD S000007294 SNR17A GO:0000154 SGD_REF:S000058471|PMID:9847166 TAS P U3 snoRNA snR17a gene taxon:4932 20010118 SGD
+SGD S000007294 SNR17A GO:0006364 SGD_REF:S000064237|PMID:7556076 IGI P U3 snoRNA snR17a gene taxon:4932 20021118 SGD
+SGD S000007294 SNR17A GO:0006364 SGD_REF:S000064237|PMID:7556076 IMP P U3 snoRNA snR17a gene taxon:4932 20021118 SGD
+SGD S000007441 SNR17B GO:0005730 SGD_REF:S000064237|PMID:7556076 IC GO:0006364 C U3 snoRNA snR17b gene taxon:4932 20021118 SGD
+SGD S000007441 SNR17B GO:0003723 SGD_REF:S000064237|PMID:7556076 IGI F U3 snoRNA snR17b gene taxon:4932 20021118 SGD
+SGD S000007441 SNR17B GO:0003723 SGD_REF:S000064237|PMID:7556076 IMP F U3 snoRNA snR17b gene taxon:4932 20021118 SGD
+SGD S000007441 SNR17B GO:0003723 SGD_REF:S000064237|PMID:7556076 ISS F U3 snoRNA snR17b gene taxon:4932 20021118 SGD
+SGD S000007441 SNR17B GO:0000154 SGD_REF:S000058471|PMID:9847166 TAS P U3 snoRNA snR17b gene taxon:4932 20010118 SGD
+SGD S000007441 SNR17B GO:0006364 SGD_REF:S000064237|PMID:7556076 IGI P U3 snoRNA snR17b gene taxon:4932 20021118 SGD
+SGD S000007441 SNR17B GO:0006364 SGD_REF:S000064237|PMID:7556076 IMP P U3 snoRNA snR17b gene taxon:4932 20021118 SGD
+SGD S000007500 SNR18 GO:0005730 SGD_REF:S000053492|PMID:10024243 TAS C C/D box snoRNA snR18 gene taxon:4932 20020306 SGD
+SGD S000007500 SNR18 GO:0030563 SGD_REF:S000053492|PMID:10024243 TAS F C/D box snoRNA snR18 gene taxon:4932 20020306 SGD
+SGD S000007500 SNR18 GO:0030563 SGD_REF:S000069247|PMID:8674114 ISS F C/D box snoRNA snR18 gene taxon:4932 20060407 SGD
+SGD S000007500 SNR18 GO:0000154 SGD_REF:S000053492|PMID:10024243 TAS P C/D box snoRNA snR18 gene taxon:4932 20020306 SGD
+SGD S000007314 SNR189 GO:0005730 SGD_REF:S000058471|PMID:9847166 TAS C H/ACA box snoRNA snR189 gene taxon:4932 20021118 SGD
+SGD S000007314 SNR189 GO:0005730 SGD_REF:S000081218|PMID:15306656 IC GO:0000154|GO:0030559 C H/ACA box snoRNA snR189 gene taxon:4932 20050422 SGD
+SGD S000007314 SNR189 GO:0030559 SGD_REF:S000058471|PMID:9847166 ISS F H/ACA box snoRNA snR189 gene taxon:4932 20020311 SGD
+SGD S000007314 SNR189 GO:0030559 SGD_REF:S000081218|PMID:15306656 IMP F H/ACA box snoRNA snR189 gene taxon:4932 20050422 SGD
+SGD S000007314 SNR189 GO:0000154 SGD_REF:S000058471|PMID:9847166 TAS P H/ACA box snoRNA snR189 gene taxon:4932 20010118 SGD
+SGD S000007314 SNR189 GO:0000154 SGD_REF:S000081218|PMID:15306656 IMP P H/ACA box snoRNA snR189 gene taxon:4932 20050422 SGD
+SGD S000007295 SNR19 GO:0000243 SGD_REF:S000087032|PMID:2529976 IDA C U1 snRNA snR19|U1 gene taxon:4932 20051031 SGD
+SGD S000007295 SNR19 GO:0005685 SGD_REF:S000050383|PMID:2440584 IDA C U1 snRNA snR19|U1 gene taxon:4932 20020715 SGD
+SGD S000007295 SNR19 GO:0030627 SGD_REF:S000051015|PMID:3056718 IMP F U1 snRNA snR19|U1 gene taxon:4932 20051027 SGD
+SGD S000007295 SNR19 GO:0030627 SGD_REF:S000082434|PMID:15989965 IMP F U1 snRNA snR19|U1 gene taxon:4932 20051027 SGD
+SGD S000007295 SNR19 GO:0030627 SGD_REF:S000082434|PMID:15989965 IGI F U1 snRNA snR19|U1 gene taxon:4932 20051027 SGD
+SGD S000007295 SNR19 GO:0030627 SGD_REF:S000051015|PMID:3056718 IGI F U1 snRNA snR19|U1 gene taxon:4932 20051027 SGD
+SGD S000007295 SNR19 GO:0000398 SGD_REF:S000050383|PMID:2440584 IDA P U1 snRNA snR19|U1 gene taxon:4932 20020715 SGD
+SGD S000006509 SNR190 GO:0005730 SGD_REF:S000040421|PMID:2850487 IDA C small nucleolar RNA U190 snR190 gene taxon:4932 20060407 SGD
+SGD S000006509 SNR190 GO:0030563 SGD_REF:S000069247|PMID:8674114 ISS F small nucleolar RNA U190 snR190 gene taxon:4932 20020306 SGD
+SGD S000006509 SNR190 GO:0000154 SGD_REF:S000069247|PMID:8674114 ISS P small nucleolar RNA U190 snR190 gene taxon:4932 20020306 SGD
+SGD S000029463 SNR191 GO:0005732 SGD_REF:S000073877|PMID:12810910 TAS C H/ACA box snoRNA snR191 gene taxon:4932 20040226 SGD
+SGD S000029463 SNR191 GO:0030559 SGD_REF:S000073877|PMID:12810910 IMP F H/ACA box snoRNA snR191 gene taxon:4932 20040226 SGD
+SGD S000029463 SNR191 GO:0000154 SGD_REF:S000073877|PMID:12810910 IMP P H/ACA box snoRNA snR191 gene taxon:4932 20040226 SGD
+SGD S000007501 SNR24 GO:0005730 SGD_REF:S000053492|PMID:10024243 TAS C C/D box snoRNA snR24|U24 gene taxon:4932 20020306 SGD
+SGD S000007501 SNR24 GO:0030563 SGD_REF:S000053492|PMID:10024243 TAS F C/D box snoRNA snR24|U24 gene taxon:4932 20020306 SGD
+SGD S000007501 SNR24 GO:0031167 SGD_REF:S000069247|PMID:8674114 IMP P C/D box snoRNA snR24|U24 gene taxon:4932 20060406 SGD
+SGD S000006492 SNR3 GO:0005730 SGD_REF:S000058471|PMID:9847166 TAS C H/ACA box snoRNA snR3 gene taxon:4932 20020311 SGD
+SGD S000006492 SNR3 GO:0005730 SGD_REF:S000081218|PMID:15306656 IC GO:0000154|GO:0030559 C H/ACA box snoRNA snR3 gene taxon:4932 20050422 SGD
+SGD S000006492 SNR3 GO:0030559 SGD_REF:S000058471|PMID:9847166 TAS F H/ACA box snoRNA snR3 gene taxon:4932 20020311 SGD
+SGD S000006492 SNR3 GO:0030559 SGD_REF:S000081218|PMID:15306656 IMP F H/ACA box snoRNA snR3 gene taxon:4932 20050422 SGD
+SGD S000006492 SNR3 GO:0000154 SGD_REF:S000058471|PMID:9847166 TAS P H/ACA box snoRNA snR3 gene taxon:4932 20010118 SGD
+SGD S000006492 SNR3 GO:0000154 SGD_REF:S000081218|PMID:15306656 IMP P H/ACA box snoRNA snR3 gene taxon:4932 20050422 SGD
+SGD S000007497 SNR30 GO:0005730 SGD_REF:S000048923|PMID:9472021 TAS C H/ACA box snoRNA snR30 gene taxon:4932 20021030 SGD
+SGD S000007497 SNR30 GO:0042134 SGD_REF:S000042548|PMID:8455623 IDA F H/ACA box snoRNA snR30 gene taxon:4932 20021118 SGD
+SGD S000007497 SNR30 GO:0006364 SGD_REF:S000048923|PMID:9472021 IMP P H/ACA box snoRNA snR30 gene taxon:4932 20021030 SGD
+SGD S000007497 SNR30 GO:0006365 SGD_REF:S000058471|PMID:9847166 TAS P H/ACA box snoRNA snR30 gene taxon:4932 20010118 SGD
+SGD S000007296 SNR31 GO:0005730 SGD_REF:S000058471|PMID:9847166 TAS C H/ACA box snoRNA snR31 gene taxon:4932 20020311 SGD
+SGD S000007296 SNR31 GO:0030559 SGD_REF:S000058471|PMID:9847166 TAS F H/ACA box snoRNA snR31 gene taxon:4932 20020311 SGD
+SGD S000007296 SNR31 GO:0000154 SGD_REF:S000058471|PMID:9847166 TAS P H/ACA box snoRNA snR31 gene taxon:4932 20010118 SGD
+SGD S000007297 SNR32 GO:0005730 SGD_REF:S000058471|PMID:9847166 TAS C H/ACA box snoRNA snR32 gene taxon:4932 20020311 SGD
+SGD S000007297 SNR32 GO:0030559 SGD_REF:S000058471|PMID:9847166 TAS F H/ACA box snoRNA snR32 gene taxon:4932 20020311 SGD
+SGD S000007297 SNR32 GO:0000154 SGD_REF:S000058471|PMID:9847166 TAS P H/ACA box snoRNA snR32 gene taxon:4932 20010118 SGD
+SGD S000007298 SNR33 GO:0005730 SGD_REF:S000058471|PMID:9847166 TAS C H/ACA box snoRNA snR33 gene taxon:4932 20020311 SGD
+SGD S000007298 SNR33 GO:0030559 SGD_REF:S000058471|PMID:9847166 TAS F H/ACA box snoRNA snR33 gene taxon:4932 20020311 SGD
+SGD S000007298 SNR33 GO:0000154 SGD_REF:S000058471|PMID:9847166 TAS P H/ACA box snoRNA snR33 gene taxon:4932 20010118 SGD
+SGD S000006500 SNR34 GO:0005730 SGD_REF:S000058471|PMID:9847166 TAS C H/ACA box snoRNA snR34 gene taxon:4932 20020311 SGD
+SGD S000006500 SNR34 GO:0030559 SGD_REF:S000058471|PMID:9847166 TAS F H/ACA box snoRNA snR34 gene taxon:4932 20020311 SGD
+SGD S000006500 SNR34 GO:0000154 SGD_REF:S000058471|PMID:9847166 TAS P H/ACA box snoRNA snR34 gene taxon:4932 20010118 SGD
+SGD S000007299 SNR35 GO:0005730 SGD_REF:S000048238|PMID:7630735 IDA C H/ACA box snoRNA snR35 gene taxon:4932 20021015 SGD
+SGD S000007299 SNR35 GO:0005730 SGD_REF:S000048238|PMID:7630735 IPI C H/ACA box snoRNA snR35 gene taxon:4932 20021015 SGD
+SGD S000007299 SNR35 GO:0030559 SGD_REF:S000058471|PMID:9847166 ISS F H/ACA box snoRNA snR35 gene taxon:4932 20020311 SGD
+SGD S000007299 SNR35 GO:0000154 SGD_REF:S000058471|PMID:9847166 TAS P H/ACA box snoRNA snR35 gene taxon:4932 20010118 SGD
+SGD S000007300 SNR36 GO:0005730 SGD_REF:S000058471|PMID:9847166 TAS C H/ACA box snoRNA snR36 gene taxon:4932 20020311 SGD
+SGD S000007300 SNR36 GO:0030559 SGD_REF:S000058471|PMID:9847166 TAS F H/ACA box snoRNA snR36 gene taxon:4932 20020311 SGD
+SGD S000007300 SNR36 GO:0000154 SGD_REF:S000058471|PMID:9847166 TAS P H/ACA box snoRNA snR36 gene taxon:4932 20010118 SGD
+SGD S000006501 SNR37 GO:0005730 SGD_REF:S000058471|PMID:9847166 TAS C H/ACA box snoRNA snR37 gene taxon:4932 20020311 SGD
+SGD S000006501 SNR37 GO:0030559 SGD_REF:S000058471|PMID:9847166 TAS F H/ACA box snoRNA snR37 gene taxon:4932 20020311 SGD
+SGD S000006501 SNR37 GO:0000154 SGD_REF:S000058471|PMID:9847166 TAS P H/ACA box snoRNA snR37 gene taxon:4932 20010118 SGD
+SGD S000007301 SNR38 GO:0005730 SGD_REF:S000053492|PMID:10024243 TAS C C/D box snoRNA snR38 gene taxon:4932 20020306 SGD
+SGD S000007301 SNR38 GO:0030563 SGD_REF:S000053492|PMID:10024243 TAS F C/D box snoRNA snR38 gene taxon:4932 20020306 SGD
+SGD S000007301 SNR38 GO:0030563 SGD_REF:S000069247|PMID:8674114 ISS F C/D box snoRNA snR38 gene taxon:4932 20060407 SGD
+SGD S000007301 SNR38 GO:0030563 SGD_REF:S000053492|PMID:10024243 ISS F C/D box snoRNA snR38 gene taxon:4932 20020306 SGD
+SGD S000007301 SNR38 GO:0000154 SGD_REF:S000053492|PMID:10024243 TAS P C/D box snoRNA snR38 gene taxon:4932 20020306 SGD
+SGD S000007301 SNR38 GO:0000154 SGD_REF:S000053492|PMID:10024243 ISS P C/D box snoRNA snR38 gene taxon:4932 20020306 SGD
+SGD S000007302 SNR39 GO:0005730 SGD_REF:S000053492|PMID:10024243 TAS C C/D box snoRNA snR39 gene taxon:4932 20020306 SGD
+SGD S000007302 SNR39 GO:0030563 SGD_REF:S000053492|PMID:10024243 TAS F C/D box snoRNA snR39 gene taxon:4932 20020306 SGD
+SGD S000007302 SNR39 GO:0030563 SGD_REF:S000069247|PMID:8674114 ISS F C/D box snoRNA snR39 gene taxon:4932 20060407 SGD
+SGD S000007302 SNR39 GO:0030563 SGD_REF:S000053492|PMID:10024243 ISS F C/D box snoRNA snR39 gene taxon:4932 20020306 SGD
+SGD S000007302 SNR39 GO:0000154 SGD_REF:S000053492|PMID:10024243 TAS P C/D box snoRNA snR39 gene taxon:4932 20020306 SGD
+SGD S000007302 SNR39 GO:0000154 SGD_REF:S000053492|PMID:10024243 ISS P C/D box snoRNA snR39 gene taxon:4932 20020306 SGD
+SGD S000007303 SNR39B GO:0005730 SGD_REF:S000053492|PMID:10024243 TAS C C/D box snoRNA snR39B gene taxon:4932 20020306 SGD
+SGD S000007303 SNR39B GO:0030563 SGD_REF:S000053492|PMID:10024243 IDA F C/D box snoRNA snR39B gene taxon:4932 20020306 SGD
+SGD S000007303 SNR39B GO:0000154 SGD_REF:S000053492|PMID:10024243 IDA P C/D box snoRNA snR39B gene taxon:4932 20010118 SGD
+SGD S000006493 SNR4 GO:0005730 SGD_REF:S000058471|PMID:9847166 TAS C small nuclear RNA snR4 snR4 gene taxon:4932 20021118 SGD
+SGD S000006493 SNR4 GO:0005554 SGD_REF:S000069584 ND F small nuclear RNA snR4 snR4 gene taxon:4932 20021118 SGD
+SGD S000006493 SNR4 GO:0000154 SGD_REF:S000058471|PMID:9847166 TAS P small nuclear RNA snR4 snR4 gene taxon:4932 20010118 SGD
+SGD S000007304 SNR40 GO:0005730 SGD_REF:S000053492|PMID:10024243 TAS C C/D box snoRNA snR40 gene taxon:4932 20020306 SGD
+SGD S000007304 SNR40 GO:0030563 SGD_REF:S000053492|PMID:10024243 IDA F C/D box snoRNA snR40 gene taxon:4932 20020306 SGD
+SGD S000007304 SNR40 GO:0030563 SGD_REF:S000069247|PMID:8674114 ISS F C/D box snoRNA snR40 gene taxon:4932 20060407 SGD
+SGD S000007304 SNR40 GO:0000154 SGD_REF:S000053492|PMID:10024243 IDA P C/D box snoRNA snR40 gene taxon:4932 20010118 SGD
+SGD S000007305 SNR41 GO:0005730 SGD_REF:S000053492|PMID:10024243 TAS C C/D box snoRNA snR41 gene taxon:4932 20020306 SGD
+SGD S000007305 SNR41 GO:0030563 SGD_REF:S000053492|PMID:10024243 IDA F C/D box snoRNA snR41 gene taxon:4932 20020306 SGD
+SGD S000007305 SNR41 GO:0030563 SGD_REF:S000069247|PMID:8674114 ISS F C/D box snoRNA snR41 gene taxon:4932 20060407 SGD
+SGD S000007305 SNR41 GO:0000154 SGD_REF:S000053492|PMID:10024243 IDA P C/D box snoRNA snR41 gene taxon:4932 20010118 SGD
+SGD S000006502 SNR42 GO:0005730 SGD_REF:S000058471|PMID:9847166 TAS C H/ACA box snoRNA snR42 gene taxon:4932 20020311 SGD
+SGD S000006502 SNR42 GO:0030559 SGD_REF:S000058471|PMID:9847166 TAS F H/ACA box snoRNA snR42 gene taxon:4932 20020311 SGD
+SGD S000006502 SNR42 GO:0000154 SGD_REF:S000058471|PMID:9847166 TAS P H/ACA box snoRNA snR42 gene taxon:4932 20010118 SGD
+SGD S000006503 SNR43 GO:0005730 SGD_REF:S000058471|PMID:9847166 TAS C H/ACA box snoRNA snR43 gene taxon:4932 20021030 SGD
+SGD S000006503 SNR43 GO:0005554 SGD_REF:S000069584 ND F H/ACA box snoRNA snR43 gene taxon:4932 20021030 SGD
+SGD S000006503 SNR43 GO:0000154 SGD_REF:S000058471|PMID:9847166 ISS P H/ACA box snoRNA snR43 gene taxon:4932 20010118 SGD
+SGD S000006504 SNR44 GO:0005730 SGD_REF:S000058471|PMID:9847166 TAS C H/ACA box snoRNA snR44 gene taxon:4932 20021030 SGD
+SGD S000006504 SNR44 GO:0005730 SGD_REF:S000081218|PMID:15306656 IC GO:0000154|GO:0030559 C H/ACA box snoRNA snR44 gene taxon:4932 20050422 SGD
+SGD S000006504 SNR44 GO:0030559 SGD_REF:S000058471|PMID:9847166 ISS F H/ACA box snoRNA snR44 gene taxon:4932 20020311 SGD
+SGD S000006504 SNR44 GO:0030559 SGD_REF:S000081218|PMID:15306656 IMP F H/ACA box snoRNA snR44 gene taxon:4932 20050422 SGD
+SGD S000006504 SNR44 GO:0000154 SGD_REF:S000058471|PMID:9847166 TAS P H/ACA box snoRNA snR44 gene taxon:4932 20010118 SGD
+SGD S000006504 SNR44 GO:0000154 SGD_REF:S000081218|PMID:15306656 IMP P H/ACA box snoRNA snR44 gene taxon:4932 20050422 SGD
+SGD S000006505 SNR45 GO:0005730 SGD_REF:S000058471|PMID:9847166 TAS C small nuclear RNA snR45 gene taxon:4932 20021118 SGD
+SGD S000006505 SNR45 GO:0005554 SGD_REF:S000069584 ND F small nuclear RNA snR45 gene taxon:4932 20021118 SGD
+SGD S000006505 SNR45 GO:0000154 SGD_REF:S000058471|PMID:9847166 ISS P small nuclear RNA snR45 gene taxon:4932 20010118 SGD
+SGD S000006506 SNR46 GO:0005730 SGD_REF:S000058471|PMID:9847166 TAS C H/ACA box snoRNA snR46 gene taxon:4932 20020311 SGD
+SGD S000006506 SNR46 GO:0030559 SGD_REF:S000058471|PMID:9847166 TAS F H/ACA box snoRNA snR46 gene taxon:4932 20020311 SGD
+SGD S000006506 SNR46 GO:0000154 SGD_REF:S000058471|PMID:9847166 TAS P H/ACA box snoRNA snR46 gene taxon:4932 20010118 SGD
+SGD S000006507 SNR47 GO:0005730 SGD_REF:S000053492|PMID:10024243 TAS C C/D box snoRNA snR47 gene taxon:4932 20020306 SGD
+SGD S000006507 SNR47 GO:0030563 SGD_REF:S000053492|PMID:10024243 IDA F C/D box snoRNA snR47 gene taxon:4932 20020306 SGD
+SGD S000006507 SNR47 GO:0000154 SGD_REF:S000053492|PMID:10024243 IDA P C/D box snoRNA snR47 gene taxon:4932 20010118 SGD
+SGD S000006440 SNR48 GO:0005730 SGD_REF:S000053492|PMID:10024243 TAS C C/D box snoRNA snR48 gene taxon:4932 20020306 SGD
+SGD S000006440 SNR48 GO:0030563 SGD_REF:S000053492|PMID:10024243 IDA F C/D box snoRNA snR48 gene taxon:4932 20020306 SGD
+SGD S000006440 SNR48 GO:0000154 SGD_REF:S000053492|PMID:10024243 IDA P C/D box snoRNA snR48 gene taxon:4932 20010118 SGD
+SGD S000007460 SNR49 GO:0005730 SGD_REF:S000058471|PMID:9847166 TAS C H/ACA box snoRNA snR49 gene taxon:4932 20021118 SGD
+SGD S000007460 SNR49 GO:0005730 SGD_REF:S000081218|PMID:15306656 IC GO:0000154|GO:0030559 C H/ACA box snoRNA snR49 gene taxon:4932 20050422 SGD
+SGD S000007460 SNR49 GO:0030559 SGD_REF:S000058471|PMID:9847166 ISS F H/ACA box snoRNA snR49 gene taxon:4932 20020311 SGD
+SGD S000007460 SNR49 GO:0030559 SGD_REF:S000081218|PMID:15306656 IMP F H/ACA box snoRNA snR49 gene taxon:4932 20050422 SGD
+SGD S000007460 SNR49 GO:0000154 SGD_REF:S000058471|PMID:9847166 TAS P H/ACA box snoRNA snR49 gene taxon:4932 20010118 SGD
+SGD S000007460 SNR49 GO:0000154 SGD_REF:S000081218|PMID:15306656 IMP P H/ACA box snoRNA snR49 gene taxon:4932 20050422 SGD
+SGD S000007291 SNR5 GO:0005730 SGD_REF:S000058471|PMID:9847166 TAS C H/ACA box snoRNA snR5 gene taxon:4932 20020311 SGD
+SGD S000007291 SNR5 GO:0030559 SGD_REF:S000058471|PMID:9847166 TAS F H/ACA box snoRNA snR5 gene taxon:4932 20020311 SGD
+SGD S000007291 SNR5 GO:0000154 SGD_REF:S000058471|PMID:9847166 TAS P H/ACA box snoRNA snR5 gene taxon:4932 20010118 SGD
+SGD S000006441 SNR50 GO:0005730 SGD_REF:S000053492|PMID:10024243 TAS C C/D box snoRNA snR50 gene taxon:4932 20020306 SGD
+SGD S000006441 SNR50 GO:0030563 SGD_REF:S000053492|PMID:10024243 IDA F C/D box snoRNA snR50 gene taxon:4932 20020306 SGD
+SGD S000006441 SNR50 GO:0000154 SGD_REF:S000053492|PMID:10024243 IDA P C/D box snoRNA snR50 gene taxon:4932 20010118 SGD
+SGD S000006442 SNR51 GO:0005730 SGD_REF:S000053492|PMID:10024243 TAS C C/D box snoRNA snR51 gene taxon:4932 20020306 SGD
+SGD S000006442 SNR51 GO:0030563 SGD_REF:S000053492|PMID:10024243 IDA F C/D box snoRNA snR51 gene taxon:4932 20020306 SGD
+SGD S000006442 SNR51 GO:0000154 SGD_REF:S000053492|PMID:10024243 IDA P C/D box snoRNA snR51 gene taxon:4932 20010118 SGD
+SGD S000006443 SNR52 GO:0005730 SGD_REF:S000053492|PMID:10024243 IC GO:0030563 C C/D box snoRNA snR52 gene taxon:4932 20060516 SGD
+SGD S000006443 SNR52 GO:0030563 SGD_REF:S000079655|PMID:15546625 IGI SGD:S000000559 F C/D box snoRNA snR52 gene taxon:4932 20041119 SGD
+SGD S000006443 SNR52 GO:0030563 SGD_REF:S000079655|PMID:15546625 IMP F C/D box snoRNA snR52 gene taxon:4932 20041119 SGD
+SGD S000006443 SNR52 GO:0030563 SGD_REF:S000053492|PMID:10024243 RCA F C/D box snoRNA snR52 gene taxon:4932 20060516 SGD
+SGD S000006443 SNR52 GO:0030563 SGD_REF:S000053492|PMID:10024243 IMP F C/D box snoRNA snR52 gene taxon:4932 20060516 SGD
+SGD S000006443 SNR52 GO:0031167 SGD_REF:S000079655|PMID:15546625 IGI SGD:S000000559 P C/D box snoRNA snR52 gene taxon:4932 20060516 SGD
+SGD S000006443 SNR52 GO:0031167 SGD_REF:S000053492|PMID:10024243 IMP P C/D box snoRNA snR52 gene taxon:4932 20060516 SGD
+SGD S000006443 SNR52 GO:0031167 SGD_REF:S000079655|PMID:15546625 IMP P C/D box snoRNA snR52 gene taxon:4932 20060516 SGD
+SGD S000006444 SNR53 GO:0005730 SGD_REF:S000053492|PMID:10024243 TAS C C/D box snoRNA snR53 gene taxon:4932 20020306 SGD
+SGD S000006444 SNR53 GO:0030563 SGD_REF:S000053492|PMID:10024243 IDA F C/D box snoRNA snR53 gene taxon:4932 20020306 SGD
+SGD S000006444 SNR53 GO:0000154 SGD_REF:S000053492|PMID:10024243 IDA P C/D box snoRNA snR53 gene taxon:4932 20010118 SGD
+SGD S000006445 SNR54 GO:0005730 SGD_REF:S000053492|PMID:10024243 TAS C C/D box snoRNA snR54 gene taxon:4932 20020306 SGD
+SGD S000006445 SNR54 GO:0030563 SGD_REF:S000053492|PMID:10024243 IDA F C/D box snoRNA snR54 gene taxon:4932 20020306 SGD
+SGD S000006445 SNR54 GO:0000154 SGD_REF:S000053492|PMID:10024243 IDA P C/D box snoRNA snR54 gene taxon:4932 20010118 SGD
+SGD S000006446 SNR55 GO:0005730 SGD_REF:S000053492|PMID:10024243 TAS C C/D box snoRNA snR55 gene taxon:4932 20020306 SGD
+SGD S000006446 SNR55 GO:0030563 SGD_REF:S000053492|PMID:10024243 ISS F C/D box snoRNA snR55 gene taxon:4932 20020306 SGD
+SGD S000006446 SNR55 GO:0000154 SGD_REF:S000053492|PMID:10024243 ISS P C/D box snoRNA snR55 gene taxon:4932 20020306 SGD
+SGD S000006447 SNR56 GO:0005730 SGD_REF:S000053492|PMID:10024243 TAS C C/D box snoRNA snR56 gene taxon:4932 20020306 SGD
+SGD S000006447 SNR56 GO:0030563 SGD_REF:S000053492|PMID:10024243 IDA F C/D box snoRNA snR56 gene taxon:4932 20020306 SGD
+SGD S000006447 SNR56 GO:0000154 SGD_REF:S000053492|PMID:10024243 IDA P C/D box snoRNA snR56 gene taxon:4932 20010118 SGD
+SGD S000006448 SNR57 GO:0005730 SGD_REF:S000053492|PMID:10024243 TAS C C/D box snoRNA snR57 gene taxon:4932 20020306 SGD
+SGD S000006448 SNR57 GO:0030563 SGD_REF:S000053492|PMID:10024243 IDA F C/D box snoRNA snR57 gene taxon:4932 20020306 SGD
+SGD S000006448 SNR57 GO:0000154 SGD_REF:S000053492|PMID:10024243 IDA P C/D box snoRNA snR57 gene taxon:4932 20010118 SGD
+SGD S000006449 SNR58 GO:0005730 SGD_REF:S000053492|PMID:10024243 TAS C C/D box snoRNA snR58 gene taxon:4932 20020306 SGD
+SGD S000006449 SNR58 GO:0030563 SGD_REF:S000053492|PMID:10024243 IDA F C/D box snoRNA snR58 gene taxon:4932 20020306 SGD
+SGD S000006449 SNR58 GO:0000154 SGD_REF:S000053492|PMID:10024243 IDA P C/D box snoRNA snR58 gene taxon:4932 20010118 SGD
+SGD S000006450 SNR59 GO:0005730 SGD_REF:S000053492|PMID:10024243 TAS C C/D box snoRNA snR59 gene taxon:4932 20020306 SGD
+SGD S000006450 SNR59 GO:0030563 SGD_REF:S000053492|PMID:10024243 ISS F C/D box snoRNA snR59 gene taxon:4932 20020306 SGD
+SGD S000006450 SNR59 GO:0000154 SGD_REF:S000053492|PMID:10024243 ISS P C/D box snoRNA snR59 gene taxon:4932 20020306 SGD
+SGD S000006494 SNR6 GO:0005688 SGD_REF:S000069987|PMID:2977088 TAS C U6 snRNA snR6 gene taxon:4932 20050219 SGD
+SGD S000006494 SNR6 GO:0005688 SGD_REF:S000066234|PMID:11720284 IDA C U6 snRNA snR6 gene taxon:4932 20051003 SGD
+SGD S000006494 SNR6 GO:0046540 SGD_REF:S000056376|PMID:10377396 IPI C U6 snRNA snR6 gene taxon:4932 20050219 SGD
+SGD S000006494 SNR6 GO:0046540 SGD_REF:S000039461|PMID:10449419 IDA C U6 snRNA snR6 gene taxon:4932 20051003 SGD
+SGD S000006494 SNR6 GO:0003723 SGD_REF:S000050382|PMID:2440583 IDA F U6 snRNA snR6 gene taxon:4932 20021118 SGD
+SGD S000006494 SNR6 contributes_to GO:0031202 SGD_REF:S000039461|PMID:10449419 IDA F U6 snRNA snR6 gene taxon:4932 20051003 SGD
+SGD S000006494 SNR6 contributes_to GO:0031202 SGD_REF:S000056376|PMID:10377396 IPI F U6 snRNA snR6 gene taxon:4932 20051003 SGD
+SGD S000006494 SNR6 GO:0000398 SGD_REF:S000050382|PMID:2440583 IPI P U6 snRNA snR6 gene taxon:4932 20021118 SGD
+SGD S000006494 SNR6 GO:0000398 SGD_REF:S000050382|PMID:2440583 ISS P U6 snRNA snR6 gene taxon:4932 20021118 SGD
+SGD S000006451 SNR60 GO:0005730 SGD_REF:S000053492|PMID:10024243 TAS C C/D box snoRNA snR60 gene taxon:4932 20020306 SGD
+SGD S000006451 SNR60 GO:0030563 SGD_REF:S000053492|PMID:10024243 IDA F C/D box snoRNA snR60 gene taxon:4932 20020306 SGD
+SGD S000006451 SNR60 GO:0000154 SGD_REF:S000053492|PMID:10024243 IDA P C/D box snoRNA snR60 gene taxon:4932 20010118 SGD
+SGD S000006452 SNR61 GO:0005730 SGD_REF:S000053492|PMID:10024243 TAS C C/D box snoRNA snR61 gene taxon:4932 20020306 SGD
+SGD S000006452 SNR61 GO:0030563 SGD_REF:S000053492|PMID:10024243 IDA F C/D box snoRNA snR61 gene taxon:4932 20020306 SGD
+SGD S000006452 SNR61 GO:0000154 SGD_REF:S000053492|PMID:10024243 IDA P C/D box snoRNA snR61 gene taxon:4932 20010118 SGD
+SGD S000006453 SNR62 GO:0005730 SGD_REF:S000053492|PMID:10024243 TAS C C/D box snoRNA snR62 gene taxon:4932 20020306 SGD
+SGD S000006453 SNR62 GO:0030563 SGD_REF:S000053492|PMID:10024243 IDA F C/D box snoRNA snR62 gene taxon:4932 20020306 SGD
+SGD S000006453 SNR62 GO:0000154 SGD_REF:S000053492|PMID:10024243 IDA P C/D box snoRNA snR62 gene taxon:4932 20010118 SGD
+SGD S000006454 SNR63 GO:0005730 SGD_REF:S000053492|PMID:10024243 TAS C C/D box snoRNA snR63 gene taxon:4932 20020306 SGD
+SGD S000006454 SNR63 GO:0030563 SGD_REF:S000053492|PMID:10024243 IDA F C/D box snoRNA snR63 gene taxon:4932 20020306 SGD
+SGD S000006454 SNR63 GO:0000154 SGD_REF:S000053492|PMID:10024243 IDA P C/D box snoRNA snR63 gene taxon:4932 20010118 SGD
+SGD S000006455 SNR64 GO:0005730 SGD_REF:S000053492|PMID:10024243 TAS C C/D box snoRNA snR64 gene taxon:4932 20020306 SGD
+SGD S000006455 SNR64 GO:0030563 SGD_REF:S000053492|PMID:10024243 IDA F C/D box snoRNA snR64 gene taxon:4932 20020306 SGD
+SGD S000006455 SNR64 GO:0000154 SGD_REF:S000053492|PMID:10024243 IDA P C/D box snoRNA snR64 gene taxon:4932 20010118 SGD
+SGD S000006456 SNR65 GO:0005730 SGD_REF:S000053492|PMID:10024243 TAS C C/D box snoRNA snR65 gene taxon:4932 20020306 SGD
+SGD S000006456 SNR65 GO:0030563 SGD_REF:S000053492|PMID:10024243 IDA F C/D box snoRNA snR65 gene taxon:4932 20020306 SGD
+SGD S000006456 SNR65 GO:0000154 SGD_REF:S000053492|PMID:10024243 IDA P C/D box snoRNA snR65 gene taxon:4932 20010118 SGD
+SGD S000006457 SNR66 GO:0005730 SGD_REF:S000053492|PMID:10024243 TAS C C/D box snoRNA snR66 gene taxon:4932 20020306 SGD
+SGD S000006457 SNR66 GO:0030563 SGD_REF:S000053492|PMID:10024243 IDA F C/D box snoRNA snR66 gene taxon:4932 20020306 SGD
+SGD S000006457 SNR66 GO:0000154 SGD_REF:S000053492|PMID:10024243 IDA P C/D box snoRNA snR66 gene taxon:4932 20010118 SGD
+SGD S000006458 SNR67 GO:0005730 SGD_REF:S000053492|PMID:10024243 TAS C C/D box snoRNA snR67 gene taxon:4932 20020306 SGD
+SGD S000006458 SNR67 GO:0030563 SGD_REF:S000053492|PMID:10024243 IDA F C/D box snoRNA snR67 gene taxon:4932 20020306 SGD
+SGD S000006458 SNR67 GO:0000154 SGD_REF:S000053492|PMID:10024243 IDA P C/D box snoRNA snR67 gene taxon:4932 20010118 SGD
+SGD S000006459 SNR68 GO:0005730 SGD_REF:S000053492|PMID:10024243 TAS C C/D box snoRNA snR68 gene taxon:4932 20020306 SGD
+SGD S000006459 SNR68 GO:0030563 SGD_REF:S000053492|PMID:10024243 IDA F C/D box snoRNA snR68 gene taxon:4932 20020306 SGD
+SGD S000006459 SNR68 GO:0000154 SGD_REF:S000053492|PMID:10024243 IDA P C/D box snoRNA snR68 gene taxon:4932 20010118 SGD
+SGD S000006460 SNR69 GO:0005730 SGD_REF:S000053492|PMID:10024243 TAS C C/D box snoRNA snR69 gene taxon:4932 20020306 SGD
+SGD S000006460 SNR69 GO:0030563 SGD_REF:S000053492|PMID:10024243 IDA F C/D box snoRNA snR69 gene taxon:4932 20020306 SGD
+SGD S000006460 SNR69 GO:0000154 SGD_REF:S000053492|PMID:10024243 IDA P C/D box snoRNA snR69 gene taxon:4932 20010118 SGD
+SGD S000006495 SNR7-L GO:0005682 SGD_REF:S000066234|PMID:11720284 IDA C U5 snRNA snR7-L|SNR7 gene taxon:4932 20020717 SGD
+SGD S000006495 SNR7-L GO:0046540 SGD_REF:S000056376|PMID:10377396 IPI C U5 snRNA snR7-L|SNR7 gene taxon:4932 20050219 SGD
+SGD S000006495 SNR7-L GO:0046540 SGD_REF:S000039461|PMID:10449419 IDA C U5 snRNA snR7-L|SNR7 gene taxon:4932 20051003 SGD
+SGD S000006495 SNR7-L GO:0030627 SGD_REF:S000070141|PMID:11453062 IDA F U5 snRNA snR7-L|SNR7 gene taxon:4932 20020717 SGD
+SGD S000006495 SNR7-L contributes_to GO:0031202 SGD_REF:S000039461|PMID:10449419 IDA F U5 snRNA snR7-L|SNR7 gene taxon:4932 20051003 SGD
+SGD S000006495 SNR7-L contributes_to GO:0031202 SGD_REF:S000056376|PMID:10377396 IPI F U5 snRNA snR7-L|SNR7 gene taxon:4932 20051003 SGD
+SGD S000006495 SNR7-L GO:0000398 SGD_REF:S000042788|PMID:3555841 IMP P U5 snRNA snR7-L|SNR7 gene taxon:4932 20020717 SGD
+SGD S000006496 SNR7-S GO:0005682 SGD_REF:S000066234|PMID:11720284 IDA C U5 snRNA snR7-S|SNR7 gene taxon:4932 20020717 SGD
+SGD S000006496 SNR7-S GO:0046540 SGD_REF:S000056376|PMID:10377396 IPI C U5 snRNA snR7-S|SNR7 gene taxon:4932 20050219 SGD
+SGD S000006496 SNR7-S GO:0046540 SGD_REF:S000039461|PMID:10449419 IDA C U5 snRNA snR7-S|SNR7 gene taxon:4932 20051003 SGD
+SGD S000006496 SNR7-S GO:0003723 SGD_REF:S000050382|PMID:2440583 IDA F U5 snRNA snR7-S|SNR7 gene taxon:4932 20021118 SGD
+SGD S000006496 SNR7-S contributes_to GO:0031202 SGD_REF:S000039461|PMID:10449419 IDA F U5 snRNA snR7-S|SNR7 gene taxon:4932 20051003 SGD
+SGD S000006496 SNR7-S contributes_to GO:0031202 SGD_REF:S000056376|PMID:10377396 IPI F U5 snRNA snR7-S|SNR7 gene taxon:4932 20051003 SGD
+SGD S000006496 SNR7-S GO:0000398 SGD_REF:S000042788|PMID:3555841 IMP P U5 snRNA snR7-S|SNR7 gene taxon:4932 20020717 SGD
+SGD S000006461 SNR70 GO:0005730 SGD_REF:S000053492|PMID:10024243 TAS C C/D box snoRNA snR70 gene taxon:4932 20020306 SGD
+SGD S000006461 SNR70 GO:0030563 SGD_REF:S000053492|PMID:10024243 ISS F C/D box snoRNA snR70 gene taxon:4932 20020306 SGD
+SGD S000006461 SNR70 GO:0000154 SGD_REF:S000053492|PMID:10024243 ISS P C/D box snoRNA snR70 gene taxon:4932 20020306 SGD
+SGD S000006462 SNR71 GO:0005730 SGD_REF:S000053492|PMID:10024243 TAS C C/D box snoRNA snR71 gene taxon:4932 20020306 SGD
+SGD S000006462 SNR71 GO:0030563 SGD_REF:S000053492|PMID:10024243 IDA F C/D box snoRNA snR71 gene taxon:4932 20020306 SGD
+SGD S000006462 SNR71 GO:0000154 SGD_REF:S000053492|PMID:10024243 IDA P C/D box snoRNA snR71 gene taxon:4932 20010118 SGD
+SGD S000007306 SNR72 GO:0005730 SGD_REF:S000053492|PMID:10024243 TAS C C/D box snoRNA snR72 gene taxon:4932 20020306 SGD
+SGD S000007306 SNR72 GO:0030563 SGD_REF:S000053492|PMID:10024243 IDA F C/D box snoRNA snR72 gene taxon:4932 20020306 SGD
+SGD S000007306 SNR72 GO:0000154 SGD_REF:S000053492|PMID:10024243 IDA P C/D box snoRNA snR72 gene taxon:4932 20010118 SGD
+SGD S000007307 SNR73 GO:0005730 SGD_REF:S000053492|PMID:10024243 TAS C C/D box snoRNA snR73 gene taxon:4932 20020306 SGD
+SGD S000007307 SNR73 GO:0030563 SGD_REF:S000053492|PMID:10024243 IDA F C/D box snoRNA snR73 gene taxon:4932 20020306 SGD
+SGD S000007307 SNR73 GO:0000154 SGD_REF:S000053492|PMID:10024243 IDA P C/D box snoRNA snR73 gene taxon:4932 20010118 SGD
+SGD S000007308 SNR74 GO:0005730 SGD_REF:S000053492|PMID:10024243 TAS C C/D box snoRNA snR74 gene taxon:4932 20020306 SGD
+SGD S000007308 SNR74 GO:0030563 SGD_REF:S000053492|PMID:10024243 IDA F C/D box snoRNA snR74 gene taxon:4932 20020306 SGD
+SGD S000007308 SNR74 GO:0000154 SGD_REF:S000053492|PMID:10024243 IDA P C/D box snoRNA snR74 gene taxon:4932 20010118 SGD
+SGD S000007309 SNR75 GO:0005730 SGD_REF:S000053492|PMID:10024243 TAS C C/D box snoRNA snR75 gene taxon:4932 20020306 SGD
+SGD S000007309 SNR75 GO:0030563 SGD_REF:S000053492|PMID:10024243 IDA F C/D box snoRNA snR75 gene taxon:4932 20020306 SGD
+SGD S000007309 SNR75 GO:0000154 SGD_REF:S000053492|PMID:10024243 IDA P C/D box snoRNA snR75 gene taxon:4932 20010118 SGD
+SGD S000007310 SNR76 GO:0005730 SGD_REF:S000053492|PMID:10024243 TAS C C/D box snoRNA snR76 gene taxon:4932 20020306 SGD
+SGD S000007310 SNR76 GO:0030563 SGD_REF:S000053492|PMID:10024243 IDA F C/D box snoRNA snR76 gene taxon:4932 20020306 SGD
+SGD S000007310 SNR76 GO:0000154 SGD_REF:S000053492|PMID:10024243 IDA P C/D box snoRNA snR76 gene taxon:4932 20010118 SGD
+SGD S000007311 SNR77 GO:0005730 SGD_REF:S000053492|PMID:10024243 TAS C C/D box snoRNA snR77 gene taxon:4932 20020306 SGD
+SGD S000007311 SNR77 GO:0030563 SGD_REF:S000053492|PMID:10024243 IDA F C/D box snoRNA snR77 gene taxon:4932 20020306 SGD
+SGD S000007311 SNR77 GO:0000154 SGD_REF:S000053492|PMID:10024243 IDA P C/D box snoRNA snR77 gene taxon:4932 20010118 SGD
+SGD S000007312 SNR78 GO:0005730 SGD_REF:S000053492|PMID:10024243 TAS C C/D box snoRNA snR78 gene taxon:4932 20020306 SGD
+SGD S000007312 SNR78 GO:0030563 SGD_REF:S000053492|PMID:10024243 IDA F C/D box snoRNA snR78 gene taxon:4932 20020306 SGD
+SGD S000007312 SNR78 GO:0000154 SGD_REF:S000053492|PMID:10024243 IDA P C/D box snoRNA snR78 gene taxon:4932 20010118 SGD
+SGD S000007313 SNR79 GO:0005730 SGD_REF:S000053492|PMID:10024243 TAS C C/D box snoRNA snR79 gene taxon:4932 20020306 SGD
+SGD S000007313 SNR79 GO:0030563 SGD_REF:S000053492|PMID:10024243 IDA F C/D box snoRNA snR79 gene taxon:4932 20020306 SGD
+SGD S000007313 SNR79 GO:0000154 SGD_REF:S000053492|PMID:10024243 IDA P C/D box snoRNA snR79 gene taxon:4932 20010118 SGD
+SGD S000006497 SNR8 GO:0005730 SGD_REF:S000058471|PMID:9847166 TAS C H/ACA box snoRNA snR8 gene taxon:4932 20020311 SGD
+SGD S000006497 SNR8 GO:0030559 SGD_REF:S000058471|PMID:9847166 TAS F H/ACA box snoRNA snR8 gene taxon:4932 20020311 SGD
+SGD S000006497 SNR8 GO:0000154 SGD_REF:S000058471|PMID:9847166 TAS P H/ACA box snoRNA snR8 gene taxon:4932 20010118 SGD
+SGD S000081374 SNR80 GO:0005730 SGD_REF:S000081218|PMID:15306656 IC GO:0000154|GO:0030559 C H/ACA box snoRNA snR80 gene taxon:4932 20050422 SGD
+SGD S000081374 SNR80 GO:0030559 SGD_REF:S000081218|PMID:15306656 IMP F H/ACA box snoRNA snR80 gene taxon:4932 20050422 SGD
+SGD S000081374 SNR80 GO:0030559 SGD_REF:S000081218|PMID:15306656 ISS F H/ACA box snoRNA snR80 gene taxon:4932 20050422 SGD
+SGD S000081374 SNR80 GO:0000154 SGD_REF:S000081218|PMID:15306656 ISS P H/ACA box snoRNA snR80 gene taxon:4932 20050422 SGD
+SGD S000081374 SNR80 GO:0000154 SGD_REF:S000081218|PMID:15306656 IMP P H/ACA box snoRNA snR80 gene taxon:4932 20050422 SGD
+SGD S000081375 SNR81 GO:0005730 SGD_REF:S000081218|PMID:15306656 IC GO:0000154|GO:0030559 C H/ACA box snoRNA snR81 gene taxon:4932 20050422 SGD
+SGD S000081375 SNR81 GO:0030559 SGD_REF:S000081218|PMID:15306656 IMP F H/ACA box snoRNA snR81 gene taxon:4932 20050422 SGD
+SGD S000081375 SNR81 GO:0030559 SGD_REF:S000081218|PMID:15306656 ISS F H/ACA box snoRNA snR81 gene taxon:4932 20050422 SGD
+SGD S000081375 SNR81 GO:0000154 SGD_REF:S000081218|PMID:15306656 ISS P H/ACA box snoRNA snR81 gene taxon:4932 20050422 SGD
+SGD S000081375 SNR81 GO:0000154 SGD_REF:S000081218|PMID:15306656 IMP P H/ACA box snoRNA snR81 gene taxon:4932 20050422 SGD
+SGD S000028467 SNR82 GO:0005730 SGD_REF:S000081218|PMID:15306656 IC GO:0000154|GO:0030559 C H/ACA box snoRNA snR82|RUF2 gene taxon:4932 20050422 SGD
+SGD S000028467 SNR82 GO:0030529 SGD_REF:S000075318|PMID:14704279 IDA C H/ACA box snoRNA snR82|RUF2 gene taxon:4932 20040401 SGD
+SGD S000028467 SNR82 GO:0030529 SGD_REF:S000075318|PMID:14704279 IPI C H/ACA box snoRNA snR82|RUF2 gene taxon:4932 20040401 SGD
+SGD S000028467 SNR82 GO:0030559 SGD_REF:S000074006|PMID:12853629 ISS F H/ACA box snoRNA snR82|RUF2 gene taxon:4932 20030923 SGD
+SGD S000028467 SNR82 GO:0030559 SGD_REF:S000081218|PMID:15306656 IMP F H/ACA box snoRNA snR82|RUF2 gene taxon:4932 20050422 SGD
+SGD S000028467 SNR82 GO:0030559 SGD_REF:S000081218|PMID:15306656 ISS F H/ACA box snoRNA snR82|RUF2 gene taxon:4932 20050422 SGD
+SGD S000028467 SNR82 GO:0000154 SGD_REF:S000074006|PMID:12853629 ISS P H/ACA box snoRNA snR82|RUF2 gene taxon:4932 20030923 SGD
+SGD S000028467 SNR82 GO:0000154 SGD_REF:S000081218|PMID:15306656 IMP P H/ACA box snoRNA snR82|RUF2 gene taxon:4932 20050422 SGD
+SGD S000028467 SNR82 GO:0000154 SGD_REF:S000081218|PMID:15306656 ISS P H/ACA box snoRNA snR82|RUF2 gene taxon:4932 20050422 SGD
+SGD S000028468 SNR83 GO:0005730 SGD_REF:S000081218|PMID:15306656 IC GO:0000154|GO:0030559 C H/ACA box snoRNA snR83|RUF3 gene taxon:4932 20050422 SGD
+SGD S000028468 SNR83 GO:0030529 SGD_REF:S000075318|PMID:14704279 IDA C H/ACA box snoRNA snR83|RUF3 gene taxon:4932 20040401 SGD
+SGD S000028468 SNR83 GO:0030529 SGD_REF:S000075318|PMID:14704279 IPI C H/ACA box snoRNA snR83|RUF3 gene taxon:4932 20040401 SGD
+SGD S000028468 SNR83 GO:0030559 SGD_REF:S000081218|PMID:15306656 IMP F H/ACA box snoRNA snR83|RUF3 gene taxon:4932 20050422 SGD
+SGD S000028468 SNR83 GO:0030559 SGD_REF:S000081218|PMID:15306656 ISS F H/ACA box snoRNA snR83|RUF3 gene taxon:4932 20050422 SGD
+SGD S000028468 SNR83 GO:0000154 SGD_REF:S000081218|PMID:15306656 ISS P H/ACA box snoRNA snR83|RUF3 gene taxon:4932 20050422 SGD
+SGD S000028468 SNR83 GO:0000154 SGD_REF:S000081218|PMID:15306656 IMP P H/ACA box snoRNA snR83|RUF3 gene taxon:4932 20050422 SGD
+SGD S000028466 SNR84 GO:0005730 SGD_REF:S000081218|PMID:15306656 IC GO:0000154|GO:0030559 C H/ACA box snoRNA snR84|RUF1 gene taxon:4932 20050422 SGD
+SGD S000028466 SNR84 GO:0030529 SGD_REF:S000075318|PMID:14704279 IDA C H/ACA box snoRNA snR84|RUF1 gene taxon:4932 20040401 SGD
+SGD S000028466 SNR84 GO:0030529 SGD_REF:S000075318|PMID:14704279 IPI C H/ACA box snoRNA snR84|RUF1 gene taxon:4932 20040401 SGD
+SGD S000028466 SNR84 GO:0030559 SGD_REF:S000081218|PMID:15306656 IMP F H/ACA box snoRNA snR84|RUF1 gene taxon:4932 20050422 SGD
+SGD S000028466 SNR84 GO:0030559 SGD_REF:S000081218|PMID:15306656 ISS F H/ACA box snoRNA snR84|RUF1 gene taxon:4932 20050422 SGD
+SGD S000028466 SNR84 GO:0000154 SGD_REF:S000081218|PMID:15306656 ISS P H/ACA box snoRNA snR84|RUF1 gene taxon:4932 20050422 SGD
+SGD S000028466 SNR84 GO:0000154 SGD_REF:S000081218|PMID:15306656 IMP P H/ACA box snoRNA snR84|RUF1 gene taxon:4932 20050422 SGD
+SGD S000081376 SNR85 GO:0005730 SGD_REF:S000081218|PMID:15306656 IC GO:0000154|GO:0030559 C H/ACA box snoRNA snR85 gene taxon:4932 20050422 SGD
+SGD S000081376 SNR85 GO:0030559 SGD_REF:S000081218|PMID:15306656 ISS F H/ACA box snoRNA snR85 gene taxon:4932 20050422 SGD
+SGD S000081376 SNR85 GO:0000154 SGD_REF:S000081218|PMID:15306656 ISS P H/ACA box snoRNA snR85 gene taxon:4932 20050422 SGD
+SGD S000114301 SNR87 GO:0005730 SGD_REF:S000114459|PMID:16484372 IC GO:0030563 C C/D box snoRNA snR87 gene taxon:4932 20060303 SGD
+SGD S000114301 SNR87 GO:0030563 SGD_REF:S000114459|PMID:16484372 IMP F C/D box snoRNA snR87 gene taxon:4932 20060303 SGD
+SGD S000114301 SNR87 GO:0000154 SGD_REF:S000114459|PMID:16484372 IMP P C/D box snoRNA snR87 gene taxon:4932 20060303 SGD
+SGD S000007292 SNR9 GO:0005730 SGD_REF:S000058471|PMID:9847166 TAS C H/ACA box snoRNA snR9 gene taxon:4932 20021118 SGD
+SGD S000007292 SNR9 GO:0005554 SGD_REF:S000069584 ND F H/ACA box snoRNA snR9 gene taxon:4932 20021118 SGD
+SGD S000007292 SNR9 GO:0000154 SGD_REF:S000058471|PMID:9847166 ISS P H/ACA box snoRNA snR9 gene taxon:4932 20010118 SGD
+SGD S000000629 SNT1 GO:0000118 SGD_REF:S000066205|PMID:11711434 IPI C YCR033W gene taxon:4932 20021010 SGD
+SGD S000000629 SNT1 contributes_to GO:0017136 SGD_REF:S000066205|PMID:11711434 IPI F YCR033W gene taxon:4932 20051128 SGD
+SGD S000000629 SNT1 GO:0045129 SGD_REF:S000066205|PMID:11711434 IPI F YCR033W gene taxon:4932 20051128 SGD
+SGD S000000629 SNT1 GO:0016575 SGD_REF:S000066205|PMID:11711434 IDA P YCR033W gene taxon:4932 20021010 SGD
+SGD S000000629 SNT1 GO:0016575 SGD_REF:S000066205|PMID:11711434 IPI P YCR033W gene taxon:4932 20021010 SGD
+SGD S000000629 SNT1 GO:0045835 SGD_REF:S000066205|PMID:11711434 IPI P YCR033W gene taxon:4932 20021010 SGD
+SGD S000003099 SNT2 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YGL131C gene taxon:4932 20031028 SGD
+SGD S000003099 SNT2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YGL131C gene taxon:4932 20031028 SGD
+SGD S000003099 SNT2 GO:0003677 SGD_REF:S000081155|PMID:15343339 IPI F YGL131C gene taxon:4932 20050331 SGD
+SGD S000003099 SNT2 GO:0000004 SGD_REF:S000069584 ND P YGL131C gene taxon:4932 20021029 SGD
+SGD S000006305 SNT309 GO:0005681 SGD_REF:S000070110|PMID:12088152 IDA C YPR101W|NTC25 gene taxon:4932 20020905 SGD
+SGD S000006305 SNT309 GO:0005515 SGD_REF:S000056365|PMID:10318896 IPI SGD:S000003959 F YPR101W|NTC25 gene taxon:4932 20050923 SGD
+SGD S000006305 SNT309 contributes_to GO:0031202 SGD_REF:S000052139|PMID:9528791 IMP F YPR101W|NTC25 gene taxon:4932 20050923 SGD
+SGD S000006305 SNT309 GO:0000398 SGD_REF:S000070110|PMID:12088152 IGI P YPR101W|NTC25 gene taxon:4932 20020905 SGD
+SGD S000006305 SNT309 GO:0000398 SGD_REF:S000052139|PMID:9528791 IMP P YPR101W|NTC25 gene taxon:4932 20050923 SGD
+SGD S000006305 SNT309 GO:0000398 SGD_REF:S000070110|PMID:12088152 IPI P YPR101W|NTC25 gene taxon:4932 20020905 SGD
+SGD S000001656 SNU114 GO:0005682 SGD_REF:S000066234|PMID:11720284 IPI C U5 snRNP-specific protein related to EF-2 YKL173W|GIN10 gene taxon:4932 20051003 SGD
+SGD S000001656 SNU114 GO:0046540 SGD_REF:S000056376|PMID:10377396 IPI C U5 snRNP-specific protein related to EF-2 YKL173W|GIN10 gene taxon:4932 20050219 SGD
+SGD S000001656 SNU114 GO:0046540 SGD_REF:S000039461|PMID:10449419 IDA C U5 snRNP-specific protein related to EF-2 YKL173W|GIN10 gene taxon:4932 20050926 SGD
+SGD S000001656 SNU114 GO:0003924 SGD_REF:S000048254|PMID:9233818 IMP F U5 snRNP-specific protein related to EF-2 YKL173W|GIN10 gene taxon:4932 20050527 SGD
+SGD S000001656 SNU114 GO:0003924 SGD_REF:S000048254|PMID:9233818 ISS UniProt:P13639|UniProt:P13551 F U5 snRNP-specific protein related to EF-2 YKL173W|GIN10 gene taxon:4932 20050527 SGD
+SGD S000001656 SNU114 GO:0005525 SGD_REF:S000048254|PMID:9233818 ISS protein_id:D21163 F U5 snRNP-specific protein related to EF-2 YKL173W|GIN10 gene taxon:4932 20050527 SGD
+SGD S000001656 SNU114 GO:0030623 SGD_REF:S000039943|PMID:9848662 IDA F U5 snRNP-specific protein related to EF-2 YKL173W|GIN10 gene taxon:4932 20051006 SGD
+SGD S000001656 SNU114 contributes_to GO:0031202 SGD_REF:S000039461|PMID:10449419 IDA F U5 snRNP-specific protein related to EF-2 YKL173W|GIN10 gene taxon:4932 20051003 SGD
+SGD S000001656 SNU114 contributes_to GO:0031202 SGD_REF:S000056376|PMID:10377396 IPI F U5 snRNP-specific protein related to EF-2 YKL173W|GIN10 gene taxon:4932 20051003 SGD
+SGD S000001656 SNU114 GO:0000349 SGD_REF:S000081766|PMID:15911574 IGI SGD:S000002242|SGD:S000000974|SGD:S000002651|SGD:S000001208|SGD:S000006261|SGD:S000005835|SGD:S000005294|SGD:S000004881|SGD:S000003959|SGD:S000001901 P U5 snRNP-specific protein related to EF-2 YKL173W|GIN10 gene taxon:4932 20051004 SGD
+SGD S000001656 SNU114 GO:0000398 SGD_REF:S000058281|PMID:9476892 TAS P U5 snRNP-specific protein related to EF-2 YKL173W|GIN10 gene taxon:4932 20010118 SGD
+SGD S000001656 SNU114 GO:0000398 SGD_REF:S000048254|PMID:9233818 IMP P U5 snRNP-specific protein related to EF-2 YKL173W|GIN10 gene taxon:4932 20051006 SGD
+SGD S000000752 SNU13 GO:0005730 SGD_REF:S000056415|PMID:10684247 IDA C U3 snoRNP protein, U4/U6.U5 snRNP component YEL026W gene taxon:4932 20020620 SGD
+SGD S000000752 SNU13 GO:0005732 SGD_REF:S000070145|PMID:12068309 IPI C U3 snoRNP protein, U4/U6.U5 snRNP component YEL026W gene taxon:4932 20030224 SGD
+SGD S000000752 SNU13 GO:0046540 SGD_REF:S000056376|PMID:10377396 IPI C U3 snoRNP protein, U4/U6.U5 snRNP component YEL026W gene taxon:4932 20050219 SGD
+SGD S000000752 SNU13 GO:0046540 SGD_REF:S000039461|PMID:10449419 IDA C U3 snoRNP protein, U4/U6.U5 snRNP component YEL026W gene taxon:4932 20050926 SGD
+SGD S000000752 SNU13 GO:0003723 SGD_REF:S000075483|PMID:14730029 IMP F U3 snoRNP protein, U4/U6.U5 snRNP component YEL026W gene taxon:4932 20050223 SGD
+SGD S000000752 SNU13 GO:0003723 SGD_REF:S000075483|PMID:14730029 ISS F U3 snoRNP protein, U4/U6.U5 snRNP component YEL026W gene taxon:4932 20050223 SGD
+SGD S000000752 SNU13 contributes_to GO:0031202 SGD_REF:S000039461|PMID:10449419 IDA F U3 snoRNP protein, U4/U6.U5 snRNP component YEL026W gene taxon:4932 20051003 SGD
+SGD S000000752 SNU13 contributes_to GO:0031202 SGD_REF:S000056376|PMID:10377396 IPI F U3 snoRNP protein, U4/U6.U5 snRNP component YEL026W gene taxon:4932 20051003 SGD
+SGD S000000752 SNU13 GO:0000398 SGD_REF:S000056376|PMID:10377396 IPI P U3 snoRNP protein, U4/U6.U5 snRNP component YEL026W gene taxon:4932 20020620 SGD
+SGD S000000752 SNU13 GO:0000398 SGD_REF:S000075483|PMID:14730029 IMP P U3 snoRNP protein, U4/U6.U5 snRNP component YEL026W gene taxon:4932 20050223 SGD
+SGD S000000752 SNU13 GO:0000398 SGD_REF:S000066234|PMID:11720284 IMP P U3 snoRNP protein, U4/U6.U5 snRNP component YEL026W gene taxon:4932 20051004 SGD
+SGD S000000752 SNU13 GO:0030490 SGD_REF:S000070145|PMID:12068309 IPI P U3 snoRNP protein, U4/U6.U5 snRNP component YEL026W gene taxon:4932 20020905 SGD
+SGD S000000752 SNU13 GO:0030490 SGD_REF:S000075483|PMID:14730029 IMP P U3 snoRNP protein, U4/U6.U5 snRNP component YEL026W gene taxon:4932 20050223 SGD
+SGD S000002256 SNU23 GO:0046540 SGD_REF:S000056376|PMID:10377396 IPI C YDL098C gene taxon:4932 20050219 SGD
+SGD S000002256 SNU23 GO:0046540 SGD_REF:S000039461|PMID:10449419 IDA C YDL098C gene taxon:4932 20050926 SGD
+SGD S000002256 SNU23 contributes_to GO:0031202 SGD_REF:S000056376|PMID:10377396 IPI F YDL098C gene taxon:4932 20020620 SGD
+SGD S000002256 SNU23 contributes_to GO:0031202 SGD_REF:S000039461|PMID:10449419 IDA F YDL098C gene taxon:4932 20051003 SGD
+SGD S000002256 SNU23 contributes_to GO:0031202 SGD_REF:S000039461|PMID:10449419 IMP F YDL098C gene taxon:4932 20051003 SGD
+SGD S000002256 SNU23 GO:0000398 SGD_REF:S000056376|PMID:10377396 IPI P YDL098C gene taxon:4932 20020620 SGD
+SGD S000002256 SNU23 GO:0000398 SGD_REF:S000039461|PMID:10449419 IMP P YDL098C gene taxon:4932 20051003 SGD
+SGD S000002256 SNU23 GO:0000398 SGD_REF:S000066234|PMID:11720284 IMP P YDL098C gene taxon:4932 20051004 SGD
+SGD S000002648 SNU56 GO:0000243 SGD_REF:S000064189|PMID:10072386 IPI C U1 snRNP protein YDR240C|MUD10 gene taxon:4932 20020405 SGD
+SGD S000002648 SNU56 GO:0005685 SGD_REF:S000069986|PMID:11804584 IDA C U1 snRNP protein YDR240C|MUD10 gene taxon:4932 20020621 SGD
+SGD S000002648 SNU56 GO:0005685 SGD_REF:S000044485|PMID:9630245 IDA C U1 snRNP protein YDR240C|MUD10 gene taxon:4932 20050929 SGD
+SGD S000002648 SNU56 GO:0003729 SGD_REF:S000064189|PMID:10072386 IPI F U1 snRNP protein YDR240C|MUD10 gene taxon:4932 20020729 SGD
+SGD S000002648 SNU56 GO:0000398 SGD_REF:S000064189|PMID:10072386 IPI P U1 snRNP protein YDR240C|MUD10 gene taxon:4932 20020729 SGD
+SGD S000005835 SNU66 GO:0046540 SGD_REF:S000056376|PMID:10377396 IPI C YOR308C gene taxon:4932 20050219 SGD
+SGD S000005835 SNU66 GO:0046540 SGD_REF:S000039461|PMID:10449419 IDA C YOR308C gene taxon:4932 20050926 SGD
+SGD S000005835 SNU66 contributes_to GO:0031202 SGD_REF:S000056376|PMID:10377396 IPI F YOR308C gene taxon:4932 20020620 SGD
+SGD S000005835 SNU66 contributes_to GO:0031202 SGD_REF:S000039461|PMID:10449419 IMP F YOR308C gene taxon:4932 20051003 SGD
+SGD S000005835 SNU66 contributes_to GO:0031202 SGD_REF:S000039461|PMID:10449419 IDA F YOR308C gene taxon:4932 20051003 SGD
+SGD S000005835 SNU66 GO:0000398 SGD_REF:S000056376|PMID:10377396 IPI P YOR308C gene taxon:4932 20020620 SGD
+SGD S000005835 SNU66 GO:0000398 SGD_REF:S000066234|PMID:11720284 IMP P YOR308C gene taxon:4932 20051004 SGD
+SGD S000005835 SNU66 GO:0000398 SGD_REF:S000039461|PMID:10449419 IMP P YOR308C gene taxon:4932 20051003 SGD
+SGD S000003245 SNU71 GO:0005685 SGD_REF:S000069986|PMID:11804584 IDA C U1 snRNP protein YGR013W gene taxon:4932 20020621 SGD
+SGD S000003245 SNU71 GO:0005685 SGD_REF:S000044485|PMID:9630245 IDA C U1 snRNP protein YGR013W gene taxon:4932 20050929 SGD
+SGD S000003245 SNU71 GO:0003723 SGD_REF:S000044485|PMID:9630245 IDA F U1 snRNP protein YGR013W gene taxon:4932 20021030 SGD
+SGD S000003245 SNU71 GO:0000398 SGD_REF:S000044485|PMID:9630245 IPI P U1 snRNP protein YGR013W gene taxon:4932 20021030 SGD
+SGD S000005884 SNX3 GO:0005829 SGD_REF:S000050763|PMID:9456318 IDA C sorting nexin YOR357C|GRD19 gene taxon:4932 20020617 SGD
+SGD S000005884 SNX3 GO:0005515 SGD_REF:S000050763|PMID:9456318 IDA F sorting nexin YOR357C|GRD19 gene taxon:4932 20021101 SGD
+SGD S000005884 SNX3 GO:0008104 SGD_REF:S000050763|PMID:9456318 IMP P sorting nexin YOR357C|GRD19 gene taxon:4932 20020617 SGD
+SGD S000003573 SNX4 GO:0016020 SGD_REF:S000070289|PMID:12048214 IPI C YJL036W|ATG24|CVT13 gene taxon:4932 20021003 SGD
+SGD S000003573 SNX4 GO:0008289 SGD_REF:S000070289|PMID:12048214 IDA F YJL036W|ATG24|CVT13 gene taxon:4932 20021003 SGD
+SGD S000003573 SNX4 GO:0006810 SGD_REF:S000070289|PMID:12048214 IDA P YJL036W|ATG24|CVT13 gene taxon:4932 20020821 SGD
+SGD S000003573 SNX4 GO:0006914 SGD_REF:S000070289|PMID:12048214 IDA P YJL036W|ATG24|CVT13 gene taxon:4932 20020821 SGD
+SGD S000002833 SNX41 GO:0005768 SGD_REF:S000072811|PMID:12554655 IDA C YDR425W gene taxon:4932 20030402 SGD
+SGD S000002833 SNX41 GO:0008565 SGD_REF:S000072811|PMID:12554655 IDA F YDR425W gene taxon:4932 20030402 SGD
+SGD S000002833 SNX41 GO:0015031 SGD_REF:S000072811|PMID:12554655 IDA P YDR425W gene taxon:4932 20030402 SGD
+SGD S000004702 SNZ1 GO:0008372 SGD_REF:S000069584 ND C highly conserved 35 kDa protein that shows increased expression after entry into stationary phase YMR096W gene taxon:4932 20030602 SGD
+SGD S000004702 SNZ1 GO:0005515 SGD_REF:S000043128|PMID:10688190 IPI SGD:S000001834|SGD:S000004941|SGD:S000004701 F highly conserved 35 kDa protein that shows increased expression after entry into stationary phase YMR096W gene taxon:4932 20030602 SGD
+SGD S000004702 SNZ1 GO:0005515 SGD_REF:S000053723|PMID:9791124 IPI SGD:S000004701|SGD:S000004702|SGD:S000005277 F highly conserved 35 kDa protein that shows increased expression after entry into stationary phase YMR096W gene taxon:4932 20030602 SGD
+SGD S000004702 SNZ1 GO:0005515 SGD_REF:S000071751|PMID:12271461 IPI SGD:S000001241 F highly conserved 35 kDa protein that shows increased expression after entry into stationary phase YMR096W gene taxon:4932 20030602 SGD
+SGD S000004702 SNZ1 GO:0008614 SGD_REF:S000060055|PMID:11238395 ISS P highly conserved 35 kDa protein that shows increased expression after entry into stationary phase YMR096W gene taxon:4932 20020524 SGD
+SGD S000004702 SNZ1 GO:0008614 SGD_REF:S000053723|PMID:9791124 IDA P highly conserved 35 kDa protein that shows increased expression after entry into stationary phase YMR096W gene taxon:4932 20020524 SGD
+SGD S000004702 SNZ1 GO:0008614 SGD_REF:S000065170|PMID:10438537 ISS P highly conserved 35 kDa protein that shows increased expression after entry into stationary phase YMR096W gene taxon:4932 20020524 SGD
+SGD S000004702 SNZ1 NOT GO:0009228 SGD_REF:S000071751|PMID:12271461 IMP P highly conserved 35 kDa protein that shows increased expression after entry into stationary phase YMR096W gene taxon:4932 20021205 SGD
+SGD S000005277 SNZ2 GO:0008372 SGD_REF:S000069584 ND C YNL333W gene taxon:4932 20030602 SGD
+SGD S000005277 SNZ2 GO:0005515 SGD_REF:S000073225|PMID:10655498 IPI SGD:S000001835|SGD:S000004701|SGD:S000005278|SGD:S000005277 F YNL333W gene taxon:4932 20030602 SGD
+SGD S000005277 SNZ2 GO:0005515 SGD_REF:S000071751|PMID:12271461 IPI SGD:S000003917 F YNL333W gene taxon:4932 20030602 SGD
+SGD S000005277 SNZ2 GO:0005515 SGD_REF:S000043128|PMID:10688190 IPI SGD:S000004529|SGD:S000004941 F YNL333W gene taxon:4932 20030602 SGD
+SGD S000005277 SNZ2 GO:0005515 SGD_REF:S000053723|PMID:9791124 IPI SGD:S000004702 F YNL333W gene taxon:4932 20030602 SGD
+SGD S000005277 SNZ2 GO:0008614 SGD_REF:S000060055|PMID:11238395 ISS P YNL333W gene taxon:4932 20020524 SGD
+SGD S000005277 SNZ2 GO:0008614 SGD_REF:S000065170|PMID:10438537 ISS P YNL333W gene taxon:4932 20020524 SGD
+SGD S000005277 SNZ2 GO:0008614 SGD_REF:S000053723|PMID:9791124 IDA P YNL333W gene taxon:4932 20020524 SGD
+SGD S000005277 SNZ2 GO:0009228 SGD_REF:S000071751|PMID:12271461 IMP P YNL333W gene taxon:4932 20021205 SGD
+SGD S000001835 SNZ3 GO:0008372 SGD_REF:S000069584 ND C YFL059W gene taxon:4932 20030602 SGD
+SGD S000001835 SNZ3 GO:0005515 SGD_REF:S000073225|PMID:10655498 IPI SGD:S000002217|SGD:S000004701|SGD:S000005277|SGD:S000005278|SGD:S000001835 F YFL059W gene taxon:4932 20030602 SGD
+SGD S000001835 SNZ3 GO:0005515 SGD_REF:S000043128|PMID:10688190 IPI SGD:S000001834|SGD:S000004941|SGD:S000004701 F YFL059W gene taxon:4932 20030602 SGD
+SGD S000001835 SNZ3 GO:0008614 SGD_REF:S000060055|PMID:11238395 ISS P YFL059W gene taxon:4932 20020524 SGD
+SGD S000001835 SNZ3 GO:0008614 SGD_REF:S000065170|PMID:10438537 ISS P YFL059W gene taxon:4932 20020524 SGD
+SGD S000001835 SNZ3 GO:0008614 SGD_REF:S000053723|PMID:9791124 IDA P YFL059W gene taxon:4932 20020524 SGD
+SGD S000001835 SNZ3 GO:0009228 SGD_REF:S000071751|PMID:12271461 IMP P YFL059W gene taxon:4932 20021205 SGD
+SGD S000003865 SOD1 GO:0005758 SGD_REF:S000068943|PMID:11500508 IDA C Cu, Zn superoxide dismutase YJR104C|CRS4 gene taxon:4932 20021001 SGD
+SGD S000003865 SOD1 GO:0005829 SGD_REF:S000068943|PMID:11500508 IDA C Cu, Zn superoxide dismutase YJR104C|CRS4 gene taxon:4932 20021001 SGD
+SGD S000003865 SOD1 GO:0004785 SGD_REF:S000057058|PMID:3290902 IDA F Cu, Zn superoxide dismutase YJR104C|CRS4 gene taxon:4932 20021001 SGD
+SGD S000003865 SOD1 GO:0001320 SGD_REF:S000074467|PMID:12966141 TAS P Cu, Zn superoxide dismutase YJR104C|CRS4 gene taxon:4932 20050323 SGD
+SGD S000003865 SOD1 GO:0006801 SGD_REF:S000057058|PMID:3290902 IMP P Cu, Zn superoxide dismutase YJR104C|CRS4 gene taxon:4932 20021001 SGD
+SGD S000003865 SOD1 GO:0006878 SGD_REF:S000049199|PMID:8530401 IGI P Cu, Zn superoxide dismutase YJR104C|CRS4 gene taxon:4932 20021001 SGD
+SGD S000003865 SOD1 GO:0006882 SGD_REF:S000066265|PMID:11581253 IGI P Cu, Zn superoxide dismutase YJR104C|CRS4 gene taxon:4932 20030127 SGD
+SGD S000003865 SOD1 GO:0006882 SGD_REF:S000066265|PMID:11581253 IMP P Cu, Zn superoxide dismutase YJR104C|CRS4 gene taxon:4932 20030127 SGD
+SGD S000001050 SOD2 GO:0005739 SGD_REF:S000069459|PMID:11914276 IDA C Mn-containing superoxide dismutase YHR008C gene taxon:4932 20020507 SGD
+SGD S000001050 SOD2 GO:0005739 SGD_REF:S000081472|PMID:15851472 IDA C Mn-containing superoxide dismutase YHR008C gene taxon:4932 20050503 SGD
+SGD S000001050 SOD2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C Mn-containing superoxide dismutase YHR008C gene taxon:4932 20040924 SGD
+SGD S000001050 SOD2 GO:0005759 SGD_REF:S000056841|PMID:238997 IDA C Mn-containing superoxide dismutase YHR008C gene taxon:4932 20021001 SGD
+SGD S000001050 SOD2 GO:0008383 SGD_REF:S000056841|PMID:238997 IDA F Mn-containing superoxide dismutase YHR008C gene taxon:4932 20021001 SGD
+SGD S000001050 SOD2 GO:0008383 SGD_REF:S000081472|PMID:15851472 IDA F Mn-containing superoxide dismutase YHR008C gene taxon:4932 20050503 SGD
+SGD S000001050 SOD2 GO:0001302 SGD_REF:S000075416|PMID:14741356 IMP P Mn-containing superoxide dismutase YHR008C gene taxon:4932 20041025 SGD
+SGD S000001050 SOD2 GO:0001320 SGD_REF:S000061085|PMID:10222047 IMP P Mn-containing superoxide dismutase YHR008C gene taxon:4932 20050323 SGD
+SGD S000001050 SOD2 GO:0001324 SGD_REF:S000060129|PMID:11292860 IMP P Mn-containing superoxide dismutase YHR008C gene taxon:4932 20041025 SGD
+SGD S000001050 SOD2 GO:0006800 SGD_REF:S000057104|PMID:3520557 IMP P Mn-containing superoxide dismutase YHR008C gene taxon:4932 20021001 SGD
+SGD S000006553 SOE1 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tRNA-Glu tE(UUC)G1 gene taxon:4932 20030507 SGD
+SGD S000006553 SOE1 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tRNA-Glu tE(UUC)G1 gene taxon:4932 20030507 SGD
+SGD S000006553 SOE1 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tRNA-Glu tE(UUC)G1 gene taxon:4932 20030507 SGD
+SGD S000003934 SOF1 GO:0005730 SGD_REF:S000077530|PMID:15367670 IDA C U3 snoRNP protein YLL011W gene taxon:4932 20050616 SGD
+SGD S000003934 SOF1 GO:0005732 SGD_REF:S000058443|PMID:10690410 TAS C U3 snoRNP protein YLL011W gene taxon:4932 20010118 SGD
+SGD S000003934 SOF1 GO:0005732 SGD_REF:S000070145|PMID:12068309 IPI C U3 snoRNP protein YLL011W gene taxon:4932 20030224 SGD
+SGD S000003934 SOF1 GO:0030532 SGD_REF:S000058443|PMID:10690410 TAS C U3 snoRNP protein YLL011W gene taxon:4932 20020219 SGD
+SGD S000003934 SOF1 GO:0030515 SGD_REF:S000054600|PMID:8508778 IPI F U3 snoRNP protein YLL011W gene taxon:4932 20030224 SGD
+SGD S000003934 SOF1 GO:0000154 SGD_REF:S000058443|PMID:10690410 TAS P U3 snoRNP protein YLL011W gene taxon:4932 20010118 SGD
+SGD S000003934 SOF1 GO:0006365 SGD_REF:S000058443|PMID:10690410 TAS P U3 snoRNP protein YLL011W gene taxon:4932 20010118 SGD
+SGD S000003934 SOF1 GO:0030490 SGD_REF:S000070145|PMID:12068309 IPI P U3 snoRNP protein YLL011W gene taxon:4932 20020905 SGD
+SGD S000005880 SOG2 GO:0000131 SGD_REF:S000074101|PMID:12972564 IDA C YOR353C gene taxon:4932 20031016 SGD
+SGD S000005880 SOG2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YOR353C gene taxon:4932 20031028 SGD
+SGD S000005880 SOG2 GO:0005933 SGD_REF:S000074101|PMID:12972564 IDA C YOR353C gene taxon:4932 20031016 SGD
+SGD S000005880 SOG2 GO:0043332 SGD_REF:S000074101|PMID:12972564 IDA C YOR353C gene taxon:4932 20031016 SGD
+SGD S000005880 SOG2 GO:0005554 SGD_REF:S000069584 ND F YOR353C gene taxon:4932 20021011 SGD
+SGD S000005880 SOG2 GO:0000903 SGD_REF:S000074101|PMID:12972564 IGI P YOR353C gene taxon:4932 20050420 SGD
+SGD S000003095 SOH1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YGL127C|MED31 gene taxon:4932 20031028 SGD
+SGD S000003095 SOH1 GO:0005554 SGD_REF:S000069584 ND F YGL127C|MED31 gene taxon:4932 20021009 SGD
+SGD S000003095 SOH1 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P YGL127C|MED31 gene taxon:4932 20060203 SGD
+SGD S000003095 SOH1 GO:0006281 SGD_REF:S000051944|PMID:8849885 IPI P YGL127C|MED31 gene taxon:4932 20021009 SGD
+SGD S000003095 SOH1 GO:0006366 SGD_REF:S000051944|PMID:8849885 IGI P YGL127C|MED31 gene taxon:4932 20021009 SGD
+SGD S000002413 SOK1 GO:0005634 SGD_REF:S000057589|PMID:8065298 IDA C YDR006C gene taxon:4932 20021016 SGD
+SGD S000002413 SOK1 GO:0005554 SGD_REF:S000069584 ND F YDR006C gene taxon:4932 20021016 SGD
+SGD S000002413 SOK1 GO:0019933 SGD_REF:S000057589|PMID:8065298 IGI P YDR006C gene taxon:4932 20021016 SGD
+SGD S000004618 SOK2 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C transcription factor (putative) YMR016C gene taxon:4932 20031028 SGD
+SGD S000004618 SOK2 GO:0003700 SGD_REF:S000051553|PMID:8524252 ISS F transcription factor (putative) YMR016C gene taxon:4932 20010626 SGD
+SGD S000004618 SOK2 GO:0007124 SGD_REF:S000051553|PMID:8524252 IMP P transcription factor (putative) YMR016C gene taxon:4932 20010626 SGD
+SGD S000004618 SOK2 GO:0007124 SGD_REF:S000059111|PMID:11046133 IMP P transcription factor (putative) YMR016C gene taxon:4932 20010626 SGD
+SGD S000005317 SOL1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YNR034W gene taxon:4932 20031028 SGD
+SGD S000005317 SOL1 GO:0005634 SGD_REF:S000079013|PMID:15454531 IDA C YNR034W gene taxon:4932 20050121 SGD
+SGD S000005317 SOL1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YNR034W gene taxon:4932 20031028 SGD
+SGD S000005317 SOL1 GO:0005554 SGD_REF:S000069584 ND F YNR034W gene taxon:4932 20050124 SGD
+SGD S000005317 SOL1 NOT GO:0017057 SGD_REF:S000079013|PMID:15454531 IDA F YNR034W gene taxon:4932 20050121 SGD
+SGD S000005317 SOL1 GO:0006409 SGD_REF:S000079013|PMID:15454531 IGI P YNR034W gene taxon:4932 20050121 SGD
+SGD S000005317 SOL1 GO:0006409 SGD_REF:S000079013|PMID:15454531 IMP P YNR034W gene taxon:4932 20050121 SGD
+SGD S000005317 SOL1 GO:0008033 SGD_REF:S000046777|PMID:8725220 IGI P YNR034W gene taxon:4932 20020927 SGD
+SGD S000005317 SOL1 GO:0008033 SGD_REF:S000046777|PMID:8725220 IMP P YNR034W gene taxon:4932 20020927 SGD
+SGD S000000718 SOL2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YCR073W-A|YCRX13W gene taxon:4932 20031028 SGD
+SGD S000000718 SOL2 GO:0005829 SGD_REF:S000079013|PMID:15454531 IDA C YCR073W-A|YCRX13W gene taxon:4932 20050121 SGD
+SGD S000000718 SOL2 GO:0005554 SGD_REF:S000069584 ND F YCR073W-A|YCRX13W gene taxon:4932 20050124 SGD
+SGD S000000718 SOL2 NOT GO:0017057 SGD_REF:S000079013|PMID:15454531 IDA F YCR073W-A|YCRX13W gene taxon:4932 20050121 SGD
+SGD S000000718 SOL2 GO:0006409 SGD_REF:S000079013|PMID:15454531 IGI P YCR073W-A|YCRX13W gene taxon:4932 20050121 SGD
+SGD S000000718 SOL2 GO:0006409 SGD_REF:S000079013|PMID:15454531 IMP P YCR073W-A|YCRX13W gene taxon:4932 20050121 SGD
+SGD S000000718 SOL2 GO:0008033 SGD_REF:S000046777|PMID:8725220 IGI P YCR073W-A|YCRX13W gene taxon:4932 20020927 SGD
+SGD S000000718 SOL2 GO:0008033 SGD_REF:S000046777|PMID:8725220 IMP P YCR073W-A|YCRX13W gene taxon:4932 20020927 SGD
+SGD S000001206 SOL3 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C 6-phosphogluconolactonase YHR163W gene taxon:4932 20031028 SGD
+SGD S000001206 SOL3 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C 6-phosphogluconolactonase YHR163W gene taxon:4932 20031028 SGD
+SGD S000001206 SOL3 GO:0017057 SGD_REF:S000074038|PMID:10518023 ISS F 6-phosphogluconolactonase YHR163W gene taxon:4932 20031104 SGD
+SGD S000001206 SOL3 GO:0017057 SGD_REF:S000079013|PMID:15454531 IDA F 6-phosphogluconolactonase YHR163W gene taxon:4932 20050121 SGD
+SGD S000001206 SOL3 GO:0009051 SGD_REF:S000072715|PMID:12570990 IEP P 6-phosphogluconolactonase YHR163W gene taxon:4932 20030310 SGD
+SGD S000001206 SOL3 GO:0009051 SGD_REF:S000072715|PMID:12570990 ISS P 6-phosphogluconolactonase YHR163W gene taxon:4932 20030310 SGD
+SGD S000003480 SOL4 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C 6-phosphogluconolactonase YGR248W gene taxon:4932 20031028 SGD
+SGD S000003480 SOL4 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C 6-phosphogluconolactonase YGR248W gene taxon:4932 20031028 SGD
+SGD S000003480 SOL4 GO:0005829 SGD_REF:S000079013|PMID:15454531 IDA C 6-phosphogluconolactonase YGR248W gene taxon:4932 20050121 SGD
+SGD S000003480 SOL4 GO:0017057 SGD_REF:S000074038|PMID:10518023 ISS F 6-phosphogluconolactonase YGR248W gene taxon:4932 20031104 SGD
+SGD S000003480 SOL4 GO:0017057 SGD_REF:S000079013|PMID:15454531 IDA F 6-phosphogluconolactonase YGR248W gene taxon:4932 20050121 SGD
+SGD S000003480 SOL4 GO:0009051 SGD_REF:S000079013|PMID:15454531 IC GO:0017057 P 6-phosphogluconolactonase YGR248W gene taxon:4932 20050802 SGD
+SGD S000002954 SOM1 GO:0005743 SGD_REF:S000044726|PMID:9604886 IDA C YEL059C-A gene taxon:4932 20020927 SGD
+SGD S000002954 SOM1 GO:0042720 SGD_REF:S000063720|PMID:10821182 IPI C YEL059C-A gene taxon:4932 20030430 SGD
+SGD S000002954 SOM1 GO:0005554 SGD_REF:S000069584 ND F YEL059C-A gene taxon:4932 20020927 SGD
+SGD S000002954 SOM1 GO:0006508 SGD_REF:S000040966|PMID:8879245 IGI P YEL059C-A gene taxon:4932 20020927 SGD
+SGD S000002954 SOM1 GO:0006508 SGD_REF:S000040966|PMID:8879245 ISS P YEL059C-A gene taxon:4932 20020927 SGD
+SGD S000002954 SOM1 GO:0006508 SGD_REF:S000063720|PMID:10821182 IMP P YEL059C-A gene taxon:4932 20020927 SGD
+SGD S000002954 SOM1 GO:0006508 SGD_REF:S000063720|PMID:10821182 IPI P YEL059C-A gene taxon:4932 20020927 SGD
+SGD S000002954 SOM1 GO:0006508 SGD_REF:S000063720|PMID:10821182 IGI P YEL059C-A gene taxon:4932 20020927 SGD
+SGD S000003728 SOP4 GO:0000299 SGD_REF:S000072752|PMID:12230471 IDA C YJL192C gene taxon:4932 20030321 SGD
+SGD S000003728 SOP4 GO:0005783 SGD_REF:S000072752|PMID:12230471 IDA C YJL192C gene taxon:4932 20030321 SGD
+SGD S000003728 SOP4 GO:0005554 SGD_REF:S000069584 ND F YJL192C gene taxon:4932 20030321 SGD
+SGD S000003728 SOP4 GO:0006888 SGD_REF:S000072752|PMID:12230471 IMP P YJL192C gene taxon:4932 20030321 SGD
+SGD S000003920 SOR1 GO:0008372 SGD_REF:S000069584 ND C sorbitol dehydrogenase, sorbitol-induced YJR159W|SDH1 gene taxon:4932 20021031 SGD
+SGD S000003920 SOR1 GO:0003939 SGD_REF:S000057608|PMID:8125328 ISS F sorbitol dehydrogenase, sorbitol-induced YJR159W|SDH1 gene taxon:4932 20020930 SGD
+SGD S000003920 SOR1 GO:0006000 SGD_REF:S000071379|PMID:11752249 NAS P sorbitol dehydrogenase, sorbitol-induced YJR159W|SDH1 gene taxon:4932 20020930 SGD
+SGD S000003920 SOR1 GO:0006013 SGD_REF:S000071379|PMID:11752249 NAS P sorbitol dehydrogenase, sorbitol-induced YJR159W|SDH1 gene taxon:4932 20020930 SGD
+SGD S000002405 SOR2 GO:0008372 SGD_REF:S000069584 ND C YDL246C gene taxon:4932 20060315 SGD
+SGD S000002405 SOR2 GO:0016616 SGD_REF:S000056335|PMID:10938079 ISS F YDL246C gene taxon:4932 20030122 SGD
+SGD S000002405 SOR2 GO:0019318 SGD_REF:S000074191|PMID:14566057 RCA P YDL246C gene taxon:4932 20050608 SGD
+SGD S000004670 SOV1 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YMR066W gene taxon:4932 20031028 SGD
+SGD S000004670 SOV1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YMR066W gene taxon:4932 20040924 SGD
+SGD S000004670 SOV1 GO:0005554 SGD_REF:S000069584 ND F YMR066W gene taxon:4932 20050725 SGD
+SGD S000004670 SOV1 GO:0000004 SGD_REF:S000069584 ND P YMR066W gene taxon:4932 20050725 SGD
+SGD S000000398 SOY1 GO:0005737 SGD_REF:S000056415|PMID:10684247 IDA C YBR194W gene taxon:4932 20001207 SGD
+SGD S000000398 SOY1 GO:0005554 SGD_REF:S000069584 ND F YBR194W gene taxon:4932 20020425 SGD
+SGD S000000398 SOY1 GO:0000004 SGD_REF:S000069584 ND P YBR194W gene taxon:4932 20020425 SGD
+SGD S000029478 SPA1 GO:0008372 SGD_REF:S000069584 ND C spindle pole antigen gene taxon:4932 20020617 SGD
+SGD S000029478 SPA1 GO:0005554 SGD_REF:S000069584 ND F spindle pole antigen gene taxon:4932 20020617 SGD
+SGD S000029478 SPA1 GO:0007059 SGD_REF:S000043736|PMID:3044610 IMP P spindle pole antigen gene taxon:4932 20020617 SGD
+SGD S000029478 SPA1 GO:0007097 SGD_REF:S000043736|PMID:3044610 IMP P spindle pole antigen gene taxon:4932 20020617 SGD
+SGD S000003944 SPA2 GO:0000131 SGD_REF:S000040502|PMID:9214378 IDA C YLL021W|FUS6|PEA1 gene taxon:4932 20030827 SGD
+SGD S000003944 SPA2 GO:0000133 SGD_REF:S000046605|PMID:10639324 TAS C YLL021W|FUS6|PEA1 gene taxon:4932 20010118 SGD
+SGD S000003944 SPA2 GO:0005934 SGD_REF:S000073832|PMID:12361575 IDA C YLL021W|FUS6|PEA1 gene taxon:4932 20030827 SGD
+SGD S000003944 SPA2 GO:0005935 SGD_REF:S000040502|PMID:9214378 IDA C YLL021W|FUS6|PEA1 gene taxon:4932 20030827 SGD
+SGD S000003944 SPA2 GO:0043332 SGD_REF:S000040502|PMID:9214378 IDA C YLL021W|FUS6|PEA1 gene taxon:4932 20030827 SGD
+SGD S000003944 SPA2 GO:0005519 SGD_REF:S000046605|PMID:10639324 IPI F YLL021W|FUS6|PEA1 gene taxon:4932 20010118 SGD
+SGD S000003944 SPA2 GO:0007015 SGD_REF:S000046605|PMID:10639324 IPI P YLL021W|FUS6|PEA1 gene taxon:4932 20010118 SGD
+SGD S000003944 SPA2 GO:0007121 SGD_REF:S000041005|PMID:10652251 TAS P YLL021W|FUS6|PEA1 gene taxon:4932 20010118 SGD
+SGD S000003944 SPA2 GO:0007124 SGD_REF:S000045317|PMID:9443897 IMP P YLL021W|FUS6|PEA1 gene taxon:4932 20010118 SGD
+SGD S000003944 SPA2 GO:0007266 SGD_REF:S000046605|PMID:10639324 IPI P YLL021W|FUS6|PEA1 gene taxon:4932 20010118 SGD
+SGD S000003944 SPA2 GO:0030468 SGD_REF:S000046605|PMID:10639324 IMP P YLL021W|FUS6|PEA1 gene taxon:4932 20010302 SGD
+SGD S000003944 SPA2 GO:0030468 SGD_REF:S000046605|PMID:10639324 IPI P YLL021W|FUS6|PEA1 gene taxon:4932 20010302 SGD
+SGD S000003944 SPA2 GO:0031384 SGD_REF:S000077102|PMID:14734532 IMP P YLL021W|FUS6|PEA1 gene taxon:4932 20050719 SGD
+SGD S000003944 SPA2 GO:0031385 SGD_REF:S000077102|PMID:14734532 IMP P YLL021W|FUS6|PEA1 gene taxon:4932 20050719 SGD
+SGD S000000559 SPB1 GO:0005634 SGD_REF:S000042751|PMID:10556316 IDA C AdoMet-dependent rRNA methyltransferase YCL054W gene taxon:4932 20010118 SGD
+SGD S000000559 SPB1 GO:0005730 SGD_REF:S000042751|PMID:10556316 IDA C AdoMet-dependent rRNA methyltransferase YCL054W gene taxon:4932 20010118 SGD
+SGD S000000559 SPB1 GO:0005730 SGD_REF:S000050020|PMID:10648622 IDA C AdoMet-dependent rRNA methyltransferase YCL054W gene taxon:4932 20041122 SGD
+SGD S000000559 SPB1 GO:0008650 SGD_REF:S000075306|PMID:14636587 IGI SGD:S000006443 F AdoMet-dependent rRNA methyltransferase YCL054W gene taxon:4932 20060512 SGD
+SGD S000000559 SPB1 GO:0016435 SGD_REF:S000079655|PMID:15546625 IDA F AdoMet-dependent rRNA methyltransferase YCL054W gene taxon:4932 20060512 SGD
+SGD S000000559 SPB1 GO:0030489 SGD_REF:S000042751|PMID:10556316 IMP P AdoMet-dependent rRNA methyltransferase YCL054W gene taxon:4932 20040709 SGD
+SGD S000000559 SPB1 GO:0030489 SGD_REF:S000050020|PMID:10648622 IMP P AdoMet-dependent rRNA methyltransferase YCL054W gene taxon:4932 20060512 SGD
+SGD S000000559 SPB1 GO:0030489 SGD_REF:S000079655|PMID:15546625 IDA P AdoMet-dependent rRNA methyltransferase YCL054W gene taxon:4932 20060512 SGD
+SGD S000000559 SPB1 GO:0031167 SGD_REF:S000075306|PMID:14636587 IGI SGD:S000006443 P AdoMet-dependent rRNA methyltransferase YCL054W gene taxon:4932 20060512 SGD
+SGD S000000559 SPB1 GO:0031167 SGD_REF:S000079655|PMID:15546625 IMP P AdoMet-dependent rRNA methyltransferase YCL054W gene taxon:4932 20060512 SGD
+SGD S000000559 SPB1 GO:0031167 SGD_REF:S000079655|PMID:15546625 IDA P AdoMet-dependent rRNA methyltransferase YCL054W gene taxon:4932 20060512 SGD
+SGD S000000559 SPB1 GO:0031167 SGD_REF:S000079655|PMID:15546625 IGI SGD:S000006443 P AdoMet-dependent rRNA methyltransferase YCL054W gene taxon:4932 20060512 SGD
+SGD S000001894 SPB4 GO:0005730 SGD_REF:S000058443|PMID:10690410 TAS C ATP dependent RNA helicase YFL002C gene taxon:4932 20010118 SGD
+SGD S000001894 SPB4 GO:0004004 SGD_REF:S000058443|PMID:10690410 TAS F ATP dependent RNA helicase YFL002C gene taxon:4932 20010118 SGD
+SGD S000001894 SPB4 GO:0000027 SGD_REF:S000058443|PMID:10690410 TAS P ATP dependent RNA helicase YFL002C gene taxon:4932 20010118 SGD
+SGD S000001894 SPB4 GO:0006365 SGD_REF:S000058443|PMID:10690410 TAS P ATP dependent RNA helicase YFL002C gene taxon:4932 20010118 SGD
+SGD S000003770 SPC1 GO:0005787 SGD_REF:S000056198|PMID:1846444 IDA C YJR010C-A gene taxon:4932 20010118 SGD
+SGD S000003770 SPC1 GO:0005554 SGD_REF:S000058467|PMID:10921929 TAS F YJR010C-A gene taxon:4932 20010118 SGD
+SGD S000003770 SPC1 GO:0006465 SGD_REF:S000051985|PMID:8663399 IPI P YJR010C-A gene taxon:4932 20010118 SGD
+SGD S000003770 SPC1 GO:0006465 SGD_REF:S000056198|PMID:1846444 IPI P YJR010C-A gene taxon:4932 20010118 SGD
+SGD S000003770 SPC1 GO:0006465 SGD_REF:S000051985|PMID:8663399 IMP P YJR010C-A gene taxon:4932 20010118 SGD
+SGD S000003770 SPC1 GO:0006465 SGD_REF:S000051985|PMID:8663399 ISS P YJR010C-A gene taxon:4932 20010118 SGD
+SGD S000003770 SPC1 GO:0006465 SGD_REF:S000051985|PMID:8663399 IGI P YJR010C-A gene taxon:4932 20010118 SGD
+SGD S000003061 SPC105 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C spindle pole component YGL093W gene taxon:4932 20040928 SGD
+SGD S000003061 SPC105 GO:0005816 SGD_REF:S000047788|PMID:9585415 IDA C spindle pole component YGL093W gene taxon:4932 20010118 SGD
+SGD S000003061 SPC105 GO:0005200 SGD_REF:S000047788|PMID:9585415 IPI F spindle pole component YGL093W gene taxon:4932 20010118 SGD
+SGD S000003061 SPC105 GO:0007020 SGD_REF:S000058447|PMID:9153752 IPI P spindle pole component YGL093W gene taxon:4932 20010118 SGD
+SGD S000002764 SPC110 GO:0005822 SGD_REF:S000043896|PMID:9215630 IDA C interacts with Spc42p, calmodulin, and a 35 kDa protein, spindle pole body component YDR356W|NUF1|XCM1 gene taxon:4932 20010118 SGD
+SGD S000002764 SPC110 GO:0005823 SGD_REF:S000043896|PMID:9215630 IDA C interacts with Spc42p, calmodulin, and a 35 kDa protein, spindle pole body component YDR356W|NUF1|XCM1 gene taxon:4932 20010118 SGD
+SGD S000002764 SPC110 GO:0005200 SGD_REF:S000043896|PMID:9215630 IPI F interacts with Spc42p, calmodulin, and a 35 kDa protein, spindle pole body component YDR356W|NUF1|XCM1 gene taxon:4932 20010118 SGD
+SGD S000002764 SPC110 GO:0007020 SGD_REF:S000058447|PMID:9153752 IPI P interacts with Spc42p, calmodulin, and a 35 kDa protein, spindle pole body component YDR356W|NUF1|XCM1 gene taxon:4932 20010118 SGD
+SGD S000002609 SPC19 GO:0000778 SGD_REF:S000069091|PMID:11756468 IDA C spindle pole component YDR201W gene taxon:4932 20021008 SGD
+SGD S000002609 SPC19 GO:0000778 SGD_REF:S000080960|PMID:11511347 IDA C spindle pole component YDR201W gene taxon:4932 20050307 SGD
+SGD S000002609 SPC19 GO:0005816 SGD_REF:S000047788|PMID:9585415 IDA C spindle pole component YDR201W gene taxon:4932 20010118 SGD
+SGD S000002609 SPC19 GO:0005819 SGD_REF:S000069091|PMID:11756468 IDA C spindle pole component YDR201W gene taxon:4932 20021008 SGD
+SGD S000002609 SPC19 GO:0005876 SGD_REF:S000080960|PMID:11511347 IDA C spindle pole component YDR201W gene taxon:4932 20050307 SGD
+SGD S000002609 SPC19 GO:0042729 SGD_REF:S000069052|PMID:11799062 IDA C spindle pole component YDR201W gene taxon:4932 20040122 SGD
+SGD S000002609 SPC19 GO:0042729 SGD_REF:S000080444|PMID:15640796 IPI C spindle pole component YDR201W gene taxon:4932 20050328 SGD
+SGD S000002609 SPC19 GO:0042729 SGD_REF:S000080667|PMID:15664196 IPI C spindle pole component YDR201W gene taxon:4932 20050328 SGD
+SGD S000002609 SPC19 GO:0042729 SGD_REF:S000080667|PMID:15664196 IDA C spindle pole component YDR201W gene taxon:4932 20050328 SGD
+SGD S000002609 SPC19 GO:0042729 SGD_REF:S000080444|PMID:15640796 IDA C spindle pole component YDR201W gene taxon:4932 20050328 SGD
+SGD S000002609 SPC19 GO:0042729 SGD_REF:S000069052|PMID:11799062 IPI C spindle pole component YDR201W gene taxon:4932 20040122 SGD
+SGD S000002609 SPC19 GO:0005200 SGD_REF:S000047788|PMID:9585415 IPI F spindle pole component YDR201W gene taxon:4932 20010118 SGD
+SGD S000002609 SPC19 GO:0007020 SGD_REF:S000058447|PMID:9153752 IPI P spindle pole component YDR201W gene taxon:4932 20010118 SGD
+SGD S000002609 SPC19 GO:0030472 SGD_REF:S000069091|PMID:11756468 IPI P spindle pole component YDR201W gene taxon:4932 20021008 SGD
+SGD S000002609 SPC19 GO:0031110 SGD_REF:S000080667|PMID:15664196 IPI P spindle pole component YDR201W gene taxon:4932 20050328 SGD
+SGD S000002609 SPC19 GO:0031110 SGD_REF:S000080667|PMID:15664196 IDA P spindle pole component YDR201W gene taxon:4932 20050328 SGD
+SGD S000004519 SPC2 GO:0005787 SGD_REF:S000056198|PMID:1846444 IDA C signal peptidase complex subunit, similar to mammalian protein SPC25 YML055W|SPY1 gene taxon:4932 20010118 SGD
+SGD S000004519 SPC2 GO:0005515 SGD_REF:S000058467|PMID:10921929 IMP F signal peptidase complex subunit, similar to mammalian protein SPC25 YML055W|SPY1 gene taxon:4932 20010118 SGD
+SGD S000004519 SPC2 GO:0006465 SGD_REF:S000058467|PMID:10921929 IMP P signal peptidase complex subunit, similar to mammalian protein SPC25 YML055W|SPY1 gene taxon:4932 20010118 SGD
+SGD S000004519 SPC2 GO:0006465 SGD_REF:S000047958|PMID:8910564 IPI P signal peptidase complex subunit, similar to mammalian protein SPC25 YML055W|SPY1 gene taxon:4932 20010118 SGD
+SGD S000004519 SPC2 GO:0006465 SGD_REF:S000047958|PMID:8910564 ISS P signal peptidase complex subunit, similar to mammalian protein SPC25 YML055W|SPY1 gene taxon:4932 20010118 SGD
+SGD S000004519 SPC2 GO:0006465 SGD_REF:S000047958|PMID:8910564 IGI P signal peptidase complex subunit, similar to mammalian protein SPC25 YML055W|SPY1 gene taxon:4932 20010118 SGD
+SGD S000004519 SPC2 GO:0006465 SGD_REF:S000058467|PMID:10921929 IPI P signal peptidase complex subunit, similar to mammalian protein SPC25 YML055W|SPY1 gene taxon:4932 20010118 SGD
+SGD S000004723 SPC24 GO:0000778 SGD_REF:S000062011|PMID:11179222 IMP C spindle pole component YMR117C gene taxon:4932 20030403 SGD
+SGD S000004723 SPC24 GO:0000778 SGD_REF:S000080960|PMID:11511347 IDA C spindle pole component YMR117C gene taxon:4932 20050307 SGD
+SGD S000004723 SPC24 GO:0000778 SGD_REF:S000062011|PMID:11179222 IPI C spindle pole component YMR117C gene taxon:4932 20030403 SGD
+SGD S000004723 SPC24 GO:0000780 SGD_REF:S000059963|PMID:11266451 IGI C spindle pole component YMR117C gene taxon:4932 20030404 SGD
+SGD S000004723 SPC24 GO:0000780 SGD_REF:S000059963|PMID:11266451 IPI C spindle pole component YMR117C gene taxon:4932 20030404 SGD
+SGD S000004723 SPC24 GO:0031262 SGD_REF:S000059963|PMID:11266451 IDA C spindle pole component YMR117C gene taxon:4932 20050303 SGD
+SGD S000004723 SPC24 GO:0031262 SGD_REF:S000062011|PMID:11179222 IDA C spindle pole component YMR117C gene taxon:4932 20050303 SGD
+SGD S000004723 SPC24 GO:0005200 SGD_REF:S000047788|PMID:9585415 IPI F spindle pole component YMR117C gene taxon:4932 20010118 SGD
+SGD S000004723 SPC24 GO:0007020 SGD_REF:S000058447|PMID:9153752 IPI P spindle pole component YMR117C gene taxon:4932 20010118 SGD
+SGD S000004723 SPC24 GO:0007059 SGD_REF:S000059963|PMID:11266451 IMP P spindle pole component YMR117C gene taxon:4932 20020214 SGD
+SGD S000004723 SPC24 GO:0007059 SGD_REF:S000059963|PMID:11266451 IGI P spindle pole component YMR117C gene taxon:4932 20020214 SGD
+SGD S000000820 SPC25 GO:0000778 SGD_REF:S000062011|PMID:11179222 IMP C spindle pole component YER018C gene taxon:4932 20030404 SGD
+SGD S000000820 SPC25 GO:0000778 SGD_REF:S000080960|PMID:11511347 IDA C spindle pole component YER018C gene taxon:4932 20050307 SGD
+SGD S000000820 SPC25 GO:0000778 SGD_REF:S000062011|PMID:11179222 IPI C spindle pole component YER018C gene taxon:4932 20030404 SGD
+SGD S000000820 SPC25 GO:0000780 SGD_REF:S000059963|PMID:11266451 IGI C spindle pole component YER018C gene taxon:4932 20030404 SGD
+SGD S000000820 SPC25 GO:0000780 SGD_REF:S000059963|PMID:11266451 IPI C spindle pole component YER018C gene taxon:4932 20030404 SGD
+SGD S000000820 SPC25 GO:0031262 SGD_REF:S000059963|PMID:11266451 IDA C spindle pole component YER018C gene taxon:4932 20050303 SGD
+SGD S000000820 SPC25 GO:0031262 SGD_REF:S000062011|PMID:11179222 IPI SGD:S000004723|SGD:S000005430 C spindle pole component YER018C gene taxon:4932 20050303 SGD
+SGD S000000820 SPC25 GO:0031262 SGD_REF:S000062011|PMID:11179222 IDA C spindle pole component YER018C gene taxon:4932 20050303 SGD
+SGD S000000820 SPC25 GO:0005200 SGD_REF:S000047788|PMID:9585415 IPI F spindle pole component YER018C gene taxon:4932 20010118 SGD
+SGD S000000820 SPC25 GO:0007020 SGD_REF:S000058447|PMID:9153752 IPI P spindle pole component YER018C gene taxon:4932 20010118 SGD
+SGD S000000820 SPC25 GO:0007059 SGD_REF:S000059963|PMID:11266451 IMP P spindle pole component YER018C gene taxon:4932 20020214 SGD
+SGD S000000820 SPC25 GO:0007059 SGD_REF:S000059963|PMID:11266451 IGI P spindle pole component YER018C gene taxon:4932 20020214 SGD
+SGD S000006045 SPC29 GO:0005823 SGD_REF:S000048648|PMID:10339566 IDA C YPL124W|LPH3|NIP29 gene taxon:4932 20010118 SGD
+SGD S000006045 SPC29 GO:0005200 SGD_REF:S000048648|PMID:10339566 IPI F YPL124W|LPH3|NIP29 gene taxon:4932 20010118 SGD
+SGD S000006045 SPC29 GO:0007020 SGD_REF:S000058447|PMID:9153752 IPI P YPL124W|LPH3|NIP29 gene taxon:4932 20010118 SGD
+SGD S000006045 SPC29 GO:0007103 SGD_REF:S000050270|PMID:10330408 IMP P YPL124W|LPH3|NIP29 gene taxon:4932 20010118 SGD
+SGD S000004056 SPC3 GO:0005787 SGD_REF:S000056198|PMID:1846444 IDA C YLR066W gene taxon:4932 20010118 SGD
+SGD S000004056 SPC3 GO:0009003 SGD_REF:S000055094|PMID:9148930 IMP F YLR066W gene taxon:4932 20010118 SGD
+SGD S000004056 SPC3 GO:0009003 SGD_REF:S000055096|PMID:9148931 IMP F YLR066W gene taxon:4932 20010118 SGD
+SGD S000004056 SPC3 GO:0006465 SGD_REF:S000055094|PMID:9148930 IMP P YLR066W gene taxon:4932 20010118 SGD
+SGD S000004056 SPC3 GO:0006465 SGD_REF:S000055096|PMID:9148931 IMP P YLR066W gene taxon:4932 20010118 SGD
+SGD S000004056 SPC3 GO:0006465 SGD_REF:S000055096|PMID:9148931 IDA P YLR066W gene taxon:4932 20010118 SGD
+SGD S000004056 SPC3 GO:0006465 SGD_REF:S000055094|PMID:9148930 ISS P YLR066W gene taxon:4932 20010118 SGD
+SGD S000004056 SPC3 GO:0006465 SGD_REF:S000055094|PMID:9148930 IGI P YLR066W gene taxon:4932 20010118 SGD
+SGD S000004056 SPC3 GO:0006465 SGD_REF:S000055096|PMID:9148931 ISS P YLR066W gene taxon:4932 20010118 SGD
+SGD S000004056 SPC3 GO:0006465 SGD_REF:S000055096|PMID:9148931 IPI P YLR066W gene taxon:4932 20010118 SGD
+SGD S000001745 SPC34 GO:0000778 SGD_REF:S000069091|PMID:11756468 IDA C spindle pole component YKR037C gene taxon:4932 20021008 SGD
+SGD S000001745 SPC34 GO:0000778 SGD_REF:S000080960|PMID:11511347 IDA C spindle pole component YKR037C gene taxon:4932 20050307 SGD
+SGD S000001745 SPC34 GO:0005816 SGD_REF:S000047788|PMID:9585415 IDA C spindle pole component YKR037C gene taxon:4932 20010118 SGD
+SGD S000001745 SPC34 GO:0005819 SGD_REF:S000069091|PMID:11756468 IDA C spindle pole component YKR037C gene taxon:4932 20021008 SGD
+SGD S000001745 SPC34 GO:0005876 SGD_REF:S000080960|PMID:11511347 IDA C spindle pole component YKR037C gene taxon:4932 20050307 SGD
+SGD S000001745 SPC34 GO:0042729 SGD_REF:S000069052|PMID:11799062 IDA C spindle pole component YKR037C gene taxon:4932 20040122 SGD
+SGD S000001745 SPC34 GO:0042729 SGD_REF:S000080667|PMID:15664196 IPI C spindle pole component YKR037C gene taxon:4932 20050328 SGD
+SGD S000001745 SPC34 GO:0042729 SGD_REF:S000080444|PMID:15640796 IDA C spindle pole component YKR037C gene taxon:4932 20050328 SGD
+SGD S000001745 SPC34 GO:0042729 SGD_REF:S000080444|PMID:15640796 IPI C spindle pole component YKR037C gene taxon:4932 20050328 SGD
+SGD S000001745 SPC34 GO:0042729 SGD_REF:S000080667|PMID:15664196 IDA C spindle pole component YKR037C gene taxon:4932 20050328 SGD
+SGD S000001745 SPC34 GO:0042729 SGD_REF:S000069052|PMID:11799062 IPI C spindle pole component YKR037C gene taxon:4932 20040122 SGD
+SGD S000001745 SPC34 GO:0005200 SGD_REF:S000047788|PMID:9585415 IPI F spindle pole component YKR037C gene taxon:4932 20010118 SGD
+SGD S000001745 SPC34 GO:0007020 SGD_REF:S000058447|PMID:9153752 IPI P spindle pole component YKR037C gene taxon:4932 20010118 SGD
+SGD S000001745 SPC34 GO:0030472 SGD_REF:S000069091|PMID:11756468 IPI P spindle pole component YKR037C gene taxon:4932 20021008 SGD
+SGD S000001745 SPC34 GO:0031110 SGD_REF:S000080667|PMID:15664196 IPI P spindle pole component YKR037C gene taxon:4932 20050328 SGD
+SGD S000001745 SPC34 GO:0031110 SGD_REF:S000080667|PMID:15664196 IDA P spindle pole component YKR037C gene taxon:4932 20050328 SGD
+SGD S000001525 SPC42 GO:0005821 SGD_REF:S000043896|PMID:9215630 IDA C spindle pole body component YKL042W gene taxon:4932 20010118 SGD
+SGD S000001525 SPC42 GO:0005823 SGD_REF:S000043896|PMID:9215630 IDA C spindle pole body component YKL042W gene taxon:4932 20020807 SGD
+SGD S000001525 SPC42 GO:0005200 SGD_REF:S000043896|PMID:9215630 IPI F spindle pole body component YKL042W gene taxon:4932 20010118 SGD
+SGD S000001525 SPC42 GO:0007020 SGD_REF:S000058447|PMID:9153752 IPI P spindle pole body component YKL042W gene taxon:4932 20010118 SGD
+SGD S000001525 SPC42 GO:0007103 SGD_REF:S000058447|PMID:9153752 IMP P spindle pole body component YKL042W gene taxon:4932 20010118 SGD
+SGD S000000045 SPC72 GO:0005824 SGD_REF:S000039737|PMID:9670012 IDA C YAL047C|LDB4 gene taxon:4932 20010118 SGD
+SGD S000000045 SPC72 GO:0005200 SGD_REF:S000044510|PMID:9606209 IPI F YAL047C|LDB4 gene taxon:4932 20010118 SGD
+SGD S000000045 SPC72 GO:0000022 SGD_REF:S000039737|PMID:9670012 IMP P YAL047C|LDB4 gene taxon:4932 20010118 SGD
+SGD S000000045 SPC72 GO:0000070 SGD_REF:S000044510|PMID:9606209 IMP P YAL047C|LDB4 gene taxon:4932 20030213 SGD
+SGD S000000045 SPC72 GO:0007020 SGD_REF:S000058447|PMID:9153752 IPI P YAL047C|LDB4 gene taxon:4932 20010118 SGD
+SGD S000000045 SPC72 GO:0030473 SGD_REF:S000039737|PMID:9670012 IMP P YAL047C|LDB4 gene taxon:4932 20010118 SGD
+SGD S000001215 SPC97 GO:0000928 SGD_REF:S000053189|PMID:9384578 IPI C gamma-tubulin complex component YHR172W gene taxon:4932 20040802 SGD
+SGD S000001215 SPC97 GO:0005822 SGD_REF:S000043896|PMID:9215630 IDA C gamma-tubulin complex component YHR172W gene taxon:4932 20010118 SGD
+SGD S000001215 SPC97 GO:0005824 SGD_REF:S000043896|PMID:9215630 IDA C gamma-tubulin complex component YHR172W gene taxon:4932 20010118 SGD
+SGD S000001215 SPC97 GO:0005200 SGD_REF:S000043896|PMID:9215630 IPI F gamma-tubulin complex component YHR172W gene taxon:4932 20010118 SGD
+SGD S000001215 SPC97 GO:0007020 SGD_REF:S000058447|PMID:9153752 TAS P gamma-tubulin complex component YHR172W gene taxon:4932 20040802 SGD
+SGD S000005070 SPC98 GO:0000928 SGD_REF:S000053189|PMID:9384578 IPI C gamma-tubulin complex component YNL126W gene taxon:4932 20040802 SGD
+SGD S000005070 SPC98 GO:0005822 SGD_REF:S000043896|PMID:9215630 IDA C gamma-tubulin complex component YNL126W gene taxon:4932 20010118 SGD
+SGD S000005070 SPC98 GO:0005824 SGD_REF:S000043896|PMID:9215630 IDA C gamma-tubulin complex component YNL126W gene taxon:4932 20010118 SGD
+SGD S000005070 SPC98 GO:0005200 SGD_REF:S000043896|PMID:9215630 IPI F gamma-tubulin complex component YNL126W gene taxon:4932 20010118 SGD
+SGD S000005070 SPC98 GO:0007020 SGD_REF:S000058447|PMID:9153752 IPI P gamma-tubulin complex component YNL126W gene taxon:4932 20010118 SGD
+SGD S000005070 SPC98 GO:0030472 SGD_REF:S000058447|PMID:9153752 IMP P gamma-tubulin complex component YNL126W gene taxon:4932 20010118 SGD
+SGD S000001667 SPE1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C ornithine decarboxylase YKL184W|ORD1|SPE10 gene taxon:4932 20031028 SGD
+SGD S000001667 SPE1 GO:0004586 SGD_REF:S000056915|PMID:2681188 IDA F ornithine decarboxylase YKL184W|ORD1|SPE10 gene taxon:4932 20021114 SGD
+SGD S000001667 SPE1 GO:0009446 SGD_REF:S000055129|PMID:7929015 IMP P ornithine decarboxylase YKL184W|ORD1|SPE10 gene taxon:4932 20050416 SGD
+SGD S000001667 SPE1 GO:0015940 SGD_REF:S000060103|PMID:11154694 IMP P ornithine decarboxylase YKL184W|ORD1|SPE10 gene taxon:4932 20020801 SGD
+SGD S000005412 SPE2 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YOL052C gene taxon:4932 20031028 SGD
+SGD S000005412 SPE2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YOL052C gene taxon:4932 20031028 SGD
+SGD S000005412 SPE2 GO:0004014 SGD_REF:S000056828|PMID:2266128 IDA F YOL052C gene taxon:4932 20021114 SGD
+SGD S000005412 SPE2 GO:0006597 SGD_REF:S000055129|PMID:7929015 IMP P YOL052C gene taxon:4932 20050416 SGD
+SGD S000005412 SPE2 GO:0008295 SGD_REF:S000055129|PMID:7929015 IMP P YOL052C gene taxon:4932 20050416 SGD
+SGD S000005412 SPE2 GO:0015940 SGD_REF:S000060103|PMID:11154694 IMP P YOL052C gene taxon:4932 20020801 SGD
+SGD S000006273 SPE3 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C putrescine aminopropyltransferase (spermidine synthase) YPR069C gene taxon:4932 20031028 SGD
+SGD S000006273 SPE3 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C putrescine aminopropyltransferase (spermidine synthase) YPR069C gene taxon:4932 20031028 SGD
+SGD S000006273 SPE3 GO:0004766 SGD_REF:S000045920|PMID:9073064 IMP F putrescine aminopropyltransferase (spermidine synthase) YPR069C gene taxon:4932 20021111 SGD
+SGD S000006273 SPE3 GO:0004766 SGD_REF:S000045920|PMID:9073064 ISS F putrescine aminopropyltransferase (spermidine synthase) YPR069C gene taxon:4932 20021111 SGD
+SGD S000006273 SPE3 GO:0008295 SGD_REF:S000045920|PMID:9073064 IMP P putrescine aminopropyltransferase (spermidine synthase) YPR069C gene taxon:4932 20021111 SGD
+SGD S000006273 SPE3 GO:0015940 SGD_REF:S000060103|PMID:11154694 IMP P putrescine aminopropyltransferase (spermidine synthase) YPR069C gene taxon:4932 20020801 SGD
+SGD S000004136 SPE4 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C spermine synthase YLR146C gene taxon:4932 20031028 SGD
+SGD S000004136 SPE4 GO:0016768 SGD_REF:S000040546|PMID:9573363 IMP F spermine synthase YLR146C gene taxon:4932 20021111 SGD
+SGD S000004136 SPE4 GO:0006597 SGD_REF:S000040546|PMID:9573363 IMP P spermine synthase YLR146C gene taxon:4932 20021111 SGD
+SGD S000004136 SPE4 GO:0015940 SGD_REF:S000060103|PMID:11154694 IMP P spermine synthase YLR146C gene taxon:4932 20020801 SGD
+SGD S000000757 SPF1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C P-type ATPase YEL031W|COD1|PER9|PIO1 gene taxon:4932 20040928 SGD
+SGD S000000757 SPF1 GO:0005789 SGD_REF:S000070157|PMID:12058017 IDA C P-type ATPase YEL031W|COD1|PER9|PIO1 gene taxon:4932 20020817 SGD
+SGD S000000757 SPF1 GO:0015662 SGD_REF:S000070157|PMID:12058017 IDA F P-type ATPase YEL031W|COD1|PER9|PIO1 gene taxon:4932 20021003 SGD
+SGD S000000757 SPF1 GO:0006486 SGD_REF:S000070159|PMID:11791712 IMP P P-type ATPase YEL031W|COD1|PER9|PIO1 gene taxon:4932 20021003 SGD
+SGD S000000757 SPF1 GO:0006874 SGD_REF:S000070157|PMID:12058017 IMP P P-type ATPase YEL031W|COD1|PER9|PIO1 gene taxon:4932 20021003 SGD
+SGD S000003468 SPG1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YGR236C gene taxon:4932 20040923 SGD
+SGD S000003468 SPG1 GO:0005554 SGD_REF:S000069584 ND F YGR236C gene taxon:4932 20020930 SGD
+SGD S000003468 SPG1 GO:0000004 SGD_REF:S000069584 ND P YGR236C gene taxon:4932 20020930 SGD
+SGD S000002912 SPG3 GO:0008372 SGD_REF:S000069584 ND C YDR504C gene taxon:4932 20021126 SGD
+SGD S000002912 SPG3 GO:0005554 SGD_REF:S000069584 ND F YDR504C gene taxon:4932 20021126 SGD
+SGD S000002912 SPG3 GO:0000004 SGD_REF:S000069584 ND P YDR504C gene taxon:4932 20021126 SGD
+SGD S000004713 SPG4 GO:0008372 SGD_REF:S000069584 ND C YMR107W gene taxon:4932 20030203 SGD
+SGD S000004713 SPG4 GO:0005554 SGD_REF:S000069584 ND F YMR107W gene taxon:4932 20030203 SGD
+SGD S000004713 SPG4 GO:0000004 SGD_REF:S000069584 ND P YMR107W gene taxon:4932 20030203 SGD
+SGD S000004803 SPG5 GO:0008372 SGD_REF:S000069584 ND C YMR191W gene taxon:4932 20021126 SGD
+SGD S000004803 SPG5 GO:0005554 SGD_REF:S000069584 ND F YMR191W gene taxon:4932 20021126 SGD
+SGD S000004803 SPG5 GO:0000004 SGD_REF:S000069584 ND P YMR191W gene taxon:4932 20021126 SGD
+SGD S000004305 SPH1 GO:0000131 SGD_REF:S000040502|PMID:9214378 IDA C Spa2p homolog YLR313C gene taxon:4932 20030827 SGD
+SGD S000004305 SPH1 GO:0000133 SGD_REF:S000046605|PMID:10639324 TAS C Spa2p homolog YLR313C gene taxon:4932 20010118 SGD
+SGD S000004305 SPH1 GO:0005934 SGD_REF:S000040502|PMID:9214378 IDA C Spa2p homolog YLR313C gene taxon:4932 20030827 SGD
+SGD S000004305 SPH1 GO:0005934 SGD_REF:S000077144|PMID:15282802 IDA C Spa2p homolog YLR313C gene taxon:4932 20041008 SGD
+SGD S000004305 SPH1 GO:0005935 SGD_REF:S000040502|PMID:9214378 IDA C Spa2p homolog YLR313C gene taxon:4932 20030827 SGD
+SGD S000004305 SPH1 GO:0005935 SGD_REF:S000077144|PMID:15282802 IDA C Spa2p homolog YLR313C gene taxon:4932 20041008 SGD
+SGD S000004305 SPH1 GO:0005937 SGD_REF:S000069496|PMID:11923536 IDA C Spa2p homolog YLR313C gene taxon:4932 20030624 SGD
+SGD S000004305 SPH1 GO:0005937 SGD_REF:S000040502|PMID:9214378 IDA C Spa2p homolog YLR313C gene taxon:4932 20030827 SGD
+SGD S000004305 SPH1 GO:0005519 SGD_REF:S000046605|PMID:10639324 IPI F Spa2p homolog YLR313C gene taxon:4932 20010118 SGD
+SGD S000004305 SPH1 GO:0007015 SGD_REF:S000046605|PMID:10639324 IPI P Spa2p homolog YLR313C gene taxon:4932 20010118 SGD
+SGD S000004305 SPH1 GO:0007121 SGD_REF:S000041005|PMID:10652251 TAS P Spa2p homolog YLR313C gene taxon:4932 20010118 SGD
+SGD S000004305 SPH1 GO:0007124 SGD_REF:S000045317|PMID:9443897 IMP P Spa2p homolog YLR313C gene taxon:4932 20010118 SGD
+SGD S000004305 SPH1 GO:0007266 SGD_REF:S000046605|PMID:10639324 IPI P Spa2p homolog YLR313C gene taxon:4932 20010118 SGD
+SGD S000004305 SPH1 GO:0030468 SGD_REF:S000046605|PMID:10639324 IMP P Spa2p homolog YLR313C gene taxon:4932 20010302 SGD
+SGD S000004305 SPH1 GO:0030468 SGD_REF:S000046605|PMID:10639324 IPI P Spa2p homolog YLR313C gene taxon:4932 20010302 SGD
+SGD S000000952 SPI1 GO:0009277 SGD_REF:S000059732|PMID:9613572 ISS C YER150W gene taxon:4932 20010306 SGD
+SGD S000000952 SPI1 GO:0009277 SGD_REF:S000059732|PMID:9613572 IDA C YER150W gene taxon:4932 20010306 SGD
+SGD S000000952 SPI1 GO:0005554 SGD_REF:S000069584 ND F YER150W gene taxon:4932 20030108 SGD
+SGD S000000952 SPI1 GO:0000004 SGD_REF:S000069584 ND P YER150W gene taxon:4932 20030108 SGD
+SGD S000001178 SPL2 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YHR136C gene taxon:4932 20020507 SGD
+SGD S000001178 SPL2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YHR136C gene taxon:4932 20031028 SGD
+SGD S000001178 SPL2 GO:0004857 SGD_REF:S000040619|PMID:9475719 ISS F YHR136C gene taxon:4932 20030122 SGD
+SGD S000001178 SPL2 GO:0009266 SGD_REF:S000040619|PMID:9475719 IGI SGD:S000006189 P YHR136C gene taxon:4932 20030122 SGD
+SGD S000006337 SPN1 GO:0008023 SGD_REF:S000071357|PMID:12242279 IPI C involved in transcriptional elongation YPR133C|IWS1 gene taxon:4932 20021004 SGD
+SGD S000006337 SPN1 GO:0016944 SGD_REF:S000071357|PMID:12242279 IPI F involved in transcriptional elongation YPR133C|IWS1 gene taxon:4932 20021004 SGD
+SGD S000006337 SPN1 GO:0006368 SGD_REF:S000071357|PMID:12242279 IPI P involved in transcriptional elongation YPR133C|IWS1 gene taxon:4932 20021004 SGD
+SGD S000004957 SPO1 GO:0005634 SGD_REF:S000040907|PMID:10855497 IDA C similar to phospholipase B YNL012W gene taxon:4932 20010118 SGD
+SGD S000004957 SPO1 GO:0004620 SGD_REF:S000054738|PMID:8921875 ISS F similar to phospholipase B YNL012W gene taxon:4932 20010118 SGD
+SGD S000004957 SPO1 GO:0007126 SGD_REF:S000040907|PMID:10855497 IMP P similar to phospholipase B YNL012W gene taxon:4932 20010118 SGD
+SGD S000001014 SPO11 GO:0000228 SGD_REF:S000044006|PMID:9039264 IPI C early meiosis-specific recombination protein YHL022C gene taxon:4932 20030403 SGD
+SGD S000001014 SPO11 GO:0016889 SGD_REF:S000069201|PMID:11809802 IMP F early meiosis-specific recombination protein YHL022C gene taxon:4932 20020708 SGD
+SGD S000001014 SPO11 GO:0016889 SGD_REF:S000071541|PMID:12408862 IDA F early meiosis-specific recombination protein YHL022C gene taxon:4932 20030616 SGD
+SGD S000001014 SPO11 GO:0042138 SGD_REF:S000069981|PMID:9334324 TAS P early meiosis-specific recombination protein YHL022C gene taxon:4932 20020708 SGD
+SGD S000001195 SPO12 GO:0005634 SGD_REF:S000066256|PMID:11729145 IDA C 20 kDa protein with negatively charged C-terminus required for function, positive regulator of exit from M-phase in mitosis and meiosis (putative) YHR152W gene taxon:4932 20020529 SGD
+SGD S000001195 SPO12 GO:0005730 SGD_REF:S000066256|PMID:11729145 IDA C 20 kDa protein with negatively charged C-terminus required for function, positive regulator of exit from M-phase in mitosis and meiosis (putative) YHR152W gene taxon:4932 20020529 SGD
+SGD S000001195 SPO12 GO:0005554 SGD_REF:S000069584 ND F 20 kDa protein with negatively charged C-terminus required for function, positive regulator of exit from M-phase in mitosis and meiosis (putative) YHR152W gene taxon:4932 20010119 SGD
+SGD S000001195 SPO12 GO:0000278 SGD_REF:S000056480|PMID:1333584 IGI P 20 kDa protein with negatively charged C-terminus required for function, positive regulator of exit from M-phase in mitosis and meiosis (putative) YHR152W gene taxon:4932 20020529 SGD
+SGD S000001195 SPO12 GO:0000278 SGD_REF:S000056480|PMID:1333584 IEP P 20 kDa protein with negatively charged C-terminus required for function, positive regulator of exit from M-phase in mitosis and meiosis (putative) YHR152W gene taxon:4932 20020529 SGD
+SGD S000001195 SPO12 GO:0007096 SGD_REF:S000069394|PMID:11832211 IGI P 20 kDa protein with negatively charged C-terminus required for function, positive regulator of exit from M-phase in mitosis and meiosis (putative) YHR152W gene taxon:4932 20020529 SGD
+SGD S000001195 SPO12 GO:0007127 SGD_REF:S000045807|PMID:7021311 IMP P 20 kDa protein with negatively charged C-terminus required for function, positive regulator of exit from M-phase in mitosis and meiosis (putative) YHR152W gene taxon:4932 20010118 SGD
+SGD S000001056 SPO13 GO:0000780 SGD_REF:S000080084|PMID:15620645 IDA C YHR014W gene taxon:4932 20051121 SGD
+SGD S000001056 SPO13 GO:0005634 SGD_REF:S000070315|PMID:12101125 IDA C YHR014W gene taxon:4932 20020911 SGD
+SGD S000001056 SPO13 GO:0005515 SGD_REF:S000070315|PMID:12101125 IDA F YHR014W gene taxon:4932 20021112 SGD
+SGD S000001056 SPO13 GO:0005515 SGD_REF:S000070315|PMID:12101125 IMP F YHR014W gene taxon:4932 20021112 SGD
+SGD S000001056 SPO13 GO:0045876 SGD_REF:S000070315|PMID:12101125 IPI P YHR014W gene taxon:4932 20021112 SGD
+SGD S000001056 SPO13 GO:0045876 SGD_REF:S000070315|PMID:12101125 IGI P YHR014W gene taxon:4932 20021112 SGD
+SGD S000001056 SPO13 GO:0051177 SGD_REF:S000080084|PMID:15620645 IMP P YHR014W gene taxon:4932 20051121 SGD
+SGD S000001056 SPO13 GO:0051177 SGD_REF:S000081577|PMID:15620644 IPI P YHR014W gene taxon:4932 20051121 SGD
+SGD S000001056 SPO13 GO:0051177 SGD_REF:S000081577|PMID:15620644 IGI P YHR014W gene taxon:4932 20051121 SGD
+SGD S000001056 SPO13 GO:0051177 SGD_REF:S000081577|PMID:15620644 IMP P YHR014W gene taxon:4932 20051121 SGD
+SGD S000001739 SPO14 GO:0005628 SGD_REF:S000052858|PMID:9693364 IDA C phospholipase D YKR031C|PLD1 gene taxon:4932 20020916 SGD
+SGD S000001739 SPO14 GO:0005768 SGD_REF:S000043659|PMID:10848624 IDA C phospholipase D YKR031C|PLD1 gene taxon:4932 20030305 SGD
+SGD S000001739 SPO14 GO:0004630 SGD_REF:S000061199|PMID:11514437 IDA F phospholipase D YKR031C|PLD1 gene taxon:4932 20030109 SGD
+SGD S000001739 SPO14 GO:0006644 SGD_REF:S000053680|PMID:8576189 IDA P phospholipase D YKR031C|PLD1 gene taxon:4932 20030305 SGD
+SGD S000001739 SPO14 GO:0006644 SGD_REF:S000053680|PMID:8576189 IMP P phospholipase D YKR031C|PLD1 gene taxon:4932 20030305 SGD
+SGD S000001739 SPO14 GO:0006887 SGD_REF:S000061199|PMID:11514437 IGI P phospholipase D YKR031C|PLD1 gene taxon:4932 20030305 SGD
+SGD S000001739 SPO14 GO:0006887 SGD_REF:S000043659|PMID:10848624 IGI P phospholipase D YKR031C|PLD1 gene taxon:4932 20030305 SGD
+SGD S000001739 SPO14 GO:0030437 SGD_REF:S000060175|PMID:11283284 TAS P phospholipase D YKR031C|PLD1 gene taxon:4932 20020916 SGD
+SGD S000001196 SPO16 GO:0008372 SGD_REF:S000069584 ND C YHR153C gene taxon:4932 20020930 SGD
+SGD S000001196 SPO16 GO:0005554 SGD_REF:S000069584 ND F YHR153C gene taxon:4932 20020930 SGD
+SGD S000001196 SPO16 GO:0030437 SGD_REF:S000040334|PMID:2188099 IMP P YHR153C gene taxon:4932 20020930 SGD
+SGD S000006051 SPO19 GO:0009277 SGD_REF:S000040179|PMID:10383953 IDA C meiosis-specific GPI-protein YPL130W gene taxon:4932 20020617 SGD
+SGD S000006051 SPO19 GO:0005554 SGD_REF:S000069584 ND F meiosis-specific GPI-protein YPL130W gene taxon:4932 20020930 SGD
+SGD S000006051 SPO19 GO:0007126 SGD_REF:S000059486|PMID:11101837 IEP P meiosis-specific GPI-protein YPL130W gene taxon:4932 20020930 SGD
+SGD S000004619 SPO20 GO:0005628 SGD_REF:S000055334|PMID:9425151 IMP C SNAP 25 homolog YMR017W|DBI9 gene taxon:4932 20010118 SGD
+SGD S000004619 SPO20 GO:0005628 SGD_REF:S000055334|PMID:9425151 ISS C SNAP 25 homolog YMR017W|DBI9 gene taxon:4932 20010118 SGD
+SGD S000004619 SPO20 GO:0005486 SGD_REF:S000052179|PMID:10924463 IPI F SNAP 25 homolog YMR017W|DBI9 gene taxon:4932 20031230 SGD
+SGD S000004619 SPO20 GO:0005486 SGD_REF:S000055334|PMID:9425151 ISS F SNAP 25 homolog YMR017W|DBI9 gene taxon:4932 20031230 SGD
+SGD S000004619 SPO20 GO:0006906 SGD_REF:S000058453|PMID:10047442 TAS P SNAP 25 homolog YMR017W|DBI9 gene taxon:4932 20010118 SGD
+SGD S000004619 SPO20 GO:0030476 SGD_REF:S000055334|PMID:9425151 IMP P SNAP 25 homolog YMR017W|DBI9 gene taxon:4932 20010118 SGD
+SGD S000005451 SPO21 GO:0005816 SGD_REF:S000061397|PMID:10899120 IDA C YOL091W|MPC70 gene taxon:4932 20020920 SGD
+SGD S000005451 SPO21 GO:0005198 SGD_REF:S000073593|PMID:12796288 IDA F YOL091W|MPC70 gene taxon:4932 20030708 SGD
+SGD S000005451 SPO21 GO:0005198 SGD_REF:S000073593|PMID:12796288 IMP F YOL091W|MPC70 gene taxon:4932 20030708 SGD
+SGD S000005451 SPO21 GO:0007126 SGD_REF:S000069721|PMID:11973299 TAS P YOL091W|MPC70 gene taxon:4932 20030107 SGD
+SGD S000005451 SPO21 GO:0030476 SGD_REF:S000061397|PMID:10899120 IMP P YOL091W|MPC70 gene taxon:4932 20020920 SGD
+SGD S000001335 SPO22 GO:0008372 SGD_REF:S000069584 ND C meiosis-specific phospholipase A2 homolog YIL073C gene taxon:4932 20021031 SGD
+SGD S000001335 SPO22 GO:0005554 SGD_REF:S000069584 ND F meiosis-specific phospholipase A2 homolog YIL073C gene taxon:4932 20021031 SGD
+SGD S000001335 SPO22 GO:0007126 SGD_REF:S000059486|PMID:11101837 IEP P meiosis-specific phospholipase A2 homolog YIL073C gene taxon:4932 20020617 SGD
+SGD S000000007 SPO7 GO:0016021 SGD_REF:S000040050|PMID:9822591 IDA C YAL009W gene taxon:4932 20021002 SGD
+SGD S000000007 SPO7 GO:0016021 SGD_REF:S000040050|PMID:9822591 ISS C YAL009W gene taxon:4932 20021002 SGD
+SGD S000000007 SPO7 GO:0042175 SGD_REF:S000040050|PMID:9822591 IDA C YAL009W gene taxon:4932 20021002 SGD
+SGD S000000007 SPO7 GO:0005554 SGD_REF:S000069584 ND F YAL009W gene taxon:4932 20021002 SGD
+SGD S000000007 SPO7 GO:0006997 SGD_REF:S000040050|PMID:9822591 IGI P YAL009W gene taxon:4932 20021002 SGD
+SGD S000000007 SPO7 GO:0006997 SGD_REF:S000040050|PMID:9822591 IMP P YAL009W gene taxon:4932 20021002 SGD
+SGD S000000007 SPO7 GO:0007126 SGD_REF:S000057191|PMID:4613605 IMP P YAL009W gene taxon:4932 20021002 SGD
+SGD S000000007 SPO7 GO:0030437 SGD_REF:S000040050|PMID:9822591 IMP P YAL009W gene taxon:4932 20021002 SGD
+SGD S000002511 SPO71 GO:0005619 SGD_REF:S000055354|PMID:9784122 ISS C YDR104C gene taxon:4932 20020930 SGD
+SGD S000002511 SPO71 GO:0005619 SGD_REF:S000055354|PMID:9784122 IMP C YDR104C gene taxon:4932 20020930 SGD
+SGD S000002511 SPO71 GO:0005554 SGD_REF:S000069584 ND F YDR104C gene taxon:4932 20020930 SGD
+SGD S000002511 SPO71 GO:0030476 SGD_REF:S000055354|PMID:9784122 IMP P YDR104C gene taxon:4932 20020930 SGD
+SGD S000002511 SPO71 GO:0030476 SGD_REF:S000055354|PMID:9784122 IEP P YDR104C gene taxon:4932 20020930 SGD
+SGD S000000848 SPO73 GO:0005829 SGD_REF:S000079982|PMID:15590821 IDA C YER046W gene taxon:4932 20050127 SGD
+SGD S000000848 SPO73 GO:0005554 SGD_REF:S000069584 ND F YER046W gene taxon:4932 20021029 SGD
+SGD S000000848 SPO73 GO:0030437 SGD_REF:S000060989|PMID:11470404 IMP P YER046W gene taxon:4932 20021029 SGD
+SGD S000000848 SPO73 GO:0030476 SGD_REF:S000079982|PMID:15590821 IMP P YER046W gene taxon:4932 20050127 SGD
+SGD S000003138 SPO74 GO:0005816 SGD_REF:S000073593|PMID:12796288 IDA C YGL170C gene taxon:4932 20030708 SGD
+SGD S000003138 SPO74 GO:0005816 SGD_REF:S000073593|PMID:12796288 IMP C YGL170C gene taxon:4932 20030708 SGD
+SGD S000003138 SPO74 GO:0005198 SGD_REF:S000073593|PMID:12796288 IDA F YGL170C gene taxon:4932 20030708 SGD
+SGD S000003138 SPO74 GO:0005198 SGD_REF:S000073593|PMID:12796288 IMP F YGL170C gene taxon:4932 20030708 SGD
+SGD S000003138 SPO74 GO:0030437 SGD_REF:S000060989|PMID:11470404 IMP P YGL170C gene taxon:4932 20021029 SGD
+SGD S000003928 SPO75 GO:0008372 SGD_REF:S000069584 ND C YLL005C gene taxon:4932 20021016 SGD
+SGD S000003928 SPO75 GO:0005554 SGD_REF:S000069584 ND F YLL005C gene taxon:4932 20021016 SGD
+SGD S000003928 SPO75 GO:0030437 SGD_REF:S000060989|PMID:11470404 IMP P YLL005C gene taxon:4932 20021016 SGD
+SGD S000003928 SPO75 GO:0030476 SGD_REF:S000079982|PMID:15590821 IMP P YLL005C gene taxon:4932 20050127 SGD
+SGD S000004333 SPO77 GO:0005622 SGD_REF:S000079982|PMID:15590821 IDA C YLR341W gene taxon:4932 20050127 SGD
+SGD S000004333 SPO77 GO:0005554 SGD_REF:S000069584 ND F YLR341W gene taxon:4932 20050127 SGD
+SGD S000004333 SPO77 GO:0030437 SGD_REF:S000060989|PMID:11470404 IMP P YLR341W gene taxon:4932 20021029 SGD
+SGD S000004333 SPO77 GO:0030476 SGD_REF:S000079982|PMID:15590821 IMP P YLR341W gene taxon:4932 20050127 SGD
+SGD S000006059 SPP1 GO:0048188 SGD_REF:S000068991|PMID:11752412 IPI SGD:S000000064|SGD:S000002877|SGD:S000001501|SGD:S000004005|SGD:S000001161|SGD:S000000379 C compass (complex proteins associated with Set1p) component YPL138C|CPS40|SAF41 gene taxon:4932 20050524 SGD
+SGD S000006059 SPP1 GO:0048188 SGD_REF:S000068755|PMID:11742990 IPI SGD:S000000064|SGD:S000004005|SGD:S000001501|SGD:S000001161|SGD:S000002877|SGD:S000000462|SGD:S000000379 C compass (complex proteins associated with Set1p) component YPL138C|CPS40|SAF41 gene taxon:4932 20050524 SGD
+SGD S000006059 SPP1 GO:0048188 SGD_REF:S000066156|PMID:11687631 IPI SGD:S000000064|SGD:S000000379|SGD:S000002877|SGD:S000001161|SGD:S000004005|SGD:S000001501 C compass (complex proteins associated with Set1p) component YPL138C|CPS40|SAF41 gene taxon:4932 20050524 SGD
+SGD S000006059 SPP1 contributes_to GO:0042800 SGD_REF:S000068991|PMID:11752412 IMP F compass (complex proteins associated with Set1p) component YPL138C|CPS40|SAF41 gene taxon:4932 20050524 SGD
+SGD S000006059 SPP1 contributes_to GO:0042800 SGD_REF:S000069538|PMID:11805083 IDA F compass (complex proteins associated with Set1p) component YPL138C|CPS40|SAF41 gene taxon:4932 20050525 SGD
+SGD S000006059 SPP1 contributes_to GO:0042800 SGD_REF:S000068755|PMID:11742990 IDA F compass (complex proteins associated with Set1p) component YPL138C|CPS40|SAF41 gene taxon:4932 20050525 SGD
+SGD S000006059 SPP1 GO:0006348 SGD_REF:S000066156|PMID:11687631 IMP P compass (complex proteins associated with Set1p) component YPL138C|CPS40|SAF41 gene taxon:4932 20020212 SGD
+SGD S000006059 SPP1 GO:0006348 SGD_REF:S000069538|PMID:11805083 IMP P compass (complex proteins associated with Set1p) component YPL138C|CPS40|SAF41 gene taxon:4932 20050525 SGD
+SGD S000006059 SPP1 GO:0006348 SGD_REF:S000068991|PMID:11752412 IMP P compass (complex proteins associated with Set1p) component YPL138C|CPS40|SAF41 gene taxon:4932 20050524 SGD
+SGD S000006059 SPP1 GO:0006355 SGD_REF:S000066156|PMID:11687631 IMP P compass (complex proteins associated with Set1p) component YPL138C|CPS40|SAF41 gene taxon:4932 20020212 SGD
+SGD S000006059 SPP1 GO:0016571 SGD_REF:S000068755|PMID:11742990 IDA P compass (complex proteins associated with Set1p) component YPL138C|CPS40|SAF41 gene taxon:4932 20020212 SGD
+SGD S000006059 SPP1 GO:0016571 SGD_REF:S000069538|PMID:11805083 IDA P compass (complex proteins associated with Set1p) component YPL138C|CPS40|SAF41 gene taxon:4932 20050525 SGD
+SGD S000006059 SPP1 GO:0016571 SGD_REF:S000068991|PMID:11752412 IMP P compass (complex proteins associated with Set1p) component YPL138C|CPS40|SAF41 gene taxon:4932 20050524 SGD
+SGD S000006059 SPP1 GO:0016571 SGD_REF:S000068991|PMID:11752412 IDA P compass (complex proteins associated with Set1p) component YPL138C|CPS40|SAF41 gene taxon:4932 20050524 SGD
+SGD S000005674 SPP2 GO:0005681 SGD_REF:S000042497|PMID:7493316 IDA C YOR148C gene taxon:4932 20021104 SGD
+SGD S000005674 SPP2 GO:0005554 SGD_REF:S000069584 ND F YOR148C gene taxon:4932 20021104 SGD
+SGD S000005674 SPP2 GO:0000398 SGD_REF:S000042497|PMID:7493316 IMP P YOR148C gene taxon:4932 20021104 SGD
+SGD S000000356 SPP381 GO:0046540 SGD_REF:S000042712|PMID:9858581 IDA C U4/U6/U5 snRNP-associated protein, contains PEST proteolysis motif YBR152W gene taxon:4932 20050923 SGD
+SGD S000000356 SPP381 GO:0046540 SGD_REF:S000039461|PMID:10449419 IDA C U4/U6/U5 snRNP-associated protein, contains PEST proteolysis motif YBR152W gene taxon:4932 20050926 SGD
+SGD S000000356 SPP381 GO:0005515 SGD_REF:S000042712|PMID:9858581 IPI SGD:S000003307 F U4/U6/U5 snRNP-associated protein, contains PEST proteolysis motif YBR152W gene taxon:4932 20050926 SGD
+SGD S000000356 SPP381 contributes_to GO:0031202 SGD_REF:S000042712|PMID:9858581 IGI SGD:S000003307 F U4/U6/U5 snRNP-associated protein, contains PEST proteolysis motif YBR152W gene taxon:4932 20050926 SGD
+SGD S000000356 SPP381 contributes_to GO:0031202 SGD_REF:S000039461|PMID:10449419 IDA F U4/U6/U5 snRNP-associated protein, contains PEST proteolysis motif YBR152W gene taxon:4932 20051003 SGD
+SGD S000000356 SPP381 contributes_to GO:0031202 SGD_REF:S000039461|PMID:10449419 IMP F U4/U6/U5 snRNP-associated protein, contains PEST proteolysis motif YBR152W gene taxon:4932 20051003 SGD
+SGD S000000356 SPP381 contributes_to GO:0031202 SGD_REF:S000042712|PMID:9858581 IMP F U4/U6/U5 snRNP-associated protein, contains PEST proteolysis motif YBR152W gene taxon:4932 20050926 SGD
+SGD S000000356 SPP381 GO:0000349 SGD_REF:S000042712|PMID:9858581 IGI SGD:S000003307 P U4/U6/U5 snRNP-associated protein, contains PEST proteolysis motif YBR152W gene taxon:4932 20050926 SGD
+SGD S000000356 SPP381 GO:0000398 SGD_REF:S000042712|PMID:9858581 IMP P U4/U6/U5 snRNP-associated protein, contains PEST proteolysis motif YBR152W gene taxon:4932 20050923 SGD
+SGD S000000356 SPP381 GO:0000398 SGD_REF:S000039461|PMID:10449419 IMP P U4/U6/U5 snRNP-associated protein, contains PEST proteolysis motif YBR152W gene taxon:4932 20050926 SGD
+SGD S000004416 SPP382 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YLR424W|CCF8|NTR1 gene taxon:4932 20031028 SGD
+SGD S000004416 SPP382 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YLR424W|CCF8|NTR1 gene taxon:4932 20031028 SGD
+SGD S000004416 SPP382 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YLR424W|CCF8|NTR1 gene taxon:4932 20040928 SGD
+SGD S000004416 SPP382 GO:0003723 SGD_REF:S000075214|PMID:14690591 ISS F YLR424W|CCF8|NTR1 gene taxon:4932 20031230 SGD
+SGD S000004416 SPP382 GO:0000391 SGD_REF:S000113869|PMID:16357217 IDA P YLR424W|CCF8|NTR1 gene taxon:4932 20051222 SGD
+SGD S000004416 SPP382 GO:0000398 SGD_REF:S000075214|PMID:14690591 IPI P YLR424W|CCF8|NTR1 gene taxon:4932 20031230 SGD
+SGD S000002872 SPP41 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C negative transcriptional regulator of prp spliceosome genes YDR464W gene taxon:4932 20031028 SGD
+SGD S000002872 SPP41 GO:0005554 SGD_REF:S000069584 ND F negative transcriptional regulator of prp spliceosome genes YDR464W gene taxon:4932 20021031 SGD
+SGD S000002872 SPP41 GO:0000122 SGD_REF:S000054901|PMID:8005438 IGI P negative transcriptional regulator of prp spliceosome genes YDR464W gene taxon:4932 20020617 SGD
+SGD S000005716 SPR1 GO:0009277 SGD_REF:S000051171|PMID:8419289 IMP C exo-1,3-beta-glucanase, sporulation-specific YOR190W|SSG1 gene taxon:4932 20020924 SGD
+SGD S000005716 SPR1 GO:0004338 SGD_REF:S000045045|PMID:7875558 IDA F exo-1,3-beta-glucanase, sporulation-specific YOR190W|SSG1 gene taxon:4932 20020924 SGD
+SGD S000005716 SPR1 GO:0030437 SGD_REF:S000051171|PMID:8419289 IMP P exo-1,3-beta-glucanase, sporulation-specific YOR190W|SSG1 gene taxon:4932 20020924 SGD
+SGD S000002626 SPR28 GO:0000144 SGD_REF:S000057920|PMID:8791410 TAS C septin YDR218C gene taxon:4932 20010118 SGD
+SGD S000002626 SPR28 GO:0005200 SGD_REF:S000057920|PMID:8791410 TAS F septin YDR218C gene taxon:4932 20010118 SGD
+SGD S000002626 SPR28 GO:0000902 SGD_REF:S000057920|PMID:8791410 TAS P septin YDR218C gene taxon:4932 20021108 SGD
+SGD S000002626 SPR28 GO:0007047 SGD_REF:S000057920|PMID:8791410 TAS P septin YDR218C gene taxon:4932 20010118 SGD
+SGD S000003291 SPR3 GO:0000144 SGD_REF:S000057920|PMID:8791410 TAS C septin YGR059W gene taxon:4932 20010118 SGD
+SGD S000003291 SPR3 GO:0005619 SGD_REF:S000057920|PMID:8791410 TAS C septin YGR059W gene taxon:4932 20010118 SGD
+SGD S000003291 SPR3 GO:0005628 SGD_REF:S000057920|PMID:8791410 TAS C septin YGR059W gene taxon:4932 20010118 SGD
+SGD S000003291 SPR3 GO:0005200 SGD_REF:S000057920|PMID:8791410 TAS F septin YGR059W gene taxon:4932 20010118 SGD
+SGD S000003291 SPR3 GO:0000753 SGD_REF:S000057920|PMID:8791410 TAS P septin YGR059W gene taxon:4932 20021206 SGD
+SGD S000003291 SPR3 GO:0000902 SGD_REF:S000057920|PMID:8791410 TAS P septin YGR059W gene taxon:4932 20021107 SGD
+SGD S000003291 SPR3 GO:0007047 SGD_REF:S000057920|PMID:8791410 TAS P septin YGR059W gene taxon:4932 20010118 SGD
+SGD S000003291 SPR3 GO:0030476 SGD_REF:S000057920|PMID:8791410 TAS P septin YGR059W gene taxon:4932 20010118 SGD
+SGD S000000917 SPR6 GO:0008372 SGD_REF:S000069584 ND C YER115C gene taxon:4932 20020930 SGD
+SGD S000000917 SPR6 GO:0005554 SGD_REF:S000069584 ND F YER115C gene taxon:4932 20020930 SGD
+SGD S000000917 SPR6 GO:0030437 SGD_REF:S000045861|PMID:2253272 IEP P YER115C gene taxon:4932 20020930 SGD
+SGD S000002931 SPS1 GO:0005628 SGD_REF:S000081076|PMID:15755916 IDA C YDR523C gene taxon:4932 20050324 SGD
+SGD S000002931 SPS1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YDR523C gene taxon:4932 20031028 SGD
+SGD S000002931 SPS1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDR523C gene taxon:4932 20031028 SGD
+SGD S000002931 SPS1 GO:0004674 SGD_REF:S000050828|PMID:7958886 ISS F YDR523C gene taxon:4932 20020822 SGD
+SGD S000002931 SPS1 GO:0006468 SGD_REF:S000050828|PMID:7958886 ISS P YDR523C gene taxon:4932 20020822 SGD
+SGD S000002931 SPS1 GO:0030437 SGD_REF:S000054637|PMID:3023934 IMP P YDR523C gene taxon:4932 20020822 SGD
+SGD S000002931 SPS1 GO:0030476 SGD_REF:S000081076|PMID:15755916 IMP P YDR523C gene taxon:4932 20050324 SGD
+SGD S000001181 SPS100 GO:0005619 SGD_REF:S000045684|PMID:3280971 ISS C sporulation-specific cell wall maturation protein YHR139C gene taxon:4932 20020620 SGD
+SGD S000001181 SPS100 GO:0005554 SGD_REF:S000069584 ND F sporulation-specific cell wall maturation protein YHR139C gene taxon:4932 20020620 SGD
+SGD S000001181 SPS100 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P sporulation-specific cell wall maturation protein YHR139C gene taxon:4932 20060214 SGD
+SGD S000001181 SPS100 GO:0030476 SGD_REF:S000045684|PMID:3280971 IMP P sporulation-specific cell wall maturation protein YHR139C gene taxon:4932 20020620 SGD
+SGD S000005148 SPS18 GO:0008372 SGD_REF:S000069584 ND C transcription factor YNL204C|SPX18 gene taxon:4932 20021001 SGD
+SGD S000005148 SPS18 GO:0005554 SGD_REF:S000069584 ND F transcription factor YNL204C|SPX18 gene taxon:4932 20021001 SGD
+SGD S000005148 SPS18 GO:0030435 SGD_REF:S000051124|PMID:7969036 IMP P transcription factor YNL204C|SPX18 gene taxon:4932 20021001 SGD
+SGD S000005146 SPS19 GO:0005782 SGD_REF:S000046425|PMID:9268358 IDA C 2,4-dienoyl-CoA reductase YNL202W|SPX19 gene taxon:4932 20010118 SGD
+SGD S000005146 SPS19 GO:0008670 SGD_REF:S000046425|PMID:9268358 IDA F 2,4-dienoyl-CoA reductase YNL202W|SPX19 gene taxon:4932 20010118 SGD
+SGD S000005146 SPS19 GO:0008670 SGD_REF:S000046425|PMID:9268358 ISS F 2,4-dienoyl-CoA reductase YNL202W|SPX19 gene taxon:4932 20010118 SGD
+SGD S000005146 SPS19 GO:0009062 SGD_REF:S000046425|PMID:9268358 IDA P 2,4-dienoyl-CoA reductase YNL202W|SPX19 gene taxon:4932 20010118 SGD
+SGD S000005146 SPS19 GO:0009062 SGD_REF:S000046425|PMID:9268358 ISS P 2,4-dienoyl-CoA reductase YNL202W|SPX19 gene taxon:4932 20010118 SGD
+SGD S000005146 SPS19 GO:0030437 SGD_REF:S000051124|PMID:7969036 IMP P 2,4-dienoyl-CoA reductase YNL202W|SPX19 gene taxon:4932 20010118 SGD
+SGD S000005146 SPS19 GO:0030437 SGD_REF:S000051124|PMID:7969036 IEP P 2,4-dienoyl-CoA reductase YNL202W|SPX19 gene taxon:4932 20010118 SGD
+SGD S000002930 SPS2 GO:0009277 SGD_REF:S000040179|PMID:10383953 IDA C YDR522C gene taxon:4932 20020617 SGD
+SGD S000002930 SPS2 GO:0005554 SGD_REF:S000069584 ND F YDR522C gene taxon:4932 20030108 SGD
+SGD S000002930 SPS2 GO:0030437 SGD_REF:S000054637|PMID:3023934 IEP P YDR522C gene taxon:4932 20030108 SGD
+SGD S000002930 SPS2 GO:0030476 SGD_REF:S000079982|PMID:15590821 IMP P YDR522C gene taxon:4932 20050127 SGD
+SGD S000000553 SPS22 GO:0005886 SGD_REF:S000077542|PMID:15470113 ISS C YCL048W gene taxon:4932 20041109 SGD
+SGD S000000553 SPS22 GO:0005554 SGD_REF:S000069584 ND F YCL048W gene taxon:4932 20021126 SGD
+SGD S000000553 SPS22 GO:0007047 SGD_REF:S000077542|PMID:15470113 ISS P YCL048W gene taxon:4932 20041109 SGD
+SGD S000000553 SPS22 GO:0030476 SGD_REF:S000079982|PMID:15590821 IMP P YCL048W gene taxon:4932 20050127 SGD
+SGD S000005840 SPS4 GO:0008372 SGD_REF:S000069584 ND C YOR313C gene taxon:4932 20020822 SGD
+SGD S000005840 SPS4 GO:0005554 SGD_REF:S000069584 ND F YOR313C gene taxon:4932 20020822 SGD
+SGD S000005840 SPS4 GO:0006259 SGD_REF:S000043176|PMID:10051619 IGI P YOR313C gene taxon:4932 20021004 SGD
+SGD S000005840 SPS4 GO:0007126 SGD_REF:S000043176|PMID:10051619 IEP P YOR313C gene taxon:4932 20021004 SGD
+SGD S000005840 SPS4 GO:0030437 SGD_REF:S000047248|PMID:3540611 IEP P YOR313C gene taxon:4932 20020822 SGD
+SGD S000003663 SPT10 GO:0005634 SGD_REF:S000049994|PMID:8264536 TAS C transcriptional regulator YJL127C|CRE1|SUD1 gene taxon:4932 20010118 SGD
+SGD S000003663 SPT10 GO:0004402 SGD_REF:S000071387|PMID:12192040 IDA F transcriptional regulator YJL127C|CRE1|SUD1 gene taxon:4932 20021008 SGD
+SGD S000003663 SPT10 GO:0006338 SGD_REF:S000043773|PMID:8007957 TAS P transcriptional regulator YJL127C|CRE1|SUD1 gene taxon:4932 20010118 SGD
+SGD S000003663 SPT10 GO:0006358 SGD_REF:S000043773|PMID:8007957 TAS P transcriptional regulator YJL127C|CRE1|SUD1 gene taxon:4932 20010118 SGD
+SGD S000006096 SPT14 GO:0000506 SGD_REF:S000062716|PMID:11102867 TAS C N-acetylglucosaminyl-phosphatidylinositol biosynthetic protein YPL175W|CWH6|GPI3 gene taxon:4932 20050713 SGD
+SGD S000006096 SPT14 GO:0005783 SGD_REF:S000043857|PMID:9079905 IMP C N-acetylglucosaminyl-phosphatidylinositol biosynthetic protein YPL175W|CWH6|GPI3 gene taxon:4932 20020813 SGD
+SGD S000006096 SPT14 GO:0008194 SGD_REF:S000063370|PMID:10970797 IPI F N-acetylglucosaminyl-phosphatidylinositol biosynthetic protein YPL175W|CWH6|GPI3 gene taxon:4932 20050713 SGD
+SGD S000006096 SPT14 GO:0008194 SGD_REF:S000063370|PMID:10970797 ISS F N-acetylglucosaminyl-phosphatidylinositol biosynthetic protein YPL175W|CWH6|GPI3 gene taxon:4932 20050713 SGD
+SGD S000006096 SPT14 GO:0006506 SGD_REF:S000049681|PMID:8806613 TAS P N-acetylglucosaminyl-phosphatidylinositol biosynthetic protein YPL175W|CWH6|GPI3 gene taxon:4932 20010118 SGD
+SGD S000000950 SPT15 GO:0000120 SGD_REF:S000058402|PMID:9932458 TAS C TFIID subunit YER148W|BTF1|TBP|TBP1 gene taxon:4932 20010118 SGD
+SGD S000000950 SPT15 GO:0000126 SGD_REF:S000058323|PMID:9585500 TAS C TFIID subunit YER148W|BTF1|TBP|TBP1 gene taxon:4932 20010118 SGD
+SGD S000000950 SPT15 GO:0000126 SGD_REF:S000041451|PMID:1458536 IDA C TFIID subunit YER148W|BTF1|TBP|TBP1 gene taxon:4932 20051128 SGD
+SGD S000000950 SPT15 GO:0005634 SGD_REF:S000065234|PMID:9818719 IDA C TFIID subunit YER148W|BTF1|TBP|TBP1 gene taxon:4932 20020319 SGD
+SGD S000000950 SPT15 GO:0005669 SGD_REF:S000058086|PMID:9118213 TAS C TFIID subunit YER148W|BTF1|TBP|TBP1 gene taxon:4932 20010118 SGD
+SGD S000000950 SPT15 GO:0005669 SGD_REF:S000079756|PMID:15448131 IDA C TFIID subunit YER148W|BTF1|TBP|TBP1 gene taxon:4932 20041215 SGD
+SGD S000000950 SPT15 GO:0003677 SGD_REF:S000055990|PMID:7723829 IPI F TFIID subunit YER148W|BTF1|TBP|TBP1 gene taxon:4932 20020319 SGD
+SGD S000000950 SPT15 GO:0003677 SGD_REF:S000055990|PMID:7723829 TAS F TFIID subunit YER148W|BTF1|TBP|TBP1 gene taxon:4932 20020319 SGD
+SGD S000000950 SPT15 GO:0003701 SGD_REF:S000058402|PMID:9932458 TAS F TFIID subunit YER148W|BTF1|TBP|TBP1 gene taxon:4932 20010118 SGD
+SGD S000000950 SPT15 GO:0003701 SGD_REF:S000055819|PMID:1586947 IMP F TFIID subunit YER148W|BTF1|TBP|TBP1 gene taxon:4932 20051117 SGD
+SGD S000000950 SPT15 GO:0003709 SGD_REF:S000058323|PMID:9585500 TAS F TFIID subunit YER148W|BTF1|TBP|TBP1 gene taxon:4932 20010118 SGD
+SGD S000000950 SPT15 GO:0003709 SGD_REF:S000055819|PMID:1586947 IMP F TFIID subunit YER148W|BTF1|TBP|TBP1 gene taxon:4932 20051117 SGD
+SGD S000000950 SPT15 GO:0008301 SGD_REF:S000043192|PMID:8413604 IDA F TFIID subunit YER148W|BTF1|TBP|TBP1 gene taxon:4932 20051117 SGD
+SGD S000000950 SPT15 GO:0016251 SGD_REF:S000058086|PMID:9118213 TAS F TFIID subunit YER148W|BTF1|TBP|TBP1 gene taxon:4932 20010119 SGD
+SGD S000000950 SPT15 GO:0016251 SGD_REF:S000055819|PMID:1586947 IMP F TFIID subunit YER148W|BTF1|TBP|TBP1 gene taxon:4932 20051117 SGD
+SGD S000000950 SPT15 GO:0042803 SGD_REF:S000041700|PMID:10394360 IMP F TFIID subunit YER148W|BTF1|TBP|TBP1 gene taxon:4932 20051117 SGD
+SGD S000000950 SPT15 GO:0006360 SGD_REF:S000058402|PMID:9932458 TAS P TFIID subunit YER148W|BTF1|TBP|TBP1 gene taxon:4932 20010118 SGD
+SGD S000000950 SPT15 GO:0006360 SGD_REF:S000055819|PMID:1586947 IMP P TFIID subunit YER148W|BTF1|TBP|TBP1 gene taxon:4932 20051117 SGD
+SGD S000000950 SPT15 GO:0006366 SGD_REF:S000055819|PMID:1586947 IMP P TFIID subunit YER148W|BTF1|TBP|TBP1 gene taxon:4932 20051117 SGD
+SGD S000000950 SPT15 GO:0006367 SGD_REF:S000056378|PMID:10384286 TAS P TFIID subunit YER148W|BTF1|TBP|TBP1 gene taxon:4932 20010118 SGD
+SGD S000000950 SPT15 GO:0006367 SGD_REF:S000058086|PMID:9118213 TAS P TFIID subunit YER148W|BTF1|TBP|TBP1 gene taxon:4932 20010118 SGD
+SGD S000000950 SPT15 GO:0006367 SGD_REF:S000056377|PMID:10384273 TAS P TFIID subunit YER148W|BTF1|TBP|TBP1 gene taxon:4932 20010118 SGD
+SGD S000000950 SPT15 GO:0006383 SGD_REF:S000055819|PMID:1586947 IMP P TFIID subunit YER148W|BTF1|TBP|TBP1 gene taxon:4932 20051117 SGD
+SGD S000000950 SPT15 GO:0006384 SGD_REF:S000058323|PMID:9585500 TAS P TFIID subunit YER148W|BTF1|TBP|TBP1 gene taxon:4932 20010118 SGD
+SGD S000003175 SPT16 GO:0000790 SGD_REF:S000054316|PMID:10413469 TAS C YGL207W|CDC68|SSF1 gene taxon:4932 20010118 SGD
+SGD S000003175 SPT16 GO:0005658 SGD_REF:S000054316|PMID:10413469 IDA C YGL207W|CDC68|SSF1 gene taxon:4932 20010118 SGD
+SGD S000003175 SPT16 GO:0008023 SGD_REF:S000071357|PMID:12242279 IPI C YGL207W|CDC68|SSF1 gene taxon:4932 20021004 SGD
+SGD S000003175 SPT16 GO:0035101 SGD_REF:S000061420|PMID:11432837 IGI C YGL207W|CDC68|SSF1 gene taxon:4932 20041021 SGD
+SGD S000003175 SPT16 GO:0035101 SGD_REF:S000061420|PMID:11432837 IPI C YGL207W|CDC68|SSF1 gene taxon:4932 20041021 SGD
+SGD S000003175 SPT16 GO:0003711 SGD_REF:S000066118|PMID:11606527 TAS F YGL207W|CDC68|SSF1 gene taxon:4932 20020807 SGD
+SGD S000003175 SPT16 GO:0016944 SGD_REF:S000071357|PMID:12242279 IPI F YGL207W|CDC68|SSF1 gene taxon:4932 20021004 SGD
+SGD S000003175 SPT16 GO:0006338 SGD_REF:S000054316|PMID:10413469 TAS P YGL207W|CDC68|SSF1 gene taxon:4932 20010118 SGD
+SGD S000003175 SPT16 GO:0006358 SGD_REF:S000054316|PMID:10413469 TAS P YGL207W|CDC68|SSF1 gene taxon:4932 20010118 SGD
+SGD S000003175 SPT16 GO:0006367 SGD_REF:S000082428|PMID:15987999 IDA P YGL207W|CDC68|SSF1 gene taxon:4932 20051114 SGD
+SGD S000003175 SPT16 GO:0006367 SGD_REF:S000082428|PMID:15987999 IMP P YGL207W|CDC68|SSF1 gene taxon:4932 20051114 SGD
+SGD S000003175 SPT16 GO:0006368 SGD_REF:S000071357|PMID:12242279 IPI P YGL207W|CDC68|SSF1 gene taxon:4932 20021004 SGD
+SGD S000000963 SPT2 GO:0005634 SGD_REF:S000043877|PMID:2072912 IDA C non-specific DNA binding protein YER161C|EXA1|SIN1 gene taxon:4932 20020807 SGD
+SGD S000000963 SPT2 GO:0003677 SGD_REF:S000043877|PMID:2072912 IDA F non-specific DNA binding protein YER161C|EXA1|SIN1 gene taxon:4932 20020807 SGD
+SGD S000000963 SPT2 GO:0000122 SGD_REF:S000043877|PMID:2072912 IMP P non-specific DNA binding protein YER161C|EXA1|SIN1 gene taxon:4932 20020807 SGD
+SGD S000005508 SPT20 GO:0000124 SGD_REF:S000048255|PMID:9674426 IDA C histone acetyltransferase SAGA complex member, transcription factor YOL148C|ADA5 gene taxon:4932 20010221 SGD
+SGD S000005508 SPT20 GO:0046695 SGD_REF:S000071997|PMID:12446794 IPI C histone acetyltransferase SAGA complex member, transcription factor YOL148C|ADA5 gene taxon:4932 20041024 SGD
+SGD S000005508 SPT20 GO:0003712 SGD_REF:S000055789|PMID:8649430 IGI F histone acetyltransferase SAGA complex member, transcription factor YOL148C|ADA5 gene taxon:4932 20021114 SGD
+SGD S000005508 SPT20 GO:0003712 SGD_REF:S000055789|PMID:8649430 IPI F histone acetyltransferase SAGA complex member, transcription factor YOL148C|ADA5 gene taxon:4932 20021114 SGD
+SGD S000005508 SPT20 GO:0003712 SGD_REF:S000055789|PMID:8649430 IMP F histone acetyltransferase SAGA complex member, transcription factor YOL148C|ADA5 gene taxon:4932 20021114 SGD
+SGD S000005508 SPT20 GO:0016568 SGD_REF:S000061032|PMID:10839822 TAS P histone acetyltransferase SAGA complex member, transcription factor YOL148C|ADA5 gene taxon:4932 20020426 SGD
+SGD S000005508 SPT20 GO:0016573 SGD_REF:S000061032|PMID:10839822 TAS P histone acetyltransferase SAGA complex member, transcription factor YOL148C|ADA5 gene taxon:4932 20020426 SGD
+SGD S000004791 SPT21 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C non-specific DNA binding protein YMR179W gene taxon:4932 20031028 SGD
+SGD S000004791 SPT21 GO:0005554 SGD_REF:S000069584 ND F non-specific DNA binding protein YMR179W gene taxon:4932 20021114 SGD
+SGD S000004791 SPT21 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P non-specific DNA binding protein YMR179W gene taxon:4932 20060203 SGD
+SGD S000004791 SPT21 GO:0006357 SGD_REF:S000049742|PMID:8035801 IMP P non-specific DNA binding protein YMR179W gene taxon:4932 20021114 SGD
+SGD S000001503 SPT23 GO:0005634 SGD_REF:S000081155|PMID:15343339 IC GO:0003677 C YKL020C gene taxon:4932 20050331 SGD
+SGD S000001503 SPT23 GO:0005789 SGD_REF:S000066217|PMID:11557770 TAS C YKL020C gene taxon:4932 20021015 SGD
+SGD S000001503 SPT23 GO:0005789 SGD_REF:S000066217|PMID:11557770 IDA C YKL020C gene taxon:4932 20021023 SGD
+SGD S000001503 SPT23 GO:0003677 SGD_REF:S000081155|PMID:15343339 IPI F YKL020C gene taxon:4932 20050331 SGD
+SGD S000001503 SPT23 GO:0016563 SGD_REF:S000066217|PMID:11557770 IMP F YKL020C gene taxon:4932 20021023 SGD
+SGD S000001503 SPT23 GO:0006631 SGD_REF:S000066217|PMID:11557770 IMP P YKL020C gene taxon:4932 20021023 SGD
+SGD S000001503 SPT23 GO:0009409 SGD_REF:S000069399|PMID:11855848 IEP P YKL020C gene taxon:4932 20021023 SGD
+SGD S000001503 SPT23 GO:0009409 SGD_REF:S000069399|PMID:11855848 IMP P YKL020C gene taxon:4932 20021023 SGD
+SGD S000001503 SPT23 GO:0045944 SGD_REF:S000066217|PMID:11557770 IMP P YKL020C gene taxon:4932 20021023 SGD
+SGD S000002800 SPT3 GO:0000124 SGD_REF:S000048255|PMID:9674426 IDA C histone acetyltransferase SAGA complex member, transcription factor YDR392W gene taxon:4932 20010221 SGD
+SGD S000002800 SPT3 GO:0046695 SGD_REF:S000071997|PMID:12446794 IPI C histone acetyltransferase SAGA complex member, transcription factor YDR392W gene taxon:4932 20041024 SGD
+SGD S000002800 SPT3 GO:0003712 SGD_REF:S000042609|PMID:9858534 IMP F histone acetyltransferase SAGA complex member, transcription factor YDR392W gene taxon:4932 20030325 SGD
+SGD S000002800 SPT3 GO:0003712 SGD_REF:S000061217|PMID:11485989 IDA F histone acetyltransferase SAGA complex member, transcription factor YDR392W gene taxon:4932 20030325 SGD
+SGD S000002800 SPT3 GO:0000747 SGD_REF:S000070081|PMID:12072450 TAS P histone acetyltransferase SAGA complex member, transcription factor YDR392W gene taxon:4932 20021206 SGD
+SGD S000002800 SPT3 GO:0001403 SGD_REF:S000070081|PMID:12072450 IDA P histone acetyltransferase SAGA complex member, transcription factor YDR392W gene taxon:4932 20021101 SGD
+SGD S000002800 SPT3 GO:0007124 SGD_REF:S000070081|PMID:12072450 IDA P histone acetyltransferase SAGA complex member, transcription factor YDR392W gene taxon:4932 20030404 SGD
+SGD S000002800 SPT3 GO:0016568 SGD_REF:S000061032|PMID:10839822 TAS P histone acetyltransferase SAGA complex member, transcription factor YDR392W gene taxon:4932 20020426 SGD
+SGD S000002800 SPT3 GO:0016573 SGD_REF:S000061032|PMID:10839822 TAS P histone acetyltransferase SAGA complex member, transcription factor YDR392W gene taxon:4932 20020426 SGD
+SGD S000002800 SPT3 GO:0030437 SGD_REF:S000070081|PMID:12072450 TAS P histone acetyltransferase SAGA complex member, transcription factor YDR392W gene taxon:4932 20021101 SGD
+SGD S000003295 SPT4 GO:0000776 SGD_REF:S000075983|PMID:15057281 IDA C transcriptional regulator, zinc finger protein YGR063C gene taxon:4932 20040714 SGD
+SGD S000003295 SPT4 GO:0000784 SGD_REF:S000075983|PMID:15057281 IDA C transcriptional regulator, zinc finger protein YGR063C gene taxon:4932 20040714 SGD
+SGD S000003295 SPT4 GO:0005634 SGD_REF:S000044170|PMID:9450930 IPI C transcriptional regulator, zinc finger protein YGR063C gene taxon:4932 20011205 SGD
+SGD S000003295 SPT4 GO:0008023 SGD_REF:S000071357|PMID:12242279 IPI C transcriptional regulator, zinc finger protein YGR063C gene taxon:4932 20021004 SGD
+SGD S000003295 SPT4 GO:0032044 SGD_REF:S000044170|PMID:9450930 IPI SGD:S000004470 C transcriptional regulator, zinc finger protein YGR063C gene taxon:4932 20060421 SGD
+SGD S000003295 SPT4 GO:0016944 SGD_REF:S000044170|PMID:9450930 IMP F transcriptional regulator, zinc finger protein YGR063C gene taxon:4932 20011205 SGD
+SGD S000003295 SPT4 GO:0016944 SGD_REF:S000044170|PMID:9450930 ISS F transcriptional regulator, zinc finger protein YGR063C gene taxon:4932 20011205 SGD
+SGD S000003295 SPT4 GO:0006325 SGD_REF:S000057934|PMID:8805244 TAS P transcriptional regulator, zinc finger protein YGR063C gene taxon:4932 20011205 SGD
+SGD S000003295 SPT4 GO:0006342 SGD_REF:S000075983|PMID:15057281 IMP P transcriptional regulator, zinc finger protein YGR063C gene taxon:4932 20040714 SGD
+SGD S000003295 SPT4 GO:0006355 SGD_REF:S000044170|PMID:9450930 ISS P transcriptional regulator, zinc finger protein YGR063C gene taxon:4932 20011205 SGD
+SGD S000003295 SPT4 GO:0006355 SGD_REF:S000044170|PMID:9450930 IMP P transcriptional regulator, zinc finger protein YGR063C gene taxon:4932 20011205 SGD
+SGD S000003295 SPT4 GO:0006368 SGD_REF:S000071357|PMID:12242279 IPI P transcriptional regulator, zinc finger protein YGR063C gene taxon:4932 20021004 SGD
+SGD S000003295 SPT4 GO:0007059 SGD_REF:S000055342|PMID:8649393 IMP P transcriptional regulator, zinc finger protein YGR063C gene taxon:4932 20030721 SGD
+SGD S000004470 SPT5 GO:0005634 SGD_REF:S000047378|PMID:1840633 IDA C transcription factor YML010W gene taxon:4932 20011205 SGD
+SGD S000004470 SPT5 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C transcription factor YML010W gene taxon:4932 20040928 SGD
+SGD S000004470 SPT5 GO:0008023 SGD_REF:S000071357|PMID:12242279 IPI C transcription factor YML010W gene taxon:4932 20021004 SGD
+SGD S000004470 SPT5 GO:0032044 SGD_REF:S000044170|PMID:9450930 IPI SGD:S000003295 C transcription factor YML010W gene taxon:4932 20060421 SGD
+SGD S000004470 SPT5 GO:0016944 SGD_REF:S000044170|PMID:9450930 IMP F transcription factor YML010W gene taxon:4932 20011205 SGD
+SGD S000004470 SPT5 GO:0016944 SGD_REF:S000044170|PMID:9450930 IPI F transcription factor YML010W gene taxon:4932 20011205 SGD
+SGD S000004470 SPT5 GO:0016944 SGD_REF:S000044170|PMID:9450930 IGI F transcription factor YML010W gene taxon:4932 20011205 SGD
+SGD S000004470 SPT5 GO:0006325 SGD_REF:S000057934|PMID:8805244 TAS P transcription factor YML010W gene taxon:4932 20011205 SGD
+SGD S000004470 SPT5 GO:0006355 SGD_REF:S000044170|PMID:9450930 IMP P transcription factor YML010W gene taxon:4932 20011205 SGD
+SGD S000004470 SPT5 GO:0006355 SGD_REF:S000044170|PMID:9450930 IPI P transcription factor YML010W gene taxon:4932 20011205 SGD
+SGD S000004470 SPT5 GO:0006355 SGD_REF:S000044170|PMID:9450930 IGI P transcription factor YML010W gene taxon:4932 20011205 SGD
+SGD S000004470 SPT5 GO:0006368 SGD_REF:S000071357|PMID:12242279 IPI P transcription factor YML010W gene taxon:4932 20021004 SGD
+SGD S000003348 SPT6 GO:0005634 SGD_REF:S000041314|PMID:8633238 IPI C interacts with histones, primarily histone H3, possesses nucleosome assembly activity, transcriptional regulator YGR116W|CRE2|SSN20 gene taxon:4932 20011205 SGD
+SGD S000003348 SPT6 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C interacts with histones, primarily histone H3, possesses nucleosome assembly activity, transcriptional regulator YGR116W|CRE2|SSN20 gene taxon:4932 20040928 SGD
+SGD S000003348 SPT6 GO:0008023 SGD_REF:S000071357|PMID:12242279 IPI C interacts with histones, primarily histone H3, possesses nucleosome assembly activity, transcriptional regulator YGR116W|CRE2|SSN20 gene taxon:4932 20021004 SGD
+SGD S000003348 SPT6 GO:0016944 SGD_REF:S000044170|PMID:9450930 IMP F interacts with histones, primarily histone H3, possesses nucleosome assembly activity, transcriptional regulator YGR116W|CRE2|SSN20 gene taxon:4932 20011205 SGD
+SGD S000003348 SPT6 GO:0006325 SGD_REF:S000057934|PMID:8805244 TAS P interacts with histones, primarily histone H3, possesses nucleosome assembly activity, transcriptional regulator YGR116W|CRE2|SSN20 gene taxon:4932 20011205 SGD
+SGD S000003348 SPT6 GO:0006334 SGD_REF:S000041314|PMID:8633238 IDA P interacts with histones, primarily histone H3, possesses nucleosome assembly activity, transcriptional regulator YGR116W|CRE2|SSN20 gene taxon:4932 20011205 SGD
+SGD S000003348 SPT6 GO:0006355 SGD_REF:S000044170|PMID:9450930 IMP P interacts with histones, primarily histone H3, possesses nucleosome assembly activity, transcriptional regulator YGR116W|CRE2|SSN20 gene taxon:4932 20011205 SGD
+SGD S000003348 SPT6 GO:0006368 SGD_REF:S000071357|PMID:12242279 IPI P interacts with histones, primarily histone H3, possesses nucleosome assembly activity, transcriptional regulator YGR116W|CRE2|SSN20 gene taxon:4932 20021004 SGD
+SGD S000000285 SPT7 GO:0000124 SGD_REF:S000048255|PMID:9674426 IDA C histone acetyltransferase SAGA complex member, transcription factor YBR081C|GIT2 gene taxon:4932 20010221 SGD
+SGD S000000285 SPT7 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C histone acetyltransferase SAGA complex member, transcription factor YBR081C|GIT2 gene taxon:4932 20040928 SGD
+SGD S000000285 SPT7 GO:0046695 SGD_REF:S000071997|PMID:12446794 IPI C histone acetyltransferase SAGA complex member, transcription factor YBR081C|GIT2 gene taxon:4932 20041024 SGD
+SGD S000000285 SPT7 GO:0005198 SGD_REF:S000070424|PMID:12101232 IDA F histone acetyltransferase SAGA complex member, transcription factor YBR081C|GIT2 gene taxon:4932 20030404 SGD
+SGD S000000285 SPT7 GO:0005198 SGD_REF:S000042609|PMID:9858534 IMP F histone acetyltransferase SAGA complex member, transcription factor YBR081C|GIT2 gene taxon:4932 20030404 SGD
+SGD S000000285 SPT7 GO:0000747 SGD_REF:S000050405|PMID:7713415 IMP P histone acetyltransferase SAGA complex member, transcription factor YBR081C|GIT2 gene taxon:4932 20030404 SGD
+SGD S000000285 SPT7 GO:0006461 SGD_REF:S000070424|PMID:12101232 IMP P histone acetyltransferase SAGA complex member, transcription factor YBR081C|GIT2 gene taxon:4932 20030609 SGD
+SGD S000000285 SPT7 GO:0006461 SGD_REF:S000042609|PMID:9858534 IMP P histone acetyltransferase SAGA complex member, transcription factor YBR081C|GIT2 gene taxon:4932 20030609 SGD
+SGD S000000285 SPT7 GO:0016568 SGD_REF:S000061032|PMID:10839822 TAS P histone acetyltransferase SAGA complex member, transcription factor YBR081C|GIT2 gene taxon:4932 20020426 SGD
+SGD S000000285 SPT7 GO:0016573 SGD_REF:S000061032|PMID:10839822 TAS P histone acetyltransferase SAGA complex member, transcription factor YBR081C|GIT2 gene taxon:4932 20020426 SGD
+SGD S000004045 SPT8 GO:0000124 SGD_REF:S000048255|PMID:9674426 IDA C probable member of histone acetyltransferase SAGA complex, transcription factor YLR055C gene taxon:4932 20010221 SGD
+SGD S000004045 SPT8 GO:0005634 SGD_REF:S000069459|PMID:11914276 IDA C probable member of histone acetyltransferase SAGA complex, transcription factor YLR055C gene taxon:4932 20020507 SGD
+SGD S000004045 SPT8 GO:0003712 SGD_REF:S000042609|PMID:9858534 IMP F probable member of histone acetyltransferase SAGA complex, transcription factor YLR055C gene taxon:4932 20021114 SGD
+SGD S000004045 SPT8 GO:0003712 SGD_REF:S000042609|PMID:9858534 IPI F probable member of histone acetyltransferase SAGA complex, transcription factor YLR055C gene taxon:4932 20021114 SGD
+SGD S000004045 SPT8 GO:0016568 SGD_REF:S000061032|PMID:10839822 TAS P probable member of histone acetyltransferase SAGA complex, transcription factor YLR055C gene taxon:4932 20020426 SGD
+SGD S000004045 SPT8 GO:0016573 SGD_REF:S000061032|PMID:10839822 TAS P probable member of histone acetyltransferase SAGA complex, transcription factor YLR055C gene taxon:4932 20020426 SGD
+SGD S000001451 SQT1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YIR012W gene taxon:4932 20020507 SGD
+SGD S000001451 SQT1 GO:0005829 SGD_REF:S000055440|PMID:9271392 IDA C YIR012W gene taxon:4932 20010118 SGD
+SGD S000001451 SQT1 GO:0005830 SGD_REF:S000055440|PMID:9271392 IDA C YIR012W gene taxon:4932 20010118 SGD
+SGD S000001451 SQT1 GO:0005554 SGD_REF:S000069584 ND F YIR012W gene taxon:4932 20010119 SGD
+SGD S000001451 SQT1 GO:0000027 SGD_REF:S000055440|PMID:9271392 IMP P YIR012W gene taxon:4932 20010118 SGD
+SGD S000001451 SQT1 GO:0000027 SGD_REF:S000055440|PMID:9271392 IGI P YIR012W gene taxon:4932 20010118 SGD
+SGD S000001083 SRB2 GO:0000119 SGD_REF:S000048078|PMID:9420330 IDA C RNA polymerase II holoenzyme/mediator subunit YHR041C|HRS2|MED20 gene taxon:4932 20010118 SGD
+SGD S000001083 SRB2 GO:0016455 SGD_REF:S000048078|PMID:9420330 IDA F RNA polymerase II holoenzyme/mediator subunit YHR041C|HRS2|MED20 gene taxon:4932 20010302 SGD
+SGD S000001083 SRB2 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P RNA polymerase II holoenzyme/mediator subunit YHR041C|HRS2|MED20 gene taxon:4932 20060203 SGD
+SGD S000001083 SRB2 GO:0006366 SGD_REF:S000048078|PMID:9420330 IDA P RNA polymerase II holoenzyme/mediator subunit YHR041C|HRS2|MED20 gene taxon:4932 20010118 SGD
+SGD S000000824 SRB4 GO:0000119 SGD_REF:S000048078|PMID:9420330 IDA C RNA polymerase II holoenzyme/mediator subunit YER022W|MED17 gene taxon:4932 20010118 SGD
+SGD S000000824 SRB4 GO:0016455 SGD_REF:S000048078|PMID:9420330 IDA F RNA polymerase II holoenzyme/mediator subunit YER022W|MED17 gene taxon:4932 20010302 SGD
+SGD S000000824 SRB4 GO:0006366 SGD_REF:S000048078|PMID:9420330 IDA P RNA polymerase II holoenzyme/mediator subunit YER022W|MED17 gene taxon:4932 20010118 SGD
+SGD S000003336 SRB5 GO:0000119 SGD_REF:S000048078|PMID:9420330 IDA C RNA polymerase II holoenzyme/mediator subunit YGR104C|MED18 gene taxon:4932 20010118 SGD
+SGD S000003336 SRB5 GO:0016455 SGD_REF:S000048078|PMID:9420330 IDA F RNA polymerase II holoenzyme/mediator subunit YGR104C|MED18 gene taxon:4932 20010302 SGD
+SGD S000003336 SRB5 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P RNA polymerase II holoenzyme/mediator subunit YGR104C|MED18 gene taxon:4932 20060203 SGD
+SGD S000003336 SRB5 GO:0006366 SGD_REF:S000048078|PMID:9420330 IDA P RNA polymerase II holoenzyme/mediator subunit YGR104C|MED18 gene taxon:4932 20010118 SGD
+SGD S000000457 SRB6 GO:0000119 SGD_REF:S000048078|PMID:9420330 IDA C part of Srb/Mediator complex, transcription factor YBR253W|MED22 gene taxon:4932 20010118 SGD
+SGD S000000457 SRB6 GO:0016455 SGD_REF:S000048078|PMID:9420330 IDA F part of Srb/Mediator complex, transcription factor YBR253W|MED22 gene taxon:4932 20010302 SGD
+SGD S000000457 SRB6 GO:0006366 SGD_REF:S000048078|PMID:9420330 IDA P part of Srb/Mediator complex, transcription factor YBR253W|MED22 gene taxon:4932 20010118 SGD
+SGD S000002716 SRB7 GO:0000119 SGD_REF:S000048078|PMID:9420330 IDA C RNA polymerase II holoenzyme/mediator subunit YDR308C|MED21 gene taxon:4932 20010118 SGD
+SGD S000002716 SRB7 GO:0016455 SGD_REF:S000048078|PMID:9420330 IDA F RNA polymerase II holoenzyme/mediator subunit YDR308C|MED21 gene taxon:4932 20010302 SGD
+SGD S000002716 SRB7 GO:0006366 SGD_REF:S000048078|PMID:9420330 IDA P RNA polymerase II holoenzyme/mediator subunit YDR308C|MED21 gene taxon:4932 20010118 SGD
+SGD S000000677 SRB8 GO:0005667 SGD_REF:S000058446|PMID:9774381 TAS C YCR081W|GIG1|MED12|NUT6|SSN5|YCR080W gene taxon:4932 20010118 SGD
+SGD S000000677 SRB8 GO:0016455 SGD_REF:S000058446|PMID:9774381 TAS F YCR081W|GIG1|MED12|NUT6|SSN5|YCR080W gene taxon:4932 20010302 SGD
+SGD S000000677 SRB8 GO:0000122 SGD_REF:S000058446|PMID:9774381 TAS P YCR081W|GIG1|MED12|NUT6|SSN5|YCR080W gene taxon:4932 20010118 SGD
+SGD S000004497 SRC1 GO:0008372 SGD_REF:S000069584 ND C YML034W|YML033W gene taxon:4932 20021009 SGD
+SGD S000004497 SRC1 GO:0005554 SGD_REF:S000069584 ND F YML034W|YML033W gene taxon:4932 20021009 SGD
+SGD S000004497 SRC1 GO:0000070 SGD_REF:S000069006|PMID:11754482 IGI P YML034W|YML033W gene taxon:4932 20021009 SGD
+SGD S000000611 SRD1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YCR018C gene taxon:4932 20031028 SGD
+SGD S000000611 SRD1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YCR018C gene taxon:4932 20031028 SGD
+SGD S000000611 SRD1 GO:0005554 SGD_REF:S000069584 ND F YCR018C gene taxon:4932 20010119 SGD
+SGD S000000611 SRD1 GO:0006364 SGD_REF:S000055913|PMID:2179050 IGI P YCR018C gene taxon:4932 20010118 SGD
+SGD S000029010 SRG1 GO:0005634 SGD_REF:S000076449|PMID:15175754 IC GO:0045892 C gene taxon:4932 20040607 SGD
+SGD S000029010 SRG1 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20040907 SGD
+SGD S000029010 SRG1 GO:0045892 SGD_REF:S000076449|PMID:15175754 IEP P gene taxon:4932 20040607 SGD
+SGD S000029010 SRG1 GO:0045892 SGD_REF:S000076449|PMID:15175754 IMP P gene taxon:4932 20040607 SGD
+SGD S000005773 SRL1 GO:0000324 SGD_REF:S000074185|PMID:14562095 IDA C YOR247W gene taxon:4932 20031028 SGD
+SGD S000005773 SRL1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YOR247W gene taxon:4932 20031028 SGD
+SGD S000005773 SRL1 GO:0005934 SGD_REF:S000074060|PMID:13679573 IDA C YOR247W gene taxon:4932 20040115 SGD
+SGD S000005773 SRL1 GO:0009277 SGD_REF:S000075303|PMID:11935221 IDA C YOR247W gene taxon:4932 20040114 SGD
+SGD S000005773 SRL1 GO:0005554 SGD_REF:S000046108|PMID:9744871 ISS F YOR247W gene taxon:4932 20011101 SGD
+SGD S000005773 SRL1 GO:0006139 SGD_REF:S000046108|PMID:9744871 IGI P YOR247W gene taxon:4932 20011101 SGD
+SGD S000004072 SRL2 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YLR082C gene taxon:4932 20031028 SGD
+SGD S000004072 SRL2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YLR082C gene taxon:4932 20031028 SGD
+SGD S000004072 SRL2 GO:0005554 SGD_REF:S000046108|PMID:9744871 ISS F YLR082C gene taxon:4932 20011101 SGD
+SGD S000004072 SRL2 GO:0006139 SGD_REF:S000046108|PMID:9744871 IGI P YLR082C gene taxon:4932 20011101 SGD
+SGD S000001799 SRL3 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YKR091W gene taxon:4932 20020507 SGD
+SGD S000001799 SRL3 GO:0005554 SGD_REF:S000046108|PMID:9744871 ISS F YKR091W gene taxon:4932 20011101 SGD
+SGD S000001799 SRL3 GO:0006139 SGD_REF:S000046108|PMID:9744871 IGI P YKR091W gene taxon:4932 20011101 SGD
+SGD S000003065 SRM1 GO:0000790 SGD_REF:S000114102|PMID:16365162 IDA C pheromone response pathway suppressor YGL097W|MTR1|PRP20 gene taxon:4932 20060210 SGD
+SGD S000003065 SRM1 GO:0005634 SGD_REF:S000051250|PMID:1666302 TAS C pheromone response pathway suppressor YGL097W|MTR1|PRP20 gene taxon:4932 20021004 SGD
+SGD S000003065 SRM1 GO:0004871 SGD_REF:S000049056|PMID:2548085 IMP F pheromone response pathway suppressor YGL097W|MTR1|PRP20 gene taxon:4932 20021004 SGD
+SGD S000003065 SRM1 GO:0000054 SGD_REF:S000067496|PMID:11739405 IMP P pheromone response pathway suppressor YGL097W|MTR1|PRP20 gene taxon:4932 20020313 SGD
+SGD S000003065 SRM1 GO:0006407 SGD_REF:S000067496|PMID:11739405 IMP P pheromone response pathway suppressor YGL097W|MTR1|PRP20 gene taxon:4932 20020313 SGD
+SGD S000004109 SRN2 GO:0000813 SGD_REF:S000078323|PMID:15044434 IDA C YLR119W|SRN10|VPS37 gene taxon:4932 20041117 SGD
+SGD S000004109 SRN2 GO:0000813 SGD_REF:S000061300|PMID:11511343 IPI C YLR119W|SRN10|VPS37 gene taxon:4932 20060314 SGD
+SGD S000004109 SRN2 GO:0005768 SGD_REF:S000061300|PMID:11511343 IPI C YLR119W|SRN10|VPS37 gene taxon:4932 20020827 SGD
+SGD S000004109 SRN2 GO:0005515 SGD_REF:S000061300|PMID:11511343 IPI F YLR119W|SRN10|VPS37 gene taxon:4932 20060314 SGD
+SGD S000004109 SRN2 GO:0006612 SGD_REF:S000061300|PMID:11511343 IMP P YLR119W|SRN10|VPS37 gene taxon:4932 20020827 SGD
+SGD S000004109 SRN2 GO:0006612 SGD_REF:S000061300|PMID:11511343 IPI P YLR119W|SRN10|VPS37 gene taxon:4932 20020827 SGD
+SGD S000004109 SRN2 GO:0006623 SGD_REF:S000061300|PMID:11511343 IMP P YLR119W|SRN10|VPS37 gene taxon:4932 20020827 SGD
+SGD S000004109 SRN2 GO:0006623 SGD_REF:S000061300|PMID:11511343 IPI P YLR119W|SRN10|VPS37 gene taxon:4932 20020827 SGD
+SGD S000004109 SRN2 GO:0043162 SGD_REF:S000075969|PMID:15086794 IC GO:0000813 P YLR119W|SRN10|VPS37 gene taxon:4932 20050125 SGD
+SGD S000006236 SRO7 GO:0005829 SGD_REF:S000049244|PMID:10402465 IDA C yeast homolog of the Drosophila tumor suppressor, lethal giant larvae YPR032W|SNI1|SOP1 gene taxon:4932 20020708 SGD
+SGD S000006236 SRO7 GO:0005886 SGD_REF:S000049244|PMID:10402465 IDA C yeast homolog of the Drosophila tumor suppressor, lethal giant larvae YPR032W|SNI1|SOP1 gene taxon:4932 20020708 SGD
+SGD S000006236 SRO7 GO:0000149 SGD_REF:S000082378|PMID:15964280 IPI SGD:S000003241 F yeast homolog of the Drosophila tumor suppressor, lethal giant larvae YPR032W|SNI1|SOP1 gene taxon:4932 20060118 SGD
+SGD S000006236 SRO7 GO:0005554 SGD_REF:S000069584 ND F yeast homolog of the Drosophila tumor suppressor, lethal giant larvae YPR032W|SNI1|SOP1 gene taxon:4932 20020708 SGD
+SGD S000006236 SRO7 GO:0006887 SGD_REF:S000049244|PMID:10402465 IGI P yeast homolog of the Drosophila tumor suppressor, lethal giant larvae YPR032W|SNI1|SOP1 gene taxon:4932 20030122 SGD
+SGD S000006236 SRO7 GO:0006893 SGD_REF:S000049244|PMID:10402465 IGI P yeast homolog of the Drosophila tumor suppressor, lethal giant larvae YPR032W|SNI1|SOP1 gene taxon:4932 20030122 SGD
+SGD S000006236 SRO7 GO:0006893 SGD_REF:S000049244|PMID:10402465 IPI P yeast homolog of the Drosophila tumor suppressor, lethal giant larvae YPR032W|SNI1|SOP1 gene taxon:4932 20030122 SGD
+SGD S000006236 SRO7 GO:0030468 SGD_REF:S000082378|PMID:15964280 IPI SGD:S000003241|SGD:S000005853 P yeast homolog of the Drosophila tumor suppressor, lethal giant larvae YPR032W|SNI1|SOP1 gene taxon:4932 20060118 SGD
+SGD S000000202 SRO77 GO:0005886 SGD_REF:S000049244|PMID:10402465 IPI C yeast homolog of the Drosophila tumor suppressor, lethal giant larvae YBL106C|SNI2|SOP2 gene taxon:4932 20030122 SGD
+SGD S000000202 SRO77 GO:0005886 SGD_REF:S000049244|PMID:10402465 ISS C yeast homolog of the Drosophila tumor suppressor, lethal giant larvae YBL106C|SNI2|SOP2 gene taxon:4932 20030122 SGD
+SGD S000000202 SRO77 GO:0005554 SGD_REF:S000069584 ND F yeast homolog of the Drosophila tumor suppressor, lethal giant larvae YBL106C|SNI2|SOP2 gene taxon:4932 20030122 SGD
+SGD S000000202 SRO77 GO:0006887 SGD_REF:S000049244|PMID:10402465 IGI P yeast homolog of the Drosophila tumor suppressor, lethal giant larvae YBL106C|SNI2|SOP2 gene taxon:4932 20030122 SGD
+SGD S000000202 SRO77 GO:0006893 SGD_REF:S000049244|PMID:10402465 IGI P yeast homolog of the Drosophila tumor suppressor, lethal giant larvae YBL106C|SNI2|SOP2 gene taxon:4932 20030122 SGD
+SGD S000000202 SRO77 GO:0006893 SGD_REF:S000049244|PMID:10402465 IPI P yeast homolog of the Drosophila tumor suppressor, lethal giant larvae YBL106C|SNI2|SOP2 gene taxon:4932 20030122 SGD
+SGD S000000542 SRO9 GO:0005844 SGD_REF:S000042217|PMID:10564276 IDA C YCL037C gene taxon:4932 20020826 SGD
+SGD S000000542 SRO9 GO:0003723 SGD_REF:S000042217|PMID:10564276 IDA F YCL037C gene taxon:4932 20020826 SGD
+SGD S000000542 SRO9 GO:0006412 SGD_REF:S000042217|PMID:10564276 IPI P YCL037C gene taxon:4932 20021001 SGD
+SGD S000005133 SRP1 GO:0005634 SGD_REF:S000041520|PMID:10725229 IDA C karyopherin alpha YNL189W|KAP60|SCM1 gene taxon:4932 20021205 SGD
+SGD S000005133 SRP1 GO:0005634 SGD_REF:S000069459|PMID:11914276 IDA C karyopherin alpha YNL189W|KAP60|SCM1 gene taxon:4932 20020507 SGD
+SGD S000005133 SRP1 GO:0005737 SGD_REF:S000041520|PMID:10725229 IDA C karyopherin alpha YNL189W|KAP60|SCM1 gene taxon:4932 20021205 SGD
+SGD S000005133 SRP1 GO:0008320 SGD_REF:S000058277|PMID:9442897 TAS F karyopherin alpha YNL189W|KAP60|SCM1 gene taxon:4932 20010118 SGD
+SGD S000005133 SRP1 GO:0006913 SGD_REF:S000058277|PMID:9442897 TAS P karyopherin alpha YNL189W|KAP60|SCM1 gene taxon:4932 20010118 SGD
+SGD S000002700 SRP101 GO:0005785 SGD_REF:S000054980|PMID:9679135 TAS C YDR292C gene taxon:4932 20050124 SGD
+SGD S000002700 SRP101 GO:0005789 SGD_REF:S000054980|PMID:9679135 IDA C YDR292C gene taxon:4932 20020822 SGD
+SGD S000002700 SRP101 GO:0005047 SGD_REF:S000040045|PMID:1327299 ISS F YDR292C gene taxon:4932 20020822 SGD
+SGD S000002700 SRP101 GO:0005047 SGD_REF:S000040045|PMID:1327299 IMP F YDR292C gene taxon:4932 20020822 SGD
+SGD S000002700 SRP101 GO:0005525 SGD_REF:S000080477|PMID:7844142 IPI F YDR292C gene taxon:4932 20050128 SGD
+SGD S000002700 SRP101 GO:0006614 SGD_REF:S000080477|PMID:7844142 IC GO:0005785 P YDR292C gene taxon:4932 20050128 SGD
+SGD S000002700 SRP101 GO:0006614 SGD_REF:S000080477|PMID:7844142 TAS P YDR292C gene taxon:4932 20050128 SGD
+SGD S000002700 SRP101 GO:0045047 SGD_REF:S000040045|PMID:1327299 IMP P YDR292C gene taxon:4932 20020822 SGD
+SGD S000001637 SRP102 GO:0005785 SGD_REF:S000054980|PMID:9679135 TAS C YKL154W gene taxon:4932 20050124 SGD
+SGD S000001637 SRP102 GO:0030176 SGD_REF:S000054980|PMID:9679135 IDA C YKL154W gene taxon:4932 20020822 SGD
+SGD S000001637 SRP102 GO:0003924 SGD_REF:S000080477|PMID:7844142 ISS protein_id:AAA35552.1 F YKL154W gene taxon:4932 20050128 SGD
+SGD S000001637 SRP102 GO:0005047 SGD_REF:S000054980|PMID:9679135 ISS F YKL154W gene taxon:4932 20020822 SGD
+SGD S000001637 SRP102 GO:0005047 SGD_REF:S000054980|PMID:9679135 IPI F YKL154W gene taxon:4932 20020822 SGD
+SGD S000001637 SRP102 GO:0005047 SGD_REF:S000054980|PMID:9679135 IMP F YKL154W gene taxon:4932 20020822 SGD
+SGD S000001637 SRP102 GO:0005525 SGD_REF:S000080477|PMID:7844142 IPI F YKL154W gene taxon:4932 20050128 SGD
+SGD S000001637 SRP102 GO:0006614 SGD_REF:S000080477|PMID:7844142 IC GO:0005785 P YKL154W gene taxon:4932 20050128 SGD
+SGD S000001637 SRP102 GO:0006614 SGD_REF:S000080477|PMID:7844142 TAS P YKL154W gene taxon:4932 20050128 SGD
+SGD S000001637 SRP102 GO:0045047 SGD_REF:S000054980|PMID:9679135 IMP P YKL154W gene taxon:4932 20020822 SGD
+SGD S000002250 SRP14 GO:0005786 SGD_REF:S000049731|PMID:7925282 IDA C YDL092W gene taxon:4932 20020620 SGD
+SGD S000002250 SRP14 GO:0005048 SGD_REF:S000049731|PMID:7925282 IPI F YDL092W gene taxon:4932 20030527 SGD
+SGD S000002250 SRP14 GO:0006617 SGD_REF:S000049731|PMID:7925282 IC GO:0005786 P YDL092W gene taxon:4932 20050131 SGD
+SGD S000002250 SRP14 GO:0045047 SGD_REF:S000049731|PMID:7925282 IPI P YDL092W gene taxon:4932 20020620 SGD
+SGD S000001605 SRP21 GO:0005634 SGD_REF:S000069459|PMID:11914276 IDA C signal recognition particle component YKL122C gene taxon:4932 20020507 SGD
+SGD S000001605 SRP21 GO:0005786 SGD_REF:S000049731|PMID:7925282 IDA C signal recognition particle component YKL122C gene taxon:4932 20020620 SGD
+SGD S000001605 SRP21 GO:0005048 SGD_REF:S000049731|PMID:7925282 IPI F signal recognition particle component YKL122C gene taxon:4932 20030527 SGD
+SGD S000001605 SRP21 GO:0006617 SGD_REF:S000049731|PMID:7925282 IC GO:0005786 P signal recognition particle component YKL122C gene taxon:4932 20050128 SGD
+SGD S000001605 SRP21 GO:0045047 SGD_REF:S000049731|PMID:7925282 IPI P signal recognition particle component YKL122C gene taxon:4932 20020620 SGD
+SGD S000001800 SRP40 GO:0005730 SGD_REF:S000054828|PMID:8702624 IDA C Nopp140 homolog, a nonribosomal protein of the nucleolus and coiled bodies, nucleolar protein YKR092C gene taxon:4932 20010118 SGD
+SGD S000001800 SRP40 GO:0051082 SGD_REF:S000054828|PMID:8702624 ISS F Nopp140 homolog, a nonribosomal protein of the nucleolus and coiled bodies, nucleolar protein YKR092C gene taxon:4932 20010118 SGD
+SGD S000001800 SRP40 GO:0006913 SGD_REF:S000054828|PMID:8702624 ISS P Nopp140 homolog, a nonribosomal protein of the nucleolus and coiled bodies, nucleolar protein YKR092C gene taxon:4932 20010118 SGD
+SGD S000029506 SRP5 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20010119 SGD
+SGD S000029506 SRP5 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20010119 SGD
+SGD S000029506 SRP5 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20010119 SGD
+SGD S000006292 SRP54 GO:0005786 SGD_REF:S000049731|PMID:7925282 IDA C YPR088C|SRH1 gene taxon:4932 20020620 SGD
+SGD S000006292 SRP54 GO:0005048 SGD_REF:S000049731|PMID:7925282 IPI F YPR088C|SRH1 gene taxon:4932 20030527 SGD
+SGD S000006292 SRP54 GO:0006617 SGD_REF:S000049731|PMID:7925282 IC GO:0005786 P YPR088C|SRH1 gene taxon:4932 20050128 SGD
+SGD S000006292 SRP54 GO:0045047 SGD_REF:S000049731|PMID:7925282 IPI P YPR088C|SRH1 gene taxon:4932 20020620 SGD
+SGD S000006164 SRP68 GO:0005786 SGD_REF:S000049731|PMID:7925282 IDA C signal recognition particle component YPL243W gene taxon:4932 20020620 SGD
+SGD S000006164 SRP68 GO:0005048 SGD_REF:S000049731|PMID:7925282 IPI F signal recognition particle component YPL243W gene taxon:4932 20030527 SGD
+SGD S000006164 SRP68 GO:0006617 SGD_REF:S000049731|PMID:7925282 IC GO:0005786 P signal recognition particle component YPL243W gene taxon:4932 20050128 SGD
+SGD S000006164 SRP68 GO:0045047 SGD_REF:S000049731|PMID:7925282 IPI P signal recognition particle component YPL243W gene taxon:4932 20020620 SGD
+SGD S000006131 SRP72 GO:0005786 SGD_REF:S000049731|PMID:7925282 IDA C signal recognition particle component YPL210C gene taxon:4932 20020620 SGD
+SGD S000006131 SRP72 GO:0005048 SGD_REF:S000049731|PMID:7925282 IPI F signal recognition particle component YPL210C gene taxon:4932 20030527 SGD
+SGD S000006131 SRP72 GO:0006617 SGD_REF:S000049731|PMID:7925282 IC GO:0005786 P signal recognition particle component YPL210C gene taxon:4932 20050128 SGD
+SGD S000006131 SRP72 GO:0045047 SGD_REF:S000049731|PMID:7925282 IPI P signal recognition particle component YPL210C gene taxon:4932 20020620 SGD
+SGD S000004707 SRT1 GO:0005811 SGD_REF:S000060857|PMID:11442630 IDA C cis-prenyltransferase YMR101C gene taxon:4932 20020307 SGD
+SGD S000004707 SRT1 GO:0045547 SGD_REF:S000060857|PMID:11442630 ISS F cis-prenyltransferase YMR101C gene taxon:4932 20050708 SGD
+SGD S000004707 SRT1 GO:0045547 SGD_REF:S000060857|PMID:11442630 IDA F cis-prenyltransferase YMR101C gene taxon:4932 20050708 SGD
+SGD S000004707 SRT1 GO:0006486 SGD_REF:S000060857|PMID:11442630 IMP P cis-prenyltransferase YMR101C gene taxon:4932 20020307 SGD
+SGD S000004707 SRT1 GO:0006486 SGD_REF:S000060857|PMID:11442630 IDA P cis-prenyltransferase YMR101C gene taxon:4932 20020307 SGD
+SGD S000005082 SRV2 GO:0030479 SGD_REF:S000054269|PMID:9190214 TAS C 70 kDa adenylyl cyclase-associated protein YNL138W|CAP gene taxon:4932 20010118 SGD
+SGD S000005082 SRV2 GO:0008092 SGD_REF:S000039306|PMID:8552082 TAS F 70 kDa adenylyl cyclase-associated protein YNL138W|CAP gene taxon:4932 20010118 SGD
+SGD S000005082 SRV2 GO:0008179 SGD_REF:S000039306|PMID:8552082 TAS F 70 kDa adenylyl cyclase-associated protein YNL138W|CAP gene taxon:4932 20010118 SGD
+SGD S000005082 SRV2 GO:0007010 SGD_REF:S000039306|PMID:8552082 TAS P 70 kDa adenylyl cyclase-associated protein YNL138W|CAP gene taxon:4932 20010118 SGD
+SGD S000005082 SRV2 GO:0007265 SGD_REF:S000053841|PMID:9774417 IMP P 70 kDa adenylyl cyclase-associated protein YNL138W|CAP gene taxon:4932 20010118 SGD
+SGD S000001569 SRX1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C ATP-dependent cysteine sulfinic acid reductase YKL086W gene taxon:4932 20031028 SGD
+SGD S000001569 SRX1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C ATP-dependent cysteine sulfinic acid reductase YKL086W gene taxon:4932 20031028 SGD
+SGD S000001569 SRX1 GO:0016667 SGD_REF:S000075134|PMID:14586471 IDA F ATP-dependent cysteine sulfinic acid reductase YKL086W gene taxon:4932 20040304 SGD
+SGD S000001569 SRX1 GO:0006979 SGD_REF:S000075134|PMID:14586471 IMP P ATP-dependent cysteine sulfinic acid reductase YKL086W gene taxon:4932 20040304 SGD
+SGD S000001701 SRY1 GO:0008372 SGD_REF:S000069584 ND C YKL218C gene taxon:4932 20030324 SGD
+SGD S000001701 SRY1 NOT GO:0030378 SGD_REF:S000076238|PMID:12951240 IDA F YKL218C gene taxon:4932 20040524 SGD
+SGD S000001701 SRY1 GO:0030848 SGD_REF:S000076238|PMID:12951240 IDA F YKL218C gene taxon:4932 20040614 SGD
+SGD S000001701 SRY1 GO:0042219 SGD_REF:S000076238|PMID:12951240 IMP P YKL218C gene taxon:4932 20040524 SGD
+SGD S000000004 SSA1 GO:0000329 SGD_REF:S000047102|PMID:10745074 IDA C heat shock protein of HSP70 family YAL005C|YG100 gene taxon:4932 20030306 SGD
+SGD S000000004 SSA1 GO:0005634 SGD_REF:S000046800|PMID:10347213 IDA C heat shock protein of HSP70 family YAL005C|YG100 gene taxon:4932 20010118 SGD
+SGD S000000004 SSA1 GO:0005634 SGD_REF:S000069459|PMID:11914276 IDA C heat shock protein of HSP70 family YAL005C|YG100 gene taxon:4932 20020507 SGD
+SGD S000000004 SSA1 GO:0005737 SGD_REF:S000043439|PMID:8755907 IDA C heat shock protein of HSP70 family YAL005C|YG100 gene taxon:4932 20010118 SGD
+SGD S000000004 SSA1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C heat shock protein of HSP70 family YAL005C|YG100 gene taxon:4932 20020507 SGD
+SGD S000000004 SSA1 GO:0005832 SGD_REF:S000080727|PMID:15704212 IPI SGD:S000002596 C heat shock protein of HSP70 family YAL005C|YG100 gene taxon:4932 20050307 SGD
+SGD S000000004 SSA1 GO:0009277 SGD_REF:S000043439|PMID:8755907 IDA C heat shock protein of HSP70 family YAL005C|YG100 gene taxon:4932 20010118 SGD
+SGD S000000004 SSA1 GO:0016887 SGD_REF:S000049386|PMID:7737974 IDA F heat shock protein of HSP70 family YAL005C|YG100 gene taxon:4932 20010118 SGD
+SGD S000000004 SSA1 GO:0051082 SGD_REF:S000045677|PMID:9789005 IDA F heat shock protein of HSP70 family YAL005C|YG100 gene taxon:4932 20021119 SGD
+SGD S000000004 SSA1 GO:0000060 SGD_REF:S000046800|PMID:10347213 IDA P heat shock protein of HSP70 family YAL005C|YG100 gene taxon:4932 20010118 SGD
+SGD S000000004 SSA1 GO:0006457 SGD_REF:S000052334|PMID:8947547 IDA P heat shock protein of HSP70 family YAL005C|YG100 gene taxon:4932 20010118 SGD
+SGD S000000004 SSA1 GO:0006616 SGD_REF:S000041237|PMID:8754838 IDA P heat shock protein of HSP70 family YAL005C|YG100 gene taxon:4932 20010118 SGD
+SGD S000000004 SSA1 GO:0006626 SGD_REF:S000041237|PMID:8754838 IMP P heat shock protein of HSP70 family YAL005C|YG100 gene taxon:4932 20060227 SGD
+SGD S000000004 SSA1 GO:0006950 SGD_REF:S000043741|PMID:3302682 IMP P heat shock protein of HSP70 family YAL005C|YG100 gene taxon:4932 20060511 SGD
+SGD S000000004 SSA1 GO:0043037 SGD_REF:S000060234|PMID:11279042 IMP P heat shock protein of HSP70 family YAL005C|YG100 gene taxon:4932 20060227 SGD
+SGD S000003947 SSA2 GO:0000329 SGD_REF:S000047102|PMID:10745074 IDA C HSP70 family YLL024C|YG102 gene taxon:4932 20030306 SGD
+SGD S000003947 SSA2 GO:0005737 SGD_REF:S000043439|PMID:8755907 IDA C HSP70 family YLL024C|YG102 gene taxon:4932 20010118 SGD
+SGD S000003947 SSA2 GO:0005832 SGD_REF:S000080727|PMID:15704212 IPI SGD:S000002596 C HSP70 family YLL024C|YG102 gene taxon:4932 20050307 SGD
+SGD S000003947 SSA2 GO:0009277 SGD_REF:S000043439|PMID:8755907 IDA C HSP70 family YLL024C|YG102 gene taxon:4932 20010118 SGD
+SGD S000003947 SSA2 GO:0005524 SGD_REF:S000049670|PMID:10893257 IDA F HSP70 family YLL024C|YG102 gene taxon:4932 20040716 SGD
+SGD S000003947 SSA2 GO:0016887 SGD_REF:S000054673|PMID:8151709 ISS SGD:S000000004 F HSP70 family YLL024C|YG102 gene taxon:4932 20060511 SGD
+SGD S000003947 SSA2 GO:0051082 SGD_REF:S000045677|PMID:9789005 IGI SGD:S000000004|SGD:S000000905|SGD:S000000171 F HSP70 family YLL024C|YG102 gene taxon:4932 20060511 SGD
+SGD S000003947 SSA2 GO:0051082 SGD_REF:S000054673|PMID:8151709 ISS SGD:S000000004 F HSP70 family YLL024C|YG102 gene taxon:4932 20060511 SGD
+SGD S000003947 SSA2 GO:0006457 SGD_REF:S000049179|PMID:9448096 IMP P HSP70 family YLL024C|YG102 gene taxon:4932 20010118 SGD
+SGD S000003947 SSA2 GO:0006457 SGD_REF:S000046286|PMID:7867784 IDA P HSP70 family YLL024C|YG102 gene taxon:4932 20060511 SGD
+SGD S000003947 SSA2 GO:0006616 SGD_REF:S000041237|PMID:8754838 IMP P HSP70 family YLL024C|YG102 gene taxon:4932 20060511 SGD
+SGD S000003947 SSA2 GO:0006950 SGD_REF:S000043741|PMID:3302682 IMP P HSP70 family YLL024C|YG102 gene taxon:4932 20060511 SGD
+SGD S000000171 SSA3 GO:0005829 SGD_REF:S000047102|PMID:10745074 IDA C heat shock protein of HSP70 family YBL075C|YG106 gene taxon:4932 20060511 SGD
+SGD S000000171 SSA3 GO:0016887 SGD_REF:S000043741|PMID:3302682 IGI SGD:S000000004 F heat shock protein of HSP70 family YBL075C|YG106 gene taxon:4932 20060511 SGD
+SGD S000000171 SSA3 GO:0016887 SGD_REF:S000054673|PMID:8151709 ISS SGD:S000000004 F heat shock protein of HSP70 family YBL075C|YG106 gene taxon:4932 20060511 SGD
+SGD S000000171 SSA3 GO:0051082 SGD_REF:S000054673|PMID:8151709 ISS SGD:S000000004 F heat shock protein of HSP70 family YBL075C|YG106 gene taxon:4932 20060511 SGD
+SGD S000000171 SSA3 GO:0051082 SGD_REF:S000045677|PMID:9789005 IGI SGD:S000000004|SGD:S000003947|SGD:S000000905 F heat shock protein of HSP70 family YBL075C|YG106 gene taxon:4932 20060511 SGD
+SGD S000000171 SSA3 GO:0006457 SGD_REF:S000045677|PMID:9789005 IGI SGD:S000000004|SGD:S000003947|SGD:S000000905 P heat shock protein of HSP70 family YBL075C|YG106 gene taxon:4932 20060511 SGD
+SGD S000000171 SSA3 GO:0006616 SGD_REF:S000041237|PMID:8754838 IMP P heat shock protein of HSP70 family YBL075C|YG106 gene taxon:4932 20010118 SGD
+SGD S000000171 SSA3 GO:0006950 SGD_REF:S000043741|PMID:3302682 IMP P heat shock protein of HSP70 family YBL075C|YG106 gene taxon:4932 20010118 SGD
+SGD S000000905 SSA4 GO:0005634 SGD_REF:S000060873|PMID:11279056 IDA C HSP70 family YER103W|YG107 gene taxon:4932 20030331 SGD
+SGD S000000905 SSA4 GO:0005737 SGD_REF:S000060873|PMID:11279056 IDA C HSP70 family YER103W|YG107 gene taxon:4932 20030331 SGD
+SGD S000000905 SSA4 GO:0016887 SGD_REF:S000054673|PMID:8151709 ISS SGD:S000000004 F HSP70 family YER103W|YG107 gene taxon:4932 20060511 SGD
+SGD S000000905 SSA4 GO:0051082 SGD_REF:S000054673|PMID:8151709 ISS SGD:S000000004 F HSP70 family YER103W|YG107 gene taxon:4932 20060511 SGD
+SGD S000000905 SSA4 GO:0051082 SGD_REF:S000045677|PMID:9789005 IGI SGD:S000000004|SGD:S000000171|SGD:S000003947 F HSP70 family YER103W|YG107 gene taxon:4932 20060511 SGD
+SGD S000000905 SSA4 GO:0006457 SGD_REF:S000045677|PMID:9789005 IGI SGD:S000000004|SGD:S000003947|SGD:S000000171 P HSP70 family YER103W|YG107 gene taxon:4932 20060511 SGD
+SGD S000000905 SSA4 GO:0006616 SGD_REF:S000041237|PMID:8754838 IMP P HSP70 family YER103W|YG107 gene taxon:4932 20010118 SGD
+SGD S000000905 SSA4 GO:0006950 SGD_REF:S000047372|PMID:2121731 IDA P HSP70 family YER103W|YG107 gene taxon:4932 20010118 SGD
+SGD S000002388 SSB1 GO:0005625 SGD_REF:S000068747|PMID:11746603 IDA C HSP70 family YDL229W|YG101 gene taxon:4932 20030130 SGD
+SGD S000002388 SSB1 GO:0005844 SGD_REF:S000041887|PMID:1394434 IDA C HSP70 family YDL229W|YG101 gene taxon:4932 20060227 SGD
+SGD S000002388 SSB1 GO:0016887 SGD_REF:S000052276|PMID:9860955 IDA F HSP70 family YDL229W|YG101 gene taxon:4932 20030331 SGD
+SGD S000002388 SSB1 GO:0051082 SGD_REF:S000039738|PMID:9670014 IDA F HSP70 family YDL229W|YG101 gene taxon:4932 20060227 SGD
+SGD S000002388 SSB1 GO:0006412 SGD_REF:S000041887|PMID:1394434 IMP P HSP70 family YDL229W|YG101 gene taxon:4932 20060227 SGD
+SGD S000002388 SSB1 GO:0006412 SGD_REF:S000041887|PMID:1394434 IPI SGD:S000001395|SGD:S000005013 P HSP70 family YDL229W|YG101 gene taxon:4932 20060227 SGD
+SGD S000002388 SSB1 GO:0006450 SGD_REF:S000077503|PMID:15456889 IMP P HSP70 family YDL229W|YG101 gene taxon:4932 20060124 SGD
+SGD S000002388 SSB1 GO:0051083 SGD_REF:S000039738|PMID:9670014 IDA P HSP70 family YDL229W|YG101 gene taxon:4932 20060227 SGD
+SGD S000005153 SSB2 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C SSB1 homolog, heat shock protein of HSP70 family YNL209W|YG103 gene taxon:4932 20020507 SGD
+SGD S000005153 SSB2 GO:0005844 SGD_REF:S000041887|PMID:1394434 IDA C SSB1 homolog, heat shock protein of HSP70 family YNL209W|YG103 gene taxon:4932 20060227 SGD
+SGD S000005153 SSB2 GO:0016887 SGD_REF:S000052276|PMID:9860955 IDA F SSB1 homolog, heat shock protein of HSP70 family YNL209W|YG103 gene taxon:4932 20030331 SGD
+SGD S000005153 SSB2 GO:0051082 SGD_REF:S000039738|PMID:9670014 IDA F SSB1 homolog, heat shock protein of HSP70 family YNL209W|YG103 gene taxon:4932 20060227 SGD
+SGD S000005153 SSB2 GO:0006412 SGD_REF:S000041887|PMID:1394434 IMP P SSB1 homolog, heat shock protein of HSP70 family YNL209W|YG103 gene taxon:4932 20060227 SGD
+SGD S000005153 SSB2 GO:0006412 SGD_REF:S000041887|PMID:1394434 IPI SGD:S000001395|SGD:S000005013 P SSB1 homolog, heat shock protein of HSP70 family YNL209W|YG103 gene taxon:4932 20060227 SGD
+SGD S000005153 SSB2 GO:0006450 SGD_REF:S000077503|PMID:15456889 IMP P SSB1 homolog, heat shock protein of HSP70 family YNL209W|YG103 gene taxon:4932 20060124 SGD
+SGD S000005153 SSB2 GO:0051083 SGD_REF:S000039738|PMID:9670014 IDA P SSB1 homolog, heat shock protein of HSP70 family YNL209W|YG103 gene taxon:4932 20060227 SGD
+SGD S000003806 SSC1 GO:0001405 SGD_REF:S000074354|PMID:14638855 IPI C Endo.SceI endonuclease subunit, mitochondrial matrix protein involved in protein import YJR045C|ENS1|mtHSP70 gene taxon:4932 20031218 SGD
+SGD S000003806 SSC1 GO:0001405 SGD_REF:S000074353|PMID:14517234 IPI C Endo.SceI endonuclease subunit, mitochondrial matrix protein involved in protein import YJR045C|ENS1|mtHSP70 gene taxon:4932 20031218 SGD
+SGD S000003806 SSC1 GO:0005739 SGD_REF:S000069459|PMID:11914276 IDA C Endo.SceI endonuclease subunit, mitochondrial matrix protein involved in protein import YJR045C|ENS1|mtHSP70 gene taxon:4932 20020507 SGD
+SGD S000003806 SSC1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C Endo.SceI endonuclease subunit, mitochondrial matrix protein involved in protein import YJR045C|ENS1|mtHSP70 gene taxon:4932 20040924 SGD
+SGD S000003806 SSC1 GO:0005743 SGD_REF:S000039851|PMID:7935837 IDA C Endo.SceI endonuclease subunit, mitochondrial matrix protein involved in protein import YJR045C|ENS1|mtHSP70 gene taxon:4932 20010118 SGD
+SGD S000003806 SSC1 GO:0042645 SGD_REF:S000080741|PMID:15692048 IDA C Endo.SceI endonuclease subunit, mitochondrial matrix protein involved in protein import YJR045C|ENS1|mtHSP70 gene taxon:4932 20050401 SGD
+SGD S000003806 SSC1 GO:0008565 SGD_REF:S000048120|PMID:10779357 IMP F Endo.SceI endonuclease subunit, mitochondrial matrix protein involved in protein import YJR045C|ENS1|mtHSP70 gene taxon:4932 20030210 SGD
+SGD S000003806 SSC1 GO:0016887 SGD_REF:S000079344|PMID:11096111 IDA F Endo.SceI endonuclease subunit, mitochondrial matrix protein involved in protein import YJR045C|ENS1|mtHSP70 gene taxon:4932 20050406 SGD
+SGD S000003806 SSC1 GO:0030234 SGD_REF:S000054598|PMID:10464305 IDA F Endo.SceI endonuclease subunit, mitochondrial matrix protein involved in protein import YJR045C|ENS1|mtHSP70 gene taxon:4932 20030227 SGD
+SGD S000003806 SSC1 GO:0006457 SGD_REF:S000050255|PMID:8654364 IDA P Endo.SceI endonuclease subunit, mitochondrial matrix protein involved in protein import YJR045C|ENS1|mtHSP70 gene taxon:4932 20010118 SGD
+SGD S000003806 SSC1 GO:0030150 SGD_REF:S000050255|PMID:8654364 IDA P Endo.SceI endonuclease subunit, mitochondrial matrix protein involved in protein import YJR045C|ENS1|mtHSP70 gene taxon:4932 20031119 SGD
+SGD S000003806 SSC1 GO:0042026 SGD_REF:S000114353|PMID:16460754 IMP P Endo.SceI endonuclease subunit, mitochondrial matrix protein involved in protein import YJR045C|ENS1|mtHSP70 gene taxon:4932 20060530 SGD
+SGD S000002701 SSD1 GO:0005737 SGD_REF:S000049246|PMID:9195905 IDA C YDR293C|CLA1|MCS1|RLT1|SRK1 gene taxon:4932 20010118 SGD
+SGD S000002701 SSD1 GO:0003723 SGD_REF:S000049246|PMID:9195905 IDA F YDR293C|CLA1|MCS1|RLT1|SRK1 gene taxon:4932 20010118 SGD
+SGD S000002701 SSD1 GO:0007047 SGD_REF:S000069081|PMID:11805047 IGI P YDR293C|CLA1|MCS1|RLT1|SRK1 gene taxon:4932 20030128 SGD
+SGD S000006027 SSE1 GO:0005737 SGD_REF:S000058920|PMID:15028727 IC GO:0030188|GO:0051082 C HSP70 family, SSA1 SSE2 homolog YPL106C|LPG3|MSI3 gene taxon:4932 20050715 SGD
+SGD S000006027 SSE1 GO:0005524 SGD_REF:S000058920|PMID:15028727 IDA F HSP70 family, SSA1 SSE2 homolog YPL106C|LPG3|MSI3 gene taxon:4932 20050715 SGD
+SGD S000006027 SSE1 GO:0005524 SGD_REF:S000058920|PMID:15028727 IMP F HSP70 family, SSA1 SSE2 homolog YPL106C|LPG3|MSI3 gene taxon:4932 20050715 SGD
+SGD S000006027 SSE1 GO:0030188 SGD_REF:S000058920|PMID:15028727 IGI SGD:S000005008 F HSP70 family, SSA1 SSE2 homolog YPL106C|LPG3|MSI3 gene taxon:4932 20060608 SGD
+SGD S000006027 SSE1 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P HSP70 family, SSA1 SSE2 homolog YPL106C|LPG3|MSI3 gene taxon:4932 20060221 SGD
+SGD S000006027 SSE1 GO:0006457 SGD_REF:S000040113|PMID:10480867 IMP P HSP70 family, SSA1 SSE2 homolog YPL106C|LPG3|MSI3 gene taxon:4932 20010118 SGD
+SGD S000006027 SSE1 GO:0006457 SGD_REF:S000058920|PMID:15028727 IC GO:0030188 P HSP70 family, SSA1 SSE2 homolog YPL106C|LPG3|MSI3 gene taxon:4932 20060608 SGD
+SGD S000000373 SSE2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C HSP70 family, SSE1 homolog YBR169C gene taxon:4932 20031028 SGD
+SGD S000000373 SSE2 GO:0005554 SGD_REF:S000069584 ND F HSP70 family, SSE1 homolog YBR169C gene taxon:4932 20040716 SGD
+SGD S000000373 SSE2 GO:0006457 SGD_REF:S000041547|PMID:8406043 ISS P HSP70 family, SSE1 homolog YBR169C gene taxon:4932 20010118 SGD
+SGD S000001108 SSF1 GO:0005730 SGD_REF:S000039858|PMID:9611192 IDA C Ssf2p homolog YHR066W gene taxon:4932 20020826 SGD
+SGD S000001108 SSF1 GO:0019843 SGD_REF:S000069545|PMID:11864606 IPI F Ssf2p homolog YHR066W gene taxon:4932 20030220 SGD
+SGD S000001108 SSF1 GO:0000027 SGD_REF:S000069545|PMID:11864606 IMP P Ssf2p homolog YHR066W gene taxon:4932 20030220 SGD
+SGD S000001108 SSF1 GO:0000027 SGD_REF:S000069532|PMID:11864607 IPI P Ssf2p homolog YHR066W gene taxon:4932 20020826 SGD
+SGD S000001108 SSF1 GO:0000747 SGD_REF:S000051561|PMID:7748491 IGI P Ssf2p homolog YHR066W gene taxon:4932 20020826 SGD
+SGD S000002720 SSF2 GO:0005730 SGD_REF:S000069532|PMID:11864607 ISS C YDR312W gene taxon:4932 20020826 SGD
+SGD S000002720 SSF2 GO:0005730 SGD_REF:S000068847|PMID:12702244 IDA C YDR312W gene taxon:4932 20030731 SGD
+SGD S000002720 SSF2 GO:0019843 SGD_REF:S000069545|PMID:11864606 IPI F YDR312W gene taxon:4932 20030220 SGD
+SGD S000002720 SSF2 GO:0000027 SGD_REF:S000069545|PMID:11864606 IMP P YDR312W gene taxon:4932 20030220 SGD
+SGD S000002720 SSF2 GO:0000027 SGD_REF:S000069532|PMID:11864607 ISS P YDR312W gene taxon:4932 20020826 SGD
+SGD S000002720 SSF2 GO:0000747 SGD_REF:S000051561|PMID:7748491 IGI P YDR312W gene taxon:4932 20020826 SGD
+SGD S000000487 SSH1 GO:0005784 SGD_REF:S000058467|PMID:10921929 TAS C YBR283C gene taxon:4932 20010118 SGD
+SGD S000000487 SSH1 GO:0005789 SGD_REF:S000068896|PMID:11702951 IDA C YBR283C gene taxon:4932 20020830 SGD
+SGD S000000487 SSH1 GO:0042175 SGD_REF:S000071811|PMID:12206772 IDA C YBR283C gene taxon:4932 20030226 SGD
+SGD S000000487 SSH1 GO:0008565 SGD_REF:S000058467|PMID:10921929 TAS F YBR283C gene taxon:4932 20010118 SGD
+SGD S000000487 SSH1 GO:0006613 SGD_REF:S000058467|PMID:10921929 TAS P YBR283C gene taxon:4932 20010118 SGD
+SGD S000001607 SSH4 GO:0008372 SGD_REF:S000069584 ND C YKL124W|MLF4 gene taxon:4932 20021009 SGD
+SGD S000001607 SSH4 GO:0005554 SGD_REF:S000069584 ND F YKL124W|MLF4 gene taxon:4932 20021009 SGD
+SGD S000001607 SSH4 GO:0000004 SGD_REF:S000069584 ND P YKL124W|MLF4 gene taxon:4932 20021009 SGD
+SGD S000003996 SSK1 GO:0005737 SGD_REF:S000053117|PMID:8808622 TAS C two-component signal transducer that with Sln1p regulates osmosensing MAP kinase cascade(suppressor of sensor kinase) YLR006C gene taxon:4932 20030213 SGD
+SGD S000003996 SSK1 GO:0000156 SGD_REF:S000056287|PMID:9482735 TAS F two-component signal transducer that with Sln1p regulates osmosensing MAP kinase cascade(suppressor of sensor kinase) YLR006C gene taxon:4932 20010118 SGD
+SGD S000003996 SSK1 GO:0008047 SGD_REF:S000056287|PMID:9482735 TAS F two-component signal transducer that with Sln1p regulates osmosensing MAP kinase cascade(suppressor of sensor kinase) YLR006C gene taxon:4932 20010118 SGD
+SGD S000003996 SSK1 GO:0007234 SGD_REF:S000048289|PMID:8183345 TAS P two-component signal transducer that with Sln1p regulates osmosensing MAP kinase cascade(suppressor of sensor kinase) YLR006C gene taxon:4932 20010118 SGD
+SGD S000003996 SSK1 GO:0007234 SGD_REF:S000053117|PMID:8808622 IDA P two-component signal transducer that with Sln1p regulates osmosensing MAP kinase cascade(suppressor of sensor kinase) YLR006C gene taxon:4932 20030226 SGD
+SGD S000003996 SSK1 GO:0042542 SGD_REF:S000059181|PMID:11084293 IMP P two-component signal transducer that with Sln1p regulates osmosensing MAP kinase cascade(suppressor of sensor kinase) YLR006C gene taxon:4932 20030213 SGD
+SGD S000005314 SSK2 GO:0005829 SGD_REF:S000070407|PMID:12181352 IDA C MAP kinase kinase kinase, activator of Pbs2p YNR031C gene taxon:4932 20030214 SGD
+SGD S000005314 SSK2 GO:0005934 SGD_REF:S000075961|PMID:12857882 IDA C MAP kinase kinase kinase, activator of Pbs2p YNR031C gene taxon:4932 20050303 SGD
+SGD S000005314 SSK2 GO:0005935 SGD_REF:S000075961|PMID:12857882 IDA C MAP kinase kinase kinase, activator of Pbs2p YNR031C gene taxon:4932 20050303 SGD
+SGD S000005314 SSK2 GO:0004709 SGD_REF:S000051778|PMID:7624781 TAS F MAP kinase kinase kinase, activator of Pbs2p YNR031C gene taxon:4932 20010118 SGD
+SGD S000005314 SSK2 GO:0000168 SGD_REF:S000051778|PMID:7624781 TAS P MAP kinase kinase kinase, activator of Pbs2p YNR031C gene taxon:4932 20010118 SGD
+SGD S000005314 SSK2 GO:0006468 SGD_REF:S000051778|PMID:7624781 TAS P MAP kinase kinase kinase, activator of Pbs2p YNR031C gene taxon:4932 20010118 SGD
+SGD S000005314 SSK2 GO:0006970 SGD_REF:S000075961|PMID:12857882 IMP P MAP kinase kinase kinase, activator of Pbs2p YNR031C gene taxon:4932 20050303 SGD
+SGD S000005314 SSK2 GO:0006970 SGD_REF:S000075961|PMID:12857882 IGI P MAP kinase kinase kinase, activator of Pbs2p YNR031C gene taxon:4932 20050303 SGD
+SGD S000005314 SSK2 GO:0007231 SGD_REF:S000051778|PMID:7624781 TAS P MAP kinase kinase kinase, activator of Pbs2p YNR031C gene taxon:4932 20010118 SGD
+SGD S000005314 SSK2 GO:0030036 SGD_REF:S000070407|PMID:12181352 IDA P MAP kinase kinase kinase, activator of Pbs2p YNR031C gene taxon:4932 20030214 SGD
+SGD S000000669 SSK22 GO:0008372 SGD_REF:S000069584 ND C YCR073C gene taxon:4932 20030211 SGD
+SGD S000000669 SSK22 GO:0004709 SGD_REF:S000058202|PMID:9305639 TAS F YCR073C gene taxon:4932 20010118 SGD
+SGD S000000669 SSK22 GO:0000168 SGD_REF:S000058202|PMID:9305639 TAS P YCR073C gene taxon:4932 20010118 SGD
+SGD S000000669 SSK22 GO:0006468 SGD_REF:S000058202|PMID:9305639 TAS P YCR073C gene taxon:4932 20010118 SGD
+SGD S000000669 SSK22 GO:0007231 SGD_REF:S000051778|PMID:7624781 TAS P YCR073C gene taxon:4932 20010118 SGD
+SGD S000003995 SSL1 GO:0000112 SGD_REF:S000070118|PMID:10915862 TAS C RNA polymerase transcription factor TFIIH component YLR005W gene taxon:4932 20020710 SGD
+SGD S000003995 SSL1 GO:0005675 SGD_REF:S000058446|PMID:9774381 TAS C RNA polymerase transcription factor TFIIH component YLR005W gene taxon:4932 20010118 SGD
+SGD S000003995 SSL1 GO:0005675 SGD_REF:S000075290|PMID:14500720 IDA C RNA polymerase transcription factor TFIIH component YLR005W gene taxon:4932 20041013 SGD
+SGD S000003995 SSL1 GO:0016251 SGD_REF:S000058446|PMID:9774381 TAS F RNA polymerase transcription factor TFIIH component YLR005W gene taxon:4932 20010119 SGD
+SGD S000003995 SSL1 GO:0000717 SGD_REF:S000070118|PMID:10915862 TAS P RNA polymerase transcription factor TFIIH component YLR005W gene taxon:4932 20020726 SGD
+SGD S000003995 SSL1 GO:0006289 SGD_REF:S000058446|PMID:9774381 TAS P RNA polymerase transcription factor TFIIH component YLR005W gene taxon:4932 20010118 SGD
+SGD S000003995 SSL1 GO:0006367 SGD_REF:S000056378|PMID:10384286 TAS P RNA polymerase transcription factor TFIIH component YLR005W gene taxon:4932 20010118 SGD
+SGD S000003995 SSL1 GO:0006367 SGD_REF:S000056377|PMID:10384273 TAS P RNA polymerase transcription factor TFIIH component YLR005W gene taxon:4932 20010118 SGD
+SGD S000003995 SSL1 GO:0007070 SGD_REF:S000056377|PMID:10384273 TAS P RNA polymerase transcription factor TFIIH component YLR005W gene taxon:4932 20010118 SGD
+SGD S000001405 SSL2 GO:0000112 SGD_REF:S000070118|PMID:10915862 TAS C DNA helicase, human XPBC, ERCC3 homolog YIL143C|LOM3|RAD25 gene taxon:4932 20020710 SGD
+SGD S000001405 SSL2 GO:0005675 SGD_REF:S000058446|PMID:9774381 TAS C DNA helicase, human XPBC, ERCC3 homolog YIL143C|LOM3|RAD25 gene taxon:4932 20010118 SGD
+SGD S000001405 SSL2 GO:0003678 SGD_REF:S000058446|PMID:9774381 TAS F DNA helicase, human XPBC, ERCC3 homolog YIL143C|LOM3|RAD25 gene taxon:4932 20010118 SGD
+SGD S000001405 SSL2 GO:0016251 SGD_REF:S000058446|PMID:9774381 TAS F DNA helicase, human XPBC, ERCC3 homolog YIL143C|LOM3|RAD25 gene taxon:4932 20010119 SGD
+SGD S000001405 SSL2 GO:0000717 SGD_REF:S000070118|PMID:10915862 TAS P DNA helicase, human XPBC, ERCC3 homolog YIL143C|LOM3|RAD25 gene taxon:4932 20020726 SGD
+SGD S000001405 SSL2 GO:0006367 SGD_REF:S000056378|PMID:10384286 TAS P DNA helicase, human XPBC, ERCC3 homolog YIL143C|LOM3|RAD25 gene taxon:4932 20010118 SGD
+SGD S000001405 SSL2 GO:0006367 SGD_REF:S000056377|PMID:10384273 TAS P DNA helicase, human XPBC, ERCC3 homolog YIL143C|LOM3|RAD25 gene taxon:4932 20010118 SGD
+SGD S000001405 SSL2 GO:0007070 SGD_REF:S000056377|PMID:10384273 TAS P DNA helicase, human XPBC, ERCC3 homolog YIL143C|LOM3|RAD25 gene taxon:4932 20010118 SGD
+SGD S000001292 SSM4 GO:0005635 SGD_REF:S000041084|PMID:8917313 TAS C integral membrane protein YIL030C|DOA10 gene taxon:4932 20010118 SGD
+SGD S000001292 SSM4 GO:0005635 SGD_REF:S000068873|PMID:11641273 IDA C integral membrane protein YIL030C|DOA10 gene taxon:4932 20050508 SGD
+SGD S000001292 SSM4 GO:0030176 SGD_REF:S000068873|PMID:11641273 IDA C integral membrane protein YIL030C|DOA10 gene taxon:4932 20050508 SGD
+SGD S000001292 SSM4 GO:0004842 SGD_REF:S000068873|PMID:11641273 IDA F integral membrane protein YIL030C|DOA10 gene taxon:4932 20020110 SGD
+SGD S000001292 SSM4 GO:0030433 SGD_REF:S000068873|PMID:11641273 IMP P integral membrane protein YIL030C|DOA10 gene taxon:4932 20050714 SGD
+SGD S000001292 SSM4 GO:0030433 SGD_REF:S000077133|PMID:15252059 IMP P integral membrane protein YIL030C|DOA10 gene taxon:4932 20050714 SGD
+SGD S000002851 SSN2 GO:0005667 SGD_REF:S000058446|PMID:9774381 TAS C transcription factor YDR443C|MED13|NUT8|RYE3|SCA1|SRB9|UME2 gene taxon:4932 20010118 SGD
+SGD S000002851 SSN2 GO:0016251 SGD_REF:S000058446|PMID:9774381 TAS F transcription factor YDR443C|MED13|NUT8|RYE3|SCA1|SRB9|UME2 gene taxon:4932 20020528 SGD
+SGD S000002851 SSN2 GO:0000122 SGD_REF:S000058446|PMID:9774381 TAS P transcription factor YDR443C|MED13|NUT8|RYE3|SCA1|SRB9|UME2 gene taxon:4932 20010118 SGD
+SGD S000005963 SSN3 GO:0005667 SGD_REF:S000058446|PMID:9774381 TAS C cyclin (SSN8)-dependent serine/threonine protein kinase YPL042C|CDK8|GIG2|NUT7|RYE5|SRB10|UME5 gene taxon:4932 20010118 SGD
+SGD S000005963 SSN3 GO:0004693 SGD_REF:S000058446|PMID:9774381 TAS F cyclin (SSN8)-dependent serine/threonine protein kinase YPL042C|CDK8|GIG2|NUT7|RYE5|SRB10|UME5 gene taxon:4932 20010118 SGD
+SGD S000005963 SSN3 GO:0016251 SGD_REF:S000058446|PMID:9774381 TAS F cyclin (SSN8)-dependent serine/threonine protein kinase YPL042C|CDK8|GIG2|NUT7|RYE5|SRB10|UME5 gene taxon:4932 20020528 SGD
+SGD S000005963 SSN3 GO:0000122 SGD_REF:S000058446|PMID:9774381 TAS P cyclin (SSN8)-dependent serine/threonine protein kinase YPL042C|CDK8|GIG2|NUT7|RYE5|SRB10|UME5 gene taxon:4932 20010118 SGD
+SGD S000005963 SSN3 GO:0006468 SGD_REF:S000058446|PMID:9774381 TAS P cyclin (SSN8)-dependent serine/threonine protein kinase YPL042C|CDK8|GIG2|NUT7|RYE5|SRB10|UME5 gene taxon:4932 20010118 SGD
+SGD S000005963 SSN3 GO:0007126 SGD_REF:S000071723|PMID:12455972 TAS P cyclin (SSN8)-dependent serine/threonine protein kinase YPL042C|CDK8|GIG2|NUT7|RYE5|SRB10|UME5 gene taxon:4932 20030502 SGD
+SGD S000005963 SSN3 GO:0045449 SGD_REF:S000065953|PMID:11486018 IMP P cyclin (SSN8)-dependent serine/threonine protein kinase YPL042C|CDK8|GIG2|NUT7|RYE5|SRB10|UME5 gene taxon:4932 20030502 SGD
+SGD S000005963 SSN3 GO:0045449 SGD_REF:S000065953|PMID:11486018 IPI P cyclin (SSN8)-dependent serine/threonine protein kinase YPL042C|CDK8|GIG2|NUT7|RYE5|SRB10|UME5 gene taxon:4932 20030502 SGD
+SGD S000004970 SSN8 GO:0005667 SGD_REF:S000058446|PMID:9774381 TAS C C-type cyclin, associates with the Ssn3p cyclin-dependent kinase YNL025C|CycC|GIG3|NUT9|RYE2|SRB11|UME3 gene taxon:4932 20010118 SGD
+SGD S000004970 SSN8 GO:0016251 SGD_REF:S000058446|PMID:9774381 TAS F C-type cyclin, associates with the Ssn3p cyclin-dependent kinase YNL025C|CycC|GIG3|NUT9|RYE2|SRB11|UME3 gene taxon:4932 20020528 SGD
+SGD S000004970 SSN8 GO:0016538 SGD_REF:S000058446|PMID:9774381 TAS F C-type cyclin, associates with the Ssn3p cyclin-dependent kinase YNL025C|CycC|GIG3|NUT9|RYE2|SRB11|UME3 gene taxon:4932 20020208 SGD
+SGD S000004970 SSN8 GO:0000122 SGD_REF:S000058446|PMID:9774381 TAS P C-type cyclin, associates with the Ssn3p cyclin-dependent kinase YNL025C|CycC|GIG3|NUT9|RYE2|SRB11|UME3 gene taxon:4932 20010118 SGD
+SGD S000004970 SSN8 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P C-type cyclin, associates with the Ssn3p cyclin-dependent kinase YNL025C|CycC|GIG3|NUT9|RYE2|SRB11|UME3 gene taxon:4932 20060202 SGD
+SGD S000004970 SSN8 GO:0007126 SGD_REF:S000071723|PMID:12455972 IGI P C-type cyclin, associates with the Ssn3p cyclin-dependent kinase YNL025C|CycC|GIG3|NUT9|RYE2|SRB11|UME3 gene taxon:4932 20030502 SGD
+SGD S000004970 SSN8 GO:0007126 SGD_REF:S000071723|PMID:12455972 IMP P C-type cyclin, associates with the Ssn3p cyclin-dependent kinase YNL025C|CycC|GIG3|NUT9|RYE2|SRB11|UME3 gene taxon:4932 20030502 SGD
+SGD S000006153 SSO1 GO:0005887 SGD_REF:S000058453|PMID:10047442 TAS C t-SNARE YPL232W gene taxon:4932 20010118 SGD
+SGD S000006153 SSO1 GO:0031201 SGD_REF:S000058139|PMID:9195974 IDA C t-SNARE YPL232W gene taxon:4932 20060531 SGD
+SGD S000006153 SSO1 GO:0005486 SGD_REF:S000058453|PMID:10047442 TAS F t-SNARE YPL232W gene taxon:4932 20010118 SGD
+SGD S000006153 SSO1 GO:0006893 SGD_REF:S000058453|PMID:10047442 TAS P t-SNARE YPL232W gene taxon:4932 20010118 SGD
+SGD S000006153 SSO1 GO:0006906 SGD_REF:S000058453|PMID:10047442 TAS P t-SNARE YPL232W gene taxon:4932 20010118 SGD
+SGD S000004795 SSO2 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C t-SNARE YMR183C gene taxon:4932 20020507 SGD
+SGD S000004795 SSO2 GO:0005783 SGD_REF:S000069459|PMID:11914276 IDA C t-SNARE YMR183C gene taxon:4932 20020507 SGD
+SGD S000004795 SSO2 GO:0005887 SGD_REF:S000058453|PMID:10047442 TAS C t-SNARE YMR183C gene taxon:4932 20010118 SGD
+SGD S000004795 SSO2 GO:0005486 SGD_REF:S000058453|PMID:10047442 TAS F t-SNARE YMR183C gene taxon:4932 20010118 SGD
+SGD S000004795 SSO2 GO:0006893 SGD_REF:S000058453|PMID:10047442 TAS P t-SNARE YMR183C gene taxon:4932 20010118 SGD
+SGD S000004795 SSO2 GO:0006906 SGD_REF:S000058453|PMID:10047442 TAS P t-SNARE YMR183C gene taxon:4932 20010118 SGD
+SGD S000001227 SSP1 GO:0005628 SGD_REF:S000069149|PMID:11742972 IDA C YHR184W|SPO3 gene taxon:4932 20020920 SGD
+SGD S000001227 SSP1 GO:0005554 SGD_REF:S000069584 ND F YHR184W|SPO3 gene taxon:4932 20020920 SGD
+SGD S000001227 SSP1 GO:0006461 SGD_REF:S000069149|PMID:11742972 IMP P YHR184W|SPO3 gene taxon:4932 20020920 SGD
+SGD S000001227 SSP1 GO:0030476 SGD_REF:S000069149|PMID:11742972 IMP P YHR184W|SPO3 gene taxon:4932 20020920 SGD
+SGD S000001227 SSP1 GO:0030476 SGD_REF:S000069149|PMID:11742972 IPI P YHR184W|SPO3 gene taxon:4932 20020920 SGD
+SGD S000004240 SSP120 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YLR250W gene taxon:4932 20031028 SGD
+SGD S000004240 SSP120 GO:0005554 SGD_REF:S000069584 ND F YLR250W gene taxon:4932 20021001 SGD
+SGD S000004240 SSP120 GO:0009306 SGD_REF:S000046103|PMID:1743509 ISS P YLR250W gene taxon:4932 20021001 SGD
+SGD S000005768 SSP2 GO:0005619 SGD_REF:S000070011|PMID:12073037 IDA C YOR242C gene taxon:4932 20021001 SGD
+SGD S000005768 SSP2 GO:0005554 SGD_REF:S000069584 ND F YOR242C gene taxon:4932 20021001 SGD
+SGD S000005768 SSP2 GO:0030476 SGD_REF:S000070011|PMID:12073037 IMP P YOR242C gene taxon:4932 20021001 SGD
+SGD S000004361 SSQ1 GO:0005759 SGD_REF:S000047007|PMID:8707841 IDA C HSP70 family chaperone YLR369W|SSC2 gene taxon:4932 20010118 SGD
+SGD S000004361 SSQ1 GO:0051082 SGD_REF:S000047007|PMID:8707841 ISS F HSP70 family chaperone YLR369W|SSC2 gene taxon:4932 20010118 SGD
+SGD S000004361 SSQ1 GO:0006261 SGD_REF:S000047007|PMID:8707841 IMP P HSP70 family chaperone YLR369W|SSC2 gene taxon:4932 20010118 SGD
+SGD S000004361 SSQ1 GO:0006880 SGD_REF:S000040492|PMID:9660806 IMP P HSP70 family chaperone YLR369W|SSC2 gene taxon:4932 20010118 SGD
+SGD S000002493 SSS1 GO:0005784 SGD_REF:S000058467|PMID:10921929 TAS C ER protein, Sec61 trimeric complex component, Ssh1 trimeric complex component YDR086C gene taxon:4932 20010118 SGD
+SGD S000002493 SSS1 GO:0005784 SGD_REF:S000079534|PMID:12860997 IDA C ER protein, Sec61 trimeric complex component, Ssh1 trimeric complex component YDR086C gene taxon:4932 20041115 SGD
+SGD S000002493 SSS1 GO:0005789 SGD_REF:S000079534|PMID:12860997 IDA C ER protein, Sec61 trimeric complex component, Ssh1 trimeric complex component YDR086C gene taxon:4932 20041115 SGD
+SGD S000002493 SSS1 GO:0031206 SGD_REF:S000063769|PMID:9252322 TAS C ER protein, Sec61 trimeric complex component, Ssh1 trimeric complex component YDR086C gene taxon:4932 20050317 SGD
+SGD S000002493 SSS1 GO:0008565 SGD_REF:S000058467|PMID:10921929 TAS F ER protein, Sec61 trimeric complex component, Ssh1 trimeric complex component YDR086C gene taxon:4932 20010118 SGD
+SGD S000002493 SSS1 GO:0006616 SGD_REF:S000080325|PMID:15631991 TAS P ER protein, Sec61 trimeric complex component, Ssh1 trimeric complex component YDR086C gene taxon:4932 20050127 SGD
+SGD S000002493 SSS1 GO:0006620 SGD_REF:S000063769|PMID:9252322 TAS P ER protein, Sec61 trimeric complex component, Ssh1 trimeric complex component YDR086C gene taxon:4932 20050127 SGD
+SGD S000002493 SSS1 GO:0009306 SGD_REF:S000079534|PMID:12860997 IMP P ER protein, Sec61 trimeric complex component, Ssh1 trimeric complex component YDR086C gene taxon:4932 20041115 SGD
+SGD S000002493 SSS1 GO:0031204 SGD_REF:S000063769|PMID:9252322 TAS P ER protein, Sec61 trimeric complex component, Ssh1 trimeric complex component YDR086C gene taxon:4932 20050317 SGD
+SGD S000004444 SST2 GO:0005886 SGD_REF:S000043515|PMID:8756677 IDA C GTPase activating protein (GAP), RGS (regulator of G-protein signalling) family YLR452C gene taxon:4932 20010118 SGD
+SGD S000004444 SST2 GO:0005096 SGD_REF:S000054924|PMID:9537998 IDA F GTPase activating protein (GAP), RGS (regulator of G-protein signalling) family YLR452C gene taxon:4932 20010118 SGD
+SGD S000004444 SST2 GO:0000754 SGD_REF:S000051182|PMID:2830483 IMP P GTPase activating protein (GAP), RGS (regulator of G-protein signalling) family YLR452C gene taxon:4932 20021206 SGD
+SGD S000004444 SST2 GO:0000754 SGD_REF:S000051894|PMID:9024634 TAS P GTPase activating protein (GAP), RGS (regulator of G-protein signalling) family YLR452C gene taxon:4932 20021206 SGD
+SGD S000004444 SST2 GO:0007165 SGD_REF:S000054924|PMID:9537998 IMP P GTPase activating protein (GAP), RGS (regulator of G-protein signalling) family YLR452C gene taxon:4932 20010118 SGD
+SGD S000006013 SSU1 GO:0005886 SGD_REF:S000050324|PMID:9294463 IDA C major facilitator superfamily YPL092W|LPG16 gene taxon:4932 20020403 SGD
+SGD S000006013 SSU1 GO:0000319 SGD_REF:S000054296|PMID:10870099 IDA F major facilitator superfamily YPL092W|LPG16 gene taxon:4932 20020416 SGD
+SGD S000006013 SSU1 GO:0000316 SGD_REF:S000054296|PMID:10870099 IDA P major facilitator superfamily YPL092W|LPG16 gene taxon:4932 20020404 SGD
+SGD S000005166 SSU72 GO:0005634 SGD_REF:S000059108|PMID:11046131 IGI SGD:S000005677 C YNL222W gene taxon:4932 20021106 SGD
+SGD S000005166 SSU72 GO:0005634 SGD_REF:S000059108|PMID:11046131 IPI C YNL222W gene taxon:4932 20021106 SGD
+SGD S000005166 SSU72 GO:0005847 SGD_REF:S000074089|PMID:12819204 IPI C YNL222W gene taxon:4932 20031013 SGD
+SGD S000005166 SSU72 contributes_to GO:0003723 SGD_REF:S000074089|PMID:12819204 IC GO:0005847 F YNL222W gene taxon:4932 20050222 SGD
+SGD S000005166 SSU72 GO:0004721 SGD_REF:S000073170|PMID:12660165 IGI F YNL222W gene taxon:4932 20030624 SGD
+SGD S000005166 SSU72 GO:0004721 SGD_REF:S000073170|PMID:12660165 IPI F YNL222W gene taxon:4932 20030624 SGD
+SGD S000005166 SSU72 GO:0004725 SGD_REF:S000073338|PMID:12606538 ISS F YNL222W gene taxon:4932 20030624 SGD
+SGD S000005166 SSU72 GO:0042578 SGD_REF:S000073170|PMID:12660165 IDA F YNL222W gene taxon:4932 20030624 SGD
+SGD S000005166 SSU72 GO:0042578 SGD_REF:S000073338|PMID:12606538 IDA F YNL222W gene taxon:4932 20030624 SGD
+SGD S000005166 SSU72 GO:0006365 SGD_REF:S000073750|PMID:12837249 IMP P YNL222W gene taxon:4932 20030805 SGD
+SGD S000005166 SSU72 GO:0006367 SGD_REF:S000059108|PMID:11046131 IGI P YNL222W gene taxon:4932 20021106 SGD
+SGD S000005166 SSU72 GO:0006367 SGD_REF:S000059108|PMID:11046131 IPI P YNL222W gene taxon:4932 20021106 SGD
+SGD S000005166 SSU72 GO:0006369 SGD_REF:S000073170|PMID:12660165 IMP P YNL222W gene taxon:4932 20030624 SGD
+SGD S000005166 SSU72 GO:0009302 SGD_REF:S000073170|PMID:12660165 IMP P YNL222W gene taxon:4932 20030624 SGD
+SGD S000005166 SSU72 GO:0030846 SGD_REF:S000074053|PMID:12944462 IMP P YNL222W gene taxon:4932 20031010 SGD
+SGD S000005166 SSU72 GO:0030846 SGD_REF:S000074089|PMID:12819204 IPI P YNL222W gene taxon:4932 20031013 SGD
+SGD S000005166 SSU72 GO:0030847 SGD_REF:S000074053|PMID:12944462 IMP P YNL222W gene taxon:4932 20031010 SGD
+SGD S000005166 SSU72 GO:0030847 SGD_REF:S000074089|PMID:12819204 IPI P YNL222W gene taxon:4932 20031013 SGD
+SGD S000002567 SSY1 GO:0005886 SGD_REF:S000045243|PMID:10409731 IDA C YDR160W|SHR10 gene taxon:4932 20020920 SGD
+SGD S000002567 SSY1 GO:0016597 SGD_REF:S000045243|PMID:10409731 IGI F YDR160W|SHR10 gene taxon:4932 20020920 SGD
+SGD S000002567 SSY1 GO:0016597 SGD_REF:S000045243|PMID:10409731 IMP F YDR160W|SHR10 gene taxon:4932 20020920 SGD
+SGD S000002567 SSY1 GO:0007606 SGD_REF:S000045243|PMID:10409731 IGI P YDR160W|SHR10 gene taxon:4932 20020920 SGD
+SGD S000002567 SSY1 GO:0007606 SGD_REF:S000045243|PMID:10409731 IMP P YDR160W|SHR10 gene taxon:4932 20020920 SGD
+SGD S000003692 SSY5 GO:0019897 SGD_REF:S000059760|PMID:11154269 IDA C YJL156C gene taxon:4932 20020920 SGD
+SGD S000003692 SSY5 GO:0016597 SGD_REF:S000059760|PMID:11154269 IGI F YJL156C gene taxon:4932 20020920 SGD
+SGD S000003692 SSY5 GO:0016597 SGD_REF:S000059760|PMID:11154269 IMP F YJL156C gene taxon:4932 20020920 SGD
+SGD S000003692 SSY5 GO:0007606 SGD_REF:S000059760|PMID:11154269 IGI P YJL156C gene taxon:4932 20020920 SGD
+SGD S000003692 SSY5 GO:0007606 SGD_REF:S000059760|PMID:11154269 IMP P YJL156C gene taxon:4932 20020920 SGD
+SGD S000001106 SSZ1 GO:0005737 SGD_REF:S000045198|PMID:10792726 IDA C HSP70 family YHR064C|PDR13 gene taxon:4932 20020708 SGD
+SGD S000001106 SSZ1 GO:0051082 SGD_REF:S000059353|PMID:11054575 IGI F HSP70 family YHR064C|PDR13 gene taxon:4932 20020708 SGD
+SGD S000001106 SSZ1 GO:0051082 SGD_REF:S000059353|PMID:11054575 IPI F HSP70 family YHR064C|PDR13 gene taxon:4932 20020708 SGD
+SGD S000001106 SSZ1 GO:0051082 SGD_REF:S000047371|PMID:9488429 ISS F HSP70 family YHR064C|PDR13 gene taxon:4932 20020708 SGD
+SGD S000001106 SSZ1 GO:0006412 SGD_REF:S000069724|PMID:11929994 IGI P HSP70 family YHR064C|PDR13 gene taxon:4932 20020708 SGD
+SGD S000001106 SSZ1 GO:0006412 SGD_REF:S000059353|PMID:11054575 IGI P HSP70 family YHR064C|PDR13 gene taxon:4932 20020708 SGD
+SGD S000001106 SSZ1 GO:0006412 SGD_REF:S000059353|PMID:11054575 IPI P HSP70 family YHR064C|PDR13 gene taxon:4932 20020708 SGD
+SGD S000001106 SSZ1 GO:0006412 SGD_REF:S000069724|PMID:11929994 IMP P HSP70 family YHR064C|PDR13 gene taxon:4932 20020708 SGD
+SGD S000001106 SSZ1 GO:0006450 SGD_REF:S000077503|PMID:15456889 IMP P HSP70 family YHR064C|PDR13 gene taxon:4932 20060124 SGD
+SGD S000029522 STA1 GO:0005576 SGD_REF:S000076041|PMID:15116339 IDA C glucan 1, 4 alpha glucosidase, glucoamylase DEX2|MAL5 gene taxon:4932 20040716 SGD
+SGD S000029522 STA1 GO:0004339 SGD_REF:S000051924|PMID:9383611 TAS F glucan 1, 4 alpha glucosidase, glucoamylase DEX2|MAL5 gene taxon:4932 20010118 SGD
+SGD S000029522 STA1 GO:0004339 SGD_REF:S000076041|PMID:15116339 IDA F glucan 1, 4 alpha glucosidase, glucoamylase DEX2|MAL5 gene taxon:4932 20040716 SGD
+SGD S000029522 STA1 GO:0005975 SGD_REF:S000076041|PMID:15116339 IC GO:0004339 P glucan 1, 4 alpha glucosidase, glucoamylase DEX2|MAL5 gene taxon:4932 20040716 SGD
+SGD S000029524 STA2 GO:0005576 SGD_REF:S000050030|PMID:3014435 TAS C glucan 1, 4 alpha glucosidase, glucoamylase gene taxon:4932 20030213 SGD
+SGD S000029524 STA2 GO:0004339 SGD_REF:S000051924|PMID:9383611 TAS F glucan 1, 4 alpha glucosidase, glucoamylase gene taxon:4932 20010118 SGD
+SGD S000029524 STA2 GO:0005983 SGD_REF:S000053194|PMID:9342405 TAS P glucan 1, 4 alpha glucosidase, glucoamylase gene taxon:4932 20030213 SGD
+SGD S000005253 STB1 GO:0005634 SGD_REF:S000069459|PMID:11914276 IDA C YNL309W gene taxon:4932 20020507 SGD
+SGD S000005253 STB1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YNL309W gene taxon:4932 20031028 SGD
+SGD S000005253 STB1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YNL309W gene taxon:4932 20031028 SGD
+SGD S000005253 STB1 GO:0016580 SGD_REF:S000054148|PMID:9393435 IPI SGD:S000005364 C YNL309W gene taxon:4932 20031215 SGD
+SGD S000005253 STB1 GO:0016563 SGD_REF:S000073748|PMID:12832490 IDA F YNL309W gene taxon:4932 20030806 SGD
+SGD S000005253 STB1 GO:0000082 SGD_REF:S000045210|PMID:10409718 IGI P YNL309W gene taxon:4932 20021010 SGD
+SGD S000005253 STB1 GO:0000082 SGD_REF:S000045210|PMID:10409718 IEP P YNL309W gene taxon:4932 20021010 SGD
+SGD S000004657 STB2 GO:0005634 SGD_REF:S000054148|PMID:9393435 IPI SGD:S000005364 C YMR053C gene taxon:4932 20021030 SGD
+SGD S000004657 STB2 GO:0016580 SGD_REF:S000054148|PMID:9393435 IPI SGD:S000005364 C YMR053C gene taxon:4932 20021030 SGD
+SGD S000004657 STB2 GO:0016564 SGD_REF:S000054148|PMID:9393435 IPI SGD:S000005364 F YMR053C gene taxon:4932 20021030 SGD
+SGD S000004657 STB2 GO:0016575 SGD_REF:S000054148|PMID:9393435 IPI P YMR053C gene taxon:4932 20021016 SGD
+SGD S000002576 STB3 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDR169C gene taxon:4932 20031028 SGD
+SGD S000002576 STB3 GO:0005554 SGD_REF:S000069584 ND F YDR169C gene taxon:4932 20021029 SGD
+SGD S000002576 STB3 GO:0000004 SGD_REF:S000069584 ND P YDR169C gene taxon:4932 20021029 SGD
+SGD S000004621 STB4 GO:0005634 SGD_REF:S000054148|PMID:9393435 ISS C YMR019W gene taxon:4932 20021029 SGD
+SGD S000004621 STB4 GO:0005634 SGD_REF:S000081155|PMID:15343339 IC GO:0003677 C YMR019W gene taxon:4932 20050331 SGD
+SGD S000004621 STB4 GO:0003677 SGD_REF:S000054148|PMID:9393435 ISS F YMR019W gene taxon:4932 20021029 SGD
+SGD S000004621 STB4 GO:0003677 SGD_REF:S000081155|PMID:15343339 IPI F YMR019W gene taxon:4932 20050331 SGD
+SGD S000004621 STB4 GO:0000004 SGD_REF:S000069584 ND P YMR019W gene taxon:4932 20021029 SGD
+SGD S000001221 STB5 GO:0005634 SGD_REF:S000069947|PMID:11943786 IPI C YHR178W gene taxon:4932 20020617 SGD
+SGD S000001221 STB5 GO:0003700 SGD_REF:S000069947|PMID:11943786 IGI F YHR178W gene taxon:4932 20020617 SGD
+SGD S000001221 STB5 GO:0003700 SGD_REF:S000069947|PMID:11943786 IMP F YHR178W gene taxon:4932 20020617 SGD
+SGD S000001221 STB5 GO:0003700 SGD_REF:S000069947|PMID:11943786 IDA F YHR178W gene taxon:4932 20050114 SGD
+SGD S000001221 STB5 GO:0003700 SGD_REF:S000069947|PMID:11943786 IPI F YHR178W gene taxon:4932 20020617 SGD
+SGD S000001221 STB5 GO:0003700 SGD_REF:S000069947|PMID:11943786 ISS F YHR178W gene taxon:4932 20020617 SGD
+SGD S000001221 STB5 GO:0006350 SGD_REF:S000069947|PMID:11943786 IDA P YHR178W gene taxon:4932 20050117 SGD
+SGD S000001221 STB5 GO:0009410 SGD_REF:S000069947|PMID:11943786 IMP P YHR178W gene taxon:4932 20020617 SGD
+SGD S000001555 STB6 GO:0008372 SGD_REF:S000069584 ND C YKL072W gene taxon:4932 20021029 SGD
+SGD S000001555 STB6 GO:0005554 SGD_REF:S000069584 ND F YKL072W gene taxon:4932 20021029 SGD
+SGD S000001555 STB6 GO:0000004 SGD_REF:S000069584 ND P YKL072W gene taxon:4932 20021029 SGD
+SGD S000005573 STD1 GO:0005634 SGD_REF:S000051846|PMID:10373505 IDA C MTH1 homolog YOR047C|MSN3|SFS3 gene taxon:4932 20020716 SGD
+SGD S000005573 STD1 GO:0005886 SGD_REF:S000051846|PMID:10373505 IDA C MTH1 homolog YOR047C|MSN3|SFS3 gene taxon:4932 20020716 SGD
+SGD S000005573 STD1 GO:0030295 SGD_REF:S000072726|PMID:12618390 IGI F MTH1 homolog YOR047C|MSN3|SFS3 gene taxon:4932 20030313 SGD
+SGD S000005573 STD1 GO:0030295 SGD_REF:S000072726|PMID:12618390 IPI F MTH1 homolog YOR047C|MSN3|SFS3 gene taxon:4932 20030313 SGD
+SGD S000005573 STD1 GO:0006006 SGD_REF:S000051846|PMID:10373505 IMP P MTH1 homolog YOR047C|MSN3|SFS3 gene taxon:4932 20020716 SGD
+SGD S000005573 STD1 GO:0006357 SGD_REF:S000048642|PMID:7667094 IMP P MTH1 homolog YOR047C|MSN3|SFS3 gene taxon:4932 20020716 SGD
+SGD S000005573 STD1 GO:0006357 SGD_REF:S000048642|PMID:7667094 IPI P MTH1 homolog YOR047C|MSN3|SFS3 gene taxon:4932 20020716 SGD
+SGD S000005573 STD1 GO:0007165 SGD_REF:S000051846|PMID:10373505 IMP P MTH1 homolog YOR047C|MSN3|SFS3 gene taxon:4932 20020716 SGD
+SGD S000005573 STD1 GO:0009651 SGD_REF:S000041177|PMID:9725828 IMP P MTH1 homolog YOR047C|MSN3|SFS3 gene taxon:4932 20020716 SGD
+SGD S000004354 STE11 GO:0005737 SGD_REF:S000058374|PMID:9755161 IDA C YLR362W gene taxon:4932 20010118 SGD
+SGD S000004354 STE11 GO:0004709 SGD_REF:S000050765|PMID:8159759 TAS F YLR362W gene taxon:4932 20010118 SGD
+SGD S000004354 STE11 GO:0000750 SGD_REF:S000050425|PMID:8001818 TAS P YLR362W gene taxon:4932 20021206 SGD
+SGD S000004354 STE11 GO:0001403 SGD_REF:S000050425|PMID:8001818 IMP P YLR362W gene taxon:4932 20050218 SGD
+SGD S000004354 STE11 GO:0006468 SGD_REF:S000050765|PMID:8159759 TAS P YLR362W gene taxon:4932 20010118 SGD
+SGD S000004354 STE11 GO:0007124 SGD_REF:S000050425|PMID:8001818 TAS P YLR362W gene taxon:4932 20010118 SGD
+SGD S000001126 STE12 GO:0005634 SGD_REF:S000048594|PMID:7834739 TAS C transcription factor YHR084W gene taxon:4932 20010118 SGD
+SGD S000001126 STE12 GO:0003700 SGD_REF:S000052446|PMID:2558054 IPI F transcription factor YHR084W gene taxon:4932 20010118 SGD
+SGD S000001126 STE12 GO:0000747 SGD_REF:S000051834|PMID:10704467 TAS P transcription factor YHR084W gene taxon:4932 20020918 SGD
+SGD S000001126 STE12 GO:0001403 SGD_REF:S000050425|PMID:8001818 IMP P transcription factor YHR084W gene taxon:4932 20010118 SGD
+SGD S000001126 STE12 GO:0007124 SGD_REF:S000055060|PMID:8259520 IMP P transcription factor YHR084W gene taxon:4932 20010118 SGD
+SGD S000001126 STE12 GO:0007329 SGD_REF:S000048594|PMID:7834739 IMP P transcription factor YHR084W gene taxon:4932 20010118 SGD
+SGD S000005745 STE13 GO:0005802 SGD_REF:S000039541|PMID:8308064 IDA C dipeptidyl aminopeptidase YOR219C|YCI1|yscIV gene taxon:4932 20020904 SGD
+SGD S000005745 STE13 GO:0004177 SGD_REF:S000052020|PMID:6339075 IDA F dipeptidyl aminopeptidase YOR219C|YCI1|yscIV gene taxon:4932 20021112 SGD
+SGD S000005745 STE13 GO:0007323 SGD_REF:S000052020|PMID:6339075 IDA P dipeptidyl aminopeptidase YOR219C|YCI1|yscIV gene taxon:4932 20021112 SGD
+SGD S000005745 STE13 GO:0007323 SGD_REF:S000052020|PMID:6339075 IMP P dipeptidyl aminopeptidase YOR219C|YCI1|yscIV gene taxon:4932 20021112 SGD
+SGD S000002818 STE14 GO:0005789 SGD_REF:S000061387|PMID:11451995 IDA C farnesyl cysteine-carboxyl methyltransferase YDR410C gene taxon:4932 20021001 SGD
+SGD S000002818 STE14 GO:0005789 SGD_REF:S000052884|PMID:9693378 IDA C farnesyl cysteine-carboxyl methyltransferase YDR410C gene taxon:4932 20041216 SGD
+SGD S000002818 STE14 GO:0004671 SGD_REF:S000061387|PMID:11451995 IMP F farnesyl cysteine-carboxyl methyltransferase YDR410C gene taxon:4932 20021001 SGD
+SGD S000002818 STE14 GO:0004671 SGD_REF:S000061387|PMID:11451995 TAS F farnesyl cysteine-carboxyl methyltransferase YDR410C gene taxon:4932 20021001 SGD
+SGD S000002818 STE14 GO:0004671 SGD_REF:S000046550|PMID:2050108 IDA F farnesyl cysteine-carboxyl methyltransferase YDR410C gene taxon:4932 20041216 SGD
+SGD S000002818 STE14 GO:0007323 SGD_REF:S000048018|PMID:9015298 TAS P farnesyl cysteine-carboxyl methyltransferase YDR410C gene taxon:4932 20021001 SGD
+SGD S000002818 STE14 GO:0007323 SGD_REF:S000046550|PMID:2050108 IMP P farnesyl cysteine-carboxyl methyltransferase YDR410C gene taxon:4932 20041216 SGD
+SGD S000003846 STE18 GO:0005737 SGD_REF:S000046375|PMID:8995254 IDA C G protein gamma subunit, coupled to mating factor receptor YJR086W gene taxon:4932 20010118 SGD
+SGD S000003846 STE18 GO:0005834 SGD_REF:S000046375|PMID:8995254 IDA C G protein gamma subunit, coupled to mating factor receptor YJR086W gene taxon:4932 20010118 SGD
+SGD S000003846 STE18 GO:0005886 SGD_REF:S000046375|PMID:8995254 IDA C G protein gamma subunit, coupled to mating factor receptor YJR086W gene taxon:4932 20010118 SGD
+SGD S000003846 STE18 GO:0003924 SGD_REF:S000058498 TAS F G protein gamma subunit, coupled to mating factor receptor YJR086W gene taxon:4932 20010119 SGD
+SGD S000003846 STE18 GO:0000750 SGD_REF:S000044693|PMID:3151178 IMP P G protein gamma subunit, coupled to mating factor receptor YJR086W gene taxon:4932 20021206 SGD
+SGD S000001868 STE2 GO:0005887 SGD_REF:S000049330|PMID:2839507 IDA C G protein coupled receptor (GPCR), alpha-factor pheromone receptor, seven-transmembrane domain protein YFL026W gene taxon:4932 20021122 SGD
+SGD S000001868 STE2 GO:0004934 SGD_REF:S000042841|PMID:3001640 ISS F G protein coupled receptor (GPCR), alpha-factor pheromone receptor, seven-transmembrane domain protein YFL026W gene taxon:4932 20010118 SGD
+SGD S000001868 STE2 GO:0004934 SGD_REF:S000056023|PMID:9742115 IMP F G protein coupled receptor (GPCR), alpha-factor pheromone receptor, seven-transmembrane domain protein YFL026W gene taxon:4932 20050512 SGD
+SGD S000001868 STE2 GO:0004934 SGD_REF:S000056023|PMID:9742115 IGI SGD:S000001047|SGD:S000003846|SGD:S000005738 F G protein coupled receptor (GPCR), alpha-factor pheromone receptor, seven-transmembrane domain protein YFL026W gene taxon:4932 20050512 SGD
+SGD S000001868 STE2 GO:0004934 SGD_REF:S000042026|PMID:2161538 IDA F G protein coupled receptor (GPCR), alpha-factor pheromone receptor, seven-transmembrane domain protein YFL026W gene taxon:4932 20050512 SGD
+SGD S000001868 STE2 GO:0000749 SGD_REF:S000042841|PMID:3001640 TAS P G protein coupled receptor (GPCR), alpha-factor pheromone receptor, seven-transmembrane domain protein YFL026W gene taxon:4932 20010118 SGD
+SGD S000001868 STE2 GO:0030031 SGD_REF:S000071985|PMID:12378535 IMP P G protein coupled receptor (GPCR), alpha-factor pheromone receptor, seven-transmembrane domain protein YFL026W gene taxon:4932 20030207 SGD
+SGD S000000999 STE20 GO:0000131 SGD_REF:S000044194|PMID:9003780 IDA C YHL007C gene taxon:4932 20010118 SGD
+SGD S000000999 STE20 GO:0043332 SGD_REF:S000044194|PMID:9003780 IDA C YHL007C gene taxon:4932 20010118 SGD
+SGD S000000999 STE20 GO:0004674 SGD_REF:S000048267|PMID:7608157 IDA F YHL007C gene taxon:4932 20021010 SGD
+SGD S000000999 STE20 GO:0000282 SGD_REF:S000061390|PMID:11452010 IMP P YHL007C gene taxon:4932 20021010 SGD
+SGD S000000999 STE20 GO:0000750 SGD_REF:S000051894|PMID:9024634 TAS P YHL007C gene taxon:4932 20021206 SGD
+SGD S000000999 STE20 GO:0001403 SGD_REF:S000050425|PMID:8001818 IMP P YHL007C gene taxon:4932 20050218 SGD
+SGD S000000999 STE20 GO:0006468 SGD_REF:S000048267|PMID:7608157 IDA P YHL007C gene taxon:4932 20021010 SGD
+SGD S000000999 STE20 GO:0007096 SGD_REF:S000071653|PMID:12234925 IMP P YHL007C gene taxon:4932 20050324 SGD
+SGD S000000999 STE20 GO:0007124 SGD_REF:S000051894|PMID:9024634 TAS P YHL007C gene taxon:4932 20010118 SGD
+SGD S000004381 STE23 GO:0016021 SGD_REF:S000041192|PMID:9725832 TAS C YLR389C gene taxon:4932 20021119 SGD
+SGD S000004381 STE23 GO:0008237 SGD_REF:S000041192|PMID:9725832 TAS F YLR389C gene taxon:4932 20021119 SGD
+SGD S000004381 STE23 GO:0008237 SGD_REF:S000051760|PMID:7569998 ISS F YLR389C gene taxon:4932 20050103 SGD
+SGD S000004381 STE23 GO:0006508 SGD_REF:S000041192|PMID:9725832 TAS P YLR389C gene taxon:4932 20021119 SGD
+SGD S000004381 STE23 GO:0007323 SGD_REF:S000041192|PMID:9725832 TAS P YLR389C gene taxon:4932 20021119 SGD
+SGD S000004381 STE23 GO:0007323 SGD_REF:S000051760|PMID:7569998 IMP P YLR389C gene taxon:4932 20050103 SGD
+SGD S000003878 STE24 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C zinc metallo-protease YJR117W|AFC1|PIO2 gene taxon:4932 20060317 SGD
+SGD S000003878 STE24 GO:0030176 SGD_REF:S000068762|PMID:11581258 IDA C zinc metallo-protease YJR117W|AFC1|PIO2 gene taxon:4932 20020717 SGD
+SGD S000003878 STE24 GO:0004222 SGD_REF:S000068762|PMID:11581258 IDA F zinc metallo-protease YJR117W|AFC1|PIO2 gene taxon:4932 20020717 SGD
+SGD S000003878 STE24 GO:0004222 SGD_REF:S000048235|PMID:9065405 ISS F zinc metallo-protease YJR117W|AFC1|PIO2 gene taxon:4932 20050103 SGD
+SGD S000003878 STE24 GO:0008487 SGD_REF:S000068762|PMID:11581258 IDA F zinc metallo-protease YJR117W|AFC1|PIO2 gene taxon:4932 20020717 SGD
+SGD S000003878 STE24 GO:0008487 SGD_REF:S000048235|PMID:9065405 IDA F zinc metallo-protease YJR117W|AFC1|PIO2 gene taxon:4932 20050103 SGD
+SGD S000003878 STE24 GO:0007323 SGD_REF:S000068762|PMID:11581258 IDA P zinc metallo-protease YJR117W|AFC1|PIO2 gene taxon:4932 20020717 SGD
+SGD S000003878 STE24 GO:0007323 SGD_REF:S000048235|PMID:9065405 IMP P zinc metallo-protease YJR117W|AFC1|PIO2 gene taxon:4932 20050103 SGD
+SGD S000001661 STE3 GO:0005887 SGD_REF:S000047820|PMID:3006051 IDA C G protein coupled receptor (GPCR), a-factor receptor YKL178C|DAF2 gene taxon:4932 20030213 SGD
+SGD S000001661 STE3 GO:0005887 SGD_REF:S000047820|PMID:3006051 ISS C G protein coupled receptor (GPCR), a-factor receptor YKL178C|DAF2 gene taxon:4932 20030213 SGD
+SGD S000001661 STE3 GO:0004933 SGD_REF:S000047820|PMID:3006051 IMP F G protein coupled receptor (GPCR), a-factor receptor YKL178C|DAF2 gene taxon:4932 20010118 SGD
+SGD S000001661 STE3 GO:0004933 SGD_REF:S000047820|PMID:3006051 ISS F G protein coupled receptor (GPCR), a-factor receptor YKL178C|DAF2 gene taxon:4932 20010118 SGD
+SGD S000001661 STE3 GO:0000750 SGD_REF:S000047820|PMID:3006051 IMP P G protein coupled receptor (GPCR), a-factor receptor YKL178C|DAF2 gene taxon:4932 20021206 SGD
+SGD S000001661 STE3 GO:0000750 SGD_REF:S000047820|PMID:3006051 ISS P G protein coupled receptor (GPCR), a-factor receptor YKL178C|DAF2 gene taxon:4932 20021206 SGD
+SGD S000005738 STE4 GO:0005834 SGD_REF:S000046375|PMID:8995254 IDA C G protein beta subunit, coupled to mating factor receptor YOR212W|HMD2 gene taxon:4932 20010118 SGD
+SGD S000005738 STE4 GO:0005886 SGD_REF:S000046375|PMID:8995254 IDA C G protein beta subunit, coupled to mating factor receptor YOR212W|HMD2 gene taxon:4932 20010118 SGD
+SGD S000005738 STE4 GO:0005937 SGD_REF:S000059571|PMID:11073983 IDA C G protein beta subunit, coupled to mating factor receptor YOR212W|HMD2 gene taxon:4932 20030622 SGD
+SGD S000005738 STE4 GO:0003924 SGD_REF:S000058498 TAS F G protein beta subunit, coupled to mating factor receptor YOR212W|HMD2 gene taxon:4932 20010119 SGD
+SGD S000005738 STE4 GO:0000750 SGD_REF:S000043671|PMID:10087263 IGI P G protein beta subunit, coupled to mating factor receptor YOR212W|HMD2 gene taxon:4932 20021206 SGD
+SGD S000005738 STE4 GO:0000750 SGD_REF:S000043671|PMID:10087263 IPI P G protein beta subunit, coupled to mating factor receptor YOR212W|HMD2 gene taxon:4932 20021206 SGD
+SGD S000005738 STE4 GO:0000750 SGD_REF:S000043671|PMID:10087263 TAS P G protein beta subunit, coupled to mating factor receptor YOR212W|HMD2 gene taxon:4932 20021206 SGD
+SGD S000005738 STE4 GO:0001403 SGD_REF:S000082049|PMID:15192700 IMP P G protein beta subunit, coupled to mating factor receptor YOR212W|HMD2 gene taxon:4932 20050930 SGD
+SGD S000002510 STE5 GO:0005634 SGD_REF:S000053527|PMID:9732267 IDA C YDR103W|HMD3|NUL3 gene taxon:4932 20010118 SGD
+SGD S000002510 STE5 GO:0005737 SGD_REF:S000069153|PMID:11781566 IDA C YDR103W|HMD3|NUL3 gene taxon:4932 20020829 SGD
+SGD S000002510 STE5 GO:0005886 SGD_REF:S000053527|PMID:9732267 IDA C YDR103W|HMD3|NUL3 gene taxon:4932 20010118 SGD
+SGD S000002510 STE5 GO:0043332 SGD_REF:S000069153|PMID:11781566 IDA C YDR103W|HMD3|NUL3 gene taxon:4932 20020829 SGD
+SGD S000002510 STE5 GO:0005078 SGD_REF:S000050302|PMID:7851759 IPI F YDR103W|HMD3|NUL3 gene taxon:4932 20010118 SGD
+SGD S000002510 STE5 GO:0005078 SGD_REF:S000051962|PMID:8062390 IPI F YDR103W|HMD3|NUL3 gene taxon:4932 20020403 SGD
+SGD S000002510 STE5 GO:0000750 SGD_REF:S000051962|PMID:8062390 IDA P YDR103W|HMD3|NUL3 gene taxon:4932 20021206 SGD
+SGD S000002510 STE5 GO:0000750 SGD_REF:S000051962|PMID:8062390 IPI P YDR103W|HMD3|NUL3 gene taxon:4932 20021206 SGD
+SGD S000002510 STE5 GO:0001403 SGD_REF:S000082049|PMID:15192700 IMP P YDR103W|HMD3|NUL3 gene taxon:4932 20050930 SGD
+SGD S000000537 STE50 GO:0005737 SGD_REF:S000065130|PMID:9742096 IDA C contains SAM (sterile alpha motif) YCL032W gene taxon:4932 20020731 SGD
+SGD S000000537 STE50 GO:0019887 SGD_REF:S000049071|PMID:10397774 IDA F contains SAM (sterile alpha motif) YCL032W gene taxon:4932 20020731 SGD
+SGD S000000537 STE50 GO:0019887 SGD_REF:S000049071|PMID:10397774 IPI F contains SAM (sterile alpha motif) YCL032W gene taxon:4932 20020731 SGD
+SGD S000000537 STE50 GO:0000161 SGD_REF:S000065130|PMID:9742096 IMP P contains SAM (sterile alpha motif) YCL032W gene taxon:4932 20020731 SGD
+SGD S000000537 STE50 GO:0000161 SGD_REF:S000065130|PMID:9742096 IPI P contains SAM (sterile alpha motif) YCL032W gene taxon:4932 20020731 SGD
+SGD S000000537 STE50 GO:0000750 SGD_REF:S000053027|PMID:8793874 IMP P contains SAM (sterile alpha motif) YCL032W gene taxon:4932 20021206 SGD
+SGD S000000537 STE50 GO:0000750 SGD_REF:S000053027|PMID:8793874 IPI P contains SAM (sterile alpha motif) YCL032W gene taxon:4932 20021206 SGD
+SGD S000000537 STE50 GO:0001402 SGD_REF:S000049635|PMID:9738877 IMP P contains SAM (sterile alpha motif) YCL032W gene taxon:4932 20020731 SGD
+SGD S000000537 STE50 GO:0001402 SGD_REF:S000049635|PMID:9738877 IPI P contains SAM (sterile alpha motif) YCL032W gene taxon:4932 20020731 SGD
+SGD S000000537 STE50 GO:0019236 SGD_REF:S000072519|PMID:10417390 IDA P contains SAM (sterile alpha motif) YCL032W gene taxon:4932 20030213 SGD
+SGD S000001692 STE6 GO:0005887 SGD_REF:S000052426|PMID:8095825 TAS C ABC transporter, glycoprotein YKL209C gene taxon:4932 20010118 SGD
+SGD S000001692 STE6 GO:0043332 SGD_REF:S000071843|PMID:12374868 IDA C ABC transporter, glycoprotein YKL209C gene taxon:4932 20030129 SGD
+SGD S000001692 STE6 GO:0042626 SGD_REF:S000065827|PMID:11389139 IDA F ABC transporter, glycoprotein YKL209C gene taxon:4932 20030616 SGD
+SGD S000001692 STE6 GO:0042626 SGD_REF:S000052426|PMID:8095825 TAS F ABC transporter, glycoprotein YKL209C gene taxon:4932 20010118 SGD
+SGD S000001692 STE6 GO:0000770 SGD_REF:S000052426|PMID:8095825 TAS P ABC transporter, glycoprotein YKL209C gene taxon:4932 20010118 SGD
+SGD S000002318 STE7 GO:0005737 SGD_REF:S000069153|PMID:11781566 IDA C MAP kinase kinase (MEK) YDL159W gene taxon:4932 20020829 SGD
+SGD S000002318 STE7 GO:0043332 SGD_REF:S000069153|PMID:11781566 IDA C MAP kinase kinase (MEK) YDL159W gene taxon:4932 20020829 SGD
+SGD S000002318 STE7 GO:0004708 SGD_REF:S000069153|PMID:11781566 TAS F MAP kinase kinase (MEK) YDL159W gene taxon:4932 20030204 SGD
+SGD S000002318 STE7 GO:0000750 SGD_REF:S000042129|PMID:8607979 TAS P MAP kinase kinase (MEK) YDL159W gene taxon:4932 20021206 SGD
+SGD S000002318 STE7 GO:0001403 SGD_REF:S000050425|PMID:8001818 IMP P MAP kinase kinase (MEK) YDL159W gene taxon:4932 20050218 SGD
+SGD S000002318 STE7 GO:0006468 SGD_REF:S000044366|PMID:3532111 ISS P MAP kinase kinase (MEK) YDL159W gene taxon:4932 20010118 SGD
+SGD S000002318 STE7 GO:0007124 SGD_REF:S000046347|PMID:8643578 IMP P MAP kinase kinase (MEK) YDL159W gene taxon:4932 20010118 SGD
+SGD S000007232 STF1 GO:0005753 SGD_REF:S000058444|PMID:10838056 TAS C YDL130W-A|AIS2 gene taxon:4932 20010118 SGD
+SGD S000007232 STF1 GO:0005554 SGD_REF:S000058444|PMID:10838056 TAS F YDL130W-A|AIS2 gene taxon:4932 20010118 SGD
+SGD S000007232 STF1 GO:0015986 SGD_REF:S000058444|PMID:10838056 TAS P YDL130W-A|AIS2 gene taxon:4932 20010118 SGD
+SGD S000003240 STF2 GO:0005753 SGD_REF:S000058444|PMID:10838056 TAS C ATPase stabilizing factor YGR008C gene taxon:4932 20010118 SGD
+SGD S000003240 STF2 GO:0005554 SGD_REF:S000058444|PMID:10838056 TAS F ATPase stabilizing factor YGR008C gene taxon:4932 20010118 SGD
+SGD S000003240 STF2 GO:0009269 SGD_REF:S000063137|PMID:10681550 IEP P ATPase stabilizing factor YGR008C gene taxon:4932 20030210 SGD
+SGD S000003240 STF2 GO:0015986 SGD_REF:S000058444|PMID:10838056 TAS P ATPase stabilizing factor YGR008C gene taxon:4932 20010118 SGD
+SGD S000001388 STH1 GO:0016586 SGD_REF:S000052087|PMID:8980231 IPI C helicase related protein, snf2 homolog YIL126W|NPS1 gene taxon:4932 20041020 SGD
+SGD S000001388 STH1 GO:0003678 SGD_REF:S000042978|PMID:1549132 ISS F helicase related protein, snf2 homolog YIL126W|NPS1 gene taxon:4932 20010118 SGD
+SGD S000001388 STH1 GO:0016887 SGD_REF:S000050376|PMID:9799253 IDA F helicase related protein, snf2 homolog YIL126W|NPS1 gene taxon:4932 20010118 SGD
+SGD S000001388 STH1 GO:0006338 SGD_REF:S000052087|PMID:8980231 IDA P helicase related protein, snf2 homolog YIL126W|NPS1 gene taxon:4932 20010118 SGD
+SGD S000001388 STH1 GO:0007126 SGD_REF:S000047042|PMID:10320476 IMP P helicase related protein, snf2 homolog YIL126W|NPS1 gene taxon:4932 20010118 SGD
+SGD S000005553 STI1 GO:0005737 SGD_REF:S000072814|PMID:12525481 IPI SGD:S000006161 C heat shock protein also induced by canavanine and entry into stationary phase YOR027W gene taxon:4932 20030424 SGD
+SGD S000005553 STI1 GO:0004857 SGD_REF:S000072814|PMID:12525481 IDA F heat shock protein also induced by canavanine and entry into stationary phase YOR027W gene taxon:4932 20030424 SGD
+SGD S000005553 STI1 GO:0051082 SGD_REF:S000070059|PMID:11923285 TAS F heat shock protein also induced by canavanine and entry into stationary phase YOR027W gene taxon:4932 20020713 SGD
+SGD S000005553 STI1 GO:0006457 SGD_REF:S000052089|PMID:8972212 IMP P heat shock protein also induced by canavanine and entry into stationary phase YOR027W gene taxon:4932 20010118 SGD
+SGD S000005553 STI1 GO:0006457 SGD_REF:S000052089|PMID:8972212 IGI P heat shock protein also induced by canavanine and entry into stationary phase YOR027W gene taxon:4932 20010118 SGD
+SGD S000002944 STL1 GO:0005886 SGD_REF:S000080701|PMID:15703210 TAS C sugar transporter-like protein YDR536W gene taxon:4932 20050215 SGD
+SGD S000002944 STL1 GO:0016020 SGD_REF:S000047431|PMID:8076821 ISS C sugar transporter-like protein YDR536W gene taxon:4932 20021003 SGD
+SGD S000002944 STL1 GO:0005215 SGD_REF:S000047431|PMID:8076821 ISS F sugar transporter-like protein YDR536W gene taxon:4932 20021003 SGD
+SGD S000002944 STL1 GO:0006810 SGD_REF:S000047431|PMID:8076821 ISS P sugar transporter-like protein YDR536W gene taxon:4932 20021003 SGD
+SGD S000002944 STL1 GO:0015793 SGD_REF:S000080701|PMID:15703210 IMP P sugar transporter-like protein YDR536W gene taxon:4932 20050215 SGD
+SGD S000004140 STM1 GO:0000783 SGD_REF:S000071136|PMID:12207228 IGI C purine motif triplex-binding protein YLR150W|MPT4 gene taxon:4932 20030403 SGD
+SGD S000004140 STM1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C purine motif triplex-binding protein YLR150W|MPT4 gene taxon:4932 20020507 SGD
+SGD S000004140 STM1 GO:0005830 SGD_REF:S000076387|PMID:15044472 IDA C purine motif triplex-binding protein YLR150W|MPT4 gene taxon:4932 20040805 SGD
+SGD S000004140 STM1 GO:0003677 SGD_REF:S000080419|PMID:15654430 IDA F purine motif triplex-binding protein YLR150W|MPT4 gene taxon:4932 20050218 SGD
+SGD S000004140 STM1 GO:0042162 SGD_REF:S000071136|PMID:12207228 TAS F purine motif triplex-binding protein YLR150W|MPT4 gene taxon:4932 20030108 SGD
+SGD S000004140 STM1 GO:0000723 SGD_REF:S000071136|PMID:12207228 IMP P purine motif triplex-binding protein YLR150W|MPT4 gene taxon:4932 20030403 SGD
+SGD S000004140 STM1 GO:0006916 SGD_REF:S000069080|PMID:11514626 IDA P purine motif triplex-binding protein YLR150W|MPT4 gene taxon:4932 20020721 SGD
+SGD S000002489 STN1 GO:0000783 SGD_REF:S000070037|PMID:11352055 TAS C YDR082W gene taxon:4932 20030403 SGD
+SGD S000002489 STN1 GO:0005515 SGD_REF:S000059835|PMID:11230140 IDA F YDR082W gene taxon:4932 20021111 SGD
+SGD S000002489 STN1 GO:0016233 SGD_REF:S000070037|PMID:11352055 TAS P YDR082W gene taxon:4932 20020625 SGD
+SGD S000004732 STO1 GO:0000243 SGD_REF:S000064189|PMID:10072386 IPI C Large subunit of the nuclear cap-binding protein complex YMR125W|CBC1|CBP80|GCR3|SUT1 gene taxon:4932 20020729 SGD
+SGD S000004732 STO1 GO:0005846 SGD_REF:S000057938|PMID:8811086 IDA C Large subunit of the nuclear cap-binding protein complex YMR125W|CBC1|CBP80|GCR3|SUT1 gene taxon:4932 20020730 SGD
+SGD S000004732 STO1 GO:0003729 SGD_REF:S000064189|PMID:10072386 IPI F Large subunit of the nuclear cap-binding protein complex YMR125W|CBC1|CBP80|GCR3|SUT1 gene taxon:4932 20020729 SGD
+SGD S000004732 STO1 GO:0000184 SGD_REF:S000080989|PMID:15753296 IDA P Large subunit of the nuclear cap-binding protein complex YMR125W|CBC1|CBP80|GCR3|SUT1 gene taxon:4932 20050315 SGD
+SGD S000004732 STO1 GO:0000184 SGD_REF:S000080989|PMID:15753296 IPI P Large subunit of the nuclear cap-binding protein complex YMR125W|CBC1|CBP80|GCR3|SUT1 gene taxon:4932 20050315 SGD
+SGD S000004732 STO1 GO:0000398 SGD_REF:S000064189|PMID:10072386 IPI P Large subunit of the nuclear cap-binding protein complex YMR125W|CBC1|CBP80|GCR3|SUT1 gene taxon:4932 20020729 SGD
+SGD S000004732 STO1 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P Large subunit of the nuclear cap-binding protein complex YMR125W|CBC1|CBP80|GCR3|SUT1 gene taxon:4932 20060203 SGD
+SGD S000002871 STP1 GO:0005634 SGD_REF:S000041872|PMID:1588961 IDA C zinc finger motif protein YDR463W|BAP1|SSY2 gene taxon:4932 20021023 SGD
+SGD S000002871 STP1 GO:0003700 SGD_REF:S000059562|PMID:11212916 IDA F zinc finger motif protein YDR463W|BAP1|SSY2 gene taxon:4932 20050117 SGD
+SGD S000002871 STP1 GO:0003704 SGD_REF:S000050738|PMID:10648791 IGI F zinc finger motif protein YDR463W|BAP1|SSY2 gene taxon:4932 20021023 SGD
+SGD S000002871 STP1 GO:0003704 SGD_REF:S000050738|PMID:10648791 IMP F zinc finger motif protein YDR463W|BAP1|SSY2 gene taxon:4932 20021023 SGD
+SGD S000002871 STP1 GO:0003704 SGD_REF:S000050738|PMID:10648791 ISS F zinc finger motif protein YDR463W|BAP1|SSY2 gene taxon:4932 20021023 SGD
+SGD S000002871 STP1 GO:0006388 SGD_REF:S000041872|PMID:1588961 IMP P zinc finger motif protein YDR463W|BAP1|SSY2 gene taxon:4932 20021023 SGD
+SGD S000002871 STP1 GO:0045941 SGD_REF:S000059562|PMID:11212916 IDA P zinc finger motif protein YDR463W|BAP1|SSY2 gene taxon:4932 20050117 SGD
+SGD S000002871 STP1 GO:0045944 SGD_REF:S000050738|PMID:10648791 IGI P zinc finger motif protein YDR463W|BAP1|SSY2 gene taxon:4932 20021023 SGD
+SGD S000002871 STP1 GO:0045944 SGD_REF:S000050738|PMID:10648791 IMP P zinc finger motif protein YDR463W|BAP1|SSY2 gene taxon:4932 20021023 SGD
+SGD S000002871 STP1 GO:0045944 SGD_REF:S000050738|PMID:10648791 ISS P zinc finger motif protein YDR463W|BAP1|SSY2 gene taxon:4932 20021023 SGD
+SGD S000001048 STP2 GO:0005634 SGD_REF:S000050738|PMID:10648791 IPI C YHR006W gene taxon:4932 20021023 SGD
+SGD S000001048 STP2 GO:0003704 SGD_REF:S000050738|PMID:10648791 IGI F YHR006W gene taxon:4932 20021023 SGD
+SGD S000001048 STP2 GO:0003704 SGD_REF:S000050738|PMID:10648791 IMP F YHR006W gene taxon:4932 20021023 SGD
+SGD S000001048 STP2 GO:0003704 SGD_REF:S000050738|PMID:10648791 ISS F YHR006W gene taxon:4932 20021023 SGD
+SGD S000001048 STP2 GO:0045944 SGD_REF:S000050738|PMID:10648791 IGI P YHR006W gene taxon:4932 20021023 SGD
+SGD S000001048 STP2 GO:0045944 SGD_REF:S000050738|PMID:10648791 ISS P YHR006W gene taxon:4932 20021023 SGD
+SGD S000001048 STP2 GO:0045944 SGD_REF:S000050738|PMID:10648791 IMP P YHR006W gene taxon:4932 20021023 SGD
+SGD S000000514 STP22 GO:0000813 SGD_REF:S000073987|PMID:12900393 TAS C putative ubiquitin receptor YCL008C|VPS23 gene taxon:4932 20040618 SGD
+SGD S000000514 STP22 GO:0000813 SGD_REF:S000078323|PMID:15044434 IDA C putative ubiquitin receptor YCL008C|VPS23 gene taxon:4932 20041117 SGD
+SGD S000000514 STP22 GO:0005768 SGD_REF:S000061300|PMID:11511343 IDA C putative ubiquitin receptor YCL008C|VPS23 gene taxon:4932 20020827 SGD
+SGD S000000514 STP22 GO:0005768 SGD_REF:S000061300|PMID:11511343 IPI C putative ubiquitin receptor YCL008C|VPS23 gene taxon:4932 20020827 SGD
+SGD S000000514 STP22 GO:0005515 SGD_REF:S000061300|PMID:11511343 IDA F putative ubiquitin receptor YCL008C|VPS23 gene taxon:4932 20020827 SGD
+SGD S000000514 STP22 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P putative ubiquitin receptor YCL008C|VPS23 gene taxon:4932 20060209 SGD
+SGD S000000514 STP22 GO:0006612 SGD_REF:S000061300|PMID:11511343 IMP P putative ubiquitin receptor YCL008C|VPS23 gene taxon:4932 20020827 SGD
+SGD S000000514 STP22 GO:0006612 SGD_REF:S000061300|PMID:11511343 IPI P putative ubiquitin receptor YCL008C|VPS23 gene taxon:4932 20020827 SGD
+SGD S000000514 STP22 GO:0006623 SGD_REF:S000061300|PMID:11511343 IMP P putative ubiquitin receptor YCL008C|VPS23 gene taxon:4932 20020827 SGD
+SGD S000000514 STP22 GO:0006623 SGD_REF:S000061300|PMID:11511343 IPI P putative ubiquitin receptor YCL008C|VPS23 gene taxon:4932 20020827 SGD
+SGD S000000514 STP22 GO:0043162 SGD_REF:S000075969|PMID:15086794 IC GO:0000813 P putative ubiquitin receptor YCL008C|VPS23 gene taxon:4932 20050125 SGD
+SGD S000004367 STP3 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YLR375W gene taxon:4932 20031028 SGD
+SGD S000004367 STP3 GO:0005554 SGD_REF:S000069584 ND F YLR375W gene taxon:4932 20050725 SGD
+SGD S000004367 STP3 GO:0000004 SGD_REF:S000069584 ND P YLR375W gene taxon:4932 20050725 SGD
+SGD S000002206 STP4 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YDL048C gene taxon:4932 20031028 SGD
+SGD S000002206 STP4 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDL048C gene taxon:4932 20031028 SGD
+SGD S000002206 STP4 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YDL048C gene taxon:4932 20031028 SGD
+SGD S000002206 STP4 GO:0005554 SGD_REF:S000069584 ND F YDL048C gene taxon:4932 20021125 SGD
+SGD S000002206 STP4 GO:0000004 SGD_REF:S000069584 ND P YDL048C gene taxon:4932 20021125 SGD
+SGD S000003891 STR2 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C cystathionine gamma-synthase YJR130C gene taxon:4932 20031028 SGD
+SGD S000003891 STR2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C cystathionine gamma-synthase YJR130C gene taxon:4932 20031028 SGD
+SGD S000003891 STR2 GO:0003962 SGD_REF:S000039910|PMID:10821189 IMP F cystathionine gamma-synthase YJR130C gene taxon:4932 20030515 SGD
+SGD S000003891 STR2 GO:0006790 SGD_REF:S000039910|PMID:10821189 IMP P cystathionine gamma-synthase YJR130C gene taxon:4932 20021001 SGD
+SGD S000003152 STR3 GO:0008372 SGD_REF:S000069584 ND C cystathionine beta-lyase YGL184C gene taxon:4932 20051214 SGD
+SGD S000003152 STR3 GO:0004121 SGD_REF:S000039910|PMID:10821189 IMP F cystathionine beta-lyase YGL184C gene taxon:4932 20021104 SGD
+SGD S000003152 STR3 GO:0004121 SGD_REF:S000039910|PMID:10821189 ISS F cystathionine beta-lyase YGL184C gene taxon:4932 20021104 SGD
+SGD S000003152 STR3 GO:0009086 SGD_REF:S000039910|PMID:10821189 IMP P cystathionine beta-lyase YGL184C gene taxon:4932 20021104 SGD
+SGD S000001450 STS1 GO:0005634 SGD_REF:S000045318|PMID:10913188 IDA C YIR011C|DBF8|SSM5 gene taxon:4932 20020826 SGD
+SGD S000001450 STS1 GO:0005554 SGD_REF:S000069584 ND F YIR011C|DBF8|SSM5 gene taxon:4932 20020826 SGD
+SGD S000001450 STS1 GO:0006511 SGD_REF:S000045318|PMID:10913188 IGI P YIR011C|DBF8|SSM5 gene taxon:4932 20020826 SGD
+SGD S000001450 STS1 GO:0006511 SGD_REF:S000045318|PMID:10913188 IPI P YIR011C|DBF8|SSM5 gene taxon:4932 20020826 SGD
+SGD S000001450 STS1 GO:0007059 SGD_REF:S000039423|PMID:8065366 IMP P YIR011C|DBF8|SSM5 gene taxon:4932 20020826 SGD
+SGD S000002990 STT3 GO:0008250 SGD_REF:S000050823|PMID:10358084 IPI C integral ER membrane protein, oligosaccharyltransferase complex subunit (putative) YGL022W gene taxon:4932 20020328 SGD
+SGD S000002990 STT3 GO:0008250 SGD_REF:S000113605|PMID:16297388 IPI C integral ER membrane protein, oligosaccharyltransferase complex subunit (putative) YGL022W gene taxon:4932 20060203 SGD
+SGD S000002990 STT3 GO:0008250 SGD_REF:S000050479|PMID:9405463 IPI C integral ER membrane protein, oligosaccharyltransferase complex subunit (putative) YGL022W gene taxon:4932 20050504 SGD
+SGD S000002990 STT3 GO:0004579 SGD_REF:S000050479|PMID:9405463 IPI F integral ER membrane protein, oligosaccharyltransferase complex subunit (putative) YGL022W gene taxon:4932 20021001 SGD
+SGD S000002990 STT3 GO:0006487 SGD_REF:S000050479|PMID:9405463 IPI P integral ER membrane protein, oligosaccharyltransferase complex subunit (putative) YGL022W gene taxon:4932 20021001 SGD
+SGD S000004296 STT4 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C phosphatidylinositol-4-kinase, similar to VPC34 YLR305C|BLM1 gene taxon:4932 20040928 SGD
+SGD S000004296 STT4 GO:0005886 SGD_REF:S000069992|PMID:12015967 IDA C phosphatidylinositol-4-kinase, similar to VPC34 YLR305C|BLM1 gene taxon:4932 20020821 SGD
+SGD S000004296 STT4 GO:0004430 SGD_REF:S000045970|PMID:8288577 IMP F phosphatidylinositol-4-kinase, similar to VPC34 YLR305C|BLM1 gene taxon:4932 20021001 SGD
+SGD S000004296 STT4 GO:0000165 SGD_REF:S000069992|PMID:12015967 IDA P phosphatidylinositol-4-kinase, similar to VPC34 YLR305C|BLM1 gene taxon:4932 20030721 SGD
+SGD S000004296 STT4 GO:0000165 SGD_REF:S000069992|PMID:12015967 IMP P phosphatidylinositol-4-kinase, similar to VPC34 YLR305C|BLM1 gene taxon:4932 20030721 SGD
+SGD S000004296 STT4 GO:0006646 SGD_REF:S000042243|PMID:9582361 IMP P phosphatidylinositol-4-kinase, similar to VPC34 YLR305C|BLM1 gene taxon:4932 20021001 SGD
+SGD S000004296 STT4 NOT GO:0009306 SGD_REF:S000059350|PMID:10930462 IMP P phosphatidylinositol-4-kinase, similar to VPC34 YLR305C|BLM1 gene taxon:4932 20021001 SGD
+SGD S000004296 STT4 GO:0030036 SGD_REF:S000059350|PMID:10930462 IMP P phosphatidylinositol-4-kinase, similar to VPC34 YLR305C|BLM1 gene taxon:4932 20021001 SGD
+SGD S000004296 STT4 GO:0046854 SGD_REF:S000045970|PMID:8288577 IMP P phosphatidylinositol-4-kinase, similar to VPC34 YLR305C|BLM1 gene taxon:4932 20050420 SGD
+SGD S000004296 STT4 GO:0048017 SGD_REF:S000045970|PMID:8288577 TAS P phosphatidylinositol-4-kinase, similar to VPC34 YLR305C|BLM1 gene taxon:4932 20050524 SGD
+SGD S000000130 STU1 GO:0005816 SGD_REF:S000047788|PMID:9585415 IDA C YBL034C gene taxon:4932 20010118 SGD
+SGD S000000130 STU1 GO:0005200 SGD_REF:S000047788|PMID:9585415 IPI F YBL034C gene taxon:4932 20010118 SGD
+SGD S000000130 STU1 GO:0007020 SGD_REF:S000058447|PMID:9153752 IPI P YBL034C gene taxon:4932 20010118 SGD
+SGD S000004035 STU2 GO:0000776 SGD_REF:S000068994|PMID:11553724 IDA C YLR045C gene taxon:4932 20040927 SGD
+SGD S000004035 STU2 GO:0000778 SGD_REF:S000080960|PMID:11511347 IDA C YLR045C gene taxon:4932 20050307 SGD
+SGD S000004035 STU2 GO:0005816 SGD_REF:S000044510|PMID:9606209 IDA C YLR045C gene taxon:4932 20010118 SGD
+SGD S000004035 STU2 GO:0005876 SGD_REF:S000080960|PMID:11511347 IDA C YLR045C gene taxon:4932 20050307 SGD
+SGD S000004035 STU2 GO:0005938 SGD_REF:S000080960|PMID:11511347 IDA C YLR045C gene taxon:4932 20050307 SGD
+SGD S000004035 STU2 GO:0005200 SGD_REF:S000044510|PMID:9606209 IPI F YLR045C gene taxon:4932 20010118 SGD
+SGD S000004035 STU2 GO:0008017 SGD_REF:S000068994|PMID:11553724 IMP F YLR045C gene taxon:4932 20030505 SGD
+SGD S000004035 STU2 GO:0007020 SGD_REF:S000058447|PMID:9153752 IPI P YLR045C gene taxon:4932 20010118 SGD
+SGD S000004035 STU2 GO:0030472 SGD_REF:S000069091|PMID:11756468 IGI P YLR045C gene taxon:4932 20021008 SGD
+SGD S000004658 STV1 GO:0000220 SGD_REF:S000041762|PMID:7514599 IGI C 110 kDa subunit; not in vacuole membrane, vacuolar H-ATPase YMR054W gene taxon:4932 20060411 SGD
+SGD S000004658 STV1 GO:0000220 SGD_REF:S000041762|PMID:7514599 IMP C 110 kDa subunit; not in vacuole membrane, vacuolar H-ATPase YMR054W gene taxon:4932 20060411 SGD
+SGD S000004658 STV1 GO:0000220 SGD_REF:S000041762|PMID:7514599 ISS SGD:S000005796 C 110 kDa subunit; not in vacuole membrane, vacuolar H-ATPase YMR054W gene taxon:4932 20060411 SGD
+SGD S000004658 STV1 GO:0000220 SGD_REF:S000041762|PMID:7514599 IPI C 110 kDa subunit; not in vacuole membrane, vacuolar H-ATPase YMR054W gene taxon:4932 20060411 SGD
+SGD S000004658 STV1 GO:0005770 SGD_REF:S000060801|PMID:11278748 IMP C 110 kDa subunit; not in vacuole membrane, vacuolar H-ATPase YMR054W gene taxon:4932 20060411 SGD
+SGD S000004658 STV1 GO:0005770 SGD_REF:S000060801|PMID:11278748 IDA C 110 kDa subunit; not in vacuole membrane, vacuolar H-ATPase YMR054W gene taxon:4932 20060411 SGD
+SGD S000004658 STV1 GO:0005794 SGD_REF:S000060801|PMID:11278748 IDA C 110 kDa subunit; not in vacuole membrane, vacuolar H-ATPase YMR054W gene taxon:4932 20030305 SGD
+SGD S000004658 STV1 GO:0005794 SGD_REF:S000069939|PMID:11948198 IDA C 110 kDa subunit; not in vacuole membrane, vacuolar H-ATPase YMR054W gene taxon:4932 20060411 SGD
+SGD S000004658 STV1 GO:0046961 SGD_REF:S000041762|PMID:7514599 IGI F 110 kDa subunit; not in vacuole membrane, vacuolar H-ATPase YMR054W gene taxon:4932 20060411 SGD
+SGD S000004658 STV1 GO:0046961 SGD_REF:S000041762|PMID:7514599 IMP F 110 kDa subunit; not in vacuole membrane, vacuolar H-ATPase YMR054W gene taxon:4932 20060411 SGD
+SGD S000004658 STV1 GO:0046961 SGD_REF:S000041762|PMID:7514599 IPI F 110 kDa subunit; not in vacuole membrane, vacuolar H-ATPase YMR054W gene taxon:4932 20060411 SGD
+SGD S000004658 STV1 GO:0046961 SGD_REF:S000041762|PMID:7514599 ISS SGD:S000005796 F 110 kDa subunit; not in vacuole membrane, vacuolar H-ATPase YMR054W gene taxon:4932 20060411 SGD
+SGD S000004658 STV1 GO:0046961 SGD_REF:S000041762|PMID:7514599 IEP F 110 kDa subunit; not in vacuole membrane, vacuolar H-ATPase YMR054W gene taxon:4932 20060411 SGD
+SGD S000004658 STV1 GO:0007035 SGD_REF:S000060801|PMID:11278748 IGI P 110 kDa subunit; not in vacuole membrane, vacuolar H-ATPase YMR054W gene taxon:4932 20060411 SGD
+SGD S000004658 STV1 GO:0007035 SGD_REF:S000060801|PMID:11278748 IEP P 110 kDa subunit; not in vacuole membrane, vacuolar H-ATPase YMR054W gene taxon:4932 20060411 SGD
+SGD S000004658 STV1 GO:0007035 SGD_REF:S000041762|PMID:7514599 IMP P 110 kDa subunit; not in vacuole membrane, vacuolar H-ATPase YMR054W gene taxon:4932 20060411 SGD
+SGD S000004658 STV1 GO:0007035 SGD_REF:S000041762|PMID:7514599 IGI P 110 kDa subunit; not in vacuole membrane, vacuolar H-ATPase YMR054W gene taxon:4932 20060411 SGD
+SGD S000004658 STV1 GO:0007035 SGD_REF:S000060801|PMID:11278748 ISS SGD:S000005796 P 110 kDa subunit; not in vacuole membrane, vacuolar H-ATPase YMR054W gene taxon:4932 20060411 SGD
+SGD S000004658 STV1 GO:0007035 SGD_REF:S000060801|PMID:11278748 IMP P 110 kDa subunit; not in vacuole membrane, vacuolar H-ATPase YMR054W gene taxon:4932 20060411 SGD
+SGD S000003137 SUA5 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YGL169W gene taxon:4932 20031028 SGD
+SGD S000003137 SUA5 GO:0005554 SGD_REF:S000069584 ND F YGL169W gene taxon:4932 20020827 SGD
+SGD S000003137 SUA5 GO:0009060 SGD_REF:S000054670|PMID:1325384 IMP P YGL169W gene taxon:4932 20041215 SGD
+SGD S000006290 SUA7 GO:0005654 SGD_REF:S000056392|PMID:10438492 IPI C transcription factor TFIIB homolog YPR086W|SOH4|TFIIB gene taxon:4932 20010118 SGD
+SGD S000006290 SUA7 GO:0005654 SGD_REF:S000054651|PMID:10464320 IPI C transcription factor TFIIB homolog YPR086W|SOH4|TFIIB gene taxon:4932 20010118 SGD
+SGD S000006290 SUA7 GO:0016251 SGD_REF:S000056392|PMID:10438492 IPI F transcription factor TFIIB homolog YPR086W|SOH4|TFIIB gene taxon:4932 20010119 SGD
+SGD S000006290 SUA7 GO:0016251 SGD_REF:S000054651|PMID:10464320 IDA F transcription factor TFIIB homolog YPR086W|SOH4|TFIIB gene taxon:4932 20010119 SGD
+SGD S000006290 SUA7 GO:0016251 SGD_REF:S000056392|PMID:10438492 IDA F transcription factor TFIIB homolog YPR086W|SOH4|TFIIB gene taxon:4932 20010119 SGD
+SGD S000006290 SUA7 GO:0016251 SGD_REF:S000056392|PMID:10438492 ISS F transcription factor TFIIB homolog YPR086W|SOH4|TFIIB gene taxon:4932 20010119 SGD
+SGD S000006290 SUA7 GO:0016251 SGD_REF:S000054651|PMID:10464320 IPI F transcription factor TFIIB homolog YPR086W|SOH4|TFIIB gene taxon:4932 20010119 SGD
+SGD S000006290 SUA7 GO:0006367 SGD_REF:S000056392|PMID:10438492 IDA P transcription factor TFIIB homolog YPR086W|SOH4|TFIIB gene taxon:4932 20010118 SGD
+SGD S000006290 SUA7 GO:0006367 SGD_REF:S000054651|PMID:10464320 IDA P transcription factor TFIIB homolog YPR086W|SOH4|TFIIB gene taxon:4932 20010118 SGD
+SGD S000006290 SUA7 GO:0006367 SGD_REF:S000056392|PMID:10438492 ISS P transcription factor TFIIB homolog YPR086W|SOH4|TFIIB gene taxon:4932 20010118 SGD
+SGD S000006290 SUA7 GO:0006367 SGD_REF:S000054651|PMID:10464320 IPI P transcription factor TFIIB homolog YPR086W|SOH4|TFIIB gene taxon:4932 20010118 SGD
+SGD S000006290 SUA7 GO:0006367 SGD_REF:S000056392|PMID:10438492 IPI P transcription factor TFIIB homolog YPR086W|SOH4|TFIIB gene taxon:4932 20010118 SGD
+SGD S000004642 SUB1 GO:0005634 SGD_REF:S000041407|PMID:8617240 IC GO:0003713 C transcriptional coactivator YMR039C|TSP1 gene taxon:4932 20021106 SGD
+SGD S000004642 SUB1 GO:0003713 SGD_REF:S000041407|PMID:8617240 IGI F transcriptional coactivator YMR039C|TSP1 gene taxon:4932 20021106 SGD
+SGD S000004642 SUB1 GO:0003713 SGD_REF:S000041407|PMID:8617240 IPI F transcriptional coactivator YMR039C|TSP1 gene taxon:4932 20021106 SGD
+SGD S000004642 SUB1 GO:0003713 SGD_REF:S000041407|PMID:8617240 ISS F transcriptional coactivator YMR039C|TSP1 gene taxon:4932 20021106 SGD
+SGD S000004642 SUB1 GO:0006369 SGD_REF:S000060779|PMID:11389848 IGI P transcriptional coactivator YMR039C|TSP1 gene taxon:4932 20021106 SGD
+SGD S000004642 SUB1 GO:0045944 SGD_REF:S000041407|PMID:8617240 IGI P transcriptional coactivator YMR039C|TSP1 gene taxon:4932 20021106 SGD
+SGD S000004642 SUB1 GO:0045944 SGD_REF:S000041407|PMID:8617240 IPI P transcriptional coactivator YMR039C|TSP1 gene taxon:4932 20021106 SGD
+SGD S000004642 SUB1 GO:0045944 SGD_REF:S000041407|PMID:8617240 ISS P transcriptional coactivator YMR039C|TSP1 gene taxon:4932 20021106 SGD
+SGD S000002242 SUB2 GO:0000346 SGD_REF:S000069956|PMID:11979277 IPI C ATP-dependent RNA helicase YDL084W gene taxon:4932 20030221 SGD
+SGD S000002242 SUB2 GO:0000781 SGD_REF:S000081848|PMID:15942929 IPI C ATP-dependent RNA helicase YDL084W gene taxon:4932 20050817 SGD
+SGD S000002242 SUB2 GO:0005634 SGD_REF:S000069459|PMID:11914276 IDA C ATP-dependent RNA helicase YDL084W gene taxon:4932 20020507 SGD
+SGD S000002242 SUB2 GO:0005681 SGD_REF:S000058281|PMID:9476892 TAS C ATP-dependent RNA helicase YDL084W gene taxon:4932 20010118 SGD
+SGD S000002242 SUB2 GO:0003723 SGD_REF:S000082053|PMID:15192704 IPI F ATP-dependent RNA helicase YDL084W gene taxon:4932 20050705 SGD
+SGD S000002242 SUB2 GO:0004004 SGD_REF:S000058281|PMID:9476892 TAS F ATP-dependent RNA helicase YDL084W gene taxon:4932 20010118 SGD
+SGD S000002242 SUB2 GO:0005515 SGD_REF:S000071844|PMID:12411502 IPI SGD:S000002566 F ATP-dependent RNA helicase YDL084W gene taxon:4932 20030605 SGD
+SGD S000002242 SUB2 GO:0031202 SGD_REF:S000059117|PMID:11156602 ISS F ATP-dependent RNA helicase YDL084W gene taxon:4932 20050223 SGD
+SGD S000002242 SUB2 GO:0000370 SGD_REF:S000058281|PMID:9476892 TAS P ATP-dependent RNA helicase YDL084W gene taxon:4932 20030825 SGD
+SGD S000002242 SUB2 GO:0000370 SGD_REF:S000073846 TAS P ATP-dependent RNA helicase YDL084W gene taxon:4932 20030825 SGD
+SGD S000002242 SUB2 GO:0000398 SGD_REF:S000059117|PMID:11156602 IMP P ATP-dependent RNA helicase YDL084W gene taxon:4932 20050711 SGD
+SGD S000002242 SUB2 GO:0006348 SGD_REF:S000081848|PMID:15942929 IMP P ATP-dependent RNA helicase YDL084W gene taxon:4932 20050817 SGD
+SGD S000002242 SUB2 GO:0006406 SGD_REF:S000066178|PMID:11696331 IMP P ATP-dependent RNA helicase YDL084W gene taxon:4932 20020213 SGD
+SGD S000002242 SUB2 GO:0006406 SGD_REF:S000068901|PMID:11675790 IPI P ATP-dependent RNA helicase YDL084W gene taxon:4932 20020213 SGD
+SGD S000002242 SUB2 GO:0006406 SGD_REF:S000068901|PMID:11675790 IMP P ATP-dependent RNA helicase YDL084W gene taxon:4932 20020213 SGD
+SGD S000002242 SUB2 GO:0006406 SGD_REF:S000068901|PMID:11675790 IDA P ATP-dependent RNA helicase YDL084W gene taxon:4932 20020213 SGD
+SGD S000002242 SUB2 GO:0006406 SGD_REF:S000066178|PMID:11696331 IDA P ATP-dependent RNA helicase YDL084W gene taxon:4932 20020213 SGD
+SGD S000029531 SUC1 GO:0009277 SGD_REF:S000071598 TAS C invertase (sucrose hydrolyzing enzyme) gene taxon:4932 20021112 SGD
+SGD S000029531 SUC1 GO:0004564 SGD_REF:S000055541|PMID:2834091 IMP F invertase (sucrose hydrolyzing enzyme) gene taxon:4932 20010118 SGD
+SGD S000029531 SUC1 GO:0005987 SGD_REF:S000058499 TAS P invertase (sucrose hydrolyzing enzyme) gene taxon:4932 20010119 SGD
+SGD S000001424 SUC2 GO:0005576 SGD_REF:S000046316|PMID:6341817 IDA C invertase (sucrose hydrolyzing enzyme) YIL162W gene taxon:4932 20021002 SGD
+SGD S000001424 SUC2 GO:0005737 SGD_REF:S000046316|PMID:6341817 IDA C invertase (sucrose hydrolyzing enzyme) YIL162W gene taxon:4932 20021002 SGD
+SGD S000001424 SUC2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C invertase (sucrose hydrolyzing enzyme) YIL162W gene taxon:4932 20040813 SGD
+SGD S000001424 SUC2 GO:0004564 SGD_REF:S000055541|PMID:2834091 IMP F invertase (sucrose hydrolyzing enzyme) YIL162W gene taxon:4932 20010118 SGD
+SGD S000001424 SUC2 GO:0005987 SGD_REF:S000058499 TAS P invertase (sucrose hydrolyzing enzyme) YIL162W gene taxon:4932 20010119 SGD
+SGD S000029532 SUC3 GO:0008372 SGD_REF:S000069584 ND C invertase (sucrose hydrolyzing enzyme) gene taxon:4932 20021115 SGD
+SGD S000029532 SUC3 GO:0004564 SGD_REF:S000055541|PMID:2834091 IMP F invertase (sucrose hydrolyzing enzyme) gene taxon:4932 20010118 SGD
+SGD S000029532 SUC3 GO:0005987 SGD_REF:S000058499 TAS P invertase (sucrose hydrolyzing enzyme) gene taxon:4932 20010119 SGD
+SGD S000029533 SUC4 GO:0008372 SGD_REF:S000069584 ND C invertase (sucrose hydrolyzing enzyme) gene taxon:4932 20021115 SGD
+SGD S000029533 SUC4 GO:0004564 SGD_REF:S000055541|PMID:2834091 IMP F invertase (sucrose hydrolyzing enzyme) gene taxon:4932 20010118 SGD
+SGD S000029533 SUC4 GO:0005987 SGD_REF:S000058499 TAS P invertase (sucrose hydrolyzing enzyme) gene taxon:4932 20010119 SGD
+SGD S000029534 SUC5 GO:0008372 SGD_REF:S000069584 ND C invertase (sucrose hydrolyzing enzyme) gene taxon:4932 20021115 SGD
+SGD S000029534 SUC5 GO:0004564 SGD_REF:S000055541|PMID:2834091 IMP F invertase (sucrose hydrolyzing enzyme) gene taxon:4932 20010118 SGD
+SGD S000029534 SUC5 GO:0005987 SGD_REF:S000058499 TAS P invertase (sucrose hydrolyzing enzyme) gene taxon:4932 20010119 SGD
+SGD S000029535 SUC7 GO:0008372 SGD_REF:S000069584 ND C invertase (sucrose hydrolyzing enzyme) gene taxon:4932 20021115 SGD
+SGD S000029535 SUC7 GO:0004564 SGD_REF:S000039524|PMID:3018485 NAS F invertase (sucrose hydrolyzing enzyme) gene taxon:4932 20010118 SGD
+SGD S000029535 SUC7 GO:0005987 SGD_REF:S000058499 TAS P invertase (sucrose hydrolyzing enzyme) gene taxon:4932 20010119 SGD
+SGD S000006355 SUE1 GO:0005740 SGD_REF:S000076908|PMID:15123691 IDA C YPR151C gene taxon:4932 20040917 SGD
+SGD S000006355 SUE1 GO:0005554 SGD_REF:S000069584 ND F YPR151C gene taxon:4932 20030203 SGD
+SGD S000006355 SUE1 GO:0030163 SGD_REF:S000076908|PMID:15123691 IMP P YPR151C gene taxon:4932 20040917 SGD
+SGD S000006592 SUF1 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tRNA-Gly tG(UCC)O gene taxon:4932 20030507 SGD
+SGD S000006592 SUF1 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tRNA-Gly tG(UCC)O gene taxon:4932 20030507 SGD
+SGD S000006592 SUF1 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tRNA-Gly tG(UCC)O gene taxon:4932 20030507 SGD
+SGD S000006679 SUF10 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tP(AGG)N gene taxon:4932 20030507 SGD
+SGD S000006679 SUF10 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tP(AGG)N gene taxon:4932 20030507 SGD
+SGD S000006679 SUF10 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tP(AGG)N gene taxon:4932 20030507 SGD
+SGD S000006688 SUF11 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tRNA-Pro tP(UGG)O2 gene taxon:4932 20030507 SGD
+SGD S000006688 SUF11 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tRNA-Pro tP(UGG)O2 gene taxon:4932 20030507 SGD
+SGD S000006688 SUF11 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tRNA-Pro tP(UGG)O2 gene taxon:4932 20030507 SGD
+SGD S000006575 SUF16 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tRNA-Gly tG(GCC)C gene taxon:4932 20030507 SGD
+SGD S000006575 SUF16 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tRNA-Gly tG(GCC)C gene taxon:4932 20030507 SGD
+SGD S000006575 SUF16 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tRNA-Gly tG(GCC)C gene taxon:4932 20030507 SGD
+SGD S000006587 SUF17 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tRNA-Gly tG(GCC)O2 gene taxon:4932 20030507 SGD
+SGD S000006587 SUF17 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tRNA-Gly tG(GCC)O2 gene taxon:4932 20030507 SGD
+SGD S000006587 SUF17 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tRNA-Gly tG(GCC)O2 gene taxon:4932 20030507 SGD
+SGD S000006678 SUF2 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tP(AGG)C gene taxon:4932 20030507 SGD
+SGD S000006678 SUF2 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tP(AGG)C gene taxon:4932 20030507 SGD
+SGD S000006678 SUF2 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tP(AGG)C gene taxon:4932 20030507 SGD
+SGD S000006579 SUF20 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tRNA-Gly tG(GCC)F1 gene taxon:4932 20030507 SGD
+SGD S000006579 SUF20 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tRNA-Gly tG(GCC)F1 gene taxon:4932 20030507 SGD
+SGD S000006579 SUF20 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tRNA-Gly tG(GCC)F1 gene taxon:4932 20030507 SGD
+SGD S000006572 SUF3 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tRNA-Gly tG(CCC)D gene taxon:4932 20030507 SGD
+SGD S000006572 SUF3 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tRNA-Gly tG(CCC)D gene taxon:4932 20030507 SGD
+SGD S000006572 SUF3 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tRNA-Gly tG(CCC)D gene taxon:4932 20030507 SGD
+SGD S000006590 SUF4 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tRNA-Gly tG(UCC)G gene taxon:4932 20030507 SGD
+SGD S000006590 SUF4 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tRNA-Gly tG(UCC)G gene taxon:4932 20030507 SGD
+SGD S000006590 SUF4 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tRNA-Gly tG(UCC)G gene taxon:4932 20030507 SGD
+SGD S000006573 SUF5 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tRNA-Gly tG(CCC)O gene taxon:4932 20030507 SGD
+SGD S000006573 SUF5 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tRNA-Gly tG(CCC)O gene taxon:4932 20030507 SGD
+SGD S000006573 SUF5 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tRNA-Gly tG(CCC)O gene taxon:4932 20030507 SGD
+SGD S000006591 SUF6 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tRNA-Gly tG(UCC)N gene taxon:4932 20030507 SGD
+SGD S000006591 SUF6 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tRNA-Gly tG(UCC)N gene taxon:4932 20030507 SGD
+SGD S000006591 SUF6 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tRNA-Gly tG(UCC)N gene taxon:4932 20030507 SGD
+SGD S000006684 SUF7 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tRNA-Pro tP(UGG)M gene taxon:4932 20030507 SGD
+SGD S000006684 SUF7 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tRNA-Pro tP(UGG)M gene taxon:4932 20030507 SGD
+SGD S000006684 SUF7 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tRNA-Pro tP(UGG)M gene taxon:4932 20030507 SGD
+SGD S000006682 SUF8 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tRNA-Pro tP(UGG)H gene taxon:4932 20030507 SGD
+SGD S000006682 SUF8 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tRNA-Pro tP(UGG)H gene taxon:4932 20030507 SGD
+SGD S000006682 SUF8 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tRNA-Pro tP(UGG)H gene taxon:4932 20030507 SGD
+SGD S000006681 SUF9 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tRNA-Pro tP(UGG)F gene taxon:4932 20030507 SGD
+SGD S000006681 SUF9 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tRNA-Pro tP(UGG)F gene taxon:4932 20030507 SGD
+SGD S000006681 SUF9 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tRNA-Pro tP(UGG)F gene taxon:4932 20030507 SGD
+SGD S000005188 SUI1 GO:0043614 SGD_REF:S000082127|PMID:11018020 IDA C translation initiation factor eIF1 YNL244C|MOF2|RFR1|eIF-1|eIF1 gene taxon:4932 20060427 SGD
+SGD S000005188 SUI1 GO:0003743 SGD_REF:S000058753|PMID:9841679 TAS F translation initiation factor eIF1 YNL244C|MOF2|RFR1|eIF-1|eIF1 gene taxon:4932 20010124 SGD
+SGD S000005188 SUI1 GO:0006413 SGD_REF:S000058753|PMID:9841679 TAS P translation initiation factor eIF1 YNL244C|MOF2|RFR1|eIF-1|eIF1 gene taxon:4932 20010124 SGD
+SGD S000003767 SUI2 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C Translation initiation factor eIF-2 alpha subunit YJR007W|eIF2 alpha gene taxon:4932 20020507 SGD
+SGD S000003767 SUI2 GO:0005840 SGD_REF:S000058753|PMID:9841679 TAS C Translation initiation factor eIF-2 alpha subunit YJR007W|eIF2 alpha gene taxon:4932 20010124 SGD
+SGD S000003767 SUI2 GO:0005850 SGD_REF:S000043546|PMID:2649894 IMP C Translation initiation factor eIF-2 alpha subunit YJR007W|eIF2 alpha gene taxon:4932 20050105 SGD
+SGD S000003767 SUI2 GO:0005850 SGD_REF:S000043546|PMID:2649894 ISS C Translation initiation factor eIF-2 alpha subunit YJR007W|eIF2 alpha gene taxon:4932 20050105 SGD
+SGD S000003767 SUI2 GO:0043614 SGD_REF:S000082127|PMID:11018020 IDA C Translation initiation factor eIF-2 alpha subunit YJR007W|eIF2 alpha gene taxon:4932 20060427 SGD
+SGD S000003767 SUI2 GO:0003743 SGD_REF:S000058753|PMID:9841679 TAS F Translation initiation factor eIF-2 alpha subunit YJR007W|eIF2 alpha gene taxon:4932 20010124 SGD
+SGD S000003767 SUI2 GO:0006413 SGD_REF:S000058753|PMID:9841679 TAS P Translation initiation factor eIF-2 alpha subunit YJR007W|eIF2 alpha gene taxon:4932 20010124 SGD
+SGD S000006158 SUI3 GO:0005840 SGD_REF:S000058753|PMID:9841679 TAS C translation initiation factor eIF-2 beta subunit YPL237W|eIF2 beta gene taxon:4932 20010124 SGD
+SGD S000006158 SUI3 GO:0005850 SGD_REF:S000051045|PMID:3136928 IMP C translation initiation factor eIF-2 beta subunit YPL237W|eIF2 beta gene taxon:4932 20050105 SGD
+SGD S000006158 SUI3 GO:0005850 SGD_REF:S000051045|PMID:3136928 ISS C translation initiation factor eIF-2 beta subunit YPL237W|eIF2 beta gene taxon:4932 20050105 SGD
+SGD S000006158 SUI3 GO:0043614 SGD_REF:S000082127|PMID:11018020 IDA C translation initiation factor eIF-2 beta subunit YPL237W|eIF2 beta gene taxon:4932 20060427 SGD
+SGD S000006158 SUI3 GO:0003743 SGD_REF:S000058753|PMID:9841679 TAS F translation initiation factor eIF-2 beta subunit YPL237W|eIF2 beta gene taxon:4932 20010124 SGD
+SGD S000006158 SUI3 GO:0006413 SGD_REF:S000058753|PMID:9841679 TAS P translation initiation factor eIF-2 beta subunit YPL237W|eIF2 beta gene taxon:4932 20010124 SGD
+SGD S000000498 SUL1 GO:0005886 SGD_REF:S000053006|PMID:7616962 ISS C YBR294W|SFP2 gene taxon:4932 20021002 SGD
+SGD S000000498 SUL1 GO:0005886 SGD_REF:S000053006|PMID:7616962 IMP C YBR294W|SFP2 gene taxon:4932 20021002 SGD
+SGD S000000498 SUL1 GO:0015116 SGD_REF:S000053006|PMID:7616962 IGI F YBR294W|SFP2 gene taxon:4932 20021002 SGD
+SGD S000000498 SUL1 GO:0015116 SGD_REF:S000053006|PMID:7616962 IMP F YBR294W|SFP2 gene taxon:4932 20021002 SGD
+SGD S000000498 SUL1 GO:0008272 SGD_REF:S000053006|PMID:7616962 IGI P YBR294W|SFP2 gene taxon:4932 20021002 SGD
+SGD S000000498 SUL1 GO:0008272 SGD_REF:S000053006|PMID:7616962 IMP P YBR294W|SFP2 gene taxon:4932 20021002 SGD
+SGD S000004082 SUL2 GO:0005886 SGD_REF:S000042768|PMID:9055073 ISS C high affinity sulfate permease YLR092W gene taxon:4932 20021002 SGD
+SGD S000004082 SUL2 GO:0005886 SGD_REF:S000042768|PMID:9055073 IMP C high affinity sulfate permease YLR092W gene taxon:4932 20021002 SGD
+SGD S000004082 SUL2 GO:0015116 SGD_REF:S000042768|PMID:9055073 IMP F high affinity sulfate permease YLR092W gene taxon:4932 20021002 SGD
+SGD S000004082 SUL2 GO:0008272 SGD_REF:S000042768|PMID:9055073 IMP P high affinity sulfate permease YLR092W gene taxon:4932 20021002 SGD
+SGD S000002718 SUM1 GO:0000118 SGD_REF:S000066205|PMID:11711434 IDA C YDR310C gene taxon:4932 20020814 SGD
+SGD S000002718 SUM1 GO:0000118 SGD_REF:S000066205|PMID:11711434 IPI C YDR310C gene taxon:4932 20020814 SGD
+SGD S000002718 SUM1 GO:0005634 SGD_REF:S000041222|PMID:8754829 IDA C YDR310C gene taxon:4932 20010118 SGD
+SGD S000002718 SUM1 GO:0016564 SGD_REF:S000071388|PMID:12192041 TAS F YDR310C gene taxon:4932 20021130 SGD
+SGD S000002718 SUM1 GO:0016564 SGD_REF:S000073726|PMID:12832469 IDA F YDR310C gene taxon:4932 20050117 SGD
+SGD S000002718 SUM1 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P YDR310C gene taxon:4932 20060203 SGD
+SGD S000002718 SUM1 GO:0006348 SGD_REF:S000041222|PMID:8754829 IMP P YDR310C gene taxon:4932 20010118 SGD
+SGD S000002718 SUM1 GO:0007088 SGD_REF:S000040525|PMID:10562556 IPI P YDR310C gene taxon:4932 20010118 SGD
+SGD S000002718 SUM1 GO:0007088 SGD_REF:S000040525|PMID:10562556 IMP P YDR310C gene taxon:4932 20010118 SGD
+SGD S000002718 SUM1 GO:0016481 SGD_REF:S000073726|PMID:12832469 IDA P YDR310C gene taxon:4932 20050117 SGD
+SGD S000002718 SUM1 GO:0030466 SGD_REF:S000041222|PMID:8754829 IMP P YDR310C gene taxon:4932 20010118 SGD
+SGD S000005010 SUN4 GO:0005759 SGD_REF:S000069559|PMID:11958935 TAS C YNL066W|SCW3 gene taxon:4932 20020721 SGD
+SGD S000005010 SUN4 GO:0009277 SGD_REF:S000069559|PMID:11958935 IDA C YNL066W|SCW3 gene taxon:4932 20020721 SGD
+SGD S000005010 SUN4 GO:0015926 SGD_REF:S000050571|PMID:9748433 ISS F YNL066W|SCW3 gene taxon:4932 20021108 SGD
+SGD S000005010 SUN4 GO:0007005 SGD_REF:S000069559|PMID:11958935 TAS P YNL066W|SCW3 gene taxon:4932 20020721 SGD
+SGD S000029700 SUP-1A GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20010119 SGD
+SGD S000029700 SUP-1A GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20010119 SGD
+SGD S000029700 SUP-1A GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20010119 SGD
+SGD S000006779 SUP11 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tY(GUA)F1 gene taxon:4932 20030507 SGD
+SGD S000006779 SUP11 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tY(GUA)F1 gene taxon:4932 20030507 SGD
+SGD S000006779 SUP11 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tY(GUA)F1 gene taxon:4932 20030507 SGD
+SGD S000029548 SUP111 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20010119 SGD
+SGD S000029548 SUP111 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20010119 SGD
+SGD S000029548 SUP111 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20010119 SGD
+SGD S000029549 SUP112 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20010119 SGD
+SGD S000029549 SUP112 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20010119 SGD
+SGD S000029549 SUP112 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20010119 SGD
+SGD S000029550 SUP113 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20010119 SGD
+SGD S000029550 SUP113 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20010119 SGD
+SGD S000029550 SUP113 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20010119 SGD
+SGD S000029551 SUP139 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20010119 SGD
+SGD S000029551 SUP139 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20010119 SGD
+SGD S000029551 SUP139 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20010119 SGD
+SGD S000029552 SUP15 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20010119 SGD
+SGD S000029552 SUP15 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20010119 SGD
+SGD S000029552 SUP15 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20010119 SGD
+SGD S000029553 SUP150 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20010119 SGD
+SGD S000029553 SUP150 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20010119 SGD
+SGD S000029553 SUP150 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20010119 SGD
+SGD S000029554 SUP154 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20010119 SGD
+SGD S000029554 SUP154 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20010119 SGD
+SGD S000029554 SUP154 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20010119 SGD
+SGD S000029555 SUP155 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20010119 SGD
+SGD S000029555 SUP155 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20010119 SGD
+SGD S000029555 SUP155 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20010119 SGD
+SGD S000006736 SUP16 GO:0005737 SGD_REF:S000054473|PMID:7024909 IDA C tS(UGA)P|SUQ5 gene taxon:4932 20051024 SGD
+SGD S000006736 SUP16 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tS(UGA)P|SUQ5 gene taxon:4932 20030507 SGD
+SGD S000006736 SUP16 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tS(UGA)P|SUQ5 gene taxon:4932 20030507 SGD
+SGD S000006736 SUP16 GO:0030533 SGD_REF:S000054473|PMID:7024909 IDA F tS(UGA)P|SUQ5 gene taxon:4932 20051024 SGD
+SGD S000006736 SUP16 GO:0006412 SGD_REF:S000054473|PMID:7024909 ISS P tS(UGA)P|SUQ5 gene taxon:4932 20051024 SGD
+SGD S000006736 SUP16 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tS(UGA)P|SUQ5 gene taxon:4932 20030507 SGD
+SGD S000029557 SUP160 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20010119 SGD
+SGD S000029557 SUP160 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20010119 SGD
+SGD S000029557 SUP160 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20010119 SGD
+SGD S000029558 SUP165 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20010119 SGD
+SGD S000029558 SUP165 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20010119 SGD
+SGD S000029558 SUP165 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20010119 SGD
+SGD S000006735 SUP17 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tS(UGA)I gene taxon:4932 20030507 SGD
+SGD S000006735 SUP17 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tS(UGA)I gene taxon:4932 20030507 SGD
+SGD S000006735 SUP17 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tS(UGA)I gene taxon:4932 20030507 SGD
+SGD S000006734 SUP19 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tRNA-Ser tS(UGA)E|SUP20 gene taxon:4932 20030507 SGD
+SGD S000006734 SUP19 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tRNA-Ser tS(UGA)E|SUP20 gene taxon:4932 20030507 SGD
+SGD S000006734 SUP19 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tRNA-Ser tS(UGA)E|SUP20 gene taxon:4932 20030507 SGD
+SGD S000006778 SUP2 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tY(GUA)D gene taxon:4932 20030507 SGD
+SGD S000006778 SUP2 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tY(GUA)D gene taxon:4932 20030507 SGD
+SGD S000006778 SUP2 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tY(GUA)D gene taxon:4932 20030507 SGD
+SGD S000029559 SUP22 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20010119 SGD
+SGD S000029559 SUP22 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20010119 SGD
+SGD S000029559 SUP22 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20010119 SGD
+SGD S000029560 SUP25 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20010119 SGD
+SGD S000029560 SUP25 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20010119 SGD
+SGD S000029560 SUP25 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20010119 SGD
+SGD S000029561 SUP26 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20010119 SGD
+SGD S000029561 SUP26 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20010119 SGD
+SGD S000029561 SUP26 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20010119 SGD
+SGD S000029562 SUP27 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20010119 SGD
+SGD S000029562 SUP27 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20010119 SGD
+SGD S000029562 SUP27 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20010119 SGD
+SGD S000029563 SUP28 GO:0008372 SGD_REF:S000069584 ND C leucine-inserting UAA suppressors gene taxon:4932 20010119 SGD
+SGD S000029563 SUP28 GO:0005554 SGD_REF:S000069584 ND F leucine-inserting UAA suppressors gene taxon:4932 20010119 SGD
+SGD S000029563 SUP28 GO:0000004 SGD_REF:S000069584 ND P leucine-inserting UAA suppressors gene taxon:4932 20010119 SGD
+SGD S000029564 SUP29 GO:0008372 SGD_REF:S000069584 ND C SUP30 gene taxon:4932 20010119 SGD
+SGD S000029564 SUP29 GO:0005554 SGD_REF:S000069584 ND F SUP30 gene taxon:4932 20010119 SGD
+SGD S000029564 SUP29 GO:0000004 SGD_REF:S000069584 ND P SUP30 gene taxon:4932 20010119 SGD
+SGD S000006785 SUP3 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tRNA-Tyr tY(GUA)O gene taxon:4932 20030507 SGD
+SGD S000006785 SUP3 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tRNA-Tyr tY(GUA)O gene taxon:4932 20030507 SGD
+SGD S000006785 SUP3 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tRNA-Tyr tY(GUA)O gene taxon:4932 20030507 SGD
+SGD S000029565 SUP33 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20010119 SGD
+SGD S000029565 SUP33 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20010119 SGD
+SGD S000029565 SUP33 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20010119 SGD
+SGD S000002579 SUP35 GO:0005829 SGD_REF:S000040067|PMID:8082183 TAS C translation termination factor eRF3 YDR172W|GST1|PNM2|SAL3|SUF12|SUP2|SUP36|[PSI(+)]|[PSI]|eRF3 gene taxon:4932 20010118 SGD
+SGD S000002579 SUP35 GO:0018444 SGD_REF:S000055465|PMID:7556078 IDA C translation termination factor eRF3 YDR172W|GST1|PNM2|SAL3|SUF12|SUP2|SUP36|[PSI(+)]|[PSI]|eRF3 gene taxon:4932 20050105 SGD
+SGD S000002579 SUP35 GO:0003747 SGD_REF:S000040067|PMID:8082183 TAS F translation termination factor eRF3 YDR172W|GST1|PNM2|SAL3|SUF12|SUP2|SUP36|[PSI(+)]|[PSI]|eRF3 gene taxon:4932 20010118 SGD
+SGD S000002579 SUP35 GO:0000288 SGD_REF:S000074117|PMID:12923185 IMP P translation termination factor eRF3 YDR172W|GST1|PNM2|SAL3|SUF12|SUP2|SUP36|[PSI(+)]|[PSI]|eRF3 gene taxon:4932 20031228 SGD
+SGD S000002579 SUP35 GO:0000288 SGD_REF:S000074117|PMID:12923185 IPI P translation termination factor eRF3 YDR172W|GST1|PNM2|SAL3|SUF12|SUP2|SUP36|[PSI(+)]|[PSI]|eRF3 gene taxon:4932 20031228 SGD
+SGD S000002579 SUP35 GO:0006415 SGD_REF:S000040067|PMID:8082183 TAS P translation termination factor eRF3 YDR172W|GST1|PNM2|SAL3|SUF12|SUP2|SUP36|[PSI(+)]|[PSI]|eRF3 gene taxon:4932 20010118 SGD
+SGD S000029566 SUP37 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20010119 SGD
+SGD S000029566 SUP37 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20010119 SGD
+SGD S000029566 SUP37 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20010119 SGD
+SGD S000006782 SUP4 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tRNA-Tyr tY(GUA)J2 gene taxon:4932 20030507 SGD
+SGD S000006782 SUP4 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tRNA-Tyr tY(GUA)J2 gene taxon:4932 20030507 SGD
+SGD S000006782 SUP4 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tRNA-Tyr tY(GUA)J2 gene taxon:4932 20030507 SGD
+SGD S000029567 SUP40 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20010119 SGD
+SGD S000029567 SUP40 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20010119 SGD
+SGD S000029567 SUP40 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20010119 SGD
+SGD S000029568 SUP42 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20010119 SGD
+SGD S000029568 SUP42 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20010119 SGD
+SGD S000029568 SUP42 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20010119 SGD
+SGD S000029569 SUP43 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20010119 SGD
+SGD S000029569 SUP43 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20010119 SGD
+SGD S000029569 SUP43 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20010119 SGD
+SGD S000000347 SUP45 GO:0005829 SGD_REF:S000043151|PMID:1474892 IPI C eRF1 (eukaryotic Release Factor 1) homolog YBR143C|SAL4|SUP1|SUP47|eRF1 gene taxon:4932 20010118 SGD
+SGD S000000347 SUP45 GO:0018444 SGD_REF:S000055465|PMID:7556078 IDA C eRF1 (eukaryotic Release Factor 1) homolog YBR143C|SAL4|SUP1|SUP47|eRF1 gene taxon:4932 20050105 SGD
+SGD S000000347 SUP45 GO:0016149 SGD_REF:S000041068|PMID:9182990 IMP F eRF1 (eukaryotic Release Factor 1) homolog YBR143C|SAL4|SUP1|SUP47|eRF1 gene taxon:4932 20010118 SGD
+SGD S000000347 SUP45 GO:0016149 SGD_REF:S000041068|PMID:9182990 ISS F eRF1 (eukaryotic Release Factor 1) homolog YBR143C|SAL4|SUP1|SUP47|eRF1 gene taxon:4932 20010118 SGD
+SGD S000000347 SUP45 GO:0000910 SGD_REF:S000080604|PMID:15228544 IGI P eRF1 (eukaryotic Release Factor 1) homolog YBR143C|SAL4|SUP1|SUP47|eRF1 gene taxon:4932 20050329 SGD
+SGD S000000347 SUP45 GO:0000910 SGD_REF:S000080604|PMID:15228544 IMP P eRF1 (eukaryotic Release Factor 1) homolog YBR143C|SAL4|SUP1|SUP47|eRF1 gene taxon:4932 20050329 SGD
+SGD S000000347 SUP45 GO:0006415 SGD_REF:S000041068|PMID:9182990 IMP P eRF1 (eukaryotic Release Factor 1) homolog YBR143C|SAL4|SUP1|SUP47|eRF1 gene taxon:4932 20010118 SGD
+SGD S000000347 SUP45 GO:0006415 SGD_REF:S000041068|PMID:9182990 ISS P eRF1 (eukaryotic Release Factor 1) homolog YBR143C|SAL4|SUP1|SUP47|eRF1 gene taxon:4932 20010118 SGD
+SGD S000006783 SUP5 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tY(GUA)M1 gene taxon:4932 20030507 SGD
+SGD S000006783 SUP5 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tY(GUA)M1 gene taxon:4932 20030507 SGD
+SGD S000006783 SUP5 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tY(GUA)M1 gene taxon:4932 20030507 SGD
+SGD S000029570 SUP50 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20010119 SGD
+SGD S000029570 SUP50 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20010119 SGD
+SGD S000029570 SUP50 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20010119 SGD
+SGD S000006650 SUP51 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tRNA-Leu tL(UAA)J|SUP52 gene taxon:4932 20030507 SGD
+SGD S000006650 SUP51 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tRNA-Leu tL(UAA)J|SUP52 gene taxon:4932 20030507 SGD
+SGD S000006650 SUP51 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tRNA-Leu tL(UAA)J|SUP52 gene taxon:4932 20030507 SGD
+SGD S000006637 SUP53 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tRNA-Leu tL(CAA)C gene taxon:4932 20030507 SGD
+SGD S000006637 SUP53 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tRNA-Leu tL(CAA)C gene taxon:4932 20030507 SGD
+SGD S000006637 SUP53 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tRNA-Leu tL(CAA)C gene taxon:4932 20030507 SGD
+SGD S000006640 SUP54 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tRNA-Leu tL(CAA)G2 gene taxon:4932 20030507 SGD
+SGD S000006640 SUP54 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tRNA-Leu tL(CAA)G2 gene taxon:4932 20030507 SGD
+SGD S000006640 SUP54 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tRNA-Leu tL(CAA)G2 gene taxon:4932 20030507 SGD
+SGD S000006636 SUP56 GO:0005829 SGD_REF:S000048408|PMID:6387150 TAS C tRNA-Leu tL(CAA)A gene taxon:4932 20010118 SGD
+SGD S000006636 SUP56 GO:0030533 SGD_REF:S000048408|PMID:6387150 TAS F tRNA-Leu tL(CAA)A gene taxon:4932 20020220 SGD
+SGD S000006636 SUP56 GO:0006414 SGD_REF:S000048408|PMID:6387150 TAS P tRNA-Leu tL(CAA)A gene taxon:4932 20010118 SGD
+SGD S000029571 SUP57 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20010119 SGD
+SGD S000029571 SUP57 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20010119 SGD
+SGD S000029571 SUP57 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20010119 SGD
+SGD S000029572 SUP58 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20010119 SGD
+SGD S000029572 SUP58 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20010119 SGD
+SGD S000029572 SUP58 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20010119 SGD
+SGD S000006780 SUP6 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tRNA-Tyr tY(GUA)F2 gene taxon:4932 20030507 SGD
+SGD S000006780 SUP6 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tRNA-Tyr tY(GUA)F2 gene taxon:4932 20030507 SGD
+SGD S000006780 SUP6 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tRNA-Tyr tY(GUA)F2 gene taxon:4932 20030507 SGD
+SGD S000006730 SUP61 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tRNA-Ser tS(CGA)C gene taxon:4932 20030507 SGD
+SGD S000006730 SUP61 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tRNA-Ser tS(CGA)C gene taxon:4932 20030507 SGD
+SGD S000006730 SUP61 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tRNA-Ser tS(CGA)C gene taxon:4932 20030507 SGD
+SGD S000006781 SUP7 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tY(GUA)J1 gene taxon:4932 20030507 SGD
+SGD S000006781 SUP7 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tY(GUA)J1 gene taxon:4932 20030507 SGD
+SGD S000006781 SUP7 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tY(GUA)J1 gene taxon:4932 20030507 SGD
+SGD S000029573 SUP71 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20010119 SGD
+SGD S000029573 SUP71 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20010119 SGD
+SGD S000029573 SUP71 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20010119 SGD
+SGD S000029574 SUP72 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20010119 SGD
+SGD S000029574 SUP72 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20010119 SGD
+SGD S000029574 SUP72 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20010119 SGD
+SGD S000029575 SUP73 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20010119 SGD
+SGD S000029575 SUP73 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20010119 SGD
+SGD S000029575 SUP73 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20010119 SGD
+SGD S000029576 SUP74 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20010119 SGD
+SGD S000029576 SUP74 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20010119 SGD
+SGD S000029576 SUP74 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20010119 SGD
+SGD S000029577 SUP75 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20010119 SGD
+SGD S000029577 SUP75 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20010119 SGD
+SGD S000029577 SUP75 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20010119 SGD
+SGD S000029578 SUP76 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20010119 SGD
+SGD S000029578 SUP76 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20010119 SGD
+SGD S000029578 SUP76 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20010119 SGD
+SGD S000029579 SUP77 GO:0008372 SGD_REF:S000069584 ND C SUP166 gene taxon:4932 20010119 SGD
+SGD S000029579 SUP77 GO:0005554 SGD_REF:S000069584 ND F SUP166 gene taxon:4932 20010119 SGD
+SGD S000029579 SUP77 GO:0000004 SGD_REF:S000069584 ND P SUP166 gene taxon:4932 20010119 SGD
+SGD S000029580 SUP78 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20010119 SGD
+SGD S000029580 SUP78 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20010119 SGD
+SGD S000029580 SUP78 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20010119 SGD
+SGD S000029581 SUP79 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20010119 SGD
+SGD S000029581 SUP79 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20010119 SGD
+SGD S000029581 SUP79 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20010119 SGD
+SGD S000006784 SUP8 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tRNA-Tyr tY(GUA)M2 gene taxon:4932 20030507 SGD
+SGD S000006784 SUP8 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tRNA-Tyr tY(GUA)M2 gene taxon:4932 20030507 SGD
+SGD S000006784 SUP8 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tRNA-Tyr tY(GUA)M2 gene taxon:4932 20030507 SGD
+SGD S000029582 SUP80 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20010119 SGD
+SGD S000029582 SUP80 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20010119 SGD
+SGD S000029582 SUP80 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20010119 SGD
+SGD S000029583 SUP85 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20010119 SGD
+SGD S000029583 SUP85 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20010119 SGD
+SGD S000029583 SUP85 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20010119 SGD
+SGD S000029584 SUP86 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20010119 SGD
+SGD S000029584 SUP86 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20010119 SGD
+SGD S000029584 SUP86 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20010119 SGD
+SGD S000029585 SUP87 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20010119 SGD
+SGD S000029585 SUP87 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20010119 SGD
+SGD S000029585 SUP87 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20010119 SGD
+SGD S000029586 SUP88 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20010119 SGD
+SGD S000029586 SUP88 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20010119 SGD
+SGD S000029586 SUP88 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20010119 SGD
+SGD S000029587 SUPX GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20010119 SGD
+SGD S000029587 SUPX GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20010119 SGD
+SGD S000029587 SUPX GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20010119 SGD
+SGD S000029588 SUPY GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20010119 SGD
+SGD S000029588 SUPY GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20010119 SGD
+SGD S000029588 SUPY GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20010119 SGD
+SGD S000005978 SUR1 GO:0005622 SGD_REF:S000053322|PMID:10931938 IC GO:0030148 C integral membrane protein YPL057C|BCL21|CSG1|LPE15 gene taxon:4932 20030311 SGD
+SGD S000005978 SUR1 GO:0000030 SGD_REF:S000075191|PMID:12954640 IGI F integral membrane protein YPL057C|BCL21|CSG1|LPE15 gene taxon:4932 20040102 SGD
+SGD S000005978 SUR1 GO:0000030 SGD_REF:S000075191|PMID:12954640 IMP F integral membrane protein YPL057C|BCL21|CSG1|LPE15 gene taxon:4932 20040102 SGD
+SGD S000005978 SUR1 GO:0016757 SGD_REF:S000055539|PMID:9653120 ISS F integral membrane protein YPL057C|BCL21|CSG1|LPE15 gene taxon:4932 20021204 SGD
+SGD S000005978 SUR1 GO:0006675 SGD_REF:S000047688|PMID:9323360 IMP P integral membrane protein YPL057C|BCL21|CSG1|LPE15 gene taxon:4932 20010118 SGD
+SGD S000005978 SUR1 GO:0006688 SGD_REF:S000047688|PMID:9323360 IMP P integral membrane protein YPL057C|BCL21|CSG1|LPE15 gene taxon:4932 20050301 SGD
+SGD S000005978 SUR1 GO:0006688 SGD_REF:S000047688|PMID:9323360 ISS P integral membrane protein YPL057C|BCL21|CSG1|LPE15 gene taxon:4932 20050301 SGD
+SGD S000005978 SUR1 GO:0030148 SGD_REF:S000061818|PMID:10366774 TAS P integral membrane protein YPL057C|BCL21|CSG1|LPE15 gene taxon:4932 20030311 SGD
+SGD S000005978 SUR1 GO:0030148 SGD_REF:S000075191|PMID:12954640 IMP P integral membrane protein YPL057C|BCL21|CSG1|LPE15 gene taxon:4932 20040102 SGD
+SGD S000002705 SUR2 GO:0005783 SGD_REF:S000040185|PMID:9556590 TAS C sphingosine hydroxylase YDR297W|SYR2 gene taxon:4932 20010118 SGD
+SGD S000002705 SUR2 GO:0000170 SGD_REF:S000040185|PMID:9556590 IMP F sphingosine hydroxylase YDR297W|SYR2 gene taxon:4932 20010118 SGD
+SGD S000002705 SUR2 GO:0000170 SGD_REF:S000040185|PMID:9556590 ISS F sphingosine hydroxylase YDR297W|SYR2 gene taxon:4932 20010118 SGD
+SGD S000002705 SUR2 GO:0006665 SGD_REF:S000040185|PMID:9556590 IMP P sphingosine hydroxylase YDR297W|SYR2 gene taxon:4932 20010118 SGD
+SGD S000002705 SUR2 GO:0006665 SGD_REF:S000040185|PMID:9556590 ISS P sphingosine hydroxylase YDR297W|SYR2 gene taxon:4932 20010118 SGD
+SGD S000002705 SUR2 GO:0030148 SGD_REF:S000061818|PMID:10366774 TAS P sphingosine hydroxylase YDR297W|SYR2 gene taxon:4932 20030311 SGD
+SGD S000004364 SUR4 GO:0005783 SGD_REF:S000071362|PMID:12087109 IDA C elongase YLR372W|APA1|ELO3|SRE1|VBM1 gene taxon:4932 20021120 SGD
+SGD S000004364 SUR4 GO:0005789 SGD_REF:S000041813|PMID:9988704 TAS C elongase YLR372W|APA1|ELO3|SRE1|VBM1 gene taxon:4932 20010118 SGD
+SGD S000004364 SUR4 GO:0009922 SGD_REF:S000073534|PMID:12684876 IMP F elongase YLR372W|APA1|ELO3|SRE1|VBM1 gene taxon:4932 20030708 SGD
+SGD S000004364 SUR4 GO:0009922 SGD_REF:S000073534|PMID:12684876 TAS F elongase YLR372W|APA1|ELO3|SRE1|VBM1 gene taxon:4932 20030708 SGD
+SGD S000004364 SUR4 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P elongase YLR372W|APA1|ELO3|SRE1|VBM1 gene taxon:4932 20060210 SGD
+SGD S000004364 SUR4 GO:0006633 SGD_REF:S000055688|PMID:9211877 IMP P elongase YLR372W|APA1|ELO3|SRE1|VBM1 gene taxon:4932 20010118 SGD
+SGD S000004364 SUR4 GO:0006892 SGD_REF:S000043234|PMID:9832547 IGI P elongase YLR372W|APA1|ELO3|SRE1|VBM1 gene taxon:4932 20010118 SGD
+SGD S000004364 SUR4 GO:0030148 SGD_REF:S000055688|PMID:9211877 IMP P elongase YLR372W|APA1|ELO3|SRE1|VBM1 gene taxon:4932 20020923 SGD
+SGD S000004364 SUR4 GO:0030497 SGD_REF:S000055688|PMID:9211877 IMP P elongase YLR372W|APA1|ELO3|SRE1|VBM1 gene taxon:4932 20020923 SGD
+SGD S000004516 SUR7 GO:0005619 SGD_REF:S000069238|PMID:11784867 IDA C integral membrane protein YML052W gene taxon:4932 20060306 SGD
+SGD S000004516 SUR7 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C integral membrane protein YML052W gene taxon:4932 20040928 SGD
+SGD S000004516 SUR7 GO:0005938 SGD_REF:S000069238|PMID:11784867 IDA C integral membrane protein YML052W gene taxon:4932 20020612 SGD
+SGD S000004516 SUR7 GO:0016021 SGD_REF:S000069238|PMID:11784867 ISS C integral membrane protein YML052W gene taxon:4932 20020612 SGD
+SGD S000004516 SUR7 GO:0016021 SGD_REF:S000048799|PMID:9219339 ISS C integral membrane protein YML052W gene taxon:4932 20020612 SGD
+SGD S000004516 SUR7 NOT GO:0030479 SGD_REF:S000069238|PMID:11784867 IDA C integral membrane protein YML052W gene taxon:4932 20020612 SGD
+SGD S000004516 SUR7 GO:0045121 SGD_REF:S000079755|PMID:15536122 IDA C integral membrane protein YML052W gene taxon:4932 20041215 SGD
+SGD S000004516 SUR7 GO:0005554 SGD_REF:S000069584 ND F integral membrane protein YML052W gene taxon:4932 20020612 SGD
+SGD S000004516 SUR7 GO:0006897 SGD_REF:S000114479|PMID:16496001 IGI P integral membrane protein YML052W gene taxon:4932 20060303 SGD
+SGD S000004516 SUR7 GO:0006897 SGD_REF:S000114479|PMID:16496001 IMP P integral membrane protein YML052W gene taxon:4932 20060303 SGD
+SGD S000004516 SUR7 GO:0030437 SGD_REF:S000069238|PMID:11784867 IMP P integral membrane protein YML052W gene taxon:4932 20020612 SGD
+SGD S000028510 SUS1 GO:0000124 SGD_REF:S000074416|PMID:14718168 IDA C YBR111W-A gene taxon:4932 20040215 SGD
+SGD S000028510 SUS1 GO:0005643 SGD_REF:S000074416|PMID:14718168 IDA C YBR111W-A gene taxon:4932 20040215 SGD
+SGD S000028510 SUS1 GO:0005554 SGD_REF:S000069584 ND F YBR111W-A gene taxon:4932 20030730 SGD
+SGD S000028510 SUS1 GO:0006406 SGD_REF:S000074416|PMID:14718168 IMP P YBR111W-A gene taxon:4932 20040215 SGD
+SGD S000028510 SUS1 GO:0045944 SGD_REF:S000074416|PMID:14718168 IMP P YBR111W-A gene taxon:4932 20040215 SGD
+SGD S000028510 SUS1 GO:0045944 SGD_REF:S000074416|PMID:14718168 IPI P YBR111W-A gene taxon:4932 20040215 SGD
+SGD S000003130 SUT1 GO:0005634 SGD_REF:S000060057|PMID:11248676 IDA C YGL162W gene taxon:4932 20021003 SGD
+SGD S000003130 SUT1 GO:0003700 SGD_REF:S000060825|PMID:11401714 IDA F YGL162W gene taxon:4932 20050117 SGD
+SGD S000003130 SUT1 GO:0003704 SGD_REF:S000060057|PMID:11248676 ISS F YGL162W gene taxon:4932 20021003 SGD
+SGD S000003130 SUT1 GO:0003704 SGD_REF:S000060057|PMID:11248676 IMP F YGL162W gene taxon:4932 20021003 SGD
+SGD S000003130 SUT1 GO:0006357 SGD_REF:S000060057|PMID:11248676 ISS P YGL162W gene taxon:4932 20021003 SGD
+SGD S000003130 SUT1 GO:0006357 SGD_REF:S000060057|PMID:11248676 IMP P YGL162W gene taxon:4932 20021003 SGD
+SGD S000003130 SUT1 GO:0015918 SGD_REF:S000060057|PMID:11248676 IMP P YGL162W gene taxon:4932 20021003 SGD
+SGD S000003130 SUT1 GO:0045449 SGD_REF:S000060825|PMID:11401714 IDA P YGL162W gene taxon:4932 20050117 SGD
+SGD S000006213 SUT2 GO:0005634 SGD_REF:S000076483|PMID:15030478 IDA C YPR009W gene taxon:4932 20040602 SGD
+SGD S000006213 SUT2 GO:0003704 SGD_REF:S000060057|PMID:11248676 ISS F YPR009W gene taxon:4932 20021003 SGD
+SGD S000006213 SUT2 GO:0003704 SGD_REF:S000060057|PMID:11248676 IMP F YPR009W gene taxon:4932 20021003 SGD
+SGD S000006213 SUT2 GO:0006357 SGD_REF:S000060057|PMID:11248676 ISS P YPR009W gene taxon:4932 20021003 SGD
+SGD S000006213 SUT2 GO:0006357 SGD_REF:S000060057|PMID:11248676 IMP P YPR009W gene taxon:4932 20021003 SGD
+SGD S000006213 SUT2 GO:0015918 SGD_REF:S000060057|PMID:11248676 IMP P YPR009W gene taxon:4932 20021003 SGD
+SGD S000005950 SUV3 GO:0005739 SGD_REF:S000048020|PMID:8565066 IDA C YPL029W|LPB2 gene taxon:4932 20021001 SGD
+SGD S000005950 SUV3 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YPL029W|LPB2 gene taxon:4932 20040924 SGD
+SGD S000005950 SUV3 GO:0005759 SGD_REF:S000072589|PMID:12426313 IDA C YPL029W|LPB2 gene taxon:4932 20030225 SGD
+SGD S000005950 SUV3 GO:0004004 SGD_REF:S000072589|PMID:12426313 IDA F YPL029W|LPB2 gene taxon:4932 20030225 SGD
+SGD S000005950 SUV3 GO:0006401 SGD_REF:S000072589|PMID:12426313 IDA P YPL029W|LPB2 gene taxon:4932 20030225 SGD
+SGD S000005950 SUV3 GO:0006401 SGD_REF:S000072589|PMID:12426313 IMP P YPL029W|LPB2 gene taxon:4932 20030225 SGD
+SGD S000002754 SVF1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YDR346C|SGI1 gene taxon:4932 20031028 SGD
+SGD S000002754 SVF1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDR346C|SGI1 gene taxon:4932 20031028 SGD
+SGD S000002754 SVF1 GO:0005554 SGD_REF:S000069584 ND F YDR346C|SGI1 gene taxon:4932 20030609 SGD
+SGD S000002754 SVF1 GO:0006979 SGD_REF:S000082333|PMID:16034825 IMP P YDR346C|SGI1 gene taxon:4932 20050725 SGD
+SGD S000005953 SVL3 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YPL032C gene taxon:4932 20031028 SGD
+SGD S000005953 SVL3 GO:0005933 SGD_REF:S000074185|PMID:14562095 IDA C YPL032C gene taxon:4932 20031028 SGD
+SGD S000005953 SVL3 GO:0005935 SGD_REF:S000074185|PMID:14562095 IDA C YPL032C gene taxon:4932 20031028 SGD
+SGD S000005953 SVL3 GO:0005554 SGD_REF:S000069584 ND F YPL032C gene taxon:4932 20021211 SGD
+SGD S000005953 SVL3 GO:0006897 SGD_REF:S000043885|PMID:9751732 IMP P YPL032C gene taxon:4932 20010118 SGD
+SGD S000001224 SVP26 GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C integral membrane protein YHR181W gene taxon:4932 20031028 SGD
+SGD S000001224 SVP26 GO:0030173 SGD_REF:S000086147|PMID:16107716 IDA C integral membrane protein YHR181W gene taxon:4932 20050823 SGD
+SGD S000001224 SVP26 GO:0005515 SGD_REF:S000086147|PMID:16107716 IDA F integral membrane protein YHR181W gene taxon:4932 20050823 SGD
+SGD S000001224 SVP26 GO:0006496 SGD_REF:S000086147|PMID:16107716 IMP P integral membrane protein YHR181W gene taxon:4932 20050823 SGD
+SGD S000001224 SVP26 GO:0031505 SGD_REF:S000086147|PMID:16107716 IGI P integral membrane protein YHR181W gene taxon:4932 20050823 SGD
+SGD S000001224 SVP26 GO:0031505 SGD_REF:S000086147|PMID:16107716 IMP P integral membrane protein YHR181W gene taxon:4932 20050823 SGD
+SGD S000001224 SVP26 GO:0045053 SGD_REF:S000086147|PMID:16107716 IMP P integral membrane protein YHR181W gene taxon:4932 20050823 SGD
+SGD S000006084 SVS1 GO:0000324 SGD_REF:S000074185|PMID:14562095 IDA C YPL163C gene taxon:4932 20031028 SGD
+SGD S000006084 SVS1 GO:0009277 SGD_REF:S000075303|PMID:11935221 IDA C YPL163C gene taxon:4932 20040114 SGD
+SGD S000006084 SVS1 GO:0005554 SGD_REF:S000069584 ND F YPL163C gene taxon:4932 20021001 SGD
+SGD S000006084 SVS1 GO:0042221 SGD_REF:S000052842|PMID:7489911 IMP P YPL163C gene taxon:4932 20021001 SGD
+SGD S000002728 SWA2 GO:0005789 SGD_REF:S000065967|PMID:11553703 IDA C auxilin-like protein YDR320C|AUX1|BUD24 gene taxon:4932 20021001 SGD
+SGD S000002728 SWA2 GO:0005515 SGD_REF:S000074415|PMID:14997574 ISS F auxilin-like protein YDR320C|AUX1|BUD24 gene taxon:4932 20041012 SGD
+SGD S000002728 SWA2 GO:0007029 SGD_REF:S000065967|PMID:11553703 IMP P auxilin-like protein YDR320C|AUX1|BUD24 gene taxon:4932 20021001 SGD
+SGD S000000009 SWC3 GO:0000812 SGD_REF:S000074662|PMID:14645854 IPI C YAL011W|SWC1 gene taxon:4932 20040412 SGD
+SGD S000000009 SWC3 GO:0000812 SGD_REF:S000075430|PMID:14690608 IPI C YAL011W|SWC1 gene taxon:4932 20040412 SGD
+SGD S000000009 SWC3 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YAL011W|SWC1 gene taxon:4932 20031028 SGD
+SGD S000000009 SWC3 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YAL011W|SWC1 gene taxon:4932 20040928 SGD
+SGD S000000009 SWC3 GO:0005554 SGD_REF:S000069584 ND F YAL011W|SWC1 gene taxon:4932 20021119 SGD
+SGD S000000009 SWC3 GO:0006338 SGD_REF:S000074662|PMID:14645854 IDA P YAL011W|SWC1 gene taxon:4932 20040322 SGD
+SGD S000000009 SWC3 GO:0006338 SGD_REF:S000075430|PMID:14690608 IGI P YAL011W|SWC1 gene taxon:4932 20040323 SGD
+SGD S000000009 SWC3 GO:0006338 SGD_REF:S000075430|PMID:14690608 IPI P YAL011W|SWC1 gene taxon:4932 20040323 SGD
+SGD S000000009 SWC3 GO:0007029 SGD_REF:S000074251|PMID:12868057 IMP P YAL011W|SWC1 gene taxon:4932 20040329 SGD
+SGD S000003234 SWC4 GO:0000123 SGD_REF:S000073630|PMID:12672825 IPI C YGR002C|EAF2|GOD1 gene taxon:4932 20040105 SGD
+SGD S000003234 SWC4 GO:0000812 SGD_REF:S000074662|PMID:14645854 IPI C YGR002C|EAF2|GOD1 gene taxon:4932 20040412 SGD
+SGD S000003234 SWC4 GO:0000812 SGD_REF:S000075430|PMID:14690608 IPI C YGR002C|EAF2|GOD1 gene taxon:4932 20040412 SGD
+SGD S000003234 SWC4 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YGR002C|EAF2|GOD1 gene taxon:4932 20031028 SGD
+SGD S000003234 SWC4 GO:0005634 SGD_REF:S000075214|PMID:14690591 IDA C YGR002C|EAF2|GOD1 gene taxon:4932 20031231 SGD
+SGD S000003234 SWC4 GO:0043189 SGD_REF:S000079775|PMID:15485911 IPI C YGR002C|EAF2|GOD1 gene taxon:4932 20050207 SGD
+SGD S000003234 SWC4 GO:0043189 SGD_REF:S000077129|PMID:15353583 IPI C YGR002C|EAF2|GOD1 gene taxon:4932 20050207 SGD
+SGD S000003234 SWC4 GO:0003677 SGD_REF:S000075214|PMID:14690591 ISS F YGR002C|EAF2|GOD1 gene taxon:4932 20031231 SGD
+SGD S000003234 SWC4 GO:0006338 SGD_REF:S000074662|PMID:14645854 IDA P YGR002C|EAF2|GOD1 gene taxon:4932 20040322 SGD
+SGD S000003234 SWC4 GO:0006338 SGD_REF:S000075430|PMID:14690608 IPI P YGR002C|EAF2|GOD1 gene taxon:4932 20040323 SGD
+SGD S000003234 SWC4 GO:0016568 SGD_REF:S000073630|PMID:12672825 IPI P YGR002C|EAF2|GOD1 gene taxon:4932 20040105 SGD
+SGD S000003234 SWC4 GO:0016573 SGD_REF:S000075214|PMID:14690591 IPI SGD:S000005770 P YGR002C|EAF2|GOD1 gene taxon:4932 20031231 SGD
+SGD S000000435 SWC5 GO:0000812 SGD_REF:S000074662|PMID:14645854 IPI C YBR231C|AOR1 gene taxon:4932 20040412 SGD
+SGD S000000435 SWC5 GO:0000812 SGD_REF:S000075430|PMID:14690608 IPI C YBR231C|AOR1 gene taxon:4932 20040412 SGD
+SGD S000000435 SWC5 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YBR231C|AOR1 gene taxon:4932 20031028 SGD
+SGD S000000435 SWC5 GO:0005554 SGD_REF:S000069584 ND F YBR231C|AOR1 gene taxon:4932 20021209 SGD
+SGD S000000435 SWC5 GO:0006338 SGD_REF:S000074662|PMID:14645854 IDA P YBR231C|AOR1 gene taxon:4932 20040322 SGD
+SGD S000000435 SWC5 GO:0006338 SGD_REF:S000075430|PMID:14690608 IGI P YBR231C|AOR1 gene taxon:4932 20040323 SGD
+SGD S000000435 SWC5 GO:0006338 SGD_REF:S000075430|PMID:14690608 IPI P YBR231C|AOR1 gene taxon:4932 20040323 SGD
+SGD S000004377 SWC7 GO:0000812 SGD_REF:S000075430|PMID:14690608 IPI C YLR385C|AWS1 gene taxon:4932 20040412 SGD
+SGD S000004377 SWC7 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YLR385C|AWS1 gene taxon:4932 20031028 SGD
+SGD S000004377 SWC7 GO:0005554 SGD_REF:S000069584 ND F YLR385C|AWS1 gene taxon:4932 20021126 SGD
+SGD S000004377 SWC7 GO:0006338 SGD_REF:S000075430|PMID:14690608 IPI P YLR385C|AWS1 gene taxon:4932 20040322 SGD
+SGD S000000064 SWD1 GO:0048188 SGD_REF:S000066156|PMID:11687631 IPI SGD:S000000379|SGD:S000002877|SGD:S000001161|SGD:S000004005|SGD:S000006059|SGD:S000001501 C compass (complex proteins associated with Set1p) component YAR003W|CPS50|FUN16|SAF49 gene taxon:4932 20050524 SGD
+SGD S000000064 SWD1 GO:0048188 SGD_REF:S000068991|PMID:11752412 IPI SGD:S000000379|SGD:S000002877|SGD:S000001501|SGD:S000006059|SGD:S000004005|SGD:S000001161 C compass (complex proteins associated with Set1p) component YAR003W|CPS50|FUN16|SAF49 gene taxon:4932 20050524 SGD
+SGD S000000064 SWD1 GO:0048188 SGD_REF:S000068755|PMID:11742990 IPI SGD:S000000379|SGD:S000000462|SGD:S000006059|SGD:S000004005|SGD:S000001501|SGD:S000001161|SGD:S000002877 C compass (complex proteins associated with Set1p) component YAR003W|CPS50|FUN16|SAF49 gene taxon:4932 20050524 SGD
+SGD S000000064 SWD1 contributes_to GO:0042800 SGD_REF:S000068991|PMID:11752412 IMP F compass (complex proteins associated with Set1p) component YAR003W|CPS50|FUN16|SAF49 gene taxon:4932 20050524 SGD
+SGD S000000064 SWD1 contributes_to GO:0042800 SGD_REF:S000068755|PMID:11742990 IDA F compass (complex proteins associated with Set1p) component YAR003W|CPS50|FUN16|SAF49 gene taxon:4932 20050525 SGD
+SGD S000000064 SWD1 contributes_to GO:0042800 SGD_REF:S000069538|PMID:11805083 IDA F compass (complex proteins associated with Set1p) component YAR003W|CPS50|FUN16|SAF49 gene taxon:4932 20050525 SGD
+SGD S000000064 SWD1 contributes_to GO:0042800 SGD_REF:S000069538|PMID:11805083 IMP F compass (complex proteins associated with Set1p) component YAR003W|CPS50|FUN16|SAF49 gene taxon:4932 20050525 SGD
+SGD S000000064 SWD1 GO:0000723 SGD_REF:S000068755|PMID:11742990 IMP P compass (complex proteins associated with Set1p) component YAR003W|CPS50|FUN16|SAF49 gene taxon:4932 20050525 SGD
+SGD S000000064 SWD1 GO:0006348 SGD_REF:S000066156|PMID:11687631 IMP P compass (complex proteins associated with Set1p) component YAR003W|CPS50|FUN16|SAF49 gene taxon:4932 20020212 SGD
+SGD S000000064 SWD1 GO:0006348 SGD_REF:S000069538|PMID:11805083 IMP P compass (complex proteins associated with Set1p) component YAR003W|CPS50|FUN16|SAF49 gene taxon:4932 20050525 SGD
+SGD S000000064 SWD1 GO:0006348 SGD_REF:S000068991|PMID:11752412 IMP P compass (complex proteins associated with Set1p) component YAR003W|CPS50|FUN16|SAF49 gene taxon:4932 20050524 SGD
+SGD S000000064 SWD1 GO:0006355 SGD_REF:S000066156|PMID:11687631 IMP P compass (complex proteins associated with Set1p) component YAR003W|CPS50|FUN16|SAF49 gene taxon:4932 20050524 SGD
+SGD S000000064 SWD1 GO:0016571 SGD_REF:S000068755|PMID:11742990 IDA P compass (complex proteins associated with Set1p) component YAR003W|CPS50|FUN16|SAF49 gene taxon:4932 20020212 SGD
+SGD S000000064 SWD1 GO:0016571 SGD_REF:S000068991|PMID:11752412 IDA P compass (complex proteins associated with Set1p) component YAR003W|CPS50|FUN16|SAF49 gene taxon:4932 20050524 SGD
+SGD S000000064 SWD1 GO:0016571 SGD_REF:S000069538|PMID:11805083 IDA P compass (complex proteins associated with Set1p) component YAR003W|CPS50|FUN16|SAF49 gene taxon:4932 20050525 SGD
+SGD S000000064 SWD1 GO:0016571 SGD_REF:S000069538|PMID:11805083 IMP P compass (complex proteins associated with Set1p) component YAR003W|CPS50|FUN16|SAF49 gene taxon:4932 20050525 SGD
+SGD S000000064 SWD1 GO:0016571 SGD_REF:S000068991|PMID:11752412 IMP P compass (complex proteins associated with Set1p) component YAR003W|CPS50|FUN16|SAF49 gene taxon:4932 20050524 SGD
+SGD S000001501 SWD2 GO:0005847 SGD_REF:S000074089|PMID:12819204 IPI C compass (complex proteins associated with Set1p) component YKL018W|CPS35|SAF37 gene taxon:4932 20031013 SGD
+SGD S000001501 SWD2 GO:0048188 SGD_REF:S000066156|PMID:11687631 IPI SGD:S000000064|SGD:S000000379|SGD:S000002877|SGD:S000006059|SGD:S000004005|SGD:S000001161 C compass (complex proteins associated with Set1p) component YKL018W|CPS35|SAF37 gene taxon:4932 20050524 SGD
+SGD S000001501 SWD2 GO:0048188 SGD_REF:S000068991|PMID:11752412 IPI SGD:S000000064|SGD:S000000379|SGD:S000006059|SGD:S000004005|SGD:S000001161|SGD:S000002877 C compass (complex proteins associated with Set1p) component YKL018W|CPS35|SAF37 gene taxon:4932 20050524 SGD
+SGD S000001501 SWD2 GO:0048188 SGD_REF:S000068755|PMID:11742990 IPI SGD:S000000064|SGD:S000000379|SGD:S000006059|SGD:S000004005|SGD:S000001161|SGD:S000002877|SGD:S000000462 C compass (complex proteins associated with Set1p) component YKL018W|CPS35|SAF37 gene taxon:4932 20050524 SGD
+SGD S000001501 SWD2 contributes_to GO:0042800 SGD_REF:S000069538|PMID:11805083 IDA F compass (complex proteins associated with Set1p) component YKL018W|CPS35|SAF37 gene taxon:4932 20050525 SGD
+SGD S000001501 SWD2 contributes_to GO:0042800 SGD_REF:S000068755|PMID:11742990 IDA F compass (complex proteins associated with Set1p) component YKL018W|CPS35|SAF37 gene taxon:4932 20050525 SGD
+SGD S000001501 SWD2 GO:0000723 SGD_REF:S000058995|PMID:15146080 IMP P compass (complex proteins associated with Set1p) component YKL018W|CPS35|SAF37 gene taxon:4932 20050826 SGD
+SGD S000001501 SWD2 GO:0016571 SGD_REF:S000068755|PMID:11742990 IDA P compass (complex proteins associated with Set1p) component YKL018W|CPS35|SAF37 gene taxon:4932 20020212 SGD
+SGD S000001501 SWD2 GO:0016571 SGD_REF:S000069538|PMID:11805083 IDA P compass (complex proteins associated with Set1p) component YKL018W|CPS35|SAF37 gene taxon:4932 20050525 SGD
+SGD S000001501 SWD2 GO:0016571 SGD_REF:S000068991|PMID:11752412 IDA P compass (complex proteins associated with Set1p) component YKL018W|CPS35|SAF37 gene taxon:4932 20050524 SGD
+SGD S000001501 SWD2 GO:0030846 SGD_REF:S000074089|PMID:12819204 IPI P compass (complex proteins associated with Set1p) component YKL018W|CPS35|SAF37 gene taxon:4932 20031013 SGD
+SGD S000001501 SWD2 GO:0030847 SGD_REF:S000074089|PMID:12819204 IPI P compass (complex proteins associated with Set1p) component YKL018W|CPS35|SAF37 gene taxon:4932 20031013 SGD
+SGD S000001501 SWD2 GO:0031124 SGD_REF:S000058995|PMID:15146080 IMP P compass (complex proteins associated with Set1p) component YKL018W|CPS35|SAF37 gene taxon:4932 20050826 SGD
+SGD S000001501 SWD2 GO:0031126 SGD_REF:S000058995|PMID:15146080 IMP P compass (complex proteins associated with Set1p) component YKL018W|CPS35|SAF37 gene taxon:4932 20050826 SGD
+SGD S000000379 SWD3 GO:0048188 SGD_REF:S000066156|PMID:11687631 IPI SGD:S000000064|SGD:S000001501|SGD:S000006059|SGD:S000004005|SGD:S000001161|SGD:S000002877 C compass (complex proteins associated with Set1p) component YBR175W|CPS30|SAF35 gene taxon:4932 20050524 SGD
+SGD S000000379 SWD3 GO:0048188 SGD_REF:S000068991|PMID:11752412 IPI SGD:S000000064|SGD:S000001161|SGD:S000002877|SGD:S000006059|SGD:S000004005|SGD:S000001501 C compass (complex proteins associated with Set1p) component YBR175W|CPS30|SAF35 gene taxon:4932 20050524 SGD
+SGD S000000379 SWD3 GO:0048188 SGD_REF:S000068755|PMID:11742990 IPI SGD:S000000064|SGD:S000002877|SGD:S000001161|SGD:S000000462|SGD:S000001501|SGD:S000006059|SGD:S000004005 C compass (complex proteins associated with Set1p) component YBR175W|CPS30|SAF35 gene taxon:4932 20050524 SGD
+SGD S000000379 SWD3 contributes_to GO:0042800 SGD_REF:S000068991|PMID:11752412 IMP F compass (complex proteins associated with Set1p) component YBR175W|CPS30|SAF35 gene taxon:4932 20050524 SGD
+SGD S000000379 SWD3 contributes_to GO:0042800 SGD_REF:S000068755|PMID:11742990 IDA F compass (complex proteins associated with Set1p) component YBR175W|CPS30|SAF35 gene taxon:4932 20050525 SGD
+SGD S000000379 SWD3 contributes_to GO:0042800 SGD_REF:S000069538|PMID:11805083 IDA F compass (complex proteins associated with Set1p) component YBR175W|CPS30|SAF35 gene taxon:4932 20050525 SGD
+SGD S000000379 SWD3 contributes_to GO:0042800 SGD_REF:S000069538|PMID:11805083 IMP F compass (complex proteins associated with Set1p) component YBR175W|CPS30|SAF35 gene taxon:4932 20050525 SGD
+SGD S000000379 SWD3 GO:0000723 SGD_REF:S000068755|PMID:11742990 IMP P compass (complex proteins associated with Set1p) component YBR175W|CPS30|SAF35 gene taxon:4932 20050525 SGD
+SGD S000000379 SWD3 GO:0006348 SGD_REF:S000066156|PMID:11687631 IMP P compass (complex proteins associated with Set1p) component YBR175W|CPS30|SAF35 gene taxon:4932 20020212 SGD
+SGD S000000379 SWD3 GO:0006348 SGD_REF:S000069538|PMID:11805083 IMP P compass (complex proteins associated with Set1p) component YBR175W|CPS30|SAF35 gene taxon:4932 20050525 SGD
+SGD S000000379 SWD3 GO:0006348 SGD_REF:S000068991|PMID:11752412 IMP P compass (complex proteins associated with Set1p) component YBR175W|CPS30|SAF35 gene taxon:4932 20050524 SGD
+SGD S000000379 SWD3 GO:0016571 SGD_REF:S000068755|PMID:11742990 IDA P compass (complex proteins associated with Set1p) component YBR175W|CPS30|SAF35 gene taxon:4932 20020212 SGD
+SGD S000000379 SWD3 GO:0016571 SGD_REF:S000069538|PMID:11805083 IDA P compass (complex proteins associated with Set1p) component YBR175W|CPS30|SAF35 gene taxon:4932 20050525 SGD
+SGD S000000379 SWD3 GO:0016571 SGD_REF:S000069538|PMID:11805083 IMP P compass (complex proteins associated with Set1p) component YBR175W|CPS30|SAF35 gene taxon:4932 20050525 SGD
+SGD S000000379 SWD3 GO:0016571 SGD_REF:S000068991|PMID:11752412 IMP P compass (complex proteins associated with Set1p) component YBR175W|CPS30|SAF35 gene taxon:4932 20050524 SGD
+SGD S000000379 SWD3 GO:0016571 SGD_REF:S000068991|PMID:11752412 IDA P compass (complex proteins associated with Set1p) component YBR175W|CPS30|SAF35 gene taxon:4932 20050524 SGD
+SGD S000003723 SWE1 GO:0005634 SGD_REF:S000043338|PMID:10805747 IDA C tyrosine kinase YJL187C|WEE1 gene taxon:4932 20020128 SGD
+SGD S000003723 SWE1 GO:0005634 SGD_REF:S000077144|PMID:15282802 IDA C tyrosine kinase YJL187C|WEE1 gene taxon:4932 20041008 SGD
+SGD S000003723 SWE1 GO:0005935 SGD_REF:S000043338|PMID:10805747 IDA C tyrosine kinase YJL187C|WEE1 gene taxon:4932 20020128 SGD
+SGD S000003723 SWE1 GO:0005935 SGD_REF:S000077144|PMID:15282802 IDA C tyrosine kinase YJL187C|WEE1 gene taxon:4932 20041008 SGD
+SGD S000003723 SWE1 GO:0004672 SGD_REF:S000042140|PMID:8253069 IDA F tyrosine kinase YJL187C|WEE1 gene taxon:4932 20030827 SGD
+SGD S000003723 SWE1 GO:0000078 SGD_REF:S000056303|PMID:8930890 IDA P tyrosine kinase YJL187C|WEE1 gene taxon:4932 20020128 SGD
+SGD S000003723 SWE1 GO:0000078 SGD_REF:S000046113|PMID:9744879 IEP P tyrosine kinase YJL187C|WEE1 gene taxon:4932 20060331 SGD
+SGD S000003723 SWE1 GO:0000078 SGD_REF:S000046113|PMID:9744879 IMP P tyrosine kinase YJL187C|WEE1 gene taxon:4932 20060331 SGD
+SGD S000003723 SWE1 GO:0000079 SGD_REF:S000042140|PMID:8253069 IDA P tyrosine kinase YJL187C|WEE1 gene taxon:4932 20020128 SGD
+SGD S000003723 SWE1 GO:0000086 SGD_REF:S000042140|PMID:8253069 IMP P tyrosine kinase YJL187C|WEE1 gene taxon:4932 20020320 SGD
+SGD S000003723 SWE1 GO:0000086 SGD_REF:S000042140|PMID:8253069 IDA P tyrosine kinase YJL187C|WEE1 gene taxon:4932 20020320 SGD
+SGD S000003723 SWE1 GO:0000086 SGD_REF:S000042140|PMID:8253069 ISS P tyrosine kinase YJL187C|WEE1 gene taxon:4932 20020320 SGD
+SGD S000003723 SWE1 NOT GO:0031569 SGD_REF:S000113890|PMID:16360682 IMP P tyrosine kinase YJL187C|WEE1 gene taxon:4932 20060327 SGD
+SGD S000003723 SWE1 NOT GO:0031569 SGD_REF:S000113890|PMID:16360682 IEP P tyrosine kinase YJL187C|WEE1 gene taxon:4932 20060327 SGD
+SGD S000003723 SWE1 GO:0040020 SGD_REF:S000055580|PMID:10619027 IGI P tyrosine kinase YJL187C|WEE1 gene taxon:4932 20020618 SGD
+SGD S000003723 SWE1 GO:0040020 SGD_REF:S000055580|PMID:10619027 IMP P tyrosine kinase YJL187C|WEE1 gene taxon:4932 20020618 SGD
+SGD S000003723 SWE1 GO:0040020 SGD_REF:S000055580|PMID:10619027 IEP P tyrosine kinase YJL187C|WEE1 gene taxon:4932 20020618 SGD
+SGD S000002533 SWF1 GO:0016021 SGD_REF:S000042150|PMID:10490616 ISS C YDR126W|PSL10 gene taxon:4932 20021125 SGD
+SGD S000002533 SWF1 GO:0042175 SGD_REF:S000082414|PMID:15973437 IDA C YDR126W|PSL10 gene taxon:4932 20051017 SGD
+SGD S000002533 SWF1 GO:0019706 SGD_REF:S000082414|PMID:15973437 IMP F YDR126W|PSL10 gene taxon:4932 20051017 SGD
+SGD S000002533 SWF1 GO:0019706 SGD_REF:S000082414|PMID:15973437 ISS F YDR126W|PSL10 gene taxon:4932 20051017 SGD
+SGD S000002533 SWF1 GO:0018318 SGD_REF:S000082414|PMID:15973437 IMP P YDR126W|PSL10 gene taxon:4932 20051017 SGD
+SGD S000002533 SWF1 GO:0030476 SGD_REF:S000072583|PMID:12586695 IMP P YDR126W|PSL10 gene taxon:4932 20050510 SGD
+SGD S000002533 SWF1 GO:0042144 SGD_REF:S000086830|PMID:16186255 IGI P YDR126W|PSL10 gene taxon:4932 20051017 SGD
+SGD S000000081 SWH1 GO:0000138 SGD_REF:S000060812|PMID:11408574 IDA C YAR042W|OSH1|YAR044W gene taxon:4932 20041123 SGD
+SGD S000000081 SWH1 GO:0005769 SGD_REF:S000060812|PMID:11408574 IDA C YAR042W|OSH1|YAR044W gene taxon:4932 20041123 SGD
+SGD S000000081 SWH1 GO:0005783 SGD_REF:S000073325|PMID:12727870 IDA C YAR042W|OSH1|YAR044W gene taxon:4932 20041123 SGD
+SGD S000000081 SWH1 GO:0005545 SGD_REF:S000059993|PMID:11238399 ISS F YAR042W|OSH1|YAR044W gene taxon:4932 20041123 SGD
+SGD S000000081 SWH1 GO:0005545 SGD_REF:S000071353|PMID:9651677 IDA F YAR042W|OSH1|YAR044W gene taxon:4932 20041123 SGD
+SGD S000000081 SWH1 GO:0006694 SGD_REF:S000059993|PMID:11238399 IGI P YAR042W|OSH1|YAR044W gene taxon:4932 20041123 SGD
+SGD S000000081 SWH1 GO:0006694 SGD_REF:S000059993|PMID:11238399 IMP P YAR042W|OSH1|YAR044W gene taxon:4932 20041123 SGD
+SGD S000005937 SWI1 GO:0016514 SGD_REF:S000043500|PMID:9726966 TAS C zinc finger transcription factor YPL016W|ADR6|GAM3|LPA1 gene taxon:4932 20030513 SGD
+SGD S000005937 SWI1 GO:0016585 SGD_REF:S000058455|PMID:9048886 TAS C zinc finger transcription factor YPL016W|ADR6|GAM3|LPA1 gene taxon:4932 20010118 SGD
+SGD S000005937 SWI1 GO:0016251 SGD_REF:S000058455|PMID:9048886 TAS F zinc finger transcription factor YPL016W|ADR6|GAM3|LPA1 gene taxon:4932 20020528 SGD
+SGD S000005937 SWI1 GO:0006338 SGD_REF:S000058455|PMID:9048886 TAS P zinc finger transcription factor YPL016W|ADR6|GAM3|LPA1 gene taxon:4932 20010118 SGD
+SGD S000003712 SWI3 GO:0016514 SGD_REF:S000043500|PMID:9726966 TAS C transcription factor YJL176C|TYE2 gene taxon:4932 20030513 SGD
+SGD S000003712 SWI3 GO:0016585 SGD_REF:S000058455|PMID:9048886 TAS C transcription factor YJL176C|TYE2 gene taxon:4932 20010118 SGD
+SGD S000003712 SWI3 GO:0016251 SGD_REF:S000058455|PMID:9048886 TAS F transcription factor YJL176C|TYE2 gene taxon:4932 20020528 SGD
+SGD S000003712 SWI3 GO:0006338 SGD_REF:S000058455|PMID:9048886 TAS P transcription factor YJL176C|TYE2 gene taxon:4932 20010118 SGD
+SGD S000000913 SWI4 GO:0005634 SGD_REF:S000042146|PMID:10490612 IDA C transcription factor YER111C|ART1 gene taxon:4932 20020215 SGD
+SGD S000000913 SWI4 GO:0003677 SGD_REF:S000040007|PMID:2649246 IDA F transcription factor YER111C|ART1 gene taxon:4932 20060516 SGD
+SGD S000000913 SWI4 GO:0003700 SGD_REF:S000048261|PMID:3542227 IMP F transcription factor YER111C|ART1 gene taxon:4932 20060516 SGD
+SGD S000000913 SWI4 GO:0003700 SGD_REF:S000040007|PMID:2649246 IPI F transcription factor YER111C|ART1 gene taxon:4932 20060516 SGD
+SGD S000000913 SWI4 GO:0000082 SGD_REF:S000072514|PMID:12518319 IGI P transcription factor YER111C|ART1 gene taxon:4932 20030217 SGD
+SGD S000000913 SWI4 GO:0006350 SGD_REF:S000048261|PMID:3542227 IMP P transcription factor YER111C|ART1 gene taxon:4932 20060516 SGD
+SGD S000002553 SWI5 GO:0005634 SGD_REF:S000051979|PMID:8816483 IDA C transcriptional activator YDR146C gene taxon:4932 20020709 SGD
+SGD S000002553 SWI5 GO:0005737 SGD_REF:S000051979|PMID:8816483 IDA C transcriptional activator YDR146C gene taxon:4932 20020709 SGD
+SGD S000002553 SWI5 GO:0016563 SGD_REF:S000044727|PMID:10409653 IDA F transcriptional activator YDR146C gene taxon:4932 20010926 SGD
+SGD S000002553 SWI5 GO:0000114 SGD_REF:S000044727|PMID:10409653 IDA P transcriptional activator YDR146C gene taxon:4932 20010118 SGD
+SGD S000004172 SWI6 GO:0005634 SGD_REF:S000053728|PMID:8590795 IDA C transcription factor YLR182W|PSL8|SDS11 gene taxon:4932 20021007 SGD
+SGD S000004172 SWI6 GO:0005634 SGD_REF:S000073233|PMID:12697814 IDA C transcription factor YLR182W|PSL8|SDS11 gene taxon:4932 20030618 SGD
+SGD S000004172 SWI6 GO:0005737 SGD_REF:S000053728|PMID:8590795 IDA C transcription factor YLR182W|PSL8|SDS11 gene taxon:4932 20021007 SGD
+SGD S000004172 SWI6 GO:0005737 SGD_REF:S000073233|PMID:12697814 IDA C transcription factor YLR182W|PSL8|SDS11 gene taxon:4932 20030618 SGD
+SGD S000004172 SWI6 GO:0003713 SGD_REF:S000047316|PMID:8423776 TAS F transcription factor YLR182W|PSL8|SDS11 gene taxon:4932 20030311 SGD
+SGD S000004172 SWI6 GO:0005515 SGD_REF:S000073233|PMID:12697814 IPI SGD:S000002743 F transcription factor YLR182W|PSL8|SDS11 gene taxon:4932 20030618 SGD
+SGD S000004172 SWI6 GO:0000083 SGD_REF:S000041257|PMID:9628912 TAS P transcription factor YLR182W|PSL8|SDS11 gene taxon:4932 20021007 SGD
+SGD S000004172 SWI6 GO:0006350 SGD_REF:S000041257|PMID:9628912 TAS P transcription factor YLR182W|PSL8|SDS11 gene taxon:4932 20021007 SGD
+SGD S000004172 SWI6 GO:0007126 SGD_REF:S000041257|PMID:9628912 IGI P transcription factor YLR182W|PSL8|SDS11 gene taxon:4932 20021007 SGD
+SGD S000004172 SWI6 GO:0007126 SGD_REF:S000041257|PMID:9628912 IMP P transcription factor YLR182W|PSL8|SDS11 gene taxon:4932 20021007 SGD
+SGD S000002668 SWM1 GO:0005634 SGD_REF:S000053651|PMID:10022899 IDA C YDR260C gene taxon:4932 20021001 SGD
+SGD S000002668 SWM1 GO:0005680 SGD_REF:S000072817|PMID:12574115 IDA C YDR260C gene taxon:4932 20030402 SGD
+SGD S000002668 SWM1 GO:0005554 SGD_REF:S000069584 ND F YDR260C gene taxon:4932 20021001 SGD
+SGD S000002668 SWM1 GO:0016567 SGD_REF:S000073158|PMID:12609981 IPI P YDR260C gene taxon:4932 20050407 SGD
+SGD S000002668 SWM1 GO:0030071 SGD_REF:S000073158|PMID:12609981 IMP P YDR260C gene taxon:4932 20030611 SGD
+SGD S000002668 SWM1 GO:0030476 SGD_REF:S000053651|PMID:10022899 IMP P YDR260C gene taxon:4932 20021001 SGD
+SGD S000002668 SWM1 GO:0031145 SGD_REF:S000073158|PMID:12609981 IPI P YDR260C gene taxon:4932 20050407 SGD
+SGD S000004757 SWP1 GO:0008250 SGD_REF:S000050823|PMID:10358084 IPI C oligosaccharyl transferase glycoprotein complex, delta subunit YMR149W gene taxon:4932 20020328 SGD
+SGD S000004757 SWP1 GO:0008250 SGD_REF:S000050479|PMID:9405463 IPI C oligosaccharyl transferase glycoprotein complex, delta subunit YMR149W gene taxon:4932 20050504 SGD
+SGD S000004757 SWP1 GO:0008250 SGD_REF:S000113605|PMID:16297388 IPI C oligosaccharyl transferase glycoprotein complex, delta subunit YMR149W gene taxon:4932 20060203 SGD
+SGD S000004757 SWP1 GO:0004579 SGD_REF:S000050479|PMID:9405463 IPI F oligosaccharyl transferase glycoprotein complex, delta subunit YMR149W gene taxon:4932 20021001 SGD
+SGD S000004757 SWP1 GO:0006487 SGD_REF:S000050479|PMID:9405463 IPI P oligosaccharyl transferase glycoprotein complex, delta subunit YMR149W gene taxon:4932 20021001 SGD
+SGD S000001845 SWP82 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YFL049W gene taxon:4932 20031028 SGD
+SGD S000001845 SWP82 GO:0016514 SGD_REF:S000086800|PMID:16204215 IPI SGD:S000003712|SGD:S000005306 C YFL049W gene taxon:4932 20060213 SGD
+SGD S000001845 SWP82 GO:0016563 SGD_REF:S000114441|PMID:16464826 IPI SGD:S000000493|SGD:S000005816|SGD:S000003507 F YFL049W gene taxon:4932 20060324 SGD
+SGD S000001845 SWP82 GO:0006338 SGD_REF:S000072677|PMID:12524530 IC GO:0016514 P YFL049W gene taxon:4932 20060324 SGD
+SGD S000001845 SWP82 GO:0030433 SGD_REF:S000115312|PMID:12711700 IMP P YFL049W gene taxon:4932 20060511 SGD
+SGD S000001845 SWP82 GO:0045449 SGD_REF:S000086800|PMID:16204215 IC GO:0016514 P YFL049W gene taxon:4932 20060213 SGD
+SGD S000002742 SWR1 GO:0000812 SGD_REF:S000074662|PMID:14645854 IPI C YDR334W gene taxon:4932 20040412 SGD
+SGD S000002742 SWR1 GO:0000812 SGD_REF:S000075430|PMID:14690608 IPI C YDR334W gene taxon:4932 20040412 SGD
+SGD S000002742 SWR1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YDR334W gene taxon:4932 20031028 SGD
+SGD S000002742 SWR1 GO:0004386 SGD_REF:S000039134|PMID:10077188 ISS F YDR334W gene taxon:4932 20030407 SGD
+SGD S000002742 SWR1 GO:0006338 SGD_REF:S000074662|PMID:14645854 IDA P YDR334W gene taxon:4932 20040322 SGD
+SGD S000002742 SWR1 GO:0006338 SGD_REF:S000075430|PMID:14690608 IGI P YDR334W gene taxon:4932 20040323 SGD
+SGD S000002742 SWR1 GO:0006338 SGD_REF:S000075430|PMID:14690608 IPI P YDR334W gene taxon:4932 20040323 SGD
+SGD S000005025 SWS2 GO:0005737 SGD_REF:S000050617|PMID:10649453 IDA C YNL081C gene taxon:4932 20030130 SGD
+SGD S000005025 SWS2 GO:0005739 SGD_REF:S000050617|PMID:10649453 ISS C YNL081C gene taxon:4932 20030206 SGD
+SGD S000005025 SWS2 GO:0005763 SGD_REF:S000071753|PMID:12392552 ISS C YNL081C gene taxon:4932 20040203 SGD
+SGD S000005025 SWS2 GO:0003735 SGD_REF:S000071753|PMID:12392552 ISS F YNL081C gene taxon:4932 20040203 SGD
+SGD S000005025 SWS2 GO:0043037 SGD_REF:S000071753|PMID:12392552 ISS P YNL081C gene taxon:4932 20040203 SGD
+SGD S000002803 SXM1 GO:0005634 SGD_REF:S000052126|PMID:9238021 IDA C karyopherin beta family member YDR395W|KAP108 gene taxon:4932 20020624 SGD
+SGD S000002803 SXM1 GO:0008320 SGD_REF:S000052126|PMID:9238021 IGI F karyopherin beta family member YDR395W|KAP108 gene taxon:4932 20020624 SGD
+SGD S000002803 SXM1 GO:0008320 SGD_REF:S000052126|PMID:9238021 ISS F karyopherin beta family member YDR395W|KAP108 gene taxon:4932 20020624 SGD
+SGD S000002803 SXM1 GO:0006406 SGD_REF:S000052126|PMID:9238021 IGI P karyopherin beta family member YDR395W|KAP108 gene taxon:4932 20020624 SGD
+SGD S000002803 SXM1 GO:0006913 SGD_REF:S000052126|PMID:9238021 IGI P karyopherin beta family member YDR395W|KAP108 gene taxon:4932 20020624 SGD
+SGD S000005705 SYC1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YOR179C gene taxon:4932 20031028 SGD
+SGD S000005705 SYC1 GO:0005847 SGD_REF:S000074089|PMID:12819204 IPI C YOR179C gene taxon:4932 20031013 SGD
+SGD S000005705 SYC1 contributes_to GO:0003723 SGD_REF:S000074089|PMID:12819204 IC GO:0005847 F YOR179C gene taxon:4932 20050222 SGD
+SGD S000005705 SYC1 GO:0030846 SGD_REF:S000074089|PMID:12819204 IPI P YOR179C gene taxon:4932 20031013 SGD
+SGD S000005705 SYC1 GO:0030847 SGD_REF:S000074089|PMID:12819204 IPI P YOR179C gene taxon:4932 20031013 SGD
+SGD S000002824 SYF1 GO:0005681 SGD_REF:S000070110|PMID:12088152 IDA C YDR416W|NTC90 gene taxon:4932 20020905 SGD
+SGD S000002824 SYF1 GO:0005554 SGD_REF:S000069584 ND F YDR416W|NTC90 gene taxon:4932 20020905 SGD
+SGD S000002824 SYF1 GO:0000398 SGD_REF:S000070110|PMID:12088152 IPI P YDR416W|NTC90 gene taxon:4932 20020905 SGD
+SGD S000002824 SYF1 GO:0000398 SGD_REF:S000059451|PMID:11102353 TAS P YDR416W|NTC90 gene taxon:4932 20010209 SGD
+SGD S000002824 SYF1 GO:0007049 SGD_REF:S000059451|PMID:11102353 TAS P YDR416W|NTC90 gene taxon:4932 20010209 SGD
+SGD S000003361 SYF2 GO:0005681 SGD_REF:S000070110|PMID:12088152 IDA C YGR129W|NTC31 gene taxon:4932 20021008 SGD
+SGD S000003361 SYF2 GO:0031202 SGD_REF:S000071476|PMID:12384582 IMP F YGR129W|NTC31 gene taxon:4932 20030128 SGD
+SGD S000003361 SYF2 GO:0000398 SGD_REF:S000059451|PMID:11102353 TAS P YGR129W|NTC31 gene taxon:4932 20010209 SGD
+SGD S000003361 SYF2 GO:0007049 SGD_REF:S000059451|PMID:11102353 TAS P YGR129W|NTC31 gene taxon:4932 20010209 SGD
+SGD S000001309 SYG1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C plasma membrane protein YIL047C gene taxon:4932 20040928 SGD
+SGD S000001309 SYG1 GO:0005886 SGD_REF:S000048600|PMID:7592711 IDA C plasma membrane protein YIL047C gene taxon:4932 20010118 SGD
+SGD S000001309 SYG1 GO:0005554 SGD_REF:S000069584 ND F plasma membrane protein YIL047C gene taxon:4932 20010119 SGD
+SGD S000001309 SYG1 GO:0007165 SGD_REF:S000048600|PMID:7592711 IMP P plasma membrane protein YIL047C gene taxon:4932 20010118 SGD
+SGD S000004241 SYM1 GO:0005743 SGD_REF:S000059075|PMID:15189984 IDA C YLR251W gene taxon:4932 20040706 SGD
+SGD S000004241 SYM1 GO:0005554 SGD_REF:S000069584 ND F YLR251W gene taxon:4932 20021125 SGD
+SGD S000004241 SYM1 GO:0006067 SGD_REF:S000059075|PMID:15189984 IMP P YLR251W gene taxon:4932 20040706 SGD
+SGD S000000012 SYN8 GO:0005768 SGD_REF:S000073333|PMID:12453154 TAS C syntaxin family YAL014C|SLT2|UIP2 gene taxon:4932 20030630 SGD
+SGD S000000012 SYN8 GO:0005484 SGD_REF:S000073333|PMID:12453154 IDA F syntaxin family YAL014C|SLT2|UIP2 gene taxon:4932 20030630 SGD
+SGD S000000012 SYN8 GO:0006810 SGD_REF:S000073333|PMID:12453154 IMP P syntaxin family YAL014C|SLT2|UIP2 gene taxon:4932 20030630 SGD
+SGD S000000012 SYN8 GO:0006810 SGD_REF:S000073333|PMID:12453154 IPI SGD:S000004810|SGD:S000005562 P syntaxin family YAL014C|SLT2|UIP2 gene taxon:4932 20030630 SGD
+SGD S000000626 SYP1 GO:0001400 SGD_REF:S000059326|PMID:11014808 IDA C YCR030C|YCR029C-A gene taxon:4932 20050124 SGD
+SGD S000000626 SYP1 GO:0005934 SGD_REF:S000059326|PMID:11014808 IDA C YCR030C|YCR029C-A gene taxon:4932 20020618 SGD
+SGD S000000626 SYP1 GO:0005935 SGD_REF:S000059326|PMID:11014808 IDA C YCR030C|YCR029C-A gene taxon:4932 20020618 SGD
+SGD S000000626 SYP1 GO:0005554 SGD_REF:S000069584 ND F YCR030C|YCR029C-A gene taxon:4932 20020618 SGD
+SGD S000000626 SYP1 GO:0000004 SGD_REF:S000069584 ND P YCR030C|YCR029C-A gene taxon:4932 20020618 SGD
+SGD S000003541 SYS1 GO:0005802 SGD_REF:S000076519|PMID:15077113 IDA C YJL004C gene taxon:4932 20050523 SGD
+SGD S000003541 SYS1 GO:0030173 SGD_REF:S000069020|PMID:11726510 IDA C YJL004C gene taxon:4932 20021001 SGD
+SGD S000003541 SYS1 GO:0005554 SGD_REF:S000069584 ND F YJL004C gene taxon:4932 20021001 SGD
+SGD S000003541 SYS1 GO:0006895 SGD_REF:S000054514|PMID:8923208 IGI P YJL004C gene taxon:4932 20021001 SGD
+SGD S000003541 SYS1 GO:0016050 SGD_REF:S000069020|PMID:11726510 IPI P YJL004C gene taxon:4932 20021001 SGD
+SGD S000006299 SYT1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YPR095C gene taxon:4932 20040813 SGD
+SGD S000006299 SYT1 GO:0005086 SGD_REF:S000039833|PMID:10430582 IDA F YPR095C gene taxon:4932 20021016 SGD
+SGD S000006299 SYT1 GO:0016192 SGD_REF:S000039833|PMID:10430582 IGI P YPR095C gene taxon:4932 20050426 SGD
+SGD S000006299 SYT1 GO:0045045 SGD_REF:S000039833|PMID:10430582 IGI P YPR095C gene taxon:4932 20021016 SGD
+SGD S000003212 TAD1 GO:0005634 SGD_REF:S000069459|PMID:11914276 IDA C tRNA-specific adenosine deaminase subunit YGL243W gene taxon:4932 20020507 SGD
+SGD S000003212 TAD1 GO:0008251 SGD_REF:S000053048|PMID:9707437 IDA F tRNA-specific adenosine deaminase subunit YGL243W gene taxon:4932 20021030 SGD
+SGD S000003212 TAD1 GO:0006400 SGD_REF:S000053048|PMID:9707437 IDA P tRNA-specific adenosine deaminase subunit YGL243W gene taxon:4932 20021030 SGD
+SGD S000003572 TAD2 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C tRNA-specific adenosine deaminase subunit YJL035C gene taxon:4932 20031028 SGD
+SGD S000003572 TAD2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C tRNA-specific adenosine deaminase subunit YJL035C gene taxon:4932 20031028 SGD
+SGD S000003572 TAD2 GO:0008251 SGD_REF:S000048334|PMID:10550050 IDA F tRNA-specific adenosine deaminase subunit YJL035C gene taxon:4932 20021030 SGD
+SGD S000003572 TAD2 GO:0006400 SGD_REF:S000048334|PMID:10550050 IDA P tRNA-specific adenosine deaminase subunit YJL035C gene taxon:4932 20021030 SGD
+SGD S000004308 TAD3 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C tRNA-specific adenosine deaminase subunit YLR316C gene taxon:4932 20031028 SGD
+SGD S000004308 TAD3 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C tRNA-specific adenosine deaminase subunit YLR316C gene taxon:4932 20031028 SGD
+SGD S000004308 TAD3 GO:0008251 SGD_REF:S000048334|PMID:10550050 IDA F tRNA-specific adenosine deaminase subunit YLR316C gene taxon:4932 20021030 SGD
+SGD S000004308 TAD3 GO:0006400 SGD_REF:S000048334|PMID:10550050 IDA P tRNA-specific adenosine deaminase subunit YLR316C gene taxon:4932 20021030 SGD
+SGD S000003506 TAF1 GO:0005669 SGD_REF:S000058086|PMID:9118213 TAS C YGR274C|TAF130|TAF145|TafII130|TafII145 gene taxon:4932 20010118 SGD
+SGD S000003506 TAF1 GO:0005669 SGD_REF:S000079756|PMID:15448131 IDA C YGR274C|TAF130|TAF145|TafII130|TafII145 gene taxon:4932 20041215 SGD
+SGD S000003506 TAF1 GO:0004402 SGD_REF:S000052091|PMID:8980232 IDA F YGR274C|TAF130|TAF145|TafII130|TafII145 gene taxon:4932 20010118 SGD
+SGD S000003506 TAF1 GO:0004674 SGD_REF:S000058086|PMID:9118213 ISS F YGR274C|TAF130|TAF145|TafII130|TafII145 gene taxon:4932 20010118 SGD
+SGD S000003506 TAF1 GO:0016251 SGD_REF:S000058086|PMID:9118213 TAS F YGR274C|TAF130|TAF145|TafII130|TafII145 gene taxon:4932 20010119 SGD
+SGD S000003506 TAF1 GO:0000114 SGD_REF:S000055374|PMID:9288741 IMP P YGR274C|TAF130|TAF145|TafII130|TafII145 gene taxon:4932 20010118 SGD
+SGD S000003506 TAF1 GO:0000114 SGD_REF:S000055374|PMID:9288741 IGI P YGR274C|TAF130|TAF145|TafII130|TafII145 gene taxon:4932 20010118 SGD
+SGD S000003506 TAF1 GO:0006367 SGD_REF:S000056378|PMID:10384286 TAS P YGR274C|TAF130|TAF145|TafII130|TafII145 gene taxon:4932 20010118 SGD
+SGD S000003506 TAF1 GO:0006367 SGD_REF:S000058086|PMID:9118213 TAS P YGR274C|TAF130|TAF145|TafII130|TafII145 gene taxon:4932 20010118 SGD
+SGD S000003506 TAF1 GO:0006367 SGD_REF:S000056377|PMID:10384273 TAS P YGR274C|TAF130|TAF145|TafII130|TafII145 gene taxon:4932 20010118 SGD
+SGD S000003506 TAF1 GO:0006468 SGD_REF:S000058086|PMID:9118213 ISS P YGR274C|TAF130|TAF145|TafII130|TafII145 gene taxon:4932 20010118 SGD
+SGD S000002574 TAF10 GO:0000124 SGD_REF:S000048255|PMID:9674426 IDA C TFIID subunit YDR167W|TAF23|TAF25|TafII25 gene taxon:4932 20010118 SGD
+SGD S000002574 TAF10 GO:0005669 SGD_REF:S000058086|PMID:9118213 TAS C TFIID subunit YDR167W|TAF23|TAF25|TafII25 gene taxon:4932 20010118 SGD
+SGD S000002574 TAF10 GO:0005669 SGD_REF:S000079756|PMID:15448131 IDA C TFIID subunit YDR167W|TAF23|TAF25|TafII25 gene taxon:4932 20041215 SGD
+SGD S000002574 TAF10 GO:0046695 SGD_REF:S000071997|PMID:12446794 IPI C TFIID subunit YDR167W|TAF23|TAF25|TafII25 gene taxon:4932 20041024 SGD
+SGD S000002574 TAF10 GO:0016251 SGD_REF:S000058086|PMID:9118213 TAS F TFIID subunit YDR167W|TAF23|TAF25|TafII25 gene taxon:4932 20010119 SGD
+SGD S000002574 TAF10 GO:0000114 SGD_REF:S000058086|PMID:9118213 IPI P TFIID subunit YDR167W|TAF23|TAF25|TafII25 gene taxon:4932 20010118 SGD
+SGD S000002574 TAF10 GO:0000114 SGD_REF:S000055374|PMID:9288741 IPI P TFIID subunit YDR167W|TAF23|TAF25|TafII25 gene taxon:4932 20010118 SGD
+SGD S000002574 TAF10 GO:0006325 SGD_REF:S000048255|PMID:9674426 IPI P TFIID subunit YDR167W|TAF23|TAF25|TafII25 gene taxon:4932 20010118 SGD
+SGD S000002574 TAF10 GO:0006367 SGD_REF:S000056378|PMID:10384286 TAS P TFIID subunit YDR167W|TAF23|TAF25|TafII25 gene taxon:4932 20010118 SGD
+SGD S000002574 TAF10 GO:0006367 SGD_REF:S000056377|PMID:10384273 TAS P TFIID subunit YDR167W|TAF23|TAF25|TafII25 gene taxon:4932 20010118 SGD
+SGD S000002574 TAF10 GO:0006367 SGD_REF:S000058086|PMID:9118213 TAS P TFIID subunit YDR167W|TAF23|TAF25|TafII25 gene taxon:4932 20010118 SGD
+SGD S000002574 TAF10 GO:0006473 SGD_REF:S000048255|PMID:9674426 IPI P TFIID subunit YDR167W|TAF23|TAF25|TafII25 gene taxon:4932 20010118 SGD
+SGD S000002574 TAF10 GO:0016568 SGD_REF:S000061032|PMID:10839822 TAS P TFIID subunit YDR167W|TAF23|TAF25|TafII25 gene taxon:4932 20020426 SGD
+SGD S000002574 TAF10 GO:0016573 SGD_REF:S000061032|PMID:10839822 TAS P TFIID subunit YDR167W|TAF23|TAF25|TafII25 gene taxon:4932 20020426 SGD
+SGD S000004477 TAF11 GO:0005669 SGD_REF:S000058086|PMID:9118213 TAS C TFIID subunit YML015C|TAF40|TafII40 gene taxon:4932 20010118 SGD
+SGD S000004477 TAF11 GO:0005669 SGD_REF:S000079756|PMID:15448131 IDA C TFIID subunit YML015C|TAF40|TafII40 gene taxon:4932 20041215 SGD
+SGD S000004477 TAF11 GO:0016251 SGD_REF:S000058086|PMID:9118213 TAS F TFIID subunit YML015C|TAF40|TafII40 gene taxon:4932 20010119 SGD
+SGD S000004477 TAF11 GO:0000114 SGD_REF:S000058086|PMID:9118213 IPI P TFIID subunit YML015C|TAF40|TafII40 gene taxon:4932 20010118 SGD
+SGD S000004477 TAF11 GO:0000114 SGD_REF:S000055374|PMID:9288741 IPI P TFIID subunit YML015C|TAF40|TafII40 gene taxon:4932 20010118 SGD
+SGD S000004477 TAF11 GO:0006367 SGD_REF:S000056378|PMID:10384286 TAS P TFIID subunit YML015C|TAF40|TafII40 gene taxon:4932 20010118 SGD
+SGD S000004477 TAF11 GO:0006367 SGD_REF:S000056377|PMID:10384273 TAS P TFIID subunit YML015C|TAF40|TafII40 gene taxon:4932 20010118 SGD
+SGD S000004477 TAF11 GO:0006367 SGD_REF:S000058086|PMID:9118213 TAS P TFIID subunit YML015C|TAF40|TafII40 gene taxon:4932 20010118 SGD
+SGD S000002552 TAF12 GO:0000124 SGD_REF:S000048255|PMID:9674426 IDA C TFIID subunit YDR145W|TAF61|TAF68|TafII61|TafII68 gene taxon:4932 20010118 SGD
+SGD S000002552 TAF12 GO:0005669 SGD_REF:S000058086|PMID:9118213 TAS C TFIID subunit YDR145W|TAF61|TAF68|TafII61|TafII68 gene taxon:4932 20010118 SGD
+SGD S000002552 TAF12 GO:0005669 SGD_REF:S000079756|PMID:15448131 IDA C TFIID subunit YDR145W|TAF61|TAF68|TafII61|TafII68 gene taxon:4932 20041215 SGD
+SGD S000002552 TAF12 GO:0046695 SGD_REF:S000071997|PMID:12446794 IPI C TFIID subunit YDR145W|TAF61|TAF68|TafII61|TafII68 gene taxon:4932 20041024 SGD
+SGD S000002552 TAF12 GO:0016251 SGD_REF:S000058086|PMID:9118213 TAS F TFIID subunit YDR145W|TAF61|TAF68|TafII61|TafII68 gene taxon:4932 20010119 SGD
+SGD S000002552 TAF12 GO:0000114 SGD_REF:S000058086|PMID:9118213 IPI P TFIID subunit YDR145W|TAF61|TAF68|TafII61|TafII68 gene taxon:4932 20010118 SGD
+SGD S000002552 TAF12 GO:0000114 SGD_REF:S000055374|PMID:9288741 IPI P TFIID subunit YDR145W|TAF61|TAF68|TafII61|TafII68 gene taxon:4932 20010118 SGD
+SGD S000002552 TAF12 GO:0006325 SGD_REF:S000048255|PMID:9674426 IPI P TFIID subunit YDR145W|TAF61|TAF68|TafII61|TafII68 gene taxon:4932 20010118 SGD
+SGD S000002552 TAF12 GO:0006367 SGD_REF:S000056378|PMID:10384286 TAS P TFIID subunit YDR145W|TAF61|TAF68|TafII61|TafII68 gene taxon:4932 20010118 SGD
+SGD S000002552 TAF12 GO:0006367 SGD_REF:S000058086|PMID:9118213 TAS P TFIID subunit YDR145W|TAF61|TAF68|TafII61|TafII68 gene taxon:4932 20010118 SGD
+SGD S000002552 TAF12 GO:0006367 SGD_REF:S000056377|PMID:10384273 TAS P TFIID subunit YDR145W|TAF61|TAF68|TafII61|TafII68 gene taxon:4932 20010118 SGD
+SGD S000002552 TAF12 GO:0006473 SGD_REF:S000048255|PMID:9674426 IPI P TFIID subunit YDR145W|TAF61|TAF68|TafII61|TafII68 gene taxon:4932 20010118 SGD
+SGD S000002552 TAF12 GO:0016568 SGD_REF:S000061032|PMID:10839822 TAS P TFIID subunit YDR145W|TAF61|TAF68|TafII61|TafII68 gene taxon:4932 20020426 SGD
+SGD S000002552 TAF12 GO:0016573 SGD_REF:S000061032|PMID:10839822 TAS P TFIID subunit YDR145W|TAF61|TAF68|TafII61|TafII68 gene taxon:4932 20020426 SGD
+SGD S000004564 TAF13 GO:0005634 SGD_REF:S000069459|PMID:11914276 IDA C TFIID subunit YML098W|FUN81|TAF19|TafII19 gene taxon:4932 20020507 SGD
+SGD S000004564 TAF13 GO:0005669 SGD_REF:S000058086|PMID:9118213 TAS C TFIID subunit YML098W|FUN81|TAF19|TafII19 gene taxon:4932 20010118 SGD
+SGD S000004564 TAF13 GO:0005669 SGD_REF:S000079756|PMID:15448131 IDA C TFIID subunit YML098W|FUN81|TAF19|TafII19 gene taxon:4932 20041215 SGD
+SGD S000004564 TAF13 GO:0016251 SGD_REF:S000058086|PMID:9118213 TAS F TFIID subunit YML098W|FUN81|TAF19|TafII19 gene taxon:4932 20010119 SGD
+SGD S000004564 TAF13 GO:0000114 SGD_REF:S000058086|PMID:9118213 IPI P TFIID subunit YML098W|FUN81|TAF19|TafII19 gene taxon:4932 20010118 SGD
+SGD S000004564 TAF13 GO:0000114 SGD_REF:S000055374|PMID:9288741 IPI P TFIID subunit YML098W|FUN81|TAF19|TafII19 gene taxon:4932 20010118 SGD
+SGD S000004564 TAF13 GO:0006367 SGD_REF:S000056378|PMID:10384286 TAS P TFIID subunit YML098W|FUN81|TAF19|TafII19 gene taxon:4932 20010118 SGD
+SGD S000004564 TAF13 GO:0006367 SGD_REF:S000058086|PMID:9118213 TAS P TFIID subunit YML098W|FUN81|TAF19|TafII19 gene taxon:4932 20010118 SGD
+SGD S000004564 TAF13 GO:0006367 SGD_REF:S000056377|PMID:10384273 TAS P TFIID subunit YML098W|FUN81|TAF19|TafII19 gene taxon:4932 20010118 SGD
+SGD S000006050 TAF14 GO:0000119 SGD_REF:S000039918|PMID:7995524 IPI C transcription initiation factor TFIIF small subunit YPL129W|ANC1|SWP29|TAF30|TFG3|TafII30 gene taxon:4932 20041007 SGD
+SGD S000006050 TAF14 GO:0000123 SGD_REF:S000050029|PMID:10817755 IPI C transcription initiation factor TFIIF small subunit YPL129W|ANC1|SWP29|TAF30|TFG3|TafII30 gene taxon:4932 20041007 SGD
+SGD S000006050 TAF14 GO:0005669 SGD_REF:S000058086|PMID:9118213 TAS C transcription initiation factor TFIIF small subunit YPL129W|ANC1|SWP29|TAF30|TFG3|TafII30 gene taxon:4932 20010118 SGD
+SGD S000006050 TAF14 GO:0005669 SGD_REF:S000079756|PMID:15448131 IDA C transcription initiation factor TFIIF small subunit YPL129W|ANC1|SWP29|TAF30|TFG3|TafII30 gene taxon:4932 20041215 SGD
+SGD S000006050 TAF14 GO:0005674 SGD_REF:S000058446|PMID:9774381 TAS C transcription initiation factor TFIIF small subunit YPL129W|ANC1|SWP29|TAF30|TFG3|TafII30 gene taxon:4932 20010118 SGD
+SGD S000006050 TAF14 GO:0005674 SGD_REF:S000081997|PMID:15896708 IPI SGD:S000003418 C transcription initiation factor TFIIF small subunit YPL129W|ANC1|SWP29|TAF30|TFG3|TafII30 gene taxon:4932 20060313 SGD
+SGD S000006050 TAF14 GO:0016514 SGD_REF:S000041724|PMID:8668146 IPI C transcription initiation factor TFIIF small subunit YPL129W|ANC1|SWP29|TAF30|TFG3|TafII30 gene taxon:4932 20041007 SGD
+SGD S000006050 TAF14 GO:0031011 SGD_REF:S000073963|PMID:12887900 IPI C transcription initiation factor TFIIF small subunit YPL129W|ANC1|SWP29|TAF30|TFG3|TafII30 gene taxon:4932 20041007 SGD
+SGD S000006050 TAF14 GO:0016251 SGD_REF:S000058455|PMID:9048886 TAS F transcription initiation factor TFIIF small subunit YPL129W|ANC1|SWP29|TAF30|TFG3|TafII30 gene taxon:4932 20020528 SGD
+SGD S000006050 TAF14 GO:0016251 SGD_REF:S000058446|PMID:9774381 TAS F transcription initiation factor TFIIF small subunit YPL129W|ANC1|SWP29|TAF30|TFG3|TafII30 gene taxon:4932 20020528 SGD
+SGD S000006050 TAF14 GO:0000114 SGD_REF:S000058086|PMID:9118213 IPI P transcription initiation factor TFIIF small subunit YPL129W|ANC1|SWP29|TAF30|TFG3|TafII30 gene taxon:4932 20010118 SGD
+SGD S000006050 TAF14 GO:0000114 SGD_REF:S000055374|PMID:9288741 IPI P transcription initiation factor TFIIF small subunit YPL129W|ANC1|SWP29|TAF30|TFG3|TafII30 gene taxon:4932 20010118 SGD
+SGD S000006050 TAF14 GO:0006338 SGD_REF:S000058455|PMID:9048886 TAS P transcription initiation factor TFIIF small subunit YPL129W|ANC1|SWP29|TAF30|TFG3|TafII30 gene taxon:4932 20010118 SGD
+SGD S000006050 TAF14 GO:0006367 SGD_REF:S000056378|PMID:10384286 TAS P transcription initiation factor TFIIF small subunit YPL129W|ANC1|SWP29|TAF30|TFG3|TafII30 gene taxon:4932 20010118 SGD
+SGD S000006050 TAF14 GO:0006367 SGD_REF:S000056377|PMID:10384273 TAS P transcription initiation factor TFIIF small subunit YPL129W|ANC1|SWP29|TAF30|TFG3|TafII30 gene taxon:4932 20010118 SGD
+SGD S000000638 TAF2 GO:0005669 SGD_REF:S000058086|PMID:9118213 TAS C TATA binding protein-associated factor YCR042C|TAF150|TSM1|TafII150 gene taxon:4932 20010118 SGD
+SGD S000000638 TAF2 GO:0005669 SGD_REF:S000079756|PMID:15448131 IDA C TATA binding protein-associated factor YCR042C|TAF150|TSM1|TafII150 gene taxon:4932 20041215 SGD
+SGD S000000638 TAF2 GO:0016251 SGD_REF:S000058086|PMID:9118213 TAS F TATA binding protein-associated factor YCR042C|TAF150|TSM1|TafII150 gene taxon:4932 20010119 SGD
+SGD S000000638 TAF2 GO:0000114 SGD_REF:S000055374|PMID:9288741 IMP P TATA binding protein-associated factor YCR042C|TAF150|TSM1|TafII150 gene taxon:4932 20010118 SGD
+SGD S000000638 TAF2 GO:0006367 SGD_REF:S000056378|PMID:10384286 TAS P TATA binding protein-associated factor YCR042C|TAF150|TSM1|TafII150 gene taxon:4932 20010118 SGD
+SGD S000000638 TAF2 GO:0006367 SGD_REF:S000058086|PMID:9118213 TAS P TATA binding protein-associated factor YCR042C|TAF150|TSM1|TafII150 gene taxon:4932 20010118 SGD
+SGD S000000638 TAF2 GO:0006367 SGD_REF:S000056377|PMID:10384273 TAS P TATA binding protein-associated factor YCR042C|TAF150|TSM1|TafII150 gene taxon:4932 20010118 SGD
+SGD S000005932 TAF3 GO:0005669 SGD_REF:S000058086|PMID:9118213 TAS C TAF(II) complex component YPL011C|TAF47|TafII47 gene taxon:4932 20010118 SGD
+SGD S000005932 TAF3 GO:0005669 SGD_REF:S000079756|PMID:15448131 IDA C TAF(II) complex component YPL011C|TAF47|TafII47 gene taxon:4932 20041215 SGD
+SGD S000005932 TAF3 GO:0016251 SGD_REF:S000058086|PMID:9118213 TAS F TAF(II) complex component YPL011C|TAF47|TafII47 gene taxon:4932 20010119 SGD
+SGD S000005932 TAF3 GO:0000114 SGD_REF:S000058086|PMID:9118213 IPI P TAF(II) complex component YPL011C|TAF47|TafII47 gene taxon:4932 20010118 SGD
+SGD S000005932 TAF3 GO:0000114 SGD_REF:S000055374|PMID:9288741 IPI P TAF(II) complex component YPL011C|TAF47|TafII47 gene taxon:4932 20010118 SGD
+SGD S000005932 TAF3 GO:0006367 SGD_REF:S000056378|PMID:10384286 TAS P TAF(II) complex component YPL011C|TAF47|TafII47 gene taxon:4932 20010118 SGD
+SGD S000005932 TAF3 GO:0006367 SGD_REF:S000056377|PMID:10384273 TAS P TAF(II) complex component YPL011C|TAF47|TafII47 gene taxon:4932 20010118 SGD
+SGD S000005932 TAF3 GO:0006367 SGD_REF:S000058086|PMID:9118213 TAS P TAF(II) complex component YPL011C|TAF47|TafII47 gene taxon:4932 20010118 SGD
+SGD S000004607 TAF4 GO:0005669 SGD_REF:S000045781|PMID:10751405 IDA C TFIID subunit YMR005W|MPT1|TAF48|TSG2|TafII48 gene taxon:4932 20010118 SGD
+SGD S000004607 TAF4 GO:0005669 SGD_REF:S000079756|PMID:15448131 IDA C TFIID subunit YMR005W|MPT1|TAF48|TSG2|TafII48 gene taxon:4932 20041215 SGD
+SGD S000004607 TAF4 GO:0005669 SGD_REF:S000050873|PMID:10788514 IDA C TFIID subunit YMR005W|MPT1|TAF48|TSG2|TafII48 gene taxon:4932 20010118 SGD
+SGD S000004607 TAF4 GO:0003702 SGD_REF:S000045781|PMID:10751405 IDA F TFIID subunit YMR005W|MPT1|TAF48|TSG2|TafII48 gene taxon:4932 20010118 SGD
+SGD S000004607 TAF4 GO:0006366 SGD_REF:S000045781|PMID:10751405 IDA P TFIID subunit YMR005W|MPT1|TAF48|TSG2|TafII48 gene taxon:4932 20010118 SGD
+SGD S000000402 TAF5 GO:0000124 SGD_REF:S000048255|PMID:9674426 IDA C YBR198C|TAF90|TafII90 gene taxon:4932 20010118 SGD
+SGD S000000402 TAF5 GO:0005669 SGD_REF:S000058086|PMID:9118213 TAS C YBR198C|TAF90|TafII90 gene taxon:4932 20010118 SGD
+SGD S000000402 TAF5 GO:0005669 SGD_REF:S000079756|PMID:15448131 IDA C YBR198C|TAF90|TafII90 gene taxon:4932 20041215 SGD
+SGD S000000402 TAF5 GO:0046695 SGD_REF:S000071997|PMID:12446794 IPI C YBR198C|TAF90|TafII90 gene taxon:4932 20041024 SGD
+SGD S000000402 TAF5 GO:0016251 SGD_REF:S000058086|PMID:9118213 TAS F YBR198C|TAF90|TafII90 gene taxon:4932 20010119 SGD
+SGD S000000402 TAF5 GO:0000114 SGD_REF:S000055374|PMID:9288741 IMP P YBR198C|TAF90|TafII90 gene taxon:4932 20010118 SGD
+SGD S000000402 TAF5 GO:0006325 SGD_REF:S000048255|PMID:9674426 IPI P YBR198C|TAF90|TafII90 gene taxon:4932 20010118 SGD
+SGD S000000402 TAF5 GO:0006367 SGD_REF:S000056378|PMID:10384286 TAS P YBR198C|TAF90|TafII90 gene taxon:4932 20010118 SGD
+SGD S000000402 TAF5 GO:0006367 SGD_REF:S000056377|PMID:10384273 TAS P YBR198C|TAF90|TafII90 gene taxon:4932 20010118 SGD
+SGD S000000402 TAF5 GO:0006367 SGD_REF:S000058086|PMID:9118213 TAS P YBR198C|TAF90|TafII90 gene taxon:4932 20010118 SGD
+SGD S000000402 TAF5 GO:0006473 SGD_REF:S000048255|PMID:9674426 IPI P YBR198C|TAF90|TafII90 gene taxon:4932 20010118 SGD
+SGD S000000402 TAF5 GO:0016568 SGD_REF:S000061032|PMID:10839822 TAS P YBR198C|TAF90|TafII90 gene taxon:4932 20020426 SGD
+SGD S000000402 TAF5 GO:0016573 SGD_REF:S000061032|PMID:10839822 TAS P YBR198C|TAF90|TafII90 gene taxon:4932 20020426 SGD
+SGD S000003080 TAF6 GO:0000124 SGD_REF:S000048255|PMID:9674426 IDA C TATA-binding protein-associated-factor YGL112C|TAF60|TafII60 gene taxon:4932 20010118 SGD
+SGD S000003080 TAF6 GO:0005669 SGD_REF:S000058086|PMID:9118213 TAS C TATA-binding protein-associated-factor YGL112C|TAF60|TafII60 gene taxon:4932 20010118 SGD
+SGD S000003080 TAF6 GO:0005669 SGD_REF:S000079756|PMID:15448131 IDA C TATA-binding protein-associated-factor YGL112C|TAF60|TafII60 gene taxon:4932 20041215 SGD
+SGD S000003080 TAF6 GO:0046695 SGD_REF:S000071997|PMID:12446794 IPI C TATA-binding protein-associated-factor YGL112C|TAF60|TafII60 gene taxon:4932 20041024 SGD
+SGD S000003080 TAF6 GO:0016251 SGD_REF:S000058086|PMID:9118213 TAS F TATA-binding protein-associated-factor YGL112C|TAF60|TafII60 gene taxon:4932 20010119 SGD
+SGD S000003080 TAF6 GO:0000114 SGD_REF:S000058086|PMID:9118213 IPI P TATA-binding protein-associated-factor YGL112C|TAF60|TafII60 gene taxon:4932 20010118 SGD
+SGD S000003080 TAF6 GO:0000114 SGD_REF:S000055374|PMID:9288741 IPI P TATA-binding protein-associated-factor YGL112C|TAF60|TafII60 gene taxon:4932 20010118 SGD
+SGD S000003080 TAF6 GO:0006325 SGD_REF:S000048255|PMID:9674426 IPI P TATA-binding protein-associated-factor YGL112C|TAF60|TafII60 gene taxon:4932 20010118 SGD
+SGD S000003080 TAF6 GO:0006367 SGD_REF:S000056378|PMID:10384286 TAS P TATA-binding protein-associated-factor YGL112C|TAF60|TafII60 gene taxon:4932 20010118 SGD
+SGD S000003080 TAF6 GO:0006367 SGD_REF:S000056377|PMID:10384273 TAS P TATA-binding protein-associated-factor YGL112C|TAF60|TafII60 gene taxon:4932 20010118 SGD
+SGD S000003080 TAF6 GO:0006367 SGD_REF:S000058086|PMID:9118213 TAS P TATA-binding protein-associated-factor YGL112C|TAF60|TafII60 gene taxon:4932 20010118 SGD
+SGD S000003080 TAF6 GO:0006473 SGD_REF:S000048255|PMID:9674426 IPI P TATA-binding protein-associated-factor YGL112C|TAF60|TafII60 gene taxon:4932 20010118 SGD
+SGD S000003080 TAF6 GO:0016568 SGD_REF:S000061032|PMID:10839822 TAS P TATA-binding protein-associated-factor YGL112C|TAF60|TafII60 gene taxon:4932 20020426 SGD
+SGD S000003080 TAF6 GO:0016573 SGD_REF:S000061032|PMID:10839822 TAS P TATA-binding protein-associated-factor YGL112C|TAF60|TafII60 gene taxon:4932 20020426 SGD
+SGD S000004840 TAF7 GO:0005634 SGD_REF:S000069459|PMID:11914276 IDA C TFIID subunit YMR227C|TAF67|TafII67 gene taxon:4932 20020507 SGD
+SGD S000004840 TAF7 GO:0005669 SGD_REF:S000058086|PMID:9118213 TAS C TFIID subunit YMR227C|TAF67|TafII67 gene taxon:4932 20010118 SGD
+SGD S000004840 TAF7 GO:0005669 SGD_REF:S000079756|PMID:15448131 IDA C TFIID subunit YMR227C|TAF67|TafII67 gene taxon:4932 20041215 SGD
+SGD S000004840 TAF7 GO:0016251 SGD_REF:S000058086|PMID:9118213 TAS F TFIID subunit YMR227C|TAF67|TafII67 gene taxon:4932 20010119 SGD
+SGD S000004840 TAF7 GO:0000114 SGD_REF:S000058086|PMID:9118213 IPI P TFIID subunit YMR227C|TAF67|TafII67 gene taxon:4932 20010118 SGD
+SGD S000004840 TAF7 GO:0000114 SGD_REF:S000055374|PMID:9288741 IPI P TFIID subunit YMR227C|TAF67|TafII67 gene taxon:4932 20010118 SGD
+SGD S000004840 TAF7 GO:0006367 SGD_REF:S000056378|PMID:10384286 TAS P TFIID subunit YMR227C|TAF67|TafII67 gene taxon:4932 20010118 SGD
+SGD S000004840 TAF7 GO:0006367 SGD_REF:S000056377|PMID:10384273 TAS P TFIID subunit YMR227C|TAF67|TafII67 gene taxon:4932 20010118 SGD
+SGD S000004840 TAF7 GO:0006367 SGD_REF:S000058086|PMID:9118213 TAS P TFIID subunit YMR227C|TAF67|TafII67 gene taxon:4932 20010118 SGD
+SGD S000004582 TAF8 GO:0005634 SGD_REF:S000069459|PMID:11914276 IDA C TFIID subunit YML114C|TAF65|TafII65 gene taxon:4932 20020507 SGD
+SGD S000004582 TAF8 GO:0005669 SGD_REF:S000050873|PMID:10788514 IDA C TFIID subunit YML114C|TAF65|TafII65 gene taxon:4932 20021106 SGD
+SGD S000004582 TAF8 GO:0005669 SGD_REF:S000079756|PMID:15448131 IDA C TFIID subunit YML114C|TAF65|TafII65 gene taxon:4932 20041215 SGD
+SGD S000004582 TAF8 GO:0003702 SGD_REF:S000050873|PMID:10788514 IPI F TFIID subunit YML114C|TAF65|TafII65 gene taxon:4932 20021106 SGD
+SGD S000004582 TAF8 GO:0006366 SGD_REF:S000050873|PMID:10788514 IPI P TFIID subunit YML114C|TAF65|TafII65 gene taxon:4932 20021106 SGD
+SGD S000004849 TAF9 GO:0000124 SGD_REF:S000048255|PMID:9674426 IDA C TFIID subunit YMR236W|TAF17|TafII17 gene taxon:4932 20010118 SGD
+SGD S000004849 TAF9 GO:0005669 SGD_REF:S000058086|PMID:9118213 TAS C TFIID subunit YMR236W|TAF17|TafII17 gene taxon:4932 20010118 SGD
+SGD S000004849 TAF9 GO:0005669 SGD_REF:S000079756|PMID:15448131 IDA C TFIID subunit YMR236W|TAF17|TafII17 gene taxon:4932 20041215 SGD
+SGD S000004849 TAF9 GO:0046695 SGD_REF:S000071997|PMID:12446794 IPI C TFIID subunit YMR236W|TAF17|TafII17 gene taxon:4932 20041024 SGD
+SGD S000004849 TAF9 GO:0016251 SGD_REF:S000058086|PMID:9118213 TAS F TFIID subunit YMR236W|TAF17|TafII17 gene taxon:4932 20010119 SGD
+SGD S000004849 TAF9 GO:0000114 SGD_REF:S000058086|PMID:9118213 IPI P TFIID subunit YMR236W|TAF17|TafII17 gene taxon:4932 20010118 SGD
+SGD S000004849 TAF9 GO:0000114 SGD_REF:S000055374|PMID:9288741 IPI P TFIID subunit YMR236W|TAF17|TafII17 gene taxon:4932 20010118 SGD
+SGD S000004849 TAF9 GO:0006325 SGD_REF:S000048255|PMID:9674426 IPI P TFIID subunit YMR236W|TAF17|TafII17 gene taxon:4932 20010118 SGD
+SGD S000004849 TAF9 GO:0006367 SGD_REF:S000056378|PMID:10384286 TAS P TFIID subunit YMR236W|TAF17|TafII17 gene taxon:4932 20010118 SGD
+SGD S000004849 TAF9 GO:0006367 SGD_REF:S000058086|PMID:9118213 TAS P TFIID subunit YMR236W|TAF17|TafII17 gene taxon:4932 20010118 SGD
+SGD S000004849 TAF9 GO:0006367 SGD_REF:S000056377|PMID:10384273 TAS P TFIID subunit YMR236W|TAF17|TafII17 gene taxon:4932 20010118 SGD
+SGD S000004849 TAF9 GO:0006473 SGD_REF:S000048255|PMID:9674426 IPI P TFIID subunit YMR236W|TAF17|TafII17 gene taxon:4932 20010118 SGD
+SGD S000004849 TAF9 GO:0016568 SGD_REF:S000061032|PMID:10839822 TAS P TFIID subunit YMR236W|TAF17|TafII17 gene taxon:4932 20020426 SGD
+SGD S000004849 TAF9 GO:0016573 SGD_REF:S000061032|PMID:10839822 TAS P TFIID subunit YMR236W|TAF17|TafII17 gene taxon:4932 20020426 SGD
+SGD S000000656 TAH1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YCR060W gene taxon:4932 20031028 SGD
+SGD S000000656 TAH1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YCR060W gene taxon:4932 20031028 SGD
+SGD S000000656 TAH1 GO:0051087 SGD_REF:S000081009|PMID:15766533 IMP F YCR060W gene taxon:4932 20050316 SGD
+SGD S000000656 TAH1 GO:0051087 SGD_REF:S000081009|PMID:15766533 IPI SGD:S000006161 F YCR060W gene taxon:4932 20050316 SGD
+SGD S000000656 TAH1 GO:0006457 SGD_REF:S000081009|PMID:15766533 IMP P YCR060W gene taxon:4932 20050316 SGD
+SGD S000000656 TAH1 GO:0006457 SGD_REF:S000081009|PMID:15766533 IGI SGD:S000006161 P YCR060W gene taxon:4932 20050317 SGD
+SGD S000000656 TAH1 GO:0006457 SGD_REF:S000081009|PMID:15766533 IPI SGD:S000006161 P YCR060W gene taxon:4932 20050317 SGD
+SGD S000003807 TAH11 GO:0005634 SGD_REF:S000069529|PMID:11836525 IDA C YJR046W|CDT1|SID2 gene taxon:4932 20021115 SGD
+SGD S000003807 TAH11 GO:0005656 SGD_REF:S000069594|PMID:11967159 IMP C YJR046W|CDT1|SID2 gene taxon:4932 20041104 SGD
+SGD S000003807 TAH11 GO:0005737 SGD_REF:S000069529|PMID:11836525 IDA C YJR046W|CDT1|SID2 gene taxon:4932 20021115 SGD
+SGD S000003807 TAH11 GO:0005554 SGD_REF:S000069584 ND F YJR046W|CDT1|SID2 gene taxon:4932 20021115 SGD
+SGD S000003807 TAH11 GO:0030174 SGD_REF:S000069594|PMID:11967159 IDA P YJR046W|CDT1|SID2 gene taxon:4932 20020909 SGD
+SGD S000006252 TAH18 GO:0008372 SGD_REF:S000069584 ND C YPR048W gene taxon:4932 20021125 SGD
+SGD S000006252 TAH18 GO:0005554 SGD_REF:S000069584 ND F YPR048W gene taxon:4932 20021125 SGD
+SGD S000006252 TAH18 GO:0000004 SGD_REF:S000069584 ND P YPR048W gene taxon:4932 20021125 SGD
+SGD S000004346 TAL1 GO:0005737 SGD_REF:S000071382|PMID:2843500 ISS C transaldolase, enzyme in the pentose phosphate pathway YLR354C gene taxon:4932 20020930 SGD
+SGD S000004346 TAL1 GO:0004801 SGD_REF:S000053822|PMID:8534086 TAS F transaldolase, enzyme in the pentose phosphate pathway YLR354C gene taxon:4932 20020930 SGD
+SGD S000004346 TAL1 GO:0006098 SGD_REF:S000053822|PMID:8534086 TAS P transaldolase, enzyme in the pentose phosphate pathway YLR354C gene taxon:4932 20020930 SGD
+SGD S000004346 TAL1 GO:0006098 SGD_REF:S000048672|PMID:8299150 IMP P transaldolase, enzyme in the pentose phosphate pathway YLR354C gene taxon:4932 20020930 SGD
+SGD S000003201 TAN1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YGL232W gene taxon:4932 20031028 SGD
+SGD S000003201 TAN1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YGL232W gene taxon:4932 20031028 SGD
+SGD S000003201 TAN1 GO:0003723 SGD_REF:S000076105|PMID:15037780 IDA F YGL232W gene taxon:4932 20040519 SGD
+SGD S000003201 TAN1 GO:0006400 SGD_REF:S000076105|PMID:15037780 IMP P YGL232W gene taxon:4932 20040519 SGD
+SGD S000001391 TAO3 GO:0000131 SGD_REF:S000069215|PMID:11854408 IDA C YIL129C|PAG1 gene taxon:4932 20020930 SGD
+SGD S000001391 TAO3 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YIL129C|PAG1 gene taxon:4932 20040928 SGD
+SGD S000001391 TAO3 GO:0005933 SGD_REF:S000074101|PMID:12972564 IDA C YIL129C|PAG1 gene taxon:4932 20031016 SGD
+SGD S000001391 TAO3 GO:0043332 SGD_REF:S000074101|PMID:12972564 IDA C YIL129C|PAG1 gene taxon:4932 20031016 SGD
+SGD S000001391 TAO3 GO:0005554 SGD_REF:S000069584 ND F YIL129C|PAG1 gene taxon:4932 20020930 SGD
+SGD S000001391 TAO3 GO:0000902 SGD_REF:S000069215|PMID:11854408 IGI P YIL129C|PAG1 gene taxon:4932 20021108 SGD
+SGD S000001391 TAO3 GO:0000902 SGD_REF:S000069215|PMID:11854408 IMP P YIL129C|PAG1 gene taxon:4932 20021108 SGD
+SGD S000001391 TAO3 GO:0000903 SGD_REF:S000074101|PMID:12972564 IGI P YIL129C|PAG1 gene taxon:4932 20050420 SGD
+SGD S000001391 TAO3 GO:0007114 SGD_REF:S000069215|PMID:11854408 IGI P YIL129C|PAG1 gene taxon:4932 20020930 SGD
+SGD S000001391 TAO3 GO:0007114 SGD_REF:S000069215|PMID:11854408 IMP P YIL129C|PAG1 gene taxon:4932 20020930 SGD
+SGD S000004630 TAP42 GO:0008372 SGD_REF:S000069584 ND C 42 kDa protein that physically associates with the PP2A and SIT4 protein phosphatase catalytic subunits YMR028W gene taxon:4932 20021211 SGD
+SGD S000004630 TAP42 GO:0005515 SGD_REF:S000041697|PMID:8756348 TAS F 42 kDa protein that physically associates with the PP2A and SIT4 protein phosphatase catalytic subunits YMR028W gene taxon:4932 20010118 SGD
+SGD S000004630 TAP42 GO:0007165 SGD_REF:S000041697|PMID:8756348 IMP P 42 kDa protein that physically associates with the PP2A and SIT4 protein phosphatase catalytic subunits YMR028W gene taxon:4932 20010118 SGD
+SGD S000028422 TAR1 GO:0005739 SGD_REF:S000071584|PMID:12414727 IMP C YLR154W-C|YLR154W-A gene taxon:4932 20021112 SGD
+SGD S000028422 TAR1 GO:0005554 SGD_REF:S000069584 ND F YLR154W-C|YLR154W-A gene taxon:4932 20020925 SGD
+SGD S000028422 TAR1 GO:0000004 SGD_REF:S000069584 ND P YLR154W-C|YLR154W-A gene taxon:4932 20020925 SGD
+SGD S000000273 TAT1 GO:0005886 SGD_REF:S000043244|PMID:10654085 ISS C amino acid transport protein for valine, leucine, isoleucine, and tyrosine YBR069C|VAP1 gene taxon:4932 20021002 SGD
+SGD S000000273 TAT1 GO:0015171 SGD_REF:S000043244|PMID:10654085 IDA F amino acid transport protein for valine, leucine, isoleucine, and tyrosine YBR069C|VAP1 gene taxon:4932 20021002 SGD
+SGD S000000273 TAT1 GO:0006865 SGD_REF:S000043244|PMID:10654085 IDA P amino acid transport protein for valine, leucine, isoleucine, and tyrosine YBR069C|VAP1 gene taxon:4932 20021002 SGD
+SGD S000005380 TAT2 GO:0005886 SGD_REF:S000043244|PMID:10654085 ISS C tryptophan permease, high affinity YOL020W|LTG3|SAB2|SCM2|TAP2 gene taxon:4932 20020806 SGD
+SGD S000005380 TAT2 GO:0005886 SGD_REF:S000073805|PMID:12810702 IDA C tryptophan permease, high affinity YOL020W|LTG3|SAB2|SCM2|TAP2 gene taxon:4932 20030908 SGD
+SGD S000005380 TAT2 GO:0015173 SGD_REF:S000043244|PMID:10654085 IDA F tryptophan permease, high affinity YOL020W|LTG3|SAB2|SCM2|TAP2 gene taxon:4932 20020806 SGD
+SGD S000005380 TAT2 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P tryptophan permease, high affinity YOL020W|LTG3|SAB2|SCM2|TAP2 gene taxon:4932 20060227 SGD
+SGD S000005380 TAT2 GO:0015801 SGD_REF:S000043244|PMID:10654085 IDA P tryptophan permease, high affinity YOL020W|LTG3|SAB2|SCM2|TAP2 gene taxon:4932 20020806 SGD
+SGD S000003619 TAX4 GO:0008372 SGD_REF:S000069584 ND C YJL083W gene taxon:4932 20021223 SGD
+SGD S000003619 TAX4 GO:0005554 SGD_REF:S000069584 ND F YJL083W gene taxon:4932 20021223 SGD
+SGD S000003619 TAX4 GO:0007047 SGD_REF:S000077163|PMID:15265867 IGI P YJL083W gene taxon:4932 20041004 SGD
+SGD S000003619 TAX4 GO:0048017 SGD_REF:S000077163|PMID:15265867 IGI P YJL083W gene taxon:4932 20050524 SGD
+SGD S000006344 TAZ1 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YPR140W gene taxon:4932 20031028 SGD
+SGD S000006344 TAZ1 GO:0005739 SGD_REF:S000079834|PMID:15304507 IDA C YPR140W gene taxon:4932 20041220 SGD
+SGD S000006344 TAZ1 GO:0005739 SGD_REF:S000080116|PMID:15588229 IDA C YPR140W gene taxon:4932 20050209 SGD
+SGD S000006344 TAZ1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YPR140W gene taxon:4932 20040924 SGD
+SGD S000006344 TAZ1 GO:0008415 SGD_REF:S000065692|PMID:9259571 ISS F YPR140W gene taxon:4932 20030423 SGD
+SGD S000006344 TAZ1 GO:0008415 SGD_REF:S000080116|PMID:15588229 IMP F YPR140W gene taxon:4932 20050209 SGD
+SGD S000006344 TAZ1 GO:0007007 SGD_REF:S000075500|PMID:14651618 IMP P YPR140W gene taxon:4932 20040302 SGD
+SGD S000006344 TAZ1 GO:0008654 SGD_REF:S000065692|PMID:9259571 ISS P YPR140W gene taxon:4932 20030423 SGD
+SGD S000006344 TAZ1 GO:0008654 SGD_REF:S000080116|PMID:15588229 IMP P YPR140W gene taxon:4932 20050209 SGD
+SGD S000006344 TAZ1 GO:0008654 SGD_REF:S000075500|PMID:14651618 IMP P YPR140W gene taxon:4932 20040302 SGD
+SGD S000006344 TAZ1 GO:0042775 SGD_REF:S000079834|PMID:15304507 IMP P YPR140W gene taxon:4932 20041220 SGD
+SGD S000006049 TBF1 GO:0000228 SGD_REF:S000040662|PMID:10871401 IPI C TTAGGG repeat binding factor YPL128C|LPI16 gene taxon:4932 20030403 SGD
+SGD S000006049 TBF1 GO:0000784 SGD_REF:S000040662|PMID:10871401 TAS C TTAGGG repeat binding factor YPL128C|LPI16 gene taxon:4932 20030403 SGD
+SGD S000006049 TBF1 GO:0005634 SGD_REF:S000069459|PMID:11914276 IDA C TTAGGG repeat binding factor YPL128C|LPI16 gene taxon:4932 20020507 SGD
+SGD S000006049 TBF1 GO:0003677 SGD_REF:S000040662|PMID:10871401 IPI F TTAGGG repeat binding factor YPL128C|LPI16 gene taxon:4932 20020930 SGD
+SGD S000006049 TBF1 GO:0003700 SGD_REF:S000071586|PMID:12200417 TAS F TTAGGG repeat binding factor YPL128C|LPI16 gene taxon:4932 20021124 SGD
+SGD S000006049 TBF1 GO:0043035 SGD_REF:S000060749|PMID:11258704 IDA F TTAGGG repeat binding factor YPL128C|LPI16 gene taxon:4932 20050415 SGD
+SGD S000006049 TBF1 GO:0006345 SGD_REF:S000060749|PMID:11258704 IDA P TTAGGG repeat binding factor YPL128C|LPI16 gene taxon:4932 20020930 SGD
+SGD S000000354 TBS1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YBR150C gene taxon:4932 20031028 SGD
+SGD S000000354 TBS1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YBR150C gene taxon:4932 20031028 SGD
+SGD S000000354 TBS1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YBR150C gene taxon:4932 20040813 SGD
+SGD S000000354 TBS1 GO:0005554 SGD_REF:S000069584 ND F YBR150C gene taxon:4932 20020930 SGD
+SGD S000000354 TBS1 GO:0000004 SGD_REF:S000069584 ND P YBR150C gene taxon:4932 20020930 SGD
+SGD S000005612 TCB1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YOR086C gene taxon:4932 20040923 SGD
+SGD S000005612 TCB1 GO:0008289 SGD_REF:S000076710|PMID:15049706 IDA F YOR086C gene taxon:4932 20041006 SGD
+SGD S000005612 TCB1 GO:0000004 SGD_REF:S000069584 ND P YOR086C gene taxon:4932 20030410 SGD
+SGD S000005031 TCB2 GO:0005933 SGD_REF:S000074060|PMID:13679573 IDA C YNL087W gene taxon:4932 20040115 SGD
+SGD S000005031 TCB2 GO:0005554 SGD_REF:S000069584 ND F YNL087W gene taxon:4932 20030421 SGD
+SGD S000005031 TCB2 GO:0000004 SGD_REF:S000069584 ND P YNL087W gene taxon:4932 20030421 SGD
+SGD S000004537 TCB3 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YML072C gene taxon:4932 20040928 SGD
+SGD S000004537 TCB3 GO:0005933 SGD_REF:S000074060|PMID:13679573 IDA C YML072C gene taxon:4932 20040115 SGD
+SGD S000004537 TCB3 GO:0008289 SGD_REF:S000076710|PMID:15049706 IDA F YML072C gene taxon:4932 20041006 SGD
+SGD S000004537 TCB3 GO:0000004 SGD_REF:S000069584 ND P YML072C gene taxon:4932 20021126 SGD
+SGD S000002758 TCM10 GO:0005743 SGD_REF:S000073291|PMID:12646576 IDA C YDR350C|ATP22 gene taxon:4932 20030618 SGD
+SGD S000002758 TCM10 GO:0005554 SGD_REF:S000069584 ND F YDR350C|ATP22 gene taxon:4932 20021125 SGD
+SGD S000002758 TCM10 GO:0006461 SGD_REF:S000073291|PMID:12646576 IDA P YDR350C|ATP22 gene taxon:4932 20030618 SGD
+SGD S000002758 TCM10 GO:0006461 SGD_REF:S000073291|PMID:12646576 IMP P YDR350C|ATP22 gene taxon:4932 20030618 SGD
+SGD S000000248 TCM62 GO:0005743 SGD_REF:S000040536|PMID:9822678 IDA C chaperone (putative) YBR044C gene taxon:4932 20010118 SGD
+SGD S000000248 TCM62 GO:0051082 SGD_REF:S000040536|PMID:9822678 IMP F chaperone (putative) YBR044C gene taxon:4932 20010118 SGD
+SGD S000000248 TCM62 GO:0006461 SGD_REF:S000040536|PMID:9822678 IPI P chaperone (putative) YBR044C gene taxon:4932 20010118 SGD
+SGD S000000248 TCM62 GO:0006461 SGD_REF:S000040536|PMID:9822678 IMP P chaperone (putative) YBR044C gene taxon:4932 20010118 SGD
+SGD S000006101 TCO89 GO:0000306 SGD_REF:S000075967|PMID:14736892 IDA C YPL180W gene taxon:4932 20051103 SGD
+SGD S000006101 TCO89 GO:0000329 SGD_REF:S000074185|PMID:14562095 IDA C YPL180W gene taxon:4932 20031028 SGD
+SGD S000006101 TCO89 GO:0031234 SGD_REF:S000075967|PMID:14736892 IDA C YPL180W gene taxon:4932 20051103 SGD
+SGD S000006101 TCO89 GO:0031931 SGD_REF:S000075967|PMID:14736892 IPI C YPL180W gene taxon:4932 20051130 SGD
+SGD S000006101 TCO89 GO:0005554 SGD_REF:S000069584 ND F YPL180W gene taxon:4932 20021204 SGD
+SGD S000006101 TCO89 GO:0001558 SGD_REF:S000075967|PMID:14736892 IPI SGD:S000003827 P YPL180W gene taxon:4932 20051104 SGD
+SGD S000006101 TCO89 GO:0006071 SGD_REF:S000049737|PMID:10931309 IGI P YPL180W gene taxon:4932 20021204 SGD
+SGD S000006101 TCO89 GO:0031505 SGD_REF:S000075967|PMID:14736892 IMP P YPL180W gene taxon:4932 20051103 SGD
+SGD S000002620 TCP1 GO:0005737 SGD_REF:S000042209|PMID:8771707 TAS C chaperonin subunit alpha YDR212W|CCT1 gene taxon:4932 20010118 SGD
+SGD S000002620 TCP1 GO:0005832 SGD_REF:S000042209|PMID:8771707 TAS C chaperonin subunit alpha YDR212W|CCT1 gene taxon:4932 20031215 SGD
+SGD S000002620 TCP1 GO:0005832 SGD_REF:S000080727|PMID:15704212 IPI SGD:S000002596 C chaperonin subunit alpha YDR212W|CCT1 gene taxon:4932 20050307 SGD
+SGD S000002620 TCP1 GO:0005856 SGD_REF:S000042209|PMID:8771707 TAS C chaperonin subunit alpha YDR212W|CCT1 gene taxon:4932 20010118 SGD
+SGD S000002620 TCP1 GO:0051082 SGD_REF:S000042209|PMID:8771707 TAS F chaperonin subunit alpha YDR212W|CCT1 gene taxon:4932 20010118 SGD
+SGD S000002620 TCP1 GO:0006457 SGD_REF:S000042209|PMID:8771707 TAS P chaperonin subunit alpha YDR212W|CCT1 gene taxon:4932 20010118 SGD
+SGD S000002620 TCP1 GO:0007010 SGD_REF:S000042209|PMID:8771707 TAS P chaperonin subunit alpha YDR212W|CCT1 gene taxon:4932 20010118 SGD
+SGD S000003588 TDH1 GO:0005737 SGD_REF:S000059685|PMID:11158358 IDA C glyceraldehyde-3-phosphate dehydrogenase 1 YJL052W|GLD3 gene taxon:4932 20050616 SGD
+SGD S000003588 TDH1 GO:0005811 SGD_REF:S000048561|PMID:10515935 IDA C glyceraldehyde-3-phosphate dehydrogenase 1 YJL052W|GLD3 gene taxon:4932 20010118 SGD
+SGD S000003588 TDH1 GO:0009277 SGD_REF:S000059685|PMID:11158358 IDA C glyceraldehyde-3-phosphate dehydrogenase 1 YJL052W|GLD3 gene taxon:4932 20030416 SGD
+SGD S000003588 TDH1 GO:0004365 SGD_REF:S000047727|PMID:3905788 IDA F glyceraldehyde-3-phosphate dehydrogenase 1 YJL052W|GLD3 gene taxon:4932 20010118 SGD
+SGD S000003588 TDH1 GO:0006094 SGD_REF:S000047727|PMID:3905788 IEP P glyceraldehyde-3-phosphate dehydrogenase 1 YJL052W|GLD3 gene taxon:4932 20050525 SGD
+SGD S000003588 TDH1 GO:0006096 SGD_REF:S000047727|PMID:3905788 IEP P glyceraldehyde-3-phosphate dehydrogenase 1 YJL052W|GLD3 gene taxon:4932 20050525 SGD
+SGD S000003769 TDH2 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C glyceraldehyde 3-phosphate dehydrogenase YJR009C|GLD2 gene taxon:4932 20020507 SGD
+SGD S000003769 TDH2 GO:0005737 SGD_REF:S000059685|PMID:11158358 IDA C glyceraldehyde 3-phosphate dehydrogenase YJR009C|GLD2 gene taxon:4932 20050616 SGD
+SGD S000003769 TDH2 GO:0005811 SGD_REF:S000048561|PMID:10515935 IDA C glyceraldehyde 3-phosphate dehydrogenase YJR009C|GLD2 gene taxon:4932 20010118 SGD
+SGD S000003769 TDH2 GO:0009277 SGD_REF:S000059685|PMID:11158358 IDA C glyceraldehyde 3-phosphate dehydrogenase YJR009C|GLD2 gene taxon:4932 20030416 SGD
+SGD S000003769 TDH2 GO:0004365 SGD_REF:S000047727|PMID:3905788 IDA F glyceraldehyde 3-phosphate dehydrogenase YJR009C|GLD2 gene taxon:4932 20010118 SGD
+SGD S000003769 TDH2 GO:0006094 SGD_REF:S000047727|PMID:3905788 IEP P glyceraldehyde 3-phosphate dehydrogenase YJR009C|GLD2 gene taxon:4932 20050525 SGD
+SGD S000003769 TDH2 GO:0006096 SGD_REF:S000047727|PMID:3905788 IEP P glyceraldehyde 3-phosphate dehydrogenase YJR009C|GLD2 gene taxon:4932 20050525 SGD
+SGD S000003424 TDH3 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C glyceraldehyde-3-phosphate dehydrogenase 3 YGR192C|GLD1|HSP35|HSP36|SSS2 gene taxon:4932 20020507 SGD
+SGD S000003424 TDH3 GO:0005737 SGD_REF:S000059685|PMID:11158358 IDA C glyceraldehyde-3-phosphate dehydrogenase 3 YGR192C|GLD1|HSP35|HSP36|SSS2 gene taxon:4932 20050616 SGD
+SGD S000003424 TDH3 GO:0005811 SGD_REF:S000048561|PMID:10515935 IDA C glyceraldehyde-3-phosphate dehydrogenase 3 YGR192C|GLD1|HSP35|HSP36|SSS2 gene taxon:4932 20010118 SGD
+SGD S000003424 TDH3 GO:0009277 SGD_REF:S000059685|PMID:11158358 IDA C glyceraldehyde-3-phosphate dehydrogenase 3 YGR192C|GLD1|HSP35|HSP36|SSS2 gene taxon:4932 20030416 SGD
+SGD S000003424 TDH3 GO:0004365 SGD_REF:S000047727|PMID:3905788 IDA F glyceraldehyde-3-phosphate dehydrogenase 3 YGR192C|GLD1|HSP35|HSP36|SSS2 gene taxon:4932 20010118 SGD
+SGD S000003424 TDH3 GO:0006094 SGD_REF:S000047727|PMID:3905788 IEP P glyceraldehyde-3-phosphate dehydrogenase 3 YGR192C|GLD1|HSP35|HSP36|SSS2 gene taxon:4932 20050525 SGD
+SGD S000003424 TDH3 GO:0006096 SGD_REF:S000047727|PMID:3905788 IEP P glyceraldehyde-3-phosphate dehydrogenase 3 YGR192C|GLD1|HSP35|HSP36|SSS2 gene taxon:4932 20050525 SGD
+SGD S000000427 TDP1 GO:0005634 SGD_REF:S000071811|PMID:12206772 IDA C YBR223C gene taxon:4932 20021210 SGD
+SGD S000000427 TDP1 GO:0005634 SGD_REF:S000064819|PMID:10521354 IMP C YBR223C gene taxon:4932 20021009 SGD
+SGD S000000427 TDP1 GO:0017005 SGD_REF:S000064819|PMID:10521354 IDA F YBR223C gene taxon:4932 20021204 SGD
+SGD S000000427 TDP1 GO:0006281 SGD_REF:S000064819|PMID:10521354 IMP P YBR223C gene taxon:4932 20021009 SGD
+SGD S000005864 TEA1 GO:0005634 SGD_REF:S000052082|PMID:8524314 IGI C YOR337W gene taxon:4932 20021106 SGD
+SGD S000005864 TEA1 GO:0005634 SGD_REF:S000052082|PMID:8524314 IPI C YOR337W gene taxon:4932 20021106 SGD
+SGD S000005864 TEA1 GO:0003677 SGD_REF:S000052082|PMID:8524314 IDA F YOR337W gene taxon:4932 20021106 SGD
+SGD S000005864 TEA1 GO:0006350 SGD_REF:S000052082|PMID:8524314 IGI P YOR337W gene taxon:4932 20021106 SGD
+SGD S000005864 TEA1 GO:0006350 SGD_REF:S000052082|PMID:8524314 IPI P YOR337W gene taxon:4932 20021106 SGD
+SGD S000000287 TEC1 GO:0005634 SGD_REF:S000042365|PMID:9036858 IC GO:0003704 C TEA/ATTS DNA-binding domain family transcription factor YBR083W|ROC1 gene taxon:4932 20021209 SGD
+SGD S000000287 TEC1 GO:0003704 SGD_REF:S000042365|PMID:9036858 IDA F TEA/ATTS DNA-binding domain family transcription factor YBR083W|ROC1 gene taxon:4932 20010118 SGD
+SGD S000000287 TEC1 GO:0001403 SGD_REF:S000080086|PMID:15620357 TAS P TEA/ATTS DNA-binding domain family transcription factor YBR083W|ROC1 gene taxon:4932 20050218 SGD
+SGD S000000287 TEC1 GO:0007124 SGD_REF:S000042365|PMID:9036858 IMP P TEA/ATTS DNA-binding domain family transcription factor YBR083W|ROC1 gene taxon:4932 20010118 SGD
+SGD S000000287 TEC1 GO:0007124 SGD_REF:S000042365|PMID:9036858 IDA P TEA/ATTS DNA-binding domain family transcription factor YBR083W|ROC1 gene taxon:4932 20010118 SGD
+SGD S000000287 TEC1 GO:0007124 SGD_REF:S000045194|PMID:8730867 IMP P TEA/ATTS DNA-binding domain family transcription factor YBR083W|ROC1 gene taxon:4932 20050218 SGD
+SGD S000000287 TEC1 GO:0045944 SGD_REF:S000042365|PMID:9036858 IDA P TEA/ATTS DNA-binding domain family transcription factor YBR083W|ROC1 gene taxon:4932 20021209 SGD
+SGD S000006284 TEF1 GO:0005840 SGD_REF:S000058753|PMID:9841679 TAS C translational elongation factor EF-1 alpha YPR080W|EF-1 alpha|eEF1A gene taxon:4932 20010124 SGD
+SGD S000006284 TEF1 GO:0005853 SGD_REF:S000075853|PMID:3026912 ISS C translational elongation factor EF-1 alpha YPR080W|EF-1 alpha|eEF1A gene taxon:4932 20050105 SGD
+SGD S000006284 TEF1 GO:0003746 SGD_REF:S000058753|PMID:9841679 TAS F translational elongation factor EF-1 alpha YPR080W|EF-1 alpha|eEF1A gene taxon:4932 20010125 SGD
+SGD S000006284 TEF1 GO:0006414 SGD_REF:S000058753|PMID:9841679 TAS P translational elongation factor EF-1 alpha YPR080W|EF-1 alpha|eEF1A gene taxon:4932 20010125 SGD
+SGD S000000322 TEF2 GO:0005840 SGD_REF:S000058753|PMID:9841679 TAS C translational elongation factor EF-1 alpha YBR118W|EF-1 alpha|eEF1A gene taxon:4932 20010124 SGD
+SGD S000000322 TEF2 GO:0005853 SGD_REF:S000075853|PMID:3026912 ISS C translational elongation factor EF-1 alpha YBR118W|EF-1 alpha|eEF1A gene taxon:4932 20050105 SGD
+SGD S000000322 TEF2 GO:0003746 SGD_REF:S000058753|PMID:9841679 TAS F translational elongation factor EF-1 alpha YBR118W|EF-1 alpha|eEF1A gene taxon:4932 20010125 SGD
+SGD S000000322 TEF2 GO:0006414 SGD_REF:S000058753|PMID:9841679 TAS P translational elongation factor EF-1 alpha YBR118W|EF-1 alpha|eEF1A gene taxon:4932 20010125 SGD
+SGD S000001564 TEF4 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C translation elongation factor EF-1gamma YKL081W|EFC1 gene taxon:4932 20040928 SGD
+SGD S000001564 TEF4 GO:0005840 SGD_REF:S000058753|PMID:9841679 TAS C translation elongation factor EF-1gamma YKL081W|EFC1 gene taxon:4932 20010124 SGD
+SGD S000001564 TEF4 GO:0005853 SGD_REF:S000045141|PMID:8041634 ISS C translation elongation factor EF-1gamma YKL081W|EFC1 gene taxon:4932 20050105 SGD
+SGD S000001564 TEF4 GO:0003746 SGD_REF:S000058753|PMID:9841679 TAS F translation elongation factor EF-1gamma YKL081W|EFC1 gene taxon:4932 20010125 SGD
+SGD S000001564 TEF4 GO:0006414 SGD_REF:S000058753|PMID:9841679 TAS P translation elongation factor EF-1gamma YKL081W|EFC1 gene taxon:4932 20010125 SGD
+SGD S000000184 TEL1 GO:0005634 SGD_REF:S000062066|PMID:8982452 TAS C YBL088C gene taxon:4932 20030324 SGD
+SGD S000000184 TEL1 GO:0005634 SGD_REF:S000039465|PMID:3513174 IC GO:0007004 C YBL088C gene taxon:4932 20030324 SGD
+SGD S000000184 TEL1 GO:0005634 SGD_REF:S000057375|PMID:7569949 IC GO:0006974 C YBL088C gene taxon:4932 20030324 SGD
+SGD S000000184 TEL1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YBL088C gene taxon:4932 20040928 SGD
+SGD S000000184 TEL1 GO:0004672 SGD_REF:S000059421|PMID:11095737 IDA F YBL088C gene taxon:4932 20040311 SGD
+SGD S000000184 TEL1 GO:0006974 SGD_REF:S000057375|PMID:7569949 TAS P YBL088C gene taxon:4932 20010118 SGD
+SGD S000000184 TEL1 GO:0007004 SGD_REF:S000039465|PMID:3513174 IMP P YBL088C gene taxon:4932 20010118 SGD
+SGD S000000184 TEL1 GO:0016310 SGD_REF:S000073980|PMID:12923051 TAS P YBL088C gene taxon:4932 20040328 SGD
+SGD S000003331 TEL2 GO:0000783 SGD_REF:S000039507|PMID:9490802 IDA C telomere binding protein YGR099W gene taxon:4932 20030403 SGD
+SGD S000003331 TEL2 GO:0042162 SGD_REF:S000052011|PMID:10525964 IDA F telomere binding protein YGR099W gene taxon:4932 20020711 SGD
+SGD S000003331 TEL2 GO:0007004 SGD_REF:S000055772|PMID:8649421 IMP P telomere binding protein YGR099W gene taxon:4932 20020711 SGD
+SGD S000004529 TEM1 GO:0005816 SGD_REF:S000060813|PMID:11434459 TAS C GTP-binding protein, ras family YML064C gene taxon:4932 20020930 SGD
+SGD S000004529 TEM1 GO:0003924 SGD_REF:S000054199|PMID:7935462 ISS F GTP-binding protein, ras family YML064C gene taxon:4932 20010118 SGD
+SGD S000004529 TEM1 GO:0005515 SGD_REF:S000043128|PMID:10688190 IPI SGD:S000001241|SGD:S000005277 F GTP-binding protein, ras family YML064C gene taxon:4932 20030602 SGD
+SGD S000004529 TEM1 GO:0007096 SGD_REF:S000086185|PMID:16039591 TAS P GTP-binding protein, ras family YML064C gene taxon:4932 20060314 SGD
+SGD S000004000 TEN1 GO:0000783 SGD_REF:S000070037|PMID:11352055 TAS C YLR010C gene taxon:4932 20030403 SGD
+SGD S000004000 TEN1 GO:0005554 SGD_REF:S000069584 ND F YLR010C gene taxon:4932 20021030 SGD
+SGD S000004000 TEN1 GO:0016233 SGD_REF:S000070037|PMID:11352055 TAS P YLR010C gene taxon:4932 20020625 SGD
+SGD S000005072 TEP1 GO:0008372 SGD_REF:S000069584 ND C tyrosine phosphatase (putative) YNL128W gene taxon:4932 20021009 SGD
+SGD S000005072 TEP1 GO:0004437 SGD_REF:S000059409|PMID:11070083 IDA F tyrosine phosphatase (putative) YNL128W gene taxon:4932 20021009 SGD
+SGD S000005072 TEP1 GO:0030476 SGD_REF:S000059409|PMID:11070083 IMP P tyrosine phosphatase (putative) YNL128W gene taxon:4932 20021009 SGD
+SGD S000005072 TEP1 GO:0046856 SGD_REF:S000059409|PMID:11070083 IDA P tyrosine phosphatase (putative) YNL128W gene taxon:4932 20050331 SGD
+SGD S000005072 TEP1 GO:0048017 SGD_REF:S000059409|PMID:11070083 IMP P tyrosine phosphatase (putative) YNL128W gene taxon:4932 20050524 SGD
+SGD S000003780 TES1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C acyl-CoA thioesterase YJR019C|PTE1 gene taxon:4932 20040928 SGD
+SGD S000003780 TES1 GO:0005777 SGD_REF:S000040379|PMID:10092594 IDA C acyl-CoA thioesterase YJR019C|PTE1 gene taxon:4932 20050526 SGD
+SGD S000003780 TES1 GO:0016291 SGD_REF:S000040379|PMID:10092594 IDA F acyl-CoA thioesterase YJR019C|PTE1 gene taxon:4932 20021021 SGD
+SGD S000003780 TES1 GO:0019395 SGD_REF:S000040379|PMID:10092594 IMP P acyl-CoA thioesterase YJR019C|PTE1 gene taxon:4932 20050526 SGD
+SGD S000003780 TES1 GO:0019395 SGD_REF:S000040379|PMID:10092594 IEP P acyl-CoA thioesterase YJR019C|PTE1 gene taxon:4932 20050526 SGD
+SGD S000005197 TEX1 GO:0000346 SGD_REF:S000069956|PMID:11979277 IPI C YNL253W gene taxon:4932 20030221 SGD
+SGD S000005197 TEX1 GO:0005554 SGD_REF:S000069584 ND F YNL253W gene taxon:4932 20030221 SGD
+SGD S000005197 TEX1 GO:0006406 SGD_REF:S000069956|PMID:11979277 IC GO:0000346 P YNL253W gene taxon:4932 20030221 SGD
+SGD S000001511 TFA1 GO:0005673 SGD_REF:S000058446|PMID:9774381 TAS C transcription factor tfIIE large subunit YKL028W gene taxon:4932 20010118 SGD
+SGD S000001511 TFA1 GO:0016251 SGD_REF:S000058446|PMID:9774381 TAS F transcription factor tfIIE large subunit YKL028W gene taxon:4932 20010119 SGD
+SGD S000001511 TFA1 GO:0006367 SGD_REF:S000056378|PMID:10384286 TAS P transcription factor tfIIE large subunit YKL028W gene taxon:4932 20010118 SGD
+SGD S000001511 TFA1 GO:0006367 SGD_REF:S000056377|PMID:10384273 TAS P transcription factor tfIIE large subunit YKL028W gene taxon:4932 20010118 SGD
+SGD S000001770 TFA2 GO:0005673 SGD_REF:S000058446|PMID:9774381 TAS C transcription factor TFIIE subunit YKR062W gene taxon:4932 20010118 SGD
+SGD S000001770 TFA2 GO:0016251 SGD_REF:S000058446|PMID:9774381 TAS F transcription factor TFIIE subunit YKR062W gene taxon:4932 20010119 SGD
+SGD S000001770 TFA2 GO:0006367 SGD_REF:S000056378|PMID:10384286 TAS P transcription factor TFIIE subunit YKR062W gene taxon:4932 20010118 SGD
+SGD S000001770 TFA2 GO:0006367 SGD_REF:S000056377|PMID:10384273 TAS P transcription factor TFIIE subunit YKR062W gene taxon:4932 20010118 SGD
+SGD S000002719 TFB1 GO:0000112 SGD_REF:S000070118|PMID:10915862 TAS C transcription initiation factor IIb, 75 kDa subunit component YDR311W gene taxon:4932 20020710 SGD
+SGD S000002719 TFB1 GO:0005675 SGD_REF:S000058446|PMID:9774381 TAS C transcription initiation factor IIb, 75 kDa subunit component YDR311W gene taxon:4932 20010118 SGD
+SGD S000002719 TFB1 GO:0005675 SGD_REF:S000075290|PMID:14500720 IDA C transcription initiation factor IIb, 75 kDa subunit component YDR311W gene taxon:4932 20041013 SGD
+SGD S000002719 TFB1 GO:0016251 SGD_REF:S000058446|PMID:9774381 TAS F transcription initiation factor IIb, 75 kDa subunit component YDR311W gene taxon:4932 20010119 SGD
+SGD S000002719 TFB1 GO:0000717 SGD_REF:S000070118|PMID:10915862 TAS P transcription initiation factor IIb, 75 kDa subunit component YDR311W gene taxon:4932 20020726 SGD
+SGD S000002719 TFB1 GO:0006289 SGD_REF:S000058446|PMID:9774381 TAS P transcription initiation factor IIb, 75 kDa subunit component YDR311W gene taxon:4932 20010118 SGD
+SGD S000002719 TFB1 GO:0006367 SGD_REF:S000056378|PMID:10384286 TAS P transcription initiation factor IIb, 75 kDa subunit component YDR311W gene taxon:4932 20010118 SGD
+SGD S000002719 TFB1 GO:0006367 SGD_REF:S000056377|PMID:10384273 TAS P transcription initiation factor IIb, 75 kDa subunit component YDR311W gene taxon:4932 20010118 SGD
+SGD S000002719 TFB1 GO:0007070 SGD_REF:S000056377|PMID:10384273 TAS P transcription initiation factor IIb, 75 kDa subunit component YDR311W gene taxon:4932 20010118 SGD
+SGD S000006043 TFB2 GO:0000112 SGD_REF:S000070118|PMID:10915862 TAS C TFIIH subunit YPL122C gene taxon:4932 20020710 SGD
+SGD S000006043 TFB2 GO:0005675 SGD_REF:S000058446|PMID:9774381 TAS C TFIIH subunit YPL122C gene taxon:4932 20010118 SGD
+SGD S000006043 TFB2 GO:0005675 SGD_REF:S000075290|PMID:14500720 IDA C TFIIH subunit YPL122C gene taxon:4932 20041013 SGD
+SGD S000006043 TFB2 GO:0016251 SGD_REF:S000058446|PMID:9774381 TAS F TFIIH subunit YPL122C gene taxon:4932 20010119 SGD
+SGD S000006043 TFB2 GO:0000717 SGD_REF:S000070118|PMID:10915862 TAS P TFIIH subunit YPL122C gene taxon:4932 20020726 SGD
+SGD S000006043 TFB2 GO:0006289 SGD_REF:S000058446|PMID:9774381 TAS P TFIIH subunit YPL122C gene taxon:4932 20010118 SGD
+SGD S000006043 TFB2 GO:0006367 SGD_REF:S000056378|PMID:10384286 TAS P TFIIH subunit YPL122C gene taxon:4932 20010118 SGD
+SGD S000006043 TFB2 GO:0006367 SGD_REF:S000056377|PMID:10384273 TAS P TFIIH subunit YPL122C gene taxon:4932 20010118 SGD
+SGD S000006043 TFB2 GO:0007070 SGD_REF:S000056377|PMID:10384273 TAS P TFIIH subunit YPL122C gene taxon:4932 20010118 SGD
+SGD S000002868 TFB3 GO:0000112 SGD_REF:S000070118|PMID:10915862 TAS C TFIIH subunit YDR460W|RIG2 gene taxon:4932 20020710 SGD
+SGD S000002868 TFB3 GO:0005675 SGD_REF:S000058446|PMID:9774381 TAS C TFIIH subunit YDR460W|RIG2 gene taxon:4932 20041013 SGD
+SGD S000002868 TFB3 GO:0005675 SGD_REF:S000075290|PMID:14500720 IDA C TFIIH subunit YDR460W|RIG2 gene taxon:4932 20041013 SGD
+SGD S000002868 TFB3 GO:0016251 SGD_REF:S000058446|PMID:9774381 TAS F TFIIH subunit YDR460W|RIG2 gene taxon:4932 20010119 SGD
+SGD S000002868 TFB3 GO:0000717 SGD_REF:S000070118|PMID:10915862 TAS P TFIIH subunit YDR460W|RIG2 gene taxon:4932 20020726 SGD
+SGD S000002868 TFB3 GO:0006289 SGD_REF:S000058446|PMID:9774381 TAS P TFIIH subunit YDR460W|RIG2 gene taxon:4932 20010118 SGD
+SGD S000002868 TFB3 GO:0006367 SGD_REF:S000056378|PMID:10384286 TAS P TFIIH subunit YDR460W|RIG2 gene taxon:4932 20010118 SGD
+SGD S000002868 TFB3 GO:0006367 SGD_REF:S000056377|PMID:10384273 TAS P TFIIH subunit YDR460W|RIG2 gene taxon:4932 20010118 SGD
+SGD S000002868 TFB3 GO:0007070 SGD_REF:S000056377|PMID:10384273 TAS P TFIIH subunit YDR460W|RIG2 gene taxon:4932 20010118 SGD
+SGD S000006260 TFB4 GO:0005675 SGD_REF:S000058446|PMID:9774381 TAS C transcription initiation factor TFIIH subunit YPR056W gene taxon:4932 20010118 SGD
+SGD S000006260 TFB4 GO:0005675 SGD_REF:S000075290|PMID:14500720 IDA C transcription initiation factor TFIIH subunit YPR056W gene taxon:4932 20041013 SGD
+SGD S000006260 TFB4 GO:0016251 SGD_REF:S000058446|PMID:9774381 TAS F transcription initiation factor TFIIH subunit YPR056W gene taxon:4932 20010119 SGD
+SGD S000006260 TFB4 GO:0006367 SGD_REF:S000056378|PMID:10384286 TAS P transcription initiation factor TFIIH subunit YPR056W gene taxon:4932 20010118 SGD
+SGD S000006260 TFB4 GO:0006367 SGD_REF:S000056377|PMID:10384273 TAS P transcription initiation factor TFIIH subunit YPR056W gene taxon:4932 20010118 SGD
+SGD S000006260 TFB4 GO:0007070 SGD_REF:S000056377|PMID:10384273 TAS P transcription initiation factor TFIIH subunit YPR056W gene taxon:4932 20010118 SGD
+SGD S000007603 TFB5 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C transcription initiation/DNA repair factor TFIIH subunit YDR079C-A gene taxon:4932 20031028 SGD
+SGD S000007603 TFB5 GO:0005675 SGD_REF:S000076786|PMID:15220919 IDA C transcription initiation/DNA repair factor TFIIH subunit YDR079C-A gene taxon:4932 20040811 SGD
+SGD S000007603 TFB5 GO:0005554 SGD_REF:S000069584 ND F transcription initiation/DNA repair factor TFIIH subunit YDR079C-A gene taxon:4932 20020425 SGD
+SGD S000007603 TFB5 GO:0016251 SGD_REF:S000076786|PMID:15220919 IDA F transcription initiation/DNA repair factor TFIIH subunit YDR079C-A gene taxon:4932 20040811 SGD
+SGD S000007603 TFB5 GO:0006281 SGD_REF:S000073478|PMID:12697762 ISS P transcription initiation/DNA repair factor TFIIH subunit YDR079C-A gene taxon:4932 20030702 SGD
+SGD S000007603 TFB5 GO:0006367 SGD_REF:S000076786|PMID:15220919 IDA P transcription initiation/DNA repair factor TFIIH subunit YDR079C-A gene taxon:4932 20040811 SGD
+SGD S000000327 TFC1 GO:0000127 SGD_REF:S000058472|PMID:10384303 TAS C 95 kDa, transcription factor tau (TFIIIC) subunit YBR123C gene taxon:4932 20010118 SGD
+SGD S000000327 TFC1 GO:0003709 SGD_REF:S000058472|PMID:10384303 TAS F 95 kDa, transcription factor tau (TFIIIC) subunit YBR123C gene taxon:4932 20010118 SGD
+SGD S000000327 TFC1 GO:0006384 SGD_REF:S000058472|PMID:10384303 TAS P 95 kDa, transcription factor tau (TFIIIC) subunit YBR123C gene taxon:4932 20010118 SGD
+SGD S000000001 TFC3 GO:0000127 SGD_REF:S000058472|PMID:10384303 TAS C transcription factor tau (TFIIIC) subunit YAL001C|FUN24|TSV115 gene taxon:4932 20010118 SGD
+SGD S000000001 TFC3 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C transcription factor tau (TFIIIC) subunit YAL001C|FUN24|TSV115 gene taxon:4932 20040928 SGD
+SGD S000000001 TFC3 GO:0003709 SGD_REF:S000058472|PMID:10384303 TAS F transcription factor tau (TFIIIC) subunit YAL001C|FUN24|TSV115 gene taxon:4932 20010118 SGD
+SGD S000000001 TFC3 GO:0006384 SGD_REF:S000058472|PMID:10384303 TAS P transcription factor tau (TFIIIC) subunit YAL001C|FUN24|TSV115 gene taxon:4932 20010118 SGD
+SGD S000003279 TFC4 GO:0000127 SGD_REF:S000058472|PMID:10384303 TAS C 131 kDa, transcription factor tau (TFIIIC) subunit YGR047C|PCF1 gene taxon:4932 20010118 SGD
+SGD S000003279 TFC4 GO:0003709 SGD_REF:S000058472|PMID:10384303 TAS F 131 kDa, transcription factor tau (TFIIIC) subunit YGR047C|PCF1 gene taxon:4932 20010118 SGD
+SGD S000003279 TFC4 GO:0006384 SGD_REF:S000058472|PMID:10384303 TAS P 131 kDa, transcription factor tau (TFIIIC) subunit YGR047C|PCF1 gene taxon:4932 20010118 SGD
+SGD S000002770 TFC6 GO:0000127 SGD_REF:S000058472|PMID:10384303 TAS C 91 kDa tau91 subunit of transcription factor IIIC (TFIIIC) YDR362C gene taxon:4932 20010118 SGD
+SGD S000002770 TFC6 GO:0003709 SGD_REF:S000058472|PMID:10384303 TAS F 91 kDa tau91 subunit of transcription factor IIIC (TFIIIC) YDR362C gene taxon:4932 20010118 SGD
+SGD S000002770 TFC6 GO:0006384 SGD_REF:S000058472|PMID:10384303 TAS P 91 kDa tau91 subunit of transcription factor IIIC (TFIIIC) YDR362C gene taxon:4932 20010118 SGD
+SGD S000005636 TFC7 GO:0000127 SGD_REF:S000058472|PMID:10384303 TAS C TFIIIC (tau55) 55 kDa subunit YOR110W gene taxon:4932 20010118 SGD
+SGD S000005636 TFC7 GO:0003709 SGD_REF:S000058472|PMID:10384303 TAS F TFIIIC (tau55) 55 kDa subunit YOR110W gene taxon:4932 20010118 SGD
+SGD S000005636 TFC7 GO:0006384 SGD_REF:S000058472|PMID:10384303 TAS P TFIIIC (tau55) 55 kDa subunit YOR110W gene taxon:4932 20010118 SGD
+SGD S000005928 TFC8 GO:0000127 SGD_REF:S000058472|PMID:10384303 TAS C TFIIIC (tau60) 60 kDa subunit YPL007C gene taxon:4932 20010118 SGD
+SGD S000005928 TFC8 GO:0003709 SGD_REF:S000058472|PMID:10384303 TAS F TFIIIC (tau60) 60 kDa subunit YPL007C gene taxon:4932 20010118 SGD
+SGD S000005928 TFC8 GO:0006384 SGD_REF:S000058472|PMID:10384303 TAS P TFIIIC (tau60) 60 kDa subunit YPL007C gene taxon:4932 20010118 SGD
+SGD S000003418 TFG1 GO:0005674 SGD_REF:S000058446|PMID:9774381 TAS C transcription factor TFIIF large subunit YGR186W|RAP74|SSU71 gene taxon:4932 20010118 SGD
+SGD S000003418 TFG1 GO:0016251 SGD_REF:S000058446|PMID:9774381 TAS F transcription factor TFIIF large subunit YGR186W|RAP74|SSU71 gene taxon:4932 20010119 SGD
+SGD S000003418 TFG1 GO:0006367 SGD_REF:S000056378|PMID:10384286 TAS P transcription factor TFIIF large subunit YGR186W|RAP74|SSU71 gene taxon:4932 20010118 SGD
+SGD S000003418 TFG1 GO:0006367 SGD_REF:S000056377|PMID:10384273 TAS P transcription factor TFIIF large subunit YGR186W|RAP74|SSU71 gene taxon:4932 20010118 SGD
+SGD S000003237 TFG2 GO:0005674 SGD_REF:S000058446|PMID:9774381 TAS C transcription initiation factor TFIIF middle subunit YGR005C gene taxon:4932 20010118 SGD
+SGD S000003237 TFG2 GO:0016251 SGD_REF:S000058446|PMID:9774381 TAS F transcription initiation factor TFIIF middle subunit YGR005C gene taxon:4932 20010119 SGD
+SGD S000003237 TFG2 GO:0006367 SGD_REF:S000056378|PMID:10384286 TAS P transcription initiation factor TFIIF middle subunit YGR005C gene taxon:4932 20010118 SGD
+SGD S000003237 TFG2 GO:0006367 SGD_REF:S000056377|PMID:10384273 TAS P transcription initiation factor TFIIF middle subunit YGR005C gene taxon:4932 20010118 SGD
+SGD S000002344 TFP1 GO:0000221 SGD_REF:S000056362|PMID:10224039 TAS C protein with three regions (ABC) that are spliced to yield the extein AC and the intein B; AC is a 69K vacuolar (H+)-ATPase, and B is a 50K site-specfic endonuclease named VDE (PI-SceI) that is homologous to HO. Cleavage is meiosis-specific and induces ge, site-specific endonuclease VDE (PI-SceI), vacuolar ATPase V1 domain subunit A (69 kDa) YDL185W|CLS8|VMA1 gene taxon:4932 20010118 SGD
+SGD S000002344 TFP1 GO:0000221 SGD_REF:S000058276|PMID:9442887 TAS C protein with three regions (ABC) that are spliced to yield the extein AC and the intein B; AC is a 69K vacuolar (H+)-ATPase, and B is a 50K site-specfic endonuclease named VDE (PI-SceI) that is homologous to HO. Cleavage is meiosis-specific and induces ge, site-specific endonuclease VDE (PI-SceI), vacuolar ATPase V1 domain subunit A (69 kDa) YDL185W|CLS8|VMA1 gene taxon:4932 20010118 SGD
+SGD S000002344 TFP1 GO:0000329 SGD_REF:S000056306|PMID:7775427 IDA C protein with three regions (ABC) that are spliced to yield the extein AC and the intein B; AC is a 69K vacuolar (H+)-ATPase, and B is a 50K site-specfic endonuclease named VDE (PI-SceI) that is homologous to HO. Cleavage is meiosis-specific and induces ge, site-specific endonuclease VDE (PI-SceI), vacuolar ATPase V1 domain subunit A (69 kDa) YDL185W|CLS8|VMA1 gene taxon:4932 20030225 SGD
+SGD S000002344 TFP1 GO:0004520 SGD_REF:S000048617|PMID:1534148 TAS F protein with three regions (ABC) that are spliced to yield the extein AC and the intein B; AC is a 69K vacuolar (H+)-ATPase, and B is a 50K site-specfic endonuclease named VDE (PI-SceI) that is homologous to HO. Cleavage is meiosis-specific and induces ge, site-specific endonuclease VDE (PI-SceI), vacuolar ATPase V1 domain subunit A (69 kDa) YDL185W|CLS8|VMA1 gene taxon:4932 20010118 SGD
+SGD S000002344 TFP1 GO:0046961 SGD_REF:S000056362|PMID:10224039 TAS F protein with three regions (ABC) that are spliced to yield the extein AC and the intein B; AC is a 69K vacuolar (H+)-ATPase, and B is a 50K site-specfic endonuclease named VDE (PI-SceI) that is homologous to HO. Cleavage is meiosis-specific and induces ge, site-specific endonuclease VDE (PI-SceI), vacuolar ATPase V1 domain subunit A (69 kDa) YDL185W|CLS8|VMA1 gene taxon:4932 20030716 SGD
+SGD S000002344 TFP1 GO:0046961 SGD_REF:S000058276|PMID:9442887 TAS F protein with three regions (ABC) that are spliced to yield the extein AC and the intein B; AC is a 69K vacuolar (H+)-ATPase, and B is a 50K site-specfic endonuclease named VDE (PI-SceI) that is homologous to HO. Cleavage is meiosis-specific and induces ge, site-specific endonuclease VDE (PI-SceI), vacuolar ATPase V1 domain subunit A (69 kDa) YDL185W|CLS8|VMA1 gene taxon:4932 20030716 SGD
+SGD S000002344 TFP1 GO:0006314 SGD_REF:S000048617|PMID:1534148 TAS P protein with three regions (ABC) that are spliced to yield the extein AC and the intein B; AC is a 69K vacuolar (H+)-ATPase, and B is a 50K site-specfic endonuclease named VDE (PI-SceI) that is homologous to HO. Cleavage is meiosis-specific and induces ge, site-specific endonuclease VDE (PI-SceI), vacuolar ATPase V1 domain subunit A (69 kDa) YDL185W|CLS8|VMA1 gene taxon:4932 20010118 SGD
+SGD S000002344 TFP1 GO:0007035 SGD_REF:S000056362|PMID:10224039 TAS P protein with three regions (ABC) that are spliced to yield the extein AC and the intein B; AC is a 69K vacuolar (H+)-ATPase, and B is a 50K site-specfic endonuclease named VDE (PI-SceI) that is homologous to HO. Cleavage is meiosis-specific and induces ge, site-specific endonuclease VDE (PI-SceI), vacuolar ATPase V1 domain subunit A (69 kDa) YDL185W|CLS8|VMA1 gene taxon:4932 20010118 SGD
+SGD S000002344 TFP1 GO:0007035 SGD_REF:S000058276|PMID:9442887 TAS P protein with three regions (ABC) that are spliced to yield the extein AC and the intein B; AC is a 69K vacuolar (H+)-ATPase, and B is a 50K site-specfic endonuclease named VDE (PI-SceI) that is homologous to HO. Cleavage is meiosis-specific and induces ge, site-specific endonuclease VDE (PI-SceI), vacuolar ATPase V1 domain subunit A (69 kDa) YDL185W|CLS8|VMA1 gene taxon:4932 20010118 SGD
+SGD S000002344 TFP1 GO:0019538 SGD_REF:S000054623|PMID:8508780 IDA P protein with three regions (ABC) that are spliced to yield the extein AC and the intein B; AC is a 69K vacuolar (H+)-ATPase, and B is a 50K site-specfic endonuclease named VDE (PI-SceI) that is homologous to HO. Cleavage is meiosis-specific and induces ge, site-specific endonuclease VDE (PI-SceI), vacuolar ATPase V1 domain subunit A (69 kDa) YDL185W|CLS8|VMA1 gene taxon:4932 20010118 SGD
+SGD S000006155 TFP3 GO:0000220 SGD_REF:S000056362|PMID:10224039 TAS C vacuolar ATPase V0 domain subunit c' (17 kDa), vacuolar H(+) ATPase 17 kDa subunit C YPL234C|CLS9|VMA11 gene taxon:4932 20010118 SGD
+SGD S000006155 TFP3 GO:0000220 SGD_REF:S000058276|PMID:9442887 TAS C vacuolar ATPase V0 domain subunit c' (17 kDa), vacuolar H(+) ATPase 17 kDa subunit C YPL234C|CLS9|VMA11 gene taxon:4932 20010118 SGD
+SGD S000006155 TFP3 GO:0016021 SGD_REF:S000077169|PMID:15252052 IDA C vacuolar ATPase V0 domain subunit c' (17 kDa), vacuolar H(+) ATPase 17 kDa subunit C YPL234C|CLS9|VMA11 gene taxon:4932 20040929 SGD
+SGD S000006155 TFP3 GO:0046961 SGD_REF:S000056362|PMID:10224039 TAS F vacuolar ATPase V0 domain subunit c' (17 kDa), vacuolar H(+) ATPase 17 kDa subunit C YPL234C|CLS9|VMA11 gene taxon:4932 20030716 SGD
+SGD S000006155 TFP3 GO:0046961 SGD_REF:S000058276|PMID:9442887 TAS F vacuolar ATPase V0 domain subunit c' (17 kDa), vacuolar H(+) ATPase 17 kDa subunit C YPL234C|CLS9|VMA11 gene taxon:4932 20030716 SGD
+SGD S000006155 TFP3 GO:0007035 SGD_REF:S000056362|PMID:10224039 TAS P vacuolar ATPase V0 domain subunit c' (17 kDa), vacuolar H(+) ATPase 17 kDa subunit C YPL234C|CLS9|VMA11 gene taxon:4932 20010118 SGD
+SGD S000006155 TFP3 GO:0007035 SGD_REF:S000058276|PMID:9442887 TAS P vacuolar ATPase V0 domain subunit c' (17 kDa), vacuolar H(+) ATPase 17 kDa subunit C YPL234C|CLS9|VMA11 gene taxon:4932 20010118 SGD
+SGD S000004168 TFS1 GO:0005625 SGD_REF:S000039310|PMID:9521655 IDA C lipid binding protein (putative), supressor of a cdc25 mutation YLR178C|DKA1 gene taxon:4932 20030110 SGD
+SGD S000004168 TFS1 GO:0008289 SGD_REF:S000039310|PMID:9521655 ISS F lipid binding protein (putative), supressor of a cdc25 mutation YLR178C|DKA1 gene taxon:4932 20020620 SGD
+SGD S000004168 TFS1 GO:0030414 SGD_REF:S000039310|PMID:9521655 IDA F lipid binding protein (putative), supressor of a cdc25 mutation YLR178C|DKA1 gene taxon:4932 20020620 SGD
+SGD S000004168 TFS1 GO:0030162 SGD_REF:S000039310|PMID:9521655 IDA P lipid binding protein (putative), supressor of a cdc25 mutation YLR178C|DKA1 gene taxon:4932 20030110 SGD
+SGD S000004168 TFS1 GO:0030162 SGD_REF:S000039310|PMID:9521655 IPI P lipid binding protein (putative), supressor of a cdc25 mutation YLR178C|DKA1 gene taxon:4932 20030110 SGD
+SGD S000001623 TGL1 GO:0005811 SGD_REF:S000048561|PMID:10515935 IDA C cholesterol esterase, triglyceride lipase YKL140W|YKL5 gene taxon:4932 20010626 SGD
+SGD S000001623 TGL1 GO:0005811 SGD_REF:S000080917|PMID:15713625 IDA C cholesterol esterase, triglyceride lipase YKL140W|YKL5 gene taxon:4932 20050302 SGD
+SGD S000001623 TGL1 GO:0016021 SGD_REF:S000080917|PMID:15713625 IDA C cholesterol esterase, triglyceride lipase YKL140W|YKL5 gene taxon:4932 20050302 SGD
+SGD S000001623 TGL1 GO:0004771 SGD_REF:S000080917|PMID:15713625 IDA F cholesterol esterase, triglyceride lipase YKL140W|YKL5 gene taxon:4932 20050302 SGD
+SGD S000001623 TGL1 GO:0016298 SGD_REF:S000049173|PMID:1574929 ISS F cholesterol esterase, triglyceride lipase YKL140W|YKL5 gene taxon:4932 20021031 SGD
+SGD S000001623 TGL1 GO:0006629 SGD_REF:S000048561|PMID:10515935 IMP P cholesterol esterase, triglyceride lipase YKL140W|YKL5 gene taxon:4932 20010626 SGD
+SGD S000001623 TGL1 GO:0016125 SGD_REF:S000080917|PMID:15713625 IMP P cholesterol esterase, triglyceride lipase YKL140W|YKL5 gene taxon:4932 20050302 SGD
+SGD S000002465 TGL2 GO:0008372 SGD_REF:S000069584 ND C triglyceride lipase YDR058C gene taxon:4932 20020930 SGD
+SGD S000002465 TGL2 GO:0004806 SGD_REF:S000049012|PMID:9544243 IDA F triglyceride lipase YDR058C gene taxon:4932 20020930 SGD
+SGD S000002465 TGL2 GO:0004806 SGD_REF:S000049012|PMID:9544243 IMP F triglyceride lipase YDR058C gene taxon:4932 20020930 SGD
+SGD S000002465 TGL2 GO:0006629 SGD_REF:S000049012|PMID:9544243 ISS P triglyceride lipase YDR058C gene taxon:4932 20020930 SGD
+SGD S000004930 TGL3 GO:0005811 SGD_REF:S000048561|PMID:10515935 IDA C triacylglycerol lipase YMR313C gene taxon:4932 20010626 SGD
+SGD S000004930 TGL3 colocalizes_with GO:0005811 SGD_REF:S000087074|PMID:16267052 IDA C triacylglycerol lipase YMR313C gene taxon:4932 20060522 SGD
+SGD S000004930 TGL3 GO:0004806 SGD_REF:S000073557|PMID:12682047 IDA F triacylglycerol lipase YMR313C gene taxon:4932 20030707 SGD
+SGD S000004930 TGL3 GO:0004806 SGD_REF:S000073557|PMID:12682047 IMP F triacylglycerol lipase YMR313C gene taxon:4932 20030707 SGD
+SGD S000004930 TGL3 GO:0006629 SGD_REF:S000048561|PMID:10515935 IMP P triacylglycerol lipase YMR313C gene taxon:4932 20010626 SGD
+SGD S000004930 TGL3 GO:0019433 SGD_REF:S000087074|PMID:16267052 IGI SGD:S000001797 P triacylglycerol lipase YMR313C gene taxon:4932 20060522 SGD
+SGD S000004930 TGL3 GO:0019433 SGD_REF:S000087074|PMID:16267052 IMP P triacylglycerol lipase YMR313C gene taxon:4932 20060522 SGD
+SGD S000001797 TGL4 GO:0005811 SGD_REF:S000074185|PMID:14562095 IDA C triacylglycerol lipase YKR089C|STC1 gene taxon:4932 20031028 SGD
+SGD S000001797 TGL4 colocalizes_with GO:0005811 SGD_REF:S000087074|PMID:16267052 IDA C triacylglycerol lipase YKR089C|STC1 gene taxon:4932 20060522 SGD
+SGD S000001797 TGL4 GO:0005811 SGD_REF:S000086466|PMID:16135509 IDA C triacylglycerol lipase YKR089C|STC1 gene taxon:4932 20050919 SGD
+SGD S000001797 TGL4 GO:0004806 SGD_REF:S000086466|PMID:16135509 IDA F triacylglycerol lipase YKR089C|STC1 gene taxon:4932 20050919 SGD
+SGD S000001797 TGL4 GO:0004806 SGD_REF:S000086466|PMID:16135509 IMP F triacylglycerol lipase YKR089C|STC1 gene taxon:4932 20050919 SGD
+SGD S000001797 TGL4 GO:0006642 SGD_REF:S000086466|PMID:16135509 IDA P triacylglycerol lipase YKR089C|STC1 gene taxon:4932 20050919 SGD
+SGD S000001797 TGL4 GO:0006642 SGD_REF:S000086466|PMID:16135509 IMP P triacylglycerol lipase YKR089C|STC1 gene taxon:4932 20050919 SGD
+SGD S000001797 TGL4 GO:0019433 SGD_REF:S000087074|PMID:16267052 IGI SGD:S000004930 P triacylglycerol lipase YKR089C|STC1 gene taxon:4932 20060522 SGD
+SGD S000001797 TGL4 GO:0019433 SGD_REF:S000087074|PMID:16267052 IMP P triacylglycerol lipase YKR089C|STC1 gene taxon:4932 20060522 SGD
+SGD S000005607 TGL5 GO:0005811 SGD_REF:S000074185|PMID:14562095 IDA C triacylglycerol lipase YOR081C|STC2 gene taxon:4932 20031028 SGD
+SGD S000005607 TGL5 GO:0005811 SGD_REF:S000086466|PMID:16135509 IDA C triacylglycerol lipase YOR081C|STC2 gene taxon:4932 20050919 SGD
+SGD S000005607 TGL5 GO:0004806 SGD_REF:S000086466|PMID:16135509 IDA F triacylglycerol lipase YOR081C|STC2 gene taxon:4932 20050919 SGD
+SGD S000005607 TGL5 GO:0004806 SGD_REF:S000086466|PMID:16135509 IMP F triacylglycerol lipase YOR081C|STC2 gene taxon:4932 20050919 SGD
+SGD S000005607 TGL5 GO:0006642 SGD_REF:S000086466|PMID:16135509 IDA P triacylglycerol lipase YOR081C|STC2 gene taxon:4932 20050919 SGD
+SGD S000005607 TGL5 GO:0006642 SGD_REF:S000086466|PMID:16135509 IMP P triacylglycerol lipase YOR081C|STC2 gene taxon:4932 20050919 SGD
+SGD S000006078 TGS1 GO:0005730 SGD_REF:S000070025|PMID:11983179 IDA C YPL157W gene taxon:4932 20021125 SGD
+SGD S000006078 TGS1 GO:0008173 SGD_REF:S000070025|PMID:11983179 IMP F YPL157W gene taxon:4932 20021125 SGD
+SGD S000006078 TGS1 GO:0008173 SGD_REF:S000080117|PMID:15590684 IDA F YPL157W gene taxon:4932 20050207 SGD
+SGD S000006078 TGS1 GO:0008173 SGD_REF:S000070025|PMID:11983179 ISS protein_id:AAK47145 F YPL157W gene taxon:4932 20021125 SGD
+SGD S000006078 TGS1 GO:0006387 SGD_REF:S000070025|PMID:11983179 IMP P YPL157W gene taxon:4932 20021125 SGD
+SGD S000006078 TGS1 GO:0007000 SGD_REF:S000077190|PMID:15340060 IMP P YPL157W gene taxon:4932 20050531 SGD
+SGD S000006078 TGS1 GO:0007046 SGD_REF:S000077190|PMID:15340060 IMP P YPL157W gene taxon:4932 20050531 SGD
+SGD S000003256 THG1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YGR024C gene taxon:4932 20031028 SGD
+SGD S000003256 THG1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YGR024C gene taxon:4932 20031028 SGD
+SGD S000003256 THG1 GO:0008193 SGD_REF:S000075143|PMID:14633974 IDA F YGR024C gene taxon:4932 20031215 SGD
+SGD S000003256 THG1 GO:0006400 SGD_REF:S000075143|PMID:14633974 IDA P YGR024C gene taxon:4932 20031215 SGD
+SGD S000003917 THI11 GO:0008372 SGD_REF:S000069584 ND C thiamine biosynthetic enzyme YJR156C gene taxon:4932 20010119 SGD
+SGD S000003917 THI11 GO:0005515 SGD_REF:S000071751|PMID:12271461 IPI SGD:S000005277 F thiamine biosynthetic enzyme YJR156C gene taxon:4932 20030602 SGD
+SGD S000003917 THI11 GO:0009228 SGD_REF:S000046055|PMID:9655908 TAS P thiamine biosynthetic enzyme YJR156C gene taxon:4932 20010118 SGD
+SGD S000005276 THI12 GO:0008372 SGD_REF:S000069584 ND C YNL332W gene taxon:4932 20010119 SGD
+SGD S000005276 THI12 GO:0005554 SGD_REF:S000069584 ND F YNL332W gene taxon:4932 20030318 SGD
+SGD S000005276 THI12 GO:0009228 SGD_REF:S000046055|PMID:9655908 TAS P YNL332W gene taxon:4932 20010118 SGD
+SGD S000002403 THI13 GO:0008372 SGD_REF:S000069584 ND C YDL244W gene taxon:4932 20010119 SGD
+SGD S000002403 THI13 GO:0005554 SGD_REF:S000069584 ND F YDL244W gene taxon:4932 20030318 SGD
+SGD S000002403 THI13 GO:0009228 SGD_REF:S000046055|PMID:9655908 TAS P YDL244W gene taxon:4932 20010118 SGD
+SGD S000000444 THI2 GO:0005634 SGD_REF:S000046951|PMID:8394343 IC GO:0016563 C YBR240C|PHO6 gene taxon:4932 20040707 SGD
+SGD S000000444 THI2 GO:0005634 SGD_REF:S000086808|PMID:16194233 IDA C YBR240C|PHO6 gene taxon:4932 20060315 SGD
+SGD S000000444 THI2 GO:0016563 SGD_REF:S000046951|PMID:8394343 IMP F YBR240C|PHO6 gene taxon:4932 20010926 SGD
+SGD S000000444 THI2 GO:0016563 SGD_REF:S000069948|PMID:11353088 ISS F YBR240C|PHO6 gene taxon:4932 20040707 SGD
+SGD S000000444 THI2 GO:0009228 SGD_REF:S000046055|PMID:9655908 TAS P YBR240C|PHO6 gene taxon:4932 20010118 SGD
+SGD S000000444 THI2 GO:0009228 SGD_REF:S000086808|PMID:16194233 IPI SGD:S000002238 P YBR240C|PHO6 gene taxon:4932 20060315 SGD
+SGD S000000444 THI2 GO:0009228 SGD_REF:S000086808|PMID:16194233 IMP P YBR240C|PHO6 gene taxon:4932 20060315 SGD
+SGD S000000444 THI2 GO:0045944 SGD_REF:S000046951|PMID:8394343 IMP P YBR240C|PHO6 gene taxon:4932 20040707 SGD
+SGD S000000444 THI2 GO:0045944 SGD_REF:S000069948|PMID:11353088 ISS P YBR240C|PHO6 gene taxon:4932 20040707 SGD
+SGD S000005416 THI20 GO:0008372 SGD_REF:S000069584 ND C YOL055C gene taxon:4932 20010119 SGD
+SGD S000005416 THI20 GO:0008902 SGD_REF:S000080147|PMID:15614489 IDA F YOL055C gene taxon:4932 20050216 SGD
+SGD S000005416 THI20 GO:0008902 SGD_REF:S000080147|PMID:15614489 IMP F YOL055C gene taxon:4932 20050216 SGD
+SGD S000005416 THI20 GO:0008972 SGD_REF:S000056318|PMID:10383756 ISS F YOL055C gene taxon:4932 20010118 SGD
+SGD S000005416 THI20 GO:0009228 SGD_REF:S000056318|PMID:10383756 IGI P YOL055C gene taxon:4932 20010118 SGD
+SGD S000005416 THI20 GO:0009228 SGD_REF:S000056318|PMID:10383756 IEP P YOL055C gene taxon:4932 20010118 SGD
+SGD S000006179 THI21 GO:0008372 SGD_REF:S000069584 ND C YPL258C gene taxon:4932 20010119 SGD
+SGD S000006179 THI21 GO:0008902 SGD_REF:S000080147|PMID:15614489 IDA F YPL258C gene taxon:4932 20050216 SGD
+SGD S000006179 THI21 GO:0008902 SGD_REF:S000080147|PMID:15614489 IMP F YPL258C gene taxon:4932 20050216 SGD
+SGD S000006179 THI21 GO:0008972 SGD_REF:S000056318|PMID:10383756 ISS F YPL258C gene taxon:4932 20010118 SGD
+SGD S000006179 THI21 GO:0009228 SGD_REF:S000056318|PMID:10383756 IGI P YPL258C gene taxon:4932 20010118 SGD
+SGD S000006179 THI21 GO:0009228 SGD_REF:S000056318|PMID:10383756 IEP P YPL258C gene taxon:4932 20010118 SGD
+SGD S000006325 THI22 GO:0008372 SGD_REF:S000069584 ND C YPR121W gene taxon:4932 20010119 SGD
+SGD S000006325 THI22 GO:0008972 SGD_REF:S000056318|PMID:10383756 ISS F YPR121W gene taxon:4932 20010118 SGD
+SGD S000006325 THI22 GO:0009228 SGD_REF:S000056318|PMID:10383756 IGI P YPR121W gene taxon:4932 20010118 SGD
+SGD S000006325 THI22 GO:0009228 SGD_REF:S000056318|PMID:10383756 IEP P YPR121W gene taxon:4932 20010118 SGD
+SGD S000002238 THI3 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C alpha-ketoisocaproate decarboxylase YDL080C|KID1 gene taxon:4932 20031028 SGD
+SGD S000002238 THI3 GO:0005634 SGD_REF:S000086808|PMID:16194233 IDA C alpha-ketoisocaproate decarboxylase YDL080C|KID1 gene taxon:4932 20060315 SGD
+SGD S000002238 THI3 GO:0016563 SGD_REF:S000046951|PMID:8394343 IMP F alpha-ketoisocaproate decarboxylase YDL080C|KID1 gene taxon:4932 20010926 SGD
+SGD S000002238 THI3 GO:0016831 SGD_REF:S000051759|PMID:10753893 IMP F alpha-ketoisocaproate decarboxylase YDL080C|KID1 gene taxon:4932 20030321 SGD
+SGD S000002238 THI3 GO:0016831 SGD_REF:S000051759|PMID:10753893 ISS F alpha-ketoisocaproate decarboxylase YDL080C|KID1 gene taxon:4932 20030321 SGD
+SGD S000002238 THI3 GO:0009228 SGD_REF:S000046055|PMID:9655908 TAS P alpha-ketoisocaproate decarboxylase YDL080C|KID1 gene taxon:4932 20010118 SGD
+SGD S000002238 THI3 GO:0009228 SGD_REF:S000086808|PMID:16194233 IPI SGD:S000000444 P alpha-ketoisocaproate decarboxylase YDL080C|KID1 gene taxon:4932 20060315 SGD
+SGD S000002238 THI3 GO:0009228 SGD_REF:S000086808|PMID:16194233 IMP P alpha-ketoisocaproate decarboxylase YDL080C|KID1 gene taxon:4932 20060315 SGD
+SGD S000002238 THI3 GO:0045944 SGD_REF:S000086808|PMID:16194233 IMP P alpha-ketoisocaproate decarboxylase YDL080C|KID1 gene taxon:4932 20060315 SGD
+SGD S000003376 THI4 GO:0005739 SGD_REF:S000052703|PMID:9367751 IMP C biosynthetic pathway component producing the thiazole precursor of thiamine YGR144W|ESP35|MOL1 gene taxon:4932 20010118 SGD
+SGD S000003376 THI4 GO:0005829 SGD_REF:S000079801|PMID:15544818 IDA C biosynthetic pathway component producing the thiazole precursor of thiamine YGR144W|ESP35|MOL1 gene taxon:4932 20041212 SGD
+SGD S000003376 THI4 GO:0005554 SGD_REF:S000069584 ND F biosynthetic pathway component producing the thiazole precursor of thiamine YGR144W|ESP35|MOL1 gene taxon:4932 20030318 SGD
+SGD S000003376 THI4 GO:0000002 SGD_REF:S000052703|PMID:9367751 IMP P biosynthetic pathway component producing the thiazole precursor of thiamine YGR144W|ESP35|MOL1 gene taxon:4932 20040707 SGD
+SGD S000003376 THI4 GO:0009228 SGD_REF:S000046055|PMID:9655908 TAS P biosynthetic pathway component producing the thiazole precursor of thiamine YGR144W|ESP35|MOL1 gene taxon:4932 20010118 SGD
+SGD S000001836 THI5 GO:0008372 SGD_REF:S000069584 ND C thiamine regulated pyrimidine precursor biosynthesis enzyme YFL058W gene taxon:4932 20010119 SGD
+SGD S000001836 THI5 GO:0005554 SGD_REF:S000069584 ND F thiamine regulated pyrimidine precursor biosynthesis enzyme YFL058W gene taxon:4932 20030318 SGD
+SGD S000001836 THI5 GO:0009228 SGD_REF:S000046055|PMID:9655908 TAS P thiamine regulated pyrimidine precursor biosynthesis enzyme YFL058W gene taxon:4932 20010118 SGD
+SGD S000006135 THI6 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C TMP pyrophosphorylase, hydroxyethylthiazole kinase YPL214C gene taxon:4932 20020507 SGD
+SGD S000006135 THI6 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C TMP pyrophosphorylase, hydroxyethylthiazole kinase YPL214C gene taxon:4932 20031028 SGD
+SGD S000006135 THI6 GO:0004417 SGD_REF:S000046055|PMID:9655908 TAS F TMP pyrophosphorylase, hydroxyethylthiazole kinase YPL214C gene taxon:4932 20010118 SGD
+SGD S000006135 THI6 GO:0004789 SGD_REF:S000046055|PMID:9655908 TAS F TMP pyrophosphorylase, hydroxyethylthiazole kinase YPL214C gene taxon:4932 20010118 SGD
+SGD S000006135 THI6 GO:0009228 SGD_REF:S000046055|PMID:9655908 TAS P TMP pyrophosphorylase, hydroxyethylthiazole kinase YPL214C gene taxon:4932 20010118 SGD
+SGD S000004227 THI7 GO:0005886 SGD_REF:S000052268|PMID:9235906 IMP C thiamine transporter YLR237W|THI10 gene taxon:4932 20010118 SGD
+SGD S000004227 THI7 GO:0005886 SGD_REF:S000052268|PMID:9235906 ISS C thiamine transporter YLR237W|THI10 gene taxon:4932 20010118 SGD
+SGD S000004227 THI7 GO:0015234 SGD_REF:S000046055|PMID:9655908 TAS F thiamine transporter YLR237W|THI10 gene taxon:4932 20010118 SGD
+SGD S000004227 THI7 GO:0015888 SGD_REF:S000046055|PMID:9655908 TAS P thiamine transporter YLR237W|THI10 gene taxon:4932 20010118 SGD
+SGD S000005669 THI80 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C thiamin pyrophosphokinase YOR143C gene taxon:4932 20031028 SGD
+SGD S000005669 THI80 GO:0004788 SGD_REF:S000046951|PMID:8394343 IMP F thiamin pyrophosphokinase YOR143C gene taxon:4932 20010118 SGD
+SGD S000005669 THI80 GO:0004788 SGD_REF:S000046951|PMID:8394343 IDA F thiamin pyrophosphokinase YOR143C gene taxon:4932 20010118 SGD
+SGD S000005669 THI80 GO:0009229 SGD_REF:S000046055|PMID:9655908 TAS P thiamin pyrophosphokinase YOR143C gene taxon:4932 20040713 SGD
+SGD S000005669 THI80 GO:0009229 SGD_REF:S000046951|PMID:8394343 IMP P thiamin pyrophosphokinase YOR143C gene taxon:4932 20040713 SGD
+SGD S000000865 THO1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YER063W gene taxon:4932 20031028 SGD
+SGD S000000865 THO1 GO:0005554 SGD_REF:S000069584 ND F YER063W gene taxon:4932 20020930 SGD
+SGD S000000865 THO1 GO:0006351 SGD_REF:S000058360|PMID:9707445 IGI P YER063W gene taxon:4932 20020930 SGD
+SGD S000005433 THP1 GO:0005643 SGD_REF:S000071844|PMID:12411502 IGI C YOL072W|BUD29 gene taxon:4932 20030605 SGD
+SGD S000005433 THP1 GO:0005643 SGD_REF:S000071844|PMID:12411502 IDA C YOL072W|BUD29 gene taxon:4932 20030605 SGD
+SGD S000005433 THP1 GO:0042175 SGD_REF:S000071811|PMID:12206772 IDA C YOL072W|BUD29 gene taxon:4932 20030605 SGD
+SGD S000005433 THP1 GO:0005515 SGD_REF:S000071844|PMID:12411502 IPI SGD:S000002566 F YOL072W|BUD29 gene taxon:4932 20030605 SGD
+SGD S000005433 THP1 GO:0000282 SGD_REF:S000061390|PMID:11452010 IMP P YOL072W|BUD29 gene taxon:4932 20021010 SGD
+SGD S000005433 THP1 GO:0006310 SGD_REF:S000059944|PMID:11139493 IMP P YOL072W|BUD29 gene taxon:4932 20021010 SGD
+SGD S000005433 THP1 GO:0006368 SGD_REF:S000059944|PMID:11139493 IMP P YOL072W|BUD29 gene taxon:4932 20021010 SGD
+SGD S000005433 THP1 GO:0006405 SGD_REF:S000071844|PMID:12411502 IMP P YOL072W|BUD29 gene taxon:4932 20030605 SGD
+SGD S000001210 THP2 GO:0000347 SGD_REF:S000059208|PMID:11060033 IMP C YHR167W gene taxon:4932 20030221 SGD
+SGD S000001210 THP2 GO:0000347 SGD_REF:S000059208|PMID:11060033 IPI C YHR167W gene taxon:4932 20030221 SGD
+SGD S000001210 THP2 GO:0003676 SGD_REF:S000070300|PMID:12093753 IDA F YHR167W gene taxon:4932 20021118 SGD
+SGD S000001210 THP2 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P YHR167W gene taxon:4932 20060203 SGD
+SGD S000001210 THP2 GO:0006310 SGD_REF:S000059208|PMID:11060033 IMP P YHR167W gene taxon:4932 20030221 SGD
+SGD S000001210 THP2 GO:0006368 SGD_REF:S000070300|PMID:12093753 IMP P YHR167W gene taxon:4932 20021118 SGD
+SGD S000001210 THP2 GO:0006406 SGD_REF:S000069956|PMID:11979277 IMP P YHR167W gene taxon:4932 20030214 SGD
+SGD S000001067 THR1 GO:0008372 SGD_REF:S000069584 ND C homoserine kinase YHR025W gene taxon:4932 20020930 SGD
+SGD S000001067 THR1 GO:0004413 SGD_REF:S000065394|PMID:8973190 ISS F homoserine kinase YHR025W gene taxon:4932 20020930 SGD
+SGD S000001067 THR1 GO:0004413 SGD_REF:S000051057|PMID:2165904 IDA F homoserine kinase YHR025W gene taxon:4932 20020930 SGD
+SGD S000001067 THR1 GO:0006549 SGD_REF:S000065394|PMID:8973190 TAS P homoserine kinase YHR025W gene taxon:4932 20020930 SGD
+SGD S000001067 THR1 GO:0006555 SGD_REF:S000065394|PMID:8973190 TAS P homoserine kinase YHR025W gene taxon:4932 20020930 SGD
+SGD S000001067 THR1 GO:0006566 SGD_REF:S000065394|PMID:8973190 TAS P homoserine kinase YHR025W gene taxon:4932 20020930 SGD
+SGD S000001067 THR1 GO:0009092 SGD_REF:S000051057|PMID:2165904 IDA P homoserine kinase YHR025W gene taxon:4932 20020930 SGD
+SGD S000000649 THR4 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C threonine synthase YCR053W gene taxon:4932 20031028 SGD
+SGD S000000649 THR4 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C threonine synthase YCR053W gene taxon:4932 20031028 SGD
+SGD S000000649 THR4 GO:0004795 SGD_REF:S000043523|PMID:8082795 IDA F threonine synthase YCR053W gene taxon:4932 20020930 SGD
+SGD S000000649 THR4 GO:0006566 SGD_REF:S000071379|PMID:11752249 TAS P threonine synthase YCR053W gene taxon:4932 20020930 SGD
+SGD S000000649 THR4 GO:0006897 SGD_REF:S000075617|PMID:15020461 IMP P threonine synthase YCR053W gene taxon:4932 20040712 SGD
+SGD S000001340 THS1 GO:0005737 SGD_REF:S000053144|PMID:2995918 IMP C threonine-tRNA ligase YIL078W gene taxon:4932 20020930 SGD
+SGD S000001340 THS1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C threonine-tRNA ligase YIL078W gene taxon:4932 20040813 SGD
+SGD S000001340 THS1 GO:0004829 SGD_REF:S000053144|PMID:2995918 ISS F threonine-tRNA ligase YIL078W gene taxon:4932 20020930 SGD
+SGD S000001340 THS1 GO:0006412 SGD_REF:S000054755|PMID:10471698 IMP P threonine-tRNA ligase YIL078W gene taxon:4932 20020930 SGD
+SGD S000001406 TID3 GO:0000778 SGD_REF:S000062011|PMID:11179222 IMP C YIL144W|HEC1|NDC80 gene taxon:4932 20030404 SGD
+SGD S000001406 TID3 GO:0000778 SGD_REF:S000062011|PMID:11179222 IPI C YIL144W|HEC1|NDC80 gene taxon:4932 20030404 SGD
+SGD S000001406 TID3 GO:0000778 SGD_REF:S000080960|PMID:11511347 IDA C YIL144W|HEC1|NDC80 gene taxon:4932 20050307 SGD
+SGD S000001406 TID3 GO:0000780 SGD_REF:S000059963|PMID:11266451 IDA C YIL144W|HEC1|NDC80 gene taxon:4932 20030404 SGD
+SGD S000001406 TID3 GO:0000780 SGD_REF:S000059963|PMID:11266451 IGI C YIL144W|HEC1|NDC80 gene taxon:4932 20030404 SGD
+SGD S000001406 TID3 GO:0000780 SGD_REF:S000059963|PMID:11266451 IPI C YIL144W|HEC1|NDC80 gene taxon:4932 20030404 SGD
+SGD S000001406 TID3 GO:0031262 SGD_REF:S000059963|PMID:11266451 IDA C YIL144W|HEC1|NDC80 gene taxon:4932 20050303 SGD
+SGD S000001406 TID3 GO:0031262 SGD_REF:S000062011|PMID:11179222 IDA C YIL144W|HEC1|NDC80 gene taxon:4932 20050303 SGD
+SGD S000001406 TID3 GO:0031262 SGD_REF:S000062011|PMID:11179222 IPI SGD:S000000820|SGD:S000004723|SGD:S000005430 C YIL144W|HEC1|NDC80 gene taxon:4932 20050303 SGD
+SGD S000001406 TID3 GO:0005200 SGD_REF:S000047788|PMID:9585415 IPI F YIL144W|HEC1|NDC80 gene taxon:4932 20010118 SGD
+SGD S000001406 TID3 GO:0007020 SGD_REF:S000058447|PMID:9153752 IPI P YIL144W|HEC1|NDC80 gene taxon:4932 20010118 SGD
+SGD S000001406 TID3 GO:0007059 SGD_REF:S000059963|PMID:11266451 IMP P YIL144W|HEC1|NDC80 gene taxon:4932 20020214 SGD
+SGD S000001406 TID3 GO:0007059 SGD_REF:S000059963|PMID:11266451 IGI P YIL144W|HEC1|NDC80 gene taxon:4932 20020214 SGD
+SGD S000001767 TIF1 GO:0005840 SGD_REF:S000058753|PMID:9841679 TAS C translation initiation factor eIF4A subunit YKR059W gene taxon:4932 20010124 SGD
+SGD S000001767 TIF1 GO:0016281 SGD_REF:S000056385|PMID:10409745 IGI C translation initiation factor eIF4A subunit YKR059W gene taxon:4932 20050105 SGD
+SGD S000001767 TIF1 GO:0016281 SGD_REF:S000056288|PMID:2648398 IGI C translation initiation factor eIF4A subunit YKR059W gene taxon:4932 20050105 SGD
+SGD S000001767 TIF1 GO:0016281 SGD_REF:S000056288|PMID:2648398 ISS C translation initiation factor eIF4A subunit YKR059W gene taxon:4932 20050105 SGD
+SGD S000001767 TIF1 GO:0003743 SGD_REF:S000058753|PMID:9841679 TAS F translation initiation factor eIF4A subunit YKR059W gene taxon:4932 20010124 SGD
+SGD S000001767 TIF1 GO:0006413 SGD_REF:S000058753|PMID:9841679 TAS P translation initiation factor eIF4A subunit YKR059W gene taxon:4932 20010124 SGD
+SGD S000004873 TIF11 GO:0005840 SGD_REF:S000058753|PMID:9841679 TAS C translation initiation factor eIF1A YMR260C|eIF1A gene taxon:4932 20010124 SGD
+SGD S000004873 TIF11 GO:0003743 SGD_REF:S000058753|PMID:9841679 TAS F translation initiation factor eIF1A YMR260C|eIF1A gene taxon:4932 20010124 SGD
+SGD S000004873 TIF11 GO:0006413 SGD_REF:S000058753|PMID:9841679 TAS P translation initiation factor eIF1A YMR260C|eIF1A gene taxon:4932 20010124 SGD
+SGD S000003674 TIF2 GO:0005737 SGD_REF:S000056288|PMID:2648398 ISS C translation initiation factor eIF4A subunit YJL138C gene taxon:4932 20010118 SGD
+SGD S000003674 TIF2 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C translation initiation factor eIF4A subunit YJL138C gene taxon:4932 20020507 SGD
+SGD S000003674 TIF2 GO:0005840 SGD_REF:S000058753|PMID:9841679 TAS C translation initiation factor eIF4A subunit YJL138C gene taxon:4932 20010124 SGD
+SGD S000003674 TIF2 GO:0016281 SGD_REF:S000056385|PMID:10409745 IGI C translation initiation factor eIF4A subunit YJL138C gene taxon:4932 20050105 SGD
+SGD S000003674 TIF2 GO:0016281 SGD_REF:S000056288|PMID:2648398 IGI C translation initiation factor eIF4A subunit YJL138C gene taxon:4932 20050105 SGD
+SGD S000003674 TIF2 GO:0016281 SGD_REF:S000056288|PMID:2648398 ISS C translation initiation factor eIF4A subunit YJL138C gene taxon:4932 20050105 SGD
+SGD S000003674 TIF2 GO:0003724 SGD_REF:S000056536|PMID:1502180 IDA F translation initiation factor eIF4A subunit YJL138C gene taxon:4932 20010118 SGD
+SGD S000003674 TIF2 GO:0003743 SGD_REF:S000056288|PMID:2648398 ISS F translation initiation factor eIF4A subunit YJL138C gene taxon:4932 20010118 SGD
+SGD S000003674 TIF2 GO:0003743 SGD_REF:S000056536|PMID:1502180 IDA F translation initiation factor eIF4A subunit YJL138C gene taxon:4932 20010118 SGD
+SGD S000003674 TIF2 GO:0003743 SGD_REF:S000058753|PMID:9841679 TAS F translation initiation factor eIF4A subunit YJL138C gene taxon:4932 20010124 SGD
+SGD S000003674 TIF2 GO:0006413 SGD_REF:S000058753|PMID:9841679 TAS P translation initiation factor eIF4A subunit YJL138C gene taxon:4932 20010124 SGD
+SGD S000003674 TIF2 GO:0006446 SGD_REF:S000056288|PMID:2648398 ISS P translation initiation factor eIF4A subunit YJL138C gene taxon:4932 20010118 SGD
+SGD S000006367 TIF3 GO:0005840 SGD_REF:S000058753|PMID:9841679 TAS C translation initiation factor eIF-4B YPR163C|RBL3|STM1 gene taxon:4932 20010124 SGD
+SGD S000006367 TIF3 GO:0003743 SGD_REF:S000058753|PMID:9841679 TAS F translation initiation factor eIF-4B YPR163C|RBL3|STM1 gene taxon:4932 20010124 SGD
+SGD S000006367 TIF3 GO:0006413 SGD_REF:S000058753|PMID:9841679 TAS P translation initiation factor eIF-4B YPR163C|RBL3|STM1 gene taxon:4932 20010124 SGD
+SGD S000004754 TIF34 GO:0005852 SGD_REF:S000043795|PMID:9671501 IPI C translation initiation factor eIF3 subunit YMR146C gene taxon:4932 20020116 SGD
+SGD S000004754 TIF34 GO:0005852 SGD_REF:S000043795|PMID:9671501 IDA C translation initiation factor eIF3 subunit YMR146C gene taxon:4932 20020116 SGD
+SGD S000004754 TIF34 GO:0005852 SGD_REF:S000040522|PMID:9660829 IPI SGD:S000002837|SGD:S000005888 C translation initiation factor eIF3 subunit YMR146C gene taxon:4932 20060118 SGD
+SGD S000004754 TIF34 GO:0005852 SGD_REF:S000040522|PMID:9660829 IDA C translation initiation factor eIF3 subunit YMR146C gene taxon:4932 20060118 SGD
+SGD S000004754 TIF34 GO:0043614 SGD_REF:S000082127|PMID:11018020 IDA C translation initiation factor eIF3 subunit YMR146C gene taxon:4932 20060427 SGD
+SGD S000004754 TIF34 GO:0003743 SGD_REF:S000043795|PMID:9671501 IDA F translation initiation factor eIF3 subunit YMR146C gene taxon:4932 20020116 SGD
+SGD S000004754 TIF34 GO:0006413 SGD_REF:S000043795|PMID:9671501 IDA P translation initiation factor eIF3 subunit YMR146C gene taxon:4932 20020116 SGD
+SGD S000002837 TIF35 GO:0005852 SGD_REF:S000043795|PMID:9671501 IPI C translation initiation factor eIF3 subunit YDR429C gene taxon:4932 20020116 SGD
+SGD S000002837 TIF35 GO:0005852 SGD_REF:S000040522|PMID:9660829 IPI SGD:S000004754|SGD:S000005888 C translation initiation factor eIF3 subunit YDR429C gene taxon:4932 20060118 SGD
+SGD S000002837 TIF35 GO:0005852 SGD_REF:S000040522|PMID:9660829 IDA C translation initiation factor eIF3 subunit YDR429C gene taxon:4932 20060118 SGD
+SGD S000002837 TIF35 GO:0005852 SGD_REF:S000043795|PMID:9671501 IDA C translation initiation factor eIF3 subunit YDR429C gene taxon:4932 20020116 SGD
+SGD S000002837 TIF35 GO:0003743 SGD_REF:S000043795|PMID:9671501 IDA F translation initiation factor eIF3 subunit YDR429C gene taxon:4932 20020116 SGD
+SGD S000002837 TIF35 GO:0006413 SGD_REF:S000043795|PMID:9671501 IDA P translation initiation factor eIF3 subunit YDR429C gene taxon:4932 20020116 SGD
+SGD S000003394 TIF4631 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C 150 kDa subunit, Tif4632p and mammalian p220 homolog, mRNA cap binding protein eIF-4F YGR162W gene taxon:4932 20040928 SGD
+SGD S000003394 TIF4631 GO:0005840 SGD_REF:S000058753|PMID:9841679 TAS C 150 kDa subunit, Tif4632p and mammalian p220 homolog, mRNA cap binding protein eIF-4F YGR162W gene taxon:4932 20010124 SGD
+SGD S000003394 TIF4631 GO:0016281 SGD_REF:S000050035|PMID:8336723 IGI C 150 kDa subunit, Tif4632p and mammalian p220 homolog, mRNA cap binding protein eIF-4F YGR162W gene taxon:4932 20050105 SGD
+SGD S000003394 TIF4631 GO:0016281 SGD_REF:S000050035|PMID:8336723 IMP C 150 kDa subunit, Tif4632p and mammalian p220 homolog, mRNA cap binding protein eIF-4F YGR162W gene taxon:4932 20050105 SGD
+SGD S000003394 TIF4631 GO:0016281 SGD_REF:S000050035|PMID:8336723 ISS C 150 kDa subunit, Tif4632p and mammalian p220 homolog, mRNA cap binding protein eIF-4F YGR162W gene taxon:4932 20050105 SGD
+SGD S000003394 TIF4631 GO:0003743 SGD_REF:S000058753|PMID:9841679 TAS F 150 kDa subunit, Tif4632p and mammalian p220 homolog, mRNA cap binding protein eIF-4F YGR162W gene taxon:4932 20010124 SGD
+SGD S000003394 TIF4631 GO:0006413 SGD_REF:S000058753|PMID:9841679 TAS P 150 kDa subunit, Tif4632p and mammalian p220 homolog, mRNA cap binding protein eIF-4F YGR162W gene taxon:4932 20010124 SGD
+SGD S000003017 TIF4632 GO:0005840 SGD_REF:S000058753|PMID:9841679 TAS C 150 kDa, eIF-4F mRNA cap-binding complex subunit, eIF-4G homolog YGL049C gene taxon:4932 20010124 SGD
+SGD S000003017 TIF4632 GO:0016281 SGD_REF:S000050035|PMID:8336723 IGI C 150 kDa, eIF-4F mRNA cap-binding complex subunit, eIF-4G homolog YGL049C gene taxon:4932 20050105 SGD
+SGD S000003017 TIF4632 GO:0016281 SGD_REF:S000050035|PMID:8336723 ISS C 150 kDa, eIF-4F mRNA cap-binding complex subunit, eIF-4G homolog YGL049C gene taxon:4932 20050105 SGD
+SGD S000003017 TIF4632 GO:0003743 SGD_REF:S000058753|PMID:9841679 TAS F 150 kDa, eIF-4F mRNA cap-binding complex subunit, eIF-4G homolog YGL049C gene taxon:4932 20010124 SGD
+SGD S000003017 TIF4632 GO:0006413 SGD_REF:S000058753|PMID:9841679 TAS P 150 kDa, eIF-4F mRNA cap-binding complex subunit, eIF-4G homolog YGL049C gene taxon:4932 20010124 SGD
+SGD S000006245 TIF5 GO:0005843 SGD_REF:S000043795|PMID:9671501 IPI C Translation initiation factor eIF5 YPR041W|SUI5|eIF5 gene taxon:4932 20021008 SGD
+SGD S000006245 TIF5 GO:0043614 SGD_REF:S000082127|PMID:11018020 IDA C Translation initiation factor eIF5 YPR041W|SUI5|eIF5 gene taxon:4932 20060427 SGD
+SGD S000006245 TIF5 GO:0003743 SGD_REF:S000063195|PMID:9395514 ISS F Translation initiation factor eIF5 YPR041W|SUI5|eIF5 gene taxon:4932 20020410 SGD
+SGD S000006245 TIF5 GO:0003743 SGD_REF:S000054790|PMID:8486705 ISS F Translation initiation factor eIF5 YPR041W|SUI5|eIF5 gene taxon:4932 20020410 SGD
+SGD S000006245 TIF5 GO:0005096 SGD_REF:S000065405|PMID:11092890 ISS F Translation initiation factor eIF5 YPR041W|SUI5|eIF5 gene taxon:4932 20020410 SGD
+SGD S000006245 TIF5 GO:0005096 SGD_REF:S000063195|PMID:9395514 IPI F Translation initiation factor eIF5 YPR041W|SUI5|eIF5 gene taxon:4932 20020410 SGD
+SGD S000006245 TIF5 GO:0006446 SGD_REF:S000060440|PMID:11331597 IMP P Translation initiation factor eIF5 YPR041W|SUI5|eIF5 gene taxon:4932 20020410 SGD
+SGD S000006245 TIF5 GO:0006446 SGD_REF:S000060440|PMID:11331597 IPI P Translation initiation factor eIF5 YPR041W|SUI5|eIF5 gene taxon:4932 20020410 SGD
+SGD S000006245 TIF5 GO:0042256 SGD_REF:S000060440|PMID:11331597 IMP P Translation initiation factor eIF5 YPR041W|SUI5|eIF5 gene taxon:4932 20020424 SGD
+SGD S000006220 TIF6 GO:0005634 SGD_REF:S000059899|PMID:11238882 IDA C YPR016C|CDC95 gene taxon:4932 20020930 SGD
+SGD S000006220 TIF6 GO:0005737 SGD_REF:S000059899|PMID:11238882 IDA C YPR016C|CDC95 gene taxon:4932 20020930 SGD
+SGD S000006220 TIF6 GO:0005554 SGD_REF:S000069584 ND F YPR016C|CDC95 gene taxon:4932 20020930 SGD
+SGD S000006220 TIF6 GO:0030489 SGD_REF:S000059899|PMID:11238882 IMP P YPR016C|CDC95 gene taxon:4932 20020930 SGD
+SGD S000006220 TIF6 GO:0042273 SGD_REF:S000059899|PMID:11238882 IMP P YPR016C|CDC95 gene taxon:4932 20020930 SGD
+SGD S000006220 TIF6 GO:0042273 SGD_REF:S000076470|PMID:15100437 IPI P YPR016C|CDC95 gene taxon:4932 20050407 SGD
+SGD S000007255 TIM11 GO:0000276 SGD_REF:S000054771|PMID:9271204 IPI C mitochondrial F1F0-ATPase subunit e YDR322C-A|ATP21 gene taxon:4932 20010118 SGD
+SGD S000007255 TIM11 GO:0000276 SGD_REF:S000055993|PMID:9857174 IPI C mitochondrial F1F0-ATPase subunit e YDR322C-A|ATP21 gene taxon:4932 20010118 SGD
+SGD S000007255 TIM11 GO:0000276 SGD_REF:S000054771|PMID:9271204 ISS C mitochondrial F1F0-ATPase subunit e YDR322C-A|ATP21 gene taxon:4932 20010118 SGD
+SGD S000007255 TIM11 GO:0000276 SGD_REF:S000055993|PMID:9857174 IMP C mitochondrial F1F0-ATPase subunit e YDR322C-A|ATP21 gene taxon:4932 20010118 SGD
+SGD S000007255 TIM11 GO:0005198 SGD_REF:S000055993|PMID:9857174 IMP F mitochondrial F1F0-ATPase subunit e YDR322C-A|ATP21 gene taxon:4932 20010118 SGD
+SGD S000007255 TIM11 GO:0005198 SGD_REF:S000055993|PMID:9857174 IPI F mitochondrial F1F0-ATPase subunit e YDR322C-A|ATP21 gene taxon:4932 20010118 SGD
+SGD S000007255 TIM11 GO:0015986 SGD_REF:S000054771|PMID:9271204 IPI P mitochondrial F1F0-ATPase subunit e YDR322C-A|ATP21 gene taxon:4932 20010118 SGD
+SGD S000007255 TIM11 GO:0015986 SGD_REF:S000054771|PMID:9271204 ISS P mitochondrial F1F0-ATPase subunit e YDR322C-A|ATP21 gene taxon:4932 20010118 SGD
+SGD S000007255 TIM11 GO:0015986 SGD_REF:S000055993|PMID:9857174 IPI P mitochondrial F1F0-ATPase subunit e YDR322C-A|ATP21 gene taxon:4932 20010118 SGD
+SGD S000007255 TIM11 GO:0015986 SGD_REF:S000055993|PMID:9857174 IMP P mitochondrial F1F0-ATPase subunit e YDR322C-A|ATP21 gene taxon:4932 20010118 SGD
+SGD S000003413 TIM13 GO:0005758 SGD_REF:S000043156|PMID:10051608 IDA C YGR181W gene taxon:4932 20010118 SGD
+SGD S000003413 TIM13 GO:0005758 SGD_REF:S000064131|PMID:10397776 IDA C YGR181W gene taxon:4932 20020410 SGD
+SGD S000003413 TIM13 GO:0042719 SGD_REF:S000071489|PMID:12221072 IDA C YGR181W gene taxon:4932 20030430 SGD
+SGD S000003413 TIM13 GO:0008565 SGD_REF:S000043156|PMID:10051608 IPI F YGR181W gene taxon:4932 20010118 SGD
+SGD S000003413 TIM13 GO:0008565 SGD_REF:S000047441|PMID:10469659 IPI F YGR181W gene taxon:4932 20010118 SGD
+SGD S000003413 TIM13 GO:0008565 SGD_REF:S000047441|PMID:10469659 IMP F YGR181W gene taxon:4932 20010118 SGD
+SGD S000003413 TIM13 GO:0045039 SGD_REF:S000043156|PMID:10051608 IPI P YGR181W gene taxon:4932 20031201 SGD
+SGD S000003413 TIM13 GO:0045039 SGD_REF:S000047441|PMID:10469659 IMP P YGR181W gene taxon:4932 20031201 SGD
+SGD S000003413 TIM13 GO:0045039 SGD_REF:S000047441|PMID:10469659 IPI P YGR181W gene taxon:4932 20031201 SGD
+SGD S000003679 TIM17 GO:0005744 SGD_REF:S000058449|PMID:10744987 TAS C 16.5 kDa inner membrane protein required for import of mitochondrial precursor proteins YJL143W|MIM17|MPI2|SMS1 gene taxon:4932 20010118 SGD
+SGD S000003679 TIM17 GO:0005744 SGD_REF:S000081320|PMID:15618217 IDA C 16.5 kDa inner membrane protein required for import of mitochondrial precursor proteins YJL143W|MIM17|MPI2|SMS1 gene taxon:4932 20050420 SGD
+SGD S000003679 TIM17 GO:0008565 SGD_REF:S000058449|PMID:10744987 TAS F 16.5 kDa inner membrane protein required for import of mitochondrial precursor proteins YJL143W|MIM17|MPI2|SMS1 gene taxon:4932 20010118 SGD
+SGD S000003679 TIM17 GO:0030150 SGD_REF:S000061378|PMID:11344168 IMP P 16.5 kDa inner membrane protein required for import of mitochondrial precursor proteins YJL143W|MIM17|MPI2|SMS1 gene taxon:4932 20031201 SGD
+SGD S000003679 TIM17 GO:0030150 SGD_REF:S000081320|PMID:15618217 IDA P 16.5 kDa inner membrane protein required for import of mitochondrial precursor proteins YJL143W|MIM17|MPI2|SMS1 gene taxon:4932 20050420 SGD
+SGD S000005823 TIM18 GO:0042721 SGD_REF:S000042844|PMID:10637294 IDA C translocase YOR297C gene taxon:4932 20030430 SGD
+SGD S000005823 TIM18 GO:0008565 SGD_REF:S000042844|PMID:10637294 IPI F translocase YOR297C gene taxon:4932 20030430 SGD
+SGD S000005823 TIM18 GO:0006612 SGD_REF:S000042844|PMID:10637294 IPI P translocase YOR297C gene taxon:4932 20010118 SGD
+SGD S000005823 TIM18 GO:0006612 SGD_REF:S000042844|PMID:10637294 IGI P translocase YOR297C gene taxon:4932 20010118 SGD
+SGD S000005823 TIM18 GO:0006626 SGD_REF:S000042844|PMID:10637294 IGI P translocase YOR297C gene taxon:4932 20010118 SGD
+SGD S000005823 TIM18 GO:0006626 SGD_REF:S000042844|PMID:10637294 IPI P translocase YOR297C gene taxon:4932 20010118 SGD
+SGD S000003265 TIM21 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YGR033C|FMP17 gene taxon:4932 20031028 SGD
+SGD S000003265 TIM21 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YGR033C|FMP17 gene taxon:4932 20040924 SGD
+SGD S000003265 TIM21 GO:0005744 SGD_REF:S000081217|PMID:15797382 IPI C YGR033C|FMP17 gene taxon:4932 20050405 SGD
+SGD S000003265 TIM21 GO:0005554 SGD_REF:S000069584 ND F YGR033C|FMP17 gene taxon:4932 20021126 SGD
+SGD S000003265 TIM21 GO:0030150 SGD_REF:S000081217|PMID:15797382 IPI P YGR033C|FMP17 gene taxon:4932 20050405 SGD
+SGD S000002376 TIM22 GO:0042721 SGD_REF:S000042844|PMID:10637294 IDA C YDL217C gene taxon:4932 20030430 SGD
+SGD S000002376 TIM22 GO:0008565 SGD_REF:S000047441|PMID:10469659 TAS F YDL217C gene taxon:4932 20010118 SGD
+SGD S000002376 TIM22 GO:0045039 SGD_REF:S000049981|PMID:10648604 IMP P YDL217C gene taxon:4932 20031201 SGD
+SGD S000002376 TIM22 GO:0045039 SGD_REF:S000049981|PMID:10648604 IPI P YDL217C gene taxon:4932 20031201 SGD
+SGD S000001284 TIM44 GO:0001405 SGD_REF:S000074354|PMID:14638855 IPI C YIL022W|ISP45|MIM44|MPI1 gene taxon:4932 20031218 SGD
+SGD S000001284 TIM44 GO:0001405 SGD_REF:S000074353|PMID:14517234 IPI C YIL022W|ISP45|MIM44|MPI1 gene taxon:4932 20031218 SGD
+SGD S000001284 TIM44 GO:0005759 SGD_REF:S000058449|PMID:10744987 TAS C YIL022W|ISP45|MIM44|MPI1 gene taxon:4932 20010118 SGD
+SGD S000001284 TIM44 GO:0008565 SGD_REF:S000058449|PMID:10744987 TAS F YIL022W|ISP45|MIM44|MPI1 gene taxon:4932 20010118 SGD
+SGD S000001284 TIM44 GO:0030150 SGD_REF:S000045295|PMID:10913171 TAS P YIL022W|ISP45|MIM44|MPI1 gene taxon:4932 20031201 SGD
+SGD S000005984 TIM50 GO:0005744 SGD_REF:S000071904|PMID:12437924 IDA C YPL063W gene taxon:4932 20030106 SGD
+SGD S000005984 TIM50 GO:0005744 SGD_REF:S000071906|PMID:12437925 IDA C YPL063W gene taxon:4932 20030106 SGD
+SGD S000005984 TIM50 GO:0005554 SGD_REF:S000069584 ND F YPL063W gene taxon:4932 20030106 SGD
+SGD S000005984 TIM50 GO:0030150 SGD_REF:S000071904|PMID:12437924 IDA P YPL063W gene taxon:4932 20030106 SGD
+SGD S000005984 TIM50 GO:0030150 SGD_REF:S000071906|PMID:12437925 IDA P YPL063W gene taxon:4932 20030106 SGD
+SGD S000003590 TIM54 GO:0042721 SGD_REF:S000042844|PMID:10637294 IDA C YJL054W gene taxon:4932 20030430 SGD
+SGD S000003590 TIM54 GO:0008565 SGD_REF:S000048711|PMID:9412462 IPI F YJL054W gene taxon:4932 20010118 SGD
+SGD S000003590 TIM54 GO:0008565 SGD_REF:S000048711|PMID:9412462 IGI F YJL054W gene taxon:4932 20010118 SGD
+SGD S000003590 TIM54 GO:0045039 SGD_REF:S000048711|PMID:9412462 IGI P YJL054W gene taxon:4932 20031202 SGD
+SGD S000003590 TIM54 GO:0045039 SGD_REF:S000048711|PMID:9412462 IPI P YJL054W gene taxon:4932 20031202 SGD
+SGD S000007348 TIM8 GO:0042719 SGD_REF:S000071489|PMID:12221072 IDA C mitochondrial protein import machinery subunit YJR135W-A gene taxon:4932 20030430 SGD
+SGD S000007348 TIM8 GO:0008565 SGD_REF:S000043156|PMID:10051608 IPI F mitochondrial protein import machinery subunit YJR135W-A gene taxon:4932 20010118 SGD
+SGD S000007348 TIM8 GO:0008565 SGD_REF:S000047441|PMID:10469659 IPI F mitochondrial protein import machinery subunit YJR135W-A gene taxon:4932 20010118 SGD
+SGD S000007348 TIM8 GO:0008565 SGD_REF:S000047441|PMID:10469659 IMP F mitochondrial protein import machinery subunit YJR135W-A gene taxon:4932 20010118 SGD
+SGD S000007348 TIM8 GO:0045039 SGD_REF:S000043156|PMID:10051608 IGI P mitochondrial protein import machinery subunit YJR135W-A gene taxon:4932 20031119 SGD
+SGD S000007348 TIM8 GO:0045039 SGD_REF:S000043156|PMID:10051608 IPI P mitochondrial protein import machinery subunit YJR135W-A gene taxon:4932 20031119 SGD
+SGD S000007348 TIM8 GO:0045039 SGD_REF:S000047441|PMID:10469659 IMP P mitochondrial protein import machinery subunit YJR135W-A gene taxon:4932 20031119 SGD
+SGD S000007348 TIM8 GO:0045039 SGD_REF:S000047441|PMID:10469659 IPI P mitochondrial protein import machinery subunit YJR135W-A gene taxon:4932 20031119 SGD
+SGD S000007256 TIM9 GO:0005758 SGD_REF:S000040056|PMID:9822593 IDA C YEL020W-A gene taxon:4932 20010118 SGD
+SGD S000007256 TIM9 GO:0042719 SGD_REF:S000040056|PMID:9822593 IDA C YEL020W-A gene taxon:4932 20030430 SGD
+SGD S000007256 TIM9 GO:0008565 SGD_REF:S000040056|PMID:9822593 IPI F YEL020W-A gene taxon:4932 20010118 SGD
+SGD S000007256 TIM9 GO:0008565 SGD_REF:S000040056|PMID:9822593 ISS F YEL020W-A gene taxon:4932 20010118 SGD
+SGD S000007256 TIM9 GO:0008565 SGD_REF:S000040056|PMID:9822593 IGI F YEL020W-A gene taxon:4932 20010118 SGD
+SGD S000007256 TIM9 GO:0051082 SGD_REF:S000071708|PMID:12138093 IDA F YEL020W-A gene taxon:4932 20030121 SGD
+SGD S000007256 TIM9 GO:0045039 SGD_REF:S000040056|PMID:9822593 IGI P YEL020W-A gene taxon:4932 20031120 SGD
+SGD S000007256 TIM9 GO:0045039 SGD_REF:S000040056|PMID:9822593 IPI P YEL020W-A gene taxon:4932 20031120 SGD
+SGD S000007256 TIM9 GO:0045039 SGD_REF:S000047441|PMID:10469659 IPI P YEL020W-A gene taxon:4932 20031120 SGD
+SGD S000007256 TIM9 GO:0045039 SGD_REF:S000040056|PMID:9822593 ISS P YEL020W-A gene taxon:4932 20031120 SGD
+SGD S000000271 TIP1 GO:0009277 SGD_REF:S000047063|PMID:10216230 IDA C cell wall mannoprotein YBR067C gene taxon:4932 20020726 SGD
+SGD S000000271 TIP1 GO:0009277 SGD_REF:S000081097|PMID:15781460 IDA C cell wall mannoprotein YBR067C gene taxon:4932 20050601 SGD
+SGD S000000271 TIP1 GO:0005199 SGD_REF:S000047063|PMID:10216230 IDA F cell wall mannoprotein YBR067C gene taxon:4932 20020726 SGD
+SGD S000000271 TIP1 GO:0016298 SGD_REF:S000047829|PMID:9818717 ISS F cell wall mannoprotein YBR067C gene taxon:4932 20020916 SGD
+SGD S000000271 TIP1 GO:0007047 SGD_REF:S000047063|PMID:10216230 IDA P cell wall mannoprotein YBR067C gene taxon:4932 20020726 SGD
+SGD S000003113 TIP20 GO:0005783 SGD_REF:S000069880|PMID:11739780 IDA C transport protein that interacts with Sec20p; required for protein transport from the endoplasmic reticulum to the golgi apparatus YGL145W|TIP1 gene taxon:4932 20020814 SGD
+SGD S000003113 TIP20 GO:0005554 SGD_REF:S000069584 ND F transport protein that interacts with Sec20p; required for protein transport from the endoplasmic reticulum to the golgi apparatus YGL145W|TIP1 gene taxon:4932 20020930 SGD
+SGD S000003113 TIP20 GO:0006890 SGD_REF:S000042789|PMID:9639310 IGI P transport protein that interacts with Sec20p; required for protein transport from the endoplasmic reticulum to the golgi apparatus YGL145W|TIP1 gene taxon:4932 20020930 SGD
+SGD S000006244 TIP41 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YPR040W gene taxon:4932 20031028 SGD
+SGD S000006244 TIP41 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YPR040W gene taxon:4932 20020507 SGD
+SGD S000006244 TIP41 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YPR040W gene taxon:4932 20031028 SGD
+SGD S000006244 TIP41 GO:0005554 SGD_REF:S000069584 ND F YPR040W gene taxon:4932 20030108 SGD
+SGD S000006244 TIP41 GO:0007165 SGD_REF:S000067486|PMID:11741537 IMP P YPR040W gene taxon:4932 20030108 SGD
+SGD S000006244 TIP41 GO:0007165 SGD_REF:S000067486|PMID:11741537 IPI P YPR040W gene taxon:4932 20030108 SGD
+SGD S000000813 TIR1 GO:0009277 SGD_REF:S000046780|PMID:8733242 IDA C YER011W|SRP1 gene taxon:4932 20010118 SGD
+SGD S000000813 TIR1 GO:0009277 SGD_REF:S000081097|PMID:15781460 IDA C YER011W|SRP1 gene taxon:4932 20050601 SGD
+SGD S000000813 TIR1 GO:0005199 SGD_REF:S000045833|PMID:9363789 IDA F YER011W|SRP1 gene taxon:4932 20010118 SGD
+SGD S000000813 TIR1 GO:0006950 SGD_REF:S000046780|PMID:8733242 ISS P YER011W|SRP1 gene taxon:4932 20010118 SGD
+SGD S000005536 TIR2 GO:0009277 SGD_REF:S000046297|PMID:7746155 ISS C YOR010C|SRP2 gene taxon:4932 20010118 SGD
+SGD S000005536 TIR2 GO:0005554 SGD_REF:S000069584 ND F YOR010C|SRP2 gene taxon:4932 20021209 SGD
+SGD S000005536 TIR2 GO:0006950 SGD_REF:S000046297|PMID:7746155 IDA P YOR010C|SRP2 gene taxon:4932 20010118 SGD
+SGD S000001273 TIR3 GO:0009277 SGD_REF:S000040179|PMID:10383953 IDA C cell wall mannoprotein YIL011W|YIB1 gene taxon:4932 20020617 SGD
+SGD S000001273 TIR3 GO:0005554 SGD_REF:S000069584 ND F cell wall mannoprotein YIL011W|YIB1 gene taxon:4932 20021216 SGD
+SGD S000001273 TIR3 GO:0000004 SGD_REF:S000069584 ND P cell wall mannoprotein YIL011W|YIB1 gene taxon:4932 20021216 SGD
+SGD S000005535 TIR4 GO:0009277 SGD_REF:S000040179|PMID:10383953 IDA C cell wall mannoprotein YOR009W gene taxon:4932 20020617 SGD
+SGD S000005535 TIR4 GO:0005554 SGD_REF:S000069584 ND F cell wall mannoprotein YOR009W gene taxon:4932 20021216 SGD
+SGD S000005535 TIR4 GO:0000004 SGD_REF:S000069584 ND P cell wall mannoprotein YOR009W gene taxon:4932 20021216 SGD
+SGD S000004126 TIS11 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YLR136C|CTH2 gene taxon:4932 20031028 SGD
+SGD S000004126 TIS11 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YLR136C|CTH2 gene taxon:4932 20031028 SGD
+SGD S000004126 TIS11 GO:0003729 SGD_REF:S000080432|PMID:15652485 IDA F YLR136C|CTH2 gene taxon:4932 20050217 SGD
+SGD S000004126 TIS11 GO:0006402 SGD_REF:S000080432|PMID:15652485 IMP P YLR136C|CTH2 gene taxon:4932 20050217 SGD
+SGD S000004126 TIS11 GO:0006879 SGD_REF:S000080432|PMID:15652485 IMP P YLR136C|CTH2 gene taxon:4932 20050217 SGD
+SGD S000006278 TKL1 GO:0005737 SGD_REF:S000071382|PMID:2843500 ISS C transketolase 1 YPR074C gene taxon:4932 20020930 SGD
+SGD S000006278 TKL1 GO:0004802 SGD_REF:S000042440|PMID:8226984 ISS F transketolase 1 YPR074C gene taxon:4932 20020930 SGD
+SGD S000006278 TKL1 GO:0004802 SGD_REF:S000042440|PMID:8226984 IMP F transketolase 1 YPR074C gene taxon:4932 20020930 SGD
+SGD S000006278 TKL1 GO:0006098 SGD_REF:S000053822|PMID:8534086 TAS P transketolase 1 YPR074C gene taxon:4932 20020930 SGD
+SGD S000006278 TKL1 GO:0006098 SGD_REF:S000048672|PMID:8299150 IMP P transketolase 1 YPR074C gene taxon:4932 20020930 SGD
+SGD S000000321 TKL2 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C transketolase, similar to TKL1 YBR117C gene taxon:4932 20031028 SGD
+SGD S000000321 TKL2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C transketolase, similar to TKL1 YBR117C gene taxon:4932 20031028 SGD
+SGD S000000321 TKL2 GO:0004802 SGD_REF:S000050393|PMID:7916691 ISS F transketolase, similar to TKL1 YBR117C gene taxon:4932 20020930 SGD
+SGD S000000321 TKL2 GO:0006098 SGD_REF:S000050393|PMID:7916691 IGI P transketolase, similar to TKL1 YBR117C gene taxon:4932 20020930 SGD
+SGD S000006657 TLC1 GO:0000333 SGD_REF:S000069751|PMID:11884619 TAS C RNA template component of telomerase TER1 gene taxon:4932 20020625 SGD
+SGD S000006657 TLC1 GO:0000333 SGD_REF:S000081300|PMID:15813705 IPI C RNA template component of telomerase TER1 gene taxon:4932 20050421 SGD
+SGD S000006657 TLC1 GO:0000333 SGD_REF:S000081300|PMID:15813705 IDA C RNA template component of telomerase TER1 gene taxon:4932 20050421 SGD
+SGD S000006657 TLC1 GO:0005634 SGD_REF:S000070205|PMID:12101098 IDA C RNA template component of telomerase TER1 gene taxon:4932 20020828 SGD
+SGD S000006657 TLC1 GO:0005697 SGD_REF:S000044698|PMID:10898986 IDA C RNA template component of telomerase TER1 gene taxon:4932 20030619 SGD
+SGD S000006657 TLC1 GO:0005697 SGD_REF:S000044698|PMID:10898986 IPI C RNA template component of telomerase TER1 gene taxon:4932 20030619 SGD
+SGD S000006657 TLC1 GO:0005737 SGD_REF:S000070205|PMID:12101098 IDA C RNA template component of telomerase TER1 gene taxon:4932 20020828 SGD
+SGD S000006657 TLC1 GO:0000332 SGD_REF:S000069751|PMID:11884619 TAS F RNA template component of telomerase TER1 gene taxon:4932 20020625 SGD
+SGD S000006657 TLC1 contributes_to GO:0003720 SGD_REF:S000081300|PMID:15813705 IDA F RNA template component of telomerase TER1 gene taxon:4932 20050421 SGD
+SGD S000006657 TLC1 GO:0007004 SGD_REF:S000069751|PMID:11884619 TAS P RNA template component of telomerase TER1 gene taxon:4932 20020625 SGD
+SGD S000006657 TLC1 GO:0007004 SGD_REF:S000081300|PMID:15813705 IMP P RNA template component of telomerase TER1 gene taxon:4932 20050421 SGD
+SGD S000006657 TLC1 GO:0007004 SGD_REF:S000081300|PMID:15813705 IDA P RNA template component of telomerase TER1 gene taxon:4932 20050421 SGD
+SGD S000002876 TLG1 GO:0000138 SGD_REF:S000058453|PMID:10047442 TAS C tSNARE that affects a late Golgi compartment YDR468C gene taxon:4932 20010118 SGD
+SGD S000002876 TLG1 GO:0005769 SGD_REF:S000058453|PMID:10047442 TAS C tSNARE that affects a late Golgi compartment YDR468C gene taxon:4932 20010118 SGD
+SGD S000002876 TLG1 GO:0005802 SGD_REF:S000058453|PMID:10047442 TAS C tSNARE that affects a late Golgi compartment YDR468C gene taxon:4932 20010118 SGD
+SGD S000002876 TLG1 GO:0005485 SGD_REF:S000058453|PMID:10047442 TAS F tSNARE that affects a late Golgi compartment YDR468C gene taxon:4932 20010118 SGD
+SGD S000002876 TLG1 GO:0005486 SGD_REF:S000058453|PMID:10047442 TAS F tSNARE that affects a late Golgi compartment YDR468C gene taxon:4932 20010118 SGD
+SGD S000002876 TLG1 GO:0005486 SGD_REF:S000076087|PMID:14981247 IDA F tSNARE that affects a late Golgi compartment YDR468C gene taxon:4932 20050614 SGD
+SGD S000002876 TLG1 GO:0006906 SGD_REF:S000058453|PMID:10047442 TAS P tSNARE that affects a late Golgi compartment YDR468C gene taxon:4932 20010118 SGD
+SGD S000005378 TLG2 GO:0000138 SGD_REF:S000058453|PMID:10047442 TAS C tSNARE that affects a late Golgi compartment YOL018C gene taxon:4932 20010118 SGD
+SGD S000005378 TLG2 GO:0005769 SGD_REF:S000058453|PMID:10047442 TAS C tSNARE that affects a late Golgi compartment YOL018C gene taxon:4932 20010118 SGD
+SGD S000005378 TLG2 GO:0005802 SGD_REF:S000058453|PMID:10047442 TAS C tSNARE that affects a late Golgi compartment YOL018C gene taxon:4932 20010118 SGD
+SGD S000005378 TLG2 GO:0005485 SGD_REF:S000058453|PMID:10047442 TAS F tSNARE that affects a late Golgi compartment YOL018C gene taxon:4932 20010118 SGD
+SGD S000005378 TLG2 GO:0005486 SGD_REF:S000058453|PMID:10047442 TAS F tSNARE that affects a late Golgi compartment YOL018C gene taxon:4932 20010118 SGD
+SGD S000005378 TLG2 GO:0006906 SGD_REF:S000058453|PMID:10047442 TAS P tSNARE that affects a late Golgi compartment YOL018C gene taxon:4932 20010118 SGD
+SGD S000004319 TMA10 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YLR327C|RBF9 gene taxon:4932 20031028 SGD
+SGD S000004319 TMA10 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YLR327C|RBF9 gene taxon:4932 20031028 SGD
+SGD S000004319 TMA10 GO:0005554 SGD_REF:S000069584 ND F YLR327C|RBF9 gene taxon:4932 20021126 SGD
+SGD S000004319 TMA10 GO:0000004 SGD_REF:S000069584 ND P YLR327C|RBF9 gene taxon:4932 20021126 SGD
+SGD S000001399 TMA108 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YIL137C|RBF108 gene taxon:4932 20031028 SGD
+SGD S000001399 TMA108 GO:0004222 SGD_REF:S000080056|PMID:15606766 ISS F YIL137C|RBF108 gene taxon:4932 20050415 SGD
+SGD S000001399 TMA108 GO:0006508 SGD_REF:S000080056|PMID:15606766 ISS P YIL137C|RBF108 gene taxon:4932 20050415 SGD
+SGD S000005778 TMA16 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YOR252W|RBF17 gene taxon:4932 20031028 SGD
+SGD S000005778 TMA16 GO:0005554 SGD_REF:S000069584 ND F YOR252W|RBF17 gene taxon:4932 20021126 SGD
+SGD S000005778 TMA16 GO:0000004 SGD_REF:S000069584 ND P YOR252W|RBF17 gene taxon:4932 20021126 SGD
+SGD S000002268 TMA17 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YDL110C gene taxon:4932 20031028 SGD
+SGD S000002268 TMA17 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDL110C gene taxon:4932 20031028 SGD
+SGD S000002268 TMA17 GO:0005554 SGD_REF:S000069584 ND F YDL110C gene taxon:4932 20030422 SGD
+SGD S000002268 TMA17 GO:0000004 SGD_REF:S000069584 ND P YDL110C gene taxon:4932 20030422 SGD
+SGD S000001539 TMA19 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YKL056C|RBF18 gene taxon:4932 20031028 SGD
+SGD S000001539 TMA19 GO:0005554 SGD_REF:S000069584 ND F YKL056C|RBF18 gene taxon:4932 20030203 SGD
+SGD S000001539 TMA19 GO:0043037 SGD_REF:S000115662|PMID:16702403 IMP P YKL056C|RBF18 gene taxon:4932 20060521 SGD
+SGD S000002957 TMA20 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YER007C-A|RBF20 gene taxon:4932 20031028 SGD
+SGD S000002957 TMA20 GO:0003723 SGD_REF:S000062013|PMID:10093218 ISS F YER007C-A|RBF20 gene taxon:4932 20030421 SGD
+SGD S000002957 TMA20 GO:0007046 SGD_REF:S000115662|PMID:16702403 IMP P YER007C-A|RBF20 gene taxon:4932 20060521 SGD
+SGD S000003775 TMA22 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YJR014W|RBF22 gene taxon:4932 20031028 SGD
+SGD S000003775 TMA22 GO:0003723 SGD_REF:S000062013|PMID:10093218 ISS F YJR014W|RBF22 gene taxon:4932 20030421 SGD
+SGD S000003775 TMA22 GO:0000004 SGD_REF:S000069584 ND P YJR014W|RBF22 gene taxon:4932 20030203 SGD
+SGD S000004882 TMA23 GO:0005730 SGD_REF:S000074185|PMID:14562095 IDA C YMR269W|YMR268W-A gene taxon:4932 20031028 SGD
+SGD S000004882 TMA23 GO:0005554 SGD_REF:S000069582|PMID:11806920 ND F YMR269W|YMR268W-A gene taxon:4932 20030428 SGD
+SGD S000004882 TMA23 GO:0000004 SGD_REF:S000069584 ND P YMR269W|YMR268W-A gene taxon:4932 20041215 SGD
+SGD S000004839 TMA29 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YMR226C gene taxon:4932 20031028 SGD
+SGD S000004839 TMA29 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YMR226C gene taxon:4932 20031028 SGD
+SGD S000004839 TMA29 GO:0016620 SGD_REF:S000072467|PMID:12535615 IDA F YMR226C gene taxon:4932 20030212 SGD
+SGD S000004839 TMA29 GO:0008152 SGD_REF:S000072467|PMID:12535615 IC GO:0016620 P YMR226C gene taxon:4932 20041220 SGD
+SGD S000005617 TMA46 GO:0005737 SGD_REF:S000056415|PMID:10684247 IDA C YOR091W|RBF46 gene taxon:4932 20010301 SGD
+SGD S000005617 TMA46 GO:0005554 SGD_REF:S000069584 ND F YOR091W|RBF46 gene taxon:4932 20010119 SGD
+SGD S000005617 TMA46 GO:0000004 SGD_REF:S000069584 ND P YOR091W|RBF46 gene taxon:4932 20010119 SGD
+SGD S000002524 TMA64 GO:0008372 SGD_REF:S000069584 ND C YDR117C|RBF64 gene taxon:4932 20030203 SGD
+SGD S000002524 TMA64 GO:0003723 SGD_REF:S000062013|PMID:10093218 ISS F YDR117C|RBF64 gene taxon:4932 20030421 SGD
+SGD S000002524 TMA64 GO:0000004 SGD_REF:S000069584 ND P YDR117C|RBF64 gene taxon:4932 20030203 SGD
+SGD S000007246 TMA7 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YLR262C-A|RBF7 gene taxon:4932 20031028 SGD
+SGD S000007246 TMA7 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YLR262C-A|RBF7 gene taxon:4932 20031028 SGD
+SGD S000007246 TMA7 GO:0005554 SGD_REF:S000069584 ND F YLR262C-A|RBF7 gene taxon:4932 20021126 SGD
+SGD S000007246 TMA7 GO:0043037 SGD_REF:S000115662|PMID:16702403 IMP P YLR262C-A|RBF7 gene taxon:4932 20060521 SGD
+SGD S000002512 TMS1 GO:0005774 SGD_REF:S000074185|PMID:14562095 IDA C YDR105C gene taxon:4932 20050511 SGD
+SGD S000002512 TMS1 GO:0016020 SGD_REF:S000065710|PMID:10637174 ISS C YDR105C gene taxon:4932 20030424 SGD
+SGD S000002512 TMS1 GO:0005554 SGD_REF:S000069584 ND F YDR105C gene taxon:4932 20030424 SGD
+SGD S000002512 TMS1 GO:0000004 SGD_REF:S000069584 ND P YDR105C gene taxon:4932 20030424 SGD
+SGD S000000977 TMT1 GO:0005829 SGD_REF:S000066185|PMID:11695919 IDA C YER175C|TAM1 gene taxon:4932 20021010 SGD
+SGD S000000977 TMT1 GO:0046547 SGD_REF:S000066185|PMID:11695919 IDA F YER175C|TAM1 gene taxon:4932 20021014 SGD
+SGD S000000977 TMT1 GO:0000004 SGD_REF:S000069584 ND P YER175C|TAM1 gene taxon:4932 20021010 SGD
+SGD S000003492 TNA1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C high affinity nicotinic acid plasma membrane permease YGR260W gene taxon:4932 20040928 SGD
+SGD S000003492 TNA1 GO:0005887 SGD_REF:S000058352|PMID:9678606 ISS C high affinity nicotinic acid plasma membrane permease YGR260W gene taxon:4932 20010118 SGD
+SGD S000003492 TNA1 GO:0015664 SGD_REF:S000051510|PMID:10869563 IMP F high affinity nicotinic acid plasma membrane permease YGR260W gene taxon:4932 20010118 SGD
+SGD S000003492 TNA1 GO:0015664 SGD_REF:S000051510|PMID:10869563 IEP F high affinity nicotinic acid plasma membrane permease YGR260W gene taxon:4932 20010118 SGD
+SGD S000003492 TNA1 GO:0015890 SGD_REF:S000051510|PMID:10869563 IMP P high affinity nicotinic acid plasma membrane permease YGR260W gene taxon:4932 20010118 SGD
+SGD S000003492 TNA1 GO:0015890 SGD_REF:S000051510|PMID:10869563 IEP P high affinity nicotinic acid plasma membrane permease YGR260W gene taxon:4932 20010118 SGD
+SGD S000005720 TOA1 GO:0005672 SGD_REF:S000057513|PMID:7862117 IDA C transcription factor IIA subunit alpha YOR194C gene taxon:4932 20010118 SGD
+SGD S000005720 TOA1 GO:0016251 SGD_REF:S000057513|PMID:7862117 IDA F transcription factor IIA subunit alpha YOR194C gene taxon:4932 20010119 SGD
+SGD S000005720 TOA1 GO:0006367 SGD_REF:S000057513|PMID:7862117 IDA P transcription factor IIA subunit alpha YOR194C gene taxon:4932 20010118 SGD
+SGD S000001541 TOA2 GO:0005672 SGD_REF:S000057513|PMID:7862117 IDA C beta, transcription factor IIA subunit YKL058W gene taxon:4932 20010118 SGD
+SGD S000001541 TOA2 GO:0016251 SGD_REF:S000057513|PMID:7862117 IDA F beta, transcription factor IIA subunit YKL058W gene taxon:4932 20010119 SGD
+SGD S000001541 TOA2 GO:0006367 SGD_REF:S000057513|PMID:7862117 IDA P beta, transcription factor IIA subunit YKL058W gene taxon:4932 20010118 SGD
+SGD S000005217 TOF1 GO:0000228 SGD_REF:S000073860|PMID:12944972 IPI C YNL273W gene taxon:4932 20040210 SGD
+SGD S000005217 TOF1 GO:0005554 SGD_REF:S000042267|PMID:10028183 TAS F YNL273W gene taxon:4932 20010118 SGD
+SGD S000005217 TOF1 GO:0000076 SGD_REF:S000073860|PMID:12944972 IMP P YNL273W gene taxon:4932 20040210 SGD
+SGD S000005217 TOF1 GO:0000076 SGD_REF:S000073860|PMID:12944972 IPI P YNL273W gene taxon:4932 20040210 SGD
+SGD S000005217 TOF1 GO:0006265 SGD_REF:S000042267|PMID:10028183 IPI P YNL273W gene taxon:4932 20010118 SGD
+SGD S000005217 TOF1 GO:0007064 SGD_REF:S000076127|PMID:14742714 IGI SGD:S000001234 P YNL273W gene taxon:4932 20050513 SGD
+SGD S000005217 TOF1 GO:0007064 SGD_REF:S000076127|PMID:14742714 IMP P YNL273W gene taxon:4932 20050513 SGD
+SGD S000001718 TOF2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YKR010C gene taxon:4932 20040928 SGD
+SGD S000001718 TOF2 GO:0005554 SGD_REF:S000042267|PMID:10028183 TAS F YKR010C gene taxon:4932 20010118 SGD
+SGD S000001718 TOF2 GO:0006265 SGD_REF:S000042267|PMID:10028183 IPI P YKR010C gene taxon:4932 20010118 SGD
+SGD S000003629 TOK1 GO:0005886 SGD_REF:S000055368|PMID:7651518 IMP C outward-rectifier potassium channel YJL093C|DUK1|YKC1|YORK|YPK1 gene taxon:4932 20020305 SGD
+SGD S000003629 TOK1 GO:0005886 SGD_REF:S000055368|PMID:7651518 IDA C outward-rectifier potassium channel YJL093C|DUK1|YKC1|YORK|YPK1 gene taxon:4932 20020305 SGD
+SGD S000003629 TOK1 GO:0005267 SGD_REF:S000055368|PMID:7651518 IMP F outward-rectifier potassium channel YJL093C|DUK1|YKC1|YORK|YPK1 gene taxon:4932 20020305 SGD
+SGD S000003629 TOK1 GO:0005267 SGD_REF:S000055368|PMID:7651518 ISS F outward-rectifier potassium channel YJL093C|DUK1|YKC1|YORK|YPK1 gene taxon:4932 20020305 SGD
+SGD S000003629 TOK1 GO:0005267 SGD_REF:S000055368|PMID:7651518 IDA F outward-rectifier potassium channel YJL093C|DUK1|YKC1|YORK|YPK1 gene taxon:4932 20020305 SGD
+SGD S000003629 TOK1 GO:0030007 SGD_REF:S000055368|PMID:7651518 IMP P outward-rectifier potassium channel YJL093C|DUK1|YKC1|YORK|YPK1 gene taxon:4932 20020305 SGD
+SGD S000003629 TOK1 GO:0030007 SGD_REF:S000055368|PMID:7651518 IDA P outward-rectifier potassium channel YJL093C|DUK1|YKC1|YORK|YPK1 gene taxon:4932 20020305 SGD
+SGD S000002865 TOM1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YDR457W gene taxon:4932 20031028 SGD
+SGD S000002865 TOM1 GO:0005730 SGD_REF:S000074185|PMID:14562095 IDA C YDR457W gene taxon:4932 20031028 SGD
+SGD S000002865 TOM1 GO:0004842 SGD_REF:S000058010|PMID:8982460 TAS F YDR457W gene taxon:4932 20010118 SGD
+SGD S000002865 TOM1 GO:0000209 SGD_REF:S000058010|PMID:8982460 TAS P YDR457W gene taxon:4932 20010118 SGD
+SGD S000002865 TOM1 GO:0006513 SGD_REF:S000058010|PMID:8982460 TAS P YDR457W gene taxon:4932 20010118 SGD
+SGD S000002865 TOM1 GO:0006913 SGD_REF:S000046718|PMID:10395901 IMP P YDR457W gene taxon:4932 20010118 SGD
+SGD S000002865 TOM1 GO:0006997 SGD_REF:S000046718|PMID:10395901 IMP P YDR457W gene taxon:4932 20010118 SGD
+SGD S000002865 TOM1 GO:0007067 SGD_REF:S000046718|PMID:10395901 IMP P YDR457W gene taxon:4932 20010118 SGD
+SGD S000003314 TOM20 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C 20 kDa mitochondrial outer membrane protein import receptor YGR082W|MAS20|MOM19 gene taxon:4932 20060317 SGD
+SGD S000003314 TOM20 GO:0005742 SGD_REF:S000055040|PMID:9774667 TAS C 20 kDa mitochondrial outer membrane protein import receptor YGR082W|MAS20|MOM19 gene taxon:4932 20010118 SGD
+SGD S000003314 TOM20 GO:0031307 SGD_REF:S000115559|PMID:16689936 IDA C 20 kDa mitochondrial outer membrane protein import receptor YGR082W|MAS20|MOM19 gene taxon:4932 20060515 SGD
+SGD S000003314 TOM20 GO:0008565 SGD_REF:S000055040|PMID:9774667 TAS F 20 kDa mitochondrial outer membrane protein import receptor YGR082W|MAS20|MOM19 gene taxon:4932 20010118 SGD
+SGD S000003314 TOM20 GO:0008565 SGD_REF:S000058473|PMID:9252394 IPI F 20 kDa mitochondrial outer membrane protein import receptor YGR082W|MAS20|MOM19 gene taxon:4932 20010118 SGD
+SGD S000003314 TOM20 GO:0030150 SGD_REF:S000055040|PMID:9774667 IMP P 20 kDa mitochondrial outer membrane protein import receptor YGR082W|MAS20|MOM19 gene taxon:4932 20031202 SGD
+SGD S000003314 TOM20 GO:0030150 SGD_REF:S000055040|PMID:9774667 IPI P 20 kDa mitochondrial outer membrane protein import receptor YGR082W|MAS20|MOM19 gene taxon:4932 20031202 SGD
+SGD S000005075 TOM22 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C mitochondrial import receptor protein YNL131W|MAS17|MAS22|MOM22 gene taxon:4932 20060317 SGD
+SGD S000005075 TOM22 GO:0005742 SGD_REF:S000039163|PMID:7709435 TAS C mitochondrial import receptor protein YNL131W|MAS17|MAS22|MOM22 gene taxon:4932 20010118 SGD
+SGD S000005075 TOM22 GO:0005742 SGD_REF:S000057822|PMID:8599107 TAS C mitochondrial import receptor protein YNL131W|MAS17|MAS22|MOM22 gene taxon:4932 20010118 SGD
+SGD S000005075 TOM22 GO:0031307 SGD_REF:S000115559|PMID:16689936 IDA C mitochondrial import receptor protein YNL131W|MAS17|MAS22|MOM22 gene taxon:4932 20060515 SGD
+SGD S000005075 TOM22 GO:0008565 SGD_REF:S000039163|PMID:7709435 TAS F mitochondrial import receptor protein YNL131W|MAS17|MAS22|MOM22 gene taxon:4932 20010118 SGD
+SGD S000005075 TOM22 GO:0008565 SGD_REF:S000057822|PMID:8599107 TAS F mitochondrial import receptor protein YNL131W|MAS17|MAS22|MOM22 gene taxon:4932 20010118 SGD
+SGD S000005075 TOM22 GO:0030150 SGD_REF:S000055040|PMID:9774667 IMP P mitochondrial import receptor protein YNL131W|MAS17|MAS22|MOM22 gene taxon:4932 20031202 SGD
+SGD S000005075 TOM22 GO:0030150 SGD_REF:S000055040|PMID:9774667 IPI P mitochondrial import receptor protein YNL131W|MAS17|MAS22|MOM22 gene taxon:4932 20031202 SGD
+SGD S000004816 TOM40 GO:0005739 SGD_REF:S000069459|PMID:11914276 IDA C mitochondrial outer membrane protein YMR203W|ISP42|MOM38 gene taxon:4932 20020507 SGD
+SGD S000004816 TOM40 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C mitochondrial outer membrane protein YMR203W|ISP42|MOM38 gene taxon:4932 20040924 SGD
+SGD S000004816 TOM40 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C mitochondrial outer membrane protein YMR203W|ISP42|MOM38 gene taxon:4932 20060317 SGD
+SGD S000004816 TOM40 GO:0005742 SGD_REF:S000055961|PMID:8119994 IPI C mitochondrial outer membrane protein YMR203W|ISP42|MOM38 gene taxon:4932 20010118 SGD
+SGD S000004816 TOM40 GO:0008565 SGD_REF:S000043691|PMID:2250717 IMP F mitochondrial outer membrane protein YMR203W|ISP42|MOM38 gene taxon:4932 20010118 SGD
+SGD S000004816 TOM40 GO:0030150 SGD_REF:S000055040|PMID:9774667 IPI P mitochondrial outer membrane protein YMR203W|ISP42|MOM38 gene taxon:4932 20031202 SGD
+SGD S000006433 TOM5 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C YPR133W-A|MOM8A gene taxon:4932 20060317 SGD
+SGD S000006433 TOM5 GO:0005742 SGD_REF:S000044379|PMID:9217162 IPI C YPR133W-A|MOM8A gene taxon:4932 20010118 SGD
+SGD S000006433 TOM5 GO:0008565 SGD_REF:S000044379|PMID:9217162 IMP F YPR133W-A|MOM8A gene taxon:4932 20010118 SGD
+SGD S000006433 TOM5 GO:0008565 SGD_REF:S000044379|PMID:9217162 IPI F YPR133W-A|MOM8A gene taxon:4932 20010118 SGD
+SGD S000006433 TOM5 GO:0030150 SGD_REF:S000044379|PMID:9217162 IMP P YPR133W-A|MOM8A gene taxon:4932 20031202 SGD
+SGD S000006433 TOM5 GO:0030150 SGD_REF:S000044379|PMID:9217162 IPI P YPR133W-A|MOM8A gene taxon:4932 20031202 SGD
+SGD S000005571 TOM6 GO:0005742 SGD_REF:S000043858|PMID:7565772 IMP C associates with TOM40, protein translocation complex component YOR045W|ISP6|MOM8B gene taxon:4932 20010118 SGD
+SGD S000005571 TOM6 GO:0005742 SGD_REF:S000055040|PMID:9774667 IPI C associates with TOM40, protein translocation complex component YOR045W|ISP6|MOM8B gene taxon:4932 20010118 SGD
+SGD S000005571 TOM6 GO:0008565 SGD_REF:S000043858|PMID:7565772 IMP F associates with TOM40, protein translocation complex component YOR045W|ISP6|MOM8B gene taxon:4932 20010118 SGD
+SGD S000005571 TOM6 GO:0008565 SGD_REF:S000045501|PMID:9710610 IPI F associates with TOM40, protein translocation complex component YOR045W|ISP6|MOM8B gene taxon:4932 20010118 SGD
+SGD S000005571 TOM6 GO:0030150 SGD_REF:S000055040|PMID:9774667 IMP P associates with TOM40, protein translocation complex component YOR045W|ISP6|MOM8B gene taxon:4932 20031202 SGD
+SGD S000005571 TOM6 GO:0030150 SGD_REF:S000055040|PMID:9774667 IPI P associates with TOM40, protein translocation complex component YOR045W|ISP6|MOM8B gene taxon:4932 20031202 SGD
+SGD S000005014 TOM7 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C translocase of the outer mitochondrial membrane YNL070W|MOM7|YOK22 gene taxon:4932 20060317 SGD
+SGD S000005014 TOM7 GO:0005742 SGD_REF:S000055040|PMID:9774667 IPI C translocase of the outer mitochondrial membrane YNL070W|MOM7|YOK22 gene taxon:4932 20010118 SGD
+SGD S000005014 TOM7 GO:0005742 SGD_REF:S000057853|PMID:8641278 IMP C translocase of the outer mitochondrial membrane YNL070W|MOM7|YOK22 gene taxon:4932 20010118 SGD
+SGD S000005014 TOM7 GO:0008565 SGD_REF:S000057853|PMID:8641278 IMP F translocase of the outer mitochondrial membrane YNL070W|MOM7|YOK22 gene taxon:4932 20010118 SGD
+SGD S000005014 TOM7 GO:0030150 SGD_REF:S000057853|PMID:8641278 IMP P translocase of the outer mitochondrial membrane YNL070W|MOM7|YOK22 gene taxon:4932 20031202 SGD
+SGD S000005014 TOM7 GO:0030150 SGD_REF:S000057853|PMID:8641278 IPI P translocase of the outer mitochondrial membrane YNL070W|MOM7|YOK22 gene taxon:4932 20031202 SGD
+SGD S000005014 TOM7 GO:0045040 SGD_REF:S000057853|PMID:8641278 IMP P translocase of the outer mitochondrial membrane YNL070W|MOM7|YOK22 gene taxon:4932 20031202 SGD
+SGD S000005065 TOM70 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C 70 kDa mitochondrial specialized import receptor of the outer membrane YNL121C|MAS70|MOM72|OMP1 gene taxon:4932 20060317 SGD
+SGD S000005065 TOM70 GO:0005742 SGD_REF:S000055040|PMID:9774667 TAS C 70 kDa mitochondrial specialized import receptor of the outer membrane YNL121C|MAS70|MOM72|OMP1 gene taxon:4932 20010118 SGD
+SGD S000005065 TOM70 GO:0031307 SGD_REF:S000115559|PMID:16689936 IDA C 70 kDa mitochondrial specialized import receptor of the outer membrane YNL121C|MAS70|MOM72|OMP1 gene taxon:4932 20060515 SGD
+SGD S000005065 TOM70 GO:0008565 SGD_REF:S000055040|PMID:9774667 TAS F 70 kDa mitochondrial specialized import receptor of the outer membrane YNL121C|MAS70|MOM72|OMP1 gene taxon:4932 20010118 SGD
+SGD S000005065 TOM70 GO:0008565 SGD_REF:S000058473|PMID:9252394 IPI F 70 kDa mitochondrial specialized import receptor of the outer membrane YNL121C|MAS70|MOM72|OMP1 gene taxon:4932 20010118 SGD
+SGD S000005065 TOM70 GO:0030150 SGD_REF:S000073048|PMID:12581629 TAS P 70 kDa mitochondrial specialized import receptor of the outer membrane YNL121C|MAS70|MOM72|OMP1 gene taxon:4932 20031203 SGD
+SGD S000005065 TOM70 GO:0045039 SGD_REF:S000073048|PMID:12581629 TAS P 70 kDa mitochondrial specialized import receptor of the outer membrane YNL121C|MAS70|MOM72|OMP1 gene taxon:4932 20031203 SGD
+SGD S000001159 TOM71 GO:0005741 SGD_REF:S000051982|PMID:8663394 IDA C protein translocase 71 kDa component of the outer membrane of mitochondria YHR117W|TOM72 gene taxon:4932 20010118 SGD
+SGD S000001159 TOM71 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C protein translocase 71 kDa component of the outer membrane of mitochondria YHR117W|TOM72 gene taxon:4932 20060317 SGD
+SGD S000001159 TOM71 GO:0031307 SGD_REF:S000115559|PMID:16689936 IDA C protein translocase 71 kDa component of the outer membrane of mitochondria YHR117W|TOM72 gene taxon:4932 20060515 SGD
+SGD S000001159 TOM71 GO:0008565 SGD_REF:S000051982|PMID:8663394 IPI F protein translocase 71 kDa component of the outer membrane of mitochondria YHR117W|TOM72 gene taxon:4932 20010118 SGD
+SGD S000001159 TOM71 GO:0008565 SGD_REF:S000051982|PMID:8663394 ISS F protein translocase 71 kDa component of the outer membrane of mitochondria YHR117W|TOM72 gene taxon:4932 20010118 SGD
+SGD S000001159 TOM71 GO:0000004 SGD_REF:S000051982|PMID:8663394 IMP P protein translocase 71 kDa component of the outer membrane of mitochondria YHR117W|TOM72 gene taxon:4932 20010118 SGD
+SGD S000005366 TOP1 GO:0005634 SGD_REF:S000058487|PMID:6088500 IDA C topoisomerase I YOL006C|MAK1|MAK17 gene taxon:4932 20010118 SGD
+SGD S000005366 TOP1 GO:0003917 SGD_REF:S000058487|PMID:6088500 IDA F topoisomerase I YOL006C|MAK1|MAK17 gene taxon:4932 20010118 SGD
+SGD S000005366 TOP1 GO:0003917 SGD_REF:S000055801|PMID:2989818 IDA F topoisomerase I YOL006C|MAK1|MAK17 gene taxon:4932 20010118 SGD
+SGD S000005366 TOP1 GO:0000019 SGD_REF:S000052967|PMID:2902925 IMP P topoisomerase I YOL006C|MAK1|MAK17 gene taxon:4932 20030814 SGD
+SGD S000005366 TOP1 GO:0006265 SGD_REF:S000058487|PMID:6088500 IDA P topoisomerase I YOL006C|MAK1|MAK17 gene taxon:4932 20010118 SGD
+SGD S000005366 TOP1 GO:0006265 SGD_REF:S000055801|PMID:2989818 IDA P topoisomerase I YOL006C|MAK1|MAK17 gene taxon:4932 20010118 SGD
+SGD S000005366 TOP1 GO:0006271 SGD_REF:S000051896|PMID:2549254 IMP P topoisomerase I YOL006C|MAK1|MAK17 gene taxon:4932 20010118 SGD
+SGD S000005366 TOP1 GO:0006333 SGD_REF:S000052145|PMID:9199287 IMP P topoisomerase I YOL006C|MAK1|MAK17 gene taxon:4932 20010118 SGD
+SGD S000005366 TOP1 GO:0006357 SGD_REF:S000044098|PMID:1660829 IMP P topoisomerase I YOL006C|MAK1|MAK17 gene taxon:4932 20010118 SGD
+SGD S000005366 TOP1 GO:0006368 SGD_REF:S000044098|PMID:1660829 IMP P topoisomerase I YOL006C|MAK1|MAK17 gene taxon:4932 20010118 SGD
+SGD S000005366 TOP1 GO:0007076 SGD_REF:S000043188|PMID:8895658 IMP P topoisomerase I YOL006C|MAK1|MAK17 gene taxon:4932 20010118 SGD
+SGD S000005366 TOP1 GO:0007076 SGD_REF:S000043188|PMID:8895658 IGI P topoisomerase I YOL006C|MAK1|MAK17 gene taxon:4932 20010118 SGD
+SGD S000005366 TOP1 GO:0007097 SGD_REF:S000043188|PMID:8895658 IGI P topoisomerase I YOL006C|MAK1|MAK17 gene taxon:4932 20010118 SGD
+SGD S000005366 TOP1 GO:0007097 SGD_REF:S000043188|PMID:8895658 IMP P topoisomerase I YOL006C|MAK1|MAK17 gene taxon:4932 20010118 SGD
+SGD S000005032 TOP2 GO:0000795 SGD_REF:S000053634|PMID:1315786 IDA C topoisomerase II YNL088W|TOR3|TRF3 gene taxon:4932 20010118 SGD
+SGD S000005032 TOP2 GO:0005634 SGD_REF:S000058487|PMID:6088500 IDA C topoisomerase II YNL088W|TOR3|TRF3 gene taxon:4932 20010118 SGD
+SGD S000005032 TOP2 GO:0003918 SGD_REF:S000055795|PMID:6323017 IDA F topoisomerase II YNL088W|TOR3|TRF3 gene taxon:4932 20010118 SGD
+SGD S000005032 TOP2 GO:0003918 SGD_REF:S000058487|PMID:6088500 IDA F topoisomerase II YNL088W|TOR3|TRF3 gene taxon:4932 20010118 SGD
+SGD S000005032 TOP2 GO:0000019 SGD_REF:S000052967|PMID:2902925 IMP P topoisomerase II YNL088W|TOR3|TRF3 gene taxon:4932 20030814 SGD
+SGD S000005032 TOP2 GO:0006265 SGD_REF:S000058487|PMID:6088500 IDA P topoisomerase II YNL088W|TOR3|TRF3 gene taxon:4932 20010118 SGD
+SGD S000005032 TOP2 GO:0006271 SGD_REF:S000051896|PMID:2549254 IMP P topoisomerase II YNL088W|TOR3|TRF3 gene taxon:4932 20010118 SGD
+SGD S000005032 TOP2 GO:0006333 SGD_REF:S000052145|PMID:9199287 IMP P topoisomerase II YNL088W|TOR3|TRF3 gene taxon:4932 20010118 SGD
+SGD S000005032 TOP2 GO:0007131 SGD_REF:S000047736|PMID:2156624 IMP P topoisomerase II YNL088W|TOR3|TRF3 gene taxon:4932 20010118 SGD
+SGD S000004224 TOP3 GO:0005634 SGD_REF:S000056212|PMID:1324925 IC GO:0003917 C DNA topoisomerase III YLR234W|EDR1 gene taxon:4932 20021105 SGD
+SGD S000004224 TOP3 GO:0031422 SGD_REF:S000081006|PMID:15889139 IPI SGD:S000004802|SGD:S000005945 C DNA topoisomerase III YLR234W|EDR1 gene taxon:4932 20050606 SGD
+SGD S000004224 TOP3 GO:0003917 SGD_REF:S000056212|PMID:1324925 IDA F DNA topoisomerase III YLR234W|EDR1 gene taxon:4932 20010118 SGD
+SGD S000004224 TOP3 GO:0000018 SGD_REF:S000045002|PMID:1328869 IMP P DNA topoisomerase III YLR234W|EDR1 gene taxon:4932 20010118 SGD
+SGD S000004224 TOP3 GO:0007004 SGD_REF:S000039158|PMID:7708702 IMP P DNA topoisomerase III YLR234W|EDR1 gene taxon:4932 20010118 SGD
+SGD S000004224 TOP3 GO:0007131 SGD_REF:S000045002|PMID:1328869 IMP P DNA topoisomerase III YLR234W|EDR1 gene taxon:4932 20010118 SGD
+SGD S000004224 TOP3 GO:0007131 SGD_REF:S000045002|PMID:1328869 IGI P DNA topoisomerase III YLR234W|EDR1 gene taxon:4932 20010118 SGD
+SGD S000003827 TOR1 GO:0000139 SGD_REF:S000072954|PMID:12719473 IDA C phosphatidylinositol kinase homolog YJR066W|DRR1 gene taxon:4932 20030507 SGD
+SGD S000003827 TOR1 GO:0005774 SGD_REF:S000072954|PMID:12719473 IDA C phosphatidylinositol kinase homolog YJR066W|DRR1 gene taxon:4932 20030507 SGD
+SGD S000003827 TOR1 GO:0005886 SGD_REF:S000059103|PMID:10973982 IDA C phosphatidylinositol kinase homolog YJR066W|DRR1 gene taxon:4932 20021209 SGD
+SGD S000003827 TOR1 GO:0010008 SGD_REF:S000072954|PMID:12719473 IDA C phosphatidylinositol kinase homolog YJR066W|DRR1 gene taxon:4932 20030507 SGD
+SGD S000003827 TOR1 GO:0031234 SGD_REF:S000072891|PMID:12631735 IDA C phosphatidylinositol kinase homolog YJR066W|DRR1 gene taxon:4932 20051104 SGD
+SGD S000003827 TOR1 GO:0031931 SGD_REF:S000071528|PMID:12408816 IPI C phosphatidylinositol kinase homolog YJR066W|DRR1 gene taxon:4932 20051130 SGD
+SGD S000003827 TOR1 GO:0004672 SGD_REF:S000045742|PMID:10329624 IMP F phosphatidylinositol kinase homolog YJR066W|DRR1 gene taxon:4932 20051028 SGD
+SGD S000003827 TOR1 GO:0005515 SGD_REF:S000072891|PMID:12631735 IPI SGD:S000001229|SGD:S000004951 F phosphatidylinositol kinase homolog YJR066W|DRR1 gene taxon:4932 20030604 SGD
+SGD S000003827 TOR1 GO:0016303 SGD_REF:S000050240|PMID:8741837 TAS F phosphatidylinositol kinase homolog YJR066W|DRR1 gene taxon:4932 20010302 SGD
+SGD S000003827 TOR1 GO:0000074 SGD_REF:S000050240|PMID:8741837 IMP P phosphatidylinositol kinase homolog YJR066W|DRR1 gene taxon:4932 20010118 SGD
+SGD S000003827 TOR1 GO:0000080 SGD_REF:S000050240|PMID:8741837 IMP P phosphatidylinositol kinase homolog YJR066W|DRR1 gene taxon:4932 20010118 SGD
+SGD S000003827 TOR1 GO:0001558 SGD_REF:S000087059|PMID:11057898 TAS P phosphatidylinositol kinase homolog YJR066W|DRR1 gene taxon:4932 20051104 SGD
+SGD S000003827 TOR1 GO:0001558 SGD_REF:S000071617|PMID:12171921 IMP P phosphatidylinositol kinase homolog YJR066W|DRR1 gene taxon:4932 20051104 SGD
+SGD S000003827 TOR1 GO:0007046 SGD_REF:S000053128|PMID:10198052 IMP P phosphatidylinositol kinase homolog YJR066W|DRR1 gene taxon:4932 20010118 SGD
+SGD S000003827 TOR1 GO:0007126 SGD_REF:S000041984|PMID:9096347 IMP P phosphatidylinositol kinase homolog YJR066W|DRR1 gene taxon:4932 20010118 SGD
+SGD S000003827 TOR1 GO:0007165 SGD_REF:S000050240|PMID:8741837 TAS P phosphatidylinositol kinase homolog YJR066W|DRR1 gene taxon:4932 20010118 SGD
+SGD S000003827 TOR1 GO:0031505 SGD_REF:S000075967|PMID:14736892 IMP P phosphatidylinositol kinase homolog YJR066W|DRR1 gene taxon:4932 20051108 SGD
+SGD S000003827 TOR1 GO:0031930 SGD_REF:S000070023|PMID:11997479 IMP P phosphatidylinositol kinase homolog YJR066W|DRR1 gene taxon:4932 20051130 SGD
+SGD S000001686 TOR2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YKL203C|DRR2 gene taxon:4932 20040928 SGD
+SGD S000001686 TOR2 GO:0005774 SGD_REF:S000046182|PMID:8846782 IDA C YKL203C|DRR2 gene taxon:4932 20010118 SGD
+SGD S000001686 TOR2 GO:0005886 SGD_REF:S000059103|PMID:10973982 IDA C YKL203C|DRR2 gene taxon:4932 20021209 SGD
+SGD S000001686 TOR2 GO:0031234 SGD_REF:S000072891|PMID:12631735 IDA C YKL203C|DRR2 gene taxon:4932 20051104 SGD
+SGD S000001686 TOR2 GO:0031931 SGD_REF:S000071528|PMID:12408816 IPI C YKL203C|DRR2 gene taxon:4932 20051130 SGD
+SGD S000001686 TOR2 GO:0031932 SGD_REF:S000071528|PMID:12408816 IPI C YKL203C|DRR2 gene taxon:4932 20051130 SGD
+SGD S000001686 TOR2 GO:0004674 SGD_REF:S000086220|PMID:16055732 IDA F YKL203C|DRR2 gene taxon:4932 20051028 SGD
+SGD S000001686 TOR2 GO:0005515 SGD_REF:S000072891|PMID:12631735 IPI SGD:S000000895|SGD:S000005438|SGD:S000004951|SGD:S000004672 F YKL203C|DRR2 gene taxon:4932 20030530 SGD
+SGD S000001686 TOR2 GO:0016303 SGD_REF:S000053983|PMID:8186460 TAS F YKL203C|DRR2 gene taxon:4932 20010302 SGD
+SGD S000001686 TOR2 GO:0000074 SGD_REF:S000040642|PMID:9475724 TAS P YKL203C|DRR2 gene taxon:4932 20010118 SGD
+SGD S000001686 TOR2 GO:0000080 SGD_REF:S000053983|PMID:8186460 TAS P YKL203C|DRR2 gene taxon:4932 20010118 SGD
+SGD S000001686 TOR2 GO:0001558 SGD_REF:S000087059|PMID:11057898 TAS P YKL203C|DRR2 gene taxon:4932 20051104 SGD
+SGD S000001686 TOR2 GO:0006897 SGD_REF:S000075861|PMID:14593073 IMP P YKL203C|DRR2 gene taxon:4932 20050505 SGD
+SGD S000001686 TOR2 GO:0007010 SGD_REF:S000040642|PMID:9475724 IMP P YKL203C|DRR2 gene taxon:4932 20010118 SGD
+SGD S000001686 TOR2 GO:0007046 SGD_REF:S000053128|PMID:10198052 IMP P YKL203C|DRR2 gene taxon:4932 20010118 SGD
+SGD S000001686 TOR2 GO:0007165 SGD_REF:S000053983|PMID:8186460 TAS P YKL203C|DRR2 gene taxon:4932 20010118 SGD
+SGD S000001686 TOR2 GO:0007266 SGD_REF:S000042831|PMID:9038344 IMP P YKL203C|DRR2 gene taxon:4932 20010118 SGD
+SGD S000001686 TOR2 GO:0030037 SGD_REF:S000042831|PMID:9038344 TAS P YKL203C|DRR2 gene taxon:4932 20011217 SGD
+SGD S000001686 TOR2 GO:0030950 SGD_REF:S000071528|PMID:12408816 IMP P YKL203C|DRR2 gene taxon:4932 20051104 SGD
+SGD S000000366 TOS1 GO:0000324 SGD_REF:S000074185|PMID:14562095 IDA C YBR162C gene taxon:4932 20031028 SGD
+SGD S000000366 TOS1 GO:0009277 SGD_REF:S000075303|PMID:11935221 IDA C YBR162C gene taxon:4932 20040114 SGD
+SGD S000000366 TOS1 GO:0009277 SGD_REF:S000081097|PMID:15781460 IDA C YBR162C gene taxon:4932 20050601 SGD
+SGD S000000366 TOS1 GO:0005554 SGD_REF:S000069584 ND F YBR162C gene taxon:4932 20020809 SGD
+SGD S000000366 TOS1 GO:0000004 SGD_REF:S000069584 ND P YBR162C gene taxon:4932 20020809 SGD
+SGD S000003453 TOS2 GO:0005934 SGD_REF:S000061434|PMID:11489916 IDA C YGR221C gene taxon:4932 20030512 SGD
+SGD S000003453 TOS2 GO:0005934 SGD_REF:S000077144|PMID:15282802 IDA C YGR221C gene taxon:4932 20041008 SGD
+SGD S000003453 TOS2 GO:0005935 SGD_REF:S000061434|PMID:11489916 IDA C YGR221C gene taxon:4932 20030512 SGD
+SGD S000003453 TOS2 GO:0005935 SGD_REF:S000077144|PMID:15282802 IDA C YGR221C gene taxon:4932 20041008 SGD
+SGD S000003453 TOS2 GO:0005554 SGD_REF:S000069584 ND F YGR221C gene taxon:4932 20040922 SGD
+SGD S000003453 TOS2 GO:0007117 SGD_REF:S000076521|PMID:14872283 IMP P YGR221C gene taxon:4932 20040922 SGD
+SGD S000003453 TOS2 GO:0007117 SGD_REF:S000076521|PMID:14872283 IPI SGD:S000000039 P YGR221C gene taxon:4932 20040922 SGD
+SGD S000003147 TOS3 NOT GO:0005634 SGD_REF:S000081815|PMID:15879520 IDA C YGL179C gene taxon:4932 20050609 SGD
+SGD S000003147 TOS3 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YGL179C gene taxon:4932 20020816 SGD
+SGD S000003147 TOS3 GO:0005737 SGD_REF:S000081815|PMID:15879520 IDA C YGL179C gene taxon:4932 20050609 SGD
+SGD S000003147 TOS3 GO:0004672 SGD_REF:S000058030|PMID:9020587 ISS F YGL179C gene taxon:4932 20030820 SGD
+SGD S000003147 TOS3 GO:0006006 SGD_REF:S000077210|PMID:15340085 IGI P YGL179C gene taxon:4932 20050512 SGD
+SGD S000003147 TOS3 GO:0006006 SGD_REF:S000077210|PMID:15340085 IMP P YGL179C gene taxon:4932 20050512 SGD
+SGD S000004173 TOS4 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YLR183C gene taxon:4932 20031028 SGD
+SGD S000004173 TOS4 GO:0005634 SGD_REF:S000077144|PMID:15282802 IDA C YLR183C gene taxon:4932 20041008 SGD
+SGD S000004173 TOS4 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YLR183C gene taxon:4932 20031028 SGD
+SGD S000004173 TOS4 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YLR183C gene taxon:4932 20040928 SGD
+SGD S000004173 TOS4 GO:0003700 SGD_REF:S000071810|PMID:12464632 IPI F YLR183C gene taxon:4932 20050603 SGD
+SGD S000004173 TOS4 GO:0000083 SGD_REF:S000071810|PMID:12464632 IPI P YLR183C gene taxon:4932 20050603 SGD
+SGD S000003064 TOS8 GO:0005634 SGD_REF:S000071810|PMID:12464632 IC GO:0003700 C YGL096W gene taxon:4932 20050603 SGD
+SGD S000003064 TOS8 GO:0003700 SGD_REF:S000071810|PMID:12464632 IPI F YGL096W gene taxon:4932 20050603 SGD
+SGD S000003064 TOS8 GO:0003700 SGD_REF:S000071810|PMID:12464632 NAS F YGL096W gene taxon:4932 20050603 SGD
+SGD S000003064 TOS8 GO:0000083 SGD_REF:S000071810|PMID:12464632 IPI P YGL096W gene taxon:4932 20050603 SGD
+SGD S000000851 TPA1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YER049W gene taxon:4932 20031028 SGD
+SGD S000000851 TPA1 GO:0005554 SGD_REF:S000069584 ND F YER049W gene taxon:4932 20010119 SGD
+SGD S000000851 TPA1 GO:0000004 SGD_REF:S000069584 ND P YER049W gene taxon:4932 20010119 SGD
+SGD S000003328 TPC1 GO:0005740 SGD_REF:S000073517|PMID:12411483 IDA C mitochondrial thiamine pyrophosphate transporter YGR096W gene taxon:4932 20030722 SGD
+SGD S000003328 TPC1 GO:0005743 SGD_REF:S000049213|PMID:10930523 ISS C mitochondrial thiamine pyrophosphate transporter YGR096W gene taxon:4932 20021017 SGD
+SGD S000003328 TPC1 GO:0005215 SGD_REF:S000049213|PMID:10930523 ISS F mitochondrial thiamine pyrophosphate transporter YGR096W gene taxon:4932 20021017 SGD
+SGD S000003328 TPC1 GO:0005215 SGD_REF:S000073517|PMID:12411483 IDA F mitochondrial thiamine pyrophosphate transporter YGR096W gene taxon:4932 20030722 SGD
+SGD S000003328 TPC1 GO:0006810 SGD_REF:S000049213|PMID:10930523 ISS P mitochondrial thiamine pyrophosphate transporter YGR096W gene taxon:4932 20021017 SGD
+SGD S000003328 TPC1 GO:0006810 SGD_REF:S000073517|PMID:12411483 IDA P mitochondrial thiamine pyrophosphate transporter YGR096W gene taxon:4932 20030722 SGD
+SGD S000003328 TPC1 GO:0006810 SGD_REF:S000073517|PMID:12411483 IMP P mitochondrial thiamine pyrophosphate transporter YGR096W gene taxon:4932 20030722 SGD
+SGD S000000014 TPD3 GO:0000159 SGD_REF:S000045742|PMID:10329624 TAS C protein phosphatase 2A regulatory subunit A YAL016W|FUN32 gene taxon:4932 20010118 SGD
+SGD S000000014 TPD3 GO:0005634 SGD_REF:S000071578|PMID:12388751 IDA C protein phosphatase 2A regulatory subunit A YAL016W|FUN32 gene taxon:4932 20030430 SGD
+SGD S000000014 TPD3 GO:0005737 SGD_REF:S000071578|PMID:12388751 IDA C protein phosphatase 2A regulatory subunit A YAL016W|FUN32 gene taxon:4932 20030430 SGD
+SGD S000000014 TPD3 GO:0005816 SGD_REF:S000071578|PMID:12388751 IDA C protein phosphatase 2A regulatory subunit A YAL016W|FUN32 gene taxon:4932 20030430 SGD
+SGD S000000014 TPD3 GO:0005934 SGD_REF:S000071578|PMID:12388751 IDA C protein phosphatase 2A regulatory subunit A YAL016W|FUN32 gene taxon:4932 20030430 SGD
+SGD S000000014 TPD3 GO:0005935 SGD_REF:S000071578|PMID:12388751 IDA C protein phosphatase 2A regulatory subunit A YAL016W|FUN32 gene taxon:4932 20030430 SGD
+SGD S000000014 TPD3 GO:0043332 SGD_REF:S000071578|PMID:12388751 IDA C protein phosphatase 2A regulatory subunit A YAL016W|FUN32 gene taxon:4932 20030430 SGD
+SGD S000000014 TPD3 GO:0000158 SGD_REF:S000045742|PMID:10329624 TAS F protein phosphatase 2A regulatory subunit A YAL016W|FUN32 gene taxon:4932 20010118 SGD
+SGD S000000014 TPD3 GO:0006412 SGD_REF:S000045742|PMID:10329624 IMP P protein phosphatase 2A regulatory subunit A YAL016W|FUN32 gene taxon:4932 20010118 SGD
+SGD S000000014 TPD3 GO:0006470 SGD_REF:S000055155|PMID:9001215 TAS P protein phosphatase 2A regulatory subunit A YAL016W|FUN32 gene taxon:4932 20030430 SGD
+SGD S000000014 TPD3 GO:0007015 SGD_REF:S000055155|PMID:9001215 TAS P protein phosphatase 2A regulatory subunit A YAL016W|FUN32 gene taxon:4932 20010118 SGD
+SGD S000000014 TPD3 GO:0007094 SGD_REF:S000055155|PMID:9001215 IMP P protein phosphatase 2A regulatory subunit A YAL016W|FUN32 gene taxon:4932 20010118 SGD
+SGD S000000014 TPD3 GO:0007117 SGD_REF:S000055155|PMID:9001215 TAS P protein phosphatase 2A regulatory subunit A YAL016W|FUN32 gene taxon:4932 20010118 SGD
+SGD S000002457 TPI1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C triosephosphate isomerase YDR050C gene taxon:4932 20020507 SGD
+SGD S000002457 TPI1 GO:0004807 SGD_REF:S000049276|PMID:6759603 IMP F triosephosphate isomerase YDR050C gene taxon:4932 20010118 SGD
+SGD S000002457 TPI1 GO:0004807 SGD_REF:S000049276|PMID:6759603 ISS F triosephosphate isomerase YDR050C gene taxon:4932 20010118 SGD
+SGD S000002457 TPI1 GO:0006096 SGD_REF:S000060352|PMID:11329176 IMP P triosephosphate isomerase YDR050C gene taxon:4932 20050524 SGD
+SGD S000003700 TPK1 GO:0005737 SGD_REF:S000046426|PMID:7826397 TAS C cAMP-dependent protein kinase catalytic subunit (putative) YJL164C|PKA1|SRA3 gene taxon:4932 20010118 SGD
+SGD S000003700 TPK1 GO:0005952 SGD_REF:S000046426|PMID:7826397 TAS C cAMP-dependent protein kinase catalytic subunit (putative) YJL164C|PKA1|SRA3 gene taxon:4932 20010118 SGD
+SGD S000003700 TPK1 GO:0005952 SGD_REF:S000042132|PMID:3036373 IMP C cAMP-dependent protein kinase catalytic subunit (putative) YJL164C|PKA1|SRA3 gene taxon:4932 20050630 SGD
+SGD S000003700 TPK1 GO:0004674 SGD_REF:S000051004|PMID:2823100 TAS F cAMP-dependent protein kinase catalytic subunit (putative) YJL164C|PKA1|SRA3 gene taxon:4932 20010118 SGD
+SGD S000003700 TPK1 GO:0004691 SGD_REF:S000051004|PMID:2823100 TAS F cAMP-dependent protein kinase catalytic subunit (putative) YJL164C|PKA1|SRA3 gene taxon:4932 20010118 SGD
+SGD S000003700 TPK1 GO:0006468 SGD_REF:S000051004|PMID:2823100 TAS P cAMP-dependent protein kinase catalytic subunit (putative) YJL164C|PKA1|SRA3 gene taxon:4932 20010118 SGD
+SGD S000003700 TPK1 GO:0007124 SGD_REF:S000051906|PMID:10373537 IMP P cAMP-dependent protein kinase catalytic subunit (putative) YJL164C|PKA1|SRA3 gene taxon:4932 20010627 SGD
+SGD S000003700 TPK1 GO:0007265 SGD_REF:S000051004|PMID:2823100 IMP P cAMP-dependent protein kinase catalytic subunit (putative) YJL164C|PKA1|SRA3 gene taxon:4932 20010118 SGD
+SGD S000006124 TPK2 GO:0005737 SGD_REF:S000046426|PMID:7826397 TAS C cAMP-dependent protein kinase catalytic subunit YPL203W|PKA2|PKA3|YKR1 gene taxon:4932 20010118 SGD
+SGD S000006124 TPK2 GO:0005952 SGD_REF:S000046426|PMID:7826397 TAS C cAMP-dependent protein kinase catalytic subunit YPL203W|PKA2|PKA3|YKR1 gene taxon:4932 20010118 SGD
+SGD S000006124 TPK2 GO:0005952 SGD_REF:S000042132|PMID:3036373 IMP C cAMP-dependent protein kinase catalytic subunit YPL203W|PKA2|PKA3|YKR1 gene taxon:4932 20050630 SGD
+SGD S000006124 TPK2 GO:0005952 SGD_REF:S000042132|PMID:3036373 ISS C cAMP-dependent protein kinase catalytic subunit YPL203W|PKA2|PKA3|YKR1 gene taxon:4932 20050630 SGD
+SGD S000006124 TPK2 GO:0004674 SGD_REF:S000052444|PMID:2558053 TAS F cAMP-dependent protein kinase catalytic subunit YPL203W|PKA2|PKA3|YKR1 gene taxon:4932 20010118 SGD
+SGD S000006124 TPK2 GO:0004691 SGD_REF:S000052444|PMID:2558053 TAS F cAMP-dependent protein kinase catalytic subunit YPL203W|PKA2|PKA3|YKR1 gene taxon:4932 20010118 SGD
+SGD S000006124 TPK2 GO:0006468 SGD_REF:S000052444|PMID:2558053 TAS P cAMP-dependent protein kinase catalytic subunit YPL203W|PKA2|PKA3|YKR1 gene taxon:4932 20010118 SGD
+SGD S000006124 TPK2 GO:0007124 SGD_REF:S000051906|PMID:10373537 IMP P cAMP-dependent protein kinase catalytic subunit YPL203W|PKA2|PKA3|YKR1 gene taxon:4932 20010118 SGD
+SGD S000006124 TPK2 GO:0007265 SGD_REF:S000040413|PMID:8090204 TAS P cAMP-dependent protein kinase catalytic subunit YPL203W|PKA2|PKA3|YKR1 gene taxon:4932 20010118 SGD
+SGD S000001649 TPK3 GO:0005737 SGD_REF:S000046426|PMID:7826397 TAS C cAMP-dependent protein kinase catalytic subunit YKL166C gene taxon:4932 20010118 SGD
+SGD S000001649 TPK3 GO:0005952 SGD_REF:S000046426|PMID:7826397 TAS C cAMP-dependent protein kinase catalytic subunit YKL166C gene taxon:4932 20010118 SGD
+SGD S000001649 TPK3 GO:0005952 SGD_REF:S000042132|PMID:3036373 IMP C cAMP-dependent protein kinase catalytic subunit YKL166C gene taxon:4932 20050630 SGD
+SGD S000001649 TPK3 GO:0005952 SGD_REF:S000042132|PMID:3036373 ISS C cAMP-dependent protein kinase catalytic subunit YKL166C gene taxon:4932 20050630 SGD
+SGD S000001649 TPK3 GO:0004674 SGD_REF:S000052444|PMID:2558053 TAS F cAMP-dependent protein kinase catalytic subunit YKL166C gene taxon:4932 20010118 SGD
+SGD S000001649 TPK3 GO:0004691 SGD_REF:S000052444|PMID:2558053 TAS F cAMP-dependent protein kinase catalytic subunit YKL166C gene taxon:4932 20010118 SGD
+SGD S000001649 TPK3 GO:0006468 SGD_REF:S000052444|PMID:2558053 TAS P cAMP-dependent protein kinase catalytic subunit YKL166C gene taxon:4932 20010118 SGD
+SGD S000001649 TPK3 GO:0007124 SGD_REF:S000051906|PMID:10373537 IMP P cAMP-dependent protein kinase catalytic subunit YKL166C gene taxon:4932 20010118 SGD
+SGD S000005023 TPM1 GO:0000142 SGD_REF:S000055444|PMID:9864365 IDA C tropomyosin I YNL079C|tropomyosin gene taxon:4932 20030902 SGD
+SGD S000005023 TPM1 GO:0030482 SGD_REF:S000055444|PMID:9864365 IDA C tropomyosin I YNL079C|tropomyosin gene taxon:4932 20030902 SGD
+SGD S000005023 TPM1 GO:0003786 SGD_REF:S000058447|PMID:9153752 TAS F tropomyosin I YNL079C|tropomyosin gene taxon:4932 20010118 SGD
+SGD S000005023 TPM1 GO:0000001 SGD_REF:S000041005|PMID:10652251 TAS P tropomyosin I YNL079C|tropomyosin gene taxon:4932 20010118 SGD
+SGD S000005023 TPM1 GO:0000011 SGD_REF:S000041005|PMID:10652251 TAS P tropomyosin I YNL079C|tropomyosin gene taxon:4932 20010118 SGD
+SGD S000005023 TPM1 GO:0006887 SGD_REF:S000041005|PMID:10652251 TAS P tropomyosin I YNL079C|tropomyosin gene taxon:4932 20010118 SGD
+SGD S000005023 TPM1 GO:0007015 SGD_REF:S000041005|PMID:10652251 IPI P tropomyosin I YNL079C|tropomyosin gene taxon:4932 20010118 SGD
+SGD S000005023 TPM1 GO:0007118 SGD_REF:S000041005|PMID:10652251 IMP P tropomyosin I YNL079C|tropomyosin gene taxon:4932 20010118 SGD
+SGD S000005023 TPM1 GO:0007118 SGD_REF:S000041005|PMID:10652251 IPI P tropomyosin I YNL079C|tropomyosin gene taxon:4932 20010118 SGD
+SGD S000005023 TPM1 GO:0007118 SGD_REF:S000041005|PMID:10652251 IGI P tropomyosin I YNL079C|tropomyosin gene taxon:4932 20010118 SGD
+SGD S000005023 TPM1 GO:0007119 SGD_REF:S000041005|PMID:10652251 IMP P tropomyosin I YNL079C|tropomyosin gene taxon:4932 20010118 SGD
+SGD S000005023 TPM1 GO:0007119 SGD_REF:S000041005|PMID:10652251 IPI P tropomyosin I YNL079C|tropomyosin gene taxon:4932 20010118 SGD
+SGD S000005023 TPM1 GO:0007119 SGD_REF:S000041005|PMID:10652251 IGI P tropomyosin I YNL079C|tropomyosin gene taxon:4932 20010118 SGD
+SGD S000005023 TPM1 GO:0008154 SGD_REF:S000041005|PMID:10652251 IGI P tropomyosin I YNL079C|tropomyosin gene taxon:4932 20010118 SGD
+SGD S000005023 TPM1 GO:0008154 SGD_REF:S000041005|PMID:10652251 IMP P tropomyosin I YNL079C|tropomyosin gene taxon:4932 20010118 SGD
+SGD S000005023 TPM1 GO:0008154 SGD_REF:S000041005|PMID:10652251 IPI P tropomyosin I YNL079C|tropomyosin gene taxon:4932 20010118 SGD
+SGD S000005023 TPM1 GO:0008298 SGD_REF:S000041005|PMID:10652251 TAS P tropomyosin I YNL079C|tropomyosin gene taxon:4932 20010118 SGD
+SGD S000005023 TPM1 GO:0016192 SGD_REF:S000041005|PMID:10652251 TAS P tropomyosin I YNL079C|tropomyosin gene taxon:4932 20010118 SGD
+SGD S000005023 TPM1 GO:0030447 SGD_REF:S000080384|PMID:15645503 IMP P tropomyosin I YNL079C|tropomyosin gene taxon:4932 20050621 SGD
+SGD S000005023 TPM1 GO:0030468 SGD_REF:S000041005|PMID:10652251 IMP P tropomyosin I YNL079C|tropomyosin gene taxon:4932 20010302 SGD
+SGD S000005023 TPM1 GO:0030468 SGD_REF:S000041005|PMID:10652251 IGI P tropomyosin I YNL079C|tropomyosin gene taxon:4932 20010302 SGD
+SGD S000005023 TPM1 GO:0030468 SGD_REF:S000041005|PMID:10652251 IPI P tropomyosin I YNL079C|tropomyosin gene taxon:4932 20010302 SGD
+SGD S000005023 TPM1 GO:0045011 SGD_REF:S000055444|PMID:9864365 IGI P tropomyosin I YNL079C|tropomyosin gene taxon:4932 20030827 SGD
+SGD S000001400 TPM2 GO:0000142 SGD_REF:S000055444|PMID:9864365 IDA C tropomyosin isoform II YIL138C|tropomyosin gene taxon:4932 20030902 SGD
+SGD S000001400 TPM2 GO:0030482 SGD_REF:S000055444|PMID:9864365 IDA C tropomyosin isoform II YIL138C|tropomyosin gene taxon:4932 20030902 SGD
+SGD S000001400 TPM2 GO:0003786 SGD_REF:S000058447|PMID:9153752 TAS F tropomyosin isoform II YIL138C|tropomyosin gene taxon:4932 20010118 SGD
+SGD S000001400 TPM2 GO:0000001 SGD_REF:S000041005|PMID:10652251 TAS P tropomyosin isoform II YIL138C|tropomyosin gene taxon:4932 20010118 SGD
+SGD S000001400 TPM2 GO:0000011 SGD_REF:S000041005|PMID:10652251 TAS P tropomyosin isoform II YIL138C|tropomyosin gene taxon:4932 20010118 SGD
+SGD S000001400 TPM2 GO:0006887 SGD_REF:S000041005|PMID:10652251 TAS P tropomyosin isoform II YIL138C|tropomyosin gene taxon:4932 20010118 SGD
+SGD S000001400 TPM2 GO:0007015 SGD_REF:S000041005|PMID:10652251 IPI P tropomyosin isoform II YIL138C|tropomyosin gene taxon:4932 20010118 SGD
+SGD S000001400 TPM2 GO:0007118 SGD_REF:S000041005|PMID:10652251 IGI P tropomyosin isoform II YIL138C|tropomyosin gene taxon:4932 20010118 SGD
+SGD S000001400 TPM2 GO:0007118 SGD_REF:S000041005|PMID:10652251 IPI P tropomyosin isoform II YIL138C|tropomyosin gene taxon:4932 20010118 SGD
+SGD S000001400 TPM2 GO:0007118 SGD_REF:S000041005|PMID:10652251 IMP P tropomyosin isoform II YIL138C|tropomyosin gene taxon:4932 20010118 SGD
+SGD S000001400 TPM2 GO:0007119 SGD_REF:S000041005|PMID:10652251 IMP P tropomyosin isoform II YIL138C|tropomyosin gene taxon:4932 20010118 SGD
+SGD S000001400 TPM2 GO:0007119 SGD_REF:S000041005|PMID:10652251 IPI P tropomyosin isoform II YIL138C|tropomyosin gene taxon:4932 20010118 SGD
+SGD S000001400 TPM2 GO:0007119 SGD_REF:S000041005|PMID:10652251 IGI P tropomyosin isoform II YIL138C|tropomyosin gene taxon:4932 20010118 SGD
+SGD S000001400 TPM2 GO:0008154 SGD_REF:S000041005|PMID:10652251 IMP P tropomyosin isoform II YIL138C|tropomyosin gene taxon:4932 20010118 SGD
+SGD S000001400 TPM2 GO:0008154 SGD_REF:S000041005|PMID:10652251 IPI P tropomyosin isoform II YIL138C|tropomyosin gene taxon:4932 20010118 SGD
+SGD S000001400 TPM2 GO:0008154 SGD_REF:S000041005|PMID:10652251 IGI P tropomyosin isoform II YIL138C|tropomyosin gene taxon:4932 20010118 SGD
+SGD S000001400 TPM2 GO:0008298 SGD_REF:S000041005|PMID:10652251 TAS P tropomyosin isoform II YIL138C|tropomyosin gene taxon:4932 20010118 SGD
+SGD S000001400 TPM2 GO:0016192 SGD_REF:S000041005|PMID:10652251 TAS P tropomyosin isoform II YIL138C|tropomyosin gene taxon:4932 20010118 SGD
+SGD S000001400 TPM2 GO:0030468 SGD_REF:S000041005|PMID:10652251 IMP P tropomyosin isoform II YIL138C|tropomyosin gene taxon:4932 20010302 SGD
+SGD S000001400 TPM2 GO:0030468 SGD_REF:S000041005|PMID:10652251 IPI P tropomyosin isoform II YIL138C|tropomyosin gene taxon:4932 20010302 SGD
+SGD S000001400 TPM2 GO:0030468 SGD_REF:S000041005|PMID:10652251 IGI P tropomyosin isoform II YIL138C|tropomyosin gene taxon:4932 20010302 SGD
+SGD S000001400 TPM2 GO:0045011 SGD_REF:S000055444|PMID:9864365 IGI P tropomyosin isoform II YIL138C|tropomyosin gene taxon:4932 20030827 SGD
+SGD S000003154 TPN1 GO:0005886 SGD_REF:S000073218|PMID:12649274 IDA C plasma membrane pyridoxine transport protein YGL186C gene taxon:4932 20030603 SGD
+SGD S000003154 TPN1 GO:0051183 SGD_REF:S000073218|PMID:12649274 IDA F plasma membrane pyridoxine transport protein YGL186C gene taxon:4932 20041006 SGD
+SGD S000003154 TPN1 GO:0051180 SGD_REF:S000073218|PMID:12649274 IDA P plasma membrane pyridoxine transport protein YGL186C gene taxon:4932 20041006 SGD
+SGD S000003951 TPO1 GO:0005774 SGD_REF:S000066148|PMID:11171066 IMP C YLL028W gene taxon:4932 20021127 SGD
+SGD S000003951 TPO1 GO:0005886 SGD_REF:S000072984|PMID:12562762 IDA C YLL028W gene taxon:4932 20030422 SGD
+SGD S000003951 TPO1 GO:0005886 SGD_REF:S000080343|PMID:15637075 IDA C YLL028W gene taxon:4932 20050126 SGD
+SGD S000003951 TPO1 GO:0005934 SGD_REF:S000074060|PMID:13679573 IDA C YLL028W gene taxon:4932 20040115 SGD
+SGD S000003951 TPO1 GO:0000297 SGD_REF:S000066148|PMID:11171066 IMP F YLL028W gene taxon:4932 20021127 SGD
+SGD S000003951 TPO1 GO:0000297 SGD_REF:S000080343|PMID:15637075 IDA F YLL028W gene taxon:4932 20050126 SGD
+SGD S000003951 TPO1 GO:0015606 SGD_REF:S000066148|PMID:11171066 IMP F YLL028W gene taxon:4932 20021127 SGD
+SGD S000003951 TPO1 GO:0015846 SGD_REF:S000066148|PMID:11171066 IMP P YLL028W gene taxon:4932 20021127 SGD
+SGD S000003370 TPO2 GO:0005774 SGD_REF:S000066148|PMID:11171066 IMP C YGR138C gene taxon:4932 20021127 SGD
+SGD S000003370 TPO2 GO:0005886 SGD_REF:S000072984|PMID:12562762 IDA C YGR138C gene taxon:4932 20030422 SGD
+SGD S000003370 TPO2 GO:0000297 SGD_REF:S000066148|PMID:11171066 IMP F YGR138C gene taxon:4932 20021127 SGD
+SGD S000003370 TPO2 GO:0015846 SGD_REF:S000066148|PMID:11171066 IMP P YGR138C gene taxon:4932 20021127 SGD
+SGD S000006360 TPO3 GO:0005774 SGD_REF:S000066148|PMID:11171066 IMP C YPR156C gene taxon:4932 20021127 SGD
+SGD S000006360 TPO3 GO:0005886 SGD_REF:S000072984|PMID:12562762 IDA C YPR156C gene taxon:4932 20030422 SGD
+SGD S000006360 TPO3 GO:0000297 SGD_REF:S000066148|PMID:11171066 IMP F YPR156C gene taxon:4932 20021127 SGD
+SGD S000006360 TPO3 GO:0015846 SGD_REF:S000066148|PMID:11171066 IMP P YPR156C gene taxon:4932 20021127 SGD
+SGD S000005799 TPO4 GO:0005774 SGD_REF:S000066148|PMID:11171066 IMP C YOR273C gene taxon:4932 20021127 SGD
+SGD S000005799 TPO4 GO:0005886 SGD_REF:S000072984|PMID:12562762 IDA C YOR273C gene taxon:4932 20030422 SGD
+SGD S000005799 TPO4 GO:0000297 SGD_REF:S000066148|PMID:11171066 IMP F YOR273C gene taxon:4932 20021127 SGD
+SGD S000005799 TPO4 GO:0015606 SGD_REF:S000066148|PMID:11171066 IMP F YOR273C gene taxon:4932 20021127 SGD
+SGD S000005799 TPO4 GO:0015846 SGD_REF:S000066148|PMID:11171066 IMP P YOR273C gene taxon:4932 20021127 SGD
+SGD S000001657 TPO5 GO:0005794 SGD_REF:S000080556|PMID:15668236 IDA C YKL174C gene taxon:4932 20050208 SGD
+SGD S000001657 TPO5 GO:0015203 SGD_REF:S000080556|PMID:15668236 IMP F YKL174C gene taxon:4932 20050208 SGD
+SGD S000001657 TPO5 GO:0015203 SGD_REF:S000080556|PMID:15668236 ISS SGD:S000002369 F YKL174C gene taxon:4932 20050208 SGD
+SGD S000001657 TPO5 GO:0015846 SGD_REF:S000080556|PMID:15668236 IMP P YKL174C gene taxon:4932 20050208 SGD
+SGD S000004765 TPP1 GO:0008372 SGD_REF:S000069584 ND C DNA 3' phosphatase YMR156C gene taxon:4932 20010119 SGD
+SGD S000004765 TPP1 GO:0046403 SGD_REF:S000073824|PMID:12783866 IDA F DNA 3' phosphatase YMR156C gene taxon:4932 20040619 SGD
+SGD S000004765 TPP1 GO:0046403 SGD_REF:S000073824|PMID:12783866 TAS F DNA 3' phosphatase YMR156C gene taxon:4932 20040619 SGD
+SGD S000004765 TPP1 GO:0006281 SGD_REF:S000073824|PMID:12783866 IDA P DNA 3' phosphatase YMR156C gene taxon:4932 20040619 SGD
+SGD S000004765 TPP1 GO:0006281 SGD_REF:S000073824|PMID:12783866 IMP P DNA 3' phosphatase YMR156C gene taxon:4932 20040619 SGD
+SGD S000000330 TPS1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C trehalose-6-phosphate synthase/phosphatase complex 56 kDa synthase subunit YBR126C|BYP1|CIF1|FDP1|GGS1|GLC6|TSS1 gene taxon:4932 20020507 SGD
+SGD S000000330 TPS1 GO:0005946 SGD_REF:S000044803|PMID:1425702 IMP C trehalose-6-phosphate synthase/phosphatase complex 56 kDa synthase subunit YBR126C|BYP1|CIF1|FDP1|GGS1|GLC6|TSS1 gene taxon:4932 20010118 SGD
+SGD S000000330 TPS1 GO:0005946 SGD_REF:S000053932|PMID:9837904 IMP C trehalose-6-phosphate synthase/phosphatase complex 56 kDa synthase subunit YBR126C|BYP1|CIF1|FDP1|GGS1|GLC6|TSS1 gene taxon:4932 20020423 SGD
+SGD S000000330 TPS1 GO:0005946 SGD_REF:S000053932|PMID:9837904 IPI C trehalose-6-phosphate synthase/phosphatase complex 56 kDa synthase subunit YBR126C|BYP1|CIF1|FDP1|GGS1|GLC6|TSS1 gene taxon:4932 20020423 SGD
+SGD S000000330 TPS1 GO:0005946 SGD_REF:S000053932|PMID:9837904 IGI C trehalose-6-phosphate synthase/phosphatase complex 56 kDa synthase subunit YBR126C|BYP1|CIF1|FDP1|GGS1|GLC6|TSS1 gene taxon:4932 20020423 SGD
+SGD S000000330 TPS1 GO:0005946 SGD_REF:S000044803|PMID:1425702 IDA C trehalose-6-phosphate synthase/phosphatase complex 56 kDa synthase subunit YBR126C|BYP1|CIF1|FDP1|GGS1|GLC6|TSS1 gene taxon:4932 20010118 SGD
+SGD S000000330 TPS1 GO:0003825 SGD_REF:S000044803|PMID:1425702 IMP F trehalose-6-phosphate synthase/phosphatase complex 56 kDa synthase subunit YBR126C|BYP1|CIF1|FDP1|GGS1|GLC6|TSS1 gene taxon:4932 20010118 SGD
+SGD S000000330 TPS1 GO:0003825 SGD_REF:S000044803|PMID:1425702 IDA F trehalose-6-phosphate synthase/phosphatase complex 56 kDa synthase subunit YBR126C|BYP1|CIF1|FDP1|GGS1|GLC6|TSS1 gene taxon:4932 20010118 SGD
+SGD S000000330 TPS1 GO:0005975 SGD_REF:S000044803|PMID:1425702 IMP P trehalose-6-phosphate synthase/phosphatase complex 56 kDa synthase subunit YBR126C|BYP1|CIF1|FDP1|GGS1|GLC6|TSS1 gene taxon:4932 20010118 SGD
+SGD S000000330 TPS1 GO:0005975 SGD_REF:S000044803|PMID:1425702 IDA P trehalose-6-phosphate synthase/phosphatase complex 56 kDa synthase subunit YBR126C|BYP1|CIF1|FDP1|GGS1|GLC6|TSS1 gene taxon:4932 20010118 SGD
+SGD S000000330 TPS1 GO:0005992 SGD_REF:S000044803|PMID:1425702 IDA P trehalose-6-phosphate synthase/phosphatase complex 56 kDa synthase subunit YBR126C|BYP1|CIF1|FDP1|GGS1|GLC6|TSS1 gene taxon:4932 20050804 SGD
+SGD S000000330 TPS1 GO:0005992 SGD_REF:S000044803|PMID:1425702 IMP P trehalose-6-phosphate synthase/phosphatase complex 56 kDa synthase subunit YBR126C|BYP1|CIF1|FDP1|GGS1|GLC6|TSS1 gene taxon:4932 20050804 SGD
+SGD S000000330 TPS1 GO:0006950 SGD_REF:S000058488|PMID:9660948 IDA P trehalose-6-phosphate synthase/phosphatase complex 56 kDa synthase subunit YBR126C|BYP1|CIF1|FDP1|GGS1|GLC6|TSS1 gene taxon:4932 20010118 SGD
+SGD S000000330 TPS1 GO:0006950 SGD_REF:S000061163|PMID:11483159 IGI P trehalose-6-phosphate synthase/phosphatase complex 56 kDa synthase subunit YBR126C|BYP1|CIF1|FDP1|GGS1|GLC6|TSS1 gene taxon:4932 20020423 SGD
+SGD S000000330 TPS1 GO:0006950 SGD_REF:S000061163|PMID:11483159 IMP P trehalose-6-phosphate synthase/phosphatase complex 56 kDa synthase subunit YBR126C|BYP1|CIF1|FDP1|GGS1|GLC6|TSS1 gene taxon:4932 20020423 SGD
+SGD S000002481 TPS2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C trehalose-6-phosphate phosphatase YDR074W|HOG2|PFK3 gene taxon:4932 20040928 SGD
+SGD S000002481 TPS2 GO:0005946 SGD_REF:S000053932|PMID:9837904 IMP C trehalose-6-phosphate phosphatase YDR074W|HOG2|PFK3 gene taxon:4932 20020423 SGD
+SGD S000002481 TPS2 GO:0005946 SGD_REF:S000053932|PMID:9837904 IGI C trehalose-6-phosphate phosphatase YDR074W|HOG2|PFK3 gene taxon:4932 20020423 SGD
+SGD S000002481 TPS2 GO:0005946 SGD_REF:S000053932|PMID:9837904 IPI C trehalose-6-phosphate phosphatase YDR074W|HOG2|PFK3 gene taxon:4932 20020423 SGD
+SGD S000002481 TPS2 GO:0004805 SGD_REF:S000052198|PMID:8444170 IMP F trehalose-6-phosphate phosphatase YDR074W|HOG2|PFK3 gene taxon:4932 20010118 SGD
+SGD S000002481 TPS2 GO:0005992 SGD_REF:S000052198|PMID:8444170 IMP P trehalose-6-phosphate phosphatase YDR074W|HOG2|PFK3 gene taxon:4932 20050713 SGD
+SGD S000002481 TPS2 GO:0005992 SGD_REF:S000043480|PMID:8203161 IMP P trehalose-6-phosphate phosphatase YDR074W|HOG2|PFK3 gene taxon:4932 20050713 SGD
+SGD S000002481 TPS2 GO:0006950 SGD_REF:S000052198|PMID:8444170 IDA P trehalose-6-phosphate phosphatase YDR074W|HOG2|PFK3 gene taxon:4932 20010118 SGD
+SGD S000002481 TPS2 GO:0006950 SGD_REF:S000043480|PMID:8203161 IMP P trehalose-6-phosphate phosphatase YDR074W|HOG2|PFK3 gene taxon:4932 20050713 SGD
+SGD S000004874 TPS3 GO:0005946 SGD_REF:S000053932|PMID:9837904 IMP C trehalose-6-phosphate synthase/phosphatase complex 115 kDa regulatory subunit YMR261C gene taxon:4932 20020423 SGD
+SGD S000004874 TPS3 GO:0005946 SGD_REF:S000053932|PMID:9837904 IPI C trehalose-6-phosphate synthase/phosphatase complex 115 kDa regulatory subunit YMR261C gene taxon:4932 20020423 SGD
+SGD S000004874 TPS3 GO:0005946 SGD_REF:S000053932|PMID:9837904 IGI C trehalose-6-phosphate synthase/phosphatase complex 115 kDa regulatory subunit YMR261C gene taxon:4932 20020423 SGD
+SGD S000004874 TPS3 contributes_to GO:0003825 SGD_REF:S000053932|PMID:9837904 IMP F trehalose-6-phosphate synthase/phosphatase complex 115 kDa regulatory subunit YMR261C gene taxon:4932 20050729 SGD
+SGD S000004874 TPS3 contributes_to GO:0003825 SGD_REF:S000053932|PMID:9837904 ISS F trehalose-6-phosphate synthase/phosphatase complex 115 kDa regulatory subunit YMR261C gene taxon:4932 20050729 SGD
+SGD S000004874 TPS3 contributes_to GO:0004805 SGD_REF:S000053932|PMID:9837904 IGI SGD:S000004566 F trehalose-6-phosphate synthase/phosphatase complex 115 kDa regulatory subunit YMR261C gene taxon:4932 20050729 SGD
+SGD S000004874 TPS3 GO:0030234 SGD_REF:S000053932|PMID:9837904 IMP F trehalose-6-phosphate synthase/phosphatase complex 115 kDa regulatory subunit YMR261C gene taxon:4932 20050729 SGD
+SGD S000004874 TPS3 GO:0030234 SGD_REF:S000053932|PMID:9837904 ISS F trehalose-6-phosphate synthase/phosphatase complex 115 kDa regulatory subunit YMR261C gene taxon:4932 20050729 SGD
+SGD S000004874 TPS3 GO:0005992 SGD_REF:S000053932|PMID:9837904 IMP P trehalose-6-phosphate synthase/phosphatase complex 115 kDa regulatory subunit YMR261C gene taxon:4932 20020423 SGD
+SGD S000004874 TPS3 GO:0005992 SGD_REF:S000053932|PMID:9837904 IGI P trehalose-6-phosphate synthase/phosphatase complex 115 kDa regulatory subunit YMR261C gene taxon:4932 20020423 SGD
+SGD S000004874 TPS3 GO:0005992 SGD_REF:S000053932|PMID:9837904 IPI P trehalose-6-phosphate synthase/phosphatase complex 115 kDa regulatory subunit YMR261C gene taxon:4932 20020423 SGD
+SGD S000004874 TPS3 GO:0006950 SGD_REF:S000053932|PMID:9837904 IMP P trehalose-6-phosphate synthase/phosphatase complex 115 kDa regulatory subunit YMR261C gene taxon:4932 20020423 SGD
+SGD S000005462 TPT1 GO:0005634 SGD_REF:S000058320|PMID:9582290 TAS C tRNA 2'-phosphotransferase YOL102C gene taxon:4932 20010118 SGD
+SGD S000005462 TPT1 GO:0000215 SGD_REF:S000058320|PMID:9582290 TAS F tRNA 2'-phosphotransferase YOL102C gene taxon:4932 20010118 SGD
+SGD S000005462 TPT1 GO:0006388 SGD_REF:S000058320|PMID:9582290 TAS P tRNA 2'-phosphotransferase YOL102C gene taxon:4932 20010118 SGD
+SGD S000001141 TRA1 GO:0000123 SGD_REF:S000046619|PMID:10911987 IPI C ATM/Mec1/TOR1/TOR2-related, NuA4 complex component YHR099W gene taxon:4932 20020918 SGD
+SGD S000001141 TRA1 GO:0043189 SGD_REF:S000051286|PMID:10487762 IPI C ATM/Mec1/TOR1/TOR2-related, NuA4 complex component YHR099W gene taxon:4932 20050207 SGD
+SGD S000001141 TRA1 GO:0046695 SGD_REF:S000071997|PMID:12446794 IPI C ATM/Mec1/TOR1/TOR2-related, NuA4 complex component YHR099W gene taxon:4932 20041024 SGD
+SGD S000001141 TRA1 GO:0004402 SGD_REF:S000046619|PMID:10911987 IDA F ATM/Mec1/TOR1/TOR2-related, NuA4 complex component YHR099W gene taxon:4932 20020918 SGD
+SGD S000001141 TRA1 GO:0006357 SGD_REF:S000046619|PMID:10911987 IPI P ATM/Mec1/TOR1/TOR2-related, NuA4 complex component YHR099W gene taxon:4932 20020918 SGD
+SGD S000001141 TRA1 GO:0016573 SGD_REF:S000046619|PMID:10911987 IPI P ATM/Mec1/TOR1/TOR2-related, NuA4 complex component YHR099W gene taxon:4932 20020422 SGD
+SGD S000001141 TRA1 GO:0016573 SGD_REF:S000047630|PMID:9885573 IPI P ATM/Mec1/TOR1/TOR2-related, NuA4 complex component YHR099W gene taxon:4932 20020422 SGD
+SGD S000001141 TRA1 GO:0016573 SGD_REF:S000046619|PMID:10911987 IDA P ATM/Mec1/TOR1/TOR2-related, NuA4 complex component YHR099W gene taxon:4932 20020422 SGD
+SGD S000006097 TRE1 GO:0005886 SGD_REF:S000071843|PMID:12374868 IDA C YPL176C gene taxon:4932 20030129 SGD
+SGD S000006097 TRE1 GO:0004872 SGD_REF:S000071843|PMID:12374868 ISS F YPL176C gene taxon:4932 20030129 SGD
+SGD S000006097 TRE1 GO:0000004 SGD_REF:S000069584 ND P YPL176C gene taxon:4932 20021126 SGD
+SGD S000005782 TRE2 GO:0008372 SGD_REF:S000069584 ND C YOR256C gene taxon:4932 20021126 SGD
+SGD S000005782 TRE2 GO:0005554 SGD_REF:S000069584 ND F YOR256C gene taxon:4932 20021126 SGD
+SGD S000005782 TRE2 GO:0000004 SGD_REF:S000069584 ND P YOR256C gene taxon:4932 20021126 SGD
+SGD S000005243 TRF5 GO:0005634 SGD_REF:S000055910|PMID:10926539 ISS C DNA polymerase sigma YNL299W gene taxon:4932 20010118 SGD
+SGD S000005243 TRF5 GO:0005730 SGD_REF:S000074185|PMID:14562095 IDA C DNA polymerase sigma YNL299W gene taxon:4932 20050616 SGD
+SGD S000005243 TRF5 GO:0003887 SGD_REF:S000055910|PMID:10926539 ISS F DNA polymerase sigma YNL299W gene taxon:4932 20010118 SGD
+SGD S000005243 TRF5 NOT GO:0003887 SGD_REF:S000087060|PMID:16260630 IDA F DNA polymerase sigma YNL299W gene taxon:4932 20051108 SGD
+SGD S000005243 TRF5 GO:0004652 SGD_REF:S000081843|PMID:15935758 IGI SGD:S000005475 F DNA polymerase sigma YNL299W gene taxon:4932 20050616 SGD
+SGD S000005243 TRF5 GO:0004652 SGD_REF:S000114120|PMID:16374505 IMP F DNA polymerase sigma YNL299W gene taxon:4932 20060120 SGD
+SGD S000005243 TRF5 GO:0004652 SGD_REF:S000114120|PMID:16374505 IDA F DNA polymerase sigma YNL299W gene taxon:4932 20060120 SGD
+SGD S000005243 TRF5 GO:0004652 SGD_REF:S000114120|PMID:16374505 IGI SGD:S000005475|SGD:S000005527 F DNA polymerase sigma YNL299W gene taxon:4932 20060120 SGD
+SGD S000005243 TRF5 GO:0004652 SGD_REF:S000081438|PMID:15828860 ISS SGD:S000005475 F DNA polymerase sigma YNL299W gene taxon:4932 20050616 SGD
+SGD S000005243 TRF5 GO:0004652 SGD_REF:S000081843|PMID:15935758 IMP F DNA polymerase sigma YNL299W gene taxon:4932 20050616 SGD
+SGD S000005243 TRF5 GO:0004652 SGD_REF:S000081843|PMID:15935758 ISS SGD:S000005475 F DNA polymerase sigma YNL299W gene taxon:4932 20050616 SGD
+SGD S000005243 TRF5 GO:0004652 SGD_REF:S000087060|PMID:16260630 IDA F DNA polymerase sigma YNL299W gene taxon:4932 20051108 SGD
+SGD S000005243 TRF5 GO:0007062 SGD_REF:S000055910|PMID:10926539 IMP P DNA polymerase sigma YNL299W gene taxon:4932 20010118 SGD
+SGD S000005243 TRF5 GO:0007062 SGD_REF:S000055910|PMID:10926539 IGI P DNA polymerase sigma YNL299W gene taxon:4932 20010118 SGD
+SGD S000005243 TRF5 GO:0016075 SGD_REF:S000081843|PMID:15935758 IMP P DNA polymerase sigma YNL299W gene taxon:4932 20050610 SGD
+SGD S000005243 TRF5 GO:0016077 SGD_REF:S000081843|PMID:15935758 IGI SGD:S000005475 P DNA polymerase sigma YNL299W gene taxon:4932 20050610 SGD
+SGD S000003665 TRK1 GO:0005886 SGD_REF:S000039655|PMID:3043197 TAS C 180 kDa high affinity potassium transporter YJL129C gene taxon:4932 20020307 SGD
+SGD S000003665 TRK1 GO:0015079 SGD_REF:S000039655|PMID:3043197 IDA F 180 kDa high affinity potassium transporter YJL129C gene taxon:4932 20020307 SGD
+SGD S000003665 TRK1 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P 180 kDa high affinity potassium transporter YJL129C gene taxon:4932 20060214 SGD
+SGD S000003665 TRK1 GO:0030007 SGD_REF:S000039655|PMID:3043197 IDA P 180 kDa high affinity potassium transporter YJL129C gene taxon:4932 20020307 SGD
+SGD S000001758 TRK2 GO:0005886 SGD_REF:S000043882|PMID:2072919 TAS C low affinity potassium transport, membrane protein YKR050W|RPD2 gene taxon:4932 20020307 SGD
+SGD S000001758 TRK2 GO:0015079 SGD_REF:S000043882|PMID:2072919 IDA F low affinity potassium transport, membrane protein YKR050W|RPD2 gene taxon:4932 20020307 SGD
+SGD S000001758 TRK2 GO:0015079 SGD_REF:S000043882|PMID:2072919 ISS F low affinity potassium transport, membrane protein YKR050W|RPD2 gene taxon:4932 20020307 SGD
+SGD S000001758 TRK2 GO:0030007 SGD_REF:S000043882|PMID:2072919 IDA P low affinity potassium transport, membrane protein YKR050W|RPD2 gene taxon:4932 20020307 SGD
+SGD S000003623 TRL1 GO:0005637 SGD_REF:S000057073|PMID:3312232 IDA C tRNA ligase YJL087C|LIG1|RLG1 gene taxon:4932 20010118 SGD
+SGD S000003623 TRL1 GO:0005654 SGD_REF:S000057073|PMID:3312232 IDA C tRNA ligase YJL087C|LIG1|RLG1 gene taxon:4932 20010118 SGD
+SGD S000003623 TRL1 GO:0003972 SGD_REF:S000057099|PMID:3512545 IDA F tRNA ligase YJL087C|LIG1|RLG1 gene taxon:4932 20010118 SGD
+SGD S000003623 TRL1 GO:0003972 SGD_REF:S000057046|PMID:3277966 IDA F tRNA ligase YJL087C|LIG1|RLG1 gene taxon:4932 20010118 SGD
+SGD S000003623 TRL1 GO:0004113 SGD_REF:S000113723|PMID:6297798 IDA F tRNA ligase YJL087C|LIG1|RLG1 gene taxon:4932 20051212 SGD
+SGD S000003623 TRL1 GO:0051730 SGD_REF:S000057745|PMID:8428918 IDA F tRNA ligase YJL087C|LIG1|RLG1 gene taxon:4932 20051215 SGD
+SGD S000003623 TRL1 GO:0006388 SGD_REF:S000056811|PMID:2207062 IDA P tRNA ligase YJL087C|LIG1|RLG1 gene taxon:4932 20010118 SGD
+SGD S000003623 TRL1 GO:0006388 SGD_REF:S000056555|PMID:1537841 IMP P tRNA ligase YJL087C|LIG1|RLG1 gene taxon:4932 20010118 SGD
+SGD S000003623 TRL1 GO:0030969 SGD_REF:S000048580|PMID:10346810 TAS P tRNA ligase YJL087C|LIG1|RLG1 gene taxon:4932 20040722 SGD
+SGD S000002527 TRM1 GO:0005635 SGD_REF:S000040259|PMID:7599275 IDA C N2,N2-dimethylguanosine-specific tRNA methyltransferase YDR120C gene taxon:4932 20050527 SGD
+SGD S000002527 TRM1 GO:0005637 SGD_REF:S000081760|PMID:15911569 TAS C N2,N2-dimethylguanosine-specific tRNA methyltransferase YDR120C gene taxon:4932 20050527 SGD
+SGD S000002527 TRM1 GO:0005739 SGD_REF:S000040259|PMID:7599275 TAS C N2,N2-dimethylguanosine-specific tRNA methyltransferase YDR120C gene taxon:4932 20020930 SGD
+SGD S000002527 TRM1 GO:0004809 SGD_REF:S000058381|PMID:9801306 IDA F N2,N2-dimethylguanosine-specific tRNA methyltransferase YDR120C gene taxon:4932 20020930 SGD
+SGD S000002527 TRM1 GO:0004809 SGD_REF:S000058381|PMID:9801306 IMP F N2,N2-dimethylguanosine-specific tRNA methyltransferase YDR120C gene taxon:4932 20020930 SGD
+SGD S000002527 TRM1 GO:0030488 SGD_REF:S000052056|PMID:2426253 IMP P N2,N2-dimethylguanosine-specific tRNA methyltransferase YDR120C gene taxon:4932 20020930 SGD
+SGD S000005453 TRM10 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YOL093W gene taxon:4932 20031028 SGD
+SGD S000005453 TRM10 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YOL093W gene taxon:4932 20031028 SGD
+SGD S000005453 TRM10 GO:0016423 SGD_REF:S000073304|PMID:12702816 IDA F YOL093W gene taxon:4932 20030618 SGD
+SGD S000005453 TRM10 GO:0030488 SGD_REF:S000073304|PMID:12702816 IDA P YOL093W gene taxon:4932 20030618 SGD
+SGD S000005484 TRM11 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C N2-monomethylguanosine-specific tRNA methyltransferase YOL124C gene taxon:4932 20031028 SGD
+SGD S000005484 TRM11 GO:0005737 SGD_REF:S000081761|PMID:15899842 IDA C N2-monomethylguanosine-specific tRNA methyltransferase YOL124C gene taxon:4932 20050601 SGD
+SGD S000005484 TRM11 GO:0003723 SGD_REF:S000081761|PMID:15899842 ISS F N2-monomethylguanosine-specific tRNA methyltransferase YOL124C gene taxon:4932 20050601 SGD
+SGD S000005484 TRM11 GO:0004809 SGD_REF:S000081761|PMID:15899842 IDA F N2-monomethylguanosine-specific tRNA methyltransferase YOL124C gene taxon:4932 20050601 SGD
+SGD S000005484 TRM11 GO:0004809 SGD_REF:S000081761|PMID:15899842 IMP F N2-monomethylguanosine-specific tRNA methyltransferase YOL124C gene taxon:4932 20050601 SGD
+SGD S000005484 TRM11 GO:0008757 SGD_REF:S000074033|PMID:12872006 ISS F N2-monomethylguanosine-specific tRNA methyltransferase YOL124C gene taxon:4932 20031001 SGD
+SGD S000005484 TRM11 GO:0008757 SGD_REF:S000081761|PMID:15899842 ISS F N2-monomethylguanosine-specific tRNA methyltransferase YOL124C gene taxon:4932 20050601 SGD
+SGD S000005484 TRM11 GO:0030488 SGD_REF:S000081761|PMID:15899842 IDA P N2-monomethylguanosine-specific tRNA methyltransferase YOL124C gene taxon:4932 20050601 SGD
+SGD S000005484 TRM11 GO:0030488 SGD_REF:S000081761|PMID:15899842 IMP P N2-monomethylguanosine-specific tRNA methyltransferase YOL124C gene taxon:4932 20050601 SGD
+SGD S000005329 TRM112 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YNR046W gene taxon:4932 20031028 SGD
+SGD S000005329 TRM112 GO:0005634 SGD_REF:S000075214|PMID:14690591 IDA C YNR046W gene taxon:4932 20040105 SGD
+SGD S000005329 TRM112 GO:0005730 SGD_REF:S000075214|PMID:14690591 IDA C YNR046W gene taxon:4932 20040105 SGD
+SGD S000005329 TRM112 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YNR046W gene taxon:4932 20031028 SGD
+SGD S000005329 TRM112 GO:0005737 SGD_REF:S000075214|PMID:14690591 IDA C YNR046W gene taxon:4932 20040105 SGD
+SGD S000005329 TRM112 contributes_to GO:0004809 SGD_REF:S000081761|PMID:15899842 IDA F YNR046W gene taxon:4932 20050601 SGD
+SGD S000005329 TRM112 contributes_to GO:0004809 SGD_REF:S000081761|PMID:15899842 IMP F YNR046W gene taxon:4932 20050601 SGD
+SGD S000005329 TRM112 GO:0008270 SGD_REF:S000081761|PMID:15899842 ISS F YNR046W gene taxon:4932 20050601 SGD
+SGD S000005329 TRM112 GO:0030488 SGD_REF:S000081761|PMID:15899842 IMP P YNR046W gene taxon:4932 20050601 SGD
+SGD S000004464 TRM12 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C tRNA methyltransferase YML005W|TYW2 gene taxon:4932 20031028 SGD
+SGD S000004464 TRM12 GO:0008757 SGD_REF:S000074033|PMID:12872006 ISS F tRNA methyltransferase YML005W|TYW2 gene taxon:4932 20031001 SGD
+SGD S000004464 TRM12 GO:0008757 SGD_REF:S000082265|PMID:16005430 IDA F tRNA methyltransferase YML005W|TYW2 gene taxon:4932 20050715 SGD
+SGD S000004464 TRM12 GO:0030488 SGD_REF:S000082265|PMID:16005430 IDA P tRNA methyltransferase YML005W|TYW2 gene taxon:4932 20050715 SGD
+SGD S000001764 TRM2 GO:0008372 SGD_REF:S000069584 ND C tRNA methyltransferase YKR056W|NUC2|NUD1|RNC1 gene taxon:4932 20021118 SGD
+SGD S000001764 TRM2 GO:0030696 SGD_REF:S000040190|PMID:10864043 IDA F tRNA methyltransferase YKR056W|NUC2|NUD1|RNC1 gene taxon:4932 20050701 SGD
+SGD S000001764 TRM2 GO:0030696 SGD_REF:S000040190|PMID:10864043 IMP F tRNA methyltransferase YKR056W|NUC2|NUD1|RNC1 gene taxon:4932 20050701 SGD
+SGD S000001764 TRM2 GO:0006400 SGD_REF:S000040190|PMID:10864043 IDA P tRNA methyltransferase YKR056W|NUC2|NUD1|RNC1 gene taxon:4932 20010830 SGD
+SGD S000002270 TRM3 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C tRNA (Gm18) ribose methylase YDL112W gene taxon:4932 20031028 SGD
+SGD S000002270 TRM3 GO:0016424 SGD_REF:S000047696|PMID:9917067 IDA F tRNA (Gm18) ribose methylase YDL112W gene taxon:4932 20021104 SGD
+SGD S000002270 TRM3 GO:0030488 SGD_REF:S000047696|PMID:9917067 IDA P tRNA (Gm18) ribose methylase YDL112W gene taxon:4932 20021104 SGD
+SGD S000001112 TRM5 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YHR070W gene taxon:4932 20031028 SGD
+SGD S000001112 TRM5 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YHR070W gene taxon:4932 20020507 SGD
+SGD S000001112 TRM5 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YHR070W gene taxon:4932 20031028 SGD
+SGD S000001112 TRM5 GO:0016423 SGD_REF:S000060299|PMID:11226173 IGI F YHR070W gene taxon:4932 20030108 SGD
+SGD S000001112 TRM5 GO:0016423 SGD_REF:S000060299|PMID:11226173 ISS F YHR070W gene taxon:4932 20030108 SGD
+SGD S000001112 TRM5 GO:0016423 SGD_REF:S000060299|PMID:11226173 IMP F YHR070W gene taxon:4932 20030108 SGD
+SGD S000001112 TRM5 GO:0030488 SGD_REF:S000060299|PMID:11226173 IGI P YHR070W gene taxon:4932 20030108 SGD
+SGD S000001112 TRM5 GO:0030488 SGD_REF:S000060299|PMID:11226173 ISS P YHR070W gene taxon:4932 20030108 SGD
+SGD S000001112 TRM5 GO:0030488 SGD_REF:S000060299|PMID:11226173 IMP P YHR070W gene taxon:4932 20030108 SGD
+SGD S000000265 TRM7 GO:0005737 SGD_REF:S000069485|PMID:11927565 IDA C 2'-O-ribose tRNA anticodon loop methyltransferase YBR061C gene taxon:4932 20021018 SGD
+SGD S000000265 TRM7 GO:0008175 SGD_REF:S000069485|PMID:11927565 IDA F 2'-O-ribose tRNA anticodon loop methyltransferase YBR061C gene taxon:4932 20021018 SGD
+SGD S000000265 TRM7 GO:0008175 SGD_REF:S000047696|PMID:9917067 IMP F 2'-O-ribose tRNA anticodon loop methyltransferase YBR061C gene taxon:4932 20020809 SGD
+SGD S000000265 TRM7 GO:0008175 SGD_REF:S000047696|PMID:9917067 ISS F 2'-O-ribose tRNA anticodon loop methyltransferase YBR061C gene taxon:4932 20020809 SGD
+SGD S000000265 TRM7 GO:0006412 SGD_REF:S000069485|PMID:11927565 IMP P 2'-O-ribose tRNA anticodon loop methyltransferase YBR061C gene taxon:4932 20021018 SGD
+SGD S000000265 TRM7 GO:0030488 SGD_REF:S000069485|PMID:11927565 IDA P 2'-O-ribose tRNA anticodon loop methyltransferase YBR061C gene taxon:4932 20021018 SGD
+SGD S000002360 TRM8 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YDL201W gene taxon:4932 20031028 SGD
+SGD S000002360 TRM8 GO:0005515 SGD_REF:S000071564|PMID:12403464 IPI SGD:S000002572 F YDL201W gene taxon:4932 20030718 SGD
+SGD S000002360 TRM8 GO:0008176 SGD_REF:S000071564|PMID:12403464 ISS F YDL201W gene taxon:4932 20060223 SGD
+SGD S000002360 TRM8 contributes_to GO:0008176 SGD_REF:S000071564|PMID:12403464 IMP F YDL201W gene taxon:4932 20060223 SGD
+SGD S000002360 TRM8 GO:0030488 SGD_REF:S000071564|PMID:12403464 IMP P YDL201W gene taxon:4932 20021107 SGD
+SGD S000002572 TRM82 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YDR165W gene taxon:4932 20031028 SGD
+SGD S000002572 TRM82 GO:0005515 SGD_REF:S000071564|PMID:12403464 IPI SGD:S000002360 F YDR165W gene taxon:4932 20030718 SGD
+SGD S000002572 TRM82 contributes_to GO:0008176 SGD_REF:S000071564|PMID:12403464 IMP F YDR165W gene taxon:4932 20060223 SGD
+SGD S000002572 TRM82 GO:0030488 SGD_REF:S000071564|PMID:12403464 IMP P YDR165W gene taxon:4932 20021107 SGD
+SGD S000004476 TRM9 GO:0005634 SGD_REF:S000075253|PMID:14645538 IDA C mcm5U/mcm5s2U tRNA carboxyl methyltransferase YML014W gene taxon:4932 20040103 SGD
+SGD S000004476 TRM9 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C mcm5U/mcm5s2U tRNA carboxyl methyltransferase YML014W gene taxon:4932 20031028 SGD
+SGD S000004476 TRM9 GO:0005737 SGD_REF:S000075253|PMID:14645538 IDA C mcm5U/mcm5s2U tRNA carboxyl methyltransferase YML014W gene taxon:4932 20040103 SGD
+SGD S000004476 TRM9 GO:0016431 SGD_REF:S000075253|PMID:14645538 IDA F mcm5U/mcm5s2U tRNA carboxyl methyltransferase YML014W gene taxon:4932 20050630 SGD
+SGD S000004476 TRM9 GO:0006950 SGD_REF:S000075253|PMID:14645538 IMP P mcm5U/mcm5s2U tRNA carboxyl methyltransferase YML014W gene taxon:4932 20040103 SGD
+SGD S000004476 TRM9 GO:0030488 SGD_REF:S000075253|PMID:14645538 IDA P mcm5U/mcm5s2U tRNA carboxyl methyltransferase YML014W gene taxon:4932 20050630 SGD
+SGD S000006680 TRN1 GO:0005829 SGD_REF:S000054194|PMID:3894935 ISS C tRNA-Pro tP(UGG)A gene taxon:4932 20020617 SGD
+SGD S000006680 TRN1 GO:0030533 SGD_REF:S000054194|PMID:3894935 ISS F tRNA-Pro tP(UGG)A gene taxon:4932 20020617 SGD
+SGD S000006680 TRN1 GO:0006414 SGD_REF:S000054194|PMID:3894935 ISS P tRNA-Pro tP(UGG)A gene taxon:4932 20020617 SGD
+SGD S000002414 TRP1 GO:0005737 SGD_REF:S000042328|PMID:1943992 TAS C N-(5'-phosphoribosyl)-anthranilate isomerase YDR007W gene taxon:4932 20010118 SGD
+SGD S000002414 TRP1 GO:0004640 SGD_REF:S000065555|PMID:348687 IMP F N-(5'-phosphoribosyl)-anthranilate isomerase YDR007W gene taxon:4932 20060301 SGD
+SGD S000002414 TRP1 GO:0004640 SGD_REF:S000054169|PMID:3286643 IDA F N-(5'-phosphoribosyl)-anthranilate isomerase YDR007W gene taxon:4932 20060301 SGD
+SGD S000002414 TRP1 GO:0000162 SGD_REF:S000041474|PMID:10790693 TAS P N-(5'-phosphoribosyl)-anthranilate isomerase YDR007W gene taxon:4932 20020419 SGD
+SGD S000002414 TRP1 GO:0000162 SGD_REF:S000054169|PMID:3286643 IDA P N-(5'-phosphoribosyl)-anthranilate isomerase YDR007W gene taxon:4932 20060301 SGD
+SGD S000002414 TRP1 GO:0000162 SGD_REF:S000065555|PMID:348687 IMP P N-(5'-phosphoribosyl)-anthranilate isomerase YDR007W gene taxon:4932 20060301 SGD
+SGD S000002414 TRP1 GO:0006520 SGD_REF:S000042328|PMID:1943992 TAS P N-(5'-phosphoribosyl)-anthranilate isomerase YDR007W gene taxon:4932 20010118 SGD
+SGD S000000892 TRP2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C anthranilate synthase component I YER090W gene taxon:4932 20031028 SGD
+SGD S000000892 TRP2 GO:0005950 SGD_REF:S000041757|PMID:3881257 IPI C anthranilate synthase component I YER090W gene taxon:4932 20050126 SGD
+SGD S000000892 TRP2 GO:0004049 SGD_REF:S000040822|PMID:6323449 IGI F anthranilate synthase component I YER090W gene taxon:4932 20020419 SGD
+SGD S000000892 TRP2 GO:0004049 SGD_REF:S000040822|PMID:6323449 ISS F anthranilate synthase component I YER090W gene taxon:4932 20020419 SGD
+SGD S000000892 TRP2 GO:0004049 SGD_REF:S000041757|PMID:3881257 IDA F anthranilate synthase component I YER090W gene taxon:4932 20020419 SGD
+SGD S000000892 TRP2 GO:0000162 SGD_REF:S000048355|PMID:8432699 IMP P anthranilate synthase component I YER090W gene taxon:4932 20020419 SGD
+SGD S000000892 TRP2 GO:0000162 SGD_REF:S000041757|PMID:3881257 TAS P anthranilate synthase component I YER090W gene taxon:4932 20020419 SGD
+SGD S000001694 TRP3 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C anthranilate synthase component II, indole-3-phosphate YKL211C gene taxon:4932 20031028 SGD
+SGD S000001694 TRP3 GO:0005950 SGD_REF:S000041757|PMID:3881257 IPI C anthranilate synthase component II, indole-3-phosphate YKL211C gene taxon:4932 20050126 SGD
+SGD S000001694 TRP3 GO:0004049 SGD_REF:S000048747|PMID:8001582 IDA F anthranilate synthase component II, indole-3-phosphate YKL211C gene taxon:4932 20021112 SGD
+SGD S000001694 TRP3 GO:0004425 SGD_REF:S000040822|PMID:6323449 IGI F anthranilate synthase component II, indole-3-phosphate YKL211C gene taxon:4932 20020419 SGD
+SGD S000001694 TRP3 GO:0004425 SGD_REF:S000041757|PMID:3881257 IDA F anthranilate synthase component II, indole-3-phosphate YKL211C gene taxon:4932 20020419 SGD
+SGD S000001694 TRP3 GO:0004425 SGD_REF:S000040822|PMID:6323449 ISS F anthranilate synthase component II, indole-3-phosphate YKL211C gene taxon:4932 20020419 SGD
+SGD S000001694 TRP3 GO:0000162 SGD_REF:S000041757|PMID:3881257 TAS P anthranilate synthase component II, indole-3-phosphate YKL211C gene taxon:4932 20020419 SGD
+SGD S000002762 TRP4 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C anthranilate phosphoribosyl transferase YDR354W gene taxon:4932 20031028 SGD
+SGD S000002762 TRP4 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C anthranilate phosphoribosyl transferase YDR354W gene taxon:4932 20031028 SGD
+SGD S000002762 TRP4 GO:0004048 SGD_REF:S000054204|PMID:2428012 ISS F anthranilate phosphoribosyl transferase YDR354W gene taxon:4932 20020419 SGD
+SGD S000002762 TRP4 GO:0000162 SGD_REF:S000041474|PMID:10790693 IMP P anthranilate phosphoribosyl transferase YDR354W gene taxon:4932 20020419 SGD
+SGD S000002762 TRP4 GO:0000162 SGD_REF:S000054204|PMID:2428012 TAS P anthranilate phosphoribosyl transferase YDR354W gene taxon:4932 20020419 SGD
+SGD S000002994 TRP5 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C tryptophan synthase YGL026C gene taxon:4932 20031028 SGD
+SGD S000002994 TRP5 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C tryptophan synthase YGL026C gene taxon:4932 20020507 SGD
+SGD S000002994 TRP5 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C tryptophan synthase YGL026C gene taxon:4932 20031028 SGD
+SGD S000002994 TRP5 GO:0004834 SGD_REF:S000039832|PMID:6276387 ISS F tryptophan synthase YGL026C gene taxon:4932 20020419 SGD
+SGD S000002994 TRP5 GO:0004834 SGD_REF:S000065562|PMID:6342605 IDA F tryptophan synthase YGL026C gene taxon:4932 20020419 SGD
+SGD S000002994 TRP5 GO:0004834 SGD_REF:S000065562|PMID:6342605 ISS F tryptophan synthase YGL026C gene taxon:4932 20020419 SGD
+SGD S000002994 TRP5 GO:0000162 SGD_REF:S000041474|PMID:10790693 IMP P tryptophan synthase YGL026C gene taxon:4932 20020419 SGD
+SGD S000002994 TRP5 GO:0000162 SGD_REF:S000043870|PMID:1946350 TAS P tryptophan synthase YGL026C gene taxon:4932 20020419 SGD
+SGD S000002761 TRR1 GO:0005737 SGD_REF:S000047291|PMID:10037727 TAS C EC 1.6.4.5, thioredoxin reductase YDR353W gene taxon:4932 20021015 SGD
+SGD S000002761 TRR1 GO:0004791 SGD_REF:S000059620|PMID:11169101 TAS F EC 1.6.4.5, thioredoxin reductase YDR353W gene taxon:4932 20020411 SGD
+SGD S000002761 TRR1 GO:0030503 SGD_REF:S000061564|PMID:11169096 TAS P EC 1.6.4.5, thioredoxin reductase YDR353W gene taxon:4932 20020411 SGD
+SGD S000002761 TRR1 GO:0030503 SGD_REF:S000053996|PMID:9571241 IDA P EC 1.6.4.5, thioredoxin reductase YDR353W gene taxon:4932 20020411 SGD
+SGD S000002761 TRR1 GO:0030503 SGD_REF:S000053996|PMID:9571241 IMP P EC 1.6.4.5, thioredoxin reductase YDR353W gene taxon:4932 20020411 SGD
+SGD S000001148 TRR2 GO:0005739 SGD_REF:S000047291|PMID:10037727 IDA C thioredoxin reductase YHR106W gene taxon:4932 20010118 SGD
+SGD S000001148 TRR2 GO:0004791 SGD_REF:S000047291|PMID:10037727 IDA F thioredoxin reductase YHR106W gene taxon:4932 20010118 SGD
+SGD S000001148 TRR2 GO:0006979 SGD_REF:S000047291|PMID:10037727 IMP P thioredoxin reductase YHR106W gene taxon:4932 20010118 SGD
+SGD S000006706 TRR4 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tRNA-Arg tR(CCG)L gene taxon:4932 20030507 SGD
+SGD S000006706 TRR4 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tRNA-Arg tR(CCG)L gene taxon:4932 20030507 SGD
+SGD S000006706 TRR4 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tRNA-Arg tR(CCG)L gene taxon:4932 20030507 SGD
+SGD S000002815 TRS120 GO:0030008 SGD_REF:S000043703|PMID:10727015 IDA C YDR407C gene taxon:4932 20020716 SGD
+SGD S000002815 TRS120 GO:0005554 SGD_REF:S000069584 ND F YDR407C gene taxon:4932 20020716 SGD
+SGD S000002815 TRS120 GO:0006888 SGD_REF:S000043703|PMID:10727015 IMP P YDR407C gene taxon:4932 20020716 SGD
+SGD S000004831 TRS130 GO:0030008 SGD_REF:S000043703|PMID:10727015 IDA C YMR218C gene taxon:4932 20020716 SGD
+SGD S000004831 TRS130 GO:0005554 SGD_REF:S000069584 ND F YMR218C gene taxon:4932 20020716 SGD
+SGD S000004831 TRS130 GO:0006888 SGD_REF:S000043703|PMID:10727015 IMP P YMR218C gene taxon:4932 20020716 SGD
+SGD S000000458 TRS20 GO:0030008 SGD_REF:S000043703|PMID:10727015 IDA C YBR254C gene taxon:4932 20020716 SGD
+SGD S000000458 TRS20 GO:0005554 SGD_REF:S000069584 ND F YBR254C gene taxon:4932 20020716 SGD
+SGD S000000458 TRS20 GO:0006888 SGD_REF:S000043703|PMID:10727015 IMP P YBR254C gene taxon:4932 20020716 SGD
+SGD S000002654 TRS23 GO:0030008 SGD_REF:S000043703|PMID:10727015 IDA C YDR246W gene taxon:4932 20020716 SGD
+SGD S000002654 TRS23 GO:0005554 SGD_REF:S000069584 ND F YDR246W gene taxon:4932 20020716 SGD
+SGD S000002654 TRS23 GO:0006888 SGD_REF:S000043703|PMID:10727015 IMP P YDR246W gene taxon:4932 20020716 SGD
+SGD S000002880 TRS31 GO:0030008 SGD_REF:S000043703|PMID:10727015 IDA C YDR472W gene taxon:4932 20020716 SGD
+SGD S000002880 TRS31 GO:0005554 SGD_REF:S000069584 ND F YDR472W gene taxon:4932 20020716 SGD
+SGD S000002880 TRS31 GO:0006888 SGD_REF:S000043703|PMID:10727015 IMP P YDR472W gene taxon:4932 20020716 SGD
+SGD S000005641 TRS33 GO:0030008 SGD_REF:S000043703|PMID:10727015 IDA C YOR115C gene taxon:4932 20020716 SGD
+SGD S000005641 TRS33 GO:0005554 SGD_REF:S000069584 ND F YOR115C gene taxon:4932 20020716 SGD
+SGD S000005641 TRS33 GO:0006888 SGD_REF:S000043703|PMID:10727015 IMP P YOR115C gene taxon:4932 20020716 SGD
+SGD S000006748 TRT2 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tRNA-Thr tT(CGU)K gene taxon:4932 20030507 SGD
+SGD S000006748 TRT2 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tRNA-Thr tT(CGU)K gene taxon:4932 20030507 SGD
+SGD S000006748 TRT2 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tRNA-Thr tT(CGU)K gene taxon:4932 20030507 SGD
+SGD S000004033 TRX1 GO:0000324 SGD_REF:S000044876|PMID:9657146 IPI C EC 1.8.4.8, thioredoxin YLR043C|LMA1 gene taxon:4932 20020411 SGD
+SGD S000004033 TRX1 GO:0005829 SGD_REF:S000057828|PMID:8603912 IDA C EC 1.8.4.8, thioredoxin YLR043C|LMA1 gene taxon:4932 20010118 SGD
+SGD S000004033 TRX1 GO:0030508 SGD_REF:S000056704|PMID:1988444 ISS F EC 1.8.4.8, thioredoxin YLR043C|LMA1 gene taxon:4932 20020111 SGD
+SGD S000004033 TRX1 GO:0000011 SGD_REF:S000057828|PMID:8603912 IMP P EC 1.8.4.8, thioredoxin YLR043C|LMA1 gene taxon:4932 20010118 SGD
+SGD S000004033 TRX1 GO:0000011 SGD_REF:S000048402|PMID:9015301 IMP P EC 1.8.4.8, thioredoxin YLR043C|LMA1 gene taxon:4932 20010118 SGD
+SGD S000004033 TRX1 GO:0000103 SGD_REF:S000049592|PMID:2026619 IGI SGD:S000003441 P EC 1.8.4.8, thioredoxin YLR043C|LMA1 gene taxon:4932 20050617 SGD
+SGD S000004033 TRX1 GO:0006261 SGD_REF:S000055665|PMID:7929110 IMP P EC 1.8.4.8, thioredoxin YLR043C|LMA1 gene taxon:4932 20010118 SGD
+SGD S000004033 TRX1 GO:0006261 SGD_REF:S000040896|PMID:7733663 IMP P EC 1.8.4.8, thioredoxin YLR043C|LMA1 gene taxon:4932 20010118 SGD
+SGD S000004033 TRX1 GO:0006888 SGD_REF:S000052969|PMID:9813082 IDA P EC 1.8.4.8, thioredoxin YLR043C|LMA1 gene taxon:4932 20050621 SGD
+SGD S000004033 TRX1 GO:0006890 SGD_REF:S000052969|PMID:9813082 IDA P EC 1.8.4.8, thioredoxin YLR043C|LMA1 gene taxon:4932 20050621 SGD
+SGD S000004033 TRX1 GO:0006979 SGD_REF:S000056704|PMID:1988444 ISS P EC 1.8.4.8, thioredoxin YLR043C|LMA1 gene taxon:4932 20010118 SGD
+SGD S000004033 TRX1 GO:0030503 SGD_REF:S000061564|PMID:11169096 TAS P EC 1.8.4.8, thioredoxin YLR043C|LMA1 gene taxon:4932 20020411 SGD
+SGD S000004033 TRX1 GO:0042144 SGD_REF:S000044876|PMID:9657146 IDA P EC 1.8.4.8, thioredoxin YLR043C|LMA1 gene taxon:4932 20020411 SGD
+SGD S000003441 TRX2 GO:0000324 SGD_REF:S000044876|PMID:9657146 IPI C EC 1.8.4.8, thioredoxin YGR209C|LMA1 gene taxon:4932 20020411 SGD
+SGD S000003441 TRX2 GO:0005829 SGD_REF:S000057828|PMID:8603912 IDA C EC 1.8.4.8, thioredoxin YGR209C|LMA1 gene taxon:4932 20010118 SGD
+SGD S000003441 TRX2 GO:0030508 SGD_REF:S000056704|PMID:1988444 ISS F EC 1.8.4.8, thioredoxin YGR209C|LMA1 gene taxon:4932 20020111 SGD
+SGD S000003441 TRX2 GO:0000011 SGD_REF:S000057828|PMID:8603912 IMP P EC 1.8.4.8, thioredoxin YGR209C|LMA1 gene taxon:4932 20010118 SGD
+SGD S000003441 TRX2 GO:0000011 SGD_REF:S000048402|PMID:9015301 IMP P EC 1.8.4.8, thioredoxin YGR209C|LMA1 gene taxon:4932 20010118 SGD
+SGD S000003441 TRX2 GO:0000103 SGD_REF:S000049592|PMID:2026619 IGI SGD:S000004033 P EC 1.8.4.8, thioredoxin YGR209C|LMA1 gene taxon:4932 20050617 SGD
+SGD S000003441 TRX2 GO:0006261 SGD_REF:S000055665|PMID:7929110 IMP P EC 1.8.4.8, thioredoxin YGR209C|LMA1 gene taxon:4932 20010118 SGD
+SGD S000003441 TRX2 GO:0006261 SGD_REF:S000040896|PMID:7733663 IMP P EC 1.8.4.8, thioredoxin YGR209C|LMA1 gene taxon:4932 20010118 SGD
+SGD S000003441 TRX2 GO:0006888 SGD_REF:S000052969|PMID:9813082 IDA P EC 1.8.4.8, thioredoxin YGR209C|LMA1 gene taxon:4932 20050621 SGD
+SGD S000003441 TRX2 GO:0006890 SGD_REF:S000052969|PMID:9813082 IDA P EC 1.8.4.8, thioredoxin YGR209C|LMA1 gene taxon:4932 20050621 SGD
+SGD S000003441 TRX2 GO:0006979 SGD_REF:S000056704|PMID:1988444 ISS P EC 1.8.4.8, thioredoxin YGR209C|LMA1 gene taxon:4932 20010118 SGD
+SGD S000003441 TRX2 GO:0030503 SGD_REF:S000061564|PMID:11169096 TAS P EC 1.8.4.8, thioredoxin YGR209C|LMA1 gene taxon:4932 20020411 SGD
+SGD S000003441 TRX2 GO:0042144 SGD_REF:S000044876|PMID:9657146 IDA P EC 1.8.4.8, thioredoxin YGR209C|LMA1 gene taxon:4932 20020411 SGD
+SGD S000000679 TRX3 GO:0005739 SGD_REF:S000047291|PMID:10037727 IDA C thioredoxin YCR083W gene taxon:4932 20010118 SGD
+SGD S000000679 TRX3 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C thioredoxin YCR083W gene taxon:4932 20040924 SGD
+SGD S000000679 TRX3 GO:0030508 SGD_REF:S000047291|PMID:10037727 IDA F thioredoxin YCR083W gene taxon:4932 20020111 SGD
+SGD S000000679 TRX3 GO:0006979 SGD_REF:S000047291|PMID:10037727 IMP P thioredoxin YCR083W gene taxon:4932 20010118 SGD
+SGD S000001787 TRZ1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C tRNA 3' processing endoribonuclease YKR079C gene taxon:4932 20031028 SGD
+SGD S000001787 TRZ1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C tRNA 3' processing endoribonuclease YKR079C gene taxon:4932 20031028 SGD
+SGD S000001787 TRZ1 GO:0005739 SGD_REF:S000075214|PMID:14690591 IDA C tRNA 3' processing endoribonuclease YKR079C gene taxon:4932 20031230 SGD
+SGD S000001787 TRZ1 GO:0017076 SGD_REF:S000064721|PMID:11175785 ISS F tRNA 3' processing endoribonuclease YKR079C gene taxon:4932 20030211 SGD
+SGD S000001787 TRZ1 GO:0042781 SGD_REF:S000073180|PMID:12711671 IDA F tRNA 3' processing endoribonuclease YKR079C gene taxon:4932 20030709 SGD
+SGD S000001787 TRZ1 GO:0042779 SGD_REF:S000073180|PMID:12711671 IDA P tRNA 3' processing endoribonuclease YKR079C gene taxon:4932 20030709 SGD
+SGD S000004490 TSA1 GO:0005737 SGD_REF:S000057702|PMID:8344960 IDA C thioredoxin peroxidase YML028W|TPX1|ZRG14|cTPxI gene taxon:4932 20020411 SGD
+SGD S000004490 TSA1 GO:0005737 SGD_REF:S000061563|PMID:10681558 IDA C thioredoxin peroxidase YML028W|TPX1|ZRG14|cTPxI gene taxon:4932 20050624 SGD
+SGD S000004490 TSA1 GO:0008379 SGD_REF:S000052194|PMID:9799566 IMP F thioredoxin peroxidase YML028W|TPX1|ZRG14|cTPxI gene taxon:4932 20020411 SGD
+SGD S000004490 TSA1 GO:0008379 SGD_REF:S000057553|PMID:7961686 IMP F thioredoxin peroxidase YML028W|TPX1|ZRG14|cTPxI gene taxon:4932 20050622 SGD
+SGD S000004490 TSA1 GO:0008379 SGD_REF:S000057553|PMID:7961686 IDA F thioredoxin peroxidase YML028W|TPX1|ZRG14|cTPxI gene taxon:4932 20050622 SGD
+SGD S000004490 TSA1 GO:0008379 SGD_REF:S000052194|PMID:9799566 IDA F thioredoxin peroxidase YML028W|TPX1|ZRG14|cTPxI gene taxon:4932 20020411 SGD
+SGD S000004490 TSA1 GO:0006979 SGD_REF:S000057702|PMID:8344960 IMP P thioredoxin peroxidase YML028W|TPX1|ZRG14|cTPxI gene taxon:4932 20020411 SGD
+SGD S000004490 TSA1 GO:0006979 SGD_REF:S000057702|PMID:8344960 IDA P thioredoxin peroxidase YML028W|TPX1|ZRG14|cTPxI gene taxon:4932 20020411 SGD
+SGD S000004490 TSA1 GO:0030503 SGD_REF:S000057702|PMID:8344960 IMP P thioredoxin peroxidase YML028W|TPX1|ZRG14|cTPxI gene taxon:4932 20020411 SGD
+SGD S000004490 TSA1 GO:0030503 SGD_REF:S000057702|PMID:8344960 IDA P thioredoxin peroxidase YML028W|TPX1|ZRG14|cTPxI gene taxon:4932 20020411 SGD
+SGD S000004490 TSA1 GO:0030503 SGD_REF:S000052194|PMID:9799566 IMP P thioredoxin peroxidase YML028W|TPX1|ZRG14|cTPxI gene taxon:4932 20020411 SGD
+SGD S000002861 TSA2 GO:0005737 SGD_REF:S000061563|PMID:10681558 IDA C YDR453C|cTPxII gene taxon:4932 20050624 SGD
+SGD S000002861 TSA2 GO:0008379 SGD_REF:S000061563|PMID:10681558 IMP F YDR453C|cTPxII gene taxon:4932 20020411 SGD
+SGD S000002861 TSA2 GO:0008379 SGD_REF:S000061563|PMID:10681558 IDA F YDR453C|cTPxII gene taxon:4932 20020411 SGD
+SGD S000002861 TSA2 GO:0008379 SGD_REF:S000061563|PMID:10681558 ISS F YDR453C|cTPxII gene taxon:4932 20020411 SGD
+SGD S000002861 TSA2 GO:0030503 SGD_REF:S000061563|PMID:10681558 IMP P YDR453C|cTPxII gene taxon:4932 20020411 SGD
+SGD S000002861 TSA2 GO:0030503 SGD_REF:S000061563|PMID:10681558 IDA P YDR453C|cTPxII gene taxon:4932 20020411 SGD
+SGD S000000469 TSC10 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C 3-ketosphinganine reductase YBR265W gene taxon:4932 20020507 SGD
+SGD S000000469 TSC10 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C 3-ketosphinganine reductase YBR265W gene taxon:4932 20060317 SGD
+SGD S000000469 TSC10 GO:0005783 SGD_REF:S000069459|PMID:11914276 IDA C 3-ketosphinganine reductase YBR265W gene taxon:4932 20020507 SGD
+SGD S000000469 TSC10 GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C 3-ketosphinganine reductase YBR265W gene taxon:4932 20031028 SGD
+SGD S000000469 TSC10 GO:0016651 SGD_REF:S000055689|PMID:9804843 IDA F 3-ketosphinganine reductase YBR265W gene taxon:4932 20021030 SGD
+SGD S000000469 TSC10 GO:0006666 SGD_REF:S000055689|PMID:9804843 IDA P 3-ketosphinganine reductase YBR265W gene taxon:4932 20021030 SGD
+SGD S000000469 TSC10 GO:0030148 SGD_REF:S000055689|PMID:9804843 IMP P 3-ketosphinganine reductase YBR265W gene taxon:4932 20020312 SGD
+SGD S000000469 TSC10 GO:0030148 SGD_REF:S000055689|PMID:9804843 ISS P 3-ketosphinganine reductase YBR265W gene taxon:4932 20020312 SGD
+SGD S000000469 TSC10 GO:0030148 SGD_REF:S000055689|PMID:9804843 IDA P 3-ketosphinganine reductase YBR265W gene taxon:4932 20020312 SGD
+SGD S000000895 TSC11 GO:0031932 SGD_REF:S000071528|PMID:12408816 IPI C YER093C|AVO3 gene taxon:4932 20051130 SGD
+SGD S000000895 TSC11 GO:0005515 SGD_REF:S000072891|PMID:12631735 IPI SGD:S000001686 F YER093C|AVO3 gene taxon:4932 20030604 SGD
+SGD S000000895 TSC11 GO:0001558 SGD_REF:S000071528|PMID:12408816 IPI SGD:S000001686 P YER093C|AVO3 gene taxon:4932 20051108 SGD
+SGD S000000895 TSC11 GO:0007047 SGD_REF:S000081257|PMID:15809876 IMP P YER093C|AVO3 gene taxon:4932 20050418 SGD
+SGD S000000895 TSC11 GO:0007047 SGD_REF:S000081257|PMID:15809876 IGI SGD:S000000201 P YER093C|AVO3 gene taxon:4932 20050418 SGD
+SGD S000000895 TSC11 GO:0030148 SGD_REF:S000055689|PMID:9804843 IGI P YER093C|AVO3 gene taxon:4932 20021030 SGD
+SGD S000000895 TSC11 GO:0030950 SGD_REF:S000071528|PMID:12408816 IPI SGD:S000001686 P YER093C|AVO3 gene taxon:4932 20051108 SGD
+SGD S000000895 TSC11 GO:0030950 SGD_REF:S000081257|PMID:15809876 IMP P YER093C|AVO3 gene taxon:4932 20051108 SGD
+SGD S000002173 TSC13 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C enoyl reductase YDL015C gene taxon:4932 20040928 SGD
+SGD S000002173 TSC13 GO:0005789 SGD_REF:S000059092|PMID:11113186 IDA C enoyl reductase YDL015C gene taxon:4932 20010710 SGD
+SGD S000002173 TSC13 GO:0005789 SGD_REF:S000059092|PMID:11113186 IGI C enoyl reductase YDL015C gene taxon:4932 20010710 SGD
+SGD S000002173 TSC13 GO:0005789 SGD_REF:S000059092|PMID:11113186 ISS C enoyl reductase YDL015C gene taxon:4932 20010710 SGD
+SGD S000002173 TSC13 GO:0016491 SGD_REF:S000059092|PMID:11113186 IMP F enoyl reductase YDL015C gene taxon:4932 20010710 SGD
+SGD S000002173 TSC13 GO:0016491 SGD_REF:S000059092|PMID:11113186 ISS F enoyl reductase YDL015C gene taxon:4932 20010710 SGD
+SGD S000002173 TSC13 GO:0000038 SGD_REF:S000059092|PMID:11113186 IMP P enoyl reductase YDL015C gene taxon:4932 20010710 SGD
+SGD S000002173 TSC13 GO:0000038 SGD_REF:S000059092|PMID:11113186 IPI P enoyl reductase YDL015C gene taxon:4932 20010710 SGD
+SGD S000002173 TSC13 GO:0000038 SGD_REF:S000059092|PMID:11113186 IGI P enoyl reductase YDL015C gene taxon:4932 20010710 SGD
+SGD S000007521 TSC3 GO:0005624 SGD_REF:S000051148|PMID:10713067 IDA C YBR058C-A gene taxon:4932 20010118 SGD
+SGD S000007521 TSC3 GO:0005792 SGD_REF:S000051148|PMID:10713067 IDA C YBR058C-A gene taxon:4932 20010118 SGD
+SGD S000007521 TSC3 GO:0008047 SGD_REF:S000051148|PMID:10713067 IDA F YBR058C-A gene taxon:4932 20020925 SGD
+SGD S000007521 TSC3 GO:0006666 SGD_REF:S000051148|PMID:10713067 IPI P YBR058C-A gene taxon:4932 20010118 SGD
+SGD S000007521 TSC3 GO:0030148 SGD_REF:S000070324|PMID:12185836 TAS P YBR058C-A gene taxon:4932 20020826 SGD
+SGD S000029608 TSF1 GO:0008372 SGD_REF:S000069584 ND C may encode a factor that controls the function of the basic RNA polymerase II transcriptional machinery gene taxon:4932 20020617 SGD
+SGD S000029608 TSF1 GO:0005554 SGD_REF:S000069584 ND F may encode a factor that controls the function of the basic RNA polymerase II transcriptional machinery gene taxon:4932 20020617 SGD
+SGD S000029608 TSF1 GO:0006366 SGD_REF:S000054931|PMID:8349104 IGI P may encode a factor that controls the function of the basic RNA polymerase II transcriptional machinery gene taxon:4932 20020617 SGD
+SGD S000004566 TSL1 GO:0005946 SGD_REF:S000053932|PMID:9837904 IMP C similar to TPS3 gene product, trehalose-6-phosphate synthase/phosphatase complex 123 kDa regulatory subunit YML100W gene taxon:4932 20020423 SGD
+SGD S000004566 TSL1 GO:0005946 SGD_REF:S000053932|PMID:9837904 IPI C similar to TPS3 gene product, trehalose-6-phosphate synthase/phosphatase complex 123 kDa regulatory subunit YML100W gene taxon:4932 20020423 SGD
+SGD S000004566 TSL1 GO:0005946 SGD_REF:S000053932|PMID:9837904 IGI C similar to TPS3 gene product, trehalose-6-phosphate synthase/phosphatase complex 123 kDa regulatory subunit YML100W gene taxon:4932 20020423 SGD
+SGD S000004566 TSL1 contributes_to GO:0003825 SGD_REF:S000053932|PMID:9837904 IMP F similar to TPS3 gene product, trehalose-6-phosphate synthase/phosphatase complex 123 kDa regulatory subunit YML100W gene taxon:4932 20050729 SGD
+SGD S000004566 TSL1 contributes_to GO:0004805 SGD_REF:S000053932|PMID:9837904 IGI SGD:S000004874 F similar to TPS3 gene product, trehalose-6-phosphate synthase/phosphatase complex 123 kDa regulatory subunit YML100W gene taxon:4932 20050729 SGD
+SGD S000004566 TSL1 GO:0030234 SGD_REF:S000043344|PMID:8404905 IDA F similar to TPS3 gene product, trehalose-6-phosphate synthase/phosphatase complex 123 kDa regulatory subunit YML100W gene taxon:4932 20030122 SGD
+SGD S000004566 TSL1 GO:0005992 SGD_REF:S000053932|PMID:9837904 IMP P similar to TPS3 gene product, trehalose-6-phosphate synthase/phosphatase complex 123 kDa regulatory subunit YML100W gene taxon:4932 20020423 SGD
+SGD S000004566 TSL1 GO:0005992 SGD_REF:S000053932|PMID:9837904 IPI P similar to TPS3 gene product, trehalose-6-phosphate synthase/phosphatase complex 123 kDa regulatory subunit YML100W gene taxon:4932 20020423 SGD
+SGD S000004566 TSL1 GO:0005992 SGD_REF:S000053932|PMID:9837904 IGI P similar to TPS3 gene product, trehalose-6-phosphate synthase/phosphatase complex 123 kDa regulatory subunit YML100W gene taxon:4932 20020423 SGD
+SGD S000004566 TSL1 GO:0006950 SGD_REF:S000053932|PMID:9837904 IMP P similar to TPS3 gene product, trehalose-6-phosphate synthase/phosphatase complex 123 kDa regulatory subunit YML100W gene taxon:4932 20020423 SGD
+SGD S000002218 TSR1 GO:0005730 SGD_REF:S000076341|PMID:15167894 IDA C YDL060W gene taxon:4932 20040719 SGD
+SGD S000002218 TSR1 GO:0005730 SGD_REF:S000065947|PMID:11565749 IDA C YDL060W gene taxon:4932 20021009 SGD
+SGD S000002218 TSR1 GO:0005737 SGD_REF:S000076341|PMID:15167894 IDA C YDL060W gene taxon:4932 20040719 SGD
+SGD S000002218 TSR1 GO:0043021 SGD_REF:S000076341|PMID:15167894 IDA F YDL060W gene taxon:4932 20040719 SGD
+SGD S000002218 TSR1 GO:0006364 SGD_REF:S000073209|PMID:12089522 IMP P YDL060W gene taxon:4932 20030530 SGD
+SGD S000002218 TSR1 GO:0042254 SGD_REF:S000065947|PMID:11565749 IMP P YDL060W gene taxon:4932 20021009 SGD
+SGD S000004427 TSR2 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YLR435W gene taxon:4932 20031028 SGD
+SGD S000004427 TSR2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YLR435W gene taxon:4932 20031028 SGD
+SGD S000004427 TSR2 GO:0005554 SGD_REF:S000069584 ND F YLR435W gene taxon:4932 20021126 SGD
+SGD S000004427 TSR2 GO:0030490 SGD_REF:S000073750|PMID:12837249 IMP P YLR435W gene taxon:4932 20030804 SGD
+SGD S000004550 TUB1 GO:0005816 SGD_REF:S000047788|PMID:9585415 IDA C alpha-tubulin YML085C gene taxon:4932 20010118 SGD
+SGD S000004550 TUB1 GO:0005827 SGD_REF:S000058492 TAS C alpha-tubulin YML085C gene taxon:4932 20010119 SGD
+SGD S000004550 TUB1 GO:0005827 SGD_REF:S000058447|PMID:9153752 TAS C alpha-tubulin YML085C gene taxon:4932 20010118 SGD
+SGD S000004550 TUB1 GO:0005828 SGD_REF:S000058492 TAS C alpha-tubulin YML085C gene taxon:4932 20010119 SGD
+SGD S000004550 TUB1 GO:0005828 SGD_REF:S000058447|PMID:9153752 TAS C alpha-tubulin YML085C gene taxon:4932 20010118 SGD
+SGD S000004550 TUB1 GO:0005880 SGD_REF:S000058492 TAS C alpha-tubulin YML085C gene taxon:4932 20010119 SGD
+SGD S000004550 TUB1 GO:0005880 SGD_REF:S000058447|PMID:9153752 TAS C alpha-tubulin YML085C gene taxon:4932 20010118 SGD
+SGD S000004550 TUB1 GO:0005881 SGD_REF:S000058492 TAS C alpha-tubulin YML085C gene taxon:4932 20010119 SGD
+SGD S000004550 TUB1 GO:0005881 SGD_REF:S000058447|PMID:9153752 TAS C alpha-tubulin YML085C gene taxon:4932 20010118 SGD
+SGD S000004550 TUB1 GO:0045298 SGD_REF:S000058492 TAS C alpha-tubulin YML085C gene taxon:4932 20041214 SGD
+SGD S000004550 TUB1 GO:0005200 SGD_REF:S000058492 TAS F alpha-tubulin YML085C gene taxon:4932 20010119 SGD
+SGD S000004550 TUB1 GO:0005200 SGD_REF:S000058447|PMID:9153752 TAS F alpha-tubulin YML085C gene taxon:4932 20010118 SGD
+SGD S000004550 TUB1 GO:0000070 SGD_REF:S000058492 TAS P alpha-tubulin YML085C gene taxon:4932 20010119 SGD
+SGD S000004550 TUB1 GO:0000070 SGD_REF:S000058447|PMID:9153752 TAS P alpha-tubulin YML085C gene taxon:4932 20010118 SGD
+SGD S000004550 TUB1 GO:0000743 SGD_REF:S000058492 TAS P alpha-tubulin YML085C gene taxon:4932 20010119 SGD
+SGD S000004550 TUB1 GO:0000743 SGD_REF:S000058447|PMID:9153752 TAS P alpha-tubulin YML085C gene taxon:4932 20010118 SGD
+SGD S000004550 TUB1 GO:0030473 SGD_REF:S000058492 TAS P alpha-tubulin YML085C gene taxon:4932 20010119 SGD
+SGD S000004550 TUB1 GO:0030473 SGD_REF:S000058447|PMID:9153752 TAS P alpha-tubulin YML085C gene taxon:4932 20010118 SGD
+SGD S000004550 TUB1 GO:0045143 SGD_REF:S000058492 TAS P alpha-tubulin YML085C gene taxon:4932 20010119 SGD
+SGD S000004550 TUB1 GO:0045143 SGD_REF:S000058447|PMID:9153752 TAS P alpha-tubulin YML085C gene taxon:4932 20010118 SGD
+SGD S000001857 TUB2 GO:0005816 SGD_REF:S000047788|PMID:9585415 IDA C beta-tubulin YFL037W|ARM10|SHE8 gene taxon:4932 20010118 SGD
+SGD S000001857 TUB2 GO:0005827 SGD_REF:S000058492 TAS C beta-tubulin YFL037W|ARM10|SHE8 gene taxon:4932 20010119 SGD
+SGD S000001857 TUB2 GO:0005827 SGD_REF:S000058447|PMID:9153752 TAS C beta-tubulin YFL037W|ARM10|SHE8 gene taxon:4932 20010118 SGD
+SGD S000001857 TUB2 GO:0005828 SGD_REF:S000058492 TAS C beta-tubulin YFL037W|ARM10|SHE8 gene taxon:4932 20010119 SGD
+SGD S000001857 TUB2 GO:0005828 SGD_REF:S000058447|PMID:9153752 TAS C beta-tubulin YFL037W|ARM10|SHE8 gene taxon:4932 20010118 SGD
+SGD S000001857 TUB2 GO:0005880 SGD_REF:S000058447|PMID:9153752 TAS C beta-tubulin YFL037W|ARM10|SHE8 gene taxon:4932 20010118 SGD
+SGD S000001857 TUB2 GO:0005881 SGD_REF:S000058492 TAS C beta-tubulin YFL037W|ARM10|SHE8 gene taxon:4932 20010119 SGD
+SGD S000001857 TUB2 GO:0005881 SGD_REF:S000058447|PMID:9153752 TAS C beta-tubulin YFL037W|ARM10|SHE8 gene taxon:4932 20010118 SGD
+SGD S000001857 TUB2 GO:0045298 SGD_REF:S000058492 TAS C beta-tubulin YFL037W|ARM10|SHE8 gene taxon:4932 20041214 SGD
+SGD S000001857 TUB2 GO:0005200 SGD_REF:S000058492 TAS F beta-tubulin YFL037W|ARM10|SHE8 gene taxon:4932 20010119 SGD
+SGD S000001857 TUB2 GO:0005200 SGD_REF:S000058447|PMID:9153752 TAS F beta-tubulin YFL037W|ARM10|SHE8 gene taxon:4932 20010118 SGD
+SGD S000001857 TUB2 GO:0000070 SGD_REF:S000058492 TAS P beta-tubulin YFL037W|ARM10|SHE8 gene taxon:4932 20010119 SGD
+SGD S000001857 TUB2 GO:0000070 SGD_REF:S000058447|PMID:9153752 TAS P beta-tubulin YFL037W|ARM10|SHE8 gene taxon:4932 20010118 SGD
+SGD S000001857 TUB2 GO:0000743 SGD_REF:S000058492 TAS P beta-tubulin YFL037W|ARM10|SHE8 gene taxon:4932 20010119 SGD
+SGD S000001857 TUB2 GO:0000743 SGD_REF:S000058447|PMID:9153752 TAS P beta-tubulin YFL037W|ARM10|SHE8 gene taxon:4932 20010118 SGD
+SGD S000001857 TUB2 GO:0030473 SGD_REF:S000058492 TAS P beta-tubulin YFL037W|ARM10|SHE8 gene taxon:4932 20010119 SGD
+SGD S000001857 TUB2 GO:0030473 SGD_REF:S000058447|PMID:9153752 TAS P beta-tubulin YFL037W|ARM10|SHE8 gene taxon:4932 20010118 SGD
+SGD S000001857 TUB2 GO:0045143 SGD_REF:S000058492 TAS P beta-tubulin YFL037W|ARM10|SHE8 gene taxon:4932 20010119 SGD
+SGD S000001857 TUB2 GO:0045143 SGD_REF:S000058447|PMID:9153752 TAS P beta-tubulin YFL037W|ARM10|SHE8 gene taxon:4932 20010118 SGD
+SGD S000004593 TUB3 GO:0005816 SGD_REF:S000047788|PMID:9585415 IDA C alpha-tubulin YML124C gene taxon:4932 20010118 SGD
+SGD S000004593 TUB3 GO:0005827 SGD_REF:S000058492 TAS C alpha-tubulin YML124C gene taxon:4932 20010119 SGD
+SGD S000004593 TUB3 GO:0005827 SGD_REF:S000058447|PMID:9153752 TAS C alpha-tubulin YML124C gene taxon:4932 20010118 SGD
+SGD S000004593 TUB3 GO:0005828 SGD_REF:S000058492 TAS C alpha-tubulin YML124C gene taxon:4932 20010119 SGD
+SGD S000004593 TUB3 GO:0005828 SGD_REF:S000058447|PMID:9153752 TAS C alpha-tubulin YML124C gene taxon:4932 20010118 SGD
+SGD S000004593 TUB3 GO:0005880 SGD_REF:S000058492 TAS C alpha-tubulin YML124C gene taxon:4932 20010119 SGD
+SGD S000004593 TUB3 GO:0005880 SGD_REF:S000058447|PMID:9153752 TAS C alpha-tubulin YML124C gene taxon:4932 20010118 SGD
+SGD S000004593 TUB3 GO:0005881 SGD_REF:S000058492 TAS C alpha-tubulin YML124C gene taxon:4932 20010119 SGD
+SGD S000004593 TUB3 GO:0005881 SGD_REF:S000058447|PMID:9153752 TAS C alpha-tubulin YML124C gene taxon:4932 20010118 SGD
+SGD S000004593 TUB3 GO:0045298 SGD_REF:S000058492 TAS C alpha-tubulin YML124C gene taxon:4932 20041214 SGD
+SGD S000004593 TUB3 GO:0005200 SGD_REF:S000058492 TAS F alpha-tubulin YML124C gene taxon:4932 20010119 SGD
+SGD S000004593 TUB3 GO:0005200 SGD_REF:S000058447|PMID:9153752 TAS F alpha-tubulin YML124C gene taxon:4932 20010118 SGD
+SGD S000004593 TUB3 GO:0000070 SGD_REF:S000058492 TAS P alpha-tubulin YML124C gene taxon:4932 20010119 SGD
+SGD S000004593 TUB3 GO:0000070 SGD_REF:S000058447|PMID:9153752 TAS P alpha-tubulin YML124C gene taxon:4932 20010118 SGD
+SGD S000004593 TUB3 GO:0000743 SGD_REF:S000058492 TAS P alpha-tubulin YML124C gene taxon:4932 20010119 SGD
+SGD S000004593 TUB3 GO:0000743 SGD_REF:S000058447|PMID:9153752 TAS P alpha-tubulin YML124C gene taxon:4932 20010118 SGD
+SGD S000004593 TUB3 GO:0030473 SGD_REF:S000058492 TAS P alpha-tubulin YML124C gene taxon:4932 20010119 SGD
+SGD S000004593 TUB3 GO:0030473 SGD_REF:S000058447|PMID:9153752 TAS P alpha-tubulin YML124C gene taxon:4932 20010118 SGD
+SGD S000004593 TUB3 GO:0045143 SGD_REF:S000058492 TAS P alpha-tubulin YML124C gene taxon:4932 20010119 SGD
+SGD S000004593 TUB3 GO:0045143 SGD_REF:S000058447|PMID:9153752 TAS P alpha-tubulin YML124C gene taxon:4932 20010118 SGD
+SGD S000004202 TUB4 GO:0000928 SGD_REF:S000053189|PMID:9384578 IPI C gamma tubulin YLR212C gene taxon:4932 20040802 SGD
+SGD S000004202 TUB4 GO:0005822 SGD_REF:S000043896|PMID:9215630 IDA C gamma tubulin YLR212C gene taxon:4932 20010118 SGD
+SGD S000004202 TUB4 GO:0005824 SGD_REF:S000043896|PMID:9215630 IDA C gamma tubulin YLR212C gene taxon:4932 20010118 SGD
+SGD S000004202 TUB4 GO:0005200 SGD_REF:S000043896|PMID:9215630 IPI F gamma tubulin YLR212C gene taxon:4932 20010118 SGD
+SGD S000004202 TUB4 GO:0007020 SGD_REF:S000058447|PMID:9153752 IPI P gamma tubulin YLR212C gene taxon:4932 20010118 SGD
+SGD S000004202 TUB4 GO:0030472 SGD_REF:S000058447|PMID:9153752 IMP P gamma tubulin YLR212C gene taxon:4932 20010118 SGD
+SGD S000005713 TUF1 GO:0005759 SGD_REF:S000057264|PMID:6353412 ISS C translation elongation factor Tu, mitochondrial YOR187W gene taxon:4932 20020711 SGD
+SGD S000005713 TUF1 GO:0003746 SGD_REF:S000057264|PMID:6353412 ISS F translation elongation factor Tu, mitochondrial YOR187W gene taxon:4932 20020711 SGD
+SGD S000005713 TUF1 GO:0003746 SGD_REF:S000080856|PMID:15695360 ISS F translation elongation factor Tu, mitochondrial YOR187W gene taxon:4932 20050223 SGD
+SGD S000005713 TUF1 GO:0003746 SGD_REF:S000080856|PMID:15695360 IGI F translation elongation factor Tu, mitochondrial YOR187W gene taxon:4932 20050223 SGD
+SGD S000005713 TUF1 GO:0003924 SGD_REF:S000080856|PMID:15695360 IGI F translation elongation factor Tu, mitochondrial YOR187W gene taxon:4932 20050223 SGD
+SGD S000005713 TUF1 GO:0003924 SGD_REF:S000080856|PMID:15695360 ISS F translation elongation factor Tu, mitochondrial YOR187W gene taxon:4932 20050223 SGD
+SGD S000005713 TUF1 GO:0006414 SGD_REF:S000058291|PMID:9506898 IGI P translation elongation factor Tu, mitochondrial YOR187W gene taxon:4932 20020711 SGD
+SGD S000005713 TUF1 GO:0006414 SGD_REF:S000080856|PMID:15695360 IGI P translation elongation factor Tu, mitochondrial YOR187W gene taxon:4932 20050223 SGD
+SGD S000005713 TUF1 GO:0006414 SGD_REF:S000080856|PMID:15695360 ISS P translation elongation factor Tu, mitochondrial YOR187W gene taxon:4932 20050223 SGD
+SGD S000001517 TUL1 GO:0005794 SGD_REF:S000074470|PMID:11788821 IDA C RING-domain E3 ubiquitin ligase YKL034W gene taxon:4932 20050421 SGD
+SGD S000001517 TUL1 GO:0004842 SGD_REF:S000074470|PMID:11788821 ISS F RING-domain E3 ubiquitin ligase YKL034W gene taxon:4932 20050421 SGD
+SGD S000001517 TUL1 GO:0004842 SGD_REF:S000074470|PMID:11788821 IPI SGD:S000000286 F RING-domain E3 ubiquitin ligase YKL034W gene taxon:4932 20050421 SGD
+SGD S000001517 TUL1 GO:0016567 SGD_REF:S000074470|PMID:11788821 IMP P RING-domain E3 ubiquitin ligase YKL034W gene taxon:4932 20050421 SGD
+SGD S000001517 TUL1 GO:0043162 SGD_REF:S000074470|PMID:11788821 IMP P RING-domain E3 ubiquitin ligase YKL034W gene taxon:4932 20050421 SGD
+SGD S000000680 TUP1 GO:0005634 SGD_REF:S000055359|PMID:1739976 IPI C YCR084C|AAR1|AER2|AMM1|CRT4|CYC9|FLK1|ROX4|SFL2|UMR7 gene taxon:4932 20020311 SGD
+SGD S000000680 TUP1 GO:0005634 SGD_REF:S000055359|PMID:1739976 IDA C YCR084C|AAR1|AER2|AMM1|CRT4|CYC9|FLK1|ROX4|SFL2|UMR7 gene taxon:4932 20020311 SGD
+SGD S000000680 TUP1 GO:0016565 SGD_REF:S000055359|PMID:1739976 IMP F YCR084C|AAR1|AER2|AMM1|CRT4|CYC9|FLK1|ROX4|SFL2|UMR7 gene taxon:4932 20020311 SGD
+SGD S000000680 TUP1 GO:0016565 SGD_REF:S000055359|PMID:1739976 IPI F YCR084C|AAR1|AER2|AMM1|CRT4|CYC9|FLK1|ROX4|SFL2|UMR7 gene taxon:4932 20020311 SGD
+SGD S000000680 TUP1 GO:0016565 SGD_REF:S000055359|PMID:1739976 IDA F YCR084C|AAR1|AER2|AMM1|CRT4|CYC9|FLK1|ROX4|SFL2|UMR7 gene taxon:4932 20020311 SGD
+SGD S000000680 TUP1 GO:0016481 SGD_REF:S000055359|PMID:1739976 IMP P YCR084C|AAR1|AER2|AMM1|CRT4|CYC9|FLK1|ROX4|SFL2|UMR7 gene taxon:4932 20020311 SGD
+SGD S000000680 TUP1 GO:0016481 SGD_REF:S000055359|PMID:1739976 IDA P YCR084C|AAR1|AER2|AMM1|CRT4|CYC9|FLK1|ROX4|SFL2|UMR7 gene taxon:4932 20020311 SGD
+SGD S000000680 TUP1 GO:0016481 SGD_REF:S000055359|PMID:1739976 IPI P YCR084C|AAR1|AER2|AMM1|CRT4|CYC9|FLK1|ROX4|SFL2|UMR7 gene taxon:4932 20020311 SGD
+SGD S000000680 TUP1 GO:0016584 SGD_REF:S000076511|PMID:15116071 IDA P YCR084C|AAR1|AER2|AMM1|CRT4|CYC9|FLK1|ROX4|SFL2|UMR7 gene taxon:4932 20041025 SGD
+SGD S000004417 TUS1 GO:0008372 SGD_REF:S000069584 ND C YLR425W|SOP10 gene taxon:4932 20021030 SGD
+SGD S000004417 TUS1 GO:0005089 SGD_REF:S000069495|PMID:11839800 IDA F YLR425W|SOP10 gene taxon:4932 20021030 SGD
+SGD S000004417 TUS1 GO:0007047 SGD_REF:S000069495|PMID:11839800 IGI P YLR425W|SOP10 gene taxon:4932 20021030 SGD
+SGD S000004417 TUS1 GO:0007047 SGD_REF:S000069495|PMID:11839800 IMP P YLR425W|SOP10 gene taxon:4932 20021030 SGD
+SGD S000004417 TUS1 GO:0007165 SGD_REF:S000069495|PMID:11839800 IGI P YLR425W|SOP10 gene taxon:4932 20021030 SGD
+SGD S000004417 TUS1 GO:0007165 SGD_REF:S000069495|PMID:11839800 IMP P YLR425W|SOP10 gene taxon:4932 20021030 SGD
+SGD S000002507 TVP15 colocalizes_with GO:0030137 SGD_REF:S000074185|PMID:14562095 IDA C integral membrane protein YDR100W gene taxon:4932 20031028 SGD
+SGD S000002507 TVP15 GO:0030173 SGD_REF:S000086147|PMID:16107716 IDA C integral membrane protein YDR100W gene taxon:4932 20050823 SGD
+SGD S000002507 TVP15 GO:0005554 SGD_REF:S000069584 ND F integral membrane protein YDR100W gene taxon:4932 20021126 SGD
+SGD S000002507 TVP15 GO:0000004 SGD_REF:S000069584 ND P integral membrane protein YDR100W gene taxon:4932 20021126 SGD
+SGD S000004675 TVP18 colocalizes_with GO:0030136 SGD_REF:S000074185|PMID:14562095 IDA C integral membrane protein YMR071C gene taxon:4932 20031028 SGD
+SGD S000004675 TVP18 GO:0030173 SGD_REF:S000086147|PMID:16107716 IDA C integral membrane protein YMR071C gene taxon:4932 20050823 SGD
+SGD S000004675 TVP18 GO:0005554 SGD_REF:S000069584 ND F integral membrane protein YMR071C gene taxon:4932 20021126 SGD
+SGD S000004675 TVP18 GO:0000004 SGD_REF:S000069584 ND P integral membrane protein YMR071C gene taxon:4932 20021126 SGD
+SGD S000002491 TVP23 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C integral membrane protein YDR084C gene taxon:4932 20031028 SGD
+SGD S000002491 TVP23 GO:0030173 SGD_REF:S000086147|PMID:16107716 IDA C integral membrane protein YDR084C gene taxon:4932 20050823 SGD
+SGD S000002491 TVP23 GO:0005554 SGD_REF:S000069584 ND F integral membrane protein YDR084C gene taxon:4932 20030203 SGD
+SGD S000002491 TVP23 GO:0000004 SGD_REF:S000069584 ND P integral membrane protein YDR084C gene taxon:4932 20030203 SGD
+SGD S000001796 TVP38 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C integral membrane protein YKR088C gene taxon:4932 20031028 SGD
+SGD S000001796 TVP38 GO:0030173 SGD_REF:S000086147|PMID:16107716 IDA C integral membrane protein YKR088C gene taxon:4932 20050823 SGD
+SGD S000001796 TVP38 GO:0005554 SGD_REF:S000069584 ND F integral membrane protein YKR088C gene taxon:4932 20030418 SGD
+SGD S000001796 TVP38 GO:0000004 SGD_REF:S000069584 ND P integral membrane protein YKR088C gene taxon:4932 20030418 SGD
+SGD S000003312 TWF1 GO:0030479 SGD_REF:S000041005|PMID:10652251 IDA C twinfilin A, an actin monomer sequestering protein YGR080W gene taxon:4932 20010118 SGD
+SGD S000003312 TWF1 GO:0003785 SGD_REF:S000039446|PMID:9700161 IDA F twinfilin A, an actin monomer sequestering protein YGR080W gene taxon:4932 20010118 SGD
+SGD S000003312 TWF1 GO:0007121 SGD_REF:S000041005|PMID:10652251 IMP P twinfilin A, an actin monomer sequestering protein YGR080W gene taxon:4932 20010118 SGD
+SGD S000003312 TWF1 GO:0008154 SGD_REF:S000041005|PMID:10652251 IMP P twinfilin A, an actin monomer sequestering protein YGR080W gene taxon:4932 20010118 SGD
+SGD S000003312 TWF1 GO:0008154 SGD_REF:S000041005|PMID:10652251 IPI P twinfilin A, an actin monomer sequestering protein YGR080W gene taxon:4932 20010118 SGD
+SGD S000003312 TWF1 GO:0042989 SGD_REF:S000039446|PMID:9700161 IDA P twinfilin A, an actin monomer sequestering protein YGR080W gene taxon:4932 20031016 SGD
+SGD S000005871 TYE7 GO:0005634 SGD_REF:S000051377|PMID:10606743 IC GO:0003677 C YOR344C|SGC1 gene taxon:4932 20021111 SGD
+SGD S000005871 TYE7 GO:0003700 SGD_REF:S000051377|PMID:10606743 IGI F YOR344C|SGC1 gene taxon:4932 20030403 SGD
+SGD S000005871 TYE7 GO:0003700 SGD_REF:S000051377|PMID:10606743 IPI F YOR344C|SGC1 gene taxon:4932 20030403 SGD
+SGD S000005871 TYE7 GO:0003700 SGD_REF:S000051377|PMID:10606743 ISS F YOR344C|SGC1 gene taxon:4932 20030403 SGD
+SGD S000005871 TYE7 GO:0003700 SGD_REF:S000051377|PMID:10606743 IDA F YOR344C|SGC1 gene taxon:4932 20050117 SGD
+SGD S000005871 TYE7 GO:0003700 SGD_REF:S000071810|PMID:12464632 IPI F YOR344C|SGC1 gene taxon:4932 20050603 SGD
+SGD S000005871 TYE7 GO:0000083 SGD_REF:S000071810|PMID:12464632 IPI P YOR344C|SGC1 gene taxon:4932 20050603 SGD
+SGD S000005871 TYE7 GO:0006350 SGD_REF:S000051377|PMID:10606743 IGI P YOR344C|SGC1 gene taxon:4932 20030403 SGD
+SGD S000005871 TYE7 GO:0006350 SGD_REF:S000051377|PMID:10606743 IPI P YOR344C|SGC1 gene taxon:4932 20030403 SGD
+SGD S000005871 TYE7 GO:0006350 SGD_REF:S000051377|PMID:10606743 IDA P YOR344C|SGC1 gene taxon:4932 20050117 SGD
+SGD S000005871 TYE7 GO:0045821 SGD_REF:S000051377|PMID:10606743 IGI SGD:S000005143 P YOR344C|SGC1 gene taxon:4932 20021108 SGD
+SGD S000005871 TYE7 GO:0045821 SGD_REF:S000051377|PMID:10606743 IMP P YOR344C|SGC1 gene taxon:4932 20021108 SGD
+SGD S000000370 TYR1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C prephenate dehydrogenase (NADP+) YBR166C gene taxon:4932 20031028 SGD
+SGD S000000370 TYR1 GO:0008977 SGD_REF:S000055495|PMID:2697638 ISS F prephenate dehydrogenase (NADP+) YBR166C gene taxon:4932 20020930 SGD
+SGD S000000370 TYR1 GO:0006570 SGD_REF:S000071379|PMID:11752249 NAS P prephenate dehydrogenase (NADP+) YBR166C gene taxon:4932 20020930 SGD
+SGD S000003417 TYS1 GO:0005634 SGD_REF:S000063706|PMID:11359929 IMP C tyrosine-tRNA ligase YGR185C|TTS1|TyrRS gene taxon:4932 20020405 SGD
+SGD S000003417 TYS1 GO:0005634 SGD_REF:S000063706|PMID:11359929 ISS C tyrosine-tRNA ligase YGR185C|TTS1|TyrRS gene taxon:4932 20020405 SGD
+SGD S000003417 TYS1 GO:0005634 SGD_REF:S000063706|PMID:11359929 IDA C tyrosine-tRNA ligase YGR185C|TTS1|TyrRS gene taxon:4932 20020405 SGD
+SGD S000003417 TYS1 GO:0005737 SGD_REF:S000063706|PMID:11359929 IDA C tyrosine-tRNA ligase YGR185C|TTS1|TyrRS gene taxon:4932 20020405 SGD
+SGD S000003417 TYS1 GO:0004831 SGD_REF:S000054421|PMID:8509419 IDA F tyrosine-tRNA ligase YGR185C|TTS1|TyrRS gene taxon:4932 20021203 SGD
+SGD S000003417 TYS1 GO:0004831 SGD_REF:S000054421|PMID:8509419 ISS F tyrosine-tRNA ligase YGR185C|TTS1|TyrRS gene taxon:4932 20021203 SGD
+SGD S000003417 TYS1 GO:0006437 SGD_REF:S000054421|PMID:8509419 IDA P tyrosine-tRNA ligase YGR185C|TTS1|TyrRS gene taxon:4932 20021203 SGD
+SGD S000006128 TYW1 GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YPL207W gene taxon:4932 20031028 SGD
+SGD S000006128 TYW1 GO:0005554 SGD_REF:S000069584 ND F YPL207W gene taxon:4932 20021126 SGD
+SGD S000006128 TYW1 GO:0000004 SGD_REF:S000069584 ND P YPL207W gene taxon:4932 20021126 SGD
+SGD S000003018 TYW3 GO:0008372 SGD_REF:S000069584 ND C YGL050W gene taxon:4932 20030203 SGD
+SGD S000003018 TYW3 GO:0005554 SGD_REF:S000069584 ND F YGL050W gene taxon:4932 20030203 SGD
+SGD S000003018 TYW3 GO:0000004 SGD_REF:S000069584 ND P YGL050W gene taxon:4932 20030203 SGD
+SGD S000005821 UAF30 GO:0000500 SGD_REF:S000061332|PMID:11500378 IMP C YOR295W gene taxon:4932 20011212 SGD
+SGD S000005821 UAF30 GO:0000500 SGD_REF:S000061332|PMID:11500378 IPI C YOR295W gene taxon:4932 20011212 SGD
+SGD S000005821 UAF30 GO:0000500 SGD_REF:S000061332|PMID:11500378 TAS C YOR295W gene taxon:4932 20011212 SGD
+SGD S000005821 UAF30 GO:0000182 SGD_REF:S000061332|PMID:11500378 IMP F YOR295W gene taxon:4932 20011212 SGD
+SGD S000005821 UAF30 GO:0000182 SGD_REF:S000061332|PMID:11500378 IPI F YOR295W gene taxon:4932 20011212 SGD
+SGD S000005821 UAF30 GO:0003701 SGD_REF:S000061332|PMID:11500378 IMP F YOR295W gene taxon:4932 20011205 SGD
+SGD S000005821 UAF30 GO:0003701 SGD_REF:S000061332|PMID:11500378 IPI F YOR295W gene taxon:4932 20011205 SGD
+SGD S000005821 UAF30 GO:0006360 SGD_REF:S000061332|PMID:11500378 IMP P YOR295W gene taxon:4932 20011212 SGD
+SGD S000005821 UAF30 GO:0006360 SGD_REF:S000061332|PMID:11500378 IPI P YOR295W gene taxon:4932 20011212 SGD
+SGD S000001693 UBA1 GO:0005634 SGD_REF:S000039750|PMID:7629121 IDA C ubiquitin activating enzyme e1 YKL210W gene taxon:4932 20010118 SGD
+SGD S000001693 UBA1 GO:0005737 SGD_REF:S000039750|PMID:7629121 IDA C ubiquitin activating enzyme e1 YKL210W gene taxon:4932 20010118 SGD
+SGD S000001693 UBA1 GO:0004839 SGD_REF:S000058010|PMID:8982460 TAS F ubiquitin activating enzyme e1 YKL210W gene taxon:4932 20010118 SGD
+SGD S000001693 UBA1 GO:0006512 SGD_REF:S000058010|PMID:8982460 TAS P ubiquitin activating enzyme e1 YKL210W gene taxon:4932 20010118 SGD
+SGD S000002798 UBA2 GO:0005634 SGD_REF:S000039750|PMID:7629121 IDA C YDR390C|UAL1 gene taxon:4932 20010118 SGD
+SGD S000002798 UBA2 GO:0019948 SGD_REF:S000040819|PMID:9312010 IDA F YDR390C|UAL1 gene taxon:4932 20020610 SGD
+SGD S000002798 UBA2 GO:0019948 SGD_REF:S000040819|PMID:9312010 IMP F YDR390C|UAL1 gene taxon:4932 20020610 SGD
+SGD S000002798 UBA2 GO:0019948 SGD_REF:S000040819|PMID:9312010 IPI F YDR390C|UAL1 gene taxon:4932 20020610 SGD
+SGD S000002798 UBA2 GO:0016925 SGD_REF:S000040819|PMID:9312010 IMP P YDR390C|UAL1 gene taxon:4932 20020404 SGD
+SGD S000002798 UBA2 GO:0016925 SGD_REF:S000040819|PMID:9312010 IDA P YDR390C|UAL1 gene taxon:4932 20020404 SGD
+SGD S000006270 UBA3 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C ubiquitin-like protein activating enzyme YPR066W gene taxon:4932 20031028 SGD
+SGD S000006270 UBA3 GO:0019781 SGD_REF:S000050724|PMID:9545234 IDA F ubiquitin-like protein activating enzyme YPR066W gene taxon:4932 20020717 SGD
+SGD S000006270 UBA3 GO:0019781 SGD_REF:S000050724|PMID:9545234 ISS SGD:S000002798 F ubiquitin-like protein activating enzyme YPR066W gene taxon:4932 20051018 SGD
+SGD S000006270 UBA3 GO:0045116 SGD_REF:S000050724|PMID:9545234 IDA P ubiquitin-like protein activating enzyme YPR066W gene taxon:4932 20030721 SGD
+SGD S000006270 UBA3 GO:0045116 SGD_REF:S000050724|PMID:9545234 IMP P ubiquitin-like protein activating enzyme YPR066W gene taxon:4932 20051018 SGD
+SGD S000006270 UBA3 GO:0045116 SGD_REF:S000050724|PMID:9545234 ISS SGD:S000002798 P ubiquitin-like protein activating enzyme YPR066W gene taxon:4932 20051018 SGD
+SGD S000001153 UBA4 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YHR111W|YHR1 gene taxon:4932 20031028 SGD
+SGD S000001153 UBA4 GO:0042292 SGD_REF:S000051101|PMID:10713047 IDA F YHR111W|YHR1 gene taxon:4932 20021030 SGD
+SGD S000001153 UBA4 GO:0042292 SGD_REF:S000051101|PMID:10713047 ISS SGD:S000001693 F YHR111W|YHR1 gene taxon:4932 20051021 SGD
+SGD S000001153 UBA4 GO:0042292 SGD_REF:S000074238|PMID:14555475 IMP F YHR111W|YHR1 gene taxon:4932 20051018 SGD
+SGD S000001153 UBA4 GO:0001403 SGD_REF:S000075061|PMID:14551258 IGI SGD:S000000999 P YHR111W|YHR1 gene taxon:4932 20051021 SGD
+SGD S000001153 UBA4 GO:0001403 SGD_REF:S000075061|PMID:14551258 IMP P YHR111W|YHR1 gene taxon:4932 20051021 SGD
+SGD S000001153 UBA4 GO:0006464 SGD_REF:S000051101|PMID:10713047 IDA P YHR111W|YHR1 gene taxon:4932 20021030 SGD
+SGD S000001153 UBA4 GO:0006464 SGD_REF:S000074238|PMID:14555475 IMP P YHR111W|YHR1 gene taxon:4932 20051018 SGD
+SGD S000001153 UBA4 GO:0006979 SGD_REF:S000074238|PMID:14555475 IMP P YHR111W|YHR1 gene taxon:4932 20051021 SGD
+SGD S000001153 UBA4 GO:0007114 SGD_REF:S000075061|PMID:14551258 IGI SGD:S000005242 P YHR111W|YHR1 gene taxon:4932 20051021 SGD
+SGD S000001153 UBA4 GO:0007124 SGD_REF:S000075061|PMID:14551258 IMP P YHR111W|YHR1 gene taxon:4932 20051021 SGD
+SGD S000002584 UBC1 GO:0000502 SGD_REF:S000064672|PMID:10848595 IPI C ubiquitin-conjugating enzyme YDR177W gene taxon:4932 20030520 SGD
+SGD S000002584 UBC1 GO:0004840 SGD_REF:S000054903|PMID:2265617 ISS SGD:S000000286|SGD:S000002466 F ubiquitin-conjugating enzyme YDR177W gene taxon:4932 20051026 SGD
+SGD S000002584 UBC1 GO:0004840 SGD_REF:S000054903|PMID:2265617 IDA F ubiquitin-conjugating enzyme YDR177W gene taxon:4932 20051026 SGD
+SGD S000002584 UBC1 GO:0000209 SGD_REF:S000058010|PMID:8982460 TAS P ubiquitin-conjugating enzyme YDR177W gene taxon:4932 20010118 SGD
+SGD S000002584 UBC1 GO:0006513 SGD_REF:S000058010|PMID:8982460 TAS P ubiquitin-conjugating enzyme YDR177W gene taxon:4932 20010118 SGD
+SGD S000002584 UBC1 GO:0006897 SGD_REF:S000058010|PMID:8982460 TAS P ubiquitin-conjugating enzyme YDR177W gene taxon:4932 20010118 SGD
+SGD S000002584 UBC1 GO:0009847 SGD_REF:S000058010|PMID:8982460 TAS P ubiquitin-conjugating enzyme YDR177W gene taxon:4932 20010118 SGD
+SGD S000002584 UBC1 GO:0016050 SGD_REF:S000060014|PMID:11134048 IMP P ubiquitin-conjugating enzyme YDR177W gene taxon:4932 20051026 SGD
+SGD S000002584 UBC1 GO:0030433 SGD_REF:S000054799|PMID:10878801 IGI SGD:S000004624 P ubiquitin-conjugating enzyme YDR177W gene taxon:4932 20051026 SGD
+SGD S000002584 UBC1 GO:0030433 SGD_REF:S000054799|PMID:10878801 IMP P ubiquitin-conjugating enzyme YDR177W gene taxon:4932 20051026 SGD
+SGD S000002584 UBC1 GO:0042787 SGD_REF:S000054903|PMID:2265617 IGI SGD:S000000286|SGD:S000002466 P ubiquitin-conjugating enzyme YDR177W gene taxon:4932 20051026 SGD
+SGD S000002584 UBC1 GO:0042787 SGD_REF:S000054903|PMID:2265617 IMP P ubiquitin-conjugating enzyme YDR177W gene taxon:4932 20051026 SGD
+SGD S000002584 UBC1 GO:0042787 SGD_REF:S000060014|PMID:11134048 IMP P ubiquitin-conjugating enzyme YDR177W gene taxon:4932 20051026 SGD
+SGD S000005866 UBC11 GO:0005737 SGD_REF:S000058010|PMID:8982460 IC GO:0004840 C YOR339C gene taxon:4932 20021205 SGD
+SGD S000005866 UBC11 GO:0004840 SGD_REF:S000052335|PMID:9675819 ISS F YOR339C gene taxon:4932 20051026 SGD
+SGD S000005866 UBC11 GO:0000209 SGD_REF:S000058010|PMID:8982460 TAS P YOR339C gene taxon:4932 20010118 SGD
+SGD S000005866 UBC11 GO:0006513 SGD_REF:S000058010|PMID:8982460 TAS P YOR339C gene taxon:4932 20010118 SGD
+SGD S000004297 UBC12 GO:0008372 SGD_REF:S000069584 ND C YLR306W gene taxon:4932 20020717 SGD
+SGD S000004297 UBC12 GO:0016976 SGD_REF:S000050724|PMID:9545234 IDA F YLR306W gene taxon:4932 20051018 SGD
+SGD S000004297 UBC12 GO:0016976 SGD_REF:S000050724|PMID:9545234 IMP F YLR306W gene taxon:4932 20051018 SGD
+SGD S000004297 UBC12 GO:0016976 SGD_REF:S000050724|PMID:9545234 ISS F YLR306W gene taxon:4932 20051018 SGD
+SGD S000004297 UBC12 GO:0045116 SGD_REF:S000050724|PMID:9545234 IDA P YLR306W gene taxon:4932 20030721 SGD
+SGD S000004297 UBC12 GO:0045116 SGD_REF:S000050724|PMID:9545234 ISS P YLR306W gene taxon:4932 20051018 SGD
+SGD S000004297 UBC12 GO:0045116 SGD_REF:S000050724|PMID:9545234 IMP P YLR306W gene taxon:4932 20051018 SGD
+SGD S000002499 UBC13 GO:0005634 SGD_REF:S000042429|PMID:10880451 IDA C ubiquitin-conjugating enzyme YDR092W gene taxon:4932 20020806 SGD
+SGD S000002499 UBC13 GO:0005737 SGD_REF:S000042429|PMID:10880451 IDA C ubiquitin-conjugating enzyme YDR092W gene taxon:4932 20020806 SGD
+SGD S000002499 UBC13 GO:0031371 SGD_REF:S000050556|PMID:10089880 IPI SGD:S000003055 C ubiquitin-conjugating enzyme YDR092W gene taxon:4932 20051028 SGD
+SGD S000002499 UBC13 contributes_to GO:0004840 SGD_REF:S000050556|PMID:10089880 IDA F ubiquitin-conjugating enzyme YDR092W gene taxon:4932 20051028 SGD
+SGD S000002499 UBC13 GO:0000209 SGD_REF:S000050556|PMID:10089880 IDA P ubiquitin-conjugating enzyme YDR092W gene taxon:4932 20051026 SGD
+SGD S000002499 UBC13 GO:0006301 SGD_REF:S000050556|PMID:10089880 IMP P ubiquitin-conjugating enzyme YDR092W gene taxon:4932 20010118 SGD
+SGD S000002499 UBC13 GO:0006301 SGD_REF:S000050556|PMID:10089880 IGI SGD:S000003055 P ubiquitin-conjugating enzyme YDR092W gene taxon:4932 20051028 SGD
+SGD S000002499 UBC13 GO:0006513 SGD_REF:S000058010|PMID:8982460 TAS P ubiquitin-conjugating enzyme YDR092W gene taxon:4932 20010118 SGD
+SGD S000000286 UBC4 GO:0000502 SGD_REF:S000064672|PMID:10848595 IPI C ubiquitin conjugating enzyme e2 YBR082C gene taxon:4932 20030520 SGD
+SGD S000000286 UBC4 GO:0004840 SGD_REF:S000042741|PMID:2154373 IDA F ubiquitin conjugating enzyme e2 YBR082C gene taxon:4932 20050103 SGD
+SGD S000000286 UBC4 GO:0000209 SGD_REF:S000042741|PMID:2154373 IDA P ubiquitin conjugating enzyme e2 YBR082C gene taxon:4932 20050103 SGD
+SGD S000000286 UBC4 GO:0006513 SGD_REF:S000042559|PMID:8391479 IDA P ubiquitin conjugating enzyme e2 YBR082C gene taxon:4932 20050103 SGD
+SGD S000000286 UBC4 GO:0006950 SGD_REF:S000058010|PMID:8982460 TAS P ubiquitin conjugating enzyme e2 YBR082C gene taxon:4932 20010118 SGD
+SGD S000000286 UBC4 GO:0006950 SGD_REF:S000042741|PMID:2154373 IDA P ubiquitin conjugating enzyme e2 YBR082C gene taxon:4932 20050103 SGD
+SGD S000000286 UBC4 GO:0030437 SGD_REF:S000058010|PMID:8982460 TAS P ubiquitin conjugating enzyme e2 YBR082C gene taxon:4932 20010118 SGD
+SGD S000000286 UBC4 GO:0043162 SGD_REF:S000074470|PMID:11788821 IMP P ubiquitin conjugating enzyme e2 YBR082C gene taxon:4932 20050421 SGD
+SGD S000002466 UBC5 GO:0000502 SGD_REF:S000064672|PMID:10848595 IPI C ubiquitin-conjugating enzyme YDR059C gene taxon:4932 20030520 SGD
+SGD S000002466 UBC5 GO:0004840 SGD_REF:S000042741|PMID:2154373 IDA F ubiquitin-conjugating enzyme YDR059C gene taxon:4932 20050103 SGD
+SGD S000002466 UBC5 GO:0000209 SGD_REF:S000042741|PMID:2154373 IDA P ubiquitin-conjugating enzyme YDR059C gene taxon:4932 20050103 SGD
+SGD S000002466 UBC5 GO:0006897 SGD_REF:S000058010|PMID:8982460 TAS P ubiquitin-conjugating enzyme YDR059C gene taxon:4932 20010118 SGD
+SGD S000002466 UBC5 GO:0006950 SGD_REF:S000042741|PMID:2154373 IDA P ubiquitin-conjugating enzyme YDR059C gene taxon:4932 20050103 SGD
+SGD S000002466 UBC5 GO:0006986 SGD_REF:S000058010|PMID:8982460 TAS P ubiquitin-conjugating enzyme YDR059C gene taxon:4932 20010118 SGD
+SGD S000002466 UBC5 GO:0030437 SGD_REF:S000058010|PMID:8982460 TAS P ubiquitin-conjugating enzyme YDR059C gene taxon:4932 20010118 SGD
+SGD S000000902 UBC6 GO:0005789 SGD_REF:S000052708|PMID:8396728 IDA C ubiquitin-conjugating enzyme YER100W|DOA2 gene taxon:4932 20051026 SGD
+SGD S000000902 UBC6 GO:0004840 SGD_REF:S000052708|PMID:8396728 IDA F ubiquitin-conjugating enzyme YER100W|DOA2 gene taxon:4932 20051026 SGD
+SGD S000000902 UBC6 GO:0004840 SGD_REF:S000052708|PMID:8396728 IMP F ubiquitin-conjugating enzyme YER100W|DOA2 gene taxon:4932 20051026 SGD
+SGD S000000902 UBC6 GO:0000209 SGD_REF:S000058010|PMID:8982460 TAS P ubiquitin-conjugating enzyme YER100W|DOA2 gene taxon:4932 20010118 SGD
+SGD S000000902 UBC6 GO:0006513 SGD_REF:S000058010|PMID:8982460 TAS P ubiquitin-conjugating enzyme YER100W|DOA2 gene taxon:4932 20010118 SGD
+SGD S000000902 UBC6 GO:0030433 SGD_REF:S000057852|PMID:8641272 IGI SGD:S000004370|SGD:S000004624 P ubiquitin-conjugating enzyme YER100W|DOA2 gene taxon:4932 20051026 SGD
+SGD S000000902 UBC6 GO:0030433 SGD_REF:S000057852|PMID:8641272 IMP P ubiquitin-conjugating enzyme YER100W|DOA2 gene taxon:4932 20051026 SGD
+SGD S000000902 UBC6 GO:0030433 SGD_REF:S000042723|PMID:8781238 IMP P ubiquitin-conjugating enzyme YER100W|DOA2 gene taxon:4932 20051026 SGD
+SGD S000000902 UBC6 GO:0030433 SGD_REF:S000052708|PMID:8396728 IGI SGD:S000004370 P ubiquitin-conjugating enzyme YER100W|DOA2 gene taxon:4932 20051026 SGD
+SGD S000000902 UBC6 GO:0030433 SGD_REF:S000042723|PMID:8781238 IGI SGD:S000004624 P ubiquitin-conjugating enzyme YER100W|DOA2 gene taxon:4932 20051026 SGD
+SGD S000000738 UBC8 GO:0005737 SGD_REF:S000039699|PMID:10811607 IDA C ubiquitin-conjugating enzyme YEL012W|GID3 gene taxon:4932 20051026 SGD
+SGD S000000738 UBC8 GO:0004840 SGD_REF:S000051223|PMID:1869573 IDA F ubiquitin-conjugating enzyme YEL012W|GID3 gene taxon:4932 20051026 SGD
+SGD S000000738 UBC8 GO:0004840 SGD_REF:S000051223|PMID:1869573 ISS SGD:S000003026 F ubiquitin-conjugating enzyme YEL012W|GID3 gene taxon:4932 20051026 SGD
+SGD S000000738 UBC8 GO:0000209 SGD_REF:S000058010|PMID:8982460 TAS P ubiquitin-conjugating enzyme YEL012W|GID3 gene taxon:4932 20010118 SGD
+SGD S000000738 UBC8 GO:0006513 SGD_REF:S000058010|PMID:8982460 TAS P ubiquitin-conjugating enzyme YEL012W|GID3 gene taxon:4932 20010118 SGD
+SGD S000000738 UBC8 GO:0042787 SGD_REF:S000039699|PMID:10811607 IMP P ubiquitin-conjugating enzyme YEL012W|GID3 gene taxon:4932 20051026 SGD
+SGD S000000738 UBC8 GO:0045721 SGD_REF:S000072993|PMID:12686616 IMP P ubiquitin-conjugating enzyme YEL012W|GID3 gene taxon:4932 20030708 SGD
+SGD S000002222 UBC9 GO:0005634 SGD_REF:S000045200|PMID:7800043 IDA C SUMO-conjugating enzyme YDL064W gene taxon:4932 20051014 SGD
+SGD S000002222 UBC9 GO:0019949 SGD_REF:S000086627|PMID:9435231 IDA F SUMO-conjugating enzyme YDL064W gene taxon:4932 20051017 SGD
+SGD S000002222 UBC9 GO:0019949 SGD_REF:S000086627|PMID:9435231 IMP F SUMO-conjugating enzyme YDL064W gene taxon:4932 20051017 SGD
+SGD S000002222 UBC9 GO:0019949 SGD_REF:S000049728|PMID:9341106 IDA F SUMO-conjugating enzyme YDL064W gene taxon:4932 20051017 SGD
+SGD S000002222 UBC9 GO:0000022 SGD_REF:S000045200|PMID:7800043 IMP P SUMO-conjugating enzyme YDL064W gene taxon:4932 20030213 SGD
+SGD S000002222 UBC9 GO:0000086 SGD_REF:S000058010|PMID:8982460 TAS P SUMO-conjugating enzyme YDL064W gene taxon:4932 20030122 SGD
+SGD S000002222 UBC9 GO:0016925 SGD_REF:S000049728|PMID:9341106 IDA P SUMO-conjugating enzyme YDL064W gene taxon:4932 20051017 SGD
+SGD S000002222 UBC9 GO:0016925 SGD_REF:S000049728|PMID:9341106 IMP P SUMO-conjugating enzyme YDL064W gene taxon:4932 20051017 SGD
+SGD S000002222 UBC9 GO:0016925 SGD_REF:S000086627|PMID:9435231 IDA P SUMO-conjugating enzyme YDL064W gene taxon:4932 20051017 SGD
+SGD S000002222 UBC9 GO:0016925 SGD_REF:S000086627|PMID:9435231 IMP P SUMO-conjugating enzyme YDL064W gene taxon:4932 20051017 SGD
+SGD S000002222 UBC9 GO:0016925 SGD_REF:S000049728|PMID:9341106 IPI P SUMO-conjugating enzyme YDL064W gene taxon:4932 20051017 SGD
+SGD S000003962 UBI4 GO:0005737 SGD_REF:S000058010|PMID:8982460 IC GO:0000209 C poly-ubiquitin, ubiquitin YLL039C|SCD2|UB14 gene taxon:4932 20040126 SGD
+SGD S000003962 UBI4 GO:0031386 SGD_REF:S000056997|PMID:3038523 ISS F poly-ubiquitin, ubiquitin YLL039C|SCD2|UB14 gene taxon:4932 20050525 SGD
+SGD S000003962 UBI4 GO:0043008 SGD_REF:S000058010|PMID:8982460 TAS F poly-ubiquitin, ubiquitin YLL039C|SCD2|UB14 gene taxon:4932 20040123 SGD
+SGD S000003962 UBI4 GO:0000209 SGD_REF:S000058010|PMID:8982460 TAS P poly-ubiquitin, ubiquitin YLL039C|SCD2|UB14 gene taxon:4932 20010118 SGD
+SGD S000003962 UBI4 GO:0006513 SGD_REF:S000058010|PMID:8982460 TAS P poly-ubiquitin, ubiquitin YLL039C|SCD2|UB14 gene taxon:4932 20010118 SGD
+SGD S000003962 UBI4 GO:0006950 SGD_REF:S000058010|PMID:8982460 TAS P poly-ubiquitin, ubiquitin YLL039C|SCD2|UB14 gene taxon:4932 20010118 SGD
+SGD S000003962 UBI4 GO:0016567 SGD_REF:S000049784|PMID:8035826 IMP P poly-ubiquitin, ubiquitin YLL039C|SCD2|UB14 gene taxon:4932 20050407 SGD
+SGD S000003962 UBI4 GO:0016579 SGD_REF:S000058010|PMID:8982460 TAS P poly-ubiquitin, ubiquitin YLL039C|SCD2|UB14 gene taxon:4932 20010118 SGD
+SGD S000003962 UBI4 GO:0030437 SGD_REF:S000058010|PMID:8982460 TAS P poly-ubiquitin, ubiquitin YLL039C|SCD2|UB14 gene taxon:4932 20010118 SGD
+SGD S000002280 UBP1 GO:0005737 SGD_REF:S000051210|PMID:1429680 IC GO:0004843 C ubiquitin-specific protease YDL122W gene taxon:4932 20021205 SGD
+SGD S000002280 UBP1 GO:0005737 SGD_REF:S000080348|PMID:15635103 IDA C ubiquitin-specific protease YDL122W gene taxon:4932 20050211 SGD
+SGD S000002280 UBP1 GO:0005783 SGD_REF:S000080348|PMID:15635103 IDA C ubiquitin-specific protease YDL122W gene taxon:4932 20050211 SGD
+SGD S000002280 UBP1 GO:0004843 SGD_REF:S000051210|PMID:1429680 IDA F ubiquitin-specific protease YDL122W gene taxon:4932 20010118 SGD
+SGD S000002280 UBP1 GO:0016579 SGD_REF:S000058010|PMID:8982460 TAS P ubiquitin-specific protease YDL122W gene taxon:4932 20010118 SGD
+SGD S000005130 UBP10 GO:0005634 SGD_REF:S000042118|PMID:10490600 IDA C YNL186W|DOT4 gene taxon:4932 20010118 SGD
+SGD S000005130 UBP10 GO:0005634 SGD_REF:S000069459|PMID:11914276 IDA C YNL186W|DOT4 gene taxon:4932 20020507 SGD
+SGD S000005130 UBP10 GO:0004843 SGD_REF:S000042118|PMID:10490600 IDA F YNL186W|DOT4 gene taxon:4932 20010118 SGD
+SGD S000005130 UBP10 GO:0006348 SGD_REF:S000080866|PMID:15721261 IMP P YNL186W|DOT4 gene taxon:4932 20050324 SGD
+SGD S000005130 UBP10 GO:0016579 SGD_REF:S000058010|PMID:8982460 TAS P YNL186W|DOT4 gene taxon:4932 20010118 SGD
+SGD S000005130 UBP10 GO:0016579 SGD_REF:S000080866|PMID:15721261 IDA P YNL186W|DOT4 gene taxon:4932 20050324 SGD
+SGD S000005130 UBP10 GO:0016579 SGD_REF:S000080866|PMID:15721261 IMP P YNL186W|DOT4 gene taxon:4932 20050324 SGD
+SGD S000001806 UBP11 GO:0008372 SGD_REF:S000069584 ND C ubiquitin-specific protease YKR098C gene taxon:4932 20021002 SGD
+SGD S000001806 UBP11 GO:0004843 SGD_REF:S000052610|PMID:10527495 IDA F ubiquitin-specific protease YKR098C gene taxon:4932 20021002 SGD
+SGD S000001806 UBP11 GO:0000004 SGD_REF:S000069584 ND P ubiquitin-specific protease YKR098C gene taxon:4932 20021002 SGD
+SGD S000003733 UBP12 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C ubiquitin carboxyl-terminal hydrolase YJL197W gene taxon:4932 20031028 SGD
+SGD S000003733 UBP12 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C ubiquitin carboxyl-terminal hydrolase YJL197W gene taxon:4932 20031028 SGD
+SGD S000003733 UBP12 GO:0004843 SGD_REF:S000058010|PMID:8982460 TAS F ubiquitin carboxyl-terminal hydrolase YJL197W gene taxon:4932 20021002 SGD
+SGD S000003733 UBP12 GO:0000004 SGD_REF:S000069584 ND P ubiquitin carboxyl-terminal hydrolase YJL197W gene taxon:4932 20021002 SGD
+SGD S000000163 UBP13 GO:0008372 SGD_REF:S000069584 ND C ubiquitin carboxyl-terminal hydrolase YBL067C gene taxon:4932 20021002 SGD
+SGD S000000163 UBP13 GO:0004843 SGD_REF:S000058010|PMID:8982460 TAS F ubiquitin carboxyl-terminal hydrolase YBL067C gene taxon:4932 20021002 SGD
+SGD S000000163 UBP13 GO:0000004 SGD_REF:S000069584 ND P ubiquitin carboxyl-terminal hydrolase YBL067C gene taxon:4932 20021002 SGD
+SGD S000000262 UBP14 GO:0005737 SGD_REF:S000058010|PMID:8982460 IC GO:0004843 C ubiquitin-specific protease YBR058C|GID6 gene taxon:4932 20021205 SGD
+SGD S000000262 UBP14 GO:0004843 SGD_REF:S000058010|PMID:8982460 TAS F ubiquitin-specific protease YBR058C|GID6 gene taxon:4932 20010118 SGD
+SGD S000000262 UBP14 GO:0016579 SGD_REF:S000058010|PMID:8982460 TAS P ubiquitin-specific protease YBR058C|GID6 gene taxon:4932 20010118 SGD
+SGD S000000262 UBP14 GO:0045721 SGD_REF:S000072993|PMID:12686616 IMP P ubiquitin-specific protease YBR058C|GID6 gene taxon:4932 20030708 SGD
+SGD S000004920 UBP15 GO:0005737 SGD_REF:S000058010|PMID:8982460 IC GO:0004843 C YMR304W gene taxon:4932 20021205 SGD
+SGD S000004920 UBP15 GO:0004843 SGD_REF:S000058010|PMID:8982460 TAS F YMR304W gene taxon:4932 20010118 SGD
+SGD S000004920 UBP15 GO:0016579 SGD_REF:S000058010|PMID:8982460 TAS P YMR304W gene taxon:4932 20010118 SGD
+SGD S000005993 UBP16 GO:0005737 SGD_REF:S000058010|PMID:8982460 IC GO:0004843 C deubiquitinating enzyme (putative) YPL072W gene taxon:4932 20021205 SGD
+SGD S000005993 UBP16 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C deubiquitinating enzyme (putative) YPL072W gene taxon:4932 20060317 SGD
+SGD S000005993 UBP16 GO:0005741 SGD_REF:S000116272|PMID:12914939 IDA C deubiquitinating enzyme (putative) YPL072W gene taxon:4932 20060612 SGD
+SGD S000005993 UBP16 GO:0004843 SGD_REF:S000058010|PMID:8982460 TAS F deubiquitinating enzyme (putative) YPL072W gene taxon:4932 20010118 SGD
+SGD S000005993 UBP16 GO:0016579 SGD_REF:S000058010|PMID:8982460 TAS P deubiquitinating enzyme (putative) YPL072W gene taxon:4932 20010118 SGD
+SGD S000005650 UBP2 GO:0005737 SGD_REF:S000051210|PMID:1429680 IC GO:0004843 C ubiquitin-specific protease YOR124C gene taxon:4932 20021205 SGD
+SGD S000005650 UBP2 GO:0004843 SGD_REF:S000051210|PMID:1429680 IDA F ubiquitin-specific protease YOR124C gene taxon:4932 20010118 SGD
+SGD S000005650 UBP2 GO:0016579 SGD_REF:S000081856|PMID:15933713 IDA P ubiquitin-specific protease YOR124C gene taxon:4932 20050715 SGD
+SGD S000000953 UBP3 GO:0005737 SGD_REF:S000051210|PMID:1429680 IC GO:0004843 C ubiquitin-specific protease YER151C gene taxon:4932 20021205 SGD
+SGD S000000953 UBP3 GO:0004843 SGD_REF:S000051210|PMID:1429680 IDA F ubiquitin-specific protease YER151C gene taxon:4932 20010118 SGD
+SGD S000000953 UBP3 GO:0016579 SGD_REF:S000058010|PMID:8982460 TAS P ubiquitin-specific protease YER151C gene taxon:4932 20010118 SGD
+SGD S000000946 UBP5 GO:0005737 SGD_REF:S000058010|PMID:8982460 IC GO:0004843 C ubiquitin-specific protease (putative) YER144C gene taxon:4932 20021205 SGD
+SGD S000000946 UBP5 GO:0004843 SGD_REF:S000058010|PMID:8982460 TAS F ubiquitin-specific protease (putative) YER144C gene taxon:4932 20010118 SGD
+SGD S000000946 UBP5 GO:0016579 SGD_REF:S000058010|PMID:8982460 TAS P ubiquitin-specific protease (putative) YER144C gene taxon:4932 20010118 SGD
+SGD S000001906 UBP6 GO:0005838 SGD_REF:S000056447|PMID:11029046 IPI C YFR010W gene taxon:4932 20020403 SGD
+SGD S000001906 UBP6 GO:0004843 SGD_REF:S000058010|PMID:8982460 TAS F YFR010W gene taxon:4932 20010118 SGD
+SGD S000001906 UBP6 GO:0016579 SGD_REF:S000058010|PMID:8982460 TAS P YFR010W gene taxon:4932 20010118 SGD
+SGD S000001418 UBP7 GO:0005737 SGD_REF:S000058010|PMID:8982460 IC GO:0004843 C ubiquitin-specific protease YIL156W gene taxon:4932 20021205 SGD
+SGD S000001418 UBP7 GO:0004843 SGD_REF:S000058010|PMID:8982460 TAS F ubiquitin-specific protease YIL156W gene taxon:4932 20010118 SGD
+SGD S000001418 UBP7 GO:0016579 SGD_REF:S000058010|PMID:8982460 TAS P ubiquitin-specific protease YIL156W gene taxon:4932 20010118 SGD
+SGD S000004836 UBP8 GO:0000124 SGD_REF:S000070225|PMID:12052880 IDA C YMR223W gene taxon:4932 20020925 SGD
+SGD S000004836 UBP8 GO:0004843 SGD_REF:S000058010|PMID:8982460 TAS F YMR223W gene taxon:4932 20010118 SGD
+SGD S000004836 UBP8 GO:0016579 SGD_REF:S000058010|PMID:8982460 TAS P YMR223W gene taxon:4932 20010118 SGD
+SGD S000000900 UBP9 GO:0005737 SGD_REF:S000058010|PMID:8982460 IC GO:0004843 C ubiquitin carboxyl-terminal hydrolase YER098W gene taxon:4932 20021205 SGD
+SGD S000000900 UBP9 GO:0004843 SGD_REF:S000058010|PMID:8982460 TAS F ubiquitin carboxyl-terminal hydrolase YER098W gene taxon:4932 20010118 SGD
+SGD S000000900 UBP9 GO:0016579 SGD_REF:S000058010|PMID:8982460 TAS P ubiquitin carboxyl-terminal hydrolase YER098W gene taxon:4932 20010118 SGD
+SGD S000003416 UBR1 GO:0000502 SGD_REF:S000064672|PMID:10848595 IPI C ubiquitin-protein ligase YGR184C|PTR1 gene taxon:4932 20030520 SGD
+SGD S000003416 UBR1 GO:0004842 SGD_REF:S000058010|PMID:8982460 TAS F ubiquitin-protein ligase YGR184C|PTR1 gene taxon:4932 20010118 SGD
+SGD S000003416 UBR1 GO:0000209 SGD_REF:S000058010|PMID:8982460 TAS P ubiquitin-protein ligase YGR184C|PTR1 gene taxon:4932 20010118 SGD
+SGD S000003416 UBR1 GO:0006513 SGD_REF:S000058010|PMID:8982460 TAS P ubiquitin-protein ligase YGR184C|PTR1 gene taxon:4932 20010118 SGD
+SGD S000004014 UBR2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C ubiquitin-protein ligase (E3) YLR024C gene taxon:4932 20031028 SGD
+SGD S000004014 UBR2 GO:0004842 SGD_REF:S000058010|PMID:8982460 TAS F ubiquitin-protein ligase (E3) YLR024C gene taxon:4932 20010118 SGD
+SGD S000004014 UBR2 GO:0000209 SGD_REF:S000058010|PMID:8982460 TAS P ubiquitin-protein ligase (E3) YLR024C gene taxon:4932 20010118 SGD
+SGD S000004014 UBR2 GO:0006513 SGD_REF:S000058010|PMID:8982460 TAS P ubiquitin-protein ligase (E3) YLR024C gene taxon:4932 20010118 SGD
+SGD S000000369 UBS1 GO:0005634 SGD_REF:S000059718|PMID:10991951 IDA C YBR165W gene taxon:4932 20020827 SGD
+SGD S000000369 UBS1 GO:0005554 SGD_REF:S000069584 ND F YBR165W gene taxon:4932 20020827 SGD
+SGD S000000369 UBS1 GO:0006611 SGD_REF:S000059718|PMID:10991951 IGI P YBR165W gene taxon:4932 20020827 SGD
+SGD S000000369 UBS1 GO:0016567 SGD_REF:S000059718|PMID:10991951 IGI P YBR165W gene taxon:4932 20020827 SGD
+SGD S000002249 UBX3 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDL091C gene taxon:4932 20031028 SGD
+SGD S000002249 UBX3 GO:0005554 SGD_REF:S000069584 ND F YDL091C gene taxon:4932 20030203 SGD
+SGD S000002249 UBX3 GO:0000004 SGD_REF:S000069584 ND P YDL091C gene taxon:4932 20030203 SGD
+SGD S000004671 UBX4 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YMR067C|CUI1 gene taxon:4932 20031028 SGD
+SGD S000004671 UBX4 GO:0005634 SGD_REF:S000075985|PMID:14755638 IDA C YMR067C|CUI1 gene taxon:4932 20050331 SGD
+SGD S000004671 UBX4 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YMR067C|CUI1 gene taxon:4932 20031028 SGD
+SGD S000004671 UBX4 GO:0005554 SGD_REF:S000069584 ND F YMR067C|CUI1 gene taxon:4932 20021126 SGD
+SGD S000004671 UBX4 GO:0006511 SGD_REF:S000075985|PMID:14755638 IMP P YMR067C|CUI1 gene taxon:4932 20050331 SGD
+SGD S000004671 UBX4 GO:0030435 SGD_REF:S000075985|PMID:14755638 IMP P YMR067C|CUI1 gene taxon:4932 20050331 SGD
+SGD S000002738 UBX5 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YDR330W gene taxon:4932 20031028 SGD
+SGD S000002738 UBX5 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDR330W gene taxon:4932 20031028 SGD
+SGD S000002738 UBX5 GO:0005554 SGD_REF:S000069584 ND F YDR330W gene taxon:4932 20030203 SGD
+SGD S000002738 UBX5 GO:0006511 SGD_REF:S000061788|PMID:10618406 IEP P YDR330W gene taxon:4932 20030205 SGD
+SGD S000003584 UBX6 GO:0005634 SGD_REF:S000075985|PMID:14755638 IDA C YJL048C|CUI2 gene taxon:4932 20050331 SGD
+SGD S000003584 UBX6 GO:0005554 SGD_REF:S000069584 ND F YJL048C|CUI2 gene taxon:4932 20030421 SGD
+SGD S000003584 UBX6 GO:0006511 SGD_REF:S000075985|PMID:14755638 IMP P YJL048C|CUI2 gene taxon:4932 20050331 SGD
+SGD S000003584 UBX6 GO:0030435 SGD_REF:S000075985|PMID:14755638 IMP P YJL048C|CUI2 gene taxon:4932 20050331 SGD
+SGD S000000477 UBX7 GO:0005635 SGD_REF:S000075985|PMID:14755638 IDA C YBR273C|CUI3 gene taxon:4932 20050331 SGD
+SGD S000000477 UBX7 GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YBR273C|CUI3 gene taxon:4932 20031028 SGD
+SGD S000000477 UBX7 GO:0005554 SGD_REF:S000069584 ND F YBR273C|CUI3 gene taxon:4932 20021126 SGD
+SGD S000000477 UBX7 GO:0006511 SGD_REF:S000075985|PMID:14755638 IMP P YBR273C|CUI3 gene taxon:4932 20050331 SGD
+SGD S000000477 UBX7 GO:0030435 SGD_REF:S000075985|PMID:14755638 IMP P YBR273C|CUI3 gene taxon:4932 20050331 SGD
+SGD S000003280 UFD1 GO:0005783 SGD_REF:S000069082|PMID:11740563 IDA C YGR048W gene taxon:4932 20020906 SGD
+SGD S000003280 UFD1 GO:0005515 SGD_REF:S000071485|PMID:12015140 TAS F YGR048W gene taxon:4932 20030222 SGD
+SGD S000003280 UFD1 GO:0006397 SGD_REF:S000068893|PMID:11574150 TAS P YGR048W gene taxon:4932 20020906 SGD
+SGD S000003280 UFD1 GO:0006511 SGD_REF:S000071485|PMID:12015140 TAS P YGR048W gene taxon:4932 20030222 SGD
+SGD S000003280 UFD1 GO:0015031 SGD_REF:S000069082|PMID:11740563 IDA P YGR048W gene taxon:4932 20020906 SGD
+SGD S000002349 UFD2 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C ubiquitin conjugating factor e4 YDL190C gene taxon:4932 20031028 SGD
+SGD S000002349 UFD2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C ubiquitin conjugating factor e4 YDL190C gene taxon:4932 20031028 SGD
+SGD S000002349 UFD2 GO:0004840 SGD_REF:S000050532|PMID:10089879 IMP F ubiquitin conjugating factor e4 YDL190C gene taxon:4932 20020927 SGD
+SGD S000002349 UFD2 GO:0004840 SGD_REF:S000050532|PMID:10089879 IPI F ubiquitin conjugating factor e4 YDL190C gene taxon:4932 20020927 SGD
+SGD S000002349 UFD2 GO:0006511 SGD_REF:S000050532|PMID:10089879 IMP P ubiquitin conjugating factor e4 YDL190C gene taxon:4932 20020927 SGD
+SGD S000002349 UFD2 GO:0006511 SGD_REF:S000050532|PMID:10089879 IPI P ubiquitin conjugating factor e4 YDL190C gene taxon:4932 20020927 SGD
+SGD S000002349 UFD2 GO:0006511 SGD_REF:S000048830|PMID:7615550 IMP P ubiquitin conjugating factor e4 YDL190C gene taxon:4932 20020927 SGD
+SGD S000002349 UFD2 GO:0006512 SGD_REF:S000114196|PMID:16427015 IMP P ubiquitin conjugating factor e4 YDL190C gene taxon:4932 20060203 SGD
+SGD S000002349 UFD2 GO:0006512 SGD_REF:S000114196|PMID:16427015 IGI P ubiquitin conjugating factor e4 YDL190C gene taxon:4932 20060203 SGD
+SGD S000002349 UFD2 GO:0006512 SGD_REF:S000114196|PMID:16427015 IPI P ubiquitin conjugating factor e4 YDL190C gene taxon:4932 20060203 SGD
+SGD S000002349 UFD2 GO:0006950 SGD_REF:S000050532|PMID:10089879 IMP P ubiquitin conjugating factor e4 YDL190C gene taxon:4932 20020927 SGD
+SGD S000001493 UFD4 GO:0005737 SGD_REF:S000047686|PMID:10688918 IPI C ubiquitin ligase e3 YKL010C gene taxon:4932 20021209 SGD
+SGD S000001493 UFD4 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C ubiquitin ligase e3 YKL010C gene taxon:4932 20040813 SGD
+SGD S000001493 UFD4 GO:0004842 SGD_REF:S000058010|PMID:8982460 TAS F ubiquitin ligase e3 YKL010C gene taxon:4932 20010118 SGD
+SGD S000001493 UFD4 GO:0000209 SGD_REF:S000058010|PMID:8982460 TAS P ubiquitin ligase e3 YKL010C gene taxon:4932 20010118 SGD
+SGD S000001493 UFD4 GO:0006513 SGD_REF:S000058010|PMID:8982460 TAS P ubiquitin ligase e3 YKL010C gene taxon:4932 20010118 SGD
+SGD S000005601 UFE1 GO:0005789 SGD_REF:S000058453|PMID:10047442 TAS C t-SNARE (ER) YOR075W|YOR29-26 gene taxon:4932 20010118 SGD
+SGD S000005601 UFE1 GO:0005486 SGD_REF:S000058453|PMID:10047442 TAS F t-SNARE (ER) YOR075W|YOR29-26 gene taxon:4932 20010118 SGD
+SGD S000005601 UFE1 GO:0006890 SGD_REF:S000058453|PMID:10047442 TAS P t-SNARE (ER) YOR075W|YOR29-26 gene taxon:4932 20010118 SGD
+SGD S000005601 UFE1 GO:0006906 SGD_REF:S000058453|PMID:10047442 TAS P t-SNARE (ER) YOR075W|YOR29-26 gene taxon:4932 20010118 SGD
+SGD S000004553 UFO1 GO:0005634 SGD_REF:S000075471|PMID:14506225 IDA C F-box protein YML088W gene taxon:4932 20040224 SGD
+SGD S000004553 UFO1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C F-box protein YML088W gene taxon:4932 20031028 SGD
+SGD S000004553 UFO1 GO:0005737 SGD_REF:S000075471|PMID:14506225 IDA C F-box protein YML088W gene taxon:4932 20040224 SGD
+SGD S000004553 UFO1 GO:0019005 SGD_REF:S000075471|PMID:14506225 IPI C F-box protein YML088W gene taxon:4932 20040224 SGD
+SGD S000004553 UFO1 GO:0004842 SGD_REF:S000047541|PMID:10963670 IMP F F-box protein YML088W gene taxon:4932 20020927 SGD
+SGD S000004553 UFO1 GO:0005515 SGD_REF:S000075471|PMID:14506225 IDA F F-box protein YML088W gene taxon:4932 20040224 SGD
+SGD S000004553 UFO1 GO:0006511 SGD_REF:S000047541|PMID:10963670 IMP P F-box protein YML088W gene taxon:4932 20020927 SGD
+SGD S000004553 UFO1 GO:0006511 SGD_REF:S000075471|PMID:14506225 IPI P F-box protein YML088W gene taxon:4932 20040224 SGD
+SGD S000004553 UFO1 GO:0006974 SGD_REF:S000047541|PMID:10963670 IMP P F-box protein YML088W gene taxon:4932 20020927 SGD
+SGD S000004553 UFO1 GO:0006974 SGD_REF:S000075471|PMID:14506225 IPI P F-box protein YML088W gene taxon:4932 20040224 SGD
+SGD S000003251 UGA1 GO:0005622 SGD_REF:S000042602|PMID:11031268 IC GO:0019740 C gamma-aminobutyrate (GABA) transaminase (4-aminobutyrate aminotransferase) YGR019W gene taxon:4932 20021122 SGD
+SGD S000003251 UGA1 GO:0003867 SGD_REF:S000046583|PMID:10590462 TAS F gamma-aminobutyrate (GABA) transaminase (4-aminobutyrate aminotransferase) YGR019W gene taxon:4932 20020927 SGD
+SGD S000003251 UGA1 GO:0019740 SGD_REF:S000054048|PMID:2653828 TAS P gamma-aminobutyrate (GABA) transaminase (4-aminobutyrate aminotransferase) YGR019W gene taxon:4932 20020927 SGD
+SGD S000000210 UGA2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C succinate semialdehyde dehydrogenase YBR006W|UGA5 gene taxon:4932 20031028 SGD
+SGD S000000210 UGA2 GO:0009013 SGD_REF:S000042602|PMID:11031268 IMP F succinate semialdehyde dehydrogenase YBR006W|UGA5 gene taxon:4932 20010118 SGD
+SGD S000000210 UGA2 GO:0009013 SGD_REF:S000042602|PMID:11031268 ISS F succinate semialdehyde dehydrogenase YBR006W|UGA5 gene taxon:4932 20010118 SGD
+SGD S000000210 UGA2 GO:0006538 SGD_REF:S000042602|PMID:11031268 IMP P succinate semialdehyde dehydrogenase YBR006W|UGA5 gene taxon:4932 20010118 SGD
+SGD S000000210 UGA2 GO:0006538 SGD_REF:S000042602|PMID:11031268 IEP P succinate semialdehyde dehydrogenase YBR006W|UGA5 gene taxon:4932 20010118 SGD
+SGD S000000210 UGA2 GO:0006538 SGD_REF:S000042602|PMID:11031268 ISS P succinate semialdehyde dehydrogenase YBR006W|UGA5 gene taxon:4932 20010118 SGD
+SGD S000000210 UGA2 GO:0006979 SGD_REF:S000042602|PMID:11031268 IMP P succinate semialdehyde dehydrogenase YBR006W|UGA5 gene taxon:4932 20010118 SGD
+SGD S000000210 UGA2 GO:0006979 SGD_REF:S000042602|PMID:11031268 IGI P succinate semialdehyde dehydrogenase YBR006W|UGA5 gene taxon:4932 20010118 SGD
+SGD S000000210 UGA2 GO:0006979 SGD_REF:S000042602|PMID:11031268 IEP P succinate semialdehyde dehydrogenase YBR006W|UGA5 gene taxon:4932 20010118 SGD
+SGD S000002329 UGA3 GO:0005634 SGD_REF:S000058344|PMID:9651335 IC GO:0003704 C zinc finger transcription factor of the Zn(2)-Cys(6) binuclear cluster domain type YDL170W gene taxon:4932 20021111 SGD
+SGD S000002329 UGA3 GO:0003700 SGD_REF:S000071820|PMID:12235130 IDA F zinc finger transcription factor of the Zn(2)-Cys(6) binuclear cluster domain type YDL170W gene taxon:4932 20050119 SGD
+SGD S000002329 UGA3 GO:0003704 SGD_REF:S000058344|PMID:9651335 IPI F zinc finger transcription factor of the Zn(2)-Cys(6) binuclear cluster domain type YDL170W gene taxon:4932 20021111 SGD
+SGD S000002329 UGA3 GO:0006357 SGD_REF:S000055594|PMID:7899074 IMP P zinc finger transcription factor of the Zn(2)-Cys(6) binuclear cluster domain type YDL170W gene taxon:4932 20021111 SGD
+SGD S000002329 UGA3 GO:0019740 SGD_REF:S000055594|PMID:7899074 IMP P zinc finger transcription factor of the Zn(2)-Cys(6) binuclear cluster domain type YDL170W gene taxon:4932 20021111 SGD
+SGD S000002329 UGA3 GO:0045893 SGD_REF:S000071820|PMID:12235130 IDA P zinc finger transcription factor of the Zn(2)-Cys(6) binuclear cluster domain type YDL170W gene taxon:4932 20050119 SGD
+SGD S000002369 UGA4 GO:0000329 SGD_REF:S000075681|PMID:14985124 IDA C GABA-specific transport protein YDL210W gene taxon:4932 20040329 SGD
+SGD S000002369 UGA4 GO:0015489 SGD_REF:S000075681|PMID:14985124 IDA F GABA-specific transport protein YDL210W gene taxon:4932 20040329 SGD
+SGD S000002369 UGA4 GO:0015495 SGD_REF:S000041981|PMID:8455553 ISS F GABA-specific transport protein YDL210W gene taxon:4932 20020403 SGD
+SGD S000002369 UGA4 GO:0006810 SGD_REF:S000053149|PMID:9416005 TAS P GABA-specific transport protein YDL210W gene taxon:4932 20020403 SGD
+SGD S000002369 UGA4 GO:0015847 SGD_REF:S000075681|PMID:14985124 IDA P GABA-specific transport protein YDL210W gene taxon:4932 20040329 SGD
+SGD S000002878 UGO1 GO:0005741 SGD_REF:S000059950|PMID:11257114 IDA C outer membrane protein YDR470C gene taxon:4932 20010328 SGD
+SGD S000002878 UGO1 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C outer membrane protein YDR470C gene taxon:4932 20060317 SGD
+SGD S000002878 UGO1 GO:0005215 SGD_REF:S000049213|PMID:10930523 ISS F outer membrane protein YDR470C gene taxon:4932 20021017 SGD
+SGD S000002878 UGO1 GO:0000002 SGD_REF:S000076835|PMID:15087460 IMP P outer membrane protein YDR470C gene taxon:4932 20050307 SGD
+SGD S000002878 UGO1 GO:0006810 SGD_REF:S000049213|PMID:10930523 ISS P outer membrane protein YDR470C gene taxon:4932 20021017 SGD
+SGD S000002878 UGO1 GO:0008053 SGD_REF:S000059950|PMID:11257114 IMP P outer membrane protein YDR470C gene taxon:4932 20010328 SGD
+SGD S000002878 UGO1 GO:0008053 SGD_REF:S000059950|PMID:11257114 IGI P outer membrane protein YDR470C gene taxon:4932 20010328 SGD
+SGD S000002878 UGO1 GO:0008053 SGD_REF:S000073565|PMID:12808034 IPI P outer membrane protein YDR470C gene taxon:4932 20030710 SGD
+SGD S000002878 UGO1 GO:0008053 SGD_REF:S000073565|PMID:12808034 IMP P outer membrane protein YDR470C gene taxon:4932 20030710 SGD
+SGD S000002878 UGO1 GO:0030447 SGD_REF:S000080384|PMID:15645503 IMP P outer membrane protein YDR470C gene taxon:4932 20050621 SGD
+SGD S000001518 UGP1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C uridinephosphoglucose pyrophosphorylase YKL035W gene taxon:4932 20031028 SGD
+SGD S000001518 UGP1 GO:0003983 SGD_REF:S000055499|PMID:7588797 IMP F uridinephosphoglucose pyrophosphorylase YKL035W gene taxon:4932 20020403 SGD
+SGD S000001518 UGP1 GO:0003983 SGD_REF:S000055499|PMID:7588797 ISS F uridinephosphoglucose pyrophosphorylase YKL035W gene taxon:4932 20020403 SGD
+SGD S000001518 UGP1 GO:0006011 SGD_REF:S000055499|PMID:7588797 IMP P uridinephosphoglucose pyrophosphorylase YKL035W gene taxon:4932 20020403 SGD
+SGD S000001518 UGP1 GO:0006486 SGD_REF:S000069480|PMID:7926366 TAS P uridinephosphoglucose pyrophosphorylase YKL035W gene taxon:4932 20020403 SGD
+SGD S000002328 UGX2 GO:0008372 SGD_REF:S000069584 ND C YDL169C gene taxon:4932 20021030 SGD
+SGD S000002328 UGX2 GO:0005554 SGD_REF:S000069584 ND F YDL169C gene taxon:4932 20021030 SGD
+SGD S000002328 UGX2 GO:0000004 SGD_REF:S000069584 ND P YDL169C gene taxon:4932 20021030 SGD
+SGD S000000075 UIP3 GO:0005635 SGD_REF:S000066186|PMID:11056382 IDA C YAR027W gene taxon:4932 20050422 SGD
+SGD S000000075 UIP3 GO:0005554 SGD_REF:S000069584 ND F YAR027W gene taxon:4932 20021018 SGD
+SGD S000000075 UIP3 GO:0000004 SGD_REF:S000069584 ND P YAR027W gene taxon:4932 20021018 SGD
+SGD S000006107 UIP4 GO:0005635 SGD_REF:S000066186|PMID:11056382 IDA C YPL186C gene taxon:4932 20050422 SGD
+SGD S000006107 UIP4 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C YPL186C gene taxon:4932 20060317 SGD
+SGD S000006107 UIP4 GO:0005783 SGD_REF:S000066186|PMID:11056382 IDA C YPL186C gene taxon:4932 20050422 SGD
+SGD S000006107 UIP4 GO:0005554 SGD_REF:S000069584 ND F YPL186C gene taxon:4932 20021018 SGD
+SGD S000006107 UIP4 GO:0000004 SGD_REF:S000069584 ND P YPL186C gene taxon:4932 20021018 SGD
+SGD S000001752 UIP5 GO:0005635 SGD_REF:S000066186|PMID:11056382 IDA C YKR044W gene taxon:4932 20050422 SGD
+SGD S000001752 UIP5 GO:0005554 SGD_REF:S000069584 ND F YKR044W gene taxon:4932 20021018 SGD
+SGD S000001752 UIP5 GO:0000004 SGD_REF:S000069584 ND P YKR044W gene taxon:4932 20021018 SGD
+SGD S000005924 ULA1 GO:0008372 SGD_REF:S000069584 ND C YPL003W|ENR2 gene taxon:4932 20020717 SGD
+SGD S000005924 ULA1 GO:0019781 SGD_REF:S000050724|PMID:9545234 IDA F YPL003W|ENR2 gene taxon:4932 20020717 SGD
+SGD S000005924 ULA1 GO:0019781 SGD_REF:S000050724|PMID:9545234 ISS SGD:S000006384 F YPL003W|ENR2 gene taxon:4932 20051018 SGD
+SGD S000005924 ULA1 GO:0019781 SGD_REF:S000042395|PMID:9531531 IMP F YPL003W|ENR2 gene taxon:4932 20051018 SGD
+SGD S000005924 ULA1 GO:0019781 SGD_REF:S000042395|PMID:9531531 ISS SGD:S000006384|TAIR:2062571|protein_id:AAC50477 F YPL003W|ENR2 gene taxon:4932 20051018 SGD
+SGD S000005924 ULA1 GO:0045116 SGD_REF:S000050724|PMID:9545234 IDA P YPL003W|ENR2 gene taxon:4932 20030721 SGD
+SGD S000005924 ULA1 GO:0045116 SGD_REF:S000050724|PMID:9545234 ISS SGD:S000006384 P YPL003W|ENR2 gene taxon:4932 20051018 SGD
+SGD S000005924 ULA1 GO:0045116 SGD_REF:S000042395|PMID:9531531 ISS TAIR:2062571|protein_id:AAC50477 P YPL003W|ENR2 gene taxon:4932 20051018 SGD
+SGD S000005924 ULA1 GO:0045116 SGD_REF:S000050724|PMID:9545234 IMP P YPL003W|ENR2 gene taxon:4932 20051018 SGD
+SGD S000005941 ULP1 GO:0005635 SGD_REF:S000051720|PMID:10713161 IDA C Smt3-specific protease YPL020C|NIB1 gene taxon:4932 20010118 SGD
+SGD S000005941 ULP1 GO:0005643 SGD_REF:S000072663|PMID:12471376 IDA C Smt3-specific protease YPL020C|NIB1 gene taxon:4932 20030304 SGD
+SGD S000005941 ULP1 GO:0008234 SGD_REF:S000040761|PMID:10094048 IDA F Smt3-specific protease YPL020C|NIB1 gene taxon:4932 20010118 SGD
+SGD S000005941 ULP1 GO:0008234 SGD_REF:S000040761|PMID:10094048 ISS F Smt3-specific protease YPL020C|NIB1 gene taxon:4932 20020403 SGD
+SGD S000005941 ULP1 GO:0016929 SGD_REF:S000040761|PMID:10094048 IMP F Smt3-specific protease YPL020C|NIB1 gene taxon:4932 20020403 SGD
+SGD S000005941 ULP1 GO:0016929 SGD_REF:S000040761|PMID:10094048 IDA F Smt3-specific protease YPL020C|NIB1 gene taxon:4932 20020403 SGD
+SGD S000005941 ULP1 GO:0000086 SGD_REF:S000040761|PMID:10094048 IMP P Smt3-specific protease YPL020C|NIB1 gene taxon:4932 20010118 SGD
+SGD S000005941 ULP1 GO:0016926 SGD_REF:S000040761|PMID:10094048 IMP P Smt3-specific protease YPL020C|NIB1 gene taxon:4932 20020403 SGD
+SGD S000005941 ULP1 GO:0016926 SGD_REF:S000040761|PMID:10094048 IDA P Smt3-specific protease YPL020C|NIB1 gene taxon:4932 20020403 SGD
+SGD S000001293 ULP2 GO:0005634 SGD_REF:S000051720|PMID:10713161 IDA C YIL031W|SMT4 gene taxon:4932 20010118 SGD
+SGD S000001293 ULP2 GO:0008234 SGD_REF:S000051720|PMID:10713161 IDA F YIL031W|SMT4 gene taxon:4932 20010118 SGD
+SGD S000001293 ULP2 GO:0008234 SGD_REF:S000040761|PMID:10094048 ISS F YIL031W|SMT4 gene taxon:4932 20020403 SGD
+SGD S000001293 ULP2 GO:0016929 SGD_REF:S000051720|PMID:10713161 IMP F YIL031W|SMT4 gene taxon:4932 20020403 SGD
+SGD S000001293 ULP2 GO:0016929 SGD_REF:S000051720|PMID:10713161 IDA F YIL031W|SMT4 gene taxon:4932 20020403 SGD
+SGD S000001293 ULP2 GO:0006276 SGD_REF:S000051720|PMID:10713161 IMP P YIL031W|SMT4 gene taxon:4932 20020403 SGD
+SGD S000001293 ULP2 GO:0006276 SGD_REF:S000060387|PMID:11333221 IMP P YIL031W|SMT4 gene taxon:4932 20020403 SGD
+SGD S000001293 ULP2 GO:0007094 SGD_REF:S000051723|PMID:10713162 IMP P YIL031W|SMT4 gene taxon:4932 20020403 SGD
+SGD S000001293 ULP2 GO:0007094 SGD_REF:S000051723|PMID:10713162 IGI P YIL031W|SMT4 gene taxon:4932 20020403 SGD
+SGD S000001293 ULP2 GO:0016926 SGD_REF:S000051720|PMID:10713161 IMP P YIL031W|SMT4 gene taxon:4932 20020403 SGD
+SGD S000001293 ULP2 GO:0016926 SGD_REF:S000051720|PMID:10713161 IDA P YIL031W|SMT4 gene taxon:4932 20020403 SGD
+SGD S000001293 ULP2 GO:0030261 SGD_REF:S000060387|PMID:11333221 IMP P YIL031W|SMT4 gene taxon:4932 20031228 SGD
+SGD S000006060 UME1 GO:0005634 SGD_REF:S000049423|PMID:9234739 IDA C transcriptional modulator YPL139C|WTM3 gene taxon:4932 20021030 SGD
+SGD S000006060 UME1 GO:0003714 SGD_REF:S000049423|PMID:9234739 IDA F transcriptional modulator YPL139C|WTM3 gene taxon:4932 20021030 SGD
+SGD S000006060 UME1 GO:0040020 SGD_REF:S000049423|PMID:9234739 IGI P transcriptional modulator YPL139C|WTM3 gene taxon:4932 20021030 SGD
+SGD S000002615 UME6 GO:0005634 SGD_REF:S000046897|PMID:8628320 IPI C C6 zinc finger URS1-binding protein YDR207C|CAR80|NIM2|RIM16 gene taxon:4932 20020226 SGD
+SGD S000002615 UME6 GO:0003677 SGD_REF:S000054292|PMID:7926768 IDA F C6 zinc finger URS1-binding protein YDR207C|CAR80|NIM2|RIM16 gene taxon:4932 20020305 SGD
+SGD S000002615 UME6 GO:0030528 SGD_REF:S000046897|PMID:8628320 IMP F C6 zinc finger URS1-binding protein YDR207C|CAR80|NIM2|RIM16 gene taxon:4932 20020226 SGD
+SGD S000002615 UME6 GO:0030528 SGD_REF:S000058110|PMID:9150136 IDA F C6 zinc finger URS1-binding protein YDR207C|CAR80|NIM2|RIM16 gene taxon:4932 20020226 SGD
+SGD S000002615 UME6 GO:0030528 SGD_REF:S000046897|PMID:8628320 IDA F C6 zinc finger URS1-binding protein YDR207C|CAR80|NIM2|RIM16 gene taxon:4932 20020226 SGD
+SGD S000002615 UME6 GO:0030528 SGD_REF:S000058110|PMID:9150136 IMP F C6 zinc finger URS1-binding protein YDR207C|CAR80|NIM2|RIM16 gene taxon:4932 20020226 SGD
+SGD S000002615 UME6 GO:0007001 SGD_REF:S000077815|PMID:11533234 IMP P C6 zinc finger URS1-binding protein YDR207C|CAR80|NIM2|RIM16 gene taxon:4932 20050407 SGD
+SGD S000002615 UME6 GO:0007068 SGD_REF:S000054292|PMID:7926768 IMP P C6 zinc finger URS1-binding protein YDR207C|CAR80|NIM2|RIM16 gene taxon:4932 20020226 SGD
+SGD S000002615 UME6 GO:0007131 SGD_REF:S000047047|PMID:8618927 IMP P C6 zinc finger URS1-binding protein YDR207C|CAR80|NIM2|RIM16 gene taxon:4932 20050513 SGD
+SGD S000002615 UME6 GO:0030437 SGD_REF:S000047047|PMID:8618927 IMP P C6 zinc finger URS1-binding protein YDR207C|CAR80|NIM2|RIM16 gene taxon:4932 20050513 SGD
+SGD S000002615 UME6 GO:0045836 SGD_REF:S000047047|PMID:8618927 IMP P C6 zinc finger URS1-binding protein YDR207C|CAR80|NIM2|RIM16 gene taxon:4932 20050513 SGD
+SGD S000000377 UMP1 GO:0005634 SGD_REF:S000069839|PMID:11922673 IDA C 20S proteasome maturation factor YBR173C gene taxon:4932 20041115 SGD
+SGD S000000377 UMP1 GO:0005737 SGD_REF:S000069839|PMID:11922673 IDA C 20S proteasome maturation factor YBR173C gene taxon:4932 20041115 SGD
+SGD S000000377 UMP1 GO:0008538 SGD_REF:S000041323|PMID:9491890 IMP F 20S proteasome maturation factor YBR173C gene taxon:4932 20020313 SGD
+SGD S000000377 UMP1 GO:0008538 SGD_REF:S000041323|PMID:9491890 IDA F 20S proteasome maturation factor YBR173C gene taxon:4932 20020313 SGD
+SGD S000000377 UMP1 GO:0006511 SGD_REF:S000041323|PMID:9491890 IMP P 20S proteasome maturation factor YBR173C gene taxon:4932 20041116 SGD
+SGD S000000377 UMP1 GO:0006974 SGD_REF:S000059223|PMID:10975253 IDA P 20S proteasome maturation factor YBR173C gene taxon:4932 20041116 SGD
+SGD S000000377 UMP1 GO:0006974 SGD_REF:S000059223|PMID:10975253 IEP P 20S proteasome maturation factor YBR173C gene taxon:4932 20041116 SGD
+SGD S000000377 UMP1 GO:0043248 SGD_REF:S000041323|PMID:9491890 IMP P 20S proteasome maturation factor YBR173C gene taxon:4932 20041115 SGD
+SGD S000004483 UNG1 GO:0005634 SGD_REF:S000069098|PMID:11812822 IDA C uracil DNA glycosylase YML021C gene taxon:4932 20021023 SGD
+SGD S000004483 UNG1 GO:0005739 SGD_REF:S000069098|PMID:11812822 IDA C uracil DNA glycosylase YML021C gene taxon:4932 20021023 SGD
+SGD S000004483 UNG1 GO:0004844 SGD_REF:S000048957|PMID:2644266 IDA F uracil DNA glycosylase YML021C gene taxon:4932 20021023 SGD
+SGD S000004483 UNG1 GO:0006281 SGD_REF:S000046772|PMID:1938887 IMP P uracil DNA glycosylase YML021C gene taxon:4932 20021023 SGD
+SGD S000002621 UPC2 GO:0005634 SGD_REF:S000066114|PMID:11533229 IPI C zinc finger transcription factor of the Zn(2)-Cys(6) binuclear cluster domain type YDR213W|MOX4 gene taxon:4932 20020918 SGD
+SGD S000002621 UPC2 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C zinc finger transcription factor of the Zn(2)-Cys(6) binuclear cluster domain type YDR213W|MOX4 gene taxon:4932 20020507 SGD
+SGD S000002621 UPC2 GO:0003702 SGD_REF:S000042754|PMID:9696767 ISS F zinc finger transcription factor of the Zn(2)-Cys(6) binuclear cluster domain type YDR213W|MOX4 gene taxon:4932 20010118 SGD
+SGD S000002621 UPC2 GO:0003702 SGD_REF:S000066114|PMID:11533229 IDA F zinc finger transcription factor of the Zn(2)-Cys(6) binuclear cluster domain type YDR213W|MOX4 gene taxon:4932 20020918 SGD
+SGD S000002621 UPC2 GO:0008202 SGD_REF:S000042754|PMID:9696767 IMP P zinc finger transcription factor of the Zn(2)-Cys(6) binuclear cluster domain type YDR213W|MOX4 gene taxon:4932 20010118 SGD
+SGD S000002621 UPC2 GO:0016126 SGD_REF:S000066114|PMID:11533229 IMP P zinc finger transcription factor of the Zn(2)-Cys(6) binuclear cluster domain type YDR213W|MOX4 gene taxon:4932 20020918 SGD
+SGD S000003304 UPF3 GO:0005634 SGD_REF:S000049319|PMID:9763508 IDA C YGR072W|SUA6 gene taxon:4932 20050301 SGD
+SGD S000003304 UPF3 GO:0005737 SGD_REF:S000059900|PMID:11238889 TAS C YGR072W|SUA6 gene taxon:4932 20020528 SGD
+SGD S000003304 UPF3 GO:0005844 SGD_REF:S000046443|PMID:9268361 IDA C YGR072W|SUA6 gene taxon:4932 20020528 SGD
+SGD S000003304 UPF3 GO:0005554 SGD_REF:S000069584 ND F YGR072W|SUA6 gene taxon:4932 20030108 SGD
+SGD S000003304 UPF3 GO:0000184 SGD_REF:S000049793|PMID:10098411 TAS P YGR072W|SUA6 gene taxon:4932 20020528 SGD
+SGD S000003304 UPF3 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P YGR072W|SUA6 gene taxon:4932 20060203 SGD
+SGD S000003304 UPF3 GO:0006402 SGD_REF:S000058753|PMID:9841679 TAS P YGR072W|SUA6 gene taxon:4932 20010124 SGD
+SGD S000003304 UPF3 NOT GO:0006452 SGD_REF:S000079922|PMID:15388879 IMP P YGR072W|SUA6 gene taxon:4932 20050301 SGD
+SGD S000001699 URA1 GO:0005737 SGD_REF:S000044017|PMID:1409592 IDA C dihydroorotate dehydrogenase YKL216W gene taxon:4932 20020208 SGD
+SGD S000001699 URA1 GO:0019898 SGD_REF:S000069514|PMID:11921093 IDA C dihydroorotate dehydrogenase YKL216W gene taxon:4932 20051216 SGD
+SGD S000001699 URA1 GO:0004152 SGD_REF:S000041097|PMID:1511880 IDA F dihydroorotate dehydrogenase YKL216W gene taxon:4932 20020208 SGD
+SGD S000001699 URA1 GO:0006207 SGD_REF:S000053452|PMID:2679804 TAS P dihydroorotate dehydrogenase YKL216W gene taxon:4932 20050614 SGD
+SGD S000004884 URA10 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C orotate phosphoribosyltransferase 2 YMR271C gene taxon:4932 20031028 SGD
+SGD S000004884 URA10 GO:0004588 SGD_REF:S000053452|PMID:2679804 TAS F orotate phosphoribosyltransferase 2 YMR271C gene taxon:4932 20020927 SGD
+SGD S000004884 URA10 GO:0006207 SGD_REF:S000053452|PMID:2679804 TAS P orotate phosphoribosyltransferase 2 YMR271C gene taxon:4932 20050614 SGD
+SGD S000003666 URA2 GO:0005737 SGD_REF:S000059391|PMID:11015727 IDA C aspartate transcarbamylase, carbamoyl phosphate synthetase (CPSase), glutamine amidotransferase YJL130C gene taxon:4932 20020208 SGD
+SGD S000003666 URA2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C aspartate transcarbamylase, carbamoyl phosphate synthetase (CPSase), glutamine amidotransferase YJL130C gene taxon:4932 20040813 SGD
+SGD S000003666 URA2 GO:0016021 SGD_REF:S000069514|PMID:11921093 IDA C aspartate transcarbamylase, carbamoyl phosphate synthetase (CPSase), glutamine amidotransferase YJL130C gene taxon:4932 20051216 SGD
+SGD S000003666 URA2 GO:0004070 SGD_REF:S000050154|PMID:10446140 IDA F aspartate transcarbamylase, carbamoyl phosphate synthetase (CPSase), glutamine amidotransferase YJL130C gene taxon:4932 20030121 SGD
+SGD S000003666 URA2 GO:0004088 SGD_REF:S000065636|PMID:5776390 IDA F aspartate transcarbamylase, carbamoyl phosphate synthetase (CPSase), glutamine amidotransferase YJL130C gene taxon:4932 20051216 SGD
+SGD S000003666 URA2 GO:0006207 SGD_REF:S000053452|PMID:2679804 TAS P aspartate transcarbamylase, carbamoyl phosphate synthetase (CPSase), glutamine amidotransferase YJL130C gene taxon:4932 20050614 SGD
+SGD S000003666 URA2 GO:0006541 SGD_REF:S000065623|PMID:5651325 IDA P aspartate transcarbamylase, carbamoyl phosphate synthetase (CPSase), glutamine amidotransferase YJL130C gene taxon:4932 20050615 SGD
+SGD S000003666 URA2 GO:0019856 SGD_REF:S000054034|PMID:181668 IDA P aspartate transcarbamylase, carbamoyl phosphate synthetase (CPSase), glutamine amidotransferase YJL130C gene taxon:4932 20020208 SGD
+SGD S000000747 URA3 GO:0005829 SGD_REF:S000086114|PMID:5010292 ISS C orotidine-5'-phosphate decarboxylase YEL021W gene taxon:4932 20050818 SGD
+SGD S000000747 URA3 GO:0004590 SGD_REF:S000046487|PMID:3311876 IDA F orotidine-5'-phosphate decarboxylase YEL021W gene taxon:4932 20030121 SGD
+SGD S000000747 URA3 GO:0006207 SGD_REF:S000053452|PMID:2679804 TAS P orotidine-5'-phosphate decarboxylase YEL021W gene taxon:4932 20050614 SGD
+SGD S000000747 URA3 GO:0019856 SGD_REF:S000056535|PMID:1499340 TAS P orotidine-5'-phosphate decarboxylase YEL021W gene taxon:4932 20020208 SGD
+SGD S000004412 URA4 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C dihydroorotase YLR420W gene taxon:4932 20031028 SGD
+SGD S000004412 URA4 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C dihydroorotase YLR420W gene taxon:4932 20031028 SGD
+SGD S000004412 URA4 GO:0004151 SGD_REF:S000049153|PMID:2897615 IMP F dihydroorotase YLR420W gene taxon:4932 20021114 SGD
+SGD S000004412 URA4 GO:0004151 SGD_REF:S000049153|PMID:2897615 ISS F dihydroorotase YLR420W gene taxon:4932 20021114 SGD
+SGD S000004412 URA4 GO:0006207 SGD_REF:S000053452|PMID:2679804 TAS P dihydroorotase YLR420W gene taxon:4932 20050614 SGD
+SGD S000004412 URA4 GO:0006221 SGD_REF:S000049153|PMID:2897615 IMP P dihydroorotase YLR420W gene taxon:4932 20021114 SGD
+SGD S000004574 URA5 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C orotate phosphoribosyltransferase 1 YML106W|PYR5 gene taxon:4932 20031028 SGD
+SGD S000004574 URA5 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C orotate phosphoribosyltransferase 1 YML106W|PYR5 gene taxon:4932 20020927 SGD
+SGD S000004574 URA5 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C orotate phosphoribosyltransferase 1 YML106W|PYR5 gene taxon:4932 20031028 SGD
+SGD S000004574 URA5 GO:0004588 SGD_REF:S000053452|PMID:2679804 TAS F orotate phosphoribosyltransferase 1 YML106W|PYR5 gene taxon:4932 20020927 SGD
+SGD S000004574 URA5 GO:0006207 SGD_REF:S000053452|PMID:2679804 TAS P orotate phosphoribosyltransferase 1 YML106W|PYR5 gene taxon:4932 20050614 SGD
+SGD S000001507 URA6 GO:0005634 SGD_REF:S000044310|PMID:8391780 IDA C uridine-monophosphate kinase (uridylate kinase) YKL024C|SOC8 gene taxon:4932 20010118 SGD
+SGD S000001507 URA6 GO:0005737 SGD_REF:S000044310|PMID:8391780 IDA C uridine-monophosphate kinase (uridylate kinase) YKL024C|SOC8 gene taxon:4932 20010118 SGD
+SGD S000001507 URA6 GO:0004849 SGD_REF:S000050748|PMID:2549068 IDA F uridine-monophosphate kinase (uridylate kinase) YKL024C|SOC8 gene taxon:4932 20010118 SGD
+SGD S000001507 URA6 GO:0004849 SGD_REF:S000048552|PMID:1655742 IDA F uridine-monophosphate kinase (uridylate kinase) YKL024C|SOC8 gene taxon:4932 20010118 SGD
+SGD S000001507 URA6 GO:0006139 SGD_REF:S000050748|PMID:2549068 IDA P uridine-monophosphate kinase (uridylate kinase) YKL024C|SOC8 gene taxon:4932 20010118 SGD
+SGD S000001507 URA6 GO:0006207 SGD_REF:S000044310|PMID:8391780 IDA P uridine-monophosphate kinase (uridylate kinase) YKL024C|SOC8 gene taxon:4932 20050616 SGD
+SGD S000000135 URA7 GO:0005829 SGD_REF:S000049478|PMID:9668079 TAS C CTP synthase YBL039C gene taxon:4932 20020927 SGD
+SGD S000000135 URA7 GO:0003883 SGD_REF:S000051954|PMID:1753946 ISS F CTP synthase YBL039C gene taxon:4932 20020927 SGD
+SGD S000000135 URA7 GO:0003883 SGD_REF:S000041184|PMID:8075080 IDA F CTP synthase YBL039C gene taxon:4932 20060123 SGD
+SGD S000000135 URA7 GO:0003883 SGD_REF:S000051954|PMID:1753946 IMP F CTP synthase YBL039C gene taxon:4932 20020927 SGD
+SGD S000000135 URA7 GO:0006241 SGD_REF:S000057492|PMID:7797479 TAS P CTP synthase YBL039C gene taxon:4932 20030625 SGD
+SGD S000000135 URA7 GO:0006241 SGD_REF:S000041184|PMID:8075080 IDA P CTP synthase YBL039C gene taxon:4932 20060123 SGD
+SGD S000000135 URA7 GO:0008654 SGD_REF:S000049478|PMID:9668079 IMP P CTP synthase YBL039C gene taxon:4932 20060123 SGD
+SGD S000000135 URA7 GO:0019856 SGD_REF:S000051954|PMID:1753946 IMP P CTP synthase YBL039C gene taxon:4932 20060123 SGD
+SGD S000003864 URA8 GO:0005829 SGD_REF:S000049478|PMID:9668079 TAS C CTP synthase YJR103W gene taxon:4932 20020927 SGD
+SGD S000003864 URA8 GO:0003883 SGD_REF:S000042459|PMID:8121398 IGI F CTP synthase YJR103W gene taxon:4932 20020927 SGD
+SGD S000003864 URA8 GO:0003883 SGD_REF:S000042459|PMID:8121398 ISS F CTP synthase YJR103W gene taxon:4932 20020927 SGD
+SGD S000003864 URA8 GO:0003883 SGD_REF:S000046523|PMID:7559626 IDA F CTP synthase YJR103W gene taxon:4932 20060123 SGD
+SGD S000003864 URA8 GO:0003883 SGD_REF:S000042459|PMID:8121398 IMP F CTP synthase YJR103W gene taxon:4932 20020927 SGD
+SGD S000003864 URA8 GO:0006241 SGD_REF:S000046523|PMID:7559626 IDA P CTP synthase YJR103W gene taxon:4932 20060123 SGD
+SGD S000003864 URA8 GO:0008654 SGD_REF:S000049478|PMID:9668079 TAS P CTP synthase YJR103W gene taxon:4932 20020927 SGD
+SGD S000003864 URA8 GO:0019856 SGD_REF:S000042459|PMID:8121398 TAS P CTP synthase YJR103W gene taxon:4932 20020927 SGD
+SGD S000003864 URA8 GO:0019856 SGD_REF:S000046523|PMID:7559626 IMP P CTP synthase YJR103W gene taxon:4932 20060123 SGD
+SGD S000001497 URB1 GO:0005730 SGD_REF:S000074185|PMID:14562095 IDA C YKL014C|NPA1 gene taxon:4932 20031028 SGD
+SGD S000001497 URB1 GO:0005730 SGD_REF:S000076599|PMID:15208443 IDA C YKL014C|NPA1 gene taxon:4932 20040713 SGD
+SGD S000001497 URB1 GO:0005554 SGD_REF:S000069584 ND F YKL014C|NPA1 gene taxon:4932 20021126 SGD
+SGD S000001497 URB1 GO:0006364 SGD_REF:S000076598|PMID:15242642 IMP P YKL014C|NPA1 gene taxon:4932 20040713 SGD
+SGD S000001497 URB1 GO:0030489 SGD_REF:S000076599|PMID:15208443 IMP P YKL014C|NPA1 gene taxon:4932 20040713 SGD
+SGD S000001497 URB1 GO:0030489 SGD_REF:S000076599|PMID:15208443 IGI SGD:S000004211 P YKL014C|NPA1 gene taxon:4932 20040713 SGD
+SGD S000003802 URB2 GO:0005730 SGD_REF:S000074185|PMID:14562095 IDA C YJR041C|NPA2 gene taxon:4932 20031028 SGD
+SGD S000003802 URB2 GO:0005730 SGD_REF:S000076600|PMID:15226434 IDA C YJR041C|NPA2 gene taxon:4932 20040713 SGD
+SGD S000003802 URB2 GO:0005554 SGD_REF:S000069584 ND F YJR041C|NPA2 gene taxon:4932 20030425 SGD
+SGD S000003802 URB2 GO:0007046 SGD_REF:S000076600|PMID:15226434 IPI SGD:S000001497 P YJR041C|NPA2 gene taxon:4932 20040713 SGD
+SGD S000003802 URB2 GO:0016072 SGD_REF:S000076598|PMID:15242642 IMP P YJR041C|NPA2 gene taxon:4932 20040714 SGD
+SGD S000005173 URE2 GO:0005625 SGD_REF:S000046423|PMID:10224139 IDA C prion, transcriptional regulator YNL229C|[URE3] gene taxon:4932 20010223 SGD
+SGD S000005173 URE2 GO:0005829 SGD_REF:S000052173|PMID:10748041 IDA C prion, transcriptional regulator YNL229C|[URE3] gene taxon:4932 20050926 SGD
+SGD S000005173 URE2 GO:0003714 SGD_REF:S000043452|PMID:8755910 IPI F prion, transcriptional regulator YNL229C|[URE3] gene taxon:4932 20010223 SGD
+SGD S000005173 URE2 GO:0003714 SGD_REF:S000043452|PMID:8755910 IGI F prion, transcriptional regulator YNL229C|[URE3] gene taxon:4932 20010223 SGD
+SGD S000005173 URE2 GO:0051219 SGD_REF:S000046200|PMID:10604478 IDA F prion, transcriptional regulator YNL229C|[URE3] gene taxon:4932 20050926 SGD
+SGD S000005173 URE2 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P prion, transcriptional regulator YNL229C|[URE3] gene taxon:4932 20060227 SGD
+SGD S000005173 URE2 GO:0006808 SGD_REF:S000043452|PMID:8755910 IPI P prion, transcriptional regulator YNL229C|[URE3] gene taxon:4932 20010223 SGD
+SGD S000005173 URE2 GO:0006808 SGD_REF:S000043452|PMID:8755910 IGI P prion, transcriptional regulator YNL229C|[URE3] gene taxon:4932 20010223 SGD
+SGD S000005173 URE2 GO:0006808 SGD_REF:S000050476|PMID:8002570 IMP P prion, transcriptional regulator YNL229C|[URE3] gene taxon:4932 20010223 SGD
+SGD S000005173 URE2 GO:0010044 SGD_REF:S000058960|PMID:15133656 IMP P prion, transcriptional regulator YNL229C|[URE3] gene taxon:4932 20040714 SGD
+SGD S000005173 URE2 GO:0042994 SGD_REF:S000052173|PMID:10748041 IMP P prion, transcriptional regulator YNL229C|[URE3] gene taxon:4932 20050926 SGD
+SGD S000002808 URH1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C uridine nucleosidase (uridine ribohydrolase); EC 3.2.2.3 YDR400W gene taxon:4932 20031028 SGD
+SGD S000002808 URH1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C uridine nucleosidase (uridine ribohydrolase); EC 3.2.2.3 YDR400W gene taxon:4932 20031028 SGD
+SGD S000002808 URH1 GO:0050263 SGD_REF:S000069484|PMID:11872485 IDA F uridine nucleosidase (uridine ribohydrolase); EC 3.2.2.3 YDR400W gene taxon:4932 20051130 SGD
+SGD S000002808 URH1 GO:0050263 SGD_REF:S000070131|PMID:12111094 IDA F uridine nucleosidase (uridine ribohydrolase); EC 3.2.2.3 YDR400W gene taxon:4932 20051130 SGD
+SGD S000002808 URH1 GO:0008655 SGD_REF:S000069484|PMID:11872485 IMP P uridine nucleosidase (uridine ribohydrolase); EC 3.2.2.3 YDR400W gene taxon:4932 20020617 SGD
+SGD S000002808 URH1 GO:0030433 SGD_REF:S000115312|PMID:12711700 IMP P uridine nucleosidase (uridine ribohydrolase); EC 3.2.2.3 YDR400W gene taxon:4932 20060511 SGD
+SGD S000002808 URH1 GO:0046135 SGD_REF:S000070131|PMID:12111094 IDA P uridine nucleosidase (uridine ribohydrolase); EC 3.2.2.3 YDR400W gene taxon:4932 20051130 SGD
+SGD S000002808 URH1 GO:0046135 SGD_REF:S000069484|PMID:11872485 IDA P uridine nucleosidase (uridine ribohydrolase); EC 3.2.2.3 YDR400W gene taxon:4932 20051130 SGD
+SGD S000005295 URK1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C uridine kinase YNR012W gene taxon:4932 20031028 SGD
+SGD S000005295 URK1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C uridine kinase YNR012W gene taxon:4932 20031028 SGD
+SGD S000005295 URK1 GO:0004849 SGD_REF:S000055858|PMID:10501935 IMP F uridine kinase YNR012W gene taxon:4932 20020927 SGD
+SGD S000005295 URK1 GO:0008655 SGD_REF:S000069484|PMID:11872485 IGI P uridine kinase YNR012W gene taxon:4932 20020927 SGD
+SGD S000005295 URK1 GO:0008655 SGD_REF:S000069484|PMID:11872485 IMP P uridine kinase YNR012W gene taxon:4932 20020927 SGD
+SGD S000001270 URM1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C ubiquitin-like protein YIL008W gene taxon:4932 20031028 SGD
+SGD S000001270 URM1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C ubiquitin-like protein YIL008W gene taxon:4932 20031028 SGD
+SGD S000001270 URM1 GO:0005737 SGD_REF:S000075061|PMID:14551258 IDA C ubiquitin-like protein YIL008W gene taxon:4932 20051021 SGD
+SGD S000001270 URM1 GO:0031386 SGD_REF:S000075061|PMID:14551258 IDA F ubiquitin-like protein YIL008W gene taxon:4932 20050525 SGD
+SGD S000001270 URM1 GO:0031386 SGD_REF:S000075061|PMID:14551258 IMP F ubiquitin-like protein YIL008W gene taxon:4932 20050525 SGD
+SGD S000001270 URM1 GO:0031386 SGD_REF:S000051101|PMID:10713047 IDA F ubiquitin-like protein YIL008W gene taxon:4932 20051021 SGD
+SGD S000001270 URM1 GO:0001403 SGD_REF:S000075061|PMID:14551258 IGI SGD:S000000999 P ubiquitin-like protein YIL008W gene taxon:4932 20051021 SGD
+SGD S000001270 URM1 GO:0001403 SGD_REF:S000075061|PMID:14551258 IMP P ubiquitin-like protein YIL008W gene taxon:4932 20051021 SGD
+SGD S000001270 URM1 GO:0006464 SGD_REF:S000051101|PMID:10713047 IDA P ubiquitin-like protein YIL008W gene taxon:4932 20010801 SGD
+SGD S000001270 URM1 GO:0006979 SGD_REF:S000074238|PMID:14555475 IMP P ubiquitin-like protein YIL008W gene taxon:4932 20051021 SGD
+SGD S000001270 URM1 GO:0007114 SGD_REF:S000075061|PMID:14551258 IGI SGD:S000005242 P ubiquitin-like protein YIL008W gene taxon:4932 20051021 SGD
+SGD S000006356 URN1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C pre-mRNA splicing factor YPR152C gene taxon:4932 20031028 SGD
+SGD S000006356 URN1 GO:0005554 SGD_REF:S000069584 ND F pre-mRNA splicing factor YPR152C gene taxon:4932 20030203 SGD
+SGD S000006356 URN1 GO:0000004 SGD_REF:S000069584 ND P pre-mRNA splicing factor YPR152C gene taxon:4932 20030203 SGD
+SGD S000029631 URR1 GO:0008372 SGD_REF:S000069584 ND C transcriptional repressor gene taxon:4932 20020522 SGD
+SGD S000029631 URR1 GO:0005554 SGD_REF:S000069584 ND F transcriptional repressor gene taxon:4932 20020522 SGD
+SGD S000029631 URR1 GO:0006355 SGD_REF:S000048176|PMID:1541392 IGI P transcriptional repressor gene taxon:4932 20020522 SGD
+SGD S000029632 URR3 GO:0008372 SGD_REF:S000069584 ND C transcriptional repressor gene taxon:4932 20020522 SGD
+SGD S000029632 URR3 GO:0005554 SGD_REF:S000069584 ND F transcriptional repressor gene taxon:4932 20020522 SGD
+SGD S000029632 URR3 GO:0006355 SGD_REF:S000048176|PMID:1541392 IGI P transcriptional repressor gene taxon:4932 20020522 SGD
+SGD S000029633 URR4 GO:0008372 SGD_REF:S000069584 ND C transcriptional repressor gene taxon:4932 20020522 SGD
+SGD S000029633 URR4 GO:0005554 SGD_REF:S000069584 ND F transcriptional repressor gene taxon:4932 20020522 SGD
+SGD S000029633 URR4 GO:0006355 SGD_REF:S000048176|PMID:1541392 IGI P transcriptional repressor gene taxon:4932 20020522 SGD
+SGD S000004491 USA1 GO:0008372 SGD_REF:S000069584 ND C pre-mRNA splicing factor (putative) YML029W gene taxon:4932 20010629 SGD
+SGD S000004491 USA1 GO:0005554 SGD_REF:S000069584 ND F pre-mRNA splicing factor (putative) YML029W gene taxon:4932 20030108 SGD
+SGD S000004491 USA1 GO:0000398 SGD_REF:S000069169|PMID:11425851 IPI P pre-mRNA splicing factor (putative) YML029W gene taxon:4932 20040610 SGD
+SGD S000003066 USE1 GO:0005783 SGD_REF:S000073644|PMID:12853481 IDA C YGL098W|SLT1 gene taxon:4932 20030717 SGD
+SGD S000003066 USE1 GO:0005484 SGD_REF:S000073644|PMID:12853481 IGI F YGL098W|SLT1 gene taxon:4932 20030717 SGD
+SGD S000003066 USE1 GO:0005484 SGD_REF:S000073644|PMID:12853481 ISS F YGL098W|SLT1 gene taxon:4932 20030717 SGD
+SGD S000003066 USE1 GO:0005484 SGD_REF:S000073644|PMID:12853481 IPI F YGL098W|SLT1 gene taxon:4932 20030717 SGD
+SGD S000003066 USE1 GO:0006888 SGD_REF:S000076242|PMID:12911815 IMP P YGL098W|SLT1 gene taxon:4932 20050712 SGD
+SGD S000003066 USE1 GO:0006890 SGD_REF:S000073644|PMID:12853481 IGI P YGL098W|SLT1 gene taxon:4932 20030717 SGD
+SGD S000003066 USE1 GO:0006890 SGD_REF:S000073644|PMID:12853481 IMP P YGL098W|SLT1 gene taxon:4932 20030717 SGD
+SGD S000002216 USO1 GO:0005625 SGD_REF:S000048978|PMID:8166741 IDA C integrin analogue gene YDL058W|INT1 gene taxon:4932 20020731 SGD
+SGD S000002216 USO1 GO:0005554 SGD_REF:S000069584 ND F integrin analogue gene YDL058W|INT1 gene taxon:4932 20021112 SGD
+SGD S000002216 USO1 GO:0006461 SGD_REF:S000052788|PMID:8603910 IDA P integrin analogue gene YDL058W|INT1 gene taxon:4932 20020731 SGD
+SGD S000002216 USO1 GO:0006888 SGD_REF:S000052582|PMID:2010462 IMP P integrin analogue gene YDL058W|INT1 gene taxon:4932 20020731 SGD
+SGD S000001750 UTH1 GO:0005741 SGD_REF:S000069559|PMID:11958935 TAS C YKR042W gene taxon:4932 20020721 SGD
+SGD S000001750 UTH1 GO:0009277 SGD_REF:S000069559|PMID:11958935 IDA C YKR042W gene taxon:4932 20020721 SGD
+SGD S000001750 UTH1 GO:0005554 SGD_REF:S000069584 ND F YKR042W gene taxon:4932 20030108 SGD
+SGD S000001750 UTH1 GO:0001308 SGD_REF:S000074467|PMID:12966141 TAS P YKR042W gene taxon:4932 20050323 SGD
+SGD S000001750 UTH1 GO:0007005 SGD_REF:S000069559|PMID:11958935 TAS P YKR042W gene taxon:4932 20020721 SGD
+SGD S000003645 UTP10 GO:0005732 SGD_REF:S000070145|PMID:12068309 IPI C U3 snoRNP protein YJL109C gene taxon:4932 20030224 SGD
+SGD S000003645 UTP10 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C U3 snoRNP protein YJL109C gene taxon:4932 20040928 SGD
+SGD S000003645 UTP10 GO:0030515 SGD_REF:S000070145|PMID:12068309 IPI F U3 snoRNP protein YJL109C gene taxon:4932 20030224 SGD
+SGD S000003645 UTP10 GO:0030490 SGD_REF:S000070145|PMID:12068309 IMP P U3 snoRNP protein YJL109C gene taxon:4932 20020906 SGD
+SGD S000003645 UTP10 GO:0030490 SGD_REF:S000070145|PMID:12068309 IPI P U3 snoRNP protein YJL109C gene taxon:4932 20020906 SGD
+SGD S000001582 UTP11 GO:0005732 SGD_REF:S000070145|PMID:12068309 IPI C U3 snoRNP protein YKL099C gene taxon:4932 20030224 SGD
+SGD S000001582 UTP11 GO:0030515 SGD_REF:S000070145|PMID:12068309 IPI F U3 snoRNP protein YKL099C gene taxon:4932 20030224 SGD
+SGD S000001582 UTP11 GO:0030490 SGD_REF:S000070145|PMID:12068309 IMP P U3 snoRNP protein YKL099C gene taxon:4932 20020906 SGD
+SGD S000001582 UTP11 GO:0030490 SGD_REF:S000070145|PMID:12068309 IPI P U3 snoRNP protein YKL099C gene taxon:4932 20020906 SGD
+SGD S000004212 UTP13 GO:0005732 SGD_REF:S000070145|PMID:12068309 IPI C U3 snoRNP protein YLR222C gene taxon:4932 20030224 SGD
+SGD S000004212 UTP13 GO:0030515 SGD_REF:S000070145|PMID:12068309 IPI F U3 snoRNP protein YLR222C gene taxon:4932 20030224 SGD
+SGD S000004212 UTP13 GO:0030490 SGD_REF:S000070145|PMID:12068309 IMP P U3 snoRNP protein YLR222C gene taxon:4932 20020906 SGD
+SGD S000004212 UTP13 GO:0030490 SGD_REF:S000070145|PMID:12068309 IPI P U3 snoRNP protein YLR222C gene taxon:4932 20020906 SGD
+SGD S000004558 UTP14 GO:0005732 SGD_REF:S000070145|PMID:12068309 IPI C U3 snoRNP protein YML093W gene taxon:4932 20030224 SGD
+SGD S000004558 UTP14 GO:0030515 SGD_REF:S000070145|PMID:12068309 IPI F U3 snoRNP protein YML093W gene taxon:4932 20030224 SGD
+SGD S000004558 UTP14 GO:0030490 SGD_REF:S000070145|PMID:12068309 IMP P U3 snoRNP protein YML093W gene taxon:4932 20020906 SGD
+SGD S000004558 UTP14 GO:0030490 SGD_REF:S000070145|PMID:12068309 IPI P U3 snoRNP protein YML093W gene taxon:4932 20020906 SGD
+SGD S000004699 UTP15 GO:0005732 SGD_REF:S000070145|PMID:12068309 IPI C U3 snoRNP protein YMR093W gene taxon:4932 20030224 SGD
+SGD S000004699 UTP15 GO:0030515 SGD_REF:S000070145|PMID:12068309 IPI F U3 snoRNP protein YMR093W gene taxon:4932 20030224 SGD
+SGD S000004699 UTP15 GO:0030490 SGD_REF:S000070145|PMID:12068309 IMP P U3 snoRNP protein YMR093W gene taxon:4932 20020906 SGD
+SGD S000004699 UTP15 GO:0030490 SGD_REF:S000070145|PMID:12068309 IPI P U3 snoRNP protein YMR093W gene taxon:4932 20020906 SGD
+SGD S000003605 UTP18 GO:0005730 SGD_REF:S000074185|PMID:14562095 IDA C U3 snoRNA associated protein, U3 snoRNP protein YJL069C gene taxon:4932 20031028 SGD
+SGD S000003605 UTP18 GO:0005730 SGD_REF:S000079989|PMID:15590835 IDA C U3 snoRNA associated protein, U3 snoRNP protein YJL069C gene taxon:4932 20060315 SGD
+SGD S000003605 UTP18 GO:0005732 SGD_REF:S000079989|PMID:15590835 IPI SGD:S000003762|SGD:S000007294|SGD:S000007441 C U3 snoRNA associated protein, U3 snoRNP protein YJL069C gene taxon:4932 20050518 SGD
+SGD S000003605 UTP18 GO:0005554 SGD_REF:S000069584 ND F U3 snoRNA associated protein, U3 snoRNP protein YJL069C gene taxon:4932 20050516 SGD
+SGD S000003605 UTP18 GO:0006365 SGD_REF:S000079989|PMID:15590835 IMP P U3 snoRNA associated protein, U3 snoRNP protein YJL069C gene taxon:4932 20050516 SGD
+SGD S000003605 UTP18 GO:0006365 SGD_REF:S000079989|PMID:15590835 IPI SGD:S000003762|SGD:S000007294|SGD:S000007441 P U3 snoRNA associated protein, U3 snoRNP protein YJL069C gene taxon:4932 20050516 SGD
+SGD S000000100 UTP20 GO:0005730 SGD_REF:S000074185|PMID:14562095 IDA C U3 snoRNP protein YBL004W gene taxon:4932 20031028 SGD
+SGD S000000100 UTP20 GO:0005730 SGD_REF:S000079989|PMID:15590835 IDA C U3 snoRNP protein YBL004W gene taxon:4932 20060315 SGD
+SGD S000000100 UTP20 GO:0005732 SGD_REF:S000079989|PMID:15590835 IPI SGD:S000003762 C U3 snoRNP protein YBL004W gene taxon:4932 20050124 SGD
+SGD S000000100 UTP20 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C U3 snoRNP protein YBL004W gene taxon:4932 20031028 SGD
+SGD S000000100 UTP20 GO:0030515 SGD_REF:S000074191|PMID:14566057 RCA F U3 snoRNP protein YBL004W gene taxon:4932 20050608 SGD
+SGD S000000100 UTP20 GO:0006365 SGD_REF:S000079989|PMID:15590835 IMP P U3 snoRNP protein YBL004W gene taxon:4932 20050518 SGD
+SGD S000000100 UTP20 GO:0006365 SGD_REF:S000079989|PMID:15590835 IPI SGD:S000003762|SGD:S000007294|SGD:S000007441 P U3 snoRNP protein YBL004W gene taxon:4932 20050518 SGD
+SGD S000004401 UTP21 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C U3 snoRNP protein YLR409C gene taxon:4932 20031028 SGD
+SGD S000004401 UTP21 GO:0005730 SGD_REF:S000079989|PMID:15590835 IDA C U3 snoRNP protein YLR409C gene taxon:4932 20060315 SGD
+SGD S000004401 UTP21 GO:0005732 SGD_REF:S000079989|PMID:15590835 IPI SGD:S000003762 C U3 snoRNP protein YLR409C gene taxon:4932 20050124 SGD
+SGD S000004401 UTP21 GO:0030515 SGD_REF:S000074191|PMID:14566057 RCA F U3 snoRNP protein YLR409C gene taxon:4932 20050608 SGD
+SGD S000004401 UTP21 GO:0006365 SGD_REF:S000079989|PMID:15590835 IPI SGD:S000003762|SGD:S000007294|SGD:S000007441 P U3 snoRNP protein YLR409C gene taxon:4932 20050518 SGD
+SGD S000004401 UTP21 GO:0006365 SGD_REF:S000074191|PMID:14566057 RCA P U3 snoRNP protein YLR409C gene taxon:4932 20050608 SGD
+SGD S000003322 UTP22 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YGR090W gene taxon:4932 20031028 SGD
+SGD S000003322 UTP22 GO:0005730 SGD_REF:S000074185|PMID:14562095 IDA C YGR090W gene taxon:4932 20031028 SGD
+SGD S000003322 UTP22 GO:0005730 SGD_REF:S000079989|PMID:15590835 IDA C YGR090W gene taxon:4932 20060315 SGD
+SGD S000003322 UTP22 GO:0005732 SGD_REF:S000079989|PMID:15590835 IPI SGD:S000003762 C YGR090W gene taxon:4932 20050124 SGD
+SGD S000003322 UTP22 GO:0030515 SGD_REF:S000074191|PMID:14566057 RCA F YGR090W gene taxon:4932 20050608 SGD
+SGD S000003322 UTP22 GO:0006365 SGD_REF:S000073750|PMID:12837249 IMP P YGR090W gene taxon:4932 20050518 SGD
+SGD S000003322 UTP22 GO:0006365 SGD_REF:S000079989|PMID:15590835 IPI SGD:S000003762|SGD:S000007441|SGD:S000007294 P YGR090W gene taxon:4932 20050518 SGD
+SGD S000005530 UTP23 GO:0005730 SGD_REF:S000075214|PMID:14690591 IDA C SSU processome protein YOR004W gene taxon:4932 20040105 SGD
+SGD S000005530 UTP23 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C SSU processome protein YOR004W gene taxon:4932 20031028 SGD
+SGD S000005530 UTP23 GO:0005554 SGD_REF:S000069584 ND F SSU processome protein YOR004W gene taxon:4932 20030429 SGD
+SGD S000005530 UTP23 GO:0006364 SGD_REF:S000073209|PMID:12089522 IMP P SSU processome protein YOR004W gene taxon:4932 20030530 SGD
+SGD S000005530 UTP23 GO:0030490 SGD_REF:S000073750|PMID:12837249 IMP P SSU processome protein YOR004W gene taxon:4932 20030805 SGD
+SGD S000001768 UTP30 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YKR060W gene taxon:4932 20031028 SGD
+SGD S000001768 UTP30 GO:0005730 SGD_REF:S000074185|PMID:14562095 IDA C YKR060W gene taxon:4932 20031028 SGD
+SGD S000001768 UTP30 GO:0005554 SGD_REF:S000069584 ND F YKR060W gene taxon:4932 20060317 SGD
+SGD S000001768 UTP30 GO:0006365 SGD_REF:S000074191|PMID:14566057 RCA P YKR060W gene taxon:4932 20050608 SGD
+SGD S000002732 UTP4 GO:0005732 SGD_REF:S000070145|PMID:12068309 IPI C U3 snoRNP protein YDR324C gene taxon:4932 20030224 SGD
+SGD S000002732 UTP4 GO:0030515 SGD_REF:S000070145|PMID:12068309 IPI F U3 snoRNP protein YDR324C gene taxon:4932 20030224 SGD
+SGD S000002732 UTP4 GO:0030490 SGD_REF:S000070145|PMID:12068309 IMP P U3 snoRNP protein YDR324C gene taxon:4932 20020906 SGD
+SGD S000002732 UTP4 GO:0030490 SGD_REF:S000070145|PMID:12068309 IPI P U3 snoRNP protein YDR324C gene taxon:4932 20020906 SGD
+SGD S000002806 UTP5 GO:0005732 SGD_REF:S000070145|PMID:12068309 IPI C U3 snoRNP protein YDR398W gene taxon:4932 20030224 SGD
+SGD S000002806 UTP5 GO:0030515 SGD_REF:S000070145|PMID:12068309 IPI F U3 snoRNP protein YDR398W gene taxon:4932 20030224 SGD
+SGD S000002806 UTP5 GO:0030490 SGD_REF:S000070145|PMID:12068309 IMP P U3 snoRNP protein YDR398W gene taxon:4932 20020906 SGD
+SGD S000002806 UTP5 GO:0030490 SGD_REF:S000070145|PMID:12068309 IPI P U3 snoRNP protein YDR398W gene taxon:4932 20020906 SGD
+SGD S000002857 UTP6 GO:0005732 SGD_REF:S000070145|PMID:12068309 IPI C U3 snoRNP protein YDR449C gene taxon:4932 20030224 SGD
+SGD S000002857 UTP6 GO:0030515 SGD_REF:S000070145|PMID:12068309 IPI F U3 snoRNP protein YDR449C gene taxon:4932 20030224 SGD
+SGD S000002857 UTP6 GO:0030490 SGD_REF:S000070145|PMID:12068309 IMP P U3 snoRNP protein YDR449C gene taxon:4932 20020906 SGD
+SGD S000002857 UTP6 GO:0030490 SGD_REF:S000070145|PMID:12068309 IPI P U3 snoRNP protein YDR449C gene taxon:4932 20020906 SGD
+SGD S000000884 UTP7 GO:0005732 SGD_REF:S000070145|PMID:12068309 IPI C U3 snoRNP protein YER082C|KRE31 gene taxon:4932 20030224 SGD
+SGD S000000884 UTP7 GO:0030515 SGD_REF:S000070145|PMID:12068309 IPI F U3 snoRNP protein YER082C|KRE31 gene taxon:4932 20030224 SGD
+SGD S000000884 UTP7 GO:0006364 SGD_REF:S000070145|PMID:12068309 IMP P U3 snoRNP protein YER082C|KRE31 gene taxon:4932 20050518 SGD
+SGD S000000884 UTP7 GO:0006364 SGD_REF:S000070145|PMID:12068309 IPI P U3 snoRNP protein YER082C|KRE31 gene taxon:4932 20050518 SGD
+SGD S000000884 UTP7 GO:0006365 SGD_REF:S000079989|PMID:15590835 IMP P U3 snoRNP protein YER082C|KRE31 gene taxon:4932 20060315 SGD
+SGD S000003360 UTP8 GO:0005732 SGD_REF:S000070145|PMID:12068309 IPI C U3 snoRNP protein YGR128C gene taxon:4932 20030224 SGD
+SGD S000003360 UTP8 GO:0030515 SGD_REF:S000070145|PMID:12068309 IPI F U3 snoRNP protein YGR128C gene taxon:4932 20030224 SGD
+SGD S000003360 UTP8 GO:0030490 SGD_REF:S000070145|PMID:12068309 IMP P U3 snoRNP protein YGR128C gene taxon:4932 20020906 SGD
+SGD S000003360 UTP8 GO:0030490 SGD_REF:S000070145|PMID:12068309 IPI P U3 snoRNP protein YGR128C gene taxon:4932 20020906 SGD
+SGD S000001239 UTP9 GO:0005634 SGD_REF:S000069459|PMID:11914276 IDA C U3 snoRNP protein YHR196W gene taxon:4932 20020507 SGD
+SGD S000001239 UTP9 GO:0005730 SGD_REF:S000069459|PMID:11914276 IDA C U3 snoRNP protein YHR196W gene taxon:4932 20020507 SGD
+SGD S000001239 UTP9 GO:0005732 SGD_REF:S000070145|PMID:12068309 IPI C U3 snoRNP protein YHR196W gene taxon:4932 20030224 SGD
+SGD S000001239 UTP9 GO:0030515 SGD_REF:S000070145|PMID:12068309 IPI F U3 snoRNP protein YHR196W gene taxon:4932 20030224 SGD
+SGD S000001239 UTP9 GO:0030490 SGD_REF:S000070145|PMID:12068309 IMP P U3 snoRNP protein YHR196W gene taxon:4932 20020906 SGD
+SGD S000001239 UTP9 GO:0030490 SGD_REF:S000070145|PMID:12068309 IPI P U3 snoRNP protein YHR196W gene taxon:4932 20020906 SGD
+SGD S000003810 UTR1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YJR049C gene taxon:4932 20031028 SGD
+SGD S000003810 UTR1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YJR049C gene taxon:4932 20031028 SGD
+SGD S000003810 UTR1 GO:0003951 SGD_REF:S000060758|PMID:11425472 IDA F YJR049C gene taxon:4932 20021008 SGD
+SGD S000003810 UTR1 GO:0042736 SGD_REF:S000086067|PMID:15978040 IDA F YJR049C gene taxon:4932 20060301 SGD
+SGD S000003810 UTR1 GO:0006741 SGD_REF:S000060758|PMID:11425472 IDA P YJR049C gene taxon:4932 20060301 SGD
+SGD S000003810 UTR1 GO:0006741 SGD_REF:S000086067|PMID:15978040 IDA P YJR049C gene taxon:4932 20060301 SGD
+SGD S000003810 UTR1 GO:0006879 SGD_REF:S000053127|PMID:8662826 IGI P YJR049C gene taxon:4932 20021008 SGD
+SGD S000000766 UTR2 GO:0000144 SGD_REF:S000069993|PMID:12045225 IDA C YEL040W|CRH2 gene taxon:4932 20020723 SGD
+SGD S000000766 UTR2 GO:0009277 SGD_REF:S000040179|PMID:10383953 IDA C YEL040W|CRH2 gene taxon:4932 20020617 SGD
+SGD S000000766 UTR2 GO:0009277 SGD_REF:S000081097|PMID:15781460 IDA C YEL040W|CRH2 gene taxon:4932 20050601 SGD
+SGD S000000766 UTR2 GO:0005554 SGD_REF:S000069584 ND F YEL040W|CRH2 gene taxon:4932 20021201 SGD
+SGD S000000766 UTR2 GO:0007047 SGD_REF:S000069993|PMID:12045225 TAS P YEL040W|CRH2 gene taxon:4932 20020723 SGD
+SGD S000000764 UTR4 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YEL038W gene taxon:4932 20031028 SGD
+SGD S000000764 UTR4 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YEL038W gene taxon:4932 20031028 SGD
+SGD S000000764 UTR4 GO:0005554 SGD_REF:S000069584 ND F YEL038W gene taxon:4932 20021030 SGD
+SGD S000000764 UTR4 GO:0000004 SGD_REF:S000069584 ND P YEL038W gene taxon:4932 20021030 SGD
+SGD S000000761 UTR5 GO:0008372 SGD_REF:S000069584 ND C YEL035C gene taxon:4932 20021007 SGD
+SGD S000000761 UTR5 GO:0005554 SGD_REF:S000069584 ND F YEL035C gene taxon:4932 20021007 SGD
+SGD S000000761 UTR5 GO:0000004 SGD_REF:S000069584 ND P YEL035C gene taxon:4932 20021007 SGD
+SGD S000000731 VAB2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YEL005C|VAB31 gene taxon:4932 20031028 SGD
+SGD S000000731 VAB2 GO:0005515 SGD_REF:S000039257|PMID:10888680 IPI F YEL005C|VAB31 gene taxon:4932 20020927 SGD
+SGD S000000731 VAB2 GO:0000004 SGD_REF:S000069584 ND P YEL005C|VAB31 gene taxon:4932 20020927 SGD
+SGD S000004378 VAC14 GO:0000329 SGD_REF:S000074437|PMID:14528018 IDA C Activator of Fab1p YLR386W gene taxon:4932 20041004 SGD
+SGD S000004378 VAC14 GO:0005773 SGD_REF:S000069781|PMID:11889142 IDA C Activator of Fab1p YLR386W gene taxon:4932 20021031 SGD
+SGD S000004378 VAC14 GO:0008047 SGD_REF:S000069781|PMID:11889142 IMP F Activator of Fab1p YLR386W gene taxon:4932 20021031 SGD
+SGD S000004378 VAC14 GO:0000011 SGD_REF:S000048576|PMID:9372916 IMP P Activator of Fab1p YLR386W gene taxon:4932 20020312 SGD
+SGD S000004378 VAC14 GO:0006644 SGD_REF:S000048576|PMID:9372916 IMP P Activator of Fab1p YLR386W gene taxon:4932 20020312 SGD
+SGD S000004378 VAC14 GO:0006644 SGD_REF:S000048576|PMID:9372916 IGI P Activator of Fab1p YLR386W gene taxon:4932 20020312 SGD
+SGD S000000568 VAC17 GO:0005774 SGD_REF:S000072665|PMID:12594460 IDA C the vacuole-specific receptor of Myo2p, a class V myosin YCL063W gene taxon:4932 20030307 SGD
+SGD S000000568 VAC17 GO:0004872 SGD_REF:S000072781|PMID:12642614 IPI F the vacuole-specific receptor of Myo2p, a class V myosin YCL063W gene taxon:4932 20030325 SGD
+SGD S000000568 VAC17 GO:0000011 SGD_REF:S000072665|PMID:12594460 IMP P the vacuole-specific receptor of Myo2p, a class V myosin YCL063W gene taxon:4932 20030307 SGD
+SGD S000004999 VAC7 GO:0000324 SGD_REF:S000048576|PMID:9372916 IDA C YNL054W gene taxon:4932 20020312 SGD
+SGD S000004999 VAC7 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YNL054W gene taxon:4932 20020507 SGD
+SGD S000004999 VAC7 GO:0016021 SGD_REF:S000048576|PMID:9372916 IDA C YNL054W gene taxon:4932 20020312 SGD
+SGD S000004999 VAC7 GO:0030234 SGD_REF:S000069689|PMID:11950935 IGI F YNL054W gene taxon:4932 20021118 SGD
+SGD S000004999 VAC7 GO:0000011 SGD_REF:S000048576|PMID:9372916 IMP P YNL054W gene taxon:4932 20020312 SGD
+SGD S000004999 VAC7 GO:0006644 SGD_REF:S000048576|PMID:9372916 IMP P YNL054W gene taxon:4932 20020312 SGD
+SGD S000004999 VAC7 GO:0006644 SGD_REF:S000048576|PMID:9372916 IGI P YNL054W gene taxon:4932 20020312 SGD
+SGD S000000739 VAC8 GO:0000324 SGD_REF:S000046657|PMID:9739084 IDA C YEL013W|YEB3 gene taxon:4932 20010118 SGD
+SGD S000000739 VAC8 GO:0005515 SGD_REF:S000039257|PMID:10888680 IPI F YEL013W|YEB3 gene taxon:4932 20020927 SGD
+SGD S000000739 VAC8 GO:0000011 SGD_REF:S000042692|PMID:9664035 IMP P YEL013W|YEB3 gene taxon:4932 20010118 SGD
+SGD S000000739 VAC8 GO:0006623 SGD_REF:S000056230|PMID:9490720 IMP P YEL013W|YEB3 gene taxon:4932 20010118 SGD
+SGD S000000739 VAC8 GO:0016237 SGD_REF:S000072498|PMID:12529432 IMP P YEL013W|YEB3 gene taxon:4932 20030213 SGD
+SGD S000000739 VAC8 GO:0042144 SGD_REF:S000065870|PMID:11441010 IMP P YEL013W|YEB3 gene taxon:4932 20020312 SGD
+SGD S000000739 VAC8 GO:0042144 SGD_REF:S000065870|PMID:11441010 IDA P YEL013W|YEB3 gene taxon:4932 20020312 SGD
+SGD S000029635 VAL1 GO:0008372 SGD_REF:S000069584 ND C tRNA-Val gene taxon:4932 20020522 SGD
+SGD S000029635 VAL1 GO:0005554 SGD_REF:S000069584 ND F tRNA-Val gene taxon:4932 20020522 SGD
+SGD S000029635 VAL1 GO:0000004 SGD_REF:S000069584 ND P tRNA-Val gene taxon:4932 20020522 SGD
+SGD S000005594 VAM10 GO:0005774 SGD_REF:S000073403|PMID:12748377 IC GO:0042144 C Required for normal tethering of vacuoles prior to fusion. YOR068C|YOR29-19 gene taxon:4932 20030808 SGD
+SGD S000005594 VAM10 GO:0005554 SGD_REF:S000069584 ND F Required for normal tethering of vacuoles prior to fusion. YOR068C|YOR29-19 gene taxon:4932 20030808 SGD
+SGD S000005594 VAM10 GO:0042144 SGD_REF:S000073403|PMID:12748377 IMP P Required for normal tethering of vacuoles prior to fusion. YOR068C|YOR29-19 gene taxon:4932 20030808 SGD
+SGD S000005632 VAM3 GO:0005774 SGD_REF:S000040637|PMID:9475723 IDA C syntaxin family YOR106W|PTH1 gene taxon:4932 20020130 SGD
+SGD S000005632 VAM3 GO:0005486 SGD_REF:S000058453|PMID:10047442 TAS F syntaxin family YOR106W|PTH1 gene taxon:4932 20010118 SGD
+SGD S000005632 VAM3 GO:0006896 SGD_REF:S000058453|PMID:10047442 TAS P syntaxin family YOR106W|PTH1 gene taxon:4932 20010118 SGD
+SGD S000005632 VAM3 GO:0006906 SGD_REF:S000058453|PMID:10047442 TAS P syntaxin family YOR106W|PTH1 gene taxon:4932 20010118 SGD
+SGD S000002235 VAM6 GO:0000324 SGD_REF:S000045452|PMID:9111041 IDA C YDL077C|CVT4|VPL18|VPL22|VPS39 gene taxon:4932 20020313 SGD
+SGD S000002235 VAM6 GO:0005774 SGD_REF:S000045452|PMID:9111041 IDA C YDL077C|CVT4|VPL18|VPL22|VPS39 gene taxon:4932 20020313 SGD
+SGD S000002235 VAM6 GO:0030897 SGD_REF:S000040175|PMID:10944212 IPI C YDL077C|CVT4|VPL18|VPL22|VPS39 gene taxon:4932 20041024 SGD
+SGD S000002235 VAM6 GO:0017112 SGD_REF:S000059565|PMID:11062257 IDA F YDL077C|CVT4|VPL18|VPL22|VPS39 gene taxon:4932 20021113 SGD
+SGD S000002235 VAM6 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P YDL077C|CVT4|VPL18|VPL22|VPS39 gene taxon:4932 20060210 SGD
+SGD S000002235 VAM6 GO:0007033 SGD_REF:S000045452|PMID:9111041 IMP P YDL077C|CVT4|VPL18|VPL22|VPS39 gene taxon:4932 20020313 SGD
+SGD S000002235 VAM6 GO:0042144 SGD_REF:S000040175|PMID:10944212 IMP P YDL077C|CVT4|VPL18|VPL22|VPS39 gene taxon:4932 20020313 SGD
+SGD S000002235 VAM6 GO:0042144 SGD_REF:S000040175|PMID:10944212 IDA P YDL077C|CVT4|VPL18|VPL22|VPS39 gene taxon:4932 20020313 SGD
+SGD S000003180 VAM7 GO:0000329 SGD_REF:S000065857|PMID:11433291 IDA C heptad repeat motif, hydrophilic protein YGL212W|VPS43 gene taxon:4932 20020917 SGD
+SGD S000003180 VAM7 GO:0005485 SGD_REF:S000058453|PMID:10047442 TAS F heptad repeat motif, hydrophilic protein YGL212W|VPS43 gene taxon:4932 20010118 SGD
+SGD S000003180 VAM7 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P heptad repeat motif, hydrophilic protein YGL212W|VPS43 gene taxon:4932 20060210 SGD
+SGD S000003180 VAM7 GO:0006896 SGD_REF:S000058453|PMID:10047442 TAS P heptad repeat motif, hydrophilic protein YGL212W|VPS43 gene taxon:4932 20010118 SGD
+SGD S000003180 VAM7 GO:0006906 SGD_REF:S000058453|PMID:10047442 TAS P heptad repeat motif, hydrophilic protein YGL212W|VPS43 gene taxon:4932 20010118 SGD
+SGD S000004583 VAN1 GO:0000136 SGD_REF:S000053242|PMID:9430634 IPI C mannosyltransferase YML115C|LDB13|VRG7|VRG8 gene taxon:4932 20020213 SGD
+SGD S000004583 VAN1 GO:0005801 SGD_REF:S000049702|PMID:10500155 TAS C mannosyltransferase YML115C|LDB13|VRG7|VRG8 gene taxon:4932 20030224 SGD
+SGD S000004583 VAN1 GO:0016020 SGD_REF:S000049702|PMID:10500155 TAS C mannosyltransferase YML115C|LDB13|VRG7|VRG8 gene taxon:4932 20030224 SGD
+SGD S000004583 VAN1 GO:0000030 SGD_REF:S000043074|PMID:9434768 ISS F mannosyltransferase YML115C|LDB13|VRG7|VRG8 gene taxon:4932 20020213 SGD
+SGD S000004583 VAN1 GO:0006487 SGD_REF:S000053242|PMID:9430634 IMP P mannosyltransferase YML115C|LDB13|VRG7|VRG8 gene taxon:4932 20020213 SGD
+SGD S000004583 VAN1 GO:0006487 SGD_REF:S000053242|PMID:9430634 IDA P mannosyltransferase YML115C|LDB13|VRG7|VRG8 gene taxon:4932 20020213 SGD
+SGD S000007275 VAR1 GO:0005763 SGD_REF:S000058278|PMID:9445368 TAS C mitochondrial ribosomal protein Q0140|VARI gene taxon:4932 20010118 SGD
+SGD S000007275 VAR1 GO:0005763 SGD_REF:S000060645|PMID:11278769 IDA C mitochondrial ribosomal protein Q0140|VARI gene taxon:4932 20010918 SGD
+SGD S000007275 VAR1 GO:0003735 SGD_REF:S000058278|PMID:9445368 TAS F mitochondrial ribosomal protein Q0140|VARI gene taxon:4932 20010118 SGD
+SGD S000007275 VAR1 GO:0003735 SGD_REF:S000060645|PMID:11278769 IDA F mitochondrial ribosomal protein Q0140|VARI gene taxon:4932 20010918 SGD
+SGD S000007275 VAR1 GO:0000028 SGD_REF:S000058278|PMID:9445368 IMP P mitochondrial ribosomal protein Q0140|VARI gene taxon:4932 20010118 SGD
+SGD S000007275 VAR1 GO:0043037 SGD_REF:S000058278|PMID:9445368 TAS P mitochondrial ribosomal protein Q0140|VARI gene taxon:4932 20010118 SGD
+SGD S000007275 VAR1 GO:0043037 SGD_REF:S000060645|PMID:11278769 IDA P mitochondrial ribosomal protein Q0140|VARI gene taxon:4932 20010918 SGD
+SGD S000003326 VAS1 GO:0005737 SGD_REF:S000049099|PMID:3275649 IMP C valine-tRNA ligase YGR094W gene taxon:4932 20020927 SGD
+SGD S000003326 VAS1 GO:0005739 SGD_REF:S000049099|PMID:3275649 IMP C valine-tRNA ligase YGR094W gene taxon:4932 20020927 SGD
+SGD S000003326 VAS1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C valine-tRNA ligase YGR094W gene taxon:4932 20040813 SGD
+SGD S000003326 VAS1 GO:0004832 SGD_REF:S000057061|PMID:3294828 ISS F valine-tRNA ligase YGR094W gene taxon:4932 20020927 SGD
+SGD S000003326 VAS1 GO:0006438 SGD_REF:S000071360|PMID:782885 IDA P valine-tRNA ligase YGR094W gene taxon:4932 20020927 SGD
+SGD S000004694 VBA1 GO:0000329 SGD_REF:S000080221|PMID:15572352 IDA C YMR088C gene taxon:4932 20050119 SGD
+SGD S000004694 VBA1 GO:0005286 SGD_REF:S000080221|PMID:15572352 IDA F YMR088C gene taxon:4932 20050119 SGD
+SGD S000004694 VBA1 GO:0005286 SGD_REF:S000080221|PMID:15572352 IMP F YMR088C gene taxon:4932 20050119 SGD
+SGD S000004694 VBA1 GO:0015802 SGD_REF:S000080221|PMID:15572352 IMP P YMR088C gene taxon:4932 20050119 SGD
+SGD S000000497 VBA2 GO:0000329 SGD_REF:S000080221|PMID:15572352 IDA C YBR293W gene taxon:4932 20050119 SGD
+SGD S000000497 VBA2 GO:0005286 SGD_REF:S000080221|PMID:15572352 IDA F YBR293W gene taxon:4932 20050119 SGD
+SGD S000000497 VBA2 GO:0005286 SGD_REF:S000080221|PMID:15572352 IMP F YBR293W gene taxon:4932 20050119 SGD
+SGD S000000497 VBA2 GO:0015239 SGD_REF:S000065696|PMID:9710608 ISS protein_id:AF029304 F YBR293W gene taxon:4932 20040212 SGD
+SGD S000000497 VBA2 GO:0015802 SGD_REF:S000080221|PMID:15572352 IMP P YBR293W gene taxon:4932 20050119 SGD
+SGD S000000574 VBA3 GO:0000329 SGD_REF:S000080221|PMID:15572352 IDA C YCL069W gene taxon:4932 20050119 SGD
+SGD S000000574 VBA3 GO:0005286 SGD_REF:S000080221|PMID:15572352 IDA F YCL069W gene taxon:4932 20050119 SGD
+SGD S000000574 VBA3 GO:0005286 SGD_REF:S000080221|PMID:15572352 IMP F YCL069W gene taxon:4932 20050119 SGD
+SGD S000000574 VBA3 GO:0015802 SGD_REF:S000080221|PMID:15572352 IMP P YCL069W gene taxon:4932 20050119 SGD
+SGD S000002286 VCX1 GO:0000324 SGD_REF:S000046399|PMID:8628289 IDA C vacuolar H+/Ca2+ exchanger YDL128W|HUM1|MNR1 gene taxon:4932 20020307 SGD
+SGD S000002286 VCX1 GO:0005774 SGD_REF:S000046399|PMID:8628289 ISS C vacuolar H+/Ca2+ exchanger YDL128W|HUM1|MNR1 gene taxon:4932 20020307 SGD
+SGD S000002286 VCX1 GO:0015085 SGD_REF:S000046399|PMID:8628289 IMP F vacuolar H+/Ca2+ exchanger YDL128W|HUM1|MNR1 gene taxon:4932 20020307 SGD
+SGD S000002286 VCX1 GO:0015085 SGD_REF:S000046399|PMID:8628289 IDA F vacuolar H+/Ca2+ exchanger YDL128W|HUM1|MNR1 gene taxon:4932 20020307 SGD
+SGD S000002286 VCX1 GO:0015085 SGD_REF:S000046399|PMID:8628289 ISS F vacuolar H+/Ca2+ exchanger YDL128W|HUM1|MNR1 gene taxon:4932 20020307 SGD
+SGD S000002286 VCX1 GO:0015369 SGD_REF:S000059425|PMID:10991947 TAS F vacuolar H+/Ca2+ exchanger YDL128W|HUM1|MNR1 gene taxon:4932 20020307 SGD
+SGD S000002286 VCX1 GO:0006816 SGD_REF:S000046399|PMID:8628289 IMP P vacuolar H+/Ca2+ exchanger YDL128W|HUM1|MNR1 gene taxon:4932 20020307 SGD
+SGD S000002286 VCX1 GO:0006816 SGD_REF:S000046399|PMID:8628289 IDA P vacuolar H+/Ca2+ exchanger YDL128W|HUM1|MNR1 gene taxon:4932 20020307 SGD
+SGD S000002286 VCX1 NOT GO:0006828 SGD_REF:S000079764|PMID:15522090 IDA P vacuolar H+/Ca2+ exchanger YDL128W|HUM1|MNR1 gene taxon:4932 20041206 SGD
+SGD S000002286 VCX1 GO:0006874 SGD_REF:S000046399|PMID:8628289 IMP P vacuolar H+/Ca2+ exchanger YDL128W|HUM1|MNR1 gene taxon:4932 20020307 SGD
+SGD S000003227 VEL1 GO:0005625 SGD_REF:S000075303|PMID:11935221 IDA C YGL258W gene taxon:4932 20040114 SGD
+SGD S000003227 VEL1 GO:0005554 SGD_REF:S000069584 ND F YGL258W gene taxon:4932 20021030 SGD
+SGD S000003227 VEL1 GO:0000004 SGD_REF:S000069584 ND P YGL258W gene taxon:4932 20021030 SGD
+SGD S000001318 VHR1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C transcription factor YIL056W gene taxon:4932 20031028 SGD
+SGD S000001318 VHR1 GO:0005634 SGD_REF:S000114633|PMID:16533810 IDA C transcription factor YIL056W gene taxon:4932 20060327 SGD
+SGD S000001318 VHR1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C transcription factor YIL056W gene taxon:4932 20031028 SGD
+SGD S000001318 VHR1 GO:0003677 SGD_REF:S000114633|PMID:16533810 IDA F transcription factor YIL056W gene taxon:4932 20060322 SGD
+SGD S000001318 VHR1 GO:0016563 SGD_REF:S000114633|PMID:16533810 IDA F transcription factor YIL056W gene taxon:4932 20060322 SGD
+SGD S000001318 VHR1 GO:0006357 SGD_REF:S000114633|PMID:16533810 IMP P transcription factor YIL056W gene taxon:4932 20060327 SGD
+SGD S000001318 VHR1 GO:0009102 SGD_REF:S000114633|PMID:16533810 IMP P transcription factor YIL056W gene taxon:4932 20060327 SGD
+SGD S000002655 VHS1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDR247W gene taxon:4932 20031028 SGD
+SGD S000002655 VHS1 GO:0004672 SGD_REF:S000058030|PMID:9020587 ISS F YDR247W gene taxon:4932 20030204 SGD
+SGD S000002655 VHS1 GO:0004674 SGD_REF:S000072514|PMID:12518319 ISS F YDR247W gene taxon:4932 20030217 SGD
+SGD S000002655 VHS1 GO:0000082 SGD_REF:S000072514|PMID:12518319 IGI P YDR247W gene taxon:4932 20030217 SGD
+SGD S000002655 VHS1 GO:0006468 SGD_REF:S000072514|PMID:12518319 ISS P YDR247W gene taxon:4932 20030217 SGD
+SGD S000001397 VHS2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YIL135C gene taxon:4932 20031028 SGD
+SGD S000001397 VHS2 GO:0005554 SGD_REF:S000069584 ND F YIL135C gene taxon:4932 20021126 SGD
+SGD S000001397 VHS2 GO:0000082 SGD_REF:S000072514|PMID:12518319 IGI P YIL135C gene taxon:4932 20030217 SGD
+SGD S000005580 VHS3 GO:0008372 SGD_REF:S000069584 ND C YOR054C|YOR29-05 gene taxon:4932 20030203 SGD
+SGD S000005580 VHS3 GO:0004633 SGD_REF:S000072463|PMID:10592175 ISS F YOR054C|YOR29-05 gene taxon:4932 20030619 SGD
+SGD S000005580 VHS3 GO:0004864 SGD_REF:S000076909|PMID:15192104 IDA F YOR054C|YOR29-05 gene taxon:4932 20040922 SGD
+SGD S000005580 VHS3 GO:0000082 SGD_REF:S000072514|PMID:12518319 IGI P YOR054C|YOR29-05 gene taxon:4932 20030217 SGD
+SGD S000005580 VHS3 GO:0015937 SGD_REF:S000072463|PMID:10592175 ISS P YOR054C|YOR29-05 gene taxon:4932 20030619 SGD
+SGD S000005580 VHS3 GO:0030004 SGD_REF:S000076909|PMID:15192104 IGI SGD:S000004478 P YOR054C|YOR29-05 gene taxon:4932 20040922 SGD
+SGD S000005580 VHS3 GO:0030004 SGD_REF:S000076909|PMID:15192104 IPI SGD:S000004478 P YOR054C|YOR29-05 gene taxon:4932 20040922 SGD
+SGD S000003297 VHT1 GO:0005886 SGD_REF:S000051408|PMID:10373489 IDA C H+-biotin symporter YGR065C gene taxon:4932 20021002 SGD
+SGD S000003297 VHT1 GO:0015225 SGD_REF:S000051408|PMID:10373489 IDA F H+-biotin symporter YGR065C gene taxon:4932 20021002 SGD
+SGD S000003297 VHT1 GO:0015878 SGD_REF:S000051408|PMID:10373489 IDA P H+-biotin symporter YGR065C gene taxon:4932 20021002 SGD
+SGD S000002767 VID21 GO:0000123 SGD_REF:S000073630|PMID:12672825 IPI C YDR359C|EAF1 gene taxon:4932 20040105 SGD
+SGD S000002767 VID21 GO:0043189 SGD_REF:S000079775|PMID:15485911 IPI C YDR359C|EAF1 gene taxon:4932 20050207 SGD
+SGD S000002767 VID21 GO:0043189 SGD_REF:S000077129|PMID:15353583 IPI C YDR359C|EAF1 gene taxon:4932 20050207 SGD
+SGD S000002767 VID21 GO:0005554 SGD_REF:S000069584 ND F YDR359C|EAF1 gene taxon:4932 20020927 SGD
+SGD S000002767 VID21 GO:0016568 SGD_REF:S000073630|PMID:12672825 IPI P YDR359C|EAF1 gene taxon:4932 20040105 SGD
+SGD S000004365 VID22 GO:0005887 SGD_REF:S000069403|PMID:11861771 IDA C YLR373C gene taxon:4932 20020927 SGD
+SGD S000004365 VID22 GO:0005554 SGD_REF:S000069584 ND F YLR373C gene taxon:4932 20020927 SGD
+SGD S000004365 VID22 GO:0007039 SGD_REF:S000069403|PMID:11861771 IMP P YLR373C gene taxon:4932 20020927 SGD
+SGD S000000309 VID24 GO:0016023 SGD_REF:S000045301|PMID:9508768 IDA C peripheral vesicle membrane protein YBR105C|GID4 gene taxon:4932 20020711 SGD
+SGD S000000309 VID24 GO:0019898 SGD_REF:S000045301|PMID:9508768 IDA C peripheral vesicle membrane protein YBR105C|GID4 gene taxon:4932 20020711 SGD
+SGD S000000309 VID24 GO:0005554 SGD_REF:S000069584 ND F peripheral vesicle membrane protein YBR105C|GID4 gene taxon:4932 20020711 SGD
+SGD S000000309 VID24 GO:0016192 SGD_REF:S000045301|PMID:9508768 IMP P peripheral vesicle membrane protein YBR105C|GID4 gene taxon:4932 20020711 SGD
+SGD S000000309 VID24 GO:0045721 SGD_REF:S000072993|PMID:12686616 IMP P peripheral vesicle membrane protein YBR105C|GID4 gene taxon:4932 20030708 SGD
+SGD S000005156 VID27 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YNL212W gene taxon:4932 20031028 SGD
+SGD S000005156 VID27 GO:0005554 SGD_REF:S000069584 ND F YNL212W gene taxon:4932 20020927 SGD
+SGD S000005156 VID27 GO:0000004 SGD_REF:S000069584 ND P YNL212W gene taxon:4932 20020927 SGD
+SGD S000001279 VID28 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YIL017C|GID5 gene taxon:4932 20031028 SGD
+SGD S000001279 VID28 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YIL017C|GID5 gene taxon:4932 20031028 SGD
+SGD S000001279 VID28 GO:0005554 SGD_REF:S000069584 ND F YIL017C|GID5 gene taxon:4932 20020927 SGD
+SGD S000001279 VID28 GO:0045721 SGD_REF:S000072993|PMID:12686616 IMP P YIL017C|GID5 gene taxon:4932 20030708 SGD
+SGD S000003196 VID30 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YGL227W|GID1 gene taxon:4932 20031028 SGD
+SGD S000003196 VID30 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YGL227W|GID1 gene taxon:4932 20031028 SGD
+SGD S000003196 VID30 GO:0005554 SGD_REF:S000069584 ND F YGL227W|GID1 gene taxon:4932 20020927 SGD
+SGD S000003196 VID30 GO:0006808 SGD_REF:S000061424|PMID:11356843 IMP P YGL227W|GID1 gene taxon:4932 20020927 SGD
+SGD S000003196 VID30 GO:0007039 SGD_REF:S000057954|PMID:8844145 IMP P YGL227W|GID1 gene taxon:4932 20050509 SGD
+SGD S000003196 VID30 GO:0043161 SGD_REF:S000080362|PMID:15358789 IMP P YGL227W|GID1 gene taxon:4932 20050509 SGD
+SGD S000003196 VID30 GO:0045721 SGD_REF:S000072993|PMID:12686616 IMP P YGL227W|GID1 gene taxon:4932 20030708 SGD
+SGD S000006174 VIK1 GO:0005816 SGD_REF:S000043673|PMID:10087265 IDA C YPL253C gene taxon:4932 20010118 SGD
+SGD S000006174 VIK1 GO:0005816 SGD_REF:S000066252|PMID:11729143 IDA C YPL253C gene taxon:4932 20020208 SGD
+SGD S000006174 VIK1 GO:0005871 SGD_REF:S000043673|PMID:10087265 IDA C YPL253C gene taxon:4932 20020208 SGD
+SGD S000006174 VIK1 GO:0003777 SGD_REF:S000043673|PMID:10087265 ISS F YPL253C gene taxon:4932 20010118 SGD
+SGD S000006174 VIK1 GO:0007017 SGD_REF:S000043673|PMID:10087265 IMP P YPL253C gene taxon:4932 20010118 SGD
+SGD S000006174 VIK1 GO:0007017 SGD_REF:S000043673|PMID:10087265 IPI P YPL253C gene taxon:4932 20010118 SGD
+SGD S000006174 VIK1 GO:0007064 SGD_REF:S000076127|PMID:14742714 IGI SGD:S000001234 P YPL253C gene taxon:4932 20050513 SGD
+SGD S000006174 VIK1 GO:0007064 SGD_REF:S000076127|PMID:14742714 IMP P YPL253C gene taxon:4932 20050513 SGD
+SGD S000004402 VIP1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YLR410W gene taxon:4932 20031028 SGD
+SGD S000004402 VIP1 GO:0005554 SGD_REF:S000069584 ND F YLR410W gene taxon:4932 20021016 SGD
+SGD S000004402 VIP1 GO:0030036 SGD_REF:S000047948|PMID:10388810 IGI P YLR410W gene taxon:4932 20021016 SGD
+SGD S000002100 VMA10 GO:0000221 SGD_REF:S000056362|PMID:10224039 TAS C vacuolar ATPase V1 domain subunit G (13 kDa) YHR039C-A|YHR039BC|YHR039C-B gene taxon:4932 20010118 SGD
+SGD S000002100 VMA10 GO:0000221 SGD_REF:S000058276|PMID:9442887 TAS C vacuolar ATPase V1 domain subunit G (13 kDa) YHR039C-A|YHR039BC|YHR039C-B gene taxon:4932 20010118 SGD
+SGD S000002100 VMA10 GO:0046961 SGD_REF:S000056362|PMID:10224039 TAS F vacuolar ATPase V1 domain subunit G (13 kDa) YHR039C-A|YHR039BC|YHR039C-B gene taxon:4932 20030716 SGD
+SGD S000002100 VMA10 GO:0046961 SGD_REF:S000058276|PMID:9442887 TAS F vacuolar ATPase V1 domain subunit G (13 kDa) YHR039C-A|YHR039BC|YHR039C-B gene taxon:4932 20030716 SGD
+SGD S000002100 VMA10 GO:0005977 SGD_REF:S000070094|PMID:12096123 IDA P vacuolar ATPase V1 domain subunit G (13 kDa) YHR039C-A|YHR039BC|YHR039C-B gene taxon:4932 20020821 SGD
+SGD S000002100 VMA10 GO:0007035 SGD_REF:S000056362|PMID:10224039 TAS P vacuolar ATPase V1 domain subunit G (13 kDa) YHR039C-A|YHR039BC|YHR039C-B gene taxon:4932 20010118 SGD
+SGD S000002100 VMA10 GO:0007035 SGD_REF:S000058276|PMID:9442887 TAS P vacuolar ATPase V1 domain subunit G (13 kDa) YHR039C-A|YHR039BC|YHR039C-B gene taxon:4932 20010118 SGD
+SGD S000006240 VMA13 GO:0000221 SGD_REF:S000056362|PMID:10224039 TAS C vacuolar H(+) ATPase V1 sector 54 kDa subunit YPR036W|CLS11 gene taxon:4932 20010118 SGD
+SGD S000006240 VMA13 GO:0000221 SGD_REF:S000058276|PMID:9442887 TAS C vacuolar H(+) ATPase V1 sector 54 kDa subunit YPR036W|CLS11 gene taxon:4932 20010118 SGD
+SGD S000006240 VMA13 GO:0000329 SGD_REF:S000069241|PMID:11717306 TAS C vacuolar H(+) ATPase V1 sector 54 kDa subunit YPR036W|CLS11 gene taxon:4932 20020728 SGD
+SGD S000006240 VMA13 GO:0046961 SGD_REF:S000056362|PMID:10224039 TAS F vacuolar H(+) ATPase V1 sector 54 kDa subunit YPR036W|CLS11 gene taxon:4932 20030716 SGD
+SGD S000006240 VMA13 GO:0046961 SGD_REF:S000058276|PMID:9442887 TAS F vacuolar H(+) ATPase V1 sector 54 kDa subunit YPR036W|CLS11 gene taxon:4932 20030716 SGD
+SGD S000006240 VMA13 GO:0007035 SGD_REF:S000056362|PMID:10224039 TAS P vacuolar H(+) ATPase V1 sector 54 kDa subunit YPR036W|CLS11 gene taxon:4932 20010118 SGD
+SGD S000006240 VMA13 GO:0007035 SGD_REF:S000058276|PMID:9442887 TAS P vacuolar H(+) ATPase V1 sector 54 kDa subunit YPR036W|CLS11 gene taxon:4932 20010118 SGD
+SGD S000000331 VMA2 GO:0000221 SGD_REF:S000056362|PMID:10224039 TAS C vacuolar ATPase V1 domain subunit B (60 kDa) YBR127C|ATPSV|VAT2 gene taxon:4932 20010118 SGD
+SGD S000000331 VMA2 GO:0000221 SGD_REF:S000058276|PMID:9442887 TAS C vacuolar ATPase V1 domain subunit B (60 kDa) YBR127C|ATPSV|VAT2 gene taxon:4932 20010118 SGD
+SGD S000000331 VMA2 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C vacuolar ATPase V1 domain subunit B (60 kDa) YBR127C|ATPSV|VAT2 gene taxon:4932 20020507 SGD
+SGD S000000331 VMA2 GO:0046961 SGD_REF:S000056362|PMID:10224039 TAS F vacuolar ATPase V1 domain subunit B (60 kDa) YBR127C|ATPSV|VAT2 gene taxon:4932 20030716 SGD
+SGD S000000331 VMA2 GO:0046961 SGD_REF:S000058276|PMID:9442887 TAS F vacuolar ATPase V1 domain subunit B (60 kDa) YBR127C|ATPSV|VAT2 gene taxon:4932 20030716 SGD
+SGD S000000331 VMA2 GO:0007035 SGD_REF:S000056362|PMID:10224039 TAS P vacuolar ATPase V1 domain subunit B (60 kDa) YBR127C|ATPSV|VAT2 gene taxon:4932 20010118 SGD
+SGD S000000331 VMA2 GO:0007035 SGD_REF:S000058276|PMID:9442887 TAS P vacuolar ATPase V1 domain subunit B (60 kDa) YBR127C|ATPSV|VAT2 gene taxon:4932 20010118 SGD
+SGD S000003337 VMA21 GO:0005783 SGD_REF:S000040585|PMID:9660861 TAS C YGR105W gene taxon:4932 20020727 SGD
+SGD S000003337 VMA21 GO:0005789 SGD_REF:S000040585|PMID:9660861 IDA C YGR105W gene taxon:4932 20021113 SGD
+SGD S000003337 VMA21 GO:0005554 SGD_REF:S000069584 ND F YGR105W gene taxon:4932 20021113 SGD
+SGD S000003337 VMA21 GO:0006461 SGD_REF:S000040585|PMID:9660861 IMP P YGR105W gene taxon:4932 20021113 SGD
+SGD S000003337 VMA21 GO:0006461 SGD_REF:S000040585|PMID:9660861 IPI P YGR105W gene taxon:4932 20021113 SGD
+SGD S000001102 VMA22 GO:0005789 SGD_REF:S000040585|PMID:9660861 TAS C YHR060W|CEV1|VPH6 gene taxon:4932 20020727 SGD
+SGD S000001102 VMA22 GO:0051082 SGD_REF:S000046211|PMID:7673216 IMP F YHR060W|CEV1|VPH6 gene taxon:4932 20030328 SGD
+SGD S000001102 VMA22 GO:0051082 SGD_REF:S000046211|PMID:7673216 IGI F YHR060W|CEV1|VPH6 gene taxon:4932 20030328 SGD
+SGD S000001102 VMA22 GO:0051082 SGD_REF:S000053116|PMID:8582630 IMP F YHR060W|CEV1|VPH6 gene taxon:4932 20030328 SGD
+SGD S000001102 VMA22 GO:0051082 SGD_REF:S000046211|PMID:7673216 IPI F YHR060W|CEV1|VPH6 gene taxon:4932 20030328 SGD
+SGD S000001102 VMA22 GO:0005977 SGD_REF:S000070094|PMID:12096123 IDA P YHR060W|CEV1|VPH6 gene taxon:4932 20020821 SGD
+SGD S000001102 VMA22 GO:0006461 SGD_REF:S000046211|PMID:7673216 IMP P YHR060W|CEV1|VPH6 gene taxon:4932 20010118 SGD
+SGD S000001102 VMA22 GO:0007035 SGD_REF:S000044189|PMID:1628805 IMP P YHR060W|CEV1|VPH6 gene taxon:4932 20010118 SGD
+SGD S000005859 VMA4 GO:0000221 SGD_REF:S000056362|PMID:10224039 TAS C E subunit of V1 sector, vacuolar H(+) ATPase 27 kDa subunit YOR332W gene taxon:4932 20010118 SGD
+SGD S000005859 VMA4 GO:0000221 SGD_REF:S000058276|PMID:9442887 TAS C E subunit of V1 sector, vacuolar H(+) ATPase 27 kDa subunit YOR332W gene taxon:4932 20010118 SGD
+SGD S000005859 VMA4 GO:0000329 SGD_REF:S000069241|PMID:11717306 TAS C E subunit of V1 sector, vacuolar H(+) ATPase 27 kDa subunit YOR332W gene taxon:4932 20020728 SGD
+SGD S000005859 VMA4 GO:0046961 SGD_REF:S000056362|PMID:10224039 TAS F E subunit of V1 sector, vacuolar H(+) ATPase 27 kDa subunit YOR332W gene taxon:4932 20030710 SGD
+SGD S000005859 VMA4 GO:0046961 SGD_REF:S000058276|PMID:9442887 TAS F E subunit of V1 sector, vacuolar H(+) ATPase 27 kDa subunit YOR332W gene taxon:4932 20030710 SGD
+SGD S000005859 VMA4 GO:0007035 SGD_REF:S000056362|PMID:10224039 TAS P E subunit of V1 sector, vacuolar H(+) ATPase 27 kDa subunit YOR332W gene taxon:4932 20010118 SGD
+SGD S000005859 VMA4 GO:0007035 SGD_REF:S000058276|PMID:9442887 TAS P E subunit of V1 sector, vacuolar H(+) ATPase 27 kDa subunit YOR332W gene taxon:4932 20010118 SGD
+SGD S000001563 VMA5 GO:0000221 SGD_REF:S000056362|PMID:10224039 TAS C V1 sector hydrophilic subunit C, vacuolar ATPase V1 domain subunit C (42 kDa), vacuolar H-ATPase YKL080W|CSL5|VAT3 gene taxon:4932 20010118 SGD
+SGD S000001563 VMA5 GO:0000221 SGD_REF:S000058276|PMID:9442887 TAS C V1 sector hydrophilic subunit C, vacuolar ATPase V1 domain subunit C (42 kDa), vacuolar H-ATPase YKL080W|CSL5|VAT3 gene taxon:4932 20010118 SGD
+SGD S000001563 VMA5 GO:0000329 SGD_REF:S000069241|PMID:11717306 TAS C V1 sector hydrophilic subunit C, vacuolar ATPase V1 domain subunit C (42 kDa), vacuolar H-ATPase YKL080W|CSL5|VAT3 gene taxon:4932 20020728 SGD
+SGD S000001563 VMA5 GO:0046961 SGD_REF:S000056362|PMID:10224039 TAS F V1 sector hydrophilic subunit C, vacuolar ATPase V1 domain subunit C (42 kDa), vacuolar H-ATPase YKL080W|CSL5|VAT3 gene taxon:4932 20030710 SGD
+SGD S000001563 VMA5 GO:0046961 SGD_REF:S000058276|PMID:9442887 TAS F V1 sector hydrophilic subunit C, vacuolar ATPase V1 domain subunit C (42 kDa), vacuolar H-ATPase YKL080W|CSL5|VAT3 gene taxon:4932 20030710 SGD
+SGD S000001563 VMA5 GO:0007035 SGD_REF:S000056362|PMID:10224039 TAS P V1 sector hydrophilic subunit C, vacuolar ATPase V1 domain subunit C (42 kDa), vacuolar H-ATPase YKL080W|CSL5|VAT3 gene taxon:4932 20010118 SGD
+SGD S000001563 VMA5 GO:0007035 SGD_REF:S000058276|PMID:9442887 TAS P V1 sector hydrophilic subunit C, vacuolar ATPase V1 domain subunit C (42 kDa), vacuolar H-ATPase YKL080W|CSL5|VAT3 gene taxon:4932 20010118 SGD
+SGD S000004439 VMA6 GO:0000220 SGD_REF:S000056362|PMID:10224039 TAS C vacuolar ATPase V0 domain subunit d (36 kDa), vacuolar H(+) ATPase 36 kDa subunit (D subunit of VO sector) YLR447C gene taxon:4932 20010118 SGD
+SGD S000004439 VMA6 GO:0000220 SGD_REF:S000058276|PMID:9442887 TAS C vacuolar ATPase V0 domain subunit d (36 kDa), vacuolar H(+) ATPase 36 kDa subunit (D subunit of VO sector) YLR447C gene taxon:4932 20010118 SGD
+SGD S000004439 VMA6 GO:0005774 SGD_REF:S000054409|PMID:8509410 IDA C vacuolar ATPase V0 domain subunit d (36 kDa), vacuolar H(+) ATPase 36 kDa subunit (D subunit of VO sector) YLR447C gene taxon:4932 20010118 SGD
+SGD S000004439 VMA6 GO:0046961 SGD_REF:S000054409|PMID:8509410 IDA F vacuolar ATPase V0 domain subunit d (36 kDa), vacuolar H(+) ATPase 36 kDa subunit (D subunit of VO sector) YLR447C gene taxon:4932 20030710 SGD
+SGD S000004439 VMA6 GO:0046961 SGD_REF:S000054409|PMID:8509410 IMP F vacuolar ATPase V0 domain subunit d (36 kDa), vacuolar H(+) ATPase 36 kDa subunit (D subunit of VO sector) YLR447C gene taxon:4932 20030710 SGD
+SGD S000004439 VMA6 GO:0007034 SGD_REF:S000054409|PMID:8509410 IMP P vacuolar ATPase V0 domain subunit d (36 kDa), vacuolar H(+) ATPase 36 kDa subunit (D subunit of VO sector) YLR447C gene taxon:4932 20010118 SGD
+SGD S000004439 VMA6 GO:0007034 SGD_REF:S000054409|PMID:8509410 IDA P vacuolar ATPase V0 domain subunit d (36 kDa), vacuolar H(+) ATPase 36 kDa subunit (D subunit of VO sector) YLR447C gene taxon:4932 20010118 SGD
+SGD S000004439 VMA6 GO:0007035 SGD_REF:S000056362|PMID:10224039 TAS P vacuolar ATPase V0 domain subunit d (36 kDa), vacuolar H(+) ATPase 36 kDa subunit (D subunit of VO sector) YLR447C gene taxon:4932 20010118 SGD
+SGD S000004439 VMA6 GO:0007035 SGD_REF:S000058276|PMID:9442887 TAS P vacuolar ATPase V0 domain subunit d (36 kDa), vacuolar H(+) ATPase 36 kDa subunit (D subunit of VO sector) YLR447C gene taxon:4932 20010118 SGD
+SGD S000003252 VMA7 GO:0000221 SGD_REF:S000056362|PMID:10224039 TAS C vacuolar ATPase V1 domain subunit F (14 kDa) YGR020C gene taxon:4932 20010118 SGD
+SGD S000003252 VMA7 GO:0000221 SGD_REF:S000058276|PMID:9442887 TAS C vacuolar ATPase V1 domain subunit F (14 kDa) YGR020C gene taxon:4932 20010118 SGD
+SGD S000003252 VMA7 GO:0000329 SGD_REF:S000068878|PMID:11780757 TAS C vacuolar ATPase V1 domain subunit F (14 kDa) YGR020C gene taxon:4932 20020728 SGD
+SGD S000003252 VMA7 GO:0046961 SGD_REF:S000056362|PMID:10224039 TAS F vacuolar ATPase V1 domain subunit F (14 kDa) YGR020C gene taxon:4932 20030710 SGD
+SGD S000003252 VMA7 GO:0046961 SGD_REF:S000058276|PMID:9442887 TAS F vacuolar ATPase V1 domain subunit F (14 kDa) YGR020C gene taxon:4932 20030710 SGD
+SGD S000003252 VMA7 GO:0007035 SGD_REF:S000056362|PMID:10224039 TAS P vacuolar ATPase V1 domain subunit F (14 kDa) YGR020C gene taxon:4932 20010118 SGD
+SGD S000003252 VMA7 GO:0007035 SGD_REF:S000058276|PMID:9442887 TAS P vacuolar ATPase V1 domain subunit F (14 kDa) YGR020C gene taxon:4932 20010118 SGD
+SGD S000000777 VMA8 GO:0000221 SGD_REF:S000056362|PMID:10224039 TAS C V1 catalytic sector D subunit, vacuolar H-ATPase YEL051W gene taxon:4932 20010118 SGD
+SGD S000000777 VMA8 GO:0000221 SGD_REF:S000058276|PMID:9442887 TAS C V1 catalytic sector D subunit, vacuolar H-ATPase YEL051W gene taxon:4932 20010118 SGD
+SGD S000000777 VMA8 GO:0000329 SGD_REF:S000069241|PMID:11717306 TAS C V1 catalytic sector D subunit, vacuolar H-ATPase YEL051W gene taxon:4932 20020728 SGD
+SGD S000000777 VMA8 GO:0046961 SGD_REF:S000056362|PMID:10224039 TAS F V1 catalytic sector D subunit, vacuolar H-ATPase YEL051W gene taxon:4932 20030710 SGD
+SGD S000000777 VMA8 GO:0046961 SGD_REF:S000058276|PMID:9442887 TAS F V1 catalytic sector D subunit, vacuolar H-ATPase YEL051W gene taxon:4932 20030710 SGD
+SGD S000000777 VMA8 GO:0007035 SGD_REF:S000056362|PMID:10224039 TAS P V1 catalytic sector D subunit, vacuolar H-ATPase YEL051W gene taxon:4932 20010118 SGD
+SGD S000000777 VMA8 GO:0007035 SGD_REF:S000058276|PMID:9442887 TAS P V1 catalytic sector D subunit, vacuolar H-ATPase YEL051W gene taxon:4932 20010118 SGD
+SGD S000028508 VMA9 GO:0000220 SGD_REF:S000075978|PMID:14970230 IMP C Subunit e of the Vo (membrane) sector of the vacuolar H+-ATPase YCL005W-A|CWH36|LDB10 gene taxon:4932 20040427 SGD
+SGD S000028508 VMA9 GO:0005774 SGD_REF:S000075978|PMID:14970230 IMP C Subunit e of the Vo (membrane) sector of the vacuolar H+-ATPase YCL005W-A|CWH36|LDB10 gene taxon:4932 20040427 SGD
+SGD S000028508 VMA9 GO:0042625 SGD_REF:S000075978|PMID:14970230 IMP F Subunit e of the Vo (membrane) sector of the vacuolar H+-ATPase YCL005W-A|CWH36|LDB10 gene taxon:4932 20040427 SGD
+SGD S000028508 VMA9 GO:0042625 SGD_REF:S000075978|PMID:14970230 ISS F Subunit e of the Vo (membrane) sector of the vacuolar H+-ATPase YCL005W-A|CWH36|LDB10 gene taxon:4932 20040427 SGD
+SGD S000028508 VMA9 GO:0000032 SGD_REF:S000075422|PMID:14734024 IMP P Subunit e of the Vo (membrane) sector of the vacuolar H+-ATPase YCL005W-A|CWH36|LDB10 gene taxon:4932 20040206 SGD
+SGD S000028508 VMA9 GO:0007035 SGD_REF:S000075978|PMID:14970230 IMP P Subunit e of the Vo (membrane) sector of the vacuolar H+-ATPase YCL005W-A|CWH36|LDB10 gene taxon:4932 20040427 SGD
+SGD S000001027 VMR1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C ABC transporter YHL035C gene taxon:4932 20040928 SGD
+SGD S000001027 VMR1 GO:0016021 SGD_REF:S000073594|PMID:12755704 ISS C ABC transporter YHL035C gene taxon:4932 20030706 SGD
+SGD S000001027 VMR1 GO:0042626 SGD_REF:S000073594|PMID:12755704 ISS F ABC transporter YHL035C gene taxon:4932 20030706 SGD
+SGD S000001027 VMR1 GO:0006810 SGD_REF:S000073594|PMID:12755704 ISS P ABC transporter YHL035C gene taxon:4932 20030706 SGD
+SGD S000005796 VPH1 GO:0000220 SGD_REF:S000056362|PMID:10224039 TAS C V0 sector subunit, essential for vacuolar acidification and vacuolar H-ATPase activity, vacuolar ATPase V0 domain subunit a (100 kDa), vacuolar H-ATPase YOR270C gene taxon:4932 20010118 SGD
+SGD S000005796 VPH1 GO:0000220 SGD_REF:S000058276|PMID:9442887 TAS C V0 sector subunit, essential for vacuolar acidification and vacuolar H-ATPase activity, vacuolar ATPase V0 domain subunit a (100 kDa), vacuolar H-ATPase YOR270C gene taxon:4932 20010118 SGD
+SGD S000005796 VPH1 GO:0005773 SGD_REF:S000060801|PMID:11278748 IDA C V0 sector subunit, essential for vacuolar acidification and vacuolar H-ATPase activity, vacuolar ATPase V0 domain subunit a (100 kDa), vacuolar H-ATPase YOR270C gene taxon:4932 20030305 SGD
+SGD S000005796 VPH1 GO:0005773 SGD_REF:S000069939|PMID:11948198 IDA C V0 sector subunit, essential for vacuolar acidification and vacuolar H-ATPase activity, vacuolar ATPase V0 domain subunit a (100 kDa), vacuolar H-ATPase YOR270C gene taxon:4932 20030305 SGD
+SGD S000005796 VPH1 GO:0046961 SGD_REF:S000056362|PMID:10224039 TAS F V0 sector subunit, essential for vacuolar acidification and vacuolar H-ATPase activity, vacuolar ATPase V0 domain subunit a (100 kDa), vacuolar H-ATPase YOR270C gene taxon:4932 20030710 SGD
+SGD S000005796 VPH1 GO:0046961 SGD_REF:S000058276|PMID:9442887 TAS F V0 sector subunit, essential for vacuolar acidification and vacuolar H-ATPase activity, vacuolar ATPase V0 domain subunit a (100 kDa), vacuolar H-ATPase YOR270C gene taxon:4932 20030710 SGD
+SGD S000005796 VPH1 GO:0006797 SGD_REF:S000050412|PMID:9933515 IMP P V0 sector subunit, essential for vacuolar acidification and vacuolar H-ATPase activity, vacuolar ATPase V0 domain subunit a (100 kDa), vacuolar H-ATPase YOR270C gene taxon:4932 20010118 SGD
+SGD S000005796 VPH1 GO:0007035 SGD_REF:S000056362|PMID:10224039 TAS P V0 sector subunit, essential for vacuolar acidification and vacuolar H-ATPase activity, vacuolar ATPase V0 domain subunit a (100 kDa), vacuolar H-ATPase YOR270C gene taxon:4932 20010118 SGD
+SGD S000005796 VPH1 GO:0007035 SGD_REF:S000058276|PMID:9442887 TAS P V0 sector subunit, essential for vacuolar acidification and vacuolar H-ATPase activity, vacuolar ATPase V0 domain subunit a (100 kDa), vacuolar H-ATPase YOR270C gene taxon:4932 20010118 SGD
+SGD S000001602 VPH2 GO:0005789 SGD_REF:S000050957|PMID:9325326 IDA C 25.2 kDa protein involved in assembly of vacuolar H(+) ATPase YKL119C|CLS10|VMA12 gene taxon:4932 20010118 SGD
+SGD S000001602 VPH2 GO:0005554 SGD_REF:S000069584 ND F 25.2 kDa protein involved in assembly of vacuolar H(+) ATPase YKL119C|CLS10|VMA12 gene taxon:4932 20010119 SGD
+SGD S000001602 VPH2 GO:0006461 SGD_REF:S000050957|PMID:9325326 IMP P 25.2 kDa protein involved in assembly of vacuolar H(+) ATPase YKL119C|CLS10|VMA12 gene taxon:4932 20010118 SGD
+SGD S000001602 VPH2 GO:0007035 SGD_REF:S000044189|PMID:1628805 IMP P 25.2 kDa protein involved in assembly of vacuolar H(+) ATPase YKL119C|CLS10|VMA12 gene taxon:4932 20010118 SGD
+SGD S000001709 VPS1 GO:0005624 SGD_REF:S000050411|PMID:8299420 IDA C GTP-binding protein (putative), dynamin GTPase family member, similar to mammalian Mx proteins YKR001C|GRD1|LAM1|SPO15|VPL1|VPT26 gene taxon:4932 20010118 SGD
+SGD S000001709 VPS1 GO:0005737 SGD_REF:S000076998|PMID:15265985 IDA C GTP-binding protein (putative), dynamin GTPase family member, similar to mammalian Mx proteins YKR001C|GRD1|LAM1|SPO15|VPL1|VPT26 gene taxon:4932 20041018 SGD
+SGD S000001709 VPS1 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C GTP-binding protein (putative), dynamin GTPase family member, similar to mammalian Mx proteins YKR001C|GRD1|LAM1|SPO15|VPL1|VPT26 gene taxon:4932 20060317 SGD
+SGD S000001709 VPS1 GO:0003924 SGD_REF:S000050411|PMID:8299420 IDA F GTP-binding protein (putative), dynamin GTPase family member, similar to mammalian Mx proteins YKR001C|GRD1|LAM1|SPO15|VPL1|VPT26 gene taxon:4932 20010118 SGD
+SGD S000001709 VPS1 GO:0003924 SGD_REF:S000050411|PMID:8299420 ISS F GTP-binding protein (putative), dynamin GTPase family member, similar to mammalian Mx proteins YKR001C|GRD1|LAM1|SPO15|VPL1|VPT26 gene taxon:4932 20010118 SGD
+SGD S000001709 VPS1 GO:0006623 SGD_REF:S000050411|PMID:8299420 IMP P GTP-binding protein (putative), dynamin GTPase family member, similar to mammalian Mx proteins YKR001C|GRD1|LAM1|SPO15|VPL1|VPT26 gene taxon:4932 20010118 SGD
+SGD S000001709 VPS1 GO:0007031 SGD_REF:S000073055|PMID:12707309 IGI P GTP-binding protein (putative), dynamin GTPase family member, similar to mammalian Mx proteins YKR001C|GRD1|LAM1|SPO15|VPL1|VPT26 gene taxon:4932 20030506 SGD
+SGD S000001709 VPS1 GO:0007031 SGD_REF:S000073055|PMID:12707309 IMP P GTP-binding protein (putative), dynamin GTPase family member, similar to mammalian Mx proteins YKR001C|GRD1|LAM1|SPO15|VPL1|VPT26 gene taxon:4932 20030506 SGD
+SGD S000001709 VPS1 GO:0007031 SGD_REF:S000073055|PMID:12707309 IDA P GTP-binding protein (putative), dynamin GTPase family member, similar to mammalian Mx proteins YKR001C|GRD1|LAM1|SPO15|VPL1|VPT26 gene taxon:4932 20030506 SGD
+SGD S000001709 VPS1 GO:0007034 SGD_REF:S000050411|PMID:8299420 IMP P GTP-binding protein (putative), dynamin GTPase family member, similar to mammalian Mx proteins YKR001C|GRD1|LAM1|SPO15|VPL1|VPT26 gene taxon:4932 20010118 SGD
+SGD S000001709 VPS1 GO:0030036 SGD_REF:S000076998|PMID:15265985 IGI P GTP-binding protein (putative), dynamin GTPase family member, similar to mammalian Mx proteins YKR001C|GRD1|LAM1|SPO15|VPL1|VPT26 gene taxon:4932 20041018 SGD
+SGD S000001709 VPS1 GO:0030036 SGD_REF:S000076998|PMID:15265985 IMP P GTP-binding protein (putative), dynamin GTPase family member, similar to mammalian Mx proteins YKR001C|GRD1|LAM1|SPO15|VPL1|VPT26 gene taxon:4932 20041018 SGD
+SGD S000001709 VPS1 GO:0030036 SGD_REF:S000076998|PMID:15265985 IPI P GTP-binding protein (putative), dynamin GTPase family member, similar to mammalian Mx proteins YKR001C|GRD1|LAM1|SPO15|VPL1|VPT26 gene taxon:4932 20041018 SGD
+SGD S000001709 VPS1 GO:0045053 SGD_REF:S000057861|PMID:8649377 IMP P GTP-binding protein (putative), dynamin GTPase family member, similar to mammalian Mx proteins YKR001C|GRD1|LAM1|SPO15|VPL1|VPT26 gene taxon:4932 20020716 SGD
+SGD S000003963 VPS13 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YLL040C|SOI1|VPT2 gene taxon:4932 20040928 SGD
+SGD S000003963 VPS13 colocalizes_with GO:0005768 SGD_REF:S000074185|PMID:14562095 IDA C YLL040C|SOI1|VPT2 gene taxon:4932 20050422 SGD
+SGD S000003963 VPS13 GO:0019898 SGD_REF:S000047092|PMID:9314526 IDA C YLL040C|SOI1|VPT2 gene taxon:4932 20020826 SGD
+SGD S000003963 VPS13 GO:0005554 SGD_REF:S000069584 ND F YLL040C|SOI1|VPT2 gene taxon:4932 20020826 SGD
+SGD S000003963 VPS13 GO:0007039 SGD_REF:S000043240|PMID:8887651 IMP P YLL040C|SOI1|VPT2 gene taxon:4932 20050422 SGD
+SGD S000003963 VPS13 GO:0030437 SGD_REF:S000047092|PMID:9314526 IMP P YLL040C|SOI1|VPT2 gene taxon:4932 20050422 SGD
+SGD S000003963 VPS13 GO:0045053 SGD_REF:S000047092|PMID:9314526 IMP P YLL040C|SOI1|VPT2 gene taxon:4932 20020826 SGD
+SGD S000003963 VPS13 GO:0045324 SGD_REF:S000043091|PMID:9265642 IGI P YLL040C|SOI1|VPT2 gene taxon:4932 20020930 SGD
+SGD S000003963 VPS13 GO:0045324 SGD_REF:S000043091|PMID:9265642 IMP P YLL040C|SOI1|VPT2 gene taxon:4932 20020930 SGD
+SGD S000000301 VPS15 GO:0000139 SGD_REF:S000052485|PMID:8689553 TAS C serine/threonine protein kinase YBR097W|GRD8|VAC4|VPL19 gene taxon:4932 20010118 SGD
+SGD S000000301 VPS15 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C serine/threonine protein kinase YBR097W|GRD8|VAC4|VPL19 gene taxon:4932 20040928 SGD
+SGD S000000301 VPS15 GO:0004674 SGD_REF:S000042062|PMID:7989323 IDA F serine/threonine protein kinase YBR097W|GRD8|VAC4|VPL19 gene taxon:4932 20030213 SGD
+SGD S000000301 VPS15 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P serine/threonine protein kinase YBR097W|GRD8|VAC4|VPL19 gene taxon:4932 20060209 SGD
+SGD S000000301 VPS15 GO:0006468 SGD_REF:S000042062|PMID:7989323 IDA P serine/threonine protein kinase YBR097W|GRD8|VAC4|VPL19 gene taxon:4932 20030213 SGD
+SGD S000000301 VPS15 GO:0006623 SGD_REF:S000052485|PMID:8689553 TAS P serine/threonine protein kinase YBR097W|GRD8|VAC4|VPL19 gene taxon:4932 20010118 SGD
+SGD S000000301 VPS15 GO:0007034 SGD_REF:S000052485|PMID:8689553 TAS P serine/threonine protein kinase YBR097W|GRD8|VAC4|VPL19 gene taxon:4932 20010118 SGD
+SGD S000000301 VPS15 GO:0045053 SGD_REF:S000057861|PMID:8649377 IMP P serine/threonine protein kinase YBR097W|GRD8|VAC4|VPL19 gene taxon:4932 20020716 SGD
+SGD S000005966 VPS16 GO:0000329 SGD_REF:S000040175|PMID:10944212 IDA C YPL045W|SVL6|VAM9|VPT16 gene taxon:4932 20020827 SGD
+SGD S000005966 VPS16 GO:0005774 SGD_REF:S000040212|PMID:9362071 IDA C YPL045W|SVL6|VAM9|VPT16 gene taxon:4932 20010118 SGD
+SGD S000005966 VPS16 GO:0030897 SGD_REF:S000040175|PMID:10944212 IPI C YPL045W|SVL6|VAM9|VPT16 gene taxon:4932 20041024 SGD
+SGD S000005966 VPS16 GO:0005554 SGD_REF:S000069584 ND F YPL045W|SVL6|VAM9|VPT16 gene taxon:4932 20020827 SGD
+SGD S000005966 VPS16 GO:0006623 SGD_REF:S000040212|PMID:9362071 IMP P YPL045W|SVL6|VAM9|VPT16 gene taxon:4932 20010118 SGD
+SGD S000005966 VPS16 GO:0006895 SGD_REF:S000066047|PMID:11422941 IGI P YPL045W|SVL6|VAM9|VPT16 gene taxon:4932 20020827 SGD
+SGD S000005966 VPS16 GO:0007033 SGD_REF:S000040212|PMID:9362071 IMP P YPL045W|SVL6|VAM9|VPT16 gene taxon:4932 20010118 SGD
+SGD S000005966 VPS16 GO:0042144 SGD_REF:S000040175|PMID:10944212 IDA P YPL045W|SVL6|VAM9|VPT16 gene taxon:4932 20020827 SGD
+SGD S000005966 VPS16 GO:0045324 SGD_REF:S000066047|PMID:11422941 IGI P YPL045W|SVL6|VAM9|VPT16 gene taxon:4932 20020827 SGD
+SGD S000005658 VPS17 GO:0005768 SGD_REF:S000039451|PMID:9700157 IPI C YOR132W|PEP21 gene taxon:4932 20020826 SGD
+SGD S000005658 VPS17 GO:0030904 SGD_REF:S000074969|PMID:11598206 TAS C YOR132W|PEP21 gene taxon:4932 20040804 SGD
+SGD S000005658 VPS17 GO:0005554 SGD_REF:S000069584 ND F YOR132W|PEP21 gene taxon:4932 20020826 SGD
+SGD S000005658 VPS17 contributes_to GO:0008565 SGD_REF:S000039451|PMID:9700157 IMP F YOR132W|PEP21 gene taxon:4932 20060426 SGD
+SGD S000005658 VPS17 contributes_to GO:0008565 SGD_REF:S000039451|PMID:9700157 IPI F YOR132W|PEP21 gene taxon:4932 20060426 SGD
+SGD S000005658 VPS17 GO:0042147 SGD_REF:S000039451|PMID:9700157 IPI P YOR132W|PEP21 gene taxon:4932 20020826 SGD
+SGD S000004682 VPS20 GO:0000815 SGD_REF:S000071351|PMID:12194857 IDA C YMR077C|CHM6|VPL10|VPT20 gene taxon:4932 20040701 SGD
+SGD S000004682 VPS20 GO:0005737 SGD_REF:S000071351|PMID:12194857 IDA C YMR077C|CHM6|VPL10|VPT20 gene taxon:4932 20021021 SGD
+SGD S000004682 VPS20 GO:0005515 SGD_REF:S000071351|PMID:12194857 IDA F YMR077C|CHM6|VPL10|VPT20 gene taxon:4932 20060308 SGD
+SGD S000004682 VPS20 GO:0005515 SGD_REF:S000075969|PMID:15086794 IDA F YMR077C|CHM6|VPL10|VPT20 gene taxon:4932 20060308 SGD
+SGD S000004682 VPS20 GO:0043162 SGD_REF:S000075969|PMID:15086794 IC GO:0000815 P YMR077C|CHM6|VPL10|VPT20 gene taxon:4932 20050125 SGD
+SGD S000004682 VPS20 GO:0045324 SGD_REF:S000071351|PMID:12194857 IPI P YMR077C|CHM6|VPL10|VPT20 gene taxon:4932 20021021 SGD
+SGD S000004682 VPS20 GO:0045324 SGD_REF:S000073931|PMID:12953057 IMP P YMR077C|CHM6|VPL10|VPT20 gene taxon:4932 20030909 SGD
+SGD S000004682 VPS20 GO:0045324 SGD_REF:S000073931|PMID:12953057 IPI P YMR077C|CHM6|VPL10|VPT20 gene taxon:4932 20030909 SGD
+SGD S000005615 VPS21 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C small GTP-binding protein YOR089C|VPS12|VPT12|YPT21|YPT51 gene taxon:4932 20040928 SGD
+SGD S000005615 VPS21 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C small GTP-binding protein YOR089C|VPS12|VPT12|YPT21|YPT51 gene taxon:4932 20060317 SGD
+SGD S000005615 VPS21 GO:0005770 SGD_REF:S000069952|PMID:11872141 IMP C small GTP-binding protein YOR089C|VPS12|VPT12|YPT21|YPT51 gene taxon:4932 20021003 SGD
+SGD S000005615 VPS21 GO:0003924 SGD_REF:S000070388|PMID:12204334 TAS F small GTP-binding protein YOR089C|VPS12|VPT12|YPT21|YPT51 gene taxon:4932 20021003 SGD
+SGD S000005615 VPS21 GO:0003924 SGD_REF:S000042833|PMID:8163546 IMP F small GTP-binding protein YOR089C|VPS12|VPT12|YPT21|YPT51 gene taxon:4932 20021113 SGD
+SGD S000005615 VPS21 GO:0003924 SGD_REF:S000042833|PMID:8163546 ISS F small GTP-binding protein YOR089C|VPS12|VPT12|YPT21|YPT51 gene taxon:4932 20021113 SGD
+SGD S000005615 VPS21 GO:0006623 SGD_REF:S000042833|PMID:8163546 IMP P small GTP-binding protein YOR089C|VPS12|VPT12|YPT21|YPT51 gene taxon:4932 20021113 SGD
+SGD S000005615 VPS21 GO:0006897 SGD_REF:S000042833|PMID:8163546 IMP P small GTP-binding protein YOR089C|VPS12|VPT12|YPT21|YPT51 gene taxon:4932 20021113 SGD
+SGD S000001524 VPS24 GO:0000815 SGD_REF:S000071351|PMID:12194857 IDA C YKL041W|DID3 gene taxon:4932 20040701 SGD
+SGD S000001524 VPS24 GO:0005737 SGD_REF:S000044124|PMID:9606181 IDA C YKL041W|DID3 gene taxon:4932 20020826 SGD
+SGD S000001524 VPS24 GO:0005515 SGD_REF:S000071351|PMID:12194857 IDA F YKL041W|DID3 gene taxon:4932 20060310 SGD
+SGD S000001524 VPS24 GO:0043162 SGD_REF:S000075969|PMID:15086794 IC GO:0000815 P YKL041W|DID3 gene taxon:4932 20050125 SGD
+SGD S000001524 VPS24 GO:0045324 SGD_REF:S000044124|PMID:9606181 IMP P YKL041W|DID3 gene taxon:4932 20020826 SGD
+SGD S000003863 VPS25 GO:0000814 SGD_REF:S000071345|PMID:12194858 IDA C YJR102C|VPT25 gene taxon:4932 20040701 SGD
+SGD S000003863 VPS25 GO:0005515 SGD_REF:S000079899|PMID:15469844 IDA F YJR102C|VPT25 gene taxon:4932 20060208 SGD
+SGD S000003863 VPS25 GO:0005515 SGD_REF:S000075969|PMID:15086794 IDA F YJR102C|VPT25 gene taxon:4932 20060208 SGD
+SGD S000003863 VPS25 GO:0005515 SGD_REF:S000082009|PMID:15913810 IDA F YJR102C|VPT25 gene taxon:4932 20060208 SGD
+SGD S000003863 VPS25 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P YJR102C|VPT25 gene taxon:4932 20060209 SGD
+SGD S000003863 VPS25 GO:0006623 SGD_REF:S000071345|PMID:12194858 IMP P YJR102C|VPT25 gene taxon:4932 20021001 SGD
+SGD S000003863 VPS25 GO:0006623 SGD_REF:S000071345|PMID:12194858 IPI P YJR102C|VPT25 gene taxon:4932 20021001 SGD
+SGD S000003863 VPS25 GO:0043162 SGD_REF:S000075969|PMID:15086794 IC GO:0000814 P YJR102C|VPT25 gene taxon:4932 20050125 SGD
+SGD S000003863 VPS25 GO:0045014 SGD_REF:S000060285|PMID:11278625 IMP P YJR102C|VPT25 gene taxon:4932 20021001 SGD
+SGD S000005289 VPS27 GO:0005768 SGD_REF:S000070211|PMID:12055639 IDA C cysteine rich putative zinc finger essential for function, hydrophilic protein YNR006W|DID7|GRD11|SSV17|VPL23|VPL27|VPT27 gene taxon:4932 20020804 SGD
+SGD S000005289 VPS27 GO:0005515 SGD_REF:S000070211|PMID:12055639 IDA F cysteine rich putative zinc finger essential for function, hydrophilic protein YNR006W|DID7|GRD11|SSV17|VPL23|VPL27|VPT27 gene taxon:4932 20021112 SGD
+SGD S000005289 VPS27 GO:0006605 SGD_REF:S000074213|PMID:12970172 TAS P cysteine rich putative zinc finger essential for function, hydrophilic protein YNR006W|DID7|GRD11|SSV17|VPL23|VPL27|VPT27 gene taxon:4932 20031202 SGD
+SGD S000005289 VPS27 GO:0016197 SGD_REF:S000046976|PMID:7593183 IMP P cysteine rich putative zinc finger essential for function, hydrophilic protein YNR006W|DID7|GRD11|SSV17|VPL23|VPL27|VPT27 gene taxon:4932 20050609 SGD
+SGD S000005289 VPS27 GO:0045053 SGD_REF:S000057861|PMID:8649377 IMP P cysteine rich putative zinc finger essential for function, hydrophilic protein YNR006W|DID7|GRD11|SSV17|VPL23|VPL27|VPT27 gene taxon:4932 20020716 SGD
+SGD S000005986 VPS28 GO:0000813 SGD_REF:S000078323|PMID:15044434 IDA C YPL065W|VPT28 gene taxon:4932 20041117 SGD
+SGD S000005986 VPS28 GO:0000813 SGD_REF:S000061300|PMID:11511343 IPI C YPL065W|VPT28 gene taxon:4932 20060314 SGD
+SGD S000005986 VPS28 GO:0005768 SGD_REF:S000061300|PMID:11511343 IDA C YPL065W|VPT28 gene taxon:4932 20021113 SGD
+SGD S000005986 VPS28 GO:0005515 SGD_REF:S000061300|PMID:11511343 IPI F YPL065W|VPT28 gene taxon:4932 20060314 SGD
+SGD S000005986 VPS28 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P YPL065W|VPT28 gene taxon:4932 20060209 SGD
+SGD S000005986 VPS28 GO:0006612 SGD_REF:S000061300|PMID:11511343 IMP P YPL065W|VPT28 gene taxon:4932 20020827 SGD
+SGD S000005986 VPS28 GO:0006612 SGD_REF:S000061300|PMID:11511343 IPI P YPL065W|VPT28 gene taxon:4932 20020827 SGD
+SGD S000005986 VPS28 GO:0006623 SGD_REF:S000061300|PMID:11511343 IMP P YPL065W|VPT28 gene taxon:4932 20020827 SGD
+SGD S000005986 VPS28 GO:0006623 SGD_REF:S000061300|PMID:11511343 IPI P YPL065W|VPT28 gene taxon:4932 20020827 SGD
+SGD S000005986 VPS28 GO:0043162 SGD_REF:S000075969|PMID:15086794 IC GO:0000813 P YPL065W|VPT28 gene taxon:4932 20050125 SGD
+SGD S000001054 VPS29 GO:0005768 SGD_REF:S000039451|PMID:9700157 IPI C YHR012W|PEP11 gene taxon:4932 20020826 SGD
+SGD S000001054 VPS29 GO:0030904 SGD_REF:S000074969|PMID:11598206 TAS C YHR012W|PEP11 gene taxon:4932 20040804 SGD
+SGD S000001054 VPS29 GO:0005554 SGD_REF:S000069584 ND F YHR012W|PEP11 gene taxon:4932 20020826 SGD
+SGD S000001054 VPS29 contributes_to GO:0008565 SGD_REF:S000039451|PMID:9700157 IMP F YHR012W|PEP11 gene taxon:4932 20060426 SGD
+SGD S000001054 VPS29 contributes_to GO:0008565 SGD_REF:S000039451|PMID:9700157 IPI F YHR012W|PEP11 gene taxon:4932 20060426 SGD
+SGD S000001054 VPS29 GO:0042147 SGD_REF:S000039451|PMID:9700157 IPI P YHR012W|PEP11 gene taxon:4932 20020826 SGD
+SGD S000002903 VPS3 GO:0005737 SGD_REF:S000047885|PMID:2202738 TAS C YDR495C|PEP6|VPL3|VPT17 gene taxon:4932 20020827 SGD
+SGD S000002903 VPS3 GO:0005554 SGD_REF:S000069584 ND F YDR495C|PEP6|VPL3|VPT17 gene taxon:4932 20020827 SGD
+SGD S000002903 VPS3 GO:0000011 SGD_REF:S000075440|PMID:14616069 TAS P YDR495C|PEP6|VPL3|VPT17 gene taxon:4932 20050920 SGD
+SGD S000002903 VPS3 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P YDR495C|PEP6|VPL3|VPT17 gene taxon:4932 20060209 SGD
+SGD S000002903 VPS3 GO:0006623 SGD_REF:S000047885|PMID:2202738 IMP P YDR495C|PEP6|VPL3|VPT17 gene taxon:4932 20020827 SGD
+SGD S000002903 VPS3 GO:0007035 SGD_REF:S000047885|PMID:2202738 IMP P YDR495C|PEP6|VPL3|VPT17 gene taxon:4932 20050531 SGD
+SGD S000006041 VPS30 GO:0005624 SGD_REF:S000050199|PMID:9712845 IDA C YPL120W|APG6|ATG6|VPT30 gene taxon:4932 20050601 SGD
+SGD S000006041 VPS30 GO:0005554 SGD_REF:S000069584 ND F YPL120W|APG6|ATG6|VPT30 gene taxon:4932 20010119 SGD
+SGD S000006041 VPS30 GO:0006623 SGD_REF:S000050199|PMID:9712845 IMP P YPL120W|APG6|ATG6|VPT30 gene taxon:4932 20010118 SGD
+SGD S000006041 VPS30 GO:0006623 SGD_REF:S000048895|PMID:9105038 IMP P YPL120W|APG6|ATG6|VPT30 gene taxon:4932 20010118 SGD
+SGD S000006041 VPS30 GO:0006914 SGD_REF:S000050199|PMID:9712845 IMP P YPL120W|APG6|ATG6|VPT30 gene taxon:4932 20010118 SGD
+SGD S000004388 VPS33 GO:0000329 SGD_REF:S000040175|PMID:10944212 IDA C YLR396C|CLS14|MET27|PEP14|SLP1|VAM5|VPL25|VPT33 gene taxon:4932 20020827 SGD
+SGD S000004388 VPS33 GO:0000329 SGD_REF:S000047466|PMID:9624182 IDA C YLR396C|CLS14|MET27|PEP14|SLP1|VAM5|VPL25|VPT33 gene taxon:4932 20020827 SGD
+SGD S000004388 VPS33 GO:0005829 SGD_REF:S000047466|PMID:9624182 IDA C YLR396C|CLS14|MET27|PEP14|SLP1|VAM5|VPL25|VPT33 gene taxon:4932 20020827 SGD
+SGD S000004388 VPS33 GO:0030897 SGD_REF:S000040175|PMID:10944212 IPI C YLR396C|CLS14|MET27|PEP14|SLP1|VAM5|VPL25|VPT33 gene taxon:4932 20041024 SGD
+SGD S000004388 VPS33 GO:0005524 SGD_REF:S000040175|PMID:10944212 ISS F YLR396C|CLS14|MET27|PEP14|SLP1|VAM5|VPL25|VPT33 gene taxon:4932 20020827 SGD
+SGD S000004388 VPS33 GO:0005524 SGD_REF:S000040175|PMID:10944212 IMP F YLR396C|CLS14|MET27|PEP14|SLP1|VAM5|VPL25|VPT33 gene taxon:4932 20020827 SGD
+SGD S000004388 VPS33 GO:0006895 SGD_REF:S000066047|PMID:11422941 IGI P YLR396C|CLS14|MET27|PEP14|SLP1|VAM5|VPL25|VPT33 gene taxon:4932 20020827 SGD
+SGD S000004388 VPS33 GO:0042144 SGD_REF:S000040175|PMID:10944212 IDA P YLR396C|CLS14|MET27|PEP14|SLP1|VAM5|VPL25|VPT33 gene taxon:4932 20020827 SGD
+SGD S000004388 VPS33 GO:0045324 SGD_REF:S000066047|PMID:11422941 IGI P YLR396C|CLS14|MET27|PEP14|SLP1|VAM5|VPL25|VPT33 gene taxon:4932 20020827 SGD
+SGD S000004230 VPS34 GO:0005624 SGD_REF:S000053384|PMID:7721937 IDA C phosphatidylinositol 3-kinase YLR240W|END12|PEP15|VPL7|VPT29 gene taxon:4932 20010118 SGD
+SGD S000004230 VPS34 GO:0004672 SGD_REF:S000042062|PMID:7989323 IDA F phosphatidylinositol 3-kinase YLR240W|END12|PEP15|VPL7|VPT29 gene taxon:4932 20010118 SGD
+SGD S000004230 VPS34 GO:0016303 SGD_REF:S000042062|PMID:7989323 IDA F phosphatidylinositol 3-kinase YLR240W|END12|PEP15|VPL7|VPT29 gene taxon:4932 20010202 SGD
+SGD S000004230 VPS34 GO:0000011 SGD_REF:S000048206|PMID:2247081 IMP P phosphatidylinositol 3-kinase YLR240W|END12|PEP15|VPL7|VPT29 gene taxon:4932 20010118 SGD
+SGD S000004230 VPS34 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P phosphatidylinositol 3-kinase YLR240W|END12|PEP15|VPL7|VPT29 gene taxon:4932 20060210 SGD
+SGD S000004230 VPS34 GO:0006468 SGD_REF:S000042062|PMID:7989323 IDA P phosphatidylinositol 3-kinase YLR240W|END12|PEP15|VPL7|VPT29 gene taxon:4932 20010118 SGD
+SGD S000004230 VPS34 GO:0006623 SGD_REF:S000042062|PMID:7989323 IDA P phosphatidylinositol 3-kinase YLR240W|END12|PEP15|VPL7|VPT29 gene taxon:4932 20010118 SGD
+SGD S000004230 VPS34 GO:0007034 SGD_REF:S000048206|PMID:2247081 IMP P phosphatidylinositol 3-kinase YLR240W|END12|PEP15|VPL7|VPT29 gene taxon:4932 20010118 SGD
+SGD S000004230 VPS34 GO:0046854 SGD_REF:S000042062|PMID:7989323 IDA P phosphatidylinositol 3-kinase YLR240W|END12|PEP15|VPL7|VPT29 gene taxon:4932 20050111 SGD
+SGD S000004230 VPS34 GO:0048017 SGD_REF:S000042062|PMID:7989323 TAS P phosphatidylinositol 3-kinase YLR240W|END12|PEP15|VPL7|VPT29 gene taxon:4932 20050524 SGD
+SGD S000003690 VPS35 GO:0005768 SGD_REF:S000039451|PMID:9700157 IPI C retromer complex component YJL154C|GRD9|VPT7 gene taxon:4932 20020826 SGD
+SGD S000003690 VPS35 GO:0030904 SGD_REF:S000074969|PMID:11598206 TAS C retromer complex component YJL154C|GRD9|VPT7 gene taxon:4932 20040804 SGD
+SGD S000003690 VPS35 GO:0005554 SGD_REF:S000069584 ND F retromer complex component YJL154C|GRD9|VPT7 gene taxon:4932 20020826 SGD
+SGD S000003690 VPS35 contributes_to GO:0008565 SGD_REF:S000039451|PMID:9700157 IMP F retromer complex component YJL154C|GRD9|VPT7 gene taxon:4932 20060426 SGD
+SGD S000003690 VPS35 contributes_to GO:0008565 SGD_REF:S000039451|PMID:9700157 IPI F retromer complex component YJL154C|GRD9|VPT7 gene taxon:4932 20060426 SGD
+SGD S000003690 VPS35 GO:0042147 SGD_REF:S000039451|PMID:9700157 IPI P retromer complex component YJL154C|GRD9|VPT7 gene taxon:4932 20020826 SGD
+SGD S000003690 VPS35 GO:0045053 SGD_REF:S000057861|PMID:8649377 IMP P retromer complex component YJL154C|GRD9|VPT7 gene taxon:4932 20020716 SGD
+SGD S000004409 VPS36 GO:0000814 SGD_REF:S000071345|PMID:12194858 IDA C YLR417W|GRD12|VAC3|VPL11 gene taxon:4932 20040701 SGD
+SGD S000004409 VPS36 GO:0016299 SGD_REF:S000070055|PMID:11940600 IMP F YLR417W|GRD12|VAC3|VPL11 gene taxon:4932 20030226 SGD
+SGD S000004409 VPS36 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P YLR417W|GRD12|VAC3|VPL11 gene taxon:4932 20060209 SGD
+SGD S000004409 VPS36 GO:0006623 SGD_REF:S000071345|PMID:12194858 IMP P YLR417W|GRD12|VAC3|VPL11 gene taxon:4932 20021001 SGD
+SGD S000004409 VPS36 GO:0006623 SGD_REF:S000071345|PMID:12194858 IPI P YLR417W|GRD12|VAC3|VPL11 gene taxon:4932 20021001 SGD
+SGD S000004409 VPS36 GO:0043162 SGD_REF:S000075969|PMID:15086794 IC GO:0000814 P YLR417W|GRD12|VAC3|VPL11 gene taxon:4932 20050125 SGD
+SGD S000004409 VPS36 GO:0045014 SGD_REF:S000060285|PMID:11278625 IMP P YLR417W|GRD12|VAC3|VPL11 gene taxon:4932 20021001 SGD
+SGD S000004409 VPS36 GO:0045053 SGD_REF:S000057861|PMID:8649377 IMP P YLR417W|GRD12|VAC3|VPL11 gene taxon:4932 20020716 SGD
+SGD S000004352 VPS38 GO:0008372 SGD_REF:S000069584 ND C YLR360W|VPL17 gene taxon:4932 20050601 SGD
+SGD S000004352 VPS38 GO:0005554 SGD_REF:S000069584 ND F YLR360W|VPL17 gene taxon:4932 20020930 SGD
+SGD S000004352 VPS38 GO:0045324 SGD_REF:S000043091|PMID:9265642 IGI P YLR360W|VPL17 gene taxon:4932 20020930 SGD
+SGD S000004352 VPS38 GO:0045324 SGD_REF:S000043091|PMID:9265642 IMP P YLR360W|VPL17 gene taxon:4932 20020930 SGD
+SGD S000006377 VPS4 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C AAA ATPase YPR173C|CSC1|DID6|END13|GRD13|VPL4|VPT10 gene taxon:4932 20020507 SGD
+SGD S000006377 VPS4 GO:0005783 SGD_REF:S000069459|PMID:11914276 IDA C AAA ATPase YPR173C|CSC1|DID6|END13|GRD13|VPL4|VPT10 gene taxon:4932 20020507 SGD
+SGD S000006377 VPS4 GO:0016887 SGD_REF:S000044124|PMID:9606181 IDA F AAA ATPase YPR173C|CSC1|DID6|END13|GRD13|VPL4|VPT10 gene taxon:4932 20020826 SGD
+SGD S000006377 VPS4 GO:0045053 SGD_REF:S000057861|PMID:8649377 IMP P AAA ATPase YPR173C|CSC1|DID6|END13|GRD13|VPL4|VPT10 gene taxon:4932 20020716 SGD
+SGD S000006377 VPS4 GO:0045324 SGD_REF:S000044124|PMID:9606181 IMP P AAA ATPase YPR173C|CSC1|DID6|END13|GRD13|VPL4|VPT10 gene taxon:4932 20020826 SGD
+SGD S000006377 VPS4 GO:0045324 SGD_REF:S000044124|PMID:9606181 IPI P AAA ATPase YPR173C|CSC1|DID6|END13|GRD13|VPL4|VPT10 gene taxon:4932 20020826 SGD
+SGD S000002487 VPS41 GO:0000324 SGD_REF:S000045452|PMID:9111041 IDA C YDR080W|CVT8|FET2|SVL2|VAM2|VPL20 gene taxon:4932 20020313 SGD
+SGD S000002487 VPS41 GO:0005768 SGD_REF:S000074185|PMID:14562095 IDA C YDR080W|CVT8|FET2|SVL2|VAM2|VPL20 gene taxon:4932 20031028 SGD
+SGD S000002487 VPS41 GO:0005774 SGD_REF:S000045452|PMID:9111041 IDA C YDR080W|CVT8|FET2|SVL2|VAM2|VPL20 gene taxon:4932 20020313 SGD
+SGD S000002487 VPS41 GO:0030897 SGD_REF:S000040175|PMID:10944212 IPI C YDR080W|CVT8|FET2|SVL2|VAM2|VPL20 gene taxon:4932 20041024 SGD
+SGD S000002487 VPS41 GO:0017112 SGD_REF:S000059565|PMID:11062257 IPI F YDR080W|CVT8|FET2|SVL2|VAM2|VPL20 gene taxon:4932 20021113 SGD
+SGD S000002487 VPS41 GO:0006827 SGD_REF:S000044014|PMID:9614122 TAS P YDR080W|CVT8|FET2|SVL2|VAM2|VPL20 gene taxon:4932 20030227 SGD
+SGD S000002487 VPS41 GO:0007033 SGD_REF:S000045452|PMID:9111041 IMP P YDR080W|CVT8|FET2|SVL2|VAM2|VPL20 gene taxon:4932 20020313 SGD
+SGD S000002487 VPS41 GO:0015031 SGD_REF:S000040248|PMID:9184222 IMP P YDR080W|CVT8|FET2|SVL2|VAM2|VPL20 gene taxon:4932 20030227 SGD
+SGD S000002487 VPS41 GO:0042144 SGD_REF:S000040175|PMID:10944212 IMP P YDR080W|CVT8|FET2|SVL2|VAM2|VPL20 gene taxon:4932 20020313 SGD
+SGD S000002487 VPS41 GO:0042144 SGD_REF:S000040175|PMID:10944212 IDA P YDR080W|CVT8|FET2|SVL2|VAM2|VPL20 gene taxon:4932 20020313 SGD
+SGD S000003063 VPS45 GO:0000139 SGD_REF:S000050447|PMID:7720726 IDA C YGL095C|STT10|VPL28 gene taxon:4932 20020917 SGD
+SGD S000003063 VPS45 GO:0005829 SGD_REF:S000047466|PMID:9624182 IDA C YGL095C|STT10|VPL28 gene taxon:4932 20030227 SGD
+SGD S000003063 VPS45 GO:0019898 SGD_REF:S000050447|PMID:7720726 IDA C YGL095C|STT10|VPL28 gene taxon:4932 20020917 SGD
+SGD S000003063 VPS45 GO:0051082 SGD_REF:S000061408|PMID:11432826 IMP F YGL095C|STT10|VPL28 gene taxon:4932 20020917 SGD
+SGD S000003063 VPS45 GO:0006461 SGD_REF:S000061408|PMID:11432826 IMP P YGL095C|STT10|VPL28 gene taxon:4932 20020917 SGD
+SGD S000003063 VPS45 GO:0006896 SGD_REF:S000050447|PMID:7720726 IMP P YGL095C|STT10|VPL28 gene taxon:4932 20010118 SGD
+SGD S000003063 VPS45 GO:0007033 SGD_REF:S000054176|PMID:9650782 IMP P YGL095C|STT10|VPL28 gene taxon:4932 20010118 SGD
+SGD S000003063 VPS45 GO:0018987 SGD_REF:S000044617|PMID:10514566 TAS P YGL095C|STT10|VPL28 gene taxon:4932 20030227 SGD
+SGD S000005595 VPS5 GO:0005768 SGD_REF:S000039451|PMID:9700157 IDA C simialr to sorting nexin I YOR069W|GRD2|PEP10|VPT5|YOR29-20 gene taxon:4932 20020826 SGD
+SGD S000005595 VPS5 GO:0005768 SGD_REF:S000041460|PMID:9175702 IDA C simialr to sorting nexin I YOR069W|GRD2|PEP10|VPT5|YOR29-20 gene taxon:4932 20050712 SGD
+SGD S000005595 VPS5 GO:0005829 SGD_REF:S000041460|PMID:9175702 IDA C simialr to sorting nexin I YOR069W|GRD2|PEP10|VPT5|YOR29-20 gene taxon:4932 20050712 SGD
+SGD S000005595 VPS5 GO:0030904 SGD_REF:S000074969|PMID:11598206 TAS C simialr to sorting nexin I YOR069W|GRD2|PEP10|VPT5|YOR29-20 gene taxon:4932 20040804 SGD
+SGD S000005595 VPS5 contributes_to GO:0008565 SGD_REF:S000039451|PMID:9700157 IMP F simialr to sorting nexin I YOR069W|GRD2|PEP10|VPT5|YOR29-20 gene taxon:4932 20060426 SGD
+SGD S000005595 VPS5 contributes_to GO:0008565 SGD_REF:S000039451|PMID:9700157 IPI F simialr to sorting nexin I YOR069W|GRD2|PEP10|VPT5|YOR29-20 gene taxon:4932 20060426 SGD
+SGD S000005595 VPS5 GO:0042147 SGD_REF:S000039451|PMID:9700157 IPI P simialr to sorting nexin I YOR069W|GRD2|PEP10|VPT5|YOR29-20 gene taxon:4932 20020826 SGD
+SGD S000005595 VPS5 GO:0045053 SGD_REF:S000057861|PMID:8649377 IMP P simialr to sorting nexin I YOR069W|GRD2|PEP10|VPT5|YOR29-20 gene taxon:4932 20020716 SGD
+SGD S000001728 VPS51 GO:0000938 SGD_REF:S000073099|PMID:12446664 IPI C function unknown YKR020W|API3|VPS67|WHI6 gene taxon:4932 20030625 SGD
+SGD S000001728 VPS51 GO:0000938 SGD_REF:S000071839|PMID:12377769 IPI C function unknown YKR020W|API3|VPS67|WHI6 gene taxon:4932 20030625 SGD
+SGD S000001728 VPS51 GO:0005794 SGD_REF:S000071839|PMID:12377769 IDA C function unknown YKR020W|API3|VPS67|WHI6 gene taxon:4932 20030625 SGD
+SGD S000001728 VPS51 GO:0005515 SGD_REF:S000071839|PMID:12377769 IPI SGD:S000002876 F function unknown YKR020W|API3|VPS67|WHI6 gene taxon:4932 20030625 SGD
+SGD S000001728 VPS51 GO:0006623 SGD_REF:S000070264|PMID:12134085 IMP P function unknown YKR020W|API3|VPS67|WHI6 gene taxon:4932 20021016 SGD
+SGD S000001728 VPS51 GO:0007118 SGD_REF:S000069686|PMID:11957109 IDA P function unknown YKR020W|API3|VPS67|WHI6 gene taxon:4932 20020629 SGD
+SGD S000001728 VPS51 GO:0016050 SGD_REF:S000073099|PMID:12446664 IMP P function unknown YKR020W|API3|VPS67|WHI6 gene taxon:4932 20030613 SGD
+SGD S000001728 VPS51 GO:0042147 SGD_REF:S000073382|PMID:12686613 IDA P function unknown YKR020W|API3|VPS67|WHI6 gene taxon:4932 20031124 SGD
+SGD S000002892 VPS52 GO:0000938 SGD_REF:S000043232|PMID:10637310 IPI C YDR484W|SAC2 gene taxon:4932 20030625 SGD
+SGD S000002892 VPS52 GO:0005794 SGD_REF:S000068970|PMID:11689439 TAS C YDR484W|SAC2 gene taxon:4932 20020707 SGD
+SGD S000002892 VPS52 GO:0005794 SGD_REF:S000043232|PMID:10637310 IDA C YDR484W|SAC2 gene taxon:4932 20030625 SGD
+SGD S000002892 VPS52 GO:0005515 SGD_REF:S000071839|PMID:12377769 IPI SGD:S000004252 F YDR484W|SAC2 gene taxon:4932 20030625 SGD
+SGD S000002892 VPS52 GO:0006896 SGD_REF:S000043232|PMID:10637310 IMP P YDR484W|SAC2 gene taxon:4932 20020930 SGD
+SGD S000002892 VPS52 GO:0030029 SGD_REF:S000058447|PMID:9153752 IGI P YDR484W|SAC2 gene taxon:4932 20010620 SGD
+SGD S000002892 VPS52 GO:0042147 SGD_REF:S000073382|PMID:12686613 IDA P YDR484W|SAC2 gene taxon:4932 20031124 SGD
+SGD S000003566 VPS53 GO:0000938 SGD_REF:S000043232|PMID:10637310 IPI C hydrophilic protein that is peripherally associated with the late Golgi and forms a stable complex with Vps52p and Vps54p YJL029C gene taxon:4932 20030625 SGD
+SGD S000003566 VPS53 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C hydrophilic protein that is peripherally associated with the late Golgi and forms a stable complex with Vps52p and Vps54p YJL029C gene taxon:4932 20020507 SGD
+SGD S000003566 VPS53 GO:0005794 SGD_REF:S000068970|PMID:11689439 TAS C hydrophilic protein that is peripherally associated with the late Golgi and forms a stable complex with Vps52p and Vps54p YJL029C gene taxon:4932 20020707 SGD
+SGD S000003566 VPS53 GO:0005794 SGD_REF:S000043232|PMID:10637310 IDA C hydrophilic protein that is peripherally associated with the late Golgi and forms a stable complex with Vps52p and Vps54p YJL029C gene taxon:4932 20030625 SGD
+SGD S000003566 VPS53 GO:0005515 SGD_REF:S000071839|PMID:12377769 IPI F hydrophilic protein that is peripherally associated with the late Golgi and forms a stable complex with Vps52p and Vps54p YJL029C gene taxon:4932 20050713 SGD
+SGD S000003566 VPS53 GO:0006896 SGD_REF:S000043232|PMID:10637310 IMP P hydrophilic protein that is peripherally associated with the late Golgi and forms a stable complex with Vps52p and Vps54p YJL029C gene taxon:4932 20020930 SGD
+SGD S000003566 VPS53 GO:0042147 SGD_REF:S000073382|PMID:12686613 IDA P hydrophilic protein that is peripherally associated with the late Golgi and forms a stable complex with Vps52p and Vps54p YJL029C gene taxon:4932 20031124 SGD
+SGD S000002434 VPS54 GO:0000938 SGD_REF:S000043232|PMID:10637310 IPI C YDR027C|CGP1|LUV1|TCS3 gene taxon:4932 20030625 SGD
+SGD S000002434 VPS54 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YDR027C|CGP1|LUV1|TCS3 gene taxon:4932 20040928 SGD
+SGD S000002434 VPS54 GO:0005794 SGD_REF:S000068970|PMID:11689439 TAS C YDR027C|CGP1|LUV1|TCS3 gene taxon:4932 20020707 SGD
+SGD S000002434 VPS54 GO:0005794 SGD_REF:S000043232|PMID:10637310 IDA C YDR027C|CGP1|LUV1|TCS3 gene taxon:4932 20030625 SGD
+SGD S000002434 VPS54 GO:0005554 SGD_REF:S000069584 ND F YDR027C|CGP1|LUV1|TCS3 gene taxon:4932 20021211 SGD
+SGD S000002434 VPS54 GO:0006896 SGD_REF:S000043232|PMID:10637310 IMP P YDR027C|CGP1|LUV1|TCS3 gene taxon:4932 20020930 SGD
+SGD S000002434 VPS54 GO:0042147 SGD_REF:S000073382|PMID:12686613 IDA P YDR027C|CGP1|LUV1|TCS3 gene taxon:4932 20031124 SGD
+SGD S000003805 VPS55 GO:0005770 SGD_REF:S000069841|PMID:12006663 IDA C Involved in Golgi to vacuolar targeting YJR044C gene taxon:4932 20021010 SGD
+SGD S000003805 VPS55 GO:0005554 SGD_REF:S000069584 ND F Involved in Golgi to vacuolar targeting YJR044C gene taxon:4932 20021010 SGD
+SGD S000003805 VPS55 GO:0045324 SGD_REF:S000069841|PMID:12006663 IMP P Involved in Golgi to vacuolar targeting YJR044C gene taxon:4932 20021010 SGD
+SGD S000002894 VPS60 GO:0000329 SGD_REF:S000074185|PMID:14562095 IDA C YDR486C|CHM5|MOS10 gene taxon:4932 20031028 SGD
+SGD S000002894 VPS60 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YDR486C|CHM5|MOS10 gene taxon:4932 20020507 SGD
+SGD S000002894 VPS60 GO:0005554 SGD_REF:S000069584 ND F YDR486C|CHM5|MOS10 gene taxon:4932 20010201 SGD
+SGD S000002894 VPS60 GO:0030447 SGD_REF:S000074064|PMID:12940986 IMP P YDR486C|CHM5|MOS10 gene taxon:4932 20041012 SGD
+SGD S000002894 VPS60 GO:0045324 SGD_REF:S000071351|PMID:12194857 IMP P YDR486C|CHM5|MOS10 gene taxon:4932 20050125 SGD
+SGD S000003373 VPS62 GO:0008372 SGD_REF:S000069584 ND C YGR141W gene taxon:4932 20021016 SGD
+SGD S000003373 VPS62 GO:0005554 SGD_REF:S000069584 ND F YGR141W gene taxon:4932 20021016 SGD
+SGD S000003373 VPS62 GO:0006623 SGD_REF:S000070264|PMID:12134085 IMP P YGR141W gene taxon:4932 20021016 SGD
+SGD S000002608 VPS64 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDR200C|FAR9 gene taxon:4932 20031028 SGD
+SGD S000002608 VPS64 GO:0005789 SGD_REF:S000072636|PMID:12514182 IDA C YDR200C|FAR9 gene taxon:4932 20031014 SGD
+SGD S000002608 VPS64 GO:0005554 SGD_REF:S000069584 ND F YDR200C|FAR9 gene taxon:4932 20021016 SGD
+SGD S000002608 VPS64 GO:0000751 SGD_REF:S000072607|PMID:12588993 IMP P YDR200C|FAR9 gene taxon:4932 20030314 SGD
+SGD S000002608 VPS64 GO:0000751 SGD_REF:S000072607|PMID:12588993 IPI P YDR200C|FAR9 gene taxon:4932 20030314 SGD
+SGD S000002608 VPS64 GO:0006623 SGD_REF:S000070264|PMID:12134085 IMP P YDR200C|FAR9 gene taxon:4932 20021016 SGD
+SGD S000006343 VPS66 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YPR139C gene taxon:4932 20020507 SGD
+SGD S000006343 VPS66 GO:0005554 SGD_REF:S000069584 ND F YPR139C gene taxon:4932 20021016 SGD
+SGD S000006343 VPS66 GO:0006623 SGD_REF:S000070264|PMID:12134085 IMP P YPR139C gene taxon:4932 20021016 SGD
+SGD S000005489 VPS68 GO:0000329 SGD_REF:S000074185|PMID:14562095 IDA C YOL129W gene taxon:4932 20031028 SGD
+SGD S000005489 VPS68 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YOL129W gene taxon:4932 20040928 SGD
+SGD S000005489 VPS68 GO:0005554 SGD_REF:S000069584 ND F YOL129W gene taxon:4932 20021016 SGD
+SGD S000005489 VPS68 GO:0006623 SGD_REF:S000070264|PMID:12134085 IMP P YOL129W gene taxon:4932 20021016 SGD
+SGD S000003887 VPS70 GO:0008372 SGD_REF:S000069584 ND C YJR126C gene taxon:4932 20021016 SGD
+SGD S000003887 VPS70 GO:0005554 SGD_REF:S000069584 ND F YJR126C gene taxon:4932 20021016 SGD
+SGD S000003887 VPS70 GO:0006623 SGD_REF:S000070264|PMID:12134085 IMP P YJR126C gene taxon:4932 20021016 SGD
+SGD S000004505 VPS71 GO:0000812 SGD_REF:S000074662|PMID:14645854 IPI C YML041C|SWC6 gene taxon:4932 20040412 SGD
+SGD S000004505 VPS71 GO:0000812 SGD_REF:S000075430|PMID:14690608 IPI C YML041C|SWC6 gene taxon:4932 20040412 SGD
+SGD S000004505 VPS71 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YML041C|SWC6 gene taxon:4932 20031028 SGD
+SGD S000004505 VPS71 GO:0005554 SGD_REF:S000069584 ND F YML041C|SWC6 gene taxon:4932 20021016 SGD
+SGD S000004505 VPS71 GO:0006338 SGD_REF:S000074662|PMID:14645854 IDA P YML041C|SWC6 gene taxon:4932 20040322 SGD
+SGD S000004505 VPS71 GO:0006338 SGD_REF:S000075430|PMID:14690608 IGI P YML041C|SWC6 gene taxon:4932 20040323 SGD
+SGD S000004505 VPS71 GO:0006338 SGD_REF:S000075430|PMID:14690608 IPI P YML041C|SWC6 gene taxon:4932 20040323 SGD
+SGD S000004505 VPS71 GO:0006623 SGD_REF:S000070264|PMID:12134085 IMP P YML041C|SWC6 gene taxon:4932 20021016 SGD
+SGD S000002893 VPS72 GO:0000812 SGD_REF:S000074662|PMID:14645854 IPI C YDR485C|SWC2 gene taxon:4932 20040412 SGD
+SGD S000002893 VPS72 GO:0000812 SGD_REF:S000075430|PMID:14690608 IPI C YDR485C|SWC2 gene taxon:4932 20040412 SGD
+SGD S000002893 VPS72 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YDR485C|SWC2 gene taxon:4932 20031028 SGD
+SGD S000002893 VPS72 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YDR485C|SWC2 gene taxon:4932 20020507 SGD
+SGD S000002893 VPS72 GO:0005554 SGD_REF:S000069584 ND F YDR485C|SWC2 gene taxon:4932 20021016 SGD
+SGD S000002893 VPS72 GO:0006338 SGD_REF:S000074662|PMID:14645854 IDA P YDR485C|SWC2 gene taxon:4932 20040322 SGD
+SGD S000002893 VPS72 GO:0006338 SGD_REF:S000075430|PMID:14690608 IPI P YDR485C|SWC2 gene taxon:4932 20040323 SGD
+SGD S000002893 VPS72 GO:0006338 SGD_REF:S000075430|PMID:14690608 IGI P YDR485C|SWC2 gene taxon:4932 20040323 SGD
+SGD S000002893 VPS72 GO:0006623 SGD_REF:S000070264|PMID:12134085 IMP P YDR485C|SWC2 gene taxon:4932 20021016 SGD
+SGD S000003072 VPS73 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YGL104C gene taxon:4932 20040813 SGD
+SGD S000003072 VPS73 GO:0005554 SGD_REF:S000069584 ND F YGL104C gene taxon:4932 20021016 SGD
+SGD S000003072 VPS73 GO:0006623 SGD_REF:S000070264|PMID:12134085 IMP P YGL104C gene taxon:4932 20021016 SGD
+SGD S000002780 VPS74 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YDR372C|API1 gene taxon:4932 20031028 SGD
+SGD S000002780 VPS74 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDR372C|API1 gene taxon:4932 20031028 SGD
+SGD S000002780 VPS74 GO:0005554 SGD_REF:S000069584 ND F YDR372C|API1 gene taxon:4932 20021016 SGD
+SGD S000002780 VPS74 GO:0006623 SGD_REF:S000070264|PMID:12134085 IMP P YDR372C|API1 gene taxon:4932 20021016 SGD
+SGD S000005190 VPS75 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YNL246W gene taxon:4932 20031028 SGD
+SGD S000005190 VPS75 GO:0005554 SGD_REF:S000069584 ND F YNL246W gene taxon:4932 20021016 SGD
+SGD S000005190 VPS75 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P YNL246W gene taxon:4932 20060210 SGD
+SGD S000005190 VPS75 GO:0006623 SGD_REF:S000070264|PMID:12134085 IMP P YNL246W gene taxon:4932 20021016 SGD
+SGD S000000002 VPS8 GO:0005624 SGD_REF:S000043076|PMID:8969229 IDA C membrane-associated hydrophilic protein which contains a C-terminal cysteine-rich region that conforms to the H2 variant of the RING finger Zn2+ binding motif YAL002W|FUN15|VPT8 gene taxon:4932 20020930 SGD
+SGD S000000002 VPS8 GO:0005554 SGD_REF:S000069584 ND F membrane-associated hydrophilic protein which contains a C-terminal cysteine-rich region that conforms to the H2 variant of the RING finger Zn2+ binding motif YAL002W|FUN15|VPT8 gene taxon:4932 20020930 SGD
+SGD S000000002 VPS8 GO:0045324 SGD_REF:S000043091|PMID:9265642 IGI P membrane-associated hydrophilic protein which contains a C-terminal cysteine-rich region that conforms to the H2 variant of the RING finger Zn2+ binding motif YAL002W|FUN15|VPT8 gene taxon:4932 20020930 SGD
+SGD S000000002 VPS8 GO:0045324 SGD_REF:S000043091|PMID:9265642 IMP P membrane-associated hydrophilic protein which contains a C-terminal cysteine-rich region that conforms to the H2 variant of the RING finger Zn2+ binding motif YAL002W|FUN15|VPT8 gene taxon:4932 20020930 SGD
+SGD S000004563 VPS9 GO:0005829 SGD_REF:S000046859|PMID:8628304 IDA C YML097C|VPL31|VPT9 gene taxon:4932 20020827 SGD
+SGD S000004563 VPS9 GO:0005085 SGD_REF:S000046430|PMID:10329739 IDA F YML097C|VPL31|VPT9 gene taxon:4932 20020827 SGD
+SGD S000004563 VPS9 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P YML097C|VPL31|VPT9 gene taxon:4932 20060209 SGD
+SGD S000004563 VPS9 GO:0006623 SGD_REF:S000046859|PMID:8628304 IMP P YML097C|VPL31|VPT9 gene taxon:4932 20020827 SGD
+SGD S000003193 VRG4 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YGL225W|GOG5|LDB3|VAN2|VIG4 gene taxon:4932 20040928 SGD
+SGD S000003193 VRG4 GO:0005794 SGD_REF:S000040647|PMID:9395539 IDA C YGL225W|GOG5|LDB3|VAN2|VIG4 gene taxon:4932 20020528 SGD
+SGD S000003193 VRG4 GO:0005338 SGD_REF:S000040647|PMID:9395539 ISS F YGL225W|GOG5|LDB3|VAN2|VIG4 gene taxon:4932 20020528 SGD
+SGD S000003193 VRG4 GO:0005338 SGD_REF:S000040647|PMID:9395539 IMP F YGL225W|GOG5|LDB3|VAN2|VIG4 gene taxon:4932 20020528 SGD
+SGD S000003193 VRG4 GO:0006487 SGD_REF:S000040647|PMID:9395539 IMP P YGL225W|GOG5|LDB3|VAN2|VIG4 gene taxon:4932 20020528 SGD
+SGD S000003193 VRG4 GO:0015780 SGD_REF:S000040647|PMID:9395539 IDA P YGL225W|GOG5|LDB3|VAN2|VIG4 gene taxon:4932 20020528 SGD
+SGD S000003193 VRG4 GO:0015780 SGD_REF:S000040647|PMID:9395539 IMP P YGL225W|GOG5|LDB3|VAN2|VIG4 gene taxon:4932 20020528 SGD
+SGD S000003193 VRG4 GO:0030259 SGD_REF:S000040647|PMID:9395539 IMP P YGL225W|GOG5|LDB3|VAN2|VIG4 gene taxon:4932 20020528 SGD
+SGD S000004329 VRP1 GO:0030479 SGD_REF:S000041005|PMID:10652251 IDA C proline-rich protein verprolin YLR337C|END5|MDP2|YLR337W gene taxon:4932 20010118 SGD
+SGD S000004329 VRP1 GO:0003779 SGD_REF:S000048725|PMID:9412475 IDA F proline-rich protein verprolin YLR337C|END5|MDP2|YLR337W gene taxon:4932 20010118 SGD
+SGD S000004329 VRP1 GO:0006897 SGD_REF:S000041005|PMID:10652251 IMP P proline-rich protein verprolin YLR337C|END5|MDP2|YLR337W gene taxon:4932 20010118 SGD
+SGD S000004329 VRP1 GO:0006970 SGD_REF:S000041005|PMID:10652251 IMP P proline-rich protein verprolin YLR337C|END5|MDP2|YLR337W gene taxon:4932 20010118 SGD
+SGD S000004329 VRP1 GO:0007015 SGD_REF:S000048725|PMID:9412475 IPI P proline-rich protein verprolin YLR337C|END5|MDP2|YLR337W gene taxon:4932 20010118 SGD
+SGD S000004329 VRP1 GO:0007121 SGD_REF:S000041005|PMID:10652251 IMP P proline-rich protein verprolin YLR337C|END5|MDP2|YLR337W gene taxon:4932 20010118 SGD
+SGD S000004171 VTA1 GO:0005768 SGD_REF:S000074185|PMID:14562095 IDA C YLR181C gene taxon:4932 20031028 SGD
+SGD S000004171 VTA1 GO:0005771 SGD_REF:S000075670|PMID:14701806 IDA C YLR181C gene taxon:4932 20040723 SGD
+SGD S000004171 VTA1 GO:0005554 SGD_REF:S000069584 ND F YLR181C gene taxon:4932 20021125 SGD
+SGD S000004171 VTA1 GO:0045324 SGD_REF:S000073931|PMID:12953057 IMP P YLR181C gene taxon:4932 20030909 SGD
+SGD S000004171 VTA1 GO:0045324 SGD_REF:S000073931|PMID:12953057 IPI P YLR181C gene taxon:4932 20030909 SGD
+SGD S000000874 VTC1 GO:0031310 SGD_REF:S000074092|PMID:12584253 IDA C S. pombe Nrf1p homolog (97% identical in predicted amino acid sequence) YER072W|NRF1|PHM4 gene taxon:4932 20050505 SGD
+SGD S000000874 VTC1 GO:0005554 SGD_REF:S000069584 ND F S. pombe Nrf1p homolog (97% identical in predicted amino acid sequence) YER072W|NRF1|PHM4 gene taxon:4932 20020715 SGD
+SGD S000000874 VTC1 GO:0042144 SGD_REF:S000069426|PMID:11823419 IMP P S. pombe Nrf1p homolog (97% identical in predicted amino acid sequence) YER072W|NRF1|PHM4 gene taxon:4932 20020715 SGD
+SGD S000001890 VTC2 GO:0005774 SGD_REF:S000069426|PMID:11823419 IDA C polyphosphate synthetase (putative) YFL004W|PHM1 gene taxon:4932 20020715 SGD
+SGD S000001890 VTC2 GO:0005554 SGD_REF:S000069584 ND F polyphosphate synthetase (putative) YFL004W|PHM1 gene taxon:4932 20020617 SGD
+SGD S000001890 VTC2 GO:0008104 SGD_REF:S000040168|PMID:10480897 IMP P polyphosphate synthetase (putative) YFL004W|PHM1 gene taxon:4932 20020617 SGD
+SGD S000001890 VTC2 GO:0042144 SGD_REF:S000069426|PMID:11823419 IMP P polyphosphate synthetase (putative) YFL004W|PHM1 gene taxon:4932 20020715 SGD
+SGD S000001890 VTC2 GO:0042144 SGD_REF:S000069426|PMID:11823419 IPI P polyphosphate synthetase (putative) YFL004W|PHM1 gene taxon:4932 20020715 SGD
+SGD S000005940 VTC3 GO:0005774 SGD_REF:S000059109|PMID:11102525 IDA C polyphosphate synthetase (putative) YPL019C|PHM2 gene taxon:4932 20020715 SGD
+SGD S000005940 VTC3 GO:0005774 SGD_REF:S000069426|PMID:11823419 IDA C polyphosphate synthetase (putative) YPL019C|PHM2 gene taxon:4932 20020715 SGD
+SGD S000005940 VTC3 GO:0005554 SGD_REF:S000069584 ND F polyphosphate synthetase (putative) YPL019C|PHM2 gene taxon:4932 20020715 SGD
+SGD S000005940 VTC3 GO:0042144 SGD_REF:S000069426|PMID:11823419 IMP P polyphosphate synthetase (putative) YPL019C|PHM2 gene taxon:4932 20020715 SGD
+SGD S000003549 VTC4 GO:0031310 SGD_REF:S000074092|PMID:12584253 IDA C polyphosphate synthetase (putative) YJL012C|PHM3|YJL012C-A gene taxon:4932 20050505 SGD
+SGD S000003549 VTC4 GO:0005554 SGD_REF:S000069584 ND F polyphosphate synthetase (putative) YJL012C|PHM3|YJL012C-A gene taxon:4932 20020715 SGD
+SGD S000003549 VTC4 GO:0042144 SGD_REF:S000069426|PMID:11823419 IMP P polyphosphate synthetase (putative) YJL012C|PHM3|YJL012C-A gene taxon:4932 20020715 SGD
+SGD S000001435 VTH1 GO:0005768 SGD_REF:S000074185|PMID:14562095 IDA C potential membrane glycoprotein (putative), strong similarity to Vth2 and Pep1/Vps10 YIL173W gene taxon:4932 20031028 SGD
+SGD S000001435 VTH1 GO:0005048 SGD_REF:S000051953|PMID:8662642 ISS F potential membrane glycoprotein (putative), strong similarity to Vth2 and Pep1/Vps10 YIL173W gene taxon:4932 20030527 SGD
+SGD S000001435 VTH1 GO:0006896 SGD_REF:S000051953|PMID:8662642 IMP P potential membrane glycoprotein (putative), strong similarity to Vth2 and Pep1/Vps10 YIL173W gene taxon:4932 20020930 SGD
+SGD S000003758 VTH2 GO:0008372 SGD_REF:S000069584 ND C potential membrane glycoprotein, strong similarity to Vth1 and Pep1 YJL222W gene taxon:4932 20020930 SGD
+SGD S000003758 VTH2 GO:0005048 SGD_REF:S000051953|PMID:8662642 ISS F potential membrane glycoprotein, strong similarity to Vth1 and Pep1 YJL222W gene taxon:4932 20030527 SGD
+SGD S000003758 VTH2 GO:0006896 SGD_REF:S000051953|PMID:8662642 ISS P potential membrane glycoprotein, strong similarity to Vth1 and Pep1 YJL222W gene taxon:4932 20020930 SGD
+SGD S000004810 VTI1 GO:0030173 SGD_REF:S000046284|PMID:9398683 IDA C interacts with two t-SNARES, Sed5p and Pep12p, v-SNARE YMR197C gene taxon:4932 20020917 SGD
+SGD S000004810 VTI1 GO:0005485 SGD_REF:S000058453|PMID:10047442 TAS F interacts with two t-SNARES, Sed5p and Pep12p, v-SNARE YMR197C gene taxon:4932 20010118 SGD
+SGD S000004810 VTI1 GO:0006891 SGD_REF:S000058453|PMID:10047442 TAS P interacts with two t-SNARES, Sed5p and Pep12p, v-SNARE YMR197C gene taxon:4932 20010118 SGD
+SGD S000004810 VTI1 GO:0006896 SGD_REF:S000058453|PMID:10047442 TAS P interacts with two t-SNARES, Sed5p and Pep12p, v-SNARE YMR197C gene taxon:4932 20010118 SGD
+SGD S000004810 VTI1 GO:0006906 SGD_REF:S000058453|PMID:10047442 TAS P interacts with two t-SNARES, Sed5p and Pep12p, v-SNARE YMR197C gene taxon:4932 20010118 SGD
+SGD S000004810 VTI1 GO:0008333 SGD_REF:S000058453|PMID:10047442 TAS P interacts with two t-SNARES, Sed5p and Pep12p, v-SNARE YMR197C gene taxon:4932 20010118 SGD
+SGD S000005886 VTS1 GO:0005829 SGD_REF:S000066006|PMID:11445562 IDA C YOR359W gene taxon:4932 20021018 SGD
+SGD S000005886 VTS1 GO:0003723 SGD_REF:S000073913|PMID:12858164 IDA F YOR359W gene taxon:4932 20031014 SGD
+SGD S000005886 VTS1 GO:0005478 SGD_REF:S000066006|PMID:11445562 IGI SGD:S000004810 F YOR359W gene taxon:4932 20021030 SGD
+SGD S000005886 VTS1 GO:0006623 SGD_REF:S000066006|PMID:11445562 IGI P YOR359W gene taxon:4932 20021018 SGD
+SGD S000004541 WAR1 GO:0005634 SGD_REF:S000072659|PMID:12588995 IDA C YML076C gene taxon:4932 20030509 SGD
+SGD S000004541 WAR1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YML076C gene taxon:4932 20040928 SGD
+SGD S000004541 WAR1 GO:0003700 SGD_REF:S000072659|PMID:12588995 IMP F YML076C gene taxon:4932 20030509 SGD
+SGD S000004541 WAR1 GO:0003700 SGD_REF:S000072659|PMID:12588995 ISS F YML076C gene taxon:4932 20030509 SGD
+SGD S000004541 WAR1 GO:0001101 SGD_REF:S000072659|PMID:12588995 IMP P YML076C gene taxon:4932 20030528 SGD
+SGD S000000728 WBP1 GO:0005635 SGD_REF:S000042470|PMID:1724755 IDA C oligosaccharyl transferase glycoprotein complex, beta subunit YEL002C gene taxon:4932 20020928 SGD
+SGD S000000728 WBP1 GO:0005783 SGD_REF:S000042470|PMID:1724755 IDA C oligosaccharyl transferase glycoprotein complex, beta subunit YEL002C gene taxon:4932 20020928 SGD
+SGD S000000728 WBP1 GO:0005783 SGD_REF:S000079534|PMID:12860997 IDA C oligosaccharyl transferase glycoprotein complex, beta subunit YEL002C gene taxon:4932 20041115 SGD
+SGD S000000728 WBP1 GO:0008250 SGD_REF:S000050823|PMID:10358084 IPI C oligosaccharyl transferase glycoprotein complex, beta subunit YEL002C gene taxon:4932 20020328 SGD
+SGD S000000728 WBP1 GO:0008250 SGD_REF:S000113605|PMID:16297388 IPI C oligosaccharyl transferase glycoprotein complex, beta subunit YEL002C gene taxon:4932 20060203 SGD
+SGD S000000728 WBP1 GO:0008250 SGD_REF:S000050479|PMID:9405463 IPI C oligosaccharyl transferase glycoprotein complex, beta subunit YEL002C gene taxon:4932 20050504 SGD
+SGD S000000728 WBP1 GO:0004579 SGD_REF:S000050479|PMID:9405463 IPI F oligosaccharyl transferase glycoprotein complex, beta subunit YEL002C gene taxon:4932 20021001 SGD
+SGD S000000728 WBP1 GO:0006487 SGD_REF:S000050479|PMID:9405463 IPI P oligosaccharyl transferase glycoprotein complex, beta subunit YEL002C gene taxon:4932 20021001 SGD
+SGD S000000728 WBP1 GO:0007049 SGD_REF:S000042470|PMID:1724755 IDA P oligosaccharyl transferase glycoprotein complex, beta subunit YEL002C gene taxon:4932 20020928 SGD
+SGD S000005569 WHI2 GO:0008372 SGD_REF:S000069584 ND C YOR043W gene taxon:4932 20021111 SGD
+SGD S000005569 WHI2 GO:0019211 SGD_REF:S000070097|PMID:12090248 IMP F YOR043W gene taxon:4932 20021111 SGD
+SGD S000005569 WHI2 GO:0019211 SGD_REF:S000070097|PMID:12090248 IPI F YOR043W gene taxon:4932 20021111 SGD
+SGD S000005569 WHI2 GO:0006897 SGD_REF:S000075617|PMID:15020461 IMP P YOR043W gene taxon:4932 20040712 SGD
+SGD S000005569 WHI2 GO:0006950 SGD_REF:S000070097|PMID:12090248 TAS P YOR043W gene taxon:4932 20020728 SGD
+SGD S000005569 WHI2 GO:0007015 SGD_REF:S000075617|PMID:15020461 IMP P YOR043W gene taxon:4932 20040712 SGD
+SGD S000005569 WHI2 GO:0040008 SGD_REF:S000050739|PMID:2204680 IMP P YOR043W gene taxon:4932 20021111 SGD
+SGD S000005141 WHI3 GO:0005737 SGD_REF:S000073973|PMID:11691832 IDA C RNA binding protein (putative) YNL197C gene taxon:4932 20030918 SGD
+SGD S000005141 WHI3 GO:0003723 SGD_REF:S000060206|PMID:11290704 ISS F RNA binding protein (putative) YNL197C gene taxon:4932 20020321 SGD
+SGD S000005141 WHI3 GO:0003723 SGD_REF:S000073973|PMID:11691832 IMP F RNA binding protein (putative) YNL197C gene taxon:4932 20030918 SGD
+SGD S000005141 WHI3 GO:0003723 SGD_REF:S000073973|PMID:11691832 IDA F RNA binding protein (putative) YNL197C gene taxon:4932 20030918 SGD
+SGD S000005141 WHI3 GO:0008361 SGD_REF:S000060206|PMID:11290704 IMP P RNA binding protein (putative) YNL197C gene taxon:4932 20020321 SGD
+SGD S000005141 WHI3 GO:0008361 SGD_REF:S000060206|PMID:11290704 IGI P RNA binding protein (putative) YNL197C gene taxon:4932 20020321 SGD
+SGD S000002383 WHI4 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C RNA binding protein (putative), WHI3 homolog YDL224C gene taxon:4932 20031028 SGD
+SGD S000002383 WHI4 GO:0003723 SGD_REF:S000060206|PMID:11290704 ISS F RNA binding protein (putative), WHI3 homolog YDL224C gene taxon:4932 20020321 SGD
+SGD S000002383 WHI4 GO:0008361 SGD_REF:S000060206|PMID:11290704 IGI P RNA binding protein (putative), WHI3 homolog YDL224C gene taxon:4932 20020321 SGD
+SGD S000005609 WHI5 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C transcriptional repressor YOR083W gene taxon:4932 20031028 SGD
+SGD S000005609 WHI5 GO:0005634 SGD_REF:S000076665|PMID:15210111 IDA C transcriptional repressor YOR083W gene taxon:4932 20040726 SGD
+SGD S000005609 WHI5 GO:0005634 SGD_REF:S000076665|PMID:15210111 IMP C transcriptional repressor YOR083W gene taxon:4932 20040726 SGD
+SGD S000005609 WHI5 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C transcriptional repressor YOR083W gene taxon:4932 20031028 SGD
+SGD S000005609 WHI5 GO:0005737 SGD_REF:S000076665|PMID:15210111 IDA C transcriptional repressor YOR083W gene taxon:4932 20040726 SGD
+SGD S000005609 WHI5 GO:0005737 SGD_REF:S000076665|PMID:15210111 IMP C transcriptional repressor YOR083W gene taxon:4932 20040726 SGD
+SGD S000005609 WHI5 GO:0016564 SGD_REF:S000076665|PMID:15210111 IMP F transcriptional repressor YOR083W gene taxon:4932 20040726 SGD
+SGD S000005609 WHI5 GO:0016564 SGD_REF:S000076664|PMID:15210110 IMP F transcriptional repressor YOR083W gene taxon:4932 20040726 SGD
+SGD S000005609 WHI5 GO:0000082 SGD_REF:S000076665|PMID:15210111 IMP P transcriptional repressor YOR083W gene taxon:4932 20040726 SGD
+SGD S000005609 WHI5 GO:0000082 SGD_REF:S000076664|PMID:15210110 IMP P transcriptional repressor YOR083W gene taxon:4932 20040726 SGD
+SGD S000005609 WHI5 GO:0008361 SGD_REF:S000070190|PMID:12089449 IDA P transcriptional repressor YOR083W gene taxon:4932 20020730 SGD
+SGD S000005457 WRS1 GO:0005737 SGD_REF:S000061571|PMID:10950302 TAS C tryptophan-tRNA ligase YOL097C|HRE342 gene taxon:4932 20020928 SGD
+SGD S000005457 WRS1 GO:0004830 SGD_REF:S000041130|PMID:9046085 IDA F tryptophan-tRNA ligase YOL097C|HRE342 gene taxon:4932 20030109 SGD
+SGD S000005457 WRS1 GO:0006436 SGD_REF:S000061571|PMID:10950302 TAS P tryptophan-tRNA ligase YOL097C|HRE342 gene taxon:4932 20020928 SGD
+SGD S000005227 WSC2 GO:0005624 SGD_REF:S000052074|PMID:10348843 ISS C contains novel cysteine motif, integral membrane protein (putative), similar to SLG1 (WSC1), WSC3 and WSC4 YNL283C|STA3 gene taxon:4932 20010118 SGD
+SGD S000005227 WSC2 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C contains novel cysteine motif, integral membrane protein (putative), similar to SLG1 (WSC1), WSC3 and WSC4 YNL283C|STA3 gene taxon:4932 20020507 SGD
+SGD S000005227 WSC2 GO:0030427 SGD_REF:S000077921|PMID:11545731 IDA C contains novel cysteine motif, integral membrane protein (putative), similar to SLG1 (WSC1), WSC3 and WSC4 YNL283C|STA3 gene taxon:4932 20050503 SGD
+SGD S000005227 WSC2 GO:0004888 SGD_REF:S000039898|PMID:10430578 IGI F contains novel cysteine motif, integral membrane protein (putative), similar to SLG1 (WSC1), WSC3 and WSC4 YNL283C|STA3 gene taxon:4932 20021206 SGD
+SGD S000005227 WSC2 GO:0004888 SGD_REF:S000039898|PMID:10430578 ISS F contains novel cysteine motif, integral membrane protein (putative), similar to SLG1 (WSC1), WSC3 and WSC4 YNL283C|STA3 gene taxon:4932 20021206 SGD
+SGD S000005227 WSC2 GO:0007047 SGD_REF:S000052074|PMID:10348843 IGI P contains novel cysteine motif, integral membrane protein (putative), similar to SLG1 (WSC1), WSC3 and WSC4 YNL283C|STA3 gene taxon:4932 20010118 SGD
+SGD S000005227 WSC2 GO:0007047 SGD_REF:S000052074|PMID:10348843 IMP P contains novel cysteine motif, integral membrane protein (putative), similar to SLG1 (WSC1), WSC3 and WSC4 YNL283C|STA3 gene taxon:4932 20010118 SGD
+SGD S000005227 WSC2 GO:0007266 SGD_REF:S000052074|PMID:10348843 IGI P contains novel cysteine motif, integral membrane protein (putative), similar to SLG1 (WSC1), WSC3 and WSC4 YNL283C|STA3 gene taxon:4932 20010118 SGD
+SGD S000005227 WSC2 GO:0007266 SGD_REF:S000049820|PMID:10508863 ISS P contains novel cysteine motif, integral membrane protein (putative), similar to SLG1 (WSC1), WSC3 and WSC4 YNL283C|STA3 gene taxon:4932 20010118 SGD
+SGD S000005227 WSC2 GO:0009408 SGD_REF:S000049820|PMID:10508863 ISS P contains novel cysteine motif, integral membrane protein (putative), similar to SLG1 (WSC1), WSC3 and WSC4 YNL283C|STA3 gene taxon:4932 20010118 SGD
+SGD S000005227 WSC2 GO:0009408 SGD_REF:S000052074|PMID:10348843 IGI P contains novel cysteine motif, integral membrane protein (putative), similar to SLG1 (WSC1), WSC3 and WSC4 YNL283C|STA3 gene taxon:4932 20010118 SGD
+SGD S000005227 WSC2 GO:0030036 SGD_REF:S000049820|PMID:10508863 TAS P contains novel cysteine motif, integral membrane protein (putative), similar to SLG1 (WSC1), WSC3 and WSC4 YNL283C|STA3 gene taxon:4932 20030116 SGD
+SGD S000005465 WSC3 GO:0005624 SGD_REF:S000052074|PMID:10348843 ISS C contains novel cysteine motif, integral membrane protein (putative), similar to SLG1 (WSC1), WSC2 and WSC4 YOL105C gene taxon:4932 20010118 SGD
+SGD S000005465 WSC3 GO:0004888 SGD_REF:S000039898|PMID:10430578 IGI F contains novel cysteine motif, integral membrane protein (putative), similar to SLG1 (WSC1), WSC2 and WSC4 YOL105C gene taxon:4932 20021206 SGD
+SGD S000005465 WSC3 GO:0004888 SGD_REF:S000039898|PMID:10430578 ISS F contains novel cysteine motif, integral membrane protein (putative), similar to SLG1 (WSC1), WSC2 and WSC4 YOL105C gene taxon:4932 20021206 SGD
+SGD S000005465 WSC3 GO:0007047 SGD_REF:S000052074|PMID:10348843 TAS P contains novel cysteine motif, integral membrane protein (putative), similar to SLG1 (WSC1), WSC2 and WSC4 YOL105C gene taxon:4932 20010118 SGD
+SGD S000005465 WSC3 GO:0007266 SGD_REF:S000049820|PMID:10508863 ISS P contains novel cysteine motif, integral membrane protein (putative), similar to SLG1 (WSC1), WSC2 and WSC4 YOL105C gene taxon:4932 20010118 SGD
+SGD S000005465 WSC3 GO:0007266 SGD_REF:S000052074|PMID:10348843 IGI P contains novel cysteine motif, integral membrane protein (putative), similar to SLG1 (WSC1), WSC2 and WSC4 YOL105C gene taxon:4932 20010118 SGD
+SGD S000005465 WSC3 GO:0009408 SGD_REF:S000049820|PMID:10508863 ISS P contains novel cysteine motif, integral membrane protein (putative), similar to SLG1 (WSC1), WSC2 and WSC4 YOL105C gene taxon:4932 20010118 SGD
+SGD S000005465 WSC3 GO:0009408 SGD_REF:S000052074|PMID:10348843 IGI P contains novel cysteine motif, integral membrane protein (putative), similar to SLG1 (WSC1), WSC2 and WSC4 YOL105C gene taxon:4932 20010118 SGD
+SGD S000005465 WSC3 GO:0030036 SGD_REF:S000049820|PMID:10508863 TAS P contains novel cysteine motif, integral membrane protein (putative), similar to SLG1 (WSC1), WSC2 and WSC4 YOL105C gene taxon:4932 20030116 SGD
+SGD S000001020 WSC4 GO:0005624 SGD_REF:S000052074|PMID:10348843 ISS C contains novel cysteine motif, integral membrane protein (putative), similar to SLG1 (WSC1), WSC2 and WSC3 YHL028W|YFW1|YHC8 gene taxon:4932 20010118 SGD
+SGD S000001020 WSC4 GO:0005789 SGD_REF:S000050779|PMID:10196219 IDA C contains novel cysteine motif, integral membrane protein (putative), similar to SLG1 (WSC1), WSC2 and WSC3 YHL028W|YFW1|YHC8 gene taxon:4932 20040109 SGD
+SGD S000001020 WSC4 GO:0004888 SGD_REF:S000039898|PMID:10430578 IGI F contains novel cysteine motif, integral membrane protein (putative), similar to SLG1 (WSC1), WSC2 and WSC3 YHL028W|YFW1|YHC8 gene taxon:4932 20021206 SGD
+SGD S000001020 WSC4 GO:0004888 SGD_REF:S000039898|PMID:10430578 ISS F contains novel cysteine motif, integral membrane protein (putative), similar to SLG1 (WSC1), WSC2 and WSC3 YHL028W|YFW1|YHC8 gene taxon:4932 20021206 SGD
+SGD S000001020 WSC4 GO:0006616 SGD_REF:S000042726|PMID:8798620 ISS UniProt:Q6C2X8_YARLI P contains novel cysteine motif, integral membrane protein (putative), similar to SLG1 (WSC1), WSC2 and WSC3 YHL028W|YFW1|YHC8 gene taxon:4932 20050711 SGD
+SGD S000001020 WSC4 GO:0006950 SGD_REF:S000066017|PMID:11589572 IGI SGD:S000005534 P contains novel cysteine motif, integral membrane protein (putative), similar to SLG1 (WSC1), WSC2 and WSC3 YHL028W|YFW1|YHC8 gene taxon:4932 20050711 SGD
+SGD S000001020 WSC4 GO:0009408 SGD_REF:S000049820|PMID:10508863 ISS P contains novel cysteine motif, integral membrane protein (putative), similar to SLG1 (WSC1), WSC2 and WSC3 YHL028W|YFW1|YHC8 gene taxon:4932 20010118 SGD
+SGD S000001020 WSC4 GO:0009408 SGD_REF:S000066017|PMID:11589572 IGI SGD:S000005534 P contains novel cysteine motif, integral membrane protein (putative), similar to SLG1 (WSC1), WSC2 and WSC3 YHL028W|YFW1|YHC8 gene taxon:4932 20050711 SGD
+SGD S000001020 WSC4 GO:0009408 SGD_REF:S000052074|PMID:10348843 ISS P contains novel cysteine motif, integral membrane protein (putative), similar to SLG1 (WSC1), WSC2 and WSC3 YHL028W|YFW1|YHC8 gene taxon:4932 20010118 SGD
+SGD S000001020 WSC4 GO:0045047 SGD_REF:S000050779|PMID:10196219 IMP P contains novel cysteine motif, integral membrane protein (putative), similar to SLG1 (WSC1), WSC2 and WSC3 YHL028W|YFW1|YHC8 gene taxon:4932 20050711 SGD
+SGD S000005746 WSP1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YOR220W gene taxon:4932 20031028 SGD
+SGD S000005746 WSP1 GO:0005554 SGD_REF:S000069584 ND F YOR220W gene taxon:4932 20030203 SGD
+SGD S000005746 WSP1 GO:0000004 SGD_REF:S000069584 ND P YOR220W gene taxon:4932 20030203 SGD
+SGD S000001176 WSS1 GO:0008372 SGD_REF:S000069584 ND C YHR134W gene taxon:4932 20021030 SGD
+SGD S000001176 WSS1 GO:0005554 SGD_REF:S000069584 ND F YHR134W gene taxon:4932 20021030 SGD
+SGD S000001176 WSS1 GO:0010224 SGD_REF:S000081216|PMID:11606770 IMP P YHR134W gene taxon:4932 20050713 SGD
+SGD S000001176 WSS1 GO:0010224 SGD_REF:S000080171|PMID:15598824 IMP P YHR134W gene taxon:4932 20050713 SGD
+SGD S000001176 WSS1 GO:0010225 SGD_REF:S000081216|PMID:11606770 IMP P YHR134W gene taxon:4932 20050713 SGD
+SGD S000001176 WSS1 GO:0010225 SGD_REF:S000080171|PMID:15598824 IMP P YHR134W gene taxon:4932 20050713 SGD
+SGD S000001176 WSS1 GO:0016925 SGD_REF:S000066115|PMID:11606525 IGI SGD:S000002918 P YHR134W gene taxon:4932 20021030 SGD
+SGD S000005756 WTM1 GO:0005634 SGD_REF:S000069459|PMID:11914276 IDA C transcriptional modulator YOR230W gene taxon:4932 20020507 SGD
+SGD S000005756 WTM1 GO:0005634 SGD_REF:S000049423|PMID:9234739 IDA C transcriptional modulator YOR230W gene taxon:4932 20021030 SGD
+SGD S000005756 WTM1 GO:0003714 SGD_REF:S000049423|PMID:9234739 IDA F transcriptional modulator YOR230W gene taxon:4932 20021030 SGD
+SGD S000005756 WTM1 GO:0040020 SGD_REF:S000049423|PMID:9234739 IGI P transcriptional modulator YOR230W gene taxon:4932 20021030 SGD
+SGD S000005755 WTM2 GO:0005634 SGD_REF:S000049423|PMID:9234739 IDA C transcriptional modulator YOR229W gene taxon:4932 20021030 SGD
+SGD S000005755 WTM2 GO:0003714 SGD_REF:S000049423|PMID:9234739 IDA F transcriptional modulator YOR229W gene taxon:4932 20021030 SGD
+SGD S000005755 WTM2 GO:0040020 SGD_REF:S000049423|PMID:9234739 IGI P transcriptional modulator YOR229W gene taxon:4932 20021030 SGD
+SGD S000001884 WWM1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YFL010C gene taxon:4932 20031028 SGD
+SGD S000001884 WWM1 GO:0005634 SGD_REF:S000069959|PMID:12062425 IDA C YFL010C gene taxon:4932 20050718 SGD
+SGD S000001884 WWM1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YFL010C gene taxon:4932 20020507 SGD
+SGD S000001884 WWM1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YFL010C gene taxon:4932 20031028 SGD
+SGD S000001884 WWM1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YFL010C gene taxon:4932 20040928 SGD
+SGD S000001884 WWM1 GO:0005554 SGD_REF:S000069584 ND F YFL010C gene taxon:4932 20021216 SGD
+SGD S000001884 WWM1 GO:0000004 SGD_REF:S000069584 ND P YFL010C gene taxon:4932 20060412 SGD
+SGD S000001363 XBP1 GO:0005634 SGD_REF:S000054825|PMID:9343412 IPI C transcriptional repressor YIL101C gene taxon:4932 20020221 SGD
+SGD S000001363 XBP1 GO:0005634 SGD_REF:S000054825|PMID:9343412 IDA C transcriptional repressor YIL101C gene taxon:4932 20020221 SGD
+SGD S000001363 XBP1 GO:0003700 SGD_REF:S000054825|PMID:9343412 IDA F transcriptional repressor YIL101C gene taxon:4932 20020221 SGD
+SGD S000001363 XBP1 GO:0006950 SGD_REF:S000054825|PMID:9343412 IMP P transcriptional repressor YIL101C gene taxon:4932 20020221 SGD
+SGD S000001363 XBP1 GO:0006950 SGD_REF:S000054825|PMID:9343412 IDA P transcriptional repressor YIL101C gene taxon:4932 20020221 SGD
+SGD S000004080 XDJ1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YLR090W gene taxon:4932 20031028 SGD
+SGD S000004080 XDJ1 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YLR090W gene taxon:4932 20031028 SGD
+SGD S000004080 XDJ1 GO:0030188 SGD_REF:S000050768|PMID:8045410 ISS SGD:S000005008 F YLR090W gene taxon:4932 20021030 SGD
+SGD S000004080 XDJ1 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P YLR090W gene taxon:4932 20060221 SGD
+SGD S000003426 XKS1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C xylulokinase YGR194C gene taxon:4932 20031028 SGD
+SGD S000003426 XKS1 GO:0004856 SGD_REF:S000052436|PMID:9595677 IMP F xylulokinase YGR194C gene taxon:4932 20021115 SGD
+SGD S000003426 XKS1 GO:0004856 SGD_REF:S000052436|PMID:9595677 ISS F xylulokinase YGR194C gene taxon:4932 20021115 SGD
+SGD S000003426 XKS1 GO:0005998 SGD_REF:S000059295|PMID:10981687 IDA P xylulokinase YGR194C gene taxon:4932 20020930 SGD
+SGD S000003894 XPT1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C xanthine phosphoribosyl transferase YJR133W gene taxon:4932 20031028 SGD
+SGD S000003894 XPT1 GO:0000310 SGD_REF:S000051783|PMID:10217799 IGI F xanthine phosphoribosyl transferase YJR133W gene taxon:4932 20050621 SGD
+SGD S000003894 XPT1 GO:0000310 SGD_REF:S000051783|PMID:10217799 IMP F xanthine phosphoribosyl transferase YJR133W gene taxon:4932 20050621 SGD
+SGD S000003894 XPT1 GO:0000310 SGD_REF:S000051783|PMID:10217799 ISS F xanthine phosphoribosyl transferase YJR133W gene taxon:4932 20050621 SGD
+SGD S000003894 XPT1 GO:0006164 SGD_REF:S000051783|PMID:10217799 TAS P xanthine phosphoribosyl transferase YJR133W gene taxon:4932 20020321 SGD
+SGD S000002777 XRS2 GO:0005634 SGD_REF:S000050527|PMID:9845372 IDA C DNA repair protein YDR369C gene taxon:4932 20030403 SGD
+SGD S000002777 XRS2 GO:0030870 SGD_REF:S000050527|PMID:9845372 IPI C DNA repair protein YDR369C gene taxon:4932 20041024 SGD
+SGD S000002777 XRS2 GO:0030870 SGD_REF:S000082253|PMID:15548595 IPI C DNA repair protein YDR369C gene taxon:4932 20050808 SGD
+SGD S000002777 XRS2 GO:0003677 SGD_REF:S000075122|PMID:14522986 IDA F DNA repair protein YDR369C gene taxon:4932 20040528 SGD
+SGD S000002777 XRS2 GO:0005515 SGD_REF:S000050527|PMID:9845372 IPI F DNA repair protein YDR369C gene taxon:4932 20020925 SGD
+SGD S000002777 XRS2 GO:0042162 SGD_REF:S000080865|PMID:15721260 IDA F DNA repair protein YDR369C gene taxon:4932 20050712 SGD
+SGD S000002777 XRS2 GO:0000723 SGD_REF:S000082253|PMID:15548595 IMP P DNA repair protein YDR369C gene taxon:4932 20050808 SGD
+SGD S000002777 XRS2 GO:0000727 SGD_REF:S000060952|PMID:11459961 TAS P DNA repair protein YDR369C gene taxon:4932 20020925 SGD
+SGD S000002777 XRS2 GO:0006303 SGD_REF:S000073203|PMID:12399380 IMP P DNA repair protein YDR369C gene taxon:4932 20030528 SGD
+SGD S000002777 XRS2 GO:0030435 SGD_REF:S000082253|PMID:15548595 IMP P DNA repair protein YDR369C gene taxon:4932 20050808 SGD
+SGD S000002777 XRS2 GO:0042138 SGD_REF:S000082253|PMID:15548595 IMP P DNA repair protein YDR369C gene taxon:4932 20050808 SGD
+SGD S000004060 XYL2 GO:0008372 SGD_REF:S000069584 ND C Xylitol Dehydrogenase YLR070C gene taxon:4932 20021009 SGD
+SGD S000004060 XYL2 GO:0046526 SGD_REF:S000056333|PMID:10486580 IDA F Xylitol Dehydrogenase YLR070C gene taxon:4932 20021009 SGD
+SGD S000004060 XYL2 GO:0005996 SGD_REF:S000056333|PMID:10486580 IDA P Xylitol Dehydrogenase YLR070C gene taxon:4932 20021009 SGD
+SGD S000003828 YAE1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YJR067C gene taxon:4932 20031028 SGD
+SGD S000003828 YAE1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YJR067C gene taxon:4932 20031028 SGD
+SGD S000003828 YAE1 GO:0005554 SGD_REF:S000069584 ND F YJR067C gene taxon:4932 20021125 SGD
+SGD S000003828 YAE1 GO:0000004 SGD_REF:S000069584 ND P YJR067C gene taxon:4932 20021125 SGD
+SGD S000005051 YAF9 GO:0000812 SGD_REF:S000074662|PMID:14645854 IPI C YNL107W gene taxon:4932 20040412 SGD
+SGD S000005051 YAF9 GO:0000812 SGD_REF:S000075430|PMID:14690608 IPI C YNL107W gene taxon:4932 20040412 SGD
+SGD S000005051 YAF9 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YNL107W gene taxon:4932 20031028 SGD
+SGD S000005051 YAF9 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YNL107W gene taxon:4932 20031028 SGD
+SGD S000005051 YAF9 GO:0043189 SGD_REF:S000079775|PMID:15485911 IPI C YNL107W gene taxon:4932 20050207 SGD
+SGD S000005051 YAF9 GO:0005554 SGD_REF:S000069584 ND F YNL107W gene taxon:4932 20021125 SGD
+SGD S000005051 YAF9 GO:0006338 SGD_REF:S000074662|PMID:14645854 IDA P YNL107W gene taxon:4932 20040322 SGD
+SGD S000005051 YAF9 GO:0006338 SGD_REF:S000075430|PMID:14690608 IGI P YNL107W gene taxon:4932 20040323 SGD
+SGD S000005051 YAF9 GO:0006338 SGD_REF:S000075430|PMID:14690608 IPI P YNL107W gene taxon:4932 20040323 SGD
+SGD S000005051 YAF9 GO:0006348 SGD_REF:S000079775|PMID:15485911 IMP P YNL107W gene taxon:4932 20050207 SGD
+SGD S000006173 YAH1 GO:0005759 SGD_REF:S000055753|PMID:10375636 IDA C iron-sulfur protein similar to human adrenodoxin YPL252C gene taxon:4932 20020903 SGD
+SGD S000006173 YAH1 GO:0009055 SGD_REF:S000055753|PMID:10375636 IMP F iron-sulfur protein similar to human adrenodoxin YPL252C gene taxon:4932 20030224 SGD
+SGD S000006173 YAH1 GO:0009055 SGD_REF:S000055753|PMID:10375636 ISS F iron-sulfur protein similar to human adrenodoxin YPL252C gene taxon:4932 20030224 SGD
+SGD S000006173 YAH1 GO:0006784 SGD_REF:S000069465|PMID:11788607 IGI P iron-sulfur protein similar to human adrenodoxin YPL252C gene taxon:4932 20020903 SGD
+SGD S000006173 YAH1 GO:0006784 SGD_REF:S000069465|PMID:11788607 IMP P iron-sulfur protein similar to human adrenodoxin YPL252C gene taxon:4932 20020903 SGD
+SGD S000003677 YAK1 GO:0005634 SGD_REF:S000060336|PMID:11358866 IDA C YJL141C gene taxon:4932 20020828 SGD
+SGD S000003677 YAK1 GO:0005737 SGD_REF:S000060336|PMID:11358866 IDA C YJL141C gene taxon:4932 20020828 SGD
+SGD S000003677 YAK1 GO:0004672 SGD_REF:S000043869|PMID:2072907 IDA F YJL141C gene taxon:4932 20020828 SGD
+SGD S000003677 YAK1 GO:0006468 SGD_REF:S000043869|PMID:2072907 IDA P YJL141C gene taxon:4932 20020828 SGD
+SGD S000004466 YAP1 GO:0005634 SGD_REF:S000069459|PMID:11914276 IDA C jun-like transcription factor YML007W|PAR1|SNQ3 gene taxon:4932 20020507 SGD
+SGD S000004466 YAP1 GO:0005634 SGD_REF:S000072694|PMID:12582119 IDA C jun-like transcription factor YML007W|PAR1|SNQ3 gene taxon:4932 20030313 SGD
+SGD S000004466 YAP1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C jun-like transcription factor YML007W|PAR1|SNQ3 gene taxon:4932 20020507 SGD
+SGD S000004466 YAP1 GO:0005737 SGD_REF:S000072694|PMID:12582119 IDA C jun-like transcription factor YML007W|PAR1|SNQ3 gene taxon:4932 20030313 SGD
+SGD S000004466 YAP1 GO:0003700 SGD_REF:S000060938|PMID:11274141 TAS F jun-like transcription factor YML007W|PAR1|SNQ3 gene taxon:4932 20020926 SGD
+SGD S000004466 YAP1 GO:0003700 SGD_REF:S000058433|PMID:11056165 IDA F jun-like transcription factor YML007W|PAR1|SNQ3 gene taxon:4932 20050117 SGD
+SGD S000004466 YAP1 GO:0006350 SGD_REF:S000072617|PMID:12464172 TAS P jun-like transcription factor YML007W|PAR1|SNQ3 gene taxon:4932 20030306 SGD
+SGD S000004466 YAP1 GO:0006350 SGD_REF:S000058433|PMID:11056165 IDA P jun-like transcription factor YML007W|PAR1|SNQ3 gene taxon:4932 20050117 SGD
+SGD S000004466 YAP1 GO:0006979 SGD_REF:S000043684|PMID:9922230 TAS P jun-like transcription factor YML007W|PAR1|SNQ3 gene taxon:4932 20020904 SGD
+SGD S000004466 YAP1 GO:0042493 SGD_REF:S000043684|PMID:9922230 TAS P jun-like transcription factor YML007W|PAR1|SNQ3 gene taxon:4932 20021111 SGD
+SGD S000004466 YAP1 GO:0042493 SGD_REF:S000080916|PMID:15713640 IMP P jun-like transcription factor YML007W|PAR1|SNQ3 gene taxon:4932 20050816 SGD
+SGD S000004466 YAP1 GO:0046685 SGD_REF:S000080191|PMID:15575969 IMP P jun-like transcription factor YML007W|PAR1|SNQ3 gene taxon:4932 20050331 SGD
+SGD S000004466 YAP1 GO:0046685 SGD_REF:S000080191|PMID:15575969 IEP P jun-like transcription factor YML007W|PAR1|SNQ3 gene taxon:4932 20050331 SGD
+SGD S000001204 YAP1801 GO:0030479 SGD_REF:S000041005|PMID:10652251 IDA C YHR161C gene taxon:4932 20010118 SGD
+SGD S000001204 YAP1801 GO:0030276 SGD_REF:S000075278|PMID:12461563 TAS F YHR161C gene taxon:4932 20040107 SGD
+SGD S000001204 YAP1801 GO:0006897 SGD_REF:S000042411|PMID:9531549 IPI P YHR161C gene taxon:4932 20010118 SGD
+SGD S000001204 YAP1801 GO:0006897 SGD_REF:S000042411|PMID:9531549 ISS P YHR161C gene taxon:4932 20010118 SGD
+SGD S000003473 YAP1802 GO:0030479 SGD_REF:S000041005|PMID:10652251 IDA C YGR241C gene taxon:4932 20010118 SGD
+SGD S000003473 YAP1802 GO:0030276 SGD_REF:S000075278|PMID:12461563 TAS F YGR241C gene taxon:4932 20040107 SGD
+SGD S000003473 YAP1802 GO:0006897 SGD_REF:S000042411|PMID:9531549 IPI P YGR241C gene taxon:4932 20010118 SGD
+SGD S000003473 YAP1802 GO:0006897 SGD_REF:S000042411|PMID:9531549 ISS P YGR241C gene taxon:4932 20010118 SGD
+SGD S000001001 YAP3 GO:0005634 SGD_REF:S000048602|PMID:9372930 IPI C YHL009C gene taxon:4932 20021021 SGD
+SGD S000001001 YAP3 GO:0003700 SGD_REF:S000048602|PMID:9372930 IDA F YHL009C gene taxon:4932 20021021 SGD
+SGD S000001001 YAP3 GO:0006357 SGD_REF:S000048602|PMID:9372930 IDA P YHL009C gene taxon:4932 20021021 SGD
+SGD S000001457 YAP5 GO:0005634 SGD_REF:S000048602|PMID:9372930 IC GO:0003702 C bZIP (basic-leucine zipper) protein, transcription factor YIR018W gene taxon:4932 20021031 SGD
+SGD S000001457 YAP5 GO:0003702 SGD_REF:S000048602|PMID:9372930 IDA F bZIP (basic-leucine zipper) protein, transcription factor YIR018W gene taxon:4932 20021031 SGD
+SGD S000001457 YAP5 GO:0000083 SGD_REF:S000071810|PMID:12464632 IPI P bZIP (basic-leucine zipper) protein, transcription factor YIR018W gene taxon:4932 20050603 SGD
+SGD S000001457 YAP5 GO:0045944 SGD_REF:S000048602|PMID:9372930 IDA P bZIP (basic-leucine zipper) protein, transcription factor YIR018W gene taxon:4932 20021031 SGD
+SGD S000002667 YAP6 GO:0005634 SGD_REF:S000060008|PMID:11179441 IDA C YDR259C|HAL7 gene taxon:4932 20020828 SGD
+SGD S000002667 YAP6 GO:0003702 SGD_REF:S000048602|PMID:9372930 ISS F YDR259C|HAL7 gene taxon:4932 20021031 SGD
+SGD S000002667 YAP6 GO:0045944 SGD_REF:S000048602|PMID:9372930 ISS P YDR259C|HAL7 gene taxon:4932 20021031 SGD
+SGD S000005388 YAP7 GO:0005634 SGD_REF:S000048602|PMID:9372930 IC GO:0003702 C basic leucine zipper (bZIP) transcription factor YOL028C gene taxon:4932 20021031 SGD
+SGD S000005388 YAP7 GO:0005634 SGD_REF:S000048602|PMID:9372930 ISS C basic leucine zipper (bZIP) transcription factor YOL028C gene taxon:4932 20021031 SGD
+SGD S000005388 YAP7 GO:0003702 SGD_REF:S000048602|PMID:9372930 ISS F basic leucine zipper (bZIP) transcription factor YOL028C gene taxon:4932 20021031 SGD
+SGD S000005388 YAP7 GO:0045944 SGD_REF:S000048602|PMID:9372930 ISS P basic leucine zipper (bZIP) transcription factor YOL028C gene taxon:4932 20021031 SGD
+SGD S000006160 YAR1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C 200-amino-acid protein with two ANK repeat motifs and an acidic C terminus rich in PEST-like sequences YPL239W gene taxon:4932 20031028 SGD
+SGD S000006160 YAR1 GO:0005554 SGD_REF:S000069584 ND F 200-amino-acid protein with two ANK repeat motifs and an acidic C terminus rich in PEST-like sequences YPL239W gene taxon:4932 20021029 SGD
+SGD S000006160 YAR1 GO:0006970 SGD_REF:S000080092|PMID:15611164 IMP P 200-amino-acid protein with two ANK repeat motifs and an acidic C terminus rich in PEST-like sequences YPL239W gene taxon:4932 20050503 SGD
+SGD S000006160 YAR1 GO:0006979 SGD_REF:S000080092|PMID:15611164 IMP P 200-amino-acid protein with two ANK repeat motifs and an acidic C terminus rich in PEST-like sequences YPL239W gene taxon:4932 20050503 SGD
+SGD S000006160 YAR1 GO:0042274 SGD_REF:S000080092|PMID:15611164 IGI SGD:S000005122 P 200-amino-acid protein with two ANK repeat motifs and an acidic C terminus rich in PEST-like sequences YPL239W gene taxon:4932 20050503 SGD
+SGD S000006160 YAR1 GO:0042274 SGD_REF:S000080092|PMID:15611164 IMP P 200-amino-acid protein with two ANK repeat motifs and an acidic C terminus rich in PEST-like sequences YPL239W gene taxon:4932 20050503 SGD
+SGD S000000080 YAT1 GO:0005739 SGD_REF:S000069459|PMID:11914276 IDA C carnitine acetyltransferase YAR035W gene taxon:4932 20020507 SGD
+SGD S000000080 YAT1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C carnitine acetyltransferase YAR035W gene taxon:4932 20040924 SGD
+SGD S000000080 YAT1 GO:0004092 SGD_REF:S000060344|PMID:11329169 ISS F carnitine acetyltransferase YAR035W gene taxon:4932 20020927 SGD
+SGD S000000080 YAT1 GO:0006066 SGD_REF:S000060344|PMID:11329169 IGI P carnitine acetyltransferase YAR035W gene taxon:4932 20020927 SGD
+SGD S000000080 YAT1 GO:0009437 SGD_REF:S000060344|PMID:11329169 IMP P carnitine acetyltransferase YAR035W gene taxon:4932 20021204 SGD
+SGD S000000826 YAT2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C carnitine acetyltransferase YER024W gene taxon:4932 20031028 SGD
+SGD S000000826 YAT2 GO:0004092 SGD_REF:S000060344|PMID:11329169 IMP F carnitine acetyltransferase YER024W gene taxon:4932 20020927 SGD
+SGD S000000826 YAT2 GO:0006066 SGD_REF:S000060344|PMID:11329169 IGI P carnitine acetyltransferase YER024W gene taxon:4932 20020927 SGD
+SGD S000000826 YAT2 GO:0006066 SGD_REF:S000060344|PMID:11329169 IMP P carnitine acetyltransferase YER024W gene taxon:4932 20020927 SGD
+SGD S000000826 YAT2 GO:0009437 SGD_REF:S000060344|PMID:11329169 IMP P carnitine acetyltransferase YER024W gene taxon:4932 20021204 SGD
+SGD S000000420 YBP1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C redox regulator YBR216C gene taxon:4932 20031028 SGD
+SGD S000000420 YBP1 GO:0005554 SGD_REF:S000069584 ND F redox regulator YBR216C gene taxon:4932 20021126 SGD
+SGD S000000420 YBP1 GO:0006979 SGD_REF:S000073844|PMID:12743123 IDA P redox regulator YBR216C gene taxon:4932 20030904 SGD
+SGD S000003028 YBP2 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YGL060W gene taxon:4932 20031028 SGD
+SGD S000003028 YBP2 GO:0005554 SGD_REF:S000069584 ND F YGL060W gene taxon:4932 20020425 SGD
+SGD S000003028 YBP2 GO:0000004 SGD_REF:S000069584 ND P YGL060W gene taxon:4932 20020425 SGD
+SGD S000003971 YBT1 GO:0000324 SGD_REF:S000056008|PMID:9182565 IDA C YLL048C|BAT1 gene taxon:4932 20021002 SGD
+SGD S000003971 YBT1 GO:0015125 SGD_REF:S000056008|PMID:9182565 IMP F YLL048C|BAT1 gene taxon:4932 20021002 SGD
+SGD S000003971 YBT1 GO:0042626 SGD_REF:S000056008|PMID:9182565 ISS F YLL048C|BAT1 gene taxon:4932 20021002 SGD
+SGD S000003971 YBT1 GO:0015721 SGD_REF:S000056008|PMID:9182565 IMP P YLL048C|BAT1 gene taxon:4932 20021002 SGD
+SGD S000002542 YCF1 GO:0005774 SGD_REF:S000045628|PMID:8692889 IDA C YDR135C gene taxon:4932 20010118 SGD
+SGD S000002542 YCF1 GO:0015127 SGD_REF:S000041475|PMID:10790694 IMP F YDR135C gene taxon:4932 20010118 SGD
+SGD S000002542 YCF1 GO:0015127 SGD_REF:S000041475|PMID:10790694 IGI F YDR135C gene taxon:4932 20010118 SGD
+SGD S000002542 YCF1 GO:0015431 SGD_REF:S000058155|PMID:9217966 IDA F YDR135C gene taxon:4932 20040511 SGD
+SGD S000002542 YCF1 GO:0015431 SGD_REF:S000041439|PMID:10220408 IDA F YDR135C gene taxon:4932 20040511 SGD
+SGD S000002542 YCF1 GO:0015431 SGD_REF:S000073594|PMID:12755704 IDA F YDR135C gene taxon:4932 20040511 SGD
+SGD S000002542 YCF1 GO:0015431 SGD_REF:S000071492|PMID:12383937 IDA F YDR135C gene taxon:4932 20040511 SGD
+SGD S000002542 YCF1 GO:0010038 SGD_REF:S000041439|PMID:10220408 IDA P YDR135C gene taxon:4932 20040511 SGD
+SGD S000002542 YCF1 GO:0010038 SGD_REF:S000058155|PMID:9217966 IDA P YDR135C gene taxon:4932 20040511 SGD
+SGD S000002542 YCF1 GO:0010038 SGD_REF:S000073594|PMID:12755704 IDA P YDR135C gene taxon:4932 20040511 SGD
+SGD S000002542 YCF1 GO:0010038 SGD_REF:S000058155|PMID:9217966 TAS P YDR135C gene taxon:4932 20040511 SGD
+SGD S000002542 YCF1 GO:0015723 SGD_REF:S000041475|PMID:10790694 IMP P YDR135C gene taxon:4932 20010118 SGD
+SGD S000002542 YCF1 GO:0015723 SGD_REF:S000041475|PMID:10790694 IGI P YDR135C gene taxon:4932 20010118 SGD
+SGD S000002733 YCG1 GO:0000799 SGD_REF:S000041579|PMID:10749931 IGI C condensin YDR325W|TIE1|YCS5 gene taxon:4932 20010118 SGD
+SGD S000002733 YCG1 GO:0000799 SGD_REF:S000041579|PMID:10749931 ISS C condensin YDR325W|TIE1|YCS5 gene taxon:4932 20010118 SGD
+SGD S000002733 YCG1 GO:0005554 SGD_REF:S000069584 ND F condensin YDR325W|TIE1|YCS5 gene taxon:4932 20010119 SGD
+SGD S000002733 YCG1 GO:0000070 SGD_REF:S000069542|PMID:11864994 IMP P condensin YDR325W|TIE1|YCS5 gene taxon:4932 20050718 SGD
+SGD S000002733 YCG1 GO:0007076 SGD_REF:S000041579|PMID:10749931 IGI P condensin YDR325W|TIE1|YCS5 gene taxon:4932 20010118 SGD
+SGD S000002733 YCG1 GO:0007076 SGD_REF:S000069542|PMID:11864994 IMP P condensin YDR325W|TIE1|YCS5 gene taxon:4932 20050718 SGD
+SGD S000002733 YCG1 GO:0007076 SGD_REF:S000040443|PMID:10811823 TAS P condensin YDR325W|TIE1|YCS5 gene taxon:4932 20010118 SGD
+SGD S000002733 YCG1 GO:0010032 SGD_REF:S000075135|PMID:14662740 IMP P condensin YDR325W|TIE1|YCS5 gene taxon:4932 20050719 SGD
+SGD S000001177 YCK1 GO:0005783 SGD_REF:S000069459|PMID:11914276 IDA C casein kinase I homolog YHR135C|CKI2 gene taxon:4932 20020507 SGD
+SGD S000001177 YCK1 GO:0005886 SGD_REF:S000047008|PMID:8034689 IDA C casein kinase I homolog YHR135C|CKI2 gene taxon:4932 20010118 SGD
+SGD S000001177 YCK1 GO:0005886 SGD_REF:S000042524|PMID:1627830 IDA C casein kinase I homolog YHR135C|CKI2 gene taxon:4932 20010118 SGD
+SGD S000001177 YCK1 GO:0004681 SGD_REF:S000050372|PMID:1729698 IMP F casein kinase I homolog YHR135C|CKI2 gene taxon:4932 20010118 SGD
+SGD S000001177 YCK1 GO:0004681 SGD_REF:S000050372|PMID:1729698 ISS F casein kinase I homolog YHR135C|CKI2 gene taxon:4932 20010118 SGD
+SGD S000001177 YCK1 GO:0000902 SGD_REF:S000053135|PMID:10198058 IGI P casein kinase I homolog YHR135C|CKI2 gene taxon:4932 20030131 SGD
+SGD S000001177 YCK1 GO:0000910 SGD_REF:S000053135|PMID:10198058 IGI P casein kinase I homolog YHR135C|CKI2 gene taxon:4932 20030131 SGD
+SGD S000001177 YCK1 GO:0006468 SGD_REF:S000050372|PMID:1729698 ISS P casein kinase I homolog YHR135C|CKI2 gene taxon:4932 20010118 SGD
+SGD S000001177 YCK1 GO:0006468 SGD_REF:S000050372|PMID:1729698 IMP P casein kinase I homolog YHR135C|CKI2 gene taxon:4932 20010118 SGD
+SGD S000001177 YCK1 GO:0006897 SGD_REF:S000053135|PMID:10198058 IGI P casein kinase I homolog YHR135C|CKI2 gene taxon:4932 20030131 SGD
+SGD S000001177 YCK1 GO:0009749 SGD_REF:S000074769|PMID:14755054 IMP P casein kinase I homolog YHR135C|CKI2 gene taxon:4932 20040709 SGD
+SGD S000005098 YCK2 GO:0005886 SGD_REF:S000047008|PMID:8034689 IDA C casein kinase I homolog YNL154C gene taxon:4932 20010118 SGD
+SGD S000005098 YCK2 GO:0005886 SGD_REF:S000042524|PMID:1627830 IDA C casein kinase I homolog YNL154C gene taxon:4932 20010118 SGD
+SGD S000005098 YCK2 GO:0005935 SGD_REF:S000053135|PMID:10198058 IDA C casein kinase I homolog YNL154C gene taxon:4932 20030131 SGD
+SGD S000005098 YCK2 GO:0005937 SGD_REF:S000053135|PMID:10198058 IDA C casein kinase I homolog YNL154C gene taxon:4932 20050505 SGD
+SGD S000005098 YCK2 GO:0004681 SGD_REF:S000050372|PMID:1729698 ISS F casein kinase I homolog YNL154C gene taxon:4932 20010118 SGD
+SGD S000005098 YCK2 GO:0004681 SGD_REF:S000050372|PMID:1729698 IMP F casein kinase I homolog YNL154C gene taxon:4932 20010118 SGD
+SGD S000005098 YCK2 GO:0004681 SGD_REF:S000046342|PMID:8474447 IDA F casein kinase I homolog YNL154C gene taxon:4932 20050505 SGD
+SGD S000005098 YCK2 GO:0000902 SGD_REF:S000053135|PMID:10198058 IGI P casein kinase I homolog YNL154C gene taxon:4932 20030131 SGD
+SGD S000005098 YCK2 GO:0000902 SGD_REF:S000046342|PMID:8474447 IGI SGD:S000001177 P casein kinase I homolog YNL154C gene taxon:4932 20050505 SGD
+SGD S000005098 YCK2 GO:0000910 SGD_REF:S000053135|PMID:10198058 IGI P casein kinase I homolog YNL154C gene taxon:4932 20030131 SGD
+SGD S000005098 YCK2 GO:0000910 SGD_REF:S000046342|PMID:8474447 IGI SGD:S000001177 P casein kinase I homolog YNL154C gene taxon:4932 20050505 SGD
+SGD S000005098 YCK2 GO:0006468 SGD_REF:S000050372|PMID:1729698 IMP P casein kinase I homolog YNL154C gene taxon:4932 20010118 SGD
+SGD S000005098 YCK2 GO:0006468 SGD_REF:S000050372|PMID:1729698 ISS P casein kinase I homolog YNL154C gene taxon:4932 20010118 SGD
+SGD S000005098 YCK2 GO:0006897 SGD_REF:S000053135|PMID:10198058 IGI P casein kinase I homolog YNL154C gene taxon:4932 20030131 SGD
+SGD S000005098 YCK2 GO:0009749 SGD_REF:S000074769|PMID:14755054 IMP P casein kinase I homolog YNL154C gene taxon:4932 20040709 SGD
+SGD S000000925 YCK3 GO:0000329 SGD_REF:S000077538|PMID:14668479 IDA C casein kinase I homolog YER123W|CKI3 gene taxon:4932 20041202 SGD
+SGD S000000925 YCK3 GO:0005634 SGD_REF:S000051920|PMID:8816449 IDA C casein kinase I homolog YER123W|CKI3 gene taxon:4932 20021025 SGD
+SGD S000000925 YCK3 GO:0005886 SGD_REF:S000051920|PMID:8816449 IDA C casein kinase I homolog YER123W|CKI3 gene taxon:4932 20021025 SGD
+SGD S000000925 YCK3 GO:0004681 SGD_REF:S000051920|PMID:8816449 ISS SGD:S000001177 F casein kinase I homolog YER123W|CKI3 gene taxon:4932 20021025 SGD
+SGD S000000925 YCK3 GO:0006468 SGD_REF:S000051920|PMID:8816449 ISS SGD:S000001177 P casein kinase I homolog YER123W|CKI3 gene taxon:4932 20021025 SGD
+SGD S000000597 YCP4 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YCR004C gene taxon:4932 20031028 SGD
+SGD S000000597 YCP4 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YCR004C gene taxon:4932 20040928 SGD
+SGD S000000597 YCP4 GO:0009055 SGD_REF:S000054405|PMID:7756978 ISS F YCR004C gene taxon:4932 20060324 SGD
+SGD S000000597 YCP4 GO:0000004 SGD_REF:S000069584 ND P YCR004C gene taxon:4932 20021010 SGD
+SGD S000004262 YCS4 GO:0000799 SGD_REF:S000040443|PMID:10811823 IPI C YLR272C|LOC7 gene taxon:4932 20010118 SGD
+SGD S000004262 YCS4 GO:0000799 SGD_REF:S000058398|PMID:9887095 TAS C YLR272C|LOC7 gene taxon:4932 20010118 SGD
+SGD S000004262 YCS4 GO:0005730 SGD_REF:S000082292|PMID:11854418 IDA C YLR272C|LOC7 gene taxon:4932 20050720 SGD
+SGD S000004262 YCS4 GO:0005554 SGD_REF:S000069584 ND F YLR272C|LOC7 gene taxon:4932 20010119 SGD
+SGD S000004262 YCS4 GO:0000070 SGD_REF:S000069542|PMID:11864994 IMP P YLR272C|LOC7 gene taxon:4932 20050718 SGD
+SGD S000004262 YCS4 GO:0000070 SGD_REF:S000082292|PMID:11854418 IMP P YLR272C|LOC7 gene taxon:4932 20050720 SGD
+SGD S000004262 YCS4 GO:0007076 SGD_REF:S000040443|PMID:10811823 IPI P YLR272C|LOC7 gene taxon:4932 20010118 SGD
+SGD S000004262 YCS4 GO:0007076 SGD_REF:S000082292|PMID:11854418 IMP P YLR272C|LOC7 gene taxon:4932 20050720 SGD
+SGD S000004262 YCS4 GO:0007076 SGD_REF:S000058398|PMID:9887095 TAS P YLR272C|LOC7 gene taxon:4932 20010118 SGD
+SGD S000004262 YCS4 GO:0007076 SGD_REF:S000069542|PMID:11864994 IMP P YLR272C|LOC7 gene taxon:4932 20050718 SGD
+SGD S000004262 YCS4 GO:0010032 SGD_REF:S000075135|PMID:14662740 IMP P YLR272C|LOC7 gene taxon:4932 20050719 SGD
+SGD S000004262 YCS4 GO:0030466 SGD_REF:S000082292|PMID:11854418 IMP P YLR272C|LOC7 gene taxon:4932 20050720 SGD
+SGD S000006008 YDC1 GO:0005783 SGD_REF:S000059207|PMID:10900202 IDA C alkaline dihydroceramidase with minor reverse activity YPL087W gene taxon:4932 20021101 SGD
+SGD S000006008 YDC1 GO:0017040 SGD_REF:S000059207|PMID:10900202 IDA F alkaline dihydroceramidase with minor reverse activity YPL087W gene taxon:4932 20021101 SGD
+SGD S000006008 YDC1 GO:0006672 SGD_REF:S000059207|PMID:10900202 IMP P alkaline dihydroceramidase with minor reverse activity YPL087W gene taxon:4932 20021101 SGD
+SGD S000006008 YDC1 GO:0009408 SGD_REF:S000059207|PMID:10900202 IMP P alkaline dihydroceramidase with minor reverse activity YPL087W gene taxon:4932 20021101 SGD
+SGD S000005008 YDJ1 GO:0005829 SGD_REF:S000055246|PMID:8144572 IDA C heat shock protein, yeast dnaJ homolog (nuclear envelope protein) YNL064C|HSP40|MAS5 gene taxon:4932 20020806 SGD
+SGD S000005008 YDJ1 GO:0001671 SGD_REF:S000045398|PMID:1400408 IDA F heat shock protein, yeast dnaJ homolog (nuclear envelope protein) YNL064C|HSP40|MAS5 gene taxon:4932 20020806 SGD
+SGD S000005008 YDJ1 GO:0001671 SGD_REF:S000077458|PMID:15342786 IDA F heat shock protein, yeast dnaJ homolog (nuclear envelope protein) YNL064C|HSP40|MAS5 gene taxon:4932 20041102 SGD
+SGD S000005008 YDJ1 GO:0030188 SGD_REF:S000048634|PMID:7761857 IGI F heat shock protein, yeast dnaJ homolog (nuclear envelope protein) YNL064C|HSP40|MAS5 gene taxon:4932 20020806 SGD
+SGD S000005008 YDJ1 GO:0030188 SGD_REF:S000048634|PMID:7761857 IPI F heat shock protein, yeast dnaJ homolog (nuclear envelope protein) YNL064C|HSP40|MAS5 gene taxon:4932 20020806 SGD
+SGD S000005008 YDJ1 GO:0030192 SGD_REF:S000055246|PMID:8144572 IDA F heat shock protein, yeast dnaJ homolog (nuclear envelope protein) YNL064C|HSP40|MAS5 gene taxon:4932 20020806 SGD
+SGD S000005008 YDJ1 GO:0006626 SGD_REF:S000050215|PMID:1729605 IMP P heat shock protein, yeast dnaJ homolog (nuclear envelope protein) YNL064C|HSP40|MAS5 gene taxon:4932 20020806 SGD
+SGD S000005008 YDJ1 GO:0030433 SGD_REF:S000077133|PMID:15252059 IMP P heat shock protein, yeast dnaJ homolog (nuclear envelope protein) YNL064C|HSP40|MAS5 gene taxon:4932 20041102 SGD
+SGD S000005008 YDJ1 GO:0030433 SGD_REF:S000077458|PMID:15342786 IMP P heat shock protein, yeast dnaJ homolog (nuclear envelope protein) YNL064C|HSP40|MAS5 gene taxon:4932 20041102 SGD
+SGD S000005008 YDJ1 GO:0030433 SGD_REF:S000077458|PMID:15342786 IGI P heat shock protein, yeast dnaJ homolog (nuclear envelope protein) YNL064C|HSP40|MAS5 gene taxon:4932 20041102 SGD
+SGD S000000730 YEA4 GO:0005783 SGD_REF:S000060113|PMID:11278413 IDA C YEL004W gene taxon:4932 20010706 SGD
+SGD S000000730 YEA4 GO:0005462 SGD_REF:S000060113|PMID:11278413 IMP F YEL004W gene taxon:4932 20010706 SGD
+SGD S000000730 YEA4 GO:0005462 SGD_REF:S000060113|PMID:11278413 ISS F YEL004W gene taxon:4932 20010706 SGD
+SGD S000000730 YEA4 GO:0006038 SGD_REF:S000060113|PMID:11278413 IMP P YEL004W gene taxon:4932 20010706 SGD
+SGD S000000730 YEA4 GO:0015788 SGD_REF:S000060113|PMID:11278413 IMP P YEL004W gene taxon:4932 20010706 SGD
+SGD S000000732 YEA6 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C NAD+ transporter YEL006W|NDT2 gene taxon:4932 20051123 SGD
+SGD S000000732 YEA6 GO:0005743 SGD_REF:S000049213|PMID:10930523 ISS C NAD+ transporter YEL006W|NDT2 gene taxon:4932 20021017 SGD
+SGD S000000732 YEA6 GO:0005215 SGD_REF:S000049213|PMID:10930523 ISS F NAD+ transporter YEL006W|NDT2 gene taxon:4932 20021017 SGD
+SGD S000000732 YEA6 GO:0051724 SGD_REF:S000113591|PMID:16291748 IGI SGD:S000001268 F NAD+ transporter YEL006W|NDT2 gene taxon:4932 20051214 SGD
+SGD S000000732 YEA6 GO:0051724 SGD_REF:S000113591|PMID:16291748 IMP F NAD+ transporter YEL006W|NDT2 gene taxon:4932 20051214 SGD
+SGD S000000732 YEA6 GO:0051724 SGD_REF:S000113591|PMID:16291748 ISS SGD:S000001268 F NAD+ transporter YEL006W|NDT2 gene taxon:4932 20051214 SGD
+SGD S000000732 YEA6 GO:0006810 SGD_REF:S000049213|PMID:10930523 ISS P NAD+ transporter YEL006W|NDT2 gene taxon:4932 20021017 SGD
+SGD S000000732 YEA6 GO:0043132 SGD_REF:S000113591|PMID:16291748 IMP P NAD+ transporter YEL006W|NDT2 gene taxon:4932 20051123 SGD
+SGD S000000732 YEA6 GO:0043132 SGD_REF:S000113591|PMID:16291748 ISS SGD:S000001268 P NAD+ transporter YEL006W|NDT2 gene taxon:4932 20051123 SGD
+SGD S000000732 YEA6 GO:0043132 SGD_REF:S000113591|PMID:16291748 IGI SGD:S000001268 P NAD+ transporter YEL006W|NDT2 gene taxon:4932 20051123 SGD
+SGD S000000767 YEF1 GO:0008372 SGD_REF:S000069584 ND C YEL041W gene taxon:4932 20021126 SGD
+SGD S000000767 YEF1 GO:0003951 SGD_REF:S000086067|PMID:15978040 IDA F YEL041W gene taxon:4932 20060301 SGD
+SGD S000000767 YEF1 GO:0042736 SGD_REF:S000086067|PMID:15978040 IDA F YEL041W gene taxon:4932 20060215 SGD
+SGD S000000767 YEF1 GO:0006741 SGD_REF:S000086067|PMID:15978040 IDA P YEL041W gene taxon:4932 20060301 SGD
+SGD S000004239 YEF3 GO:0005840 SGD_REF:S000058754|PMID:9553076 IDA C Translation elongation factor 3 (EF-3) YLR249W|EF-3|TEF3 gene taxon:4932 20010123 SGD
+SGD S000004239 YEF3 GO:0003746 SGD_REF:S000058753|PMID:9841679 TAS F Translation elongation factor 3 (EF-3) YLR249W|EF-3|TEF3 gene taxon:4932 20010123 SGD
+SGD S000004239 YEF3 GO:0006414 SGD_REF:S000058753|PMID:9841679 TAS P Translation elongation factor 3 (EF-3) YLR249W|EF-3|TEF3 gene taxon:4932 20010123 SGD
+SGD S000003935 YEH1 GO:0005811 SGD_REF:S000074185|PMID:14562095 IDA C steryl ester hydrolase YLL012W gene taxon:4932 20031028 SGD
+SGD S000003935 YEH1 GO:0005811 SGD_REF:S000080917|PMID:15713625 IDA C steryl ester hydrolase YLL012W gene taxon:4932 20050302 SGD
+SGD S000003935 YEH1 GO:0016021 SGD_REF:S000080917|PMID:15713625 IDA C steryl ester hydrolase YLL012W gene taxon:4932 20050302 SGD
+SGD S000003935 YEH1 GO:0004771 SGD_REF:S000080917|PMID:15713625 IDA F steryl ester hydrolase YLL012W gene taxon:4932 20050302 SGD
+SGD S000003935 YEH1 GO:0016125 SGD_REF:S000080917|PMID:15713625 IMP P steryl ester hydrolase YLL012W gene taxon:4932 20050302 SGD
+SGD S000004010 YEH2 GO:0005886 SGD_REF:S000080289|PMID:15632184 IDA C steryl ester hydrolase YLR020C gene taxon:4932 20050111 SGD
+SGD S000004010 YEH2 GO:0016021 SGD_REF:S000080917|PMID:15713625 IDA C steryl ester hydrolase YLR020C gene taxon:4932 20050302 SGD
+SGD S000004010 YEH2 GO:0004771 SGD_REF:S000080289|PMID:15632184 IDA F steryl ester hydrolase YLR020C gene taxon:4932 20050111 SGD
+SGD S000004010 YEH2 GO:0004771 SGD_REF:S000080917|PMID:15713625 IDA F steryl ester hydrolase YLR020C gene taxon:4932 20050302 SGD
+SGD S000004010 YEH2 GO:0004771 SGD_REF:S000080289|PMID:15632184 IMP F steryl ester hydrolase YLR020C gene taxon:4932 20050111 SGD
+SGD S000004010 YEH2 GO:0000032 SGD_REF:S000075144|PMID:14587103 IMP P steryl ester hydrolase YLR020C gene taxon:4932 20031229 SGD
+SGD S000004010 YEH2 GO:0016125 SGD_REF:S000080289|PMID:15632184 IMP P steryl ester hydrolase YLR020C gene taxon:4932 20050111 SGD
+SGD S000004010 YEH2 GO:0016125 SGD_REF:S000080917|PMID:15713625 IMP P steryl ester hydrolase YLR020C gene taxon:4932 20050302 SGD
+SGD S000000843 YEN1 GO:0005634 SGD_REF:S000051194|PMID:9683672 ISS C YER041W gene taxon:4932 20021029 SGD
+SGD S000000843 YEN1 GO:0000014 SGD_REF:S000051194|PMID:9683672 ISS F YER041W gene taxon:4932 20021029 SGD
+SGD S000000843 YEN1 GO:0000004 SGD_REF:S000069584 ND P YER041W gene taxon:4932 20021029 SGD
+SGD S000001548 YET1 GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C homolog of mammalian BAP31 YKL065C gene taxon:4932 20031028 SGD
+SGD S000001548 YET1 GO:0005554 SGD_REF:S000069584 ND F homolog of mammalian BAP31 YKL065C gene taxon:4932 20021120 SGD
+SGD S000001548 YET1 GO:0000004 SGD_REF:S000069584 ND P homolog of mammalian BAP31 YKL065C gene taxon:4932 20021120 SGD
+SGD S000004643 YET2 GO:0016021 SGD_REF:S000072825|PMID:12524434 ISS C homolog of mammalian BAP31 YMR040W gene taxon:4932 20030409 SGD
+SGD S000004643 YET2 GO:0005554 SGD_REF:S000069584 ND F homolog of mammalian BAP31 YMR040W gene taxon:4932 20030203 SGD
+SGD S000004643 YET2 GO:0000004 SGD_REF:S000069584 ND P homolog of mammalian BAP31 YMR040W gene taxon:4932 20030203 SGD
+SGD S000002230 YET3 GO:0005783 SGD_REF:S000069459|PMID:11914276 IDA C homolog of mammalian BAP31 YDL072C gene taxon:4932 20020507 SGD
+SGD S000002230 YET3 GO:0005554 SGD_REF:S000069584 ND F homolog of mammalian BAP31 YDL072C gene taxon:4932 20030429 SGD
+SGD S000002230 YET3 GO:0000004 SGD_REF:S000069584 ND P homolog of mammalian BAP31 YDL072C gene taxon:4932 20030429 SGD
+SGD S000002278 YFH1 GO:0005739 SGD_REF:S000049863|PMID:9180083 IDA C YDL120W gene taxon:4932 20020828 SGD
+SGD S000002278 YFH1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YDL120W gene taxon:4932 20040924 SGD
+SGD S000002278 YFH1 GO:0005759 SGD_REF:S000050931|PMID:10428860 IDA C YDL120W gene taxon:4932 20040106 SGD
+SGD S000002278 YFH1 GO:0030234 SGD_REF:S000072956|PMID:12668611 IMP F YDL120W gene taxon:4932 20030421 SGD
+SGD S000002278 YFH1 GO:0030234 SGD_REF:S000072956|PMID:12668611 IPI F YDL120W gene taxon:4932 20030421 SGD
+SGD S000002278 YFH1 GO:0006800 SGD_REF:S000071460|PMID:12019217 IMP P YDL120W gene taxon:4932 20030128 SGD
+SGD S000002278 YFH1 GO:0006879 SGD_REF:S000069054|PMID:11734220 IGI P YDL120W gene taxon:4932 20020828 SGD
+SGD S000002278 YFH1 GO:0006879 SGD_REF:S000049863|PMID:9180083 IGI P YDL120W gene taxon:4932 20020828 SGD
+SGD S000002278 YFH1 GO:0006879 SGD_REF:S000049863|PMID:9180083 IDA P YDL120W gene taxon:4932 20020828 SGD
+SGD S000002278 YFH1 GO:0006879 SGD_REF:S000049863|PMID:9180083 IMP P YDL120W gene taxon:4932 20020828 SGD
+SGD S000002278 YFH1 GO:0006879 SGD_REF:S000069054|PMID:11734220 IMP P YDL120W gene taxon:4932 20020828 SGD
+SGD S000002278 YFH1 GO:0018283 SGD_REF:S000070337|PMID:12065597 IGI P YDL120W gene taxon:4932 20020828 SGD
+SGD S000002278 YFH1 GO:0018283 SGD_REF:S000070337|PMID:12065597 IMP P YDL120W gene taxon:4932 20020828 SGD
+SGD S000005488 YGK3 GO:0008372 SGD_REF:S000069584 ND C protein kinase YOL128C gene taxon:4932 20021011 SGD
+SGD S000005488 YGK3 GO:0004696 SGD_REF:S000052678|PMID:10958669 IGI F protein kinase YOL128C gene taxon:4932 20021009 SGD
+SGD S000005488 YGK3 GO:0004696 SGD_REF:S000052678|PMID:10958669 ISS F protein kinase YOL128C gene taxon:4932 20021009 SGD
+SGD S000005488 YGK3 GO:0006468 SGD_REF:S000052678|PMID:10958669 IGI P protein kinase YOL128C gene taxon:4932 20021009 SGD
+SGD S000005488 YGK3 GO:0006468 SGD_REF:S000052678|PMID:10958669 ISS P protein kinase YOL128C gene taxon:4932 20021009 SGD
+SGD S000005488 YGK3 GO:0006508 SGD_REF:S000052678|PMID:10958669 IGI P protein kinase YOL128C gene taxon:4932 20021009 SGD
+SGD S000005488 YGK3 GO:0006950 SGD_REF:S000072503|PMID:12529445 IGI P protein kinase YOL128C gene taxon:4932 20030219 SGD
+SGD S000005488 YGK3 GO:0006950 SGD_REF:S000072503|PMID:12529445 IMP P protein kinase YOL128C gene taxon:4932 20030219 SGD
+SGD S000005104 YGP1 GO:0009277 SGD_REF:S000071368|PMID:11136466 TAS C gp37, a glycoprotein synthesized in response to nutrient limitation which is homologous to the sporulation-specific SPS100 gene YNL160W gene taxon:4932 20021002 SGD
+SGD S000005104 YGP1 GO:0005554 SGD_REF:S000069584 ND F gp37, a glycoprotein synthesized in response to nutrient limitation which is homologous to the sporulation-specific SPS100 gene YNL160W gene taxon:4932 20030108 SGD
+SGD S000005104 YGP1 GO:0006950 SGD_REF:S000042954|PMID:8139573 IEP P gp37, a glycoprotein synthesized in response to nutrient limitation which is homologous to the sporulation-specific SPS100 gene YNL160W gene taxon:4932 20010306 SGD
+SGD S000005104 YGP1 GO:0007584 SGD_REF:S000042954|PMID:8139573 IEP P gp37, a glycoprotein synthesized in response to nutrient limitation which is homologous to the sporulation-specific SPS100 gene YNL160W gene taxon:4932 20010306 SGD
+SGD S000003466 YHB1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C flavohemoglobin YGR234W|YHB4 gene taxon:4932 20031028 SGD
+SGD S000003466 YHB1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C flavohemoglobin YGR234W|YHB4 gene taxon:4932 20040813 SGD
+SGD S000003466 YHB1 GO:0005759 SGD_REF:S000080149|PMID:15611069 IDA C flavohemoglobin YGR234W|YHB4 gene taxon:4932 20050221 SGD
+SGD S000003466 YHB1 GO:0005829 SGD_REF:S000080149|PMID:15611069 IDA C flavohemoglobin YGR234W|YHB4 gene taxon:4932 20050221 SGD
+SGD S000003466 YHB1 GO:0016966 SGD_REF:S000080149|PMID:15611069 IMP F flavohemoglobin YGR234W|YHB4 gene taxon:4932 20050221 SGD
+SGD S000003466 YHB1 GO:0016966 SGD_REF:S000055966|PMID:10758168 IMP F flavohemoglobin YGR234W|YHB4 gene taxon:4932 20050428 SGD
+SGD S000003466 YHB1 GO:0006950 SGD_REF:S000050798|PMID:9545281 IDA P flavohemoglobin YGR234W|YHB4 gene taxon:4932 20010118 SGD
+SGD S000003466 YHB1 GO:0006950 SGD_REF:S000040653|PMID:8810268 IDA P flavohemoglobin YGR234W|YHB4 gene taxon:4932 20010118 SGD
+SGD S000004289 YHC1 GO:0000243 SGD_REF:S000064189|PMID:10072386 IPI C YLR298C|U1-C|U1C gene taxon:4932 20020729 SGD
+SGD S000004289 YHC1 GO:0005685 SGD_REF:S000069986|PMID:11804584 IDA C YLR298C|U1-C|U1C gene taxon:4932 20020621 SGD
+SGD S000004289 YHC1 GO:0005685 SGD_REF:S000044485|PMID:9630245 IDA C YLR298C|U1-C|U1C gene taxon:4932 20050929 SGD
+SGD S000004289 YHC1 GO:0003729 SGD_REF:S000064189|PMID:10072386 IPI F YLR298C|U1-C|U1C gene taxon:4932 20020729 SGD
+SGD S000004289 YHC1 GO:0000398 SGD_REF:S000064189|PMID:10072386 IPI P YLR298C|U1-C|U1C gene taxon:4932 20020729 SGD
+SGD S000003595 YHC3 GO:0000324 SGD_REF:S000046600|PMID:9753630 IDA C YJL059W|BTN1 gene taxon:4932 20021007 SGD
+SGD S000003595 YHC3 GO:0015174 SGD_REF:S000075209|PMID:14660799 IGI F YJL059W|BTN1 gene taxon:4932 20031228 SGD
+SGD S000003595 YHC3 GO:0015174 SGD_REF:S000075209|PMID:14660799 IMP F YJL059W|BTN1 gene taxon:4932 20031228 SGD
+SGD S000003595 YHC3 GO:0006886 SGD_REF:S000072803|PMID:12615067 IMP P YJL059W|BTN1 gene taxon:4932 20030324 SGD
+SGD S000003595 YHC3 GO:0015802 SGD_REF:S000075209|PMID:14660799 IGI P YJL059W|BTN1 gene taxon:4932 20031228 SGD
+SGD S000003595 YHC3 GO:0015802 SGD_REF:S000075209|PMID:14660799 IMP P YJL059W|BTN1 gene taxon:4932 20031228 SGD
+SGD S000001071 YHI9 GO:0008372 SGD_REF:S000069584 ND C YHR029C gene taxon:4932 20030203 SGD
+SGD S000001071 YHI9 GO:0005554 SGD_REF:S000069584 ND F YHR029C gene taxon:4932 20030203 SGD
+SGD S000001071 YHI9 GO:0000004 SGD_REF:S000069584 ND P YHR029C gene taxon:4932 20030203 SGD
+SGD S000004854 YHM2 GO:0005743 SGD_REF:S000061777|PMID:9559855 ISS C DNA binding protein, mtDNA stabilizing protein, mitochondrial inner membrane protein with low homology to RIM2 YMR241W gene taxon:4932 20021017 SGD
+SGD S000004854 YHM2 GO:0042645 SGD_REF:S000055577|PMID:9742088 IDA C DNA binding protein, mtDNA stabilizing protein, mitochondrial inner membrane protein with low homology to RIM2 YMR241W gene taxon:4932 20050623 SGD
+SGD S000004854 YHM2 GO:0003677 SGD_REF:S000055577|PMID:9742088 IDA F DNA binding protein, mtDNA stabilizing protein, mitochondrial inner membrane protein with low homology to RIM2 YMR241W gene taxon:4932 20050623 SGD
+SGD S000004854 YHM2 GO:0005371 SGD_REF:S000061777|PMID:9559855 IDA F DNA binding protein, mtDNA stabilizing protein, mitochondrial inner membrane protein with low homology to RIM2 YMR241W gene taxon:4932 20021017 SGD
+SGD S000004854 YHM2 GO:0000002 SGD_REF:S000055577|PMID:9742088 IGI SGD:S000004676 P DNA binding protein, mtDNA stabilizing protein, mitochondrial inner membrane protein with low homology to RIM2 YMR241W gene taxon:4932 20050623 SGD
+SGD S000004854 YHM2 GO:0000002 SGD_REF:S000055577|PMID:9742088 IMP P DNA binding protein, mtDNA stabilizing protein, mitochondrial inner membrane protein with low homology to RIM2 YMR241W gene taxon:4932 20050623 SGD
+SGD S000004854 YHM2 GO:0006842 SGD_REF:S000061777|PMID:9559855 IDA P DNA binding protein, mtDNA stabilizing protein, mitochondrial inner membrane protein with low homology to RIM2 YMR241W gene taxon:4932 20021017 SGD
+SGD S000002859 YHP1 GO:0000228 SGD_REF:S000053020|PMID:10705372 IDA C YDR451C gene taxon:4932 20021014 SGD
+SGD S000002859 YHP1 GO:0003677 SGD_REF:S000072304|PMID:12464633 IDA F YDR451C gene taxon:4932 20050509 SGD
+SGD S000002859 YHP1 GO:0016566 SGD_REF:S000053020|PMID:10705372 IDA F YDR451C gene taxon:4932 20050509 SGD
+SGD S000002859 YHP1 GO:0016566 SGD_REF:S000072304|PMID:12464633 IGI SGD:S000004489 F YDR451C gene taxon:4932 20050509 SGD
+SGD S000002859 YHP1 GO:0016566 SGD_REF:S000053020|PMID:10705372 IPI F YDR451C gene taxon:4932 20050509 SGD
+SGD S000002859 YHP1 GO:0000083 SGD_REF:S000071810|PMID:12464632 IPI P YDR451C gene taxon:4932 20050603 SGD
+SGD S000002859 YHP1 GO:0000122 SGD_REF:S000053020|PMID:10705372 IEP P YDR451C gene taxon:4932 20021014 SGD
+SGD S000002859 YHP1 GO:0000122 SGD_REF:S000072304|PMID:12464633 IDA P YDR451C gene taxon:4932 20050509 SGD
+SGD S000002859 YHP1 GO:0000122 SGD_REF:S000053020|PMID:10705372 IPI P YDR451C gene taxon:4932 20021014 SGD
+SGD S000002859 YHP1 GO:0000122 SGD_REF:S000072304|PMID:12464633 IGI SGD:S000004489 P YDR451C gene taxon:4932 20050509 SGD
+SGD S000002859 YHP1 GO:0007346 SGD_REF:S000072304|PMID:12464633 IMP P YDR451C gene taxon:4932 20050509 SGD
+SGD S000002859 YHP1 GO:0040020 SGD_REF:S000053020|PMID:10705372 IEP P YDR451C gene taxon:4932 20021014 SGD
+SGD S000002859 YHP1 GO:0040020 SGD_REF:S000053020|PMID:10705372 IPI P YDR451C gene taxon:4932 20021014 SGD
+SGD S000001268 YIA6 GO:0005739 SGD_REF:S000113591|PMID:16291748 IDA C NAD+ transporter YIL006W|NDT1 gene taxon:4932 20051123 SGD
+SGD S000001268 YIA6 GO:0005743 SGD_REF:S000049213|PMID:10930523 ISS C NAD+ transporter YIL006W|NDT1 gene taxon:4932 20021017 SGD
+SGD S000001268 YIA6 GO:0005215 SGD_REF:S000049213|PMID:10930523 ISS F NAD+ transporter YIL006W|NDT1 gene taxon:4932 20021017 SGD
+SGD S000001268 YIA6 GO:0005477 SGD_REF:S000073975|PMID:12887330 IMP F NAD+ transporter YIL006W|NDT1 gene taxon:4932 20031222 SGD
+SGD S000001268 YIA6 NOT GO:0005477 SGD_REF:S000113591|PMID:16291748 IDA F NAD+ transporter YIL006W|NDT1 gene taxon:4932 20051123 SGD
+SGD S000001268 YIA6 GO:0051724 SGD_REF:S000113591|PMID:16291748 IGI SGD:S000000732 F NAD+ transporter YIL006W|NDT1 gene taxon:4932 20051214 SGD
+SGD S000001268 YIA6 GO:0051724 SGD_REF:S000113591|PMID:16291748 IDA F NAD+ transporter YIL006W|NDT1 gene taxon:4932 20051214 SGD
+SGD S000001268 YIA6 GO:0051724 SGD_REF:S000113591|PMID:16291748 IMP F NAD+ transporter YIL006W|NDT1 gene taxon:4932 20051214 SGD
+SGD S000001268 YIA6 GO:0006810 SGD_REF:S000049213|PMID:10930523 ISS P NAD+ transporter YIL006W|NDT1 gene taxon:4932 20021017 SGD
+SGD S000001268 YIA6 GO:0006850 SGD_REF:S000073975|PMID:12887330 IMP P NAD+ transporter YIL006W|NDT1 gene taxon:4932 20031222 SGD
+SGD S000001268 YIA6 NOT GO:0006850 SGD_REF:S000113591|PMID:16291748 IDA P NAD+ transporter YIL006W|NDT1 gene taxon:4932 20051123 SGD
+SGD S000001268 YIA6 GO:0043132 SGD_REF:S000113591|PMID:16291748 IGI SGD:S000000732 P NAD+ transporter YIL006W|NDT1 gene taxon:4932 20051123 SGD
+SGD S000001268 YIA6 GO:0043132 SGD_REF:S000113591|PMID:16291748 IDA P NAD+ transporter YIL006W|NDT1 gene taxon:4932 20051123 SGD
+SGD S000001268 YIA6 GO:0043132 SGD_REF:S000113591|PMID:16291748 IMP P NAD+ transporter YIL006W|NDT1 gene taxon:4932 20051123 SGD
+SGD S000005207 YIF1 GO:0005789 SGD_REF:S000080565|PMID:15659647 IPI SGD:S000007651 C YNL263C gene taxon:4932 20050623 SGD
+SGD S000005207 YIF1 GO:0030134 SGD_REF:S000061877|PMID:11157978 IDA C YNL263C gene taxon:4932 20020716 SGD
+SGD S000005207 YIF1 GO:0030173 SGD_REF:S000078612|PMID:10970842 IDA C YNL263C gene taxon:4932 20050621 SGD
+SGD S000005207 YIF1 GO:0005554 SGD_REF:S000069584 ND F YNL263C gene taxon:4932 20020716 SGD
+SGD S000005207 YIF1 GO:0006888 SGD_REF:S000061877|PMID:11157978 IPI P YNL263C gene taxon:4932 20020716 SGD
+SGD S000006122 YIG1 GO:0005634 SGD_REF:S000113896|PMID:16358322 IDA C YPL201C gene taxon:4932 20060111 SGD
+SGD S000006122 YIG1 GO:0005829 SGD_REF:S000113896|PMID:16358322 IDA C YPL201C gene taxon:4932 20060111 SGD
+SGD S000006122 YIG1 GO:0005554 SGD_REF:S000069584 ND F YPL201C gene taxon:4932 20021126 SGD
+SGD S000006122 YIG1 GO:0006114 SGD_REF:S000113896|PMID:16358322 IMP P YPL201C gene taxon:4932 20060111 SGD
+SGD S000000655 YIH1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YCR059C gene taxon:4932 20031028 SGD
+SGD S000000655 YIH1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YCR059C gene taxon:4932 20031028 SGD
+SGD S000000655 YIH1 GO:0005554 SGD_REF:S000069584 ND F YCR059C gene taxon:4932 20010308 SGD
+SGD S000000655 YIH1 GO:0006521 SGD_REF:S000054053|PMID:10801780 IPI P YCR059C gene taxon:4932 20010308 SGD
+SGD S000000655 YIH1 GO:0006521 SGD_REF:S000054053|PMID:10801780 IMP P YCR059C gene taxon:4932 20010308 SGD
+SGD S000004760 YIM1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YMR152W gene taxon:4932 20020507 SGD
+SGD S000004760 YIM1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YMR152W gene taxon:4932 20051017 SGD
+SGD S000004760 YIM1 GO:0005811 SGD_REF:S000048561|PMID:10515935 IDA C YMR152W gene taxon:4932 20010118 SGD
+SGD S000004760 YIM1 GO:0005554 SGD_REF:S000069584 ND F YMR152W gene taxon:4932 20051017 SGD
+SGD S000004760 YIM1 GO:0006974 SGD_REF:S000081213|PMID:12077312 IMP P YMR152W gene taxon:4932 20050803 SGD
+SGD S000003404 YIP1 GO:0005789 SGD_REF:S000074554|PMID:14557247 IDA C YGR172C gene taxon:4932 20050208 SGD
+SGD S000003404 YIP1 GO:0005789 SGD_REF:S000080565|PMID:15659647 IDA C YGR172C gene taxon:4932 20050208 SGD
+SGD S000003404 YIP1 GO:0030134 SGD_REF:S000080565|PMID:15659647 IDA C YGR172C gene taxon:4932 20050623 SGD
+SGD S000003404 YIP1 GO:0030134 SGD_REF:S000080565|PMID:15659647 IPI SGD:S000007651 C YGR172C gene taxon:4932 20050623 SGD
+SGD S000003404 YIP1 GO:0030173 SGD_REF:S000055649|PMID:9724632 IDA C YGR172C gene taxon:4932 20050208 SGD
+SGD S000003404 YIP1 GO:0005554 SGD_REF:S000069584 ND F YGR172C gene taxon:4932 20020624 SGD
+SGD S000003404 YIP1 GO:0006888 SGD_REF:S000080565|PMID:15659647 IMP P YGR172C gene taxon:4932 20050208 SGD
+SGD S000003404 YIP1 GO:0016192 SGD_REF:S000055649|PMID:9724632 IMP P YGR172C gene taxon:4932 20020624 SGD
+SGD S000003404 YIP1 GO:0048280 SGD_REF:S000073622|PMID:12657649 IMP P YGR172C gene taxon:4932 20050208 SGD
+SGD S000004989 YIP3 GO:0005783 SGD_REF:S000082473|PMID:16002643 IDA C YNL044W gene taxon:4932 20060426 SGD
+SGD S000004989 YIP3 GO:0005794 SGD_REF:S000082473|PMID:16002643 IDA C YNL044W gene taxon:4932 20060426 SGD
+SGD S000004989 YIP3 GO:0030134 SGD_REF:S000061877|PMID:11157978 IDA C YNL044W gene taxon:4932 20020716 SGD
+SGD S000004989 YIP3 GO:0005554 SGD_REF:S000069584 ND F YNL044W gene taxon:4932 20050623 SGD
+SGD S000004989 YIP3 GO:0006888 SGD_REF:S000061877|PMID:11157978 IPI P YNL044W gene taxon:4932 20020716 SGD
+SGD S000003166 YIP4 GO:0016020 SGD_REF:S000069836|PMID:11943201 ISS C YGL198W gene taxon:4932 20030117 SGD
+SGD S000003166 YIP4 GO:0017137 SGD_REF:S000069836|PMID:11943201 IPI SGD:S000001856 F YGL198W gene taxon:4932 20030117 SGD
+SGD S000003166 YIP4 GO:0016192 SGD_REF:S000074191|PMID:14566057 RCA P YGL198W gene taxon:4932 20050608 SGD
+SGD S000003129 YIP5 GO:0016020 SGD_REF:S000069836|PMID:11943201 ISS C YGL161C gene taxon:4932 20030117 SGD
+SGD S000003129 YIP5 GO:0017137 SGD_REF:S000069836|PMID:11943201 IPI SGD:S000001856 F YGL161C gene taxon:4932 20030117 SGD
+SGD S000003129 YIP5 GO:0016192 SGD_REF:S000074191|PMID:14566057 RCA P YGL161C gene taxon:4932 20050608 SGD
+SGD S000001578 YJU2 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YKL095W|CWC16 gene taxon:4932 20031028 SGD
+SGD S000001578 YJU2 GO:0005554 SGD_REF:S000069584 ND F YKL095W|CWC16 gene taxon:4932 20021030 SGD
+SGD S000001578 YJU2 GO:0000398 SGD_REF:S000074191|PMID:14566057 RCA P YKL095W|CWC16 gene taxon:4932 20050608 SGD
+SGD S000001577 YJU3 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YKL094W gene taxon:4932 20020507 SGD
+SGD S000001577 YJU3 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C YKL094W gene taxon:4932 20060317 SGD
+SGD S000001577 YJU3 GO:0005811 SGD_REF:S000048561|PMID:10515935 IDA C YKL094W gene taxon:4932 20020917 SGD
+SGD S000001577 YJU3 GO:0017171 SGD_REF:S000076484|PMID:14645503 IDA F YKL094W gene taxon:4932 20040604 SGD
+SGD S000001577 YJU3 GO:0017171 SGD_REF:S000076484|PMID:14645503 RCA F YKL094W gene taxon:4932 20060421 SGD
+SGD S000001577 YJU3 GO:0000004 SGD_REF:S000069584 ND P YKL094W gene taxon:4932 20030108 SGD
+SGD S000004190 YKE2 GO:0005737 SGD_REF:S000049112|PMID:9463374 IDA C bovine NABC complex component homolog, non-native actin binding complex polypeptide 6, prefoldin complex subunit YLR200W|GIM1|PFD6 gene taxon:4932 20020617 SGD
+SGD S000004190 YKE2 GO:0016272 SGD_REF:S000049112|PMID:9463374 IPI SGD:S000003310|SGD:S000004559 C bovine NABC complex component homolog, non-native actin binding complex polypeptide 6, prefoldin complex subunit YLR200W|GIM1|PFD6 gene taxon:4932 20031215 SGD
+SGD S000004190 YKE2 GO:0016272 SGD_REF:S000058336|PMID:9630229 ISS C bovine NABC complex component homolog, non-native actin binding complex polypeptide 6, prefoldin complex subunit YLR200W|GIM1|PFD6 gene taxon:4932 20031215 SGD
+SGD S000004190 YKE2 GO:0015631 SGD_REF:S000049112|PMID:9463374 IDA F bovine NABC complex component homolog, non-native actin binding complex polypeptide 6, prefoldin complex subunit YLR200W|GIM1|PFD6 gene taxon:4932 20021101 SGD
+SGD S000004190 YKE2 GO:0006457 SGD_REF:S000049112|PMID:9463374 ISS P bovine NABC complex component homolog, non-native actin binding complex polypeptide 6, prefoldin complex subunit YLR200W|GIM1|PFD6 gene taxon:4932 20020617 SGD
+SGD S000004190 YKE2 GO:0006457 SGD_REF:S000049112|PMID:9463374 IMP P bovine NABC complex component homolog, non-native actin binding complex polypeptide 6, prefoldin complex subunit YLR200W|GIM1|PFD6 gene taxon:4932 20020617 SGD
+SGD S000004190 YKE2 GO:0007021 SGD_REF:S000049112|PMID:9463374 ISS P bovine NABC complex component homolog, non-native actin binding complex polypeptide 6, prefoldin complex subunit YLR200W|GIM1|PFD6 gene taxon:4932 20020617 SGD
+SGD S000004190 YKE2 GO:0007021 SGD_REF:S000049112|PMID:9463374 IMP P bovine NABC complex component homolog, non-native actin binding complex polypeptide 6, prefoldin complex subunit YLR200W|GIM1|PFD6 gene taxon:4932 20020617 SGD
+SGD S000001285 YKE4 GO:0008372 SGD_REF:S000069584 ND C ER zinc transporter YIL023C gene taxon:4932 20021126 SGD
+SGD S000001285 YKE4 GO:0005554 SGD_REF:S000069584 ND F ER zinc transporter YIL023C gene taxon:4932 20021126 SGD
+SGD S000001285 YKE4 GO:0000004 SGD_REF:S000069584 ND P ER zinc transporter YIL023C gene taxon:4932 20021126 SGD
+SGD S000001679 YKT6 GO:0000324 SGD_REF:S000080980|PMID:15723044 IDA C v-SNARE YKL196C gene taxon:4932 20050315 SGD
+SGD S000001679 YKT6 GO:0005625 SGD_REF:S000080980|PMID:15723044 IDA C v-SNARE YKL196C gene taxon:4932 20050315 SGD
+SGD S000001679 YKT6 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C v-SNARE YKL196C gene taxon:4932 20040928 SGD
+SGD S000001679 YKT6 GO:0016020 SGD_REF:S000056190|PMID:9211930 IDA C v-SNARE YKL196C gene taxon:4932 20020827 SGD
+SGD S000001679 YKT6 GO:0005485 SGD_REF:S000058453|PMID:10047442 TAS F v-SNARE YKL196C gene taxon:4932 20010118 SGD
+SGD S000001679 YKT6 GO:0016409 SGD_REF:S000076866|PMID:14685280 IDA F v-SNARE YKL196C gene taxon:4932 20050914 SGD
+SGD S000001679 YKT6 GO:0006891 SGD_REF:S000058453|PMID:10047442 TAS P v-SNARE YKL196C gene taxon:4932 20010118 SGD
+SGD S000001679 YKT6 GO:0006906 SGD_REF:S000058453|PMID:10047442 TAS P v-SNARE YKL196C gene taxon:4932 20010118 SGD
+SGD S000004897 YKU70 GO:0000790 SGD_REF:S000039233|PMID:10367891 TAS C DNA binding protein YMR284W|HDF1|KU70|NES24 gene taxon:4932 20021101 SGD
+SGD S000004897 YKU70 GO:0005635 SGD_REF:S000056414|PMID:10638763 IDA C DNA binding protein YMR284W|HDF1|KU70|NES24 gene taxon:4932 20021025 SGD
+SGD S000004897 YKU70 GO:0005724 SGD_REF:S000070058|PMID:12080091 TAS C DNA binding protein YMR284W|HDF1|KU70|NES24 gene taxon:4932 20021101 SGD
+SGD S000004897 YKU70 GO:0003684 SGD_REF:S000039233|PMID:10367891 TAS F DNA binding protein YMR284W|HDF1|KU70|NES24 gene taxon:4932 20021101 SGD
+SGD S000004897 YKU70 GO:0003723 SGD_REF:S000074098|PMID:12975323 IDA F DNA binding protein YMR284W|HDF1|KU70|NES24 gene taxon:4932 20040327 SGD
+SGD S000004897 YKU70 GO:0000723 SGD_REF:S000047753|PMID:10818099 IMP P DNA binding protein YMR284W|HDF1|KU70|NES24 gene taxon:4932 20021101 SGD
+SGD S000004897 YKU70 GO:0000724 SGD_REF:S000059175|PMID:11016833 IMP P DNA binding protein YMR284W|HDF1|KU70|NES24 gene taxon:4932 20021101 SGD
+SGD S000004897 YKU70 GO:0006303 SGD_REF:S000051563|PMID:10908335 IDA P DNA binding protein YMR284W|HDF1|KU70|NES24 gene taxon:4932 20021101 SGD
+SGD S000004897 YKU70 GO:0006333 SGD_REF:S000068980|PMID:11553718 IDA P DNA binding protein YMR284W|HDF1|KU70|NES24 gene taxon:4932 20021101 SGD
+SGD S000004897 YKU70 GO:0006342 SGD_REF:S000047483|PMID:9501103 IMP P DNA binding protein YMR284W|HDF1|KU70|NES24 gene taxon:4932 20030617 SGD
+SGD S000004897 YKU70 GO:0006342 SGD_REF:S000047483|PMID:9501103 IDA P DNA binding protein YMR284W|HDF1|KU70|NES24 gene taxon:4932 20030617 SGD
+SGD S000004712 YKU80 GO:0000790 SGD_REF:S000039233|PMID:10367891 TAS C Ku80 homolog YMR106C|HDF2 gene taxon:4932 20021101 SGD
+SGD S000004712 YKU80 GO:0005724 SGD_REF:S000070058|PMID:12080091 TAS C Ku80 homolog YMR106C|HDF2 gene taxon:4932 20021101 SGD
+SGD S000004712 YKU80 GO:0003677 SGD_REF:S000086738|PMID:16166630 IDA F Ku80 homolog YMR106C|HDF2 gene taxon:4932 20051003 SGD
+SGD S000004712 YKU80 GO:0003684 SGD_REF:S000039233|PMID:10367891 TAS F Ku80 homolog YMR106C|HDF2 gene taxon:4932 20021101 SGD
+SGD S000004712 YKU80 GO:0003723 SGD_REF:S000074098|PMID:12975323 IDA F Ku80 homolog YMR106C|HDF2 gene taxon:4932 20040327 SGD
+SGD S000004712 YKU80 GO:0000723 SGD_REF:S000047753|PMID:10818099 IMP P Ku80 homolog YMR106C|HDF2 gene taxon:4932 20021101 SGD
+SGD S000004712 YKU80 GO:0000724 SGD_REF:S000059175|PMID:11016833 IMP P Ku80 homolog YMR106C|HDF2 gene taxon:4932 20021101 SGD
+SGD S000004712 YKU80 GO:0006303 SGD_REF:S000051563|PMID:10908335 IDA P Ku80 homolog YMR106C|HDF2 gene taxon:4932 20021101 SGD
+SGD S000004712 YKU80 GO:0006333 SGD_REF:S000068980|PMID:11553718 IDA P Ku80 homolog YMR106C|HDF2 gene taxon:4932 20021101 SGD
+SGD S000004712 YKU80 GO:0006342 SGD_REF:S000047483|PMID:9501103 IMP P Ku80 homolog YMR106C|HDF2 gene taxon:4932 20030617 SGD
+SGD S000004712 YKU80 GO:0006342 SGD_REF:S000047483|PMID:9501103 IDA P Ku80 homolog YMR106C|HDF2 gene taxon:4932 20030617 SGD
+SGD S000004712 YKU80 GO:0031494 SGD_REF:S000086738|PMID:16166630 IDA P Ku80 homolog YMR106C|HDF2 gene taxon:4932 20051003 SGD
+SGD S000004712 YKU80 GO:0031494 SGD_REF:S000086738|PMID:16166630 IMP P Ku80 homolog YMR106C|HDF2 gene taxon:4932 20051003 SGD
+SGD S000001006 YLF2 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YHL014C|YLF1 gene taxon:4932 20031028 SGD
+SGD S000001006 YLF2 GO:0005525 SGD_REF:S000040292|PMID:8021936 ISS protein_id:U02423 F YHL014C|YLF1 gene taxon:4932 20050802 SGD
+SGD S000001006 YLF2 GO:0000004 SGD_REF:S000069584 ND P YHL014C|YLF1 gene taxon:4932 20021029 SGD
+SGD S000006329 YLH47 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YPR125W gene taxon:4932 20031028 SGD
+SGD S000006329 YLH47 GO:0005743 SGD_REF:S000114395|PMID:16476776 IDA C YPR125W gene taxon:4932 20060216 SGD
+SGD S000006329 YLH47 GO:0005743 SGD_REF:S000114395|PMID:16476776 ISS C YPR125W gene taxon:4932 20060216 SGD
+SGD S000006329 YLH47 GO:0005554 SGD_REF:S000069584 ND F YPR125W gene taxon:4932 20060216 SGD
+SGD S000006329 YLH47 GO:0051204 SGD_REF:S000114395|PMID:16476776 IMP P YPR125W gene taxon:4932 20060410 SGD
+SGD S000006262 YMC1 GO:0005743 SGD_REF:S000049213|PMID:10930523 ISS C YPR058W gene taxon:4932 20021017 SGD
+SGD S000006262 YMC1 GO:0005215 SGD_REF:S000040778|PMID:8488731 ISS F YPR058W gene taxon:4932 20021002 SGD
+SGD S000006262 YMC1 GO:0006810 SGD_REF:S000040778|PMID:8488731 ISS P YPR058W gene taxon:4932 20021002 SGD
+SGD S000000308 YMC2 GO:0005743 SGD_REF:S000049213|PMID:10930523 ISS C YBR104W gene taxon:4932 20021017 SGD
+SGD S000000308 YMC2 GO:0005215 SGD_REF:S000049213|PMID:10930523 ISS F YBR104W gene taxon:4932 20021017 SGD
+SGD S000000308 YMC2 GO:0006810 SGD_REF:S000049213|PMID:10930523 ISS P YBR104W gene taxon:4932 20021017 SGD
+SGD S000004502 YMD8 colocalizes_with GO:0030137 SGD_REF:S000074185|PMID:14562095 IDA C YML038C gene taxon:4932 20031028 SGD
+SGD S000004502 YMD8 GO:0005338 SGD_REF:S000040647|PMID:9395539 ISS SGD:S000003193 F YML038C gene taxon:4932 20021030 SGD
+SGD S000004502 YMD8 GO:0015780 SGD_REF:S000040647|PMID:9395539 ISS SGD:S000003193 P YML038C gene taxon:4932 20021030 SGD
+SGD S000006228 YME1 GO:0005739 SGD_REF:S000069459|PMID:11914276 IDA C YPR024W|OSD1|YTA11 gene taxon:4932 20020507 SGD
+SGD S000006228 YME1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YPR024W|OSD1|YTA11 gene taxon:4932 20040924 SGD
+SGD S000006228 YME1 GO:0005743 SGD_REF:S000058450|PMID:9891785 TAS C YPR024W|OSD1|YTA11 gene taxon:4932 20010118 SGD
+SGD S000006228 YME1 GO:0031942 SGD_REF:S000113568|PMID:16267274 IDA C YPR024W|OSD1|YTA11 gene taxon:4932 20051129 SGD
+SGD S000006228 YME1 GO:0004176 SGD_REF:S000058450|PMID:9891785 TAS F YPR024W|OSD1|YTA11 gene taxon:4932 20010118 SGD
+SGD S000006228 YME1 GO:0007005 SGD_REF:S000058450|PMID:9891785 TAS P YPR024W|OSD1|YTA11 gene taxon:4932 20010118 SGD
+SGD S000004917 YME2 GO:0005743 SGD_REF:S000055327|PMID:8649384 TAS C exonuclease (putative), integral membrane protein YMR302C|PRP12|RNA12 gene taxon:4932 20010118 SGD
+SGD S000004917 YME2 GO:0004527 SGD_REF:S000049298|PMID:9933355 ISS F exonuclease (putative), integral membrane protein YMR302C|PRP12|RNA12 gene taxon:4932 20010118 SGD
+SGD S000004917 YME2 GO:0000002 SGD_REF:S000047590|PMID:8514129 IMP P exonuclease (putative), integral membrane protein YMR302C|PRP12|RNA12 gene taxon:4932 20010118 SGD
+SGD S000004917 YME2 GO:0006364 SGD_REF:S000042396|PMID:1557037 IMP P exonuclease (putative), integral membrane protein YMR302C|PRP12|RNA12 gene taxon:4932 20010118 SGD
+SGD S000004487 YML6 GO:0005762 SGD_REF:S000058278|PMID:9445368 TAS C YML025C gene taxon:4932 20001002 SGD
+SGD S000004487 YML6 GO:0003735 SGD_REF:S000058278|PMID:9445368 TAS F YML025C gene taxon:4932 20001002 SGD
+SGD S000004487 YML6 GO:0000027 SGD_REF:S000058278|PMID:9445368 ISS P YML025C gene taxon:4932 20001002 SGD
+SGD S000004487 YML6 GO:0043037 SGD_REF:S000058278|PMID:9445368 TAS P YML025C gene taxon:4932 20001002 SGD
+SGD S000003871 YMR1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YJR110W gene taxon:4932 20031028 SGD
+SGD S000003871 YMR1 GO:0004438 SGD_REF:S000076957|PMID:15169871 IDA F YJR110W gene taxon:4932 20041008 SGD
+SGD S000003871 YMR1 GO:0004438 SGD_REF:S000076957|PMID:15169871 IMP F YJR110W gene taxon:4932 20041008 SGD
+SGD S000003871 YMR1 GO:0016791 SGD_REF:S000065754|PMID:9736772 ISS F YJR110W gene taxon:4932 20030121 SGD
+SGD S000003871 YMR1 GO:0016192 SGD_REF:S000076957|PMID:15169871 IMP P YJR110W gene taxon:4932 20041008 SGD
+SGD S000003871 YMR1 GO:0046856 SGD_REF:S000076957|PMID:15169871 IDA P YJR110W gene taxon:4932 20041008 SGD
+SGD S000003871 YMR1 GO:0046856 SGD_REF:S000076957|PMID:15169871 IMP P YJR110W gene taxon:4932 20041008 SGD
+SGD S000003871 YMR1 GO:0048017 SGD_REF:S000076957|PMID:15169871 IMP P YJR110W gene taxon:4932 20050524 SGD
+SGD S000001945 YMR31 GO:0005763 SGD_REF:S000058278|PMID:9445368 TAS C mitochondrial ribosomal protein YFR049W gene taxon:4932 20010118 SGD
+SGD S000001945 YMR31 GO:0003735 SGD_REF:S000058278|PMID:9445368 TAS F mitochondrial ribosomal protein YFR049W gene taxon:4932 20010118 SGD
+SGD S000001945 YMR31 GO:0043037 SGD_REF:S000058278|PMID:9445368 TAS P mitochondrial ribosomal protein YFR049W gene taxon:4932 20010118 SGD
+SGD S000000807 YND1 GO:0005794 SGD_REF:S000074185|PMID:14562095 IDA C apyrase (NDPase/NTPase) YER005W|YEJ5 gene taxon:4932 20031028 SGD
+SGD S000000807 YND1 colocalizes_with GO:0030137 SGD_REF:S000074185|PMID:14562095 IDA C apyrase (NDPase/NTPase) YER005W|YEJ5 gene taxon:4932 20031028 SGD
+SGD S000000807 YND1 GO:0017110 SGD_REF:S000045197|PMID:10409709 IDA F apyrase (NDPase/NTPase) YER005W|YEJ5 gene taxon:4932 20020617 SGD
+SGD S000000807 YND1 GO:0006486 SGD_REF:S000045197|PMID:10409709 IMP P apyrase (NDPase/NTPase) YER005W|YEJ5 gene taxon:4932 20020617 SGD
+SGD S000005590 YNG1 GO:0000123 SGD_REF:S000070253|PMID:12077334 IDA C histone acetyltransferase complex component YOR064C|YOR29-15 gene taxon:4932 20021104 SGD
+SGD S000005590 YNG1 GO:0000788 SGD_REF:S000070253|PMID:12077334 TAS C histone acetyltransferase complex component YOR064C|YOR29-15 gene taxon:4932 20020807 SGD
+SGD S000005590 YNG1 contributes_to GO:0004402 SGD_REF:S000070253|PMID:12077334 IMP F histone acetyltransferase complex component YOR064C|YOR29-15 gene taxon:4932 20050629 SGD
+SGD S000005590 YNG1 GO:0016568 SGD_REF:S000043268|PMID:10805724 IMP P histone acetyltransferase complex component YOR064C|YOR29-15 gene taxon:4932 20020321 SGD
+SGD S000005590 YNG1 GO:0016568 SGD_REF:S000043268|PMID:10805724 ISS P histone acetyltransferase complex component YOR064C|YOR29-15 gene taxon:4932 20020321 SGD
+SGD S000005590 YNG1 GO:0016568 SGD_REF:S000043268|PMID:10805724 IPI P histone acetyltransferase complex component YOR064C|YOR29-15 gene taxon:4932 20020321 SGD
+SGD S000005590 YNG1 GO:0016573 SGD_REF:S000070253|PMID:12077334 IDA P histone acetyltransferase complex component YOR064C|YOR29-15 gene taxon:4932 20021104 SGD
+SGD S000001132 YNG2 GO:0000123 SGD_REF:S000068948|PMID:11604499 IDA C NuA4 histone acetyltransferase complex component YHR090C|EAF4|NBN1 gene taxon:4932 20021106 SGD
+SGD S000001132 YNG2 GO:0005634 SGD_REF:S000043268|PMID:10805724 IDA C NuA4 histone acetyltransferase complex component YHR090C|EAF4|NBN1 gene taxon:4932 20020321 SGD
+SGD S000001132 YNG2 GO:0043189 SGD_REF:S000079775|PMID:15485911 IPI C NuA4 histone acetyltransferase complex component YHR090C|EAF4|NBN1 gene taxon:4932 20050207 SGD
+SGD S000001132 YNG2 GO:0008047 SGD_REF:S000068990|PMID:11544250 IMP F NuA4 histone acetyltransferase complex component YHR090C|EAF4|NBN1 gene taxon:4932 20021106 SGD
+SGD S000001132 YNG2 GO:0016568 SGD_REF:S000043268|PMID:10805724 IMP P NuA4 histone acetyltransferase complex component YHR090C|EAF4|NBN1 gene taxon:4932 20020321 SGD
+SGD S000001132 YNG2 GO:0016568 SGD_REF:S000043268|PMID:10805724 IPI P NuA4 histone acetyltransferase complex component YHR090C|EAF4|NBN1 gene taxon:4932 20020321 SGD
+SGD S000001132 YNG2 GO:0016568 SGD_REF:S000043268|PMID:10805724 ISS P NuA4 histone acetyltransferase complex component YHR090C|EAF4|NBN1 gene taxon:4932 20020321 SGD
+SGD S000001550 YNK1 GO:0005758 SGD_REF:S000072775|PMID:12472466 IDA C nucleoside diphosphate kinase YKL067W|NDK1 gene taxon:4932 20030324 SGD
+SGD S000001550 YNK1 GO:0005829 SGD_REF:S000072775|PMID:12472466 IDA C nucleoside diphosphate kinase YKL067W|NDK1 gene taxon:4932 20030324 SGD
+SGD S000001550 YNK1 GO:0004550 SGD_REF:S000052142|PMID:7499258 ISS F nucleoside diphosphate kinase YKL067W|NDK1 gene taxon:4932 20020927 SGD
+SGD S000001550 YNK1 GO:0004550 SGD_REF:S000072775|PMID:12472466 IDA F nucleoside diphosphate kinase YKL067W|NDK1 gene taxon:4932 20051025 SGD
+SGD S000001550 YNK1 GO:0006164 SGD_REF:S000060059|PMID:11035032 TAS P nucleoside diphosphate kinase YKL067W|NDK1 gene taxon:4932 20030326 SGD
+SGD S000001550 YNK1 GO:0006165 SGD_REF:S000065769|PMID:1659321 IDA P nucleoside diphosphate kinase YKL067W|NDK1 gene taxon:4932 20051025 SGD
+SGD S000001550 YNK1 GO:0006259 SGD_REF:S000065769|PMID:1659321 IDA P nucleoside diphosphate kinase YKL067W|NDK1 gene taxon:4932 20030326 SGD
+SGD S000001550 YNK1 GO:0009117 SGD_REF:S000072775|PMID:12472466 TAS P nucleoside diphosphate kinase YKL067W|NDK1 gene taxon:4932 20030324 SGD
+SGD S000001550 YNK1 GO:0009142 SGD_REF:S000065769|PMID:1659321 IDA P nucleoside diphosphate kinase YKL067W|NDK1 gene taxon:4932 20051025 SGD
+SGD S000001550 YNK1 GO:0016070 SGD_REF:S000065769|PMID:1659321 IDA P nucleoside diphosphate kinase YKL067W|NDK1 gene taxon:4932 20030326 SGD
+SGD S000006232 YOP1 GO:0016021 SGD_REF:S000060113|PMID:11278413 IDA C YPR028W|YIP2 gene taxon:4932 20050208 SGD
+SGD S000006232 YOP1 GO:0005515 SGD_REF:S000060113|PMID:11278413 IDA F YPR028W|YIP2 gene taxon:4932 20040914 SGD
+SGD S000006232 YOP1 GO:0016192 SGD_REF:S000071802|PMID:12427979 IMP P YPR028W|YIP2 gene taxon:4932 20050208 SGD
+SGD S000006232 YOP1 GO:0016192 SGD_REF:S000060113|PMID:11278413 IPI P YPR028W|YIP2 gene taxon:4932 20050208 SGD
+SGD S000006232 YOP1 GO:0016192 SGD_REF:S000060113|PMID:11278413 IMP P YPR028W|YIP2 gene taxon:4932 20050208 SGD
+SGD S000003513 YOR1 GO:0005886 SGD_REF:S000043289|PMID:9575223 IDA C ABC transporter YGR281W|YRS1 gene taxon:4932 20021003 SGD
+SGD S000003513 YOR1 GO:0008559 SGD_REF:S000069766|PMID:11421285 TAS F ABC transporter YGR281W|YRS1 gene taxon:4932 20020607 SGD
+SGD S000003513 YOR1 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P ABC transporter YGR281W|YRS1 gene taxon:4932 20060227 SGD
+SGD S000003513 YOR1 GO:0006810 SGD_REF:S000069766|PMID:11421285 TAS P ABC transporter YGR281W|YRS1 gene taxon:4932 20020607 SGD
+SGD S000003513 YOR1 GO:0042493 SGD_REF:S000069766|PMID:11421285 TAS P ABC transporter YGR281W|YRS1 gene taxon:4932 20021111 SGD
+SGD S000007651 YOS1 GO:0005789 SGD_REF:S000080565|PMID:15659647 IDA C YER074W-A gene taxon:4932 20050623 SGD
+SGD S000007651 YOS1 GO:0005789 SGD_REF:S000080565|PMID:15659647 IPI SGD:S000003404|SGD:S000005207 C YER074W-A gene taxon:4932 20050623 SGD
+SGD S000007651 YOS1 GO:0030134 SGD_REF:S000080565|PMID:15659647 IDA C YER074W-A gene taxon:4932 20050623 SGD
+SGD S000007651 YOS1 GO:0030134 SGD_REF:S000080565|PMID:15659647 IPI SGD:S000003404|SGD:S000005207 C YER074W-A gene taxon:4932 20050623 SGD
+SGD S000007651 YOS1 GO:0030173 SGD_REF:S000080565|PMID:15659647 IPI SGD:S000003404|SGD:S000005207 C YER074W-A gene taxon:4932 20050623 SGD
+SGD S000007651 YOS1 GO:0030173 SGD_REF:S000080565|PMID:15659647 IDA C YER074W-A gene taxon:4932 20050623 SGD
+SGD S000007651 YOS1 GO:0005554 SGD_REF:S000069584 ND F YER074W-A gene taxon:4932 20050623 SGD
+SGD S000007651 YOS1 GO:0006888 SGD_REF:S000080565|PMID:15659647 IMP P YER074W-A gene taxon:4932 20050623 SGD
+SGD S000002464 YOS9 GO:0005783 SGD_REF:S000071361|PMID:12077121 TAS C membrane-associated glycoprotein YDR057W gene taxon:4932 20021002 SGD
+SGD S000002464 YOS9 GO:0005529 SGD_REF:S000086711|PMID:16168372 IMP F membrane-associated glycoprotein YDR057W gene taxon:4932 20051209 SGD
+SGD S000002464 YOS9 GO:0005529 SGD_REF:S000086711|PMID:16168372 ISS F membrane-associated glycoprotein YDR057W gene taxon:4932 20051209 SGD
+SGD S000002464 YOS9 GO:0030433 SGD_REF:S000086775|PMID:16168370 IMP P membrane-associated glycoprotein YDR057W gene taxon:4932 20051209 SGD
+SGD S000002464 YOS9 GO:0030433 SGD_REF:S000113700|PMID:16168371 IMP P membrane-associated glycoprotein YDR057W gene taxon:4932 20051209 SGD
+SGD S000002464 YOS9 GO:0030433 SGD_REF:S000086711|PMID:16168372 IMP P membrane-associated glycoprotein YDR057W gene taxon:4932 20051209 SGD
+SGD S000004489 YOX1 GO:0005634 SGD_REF:S000072304|PMID:12464633 IC GO:0016566 C homeobox-domain containing protein YML027W gene taxon:4932 20030325 SGD
+SGD S000004489 YOX1 GO:0005634 SGD_REF:S000077144|PMID:15282802 IDA C homeobox-domain containing protein YML027W gene taxon:4932 20041008 SGD
+SGD S000004489 YOX1 GO:0003677 SGD_REF:S000050068|PMID:8096171 IDA F homeobox-domain containing protein YML027W gene taxon:4932 20021030 SGD
+SGD S000004489 YOX1 GO:0003677 SGD_REF:S000072304|PMID:12464633 IDA F homeobox-domain containing protein YML027W gene taxon:4932 20050509 SGD
+SGD S000004489 YOX1 GO:0016566 SGD_REF:S000072304|PMID:12464633 IDA F homeobox-domain containing protein YML027W gene taxon:4932 20030325 SGD
+SGD S000004489 YOX1 GO:0016566 SGD_REF:S000072304|PMID:12464633 IMP F homeobox-domain containing protein YML027W gene taxon:4932 20050509 SGD
+SGD S000004489 YOX1 GO:0016566 SGD_REF:S000072304|PMID:12464633 IGI SGD:S000002859 F homeobox-domain containing protein YML027W gene taxon:4932 20050509 SGD
+SGD S000004489 YOX1 GO:0000083 SGD_REF:S000071810|PMID:12464632 IPI P homeobox-domain containing protein YML027W gene taxon:4932 20050603 SGD
+SGD S000004489 YOX1 GO:0000122 SGD_REF:S000072304|PMID:12464633 IGI SGD:S000002859 P homeobox-domain containing protein YML027W gene taxon:4932 20050509 SGD
+SGD S000004489 YOX1 GO:0000122 SGD_REF:S000072304|PMID:12464633 IDA P homeobox-domain containing protein YML027W gene taxon:4932 20050509 SGD
+SGD S000004489 YOX1 GO:0000122 SGD_REF:S000072304|PMID:12464633 IMP P homeobox-domain containing protein YML027W gene taxon:4932 20050509 SGD
+SGD S000004489 YOX1 GO:0007346 SGD_REF:S000072304|PMID:12464633 IMP P homeobox-domain containing protein YML027W gene taxon:4932 20030325 SGD
+SGD S000000387 YPC1 GO:0005783 SGD_REF:S000059207|PMID:10900202 IDA C alkaline ceramidase with reverse activity YBR183W gene taxon:4932 20021101 SGD
+SGD S000000387 YPC1 GO:0017040 SGD_REF:S000059207|PMID:10900202 IDA F alkaline ceramidase with reverse activity YBR183W gene taxon:4932 20021101 SGD
+SGD S000000387 YPC1 GO:0006672 SGD_REF:S000059207|PMID:10900202 IMP P alkaline ceramidase with reverse activity YBR183W gene taxon:4932 20021101 SGD
+SGD S000002394 YPD1 GO:0005737 SGD_REF:S000053117|PMID:8808622 TAS C two-component phosphorelay intermediate YDL235C gene taxon:4932 20020726 SGD
+SGD S000002394 YPD1 GO:0016772 SGD_REF:S000053117|PMID:8808622 IDA F two-component phosphorelay intermediate YDL235C gene taxon:4932 20020726 SGD
+SGD S000002394 YPD1 GO:0006970 SGD_REF:S000053117|PMID:8808622 TAS P two-component phosphorelay intermediate YDL235C gene taxon:4932 20020726 SGD
+SGD S000002394 YPD1 GO:0007234 SGD_REF:S000053117|PMID:8808622 IDA P two-component phosphorelay intermediate YDL235C gene taxon:4932 20020726 SGD
+SGD S000002394 YPD1 GO:0007234 SGD_REF:S000053117|PMID:8808622 IMP P two-component phosphorelay intermediate YDL235C gene taxon:4932 20020726 SGD
+SGD S000001899 YPI1 GO:0008372 SGD_REF:S000069584 ND C PP1 phosphatase inhibitor YFR003C gene taxon:4932 20020425 SGD
+SGD S000001899 YPI1 GO:0004864 SGD_REF:S000074628|PMID:14506263 IDA F PP1 phosphatase inhibitor YFR003C gene taxon:4932 20031212 SGD
+SGD S000001899 YPI1 GO:0005977 SGD_REF:S000074628|PMID:14506263 IMP P PP1 phosphatase inhibitor YFR003C gene taxon:4932 20031212 SGD
+SGD S000001899 YPI1 GO:0006470 SGD_REF:S000074628|PMID:14506263 IDA P PP1 phosphatase inhibitor YFR003C gene taxon:4932 20031212 SGD
+SGD S000001609 YPK1 GO:0005829 SGD_REF:S000046994|PMID:10825204 IDA C 76.5 kDa serine/threonine protein kinase, similarity to protein kinase C, is 90% identical to Ypk2p YKL126W|SLI2 gene taxon:4932 20021007 SGD
+SGD S000001609 YPK1 GO:0005886 SGD_REF:S000046994|PMID:10825204 IDA C 76.5 kDa serine/threonine protein kinase, similarity to protein kinase C, is 90% identical to Ypk2p YKL126W|SLI2 gene taxon:4932 20021007 SGD
+SGD S000001609 YPK1 GO:0005935 SGD_REF:S000046994|PMID:10825204 IDA C 76.5 kDa serine/threonine protein kinase, similarity to protein kinase C, is 90% identical to Ypk2p YKL126W|SLI2 gene taxon:4932 20021007 SGD
+SGD S000001609 YPK1 GO:0004674 SGD_REF:S000046994|PMID:10825204 ISS F 76.5 kDa serine/threonine protein kinase, similarity to protein kinase C, is 90% identical to Ypk2p YKL126W|SLI2 gene taxon:4932 20021007 SGD
+SGD S000001609 YPK1 GO:0004674 SGD_REF:S000046994|PMID:10825204 IMP F 76.5 kDa serine/threonine protein kinase, similarity to protein kinase C, is 90% identical to Ypk2p YKL126W|SLI2 gene taxon:4932 20021007 SGD
+SGD S000001609 YPK1 GO:0006468 SGD_REF:S000046994|PMID:10825204 ISS P 76.5 kDa serine/threonine protein kinase, similarity to protein kinase C, is 90% identical to Ypk2p YKL126W|SLI2 gene taxon:4932 20021007 SGD
+SGD S000001609 YPK1 GO:0006468 SGD_REF:S000046994|PMID:10825204 IMP P 76.5 kDa serine/threonine protein kinase, similarity to protein kinase C, is 90% identical to Ypk2p YKL126W|SLI2 gene taxon:4932 20021007 SGD
+SGD S000001609 YPK1 GO:0006665 SGD_REF:S000046994|PMID:10825204 IMP P 76.5 kDa serine/threonine protein kinase, similarity to protein kinase C, is 90% identical to Ypk2p YKL126W|SLI2 gene taxon:4932 20021007 SGD
+SGD S000001609 YPK1 GO:0006897 SGD_REF:S000069470|PMID:11807089 IMP P 76.5 kDa serine/threonine protein kinase, similarity to protein kinase C, is 90% identical to Ypk2p YKL126W|SLI2 gene taxon:4932 20021007 SGD
+SGD S000004710 YPK2 GO:0005634 SGD_REF:S000071423|PMID:12221112 IDA C protein kinase YMR104C|YKR2 gene taxon:4932 20021008 SGD
+SGD S000004710 YPK2 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C protein kinase YMR104C|YKR2 gene taxon:4932 20020507 SGD
+SGD S000004710 YPK2 GO:0004672 SGD_REF:S000053842|PMID:10074427 ISS F protein kinase YMR104C|YKR2 gene taxon:4932 20021008 SGD
+SGD S000004710 YPK2 GO:0006468 SGD_REF:S000053842|PMID:10074427 ISS P protein kinase YMR104C|YKR2 gene taxon:4932 20021008 SGD
+SGD S000002776 YPR1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YDR368W gene taxon:4932 20031028 SGD
+SGD S000002776 YPR1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDR368W gene taxon:4932 20031028 SGD
+SGD S000002776 YPR1 GO:0004032 SGD_REF:S000060122|PMID:11306085 IDA F YDR368W gene taxon:4932 20030912 SGD
+SGD S000002776 YPR1 GO:0004033 SGD_REF:S000060122|PMID:11306085 ISS F YDR368W gene taxon:4932 20030912 SGD
+SGD S000002776 YPR1 GO:0016491 SGD_REF:S000060971|PMID:11456752 IDA F YDR368W gene taxon:4932 20021009 SGD
+SGD S000002776 YPR1 GO:0019568 SGD_REF:S000071519|PMID:12271459 IDA P YDR368W gene taxon:4932 20050131 SGD
+SGD S000002776 YPR1 GO:0019568 SGD_REF:S000071519|PMID:12271459 IMP P YDR368W gene taxon:4932 20050131 SGD
+SGD S000002776 YPR1 GO:0042843 SGD_REF:S000071519|PMID:12271459 IDA P YDR368W gene taxon:4932 20050131 SGD
+SGD S000004110 YPS1 GO:0009277 SGD_REF:S000040179|PMID:10383953 IDA C GPI-anchored aspartic protease YLR120C|YAP3 gene taxon:4932 20020617 SGD
+SGD S000004110 YPS1 GO:0004190 SGD_REF:S000057719|PMID:8389368 IDA F GPI-anchored aspartic protease YLR120C|YAP3 gene taxon:4932 20020927 SGD
+SGD S000004110 YPS1 GO:0016485 SGD_REF:S000057846|PMID:8626758 IDA P GPI-anchored aspartic protease YLR120C|YAP3 gene taxon:4932 20020927 SGD
+SGD S000004111 YPS3 GO:0005886 SGD_REF:S000042463|PMID:10191273 ISS C GPI-anchored aspartic protease YLR121C|YPS4 gene taxon:4932 20010118 SGD
+SGD S000004111 YPS3 GO:0005886 SGD_REF:S000042463|PMID:10191273 IDA C GPI-anchored aspartic protease YLR121C|YPS4 gene taxon:4932 20010118 SGD
+SGD S000004111 YPS3 GO:0046658 SGD_REF:S000059176|PMID:11016834 IDA C GPI-anchored aspartic protease YLR121C|YPS4 gene taxon:4932 20060405 SGD
+SGD S000004111 YPS3 GO:0046658 SGD_REF:S000059176|PMID:11016834 IPI C GPI-anchored aspartic protease YLR121C|YPS4 gene taxon:4932 20060405 SGD
+SGD S000004111 YPS3 GO:0004190 SGD_REF:S000042463|PMID:10191273 ISS F GPI-anchored aspartic protease YLR121C|YPS4 gene taxon:4932 20010118 SGD
+SGD S000004111 YPS3 GO:0004190 SGD_REF:S000042463|PMID:10191273 IDA F GPI-anchored aspartic protease YLR121C|YPS4 gene taxon:4932 20010118 SGD
+SGD S000004111 YPS3 GO:0005199 SGD_REF:S000059176|PMID:11016834 IPI F GPI-anchored aspartic protease YLR121C|YPS4 gene taxon:4932 20060405 SGD
+SGD S000004111 YPS3 GO:0019538 SGD_REF:S000042463|PMID:10191273 IDA P GPI-anchored aspartic protease YLR121C|YPS4 gene taxon:4932 20010118 SGD
+SGD S000004111 YPS3 GO:0019538 SGD_REF:S000042463|PMID:10191273 ISS P GPI-anchored aspartic protease YLR121C|YPS4 gene taxon:4932 20010118 SGD
+SGD S000004111 YPS3 GO:0031505 SGD_REF:S000059176|PMID:11016834 IPI P GPI-anchored aspartic protease YLR121C|YPS4 gene taxon:4932 20060405 SGD
+SGD S000004111 YPS3 GO:0031505 SGD_REF:S000059176|PMID:11016834 IEP P GPI-anchored aspartic protease YLR121C|YPS4 gene taxon:4932 20060405 SGD
+SGD S000003228 YPS5 GO:0008372 SGD_REF:S000069584 ND C GPI-anchored aspartic protease YGL259W gene taxon:4932 20020927 SGD
+SGD S000003228 YPS5 GO:0004190 SGD_REF:S000042463|PMID:10191273 ISS F GPI-anchored aspartic protease YGL259W gene taxon:4932 20020927 SGD
+SGD S000003228 YPS5 GO:0000004 SGD_REF:S000069584 ND P GPI-anchored aspartic protease YGL259W gene taxon:4932 20020927 SGD
+SGD S000001478 YPS6 GO:0009277 SGD_REF:S000040179|PMID:10383953 IDA C GPI-anchored aspartic protease YIR039C gene taxon:4932 20020617 SGD
+SGD S000001478 YPS6 GO:0004190 SGD_REF:S000042463|PMID:10191273 ISS F GPI-anchored aspartic protease YIR039C gene taxon:4932 20020927 SGD
+SGD S000001478 YPS6 GO:0000004 SGD_REF:S000069584 ND P GPI-anchored aspartic protease YIR039C gene taxon:4932 20020927 SGD
+SGD S000002757 YPS7 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C GPI-anchored aspartic protease YDR349C gene taxon:4932 20031028 SGD
+SGD S000002757 YPS7 GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C GPI-anchored aspartic protease YDR349C gene taxon:4932 20031028 SGD
+SGD S000002757 YPS7 GO:0004190 SGD_REF:S000042463|PMID:10191273 ISS F GPI-anchored aspartic protease YDR349C gene taxon:4932 20020927 SGD
+SGD S000002757 YPS7 GO:0000004 SGD_REF:S000069584 ND P GPI-anchored aspartic protease YDR349C gene taxon:4932 20020927 SGD
+SGD S000001856 YPT1 GO:0000139 SGD_REF:S000050496|PMID:10747087 IDA C GTP-binding protein, ras homolog, similar to mammalian Rab1A protein YFL038C|YP2 gene taxon:4932 20010118 SGD
+SGD S000001856 YPT1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C GTP-binding protein, ras homolog, similar to mammalian Rab1A protein YFL038C|YP2 gene taxon:4932 20040928 SGD
+SGD S000001856 YPT1 GO:0005789 SGD_REF:S000050496|PMID:10747087 IDA C GTP-binding protein, ras homolog, similar to mammalian Rab1A protein YFL038C|YP2 gene taxon:4932 20010118 SGD
+SGD S000001856 YPT1 GO:0003924 SGD_REF:S000055253|PMID:9433126 TAS F GTP-binding protein, ras homolog, similar to mammalian Rab1A protein YFL038C|YP2 gene taxon:4932 20010118 SGD
+SGD S000001856 YPT1 GO:0006461 SGD_REF:S000052788|PMID:8603910 IDA P GTP-binding protein, ras homolog, similar to mammalian Rab1A protein YFL038C|YP2 gene taxon:4932 20020731 SGD
+SGD S000001856 YPT1 GO:0006888 SGD_REF:S000055253|PMID:9433126 TAS P GTP-binding protein, ras homolog, similar to mammalian Rab1A protein YFL038C|YP2 gene taxon:4932 20010118 SGD
+SGD S000000468 YPT10 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YBR264C gene taxon:4932 20031028 SGD
+SGD S000000468 YPT10 GO:0003924 SGD_REF:S000055253|PMID:9433126 ISS SGD:S000001856 F YBR264C gene taxon:4932 20050622 SGD
+SGD S000000468 YPT10 GO:0019001 SGD_REF:S000044599|PMID:10394895 IDA F YBR264C gene taxon:4932 20021009 SGD
+SGD S000000468 YPT10 GO:0007030 SGD_REF:S000044599|PMID:10394895 IGI P YBR264C gene taxon:4932 20021009 SGD
+SGD S000005248 YPT11 GO:0000131 SGD_REF:S000071794|PMID:12391144 IDA C YNL304W gene taxon:4932 20021212 SGD
+SGD S000005248 YPT11 GO:0005934 SGD_REF:S000071794|PMID:12391144 IDA C YNL304W gene taxon:4932 20021212 SGD
+SGD S000005248 YPT11 GO:0005935 SGD_REF:S000071794|PMID:12391144 IDA C YNL304W gene taxon:4932 20021212 SGD
+SGD S000005248 YPT11 GO:0003924 SGD_REF:S000071794|PMID:12391144 IPI F YNL304W gene taxon:4932 20021210 SGD
+SGD S000005248 YPT11 GO:0000001 SGD_REF:S000071794|PMID:12391144 IGI P YNL304W gene taxon:4932 20021212 SGD
+SGD S000000833 YPT31 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C GTPase, YPT32 homolog, ras homolog YER031C|YPT8 gene taxon:4932 20060317 SGD
+SGD S000000833 YPT31 GO:0005768 SGD_REF:S000082256|PMID:15537705 IDA C GTPase, YPT32 homolog, ras homolog YER031C|YPT8 gene taxon:4932 20050711 SGD
+SGD S000000833 YPT31 GO:0005794 SGD_REF:S000072743|PMID:12221137 TAS C GTPase, YPT32 homolog, ras homolog YER031C|YPT8 gene taxon:4932 20030428 SGD
+SGD S000000833 YPT31 GO:0005794 SGD_REF:S000082256|PMID:15537705 IDA C GTPase, YPT32 homolog, ras homolog YER031C|YPT8 gene taxon:4932 20050711 SGD
+SGD S000000833 YPT31 GO:0003924 SGD_REF:S000044888|PMID:9151665 ISS F GTPase, YPT32 homolog, ras homolog YER031C|YPT8 gene taxon:4932 20020624 SGD
+SGD S000000833 YPT31 GO:0003924 SGD_REF:S000047577|PMID:10071213 IPI F GTPase, YPT32 homolog, ras homolog YER031C|YPT8 gene taxon:4932 20020624 SGD
+SGD S000000833 YPT31 GO:0006887 SGD_REF:S000044888|PMID:9151665 IMP P GTPase, YPT32 homolog, ras homolog YER031C|YPT8 gene taxon:4932 20020624 SGD
+SGD S000000833 YPT31 GO:0016192 SGD_REF:S000044888|PMID:9151665 IGI P GTPase, YPT32 homolog, ras homolog YER031C|YPT8 gene taxon:4932 20020624 SGD
+SGD S000000833 YPT31 GO:0016192 SGD_REF:S000044888|PMID:9151665 IMP P GTPase, YPT32 homolog, ras homolog YER031C|YPT8 gene taxon:4932 20020624 SGD
+SGD S000003178 YPT32 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C GTPase, YPT31 homolog, ras homolog YGL210W gene taxon:4932 20060317 SGD
+SGD S000003178 YPT32 GO:0005768 SGD_REF:S000082256|PMID:15537705 IDA C GTPase, YPT31 homolog, ras homolog YGL210W gene taxon:4932 20050711 SGD
+SGD S000003178 YPT32 GO:0005794 SGD_REF:S000072743|PMID:12221137 TAS C GTPase, YPT31 homolog, ras homolog YGL210W gene taxon:4932 20030428 SGD
+SGD S000003178 YPT32 GO:0005794 SGD_REF:S000082256|PMID:15537705 IDA C GTPase, YPT31 homolog, ras homolog YGL210W gene taxon:4932 20050711 SGD
+SGD S000003178 YPT32 GO:0003924 SGD_REF:S000044888|PMID:9151665 ISS F GTPase, YPT31 homolog, ras homolog YGL210W gene taxon:4932 20020624 SGD
+SGD S000003178 YPT32 GO:0003924 SGD_REF:S000047577|PMID:10071213 IPI F GTPase, YPT31 homolog, ras homolog YGL210W gene taxon:4932 20020624 SGD
+SGD S000003178 YPT32 GO:0006887 SGD_REF:S000044888|PMID:9151665 IMP P GTPase, YPT31 homolog, ras homolog YGL210W gene taxon:4932 20020624 SGD
+SGD S000003178 YPT32 GO:0016192 SGD_REF:S000044888|PMID:9151665 IGI P GTPase, YPT31 homolog, ras homolog YGL210W gene taxon:4932 20020624 SGD
+SGD S000003178 YPT32 GO:0016192 SGD_REF:S000044888|PMID:9151665 IMP P GTPase, YPT31 homolog, ras homolog YGL210W gene taxon:4932 20020624 SGD
+SGD S000001147 YPT35 GO:0005768 SGD_REF:S000074185|PMID:14562095 IDA C YHR105W gene taxon:4932 20031028 SGD
+SGD S000001147 YPT35 GO:0005554 SGD_REF:S000069584 ND F YHR105W gene taxon:4932 20030114 SGD
+SGD S000001147 YPT35 GO:0000004 SGD_REF:S000069584 ND P YHR105W gene taxon:4932 20030114 SGD
+SGD S000001722 YPT52 GO:0005770 SGD_REF:S000069952|PMID:11872141 IMP C YKR014C gene taxon:4932 20021003 SGD
+SGD S000001722 YPT52 GO:0003924 SGD_REF:S000042833|PMID:8163546 IMP F YKR014C gene taxon:4932 20021113 SGD
+SGD S000001722 YPT52 GO:0003924 SGD_REF:S000042833|PMID:8163546 ISS F YKR014C gene taxon:4932 20021113 SGD
+SGD S000001722 YPT52 GO:0006623 SGD_REF:S000042833|PMID:8163546 IMP P YKR014C gene taxon:4932 20021113 SGD
+SGD S000001722 YPT52 GO:0006897 SGD_REF:S000042833|PMID:8163546 IMP P YKR014C gene taxon:4932 20021113 SGD
+SGD S000005037 YPT53 GO:0005770 SGD_REF:S000069952|PMID:11872141 IMP C GTP-binding protein, rab family YNL093W gene taxon:4932 20021003 SGD
+SGD S000005037 YPT53 GO:0003924 SGD_REF:S000042833|PMID:8163546 IMP F GTP-binding protein, rab family YNL093W gene taxon:4932 20021113 SGD
+SGD S000005037 YPT53 GO:0003924 SGD_REF:S000042833|PMID:8163546 ISS F GTP-binding protein, rab family YNL093W gene taxon:4932 20021113 SGD
+SGD S000005037 YPT53 GO:0006623 SGD_REF:S000042833|PMID:8163546 IMP P GTP-binding protein, rab family YNL093W gene taxon:4932 20021113 SGD
+SGD S000005037 YPT53 GO:0006897 SGD_REF:S000042833|PMID:8163546 IMP P GTP-binding protein, rab family YNL093W gene taxon:4932 20021113 SGD
+SGD S000004252 YPT6 GO:0005794 SGD_REF:S000068970|PMID:11689439 TAS C similar to the human GTPase, Rab6 YLR262C gene taxon:4932 20020707 SGD
+SGD S000004252 YPT6 GO:0003924 SGD_REF:S000055253|PMID:9433126 ISS F similar to the human GTPase, Rab6 YLR262C gene taxon:4932 20021001 SGD
+SGD S000004252 YPT6 GO:0003924 SGD_REF:S000055253|PMID:9433126 TAS F similar to the human GTPase, Rab6 YLR262C gene taxon:4932 20021001 SGD
+SGD S000004252 YPT6 GO:0006886 SGD_REF:S000071749|PMID:10990452 IGI P similar to the human GTPase, Rab6 YLR262C gene taxon:4932 20021203 SGD
+SGD S000004252 YPT6 GO:0006886 SGD_REF:S000071749|PMID:10990452 TAS P similar to the human GTPase, Rab6 YLR262C gene taxon:4932 20021203 SGD
+SGD S000004252 YPT6 GO:0042147 SGD_REF:S000059520|PMID:11160819 IMP P similar to the human GTPase, Rab6 YLR262C gene taxon:4932 20021001 SGD
+SGD S000004252 YPT6 GO:0042147 SGD_REF:S000059520|PMID:11160819 TAS P similar to the human GTPase, Rab6 YLR262C gene taxon:4932 20021001 SGD
+SGD S000004460 YPT7 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C GTP-binding protein, rab family YML001W|AST4|VAM4 gene taxon:4932 20060317 SGD
+SGD S000004460 YPT7 GO:0005773 SGD_REF:S000066015|PMID:11590240 IDA C GTP-binding protein, rab family YML001W|AST4|VAM4 gene taxon:4932 20020817 SGD
+SGD S000004460 YPT7 GO:0003924 SGD_REF:S000058365|PMID:9714809 TAS F GTP-binding protein, rab family YML001W|AST4|VAM4 gene taxon:4932 20010118 SGD
+SGD S000004460 YPT7 GO:0000011 SGD_REF:S000051599|PMID:7489715 IDA P GTP-binding protein, rab family YML001W|AST4|VAM4 gene taxon:4932 20010118 SGD
+SGD S000004460 YPT7 GO:0006896 SGD_REF:S000058365|PMID:9714809 TAS P GTP-binding protein, rab family YML001W|AST4|VAM4 gene taxon:4932 20010118 SGD
+SGD S000004460 YPT7 GO:0016192 SGD_REF:S000048403|PMID:9015302 IDA P GTP-binding protein, rab family YML001W|AST4|VAM4 gene taxon:4932 20010118 SGD
+SGD S000004460 YPT7 GO:0042144 SGD_REF:S000051599|PMID:7489715 IMP P GTP-binding protein, rab family YML001W|AST4|VAM4 gene taxon:4932 20050914 SGD
+SGD S000002789 YRA1 GO:0000346 SGD_REF:S000069956|PMID:11979277 IPI C RNA-binding RNA annealing protein YDR381W|SHE11 gene taxon:4932 20030221 SGD
+SGD S000002789 YRA1 GO:0003723 SGD_REF:S000061447|PMID:11390651 IDA F RNA-binding RNA annealing protein YDR381W|SHE11 gene taxon:4932 20021030 SGD
+SGD S000002789 YRA1 GO:0006406 SGD_REF:S000069956|PMID:11979277 IGI P RNA-binding RNA annealing protein YDR381W|SHE11 gene taxon:4932 20030214 SGD
+SGD S000001697 YRA2 GO:0005634 SGD_REF:S000061447|PMID:11390651 IDA C YKL214C gene taxon:4932 20021030 SGD
+SGD S000001697 YRA2 GO:0003723 SGD_REF:S000061447|PMID:11390651 IDA F YKL214C gene taxon:4932 20021030 SGD
+SGD S000001697 YRA2 GO:0016973 SGD_REF:S000061447|PMID:11390651 IGI P YKL214C gene taxon:4932 20021030 SGD
+SGD S000002409 YRB1 GO:0005634 SGD_REF:S000046566|PMID:10825193 IDA C YDR002W|CST20|HTN1|SFO1 gene taxon:4932 20020829 SGD
+SGD S000002409 YRB1 GO:0005737 SGD_REF:S000046566|PMID:10825193 IDA C YDR002W|CST20|HTN1|SFO1 gene taxon:4932 20020829 SGD
+SGD S000002409 YRB1 GO:0008536 SGD_REF:S000050246|PMID:7836422 IDA F YDR002W|CST20|HTN1|SFO1 gene taxon:4932 20020829 SGD
+SGD S000002409 YRB1 GO:0000082 SGD_REF:S000059718|PMID:10991951 IMP P YDR002W|CST20|HTN1|SFO1 gene taxon:4932 20020829 SGD
+SGD S000002409 YRB1 GO:0006405 SGD_REF:S000051618|PMID:7489726 IMP P YDR002W|CST20|HTN1|SFO1 gene taxon:4932 20020829 SGD
+SGD S000002409 YRB1 GO:0006511 SGD_REF:S000059718|PMID:10991951 IMP P YDR002W|CST20|HTN1|SFO1 gene taxon:4932 20020829 SGD
+SGD S000002409 YRB1 GO:0006606 SGD_REF:S000051618|PMID:7489726 IMP P YDR002W|CST20|HTN1|SFO1 gene taxon:4932 20020829 SGD
+SGD S000001325 YRB2 GO:0005634 SGD_REF:S000040644|PMID:9395535 IDA C nuclear protein that interacts with Gsp1p and Crm1p YIL063C gene taxon:4932 20050928 SGD
+SGD S000001325 YRB2 GO:0005634 SGD_REF:S000058090|PMID:9121474 IDA C nuclear protein that interacts with Gsp1p and Crm1p YIL063C gene taxon:4932 20050928 SGD
+SGD S000001325 YRB2 GO:0005643 SGD_REF:S000056415|PMID:10684247 IDA C nuclear protein that interacts with Gsp1p and Crm1p YIL063C gene taxon:4932 20050928 SGD
+SGD S000001325 YRB2 GO:0005554 SGD_REF:S000069584 ND F nuclear protein that interacts with Gsp1p and Crm1p YIL063C gene taxon:4932 20050928 SGD
+SGD S000001325 YRB2 GO:0006611 SGD_REF:S000054077|PMID:9636166 IMP P nuclear protein that interacts with Gsp1p and Crm1p YIL063C gene taxon:4932 20010118 SGD
+SGD S000003132 YRB30 GO:0005634 SGD_REF:S000073057|PMID:12578832 IMP C YGL164C gene taxon:4932 20030506 SGD
+SGD S000003132 YRB30 GO:0005634 SGD_REF:S000073057|PMID:12578832 ISS C YGL164C gene taxon:4932 20030506 SGD
+SGD S000003132 YRB30 GO:0005737 SGD_REF:S000073057|PMID:12578832 IDA C YGL164C gene taxon:4932 20030506 SGD
+SGD S000003132 YRB30 GO:0005515 SGD_REF:S000073057|PMID:12578832 IDA F YGL164C gene taxon:4932 20030506 SGD
+SGD S000003132 YRB30 GO:0030695 SGD_REF:S000073057|PMID:12578832 IPI SGD:S000004284 F YGL164C gene taxon:4932 20051205 SGD
+SGD S000003132 YRB30 GO:0030695 SGD_REF:S000073057|PMID:12578832 IDA F YGL164C gene taxon:4932 20051205 SGD
+SGD S000003132 YRB30 GO:0000004 SGD_REF:S000069584 ND P YGL164C gene taxon:4932 20021126 SGD
+SGD S000002953 YRF1-1 GO:0005634 SGD_REF:S000073348 IC GO:0000722 C Y'-helicase protein 1 YDR545W|YRF1 gene taxon:4932 20040324 SGD
+SGD S000002953 YRF1-1 GO:0003678 SGD_REF:S000053946|PMID:9837911 IDA F Y'-helicase protein 1 YDR545W|YRF1 gene taxon:4932 20031203 SGD
+SGD S000002953 YRF1-1 GO:0000722 SGD_REF:S000053946|PMID:9837911 IGI P Y'-helicase protein 1 YDR545W|YRF1 gene taxon:4932 20031203 SGD
+SGD S000000992 YRF1-2 GO:0005634 SGD_REF:S000073348 IC GO:0000722 C Y'-helicase protein 1 YER190W|YRF1 gene taxon:4932 20040324 SGD
+SGD S000000992 YRF1-2 GO:0003678 SGD_REF:S000053946|PMID:9837911 IDA F Y'-helicase protein 1 YER190W|YRF1 gene taxon:4932 20031203 SGD
+SGD S000000992 YRF1-2 GO:0000722 SGD_REF:S000053946|PMID:9837911 IGI P Y'-helicase protein 1 YER190W|YRF1 gene taxon:4932 20031203 SGD
+SGD S000003528 YRF1-3 GO:0005634 SGD_REF:S000073348 IC GO:0000722 C Y'-helicase protein 1 YGR296W|YRF1 gene taxon:4932 20040324 SGD
+SGD S000003528 YRF1-3 GO:0003678 SGD_REF:S000053946|PMID:9837911 IDA F Y'-helicase protein 1 YGR296W|YRF1 gene taxon:4932 20031203 SGD
+SGD S000003528 YRF1-3 GO:0000722 SGD_REF:S000053946|PMID:9837911 IGI P Y'-helicase protein 1 YGR296W|YRF1 gene taxon:4932 20031203 SGD
+SGD S000004458 YRF1-4 GO:0005634 SGD_REF:S000073348 IC GO:0000722 C Y'-helicase protein 1 YLR466W|YRF1 gene taxon:4932 20040324 SGD
+SGD S000004458 YRF1-4 GO:0003678 SGD_REF:S000053946|PMID:9837911 IDA F Y'-helicase protein 1 YLR466W|YRF1 gene taxon:4932 20031203 SGD
+SGD S000004458 YRF1-4 GO:0000722 SGD_REF:S000053946|PMID:9837911 IGI P Y'-helicase protein 1 YLR466W|YRF1 gene taxon:4932 20031203 SGD
+SGD S000004459 YRF1-5 GO:0005634 SGD_REF:S000073348 IC GO:0000722 C Y'-helicase protein 1 YLR467W|YRF1 gene taxon:4932 20040324 SGD
+SGD S000004459 YRF1-5 GO:0003678 SGD_REF:S000053946|PMID:9837911 IDA F Y'-helicase protein 1 YLR467W|YRF1 gene taxon:4932 20031203 SGD
+SGD S000004459 YRF1-5 GO:0000722 SGD_REF:S000053946|PMID:9837911 IGI P Y'-helicase protein 1 YLR467W|YRF1 gene taxon:4932 20031203 SGD
+SGD S000005283 YRF1-6 GO:0005634 SGD_REF:S000073348 IC GO:0000722 C Y'-helicase protein 1 YNL339C|YRF1 gene taxon:4932 20040324 SGD
+SGD S000005283 YRF1-6 GO:0003678 SGD_REF:S000053946|PMID:9837911 IDA F Y'-helicase protein 1 YNL339C|YRF1 gene taxon:4932 20031203 SGD
+SGD S000005283 YRF1-6 GO:0000722 SGD_REF:S000053946|PMID:9837911 IGI P Y'-helicase protein 1 YNL339C|YRF1 gene taxon:4932 20031203 SGD
+SGD S000006204 YRF1-7 GO:0005634 SGD_REF:S000073348 IC GO:0000722 C Y'-helicase protein 1 YPL283C|YRF1 gene taxon:4932 20040324 SGD
+SGD S000006204 YRF1-7 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C Y'-helicase protein 1 YPL283C|YRF1 gene taxon:4932 20040928 SGD
+SGD S000006204 YRF1-7 GO:0003678 SGD_REF:S000053946|PMID:9837911 IDA F Y'-helicase protein 1 YPL283C|YRF1 gene taxon:4932 20031203 SGD
+SGD S000006204 YRF1-7 GO:0000722 SGD_REF:S000053946|PMID:9837911 IGI P Y'-helicase protein 1 YPL283C|YRF1 gene taxon:4932 20031203 SGD
+SGD S000005698 YRM1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C zinc finger transcription factor YOR172W gene taxon:4932 20031028 SGD
+SGD S000005698 YRM1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C zinc finger transcription factor YOR172W gene taxon:4932 20031028 SGD
+SGD S000005698 YRM1 GO:0003704 SGD_REF:S000074423|PMID:14512416 IDA F zinc finger transcription factor YOR172W gene taxon:4932 20040225 SGD
+SGD S000005698 YRM1 GO:0006855 SGD_REF:S000074423|PMID:14512416 IMP P zinc finger transcription factor YOR172W gene taxon:4932 20040225 SGD
+SGD S000005698 YRM1 GO:0045944 SGD_REF:S000074423|PMID:14512416 IDA P zinc finger transcription factor YOR172W gene taxon:4932 20040225 SGD
+SGD S000000258 YRO2 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YBR054W gene taxon:4932 20040928 SGD
+SGD S000000258 YRO2 GO:0005933 SGD_REF:S000074185|PMID:14562095 IDA C YBR054W gene taxon:4932 20031028 SGD
+SGD S000000258 YRO2 GO:0005554 SGD_REF:S000069584 ND F YBR054W gene taxon:4932 20021014 SGD
+SGD S000000258 YRO2 GO:0000004 SGD_REF:S000069584 ND P YBR054W gene taxon:4932 20021014 SGD
+SGD S000005688 YRR1 GO:0005634 SGD_REF:S000069687|PMID:11909958 IPI C transcription factor YOR162C|PDR2 gene taxon:4932 20021003 SGD
+SGD S000005688 YRR1 GO:0003704 SGD_REF:S000069687|PMID:11909958 IMP F transcription factor YOR162C|PDR2 gene taxon:4932 20021003 SGD
+SGD S000005688 YRR1 GO:0003704 SGD_REF:S000069687|PMID:11909958 IPI F transcription factor YOR162C|PDR2 gene taxon:4932 20021003 SGD
+SGD S000005688 YRR1 GO:0006855 SGD_REF:S000069687|PMID:11909958 IMP P transcription factor YOR162C|PDR2 gene taxon:4932 20021003 SGD
+SGD S000005688 YRR1 GO:0006855 SGD_REF:S000069687|PMID:11909958 IPI P transcription factor YOR162C|PDR2 gene taxon:4932 20021003 SGD
+SGD S000005688 YRR1 GO:0045944 SGD_REF:S000056136|PMID:9767597 IMP P transcription factor YOR162C|PDR2 gene taxon:4932 20021003 SGD
+SGD S000000315 YSA1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YBR111C|RMA2 gene taxon:4932 20031028 SGD
+SGD S000000315 YSA1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YBR111C|RMA2 gene taxon:4932 20031028 SGD
+SGD S000000315 YSA1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YBR111C|RMA2 gene taxon:4932 20040928 SGD
+SGD S000000315 YSA1 GO:0004636 SGD_REF:S000049587|PMID:10542272 IDA F YBR111C|RMA2 gene taxon:4932 20021010 SGD
+SGD S000000315 YSA1 GO:0000004 SGD_REF:S000069584 ND P YBR111C|RMA2 gene taxon:4932 20021010 SGD
+SGD S000001059 YSC83 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YHR017W gene taxon:4932 20040813 SGD
+SGD S000001059 YSC83 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C YHR017W gene taxon:4932 20060317 SGD
+SGD S000001059 YSC83 GO:0005554 SGD_REF:S000069584 ND F YHR017W gene taxon:4932 20021014 SGD
+SGD S000001059 YSC83 GO:0000004 SGD_REF:S000069584 ND P YHR017W gene taxon:4932 20021014 SGD
+SGD S000001058 YSC84 GO:0030479 SGD_REF:S000071530|PMID:12388763 IDA C YHR016C|LSB4 gene taxon:4932 20021114 SGD
+SGD S000001058 YSC84 GO:0005554 SGD_REF:S000069584 ND F YHR016C|LSB4 gene taxon:4932 20021010 SGD
+SGD S000001058 YSC84 GO:0006897 SGD_REF:S000071530|PMID:12388763 IMP P YHR016C|LSB4 gene taxon:4932 20021114 SGD
+SGD S000001058 YSC84 GO:0007015 SGD_REF:S000043043|PMID:10512884 IPI P YHR016C|LSB4 gene taxon:4932 20021010 SGD
+SGD S000028509 YSF3 colocalizes_with GO:0005686 SGD_REF:S000080993|PMID:15565172 IDA C U2 snRNP subunit, SF3b associated YNL138W-A|RCP10 gene taxon:4932 20051006 SGD
+SGD S000028509 YSF3 GO:0008372 SGD_REF:S000069584 ND C U2 snRNP subunit, SF3b associated YNL138W-A|RCP10 gene taxon:4932 20030730 SGD
+SGD S000028509 YSF3 GO:0005554 SGD_REF:S000069584 ND F U2 snRNP subunit, SF3b associated YNL138W-A|RCP10 gene taxon:4932 20030730 SGD
+SGD S000028509 YSF3 GO:0000004 SGD_REF:S000069584 ND P U2 snRNP subunit, SF3b associated YNL138W-A|RCP10 gene taxon:4932 20030730 SGD
+SGD S000004267 YSH1 GO:0005847 SGD_REF:S000046866|PMID:10523662 IPI C cleavage factor II (CF II) component, polyadenylation factor I (PF I) YLR277C|BRR5 gene taxon:4932 20040928 SGD
+SGD S000004267 YSH1 GO:0005847 SGD_REF:S000049364|PMID:9099738 IPI C cleavage factor II (CF II) component, polyadenylation factor I (PF I) YLR277C|BRR5 gene taxon:4932 20040928 SGD
+SGD S000004267 YSH1 GO:0005849 SGD_REF:S000049364|PMID:9099738 IPI C cleavage factor II (CF II) component, polyadenylation factor I (PF I) YLR277C|BRR5 gene taxon:4932 20020410 SGD
+SGD S000004267 YSH1 contributes_to GO:0003723 SGD_REF:S000049364|PMID:9099738 IC GO:0005847 F cleavage factor II (CF II) component, polyadenylation factor I (PF I) YLR277C|BRR5 gene taxon:4932 20050218 SGD
+SGD S000004267 YSH1 GO:0004521 SGD_REF:S000076088|PMID:15037765 IMP F cleavage factor II (CF II) component, polyadenylation factor I (PF I) YLR277C|BRR5 gene taxon:4932 20050629 SGD
+SGD S000004267 YSH1 GO:0004521 SGD_REF:S000076088|PMID:15037765 ISS F cleavage factor II (CF II) component, polyadenylation factor I (PF I) YLR277C|BRR5 gene taxon:4932 20050629 SGD
+SGD S000004267 YSH1 GO:0006378 SGD_REF:S000060315|PMID:11344258 IDA P cleavage factor II (CF II) component, polyadenylation factor I (PF I) YLR277C|BRR5 gene taxon:4932 20020410 SGD
+SGD S000004267 YSH1 GO:0006378 SGD_REF:S000060315|PMID:11344258 TAS P cleavage factor II (CF II) component, polyadenylation factor I (PF I) YLR277C|BRR5 gene taxon:4932 20020410 SGD
+SGD S000004267 YSH1 GO:0006379 SGD_REF:S000060315|PMID:11344258 IDA P cleavage factor II (CF II) component, polyadenylation factor I (PF I) YLR277C|BRR5 gene taxon:4932 20020410 SGD
+SGD S000004267 YSH1 GO:0006379 SGD_REF:S000060315|PMID:11344258 TAS P cleavage factor II (CF II) component, polyadenylation factor I (PF I) YLR277C|BRR5 gene taxon:4932 20020410 SGD
+SGD S000005348 YSN1 GO:0008372 SGD_REF:S000069584 ND C YNR065C gene taxon:4932 20021029 SGD
+SGD S000005348 YSN1 GO:0005554 SGD_REF:S000069584 ND F YNR065C gene taxon:4932 20021029 SGD
+SGD S000005348 YSN1 GO:0000004 SGD_REF:S000069584 ND P YNR065C gene taxon:4932 20021029 SGD
+SGD S000001198 YSP1 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YHR155W gene taxon:4932 20031028 SGD
+SGD S000001198 YSP1 GO:0005739 SGD_REF:S000080563|PMID:15657396 IDA C YHR155W gene taxon:4932 20050816 SGD
+SGD S000001198 YSP1 GO:0005554 SGD_REF:S000069584 ND F YHR155W gene taxon:4932 20021126 SGD
+SGD S000001198 YSP1 GO:0000004 SGD_REF:S000069584 ND P YHR155W gene taxon:4932 20021126 SGD
+SGD S000005529 YSP3 GO:0008372 SGD_REF:S000069584 ND C subtilisin-like protease III YOR003W gene taxon:4932 20020830 SGD
+SGD S000005529 YSP3 GO:0008233 SGD_REF:S000066038|PMID:8896276 ISS F subtilisin-like protease III YOR003W gene taxon:4932 20020830 SGD
+SGD S000005529 YSP3 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P subtilisin-like protease III YOR003W gene taxon:4932 20060210 SGD
+SGD S000005529 YSP3 GO:0030163 SGD_REF:S000066038|PMID:8896276 ISS P subtilisin-like protease III YOR003W gene taxon:4932 20020830 SGD
+SGD S000001761 YSR3 GO:0005783 SGD_REF:S000045004|PMID:10531356 IDA C DHS-1-P phosphatase YKR053C|LBP2 gene taxon:4932 20020821 SGD
+SGD S000001761 YSR3 GO:0005783 SGD_REF:S000044959|PMID:10477278 IDA C DHS-1-P phosphatase YKR053C|LBP2 gene taxon:4932 20020925 SGD
+SGD S000001761 YSR3 GO:0042392 SGD_REF:S000041358|PMID:10856228 IDA F DHS-1-P phosphatase YKR053C|LBP2 gene taxon:4932 20020925 SGD
+SGD S000001761 YSR3 GO:0030148 SGD_REF:S000041039|PMID:10563329 TAS P DHS-1-P phosphatase YKR053C|LBP2 gene taxon:4932 20020821 SGD
+SGD S000000352 YSW1 GO:0008372 SGD_REF:S000069584 ND C YBR148W gene taxon:4932 20021120 SGD
+SGD S000000352 YSW1 GO:0005554 SGD_REF:S000069584 ND F YBR148W gene taxon:4932 20021120 SGD
+SGD S000000352 YSW1 GO:0000004 SGD_REF:S000069584 ND P YBR148W gene taxon:4932 20021120 SGD
+SGD S000002158 YSY6 GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YBR162W-A gene taxon:4932 20031028 SGD
+SGD S000002158 YSY6 GO:0005554 SGD_REF:S000069584 ND F YBR162W-A gene taxon:4932 20020927 SGD
+SGD S000002158 YSY6 GO:0009306 SGD_REF:S000065792|PMID:10469658 ISS P YBR162W-A gene taxon:4932 20020927 SGD
+SGD S000004695 YTA12 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C ATPase, CDC48/PAS1/SEC18 (AAA) family YMR089C|RCA1 gene taxon:4932 20020507 SGD
+SGD S000004695 YTA12 GO:0005739 SGD_REF:S000069459|PMID:11914276 IDA C ATPase, CDC48/PAS1/SEC18 (AAA) family YMR089C|RCA1 gene taxon:4932 20020507 SGD
+SGD S000004695 YTA12 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C ATPase, CDC48/PAS1/SEC18 (AAA) family YMR089C|RCA1 gene taxon:4932 20040924 SGD
+SGD S000004695 YTA12 GO:0005743 SGD_REF:S000039413|PMID:7929327 IDA C ATPase, CDC48/PAS1/SEC18 (AAA) family YMR089C|RCA1 gene taxon:4932 20010118 SGD
+SGD S000004695 YTA12 GO:0005745 SGD_REF:S000055187|PMID:8681382 IDA C ATPase, CDC48/PAS1/SEC18 (AAA) family YMR089C|RCA1 gene taxon:4932 20030430 SGD
+SGD S000004695 YTA12 GO:0008237 SGD_REF:S000055187|PMID:8681382 IMP F ATPase, CDC48/PAS1/SEC18 (AAA) family YMR089C|RCA1 gene taxon:4932 20010118 SGD
+SGD S000004695 YTA12 GO:0016887 SGD_REF:S000039413|PMID:7929327 ISS F ATPase, CDC48/PAS1/SEC18 (AAA) family YMR089C|RCA1 gene taxon:4932 20010118 SGD
+SGD S000004695 YTA12 GO:0006461 SGD_REF:S000055187|PMID:8681382 IMP P ATPase, CDC48/PAS1/SEC18 (AAA) family YMR089C|RCA1 gene taxon:4932 20010118 SGD
+SGD S000004695 YTA12 GO:0006465 SGD_REF:S000071826|PMID:12417197 IMP P ATPase, CDC48/PAS1/SEC18 (AAA) family YMR089C|RCA1 gene taxon:4932 20050503 SGD
+SGD S000004695 YTA12 GO:0006508 SGD_REF:S000055187|PMID:8681382 IMP P ATPase, CDC48/PAS1/SEC18 (AAA) family YMR089C|RCA1 gene taxon:4932 20010118 SGD
+SGD S000004695 YTA12 GO:0045041 SGD_REF:S000071826|PMID:12417197 TAS P ATPase, CDC48/PAS1/SEC18 (AAA) family YMR089C|RCA1 gene taxon:4932 20021212 SGD
+SGD S000005995 YTA6 GO:0005938 SGD_REF:S000068954|PMID:11553699 IDA C AAA ATPase YPL074W gene taxon:4932 20021018 SGD
+SGD S000005995 YTA6 GO:0016887 SGD_REF:S000057468|PMID:7754704 ISS F AAA ATPase YPL074W gene taxon:4932 20021018 SGD
+SGD S000005995 YTA6 GO:0000004 SGD_REF:S000069584 ND P AAA ATPase YPL074W gene taxon:4932 20021018 SGD
+SGD S000003502 YTA7 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YGR270W gene taxon:4932 20031028 SGD
+SGD S000003502 YTA7 GO:0016887 SGD_REF:S000044551|PMID:9605509 ISS F YGR270W gene taxon:4932 20020829 SGD
+SGD S000003502 YTA7 GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P YGR270W gene taxon:4932 20060210 SGD
+SGD S000003502 YTA7 GO:0030163 SGD_REF:S000044551|PMID:9605509 ISS P YGR270W gene taxon:4932 20020829 SGD
+SGD S000006311 YTH1 GO:0005847 SGD_REF:S000060315|PMID:11344258 TAS C polyadenylation factor subunit YPR107C gene taxon:4932 20020410 SGD
+SGD S000006311 YTH1 GO:0005847 SGD_REF:S000074089|PMID:12819204 IPI C polyadenylation factor subunit YPR107C gene taxon:4932 20031013 SGD
+SGD S000006311 YTH1 GO:0003723 SGD_REF:S000045965|PMID:9224719 IDA F polyadenylation factor subunit YPR107C gene taxon:4932 20040506 SGD
+SGD S000006311 YTH1 GO:0006378 SGD_REF:S000060315|PMID:11344258 IDA P polyadenylation factor subunit YPR107C gene taxon:4932 20020410 SGD
+SGD S000006311 YTH1 GO:0006378 SGD_REF:S000060315|PMID:11344258 TAS P polyadenylation factor subunit YPR107C gene taxon:4932 20020410 SGD
+SGD S000006311 YTH1 GO:0006378 SGD_REF:S000041731|PMID:10899131 IMP P polyadenylation factor subunit YPR107C gene taxon:4932 20020410 SGD
+SGD S000006311 YTH1 GO:0006379 SGD_REF:S000060315|PMID:11344258 IDA P polyadenylation factor subunit YPR107C gene taxon:4932 20020410 SGD
+SGD S000006311 YTH1 GO:0006379 SGD_REF:S000060315|PMID:11344258 TAS P polyadenylation factor subunit YPR107C gene taxon:4932 20020410 SGD
+SGD S000006311 YTH1 GO:0006379 SGD_REF:S000041731|PMID:10899131 IMP P polyadenylation factor subunit YPR107C gene taxon:4932 20020410 SGD
+SGD S000005798 YTM1 GO:0005634 SGD_REF:S000069459|PMID:11914276 IDA C microtubule-associated protein YOR272W gene taxon:4932 20020507 SGD
+SGD S000005798 YTM1 GO:0005730 SGD_REF:S000066002|PMID:11583614 IDA C microtubule-associated protein YOR272W gene taxon:4932 20020927 SGD
+SGD S000005798 YTM1 GO:0005554 SGD_REF:S000069584 ND F microtubule-associated protein YOR272W gene taxon:4932 20021205 SGD
+SGD S000005798 YTM1 GO:0007001 SGD_REF:S000052609|PMID:10454593 IGI P microtubule-associated protein YOR272W gene taxon:4932 20021205 SGD
+SGD S000005798 YTM1 GO:0042273 SGD_REF:S000066002|PMID:11583614 IMP P microtubule-associated protein YOR272W gene taxon:4932 20020927 SGD
+SGD S000005798 YTM1 GO:0042273 SGD_REF:S000066002|PMID:11583614 IPI P microtubule-associated protein YOR272W gene taxon:4932 20020927 SGD
+SGD S000005798 YTM1 GO:0042273 SGD_REF:S000076470|PMID:15100437 IPI P microtubule-associated protein YOR272W gene taxon:4932 20050407 SGD
+SGD S000005181 YTP1 GO:0016020 SGD_REF:S000047556|PMID:8635735 ISS C YNL237W gene taxon:4932 20021011 SGD
+SGD S000005181 YTP1 GO:0005554 SGD_REF:S000069584 ND F YNL237W gene taxon:4932 20021011 SGD
+SGD S000005181 YTP1 GO:0000004 SGD_REF:S000069584 ND P YNL237W gene taxon:4932 20021011 SGD
+SGD S000003860 YUH1 GO:0005737 SGD_REF:S000051210|PMID:1429680 IC GO:0004843 C ubiquitin hydrolase YJR099W gene taxon:4932 20021209 SGD
+SGD S000003860 YUH1 GO:0004843 SGD_REF:S000051210|PMID:1429680 TAS F ubiquitin hydrolase YJR099W gene taxon:4932 20010118 SGD
+SGD S000003860 YUH1 GO:0016579 SGD_REF:S000058010|PMID:8982460 TAS P ubiquitin hydrolase YJR099W gene taxon:4932 20010118 SGD
+SGD S000003675 YUR1 GO:0005794 SGD_REF:S000041908|PMID:8631921 IDA C mannosyltransferase YJL139C gene taxon:4932 20010118 SGD
+SGD S000003675 YUR1 GO:0000030 SGD_REF:S000041908|PMID:8631921 IDA F mannosyltransferase YJL139C gene taxon:4932 20010118 SGD
+SGD S000003675 YUR1 GO:0000032 SGD_REF:S000041908|PMID:8631921 IMP P mannosyltransferase YJL139C gene taxon:4932 20010118 SGD
+SGD S000003675 YUR1 GO:0006487 SGD_REF:S000041908|PMID:8631921 IMP P mannosyltransferase YJL139C gene taxon:4932 20010118 SGD
+SGD S000005613 YVC1 GO:0000324 SGD_REF:S000069157|PMID:11781332 IDA C YOR087W|YOR088W gene taxon:4932 20020307 SGD
+SGD S000005613 YVC1 GO:0000324 SGD_REF:S000069248|PMID:11427713 IDA C YOR087W|YOR088W gene taxon:4932 20020307 SGD
+SGD S000005613 YVC1 GO:0005227 SGD_REF:S000069249|PMID:1700419 IDA F YOR087W|YOR088W gene taxon:4932 20020308 SGD
+SGD S000005613 YVC1 GO:0005244 SGD_REF:S000069249|PMID:1700419 IDA F YOR087W|YOR088W gene taxon:4932 20020308 SGD
+SGD S000005613 YVC1 GO:0005262 SGD_REF:S000069157|PMID:11781332 IDA F YOR087W|YOR088W gene taxon:4932 20020308 SGD
+SGD S000005613 YVC1 GO:0005267 SGD_REF:S000069249|PMID:1700419 IDA F YOR087W|YOR088W gene taxon:4932 20020308 SGD
+SGD S000005613 YVC1 GO:0005272 SGD_REF:S000069249|PMID:1700419 IDA F YOR087W|YOR088W gene taxon:4932 20020308 SGD
+SGD S000005613 YVC1 GO:0015281 SGD_REF:S000069249|PMID:1700419 IDA F YOR087W|YOR088W gene taxon:4932 20020308 SGD
+SGD S000005613 YVC1 GO:0030003 SGD_REF:S000069248|PMID:11427713 IMP P YOR087W|YOR088W gene taxon:4932 20020307 SGD
+SGD S000005613 YVC1 GO:0030003 SGD_REF:S000069157|PMID:11781332 IDA P YOR087W|YOR088W gene taxon:4932 20020307 SGD
+SGD S000005613 YVC1 GO:0030003 SGD_REF:S000069248|PMID:11427713 IDA P YOR087W|YOR088W gene taxon:4932 20020307 SGD
+SGD S000005613 YVC1 GO:0030003 SGD_REF:S000069157|PMID:11781332 IMP P YOR087W|YOR088W gene taxon:4932 20020307 SGD
+SGD S000001465 YVH1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C protein tyrosine phosphatase induced by nitrogen starvation YIR026C gene taxon:4932 20031028 SGD
+SGD S000001465 YVH1 GO:0004725 SGD_REF:S000039992|PMID:1334559 IDA F protein tyrosine phosphatase induced by nitrogen starvation YIR026C gene taxon:4932 20010118 SGD
+SGD S000001465 YVH1 GO:0008138 SGD_REF:S000039992|PMID:1334559 ISS F protein tyrosine phosphatase induced by nitrogen starvation YIR026C gene taxon:4932 20050801 SGD
+SGD S000001465 YVH1 GO:0005977 SGD_REF:S000055500|PMID:10852885 IMP P protein tyrosine phosphatase induced by nitrogen starvation YIR026C gene taxon:4932 20050801 SGD
+SGD S000001465 YVH1 GO:0007126 SGD_REF:S000042673|PMID:8896280 IMP P protein tyrosine phosphatase induced by nitrogen starvation YIR026C gene taxon:4932 20010118 SGD
+SGD S000001465 YVH1 GO:0030437 SGD_REF:S000042673|PMID:8896280 IMP P protein tyrosine phosphatase induced by nitrogen starvation YIR026C gene taxon:4932 20010118 SGD
+SGD S000003592 ZAP1 GO:0005634 SGD_REF:S000041703|PMID:10899124 IDA C YJL056C|ZRG10 gene taxon:4932 20021015 SGD
+SGD S000003592 ZAP1 GO:0003677 SGD_REF:S000072515|PMID:12549926 IDA F YJL056C|ZRG10 gene taxon:4932 20030213 SGD
+SGD S000003592 ZAP1 GO:0003704 SGD_REF:S000055420|PMID:9271382 IMP F YJL056C|ZRG10 gene taxon:4932 20010118 SGD
+SGD S000003592 ZAP1 GO:0003704 SGD_REF:S000055420|PMID:9271382 ISS F YJL056C|ZRG10 gene taxon:4932 20010118 SGD
+SGD S000003592 ZAP1 GO:0006357 SGD_REF:S000055420|PMID:9271382 IMP P YJL056C|ZRG10 gene taxon:4932 20010118 SGD
+SGD S000003592 ZAP1 GO:0006882 SGD_REF:S000055420|PMID:9271382 IMP P YJL056C|ZRG10 gene taxon:4932 20010118 SGD
+SGD S000004886 ZDS1 GO:0005643 SGD_REF:S000080156|PMID:15619606 IPI SGD:S000004868|SGD:S000005572 C YMR273C|CES1|CKM1|NRC1|OSS1 gene taxon:4932 20050105 SGD
+SGD S000004886 ZDS1 GO:0005737 SGD_REF:S000059459|PMID:11134339 IPI C YMR273C|CES1|CKM1|NRC1|OSS1 gene taxon:4932 20021114 SGD
+SGD S000004886 ZDS1 GO:0005934 SGD_REF:S000051902|PMID:8816439 IDA C YMR273C|CES1|CKM1|NRC1|OSS1 gene taxon:4932 20021114 SGD
+SGD S000004886 ZDS1 GO:0005935 SGD_REF:S000051902|PMID:8816439 IDA C YMR273C|CES1|CKM1|NRC1|OSS1 gene taxon:4932 20021114 SGD
+SGD S000004886 ZDS1 GO:0005515 SGD_REF:S000059459|PMID:11134339 IDA F YMR273C|CES1|CKM1|NRC1|OSS1 gene taxon:4932 20021114 SGD
+SGD S000004886 ZDS1 GO:0006342 SGD_REF:S000046636|PMID:10662670 IMP P YMR273C|CES1|CKM1|NRC1|OSS1 gene taxon:4932 20021114 SGD
+SGD S000004886 ZDS1 GO:0006406 SGD_REF:S000080156|PMID:15619606 IGI SGD:S000004868|SGD:S000005572 P YMR273C|CES1|CKM1|NRC1|OSS1 gene taxon:4932 20050105 SGD
+SGD S000004886 ZDS1 GO:0006406 SGD_REF:S000080156|PMID:15619606 IMP P YMR273C|CES1|CKM1|NRC1|OSS1 gene taxon:4932 20050105 SGD
+SGD S000004886 ZDS1 GO:0006406 SGD_REF:S000080156|PMID:15619606 IPI SGD:S000004868|SGD:S000005572 P YMR273C|CES1|CKM1|NRC1|OSS1 gene taxon:4932 20050105 SGD
+SGD S000004886 ZDS1 GO:0007569 SGD_REF:S000046636|PMID:10662670 IMP P YMR273C|CES1|CKM1|NRC1|OSS1 gene taxon:4932 20030814 SGD
+SGD S000004886 ZDS1 GO:0030468 SGD_REF:S000051902|PMID:8816439 IGI P YMR273C|CES1|CKM1|NRC1|OSS1 gene taxon:4932 20021204 SGD
+SGD S000004577 ZDS2 GO:0005634 SGD_REF:S000046636|PMID:10662670 IPI C YML109W|CES4 gene taxon:4932 20021018 SGD
+SGD S000004577 ZDS2 GO:0005554 SGD_REF:S000069584 ND F YML109W|CES4 gene taxon:4932 20021018 SGD
+SGD S000004577 ZDS2 GO:0000183 SGD_REF:S000046636|PMID:10662670 IMP P YML109W|CES4 gene taxon:4932 20021018 SGD
+SGD S000004577 ZDS2 GO:0007569 SGD_REF:S000046636|PMID:10662670 IMP P YML109W|CES4 gene taxon:4932 20030814 SGD
+SGD S000004577 ZDS2 GO:0030468 SGD_REF:S000051902|PMID:8816439 IMP P YML109W|CES4 gene taxon:4932 20021114 SGD
+SGD S000005469 ZEO1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YOL109W gene taxon:4932 20040928 SGD
+SGD S000005469 ZEO1 GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C YOL109W gene taxon:4932 20060317 SGD
+SGD S000005469 ZEO1 GO:0019897 SGD_REF:S000074041|PMID:12949174 IDA C YOL109W gene taxon:4932 20031017 SGD
+SGD S000005469 ZEO1 GO:0005554 SGD_REF:S000069584 ND F YOL109W gene taxon:4932 20020425 SGD
+SGD S000005469 ZEO1 GO:0006950 SGD_REF:S000074041|PMID:12949174 IGI P YOL109W gene taxon:4932 20031017 SGD
+SGD S000005469 ZEO1 GO:0006950 SGD_REF:S000074041|PMID:12949174 IMP P YOL109W gene taxon:4932 20031017 SGD
+SGD S000005469 ZEO1 GO:0007047 SGD_REF:S000074041|PMID:12949174 IGI P YOL109W gene taxon:4932 20031017 SGD
+SGD S000005469 ZEO1 GO:0007047 SGD_REF:S000074041|PMID:12949174 IMP P YOL109W gene taxon:4932 20031017 SGD
+SGD S000005254 ZIM17 GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YNL310C|FMP28|HEP1|TIM15 gene taxon:4932 20031028 SGD
+SGD S000005254 ZIM17 GO:0005739 SGD_REF:S000081479|PMID:15719019 IPI C YNL310C|FMP28|HEP1|TIM15 gene taxon:4932 20050503 SGD
+SGD S000005254 ZIM17 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YNL310C|FMP28|HEP1|TIM15 gene taxon:4932 20040924 SGD
+SGD S000005254 ZIM17 GO:0005759 SGD_REF:S000079758|PMID:15383543 IDA C YNL310C|FMP28|HEP1|TIM15 gene taxon:4932 20050103 SGD
+SGD S000005254 ZIM17 GO:0005759 SGD_REF:S000082445|PMID:15992824 IDA C YNL310C|FMP28|HEP1|TIM15 gene taxon:4932 20051118 SGD
+SGD S000005254 ZIM17 GO:0005515 SGD_REF:S000079758|PMID:15383543 ISS F YNL310C|FMP28|HEP1|TIM15 gene taxon:4932 20050103 SGD
+SGD S000005254 ZIM17 GO:0005515 SGD_REF:S000081479|PMID:15719019 IDA F YNL310C|FMP28|HEP1|TIM15 gene taxon:4932 20050503 SGD
+SGD S000005254 ZIM17 GO:0006457 SGD_REF:S000081479|PMID:15719019 IMP P YNL310C|FMP28|HEP1|TIM15 gene taxon:4932 20050503 SGD
+SGD S000005254 ZIM17 GO:0006457 SGD_REF:S000081479|PMID:15719019 IPI P YNL310C|FMP28|HEP1|TIM15 gene taxon:4932 20050503 SGD
+SGD S000005254 ZIM17 GO:0006986 SGD_REF:S000082445|PMID:15992824 IMP P YNL310C|FMP28|HEP1|TIM15 gene taxon:4932 20051118 SGD
+SGD S000005254 ZIM17 GO:0007005 SGD_REF:S000081479|PMID:15719019 IMP P YNL310C|FMP28|HEP1|TIM15 gene taxon:4932 20050503 SGD
+SGD S000005254 ZIM17 GO:0030150 SGD_REF:S000079758|PMID:15383543 IMP P YNL310C|FMP28|HEP1|TIM15 gene taxon:4932 20050103 SGD
+SGD S000002693 ZIP1 GO:0000802 SGD_REF:S000047269|PMID:10662769 IDA C YDR285W gene taxon:4932 20050802 SGD
+SGD S000002693 ZIP1 GO:0003682 SGD_REF:S000073275|PMID:12734403 TAS F YDR285W gene taxon:4932 20030630 SGD
+SGD S000002693 ZIP1 GO:0007129 SGD_REF:S000039860|PMID:9611194 IMP P YDR285W gene taxon:4932 20021111 SGD
+SGD S000002693 ZIP1 GO:0007129 SGD_REF:S000081371|PMID:15805472 IMP P YDR285W gene taxon:4932 20050802 SGD
+SGD S000002693 ZIP1 GO:0007129 SGD_REF:S000081371|PMID:15805472 IGI P YDR285W gene taxon:4932 20050802 SGD
+SGD S000003218 ZIP2 GO:0000795 SGD_REF:S000041062|PMID:9590170 IDA C YGL249W gene taxon:4932 20021113 SGD
+SGD S000003218 ZIP2 GO:0005554 SGD_REF:S000069584 ND F YGL249W gene taxon:4932 20050802 SGD
+SGD S000003218 ZIP2 GO:0007129 SGD_REF:S000081371|PMID:15805472 IGI P YGL249W gene taxon:4932 20050802 SGD
+SGD S000003218 ZIP2 GO:0007129 SGD_REF:S000081371|PMID:15805472 IMP P YGL249W gene taxon:4932 20050802 SGD
+SGD S000003218 ZIP2 GO:0007130 SGD_REF:S000041062|PMID:9590170 IMP P YGL249W gene taxon:4932 20021113 SGD
+SGD S000077071 ZOD1 GO:0008372 SGD_REF:S000069584 ND C gene taxon:4932 20040920 SGD
+SGD S000077071 ZOD1 GO:0005554 SGD_REF:S000069584 ND F gene taxon:4932 20040920 SGD
+SGD S000077071 ZOD1 GO:0000004 SGD_REF:S000069584 ND P gene taxon:4932 20040920 SGD
+SGD S000003443 ZPR1 GO:0005634 SGD_REF:S000047621|PMID:9852145 IDA C zinc finger protein YGR211W gene taxon:4932 20040415 SGD
+SGD S000003443 ZPR1 GO:0005737 SGD_REF:S000047621|PMID:9852145 IDA C zinc finger protein YGR211W gene taxon:4932 20040415 SGD
+SGD S000003443 ZPR1 GO:0005515 SGD_REF:S000047621|PMID:9852145 IDA F zinc finger protein YGR211W gene taxon:4932 20021106 SGD
+SGD S000003443 ZPR1 GO:0000074 SGD_REF:S000047621|PMID:9852145 IMP P zinc finger protein YGR211W gene taxon:4932 20021106 SGD
+SGD S000003443 ZPR1 GO:0009267 SGD_REF:S000071560|PMID:12242280 IMP P zinc finger protein YGR211W gene taxon:4932 20060119 SGD
+SGD S000005514 ZPS1 GO:0000324 SGD_REF:S000074185|PMID:14562095 IDA C YOL154W gene taxon:4932 20031028 SGD
+SGD S000005514 ZPS1 GO:0009277 SGD_REF:S000075303|PMID:11935221 IDA C YOL154W gene taxon:4932 20040114 SGD
+SGD S000005514 ZPS1 GO:0005554 SGD_REF:S000069584 ND F YOL154W gene taxon:4932 20020806 SGD
+SGD S000005514 ZPS1 GO:0000004 SGD_REF:S000069584 ND P YOL154W gene taxon:4932 20020806 SGD
+SGD S000004856 ZRC1 GO:0000324 SGD_REF:S000050176|PMID:9712830 IDA C YMR243C|OSR1 gene taxon:4932 20010302 SGD
+SGD S000004856 ZRC1 GO:0005385 SGD_REF:S000050585|PMID:2693940 IMP F YMR243C|OSR1 gene taxon:4932 20010118 SGD
+SGD S000004856 ZRC1 GO:0015082 SGD_REF:S000058475|PMID:9075641 ISS F YMR243C|OSR1 gene taxon:4932 20010118 SGD
+SGD S000004856 ZRC1 GO:0006749 SGD_REF:S000055158|PMID:8867889 NAS P YMR243C|OSR1 gene taxon:4932 20010118 SGD
+SGD S000004856 ZRC1 GO:0006824 SGD_REF:S000039447|PMID:8058041 NAS P YMR243C|OSR1 gene taxon:4932 20010118 SGD
+SGD S000004856 ZRC1 GO:0006829 SGD_REF:S000039447|PMID:8058041 NAS P YMR243C|OSR1 gene taxon:4932 20010118 SGD
+SGD S000004856 ZRC1 GO:0006882 SGD_REF:S000041386|PMID:10856230 IMP P YMR243C|OSR1 gene taxon:4932 20010118 SGD
+SGD S000005322 ZRG17 GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YNR039C gene taxon:4932 20031028 SGD
+SGD S000005322 ZRG17 GO:0005554 SGD_REF:S000069584 ND F YNR039C gene taxon:4932 20021029 SGD
+SGD S000005322 ZRG17 GO:0006829 SGD_REF:S000039372|PMID:10978274 IMP P YNR039C gene taxon:4932 20021029 SGD
+SGD S000000835 ZRG8 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YER033C gene taxon:4932 20031028 SGD
+SGD S000000835 ZRG8 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YER033C gene taxon:4932 20040813 SGD
+SGD S000000835 ZRG8 GO:0005554 SGD_REF:S000069584 ND F YER033C gene taxon:4932 20021029 SGD
+SGD S000000835 ZRG8 GO:0000004 SGD_REF:S000069584 ND P YER033C gene taxon:4932 20021029 SGD
+SGD S000003224 ZRT1 GO:0005887 SGD_REF:S000051602|PMID:8637895 ISS C YGL255W gene taxon:4932 20020917 SGD
+SGD S000003224 ZRT1 GO:0005887 SGD_REF:S000051602|PMID:8637895 IMP C YGL255W gene taxon:4932 20020917 SGD
+SGD S000003224 ZRT1 GO:0000006 SGD_REF:S000051602|PMID:8637895 ISS F YGL255W gene taxon:4932 20020917 SGD
+SGD S000003224 ZRT1 GO:0000006 SGD_REF:S000051602|PMID:8637895 IMP F YGL255W gene taxon:4932 20020917 SGD
+SGD S000003224 ZRT1 GO:0006830 SGD_REF:S000051602|PMID:8637895 IMP P YGL255W gene taxon:4932 20020917 SGD
+SGD S000004120 ZRT2 GO:0005886 SGD_REF:S000042070|PMID:8798516 ISS C low affinity zinc transport protein YLR130C gene taxon:4932 20021003 SGD
+SGD S000004120 ZRT2 GO:0005886 SGD_REF:S000042070|PMID:8798516 IMP C low affinity zinc transport protein YLR130C gene taxon:4932 20021003 SGD
+SGD S000004120 ZRT2 GO:0000007 SGD_REF:S000042070|PMID:8798516 ISS F low affinity zinc transport protein YLR130C gene taxon:4932 20021003 SGD
+SGD S000004120 ZRT2 GO:0000007 SGD_REF:S000042070|PMID:8798516 IMP F low affinity zinc transport protein YLR130C gene taxon:4932 20021003 SGD
+SGD S000004120 ZRT2 GO:0006831 SGD_REF:S000042070|PMID:8798516 ISS P low affinity zinc transport protein YLR130C gene taxon:4932 20021003 SGD
+SGD S000004120 ZRT2 GO:0006831 SGD_REF:S000042070|PMID:8798516 IMP P low affinity zinc transport protein YLR130C gene taxon:4932 20021003 SGD
+SGD S000001658 ZRT3 GO:0005774 SGD_REF:S000041386|PMID:10856230 IDA C YKL175W gene taxon:4932 20010118 SGD
+SGD S000001658 ZRT3 GO:0005385 SGD_REF:S000041386|PMID:10856230 IMP F YKL175W gene taxon:4932 20010118 SGD
+SGD S000001658 ZRT3 GO:0005385 SGD_REF:S000041386|PMID:10856230 ISS F YKL175W gene taxon:4932 20010118 SGD
+SGD S000001658 ZRT3 GO:0006829 SGD_REF:S000041386|PMID:10856230 IMP P YKL175W gene taxon:4932 20010118 SGD
+SGD S000001658 ZRT3 GO:0006829 SGD_REF:S000041386|PMID:10856230 ISS P YKL175W gene taxon:4932 20010118 SGD
+SGD S000001658 ZRT3 GO:0006882 SGD_REF:S000041386|PMID:10856230 IMP P YKL175W gene taxon:4932 20010118 SGD
+SGD S000000491 ZSP1 GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YBR287W gene taxon:4932 20031028 SGD
+SGD S000000491 ZSP1 GO:0005554 SGD_REF:S000069584 ND F YBR287W gene taxon:4932 20030423 SGD
+SGD S000000491 ZSP1 GO:0000004 SGD_REF:S000069584 ND P YBR287W gene taxon:4932 20030423 SGD
+SGD S000000250 ZTA1 GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YBR046C gene taxon:4932 20031028 SGD
+SGD S000000250 ZTA1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YBR046C gene taxon:4932 20031028 SGD
+SGD S000000250 ZTA1 GO:0005554 SGD_REF:S000069584 ND F YBR046C gene taxon:4932 20010119 SGD
+SGD S000000250 ZTA1 GO:0000004 SGD_REF:S000069584 ND P YBR046C gene taxon:4932 20010119 SGD
+SGD S000003517 ZUO1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C zuotin, Z-DNA binding protein (putative) YGR285C|zuotin gene taxon:4932 20020507 SGD
+SGD S000003517 ZUO1 GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C zuotin, Z-DNA binding protein (putative) YGR285C|zuotin gene taxon:4932 20040928 SGD
+SGD S000003517 ZUO1 GO:0005829 SGD_REF:S000053055|PMID:9707440 NAS C zuotin, Z-DNA binding protein (putative) YGR285C|zuotin gene taxon:4932 20010118 SGD
+SGD S000003517 ZUO1 GO:0005840 SGD_REF:S000053055|PMID:9707440 NAS C zuotin, Z-DNA binding protein (putative) YGR285C|zuotin gene taxon:4932 20010118 SGD
+SGD S000003517 ZUO1 GO:0051082 SGD_REF:S000053055|PMID:9707440 NAS F zuotin, Z-DNA binding protein (putative) YGR285C|zuotin gene taxon:4932 20010118 SGD
+SGD S000003517 ZUO1 GO:0006450 SGD_REF:S000077503|PMID:15456889 IMP P zuotin, Z-DNA binding protein (putative) YGR285C|zuotin gene taxon:4932 20060124 SGD
+SGD S000003517 ZUO1 GO:0006457 SGD_REF:S000053055|PMID:9707440 NAS P zuotin, Z-DNA binding protein (putative) YGR285C|zuotin gene taxon:4932 20010118 SGD
+SGD S000005185 ZWF1 GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C glucose-6-phosphate dehydrogenase YNL241C|MET19|POS10 gene taxon:4932 20020507 SGD
+SGD S000005185 ZWF1 GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C glucose-6-phosphate dehydrogenase YNL241C|MET19|POS10 gene taxon:4932 20031028 SGD
+SGD S000005185 ZWF1 GO:0004345 SGD_REF:S000043047|PMID:2269430 ISS F glucose-6-phosphate dehydrogenase YNL241C|MET19|POS10 gene taxon:4932 20021018 SGD
+SGD S000005185 ZWF1 GO:0009051 SGD_REF:S000043047|PMID:2269430 ISS P glucose-6-phosphate dehydrogenase YNL241C|MET19|POS10 gene taxon:4932 20050802 SGD
+SGD S000005185 ZWF1 GO:0042542 SGD_REF:S000048034|PMID:7586028 IMP P glucose-6-phosphate dehydrogenase YNL241C|MET19|POS10 gene taxon:4932 20050802 SGD
+SGD S000005185 ZWF1 GO:0042542 SGD_REF:S000061566|PMID:9480895 IMP P glucose-6-phosphate dehydrogenase YNL241C|MET19|POS10 gene taxon:4932 20050802 SGD
+SGD S000007282 Q0255 GO:0005739 SGD_REF:S000058438|PMID:9872396 TAS C Q0255|ORF1|RF1 gene taxon:4932 20021119 SGD
+SGD S000007282 Q0255 GO:0005554 SGD_REF:S000069584 ND F Q0255|ORF1|RF1 gene taxon:4932 20021119 SGD
+SGD S000007282 Q0255 GO:0000004 SGD_REF:S000069584 ND P Q0255|ORF1|RF1 gene taxon:4932 20021119 SGD
+SGD S000114171 RNA170 GO:0008372 SGD_REF:S000069584 ND C RNA170 gene taxon:4932 20060124 SGD
+SGD S000114171 RNA170 GO:0005554 SGD_REF:S000069584 ND F RNA170 gene taxon:4932 20060124 SGD
+SGD S000114171 RNA170 GO:0000004 SGD_REF:S000069584 ND P RNA170 gene taxon:4932 20060124 SGD
+SGD S000000016 YAL018C GO:0008372 SGD_REF:S000069584 ND C YAL018C gene taxon:4932 20021126 SGD
+SGD S000000016 YAL018C GO:0005554 SGD_REF:S000069584 ND F YAL018C gene taxon:4932 20021126 SGD
+SGD S000000016 YAL018C GO:0000004 SGD_REF:S000069584 ND P YAL018C gene taxon:4932 20021126 SGD
+SGD S000000025 YAL027W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YAL027W gene taxon:4932 20031028 SGD
+SGD S000000025 YAL027W GO:0005554 SGD_REF:S000069584 ND F YAL027W gene taxon:4932 20021126 SGD
+SGD S000000025 YAL027W GO:0000004 SGD_REF:S000069584 ND P YAL027W gene taxon:4932 20021126 SGD
+SGD S000028732 YAL037C-A GO:0008372 SGD_REF:S000069584 ND C YAL037C-A gene taxon:4932 20030730 SGD
+SGD S000028732 YAL037C-A GO:0005554 SGD_REF:S000069584 ND F YAL037C-A gene taxon:4932 20030730 SGD
+SGD S000028732 YAL037C-A GO:0000004 SGD_REF:S000069584 ND P YAL037C-A gene taxon:4932 20030730 SGD
+SGD S000000035 YAL037W GO:0008372 SGD_REF:S000069584 ND C YAL037W gene taxon:4932 20021126 SGD
+SGD S000000035 YAL037W GO:0005554 SGD_REF:S000069584 ND F YAL037W gene taxon:4932 20021126 SGD
+SGD S000000035 YAL037W GO:0000004 SGD_REF:S000069584 ND P YAL037W gene taxon:4932 20021126 SGD
+SGD S000007586 YAL044W-A GO:0008372 SGD_REF:S000069584 ND C YAL044W-A gene taxon:4932 20010130 SGD
+SGD S000007586 YAL044W-A GO:0005554 SGD_REF:S000069584 ND F YAL044W-A gene taxon:4932 20010130 SGD
+SGD S000007586 YAL044W-A GO:0000004 SGD_REF:S000069584 ND P YAL044W-A gene taxon:4932 20010130 SGD
+SGD S000000044 YAL046C GO:0008372 SGD_REF:S000069584 ND C YAL046C gene taxon:4932 20021126 SGD
+SGD S000000044 YAL046C GO:0005554 SGD_REF:S000069584 ND F YAL046C gene taxon:4932 20021126 SGD
+SGD S000000044 YAL046C GO:0000004 SGD_REF:S000069584 ND P YAL046C gene taxon:4932 20021126 SGD
+SGD S000000047 YAL049C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YAL049C gene taxon:4932 20031028 SGD
+SGD S000000047 YAL049C GO:0005554 SGD_REF:S000069584 ND F YAL049C gene taxon:4932 20021126 SGD
+SGD S000000047 YAL049C GO:0000004 SGD_REF:S000069584 ND P YAL049C gene taxon:4932 20021126 SGD
+SGD S000000057 YAL061W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YAL061W gene taxon:4932 20031028 SGD
+SGD S000000057 YAL061W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YAL061W gene taxon:4932 20031028 SGD
+SGD S000000057 YAL061W GO:0016616 SGD_REF:S000056335|PMID:10938079 ISS F YAL061W gene taxon:4932 20021126 SGD
+SGD S000000057 YAL061W GO:0000004 SGD_REF:S000069584 ND P YAL061W gene taxon:4932 20021126 SGD
+SGD S000028813 YAL063C-A GO:0008372 SGD_REF:S000069584 ND C YAL063C-A gene taxon:4932 20030730 SGD
+SGD S000028813 YAL063C-A GO:0005554 SGD_REF:S000069584 ND F YAL063C-A gene taxon:4932 20030730 SGD
+SGD S000028813 YAL063C-A GO:0000004 SGD_REF:S000069584 ND P YAL063C-A gene taxon:4932 20030730 SGD
+SGD S000002140 YAL064C-A GO:0008372 SGD_REF:S000069584 ND C YAL064C-A gene taxon:4932 20021126 SGD
+SGD S000002140 YAL064C-A GO:0005554 SGD_REF:S000069584 ND F YAL064C-A gene taxon:4932 20021126 SGD
+SGD S000002140 YAL064C-A GO:0000004 SGD_REF:S000069584 ND P YAL064C-A gene taxon:4932 20021126 SGD
+SGD S000000060 YAL064W GO:0008372 SGD_REF:S000069584 ND C YAL064W gene taxon:4932 20021126 SGD
+SGD S000000060 YAL064W GO:0005554 SGD_REF:S000069584 ND F YAL064W gene taxon:4932 20021126 SGD
+SGD S000000060 YAL064W GO:0000004 SGD_REF:S000069584 ND P YAL064W gene taxon:4932 20021126 SGD
+SGD S000002141 YAL064W-B GO:0008372 SGD_REF:S000069584 ND C YAL064W-B gene taxon:4932 20021126 SGD
+SGD S000002141 YAL064W-B GO:0005554 SGD_REF:S000069584 ND F YAL064W-B gene taxon:4932 20021126 SGD
+SGD S000002141 YAL064W-B GO:0000004 SGD_REF:S000069584 ND P YAL064W-B gene taxon:4932 20021126 SGD
+SGD S000001817 YAL065C GO:0008372 SGD_REF:S000069584 ND C YAL065C gene taxon:4932 20021126 SGD
+SGD S000001817 YAL065C GO:0005554 SGD_REF:S000069584 ND F YAL065C gene taxon:4932 20021126 SGD
+SGD S000001817 YAL065C GO:0000004 SGD_REF:S000069584 ND P YAL065C gene taxon:4932 20021126 SGD
+SGD S000028593 YAL067W-A GO:0008372 SGD_REF:S000069584 ND C YAL067W-A gene taxon:4932 20030730 SGD
+SGD S000028593 YAL067W-A GO:0005554 SGD_REF:S000069584 ND F YAL067W-A gene taxon:4932 20030730 SGD
+SGD S000028593 YAL067W-A GO:0000004 SGD_REF:S000069584 ND P YAL067W-A gene taxon:4932 20030730 SGD
+SGD S000000067 YAR009C GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YAR009C|YARCTyB1-1 gene taxon:4932 20030811 SGD
+SGD S000000067 YAR009C GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YAR009C|YARCTyB1-1 gene taxon:4932 20030811 SGD
+SGD S000000067 YAR009C GO:0003887 SGD_REF:S000072465|PMID:9582191 ISS F YAR009C|YARCTyB1-1 gene taxon:4932 20030811 SGD
+SGD S000000067 YAR009C GO:0003964 SGD_REF:S000072465|PMID:9582191 ISS F YAR009C|YARCTyB1-1 gene taxon:4932 20030811 SGD
+SGD S000000067 YAR009C GO:0004540 SGD_REF:S000072465|PMID:9582191 ISS F YAR009C|YARCTyB1-1 gene taxon:4932 20030811 SGD
+SGD S000000067 YAR009C GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YAR009C|YARCTyB1-1 gene taxon:4932 20030811 SGD
+SGD S000000067 YAR009C GO:0008233 SGD_REF:S000072465|PMID:9582191 ISS F YAR009C|YARCTyB1-1 gene taxon:4932 20030811 SGD
+SGD S000000067 YAR009C GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YAR009C|YARCTyB1-1 gene taxon:4932 20030811 SGD
+SGD S000000068 YAR010C GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YAR010C|YARCTyA1-1 gene taxon:4932 20030811 SGD
+SGD S000000068 YAR010C GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YAR010C|YARCTyA1-1 gene taxon:4932 20030811 SGD
+SGD S000000068 YAR010C GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YAR010C|YARCTyA1-1 gene taxon:4932 20030811 SGD
+SGD S000000068 YAR010C GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YAR010C|YARCTyA1-1 gene taxon:4932 20030811 SGD
+SGD S000000074 YAR023C GO:0008372 SGD_REF:S000069584 ND C YAR023C gene taxon:4932 20021126 SGD
+SGD S000000074 YAR023C GO:0005554 SGD_REF:S000069584 ND F YAR023C gene taxon:4932 20021126 SGD
+SGD S000000074 YAR023C GO:0000004 SGD_REF:S000069584 ND P YAR023C gene taxon:4932 20021126 SGD
+SGD S000000076 YAR028W GO:0008372 SGD_REF:S000069584 ND C YAR028W gene taxon:4932 20021126 SGD
+SGD S000000076 YAR028W GO:0005554 SGD_REF:S000069584 ND F YAR028W gene taxon:4932 20021126 SGD
+SGD S000000076 YAR028W GO:0000004 SGD_REF:S000069584 ND P YAR028W gene taxon:4932 20021126 SGD
+SGD S000000077 YAR029W GO:0005737 SGD_REF:S000074227|PMID:12101299 IDA C YAR029W gene taxon:4932 20031107 SGD
+SGD S000000077 YAR029W GO:0005554 SGD_REF:S000069584 ND F YAR029W gene taxon:4932 20021126 SGD
+SGD S000000077 YAR029W GO:0000004 SGD_REF:S000069584 ND P YAR029W gene taxon:4932 20021126 SGD
+SGD S000028595 YAR035C-A GO:0008372 SGD_REF:S000069584 ND C YAR035C-A gene taxon:4932 20030730 SGD
+SGD S000028595 YAR035C-A GO:0005554 SGD_REF:S000069584 ND F YAR035C-A gene taxon:4932 20030730 SGD
+SGD S000028595 YAR035C-A GO:0000004 SGD_REF:S000069584 ND P YAR035C-A gene taxon:4932 20030730 SGD
+SGD S000000087 YAR061W GO:0008372 SGD_REF:S000069584 ND C YAR061W gene taxon:4932 20021126 SGD
+SGD S000000087 YAR061W GO:0005554 SGD_REF:S000069584 ND F YAR061W gene taxon:4932 20021126 SGD
+SGD S000000087 YAR061W GO:0000004 SGD_REF:S000069584 ND P YAR061W gene taxon:4932 20021126 SGD
+SGD S000000088 YAR062W GO:0008372 SGD_REF:S000069584 ND C YAR062W gene taxon:4932 20021126 SGD
+SGD S000000088 YAR062W GO:0005554 SGD_REF:S000069584 ND F YAR062W gene taxon:4932 20021126 SGD
+SGD S000000088 YAR062W GO:0000004 SGD_REF:S000069584 ND P YAR062W gene taxon:4932 20021126 SGD
+SGD S000000089 YAR064W GO:0008372 SGD_REF:S000069584 ND C YAR064W gene taxon:4932 20021126 SGD
+SGD S000000089 YAR064W GO:0005554 SGD_REF:S000069584 ND F YAR064W gene taxon:4932 20021126 SGD
+SGD S000000089 YAR064W GO:0000004 SGD_REF:S000069584 ND P YAR064W gene taxon:4932 20021126 SGD
+SGD S000002144 YAR066W GO:0008372 SGD_REF:S000069584 ND C YAR066W gene taxon:4932 20030203 SGD
+SGD S000002144 YAR066W GO:0005554 SGD_REF:S000069584 ND F YAR066W gene taxon:4932 20030203 SGD
+SGD S000002144 YAR066W GO:0000004 SGD_REF:S000069584 ND P YAR066W gene taxon:4932 20030203 SGD
+SGD S000000091 YAR068W GO:0008372 SGD_REF:S000069584 ND C YAR068W gene taxon:4932 20021106 SGD
+SGD S000000091 YAR068W GO:0005554 SGD_REF:S000069584 ND F YAR068W gene taxon:4932 20021106 SGD
+SGD S000000091 YAR068W GO:0000004 SGD_REF:S000069584 ND P YAR068W gene taxon:4932 20021106 SGD
+SGD S000002146 YBL005W-A GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YBL005W-A gene taxon:4932 20030811 SGD
+SGD S000002146 YBL005W-A GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YBL005W-A gene taxon:4932 20030811 SGD
+SGD S000002146 YBL005W-A GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YBL005W-A gene taxon:4932 20030811 SGD
+SGD S000002146 YBL005W-A GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YBL005W-A gene taxon:4932 20030811 SGD
+SGD S000002147 YBL005W-B GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YBL005W-B gene taxon:4932 20030811 SGD
+SGD S000002147 YBL005W-B GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YBL005W-B gene taxon:4932 20030811 SGD
+SGD S000002147 YBL005W-B GO:0003887 SGD_REF:S000072465|PMID:9582191 ISS F YBL005W-B gene taxon:4932 20030811 SGD
+SGD S000002147 YBL005W-B GO:0003964 SGD_REF:S000072465|PMID:9582191 ISS F YBL005W-B gene taxon:4932 20030811 SGD
+SGD S000002147 YBL005W-B GO:0004540 SGD_REF:S000072465|PMID:9582191 ISS F YBL005W-B gene taxon:4932 20030811 SGD
+SGD S000002147 YBL005W-B GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YBL005W-B gene taxon:4932 20030811 SGD
+SGD S000002147 YBL005W-B GO:0008233 SGD_REF:S000072465|PMID:9582191 ISS F YBL005W-B gene taxon:4932 20030811 SGD
+SGD S000002147 YBL005W-B GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YBL005W-B gene taxon:4932 20030811 SGD
+SGD S000028529 YBL008W-A GO:0008372 SGD_REF:S000069584 ND C YBL008W-A gene taxon:4932 20030730 SGD
+SGD S000028529 YBL008W-A GO:0005554 SGD_REF:S000069584 ND F YBL008W-A gene taxon:4932 20030730 SGD
+SGD S000028529 YBL008W-A GO:0000004 SGD_REF:S000069584 ND P YBL008W-A gene taxon:4932 20030730 SGD
+SGD S000000105 YBL009W GO:0005634 SGD_REF:S000073149|PMID:12737306 ISS C YBL009W gene taxon:4932 20030527 SGD
+SGD S000000105 YBL009W GO:0004674 SGD_REF:S000073149|PMID:12737306 ISS F YBL009W gene taxon:4932 20030527 SGD
+SGD S000000105 YBL009W GO:0007126 SGD_REF:S000073149|PMID:12737306 IEP P YBL009W gene taxon:4932 20030527 SGD
+SGD S000000106 YBL010C colocalizes_with GO:0030136 SGD_REF:S000074185|PMID:14562095 IDA C YBL010C gene taxon:4932 20031028 SGD
+SGD S000000106 YBL010C GO:0005554 SGD_REF:S000069584 ND F YBL010C gene taxon:4932 20030203 SGD
+SGD S000000106 YBL010C GO:0000004 SGD_REF:S000069584 ND P YBL010C gene taxon:4932 20030203 SGD
+SGD S000000124 YBL028C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YBL028C gene taxon:4932 20031028 SGD
+SGD S000000124 YBL028C GO:0005730 SGD_REF:S000074185|PMID:14562095 IDA C YBL028C gene taxon:4932 20031028 SGD
+SGD S000000124 YBL028C GO:0005554 SGD_REF:S000069584 ND F YBL028C gene taxon:4932 20030203 SGD
+SGD S000000124 YBL028C GO:0000004 SGD_REF:S000069584 ND P YBL028C gene taxon:4932 20030203 SGD
+SGD S000007591 YBL029C-A GO:0008372 SGD_REF:S000069584 ND C YBL029C-A gene taxon:4932 20010226 SGD
+SGD S000007591 YBL029C-A GO:0005554 SGD_REF:S000069584 ND F YBL029C-A gene taxon:4932 20010226 SGD
+SGD S000007591 YBL029C-A GO:0000004 SGD_REF:S000069584 ND P YBL029C-A gene taxon:4932 20010226 SGD
+SGD S000000125 YBL029W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YBL029W gene taxon:4932 20031028 SGD
+SGD S000000125 YBL029W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YBL029W gene taxon:4932 20031028 SGD
+SGD S000000125 YBL029W GO:0005554 SGD_REF:S000069584 ND F YBL029W gene taxon:4932 20030203 SGD
+SGD S000000125 YBL029W GO:0000004 SGD_REF:S000069584 ND P YBL029W gene taxon:4932 20030203 SGD
+SGD S000000132 YBL036C GO:0005622 SGD_REF:S000073651|PMID:12499548 IC GO:0006520|GO:0008784 C YBL036C gene taxon:4932 20030729 SGD
+SGD S000000132 YBL036C GO:0008784 SGD_REF:S000073651|PMID:12499548 IDA F YBL036C gene taxon:4932 20030729 SGD
+SGD S000000132 YBL036C GO:0030170 SGD_REF:S000073651|PMID:12499548 IDA F YBL036C gene taxon:4932 20030729 SGD
+SGD S000000132 YBL036C GO:0006520 SGD_REF:S000073651|PMID:12499548 IDA P YBL036C gene taxon:4932 20030729 SGD
+SGD S000028517 YBL039W-B GO:0008372 SGD_REF:S000069584 ND C YBL039W-B|YBL039W-A gene taxon:4932 20030730 SGD
+SGD S000028517 YBL039W-B GO:0005554 SGD_REF:S000069584 ND F YBL039W-B|YBL039W-A gene taxon:4932 20030730 SGD
+SGD S000028517 YBL039W-B GO:0000004 SGD_REF:S000069584 ND P YBL039W-B|YBL039W-A gene taxon:4932 20030730 SGD
+SGD S000000140 YBL044W GO:0008372 SGD_REF:S000069584 ND C YBL044W gene taxon:4932 20021126 SGD
+SGD S000000140 YBL044W GO:0005554 SGD_REF:S000069584 ND F YBL044W gene taxon:4932 20021126 SGD
+SGD S000000140 YBL044W GO:0000004 SGD_REF:S000069584 ND P YBL044W gene taxon:4932 20021126 SGD
+SGD S000000150 YBL054W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YBL054W gene taxon:4932 20031028 SGD
+SGD S000000150 YBL054W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YBL054W gene taxon:4932 20031028 SGD
+SGD S000000150 YBL054W GO:0005554 SGD_REF:S000069584 ND F YBL054W gene taxon:4932 20030203 SGD
+SGD S000000150 YBL054W GO:0000004 SGD_REF:S000069584 ND P YBL054W gene taxon:4932 20030203 SGD
+SGD S000000151 YBL055C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YBL055C gene taxon:4932 20031028 SGD
+SGD S000000151 YBL055C GO:0005554 SGD_REF:S000069584 ND F YBL055C gene taxon:4932 20030203 SGD
+SGD S000000151 YBL055C GO:0000004 SGD_REF:S000069584 ND P YBL055C gene taxon:4932 20030203 SGD
+SGD S000007488 YBL059C-A GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YBL059C-A gene taxon:4932 20031028 SGD
+SGD S000007488 YBL059C-A GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YBL059C-A gene taxon:4932 20031028 SGD
+SGD S000007488 YBL059C-A GO:0005554 SGD_REF:S000069584 ND F YBL059C-A gene taxon:4932 20021126 SGD
+SGD S000007488 YBL059C-A GO:0000004 SGD_REF:S000069584 ND P YBL059C-A gene taxon:4932 20021126 SGD
+SGD S000000155 YBL059W GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YBL059W gene taxon:4932 20031028 SGD
+SGD S000000155 YBL059W GO:0005554 SGD_REF:S000069584 ND F YBL059W gene taxon:4932 20030422 SGD
+SGD S000000155 YBL059W GO:0000004 SGD_REF:S000069584 ND P YBL059W gene taxon:4932 20030422 SGD
+SGD S000000156 YBL060W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YBL060W gene taxon:4932 20031028 SGD
+SGD S000000156 YBL060W GO:0005935 SGD_REF:S000074185|PMID:14562095 IDA C YBL060W gene taxon:4932 20031028 SGD
+SGD S000000156 YBL060W GO:0005554 SGD_REF:S000069584 ND F YBL060W gene taxon:4932 20030203 SGD
+SGD S000000156 YBL060W GO:0000004 SGD_REF:S000069584 ND P YBL060W gene taxon:4932 20030203 SGD
+SGD S000028597 YBL071C-B GO:0008372 SGD_REF:S000069584 ND C YBL071C-B gene taxon:4932 20030730 SGD
+SGD S000028597 YBL071C-B GO:0005554 SGD_REF:S000069584 ND F YBL071C-B gene taxon:4932 20030730 SGD
+SGD S000028597 YBL071C-B GO:0000004 SGD_REF:S000069584 ND P YBL071C-B gene taxon:4932 20030730 SGD
+SGD S000000177 YBL081W GO:0008372 SGD_REF:S000069584 ND C YBL081W gene taxon:4932 20030203 SGD
+SGD S000000177 YBL081W GO:0005554 SGD_REF:S000069584 ND F YBL081W gene taxon:4932 20030203 SGD
+SGD S000000177 YBL081W GO:0000004 SGD_REF:S000069584 ND P YBL081W gene taxon:4932 20030203 SGD
+SGD S000000182 YBL086C GO:0008372 SGD_REF:S000069584 ND C YBL086C gene taxon:4932 20030203 SGD
+SGD S000000182 YBL086C GO:0005554 SGD_REF:S000069584 ND F YBL086C gene taxon:4932 20030203 SGD
+SGD S000000182 YBL086C GO:0000004 SGD_REF:S000069584 ND P YBL086C gene taxon:4932 20030203 SGD
+SGD S000000191 YBL095W GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YBL095W gene taxon:4932 20031028 SGD
+SGD S000000191 YBL095W GO:0005554 SGD_REF:S000069584 ND F YBL095W gene taxon:4932 20030203 SGD
+SGD S000000191 YBL095W GO:0000004 SGD_REF:S000069584 ND P YBL095W gene taxon:4932 20030203 SGD
+SGD S000002148 YBL100W-A GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YBL100W-A|TY2A_B|YBL101W-A gene taxon:4932 20030811 SGD
+SGD S000002148 YBL100W-A GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YBL100W-A|TY2A_B|YBL101W-A gene taxon:4932 20030811 SGD
+SGD S000002148 YBL100W-A GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YBL100W-A|TY2A_B|YBL101W-A gene taxon:4932 20030811 SGD
+SGD S000002148 YBL100W-A GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YBL100W-A|TY2A_B|YBL101W-A gene taxon:4932 20030811 SGD
+SGD S000002149 YBL100W-B GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YBL100W-B|TY2B_B|YBL101W-B gene taxon:4932 20030811 SGD
+SGD S000002149 YBL100W-B GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YBL100W-B|TY2B_B|YBL101W-B gene taxon:4932 20030811 SGD
+SGD S000002149 YBL100W-B GO:0003887 SGD_REF:S000072465|PMID:9582191 ISS F YBL100W-B|TY2B_B|YBL101W-B gene taxon:4932 20030811 SGD
+SGD S000002149 YBL100W-B GO:0003964 SGD_REF:S000072465|PMID:9582191 ISS F YBL100W-B|TY2B_B|YBL101W-B gene taxon:4932 20030811 SGD
+SGD S000002149 YBL100W-B GO:0004540 SGD_REF:S000072465|PMID:9582191 ISS F YBL100W-B|TY2B_B|YBL101W-B gene taxon:4932 20030811 SGD
+SGD S000002149 YBL100W-B GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YBL100W-B|TY2B_B|YBL101W-B gene taxon:4932 20030811 SGD
+SGD S000002149 YBL100W-B GO:0008233 SGD_REF:S000072465|PMID:9582191 ISS F YBL100W-B|TY2B_B|YBL101W-B gene taxon:4932 20030811 SGD
+SGD S000002149 YBL100W-B GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YBL100W-B|TY2B_B|YBL101W-B gene taxon:4932 20030811 SGD
+SGD S000028598 YBL100W-C GO:0008372 SGD_REF:S000069584 ND C YBL100W-C|YBL101W-C gene taxon:4932 20030730 SGD
+SGD S000028598 YBL100W-C GO:0005554 SGD_REF:S000069584 ND F YBL100W-C|YBL101W-C gene taxon:4932 20030730 SGD
+SGD S000028598 YBL100W-C GO:0000004 SGD_REF:S000069584 ND P YBL100W-C|YBL101W-C gene taxon:4932 20030730 SGD
+SGD S000000200 YBL104C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YBL104C|YBL103C-A gene taxon:4932 20031028 SGD
+SGD S000000200 YBL104C GO:0005554 SGD_REF:S000069584 ND F YBL104C|YBL103C-A gene taxon:4932 20021104 SGD
+SGD S000000200 YBL104C GO:0000004 SGD_REF:S000069584 ND P YBL104C|YBL103C-A gene taxon:4932 20021104 SGD
+SGD S000000203 YBL107C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YBL107C gene taxon:4932 20031028 SGD
+SGD S000000203 YBL107C GO:0005554 SGD_REF:S000069584 ND F YBL107C gene taxon:4932 20021126 SGD
+SGD S000000203 YBL107C GO:0000004 SGD_REF:S000069584 ND P YBL107C gene taxon:4932 20021126 SGD
+SGD S000002151 YBL111C GO:0008372 SGD_REF:S000069584 ND C YBL111C gene taxon:4932 20021126 SGD
+SGD S000002151 YBL111C GO:0005554 SGD_REF:S000069584 ND F YBL111C gene taxon:4932 20021126 SGD
+SGD S000002151 YBL111C GO:0000004 SGD_REF:S000069584 ND P YBL111C gene taxon:4932 20021126 SGD
+SGD S000002152 YBL112C GO:0008372 SGD_REF:S000069584 ND C YBL112C gene taxon:4932 20021126 SGD
+SGD S000002152 YBL112C GO:0005554 SGD_REF:S000069584 ND F YBL112C gene taxon:4932 20021126 SGD
+SGD S000002152 YBL112C GO:0000004 SGD_REF:S000069584 ND P YBL112C gene taxon:4932 20021126 SGD
+SGD S000002153 YBL113C GO:0008372 SGD_REF:S000069584 ND C YBL113C gene taxon:4932 20030203 SGD
+SGD S000002153 YBL113C GO:0004386 SGD_REF:S000053946|PMID:9837911 ISS F YBL113C gene taxon:4932 20040323 SGD
+SGD S000002153 YBL113C GO:0000004 SGD_REF:S000069584 ND P YBL113C gene taxon:4932 20030203 SGD
+SGD S000002154 YBR012W-A GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YBR012W-A gene taxon:4932 20030811 SGD
+SGD S000002154 YBR012W-A GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YBR012W-A gene taxon:4932 20030811 SGD
+SGD S000002154 YBR012W-A GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YBR012W-A gene taxon:4932 20030811 SGD
+SGD S000002154 YBR012W-A GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YBR012W-A gene taxon:4932 20030811 SGD
+SGD S000002155 YBR012W-B GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YBR012W-B gene taxon:4932 20030811 SGD
+SGD S000002155 YBR012W-B GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YBR012W-B gene taxon:4932 20030811 SGD
+SGD S000002155 YBR012W-B GO:0003887 SGD_REF:S000072465|PMID:9582191 ISS F YBR012W-B gene taxon:4932 20030811 SGD
+SGD S000002155 YBR012W-B GO:0003964 SGD_REF:S000072465|PMID:9582191 ISS F YBR012W-B gene taxon:4932 20030811 SGD
+SGD S000002155 YBR012W-B GO:0004540 SGD_REF:S000072465|PMID:9582191 ISS F YBR012W-B gene taxon:4932 20030811 SGD
+SGD S000002155 YBR012W-B GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YBR012W-B gene taxon:4932 20030811 SGD
+SGD S000002155 YBR012W-B GO:0008233 SGD_REF:S000072465|PMID:9582191 ISS F YBR012W-B gene taxon:4932 20030811 SGD
+SGD S000002155 YBR012W-B GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YBR012W-B gene taxon:4932 20030811 SGD
+SGD S000000217 YBR013C GO:0008372 SGD_REF:S000069584 ND C YBR013C gene taxon:4932 20021126 SGD
+SGD S000000217 YBR013C GO:0005554 SGD_REF:S000069584 ND F YBR013C gene taxon:4932 20021126 SGD
+SGD S000000217 YBR013C GO:0000004 SGD_REF:S000069584 ND P YBR013C gene taxon:4932 20021126 SGD
+SGD S000000218 YBR014C GO:0000324 SGD_REF:S000074185|PMID:14562095 IDA C YBR014C gene taxon:4932 20031028 SGD
+SGD S000000218 YBR014C GO:0005624 SGD_REF:S000075303|PMID:11935221 IDA C YBR014C gene taxon:4932 20040114 SGD
+SGD S000000218 YBR014C GO:0005554 SGD_REF:S000069584 ND F YBR014C gene taxon:4932 20030421 SGD
+SGD S000000218 YBR014C GO:0000004 SGD_REF:S000069584 ND P YBR014C gene taxon:4932 20030421 SGD
+SGD S000000220 YBR016W GO:0005886 SGD_REF:S000072636|PMID:12514182 IDA C YBR016W gene taxon:4932 20031014 SGD
+SGD S000000220 YBR016W GO:0005554 SGD_REF:S000069584 ND F YBR016W gene taxon:4932 20030210 SGD
+SGD S000000220 YBR016W GO:0009269 SGD_REF:S000063137|PMID:10681550 IEP P YBR016W gene taxon:4932 20030210 SGD
+SGD S000000229 YBR025C GO:0005737 SGD_REF:S000056415|PMID:10684247 IDA C YBR025C gene taxon:4932 20010301 SGD
+SGD S000000229 YBR025C GO:0005554 SGD_REF:S000069584 ND F YBR025C gene taxon:4932 20010119 SGD
+SGD S000000229 YBR025C GO:0000004 SGD_REF:S000069584 ND P YBR025C gene taxon:4932 20010119 SGD
+SGD S000000232 YBR028C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YBR028C gene taxon:4932 20031028 SGD
+SGD S000000232 YBR028C GO:0004672 SGD_REF:S000058030|PMID:9020587 ISS F YBR028C gene taxon:4932 20030203 SGD
+SGD S000000232 YBR028C GO:0000004 SGD_REF:S000069584 ND P YBR028C gene taxon:4932 20030203 SGD
+SGD S000000234 YBR030W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YBR030W gene taxon:4932 20031028 SGD
+SGD S000000234 YBR030W GO:0005554 SGD_REF:S000069584 ND F YBR030W gene taxon:4932 20030203 SGD
+SGD S000000234 YBR030W GO:0006644 SGD_REF:S000047944|PMID:8910557 IGI P YBR030W gene taxon:4932 20030217 SGD
+SGD S000000246 YBR042C GO:0005811 SGD_REF:S000074185|PMID:14562095 IDA C YBR042C gene taxon:4932 20031028 SGD
+SGD S000000246 YBR042C GO:0008415 SGD_REF:S000065692|PMID:9259571 ISS F YBR042C gene taxon:4932 20030423 SGD
+SGD S000000246 YBR042C GO:0008654 SGD_REF:S000065692|PMID:9259571 ISS P YBR042C gene taxon:4932 20030423 SGD
+SGD S000000257 YBR053C GO:0008372 SGD_REF:S000069584 ND C YBR053C gene taxon:4932 20030421 SGD
+SGD S000000257 YBR053C GO:0005554 SGD_REF:S000069584 ND F YBR053C gene taxon:4932 20030421 SGD
+SGD S000000257 YBR053C GO:0000004 SGD_REF:S000069584 ND P YBR053C gene taxon:4932 20030421 SGD
+SGD S000000260 YBR056W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YBR056W gene taxon:4932 20031028 SGD
+SGD S000000260 YBR056W GO:0005554 SGD_REF:S000069584 ND F YBR056W gene taxon:4932 20030203 SGD
+SGD S000000260 YBR056W GO:0000004 SGD_REF:S000069584 ND P YBR056W gene taxon:4932 20030203 SGD
+SGD S000000266 YBR062C GO:0008372 SGD_REF:S000069584 ND C YBR062C gene taxon:4932 20021126 SGD
+SGD S000000266 YBR062C GO:0005554 SGD_REF:S000069584 ND F YBR062C gene taxon:4932 20021126 SGD
+SGD S000000266 YBR062C GO:0000004 SGD_REF:S000069584 ND P YBR062C gene taxon:4932 20021126 SGD
+SGD S000000267 YBR063C GO:0008372 SGD_REF:S000069584 ND C YBR063C gene taxon:4932 20030421 SGD
+SGD S000000267 YBR063C GO:0005554 SGD_REF:S000069584 ND F YBR063C gene taxon:4932 20030421 SGD
+SGD S000000267 YBR063C GO:0000004 SGD_REF:S000069584 ND P YBR063C gene taxon:4932 20030421 SGD
+SGD S000000275 YBR071W GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YBR071W gene taxon:4932 20020507 SGD
+SGD S000000275 YBR071W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YBR071W gene taxon:4932 20031028 SGD
+SGD S000000275 YBR071W GO:0005554 SGD_REF:S000069584 ND F YBR071W gene taxon:4932 20030203 SGD
+SGD S000000275 YBR071W GO:0000004 SGD_REF:S000069584 ND P YBR071W gene taxon:4932 20030203 SGD
+SGD S000028532 YBR072C-A GO:0008372 SGD_REF:S000069584 ND C YBR072C-A gene taxon:4932 20030730 SGD
+SGD S000028532 YBR072C-A GO:0005554 SGD_REF:S000069584 ND F YBR072C-A gene taxon:4932 20030730 SGD
+SGD S000028532 YBR072C-A GO:0000004 SGD_REF:S000069584 ND P YBR072C-A gene taxon:4932 20030730 SGD
+SGD S000000278 YBR074W GO:0008372 SGD_REF:S000069584 ND C YBR074W|YBR075W gene taxon:4932 20030203 SGD
+SGD S000000278 YBR074W GO:0004222 SGD_REF:S000080056|PMID:15606766 ISS F YBR074W|YBR075W gene taxon:4932 20050415 SGD
+SGD S000000278 YBR074W GO:0006508 SGD_REF:S000080056|PMID:15606766 ISS P YBR074W|YBR075W gene taxon:4932 20050415 SGD
+SGD S000007522 YBR085C-A GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YBR085C-A gene taxon:4932 20031028 SGD
+SGD S000007522 YBR085C-A GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YBR085C-A gene taxon:4932 20031028 SGD
+SGD S000007522 YBR085C-A GO:0005554 SGD_REF:S000069584 ND F YBR085C-A gene taxon:4932 20030203 SGD
+SGD S000007522 YBR085C-A GO:0000004 SGD_REF:S000069584 ND P YBR085C-A gene taxon:4932 20030203 SGD
+SGD S000000294 YBR090C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YBR090C gene taxon:4932 20031028 SGD
+SGD S000000294 YBR090C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YBR090C gene taxon:4932 20031028 SGD
+SGD S000000294 YBR090C GO:0005554 SGD_REF:S000069584 ND F YBR090C gene taxon:4932 20030203 SGD
+SGD S000000294 YBR090C GO:0000004 SGD_REF:S000069584 ND P YBR090C gene taxon:4932 20030203 SGD
+SGD S000000298 YBR094W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YBR094W gene taxon:4932 20031028 SGD
+SGD S000000298 YBR094W GO:0005554 SGD_REF:S000069584 ND F YBR094W gene taxon:4932 20030421 SGD
+SGD S000000298 YBR094W GO:0000004 SGD_REF:S000069584 ND P YBR094W gene taxon:4932 20030421 SGD
+SGD S000000300 YBR096W GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YBR096W gene taxon:4932 20031028 SGD
+SGD S000000300 YBR096W GO:0005554 SGD_REF:S000069584 ND F YBR096W gene taxon:4932 20030421 SGD
+SGD S000000300 YBR096W GO:0000004 SGD_REF:S000069584 ND P YBR096W gene taxon:4932 20030421 SGD
+SGD S000000312 YBR108W colocalizes_with GO:0045121 SGD_REF:S000080197|PMID:15561700 IDA C YBR108W gene taxon:4932 20050111 SGD
+SGD S000000312 YBR108W GO:0005554 SGD_REF:S000069584 ND F YBR108W gene taxon:4932 20030421 SGD
+SGD S000000312 YBR108W GO:0000004 SGD_REF:S000069584 ND P YBR108W gene taxon:4932 20030421 SGD
+SGD S000000341 YBR137W GO:0005737 SGD_REF:S000059972|PMID:11266464 IDA C YBR137W gene taxon:4932 20021223 SGD
+SGD S000000341 YBR137W GO:0005554 SGD_REF:S000069584 ND F YBR137W gene taxon:4932 20021223 SGD
+SGD S000000341 YBR137W GO:0000004 SGD_REF:S000069584 ND P YBR137W gene taxon:4932 20021223 SGD
+SGD S000000342 YBR138C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YBR138C|HDR1 gene taxon:4932 20031028 SGD
+SGD S000000342 YBR138C GO:0005554 SGD_REF:S000069584 ND F YBR138C|HDR1 gene taxon:4932 20021004 SGD
+SGD S000000342 YBR138C GO:0000004 SGD_REF:S000069584 ND P YBR138C|HDR1 gene taxon:4932 20021004 SGD
+SGD S000000343 YBR139W GO:0000324 SGD_REF:S000074185|PMID:14562095 IDA C YBR139W gene taxon:4932 20031028 SGD
+SGD S000000343 YBR139W GO:0004186 SGD_REF:S000072463|PMID:10592175 ISS F YBR139W gene taxon:4932 20030204 SGD
+SGD S000000343 YBR139W GO:0017171 SGD_REF:S000076484|PMID:14645503 RCA F YBR139W gene taxon:4932 20060421 SGD
+SGD S000000343 YBR139W GO:0017171 SGD_REF:S000076484|PMID:14645503 IDA F YBR139W gene taxon:4932 20060421 SGD
+SGD S000000343 YBR139W GO:0000004 SGD_REF:S000069584 ND P YBR139W gene taxon:4932 20030204 SGD
+SGD S000000345 YBR141C GO:0005730 SGD_REF:S000074185|PMID:14562095 IDA C YBR141C gene taxon:4932 20031028 SGD
+SGD S000000345 YBR141C GO:0005554 SGD_REF:S000069584 ND F YBR141C gene taxon:4932 20030203 SGD
+SGD S000000345 YBR141C GO:0000004 SGD_REF:S000069584 ND P YBR141C gene taxon:4932 20030203 SGD
+SGD S000000351 YBR147W GO:0008372 SGD_REF:S000069584 ND C YBR147W gene taxon:4932 20021223 SGD
+SGD S000000351 YBR147W GO:0005554 SGD_REF:S000069584 ND F YBR147W gene taxon:4932 20021223 SGD
+SGD S000000351 YBR147W GO:0000004 SGD_REF:S000069584 ND P YBR147W gene taxon:4932 20021223 SGD
+SGD S000028603 YBR182C-A GO:0008372 SGD_REF:S000069584 ND C YBR182C-A gene taxon:4932 20030730 SGD
+SGD S000028603 YBR182C-A GO:0005554 SGD_REF:S000069584 ND F YBR182C-A gene taxon:4932 20030730 SGD
+SGD S000028603 YBR182C-A GO:0000004 SGD_REF:S000069584 ND P YBR182C-A gene taxon:4932 20030730 SGD
+SGD S000000388 YBR184W GO:0008372 SGD_REF:S000069584 ND C YBR184W gene taxon:4932 20030203 SGD
+SGD S000000388 YBR184W GO:0005554 SGD_REF:S000069584 ND F YBR184W gene taxon:4932 20030203 SGD
+SGD S000000388 YBR184W GO:0000004 SGD_REF:S000069584 ND P YBR184W gene taxon:4932 20030203 SGD
+SGD S000000391 YBR187W GO:0000324 SGD_REF:S000074185|PMID:14562095 IDA C YBR187W gene taxon:4932 20031028 SGD
+SGD S000000391 YBR187W GO:0005554 SGD_REF:S000069584 ND F YBR187W gene taxon:4932 20030203 SGD
+SGD S000000391 YBR187W GO:0000004 SGD_REF:S000069584 ND P YBR187W gene taxon:4932 20030203 SGD
+SGD S000028534 YBR196C-A GO:0008372 SGD_REF:S000069584 ND C YBR196C-A gene taxon:4932 20030730 SGD
+SGD S000028534 YBR196C-A GO:0005554 SGD_REF:S000069584 ND F YBR196C-A gene taxon:4932 20030730 SGD
+SGD S000028534 YBR196C-A GO:0000004 SGD_REF:S000069584 ND P YBR196C-A gene taxon:4932 20030730 SGD
+SGD S000028816 YBR196C-B GO:0008372 SGD_REF:S000069584 ND C YBR196C-B gene taxon:4932 20030730 SGD
+SGD S000028816 YBR196C-B GO:0005554 SGD_REF:S000069584 ND F YBR196C-B gene taxon:4932 20030730 SGD
+SGD S000028816 YBR196C-B GO:0000004 SGD_REF:S000069584 ND P YBR196C-B gene taxon:4932 20030730 SGD
+SGD S000000401 YBR197C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YBR197C gene taxon:4932 20031028 SGD
+SGD S000000401 YBR197C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YBR197C gene taxon:4932 20031028 SGD
+SGD S000000401 YBR197C GO:0005554 SGD_REF:S000069584 ND F YBR197C gene taxon:4932 20030421 SGD
+SGD S000000401 YBR197C GO:0000004 SGD_REF:S000069584 ND P YBR197C gene taxon:4932 20030421 SGD
+SGD S000028535 YBR200W-A GO:0008372 SGD_REF:S000069584 ND C YBR200W-A gene taxon:4932 20030730 SGD
+SGD S000028535 YBR200W-A GO:0005554 SGD_REF:S000069584 ND F YBR200W-A gene taxon:4932 20030730 SGD
+SGD S000028535 YBR200W-A GO:0000004 SGD_REF:S000069584 ND P YBR200W-A gene taxon:4932 20030730 SGD
+SGD S000087085 YBR201C-A GO:0008372 SGD_REF:S000069584 ND C YBR201C-A gene taxon:4932 20051109 SGD
+SGD S000087085 YBR201C-A GO:0005554 SGD_REF:S000069584 ND F YBR201C-A gene taxon:4932 20051109 SGD
+SGD S000087085 YBR201C-A GO:0000004 SGD_REF:S000069584 ND P YBR201C-A gene taxon:4932 20051109 SGD
+SGD S000000408 YBR204C GO:0008372 SGD_REF:S000069584 ND C YBR204C gene taxon:4932 20051214 SGD
+SGD S000000408 YBR204C GO:0017171 SGD_REF:S000076484|PMID:14645503 IDA F YBR204C gene taxon:4932 20040604 SGD
+SGD S000000408 YBR204C GO:0017171 SGD_REF:S000076484|PMID:14645503 RCA F YBR204C gene taxon:4932 20060421 SGD
+SGD S000000408 YBR204C GO:0000004 SGD_REF:S000069584 ND P YBR204C gene taxon:4932 20030203 SGD
+SGD S000000423 YBR219C GO:0008372 SGD_REF:S000069584 ND C YBR219C gene taxon:4932 20030203 SGD
+SGD S000000423 YBR219C GO:0005554 SGD_REF:S000069584 ND F YBR219C gene taxon:4932 20030203 SGD
+SGD S000000423 YBR219C GO:0000004 SGD_REF:S000069584 ND P YBR219C gene taxon:4932 20030203 SGD
+SGD S000000424 YBR220C GO:0008372 SGD_REF:S000069584 ND C YBR220C gene taxon:4932 20030422 SGD
+SGD S000000424 YBR220C GO:0005554 SGD_REF:S000069584 ND F YBR220C gene taxon:4932 20030422 SGD
+SGD S000000424 YBR220C GO:0000004 SGD_REF:S000069584 ND P YBR220C gene taxon:4932 20030422 SGD
+SGD S000028817 YBR221W-A GO:0008372 SGD_REF:S000069584 ND C YBR221W-A gene taxon:4932 20030730 SGD
+SGD S000028817 YBR221W-A GO:0005554 SGD_REF:S000069584 ND F YBR221W-A gene taxon:4932 20030730 SGD
+SGD S000028817 YBR221W-A GO:0000004 SGD_REF:S000069584 ND P YBR221W-A gene taxon:4932 20030730 SGD
+SGD S000000429 YBR225W GO:0008372 SGD_REF:S000069584 ND C YBR225W gene taxon:4932 20021126 SGD
+SGD S000000429 YBR225W GO:0005554 SGD_REF:S000069584 ND F YBR225W gene taxon:4932 20021126 SGD
+SGD S000000429 YBR225W GO:0000004 SGD_REF:S000069584 ND P YBR225W gene taxon:4932 20021126 SGD
+SGD S000029722 YBR230W-A GO:0008372 SGD_REF:S000069584 ND C YBR230W-A gene taxon:4932 20041021 SGD
+SGD S000029722 YBR230W-A GO:0005554 SGD_REF:S000069584 ND F YBR230W-A gene taxon:4932 20041021 SGD
+SGD S000029722 YBR230W-A GO:0000004 SGD_REF:S000069584 ND P YBR230W-A gene taxon:4932 20041021 SGD
+SGD S000000439 YBR235W GO:0008372 SGD_REF:S000069584 ND C YBR235W gene taxon:4932 20021204 SGD
+SGD S000000439 YBR235W GO:0015075 SGD_REF:S000056341|PMID:8526903 ISS F YBR235W gene taxon:4932 20021204 SGD
+SGD S000000439 YBR235W GO:0000004 SGD_REF:S000069584 ND P YBR235W gene taxon:4932 20021204 SGD
+SGD S000000442 YBR238C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YBR238C gene taxon:4932 20031028 SGD
+SGD S000000442 YBR238C GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YBR238C gene taxon:4932 20031028 SGD
+SGD S000000442 YBR238C GO:0005554 SGD_REF:S000069584 ND F YBR238C gene taxon:4932 20021126 SGD
+SGD S000000442 YBR238C GO:0000004 SGD_REF:S000069584 ND P YBR238C gene taxon:4932 20021126 SGD
+SGD S000000443 YBR239C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YBR239C gene taxon:4932 20031028 SGD
+SGD S000000443 YBR239C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YBR239C gene taxon:4932 20031028 SGD
+SGD S000000443 YBR239C GO:0005554 SGD_REF:S000069584 ND F YBR239C gene taxon:4932 20021126 SGD
+SGD S000000443 YBR239C GO:0000004 SGD_REF:S000069584 ND P YBR239C gene taxon:4932 20021126 SGD
+SGD S000000445 YBR241C GO:0000329 SGD_REF:S000074185|PMID:14562095 IDA C YBR241C gene taxon:4932 20031028 SGD
+SGD S000000445 YBR241C GO:0005554 SGD_REF:S000069584 ND F YBR241C gene taxon:4932 20030203 SGD
+SGD S000000445 YBR241C GO:0000004 SGD_REF:S000069584 ND P YBR241C gene taxon:4932 20030203 SGD
+SGD S000000446 YBR242W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YBR242W gene taxon:4932 20031028 SGD
+SGD S000000446 YBR242W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YBR242W gene taxon:4932 20031028 SGD
+SGD S000000446 YBR242W GO:0005554 SGD_REF:S000069584 ND F YBR242W gene taxon:4932 20030423 SGD
+SGD S000000446 YBR242W GO:0000004 SGD_REF:S000069584 ND P YBR242W gene taxon:4932 20030423 SGD
+SGD S000000450 YBR246W GO:0008372 SGD_REF:S000069584 ND C YBR246W gene taxon:4932 20021126 SGD
+SGD S000000450 YBR246W GO:0005554 SGD_REF:S000069584 ND F YBR246W gene taxon:4932 20021126 SGD
+SGD S000000450 YBR246W GO:0000004 SGD_REF:S000069584 ND P YBR246W gene taxon:4932 20021126 SGD
+SGD S000000454 YBR250W GO:0008372 SGD_REF:S000069584 ND C YBR250W gene taxon:4932 20021126 SGD
+SGD S000000454 YBR250W GO:0005554 SGD_REF:S000069584 ND F YBR250W gene taxon:4932 20021126 SGD
+SGD S000000454 YBR250W GO:0000004 SGD_REF:S000069584 ND P YBR250W gene taxon:4932 20021126 SGD
+SGD S000007649 YBR255C-A GO:0008372 SGD_REF:S000069584 ND C YBR255C-A gene taxon:4932 20010411 SGD
+SGD S000007649 YBR255C-A GO:0005554 SGD_REF:S000069584 ND F YBR255C-A gene taxon:4932 20010411 SGD
+SGD S000007649 YBR255C-A GO:0000004 SGD_REF:S000069584 ND P YBR255C-A gene taxon:4932 20010411 SGD
+SGD S000000459 YBR255W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YBR255W gene taxon:4932 20031028 SGD
+SGD S000000459 YBR255W GO:0005554 SGD_REF:S000069584 ND F YBR255W gene taxon:4932 20030423 SGD
+SGD S000000459 YBR255W GO:0000004 SGD_REF:S000069584 ND P YBR255W gene taxon:4932 20030423 SGD
+SGD S000000463 YBR259W GO:0008372 SGD_REF:S000069584 ND C YBR259W gene taxon:4932 20030423 SGD
+SGD S000000463 YBR259W GO:0005554 SGD_REF:S000069584 ND F YBR259W gene taxon:4932 20030423 SGD
+SGD S000000463 YBR259W GO:0000004 SGD_REF:S000069584 ND P YBR259W gene taxon:4932 20030423 SGD
+SGD S000000465 YBR261C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YBR261C gene taxon:4932 20031028 SGD
+SGD S000000465 YBR261C GO:0008757 SGD_REF:S000074033|PMID:12872006 ISS F YBR261C gene taxon:4932 20031001 SGD
+SGD S000000465 YBR261C GO:0000004 SGD_REF:S000069584 ND P YBR261C gene taxon:4932 20030423 SGD
+SGD S000000475 YBR271W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YBR271W gene taxon:4932 20031028 SGD
+SGD S000000475 YBR271W GO:0008757 SGD_REF:S000074033|PMID:12872006 ISS F YBR271W gene taxon:4932 20031001 SGD
+SGD S000000475 YBR271W GO:0000004 SGD_REF:S000069584 ND P YBR271W gene taxon:4932 20030203 SGD
+SGD S000000484 YBR280C GO:0008372 SGD_REF:S000069584 ND C YBR280C gene taxon:4932 20030203 SGD
+SGD S000000484 YBR280C GO:0005554 SGD_REF:S000069584 ND F YBR280C gene taxon:4932 20030203 SGD
+SGD S000000484 YBR280C GO:0000004 SGD_REF:S000069584 ND P YBR280C gene taxon:4932 20030203 SGD
+SGD S000000485 YBR281C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YBR281C gene taxon:4932 20031028 SGD
+SGD S000000485 YBR281C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YBR281C gene taxon:4932 20031028 SGD
+SGD S000000485 YBR281C GO:0005554 SGD_REF:S000069584 ND F YBR281C gene taxon:4932 20030203 SGD
+SGD S000000485 YBR281C GO:0000004 SGD_REF:S000069584 ND P YBR281C gene taxon:4932 20030203 SGD
+SGD S000000488 YBR284W GO:0008372 SGD_REF:S000069584 ND C YBR284W gene taxon:4932 20030203 SGD
+SGD S000000488 YBR284W GO:0005554 SGD_REF:S000069584 ND F YBR284W gene taxon:4932 20030203 SGD
+SGD S000000488 YBR284W GO:0000004 SGD_REF:S000069584 ND P YBR284W gene taxon:4932 20030203 SGD
+SGD S000000489 YBR285W GO:0008372 SGD_REF:S000069584 ND C YBR285W gene taxon:4932 20030203 SGD
+SGD S000000489 YBR285W GO:0005554 SGD_REF:S000069584 ND F YBR285W gene taxon:4932 20030203 SGD
+SGD S000000489 YBR285W GO:0000004 SGD_REF:S000069584 ND P YBR285W gene taxon:4932 20030203 SGD
+SGD S000028605 YBR296C-A GO:0008372 SGD_REF:S000069584 ND C YBR296C-A gene taxon:4932 20030730 SGD
+SGD S000028605 YBR296C-A GO:0005554 SGD_REF:S000069584 ND F YBR296C-A gene taxon:4932 20030730 SGD
+SGD S000028605 YBR296C-A GO:0000004 SGD_REF:S000069584 ND P YBR296C-A gene taxon:4932 20030730 SGD
+SGD S000028606 YBR298C-A GO:0008372 SGD_REF:S000069584 ND C YBR298C-A gene taxon:4932 20030730 SGD
+SGD S000028606 YBR298C-A GO:0005554 SGD_REF:S000069584 ND F YBR298C-A gene taxon:4932 20030730 SGD
+SGD S000028606 YBR298C-A GO:0000004 SGD_REF:S000069584 ND P YBR298C-A gene taxon:4932 20030730 SGD
+SGD S000007221 YCL001W-A GO:0008372 SGD_REF:S000069584 ND C YCL001W-A gene taxon:4932 20030203 SGD
+SGD S000007221 YCL001W-A GO:0005554 SGD_REF:S000069584 ND F YCL001W-A gene taxon:4932 20030203 SGD
+SGD S000007221 YCL001W-A GO:0000004 SGD_REF:S000069584 ND P YCL001W-A gene taxon:4932 20030203 SGD
+SGD S000007596 YCL001W-B GO:0008372 SGD_REF:S000069584 ND C YCL001W-B gene taxon:4932 20010226 SGD
+SGD S000007596 YCL001W-B GO:0005554 SGD_REF:S000069584 ND F YCL001W-B gene taxon:4932 20010226 SGD
+SGD S000007596 YCL001W-B GO:0000004 SGD_REF:S000069584 ND P YCL001W-B gene taxon:4932 20010226 SGD
+SGD S000000508 YCL002C GO:0008372 SGD_REF:S000069584 ND C YCL002C gene taxon:4932 20021126 SGD
+SGD S000000508 YCL002C GO:0005554 SGD_REF:S000069584 ND F YCL002C gene taxon:4932 20021126 SGD
+SGD S000000508 YCL002C GO:0000004 SGD_REF:S000069584 ND P YCL002C gene taxon:4932 20021126 SGD
+SGD S000029705 YCL012C GO:0008372 SGD_REF:S000075439|PMID:12794934 TAS C YCL012C|YCL011C-A gene taxon:4932 20040301 SGD
+SGD S000029705 YCL012C GO:0005554 SGD_REF:S000075439|PMID:12794934 TAS F YCL012C|YCL011C-A gene taxon:4932 20040301 SGD
+SGD S000029705 YCL012C GO:0000004 SGD_REF:S000075439|PMID:12794934 TAS P YCL012C|YCL011C-A gene taxon:4932 20040301 SGD
+SGD S000000524 YCL019W GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YCL019W gene taxon:4932 20030811 SGD
+SGD S000000524 YCL019W GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YCL019W gene taxon:4932 20030811 SGD
+SGD S000000524 YCL019W GO:0003887 SGD_REF:S000072465|PMID:9582191 ISS F YCL019W gene taxon:4932 20030811 SGD
+SGD S000000524 YCL019W GO:0003964 SGD_REF:S000072465|PMID:9582191 ISS F YCL019W gene taxon:4932 20030811 SGD
+SGD S000000524 YCL019W GO:0004540 SGD_REF:S000072465|PMID:9582191 ISS F YCL019W gene taxon:4932 20030811 SGD
+SGD S000000524 YCL019W GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YCL019W gene taxon:4932 20030811 SGD
+SGD S000000524 YCL019W GO:0008233 SGD_REF:S000072465|PMID:9582191 ISS F YCL019W gene taxon:4932 20030811 SGD
+SGD S000000524 YCL019W GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YCL019W gene taxon:4932 20030811 SGD
+SGD S000000525 YCL020W GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YCL020W gene taxon:4932 20030811 SGD
+SGD S000000525 YCL020W GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YCL020W gene taxon:4932 20030811 SGD
+SGD S000000525 YCL020W GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YCL020W gene taxon:4932 20030811 SGD
+SGD S000000525 YCL020W GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YCL020W gene taxon:4932 20030811 SGD
+SGD S000007549 YCL021W-A GO:0008372 SGD_REF:S000069584 ND C YCL021W-A gene taxon:4932 20010119 SGD
+SGD S000007549 YCL021W-A GO:0005554 SGD_REF:S000069584 ND F YCL021W-A gene taxon:4932 20010119 SGD
+SGD S000007549 YCL021W-A GO:0000004 SGD_REF:S000069584 ND P YCL021W-A gene taxon:4932 20010119 SGD
+SGD S000007548 YCL026C-B GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YCL026C-B|YCL027C-A gene taxon:4932 20031028 SGD
+SGD S000007548 YCL026C-B GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YCL026C-B|YCL027C-A gene taxon:4932 20031028 SGD
+SGD S000007548 YCL026C-B GO:0005554 SGD_REF:S000069584 ND F YCL026C-B|YCL027C-A gene taxon:4932 20010119 SGD
+SGD S000007548 YCL026C-B GO:0000004 SGD_REF:S000069584 ND P YCL026C-B|YCL027C-A gene taxon:4932 20010119 SGD
+SGD S000000538 YCL033C GO:0008372 SGD_REF:S000069584 ND C YCL033C|MSRB gene taxon:4932 20020405 SGD
+SGD S000000538 YCL033C GO:0000318 SGD_REF:S000069481|PMID:11929995 ISS F YCL033C|MSRB gene taxon:4932 20020408 SGD
+SGD S000000538 YCL033C GO:0006979 SGD_REF:S000069481|PMID:11929995 IEP P YCL033C|MSRB gene taxon:4932 20020405 SGD
+SGD S000000538 YCL033C GO:0006979 SGD_REF:S000069481|PMID:11929995 IMP P YCL033C|MSRB gene taxon:4932 20020405 SGD
+SGD S000000538 YCL033C GO:0006979 SGD_REF:S000069481|PMID:11929995 IGI P YCL033C|MSRB gene taxon:4932 20020405 SGD
+SGD S000000547 YCL042W GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YCL042W gene taxon:4932 20020507 SGD
+SGD S000000547 YCL042W GO:0005554 SGD_REF:S000069584 ND F YCL042W gene taxon:4932 20030203 SGD
+SGD S000000547 YCL042W GO:0000004 SGD_REF:S000069584 ND P YCL042W gene taxon:4932 20030203 SGD
+SGD S000000550 YCL045C GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YCL045C gene taxon:4932 20031028 SGD
+SGD S000000550 YCL045C GO:0005554 SGD_REF:S000069584 ND F YCL045C gene taxon:4932 20030203 SGD
+SGD S000000550 YCL045C GO:0000004 SGD_REF:S000069584 ND P YCL045C gene taxon:4932 20030203 SGD
+SGD S000000552 YCL047C GO:0008372 SGD_REF:S000069584 ND C YCL047C gene taxon:4932 20021126 SGD
+SGD S000000552 YCL047C GO:0005554 SGD_REF:S000069584 ND F YCL047C gene taxon:4932 20021126 SGD
+SGD S000000552 YCL047C GO:0000004 SGD_REF:S000069584 ND P YCL047C gene taxon:4932 20021126 SGD
+SGD S000087203 YCL048W-A GO:0008372 SGD_REF:S000069584 ND C YCL048W-A gene taxon:4932 20051114 SGD
+SGD S000087203 YCL048W-A GO:0005554 SGD_REF:S000069584 ND F YCL048W-A gene taxon:4932 20051114 SGD
+SGD S000087203 YCL048W-A GO:0000004 SGD_REF:S000069584 ND P YCL048W-A gene taxon:4932 20051114 SGD
+SGD S000000554 YCL049C GO:0005624 SGD_REF:S000075303|PMID:11935221 IDA C YCL049C gene taxon:4932 20040114 SGD
+SGD S000000554 YCL049C GO:0005554 SGD_REF:S000069584 ND F YCL049C gene taxon:4932 20021126 SGD
+SGD S000000554 YCL049C GO:0000004 SGD_REF:S000069584 ND P YCL049C gene taxon:4932 20021126 SGD
+SGD S000000561 YCL056C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YCL056C gene taxon:4932 20031028 SGD
+SGD S000000561 YCL056C GO:0005554 SGD_REF:S000069584 ND F YCL056C gene taxon:4932 20030203 SGD
+SGD S000000561 YCL056C GO:0000004 SGD_REF:S000069584 ND P YCL056C gene taxon:4932 20030203 SGD
+SGD S000007547 YCL057C-A GO:0008372 SGD_REF:S000069584 ND C YCL057C-A gene taxon:4932 20020325 SGD
+SGD S000007547 YCL057C-A GO:0005554 SGD_REF:S000069584 ND F YCL057C-A gene taxon:4932 20020325 SGD
+SGD S000007547 YCL057C-A GO:0000004 SGD_REF:S000069584 ND P YCL057C-A gene taxon:4932 20020325 SGD
+SGD S000028518 YCL058W-A GO:0008372 SGD_REF:S000069584 ND C YCL058W-A gene taxon:4932 20030730 SGD
+SGD S000028518 YCL058W-A GO:0005554 SGD_REF:S000069584 ND F YCL058W-A gene taxon:4932 20030730 SGD
+SGD S000028518 YCL058W-A GO:0000004 SGD_REF:S000069584 ND P YCL058W-A gene taxon:4932 20030730 SGD
+SGD S000000573 YCL068C GO:0008372 SGD_REF:S000069584 ND C YCL068C gene taxon:4932 20021126 SGD
+SGD S000000573 YCL068C GO:0005554 SGD_REF:S000069584 ND F YCL068C gene taxon:4932 20021126 SGD
+SGD S000000573 YCL068C GO:0000004 SGD_REF:S000069584 ND P YCL068C gene taxon:4932 20021126 SGD
+SGD S000000575 YCL073C GO:0016020 SGD_REF:S000049483|PMID:10744769 ISS C YCL073C gene taxon:4932 20021120 SGD
+SGD S000000575 YCL073C GO:0005215 SGD_REF:S000049483|PMID:10744769 ISS F YCL073C gene taxon:4932 20021120 SGD
+SGD S000000575 YCL073C GO:0006810 SGD_REF:S000049483|PMID:10744769 ISS P YCL073C gene taxon:4932 20021120 SGD
+SGD S000000579 YCL074W GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YCL074W gene taxon:4932 20030811 SGD
+SGD S000000579 YCL074W GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YCL074W gene taxon:4932 20030811 SGD
+SGD S000000579 YCL074W GO:0003887 SGD_REF:S000072465|PMID:9582191 ISS F YCL074W gene taxon:4932 20030811 SGD
+SGD S000000579 YCL074W GO:0003964 SGD_REF:S000072465|PMID:9582191 ISS F YCL074W gene taxon:4932 20030811 SGD
+SGD S000000579 YCL074W GO:0004540 SGD_REF:S000072465|PMID:9582191 ISS F YCL074W gene taxon:4932 20030811 SGD
+SGD S000000579 YCL074W GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YCL074W gene taxon:4932 20030811 SGD
+SGD S000000579 YCL074W GO:0008233 SGD_REF:S000072465|PMID:9582191 ISS F YCL074W gene taxon:4932 20030811 SGD
+SGD S000000579 YCL074W GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YCL074W gene taxon:4932 20030811 SGD
+SGD S000000580 YCL075W GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YCL075W gene taxon:4932 20030811 SGD
+SGD S000000580 YCL075W GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YCL075W gene taxon:4932 20030811 SGD
+SGD S000000580 YCL075W GO:0003887 SGD_REF:S000072465|PMID:9582191 ISS F YCL075W gene taxon:4932 20030811 SGD
+SGD S000000580 YCL075W GO:0003964 SGD_REF:S000072465|PMID:9582191 ISS F YCL075W gene taxon:4932 20030811 SGD
+SGD S000000580 YCL075W GO:0004540 SGD_REF:S000072465|PMID:9582191 ISS F YCL075W gene taxon:4932 20030811 SGD
+SGD S000000580 YCL075W GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YCL075W gene taxon:4932 20030811 SGD
+SGD S000000580 YCL075W GO:0008233 SGD_REF:S000072465|PMID:9582191 ISS F YCL075W gene taxon:4932 20030811 SGD
+SGD S000000580 YCL075W GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YCL075W gene taxon:4932 20030811 SGD
+SGD S000000600 YCR007C GO:0008372 SGD_REF:S000069584 ND C YCR007C gene taxon:4932 20021223 SGD
+SGD S000000600 YCR007C GO:0005554 SGD_REF:S000069584 ND F YCR007C gene taxon:4932 20021223 SGD
+SGD S000000600 YCR007C GO:0000004 SGD_REF:S000069584 ND P YCR007C gene taxon:4932 20021223 SGD
+SGD S000000608 YCR015C GO:0008372 SGD_REF:S000069584 ND C YCR015C gene taxon:4932 20021126 SGD
+SGD S000000608 YCR015C GO:0005554 SGD_REF:S000069584 ND F YCR015C gene taxon:4932 20021126 SGD
+SGD S000000608 YCR015C GO:0000004 SGD_REF:S000069584 ND P YCR015C gene taxon:4932 20021126 SGD
+SGD S000000609 YCR016W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YCR016W gene taxon:4932 20031028 SGD
+SGD S000000609 YCR016W GO:0005730 SGD_REF:S000074185|PMID:14562095 IDA C YCR016W gene taxon:4932 20031028 SGD
+SGD S000000609 YCR016W GO:0005554 SGD_REF:S000069584 ND F YCR016W gene taxon:4932 20021126 SGD
+SGD S000000609 YCR016W GO:0000004 SGD_REF:S000069584 ND P YCR016W gene taxon:4932 20021126 SGD
+SGD S000000617 YCR023C GO:0008372 SGD_REF:S000069584 ND C YCR023C gene taxon:4932 20021120 SGD
+SGD S000000617 YCR023C GO:0005554 SGD_REF:S000069584 ND F YCR023C gene taxon:4932 20021120 SGD
+SGD S000000617 YCR023C GO:0000004 SGD_REF:S000069584 ND P YCR023C gene taxon:4932 20021120 SGD
+SGD S000028818 YCR024C-B GO:0008372 SGD_REF:S000069584 ND C YCR024C-B gene taxon:4932 20030730 SGD
+SGD S000028818 YCR024C-B GO:0005554 SGD_REF:S000069584 ND F YCR024C-B gene taxon:4932 20030730 SGD
+SGD S000028818 YCR024C-B GO:0000004 SGD_REF:S000069584 ND P YCR024C-B gene taxon:4932 20030730 SGD
+SGD S000000639 YCR043C GO:0005794 SGD_REF:S000074185|PMID:14562095 IDA C YCR043C gene taxon:4932 20031028 SGD
+SGD S000000639 YCR043C GO:0005554 SGD_REF:S000069584 ND F YCR043C gene taxon:4932 20030203 SGD
+SGD S000000639 YCR043C GO:0000004 SGD_REF:S000069584 ND P YCR043C gene taxon:4932 20030203 SGD
+SGD S000000641 YCR045C GO:0008372 SGD_REF:S000069584 ND C YCR045C gene taxon:4932 20021126 SGD
+SGD S000000641 YCR045C GO:0008236 SGD_REF:S000072463|PMID:10592175 ISS F YCR045C gene taxon:4932 20030204 SGD
+SGD S000000641 YCR045C GO:0000004 SGD_REF:S000069584 ND P YCR045C gene taxon:4932 20021126 SGD
+SGD S000000647 YCR051W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YCR051W gene taxon:4932 20031028 SGD
+SGD S000000647 YCR051W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YCR051W gene taxon:4932 20031028 SGD
+SGD S000000647 YCR051W GO:0005554 SGD_REF:S000069584 ND F YCR051W gene taxon:4932 20021126 SGD
+SGD S000000647 YCR051W GO:0000004 SGD_REF:S000069584 ND P YCR051W gene taxon:4932 20021126 SGD
+SGD S000000657 YCR061W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YCR061W|YCR062W gene taxon:4932 20031028 SGD
+SGD S000000657 YCR061W GO:0005554 SGD_REF:S000069584 ND F YCR061W|YCR062W gene taxon:4932 20030205 SGD
+SGD S000000657 YCR061W GO:0000004 SGD_REF:S000069584 ND P YCR061W|YCR062W gene taxon:4932 20030205 SGD
+SGD S000028519 YCR075W-A GO:0008372 SGD_REF:S000069584 ND C YCR075W-A gene taxon:4932 20030730 SGD
+SGD S000028519 YCR075W-A GO:0005554 SGD_REF:S000069584 ND F YCR075W-A gene taxon:4932 20030730 SGD
+SGD S000028519 YCR075W-A GO:0000004 SGD_REF:S000069584 ND P YCR075W-A gene taxon:4932 20030730 SGD
+SGD S000000672 YCR076C GO:0008372 SGD_REF:S000069584 ND C YCR076C gene taxon:4932 20021126 SGD
+SGD S000000672 YCR076C GO:0005554 SGD_REF:S000069584 ND F YCR076C gene taxon:4932 20021126 SGD
+SGD S000000672 YCR076C GO:0000004 SGD_REF:S000069584 ND P YCR076C gene taxon:4932 20021126 SGD
+SGD S000007223 YCR087C-A GO:0005730 SGD_REF:S000074185|PMID:14562095 IDA C YCR087C-A gene taxon:4932 20031028 SGD
+SGD S000007223 YCR087C-A GO:0005554 SGD_REF:S000069584 ND F YCR087C-A gene taxon:4932 20021126 SGD
+SGD S000007223 YCR087C-A GO:0000004 SGD_REF:S000069584 ND P YCR087C-A gene taxon:4932 20021126 SGD
+SGD S000000686 YCR090C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YCR090C gene taxon:4932 20031028 SGD
+SGD S000000686 YCR090C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YCR090C gene taxon:4932 20031028 SGD
+SGD S000000686 YCR090C GO:0005554 SGD_REF:S000069584 ND F YCR090C gene taxon:4932 20030203 SGD
+SGD S000000686 YCR090C GO:0000004 SGD_REF:S000069584 ND P YCR090C gene taxon:4932 20030203 SGD
+SGD S000029724 YCR095W-A GO:0008372 SGD_REF:S000069584 ND C YCR095W-A gene taxon:4932 20040903 SGD
+SGD S000029724 YCR095W-A GO:0005554 SGD_REF:S000069584 ND F YCR095W-A gene taxon:4932 20040903 SGD
+SGD S000029724 YCR095W-A GO:0000004 SGD_REF:S000069584 ND P YCR095W-A gene taxon:4932 20040903 SGD
+SGD S000000696 YCR099C GO:0008372 SGD_REF:S000069584 ND C YCR099C gene taxon:4932 20021126 SGD
+SGD S000000696 YCR099C GO:0005554 SGD_REF:S000069584 ND F YCR099C gene taxon:4932 20021126 SGD
+SGD S000000696 YCR099C GO:0000004 SGD_REF:S000069584 ND P YCR099C gene taxon:4932 20021126 SGD
+SGD S000000697 YCR100C GO:0008372 SGD_REF:S000069584 ND C YCR100C gene taxon:4932 20021126 SGD
+SGD S000000697 YCR100C GO:0005554 SGD_REF:S000069584 ND F YCR100C gene taxon:4932 20021126 SGD
+SGD S000000697 YCR100C GO:0000004 SGD_REF:S000069584 ND P YCR100C gene taxon:4932 20021126 SGD
+SGD S000000698 YCR101C GO:0005624 SGD_REF:S000075303|PMID:11935221 IDA C YCR101C gene taxon:4932 20040114 SGD
+SGD S000000698 YCR101C GO:0005554 SGD_REF:S000069584 ND F YCR101C gene taxon:4932 20030203 SGD
+SGD S000000698 YCR101C GO:0000004 SGD_REF:S000069584 ND P YCR101C gene taxon:4932 20030203 SGD
+SGD S000000699 YCR102C GO:0008372 SGD_REF:S000069584 ND C YCR102C gene taxon:4932 20030205 SGD
+SGD S000000699 YCR102C GO:0005554 SGD_REF:S000069584 ND F YCR102C gene taxon:4932 20030205 SGD
+SGD S000000699 YCR102C GO:0046688 SGD_REF:S000081637|PMID:15886332 IMP P YCR102C gene taxon:4932 20060428 SGD
+SGD S000028536 YCR108C GO:0008372 SGD_REF:S000069584 ND C YCR108C gene taxon:4932 20030730 SGD
+SGD S000028536 YCR108C GO:0005554 SGD_REF:S000069584 ND F YCR108C gene taxon:4932 20030730 SGD
+SGD S000028536 YCR108C GO:0000004 SGD_REF:S000069584 ND P YCR108C gene taxon:4932 20030730 SGD
+SGD S000113557 YDL007C-A GO:0008372 SGD_REF:S000069584 ND C YDL007C-A gene taxon:4932 20051117 SGD
+SGD S000113557 YDL007C-A GO:0005554 SGD_REF:S000069584 ND F YDL007C-A gene taxon:4932 20051117 SGD
+SGD S000113557 YDL007C-A GO:0000004 SGD_REF:S000069584 ND P YDL007C-A gene taxon:4932 20051117 SGD
+SGD S000002168 YDL010W GO:0000324 SGD_REF:S000074185|PMID:14562095 IDA C YDL010W gene taxon:4932 20031028 SGD
+SGD S000002168 YDL010W GO:0005554 SGD_REF:S000069584 ND F YDL010W gene taxon:4932 20030423 SGD
+SGD S000002168 YDL010W GO:0000004 SGD_REF:S000069584 ND P YDL010W gene taxon:4932 20030423 SGD
+SGD S000002170 YDL012C GO:0005886 SGD_REF:S000072636|PMID:12514182 IDA C YDL012C gene taxon:4932 20031014 SGD
+SGD S000002170 YDL012C GO:0005554 SGD_REF:S000069584 ND F YDL012C gene taxon:4932 20021223 SGD
+SGD S000002170 YDL012C GO:0000004 SGD_REF:S000069584 ND P YDL012C gene taxon:4932 20021223 SGD
+SGD S000002183 YDL025C GO:0008372 SGD_REF:S000069584 ND C YDL025C gene taxon:4932 20021120 SGD
+SGD S000002183 YDL025C GO:0004672 SGD_REF:S000058030|PMID:9020587 ISS F YDL025C gene taxon:4932 20030204 SGD
+SGD S000002183 YDL025C GO:0000004 SGD_REF:S000069584 ND P YDL025C gene taxon:4932 20021120 SGD
+SGD S000002185 YDL027C GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YDL027C gene taxon:4932 20031028 SGD
+SGD S000002185 YDL027C GO:0005554 SGD_REF:S000069584 ND F YDL027C gene taxon:4932 20030203 SGD
+SGD S000002185 YDL027C GO:0000004 SGD_REF:S000069584 ND P YDL027C gene taxon:4932 20030203 SGD
+SGD S000002196 YDL038C GO:0008372 SGD_REF:S000069584 ND C YDL038C gene taxon:4932 20030203 SGD
+SGD S000002196 YDL038C GO:0005554 SGD_REF:S000069584 ND F YDL038C gene taxon:4932 20030203 SGD
+SGD S000002196 YDL038C GO:0000004 SGD_REF:S000069584 ND P YDL038C gene taxon:4932 20030203 SGD
+SGD S000002215 YDL057W GO:0008372 SGD_REF:S000069584 ND C YDL057W gene taxon:4932 20030422 SGD
+SGD S000002215 YDL057W GO:0005554 SGD_REF:S000069584 ND F YDL057W gene taxon:4932 20030422 SGD
+SGD S000002215 YDL057W GO:0000004 SGD_REF:S000069584 ND P YDL057W gene taxon:4932 20030422 SGD
+SGD S000002221 YDL063C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YDL063C gene taxon:4932 20031028 SGD
+SGD S000002221 YDL063C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDL063C gene taxon:4932 20031028 SGD
+SGD S000002221 YDL063C GO:0005554 SGD_REF:S000069584 ND F YDL063C gene taxon:4932 20030422 SGD
+SGD S000002221 YDL063C GO:0000004 SGD_REF:S000069584 ND P YDL063C gene taxon:4932 20030422 SGD
+SGD S000002231 YDL073W GO:0008372 SGD_REF:S000069584 ND C YDL073W gene taxon:4932 20030422 SGD
+SGD S000002231 YDL073W GO:0005554 SGD_REF:S000069584 ND F YDL073W gene taxon:4932 20030422 SGD
+SGD S000002231 YDL073W GO:0000004 SGD_REF:S000069584 ND P YDL073W gene taxon:4932 20030422 SGD
+SGD S000007588 YDL085C-A GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YDL085C-A gene taxon:4932 20031028 SGD
+SGD S000007588 YDL085C-A GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDL085C-A gene taxon:4932 20031028 SGD
+SGD S000007588 YDL085C-A GO:0005554 SGD_REF:S000069584 ND F YDL085C-A gene taxon:4932 20010130 SGD
+SGD S000007588 YDL085C-A GO:0000004 SGD_REF:S000069584 ND P YDL085C-A gene taxon:4932 20010130 SGD
+SGD S000002244 YDL086W GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YDL086W gene taxon:4932 20020507 SGD
+SGD S000002244 YDL086W GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YDL086W gene taxon:4932 20040928 SGD
+SGD S000002244 YDL086W GO:0008806 SGD_REF:S000072463|PMID:10592175 ISS F YDL086W gene taxon:4932 20030204 SGD
+SGD S000002244 YDL086W GO:0000004 SGD_REF:S000069584 ND P YDL086W gene taxon:4932 20021002 SGD
+SGD S000002247 YDL089W GO:0008372 SGD_REF:S000069584 ND C YDL089W gene taxon:4932 20021126 SGD
+SGD S000002247 YDL089W GO:0005554 SGD_REF:S000069584 ND F YDL089W gene taxon:4932 20021126 SGD
+SGD S000002247 YDL089W GO:0000004 SGD_REF:S000069584 ND P YDL089W gene taxon:4932 20021126 SGD
+SGD S000002267 YDL109C GO:0008372 SGD_REF:S000069584 ND C YDL109C gene taxon:4932 20021223 SGD
+SGD S000002267 YDL109C GO:0005554 SGD_REF:S000069584 ND F YDL109C gene taxon:4932 20060505 SGD
+SGD S000002267 YDL109C GO:0006629 SGD_REF:S000062226|PMID:10341423 IMP P YDL109C gene taxon:4932 20021223 SGD
+SGD S000002272 YDL114W GO:0008372 SGD_REF:S000069584 ND C YDL114W gene taxon:4932 20030203 SGD
+SGD S000002272 YDL114W GO:0005554 SGD_REF:S000069584 ND F YDL114W gene taxon:4932 20030203 SGD
+SGD S000002272 YDL114W GO:0000004 SGD_REF:S000069584 ND P YDL114W gene taxon:4932 20030203 SGD
+SGD S000002277 YDL119C GO:0005743 SGD_REF:S000049213|PMID:10930523 ISS C YDL119C gene taxon:4932 20021017 SGD
+SGD S000002277 YDL119C GO:0005215 SGD_REF:S000049213|PMID:10930523 ISS F YDL119C gene taxon:4932 20021017 SGD
+SGD S000002277 YDL119C GO:0006810 SGD_REF:S000049213|PMID:10930523 ISS P YDL119C gene taxon:4932 20021017 SGD
+SGD S000002279 YDL121C GO:0005783 SGD_REF:S000056415|PMID:10684247 IDA C YDL121C gene taxon:4932 20010301 SGD
+SGD S000002279 YDL121C GO:0005554 SGD_REF:S000069584 ND F YDL121C gene taxon:4932 20010119 SGD
+SGD S000002279 YDL121C GO:0000004 SGD_REF:S000069584 ND P YDL121C gene taxon:4932 20010119 SGD
+SGD S000002282 YDL124W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YDL124W gene taxon:4932 20031028 SGD
+SGD S000002282 YDL124W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDL124W gene taxon:4932 20031028 SGD
+SGD S000002282 YDL124W GO:0051268 SGD_REF:S000079744|PMID:15564669 IDA F YDL124W gene taxon:4932 20041130 SGD
+SGD S000002282 YDL124W GO:0051269 SGD_REF:S000079744|PMID:15564669 IDA F YDL124W gene taxon:4932 20041130 SGD
+SGD S000002282 YDL124W GO:0008152 SGD_REF:S000079744|PMID:15564669 IC GO:0051268|GO:0051269 P YDL124W gene taxon:4932 20041130 SGD
+SGD S000002287 YDL129W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YDL129W gene taxon:4932 20031028 SGD
+SGD S000002287 YDL129W GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YDL129W gene taxon:4932 20020507 SGD
+SGD S000002287 YDL129W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDL129W gene taxon:4932 20031028 SGD
+SGD S000002287 YDL129W GO:0005554 SGD_REF:S000069584 ND F YDL129W gene taxon:4932 20030203 SGD
+SGD S000002287 YDL129W GO:0000004 SGD_REF:S000069584 ND P YDL129W gene taxon:4932 20030203 SGD
+SGD S000002291 YDL133W GO:0008372 SGD_REF:S000069584 ND C YDL133W gene taxon:4932 20030203 SGD
+SGD S000002291 YDL133W GO:0005554 SGD_REF:S000069584 ND F YDL133W gene taxon:4932 20030203 SGD
+SGD S000002291 YDL133W GO:0000004 SGD_REF:S000069584 ND P YDL133W gene taxon:4932 20030203 SGD
+SGD S000002303 YDL144C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YDL144C gene taxon:4932 20031028 SGD
+SGD S000002303 YDL144C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDL144C gene taxon:4932 20031028 SGD
+SGD S000002303 YDL144C GO:0005554 SGD_REF:S000069584 ND F YDL144C gene taxon:4932 20030203 SGD
+SGD S000002303 YDL144C GO:0000004 SGD_REF:S000069584 ND P YDL144C gene taxon:4932 20030203 SGD
+SGD S000002315 YDL156W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YDL156W gene taxon:4932 20031028 SGD
+SGD S000002315 YDL156W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDL156W gene taxon:4932 20031028 SGD
+SGD S000002315 YDL156W GO:0005554 SGD_REF:S000069584 ND F YDL156W gene taxon:4932 20030203 SGD
+SGD S000002315 YDL156W GO:0000004 SGD_REF:S000069584 ND P YDL156W gene taxon:4932 20030203 SGD
+SGD S000002316 YDL157C GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YDL157C gene taxon:4932 20031028 SGD
+SGD S000002316 YDL157C GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YDL157C gene taxon:4932 20040924 SGD
+SGD S000002316 YDL157C GO:0005554 SGD_REF:S000069584 ND F YDL157C gene taxon:4932 20021126 SGD
+SGD S000002316 YDL157C GO:0000004 SGD_REF:S000069584 ND P YDL157C gene taxon:4932 20021126 SGD
+SGD S000007599 YDL159W-A GO:0008372 SGD_REF:S000069584 ND C YDL159W-A|YDL159W-B gene taxon:4932 20010226 SGD
+SGD S000007599 YDL159W-A GO:0005554 SGD_REF:S000069584 ND F YDL159W-A|YDL159W-B gene taxon:4932 20010226 SGD
+SGD S000007599 YDL159W-A GO:0000004 SGD_REF:S000069584 ND P YDL159W-A|YDL159W-B gene taxon:4932 20010226 SGD
+SGD S000028520 YDL160C-A GO:0008372 SGD_REF:S000069584 ND C YDL160C-A gene taxon:4932 20030730 SGD
+SGD S000028520 YDL160C-A GO:0005554 SGD_REF:S000069584 ND F YDL160C-A gene taxon:4932 20030730 SGD
+SGD S000028520 YDL160C-A GO:0000004 SGD_REF:S000069584 ND P YDL160C-A gene taxon:4932 20030730 SGD
+SGD S000002332 YDL173W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDL173W gene taxon:4932 20031028 SGD
+SGD S000002332 YDL173W GO:0005554 SGD_REF:S000069584 ND F YDL173W gene taxon:4932 20021126 SGD
+SGD S000002332 YDL173W GO:0000004 SGD_REF:S000069584 ND P YDL173W gene taxon:4932 20021126 SGD
+SGD S000002335 YDL176W GO:0008372 SGD_REF:S000069584 ND C YDL176W gene taxon:4932 20021126 SGD
+SGD S000002335 YDL176W GO:0005554 SGD_REF:S000069584 ND F YDL176W gene taxon:4932 20021126 SGD
+SGD S000002335 YDL176W GO:0000004 SGD_REF:S000069584 ND P YDL176W gene taxon:4932 20021126 SGD
+SGD S000002336 YDL177C GO:0008372 SGD_REF:S000069584 ND C YDL177C gene taxon:4932 20021120 SGD
+SGD S000002336 YDL177C GO:0005554 SGD_REF:S000069584 ND F YDL177C gene taxon:4932 20021120 SGD
+SGD S000002336 YDL177C GO:0000004 SGD_REF:S000069584 ND P YDL177C gene taxon:4932 20021120 SGD
+SGD S000002339 YDL180W GO:0000324 SGD_REF:S000074185|PMID:14562095 IDA C YDL180W gene taxon:4932 20031028 SGD
+SGD S000002339 YDL180W GO:0005554 SGD_REF:S000069584 ND F YDL180W gene taxon:4932 20021126 SGD
+SGD S000002339 YDL180W GO:0000004 SGD_REF:S000069584 ND P YDL180W gene taxon:4932 20021126 SGD
+SGD S000002342 YDL183C GO:0008372 SGD_REF:S000069584 ND C YDL183C gene taxon:4932 20030203 SGD
+SGD S000002342 YDL183C GO:0005554 SGD_REF:S000069584 ND F YDL183C gene taxon:4932 20030203 SGD
+SGD S000002342 YDL183C GO:0000004 SGD_REF:S000069584 ND P YDL183C gene taxon:4932 20030203 SGD
+SGD S000002345 YDL186W GO:0008372 SGD_REF:S000069584 ND C YDL186W gene taxon:4932 20030203 SGD
+SGD S000002345 YDL186W GO:0005554 SGD_REF:S000069584 ND F YDL186W gene taxon:4932 20030203 SGD
+SGD S000002345 YDL186W GO:0000004 SGD_REF:S000069584 ND P YDL186W gene taxon:4932 20030203 SGD
+SGD S000002358 YDL199C GO:0008372 SGD_REF:S000069584 ND C YDL199C gene taxon:4932 20030203 SGD
+SGD S000002358 YDL199C GO:0005554 SGD_REF:S000069584 ND F YDL199C gene taxon:4932 20030203 SGD
+SGD S000002358 YDL199C GO:0000004 SGD_REF:S000069584 ND P YDL199C gene taxon:4932 20030203 SGD
+SGD S000002365 YDL206W GO:0008372 SGD_REF:S000069584 ND C YDL206W gene taxon:4932 20030203 SGD
+SGD S000002365 YDL206W GO:0005554 SGD_REF:S000069584 ND F YDL206W gene taxon:4932 20030203 SGD
+SGD S000002365 YDL206W GO:0000004 SGD_REF:S000069584 ND P YDL206W gene taxon:4932 20030203 SGD
+SGD S000002370 YDL211C GO:0000324 SGD_REF:S000074185|PMID:14562095 IDA C YDL211C gene taxon:4932 20031028 SGD
+SGD S000002370 YDL211C GO:0005554 SGD_REF:S000069584 ND F YDL211C gene taxon:4932 20030203 SGD
+SGD S000002370 YDL211C GO:0000004 SGD_REF:S000069584 ND P YDL211C gene taxon:4932 20030203 SGD
+SGD S000002377 YDL218W GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YDL218W gene taxon:4932 20020507 SGD
+SGD S000002377 YDL218W GO:0005554 SGD_REF:S000069584 ND F YDL218W gene taxon:4932 20030203 SGD
+SGD S000002377 YDL218W GO:0000004 SGD_REF:S000069584 ND P YDL218W gene taxon:4932 20030203 SGD
+SGD S000002392 YDL233W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YDL233W gene taxon:4932 20031028 SGD
+SGD S000002392 YDL233W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDL233W gene taxon:4932 20031028 SGD
+SGD S000002392 YDL233W GO:0005554 SGD_REF:S000069584 ND F YDL233W gene taxon:4932 20021126 SGD
+SGD S000002392 YDL233W GO:0000004 SGD_REF:S000069584 ND P YDL233W gene taxon:4932 20021126 SGD
+SGD S000002396 YDL237W GO:0008372 SGD_REF:S000069584 ND C YDL237W gene taxon:4932 20030421 SGD
+SGD S000002396 YDL237W GO:0005554 SGD_REF:S000069584 ND F YDL237W gene taxon:4932 20030421 SGD
+SGD S000002396 YDL237W GO:0000004 SGD_REF:S000069584 ND P YDL237W gene taxon:4932 20030421 SGD
+SGD S000002400 YDL241W GO:0008372 SGD_REF:S000069584 ND C YDL241W gene taxon:4932 20021126 SGD
+SGD S000002400 YDL241W GO:0005554 SGD_REF:S000069584 ND F YDL241W gene taxon:4932 20021126 SGD
+SGD S000002400 YDL241W GO:0000004 SGD_REF:S000069584 ND P YDL241W gene taxon:4932 20021126 SGD
+SGD S000028819 YDR003W-A GO:0008372 SGD_REF:S000069584 ND C YDR003W-A gene taxon:4932 20030730 SGD
+SGD S000028819 YDR003W-A GO:0005554 SGD_REF:S000069584 ND F YDR003W-A gene taxon:4932 20030730 SGD
+SGD S000028819 YDR003W-A GO:0000004 SGD_REF:S000069584 ND P YDR003W-A gene taxon:4932 20030730 SGD
+SGD S000002425 YDR018C GO:0008372 SGD_REF:S000069584 ND C YDR018C gene taxon:4932 20030423 SGD
+SGD S000002425 YDR018C GO:0008415 SGD_REF:S000065692|PMID:9259571 ISS F YDR018C gene taxon:4932 20030423 SGD
+SGD S000002425 YDR018C GO:0008654 SGD_REF:S000065692|PMID:9259571 ISS P YDR018C gene taxon:4932 20030423 SGD
+SGD S000002427 YDR020C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YDR020C gene taxon:4932 20031028 SGD
+SGD S000002427 YDR020C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDR020C gene taxon:4932 20031028 SGD
+SGD S000002427 YDR020C GO:0005554 SGD_REF:S000069584 ND F YDR020C gene taxon:4932 20030423 SGD
+SGD S000002427 YDR020C GO:0000004 SGD_REF:S000069584 ND P YDR020C gene taxon:4932 20030423 SGD
+SGD S000002433 YDR026C GO:0005634 SGD_REF:S000081155|PMID:15343339 IC GO:0003677 C YDR026C gene taxon:4932 20050331 SGD
+SGD S000002433 YDR026C GO:0005730 SGD_REF:S000074185|PMID:14562095 IDA C YDR026C gene taxon:4932 20031028 SGD
+SGD S000002433 YDR026C GO:0003677 SGD_REF:S000081155|PMID:15343339 IPI F YDR026C gene taxon:4932 20050331 SGD
+SGD S000002433 YDR026C GO:0000004 SGD_REF:S000069584 ND P YDR026C gene taxon:4932 20030203 SGD
+SGD S000002438 YDR031W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YDR031W gene taxon:4932 20031028 SGD
+SGD S000002438 YDR031W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDR031W gene taxon:4932 20031028 SGD
+SGD S000002438 YDR031W GO:0005554 SGD_REF:S000069584 ND F YDR031W gene taxon:4932 20021126 SGD
+SGD S000002438 YDR031W GO:0000004 SGD_REF:S000069584 ND P YDR031W gene taxon:4932 20021126 SGD
+SGD S000007233 YDR034C-A GO:0008372 SGD_REF:S000069584 ND C YDR034C-A gene taxon:4932 20021126 SGD
+SGD S000007233 YDR034C-A GO:0005554 SGD_REF:S000069584 ND F YDR034C-A gene taxon:4932 20021126 SGD
+SGD S000007233 YDR034C-A GO:0000004 SGD_REF:S000069584 ND P YDR034C-A gene taxon:4932 20021126 SGD
+SGD S000007344 YDR034C-C GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YDR034C-C gene taxon:4932 20030811 SGD
+SGD S000007344 YDR034C-C GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YDR034C-C gene taxon:4932 20030811 SGD
+SGD S000007344 YDR034C-C GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YDR034C-C gene taxon:4932 20030811 SGD
+SGD S000007344 YDR034C-C GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YDR034C-C gene taxon:4932 20030811 SGD
+SGD S000007345 YDR034C-D GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YDR034C-D gene taxon:4932 20030811 SGD
+SGD S000007345 YDR034C-D GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YDR034C-D gene taxon:4932 20030811 SGD
+SGD S000007345 YDR034C-D GO:0003887 SGD_REF:S000072465|PMID:9582191 ISS F YDR034C-D gene taxon:4932 20030811 SGD
+SGD S000007345 YDR034C-D GO:0003964 SGD_REF:S000072465|PMID:9582191 ISS F YDR034C-D gene taxon:4932 20030811 SGD
+SGD S000007345 YDR034C-D GO:0004540 SGD_REF:S000072465|PMID:9582191 ISS F YDR034C-D gene taxon:4932 20030811 SGD
+SGD S000007345 YDR034C-D GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YDR034C-D gene taxon:4932 20030811 SGD
+SGD S000007345 YDR034C-D GO:0008233 SGD_REF:S000072465|PMID:9582191 ISS F YDR034C-D gene taxon:4932 20030811 SGD
+SGD S000007345 YDR034C-D GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YDR034C-D gene taxon:4932 20030811 SGD
+SGD S000007234 YDR034W-B GO:0008372 SGD_REF:S000069584 ND C YDR034W-B gene taxon:4932 20021126 SGD
+SGD S000007234 YDR034W-B GO:0005554 SGD_REF:S000069584 ND F YDR034W-B gene taxon:4932 20021126 SGD
+SGD S000007234 YDR034W-B GO:0000004 SGD_REF:S000069584 ND P YDR034W-B gene taxon:4932 20021126 SGD
+SGD S000002449 YDR042C GO:0008372 SGD_REF:S000069584 ND C YDR042C gene taxon:4932 20021126 SGD
+SGD S000002449 YDR042C GO:0005554 SGD_REF:S000069584 ND F YDR042C gene taxon:4932 20021126 SGD
+SGD S000002449 YDR042C GO:0000004 SGD_REF:S000069584 ND P YDR042C gene taxon:4932 20021126 SGD
+SGD S000002456 YDR049W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDR049W gene taxon:4932 20031028 SGD
+SGD S000002456 YDR049W GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YDR049W gene taxon:4932 20040928 SGD
+SGD S000002456 YDR049W GO:0005554 SGD_REF:S000069584 ND F YDR049W gene taxon:4932 20021126 SGD
+SGD S000002456 YDR049W GO:0000004 SGD_REF:S000069584 ND P YDR049W gene taxon:4932 20021126 SGD
+SGD S000002458 YDR051C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YDR051C gene taxon:4932 20031028 SGD
+SGD S000002458 YDR051C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDR051C gene taxon:4932 20031028 SGD
+SGD S000002458 YDR051C GO:0005554 SGD_REF:S000069584 ND F YDR051C gene taxon:4932 20030203 SGD
+SGD S000002458 YDR051C GO:0000004 SGD_REF:S000069584 ND P YDR051C gene taxon:4932 20030203 SGD
+SGD S000002463 YDR056C GO:0005624 SGD_REF:S000075303|PMID:11935221 IDA C YDR056C gene taxon:4932 20040114 SGD
+SGD S000002463 YDR056C GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YDR056C gene taxon:4932 20031028 SGD
+SGD S000002463 YDR056C GO:0005554 SGD_REF:S000069584 ND F YDR056C gene taxon:4932 20021126 SGD
+SGD S000002463 YDR056C GO:0000004 SGD_REF:S000069584 ND P YDR056C gene taxon:4932 20021126 SGD
+SGD S000002468 YDR061W GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YDR061W gene taxon:4932 20031028 SGD
+SGD S000002468 YDR061W GO:0042626 SGD_REF:S000044365|PMID:10581358 ISS F YDR061W gene taxon:4932 20030424 SGD
+SGD S000002468 YDR061W GO:0000004 SGD_REF:S000069584 ND P YDR061W gene taxon:4932 20030424 SGD
+SGD S000002470 YDR063W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YDR063W gene taxon:4932 20031028 SGD
+SGD S000002470 YDR063W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDR063W gene taxon:4932 20031028 SGD
+SGD S000002470 YDR063W GO:0005554 SGD_REF:S000069584 ND F YDR063W gene taxon:4932 20021126 SGD
+SGD S000002470 YDR063W GO:0000004 SGD_REF:S000069584 ND P YDR063W gene taxon:4932 20021126 SGD
+SGD S000002472 YDR065W GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YDR065W gene taxon:4932 20031028 SGD
+SGD S000002472 YDR065W GO:0005554 SGD_REF:S000069584 ND F YDR065W gene taxon:4932 20060424 SGD
+SGD S000002472 YDR065W GO:0007035 SGD_REF:S000086702|PMID:16168084 IMP P YDR065W gene taxon:4932 20060424 SGD
+SGD S000002473 YDR066C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDR066C gene taxon:4932 20031028 SGD
+SGD S000002473 YDR066C GO:0005554 SGD_REF:S000069584 ND F YDR066C gene taxon:4932 20030203 SGD
+SGD S000002473 YDR066C GO:0000004 SGD_REF:S000069584 ND P YDR066C gene taxon:4932 20030203 SGD
+SGD S000002496 YDR089W GO:0016020 SGD_REF:S000040168|PMID:10480897 ISS C YDR089W gene taxon:4932 20030424 SGD
+SGD S000002496 YDR089W GO:0005554 SGD_REF:S000069584 ND F YDR089W gene taxon:4932 20030424 SGD
+SGD S000002496 YDR089W GO:0016044 SGD_REF:S000040168|PMID:10480897 ISS P YDR089W gene taxon:4932 20030424 SGD
+SGD S000002497 YDR090C GO:0016021 SGD_REF:S000072825|PMID:12524434 ISS C YDR090C gene taxon:4932 20030409 SGD
+SGD S000002497 YDR090C GO:0005554 SGD_REF:S000069584 ND F YDR090C gene taxon:4932 20021126 SGD
+SGD S000002497 YDR090C GO:0000004 SGD_REF:S000069584 ND P YDR090C gene taxon:4932 20021126 SGD
+SGD S000007390 YDR098C-A GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YDR098C-A gene taxon:4932 20030811 SGD
+SGD S000007390 YDR098C-A GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YDR098C-A gene taxon:4932 20030811 SGD
+SGD S000007390 YDR098C-A GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YDR098C-A gene taxon:4932 20030811 SGD
+SGD S000007390 YDR098C-A GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YDR098C-A gene taxon:4932 20030811 SGD
+SGD S000007391 YDR098C-B GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YDR098C-B gene taxon:4932 20030811 SGD
+SGD S000007391 YDR098C-B GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YDR098C-B gene taxon:4932 20030811 SGD
+SGD S000007391 YDR098C-B GO:0003887 SGD_REF:S000072465|PMID:9582191 ISS F YDR098C-B gene taxon:4932 20030811 SGD
+SGD S000007391 YDR098C-B GO:0003964 SGD_REF:S000072465|PMID:9582191 ISS F YDR098C-B gene taxon:4932 20030811 SGD
+SGD S000007391 YDR098C-B GO:0004540 SGD_REF:S000072465|PMID:9582191 ISS F YDR098C-B gene taxon:4932 20030811 SGD
+SGD S000007391 YDR098C-B GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YDR098C-B gene taxon:4932 20030811 SGD
+SGD S000007391 YDR098C-B GO:0008233 SGD_REF:S000072465|PMID:9582191 ISS F YDR098C-B gene taxon:4932 20030811 SGD
+SGD S000007391 YDR098C-B GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YDR098C-B gene taxon:4932 20030811 SGD
+SGD S000002514 YDR107C GO:0005624 SGD_REF:S000045474|PMID:9729438 ISS SGD:S000004073 C YDR107C gene taxon:4932 20030204 SGD
+SGD S000002514 YDR107C GO:0005554 SGD_REF:S000069584 ND F YDR107C gene taxon:4932 20030203 SGD
+SGD S000002514 YDR107C GO:0000004 SGD_REF:S000069584 ND P YDR107C gene taxon:4932 20030203 SGD
+SGD S000002516 YDR109C GO:0008372 SGD_REF:S000069584 ND C YDR109C gene taxon:4932 20021126 SGD
+SGD S000002516 YDR109C GO:0016301 SGD_REF:S000072463|PMID:10592175 ISS F YDR109C gene taxon:4932 20030211 SGD
+SGD S000002516 YDR109C GO:0000004 SGD_REF:S000069584 ND P YDR109C gene taxon:4932 20021126 SGD
+SGD S000002522 YDR115W GO:0005762 SGD_REF:S000071753|PMID:12392552 ISS C YDR115W gene taxon:4932 20040203 SGD
+SGD S000002522 YDR115W GO:0003735 SGD_REF:S000060148|PMID:10929718 ISS F YDR115W gene taxon:4932 20020806 SGD
+SGD S000002522 YDR115W GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P YDR115W gene taxon:4932 20060227 SGD
+SGD S000002522 YDR115W GO:0009060 SGD_REF:S000060148|PMID:10929718 IMP P YDR115W gene taxon:4932 20020806 SGD
+SGD S000002522 YDR115W GO:0009060 SGD_REF:S000060148|PMID:10929718 IEP P YDR115W gene taxon:4932 20020806 SGD
+SGD S000002526 YDR119W GO:0000329 SGD_REF:S000074185|PMID:14562095 IDA C YDR119W gene taxon:4932 20031028 SGD
+SGD S000002526 YDR119W GO:0005554 SGD_REF:S000069584 ND F YDR119W gene taxon:4932 20021126 SGD
+SGD S000002526 YDR119W GO:0000004 SGD_REF:S000069584 ND P YDR119W gene taxon:4932 20021126 SGD
+SGD S000113555 YDR119W-A GO:0008372 SGD_REF:S000069584 ND C YDR119W-A gene taxon:4932 20051118 SGD
+SGD S000113555 YDR119W-A GO:0005554 SGD_REF:S000069584 ND F YDR119W-A gene taxon:4932 20051118 SGD
+SGD S000113555 YDR119W-A GO:0000004 SGD_REF:S000069584 ND P YDR119W-A gene taxon:4932 20051118 SGD
+SGD S000002531 YDR124W GO:0008372 SGD_REF:S000069584 ND C YDR124W gene taxon:4932 20030424 SGD
+SGD S000002531 YDR124W GO:0005554 SGD_REF:S000069584 ND F YDR124W gene taxon:4932 20030424 SGD
+SGD S000002531 YDR124W GO:0000004 SGD_REF:S000069584 ND P YDR124W gene taxon:4932 20030424 SGD
+SGD S000002535 YDR128W GO:0000329 SGD_REF:S000074185|PMID:14562095 IDA C YDR128W gene taxon:4932 20031028 SGD
+SGD S000002535 YDR128W GO:0005554 SGD_REF:S000069584 ND F YDR128W gene taxon:4932 20030203 SGD
+SGD S000002535 YDR128W GO:0000004 SGD_REF:S000069584 ND P YDR128W gene taxon:4932 20030203 SGD
+SGD S000002538 YDR131C GO:0000151 SGD_REF:S000058340|PMID:9635407 ISS C YDR131C gene taxon:4932 20030205 SGD
+SGD S000002538 YDR131C GO:0005515 SGD_REF:S000058340|PMID:9635407 ISS F YDR131C gene taxon:4932 20030205 SGD
+SGD S000002538 YDR131C GO:0006511 SGD_REF:S000058340|PMID:9635407 ISS P YDR131C gene taxon:4932 20030205 SGD
+SGD S000002539 YDR132C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YDR132C gene taxon:4932 20031028 SGD
+SGD S000002539 YDR132C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDR132C gene taxon:4932 20031028 SGD
+SGD S000002539 YDR132C GO:0005554 SGD_REF:S000069584 ND F YDR132C gene taxon:4932 20030203 SGD
+SGD S000002539 YDR132C GO:0000004 SGD_REF:S000069584 ND P YDR132C gene taxon:4932 20030203 SGD
+SGD S000002541 YDR134C GO:0009277 SGD_REF:S000040179|PMID:10383953 IDA C YDR134C gene taxon:4932 20020617 SGD
+SGD S000002541 YDR134C GO:0005554 SGD_REF:S000069584 ND F YDR134C gene taxon:4932 20030429 SGD
+SGD S000002541 YDR134C GO:0000004 SGD_REF:S000069584 ND P YDR134C gene taxon:4932 20030429 SGD
+SGD S000002568 YDR161W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YDR161W gene taxon:4932 20031028 SGD
+SGD S000002568 YDR161W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDR161W gene taxon:4932 20031028 SGD
+SGD S000002568 YDR161W GO:0005554 SGD_REF:S000069584 ND F YDR161W gene taxon:4932 20021120 SGD
+SGD S000002568 YDR161W GO:0000004 SGD_REF:S000069584 ND P YDR161W gene taxon:4932 20021120 SGD
+SGD S000028538 YDR169C-A GO:0008372 SGD_REF:S000069584 ND C YDR169C-A gene taxon:4932 20030730 SGD
+SGD S000028538 YDR169C-A GO:0005554 SGD_REF:S000069584 ND F YDR169C-A gene taxon:4932 20030730 SGD
+SGD S000028538 YDR169C-A GO:0000004 SGD_REF:S000069584 ND P YDR169C-A gene taxon:4932 20030730 SGD
+SGD S000007227 YDR170W-A GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YDR170W-A gene taxon:4932 20030811 SGD
+SGD S000007227 YDR170W-A GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YDR170W-A gene taxon:4932 20030811 SGD
+SGD S000007227 YDR170W-A GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YDR170W-A gene taxon:4932 20030811 SGD
+SGD S000007227 YDR170W-A GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YDR170W-A gene taxon:4932 20030811 SGD
+SGD S000002587 YDR179W-A GO:0008372 SGD_REF:S000069584 ND C YDR179W-A gene taxon:4932 20021126 SGD
+SGD S000002587 YDR179W-A GO:0005554 SGD_REF:S000069584 ND F YDR179W-A gene taxon:4932 20021126 SGD
+SGD S000002587 YDR179W-A GO:0000004 SGD_REF:S000069584 ND P YDR179W-A gene taxon:4932 20021126 SGD
+SGD S000028539 YDR182W-A GO:0008372 SGD_REF:S000069584 ND C YDR182W-A gene taxon:4932 20030730 SGD
+SGD S000028539 YDR182W-A GO:0005554 SGD_REF:S000069584 ND F YDR182W-A gene taxon:4932 20030730 SGD
+SGD S000028539 YDR182W-A GO:0000004 SGD_REF:S000069584 ND P YDR182W-A gene taxon:4932 20030730 SGD
+SGD S000002593 YDR185C GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YDR185C gene taxon:4932 20031028 SGD
+SGD S000002593 YDR185C GO:0005554 SGD_REF:S000069584 ND F YDR185C gene taxon:4932 20030203 SGD
+SGD S000002593 YDR185C GO:0000004 SGD_REF:S000069584 ND P YDR185C gene taxon:4932 20030203 SGD
+SGD S000002594 YDR186C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDR186C gene taxon:4932 20031028 SGD
+SGD S000002594 YDR186C GO:0005554 SGD_REF:S000069584 ND F YDR186C gene taxon:4932 20021126 SGD
+SGD S000002594 YDR186C GO:0000004 SGD_REF:S000069584 ND P YDR186C gene taxon:4932 20021126 SGD
+SGD S000028541 YDR194W-A GO:0008372 SGD_REF:S000069584 ND C YDR194W-A gene taxon:4932 20030730 SGD
+SGD S000028541 YDR194W-A GO:0005554 SGD_REF:S000069584 ND F YDR194W-A gene taxon:4932 20030730 SGD
+SGD S000028541 YDR194W-A GO:0000004 SGD_REF:S000069584 ND P YDR194W-A gene taxon:4932 20030730 SGD
+SGD S000002604 YDR196C GO:0005635 SGD_REF:S000075214|PMID:14690591 IDA C YDR196C gene taxon:4932 20040105 SGD
+SGD S000002604 YDR196C GO:0005783 SGD_REF:S000075214|PMID:14690591 IDA C YDR196C gene taxon:4932 20040105 SGD
+SGD S000002604 YDR196C GO:0004140 SGD_REF:S000072463|PMID:10592175 ISS F YDR196C gene taxon:4932 20030619 SGD
+SGD S000002604 YDR196C GO:0004140 SGD_REF:S000075214|PMID:14690591 ISS F YDR196C gene taxon:4932 20040105 SGD
+SGD S000002604 YDR196C GO:0015937 SGD_REF:S000072463|PMID:10592175 ISS P YDR196C gene taxon:4932 20030619 SGD
+SGD S000007409 YDR210C-C GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YDR210C-C|YDR210W-C gene taxon:4932 20030811 SGD
+SGD S000007409 YDR210C-C GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YDR210C-C|YDR210W-C gene taxon:4932 20030811 SGD
+SGD S000007409 YDR210C-C GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YDR210C-C|YDR210W-C gene taxon:4932 20030811 SGD
+SGD S000007409 YDR210C-C GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YDR210C-C|YDR210W-C gene taxon:4932 20030811 SGD
+SGD S000007410 YDR210C-D GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YDR210C-D|YDR210W-D gene taxon:4932 20030811 SGD
+SGD S000007410 YDR210C-D GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YDR210C-D|YDR210W-D gene taxon:4932 20030811 SGD
+SGD S000007410 YDR210C-D GO:0003887 SGD_REF:S000072465|PMID:9582191 ISS F YDR210C-D|YDR210W-D gene taxon:4932 20030811 SGD
+SGD S000007410 YDR210C-D GO:0003964 SGD_REF:S000072465|PMID:9582191 ISS F YDR210C-D|YDR210W-D gene taxon:4932 20030811 SGD
+SGD S000007410 YDR210C-D GO:0004540 SGD_REF:S000072465|PMID:9582191 ISS F YDR210C-D|YDR210W-D gene taxon:4932 20030811 SGD
+SGD S000007410 YDR210C-D GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YDR210C-D|YDR210W-D gene taxon:4932 20030811 SGD
+SGD S000007410 YDR210C-D GO:0008233 SGD_REF:S000072465|PMID:9582191 ISS F YDR210C-D|YDR210W-D gene taxon:4932 20030811 SGD
+SGD S000007410 YDR210C-D GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YDR210C-D|YDR210W-D gene taxon:4932 20030811 SGD
+SGD S000002618 YDR210W GO:0008372 SGD_REF:S000069584 ND C YDR210W gene taxon:4932 20021126 SGD
+SGD S000002618 YDR210W GO:0005554 SGD_REF:S000069584 ND F YDR210W gene taxon:4932 20021126 SGD
+SGD S000002618 YDR210W GO:0000004 SGD_REF:S000069584 ND P YDR210W gene taxon:4932 20021126 SGD
+SGD S000007392 YDR210W-A GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YDR210W-A gene taxon:4932 20030811 SGD
+SGD S000007392 YDR210W-A GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YDR210W-A gene taxon:4932 20030811 SGD
+SGD S000007392 YDR210W-A GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YDR210W-A gene taxon:4932 20030811 SGD
+SGD S000007392 YDR210W-A GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YDR210W-A gene taxon:4932 20030811 SGD
+SGD S000007393 YDR210W-B GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YDR210W-B gene taxon:4932 20030811 SGD
+SGD S000007393 YDR210W-B GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YDR210W-B gene taxon:4932 20030811 SGD
+SGD S000007393 YDR210W-B GO:0003887 SGD_REF:S000072465|PMID:9582191 ISS F YDR210W-B gene taxon:4932 20030811 SGD
+SGD S000007393 YDR210W-B GO:0003964 SGD_REF:S000072465|PMID:9582191 ISS F YDR210W-B gene taxon:4932 20030811 SGD
+SGD S000007393 YDR210W-B GO:0004540 SGD_REF:S000072465|PMID:9582191 ISS F YDR210W-B gene taxon:4932 20030811 SGD
+SGD S000007393 YDR210W-B GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YDR210W-B gene taxon:4932 20030811 SGD
+SGD S000007393 YDR210W-B GO:0008233 SGD_REF:S000072465|PMID:9582191 ISS F YDR210W-B gene taxon:4932 20030811 SGD
+SGD S000007393 YDR210W-B GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YDR210W-B gene taxon:4932 20030811 SGD
+SGD S000002630 YDR222W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDR222W gene taxon:4932 20031028 SGD
+SGD S000002630 YDR222W GO:0005554 SGD_REF:S000069584 ND F YDR222W gene taxon:4932 20021126 SGD
+SGD S000002630 YDR222W GO:0000004 SGD_REF:S000069584 ND P YDR222W gene taxon:4932 20021126 SGD
+SGD S000002647 YDR239C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDR239C gene taxon:4932 20031028 SGD
+SGD S000002647 YDR239C GO:0005554 SGD_REF:S000069584 ND F YDR239C gene taxon:4932 20021126 SGD
+SGD S000002647 YDR239C GO:0000004 SGD_REF:S000069584 ND P YDR239C gene taxon:4932 20021126 SGD
+SGD S000028542 YDR246W-A GO:0008372 SGD_REF:S000069584 ND C YDR246W-A gene taxon:4932 20030730 SGD
+SGD S000028542 YDR246W-A GO:0005554 SGD_REF:S000069584 ND F YDR246W-A gene taxon:4932 20030730 SGD
+SGD S000028542 YDR246W-A GO:0000004 SGD_REF:S000069584 ND P YDR246W-A gene taxon:4932 20030730 SGD
+SGD S000002656 YDR248C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDR248C gene taxon:4932 20031028 SGD
+SGD S000002656 YDR248C GO:0005554 SGD_REF:S000069584 ND F YDR248C gene taxon:4932 20021126 SGD
+SGD S000002656 YDR248C GO:0000004 SGD_REF:S000069584 ND P YDR248C gene taxon:4932 20021126 SGD
+SGD S000002657 YDR249C GO:0008372 SGD_REF:S000069584 ND C YDR249C gene taxon:4932 20021126 SGD
+SGD S000002657 YDR249C GO:0005554 SGD_REF:S000069584 ND F YDR249C gene taxon:4932 20021126 SGD
+SGD S000002657 YDR249C GO:0000004 SGD_REF:S000069584 ND P YDR249C gene taxon:4932 20021126 SGD
+SGD S000007394 YDR261C-C GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YDR261C-C gene taxon:4932 20030811 SGD
+SGD S000007394 YDR261C-C GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YDR261C-C gene taxon:4932 20030811 SGD
+SGD S000007394 YDR261C-C GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YDR261C-C gene taxon:4932 20030811 SGD
+SGD S000007394 YDR261C-C GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YDR261C-C gene taxon:4932 20030811 SGD
+SGD S000007395 YDR261C-D GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YDR261C-D gene taxon:4932 20030811 SGD
+SGD S000007395 YDR261C-D GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YDR261C-D gene taxon:4932 20030811 SGD
+SGD S000007395 YDR261C-D GO:0003887 SGD_REF:S000072465|PMID:9582191 ISS F YDR261C-D gene taxon:4932 20030811 SGD
+SGD S000007395 YDR261C-D GO:0003964 SGD_REF:S000072465|PMID:9582191 ISS F YDR261C-D gene taxon:4932 20030811 SGD
+SGD S000007395 YDR261C-D GO:0004540 SGD_REF:S000072465|PMID:9582191 ISS F YDR261C-D gene taxon:4932 20030811 SGD
+SGD S000007395 YDR261C-D GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YDR261C-D gene taxon:4932 20030811 SGD
+SGD S000007395 YDR261C-D GO:0008233 SGD_REF:S000072465|PMID:9582191 ISS F YDR261C-D gene taxon:4932 20030811 SGD
+SGD S000007395 YDR261C-D GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YDR261C-D gene taxon:4932 20030811 SGD
+SGD S000007396 YDR261W-A GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YDR261W-A gene taxon:4932 20030811 SGD
+SGD S000007396 YDR261W-A GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YDR261W-A gene taxon:4932 20030811 SGD
+SGD S000007396 YDR261W-A GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YDR261W-A gene taxon:4932 20030811 SGD
+SGD S000007396 YDR261W-A GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YDR261W-A gene taxon:4932 20030811 SGD
+SGD S000007397 YDR261W-B GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YDR261W-B gene taxon:4932 20030811 SGD
+SGD S000007397 YDR261W-B GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YDR261W-B gene taxon:4932 20030811 SGD
+SGD S000007397 YDR261W-B GO:0003887 SGD_REF:S000072465|PMID:9582191 ISS F YDR261W-B gene taxon:4932 20030811 SGD
+SGD S000007397 YDR261W-B GO:0003964 SGD_REF:S000072465|PMID:9582191 ISS F YDR261W-B gene taxon:4932 20030811 SGD
+SGD S000007397 YDR261W-B GO:0004540 SGD_REF:S000072465|PMID:9582191 ISS F YDR261W-B gene taxon:4932 20030811 SGD
+SGD S000007397 YDR261W-B GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YDR261W-B gene taxon:4932 20030811 SGD
+SGD S000007397 YDR261W-B GO:0008233 SGD_REF:S000072465|PMID:9582191 ISS F YDR261W-B gene taxon:4932 20030811 SGD
+SGD S000007397 YDR261W-B GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YDR261W-B gene taxon:4932 20030811 SGD
+SGD S000002670 YDR262W GO:0000324 SGD_REF:S000074185|PMID:14562095 IDA C YDR262W gene taxon:4932 20031028 SGD
+SGD S000002670 YDR262W GO:0005554 SGD_REF:S000069584 ND F YDR262W gene taxon:4932 20030203 SGD
+SGD S000002670 YDR262W GO:0000004 SGD_REF:S000069584 ND P YDR262W gene taxon:4932 20030203 SGD
+SGD S000002674 YDR266C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDR266C gene taxon:4932 20031028 SGD
+SGD S000002674 YDR266C GO:0005554 SGD_REF:S000069584 ND F YDR266C gene taxon:4932 20021126 SGD
+SGD S000002674 YDR266C GO:0000004 SGD_REF:S000069584 ND P YDR266C gene taxon:4932 20021126 SGD
+SGD S000002690 YDR282C GO:0008372 SGD_REF:S000069584 ND C YDR282C gene taxon:4932 20021126 SGD
+SGD S000002690 YDR282C GO:0005554 SGD_REF:S000069584 ND F YDR282C gene taxon:4932 20021126 SGD
+SGD S000002690 YDR282C GO:0000004 SGD_REF:S000069584 ND P YDR282C gene taxon:4932 20021126 SGD
+SGD S000002694 YDR286C GO:0008372 SGD_REF:S000069584 ND C YDR286C gene taxon:4932 20021126 SGD
+SGD S000002694 YDR286C GO:0005554 SGD_REF:S000069584 ND F YDR286C gene taxon:4932 20021126 SGD
+SGD S000002694 YDR286C GO:0000004 SGD_REF:S000069584 ND P YDR286C gene taxon:4932 20021126 SGD
+SGD S000002695 YDR287W GO:0008372 SGD_REF:S000069584 ND C YDR287W gene taxon:4932 20030325 SGD
+SGD S000002695 YDR287W GO:0008934 SGD_REF:S000044239|PMID:10096091 IDA F YDR287W gene taxon:4932 20030325 SGD
+SGD S000002695 YDR287W GO:0008934 SGD_REF:S000044239|PMID:10096091 ISS F YDR287W gene taxon:4932 20030325 SGD
+SGD S000002695 YDR287W GO:0046855 SGD_REF:S000044239|PMID:10096091 IDA P YDR287W gene taxon:4932 20050331 SGD
+SGD S000002714 YDR306C GO:0000151 SGD_REF:S000058340|PMID:9635407 ISS C YDR306C gene taxon:4932 20030205 SGD
+SGD S000002714 YDR306C GO:0005515 SGD_REF:S000058340|PMID:9635407 ISS F YDR306C gene taxon:4932 20030205 SGD
+SGD S000002714 YDR306C GO:0006511 SGD_REF:S000058340|PMID:9635407 ISS P YDR306C gene taxon:4932 20030205 SGD
+SGD S000002715 YDR307W GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YDR307W gene taxon:4932 20031028 SGD
+SGD S000002715 YDR307W GO:0005554 SGD_REF:S000069584 ND F YDR307W gene taxon:4932 20030203 SGD
+SGD S000002715 YDR307W GO:0000004 SGD_REF:S000069584 ND P YDR307W gene taxon:4932 20030203 SGD
+SGD S000007398 YDR316W-A GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YDR316W-A gene taxon:4932 20030811 SGD
+SGD S000007398 YDR316W-A GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YDR316W-A gene taxon:4932 20030811 SGD
+SGD S000007398 YDR316W-A GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YDR316W-A gene taxon:4932 20030811 SGD
+SGD S000007398 YDR316W-A GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YDR316W-A gene taxon:4932 20030811 SGD
+SGD S000007399 YDR316W-B GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YDR316W-B gene taxon:4932 20030811 SGD
+SGD S000007399 YDR316W-B GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YDR316W-B gene taxon:4932 20030811 SGD
+SGD S000007399 YDR316W-B GO:0003887 SGD_REF:S000072465|PMID:9582191 ISS F YDR316W-B gene taxon:4932 20030811 SGD
+SGD S000007399 YDR316W-B GO:0003964 SGD_REF:S000072465|PMID:9582191 ISS F YDR316W-B gene taxon:4932 20030811 SGD
+SGD S000007399 YDR316W-B GO:0004540 SGD_REF:S000072465|PMID:9582191 ISS F YDR316W-B gene taxon:4932 20030811 SGD
+SGD S000007399 YDR316W-B GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YDR316W-B gene taxon:4932 20030811 SGD
+SGD S000007399 YDR316W-B GO:0008233 SGD_REF:S000072465|PMID:9582191 ISS F YDR316W-B gene taxon:4932 20030811 SGD
+SGD S000007399 YDR316W-B GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YDR316W-B gene taxon:4932 20030811 SGD
+SGD S000002727 YDR319C GO:0008372 SGD_REF:S000069584 ND C YDR319C gene taxon:4932 20021126 SGD
+SGD S000002727 YDR319C GO:0005554 SGD_REF:S000069584 ND F YDR319C gene taxon:4932 20021126 SGD
+SGD S000002727 YDR319C GO:0000004 SGD_REF:S000069584 ND P YDR319C gene taxon:4932 20021126 SGD
+SGD S000002734 YDR326C GO:0008372 SGD_REF:S000069584 ND C YDR326C gene taxon:4932 20021126 SGD
+SGD S000002734 YDR326C GO:0005554 SGD_REF:S000069584 ND F YDR326C gene taxon:4932 20021126 SGD
+SGD S000002734 YDR326C GO:0000004 SGD_REF:S000069584 ND P YDR326C gene taxon:4932 20021126 SGD
+SGD S000002741 YDR333C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDR333C gene taxon:4932 20031028 SGD
+SGD S000002741 YDR333C GO:0005554 SGD_REF:S000069584 ND F YDR333C gene taxon:4932 20030203 SGD
+SGD S000002741 YDR333C GO:0000004 SGD_REF:S000069584 ND P YDR333C gene taxon:4932 20030203 SGD
+SGD S000002744 YDR336W GO:0008372 SGD_REF:S000069584 ND C YDR336W gene taxon:4932 20021126 SGD
+SGD S000002744 YDR336W GO:0005554 SGD_REF:S000069584 ND F YDR336W gene taxon:4932 20021126 SGD
+SGD S000002744 YDR336W GO:0000004 SGD_REF:S000069584 ND P YDR336W gene taxon:4932 20021126 SGD
+SGD S000002746 YDR338C GO:0008372 SGD_REF:S000069584 ND C YDR338C gene taxon:4932 20021126 SGD
+SGD S000002746 YDR338C GO:0005554 SGD_REF:S000069584 ND F YDR338C gene taxon:4932 20021126 SGD
+SGD S000002746 YDR338C GO:0000004 SGD_REF:S000069584 ND P YDR338C gene taxon:4932 20021126 SGD
+SGD S000002749 YDR341C GO:0005737 SGD_REF:S000058442|PMID:9622124 IC C YDR341C|ArgRS|RRS1 gene taxon:4932 20021205 SGD
+SGD S000002749 YDR341C GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YDR341C|ArgRS|RRS1 gene taxon:4932 20040928 SGD
+SGD S000002749 YDR341C GO:0004814 SGD_REF:S000058442|PMID:9622124 IDA F YDR341C|ArgRS|RRS1 gene taxon:4932 20010301 SGD
+SGD S000002749 YDR341C GO:0006412 SGD_REF:S000058442|PMID:9622124 IDA P YDR341C|ArgRS|RRS1 gene taxon:4932 20010301 SGD
+SGD S000002756 YDR348C GO:0005935 SGD_REF:S000074185|PMID:14562095 IDA C YDR348C gene taxon:4932 20031028 SGD
+SGD S000002756 YDR348C GO:0005554 SGD_REF:S000069584 ND F YDR348C gene taxon:4932 20021126 SGD
+SGD S000002756 YDR348C GO:0000004 SGD_REF:S000069584 ND P YDR348C gene taxon:4932 20021126 SGD
+SGD S000002760 YDR352W GO:0000329 SGD_REF:S000074185|PMID:14562095 IDA C YDR352W gene taxon:4932 20031028 SGD
+SGD S000002760 YDR352W GO:0005554 SGD_REF:S000069584 ND F YDR352W gene taxon:4932 20021126 SGD
+SGD S000002760 YDR352W GO:0000004 SGD_REF:S000069584 ND P YDR352W gene taxon:4932 20021126 SGD
+SGD S000002765 YDR357C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDR357C gene taxon:4932 20031028 SGD
+SGD S000002765 YDR357C GO:0005554 SGD_REF:S000069584 ND F YDR357C gene taxon:4932 20021126 SGD
+SGD S000002765 YDR357C GO:0000004 SGD_REF:S000069584 ND P YDR357C gene taxon:4932 20021126 SGD
+SGD S000007400 YDR365W-A GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YDR365W-A gene taxon:4932 20030811 SGD
+SGD S000007400 YDR365W-A GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YDR365W-A gene taxon:4932 20030811 SGD
+SGD S000007400 YDR365W-A GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YDR365W-A gene taxon:4932 20030811 SGD
+SGD S000007400 YDR365W-A GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YDR365W-A gene taxon:4932 20030811 SGD
+SGD S000007401 YDR365W-B GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YDR365W-B gene taxon:4932 20030811 SGD
+SGD S000007401 YDR365W-B GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YDR365W-B gene taxon:4932 20030811 SGD
+SGD S000007401 YDR365W-B GO:0003887 SGD_REF:S000072465|PMID:9582191 ISS F YDR365W-B gene taxon:4932 20030811 SGD
+SGD S000007401 YDR365W-B GO:0003964 SGD_REF:S000072465|PMID:9582191 ISS F YDR365W-B gene taxon:4932 20030811 SGD
+SGD S000007401 YDR365W-B GO:0004540 SGD_REF:S000072465|PMID:9582191 ISS F YDR365W-B gene taxon:4932 20030811 SGD
+SGD S000007401 YDR365W-B GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YDR365W-B gene taxon:4932 20030811 SGD
+SGD S000007401 YDR365W-B GO:0008233 SGD_REF:S000072465|PMID:9582191 ISS F YDR365W-B gene taxon:4932 20030811 SGD
+SGD S000007401 YDR365W-B GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YDR365W-B gene taxon:4932 20030811 SGD
+SGD S000002774 YDR366C GO:0008372 SGD_REF:S000069584 ND C YDR366C gene taxon:4932 20021126 SGD
+SGD S000002774 YDR366C GO:0005554 SGD_REF:S000069584 ND F YDR366C gene taxon:4932 20021126 SGD
+SGD S000002774 YDR366C GO:0000004 SGD_REF:S000069584 ND P YDR366C gene taxon:4932 20021126 SGD
+SGD S000002775 YDR367W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDR367W gene taxon:4932 20031028 SGD
+SGD S000002775 YDR367W GO:0005794 SGD_REF:S000075214|PMID:14690591 IDA C YDR367W gene taxon:4932 20040105 SGD
+SGD S000002775 YDR367W GO:0005554 SGD_REF:S000069584 ND F YDR367W gene taxon:4932 20030422 SGD
+SGD S000002775 YDR367W GO:0000004 SGD_REF:S000069584 ND P YDR367W gene taxon:4932 20030422 SGD
+SGD S000002778 YDR370C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDR370C gene taxon:4932 20031028 SGD
+SGD S000002778 YDR370C GO:0005554 SGD_REF:S000069584 ND F YDR370C gene taxon:4932 20030424 SGD
+SGD S000002778 YDR370C GO:0000004 SGD_REF:S000069584 ND P YDR370C gene taxon:4932 20030424 SGD
+SGD S000002782 YDR374C GO:0008372 SGD_REF:S000069584 ND C YDR374C gene taxon:4932 20021126 SGD
+SGD S000002782 YDR374C GO:0005554 SGD_REF:S000069584 ND F YDR374C gene taxon:4932 20021126 SGD
+SGD S000002782 YDR374C GO:0000004 SGD_REF:S000069584 ND P YDR374C gene taxon:4932 20021126 SGD
+SGD S000113553 YDR374W-A GO:0008372 SGD_REF:S000069584 ND C YDR374W-A gene taxon:4932 20051116 SGD
+SGD S000113553 YDR374W-A GO:0005554 SGD_REF:S000069584 ND F YDR374W-A gene taxon:4932 20051116 SGD
+SGD S000113553 YDR374W-A GO:0000004 SGD_REF:S000069584 ND P YDR374W-A gene taxon:4932 20051116 SGD
+SGD S000007605 YDR379C-A GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YDR379C-A gene taxon:4932 20031028 SGD
+SGD S000007605 YDR379C-A GO:0005554 SGD_REF:S000069584 ND F YDR379C-A gene taxon:4932 20010226 SGD
+SGD S000007605 YDR379C-A GO:0000004 SGD_REF:S000069584 ND P YDR379C-A gene taxon:4932 20010226 SGD
+SGD S000007650 YDR381C-A GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C YDR381C-A gene taxon:4932 20060317 SGD
+SGD S000007650 YDR381C-A GO:0005554 SGD_REF:S000069584 ND F YDR381C-A gene taxon:4932 20010411 SGD
+SGD S000007650 YDR381C-A GO:0000004 SGD_REF:S000069584 ND P YDR381C-A gene taxon:4932 20010411 SGD
+SGD S000002795 YDR387C GO:0008372 SGD_REF:S000069584 ND C YDR387C gene taxon:4932 20030203 SGD
+SGD S000002795 YDR387C GO:0015646 SGD_REF:S000056317|PMID:10618490 TAS F YDR387C gene taxon:4932 20030304 SGD
+SGD S000002795 YDR387C GO:0000004 SGD_REF:S000069584 ND P YDR387C gene taxon:4932 20030203 SGD
+SGD S000002799 YDR391C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YDR391C gene taxon:4932 20031028 SGD
+SGD S000002799 YDR391C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDR391C gene taxon:4932 20031028 SGD
+SGD S000002799 YDR391C GO:0005554 SGD_REF:S000069584 ND F YDR391C gene taxon:4932 20030203 SGD
+SGD S000002799 YDR391C GO:0000004 SGD_REF:S000069584 ND P YDR391C gene taxon:4932 20030203 SGD
+SGD S000002823 YDR415C GO:0008372 SGD_REF:S000069584 ND C YDR415C gene taxon:4932 20021126 SGD
+SGD S000002823 YDR415C GO:0005554 SGD_REF:S000069584 ND F YDR415C gene taxon:4932 20021126 SGD
+SGD S000002823 YDR415C GO:0000004 SGD_REF:S000069584 ND P YDR415C gene taxon:4932 20021126 SGD
+SGD S000002836 YDR428C GO:0008372 SGD_REF:S000069584 ND C YDR428C gene taxon:4932 20021126 SGD
+SGD S000002836 YDR428C GO:0005554 SGD_REF:S000069584 ND F YDR428C gene taxon:4932 20021126 SGD
+SGD S000002836 YDR428C GO:0000004 SGD_REF:S000069584 ND P YDR428C gene taxon:4932 20021126 SGD
+SGD S000002846 YDR438W GO:0016021 SGD_REF:S000072825|PMID:12524434 ISS C YDR438W gene taxon:4932 20030409 SGD
+SGD S000002846 YDR438W GO:0005554 SGD_REF:S000069584 ND F YDR438W gene taxon:4932 20021126 SGD
+SGD S000002846 YDR438W GO:0000004 SGD_REF:S000069584 ND P YDR438W gene taxon:4932 20021126 SGD
+SGD S000002852 YDR444W GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YDR444W gene taxon:4932 20020507 SGD
+SGD S000002852 YDR444W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDR444W gene taxon:4932 20031028 SGD
+SGD S000002852 YDR444W GO:0005554 SGD_REF:S000069584 ND F YDR444W gene taxon:4932 20030203 SGD
+SGD S000002852 YDR444W GO:0000004 SGD_REF:S000069584 ND P YDR444W gene taxon:4932 20030203 SGD
+SGD S000002866 YDR458C GO:0008372 SGD_REF:S000069584 ND C YDR458C gene taxon:4932 20021126 SGD
+SGD S000002866 YDR458C GO:0005554 SGD_REF:S000069584 ND F YDR458C gene taxon:4932 20021126 SGD
+SGD S000002866 YDR458C GO:0000004 SGD_REF:S000069584 ND P YDR458C gene taxon:4932 20021126 SGD
+SGD S000087209 YDR461C-A GO:0008372 SGD_REF:S000069584 ND C YDR461C-A gene taxon:4932 20051115 SGD
+SGD S000087209 YDR461C-A GO:0005554 SGD_REF:S000069584 ND F YDR461C-A gene taxon:4932 20051115 SGD
+SGD S000087209 YDR461C-A GO:0000004 SGD_REF:S000069584 ND P YDR461C-A gene taxon:4932 20051115 SGD
+SGD S000002884 YDR476C GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YDR476C gene taxon:4932 20031028 SGD
+SGD S000002884 YDR476C GO:0005554 SGD_REF:S000069584 ND F YDR476C gene taxon:4932 20021126 SGD
+SGD S000002884 YDR476C GO:0000004 SGD_REF:S000069584 ND P YDR476C gene taxon:4932 20021126 SGD
+SGD S000002914 YDR506C GO:0008372 SGD_REF:S000069584 ND C YDR506C gene taxon:4932 20021126 SGD
+SGD S000002914 YDR506C GO:0005554 SGD_REF:S000069584 ND F YDR506C gene taxon:4932 20021126 SGD
+SGD S000002914 YDR506C GO:0000004 SGD_REF:S000069584 ND P YDR506C gene taxon:4932 20021126 SGD
+SGD S000002922 YDR514C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YDR514C gene taxon:4932 20031028 SGD
+SGD S000002922 YDR514C GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YDR514C gene taxon:4932 20031028 SGD
+SGD S000002922 YDR514C GO:0005554 SGD_REF:S000069584 ND F YDR514C gene taxon:4932 20021126 SGD
+SGD S000002922 YDR514C GO:0000004 SGD_REF:S000069584 ND P YDR514C gene taxon:4932 20021126 SGD
+SGD S000002928 YDR520C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YDR520C gene taxon:4932 20031028 SGD
+SGD S000002928 YDR520C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDR520C gene taxon:4932 20031028 SGD
+SGD S000002928 YDR520C GO:0005554 SGD_REF:S000069584 ND F YDR520C gene taxon:4932 20021126 SGD
+SGD S000002928 YDR520C GO:0000004 SGD_REF:S000069584 ND P YDR520C gene taxon:4932 20021126 SGD
+SGD S000028739 YDR524C-B GO:0008372 SGD_REF:S000069584 ND C YDR524C-B gene taxon:4932 20030730 SGD
+SGD S000028739 YDR524C-B GO:0005554 SGD_REF:S000069584 ND F YDR524C-B gene taxon:4932 20030730 SGD
+SGD S000028739 YDR524C-B GO:0000004 SGD_REF:S000069584 ND P YDR524C-B gene taxon:4932 20030730 SGD
+SGD S000028740 YDR524W-C GO:0008372 SGD_REF:S000069584 ND C YDR524W-C|YDR524W-A gene taxon:4932 20030730 SGD
+SGD S000028740 YDR524W-C GO:0005554 SGD_REF:S000069584 ND F YDR524W-C|YDR524W-A gene taxon:4932 20030730 SGD
+SGD S000028740 YDR524W-C GO:0000004 SGD_REF:S000069584 ND P YDR524W-C|YDR524W-A gene taxon:4932 20030730 SGD
+SGD S000002939 YDR531W GO:0005634 SGD_REF:S000075214|PMID:14690591 IDA C YDR531W gene taxon:4932 20040105 SGD
+SGD S000002939 YDR531W GO:0005737 SGD_REF:S000075214|PMID:14690591 IDA C YDR531W gene taxon:4932 20040105 SGD
+SGD S000002939 YDR531W GO:0004594 SGD_REF:S000065722|PMID:9890959 ISS F YDR531W gene taxon:4932 20030206 SGD
+SGD S000002939 YDR531W GO:0015937 SGD_REF:S000065722|PMID:9890959 ISS P YDR531W gene taxon:4932 20030206 SGD
+SGD S000002940 YDR532C colocalizes_with GO:0005816 SGD_REF:S000074185|PMID:14562095 IDA C YDR532C gene taxon:4932 20031028 SGD
+SGD S000002940 YDR532C GO:0005554 SGD_REF:S000069584 ND F YDR532C gene taxon:4932 20021122 SGD
+SGD S000002940 YDR532C GO:0000004 SGD_REF:S000069584 ND P YDR532C gene taxon:4932 20021122 SGD
+SGD S000002947 YDR539W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YDR539W gene taxon:4932 20031028 SGD
+SGD S000002947 YDR539W GO:0005554 SGD_REF:S000069584 ND F YDR539W gene taxon:4932 20021126 SGD
+SGD S000002947 YDR539W GO:0000004 SGD_REF:S000069584 ND P YDR539W gene taxon:4932 20021126 SGD
+SGD S000002949 YDR541C GO:0008372 SGD_REF:S000069584 ND C YDR541C gene taxon:4932 20030203 SGD
+SGD S000002949 YDR541C GO:0045552 SGD_REF:S000043731|PMID:10903444 ISS F YDR541C gene taxon:4932 20030206 SGD
+SGD S000002949 YDR541C GO:0000004 SGD_REF:S000069584 ND P YDR541C gene taxon:4932 20030203 SGD
+SGD S000000727 YEL001C GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YEL001C gene taxon:4932 20031028 SGD
+SGD S000000727 YEL001C GO:0005554 SGD_REF:S000069584 ND F YEL001C gene taxon:4932 20021126 SGD
+SGD S000000727 YEL001C GO:0000004 SGD_REF:S000069584 ND P YEL001C gene taxon:4932 20021126 SGD
+SGD S000000733 YEL007W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YEL007W|TOS9 gene taxon:4932 20031028 SGD
+SGD S000000733 YEL007W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YEL007W|TOS9 gene taxon:4932 20031028 SGD
+SGD S000000733 YEL007W GO:0005554 SGD_REF:S000069584 ND F YEL007W|TOS9 gene taxon:4932 20030421 SGD
+SGD S000000733 YEL007W GO:0000004 SGD_REF:S000069584 ND P YEL007W|TOS9 gene taxon:4932 20030421 SGD
+SGD S000000746 YEL020C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YEL020C gene taxon:4932 20031028 SGD
+SGD S000000746 YEL020C GO:0005554 SGD_REF:S000069584 ND F YEL020C gene taxon:4932 20030203 SGD
+SGD S000000746 YEL020C GO:0000004 SGD_REF:S000069584 ND P YEL020C gene taxon:4932 20030203 SGD
+SGD S000000749 YEL023C GO:0008372 SGD_REF:S000069584 ND C YEL023C gene taxon:4932 20021126 SGD
+SGD S000000749 YEL023C GO:0005554 SGD_REF:S000069584 ND F YEL023C gene taxon:4932 20021126 SGD
+SGD S000000749 YEL023C GO:0000004 SGD_REF:S000069584 ND P YEL023C gene taxon:4932 20021126 SGD
+SGD S000000751 YEL025C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YEL025C|SRI1 gene taxon:4932 20031028 SGD
+SGD S000000751 YEL025C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YEL025C|SRI1 gene taxon:4932 20031028 SGD
+SGD S000000751 YEL025C GO:0005554 SGD_REF:S000069584 ND F YEL025C|SRI1 gene taxon:4932 20021125 SGD
+SGD S000000751 YEL025C GO:0000004 SGD_REF:S000069584 ND P YEL025C|SRI1 gene taxon:4932 20021125 SGD
+SGD S000000769 YEL043W GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YEL043W gene taxon:4932 20031028 SGD
+SGD S000000769 YEL043W GO:0005554 SGD_REF:S000069584 ND F YEL043W gene taxon:4932 20030424 SGD
+SGD S000000769 YEL043W GO:0000004 SGD_REF:S000069584 ND P YEL043W gene taxon:4932 20030424 SGD
+SGD S000000773 YEL047C GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YEL047C|FRDS gene taxon:4932 20040928 SGD
+SGD S000000773 YEL047C GO:0005829 SGD_REF:S000051098|PMID:9587404 IDA C YEL047C|FRDS gene taxon:4932 20040812 SGD
+SGD S000000773 YEL047C GO:0016156 SGD_REF:S000048275|PMID:8946166 IDA F YEL047C|FRDS gene taxon:4932 20010625 SGD
+SGD S000000773 YEL047C GO:0008152 SGD_REF:S000048275|PMID:8946166 TAS P YEL047C|FRDS gene taxon:4932 20010625 SGD
+SGD S000000774 YEL048C colocalizes_with GO:0030136 SGD_REF:S000074185|PMID:14562095 IDA C YEL048C gene taxon:4932 20031028 SGD
+SGD S000000774 YEL048C GO:0005554 SGD_REF:S000069584 ND F YEL048C gene taxon:4932 20021126 SGD
+SGD S000000774 YEL048C GO:0000004 SGD_REF:S000069584 ND P YEL048C gene taxon:4932 20021126 SGD
+SGD S000000783 YEL057C GO:0008372 SGD_REF:S000069584 ND C YEL057C gene taxon:4932 20030203 SGD
+SGD S000000783 YEL057C GO:0005554 SGD_REF:S000069584 ND F YEL057C gene taxon:4932 20030203 SGD
+SGD S000000783 YEL057C GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P YEL057C gene taxon:4932 20060209 SGD
+SGD S000000799 YEL073C GO:0008372 SGD_REF:S000069584 ND C YEL073C gene taxon:4932 20021126 SGD
+SGD S000000799 YEL073C GO:0005554 SGD_REF:S000069584 ND F YEL073C gene taxon:4932 20021126 SGD
+SGD S000000799 YEL073C GO:0000004 SGD_REF:S000069584 ND P YEL073C gene taxon:4932 20021126 SGD
+SGD S000000801 YEL075C GO:0008372 SGD_REF:S000069584 ND C YEL075C gene taxon:4932 20021126 SGD
+SGD S000000801 YEL075C GO:0005554 SGD_REF:S000069584 ND F YEL075C gene taxon:4932 20021126 SGD
+SGD S000000801 YEL075C GO:0000004 SGD_REF:S000069584 ND P YEL075C gene taxon:4932 20021126 SGD
+SGD S000000802 YEL076C GO:0008372 SGD_REF:S000069584 ND C YEL076C gene taxon:4932 20021126 SGD
+SGD S000000802 YEL076C GO:0005554 SGD_REF:S000069584 ND F YEL076C gene taxon:4932 20021126 SGD
+SGD S000000802 YEL076C GO:0000004 SGD_REF:S000069584 ND P YEL076C gene taxon:4932 20021126 SGD
+SGD S000002955 YEL076C-A GO:0008372 SGD_REF:S000069584 ND C YEL076C-A gene taxon:4932 20030421 SGD
+SGD S000002955 YEL076C-A GO:0005554 SGD_REF:S000069584 ND F YEL076C-A gene taxon:4932 20030421 SGD
+SGD S000002955 YEL076C-A GO:0000004 SGD_REF:S000069584 ND P YEL076C-A gene taxon:4932 20030421 SGD
+SGD S000006409 YEL077C GO:0008372 SGD_REF:S000069584 ND C YEL077C gene taxon:4932 20021126 SGD
+SGD S000006409 YEL077C GO:0004386 SGD_REF:S000053946|PMID:9837911 ISS F YEL077C gene taxon:4932 20040323 SGD
+SGD S000006409 YEL077C GO:0000004 SGD_REF:S000069584 ND P YEL077C gene taxon:4932 20021126 SGD
+SGD S000000812 YER010C GO:0008372 SGD_REF:S000069584 ND C YER010C gene taxon:4932 20021126 SGD
+SGD S000000812 YER010C GO:0005554 SGD_REF:S000069584 ND F YER010C gene taxon:4932 20021126 SGD
+SGD S000000812 YER010C GO:0000004 SGD_REF:S000069584 ND P YER010C gene taxon:4932 20021126 SGD
+SGD S000000836 YER034W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YER034W gene taxon:4932 20031028 SGD
+SGD S000000836 YER034W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YER034W gene taxon:4932 20031028 SGD
+SGD S000000836 YER034W GO:0005554 SGD_REF:S000069584 ND F YER034W gene taxon:4932 20021126 SGD
+SGD S000000836 YER034W GO:0000004 SGD_REF:S000069584 ND P YER034W gene taxon:4932 20021126 SGD
+SGD S000007226 YER039C-A GO:0008372 SGD_REF:S000069584 ND C YER039C-A gene taxon:4932 20021126 SGD
+SGD S000007226 YER039C-A GO:0005554 SGD_REF:S000069584 ND F YER039C-A gene taxon:4932 20021126 SGD
+SGD S000007226 YER039C-A GO:0000004 SGD_REF:S000069584 ND P YER039C-A gene taxon:4932 20021126 SGD
+SGD S000007523 YER053C-A GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YER053C-A gene taxon:4932 20031028 SGD
+SGD S000007523 YER053C-A GO:0005554 SGD_REF:S000069584 ND F YER053C-A gene taxon:4932 20030203 SGD
+SGD S000007523 YER053C-A GO:0000004 SGD_REF:S000069584 ND P YER053C-A gene taxon:4932 20030203 SGD
+SGD S000000866 YER064C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YER064C gene taxon:4932 20031028 SGD
+SGD S000000866 YER064C GO:0005554 SGD_REF:S000069584 ND F YER064C gene taxon:4932 20030410 SGD
+SGD S000000866 YER064C GO:0045449 SGD_REF:S000060242|PMID:11342098 IMP P YER064C gene taxon:4932 20040813 SGD
+SGD S000000868 YER066W GO:0008372 SGD_REF:S000069584 ND C YER066W gene taxon:4932 20021126 SGD
+SGD S000000868 YER066W GO:0005554 SGD_REF:S000069584 ND F YER066W gene taxon:4932 20021126 SGD
+SGD S000000868 YER066W GO:0000004 SGD_REF:S000069584 ND P YER066W gene taxon:4932 20021126 SGD
+SGD S000000869 YER067W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YER067W gene taxon:4932 20031028 SGD
+SGD S000000869 YER067W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YER067W gene taxon:4932 20031028 SGD
+SGD S000000869 YER067W GO:0005554 SGD_REF:S000069584 ND F YER067W gene taxon:4932 20021223 SGD
+SGD S000000869 YER067W GO:0000004 SGD_REF:S000069584 ND P YER067W gene taxon:4932 20021223 SGD
+SGD S000000873 YER071C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YER071C gene taxon:4932 20031028 SGD
+SGD S000000873 YER071C GO:0005554 SGD_REF:S000069584 ND F YER071C gene taxon:4932 20030424 SGD
+SGD S000000873 YER071C GO:0000004 SGD_REF:S000069584 ND P YER071C gene taxon:4932 20030424 SGD
+SGD S000000878 YER076C GO:0005624 SGD_REF:S000075303|PMID:11935221 IDA C YER076C gene taxon:4932 20040114 SGD
+SGD S000000878 YER076C GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YER076C gene taxon:4932 20040928 SGD
+SGD S000000878 YER076C GO:0005554 SGD_REF:S000069584 ND F YER076C gene taxon:4932 20030203 SGD
+SGD S000000878 YER076C GO:0000004 SGD_REF:S000069584 ND P YER076C gene taxon:4932 20030203 SGD
+SGD S000000879 YER077C GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YER077C gene taxon:4932 20031028 SGD
+SGD S000000879 YER077C GO:0005554 SGD_REF:S000069584 ND F YER077C gene taxon:4932 20030203 SGD
+SGD S000000879 YER077C GO:0000004 SGD_REF:S000069584 ND P YER077C gene taxon:4932 20030203 SGD
+SGD S000000880 YER078C GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YER078C gene taxon:4932 20031028 SGD
+SGD S000000880 YER078C GO:0005759 SGD_REF:S000081142|PMID:15772085 NAS C YER078C gene taxon:4932 20050418 SGD
+SGD S000000880 YER078C GO:0004222 SGD_REF:S000081142|PMID:15772085 NAS F YER078C gene taxon:4932 20050418 SGD
+SGD S000000880 YER078C GO:0008451 SGD_REF:S000072463|PMID:10592175 ISS F YER078C gene taxon:4932 20030205 SGD
+SGD S000000880 YER078C GO:0006508 SGD_REF:S000081142|PMID:15772085 NAS P YER078C gene taxon:4932 20050418 SGD
+SGD S000028546 YER078W-A GO:0008372 SGD_REF:S000069584 ND C YER078W-A gene taxon:4932 20030730 SGD
+SGD S000028546 YER078W-A GO:0005554 SGD_REF:S000069584 ND F YER078W-A gene taxon:4932 20030730 SGD
+SGD S000028546 YER078W-A GO:0000004 SGD_REF:S000069584 ND P YER078W-A gene taxon:4932 20030730 SGD
+SGD S000000881 YER079W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YER079W gene taxon:4932 20031028 SGD
+SGD S000000881 YER079W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YER079W gene taxon:4932 20031028 SGD
+SGD S000000881 YER079W GO:0005554 SGD_REF:S000069584 ND F YER079W gene taxon:4932 20021126 SGD
+SGD S000000881 YER079W GO:0000004 SGD_REF:S000069584 ND P YER079W gene taxon:4932 20021126 SGD
+SGD S000000887 YER085C GO:0008372 SGD_REF:S000069584 ND C YER085C gene taxon:4932 20021126 SGD
+SGD S000000887 YER085C GO:0005554 SGD_REF:S000069584 ND F YER085C gene taxon:4932 20021126 SGD
+SGD S000000887 YER085C GO:0000004 SGD_REF:S000069584 ND P YER085C gene taxon:4932 20021126 SGD
+SGD S000000889 YER087W GO:0008372 SGD_REF:S000069584 ND C YER087W gene taxon:4932 20010207 SGD
+SGD S000000889 YER087W GO:0004827 SGD_REF:S000072463|PMID:10592175 ISS F YER087W gene taxon:4932 20030205 SGD
+SGD S000000889 YER087W GO:0000004 SGD_REF:S000069584 ND P YER087W gene taxon:4932 20010207 SGD
+SGD S000002960 YER093C-A GO:0008372 SGD_REF:S000069584 ND C YER093C-A gene taxon:4932 20030422 SGD
+SGD S000002960 YER093C-A GO:0005554 SGD_REF:S000069584 ND F YER093C-A gene taxon:4932 20030422 SGD
+SGD S000002960 YER093C-A GO:0000004 SGD_REF:S000069584 ND P YER093C-A gene taxon:4932 20030422 SGD
+SGD S000000915 YER113C GO:0005794 SGD_REF:S000074185|PMID:14562095 IDA C YER113C gene taxon:4932 20031028 SGD
+SGD S000000915 YER113C colocalizes_with GO:0030137 SGD_REF:S000074185|PMID:14562095 IDA C YER113C gene taxon:4932 20031028 SGD
+SGD S000000915 YER113C GO:0005554 SGD_REF:S000069584 ND F YER113C gene taxon:4932 20030203 SGD
+SGD S000000915 YER113C GO:0000004 SGD_REF:S000069584 ND P YER113C gene taxon:4932 20030203 SGD
+SGD S000000930 YER128W GO:0008372 SGD_REF:S000069584 ND C YER128W gene taxon:4932 20021126 SGD
+SGD S000000930 YER128W GO:0005554 SGD_REF:S000069584 ND F YER128W gene taxon:4932 20021126 SGD
+SGD S000000930 YER128W GO:0000004 SGD_REF:S000069584 ND P YER128W gene taxon:4932 20021126 SGD
+SGD S000000932 YER130C GO:0008372 SGD_REF:S000069584 ND C YER130C gene taxon:4932 20021126 SGD
+SGD S000000932 YER130C GO:0005554 SGD_REF:S000069584 ND F YER130C gene taxon:4932 20021126 SGD
+SGD S000000932 YER130C GO:0000004 SGD_REF:S000069584 ND P YER130C gene taxon:4932 20021126 SGD
+SGD S000000936 YER134C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YER134C gene taxon:4932 20031028 SGD
+SGD S000000936 YER134C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YER134C gene taxon:4932 20031028 SGD
+SGD S000000936 YER134C GO:0005554 SGD_REF:S000069584 ND F YER134C gene taxon:4932 20021126 SGD
+SGD S000000936 YER134C GO:0000004 SGD_REF:S000069584 ND P YER134C gene taxon:4932 20021126 SGD
+SGD S000000939 YER137C GO:0008372 SGD_REF:S000069584 ND C YER137C gene taxon:4932 20021126 SGD
+SGD S000000939 YER137C GO:0005554 SGD_REF:S000069584 ND F YER137C gene taxon:4932 20021126 SGD
+SGD S000000939 YER137C GO:0000004 SGD_REF:S000069584 ND P YER137C gene taxon:4932 20021126 SGD
+SGD S000007402 YER137C-A GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YER137C-A gene taxon:4932 20030811 SGD
+SGD S000007402 YER137C-A GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YER137C-A gene taxon:4932 20030811 SGD
+SGD S000007402 YER137C-A GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YER137C-A gene taxon:4932 20030811 SGD
+SGD S000007402 YER137C-A GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YER137C-A gene taxon:4932 20030811 SGD
+SGD S000000940 YER138C GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YER138C gene taxon:4932 20030811 SGD
+SGD S000000940 YER138C GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YER138C gene taxon:4932 20030811 SGD
+SGD S000000940 YER138C GO:0003887 SGD_REF:S000072465|PMID:9582191 ISS F YER138C gene taxon:4932 20030811 SGD
+SGD S000000940 YER138C GO:0003964 SGD_REF:S000072465|PMID:9582191 ISS F YER138C gene taxon:4932 20030811 SGD
+SGD S000000940 YER138C GO:0004540 SGD_REF:S000072465|PMID:9582191 ISS F YER138C gene taxon:4932 20030811 SGD
+SGD S000000940 YER138C GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YER138C gene taxon:4932 20030811 SGD
+SGD S000000940 YER138C GO:0008233 SGD_REF:S000072465|PMID:9582191 ISS F YER138C gene taxon:4932 20030811 SGD
+SGD S000000940 YER138C GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YER138C gene taxon:4932 20030811 SGD
+SGD S000007239 YER138W-A GO:0008372 SGD_REF:S000069584 ND C YER138W-A gene taxon:4932 20021126 SGD
+SGD S000007239 YER138W-A GO:0005554 SGD_REF:S000069584 ND F YER138W-A gene taxon:4932 20021126 SGD
+SGD S000007239 YER138W-A GO:0000004 SGD_REF:S000069584 ND P YER138W-A gene taxon:4932 20021126 SGD
+SGD S000000941 YER139C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YER139C gene taxon:4932 20031028 SGD
+SGD S000000941 YER139C GO:0005554 SGD_REF:S000069584 ND F YER139C gene taxon:4932 20021126 SGD
+SGD S000000941 YER139C GO:0000004 SGD_REF:S000069584 ND P YER139C gene taxon:4932 20021126 SGD
+SGD S000000942 YER140W GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YER140W gene taxon:4932 20040813 SGD
+SGD S000000942 YER140W GO:0005554 SGD_REF:S000069584 ND F YER140W gene taxon:4932 20021126 SGD
+SGD S000000942 YER140W GO:0000004 SGD_REF:S000069584 ND P YER140W gene taxon:4932 20021126 SGD
+SGD S000000954 YER152C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YER152C gene taxon:4932 20031028 SGD
+SGD S000000954 YER152C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YER152C gene taxon:4932 20031028 SGD
+SGD S000000954 YER152C GO:0005554 SGD_REF:S000069584 ND F YER152C gene taxon:4932 20030424 SGD
+SGD S000000954 YER152C GO:0000004 SGD_REF:S000069584 ND P YER152C gene taxon:4932 20030424 SGD
+SGD S000000958 YER156C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YER156C gene taxon:4932 20031028 SGD
+SGD S000000958 YER156C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YER156C gene taxon:4932 20031028 SGD
+SGD S000000958 YER156C GO:0005554 SGD_REF:S000069584 ND F YER156C gene taxon:4932 20021126 SGD
+SGD S000000958 YER156C GO:0000004 SGD_REF:S000069584 ND P YER156C gene taxon:4932 20021126 SGD
+SGD S000000960 YER158C GO:0008372 SGD_REF:S000069584 ND C YER158C gene taxon:4932 20030424 SGD
+SGD S000000960 YER158C GO:0005554 SGD_REF:S000069584 ND F YER158C gene taxon:4932 20030424 SGD
+SGD S000000960 YER158C GO:0000004 SGD_REF:S000069584 ND P YER158C gene taxon:4932 20030424 SGD
+SGD S000007403 YER159C-A GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YER159C-A gene taxon:4932 20030811 SGD
+SGD S000007403 YER159C-A GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YER159C-A gene taxon:4932 20030811 SGD
+SGD S000007403 YER159C-A GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YER159C-A gene taxon:4932 20030811 SGD
+SGD S000007403 YER159C-A GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YER159C-A gene taxon:4932 20030811 SGD
+SGD S000000962 YER160C GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YER160C gene taxon:4932 20030811 SGD
+SGD S000000962 YER160C GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YER160C gene taxon:4932 20030811 SGD
+SGD S000000962 YER160C GO:0003887 SGD_REF:S000072465|PMID:9582191 ISS F YER160C gene taxon:4932 20030811 SGD
+SGD S000000962 YER160C GO:0003964 SGD_REF:S000072465|PMID:9582191 ISS F YER160C gene taxon:4932 20030811 SGD
+SGD S000000962 YER160C GO:0004540 SGD_REF:S000072465|PMID:9582191 ISS F YER160C gene taxon:4932 20030811 SGD
+SGD S000000962 YER160C GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YER160C gene taxon:4932 20030811 SGD
+SGD S000000962 YER160C GO:0008233 SGD_REF:S000072465|PMID:9582191 ISS F YER160C gene taxon:4932 20030811 SGD
+SGD S000000962 YER160C GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YER160C gene taxon:4932 20030811 SGD
+SGD S000000965 YER163C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YER163C gene taxon:4932 20031028 SGD
+SGD S000000965 YER163C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YER163C gene taxon:4932 20031028 SGD
+SGD S000000965 YER163C GO:0005554 SGD_REF:S000069584 ND F YER163C gene taxon:4932 20021126 SGD
+SGD S000000965 YER163C GO:0000004 SGD_REF:S000069584 ND P YER163C gene taxon:4932 20021126 SGD
+SGD S000028625 YER175W-A GO:0008372 SGD_REF:S000069584 ND C YER175W-A gene taxon:4932 20030730 SGD
+SGD S000028625 YER175W-A GO:0005554 SGD_REF:S000069584 ND F YER175W-A gene taxon:4932 20030730 SGD
+SGD S000028625 YER175W-A GO:0000004 SGD_REF:S000069584 ND P YER175W-A gene taxon:4932 20030730 SGD
+SGD S000000986 YER184C GO:0008372 SGD_REF:S000069584 ND C YER184C gene taxon:4932 20021205 SGD
+SGD S000000986 YER184C GO:0005554 SGD_REF:S000069584 ND F YER184C gene taxon:4932 20021205 SGD
+SGD S000000986 YER184C GO:0000004 SGD_REF:S000069584 ND P YER184C gene taxon:4932 20021205 SGD
+SGD S000000987 YER185W GO:0016021 SGD_REF:S000072825|PMID:12524434 ISS C YER185W gene taxon:4932 20030409 SGD
+SGD S000000987 YER185W GO:0005554 SGD_REF:S000069584 ND F YER185W gene taxon:4932 20030203 SGD
+SGD S000000987 YER185W GO:0000004 SGD_REF:S000069584 ND P YER185W gene taxon:4932 20030203 SGD
+SGD S000000988 YER186C GO:0008372 SGD_REF:S000069584 ND C YER186C gene taxon:4932 20021126 SGD
+SGD S000000988 YER186C GO:0005554 SGD_REF:S000069584 ND F YER186C gene taxon:4932 20021126 SGD
+SGD S000000988 YER186C GO:0000004 SGD_REF:S000069584 ND P YER186C gene taxon:4932 20021126 SGD
+SGD S000000989 YER187W GO:0008372 SGD_REF:S000069584 ND C YER187W gene taxon:4932 20030203 SGD
+SGD S000000989 YER187W GO:0005554 SGD_REF:S000069584 ND F YER187W gene taxon:4932 20030203 SGD
+SGD S000000989 YER187W GO:0000004 SGD_REF:S000069584 ND P YER187W gene taxon:4932 20030203 SGD
+SGD S000028764 YER188C-A GO:0008372 SGD_REF:S000069584 ND C YER188C-A gene taxon:4932 20030730 SGD
+SGD S000028764 YER188C-A GO:0005554 SGD_REF:S000069584 ND F YER188C-A gene taxon:4932 20030730 SGD
+SGD S000028764 YER188C-A GO:0000004 SGD_REF:S000069584 ND P YER188C-A gene taxon:4932 20030730 SGD
+SGD S000000991 YER189W GO:0008372 SGD_REF:S000069584 ND C YER189W gene taxon:4932 20021126 SGD
+SGD S000000991 YER189W GO:0005554 SGD_REF:S000069584 ND F YER189W gene taxon:4932 20021126 SGD
+SGD S000000991 YER189W GO:0000004 SGD_REF:S000069584 ND P YER189W gene taxon:4932 20021126 SGD
+SGD S000002962 YFL002W-A GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YFL002W-A gene taxon:4932 20030811 SGD
+SGD S000002962 YFL002W-A GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YFL002W-A gene taxon:4932 20030811 SGD
+SGD S000002962 YFL002W-A GO:0003887 SGD_REF:S000072465|PMID:9582191 ISS F YFL002W-A gene taxon:4932 20030811 SGD
+SGD S000002962 YFL002W-A GO:0003964 SGD_REF:S000072465|PMID:9582191 ISS F YFL002W-A gene taxon:4932 20030811 SGD
+SGD S000002962 YFL002W-A GO:0004540 SGD_REF:S000072465|PMID:9582191 ISS F YFL002W-A gene taxon:4932 20030811 SGD
+SGD S000002962 YFL002W-A GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YFL002W-A gene taxon:4932 20030811 SGD
+SGD S000002962 YFL002W-A GO:0008233 SGD_REF:S000072465|PMID:9582191 ISS F YFL002W-A gene taxon:4932 20030811 SGD
+SGD S000002962 YFL002W-A GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YFL002W-A gene taxon:4932 20030811 SGD
+SGD S000007404 YFL002W-B GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YFL002W-B gene taxon:4932 20030811 SGD
+SGD S000007404 YFL002W-B GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YFL002W-B gene taxon:4932 20030811 SGD
+SGD S000007404 YFL002W-B GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YFL002W-B gene taxon:4932 20030811 SGD
+SGD S000007404 YFL002W-B GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YFL002W-B gene taxon:4932 20030811 SGD
+SGD S000001882 YFL012W GO:0008372 SGD_REF:S000069584 ND C YFL012W gene taxon:4932 20030424 SGD
+SGD S000001882 YFL012W GO:0005554 SGD_REF:S000069584 ND F YFL012W gene taxon:4932 20030424 SGD
+SGD S000001882 YFL012W GO:0000004 SGD_REF:S000069584 ND P YFL012W gene taxon:4932 20030424 SGD
+SGD S000001860 YFL034W GO:0016021 SGD_REF:S000076737|PMID:15286401 ISS C YFL034W gene taxon:4932 20040812 SGD
+SGD S000001860 YFL034W GO:0005554 SGD_REF:S000069584 ND F YFL034W gene taxon:4932 20021126 SGD
+SGD S000001860 YFL034W GO:0000004 SGD_REF:S000069584 ND P YFL034W gene taxon:4932 20021126 SGD
+SGD S000001854 YFL040W GO:0008372 SGD_REF:S000069584 ND C YFL040W gene taxon:4932 20030203 SGD
+SGD S000001854 YFL040W GO:0005554 SGD_REF:S000069584 ND F YFL040W gene taxon:4932 20030203 SGD
+SGD S000001854 YFL040W GO:0000004 SGD_REF:S000069584 ND P YFL040W gene taxon:4932 20030203 SGD
+SGD S000028547 YFL041W-A GO:0008372 SGD_REF:S000069584 ND C YFL041W-A gene taxon:4932 20030730 SGD
+SGD S000028547 YFL041W-A GO:0005554 SGD_REF:S000069584 ND F YFL041W-A gene taxon:4932 20030730 SGD
+SGD S000028547 YFL041W-A GO:0000004 SGD_REF:S000069584 ND P YFL041W-A gene taxon:4932 20030730 SGD
+SGD S000001852 YFL042C GO:0008372 SGD_REF:S000069584 ND C YFL042C|YFL043C gene taxon:4932 20030203 SGD
+SGD S000001852 YFL042C GO:0005554 SGD_REF:S000069584 ND F YFL042C|YFL043C gene taxon:4932 20030203 SGD
+SGD S000001852 YFL042C GO:0000004 SGD_REF:S000069584 ND P YFL042C|YFL043C gene taxon:4932 20030203 SGD
+SGD S000001843 YFL051C GO:0008372 SGD_REF:S000069584 ND C YFL051C gene taxon:4932 20030203 SGD
+SGD S000001843 YFL051C GO:0005554 SGD_REF:S000069584 ND F YFL051C gene taxon:4932 20030203 SGD
+SGD S000001843 YFL051C GO:0000004 SGD_REF:S000069584 ND P YFL051C gene taxon:4932 20030203 SGD
+SGD S000001842 YFL052W GO:0008372 SGD_REF:S000069584 ND C YFL052W gene taxon:4932 20030424 SGD
+SGD S000001842 YFL052W GO:0003677 SGD_REF:S000069948|PMID:11353088 ISS F YFL052W gene taxon:4932 20030424 SGD
+SGD S000001842 YFL052W GO:0000004 SGD_REF:S000069584 ND P YFL052W gene taxon:4932 20030424 SGD
+SGD S000001840 YFL054C GO:0016021 SGD_REF:S000073532|PMID:12832087 ISS C YFL054C gene taxon:4932 20030801 SGD
+SGD S000001840 YFL054C GO:0005215 SGD_REF:S000073532|PMID:12832087 IMP F YFL054C gene taxon:4932 20030801 SGD
+SGD S000001840 YFL054C GO:0015168 SGD_REF:S000071999|PMID:12450819 ISS F YFL054C gene taxon:4932 20030402 SGD
+SGD S000001840 YFL054C GO:0015250 SGD_REF:S000046932|PMID:10400607 ISS F YFL054C gene taxon:4932 20030207 SGD
+SGD S000001840 YFL054C GO:0006833 SGD_REF:S000046932|PMID:10400607 ISS P YFL054C gene taxon:4932 20030207 SGD
+SGD S000001830 YFL064C GO:0008372 SGD_REF:S000069584 ND C YFL064C gene taxon:4932 20021126 SGD
+SGD S000001830 YFL064C GO:0005554 SGD_REF:S000069584 ND F YFL064C gene taxon:4932 20021126 SGD
+SGD S000001830 YFL064C GO:0000004 SGD_REF:S000069584 ND P YFL064C gene taxon:4932 20021126 SGD
+SGD S000001829 YFL065C GO:0008372 SGD_REF:S000069584 ND C YFL065C gene taxon:4932 20021126 SGD
+SGD S000001829 YFL065C GO:0005554 SGD_REF:S000069584 ND F YFL065C gene taxon:4932 20021126 SGD
+SGD S000001829 YFL065C GO:0000004 SGD_REF:S000069584 ND P YFL065C gene taxon:4932 20021126 SGD
+SGD S000001828 YFL066C GO:0008372 SGD_REF:S000069584 ND C YFL066C gene taxon:4932 20030203 SGD
+SGD S000001828 YFL066C GO:0005554 SGD_REF:S000069584 ND F YFL066C gene taxon:4932 20030203 SGD
+SGD S000001828 YFL066C GO:0000004 SGD_REF:S000069584 ND P YFL066C gene taxon:4932 20030203 SGD
+SGD S000001827 YFL067W GO:0008372 SGD_REF:S000069584 ND C YFL067W gene taxon:4932 20030203 SGD
+SGD S000001827 YFL067W GO:0005554 SGD_REF:S000069584 ND F YFL067W gene taxon:4932 20030203 SGD
+SGD S000001827 YFL067W GO:0000004 SGD_REF:S000069584 ND P YFL067W gene taxon:4932 20030203 SGD
+SGD S000001826 YFL068W GO:0008372 SGD_REF:S000069584 ND C YFL068W gene taxon:4932 20021126 SGD
+SGD S000001826 YFL068W GO:0005554 SGD_REF:S000069584 ND F YFL068W gene taxon:4932 20021126 SGD
+SGD S000001826 YFL068W GO:0000004 SGD_REF:S000069584 ND P YFL068W gene taxon:4932 20021126 SGD
+SGD S000001902 YFR006W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YFR006W gene taxon:4932 20031028 SGD
+SGD S000001902 YFR006W GO:0008451 SGD_REF:S000072463|PMID:10592175 ISS F YFR006W gene taxon:4932 20030205 SGD
+SGD S000001902 YFR006W GO:0000004 SGD_REF:S000069584 ND P YFR006W gene taxon:4932 20030205 SGD
+SGD S000001903 YFR007W GO:0008372 SGD_REF:S000069584 ND C YFR007W gene taxon:4932 20021126 SGD
+SGD S000001903 YFR007W GO:0005554 SGD_REF:S000069584 ND F YFR007W gene taxon:4932 20021126 SGD
+SGD S000001903 YFR007W GO:0000004 SGD_REF:S000069584 ND P YFR007W gene taxon:4932 20021126 SGD
+SGD S000001907 YFR011C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YFR011C gene taxon:4932 20031028 SGD
+SGD S000001907 YFR011C GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YFR011C gene taxon:4932 20031028 SGD
+SGD S000001907 YFR011C GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YFR011C gene taxon:4932 20040924 SGD
+SGD S000001907 YFR011C GO:0005554 SGD_REF:S000069584 ND F YFR011C gene taxon:4932 20030424 SGD
+SGD S000001907 YFR011C GO:0000004 SGD_REF:S000069584 ND P YFR011C gene taxon:4932 20030424 SGD
+SGD S000001908 YFR012W GO:0008372 SGD_REF:S000069584 ND C YFR012W gene taxon:4932 20030203 SGD
+SGD S000001908 YFR012W GO:0005554 SGD_REF:S000069584 ND F YFR012W gene taxon:4932 20030203 SGD
+SGD S000001908 YFR012W GO:0000004 SGD_REF:S000069584 ND P YFR012W gene taxon:4932 20030203 SGD
+SGD S000007606 YFR012W-A GO:0008372 SGD_REF:S000069584 ND C YFR012W-A gene taxon:4932 20010226 SGD
+SGD S000007606 YFR012W-A GO:0005554 SGD_REF:S000069584 ND F YFR012W-A gene taxon:4932 20010226 SGD
+SGD S000007606 YFR012W-A GO:0000004 SGD_REF:S000069584 ND P YFR012W-A gene taxon:4932 20010226 SGD
+SGD S000001912 YFR016C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YFR016C gene taxon:4932 20031028 SGD
+SGD S000001912 YFR016C GO:0005933 SGD_REF:S000074185|PMID:14562095 IDA C YFR016C gene taxon:4932 20031028 SGD
+SGD S000001912 YFR016C GO:0005554 SGD_REF:S000069584 ND F YFR016C gene taxon:4932 20030203 SGD
+SGD S000001912 YFR016C GO:0000004 SGD_REF:S000069584 ND P YFR016C gene taxon:4932 20030203 SGD
+SGD S000001913 YFR017C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YFR017C gene taxon:4932 20031028 SGD
+SGD S000001913 YFR017C GO:0005554 SGD_REF:S000069584 ND F YFR017C gene taxon:4932 20030424 SGD
+SGD S000001913 YFR017C GO:0000004 SGD_REF:S000069584 ND P YFR017C gene taxon:4932 20030424 SGD
+SGD S000001914 YFR018C GO:0008372 SGD_REF:S000069584 ND C YFR018C gene taxon:4932 20021126 SGD
+SGD S000001914 YFR018C GO:0005554 SGD_REF:S000069584 ND F YFR018C gene taxon:4932 20021126 SGD
+SGD S000001914 YFR018C GO:0000004 SGD_REF:S000069584 ND P YFR018C gene taxon:4932 20021126 SGD
+SGD S000001922 YFR026C GO:0008372 SGD_REF:S000069584 ND C YFR026C gene taxon:4932 20030203 SGD
+SGD S000001922 YFR026C GO:0005554 SGD_REF:S000069584 ND F YFR026C gene taxon:4932 20030203 SGD
+SGD S000001922 YFR026C GO:0000004 SGD_REF:S000069584 ND P YFR026C gene taxon:4932 20030203 SGD
+SGD S000001928 YFR032C GO:0008372 SGD_REF:S000069584 ND C YFR032C gene taxon:4932 20030424 SGD
+SGD S000001928 YFR032C GO:0005554 SGD_REF:S000069584 ND F YFR032C gene taxon:4932 20030424 SGD
+SGD S000001928 YFR032C GO:0000004 SGD_REF:S000069584 ND P YFR032C gene taxon:4932 20030424 SGD
+SGD S000028630 YFR032C-B GO:0008372 SGD_REF:S000069584 ND C YFR032C-B gene taxon:4932 20030730 SGD
+SGD S000028630 YFR032C-B GO:0005554 SGD_REF:S000069584 ND F YFR032C-B gene taxon:4932 20030730 SGD
+SGD S000028630 YFR032C-B GO:0000004 SGD_REF:S000069584 ND P YFR032C-B gene taxon:4932 20030730 SGD
+SGD S000001931 YFR035C GO:0008372 SGD_REF:S000069584 ND C YFR035C gene taxon:4932 20030203 SGD
+SGD S000001931 YFR035C GO:0005554 SGD_REF:S000069584 ND F YFR035C gene taxon:4932 20030203 SGD
+SGD S000001931 YFR035C GO:0000004 SGD_REF:S000069584 ND P YFR035C gene taxon:4932 20030203 SGD
+SGD S000001935 YFR039C GO:0008372 SGD_REF:S000069584 ND C YFR039C gene taxon:4932 20030203 SGD
+SGD S000001935 YFR039C GO:0005554 SGD_REF:S000069584 ND F YFR039C gene taxon:4932 20030203 SGD
+SGD S000001935 YFR039C GO:0000004 SGD_REF:S000069584 ND P YFR039C gene taxon:4932 20030203 SGD
+SGD S000001938 YFR042W GO:0008372 SGD_REF:S000069584 ND C YFR042W gene taxon:4932 20021126 SGD
+SGD S000001938 YFR042W GO:0005554 SGD_REF:S000069584 ND F YFR042W gene taxon:4932 20021126 SGD
+SGD S000001938 YFR042W GO:0000004 SGD_REF:S000069584 ND P YFR042W gene taxon:4932 20021126 SGD
+SGD S000001940 YFR044C GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YFR044C gene taxon:4932 20020507 SGD
+SGD S000001940 YFR044C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YFR044C gene taxon:4932 20031028 SGD
+SGD S000001940 YFR044C GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YFR044C gene taxon:4932 20031028 SGD
+SGD S000001940 YFR044C GO:0005554 SGD_REF:S000069584 ND F YFR044C gene taxon:4932 20030203 SGD
+SGD S000001940 YFR044C GO:0000004 SGD_REF:S000069584 ND P YFR044C gene taxon:4932 20030203 SGD
+SGD S000001941 YFR045W GO:0005743 SGD_REF:S000049213|PMID:10930523 ISS C YFR045W gene taxon:4932 20021017 SGD
+SGD S000001941 YFR045W GO:0005215 SGD_REF:S000049213|PMID:10930523 ISS F YFR045W gene taxon:4932 20021017 SGD
+SGD S000001941 YFR045W GO:0006810 SGD_REF:S000049213|PMID:10930523 ISS P YFR045W gene taxon:4932 20021017 SGD
+SGD S000001953 YFR057W GO:0008372 SGD_REF:S000069584 ND C YFR057W gene taxon:4932 20021126 SGD
+SGD S000001953 YFR057W GO:0005554 SGD_REF:S000069584 ND F YFR057W gene taxon:4932 20021126 SGD
+SGD S000001953 YFR057W GO:0000004 SGD_REF:S000069584 ND P YFR057W gene taxon:4932 20021126 SGD
+SGD S000028769 YGL006W-A GO:0008372 SGD_REF:S000069584 ND C YGL006W-A gene taxon:4932 20030730 SGD
+SGD S000028769 YGL006W-A GO:0005554 SGD_REF:S000069584 ND F YGL006W-A gene taxon:4932 20030730 SGD
+SGD S000028769 YGL006W-A GO:0000004 SGD_REF:S000069584 ND P YGL006W-A gene taxon:4932 20030730 SGD
+SGD S000028632 YGL007C-A GO:0008372 SGD_REF:S000069584 ND C YGL007C-A gene taxon:4932 20030730 SGD
+SGD S000028632 YGL007C-A GO:0005554 SGD_REF:S000069584 ND F YGL007C-A gene taxon:4932 20030730 SGD
+SGD S000028632 YGL007C-A GO:0000004 SGD_REF:S000069584 ND P YGL007C-A gene taxon:4932 20030730 SGD
+SGD S000002978 YGL010W GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YGL010W gene taxon:4932 20031028 SGD
+SGD S000002978 YGL010W GO:0005554 SGD_REF:S000069584 ND F YGL010W gene taxon:4932 20030422 SGD
+SGD S000002978 YGL010W GO:0000004 SGD_REF:S000069584 ND P YGL010W gene taxon:4932 20030422 SGD
+SGD S000002983 YGL015C GO:0008372 SGD_REF:S000069584 ND C YGL015C gene taxon:4932 20030203 SGD
+SGD S000002983 YGL015C GO:0005554 SGD_REF:S000069584 ND F YGL015C gene taxon:4932 20030203 SGD
+SGD S000002983 YGL015C GO:0000004 SGD_REF:S000069584 ND P YGL015C gene taxon:4932 20030203 SGD
+SGD S000003004 YGL036W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YGL036W gene taxon:4932 20031028 SGD
+SGD S000003004 YGL036W GO:0005554 SGD_REF:S000069584 ND F YGL036W gene taxon:4932 20021126 SGD
+SGD S000003004 YGL036W GO:0000004 SGD_REF:S000069584 ND P YGL036W gene taxon:4932 20021126 SGD
+SGD S000003007 YGL039W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YGL039W gene taxon:4932 20031028 SGD
+SGD S000003007 YGL039W GO:0016491 SGD_REF:S000075114|PMID:14574691 IDA F YGL039W gene taxon:4932 20031222 SGD
+SGD S000003007 YGL039W GO:0045552 SGD_REF:S000043731|PMID:10903444 ISS F YGL039W gene taxon:4932 20030224 SGD
+SGD S000003007 YGL039W GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P YGL039W gene taxon:4932 20060227 SGD
+SGD S000028548 YGL041C-B GO:0008372 SGD_REF:S000069584 ND C YGL041C-B gene taxon:4932 20030730 SGD
+SGD S000028548 YGL041C-B GO:0005554 SGD_REF:S000069584 ND F YGL041C-B gene taxon:4932 20030730 SGD
+SGD S000028548 YGL041C-B GO:0000004 SGD_REF:S000069584 ND P YGL041C-B gene taxon:4932 20030730 SGD
+SGD S000003025 YGL057C GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YGL057C gene taxon:4932 20031028 SGD
+SGD S000003025 YGL057C GO:0005554 SGD_REF:S000069584 ND F YGL057C gene taxon:4932 20011204 SGD
+SGD S000003025 YGL057C GO:0000004 SGD_REF:S000069584 ND P YGL057C gene taxon:4932 20011204 SGD
+SGD S000003027 YGL059W GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YGL059W gene taxon:4932 20031028 SGD
+SGD S000003027 YGL059W GO:0004672 SGD_REF:S000072463|PMID:10592175 ISS F YGL059W gene taxon:4932 20030211 SGD
+SGD S000003027 YGL059W GO:0000004 SGD_REF:S000069584 ND P YGL059W gene taxon:4932 20011204 SGD
+SGD S000003047 YGL079W GO:0005768 SGD_REF:S000074185|PMID:14562095 IDA C YGL079W gene taxon:4932 20031028 SGD
+SGD S000003047 YGL079W GO:0005554 SGD_REF:S000069584 ND F YGL079W gene taxon:4932 20021126 SGD
+SGD S000003047 YGL079W GO:0000004 SGD_REF:S000069584 ND P YGL079W gene taxon:4932 20021126 SGD
+SGD S000003049 YGL081W GO:0008372 SGD_REF:S000069584 ND C YGL081W gene taxon:4932 20021126 SGD
+SGD S000003049 YGL081W GO:0005554 SGD_REF:S000069584 ND F YGL081W gene taxon:4932 20021126 SGD
+SGD S000003049 YGL081W GO:0000004 SGD_REF:S000069584 ND P YGL081W gene taxon:4932 20021126 SGD
+SGD S000003050 YGL082W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YGL082W gene taxon:4932 20031028 SGD
+SGD S000003050 YGL082W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YGL082W gene taxon:4932 20031028 SGD
+SGD S000003050 YGL082W GO:0005554 SGD_REF:S000069584 ND F YGL082W gene taxon:4932 20030203 SGD
+SGD S000003050 YGL082W GO:0000004 SGD_REF:S000069584 ND P YGL082W gene taxon:4932 20030203 SGD
+SGD S000003053 YGL085W GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YGL085W gene taxon:4932 20031028 SGD
+SGD S000003053 YGL085W GO:0005554 SGD_REF:S000069584 ND F YGL085W gene taxon:4932 20021126 SGD
+SGD S000003053 YGL085W GO:0000004 SGD_REF:S000069584 ND P YGL085W gene taxon:4932 20021126 SGD
+SGD S000003069 YGL101W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YGL101W gene taxon:4932 20031028 SGD
+SGD S000003069 YGL101W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YGL101W gene taxon:4932 20031028 SGD
+SGD S000003069 YGL101W GO:0005554 SGD_REF:S000069584 ND F YGL101W gene taxon:4932 20030422 SGD
+SGD S000003069 YGL101W GO:0000004 SGD_REF:S000069584 ND P YGL101W gene taxon:4932 20030422 SGD
+SGD S000003076 YGL108C GO:0008372 SGD_REF:S000069584 ND C YGL108C gene taxon:4932 20030203 SGD
+SGD S000003076 YGL108C GO:0005554 SGD_REF:S000069584 ND F YGL108C gene taxon:4932 20030203 SGD
+SGD S000003076 YGL108C GO:0000004 SGD_REF:S000069584 ND P YGL108C gene taxon:4932 20030203 SGD
+SGD S000003082 YGL114W GO:0016020 SGD_REF:S000075656|PMID:11788967 ISS C YGL114W gene taxon:4932 20040324 SGD
+SGD S000003082 YGL114W GO:0015198 SGD_REF:S000075656|PMID:11788967 ISS F YGL114W gene taxon:4932 20040324 SGD
+SGD S000003082 YGL114W GO:0006810 SGD_REF:S000075656|PMID:11788967 IC GO:0015198 P YGL114W gene taxon:4932 20040324 SGD
+SGD S000003085 YGL117W GO:0008372 SGD_REF:S000069584 ND C YGL117W gene taxon:4932 20030203 SGD
+SGD S000003085 YGL117W GO:0005554 SGD_REF:S000069584 ND F YGL117W gene taxon:4932 20030203 SGD
+SGD S000003085 YGL117W GO:0000004 SGD_REF:S000069584 ND P YGL117W gene taxon:4932 20030203 SGD
+SGD S000003106 YGL138C GO:0008372 SGD_REF:S000069584 ND C YGL138C gene taxon:4932 20030423 SGD
+SGD S000003106 YGL138C GO:0005554 SGD_REF:S000069584 ND F YGL138C gene taxon:4932 20030423 SGD
+SGD S000003106 YGL138C GO:0000004 SGD_REF:S000069584 ND P YGL138C gene taxon:4932 20030423 SGD
+SGD S000003108 YGL140C GO:0008372 SGD_REF:S000069584 ND C YGL140C gene taxon:4932 20021119 SGD
+SGD S000003108 YGL140C GO:0005554 SGD_REF:S000069584 ND F YGL140C gene taxon:4932 20021119 SGD
+SGD S000003108 YGL140C GO:0000004 SGD_REF:S000069584 ND P YGL140C gene taxon:4932 20021119 SGD
+SGD S000003114 YGL146C GO:0016020 SGD_REF:S000041156|PMID:9046099 NAS C YGL146C gene taxon:4932 20030423 SGD
+SGD S000003114 YGL146C GO:0005554 SGD_REF:S000069584 ND F YGL146C gene taxon:4932 20030423 SGD
+SGD S000003114 YGL146C GO:0000004 SGD_REF:S000069584 ND P YGL146C gene taxon:4932 20030423 SGD
+SGD S000003125 YGL157W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YGL157W gene taxon:4932 20031028 SGD
+SGD S000003125 YGL157W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YGL157W gene taxon:4932 20031028 SGD
+SGD S000003125 YGL157W GO:0016491 SGD_REF:S000075114|PMID:14574691 IDA F YGL157W gene taxon:4932 20031222 SGD
+SGD S000003125 YGL157W GO:0045552 SGD_REF:S000043731|PMID:10903444 ISS F YGL157W gene taxon:4932 20030224 SGD
+SGD S000003125 YGL157W GO:0000004 SGD_REF:S000069584 ND P YGL157W gene taxon:4932 20030203 SGD
+SGD S000003127 YGL159W GO:0008372 SGD_REF:S000069584 ND C YGL159W gene taxon:4932 20021126 SGD
+SGD S000003127 YGL159W GO:0005554 SGD_REF:S000069584 ND F YGL159W gene taxon:4932 20021126 SGD
+SGD S000003127 YGL159W GO:0000004 SGD_REF:S000069584 ND P YGL159W gene taxon:4932 20021126 SGD
+SGD S000003128 YGL160W GO:0016020 SGD_REF:S000055262|PMID:10341420 ISS C YGL160W gene taxon:4932 20030423 SGD
+SGD S000003128 YGL160W GO:0016722 SGD_REF:S000055262|PMID:10341420 ISS F YGL160W gene taxon:4932 20050812 SGD
+SGD S000003128 YGL160W GO:0000004 SGD_REF:S000069584 ND P YGL160W gene taxon:4932 20030423 SGD
+SGD S000003144 YGL176C GO:0008372 SGD_REF:S000069584 ND C YGL176C gene taxon:4932 20030203 SGD
+SGD S000003144 YGL176C GO:0005554 SGD_REF:S000069584 ND F YGL176C gene taxon:4932 20030203 SGD
+SGD S000003144 YGL176C GO:0000004 SGD_REF:S000069584 ND P YGL176C gene taxon:4932 20030203 SGD
+SGD S000003153 YGL185C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YGL185C gene taxon:4932 20031028 SGD
+SGD S000003153 YGL185C GO:0016616 SGD_REF:S000072828|PMID:12525494 ISS F YGL185C gene taxon:4932 20030401 SGD
+SGD S000003153 YGL185C GO:0008152 SGD_REF:S000072828|PMID:12525494 ISS P YGL185C gene taxon:4932 20030401 SGD
+SGD S000028635 YGL188C-A GO:0008372 SGD_REF:S000069584 ND C YGL188C-A gene taxon:4932 20030730 SGD
+SGD S000028635 YGL188C-A GO:0005554 SGD_REF:S000069584 ND F YGL188C-A gene taxon:4932 20030730 SGD
+SGD S000028635 YGL188C-A GO:0000004 SGD_REF:S000069584 ND P YGL188C-A gene taxon:4932 20030730 SGD
+SGD S000087160 YGL194C-A GO:0008372 SGD_REF:S000069584 ND C YGL194C-A gene taxon:4932 20051111 SGD
+SGD S000087160 YGL194C-A GO:0005554 SGD_REF:S000069584 ND F YGL194C-A gene taxon:4932 20051111 SGD
+SGD S000087160 YGL194C-A GO:0000004 SGD_REF:S000069584 ND P YGL194C-A gene taxon:4932 20051111 SGD
+SGD S000003164 YGL196W GO:0008372 SGD_REF:S000069584 ND C YGL196W gene taxon:4932 20030203 SGD
+SGD S000003164 YGL196W GO:0005554 SGD_REF:S000069584 ND F YGL196W gene taxon:4932 20030203 SGD
+SGD S000003164 YGL196W GO:0000004 SGD_REF:S000069584 ND P YGL196W gene taxon:4932 20030203 SGD
+SGD S000003188 YGL220W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YGL220W gene taxon:4932 20031028 SGD
+SGD S000003188 YGL220W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YGL220W gene taxon:4932 20031028 SGD
+SGD S000003188 YGL220W GO:0005554 SGD_REF:S000069584 ND F YGL220W gene taxon:4932 20021126 SGD
+SGD S000003188 YGL220W GO:0000004 SGD_REF:S000069584 ND P YGL220W gene taxon:4932 20021126 SGD
+SGD S000003195 YGL226W GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YGL226W gene taxon:4932 20031028 SGD
+SGD S000003195 YGL226W GO:0005554 SGD_REF:S000069584 ND F YGL226W gene taxon:4932 20021126 SGD
+SGD S000003195 YGL226W GO:0000004 SGD_REF:S000069584 ND P YGL226W gene taxon:4932 20021126 SGD
+SGD S000003199 YGL230C GO:0008372 SGD_REF:S000069584 ND C YGL230C gene taxon:4932 20021126 SGD
+SGD S000003199 YGL230C GO:0005554 SGD_REF:S000069584 ND F YGL230C gene taxon:4932 20021126 SGD
+SGD S000003199 YGL230C GO:0000004 SGD_REF:S000069584 ND P YGL230C gene taxon:4932 20021126 SGD
+SGD S000003200 YGL231C GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YGL231C gene taxon:4932 20031028 SGD
+SGD S000003200 YGL231C GO:0005554 SGD_REF:S000069584 ND F YGL231C gene taxon:4932 20021126 SGD
+SGD S000003200 YGL231C GO:0000004 SGD_REF:S000069584 ND P YGL231C gene taxon:4932 20021126 SGD
+SGD S000003204 YGL235W GO:0008372 SGD_REF:S000069584 ND C YGL235W gene taxon:4932 20021126 SGD
+SGD S000003204 YGL235W GO:0005554 SGD_REF:S000069584 ND F YGL235W gene taxon:4932 20021126 SGD
+SGD S000003204 YGL235W GO:0000004 SGD_REF:S000069584 ND P YGL235W gene taxon:4932 20021126 SGD
+SGD S000003211 YGL242C GO:0008372 SGD_REF:S000069584 ND C YGL242C gene taxon:4932 20030203 SGD
+SGD S000003211 YGL242C GO:0005554 SGD_REF:S000069584 ND F YGL242C gene taxon:4932 20030203 SGD
+SGD S000003211 YGL242C GO:0000004 SGD_REF:S000069584 ND P YGL242C gene taxon:4932 20030203 SGD
+SGD S000003219 YGL250W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YGL250W gene taxon:4932 20031028 SGD
+SGD S000003219 YGL250W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YGL250W gene taxon:4932 20031028 SGD
+SGD S000003219 YGL250W GO:0005554 SGD_REF:S000069584 ND F YGL250W gene taxon:4932 20021126 SGD
+SGD S000003219 YGL250W GO:0000004 SGD_REF:S000069584 ND P YGL250W gene taxon:4932 20021126 SGD
+SGD S000007607 YGL258W-A GO:0008372 SGD_REF:S000069584 ND C YGL258W-A gene taxon:4932 20010226 SGD
+SGD S000007607 YGL258W-A GO:0005554 SGD_REF:S000069584 ND F YGL258W-A gene taxon:4932 20010226 SGD
+SGD S000007607 YGL258W-A GO:0000004 SGD_REF:S000069584 ND P YGL258W-A gene taxon:4932 20010226 SGD
+SGD S000003229 YGL260W GO:0008372 SGD_REF:S000069584 ND C YGL260W gene taxon:4932 20030203 SGD
+SGD S000003229 YGL260W GO:0005554 SGD_REF:S000069584 ND F YGL260W gene taxon:4932 20030203 SGD
+SGD S000003229 YGL260W GO:0000004 SGD_REF:S000069584 ND P YGL260W gene taxon:4932 20030203 SGD
+SGD S000003231 YGL262W GO:0008372 SGD_REF:S000069584 ND C YGL262W gene taxon:4932 20021126 SGD
+SGD S000003231 YGL262W GO:0005554 SGD_REF:S000069584 ND F YGL262W gene taxon:4932 20021126 SGD
+SGD S000003231 YGL262W GO:0000004 SGD_REF:S000069584 ND P YGL262W gene taxon:4932 20021126 SGD
+SGD S000003233 YGR001C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YGR001C gene taxon:4932 20031028 SGD
+SGD S000003233 YGR001C GO:0008168 SGD_REF:S000076596|PMID:15225602 ISS F YGR001C gene taxon:4932 20040712 SGD
+SGD S000003233 YGR001C GO:0000004 SGD_REF:S000069584 ND P YGR001C gene taxon:4932 20030422 SGD
+SGD S000003244 YGR012W GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YGR012W gene taxon:4932 20031028 SGD
+SGD S000003244 YGR012W GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YGR012W gene taxon:4932 20040924 SGD
+SGD S000003244 YGR012W GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C YGR012W gene taxon:4932 20060317 SGD
+SGD S000003244 YGR012W GO:0004124 SGD_REF:S000072463|PMID:10592175 ISS F YGR012W gene taxon:4932 20030205 SGD
+SGD S000003244 YGR012W GO:0000004 SGD_REF:S000069584 ND P YGR012W gene taxon:4932 20021002 SGD
+SGD S000003247 YGR015C GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YGR015C gene taxon:4932 20031028 SGD
+SGD S000003247 YGR015C GO:0005554 SGD_REF:S000069584 ND F YGR015C gene taxon:4932 20021126 SGD
+SGD S000003247 YGR015C GO:0000004 SGD_REF:S000069584 ND P YGR015C gene taxon:4932 20021126 SGD
+SGD S000003248 YGR016W GO:0008372 SGD_REF:S000069584 ND C YGR016W gene taxon:4932 20021126 SGD
+SGD S000003248 YGR016W GO:0005554 SGD_REF:S000069584 ND F YGR016W gene taxon:4932 20021126 SGD
+SGD S000003248 YGR016W GO:0000004 SGD_REF:S000069584 ND P YGR016W gene taxon:4932 20021126 SGD
+SGD S000003249 YGR017W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YGR017W gene taxon:4932 20031028 SGD
+SGD S000003249 YGR017W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YGR017W gene taxon:4932 20031028 SGD
+SGD S000003249 YGR017W GO:0005554 SGD_REF:S000069584 ND F YGR017W gene taxon:4932 20021126 SGD
+SGD S000003249 YGR017W GO:0000004 SGD_REF:S000069584 ND P YGR017W gene taxon:4932 20021126 SGD
+SGD S000003253 YGR021W GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YGR021W gene taxon:4932 20031028 SGD
+SGD S000003253 YGR021W GO:0005554 SGD_REF:S000069584 ND F YGR021W gene taxon:4932 20030203 SGD
+SGD S000003253 YGR021W GO:0000004 SGD_REF:S000069584 ND P YGR021W gene taxon:4932 20030203 SGD
+SGD S000003258 YGR026W GO:0008372 SGD_REF:S000069584 ND C YGR026W gene taxon:4932 20021126 SGD
+SGD S000003258 YGR026W GO:0005554 SGD_REF:S000069584 ND F YGR026W gene taxon:4932 20021126 SGD
+SGD S000003258 YGR026W GO:0000004 SGD_REF:S000069584 ND P YGR026W gene taxon:4932 20021126 SGD
+SGD S000007405 YGR027W-A GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YGR027W-A gene taxon:4932 20030811 SGD
+SGD S000007405 YGR027W-A GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YGR027W-A gene taxon:4932 20030811 SGD
+SGD S000007405 YGR027W-A GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YGR027W-A gene taxon:4932 20030811 SGD
+SGD S000007405 YGR027W-A GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YGR027W-A gene taxon:4932 20030811 SGD
+SGD S000007406 YGR027W-B GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YGR027W-B gene taxon:4932 20030811 SGD
+SGD S000007406 YGR027W-B GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YGR027W-B gene taxon:4932 20030811 SGD
+SGD S000007406 YGR027W-B GO:0003887 SGD_REF:S000072465|PMID:9582191 ISS F YGR027W-B gene taxon:4932 20030811 SGD
+SGD S000007406 YGR027W-B GO:0003964 SGD_REF:S000072465|PMID:9582191 ISS F YGR027W-B gene taxon:4932 20030811 SGD
+SGD S000007406 YGR027W-B GO:0004540 SGD_REF:S000072465|PMID:9582191 ISS F YGR027W-B gene taxon:4932 20030811 SGD
+SGD S000007406 YGR027W-B GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YGR027W-B gene taxon:4932 20030811 SGD
+SGD S000007406 YGR027W-B GO:0008233 SGD_REF:S000072465|PMID:9582191 ISS F YGR027W-B gene taxon:4932 20030811 SGD
+SGD S000007406 YGR027W-B GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YGR027W-B gene taxon:4932 20030811 SGD
+SGD S000003263 YGR031W GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YGR031W gene taxon:4932 20031028 SGD
+SGD S000003263 YGR031W GO:0005554 SGD_REF:S000069584 ND F YGR031W gene taxon:4932 20021126 SGD
+SGD S000003263 YGR031W GO:0000004 SGD_REF:S000069584 ND P YGR031W gene taxon:4932 20021126 SGD
+SGD S000003267 YGR035C GO:0008372 SGD_REF:S000069584 ND C YGR035C gene taxon:4932 20021126 SGD
+SGD S000003267 YGR035C GO:0005554 SGD_REF:S000069584 ND F YGR035C gene taxon:4932 20021126 SGD
+SGD S000003267 YGR035C GO:0000004 SGD_REF:S000069584 ND P YGR035C gene taxon:4932 20021126 SGD
+SGD S000028827 YGR035W-A GO:0008372 SGD_REF:S000069584 ND C YGR035W-A gene taxon:4932 20030730 SGD
+SGD S000028827 YGR035W-A GO:0005554 SGD_REF:S000069584 ND F YGR035W-A gene taxon:4932 20030730 SGD
+SGD S000028827 YGR035W-A GO:0000004 SGD_REF:S000069584 ND P YGR035W-A gene taxon:4932 20030730 SGD
+SGD S000007407 YGR038C-A GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YGR038C-A gene taxon:4932 20030811 SGD
+SGD S000007407 YGR038C-A GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YGR038C-A gene taxon:4932 20030811 SGD
+SGD S000007407 YGR038C-A GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YGR038C-A gene taxon:4932 20030811 SGD
+SGD S000007407 YGR038C-A GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YGR038C-A gene taxon:4932 20030811 SGD
+SGD S000007408 YGR038C-B GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YGR038C-B gene taxon:4932 20030811 SGD
+SGD S000007408 YGR038C-B GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YGR038C-B gene taxon:4932 20030811 SGD
+SGD S000007408 YGR038C-B GO:0003887 SGD_REF:S000072465|PMID:9582191 ISS F YGR038C-B gene taxon:4932 20030811 SGD
+SGD S000007408 YGR038C-B GO:0003964 SGD_REF:S000072465|PMID:9582191 ISS F YGR038C-B gene taxon:4932 20030811 SGD
+SGD S000007408 YGR038C-B GO:0004540 SGD_REF:S000072465|PMID:9582191 ISS F YGR038C-B gene taxon:4932 20030811 SGD
+SGD S000007408 YGR038C-B GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YGR038C-B gene taxon:4932 20030811 SGD
+SGD S000007408 YGR038C-B GO:0008233 SGD_REF:S000072465|PMID:9582191 ISS F YGR038C-B gene taxon:4932 20030811 SGD
+SGD S000007408 YGR038C-B GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YGR038C-B gene taxon:4932 20030811 SGD
+SGD S000003274 YGR042W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YGR042W gene taxon:4932 20031028 SGD
+SGD S000003274 YGR042W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YGR042W gene taxon:4932 20031028 SGD
+SGD S000003274 YGR042W GO:0005554 SGD_REF:S000069584 ND F YGR042W gene taxon:4932 20021126 SGD
+SGD S000003274 YGR042W GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P YGR042W gene taxon:4932 20060227 SGD
+SGD S000003275 YGR043C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YGR043C gene taxon:4932 20031028 SGD
+SGD S000003275 YGR043C GO:0004801 SGD_REF:S000072463|PMID:10592175 ISS F YGR043C gene taxon:4932 20030205 SGD
+SGD S000003275 YGR043C GO:0000004 SGD_REF:S000069584 ND P YGR043C gene taxon:4932 20021002 SGD
+SGD S000003278 YGR046W GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YGR046W gene taxon:4932 20031028 SGD
+SGD S000003278 YGR046W GO:0005739 SGD_REF:S000075214|PMID:14690591 IDA C YGR046W gene taxon:4932 20031231 SGD
+SGD S000003278 YGR046W GO:0005554 SGD_REF:S000069584 ND F YGR046W gene taxon:4932 20030423 SGD
+SGD S000003278 YGR046W GO:0030150 SGD_REF:S000075214|PMID:14690591 IPI SGD:S000004249 P YGR046W gene taxon:4932 20031231 SGD
+SGD S000003285 YGR053C GO:0008372 SGD_REF:S000069584 ND C YGR053C gene taxon:4932 20021126 SGD
+SGD S000003285 YGR053C GO:0005554 SGD_REF:S000069584 ND F YGR053C gene taxon:4932 20021126 SGD
+SGD S000003285 YGR053C GO:0000004 SGD_REF:S000069584 ND P YGR053C gene taxon:4932 20021126 SGD
+SGD S000003286 YGR054W GO:0005830 SGD_REF:S000071447|PMID:12133843 IDA C YGR054W gene taxon:4932 20021014 SGD
+SGD S000003286 YGR054W GO:0005843 SGD_REF:S000071447|PMID:12133843 IDA C YGR054W gene taxon:4932 20021014 SGD
+SGD S000003286 YGR054W GO:0003743 SGD_REF:S000071447|PMID:12133843 IMP F YGR054W gene taxon:4932 20021014 SGD
+SGD S000003286 YGR054W GO:0003743 SGD_REF:S000071447|PMID:12133843 IDA F YGR054W gene taxon:4932 20021014 SGD
+SGD S000003286 YGR054W GO:0006413 SGD_REF:S000071447|PMID:12133843 IDA P YGR054W gene taxon:4932 20021014 SGD
+SGD S000003286 YGR054W GO:0006413 SGD_REF:S000071447|PMID:12133843 IMP P YGR054W gene taxon:4932 20021014 SGD
+SGD S000003290 YGR058W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YGR058W gene taxon:4932 20031028 SGD
+SGD S000003290 YGR058W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YGR058W gene taxon:4932 20031028 SGD
+SGD S000003290 YGR058W GO:0005554 SGD_REF:S000069584 ND F YGR058W gene taxon:4932 20021126 SGD
+SGD S000003290 YGR058W GO:0000004 SGD_REF:S000069584 ND P YGR058W gene taxon:4932 20021126 SGD
+SGD S000003298 YGR066C GO:0008372 SGD_REF:S000069584 ND C YGR066C gene taxon:4932 20030203 SGD
+SGD S000003298 YGR066C GO:0005554 SGD_REF:S000069584 ND F YGR066C gene taxon:4932 20030203 SGD
+SGD S000003298 YGR066C GO:0000004 SGD_REF:S000069584 ND P YGR066C gene taxon:4932 20030203 SGD
+SGD S000003299 YGR067C GO:0008372 SGD_REF:S000069584 ND C YGR067C gene taxon:4932 20030410 SGD
+SGD S000003299 YGR067C GO:0005554 SGD_REF:S000069584 ND F YGR067C gene taxon:4932 20030410 SGD
+SGD S000003299 YGR067C GO:0000004 SGD_REF:S000069584 ND P YGR067C gene taxon:4932 20030410 SGD
+SGD S000003300 YGR068C GO:0008372 SGD_REF:S000069584 ND C YGR068C gene taxon:4932 20021126 SGD
+SGD S000003300 YGR068C GO:0005554 SGD_REF:S000069584 ND F YGR068C gene taxon:4932 20021126 SGD
+SGD S000003300 YGR068C GO:0000004 SGD_REF:S000069584 ND P YGR068C gene taxon:4932 20021126 SGD
+SGD S000003303 YGR071C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YGR071C gene taxon:4932 20031028 SGD
+SGD S000003303 YGR071C GO:0005554 SGD_REF:S000069584 ND F YGR071C gene taxon:4932 20021126 SGD
+SGD S000003303 YGR071C GO:0000004 SGD_REF:S000069584 ND P YGR071C gene taxon:4932 20021126 SGD
+SGD S000003311 YGR079W GO:0008372 SGD_REF:S000069584 ND C YGR079W gene taxon:4932 20021126 SGD
+SGD S000003311 YGR079W GO:0005554 SGD_REF:S000069584 ND F YGR079W gene taxon:4932 20021126 SGD
+SGD S000003311 YGR079W GO:0000004 SGD_REF:S000069584 ND P YGR079W gene taxon:4932 20021126 SGD
+SGD S000003325 YGR093W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YGR093W gene taxon:4932 20031028 SGD
+SGD S000003325 YGR093W GO:0005554 SGD_REF:S000069584 ND F YGR093W gene taxon:4932 20021126 SGD
+SGD S000003325 YGR093W GO:0000004 SGD_REF:S000069584 ND P YGR093W gene taxon:4932 20021126 SGD
+SGD S000003334 YGR102C GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YGR102C gene taxon:4932 20031028 SGD
+SGD S000003334 YGR102C GO:0005554 SGD_REF:S000069584 ND F YGR102C gene taxon:4932 20021126 SGD
+SGD S000003334 YGR102C GO:0000004 SGD_REF:S000069584 ND P YGR102C gene taxon:4932 20021126 SGD
+SGD S000003338 YGR106C GO:0000329 SGD_REF:S000074185|PMID:14562095 IDA C YGR106C gene taxon:4932 20031028 SGD
+SGD S000003338 YGR106C GO:0005554 SGD_REF:S000069584 ND F YGR106C gene taxon:4932 20030203 SGD
+SGD S000003338 YGR106C GO:0000004 SGD_REF:S000069584 ND P YGR106C gene taxon:4932 20030203 SGD
+SGD S000007346 YGR109W-A GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YGR109W-A gene taxon:4932 20030811 SGD
+SGD S000007346 YGR109W-A GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YGR109W-A gene taxon:4932 20030811 SGD
+SGD S000007346 YGR109W-A GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YGR109W-A gene taxon:4932 20030811 SGD
+SGD S000007346 YGR109W-A GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YGR109W-A gene taxon:4932 20030811 SGD
+SGD S000007347 YGR109W-B GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YGR109W-B gene taxon:4932 20030811 SGD
+SGD S000007347 YGR109W-B GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YGR109W-B gene taxon:4932 20030811 SGD
+SGD S000007347 YGR109W-B GO:0003887 SGD_REF:S000072465|PMID:9582191 ISS F YGR109W-B gene taxon:4932 20030811 SGD
+SGD S000007347 YGR109W-B GO:0003964 SGD_REF:S000072465|PMID:9582191 ISS F YGR109W-B gene taxon:4932 20030811 SGD
+SGD S000007347 YGR109W-B GO:0004540 SGD_REF:S000072465|PMID:9582191 ISS F YGR109W-B gene taxon:4932 20030811 SGD
+SGD S000007347 YGR109W-B GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YGR109W-B gene taxon:4932 20030811 SGD
+SGD S000007347 YGR109W-B GO:0008233 SGD_REF:S000072465|PMID:9582191 ISS F YGR109W-B gene taxon:4932 20030811 SGD
+SGD S000007347 YGR109W-B GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YGR109W-B gene taxon:4932 20030811 SGD
+SGD S000003342 YGR110W GO:0008372 SGD_REF:S000069584 ND C YGR110W gene taxon:4932 20021126 SGD
+SGD S000003342 YGR110W GO:0005554 SGD_REF:S000069584 ND F YGR110W gene taxon:4932 20021126 SGD
+SGD S000003342 YGR110W GO:0000004 SGD_REF:S000069584 ND P YGR110W gene taxon:4932 20021126 SGD
+SGD S000003343 YGR111W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YGR111W gene taxon:4932 20031028 SGD
+SGD S000003343 YGR111W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YGR111W gene taxon:4932 20031028 SGD
+SGD S000003343 YGR111W GO:0005554 SGD_REF:S000069584 ND F YGR111W gene taxon:4932 20030203 SGD
+SGD S000003343 YGR111W GO:0000004 SGD_REF:S000069584 ND P YGR111W gene taxon:4932 20030203 SGD
+SGD S000003349 YGR117C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YGR117C gene taxon:4932 20031028 SGD
+SGD S000003349 YGR117C GO:0005554 SGD_REF:S000069584 ND F YGR117C gene taxon:4932 20021126 SGD
+SGD S000003349 YGR117C GO:0000004 SGD_REF:S000069584 ND P YGR117C gene taxon:4932 20021126 SGD
+SGD S000028550 YGR121W-A GO:0008372 SGD_REF:S000069584 ND C YGR121W-A gene taxon:4932 20030730 SGD
+SGD S000028550 YGR121W-A GO:0005554 SGD_REF:S000069584 ND F YGR121W-A gene taxon:4932 20030730 SGD
+SGD S000028550 YGR121W-A GO:0000004 SGD_REF:S000069584 ND P YGR121W-A gene taxon:4932 20030730 SGD
+SGD S000003354 YGR122W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YGR122W gene taxon:4932 20031028 SGD
+SGD S000003354 YGR122W GO:0005554 SGD_REF:S000069584 ND F YGR122W gene taxon:4932 20030203 SGD
+SGD S000003354 YGR122W GO:0000122 SGD_REF:S000082525|PMID:16024810 IMP P YGR122W gene taxon:4932 20060203 SGD
+SGD S000003354 YGR122W GO:0000122 SGD_REF:S000081820|PMID:15879523 IMP P YGR122W gene taxon:4932 20060203 SGD
+SGD S000003357 YGR125W GO:0000324 SGD_REF:S000074185|PMID:14562095 IDA C YGR125W gene taxon:4932 20031028 SGD
+SGD S000003357 YGR125W GO:0005554 SGD_REF:S000069584 ND F YGR125W gene taxon:4932 20030424 SGD
+SGD S000003357 YGR125W GO:0000004 SGD_REF:S000069584 ND P YGR125W gene taxon:4932 20030424 SGD
+SGD S000003358 YGR126W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YGR126W gene taxon:4932 20031028 SGD
+SGD S000003358 YGR126W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YGR126W gene taxon:4932 20031028 SGD
+SGD S000003358 YGR126W GO:0005554 SGD_REF:S000069584 ND F YGR126W gene taxon:4932 20021126 SGD
+SGD S000003358 YGR126W GO:0000004 SGD_REF:S000069584 ND P YGR126W gene taxon:4932 20021126 SGD
+SGD S000003359 YGR127W GO:0008372 SGD_REF:S000069584 ND C YGR127W gene taxon:4932 20021126 SGD
+SGD S000003359 YGR127W GO:0005554 SGD_REF:S000069584 ND F YGR127W gene taxon:4932 20021126 SGD
+SGD S000003359 YGR127W GO:0000004 SGD_REF:S000069584 ND P YGR127W gene taxon:4932 20021126 SGD
+SGD S000003362 YGR130C GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YGR130C gene taxon:4932 20020507 SGD
+SGD S000003362 YGR130C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YGR130C gene taxon:4932 20031028 SGD
+SGD S000003362 YGR130C GO:0005554 SGD_REF:S000069584 ND F YGR130C gene taxon:4932 20030203 SGD
+SGD S000003362 YGR130C GO:0000004 SGD_REF:S000069584 ND P YGR130C gene taxon:4932 20030203 SGD
+SGD S000003363 YGR131W GO:0008372 SGD_REF:S000069584 ND C YGR131W gene taxon:4932 20021126 SGD
+SGD S000003363 YGR131W GO:0005554 SGD_REF:S000069584 ND F YGR131W gene taxon:4932 20021126 SGD
+SGD S000003363 YGR131W GO:0000004 SGD_REF:S000069584 ND P YGR131W gene taxon:4932 20021126 SGD
+SGD S000003378 YGR146C GO:0008372 SGD_REF:S000069584 ND C YGR146C gene taxon:4932 20030203 SGD
+SGD S000003378 YGR146C GO:0005554 SGD_REF:S000069584 ND F YGR146C gene taxon:4932 20030203 SGD
+SGD S000003378 YGR146C GO:0000004 SGD_REF:S000069584 ND P YGR146C gene taxon:4932 20030203 SGD
+SGD S000028638 YGR146C-A GO:0008372 SGD_REF:S000069584 ND C YGR146C-A gene taxon:4932 20030730 SGD
+SGD S000028638 YGR146C-A GO:0005554 SGD_REF:S000069584 ND F YGR146C-A gene taxon:4932 20030730 SGD
+SGD S000028638 YGR146C-A GO:0000004 SGD_REF:S000069584 ND P YGR146C-A gene taxon:4932 20030730 SGD
+SGD S000003381 YGR149W GO:0016021 SGD_REF:S000072825|PMID:12524434 ISS C YGR149W gene taxon:4932 20030409 SGD
+SGD S000003381 YGR149W GO:0005554 SGD_REF:S000069584 ND F YGR149W gene taxon:4932 20030203 SGD
+SGD S000003381 YGR149W GO:0000004 SGD_REF:S000069584 ND P YGR149W gene taxon:4932 20030203 SGD
+SGD S000003382 YGR150C GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YGR150C gene taxon:4932 20031028 SGD
+SGD S000003382 YGR150C GO:0005554 SGD_REF:S000069584 ND F YGR150C gene taxon:4932 20030203 SGD
+SGD S000003382 YGR150C GO:0000004 SGD_REF:S000069584 ND P YGR150C gene taxon:4932 20030203 SGD
+SGD S000003385 YGR153W GO:0008372 SGD_REF:S000069584 ND C YGR153W|TOS10 gene taxon:4932 20021126 SGD
+SGD S000003385 YGR153W GO:0005554 SGD_REF:S000069584 ND F YGR153W|TOS10 gene taxon:4932 20021126 SGD
+SGD S000003385 YGR153W GO:0000004 SGD_REF:S000069584 ND P YGR153W|TOS10 gene taxon:4932 20021126 SGD
+SGD S000007367 YGR161C-C GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YGR161C-C gene taxon:4932 20030811 SGD
+SGD S000007367 YGR161C-C GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YGR161C-C gene taxon:4932 20030811 SGD
+SGD S000007367 YGR161C-C GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YGR161C-C gene taxon:4932 20030811 SGD
+SGD S000007367 YGR161C-C GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YGR161C-C gene taxon:4932 20030811 SGD
+SGD S000007368 YGR161C-D GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YGR161C-D gene taxon:4932 20030811 SGD
+SGD S000007368 YGR161C-D GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YGR161C-D gene taxon:4932 20030811 SGD
+SGD S000007368 YGR161C-D GO:0003887 SGD_REF:S000072465|PMID:9582191 ISS F YGR161C-D gene taxon:4932 20030811 SGD
+SGD S000007368 YGR161C-D GO:0003964 SGD_REF:S000072465|PMID:9582191 ISS F YGR161C-D gene taxon:4932 20030811 SGD
+SGD S000007368 YGR161C-D GO:0004540 SGD_REF:S000072465|PMID:9582191 ISS F YGR161C-D gene taxon:4932 20030811 SGD
+SGD S000007368 YGR161C-D GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YGR161C-D gene taxon:4932 20030811 SGD
+SGD S000007368 YGR161C-D GO:0008233 SGD_REF:S000072465|PMID:9582191 ISS F YGR161C-D gene taxon:4932 20030811 SGD
+SGD S000007368 YGR161C-D GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YGR161C-D gene taxon:4932 20030811 SGD
+SGD S000007369 YGR161W-A GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YGR161W-A gene taxon:4932 20030811 SGD
+SGD S000007369 YGR161W-A GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YGR161W-A gene taxon:4932 20030811 SGD
+SGD S000007369 YGR161W-A GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YGR161W-A gene taxon:4932 20030811 SGD
+SGD S000007369 YGR161W-A GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YGR161W-A gene taxon:4932 20030811 SGD
+SGD S000007370 YGR161W-B GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YGR161W-B gene taxon:4932 20030811 SGD
+SGD S000007370 YGR161W-B GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YGR161W-B gene taxon:4932 20030811 SGD
+SGD S000007370 YGR161W-B GO:0003887 SGD_REF:S000072465|PMID:9582191 ISS F YGR161W-B gene taxon:4932 20030811 SGD
+SGD S000007370 YGR161W-B GO:0003964 SGD_REF:S000072465|PMID:9582191 ISS F YGR161W-B gene taxon:4932 20030811 SGD
+SGD S000007370 YGR161W-B GO:0004540 SGD_REF:S000072465|PMID:9582191 ISS F YGR161W-B gene taxon:4932 20030811 SGD
+SGD S000007370 YGR161W-B GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YGR161W-B gene taxon:4932 20030811 SGD
+SGD S000007370 YGR161W-B GO:0008233 SGD_REF:S000072465|PMID:9582191 ISS F YGR161W-B gene taxon:4932 20030811 SGD
+SGD S000007370 YGR161W-B GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YGR161W-B gene taxon:4932 20030811 SGD
+SGD S000029726 YGR161W-C GO:0008372 SGD_REF:S000069584 ND C YGR161W-C gene taxon:4932 20040903 SGD
+SGD S000029726 YGR161W-C GO:0005554 SGD_REF:S000069584 ND F YGR161W-C gene taxon:4932 20040903 SGD
+SGD S000029726 YGR161W-C GO:0000004 SGD_REF:S000069584 ND P YGR161W-C gene taxon:4932 20040903 SGD
+SGD S000003400 YGR168C GO:0008372 SGD_REF:S000069584 ND C YGR168C gene taxon:4932 20021126 SGD
+SGD S000003400 YGR168C GO:0005554 SGD_REF:S000069584 ND F YGR168C gene taxon:4932 20021126 SGD
+SGD S000003400 YGR168C GO:0000004 SGD_REF:S000069584 ND P YGR168C gene taxon:4932 20021126 SGD
+SGD S000028521 YGR169C-A GO:0008372 SGD_REF:S000069584 ND C YGR169C-A|YGR169C-C gene taxon:4932 20030730 SGD
+SGD S000028521 YGR169C-A GO:0005554 SGD_REF:S000069584 ND F YGR169C-A|YGR169C-C gene taxon:4932 20030730 SGD
+SGD S000028521 YGR169C-A GO:0000004 SGD_REF:S000069584 ND P YGR169C-A|YGR169C-C gene taxon:4932 20030730 SGD
+SGD S000028639 YGR174W-A GO:0008372 SGD_REF:S000069584 ND C YGR174W-A gene taxon:4932 20030730 SGD
+SGD S000028639 YGR174W-A GO:0005554 SGD_REF:S000069584 ND F YGR174W-A gene taxon:4932 20030730 SGD
+SGD S000028639 YGR174W-A GO:0000004 SGD_REF:S000069584 ND P YGR174W-A gene taxon:4932 20030730 SGD
+SGD S000003430 YGR198W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YGR198W gene taxon:4932 20031028 SGD
+SGD S000003430 YGR198W GO:0005886 SGD_REF:S000075214|PMID:14690591 IDA C YGR198W gene taxon:4932 20031231 SGD
+SGD S000003430 YGR198W GO:0016740 SGD_REF:S000075214|PMID:14690591 ISS F YGR198W gene taxon:4932 20031231 SGD
+SGD S000003430 YGR198W GO:0000165 SGD_REF:S000075214|PMID:14690591 IPI SGD:S000004296 P YGR198W gene taxon:4932 20031231 SGD
+SGD S000003433 YGR201C GO:0008372 SGD_REF:S000069584 ND C YGR201C gene taxon:4932 20030203 SGD
+SGD S000003433 YGR201C GO:0005554 SGD_REF:S000069584 ND F YGR201C gene taxon:4932 20030203 SGD
+SGD S000003433 YGR201C GO:0000004 SGD_REF:S000069584 ND P YGR201C gene taxon:4932 20030203 SGD
+SGD S000003435 YGR203W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YGR203W gene taxon:4932 20031028 SGD
+SGD S000003435 YGR203W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YGR203W gene taxon:4932 20031028 SGD
+SGD S000003435 YGR203W GO:0004725 SGD_REF:S000074030|PMID:14508607 ISS F YGR203W gene taxon:4932 20030930 SGD
+SGD S000003435 YGR203W GO:0004725 SGD_REF:S000074031|PMID:9818190 NAS F YGR203W gene taxon:4932 20030930 SGD
+SGD S000003435 YGR203W GO:0016791 SGD_REF:S000062704|PMID:9733650 ISS F YGR203W gene taxon:4932 20030121 SGD
+SGD S000003435 YGR203W GO:0000004 SGD_REF:S000069584 ND P YGR203W gene taxon:4932 20021223 SGD
+SGD S000028640 YGR204C-A GO:0008372 SGD_REF:S000069584 ND C YGR204C-A gene taxon:4932 20030730 SGD
+SGD S000028640 YGR204C-A GO:0005554 SGD_REF:S000069584 ND F YGR204C-A gene taxon:4932 20030730 SGD
+SGD S000028640 YGR204C-A GO:0000004 SGD_REF:S000069584 ND P YGR204C-A gene taxon:4932 20030730 SGD
+SGD S000003437 YGR205W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YGR205W gene taxon:4932 20031028 SGD
+SGD S000003437 YGR205W GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YGR205W gene taxon:4932 20020507 SGD
+SGD S000003437 YGR205W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YGR205W gene taxon:4932 20031028 SGD
+SGD S000003437 YGR205W GO:0005524 SGD_REF:S000075499|PMID:14997573 IDA F YGR205W gene taxon:4932 20040722 SGD
+SGD S000003437 YGR205W GO:0000004 SGD_REF:S000069584 ND P YGR205W gene taxon:4932 20030429 SGD
+SGD S000003438 YGR206W GO:0005768 SGD_REF:S000074185|PMID:14562095 IDA C YGR206W gene taxon:4932 20031028 SGD
+SGD S000003438 YGR206W GO:0005554 SGD_REF:S000069584 ND F YGR206W gene taxon:4932 20021126 SGD
+SGD S000003438 YGR206W GO:0000004 SGD_REF:S000069584 ND P YGR206W gene taxon:4932 20021126 SGD
+SGD S000003439 YGR207C GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YGR207C gene taxon:4932 20031028 SGD
+SGD S000003439 YGR207C GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YGR207C gene taxon:4932 20040924 SGD
+SGD S000003439 YGR207C GO:0005554 SGD_REF:S000069584 ND F YGR207C gene taxon:4932 20021120 SGD
+SGD S000003439 YGR207C GO:0000004 SGD_REF:S000069584 ND P YGR207C gene taxon:4932 20021120 SGD
+SGD S000003442 YGR210C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YGR210C gene taxon:4932 20031028 SGD
+SGD S000003442 YGR210C GO:0005554 SGD_REF:S000069584 ND F YGR210C gene taxon:4932 20030421 SGD
+SGD S000003442 YGR210C GO:0000004 SGD_REF:S000069584 ND P YGR210C gene taxon:4932 20030421 SGD
+SGD S000003467 YGR235C GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YGR235C gene taxon:4932 20031028 SGD
+SGD S000003467 YGR235C GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YGR235C gene taxon:4932 20040924 SGD
+SGD S000003467 YGR235C GO:0005554 SGD_REF:S000069584 ND F YGR235C gene taxon:4932 20021126 SGD
+SGD S000003467 YGR235C GO:0000004 SGD_REF:S000069584 ND P YGR235C gene taxon:4932 20021126 SGD
+SGD S000003469 YGR237C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YGR237C gene taxon:4932 20031028 SGD
+SGD S000003469 YGR237C GO:0005554 SGD_REF:S000069584 ND F YGR237C gene taxon:4932 20030203 SGD
+SGD S000003469 YGR237C GO:0000004 SGD_REF:S000069584 ND P YGR237C gene taxon:4932 20030203 SGD
+SGD S000028551 YGR240C-A GO:0008372 SGD_REF:S000069584 ND C YGR240C-A gene taxon:4932 20030730 SGD
+SGD S000028551 YGR240C-A GO:0005554 SGD_REF:S000069584 ND F YGR240C-A gene taxon:4932 20030730 SGD
+SGD S000028551 YGR240C-A GO:0000004 SGD_REF:S000069584 ND P YGR240C-A gene taxon:4932 20030730 SGD
+SGD S000003482 YGR250C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YGR250C gene taxon:4932 20031028 SGD
+SGD S000003482 YGR250C GO:0003723 SGD_REF:S000042255|PMID:9133742 ISS F YGR250C gene taxon:4932 20030424 SGD
+SGD S000003482 YGR250C GO:0000004 SGD_REF:S000069584 ND P YGR250C gene taxon:4932 20030424 SGD
+SGD S000003483 YGR251W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YGR251W gene taxon:4932 20031028 SGD
+SGD S000003483 YGR251W GO:0005634 SGD_REF:S000075214|PMID:14690591 IDA C YGR251W gene taxon:4932 20040105 SGD
+SGD S000003483 YGR251W GO:0005730 SGD_REF:S000074185|PMID:14562095 IDA C YGR251W gene taxon:4932 20031028 SGD
+SGD S000003483 YGR251W GO:0005730 SGD_REF:S000075214|PMID:14690591 IDA C YGR251W gene taxon:4932 20040105 SGD
+SGD S000003483 YGR251W GO:0005554 SGD_REF:S000069584 ND F YGR251W gene taxon:4932 20030424 SGD
+SGD S000003483 YGR251W GO:0006365 SGD_REF:S000073750|PMID:12837249 IMP P YGR251W gene taxon:4932 20051101 SGD
+SGD S000003495 YGR263C GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YGR263C gene taxon:4932 20031028 SGD
+SGD S000003495 YGR263C GO:0005554 SGD_REF:S000069584 ND F YGR263C gene taxon:4932 20030424 SGD
+SGD S000003495 YGR263C GO:0000004 SGD_REF:S000069584 ND P YGR263C gene taxon:4932 20030424 SGD
+SGD S000003498 YGR266W GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YGR266W gene taxon:4932 20040928 SGD
+SGD S000003498 YGR266W GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C YGR266W gene taxon:4932 20060317 SGD
+SGD S000003498 YGR266W GO:0005886 SGD_REF:S000071931|PMID:12469340 IDA C YGR266W gene taxon:4932 20030103 SGD
+SGD S000003498 YGR266W GO:0005554 SGD_REF:S000069584 ND F YGR266W gene taxon:4932 20030429 SGD
+SGD S000003498 YGR266W GO:0000004 SGD_REF:S000069584 ND P YGR266W gene taxon:4932 20030429 SGD
+SGD S000007608 YGR271C-A GO:0005730 SGD_REF:S000074185|PMID:14562095 IDA C YGR271C-A gene taxon:4932 20031028 SGD
+SGD S000007608 YGR271C-A GO:0005554 SGD_REF:S000069584 ND F YGR271C-A gene taxon:4932 20010226 SGD
+SGD S000007608 YGR271C-A GO:0000004 SGD_REF:S000069584 ND P YGR271C-A gene taxon:4932 20010226 SGD
+SGD S000003504 YGR272C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YGR272C gene taxon:4932 20031028 SGD
+SGD S000003504 YGR272C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YGR272C gene taxon:4932 20031028 SGD
+SGD S000003504 YGR272C GO:0005554 SGD_REF:S000069584 ND F YGR272C gene taxon:4932 20021120 SGD
+SGD S000003504 YGR272C GO:0006365 SGD_REF:S000073750|PMID:12837249 IMP P YGR272C gene taxon:4932 20051101 SGD
+SGD S000003505 YGR273C GO:0008372 SGD_REF:S000069584 ND C YGR273C gene taxon:4932 20030424 SGD
+SGD S000003505 YGR273C GO:0005554 SGD_REF:S000069584 ND F YGR273C gene taxon:4932 20030424 SGD
+SGD S000003505 YGR273C GO:0000004 SGD_REF:S000069584 ND P YGR273C gene taxon:4932 20030424 SGD
+SGD S000003509 YGR277C GO:0005634 SGD_REF:S000075214|PMID:14690591 IDA C YGR277C gene taxon:4932 20040105 SGD
+SGD S000003509 YGR277C GO:0005737 SGD_REF:S000075214|PMID:14690591 IDA C YGR277C gene taxon:4932 20040105 SGD
+SGD S000003509 YGR277C GO:0004595 SGD_REF:S000073342|PMID:11923312 ISS F YGR277C gene taxon:4932 20030619 SGD
+SGD S000003509 YGR277C GO:0015937 SGD_REF:S000073342|PMID:11923312 ISS P YGR277C gene taxon:4932 20030619 SGD
+SGD S000003515 YGR283C GO:0005730 SGD_REF:S000074185|PMID:14562095 IDA C YGR283C gene taxon:4932 20031028 SGD
+SGD S000003515 YGR283C GO:0005554 SGD_REF:S000069584 ND F YGR283C gene taxon:4932 20030203 SGD
+SGD S000003515 YGR283C GO:0000004 SGD_REF:S000069584 ND P YGR283C gene taxon:4932 20030203 SGD
+SGD S000003519 YGR287C GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YGR287C gene taxon:4932 20040813 SGD
+SGD S000003519 YGR287C GO:0004553 SGD_REF:S000072463|PMID:10592175 ISS F YGR287C gene taxon:4932 20030206 SGD
+SGD S000003519 YGR287C GO:0000004 SGD_REF:S000069584 ND P YGR287C gene taxon:4932 20021002 SGD
+SGD S000001000 YHL008C GO:0000324 SGD_REF:S000074185|PMID:14562095 IDA C YHL008C gene taxon:4932 20031028 SGD
+SGD S000001000 YHL008C GO:0005215 SGD_REF:S000058352|PMID:9678606 ISS F YHL008C gene taxon:4932 20030421 SGD
+SGD S000001000 YHL008C NOT GO:0008028 SGD_REF:S000065864|PMID:11536335 IMP F YHL008C gene taxon:4932 20051109 SGD
+SGD S000001000 YHL008C GO:0000004 SGD_REF:S000069584 ND P YHL008C gene taxon:4932 20030421 SGD
+SGD S000001000 YHL008C NOT GO:0015718 SGD_REF:S000065864|PMID:11536335 IMP P YHL008C gene taxon:4932 20051109 SGD
+SGD S000007371 YHL009W-A GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YHL009W-A gene taxon:4932 20030811 SGD
+SGD S000007371 YHL009W-A GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YHL009W-A gene taxon:4932 20030811 SGD
+SGD S000007371 YHL009W-A GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YHL009W-A gene taxon:4932 20030811 SGD
+SGD S000007371 YHL009W-A GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YHL009W-A gene taxon:4932 20030811 SGD
+SGD S000007372 YHL009W-B GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YHL009W-B gene taxon:4932 20030811 SGD
+SGD S000007372 YHL009W-B GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YHL009W-B gene taxon:4932 20030811 SGD
+SGD S000007372 YHL009W-B GO:0003887 SGD_REF:S000072465|PMID:9582191 ISS F YHL009W-B gene taxon:4932 20030811 SGD
+SGD S000007372 YHL009W-B GO:0003964 SGD_REF:S000072465|PMID:9582191 ISS F YHL009W-B gene taxon:4932 20030811 SGD
+SGD S000007372 YHL009W-B GO:0004540 SGD_REF:S000072465|PMID:9582191 ISS F YHL009W-B gene taxon:4932 20030811 SGD
+SGD S000007372 YHL009W-B GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YHL009W-B gene taxon:4932 20030811 SGD
+SGD S000007372 YHL009W-B GO:0008233 SGD_REF:S000072465|PMID:9582191 ISS F YHL009W-B gene taxon:4932 20030811 SGD
+SGD S000007372 YHL009W-B GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YHL009W-B gene taxon:4932 20030811 SGD
+SGD S000001002 YHL010C GO:0008372 SGD_REF:S000069584 ND C YHL010C gene taxon:4932 20030203 SGD
+SGD S000001002 YHL010C GO:0008139 SGD_REF:S000065742|PMID:9497340 IDA F YHL010C gene taxon:4932 20030206 SGD
+SGD S000001002 YHL010C GO:0000004 SGD_REF:S000069584 ND P YHL010C gene taxon:4932 20030203 SGD
+SGD S000001004 YHL012W GO:0008372 SGD_REF:S000069584 ND C YHL012W gene taxon:4932 20030428 SGD
+SGD S000001004 YHL012W GO:0005554 SGD_REF:S000069584 ND F YHL012W gene taxon:4932 20030428 SGD
+SGD S000001004 YHL012W GO:0000004 SGD_REF:S000069584 ND P YHL012W gene taxon:4932 20021002 SGD
+SGD S000028828 YHL015W-A GO:0008372 SGD_REF:S000069584 ND C YHL015W-A gene taxon:4932 20030730 SGD
+SGD S000028828 YHL015W-A GO:0005554 SGD_REF:S000069584 ND F YHL015W-A gene taxon:4932 20030730 SGD
+SGD S000028828 YHL015W-A GO:0000004 SGD_REF:S000069584 ND P YHL015W-A gene taxon:4932 20030730 SGD
+SGD S000001009 YHL017W colocalizes_with GO:0030136 SGD_REF:S000074185|PMID:14562095 IDA C YHL017W gene taxon:4932 20031028 SGD
+SGD S000001009 YHL017W GO:0005554 SGD_REF:S000069584 ND F YHL017W gene taxon:4932 20030203 SGD
+SGD S000001009 YHL017W GO:0000004 SGD_REF:S000069584 ND P YHL017W gene taxon:4932 20030203 SGD
+SGD S000001010 YHL018W GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YHL018W gene taxon:4932 20031028 SGD
+SGD S000001010 YHL018W GO:0005554 SGD_REF:S000069584 ND F YHL018W gene taxon:4932 20021126 SGD
+SGD S000001010 YHL018W GO:0000004 SGD_REF:S000069584 ND P YHL018W gene taxon:4932 20021126 SGD
+SGD S000001018 YHL026C GO:0008372 SGD_REF:S000069584 ND C YHL026C gene taxon:4932 20030203 SGD
+SGD S000001018 YHL026C GO:0005554 SGD_REF:S000069584 ND F YHL026C gene taxon:4932 20030203 SGD
+SGD S000001018 YHL026C GO:0000004 SGD_REF:S000069584 ND P YHL026C gene taxon:4932 20030203 SGD
+SGD S000001031 YHL039W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YHL039W gene taxon:4932 20031028 SGD
+SGD S000001031 YHL039W GO:0005554 SGD_REF:S000069584 ND F YHL039W gene taxon:4932 20021126 SGD
+SGD S000001031 YHL039W GO:0000004 SGD_REF:S000069584 ND P YHL039W gene taxon:4932 20021126 SGD
+SGD S000001034 YHL042W GO:0008372 SGD_REF:S000069584 ND C YHL042W gene taxon:4932 20021126 SGD
+SGD S000001034 YHL042W GO:0005554 SGD_REF:S000069584 ND F YHL042W gene taxon:4932 20021126 SGD
+SGD S000001034 YHL042W GO:0000004 SGD_REF:S000069584 ND P YHL042W gene taxon:4932 20021126 SGD
+SGD S000001036 YHL044W GO:0005886 SGD_REF:S000074227|PMID:12101299 IDA C YHL044W gene taxon:4932 20031107 SGD
+SGD S000001036 YHL044W GO:0005886 SGD_REF:S000074227|PMID:12101299 ISS C YHL044W gene taxon:4932 20031107 SGD
+SGD S000001036 YHL044W GO:0005554 SGD_REF:S000069584 ND F YHL044W gene taxon:4932 20021126 SGD
+SGD S000001036 YHL044W GO:0000004 SGD_REF:S000069584 ND P YHL044W gene taxon:4932 20021126 SGD
+SGD S000028829 YHL048C-A GO:0008372 SGD_REF:S000069584 ND C YHL048C-A gene taxon:4932 20030730 SGD
+SGD S000028829 YHL048C-A GO:0005554 SGD_REF:S000069584 ND F YHL048C-A gene taxon:4932 20030730 SGD
+SGD S000028829 YHL048C-A GO:0000004 SGD_REF:S000069584 ND P YHL048C-A gene taxon:4932 20030730 SGD
+SGD S000001041 YHL049C GO:0008372 SGD_REF:S000069584 ND C YHL049C gene taxon:4932 20021126 SGD
+SGD S000001041 YHL049C GO:0005554 SGD_REF:S000069584 ND F YHL049C gene taxon:4932 20021126 SGD
+SGD S000001041 YHL049C GO:0000004 SGD_REF:S000069584 ND P YHL049C gene taxon:4932 20021126 SGD
+SGD S000001042 YHL050C GO:0008372 SGD_REF:S000069584 ND C YHL050C gene taxon:4932 20030410 SGD
+SGD S000001042 YHL050C GO:0004386 SGD_REF:S000053946|PMID:9837911 ISS F YHL050C gene taxon:4932 20030410 SGD
+SGD S000001042 YHL050C GO:0000004 SGD_REF:S000069584 ND P YHL050C gene taxon:4932 20030410 SGD
+SGD S000001045 YHR003C GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YHR003C gene taxon:4932 20031028 SGD
+SGD S000001045 YHR003C GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YHR003C gene taxon:4932 20040924 SGD
+SGD S000001045 YHR003C GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C YHR003C gene taxon:4932 20060317 SGD
+SGD S000001045 YHR003C GO:0005554 SGD_REF:S000069584 ND F YHR003C gene taxon:4932 20030203 SGD
+SGD S000001045 YHR003C GO:0000004 SGD_REF:S000069584 ND P YHR003C gene taxon:4932 20030203 SGD
+SGD S000028830 YHR007C-A GO:0008372 SGD_REF:S000069584 ND C YHR007C-A gene taxon:4932 20030730 SGD
+SGD S000028830 YHR007C-A GO:0005554 SGD_REF:S000069584 ND F YHR007C-A gene taxon:4932 20030730 SGD
+SGD S000028830 YHR007C-A GO:0000004 SGD_REF:S000069584 ND P YHR007C-A gene taxon:4932 20030730 SGD
+SGD S000001051 YHR009C GO:0005737 SGD_REF:S000056415|PMID:10684247 IDA C YHR009C gene taxon:4932 20010301 SGD
+SGD S000001051 YHR009C GO:0005554 SGD_REF:S000069584 ND F YHR009C gene taxon:4932 20010119 SGD
+SGD S000001051 YHR009C GO:0000004 SGD_REF:S000069584 ND P YHR009C gene taxon:4932 20010119 SGD
+SGD S000001062 YHR020W GO:0008372 SGD_REF:S000069584 ND C YHR020W gene taxon:4932 20010207 SGD
+SGD S000001062 YHR020W GO:0004827 SGD_REF:S000072463|PMID:10592175 ISS F YHR020W gene taxon:4932 20030212 SGD
+SGD S000001062 YHR020W GO:0006418 SGD_REF:S000072463|PMID:10592175 ISS P YHR020W gene taxon:4932 20050217 SGD
+SGD S000001064 YHR022C GO:0008372 SGD_REF:S000069584 ND C YHR022C gene taxon:4932 20030203 SGD
+SGD S000001064 YHR022C GO:0005554 SGD_REF:S000069584 ND F YHR022C gene taxon:4932 20030203 SGD
+SGD S000001064 YHR022C GO:0000004 SGD_REF:S000069584 ND P YHR022C gene taxon:4932 20030203 SGD
+SGD S000028645 YHR022C-A GO:0008372 SGD_REF:S000069584 ND C YHR022C-A gene taxon:4932 20030730 SGD
+SGD S000028645 YHR022C-A GO:0005554 SGD_REF:S000069584 ND F YHR022C-A gene taxon:4932 20030730 SGD
+SGD S000028645 YHR022C-A GO:0000004 SGD_REF:S000069584 ND P YHR022C-A gene taxon:4932 20030730 SGD
+SGD S000001074 YHR032W GO:0008372 SGD_REF:S000069584 ND C YHR032W gene taxon:4932 20021120 SGD
+SGD S000001074 YHR032W GO:0005554 SGD_REF:S000069584 ND F YHR032W gene taxon:4932 20021120 SGD
+SGD S000001074 YHR032W GO:0000004 SGD_REF:S000069584 ND P YHR032W gene taxon:4932 20021120 SGD
+SGD S000001075 YHR033W GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YHR033W gene taxon:4932 20020507 SGD
+SGD S000001075 YHR033W GO:0005554 SGD_REF:S000069584 ND F YHR033W gene taxon:4932 20030428 SGD
+SGD S000001075 YHR033W GO:0000004 SGD_REF:S000069584 ND P YHR033W gene taxon:4932 20030428 SGD
+SGD S000001077 YHR035W GO:0008372 SGD_REF:S000069584 ND C YHR035W gene taxon:4932 20030203 SGD
+SGD S000001077 YHR035W GO:0005554 SGD_REF:S000069584 ND F YHR035W gene taxon:4932 20030203 SGD
+SGD S000001077 YHR035W GO:0000004 SGD_REF:S000069584 ND P YHR035W gene taxon:4932 20030203 SGD
+SGD S000001087 YHR045W GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YHR045W gene taxon:4932 20031028 SGD
+SGD S000001087 YHR045W GO:0005554 SGD_REF:S000069584 ND F YHR045W gene taxon:4932 20021126 SGD
+SGD S000001087 YHR045W GO:0000004 SGD_REF:S000069584 ND P YHR045W gene taxon:4932 20021126 SGD
+SGD S000001090 YHR048W GO:0016021 SGD_REF:S000073301|PMID:12697649 ISS C YHR048W|YHK8 gene taxon:4932 20030619 SGD
+SGD S000001090 YHR048W GO:0015238 SGD_REF:S000073301|PMID:12697649 IEP F YHR048W|YHK8 gene taxon:4932 20030619 SGD
+SGD S000001090 YHR048W GO:0015238 SGD_REF:S000073301|PMID:12697649 ISS F YHR048W|YHK8 gene taxon:4932 20030619 SGD
+SGD S000001090 YHR048W GO:0015893 SGD_REF:S000073301|PMID:12697649 IEP P YHR048W|YHK8 gene taxon:4932 20030619 SGD
+SGD S000001090 YHR048W GO:0015893 SGD_REF:S000073301|PMID:12697649 ISS P YHR048W|YHK8 gene taxon:4932 20030619 SGD
+SGD S000028832 YHR050W-A GO:0008372 SGD_REF:S000069584 ND C YHR050W-A gene taxon:4932 20030730 SGD
+SGD S000028832 YHR050W-A GO:0005554 SGD_REF:S000069584 ND F YHR050W-A gene taxon:4932 20030730 SGD
+SGD S000028832 YHR050W-A GO:0000004 SGD_REF:S000069584 ND P YHR050W-A gene taxon:4932 20030730 SGD
+SGD S000001096 YHR054C GO:0008372 SGD_REF:S000069584 ND C YHR054C gene taxon:4932 20021126 SGD
+SGD S000001096 YHR054C GO:0005554 SGD_REF:S000069584 ND F YHR054C gene taxon:4932 20021126 SGD
+SGD S000001096 YHR054C GO:0000004 SGD_REF:S000069584 ND P YHR054C gene taxon:4932 20021126 SGD
+SGD S000001120 YHR078W GO:0008372 SGD_REF:S000069584 ND C YHR078W gene taxon:4932 20021126 SGD
+SGD S000001120 YHR078W GO:0005554 SGD_REF:S000069584 ND F YHR078W gene taxon:4932 20021126 SGD
+SGD S000001120 YHR078W GO:0000004 SGD_REF:S000069584 ND P YHR078W gene taxon:4932 20021126 SGD
+SGD S000001122 YHR080C GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YHR080C gene taxon:4932 20040813 SGD
+SGD S000001122 YHR080C GO:0005554 SGD_REF:S000069584 ND F YHR080C gene taxon:4932 20021126 SGD
+SGD S000001122 YHR080C GO:0000004 SGD_REF:S000069584 ND P YHR080C gene taxon:4932 20021126 SGD
+SGD S000028552 YHR086W-A GO:0008372 SGD_REF:S000069584 ND C YHR086W-A gene taxon:4932 20030730 SGD
+SGD S000028552 YHR086W-A GO:0005554 SGD_REF:S000069584 ND F YHR086W-A gene taxon:4932 20030730 SGD
+SGD S000028552 YHR086W-A GO:0000004 SGD_REF:S000069584 ND P YHR086W-A gene taxon:4932 20030730 SGD
+SGD S000001129 YHR087W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YHR087W gene taxon:4932 20031028 SGD
+SGD S000001129 YHR087W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YHR087W gene taxon:4932 20031028 SGD
+SGD S000001129 YHR087W GO:0005554 SGD_REF:S000069584 ND F YHR087W gene taxon:4932 20030203 SGD
+SGD S000001129 YHR087W GO:0016070 SGD_REF:S000080732|PMID:15701634 IGI P YHR087W gene taxon:4932 20050405 SGD
+SGD S000001139 YHR097C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YHR097C gene taxon:4932 20031028 SGD
+SGD S000001139 YHR097C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YHR097C gene taxon:4932 20031028 SGD
+SGD S000001139 YHR097C GO:0005554 SGD_REF:S000069584 ND F YHR097C gene taxon:4932 20030421 SGD
+SGD S000001139 YHR097C GO:0000004 SGD_REF:S000069584 ND P YHR097C gene taxon:4932 20030421 SGD
+SGD S000001142 YHR100C GO:0008372 SGD_REF:S000069584 ND C YHR100C gene taxon:4932 20021126 SGD
+SGD S000001142 YHR100C GO:0005554 SGD_REF:S000069584 ND F YHR100C gene taxon:4932 20021126 SGD
+SGD S000001142 YHR100C GO:0000004 SGD_REF:S000069584 ND P YHR100C gene taxon:4932 20021126 SGD
+SGD S000001154 YHR112C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YHR112C gene taxon:4932 20031028 SGD
+SGD S000001154 YHR112C GO:0004121 SGD_REF:S000039910|PMID:10821189 ISS F YHR112C gene taxon:4932 20030530 SGD
+SGD S000001154 YHR112C GO:0006790 SGD_REF:S000039910|PMID:10821189 ISS P YHR112C gene taxon:4932 20030530 SGD
+SGD S000001155 YHR113W GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C aspartyl aminopeptidase YHR113W gene taxon:4932 20020507 SGD
+SGD S000001155 YHR113W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C aspartyl aminopeptidase YHR113W gene taxon:4932 20031028 SGD
+SGD S000001155 YHR113W GO:0042576 SGD_REF:S000114108|PMID:16367759 IDA F aspartyl aminopeptidase YHR113W gene taxon:4932 20060126 SGD
+SGD S000001155 YHR113W GO:0006508 SGD_REF:S000057599|PMID:8091229 ISS P aspartyl aminopeptidase YHR113W gene taxon:4932 20050415 SGD
+SGD S000001155 YHR113W GO:0006508 SGD_REF:S000080056|PMID:15606766 ISS P aspartyl aminopeptidase YHR113W gene taxon:4932 20050415 SGD
+SGD S000001164 YHR122W GO:0005634 SGD_REF:S000075214|PMID:14690591 IDA C YHR122W gene taxon:4932 20040105 SGD
+SGD S000001164 YHR122W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YHR122W gene taxon:4932 20031028 SGD
+SGD S000001164 YHR122W GO:0005737 SGD_REF:S000075214|PMID:14690591 IDA C YHR122W gene taxon:4932 20040105 SGD
+SGD S000001164 YHR122W GO:0005554 SGD_REF:S000069584 ND F YHR122W gene taxon:4932 20021126 SGD
+SGD S000001164 YHR122W GO:0006350 SGD_REF:S000075214|PMID:14690591 IPI P YHR122W gene taxon:4932 20040105 SGD
+SGD S000001168 YHR126C GO:0008372 SGD_REF:S000069584 ND C YHR126C gene taxon:4932 20030203 SGD
+SGD S000001168 YHR126C GO:0005554 SGD_REF:S000069584 ND F YHR126C gene taxon:4932 20030203 SGD
+SGD S000001168 YHR126C GO:0000004 SGD_REF:S000069584 ND P YHR126C gene taxon:4932 20030203 SGD
+SGD S000001169 YHR127W GO:0005634 SGD_REF:S000056415|PMID:10684247 IDA C YHR127W|HSN1 gene taxon:4932 20020620 SGD
+SGD S000001169 YHR127W GO:0005554 SGD_REF:S000069584 ND F YHR127W|HSN1 gene taxon:4932 20021119 SGD
+SGD S000001169 YHR127W GO:0000004 SGD_REF:S000069584 ND P YHR127W|HSN1 gene taxon:4932 20021119 SGD
+SGD S000001173 YHR131C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YHR131C gene taxon:4932 20031028 SGD
+SGD S000001173 YHR131C GO:0005554 SGD_REF:S000069584 ND F YHR131C gene taxon:4932 20030203 SGD
+SGD S000001173 YHR131C GO:0000004 SGD_REF:S000069584 ND P YHR131C gene taxon:4932 20030203 SGD
+SGD S000001180 YHR138C GO:0008372 SGD_REF:S000069584 ND C YHR138C gene taxon:4932 20030120 SGD
+SGD S000001180 YHR138C GO:0004866 SGD_REF:S000044876|PMID:9657146 ISS F YHR138C gene taxon:4932 20030120 SGD
+SGD S000001180 YHR138C GO:0004866 SGD_REF:S000044876|PMID:9657146 IGI F YHR138C gene taxon:4932 20030120 SGD
+SGD S000001180 YHR138C GO:0042144 SGD_REF:S000044876|PMID:9657146 IGI P YHR138C gene taxon:4932 20020411 SGD
+SGD S000001182 YHR140W GO:0016021 SGD_REF:S000072825|PMID:12524434 ISS C YHR140W gene taxon:4932 20030409 SGD
+SGD S000001182 YHR140W GO:0005554 SGD_REF:S000069584 ND F YHR140W gene taxon:4932 20021126 SGD
+SGD S000001182 YHR140W GO:0000004 SGD_REF:S000069584 ND P YHR140W gene taxon:4932 20021126 SGD
+SGD S000001194 YHR151C GO:0008372 SGD_REF:S000069584 ND C YHR151C gene taxon:4932 20021126 SGD
+SGD S000001194 YHR151C GO:0005554 SGD_REF:S000069584 ND F YHR151C gene taxon:4932 20021126 SGD
+SGD S000001194 YHR151C GO:0000004 SGD_REF:S000069584 ND P YHR151C gene taxon:4932 20021126 SGD
+SGD S000001202 YHR159W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YHR159W gene taxon:4932 20031028 SGD
+SGD S000001202 YHR159W GO:0005554 SGD_REF:S000069584 ND F YHR159W gene taxon:4932 20021126 SGD
+SGD S000001202 YHR159W GO:0000004 SGD_REF:S000069584 ND P YHR159W gene taxon:4932 20021126 SGD
+SGD S000001205 YHR162W GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YHR162W gene taxon:4932 20031028 SGD
+SGD S000001205 YHR162W GO:0005554 SGD_REF:S000069584 ND F YHR162W gene taxon:4932 20030421 SGD
+SGD S000001205 YHR162W GO:0000004 SGD_REF:S000069584 ND P YHR162W gene taxon:4932 20030421 SGD
+SGD S000028553 YHR175W-A GO:0008372 SGD_REF:S000069584 ND C YHR175W-A gene taxon:4932 20030730 SGD
+SGD S000028553 YHR175W-A GO:0005554 SGD_REF:S000069584 ND F YHR175W-A gene taxon:4932 20030730 SGD
+SGD S000028553 YHR175W-A GO:0000004 SGD_REF:S000069584 ND P YHR175W-A gene taxon:4932 20030730 SGD
+SGD S000001220 YHR177W GO:0008372 SGD_REF:S000069584 ND C YHR177W|GON3 gene taxon:4932 20030203 SGD
+SGD S000001220 YHR177W GO:0005554 SGD_REF:S000069584 ND F YHR177W|GON3 gene taxon:4932 20030203 SGD
+SGD S000001220 YHR177W GO:0000004 SGD_REF:S000069584 ND P YHR177W|GON3 gene taxon:4932 20030203 SGD
+SGD S000001225 YHR182W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YHR182W gene taxon:4932 20031028 SGD
+SGD S000001225 YHR182W GO:0005554 SGD_REF:S000069584 ND F YHR182W gene taxon:4932 20021126 SGD
+SGD S000001225 YHR182W GO:0000004 SGD_REF:S000069584 ND P YHR182W gene taxon:4932 20021126 SGD
+SGD S000001235 YHR192W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YHR192W gene taxon:4932 20031028 SGD
+SGD S000001235 YHR192W GO:0005554 SGD_REF:S000069584 ND F YHR192W gene taxon:4932 20021126 SGD
+SGD S000001235 YHR192W GO:0000004 SGD_REF:S000069584 ND P YHR192W gene taxon:4932 20021126 SGD
+SGD S000029704 YHR199C-A GO:0008372 SGD_REF:S000069584 ND C YHR199C-A gene taxon:4932 20040220 SGD
+SGD S000029704 YHR199C-A GO:0005554 SGD_REF:S000069584 ND F YHR199C-A gene taxon:4932 20040220 SGD
+SGD S000029704 YHR199C-A GO:0000004 SGD_REF:S000069584 ND P YHR199C-A gene taxon:4932 20040220 SGD
+SGD S000001245 YHR202W GO:0000324 SGD_REF:S000074185|PMID:14562095 IDA C YHR202W gene taxon:4932 20031028 SGD
+SGD S000001245 YHR202W GO:0005625 SGD_REF:S000075303|PMID:11935221 IDA C YHR202W gene taxon:4932 20040114 SGD
+SGD S000001245 YHR202W GO:0005554 SGD_REF:S000069584 ND F YHR202W gene taxon:4932 20021126 SGD
+SGD S000001245 YHR202W GO:0000004 SGD_REF:S000069584 ND P YHR202W gene taxon:4932 20021126 SGD
+SGD S000001252 YHR209W GO:0008372 SGD_REF:S000069584 ND C YHR209W gene taxon:4932 20030317 SGD
+SGD S000001252 YHR209W GO:0008757 SGD_REF:S000073093|PMID:9873020 ISS F YHR209W gene taxon:4932 20030507 SGD
+SGD S000001252 YHR209W GO:0000004 SGD_REF:S000069584 ND P YHR209W gene taxon:4932 20030317 SGD
+SGD S000001253 YHR210C GO:0008372 SGD_REF:S000069584 ND C YHR210C gene taxon:4932 20030203 SGD
+SGD S000001253 YHR210C GO:0005554 SGD_REF:S000069584 ND F YHR210C gene taxon:4932 20030203 SGD
+SGD S000001253 YHR210C GO:0000004 SGD_REF:S000069584 ND P YHR210C gene taxon:4932 20030203 SGD
+SGD S000028650 YHR212W-A GO:0008372 SGD_REF:S000069584 ND C YHR212W-A gene taxon:4932 20030730 SGD
+SGD S000028650 YHR212W-A GO:0005554 SGD_REF:S000069584 ND F YHR212W-A gene taxon:4932 20030730 SGD
+SGD S000028650 YHR212W-A GO:0000004 SGD_REF:S000069584 ND P YHR212W-A gene taxon:4932 20030730 SGD
+SGD S000001256 YHR213W GO:0008372 SGD_REF:S000069584 ND C YHR213W gene taxon:4932 20030410 SGD
+SGD S000001256 YHR213W GO:0005554 SGD_REF:S000069584 ND F YHR213W gene taxon:4932 20030410 SGD
+SGD S000001256 YHR213W GO:0000004 SGD_REF:S000069584 ND P YHR213W gene taxon:4932 20030410 SGD
+SGD S000028651 YHR213W-A GO:0008372 SGD_REF:S000069584 ND C YHR213W-A gene taxon:4932 20030730 SGD
+SGD S000028651 YHR213W-A GO:0005554 SGD_REF:S000069584 ND F YHR213W-A gene taxon:4932 20030730 SGD
+SGD S000028651 YHR213W-A GO:0000004 SGD_REF:S000069584 ND P YHR213W-A gene taxon:4932 20030730 SGD
+SGD S000028652 YHR213W-B GO:0008372 SGD_REF:S000069584 ND C YHR213W-B gene taxon:4932 20030730 SGD
+SGD S000028652 YHR213W-B GO:0005554 SGD_REF:S000069584 ND F YHR213W-B gene taxon:4932 20030730 SGD
+SGD S000028652 YHR213W-B GO:0000004 SGD_REF:S000069584 ND P YHR213W-B gene taxon:4932 20030730 SGD
+SGD S000003534 YHR214C-B GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YHR214C-B gene taxon:4932 20030811 SGD
+SGD S000003534 YHR214C-B GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YHR214C-B gene taxon:4932 20030811 SGD
+SGD S000003534 YHR214C-B GO:0003887 SGD_REF:S000072465|PMID:9582191 ISS F YHR214C-B gene taxon:4932 20030811 SGD
+SGD S000003534 YHR214C-B GO:0003964 SGD_REF:S000072465|PMID:9582191 ISS F YHR214C-B gene taxon:4932 20030811 SGD
+SGD S000003534 YHR214C-B GO:0004540 SGD_REF:S000072465|PMID:9582191 ISS F YHR214C-B gene taxon:4932 20030811 SGD
+SGD S000003534 YHR214C-B GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YHR214C-B gene taxon:4932 20030811 SGD
+SGD S000003534 YHR214C-B GO:0008233 SGD_REF:S000072465|PMID:9582191 ISS F YHR214C-B gene taxon:4932 20030811 SGD
+SGD S000003534 YHR214C-B GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YHR214C-B gene taxon:4932 20030811 SGD
+SGD S000007421 YHR214C-C GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YHR214C-C gene taxon:4932 20030811 SGD
+SGD S000007421 YHR214C-C GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YHR214C-C gene taxon:4932 20030811 SGD
+SGD S000007421 YHR214C-C GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YHR214C-C gene taxon:4932 20030811 SGD
+SGD S000007421 YHR214C-C GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YHR214C-C gene taxon:4932 20030811 SGD
+SGD S000028653 YHR214C-D GO:0008372 SGD_REF:S000069584 ND C YHR214C-D gene taxon:4932 20030730 SGD
+SGD S000028653 YHR214C-D GO:0005554 SGD_REF:S000069584 ND F YHR214C-D gene taxon:4932 20030730 SGD
+SGD S000028653 YHR214C-D GO:0000004 SGD_REF:S000069584 ND P YHR214C-D gene taxon:4932 20030730 SGD
+SGD S000028654 YHR214C-E GO:0008372 SGD_REF:S000069584 ND C YHR214C-E gene taxon:4932 20030730 SGD
+SGD S000028654 YHR214C-E GO:0005554 SGD_REF:S000069584 ND F YHR214C-E gene taxon:4932 20030730 SGD
+SGD S000028654 YHR214C-E GO:0000004 SGD_REF:S000069584 ND P YHR214C-E gene taxon:4932 20030730 SGD
+SGD S000001257 YHR214W GO:0008372 SGD_REF:S000069584 ND C YHR214W gene taxon:4932 20030410 SGD
+SGD S000001257 YHR214W GO:0005554 SGD_REF:S000069584 ND F YHR214W gene taxon:4932 20030410 SGD
+SGD S000001257 YHR214W GO:0000004 SGD_REF:S000069584 ND P YHR214W gene taxon:4932 20030410 SGD
+SGD S000001261 YHR218W GO:0008372 SGD_REF:S000069584 ND C YHR218W gene taxon:4932 20030203 SGD
+SGD S000001261 YHR218W GO:0005554 SGD_REF:S000069584 ND F YHR218W gene taxon:4932 20030203 SGD
+SGD S000001261 YHR218W GO:0000004 SGD_REF:S000069584 ND P YHR218W gene taxon:4932 20030203 SGD
+SGD S000001262 YHR219W GO:0008372 SGD_REF:S000069584 ND C YHR219W gene taxon:4932 20030203 SGD
+SGD S000001262 YHR219W GO:0005554 SGD_REF:S000069584 ND F YHR219W gene taxon:4932 20030203 SGD
+SGD S000001262 YHR219W GO:0000004 SGD_REF:S000069584 ND P YHR219W gene taxon:4932 20030203 SGD
+SGD S000001263 YIL001W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YIL001W gene taxon:4932 20031028 SGD
+SGD S000001263 YIL001W GO:0005554 SGD_REF:S000069584 ND F YIL001W gene taxon:4932 20030203 SGD
+SGD S000001263 YIL001W GO:0000004 SGD_REF:S000069584 ND P YIL001W gene taxon:4932 20030203 SGD
+SGD S000028835 YIL002W-A GO:0008372 SGD_REF:S000069584 ND C YIL002W-A gene taxon:4932 20030730 SGD
+SGD S000028835 YIL002W-A GO:0005554 SGD_REF:S000069584 ND F YIL002W-A gene taxon:4932 20030730 SGD
+SGD S000028835 YIL002W-A GO:0000004 SGD_REF:S000069584 ND P YIL002W-A gene taxon:4932 20030730 SGD
+SGD S000003536 YIL014C-A GO:0008372 SGD_REF:S000069584 ND C YIL014C-A|YIL015C-A gene taxon:4932 20021126 SGD
+SGD S000003536 YIL014C-A GO:0005554 SGD_REF:S000069584 ND F YIL014C-A|YIL015C-A gene taxon:4932 20021126 SGD
+SGD S000003536 YIL014C-A GO:0000004 SGD_REF:S000069584 ND P YIL014C-A|YIL015C-A gene taxon:4932 20021126 SGD
+SGD S000001286 YIL024C GO:0008372 SGD_REF:S000069584 ND C YIL024C gene taxon:4932 20021126 SGD
+SGD S000001286 YIL024C GO:0005554 SGD_REF:S000069584 ND F YIL024C gene taxon:4932 20021126 SGD
+SGD S000001286 YIL024C GO:0000004 SGD_REF:S000069584 ND P YIL024C gene taxon:4932 20021126 SGD
+SGD S000001291 YIL029C GO:0008372 SGD_REF:S000069584 ND C YIL029C gene taxon:4932 20021126 SGD
+SGD S000001291 YIL029C GO:0005554 SGD_REF:S000069584 ND F YIL029C gene taxon:4932 20021126 SGD
+SGD S000001291 YIL029C GO:0000004 SGD_REF:S000069584 ND P YIL029C gene taxon:4932 20021126 SGD
+SGD S000001301 YIL039W GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YIL039W gene taxon:4932 20031028 SGD
+SGD S000001301 YIL039W GO:0005554 SGD_REF:S000069584 ND F YIL039W gene taxon:4932 20030203 SGD
+SGD S000001301 YIL039W GO:0000004 SGD_REF:S000069584 ND P YIL039W gene taxon:4932 20030203 SGD
+SGD S000001304 YIL042C GO:0005739 SGD_REF:S000063829|PMID:10974565 ISS C YIL042C gene taxon:4932 20030130 SGD
+SGD S000001304 YIL042C GO:0016301 SGD_REF:S000063829|PMID:10974565 ISS F YIL042C gene taxon:4932 20030130 SGD
+SGD S000001304 YIL042C GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P YIL042C gene taxon:4932 20060227 SGD
+SGD S000028836 YIL046W-A GO:0008372 SGD_REF:S000069584 ND C YIL046W-A gene taxon:4932 20030730 SGD
+SGD S000028836 YIL046W-A GO:0005554 SGD_REF:S000069584 ND F YIL046W-A gene taxon:4932 20030730 SGD
+SGD S000028836 YIL046W-A GO:0000004 SGD_REF:S000069584 ND P YIL046W-A gene taxon:4932 20030730 SGD
+SGD S000001317 YIL055C GO:0008372 SGD_REF:S000069584 ND C YIL055C gene taxon:4932 20021126 SGD
+SGD S000001317 YIL055C GO:0005554 SGD_REF:S000069584 ND F YIL055C gene taxon:4932 20021126 SGD
+SGD S000001317 YIL055C GO:0000004 SGD_REF:S000069584 ND P YIL055C gene taxon:4932 20021126 SGD
+SGD S000001319 YIL057C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YIL057C gene taxon:4932 20031028 SGD
+SGD S000001319 YIL057C GO:0005554 SGD_REF:S000069584 ND F YIL057C gene taxon:4932 20030203 SGD
+SGD S000001319 YIL057C GO:0000004 SGD_REF:S000069584 ND P YIL057C gene taxon:4932 20030203 SGD
+SGD S000001322 YIL060W GO:0008372 SGD_REF:S000069584 ND C YIL060W gene taxon:4932 20021126 SGD
+SGD S000001322 YIL060W GO:0005554 SGD_REF:S000069584 ND F YIL060W gene taxon:4932 20021126 SGD
+SGD S000001322 YIL060W GO:0000004 SGD_REF:S000069584 ND P YIL060W gene taxon:4932 20021126 SGD
+SGD S000001326 YIL064W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YIL064W gene taxon:4932 20031028 SGD
+SGD S000001326 YIL064W GO:0008757 SGD_REF:S000074033|PMID:12872006 ISS F YIL064W gene taxon:4932 20031001 SGD
+SGD S000001326 YIL064W GO:0000004 SGD_REF:S000069584 ND P YIL064W gene taxon:4932 20030203 SGD
+SGD S000001329 YIL067C GO:0000324 SGD_REF:S000074185|PMID:14562095 IDA C YIL067C gene taxon:4932 20031028 SGD
+SGD S000001329 YIL067C GO:0005554 SGD_REF:S000069584 ND F YIL067C gene taxon:4932 20021126 SGD
+SGD S000001329 YIL067C GO:0000004 SGD_REF:S000069584 ND P YIL067C gene taxon:4932 20021126 SGD
+SGD S000001339 YIL077C GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YIL077C gene taxon:4932 20031028 SGD
+SGD S000001339 YIL077C GO:0005554 SGD_REF:S000069584 ND F YIL077C gene taxon:4932 20021126 SGD
+SGD S000001339 YIL077C GO:0000004 SGD_REF:S000069584 ND P YIL077C gene taxon:4932 20021126 SGD
+SGD S000001342 YIL080W GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YIL080W gene taxon:4932 20030811 SGD
+SGD S000001342 YIL080W GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YIL080W gene taxon:4932 20030811 SGD
+SGD S000001342 YIL080W GO:0003887 SGD_REF:S000072465|PMID:9582191 ISS F YIL080W gene taxon:4932 20030811 SGD
+SGD S000001342 YIL080W GO:0003964 SGD_REF:S000072465|PMID:9582191 ISS F YIL080W gene taxon:4932 20030811 SGD
+SGD S000001342 YIL080W GO:0004540 SGD_REF:S000072465|PMID:9582191 ISS F YIL080W gene taxon:4932 20030811 SGD
+SGD S000001342 YIL080W GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YIL080W gene taxon:4932 20030811 SGD
+SGD S000001342 YIL080W GO:0008233 SGD_REF:S000072465|PMID:9582191 ISS F YIL080W gene taxon:4932 20030811 SGD
+SGD S000001342 YIL080W GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YIL080W gene taxon:4932 20030811 SGD
+SGD S000003537 YIL082W-A GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YIL082W-A gene taxon:4932 20030811 SGD
+SGD S000003537 YIL082W-A GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YIL082W-A gene taxon:4932 20030811 SGD
+SGD S000003537 YIL082W-A GO:0003887 SGD_REF:S000072465|PMID:9582191 ISS F YIL082W-A gene taxon:4932 20030811 SGD
+SGD S000003537 YIL082W-A GO:0003964 SGD_REF:S000072465|PMID:9582191 ISS F YIL082W-A gene taxon:4932 20030811 SGD
+SGD S000003537 YIL082W-A GO:0004540 SGD_REF:S000072465|PMID:9582191 ISS F YIL082W-A gene taxon:4932 20030811 SGD
+SGD S000003537 YIL082W-A GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YIL082W-A gene taxon:4932 20030811 SGD
+SGD S000003537 YIL082W-A GO:0008233 SGD_REF:S000072465|PMID:9582191 ISS F YIL082W-A gene taxon:4932 20030811 SGD
+SGD S000003537 YIL082W-A GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YIL082W-A gene taxon:4932 20030811 SGD
+SGD S000001345 YIL083C GO:0005634 SGD_REF:S000075214|PMID:14690591 IDA C YIL083C gene taxon:4932 20040105 SGD
+SGD S000001345 YIL083C GO:0005737 SGD_REF:S000075214|PMID:14690591 IDA C YIL083C gene taxon:4932 20040105 SGD
+SGD S000001345 YIL083C GO:0004632 SGD_REF:S000073342|PMID:11923312 ISS F YIL083C gene taxon:4932 20030619 SGD
+SGD S000001345 YIL083C GO:0015937 SGD_REF:S000073342|PMID:11923312 ISS P YIL083C gene taxon:4932 20030619 SGD
+SGD S000001349 YIL087C GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YIL087C gene taxon:4932 20031028 SGD
+SGD S000001349 YIL087C GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YIL087C gene taxon:4932 20040924 SGD
+SGD S000001349 YIL087C GO:0005554 SGD_REF:S000069584 ND F YIL087C gene taxon:4932 20021126 SGD
+SGD S000001349 YIL087C GO:0000004 SGD_REF:S000069584 ND P YIL087C gene taxon:4932 20021126 SGD
+SGD S000001351 YIL089W GO:0008372 SGD_REF:S000069584 ND C YIL089W gene taxon:4932 20021126 SGD
+SGD S000001351 YIL089W GO:0005554 SGD_REF:S000069584 ND F YIL089W gene taxon:4932 20021126 SGD
+SGD S000001351 YIL089W GO:0000004 SGD_REF:S000069584 ND P YIL089W gene taxon:4932 20021126 SGD
+SGD S000001353 YIL091C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YIL091C gene taxon:4932 20031028 SGD
+SGD S000001353 YIL091C GO:0005634 SGD_REF:S000075214|PMID:14690591 IDA C YIL091C gene taxon:4932 20040105 SGD
+SGD S000001353 YIL091C GO:0005730 SGD_REF:S000074185|PMID:14562095 IDA C YIL091C gene taxon:4932 20031028 SGD
+SGD S000001353 YIL091C GO:0005730 SGD_REF:S000075214|PMID:14690591 IDA C YIL091C gene taxon:4932 20040105 SGD
+SGD S000001353 YIL091C GO:0003724 SGD_REF:S000075214|PMID:14690591 ISS F YIL091C gene taxon:4932 20040105 SGD
+SGD S000001353 YIL091C GO:0000004 SGD_REF:S000069584 ND P YIL091C gene taxon:4932 20021126 SGD
+SGD S000001354 YIL092W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YIL092W gene taxon:4932 20031028 SGD
+SGD S000001354 YIL092W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YIL092W gene taxon:4932 20031028 SGD
+SGD S000001354 YIL092W GO:0005554 SGD_REF:S000069584 ND F YIL092W gene taxon:4932 20021126 SGD
+SGD S000001354 YIL092W GO:0000004 SGD_REF:S000069584 ND P YIL092W gene taxon:4932 20021126 SGD
+SGD S000001358 YIL096C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YIL096C gene taxon:4932 20031028 SGD
+SGD S000001358 YIL096C GO:0005730 SGD_REF:S000074185|PMID:14562095 IDA C YIL096C gene taxon:4932 20031028 SGD
+SGD S000001358 YIL096C GO:0005554 SGD_REF:S000069584 ND F YIL096C gene taxon:4932 20021126 SGD
+SGD S000001358 YIL096C GO:0000004 SGD_REF:S000069584 ND P YIL096C gene taxon:4932 20021126 SGD
+SGD S000001364 YIL102C GO:0008372 SGD_REF:S000069584 ND C YIL102C gene taxon:4932 20021126 SGD
+SGD S000001364 YIL102C GO:0005554 SGD_REF:S000069584 ND F YIL102C gene taxon:4932 20021126 SGD
+SGD S000001364 YIL102C GO:0000004 SGD_REF:S000069584 ND P YIL102C gene taxon:4932 20021126 SGD
+SGD S000113587 YIL102C-A GO:0008372 SGD_REF:S000069584 ND C YIL102C-A gene taxon:4932 20051122 SGD
+SGD S000113587 YIL102C-A GO:0005554 SGD_REF:S000069584 ND F YIL102C-A gene taxon:4932 20051122 SGD
+SGD S000113587 YIL102C-A GO:0000004 SGD_REF:S000069584 ND P YIL102C-A gene taxon:4932 20051122 SGD
+SGD S000001370 YIL108W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YIL108W gene taxon:4932 20031028 SGD
+SGD S000001370 YIL108W GO:0004222 SGD_REF:S000080056|PMID:15606766 ISS F YIL108W gene taxon:4932 20050415 SGD
+SGD S000001370 YIL108W GO:0006508 SGD_REF:S000080056|PMID:15606766 ISS P YIL108W gene taxon:4932 20050415 SGD
+SGD S000001372 YIL110W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YIL110W gene taxon:4932 20031028 SGD
+SGD S000001372 YIL110W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YIL110W gene taxon:4932 20031028 SGD
+SGD S000001372 YIL110W GO:0008757 SGD_REF:S000074033|PMID:12872006 ISS F YIL110W gene taxon:4932 20031001 SGD
+SGD S000001372 YIL110W GO:0000004 SGD_REF:S000069584 ND P YIL110W gene taxon:4932 20021126 SGD
+SGD S000001389 YIL127C GO:0005730 SGD_REF:S000074185|PMID:14562095 IDA C YIL127C gene taxon:4932 20031028 SGD
+SGD S000001389 YIL127C GO:0005554 SGD_REF:S000069584 ND F YIL127C gene taxon:4932 20021126 SGD
+SGD S000001389 YIL127C GO:0000004 SGD_REF:S000069584 ND P YIL127C gene taxon:4932 20021126 SGD
+SGD S000028556 YIL134C-A GO:0008372 SGD_REF:S000069584 ND C YIL134C-A gene taxon:4932 20030730 SGD
+SGD S000028556 YIL134C-A GO:0005554 SGD_REF:S000069584 ND F YIL134C-A gene taxon:4932 20030730 SGD
+SGD S000028556 YIL134C-A GO:0000004 SGD_REF:S000069584 ND P YIL134C-A gene taxon:4932 20030730 SGD
+SGD S000001413 YIL151C GO:0008372 SGD_REF:S000069584 ND C YIL151C gene taxon:4932 20021126 SGD
+SGD S000001413 YIL151C GO:0005554 SGD_REF:S000069584 ND F YIL151C gene taxon:4932 20021126 SGD
+SGD S000001413 YIL151C GO:0000004 SGD_REF:S000069584 ND P YIL151C gene taxon:4932 20021126 SGD
+SGD S000001414 YIL152W GO:0008372 SGD_REF:S000069584 ND C YIL152W gene taxon:4932 20021126 SGD
+SGD S000001414 YIL152W GO:0005554 SGD_REF:S000069584 ND F YIL152W gene taxon:4932 20021126 SGD
+SGD S000001414 YIL152W GO:0000004 SGD_REF:S000069584 ND P YIL152W gene taxon:4932 20021126 SGD
+SGD S000028511 YIL156W-B GO:0008372 SGD_REF:S000069584 ND C YIL156W-B gene taxon:4932 20030730 SGD
+SGD S000028511 YIL156W-B GO:0005554 SGD_REF:S000069584 ND F YIL156W-B gene taxon:4932 20030730 SGD
+SGD S000028511 YIL156W-B GO:0000004 SGD_REF:S000069584 ND P YIL156W-B gene taxon:4932 20030730 SGD
+SGD S000001420 YIL158W GO:0000324 SGD_REF:S000074185|PMID:14562095 IDA C YIL158W gene taxon:4932 20031028 SGD
+SGD S000001420 YIL158W GO:0005554 SGD_REF:S000069584 ND F YIL158W gene taxon:4932 20030203 SGD
+SGD S000001420 YIL158W GO:0000004 SGD_REF:S000069584 ND P YIL158W gene taxon:4932 20030203 SGD
+SGD S000001423 YIL161W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YIL161W gene taxon:4932 20031028 SGD
+SGD S000001423 YIL161W GO:0005554 SGD_REF:S000069584 ND F YIL161W gene taxon:4932 20021223 SGD
+SGD S000001423 YIL161W GO:0000004 SGD_REF:S000069584 ND P YIL161W gene taxon:4932 20021223 SGD
+SGD S000001427 YIL165C GO:0008372 SGD_REF:S000069584 ND C YIL165C gene taxon:4932 20021126 SGD
+SGD S000001427 YIL165C GO:0005554 SGD_REF:S000069584 ND F YIL165C gene taxon:4932 20021126 SGD
+SGD S000001427 YIL165C GO:0000004 SGD_REF:S000069584 ND P YIL165C gene taxon:4932 20021126 SGD
+SGD S000001428 YIL166C GO:0016020 SGD_REF:S000057800|PMID:8543057 ISS SGD:S000003913 C YIL166C gene taxon:4932 20051031 SGD
+SGD S000001428 YIL166C GO:0016020 SGD_REF:S000058231|PMID:9348664 ISS SGD:S000003913 C YIL166C gene taxon:4932 20051031 SGD
+SGD S000001428 YIL166C GO:0005215 SGD_REF:S000057800|PMID:8543057 ISS SGD:S000003913 F YIL166C gene taxon:4932 20051031 SGD
+SGD S000001428 YIL166C GO:0005215 SGD_REF:S000058231|PMID:9348664 ISS SGD:S000003913 F YIL166C gene taxon:4932 20051031 SGD
+SGD S000001428 YIL166C GO:0006810 SGD_REF:S000057800|PMID:8543057 ISS SGD:S000003913 P YIL166C gene taxon:4932 20051031 SGD
+SGD S000001428 YIL166C GO:0006810 SGD_REF:S000058231|PMID:9348664 ISS SGD:S000003913 P YIL166C gene taxon:4932 20051031 SGD
+SGD S000001430 YIL168W GO:0008372 SGD_REF:S000069584 ND C YIL168W|SDL1 gene taxon:4932 20051101 SGD
+SGD S000001430 YIL168W GO:0003941 SGD_REF:S000065076|PMID:2194168 ISS F YIL168W|SDL1 gene taxon:4932 20051101 SGD
+SGD S000001430 YIL168W GO:0009069 SGD_REF:S000065076|PMID:2194168 ISS P YIL168W|SDL1 gene taxon:4932 20051101 SGD
+SGD S000001431 YIL169C GO:0008372 SGD_REF:S000069584 ND C YIL169C gene taxon:4932 20030421 SGD
+SGD S000001431 YIL169C GO:0005554 SGD_REF:S000069584 ND F YIL169C gene taxon:4932 20030421 SGD
+SGD S000001431 YIL169C GO:0000004 SGD_REF:S000069584 ND P YIL169C gene taxon:4932 20030421 SGD
+SGD S000001433 YIL171W GO:0008372 SGD_REF:S000069584 ND C YIL171W|HXT12 gene taxon:4932 20040617 SGD
+SGD S000001433 YIL171W GO:0005554 SGD_REF:S000069584 ND F YIL171W|HXT12 gene taxon:4932 20041207 SGD
+SGD S000001433 YIL171W NOT GO:0015149 SGD_REF:S000056317|PMID:10618490 IGI F YIL171W|HXT12 gene taxon:4932 20041207 SGD
+SGD S000001433 YIL171W GO:0000004 SGD_REF:S000069584 ND P YIL171W|HXT12 gene taxon:4932 20041207 SGD
+SGD S000001433 YIL171W NOT GO:0008645 SGD_REF:S000056317|PMID:10618490 IGI P YIL171W|HXT12 gene taxon:4932 20041207 SGD
+SGD S000001434 YIL172C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YIL172C gene taxon:4932 20031028 SGD
+SGD S000001434 YIL172C GO:0015926 SGD_REF:S000072463|PMID:10592175 ISS F YIL172C gene taxon:4932 20030212 SGD
+SGD S000001434 YIL172C GO:0000004 SGD_REF:S000069584 ND P YIL172C gene taxon:4932 20021002 SGD
+SGD S000001436 YIL174W GO:0008372 SGD_REF:S000069584 ND C YIL174W gene taxon:4932 20021126 SGD
+SGD S000001436 YIL174W GO:0005554 SGD_REF:S000069584 ND F YIL174W gene taxon:4932 20021126 SGD
+SGD S000001436 YIL174W GO:0000004 SGD_REF:S000069584 ND P YIL174W gene taxon:4932 20021126 SGD
+SGD S000001437 YIL175W GO:0008372 SGD_REF:S000069584 ND C YIL175W gene taxon:4932 20021126 SGD
+SGD S000001437 YIL175W GO:0005554 SGD_REF:S000069584 ND F YIL175W gene taxon:4932 20021126 SGD
+SGD S000001437 YIL175W GO:0000004 SGD_REF:S000069584 ND P YIL175W gene taxon:4932 20021126 SGD
+SGD S000001439 YIL177C GO:0008372 SGD_REF:S000069584 ND C YIL177C gene taxon:4932 20030410 SGD
+SGD S000001439 YIL177C GO:0004386 SGD_REF:S000053946|PMID:9837911 ISS F YIL177C gene taxon:4932 20030410 SGD
+SGD S000001439 YIL177C GO:0000004 SGD_REF:S000069584 ND P YIL177C gene taxon:4932 20030410 SGD
+SGD S000001442 YIR003W GO:0015629 SGD_REF:S000074185|PMID:14562095 IDA C YIR003W gene taxon:4932 20031028 SGD
+SGD S000001442 YIR003W GO:0005554 SGD_REF:S000069584 ND F YIR003W gene taxon:4932 20030203 SGD
+SGD S000001442 YIR003W GO:0000004 SGD_REF:S000069584 ND P YIR003W gene taxon:4932 20030203 SGD
+SGD S000001446 YIR007W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YIR007W gene taxon:4932 20031028 SGD
+SGD S000001446 YIR007W GO:0005554 SGD_REF:S000069584 ND F YIR007W gene taxon:4932 20030203 SGD
+SGD S000001446 YIR007W GO:0000004 SGD_REF:S000069584 ND P YIR007W gene taxon:4932 20030203 SGD
+SGD S000001453 YIR014W GO:0000324 SGD_REF:S000074185|PMID:14562095 IDA C YIR014W gene taxon:4932 20031028 SGD
+SGD S000001453 YIR014W GO:0005554 SGD_REF:S000069584 ND F YIR014W gene taxon:4932 20021126 SGD
+SGD S000001453 YIR014W GO:0000004 SGD_REF:S000069584 ND P YIR014W gene taxon:4932 20021126 SGD
+SGD S000001455 YIR016W GO:0008372 SGD_REF:S000069584 ND C YIR016W gene taxon:4932 20021126 SGD
+SGD S000001455 YIR016W GO:0005554 SGD_REF:S000069584 ND F YIR016W gene taxon:4932 20021126 SGD
+SGD S000001455 YIR016W GO:0000004 SGD_REF:S000069584 ND P YIR016W gene taxon:4932 20021126 SGD
+SGD S000028837 YIR018C-A GO:0008372 SGD_REF:S000069584 ND C YIR018C-A gene taxon:4932 20030730 SGD
+SGD S000028837 YIR018C-A GO:0005554 SGD_REF:S000069584 ND F YIR018C-A gene taxon:4932 20030730 SGD
+SGD S000028837 YIR018C-A GO:0000004 SGD_REF:S000069584 ND P YIR018C-A gene taxon:4932 20030730 SGD
+SGD S000028838 YIR021W-A GO:0008372 SGD_REF:S000069584 ND C YIR021W-A gene taxon:4932 20030730 SGD
+SGD S000028838 YIR021W-A GO:0005554 SGD_REF:S000069584 ND F YIR021W-A gene taxon:4932 20030730 SGD
+SGD S000028838 YIR021W-A GO:0000004 SGD_REF:S000069584 ND P YIR021W-A gene taxon:4932 20030730 SGD
+SGD S000001463 YIR024C GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YIR024C|GIF1 gene taxon:4932 20031028 SGD
+SGD S000001463 YIR024C GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YIR024C|GIF1 gene taxon:4932 20031210 SGD
+SGD S000001463 YIR024C GO:0005554 SGD_REF:S000069584 ND F YIR024C|GIF1 gene taxon:4932 20020930 SGD
+SGD S000001463 YIR024C GO:0000004 SGD_REF:S000069584 ND P YIR024C|GIF1 gene taxon:4932 20020930 SGD
+SGD S000001474 YIR035C GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YIR035C gene taxon:4932 20020507 SGD
+SGD S000001474 YIR035C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YIR035C gene taxon:4932 20031028 SGD
+SGD S000001474 YIR035C GO:0005554 SGD_REF:S000069584 ND F YIR035C gene taxon:4932 20030203 SGD
+SGD S000001474 YIR035C GO:0000004 SGD_REF:S000069584 ND P YIR035C gene taxon:4932 20030203 SGD
+SGD S000001475 YIR036C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YIR036C gene taxon:4932 20031028 SGD
+SGD S000001475 YIR036C GO:0005554 SGD_REF:S000069584 ND F YIR036C gene taxon:4932 20030203 SGD
+SGD S000001475 YIR036C GO:0000004 SGD_REF:S000069584 ND P YIR036C gene taxon:4932 20030203 SGD
+SGD S000001481 YIR042C GO:0008372 SGD_REF:S000069584 ND C YIR042C gene taxon:4932 20021126 SGD
+SGD S000001481 YIR042C GO:0005554 SGD_REF:S000069584 ND F YIR042C gene taxon:4932 20021126 SGD
+SGD S000001481 YIR042C GO:0000004 SGD_REF:S000069584 ND P YIR042C gene taxon:4932 20021126 SGD
+SGD S000001482 YIR043C GO:0008372 SGD_REF:S000069584 ND C YIR043C gene taxon:4932 20030203 SGD
+SGD S000001482 YIR043C GO:0005554 SGD_REF:S000069584 ND F YIR043C gene taxon:4932 20030203 SGD
+SGD S000001482 YIR043C GO:0000004 SGD_REF:S000069584 ND P YIR043C gene taxon:4932 20030203 SGD
+SGD S000001483 YIR044C GO:0008372 SGD_REF:S000069584 ND C YIR044C gene taxon:4932 20021126 SGD
+SGD S000001483 YIR044C GO:0005554 SGD_REF:S000069584 ND F YIR044C gene taxon:4932 20021126 SGD
+SGD S000001483 YIR044C GO:0000004 SGD_REF:S000069584 ND P YIR044C gene taxon:4932 20021126 SGD
+SGD S000003553 YJL016W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YJL016W|YJL017W gene taxon:4932 20031028 SGD
+SGD S000003553 YJL016W GO:0005554 SGD_REF:S000069584 ND F YJL016W|YJL017W gene taxon:4932 20021126 SGD
+SGD S000003553 YJL016W GO:0000004 SGD_REF:S000069584 ND P YJL016W|YJL017W gene taxon:4932 20021126 SGD
+SGD S000003564 YJL027C GO:0008372 SGD_REF:S000069584 ND C YJL027C gene taxon:4932 20021126 SGD
+SGD S000003564 YJL027C GO:0005554 SGD_REF:S000069584 ND F YJL027C gene taxon:4932 20021126 SGD
+SGD S000003564 YJL027C GO:0000004 SGD_REF:S000069584 ND P YJL027C gene taxon:4932 20021126 SGD
+SGD S000003574 YJL037W GO:0008372 SGD_REF:S000069584 ND C YJL037W gene taxon:4932 20021126 SGD
+SGD S000003574 YJL037W GO:0005554 SGD_REF:S000069584 ND F YJL037W gene taxon:4932 20021126 SGD
+SGD S000003574 YJL037W GO:0000004 SGD_REF:S000069584 ND P YJL037W gene taxon:4932 20021126 SGD
+SGD S000003575 YJL038C GO:0008372 SGD_REF:S000069584 ND C YJL038C gene taxon:4932 20030421 SGD
+SGD S000003575 YJL038C GO:0005554 SGD_REF:S000069584 ND F YJL038C gene taxon:4932 20030421 SGD
+SGD S000003575 YJL038C GO:0000004 SGD_REF:S000069584 ND P YJL038C gene taxon:4932 20030421 SGD
+SGD S000003579 YJL043W GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YJL043W gene taxon:4932 20020507 SGD
+SGD S000003579 YJL043W GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YJL043W gene taxon:4932 20031028 SGD
+SGD S000003579 YJL043W GO:0005554 SGD_REF:S000069584 ND F YJL043W gene taxon:4932 20021126 SGD
+SGD S000003579 YJL043W GO:0000004 SGD_REF:S000069584 ND P YJL043W gene taxon:4932 20021126 SGD
+SGD S000003581 YJL045W GO:0005739 SGD_REF:S000050086|PMID:9730279 IPI C YJL045W|SDH1b gene taxon:4932 20021223 SGD
+SGD S000003581 YJL045W GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YJL045W|SDH1b gene taxon:4932 20040928 SGD
+SGD S000003581 YJL045W GO:0008177 SGD_REF:S000050086|PMID:9730279 IGI SGD:S000001631 F YJL045W|SDH1b gene taxon:4932 20051128 SGD
+SGD S000003581 YJL045W GO:0008177 SGD_REF:S000086932|PMID:16232921 IMP F YJL045W|SDH1b gene taxon:4932 20051128 SGD
+SGD S000003581 YJL045W GO:0008177 SGD_REF:S000086932|PMID:16232921 IGI SGD:S000001631 F YJL045W|SDH1b gene taxon:4932 20051128 SGD
+SGD S000003581 YJL045W GO:0008177 SGD_REF:S000050086|PMID:9730279 ISS SGD:S000001631 F YJL045W|SDH1b gene taxon:4932 20051128 SGD
+SGD S000003581 YJL045W GO:0045333 SGD_REF:S000050086|PMID:9730279 IGI SGD:S000001631 P YJL045W|SDH1b gene taxon:4932 20051128 SGD
+SGD S000003581 YJL045W GO:0045333 SGD_REF:S000086932|PMID:16232921 IGI SGD:S000001631 P YJL045W|SDH1b gene taxon:4932 20051128 SGD
+SGD S000003581 YJL045W GO:0045333 SGD_REF:S000086932|PMID:16232921 IMP P YJL045W|SDH1b gene taxon:4932 20051128 SGD
+SGD S000003582 YJL046W GO:0008372 SGD_REF:S000069584 ND C YJL046W gene taxon:4932 20030421 SGD
+SGD S000003582 YJL046W GO:0005554 SGD_REF:S000069584 ND F YJL046W gene taxon:4932 20030421 SGD
+SGD S000003582 YJL046W GO:0000004 SGD_REF:S000069584 ND P YJL046W gene taxon:4932 20030421 SGD
+SGD S000028804 YJL047C-A GO:0008372 SGD_REF:S000069584 ND C YJL047C-A gene taxon:4932 20030730 SGD
+SGD S000028804 YJL047C-A GO:0005554 SGD_REF:S000069584 ND F YJL047C-A gene taxon:4932 20030730 SGD
+SGD S000028804 YJL047C-A GO:0000004 SGD_REF:S000069584 ND P YJL047C-A gene taxon:4932 20030730 SGD
+SGD S000003585 YJL049W GO:0008372 SGD_REF:S000069584 ND C YJL049W gene taxon:4932 20030421 SGD
+SGD S000003585 YJL049W GO:0005554 SGD_REF:S000069584 ND F YJL049W gene taxon:4932 20030421 SGD
+SGD S000003585 YJL049W GO:0000004 SGD_REF:S000069584 ND P YJL049W gene taxon:4932 20030421 SGD
+SGD S000007610 YJL052C-A GO:0008372 SGD_REF:S000069584 ND C YJL052C-A gene taxon:4932 20010226 SGD
+SGD S000007610 YJL052C-A GO:0005554 SGD_REF:S000069584 ND F YJL052C-A gene taxon:4932 20010226 SGD
+SGD S000007610 YJL052C-A GO:0000004 SGD_REF:S000069584 ND P YJL052C-A gene taxon:4932 20010226 SGD
+SGD S000003591 YJL055W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YJL055W gene taxon:4932 20031028 SGD
+SGD S000003591 YJL055W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YJL055W gene taxon:4932 20031028 SGD
+SGD S000003591 YJL055W GO:0005554 SGD_REF:S000069584 ND F YJL055W gene taxon:4932 20030421 SGD
+SGD S000003591 YJL055W GO:0000004 SGD_REF:S000069584 ND P YJL055W gene taxon:4932 20030421 SGD
+SGD S000007611 YJL062W-A GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YJL062W-A gene taxon:4932 20031028 SGD
+SGD S000007611 YJL062W-A GO:0005554 SGD_REF:S000069584 ND F YJL062W-A gene taxon:4932 20010226 SGD
+SGD S000007611 YJL062W-A GO:0000004 SGD_REF:S000069584 ND P YJL062W-A gene taxon:4932 20010226 SGD
+SGD S000003604 YJL068C GO:0005829 SGD_REF:S000065748|PMID:10427036 IDA C S-formylglutathione hydrolase YJL068C gene taxon:4932 20021126 SGD
+SGD S000003604 YJL068C GO:0018738 SGD_REF:S000065748|PMID:10427036 IDA F S-formylglutathione hydrolase YJL068C gene taxon:4932 20051208 SGD
+SGD S000003604 YJL068C GO:0046294 SGD_REF:S000065748|PMID:10427036 IMP P S-formylglutathione hydrolase YJL068C gene taxon:4932 20051208 SGD
+SGD S000003606 YJL070C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YJL070C gene taxon:4932 20031028 SGD
+SGD S000003606 YJL070C GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YJL070C gene taxon:4932 20040928 SGD
+SGD S000003606 YJL070C GO:0005554 SGD_REF:S000069584 ND F YJL070C gene taxon:4932 20030421 SGD
+SGD S000003606 YJL070C GO:0000004 SGD_REF:S000069584 ND P YJL070C gene taxon:4932 20030421 SGD
+SGD S000028662 YJL077W-B GO:0008372 SGD_REF:S000069584 ND C YJL077W-B gene taxon:4932 20030730 SGD
+SGD S000028662 YJL077W-B GO:0005554 SGD_REF:S000069584 ND F YJL077W-B gene taxon:4932 20030730 SGD
+SGD S000028662 YJL077W-B GO:0000004 SGD_REF:S000069584 ND P YJL077W-B gene taxon:4932 20030730 SGD
+SGD S000003620 YJL084C GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YJL084C gene taxon:4932 20020507 SGD
+SGD S000003620 YJL084C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YJL084C gene taxon:4932 20031028 SGD
+SGD S000003620 YJL084C GO:0030332 SGD_REF:S000070355|PMID:12098764 IDA F YJL084C gene taxon:4932 20021126 SGD
+SGD S000003620 YJL084C GO:0000004 SGD_REF:S000069584 ND P YJL084C gene taxon:4932 20021126 SGD
+SGD S000003639 YJL103C GO:0008372 SGD_REF:S000069584 ND C YJL103C gene taxon:4932 20021126 SGD
+SGD S000003639 YJL103C GO:0005554 SGD_REF:S000069584 ND F YJL103C gene taxon:4932 20021126 SGD
+SGD S000003639 YJL103C GO:0006119 SGD_REF:S000081742|PMID:15583838 ISS P YJL103C gene taxon:4932 20050527 SGD
+SGD S000003639 YJL103C GO:0006119 SGD_REF:S000081742|PMID:15583838 IEP P YJL103C gene taxon:4932 20060201 SGD
+SGD S000003643 YJL107C GO:0008372 SGD_REF:S000069584 ND C YJL107C gene taxon:4932 20030421 SGD
+SGD S000003643 YJL107C GO:0005554 SGD_REF:S000069584 ND F YJL107C gene taxon:4932 20030421 SGD
+SGD S000003643 YJL107C GO:0000004 SGD_REF:S000069584 ND P YJL107C gene taxon:4932 20030421 SGD
+SGD S000003649 YJL113W GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YJL113W gene taxon:4932 20030811 SGD
+SGD S000003649 YJL113W GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YJL113W gene taxon:4932 20040928 SGD
+SGD S000003649 YJL113W GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YJL113W gene taxon:4932 20030811 SGD
+SGD S000003649 YJL113W GO:0003887 SGD_REF:S000072465|PMID:9582191 ISS F YJL113W gene taxon:4932 20030811 SGD
+SGD S000003649 YJL113W GO:0003964 SGD_REF:S000072465|PMID:9582191 ISS F YJL113W gene taxon:4932 20030811 SGD
+SGD S000003649 YJL113W GO:0004540 SGD_REF:S000072465|PMID:9582191 ISS F YJL113W gene taxon:4932 20030811 SGD
+SGD S000003649 YJL113W GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YJL113W gene taxon:4932 20030811 SGD
+SGD S000003649 YJL113W GO:0008233 SGD_REF:S000072465|PMID:9582191 ISS F YJL113W gene taxon:4932 20030811 SGD
+SGD S000003649 YJL113W GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YJL113W gene taxon:4932 20030811 SGD
+SGD S000003650 YJL114W GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YJL114W gene taxon:4932 20030811 SGD
+SGD S000003650 YJL114W GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YJL114W gene taxon:4932 20030811 SGD
+SGD S000003650 YJL114W GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YJL114W gene taxon:4932 20030811 SGD
+SGD S000003650 YJL114W GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YJL114W gene taxon:4932 20030811 SGD
+SGD S000003654 YJL118W GO:0008372 SGD_REF:S000069584 ND C YJL118W gene taxon:4932 20021119 SGD
+SGD S000003654 YJL118W GO:0005554 SGD_REF:S000069584 ND F YJL118W gene taxon:4932 20021119 SGD
+SGD S000003654 YJL118W GO:0000004 SGD_REF:S000069584 ND P YJL118W gene taxon:4932 20021119 SGD
+SGD S000003659 YJL123C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YJL123C gene taxon:4932 20031028 SGD
+SGD S000003659 YJL123C GO:0005794 SGD_REF:S000074185|PMID:14562095 IDA C YJL123C gene taxon:4932 20031028 SGD
+SGD S000003659 YJL123C colocalizes_with GO:0030137 SGD_REF:S000074185|PMID:14562095 IDA C YJL123C gene taxon:4932 20031028 SGD
+SGD S000003659 YJL123C GO:0005554 SGD_REF:S000069584 ND F YJL123C gene taxon:4932 20030421 SGD
+SGD S000003659 YJL123C GO:0000004 SGD_REF:S000069584 ND P YJL123C gene taxon:4932 20030421 SGD
+SGD S000028522 YJL127C-B GO:0008372 SGD_REF:S000069584 ND C YJL127C-B|YJL127C-A gene taxon:4932 20030730 SGD
+SGD S000028522 YJL127C-B GO:0005554 SGD_REF:S000069584 ND F YJL127C-B|YJL127C-A gene taxon:4932 20030730 SGD
+SGD S000028522 YJL127C-B GO:0000004 SGD_REF:S000069584 ND P YJL127C-B|YJL127C-A gene taxon:4932 20030730 SGD
+SGD S000003667 YJL131C GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YJL131C gene taxon:4932 20031028 SGD
+SGD S000003667 YJL131C GO:0005554 SGD_REF:S000069584 ND F YJL131C gene taxon:4932 20030421 SGD
+SGD S000003667 YJL131C GO:0000004 SGD_REF:S000069584 ND P YJL131C gene taxon:4932 20030421 SGD
+SGD S000003668 YJL132W GO:0005624 SGD_REF:S000075303|PMID:11935221 IDA C YJL132W gene taxon:4932 20040114 SGD
+SGD S000003668 YJL132W GO:0005554 SGD_REF:S000069584 ND F YJL132W gene taxon:4932 20021119 SGD
+SGD S000003668 YJL132W GO:0000004 SGD_REF:S000069584 ND P YJL132W gene taxon:4932 20021119 SGD
+SGD S000028805 YJL133C-A GO:0008372 SGD_REF:S000069584 ND C YJL133C-A gene taxon:4932 20030730 SGD
+SGD S000028805 YJL133C-A GO:0005554 SGD_REF:S000069584 ND F YJL133C-A gene taxon:4932 20030730 SGD
+SGD S000028805 YJL133C-A GO:0000004 SGD_REF:S000069584 ND P YJL133C-A gene taxon:4932 20030730 SGD
+SGD S000028806 YJL136W-A GO:0008372 SGD_REF:S000069584 ND C YJL136W-A gene taxon:4932 20030730 SGD
+SGD S000028806 YJL136W-A GO:0005554 SGD_REF:S000069584 ND F YJL136W-A gene taxon:4932 20030730 SGD
+SGD S000028806 YJL136W-A GO:0000004 SGD_REF:S000069584 ND P YJL136W-A gene taxon:4932 20030730 SGD
+SGD S000003680 YJL144W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YJL144W gene taxon:4932 20031028 SGD
+SGD S000003680 YJL144W GO:0005554 SGD_REF:S000069584 ND F YJL144W gene taxon:4932 20030203 SGD
+SGD S000003680 YJL144W GO:0009269 SGD_REF:S000063137|PMID:10681550 IEP P YJL144W gene taxon:4932 20030210 SGD
+SGD S000003683 YJL147C GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YJL147C gene taxon:4932 20031028 SGD
+SGD S000003683 YJL147C GO:0005554 SGD_REF:S000069584 ND F YJL147C gene taxon:4932 20030203 SGD
+SGD S000003683 YJL147C GO:0000004 SGD_REF:S000069584 ND P YJL147C gene taxon:4932 20030203 SGD
+SGD S000003685 YJL149W GO:0019005 SGD_REF:S000060747|PMID:11283612 IPI C YJL149W gene taxon:4932 20030410 SGD
+SGD S000003685 YJL149W GO:0005554 SGD_REF:S000069584 ND F YJL149W gene taxon:4932 20030410 SGD
+SGD S000003685 YJL149W GO:0000004 SGD_REF:S000069584 ND P YJL149W gene taxon:4932 20030410 SGD
+SGD S000003696 YJL160C GO:0008372 SGD_REF:S000069584 ND C YJL160C gene taxon:4932 20021122 SGD
+SGD S000003696 YJL160C GO:0005554 SGD_REF:S000069584 ND F YJL160C gene taxon:4932 20021122 SGD
+SGD S000003696 YJL160C GO:0000004 SGD_REF:S000069584 ND P YJL160C gene taxon:4932 20021122 SGD
+SGD S000003699 YJL163C GO:0008372 SGD_REF:S000069584 ND C YJL163C gene taxon:4932 20021126 SGD
+SGD S000003699 YJL163C GO:0005554 SGD_REF:S000069584 ND F YJL163C gene taxon:4932 20021126 SGD
+SGD S000003699 YJL163C GO:0000004 SGD_REF:S000069584 ND P YJL163C gene taxon:4932 20021126 SGD
+SGD S000003707 YJL171C GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YJL171C gene taxon:4932 20040928 SGD
+SGD S000003707 YJL171C GO:0009277 SGD_REF:S000040179|PMID:10383953 IDA C YJL171C gene taxon:4932 20020617 SGD
+SGD S000003707 YJL171C GO:0005554 SGD_REF:S000069584 ND F YJL171C gene taxon:4932 20030421 SGD
+SGD S000003707 YJL171C GO:0000004 SGD_REF:S000069584 ND P YJL171C gene taxon:4932 20030421 SGD
+SGD S000003717 YJL181W GO:0008372 SGD_REF:S000069584 ND C YJL181W gene taxon:4932 20030203 SGD
+SGD S000003717 YJL181W GO:0005554 SGD_REF:S000069584 ND F YJL181W gene taxon:4932 20030203 SGD
+SGD S000003717 YJL181W GO:0000004 SGD_REF:S000069584 ND P YJL181W gene taxon:4932 20030203 SGD
+SGD S000003721 YJL185C GO:0008372 SGD_REF:S000069584 ND C YJL185C gene taxon:4932 20030421 SGD
+SGD S000003721 YJL185C GO:0005554 SGD_REF:S000069584 ND F YJL185C gene taxon:4932 20030421 SGD
+SGD S000003721 YJL185C GO:0000004 SGD_REF:S000069584 ND P YJL185C gene taxon:4932 20030421 SGD
+SGD S000003729 YJL193W GO:0008372 SGD_REF:S000069584 ND C YJL193W gene taxon:4932 20030203 SGD
+SGD S000003729 YJL193W GO:0005554 SGD_REF:S000069584 ND F YJL193W gene taxon:4932 20030203 SGD
+SGD S000003729 YJL193W GO:0000004 SGD_REF:S000069584 ND P YJL193W gene taxon:4932 20030203 SGD
+SGD S000003741 YJL206C GO:0008372 SGD_REF:S000069584 ND C YJL206C gene taxon:4932 20030425 SGD
+SGD S000003741 YJL206C GO:0005554 SGD_REF:S000069584 ND F YJL206C gene taxon:4932 20030425 SGD
+SGD S000003741 YJL206C GO:0000004 SGD_REF:S000069584 ND P YJL206C gene taxon:4932 20030425 SGD
+SGD S000003749 YJL213W GO:0008372 SGD_REF:S000069584 ND C YJL213W gene taxon:4932 20030425 SGD
+SGD S000003749 YJL213W GO:0005554 SGD_REF:S000069584 ND F YJL213W gene taxon:4932 20030425 SGD
+SGD S000003749 YJL213W GO:0000004 SGD_REF:S000069584 ND P YJL213W gene taxon:4932 20030425 SGD
+SGD S000003752 YJL216C GO:0008372 SGD_REF:S000069584 ND C YJL216C gene taxon:4932 20030213 SGD
+SGD S000003752 YJL216C GO:0004553 SGD_REF:S000072463|PMID:10592175 ISS F YJL216C gene taxon:4932 20030213 SGD
+SGD S000003752 YJL216C GO:0004557 SGD_REF:S000041946|PMID:7725802 ISS F YJL216C gene taxon:4932 20060217 SGD
+SGD S000003752 YJL216C GO:0004557 SGD_REF:S000047637|PMID:9090054 ISS SGD:S000000503|SGD:S000029690|SGD:S000003757|SGD:S000001434|SGD:S000003524|SGD:S000003519 F YJL216C gene taxon:4932 20060217 SGD
+SGD S000003752 YJL216C GO:0000004 SGD_REF:S000069584 ND P YJL216C gene taxon:4932 20021002 SGD
+SGD S000003753 YJL217W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YJL217W gene taxon:4932 20031028 SGD
+SGD S000003753 YJL217W GO:0005554 SGD_REF:S000069584 ND F YJL217W gene taxon:4932 20030425 SGD
+SGD S000003753 YJL217W GO:0000004 SGD_REF:S000069584 ND P YJL217W gene taxon:4932 20030425 SGD
+SGD S000003754 YJL218W GO:0008372 SGD_REF:S000069584 ND C YJL218W gene taxon:4932 20030213 SGD
+SGD S000003754 YJL218W GO:0016407 SGD_REF:S000072463|PMID:10592175 ISS F YJL218W gene taxon:4932 20030213 SGD
+SGD S000003754 YJL218W GO:0000004 SGD_REF:S000069584 ND P YJL218W gene taxon:4932 20030213 SGD
+SGD S000003760 YJL225C GO:0008372 SGD_REF:S000069584 ND C YJL225C gene taxon:4932 20030410 SGD
+SGD S000003760 YJL225C GO:0004386 SGD_REF:S000053946|PMID:9837911 ISS F YJL225C gene taxon:4932 20030410 SGD
+SGD S000003760 YJL225C GO:0000004 SGD_REF:S000069584 ND P YJL225C gene taxon:4932 20030410 SGD
+SGD S000003763 YJR003C GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YJR003C gene taxon:4932 20031028 SGD
+SGD S000003763 YJR003C GO:0005554 SGD_REF:S000069584 ND F YJR003C gene taxon:4932 20021002 SGD
+SGD S000003763 YJR003C GO:0000004 SGD_REF:S000069584 ND P YJR003C gene taxon:4932 20021002 SGD
+SGD S000028523 YJR005C-A GO:0008372 SGD_REF:S000069584 ND C YJR005C-A gene taxon:4932 20030730 SGD
+SGD S000028523 YJR005C-A GO:0005554 SGD_REF:S000069584 ND F YJR005C-A gene taxon:4932 20030730 SGD
+SGD S000028523 YJR005C-A GO:0000004 SGD_REF:S000069584 ND P YJR005C-A gene taxon:4932 20030730 SGD
+SGD S000003768 YJR008W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YJR008W gene taxon:4932 20031028 SGD
+SGD S000003768 YJR008W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YJR008W gene taxon:4932 20031028 SGD
+SGD S000003768 YJR008W GO:0005554 SGD_REF:S000069584 ND F YJR008W gene taxon:4932 20021126 SGD
+SGD S000003768 YJR008W GO:0000004 SGD_REF:S000069584 ND P YJR008W gene taxon:4932 20021126 SGD
+SGD S000003772 YJR011C GO:0008372 SGD_REF:S000069584 ND C YJR011C gene taxon:4932 20021126 SGD
+SGD S000003772 YJR011C GO:0005554 SGD_REF:S000069584 ND F YJR011C gene taxon:4932 20021126 SGD
+SGD S000003772 YJR011C GO:0000004 SGD_REF:S000069584 ND P YJR011C gene taxon:4932 20021126 SGD
+SGD S000003773 YJR012C GO:0008372 SGD_REF:S000069584 ND C YJR012C gene taxon:4932 20021126 SGD
+SGD S000003773 YJR012C GO:0005554 SGD_REF:S000069584 ND F YJR012C gene taxon:4932 20021126 SGD
+SGD S000003773 YJR012C GO:0006810 SGD_REF:S000075214|PMID:14690591 IPI P YJR012C gene taxon:4932 20040105 SGD
+SGD S000003776 YJR015W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YJR015W gene taxon:4932 20031028 SGD
+SGD S000003776 YJR015W GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YJR015W gene taxon:4932 20031028 SGD
+SGD S000003776 YJR015W GO:0005554 SGD_REF:S000069584 ND F YJR015W gene taxon:4932 20021126 SGD
+SGD S000003776 YJR015W GO:0000004 SGD_REF:S000069584 ND P YJR015W gene taxon:4932 20021126 SGD
+SGD S000003785 YJR024C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YJR024C gene taxon:4932 20031028 SGD
+SGD S000003785 YJR024C GO:0005554 SGD_REF:S000069584 ND F YJR024C gene taxon:4932 20030203 SGD
+SGD S000003785 YJR024C GO:0000004 SGD_REF:S000069584 ND P YJR024C gene taxon:4932 20030203 SGD
+SGD S000003787 YJR026W GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YJR026W gene taxon:4932 20030811 SGD
+SGD S000003787 YJR026W GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YJR026W gene taxon:4932 20030811 SGD
+SGD S000003787 YJR026W GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YJR026W gene taxon:4932 20030811 SGD
+SGD S000003787 YJR026W GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YJR026W gene taxon:4932 20030811 SGD
+SGD S000003788 YJR027W GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YJR027W gene taxon:4932 20030811 SGD
+SGD S000003788 YJR027W GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YJR027W gene taxon:4932 20030811 SGD
+SGD S000003788 YJR027W GO:0003887 SGD_REF:S000072465|PMID:9582191 ISS F YJR027W gene taxon:4932 20030811 SGD
+SGD S000003788 YJR027W GO:0003964 SGD_REF:S000072465|PMID:9582191 ISS F YJR027W gene taxon:4932 20030811 SGD
+SGD S000003788 YJR027W GO:0004540 SGD_REF:S000072465|PMID:9582191 ISS F YJR027W gene taxon:4932 20030811 SGD
+SGD S000003788 YJR027W GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YJR027W gene taxon:4932 20030811 SGD
+SGD S000003788 YJR027W GO:0008233 SGD_REF:S000072465|PMID:9582191 ISS F YJR027W gene taxon:4932 20030811 SGD
+SGD S000003788 YJR027W GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YJR027W gene taxon:4932 20030811 SGD
+SGD S000003789 YJR028W GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YJR028W gene taxon:4932 20030811 SGD
+SGD S000003789 YJR028W GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YJR028W gene taxon:4932 20030811 SGD
+SGD S000003789 YJR028W GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YJR028W gene taxon:4932 20030811 SGD
+SGD S000003789 YJR028W GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YJR028W gene taxon:4932 20030811 SGD
+SGD S000003790 YJR029W GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YJR029W gene taxon:4932 20030811 SGD
+SGD S000003790 YJR029W GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YJR029W gene taxon:4932 20030811 SGD
+SGD S000003790 YJR029W GO:0003887 SGD_REF:S000072465|PMID:9582191 ISS F YJR029W gene taxon:4932 20030819 SGD
+SGD S000003790 YJR029W GO:0003964 SGD_REF:S000072465|PMID:9582191 ISS F YJR029W gene taxon:4932 20030819 SGD
+SGD S000003790 YJR029W GO:0004540 SGD_REF:S000072465|PMID:9582191 ISS F YJR029W gene taxon:4932 20030819 SGD
+SGD S000003790 YJR029W GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YJR029W gene taxon:4932 20030811 SGD
+SGD S000003790 YJR029W GO:0008233 SGD_REF:S000072465|PMID:9582191 ISS F YJR029W gene taxon:4932 20030819 SGD
+SGD S000003790 YJR029W GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YJR029W gene taxon:4932 20030811 SGD
+SGD S000003791 YJR030C GO:0008372 SGD_REF:S000069584 ND C YJR030C gene taxon:4932 20030203 SGD
+SGD S000003791 YJR030C GO:0005554 SGD_REF:S000069584 ND F YJR030C gene taxon:4932 20030203 SGD
+SGD S000003791 YJR030C GO:0000004 SGD_REF:S000069584 ND P YJR030C gene taxon:4932 20030203 SGD
+SGD S000003800 YJR039W GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YJR039W gene taxon:4932 20040813 SGD
+SGD S000003800 YJR039W GO:0005554 SGD_REF:S000069584 ND F YJR039W gene taxon:4932 20030425 SGD
+SGD S000003800 YJR039W GO:0000004 SGD_REF:S000069584 ND P YJR039W gene taxon:4932 20030425 SGD
+SGD S000003815 YJR054W GO:0000324 SGD_REF:S000074185|PMID:14562095 IDA C YJR054W gene taxon:4932 20031028 SGD
+SGD S000003815 YJR054W GO:0005554 SGD_REF:S000069584 ND F YJR054W gene taxon:4932 20030203 SGD
+SGD S000003815 YJR054W GO:0000004 SGD_REF:S000069584 ND P YJR054W gene taxon:4932 20030203 SGD
+SGD S000003817 YJR056C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YJR056C gene taxon:4932 20031028 SGD
+SGD S000003817 YJR056C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YJR056C gene taxon:4932 20031028 SGD
+SGD S000003817 YJR056C GO:0005554 SGD_REF:S000069584 ND F YJR056C gene taxon:4932 20030203 SGD
+SGD S000003817 YJR056C GO:0000004 SGD_REF:S000069584 ND P YJR056C gene taxon:4932 20030203 SGD
+SGD S000003822 YJR061W GO:0008372 SGD_REF:S000069584 ND C YJR061W gene taxon:4932 20021223 SGD
+SGD S000003822 YJR061W GO:0005554 SGD_REF:S000069584 ISS F YJR061W gene taxon:4932 20030211 SGD
+SGD S000003822 YJR061W GO:0000004 SGD_REF:S000069584 ND P YJR061W gene taxon:4932 20021223 SGD
+SGD S000003840 YJR079W GO:0008372 SGD_REF:S000069584 ND C YJR079W gene taxon:4932 20030422 SGD
+SGD S000003840 YJR079W GO:0005554 SGD_REF:S000069584 ND F YJR079W gene taxon:4932 20030422 SGD
+SGD S000003840 YJR079W GO:0000004 SGD_REF:S000069584 ND P YJR079W gene taxon:4932 20030422 SGD
+SGD S000003845 YJR085C GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YJR085C gene taxon:4932 20040813 SGD
+SGD S000003845 YJR085C GO:0005554 SGD_REF:S000069584 ND F YJR085C gene taxon:4932 20030203 SGD
+SGD S000003845 YJR085C GO:0000004 SGD_REF:S000069584 ND P YJR085C gene taxon:4932 20030203 SGD
+SGD S000003848 YJR088C GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YJR088C gene taxon:4932 20031028 SGD
+SGD S000003848 YJR088C GO:0005554 SGD_REF:S000069584 ND F YJR088C gene taxon:4932 20030203 SGD
+SGD S000003848 YJR088C GO:0000004 SGD_REF:S000069584 ND P YJR088C gene taxon:4932 20030203 SGD
+SGD S000003857 YJR096W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YJR096W gene taxon:4932 20031028 SGD
+SGD S000003857 YJR096W GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YJR096W gene taxon:4932 20020507 SGD
+SGD S000003857 YJR096W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YJR096W gene taxon:4932 20031028 SGD
+SGD S000003857 YJR096W GO:0004032 SGD_REF:S000071519|PMID:12271459 IDA F YJR096W gene taxon:4932 20030912 SGD
+SGD S000003857 YJR096W GO:0004032 SGD_REF:S000071519|PMID:12271459 IGI F YJR096W gene taxon:4932 20030912 SGD
+SGD S000003857 YJR096W GO:0004033 SGD_REF:S000060122|PMID:11306085 ISS F YJR096W gene taxon:4932 20030912 SGD
+SGD S000003857 YJR096W GO:0019568 SGD_REF:S000071519|PMID:12271459 IDA P YJR096W gene taxon:4932 20050131 SGD
+SGD S000003857 YJR096W GO:0019568 SGD_REF:S000071519|PMID:12271459 IMP P YJR096W gene taxon:4932 20050131 SGD
+SGD S000003857 YJR096W GO:0042843 SGD_REF:S000071519|PMID:12271459 IMP P YJR096W gene taxon:4932 20050131 SGD
+SGD S000003859 YJR098C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YJR098C gene taxon:4932 20031028 SGD
+SGD S000003859 YJR098C GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YJR098C gene taxon:4932 20040928 SGD
+SGD S000003859 YJR098C GO:0005554 SGD_REF:S000069584 ND F YJR098C gene taxon:4932 20021126 SGD
+SGD S000003859 YJR098C GO:0000004 SGD_REF:S000069584 ND P YJR098C gene taxon:4932 20021126 SGD
+SGD S000003861 YJR100C GO:0008372 SGD_REF:S000069584 ND C YJR100C gene taxon:4932 20030425 SGD
+SGD S000003861 YJR100C GO:0005554 SGD_REF:S000069584 ND F YJR100C gene taxon:4932 20030425 SGD
+SGD S000003861 YJR100C GO:0000004 SGD_REF:S000069584 ND P YJR100C gene taxon:4932 20030425 SGD
+SGD S000003868 YJR107W GO:0008372 SGD_REF:S000069584 ND C YJR107W gene taxon:4932 20021002 SGD
+SGD S000003868 YJR107W GO:0016298 SGD_REF:S000072463|PMID:10592175 ISS F YJR107W gene taxon:4932 20030213 SGD
+SGD S000003868 YJR107W GO:0000004 SGD_REF:S000069584 ND P YJR107W gene taxon:4932 20021002 SGD
+SGD S000003872 YJR111C GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YJR111C gene taxon:4932 20031028 SGD
+SGD S000003872 YJR111C GO:0005554 SGD_REF:S000069584 ND F YJR111C gene taxon:4932 20030423 SGD
+SGD S000003872 YJR111C GO:0000004 SGD_REF:S000069584 ND P YJR111C gene taxon:4932 20030423 SGD
+SGD S000028513 YJR112W-A GO:0008372 SGD_REF:S000069584 ND C YJR112W-A gene taxon:4932 20030730 SGD
+SGD S000028513 YJR112W-A GO:0005554 SGD_REF:S000069584 ND F YJR112W-A gene taxon:4932 20030730 SGD
+SGD S000028513 YJR112W-A GO:0000004 SGD_REF:S000069584 ND P YJR112W-A gene taxon:4932 20030730 SGD
+SGD S000003876 YJR115W GO:0008372 SGD_REF:S000069584 ND C YJR115W gene taxon:4932 20030423 SGD
+SGD S000003876 YJR115W GO:0005554 SGD_REF:S000069584 ND F YJR115W gene taxon:4932 20030423 SGD
+SGD S000003876 YJR115W GO:0000004 SGD_REF:S000069584 ND P YJR115W gene taxon:4932 20030423 SGD
+SGD S000003877 YJR116W GO:0008372 SGD_REF:S000069584 ND C YJR116W gene taxon:4932 20021126 SGD
+SGD S000003877 YJR116W GO:0005554 SGD_REF:S000069584 ND F YJR116W gene taxon:4932 20021126 SGD
+SGD S000003877 YJR116W GO:0000004 SGD_REF:S000069584 ND P YJR116W gene taxon:4932 20021126 SGD
+SGD S000003880 YJR119C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YJR119C gene taxon:4932 20031028 SGD
+SGD S000003880 YJR119C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YJR119C gene taxon:4932 20031028 SGD
+SGD S000003880 YJR119C GO:0005554 SGD_REF:S000069584 ND F YJR119C gene taxon:4932 20021126 SGD
+SGD S000003880 YJR119C GO:0000004 SGD_REF:S000069584 ND P YJR119C gene taxon:4932 20021126 SGD
+SGD S000003881 YJR120W GO:0008372 SGD_REF:S000069584 ND C YJR120W gene taxon:4932 20030423 SGD
+SGD S000003881 YJR120W GO:0005554 SGD_REF:S000069584 ND F YJR120W gene taxon:4932 20030423 SGD
+SGD S000003881 YJR120W GO:0007005 SGD_REF:S000056413|PMID:10628851 IMP P YJR120W gene taxon:4932 20030423 SGD
+SGD S000003881 YJR120W GO:0045333 SGD_REF:S000056413|PMID:10628851 IMP P YJR120W gene taxon:4932 20030423 SGD
+SGD S000003885 YJR124C GO:0008372 SGD_REF:S000069584 ND C YJR124C gene taxon:4932 20021126 SGD
+SGD S000003885 YJR124C GO:0005554 SGD_REF:S000069584 ND F YJR124C gene taxon:4932 20021126 SGD
+SGD S000003885 YJR124C GO:0000004 SGD_REF:S000069584 ND P YJR124C gene taxon:4932 20021126 SGD
+SGD S000003890 YJR129C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YJR129C gene taxon:4932 20031028 SGD
+SGD S000003890 YJR129C GO:0008757 SGD_REF:S000074033|PMID:12872006 ISS F YJR129C gene taxon:4932 20031001 SGD
+SGD S000003890 YJR129C GO:0000004 SGD_REF:S000069584 ND P YJR129C gene taxon:4932 20030422 SGD
+SGD S000003897 YJR136C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YJR136C gene taxon:4932 20031028 SGD
+SGD S000003897 YJR136C GO:0005554 SGD_REF:S000069584 ND F YJR136C gene taxon:4932 20021126 SGD
+SGD S000003897 YJR136C GO:0006412 SGD_REF:S000075214|PMID:14690591 IPI SGD:S000003097 P YJR136C gene taxon:4932 20031231 SGD
+SGD S000003902 YJR141W GO:0008372 SGD_REF:S000069584 ND C YJR141W gene taxon:4932 20030422 SGD
+SGD S000003902 YJR141W GO:0005554 SGD_REF:S000069584 ND F YJR141W gene taxon:4932 20030422 SGD
+SGD S000003902 YJR141W GO:0006397 SGD_REF:S000075214|PMID:14690591 IPI P YJR141W gene taxon:4932 20040105 SGD
+SGD S000003903 YJR142W GO:0008372 SGD_REF:S000069584 ND C YJR142W gene taxon:4932 20030203 SGD
+SGD S000003903 YJR142W GO:0005554 SGD_REF:S000069584 ND F YJR142W gene taxon:4932 20030203 SGD
+SGD S000003903 YJR142W GO:0000004 SGD_REF:S000069584 ND P YJR142W gene taxon:4932 20030203 SGD
+SGD S000003910 YJR149W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YJR149W gene taxon:4932 20031028 SGD
+SGD S000003910 YJR149W GO:0005554 SGD_REF:S000069584 ND F YJR149W gene taxon:4932 20021126 SGD
+SGD S000003910 YJR149W GO:0000004 SGD_REF:S000069584 ND P YJR149W gene taxon:4932 20021126 SGD
+SGD S000028557 YJR151W-A GO:0008372 SGD_REF:S000069584 ND C YJR151W-A gene taxon:4932 20030730 SGD
+SGD S000028557 YJR151W-A GO:0005554 SGD_REF:S000069584 ND F YJR151W-A gene taxon:4932 20030730 SGD
+SGD S000028557 YJR151W-A GO:0000004 SGD_REF:S000069584 ND P YJR151W-A gene taxon:4932 20030730 SGD
+SGD S000003915 YJR154W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YJR154W gene taxon:4932 20031028 SGD
+SGD S000003915 YJR154W GO:0005554 SGD_REF:S000069584 ND F YJR154W gene taxon:4932 20021126 SGD
+SGD S000003915 YJR154W GO:0000004 SGD_REF:S000069584 ND P YJR154W gene taxon:4932 20021126 SGD
+SGD S000007615 YKL018C-A GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YKL018C-A gene taxon:4932 20031028 SGD
+SGD S000007615 YKL018C-A GO:0005554 SGD_REF:S000069584 ND F YKL018C-A gene taxon:4932 20010226 SGD
+SGD S000007615 YKL018C-A GO:0000004 SGD_REF:S000069584 ND P YKL018C-A gene taxon:4932 20010226 SGD
+SGD S000113559 YKL023C-A GO:0008372 SGD_REF:S000069584 ND C YKL023C-A gene taxon:4932 20051117 SGD
+SGD S000113559 YKL023C-A GO:0005554 SGD_REF:S000069584 ND F YKL023C-A gene taxon:4932 20051117 SGD
+SGD S000113559 YKL023C-A GO:0000004 SGD_REF:S000069584 ND P YKL023C-A gene taxon:4932 20051117 SGD
+SGD S000001506 YKL023W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YKL023W gene taxon:4932 20031028 SGD
+SGD S000001506 YKL023W GO:0005554 SGD_REF:S000069584 ND F YKL023W gene taxon:4932 20030203 SGD
+SGD S000001506 YKL023W GO:0000004 SGD_REF:S000069584 ND P YKL023W gene taxon:4932 20030203 SGD
+SGD S000001510 YKL027W GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YKL027W gene taxon:4932 20031028 SGD
+SGD S000001510 YKL027W GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YKL027W gene taxon:4932 20040924 SGD
+SGD S000001510 YKL027W GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C YKL027W gene taxon:4932 20060317 SGD
+SGD S000001510 YKL027W GO:0005554 SGD_REF:S000069584 ND F YKL027W gene taxon:4932 20021126 SGD
+SGD S000001510 YKL027W GO:0000004 SGD_REF:S000069584 ND P YKL027W gene taxon:4932 20021126 SGD
+SGD S000001516 YKL033W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YKL033W|FMP47 gene taxon:4932 20031028 SGD
+SGD S000001516 YKL033W GO:0005554 SGD_REF:S000069584 ND F YKL033W|FMP47 gene taxon:4932 20030203 SGD
+SGD S000001516 YKL033W GO:0000004 SGD_REF:S000069584 ND P YKL033W|FMP47 gene taxon:4932 20030203 SGD
+SGD S000007242 YKL033W-A GO:0008372 SGD_REF:S000069584 ND C YKL033W-A gene taxon:4932 20021125 SGD
+SGD S000007242 YKL033W-A GO:0005554 SGD_REF:S000069584 ND F YKL033W-A gene taxon:4932 20021125 SGD
+SGD S000007242 YKL033W-A GO:0000004 SGD_REF:S000069584 ND P YKL033W-A gene taxon:4932 20021125 SGD
+SGD S000001520 YKL037W GO:0008372 SGD_REF:S000069584 ND C YKL037W gene taxon:4932 20030203 SGD
+SGD S000001520 YKL037W GO:0005554 SGD_REF:S000069584 ND F YKL037W gene taxon:4932 20030203 SGD
+SGD S000001520 YKL037W GO:0000004 SGD_REF:S000069584 ND P YKL037W gene taxon:4932 20030203 SGD
+SGD S000001530 YKL047W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YKL047W gene taxon:4932 20031028 SGD
+SGD S000001530 YKL047W GO:0005554 SGD_REF:S000069584 ND F YKL047W gene taxon:4932 20030203 SGD
+SGD S000001530 YKL047W GO:0000004 SGD_REF:S000069584 ND P YKL047W gene taxon:4932 20030203 SGD
+SGD S000001533 YKL050C GO:0008372 SGD_REF:S000069584 ND C YKL050C gene taxon:4932 20030203 SGD
+SGD S000001533 YKL050C GO:0005554 SGD_REF:S000069584 ND F YKL050C gene taxon:4932 20030203 SGD
+SGD S000001533 YKL050C GO:0000004 SGD_REF:S000069584 ND P YKL050C gene taxon:4932 20030203 SGD
+SGD S000001544 YKL061W GO:0005768 SGD_REF:S000074185|PMID:14562095 IDA C YKL061W gene taxon:4932 20031028 SGD
+SGD S000001544 YKL061W GO:0005554 SGD_REF:S000069584 ND F YKL061W gene taxon:4932 20030203 SGD
+SGD S000001544 YKL061W GO:0000004 SGD_REF:S000069584 ND P YKL061W gene taxon:4932 20030203 SGD
+SGD S000001546 YKL063C GO:0005794 SGD_REF:S000074185|PMID:14562095 IDA C YKL063C gene taxon:4932 20031028 SGD
+SGD S000001546 YKL063C GO:0005554 SGD_REF:S000069584 ND F YKL063C gene taxon:4932 20030203 SGD
+SGD S000001546 YKL063C GO:0000004 SGD_REF:S000069584 ND P YKL063C gene taxon:4932 20030203 SGD
+SGD S000113563 YKL065W-A GO:0008372 SGD_REF:S000069584 ND C YKL065W-A gene taxon:4932 20051117 SGD
+SGD S000113563 YKL065W-A GO:0005554 SGD_REF:S000069584 ND F YKL065W-A gene taxon:4932 20051117 SGD
+SGD S000113563 YKL065W-A GO:0000004 SGD_REF:S000069584 ND P YKL065W-A gene taxon:4932 20051117 SGD
+SGD S000028524 YKL068W-A GO:0008372 SGD_REF:S000069584 ND C YKL068W-A gene taxon:4932 20030730 SGD
+SGD S000028524 YKL068W-A GO:0005554 SGD_REF:S000069584 ND F YKL068W-A gene taxon:4932 20030730 SGD
+SGD S000028524 YKL068W-A GO:0000004 SGD_REF:S000069584 ND P YKL068W-A gene taxon:4932 20030730 SGD
+SGD S000001552 YKL069W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YKL069W|YKG9 gene taxon:4932 20031028 SGD
+SGD S000001552 YKL069W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YKL069W|YKG9 gene taxon:4932 20031028 SGD
+SGD S000001552 YKL069W GO:0005554 SGD_REF:S000069584 ND F YKL069W|YKG9 gene taxon:4932 20030203 SGD
+SGD S000001552 YKL069W GO:0000004 SGD_REF:S000069584 ND P YKL069W|YKG9 gene taxon:4932 20030203 SGD
+SGD S000001553 YKL070W GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YKL070W gene taxon:4932 20040813 SGD
+SGD S000001553 YKL070W GO:0005554 SGD_REF:S000069584 ND F YKL070W gene taxon:4932 20030203 SGD
+SGD S000001553 YKL070W GO:0000004 SGD_REF:S000069584 ND P YKL070W gene taxon:4932 20030203 SGD
+SGD S000001554 YKL071W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YKL071W gene taxon:4932 20031028 SGD
+SGD S000001554 YKL071W GO:0005554 SGD_REF:S000069584 ND F YKL071W gene taxon:4932 20030421 SGD
+SGD S000001554 YKL071W GO:0000004 SGD_REF:S000069584 ND P YKL071W gene taxon:4932 20030421 SGD
+SGD S000001558 YKL075C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YKL075C gene taxon:4932 20031028 SGD
+SGD S000001558 YKL075C GO:0005554 SGD_REF:S000069584 ND F YKL075C gene taxon:4932 20060106 SGD
+SGD S000001558 YKL075C GO:0042493 SGD_REF:S000086496|PMID:16121259 IMP P YKL075C gene taxon:4932 20060106 SGD
+SGD S000001560 YKL077W GO:0000324 SGD_REF:S000074185|PMID:14562095 IDA C YKL077W gene taxon:4932 20031028 SGD
+SGD S000001560 YKL077W GO:0005554 SGD_REF:S000069584 ND F YKL077W gene taxon:4932 20030203 SGD
+SGD S000001560 YKL077W GO:0000004 SGD_REF:S000069584 ND P YKL077W gene taxon:4932 20030203 SGD
+SGD S000001571 YKL088W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YKL088W gene taxon:4932 20031028 SGD
+SGD S000001571 YKL088W GO:0005737 SGD_REF:S000075214|PMID:14690591 IDA C YKL088W gene taxon:4932 20031231 SGD
+SGD S000001571 YKL088W GO:0004633 SGD_REF:S000072463|PMID:10592175 ISS F YKL088W gene taxon:4932 20030619 SGD
+SGD S000001571 YKL088W GO:0004633 SGD_REF:S000075214|PMID:14690591 ISS F YKL088W gene taxon:4932 20031231 SGD
+SGD S000001571 YKL088W GO:0017076 SGD_REF:S000051661|PMID:7705654 ISS F YKL088W gene taxon:4932 20030212 SGD
+SGD S000001571 YKL088W GO:0009651 SGD_REF:S000040057|PMID:8923737 IGI P YKL088W gene taxon:4932 20030212 SGD
+SGD S000001571 YKL088W GO:0015937 SGD_REF:S000072463|PMID:10592175 ISS P YKL088W gene taxon:4932 20030619 SGD
+SGD S000001571 YKL088W GO:0015937 SGD_REF:S000075214|PMID:14690591 IPI SGD:S000001780|SGD:S000005580 P YKL088W gene taxon:4932 20031231 SGD
+SGD S000001574 YKL091C GO:0005634 SGD_REF:S000073885|PMID:12869188 IDA C YKL091C|SFH1 gene taxon:4932 20031001 SGD
+SGD S000001574 YKL091C GO:0005554 SGD_REF:S000069584 ND F YKL091C|SFH1 gene taxon:4932 20030422 SGD
+SGD S000001574 YKL091C GO:0000004 SGD_REF:S000069584 ND P YKL091C|SFH1 gene taxon:4932 20030422 SGD
+SGD S000028667 YKL096C-B GO:0008372 SGD_REF:S000069584 ND C YKL096C-B gene taxon:4932 20030730 SGD
+SGD S000028667 YKL096C-B GO:0005554 SGD_REF:S000069584 ND F YKL096C-B gene taxon:4932 20030730 SGD
+SGD S000028667 YKL096C-B GO:0000004 SGD_REF:S000069584 ND P YKL096C-B gene taxon:4932 20030730 SGD
+SGD S000001581 YKL098W GO:0008372 SGD_REF:S000069584 ND C YKL098W gene taxon:4932 20030203 SGD
+SGD S000001581 YKL098W GO:0005554 SGD_REF:S000069584 ND F YKL098W gene taxon:4932 20030203 SGD
+SGD S000001581 YKL098W GO:0000004 SGD_REF:S000069584 ND P YKL098W gene taxon:4932 20030203 SGD
+SGD S000001583 YKL100C GO:0008372 SGD_REF:S000069584 ND C YKL100C gene taxon:4932 20030203 SGD
+SGD S000001583 YKL100C GO:0005554 SGD_REF:S000069584 ND F YKL100C gene taxon:4932 20030203 SGD
+SGD S000001583 YKL100C GO:0000004 SGD_REF:S000069584 ND P YKL100C gene taxon:4932 20030203 SGD
+SGD S000001588 YKL105C GO:0008372 SGD_REF:S000069584 ND C YKL105C gene taxon:4932 20030203 SGD
+SGD S000001588 YKL105C GO:0005554 SGD_REF:S000069584 ND F YKL105C gene taxon:4932 20030203 SGD
+SGD S000001588 YKL105C GO:0000004 SGD_REF:S000069584 ND P YKL105C gene taxon:4932 20030203 SGD
+SGD S000007616 YKL106C-A GO:0008372 SGD_REF:S000069584 ND C YKL106C-A gene taxon:4932 20010226 SGD
+SGD S000007616 YKL106C-A GO:0005554 SGD_REF:S000069584 ND F YKL106C-A gene taxon:4932 20010226 SGD
+SGD S000007616 YKL106C-A GO:0000004 SGD_REF:S000069584 ND P YKL106C-A gene taxon:4932 20010226 SGD
+SGD S000001590 YKL107W GO:0008372 SGD_REF:S000069584 ND C YKL107W gene taxon:4932 20030203 SGD
+SGD S000001590 YKL107W GO:0005554 SGD_REF:S000069584 ND F YKL107W gene taxon:4932 20030203 SGD
+SGD S000001590 YKL107W GO:0000004 SGD_REF:S000069584 ND P YKL107W gene taxon:4932 20030203 SGD
+SGD S000001604 YKL121W GO:0008372 SGD_REF:S000069584 ND C YKL121W gene taxon:4932 20030203 SGD
+SGD S000001604 YKL121W GO:0005554 SGD_REF:S000069584 ND F YKL121W gene taxon:4932 20030203 SGD
+SGD S000001604 YKL121W GO:0000004 SGD_REF:S000069584 ND P YKL121W gene taxon:4932 20030203 SGD
+SGD S000001616 YKL133C GO:0008372 SGD_REF:S000069584 ND C YKL133C gene taxon:4932 20021126 SGD
+SGD S000001616 YKL133C GO:0005554 SGD_REF:S000069584 ND F YKL133C gene taxon:4932 20021126 SGD
+SGD S000001616 YKL133C GO:0000004 SGD_REF:S000069584 ND P YKL133C gene taxon:4932 20021126 SGD
+SGD S000001620 YKL137W GO:0008372 SGD_REF:S000069584 ND C YKL137W gene taxon:4932 20030421 SGD
+SGD S000001620 YKL137W GO:0005554 SGD_REF:S000069584 ND F YKL137W gene taxon:4932 20030421 SGD
+SGD S000001620 YKL137W GO:0000004 SGD_REF:S000069584 ND P YKL137W gene taxon:4932 20030421 SGD
+SGD S000001634 YKL151C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YKL151C gene taxon:4932 20031028 SGD
+SGD S000001634 YKL151C GO:0005554 SGD_REF:S000069584 ND F YKL151C gene taxon:4932 20030113 SGD
+SGD S000001634 YKL151C GO:0000004 SGD_REF:S000069584 ND P YKL151C gene taxon:4932 20030113 SGD
+SGD S000001644 YKL161C GO:0008372 SGD_REF:S000069584 ND C YKL161C|MLP1 gene taxon:4932 20021118 SGD
+SGD S000001644 YKL161C GO:0004672 SGD_REF:S000058030|PMID:9020587 ISS F YKL161C|MLP1 gene taxon:4932 20030204 SGD
+SGD S000001644 YKL161C GO:0000004 SGD_REF:S000069584 ND P YKL161C|MLP1 gene taxon:4932 20021118 SGD
+SGD S000001645 YKL162C GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YKL162C gene taxon:4932 20031028 SGD
+SGD S000001645 YKL162C GO:0005554 SGD_REF:S000069584 ND F YKL162C gene taxon:4932 20030421 SGD
+SGD S000001645 YKL162C GO:0000004 SGD_REF:S000069584 ND P YKL162C gene taxon:4932 20030421 SGD
+SGD S000001654 YKL171W GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YKL171W gene taxon:4932 20020507 SGD
+SGD S000001654 YKL171W GO:0004672 SGD_REF:S000058030|PMID:9020587 ISS F YKL171W gene taxon:4932 20030204 SGD
+SGD S000001654 YKL171W GO:0006508 SGD_REF:S000066003|PMID:11595789 IPI P YKL171W gene taxon:4932 20021120 SGD
+SGD S000028558 YKL183C-A GO:0008372 SGD_REF:S000069584 ND C YKL183C-A gene taxon:4932 20030730 SGD
+SGD S000028558 YKL183C-A GO:0005554 SGD_REF:S000069584 ND F YKL183C-A gene taxon:4932 20030730 SGD
+SGD S000028558 YKL183C-A GO:0000004 SGD_REF:S000069584 ND P YKL183C-A gene taxon:4932 20030730 SGD
+SGD S000001670 YKL187C GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YKL187C gene taxon:4932 20040813 SGD
+SGD S000001670 YKL187C GO:0005554 SGD_REF:S000069584 ND F YKL187C gene taxon:4932 20030203 SGD
+SGD S000001670 YKL187C GO:0000004 SGD_REF:S000069584 ND P YKL187C gene taxon:4932 20030203 SGD
+SGD S000001690 YKL207W GO:0008372 SGD_REF:S000069584 ND C YKL207W gene taxon:4932 20030203 SGD
+SGD S000001690 YKL207W GO:0005554 SGD_REF:S000069584 ND F YKL207W gene taxon:4932 20030203 SGD
+SGD S000001690 YKL207W GO:0000004 SGD_REF:S000069584 ND P YKL207W gene taxon:4932 20030203 SGD
+SGD S000001698 YKL215C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YKL215C gene taxon:4932 20031028 SGD
+SGD S000001698 YKL215C GO:0005554 SGD_REF:S000069584 ND F YKL215C gene taxon:4932 20030203 SGD
+SGD S000001698 YKL215C GO:0000004 SGD_REF:S000069584 ND P YKL215C gene taxon:4932 20030203 SGD
+SGD S000001705 YKL222C GO:0008372 SGD_REF:S000069584 ND C YKL222C gene taxon:4932 20030203 SGD
+SGD S000001705 YKL222C GO:0005554 SGD_REF:S000069584 ND F YKL222C gene taxon:4932 20030203 SGD
+SGD S000001705 YKL222C GO:0000004 SGD_REF:S000069584 ND P YKL222C gene taxon:4932 20030203 SGD
+SGD S000001713 YKR005C GO:0008372 SGD_REF:S000069584 ND C YKR005C gene taxon:4932 20030203 SGD
+SGD S000001713 YKR005C GO:0005554 SGD_REF:S000069584 ND F YKR005C gene taxon:4932 20030203 SGD
+SGD S000001713 YKR005C GO:0000004 SGD_REF:S000069584 ND P YKR005C gene taxon:4932 20030203 SGD
+SGD S000001719 YKR011C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YKR011C|TOS5 gene taxon:4932 20031028 SGD
+SGD S000001719 YKR011C GO:0005554 SGD_REF:S000069584 ND F YKR011C|TOS5 gene taxon:4932 20010119 SGD
+SGD S000001719 YKR011C GO:0000004 SGD_REF:S000069584 ND P YKR011C|TOS5 gene taxon:4932 20010119 SGD
+SGD S000001723 YKR015C GO:0008372 SGD_REF:S000069584 ND C YKR015C gene taxon:4932 20030421 SGD
+SGD S000001723 YKR015C GO:0005554 SGD_REF:S000069584 ND F YKR015C gene taxon:4932 20030421 SGD
+SGD S000001723 YKR015C GO:0000004 SGD_REF:S000069584 ND P YKR015C gene taxon:4932 20030421 SGD
+SGD S000001725 YKR017C GO:0008372 SGD_REF:S000069584 ND C YKR017C gene taxon:4932 20030113 SGD
+SGD S000001725 YKR017C GO:0005554 SGD_REF:S000069584 ND F YKR017C gene taxon:4932 20030113 SGD
+SGD S000001725 YKR017C GO:0000004 SGD_REF:S000069584 ND P YKR017C gene taxon:4932 20030113 SGD
+SGD S000001726 YKR018C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YKR018C gene taxon:4932 20031028 SGD
+SGD S000001726 YKR018C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YKR018C gene taxon:4932 20031028 SGD
+SGD S000001726 YKR018C GO:0005554 SGD_REF:S000069584 ND F YKR018C gene taxon:4932 20030421 SGD
+SGD S000001726 YKR018C GO:0000004 SGD_REF:S000069584 ND P YKR018C gene taxon:4932 20030421 SGD
+SGD S000001729 YKR021W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YKR021W gene taxon:4932 20031028 SGD
+SGD S000001729 YKR021W GO:0005554 SGD_REF:S000069584 ND F YKR021W gene taxon:4932 20030421 SGD
+SGD S000001729 YKR021W GO:0000004 SGD_REF:S000069584 ND P YKR021W gene taxon:4932 20030421 SGD
+SGD S000001731 YKR023W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YKR023W gene taxon:4932 20031028 SGD
+SGD S000001731 YKR023W GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YKR023W gene taxon:4932 20040928 SGD
+SGD S000001731 YKR023W GO:0005554 SGD_REF:S000069584 ND F YKR023W gene taxon:4932 20030421 SGD
+SGD S000001731 YKR023W GO:0000004 SGD_REF:S000069584 ND P YKR023W gene taxon:4932 20030421 SGD
+SGD S000001749 YKR041W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YKR041W gene taxon:4932 20031028 SGD
+SGD S000001749 YKR041W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YKR041W gene taxon:4932 20031028 SGD
+SGD S000001749 YKR041W GO:0005554 SGD_REF:S000069584 ND F YKR041W gene taxon:4932 20021126 SGD
+SGD S000001749 YKR041W GO:0000004 SGD_REF:S000069584 ND P YKR041W gene taxon:4932 20021126 SGD
+SGD S000001751 YKR043C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YKR043C gene taxon:4932 20031028 SGD
+SGD S000001751 YKR043C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YKR043C gene taxon:4932 20031028 SGD
+SGD S000001751 YKR043C GO:0005554 SGD_REF:S000069584 ND F YKR043C gene taxon:4932 20021126 SGD
+SGD S000001751 YKR043C GO:0000004 SGD_REF:S000069584 ND P YKR043C gene taxon:4932 20021126 SGD
+SGD S000001753 YKR045C GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YKR045C gene taxon:4932 20020507 SGD
+SGD S000001753 YKR045C GO:0005554 SGD_REF:S000069584 ND F YKR045C gene taxon:4932 20030203 SGD
+SGD S000001753 YKR045C GO:0000004 SGD_REF:S000069584 ND P YKR045C gene taxon:4932 20030203 SGD
+SGD S000001759 YKR051W GO:0008372 SGD_REF:S000069584 ND C YKR051W gene taxon:4932 20021126 SGD
+SGD S000001759 YKR051W GO:0005554 SGD_REF:S000069584 ND F YKR051W gene taxon:4932 20021126 SGD
+SGD S000001759 YKR051W GO:0000004 SGD_REF:S000069584 ND P YKR051W gene taxon:4932 20021126 SGD
+SGD S000001772 YKR064W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YKR064W gene taxon:4932 20031028 SGD
+SGD S000001772 YKR064W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YKR064W gene taxon:4932 20031028 SGD
+SGD S000001772 YKR064W GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YKR064W gene taxon:4932 20040928 SGD
+SGD S000001772 YKR064W GO:0005554 SGD_REF:S000069584 ND F YKR064W gene taxon:4932 20021126 SGD
+SGD S000001772 YKR064W GO:0000004 SGD_REF:S000069584 ND P YKR064W gene taxon:4932 20021126 SGD
+SGD S000001778 YKR070W GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YKR070W gene taxon:4932 20031028 SGD
+SGD S000001778 YKR070W GO:0005554 SGD_REF:S000069584 ND F YKR070W gene taxon:4932 20021126 SGD
+SGD S000001778 YKR070W GO:0000004 SGD_REF:S000069584 ND P YKR070W gene taxon:4932 20021126 SGD
+SGD S000001782 YKR074W GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YKR074W gene taxon:4932 20020507 SGD
+SGD S000001782 YKR074W GO:0005554 SGD_REF:S000069584 ND F YKR074W gene taxon:4932 20030203 SGD
+SGD S000001782 YKR074W GO:0000004 SGD_REF:S000069584 ND P YKR074W gene taxon:4932 20030203 SGD
+SGD S000001783 YKR075C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YKR075C gene taxon:4932 20031028 SGD
+SGD S000001783 YKR075C GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YKR075C gene taxon:4932 20020507 SGD
+SGD S000001783 YKR075C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YKR075C gene taxon:4932 20031028 SGD
+SGD S000001783 YKR075C GO:0005554 SGD_REF:S000069584 ND F YKR075C gene taxon:4932 20030203 SGD
+SGD S000001783 YKR075C GO:0000004 SGD_REF:S000069584 ND P YKR075C gene taxon:4932 20030203 SGD
+SGD S000001785 YKR077W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YKR077W gene taxon:4932 20031028 SGD
+SGD S000001785 YKR077W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YKR077W gene taxon:4932 20031028 SGD
+SGD S000001785 YKR077W GO:0005554 SGD_REF:S000069584 ND F YKR077W gene taxon:4932 20021126 SGD
+SGD S000001785 YKR077W GO:0000004 SGD_REF:S000069584 ND P YKR077W gene taxon:4932 20021126 SGD
+SGD S000001786 YKR078W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YKR078W gene taxon:4932 20031028 SGD
+SGD S000001786 YKR078W GO:0008565 SGD_REF:S000041460|PMID:9175702 ISS F YKR078W gene taxon:4932 20030211 SGD
+SGD S000001786 YKR078W GO:0015031 SGD_REF:S000041460|PMID:9175702 ISS P YKR078W gene taxon:4932 20030211 SGD
+SGD S000001804 YKR096W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YKR096W gene taxon:4932 20031028 SGD
+SGD S000001804 YKR096W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YKR096W gene taxon:4932 20031028 SGD
+SGD S000001804 YKR096W GO:0005554 SGD_REF:S000069584 ND F YKR096W gene taxon:4932 20030421 SGD
+SGD S000001804 YKR096W GO:0000004 SGD_REF:S000069584 ND P YKR096W gene taxon:4932 20030421 SGD
+SGD S000001812 YKR104W GO:0016020 SGD_REF:S000058031|PMID:9020838 ISS C YKR104W|NFT1 gene taxon:4932 20040617 SGD
+SGD S000001812 YKR104W GO:0042626 SGD_REF:S000058031|PMID:9020838 ISS F YKR104W|NFT1 gene taxon:4932 20040617 SGD
+SGD S000001812 YKR104W GO:0042626 SGD_REF:S000073529|PMID:12796304 ISS F YKR104W|NFT1 gene taxon:4932 20040617 SGD
+SGD S000001812 YKR104W GO:0006810 SGD_REF:S000058031|PMID:9020838 ISS P YKR104W|NFT1 gene taxon:4932 20040617 SGD
+SGD S000001813 YKR105C GO:0008372 SGD_REF:S000069584 ND C YKR105C gene taxon:4932 20021120 SGD
+SGD S000001813 YKR105C GO:0005554 SGD_REF:S000069584 ND F YKR105C gene taxon:4932 20021120 SGD
+SGD S000001813 YKR105C GO:0000004 SGD_REF:S000069584 ND P YKR105C gene taxon:4932 20021120 SGD
+SGD S000001814 YKR106W GO:0016020 SGD_REF:S000049483|PMID:10744769 ISS C YKR106W gene taxon:4932 20021120 SGD
+SGD S000001814 YKR106W GO:0005215 SGD_REF:S000049483|PMID:10744769 ISS F YKR106W gene taxon:4932 20021120 SGD
+SGD S000001814 YKR106W GO:0006810 SGD_REF:S000049483|PMID:10744769 ISS P YKR106W gene taxon:4932 20021120 SGD
+SGD S000028560 YLL006W-A GO:0008372 SGD_REF:S000069584 ND C YLL006W-A gene taxon:4932 20030730 SGD
+SGD S000028560 YLL006W-A GO:0005554 SGD_REF:S000069584 ND F YLL006W-A gene taxon:4932 20030730 SGD
+SGD S000028560 YLL006W-A GO:0000004 SGD_REF:S000069584 ND P YLL006W-A gene taxon:4932 20030730 SGD
+SGD S000003930 YLL007C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YLL007C gene taxon:4932 20031028 SGD
+SGD S000003930 YLL007C GO:0005554 SGD_REF:S000069584 ND F YLL007C gene taxon:4932 20030422 SGD
+SGD S000003930 YLL007C GO:0000004 SGD_REF:S000069584 ND P YLL007C gene taxon:4932 20030422 SGD
+SGD S000003937 YLL014W GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YLL014W gene taxon:4932 20031028 SGD
+SGD S000003937 YLL014W GO:0005554 SGD_REF:S000069584 ND F YLL014W gene taxon:4932 20021126 SGD
+SGD S000003937 YLL014W GO:0000004 SGD_REF:S000069584 ND P YLL014W gene taxon:4932 20021126 SGD
+SGD S000003940 YLL017W GO:0016020 SGD_REF:S000055581|PMID:10747953 IDA C YLL017W|SDC25 gene taxon:4932 20060324 SGD
+SGD S000003940 YLL017W GO:0005088 SGD_REF:S000052520|PMID:7941731 TAS F YLL017W|SDC25 gene taxon:4932 20040617 SGD
+SGD S000003940 YLL017W GO:0007265 SGD_REF:S000052520|PMID:7941731 TAS P YLL017W|SDC25 gene taxon:4932 20040617 SGD
+SGD S000003946 YLL023C GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YLL023C gene taxon:4932 20031028 SGD
+SGD S000003946 YLL023C GO:0005554 SGD_REF:S000069584 ND F YLL023C gene taxon:4932 20030424 SGD
+SGD S000003946 YLL023C GO:0000004 SGD_REF:S000069584 ND P YLL023C gene taxon:4932 20030424 SGD
+SGD S000003952 YLL029W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YLL029W gene taxon:4932 20031028 SGD
+SGD S000003952 YLL029W GO:0005554 SGD_REF:S000069584 ND F YLL029W gene taxon:4932 20030425 SGD
+SGD S000003952 YLL029W GO:0000004 SGD_REF:S000069584 ND P YLL029W gene taxon:4932 20030425 SGD
+SGD S000003955 YLL032C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YLL032C gene taxon:4932 20031028 SGD
+SGD S000003955 YLL032C GO:0005554 SGD_REF:S000069584 ND F YLL032C gene taxon:4932 20030424 SGD
+SGD S000003955 YLL032C GO:0000004 SGD_REF:S000069584 ND P YLL032C gene taxon:4932 20030424 SGD
+SGD S000003956 YLL033W GO:0008372 SGD_REF:S000069584 ND C YLL033W|GON2 gene taxon:4932 20030422 SGD
+SGD S000003956 YLL033W GO:0005554 SGD_REF:S000069584 ND F YLL033W|GON2 gene taxon:4932 20030422 SGD
+SGD S000003956 YLL033W GO:0030437 SGD_REF:S000073751|PMID:12432101 IMP P YLL033W|GON2 gene taxon:4932 20040714 SGD
+SGD S000003976 YLL053C GO:0008372 SGD_REF:S000069584 ND C YLL053C gene taxon:4932 20030410 SGD
+SGD S000003976 YLL053C GO:0005554 SGD_REF:S000069584 ND F YLL053C gene taxon:4932 20030410 SGD
+SGD S000003976 YLL053C GO:0000004 SGD_REF:S000069584 ND P YLL053C gene taxon:4932 20030410 SGD
+SGD S000003977 YLL054C GO:0005886 SGD_REF:S000059099|PMID:11113969 ISS C YLL054C gene taxon:4932 20030424 SGD
+SGD S000003977 YLL054C GO:0016563 SGD_REF:S000059099|PMID:11113969 ISS F YLL054C gene taxon:4932 20030424 SGD
+SGD S000003977 YLL054C GO:0000004 SGD_REF:S000069584 ND P YLL054C gene taxon:4932 20030424 SGD
+SGD S000003978 YLL055W GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YLL055W gene taxon:4932 20031028 SGD
+SGD S000003978 YLL055W GO:0015075 SGD_REF:S000058231|PMID:9348664 ISS F YLL055W gene taxon:4932 20060327 SGD
+SGD S000003978 YLL055W GO:0000004 SGD_REF:S000069584 ND P YLL055W gene taxon:4932 20030427 SGD
+SGD S000003979 YLL056C GO:0008372 SGD_REF:S000069584 ND C YLL056C gene taxon:4932 20030113 SGD
+SGD S000003979 YLL056C GO:0005554 SGD_REF:S000069584 ND F YLL056C gene taxon:4932 20030113 SGD
+SGD S000003979 YLL056C GO:0000004 SGD_REF:S000069584 ND P YLL056C gene taxon:4932 20030113 SGD
+SGD S000003981 YLL058W GO:0008372 SGD_REF:S000069584 ND C YLL058W gene taxon:4932 20030428 SGD
+SGD S000003981 YLL058W GO:0003962 SGD_REF:S000039910|PMID:10821189 ISS F YLL058W gene taxon:4932 20030530 SGD
+SGD S000003981 YLL058W GO:0006790 SGD_REF:S000039910|PMID:10821189 ISS P YLL058W gene taxon:4932 20030530 SGD
+SGD S000003989 YLL066C GO:0008372 SGD_REF:S000069584 ND C YLL066C gene taxon:4932 20030203 SGD
+SGD S000003989 YLL066C GO:0004386 SGD_REF:S000053946|PMID:9837911 ISS F YLL066C gene taxon:4932 20040323 SGD
+SGD S000003989 YLL066C GO:0000004 SGD_REF:S000069584 ND P YLL066C gene taxon:4932 20030203 SGD
+SGD S000028672 YLL066W-B GO:0008372 SGD_REF:S000069584 ND C YLL066W-B gene taxon:4932 20030730 SGD
+SGD S000028672 YLL066W-B GO:0005554 SGD_REF:S000069584 ND F YLL066W-B gene taxon:4932 20030730 SGD
+SGD S000028672 YLL066W-B GO:0000004 SGD_REF:S000069584 ND P YLL066W-B gene taxon:4932 20030730 SGD
+SGD S000003990 YLL067C GO:0008372 SGD_REF:S000069584 ND C YLL067C gene taxon:4932 20030203 SGD
+SGD S000003990 YLL067C GO:0004386 SGD_REF:S000053946|PMID:9837911 ISS F YLL067C gene taxon:4932 20040323 SGD
+SGD S000003990 YLL067C GO:0000004 SGD_REF:S000069584 ND P YLL067C gene taxon:4932 20030203 SGD
+SGD S000003991 YLR001C GO:0000329 SGD_REF:S000074185|PMID:14562095 IDA C YLR001C gene taxon:4932 20031028 SGD
+SGD S000003991 YLR001C GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YLR001C gene taxon:4932 20040928 SGD
+SGD S000003991 YLR001C GO:0005554 SGD_REF:S000069584 ND F YLR001C gene taxon:4932 20030203 SGD
+SGD S000003991 YLR001C GO:0000004 SGD_REF:S000069584 ND P YLR001C gene taxon:4932 20030203 SGD
+SGD S000003993 YLR003C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YLR003C|CMS1 gene taxon:4932 20031028 SGD
+SGD S000003993 YLR003C GO:0005554 SGD_REF:S000069584 ND F YLR003C|CMS1 gene taxon:4932 20030421 SGD
+SGD S000003993 YLR003C GO:0006275 SGD_REF:S000068999|PMID:11787774 IGI P YLR003C|CMS1 gene taxon:4932 20030421 SGD
+SGD S000003994 YLR004C GO:0016021 SGD_REF:S000051510|PMID:10869563 ISS SGD:S000003913 C YLR004C gene taxon:4932 20030421 SGD
+SGD S000003994 YLR004C GO:0005215 SGD_REF:S000051510|PMID:10869563 ISS SGD:S000003913 F YLR004C gene taxon:4932 20030421 SGD
+SGD S000003994 YLR004C GO:0006810 SGD_REF:S000051510|PMID:10869563 ISS SGD:S000003913 P YLR004C gene taxon:4932 20030421 SGD
+SGD S000004002 YLR012C GO:0008372 SGD_REF:S000069584 ND C YLR012C gene taxon:4932 20021126 SGD
+SGD S000004002 YLR012C GO:0005554 SGD_REF:S000069584 ND F YLR012C gene taxon:4932 20021126 SGD
+SGD S000004002 YLR012C GO:0000004 SGD_REF:S000069584 ND P YLR012C gene taxon:4932 20021126 SGD
+SGD S000004011 YLR021W GO:0008372 SGD_REF:S000069584 ND C YLR021W gene taxon:4932 20021126 SGD
+SGD S000004011 YLR021W GO:0005554 SGD_REF:S000069584 ND F YLR021W gene taxon:4932 20021126 SGD
+SGD S000004011 YLR021W GO:0000004 SGD_REF:S000069584 ND P YLR021W gene taxon:4932 20021126 SGD
+SGD S000004020 YLR030W GO:0008372 SGD_REF:S000069584 ND C YLR030W gene taxon:4932 20030203 SGD
+SGD S000004020 YLR030W GO:0005554 SGD_REF:S000069584 ND F YLR030W gene taxon:4932 20030203 SGD
+SGD S000004020 YLR030W GO:0000004 SGD_REF:S000069584 ND P YLR030W gene taxon:4932 20030203 SGD
+SGD S000004021 YLR031W GO:0008372 SGD_REF:S000069584 ND C YLR031W gene taxon:4932 20030203 SGD
+SGD S000004021 YLR031W GO:0005554 SGD_REF:S000069584 ND F YLR031W gene taxon:4932 20030203 SGD
+SGD S000004021 YLR031W GO:0000004 SGD_REF:S000069584 ND P YLR031W gene taxon:4932 20030203 SGD
+SGD S000007225 YLR035C-A GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YLR035C-A gene taxon:4932 20030811 SGD
+SGD S000007225 YLR035C-A GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YLR035C-A gene taxon:4932 20030811 SGD
+SGD S000007225 YLR035C-A GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YLR035C-A gene taxon:4932 20030811 SGD
+SGD S000007225 YLR035C-A GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YLR035C-A gene taxon:4932 20030811 SGD
+SGD S000004026 YLR036C GO:0008372 SGD_REF:S000069584 ND C YLR036C gene taxon:4932 20030427 SGD
+SGD S000004026 YLR036C GO:0005554 SGD_REF:S000069584 ND F YLR036C gene taxon:4932 20030427 SGD
+SGD S000004026 YLR036C GO:0000004 SGD_REF:S000069584 ND P YLR036C gene taxon:4932 20030427 SGD
+SGD S000004030 YLR040C GO:0009277 SGD_REF:S000040179|PMID:10383953 IDA C YLR040C gene taxon:4932 20020617 SGD
+SGD S000004030 YLR040C GO:0005554 SGD_REF:S000069584 ND F YLR040C gene taxon:4932 20030428 SGD
+SGD S000004030 YLR040C GO:0000004 SGD_REF:S000069584 ND P YLR040C gene taxon:4932 20030428 SGD
+SGD S000004032 YLR042C GO:0009277 SGD_REF:S000040179|PMID:10383953 IDA C YLR042C gene taxon:4932 20020617 SGD
+SGD S000004032 YLR042C GO:0005554 SGD_REF:S000069584 ND F YLR042C gene taxon:4932 20030428 SGD
+SGD S000004032 YLR042C GO:0000004 SGD_REF:S000069584 ND P YLR042C gene taxon:4932 20030428 SGD
+SGD S000004036 YLR046C GO:0016021 SGD_REF:S000072825|PMID:12524434 ISS C YLR046C gene taxon:4932 20030409 SGD
+SGD S000004036 YLR046C GO:0005554 SGD_REF:S000069584 ND F YLR046C gene taxon:4932 20030203 SGD
+SGD S000004036 YLR046C GO:0000004 SGD_REF:S000069584 ND P YLR046C gene taxon:4932 20030203 SGD
+SGD S000004039 YLR049C GO:0008372 SGD_REF:S000069584 ND C YLR049C gene taxon:4932 20030203 SGD
+SGD S000004039 YLR049C GO:0005554 SGD_REF:S000069584 ND F YLR049C gene taxon:4932 20030203 SGD
+SGD S000004039 YLR049C GO:0000004 SGD_REF:S000069584 ND P YLR049C gene taxon:4932 20030203 SGD
+SGD S000004040 YLR050C GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YLR050C gene taxon:4932 20031028 SGD
+SGD S000004040 YLR050C GO:0005554 SGD_REF:S000069584 ND F YLR050C gene taxon:4932 20021126 SGD
+SGD S000004040 YLR050C GO:0000004 SGD_REF:S000069584 ND P YLR050C gene taxon:4932 20021126 SGD
+SGD S000004043 YLR053C GO:0008372 SGD_REF:S000069584 ND C YLR053C gene taxon:4932 20021126 SGD
+SGD S000004043 YLR053C GO:0005554 SGD_REF:S000069584 ND F YLR053C gene taxon:4932 20021126 SGD
+SGD S000004043 YLR053C GO:0000004 SGD_REF:S000069584 ND P YLR053C gene taxon:4932 20021126 SGD
+SGD S000004047 YLR057W GO:0008372 SGD_REF:S000069584 ND C YLR057W gene taxon:4932 20030203 SGD
+SGD S000004047 YLR057W GO:0005554 SGD_REF:S000069584 ND F YLR057W gene taxon:4932 20030203 SGD
+SGD S000004047 YLR057W GO:0000004 SGD_REF:S000069584 ND P YLR057W gene taxon:4932 20030203 SGD
+SGD S000004053 YLR063W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YLR063W gene taxon:4932 20031028 SGD
+SGD S000004053 YLR063W GO:0005554 SGD_REF:S000069584 ND F YLR063W gene taxon:4932 20030211 SGD
+SGD S000004053 YLR063W GO:0000004 SGD_REF:S000069584 ND P YLR063W gene taxon:4932 20021126 SGD
+SGD S000004054 YLR064W GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YLR064W gene taxon:4932 20031028 SGD
+SGD S000004054 YLR064W GO:0005554 SGD_REF:S000069584 ND F YLR064W gene taxon:4932 20021126 SGD
+SGD S000004054 YLR064W GO:0000004 SGD_REF:S000069584 ND P YLR064W gene taxon:4932 20021126 SGD
+SGD S000004055 YLR065C GO:0008372 SGD_REF:S000069584 ND C YLR065C gene taxon:4932 20030421 SGD
+SGD S000004055 YLR065C GO:0005554 SGD_REF:S000069584 ND F YLR065C gene taxon:4932 20030421 SGD
+SGD S000004055 YLR065C GO:0000004 SGD_REF:S000069584 ND P YLR065C gene taxon:4932 20030421 SGD
+SGD S000004062 YLR072W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YLR072W gene taxon:4932 20031028 SGD
+SGD S000004062 YLR072W GO:0005554 SGD_REF:S000069584 ND F YLR072W gene taxon:4932 20021126 SGD
+SGD S000004062 YLR072W GO:0000004 SGD_REF:S000069584 ND P YLR072W gene taxon:4932 20021126 SGD
+SGD S000004063 YLR073C GO:0005768 SGD_REF:S000074185|PMID:14562095 IDA C YLR073C gene taxon:4932 20031028 SGD
+SGD S000004063 YLR073C GO:0005554 SGD_REF:S000069584 ND F YLR073C gene taxon:4932 20021126 SGD
+SGD S000004063 YLR073C GO:0000004 SGD_REF:S000069584 ND P YLR073C gene taxon:4932 20021126 SGD
+SGD S000004081 YLR091W GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YLR091W gene taxon:4932 20031028 SGD
+SGD S000004081 YLR091W GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YLR091W gene taxon:4932 20040924 SGD
+SGD S000004081 YLR091W GO:0005554 SGD_REF:S000069584 ND F YLR091W gene taxon:4932 20021126 SGD
+SGD S000004081 YLR091W GO:0000004 SGD_REF:S000069584 ND P YLR091W gene taxon:4932 20021126 SGD
+SGD S000007618 YLR099W-A GO:0008372 SGD_REF:S000069584 ND C YLR099W-A gene taxon:4932 20010226 SGD
+SGD S000007618 YLR099W-A GO:0005554 SGD_REF:S000069584 ND F YLR099W-A gene taxon:4932 20010226 SGD
+SGD S000007618 YLR099W-A GO:0000004 SGD_REF:S000069584 ND P YLR099W-A gene taxon:4932 20010226 SGD
+SGD S000004094 YLR104W GO:0008372 SGD_REF:S000069584 ND C YLR104W gene taxon:4932 20021126 SGD
+SGD S000004094 YLR104W GO:0005554 SGD_REF:S000069584 ND F YLR104W gene taxon:4932 20021126 SGD
+SGD S000004094 YLR104W GO:0000004 SGD_REF:S000069584 ND P YLR104W gene taxon:4932 20021126 SGD
+SGD S000004098 YLR108C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YLR108C gene taxon:4932 20031028 SGD
+SGD S000004098 YLR108C GO:0005554 SGD_REF:S000069584 ND F YLR108C gene taxon:4932 20030203 SGD
+SGD S000004098 YLR108C GO:0000004 SGD_REF:S000069584 ND P YLR108C gene taxon:4932 20030203 SGD
+SGD S000004108 YLR118C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C acyl-protein thioesterase YLR118C|APT1 gene taxon:4932 20031028 SGD
+SGD S000004108 YLR118C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C acyl-protein thioesterase YLR118C|APT1 gene taxon:4932 20031028 SGD
+SGD S000004108 YLR118C GO:0008474 SGD_REF:S000070379|PMID:12080046 IDA F acyl-protein thioesterase YLR118C|APT1 gene taxon:4932 20060404 SGD
+SGD S000004108 YLR118C GO:0008474 SGD_REF:S000070379|PMID:12080046 IMP F acyl-protein thioesterase YLR118C|APT1 gene taxon:4932 20060404 SGD
+SGD S000004108 YLR118C GO:0008474 SGD_REF:S000070379|PMID:12080046 ISS F acyl-protein thioesterase YLR118C|APT1 gene taxon:4932 20060404 SGD
+SGD S000004108 YLR118C GO:0000004 SGD_REF:S000069584 ND P acyl-protein thioesterase YLR118C|APT1 gene taxon:4932 20030115 SGD
+SGD S000004115 YLR125W GO:0008372 SGD_REF:S000069584 ND C YLR125W gene taxon:4932 20030422 SGD
+SGD S000004115 YLR125W GO:0005554 SGD_REF:S000069584 ND F YLR125W gene taxon:4932 20030422 SGD
+SGD S000004115 YLR125W GO:0000004 SGD_REF:S000069584 ND P YLR125W gene taxon:4932 20030422 SGD
+SGD S000004116 YLR126C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YLR126C gene taxon:4932 20031028 SGD
+SGD S000004116 YLR126C GO:0005554 SGD_REF:S000069584 ND F YLR126C gene taxon:4932 20030422 SGD
+SGD S000004116 YLR126C GO:0006878 SGD_REF:S000074663|PMID:14534306 IEP P YLR126C gene taxon:4932 20060404 SGD
+SGD S000004116 YLR126C GO:0006878 SGD_REF:S000074663|PMID:14534306 ISS P YLR126C gene taxon:4932 20060404 SGD
+SGD S000004116 YLR126C GO:0006879 SGD_REF:S000074663|PMID:14534306 IEP P YLR126C gene taxon:4932 20060404 SGD
+SGD S000004116 YLR126C GO:0006879 SGD_REF:S000074663|PMID:14534306 ISS P YLR126C gene taxon:4932 20060404 SGD
+SGD S000004122 YLR132C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YLR132C gene taxon:4932 20031028 SGD
+SGD S000004122 YLR132C GO:0005634 SGD_REF:S000075214|PMID:14690591 IDA C YLR132C gene taxon:4932 20031230 SGD
+SGD S000004122 YLR132C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YLR132C gene taxon:4932 20031028 SGD
+SGD S000004122 YLR132C GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YLR132C gene taxon:4932 20031028 SGD
+SGD S000004122 YLR132C GO:0005739 SGD_REF:S000075214|PMID:14690591 IDA C YLR132C gene taxon:4932 20031230 SGD
+SGD S000004122 YLR132C GO:0005554 SGD_REF:S000069584 ND F YLR132C gene taxon:4932 20030203 SGD
+SGD S000004122 YLR132C GO:0000398 SGD_REF:S000075214|PMID:14690591 IPI SGD:S000003959 P YLR132C gene taxon:4932 20031230 SGD
+SGD S000004122 YLR132C GO:0009060 SGD_REF:S000075214|PMID:14690591 IPI SGD:S000000141 P YLR132C gene taxon:4932 20031230 SGD
+SGD S000004127 YLR137W GO:0008372 SGD_REF:S000069584 ND C YLR137W gene taxon:4932 20021126 SGD
+SGD S000004127 YLR137W GO:0005554 SGD_REF:S000069584 ND F YLR137W gene taxon:4932 20021126 SGD
+SGD S000004127 YLR137W GO:0000004 SGD_REF:S000069584 ND P YLR137W gene taxon:4932 20021126 SGD
+SGD S000004133 YLR143W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YLR143W gene taxon:4932 20031028 SGD
+SGD S000004133 YLR143W GO:0005554 SGD_REF:S000069584 ND F YLR143W gene taxon:4932 20030422 SGD
+SGD S000004133 YLR143W GO:0000004 SGD_REF:S000069584 ND P YLR143W gene taxon:4932 20030422 SGD
+SGD S000113566 YLR146W-A GO:0008372 SGD_REF:S000069584 ND C YLR146W-A gene taxon:4932 20051117 SGD
+SGD S000113566 YLR146W-A GO:0005554 SGD_REF:S000069584 ND F YLR146W-A gene taxon:4932 20051117 SGD
+SGD S000113566 YLR146W-A GO:0000004 SGD_REF:S000069584 ND P YLR146W-A gene taxon:4932 20051117 SGD
+SGD S000004139 YLR149C GO:0008372 SGD_REF:S000069584 ND C YLR149C gene taxon:4932 20030422 SGD
+SGD S000004139 YLR149C GO:0005554 SGD_REF:S000069584 ND F YLR149C gene taxon:4932 20030422 SGD
+SGD S000004139 YLR149C GO:0000004 SGD_REF:S000069584 ND P YLR149C gene taxon:4932 20030422 SGD
+SGD S000004142 YLR152C GO:0008372 SGD_REF:S000069584 ND C YLR152C gene taxon:4932 20030422 SGD
+SGD S000004142 YLR152C GO:0005554 SGD_REF:S000069584 ND F YLR152C gene taxon:4932 20030422 SGD
+SGD S000004142 YLR152C GO:0000004 SGD_REF:S000069584 ND P YLR152C gene taxon:4932 20030422 SGD
+SGD S000028561 YLR154C-G GO:0008372 SGD_REF:S000069584 ND C YLR154C-G gene taxon:4932 20030730 SGD
+SGD S000028561 YLR154C-G GO:0005554 SGD_REF:S000069584 ND F YLR154C-G gene taxon:4932 20030730 SGD
+SGD S000028561 YLR154C-G GO:0000004 SGD_REF:S000069584 ND P YLR154C-G gene taxon:4932 20030730 SGD
+SGD S000028562 YLR154C-H GO:0008372 SGD_REF:S000069584 ND C YLR154C-H gene taxon:4932 20030730 SGD
+SGD S000028562 YLR154C-H GO:0005554 SGD_REF:S000069584 ND F YLR154C-H gene taxon:4932 20030730 SGD
+SGD S000028562 YLR154C-H GO:0000004 SGD_REF:S000069584 ND P YLR154C-H gene taxon:4932 20030730 SGD
+SGD S000028564 YLR156C-A GO:0008372 SGD_REF:S000069584 ND C YLR156C-A gene taxon:4932 20030730 SGD
+SGD S000028564 YLR156C-A GO:0005554 SGD_REF:S000069584 ND F YLR156C-A gene taxon:4932 20030730 SGD
+SGD S000028564 YLR156C-A GO:0000004 SGD_REF:S000069584 ND P YLR156C-A gene taxon:4932 20030730 SGD
+SGD S000004146 YLR156W GO:0008372 SGD_REF:S000069584 ND C YLR156W gene taxon:4932 20030203 SGD
+SGD S000004146 YLR156W GO:0005554 SGD_REF:S000069584 ND F YLR156W gene taxon:4932 20030203 SGD
+SGD S000004146 YLR156W GO:0000004 SGD_REF:S000069584 ND P YLR156W gene taxon:4932 20030203 SGD
+SGD S000007373 YLR157C-A GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YLR157C-A gene taxon:4932 20030811 SGD
+SGD S000007373 YLR157C-A GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YLR157C-A gene taxon:4932 20030811 SGD
+SGD S000007373 YLR157C-A GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YLR157C-A gene taxon:4932 20030811 SGD
+SGD S000007373 YLR157C-A GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YLR157C-A gene taxon:4932 20030811 SGD
+SGD S000007374 YLR157C-B GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YLR157C-B gene taxon:4932 20030811 SGD
+SGD S000007374 YLR157C-B GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YLR157C-B gene taxon:4932 20030811 SGD
+SGD S000007374 YLR157C-B GO:0003887 SGD_REF:S000072465|PMID:9582191 ISS F YLR157C-B gene taxon:4932 20030811 SGD
+SGD S000007374 YLR157C-B GO:0003964 SGD_REF:S000072465|PMID:9582191 ISS F YLR157C-B gene taxon:4932 20030811 SGD
+SGD S000007374 YLR157C-B GO:0004540 SGD_REF:S000072465|PMID:9582191 ISS F YLR157C-B gene taxon:4932 20030811 SGD
+SGD S000007374 YLR157C-B GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YLR157C-B gene taxon:4932 20030811 SGD
+SGD S000007374 YLR157C-B GO:0008233 SGD_REF:S000072465|PMID:9582191 ISS F YLR157C-B gene taxon:4932 20030811 SGD
+SGD S000007374 YLR157C-B GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YLR157C-B gene taxon:4932 20030811 SGD
+SGD S000028565 YLR157C-C GO:0008372 SGD_REF:S000069584 ND C YLR157C-C gene taxon:4932 20030730 SGD
+SGD S000028565 YLR157C-C GO:0005554 SGD_REF:S000069584 ND F YLR157C-C gene taxon:4932 20030730 SGD
+SGD S000028565 YLR157C-C GO:0000004 SGD_REF:S000069584 ND P YLR157C-C gene taxon:4932 20030730 SGD
+SGD S000028677 YLR157W-D GO:0008372 SGD_REF:S000069584 ND C YLR157W-D|YLR157W-A gene taxon:4932 20030730 SGD
+SGD S000028677 YLR157W-D GO:0005554 SGD_REF:S000069584 ND F YLR157W-D|YLR157W-A gene taxon:4932 20030730 SGD
+SGD S000028677 YLR157W-D GO:0000004 SGD_REF:S000069584 ND P YLR157W-D|YLR157W-A gene taxon:4932 20030730 SGD
+SGD S000028678 YLR157W-E GO:0008372 SGD_REF:S000069584 ND C YLR157W-E|YLR157W-B|YLR157W-C gene taxon:4932 20030730 SGD
+SGD S000028678 YLR157W-E GO:0005554 SGD_REF:S000069584 ND F YLR157W-E|YLR157W-B|YLR157W-C gene taxon:4932 20030730 SGD
+SGD S000028678 YLR157W-E GO:0000004 SGD_REF:S000069584 ND P YLR157W-E|YLR157W-B|YLR157W-C gene taxon:4932 20030730 SGD
+SGD S000028566 YLR159C-A GO:0008372 SGD_REF:S000069584 ND C YLR159C-A gene taxon:4932 20030730 SGD
+SGD S000028566 YLR159C-A GO:0005554 SGD_REF:S000069584 ND F YLR159C-A gene taxon:4932 20030730 SGD
+SGD S000028566 YLR159C-A GO:0000004 SGD_REF:S000069584 ND P YLR159C-A gene taxon:4932 20030730 SGD
+SGD S000004149 YLR159W GO:0008372 SGD_REF:S000069584 ND C YLR159W gene taxon:4932 20030203 SGD
+SGD S000004149 YLR159W GO:0005554 SGD_REF:S000069584 ND F YLR159W gene taxon:4932 20030203 SGD
+SGD S000004149 YLR159W GO:0000004 SGD_REF:S000069584 ND P YLR159W gene taxon:4932 20030203 SGD
+SGD S000004151 YLR161W GO:0008372 SGD_REF:S000069584 ND C YLR161W gene taxon:4932 20030203 SGD
+SGD S000004151 YLR161W GO:0005554 SGD_REF:S000069584 ND F YLR161W gene taxon:4932 20030203 SGD
+SGD S000004151 YLR161W GO:0000004 SGD_REF:S000069584 ND P YLR161W gene taxon:4932 20030203 SGD
+SGD S000004152 YLR162W GO:0008372 SGD_REF:S000069584 ND C YLR162W gene taxon:4932 20030203 SGD
+SGD S000004152 YLR162W GO:0005554 SGD_REF:S000069584 ND F YLR162W gene taxon:4932 20030203 SGD
+SGD S000004152 YLR162W GO:0000004 SGD_REF:S000069584 ND P YLR162W gene taxon:4932 20030203 SGD
+SGD S000028567 YLR162W-A GO:0008372 SGD_REF:S000069584 ND C YLR162W-A gene taxon:4932 20030730 SGD
+SGD S000028567 YLR162W-A GO:0005554 SGD_REF:S000069584 ND F YLR162W-A gene taxon:4932 20030730 SGD
+SGD S000028567 YLR162W-A GO:0000004 SGD_REF:S000069584 ND P YLR162W-A gene taxon:4932 20030730 SGD
+SGD S000004154 YLR164W GO:0005743 SGD_REF:S000042844|PMID:10637294 IDA C YLR164W gene taxon:4932 20060405 SGD
+SGD S000004154 YLR164W GO:0005554 SGD_REF:S000069584 ND F YLR164W gene taxon:4932 20030203 SGD
+SGD S000004154 YLR164W GO:0000004 SGD_REF:S000069584 ND P YLR164W gene taxon:4932 20030203 SGD
+SGD S000004158 YLR168C GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YLR168C|MSF1|MSF1' gene taxon:4932 20031028 SGD
+SGD S000004158 YLR168C GO:0005554 SGD_REF:S000069584 ND F YLR168C|MSF1|MSF1' gene taxon:4932 20021120 SGD
+SGD S000004158 YLR168C GO:0000004 SGD_REF:S000069584 ND P YLR168C|MSF1|MSF1' gene taxon:4932 20021120 SGD
+SGD S000004163 YLR173W GO:0008372 SGD_REF:S000069584 ND C YLR173W gene taxon:4932 20021126 SGD
+SGD S000004163 YLR173W GO:0005554 SGD_REF:S000069584 ND F YLR173W gene taxon:4932 20021126 SGD
+SGD S000004163 YLR173W GO:0000004 SGD_REF:S000069584 ND P YLR173W gene taxon:4932 20021126 SGD
+SGD S000004167 YLR177W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YLR177W gene taxon:4932 20031028 SGD
+SGD S000004167 YLR177W GO:0005554 SGD_REF:S000069584 ND F YLR177W gene taxon:4932 20030422 SGD
+SGD S000004167 YLR177W GO:0000004 SGD_REF:S000069584 ND P YLR177W gene taxon:4932 20030422 SGD
+SGD S000004169 YLR179C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YLR179C gene taxon:4932 20031028 SGD
+SGD S000004169 YLR179C GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YLR179C gene taxon:4932 20020507 SGD
+SGD S000004169 YLR179C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YLR179C gene taxon:4932 20031028 SGD
+SGD S000004169 YLR179C GO:0005554 SGD_REF:S000069584 ND F YLR179C gene taxon:4932 20030203 SGD
+SGD S000004169 YLR179C GO:0000004 SGD_REF:S000069584 ND P YLR179C gene taxon:4932 20030203 SGD
+SGD S000004183 YLR193C GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YLR193C gene taxon:4932 20031028 SGD
+SGD S000004183 YLR193C GO:0005554 SGD_REF:S000069584 ND F YLR193C gene taxon:4932 20030203 SGD
+SGD S000004183 YLR193C GO:0000004 SGD_REF:S000069584 ND P YLR193C gene taxon:4932 20030203 SGD
+SGD S000004184 YLR194C GO:0009277 SGD_REF:S000040179|PMID:10383953 IDA C YLR194C gene taxon:4932 20020617 SGD
+SGD S000004184 YLR194C GO:0046658 SGD_REF:S000059176|PMID:11016834 IDA C YLR194C gene taxon:4932 20060405 SGD
+SGD S000004184 YLR194C GO:0046658 SGD_REF:S000059176|PMID:11016834 IPI C YLR194C gene taxon:4932 20060405 SGD
+SGD S000004184 YLR194C GO:0005199 SGD_REF:S000059176|PMID:11016834 IPI F YLR194C gene taxon:4932 20060405 SGD
+SGD S000004184 YLR194C GO:0031505 SGD_REF:S000059176|PMID:11016834 IPI P YLR194C gene taxon:4932 20060405 SGD
+SGD S000004184 YLR194C GO:0031505 SGD_REF:S000059176|PMID:11016834 IEP P YLR194C gene taxon:4932 20060405 SGD
+SGD S000004189 YLR199C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YLR199C gene taxon:4932 20031028 SGD
+SGD S000004189 YLR199C GO:0005554 SGD_REF:S000069584 ND F YLR199C gene taxon:4932 20021126 SGD
+SGD S000004189 YLR199C GO:0000004 SGD_REF:S000069584 ND P YLR199C gene taxon:4932 20021126 SGD
+SGD S000004201 YLR211C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YLR211C gene taxon:4932 20031028 SGD
+SGD S000004201 YLR211C GO:0005554 SGD_REF:S000069584 ND F YLR211C gene taxon:4932 20030203 SGD
+SGD S000004201 YLR211C GO:0000004 SGD_REF:S000069584 ND P YLR211C gene taxon:4932 20030203 SGD
+SGD S000004208 YLR218C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YLR218C gene taxon:4932 20031028 SGD
+SGD S000004208 YLR218C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YLR218C gene taxon:4932 20031028 SGD
+SGD S000004208 YLR218C GO:0005554 SGD_REF:S000069584 ND F YLR218C gene taxon:4932 20021126 SGD
+SGD S000004208 YLR218C GO:0000004 SGD_REF:S000069584 ND P YLR218C gene taxon:4932 20021126 SGD
+SGD S000004214 YLR224W GO:0000151 SGD_REF:S000075480|PMID:14747994 IPI SGD:S000000286|SGD:S000005493|SGD:S000002290|SGD:S000002736 C YLR224W gene taxon:4932 20060410 SGD
+SGD S000004214 YLR224W GO:0000151 SGD_REF:S000058340|PMID:9635407 ISS SGD:S000001885|SGD:S000001308|SGD:S000003850 C YLR224W gene taxon:4932 20060410 SGD
+SGD S000004214 YLR224W GO:0005515 SGD_REF:S000058340|PMID:9635407 ISS SGD:S000001885|SGD:S000001308|SGD:S000003850 F YLR224W gene taxon:4932 20030205 SGD
+SGD S000004214 YLR224W GO:0005515 SGD_REF:S000075480|PMID:14747994 IPI SGD:S000002290|SGD:S000005493|SGD:S000002736 F YLR224W gene taxon:4932 20060410 SGD
+SGD S000004214 YLR224W GO:0006511 SGD_REF:S000075480|PMID:14747994 IPI SGD:S000000286|SGD:S000002290|SGD:S000005493|SGD:S000002736 P YLR224W gene taxon:4932 20060410 SGD
+SGD S000004215 YLR225C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YLR225C gene taxon:4932 20031028 SGD
+SGD S000004215 YLR225C GO:0005554 SGD_REF:S000069584 ND F YLR225C gene taxon:4932 20021126 SGD
+SGD S000004215 YLR225C GO:0000004 SGD_REF:S000069584 ND P YLR225C gene taxon:4932 20021126 SGD
+SGD S000007375 YLR227W-A GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YLR227W-A gene taxon:4932 20030811 SGD
+SGD S000007375 YLR227W-A GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YLR227W-A gene taxon:4932 20030811 SGD
+SGD S000007375 YLR227W-A GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YLR227W-A gene taxon:4932 20030811 SGD
+SGD S000007375 YLR227W-A GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YLR227W-A gene taxon:4932 20030811 SGD
+SGD S000007376 YLR227W-B GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YLR227W-B gene taxon:4932 20030811 SGD
+SGD S000007376 YLR227W-B GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YLR227W-B gene taxon:4932 20030811 SGD
+SGD S000007376 YLR227W-B GO:0003887 SGD_REF:S000072465|PMID:9582191 ISS F YLR227W-B gene taxon:4932 20030811 SGD
+SGD S000007376 YLR227W-B GO:0003964 SGD_REF:S000072465|PMID:9582191 ISS F YLR227W-B gene taxon:4932 20030811 SGD
+SGD S000007376 YLR227W-B GO:0004540 SGD_REF:S000072465|PMID:9582191 ISS F YLR227W-B gene taxon:4932 20030811 SGD
+SGD S000007376 YLR227W-B GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YLR227W-B gene taxon:4932 20030811 SGD
+SGD S000007376 YLR227W-B GO:0008233 SGD_REF:S000072465|PMID:9582191 ISS F YLR227W-B gene taxon:4932 20030811 SGD
+SGD S000007376 YLR227W-B GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YLR227W-B gene taxon:4932 20030811 SGD
+SGD S000004231 YLR241W GO:0008372 SGD_REF:S000069584 ND C YLR241W gene taxon:4932 20021120 SGD
+SGD S000004231 YLR241W GO:0005554 SGD_REF:S000069584 ND F YLR241W gene taxon:4932 20021120 SGD
+SGD S000004231 YLR241W GO:0000004 SGD_REF:S000069584 ND P YLR241W gene taxon:4932 20021120 SGD
+SGD S000004233 YLR243W GO:0008372 SGD_REF:S000069584 ND C YLR243W gene taxon:4932 20021126 SGD
+SGD S000004233 YLR243W GO:0005048 SGD_REF:S000075214|PMID:14690591 ISS F YLR243W gene taxon:4932 20040105 SGD
+SGD S000004233 YLR243W GO:0000004 SGD_REF:S000069584 ND P YLR243W gene taxon:4932 20021126 SGD
+SGD S000004237 YLR247C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YLR247C gene taxon:4932 20031028 SGD
+SGD S000004237 YLR247C GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YLR247C gene taxon:4932 20040928 SGD
+SGD S000004237 YLR247C GO:0004386 SGD_REF:S000039134|PMID:10077188 ISS F YLR247C gene taxon:4932 20011205 SGD
+SGD S000004237 YLR247C GO:0000004 SGD_REF:S000069584 ND P YLR247C gene taxon:4932 20011205 SGD
+SGD S000004243 YLR253W GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YLR253W gene taxon:4932 20031028 SGD
+SGD S000004243 YLR253W GO:0005554 SGD_REF:S000069584 ND F YLR253W gene taxon:4932 20021126 SGD
+SGD S000004243 YLR253W GO:0000004 SGD_REF:S000069584 ND P YLR253W gene taxon:4932 20021126 SGD
+SGD S000007377 YLR256W-A GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YLR256W-A gene taxon:4932 20030811 SGD
+SGD S000007377 YLR256W-A GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YLR256W-A gene taxon:4932 20030811 SGD
+SGD S000007377 YLR256W-A GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YLR256W-A gene taxon:4932 20030811 SGD
+SGD S000007377 YLR256W-A GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YLR256W-A gene taxon:4932 20030811 SGD
+SGD S000004247 YLR257W GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YLR257W gene taxon:4932 20020507 SGD
+SGD S000004247 YLR257W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YLR257W gene taxon:4932 20031028 SGD
+SGD S000004247 YLR257W GO:0005554 SGD_REF:S000069584 ND F YLR257W gene taxon:4932 20030203 SGD
+SGD S000004247 YLR257W GO:0000004 SGD_REF:S000069584 ND P YLR257W gene taxon:4932 20030203 SGD
+SGD S000028808 YLR264C-A GO:0008372 SGD_REF:S000069584 ND C YLR264C-A gene taxon:4932 20030730 SGD
+SGD S000028808 YLR264C-A GO:0005554 SGD_REF:S000069584 ND F YLR264C-A gene taxon:4932 20030730 SGD
+SGD S000028808 YLR264C-A GO:0000004 SGD_REF:S000069584 ND P YLR264C-A gene taxon:4932 20030730 SGD
+SGD S000004261 YLR271W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YLR271W gene taxon:4932 20031028 SGD
+SGD S000004261 YLR271W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YLR271W gene taxon:4932 20031028 SGD
+SGD S000004261 YLR271W GO:0005554 SGD_REF:S000069584 ND F YLR271W gene taxon:4932 20021126 SGD
+SGD S000004261 YLR271W GO:0000004 SGD_REF:S000069584 ND P YLR271W gene taxon:4932 20021126 SGD
+SGD S000004268 YLR278C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YLR278C gene taxon:4932 20031028 SGD
+SGD S000004268 YLR278C GO:0005554 SGD_REF:S000069584 ND F YLR278C gene taxon:4932 20030203 SGD
+SGD S000004268 YLR278C GO:0000004 SGD_REF:S000069584 ND P YLR278C gene taxon:4932 20030203 SGD
+SGD S000004271 YLR281C GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YLR281C gene taxon:4932 20031028 SGD
+SGD S000004271 YLR281C GO:0005554 SGD_REF:S000069584 ND F YLR281C gene taxon:4932 20021126 SGD
+SGD S000004271 YLR281C GO:0000004 SGD_REF:S000069584 ND P YLR281C gene taxon:4932 20021126 SGD
+SGD S000004273 YLR283W GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YLR283W gene taxon:4932 20031028 SGD
+SGD S000004273 YLR283W GO:0005554 SGD_REF:S000069584 ND F YLR283W gene taxon:4932 20021126 SGD
+SGD S000004273 YLR283W GO:0000004 SGD_REF:S000069584 ND P YLR283W gene taxon:4932 20021126 SGD
+SGD S000028569 YLR285C-A GO:0008372 SGD_REF:S000069584 ND C YLR285C-A gene taxon:4932 20030730 SGD
+SGD S000028569 YLR285C-A GO:0005554 SGD_REF:S000069584 ND F YLR285C-A gene taxon:4932 20030730 SGD
+SGD S000028569 YLR285C-A GO:0000004 SGD_REF:S000069584 ND P YLR285C-A gene taxon:4932 20030730 SGD
+SGD S000004277 YLR287C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YLR287C gene taxon:4932 20031028 SGD
+SGD S000004277 YLR287C GO:0005554 SGD_REF:S000069584 ND F YLR287C gene taxon:4932 20021126 SGD
+SGD S000004277 YLR287C GO:0000004 SGD_REF:S000069584 ND P YLR287C gene taxon:4932 20021126 SGD
+SGD S000004281 YLR290C GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YLR290C gene taxon:4932 20031028 SGD
+SGD S000004281 YLR290C GO:0005554 SGD_REF:S000069584 ND F YLR290C gene taxon:4932 20021126 SGD
+SGD S000004281 YLR290C GO:0000004 SGD_REF:S000069584 ND P YLR290C gene taxon:4932 20021126 SGD
+SGD S000004288 YLR297W GO:0000324 SGD_REF:S000074185|PMID:14562095 IDA C YLR297W gene taxon:4932 20031028 SGD
+SGD S000004288 YLR297W GO:0005554 SGD_REF:S000069584 ND F YLR297W gene taxon:4932 20021126 SGD
+SGD S000004288 YLR297W GO:0000004 SGD_REF:S000069584 ND P YLR297W gene taxon:4932 20021126 SGD
+SGD S000004292 YLR301W GO:0005789 SGD_REF:S000072462|PMID:12518317 IPI C YLR301W gene taxon:4932 20030207 SGD
+SGD S000004292 YLR301W GO:0005554 SGD_REF:S000069584 ND F YLR301W gene taxon:4932 20030203 SGD
+SGD S000004292 YLR301W GO:0006613 SGD_REF:S000072462|PMID:12518317 IPI P YLR301W gene taxon:4932 20030207 SGD
+SGD S000028525 YLR307C-A GO:0008372 SGD_REF:S000069584 ND C YLR307C-A gene taxon:4932 20030730 SGD
+SGD S000028525 YLR307C-A GO:0005554 SGD_REF:S000069584 ND F YLR307C-A gene taxon:4932 20030730 SGD
+SGD S000028525 YLR307C-A GO:0000004 SGD_REF:S000069584 ND P YLR307C-A gene taxon:4932 20030730 SGD
+SGD S000004303 YLR312C GO:0008372 SGD_REF:S000069584 ND C YLR312C gene taxon:4932 20021126 SGD
+SGD S000004303 YLR312C GO:0005554 SGD_REF:S000069584 ND F YLR312C gene taxon:4932 20021126 SGD
+SGD S000004303 YLR312C GO:0000004 SGD_REF:S000069584 ND P YLR312C gene taxon:4932 20021126 SGD
+SGD S000004318 YLR326W GO:0008372 SGD_REF:S000069584 ND C YLR326W gene taxon:4932 20021126 SGD
+SGD S000004318 YLR326W GO:0005554 SGD_REF:S000069584 ND F YLR326W gene taxon:4932 20021126 SGD
+SGD S000004318 YLR326W GO:0000004 SGD_REF:S000069584 ND P YLR326W gene taxon:4932 20021126 SGD
+SGD S000028571 YLR342W-A GO:0008372 SGD_REF:S000069584 ND C YLR342W-A gene taxon:4932 20030730 SGD
+SGD S000028571 YLR342W-A GO:0005554 SGD_REF:S000069584 ND F YLR342W-A gene taxon:4932 20030730 SGD
+SGD S000028571 YLR342W-A GO:0000004 SGD_REF:S000069584 ND P YLR342W-A gene taxon:4932 20030730 SGD
+SGD S000004337 YLR345W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YLR345W gene taxon:4932 20031028 SGD
+SGD S000004337 YLR345W GO:0003873 SGD_REF:S000080361|PMID:15494396 NAS F YLR345W gene taxon:4932 20060425 SGD
+SGD S000004337 YLR345W GO:0006003 SGD_REF:S000080361|PMID:15494396 NAS P YLR345W gene taxon:4932 20060425 SGD
+SGD S000004337 YLR345W GO:0006110 SGD_REF:S000080361|PMID:15494396 NAS P YLR345W gene taxon:4932 20060425 SGD
+SGD S000004338 YLR346C GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YLR346C gene taxon:4932 20031028 SGD
+SGD S000004338 YLR346C GO:0005554 SGD_REF:S000069584 ND F YLR346C gene taxon:4932 20030115 SGD
+SGD S000004338 YLR346C GO:0000004 SGD_REF:S000069584 ND P YLR346C gene taxon:4932 20030115 SGD
+SGD S000004344 YLR352W GO:0008372 SGD_REF:S000069584 ND C YLR352W gene taxon:4932 20030203 SGD
+SGD S000004344 YLR352W GO:0005554 SGD_REF:S000069584 ND F YLR352W gene taxon:4932 20030203 SGD
+SGD S000004344 YLR352W GO:0000004 SGD_REF:S000069584 ND P YLR352W gene taxon:4932 20030203 SGD
+SGD S000004348 YLR356W GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YLR356W gene taxon:4932 20031028 SGD
+SGD S000004348 YLR356W GO:0005554 SGD_REF:S000069584 ND F YLR356W gene taxon:4932 20021126 SGD
+SGD S000004348 YLR356W GO:0000004 SGD_REF:S000069584 ND P YLR356W gene taxon:4932 20021126 SGD
+SGD S000028845 YLR361C-A GO:0008372 SGD_REF:S000069584 ND C YLR361C-A gene taxon:4932 20030730 SGD
+SGD S000028845 YLR361C-A GO:0005554 SGD_REF:S000069584 ND F YLR361C-A gene taxon:4932 20030730 SGD
+SGD S000028845 YLR361C-A GO:0000004 SGD_REF:S000069584 ND P YLR361C-A gene taxon:4932 20030730 SGD
+SGD S000007620 YLR363W-A GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YLR363W-A gene taxon:4932 20031028 SGD
+SGD S000007620 YLR363W-A GO:0005554 SGD_REF:S000069584 ND F YLR363W-A gene taxon:4932 20010226 SGD
+SGD S000007620 YLR363W-A GO:0000004 SGD_REF:S000069584 ND P YLR363W-A gene taxon:4932 20010226 SGD
+SGD S000004356 YLR364W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YLR364W gene taxon:4932 20031028 SGD
+SGD S000004356 YLR364W GO:0005554 SGD_REF:S000069584 ND F YLR364W gene taxon:4932 20030203 SGD
+SGD S000004356 YLR364W GO:0000004 SGD_REF:S000069584 ND P YLR364W gene taxon:4932 20030203 SGD
+SGD S000004384 YLR392C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YLR392C gene taxon:4932 20031028 SGD
+SGD S000004384 YLR392C GO:0005554 SGD_REF:S000069584 ND F YLR392C gene taxon:4932 20030203 SGD
+SGD S000004384 YLR392C GO:0000004 SGD_REF:S000069584 ND P YLR392C gene taxon:4932 20030203 SGD
+SGD S000004396 YLR404W GO:0016021 SGD_REF:S000072825|PMID:12524434 ISS C YLR404W gene taxon:4932 20030409 SGD
+SGD S000004396 YLR404W GO:0005554 SGD_REF:S000069584 ND F YLR404W gene taxon:4932 20021126 SGD
+SGD S000004396 YLR404W GO:0000004 SGD_REF:S000069584 ND P YLR404W gene taxon:4932 20021126 SGD
+SGD S000028683 YLR406C-A GO:0008372 SGD_REF:S000069584 ND C YLR406C-A gene taxon:4932 20030730 SGD
+SGD S000028683 YLR406C-A GO:0005554 SGD_REF:S000069584 ND F YLR406C-A gene taxon:4932 20030730 SGD
+SGD S000028683 YLR406C-A GO:0000004 SGD_REF:S000069584 ND P YLR406C-A gene taxon:4932 20030730 SGD
+SGD S000004399 YLR407W GO:0008372 SGD_REF:S000069584 ND C YLR407W gene taxon:4932 20021126 SGD
+SGD S000004399 YLR407W GO:0005554 SGD_REF:S000069584 ND F YLR407W gene taxon:4932 20021126 SGD
+SGD S000004399 YLR407W GO:0000004 SGD_REF:S000069584 ND P YLR407W gene taxon:4932 20021126 SGD
+SGD S000004400 YLR408C GO:0005768 SGD_REF:S000074185|PMID:14562095 IDA C YLR408C gene taxon:4932 20031028 SGD
+SGD S000004400 YLR408C GO:0005554 SGD_REF:S000069584 ND F YLR408C gene taxon:4932 20021126 SGD
+SGD S000004400 YLR408C GO:0000004 SGD_REF:S000069584 ND P YLR408C gene taxon:4932 20021126 SGD
+SGD S000007379 YLR410W-A GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YLR410W-A gene taxon:4932 20030811 SGD
+SGD S000007379 YLR410W-A GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YLR410W-A gene taxon:4932 20030811 SGD
+SGD S000007379 YLR410W-A GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YLR410W-A gene taxon:4932 20030811 SGD
+SGD S000007379 YLR410W-A GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YLR410W-A gene taxon:4932 20030811 SGD
+SGD S000007380 YLR410W-B GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YLR410W-B gene taxon:4932 20030811 SGD
+SGD S000007380 YLR410W-B GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YLR410W-B gene taxon:4932 20030811 SGD
+SGD S000007380 YLR410W-B GO:0003887 SGD_REF:S000072465|PMID:9582191 ISS F YLR410W-B gene taxon:4932 20030811 SGD
+SGD S000007380 YLR410W-B GO:0003964 SGD_REF:S000072465|PMID:9582191 ISS F YLR410W-B gene taxon:4932 20030811 SGD
+SGD S000007380 YLR410W-B GO:0004540 SGD_REF:S000072465|PMID:9582191 ISS F YLR410W-B gene taxon:4932 20030811 SGD
+SGD S000007380 YLR410W-B GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YLR410W-B gene taxon:4932 20030811 SGD
+SGD S000007380 YLR410W-B GO:0008233 SGD_REF:S000072465|PMID:9582191 ISS F YLR410W-B gene taxon:4932 20030811 SGD
+SGD S000007380 YLR410W-B GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YLR410W-B gene taxon:4932 20030811 SGD
+SGD S000028572 YLR412C-A GO:0008372 SGD_REF:S000069584 ND C YLR412C-A gene taxon:4932 20030730 SGD
+SGD S000028572 YLR412C-A GO:0005554 SGD_REF:S000069584 ND F YLR412C-A gene taxon:4932 20030730 SGD
+SGD S000028572 YLR412C-A GO:0000004 SGD_REF:S000069584 ND P YLR412C-A gene taxon:4932 20030730 SGD
+SGD S000004404 YLR412W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YLR412W gene taxon:4932 20031028 SGD
+SGD S000004404 YLR412W GO:0005554 SGD_REF:S000069584 ND F YLR412W gene taxon:4932 20021126 SGD
+SGD S000004404 YLR412W GO:0000004 SGD_REF:S000069584 ND P YLR412W gene taxon:4932 20021126 SGD
+SGD S000004405 YLR413W GO:0008372 SGD_REF:S000069584 ND C YLR413W gene taxon:4932 20030203 SGD
+SGD S000004405 YLR413W GO:0005554 SGD_REF:S000069584 ND F YLR413W gene taxon:4932 20030203 SGD
+SGD S000004405 YLR413W GO:0000004 SGD_REF:S000069584 ND P YLR413W gene taxon:4932 20030203 SGD
+SGD S000004406 YLR414C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YLR414C gene taxon:4932 20031028 SGD
+SGD S000004406 YLR414C GO:0005933 SGD_REF:S000074185|PMID:14562095 IDA C YLR414C gene taxon:4932 20031028 SGD
+SGD S000004406 YLR414C GO:0005554 SGD_REF:S000069584 ND F YLR414C gene taxon:4932 20021126 SGD
+SGD S000004406 YLR414C GO:0000004 SGD_REF:S000069584 ND P YLR414C gene taxon:4932 20021126 SGD
+SGD S000004407 YLR415C GO:0008372 SGD_REF:S000069584 ND C YLR415C gene taxon:4932 20021126 SGD
+SGD S000004407 YLR415C GO:0005554 SGD_REF:S000069584 ND F YLR415C gene taxon:4932 20021126 SGD
+SGD S000004407 YLR415C GO:0000004 SGD_REF:S000069584 ND P YLR415C gene taxon:4932 20021126 SGD
+SGD S000004411 YLR419W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YLR419W gene taxon:4932 20031028 SGD
+SGD S000004411 YLR419W GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YLR419W gene taxon:4932 20040928 SGD
+SGD S000004411 YLR419W GO:0004386 SGD_REF:S000039134|PMID:10077188 ISS F YLR419W gene taxon:4932 20011205 SGD
+SGD S000004411 YLR419W GO:0000004 SGD_REF:S000069584 ND P YLR419W gene taxon:4932 20011205 SGD
+SGD S000004414 YLR422W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YLR422W gene taxon:4932 20031028 SGD
+SGD S000004414 YLR422W GO:0005554 SGD_REF:S000069584 ND F YLR422W gene taxon:4932 20030427 SGD
+SGD S000004414 YLR422W GO:0000004 SGD_REF:S000069584 ND P YLR422W gene taxon:4932 20030427 SGD
+SGD S000004418 YLR426W GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YLR426W gene taxon:4932 20040813 SGD
+SGD S000004418 YLR426W GO:0005554 SGD_REF:S000069584 ND F YLR426W gene taxon:4932 20060106 SGD
+SGD S000004418 YLR426W GO:0042493 SGD_REF:S000086496|PMID:16121259 IMP P YLR426W gene taxon:4932 20060106 SGD
+SGD S000004429 YLR437C GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YLR437C gene taxon:4932 20020507 SGD
+SGD S000004429 YLR437C GO:0005554 SGD_REF:S000069584 ND F YLR437C gene taxon:4932 20030203 SGD
+SGD S000004429 YLR437C GO:0000004 SGD_REF:S000069584 ND P YLR437C gene taxon:4932 20030203 SGD
+SGD S000004437 YLR445W GO:0008372 SGD_REF:S000069584 ND C YLR445W gene taxon:4932 20021126 SGD
+SGD S000004437 YLR445W GO:0005554 SGD_REF:S000069584 ND F YLR445W gene taxon:4932 20021126 SGD
+SGD S000004437 YLR445W GO:0000004 SGD_REF:S000069584 ND P YLR445W gene taxon:4932 20021126 SGD
+SGD S000004438 YLR446W GO:0008372 SGD_REF:S000069584 ND C YLR446W gene taxon:4932 20030203 SGD
+SGD S000004438 YLR446W GO:0005554 SGD_REF:S000069584 ND F YLR446W gene taxon:4932 20030203 SGD
+SGD S000004438 YLR446W GO:0000004 SGD_REF:S000069584 ND P YLR446W gene taxon:4932 20030203 SGD
+SGD S000004447 YLR455W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YLR455W gene taxon:4932 20031028 SGD
+SGD S000004447 YLR455W GO:0005554 SGD_REF:S000069584 ND F YLR455W gene taxon:4932 20021126 SGD
+SGD S000004447 YLR455W GO:0000004 SGD_REF:S000069584 ND P YLR455W gene taxon:4932 20021126 SGD
+SGD S000004448 YLR456W GO:0008372 SGD_REF:S000069584 ND C YLR456W gene taxon:4932 20021126 SGD
+SGD S000004448 YLR456W GO:0005554 SGD_REF:S000069584 ND F YLR456W gene taxon:4932 20021126 SGD
+SGD S000004448 YLR456W GO:0000004 SGD_REF:S000069584 ND P YLR456W gene taxon:4932 20021126 SGD
+SGD S000004452 YLR460C GO:0008372 SGD_REF:S000069584 ND C YLR460C gene taxon:4932 20030203 SGD
+SGD S000004452 YLR460C GO:0005554 SGD_REF:S000069584 ND F YLR460C gene taxon:4932 20030203 SGD
+SGD S000004452 YLR460C GO:0000004 SGD_REF:S000069584 ND P YLR460C gene taxon:4932 20030203 SGD
+SGD S000004454 YLR462W GO:0008372 SGD_REF:S000069584 ND C YLR462W gene taxon:4932 20021126 SGD
+SGD S000004454 YLR462W GO:0005554 SGD_REF:S000069584 ND F YLR462W gene taxon:4932 20021126 SGD
+SGD S000004454 YLR462W GO:0000004 SGD_REF:S000069584 ND P YLR462W gene taxon:4932 20021126 SGD
+SGD S000004456 YLR464W GO:0008372 SGD_REF:S000069584 ND C YLR464W gene taxon:4932 20030422 SGD
+SGD S000004456 YLR464W GO:0005554 SGD_REF:S000069584 ND F YLR464W gene taxon:4932 20030422 SGD
+SGD S000004456 YLR464W GO:0000004 SGD_REF:S000069584 ND P YLR464W gene taxon:4932 20030422 SGD
+SGD S000028686 YLR466C-B GO:0008372 SGD_REF:S000069584 ND C YLR466C-B gene taxon:4932 20030730 SGD
+SGD S000028686 YLR466C-B GO:0005554 SGD_REF:S000069584 ND F YLR466C-B gene taxon:4932 20030730 SGD
+SGD S000028686 YLR466C-B GO:0000004 SGD_REF:S000069584 ND P YLR466C-B gene taxon:4932 20030730 SGD
+SGD S000004461 YML002W GO:0008372 SGD_REF:S000069584 ND C YML002W gene taxon:4932 20021126 SGD
+SGD S000004461 YML002W GO:0005554 SGD_REF:S000069584 ND F YML002W gene taxon:4932 20021126 SGD
+SGD S000004461 YML002W GO:0000004 SGD_REF:S000069584 ND P YML002W gene taxon:4932 20021126 SGD
+SGD S000004462 YML003W GO:0008372 SGD_REF:S000069584 ND C YML003W gene taxon:4932 20021126 SGD
+SGD S000004462 YML003W GO:0005554 SGD_REF:S000069584 ND F YML003W gene taxon:4932 20021126 SGD
+SGD S000004462 YML003W GO:0000004 SGD_REF:S000069584 ND P YML003W gene taxon:4932 20021126 SGD
+SGD S000007621 YML007C-A GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YML007C-A gene taxon:4932 20031028 SGD
+SGD S000007621 YML007C-A GO:0005554 SGD_REF:S000069584 ND F YML007C-A gene taxon:4932 20010226 SGD
+SGD S000007621 YML007C-A GO:0000004 SGD_REF:S000069584 ND P YML007C-A gene taxon:4932 20010226 SGD
+SGD S000004480 YML018C GO:0000329 SGD_REF:S000074185|PMID:14562095 IDA C YML018C gene taxon:4932 20031028 SGD
+SGD S000004480 YML018C GO:0005554 SGD_REF:S000069584 ND F YML018C gene taxon:4932 20030203 SGD
+SGD S000004480 YML018C GO:0000004 SGD_REF:S000069584 ND P YML018C gene taxon:4932 20030203 SGD
+SGD S000004482 YML020W GO:0008372 SGD_REF:S000069584 ND C YML020W gene taxon:4932 20021126 SGD
+SGD S000004482 YML020W GO:0005554 SGD_REF:S000069584 ND F YML020W gene taxon:4932 20021126 SGD
+SGD S000004482 YML020W GO:0000004 SGD_REF:S000069584 ND P YML020W gene taxon:4932 20021126 SGD
+SGD S000004492 YML030W GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YML030W gene taxon:4932 20031028 SGD
+SGD S000004492 YML030W GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YML030W gene taxon:4932 20040924 SGD
+SGD S000004492 YML030W GO:0005554 SGD_REF:S000069584 ND F YML030W gene taxon:4932 20021126 SGD
+SGD S000004492 YML030W GO:0000004 SGD_REF:S000069584 ND P YML030W gene taxon:4932 20021126 SGD
+SGD S000004501 YML037C colocalizes_with GO:0030136 SGD_REF:S000074185|PMID:14562095 IDA C YML037C gene taxon:4932 20031028 SGD
+SGD S000004501 YML037C GO:0005554 SGD_REF:S000069584 ND F YML037C gene taxon:4932 20021126 SGD
+SGD S000004501 YML037C GO:0000004 SGD_REF:S000069584 ND P YML037C gene taxon:4932 20021126 SGD
+SGD S000004503 YML039W GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YML039W gene taxon:4932 20030811 SGD
+SGD S000004503 YML039W GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YML039W gene taxon:4932 20030811 SGD
+SGD S000004503 YML039W GO:0003887 SGD_REF:S000072465|PMID:9582191 ISS F YML039W gene taxon:4932 20030811 SGD
+SGD S000004503 YML039W GO:0003964 SGD_REF:S000072465|PMID:9582191 ISS F YML039W gene taxon:4932 20030811 SGD
+SGD S000004503 YML039W GO:0004540 SGD_REF:S000072465|PMID:9582191 ISS F YML039W gene taxon:4932 20030811 SGD
+SGD S000004503 YML039W GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YML039W gene taxon:4932 20030811 SGD
+SGD S000004503 YML039W GO:0008233 SGD_REF:S000072465|PMID:9582191 ISS F YML039W gene taxon:4932 20030811 SGD
+SGD S000004503 YML039W GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YML039W gene taxon:4932 20030811 SGD
+SGD S000004504 YML040W GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YML040W gene taxon:4932 20030811 SGD
+SGD S000004504 YML040W GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YML040W gene taxon:4932 20030811 SGD
+SGD S000004504 YML040W GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YML040W gene taxon:4932 20030811 SGD
+SGD S000004504 YML040W GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YML040W gene taxon:4932 20030811 SGD
+SGD S000004508 YML045W GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YML045W gene taxon:4932 20030811 SGD
+SGD S000004508 YML045W GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YML045W gene taxon:4932 20030811 SGD
+SGD S000004508 YML045W GO:0003887 SGD_REF:S000072465|PMID:9582191 ISS F YML045W gene taxon:4932 20030811 SGD
+SGD S000004508 YML045W GO:0003964 SGD_REF:S000072465|PMID:9582191 ISS F YML045W gene taxon:4932 20030811 SGD
+SGD S000004508 YML045W GO:0004540 SGD_REF:S000072465|PMID:9582191 ISS F YML045W gene taxon:4932 20030811 SGD
+SGD S000004508 YML045W GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YML045W gene taxon:4932 20030811 SGD
+SGD S000004508 YML045W GO:0008233 SGD_REF:S000072465|PMID:9582191 ISS F YML045W gene taxon:4932 20030811 SGD
+SGD S000004508 YML045W GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YML045W gene taxon:4932 20030811 SGD
+SGD S000007381 YML045W-A GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YML045W-A gene taxon:4932 20030811 SGD
+SGD S000007381 YML045W-A GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YML045W-A gene taxon:4932 20030811 SGD
+SGD S000007381 YML045W-A GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YML045W-A gene taxon:4932 20030811 SGD
+SGD S000007381 YML045W-A GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YML045W-A gene taxon:4932 20030811 SGD
+SGD S000004514 YML050W GO:0008372 SGD_REF:S000069584 ND C YML050W gene taxon:4932 20021126 SGD
+SGD S000004514 YML050W GO:0005554 SGD_REF:S000069584 ND F YML050W gene taxon:4932 20021126 SGD
+SGD S000004514 YML050W GO:0000004 SGD_REF:S000069584 ND P YML050W gene taxon:4932 20021126 SGD
+SGD S000004517 YML053C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YML053C gene taxon:4932 20031028 SGD
+SGD S000004517 YML053C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YML053C gene taxon:4932 20031028 SGD
+SGD S000004517 YML053C GO:0005554 SGD_REF:S000069584 ND F YML053C gene taxon:4932 20021126 SGD
+SGD S000004517 YML053C GO:0000004 SGD_REF:S000069584 ND P YML053C gene taxon:4932 20021126 SGD
+SGD S000028573 YML054C-A GO:0008372 SGD_REF:S000069584 ND C YML054C-A gene taxon:4932 20030730 SGD
+SGD S000028573 YML054C-A GO:0005554 SGD_REF:S000069584 ND F YML054C-A gene taxon:4932 20030730 SGD
+SGD S000028573 YML054C-A GO:0000004 SGD_REF:S000069584 ND P YML054C-A gene taxon:4932 20030730 SGD
+SGD S000004544 YML079W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YML079W gene taxon:4932 20031028 SGD
+SGD S000004544 YML079W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YML079W gene taxon:4932 20031028 SGD
+SGD S000004544 YML079W GO:0005554 SGD_REF:S000069584 ND F YML079W gene taxon:4932 20021126 SGD
+SGD S000004544 YML079W GO:0000004 SGD_REF:S000069584 ND P YML079W gene taxon:4932 20021126 SGD
+SGD S000004546 YML081W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YML081W gene taxon:4932 20031028 SGD
+SGD S000004546 YML081W GO:0005554 SGD_REF:S000069584 ND F YML081W gene taxon:4932 20021126 SGD
+SGD S000004546 YML081W GO:0000004 SGD_REF:S000069584 ND P YML081W gene taxon:4932 20021126 SGD
+SGD S000004547 YML082W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YML082W gene taxon:4932 20031028 SGD
+SGD S000004547 YML082W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YML082W gene taxon:4932 20031028 SGD
+SGD S000004547 YML082W GO:0016846 SGD_REF:S000072463|PMID:10592175 ISS F YML082W gene taxon:4932 20030213 SGD
+SGD S000004547 YML082W GO:0006790 SGD_REF:S000039910|PMID:10821189 ISS P YML082W gene taxon:4932 20030530 SGD
+SGD S000004548 YML083C GO:0008372 SGD_REF:S000069584 ND C YML083C gene taxon:4932 20021126 SGD
+SGD S000004548 YML083C GO:0005554 SGD_REF:S000069584 ND F YML083C gene taxon:4932 20021126 SGD
+SGD S000004548 YML083C GO:0000004 SGD_REF:S000069584 ND P YML083C gene taxon:4932 20021126 SGD
+SGD S000004552 YML087C GO:0008372 SGD_REF:S000069584 ND C YML087C gene taxon:4932 20021126 SGD
+SGD S000004552 YML087C GO:0005554 SGD_REF:S000069584 ND F YML087C gene taxon:4932 20021126 SGD
+SGD S000004552 YML087C GO:0000004 SGD_REF:S000069584 ND P YML087C gene taxon:4932 20021126 SGD
+SGD S000004562 YML096W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YML096W gene taxon:4932 20031028 SGD
+SGD S000004562 YML096W GO:0005554 SGD_REF:S000069584 ND F YML096W gene taxon:4932 20021126 SGD
+SGD S000004562 YML096W GO:0000004 SGD_REF:S000069584 ND P YML096W gene taxon:4932 20021126 SGD
+SGD S000028688 YML100W-A GO:0008372 SGD_REF:S000069584 ND C YML100W-A gene taxon:4932 20030730 SGD
+SGD S000028688 YML100W-A GO:0005554 SGD_REF:S000069584 ND F YML100W-A gene taxon:4932 20030730 SGD
+SGD S000028688 YML100W-A GO:0000004 SGD_REF:S000069584 ND P YML100W-A gene taxon:4932 20030730 SGD
+SGD S000004576 YML108W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YML108W gene taxon:4932 20031028 SGD
+SGD S000004576 YML108W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YML108W gene taxon:4932 20031028 SGD
+SGD S000004576 YML108W GO:0005554 SGD_REF:S000069584 ND F YML108W gene taxon:4932 20030203 SGD
+SGD S000004576 YML108W GO:0000004 SGD_REF:S000069584 ND P YML108W gene taxon:4932 20030203 SGD
+SGD S000004588 YML119W GO:0008372 SGD_REF:S000069584 ND C YML119W gene taxon:4932 20030203 SGD
+SGD S000004588 YML119W GO:0005554 SGD_REF:S000069584 ND F YML119W gene taxon:4932 20030203 SGD
+SGD S000004588 YML119W GO:0000004 SGD_REF:S000069584 ND P YML119W gene taxon:4932 20030203 SGD
+SGD S000004600 YML131W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YML131W gene taxon:4932 20031028 SGD
+SGD S000004600 YML131W GO:0005554 SGD_REF:S000069584 ND F YML131W gene taxon:4932 20030428 SGD
+SGD S000004600 YML131W GO:0000004 SGD_REF:S000069584 ND P YML131W gene taxon:4932 20030428 SGD
+SGD S000004602 YML133C GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YML133C gene taxon:4932 20040813 SGD
+SGD S000004602 YML133C GO:0004386 SGD_REF:S000053946|PMID:9837911 ISS F YML133C gene taxon:4932 20040323 SGD
+SGD S000004602 YML133C GO:0000004 SGD_REF:S000069584 ND P YML133C gene taxon:4932 20021126 SGD
+SGD S000028691 YMR001C-A GO:0008372 SGD_REF:S000069584 ND C YMR001C-A gene taxon:4932 20030730 SGD
+SGD S000028691 YMR001C-A GO:0005554 SGD_REF:S000069584 ND F YMR001C-A gene taxon:4932 20030730 SGD
+SGD S000028691 YMR001C-A GO:0000004 SGD_REF:S000069584 ND P YMR001C-A gene taxon:4932 20030730 SGD
+SGD S000004604 YMR002W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YMR002W gene taxon:4932 20031028 SGD
+SGD S000004604 YMR002W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YMR002W gene taxon:4932 20031028 SGD
+SGD S000004604 YMR002W GO:0005554 SGD_REF:S000069584 ND F YMR002W gene taxon:4932 20021126 SGD
+SGD S000004604 YMR002W GO:0000004 SGD_REF:S000069584 ND P YMR002W gene taxon:4932 20021126 SGD
+SGD S000004605 YMR003W GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YMR003W gene taxon:4932 20031028 SGD
+SGD S000004605 YMR003W GO:0005554 SGD_REF:S000069584 ND F YMR003W gene taxon:4932 20021126 SGD
+SGD S000004605 YMR003W GO:0000004 SGD_REF:S000069584 ND P YMR003W gene taxon:4932 20021126 SGD
+SGD S000004612 YMR010W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YMR010W gene taxon:4932 20031028 SGD
+SGD S000004612 YMR010W GO:0005554 SGD_REF:S000069584 ND F YMR010W gene taxon:4932 20021126 SGD
+SGD S000004612 YMR010W GO:0008152 SGD_REF:S000075216|PMID:14656964 TAS P YMR010W gene taxon:4932 20040315 SGD
+SGD S000004620 YMR018W GO:0008372 SGD_REF:S000069584 ND C YMR018W gene taxon:4932 20030427 SGD
+SGD S000004620 YMR018W GO:0005554 SGD_REF:S000069584 ND F YMR018W gene taxon:4932 20030427 SGD
+SGD S000004620 YMR018W GO:0000004 SGD_REF:S000069584 ND P YMR018W gene taxon:4932 20030427 SGD
+SGD S000004629 YMR027W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YMR027W gene taxon:4932 20031028 SGD
+SGD S000004629 YMR027W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YMR027W gene taxon:4932 20031028 SGD
+SGD S000004629 YMR027W GO:0005554 SGD_REF:S000069584 ND F YMR027W gene taxon:4932 20021001 SGD
+SGD S000004629 YMR027W GO:0000004 SGD_REF:S000069584 ND P YMR027W gene taxon:4932 20021001 SGD
+SGD S000028574 YMR030W-A GO:0008372 SGD_REF:S000069584 ND C YMR030W-A gene taxon:4932 20030730 SGD
+SGD S000028574 YMR030W-A GO:0005554 SGD_REF:S000069584 ND F YMR030W-A gene taxon:4932 20030730 SGD
+SGD S000028574 YMR030W-A GO:0000004 SGD_REF:S000069584 ND P YMR030W-A gene taxon:4932 20030730 SGD
+SGD S000004633 YMR031C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YMR031C gene taxon:4932 20031028 SGD
+SGD S000004633 YMR031C GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YMR031C gene taxon:4932 20040929 SGD
+SGD S000004633 YMR031C GO:0005554 SGD_REF:S000069584 ND F YMR031C gene taxon:4932 20030203 SGD
+SGD S000004633 YMR031C GO:0000004 SGD_REF:S000069584 ND P YMR031C gene taxon:4932 20030203 SGD
+SGD S000004637 YMR034C GO:0008372 SGD_REF:S000069584 ND C YMR034C gene taxon:4932 20030115 SGD
+SGD S000004637 YMR034C GO:0015248 SGD_REF:S000054158|PMID:10543755 ISS F YMR034C gene taxon:4932 20030115 SGD
+SGD S000004637 YMR034C GO:0000004 SGD_REF:S000069584 ND P YMR034C gene taxon:4932 20030115 SGD
+SGD S000004644 YMR041C GO:0008372 SGD_REF:S000069584 ND C YMR041C gene taxon:4932 20030203 SGD
+SGD S000004644 YMR041C GO:0005554 SGD_REF:S000069584 ND F YMR041C gene taxon:4932 20030203 SGD
+SGD S000004644 YMR041C GO:0000004 SGD_REF:S000069584 ND P YMR041C gene taxon:4932 20030203 SGD
+SGD S000004648 YMR045C GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YMR045C gene taxon:4932 20030811 SGD
+SGD S000004648 YMR045C GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YMR045C gene taxon:4932 20030811 SGD
+SGD S000004648 YMR045C GO:0003887 SGD_REF:S000072465|PMID:9582191 ISS F YMR045C gene taxon:4932 20030811 SGD
+SGD S000004648 YMR045C GO:0003964 SGD_REF:S000072465|PMID:9582191 ISS F YMR045C gene taxon:4932 20030811 SGD
+SGD S000004648 YMR045C GO:0004540 SGD_REF:S000072465|PMID:9582191 ISS F YMR045C gene taxon:4932 20030811 SGD
+SGD S000004648 YMR045C GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YMR045C gene taxon:4932 20030811 SGD
+SGD S000004648 YMR045C GO:0008233 SGD_REF:S000072465|PMID:9582191 ISS F YMR045C gene taxon:4932 20030811 SGD
+SGD S000004648 YMR045C GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YMR045C gene taxon:4932 20030811 SGD
+SGD S000004649 YMR046C GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YMR046C gene taxon:4932 20030811 SGD
+SGD S000004649 YMR046C GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YMR046C gene taxon:4932 20030811 SGD
+SGD S000004649 YMR046C GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YMR046C gene taxon:4932 20030811 SGD
+SGD S000004649 YMR046C GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YMR046C gene taxon:4932 20030811 SGD
+SGD S000004653 YMR050C GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YMR050C gene taxon:4932 20030811 SGD
+SGD S000004653 YMR050C GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YMR050C gene taxon:4932 20030811 SGD
+SGD S000004653 YMR050C GO:0003887 SGD_REF:S000072465|PMID:9582191 ISS F YMR050C gene taxon:4932 20030811 SGD
+SGD S000004653 YMR050C GO:0003964 SGD_REF:S000072465|PMID:9582191 ISS F YMR050C gene taxon:4932 20030811 SGD
+SGD S000004653 YMR050C GO:0004540 SGD_REF:S000072465|PMID:9582191 ISS F YMR050C gene taxon:4932 20030811 SGD
+SGD S000004653 YMR050C GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YMR050C gene taxon:4932 20030811 SGD
+SGD S000004653 YMR050C GO:0008233 SGD_REF:S000072465|PMID:9582191 ISS F YMR050C gene taxon:4932 20030811 SGD
+SGD S000004653 YMR050C GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YMR050C gene taxon:4932 20030811 SGD
+SGD S000004654 YMR051C GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YMR051C gene taxon:4932 20030811 SGD
+SGD S000004654 YMR051C GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YMR051C gene taxon:4932 20030811 SGD
+SGD S000004654 YMR051C GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YMR051C gene taxon:4932 20030811 SGD
+SGD S000004654 YMR051C GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YMR051C gene taxon:4932 20030811 SGD
+SGD S000004677 YMR073C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YMR073C gene taxon:4932 20031028 SGD
+SGD S000004677 YMR073C GO:0005554 SGD_REF:S000069584 ND F YMR073C gene taxon:4932 20060106 SGD
+SGD S000004677 YMR073C GO:0042493 SGD_REF:S000086496|PMID:16121259 IMP P YMR073C gene taxon:4932 20060106 SGD
+SGD S000004678 YMR074C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YMR074C gene taxon:4932 20031028 SGD
+SGD S000004678 YMR074C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YMR074C gene taxon:4932 20031028 SGD
+SGD S000004678 YMR074C GO:0005554 SGD_REF:S000069584 ND F YMR074C gene taxon:4932 20021126 SGD
+SGD S000004678 YMR074C GO:0000004 SGD_REF:S000069584 ND P YMR074C gene taxon:4932 20021126 SGD
+SGD S000004689 YMR084W GO:0008372 SGD_REF:S000069584 ND C YMR084W gene taxon:4932 20030203 SGD
+SGD S000004689 YMR084W GO:0005554 SGD_REF:S000069584 ND F YMR084W gene taxon:4932 20030203 SGD
+SGD S000004689 YMR084W GO:0000004 SGD_REF:S000069584 ND P YMR084W gene taxon:4932 20030203 SGD
+SGD S000004690 YMR085W GO:0008372 SGD_REF:S000069584 ND C YMR085W gene taxon:4932 20021126 SGD
+SGD S000004690 YMR085W GO:0005554 SGD_REF:S000069584 ND F YMR085W gene taxon:4932 20021126 SGD
+SGD S000004690 YMR085W GO:0000004 SGD_REF:S000069584 ND P YMR085W gene taxon:4932 20021126 SGD
+SGD S000004692 YMR086W GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YMR086W gene taxon:4932 20020507 SGD
+SGD S000004692 YMR086W GO:0005554 SGD_REF:S000069584 ND F YMR086W gene taxon:4932 20030428 SGD
+SGD S000004692 YMR086W GO:0000004 SGD_REF:S000069584 ND P YMR086W gene taxon:4932 20030428 SGD
+SGD S000004693 YMR087W GO:0008372 SGD_REF:S000069584 ND C YMR087W gene taxon:4932 20021126 SGD
+SGD S000004693 YMR087W GO:0016791 SGD_REF:S000080961|PMID:15722447 ISS F YMR087W gene taxon:4932 20050310 SGD
+SGD S000004693 YMR087W GO:0006388 SGD_REF:S000080961|PMID:15722447 TAS P YMR087W gene taxon:4932 20050308 SGD
+SGD S000004696 YMR090W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YMR090W gene taxon:4932 20031028 SGD
+SGD S000004696 YMR090W GO:0005554 SGD_REF:S000069584 ND F YMR090W gene taxon:4932 20021126 SGD
+SGD S000004696 YMR090W GO:0000004 SGD_REF:S000069584 ND P YMR090W gene taxon:4932 20021126 SGD
+SGD S000004704 YMR098C GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YMR098C gene taxon:4932 20031028 SGD
+SGD S000004704 YMR098C GO:0005554 SGD_REF:S000069584 ND F YMR098C gene taxon:4932 20021126 SGD
+SGD S000004704 YMR098C GO:0000004 SGD_REF:S000069584 ND P YMR098C gene taxon:4932 20021126 SGD
+SGD S000004705 YMR099C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YMR099C gene taxon:4932 20031028 SGD
+SGD S000004705 YMR099C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YMR099C gene taxon:4932 20031028 SGD
+SGD S000004705 YMR099C GO:0005554 SGD_REF:S000069584 ND F YMR099C gene taxon:4932 20030427 SGD
+SGD S000004705 YMR099C GO:0000004 SGD_REF:S000069584 ND P YMR099C gene taxon:4932 20030427 SGD
+SGD S000004708 YMR102C GO:0008372 SGD_REF:S000069584 ND C YMR102C gene taxon:4932 20021126 SGD
+SGD S000004708 YMR102C GO:0005554 SGD_REF:S000069584 ND F YMR102C gene taxon:4932 20021126 SGD
+SGD S000004708 YMR102C GO:0000004 SGD_REF:S000069584 ND P YMR102C gene taxon:4932 20021126 SGD
+SGD S000028692 YMR105W-A GO:0008372 SGD_REF:S000069584 ND C YMR105W-A gene taxon:4932 20030730 SGD
+SGD S000028692 YMR105W-A GO:0005554 SGD_REF:S000069584 ND F YMR105W-A gene taxon:4932 20030730 SGD
+SGD S000028692 YMR105W-A GO:0000004 SGD_REF:S000069584 ND P YMR105W-A gene taxon:4932 20030730 SGD
+SGD S000004717 YMR111C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YMR111C gene taxon:4932 20031028 SGD
+SGD S000004717 YMR111C GO:0005554 SGD_REF:S000069584 ND F YMR111C gene taxon:4932 20021126 SGD
+SGD S000004717 YMR111C GO:0000004 SGD_REF:S000069584 ND P YMR111C gene taxon:4932 20021126 SGD
+SGD S000004720 YMR114C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YMR114C gene taxon:4932 20031028 SGD
+SGD S000004720 YMR114C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YMR114C gene taxon:4932 20031028 SGD
+SGD S000004720 YMR114C GO:0005554 SGD_REF:S000069584 ND F YMR114C gene taxon:4932 20021126 SGD
+SGD S000004720 YMR114C GO:0000004 SGD_REF:S000069584 ND P YMR114C gene taxon:4932 20021126 SGD
+SGD S000004724 YMR118C GO:0008372 SGD_REF:S000069584 ND C YMR118C gene taxon:4932 20021126 SGD
+SGD S000004724 YMR118C GO:0005554 SGD_REF:S000069584 ND F YMR118C gene taxon:4932 20021126 SGD
+SGD S000004724 YMR118C GO:0000004 SGD_REF:S000069584 ND P YMR118C gene taxon:4932 20021126 SGD
+SGD S000007524 YMR122W-A GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YMR122W-A gene taxon:4932 20031028 SGD
+SGD S000007524 YMR122W-A GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YMR122W-A gene taxon:4932 20031028 SGD
+SGD S000007524 YMR122W-A GO:0005554 SGD_REF:S000069584 ND F YMR122W-A gene taxon:4932 20030203 SGD
+SGD S000007524 YMR122W-A GO:0000004 SGD_REF:S000069584 ND P YMR122W-A gene taxon:4932 20030203 SGD
+SGD S000004731 YMR124W GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YMR124W gene taxon:4932 20020507 SGD
+SGD S000004731 YMR124W GO:0005554 SGD_REF:S000069584 ND F YMR124W gene taxon:4932 20030428 SGD
+SGD S000004731 YMR124W GO:0000004 SGD_REF:S000069584 ND P YMR124W gene taxon:4932 20030428 SGD
+SGD S000004737 YMR130W GO:0008372 SGD_REF:S000069584 ND C YMR130W gene taxon:4932 20021126 SGD
+SGD S000004737 YMR130W GO:0005554 SGD_REF:S000069584 ND F YMR130W gene taxon:4932 20021126 SGD
+SGD S000004737 YMR130W GO:0000004 SGD_REF:S000069584 ND P YMR130W gene taxon:4932 20021126 SGD
+SGD S000004741 YMR134W GO:0005635 SGD_REF:S000075214|PMID:14690591 IDA C YMR134W gene taxon:4932 20040105 SGD
+SGD S000004741 YMR134W GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YMR134W gene taxon:4932 20020507 SGD
+SGD S000004741 YMR134W GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YMR134W gene taxon:4932 20031028 SGD
+SGD S000004741 YMR134W GO:0005783 SGD_REF:S000075214|PMID:14690591 IDA C YMR134W gene taxon:4932 20040105 SGD
+SGD S000004741 YMR134W GO:0005554 SGD_REF:S000069584 ND F YMR134W gene taxon:4932 20030203 SGD
+SGD S000004741 YMR134W GO:0006879 SGD_REF:S000049863|PMID:9180083 IGI P YMR134W gene taxon:4932 20030212 SGD
+SGD S000004741 YMR134W GO:0006879 SGD_REF:S000049863|PMID:9180083 IMP P YMR134W gene taxon:4932 20030212 SGD
+SGD S000004741 YMR134W GO:0007005 SGD_REF:S000086425|PMID:16135527 IMP P YMR134W gene taxon:4932 20051111 SGD
+SGD S000004752 YMR144W GO:0005634 SGD_REF:S000069459|PMID:11914276 IDA C YMR144W gene taxon:4932 20020507 SGD
+SGD S000004752 YMR144W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YMR144W gene taxon:4932 20031028 SGD
+SGD S000004752 YMR144W GO:0005554 SGD_REF:S000069584 ND F YMR144W gene taxon:4932 20030203 SGD
+SGD S000004752 YMR144W GO:0000004 SGD_REF:S000069584 ND P YMR144W gene taxon:4932 20030203 SGD
+SGD S000004755 YMR147W GO:0008372 SGD_REF:S000069584 ND C YMR147W gene taxon:4932 20021126 SGD
+SGD S000004755 YMR147W GO:0005554 SGD_REF:S000069584 ND F YMR147W gene taxon:4932 20021126 SGD
+SGD S000004755 YMR147W GO:0000004 SGD_REF:S000069584 ND P YMR147W gene taxon:4932 20021126 SGD
+SGD S000004756 YMR148W GO:0016021 SGD_REF:S000072825|PMID:12524434 ISS C YMR148W gene taxon:4932 20030409 SGD
+SGD S000004756 YMR148W GO:0005554 SGD_REF:S000069584 ND F YMR148W gene taxon:4932 20021126 SGD
+SGD S000004756 YMR148W GO:0000004 SGD_REF:S000069584 ND P YMR148W gene taxon:4932 20021126 SGD
+SGD S000004764 YMR155W GO:0008372 SGD_REF:S000069584 ND C YMR155W gene taxon:4932 20021126 SGD
+SGD S000004764 YMR155W GO:0005554 SGD_REF:S000069584 ND F YMR155W gene taxon:4932 20021126 SGD
+SGD S000004764 YMR155W GO:0000004 SGD_REF:S000069584 ND P YMR155W gene taxon:4932 20021126 SGD
+SGD S000007249 YMR158C-A GO:0008372 SGD_REF:S000069584 ND C YMR158C-A|YMR158C-B gene taxon:4932 20021126 SGD
+SGD S000007249 YMR158C-A GO:0005554 SGD_REF:S000069584 ND F YMR158C-A|YMR158C-B gene taxon:4932 20021126 SGD
+SGD S000007249 YMR158C-A GO:0000004 SGD_REF:S000069584 ND P YMR158C-A|YMR158C-B gene taxon:4932 20021126 SGD
+SGD S000004770 YMR160W GO:0000329 SGD_REF:S000074185|PMID:14562095 IDA C YMR160W gene taxon:4932 20031028 SGD
+SGD S000004770 YMR160W GO:0005554 SGD_REF:S000069584 ND F YMR160W gene taxon:4932 20021126 SGD
+SGD S000004770 YMR160W GO:0000004 SGD_REF:S000069584 ND P YMR160W gene taxon:4932 20021126 SGD
+SGD S000004773 YMR163C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YMR163C gene taxon:4932 20031028 SGD
+SGD S000004773 YMR163C GO:0005554 SGD_REF:S000069584 ND F YMR163C gene taxon:4932 20021126 SGD
+SGD S000004773 YMR163C GO:0000004 SGD_REF:S000069584 ND P YMR163C gene taxon:4932 20021126 SGD
+SGD S000004776 YMR166C GO:0005743 SGD_REF:S000049213|PMID:10930523 ISS C YMR166C gene taxon:4932 20021017 SGD
+SGD S000004776 YMR166C GO:0005215 SGD_REF:S000049213|PMID:10930523 ISS F YMR166C gene taxon:4932 20021017 SGD
+SGD S000004776 YMR166C GO:0006810 SGD_REF:S000049213|PMID:10930523 ISS P YMR166C gene taxon:4932 20021017 SGD
+SGD S000004781 YMR171C GO:0005768 SGD_REF:S000074185|PMID:14562095 IDA C YMR171C gene taxon:4932 20031028 SGD
+SGD S000004781 YMR171C GO:0005554 SGD_REF:S000069584 ND F YMR171C gene taxon:4932 20021126 SGD
+SGD S000004781 YMR171C GO:0000004 SGD_REF:S000069584 ND P YMR171C gene taxon:4932 20021126 SGD
+SGD S000028848 YMR175W-A GO:0008372 SGD_REF:S000069584 ND C YMR175W-A gene taxon:4932 20030730 SGD
+SGD S000028848 YMR175W-A GO:0005554 SGD_REF:S000069584 ND F YMR175W-A gene taxon:4932 20030730 SGD
+SGD S000028848 YMR175W-A GO:0000004 SGD_REF:S000069584 ND P YMR175W-A gene taxon:4932 20030730 SGD
+SGD S000004790 YMR178W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YMR178W gene taxon:4932 20031028 SGD
+SGD S000004790 YMR178W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YMR178W gene taxon:4932 20031028 SGD
+SGD S000004790 YMR178W GO:0005554 SGD_REF:S000069584 ND F YMR178W gene taxon:4932 20021126 SGD
+SGD S000004790 YMR178W GO:0000004 SGD_REF:S000069584 ND P YMR178W gene taxon:4932 20021126 SGD
+SGD S000004793 YMR181C GO:0008372 SGD_REF:S000069584 ND C YMR181C gene taxon:4932 20021126 SGD
+SGD S000004793 YMR181C GO:0005554 SGD_REF:S000069584 ND F YMR181C gene taxon:4932 20021126 SGD
+SGD S000004793 YMR181C GO:0000004 SGD_REF:S000069584 ND P YMR181C gene taxon:4932 20021126 SGD
+SGD S000028693 YMR182W-A GO:0008372 SGD_REF:S000069584 ND C YMR182W-A gene taxon:4932 20030730 SGD
+SGD S000028693 YMR182W-A GO:0005554 SGD_REF:S000069584 ND F YMR182W-A gene taxon:4932 20030730 SGD
+SGD S000028693 YMR182W-A GO:0000004 SGD_REF:S000069584 ND P YMR182W-A gene taxon:4932 20030730 SGD
+SGD S000004797 YMR185W GO:0008372 SGD_REF:S000069584 ND C YMR185W gene taxon:4932 20021126 SGD
+SGD S000004797 YMR185W GO:0005554 SGD_REF:S000069584 ND F YMR185W gene taxon:4932 20021126 SGD
+SGD S000004797 YMR185W GO:0000004 SGD_REF:S000069584 ND P YMR185W gene taxon:4932 20021126 SGD
+SGD S000004799 YMR187C GO:0008372 SGD_REF:S000069584 ND C YMR187C gene taxon:4932 20021126 SGD
+SGD S000004799 YMR187C GO:0005554 SGD_REF:S000069584 ND F YMR187C gene taxon:4932 20021126 SGD
+SGD S000004799 YMR187C GO:0000004 SGD_REF:S000069584 ND P YMR187C gene taxon:4932 20021126 SGD
+SGD S000028514 YMR194C-B GO:0008372 SGD_REF:S000069584 ND C YMR194C-B gene taxon:4932 20030730 SGD
+SGD S000028514 YMR194C-B GO:0005554 SGD_REF:S000069584 ND F YMR194C-B gene taxon:4932 20030730 SGD
+SGD S000028514 YMR194C-B GO:0000004 SGD_REF:S000069584 ND P YMR194C-B gene taxon:4932 20030730 SGD
+SGD S000004809 YMR196W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YMR196W gene taxon:4932 20031028 SGD
+SGD S000004809 YMR196W GO:0005554 SGD_REF:S000069584 ND F YMR196W gene taxon:4932 20021126 SGD
+SGD S000004809 YMR196W GO:0000004 SGD_REF:S000069584 ND P YMR196W gene taxon:4932 20021126 SGD
+SGD S000004819 YMR206W GO:0008372 SGD_REF:S000069584 ND C YMR206W gene taxon:4932 20021126 SGD
+SGD S000004819 YMR206W GO:0005554 SGD_REF:S000069584 ND F YMR206W gene taxon:4932 20021126 SGD
+SGD S000004819 YMR206W GO:0000004 SGD_REF:S000069584 ND P YMR206W gene taxon:4932 20021126 SGD
+SGD S000004822 YMR209C GO:0008372 SGD_REF:S000069584 ND C YMR209C gene taxon:4932 20021126 SGD
+SGD S000004822 YMR209C GO:0005554 SGD_REF:S000069584 ND F YMR209C gene taxon:4932 20021126 SGD
+SGD S000004822 YMR209C GO:0000004 SGD_REF:S000069584 ND P YMR209C gene taxon:4932 20021126 SGD
+SGD S000004823 YMR210W GO:0008372 SGD_REF:S000069584 ND C YMR210W gene taxon:4932 20021126 SGD
+SGD S000004823 YMR210W GO:0005554 SGD_REF:S000069584 ND F YMR210W gene taxon:4932 20021126 SGD
+SGD S000004823 YMR210W GO:0000004 SGD_REF:S000069584 ND P YMR210W gene taxon:4932 20021126 SGD
+SGD S000028576 YMR230W-A GO:0008372 SGD_REF:S000069584 ND C YMR230W-A gene taxon:4932 20030730 SGD
+SGD S000028576 YMR230W-A GO:0005554 SGD_REF:S000069584 ND F YMR230W-A gene taxon:4932 20030730 SGD
+SGD S000028576 YMR230W-A GO:0000004 SGD_REF:S000069584 ND P YMR230W-A gene taxon:4932 20030730 SGD
+SGD S000004846 YMR233W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YMR233W|TRI1 gene taxon:4932 20031028 SGD
+SGD S000004846 YMR233W GO:0005730 SGD_REF:S000074185|PMID:14562095 IDA C YMR233W|TRI1 gene taxon:4932 20031028 SGD
+SGD S000004846 YMR233W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YMR233W|TRI1 gene taxon:4932 20031028 SGD
+SGD S000004846 YMR233W GO:0005554 SGD_REF:S000069584 ND F YMR233W|TRI1 gene taxon:4932 20021125 SGD
+SGD S000004846 YMR233W GO:0000004 SGD_REF:S000069584 ND P YMR233W|TRI1 gene taxon:4932 20021125 SGD
+SGD S000028694 YMR242W-A GO:0008372 SGD_REF:S000069584 ND C YMR242W-A gene taxon:4932 20030730 SGD
+SGD S000028694 YMR242W-A GO:0005554 SGD_REF:S000069584 ND F YMR242W-A gene taxon:4932 20030730 SGD
+SGD S000028694 YMR242W-A GO:0000004 SGD_REF:S000069584 ND P YMR242W-A gene taxon:4932 20030730 SGD
+SGD S000004857 YMR244C-A GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YMR244C-A gene taxon:4932 20031028 SGD
+SGD S000004857 YMR244C-A GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YMR244C-A gene taxon:4932 20031028 SGD
+SGD S000004857 YMR244C-A GO:0005554 SGD_REF:S000069584 ND F YMR244C-A gene taxon:4932 20021126 SGD
+SGD S000004857 YMR244C-A GO:0000004 SGD_REF:S000069584 ND P YMR244C-A gene taxon:4932 20021126 SGD
+SGD S000004858 YMR244W GO:0008372 SGD_REF:S000069584 ND C YMR244W gene taxon:4932 20021126 SGD
+SGD S000004858 YMR244W GO:0005554 SGD_REF:S000069584 ND F YMR244W gene taxon:4932 20021126 SGD
+SGD S000004858 YMR244W GO:0000004 SGD_REF:S000069584 ND P YMR244W gene taxon:4932 20021126 SGD
+SGD S000028849 YMR247W-A GO:0008372 SGD_REF:S000069584 ND C YMR247W-A gene taxon:4932 20030730 SGD
+SGD S000028849 YMR247W-A GO:0005554 SGD_REF:S000069584 ND F YMR247W-A gene taxon:4932 20030730 SGD
+SGD S000028849 YMR247W-A GO:0000004 SGD_REF:S000069584 ND P YMR247W-A gene taxon:4932 20030730 SGD
+SGD S000004865 YMR252C GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YMR252C gene taxon:4932 20031028 SGD
+SGD S000004865 YMR252C GO:0005554 SGD_REF:S000069584 ND F YMR252C gene taxon:4932 20021126 SGD
+SGD S000004865 YMR252C GO:0000004 SGD_REF:S000069584 ND P YMR252C gene taxon:4932 20021126 SGD
+SGD S000004866 YMR253C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YMR253C gene taxon:4932 20031028 SGD
+SGD S000004866 YMR253C GO:0005554 SGD_REF:S000069584 ND F YMR253C gene taxon:4932 20021120 SGD
+SGD S000004866 YMR253C GO:0000004 SGD_REF:S000069584 ND P YMR253C gene taxon:4932 20021120 SGD
+SGD S000004871 YMR258C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YMR258C gene taxon:4932 20031028 SGD
+SGD S000004871 YMR258C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YMR258C gene taxon:4932 20031028 SGD
+SGD S000004871 YMR258C GO:0005554 SGD_REF:S000069584 ND F YMR258C gene taxon:4932 20030203 SGD
+SGD S000004871 YMR258C GO:0000004 SGD_REF:S000069584 ND P YMR258C gene taxon:4932 20030203 SGD
+SGD S000004872 YMR259C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YMR259C gene taxon:4932 20031028 SGD
+SGD S000004872 YMR259C GO:0005554 SGD_REF:S000069584 ND F YMR259C gene taxon:4932 20030203 SGD
+SGD S000004872 YMR259C GO:0000004 SGD_REF:S000069584 ND P YMR259C gene taxon:4932 20030203 SGD
+SGD S000004875 YMR262W GO:0008372 SGD_REF:S000069584 ND C YMR262W gene taxon:4932 20030203 SGD
+SGD S000004875 YMR262W GO:0005554 SGD_REF:S000069584 ND F YMR262W gene taxon:4932 20030203 SGD
+SGD S000004875 YMR262W GO:0000004 SGD_REF:S000069584 ND P YMR262W gene taxon:4932 20030203 SGD
+SGD S000004878 YMR265C GO:0008372 SGD_REF:S000069584 ND C YMR265C gene taxon:4932 20021029 SGD
+SGD S000004878 YMR265C GO:0005554 SGD_REF:S000069584 ND F YMR265C gene taxon:4932 20021029 SGD
+SGD S000004878 YMR265C GO:0000004 SGD_REF:S000069584 ND P YMR265C gene taxon:4932 20021029 SGD
+SGD S000028696 YMR272W-B GO:0008372 SGD_REF:S000069584 ND C YMR272W-B gene taxon:4932 20030730 SGD
+SGD S000028696 YMR272W-B GO:0005554 SGD_REF:S000069584 ND F YMR272W-B gene taxon:4932 20030730 SGD
+SGD S000028696 YMR272W-B GO:0000004 SGD_REF:S000069584 ND P YMR272W-B gene taxon:4932 20030730 SGD
+SGD S000004891 YMR278W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YMR278W gene taxon:4932 20031028 SGD
+SGD S000004891 YMR278W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YMR278W gene taxon:4932 20031028 SGD
+SGD S000004891 YMR278W GO:0005554 SGD_REF:S000069584 ND F YMR278W gene taxon:4932 20021126 SGD
+SGD S000004891 YMR278W GO:0000004 SGD_REF:S000069584 ND P YMR278W gene taxon:4932 20021126 SGD
+SGD S000004892 YMR279C GO:0008372 SGD_REF:S000069584 ND C YMR279C gene taxon:4932 20021120 SGD
+SGD S000004892 YMR279C GO:0005554 SGD_REF:S000069584 ND F YMR279C gene taxon:4932 20021120 SGD
+SGD S000004892 YMR279C GO:0000004 SGD_REF:S000069584 ND P YMR279C gene taxon:4932 20021120 SGD
+SGD S000004905 YMR291W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YMR291W gene taxon:4932 20031028 SGD
+SGD S000004905 YMR291W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YMR291W gene taxon:4932 20031028 SGD
+SGD S000004905 YMR291W GO:0004672 SGD_REF:S000058030|PMID:9020587 ISS F YMR291W gene taxon:4932 20030204 SGD
+SGD S000004905 YMR291W GO:0000004 SGD_REF:S000069584 ND P YMR291W gene taxon:4932 20021126 SGD
+SGD S000004907 YMR293C GO:0005739 SGD_REF:S000069459|PMID:11914276 IDA C YMR293C gene taxon:4932 20020806 SGD
+SGD S000004907 YMR293C GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YMR293C gene taxon:4932 20031028 SGD
+SGD S000004907 YMR293C GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YMR293C gene taxon:4932 20040924 SGD
+SGD S000004907 YMR293C GO:0004040 SGD_REF:S000072463|PMID:10592175 ISS F YMR293C gene taxon:4932 20030213 SGD
+SGD S000004907 YMR293C GO:0009060 SGD_REF:S000060148|PMID:10929718 IMP P YMR293C gene taxon:4932 20020806 SGD
+SGD S000004907 YMR293C GO:0009060 SGD_REF:S000060148|PMID:10929718 IEP P YMR293C gene taxon:4932 20020806 SGD
+SGD S000004910 YMR295C GO:0005933 SGD_REF:S000074185|PMID:14562095 IDA C YMR295C gene taxon:4932 20031028 SGD
+SGD S000004910 YMR295C GO:0005554 SGD_REF:S000069584 ND F YMR295C gene taxon:4932 20030203 SGD
+SGD S000004910 YMR295C GO:0000004 SGD_REF:S000069584 ND P YMR295C gene taxon:4932 20030203 SGD
+SGD S000004927 YMR310C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YMR310C gene taxon:4932 20031028 SGD
+SGD S000004927 YMR310C GO:0005554 SGD_REF:S000069584 ND F YMR310C gene taxon:4932 20030203 SGD
+SGD S000004927 YMR310C GO:0000004 SGD_REF:S000069584 ND P YMR310C gene taxon:4932 20030203 SGD
+SGD S000004932 YMR315W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YMR315W gene taxon:4932 20031028 SGD
+SGD S000004932 YMR315W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YMR315W gene taxon:4932 20031028 SGD
+SGD S000004932 YMR315W GO:0005554 SGD_REF:S000069584 ND F YMR315W gene taxon:4932 20021126 SGD
+SGD S000004932 YMR315W GO:0000004 SGD_REF:S000069584 ND P YMR315W gene taxon:4932 20021126 SGD
+SGD S000028697 YMR315W-A GO:0008372 SGD_REF:S000069584 ND C YMR315W-A gene taxon:4932 20030730 SGD
+SGD S000028697 YMR315W-A GO:0005554 SGD_REF:S000069584 ND F YMR315W-A gene taxon:4932 20030730 SGD
+SGD S000028697 YMR315W-A GO:0000004 SGD_REF:S000069584 ND P YMR315W-A gene taxon:4932 20030730 SGD
+SGD S000004936 YMR317W GO:0008372 SGD_REF:S000069584 ND C YMR317W gene taxon:4932 20030427 SGD
+SGD S000004936 YMR317W GO:0005554 SGD_REF:S000069584 ND F YMR317W gene taxon:4932 20030427 SGD
+SGD S000004936 YMR317W GO:0000004 SGD_REF:S000069584 ND P YMR317W gene taxon:4932 20030427 SGD
+SGD S000004940 YMR321C GO:0008372 SGD_REF:S000069584 ND C YMR321C gene taxon:4932 20021126 SGD
+SGD S000004940 YMR321C GO:0005554 SGD_REF:S000069584 ND F YMR321C gene taxon:4932 20021126 SGD
+SGD S000004940 YMR321C GO:0000004 SGD_REF:S000069584 ND P YMR321C gene taxon:4932 20021126 SGD
+SGD S000004955 YNL010W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YNL010W gene taxon:4932 20031028 SGD
+SGD S000004955 YNL010W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YNL010W gene taxon:4932 20031028 SGD
+SGD S000004955 YNL010W GO:0005554 SGD_REF:S000069584 ND F YNL010W gene taxon:4932 20030203 SGD
+SGD S000004955 YNL010W GO:0000004 SGD_REF:S000069584 ND P YNL010W gene taxon:4932 20030203 SGD
+SGD S000004956 YNL011C GO:0008372 SGD_REF:S000069584 ND C YNL011C gene taxon:4932 20030427 SGD
+SGD S000004956 YNL011C GO:0005554 SGD_REF:S000069584 ND F YNL011C gene taxon:4932 20030427 SGD
+SGD S000004956 YNL011C GO:0000004 SGD_REF:S000069584 ND P YNL011C gene taxon:4932 20030427 SGD
+SGD S000004963 YNL018C GO:0008372 SGD_REF:S000069584 ND C YNL018C gene taxon:4932 20030428 SGD
+SGD S000004963 YNL018C GO:0005554 SGD_REF:S000069584 ND F YNL018C gene taxon:4932 20030428 SGD
+SGD S000004963 YNL018C GO:0000004 SGD_REF:S000069584 ND P YNL018C gene taxon:4932 20030428 SGD
+SGD S000004964 YNL019C GO:0008372 SGD_REF:S000069584 ND C YNL019C gene taxon:4932 20030428 SGD
+SGD S000004964 YNL019C GO:0005554 SGD_REF:S000069584 ND F YNL019C gene taxon:4932 20030428 SGD
+SGD S000004964 YNL019C GO:0000004 SGD_REF:S000069584 ND P YNL019C gene taxon:4932 20030428 SGD
+SGD S000004967 YNL022C GO:0005634 SGD_REF:S000050617|PMID:10649453 IDA C YNL022C gene taxon:4932 20010626 SGD
+SGD S000004967 YNL022C GO:0005554 SGD_REF:S000069584 ND F YNL022C gene taxon:4932 20010626 SGD
+SGD S000004967 YNL022C GO:0000004 SGD_REF:S000069584 ND P YNL022C gene taxon:4932 20010626 SGD
+SGD S000004969 YNL024C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YNL024C gene taxon:4932 20031028 SGD
+SGD S000004969 YNL024C GO:0008757 SGD_REF:S000074033|PMID:12872006 ISS F YNL024C gene taxon:4932 20031001 SGD
+SGD S000004969 YNL024C GO:0000004 SGD_REF:S000069584 ND P YNL024C gene taxon:4932 20021126 SGD
+SGD S000028698 YNL024C-A GO:0008372 SGD_REF:S000069584 ND C YNL024C-A gene taxon:4932 20030730 SGD
+SGD S000028698 YNL024C-A GO:0005554 SGD_REF:S000069584 ND F YNL024C-A gene taxon:4932 20030730 SGD
+SGD S000028698 YNL024C-A GO:0000004 SGD_REF:S000069584 ND P YNL024C-A gene taxon:4932 20030730 SGD
+SGD S000004978 YNL033W GO:0008372 SGD_REF:S000069584 ND C YNL033W gene taxon:4932 20030428 SGD
+SGD S000004978 YNL033W GO:0005554 SGD_REF:S000069584 ND F YNL033W gene taxon:4932 20030428 SGD
+SGD S000004978 YNL033W GO:0000004 SGD_REF:S000069584 ND P YNL033W gene taxon:4932 20030428 SGD
+SGD S000004979 YNL034W GO:0008372 SGD_REF:S000069584 ND C YNL034W gene taxon:4932 20030428 SGD
+SGD S000004979 YNL034W GO:0005554 SGD_REF:S000069584 ND F YNL034W gene taxon:4932 20030428 SGD
+SGD S000004979 YNL034W GO:0000004 SGD_REF:S000069584 ND P YNL034W gene taxon:4932 20030428 SGD
+SGD S000004980 YNL035C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YNL035C gene taxon:4932 20031028 SGD
+SGD S000004980 YNL035C GO:0005554 SGD_REF:S000069584 ND F YNL035C gene taxon:4932 20030115 SGD
+SGD S000004980 YNL035C GO:0000004 SGD_REF:S000069584 ND P YNL035C gene taxon:4932 20030115 SGD
+SGD S000004985 YNL040W GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YNL040W gene taxon:4932 20020507 SGD
+SGD S000004985 YNL040W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YNL040W gene taxon:4932 20031028 SGD
+SGD S000004985 YNL040W GO:0005554 SGD_REF:S000069584 ND F YNL040W gene taxon:4932 20030429 SGD
+SGD S000004985 YNL040W GO:0000004 SGD_REF:S000069584 ND P YNL040W gene taxon:4932 20030429 SGD
+SGD S000028850 YNL042W-B GO:0008372 SGD_REF:S000069584 ND C YNL042W-B gene taxon:4932 20030730 SGD
+SGD S000028850 YNL042W-B GO:0005554 SGD_REF:S000069584 ND F YNL042W-B gene taxon:4932 20030730 SGD
+SGD S000028850 YNL042W-B GO:0000004 SGD_REF:S000069584 ND P YNL042W-B gene taxon:4932 20030730 SGD
+SGD S000004990 YNL045W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YNL045W gene taxon:4932 20031028 SGD
+SGD S000004990 YNL045W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YNL045W gene taxon:4932 20031028 SGD
+SGD S000004990 YNL045W GO:0004177 SGD_REF:S000065771|PMID:10574934 IDA F YNL045W gene taxon:4932 20030221 SGD
+SGD S000004990 YNL045W GO:0004301 SGD_REF:S000065771|PMID:10574934 IDA F YNL045W gene taxon:4932 20030221 SGD
+SGD S000004990 YNL045W GO:0004463 SGD_REF:S000062226|PMID:10341423 ISS F YNL045W gene taxon:4932 20030120 SGD
+SGD S000004990 YNL045W GO:0006629 SGD_REF:S000065771|PMID:10574934 IDA P YNL045W gene taxon:4932 20030221 SGD
+SGD S000004990 YNL045W GO:0006629 SGD_REF:S000062226|PMID:10341423 IMP P YNL045W gene taxon:4932 20021002 SGD
+SGD S000004990 YNL045W GO:0030163 SGD_REF:S000065771|PMID:10574934 IDA P YNL045W gene taxon:4932 20030221 SGD
+SGD S000004991 YNL046W GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YNL046W gene taxon:4932 20031028 SGD
+SGD S000004991 YNL046W GO:0005554 SGD_REF:S000069584 ND F YNL046W gene taxon:4932 20030427 SGD
+SGD S000004991 YNL046W GO:0000004 SGD_REF:S000069584 ND P YNL046W gene taxon:4932 20030427 SGD
+SGD S000004995 YNL050C GO:0008372 SGD_REF:S000069584 ND C YNL050C gene taxon:4932 20030422 SGD
+SGD S000004995 YNL050C GO:0005554 SGD_REF:S000069584 ND F YNL050C gene taxon:4932 20030422 SGD
+SGD S000004995 YNL050C GO:0000004 SGD_REF:S000069584 ND P YNL050C gene taxon:4932 20030422 SGD
+SGD S000007384 YNL054W-A GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YNL054W-A gene taxon:4932 20030811 SGD
+SGD S000007384 YNL054W-A GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YNL054W-A gene taxon:4932 20030811 SGD
+SGD S000007384 YNL054W-A GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YNL054W-A gene taxon:4932 20030811 SGD
+SGD S000007384 YNL054W-A GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YNL054W-A gene taxon:4932 20030811 SGD
+SGD S000007385 YNL054W-B GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YNL054W-B gene taxon:4932 20030811 SGD
+SGD S000007385 YNL054W-B GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YNL054W-B gene taxon:4932 20030811 SGD
+SGD S000007385 YNL054W-B GO:0003887 SGD_REF:S000072465|PMID:9582191 ISS F YNL054W-B gene taxon:4932 20030811 SGD
+SGD S000007385 YNL054W-B GO:0003964 SGD_REF:S000072465|PMID:9582191 ISS F YNL054W-B gene taxon:4932 20030811 SGD
+SGD S000007385 YNL054W-B GO:0004540 SGD_REF:S000072465|PMID:9582191 ISS F YNL054W-B gene taxon:4932 20030811 SGD
+SGD S000007385 YNL054W-B GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YNL054W-B gene taxon:4932 20030811 SGD
+SGD S000007385 YNL054W-B GO:0008233 SGD_REF:S000072465|PMID:9582191 ISS F YNL054W-B gene taxon:4932 20030811 SGD
+SGD S000007385 YNL054W-B GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YNL054W-B gene taxon:4932 20030811 SGD
+SGD S000005003 YNL058C GO:0000324 SGD_REF:S000074185|PMID:14562095 IDA C YNL058C gene taxon:4932 20031028 SGD
+SGD S000005003 YNL058C GO:0005554 SGD_REF:S000069584 ND F YNL058C gene taxon:4932 20030427 SGD
+SGD S000005003 YNL058C GO:0000004 SGD_REF:S000069584 ND P YNL058C gene taxon:4932 20030427 SGD
+SGD S000028810 YNL067W-B GO:0008372 SGD_REF:S000069584 ND C YNL067W-B|YNL067W-A gene taxon:4932 20030730 SGD
+SGD S000028810 YNL067W-B GO:0005554 SGD_REF:S000069584 ND F YNL067W-B|YNL067W-A gene taxon:4932 20030730 SGD
+SGD S000028810 YNL067W-B GO:0000004 SGD_REF:S000069584 ND P YNL067W-B|YNL067W-A gene taxon:4932 20030730 SGD
+SGD S000005024 YNL080C GO:0016020 SGD_REF:S000050617|PMID:10649453 ISS C YNL080C gene taxon:4932 20030130 SGD
+SGD S000005024 YNL080C GO:0005554 SGD_REF:S000069584 ND F YNL080C gene taxon:4932 20010626 SGD
+SGD S000005024 YNL080C GO:0000004 SGD_REF:S000069584 ND P YNL080C gene taxon:4932 20010626 SGD
+SGD S000005030 YNL086W GO:0005768 SGD_REF:S000074185|PMID:14562095 IDA C YNL086W gene taxon:4932 20031028 SGD
+SGD S000005030 YNL086W GO:0005554 SGD_REF:S000069584 ND F YNL086W gene taxon:4932 20030427 SGD
+SGD S000005030 YNL086W GO:0000004 SGD_REF:S000069584 ND P YNL086W gene taxon:4932 20030427 SGD
+SGD S000005036 YNL092W GO:0008372 SGD_REF:S000069584 ND C YNL092W gene taxon:4932 20030203 SGD
+SGD S000005036 YNL092W GO:0008757 SGD_REF:S000074033|PMID:12872006 ISS F YNL092W gene taxon:4932 20031001 SGD
+SGD S000005036 YNL092W GO:0000004 SGD_REF:S000069584 ND P YNL092W gene taxon:4932 20030203 SGD
+SGD S000005039 YNL095C GO:0016021 SGD_REF:S000042245|PMID:8771715 ISS C YNL095C gene taxon:4932 20030213 SGD
+SGD S000005039 YNL095C GO:0005554 SGD_REF:S000069584 ND F YNL095C gene taxon:4932 20030203 SGD
+SGD S000005039 YNL095C GO:0000004 SGD_REF:S000069584 ND P YNL095C gene taxon:4932 20030203 SGD
+SGD S000028699 YNL097C-B GO:0008372 SGD_REF:S000069584 ND C YNL097C-B|YNL097C-A gene taxon:4932 20030730 SGD
+SGD S000028699 YNL097C-B GO:0005554 SGD_REF:S000069584 ND F YNL097C-B|YNL097C-A gene taxon:4932 20030730 SGD
+SGD S000028699 YNL097C-B GO:0000004 SGD_REF:S000069584 ND P YNL097C-B|YNL097C-A gene taxon:4932 20030730 SGD
+SGD S000005044 YNL100W GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YNL100W gene taxon:4932 20031028 SGD
+SGD S000005044 YNL100W GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YNL100W gene taxon:4932 20040924 SGD
+SGD S000005044 YNL100W GO:0005554 SGD_REF:S000069584 ND F YNL100W gene taxon:4932 20030128 SGD
+SGD S000005044 YNL100W GO:0000004 SGD_REF:S000069584 ND P YNL100W gene taxon:4932 20030128 SGD
+SGD S000005052 YNL108C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YNL108C|HUF gene taxon:4932 20031028 SGD
+SGD S000005052 YNL108C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YNL108C|HUF gene taxon:4932 20031028 SGD
+SGD S000005052 YNL108C GO:0005554 SGD_REF:S000069584 ND F YNL108C|HUF gene taxon:4932 20021127 SGD
+SGD S000005052 YNL108C GO:0008152 SGD_REF:S000044721|PMID:10824121 IGI P YNL108C|HUF gene taxon:4932 20021127 SGD
+SGD S000005052 YNL108C GO:0008152 SGD_REF:S000044721|PMID:10824121 IMP P YNL108C|HUF gene taxon:4932 20021127 SGD
+SGD S000005059 YNL115C GO:0000324 SGD_REF:S000074185|PMID:14562095 IDA C YNL115C gene taxon:4932 20031028 SGD
+SGD S000005059 YNL115C GO:0005554 SGD_REF:S000069584 ND F YNL115C gene taxon:4932 20030428 SGD
+SGD S000005059 YNL115C GO:0000004 SGD_REF:S000069584 ND P YNL115C gene taxon:4932 20030428 SGD
+SGD S000005066 YNL122C GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YNL122C gene taxon:4932 20031028 SGD
+SGD S000005066 YNL122C GO:0005554 SGD_REF:S000069584 ND F YNL122C gene taxon:4932 20030203 SGD
+SGD S000005066 YNL122C GO:0000004 SGD_REF:S000069584 ND P YNL122C gene taxon:4932 20030203 SGD
+SGD S000028579 YNL130C-A GO:0008372 SGD_REF:S000069584 ND C YNL130C-A gene taxon:4932 20030730 SGD
+SGD S000028579 YNL130C-A GO:0005554 SGD_REF:S000069584 ND F YNL130C-A gene taxon:4932 20030730 SGD
+SGD S000028579 YNL130C-A GO:0000004 SGD_REF:S000069584 ND P YNL130C-A gene taxon:4932 20030730 SGD
+SGD S000005078 YNL134C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YNL134C gene taxon:4932 20031028 SGD
+SGD S000005078 YNL134C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YNL134C gene taxon:4932 20031028 SGD
+SGD S000005078 YNL134C GO:0008106 SGD_REF:S000046236|PMID:10347154 NAS F YNL134C gene taxon:4932 20030120 SGD
+SGD S000005078 YNL134C GO:0000004 SGD_REF:S000069584 ND P YNL134C gene taxon:4932 20030120 SGD
+SGD S000005088 YNL144C GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YNL144C gene taxon:4932 20040813 SGD
+SGD S000005088 YNL144C GO:0005554 SGD_REF:S000069584 ND F YNL144C gene taxon:4932 20030203 SGD
+SGD S000005088 YNL144C GO:0000004 SGD_REF:S000069584 ND P YNL144C gene taxon:4932 20030203 SGD
+SGD S000028851 YNL146C-A GO:0008372 SGD_REF:S000069584 ND C YNL146C-A gene taxon:4932 20030730 SGD
+SGD S000028851 YNL146C-A GO:0005554 SGD_REF:S000069584 ND F YNL146C-A gene taxon:4932 20030730 SGD
+SGD S000028851 YNL146C-A GO:0000004 SGD_REF:S000069584 ND P YNL146C-A gene taxon:4932 20030730 SGD
+SGD S000005090 YNL146W GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YNL146W gene taxon:4932 20031028 SGD
+SGD S000005090 YNL146W GO:0005554 SGD_REF:S000069584 ND F YNL146W gene taxon:4932 20030203 SGD
+SGD S000005090 YNL146W GO:0000004 SGD_REF:S000069584 ND P YNL146W gene taxon:4932 20030203 SGD
+SGD S000005096 YNL152W GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YNL152W gene taxon:4932 20020507 SGD
+SGD S000005096 YNL152W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YNL152W gene taxon:4932 20031028 SGD
+SGD S000005096 YNL152W GO:0005543 SGD_REF:S000075214|PMID:14690591 ISS F YNL152W gene taxon:4932 20040105 SGD
+SGD S000005096 YNL152W GO:0000004 SGD_REF:S000069584 ND P YNL152W gene taxon:4932 20030203 SGD
+SGD S000005099 YNL155W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YNL155W gene taxon:4932 20031028 SGD
+SGD S000005099 YNL155W GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YNL155W gene taxon:4932 20020507 SGD
+SGD S000005099 YNL155W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YNL155W gene taxon:4932 20031028 SGD
+SGD S000005099 YNL155W GO:0005554 SGD_REF:S000069584 ND F YNL155W gene taxon:4932 20030429 SGD
+SGD S000005099 YNL155W GO:0000004 SGD_REF:S000069584 ND P YNL155W gene taxon:4932 20030429 SGD
+SGD S000007624 YNL162W-A GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YNL162W-A gene taxon:4932 20031028 SGD
+SGD S000007624 YNL162W-A GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YNL162W-A gene taxon:4932 20031028 SGD
+SGD S000007624 YNL162W-A GO:0005554 SGD_REF:S000069584 ND F YNL162W-A gene taxon:4932 20010226 SGD
+SGD S000007624 YNL162W-A GO:0000004 SGD_REF:S000069584 ND P YNL162W-A gene taxon:4932 20010226 SGD
+SGD S000005109 YNL165W GO:0008372 SGD_REF:S000069584 ND C YNL165W gene taxon:4932 20030203 SGD
+SGD S000005109 YNL165W GO:0005554 SGD_REF:S000069584 ND F YNL165W gene taxon:4932 20030203 SGD
+SGD S000005109 YNL165W GO:0000004 SGD_REF:S000069584 ND P YNL165W gene taxon:4932 20030203 SGD
+SGD S000005120 YNL176C GO:0000324 SGD_REF:S000074185|PMID:14562095 IDA C YNL176C gene taxon:4932 20031028 SGD
+SGD S000005120 YNL176C GO:0005554 SGD_REF:S000069584 ND F YNL176C gene taxon:4932 20030203 SGD
+SGD S000005120 YNL176C GO:0000004 SGD_REF:S000069584 ND P YNL176C gene taxon:4932 20030203 SGD
+SGD S000005125 YNL181W GO:0005635 SGD_REF:S000075214|PMID:14690591 IDA C YNL181W gene taxon:4932 20040105 SGD
+SGD S000005125 YNL181W GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YNL181W gene taxon:4932 20031028 SGD
+SGD S000005125 YNL181W GO:0005783 SGD_REF:S000075214|PMID:14690591 IDA C YNL181W gene taxon:4932 20040105 SGD
+SGD S000005125 YNL181W GO:0016491 SGD_REF:S000075214|PMID:14690591 ISS F YNL181W gene taxon:4932 20040105 SGD
+SGD S000005125 YNL181W GO:0016726 SGD_REF:S000061895|PMID:9811845 ISS F YNL181W gene taxon:4932 20030214 SGD
+SGD S000005125 YNL181W GO:0000004 SGD_REF:S000069584 ND P YNL181W gene taxon:4932 20030214 SGD
+SGD S000005131 YNL187W GO:0005634 SGD_REF:S000075602|PMID:15020406 IMP C YNL187W gene taxon:4932 20040322 SGD
+SGD S000005131 YNL187W GO:0005634 SGD_REF:S000075602|PMID:15020406 ISS C YNL187W gene taxon:4932 20040322 SGD
+SGD S000005131 YNL187W GO:0005554 SGD_REF:S000069584 ND F YNL187W gene taxon:4932 20021126 SGD
+SGD S000005131 YNL187W GO:0006810 SGD_REF:S000075602|PMID:15020406 IMP P YNL187W gene taxon:4932 20040322 SGD
+SGD S000005131 YNL187W GO:0006810 SGD_REF:S000075602|PMID:15020406 ISS P YNL187W gene taxon:4932 20040322 SGD
+SGD S000005134 YNL190W GO:0009277 SGD_REF:S000040179|PMID:10383953 IDA C YNL190W gene taxon:4932 20020617 SGD
+SGD S000005134 YNL190W GO:0005554 SGD_REF:S000069584 ND F YNL190W gene taxon:4932 20030210 SGD
+SGD S000005134 YNL190W GO:0009269 SGD_REF:S000063137|PMID:10681550 IEP P YNL190W gene taxon:4932 20030210 SGD
+SGD S000005135 YNL191W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YNL191W gene taxon:4932 20031028 SGD
+SGD S000005135 YNL191W GO:0005554 SGD_REF:S000069584 ND F YNL191W gene taxon:4932 20030427 SGD
+SGD S000005135 YNL191W GO:0000004 SGD_REF:S000069584 ND P YNL191W gene taxon:4932 20030427 SGD
+SGD S000005137 YNL193W GO:0008372 SGD_REF:S000069584 ND C YNL193W gene taxon:4932 20021126 SGD
+SGD S000005137 YNL193W GO:0005554 SGD_REF:S000069584 ND F YNL193W gene taxon:4932 20021126 SGD
+SGD S000005137 YNL193W GO:0000004 SGD_REF:S000069584 ND P YNL193W gene taxon:4932 20021126 SGD
+SGD S000005138 YNL194C GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C integral membrane protein YNL194C gene taxon:4932 20020507 SGD
+SGD S000005138 YNL194C GO:0005783 SGD_REF:S000069459|PMID:11914276 IDA C integral membrane protein YNL194C gene taxon:4932 20020507 SGD
+SGD S000005138 YNL194C GO:0005938 SGD_REF:S000069238|PMID:11784867 IDA C integral membrane protein YNL194C gene taxon:4932 20020612 SGD
+SGD S000005138 YNL194C GO:0016021 SGD_REF:S000069238|PMID:11784867 ISS C integral membrane protein YNL194C gene taxon:4932 20020612 SGD
+SGD S000005138 YNL194C GO:0016021 SGD_REF:S000048799|PMID:9219339 ISS C integral membrane protein YNL194C gene taxon:4932 20020612 SGD
+SGD S000005138 YNL194C GO:0005554 SGD_REF:S000069584 ND F integral membrane protein YNL194C gene taxon:4932 20020612 SGD
+SGD S000005138 YNL194C GO:0030437 SGD_REF:S000069238|PMID:11784867 IGI P integral membrane protein YNL194C gene taxon:4932 20060306 SGD
+SGD S000005138 YNL194C GO:0030437 SGD_REF:S000069238|PMID:11784867 IMP P integral membrane protein YNL194C gene taxon:4932 20060306 SGD
+SGD S000005139 YNL195C GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YNL195C gene taxon:4932 20040813 SGD
+SGD S000005139 YNL195C GO:0005554 SGD_REF:S000069584 ND F YNL195C gene taxon:4932 20030203 SGD
+SGD S000005139 YNL195C GO:0000004 SGD_REF:S000069584 ND P YNL195C gene taxon:4932 20030203 SGD
+SGD S000005140 YNL196C GO:0008372 SGD_REF:S000069584 ND C YNL196C gene taxon:4932 20021029 SGD
+SGD S000005140 YNL196C GO:0005554 SGD_REF:S000069584 ND F YNL196C gene taxon:4932 20021029 SGD
+SGD S000005140 YNL196C GO:0000004 SGD_REF:S000069584 ND P YNL196C gene taxon:4932 20021029 SGD
+SGD S000005144 YNL200C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YNL200C gene taxon:4932 20031028 SGD
+SGD S000005144 YNL200C GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YNL200C gene taxon:4932 20040928 SGD
+SGD S000005144 YNL200C GO:0005554 SGD_REF:S000069584 ND F YNL200C gene taxon:4932 20030410 SGD
+SGD S000005144 YNL200C GO:0000004 SGD_REF:S000069584 ND P YNL200C gene taxon:4932 20030410 SGD
+SGD S000005152 YNL208W GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YNL208W gene taxon:4932 20040813 SGD
+SGD S000005152 YNL208W GO:0005554 SGD_REF:S000069584 ND F YNL208W gene taxon:4932 20030120 SGD
+SGD S000005152 YNL208W GO:0000004 SGD_REF:S000069584 ND P YNL208W gene taxon:4932 20030120 SGD
+SGD S000005155 YNL211C GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YNL211C gene taxon:4932 20031028 SGD
+SGD S000005155 YNL211C GO:0005554 SGD_REF:S000069584 ND F YNL211C gene taxon:4932 20030428 SGD
+SGD S000005155 YNL211C GO:0000004 SGD_REF:S000069584 ND P YNL211C gene taxon:4932 20030428 SGD
+SGD S000005157 YNL213C GO:0005739 SGD_REF:S000048525|PMID:10029995 ISS C YNL213C gene taxon:4932 20030120 SGD
+SGD S000005157 YNL213C GO:0005554 SGD_REF:S000069584 ND F YNL213C gene taxon:4932 20030120 SGD
+SGD S000005157 YNL213C GO:0007005 SGD_REF:S000048525|PMID:10029995 IMP P YNL213C gene taxon:4932 20030120 SGD
+SGD S000005161 YNL217W GO:0000324 SGD_REF:S000074185|PMID:14562095 IDA C YNL217W gene taxon:4932 20031028 SGD
+SGD S000005161 YNL217W GO:0016791 SGD_REF:S000061788|PMID:10618406 ISS F YNL217W gene taxon:4932 20030423 SGD
+SGD S000005161 YNL217W GO:0000004 SGD_REF:S000069584 ND P YNL217W gene taxon:4932 20030423 SGD
+SGD S000005168 YNL224C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YNL224C gene taxon:4932 20031028 SGD
+SGD S000005168 YNL224C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YNL224C gene taxon:4932 20031028 SGD
+SGD S000005168 YNL224C GO:0005554 SGD_REF:S000069584 ND F YNL224C gene taxon:4932 20030203 SGD
+SGD S000005168 YNL224C GO:0000004 SGD_REF:S000069584 ND P YNL224C gene taxon:4932 20030203 SGD
+SGD S000005178 YNL234W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YNL234W gene taxon:4932 20031028 SGD
+SGD S000005178 YNL234W GO:0020037 SGD_REF:S000056349|PMID:9988749 IPI F YNL234W gene taxon:4932 20021126 SGD
+SGD S000005178 YNL234W GO:0020037 SGD_REF:S000056349|PMID:9988749 ISS F YNL234W gene taxon:4932 20021126 SGD
+SGD S000005178 YNL234W GO:0006950 SGD_REF:S000056349|PMID:9988749 IEP P YNL234W gene taxon:4932 20021126 SGD
+SGD S000005191 YNL247W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YNL247W gene taxon:4932 20031028 SGD
+SGD S000005191 YNL247W GO:0004817 SGD_REF:S000056336|PMID:9523015 IDA F YNL247W gene taxon:4932 20030120 SGD
+SGD S000005191 YNL247W GO:0006423 SGD_REF:S000056336|PMID:9523015 IDA P YNL247W gene taxon:4932 20030120 SGD
+SGD S000005191 YNL247W GO:0006534 SGD_REF:S000071379|PMID:11752249 NAS P YNL247W gene taxon:4932 20021002 SGD
+SGD S000005198 YNL254C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YNL254C gene taxon:4932 20031028 SGD
+SGD S000005198 YNL254C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YNL254C gene taxon:4932 20031028 SGD
+SGD S000005198 YNL254C GO:0005554 SGD_REF:S000069584 ND F YNL254C gene taxon:4932 20030423 SGD
+SGD S000005198 YNL254C GO:0000004 SGD_REF:S000069584 ND P YNL254C gene taxon:4932 20030423 SGD
+SGD S000005204 YNL260C GO:0005634 SGD_REF:S000075214|PMID:14690591 IDA C YNL260C gene taxon:4932 20040105 SGD
+SGD S000005204 YNL260C GO:0005737 SGD_REF:S000075214|PMID:14690591 IDA C YNL260C gene taxon:4932 20040105 SGD
+SGD S000005204 YNL260C GO:0005554 SGD_REF:S000069584 ND F YNL260C gene taxon:4932 20030423 SGD
+SGD S000005204 YNL260C GO:0000004 SGD_REF:S000069584 ND P YNL260C gene taxon:4932 20030423 SGD
+SGD S000005218 YNL274C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YNL274C gene taxon:4932 20031028 SGD
+SGD S000005218 YNL274C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YNL274C gene taxon:4932 20031028 SGD
+SGD S000005218 YNL274C GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YNL274C gene taxon:4932 20040928 SGD
+SGD S000005218 YNL274C GO:0016616 SGD_REF:S000066173|PMID:9341119 ISS F YNL274C gene taxon:4932 20030401 SGD
+SGD S000005218 YNL274C GO:0008152 SGD_REF:S000066173|PMID:9341119 ISS P YNL274C gene taxon:4932 20030401 SGD
+SGD S000028852 YNL277W-A GO:0008372 SGD_REF:S000069584 ND C YNL277W-A gene taxon:4932 20030730 SGD
+SGD S000028852 YNL277W-A GO:0005554 SGD_REF:S000069584 ND F YNL277W-A gene taxon:4932 20030730 SGD
+SGD S000028852 YNL277W-A GO:0000004 SGD_REF:S000069584 ND P YNL277W-A gene taxon:4932 20030730 SGD
+SGD S000007386 YNL284C-A GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YNL284C-A gene taxon:4932 20030811 SGD
+SGD S000007386 YNL284C-A GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YNL284C-A gene taxon:4932 20030811 SGD
+SGD S000007386 YNL284C-A GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YNL284C-A gene taxon:4932 20030811 SGD
+SGD S000007386 YNL284C-A GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YNL284C-A gene taxon:4932 20030811 SGD
+SGD S000007387 YNL284C-B GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YNL284C-B gene taxon:4932 20030811 SGD
+SGD S000007387 YNL284C-B GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YNL284C-B gene taxon:4932 20030811 SGD
+SGD S000007387 YNL284C-B GO:0003887 SGD_REF:S000072465|PMID:9582191 ISS F YNL284C-B gene taxon:4932 20030811 SGD
+SGD S000007387 YNL284C-B GO:0003964 SGD_REF:S000072465|PMID:9582191 ISS F YNL284C-B gene taxon:4932 20030811 SGD
+SGD S000007387 YNL284C-B GO:0004540 SGD_REF:S000072465|PMID:9582191 ISS F YNL284C-B gene taxon:4932 20030811 SGD
+SGD S000007387 YNL284C-B GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YNL284C-B gene taxon:4932 20030811 SGD
+SGD S000007387 YNL284C-B GO:0008233 SGD_REF:S000072465|PMID:9582191 ISS F YNL284C-B gene taxon:4932 20030811 SGD
+SGD S000007387 YNL284C-B GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YNL284C-B gene taxon:4932 20030811 SGD
+SGD S000005239 YNL295W GO:0008372 SGD_REF:S000069584 ND C YNL295W gene taxon:4932 20030203 SGD
+SGD S000005239 YNL295W GO:0005554 SGD_REF:S000069584 ND F YNL295W gene taxon:4932 20030203 SGD
+SGD S000005239 YNL295W GO:0000004 SGD_REF:S000069584 ND P YNL295W gene taxon:4932 20030203 SGD
+SGD S000005244 YNL300W GO:0009277 SGD_REF:S000040179|PMID:10383953 IDA C YNL300W|TOS6 gene taxon:4932 20020617 SGD
+SGD S000005244 YNL300W GO:0005554 SGD_REF:S000069584 ND F YNL300W|TOS6 gene taxon:4932 20030429 SGD
+SGD S000005244 YNL300W GO:0000004 SGD_REF:S000069584 ND P YNL300W|TOS6 gene taxon:4932 20030429 SGD
+SGD S000005249 YNL305C GO:0000324 SGD_REF:S000074185|PMID:14562095 IDA C YNL305C gene taxon:4932 20031028 SGD
+SGD S000005249 YNL305C GO:0005554 SGD_REF:S000069584 ND F YNL305C gene taxon:4932 20021126 SGD
+SGD S000005249 YNL305C GO:0000004 SGD_REF:S000069584 ND P YNL305C gene taxon:4932 20021126 SGD
+SGD S000005257 YNL313C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YNL313C gene taxon:4932 20031028 SGD
+SGD S000005257 YNL313C GO:0005634 SGD_REF:S000075214|PMID:14690591 IDA C YNL313C gene taxon:4932 20031231 SGD
+SGD S000005257 YNL313C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YNL313C gene taxon:4932 20031028 SGD
+SGD S000005257 YNL313C GO:0005737 SGD_REF:S000075214|PMID:14690591 IDA C YNL313C gene taxon:4932 20031231 SGD
+SGD S000005257 YNL313C GO:0005554 SGD_REF:S000069584 ND F YNL313C gene taxon:4932 20030203 SGD
+SGD S000005257 YNL313C GO:0000741 SGD_REF:S000075214|PMID:14690591 IPI SGD:S000003571 P YNL313C gene taxon:4932 20031231 SGD
+SGD S000005264 YNL320W GO:0008372 SGD_REF:S000069584 ND C YNL320W gene taxon:4932 20030203 SGD
+SGD S000005264 YNL320W GO:0005554 SGD_REF:S000069584 ND F YNL320W gene taxon:4932 20030203 SGD
+SGD S000005264 YNL320W GO:0000004 SGD_REF:S000069584 ND P YNL320W gene taxon:4932 20030203 SGD
+SGD S000005265 YNL321W GO:0008372 SGD_REF:S000069584 ND C YNL321W gene taxon:4932 20030203 SGD
+SGD S000005265 YNL321W GO:0005554 SGD_REF:S000069584 ND F YNL321W gene taxon:4932 20030203 SGD
+SGD S000005265 YNL321W GO:0000004 SGD_REF:S000069584 ND P YNL321W gene taxon:4932 20030203 SGD
+SGD S000005287 YNR004W GO:0005730 SGD_REF:S000074185|PMID:14562095 IDA C YNR004W gene taxon:4932 20031028 SGD
+SGD S000005287 YNR004W GO:0005554 SGD_REF:S000069584 ND F YNR004W gene taxon:4932 20030410 SGD
+SGD S000005287 YNR004W GO:0000004 SGD_REF:S000069584 ND P YNR004W gene taxon:4932 20030410 SGD
+SGD S000005297 YNR014W GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YNR014W gene taxon:4932 20020507 SGD
+SGD S000005297 YNR014W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YNR014W gene taxon:4932 20031028 SGD
+SGD S000005297 YNR014W GO:0005554 SGD_REF:S000069584 ND F YNR014W gene taxon:4932 20030203 SGD
+SGD S000005297 YNR014W GO:0000004 SGD_REF:S000069584 ND P YNR014W gene taxon:4932 20030203 SGD
+SGD S000005301 YNR018W GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YNR018W gene taxon:4932 20031028 SGD
+SGD S000005301 YNR018W GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YNR018W gene taxon:4932 20040924 SGD
+SGD S000005301 YNR018W GO:0005554 SGD_REF:S000069584 ND F YNR018W gene taxon:4932 20021126 SGD
+SGD S000005301 YNR018W GO:0000004 SGD_REF:S000069584 ND P YNR018W gene taxon:4932 20021126 SGD
+SGD S000005303 YNR020C GO:0008372 SGD_REF:S000069584 ND C YNR020C gene taxon:4932 20021126 SGD
+SGD S000005303 YNR020C GO:0005554 SGD_REF:S000069584 ND F YNR020C gene taxon:4932 20021126 SGD
+SGD S000005303 YNR020C GO:0000004 SGD_REF:S000069584 ND P YNR020C gene taxon:4932 20021126 SGD
+SGD S000005304 YNR021W GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YNR021W gene taxon:4932 20031028 SGD
+SGD S000005304 YNR021W GO:0005554 SGD_REF:S000069584 ND F YNR021W gene taxon:4932 20030203 SGD
+SGD S000005304 YNR021W GO:0000004 SGD_REF:S000069584 ND P YNR021W gene taxon:4932 20030203 SGD
+SGD S000005307 YNR024W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YNR024W gene taxon:4932 20031028 SGD
+SGD S000005307 YNR024W GO:0005554 SGD_REF:S000069584 ND F YNR024W gene taxon:4932 20021126 SGD
+SGD S000005307 YNR024W GO:0000004 SGD_REF:S000069584 ND P YNR024W gene taxon:4932 20021126 SGD
+SGD S000005312 YNR029C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YNR029C gene taxon:4932 20031028 SGD
+SGD S000005312 YNR029C GO:0005554 SGD_REF:S000069584 ND F YNR029C gene taxon:4932 20021126 SGD
+SGD S000005312 YNR029C GO:0000004 SGD_REF:S000069584 ND P YNR029C gene taxon:4932 20021126 SGD
+SGD S000007525 YNR034W-A GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YNR034W-A gene taxon:4932 20031028 SGD
+SGD S000007525 YNR034W-A GO:0005554 SGD_REF:S000069584 ND F YNR034W-A gene taxon:4932 20030203 SGD
+SGD S000007525 YNR034W-A GO:0000004 SGD_REF:S000069584 ND P YNR034W-A gene taxon:4932 20030203 SGD
+SGD S000005319 YNR036C GO:0005763 SGD_REF:S000071753|PMID:12392552 ISS C YNR036C gene taxon:4932 20040203 SGD
+SGD S000005319 YNR036C GO:0003735 SGD_REF:S000071753|PMID:12392552 ISS F YNR036C gene taxon:4932 20040203 SGD
+SGD S000005319 YNR036C GO:0043037 SGD_REF:S000071753|PMID:12392552 ISS P YNR036C gene taxon:4932 20040203 SGD
+SGD S000005323 YNR040W GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YNR040W gene taxon:4932 20031028 SGD
+SGD S000005323 YNR040W GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YNR040W gene taxon:4932 20040924 SGD
+SGD S000005323 YNR040W GO:0005554 SGD_REF:S000069584 ND F YNR040W gene taxon:4932 20021126 SGD
+SGD S000005323 YNR040W GO:0000004 SGD_REF:S000069584 ND P YNR040W gene taxon:4932 20021126 SGD
+SGD S000005330 YNR047W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YNR047W gene taxon:4932 20031028 SGD
+SGD S000005330 YNR047W GO:0004672 SGD_REF:S000058030|PMID:9020587 ISS F YNR047W gene taxon:4932 20030203 SGD
+SGD S000005330 YNR047W GO:0019236 SGD_REF:S000061243|PMID:11337509 IMP P YNR047W gene taxon:4932 20030203 SGD
+SGD S000005331 YNR048W GO:0016021 SGD_REF:S000081887|PMID:15919184 ISS C YNR048W|CRF1 gene taxon:4932 20051212 SGD
+SGD S000005331 YNR048W contributes_to GO:0004012 SGD_REF:S000081887|PMID:15919184 ISS SGD:S000000690|SGD:S000005267 F YNR048W|CRF1 gene taxon:4932 20051212 SGD
+SGD S000005331 YNR048W GO:0042493 SGD_REF:S000074019|PMID:12842877 IMP P YNR048W|CRF1 gene taxon:4932 20051212 SGD
+SGD S000005331 YNR048W GO:0042493 SGD_REF:S000074019|PMID:12842877 IGI SGD:S000005267 P YNR048W|CRF1 gene taxon:4932 20051212 SGD
+SGD S000005344 YNR061C GO:0000324 SGD_REF:S000074185|PMID:14562095 IDA C YNR061C gene taxon:4932 20031028 SGD
+SGD S000005344 YNR061C GO:0005554 SGD_REF:S000069584 ND F YNR061C gene taxon:4932 20021126 SGD
+SGD S000005344 YNR061C GO:0000004 SGD_REF:S000069584 ND P YNR061C gene taxon:4932 20021126 SGD
+SGD S000005345 YNR062C GO:0016021 SGD_REF:S000072825|PMID:12524434 ISS C YNR062C gene taxon:4932 20030409 SGD
+SGD S000005345 YNR062C GO:0005554 SGD_REF:S000069584 ND F YNR062C gene taxon:4932 20021126 SGD
+SGD S000005345 YNR062C GO:0000004 SGD_REF:S000069584 ND P YNR062C gene taxon:4932 20021126 SGD
+SGD S000005346 YNR063W GO:0008372 SGD_REF:S000069584 ND C YNR063W gene taxon:4932 20030203 SGD
+SGD S000005346 YNR063W GO:0005554 SGD_REF:S000069584 ND F YNR063W gene taxon:4932 20030203 SGD
+SGD S000005346 YNR063W GO:0000004 SGD_REF:S000069584 ND P YNR063W gene taxon:4932 20030203 SGD
+SGD S000005347 YNR064C GO:0005625 SGD_REF:S000081135|PMID:15769598 IDA C YNR064C gene taxon:4932 20050525 SGD
+SGD S000005347 YNR064C GO:0004301 SGD_REF:S000081135|PMID:15769598 IDA F YNR064C gene taxon:4932 20050525 SGD
+SGD S000005347 YNR064C GO:0004301 SGD_REF:S000081135|PMID:15769598 ISS F YNR064C gene taxon:4932 20050525 SGD
+SGD S000005347 YNR064C GO:0009636 SGD_REF:S000081135|PMID:15769598 ISS P YNR064C gene taxon:4932 20050525 SGD
+SGD S000005349 YNR066C GO:0005624 SGD_REF:S000075303|PMID:11935221 IDA C YNR066C gene taxon:4932 20040114 SGD
+SGD S000005349 YNR066C GO:0005554 SGD_REF:S000069584 ND F YNR066C gene taxon:4932 20021126 SGD
+SGD S000005349 YNR066C GO:0000004 SGD_REF:S000069584 ND P YNR066C gene taxon:4932 20021126 SGD
+SGD S000005351 YNR068C GO:0008372 SGD_REF:S000069584 ND C YNR068C gene taxon:4932 20021126 SGD
+SGD S000005351 YNR068C GO:0005554 SGD_REF:S000069584 ND F YNR068C gene taxon:4932 20021126 SGD
+SGD S000005351 YNR068C GO:0000004 SGD_REF:S000069584 ND P YNR068C gene taxon:4932 20021126 SGD
+SGD S000005353 YNR070W GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YNR070W|PDR18 gene taxon:4932 20040928 SGD
+SGD S000005353 YNR070W GO:0016020 SGD_REF:S000044365|PMID:10581358 ISS C YNR070W|PDR18 gene taxon:4932 20030424 SGD
+SGD S000005353 YNR070W GO:0042626 SGD_REF:S000044365|PMID:10581358 ISS F YNR070W|PDR18 gene taxon:4932 20030424 SGD
+SGD S000005353 YNR070W GO:0006810 SGD_REF:S000044365|PMID:10581358 ISS P YNR070W|PDR18 gene taxon:4932 20030424 SGD
+SGD S000005354 YNR071C GO:0008372 SGD_REF:S000069584 ND C YNR071C gene taxon:4932 20021126 SGD
+SGD S000005354 YNR071C GO:0005554 SGD_REF:S000069584 ND F YNR071C gene taxon:4932 20021126 SGD
+SGD S000005354 YNR071C GO:0000004 SGD_REF:S000069584 ND P YNR071C gene taxon:4932 20021126 SGD
+SGD S000005356 YNR073C GO:0008372 SGD_REF:S000069584 ND C YNR073C gene taxon:4932 20030203 SGD
+SGD S000005356 YNR073C GO:0046029 SGD_REF:S000050135|PMID:8904342 ISS F YNR073C gene taxon:4932 20030214 SGD
+SGD S000005356 YNR073C GO:0000004 SGD_REF:S000069584 ND P YNR073C gene taxon:4932 20030203 SGD
+SGD S000028706 YNR075C-A GO:0008372 SGD_REF:S000069584 ND C YNR075C-A gene taxon:4932 20030730 SGD
+SGD S000028706 YNR075C-A GO:0005554 SGD_REF:S000069584 ND F YNR075C-A gene taxon:4932 20030730 SGD
+SGD S000028706 YNR075C-A GO:0000004 SGD_REF:S000069584 ND P YNR075C-A gene taxon:4932 20030730 SGD
+SGD S000005367 YOL007C GO:0000324 SGD_REF:S000074185|PMID:14562095 IDA C YOL007C gene taxon:4932 20031028 SGD
+SGD S000005367 YOL007C GO:0000324 SGD_REF:S000077144|PMID:15282802 IDA C YOL007C gene taxon:4932 20041008 SGD
+SGD S000005367 YOL007C GO:0005935 SGD_REF:S000077144|PMID:15282802 IDA C YOL007C gene taxon:4932 20041008 SGD
+SGD S000005367 YOL007C GO:0005554 SGD_REF:S000069584 ND F YOL007C gene taxon:4932 20021120 SGD
+SGD S000005367 YOL007C GO:0000004 SGD_REF:S000069584 ND P YOL007C gene taxon:4932 20020925 SGD
+SGD S000028811 YOL013W-A GO:0008372 SGD_REF:S000069584 ND C YOL013W-A|YOL013W-B gene taxon:4932 20030730 SGD
+SGD S000028811 YOL013W-A GO:0005554 SGD_REF:S000069584 ND F YOL013W-A|YOL013W-B gene taxon:4932 20030730 SGD
+SGD S000028811 YOL013W-A GO:0000004 SGD_REF:S000069584 ND P YOL013W-A|YOL013W-B gene taxon:4932 20030730 SGD
+SGD S000005374 YOL014W GO:0008372 SGD_REF:S000069584 ND C YOL014W gene taxon:4932 20030203 SGD
+SGD S000005374 YOL014W GO:0005554 SGD_REF:S000069584 ND F YOL014W gene taxon:4932 20030203 SGD
+SGD S000005374 YOL014W GO:0000004 SGD_REF:S000069584 ND P YOL014W gene taxon:4932 20030203 SGD
+SGD S000005379 YOL019W GO:0000324 SGD_REF:S000074185|PMID:14562095 IDA C YOL019W|TOS7 gene taxon:4932 20031028 SGD
+SGD S000005379 YOL019W GO:0005886 SGD_REF:S000077144|PMID:15282802 IDA C YOL019W|TOS7 gene taxon:4932 20041008 SGD
+SGD S000005379 YOL019W GO:0005554 SGD_REF:S000069584 ND F YOL019W|TOS7 gene taxon:4932 20030203 SGD
+SGD S000005379 YOL019W GO:0000004 SGD_REF:S000069584 ND P YOL019W|TOS7 gene taxon:4932 20030203 SGD
+SGD S000028707 YOL019W-A GO:0008372 SGD_REF:S000069584 ND C YOL019W-A gene taxon:4932 20030730 SGD
+SGD S000028707 YOL019W-A GO:0005554 SGD_REF:S000069584 ND F YOL019W-A gene taxon:4932 20030730 SGD
+SGD S000028707 YOL019W-A GO:0000004 SGD_REF:S000069584 ND P YOL019W-A gene taxon:4932 20030730 SGD
+SGD S000005382 YOL022C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YOL022C gene taxon:4932 20031028 SGD
+SGD S000005382 YOL022C GO:0005554 SGD_REF:S000069584 ND F YOL022C gene taxon:4932 20030203 SGD
+SGD S000005382 YOL022C GO:0000004 SGD_REF:S000069584 ND P YOL022C gene taxon:4932 20030203 SGD
+SGD S000005384 YOL024W GO:0008372 SGD_REF:S000069584 ND C YOL024W gene taxon:4932 20030203 SGD
+SGD S000005384 YOL024W GO:0005554 SGD_REF:S000069584 ND F YOL024W gene taxon:4932 20030203 SGD
+SGD S000005384 YOL024W GO:0000004 SGD_REF:S000069584 ND P YOL024W gene taxon:4932 20030203 SGD
+SGD S000005389 YOL029C GO:0008372 SGD_REF:S000069584 ND C YOL029C gene taxon:4932 20030203 SGD
+SGD S000005389 YOL029C GO:0005554 SGD_REF:S000069584 ND F YOL029C gene taxon:4932 20030203 SGD
+SGD S000005389 YOL029C GO:0000004 SGD_REF:S000069584 ND P YOL029C gene taxon:4932 20030203 SGD
+SGD S000005396 YOL036W GO:0008372 SGD_REF:S000069584 ND C YOL036W gene taxon:4932 20030203 SGD
+SGD S000005396 YOL036W GO:0005554 SGD_REF:S000069584 ND F YOL036W gene taxon:4932 20030203 SGD
+SGD S000005396 YOL036W GO:0000004 SGD_REF:S000069584 ND P YOL036W gene taxon:4932 20030203 SGD
+SGD S000028812 YOL038C-A GO:0008372 SGD_REF:S000069584 ND C YOL038C-A gene taxon:4932 20030730 SGD
+SGD S000028812 YOL038C-A GO:0005554 SGD_REF:S000069584 ND F YOL038C-A gene taxon:4932 20030730 SGD
+SGD S000028812 YOL038C-A GO:0000004 SGD_REF:S000069584 ND P YOL038C-A gene taxon:4932 20030730 SGD
+SGD S000005407 YOL047C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YOL047C gene taxon:4932 20031028 SGD
+SGD S000005407 YOL047C GO:0005554 SGD_REF:S000069584 ND F YOL047C gene taxon:4932 20030422 SGD
+SGD S000005407 YOL047C GO:0000004 SGD_REF:S000069584 ND P YOL047C gene taxon:4932 20030422 SGD
+SGD S000005408 YOL048C GO:0005811 SGD_REF:S000074185|PMID:14562095 IDA C YOL048C gene taxon:4932 20031028 SGD
+SGD S000005408 YOL048C GO:0005554 SGD_REF:S000069584 ND F YOL048C gene taxon:4932 20021126 SGD
+SGD S000005408 YOL048C GO:0000004 SGD_REF:S000069584 ND P YOL048C gene taxon:4932 20021126 SGD
+SGD S000005414 YOL053W GO:0008372 SGD_REF:S000069584 ND C YOL053W gene taxon:4932 20021126 SGD
+SGD S000005414 YOL053W GO:0005554 SGD_REF:S000069584 ND F YOL053W gene taxon:4932 20021126 SGD
+SGD S000005414 YOL053W GO:0000004 SGD_REF:S000069584 ND P YOL053W gene taxon:4932 20021126 SGD
+SGD S000005418 YOL057W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YOL057W gene taxon:4932 20031028 SGD
+SGD S000005418 YOL057W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YOL057W gene taxon:4932 20031028 SGD
+SGD S000005418 YOL057W GO:0004222 SGD_REF:S000080056|PMID:15606766 ISS F YOL057W gene taxon:4932 20050415 SGD
+SGD S000005418 YOL057W GO:0006508 SGD_REF:S000080056|PMID:15606766 ISS P YOL057W gene taxon:4932 20050415 SGD
+SGD S000005431 YOL070C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YOL070C gene taxon:4932 20031028 SGD
+SGD S000005431 YOL070C GO:0005935 SGD_REF:S000074185|PMID:14562095 IDA C YOL070C gene taxon:4932 20031028 SGD
+SGD S000005431 YOL070C GO:0005554 SGD_REF:S000069584 ND F YOL070C gene taxon:4932 20030203 SGD
+SGD S000005431 YOL070C GO:0000004 SGD_REF:S000069584 ND P YOL070C gene taxon:4932 20030203 SGD
+SGD S000005434 YOL073C GO:0008372 SGD_REF:S000069584 ND C YOL073C gene taxon:4932 20030203 SGD
+SGD S000005434 YOL073C GO:0005554 SGD_REF:S000069584 ND F YOL073C gene taxon:4932 20030203 SGD
+SGD S000005434 YOL073C GO:0000004 SGD_REF:S000069584 ND P YOL073C gene taxon:4932 20030203 SGD
+SGD S000005435 YOL075C GO:0016020 SGD_REF:S000058031|PMID:9020838 ISS C YOL075C gene taxon:4932 20021120 SGD
+SGD S000005435 YOL075C GO:0042626 SGD_REF:S000058031|PMID:9020838 ISS F YOL075C gene taxon:4932 20021120 SGD
+SGD S000005435 YOL075C GO:0006810 SGD_REF:S000058031|PMID:9020838 ISS P YOL075C gene taxon:4932 20021120 SGD
+SGD S000005443 YOL083W GO:0008372 SGD_REF:S000069584 ND C YOL083W gene taxon:4932 20030203 SGD
+SGD S000005443 YOL083W GO:0005554 SGD_REF:S000069584 ND F YOL083W gene taxon:4932 20030203 SGD
+SGD S000005443 YOL083W GO:0000004 SGD_REF:S000069584 ND P YOL083W gene taxon:4932 20030203 SGD
+SGD S000007626 YOL086W-A GO:0008372 SGD_REF:S000069584 ND C YOL086W-A gene taxon:4932 20010226 SGD
+SGD S000007626 YOL086W-A GO:0005554 SGD_REF:S000069584 ND F YOL086W-A gene taxon:4932 20010226 SGD
+SGD S000007626 YOL086W-A GO:0000004 SGD_REF:S000069584 ND P YOL086W-A gene taxon:4932 20010226 SGD
+SGD S000005447 YOL087C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YOL087C gene taxon:4932 20031028 SGD
+SGD S000005447 YOL087C GO:0005554 SGD_REF:S000069584 ND F YOL087C gene taxon:4932 20021121 SGD
+SGD S000005447 YOL087C GO:0000004 SGD_REF:S000069584 ND P YOL087C gene taxon:4932 20021121 SGD
+SGD S000005452 YOL092W GO:0000329 SGD_REF:S000074185|PMID:14562095 IDA C YOL092W gene taxon:4932 20031028 SGD
+SGD S000005452 YOL092W GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YOL092W gene taxon:4932 20020507 SGD
+SGD S000005452 YOL092W GO:0005554 SGD_REF:S000069584 ND F YOL092W gene taxon:4932 20030203 SGD
+SGD S000005452 YOL092W GO:0000004 SGD_REF:S000069584 ND P YOL092W gene taxon:4932 20030203 SGD
+SGD S000028854 YOL097W-A GO:0008372 SGD_REF:S000069584 ND C YOL097W-A gene taxon:4932 20030730 SGD
+SGD S000028854 YOL097W-A GO:0005554 SGD_REF:S000069584 ND F YOL097W-A gene taxon:4932 20030730 SGD
+SGD S000028854 YOL097W-A GO:0000004 SGD_REF:S000069584 ND P YOL097W-A gene taxon:4932 20030730 SGD
+SGD S000005458 YOL098C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YOL098C gene taxon:4932 20031028 SGD
+SGD S000005458 YOL098C GO:0004222 SGD_REF:S000080056|PMID:15606766 ISS F YOL098C gene taxon:4932 20050415 SGD
+SGD S000005458 YOL098C GO:0006508 SGD_REF:S000080056|PMID:15606766 ISS P YOL098C gene taxon:4932 20050415 SGD
+SGD S000007349 YOL103W-A GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YOL103W-A gene taxon:4932 20030811 SGD
+SGD S000007349 YOL103W-A GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YOL103W-A gene taxon:4932 20030811 SGD
+SGD S000007349 YOL103W-A GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YOL103W-A gene taxon:4932 20030811 SGD
+SGD S000007349 YOL103W-A GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YOL103W-A gene taxon:4932 20030811 SGD
+SGD S000007350 YOL103W-B GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YOL103W-B gene taxon:4932 20030811 SGD
+SGD S000007350 YOL103W-B GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YOL103W-B gene taxon:4932 20030811 SGD
+SGD S000007350 YOL103W-B GO:0003887 SGD_REF:S000072465|PMID:9582191 ISS F YOL103W-B gene taxon:4932 20030811 SGD
+SGD S000007350 YOL103W-B GO:0003964 SGD_REF:S000072465|PMID:9582191 ISS F YOL103W-B gene taxon:4932 20030811 SGD
+SGD S000007350 YOL103W-B GO:0004540 SGD_REF:S000072465|PMID:9582191 ISS F YOL103W-B gene taxon:4932 20030811 SGD
+SGD S000007350 YOL103W-B GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YOL103W-B gene taxon:4932 20030811 SGD
+SGD S000007350 YOL103W-B GO:0008233 SGD_REF:S000072465|PMID:9582191 ISS F YOL103W-B gene taxon:4932 20030811 SGD
+SGD S000007350 YOL103W-B GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YOL103W-B gene taxon:4932 20030811 SGD
+SGD S000005467 YOL107W GO:0005794 SGD_REF:S000074185|PMID:14562095 IDA C YOL107W gene taxon:4932 20031028 SGD
+SGD S000005467 YOL107W colocalizes_with GO:0030137 SGD_REF:S000074185|PMID:14562095 IDA C YOL107W gene taxon:4932 20031028 SGD
+SGD S000005467 YOL107W GO:0005554 SGD_REF:S000069584 ND F YOL107W gene taxon:4932 20030203 SGD
+SGD S000005467 YOL107W GO:0000004 SGD_REF:S000069584 ND P YOL107W gene taxon:4932 20030203 SGD
+SGD S000005474 YOL114C GO:0008372 SGD_REF:S000069584 ND C YOL114C gene taxon:4932 20030425 SGD
+SGD S000005474 YOL114C GO:0005554 SGD_REF:S000069584 ND F YOL114C gene taxon:4932 20030425 SGD
+SGD S000005474 YOL114C GO:0000004 SGD_REF:S000069584 ND P YOL114C gene taxon:4932 20030425 SGD
+SGD S000005485 YOL125W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YOL125W gene taxon:4932 20031028 SGD
+SGD S000005485 YOL125W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YOL125W gene taxon:4932 20031028 SGD
+SGD S000005485 YOL125W GO:0005554 SGD_REF:S000069584 ND F YOL125W gene taxon:4932 20030425 SGD
+SGD S000005485 YOL125W GO:0000004 SGD_REF:S000069584 ND P YOL125W gene taxon:4932 20030425 SGD
+SGD S000005491 YOL131W GO:0008372 SGD_REF:S000069584 ND C YOL131W gene taxon:4932 20030203 SGD
+SGD S000005491 YOL131W GO:0005554 SGD_REF:S000069584 ND F YOL131W gene taxon:4932 20030203 SGD
+SGD S000005491 YOL131W GO:0000004 SGD_REF:S000069584 ND P YOL131W gene taxon:4932 20030203 SGD
+SGD S000005498 YOL138C GO:0000324 SGD_REF:S000074185|PMID:14562095 IDA C YOL138C gene taxon:4932 20031028 SGD
+SGD S000005498 YOL138C GO:0005554 SGD_REF:S000069584 ND F YOL138C gene taxon:4932 20030203 SGD
+SGD S000005498 YOL138C GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P YOL138C gene taxon:4932 20060227 SGD
+SGD S000005513 YOL153C GO:0008372 SGD_REF:S000069584 ND C YOL153C gene taxon:4932 20021126 SGD
+SGD S000005513 YOL153C GO:0005554 SGD_REF:S000069584 ND F YOL153C gene taxon:4932 20021126 SGD
+SGD S000005513 YOL153C GO:0000004 SGD_REF:S000069584 ND P YOL153C gene taxon:4932 20021126 SGD
+SGD S000005515 YOL155C GO:0005576 SGD_REF:S000075303|PMID:11935221 IDA C YOL155C gene taxon:4932 20040114 SGD
+SGD S000005515 YOL155C GO:0009277 SGD_REF:S000068778|PMID:11748726 IDA C YOL155C gene taxon:4932 20021206 SGD
+SGD S000005515 YOL155C GO:0015926 SGD_REF:S000068778|PMID:11748726 ISS F YOL155C gene taxon:4932 20021206 SGD
+SGD S000005515 YOL155C GO:0007047 SGD_REF:S000068778|PMID:11748726 IGI P YOL155C gene taxon:4932 20021206 SGD
+SGD S000028855 YOL155W-A GO:0008372 SGD_REF:S000069584 ND C YOL155W-A gene taxon:4932 20030730 SGD
+SGD S000028855 YOL155W-A GO:0005554 SGD_REF:S000069584 ND F YOL155W-A gene taxon:4932 20030730 SGD
+SGD S000028855 YOL155W-A GO:0000004 SGD_REF:S000069584 ND P YOL155W-A gene taxon:4932 20030730 SGD
+SGD S000005517 YOL157C GO:0008372 SGD_REF:S000069584 ND C YOL157C gene taxon:4932 20021120 SGD
+SGD S000005517 YOL157C GO:0005554 SGD_REF:S000069584 ND F YOL157C gene taxon:4932 20021120 SGD
+SGD S000005517 YOL157C GO:0000004 SGD_REF:S000069584 ND P YOL157C gene taxon:4932 20021120 SGD
+SGD S000005519 YOL159C GO:0005625 SGD_REF:S000075303|PMID:11935221 IDA C YOL159C gene taxon:4932 20040114 SGD
+SGD S000005519 YOL159C GO:0005554 SGD_REF:S000069584 ND F YOL159C gene taxon:4932 20021126 SGD
+SGD S000005519 YOL159C GO:0000004 SGD_REF:S000069584 ND P YOL159C gene taxon:4932 20021126 SGD
+SGD S000007627 YOL159C-A GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YOL159C-A gene taxon:4932 20031028 SGD
+SGD S000007627 YOL159C-A GO:0005554 SGD_REF:S000069584 ND F YOL159C-A gene taxon:4932 20010226 SGD
+SGD S000007627 YOL159C-A GO:0000004 SGD_REF:S000069584 ND P YOL159C-A gene taxon:4932 20010226 SGD
+SGD S000005522 YOL162W GO:0016020 SGD_REF:S000051510|PMID:10869563 ISS C YOL162W gene taxon:4932 20030208 SGD
+SGD S000005522 YOL162W GO:0005215 SGD_REF:S000051510|PMID:10869563 ISS F YOL162W gene taxon:4932 20030208 SGD
+SGD S000005522 YOL162W GO:0006810 SGD_REF:S000051510|PMID:10869563 ISS P YOL162W gene taxon:4932 20030208 SGD
+SGD S000005523 YOL163W GO:0016020 SGD_REF:S000051510|PMID:10869563 ISS C YOL163W gene taxon:4932 20030208 SGD
+SGD S000005523 YOL163W GO:0005215 SGD_REF:S000051510|PMID:10869563 ISS F YOL163W gene taxon:4932 20030208 SGD
+SGD S000005523 YOL163W GO:0006810 SGD_REF:S000051510|PMID:10869563 ISS P YOL163W gene taxon:4932 20030208 SGD
+SGD S000028580 YOL164W-A GO:0008372 SGD_REF:S000069584 ND C YOL164W-A gene taxon:4932 20030730 SGD
+SGD S000028580 YOL164W-A GO:0005554 SGD_REF:S000069584 ND F YOL164W-A gene taxon:4932 20030730 SGD
+SGD S000028580 YOL164W-A GO:0000004 SGD_REF:S000069584 ND P YOL164W-A gene taxon:4932 20030730 SGD
+SGD S000028709 YOL166W-A GO:0008372 SGD_REF:S000069584 ND C YOL166W-A gene taxon:4932 20030730 SGD
+SGD S000028709 YOL166W-A GO:0005554 SGD_REF:S000069584 ND F YOL166W-A gene taxon:4932 20030730 SGD
+SGD S000028709 YOL166W-A GO:0000004 SGD_REF:S000069584 ND P YOL166W-A gene taxon:4932 20030730 SGD
+SGD S000005532 YOR006C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YOR006C gene taxon:4932 20031028 SGD
+SGD S000005532 YOR006C GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YOR006C gene taxon:4932 20020507 SGD
+SGD S000005532 YOR006C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YOR006C gene taxon:4932 20031028 SGD
+SGD S000005532 YOR006C GO:0005554 SGD_REF:S000069584 ND F YOR006C gene taxon:4932 20030429 SGD
+SGD S000005532 YOR006C GO:0000004 SGD_REF:S000069584 ND P YOR006C gene taxon:4932 20030429 SGD
+SGD S000006431 YOR008C-A GO:0008372 SGD_REF:S000069584 ND C YOR008C-A gene taxon:4932 20021126 SGD
+SGD S000006431 YOR008C-A GO:0005554 SGD_REF:S000069584 ND F YOR008C-A gene taxon:4932 20021126 SGD
+SGD S000006431 YOR008C-A GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P YOR008C-A gene taxon:4932 20060227 SGD
+SGD S000028581 YOR011W-A GO:0008372 SGD_REF:S000069584 ND C YOR011W-A gene taxon:4932 20030730 SGD
+SGD S000028581 YOR011W-A GO:0005554 SGD_REF:S000069584 ND F YOR011W-A gene taxon:4932 20030730 SGD
+SGD S000028581 YOR011W-A GO:0000004 SGD_REF:S000069584 ND P YOR011W-A gene taxon:4932 20030730 SGD
+SGD S000005538 YOR012W GO:0008372 SGD_REF:S000069584 ND C YOR012W gene taxon:4932 20021126 SGD
+SGD S000005538 YOR012W GO:0005554 SGD_REF:S000069584 ND F YOR012W gene taxon:4932 20021126 SGD
+SGD S000005538 YOR012W GO:0000004 SGD_REF:S000069584 ND P YOR012W gene taxon:4932 20021126 SGD
+SGD S000005545 YOR019W GO:0008372 SGD_REF:S000069584 ND C YOR019W gene taxon:4932 20030203 SGD
+SGD S000005545 YOR019W GO:0005554 SGD_REF:S000069584 ND F YOR019W gene taxon:4932 20030203 SGD
+SGD S000005545 YOR019W GO:0000004 SGD_REF:S000069584 ND P YOR019W gene taxon:4932 20030203 SGD
+SGD S000028526 YOR020W-A GO:0008372 SGD_REF:S000069584 ND C YOR020W-A gene taxon:4932 20030730 SGD
+SGD S000028526 YOR020W-A GO:0005554 SGD_REF:S000069584 ND F YOR020W-A gene taxon:4932 20030730 SGD
+SGD S000028526 YOR020W-A GO:0000004 SGD_REF:S000069584 ND P YOR020W-A gene taxon:4932 20030730 SGD
+SGD S000005547 YOR021C GO:0008372 SGD_REF:S000069584 ND C YOR021C gene taxon:4932 20030203 SGD
+SGD S000005547 YOR021C GO:0005554 SGD_REF:S000069584 ND F YOR021C gene taxon:4932 20030203 SGD
+SGD S000005547 YOR021C GO:0000004 SGD_REF:S000069584 ND P YOR021C gene taxon:4932 20030203 SGD
+SGD S000005548 YOR022C GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YOR022C gene taxon:4932 20031028 SGD
+SGD S000005548 YOR022C GO:0004620 SGD_REF:S000065776|PMID:9488669 ISS F YOR022C gene taxon:4932 20030206 SGD
+SGD S000005548 YOR022C GO:0000004 SGD_REF:S000069584 ND P YOR022C gene taxon:4932 20030203 SGD
+SGD S000028710 YOR032W-A GO:0008372 SGD_REF:S000069584 ND C YOR032W-A gene taxon:4932 20030730 SGD
+SGD S000028710 YOR032W-A GO:0005554 SGD_REF:S000069584 ND F YOR032W-A gene taxon:4932 20030730 SGD
+SGD S000028710 YOR032W-A GO:0000004 SGD_REF:S000069584 ND P YOR032W-A gene taxon:4932 20030730 SGD
+SGD S000028856 YOR034C-A GO:0008372 SGD_REF:S000069584 ND C YOR034C-A gene taxon:4932 20030730 SGD
+SGD S000028856 YOR034C-A GO:0005554 SGD_REF:S000069584 ND F YOR034C-A gene taxon:4932 20030730 SGD
+SGD S000028856 YOR034C-A GO:0000004 SGD_REF:S000069584 ND P YOR034C-A gene taxon:4932 20030730 SGD
+SGD S000005570 YOR044W GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YOR044W gene taxon:4932 20031028 SGD
+SGD S000005570 YOR044W GO:0005554 SGD_REF:S000069584 ND F YOR044W gene taxon:4932 20021126 SGD
+SGD S000005570 YOR044W GO:0000004 SGD_REF:S000069584 ND P YOR044W gene taxon:4932 20021126 SGD
+SGD S000005577 YOR051C GO:0005634 SGD_REF:S000056415|PMID:10684247 IDA C YOR051C|YOR29-02 gene taxon:4932 20010301 SGD
+SGD S000005577 YOR051C GO:0005554 SGD_REF:S000069584 ND F YOR051C|YOR29-02 gene taxon:4932 20010119 SGD
+SGD S000005577 YOR051C GO:0000004 SGD_REF:S000069584 ND P YOR051C|YOR29-02 gene taxon:4932 20010119 SGD
+SGD S000005578 YOR052C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YOR052C|YOR29-03 gene taxon:4932 20031028 SGD
+SGD S000005578 YOR052C GO:0005554 SGD_REF:S000069584 ND F YOR052C|YOR29-03 gene taxon:4932 20030203 SGD
+SGD S000005578 YOR052C GO:0000004 SGD_REF:S000069584 ND P YOR052C|YOR29-03 gene taxon:4932 20030203 SGD
+SGD S000005585 YOR059C GO:0005811 SGD_REF:S000048561|PMID:10515935 IDA C YOR059C|YOR29-10 gene taxon:4932 20020917 SGD
+SGD S000005585 YOR059C GO:0005554 SGD_REF:S000069584 ND F YOR059C|YOR29-10 gene taxon:4932 20030429 SGD
+SGD S000005585 YOR059C GO:0000004 SGD_REF:S000069584 ND P YOR059C|YOR29-10 gene taxon:4932 20030429 SGD
+SGD S000005586 YOR060C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YOR060C|YOR29-11 gene taxon:4932 20031028 SGD
+SGD S000005586 YOR060C GO:0005634 SGD_REF:S000075214|PMID:14690591 IDA C YOR060C|YOR29-11 gene taxon:4932 20040105 SGD
+SGD S000005586 YOR060C GO:0005635 SGD_REF:S000075214|PMID:14690591 IDA C YOR060C|YOR29-11 gene taxon:4932 20040105 SGD
+SGD S000005586 YOR060C GO:0005737 SGD_REF:S000075214|PMID:14690591 IDA C YOR060C|YOR29-11 gene taxon:4932 20040105 SGD
+SGD S000005586 YOR060C GO:0005783 SGD_REF:S000075214|PMID:14690591 IDA C YOR060C|YOR29-11 gene taxon:4932 20040105 SGD
+SGD S000005586 YOR060C colocalizes_with GO:0005816 SGD_REF:S000074185|PMID:14562095 IDA C YOR060C|YOR29-11 gene taxon:4932 20031028 SGD
+SGD S000005586 YOR060C GO:0005554 SGD_REF:S000069584 ND F YOR060C|YOR29-11 gene taxon:4932 20030203 SGD
+SGD S000005586 YOR060C GO:0000004 SGD_REF:S000069584 ND P YOR060C|YOR29-11 gene taxon:4932 20030203 SGD
+SGD S000005586 YOR060C GO:0007005 SGD_REF:S000086425|PMID:16135527 IMP P YOR060C|YOR29-11 gene taxon:4932 20051111 SGD
+SGD S000005588 YOR062C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YOR062C|YOR29-13 gene taxon:4932 20031028 SGD
+SGD S000005588 YOR062C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YOR062C|YOR29-13 gene taxon:4932 20031028 SGD
+SGD S000005588 YOR062C GO:0005554 SGD_REF:S000069584 ND F YOR062C|YOR29-13 gene taxon:4932 20030203 SGD
+SGD S000005588 YOR062C GO:0000004 SGD_REF:S000069584 ND P YOR062C|YOR29-13 gene taxon:4932 20030203 SGD
+SGD S000005592 YOR066W GO:0008372 SGD_REF:S000069584 ND C YOR066W|YOR29-17 gene taxon:4932 20030203 SGD
+SGD S000005592 YOR066W GO:0005554 SGD_REF:S000069584 ND F YOR066W|YOR29-17 gene taxon:4932 20030203 SGD
+SGD S000005592 YOR066W GO:0000004 SGD_REF:S000069584 ND P YOR066W|YOR29-17 gene taxon:4932 20030203 SGD
+SGD S000005597 YOR071C GO:0016020 SGD_REF:S000052268|PMID:9235906 ISS C YOR071C|YOR29-22 gene taxon:4932 20021120 SGD
+SGD S000005597 YOR071C GO:0005215 SGD_REF:S000052268|PMID:9235906 ISS F YOR071C|YOR29-22 gene taxon:4932 20021120 SGD
+SGD S000005597 YOR071C GO:0006810 SGD_REF:S000052268|PMID:9235906 ISS P YOR071C|YOR29-22 gene taxon:4932 20021120 SGD
+SGD S000028516 YOR072W-B GO:0008372 SGD_REF:S000069584 ND C YOR072W-B gene taxon:4932 20030730 SGD
+SGD S000028516 YOR072W-B GO:0005554 SGD_REF:S000069584 ND F YOR072W-B gene taxon:4932 20030730 SGD
+SGD S000028516 YOR072W-B GO:0000004 SGD_REF:S000069584 ND P YOR072W-B gene taxon:4932 20030730 SGD
+SGD S000005610 YOR084W GO:0005782 SGD_REF:S000070290|PMID:12135984 IDA C YOR084W gene taxon:4932 20020820 SGD
+SGD S000005610 YOR084W GO:0016298 SGD_REF:S000050653|PMID:9200815 ISS F YOR084W gene taxon:4932 20030206 SGD
+SGD S000005610 YOR084W GO:0007031 SGD_REF:S000070290|PMID:12135984 IEP P YOR084W gene taxon:4932 20021220 SGD
+SGD S000005619 YOR093C GO:0008372 SGD_REF:S000069584 ND C YOR093C gene taxon:4932 20030203 SGD
+SGD S000005619 YOR093C GO:0005554 SGD_REF:S000069584 ND F YOR093C gene taxon:4932 20030203 SGD
+SGD S000005619 YOR093C GO:0000004 SGD_REF:S000069584 ND P YOR093C gene taxon:4932 20030203 SGD
+SGD S000005623 YOR097C GO:0008372 SGD_REF:S000069584 ND C YOR097C gene taxon:4932 20030203 SGD
+SGD S000005623 YOR097C GO:0005554 SGD_REF:S000069584 ND F YOR097C gene taxon:4932 20030203 SGD
+SGD S000005623 YOR097C GO:0000004 SGD_REF:S000069584 ND P YOR097C gene taxon:4932 20030203 SGD
+SGD S000005637 YOR111W GO:0008372 SGD_REF:S000069584 ND C YOR111W gene taxon:4932 20030128 SGD
+SGD S000005637 YOR111W GO:0005554 SGD_REF:S000069584 ND F YOR111W gene taxon:4932 20030128 SGD
+SGD S000005637 YOR111W GO:0000004 SGD_REF:S000069584 ND P YOR111W gene taxon:4932 20030128 SGD
+SGD S000005638 YOR112W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YOR112W gene taxon:4932 20031028 SGD
+SGD S000005638 YOR112W GO:0005554 SGD_REF:S000069584 ND F YOR112W gene taxon:4932 20030203 SGD
+SGD S000005638 YOR112W GO:0000004 SGD_REF:S000069584 ND P YOR112W gene taxon:4932 20030203 SGD
+SGD S000005640 YOR114W GO:0008372 SGD_REF:S000069584 ND C YOR114W gene taxon:4932 20030203 SGD
+SGD S000005640 YOR114W GO:0005554 SGD_REF:S000069584 ND F YOR114W gene taxon:4932 20030203 SGD
+SGD S000005640 YOR114W GO:0000004 SGD_REF:S000069584 ND P YOR114W gene taxon:4932 20030203 SGD
+SGD S000005644 YOR118W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YOR118W gene taxon:4932 20031028 SGD
+SGD S000005644 YOR118W GO:0005554 SGD_REF:S000069584 ND F YOR118W gene taxon:4932 20030203 SGD
+SGD S000005644 YOR118W GO:0000004 SGD_REF:S000069584 ND P YOR118W gene taxon:4932 20030203 SGD
+SGD S000005655 YOR129C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YOR129C gene taxon:4932 20031028 SGD
+SGD S000005655 YOR129C GO:0005824 SGD_REF:S000074039|PMID:14515169 IPI C YOR129C gene taxon:4932 20031222 SGD
+SGD S000005655 YOR129C GO:0005200 SGD_REF:S000074039|PMID:14515169 IGI F YOR129C gene taxon:4932 20031222 SGD
+SGD S000005655 YOR129C GO:0005200 SGD_REF:S000074039|PMID:14515169 IPI F YOR129C gene taxon:4932 20031222 SGD
+SGD S000005655 YOR129C GO:0030003 SGD_REF:S000074039|PMID:14515169 IGI P YOR129C gene taxon:4932 20031222 SGD
+SGD S000005655 YOR129C GO:0030003 SGD_REF:S000074039|PMID:14515169 IMP P YOR129C gene taxon:4932 20031222 SGD
+SGD S000005655 YOR129C GO:0042493 SGD_REF:S000074039|PMID:14515169 IGI P YOR129C gene taxon:4932 20031222 SGD
+SGD S000005655 YOR129C GO:0042493 SGD_REF:S000074039|PMID:14515169 IMP P YOR129C gene taxon:4932 20031222 SGD
+SGD S000005657 YOR131C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YOR131C gene taxon:4932 20031028 SGD
+SGD S000005657 YOR131C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YOR131C gene taxon:4932 20031028 SGD
+SGD S000005657 YOR131C GO:0005554 SGD_REF:S000069584 ND F YOR131C gene taxon:4932 20030203 SGD
+SGD S000005657 YOR131C GO:0000004 SGD_REF:S000069584 ND P YOR131C gene taxon:4932 20030203 SGD
+SGD S000007351 YOR142W-A GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YOR142W-A gene taxon:4932 20030811 SGD
+SGD S000007351 YOR142W-A GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YOR142W-A gene taxon:4932 20030811 SGD
+SGD S000007351 YOR142W-A GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YOR142W-A gene taxon:4932 20030811 SGD
+SGD S000007351 YOR142W-A GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YOR142W-A gene taxon:4932 20030811 SGD
+SGD S000007352 YOR142W-B GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YOR142W-B gene taxon:4932 20030811 SGD
+SGD S000007352 YOR142W-B GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YOR142W-B gene taxon:4932 20030811 SGD
+SGD S000007352 YOR142W-B GO:0003887 SGD_REF:S000072465|PMID:9582191 ISS F YOR142W-B gene taxon:4932 20030811 SGD
+SGD S000007352 YOR142W-B GO:0003964 SGD_REF:S000072465|PMID:9582191 ISS F YOR142W-B gene taxon:4932 20030811 SGD
+SGD S000007352 YOR142W-B GO:0004540 SGD_REF:S000072465|PMID:9582191 ISS F YOR142W-B gene taxon:4932 20030811 SGD
+SGD S000007352 YOR142W-B GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YOR142W-B gene taxon:4932 20030811 SGD
+SGD S000007352 YOR142W-B GO:0008233 SGD_REF:S000072465|PMID:9582191 ISS F YOR142W-B gene taxon:4932 20030811 SGD
+SGD S000007352 YOR142W-B GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YOR142W-B gene taxon:4932 20030811 SGD
+SGD S000005678 YOR152C GO:0005624 SGD_REF:S000075303|PMID:11935221 IDA C YOR152C gene taxon:4932 20040114 SGD
+SGD S000005678 YOR152C GO:0005554 SGD_REF:S000069584 ND F YOR152C gene taxon:4932 20021204 SGD
+SGD S000005678 YOR152C GO:0000004 SGD_REF:S000069584 ND P YOR152C gene taxon:4932 20021204 SGD
+SGD S000005680 YOR154W GO:0008372 SGD_REF:S000069584 ND C YOR154W gene taxon:4932 20030421 SGD
+SGD S000005680 YOR154W GO:0005554 SGD_REF:S000069584 ND F YOR154W gene taxon:4932 20030421 SGD
+SGD S000005680 YOR154W GO:0000004 SGD_REF:S000069584 ND P YOR154W gene taxon:4932 20030421 SGD
+SGD S000028712 YOR161C-C GO:0008372 SGD_REF:S000069584 ND C YOR161C-C gene taxon:4932 20030730 SGD
+SGD S000028712 YOR161C-C GO:0005554 SGD_REF:S000069584 ND F YOR161C-C gene taxon:4932 20030730 SGD
+SGD S000028712 YOR161C-C GO:0000004 SGD_REF:S000069584 ND P YOR161C-C gene taxon:4932 20030730 SGD
+SGD S000005690 YOR164C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YOR164C gene taxon:4932 20031028 SGD
+SGD S000005690 YOR164C GO:0005554 SGD_REF:S000069584 ND F YOR164C gene taxon:4932 20021126 SGD
+SGD S000005690 YOR164C GO:0000004 SGD_REF:S000069584 ND P YOR164C gene taxon:4932 20021126 SGD
+SGD S000005692 YOR166C GO:0008372 SGD_REF:S000069584 ND C YOR166C gene taxon:4932 20021126 SGD
+SGD S000005692 YOR166C GO:0005554 SGD_REF:S000069584 ND F YOR166C gene taxon:4932 20021126 SGD
+SGD S000005692 YOR166C GO:0000004 SGD_REF:S000069584 ND P YOR166C gene taxon:4932 20021126 SGD
+SGD S000005701 YOR175C GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YOR175C gene taxon:4932 20031028 SGD
+SGD S000005701 YOR175C GO:0008374 SGD_REF:S000081341|PMID:10694878 ISS F YOR175C gene taxon:4932 20050419 SGD
+SGD S000005701 YOR175C GO:0000004 SGD_REF:S000069584 ND P YOR175C gene taxon:4932 20030203 SGD
+SGD S000005712 YOR186W GO:0008372 SGD_REF:S000069584 ND C YOR186W gene taxon:4932 20021126 SGD
+SGD S000005712 YOR186W GO:0005554 SGD_REF:S000069584 ND F YOR186W gene taxon:4932 20021126 SGD
+SGD S000005712 YOR186W GO:0000004 SGD_REF:S000069584 ND P YOR186W gene taxon:4932 20021126 SGD
+SGD S000005718 YOR192C GO:0016020 SGD_REF:S000052268|PMID:9235906 ISS C YOR192C gene taxon:4932 20021120 SGD
+SGD S000005718 YOR192C GO:0005215 SGD_REF:S000052268|PMID:9235906 ISS F YOR192C gene taxon:4932 20021120 SGD
+SGD S000005718 YOR192C GO:0006810 SGD_REF:S000052268|PMID:9235906 ISS P YOR192C gene taxon:4932 20021120 SGD
+SGD S000007353 YOR192C-A GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YOR192C-A gene taxon:4932 20030811 SGD
+SGD S000007353 YOR192C-A GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YOR192C-A gene taxon:4932 20030811 SGD
+SGD S000007353 YOR192C-A GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YOR192C-A gene taxon:4932 20030811 SGD
+SGD S000007353 YOR192C-A GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YOR192C-A gene taxon:4932 20030811 SGD
+SGD S000007354 YOR192C-B GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YOR192C-B gene taxon:4932 20030811 SGD
+SGD S000007354 YOR192C-B GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YOR192C-B gene taxon:4932 20030811 SGD
+SGD S000007354 YOR192C-B GO:0003887 SGD_REF:S000072465|PMID:9582191 ISS F YOR192C-B gene taxon:4932 20030811 SGD
+SGD S000007354 YOR192C-B GO:0003964 SGD_REF:S000072465|PMID:9582191 ISS F YOR192C-B gene taxon:4932 20030811 SGD
+SGD S000007354 YOR192C-B GO:0004540 SGD_REF:S000072465|PMID:9582191 ISS F YOR192C-B gene taxon:4932 20030811 SGD
+SGD S000007354 YOR192C-B GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YOR192C-B gene taxon:4932 20030811 SGD
+SGD S000007354 YOR192C-B GO:0008233 SGD_REF:S000072465|PMID:9582191 ISS F YOR192C-B gene taxon:4932 20030811 SGD
+SGD S000007354 YOR192C-B GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YOR192C-B gene taxon:4932 20030811 SGD
+SGD S000028857 YOR192C-C GO:0008372 SGD_REF:S000069584 ND C YOR192C-C gene taxon:4932 20030730 SGD
+SGD S000028857 YOR192C-C GO:0005554 SGD_REF:S000069584 ND F YOR192C-C gene taxon:4932 20030730 SGD
+SGD S000028857 YOR192C-C GO:0000004 SGD_REF:S000069584 ND P YOR192C-C gene taxon:4932 20030730 SGD
+SGD S000005740 YOR214C GO:0009277 SGD_REF:S000040179|PMID:10383953 IDA C YOR214C gene taxon:4932 20020617 SGD
+SGD S000005740 YOR214C GO:0005554 SGD_REF:S000069584 ND F YOR214C gene taxon:4932 20030429 SGD
+SGD S000005740 YOR214C GO:0000004 SGD_REF:S000069584 ND P YOR214C gene taxon:4932 20030429 SGD
+SGD S000005741 YOR215C GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YOR215C gene taxon:4932 20031028 SGD
+SGD S000005741 YOR215C GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YOR215C gene taxon:4932 20031210 SGD
+SGD S000005741 YOR215C GO:0005554 SGD_REF:S000069584 ND F YOR215C gene taxon:4932 20030203 SGD
+SGD S000005741 YOR215C GO:0000004 SGD_REF:S000069584 ND P YOR215C gene taxon:4932 20030203 SGD
+SGD S000005749 YOR223W GO:0008372 SGD_REF:S000069584 ND C YOR223W gene taxon:4932 20030203 SGD
+SGD S000005749 YOR223W GO:0005554 SGD_REF:S000069584 ND F YOR223W gene taxon:4932 20030203 SGD
+SGD S000005749 YOR223W GO:0000004 SGD_REF:S000069584 ND P YOR223W gene taxon:4932 20030203 SGD
+SGD S000005753 YOR227W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YOR227W gene taxon:4932 20031028 SGD
+SGD S000005753 YOR227W GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YOR227W gene taxon:4932 20040928 SGD
+SGD S000005753 YOR227W GO:0005554 SGD_REF:S000069584 ND F YOR227W gene taxon:4932 20030205 SGD
+SGD S000005753 YOR227W GO:0000004 SGD_REF:S000069584 ND P YOR227W gene taxon:4932 20030205 SGD
+SGD S000005754 YOR228C GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YOR228C gene taxon:4932 20031028 SGD
+SGD S000005754 YOR228C GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C YOR228C gene taxon:4932 20060317 SGD
+SGD S000005754 YOR228C GO:0005554 SGD_REF:S000069584 ND F YOR228C gene taxon:4932 20030203 SGD
+SGD S000005754 YOR228C GO:0000004 SGD_REF:S000069584 ND P YOR228C gene taxon:4932 20030203 SGD
+SGD S000005764 YOR238W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YOR238W gene taxon:4932 20031028 SGD
+SGD S000005764 YOR238W GO:0005554 SGD_REF:S000069584 ND F YOR238W gene taxon:4932 20021106 SGD
+SGD S000005764 YOR238W GO:0000004 SGD_REF:S000069584 ND P YOR238W gene taxon:4932 20021106 SGD
+SGD S000005772 YOR246C GO:0005811 SGD_REF:S000074185|PMID:14562095 IDA C YOR246C gene taxon:4932 20031028 SGD
+SGD S000005772 YOR246C GO:0016491 SGD_REF:S000053931|PMID:8972580 ISS F YOR246C gene taxon:4932 20030207 SGD
+SGD S000005772 YOR246C GO:0000004 SGD_REF:S000069584 ND P YOR246C gene taxon:4932 20030203 SGD
+SGD S000005777 YOR251C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YOR251C gene taxon:4932 20031028 SGD
+SGD S000005777 YOR251C GO:0004792 SGD_REF:S000048863|PMID:9153759 ISS F YOR251C gene taxon:4932 20030120 SGD
+SGD S000005777 YOR251C GO:0000004 SGD_REF:S000069584 ND P YOR251C gene taxon:4932 20021002 SGD
+SGD S000005788 YOR262W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YOR262W gene taxon:4932 20031028 SGD
+SGD S000005788 YOR262W GO:0005737 SGD_REF:S000075214|PMID:14690591 IDA C YOR262W gene taxon:4932 20040105 SGD
+SGD S000005788 YOR262W GO:0005554 SGD_REF:S000069584 ND F YOR262W gene taxon:4932 20021126 SGD
+SGD S000005788 YOR262W GO:0000004 SGD_REF:S000069584 ND P YOR262W gene taxon:4932 20021126 SGD
+SGD S000005794 YOR268C GO:0008372 SGD_REF:S000069584 ND C YOR268C gene taxon:4932 20021126 SGD
+SGD S000005794 YOR268C GO:0005554 SGD_REF:S000069584 ND F YOR268C gene taxon:4932 20021126 SGD
+SGD S000005794 YOR268C GO:0000004 SGD_REF:S000069584 ND P YOR268C gene taxon:4932 20021126 SGD
+SGD S000005797 YOR271C GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YOR271C gene taxon:4932 20031028 SGD
+SGD S000005797 YOR271C GO:0005554 SGD_REF:S000069584 ND F YOR271C gene taxon:4932 20030203 SGD
+SGD S000005797 YOR271C GO:0000004 SGD_REF:S000069584 ND P YOR271C gene taxon:4932 20030203 SGD
+SGD S000005809 YOR283W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YOR283W gene taxon:4932 20031028 SGD
+SGD S000005809 YOR283W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YOR283W gene taxon:4932 20031028 SGD
+SGD S000005809 YOR283W GO:0005554 SGD_REF:S000069584 ND F YOR283W gene taxon:4932 20030203 SGD
+SGD S000005809 YOR283W GO:0000004 SGD_REF:S000069584 ND P YOR283W gene taxon:4932 20030203 SGD
+SGD S000005811 YOR285W GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YOR285W gene taxon:4932 20040928 SGD
+SGD S000005811 YOR285W GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C YOR285W gene taxon:4932 20060317 SGD
+SGD S000005811 YOR285W GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YOR285W gene taxon:4932 20031028 SGD
+SGD S000005811 YOR285W GO:0005554 SGD_REF:S000069584 ND F YOR285W gene taxon:4932 20030203 SGD
+SGD S000005811 YOR285W GO:0000004 SGD_REF:S000069584 ND P YOR285W gene taxon:4932 20030203 SGD
+SGD S000005813 YOR287C GO:0008372 SGD_REF:S000069584 ND C YOR287C gene taxon:4932 20030203 SGD
+SGD S000005813 YOR287C GO:0005554 SGD_REF:S000069584 ND F YOR287C gene taxon:4932 20030203 SGD
+SGD S000005813 YOR287C GO:0030490 SGD_REF:S000073750|PMID:12837249 IMP P YOR287C gene taxon:4932 20030805 SGD
+SGD S000005815 YOR289W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YOR289W gene taxon:4932 20031028 SGD
+SGD S000005815 YOR289W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YOR289W gene taxon:4932 20031028 SGD
+SGD S000005815 YOR289W GO:0005554 SGD_REF:S000069584 ND F YOR289W gene taxon:4932 20021106 SGD
+SGD S000005815 YOR289W GO:0000004 SGD_REF:S000069584 ND P YOR289W gene taxon:4932 20021106 SGD
+SGD S000005817 YOR291W GO:0016020 SGD_REF:S000048862|PMID:9153758 ISS C YOR291W gene taxon:4932 20021204 SGD
+SGD S000005817 YOR291W GO:0005554 SGD_REF:S000069584 ND F YOR291W gene taxon:4932 20030120 SGD
+SGD S000005817 YOR291W GO:0000004 SGD_REF:S000069584 ND P YOR291W gene taxon:4932 20021204 SGD
+SGD S000005818 YOR292C GO:0000324 SGD_REF:S000074185|PMID:14562095 IDA C YOR292C gene taxon:4932 20031028 SGD
+SGD S000005818 YOR292C GO:0005554 SGD_REF:S000069584 ND F YOR292C gene taxon:4932 20030203 SGD
+SGD S000005818 YOR292C GO:0000004 SGD_REF:S000069584 ND P YOR292C gene taxon:4932 20030203 SGD
+SGD S000028858 YOR293C-A GO:0008372 SGD_REF:S000069584 ND C YOR293C-A gene taxon:4932 20030730 SGD
+SGD S000028858 YOR293C-A GO:0005554 SGD_REF:S000069584 ND F YOR293C-A gene taxon:4932 20030730 SGD
+SGD S000028858 YOR293C-A GO:0000004 SGD_REF:S000069584 ND P YOR293C-A gene taxon:4932 20030730 SGD
+SGD S000005822 YOR296W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YOR296W gene taxon:4932 20031028 SGD
+SGD S000005822 YOR296W GO:0005554 SGD_REF:S000069584 ND F YOR296W gene taxon:4932 20030203 SGD
+SGD S000005822 YOR296W GO:0000004 SGD_REF:S000069584 ND P YOR296W gene taxon:4932 20030203 SGD
+SGD S000005828 YOR302W GO:0005829 SGD_REF:S000055193|PMID:10608810 IC GO:0045182 C YOR302W gene taxon:4932 20030212 SGD
+SGD S000005828 YOR302W GO:0045182 SGD_REF:S000055193|PMID:10608810 IDA F YOR302W gene taxon:4932 20030212 SGD
+SGD S000005828 YOR302W GO:0006417 SGD_REF:S000055193|PMID:10608810 IDA P YOR302W gene taxon:4932 20030212 SGD
+SGD S000005830 YOR304C-A GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YOR304C-A gene taxon:4932 20031028 SGD
+SGD S000005830 YOR304C-A GO:0005933 SGD_REF:S000074185|PMID:14562095 IDA C YOR304C-A gene taxon:4932 20031028 SGD
+SGD S000005830 YOR304C-A GO:0005935 SGD_REF:S000074185|PMID:14562095 IDA C YOR304C-A gene taxon:4932 20031028 SGD
+SGD S000005830 YOR304C-A GO:0005554 SGD_REF:S000069584 ND F YOR304C-A gene taxon:4932 20021120 SGD
+SGD S000005830 YOR304C-A GO:0000004 SGD_REF:S000069584 ND P YOR304C-A gene taxon:4932 20021120 SGD
+SGD S000005832 YOR305W GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YOR305W gene taxon:4932 20031028 SGD
+SGD S000005832 YOR305W GO:0005554 SGD_REF:S000069584 ND F YOR305W gene taxon:4932 20030203 SGD
+SGD S000005832 YOR305W GO:0000004 SGD_REF:S000069584 ND P YOR305W gene taxon:4932 20030203 SGD
+SGD S000028584 YOR316C-A GO:0008372 SGD_REF:S000069584 ND C YOR316C-A gene taxon:4932 20030730 SGD
+SGD S000028584 YOR316C-A GO:0005554 SGD_REF:S000069584 ND F YOR316C-A gene taxon:4932 20030730 SGD
+SGD S000028584 YOR316C-A GO:0000004 SGD_REF:S000069584 ND P YOR316C-A gene taxon:4932 20030730 SGD
+SGD S000005865 YOR338W GO:0008372 SGD_REF:S000069584 ND C YOR338W gene taxon:4932 20030203 SGD
+SGD S000005865 YOR338W GO:0005554 SGD_REF:S000069584 ND F YOR338W gene taxon:4932 20030203 SGD
+SGD S000005865 YOR338W GO:0000004 SGD_REF:S000069584 ND P YOR338W gene taxon:4932 20030203 SGD
+SGD S000005869 YOR342C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YOR342C gene taxon:4932 20031028 SGD
+SGD S000005869 YOR342C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YOR342C gene taxon:4932 20031028 SGD
+SGD S000005869 YOR342C GO:0005554 SGD_REF:S000069584 ND F YOR342C gene taxon:4932 20030203 SGD
+SGD S000005869 YOR342C GO:0000004 SGD_REF:S000069584 ND P YOR342C gene taxon:4932 20030203 SGD
+SGD S000007355 YOR343W-A GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YOR343W-A|YOR343C-A gene taxon:4932 20030811 SGD
+SGD S000007355 YOR343W-A GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YOR343W-A|YOR343C-A gene taxon:4932 20030811 SGD
+SGD S000007355 YOR343W-A GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YOR343W-A|YOR343C-A gene taxon:4932 20030811 SGD
+SGD S000007355 YOR343W-A GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YOR343W-A|YOR343C-A gene taxon:4932 20030811 SGD
+SGD S000007356 YOR343W-B GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YOR343W-B|YOR343C-B gene taxon:4932 20030811 SGD
+SGD S000007356 YOR343W-B GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YOR343W-B|YOR343C-B gene taxon:4932 20030811 SGD
+SGD S000007356 YOR343W-B GO:0003887 SGD_REF:S000072465|PMID:9582191 ISS F YOR343W-B|YOR343C-B gene taxon:4932 20030811 SGD
+SGD S000007356 YOR343W-B GO:0003964 SGD_REF:S000072465|PMID:9582191 ISS F YOR343W-B|YOR343C-B gene taxon:4932 20030811 SGD
+SGD S000007356 YOR343W-B GO:0004540 SGD_REF:S000072465|PMID:9582191 ISS F YOR343W-B|YOR343C-B gene taxon:4932 20030811 SGD
+SGD S000007356 YOR343W-B GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YOR343W-B|YOR343C-B gene taxon:4932 20030811 SGD
+SGD S000007356 YOR343W-B GO:0008233 SGD_REF:S000072465|PMID:9582191 ISS F YOR343W-B|YOR343C-B gene taxon:4932 20030811 SGD
+SGD S000007356 YOR343W-B GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YOR343W-B|YOR343C-B gene taxon:4932 20030811 SGD
+SGD S000005879 YOR352W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YOR352W gene taxon:4932 20031028 SGD
+SGD S000005879 YOR352W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YOR352W gene taxon:4932 20031028 SGD
+SGD S000005879 YOR352W GO:0005554 SGD_REF:S000069584 ND F YOR352W gene taxon:4932 20021126 SGD
+SGD S000005879 YOR352W GO:0000004 SGD_REF:S000069584 ND P YOR352W gene taxon:4932 20021126 SGD
+SGD S000005883 YOR356W GO:0005739 SGD_REF:S000068875|PMID:11502169 IPI C YOR356W gene taxon:4932 20021002 SGD
+SGD S000005883 YOR356W GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YOR356W gene taxon:4932 20031210 SGD
+SGD S000005883 YOR356W GO:0016649 SGD_REF:S000072463|PMID:10592175 ISS F YOR356W gene taxon:4932 20030213 SGD
+SGD S000005883 YOR356W GO:0019677 SGD_REF:S000068875|PMID:11502169 IPI P YOR356W gene taxon:4932 20021002 SGD
+SGD S000005892 YOR365C GO:0008372 SGD_REF:S000069584 ND C YOR365C gene taxon:4932 20030203 SGD
+SGD S000005892 YOR365C GO:0005554 SGD_REF:S000069584 ND F YOR365C gene taxon:4932 20030203 SGD
+SGD S000005892 YOR365C GO:0000004 SGD_REF:S000069584 ND P YOR365C gene taxon:4932 20030203 SGD
+SGD S000028586 YOR376W-A GO:0008372 SGD_REF:S000069584 ND C YOR376W-A gene taxon:4932 20030730 SGD
+SGD S000028586 YOR376W-A GO:0005554 SGD_REF:S000069584 ND F YOR376W-A gene taxon:4932 20030730 SGD
+SGD S000028586 YOR376W-A GO:0000004 SGD_REF:S000069584 ND P YOR376W-A gene taxon:4932 20030730 SGD
+SGD S000005905 YOR378W GO:0008372 SGD_REF:S000069584 ND C YOR378W gene taxon:4932 20021126 SGD
+SGD S000005905 YOR378W GO:0005554 SGD_REF:S000069584 ND F YOR378W gene taxon:4932 20021126 SGD
+SGD S000005905 YOR378W GO:0000004 SGD_REF:S000069584 ND P YOR378W gene taxon:4932 20021126 SGD
+SGD S000028587 YOR381W-A GO:0008372 SGD_REF:S000069584 ND C YOR381W-A gene taxon:4932 20030730 SGD
+SGD S000028587 YOR381W-A GO:0005554 SGD_REF:S000069584 ND F YOR381W-A gene taxon:4932 20030730 SGD
+SGD S000028587 YOR381W-A GO:0000004 SGD_REF:S000069584 ND P YOR381W-A gene taxon:4932 20030730 SGD
+SGD S000005912 YOR385W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YOR385W gene taxon:4932 20031028 SGD
+SGD S000005912 YOR385W GO:0005554 SGD_REF:S000069584 ND F YOR385W gene taxon:4932 20021126 SGD
+SGD S000005912 YOR385W GO:0000004 SGD_REF:S000069584 ND P YOR385W gene taxon:4932 20021126 SGD
+SGD S000005914 YOR387C GO:0005625 SGD_REF:S000075303|PMID:11935221 IDA C YOR387C gene taxon:4932 20040114 SGD
+SGD S000005914 YOR387C GO:0005554 SGD_REF:S000069584 ND F YOR387C gene taxon:4932 20030205 SGD
+SGD S000005914 YOR387C GO:0000004 SGD_REF:S000069584 ND P YOR387C gene taxon:4932 20030205 SGD
+SGD S000005916 YOR389W GO:0008372 SGD_REF:S000069584 ND C YOR389W gene taxon:4932 20021126 SGD
+SGD S000005916 YOR389W GO:0005554 SGD_REF:S000069584 ND F YOR389W gene taxon:4932 20021126 SGD
+SGD S000005916 YOR389W GO:0000004 SGD_REF:S000069584 ND P YOR389W gene taxon:4932 20021126 SGD
+SGD S000005917 YOR390W GO:0008372 SGD_REF:S000069584 ND C YOR390W gene taxon:4932 20021126 SGD
+SGD S000005917 YOR390W GO:0005554 SGD_REF:S000069584 ND F YOR390W gene taxon:4932 20021126 SGD
+SGD S000005917 YOR390W GO:0000004 SGD_REF:S000069584 ND P YOR390W gene taxon:4932 20021126 SGD
+SGD S000028718 YOR394C-A GO:0008372 SGD_REF:S000069584 ND C YOR394C-A gene taxon:4932 20030730 SGD
+SGD S000028718 YOR394C-A GO:0005554 SGD_REF:S000069584 ND F YOR394C-A gene taxon:4932 20030730 SGD
+SGD S000028718 YOR394C-A GO:0000004 SGD_REF:S000069584 ND P YOR394C-A gene taxon:4932 20030730 SGD
+SGD S000007526 YOR396W GO:0008372 SGD_REF:S000069584 ND C YOR396W gene taxon:4932 20021120 SGD
+SGD S000007526 YOR396W GO:0004386 SGD_REF:S000053946|PMID:9837911 ISS F YOR396W gene taxon:4932 20040323 SGD
+SGD S000007526 YOR396W GO:0000004 SGD_REF:S000069584 ND P YOR396W gene taxon:4932 20021120 SGD
+SGD S000005930 YPL009C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YPL009C gene taxon:4932 20031028 SGD
+SGD S000005930 YPL009C GO:0005554 SGD_REF:S000069584 ND F YPL009C gene taxon:4932 20030203 SGD
+SGD S000005930 YPL009C GO:0000004 SGD_REF:S000069584 ND P YPL009C gene taxon:4932 20030203 SGD
+SGD S000005935 YPL014W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YPL014W gene taxon:4932 20031028 SGD
+SGD S000005935 YPL014W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YPL014W gene taxon:4932 20031028 SGD
+SGD S000005935 YPL014W GO:0005554 SGD_REF:S000069584 ND F YPL014W gene taxon:4932 20021126 SGD
+SGD S000005935 YPL014W GO:0000004 SGD_REF:S000069584 ND P YPL014W gene taxon:4932 20021126 SGD
+SGD S000005938 YPL017C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YPL017C gene taxon:4932 20031028 SGD
+SGD S000005938 YPL017C GO:0008757 SGD_REF:S000074033|PMID:12872006 ISS F YPL017C gene taxon:4932 20031001 SGD
+SGD S000005938 YPL017C GO:0000004 SGD_REF:S000069584 ND P YPL017C gene taxon:4932 20021108 SGD
+SGD S000005951 YPL030W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YPL030W gene taxon:4932 20031028 SGD
+SGD S000005951 YPL030W GO:0005554 SGD_REF:S000069584 ND F YPL030W gene taxon:4932 20030203 SGD
+SGD S000005951 YPL030W GO:0000004 SGD_REF:S000069584 ND P YPL030W gene taxon:4932 20030203 SGD
+SGD S000005954 YPL033C GO:0008372 SGD_REF:S000069584 ND C YPL033C gene taxon:4932 20021004 SGD
+SGD S000005954 YPL033C GO:0005554 SGD_REF:S000069584 ND F YPL033C gene taxon:4932 20021004 SGD
+SGD S000005954 YPL033C GO:0006259 SGD_REF:S000043176|PMID:10051619 IGI P YPL033C gene taxon:4932 20021004 SGD
+SGD S000005954 YPL033C GO:0007126 SGD_REF:S000043176|PMID:10051619 IEP P YPL033C gene taxon:4932 20021004 SGD
+SGD S000005955 YPL034W GO:0008372 SGD_REF:S000069584 ND C YPL034W gene taxon:4932 20021126 SGD
+SGD S000005955 YPL034W GO:0005554 SGD_REF:S000069584 ND F YPL034W gene taxon:4932 20021126 SGD
+SGD S000005955 YPL034W GO:0000004 SGD_REF:S000069584 ND P YPL034W gene taxon:4932 20021126 SGD
+SGD S000028588 YPL038W-A GO:0008372 SGD_REF:S000069584 ND C YPL038W-A gene taxon:4932 20030730 SGD
+SGD S000028588 YPL038W-A GO:0005554 SGD_REF:S000069584 ND F YPL038W-A gene taxon:4932 20030730 SGD
+SGD S000028588 YPL038W-A GO:0000004 SGD_REF:S000069584 ND P YPL038W-A gene taxon:4932 20030730 SGD
+SGD S000005960 YPL039W GO:0008372 SGD_REF:S000069584 ND C YPL039W gene taxon:4932 20021126 SGD
+SGD S000005960 YPL039W GO:0005554 SGD_REF:S000069584 ND F YPL039W gene taxon:4932 20021126 SGD
+SGD S000005960 YPL039W GO:0000004 SGD_REF:S000069584 ND P YPL039W gene taxon:4932 20021126 SGD
+SGD S000005962 YPL041C GO:0008372 SGD_REF:S000069584 ND C YPL041C gene taxon:4932 20021126 SGD
+SGD S000005962 YPL041C GO:0005554 SGD_REF:S000069584 ND F YPL041C gene taxon:4932 20021126 SGD
+SGD S000005962 YPL041C GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P YPL041C gene taxon:4932 20060202 SGD
+SGD S000005977 YPL056C GO:0008372 SGD_REF:S000069584 ND C YPL056C gene taxon:4932 20021126 SGD
+SGD S000005977 YPL056C GO:0005554 SGD_REF:S000069584 ND F YPL056C gene taxon:4932 20021126 SGD
+SGD S000005977 YPL056C GO:0000004 SGD_REF:S000069584 ND P YPL056C gene taxon:4932 20021126 SGD
+SGD S000007388 YPL060C-A GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YPL060C-A gene taxon:4932 20030811 SGD
+SGD S000007388 YPL060C-A GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YPL060C-A gene taxon:4932 20030811 SGD
+SGD S000007388 YPL060C-A GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YPL060C-A gene taxon:4932 20030811 SGD
+SGD S000007388 YPL060C-A GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YPL060C-A gene taxon:4932 20030811 SGD
+SGD S000005987 YPL066W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YPL066W gene taxon:4932 20031028 SGD
+SGD S000005987 YPL066W GO:0005935 SGD_REF:S000074185|PMID:14562095 IDA C YPL066W gene taxon:4932 20031028 SGD
+SGD S000005987 YPL066W GO:0005554 SGD_REF:S000069584 ND F YPL066W gene taxon:4932 20021126 SGD
+SGD S000005987 YPL066W GO:0000004 SGD_REF:S000069584 ND P YPL066W gene taxon:4932 20021126 SGD
+SGD S000005988 YPL067C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YPL067C gene taxon:4932 20031028 SGD
+SGD S000005988 YPL067C GO:0005554 SGD_REF:S000069584 ND F YPL067C gene taxon:4932 20030203 SGD
+SGD S000005988 YPL067C GO:0000004 SGD_REF:S000069584 ND P YPL067C gene taxon:4932 20030203 SGD
+SGD S000005989 YPL068C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YPL068C gene taxon:4932 20031028 SGD
+SGD S000005989 YPL068C GO:0005554 SGD_REF:S000069584 ND F YPL068C gene taxon:4932 20030203 SGD
+SGD S000005989 YPL068C GO:0000004 SGD_REF:S000069584 ND P YPL068C gene taxon:4932 20030203 SGD
+SGD S000005992 YPL071C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YPL071C gene taxon:4932 20031028 SGD
+SGD S000005992 YPL071C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YPL071C gene taxon:4932 20031028 SGD
+SGD S000005992 YPL071C GO:0005554 SGD_REF:S000069584 ND F YPL071C gene taxon:4932 20030203 SGD
+SGD S000005992 YPL071C GO:0000004 SGD_REF:S000069584 ND P YPL071C gene taxon:4932 20030203 SGD
+SGD S000005998 YPL077C GO:0008372 SGD_REF:S000069584 ND C YPL077C gene taxon:4932 20030203 SGD
+SGD S000005998 YPL077C GO:0005554 SGD_REF:S000069584 ND F YPL077C gene taxon:4932 20030203 SGD
+SGD S000005998 YPL077C GO:0000004 SGD_REF:S000069584 ND P YPL077C gene taxon:4932 20030203 SGD
+SGD S000006009 YPL088W GO:0008372 SGD_REF:S000069584 ND C YPL088W gene taxon:4932 20020902 SGD
+SGD S000006009 YPL088W GO:0018456 SGD_REF:S000042151|PMID:10572264 ISS F YPL088W gene taxon:4932 20020902 SGD
+SGD S000006009 YPL088W GO:0006081 SGD_REF:S000042151|PMID:10572264 ISS P YPL088W gene taxon:4932 20020902 SGD
+SGD S000006026 YPL105C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YPL105C gene taxon:4932 20031028 SGD
+SGD S000006026 YPL105C GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YPL105C gene taxon:4932 20040928 SGD
+SGD S000006026 YPL105C GO:0005554 SGD_REF:S000069584 ND F YPL105C gene taxon:4932 20030203 SGD
+SGD S000006026 YPL105C GO:0000004 SGD_REF:S000069584 ND P YPL105C gene taxon:4932 20030203 SGD
+SGD S000006028 YPL107W GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YPL107W gene taxon:4932 20031028 SGD
+SGD S000006028 YPL107W GO:0005554 SGD_REF:S000069584 ND F YPL107W gene taxon:4932 20021126 SGD
+SGD S000006028 YPL107W GO:0000004 SGD_REF:S000069584 ND P YPL107W gene taxon:4932 20021126 SGD
+SGD S000006029 YPL108W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YPL108W gene taxon:4932 20031028 SGD
+SGD S000006029 YPL108W GO:0005554 SGD_REF:S000069584 ND F YPL108W gene taxon:4932 20021126 SGD
+SGD S000006029 YPL108W GO:0000004 SGD_REF:S000069584 ND P YPL108W gene taxon:4932 20021126 SGD
+SGD S000006030 YPL109C GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YPL109C gene taxon:4932 20031028 SGD
+SGD S000006030 YPL109C GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YPL109C gene taxon:4932 20040924 SGD
+SGD S000006030 YPL109C GO:0005554 SGD_REF:S000069584 ND F YPL109C gene taxon:4932 20030203 SGD
+SGD S000006030 YPL109C GO:0000004 SGD_REF:S000069584 ND P YPL109C gene taxon:4932 20030203 SGD
+SGD S000006034 YPL113C GO:0008372 SGD_REF:S000069584 ND C YPL113C gene taxon:4932 20030203 SGD
+SGD S000006034 YPL113C GO:0016491 SGD_REF:S000072828|PMID:12525494 ISS F YPL113C gene taxon:4932 20030401 SGD
+SGD S000006034 YPL113C GO:0008152 SGD_REF:S000072828|PMID:12525494 ISS P YPL113C gene taxon:4932 20030401 SGD
+SGD S000028859 YPL119C-A GO:0008372 SGD_REF:S000069584 ND C YPL119C-A gene taxon:4932 20030730 SGD
+SGD S000028859 YPL119C-A GO:0005554 SGD_REF:S000069584 ND F YPL119C-A gene taxon:4932 20030730 SGD
+SGD S000028859 YPL119C-A GO:0000004 SGD_REF:S000069584 ND P YPL119C-A gene taxon:4932 20030730 SGD
+SGD S000006062 YPL141C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YPL141C gene taxon:4932 20031028 SGD
+SGD S000006062 YPL141C GO:0004672 SGD_REF:S000058030|PMID:9020587 ISS F YPL141C gene taxon:4932 20030203 SGD
+SGD S000006062 YPL141C GO:0000004 SGD_REF:S000069584 ND P YPL141C gene taxon:4932 20030203 SGD
+SGD S000006065 YPL144W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YPL144W gene taxon:4932 20031028 SGD
+SGD S000006065 YPL144W GO:0005554 SGD_REF:S000069584 ND F YPL144W gene taxon:4932 20030203 SGD
+SGD S000006065 YPL144W GO:0000723 SGD_REF:S000114270|PMID:15161972 IMP P YPL144W gene taxon:4932 20060214 SGD
+SGD S000006071 YPL150W GO:0008372 SGD_REF:S000069584 ND C YPL150W gene taxon:4932 20030204 SGD
+SGD S000006071 YPL150W GO:0004672 SGD_REF:S000058030|PMID:9020587 ISS F YPL150W gene taxon:4932 20030204 SGD
+SGD S000006071 YPL150W GO:0000004 SGD_REF:S000069584 ND P YPL150W gene taxon:4932 20030204 SGD
+SGD S000028721 YPL152W-A GO:0008372 SGD_REF:S000069584 ND C YPL152W-A gene taxon:4932 20030730 SGD
+SGD S000028721 YPL152W-A GO:0005554 SGD_REF:S000069584 ND F YPL152W-A gene taxon:4932 20030730 SGD
+SGD S000028721 YPL152W-A GO:0000004 SGD_REF:S000069584 ND P YPL152W-A gene taxon:4932 20030730 SGD
+SGD S000006079 YPL158C GO:0005935 SGD_REF:S000074185|PMID:14562095 IDA C YPL158C gene taxon:4932 20031028 SGD
+SGD S000006079 YPL158C GO:0005554 SGD_REF:S000069584 ND F YPL158C gene taxon:4932 20030205 SGD
+SGD S000006079 YPL158C GO:0000004 SGD_REF:S000069584 ND P YPL158C gene taxon:4932 20030205 SGD
+SGD S000006083 YPL162C GO:0000329 SGD_REF:S000074185|PMID:14562095 IDA C YPL162C gene taxon:4932 20031028 SGD
+SGD S000006083 YPL162C GO:0005554 SGD_REF:S000069584 ND F YPL162C gene taxon:4932 20030203 SGD
+SGD S000006083 YPL162C GO:0000004 SGD_REF:S000069584 ND P YPL162C gene taxon:4932 20030203 SGD
+SGD S000006089 YPL168W GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YPL168W gene taxon:4932 20031028 SGD
+SGD S000006089 YPL168W GO:0005554 SGD_REF:S000069584 ND F YPL168W gene taxon:4932 20030203 SGD
+SGD S000006089 YPL168W GO:0000004 SGD_REF:S000069584 ND P YPL168W gene taxon:4932 20030203 SGD
+SGD S000006104 YPL183C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YPL183C gene taxon:4932 20031028 SGD
+SGD S000006104 YPL183C GO:0005554 SGD_REF:S000069584 ND F YPL183C gene taxon:4932 20021126 SGD
+SGD S000006104 YPL183C GO:0000004 SGD_REF:S000069584 ND P YPL183C gene taxon:4932 20021126 SGD
+SGD S000007224 YPL183W-A GO:0005762 SGD_REF:S000071753|PMID:12392552 ISS C YPL183W-A|GON5 gene taxon:4932 20040203 SGD
+SGD S000007224 YPL183W-A GO:0003735 SGD_REF:S000058440|PMID:9392081 ISS F YPL183W-A|GON5 gene taxon:4932 20010102 SGD
+SGD S000007224 YPL183W-A GO:0043037 SGD_REF:S000058440|PMID:9392081 ISS P YPL183W-A|GON5 gene taxon:4932 20010102 SGD
+SGD S000006105 YPL184C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YPL184C gene taxon:4932 20031028 SGD
+SGD S000006105 YPL184C GO:0005554 SGD_REF:S000069584 ND F YPL184C gene taxon:4932 20021126 SGD
+SGD S000006105 YPL184C GO:0000004 SGD_REF:S000069584 ND P YPL184C gene taxon:4932 20021126 SGD
+SGD S000028527 YPL189C-A GO:0008372 SGD_REF:S000069584 ND C YPL189C-A gene taxon:4932 20030730 SGD
+SGD S000028527 YPL189C-A GO:0005554 SGD_REF:S000069584 ND F YPL189C-A gene taxon:4932 20030730 SGD
+SGD S000028527 YPL189C-A GO:0000004 SGD_REF:S000069584 ND P YPL189C-A gene taxon:4932 20030730 SGD
+SGD S000006112 YPL191C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YPL191C gene taxon:4932 20031028 SGD
+SGD S000006112 YPL191C GO:0005554 SGD_REF:S000069584 ND F YPL191C gene taxon:4932 20030203 SGD
+SGD S000006112 YPL191C GO:0000004 SGD_REF:S000069584 ND P YPL191C gene taxon:4932 20030203 SGD
+SGD S000006120 YPL199C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YPL199C gene taxon:4932 20031028 SGD
+SGD S000006120 YPL199C GO:0005554 SGD_REF:S000069584 ND F YPL199C gene taxon:4932 20021126 SGD
+SGD S000006120 YPL199C GO:0000004 SGD_REF:S000069584 ND P YPL199C gene taxon:4932 20021126 SGD
+SGD S000006127 YPL206C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YPL206C gene taxon:4932 20031028 SGD
+SGD S000006127 YPL206C GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YPL206C gene taxon:4932 20040928 SGD
+SGD S000006127 YPL206C GO:0005783 SGD_REF:S000072636|PMID:12514182 IDA C YPL206C gene taxon:4932 20031014 SGD
+SGD S000006127 YPL206C GO:0008889 SGD_REF:S000086509|PMID:16141200 ISS F YPL206C gene taxon:4932 20050923 SGD
+SGD S000006127 YPL206C GO:0046475 SGD_REF:S000086509|PMID:16141200 ISS P YPL206C gene taxon:4932 20050923 SGD
+SGD S000006137 YPL216W GO:0008372 SGD_REF:S000069584 ND C YPL216W gene taxon:4932 20030203 SGD
+SGD S000006137 YPL216W GO:0005554 SGD_REF:S000069584 ND F YPL216W gene taxon:4932 20030203 SGD
+SGD S000006137 YPL216W GO:0000004 SGD_REF:S000069584 ND P YPL216W gene taxon:4932 20030203 SGD
+SGD S000006146 YPL225W GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YPL225W gene taxon:4932 20020507 SGD
+SGD S000006146 YPL225W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YPL225W gene taxon:4932 20031028 SGD
+SGD S000006146 YPL225W GO:0005554 SGD_REF:S000069584 ND F YPL225W gene taxon:4932 20030203 SGD
+SGD S000006146 YPL225W GO:0000004 SGD_REF:S000069584 ND P YPL225W gene taxon:4932 20030203 SGD
+SGD S000006150 YPL229W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YPL229W gene taxon:4932 20031028 SGD
+SGD S000006150 YPL229W GO:0005554 SGD_REF:S000069584 ND F YPL229W gene taxon:4932 20021126 SGD
+SGD S000006150 YPL229W GO:0000004 SGD_REF:S000069584 ND P YPL229W gene taxon:4932 20021126 SGD
+SGD S000006151 YPL230W GO:0008372 SGD_REF:S000069584 ND C YPL230W gene taxon:4932 20021126 SGD
+SGD S000006151 YPL230W GO:0005554 SGD_REF:S000069584 ND F YPL230W gene taxon:4932 20021126 SGD
+SGD S000006151 YPL230W GO:0000004 SGD_REF:S000069584 ND P YPL230W gene taxon:4932 20021126 SGD
+SGD S000006157 YPL236C GO:0000329 SGD_REF:S000074185|PMID:14562095 IDA C YPL236C gene taxon:4932 20031028 SGD
+SGD S000006157 YPL236C GO:0004672 SGD_REF:S000063991|PMID:9817935 ISS F YPL236C gene taxon:4932 20030204 SGD
+SGD S000006157 YPL236C GO:0000004 SGD_REF:S000069584 ND P YPL236C gene taxon:4932 20030203 SGD
+SGD S000006166 YPL245W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YPL245W gene taxon:4932 20031028 SGD
+SGD S000006166 YPL245W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YPL245W gene taxon:4932 20031028 SGD
+SGD S000006166 YPL245W GO:0005554 SGD_REF:S000069584 ND F YPL245W gene taxon:4932 20021126 SGD
+SGD S000006166 YPL245W GO:0000004 SGD_REF:S000069584 ND P YPL245W gene taxon:4932 20021126 SGD
+SGD S000006168 YPL247C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YPL247C gene taxon:4932 20031028 SGD
+SGD S000006168 YPL247C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YPL247C gene taxon:4932 20031028 SGD
+SGD S000006168 YPL247C GO:0005554 SGD_REF:S000069584 ND F YPL247C gene taxon:4932 20030203 SGD
+SGD S000006168 YPL247C GO:0000004 SGD_REF:S000069584 ND P YPL247C gene taxon:4932 20030203 SGD
+SGD S000006178 YPL257W GO:0008372 SGD_REF:S000069584 ND C YPL257W gene taxon:4932 20021126 SGD
+SGD S000006178 YPL257W GO:0005554 SGD_REF:S000069584 ND F YPL257W gene taxon:4932 20021126 SGD
+SGD S000006178 YPL257W GO:0000004 SGD_REF:S000069584 ND P YPL257W gene taxon:4932 20021126 SGD
+SGD S000007357 YPL257W-A GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YPL257W-A gene taxon:4932 20030811 SGD
+SGD S000007357 YPL257W-A GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YPL257W-A gene taxon:4932 20030811 SGD
+SGD S000007357 YPL257W-A GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YPL257W-A gene taxon:4932 20030811 SGD
+SGD S000007357 YPL257W-A GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YPL257W-A gene taxon:4932 20030811 SGD
+SGD S000007358 YPL257W-B GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YPL257W-B gene taxon:4932 20030811 SGD
+SGD S000007358 YPL257W-B GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YPL257W-B gene taxon:4932 20030811 SGD
+SGD S000007358 YPL257W-B GO:0003887 SGD_REF:S000072465|PMID:9582191 ISS F YPL257W-B gene taxon:4932 20030819 SGD
+SGD S000007358 YPL257W-B GO:0003964 SGD_REF:S000072465|PMID:9582191 ISS F YPL257W-B gene taxon:4932 20030819 SGD
+SGD S000007358 YPL257W-B GO:0004540 SGD_REF:S000072465|PMID:9582191 ISS F YPL257W-B gene taxon:4932 20030819 SGD
+SGD S000007358 YPL257W-B GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YPL257W-B gene taxon:4932 20030811 SGD
+SGD S000007358 YPL257W-B GO:0008233 SGD_REF:S000072465|PMID:9582191 ISS F YPL257W-B gene taxon:4932 20030819 SGD
+SGD S000007358 YPL257W-B GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YPL257W-B gene taxon:4932 20030811 SGD
+SGD S000006181 YPL260W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YPL260W gene taxon:4932 20031028 SGD
+SGD S000006181 YPL260W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YPL260W gene taxon:4932 20031028 SGD
+SGD S000006181 YPL260W GO:0005554 SGD_REF:S000069584 ND F YPL260W gene taxon:4932 20030203 SGD
+SGD S000006181 YPL260W GO:0000004 SGD_REF:S000069584 ND P YPL260W gene taxon:4932 20030203 SGD
+SGD S000006185 YPL264C GO:0016021 SGD_REF:S000072825|PMID:12524434 ISS C YPL264C gene taxon:4932 20030409 SGD
+SGD S000006185 YPL264C GO:0005554 SGD_REF:S000069584 ND F YPL264C gene taxon:4932 20021120 SGD
+SGD S000006185 YPL264C GO:0000004 SGD_REF:S000069584 ND P YPL264C gene taxon:4932 20021120 SGD
+SGD S000006193 YPL272C GO:0008372 SGD_REF:S000069584 ND C YPL272C gene taxon:4932 20021126 SGD
+SGD S000006193 YPL272C GO:0005554 SGD_REF:S000069584 ND F YPL272C gene taxon:4932 20021126 SGD
+SGD S000006193 YPL272C GO:0000004 SGD_REF:S000069584 ND P YPL272C gene taxon:4932 20021126 SGD
+SGD S000006197 YPL276W GO:0008372 SGD_REF:S000069584 ND C YPL276W|FDH2 gene taxon:4932 20040617 SGD
+SGD S000006197 YPL276W GO:0008863 SGD_REF:S000069478|PMID:11921099 IGI F YPL276W|FDH2 gene taxon:4932 20040617 SGD
+SGD S000006197 YPL276W GO:0008863 SGD_REF:S000069478|PMID:11921099 ISS F YPL276W|FDH2 gene taxon:4932 20040617 SGD
+SGD S000006197 YPL276W GO:0042183 SGD_REF:S000069478|PMID:11921099 IGI P YPL276W|FDH2 gene taxon:4932 20040617 SGD
+SGD S000006197 YPL276W GO:0042183 SGD_REF:S000069478|PMID:11921099 TAS P YPL276W|FDH2 gene taxon:4932 20040617 SGD
+SGD S000006198 YPL277C GO:0005624 SGD_REF:S000075303|PMID:11935221 IDA C YPL277C gene taxon:4932 20040114 SGD
+SGD S000006198 YPL277C GO:0005554 SGD_REF:S000069584 ND F YPL277C gene taxon:4932 20030205 SGD
+SGD S000006198 YPL277C GO:0000004 SGD_REF:S000069584 ND P YPL277C gene taxon:4932 20030205 SGD
+SGD S000006199 YPL278C GO:0008372 SGD_REF:S000069584 ND C YPL278C gene taxon:4932 20021126 SGD
+SGD S000006199 YPL278C GO:0005554 SGD_REF:S000069584 ND F YPL278C gene taxon:4932 20021126 SGD
+SGD S000006199 YPL278C GO:0000004 SGD_REF:S000069584 ND P YPL278C gene taxon:4932 20021126 SGD
+SGD S000006200 YPL279C GO:0008372 SGD_REF:S000069584 ND C YPL279C gene taxon:4932 20021126 SGD
+SGD S000006200 YPL279C GO:0005554 SGD_REF:S000069584 ND F YPL279C gene taxon:4932 20021126 SGD
+SGD S000006200 YPL279C GO:0000004 SGD_REF:S000069584 ND P YPL279C gene taxon:4932 20021126 SGD
+SGD S000006207 YPR003C GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YPR003C gene taxon:4932 20031028 SGD
+SGD S000006207 YPR003C GO:0005554 SGD_REF:S000069584 ND F YPR003C gene taxon:4932 20030203 SGD
+SGD S000006207 YPR003C GO:0000004 SGD_REF:S000069584 ND P YPR003C gene taxon:4932 20030203 SGD
+SGD S000006208 YPR004C GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YPR004C gene taxon:4932 20031028 SGD
+SGD S000006208 YPR004C GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YPR004C gene taxon:4932 20031210 SGD
+SGD S000006208 YPR004C GO:0009055 SGD_REF:S000068875|PMID:11502169 NAS F YPR004C gene taxon:4932 20030224 SGD
+SGD S000006208 YPR004C GO:0000004 SGD_REF:S000069584 ND P YPR004C gene taxon:4932 20021120 SGD
+SGD S000006215 YPR011C GO:0005743 SGD_REF:S000049213|PMID:10930523 ISS C YPR011C gene taxon:4932 20021017 SGD
+SGD S000006215 YPR011C GO:0005215 SGD_REF:S000049213|PMID:10930523 ISS F YPR011C gene taxon:4932 20021017 SGD
+SGD S000006215 YPR011C GO:0006810 SGD_REF:S000049213|PMID:10930523 ISS P YPR011C gene taxon:4932 20021017 SGD
+SGD S000006217 YPR013C GO:0008372 SGD_REF:S000069584 ND C YPR013C gene taxon:4932 20021126 SGD
+SGD S000006217 YPR013C GO:0005554 SGD_REF:S000069584 ND F YPR013C gene taxon:4932 20021126 SGD
+SGD S000006217 YPR013C GO:0000004 SGD_REF:S000069584 ND P YPR013C gene taxon:4932 20021126 SGD
+SGD S000006219 YPR015C GO:0008372 SGD_REF:S000069584 ND C YPR015C gene taxon:4932 20021126 SGD
+SGD S000006219 YPR015C GO:0005554 SGD_REF:S000069584 ND F YPR015C gene taxon:4932 20021126 SGD
+SGD S000006219 YPR015C GO:0000004 SGD_REF:S000069584 ND P YPR015C gene taxon:4932 20021126 SGD
+SGD S000006226 YPR022C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YPR022C gene taxon:4932 20031028 SGD
+SGD S000006226 YPR022C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YPR022C gene taxon:4932 20031028 SGD
+SGD S000006226 YPR022C GO:0005554 SGD_REF:S000069584 ND F YPR022C gene taxon:4932 20030203 SGD
+SGD S000006226 YPR022C GO:0000004 SGD_REF:S000069584 ND P YPR022C gene taxon:4932 20030203 SGD
+SGD S000006231 YPR027C GO:0008372 SGD_REF:S000069584 ND C YPR027C gene taxon:4932 20021126 SGD
+SGD S000006231 YPR027C GO:0005554 SGD_REF:S000069584 ND F YPR027C gene taxon:4932 20021126 SGD
+SGD S000006231 YPR027C GO:0000004 SGD_REF:S000069584 ND P YPR027C gene taxon:4932 20021126 SGD
+SGD S000028425 YPR036W-A GO:0008372 SGD_REF:S000069584 ND C YPR036W-A gene taxon:4932 20020925 SGD
+SGD S000028425 YPR036W-A GO:0005554 SGD_REF:S000069584 ND F YPR036W-A gene taxon:4932 20020925 SGD
+SGD S000028425 YPR036W-A GO:0042493 SGD_REF:S000070169|PMID:11557050 IEP P YPR036W-A gene taxon:4932 20021107 SGD
+SGD S000028425 YPR036W-A GO:0042493 SGD_REF:S000070169|PMID:11557050 ISS P YPR036W-A gene taxon:4932 20021107 SGD
+SGD S000006249 YPR045C GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YPR045C gene taxon:4932 20031028 SGD
+SGD S000006249 YPR045C GO:0005554 SGD_REF:S000069584 ND F YPR045C gene taxon:4932 20030203 SGD
+SGD S000006249 YPR045C GO:0000004 SGD_REF:S000069584 ND P YPR045C gene taxon:4932 20030203 SGD
+SGD S000006267 YPR063C GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YPR063C gene taxon:4932 20031028 SGD
+SGD S000006267 YPR063C GO:0005554 SGD_REF:S000069584 ND F YPR063C gene taxon:4932 20021120 SGD
+SGD S000006267 YPR063C GO:0000004 SGD_REF:S000069584 ND P YPR063C gene taxon:4932 20021120 SGD
+SGD S000006275 YPR071W GO:0016021 SGD_REF:S000072825|PMID:12524434 ISS C YPR071W gene taxon:4932 20030409 SGD
+SGD S000006275 YPR071W GO:0005554 SGD_REF:S000069584 ND F YPR071W gene taxon:4932 20030203 SGD
+SGD S000006275 YPR071W GO:0000004 SGD_REF:S000069584 ND P YPR071W gene taxon:4932 20030203 SGD
+SGD S000006282 YPR078C GO:0008372 SGD_REF:S000069584 ND C YPR078C gene taxon:4932 20021004 SGD
+SGD S000006282 YPR078C GO:0005554 SGD_REF:S000069584 ND F YPR078C gene taxon:4932 20021004 SGD
+SGD S000006282 YPR078C GO:0006259 SGD_REF:S000043176|PMID:10051619 IGI P YPR078C gene taxon:4932 20021004 SGD
+SGD S000006282 YPR078C GO:0007126 SGD_REF:S000043176|PMID:10051619 IEP P YPR078C gene taxon:4932 20021004 SGD
+SGD S000006288 YPR084W GO:0008372 SGD_REF:S000069584 ND C YPR084W gene taxon:4932 20021126 SGD
+SGD S000006288 YPR084W GO:0005554 SGD_REF:S000069584 ND F YPR084W gene taxon:4932 20021126 SGD
+SGD S000006288 YPR084W GO:0000004 SGD_REF:S000069584 ND P YPR084W gene taxon:4932 20021126 SGD
+SGD S000006289 YPR085C GO:0008372 SGD_REF:S000069584 ND C YPR085C gene taxon:4932 20021126 SGD
+SGD S000006289 YPR085C GO:0005554 SGD_REF:S000069584 ND F YPR085C gene taxon:4932 20021126 SGD
+SGD S000006289 YPR085C GO:0000004 SGD_REF:S000069584 ND P YPR085C gene taxon:4932 20021126 SGD
+SGD S000006293 YPR089W GO:0008372 SGD_REF:S000069584 ND C YPR089W|YPR090W gene taxon:4932 20021126 SGD
+SGD S000006293 YPR089W GO:0005554 SGD_REF:S000069584 ND F YPR089W|YPR090W gene taxon:4932 20021126 SGD
+SGD S000006293 YPR089W GO:0000004 SGD_REF:S000069584 ND P YPR089W|YPR090W gene taxon:4932 20021126 SGD
+SGD S000006295 YPR091C GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YPR091C gene taxon:4932 20031028 SGD
+SGD S000006295 YPR091C GO:0005554 SGD_REF:S000069584 ND F YPR091C gene taxon:4932 20021126 SGD
+SGD S000006295 YPR091C GO:0000004 SGD_REF:S000069584 ND P YPR091C gene taxon:4932 20021126 SGD
+SGD S000006301 YPR097W GO:0005739 SGD_REF:S000075100|PMID:14576278 IDA C YPR097W gene taxon:4932 20040813 SGD
+SGD S000006301 YPR097W GO:0005554 SGD_REF:S000069584 ND F YPR097W gene taxon:4932 20030203 SGD
+SGD S000006301 YPR097W GO:0000004 SGD_REF:S000069584 ND P YPR097W gene taxon:4932 20030203 SGD
+SGD S000006302 YPR098C GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YPR098C gene taxon:4932 20031028 SGD
+SGD S000006302 YPR098C GO:0005741 SGD_REF:S000114057|PMID:16407407 IDA C YPR098C gene taxon:4932 20060317 SGD
+SGD S000006302 YPR098C GO:0005554 SGD_REF:S000069584 ND F YPR098C gene taxon:4932 20021126 SGD
+SGD S000006302 YPR098C GO:0000004 SGD_REF:S000069584 ND P YPR098C gene taxon:4932 20021126 SGD
+SGD S000028590 YPR108W-A GO:0008372 SGD_REF:S000069584 ND C YPR108W-A gene taxon:4932 20030730 SGD
+SGD S000028590 YPR108W-A GO:0005554 SGD_REF:S000069584 ND F YPR108W-A gene taxon:4932 20030730 SGD
+SGD S000028590 YPR108W-A GO:0000004 SGD_REF:S000069584 ND P YPR108W-A gene taxon:4932 20030730 SGD
+SGD S000006313 YPR109W GO:0008372 SGD_REF:S000069584 ND C YPR109W gene taxon:4932 20021126 SGD
+SGD S000006313 YPR109W GO:0005554 SGD_REF:S000069584 ND F YPR109W gene taxon:4932 20021126 SGD
+SGD S000006313 YPR109W GO:0000004 SGD_REF:S000069584 ND P YPR109W gene taxon:4932 20021126 SGD
+SGD S000006318 YPR114W GO:0005783 SGD_REF:S000074185|PMID:14562095 IDA C YPR114W gene taxon:4932 20031028 SGD
+SGD S000006318 YPR114W GO:0005554 SGD_REF:S000069584 ND F YPR114W gene taxon:4932 20021126 SGD
+SGD S000006318 YPR114W GO:0000004 SGD_REF:S000069584 ND P YPR114W gene taxon:4932 20021126 SGD
+SGD S000006319 YPR115W GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YPR115W gene taxon:4932 20020507 SGD
+SGD S000006319 YPR115W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YPR115W gene taxon:4932 20031028 SGD
+SGD S000006319 YPR115W GO:0005554 SGD_REF:S000069584 ND F YPR115W gene taxon:4932 20030203 SGD
+SGD S000006319 YPR115W GO:0000004 SGD_REF:S000069584 ND P YPR115W gene taxon:4932 20030203 SGD
+SGD S000006320 YPR116W GO:0005739 SGD_REF:S000074185|PMID:14562095 IDA C YPR116W gene taxon:4932 20031028 SGD
+SGD S000006320 YPR116W GO:0005554 SGD_REF:S000069584 ND F YPR116W gene taxon:4932 20021126 SGD
+SGD S000006320 YPR116W GO:0000004 SGD_REF:S000069584 ND P YPR116W gene taxon:4932 20021126 SGD
+SGD S000006321 YPR117W GO:0008372 SGD_REF:S000069584 ND C YPR117W gene taxon:4932 20021126 SGD
+SGD S000006321 YPR117W GO:0005554 SGD_REF:S000069584 ND F YPR117W gene taxon:4932 20021126 SGD
+SGD S000006321 YPR117W GO:0000004 SGD_REF:S000069584 ND P YPR117W gene taxon:4932 20021126 SGD
+SGD S000006322 YPR118W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YPR118W gene taxon:4932 20031028 SGD
+SGD S000006322 YPR118W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YPR118W gene taxon:4932 20031028 SGD
+SGD S000006322 YPR118W GO:0050261 SGD_REF:S000077022|PMID:15215245 ISS UniProt:O31662 F YPR118W gene taxon:4932 20040917 SGD
+SGD S000006322 YPR118W GO:0019509 SGD_REF:S000077022|PMID:15215245 IMP P YPR118W gene taxon:4932 20040917 SGD
+SGD S000006331 YPR127W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YPR127W gene taxon:4932 20031028 SGD
+SGD S000006331 YPR127W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YPR127W gene taxon:4932 20031028 SGD
+SGD S000006331 YPR127W GO:0005554 SGD_REF:S000069584 ND F YPR127W gene taxon:4932 20030203 SGD
+SGD S000006331 YPR127W GO:0000004 SGD_REF:S000069584 ND P YPR127W gene taxon:4932 20030203 SGD
+SGD S000007359 YPR137C-A GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YPR137C-A gene taxon:4932 20030811 SGD
+SGD S000007359 YPR137C-A GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YPR137C-A gene taxon:4932 20030811 SGD
+SGD S000007359 YPR137C-A GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YPR137C-A gene taxon:4932 20030811 SGD
+SGD S000007359 YPR137C-A GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YPR137C-A gene taxon:4932 20030811 SGD
+SGD S000007360 YPR137C-B GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YPR137C-B gene taxon:4932 20030811 SGD
+SGD S000007360 YPR137C-B GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YPR137C-B gene taxon:4932 20030811 SGD
+SGD S000007360 YPR137C-B GO:0003887 SGD_REF:S000072465|PMID:9582191 ISS F YPR137C-B gene taxon:4932 20030811 SGD
+SGD S000007360 YPR137C-B GO:0003964 SGD_REF:S000072465|PMID:9582191 ISS F YPR137C-B gene taxon:4932 20030811 SGD
+SGD S000007360 YPR137C-B GO:0004540 SGD_REF:S000072465|PMID:9582191 ISS F YPR137C-B gene taxon:4932 20030811 SGD
+SGD S000007360 YPR137C-B GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YPR137C-B gene taxon:4932 20030811 SGD
+SGD S000007360 YPR137C-B GO:0008233 SGD_REF:S000072465|PMID:9582191 ISS F YPR137C-B gene taxon:4932 20030811 SGD
+SGD S000007360 YPR137C-B GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YPR137C-B gene taxon:4932 20030811 SGD
+SGD S000113589 YPR145C-A GO:0008372 SGD_REF:S000069584 ND C YPR145C-A gene taxon:4932 20051121 SGD
+SGD S000113589 YPR145C-A GO:0005554 SGD_REF:S000069584 ND F YPR145C-A gene taxon:4932 20051121 SGD
+SGD S000113589 YPR145C-A GO:0000004 SGD_REF:S000069584 ND P YPR145C-A gene taxon:4932 20051121 SGD
+SGD S000006351 YPR147C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YPR147C gene taxon:4932 20031028 SGD
+SGD S000006351 YPR147C GO:0005554 SGD_REF:S000069584 ND F YPR147C gene taxon:4932 20021126 SGD
+SGD S000006351 YPR147C GO:0000004 SGD_REF:S000069584 ND P YPR147C gene taxon:4932 20021126 SGD
+SGD S000006352 YPR148C GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YPR148C gene taxon:4932 20031028 SGD
+SGD S000006352 YPR148C GO:0005554 SGD_REF:S000069584 ND F YPR148C gene taxon:4932 20021126 SGD
+SGD S000006352 YPR148C GO:0000004 SGD_REF:S000069584 ND P YPR148C gene taxon:4932 20021126 SGD
+SGD S000006357 YPR153W GO:0008372 SGD_REF:S000069584 ND C YPR153W gene taxon:4932 20021029 SGD
+SGD S000006357 YPR153W GO:0005554 SGD_REF:S000069584 ND F YPR153W gene taxon:4932 20021029 SGD
+SGD S000006357 YPR153W GO:0000004 SGD_REF:S000069584 ND P YPR153W gene taxon:4932 20021029 SGD
+SGD S000006361 YPR157W GO:0008372 SGD_REF:S000069584 ND C YPR157W gene taxon:4932 20021126 SGD
+SGD S000006361 YPR157W GO:0005554 SGD_REF:S000069584 ND F YPR157W gene taxon:4932 20021126 SGD
+SGD S000006361 YPR157W GO:0000004 SGD_REF:S000069584 ND P YPR157W gene taxon:4932 20021126 SGD
+SGD S000007361 YPR158C-C GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YPR158C-C gene taxon:4932 20030811 SGD
+SGD S000007361 YPR158C-C GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YPR158C-C gene taxon:4932 20030811 SGD
+SGD S000007361 YPR158C-C GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YPR158C-C gene taxon:4932 20030811 SGD
+SGD S000007361 YPR158C-C GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YPR158C-C gene taxon:4932 20030811 SGD
+SGD S000007362 YPR158C-D GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YPR158C-D gene taxon:4932 20030811 SGD
+SGD S000007362 YPR158C-D GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YPR158C-D gene taxon:4932 20030811 SGD
+SGD S000007362 YPR158C-D GO:0003887 SGD_REF:S000072465|PMID:9582191 ISS F YPR158C-D gene taxon:4932 20030811 SGD
+SGD S000007362 YPR158C-D GO:0003964 SGD_REF:S000072465|PMID:9582191 ISS F YPR158C-D gene taxon:4932 20030811 SGD
+SGD S000007362 YPR158C-D GO:0004540 SGD_REF:S000072465|PMID:9582191 ISS F YPR158C-D gene taxon:4932 20030811 SGD
+SGD S000007362 YPR158C-D GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YPR158C-D gene taxon:4932 20030811 SGD
+SGD S000007362 YPR158C-D GO:0008233 SGD_REF:S000072465|PMID:9582191 ISS F YPR158C-D gene taxon:4932 20030811 SGD
+SGD S000007362 YPR158C-D GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YPR158C-D gene taxon:4932 20030811 SGD
+SGD S000006362 YPR158W GO:0008372 SGD_REF:S000069584 ND C YPR158W gene taxon:4932 20010119 SGD
+SGD S000006362 YPR158W GO:0005554 SGD_REF:S000069584 ND F YPR158W gene taxon:4932 20010119 SGD
+SGD S000006362 YPR158W GO:0000004 SGD_REF:S000069584 ND P YPR158W gene taxon:4932 20010119 SGD
+SGD S000007363 YPR158W-A GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YPR158W-A gene taxon:4932 20030811 SGD
+SGD S000007363 YPR158W-A GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YPR158W-A gene taxon:4932 20030811 SGD
+SGD S000007363 YPR158W-A GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YPR158W-A gene taxon:4932 20030811 SGD
+SGD S000007363 YPR158W-A GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YPR158W-A gene taxon:4932 20030811 SGD
+SGD S000007364 YPR158W-B GO:0000943 SGD_REF:S000072465|PMID:9582191 ISS C YPR158W-B gene taxon:4932 20030811 SGD
+SGD S000007364 YPR158W-B GO:0003723 SGD_REF:S000072465|PMID:9582191 ISS F YPR158W-B gene taxon:4932 20030811 SGD
+SGD S000007364 YPR158W-B GO:0003887 SGD_REF:S000072465|PMID:9582191 ISS F YPR158W-B gene taxon:4932 20030811 SGD
+SGD S000007364 YPR158W-B GO:0003964 SGD_REF:S000072465|PMID:9582191 ISS F YPR158W-B gene taxon:4932 20030811 SGD
+SGD S000007364 YPR158W-B GO:0004540 SGD_REF:S000072465|PMID:9582191 ISS F YPR158W-B gene taxon:4932 20030811 SGD
+SGD S000007364 YPR158W-B GO:0005515 SGD_REF:S000072465|PMID:9582191 ISS F YPR158W-B gene taxon:4932 20030811 SGD
+SGD S000007364 YPR158W-B GO:0008233 SGD_REF:S000072465|PMID:9582191 ISS F YPR158W-B gene taxon:4932 20030811 SGD
+SGD S000007364 YPR158W-B GO:0006319 SGD_REF:S000072465|PMID:9582191 ISS P YPR158W-B gene taxon:4932 20030811 SGD
+SGD S000028725 YPR159C-A GO:0008372 SGD_REF:S000069584 ND C YPR159C-A gene taxon:4932 20030730 SGD
+SGD S000028725 YPR159C-A GO:0005554 SGD_REF:S000069584 ND F YPR159C-A gene taxon:4932 20030730 SGD
+SGD S000028725 YPR159C-A GO:0000004 SGD_REF:S000069584 ND P YPR159C-A gene taxon:4932 20030730 SGD
+SGD S000006376 YPR172W GO:0005634 SGD_REF:S000074185|PMID:14562095 IDA C YPR172W gene taxon:4932 20031028 SGD
+SGD S000006376 YPR172W GO:0005737 SGD_REF:S000069459|PMID:11914276 IDA C YPR172W gene taxon:4932 20020507 SGD
+SGD S000006376 YPR172W GO:0005737 SGD_REF:S000074185|PMID:14562095 IDA C YPR172W gene taxon:4932 20031028 SGD
+SGD S000006376 YPR172W GO:0005554 SGD_REF:S000069584 ND F YPR172W gene taxon:4932 20030203 SGD
+SGD S000006376 YPR172W GO:0000004 SGD_REF:S000069584 ND P YPR172W gene taxon:4932 20030203 SGD
+SGD S000006378 YPR174C GO:0005635 SGD_REF:S000077144|PMID:15282802 IDA C YPR174C gene taxon:4932 20041008 SGD
+SGD S000006378 YPR174C GO:0005816 SGD_REF:S000077144|PMID:15282802 IDA C YPR174C gene taxon:4932 20041008 SGD
+SGD S000006378 YPR174C GO:0005554 SGD_REF:S000069584 ND F YPR174C gene taxon:4932 20021126 SGD
+SGD S000006378 YPR174C GO:0000004 SGD_REF:S000069584 ND P YPR174C gene taxon:4932 20021126 SGD
+SGD S000006400 YPR196W GO:0008372 SGD_REF:S000069584 ND C YPR196W gene taxon:4932 20021205 SGD
+SGD S000006400 YPR196W GO:0005554 SGD_REF:S000069584 ND F YPR196W gene taxon:4932 20010119 SGD
+SGD S000006400 YPR196W GO:0000004 SGD_REF:S000069584 ND P YPR196W gene taxon:4932 20010119 SGD
+SGD S000006406 YPR202W GO:0008372 SGD_REF:S000069584 ND C YPR202W gene taxon:4932 20010119 SGD
+SGD S000006406 YPR202W GO:0005554 SGD_REF:S000069584 ND F YPR202W gene taxon:4932 20010119 SGD
+SGD S000006406 YPR202W GO:0000004 SGD_REF:S000069584 ND P YPR202W gene taxon:4932 20010119 SGD
+SGD S000006407 YPR203W GO:0008372 SGD_REF:S000069584 ND C YPR203W gene taxon:4932 20010119 SGD
+SGD S000006407 YPR203W GO:0005554 SGD_REF:S000069584 ND F YPR203W gene taxon:4932 20010119 SGD
+SGD S000006407 YPR203W GO:0000004 SGD_REF:S000069584 ND P YPR203W gene taxon:4932 20010119 SGD
+SGD S000006408 YPR204W GO:0008372 SGD_REF:S000069584 ND C YPR204W gene taxon:4932 20010119 SGD
+SGD S000006408 YPR204W GO:0003678 SGD_REF:S000053946|PMID:9837911 IDA F YPR204W gene taxon:4932 20010301 SGD
+SGD S000006408 YPR204W GO:0000004 SGD_REF:S000069584 ND P YPR204W gene taxon:4932 20010119 SGD
+SGD S000006510 tA(AGC)D GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tA(AGC)D gene taxon:4932 20030507 SGD
+SGD S000006510 tA(AGC)D GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tA(AGC)D gene taxon:4932 20030507 SGD
+SGD S000006510 tA(AGC)D GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tA(AGC)D gene taxon:4932 20030507 SGD
+SGD S000006511 tA(AGC)F GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tA(AGC)F gene taxon:4932 20030507 SGD
+SGD S000006511 tA(AGC)F GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tA(AGC)F gene taxon:4932 20030507 SGD
+SGD S000006511 tA(AGC)F GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tA(AGC)F gene taxon:4932 20030507 SGD
+SGD S000006512 tA(AGC)G GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tA(AGC)G gene taxon:4932 20030507 SGD
+SGD S000006512 tA(AGC)G GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tA(AGC)G gene taxon:4932 20030507 SGD
+SGD S000006512 tA(AGC)G GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tA(AGC)G gene taxon:4932 20030507 SGD
+SGD S000006513 tA(AGC)H GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tA(AGC)H gene taxon:4932 20030507 SGD
+SGD S000006513 tA(AGC)H GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tA(AGC)H gene taxon:4932 20030507 SGD
+SGD S000006513 tA(AGC)H GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tA(AGC)H gene taxon:4932 20030507 SGD
+SGD S000006514 tA(AGC)J GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tA(AGC)J gene taxon:4932 20030507 SGD
+SGD S000006514 tA(AGC)J GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tA(AGC)J gene taxon:4932 20030507 SGD
+SGD S000006514 tA(AGC)J GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tA(AGC)J gene taxon:4932 20030507 SGD
+SGD S000006515 tA(AGC)K1 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tA(AGC)K1 gene taxon:4932 20030507 SGD
+SGD S000006515 tA(AGC)K1 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tA(AGC)K1 gene taxon:4932 20030507 SGD
+SGD S000006515 tA(AGC)K1 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tA(AGC)K1 gene taxon:4932 20030507 SGD
+SGD S000006516 tA(AGC)K2 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tA(AGC)K2 gene taxon:4932 20030507 SGD
+SGD S000006516 tA(AGC)K2 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tA(AGC)K2 gene taxon:4932 20030507 SGD
+SGD S000006516 tA(AGC)K2 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tA(AGC)K2 gene taxon:4932 20030507 SGD
+SGD S000006517 tA(AGC)L GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tA(AGC)L gene taxon:4932 20030507 SGD
+SGD S000006517 tA(AGC)L GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tA(AGC)L gene taxon:4932 20030507 SGD
+SGD S000006517 tA(AGC)L GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tA(AGC)L gene taxon:4932 20030507 SGD
+SGD S000006518 tA(AGC)M1 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tA(AGC)M1 gene taxon:4932 20030507 SGD
+SGD S000006518 tA(AGC)M1 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tA(AGC)M1 gene taxon:4932 20030507 SGD
+SGD S000006518 tA(AGC)M1 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tA(AGC)M1 gene taxon:4932 20030507 SGD
+SGD S000006519 tA(AGC)M2 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tA(AGC)M2 gene taxon:4932 20030507 SGD
+SGD S000006519 tA(AGC)M2 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tA(AGC)M2 gene taxon:4932 20030507 SGD
+SGD S000006519 tA(AGC)M2 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tA(AGC)M2 gene taxon:4932 20030507 SGD
+SGD S000006520 tA(AGC)P GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tA(AGC)P gene taxon:4932 20030507 SGD
+SGD S000006520 tA(AGC)P GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tA(AGC)P gene taxon:4932 20030507 SGD
+SGD S000006520 tA(AGC)P GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tA(AGC)P gene taxon:4932 20030507 SGD
+SGD S000006521 tA(UGC)A GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tA(UGC)A gene taxon:4932 20030507 SGD
+SGD S000006521 tA(UGC)A GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tA(UGC)A gene taxon:4932 20030507 SGD
+SGD S000006521 tA(UGC)A GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tA(UGC)A gene taxon:4932 20030507 SGD
+SGD S000006522 tA(UGC)E GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tA(UGC)E gene taxon:4932 20030507 SGD
+SGD S000006522 tA(UGC)E GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tA(UGC)E gene taxon:4932 20030507 SGD
+SGD S000006522 tA(UGC)E GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tA(UGC)E gene taxon:4932 20030507 SGD
+SGD S000006523 tA(UGC)G GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tA(UGC)G gene taxon:4932 20030507 SGD
+SGD S000006523 tA(UGC)G GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tA(UGC)G gene taxon:4932 20030507 SGD
+SGD S000006523 tA(UGC)G GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tA(UGC)G gene taxon:4932 20030507 SGD
+SGD S000006524 tA(UGC)L GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tA(UGC)L gene taxon:4932 20030507 SGD
+SGD S000006524 tA(UGC)L GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tA(UGC)L gene taxon:4932 20030507 SGD
+SGD S000006524 tA(UGC)L GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tA(UGC)L gene taxon:4932 20030507 SGD
+SGD S000006525 tA(UGC)O GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tA(UGC)O gene taxon:4932 20030507 SGD
+SGD S000006525 tA(UGC)O GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tA(UGC)O gene taxon:4932 20030507 SGD
+SGD S000006525 tA(UGC)O GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tA(UGC)O gene taxon:4932 20030507 SGD
+SGD S000007315 tA(UGC)Q GO:0005739 SGD_REF:S000073094|PMID:9159473 NAS C tA(UGC)Q gene taxon:4932 20030507 SGD
+SGD S000007315 tA(UGC)Q GO:0030533 SGD_REF:S000058438|PMID:9872396 NAS F tA(UGC)Q gene taxon:4932 20020220 SGD
+SGD S000007315 tA(UGC)Q GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tA(UGC)Q gene taxon:4932 20030507 SGD
+SGD S000006526 tC(GCA)B GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tC(GCA)B gene taxon:4932 20030507 SGD
+SGD S000006526 tC(GCA)B GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tC(GCA)B gene taxon:4932 20030507 SGD
+SGD S000006526 tC(GCA)B GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tC(GCA)B gene taxon:4932 20030507 SGD
+SGD S000006527 tC(GCA)G GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tC(GCA)G gene taxon:4932 20030507 SGD
+SGD S000006527 tC(GCA)G GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tC(GCA)G gene taxon:4932 20030507 SGD
+SGD S000006527 tC(GCA)G GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tC(GCA)G gene taxon:4932 20030507 SGD
+SGD S000006528 tC(GCA)P1 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tC(GCA)P1 gene taxon:4932 20030507 SGD
+SGD S000006528 tC(GCA)P1 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tC(GCA)P1 gene taxon:4932 20030507 SGD
+SGD S000006528 tC(GCA)P1 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tC(GCA)P1 gene taxon:4932 20030507 SGD
+SGD S000006529 tC(GCA)P2 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tC(GCA)P2 gene taxon:4932 20030507 SGD
+SGD S000006529 tC(GCA)P2 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tC(GCA)P2 gene taxon:4932 20030507 SGD
+SGD S000006529 tC(GCA)P2 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tC(GCA)P2 gene taxon:4932 20030507 SGD
+SGD S000007316 tC(GCA)Q GO:0005739 SGD_REF:S000073094|PMID:9159473 NAS C tC(GCA)Q gene taxon:4932 20030507 SGD
+SGD S000007316 tC(GCA)Q GO:0030533 SGD_REF:S000058438|PMID:9872396 NAS F tC(GCA)Q gene taxon:4932 20020220 SGD
+SGD S000007316 tC(GCA)Q GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tC(GCA)Q gene taxon:4932 20030507 SGD
+SGD S000006530 tD(GUC)B GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tD(GUC)B gene taxon:4932 20030507 SGD
+SGD S000006530 tD(GUC)B GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tD(GUC)B gene taxon:4932 20030507 SGD
+SGD S000006530 tD(GUC)B GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tD(GUC)B gene taxon:4932 20030507 SGD
+SGD S000006531 tD(GUC)D GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tD(GUC)D gene taxon:4932 20030507 SGD
+SGD S000006531 tD(GUC)D GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tD(GUC)D gene taxon:4932 20030507 SGD
+SGD S000006531 tD(GUC)D GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tD(GUC)D gene taxon:4932 20030507 SGD
+SGD S000006532 tD(GUC)G1 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tD(GUC)G1 gene taxon:4932 20030507 SGD
+SGD S000006532 tD(GUC)G1 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tD(GUC)G1 gene taxon:4932 20030507 SGD
+SGD S000006532 tD(GUC)G1 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tD(GUC)G1 gene taxon:4932 20030507 SGD
+SGD S000006533 tD(GUC)G2 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tD(GUC)G2 gene taxon:4932 20030507 SGD
+SGD S000006533 tD(GUC)G2 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tD(GUC)G2 gene taxon:4932 20030507 SGD
+SGD S000006533 tD(GUC)G2 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tD(GUC)G2 gene taxon:4932 20030507 SGD
+SGD S000006534 tD(GUC)I1 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tD(GUC)I1 gene taxon:4932 20030507 SGD
+SGD S000006534 tD(GUC)I1 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tD(GUC)I1 gene taxon:4932 20030507 SGD
+SGD S000006534 tD(GUC)I1 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tD(GUC)I1 gene taxon:4932 20030507 SGD
+SGD S000006535 tD(GUC)I2 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tD(GUC)I2 gene taxon:4932 20030507 SGD
+SGD S000006535 tD(GUC)I2 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tD(GUC)I2 gene taxon:4932 20030507 SGD
+SGD S000006535 tD(GUC)I2 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tD(GUC)I2 gene taxon:4932 20030507 SGD
+SGD S000006536 tD(GUC)J1 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tD(GUC)J1 gene taxon:4932 20030507 SGD
+SGD S000006536 tD(GUC)J1 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tD(GUC)J1 gene taxon:4932 20030507 SGD
+SGD S000006536 tD(GUC)J1 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tD(GUC)J1 gene taxon:4932 20030507 SGD
+SGD S000006537 tD(GUC)J2 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tD(GUC)J2 gene taxon:4932 20030507 SGD
+SGD S000006537 tD(GUC)J2 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tD(GUC)J2 gene taxon:4932 20030507 SGD
+SGD S000006537 tD(GUC)J2 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tD(GUC)J2 gene taxon:4932 20030507 SGD
+SGD S000006538 tD(GUC)J3 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tD(GUC)J3 gene taxon:4932 20030507 SGD
+SGD S000006538 tD(GUC)J3 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tD(GUC)J3 gene taxon:4932 20030507 SGD
+SGD S000006538 tD(GUC)J3 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tD(GUC)J3 gene taxon:4932 20030507 SGD
+SGD S000006539 tD(GUC)J4 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tD(GUC)J4 gene taxon:4932 20030507 SGD
+SGD S000006539 tD(GUC)J4 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tD(GUC)J4 gene taxon:4932 20030507 SGD
+SGD S000006539 tD(GUC)J4 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tD(GUC)J4 gene taxon:4932 20030507 SGD
+SGD S000006540 tD(GUC)K GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tD(GUC)K gene taxon:4932 20030507 SGD
+SGD S000006540 tD(GUC)K GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tD(GUC)K gene taxon:4932 20030507 SGD
+SGD S000006540 tD(GUC)K GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tD(GUC)K gene taxon:4932 20030507 SGD
+SGD S000006541 tD(GUC)L1 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tD(GUC)L1 gene taxon:4932 20030507 SGD
+SGD S000006541 tD(GUC)L1 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tD(GUC)L1 gene taxon:4932 20030507 SGD
+SGD S000006541 tD(GUC)L1 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tD(GUC)L1 gene taxon:4932 20030507 SGD
+SGD S000006542 tD(GUC)L2 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tD(GUC)L2 gene taxon:4932 20030507 SGD
+SGD S000006542 tD(GUC)L2 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tD(GUC)L2 gene taxon:4932 20030507 SGD
+SGD S000006542 tD(GUC)L2 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tD(GUC)L2 gene taxon:4932 20030507 SGD
+SGD S000006543 tD(GUC)M GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tD(GUC)M gene taxon:4932 20030507 SGD
+SGD S000006543 tD(GUC)M GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tD(GUC)M gene taxon:4932 20030507 SGD
+SGD S000006543 tD(GUC)M GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tD(GUC)M gene taxon:4932 20030507 SGD
+SGD S000006544 tD(GUC)N GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tD(GUC)N gene taxon:4932 20030507 SGD
+SGD S000006544 tD(GUC)N GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tD(GUC)N gene taxon:4932 20030507 SGD
+SGD S000006544 tD(GUC)N GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tD(GUC)N gene taxon:4932 20030507 SGD
+SGD S000006545 tD(GUC)O GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tD(GUC)O gene taxon:4932 20030507 SGD
+SGD S000006545 tD(GUC)O GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tD(GUC)O gene taxon:4932 20030507 SGD
+SGD S000006545 tD(GUC)O GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tD(GUC)O gene taxon:4932 20030507 SGD
+SGD S000007317 tD(GUC)Q GO:0005739 SGD_REF:S000073094|PMID:9159473 NAS C tD(GUC)Q gene taxon:4932 20030507 SGD
+SGD S000007317 tD(GUC)Q GO:0030533 SGD_REF:S000058438|PMID:9872396 NAS F tD(GUC)Q gene taxon:4932 20020220 SGD
+SGD S000007317 tD(GUC)Q GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tD(GUC)Q gene taxon:4932 20030507 SGD
+SGD S000006546 tE(CUC)D GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tE(CUC)D gene taxon:4932 20030507 SGD
+SGD S000006546 tE(CUC)D GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tE(CUC)D gene taxon:4932 20030507 SGD
+SGD S000006546 tE(CUC)D GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tE(CUC)D gene taxon:4932 20030507 SGD
+SGD S000006547 tE(CUC)I GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tE(CUC)I gene taxon:4932 20030507 SGD
+SGD S000006547 tE(CUC)I GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tE(CUC)I gene taxon:4932 20030507 SGD
+SGD S000006547 tE(CUC)I GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tE(CUC)I gene taxon:4932 20030507 SGD
+SGD S000006548 tE(UUC)B GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tE(UUC)B gene taxon:4932 20030507 SGD
+SGD S000006548 tE(UUC)B GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tE(UUC)B gene taxon:4932 20030507 SGD
+SGD S000006548 tE(UUC)B GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tE(UUC)B gene taxon:4932 20030507 SGD
+SGD S000006549 tE(UUC)C GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tE(UUC)C gene taxon:4932 20030507 SGD
+SGD S000006549 tE(UUC)C GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tE(UUC)C gene taxon:4932 20030507 SGD
+SGD S000006549 tE(UUC)C GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tE(UUC)C gene taxon:4932 20030507 SGD
+SGD S000006550 tE(UUC)E1 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tE(UUC)E1 gene taxon:4932 20030507 SGD
+SGD S000006550 tE(UUC)E1 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tE(UUC)E1 gene taxon:4932 20030507 SGD
+SGD S000006550 tE(UUC)E1 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tE(UUC)E1 gene taxon:4932 20030507 SGD
+SGD S000006551 tE(UUC)E2 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tE(UUC)E2 gene taxon:4932 20030507 SGD
+SGD S000006551 tE(UUC)E2 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tE(UUC)E2 gene taxon:4932 20030507 SGD
+SGD S000006551 tE(UUC)E2 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tE(UUC)E2 gene taxon:4932 20030507 SGD
+SGD S000006552 tE(UUC)E3 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tE(UUC)E3 gene taxon:4932 20030507 SGD
+SGD S000006552 tE(UUC)E3 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tE(UUC)E3 gene taxon:4932 20030507 SGD
+SGD S000006552 tE(UUC)E3 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tE(UUC)E3 gene taxon:4932 20030507 SGD
+SGD S000006554 tE(UUC)G2 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tE(UUC)G2 gene taxon:4932 20030507 SGD
+SGD S000006554 tE(UUC)G2 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tE(UUC)G2 gene taxon:4932 20030507 SGD
+SGD S000006554 tE(UUC)G2 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tE(UUC)G2 gene taxon:4932 20030507 SGD
+SGD S000006555 tE(UUC)G3 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tE(UUC)G3 gene taxon:4932 20030507 SGD
+SGD S000006555 tE(UUC)G3 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tE(UUC)G3 gene taxon:4932 20030507 SGD
+SGD S000006555 tE(UUC)G3 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tE(UUC)G3 gene taxon:4932 20030507 SGD
+SGD S000006556 tE(UUC)I GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tE(UUC)I gene taxon:4932 20030507 SGD
+SGD S000006556 tE(UUC)I GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tE(UUC)I gene taxon:4932 20030507 SGD
+SGD S000006556 tE(UUC)I GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tE(UUC)I gene taxon:4932 20030507 SGD
+SGD S000006557 tE(UUC)J GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tE(UUC)J gene taxon:4932 20030507 SGD
+SGD S000006557 tE(UUC)J GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tE(UUC)J gene taxon:4932 20030507 SGD
+SGD S000006557 tE(UUC)J GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tE(UUC)J gene taxon:4932 20030507 SGD
+SGD S000006558 tE(UUC)K GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tE(UUC)K gene taxon:4932 20030507 SGD
+SGD S000006558 tE(UUC)K GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tE(UUC)K gene taxon:4932 20030507 SGD
+SGD S000006558 tE(UUC)K GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tE(UUC)K gene taxon:4932 20030507 SGD
+SGD S000006559 tE(UUC)L GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tE(UUC)L gene taxon:4932 20030507 SGD
+SGD S000006559 tE(UUC)L GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tE(UUC)L gene taxon:4932 20030507 SGD
+SGD S000006559 tE(UUC)L GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tE(UUC)L gene taxon:4932 20030507 SGD
+SGD S000006560 tE(UUC)M GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tE(UUC)M gene taxon:4932 20030507 SGD
+SGD S000006560 tE(UUC)M GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tE(UUC)M gene taxon:4932 20030507 SGD
+SGD S000006560 tE(UUC)M GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tE(UUC)M gene taxon:4932 20030507 SGD
+SGD S000006561 tE(UUC)P GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tE(UUC)P gene taxon:4932 20030507 SGD
+SGD S000006561 tE(UUC)P GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tE(UUC)P gene taxon:4932 20030507 SGD
+SGD S000006561 tE(UUC)P GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tE(UUC)P gene taxon:4932 20030507 SGD
+SGD S000007318 tE(UUC)Q GO:0005739 SGD_REF:S000073094|PMID:9159473 NAS C tE(UUC)Q gene taxon:4932 20030507 SGD
+SGD S000007318 tE(UUC)Q GO:0030533 SGD_REF:S000058438|PMID:9872396 NAS F tE(UUC)Q gene taxon:4932 20020220 SGD
+SGD S000007318 tE(UUC)Q GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tE(UUC)Q gene taxon:4932 20030507 SGD
+SGD S000006562 tF(GAA)B GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tF(GAA)B gene taxon:4932 20030507 SGD
+SGD S000006562 tF(GAA)B GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tF(GAA)B gene taxon:4932 20030507 SGD
+SGD S000006562 tF(GAA)B GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tF(GAA)B gene taxon:4932 20030507 SGD
+SGD S000006563 tF(GAA)D GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tF(GAA)D gene taxon:4932 20030507 SGD
+SGD S000006563 tF(GAA)D GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tF(GAA)D gene taxon:4932 20030507 SGD
+SGD S000006563 tF(GAA)D GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tF(GAA)D gene taxon:4932 20030507 SGD
+SGD S000006564 tF(GAA)F GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tF(GAA)F gene taxon:4932 20030507 SGD
+SGD S000006564 tF(GAA)F GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tF(GAA)F gene taxon:4932 20030507 SGD
+SGD S000006564 tF(GAA)F GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tF(GAA)F gene taxon:4932 20030507 SGD
+SGD S000006565 tF(GAA)G GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tF(GAA)G gene taxon:4932 20030507 SGD
+SGD S000006565 tF(GAA)G GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tF(GAA)G gene taxon:4932 20030507 SGD
+SGD S000006565 tF(GAA)G GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tF(GAA)G gene taxon:4932 20030507 SGD
+SGD S000006566 tF(GAA)H1 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tF(GAA)H1 gene taxon:4932 20030507 SGD
+SGD S000006566 tF(GAA)H1 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tF(GAA)H1 gene taxon:4932 20030507 SGD
+SGD S000006566 tF(GAA)H1 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tF(GAA)H1 gene taxon:4932 20030507 SGD
+SGD S000006567 tF(GAA)H2 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tF(GAA)H2 gene taxon:4932 20030507 SGD
+SGD S000006567 tF(GAA)H2 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tF(GAA)H2 gene taxon:4932 20030507 SGD
+SGD S000006567 tF(GAA)H2 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tF(GAA)H2 gene taxon:4932 20030507 SGD
+SGD S000006568 tF(GAA)M GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tF(GAA)M gene taxon:4932 20030507 SGD
+SGD S000006568 tF(GAA)M GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tF(GAA)M gene taxon:4932 20030507 SGD
+SGD S000006568 tF(GAA)M GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tF(GAA)M gene taxon:4932 20030507 SGD
+SGD S000006569 tF(GAA)N GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tF(GAA)N gene taxon:4932 20030507 SGD
+SGD S000006569 tF(GAA)N GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tF(GAA)N gene taxon:4932 20030507 SGD
+SGD S000006569 tF(GAA)N GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tF(GAA)N gene taxon:4932 20030507 SGD
+SGD S000006570 tF(GAA)P1 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tF(GAA)P1 gene taxon:4932 20030507 SGD
+SGD S000006570 tF(GAA)P1 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tF(GAA)P1 gene taxon:4932 20030507 SGD
+SGD S000006570 tF(GAA)P1 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tF(GAA)P1 gene taxon:4932 20030507 SGD
+SGD S000006571 tF(GAA)P2 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tF(GAA)P2 gene taxon:4932 20030507 SGD
+SGD S000006571 tF(GAA)P2 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tF(GAA)P2 gene taxon:4932 20030507 SGD
+SGD S000006571 tF(GAA)P2 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tF(GAA)P2 gene taxon:4932 20030507 SGD
+SGD S000007319 tF(GAA)Q GO:0005739 SGD_REF:S000073094|PMID:9159473 NAS C tF(GAA)Q gene taxon:4932 20030507 SGD
+SGD S000007319 tF(GAA)Q GO:0030533 SGD_REF:S000058438|PMID:9872396 NAS F tF(GAA)Q gene taxon:4932 20020220 SGD
+SGD S000007319 tF(GAA)Q GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tF(GAA)Q gene taxon:4932 20030507 SGD
+SGD S000006574 tG(GCC)B GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tG(GCC)B gene taxon:4932 20030507 SGD
+SGD S000006574 tG(GCC)B GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tG(GCC)B gene taxon:4932 20030507 SGD
+SGD S000006574 tG(GCC)B GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tG(GCC)B gene taxon:4932 20030507 SGD
+SGD S000006576 tG(GCC)D1 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tG(GCC)D1 gene taxon:4932 20030507 SGD
+SGD S000006576 tG(GCC)D1 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tG(GCC)D1 gene taxon:4932 20030507 SGD
+SGD S000006576 tG(GCC)D1 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tG(GCC)D1 gene taxon:4932 20030507 SGD
+SGD S000006577 tG(GCC)D2 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tG(GCC)D2 gene taxon:4932 20030507 SGD
+SGD S000006577 tG(GCC)D2 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tG(GCC)D2 gene taxon:4932 20030507 SGD
+SGD S000006577 tG(GCC)D2 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tG(GCC)D2 gene taxon:4932 20030507 SGD
+SGD S000006578 tG(GCC)E GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tG(GCC)E gene taxon:4932 20030507 SGD
+SGD S000006578 tG(GCC)E GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tG(GCC)E gene taxon:4932 20030507 SGD
+SGD S000006578 tG(GCC)E GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tG(GCC)E gene taxon:4932 20030507 SGD
+SGD S000006580 tG(GCC)F2 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tG(GCC)F2 gene taxon:4932 20030507 SGD
+SGD S000006580 tG(GCC)F2 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tG(GCC)F2 gene taxon:4932 20030507 SGD
+SGD S000006580 tG(GCC)F2 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tG(GCC)F2 gene taxon:4932 20030507 SGD
+SGD S000006581 tG(GCC)G1 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tG(GCC)G1 gene taxon:4932 20030507 SGD
+SGD S000006581 tG(GCC)G1 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tG(GCC)G1 gene taxon:4932 20030507 SGD
+SGD S000006581 tG(GCC)G1 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tG(GCC)G1 gene taxon:4932 20030507 SGD
+SGD S000006582 tG(GCC)G2 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tG(GCC)G2 gene taxon:4932 20030507 SGD
+SGD S000006582 tG(GCC)G2 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tG(GCC)G2 gene taxon:4932 20030507 SGD
+SGD S000006582 tG(GCC)G2 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tG(GCC)G2 gene taxon:4932 20030507 SGD
+SGD S000006583 tG(GCC)J1 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tG(GCC)J1 gene taxon:4932 20030507 SGD
+SGD S000006583 tG(GCC)J1 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tG(GCC)J1 gene taxon:4932 20030507 SGD
+SGD S000006583 tG(GCC)J1 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tG(GCC)J1 gene taxon:4932 20030507 SGD
+SGD S000006584 tG(GCC)J2 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tG(GCC)J2 gene taxon:4932 20030507 SGD
+SGD S000006584 tG(GCC)J2 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tG(GCC)J2 gene taxon:4932 20030507 SGD
+SGD S000006584 tG(GCC)J2 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tG(GCC)J2 gene taxon:4932 20030507 SGD
+SGD S000006585 tG(GCC)M GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tG(GCC)M gene taxon:4932 20030507 SGD
+SGD S000006585 tG(GCC)M GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tG(GCC)M gene taxon:4932 20030507 SGD
+SGD S000006585 tG(GCC)M GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tG(GCC)M gene taxon:4932 20030507 SGD
+SGD S000006586 tG(GCC)O1 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tG(GCC)O1 gene taxon:4932 20030507 SGD
+SGD S000006586 tG(GCC)O1 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tG(GCC)O1 gene taxon:4932 20030507 SGD
+SGD S000006586 tG(GCC)O1 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tG(GCC)O1 gene taxon:4932 20030507 SGD
+SGD S000006588 tG(GCC)P1 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tG(GCC)P1 gene taxon:4932 20030507 SGD
+SGD S000006588 tG(GCC)P1 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tG(GCC)P1 gene taxon:4932 20030507 SGD
+SGD S000006588 tG(GCC)P1 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tG(GCC)P1 gene taxon:4932 20030507 SGD
+SGD S000006589 tG(GCC)P2 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tG(GCC)P2 gene taxon:4932 20030507 SGD
+SGD S000006589 tG(GCC)P2 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tG(GCC)P2 gene taxon:4932 20030507 SGD
+SGD S000006589 tG(GCC)P2 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tG(GCC)P2 gene taxon:4932 20030507 SGD
+SGD S000007320 tG(UCC)Q GO:0005739 SGD_REF:S000073094|PMID:9159473 NAS C tG(UCC)Q gene taxon:4932 20030507 SGD
+SGD S000007320 tG(UCC)Q GO:0030533 SGD_REF:S000058438|PMID:9872396 NAS F tG(UCC)Q gene taxon:4932 20020220 SGD
+SGD S000007320 tG(UCC)Q GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tG(UCC)Q gene taxon:4932 20030507 SGD
+SGD S000006593 tH(GUG)E1 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tH(GUG)E1 gene taxon:4932 20030507 SGD
+SGD S000006593 tH(GUG)E1 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tH(GUG)E1 gene taxon:4932 20030507 SGD
+SGD S000006593 tH(GUG)E1 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tH(GUG)E1 gene taxon:4932 20030507 SGD
+SGD S000006594 tH(GUG)E2 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tH(GUG)E2 gene taxon:4932 20030507 SGD
+SGD S000006594 tH(GUG)E2 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tH(GUG)E2 gene taxon:4932 20030507 SGD
+SGD S000006594 tH(GUG)E2 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tH(GUG)E2 gene taxon:4932 20030507 SGD
+SGD S000006595 tH(GUG)G1 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tH(GUG)G1 gene taxon:4932 20030507 SGD
+SGD S000006595 tH(GUG)G1 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tH(GUG)G1 gene taxon:4932 20030507 SGD
+SGD S000006595 tH(GUG)G1 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tH(GUG)G1 gene taxon:4932 20030507 SGD
+SGD S000006596 tH(GUG)G2 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tH(GUG)G2 gene taxon:4932 20030507 SGD
+SGD S000006596 tH(GUG)G2 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tH(GUG)G2 gene taxon:4932 20030507 SGD
+SGD S000006596 tH(GUG)G2 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tH(GUG)G2 gene taxon:4932 20030507 SGD
+SGD S000006597 tH(GUG)H GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tH(GUG)H gene taxon:4932 20030507 SGD
+SGD S000006597 tH(GUG)H GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tH(GUG)H gene taxon:4932 20030507 SGD
+SGD S000006597 tH(GUG)H GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tH(GUG)H gene taxon:4932 20030507 SGD
+SGD S000006598 tH(GUG)K GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tH(GUG)K gene taxon:4932 20030507 SGD
+SGD S000006598 tH(GUG)K GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tH(GUG)K gene taxon:4932 20030507 SGD
+SGD S000006598 tH(GUG)K GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tH(GUG)K gene taxon:4932 20030507 SGD
+SGD S000006599 tH(GUG)M GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tH(GUG)M gene taxon:4932 20030507 SGD
+SGD S000006599 tH(GUG)M GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tH(GUG)M gene taxon:4932 20030507 SGD
+SGD S000006599 tH(GUG)M GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tH(GUG)M gene taxon:4932 20030507 SGD
+SGD S000007321 tH(GUG)Q GO:0005739 SGD_REF:S000073094|PMID:9159473 NAS C tH(GUG)Q gene taxon:4932 20030507 SGD
+SGD S000007321 tH(GUG)Q GO:0030533 SGD_REF:S000058438|PMID:9872396 NAS F tH(GUG)Q gene taxon:4932 20020220 SGD
+SGD S000007321 tH(GUG)Q GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tH(GUG)Q gene taxon:4932 20030507 SGD
+SGD S000006600 tI(AAU)B GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tI(AAU)B gene taxon:4932 20030507 SGD
+SGD S000006600 tI(AAU)B GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tI(AAU)B gene taxon:4932 20030507 SGD
+SGD S000006600 tI(AAU)B GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tI(AAU)B gene taxon:4932 20030507 SGD
+SGD S000006601 tI(AAU)D GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tI(AAU)D gene taxon:4932 20030507 SGD
+SGD S000006601 tI(AAU)D GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tI(AAU)D gene taxon:4932 20030507 SGD
+SGD S000006601 tI(AAU)D GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tI(AAU)D gene taxon:4932 20030507 SGD
+SGD S000006602 tI(AAU)E1 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tI(AAU)E1 gene taxon:4932 20030507 SGD
+SGD S000006602 tI(AAU)E1 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tI(AAU)E1 gene taxon:4932 20030507 SGD
+SGD S000006602 tI(AAU)E1 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tI(AAU)E1 gene taxon:4932 20030507 SGD
+SGD S000006603 tI(AAU)E2 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tI(AAU)E2 gene taxon:4932 20030507 SGD
+SGD S000006603 tI(AAU)E2 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tI(AAU)E2 gene taxon:4932 20030507 SGD
+SGD S000006603 tI(AAU)E2 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tI(AAU)E2 gene taxon:4932 20030507 SGD
+SGD S000006604 tI(AAU)G GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tI(AAU)G gene taxon:4932 20030507 SGD
+SGD S000006604 tI(AAU)G GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tI(AAU)G gene taxon:4932 20030507 SGD
+SGD S000006604 tI(AAU)G GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tI(AAU)G gene taxon:4932 20030507 SGD
+SGD S000006605 tI(AAU)I1 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tI(AAU)I1 gene taxon:4932 20030507 SGD
+SGD S000006605 tI(AAU)I1 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tI(AAU)I1 gene taxon:4932 20030507 SGD
+SGD S000006605 tI(AAU)I1 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tI(AAU)I1 gene taxon:4932 20030507 SGD
+SGD S000006606 tI(AAU)I2 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tI(AAU)I2 gene taxon:4932 20030507 SGD
+SGD S000006606 tI(AAU)I2 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tI(AAU)I2 gene taxon:4932 20030507 SGD
+SGD S000006606 tI(AAU)I2 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tI(AAU)I2 gene taxon:4932 20030507 SGD
+SGD S000006607 tI(AAU)L1 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tI(AAU)L1 gene taxon:4932 20030507 SGD
+SGD S000006607 tI(AAU)L1 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tI(AAU)L1 gene taxon:4932 20030507 SGD
+SGD S000006607 tI(AAU)L1 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tI(AAU)L1 gene taxon:4932 20030507 SGD
+SGD S000006608 tI(AAU)L2 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tI(AAU)L2 gene taxon:4932 20030507 SGD
+SGD S000006608 tI(AAU)L2 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tI(AAU)L2 gene taxon:4932 20030507 SGD
+SGD S000006608 tI(AAU)L2 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tI(AAU)L2 gene taxon:4932 20030507 SGD
+SGD S000006609 tI(AAU)N1 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tI(AAU)N1 gene taxon:4932 20030507 SGD
+SGD S000006609 tI(AAU)N1 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tI(AAU)N1 gene taxon:4932 20030507 SGD
+SGD S000006609 tI(AAU)N1 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tI(AAU)N1 gene taxon:4932 20030507 SGD
+SGD S000006610 tI(AAU)N2 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tI(AAU)N2 gene taxon:4932 20030507 SGD
+SGD S000006610 tI(AAU)N2 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tI(AAU)N2 gene taxon:4932 20030507 SGD
+SGD S000006610 tI(AAU)N2 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tI(AAU)N2 gene taxon:4932 20030507 SGD
+SGD S000006611 tI(AAU)P1 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tI(AAU)P1 gene taxon:4932 20030507 SGD
+SGD S000006611 tI(AAU)P1 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tI(AAU)P1 gene taxon:4932 20030507 SGD
+SGD S000006611 tI(AAU)P1 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tI(AAU)P1 gene taxon:4932 20030507 SGD
+SGD S000006612 tI(AAU)P2 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tI(AAU)P2 gene taxon:4932 20030507 SGD
+SGD S000006612 tI(AAU)P2 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tI(AAU)P2 gene taxon:4932 20030507 SGD
+SGD S000006612 tI(AAU)P2 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tI(AAU)P2 gene taxon:4932 20030507 SGD
+SGD S000007322 tI(GAU)Q GO:0005739 SGD_REF:S000073094|PMID:9159473 NAS C tI(GAU)Q gene taxon:4932 20030507 SGD
+SGD S000007322 tI(GAU)Q GO:0030533 SGD_REF:S000058438|PMID:9872396 NAS F tI(GAU)Q gene taxon:4932 20020220 SGD
+SGD S000007322 tI(GAU)Q GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tI(GAU)Q gene taxon:4932 20030507 SGD
+SGD S000006613 tI(UAU)D GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tI(UAU)D gene taxon:4932 20030507 SGD
+SGD S000006613 tI(UAU)D GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tI(UAU)D gene taxon:4932 20030507 SGD
+SGD S000006613 tI(UAU)D GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tI(UAU)D gene taxon:4932 20030507 SGD
+SGD S000006614 tI(UAU)L GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tI(UAU)L gene taxon:4932 20030507 SGD
+SGD S000006614 tI(UAU)L GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tI(UAU)L gene taxon:4932 20030507 SGD
+SGD S000006614 tI(UAU)L GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tI(UAU)L gene taxon:4932 20030507 SGD
+SGD S000006615 tK(CUU)C GO:0005739 SGD_REF:S000056222|PMID:8915539 IDA C tK(CUU)C gene taxon:4932 20010301 SGD
+SGD S000006615 tK(CUU)C GO:0005829 SGD_REF:S000056222|PMID:8915539 IDA C tK(CUU)C gene taxon:4932 20010301 SGD
+SGD S000006615 tK(CUU)C GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tK(CUU)C gene taxon:4932 20030507 SGD
+SGD S000006615 tK(CUU)C GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tK(CUU)C gene taxon:4932 20030507 SGD
+SGD S000006616 tK(CUU)D1 GO:0005739 SGD_REF:S000056222|PMID:8915539 IDA C tK(CUU)D1 gene taxon:4932 20010301 SGD
+SGD S000006616 tK(CUU)D1 GO:0005829 SGD_REF:S000056222|PMID:8915539 IDA C tK(CUU)D1 gene taxon:4932 20010301 SGD
+SGD S000006616 tK(CUU)D1 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tK(CUU)D1 gene taxon:4932 20030507 SGD
+SGD S000006616 tK(CUU)D1 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tK(CUU)D1 gene taxon:4932 20030507 SGD
+SGD S000006617 tK(CUU)D2 GO:0005739 SGD_REF:S000056222|PMID:8915539 IDA C tK(CUU)D2 gene taxon:4932 20010301 SGD
+SGD S000006617 tK(CUU)D2 GO:0005829 SGD_REF:S000056222|PMID:8915539 IDA C tK(CUU)D2 gene taxon:4932 20010301 SGD
+SGD S000006617 tK(CUU)D2 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tK(CUU)D2 gene taxon:4932 20030507 SGD
+SGD S000006617 tK(CUU)D2 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tK(CUU)D2 gene taxon:4932 20030507 SGD
+SGD S000006618 tK(CUU)E1 GO:0005739 SGD_REF:S000056222|PMID:8915539 IDA C tK(CUU)E1 gene taxon:4932 20010301 SGD
+SGD S000006618 tK(CUU)E1 GO:0005829 SGD_REF:S000056222|PMID:8915539 IDA C tK(CUU)E1 gene taxon:4932 20010301 SGD
+SGD S000006618 tK(CUU)E1 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tK(CUU)E1 gene taxon:4932 20030507 SGD
+SGD S000006618 tK(CUU)E1 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tK(CUU)E1 gene taxon:4932 20030507 SGD
+SGD S000006619 tK(CUU)E2 GO:0005739 SGD_REF:S000056222|PMID:8915539 IDA C tK(CUU)E2 gene taxon:4932 20010301 SGD
+SGD S000006619 tK(CUU)E2 GO:0005829 SGD_REF:S000056222|PMID:8915539 IDA C tK(CUU)E2 gene taxon:4932 20010301 SGD
+SGD S000006619 tK(CUU)E2 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tK(CUU)E2 gene taxon:4932 20030507 SGD
+SGD S000006619 tK(CUU)E2 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tK(CUU)E2 gene taxon:4932 20030507 SGD
+SGD S000006620 tK(CUU)F GO:0005739 SGD_REF:S000056222|PMID:8915539 IDA C tK(CUU)F gene taxon:4932 20010301 SGD
+SGD S000006620 tK(CUU)F GO:0005829 SGD_REF:S000056222|PMID:8915539 IDA C tK(CUU)F gene taxon:4932 20010301 SGD
+SGD S000006620 tK(CUU)F GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tK(CUU)F gene taxon:4932 20030507 SGD
+SGD S000006620 tK(CUU)F GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tK(CUU)F gene taxon:4932 20030507 SGD
+SGD S000006621 tK(CUU)G1 GO:0005739 SGD_REF:S000056222|PMID:8915539 IDA C tK(CUU)G1 gene taxon:4932 20010301 SGD
+SGD S000006621 tK(CUU)G1 GO:0005829 SGD_REF:S000056222|PMID:8915539 IDA C tK(CUU)G1 gene taxon:4932 20010301 SGD
+SGD S000006621 tK(CUU)G1 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tK(CUU)G1 gene taxon:4932 20030507 SGD
+SGD S000006621 tK(CUU)G1 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tK(CUU)G1 gene taxon:4932 20030507 SGD
+SGD S000006622 tK(CUU)G2 GO:0005739 SGD_REF:S000056222|PMID:8915539 IDA C tK(CUU)G2 gene taxon:4932 20010301 SGD
+SGD S000006622 tK(CUU)G2 GO:0005829 SGD_REF:S000056222|PMID:8915539 IDA C tK(CUU)G2 gene taxon:4932 20010301 SGD
+SGD S000006622 tK(CUU)G2 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tK(CUU)G2 gene taxon:4932 20030507 SGD
+SGD S000006622 tK(CUU)G2 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tK(CUU)G2 gene taxon:4932 20030507 SGD
+SGD S000006623 tK(CUU)G3 GO:0005739 SGD_REF:S000056222|PMID:8915539 IDA C tK(CUU)G3 gene taxon:4932 20010301 SGD
+SGD S000006623 tK(CUU)G3 GO:0005829 SGD_REF:S000056222|PMID:8915539 IDA C tK(CUU)G3 gene taxon:4932 20010301 SGD
+SGD S000006623 tK(CUU)G3 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tK(CUU)G3 gene taxon:4932 20030507 SGD
+SGD S000006623 tK(CUU)G3 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tK(CUU)G3 gene taxon:4932 20030507 SGD
+SGD S000006624 tK(CUU)I GO:0005739 SGD_REF:S000056222|PMID:8915539 IDA C tK(CUU)I gene taxon:4932 20010301 SGD
+SGD S000006624 tK(CUU)I GO:0005829 SGD_REF:S000056222|PMID:8915539 IDA C tK(CUU)I gene taxon:4932 20010301 SGD
+SGD S000006624 tK(CUU)I GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tK(CUU)I gene taxon:4932 20030507 SGD
+SGD S000006624 tK(CUU)I GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tK(CUU)I gene taxon:4932 20030507 SGD
+SGD S000006625 tK(CUU)J GO:0005739 SGD_REF:S000056222|PMID:8915539 IDA C tK(CUU)J gene taxon:4932 20010301 SGD
+SGD S000006625 tK(CUU)J GO:0005829 SGD_REF:S000056222|PMID:8915539 IDA C tK(CUU)J gene taxon:4932 20010301 SGD
+SGD S000006625 tK(CUU)J GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tK(CUU)J gene taxon:4932 20030507 SGD
+SGD S000006625 tK(CUU)J GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tK(CUU)J gene taxon:4932 20030507 SGD
+SGD S000006626 tK(CUU)K GO:0005739 SGD_REF:S000056222|PMID:8915539 IDA C tK(CUU)K gene taxon:4932 20010301 SGD
+SGD S000006626 tK(CUU)K GO:0005829 SGD_REF:S000056222|PMID:8915539 IDA C tK(CUU)K gene taxon:4932 20010301 SGD
+SGD S000006626 tK(CUU)K GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tK(CUU)K gene taxon:4932 20030507 SGD
+SGD S000006626 tK(CUU)K GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tK(CUU)K gene taxon:4932 20030507 SGD
+SGD S000006627 tK(CUU)M GO:0005739 SGD_REF:S000056222|PMID:8915539 IDA C tK(CUU)M gene taxon:4932 20010301 SGD
+SGD S000006627 tK(CUU)M GO:0005829 SGD_REF:S000056222|PMID:8915539 IDA C tK(CUU)M gene taxon:4932 20010301 SGD
+SGD S000006627 tK(CUU)M GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tK(CUU)M gene taxon:4932 20030507 SGD
+SGD S000006627 tK(CUU)M GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tK(CUU)M gene taxon:4932 20030507 SGD
+SGD S000006628 tK(CUU)P GO:0005739 SGD_REF:S000056222|PMID:8915539 IDA C tK(CUU)P gene taxon:4932 20010301 SGD
+SGD S000006628 tK(CUU)P GO:0005829 SGD_REF:S000056222|PMID:8915539 IDA C tK(CUU)P gene taxon:4932 20010301 SGD
+SGD S000006628 tK(CUU)P GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tK(CUU)P gene taxon:4932 20030507 SGD
+SGD S000006628 tK(CUU)P GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tK(CUU)P gene taxon:4932 20030507 SGD
+SGD S000006629 tK(UUU)D GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tK(UUU)D gene taxon:4932 20030507 SGD
+SGD S000006629 tK(UUU)D GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tK(UUU)D gene taxon:4932 20030507 SGD
+SGD S000006629 tK(UUU)D GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tK(UUU)D gene taxon:4932 20030507 SGD
+SGD S000006630 tK(UUU)G1 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tK(UUU)G1 gene taxon:4932 20030507 SGD
+SGD S000006630 tK(UUU)G1 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tK(UUU)G1 gene taxon:4932 20030507 SGD
+SGD S000006630 tK(UUU)G1 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tK(UUU)G1 gene taxon:4932 20030507 SGD
+SGD S000006631 tK(UUU)G2 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tK(UUU)G2 gene taxon:4932 20030507 SGD
+SGD S000006631 tK(UUU)G2 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tK(UUU)G2 gene taxon:4932 20030507 SGD
+SGD S000006631 tK(UUU)G2 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tK(UUU)G2 gene taxon:4932 20030507 SGD
+SGD S000006632 tK(UUU)K GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tK(UUU)K gene taxon:4932 20030507 SGD
+SGD S000006632 tK(UUU)K GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tK(UUU)K gene taxon:4932 20030507 SGD
+SGD S000006632 tK(UUU)K GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tK(UUU)K gene taxon:4932 20030507 SGD
+SGD S000006633 tK(UUU)L GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tK(UUU)L gene taxon:4932 20030507 SGD
+SGD S000006633 tK(UUU)L GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tK(UUU)L gene taxon:4932 20030507 SGD
+SGD S000006633 tK(UUU)L GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tK(UUU)L gene taxon:4932 20030507 SGD
+SGD S000006634 tK(UUU)O GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tK(UUU)O gene taxon:4932 20030507 SGD
+SGD S000006634 tK(UUU)O GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tK(UUU)O gene taxon:4932 20030507 SGD
+SGD S000006634 tK(UUU)O GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tK(UUU)O gene taxon:4932 20030507 SGD
+SGD S000006635 tK(UUU)P GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tK(UUU)P gene taxon:4932 20030507 SGD
+SGD S000006635 tK(UUU)P GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tK(UUU)P gene taxon:4932 20030507 SGD
+SGD S000006635 tK(UUU)P GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tK(UUU)P gene taxon:4932 20030507 SGD
+SGD S000007323 tK(UUU)Q GO:0005739 SGD_REF:S000073094|PMID:9159473 NAS C tK(UUU)Q gene taxon:4932 20030507 SGD
+SGD S000007323 tK(UUU)Q GO:0030533 SGD_REF:S000058438|PMID:9872396 NAS F tK(UUU)Q gene taxon:4932 20020220 SGD
+SGD S000007323 tK(UUU)Q GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tK(UUU)Q gene taxon:4932 20030507 SGD
+SGD S000006638 tL(CAA)D GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tL(CAA)D gene taxon:4932 20030507 SGD
+SGD S000006638 tL(CAA)D GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tL(CAA)D gene taxon:4932 20030507 SGD
+SGD S000006638 tL(CAA)D GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tL(CAA)D gene taxon:4932 20030507 SGD
+SGD S000006639 tL(CAA)G1 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tL(CAA)G1 gene taxon:4932 20030507 SGD
+SGD S000006639 tL(CAA)G1 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tL(CAA)G1 gene taxon:4932 20030507 SGD
+SGD S000006639 tL(CAA)G1 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tL(CAA)G1 gene taxon:4932 20030507 SGD
+SGD S000006641 tL(CAA)G3 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tL(CAA)G3 gene taxon:4932 20030507 SGD
+SGD S000006641 tL(CAA)G3 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tL(CAA)G3 gene taxon:4932 20030507 SGD
+SGD S000006641 tL(CAA)G3 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tL(CAA)G3 gene taxon:4932 20030507 SGD
+SGD S000006642 tL(CAA)K GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tL(CAA)K gene taxon:4932 20030507 SGD
+SGD S000006642 tL(CAA)K GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tL(CAA)K gene taxon:4932 20030507 SGD
+SGD S000006642 tL(CAA)K GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tL(CAA)K gene taxon:4932 20030507 SGD
+SGD S000006643 tL(CAA)L GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tL(CAA)L gene taxon:4932 20030507 SGD
+SGD S000006643 tL(CAA)L GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tL(CAA)L gene taxon:4932 20030507 SGD
+SGD S000006643 tL(CAA)L GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tL(CAA)L gene taxon:4932 20030507 SGD
+SGD S000006644 tL(CAA)M GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tL(CAA)M gene taxon:4932 20030507 SGD
+SGD S000006644 tL(CAA)M GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tL(CAA)M gene taxon:4932 20030507 SGD
+SGD S000006644 tL(CAA)M GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tL(CAA)M gene taxon:4932 20030507 SGD
+SGD S000006645 tL(CAA)N GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tL(CAA)N gene taxon:4932 20030507 SGD
+SGD S000006645 tL(CAA)N GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tL(CAA)N gene taxon:4932 20030507 SGD
+SGD S000006645 tL(CAA)N GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tL(CAA)N gene taxon:4932 20030507 SGD
+SGD S000006646 tL(GAG)G GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tL(GAG)G gene taxon:4932 20030507 SGD
+SGD S000006646 tL(GAG)G GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tL(GAG)G gene taxon:4932 20030507 SGD
+SGD S000006646 tL(GAG)G GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tL(GAG)G gene taxon:4932 20030507 SGD
+SGD S000006647 tL(UAA)B1 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tL(UAA)B1 gene taxon:4932 20030507 SGD
+SGD S000006647 tL(UAA)B1 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tL(UAA)B1 gene taxon:4932 20030507 SGD
+SGD S000006647 tL(UAA)B1 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tL(UAA)B1 gene taxon:4932 20030507 SGD
+SGD S000006648 tL(UAA)B2 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tL(UAA)B2 gene taxon:4932 20030507 SGD
+SGD S000006648 tL(UAA)B2 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tL(UAA)B2 gene taxon:4932 20030507 SGD
+SGD S000006648 tL(UAA)B2 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tL(UAA)B2 gene taxon:4932 20030507 SGD
+SGD S000006649 tL(UAA)D GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tL(UAA)D gene taxon:4932 20030507 SGD
+SGD S000006649 tL(UAA)D GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tL(UAA)D gene taxon:4932 20030507 SGD
+SGD S000006649 tL(UAA)D GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tL(UAA)D gene taxon:4932 20030507 SGD
+SGD S000006651 tL(UAA)K GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tL(UAA)K gene taxon:4932 20030507 SGD
+SGD S000006651 tL(UAA)K GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tL(UAA)K gene taxon:4932 20030507 SGD
+SGD S000006651 tL(UAA)K GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tL(UAA)K gene taxon:4932 20030507 SGD
+SGD S000006652 tL(UAA)L GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tL(UAA)L gene taxon:4932 20030507 SGD
+SGD S000006652 tL(UAA)L GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tL(UAA)L gene taxon:4932 20030507 SGD
+SGD S000006652 tL(UAA)L GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tL(UAA)L gene taxon:4932 20030507 SGD
+SGD S000006653 tL(UAA)N GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tL(UAA)N gene taxon:4932 20030507 SGD
+SGD S000006653 tL(UAA)N GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tL(UAA)N gene taxon:4932 20030507 SGD
+SGD S000006653 tL(UAA)N GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tL(UAA)N gene taxon:4932 20030507 SGD
+SGD S000007324 tL(UAA)Q GO:0005739 SGD_REF:S000073094|PMID:9159473 NAS C tL(UAA)Q gene taxon:4932 20030507 SGD
+SGD S000007324 tL(UAA)Q GO:0030533 SGD_REF:S000058438|PMID:9872396 NAS F tL(UAA)Q gene taxon:4932 20020220 SGD
+SGD S000007324 tL(UAA)Q GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tL(UAA)Q gene taxon:4932 20030507 SGD
+SGD S000006654 tL(UAG)J GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tL(UAG)J gene taxon:4932 20030507 SGD
+SGD S000006654 tL(UAG)J GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tL(UAG)J gene taxon:4932 20030507 SGD
+SGD S000006654 tL(UAG)J GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tL(UAG)J gene taxon:4932 20030507 SGD
+SGD S000006655 tL(UAG)L1 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tL(UAG)L1 gene taxon:4932 20030507 SGD
+SGD S000006655 tL(UAG)L1 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tL(UAG)L1 gene taxon:4932 20030507 SGD
+SGD S000006655 tL(UAG)L1 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tL(UAG)L1 gene taxon:4932 20030507 SGD
+SGD S000006656 tL(UAG)L2 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tL(UAG)L2 gene taxon:4932 20030507 SGD
+SGD S000006656 tL(UAG)L2 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tL(UAG)L2 gene taxon:4932 20030507 SGD
+SGD S000006656 tL(UAG)L2 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tL(UAG)L2 gene taxon:4932 20030507 SGD
+SGD S000006658 tM(CAU)C GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tM(CAU)C gene taxon:4932 20030507 SGD
+SGD S000006658 tM(CAU)C GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tM(CAU)C gene taxon:4932 20030507 SGD
+SGD S000006658 tM(CAU)C GO:0006413 SGD_REF:S000073094|PMID:9159473 NAS P tM(CAU)C gene taxon:4932 20030507 SGD
+SGD S000007325 tM(CAU)Q1 GO:0005739 SGD_REF:S000073094|PMID:9159473 NAS C tM(CAU)Q1 gene taxon:4932 20030507 SGD
+SGD S000007325 tM(CAU)Q1 GO:0030533 SGD_REF:S000058438|PMID:9872396 NAS F tM(CAU)Q1 gene taxon:4932 20020220 SGD
+SGD S000007325 tM(CAU)Q1 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tM(CAU)Q1 gene taxon:4932 20030507 SGD
+SGD S000007326 tM(CAU)Q2 GO:0005739 SGD_REF:S000073094|PMID:9159473 NAS C tM(CAU)Q2 gene taxon:4932 20030507 SGD
+SGD S000007326 tM(CAU)Q2 GO:0030533 SGD_REF:S000058438|PMID:9872396 NAS F tM(CAU)Q2 gene taxon:4932 20020220 SGD
+SGD S000007326 tM(CAU)Q2 GO:0006413 SGD_REF:S000073094|PMID:9159473 NAS P tM(CAU)Q2 gene taxon:4932 20031222 SGD
+SGD S000006668 tN(GUU)C GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tN(GUU)C gene taxon:4932 20030507 SGD
+SGD S000006668 tN(GUU)C GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tN(GUU)C gene taxon:4932 20030507 SGD
+SGD S000006668 tN(GUU)C GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tN(GUU)C gene taxon:4932 20030507 SGD
+SGD S000006669 tN(GUU)F GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tN(GUU)F gene taxon:4932 20030507 SGD
+SGD S000006669 tN(GUU)F GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tN(GUU)F gene taxon:4932 20030507 SGD
+SGD S000006669 tN(GUU)F GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tN(GUU)F gene taxon:4932 20030507 SGD
+SGD S000006670 tN(GUU)G GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tN(GUU)G gene taxon:4932 20030507 SGD
+SGD S000006670 tN(GUU)G GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tN(GUU)G gene taxon:4932 20030507 SGD
+SGD S000006670 tN(GUU)G GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tN(GUU)G gene taxon:4932 20030507 SGD
+SGD S000006671 tN(GUU)K GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tN(GUU)K gene taxon:4932 20030507 SGD
+SGD S000006671 tN(GUU)K GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tN(GUU)K gene taxon:4932 20030507 SGD
+SGD S000006671 tN(GUU)K GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tN(GUU)K gene taxon:4932 20030507 SGD
+SGD S000006672 tN(GUU)L GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tN(GUU)L gene taxon:4932 20030507 SGD
+SGD S000006672 tN(GUU)L GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tN(GUU)L gene taxon:4932 20030507 SGD
+SGD S000006672 tN(GUU)L GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tN(GUU)L gene taxon:4932 20030507 SGD
+SGD S000006673 tN(GUU)N1 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tN(GUU)N1 gene taxon:4932 20030507 SGD
+SGD S000006673 tN(GUU)N1 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tN(GUU)N1 gene taxon:4932 20030507 SGD
+SGD S000006673 tN(GUU)N1 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tN(GUU)N1 gene taxon:4932 20030507 SGD
+SGD S000006674 tN(GUU)N2 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tN(GUU)N2 gene taxon:4932 20030507 SGD
+SGD S000006674 tN(GUU)N2 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tN(GUU)N2 gene taxon:4932 20030507 SGD
+SGD S000006674 tN(GUU)N2 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tN(GUU)N2 gene taxon:4932 20030507 SGD
+SGD S000006675 tN(GUU)O1 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tN(GUU)O1 gene taxon:4932 20030507 SGD
+SGD S000006675 tN(GUU)O1 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tN(GUU)O1 gene taxon:4932 20030507 SGD
+SGD S000006675 tN(GUU)O1 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tN(GUU)O1 gene taxon:4932 20030507 SGD
+SGD S000006676 tN(GUU)O2 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tN(GUU)O2 gene taxon:4932 20030507 SGD
+SGD S000006676 tN(GUU)O2 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tN(GUU)O2 gene taxon:4932 20030507 SGD
+SGD S000006676 tN(GUU)O2 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tN(GUU)O2 gene taxon:4932 20030507 SGD
+SGD S000006677 tN(GUU)P GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tN(GUU)P gene taxon:4932 20030507 SGD
+SGD S000006677 tN(GUU)P GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tN(GUU)P gene taxon:4932 20030507 SGD
+SGD S000006677 tN(GUU)P GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tN(GUU)P gene taxon:4932 20030507 SGD
+SGD S000007327 tN(GUU)Q GO:0005739 SGD_REF:S000073094|PMID:9159473 NAS C tN(GUU)Q gene taxon:4932 20030507 SGD
+SGD S000007327 tN(GUU)Q GO:0030533 SGD_REF:S000058438|PMID:9872396 NAS F tN(GUU)Q gene taxon:4932 20020220 SGD
+SGD S000007327 tN(GUU)Q GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tN(GUU)Q gene taxon:4932 20030507 SGD
+SGD S000006683 tP(UGG)L GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tP(UGG)L gene taxon:4932 20030507 SGD
+SGD S000006683 tP(UGG)L GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tP(UGG)L gene taxon:4932 20030507 SGD
+SGD S000006683 tP(UGG)L GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tP(UGG)L gene taxon:4932 20030507 SGD
+SGD S000006685 tP(UGG)N1 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tP(UGG)N1 gene taxon:4932 20030507 SGD
+SGD S000006685 tP(UGG)N1 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tP(UGG)N1 gene taxon:4932 20030507 SGD
+SGD S000006685 tP(UGG)N1 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tP(UGG)N1 gene taxon:4932 20030507 SGD
+SGD S000006686 tP(UGG)N2 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tP(UGG)N2 gene taxon:4932 20030507 SGD
+SGD S000006686 tP(UGG)N2 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tP(UGG)N2 gene taxon:4932 20030507 SGD
+SGD S000006686 tP(UGG)N2 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tP(UGG)N2 gene taxon:4932 20030507 SGD
+SGD S000006687 tP(UGG)O1 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tP(UGG)O1 gene taxon:4932 20030507 SGD
+SGD S000006687 tP(UGG)O1 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tP(UGG)O1 gene taxon:4932 20030507 SGD
+SGD S000006687 tP(UGG)O1 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tP(UGG)O1 gene taxon:4932 20030507 SGD
+SGD S000006689 tP(UGG)O3 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tP(UGG)O3 gene taxon:4932 20030507 SGD
+SGD S000006689 tP(UGG)O3 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tP(UGG)O3 gene taxon:4932 20030507 SGD
+SGD S000006689 tP(UGG)O3 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tP(UGG)O3 gene taxon:4932 20030507 SGD
+SGD S000007328 tP(UGG)Q GO:0005739 SGD_REF:S000073094|PMID:9159473 NAS C tP(UGG)Q gene taxon:4932 20030507 SGD
+SGD S000007328 tP(UGG)Q GO:0030533 SGD_REF:S000058438|PMID:9872396 NAS F tP(UGG)Q gene taxon:4932 20020220 SGD
+SGD S000007328 tP(UGG)Q GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tP(UGG)Q gene taxon:4932 20030507 SGD
+SGD S000006691 tQ(UUG)B GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tQ(UUG)B gene taxon:4932 20030507 SGD
+SGD S000006691 tQ(UUG)B GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tQ(UUG)B gene taxon:4932 20030507 SGD
+SGD S000006691 tQ(UUG)B GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tQ(UUG)B gene taxon:4932 20030507 SGD
+SGD S000006692 tQ(UUG)C GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tQ(UUG)C gene taxon:4932 20030507 SGD
+SGD S000006692 tQ(UUG)C GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tQ(UUG)C gene taxon:4932 20030507 SGD
+SGD S000006692 tQ(UUG)C GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tQ(UUG)C gene taxon:4932 20030507 SGD
+SGD S000006693 tQ(UUG)D1 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tQ(UUG)D1 gene taxon:4932 20030507 SGD
+SGD S000006693 tQ(UUG)D1 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tQ(UUG)D1 gene taxon:4932 20030507 SGD
+SGD S000006693 tQ(UUG)D1 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tQ(UUG)D1 gene taxon:4932 20030507 SGD
+SGD S000006694 tQ(UUG)D2 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tQ(UUG)D2 gene taxon:4932 20030507 SGD
+SGD S000006694 tQ(UUG)D2 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tQ(UUG)D2 gene taxon:4932 20030507 SGD
+SGD S000006694 tQ(UUG)D2 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tQ(UUG)D2 gene taxon:4932 20030507 SGD
+SGD S000006695 tQ(UUG)D3 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tQ(UUG)D3 gene taxon:4932 20030507 SGD
+SGD S000006695 tQ(UUG)D3 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tQ(UUG)D3 gene taxon:4932 20030507 SGD
+SGD S000006695 tQ(UUG)D3 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tQ(UUG)D3 gene taxon:4932 20030507 SGD
+SGD S000006696 tQ(UUG)E1 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tQ(UUG)E1 gene taxon:4932 20030507 SGD
+SGD S000006696 tQ(UUG)E1 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tQ(UUG)E1 gene taxon:4932 20030507 SGD
+SGD S000006696 tQ(UUG)E1 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tQ(UUG)E1 gene taxon:4932 20030507 SGD
+SGD S000006697 tQ(UUG)E2 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tQ(UUG)E2 gene taxon:4932 20030507 SGD
+SGD S000006697 tQ(UUG)E2 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tQ(UUG)E2 gene taxon:4932 20030507 SGD
+SGD S000006697 tQ(UUG)E2 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tQ(UUG)E2 gene taxon:4932 20030507 SGD
+SGD S000006698 tQ(UUG)H GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tQ(UUG)H gene taxon:4932 20030507 SGD
+SGD S000006698 tQ(UUG)H GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tQ(UUG)H gene taxon:4932 20030507 SGD
+SGD S000006698 tQ(UUG)H GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tQ(UUG)H gene taxon:4932 20030507 SGD
+SGD S000006699 tQ(UUG)L GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tQ(UUG)L gene taxon:4932 20030507 SGD
+SGD S000006699 tQ(UUG)L GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tQ(UUG)L gene taxon:4932 20030507 SGD
+SGD S000006699 tQ(UUG)L GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tQ(UUG)L gene taxon:4932 20030507 SGD
+SGD S000007329 tQ(UUG)Q GO:0005739 SGD_REF:S000073094|PMID:9159473 NAS C tQ(UUG)Q gene taxon:4932 20030507 SGD
+SGD S000007329 tQ(UUG)Q GO:0030533 SGD_REF:S000058438|PMID:9872396 NAS F tQ(UUG)Q gene taxon:4932 20020220 SGD
+SGD S000007329 tQ(UUG)Q GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tQ(UUG)Q gene taxon:4932 20030507 SGD
+SGD S000006700 tR(ACG)D GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tR(ACG)D gene taxon:4932 20030507 SGD
+SGD S000006700 tR(ACG)D GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tR(ACG)D gene taxon:4932 20030507 SGD
+SGD S000006700 tR(ACG)D GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tR(ACG)D gene taxon:4932 20030507 SGD
+SGD S000006701 tR(ACG)E GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tR(ACG)E gene taxon:4932 20030507 SGD
+SGD S000006701 tR(ACG)E GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tR(ACG)E gene taxon:4932 20030507 SGD
+SGD S000006701 tR(ACG)E GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tR(ACG)E gene taxon:4932 20030507 SGD
+SGD S000006702 tR(ACG)J GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tR(ACG)J gene taxon:4932 20030507 SGD
+SGD S000006702 tR(ACG)J GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tR(ACG)J gene taxon:4932 20030507 SGD
+SGD S000006702 tR(ACG)J GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tR(ACG)J gene taxon:4932 20030507 SGD
+SGD S000006703 tR(ACG)K GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tR(ACG)K gene taxon:4932 20030507 SGD
+SGD S000006703 tR(ACG)K GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tR(ACG)K gene taxon:4932 20030507 SGD
+SGD S000006703 tR(ACG)K GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tR(ACG)K gene taxon:4932 20030507 SGD
+SGD S000006704 tR(ACG)L GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tR(ACG)L gene taxon:4932 20030507 SGD
+SGD S000006704 tR(ACG)L GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tR(ACG)L gene taxon:4932 20030507 SGD
+SGD S000006704 tR(ACG)L GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tR(ACG)L gene taxon:4932 20030507 SGD
+SGD S000006705 tR(ACG)O GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tR(ACG)O gene taxon:4932 20030507 SGD
+SGD S000006705 tR(ACG)O GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tR(ACG)O gene taxon:4932 20030507 SGD
+SGD S000006705 tR(ACG)O GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tR(ACG)O gene taxon:4932 20030507 SGD
+SGD S000007330 tR(ACG)Q2 GO:0005739 SGD_REF:S000073094|PMID:9159473 NAS C tR(ACG)Q2 gene taxon:4932 20030507 SGD
+SGD S000007330 tR(ACG)Q2 GO:0030533 SGD_REF:S000058438|PMID:9872396 NAS F tR(ACG)Q2 gene taxon:4932 20020220 SGD
+SGD S000007330 tR(ACG)Q2 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tR(ACG)Q2 gene taxon:4932 20030507 SGD
+SGD S000006708 tR(UCU)B GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tR(UCU)B gene taxon:4932 20030507 SGD
+SGD S000006708 tR(UCU)B GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tR(UCU)B gene taxon:4932 20030507 SGD
+SGD S000006708 tR(UCU)B GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tR(UCU)B gene taxon:4932 20030507 SGD
+SGD S000006709 tR(UCU)D GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tR(UCU)D gene taxon:4932 20030507 SGD
+SGD S000006709 tR(UCU)D GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tR(UCU)D gene taxon:4932 20030507 SGD
+SGD S000006709 tR(UCU)D GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tR(UCU)D gene taxon:4932 20030507 SGD
+SGD S000006710 tR(UCU)E GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tR(UCU)E gene taxon:4932 20030507 SGD
+SGD S000006710 tR(UCU)E GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tR(UCU)E gene taxon:4932 20030507 SGD
+SGD S000006710 tR(UCU)E GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tR(UCU)E gene taxon:4932 20030507 SGD
+SGD S000006711 tR(UCU)G1 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tR(UCU)G1 gene taxon:4932 20030507 SGD
+SGD S000006711 tR(UCU)G1 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tR(UCU)G1 gene taxon:4932 20030507 SGD
+SGD S000006711 tR(UCU)G1 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tR(UCU)G1 gene taxon:4932 20030507 SGD
+SGD S000006712 tR(UCU)G2 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tR(UCU)G2 gene taxon:4932 20030507 SGD
+SGD S000006712 tR(UCU)G2 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tR(UCU)G2 gene taxon:4932 20030507 SGD
+SGD S000006712 tR(UCU)G2 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tR(UCU)G2 gene taxon:4932 20030507 SGD
+SGD S000006713 tR(UCU)G3 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tR(UCU)G3 gene taxon:4932 20030507 SGD
+SGD S000006713 tR(UCU)G3 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tR(UCU)G3 gene taxon:4932 20030507 SGD
+SGD S000006713 tR(UCU)G3 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tR(UCU)G3 gene taxon:4932 20030507 SGD
+SGD S000006714 tR(UCU)J1 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tR(UCU)J1 gene taxon:4932 20030507 SGD
+SGD S000006714 tR(UCU)J1 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tR(UCU)J1 gene taxon:4932 20030507 SGD
+SGD S000006714 tR(UCU)J1 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tR(UCU)J1 gene taxon:4932 20030507 SGD
+SGD S000006715 tR(UCU)J2 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tR(UCU)J2 gene taxon:4932 20030507 SGD
+SGD S000006715 tR(UCU)J2 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tR(UCU)J2 gene taxon:4932 20030507 SGD
+SGD S000006715 tR(UCU)J2 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tR(UCU)J2 gene taxon:4932 20030507 SGD
+SGD S000006716 tR(UCU)K GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tR(UCU)K gene taxon:4932 20030507 SGD
+SGD S000006716 tR(UCU)K GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tR(UCU)K gene taxon:4932 20030507 SGD
+SGD S000006716 tR(UCU)K GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tR(UCU)K gene taxon:4932 20030507 SGD
+SGD S000006717 tR(UCU)M1 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tR(UCU)M1 gene taxon:4932 20030507 SGD
+SGD S000006717 tR(UCU)M1 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tR(UCU)M1 gene taxon:4932 20030507 SGD
+SGD S000006717 tR(UCU)M1 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tR(UCU)M1 gene taxon:4932 20030507 SGD
+SGD S000006718 tR(UCU)M2 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tR(UCU)M2 gene taxon:4932 20030507 SGD
+SGD S000006718 tR(UCU)M2 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tR(UCU)M2 gene taxon:4932 20030507 SGD
+SGD S000006718 tR(UCU)M2 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tR(UCU)M2 gene taxon:4932 20030507 SGD
+SGD S000007331 tR(UCU)Q1 GO:0005739 SGD_REF:S000073094|PMID:9159473 NAS C tR(UCU)Q1 gene taxon:4932 20030507 SGD
+SGD S000007331 tR(UCU)Q1 GO:0030533 SGD_REF:S000058438|PMID:9872396 NAS F tR(UCU)Q1 gene taxon:4932 20020220 SGD
+SGD S000007331 tR(UCU)Q1 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tR(UCU)Q1 gene taxon:4932 20030507 SGD
+SGD S000006719 tS(AGA)A GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tS(AGA)A gene taxon:4932 20030507 SGD
+SGD S000006719 tS(AGA)A GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tS(AGA)A gene taxon:4932 20030507 SGD
+SGD S000006719 tS(AGA)A GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tS(AGA)A gene taxon:4932 20030507 SGD
+SGD S000006720 tS(AGA)B GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tS(AGA)B gene taxon:4932 20030507 SGD
+SGD S000006720 tS(AGA)B GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tS(AGA)B gene taxon:4932 20030507 SGD
+SGD S000006720 tS(AGA)B GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tS(AGA)B gene taxon:4932 20030507 SGD
+SGD S000006721 tS(AGA)D1 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tS(AGA)D1 gene taxon:4932 20030507 SGD
+SGD S000006721 tS(AGA)D1 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tS(AGA)D1 gene taxon:4932 20030507 SGD
+SGD S000006721 tS(AGA)D1 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tS(AGA)D1 gene taxon:4932 20030507 SGD
+SGD S000006722 tS(AGA)D2 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tS(AGA)D2 gene taxon:4932 20030507 SGD
+SGD S000006722 tS(AGA)D2 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tS(AGA)D2 gene taxon:4932 20030507 SGD
+SGD S000006722 tS(AGA)D2 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tS(AGA)D2 gene taxon:4932 20030507 SGD
+SGD S000006723 tS(AGA)D3 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tS(AGA)D3 gene taxon:4932 20030507 SGD
+SGD S000006723 tS(AGA)D3 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tS(AGA)D3 gene taxon:4932 20030507 SGD
+SGD S000006723 tS(AGA)D3 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tS(AGA)D3 gene taxon:4932 20030507 SGD
+SGD S000006724 tS(AGA)E GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tS(AGA)E gene taxon:4932 20030507 SGD
+SGD S000006724 tS(AGA)E GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tS(AGA)E gene taxon:4932 20030507 SGD
+SGD S000006724 tS(AGA)E GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tS(AGA)E gene taxon:4932 20030507 SGD
+SGD S000006725 tS(AGA)G GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tS(AGA)G gene taxon:4932 20030507 SGD
+SGD S000006725 tS(AGA)G GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tS(AGA)G gene taxon:4932 20030507 SGD
+SGD S000006725 tS(AGA)G GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tS(AGA)G gene taxon:4932 20030507 SGD
+SGD S000006726 tS(AGA)H GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tS(AGA)H gene taxon:4932 20030507 SGD
+SGD S000006726 tS(AGA)H GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tS(AGA)H gene taxon:4932 20030507 SGD
+SGD S000006726 tS(AGA)H GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tS(AGA)H gene taxon:4932 20030507 SGD
+SGD S000006727 tS(AGA)J GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tS(AGA)J gene taxon:4932 20030507 SGD
+SGD S000006727 tS(AGA)J GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tS(AGA)J gene taxon:4932 20030507 SGD
+SGD S000006727 tS(AGA)J GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tS(AGA)J gene taxon:4932 20030507 SGD
+SGD S000006728 tS(AGA)L GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tS(AGA)L gene taxon:4932 20030507 SGD
+SGD S000006728 tS(AGA)L GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tS(AGA)L gene taxon:4932 20030507 SGD
+SGD S000006728 tS(AGA)L GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tS(AGA)L gene taxon:4932 20030507 SGD
+SGD S000006729 tS(AGA)M GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tS(AGA)M gene taxon:4932 20030507 SGD
+SGD S000006729 tS(AGA)M GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tS(AGA)M gene taxon:4932 20030507 SGD
+SGD S000006729 tS(AGA)M GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tS(AGA)M gene taxon:4932 20030507 SGD
+SGD S000006731 tS(GCU)F GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tS(GCU)F gene taxon:4932 20030507 SGD
+SGD S000006731 tS(GCU)F GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tS(GCU)F gene taxon:4932 20030507 SGD
+SGD S000006731 tS(GCU)F GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tS(GCU)F gene taxon:4932 20030507 SGD
+SGD S000006732 tS(GCU)L GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tS(GCU)L gene taxon:4932 20030507 SGD
+SGD S000006732 tS(GCU)L GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tS(GCU)L gene taxon:4932 20030507 SGD
+SGD S000006732 tS(GCU)L GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tS(GCU)L gene taxon:4932 20030507 SGD
+SGD S000006733 tS(GCU)O GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tS(GCU)O gene taxon:4932 20030507 SGD
+SGD S000006733 tS(GCU)O GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tS(GCU)O gene taxon:4932 20030507 SGD
+SGD S000006733 tS(GCU)O GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tS(GCU)O gene taxon:4932 20030507 SGD
+SGD S000007332 tS(GCU)Q1 GO:0005739 SGD_REF:S000073094|PMID:9159473 NAS C tS(GCU)Q1 gene taxon:4932 20030507 SGD
+SGD S000007332 tS(GCU)Q1 GO:0030533 SGD_REF:S000058438|PMID:9872396 NAS F tS(GCU)Q1 gene taxon:4932 20020220 SGD
+SGD S000007332 tS(GCU)Q1 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tS(GCU)Q1 gene taxon:4932 20030507 SGD
+SGD S000007333 tS(UGA)Q2 GO:0005739 SGD_REF:S000073094|PMID:9159473 NAS C tS(UGA)Q2 gene taxon:4932 20030507 SGD
+SGD S000007333 tS(UGA)Q2 GO:0030533 SGD_REF:S000058438|PMID:9872396 NAS F tS(UGA)Q2 gene taxon:4932 20020220 SGD
+SGD S000007333 tS(UGA)Q2 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tS(UGA)Q2 gene taxon:4932 20030507 SGD
+SGD S000006737 tT(AGU)B GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tT(AGU)B gene taxon:4932 20030507 SGD
+SGD S000006737 tT(AGU)B GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tT(AGU)B gene taxon:4932 20030507 SGD
+SGD S000006737 tT(AGU)B GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tT(AGU)B gene taxon:4932 20030507 SGD
+SGD S000006738 tT(AGU)C GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tT(AGU)C gene taxon:4932 20030507 SGD
+SGD S000006738 tT(AGU)C GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tT(AGU)C gene taxon:4932 20030507 SGD
+SGD S000006738 tT(AGU)C GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tT(AGU)C gene taxon:4932 20030507 SGD
+SGD S000006739 tT(AGU)D GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tT(AGU)D gene taxon:4932 20030507 SGD
+SGD S000006739 tT(AGU)D GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tT(AGU)D gene taxon:4932 20030507 SGD
+SGD S000006739 tT(AGU)D GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tT(AGU)D gene taxon:4932 20030507 SGD
+SGD S000006740 tT(AGU)H GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tT(AGU)H gene taxon:4932 20030507 SGD
+SGD S000006740 tT(AGU)H GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tT(AGU)H gene taxon:4932 20030507 SGD
+SGD S000006740 tT(AGU)H GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tT(AGU)H gene taxon:4932 20030507 SGD
+SGD S000006741 tT(AGU)I1 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tT(AGU)I1 gene taxon:4932 20030507 SGD
+SGD S000006741 tT(AGU)I1 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tT(AGU)I1 gene taxon:4932 20030507 SGD
+SGD S000006741 tT(AGU)I1 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tT(AGU)I1 gene taxon:4932 20030507 SGD
+SGD S000006742 tT(AGU)I2 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tT(AGU)I2 gene taxon:4932 20030507 SGD
+SGD S000006742 tT(AGU)I2 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tT(AGU)I2 gene taxon:4932 20030507 SGD
+SGD S000006742 tT(AGU)I2 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tT(AGU)I2 gene taxon:4932 20030507 SGD
+SGD S000006743 tT(AGU)J GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tT(AGU)J gene taxon:4932 20030507 SGD
+SGD S000006743 tT(AGU)J GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tT(AGU)J gene taxon:4932 20030507 SGD
+SGD S000006743 tT(AGU)J GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tT(AGU)J gene taxon:4932 20030507 SGD
+SGD S000006744 tT(AGU)N1 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tT(AGU)N1 gene taxon:4932 20030507 SGD
+SGD S000006744 tT(AGU)N1 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tT(AGU)N1 gene taxon:4932 20030507 SGD
+SGD S000006744 tT(AGU)N1 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tT(AGU)N1 gene taxon:4932 20030507 SGD
+SGD S000006745 tT(AGU)N2 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tT(AGU)N2 gene taxon:4932 20030507 SGD
+SGD S000006745 tT(AGU)N2 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tT(AGU)N2 gene taxon:4932 20030507 SGD
+SGD S000006745 tT(AGU)N2 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tT(AGU)N2 gene taxon:4932 20030507 SGD
+SGD S000006746 tT(AGU)O1 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tT(AGU)O1 gene taxon:4932 20030507 SGD
+SGD S000006746 tT(AGU)O1 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tT(AGU)O1 gene taxon:4932 20030507 SGD
+SGD S000006746 tT(AGU)O1 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tT(AGU)O1 gene taxon:4932 20030507 SGD
+SGD S000006747 tT(AGU)O2 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tT(AGU)O2 gene taxon:4932 20030507 SGD
+SGD S000006747 tT(AGU)O2 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tT(AGU)O2 gene taxon:4932 20030507 SGD
+SGD S000006747 tT(AGU)O2 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tT(AGU)O2 gene taxon:4932 20030507 SGD
+SGD S000006749 tT(UGU)G1 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tT(UGU)G1 gene taxon:4932 20030507 SGD
+SGD S000006749 tT(UGU)G1 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tT(UGU)G1 gene taxon:4932 20030507 SGD
+SGD S000006749 tT(UGU)G1 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tT(UGU)G1 gene taxon:4932 20030507 SGD
+SGD S000006750 tT(UGU)G2 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tT(UGU)G2 gene taxon:4932 20030507 SGD
+SGD S000006750 tT(UGU)G2 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tT(UGU)G2 gene taxon:4932 20030507 SGD
+SGD S000006750 tT(UGU)G2 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tT(UGU)G2 gene taxon:4932 20030507 SGD
+SGD S000006751 tT(UGU)H GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tT(UGU)H gene taxon:4932 20030507 SGD
+SGD S000006751 tT(UGU)H GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tT(UGU)H gene taxon:4932 20030507 SGD
+SGD S000006751 tT(UGU)H GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tT(UGU)H gene taxon:4932 20030507 SGD
+SGD S000006752 tT(UGU)P GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tT(UGU)P gene taxon:4932 20030507 SGD
+SGD S000006752 tT(UGU)P GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tT(UGU)P gene taxon:4932 20030507 SGD
+SGD S000006752 tT(UGU)P GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tT(UGU)P gene taxon:4932 20030507 SGD
+SGD S000007334 tT(UGU)Q1 GO:0005739 SGD_REF:S000073094|PMID:9159473 NAS C tT(UGU)Q1 gene taxon:4932 20030507 SGD
+SGD S000007334 tT(UGU)Q1 GO:0030533 SGD_REF:S000058438|PMID:9872396 NAS F tT(UGU)Q1 gene taxon:4932 20020220 SGD
+SGD S000007334 tT(UGU)Q1 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tT(UGU)Q1 gene taxon:4932 20030507 SGD
+SGD S000007335 tT(XXX)Q2 GO:0005739 SGD_REF:S000073094|PMID:9159473 NAS C tT(XXX)Q2 gene taxon:4932 20030507 SGD
+SGD S000007335 tT(XXX)Q2 GO:0030533 SGD_REF:S000058438|PMID:9872396 NAS F tT(XXX)Q2 gene taxon:4932 20020220 SGD
+SGD S000007335 tT(XXX)Q2 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tT(XXX)Q2 gene taxon:4932 20030507 SGD
+SGD S000006753 tV(AAC)E1 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tV(AAC)E1 gene taxon:4932 20030507 SGD
+SGD S000006753 tV(AAC)E1 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tV(AAC)E1 gene taxon:4932 20030507 SGD
+SGD S000006753 tV(AAC)E1 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tV(AAC)E1 gene taxon:4932 20030507 SGD
+SGD S000006754 tV(AAC)E2 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tV(AAC)E2 gene taxon:4932 20030507 SGD
+SGD S000006754 tV(AAC)E2 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tV(AAC)E2 gene taxon:4932 20030507 SGD
+SGD S000006754 tV(AAC)E2 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tV(AAC)E2 gene taxon:4932 20030507 SGD
+SGD S000006755 tV(AAC)G1 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tV(AAC)G1 gene taxon:4932 20030507 SGD
+SGD S000006755 tV(AAC)G1 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tV(AAC)G1 gene taxon:4932 20030507 SGD
+SGD S000006755 tV(AAC)G1 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tV(AAC)G1 gene taxon:4932 20030507 SGD
+SGD S000006756 tV(AAC)G2 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tV(AAC)G2 gene taxon:4932 20030507 SGD
+SGD S000006756 tV(AAC)G2 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tV(AAC)G2 gene taxon:4932 20030507 SGD
+SGD S000006756 tV(AAC)G2 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tV(AAC)G2 gene taxon:4932 20030507 SGD
+SGD S000006757 tV(AAC)G3 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tV(AAC)G3 gene taxon:4932 20030507 SGD
+SGD S000006757 tV(AAC)G3 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tV(AAC)G3 gene taxon:4932 20030507 SGD
+SGD S000006757 tV(AAC)G3 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tV(AAC)G3 gene taxon:4932 20030507 SGD
+SGD S000006758 tV(AAC)H GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tV(AAC)H gene taxon:4932 20030507 SGD
+SGD S000006758 tV(AAC)H GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tV(AAC)H gene taxon:4932 20030507 SGD
+SGD S000006758 tV(AAC)H GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tV(AAC)H gene taxon:4932 20030507 SGD
+SGD S000006759 tV(AAC)J GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tV(AAC)J gene taxon:4932 20030507 SGD
+SGD S000006759 tV(AAC)J GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tV(AAC)J gene taxon:4932 20030507 SGD
+SGD S000006759 tV(AAC)J GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tV(AAC)J gene taxon:4932 20030507 SGD
+SGD S000006760 tV(AAC)K1 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tV(AAC)K1 gene taxon:4932 20030507 SGD
+SGD S000006760 tV(AAC)K1 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tV(AAC)K1 gene taxon:4932 20030507 SGD
+SGD S000006760 tV(AAC)K1 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tV(AAC)K1 gene taxon:4932 20030507 SGD
+SGD S000006761 tV(AAC)K2 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tV(AAC)K2 gene taxon:4932 20030507 SGD
+SGD S000006761 tV(AAC)K2 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tV(AAC)K2 gene taxon:4932 20030507 SGD
+SGD S000006761 tV(AAC)K2 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tV(AAC)K2 gene taxon:4932 20030507 SGD
+SGD S000006762 tV(AAC)L GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tV(AAC)L gene taxon:4932 20030507 SGD
+SGD S000006762 tV(AAC)L GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tV(AAC)L gene taxon:4932 20030507 SGD
+SGD S000006762 tV(AAC)L GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tV(AAC)L gene taxon:4932 20030507 SGD
+SGD S000006763 tV(AAC)M1 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tV(AAC)M1 gene taxon:4932 20030507 SGD
+SGD S000006763 tV(AAC)M1 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tV(AAC)M1 gene taxon:4932 20030507 SGD
+SGD S000006763 tV(AAC)M1 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tV(AAC)M1 gene taxon:4932 20030507 SGD
+SGD S000006764 tV(AAC)M2 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tV(AAC)M2 gene taxon:4932 20030507 SGD
+SGD S000006764 tV(AAC)M2 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tV(AAC)M2 gene taxon:4932 20030507 SGD
+SGD S000006764 tV(AAC)M2 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tV(AAC)M2 gene taxon:4932 20030507 SGD
+SGD S000006765 tV(AAC)M3 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tV(AAC)M3 gene taxon:4932 20030507 SGD
+SGD S000006765 tV(AAC)M3 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tV(AAC)M3 gene taxon:4932 20030507 SGD
+SGD S000006765 tV(AAC)M3 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tV(AAC)M3 gene taxon:4932 20030507 SGD
+SGD S000006766 tV(AAC)O GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tV(AAC)O gene taxon:4932 20030507 SGD
+SGD S000006766 tV(AAC)O GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tV(AAC)O gene taxon:4932 20030507 SGD
+SGD S000006766 tV(AAC)O GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tV(AAC)O gene taxon:4932 20030507 SGD
+SGD S000006767 tV(CAC)D GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tV(CAC)D gene taxon:4932 20030507 SGD
+SGD S000006767 tV(CAC)D GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tV(CAC)D gene taxon:4932 20030507 SGD
+SGD S000006767 tV(CAC)D GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tV(CAC)D gene taxon:4932 20030507 SGD
+SGD S000006768 tV(CAC)H GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tV(CAC)H gene taxon:4932 20030507 SGD
+SGD S000006768 tV(CAC)H GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tV(CAC)H gene taxon:4932 20030507 SGD
+SGD S000006768 tV(CAC)H GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tV(CAC)H gene taxon:4932 20030507 SGD
+SGD S000006769 tV(UAC)B GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tV(UAC)B gene taxon:4932 20030507 SGD
+SGD S000006769 tV(UAC)B GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tV(UAC)B gene taxon:4932 20030507 SGD
+SGD S000006769 tV(UAC)B GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tV(UAC)B gene taxon:4932 20030507 SGD
+SGD S000006770 tV(UAC)D GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tV(UAC)D gene taxon:4932 20030507 SGD
+SGD S000006770 tV(UAC)D GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tV(UAC)D gene taxon:4932 20030507 SGD
+SGD S000006770 tV(UAC)D GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tV(UAC)D gene taxon:4932 20030507 SGD
+SGD S000007336 tV(UAC)Q GO:0005739 SGD_REF:S000073094|PMID:9159473 NAS C tV(UAC)Q gene taxon:4932 20030507 SGD
+SGD S000007336 tV(UAC)Q GO:0030533 SGD_REF:S000058438|PMID:9872396 NAS F tV(UAC)Q gene taxon:4932 20020220 SGD
+SGD S000007336 tV(UAC)Q GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tV(UAC)Q gene taxon:4932 20030507 SGD
+SGD S000006771 tW(CCA)G1 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tW(CCA)G1 gene taxon:4932 20030507 SGD
+SGD S000006771 tW(CCA)G1 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tW(CCA)G1 gene taxon:4932 20030507 SGD
+SGD S000006771 tW(CCA)G1 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tW(CCA)G1 gene taxon:4932 20030507 SGD
+SGD S000006772 tW(CCA)G2 GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tW(CCA)G2 gene taxon:4932 20030507 SGD
+SGD S000006772 tW(CCA)G2 GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tW(CCA)G2 gene taxon:4932 20030507 SGD
+SGD S000006772 tW(CCA)G2 GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tW(CCA)G2 gene taxon:4932 20030507 SGD
+SGD S000006773 tW(CCA)J GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tW(CCA)J gene taxon:4932 20030507 SGD
+SGD S000006773 tW(CCA)J GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tW(CCA)J gene taxon:4932 20030507 SGD
+SGD S000006773 tW(CCA)J GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tW(CCA)J gene taxon:4932 20030507 SGD
+SGD S000006774 tW(CCA)K GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tW(CCA)K gene taxon:4932 20030507 SGD
+SGD S000006774 tW(CCA)K GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tW(CCA)K gene taxon:4932 20030507 SGD
+SGD S000006774 tW(CCA)K GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tW(CCA)K gene taxon:4932 20030507 SGD
+SGD S000006775 tW(CCA)M GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tW(CCA)M gene taxon:4932 20030507 SGD
+SGD S000006775 tW(CCA)M GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tW(CCA)M gene taxon:4932 20030507 SGD
+SGD S000006775 tW(CCA)M GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tW(CCA)M gene taxon:4932 20030507 SGD
+SGD S000006776 tW(CCA)P GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tW(CCA)P gene taxon:4932 20030507 SGD
+SGD S000006776 tW(CCA)P GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tW(CCA)P gene taxon:4932 20030507 SGD
+SGD S000006776 tW(CCA)P GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tW(CCA)P gene taxon:4932 20030507 SGD
+SGD S000007337 tW(UCA)Q GO:0005739 SGD_REF:S000073094|PMID:9159473 NAS C tW(UCA)Q gene taxon:4932 20030507 SGD
+SGD S000007337 tW(UCA)Q GO:0030533 SGD_REF:S000058438|PMID:9872396 NAS F tW(UCA)Q gene taxon:4932 20020220 SGD
+SGD S000007337 tW(UCA)Q GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tW(UCA)Q gene taxon:4932 20030507 SGD
+SGD S000006777 tX(XXX)D GO:0005829 SGD_REF:S000073094|PMID:9159473 NAS C tX(XXX)D gene taxon:4932 20030507 SGD
+SGD S000006777 tX(XXX)D GO:0030533 SGD_REF:S000073095|PMID:9443958 TAS F tX(XXX)D gene taxon:4932 20030507 SGD
+SGD S000006777 tX(XXX)D GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tX(XXX)D gene taxon:4932 20030507 SGD
+SGD S000007338 tY(GUA)Q GO:0005739 SGD_REF:S000073094|PMID:9159473 NAS C tY(GUA)Q gene taxon:4932 20030507 SGD
+SGD S000007338 tY(GUA)Q GO:0030533 SGD_REF:S000058438|PMID:9872396 NAS F tY(GUA)Q gene taxon:4932 20020220 SGD
+SGD S000007338 tY(GUA)Q GO:0006414 SGD_REF:S000073094|PMID:9159473 NAS P tY(GUA)Q gene taxon:4932 20030507 SGD
diff --git a/coreplugins/TableImport/src/test/resources/annotation/goslim_generic.obo b/coreplugins/TableImport/src/test/resources/annotation/goslim_generic.obo
new file mode 100644
index 0000000..1a8d2c9
--- /dev/null
+++ b/coreplugins/TableImport/src/test/resources/annotation/goslim_generic.obo
@@ -0,0 +1,1754 @@
+format-version: 1.0
+date: 18:08:2006 15:30
+saved-by: jclark
+auto-generated-by: OBO-Edit 1.002
+subsetdef: goslim_generic "Generic GO slim"
+subsetdef: goslim_goa "GOA and proteome slim"
+subsetdef: goslim_plant "Plant GO slim"
+subsetdef: goslim_yeast "Yeast GO slim"
+subsetdef: gosubset_prok "Prokaryotic GO subset"
+default-namespace: gene_ontology
+remark: cvs version: $Revision: 1.308 $
+remark: GO_slim_name: Generic GO slim
+remark: GO_slim_authors: Suparna Mundodi and Amelia Ireland
+remark: GO_slim_contact: smundodi at acoma.stanford.edu
+
+[Term]
+id: GO:0000003
+name: reproduction
+namespace: biological_process
+alt_id: GO:0019952
+def: "The production by an organism of new individuals that contain some portion of their genetic material inherited from that organism." [GOC:go_curators, ISBN:0198506732]
+subset: goslim_generic
+subset: goslim_plant
+subset: gosubset_prok
+is_a: GO:0008150
+
+[Term]
+id: GO:0000004
+name: biological process unknown
+namespace: biological_process
+def: "Used for the annotation of gene products whose process is not known or cannot be inferred." [GOC:sgd_curators]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+is_a: GO:0008150
+
+[Term]
+id: GO:0000166
+name: nucleotide binding
+namespace: molecular_function
+def: "Interacting selectively with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety." [GOC:mah, ISBN:0198547684]
+subset: goslim_generic
+subset: goslim_plant
+subset: gosubset_prok
+is_a: GO:0005488
+
+[Term]
+id: GO:0000228
+name: nuclear chromosome
+namespace: cellular_component
+def: "A chromosome found in the nucleus of a eukaryotic cell." [GOC:mah]
+subset: goslim_generic
+narrow_synonym: "nuclear interphase chromosome" []
+relationship: part_of GO:0005634
+is_a: GO:0005694
+
+[Term]
+id: GO:0000229
+name: cytoplasmic chromosome
+namespace: cellular_component
+def: "A chromosome found in the cytoplasm." [GOC:mah]
+subset: goslim_generic
+subset: gosubset_prok
+narrow_synonym: "cytoplasmic interphase chromosome" []
+is_a: GO:0005694
+relationship: part_of GO:0005737
+
+[Term]
+id: GO:0003674
+name: molecular_function
+namespace: molecular_function
+def: "Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions." [GOC:go_curators]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+
+[Term]
+id: GO:0003676
+name: nucleic acid binding
+namespace: molecular_function
+def: "Interacting selectively with any nucleic acid." [GOC:jl]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: gosubset_prok
+is_a: GO:0005488
+
+[Term]
+id: GO:0003677
+name: DNA binding
+namespace: molecular_function
+def: "Interacting selectively with DNA (deoxyribonucleic acid)." [GOC:jl]
+subset: goslim_generic
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+related_synonym: "microtubule/chromatin interaction" []
+narrow_synonym: "plasmid binding" []
+is_a: GO:0003676
+
+[Term]
+id: GO:0003682
+name: chromatin binding
+namespace: molecular_function
+def: "Interacting selectively with chromatin, the network of fibers of DNA and protein that make up the chromosomes of the eukaryotic nucleus during interphase." [GOC:jl, ISBN:0198506732]
+subset: goslim_generic
+subset: goslim_plant
+related_synonym: "microtubule/chromatin interaction" []
+narrow_synonym: "nuclear membrane vesicle binding to chromatin" []
+broad_synonym: "lamin/chromatin binding" []
+is_a: GO:0005488
+
+[Term]
+id: GO:0003700
+name: transcription factor activity
+namespace: molecular_function
+alt_id: GO:0000130
+def: "The function of binding to a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex." [GOC:curators]
+subset: goslim_generic
+subset: goslim_plant
+subset: gosubset_prok
+is_a: GO:0003677
+is_a: GO:0030528
+
+[Term]
+id: GO:0003723
+name: RNA binding
+namespace: molecular_function
+def: "Interacting selectively with an RNA molecule or a portion thereof." [GOC:mah]
+subset: goslim_generic
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+is_a: GO:0003676
+
+[Term]
+id: GO:0003774
+name: motor activity
+namespace: molecular_function
+def: "Catalysis of movement along a polymeric molecule such as a microfilament or microtubule, coupled to the hydrolysis of a nucleoside triphosphate." [GOC:mah, ISBN:0815316194]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+is_a: GO:0003674
+
+[Term]
+id: GO:0003779
+name: actin binding
+namespace: molecular_function
+def: "Interacting selectively with monomeric or multimeric forms of actin, including actin filaments." [GOC:clt]
+subset: goslim_generic
+narrow_synonym: "membrane associated actin binding" []
+is_a: GO:0008092
+
+[Term]
+id: GO:0003824
+name: catalytic activity
+namespace: molecular_function
+def: "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." [ISBN:0198506732]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: gosubset_prok
+related_synonym: "enzyme activity" []
+is_a: GO:0003674
+
+[Term]
+id: GO:0004518
+name: nuclease activity
+namespace: molecular_function
+def: "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN:0198547684]
+comment: Consider also annotating to the molecular function term 'nucleic acid binding ; GO:0003676'.
+subset: goslim_generic
+subset: goslim_plant
+subset: gosubset_prok
+xref_analog: EC:3.1.-.-
+is_a: GO:0016787
+
+[Term]
+id: GO:0004672
+name: protein kinase activity
+namespace: molecular_function
+alt_id: GO:0050222
+def: "Catalysis of the transfer of a phosphate group, usually from ATP, to a protein substrate." [GOC:jl]
+subset: goslim_generic
+subset: goslim_yeast
+subset: gosubset_prok
+narrow_synonym: "protamine kinase activity" []
+xref_analog: EC:2.7.1.37
+xref_analog: MetaCyc:PROTEIN-KINASE-RXN
+xref_analog: Reactome:4030
+is_a: GO:0016301
+
+[Term]
+id: GO:0004721
+name: phosphoprotein phosphatase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: a phosphoprotein + H2O = a protein + phosphate. Together with protein kinases, these enzymes control the state of phosphorylation of cell proteins and thereby provide an important mechanism for regulating cellular activity." [EC:3.1.3.16, ISBN:0198547684]
+subset: goslim_generic
+subset: goslim_yeast
+subset: gosubset_prok
+exact_synonym: "protein phosphatase activity" []
+xref_analog: EC:3.1.3.16
+xref_analog: MetaCyc:3.1.3.16-RXN
+xref_analog: Reactome:113432
+xref_analog: Reactome:113757
+xref_analog: Reactome:115322
+xref_analog: Reactome:115328
+xref_analog: Reactome:115332
+xref_analog: Reactome:117849
+xref_analog: Reactome:117855
+xref_analog: Reactome:117859
+xref_analog: Reactome:117862
+xref_analog: Reactome:120480
+xref_analog: Reactome:120488
+xref_analog: Reactome:122808
+xref_analog: Reactome:122814
+xref_analog: Reactome:122818
+xref_analog: Reactome:124864
+xref_analog: Reactome:124870
+xref_analog: Reactome:1887
+xref_analog: Reactome:69198
+xref_analog: Reactome:69262
+xref_analog: Reactome:69735
+xref_analog: Reactome:69742
+is_a: GO:0016787
+
+[Term]
+id: GO:0004871
+name: signal transducer activity
+namespace: molecular_function
+def: "Mediates the transfer of a signal from the outside to the inside of a cell by means other than the introduction of the signal molecule itself into the cell." [GOC:jl, ISBN:0198506732]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+narrow_synonym: "SAP kinase 3 activity" []
+narrow_synonym: "SAP kinase 4 activity" []
+narrow_synonym: "SAP kinase 5 activity" []
+is_a: GO:0003674
+
+[Term]
+id: GO:0004872
+name: receptor activity
+namespace: molecular_function
+def: "Combining with an extracellular or intracellular messenger to initiate a change in cell activity." [GOC:ceb, ISBN:0198506732]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: gosubset_prok
+related_synonym: "immunophilin" []
+narrow_synonym: "endoplasmic reticulum receptor activity" []
+narrow_synonym: "GPI-anchored membrane-bound receptor" []
+narrow_synonym: "peroxisome integral membrane receptor" []
+narrow_synonym: "peroxisome receptor" []
+narrow_synonym: "receptor guanylate cyclase activity" []
+is_a: GO:0004871
+
+[Term]
+id: GO:0005102
+name: receptor binding
+namespace: molecular_function
+def: "Interacting selectively with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function." [GOC:bf, GOC:ceb, ISBN:0198506732]
+subset: goslim_generic
+subset: goslim_plant
+subset: gosubset_prok
+related_synonym: "adrenocorticotropin" []
+related_synonym: "allatostatin" []
+related_synonym: "alpha-2 macroglobulin receptor-associated protein activity" []
+related_synonym: "bacteriocin activity" []
+related_synonym: "cell adhesion molecule activity" []
+related_synonym: "cell adhesion receptor inhibitor activity" []
+related_synonym: "cell adhesion receptor regulator activity" []
+related_synonym: "colicin" []
+related_synonym: "insulin" []
+related_synonym: "membrane-associated guanylate kinase" []
+related_synonym: "N-methyl-D-aspartate receptor-associated protein activity" []
+related_synonym: "nicotinic acetylcholine receptor-associated protein activity" []
+related_synonym: "receptor-associated protein activity" []
+related_synonym: "selectin" []
+related_synonym: "tachykinin" []
+related_synonym: "transmembrane receptor protein serine/threonine kinase related_receptor-associated protein activity" []
+narrow_synonym: "receptor ligand" []
+is_a: GO:0004871
+is_a: GO:0005515
+
+[Term]
+id: GO:0005198
+name: structural molecule activity
+namespace: molecular_function
+def: "The action of a molecule that contributes to the structural integrity of a complex or assembly within or outside a cell." [GOC:mah]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+related_synonym: "colicin" []
+related_synonym: "pore-forming toxin activity" []
+related_synonym: "puparial glue (sensu Diptera)" []
+related_synonym: "yolk protein" []
+is_a: GO:0003674
+
+[Term]
+id: GO:0005215
+name: transporter activity
+namespace: molecular_function
+def: "Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of, within or between cells." [GOC:ai, GOC:df]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+related_synonym: "small-molecule carrier or transporter" []
+narrow_synonym: "peroxisomal membrane transporter" []
+xref_analog: Reactome:1391
+is_a: GO:0003674
+
+[Term]
+id: GO:0005216
+name: ion channel activity
+namespace: molecular_function
+def: "Allows the regulatable energy-independent passage of ions across a lipid bilayer down a concentration gradient." [GOC:cy]
+subset: goslim_generic
+subset: gosubset_prok
+is_a: GO:0005215
+
+[Term]
+id: GO:0005326
+name: neurotransmitter transporter activity
+namespace: molecular_function
+def: "Enables the directed movement of a neurotransmitter into, out of, within or between cells. Neurotransmitters are any chemical substance that is capable of transmitting (or inhibiting the transmission of) a nerve impulse from a neuron to another cell." [GOC:ai, ISBN:0198506732]
+subset: goslim_generic
+subset: gosubset_prok
+is_a: GO:0005215
+
+[Term]
+id: GO:0005488
+name: binding
+namespace: molecular_function
+def: "The selective, often stoichiometric interaction of a molecule with one or more specific sites on another molecule." [GOC:ceb, GOC:mah, ISBN:0198506732]
+comment: Note that ligand is being used in its broadest biological sense. For ligands that bind to signal transducing receptors, consider the molecular function term 'receptor binding ; GO:0005102' and its children.
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: gosubset_prok
+narrow_synonym: "ligand" []
+is_a: GO:0003674
+
+[Term]
+id: GO:0005509
+name: calcium ion binding
+namespace: molecular_function
+def: "Interacting selectively with calcium ions (Ca2+)." [GOC:ai]
+subset: goslim_generic
+subset: gosubset_prok
+related_synonym: "calcium ion storage activity" []
+related_synonym: "fibrillin" []
+is_a: GO:0005488
+
+[Term]
+id: GO:0005515
+name: protein binding
+namespace: molecular_function
+alt_id: GO:0045308
+def: "Interacting selectively with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC:go_curators]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+related_synonym: "alpha-2 macroglobulin receptor-associated protein activity" []
+related_synonym: "calcium-dependent cell adhesion molecule activity" []
+related_synonym: "calcium-independent cell adhesion molecule activity" []
+related_synonym: "cell adhesion molecule activity" []
+related_synonym: "death receptor adaptor protein activity" []
+related_synonym: "death receptor interacting protein activity" []
+related_synonym: "death receptor-associated factor activity" []
+related_synonym: "glycine receptor-associated protein" []
+related_synonym: "N-methyl-D-aspartate receptor-associated protein activity" []
+related_synonym: "nicotinic acetylcholine receptor-associated protein activity" []
+related_synonym: "protein degradation tagging activity" []
+related_synonym: "protein tagging activity" []
+related_synonym: "receptor-associated protein activity" []
+exact_synonym: "protein amino acid binding" []
+is_a: GO:0005488
+
+[Term]
+id: GO:0005554
+name: molecular function unknown
+namespace: molecular_function
+def: "Used for the annotation of gene products whose function is not known or cannot be inferred." [GOC:sgd_curators]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+is_a: GO:0003674
+
+[Term]
+id: GO:0005575
+name: cellular_component
+namespace: cellular_component
+def: "The part of a cell of which a gene product is a component; for purpose of GO includes the extracellular environment of cells; a gene product may be a component of one or more parts of a cell; this term includes gene products that are parts of macromolecular complexes, by the definition that all members of a complex normally copurify under all except extreme conditions." [GOC:go_curators]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+
+[Term]
+id: GO:0005576
+name: extracellular region
+namespace: cellular_component
+def: "The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite." [GOC:go_curators]
+comment: Note that this term is intended to annotate gene products that are not attached to the cell surface.
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+exact_synonym: "extracellular" []
+is_a: GO:0005575
+
+[Term]
+id: GO:0005578
+name: extracellular matrix (sensu Metazoa)
+namespace: cellular_component
+def: "A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity. As in, but not restricted to, the multicellular animals (Metazoa, ncbi_taxonomy_id:33208)." [ISBN:0198547684]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+narrow_synonym: "adhesive extracellular matrix constituent" []
+relationship: part_of GO:0005576
+
+[Term]
+id: GO:0005615
+name: extracellular space
+namespace: cellular_component
+def: "That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid." [ISBN:0198547684]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+related_synonym: "intercellular space" []
+relationship: part_of GO:0005576
+
+[Term]
+id: GO:0005618
+name: cell wall
+namespace: cellular_component
+def: "The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan." [ISBN:0198547684]
+subset: goslim_generic
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+is_a: GO:0030312
+
+[Term]
+id: GO:0005622
+name: intracellular
+namespace: cellular_component
+def: "The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm." [ISBN:0198506732]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: gosubset_prok
+exact_synonym: "protoplasm" []
+relationship: part_of GO:0005623
+
+[Term]
+id: GO:0005623
+name: cell
+namespace: cellular_component
+def: "The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope." [GOC:go_curators]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: gosubset_prok
+is_a: GO:0005575
+
+[Term]
+id: GO:0005634
+name: nucleus
+namespace: cellular_component
+def: "A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent." [GOC:go_curators]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: goslim_yeast
+relationship: part_of GO:0005622
+is_a: GO:0043226
+
+[Term]
+id: GO:0005635
+name: nuclear envelope
+namespace: cellular_component
+alt_id: GO:0005636
+def: "The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space)." [ISBN:0198547684]
+subset: goslim_generic
+subset: goslim_plant
+relationship: part_of GO:0005634
+
+[Term]
+id: GO:0005654
+name: nucleoplasm
+namespace: cellular_component
+def: "That part of the nuclear content other than the chromosomes or the nucleolus." [GOC:ma, ISBN:0124325653]
+subset: goslim_generic
+subset: goslim_plant
+relationship: part_of GO:0005634
+
+[Term]
+id: GO:0005694
+name: chromosome
+namespace: cellular_component
+def: "A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information." [ISBN:0198547684]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_yeast
+subset: gosubset_prok
+related_synonym: "chromatid" []
+narrow_synonym: "interphase chromosome" []
+narrow_synonym: "prophase chromosome" []
+relationship: part_of GO:0005622
+is_a: GO:0043226
+
+[Term]
+id: GO:0005730
+name: nucleolus
+namespace: cellular_component
+def: "A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association res [...]
+subset: goslim_generic
+subset: goslim_plant
+subset: goslim_yeast
+relationship: part_of GO:0005634
+
+[Term]
+id: GO:0005737
+name: cytoplasm
+namespace: cellular_component
+def: "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN:0198547684]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+relationship: part_of GO:0005622
+
+[Term]
+id: GO:0005739
+name: mitochondrion
+namespace: cellular_component
+def: "A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration." [ISBN:0198506732]
+subset: goslim_generic
+subset: goslim_plant
+subset: goslim_yeast
+exact_synonym: "mitochondria" []
+relationship: part_of GO:0005737
+is_a: GO:0043226
+
+[Term]
+id: GO:0005764
+name: lysosome
+namespace: cellular_component
+def: "Any of a group of related cytoplasmic, membrane bound organelles that are found in most animal cells and that contain a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions." [ISBN:0198506732]
+subset: goslim_generic
+subset: goslim_plant
+related_synonym: "lysosomal cysteine-type endopeptidase" []
+related_synonym: "lysosomal protein stabilization" []
+is_a: GO:0005773
+
+[Term]
+id: GO:0005768
+name: endosome
+namespace: cellular_component
+def: "A membrane-bound organelle that carries materials newly ingested by endocytosis. It passes many of the materials to lysosomes for degradation." [ISBN:0198506732]
+subset: goslim_generic
+subset: goslim_plant
+related_synonym: "endosomal oligosaccharide transporter" []
+relationship: part_of GO:0005737
+is_a: GO:0043226
+
+[Term]
+id: GO:0005773
+name: vacuole
+namespace: cellular_component
+def: "A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material." [ISBN:0198506732]
+subset: goslim_generic
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+related_synonym: "vacuolar carboxypeptidase Y" []
+relationship: part_of GO:0005737
+is_a: GO:0043226
+
+[Term]
+id: GO:0005777
+name: peroxisome
+namespace: cellular_component
+alt_id: GO:0019818
+def: "A small, membrane-bounded organelle that uses dioxygen (O2) to oxidize organic molecules; contains some enzymes that produce and others that degrade hydrogen peroxide (H2O2)." [ISBN:0815316194]
+subset: goslim_generic
+subset: goslim_plant
+subset: goslim_yeast
+related_synonym: "peroxisomal fatty acyl transporter" []
+related_synonym: "peroxisomal membrane transporter" []
+related_synonym: "peroxisome receptor" []
+broad_synonym: "peroxisome vesicle" []
+relationship: part_of GO:0005737
+is_a: GO:0043226
+
+[Term]
+id: GO:0005783
+name: endoplasmic reticulum
+namespace: cellular_component
+def: "The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached)." [ISBN:0198506732]
+subset: goslim_generic
+subset: goslim_plant
+subset: goslim_yeast
+exact_synonym: "ER" []
+relationship: part_of GO:0005737
+is_a: GO:0043226
+
+[Term]
+id: GO:0005794
+name: Golgi apparatus
+namespace: cellular_component
+def: "A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cell [...]
+comment: Note that the Golgi apparatus can be located in various places in the cytoplasm. In plants and lower animal cells, the Golgi apparatus exists as many copies of discrete stacks dispersed throughout the cytoplasm, while the Golgi apparatus of interphase mammalian cells is a juxtanuclear, often pericentriolar reticulum, where the discrete Golgi stacks are stitched together to form a compact and interconnected ribbon, sometimes called the Golgi ribbon.
+subset: goslim_generic
+subset: goslim_plant
+subset: goslim_yeast
+exact_synonym: "Golgi" []
+exact_synonym: "Golgi complex" []
+narrow_synonym: "Golgi ribbon" []
+relationship: part_of GO:0005737
+is_a: GO:0043226
+
+[Term]
+id: GO:0005811
+name: lipid particle
+namespace: cellular_component
+def: "Any particle of coalesced lipids in the cytoplasm of a cell. May include associated proteins." [GOC:mah]
+comment: Note that this term does not refer to vesicle, but instead to structures in which lipids do not necessarily form bilayers.
+subset: goslim_generic
+exact_synonym: "lipid droplet" []
+relationship: part_of GO:0005737
+
+[Term]
+id: GO:0005815
+name: microtubule organizing center
+namespace: cellular_component
+def: "A region in a eukaryotic cell, such as a centrosome or basal body, from which microtubules grow." [ISBN:0815316194]
+subset: goslim_generic
+subset: goslim_yeast
+exact_synonym: "microtubule organising centre" []
+exact_synonym: "MTOC" []
+relationship: part_of GO:0005737
+
+[Term]
+id: GO:0005829
+name: cytosol
+namespace: cellular_component
+def: "That part of the cytoplasm that does not contain membranous or particulate subcellular components." [ISBN:0198547684]
+subset: goslim_generic
+subset: goslim_plant
+subset: gosubset_prok
+relationship: part_of GO:0005737
+
+[Term]
+id: GO:0005840
+name: ribosome
+namespace: cellular_component
+def: "An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) [...]
+subset: goslim_generic
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+narrow_synonym: "ribosomal RNA" []
+relationship: part_of GO:0005737
+is_a: GO:0043226
+is_a: GO:0043234
+
+[Term]
+id: GO:0005856
+name: cytoskeleton
+namespace: cellular_component
+def: "Any of the various filamentous elements within the cytoplasm of eukaryotic cells that remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, and the microtrabecular lattice. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movem [...]
+subset: goslim_generic
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+relationship: part_of GO:0005622
+is_a: GO:0043226
+
+[Term]
+id: GO:0005886
+name: plasma membrane
+namespace: cellular_component
+def: "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN:0716731363]
+subset: goslim_generic
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+related_synonym: "plasma membrane cation-transporting ATPase" []
+related_synonym: "plasma membrane copper transporter" []
+related_synonym: "plasma membrane long-chain fatty acid transporter" []
+exact_synonym: "cell membrane" []
+exact_synonym: "cytoplasmic membrane" []
+exact_synonym: "plasmalemma" []
+narrow_synonym: "bacterial inner membrane" []
+broad_synonym: "juxtamembrane" []
+relationship: part_of GO:0005623
+
+[Term]
+id: GO:0005929
+name: cilium
+namespace: cellular_component
+def: "A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole." [GOC:kva, ISBN:0198547684]
+subset: goslim_generic
+relationship: part_of GO:0005622
+is_a: GO:0043226
+
+[Term]
+id: GO:0005941
+name: unlocalized protein complex
+namespace: cellular_component
+def: "Used as a holding place for cellular components whose precise localization is, as yet, unknown, or has not been determined by GO (the latter is the major reason for nodes to have this parent); this term should not be used for annotation of gene products." [GOC:ma]
+comment: See also the cellular component term 'cellular component unknown ; GO:0008372'.
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: gosubset_prok
+is_a: GO:0043234
+
+[Term]
+id: GO:0005975
+name: carbohydrate metabolism
+namespace: biological_process
+def: "The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y." [ISBN:0198506732]
+subset: goslim_generic
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+is_a: GO:0044238
+
+[Term]
+id: GO:0006091
+name: generation of precursor metabolites and energy
+namespace: biological_process
+def: "The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and the processes involved in the liberation of energy from these substances." [GOC:jl]
+subset: goslim_generic
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+broad_synonym: "energy pathways" []
+is_a: GO:0008152
+
+[Term]
+id: GO:0006118
+name: electron transport
+namespace: biological_process
+def: "The transport of electrons from an electron donor to an electron acceptor." [http://cancerweb.ncl.ac.uk/]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+related_synonym: "6-phosphofructokinase reduction" []
+related_synonym: "dihydrobiopterin reduction" []
+related_synonym: "dihydrolipoamide reduction" []
+related_synonym: "dihydrolipoylprotein reduction" []
+related_synonym: "dihydropteridine reduction" []
+related_synonym: "other pathways of electron transport" []
+related_synonym: "oxidized glutathione reduction" []
+related_synonym: "protein-disulfide reduction" []
+exact_synonym: "electron transfer" []
+is_a: GO:0006091
+is_a: GO:0006810
+
+[Term]
+id: GO:0006139
+name: nucleobase, nucleoside, nucleotide and nucleic acid metabolism
+namespace: biological_process
+def: "The chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids." [GOC:ai]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: gosubset_prok
+is_a: GO:0044238
+
+[Term]
+id: GO:0006259
+name: DNA metabolism
+namespace: biological_process
+def: "The chemical reactions and pathways involving DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN:0198506732]
+subset: goslim_generic
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+is_a: GO:0006139
+
+[Term]
+id: GO:0006350
+name: transcription
+namespace: biological_process
+def: "The synthesis of either RNA on a template of DNA or DNA on a template of RNA." [ISBN:0198506732]
+subset: goslim_generic
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+xref_analog: Reactome:74159
+is_a: GO:0006139
+
+[Term]
+id: GO:0006412
+name: protein biosynthesis
+namespace: biological_process
+alt_id: GO:0006416
+alt_id: GO:0006453
+def: "The chemical reactions and pathways resulting in the formation of a protein, rather than of proteins in general." [GOC:go_curators]
+subset: goslim_generic
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+related_synonym: "protein-synthesizing GTPase activity" []
+related_synonym: "protein-synthesizing GTPase activity, elongation" []
+related_synonym: "protein-synthesizing GTPase activity, initiation" []
+related_synonym: "protein-synthesizing GTPase activity, termination" []
+exact_synonym: "protein anabolism" []
+exact_synonym: "protein formation" []
+exact_synonym: "protein synthesis" []
+is_a: GO:0009058
+is_a: GO:0019538
+
+[Term]
+id: GO:0006464
+name: protein modification
+namespace: biological_process
+def: "The covalent alteration of one or more amino acid residues within a protein, resulting in a change in the properties of that protein." [GOC:go_curators]
+subset: goslim_generic
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+related_synonym: "protein tagging activity" []
+narrow_synonym: "protein-pyrroloquinoline-quinone linkage" []
+xref_analog: Reactome:163841
+is_a: GO:0019538
+
+[Term]
+id: GO:0006519
+name: amino acid and derivative metabolism
+namespace: biological_process
+def: "The chemical reactions and pathways involving amino acids, organic acids containing one or more amino substituents, and compounds derived from amino acids." [ISBN:0198506732]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+is_a: GO:0044238
+
+[Term]
+id: GO:0006629
+name: lipid metabolism
+namespace: biological_process
+def: "The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids." [GOC:ma]
+subset: goslim_generic
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+is_a: GO:0044238
+
+[Term]
+id: GO:0006810
+name: transport
+namespace: biological_process
+def: "The directed movement of substances (such as macromolecules, small molecules, ions) into, out of, within or between cells." [GOC:mah]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+related_synonym: "hydrolase activity, acting on acid anhydrides, acting on GTP, involved in cellular and subcellular movement" []
+narrow_synonym: "small molecule transport" []
+narrow_synonym: "solute:solute exchange" []
+relationship: part_of GO:0007582
+
+[Term]
+id: GO:0006811
+name: ion transport
+namespace: biological_process
+def: "The directed movement of charged atoms or small charged molecules into, out of, within or between cells." [GOC:ai]
+subset: goslim_generic
+subset: gosubset_prok
+is_a: GO:0006810
+
+[Term]
+id: GO:0006950
+name: response to stress
+namespace: biological_process
+def: "A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation)." [GOC:mah]
+subset: goslim_generic
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+is_a: GO:0008150
+
+[Term]
+id: GO:0006996
+name: organelle organization and biogenesis
+namespace: biological_process
+def: "The assembly and arrangement of any organelle within a cell." [GOC:mah]
+subset: goslim_generic
+subset: goslim_yeast
+subset: gosubset_prok
+exact_synonym: "organelle organisation and biogenesis" []
+is_a: GO:0016043
+
+[Term]
+id: GO:0007005
+name: mitochondrion organization and biogenesis
+namespace: biological_process
+def: "The assembly and arrangement of a mitochondrion, including mitochondrial morphology and distribution, and replication of the mitochondrial genome as well as synthesis of new mitochondrial components." [GOC:mah, GOC:sgd_curators, PMID:9786946]
+subset: goslim_generic
+exact_synonym: "mitochondria organization and biogenesis" []
+exact_synonym: "mitochondrion organisation and biogenesis" []
+is_a: GO:0006996
+
+[Term]
+id: GO:0007010
+name: cytoskeleton organization and biogenesis
+namespace: biological_process
+def: "The assembly and arrangement of cytoskeletal structures." [GOC:mah]
+subset: goslim_generic
+subset: goslim_yeast
+subset: gosubset_prok
+related_synonym: "cytoskeletal regulator activity" []
+related_synonym: "negative regulation of cytoskeleton" []
+related_synonym: "positive regulation of cytoskeleton" []
+related_synonym: "regulation of cytoskeleton" []
+related_synonym: "Rho small monomeric GTPase activity" []
+exact_synonym: "cytoskeleton organisation and biogenesis" []
+is_a: GO:0006996
+
+[Term]
+id: GO:0007028
+name: cytoplasm organization and biogenesis
+namespace: biological_process
+def: "The assembly and arrangement of the cytoplasm and its components." [GOC:ems]
+subset: goslim_generic
+subset: gosubset_prok
+exact_synonym: "cytoplasm organisation and biogenesis" []
+is_a: GO:0016043
+
+[Term]
+id: GO:0007049
+name: cell cycle
+namespace: biological_process
+def: "The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division." [GOC:go_curators]
+subset: goslim_generic
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+exact_synonym: "cell-division cycle" []
+is_a: GO:0007582
+
+[Term]
+id: GO:0007154
+name: cell communication
+namespace: biological_process
+def: "Any process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment." [GOC:mah]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: gosubset_prok
+is_a: GO:0008150
+
+[Term]
+id: GO:0007165
+name: signal transduction
+namespace: biological_process
+def: "The cascade of processes by which a signal interacts with a receptor, causing a change in the level or activity of a second messenger or other downstream target, and ultimately effecting a change in the functioning of the cell." [GOC:go_curators]
+subset: goslim_generic
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+narrow_synonym: "activation of MAPK during sporulation (sensu Fungi)" []
+narrow_synonym: "activation of MAPK during sporulation (sensu Saccharomyces)" []
+narrow_synonym: "activation of MAPKK during sporulation (sensu Fungi)" []
+narrow_synonym: "activation of MAPKK during sporulation (sensu Saccharomyces)" []
+narrow_synonym: "activation of MAPKKK during sporulation (sensu Fungi)" []
+narrow_synonym: "activation of MAPKKK during sporulation (sensu Saccharomyces)" []
+narrow_synonym: "inactivation of MAPK during sporulation (sensu Fungi)" []
+narrow_synonym: "inactivation of MAPK during sporulation (sensu Saccharomyces)" []
+narrow_synonym: "MAPKKK cascade during sporulation (sensu Fungi)" []
+narrow_synonym: "MAPKKK cascade during sporulation (sensu Saccharomyces)" []
+is_a: GO:0007154
+
+[Term]
+id: GO:0007267
+name: cell-cell signaling
+namespace: biological_process
+def: "Any process that mediates the transfer of information from one cell to another." [GOC:mah]
+subset: goslim_generic
+subset: goslim_plant
+subset: gosubset_prok
+exact_synonym: "cell-cell signalling" []
+is_a: GO:0007154
+
+[Term]
+id: GO:0007275
+name: development
+namespace: biological_process
+def: "The biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, a young adult or a young single celled organism) to a later condition (e.g. a multicellular animal, an aged adult or a mature single celled organism)." [GOC:ems]
+comment: Note that this term was 'developmental process'.
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: gosubset_prok
+is_a: GO:0008150
+
+[Term]
+id: GO:0007582
+name: physiological process
+namespace: biological_process
+def: "Those processes specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms." [GOC:ems, ISBN:0198506732]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: gosubset_prok
+is_a: GO:0008150
+
+[Term]
+id: GO:0007610
+name: behavior
+namespace: biological_process
+def: "The specific actions or reactions of an organism in response to external or internal stimuli. Patterned activity of a whole organism in a manner dependent upon some combination of that organism's internal state and external conditions." [GOC:ems, ISBN:0395448956]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+exact_synonym: "behavioral response to stimulus" []
+exact_synonym: "behaviour" []
+exact_synonym: "behavioural response to stimulus" []
+is_a: GO:0008150
+
+[Term]
+id: GO:0008037
+name: cell recognition
+namespace: biological_process
+def: "The process by which a cell in a multicellular organism interprets its surroundings." [GOC:go_curators]
+subset: goslim_generic
+is_a: GO:0008150
+
+[Term]
+id: GO:0008092
+name: cytoskeletal protein binding
+namespace: molecular_function
+def: "Interacting selectively with any protein component of any cytoskeleton (actin, microtubule, or intermediate filament cytoskeleton)." [GOC:mah]
+subset: goslim_generic
+subset: gosubset_prok
+is_a: GO:0005515
+
+[Term]
+id: GO:0008135
+name: translation factor activity, nucleic acid binding
+namespace: molecular_function
+def: "Functions during translation by binding nucleic acids during polypeptide synthesis at the ribosome." [GOC:ai]
+subset: goslim_generic
+subset: goslim_plant
+subset: gosubset_prok
+related_synonym: "protein-synthesizing GTPase activity" []
+is_a: GO:0003676
+is_a: GO:0045182
+
+[Term]
+id: GO:0008150
+name: biological_process
+namespace: biological_process
+def: "A phenomenon marked by changes that lead to a particular result, mediated by one or more gene products." [GOC:go_curators]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+
+[Term]
+id: GO:0008152
+name: metabolism
+namespace: biological_process
+def: "Processes that cause many of the chemical changes in living organisms, including anabolism and catabolism. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation." [GOC:go_curators, ISBN:0198547684]
+comment: Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions.
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: gosubset_prok
+exact_synonym: "metabolic process" []
+narrow_synonym: "fat body metabolism (sensu Insecta)" []
+narrow_synonym: "metabolism resulting in cell growth" []
+xref_analog: Reactome:71408
+is_a: GO:0007582
+
+[Term]
+id: GO:0008219
+name: cell death
+namespace: biological_process
+def: "The specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death." [GOC:ems]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: gosubset_prok
+related_synonym: "necrosis" []
+is_a: GO:0016265
+
+[Term]
+id: GO:0008233
+name: peptidase activity
+namespace: molecular_function
+def: "Catalysis of the hydrolysis of peptide bonds." [GOC:jl]
+subset: goslim_generic
+subset: goslim_yeast
+subset: gosubset_prok
+exact_synonym: "hydrolase, acting on peptide bonds" []
+exact_synonym: "peptide hydrolase" []
+exact_synonym: "protease" []
+narrow_synonym: "proteasome endopeptidase activity" []
+xref_analog: EC:3.4.-.-
+is_a: GO:0016787
+
+[Term]
+id: GO:0008283
+name: cell proliferation
+namespace: biological_process
+def: "The multiplication or reproduction of cells, resulting in the rapid expansion of a cell population." [GOC:mah, GOC:mb]
+subset: goslim_generic
+subset: gosubset_prok
+is_a: GO:0007582
+
+[Term]
+id: GO:0008289
+name: lipid binding
+namespace: molecular_function
+def: "Interacting selectively with a lipid." [GOC:ai]
+subset: goslim_generic
+subset: goslim_plant
+subset: gosubset_prok
+is_a: GO:0005488
+
+[Term]
+id: GO:0008372
+name: cellular component unknown
+namespace: cellular_component
+def: "Used for the annotation of gene products whose localization is not known or cannot be inferred." [GOC:ma]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+is_a: GO:0005575
+
+[Term]
+id: GO:0009055
+name: electron carrier activity
+namespace: molecular_function
+def: "Any molecular entity that serves as an electron acceptor and electron donor in an electron transport system." [ISBN:0198506732]
+subset: goslim_generic
+subset: goslim_goa
+subset: gosubset_prok
+related_synonym: "electron carrier, chlorophyll electron transport system" []
+exact_synonym: "electron transporter activity" []
+narrow_synonym: "2Fe-2S electron transfer carrier" []
+narrow_synonym: "3Fe-4S/4Fe-4S electron transfer carrier" []
+narrow_synonym: "adrenodoxin-type ferredoxin" []
+narrow_synonym: "amicyanin" []
+narrow_synonym: "azurin" []
+narrow_synonym: "bacterial-type ferredoxin" []
+narrow_synonym: "chloroplast-type ferredoxin" []
+narrow_synonym: "copper electron carrier" []
+narrow_synonym: "dicluster bacterial-type ferredoxin" []
+narrow_synonym: "electron transfer flavoprotein" []
+narrow_synonym: "electron transfer flavoprotein, group I" []
+narrow_synonym: "electron transfer flavoprotein, group II" []
+narrow_synonym: "high-potential iron-sulfur carrier" []
+narrow_synonym: "iron-sulfur electron transfer carrier" []
+narrow_synonym: "monocluster bacterial-type ferredoxin" []
+narrow_synonym: "mononuclear iron electron carrier" []
+narrow_synonym: "polyferredoxin" []
+narrow_synonym: "redox-active disulfide bond electron carrier" []
+narrow_synonym: "rubredoxin" []
+narrow_synonym: "small blue copper electron carrier" []
+narrow_synonym: "thioredoxin-like 2Fe-2S ferredoxin" []
+is_a: GO:0003824
+
+[Term]
+id: GO:0009056
+name: catabolism
+namespace: biological_process
+def: "The chemical reactions and pathways resulting in the breakdown of substances, including the breakdown of carbon compounds with the liberation of energy for use by the cell or organism." [ISBN:0198547684]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: gosubset_prok
+exact_synonym: "breakdown" []
+exact_synonym: "degradation" []
+is_a: GO:0008152
+
+[Term]
+id: GO:0009058
+name: biosynthesis
+namespace: biological_process
+def: "The energy-requiring part of metabolism in which simpler substances are transformed into more complex ones, as in growth and other biosynthetic processes." [ISBN:0198547684]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: gosubset_prok
+exact_synonym: "anabolism" []
+exact_synonym: "formation" []
+exact_synonym: "synthesis" []
+is_a: GO:0008152
+
+[Term]
+id: GO:0009536
+name: plastid
+namespace: cellular_component
+def: "Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid." [GOC:jl, ISBN:0198547684]
+subset: goslim_generic
+subset: goslim_plant
+subset: gosubset_prok
+relationship: part_of GO:0005737
+is_a: GO:0043226
+
+[Term]
+id: GO:0009579
+name: thylakoid
+namespace: cellular_component
+def: "A sac-like vesicle that bears the photosynthetic pigments in photosynthetic organisms. In prokaryotes the thylakoids are of various shapes and are attached to the plasma membrane. In eukaryotes they are flattened, membrane-bound disk-like structures located in the chloroplasts; in the chloroplasts of higher plants the thylakoids form dense stacks called grana. Isolated thylakoid preparations can carry out photosynthetic electron transport and the associated phosphorylation." [ISBN: [...]
+subset: goslim_generic
+subset: goslim_plant
+subset: gosubset_prok
+related_synonym: "photosynthetic membrane" []
+relationship: part_of GO:0005622
+is_a: GO:0043226
+
+[Term]
+id: GO:0009605
+name: response to external stimulus
+namespace: biological_process
+def: "A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an external stimulus." [GOC:hb]
+subset: goslim_generic
+subset: goslim_plant
+subset: gosubset_prok
+exact_synonym: "response to environmental stimulus" []
+is_a: GO:0008150
+
+[Term]
+id: GO:0009607
+name: response to biotic stimulus
+namespace: biological_process
+def: "A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a biotic stimulus, a stimulus caused or produced by a living organism." [GOC:hb]
+subset: goslim_generic
+subset: goslim_plant
+subset: gosubset_prok
+is_a: GO:0008150
+
+[Term]
+id: GO:0009628
+name: response to abiotic stimulus
+namespace: biological_process
+def: "A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an abiotic (non-living) stimulus." [GOC:hb]
+subset: goslim_generic
+subset: goslim_plant
+subset: gosubset_prok
+is_a: GO:0008150
+
+[Term]
+id: GO:0009653
+name: morphogenesis
+namespace: biological_process
+def: "The process by which anatomical structures are generated and organized. Morphogenesis pertains to the creation of form." [GOC:go_curators, ISBN:0521436125]
+subset: goslim_generic
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+broad_synonym: "embryogenesis and morphogenesis" []
+relationship: part_of GO:0007275
+
+[Term]
+id: GO:0009719
+name: response to endogenous stimulus
+namespace: biological_process
+def: "A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an endogenous stimulus." [GOC:sm]
+subset: goslim_generic
+subset: goslim_plant
+subset: gosubset_prok
+is_a: GO:0008150
+
+[Term]
+id: GO:0009790
+name: embryonic development
+namespace: biological_process
+alt_id: GO:0009795
+def: "The process whose specific outcome is the progression of an embryo from zygote formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific and may be somewhat arbitrary. For example, it would be at birth for mammals, larval hatching for insects and seed dormancy in plants." [GOC:go_curators]
+subset: goslim_generic
+subset: goslim_plant
+exact_synonym: "embryogenesis" []
+exact_synonym: "embryonal development" []
+broad_synonym: "embryogenesis and morphogenesis" []
+is_a: GO:0007275
+
+[Term]
+id: GO:0015031
+name: protein transport
+namespace: biological_process
+alt_id: GO:0015831
+def: "The directed movement of proteins into, out of, within or between cells." [GOC:ai]
+subset: goslim_generic
+subset: gosubset_prok
+narrow_synonym: "enzyme transport" []
+is_a: GO:0006810
+
+[Term]
+id: GO:0016023
+name: cytoplasmic membrane-bound vesicle
+namespace: cellular_component
+def: "A membrane-bound vesicle found in the cytoplasm of the cell." [GOC:ai, GOC:mah]
+subset: goslim_generic
+subset: goslim_yeast
+subset: gosubset_prok
+exact_synonym: "cytoplasmic membrane bound vesicle" []
+relationship: part_of GO:0005737
+is_a: GO:0043226
+
+[Term]
+id: GO:0016032
+name: viral life cycle
+namespace: biological_process
+def: "A set of processes by which a virus reproduces. Usually, this is by infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle." [GOC:mah]
+comment: See also the biological process terms 'viral infectious cycle ; GO:0019058' and 'lysogeny ; GO:0030069'.
+subset: goslim_generic
+related_synonym: "viral infection" []
+related_synonym: "virulence" []
+exact_synonym: "viral replication cycle" []
+is_a: GO:0008150
+
+[Term]
+id: GO:0016043
+name: cell organization and biogenesis
+namespace: biological_process
+def: "The processes involved in the assembly and arrangement of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope." [GOC:ai]
+subset: goslim_generic
+subset: goslim_plant
+subset: gosubset_prok
+exact_synonym: "cell organisation and biogenesis" []
+is_a: GO:0007582
+
+[Term]
+id: GO:0016049
+name: cell growth
+namespace: biological_process
+def: "The process by which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present." [GOC:ai]
+subset: goslim_generic
+subset: goslim_plant
+subset: gosubset_prok
+related_synonym: "cell expansion" []
+related_synonym: "metabolism resulting in cell growth" []
+exact_synonym: "cellular growth" []
+exact_synonym: "growth of cell" []
+relationship: part_of GO:0009653
+relationship: part_of GO:0016043
+is_a: GO:0040007
+
+[Term]
+id: GO:0016209
+name: antioxidant activity
+namespace: molecular_function
+def: "Inhibition of the reactions brought about by dioxygen (O2) or peroxides. Usually the antioxidant is effective because it can itself be more easily oxidized than the substance protected. The term is often applied to components that can trap free radicals, thereby breaking the chain reaction that normally leads to extensive biological damage." [ISBN:0198506732]
+subset: goslim_generic
+subset: goslim_goa
+subset: gosubset_prok
+is_a: GO:0003674
+
+[Term]
+id: GO:0016265
+name: death
+namespace: biological_process
+def: "A permanent cessation of all vital functions: the end of life; can be applied to a whole organism or to a part of an organism." [GOC:mah, ISBN:0877797099]
+comment: See also the biological process term 'apoptosis ; GO:0006915'.
+subset: goslim_generic
+subset: goslim_plant
+subset: gosubset_prok
+is_a: GO:0007582
+
+[Term]
+id: GO:0016301
+name: kinase activity
+namespace: molecular_function
+def: "Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule." [ISBN:0198506732]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: gosubset_prok
+exact_synonym: "phosphokinase" []
+xref_analog: Reactome:113431
+xref_analog: Reactome:113433
+xref_analog: Reactome:114246
+xref_analog: Reactome:115027
+xref_analog: Reactome:115715
+xref_analog: Reactome:115932
+xref_analog: Reactome:115944
+xref_analog: Reactome:115947
+xref_analog: Reactome:115951
+xref_analog: Reactome:115974
+xref_analog: Reactome:115991
+xref_analog: Reactome:116605
+xref_analog: Reactome:117491
+xref_analog: Reactome:118310
+xref_analog: Reactome:118568
+xref_analog: Reactome:118583
+xref_analog: Reactome:118586
+xref_analog: Reactome:118589
+xref_analog: Reactome:118596
+xref_analog: Reactome:118617
+xref_analog: Reactome:118965
+xref_analog: Reactome:119356
+xref_analog: Reactome:120179
+xref_analog: Reactome:120930
+xref_analog: Reactome:121183
+xref_analog: Reactome:121192
+xref_analog: Reactome:121216
+xref_analog: Reactome:121239
+xref_analog: Reactome:121274
+xref_analog: Reactome:121543
+xref_analog: Reactome:122577
+xref_analog: Reactome:123125
+xref_analog: Reactome:123301
+xref_analog: Reactome:123309
+xref_analog: Reactome:123312
+xref_analog: Reactome:123316
+xref_analog: Reactome:123331
+xref_analog: Reactome:124636
+xref_analog: Reactome:125197
+xref_analog: Reactome:125408
+xref_analog: Reactome:125423
+xref_analog: Reactome:125426
+xref_analog: Reactome:125441
+xref_analog: Reactome:1423
+xref_analog: Reactome:68385
+xref_analog: Reactome:68401
+xref_analog: Reactome:69194
+xref_analog: Reactome:69222
+xref_analog: Reactome:69246
+xref_analog: Reactome:69254
+xref_analog: Reactome:69603
+xref_analog: Reactome:69607
+xref_analog: Reactome:69716
+xref_analog: Reactome:69904
+xref_analog: Reactome:69913
+xref_analog: Reactome:75047
+xref_analog: Reactome:75051
+xref_analog: Reactome:75052
+xref_analog: Reactome:75053
+xref_analog: Reactome:75054
+xref_analog: Reactome:75225
+xref_analog: Reactome:75371
+xref_analog: Reactome:75808
+xref_analog: Reactome:75819
+xref_analog: Reactome:83536
+is_a: GO:0016740
+
+[Term]
+id: GO:0016740
+name: transferase activity
+namespace: molecular_function
+def: "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." [ISBN:0198506732]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+xref_analog: EC:2
+is_a: GO:0003824
+
+[Term]
+id: GO:0016787
+name: hydrolase activity
+namespace: molecular_function
+def: "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN:0198506732]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+xref_analog: EC:3
+is_a: GO:0003824
+
+[Term]
+id: GO:0019538
+name: protein metabolism
+namespace: biological_process
+alt_id: GO:0006411
+def: "The chemical reactions and pathways involving a specific protein, rather than of proteins in general. Includes protein modification." [GOC:ma]
+subset: goslim_generic
+subset: goslim_plant
+subset: gosubset_prok
+exact_synonym: "protein metabolism and modification" []
+is_a: GO:0044238
+
+[Term]
+id: GO:0019725
+name: cell homeostasis
+namespace: biological_process
+def: "Any of the processes involved in the maintenance of an internal equilibrium within a cell or between a cell and its external environment." [GOC:jl, ISBN:0395825172]
+subset: goslim_generic
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+is_a: GO:0007582
+
+[Term]
+id: GO:0019748
+name: secondary metabolism
+namespace: biological_process
+def: "The chemical reactions and pathways resulting in many of the chemical changes of compounds that are not necessarily required for growth and maintenance of cells, and are often unique to a taxon. In multicellular organisms secondary metabolism is generally carried out in specific cell types, and may be useful for the organism as a whole. In unicellular organisms, secondary metabolism is often used for the production of antibiotics or for the utilization and acquisition of unusual nu [...]
+subset: goslim_generic
+subset: goslim_plant
+subset: gosubset_prok
+is_a: GO:0008152
+
+[Term]
+id: GO:0019825
+name: oxygen binding
+namespace: molecular_function
+def: "Interacting selectively with oxygen (O2)." [GOC:jl]
+subset: goslim_generic
+subset: goslim_plant
+subset: gosubset_prok
+related_synonym: "cytochrome P450 activity" []
+narrow_synonym: "cytochrome P450" []
+xref_analog: Reactome:4477
+is_a: GO:0005488
+
+[Term]
+id: GO:0030154
+name: cell differentiation
+namespace: biological_process
+def: "The process whereby relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate." [ISBN:0198506732]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: gosubset_prok
+relationship: part_of GO:0007275
+
+[Term]
+id: GO:0030188
+name: chaperone regulator activity
+namespace: molecular_function
+def: "Modulates the activity of a molecular chaperone." [GOC:mah]
+subset: goslim_generic
+subset: goslim_goa
+subset: gosubset_prok
+is_a: GO:0003674
+
+[Term]
+id: GO:0030234
+name: enzyme regulator activity
+namespace: molecular_function
+def: "Modulates the activity of an enzyme." [GOC:mah]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+exact_synonym: "enzyme modulator" []
+is_a: GO:0003674
+
+[Term]
+id: GO:0030246
+name: carbohydrate binding
+namespace: molecular_function
+def: "Interacting selectively with any carbohydrate." [GOC:mah]
+subset: goslim_generic
+subset: goslim_plant
+subset: gosubset_prok
+related_synonym: "cell adhesion molecule activity" []
+related_synonym: "cell adhesion receptor activity" []
+related_synonym: "selectin" []
+is_a: GO:0005488
+
+[Term]
+id: GO:0030312
+name: external encapsulating structure
+namespace: cellular_component
+def: "A structure that lies outside the plasma membrane and surrounds the entire cell." [GOC:go_curators]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: gosubset_prok
+relationship: part_of GO:0005623
+
+[Term]
+id: GO:0030313
+name: cell envelope
+namespace: cellular_component
+def: "Everything external to, but not including, the cytoplasmic membrane of bacteria, encompassing the periplasmic space, cell wall, and outer membrane if present." [GOC:jl, http://pathmicro.med.sc.edu/fox/cell_envelope.htm]
+subset: goslim_generic
+subset: gosubset_prok
+is_a: GO:0030312
+
+[Term]
+id: GO:0030528
+name: transcription regulator activity
+namespace: molecular_function
+def: "Plays a role in regulating transcription; may bind a promoter or enhancer DNA sequence or interact with a DNA-binding transcription factor." [GOC:mah]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+is_a: GO:0003674
+
+[Term]
+id: GO:0030533
+name: triplet codon-amino acid adaptor activity
+namespace: molecular_function
+def: "Mediates the insertion of an amino acid at the correct point in the sequence of a nascent polypeptide chain during protein synthesis." [ISBN:0198506732]
+comment: Note that this term can be used in place of the obsolete term 'transfer RNA ; GO:0005563'.
+subset: goslim_generic
+exact_synonym: "transfer RNA" []
+exact_synonym: "tRNA" []
+is_a: GO:0003674
+
+[Term]
+id: GO:0031386
+name: protein tag
+namespace: molecular_function
+def: "Acting as an indicator or marker to facilitate recognition by other molecules in the cell. Recognition of the tag, which can be covalently attached to the target molecule, may result in modification, sequestration, transport or degradation of the molecule in question." [GOC:go_curators]
+subset: goslim_generic
+related_synonym: "protein tagging activity" []
+related_synonym: "ubiquitin" []
+is_a: GO:0003674
+
+[Term]
+id: GO:0040007
+name: growth
+namespace: biological_process
+def: "The increase in size or mass of an entire organism, a part of an organism or a cell." [GOC:bf, GOC:ma]
+comment: See also the biological process term 'cell growth ; GO:0016049'.
+subset: goslim_generic
+subset: goslim_plant
+subset: gosubset_prok
+related_synonym: "growth pattern" []
+is_a: GO:0008150
+
+[Term]
+id: GO:0040029
+name: regulation of gene expression, epigenetic
+namespace: biological_process
+def: "Any process that modulates the frequency, rate or extent of gene expression; the process is mitotically or meiotically heritable, or is stably self-propagated in the cytoplasm of a resting cell, and does not entail a change in DNA sequence." [PMID:10521337, PMID:11498582]
+subset: goslim_generic
+subset: goslim_plant
+subset: gosubset_prok
+is_a: GO:0050789
+
+[Term]
+id: GO:0043226
+name: organelle
+namespace: cellular_component
+def: "Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane." [GOC:go_curators]
+subset: goslim_generic
+subset: gosubset_prok
+is_a: GO:0005575
+
+[Term]
+id: GO:0043234
+name: protein complex
+namespace: cellular_component
+def: "Any protein group composed of two or more subunits, which may or may not be identical. Protein complexes may have other associated non-protein prosthetic groups, such as nucleic acids, metal ions or carbohydrate groups." [GOC:go_curators]
+comment: Note that although at some level almost all cellular components can be thought of as protein complexes, this term is intended to exclude structures composed of the same repeating subunit or subunits, for example microtubules. Protein complexes encompassed by this term are generally not structural, and usually have a defined set of subunits.
+subset: goslim_generic
+subset: gosubset_prok
+is_a: GO:0005575
+
+[Term]
+id: GO:0044238
+name: primary metabolism
+namespace: biological_process
+def: "Reactions involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism." [GOC:go_curators, http://www.metacyc.org]
+subset: goslim_generic
+subset: gosubset_prok
+is_a: GO:0008152
+
+[Term]
+id: GO:0044403
+name: symbiosis, encompassing mutualism through parasitism
+namespace: biological_process
+alt_id: GO:0043298
+alt_id: GO:0044404
+def: "An interaction between two organisms living together in more or less intimate association. The term host is usually used for the larger (macro) of the two members of a symbiosis. The smaller (micro) member is called the symbiont. Microscopic symbionts are often referred to as endosymbionts. The various forms of symbiosis include parasitism, in which the association is disadvantageous or destructive to one of the organisms; mutualism, in which the association is advantageous, or oft [...]
+comment: Note that this term encompasses all symbiotic relationships between species along a continuum from mutualism through to parasitism, as outlined in the definition.
+subset: goslim_generic
+subset: gosubset_prok
+related_synonym: "host-pathogen interaction" []
+related_synonym: "symbiotic interaction between host and other organism" []
+related_synonym: "symbiotic interaction with other non-host organism" []
+exact_synonym: "symbiotic interaction between organisms" []
+exact_synonym: "symbiotic interaction between species" []
+is_a: GO:0008150
+
+[Term]
+id: GO:0045182
+name: translation regulator activity
+namespace: molecular_function
+def: "Any substance involved in the initiation, activation, perpetuation, repression or termination of polypeptide synthesis at the ribosome." [GOC:ai]
+subset: goslim_generic
+subset: goslim_goa
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+is_a: GO:0003674
+
+[Term]
+id: GO:0045735
+name: nutrient reservoir activity
+namespace: molecular_function
+def: "Functions in the storage of nutritious substrates." [GOC:ai]
+comment: Note that this term can be used in place of the obsolete terms 'storage protein ; GO:0005187' and 'storage protein of fat body (sensu Insecta) ; GO:0008041'.
+subset: goslim_generic
+subset: gosubset_prok
+related_synonym: "storage protein" []
+related_synonym: "storage protein of fat body (sensu Insecta)" []
+related_synonym: "yolk protein" []
+is_a: GO:0003674
+
+[Term]
+id: GO:0050789
+name: regulation of biological process
+namespace: biological_process
+def: "Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule." [GOC:ai, GOC:go_curators]
+subset: goslim_generic
+subset: goslim_goa
+subset: gosubset_prok
+broad_synonym: "regulation" []
+is_a: GO:0008150
+
+[Typedef]
+id: part_of
+name: part of
+is_transitive: true
+
diff --git a/coreplugins/TableImport/src/test/resources/empty_attr_row.xls b/coreplugins/TableImport/src/test/resources/empty_attr_row.xls
new file mode 100644
index 0000000..d73aa24
Binary files /dev/null and b/coreplugins/TableImport/src/test/resources/empty_attr_row.xls differ
diff --git a/coreplugins/TableImport/src/test/resources/galFiltered.sif b/coreplugins/TableImport/src/test/resources/galFiltered.sif
new file mode 100644
index 0000000..9e71eb5
--- /dev/null
+++ b/coreplugins/TableImport/src/test/resources/galFiltered.sif
@@ -0,0 +1,362 @@
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diff --git a/coreplugins/TableImport/src/test/resources/galFiltered.txt b/coreplugins/TableImport/src/test/resources/galFiltered.txt
new file mode 100755
index 0000000..ef47648
--- /dev/null
+++ b/coreplugins/TableImport/src/test/resources/galFiltered.txt
@@ -0,0 +1,362 @@
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+YER052C YNL135C pp TRUE abcd12604 1.2344543
+YPR124W YMR021C pd TRUE abcd12605 1.2344543
+YGL166W YHR053C pd TRUE abcd12606 1.2344543
+YGL166W YHR055C pd TRUE abcd12607 1.2344543
+YGL134W YPL031C pp TRUE abcd12608 1.2344543
+YGL134W YLR258W pp TRUE abcd12609 1.2344543
+YJL194W YMR043W pd TRUE abcd12610 1.2344543
+YLR264W YER112W pp TRUE abcd12611 1.2344543
+YLR264W YOL149W pp TRUE abcd12612 1.2344543
+YLR264W YBL026W pp TRUE abcd12613 1.2344543
+YBL050W YOR036W pp TRUE abcd12614 1.2344543
+YNL145W YCL067C pd TRUE abcd12615 1.2344543
+YNL145W YHR084W pd TRUE abcd12616 1.2344543
+YBR274W YMR255W pp TRUE abcd12617 1.2344543
+YLR452C YHR005C pp TRUE abcd12618 1.2344543
+YDR299W YJL194W pd TRUE abcd12619 1.2344543
+YIL074C YNL311C pp TRUE abcd12620 1.2344543
+YLR319C YLR362W pp TRUE abcd12621 1.2344543
+YGL073W YOR178C pp TRUE abcd12622 1.2344543
+YGL073W YHR053C pd TRUE abcd12623 1.2344543
+YGL073W YHR055C pd TRUE abcd12624 1.2344543
+YGL073W YER103W pd TRUE abcd12625 1.2344543
+YOR120W YPL248C pd TRUE abcd12626 1.2344543
+YPR041W YOR361C pp TRUE abcd12627 1.2344543
+YPR041W YMR309C pp TRUE abcd12628 1.2344543
+YNL135C YDR174W pp TRUE abcd12629 1.2344543
+YBR217W YNR007C pp TRUE abcd12630 1.2344543
+YMR255W YGL122C pp TRUE abcd12631 1.2344543
+YLR258W YIL045W pp TRUE abcd12632 1.2344543
+YLR258W YBR274W pp TRUE abcd12633 1.2344543
+YDL215C YER040W pd TRUE abcd12634 1.2344543
+YDL215C YLR432W pp TRUE abcd12635 1.2344543
+YER079W YHR135C pp TRUE abcd12636 1.2344543
+YER079W YNL154C pp TRUE abcd12637 1.2344543
+YDL030W YDL013W pp TRUE abcd12638 1.2344543
+YDL030W YMR005W pp TRUE abcd12639 1.2344543
+YLR362W YER124C pp TRUE abcd12640 1.2344543
+YLR362W YMR186W pp TRUE abcd12641 1.2344543
+YLR362W YPL240C pp TRUE abcd12642 1.2344543
+YHR084W YMR043W pp TRUE abcd12643 1.2344543
+YHR084W YDR461W pd TRUE abcd12644 1.2344543
+YHR084W YFL026W pd TRUE abcd12645 1.2344543
+YGR085C YLR075W pp TRUE abcd12646 1.2344543
+YGR085C YDR395W pp TRUE abcd12647 1.2344543
+YKL074C YGL035C pp TRUE abcd12648 1.2344543
+YGR088W YLR256W pd TRUE abcd12649 1.2344543
+YER081W YIL074C pp TRUE abcd12650 1.2344543
+YPR113W YMR043W pd TRUE abcd12651 1.2344543
+YIL070C YML054C pp TRUE abcd12652 1.2344543
+YIL061C YDL013W pp TRUE abcd12653 1.2344543
+YIL061C YNL199C pp TRUE abcd12654 1.2344543
+YIL061C YLR153C pp TRUE abcd12655 1.2344543
+YGR046W YNL236W pp TRUE abcd12656 1.2344543
+YNL091W YNL164C pp TRUE abcd12657 1.2344543
+YHR030C YLL021W pp TRUE abcd12658 1.2344543
+YHR030C YER111C pp TRUE abcd12659 1.2344543
+YPR048W YOR355W pp TRUE abcd12660 1.2344543
+YPR048W YDL215C pp TRUE abcd12661 1.2344543
+YHR005C YLR362W pp TRUE abcd12662 1.2344543
+YDR070C YFL017C pp TRUE abcd12663 1.2344543
+YJL157C YAL040C pp TRUE abcd12664 1.2344543
+YJL157C YOR212W pp TRUE abcd12665 1.2344543
+YNL036W YIR009W pp TRUE abcd12666 1.2344543
+YML114C YDR167W pp TRUE abcd12667 1.2344543
+YMR117C YCL032W pp TRUE abcd12668 1.2344543
+YMR117C YPR010C pp TRUE abcd12669 1.2344543
+YHR115C YOR215C pp TRUE abcd12670 1.2344543
+YGR009C YAL030W pp TRUE abcd12671 1.2344543
+YGR009C YOR327C pp TRUE abcd12672 1.2344543
+YGR009C YDR335W pp TRUE abcd12673 1.2344543
+YGR009C YBL050W pp TRUE abcd12674 1.2344543
+YDL088C YER110C pp TRUE abcd12675 1.2344543
+YLR197W YDL014W pp TRUE abcd12676 1.2344543
+YLR197W YOR310C pp TRUE abcd12677 1.2344543
+YGL202W YGR074W pp TRUE abcd12678 1.2344543
+YIL162W YNL167C pd TRUE abcd12679 1.2344543
+YBR170C YGR048W pp TRUE abcd12680 1.2344543
+YOR212W YLR362W pp TRUE abcd12681 1.2344543
+YDR103W YLR362W pp TRUE abcd12682 1.2344543
+YDL023C YJL159W pp TRUE abcd12683 1.2344543
+YGR136W YGR058W pp TRUE abcd12684 1.2344543
+YBR109C YOR326W pp TRUE abcd12685 1.2344543
+YBR109C YFR014C pp TRUE abcd12686 1.2344543
+YDR395W YDL075W pp TRUE abcd12687 1.2344543
+YDR395W YIL133C pp TRUE abcd12688 1.2344543
+YDR395W YNL069C pp TRUE abcd12689 1.2344543
+YDR395W YER056CA pp TRUE abcd12690 1.2344543
+YDR395W YIL052C pp TRUE abcd12691 1.2344543
+YDR395W YOL127W pp TRUE abcd12692 1.2344543
+YDR395W YPR102C pp TRUE abcd12693 1.2344543
+YLR345W YLR321C pp TRUE abcd12694 1.2344543
+YBL079W YDL088C pp TRUE abcd12695 1.2344543
+YBR045C YIL045W pp TRUE abcd12696 1.2344543
+YBR045C YOR178C pp TRUE abcd12697 1.2344543
+YER054C YER133W pp TRUE abcd12698 1.2344543
+YER054C YBR045C pp TRUE abcd12699 1.2344543
+YPR145W YMR117C pp TRUE abcd12700 1.2344543
+YNR053C YJL203W pp TRUE abcd12701 1.2344543
+YNR053C YDL030W pp TRUE abcd12702 1.2344543
+YGR074W YBR043C pp TRUE abcd12703 1.2344543
+YDR277C YJR022W pp TRUE abcd12704 1.2344543
+YDR277C YDL194W pp TRUE abcd12705 1.2344543
+YBL026W YOR167C pp TRUE abcd12706 1.2344543
diff --git a/coreplugins/TableImport/src/test/resources/galFiltered.xls b/coreplugins/TableImport/src/test/resources/galFiltered.xls
new file mode 100755
index 0000000..a32578a
Binary files /dev/null and b/coreplugins/TableImport/src/test/resources/galFiltered.xls differ
diff --git a/coreplugins/TableImport/src/test/resources/galFilteredEdgeAttr.txt b/coreplugins/TableImport/src/test/resources/galFilteredEdgeAttr.txt
new file mode 100755
index 0000000..8c964c1
--- /dev/null
+++ b/coreplugins/TableImport/src/test/resources/galFilteredEdgeAttr.txt
@@ -0,0 +1,363 @@
+Edge ID Integer Attr String Attr Edge List Attr
+YGL237C (pd) YJR048W 100 test123 A|B|C|D|END
+YEL009C (pd) YMR300C 101 test124 A|B|C|D|END
+YOR120W (pd) YPL248C 102 test125 A|B|C|D|END
+YDR395W (pp) YNL069C 103 test126 A|B|C|D|END
+YPL240C (pp) YBR155W 104 test127 A|B|C|D|END
+YOR327C (pp) YER143W 105 test128 A|B|C|D|END
+YJR022W (pp) YEL015W 106 test129 A|B|C|D|END
+YOL051W (pd) YBR018C 107 test130 A|B|C|D|END
+YBR072W (pd) YGL073W 108 test131 A|B|C|D|END
+YGL073W (pp) YOR178C 109 test132 A|B|C|D|END
+YIR009W (pp) YNL091W 110 test133 A|B|C|D|END
+YNL236W (pp) YKL012W 111 test134 A|B|C|D|END
+YHR084W (pp) YMR043W 112 test135 A|B|C|D|END
+YPL075W (pd) YOL086C 113 test136 A|B|C|D|END
+YNL216W (pd) YOL120C 114 test137 A|B|C|D|END
+YLR249W (pp) YPR080W 115 test138 A|B|C|D|END
+YGL013C (pd) YJL219W 116 test139 A|B|C|D|END
+YEL009C (pd) YOR202W 117 test140 A|B|C|D|END
+YLR362W (pp) YER124C 118 test141 A|B|C|D|END
+YIR009W (pp) YDR184C 119 test142 A|B|C|D|END
+YBR217W (pp) YNR007C 120 test143 A|B|C|D|END
+YOR361C (pp) YMR309C 121 test144 A|B|C|D|END
+YNL216W (pd) YBR093C 122 test145 A|B|C|D|END
+YCL032W (pp) YLR362W 123 test146 A|B|C|D|END
+YPR113W (pd) YMR043W 124 test147 A|B|C|D|END
+YNL216W (pd) YIL069C 125 test148 A|B|C|D|END
+YOR036W (pp) YGL161C 126 test149 A|B|C|D|END
+YDR244W (pp) YDR142C 127 test150 A|B|C|D|END
+YAR007C (pd) YPL111W 128 test151 A|B|C|D|END
+YFR037C (pp) YOR290C 129 test152 A|B|C|D|END
+YBR019C (pd) YGL035C 130 test153 A|B|C|D|END
+YNL216W (pd) YGR254W 131 test154 A|B|C|D|END
+YER133W (pp) YMR311C 132 test155 A|B|C|D|END
+YNL307C (pp) YAL038W 133 test156 A|B|C|D|END
+YML123C (pd) YFR034C 134 test157 A|B|C|D|END
+YDR354W (pd) YEL009C 135 test158 A|B|C|D|END
+YOL058W (pp) YNL189W 136 test159 A|B|C|D|END
+YML024W (pd) YNL216W 137 test160 A|B|C|D|END
+YMR043W (pd) YFL026W 138 test161 A|B|C|D|END
+YGL097W (pp) YOR204W 139 test162 A|B|C|D|END
+YEL041W (pp) YHR115C 140 test163 A|B|C|D|END
+YLR452C (pp) YHR005C 141 test164 A|B|C|D|END
+YER054C (pp) YER133W 142 test165 A|B|C|D|END
+YDL215C (pd) YER040W 143 test166 A|B|C|D|END
+YLR175W (pp) YNL307C 144 test167 A|B|C|D|END
+YLR117C (pp) YBR190W 145 test168 A|B|C|D|END
+YNL091W (pp) YNL164C 146 test169 A|B|C|D|END
+YAL038W (pd) YPL075W 147 test170 A|B|C|D|END
+YER040W (pd) YGR019W 148 test171 A|B|C|D|END
+YPR145W (pp) YMR117C 149 test172 A|B|C|D|END
+YEL009C (pd) YOL058W 150 test173 A|B|C|D|END
+YGL166W (pd) YHR055C 151 test174 A|B|C|D|END
+YDR277C (pp) YDL194W 152 test175 A|B|C|D|END
+YCR084C (pp) YBR112C 153 test176 A|B|C|D|END
+YFL039C (pp) YHR179W 154 test177 A|B|C|D|END
+YMR043W (pd) YJL159W 155 test178 A|B|C|D|END
+YMR044W (pp) YIL061C 156 test179 A|B|C|D|END
+YGR009C (pp) YAL030W 157 test180 A|B|C|D|END
+YDR244W (pp) YLR191W 158 test181 A|B|C|D|END
+YGL013C (pd) YOL156W 159 test182 A|B|C|D|END
+YMR291W (pp) YGL115W 160 test183 A|B|C|D|END
+YPL248C (pd) YBR020W 161 test184 A|B|C|D|END
+YPL075W (pd) YHR174W 162 test185 A|B|C|D|END
+YBL050W (pp) YOR036W 163 test186 A|B|C|D|END
+YIL070C (pp) YML054C 164 test187 A|B|C|D|END
+YJL157C (pp) YAL040C 165 test188 A|B|C|D|END
+YPL149W (pp) YHR171W 166 test189 A|B|C|D|END
+YER062C (pp) YPL201C 167 test190 A|B|C|D|END
+YKL109W (pp) YGL237C 168 test191 A|B|C|D|END
+YIR009W (pp) YKR099W 169 test192 A|B|C|D|END
+YKL012W (pp) YKL074C 170 test193 A|B|C|D|END
+YBR109C (pp) YOR326W 171 test194 A|B|C|D|END
+YML064C (pp) YDR174W 172 test195 A|B|C|D|END
+YBR160W (pd) YMR043W 173 test196 A|B|C|D|END
+YPR041W (pp) YOR361C 174 test197 A|B|C|D|END
+YJR066W (pp) YLR116W 175 test198 A|B|C|D|END
+YDR142C (pp) YIL160C 176 test199 A|B|C|D|END
+YLR197W (pp) YOR310C 177 test200 A|B|C|D|END
+YCL067C (pd) YDR461W 178 test201 A|B|C|D|END
+YFL038C (pp) YOR036W 179 test202 A|B|C|D|END
+YMR043W (pd) YGR108W 180 test203 A|B|C|D|END
+YNL189W (pp) YER065C 181 test204 A|B|C|D|END
+YJL013C (pp) YGL229C 182 test205 A|B|C|D|END
+YNL216W (pd) YAL038W 183 test206 A|B|C|D|END
+YOL016C (pp) YBR109C 184 test207 A|B|C|D|END
+YPL248C (pd) YBR019C 185 test208 A|B|C|D|END
+YLR191W (pp) YGL153W 186 test209 A|B|C|D|END
+YDR309C (pp) YLR229C 187 test210 A|B|C|D|END
+YDR395W (pp) YER056CA 188 test211 A|B|C|D|END
+YPR048W (pp) YDL215C 189 test212 A|B|C|D|END
+YOL051W (pp) YPL248C 190 test213 A|B|C|D|END
+YPL248C (pd) YGL035C 191 test214 A|B|C|D|END
+YBL021C (pd) YJR048W 192 test215 A|B|C|D|END
+YNL199C (pp) YPR048W 193 test216 A|B|C|D|END
+YER079W (pp) YNL154C 194 test217 A|B|C|D|END
+YGR085C (pp) YDR395W 195 test218 A|B|C|D|END
+YGL073W (pd) YHR053C 196 test219 A|B|C|D|END
+YPL031C (pp) YHR071W 197 test220 A|B|C|D|END
+YNL113W (pp) YPR110C 198 test221 A|B|C|D|END
+YKR026C (pp) YGL122C 199 test222 A|B|C|D|END
+YDR299W (pd) YJL194W 200 test223 A|B|C|D|END
+YER179W (pp) YLR044C 201 test224 A|B|C|D|END
+YDR244W (pp) YDL078C 202 test225 A|B|C|D|END
+YER112W (pp) YOR167C 203 test226 A|B|C|D|END
+YCL030C (pd) YKR099W 204 test227 A|B|C|D|END
+YMR117C (pp) YCL032W 205 test228 A|B|C|D|END
+YHR030C (pp) YLL021W 206 test229 A|B|C|D|END
+YPL240C (pp) YOR036W 207 test230 A|B|C|D|END
+YER133W (pp) YBR050C 208 test231 A|B|C|D|END
+YNL098C (pp) YLR310C 209 test232 A|B|C|D|END
+YCL032W (pp) YDR103W 210 test233 A|B|C|D|END
+YIL074C (pp) YNL311C 211 test234 A|B|C|D|END
+YHR084W (pd) YDR461W 212 test235 A|B|C|D|END
+YGL122C (pp) YOL123W 213 test236 A|B|C|D|END
+YKL161C (pp) YPL089C 214 test237 A|B|C|D|END
+YER133W (pp) YDR412W 215 test238 A|B|C|D|END
+YOL051W (pd) YBR020W 216 test239 A|B|C|D|END
+YLR362W (pp) YMR186W 217 test240 A|B|C|D|END
+YGR048W (pp) YPL222W 218 test241 A|B|C|D|END
+YCL067C (pd) YFL026W 219 test242 A|B|C|D|END
+YOR039W (pp) YOR303W 220 test243 A|B|C|D|END
+YNR053C (pp) YDL030W 221 test244 A|B|C|D|END
+YMR255W (pp) YGL122C 222 test245 A|B|C|D|END
+YNL167C (pd) YOR202W 223 test246 A|B|C|D|END
+YDR395W (pp) YIL052C 224 test247 A|B|C|D|END
+YER052C (pp) YNL135C 225 test248 A|B|C|D|END
+YGR009C (pp) YDR335W 226 test249 A|B|C|D|END
+YNL216W (pd) YNL301C 227 test250 A|B|C|D|END
+YNR050C (pp) YMR138W 228 test251 A|B|C|D|END
+YFL017C (pp) YOL059W 229 test252 A|B|C|D|END
+YJL157C (pp) YOR212W 230 test253 A|B|C|D|END
+YBR109C (pp) YFR014C 231 test254 A|B|C|D|END
+YOR361C (pp) YDR429C 232 test255 A|B|C|D|END
+YKL109W (pd) YGL035C 233 test256 A|B|C|D|END
+YDL014W (pp) YOR310C 234 test257 A|B|C|D|END
+YDR412W (pp) YCR086W 235 test258 A|B|C|D|END
+YML051W (pp) YBR020W 236 test259 A|B|C|D|END
+YDR382W (pp) YDL130W 237 test260 A|B|C|D|END
+YMR043W (pd) YDR461W 238 test261 A|B|C|D|END
+YKL074C (pp) YGL035C 239 test262 A|B|C|D|END
+YLR075W (pp) YPR102C 240 test263 A|B|C|D|END
+YGL134W (pp) YPL031C 241 test264 A|B|C|D|END
+YPL075W (pd) YCR012W 242 test265 A|B|C|D|END
+YGL202W (pp) YGR074W 243 test266 A|B|C|D|END
+YEL015W (pp) YML064C 244 test267 A|B|C|D|END
+YDR323C (pp) YOR036W 245 test268 A|B|C|D|END
+YML114C (pp) YDR167W 246 test269 A|B|C|D|END
+YCR084C (pp) YCL067C 247 test270 A|B|C|D|END
+YLR293C (pp) YGL097W 248 test271 A|B|C|D|END
+YDR311W (pp) YKL028W 249 test272 A|B|C|D|END
+YLL028W (pp) YGL166W 250 test273 A|B|C|D|END
+YDR412W (pp) YGL013C 251 test274 A|B|C|D|END
+YML032C (pp) YNL312W 252 test275 A|B|C|D|END
+YBR045C (pp) YOR178C 253 test276 A|B|C|D|END
+YJL194W (pd) YMR043W 254 test277 A|B|C|D|END
+YHR171W (pp) YDR412W 255 test278 A|B|C|D|END
+YOL149W (pp) YOR167C 256 test279 A|B|C|D|END
+YPL075W (pp) YNL199C 257 test280 A|B|C|D|END
+YMR043W (pd) YKR097W 258 test281 A|B|C|D|END
+YGL073W (pd) YHR055C 259 test282 A|B|C|D|END
+YNL216W (pd) YOL127W 260 test283 A|B|C|D|END
+YJR022W (pp) YNR050C 261 test284 A|B|C|D|END
+YBL026W (pp) YOR167C 262 test285 A|B|C|D|END
+YPR041W (pp) YMR309C 263 test286 A|B|C|D|END
+YGL134W (pp) YLR258W 264 test287 A|B|C|D|END
+YGR009C (pp) YOR327C 265 test288 A|B|C|D|END
+YPL248C (pd) YLR081W 266 test289 A|B|C|D|END
+YPL149W (pp) YBR217W 267 test290 A|B|C|D|END
+YHR135C (pp) YNL116W 268 test291 A|B|C|D|END
+YEL009C (pd) YCL030C 269 test292 A|B|C|D|END
+YNR053C (pp) YJL203W 270 test293 A|B|C|D|END
+YJL089W (pd) YKR097W 271 test294 A|B|C|D|END
+YMR021C (pd) YLR214W 272 test295 A|B|C|D|END
+YLR264W (pp) YER112W 273 test296 A|B|C|D|END
+YNL189W (pp) YPR062W 274 test297 A|B|C|D|END
+YOR355W (pp) YNL091W 275 test298 A|B|C|D|END
+YGR014W (pp) YJL030W 276 test299 A|B|C|D|END
+YKL109W (pp) YBL021C 277 test300 A|B|C|D|END
+YNL216W (pd) YOL086C 278 test301 A|B|C|D|END
+YGL115W (pp) YGL208W 279 test302 A|B|C|D|END
+YDR244W (pp) YGL153W 280 test303 A|B|C|D|END
+YDR395W (pp) YDL075W 281 test304 A|B|C|D|END
+YDR103W (pp) YLR362W 282 test305 A|B|C|D|END
+YOL156W (pd) YBL005W 283 test306 A|B|C|D|END
+YKL101W (pp) YBR160W 284 test307 A|B|C|D|END
+YNL145W (pd) YCL067C 285 test308 A|B|C|D|END
+YIL061C (pp) YDL013W 286 test309 A|B|C|D|END
+YGR058W (pp) YOR264W 287 test310 A|B|C|D|END
+YLR310C (pp) YER103W 288 test311 A|B|C|D|END
+YDL030W (pp) YDL013W 289 test312 A|B|C|D|END
+? (pd) YGL035C 290 test313 A|B|C|D|END
+YBR160W (pp) YGR108W 291 test314 A|B|C|D|END
+YER110C (pp) YML007W 292 test315 A|B|C|D|END
+YEL009C (pd) YBR248C 293 test316 A|B|C|D|END
+YMR186W (pp) YBR155W 294 test317 A|B|C|D|END
+YGR088W (pd) YLR256W 295 test318 A|B|C|D|END
+YDL063C (pp) YPL131W 296 test319 A|B|C|D|END
+YBR020W (pd) YGL035C 297 test320 A|B|C|D|END
+YBL069W (pp) YGL008C 298 test321 A|B|C|D|END
+YNL216W (pd) YIL133C 299 test322 A|B|C|D|END
+YLR258W (pp) YIL045W 300 test323 A|B|C|D|END
+YMR117C (pp) YPR010C 301 test324 A|B|C|D|END
+YER179W (pp) YLR134W 302 test325 A|B|C|D|END
+YOR212W (pp) YLR362W 303 test326 A|B|C|D|END
+YJR022W (pp) YLR264W 304 test327 A|B|C|D|END
+YNL216W (pd) YHR174W 305 test328 A|B|C|D|END
+YPL248C (pd) YML051W 306 test329 A|B|C|D|END
+YJL203W (pp) YOL136C 307 test330 A|B|C|D|END
+YJL089W (pd) YLR377C 308 test331 A|B|C|D|END
+YPL248C (pd) ? 309 test332 A|B|C|D|END
+YDR167W (pp) YLR432W 310 test333 A|B|C|D|END
+YHR171W (pp) YNR007C 311 test334 A|B|C|D|END
+YHR005C (pp) YLR362W 312 test335 A|B|C|D|END
+YER133W (pp) YOR178C 313 test336 A|B|C|D|END
+YPL211W (pp) YGR014W 314 test337 A|B|C|D|END
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+YLR264W (pp) YBL026W 438 test461 A|B|C|D|END
+YJL036W (pp) YDL113C 439 test462 A|B|C|D|END
+? (pd) YKR099W 440 test463 A|B|C|D|END
+YLR249W (pp) YBR118W 441 test464 A|B|C|D|END
+YPR048W (pp) YOR355W 442 test465 A|B|C|D|END
+YDR412W (pp) YPR119W 443 test466 A|B|C|D|END
+YPL248C (pd) YJR048W 444 test467 A|B|C|D|END
+YER079W (pp) YHR135C 445 test468 A|B|C|D|END
+YJR022W (pp) YOR167C 446 test469 A|B|C|D|END
+YCL067C (pp) YMR043W 447 test470 A|B|C|D|END
+YER116C (pp) YDL013W 448 test471 A|B|C|D|END
+YDL081C (pp) YLR340W 449 test472 A|B|C|D|END
+YDR277C (pp) YJR022W 450 test473 A|B|C|D|END
+YLR256W (pd) YJR048W 451 test474 A|B|C|D|END
+YBR274W (pp) YMR255W 452 test475 A|B|C|D|END
+YMR043W (pd) YIL015W 453 test476 A|B|C|D|END
+YBR118W (pp) YAL003W 454 test477 A|B|C|D|END
+YDL088C (pp) YER110C 455 test478 A|B|C|D|END
+YGR203W (pp) YIL061C 456 test479 A|B|C|D|END
+YGR218W (pp) YGL097W 457 test480 A|B|C|D|END
+YGR046W (pp) YNL236W 458 test481 A|B|C|D|END
+YGL035C (pd) YIL162W 459 test482 A|B|C|D|END
+YJL030W (pp) YGL229C 460 test483 A|B|C|D|END
+YDR142C (pp) YGL153W 461 test484 A|B|C|D|END
diff --git a/coreplugins/TableImport/src/test/resources/galFiltered_EAttr.txt b/coreplugins/TableImport/src/test/resources/galFiltered_EAttr.txt
new file mode 100755
index 0000000..7683920
--- /dev/null
+++ b/coreplugins/TableImport/src/test/resources/galFiltered_EAttr.txt
@@ -0,0 +1,368 @@
+! This is a test data file for testing
+! Created from galFiltered.sif
+!
+! Keiichiro Ono kono at ucsd.edu
+!
+source target interaction Boolean Attr 1 String Attr 1 Float Attr 1 List Attr 1 Integer Attr 1
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+YGR218W YGL097W pp TRUE abcd12346 1.2344543 "This,is,a,string,attribute " 2
+YGL097W YOR204W pp TRUE abcd12347 1.2344543 "This,is,a,string,attribute " 3
+YLR249W YPR080W pp TRUE abcd12348 1.2344543 "This,is,a,string,attribute " 4
+YLR249W YBR118W pp TRUE abcd12349 1.2344543 "This,is,a,string,attribute " 5
+YLR293C YGL097W pp TRUE abcd12350 1.2344543 "This,is,a,string,attribute " 6
+YMR146C YDR429C pp TRUE abcd12351 1.2344543 "This,is,a,string,attribute " 7
+YDR429C YFL017C pp TRUE abcd12352 1.2344543 "This,is,a,string,attribute " 8
+YPR080W YAL003W pp TRUE abcd12353 1.2344543 "This,is,a,string,attribute " 9
+YBR118W YAL003W pp TRUE abcd12354 1.2344543 "This,is,a,string,attribute " 10
+YOL123W YGL044C pp TRUE abcd12355 1.2344543 "This,is,a,string,attribute " 11
+YPL211W YGR014W pp TRUE abcd12356 1.2344543 "This,is,a,string,attribute " 12
+YJL030W YGL229C pp TRUE abcd12357 1.2344543 "This,is,a,string,attribute " 13
+YJL013C YGL229C pp TRUE abcd12358 1.2344543 "This,is,a,string,attribute " 14
+YGL122C YOL123W pp TRUE abcd12359 1.2344543 "This,is,a,string,attribute " 15
+YGR014W YJL030W pp TRUE abcd12360 1.2344543 "This,is,a,string,attribute " 16
+YGR014W YJL013C pp TRUE abcd12361 1.2344543 "This,is,a,string,attribute " 17
+YGR203W YIL061C pp TRUE abcd12362 1.2344543 "This,is,a,string,attribute " 18
+YCR084C YBR112C pp TRUE abcd12363 1.2344543 "This,is,a,string,attribute " 19
+YCR084C YCL067C pp TRUE abcd12364 1.2344543 "This,is,a,string,attribute " 20
+YER112W YOR167C pp TRUE abcd12365 1.2344543 "This,is,a,string,attribute " 21
+YJR022W YNR050C pp TRUE abcd12366 1.2344543 "This,is,a,string,attribute " 22
+YJR022W YNL050C pp TRUE abcd12367 1.2344543 "This,is,a,string,attribute " 23
+YJR022W YEL015W pp TRUE abcd12368 1.2344543 "This,is,a,string,attribute " 24
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+YJR022W YLR264W pp TRUE abcd12370 1.2344543 "This,is,a,string,attribute " 26
+YJR022W YNR053C pp TRUE abcd12371 1.2344543 "This,is,a,string,attribute " 27
+YER116C YDL013W pp TRUE abcd12372 1.2344543 "This,is,a,string,attribute " 28
+YNL307C YAL038W pp TRUE abcd12373 1.2344543 "This,is,a,string,attribute " 29
+YNL216W YCR012W pd TRUE abcd12374 1.2344543 "This,is,a,string,attribute " 30
+YNL216W YGR254W pd TRUE abcd12375 1.2344543 "This,is,a,string,attribute " 31
+YNL216W YHR174W pd TRUE abcd12376 1.2344543 "This,is,a,string,attribute " 32
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+YNL216W YLR044C pd TRUE abcd12378 1.2344543 "This,is,a,string,attribute " 34
+YNL216W YOL120C pd TRUE abcd12379 1.2344543 "This,is,a,string,attribute " 35
+YNL216W YNL301C pd TRUE abcd12380 1.2344543 "This,is,a,string,attribute " 36
+YNL216W YCL030C pd TRUE abcd12381 1.2344543 "This,is,a,string,attribute " 37
+YNL216W YDR171W pp TRUE abcd12382 1.2344543 "This,is,a,string,attribute " 38
+YNL216W YBR093C pd TRUE abcd12383 1.2344543 "This,is,a,string,attribute " 39
+YNL216W YER074W pd TRUE abcd12384 1.2344543 "This,is,a,string,attribute " 40
+YNL216W YIL069C pd TRUE abcd12385 1.2344543 "This,is,a,string,attribute " 41
+YNL216W YAL038W pd TRUE abcd12386 1.2344543 "This,is,a,string,attribute " 42
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+YDR412W YGL013C pp TRUE abcd12394 1.2344543 "This,is,a,string,attribute " 50
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+YOR326W YGL106W pp TRUE abcd12403 1.2344543 "This,is,a,string,attribute " 59
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+YEL009C YMR108W pd TRUE abcd12405 1.2344543 "This,is,a,string,attribute " 61
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+YEL009C YBR248C pd TRUE abcd12408 1.2344543 "This,is,a,string,attribute " 64
+YEL009C YOL058W pd TRUE abcd12409 1.2344543 "This,is,a,string,attribute " 65
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+YIR009W YNL091W pp TRUE abcd12426 1.2344543 "This,is,a,string,attribute " 82
+YNL236W YKL012W pp TRUE abcd12427 1.2344543 "This,is,a,string,attribute " 83
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+YGL013C YJL219W pd TRUE abcd12459 1.2344543 "This,is,a,string,attribute " 115
+YGL013C YOL156W pd TRUE abcd12460 1.2344543 "This,is,a,string,attribute " 116
+YKL101W YBR160W pp TRUE abcd12461 1.2344543 "This,is,a,string,attribute " 117
+YCL067C YIL015W pd TRUE abcd12462 1.2344543 "This,is,a,string,attribute " 118
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+YCL067C YDR461W pd TRUE abcd12464 1.2344543 "This,is,a,string,attribute " 120
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+YLR117C YBR190W pp TRUE abcd12555 1.2344543 "This,is,a,string,attribute " 211
+YFL017C YOL059W pp TRUE abcd12556 1.2344543 "This,is,a,string,attribute " 212
+YFL017C YER102W pp TRUE abcd12557 1.2344543 "This,is,a,string,attribute " 213
+YFL017C YOR362C pp TRUE abcd12558 1.2344543 "This,is,a,string,attribute " 214
+YMR044W YIL061C pp TRUE abcd12559 1.2344543 "This,is,a,string,attribute " 215
+YOL149W YOR167C pp TRUE abcd12560 1.2344543 "This,is,a,string,attribute " 216
+YOR036W YDR100W pp TRUE abcd12561 1.2344543 "This,is,a,string,attribute " 217
+YOR036W YGL161C pp TRUE abcd12562 1.2344543 "This,is,a,string,attribute " 218
+YLR191W YGL153W pp TRUE abcd12563 1.2344543 "This,is,a,string,attribute " 219
+YER110C YML007W pp TRUE abcd12564 1.2344543 "This,is,a,string,attribute " 220
+YBR135W YER102W pp TRUE abcd12565 1.2344543 "This,is,a,string,attribute " 221
+YNL214W YGL153W pp TRUE abcd12566 1.2344543 "This,is,a,string,attribute " 222
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+YOR089C YDR323C pp TRUE abcd12568 1.2344543 "This,is,a,string,attribute " 224
+YNL117W YJL089W pd TRUE abcd12569 1.2344543 "This,is,a,string,attribute " 225
+YLR175W YNL307C pp TRUE abcd12570 1.2344543 "This,is,a,string,attribute " 226
+YDR167W YLR432W pp TRUE abcd12571 1.2344543 "This,is,a,string,attribute " 227
+YGR108W YBR135W pp TRUE abcd12572 1.2344543 "This,is,a,string,attribute " 228
+YDR244W YLR191W pp TRUE abcd12573 1.2344543 "This,is,a,string,attribute " 229
+YDR244W YGL153W pp TRUE abcd12574 1.2344543 "This,is,a,string,attribute " 230
+YDR244W YNL214W pp TRUE abcd12575 1.2344543 "This,is,a,string,attribute " 231
+YDR244W YDR142C pp TRUE abcd12576 1.2344543 "This,is,a,string,attribute " 232
+YDR244W YDL078C pp TRUE abcd12577 1.2344543 "This,is,a,string,attribute " 233
+YPR119W YMR043W pd TRUE abcd12578 1.2344543 "This,is,a,string,attribute " 234
+YDR142C YGL153W pp TRUE abcd12579 1.2344543 "This,is,a,string,attribute " 235
+YDR142C YIL160C pp TRUE abcd12580 1.2344543 "This,is,a,string,attribute " 236
+YBR020W YGL035C pd TRUE abcd12581 1.2344543 "This,is,a,string,attribute " 237
+YDR009W YGL035C pd TRUE abcd12582 1.2344543 "This,is,a,string,attribute " 238
+YPL248C YBR019C pd TRUE abcd12583 1.2344543 "This,is,a,string,attribute " 239
+YPL248C ? pd TRUE abcd12584 1.2344543 "This,is,a,string,attribute " 240
+YPL248C YJR048W pd TRUE abcd12585 1.2344543 "This,is,a,string,attribute " 241
+YPL248C YGL035C pd TRUE abcd12586 1.2344543 "This,is,a,string,attribute " 242
+YPL248C YML051W pd TRUE abcd12587 1.2344543 "This,is,a,string,attribute " 243
+YPL248C YML051W pp TRUE abcd12588 1.2344543 "This,is,a,string,attribute " 244
+YPL248C YBR020W pd TRUE abcd12589 1.2344543 "This,is,a,string,attribute " 245
+YPL248C YLR081W pd TRUE abcd12590 1.2344543 "This,is,a,string,attribute " 246
+YPL248C YBR018C pd TRUE abcd12591 1.2344543 "This,is,a,string,attribute " 247
+YAR007C YML032C pp TRUE abcd12592 1.2344543 "This,is,a,string,attribute " 248
+YAR007C YPL111W pd TRUE abcd12593 1.2344543 "This,is,a,string,attribute " 249
+YKL161C YPL089C pp TRUE abcd12594 1.2344543 "This,is,a,string,attribute " 250
+YNL312W YPL111W pd TRUE abcd12595 1.2344543 "This,is,a,string,attribute " 251
+YLR075W YPR102C pp TRUE abcd12596 1.2344543 "This,is,a,string,attribute " 252
+YLR229C YJL157C pp TRUE abcd12597 1.2344543 "This,is,a,string,attribute " 253
+YPL240C YBR155W pp TRUE abcd12598 1.2344543 "This,is,a,string,attribute " 254
+YPL240C YOR036W pp TRUE abcd12599 1.2344543 "This,is,a,string,attribute " 255
+YOL156W YBL005W pd TRUE abcd12600 1.2344543 "This,is,a,string,attribute " 256
+YML064C YHR198C pp TRUE abcd12601 1.2344543 "This,is,a,string,attribute " 257
+YML064C YLR284C pp TRUE abcd12602 1.2344543 "This,is,a,string,attribute " 258
+YML064C YDR174W pp TRUE abcd12603 1.2344543 "This,is,a,string,attribute " 259
+YER052C YNL135C pp TRUE abcd12604 1.2344543 "This,is,a,string,attribute " 260
+YPR124W YMR021C pd TRUE abcd12605 1.2344543 "This,is,a,string,attribute " 261
+YGL166W YHR053C pd TRUE abcd12606 1.2344543 "This,is,a,string,attribute " 262
+YGL166W YHR055C pd TRUE abcd12607 1.2344543 "This,is,a,string,attribute " 263
+YGL134W YPL031C pp TRUE abcd12608 1.2344543 "This,is,a,string,attribute " 264
+YGL134W YLR258W pp TRUE abcd12609 1.2344543 "This,is,a,string,attribute " 265
+YJL194W YMR043W pd TRUE abcd12610 1.2344543 "This,is,a,string,attribute " 266
+YLR264W YER112W pp TRUE abcd12611 1.2344543 "This,is,a,string,attribute " 267
+YLR264W YOL149W pp TRUE abcd12612 1.2344543 "This,is,a,string,attribute " 268
+YLR264W YBL026W pp TRUE abcd12613 1.2344543 "This,is,a,string,attribute " 269
+YBL050W YOR036W pp TRUE abcd12614 1.2344543 "This,is,a,string,attribute " 270
+YNL145W YCL067C pd TRUE abcd12615 1.2344543 "This,is,a,string,attribute " 271
+YNL145W YHR084W pd TRUE abcd12616 1.2344543 "This,is,a,string,attribute " 272
+YBR274W YMR255W pp TRUE abcd12617 1.2344543 "This,is,a,string,attribute " 273
+YLR452C YHR005C pp TRUE abcd12618 1.2344543 "This,is,a,string,attribute " 274
+YDR299W YJL194W pd TRUE abcd12619 1.2344543 "This,is,a,string,attribute " 275
+YIL074C YNL311C pp TRUE abcd12620 1.2344543 "This,is,a,string,attribute " 276
+YLR319C YLR362W pp TRUE abcd12621 1.2344543 "This,is,a,string,attribute " 277
+YGL073W YOR178C pp TRUE abcd12622 1.2344543 "This,is,a,string,attribute " 278
+YGL073W YHR053C pd TRUE abcd12623 1.2344543 "This,is,a,string,attribute " 279
+YGL073W YHR055C pd TRUE abcd12624 1.2344543 "This,is,a,string,attribute " 280
+YGL073W YER103W pd TRUE abcd12625 1.2344543 "This,is,a,string,attribute " 281
+YOR120W YPL248C pd TRUE abcd12626 1.2344543 "This,is,a,string,attribute " 282
+YPR041W YOR361C pp TRUE abcd12627 1.2344543 "This,is,a,string,attribute " 283
+YPR041W YMR309C pp TRUE abcd12628 1.2344543 "This,is,a,string,attribute " 284
+YNL135C YDR174W pp TRUE abcd12629 1.2344543 "This,is,a,string,attribute " 285
+YBR217W YNR007C pp TRUE abcd12630 1.2344543 "This,is,a,string,attribute " 286
+YMR255W YGL122C pp TRUE abcd12631 1.2344543 "This,is,a,string,attribute " 287
+YLR258W YIL045W pp TRUE abcd12632 1.2344543 "This,is,a,string,attribute " 288
+YLR258W YBR274W pp TRUE abcd12633 1.2344543 "This,is,a,string,attribute " 289
+YDL215C YER040W pd TRUE abcd12634 1.2344543 "This,is,a,string,attribute " 290
+YDL215C YLR432W pp TRUE abcd12635 1.2344543 "This,is,a,string,attribute " 291
+YER079W YHR135C pp TRUE abcd12636 1.2344543 "This,is,a,string,attribute " 292
+YER079W YNL154C pp TRUE abcd12637 1.2344543 "This,is,a,string,attribute " 293
+YDL030W YDL013W pp TRUE abcd12638 1.2344543 "This,is,a,string,attribute " 294
+YDL030W YMR005W pp TRUE abcd12639 1.2344543 "This,is,a,string,attribute " 295
+YLR362W YER124C pp TRUE abcd12640 1.2344543 "This,is,a,string,attribute " 296
+YLR362W YMR186W pp TRUE abcd12641 1.2344543 "This,is,a,string,attribute " 297
+YLR362W YPL240C pp TRUE abcd12642 1.2344543 "This,is,a,string,attribute " 298
+YHR084W YMR043W pp TRUE abcd12643 1.2344543 "This,is,a,string,attribute " 299
+YHR084W YDR461W pd TRUE abcd12644 1.2344543 "This,is,a,string,attribute " 300
+YHR084W YFL026W pd TRUE abcd12645 1.2344543 "This,is,a,string,attribute " 301
+YGR085C YLR075W pp TRUE abcd12646 1.2344543 "This,is,a,string,attribute " 302
+YGR085C YDR395W pp TRUE abcd12647 1.2344543 "This,is,a,string,attribute " 303
+YKL074C YGL035C pp TRUE abcd12648 1.2344543 "This,is,a,string,attribute " 304
+YGR088W YLR256W pd TRUE abcd12649 1.2344543 "This,is,a,string,attribute " 305
+YER081W YIL074C pp TRUE abcd12650 1.2344543 "This,is,a,string,attribute " 306
+YPR113W YMR043W pd TRUE abcd12651 1.2344543 "This,is,a,string,attribute " 307
+YIL070C YML054C pp TRUE abcd12652 1.2344543 "This,is,a,string,attribute " 308
+YIL061C YDL013W pp TRUE abcd12653 1.2344543 "This,is,a,string,attribute " 309
+YIL061C YNL199C pp TRUE abcd12654 1.2344543 "This,is,a,string,attribute " 310
+YIL061C YLR153C pp TRUE abcd12655 1.2344543 "This,is,a,string,attribute " 311
+YGR046W YNL236W pp TRUE abcd12656 1.2344543 "This,is,a,string,attribute " 312
+YNL091W YNL164C pp TRUE abcd12657 1.2344543 "This,is,a,string,attribute " 313
+YHR030C YLL021W pp TRUE abcd12658 1.2344543 "This,is,a,string,attribute " 314
+YHR030C YER111C pp TRUE abcd12659 1.2344543 "This,is,a,string,attribute " 315
+YPR048W YOR355W pp TRUE abcd12660 1.2344543 "This,is,a,string,attribute " 316
+YPR048W YDL215C pp TRUE abcd12661 1.2344543 "This,is,a,string,attribute " 317
+YHR005C YLR362W pp TRUE abcd12662 1.2344543 "This,is,a,string,attribute " 318
+YDR070C YFL017C pp TRUE abcd12663 1.2344543 "This,is,a,string,attribute " 319
+YJL157C YAL040C pp TRUE abcd12664 1.2344543 "This,is,a,string,attribute " 320
+YJL157C YOR212W pp TRUE abcd12665 1.2344543 "This,is,a,string,attribute " 321
+YNL036W YIR009W pp TRUE abcd12666 1.2344543 "This,is,a,string,attribute " 322
+YML114C YDR167W pp TRUE abcd12667 1.2344543 "This,is,a,string,attribute " 323
+YMR117C YCL032W pp TRUE abcd12668 1.2344543 "This,is,a,string,attribute " 324
+YMR117C YPR010C pp TRUE abcd12669 1.2344543 "This,is,a,string,attribute " 325
+YHR115C YOR215C pp TRUE abcd12670 1.2344543 "This,is,a,string,attribute " 326
+YGR009C YAL030W pp TRUE abcd12671 1.2344543 "This,is,a,string,attribute " 327
+YGR009C YOR327C pp TRUE abcd12672 1.2344543 "This,is,a,string,attribute " 328
+YGR009C YDR335W pp TRUE abcd12673 1.2344543 "This,is,a,string,attribute " 329
+YGR009C YBL050W pp TRUE abcd12674 1.2344543 "This,is,a,string,attribute " 330
+YDL088C YER110C pp TRUE abcd12675 1.2344543 "This,is,a,string,attribute " 331
+YLR197W YDL014W pp TRUE abcd12676 1.2344543 "This,is,a,string,attribute " 332
+YLR197W YOR310C pp TRUE abcd12677 1.2344543 "This,is,a,string,attribute " 333
+YGL202W YGR074W pp TRUE abcd12678 1.2344543 "This,is,a,string,attribute " 334
+YIL162W YNL167C pd TRUE abcd12679 1.2344543 "This,is,a,string,attribute " 335
+YBR170C YGR048W pp TRUE abcd12680 1.2344543 "This,is,a,string,attribute " 336
+YOR212W YLR362W pp TRUE abcd12681 1.2344543 "This,is,a,string,attribute " 337
+YDR103W YLR362W pp TRUE abcd12682 1.2344543 "This,is,a,string,attribute " 338
+YDL023C YJL159W pp TRUE abcd12683 1.2344543 "This,is,a,string,attribute " 339
+YGR136W YGR058W pp TRUE abcd12684 1.2344543 "This,is,a,string,attribute " 340
+YBR109C YOR326W pp TRUE abcd12685 1.2344543 "This,is,a,string,attribute " 341
+YBR109C YFR014C pp TRUE abcd12686 1.2344543 "This,is,a,string,attribute " 342
+YDR395W YDL075W pp TRUE abcd12687 1.2344543 "This,is,a,string,attribute " 343
+YDR395W YIL133C pp TRUE abcd12688 1.2344543 "This,is,a,string,attribute " 344
+YDR395W YNL069C pp TRUE abcd12689 1.2344543 "This,is,a,string,attribute " 345
+YDR395W YER056CA pp TRUE abcd12690 1.2344543 "This,is,a,string,attribute " 346
+YDR395W YIL052C pp TRUE abcd12691 1.2344543 "This,is,a,string,attribute " 347
+YDR395W YOL127W pp TRUE abcd12692 1.2344543 "This,is,a,string,attribute " 348
+YDR395W YPR102C pp TRUE abcd12693 1.2344543 "This,is,a,string,attribute " 349
+YLR345W YLR321C pp TRUE abcd12694 1.2344543 "This,is,a,string,attribute " 350
+YBL079W YDL088C pp TRUE abcd12695 1.2344543 "This,is,a,string,attribute " 351
+YBR045C YIL045W pp TRUE abcd12696 1.2344543 "This,is,a,string,attribute " 352
+YBR045C YOR178C pp TRUE abcd12697 1.2344543 "This,is,a,string,attribute " 353
+YER054C YER133W pp TRUE abcd12698 1.2344543 "This,is,a,string,attribute " 354
+YER054C YBR045C pp TRUE abcd12699 1.2344543 "This,is,a,string,attribute " 355
+YPR145W YMR117C pp TRUE abcd12700 1.2344543 "This,is,a,string,attribute " 356
+YNR053C YJL203W pp TRUE abcd12701 1.2344543 "This,is,a,string,attribute " 357
+YNR053C YDL030W pp TRUE abcd12702 1.2344543 "This,is,a,string,attribute " 358
+YGR074W YBR043C pp TRUE abcd12703 1.2344543 "This,is,a,string,attribute " 359
+YDR277C YJR022W pp TRUE abcd12704 1.2344543 "This,is,a,string,attribute " 360
+YDR277C YDL194W pp TRUE abcd12705 1.2344543 "This,is,a,string,attribute " 361
+YBL026W YOR167C pp TRUE abcd12706 1.2344543 "This,is,a,string,attribute " 362
diff --git a/coreplugins/TableImport/src/test/resources/galSubnetwork.sif b/coreplugins/TableImport/src/test/resources/galSubnetwork.sif
new file mode 100644
index 0000000..1f05c38
--- /dev/null
+++ b/coreplugins/TableImport/src/test/resources/galSubnetwork.sif
@@ -0,0 +1,15 @@
+YBL026W pp YOR167C
+YMR138W pp YLR109W
+YMR138W pp YHR141C
+YJR022W pp YNR050C
+YJR022W pp YOR167C
+YJR022W pp YNL050C
+YJR022W pp YLR264W
+YER112W pp YOR167C
+YDR277C pp YJR022W
+YDR277C pp YDL194W
+YOL149W pp YOR167C
+YNR050C pp YMR138W
+YLR264W pp YBL026W
+YLR264W pp YOL149W
+YLR264W pp YER112W
diff --git a/coreplugins/TableImport/src/test/resources/lowercase.sif b/coreplugins/TableImport/src/test/resources/lowercase.sif
new file mode 100644
index 0000000..b726dc1
--- /dev/null
+++ b/coreplugins/TableImport/src/test/resources/lowercase.sif
@@ -0,0 +1 @@
+fam62C pp mmp9
\ No newline at end of file
diff --git a/coreplugins/TableImport/src/test/resources/resources/tax_report.txt b/coreplugins/TableImport/src/test/resources/resources/tax_report.txt
new file mode 100644
index 0000000..c095751
--- /dev/null
+++ b/coreplugins/TableImport/src/test/resources/resources/tax_report.txt
@@ -0,0 +1,33 @@
+code | name | preferred name | taxid
+1 | Saccharomyces cerevisiae | | 4932
+1 | Drosophila melanogaster | | 7227
+1 | Mus musculus | | 10090
+1 | Arabidopsis thaliana | | 3702
+1 | Caenorhabditis elegans | | 6239
+1 | Rattus norvegicus | | 10116
+1 | Oryza sativa | | 4530
+1 | Danio rerio | | 7955
+1 | Dictyostelium discoideum | | 44689
+1 | Candida albicans | | 5476
+2 | Bacillus anthracis Ames | Bacillus anthracis str. Ames | 198094
+1 | Coxiella burnetii RSA 493 | | 227377
+1 | Campylobacter jejuni RM1221 | | 195099
+1 | Dehalococcoides ethenogenes 195 | | 243164
+1 | Geobacter sulfurreducens PCA | | 243231
+2 | Listeria monocytogenes 4b F2365 | Listeria monocytogenes str. 4b F2365 | 265669
+2 | Methylococcus capsulatus Bath | Methylococcus capsulatus str. Bath | 243233
+2 | Pseudomonas syringae DC3000 | Pseudomonas syringae pv. tomato str. DC3000 | 223283
+1 | Shewanella oneidensis MR-1 | | 211586
+1 | Silicibacter pomeroyi DSS-3 | | 246200
+1 | Trypanosoma brucei | | 5691
+1 | Vibrio cholerae | | 666
+1 | Arabidopsis | | 3701
+2 | Human | Homo sapiens | 9606
+2+ | Rat | Rattus | 10114
+2+ | Rat | Rattus norvegicus | 10116
+2 | Zebrafish | Danio rerio | 7955
+1 | Leishmania major | | 5664
+1 | Plasmodium falciparum | | 5833
+1 | Schizosaccharomyces pombe | | 4896
+1 | Trypanosoma brucei | | 5691
+1 | Glossina morsitans | | 7394
diff --git a/coreplugins/TableImport/src/test/resources/uppercase.sif b/coreplugins/TableImport/src/test/resources/uppercase.sif
new file mode 100644
index 0000000..6a7a7d2
--- /dev/null
+++ b/coreplugins/TableImport/src/test/resources/uppercase.sif
@@ -0,0 +1 @@
+FAM62C pp MMP9
\ No newline at end of file
diff --git a/coreplugins/TableImport/src/test/resources/yeastHQ_sub.sif b/coreplugins/TableImport/src/test/resources/yeastHQ_sub.sif
new file mode 100644
index 0000000..4d89240
--- /dev/null
+++ b/coreplugins/TableImport/src/test/resources/yeastHQ_sub.sif
@@ -0,0 +1,32 @@
+YPL256C pp YMR199W
+YPL256C pp YBR160W
+YMR199W pp YBR160W
+YLR182W pd YDR279W
+YLR182W pd YDL227C
+YLR182W pd YGL179C
+YLR182W pd YML083C
+YLR182W pd YML082W
+YLR182W pd YJL185C
+YLR182W pd YKL161C
+YLR182W pd YMR307W
+YLR182W pd YMR199W
+YLR182W pd YPL163C
+YLR182W pd YJR054W
+YLR182W pd YKR013W
+YLR182W pd YMR306C-A
+YLR182W pd YKR011C
+YLR182W pd YGL239C
+YLR182W pd YOR106W
+YLR182W pd YDL141W
+YLR182W pd YKL214C
+YLR182W pd YER140W
+YLR182W pd YNL301C
+YLR182W pd YER128W
+YLR182W pd YJL092W
+YLR182W pd YJL093C
+YLR182W pd YOR373W
+YLR182W pd YDR525W-A
+YLR182W pd YER139C
+YLR182W pd YOL114C
+YLR182W pd YDL142C
+YLR182W pd YFL055W
diff --git a/coreplugins/TableImport/src/test/resources/yeastHQ_sub.xls b/coreplugins/TableImport/src/test/resources/yeastHQ_sub.xls
new file mode 100755
index 0000000..10605f4
Binary files /dev/null and b/coreplugins/TableImport/src/test/resources/yeastHQ_sub.xls differ
diff --git a/coreplugins/browser/pom.xml b/coreplugins/browser/pom.xml
new file mode 100644
index 0000000..a49be1a
--- /dev/null
+++ b/coreplugins/browser/pom.xml
@@ -0,0 +1,56 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>parent</artifactId>
+ <version>2.8.4-SNAPSHOT</version>
+ </parent>
+
+ <artifactId>attribute-browser</artifactId>
+ <packaging>jar</packaging>
+
+ <name>Attribute Browser</name>
+
+ <!-- bootstrap for cytoscape dependencies, namely the parent POM snapshots -->
+ <repositories>
+ <repository>
+ <id>cytoscape_snapshots</id>
+ <snapshots>
+ <enabled>true</enabled>
+ </snapshots>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <name>Cytoscape Snapshots</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/</url>
+ </repository>
+ <repository>
+ <id>cytoscape_releases</id>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ <name>Cytoscape Releases</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/releases/</url>
+ </repository>
+ </repositories>
+
+ <build>
+ <plugins>
+ <plugin>
+ <artifactId>maven-assembly-plugin</artifactId>
+ <configuration>
+ <archive>
+ <manifestEntries>
+ <Cytoscape-Plugin>browser.AttributeBrowserPlugin</Cytoscape-Plugin>
+ </manifestEntries>
+ </archive>
+ </configuration>
+ </plugin>
+ </plugins>
+ </build>
+
+</project>
+
diff --git a/coreplugins/browser/src/main/java/browser/AttributeBrowser.java b/coreplugins/browser/src/main/java/browser/AttributeBrowser.java
new file mode 100644
index 0000000..5a85341
--- /dev/null
+++ b/coreplugins/browser/src/main/java/browser/AttributeBrowser.java
@@ -0,0 +1,333 @@
+/*
+ Copyright (c) 2006, 2007, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package browser;
+
+
+import giny.model.GraphObject;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Dimension;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeSupport;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTable;
+import javax.swing.SwingConstants;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ListSelectionEvent;
+import javax.swing.event.SwingPropertyChangeSupport;
+import javax.swing.event.TableColumnModelEvent;
+import javax.swing.event.TableColumnModelListener;
+import javax.swing.table.TableColumnModel;
+
+import browser.ui.AttributeBrowserToolBar;
+import browser.ui.CyAttributeBrowserTable;
+import cytoscape.Cytoscape;
+import cytoscape.data.CyAttributes;
+import cytoscape.data.CyAttributesUtils;
+import cytoscape.view.cytopanels.CytoPanelListener;
+import cytoscape.view.cytopanels.CytoPanelState;
+
+
+/**
+ * DataTable class constructs all Panels for the browser.<br>
+ * One DataTable contains the table of values and the toolbar above the table
+ * within a jpanel. This panel is then added to CytoPanel2. Tabbed browsing
+ * between attribute tables is handled by CytoPanel2.
+ *
+ * @author kono xmas
+ *
+ * Combine CytoPanel_2 and CytoPanel_3 Peng-Liang wang 9/12/2006 Move advanced
+ * panel to AttrMod Dialog Peng-Liang wang 9/28/2006
+ *
+ */
+public class AttributeBrowser implements TableColumnModelListener {
+ private static final Dimension PANEL_SIZE = new Dimension(400, 300);
+
+ protected static Object pcsO = new Object();
+ protected static PropertyChangeSupport pcs = new SwingPropertyChangeSupport(pcsO);
+
+
+ public static PropertyChangeSupport getPropertyChangeSupport() {
+ return pcs;
+ }
+
+ public static void firePropertyChange(String property_type, Object old_value, Object new_value) {
+ final PropertyChangeEvent e = new PropertyChangeEvent(pcsO, property_type, old_value, new_value);
+ getPropertyChangeSupport().firePropertyChange(e);
+ }
+
+ public static final String ID = "ID";
+
+
+ public static final String NETWORK_METADATA = "Network Metadata";
+ public static final Color DEFAULT_EDGE_COLOR = Color.RED;
+ public static final Color DEFAULT_NODE_COLOR = Color.YELLOW;
+
+ // Each Attribute Browser operates on one CytoscapeData object, and on
+ // either Nodes or Edges.
+ private final CyAttributes attributes;
+
+ // Type of attribute
+ private final DataObjectType panelType;
+
+ // Main panel for put everything
+ private JPanel mainPanel;
+
+ // Table object and its model.
+ private final DataTableModel tableModel;
+ private final CyAttributeBrowserTable attributeTable;
+
+ // Toolbar panel on the top of browser
+ private final AttributeBrowserToolBar attributeBrowserToolBar;
+
+ // Will be used to keep track of column order.
+ private List<String> orderedColumn;
+
+ // Index number for the panels
+ int attributePanelIndex;
+ int modPanelIndex;
+ int tableIndex;
+ int browserIndex;
+
+
+ /**
+ *
+ */
+ public final static String RESTORE_COLUMN = "RESTORE_COLUMN";
+ public final static String CLEAR_INTERNAL_SELECTION = "CLEAR_INTERNAL_SELECTION";
+
+ /**
+ * Browser object is one per attribute type.
+ * Users should access it through this.
+ *
+ * @param type
+ */
+ public static AttributeBrowser getBrowser(final DataObjectType type) {
+ return new AttributeBrowser(type);
+ }
+
+ protected void addMenuItem(Component newItem) {
+ attributeTable.getPopupMenu().add(newItem);
+ }
+
+ /**
+ * Creates a new DataTable object.
+ *
+ * @param attributes
+ * DOCUMENT ME!
+ * @param tableObjectType
+ * DOCUMENT ME!
+ */
+ private AttributeBrowser(final DataObjectType panelType) {
+ // set up CytoscapeData Object and GraphObject Type
+ this.attributes = panelType.getAssociatedAttributes();
+ this.panelType = panelType;
+ this.orderedColumn = new ArrayList<String>();
+
+ // Create table model.
+ tableModel = makeModel();
+
+ attributeTable = new CyAttributeBrowserTable(tableModel, panelType, this);
+ attributeTable.setAutoResizeMode(JTable.AUTO_RESIZE_OFF);
+
+ // Toolbar for selecting attributes and create new attribute.
+ attributeBrowserToolBar = new AttributeBrowserToolBar(tableModel, attributeTable,
+ new AttributeModel(attributes, this), orderedColumn,
+ panelType);
+
+ // the attribute table display: CytoPanel 2, horizontal SOUTH panel.
+ mainPanel = new JPanel();
+ mainPanel.setLayout(new BorderLayout());
+ mainPanel.setPreferredSize(PANEL_SIZE);
+ mainPanel.setBorder(null);
+
+ // If this is a network attribute browser, do not allow to swap
+ // column.
+ if (panelType == DataObjectType.NETWORK) {
+ attributeTable.getTableHeader().setReorderingAllowed(false);
+ }
+
+ attributeTable.getColumnModel().addColumnModelListener(this);
+ JScrollPane tp = new JScrollPane(attributeTable);
+ tp.addMouseListener(new MouseAdapter() {
+ public void mouseClicked(MouseEvent e) {
+ getPropertyChangeSupport().firePropertyChange(AttributeBrowser.CLEAR_INTERNAL_SELECTION, null, panelType);
+ }
+ });
+ mainPanel.setName(panelType.getDisplayName() + "AttributeBrowser");
+ mainPanel.add(tp, BorderLayout.CENTER);
+ mainPanel.add(attributeBrowserToolBar, BorderLayout.NORTH);
+
+ // Add main browser panel to CytoPanel 2 (SOUTH)
+ Cytoscape.getDesktop().getCytoPanel(SwingConstants.SOUTH)
+ .add(panelType.getDisplayName() + " Attribute Browser", mainPanel);
+ Cytoscape.getDesktop().getCytoPanel(SwingConstants.SOUTH).setState(CytoPanelState.DOCK);
+ }
+
+ void refresh() {
+ // TODO: is this correct?
+ tableModel.setTableData(null, null);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public CyAttributeBrowserTable getAttributeTable() {
+ return attributeTable;
+ }
+
+ static class Listener implements CytoPanelListener {
+ int WEST;
+ int SOUTH;
+ int EAST;
+ int myIndex;
+
+ Listener(int w, int s, int e, int my) {
+ WEST = w;
+ SOUTH = s;
+ EAST = e;
+ myIndex = my;
+ }
+
+ public void onComponentAdded(int count) {
+ }
+
+ public void onComponentRemoved(int count) {
+ }
+
+ public void onComponentSelected(int componentIndex) {
+ if (componentIndex == myIndex) {
+ if (WEST != -1) {
+ Cytoscape.getDesktop().getCytoPanel(SwingConstants.WEST).setSelectedIndex(WEST);
+ }
+
+ if (SOUTH != -1) {
+ Cytoscape.getDesktop().getCytoPanel(SwingConstants.SOUTH).setSelectedIndex(SOUTH);
+ }
+
+ if (EAST != -1) {
+ Cytoscape.getDesktop().getCytoPanel(SwingConstants.EAST).setSelectedIndex(EAST);
+ }
+ }
+ }
+
+ public void onStateChange(CytoPanelState newState) {
+ }
+ }
+
+
+ private DataTableModel makeModel() {
+ final List<String> attributeNames = CyAttributesUtils.getVisibleAttributeNames(attributes);
+ final List<GraphObject> graphObjects = getSelectedGraphObjects();
+ final DataTableModel model = new DataTableModel(graphObjects, attributeNames, panelType);
+
+ return model;
+ }
+
+ private List<GraphObject> getSelectedGraphObjects() {
+ if (panelType.equals(DataObjectType.NODES)) {
+ return new ArrayList<GraphObject>(Cytoscape.getCurrentNetwork().getSelectedNodes());
+ } else if (panelType.equals(DataObjectType.EDGES)){
+ return new ArrayList<GraphObject>(Cytoscape.getCurrentNetwork().getSelectedEdges());
+ }
+
+ return null;
+ }
+
+ /**
+ * Return selected items.
+ *
+ * @return DOCUMENT ME!
+ */
+ public List<String> getSelectedAttributes() {
+ orderedColumn.clear();
+ for(int i=0; i<attributeTable.getColumnModel().getColumnCount(); i++) {
+ orderedColumn.add(attributeTable.getColumnModel().getColumn(i).getHeaderValue().toString());
+ }
+ return orderedColumn;
+ }
+
+ public void setSelectedAttributes(final List<String> selected) {
+ orderedColumn = selected;
+ attributeBrowserToolBar.updateList(selected);
+ tableModel.setTableData(null, orderedColumn);
+ }
+
+
+ public void restoreColumnModel(TableColumnModel newModel) {
+ attributeTable.setColumnModel(newModel);
+ }
+
+ public TableColumnModel getColumnModel() {
+ return attributeTable.getColumnModel();
+ }
+
+ @Override
+ public void columnAdded(TableColumnModelEvent e) {}
+
+ @Override
+ public void columnMarginChanged(ChangeEvent e) {}
+
+ @Override
+ public void columnMoved(TableColumnModelEvent e) {
+ // Ignore if same
+ if (e.getFromIndex() == e.getToIndex())
+ return;
+
+ final int columnCount = attributeTable.getColumnCount();
+
+ //System.out.println("Ordered: " + e.getFromIndex() + " to " + e.getToIndex());
+ orderedColumn.clear();
+
+ for (int i = 0; i < columnCount; i++) {
+ //System.out.print("[" + attributeTable.getColumnName(i) + "] ");
+ orderedColumn.add(attributeTable.getColumnName(i));
+ }
+
+ // update child's column order
+ attributeBrowserToolBar.setOrderedColumnList(orderedColumn);
+
+ //System.out.println("");
+ }
+
+ @Override
+ public void columnRemoved(TableColumnModelEvent e) {}
+
+ @Override
+ public void columnSelectionChanged(ListSelectionEvent e) {}
+}
diff --git a/coreplugins/browser/src/main/java/browser/AttributeBrowserPlugin.java b/coreplugins/browser/src/main/java/browser/AttributeBrowserPlugin.java
new file mode 100755
index 0000000..4ee6681
--- /dev/null
+++ b/coreplugins/browser/src/main/java/browser/AttributeBrowserPlugin.java
@@ -0,0 +1,290 @@
+/*
+ Copyright (c) 2006, 2007, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package browser;
+
+import static browser.DataObjectType.EDGES;
+import static browser.DataObjectType.NETWORK;
+import static browser.DataObjectType.NODES;
+
+import java.awt.Component;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.text.DecimalFormat;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+import java.util.Properties;
+import java.util.Map.Entry;
+
+import cytoscape.logger.CyLogger;
+import cytoscape.plugin.CytoscapePlugin;
+import javax.swing.table.TableColumn;
+import javax.swing.table.TableColumnModel;
+import java.util.HashMap;
+
+/**
+ * Attribute browser's main class.<br>
+ *
+ * @version 0.9
+ * @since 2.2
+ * @author xmas kono ruschein
+ *
+ */
+public class AttributeBrowserPlugin extends CytoscapePlugin {
+ // Name of browser's property file.
+ private static final String PROP_FILE_NAME = "attributeBrowser.props";
+
+ // Header message in the prop file.
+ private static final String PROP_HEADER = "Cytoscape Attribute Browser Plugin Properties";
+
+ /*
+ * Static instances of browsers.
+ */
+ private static final AttributeBrowser nodeAttributeBrowser;
+ private static final AttributeBrowser edgeAttributeBrowser;
+ private static final AttributeBrowser networkAttributeBrowser;
+
+ private static CyLogger logger;
+
+ static {
+ nodeAttributeBrowser = AttributeBrowser.getBrowser(NODES);
+ edgeAttributeBrowser = AttributeBrowser.getBrowser(EDGES);
+ networkAttributeBrowser = AttributeBrowser.getBrowser(NETWORK);
+ logger = CyLogger.getLogger(AttributeBrowserPlugin.class);
+ }
+
+ // Global properties for this plugin.
+ private final Properties prop;
+
+ /**
+ * Constructor for this plugin.
+ * Call 3 tables, nodes, edges and network.<br>
+ * The DataTable class actually creates all CytoPanels.<br>
+ * Filter functions are implemented in Advanced Window.
+ *
+ */
+ public AttributeBrowserPlugin() {
+ prop = new Properties();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param targetType DOCUMENT ME!
+ * @param menuItem DOCUMENT ME!
+ */
+ public static void addMenuItem(final DataObjectType targetType, final Component menuItem) {
+ if (targetType == NODES)
+ nodeAttributeBrowser.addMenuItem(menuItem);
+ else if (targetType == EDGES)
+ edgeAttributeBrowser.addMenuItem(menuItem);
+ else
+ networkAttributeBrowser.addMenuItem(menuItem);
+ }
+
+ public static AttributeBrowser getAttributeBrowser(browser.DataObjectType pObjectType){
+ if (pObjectType == NODES)
+ return nodeAttributeBrowser;
+ else if (pObjectType == EDGES)
+ return edgeAttributeBrowser;
+
+ return networkAttributeBrowser;
+ }
+ /**
+ * DOCUMENT ME!
+ */
+ public void onCytoscapeExit() {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param pStateFileList DOCUMENT ME!
+ */
+ public void restoreSessionState(List<File> pStateFileList) {
+ if ((pStateFileList == null) || (pStateFileList.size() == 0)) {
+ logger.error("Could not find Browser property file. Using defaults.");
+ return;
+ }
+
+ try {
+ // Pick the first one since currently there is only one prop file.
+ final File browserPropfile = pStateFileList.get(0);
+ prop.clear();
+ prop.load(new FileInputStream(browserPropfile));
+
+ final List<String> nodeAttrSelected = new ArrayList<String>();
+ final List<String> edgeAttrSelected = new ArrayList<String>();
+ final List<String> networkAttrSelected = new ArrayList<String>();
+
+ List<String> nodeAttrColumnWidth = new ArrayList<String>();;
+ List<String> edgeAttrColumnWidth = new ArrayList<String>();;
+ List<String> networkAttrColumnWidth = new ArrayList<String>();;
+
+ final List<String> nodeKeys = new ArrayList<String>();
+ final List<String> edgeKeys = new ArrayList<String>();
+ final List<String> networkKeys = new ArrayList<String>();
+
+ String key;
+ String val;
+
+ for (Entry<Object, Object> set : prop.entrySet()) {
+ key = set.getKey().toString();
+ val = set.getValue().toString();
+
+ if (key.contains("node"))
+ nodeKeys.add(key);
+ else if (key.contains("edge"))
+ edgeKeys.add(key);
+ else if (key.contains("network"))
+ networkKeys.add(key);
+ else
+ System.out.println("Something wrong in the attribute browser property file");
+ }
+
+ Collections.sort(nodeKeys);
+ Collections.sort(edgeKeys);
+ Collections.sort(networkKeys);
+
+ for (String targetKey : nodeKeys) {
+ String value = prop.getProperty(targetKey);
+ String [] items = value.split("\t");
+ nodeAttrSelected.add(items[0]);
+
+ if (items.length>1)
+ nodeAttrColumnWidth.add(items[1]);
+ }
+
+ for (String targetKey : edgeKeys) {
+ String value = prop.getProperty(targetKey);
+ String [] items = value.split("\t");
+ edgeAttrSelected.add(items[0]);
+
+ if (items.length > 1)
+ edgeAttrColumnWidth.add(items[1]);
+ }
+
+ nodeAttributeBrowser.setSelectedAttributes(nodeAttrSelected);
+ edgeAttributeBrowser.setSelectedAttributes(edgeAttrSelected);
+ networkAttributeBrowser.setSelectedAttributes(networkAttrSelected);
+
+ // recover the column width
+ restoreTableColumnWidth(NODES, nodeAttrColumnWidth);
+ restoreTableColumnWidth(EDGES, edgeAttrColumnWidth);
+ restoreTableColumnWidth(NETWORK, networkAttrColumnWidth);
+ } catch (IOException e) {
+ logger.error("Could not restore browser state. Using defaults...", e);
+ }
+ }
+
+ private void restoreTableColumnWidth(DataObjectType pObjectType, List<String> attrColumnWidth){
+ AttributeBrowser attBrowser = null;
+ if (pObjectType == NODES)
+ attBrowser = nodeAttributeBrowser;
+ else if (pObjectType == EDGES)
+ attBrowser = edgeAttributeBrowser;
+ else if (pObjectType == NETWORK)
+ attBrowser = networkAttributeBrowser;
+
+ if (attrColumnWidth != null && attrColumnWidth.size() > 0){
+
+ HashMap<String, Integer> attributeColumnWidthMap = attBrowser.getAttributeTable().getColumnWidthMap();
+ TableColumnModel colModel = attBrowser.getAttributeTable().getColumnModel();
+ for (int i = 0; i< colModel.getColumnCount(); i++) {
+ colModel.getColumn(i).setPreferredWidth(new Integer(attrColumnWidth.get(i)).intValue());
+ // It's important to save this value to the map to prevent it to be overwritten by other event
+ attributeColumnWidthMap.put(colModel.getColumn(i).getIdentifier().toString(), new Integer(attrColumnWidth.get(i)).intValue());
+ }
+ }
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param fileList DOCUMENT ME!
+ */
+ public void saveSessionStateFiles(List<File> fileList) {
+ final String tmpDir = System.getProperty("java.io.tmpdir");
+ final File browserPropfile = new File(tmpDir, PROP_FILE_NAME);
+ prop.clear();
+
+ final DecimalFormat decimalFormat = new DecimalFormat("0000");
+
+ try {
+ int idx = 0;
+ List<String> nodeAttr = nodeAttributeBrowser.getSelectedAttributes();
+ for (String name : nodeAttr) {
+ TableColumnModel colModel = nodeAttributeBrowser.getAttributeTable().getColumnModel();
+ int colIndex = colModel.getColumnIndex(name);
+ Integer widthObj = new Integer(colModel.getColumn(colIndex).getWidth());
+
+ prop.setProperty("attributeBrowser.node.selectedAttr" + decimalFormat.format(idx), name + "\t" + widthObj.toString());
+ idx++;
+ }
+
+ idx = 0;
+ List<String> edgeAttr = edgeAttributeBrowser.getSelectedAttributes();
+ for (String name : edgeAttr) {
+ TableColumnModel colModel = edgeAttributeBrowser.getAttributeTable().getColumnModel();
+ int colIndex = colModel.getColumnIndex(name);
+ Integer widthObj = new Integer(colModel.getColumn(colIndex).getWidth());
+
+ prop.setProperty("attributeBrowser.edge.selectedAttr" + decimalFormat.format(idx), name + "\t" + widthObj.toString());
+ idx++;
+ }
+
+ idx = 0;
+ for (String name : networkAttributeBrowser.getSelectedAttributes()) {
+ TableColumnModel colModel = networkAttributeBrowser.getAttributeTable().getColumnModel();
+ int colIndex = colModel.getColumnIndex(name);
+ Integer widthObj = new Integer(colModel.getColumn(colIndex).getWidth());
+
+ prop.setProperty("attributeBrowser.network.selectedAttr" + decimalFormat.format(idx), name + "\t" + widthObj.toString());
+ idx++;
+ }
+
+ String key;
+ String val;
+
+ for (Entry<Object, Object> set : prop.entrySet()) {
+ key = set.getKey().toString();
+ val = set.getValue().toString();
+ // logger.debug("KEY and VAL = " + key + ", " + val);
+ }
+
+ prop.store(new FileOutputStream(browserPropfile), PROP_HEADER);
+ } catch (IOException e) {
+ logger.error("Could not save attribute browser property file.", e);
+ }
+
+ fileList.add(browserPropfile);
+ }
+}
diff --git a/coreplugins/browser/src/main/java/browser/AttributeModel.java b/coreplugins/browser/src/main/java/browser/AttributeModel.java
new file mode 100644
index 0000000..45b0371
--- /dev/null
+++ b/coreplugins/browser/src/main/java/browser/AttributeModel.java
@@ -0,0 +1,220 @@
+/*
+ Copyright (c) 2006, 2007, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package browser;
+
+
+import cytoscape.Cytoscape;
+import cytoscape.data.CyAttributes;
+import cytoscape.data.CyAttributesUtils;
+
+import cytoscape.data.attr.MultiHashMapDefinitionListener;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Set;
+import java.util.TreeSet;
+import java.util.Vector;
+
+import javax.swing.ComboBoxModel;
+import javax.swing.ListModel;
+import javax.swing.event.ListDataEvent;
+import javax.swing.event.ListDataListener;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+
+
+public class AttributeModel implements ListModel, ComboBoxModel, MultiHashMapDefinitionListener, PropertyChangeListener {
+ private final AttributeBrowser attribBrowser;
+ private Vector listeners = new Vector();
+ private final CyAttributes attributes;
+ private List<String> attributeNames;
+ private Object selection = null;
+ private Set<Byte> validAttrTypes;
+ private Set<String> newAttributeNames = new HashSet<String>();
+
+ /**
+ * Creates a new AttributeModel object.
+ *
+ * @param data DOCUMENT ME!
+ */
+ public AttributeModel(final CyAttributes data, final AttributeBrowser attribBrowser, final Set<Byte> validAttrTypes) {
+ this.attribBrowser = attribBrowser;
+ this.attributes = data;
+ this.validAttrTypes = validAttrTypes;
+ data.getMultiHashMapDefinition().addDataDefinitionListener(this);
+ sortAttributes();
+
+ Cytoscape.getPropertyChangeSupport().addPropertyChangeListener(Cytoscape.ATTRIBUTES_CHANGED, this);
+ }
+
+ @SuppressWarnings("unchecked") public AttributeModel(final CyAttributes data, final AttributeBrowser attribBrowser) {
+ this(data, attribBrowser,
+ new TreeSet<Byte>((List<Byte>)(Arrays.asList(new Byte[] {
+ CyAttributes.TYPE_BOOLEAN,
+ CyAttributes.TYPE_COMPLEX,
+ CyAttributes.TYPE_FLOATING,
+ CyAttributes.TYPE_INTEGER,
+ CyAttributes.TYPE_SIMPLE_LIST,
+ CyAttributes.TYPE_SIMPLE_MAP,
+ CyAttributes.TYPE_STRING
+ }))));
+ }
+
+ public void propertyChange(PropertyChangeEvent e) {
+ // This will handle the case for the change of attribute userVisibility
+ if (e.getPropertyName() == Cytoscape.ATTRIBUTES_CHANGED) {
+ sortAttributes();
+ if (attribBrowser != null)
+ attribBrowser.refresh();
+ }
+ }
+
+ /**
+ * Sets "attributeNames" to the sorted list of user-visible attribute names with supported data types.
+ */
+ public void sortAttributes() {
+ final Set<String> oldAttributeNames = (attributeNames == null) ? new HashSet<String>() : new HashSet<String>(attributeNames);
+ newAttributeNames = new HashSet<String>();
+
+ attributeNames = new ArrayList<String>();
+ for (final String attrName : CyAttributesUtils.getVisibleAttributeNames(attributes)) {
+ if (validAttrTypes.contains(attributes.getType(attrName))) {
+ attributeNames.add(attrName);
+ if (!oldAttributeNames.contains(attrName))
+ newAttributeNames.add(attrName);
+ }
+ }
+ Collections.sort(attributeNames);
+
+ notifyListeners(new ListDataEvent(this, ListDataEvent.CONTENTS_CHANGED, 0,
+ attributeNames.size()));
+ }
+
+ public List<String> getAttributeNames() {
+ return attributeNames;
+ }
+
+ public Set<String> getNewAttributeNames() {
+ return newAttributeNames;
+ }
+
+ /**
+ * @return the i-th attribute name
+ */
+ public Object getElementAt(int i) {
+ if (i > attributeNames.size())
+ return null;
+
+ return attributeNames.get(i);
+ }
+
+ /**
+ * @return the number of attribute names
+ */
+ public int getSize() {
+ return attributeNames.size();
+ }
+
+ // implements ComboBoxModel
+ /**
+ * DOCUMENT ME!
+ *
+ * @param anItem DOCUMENT ME!
+ */
+ public void setSelectedItem(Object anItem) {
+ selection = anItem;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object getSelectedItem() {
+ return selection;
+ }
+
+ // implements CyDataDefinitionListener
+ /**
+ * DOCUMENT ME!
+ *
+ * @param attributeName DOCUMENT ME!
+ */
+ public void attributeDefined(String attributeName) {
+ sortAttributes();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param attributeName DOCUMENT ME!
+ */
+ public void attributeUndefined(String attributeName) {
+ sortAttributes();
+ }
+
+ // implements ListModel
+ /**
+ * DOCUMENT ME!
+ *
+ * @param l DOCUMENT ME!
+ */
+ public void addListDataListener(ListDataListener l) {
+ listeners.add(l);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param l DOCUMENT ME!
+ */
+ public void removeListDataListener(ListDataListener l) {
+ listeners.remove(l);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void notifyListeners(ListDataEvent e) {
+ for (Iterator listenIt = listeners.iterator(); listenIt.hasNext();) {
+ if (e.getType() == ListDataEvent.CONTENTS_CHANGED) {
+ ((ListDataListener) listenIt.next()).contentsChanged(e);
+ } else if (e.getType() == ListDataEvent.INTERVAL_ADDED) {
+ ((ListDataListener) listenIt.next()).intervalAdded(e);
+ } else if (e.getType() == ListDataEvent.INTERVAL_REMOVED) {
+ ((ListDataListener) listenIt.next()).intervalRemoved(e);
+ }
+ }
+ }
+}
diff --git a/coreplugins/browser/src/main/java/browser/ColumnComparator.java b/coreplugins/browser/src/main/java/browser/ColumnComparator.java
new file mode 100644
index 0000000..5b3cb4e
--- /dev/null
+++ b/coreplugins/browser/src/main/java/browser/ColumnComparator.java
@@ -0,0 +1,157 @@
+/*
+ =====================================================================
+
+ ColumnComparator.java
+
+ Created by Claude Duguay
+ Copyright (c) 2002
+
+ Rewrote by Keiichiro Ono 2006
+
+ =====================================================================
+ */
+package browser;
+
+import java.util.Comparator;
+import java.util.Vector;
+
+
+import cytoscape.data.CyAttributes;
+
+/**
+ *
+ */
+public class ColumnComparator implements Comparator {
+ private static final int EMPTY_STR_LENGTH = 2;
+ protected int index;
+ protected byte internalColumnType;
+ protected boolean ascending;
+
+ /**
+ * Creates a new ColumnComparator object.
+ *
+ * @param index DOCUMENT ME!
+ * @param ascending DOCUMENT ME!
+ */
+ public ColumnComparator(final int index, final byte type, final boolean ascending) {
+ this.index = index;
+ this.internalColumnType = type;
+ this.ascending = ascending;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param obj1 DOCUMENT ME!
+ * @param obj2 DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int compare(final Object obj1, final Object obj2) {
+ if (obj1 instanceof Vector && obj2 instanceof Vector) {
+ final Object firstObj = ((Vector) obj1).elementAt(index);
+ final Object secondObj = ((Vector) obj2).elementAt(index);
+
+ if ((firstObj == null) && (secondObj == null)) {
+ return 0;
+ } else if (firstObj == null) {
+ return 1;
+ } else if (secondObj == null) {
+ return -1;
+ } else if (firstObj instanceof ValidatedObjectAndEditString && secondObj instanceof ValidatedObjectAndEditString) {
+ final ValidatedObjectAndEditString v1 = (ValidatedObjectAndEditString) firstObj;
+ final ValidatedObjectAndEditString v2 = (ValidatedObjectAndEditString) secondObj;
+ final String errorText1 = v1.getErrorText();
+ final String errorText2 = v2.getErrorText();
+ if (errorText1 != null && errorText2 != null)
+ return ascending ? errorText1.compareToIgnoreCase(errorText2) : errorText2.compareToIgnoreCase(errorText1);
+ if (errorText2 != null)
+ return ascending? 1: -1;
+ if (errorText1 != null)
+ return ascending? -1: 1;
+ final Object val1 = v1.getValidatedObject();
+ final Object val2 = v2.getValidatedObject();
+
+ if (internalColumnType == CyAttributes.TYPE_FLOATING)
+ return ascending ? doubleCompare((double)(Double)val1, (double)(Double)val2) :
+ doubleCompare((double)(Double)val2, (double)(Double)val1);
+ if (internalColumnType == CyAttributes.TYPE_INTEGER)
+ return ascending ? integerCompare((int)(Integer)val1, (int)(Integer)val2) :
+ integerCompare((int)(Integer)val2, (int)(Integer)val1);
+
+ if (internalColumnType == CyAttributes.TYPE_BOOLEAN)
+ return ascending ? booleanCompare((boolean)(Boolean)val1, (boolean)(Boolean)val2) :
+ booleanCompare((boolean)(Boolean)val2, (boolean)(Boolean)val1);
+
+ return ascending ? stringCompare(val1.toString(), val2.toString()):
+ stringCompare(val2.toString(), val1.toString());
+ } else {
+ /*
+ * If not primitive, just compare as String
+ */
+ final String str1 = firstObj.toString();
+ final String str2 = secondObj.toString();
+
+ if ((str1.length() == EMPTY_STR_LENGTH) && (str2.length() == EMPTY_STR_LENGTH)) {
+ return 0;
+ } else if (str1.length() == EMPTY_STR_LENGTH) {
+ return 1;
+ } else if (str2.length() == EMPTY_STR_LENGTH) {
+ return -1;
+ } else {
+ return ascending ? str1.compareTo(str2) : str2.compareTo(str1);
+ }
+ }
+ }
+
+ return 1;
+ }
+
+ private static int doubleCompare(final double d1, final double d2) {
+ if (d1 < d2)
+ return -1;
+ return d1 > d2 ? +1 : 0;
+ }
+
+ private static int longCompare(final long l1, final long l2) {
+ if (l1 < l2)
+ return -1;
+ return l1 > l2 ? +1 : 0;
+ }
+
+ private static int integerCompare(final int i1, int i2) {
+ if (i1 < i2)
+ return -1;
+ return i1 > i2 ? +1 : 0;
+ }
+
+ private static int booleanCompare(final boolean b1, final boolean b2) {
+ if ((b1 && b2) || (!b1 && !b2))
+ return 0;
+ return b1 ? -1 : +1;
+ }
+
+ private static int stringCompare(final String s1, final String s2) {
+ return s1.compareToIgnoreCase(s2);
+ }
+
+ /**
+ * Comparing numbers.
+ *
+ * @param number1
+ * @param number2
+ * @return
+ */
+ public int compare(final Number number1, final Number number2) {
+ final double firstNumber = number1.doubleValue();
+ final double secondNumber = number2.doubleValue();
+
+ if (firstNumber < secondNumber) {
+ return -1;
+ } else if (firstNumber > secondNumber) {
+ return 1;
+ } else {
+ return 0;
+ }
+ }
+}
diff --git a/coreplugins/browser/src/main/java/browser/DataEditAction.java b/coreplugins/browser/src/main/java/browser/DataEditAction.java
new file mode 100644
index 0000000..2bc1fbf
--- /dev/null
+++ b/coreplugins/browser/src/main/java/browser/DataEditAction.java
@@ -0,0 +1,610 @@
+/*
+ Copyright (c) 2006, 2007, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package browser;
+
+
+import static browser.DataObjectType.NETWORK;
+import browser.util.AttrUtil;
+
+import cytoscape.Cytoscape;
+import cytoscape.data.CyAttributes;
+
+import org.cytoscape.equations.BooleanList;
+import org.cytoscape.equations.EqnCompiler;
+import org.cytoscape.equations.DoubleList;
+import org.cytoscape.equations.Equation;
+import org.cytoscape.equations.FunctionUtil;
+import org.cytoscape.equations.LongList;
+import org.cytoscape.equations.StringList;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Map;
+import java.util.List;
+import java.util.TreeMap;
+import javax.swing.JOptionPane;
+import javax.swing.undo.AbstractUndoableEdit;
+
+
+/**
+ * Validate and set new value to the CyAttributes.
+ */
+public class DataEditAction extends AbstractUndoableEdit {
+ private final String attrKey;
+ private final String attrName;
+ private final Object old_value;
+ private final Object new_value;
+ private final DataObjectType objectType;
+ private final DataTableModel tableModel;
+
+ private boolean valid = false;
+ private ValidatedObjectAndEditString objectAndEditString = null;
+
+ /**
+ * Creates a new DataEditAction object.
+ *
+ * @param table DOCUMENT ME!
+ * @param attrKey DOCUMENT ME!
+ * @param attrName DOCUMENT ME!
+ * @param keys DOCUMENT ME!
+ * @param old_value DOCUMENT ME!
+ * @param new_value DOCUMENT ME!
+ * @param graphObjectType DOCUMENT ME!
+ */
+ public DataEditAction(DataTableModel table, String attrKey, String attrName,
+ Object old_value, Object new_value, DataObjectType graphObjectType)
+ {
+ this.tableModel = table;
+ this.attrKey = attrKey;
+ this.attrName = attrName;
+ this.old_value = old_value;
+ this.new_value = new_value;
+ this.objectType = graphObjectType;
+
+ redo();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getPresentationName() {
+ return attrKey + " attribute " + attrName + " changed.";
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getRedoPresentationName() {
+ return "Redo: " + attrKey + ":" + attrName + " to:" + new_value + " from " + old_value;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getUndoPresentationName() {
+ return "Undo: " + attrKey + ":" + attrName + " back to:" + old_value + " from " + new_value;
+ }
+
+ public ValidatedObjectAndEditString getValidatedObjectAndEditString() { return objectAndEditString; }
+
+ /**
+ * Set attribute value. Input validater is added.
+ *
+ * @param id
+ * @param att
+ * @param newValue
+ */
+ private void setAttributeValue(final String id, final String attrName, final Object newValue) {
+ valid = false;
+ if (newValue == null)
+ return;
+
+ final CyAttributes attrs = objectType.getAssociatedAttributes();
+
+ // Error message for the popup dialog.
+ String errMessage = null;
+
+ // Change object to String
+ final String newValueStr = newValue.toString().trim();
+
+ final byte targetType = attrs.getType(attrName);
+ if (targetType == CyAttributes.TYPE_INTEGER)
+ handleInteger(newValueStr, attrs, id);
+ else if (targetType == CyAttributes.TYPE_FLOATING)
+ handleDouble(newValueStr, attrs, id);
+ else if (targetType == CyAttributes.TYPE_BOOLEAN)
+ handleBoolean(newValueStr, attrs, id);
+ else if (targetType == CyAttributes.TYPE_STRING)
+ handleString(newValueStr, attrs, id);
+ else if (targetType == CyAttributes.TYPE_SIMPLE_LIST)
+ handleList(newValueStr, attrs, id);
+ else if (targetType == CyAttributes.TYPE_SIMPLE_MAP)
+ handleMap(newValueStr, attrs, id);
+ }
+
+ private void handleInteger(final String newValueStr, final CyAttributes attrs, final String id) {
+ // Deal with equations first:
+ if (newValueStr != null && newValueStr.length() >= 2 && newValueStr.charAt(0) == '=') {
+ final Equation equation = parseEquation(newValueStr, attrs, id, attrName);
+ if (equation == null) {
+ objectAndEditString = new ValidatedObjectAndEditString(null, newValueStr, "#PARSE");
+ attrs.deleteAttribute(id, attrName);
+ return;
+ }
+
+ final Class returnType = equation.getType();
+ if (returnType != Long.class && returnType != Double.class && returnType != Boolean.class && returnType != Object.class) {
+ showErrorWindow("Error in attribute \"" + attrName
+ + "\": equation is of type " + getLastDotComponent(returnType.toString())
+ + " but should be of type Integer!");
+ objectAndEditString = new ValidatedObjectAndEditString(null, newValueStr, "#TYPE");
+ attrs.deleteAttribute(id, attrName);
+ return;
+ }
+
+ attrs.setAttribute(id, attrName, equation);
+ final Object attrValue = attrs.getAttribute(id, attrName);
+ String errorMessage = attrs.getLastEquationError();
+ if (errorMessage != null)
+ errorMessage = "#ERROR(" + errorMessage + ")";
+ objectAndEditString = new ValidatedObjectAndEditString(attrValue, newValueStr, errorMessage);
+ valid = true;
+ return;
+ }
+
+ Integer newIntVal;
+ try {
+ newIntVal = Integer.valueOf(newValueStr);
+ attrs.setAttribute(id, attrName, newIntVal);
+ objectAndEditString = new ValidatedObjectAndEditString(newIntVal);
+ valid = true;
+ } catch (final Exception e) {
+ objectAndEditString = new ValidatedObjectAndEditString(null, newValueStr, "#ERROR");
+ attrs.deleteAttribute(id, attrName);
+ showErrorWindow("Attribute " + attrName
+ + " should be an Integer (or the number is too big/small).");
+ }
+ }
+
+ private void handleDouble(final String newValueStr, final CyAttributes attrs, final String id) {
+ // Deal with equations first:
+ if (newValueStr != null && newValueStr.length() >= 2 && newValueStr.charAt(0) == '=') {
+ final Equation equation = parseEquation(newValueStr, attrs, id, attrName);
+ if (equation == null) {
+ objectAndEditString = new ValidatedObjectAndEditString(null, newValueStr, "#PARSE");
+ attrs.deleteAttribute(id, attrName);
+ return;
+ }
+
+ final Class returnType = equation.getType();
+ if (returnType != Double.class && returnType != Long.class && returnType != Boolean.class && returnType != Object.class) {
+ showErrorWindow("Error in attribute \"" + attrName
+ + "\": equation is of type " + getLastDotComponent(returnType.toString())
+ + " but should be of type Floating Point!");
+ objectAndEditString = new ValidatedObjectAndEditString(null, newValueStr, "#TYPE");
+ attrs.deleteAttribute(id, attrName);
+ return;
+ }
+
+ attrs.setAttribute(id, attrName, equation);
+ final Object attrValue = attrs.getAttribute(id, attrName);
+ String errorMessage = attrs.getLastEquationError();
+ if (errorMessage != null)
+ errorMessage = "#ERROR(" + errorMessage + ")";
+ objectAndEditString = new ValidatedObjectAndEditString(attrValue, newValueStr, errorMessage);
+ valid = true;
+ return;
+ }
+
+ Double newDblVal;
+ try {
+ newDblVal = Double.valueOf(newValueStr);
+ attrs.setAttribute(id, attrName, newDblVal);
+ objectAndEditString = new ValidatedObjectAndEditString(newDblVal);
+ valid = true;
+ } catch (final Exception e) {
+ objectAndEditString = new ValidatedObjectAndEditString(null, newValueStr, "#ERROR");
+ attrs.deleteAttribute(id, attrName);
+ showErrorWindow("Attribute " + attrName
+ + " should be a floating point number (or the number is too big/small).");
+ }
+ }
+
+ private void handleBoolean(final String newValueStr, final CyAttributes attrs, final String id) {
+ // Deal with equations first:
+ if (newValueStr != null && newValueStr.length() >= 2 && newValueStr.charAt(0) == '=') {
+ final Equation equation = parseEquation(newValueStr, attrs, id, attrName);
+ if (equation == null) {
+ objectAndEditString = new ValidatedObjectAndEditString(null, newValueStr, "#PARSE");
+ attrs.deleteAttribute(id, attrName);
+ return;
+ }
+
+ final Class returnType = equation.getType();
+ if (returnType != Boolean.class && returnType != Long.class && returnType != Double.class && returnType != Object.class) {
+ objectAndEditString = new ValidatedObjectAndEditString(null, newValueStr, "#TYPE");
+ attrs.deleteAttribute(id, attrName);
+ showErrorWindow("Error in attribute \"" + attrName
+ + "\": equation is of type " + getLastDotComponent(returnType.toString())
+ + " but should be of type Boolean!");
+ return;
+ }
+
+ attrs.setAttribute(id, attrName, equation);
+ final Object attrValue = attrs.getAttribute(id, attrName);
+ String errorMessage = attrs.getLastEquationError();
+ if (errorMessage != null)
+ errorMessage = "#ERROR(" + errorMessage + ")";
+ objectAndEditString = new ValidatedObjectAndEditString(attrValue, newValueStr, errorMessage);
+ valid = true;
+ return;
+ }
+
+ Boolean newBoolVal = false;
+ try {
+ newBoolVal = Boolean.valueOf(newValueStr);
+ attrs.setAttribute(id, attrName, newBoolVal);
+ objectAndEditString = new ValidatedObjectAndEditString(newBoolVal);
+ valid = true;
+ } catch (final Exception e) {
+ objectAndEditString = new ValidatedObjectAndEditString(null, newValueStr, "#ERROR");
+ attrs.deleteAttribute(id, attrName);
+ showErrorWindow("Attribute " + attrName + " should be a boolean value (true/false).");
+ }
+ }
+
+ private void handleString(final String newValueStr, final CyAttributes attrs, final String id) {
+ final String newStrVal = replaceCStyleEscapes(newValueStr);
+
+ // Deal with equations first:
+ if (newValueStr != null && newValueStr.length() >= 2 && newValueStr.charAt(0) == '=') {
+ final Equation equation = parseEquation(newStrVal, attrs, id, attrName);
+ if (equation == null) {
+ objectAndEditString = new ValidatedObjectAndEditString(null, newStrVal, "#PARSE");
+ attrs.deleteAttribute(id, attrName);
+ return;
+ }
+
+ attrs.setAttribute(id, attrName, equation);
+ objectAndEditString = new ValidatedObjectAndEditString(attrs.getAttribute(id, attrName), equation.toString());
+ final Object attrValue = attrs.getAttribute(id, attrName);
+ String errorMessage = attrs.getLastEquationError();
+ if (errorMessage != null)
+ errorMessage = "#ERROR(" + errorMessage + ")";
+ objectAndEditString = new ValidatedObjectAndEditString(attrValue, newValueStr, errorMessage);
+ valid = true;
+ return;
+ }
+
+ attrs.setAttribute(id, attrName, newStrVal);
+ objectAndEditString = new ValidatedObjectAndEditString(newStrVal);
+ valid = true;
+ }
+
+ private void handleList(final String newValueStr, final CyAttributes attrs, final String id) {
+ // Deal with equations first:
+ if (newValueStr != null && newValueStr.length() >= 2 && newValueStr.charAt(0) == '=') {
+ final Equation equation = parseEquation(newValueStr, attrs, id, attrName);
+ if (equation == null) {
+ objectAndEditString = new ValidatedObjectAndEditString(null, newValueStr, "#PARSE");
+ attrs.deleteAttribute(id, attrName);
+ return;
+ }
+
+ final Class returnType = equation.getType();
+ if (!FunctionUtil.isSomeKindOfList(returnType) && returnType != Object.class) {
+ objectAndEditString = new ValidatedObjectAndEditString(null, newValueStr, "#TYPE");
+ attrs.deleteAttribute(id, attrName);
+ showErrorWindow("Error in attribute \"" + attrName
+ + "\": equation is of type " + getLastDotComponent(returnType.toString())
+ + " but should be of type List!");
+ return;
+ }
+
+ final byte listElementType = attrs.getListElementType(attrName);
+ if (returnType == DoubleList.class && listElementType != CyAttributes.TYPE_FLOATING
+ || returnType == LongList.class && listElementType != CyAttributes.TYPE_INTEGER
+ || returnType == StringList.class && listElementType != CyAttributes.TYPE_STRING
+ || returnType == BooleanList.class && listElementType != CyAttributes.TYPE_BOOLEAN)
+ {
+ objectAndEditString = new ValidatedObjectAndEditString(null, newValueStr, "#TYPE");
+ attrs.deleteAttribute(id, attrName);
+ showErrorWindow("Error in attribute \"" + attrName
+ + "\": equation is of type " + getLastDotComponent(returnType.toString())
+ + " which is the wrong type of list!");
+ return;
+ }
+
+ attrs.setListAttribute(id, attrName, equation);
+ final Object attrValue = attrs.getAttribute(id, attrName);
+ String errorMessage = attrs.getLastEquationError();
+ if (errorMessage != null)
+ errorMessage = "#ERROR(" + errorMessage + ")";
+ objectAndEditString = new ValidatedObjectAndEditString(attrValue, newValueStr, errorMessage);
+ valid = true;
+ return;
+ }
+
+ final String escapedString = replaceCStyleEscapes(newValueStr);
+ final int elementType = attrs.getListElementType(attrName);
+
+ List newList = null;
+ switch (elementType) {
+ case CyAttributes.TYPE_STRING:
+ newList = parseStringListValue(escapedString);
+ break;
+ case CyAttributes.TYPE_FLOATING:
+ newList = parseDoubleListValue(escapedString);
+ break;
+ case CyAttributes.TYPE_INTEGER:
+ newList = parseIntegerListValue(escapedString);
+ break;
+ case CyAttributes.TYPE_BOOLEAN:
+ newList = parseBooleanListValue(escapedString);
+ break;
+ default:
+ throw new ClassCastException("can't determined List type!");
+ }
+
+ if (newList == null) {
+ objectAndEditString = new ValidatedObjectAndEditString(null, newValueStr, "#ERROR");
+ attrs.deleteAttribute(id, attrName);
+ showErrorWindow("Invalid list!");
+ return;
+ }
+ else {
+ attrs.setListAttribute(id, attrName, newList);
+ objectAndEditString = new ValidatedObjectAndEditString(escapedString);
+ valid = true;
+ }
+ }
+
+ private void handleMap(final String newValueStr, final CyAttributes attrs, final String id) {
+ // Deal with equations first:
+ if (newValueStr != null && newValueStr.length() >= 2 && newValueStr.charAt(0) == '=') {
+ objectAndEditString = new ValidatedObjectAndEditString(null, newValueStr, "#ERROR");
+ attrs.deleteAttribute(id, attrName);
+ showErrorWindow("Error in attribute \"" + attrName
+ + "\": no equations are supported for maps!");
+ return;
+ }
+
+ showErrorWindow("Map editing is not supported in this version.");
+ }
+
+ /**
+ * Assumes that "s" consists of components separated by dots.
+ * @returns the last component of "s" or all of "s" if there are no dots
+ */
+ private static String getLastDotComponent(final String s) {
+ final int lastDotPos = s.lastIndexOf('.');
+ if (lastDotPos == -1)
+ return s;
+
+ return s.substring(lastDotPos + 1);
+ }
+
+ /** Does some rudimentary list syntax checking and returns the number of items in "listCandidate."
+ * @param listCandidate a string that will be analysed as to list-syntax conformance.
+ * @returns -1 if "listCandidate" does not conform to a list syntax, otherwise the number of items in the simple list.
+ */
+ private int countListItems(final String listCandidate) {
+ if (listCandidate.length() < 2 || listCandidate.charAt(0) != '[' || listCandidate.charAt(listCandidate.length() - 1) != ']')
+ return -1;
+
+ int commaCount = 0;
+ for (int charIndex = 1; charIndex < listCandidate.length() - 1; ++charIndex) {
+ if (listCandidate.charAt(charIndex) == ',')
+ ++commaCount;
+ }
+
+ return commaCount;
+ }
+
+ /** Attemps to convert "listCandidate" to a List of String.
+ * @param listCandidate hopefully a list of strings.
+ * @returns the List if "listCandidate" has been successfully parsed, else null.
+ */
+ private List parseStringListValue(final String listCandidate) {
+ final int itemCount = countListItems(listCandidate);
+ if (itemCount == -1)
+ return null;
+
+ final String bracketlessList = listCandidate.substring(1, listCandidate.length() - 1);
+ final String[] items = bracketlessList.split("\\s*,\\s*");
+
+ return Arrays.asList(items);
+ }
+
+ /** Attemps to convert "listCandidate" to a List of Double.
+ * @param listCandidate hopefully a list of doubles.
+ * @returns the List if "listCandidate" has been successfully parsed, else null.
+ */
+ private List parseDoubleListValue(final String listCandidate) {
+ final int itemCount = countListItems(listCandidate);
+ if (itemCount == -1)
+ return null;
+
+ final String bracketlessList = listCandidate.substring(1, listCandidate.length() - 1);
+ final String[] items = bracketlessList.split("\\s*,\\s*");
+
+ final List<Double> doubleList = new ArrayList<Double>(itemCount);
+ try {
+ for (final String item : items) {
+ final Double newDouble = Double.valueOf(item);
+ doubleList.add(newDouble);
+ }
+ } catch (final NumberFormatException e) {
+ return null; // At least one of the list items was not a double.
+ }
+
+ return doubleList;
+ }
+
+ /** Attemps to convert "listCandidate" to a List of Integer.
+ * @param listCandidate hopefully a list of ints.
+ * @returns the List if "listCandidate" has been successfully parsed, else null.
+ */
+ private List parseIntegerListValue(final String listCandidate) {
+ final int itemCount = countListItems(listCandidate);
+ if (itemCount == -1)
+ return null;
+
+ final String bracketlessList = listCandidate.substring(1, listCandidate.length() - 1);
+ final String[] items = bracketlessList.split("\\s*,\\s*");
+
+ final List<Integer> intList = new ArrayList<Integer>(itemCount);
+ try {
+ for (final String item : items) {
+ final Integer newInteger = Integer.valueOf(item);
+ intList.add(newInteger);
+ }
+ } catch (final NumberFormatException e) {
+ return null; // At least one of the list items was not a int.
+ }
+
+ return intList;
+ }
+
+ /** Attemps to convert "listCandidate" to a List of Boolean.
+ * @param listCandidate hopefully a list of booleans.
+ * @returns the List if "listCandidate" has been successfully parsed, else null.
+ */
+ private List parseBooleanListValue(final String listCandidate) {
+ final int itemCount = countListItems(listCandidate);
+ if (itemCount == -1)
+ return null;
+
+ final String bracketlessList = listCandidate.substring(1, listCandidate.length() - 1);
+ final String[] items = bracketlessList.split("\\s*,\\s*");
+
+ final List<Boolean> booleanList = new ArrayList<Boolean>(itemCount);
+ try {
+ for (final String item : items) {
+ final Boolean newBoolean = Boolean.valueOf(item);
+ booleanList.add(newBoolean);
+ }
+ } catch (final NumberFormatException e) {
+ return null; // At least one of the list items was not a boolean.
+ }
+
+ return booleanList;
+ }
+
+ private String replaceCStyleEscapes(String s) {
+ StringBuffer sb = new StringBuffer( s );
+ int index = 0;
+ while ( index < sb.length() ) {
+ if ( sb.charAt(index) == '\\' ) {
+ if ( sb.charAt(index+1) == 'n') {
+ sb.setCharAt(index,'\n');
+ sb.deleteCharAt(index+1);
+ index++;
+ } else if ( sb.charAt(index+1) == 'b') {
+ sb.setCharAt(index,'\b');
+ sb.deleteCharAt(index+1);
+ index++;
+ } else if ( sb.charAt(index+1) == 'r') {
+ sb.setCharAt(index,'\r');
+ sb.deleteCharAt(index+1);
+ index++;
+ } else if ( sb.charAt(index+1) == 'f') {
+ sb.setCharAt(index,'\f');
+ sb.deleteCharAt(index+1);
+ index++;
+ } else if ( sb.charAt(index+1) == 't') {
+ sb.setCharAt(index,'\t');
+ sb.deleteCharAt(index+1);
+ index++;
+ }
+ }
+ index++;
+ }
+ return sb.toString();
+ }
+
+ // Pop-up window for error message
+ private static void showErrorWindow(final String errMessage) {
+ JOptionPane.showMessageDialog(Cytoscape.getDesktop(), errMessage, "Invalid Value!",
+ JOptionPane.ERROR_MESSAGE);
+ }
+
+ /**
+ * For redo function.
+ */
+ public void redo() {
+ setAttributeValue(attrKey, attrName, new_value);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void undo() {
+ setAttributeValue(attrKey, attrName, old_value);
+
+ if (objectType != NETWORK) {
+ tableModel.setTableData();
+ } else {
+ tableModel.setNetworkTable();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isValid() {
+ return valid;
+ }
+
+ /**
+ * @returns the successfully compiled equation or null if an error occurred
+ */
+ private Equation parseEquation(final String equation, final CyAttributes attrs, final String id,
+ final String currentAttrName)
+ {
+ final Map<String, Class> attribNameToTypeMap = AttrUtil.getAttrNamesAndTypes(attrs);
+ attribNameToTypeMap.put("ID", String.class);
+
+ final EqnCompiler compiler = new EqnCompiler();
+ if (!compiler.compile(equation, attribNameToTypeMap)) {
+ showErrorWindow("Error in equation for attribute\"" + currentAttrName + "\": "
+ + compiler.getLastErrorMsg());
+ return null;
+ }
+
+ return compiler.getEquation();
+ }
+}
diff --git a/coreplugins/browser/src/main/java/browser/DataObjectType.java b/coreplugins/browser/src/main/java/browser/DataObjectType.java
new file mode 100644
index 0000000..f8daa3f
--- /dev/null
+++ b/coreplugins/browser/src/main/java/browser/DataObjectType.java
@@ -0,0 +1,102 @@
+/*
+ Copyright (c) 2006, 2007, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package browser;
+
+
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import cytoscape.data.CyAttributes;
+import giny.model.GraphObject;
+
+
+
+
+public enum DataObjectType {
+ NODES("Node"),
+ EDGES("Edge"),
+ NETWORK("Network");
+
+ private String dispName;
+
+ private DataObjectType(String dispName) {
+ this.dispName = dispName;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getDisplayName() {
+ return dispName;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public CyAttributes getAssociatedAttributes() {
+ if (this == NODES)
+ return Cytoscape.getNodeAttributes();
+ else if (this == EDGES)
+ return Cytoscape.getEdgeAttributes();
+ else if (this == NETWORK)
+ return Cytoscape.getNetworkAttributes();
+
+ return null;
+ }
+
+ public Iterable<String> getAssociatedIdentifiers() {
+ final Set<String> ids = new HashSet<String>();
+ if (this == NODES) {
+ final List<GraphObject> nodes = (List<GraphObject>)Cytoscape.getCyNodesList();
+ for (final GraphObject node : nodes)
+ ids.add(node.getIdentifier());
+ return ids;
+ }
+ else if (this == EDGES) {
+ final List<GraphObject> edges = (List<GraphObject>)Cytoscape.getCyEdgesList();
+ for (final GraphObject edge : edges)
+ ids.add(edge.getIdentifier());
+ return ids;
+ }
+ else if (this == NETWORK) {
+ final Set<CyNetwork> networks = Cytoscape.getNetworkSet();
+ for (final CyNetwork network : networks)
+ ids.add(network.getIdentifier());
+ return ids;
+ }
+
+ return null;
+ }
+}
diff --git a/coreplugins/browser/src/main/java/browser/DataTableModel.java b/coreplugins/browser/src/main/java/browser/DataTableModel.java
new file mode 100644
index 0000000..2a47b89
--- /dev/null
+++ b/coreplugins/browser/src/main/java/browser/DataTableModel.java
@@ -0,0 +1,655 @@
+/*
+ Copyright (c) 2006, 2007, 2010 The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package browser;
+
+
+import static browser.DataObjectType.NETWORK;
+import giny.model.GraphObject;
+import giny.view.EdgeView;
+import giny.view.NodeView;
+
+import java.awt.Color;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Properties;
+import java.util.Vector;
+
+import javax.swing.table.DefaultTableModel;
+
+import org.cytoscape.equations.Equation;
+
+import browser.ui.CyAttributeBrowserTable;
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import cytoscape.data.CyAttributes;
+import cytoscape.data.CyAttributesUtils;
+import cytoscape.view.CyNetworkView;
+import cytoscape.visual.GlobalAppearanceCalculator;
+
+
+/**
+ *
+ * Actual data manipulation is implemented here.<br>
+ *
+ * @author kono
+ * @author xmas
+ * @author ruschein
+ */
+public class DataTableModel extends DefaultTableModel implements SortTableModel {
+
+ private static final long serialVersionUID = -8721633060696752335L;
+
+ public static final String LS = System.getProperty("line.separator");
+ private static final Boolean DEFAULT_FLAG = false;
+
+ // Property for this browser. One for each panel.
+ private Properties props;
+
+ // Type of the object
+ private final DataObjectType objectType;
+
+ // Target CyAttributes
+ private final CyAttributes data;
+
+ // Currently selected data objects
+ private List<GraphObject> graphObjects;
+
+ // Ordered list of attribute names shown as column names.
+ private List<String> attributeNames;
+ private final GlobalAppearanceCalculator gac = Cytoscape.getVisualMappingManager()
+ .getVisualStyle()
+ .getGlobalAppearanceCalculator();
+
+ /*
+ * Selected nodes & edges color
+ */
+ private Color selectedNodeColor;
+ private Color selectedEdgeColor;
+
+ // will be used by internal selection.
+ private Map<String, Boolean> internalSelection = new HashMap<String, Boolean>();
+
+ /**
+ * Creates a new DataTableModel object.
+ *
+ * @param attributeNames DOCUMENT ME!
+ * @param type DOCUMENT ME!
+ */
+ public DataTableModel(final List<String> attributeNames, final DataObjectType type) {
+ this(null, attributeNames, type);
+ }
+
+ /**
+ * Creates a new DataTableModel object.
+ *
+ * @param graph_objects DOCUMENT ME!
+ * @param attributeNames DOCUMENT ME!
+ * @param type DOCUMENT ME!
+ */
+ public DataTableModel(final List<GraphObject> graph_objects, final List<String> attributeNames,
+ final DataObjectType type)
+ {
+ this.data = type.getAssociatedAttributes();
+ this.graphObjects = graph_objects;
+ this.attributeNames = attributeNames;
+ this.objectType = type;
+
+ props = new Properties();
+ props.setProperty("colorSwitch", "off");
+ setSelectedColor(CyAttributeBrowserTable.SELECTED_NODE);
+ setSelectedColor(CyAttributeBrowserTable.SELECTED_EDGE);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param type DOCUMENT ME!
+ */
+ public void setSelectedColor(final int type) {
+ switch (type) {
+ case CyAttributeBrowserTable.SELECTED_NODE:
+ selectedNodeColor = gac.getDefaultNodeSelectionColor();
+
+ break;
+
+ case CyAttributeBrowserTable.SELECTED_EDGE:
+ selectedEdgeColor = gac.getDefaultEdgeSelectionColor();
+
+ break;
+
+ default:
+ break;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param type DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Color getSelectedColor(final int type) {
+ final Color newColor;
+
+ switch (type) {
+ case CyAttributeBrowserTable.SELECTED_NODE:
+ newColor = gac.getDefaultNodeSelectionColor();
+ break;
+ case CyAttributeBrowserTable.SELECTED_EDGE:
+ newColor = gac.getDefaultEdgeSelectionColor();
+ break;
+ default:
+ newColor = null;
+ break;
+ }
+
+ return newColor;
+ }
+
+ protected void setColorSwitch(final boolean on) {
+ props.setProperty("colorSwitch", on ? "on" : "off");
+ }
+
+ protected boolean getColorSwitch() {
+ return props.getProperty("colorSwitch").equals("on");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param key DOCUMENT ME!
+ * @param flag DOCUMENT ME!
+ */
+ public void setSelectionArray(final String key, final boolean flag) {
+ internalSelection.put(key, new Boolean(flag));
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void resetSelectionFlags() {
+ if (this.objectType != NETWORK) {
+ for (GraphObject gObj : graphObjects) {
+ internalSelection.put(gObj.getIdentifier(), DEFAULT_FLAG);
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public List getObjects() {
+ return graphObjects;
+ }
+
+
+ public void setTableData(List cellData, List<String> attributes) {
+ if (attributes != null)
+ this.attributeNames = attributes;
+
+ if (cellData != null)
+ graphObjects = cellData;
+
+ if (objectType != NETWORK)
+ setTableData();
+ else
+ setNetworkTable();
+ }
+
+ protected void setNetworkTable() {
+ if (Cytoscape.getCurrentNetwork() == null) {
+ return;
+ }
+
+ final int att_length = attributeNames.size();
+
+ // Attribute names will be the row id, and num. of column is always
+ Object[][] data_vector = new Object[att_length][2];
+ Object[] column_names = new Object[2];
+
+ column_names[0] = "Network Attribute Name";
+ column_names[1] = "Value";
+
+ for (int i = 0; i < att_length; i++) {
+ final String attributeName = (String) attributeNames.get(i);
+ data_vector[i][0] = new ValidatedObjectAndEditString(attributeName);
+ data_vector[i][1] = getValidatedObjectAndEditString(data.getType(attributeName),
+ Cytoscape.getCurrentNetwork().getIdentifier(),
+ attributeName);
+ }
+
+ setDataVector(data_vector, column_names);
+ }
+
+ protected void setAllNetworkTable() {
+ int att_length = attributeNames.size() + 1;
+ int networkCount = Cytoscape.getNetworkSet().size();
+
+ Object[][] data_vector = new Object[networkCount][att_length];
+ Object[] column_names = new Object[att_length];
+ column_names[0] = AttributeBrowser.ID;
+
+ internalSelection = new HashMap();
+
+ Iterator it = Cytoscape.getNetworkSet().iterator();
+ int k = 0;
+
+ while (it.hasNext()) {
+ CyNetwork network = (CyNetwork) it.next();
+ String id = network.getIdentifier();
+
+ data_vector[k][0] = new ValidatedObjectAndEditString(id);
+ k++;
+ }
+
+ // Set actual data
+ for (int idx = 0; idx < attributeNames.size(); ++idx) {
+ int i = idx + 1;
+ column_names[i] = attributeNames.get(idx);
+
+ String attributeName = (String) attributeNames.get(idx);
+
+ byte type = data.getType(attributeName);
+ it = Cytoscape.getNetworkSet().iterator();
+
+ int j = 0;
+
+ while (it.hasNext()) {
+ CyNetwork network = (CyNetwork) it.next();
+ Object value = getValidatedObjectAndEditString(type, network.getIdentifier(), attributeName);
+
+ data_vector[j][i] = value;
+ j++;
+ }
+ }
+
+ setDataVector(data_vector, column_names);
+ }
+
+ /**
+ * Method to fill in table cells.
+ */
+ public void setTableData() {
+ if (graphObjects == null)
+ return;
+
+ internalSelection = new HashMap<String, Boolean>();
+
+ NodeView nv;
+ EdgeView edgeView;
+ final CyNetworkView netView = Cytoscape.getCurrentNetworkView();
+
+ if (Cytoscape.getCurrentNetworkView() != Cytoscape.getNullNetworkView()) {
+ for (GraphObject obj : graphObjects) {
+ internalSelection.put(obj.getIdentifier(), DEFAULT_FLAG);
+ }
+ }
+
+ // Selected attributes + ID
+ final int att_length = attributeNames.size();
+
+ // Number of selected objects.
+ final int go_length = graphObjects.size();
+
+ Object[][] data_vector;
+ Object[] column_names;
+
+ String attributeName;
+ byte type;
+
+ // ID only.
+ if (att_length == 0) {
+ data_vector = new Object[go_length][1];
+ column_names = new Object[1];
+ column_names[0] = AttributeBrowser.ID;
+
+ for (int j = 0; j < go_length; ++j)
+ data_vector[j][0] = new ValidatedObjectAndEditString(graphObjects.get(j).getIdentifier());
+
+ setDataVector(data_vector, column_names);
+ // Cytoscape.getDesktop().getSwingPropertyChangeSupport()
+ // .firePropertyChange(CyAttributeBrowserTable.RESTORE_COLUMN, null, null);
+ AttributeBrowser.getPropertyChangeSupport()
+ .firePropertyChange(AttributeBrowser.RESTORE_COLUMN, null,
+ objectType);
+
+ return;
+ } else if (attributeNames.contains(AttributeBrowser.ID) == false) {
+ data_vector = new Object[go_length][att_length + 1];
+ column_names = new Object[att_length + 1];
+
+ column_names[0] = AttributeBrowser.ID;
+
+ for (int j = 0; j < go_length; ++j)
+ data_vector[j][0] = new ValidatedObjectAndEditString(graphObjects.get(j).getIdentifier());
+
+ for (int i1 = 0; i1 < att_length; ++i1) {
+ column_names[i1 + 1] = attributeNames.get(i1);
+ attributeName = attributeNames.get(i1);
+ type = data.getType(attributeName);
+
+ for (int j = 0; j < go_length; ++j) {
+ data_vector[j][i1 + 1] = getValidatedObjectAndEditString(type,
+ graphObjects.get(j).getIdentifier(),
+ attributeName);
+ }
+ }
+ } else {
+ data_vector = new Object[go_length][att_length];
+ column_names = new Object[att_length];
+
+ for (int i1 = 0; i1 < att_length; ++i1) {
+ column_names[i1] = attributeNames.get(i1);
+ attributeName = (String) attributeNames.get(i1);
+ type = data.getType(attributeName);
+ for (int j = 0; j < go_length; ++j) {
+ if (attributeName.equals(AttributeBrowser.ID))
+ data_vector[j][i1] = new ValidatedObjectAndEditString(graphObjects.get(j).getIdentifier());
+ else
+ data_vector[j][i1] =
+ getValidatedObjectAndEditString(type, graphObjects.get(j).getIdentifier(),
+ attributeName);
+ }
+ }
+ }
+
+ setDataVector(data_vector, column_names);
+
+ AttributeBrowser.getPropertyChangeSupport()
+ .firePropertyChange(AttributeBrowser.RESTORE_COLUMN, null, objectType);
+ }
+
+ /**
+ * Returns a validated object and edit string which is a data structure used to display values or error messages in a
+ * browser cell.
+ *
+ * @param type the expected data type for the attribute
+ * @param id the key representing the particular node/edge/network
+ * @param attrName which attribute we're dealing with
+ *
+ * @return DOCUMENT ME!
+ */
+ public ValidatedObjectAndEditString getValidatedObjectAndEditString(final byte type, final String id, final String attrName) {
+ final Object attribValue = data.getAttribute(id, attrName);
+ final Equation equation = data.getEquation(id, attrName);
+ if (attribValue == null && equation == null)
+ return null;
+
+ final String equationFormula = equation == null ? null : equation.toString();
+ String errorMessage = data.getLastEquationError();
+ if (errorMessage != null)
+ errorMessage = "#ERROR(" + errorMessage + ")";
+
+ switch (type) {
+ case CyAttributes.TYPE_INTEGER:
+ case CyAttributes.TYPE_FLOATING:
+ case CyAttributes.TYPE_STRING:
+ case CyAttributes.TYPE_BOOLEAN:
+ case CyAttributes.TYPE_SIMPLE_LIST:
+ return new ValidatedObjectAndEditString(attribValue, equationFormula, errorMessage);
+ case CyAttributes.TYPE_SIMPLE_MAP:
+ return new ValidatedObjectAndEditString(attribValue);
+ default:
+ return null;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public List getGraphObjects() {
+ return graphObjects;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param colName DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Class getObjectTypeAt(String colName) {
+ return CyAttributesUtils.getClass(colName, data);
+ }
+
+ public byte getObjectTypeAt(int col) {
+ String columnName = getColumnName(col);
+ return data.getType(columnName);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param col DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isSortable(int col) {
+ return true;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param col DOCUMENT ME!
+ * @param ascending DOCUMENT ME!
+ */
+ public void sortColumn(int col, boolean ascending) {
+ Collections.sort(getDataVector(), new ColumnComparator(col, getObjectTypeAt(col), ascending));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param rowIndex DOCUMENT ME!
+ * @param colIndex DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isCellEditable(int rowIndex, int colIndex) {
+ if (!data.getUserEditable(getColumnName(colIndex)))
+ return false;
+
+ Class objectType = null;
+ Object selectedObj = this.getValueAt(rowIndex, colIndex);
+
+ if ((selectedObj == null) && (colIndex != 0)) {
+ return true;
+ } else if (selectedObj != null) {
+ objectType = this.getValueAt(rowIndex, colIndex).getClass();
+ }
+
+ if (objectType != null) {
+ if (colIndex == 0)
+ return false;
+ else
+ return true;
+ } else
+ return false;
+ }
+
+ /**
+ * Instead of using a listener, just overwrite this method to save time and
+ * write to the temp object
+ */
+ public void setValueAt(final Object newValue, int rowIdx, int colIdx) {
+ final int keyIndex = getKeyIndex();
+ if (keyIndex == -1)
+ return;
+
+ final DataEditAction edit = updateCell(keyIndex, rowIdx, colIdx, newValue);
+ if (edit != null)
+ cytoscape.util.undo.CyUndo.getUndoableEditSupport().postEdit(edit);
+ }
+
+ public CyAttributes getCyAttributes() { return data; }
+
+ /**
+ * Updates an entire column.
+ *
+ * @param newValue the new value to be set
+ * @param colIdx the index of the column that will be updated
+ * @param skipRowIdx a row with matching this index will not be updated
+ *
+ */
+ public void updateColumn(final Object newValue, final int colIdx, final int skipRowIdx) {
+ final int keyIndex = getKeyIndex();
+ if (keyIndex == -1)
+ return;
+
+ for (int rowIdx = 0; rowIdx < getRowCount(); ++rowIdx) {
+ if (rowIdx == skipRowIdx)
+ continue;
+
+ final DataEditAction edit = updateCell(keyIndex, rowIdx, colIdx, newValue);
+ if (edit != null)
+ cytoscape.util.undo.CyUndo.getUndoableEditSupport().postEdit(edit);
+ }
+ }
+
+ public String getRowId(final int rowIndex) {
+ final int keyIndex = getKeyIndex();
+ if (keyIndex == -1)
+ return null;
+
+ final ValidatedObjectAndEditString objectAndEditString = (ValidatedObjectAndEditString)getValueAt(rowIndex, keyIndex);
+ return (String)objectAndEditString.getValidatedObject();
+ }
+
+ private int getKeyIndex() {
+ int keyIndex = -1;
+ int columnOffset = 0;
+
+ if (attributeNames.contains(AttributeBrowser.ID) == false) {
+ // The ID is not in our attribute list, so it must be in the first column
+ // We will need to offset our index into the attribute names list to get
+ // the correct value. Note that this is only safe because AttributeBrowser.ID
+ // is not editable
+ keyIndex = 0;
+ columnOffset = 1;
+ } else {
+ for (int i = 0; i < columnIdentifiers.size(); i++) {
+ if (columnIdentifiers.get(i).equals(AttributeBrowser.ID)) {
+ keyIndex = i;
+ break;
+ }
+ }
+ }
+
+ return keyIndex;
+ }
+
+ private DataEditAction updateCell(final int keyIndex, final int rowIdx, final int colIdx, final Object newValue) {
+ final DataEditAction edit;
+ if (this.objectType != NETWORK) {
+ // This edit is for node or edge.
+ final ValidatedObjectAndEditString objectAndEditString = (ValidatedObjectAndEditString)getValueAt(rowIdx, keyIndex);
+ if (objectAndEditString == null)
+ return null;
+
+ final Object validatedObject = objectAndEditString.getValidatedObject();
+ if (validatedObject == null)
+ return null;
+
+ edit = new DataEditAction(this, validatedObject.toString(), getColumnName(colIdx),
+ getValueAt(rowIdx, colIdx), newValue, objectType);
+ } else {
+ final ValidatedObjectAndEditString objectAndEditString = (ValidatedObjectAndEditString)getValueAt(rowIdx, 0);
+ if (objectAndEditString == null)
+ return null;
+
+ final Object validatedObject = objectAndEditString.getValidatedObject();
+ if (validatedObject == null)
+ return null;
+
+ edit = new DataEditAction(this, Cytoscape.getCurrentNetwork().getIdentifier(),
+ validatedObject.toString(), getValueAt(rowIdx, colIdx),
+ newValue, objectType);
+ }
+
+ final boolean editIsValid = edit.isValid();
+
+ final Vector rowVector = (Vector) dataVector.elementAt(rowIdx);
+ rowVector.setElementAt(edit.getValidatedObjectAndEditString(), colIdx);
+ if (this.objectType != NETWORK)
+ setDataTableRow(rowIdx, colIdx);
+ else
+ setDataTableColumn();
+
+ return editIsValid ? edit : null;
+ }
+
+ /**
+ * Helper method for updateCell().
+ */
+ void setDataTableRow(final int rowIdx, final int skipIdx) {
+ final Vector rowVector = (Vector) dataVector.elementAt(rowIdx);
+ final int noOfColumns = attributeNames.contains(AttributeBrowser.ID) ? attributeNames.size() : attributeNames.size() + 1;
+ final String id = graphObjects.get(rowIdx).getIdentifier();
+ for (int colIdx = 0; colIdx < noOfColumns; ++colIdx) {
+ if (colIdx == skipIdx)
+ continue;
+
+ final String attribName = (String)columnIdentifiers.get(colIdx);
+ if (attribName.equals(AttributeBrowser.ID))
+ continue;
+
+ final byte type = data.getType(attribName);
+ final ValidatedObjectAndEditString objectAndEditString = getValidatedObjectAndEditString(type, id, attribName);
+ if (objectAndEditString != null) {
+ final int actualColIdx = findColumn(attribName);
+ rowVector.setElementAt(objectAndEditString, actualColIdx);
+ }
+ }
+ }
+
+ /**
+ * Helper method for updateCell().
+ */
+ void setDataTableColumn() {
+ final int noOfRows = attributeNames.size();
+ final String id = Cytoscape.getCurrentNetwork().getIdentifier();
+ for (int rowIdx = 1; rowIdx <= noOfRows; ++rowIdx) {
+ final String attribName = attributeNames.get(rowIdx - 1);
+ final byte type = data.getType(attribName);
+ final ValidatedObjectAndEditString objectAndEditString = getValidatedObjectAndEditString(type, id, attribName);
+ if (objectAndEditString != null) {
+ final Vector rowVector = (Vector) dataVector.elementAt(rowIdx - 1);
+ rowVector.setElementAt(objectAndEditString, 1 /* Always the 2nd column! */);
+ }
+ }
+ }
+}
diff --git a/coreplugins/browser/src/main/java/browser/MultiDataEditAction.java b/coreplugins/browser/src/main/java/browser/MultiDataEditAction.java
new file mode 100644
index 0000000..537e50c
--- /dev/null
+++ b/coreplugins/browser/src/main/java/browser/MultiDataEditAction.java
@@ -0,0 +1,584 @@
+/*
+ Copyright (c) 2006, 2007, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package browser;
+
+import browser.ui.ActionName;
+import browser.util.AttrUtil;
+import cytoscape.Cytoscape;
+
+import cytoscape.data.CyAttributes;
+
+import giny.model.GraphObject;
+
+import org.cytoscape.equations.Equation;
+import org.cytoscape.equations.EqnCompiler;
+
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+
+import javax.swing.JOptionPane;
+import javax.swing.undo.AbstractUndoableEdit;
+
+import static browser.ui.ActionName.*;
+
+
+/**
+ *
+ */
+public class MultiDataEditAction extends AbstractUndoableEdit {
+ final List<Object> objects;
+ final String attributeTo;
+ final String attributeFrom;
+ List<Object> old_values;
+ List<Object> new_values;
+ final String[] keys;
+ final DataObjectType graphObjectType;
+ final DataTableModel table;
+ final ActionName action;
+ final String input;
+ CyAttributes attrData;
+ byte attType;
+
+ /**
+ * Creates a new MultiDataEditAction object.
+ *
+ * @param input DOCUMENT ME!
+ * @param action DOCUMENT ME!
+ * @param objects DOCUMENT ME!
+ * @param attributeTo DOCUMENT ME!
+ * @param attributeFrom DOCUMENT ME!
+ * @param keys DOCUMENT ME!
+ * @param graphObjectType DOCUMENT ME!
+ * @param table DOCUMENT ME!
+ * @param dataType DOCUMENT ME!
+ */
+ public MultiDataEditAction(final String input, ActionName action, List<Object> objects, String attributeTo,
+ String attributeFrom, String[] keys, DataObjectType graphObjectType,
+ DataTableModel table)
+ {
+ if (input != null && input.length() > 0)
+ this.input = input.trim();
+ else
+ this.input = input;
+ this.action = action;
+ this.table = table;
+ this.objects = objects;
+ this.attributeTo = attributeTo;
+ this.attributeFrom = attributeFrom;
+ this.keys = keys;
+ this.graphObjectType = graphObjectType;
+
+ initEdit();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getPresentationName() {
+ return "Attribute " + attributeTo + " changed.";
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getRedoPresentationName() {
+ return "Redo: " + action;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getUndoPresentationName() {
+ return "Undo: " + action;
+ }
+
+ private void setAttributeValue(String id, String att, Object object) {
+ if (object instanceof Integer)
+ attrData.setAttribute(id, att, (Integer) object);
+ else if (object instanceof Double)
+ attrData.setAttribute(id, att, (Double) object);
+ else if (object instanceof Boolean)
+ attrData.setAttribute(id, att, (Boolean) object);
+ else if (object instanceof String)
+ attrData.setAttribute(id, att, (String) object);
+ else if (object instanceof List)
+ attrData.setListAttribute(id, att, (List) object);
+ else if (object instanceof Map)
+ attrData.setMapAttribute(id, att, (Map) object);
+ }
+
+
+ // put back the new_values
+ /**
+ * DOCUMENT ME!
+ */
+ public void redo() {
+ final int size = objects.size();
+ GraphObject go;
+ for (int i = 0; i < size; ++i) {
+ go = (GraphObject) objects.get(i);
+
+ if (new_values.get(i) == null) {
+ attrData.getMultiHashMap().removeAllAttributeValues(go.getIdentifier(), attributeTo);
+ } else {
+ setAttributeValue(go.getIdentifier(), attributeTo, new_values.get(i));
+ }
+ }
+ table.setTableData();
+ }
+
+
+ // put back the old_values
+ /**
+ * DOCUMENT ME!
+ */
+ public void undo() {
+ for (int i = 0; i < objects.size(); ++i) {
+ GraphObject go = (GraphObject) objects.get(i);
+
+ if (old_values.get(i) == null) {
+ attrData.getMultiHashMap().removeAllAttributeValues(go.getIdentifier(), attributeTo);
+ } else {
+ setAttributeValue(go.getIdentifier(), attributeTo, old_values.get(i));
+ }
+ }
+
+ table.setTableData();
+ }
+
+
+ public void initEdit() {
+ // get proper Global CytoscapeData object
+ attrData = graphObjectType.getAssociatedAttributes();
+
+ if (action == COPY) {
+ copyAtt();
+ } else if (action == CLEAR) {
+ deleteAtt();
+ } else {
+ attType = attrData.getType(attributeTo);
+ if (attType == CyAttributes.TYPE_UNDEFINED)
+ attType = CyAttributes.TYPE_STRING;
+
+ if (input.length() >= 2 && input.charAt(0) == '=') {
+ if (action != SET) {
+ showErrorWindow("Equations are only compatible with the SET operation!");
+ return;
+ }
+
+ final Map<String, Class> attribNameToTypeMap = AttrUtil.getAttrNamesAndTypes(attrData);
+
+ final EqnCompiler compiler = new EqnCompiler();
+ if (!compiler.compile(input, attribNameToTypeMap)) {
+ showErrorWindow("Error in equation in SET operation: "
+ + compiler.getLastErrorMsg());
+ return;
+ }
+
+ final Equation equation = compiler.getEquation();
+ final Class eqnType = equation.getType();
+ if (!eqnTypeIsCompatibleWithAttrType(eqnType, attType)) {
+ showErrorWindow("Equation of type \"" + eqnType
+ + "\" is incompatible with the target of the SET operation!");
+ return;
+ }
+
+ equationAction(equation);
+ }
+ else if (attType == CyAttributes.TYPE_FLOATING) {
+ Double d = new Double(input);
+ doubleAction(d.doubleValue());
+ } else if (attType == CyAttributes.TYPE_INTEGER) {
+ try {
+ Integer d = new Integer(input);
+ integerAction(d.intValue());
+ } catch (final Exception e) {
+ showErrorWindow("\"" + input + "\" is not a valid integer!");
+ }
+ } else if (attType == CyAttributes.TYPE_STRING) {
+ stringAction(input);
+ } else if (attType == CyAttributes.TYPE_BOOLEAN) {
+ booleanAction(Boolean.valueOf(input));
+ } else if (attType == CyAttributes.TYPE_SIMPLE_LIST) {
+ listAction();
+ } else if (attType == CyAttributes.TYPE_SIMPLE_MAP) {
+ // TODO: HANDLE
+ }
+ }
+
+ if (graphObjectType != DataObjectType.NETWORK) {
+ table.setTableData();
+ } else {
+ table.setNetworkTable();
+ }
+ } // initEdit
+
+ private static boolean eqnTypeIsCompatibleWithAttrType(final Class eqnType, final byte attType) {
+ if (eqnType == Integer.class || eqnType == Long.class) {
+ if (attType != CyAttributes.TYPE_INTEGER && attType != CyAttributes.TYPE_FLOATING
+ && attType != CyAttributes.TYPE_BOOLEAN && attType != CyAttributes.TYPE_STRING)
+ return false;
+ }
+ else if (eqnType == Double.class) {
+ if (attType != CyAttributes.TYPE_FLOATING && attType != CyAttributes.TYPE_BOOLEAN
+ && attType != CyAttributes.TYPE_STRING)
+ return false;
+ }
+ else if (eqnType == Boolean.class) {
+ if (attType != CyAttributes.TYPE_INTEGER && attType != CyAttributes.TYPE_FLOATING
+ && attType != CyAttributes.TYPE_BOOLEAN)
+ return false;
+ }
+ else if (eqnType == String.class) {
+ /* Everything can be turned into a String! */
+ }
+ else
+ throw new IllegalStateException("unhandled equation return type: " + eqnType + "!");
+
+ return true;
+ }
+
+ private void listAction() {
+ if ((action == DIV) || (action == MUL))
+ return;
+
+ old_values = new ArrayList(objects.size());
+ new_values = new ArrayList(objects.size());
+
+ for (final Object obj : objects) {
+ final GraphObject go = (GraphObject)obj;
+
+ // get the current value and set the old_value to it
+ final String s = (String)attrData.getAttribute(go.getIdentifier(), attributeTo);
+ old_values.add(s);
+
+ final String new_v;
+ if (action == SET)
+ new_v = input;
+ else if(action == ActionName.ADD_PREFIX) {
+ new_v = s+input;
+ } else if(action == ActionName.ADD_SUFFIX) {
+ new_v = input+s;
+ } else if(action == ActionName.REMOVE) {
+ new_v = s.replaceAll(input, "");
+ } else if(action == ActionName.REPLACE) {
+ new_v = s.replaceAll(input, "");
+ } else
+ new_v = s.concat(input);
+
+ new_values.add(new_v);
+ setAttributeValue(go.getIdentifier(), attributeTo, new_v);
+ } // iterator
+ }
+
+ /**
+ * Use the global edit variables to copy the attribute in attributeFrom to
+ * attributeTo the values that were copied will be saved to "new_values"
+ */
+ private void copyAtt() {
+ // Sanity check:
+ if (attributeFrom == null || attributeTo == null || attributeTo.equals("")) {
+ showErrorWindow("\"From\" attribute or \"To\" attribute has not been specified!");
+ return;
+ }
+
+ final byte fromType = attrData.getType(attributeFrom);
+ final byte toType = attrData.getType(attributeTo);
+ if (toType == CyAttributes.TYPE_UNDEFINED || !copyAttrsAreCompatible(fromType, toType)) {
+ showErrorWindow("Copy Failed: Incompatible data types.");
+
+ return;
+ }
+
+ new_values = new ArrayList(objects.size());
+ old_values = new ArrayList(objects.size());
+
+ for (final Object o : objects) {
+ final GraphObject go = (GraphObject)o;
+
+ final Equation equation = attrData.getEquation(go.getIdentifier(), attributeFrom);
+ if (equation != null) {
+ attrData.setAttribute(go.getIdentifier(), attributeTo, equation);
+ new_values.add(equation);
+ old_values.add(null);
+ continue;
+ }
+
+ Object value = attrData.getAttribute(go.getIdentifier(), attributeFrom);
+ new_values.add(value);
+
+ // Translate from Integer to Double?
+ if ((fromType == CyAttributes.TYPE_INTEGER) && (toType == CyAttributes.TYPE_FLOATING))
+ value = new Double((Integer)value);
+
+ setAttributeValue(go.getIdentifier(), attributeTo, value);
+ old_values.add(null);
+ }
+ }
+
+ private boolean copyAttrsAreCompatible(final byte fromType, final byte toType) {
+ if (fromType == toType)
+ return true;
+
+ return (fromType == CyAttributes.TYPE_INTEGER) && (toType == CyAttributes.TYPE_FLOATING);
+ }
+
+ /**
+ * Use the global edit variables to delete the values from the given
+ * attribute. the deleted values will be stored in "old_values"
+ */
+ private void deleteAtt() {
+ new_values = new ArrayList(objects.size());
+ old_values = new ArrayList(objects.size());
+
+ // Check data compatibility
+ for (final Object o : objects) {
+ final GraphObject go = (GraphObject)o;
+
+ final Object attr;
+ final Equation equation = attrData.getEquation(go.getIdentifier(), attributeTo);
+ if (equation != null)
+ attr = equation;
+ else
+ attr = attrData.getAttribute(go.getIdentifier(), attributeTo);
+
+ if (attr != null) {
+ old_values.add(attr);
+ attrData.getMultiHashMap().removeAllAttributeValues(go.getIdentifier(), attributeTo);
+ new_values.add(null);
+ }
+ }
+ }
+
+ // Pop-up window for error message
+ private static void showErrorWindow(final String errMessage) {
+ JOptionPane.showMessageDialog(null, errMessage, "Error!", JOptionPane.ERROR_MESSAGE);
+ }
+
+ /**
+ * save the old and new values, subsequent redo/undo will only use these
+ * values.
+ */
+ private void doubleAction(double input) {
+ // Sanity check:
+ if (action == DIV && input == 0.0) {
+ showErrorWindow("Division by zero is invalid!");
+ return;
+ }
+
+ old_values = new ArrayList(objects.size());
+ new_values = new ArrayList(objects.size());
+
+ for (final Object o : objects) {
+ final GraphObject go = (GraphObject)o;
+
+ if (action == SET) {
+ // Get the current value and set the old_value to it
+ final Equation oldEquation = attrData.getEquation(go.getIdentifier(), attributeTo);
+ if (oldEquation != null)
+ old_values.add(oldEquation);
+ else
+ old_values.add(attrData.getAttribute(go.getIdentifier(), attributeTo));
+ setAttributeValue(go.getIdentifier(), attributeTo, input);
+ new_values.add(input);
+ } else {
+ // get the current value and set the old_value to it
+ final Double d = (Double) attrData.getAttribute(go.getIdentifier(), attributeTo);
+ old_values.add(d);
+
+ double new_v;
+
+ if (action == ADD)
+ new_v = input + d;
+ else if (action == MUL)
+ new_v = input * d;
+ else if (action == DIV)
+ new_v = d / input;
+ else
+ new_v = input;
+
+ new_values.add(new Double(new_v));
+ setAttributeValue(go.getIdentifier(), attributeTo, new Double(new_v));
+ }
+ } // iterator
+ } // doubleAction
+
+ /**
+ * save the old and new values, subsequent redo/undo will only use these
+ * values.
+ */
+ private void integerAction(final int input) {
+ // Sanity check:
+ if (action == DIV && input == 0) {
+ showErrorWindow("Division by zero is invalid!");
+ return;
+ }
+
+ old_values = new ArrayList(objects.size());
+ new_values = new ArrayList(objects.size());
+
+ for (final Object o : objects) {
+ final GraphObject go = (GraphObject)o;
+
+ if (action == SET) {
+ // Get the current value and set the old_value to it
+ final Equation oldEquation = attrData.getEquation(go.getIdentifier(), attributeTo);
+ if (oldEquation != null)
+ old_values.add(oldEquation);
+ else
+ old_values.add(attrData.getAttribute(go.getIdentifier(), attributeTo));
+ setAttributeValue(go.getIdentifier(), attributeTo, input);
+ new_values.add(input);
+ } else {
+ // get the current value and set the old_value to it
+ final Integer i = (Integer)attrData.getAttribute(go.getIdentifier(), attributeTo);
+ old_values.add(i);
+
+ int new_v;
+ if (action == ADD)
+ new_v = input + i;
+ else if (action == MUL)
+ new_v = input * i;
+ else if (action == DIV)
+ new_v = i / input;
+ else
+ new_v = input;
+
+ new_values.add(new Integer(new_v));
+ setAttributeValue(go.getIdentifier(), attributeTo, new Integer(new_v));
+ }
+ } // iterator
+ } // integerAction
+
+ /**
+ * save the old and new values, subsequent redo/undo will only use these
+ * values.
+ */
+ private void stringAction(final String input) {
+ // return if number only action
+ if ((action == DIV) || (action == MUL))
+ return;
+
+ old_values = new ArrayList(objects.size());
+ new_values = new ArrayList(objects.size());
+
+ for (final Object obj : objects) {
+ final GraphObject go = (GraphObject) obj;
+
+ // get the current value and set the old_value to it
+ final String s = (String) attrData.getAttribute(go.getIdentifier(), attributeTo);
+ old_values.add(s);
+
+ if (s == null && action != SET)
+ continue;
+
+ if (action == SET) {
+ // Get the current value and set the old_value to it
+ final Equation oldEquation = attrData.getEquation(go.getIdentifier(), attributeTo);
+ if (oldEquation != null)
+ old_values.add(oldEquation);
+ else
+ old_values.add(attrData.getAttribute(go.getIdentifier(), attributeTo));
+ setAttributeValue(go.getIdentifier(), attributeTo, input);
+ new_values.add(input);
+ } else {
+ String new_v;
+ if (action == ActionName.ADD_PREFIX) {
+ new_v = input + s;
+ } else if (action == ActionName.ADD_SUFFIX) {
+ new_v = s + input;
+ } else if (action == ActionName.REMOVE) {
+ new_v = s.replaceAll(input, "");
+ } else if (action == ActionName.REPLACE) {
+ final String[] vals = input.split("\t");
+ if (vals.length == 2)
+ new_v = s.replaceAll(vals[0], vals[1]);
+ else
+ new_v = s.concat(input);
+
+ } else if (action == ActionName.TO_LOWER) {
+ new_v = s.toLowerCase();
+ } else if (action == ActionName.TO_UPPER) {
+ new_v = s.toUpperCase();
+ } else
+ new_v = s.concat(input);
+
+ new_values.add(new_v);
+ setAttributeValue(go.getIdentifier(), attributeTo, new_v);
+ }
+ } // iterator
+ } // stringAction
+
+ private void booleanAction(final Boolean input) {
+ if ((action == DIV) || (action == MUL) || (action == ADD))
+ return;
+
+ old_values = new ArrayList(objects.size());
+ new_values = new ArrayList(objects.size());
+
+ for (final Object o : objects) {
+ GraphObject go = (GraphObject)o;
+
+ // Get the current value and set the old_value to it
+ final Equation oldEquation = attrData.getEquation(go.getIdentifier(), attributeTo);
+ if (oldEquation != null)
+ old_values.add(oldEquation);
+ else
+ old_values.add(attrData.getAttribute(go.getIdentifier(), attributeTo));
+ setAttributeValue(go.getIdentifier(), attributeTo, input);
+ new_values.add(input);
+ } // iterator
+ } // booleanAction
+
+ private void equationAction(final Equation input) {
+ old_values = new ArrayList(objects.size());
+ new_values = new ArrayList(objects.size());
+
+ for (final Object o : objects) {
+ final GraphObject go = (GraphObject)o;
+
+ // Get the current value and set the old_value to it
+ final Equation oldEquation = attrData.getEquation(go.getIdentifier(), attributeTo);
+ if (oldEquation != null)
+ old_values.add(oldEquation);
+ else
+ old_values.add(attrData.getAttribute(go.getIdentifier(), attributeTo));
+ attrData.setAttribute(go.getIdentifier(), attributeTo, input);
+ new_values.add(input);
+ } // iterator
+ } // equationAction
+}
diff --git a/coreplugins/browser/src/main/java/browser/SortTableModel.java b/coreplugins/browser/src/main/java/browser/SortTableModel.java
new file mode 100644
index 0000000..807c6cd
--- /dev/null
+++ b/coreplugins/browser/src/main/java/browser/SortTableModel.java
@@ -0,0 +1,49 @@
+/*
+ * $Archive: SourceJammer$
+ * $FileName: SortTableModel.java$
+ * $FileID: 3983$
+ *
+ * Last change:
+ * $AuthorName: Timo Haberkern$
+ * $Date: 2007-12-08 03:57:44 +0100 (Sat, 08 Dec 2007) $
+ * $Comment: $
+ *
+ * $KeyWordsOff: $
+ */
+
+/*
+=====================================================================
+
+ SortTableModel.java
+
+ Created by Claude Duguay
+ Copyright (c) 2002
+
+=====================================================================
+*/
+package browser;
+
+import javax.swing.table.TableModel;
+
+
+/**
+ *
+ */
+public interface SortTableModel extends TableModel {
+ /**
+ * DOCUMENT ME!
+ *
+ * @param col DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isSortable(int col);
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param col DOCUMENT ME!
+ * @param ascending DOCUMENT ME!
+ */
+ public void sortColumn(int col, boolean ascending);
+}
diff --git a/coreplugins/browser/src/main/java/browser/ValidatedObjectAndEditString.java b/coreplugins/browser/src/main/java/browser/ValidatedObjectAndEditString.java
new file mode 100644
index 0000000..af26601
--- /dev/null
+++ b/coreplugins/browser/src/main/java/browser/ValidatedObjectAndEditString.java
@@ -0,0 +1,68 @@
+/*
+ Copyright (c) 2010 The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package browser;
+
+
+public class ValidatedObjectAndEditString {
+ private final Object validatedObject;
+ private final String editString;
+ private String errorText;
+
+ public ValidatedObjectAndEditString(final Object validatedObject, final String editString,
+ final String errorText)
+ {
+ this.validatedObject = validatedObject;
+ this.editString = editString;
+ this.errorText = errorText;
+ }
+
+ public ValidatedObjectAndEditString(final Object validatedObject, final String editString) {
+ this(validatedObject, editString, null);
+ }
+
+ public ValidatedObjectAndEditString(final Object validatedObject) {
+ this(validatedObject, null);
+ }
+
+ public Object getValidatedObject() { return validatedObject; }
+ public String getEditString() {
+ if (editString != null)
+ return editString;
+ if (validatedObject != null)
+ return validatedObject.toString();
+ return "";
+ }
+
+ public void setErrorText(final String newErrorText) { errorText = newErrorText; }
+ public String getErrorText() { return errorText; }
+
+ @Override public String toString() {
+ return "ValidatedObjectAndEditString: validatedObject=" + validatedObject
+ + ", editString=" + editString;
+ }
+}
diff --git a/coreplugins/browser/src/main/java/browser/ui/ActionName.java b/coreplugins/browser/src/main/java/browser/ui/ActionName.java
new file mode 100644
index 0000000..ad4c9a9
--- /dev/null
+++ b/coreplugins/browser/src/main/java/browser/ui/ActionName.java
@@ -0,0 +1,52 @@
+/**
+ *
+ */
+package browser.ui;
+
+public enum ActionName {
+ SET("Set"),
+ REPLACE("Replace"),
+ REMOVE("Remove"),
+ TO_UPPER("To upper-case"),
+ TO_LOWER("To lower-case"),
+ ADD_PREFIX("Add Prefix"),
+ ADD_SUFFIX("Add Suffix"),
+
+ ADD("Add Number"),
+ MUL("Mul"),
+ DIV("Div"),
+ COPY("Copy"),
+ CLEAR("Clear");
+
+ String dispName;
+
+ private ActionName(String dispName) {
+ this.dispName = dispName;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getDisplayName() {
+ return dispName;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param dispName DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static ActionName getValueOf(final String dispName) {
+ for (ActionName action : values()) {
+ if (action.dispName.equals(dispName)) {
+ return action;
+ }
+ }
+
+ return null;
+ }
+}
diff --git a/coreplugins/browser/src/main/java/browser/ui/AttributeBrowserToolBar.java b/coreplugins/browser/src/main/java/browser/ui/AttributeBrowserToolBar.java
new file mode 100644
index 0000000..a15a17e
--- /dev/null
+++ b/coreplugins/browser/src/main/java/browser/ui/AttributeBrowserToolBar.java
@@ -0,0 +1,1068 @@
+/*
+ Copyright (c) 2006, 2007, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package browser.ui;
+
+
+import static browser.DataObjectType.EDGES;
+import static browser.DataObjectType.NETWORK;
+import static browser.DataObjectType.NODES;
+
+import java.awt.BorderLayout;
+import java.awt.Dimension;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import javax.swing.ImageIcon;
+import javax.swing.JButton;
+import javax.swing.JList;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JPopupMenu;
+import javax.swing.JScrollPane;
+import javax.swing.JTable;
+import javax.swing.JToolBar;
+import javax.swing.ListSelectionModel;
+import javax.swing.SwingUtilities;
+import javax.swing.event.PopupMenuEvent;
+import javax.swing.event.PopupMenuListener;
+
+import org.jdesktop.layout.GroupLayout;
+import org.jdesktop.layout.LayoutStyle;
+
+import browser.AttributeBrowser;
+import browser.AttributeModel;
+import browser.DataObjectType;
+import browser.DataTableModel;
+import browser.ValidatedObjectAndEditString;
+import cytoscape.Cytoscape;
+import cytoscape.actions.ImportEdgeAttributesAction;
+import cytoscape.actions.ImportExpressionMatrixAction;
+import cytoscape.actions.ImportNodeAttributesAction;
+import cytoscape.data.CyAttributes;
+import cytoscape.data.CyAttributesUtils;
+import cytoscape.dialogs.NetworkMetaDataDialog;
+import cytoscape.logger.CyLogger;
+import cytoscape.util.swing.CheckBoxJList;
+
+
+/**
+ * Define toolbar for Attribute Browser.
+ */
+public class AttributeBrowserToolBar extends JPanel implements PopupMenuListener, PropertyChangeListener {
+ private static final long serialVersionUID = -508393701912596399L;
+
+ private final CyAttributes attributes;
+ private DataTableModel tableModel;
+ private final JTable table;
+ private final DataObjectType objectType;
+ private AttributeModel attrModel;
+ private String attributeType = null;
+ private CyLogger logger = null;
+ private List<String> orderedCol;
+
+ /**
+ * GUI components
+ */
+ private JPopupMenu attributeSelectionPopupMenu = null;
+ private JScrollPane jScrollPane = null;
+ private JPopupMenu jPopupMenu1 = null;
+
+ private JMenuItem jMenuItemStringAttribute = null;
+ private JMenuItem jMenuItemIntegerAttribute = null;
+ private JMenuItem jMenuItemFloatingPointAttribute = null;
+ private JMenuItem jMenuItemBooleanAttribute = null;
+
+ private JMenuItem jMenuItemStringListAttribute = null;
+ private JMenuItem jMenuItemIntegerListAttribute = null;
+ private JMenuItem jMenuItemFloatingPointListAttribute = null;
+ private JMenuItem jMenuItemBooleanListAttribute = null;
+
+ private JToolBar browserToolBar = null;
+ private JButton selectButton = null;
+ private CheckBoxJList attributeList = null;
+ private JList attrDeletionList = null;
+ private JButton createNewAttributeButton = null;
+ private JButton deleteAttributeButton = null;
+ private JButton selectAllAttributesButton = null;
+ private JButton unselectAllAttributesButton = null;
+ private JButton matrixButton = null;
+ private JButton importButton = null;
+
+ private ModDialog modDialog;
+ private FormulaBuilderDialog formulaBuilderDialog;
+
+
+ public AttributeBrowserToolBar(final DataTableModel tableModel, final CyAttributeBrowserTable table,
+ final AttributeModel a_model, final List<String> orderedCol,
+ final DataObjectType graphObjectType)
+ {
+ super();
+
+ this.tableModel = tableModel;
+ this.table = table;
+ this.attributes = graphObjectType.getAssociatedAttributes();
+ this.objectType = graphObjectType;
+ this.attrModel = a_model;
+ this.orderedCol = orderedCol;
+
+ logger = CyLogger.getLogger(AttributeBrowserToolBar.class);
+
+ initializeGUI();
+
+ Cytoscape.getPropertyChangeSupport().addPropertyChangeListener(Cytoscape.NEW_ATTRS_LOADED, this);
+ }
+
+ private void initializeGUI() {
+ this.setLayout(new BorderLayout());
+
+ this.setPreferredSize(new Dimension(210, 32));
+ this.add(getJToolBar(), java.awt.BorderLayout.CENTER);
+
+ getAttributeSelectionPopupMenu();
+ getJPopupMenu1();
+
+ modDialog = new ModDialog(tableModel, objectType, Cytoscape.getDesktop());
+ attrModButton.setVisible(objectType != NETWORK);
+ }
+
+ public void propertyChange(PropertyChangeEvent e) {
+ // This will handle the case for the change of attribute userVisibility
+ if (e.getPropertyName() == Cytoscape.NEW_ATTRS_LOADED && e.getOldValue() == attributes) {
+ final Set<String> newAttrNames = (Set<String>)e.getNewValue();
+ final int MAX_DISPLAY_COUNT = 10;
+ int displayCount = 0;
+ for (final String newAttrName : newAttrNames) {
+ orderedCol.add(newAttrName);
+ if (++displayCount > MAX_DISPLAY_COUNT)
+ break;
+ }
+ tableModel.setTableData(null, orderedCol);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getToBeDeletedAttribute() {
+ return attrDeletionList.getSelectedValue().toString();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param tableModel DOCUMENT ME!
+ */
+ public void setTableModel(DataTableModel tableModel) {
+ this.tableModel = tableModel;
+ }
+
+ /**
+ * This method initializes jPopupMenu
+ *
+ * @return javax.swing.JPopupMenu
+ */
+ private JPopupMenu getAttributeSelectionPopupMenu() {
+ if (attributeSelectionPopupMenu == null) {
+ attributeSelectionPopupMenu = new JPopupMenu();
+ attributeSelectionPopupMenu.add(getJScrollPane());
+ attributeSelectionPopupMenu.addPopupMenuListener(this);
+ }
+
+ return attributeSelectionPopupMenu;
+ }
+
+ /**
+ * This method initializes jScrollPane
+ *
+ * @return javax.swing.JScrollPane
+ */
+ private JScrollPane getJScrollPane() {
+ if (jScrollPane == null) {
+ jScrollPane = new JScrollPane();
+ jScrollPane.setPreferredSize(new Dimension(600, 300));
+ jScrollPane.setViewportView(getSelectedAttributeList());
+ }
+
+ return jScrollPane;
+ }
+
+ /**
+ * This method initializes jPopupMenu1
+ *
+ * @return javax.swing.JPopupMenu
+ */
+ private JPopupMenu getJPopupMenu1() {
+ if (jPopupMenu1 == null) {
+ jPopupMenu1 = new JPopupMenu();
+ jPopupMenu1.add(getJMenuItemIntegerAttribute());
+ jPopupMenu1.add(getJMenuItemStringAttribute());
+ jPopupMenu1.add(getJMenuItemFloatingPointAttribute());
+ jPopupMenu1.add(getJMenuItemBooleanAttribute());
+ jPopupMenu1.add(getJMenuItemIntegerListAttribute());
+ jPopupMenu1.add(getJMenuItemStringListAttribute());
+ jPopupMenu1.add(getJMenuItemFloatingPointListAttribute());
+ jPopupMenu1.add(getJMenuItemBooleanListAttribute());
+ }
+
+ return jPopupMenu1;
+ }
+
+ /**
+ * This method initializes jMenuItemStringAttribute
+ *
+ * @return javax.swing.JMenuItem
+ */
+ private JMenuItem getJMenuItemStringAttribute() {
+ if (jMenuItemStringAttribute == null) {
+ jMenuItemStringAttribute = new JMenuItem();
+ jMenuItemStringAttribute.setText("String Attribute");
+ jMenuItemStringAttribute.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent e) {
+ createNewAttribute("String");
+ }
+ });
+ }
+
+ return jMenuItemStringAttribute;
+ }
+
+ /**
+ * This method initializes jMenuItemIntegerAttribute
+ *
+ * @return javax.swing.JMenuItem
+ */
+ private JMenuItem getJMenuItemIntegerAttribute() {
+ if (jMenuItemIntegerAttribute == null) {
+ jMenuItemIntegerAttribute = new JMenuItem();
+ jMenuItemIntegerAttribute.setText("Integer Attribute");
+ jMenuItemIntegerAttribute.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent e) {
+ createNewAttribute("Integer");
+ }
+ });
+ }
+
+ return jMenuItemIntegerAttribute;
+ }
+
+ /**
+ * This method initializes jMenuItemFloatingPointAttribute
+ *
+ * @return javax.swing.JMenuItem
+ */
+ private JMenuItem getJMenuItemFloatingPointAttribute() {
+ if (jMenuItemFloatingPointAttribute == null) {
+ jMenuItemFloatingPointAttribute = new JMenuItem();
+ jMenuItemFloatingPointAttribute.setText("Floating Point Attribute");
+ jMenuItemFloatingPointAttribute.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent e) {
+ createNewAttribute("Floating Point");
+ }
+ });
+ }
+
+ return jMenuItemFloatingPointAttribute;
+ }
+
+ /**
+ * This method initializes jMenuItemBooleanAttribute
+ *
+ * @return javax.swing.JMenuItem
+ */
+ private JMenuItem getJMenuItemBooleanAttribute() {
+ if (jMenuItemBooleanAttribute == null) {
+ jMenuItemBooleanAttribute = new JMenuItem();
+ jMenuItemBooleanAttribute.setText("Boolean Attribute");
+ jMenuItemBooleanAttribute.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent e) {
+ createNewAttribute("Boolean");
+ }
+ });
+ }
+
+ return jMenuItemBooleanAttribute;
+ }
+
+ /**
+ * This method initializes jMenuItemStringListAttribute
+ *
+ * @return javax.swing.JMenuItem
+ */
+ private JMenuItem getJMenuItemStringListAttribute() {
+ if (jMenuItemStringListAttribute == null) {
+ jMenuItemStringListAttribute = new JMenuItem();
+ jMenuItemStringListAttribute.setText("String List Attribute");
+ jMenuItemStringListAttribute.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent e) {
+ createNewAttribute("String List");
+ }
+ });
+ }
+
+ return jMenuItemStringListAttribute;
+ }
+
+ /**
+ * This method initializes jMenuItemIntegerListAttribute
+ *
+ * @return javax.swing.JMenuItem
+ */
+ private JMenuItem getJMenuItemIntegerListAttribute() {
+ if (jMenuItemIntegerListAttribute == null) {
+ jMenuItemIntegerListAttribute = new JMenuItem();
+ jMenuItemIntegerListAttribute.setText("Integer List Attribute");
+ jMenuItemIntegerListAttribute.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent e) {
+ createNewAttribute("Integer List");
+ }
+ });
+ }
+
+ return jMenuItemIntegerListAttribute;
+ }
+
+ /**
+ * This method initializes jMenuItemFloatingPointListAttribute
+ *
+ * @return javax.swing.JMenuItem
+ */
+ private JMenuItem getJMenuItemFloatingPointListAttribute() {
+ if (jMenuItemFloatingPointListAttribute == null) {
+ jMenuItemFloatingPointListAttribute = new JMenuItem();
+ jMenuItemFloatingPointListAttribute.setText("Floating Point List Attribute");
+ jMenuItemFloatingPointListAttribute.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent e) {
+ createNewAttribute("Floating Point List");
+ }
+ });
+ }
+
+ return jMenuItemFloatingPointListAttribute;
+ }
+
+ /**
+ * This method initializes jMenuItemBooleanListAttribute
+ *
+ * @return javax.swing.JMenuItem
+ */
+ private JMenuItem getJMenuItemBooleanListAttribute() {
+ if (jMenuItemBooleanListAttribute == null) {
+ jMenuItemBooleanListAttribute = new JMenuItem();
+ jMenuItemBooleanListAttribute.setText("Boolean List Attribute");
+ jMenuItemBooleanListAttribute.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent e) {
+ createNewAttribute("Boolean List");
+ }
+ });
+ }
+
+ return jMenuItemBooleanListAttribute;
+ }
+
+ /**
+ * This method initializes jToolBar
+ *
+ * @return javax.swing.JToolBar
+ */
+ private JToolBar getJToolBar() {
+ if (browserToolBar == null) {
+ browserToolBar = new JToolBar();
+ browserToolBar.addMouseListener(new MouseAdapter() {
+ public void mouseClicked(MouseEvent e) {
+ AttributeBrowser.getPropertyChangeSupport().firePropertyChange(AttributeBrowser.CLEAR_INTERNAL_SELECTION, null, objectType);
+ }
+ });
+ browserToolBar.setMargin(new java.awt.Insets(0, 0, 3, 0));
+ browserToolBar.setPreferredSize(new Dimension(200, 30));
+ browserToolBar.setFloatable(false);
+ browserToolBar.setOrientation(JToolBar.HORIZONTAL);
+
+ final GroupLayout buttonBarLayout = new GroupLayout(browserToolBar);
+ browserToolBar.setLayout(buttonBarLayout);
+
+ // Layout information.
+ if (objectType == NODES) {
+ buttonBarLayout.setHorizontalGroup(buttonBarLayout.createParallelGroup(GroupLayout.LEADING)
+ .add(buttonBarLayout.createSequentialGroup()
+ .addPreferredGap(LayoutStyle.RELATED)
+ .add(getSelectButton(),
+ GroupLayout.PREFERRED_SIZE,
+ GroupLayout.DEFAULT_SIZE,
+ GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(LayoutStyle.RELATED)
+ .add(getNewButton())
+ .addPreferredGap(LayoutStyle.RELATED)
+ .add(getSelectAllButton())
+ .addPreferredGap(LayoutStyle.RELATED)
+ .add(getUnselectAllButton())
+ .addPreferredGap(LayoutStyle.RELATED)
+ .add(getDeleteButton())
+ .addPreferredGap(LayoutStyle.RELATED,
+ 28,
+ Short.MAX_VALUE)
+ .add(getAttrModButton(),
+ GroupLayout.PREFERRED_SIZE,
+ 28,
+ GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(LayoutStyle.RELATED)
+ .add(getFunctionBuilderButton(),
+ GroupLayout.PREFERRED_SIZE,
+ 28,
+ GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(LayoutStyle.RELATED)
+ .add(getImportButton(),
+ GroupLayout.PREFERRED_SIZE,
+ 28,
+ GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(LayoutStyle.RELATED)
+ .add(getMatrixButton())
+ .addPreferredGap(LayoutStyle.RELATED)));
+ buttonBarLayout.setVerticalGroup(buttonBarLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(org.jdesktop.layout.GroupLayout.CENTER,
+ selectButton,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ 27,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .add(org.jdesktop.layout.GroupLayout.CENTER,
+ createNewAttributeButton,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 27, Short.MAX_VALUE)
+ .add(org.jdesktop.layout.GroupLayout.CENTER,
+ selectAllAttributesButton,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 27, Short.MAX_VALUE)
+ .add(org.jdesktop.layout.GroupLayout.CENTER,
+ unselectAllAttributesButton,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 27, Short.MAX_VALUE)
+ .add(org.jdesktop.layout.GroupLayout.CENTER,
+ deleteAttributeButton,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 27, Short.MAX_VALUE)
+ .add(buttonBarLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.CENTER)
+ .add(matrixButton,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ 27,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .add(importButton,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ 27,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .add(attrModButton,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ 27,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .add(formulaBuilderButton,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ 27,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)));
+ } else if (objectType == NETWORK) {
+ buttonBarLayout.setHorizontalGroup(buttonBarLayout.createParallelGroup(GroupLayout.LEADING)
+ .add(buttonBarLayout.createSequentialGroup()
+ .add(getSelectButton(),
+ GroupLayout.PREFERRED_SIZE,
+ GroupLayout.DEFAULT_SIZE,
+ GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(LayoutStyle.RELATED)
+ .add(getNewButton())
+ .addPreferredGap(LayoutStyle.RELATED)
+ .add(getSelectAllButton())
+ .addPreferredGap(LayoutStyle.RELATED)
+ .add(getUnselectAllButton())
+ .addPreferredGap(LayoutStyle.RELATED)
+ .add(getDeleteButton())
+ .addPreferredGap(LayoutStyle.RELATED,
+ 320,
+ Short.MAX_VALUE)
+ .addPreferredGap(LayoutStyle.RELATED)
+ .add(getAttrModButton(),
+ GroupLayout.PREFERRED_SIZE,
+ 28,
+ GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(LayoutStyle.RELATED)
+ .add(getFunctionBuilderButton(),
+ GroupLayout.PREFERRED_SIZE,
+ 28,
+ GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(LayoutStyle.RELATED)));
+
+ buttonBarLayout.setVerticalGroup(buttonBarLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(org.jdesktop.layout.GroupLayout.CENTER,
+ selectButton,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ 27,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .add(org.jdesktop.layout.GroupLayout.CENTER,
+ createNewAttributeButton,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 27, Short.MAX_VALUE)
+ .add(org.jdesktop.layout.GroupLayout.CENTER,
+ selectAllAttributesButton,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 27, Short.MAX_VALUE)
+ .add(org.jdesktop.layout.GroupLayout.CENTER,
+ unselectAllAttributesButton,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 27, Short.MAX_VALUE)
+ .add(org.jdesktop.layout.GroupLayout.CENTER,
+ deleteAttributeButton,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 27, Short.MAX_VALUE)
+ .add(buttonBarLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.CENTER)
+ .add(attrModButton,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ 27,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .add(formulaBuilderButton,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ 27,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)));
+ } else {
+ buttonBarLayout.setHorizontalGroup(buttonBarLayout.createParallelGroup(GroupLayout.LEADING)
+ .add(buttonBarLayout.createSequentialGroup()
+ .addPreferredGap(LayoutStyle.RELATED)
+ .add(getSelectButton(),
+ GroupLayout.PREFERRED_SIZE,
+ GroupLayout.DEFAULT_SIZE,
+ GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(LayoutStyle.RELATED)
+ .add(getNewButton())
+ .addPreferredGap(LayoutStyle.RELATED)
+ .add(getSelectAllButton())
+ .addPreferredGap(LayoutStyle.RELATED)
+ .add(getUnselectAllButton())
+ .addPreferredGap(LayoutStyle.RELATED)
+ .add(getDeleteButton())
+ .addPreferredGap(LayoutStyle.RELATED,
+ 150,
+ Short.MAX_VALUE)
+ .add(getAttrModButton(),
+ GroupLayout.PREFERRED_SIZE,
+ 28,
+ GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(LayoutStyle.RELATED)
+ .add(getFunctionBuilderButton(),
+ GroupLayout.PREFERRED_SIZE,
+ 28,
+ GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(LayoutStyle.RELATED)
+ .add(getImportButton(),
+ GroupLayout.PREFERRED_SIZE,
+ 28,
+ GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(LayoutStyle.RELATED)));
+ buttonBarLayout.setVerticalGroup(buttonBarLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(org.jdesktop.layout.GroupLayout.CENTER,
+ selectButton,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ 27,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .add(org.jdesktop.layout.GroupLayout.CENTER,
+ createNewAttributeButton,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 27, Short.MAX_VALUE)
+ .add(org.jdesktop.layout.GroupLayout.CENTER,
+ selectAllAttributesButton,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 27, Short.MAX_VALUE)
+ .add(org.jdesktop.layout.GroupLayout.CENTER,
+ unselectAllAttributesButton,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 27, Short.MAX_VALUE)
+ .add(org.jdesktop.layout.GroupLayout.CENTER,
+ deleteAttributeButton,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 27, Short.MAX_VALUE)
+ .add(buttonBarLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.CENTER)
+ .add(importButton,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ 27,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .add(formulaBuilderButton,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ 27,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+ .add(attrModButton,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+ 27,
+ org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)));
+ }
+ }
+
+ return browserToolBar;
+ }
+
+ /**
+ * This method initializes jButton
+ *
+ * @return javax.swing.JButton
+ */
+ private JButton getSelectButton() {
+ if (selectButton == null) {
+ selectButton = new JButton();
+ selectButton.setBorder(null);
+ selectButton.setMargin(new java.awt.Insets(0, 0, 0, 0));
+ selectButton.setIcon(new ImageIcon(AttributeBrowser.class.getResource("images/stock_select-row.png")));
+ selectButton.setToolTipText("Select Attributes");
+
+ selectButton.addMouseListener(new MouseAdapter() {
+ public void mouseClicked(java.awt.event.MouseEvent e) {
+ attributeList.setSelectedItems(orderedCol);
+ attributeSelectionPopupMenu.show(e.getComponent(), e.getX(), e.getY());
+ }
+ });
+ }
+
+ return selectButton;
+ }
+
+ private JButton getImportButton() {
+ if (importButton == null) {
+ importButton = new JButton();
+ importButton.setBorder(null);
+ importButton.setIcon(new ImageIcon(AttributeBrowser.class.getResource("images/stock_open.png")));
+ importButton.setToolTipText("Import attributes from file...");
+ importButton.setMargin(new java.awt.Insets(0, 0, 0, 0));
+ importButton.addMouseListener(new java.awt.event.MouseAdapter() {
+ public void mouseClicked(java.awt.event.MouseEvent e) {
+ importAttributes();
+ }
+ });
+ }
+
+ return importButton;
+ }
+
+ private JButton getMatrixButton() {
+ if (matrixButton == null) {
+ matrixButton = new JButton();
+ matrixButton.setBorder(null);
+ matrixButton.setMargin(new java.awt.Insets(0, 0, 0, 0));
+ matrixButton.setIcon(new javax.swing.ImageIcon(AttributeBrowser.class.getResource("images/microarray_24.png")));
+ matrixButton.setToolTipText("Import Expression Matrix Data...");
+
+ matrixButton.addMouseListener(new java.awt.event.MouseAdapter() {
+ public void mouseClicked(java.awt.event.MouseEvent e) {
+ importMatrix();
+ }
+ });
+ }
+
+ return matrixButton;
+ }
+
+ private JButton attrModButton = null;
+
+ private JButton getAttrModButton() {
+ if (attrModButton == null) {
+ attrModButton = new JButton();
+ attrModButton.setBorder(null);
+ attrModButton.setIcon(new javax.swing.ImageIcon(AttributeBrowser.class.getResource("images/stock_insert-columns.png")));
+ attrModButton.setToolTipText("Attribute Batch Editor");
+ attrModButton.setMargin(new java.awt.Insets(0, 0, 0, 0));
+
+ attrModButton.addMouseListener(new java.awt.event.MouseAdapter() {
+ public void mouseClicked(java.awt.event.MouseEvent e) {
+ modDialog.setLocationRelativeTo(Cytoscape.getDesktop());
+ modDialog.setVisible(true);
+ }
+ });
+ }
+
+ return attrModButton;
+ }
+
+ private JButton formulaBuilderButton = null;
+
+ private JButton getFunctionBuilderButton() {
+ if (formulaBuilderButton == null) {
+ formulaBuilderButton = new JButton();
+ formulaBuilderButton.setBorder(null);
+ formulaBuilderButton.setIcon(new ImageIcon(AttributeBrowser.class.getResource("images/fx.png")));
+ formulaBuilderButton.setToolTipText("Function Builder");
+ formulaBuilderButton.setMargin(new java.awt.Insets(1, 1, 1, 1));
+
+ formulaBuilderButton.addMouseListener(new java.awt.event.MouseAdapter() {
+ public void mouseClicked(java.awt.event.MouseEvent e) {
+ // Do not allow opening of the formula builder dialog while a cell is being edited!
+ if (table.getCellEditor() != null)
+ return;
+
+ final int cellRow = table.getSelectedRow();
+ final int cellColumn = table.getSelectedColumn();
+ if (cellRow == -1 || cellColumn == -1 || !tableModel.isCellEditable(cellRow, cellColumn))
+ JOptionPane.showMessageDialog(Cytoscape.getDesktop(),
+ "Can't enter a formula w/o a selected cell!",
+ "Information", JOptionPane.INFORMATION_MESSAGE);
+ else {
+ final String attrName = getAttribName(cellRow, cellColumn);
+ final Map<String, Class> attribNameToTypeMap = new HashMap<String, Class>();
+ Util.initAttribNameToTypeMap(objectType, attrName, attribNameToTypeMap);
+ formulaBuilderDialog =
+ new FormulaBuilderDialog(tableModel, table, objectType, Cytoscape.getDesktop(),
+ attribNameToTypeMap, attrName);
+ formulaBuilderDialog.setLocationRelativeTo(Cytoscape.getDesktop());
+ formulaBuilderDialog.setVisible(true);
+ }
+ }
+ });
+ }
+
+ return formulaBuilderButton;
+ }
+
+ private String getAttribName(final int cellRow, final int cellColumn) {
+ if (objectType == NETWORK)
+ return ((ValidatedObjectAndEditString)(tableModel.getValueAt(cellRow, 0))).getValidatedObject().toString();
+ else
+ return tableModel.getColumnName(cellColumn);
+ }
+
+ protected void editMetadata() {
+ NetworkMetaDataDialog mdd = new NetworkMetaDataDialog(Cytoscape.getDesktop(), false,
+ Cytoscape.getCurrentNetwork());
+ mdd.setVisible(true);
+ }
+
+ protected void importAttributes() {
+ if (objectType == NODES) {
+ ImportNodeAttributesAction nodeAction = new ImportNodeAttributesAction();
+ nodeAction.actionPerformed(null);
+ } else if (objectType == EDGES) {
+ ImportEdgeAttributesAction edgeAction = new ImportEdgeAttributesAction();
+ edgeAction.actionPerformed(null);
+ } else { // case for Network
+ logger.warn("Network Attribute import not implemented yet");
+ }
+ }
+
+ protected void importMatrix() {
+ ImportExpressionMatrixAction matrixAction = new ImportExpressionMatrixAction();
+ matrixAction.actionPerformed(null);
+ }
+
+ private JButton getDeleteButton() {
+ if (deleteAttributeButton == null) {
+ deleteAttributeButton = new JButton();
+ deleteAttributeButton.setBorder(null);
+ deleteAttributeButton.setMargin(new java.awt.Insets(0, 0, 0, 0));
+ deleteAttributeButton.setIcon(new javax.swing.ImageIcon(AttributeBrowser.class
+ [...]
+ deleteAttributeButton.setToolTipText("Delete Attributes...");
+
+ // Create pop-up window for deletion
+ deleteAttributeButton.addMouseListener(new java.awt.event.MouseAdapter() {
+ public void mouseClicked(java.awt.event.MouseEvent e) {
+ removeAttribute(e);
+ }
+ });
+ }
+
+ return deleteAttributeButton;
+ }
+
+ private JButton getSelectAllButton() {
+ if (selectAllAttributesButton == null) {
+ selectAllAttributesButton = new JButton();
+ selectAllAttributesButton.setBorder(null);
+ selectAllAttributesButton.setMargin(new java.awt.Insets(0, 0, 0, 0));
+ selectAllAttributesButton.setIcon(new javax.swing.ImageIcon(AttributeBrowser.class.getResource("images/select_all.png")));
+ selectAllAttributesButton.setToolTipText("Select All Attributes");
+
+ selectAllAttributesButton.addMouseListener(new java.awt.event.MouseAdapter() {
+ public void mouseClicked(java.awt.event.MouseEvent e) {
+ updateList(attrModel.getAttributeNames());
+ try {
+// getUpdatedSelectedList();
+ updateSelectedColumn();
+ tableModel.setTableData(null, orderedCol);
+ } catch (Exception ex) {
+ attributeList.clearSelection();
+ }
+ }
+ });
+ }
+
+ return selectAllAttributesButton;
+ }
+
+ private JButton getUnselectAllButton() {
+ if (unselectAllAttributesButton == null) {
+ unselectAllAttributesButton = new JButton();
+ unselectAllAttributesButton.setBorder(null);
+ unselectAllAttributesButton.setMargin(new java.awt.Insets(0, 0, 0, 0));
+ unselectAllAttributesButton.setIcon(new javax.swing.ImageIcon(AttributeBrowser.class.getResource("images/unselect_all.png")));
+ unselectAllAttributesButton.setToolTipText("Unselect All Attributes");
+
+ unselectAllAttributesButton.addMouseListener(new java.awt.event.MouseAdapter() {
+ public void mouseClicked(java.awt.event.MouseEvent e) {
+ final List<String> emptyList = new ArrayList<String>();
+ updateList(emptyList);
+ try {
+// getUpdatedSelectedList();
+ updateSelectedColumn();
+ tableModel.setTableData(null, orderedCol);
+ } catch (Exception ex) {
+ attributeList.clearSelection();
+ }
+ }
+ });
+ }
+ return unselectAllAttributesButton;
+ }
+
+ private void removeAttribute(final MouseEvent e) {
+ final String[] attrArray = getAttributeArray();
+ Arrays.sort(attrArray);
+
+ final DeletionDialog dDialog = new DeletionDialog(Cytoscape.getDesktop(), true, attrArray,
+ attributeType, tableModel);
+
+ dDialog.pack();
+ dDialog.setLocationRelativeTo(browserToolBar);
+ dDialog.setVisible(true);
+ attrModel.sortAttributes();
+
+ final List<String> atNames = new ArrayList<String>();
+ for (String attName: CyAttributesUtils.getVisibleAttributeNames(attributes))
+ atNames.add(attName);
+ final List<String> toBeRemoved = new ArrayList<String>();
+ for (String colName: orderedCol) {
+ if (atNames.contains(colName) == false)
+ toBeRemoved.add(colName);
+ }
+
+ for (String rem: toBeRemoved)
+ orderedCol.remove(rem);
+
+ tableModel.setTableData(null, orderedCol);
+ AttributeBrowser.firePropertyChange(AttributeBrowser.RESTORE_COLUMN, null, objectType);
+
+ }
+
+
+ private JList getSelectedAttributeList() {
+ if (attributeList == null) {
+ attributeList = new CheckBoxJList();
+ attributeList.setModel(attrModel);
+ attributeList.setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION);
+ attributeList.addMouseListener(new MouseAdapter() {
+ public void mouseClicked(MouseEvent e) {
+ if (SwingUtilities.isRightMouseButton(e)) {
+ attributeSelectionPopupMenu.setVisible(false);
+ }
+ }
+ });
+ }
+ return attributeList;
+ }
+
+ private String[] getAttributeArray() {
+ final CyAttributes currentAttributes;
+
+ if (objectType == NODES) {
+ attributeType = "Node";
+ currentAttributes = Cytoscape.getNodeAttributes();
+ } else if (objectType == EDGES) {
+ attributeType = "Edge";
+ currentAttributes = Cytoscape.getEdgeAttributes();
+ } else if (objectType == NETWORK) {
+ attributeType = "Network";
+ currentAttributes = Cytoscape.getNetworkAttributes();
+ } else {
+ return new String[0];
+ }
+
+ return CyAttributesUtils.getVisibleAttributeNames(currentAttributes).toArray(new String[0]);
+ }
+
+ /**
+ * This method initializes createNewAttributeButton
+ *
+ * @return javax.swing.JButton
+ */
+ private JButton getNewButton() {
+ if (createNewAttributeButton == null) {
+ createNewAttributeButton = new JButton();
+ createNewAttributeButton.setBorder(null);
+
+ createNewAttributeButton.setFont(new java.awt.Font("Dialog", java.awt.Font.PLAIN, 12));
+ createNewAttributeButton.setHorizontalTextPosition(javax.swing.SwingConstants.CENTER);
+ createNewAttributeButton.setMargin(new java.awt.Insets(0, 0, 0, 0));
+ createNewAttributeButton.setToolTipText("Create New Attribute");
+ createNewAttributeButton.setIcon(new javax.swing.ImageIcon(AttributeBrowser.class
+ [...]
+ createNewAttributeButton.addMouseListener(new java.awt.event.MouseAdapter() {
+ public void mouseClicked(java.awt.event.MouseEvent e) {
+ jPopupMenu1.show(e.getComponent(), e.getX(), e.getY());
+ }
+ });
+ }
+
+ return createNewAttributeButton;
+ }
+
+ // Create a whole new attribute and set a default value.
+ //
+ private void createNewAttribute(final String type) {
+ final String[] existingAttrs = CyAttributesUtils.getVisibleAttributeNames(attributes).toArray(new String[0]);
+ String newAttribName = null;
+ do {
+ newAttribName = JOptionPane.showInputDialog(this, "Please enter new attribute name: ",
+ "Create New " + type + " Attribute",
+ JOptionPane.QUESTION_MESSAGE);
+ if (newAttribName == null)
+ return;
+
+ if (Arrays.binarySearch(existingAttrs, newAttribName) >= 0) {
+ JOptionPane.showMessageDialog(Cytoscape.getDesktop(),
+ "Attribute " + newAttribName + " already exists.",
+ "Error!", JOptionPane.ERROR_MESSAGE);
+ newAttribName = null;
+ }
+ } while (newAttribName == null);
+
+ final String testVal = "dummy";
+
+ if (type.equals("String"))
+ attributes.setAttribute(testVal, newAttribName, new String());
+ else if (type.equals("Floating Point"))
+ attributes.setAttribute(testVal, newAttribName, new Double(0));
+ else if (type.equals("Integer"))
+ attributes.setAttribute(testVal, newAttribName, new Integer(0));
+ else if (type.equals("Boolean"))
+ attributes.setAttribute(testVal, newAttribName, new Boolean(false));
+ else if (type.equals("String List")) {
+ final List<String> newStringList = new ArrayList<String>();
+ newStringList.add("dummy");
+ attributes.setListAttribute(testVal, newAttribName, newStringList);
+ } else if (type.equals("Floating Point List")) {
+ final List<Double> newDoubleList = new ArrayList<Double>();
+ newDoubleList.add(0.0);
+ attributes.setListAttribute(testVal, newAttribName, newDoubleList);
+ } else if (type.equals("Integer List")) {
+ final List<Integer> newIntList = new ArrayList<Integer>();
+ newIntList.add(0);
+ attributes.setListAttribute(testVal, newAttribName, newIntList);
+ } else if (type.equals("Boolean List")) {
+ final List<Boolean> newBooleanList = new ArrayList<Boolean>();
+ newBooleanList.add(true);
+ attributes.setListAttribute(testVal, newAttribName, newBooleanList);
+ } else
+ throw new IllegalArgumentException("unknown attribute type \"" + type + "\"!");
+
+ attributes.deleteAttribute(testVal, newAttribName);
+
+ // Update list selection
+ orderedCol.add(newAttribName);
+ Cytoscape.getSwingPropertyChangeSupport()
+ .firePropertyChange(Cytoscape.ATTRIBUTES_CHANGED, null, null);
+ Cytoscape.getPropertyChangeSupport().firePropertyChange(Cytoscape.ATTRIBUTES_CHANGED, null, null);
+
+ tableModel.setTableData(null, orderedCol);
+ }
+
+ @Override
+ public void popupMenuCanceled(PopupMenuEvent e) {}
+
+ @Override
+ public void popupMenuWillBecomeInvisible(PopupMenuEvent e) {
+ // Update actual table
+ try {
+ updateSelectedColumn();
+ tableModel.setTableData(null, orderedCol);
+ } catch (Exception ex) {
+ attributeList.clearSelection();
+ }
+ }
+
+ private void updateSelectedColumn() {
+
+ final Object[] selected = attributeList.getSelectedValues();
+ final List<String> list = new ArrayList<String>();
+ for(final Object name: selected)
+ list.add(name.toString());
+ updateList(list);
+ }
+
+ public void setOrderedColumnList(final List<String> newSelection) {
+ orderedCol = new ArrayList<String>(newSelection);
+ attributeList.setSelectedItems(orderedCol);
+ }
+ public void updateList(List<String> newSelection) {
+ //System.out.println("Update called. new List: " + newSelection);
+ //System.out.println("Update called. OLD List: " + orderedCol);
+ final List<String> tempList = new ArrayList<String>(orderedCol);
+
+ // Special cases: original or new List is empty
+ if(orderedCol.size() == 0 || orderedCol.size() == 1) {
+ orderedCol = new ArrayList<String>(newSelection);
+ attributeList.setSelectedItems(orderedCol);
+ return;
+ } else if(newSelection.size() == 0) {
+ orderedCol = new ArrayList<String>();
+ attributeList.setSelectedItems(orderedCol);
+ return;
+ }
+
+ // First, remove unnecessary column from the original ordered list
+ for(final String currentColName: orderedCol) {
+ if(currentColName.equals("ID") == false && newSelection.contains(currentColName) == false) {
+ //System.out.println(" Removed: " + currentColName);
+ tempList.remove(currentColName);
+ }
+ }
+
+ // Then add the new column anames to the end of list
+ for(final String currentColName: newSelection) {
+ if(currentColName.equals("ID") == false && tempList.contains(currentColName) == false) {
+ //System.out.println(" Adding: " + currentColName);
+ tempList.add(currentColName);
+ }
+ }
+
+ // Copy it to the sorted list
+ orderedCol = new ArrayList<String>(tempList);
+ //System.out.println("======> ORDERED: " + orderedCol);
+ attributeList.setSelectedItems(orderedCol);
+ }
+
+ @Override
+ public void popupMenuWillBecomeVisible(PopupMenuEvent e) {}
+}
diff --git a/coreplugins/browser/src/main/java/browser/ui/BrowserTableCellRenderer.java b/coreplugins/browser/src/main/java/browser/ui/BrowserTableCellRenderer.java
new file mode 100644
index 0000000..072c57c
--- /dev/null
+++ b/coreplugins/browser/src/main/java/browser/ui/BrowserTableCellRenderer.java
@@ -0,0 +1,174 @@
+package browser.ui;
+
+import static browser.DataObjectType.EDGES;
+import static browser.DataObjectType.NETWORK;
+import static browser.DataObjectType.NODES;
+import giny.model.Edge;
+import giny.model.Node;
+import giny.view.EdgeView;
+import giny.view.NodeView;
+
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Font;
+import java.util.List;
+import java.util.Map;
+
+import javax.swing.BorderFactory;
+import javax.swing.JLabel;
+import javax.swing.JTable;
+import javax.swing.border.Border;
+import javax.swing.table.TableCellRenderer;
+
+import browser.AttributeBrowser;
+import browser.DataObjectType;
+import browser.ValidatedObjectAndEditString;
+import cytoscape.Cytoscape;
+import cytoscape.data.CyAttributes;
+import cytoscape.view.CyNetworkView;
+
+/**
+ *
+ * Cell renderer for preview table.<br>
+ * Coloring function is added. This will sync node color and cell colors.<br>
+ *
+ * @version 0.6
+ * @since Cytoscape 2.3
+ *
+ * @author kono
+ *
+ */
+class BrowserTableCellRenderer extends JLabel implements TableCellRenderer {
+ private static final String HTML_BEG = "<html><body topmargin=\"5\" leftmargin=\"0\" marginheight=\"5\" marginwidth=\"5\" "
+ + "bgcolor=\"#ffffff\" text=\"#595959\" link=\"#0000ff\" vlink=\"#800080\" alink=\"#ff0000\">";
+ private static final String HTML_STYLE = "<div style=\"width: 200px; background-color: #ffffff; padding: 3px;\"> ";
+
+ // Define fonts & colors for the cells
+ private Font labelFont = new Font("Sans-serif", Font.BOLD, 12);
+ private Font normalFont = new Font("Sans-serif", Font.PLAIN, 12);
+ private final Color metadataBackground = new Color(255, 210, 255);
+ private static final Color NON_EDITABLE_COLOR = new Color(235, 235, 235, 100);
+ private static final Color SELECTED_CELL_COLOR = new Color(0, 100, 255, 40);
+ private static final Color SELECTED_LABEL_COLOR = Color.black.brighter();
+ private DataObjectType type = DataObjectType.NODES;
+ private boolean coloring;
+
+ /**
+ * Creates a new BrowserTableCellRenderer object.
+ *
+ * @param coloring DOCUMENT ME!
+ * @param type DOCUMENT ME!
+ */
+ public BrowserTableCellRenderer(boolean coloring, DataObjectType type) {
+ super();
+ this.type = type;
+ this.coloring = coloring;
+ setOpaque(true);
+ setBorder(BorderFactory.createEmptyBorder(0, 5, 0, 5));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param table DOCUMENT ME!
+ * @param value DOCUMENT ME!
+ * @param isSelected DOCUMENT ME!
+ * @param hasFocus DOCUMENT ME!
+ * @param row DOCUMENT ME!
+ * @param column DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Component getTableCellRendererComponent(final JTable table, final Object value, final boolean isSelected,
+ final boolean hasFocus, final int row, final int column)
+ {
+ setHorizontalAlignment(JLabel.LEFT);
+
+ final ValidatedObjectAndEditString objectAndEditString = (ValidatedObjectAndEditString)value;
+ final String colName = table.getColumnName(column);
+
+ // First, set values
+ if (objectAndEditString == null
+ || (objectAndEditString.getValidatedObject() == null && objectAndEditString.getErrorText() == null))
+ setText("");
+ else {
+ final String displayText = (objectAndEditString.getErrorText() != null)
+ ? objectAndEditString.getErrorText()
+ : objectAndEditString.getValidatedObject().toString();
+ setText(displayText);
+ }
+
+ // If selected, return
+ if (isSelected) {
+ setFont(labelFont);
+ setForeground(SELECTED_LABEL_COLOR);
+ setBackground(SELECTED_CELL_COLOR);
+
+ return this;
+ }
+
+ // set default colorings
+ setForeground(table.getForeground());
+ setFont(normalFont);
+ setBackground(table.getBackground());
+
+ final CyAttributes attribs = type.getAssociatedAttributes();
+
+ if (attribs == null)
+ return this;
+
+ // check for non-editable columns
+ if (attribs.getUserEditable(colName) == false) {
+ setBackground(NON_EDITABLE_COLOR);
+ }
+
+ // If ID, return default.
+ if (colName.equals(AttributeBrowser.ID)) {
+ setFont(labelFont);
+ setBackground(NON_EDITABLE_COLOR);
+ }
+
+ // handle special NETWORK coloring
+ if ((type == NETWORK) && (value != null)) {
+ if (colName.equals("Network Attribute Name") && !value.equals("Network Metadata")) {
+ setFont(labelFont);
+ setBackground(NON_EDITABLE_COLOR);
+ } else if (value.equals("Network Metadata")) {
+ setBackground(metadataBackground);
+ setFont(labelFont);
+ }
+ }
+
+ // if we're not coloring the ID column we're done
+ if ((coloring == false) || !colName.equals(AttributeBrowser.ID))
+ return this;
+
+ // handle colors for the the ID column
+ CyNetworkView netview = Cytoscape.getCurrentNetworkView();
+
+ if (type == NODES) {
+ if (netview != Cytoscape.getNullNetworkView()) {
+ NodeView nodeView = netview.getNodeView(Cytoscape.getCyNode((String) table.getValueAt(row, column)));
+
+ if (nodeView != null) {
+ Color nodeColor = (Color) nodeView.getUnselectedPaint();
+ setBackground(nodeColor);
+ }
+ }
+ } else if (type == EDGES) {
+ if (netview != Cytoscape.getNullNetworkView()) {
+ final String edgeName = (String) table.getValueAt(row, column);
+ final EdgeView edgeView = netview.getEdgeView(((CyAttributeBrowserTable) table).getEdge(edgeName));
+
+ if (edgeView != null) {
+ Color edgeColor = (Color) edgeView.getUnselectedPaint();
+ setBackground(edgeColor);
+ }
+ }
+ }
+
+ return this;
+ }
+}
+
+
diff --git a/coreplugins/browser/src/main/java/browser/ui/CyAttributeBrowserTable.java b/coreplugins/browser/src/main/java/browser/ui/CyAttributeBrowserTable.java
new file mode 100644
index 0000000..9755144
--- /dev/null
+++ b/coreplugins/browser/src/main/java/browser/ui/CyAttributeBrowserTable.java
@@ -0,0 +1,1622 @@
+/*
+ =====================================================================
+
+ JSortTable.java
+
+ Created by Claude Duguay
+ Copyright (c) 2002
+
+ =====================================================================
+ */
+package browser.ui;
+
+import static browser.DataObjectType.EDGES;
+import static browser.DataObjectType.NETWORK;
+import static browser.DataObjectType.NODES;
+import giny.model.Edge;
+import giny.model.GraphObject;
+import giny.model.Node;
+import giny.view.EdgeView;
+import giny.view.NodeView;
+
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Cursor;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.Graphics;
+import java.awt.KeyboardFocusManager;
+import java.awt.Rectangle;
+import java.awt.Toolkit;
+import java.awt.Window;
+import java.awt.datatransfer.Clipboard;
+import java.awt.datatransfer.StringSelection;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.KeyEvent;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.EventObject;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Properties;
+
+import javax.swing.BorderFactory;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JComponent;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JPopupMenu;
+import javax.swing.JTable;
+import javax.swing.JViewport;
+import javax.swing.KeyStroke;
+import javax.swing.ListSelectionModel;
+import javax.swing.SwingUtilities;
+import javax.swing.border.Border;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ListSelectionEvent;
+import javax.swing.table.JTableHeader;
+import javax.swing.table.TableCellEditor;
+import javax.swing.table.TableColumn;
+import javax.swing.table.TableColumnModel;
+
+import org.cytoscape.equations.Equation;
+
+import browser.AttributeBrowser;
+import browser.DataObjectType;
+import browser.DataTableModel;
+import browser.SortTableModel;
+import browser.ValidatedObjectAndEditString;
+import browser.util.HyperLinkOut;
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import cytoscape.CytoscapeInit;
+import cytoscape.data.CyAttributes;
+import cytoscape.data.CyAttributesUtils;
+import cytoscape.data.SelectEvent;
+import cytoscape.data.SelectEventListener;
+import cytoscape.data.Semantics;
+import cytoscape.dialogs.NetworkMetaDataDialog;
+import cytoscape.logger.CyLogger;
+import cytoscape.util.CyFileFilter;
+import cytoscape.util.FileUtil;
+import cytoscape.util.OpenBrowser;
+import cytoscape.util.swing.ColumnResizer;
+import cytoscape.view.CyNetworkView;
+import cytoscape.view.CytoscapeDesktop;
+import cytoscape.visual.GlobalAppearanceCalculator;
+import cytoscape.visual.VisualMappingManager;
+
+
+/**
+ * Table for browser based on JSortTable
+ */
+public class CyAttributeBrowserTable extends JTable implements MouseListener, ActionListener, PropertyChangeListener,
+ SelectEventListener, MouseMotionListener {
+
+ private static final long serialVersionUID = -6870984215180716506L;
+
+ public static final int SELECTED_NODE = 1;
+ public static final int REV_SELECTED_NODE = 2;
+ public static final int SELECTED_EDGE = 3;
+ public static final int REV_SELECTED_EDGE = 4;
+
+ // Target network to watch selection
+ CyNetwork currentNetwork;
+
+ // Global calcs used for coloring
+ private VisualMappingManager vmm = Cytoscape.getVisualMappingManager();
+ private GlobalAppearanceCalculator gac;
+ protected int sortedColumnIndex = -1;
+ protected boolean sortedColumnAscending = true;
+ private Color selectedNodeColor;
+ private Color selectedEdgeColor;
+ private Color reverseSelectedNodeColor;
+ private Color reverseSelectedEdgeColor;
+
+ // For right-click menu
+ private JPopupMenu rightClickPopupMenu;
+ private JPopupMenu rightClickHeaderPopupMenu;
+ private JPopupMenu cellMenu;
+ private JMenuItem openFormulaBuilderMenuItem = null;
+ private JMenuItem copyMenuItem = null;
+ private JMenuItem copyToCurrentSelectionMenuItem = null;
+ private JMenuItem copyFormulaToCurrentSelectionMenuItem = null;
+ private JMenuItem copyToEntireAttributeMenuItem = null;
+ private JMenuItem copyFormulaToEntireAttributeMenuItem = null;
+ private JMenu exportMenu = null;
+ private JMenuItem exportCellsMenuItem = null;
+ private JMenuItem exportTableMenuItem = null;
+ private JMenuItem selectAllMenuItem = null;
+ private JMenuItem newSelectionMenuItem = null;
+ private JCheckBoxMenuItem coloringMenuItem = null;
+ private Clipboard systemClipboard;
+ private StringSelection stsel;
+ private DataTableModel tableModel;
+ private DataObjectType objectType;
+ private Map<String, Map<String, String>> linkoutProps;
+ private CyLogger logger = null;
+ private FormulaBuilderDialog formulaBuilderDialog = null;
+ private int mouseX;
+ private static final Font BORDER_FONT = new Font("Sans-serif", Font.BOLD, 12);
+
+ private HashMap<String, Integer> columnWidthMap = new HashMap<String, Integer>();
+ private final AttributeBrowser parent;
+
+ // For turning off listener during session loading
+ private boolean ignore = false;
+
+ /**
+ * String used to compare against os.name System property -
+ * to determine if we are running on Windows platform.
+ */
+ static final String MAC_OS_ID = "mac";
+
+ /**
+ * Routine which determines if we are running on mac platform
+ *
+ * @return boolean
+ */
+ private boolean isMacPlatform() {
+ String os = System.getProperty("os.name");
+ return os.regionMatches(true, 0, MAC_OS_ID, 0, MAC_OS_ID.length());
+ }
+
+ protected static final String LS = System.getProperty("line.separator");
+
+ public CyAttributeBrowserTable(DataTableModel model, DataObjectType objectType, final AttributeBrowser parent) {
+ super(model);
+ this.parent = parent;
+ logger = CyLogger.getLogger(CyAttributeBrowserTable.class);
+ initSortHeader();
+
+ this.tableModel = model;
+ this.objectType = objectType;
+
+ initialize();
+ }
+
+ // Initialize some attributes of this table
+ private void initialize() {
+ this.setSize(400, 300);
+ this.setCellSelectionEnabled(true);
+ this.getPopupMenu();
+ this.getHeaderPopupMenu();
+
+
+ setKeyStroke();
+ Cytoscape.getSwingPropertyChangeSupport().addPropertyChangeListener(this);
+
+ setSelectedColor(SELECTED_NODE);
+ setSelectedColor(REV_SELECTED_NODE);
+ setSelectedColor(SELECTED_EDGE);
+ setSelectedColor(REV_SELECTED_EDGE);
+
+ this.setDefaultRenderer(Object.class, new BrowserTableCellRenderer(false, objectType));
+ this.getColumnModel().addColumnModelListener(this);
+ this.setDefaultEditor(Object.class, new MultiLineTableCellEditor() );
+
+ this.getTableHeader().addMouseMotionListener(this);
+ }
+
+ public void valueChanged(final ListSelectionEvent event) {
+ super.valueChanged(event);
+
+ final boolean singleCellSelected = getSelectedRowCount() == 1 && getSelectedColumnCount() == 1;
+ if (singleCellSelected) {
+ copyToCurrentSelectionMenuItem.setEnabled(true);
+ copyFormulaToCurrentSelectionMenuItem.setEnabled(true);
+ copyToEntireAttributeMenuItem.setEnabled(true);
+ copyFormulaToEntireAttributeMenuItem.setEnabled(true);
+ }
+ else {
+ copyToCurrentSelectionMenuItem.setEnabled(false);
+ copyFormulaToCurrentSelectionMenuItem.setEnabled(false);
+ copyToEntireAttributeMenuItem.setEnabled(false);
+ copyFormulaToEntireAttributeMenuItem.setEnabled(false);
+ }
+ }
+
+ private void setKeyStroke() {
+ KeyStroke copy = KeyStroke.getKeyStroke(KeyEvent.VK_C, ActionEvent.CTRL_MASK, false);
+ // Identifying the copy KeyStroke user can modify this
+ // to copy on some other Key combination.
+ this.registerKeyboardAction(this, "Copy", copy, JComponent.WHEN_FOCUSED);
+ systemClipboard = Toolkit.getDefaultToolkit().getSystemClipboard();
+ }
+
+ protected void setSelectedColor(final int type) {
+ gac = vmm.getVisualStyle().getGlobalAppearanceCalculator();
+
+ switch (type) {
+ case SELECTED_NODE:
+ selectedNodeColor = gac.getDefaultNodeSelectionColor();
+ break;
+ case REV_SELECTED_NODE:
+ reverseSelectedNodeColor = gac.getDefaultNodeReverseSelectionColor();
+ break;
+ case SELECTED_EDGE:
+ selectedEdgeColor = gac.getDefaultEdgeSelectionColor();
+ break;
+ case REV_SELECTED_EDGE:
+ reverseSelectedEdgeColor = gac.getDefaultEdgeReverseSelectionColor();
+ break;
+ default:
+ break;
+ }
+ }
+
+ protected Color getSelectedColor(final int type) {
+ Color newColor;
+ gac = vmm.getVisualStyle().getGlobalAppearanceCalculator();
+
+ switch (type) {
+ case SELECTED_NODE:
+ newColor = gac.getDefaultNodeSelectionColor();
+ break;
+ case REV_SELECTED_NODE:
+ newColor = gac.getDefaultNodeReverseSelectionColor();
+ break;
+ case SELECTED_EDGE:
+ newColor = gac.getDefaultEdgeSelectionColor();
+ break;
+ case REV_SELECTED_EDGE:
+ newColor = gac.getDefaultEdgeReverseSelectionColor();
+ break;
+ default:
+ newColor = null;
+ break;
+ }
+
+ return newColor;
+ }
+
+ protected Edge getEdge(final String edgeString) {
+ String[] edgeNameParts = edgeString.split(" \\(");
+ final Node source = Cytoscape.getCyNode(edgeNameParts[0]);
+ edgeNameParts = edgeNameParts[1].split("\\) ");
+
+ final String interaction = edgeNameParts[0];
+ final Node target = Cytoscape.getCyNode(edgeNameParts[1]);
+
+ return Cytoscape.getCyEdge(source, target, Semantics.INTERACTION, interaction, false);
+ }
+
+ private Map<String, GraphObject> paintNodesAndEdges(int idLocation) {
+ final int[] rowsSelected = getSelectedRows();
+ final Map<String, GraphObject> selectedMap = new HashMap<String, GraphObject>();
+ final int selectedRowLength = rowsSelected.length;
+ final CyNetworkView netView = Cytoscape.getCurrentNetworkView();
+
+ for (int idx = 0; idx < selectedRowLength; idx++) {
+ final ValidatedObjectAndEditString objectAndEditString =
+ (ValidatedObjectAndEditString)getValueAt(rowsSelected[idx], idLocation);
+ if (objectAndEditString == null)
+ continue;
+
+ final String selectedName = (String)objectAndEditString.getValidatedObject();
+ if (selectedName == null)
+ continue;
+
+ if (objectType == NODES) {
+ // Change node color
+ final Node selectedNode = Cytoscape.getCyNode(selectedName);
+ selectedMap.put(selectedName, selectedNode);
+
+ if (netView != Cytoscape.getNullNetworkView()) {
+ final NodeView nv = netView.getNodeView(selectedNode);
+ if (nv != null)
+ nv.setSelectedPaint(reverseSelectedNodeColor);
+ }
+ } else if (objectType == EDGES) {
+ final Edge selectedEdge = getEdge(selectedName);
+ selectedMap.put(selectedName, selectedEdge);
+
+ if (netView != Cytoscape.getNullNetworkView()) {
+ final EdgeView ev = netView.getEdgeView(selectedEdge);
+ if (ev != null)
+ ev.setSelectedPaint(reverseSelectedEdgeColor);
+ }
+ }
+ }
+
+ return selectedMap;
+ }
+
+ private void resetObjectColor(int idLocation) {
+ final CyNetworkView view = Cytoscape.getCurrentNetworkView();
+ if ((view == Cytoscape.getNullNetworkView()) || (view == null))
+ return;
+
+ final int rowCount = dataModel.getRowCount();
+ for (int idx = 0; idx < rowCount; idx++) {
+ final ValidatedObjectAndEditString val = (ValidatedObjectAndEditString)dataModel.getValueAt(idx, idLocation);
+ final String objectName;
+ try {
+ objectName = (String)val.getValidatedObject();
+ } catch (final Exception e) {
+ continue;
+ }
+
+ if (objectType == NODES) {
+ final Node selectedNode = Cytoscape.getCyNode(objectName);
+
+ // Set to the original color
+ if (selectedNode != null) {
+ final NodeView nv = view.getNodeView(selectedNode);
+ if (nv != null)
+ nv.setSelectedPaint(selectedNodeColor);
+ }
+ } else if (objectType == EDGES) {
+ final Edge selectedEdge = this.getEdge(objectName);
+ if (selectedEdge != null) {
+ final EdgeView ev = view.getEdgeView(selectedEdge);
+ if (ev != null)
+ ev.setSelectedPaint(selectedEdgeColor);
+ }
+ }
+ }
+ }
+
+ /**
+ * This method initializes rightClickPopupMenu
+ *
+ * @return the inilialised pop-up menu
+ */
+ public JPopupMenu getPopupMenu() {
+ if (rightClickPopupMenu != null)
+ return rightClickPopupMenu;
+
+ rightClickPopupMenu = new JPopupMenu();
+
+ openFormulaBuilderMenuItem = new JMenuItem("Open Formula Builder");
+ copyMenuItem = new JMenuItem("Copy");
+ copyToCurrentSelectionMenuItem = new JMenuItem("Copy to Current Selection");
+ copyToCurrentSelectionMenuItem.setEnabled(false);
+ copyFormulaToCurrentSelectionMenuItem = new JMenuItem("Copy Formula to Current Selection");
+ copyFormulaToCurrentSelectionMenuItem.setEnabled(false);
+ copyToEntireAttributeMenuItem = new JMenuItem("Copy to Entire Attribute");
+ copyToEntireAttributeMenuItem.setEnabled(false);
+ copyFormulaToEntireAttributeMenuItem = new JMenuItem("Copy Formula to Entire Attribute");
+ copyFormulaToEntireAttributeMenuItem.setEnabled(false);
+ newSelectionMenuItem = new JMenuItem("Select from Table");
+ exportMenu = new JMenu("Export...");
+ exportCellsMenuItem = new JMenuItem("Selected Cells");
+ exportTableMenuItem = new JMenuItem("Entire Table");
+ selectAllMenuItem = new JMenuItem("Select All");
+
+ coloringMenuItem = new JCheckBoxMenuItem("On/Off Coloring");
+
+ final JTable table = this;
+ openFormulaBuilderMenuItem.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(final ActionEvent e) {
+ final int cellRow = table.getSelectedRow();
+ final int cellColumn = table.getSelectedColumn();
+ if (cellRow == -1 || cellColumn == -1 || !tableModel.isCellEditable(cellRow, cellColumn))
+ JOptionPane.showMessageDialog(Cytoscape.getDesktop(),
+ "Can't enter a formula w/o a selected cell!",
+ "Information", JOptionPane.INFORMATION_MESSAGE);
+ else {
+ final String columnName = tableModel.getColumnName(cellColumn);
+ final Map<String, Class> attribNameToTypeMap = new HashMap<String, Class>();
+ initAttribNameToTypeMap(objectType, columnName, attribNameToTypeMap);
+ formulaBuilderDialog =
+ new FormulaBuilderDialog(tableModel, table, objectType, Cytoscape.getDesktop(),
+ attribNameToTypeMap, columnName);
+ formulaBuilderDialog.setLocationRelativeTo(Cytoscape.getDesktop());
+ formulaBuilderDialog.setVisible(true);
+ }
+ }
+ });
+
+ copyMenuItem.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent e) {
+ copyToClipBoard();
+ }
+ });
+
+ copyToCurrentSelectionMenuItem.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent e) {
+ copyToCurrentSelection();
+ }
+ });
+
+ copyFormulaToCurrentSelectionMenuItem.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(final ActionEvent e) {
+ copyFormulaToCurrentSelection();
+ }
+ });
+
+ copyToEntireAttributeMenuItem.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(final ActionEvent e) {
+ copyToEntireAttribute();
+ }
+ });
+
+ copyFormulaToEntireAttributeMenuItem.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(final ActionEvent e) {
+ copyFormulaToEntireAttribute();
+ }
+ });
+
+ exportCellsMenuItem.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(final ActionEvent e) {
+ export(false);
+ }
+ });
+
+ exportTableMenuItem.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(final ActionEvent e) {
+ export(true);
+ }
+ });
+
+ selectAllMenuItem.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(final ActionEvent e) {
+ selectAll();
+ }
+ });
+
+ newSelectionMenuItem.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(final ActionEvent e) {
+ final int idLocation = getIdColumn();
+ final Map<String, GraphObject> selectedMap = paintNodesAndEdges(idLocation);
+ final CyNetwork curNet = Cytoscape.getCurrentNetwork();
+
+ final List<GraphObject> nonSelectedObjects = new ArrayList<GraphObject>();
+
+ GraphObject fromMap;
+
+ if (objectType == NODES) {
+ for (Object curNode : curNet.getSelectedNodes()) {
+ fromMap = selectedMap.get(((Node) curNode).getIdentifier());
+
+ if (fromMap == null) {
+ nonSelectedObjects.add((GraphObject) curNode);
+ }
+ }
+
+ resetObjectColor(idLocation);
+ curNet.setSelectedNodeState(nonSelectedObjects, false);
+ } else {
+ for (Object curEdge : curNet.getSelectedEdges()) {
+ fromMap = selectedMap.get(((Edge) curEdge).getIdentifier());
+
+ if (fromMap == null) {
+ nonSelectedObjects.add((GraphObject) curEdge);
+ }
+ }
+
+ resetObjectColor(idLocation);
+ curNet.setSelectedEdgeState(nonSelectedObjects, false);
+ }
+
+ if (Cytoscape.getCurrentNetworkView() != Cytoscape.getNullNetworkView()) {
+ Cytoscape.getCurrentNetworkView().updateView();
+ }
+ }
+ });
+
+ coloringMenuItem.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent e) {
+ if (Cytoscape.getCurrentNetworkView() != Cytoscape.getNullNetworkView()) {
+ if (coloringMenuItem.isSelected() == true) {
+ logger.debug("color ON");
+ setNewRenderer(true);
+ } else {
+ logger.debug("color OFF");
+ setNewRenderer(false);
+ }
+ }
+ }
+ });
+
+ exportMenu.add(exportCellsMenuItem);
+ exportMenu.add(exportTableMenuItem);
+
+ if (objectType != NETWORK)
+ rightClickPopupMenu.add(newSelectionMenuItem);
+
+ rightClickPopupMenu.add(openFormulaBuilderMenuItem);
+ rightClickPopupMenu.add(copyMenuItem);
+ rightClickPopupMenu.add(copyToCurrentSelectionMenuItem);
+ rightClickPopupMenu.add(copyFormulaToCurrentSelectionMenuItem);
+ rightClickPopupMenu.add(copyToEntireAttributeMenuItem);
+ rightClickPopupMenu.add(copyFormulaToEntireAttributeMenuItem);
+ rightClickPopupMenu.add(selectAllMenuItem);
+ rightClickPopupMenu.add(exportMenu);
+
+ if (objectType != NETWORK) {
+ rightClickPopupMenu.addSeparator();
+ rightClickPopupMenu.add(coloringMenuItem);
+ }
+
+ return rightClickPopupMenu;
+ }
+
+ private JPopupMenu getHeaderPopupMenu() {
+ if (objectType == NETWORK)
+ return null;
+
+ if (rightClickHeaderPopupMenu != null)
+ return rightClickHeaderPopupMenu;
+
+ rightClickHeaderPopupMenu = new JPopupMenu();
+ final JMenuItem openFormulaBuilderMenuItem = new JMenuItem("Open Formula Builder");
+ final TableColumnModel columnModel = getColumnModel();
+ final JTable table = this;
+ openFormulaBuilderMenuItem.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(final ActionEvent event) {
+ final int cellColumn = columnModel.getColumnIndexAtX(mouseX);
+ final String columnName = tableModel.getColumnName(cellColumn);
+ final Map<String, Class> attribNameToTypeMap = new HashMap<String, Class>();
+ initAttribNameToTypeMap(objectType, columnName, attribNameToTypeMap);
+ formulaBuilderDialog =
+ new FormulaBuilderDialog(tableModel, table, objectType, Cytoscape.getDesktop(),
+ attribNameToTypeMap, columnName);
+ formulaBuilderDialog.setLocationRelativeTo(Cytoscape.getDesktop());
+ formulaBuilderDialog.setVisible(true);
+ }
+ });
+ rightClickHeaderPopupMenu.add(openFormulaBuilderMenuItem);
+
+ return rightClickHeaderPopupMenu;
+ }
+
+ private void setNewRenderer(boolean colorSwitch) {
+ this.setDefaultRenderer(Object.class, new BrowserTableCellRenderer(colorSwitch, objectType));
+ this.repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param all DOCUMENT ME!
+ */
+ public void export(final boolean all) {
+ // Do this in the GUI Event Dispatch thread...
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ final String name;
+
+ try {
+ name = FileUtil.getFile("Export Table", FileUtil.SAVE,
+ new CyFileFilter[] { }).toString();
+ } catch (Exception exp) {
+ // this is because the selection was canceled
+ return;
+ }
+
+ String export = exportTable(all);
+ export = export.replace("[", "\"");
+ export = export.replace("]", "\"");
+
+ try {
+ final BufferedWriter writer = new BufferedWriter(new FileWriter(new File(name)));
+ writer.write(export);
+ writer.close();
+ export = null;
+ } catch (Exception ex) {
+ logger.error("Table Export Write error",ex);
+ }
+ }
+ });
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String exportTable() {
+ return exportTable("\t", LS, false);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param all DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String exportTable(boolean all) {
+ return exportTable("\t", LS, all);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param element_delim DOCUMENT ME!
+ * @param eol_delim DOCUMENT ME!
+ * @param all DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String exportTable(final String element_delim, final String eol_delim, boolean all) {
+ if (all == true) {
+ this.selectAll();
+ }
+
+ final int[] selectedCols = this.getSelectedColumns();
+ final StringBuffer buf = new StringBuffer();
+
+ for (int i = 0; i < selectedCols.length; i++) {
+ buf.append(this.getColumnName(selectedCols[i]) + "\t");
+ }
+
+ buf.append(LS);
+
+ return buf.toString() + copyToClipBoard();
+ }
+
+ private void getSelected() {
+ int selectedCol = this.getSelectedColumn();
+ this.getSelectedRows();
+ }
+
+ protected void initSortHeader() {
+ JTableHeader header = getTableHeader();
+ header.setDefaultRenderer(new SortHeaderRenderer());
+ header.addMouseListener(this);
+
+ setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION);
+
+ //
+ // Event handler. Define actions when mouse is clicked.
+ //
+ addMouseListener(new MouseAdapter() {
+ public void mouseClicked(MouseEvent e) {
+ final int column = getColumnModel().getColumnIndexAtX(e.getX());
+ final int row = e.getY() / getRowHeight();
+
+ // Bail out if we're dealing w/ network attributes or we are at the ID column:
+ if (objectType == NETWORK || column == getIdColumn())
+
+ // Make sure the column and row we're clicking on actually exists!
+ if (column >= tableModel.getColumnCount() || row >= tableModel.getRowCount())
+ return;
+
+ ValidatedObjectAndEditString objectAndEditString = null;
+ try {
+ objectAndEditString = (ValidatedObjectAndEditString)getValueAt(row, column);
+ }
+ catch (Exception ex){
+ // If user clicks outside the table, just ignore
+ return;
+ }
+
+ getSelected();
+
+ // If action is right click, then show edit pop-up menu
+ if ((SwingUtilities.isRightMouseButton(e)) || (isMacPlatform() && e.isControlDown())){
+ if (objectAndEditString != null) {
+ // Remove the last menuItem
+ rightClickPopupMenu.remove(rightClickPopupMenu.getComponentCount() - 1);
+
+ final Object validatedObject = objectAndEditString.getValidatedObject();
+ if (validatedObject != null){
+
+ // If there is already an menuItem "Open this URL in a browser", remove it
+ for (int i=0; i<rightClickPopupMenu.getComponentCount(); i++){
+ Object obj = rightClickPopupMenu.getComponent(i);
+ if (obj instanceof JMenuItem){
+ JMenuItem menuItem = (JMenuItem) obj;
+ if (menuItem.getText().equalsIgnoreCase("<html>Open this URL in a browser</html>")){
+ rightClickPopupMenu.remove(i);
+ break;
+ }
+ }
+ }
+
+ // Check if this is a URL
+ URL url = null;
+ try {
+ url = new URL(objectAndEditString.getValidatedObject().toString());
+ } catch (final MalformedURLException e1) {
+ // If invalid, just ignore.
+ }
+
+ if (url !=null){
+ // It is a URL, add a menuItem 'Open this URL in a browser'
+ rightClickPopupMenu.add(new OpenNewBrowser(url));
+ }
+
+ // Add last menuItem to right-click menu
+ rightClickPopupMenu.add(new HyperLinkOut(validatedObject.toString(), linkoutProps));
+ }
+ rightClickPopupMenu.show(e.getComponent(), e.getX(), e.getY());
+
+ }
+ } else if (SwingUtilities.isLeftMouseButton(e) && (getSelectedRows().length != 0)) {
+
+ showListContents(e);
+
+ if (row >= getRowCount() || row < 0 || column >= getColumnCount() || column < 0)
+ return;
+ }
+ } // mouseClicked
+
+
+ public void mouseReleased(MouseEvent e) {
+ // When the mouse is released, fire signal to pass the selected
+ // objects in the table.
+ // Get selected object names
+ final int[] rowsSelected = getSelectedRows();
+
+ if (rowsSelected.length == 0) {
+ return;
+ }
+
+ final int columnCount = getColumnCount();
+ int idLocation = 0;
+
+ // First, find the location of the ID column
+ for (int idx = 0; idx < columnCount; idx++) {
+ if (getColumnName(idx).equals(AttributeBrowser.ID)) {
+ idLocation = idx;
+
+ break;
+ }
+ }
+
+ // Initialize internal selection table
+ ((DataTableModel) dataModel).resetSelectionFlags();
+
+ setSelectedColor(SELECTED_NODE);
+ setSelectedColor(REV_SELECTED_NODE);
+ setSelectedColor(SELECTED_EDGE);
+ setSelectedColor(REV_SELECTED_EDGE);
+
+ resetObjectColor(idLocation);
+ paintNodesAndEdges(idLocation);
+
+ if (Cytoscape.getCurrentNetworkView() != Cytoscape.getNullNetworkView()) {
+ Cytoscape.getCurrentNetworkView().updateView();
+ }
+ }
+ });
+ }
+
+ class OpenNewBrowser extends JMenuItem implements ActionListener{
+ URL url;
+ public OpenNewBrowser(URL url){
+ this.url=url;
+ this.setText("<html>Open this URL in a browser</html>");
+ this.addActionListener(this);
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ cytoscape.util.OpenBrowser.openURL(url.toString());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getSortedColumnIndex() {
+ return sortedColumnIndex;
+ }
+
+
+ public boolean isSortedColumnAscending() {
+ return sortedColumnAscending;
+ }
+
+
+ @Override
+ public void mouseReleased(MouseEvent event) {}
+
+ @Override
+ public void mousePressed(MouseEvent event) {}
+
+ @Override
+ public void mouseClicked(MouseEvent event) {
+ final int cursorType = getTableHeader().getCursor().getType();
+ if ((event.getButton() == MouseEvent.BUTTON1) && (cursorType != Cursor.E_RESIZE_CURSOR)
+ && (cursorType != Cursor.W_RESIZE_CURSOR)) {
+ final int index = getColumnModel().getColumnIndexAtX(event.getX());
+
+ if (index >= 0) {
+ final int modelIndex = getColumnModel().getColumn(index).getModelIndex();
+
+ final SortTableModel model = (SortTableModel) getModel();
+
+ if (model.isSortable(modelIndex)) {
+ // toggle ascension, if already sorted
+ if (sortedColumnIndex == index) {
+ sortedColumnAscending = !sortedColumnAscending;
+ }
+
+ sortedColumnIndex = index;
+
+ model.sortColumn(modelIndex, sortedColumnAscending);
+ }
+ }
+ }
+ else if (event.getButton() == MouseEvent.BUTTON3) {
+ // Don't do anything if we're displaying network attributes:
+ if (objectType == NETWORK)
+ return;
+
+ final int column = getColumnModel().getColumnIndexAtX(event.getX());
+
+ // Make sure the column we're clicking on actually exists!
+ if (column >= tableModel.getColumnCount() || column < 0)
+ return;
+
+ // Ignore clicks on the ID column:
+ if (column == getIdColumn())
+ return;
+
+ mouseX = event.getX();
+ rightClickHeaderPopupMenu.show(event.getComponent(), event.getX(), event.getY());
+ }
+ }
+
+ @Override
+ public void mouseEntered(MouseEvent event) {}
+
+ @Override
+ public void mouseExited(MouseEvent event) {}
+
+ @Override
+ public void actionPerformed(ActionEvent event) {
+ if (event.getActionCommand().compareTo("Copy") == 0) {
+ logger.debug("Cells copied to clipboard.");
+ copyToClipBoard();
+ }
+ }
+
+ // Display elements in te list & map objects
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void showListContents(MouseEvent e) {
+ int column = 0;
+ int row = 0;
+ row = this.getSelectedRow();
+ column = this.getSelectedColumn();
+
+ DataTableModel model = (DataTableModel) tableModel;
+
+ // List tester = new ArrayList();
+ Class tester = model.getObjectTypeAt(this.getColumnName(column));
+
+ Object value = model.getValueAt(row, column);
+
+ if ((tester != null) && tester.equals(List.class)) {
+ int idCol = 0;
+
+ for (int i = 0; i < this.getColumnCount(); i++) {
+ if (this.getColumnName(i).equals(AttributeBrowser.ID)) {
+ idCol = i;
+
+ break;
+ }
+ }
+
+ final String idField = (String) ((ValidatedObjectAndEditString)this.getValueAt(row, idCol)).getValidatedObject();
+ List contents = (List) model.getValidatedObjectAndEditString(CyAttributes.TYPE_SIMPLE_LIST, idField,
+ this.getColumnName(column)).getValidatedObject();
+ cellMenu = new JPopupMenu();
+
+ Object[] listItems = contents.toArray();
+
+ if (listItems.length != 0)
+ getCellContentView(CyAttributes.TYPE_SIMPLE_LIST, listItems, idField, e);
+ } else if ((value != null) && (value instanceof Map)
+ && model.getValueAt(row, 0).equals(AttributeBrowser.NETWORK_METADATA)) {
+ NetworkMetaDataDialog mdd = new NetworkMetaDataDialog(Cytoscape.getDesktop(), false,
+ Cytoscape.getCurrentNetwork());
+ mdd.setLocationRelativeTo(Cytoscape.getDesktop());
+ mdd.setVisible(true);
+ } else if ((tester != null) && tester.equals(Map.class)) {
+ int idCol = 0;
+
+ for (int i = 0; i < this.getColumnCount(); i++) {
+ if (this.getColumnName(i).equals(AttributeBrowser.ID)) {
+ idCol = i;
+
+ break;
+ }
+ }
+
+ String idField = (String) this.getValueAt(row, idCol);
+
+ Map<String, Object> contents = (Map) model.getValidatedObjectAndEditString(CyAttributes.TYPE_SIMPLE_MAP,
+ idField,
+ this.getColumnName(column)).getValidatedObject();
+
+ if ((contents != null) && (contents.size() != 0)) {
+ Object[] listItems = new Object[contents.size()];
+ Object[] keySet = contents.keySet().toArray();
+
+ for (int i = 0; i < contents.keySet().size(); i++) {
+ // System.out.println("Key = " + key + ", Val = " +
+ // contents.get(key));
+ listItems[i] = keySet[i] + " = " + contents.get(keySet[i]);
+ }
+
+ cellMenu = new JPopupMenu();
+ getCellContentView(CyAttributes.TYPE_SIMPLE_MAP, listItems, idField, e);
+ }
+ }
+ }
+
+ private void getCellContentView(final Byte type, final Object[] listItems, final String idField,
+ final MouseEvent e)
+ {
+ final int column = getColumnModel().getColumnIndexAtX(e.getX());
+ final int row = e.getY() / getRowHeight();
+
+ JMenu curItem = null;
+
+ String dispName;
+
+ for (final Object item : listItems) {
+ dispName = item.toString();
+
+ if (dispName.length() > 60) {
+ dispName = dispName.substring(0, 59) + " ...";
+ }
+
+ curItem = new JMenu(dispName);
+ curItem.setBackground(Color.white);
+ curItem.add(getPopupMenu());
+
+ JMenuItem openURL = new JMenuItem("Open as hyper link...");
+
+ openURL.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent e) {
+ logger.debug(item.toString());
+ OpenBrowser.openURL(item.toString());
+ }
+ });
+ curItem.add(openURL);
+
+ JMenuItem copyAll = new JMenuItem("Copy all");
+ copyAll.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent arg0) {
+ StringBuilder builder = new StringBuilder();
+
+ for (Object oneEntry : listItems) {
+ builder.append(oneEntry.toString() + "\t");
+ }
+
+ stsel = new StringSelection(builder.toString());
+ systemClipboard = Toolkit.getDefaultToolkit().getSystemClipboard();
+ systemClipboard.setContents(stsel, stsel);
+ }
+ });
+ curItem.add(copyAll);
+
+ JMenuItem copy = new JMenuItem("Copy one entry");
+ copy.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent arg0) {
+ stsel = new StringSelection(item.toString());
+ systemClipboard = Toolkit.getDefaultToolkit().getSystemClipboard();
+ systemClipboard.setContents(stsel, stsel);
+ }
+ });
+ curItem.add(copy);
+
+ if (item.toString().startsWith("http://")) {
+ curItem.getMenuComponent(1).setEnabled(true);
+ } else
+ curItem.getMenuComponent(1).setEnabled(false);
+
+ curItem.getMenuComponent(2).setEnabled(true);
+
+ if (type == CyAttributes.TYPE_SIMPLE_LIST) {
+ curItem.add(new HyperLinkOut(item.toString(), linkoutProps));
+ } else {
+ curItem.add(new HyperLinkOut(item.toString().split("=")[1], linkoutProps));
+ }
+
+ cellMenu.add(curItem);
+ }
+
+ final Border popupBorder = BorderFactory.createTitledBorder(null, idField,
+ javax.swing.border.TitledBorder.DEFAULT_JUSTIFICATION,
+ javax.swing.border.TitledBorder.DEFAULT_POSITION,
+ BORDER_FONT, Color.BLUE);
+ cellMenu.setBorder(popupBorder);
+ cellMenu.setBackground(Color.WHITE);
+ cellMenu.show(e.getComponent(), e.getX(), e.getY());
+ }
+
+ private String copyToClipBoard() {
+ final StringBuffer sbf = new StringBuffer();
+
+ /*
+ * Check to ensure we have selected only a contiguous block of cells.
+ */
+ final int numcols = this.getSelectedColumnCount();
+ final int numrows = this.getSelectedRowCount();
+
+ final int[] rowsselected = this.getSelectedRows();
+ final int[] colsselected = this.getSelectedColumns();
+
+ // Return if no cell is selected.
+ if (numcols == 0 && numrows == 0)
+ return null;
+
+ if (!((numrows - 1 == rowsselected[rowsselected.length - 1] - rowsselected[0]
+ && numrows == rowsselected.length)
+ && (numcols - 1 == colsselected[colsselected.length - 1] - colsselected[0]
+ && numcols == colsselected.length))) {
+ JOptionPane.showMessageDialog(Cytoscape.getDesktop(), "Invalid Copy Selection",
+ "Invalid Copy Selection", JOptionPane.ERROR_MESSAGE);
+
+ return null;
+ }
+
+ for (int i = 0; i < numrows; i++) {
+ for (int j = 0; j < numcols; j++) {
+ final Object cellValue = this.getValueAt(rowsselected[i], colsselected[j]);
+ final String cellText =
+ cellValue == null ? "null" :((ValidatedObjectAndEditString)cellValue).getEditString();
+ sbf.append(cellText);
+
+ if (j < (numcols - 1))
+ sbf.append("\t");
+ }
+
+ sbf.append(LS);
+ }
+
+ stsel = new StringSelection(sbf.toString());
+ systemClipboard = Toolkit.getDefaultToolkit().getSystemClipboard();
+ systemClipboard.setContents(stsel, stsel);
+
+ return sbf.toString();
+ }
+
+ private void copyToCurrentSelection() {
+ final int tableRow = this.getSelectedRow();
+ final int tableColumn = this.getSelectedColumn();
+ if (tableRow == -1 || tableColumn == -1)
+ return;
+
+ final String attribName = tableModel.getColumnName(tableColumn);
+ final String rowId = tableModel.getRowId(tableRow);
+ final CyAttributes attribs = tableModel.getCyAttributes();
+
+ // Check for copying of an empty cell:
+ if (attribs.getAttribute(rowId, attribName) == null) {
+ if (JOptionPane.showConfirmDialog(null, "Are you sure you want to copy an empty value?",
+ "Confirmation", JOptionPane.YES_NO_OPTION)
+ != JOptionPane.YES_OPTION)
+ return;
+ }
+
+ final List<GraphObject> selectedGraphObjects = tableModel.getObjects();
+ final StringBuilder errorMessage = new StringBuilder();
+ for (final GraphObject graphObject : selectedGraphObjects)
+ CyAttributesUtils.copyAttribute(attribs, rowId, graphObject.getIdentifier(),
+ attribName, /* copyEquation = */ false, errorMessage);
+ tableModel.updateColumn(attribs.getAttribute(rowId, attribName), tableColumn, tableRow);
+ }
+
+ private void copyFormulaToCurrentSelection() {
+ final int tableRow = this.getSelectedRow();
+ final int tableColumn = this.getSelectedColumn();
+ if (tableRow == -1 || tableColumn == -1)
+ return;
+
+ final String attribName = tableModel.getColumnName(tableColumn);
+ final String rowId = tableModel.getRowId(tableRow);
+ final CyAttributes attribs = tableModel.getCyAttributes();
+
+ // Check for copying of an empty cell:
+ if (attribs.getEquation(rowId, attribName) == null) {
+ if (JOptionPane.showConfirmDialog(null, "Are you sure you want to copy an empty equation?",
+ "Confirmation", JOptionPane.YES_NO_OPTION)
+ != JOptionPane.YES_OPTION)
+ return;
+ }
+
+ final List<GraphObject> selectedGraphObjects = tableModel.getObjects();
+ final StringBuilder errorMessage = new StringBuilder();
+ for (final GraphObject graphObject : selectedGraphObjects)
+ CyAttributesUtils.copyAttribute(attribs, rowId, graphObject.getIdentifier(),
+ attribName, /* copyEquation = */ true, errorMessage);
+ final Equation equation = attribs.getEquation(rowId, attribName);
+ tableModel.updateColumn(equation != null ? equation : attribs.getAttribute(rowId, attribName),
+ tableColumn, tableRow);
+ }
+
+ private void copyToEntireAttribute() {
+ final int tableRow = this.getSelectedRow();
+ final int tableColumn = this.getSelectedColumn();
+ if (tableRow == -1 || tableColumn == -1)
+ return;
+
+ final String attribName = tableModel.getColumnName(tableColumn);
+ final String rowId = tableModel.getRowId(tableRow);
+ final CyAttributes attribs = tableModel.getCyAttributes();
+
+ // Check for copying of an empty cell:
+ if (attribs.getAttribute(rowId, attribName) == null) {
+ if (JOptionPane.showConfirmDialog(null, "Are you sure you want to copy an empty value?",
+ "Confirmation", JOptionPane.YES_NO_OPTION)
+ != JOptionPane.YES_OPTION)
+ return;
+ }
+
+ final Iterable<String> ids = objectType.getAssociatedIdentifiers();
+ final StringBuilder errorMessage = new StringBuilder();
+ for (final String id : ids)
+ CyAttributesUtils.copyAttribute(attribs, rowId, id, attribName,
+ /* copyEquations = */false, errorMessage);
+
+
+ tableModel.updateColumn(attribs.getAttribute(rowId, attribName), tableColumn, tableRow);
+ }
+
+ private void copyFormulaToEntireAttribute() {
+ final int tableRow = this.getSelectedRow();
+ final int tableColumn = this.getSelectedColumn();
+ if (tableRow == -1 || tableColumn == -1)
+ return;
+
+ final String attribName = tableModel.getColumnName(tableColumn);
+ final String rowId = tableModel.getRowId(tableRow);
+ final CyAttributes attribs = tableModel.getCyAttributes();
+
+ // Check for copying of an empty cell:
+ if (attribs.getEquation(rowId, attribName) == null) {
+ if (JOptionPane.showConfirmDialog(null, "Are you sure you want to copy an empty equation?",
+ "Confirmation", JOptionPane.YES_NO_OPTION)
+ != JOptionPane.YES_OPTION)
+ return;
+ }
+
+ final Iterable<String> ids = objectType.getAssociatedIdentifiers();
+ final StringBuilder errorMessage = new StringBuilder();
+ for (final String id : ids)
+ CyAttributesUtils.copyAttribute(attribs, rowId, id, attribName,
+ /* copyEquations = */true, errorMessage);
+ final Equation equation = attribs.getEquation(rowId, attribName);
+ tableModel.updateColumn(equation != null ? equation : attribs.getAttribute(rowId, attribName),
+ tableColumn, tableRow);
+ }
+
+ private void adjustColWidth() {
+ final HashMap<String, Integer> widthMap = ColumnResizer.getColumnPreferredWidths(this);
+
+ // Save the width if it does not exist
+ Iterator<String> it = widthMap.keySet().iterator();
+ while (it.hasNext()) {
+ String key = it.next();
+
+ // make exception for the first column (ID), save it only when the table is not empty
+ if (this.getModel().getRowCount() == 0 && key.equalsIgnoreCase("ID"))
+ continue;
+
+ if (!this.columnWidthMap.containsKey(key))
+ this.columnWidthMap.put(key, widthMap.get(key));
+ }
+
+ // adjust column width
+ for (int i = 0; i < this.getColumnCount(); i++) {
+ TableColumn col = this.getColumnModel().getColumn(i);
+ if (this.columnWidthMap.containsKey(this.getColumnName(i)))
+ col.setPreferredWidth(this.columnWidthMap.get(this.getColumnName(i)).intValue());
+ }
+ }
+
+ public HashMap<String, Integer> getColumnWidthMap() {
+ return this.columnWidthMap;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void propertyChange(PropertyChangeEvent e) {
+ if (e.getPropertyName().equals(Integer.toString(Cytoscape.SESSION_OPENED)))
+ ignore = true;
+ else if (e.getPropertyName().equals(Cytoscape.CYTOSCAPE_INITIALIZED) || e.getPropertyName().equals(Cytoscape.SESSION_LOADED))
+ ignore = false;
+
+ // Ignore all signal if this flag is on.
+ if (ignore)
+ return;
+
+
+ if (e.getPropertyName().equals(AttributeBrowser.RESTORE_COLUMN)
+ && e.getNewValue() != null && e.getNewValue().equals(objectType))
+ {
+ this.adjustColWidth();
+ return;
+ }
+
+ if (e.getPropertyName().equals(AttributeBrowser.CLEAR_INTERNAL_SELECTION)) {
+ if (e.getNewValue() != null && e.getNewValue().equals(objectType)) {
+ getSelectionModel().clearSelection();
+ Cytoscape.getCurrentNetworkView().redrawGraph(false, true);
+ }
+ }
+
+ if (e.getPropertyName().equals(Cytoscape.CYTOSCAPE_INITIALIZED)) {
+ Cytoscape.getDesktop().getSwingPropertyChangeSupport().addPropertyChangeListener(this);
+ AttributeBrowser.getPropertyChangeSupport().addPropertyChangeListener(this);
+ }
+
+ if (e.getPropertyName().equals(Cytoscape.NETWORK_CREATED)
+ || e.getPropertyName().equals(Cytoscape.NETWORK_DESTROYED))
+ tableModel.setTableData();
+
+ if ((e.getPropertyName() == CytoscapeDesktop.NETWORK_VIEW_FOCUS)
+ || e.getPropertyName().equals(Cytoscape.SESSION_LOADED)
+ || e.getPropertyName().equals(Cytoscape.CYTOSCAPE_INITIALIZED)) {
+ if (currentNetwork != null)
+ currentNetwork.removeSelectEventListener(this);
+
+ // Change the target network
+ currentNetwork = Cytoscape.getCurrentNetwork();
+
+ if (currentNetwork != null) {
+ currentNetwork.addSelectEventListener(this);
+
+ if (objectType == NODES) {
+ tableModel.setTableData(new ArrayList(Cytoscape.getCurrentNetwork().getSelectedNodes()), parent.getSelectedAttributes());
+ } else if (objectType == EDGES) {
+ tableModel.setTableData(new ArrayList(Cytoscape.getCurrentNetwork().getSelectedEdges()), parent.getSelectedAttributes());
+ } else {
+ // Network Attribute
+ tableModel.setTableData(null, null);
+ adjustColWidth();
+ }
+ }
+
+ setSelectedColor(SELECTED_NODE);
+ setSelectedColor(REV_SELECTED_NODE);
+ setSelectedColor(SELECTED_EDGE);
+ setSelectedColor(REV_SELECTED_EDGE);
+ }
+
+ // If initialized, check linkout props.
+ if (e.getPropertyName().equals(Cytoscape.CYTOSCAPE_INITIALIZED)) {
+ // First, load existing property
+ Properties props = CytoscapeInit.getProperties();
+
+ // Use reflection to get resource
+ Class linkout = null;
+
+ try {
+ linkout = Class.forName("linkout.LinkOut");
+ } catch (ClassNotFoundException e1) {
+ logger.error("Could't create LinkOut class",e1);
+
+ return;
+ }
+
+ final ClassLoader cl = linkout.getClassLoader();
+
+ try {
+ props.load(cl.getResource("linkout.props").openStream());
+ } catch (IOException e1) {
+ logger.warn("Could't read linkout.props",e1);
+ }
+
+ linkoutProps = new HashMap<String, Map<String, String>>();
+
+ final String nodeLink = "nodelinkouturl";
+
+ String[] parts = null;
+
+ for (Entry<Object, Object> entry : props.entrySet()) {
+ Map<String, String> pair = null;
+
+ if (entry.getKey().toString().startsWith(nodeLink)) {
+ parts = entry.getKey().toString().split("\\.");
+
+ if (parts.length == 3) {
+ pair = linkoutProps.get(parts[1]);
+
+ if (pair == null) {
+ pair = new HashMap<String, String>();
+ linkoutProps.put(parts[1], pair);
+ }
+
+ pair.put(parts[2], entry.getValue().toString());
+ }
+ }
+ }
+ }
+ }
+
+
+ /**
+ * Will be called when node/edge selection state had been updated.
+ */
+ @Override
+ public void onSelectEvent(SelectEvent event) {
+ if(this.objectType.equals(NETWORK))
+ return;
+
+ if ((objectType == NODES)
+ && ((event.getTargetType() == SelectEvent.SINGLE_NODE) || (event.getTargetType() == SelectEvent.NODE_SET))) {
+
+ // node selection updated
+ tableModel.setSelectedColor(CyAttributeBrowserTable.SELECTED_NODE);
+ tableModel.setSelectedColor(CyAttributeBrowserTable.REV_SELECTED_NODE);
+
+ tableModel.setTableData(new ArrayList<GraphObject>(Cytoscape.getCurrentNetwork().getSelectedNodes()), parent.getSelectedAttributes());
+ } else if ((objectType == EDGES)
+ && ((event.getTargetType() == SelectEvent.SINGLE_EDGE) || (event.getTargetType() == SelectEvent.EDGE_SET))) {
+ // edge selection updated
+ tableModel.setSelectedColor(CyAttributeBrowserTable.SELECTED_EDGE);
+ tableModel.setSelectedColor(CyAttributeBrowserTable.REV_SELECTED_EDGE);
+ tableModel.setTableData(new ArrayList<GraphObject>(Cytoscape.getCurrentNetwork().getSelectedEdges()), parent.getSelectedAttributes());
+ }
+
+ this.adjustColWidth();
+
+ setSelectedColor(SELECTED_NODE);
+ setSelectedColor(REV_SELECTED_NODE);
+ setSelectedColor(SELECTED_EDGE);
+ setSelectedColor(REV_SELECTED_EDGE);
+ }
+
+
+ public void editingStopped(ChangeEvent e) {
+ super.editingStopped(e);
+ Cytoscape.getVisualMappingManager().getNetworkView().redrawGraph(false, true);
+
+ final int currentRow = getEditingRow();
+ final int currentColumn = getEditingColumn();
+
+ int nextRow, nextColumn;
+
+ final int rowCount = getRowCount();
+ if (currentRow < getRowCount() - 1) {
+ nextRow = currentRow + 1;
+ nextColumn = currentColumn;
+ } else {
+ nextRow = 0;
+
+ // First, find the location of the ID column
+ int idColumn = -1;
+ final int columnCount = getColumnCount();
+ for (int idx = 0; idx < columnCount; idx++) {
+ if (getColumnName(idx).equals(AttributeBrowser.ID)) {
+ idColumn = idx;
+ break;
+ }
+ }
+
+ nextColumn = currentColumn + 1;
+ if (nextColumn == idColumn)
+ ++nextColumn;
+ if (nextColumn == columnCount)
+ nextColumn = 0;
+ if (nextColumn == idColumn)
+ ++nextColumn;
+ }
+
+ changeSelection(nextRow, nextColumn, false, false);
+ }
+
+ public void mouseDragged(MouseEvent e) {
+ // save the column width, if user adjust column width manually
+ if (e.getSource() instanceof JTableHeader){
+ final int index = getColumnModel().getColumnIndexAtX(e.getX());
+ if (index != -1){
+ // Save the column width for the adjusted column only
+// int colWidth = getColumnModel().getColumn(index).getWidth();
+// this.columnWidthMap.put(this.getColumnName(index), new Integer(colWidth));
+
+ // Save the column widths for all the columns, 01/18/2011
+ int columnCount = getColumnModel().getColumnCount();
+ for (int i=0; i< columnCount; i++){
+ int columnWidth = getColumnModel().getColumn(i).getWidth();
+ this.columnWidthMap.put(this.getColumnName(i), new Integer(columnWidth));
+ }
+ }
+ }
+ }
+
+ public void mouseMoved(MouseEvent e) {
+
+ }
+
+ // =========================================================================================
+ // BEGIN special cell editing code...
+ //
+ public boolean editCellAt(int row, int column, EventObject e) {
+ if ((cellEditor != null) && !cellEditor.stopCellEditing()) {
+ return false;
+ }
+
+ if ((row < 0) || (row >= getRowCount()) || (column < 0) || (column >= getColumnCount())) {
+ return false;
+ }
+
+ if (!isCellEditable(row, column))
+ return false;
+
+ if (editorRemover == null) {
+ KeyboardFocusManager fm = KeyboardFocusManager.getCurrentKeyboardFocusManager();
+ editorRemover = new CellEditorRemover(fm);
+ fm.addPropertyChangeListener("permanentFocusOwner", editorRemover);
+ }
+
+ TableCellEditor editor = getCellEditor(row, column);
+
+ if ((editor != null) && editor.isCellEditable(e)) {
+
+ // Do this first so that the bounds of the JTextArea editor
+ // will be correct.
+ setEditingRow(row);
+ setEditingColumn(column);
+ setCellEditor(editor);
+ editor.addCellEditorListener(this);
+
+ editorComp = prepareEditor(editor, row, column);
+
+ if (editorComp == null) {
+ removeEditor();
+ return false;
+ }
+
+ Rectangle cellRect = getCellRect(row, column, false);
+
+ if (editor instanceof MultiLineTableCellEditor) {
+ Dimension prefSize = editorComp.getPreferredSize();
+ ((JComponent) editorComp).putClientProperty(MultiLineTableCellEditor.UPDATE_BOUNDS,
+ Boolean.TRUE);
+ editorComp.setBounds(cellRect.x, cellRect.y,
+ Math.max(cellRect.width, prefSize.width),
+ Math.max(cellRect.height, prefSize.height));
+ ((JComponent) editorComp).putClientProperty(MultiLineTableCellEditor.UPDATE_BOUNDS,
+ Boolean.FALSE);
+ } else
+ editorComp.setBounds(cellRect);
+
+ add(editorComp);
+ editorComp.validate();
+
+ return true;
+ }
+
+ return false;
+ }
+
+ protected void paintComponent(Graphics g) {
+ super.paintComponent(g);
+
+ if (isEditing()) {
+ Component component = getEditorComponent();
+ component.repaint();
+ }
+ }
+
+ public void removeNotify() {
+ KeyboardFocusManager.getCurrentKeyboardFocusManager()
+ .removePropertyChangeListener("permanentFocusOwner", editorRemover);
+ editorRemover = null;
+ super.removeNotify();
+ }
+
+ public void removeEditor() {
+ KeyboardFocusManager.getCurrentKeyboardFocusManager()
+ .removePropertyChangeListener("permanentFocusOwner", editorRemover);
+ editorRemover = null;
+
+ TableCellEditor editor = getCellEditor();
+
+ if (editor != null) {
+ editor.removeCellEditorListener(this);
+
+ Rectangle cellRect = getCellRect(editingRow, editingColumn, false);
+
+ if (editorComp != null) {
+ cellRect = cellRect.union(editorComp.getBounds());
+ remove(editorComp);
+ }
+
+ setCellEditor(null);
+ editorComp = null;
+ repaint(cellRect);
+ }
+ }
+
+ public boolean getScrollableTracksViewportHeight() {
+ if (getParent() instanceof JViewport)
+ return getParent().getHeight() > getPreferredSize().height;
+ else
+ return false;
+ }
+
+ private PropertyChangeListener editorRemover = null;
+
+ private class CellEditorRemover implements PropertyChangeListener {
+ KeyboardFocusManager focusManager;
+
+ public CellEditorRemover(KeyboardFocusManager fm) {
+ this.focusManager = fm;
+ }
+
+ public void propertyChange(PropertyChangeEvent ev) {
+ if (!isEditing() || (getClientProperty("terminateEditOnFocusLost") != Boolean.TRUE)) {
+ return;
+ }
+
+ Component c = focusManager.getPermanentFocusOwner();
+
+ while (c != null) {
+ if (c == CyAttributeBrowserTable.this) {
+ // focus remains inside the table
+ return;
+ } else if (c instanceof Window) {
+ if (c == SwingUtilities.getRoot(CyAttributeBrowserTable.this)) {
+ if (!getCellEditor().stopCellEditing()) {
+ getCellEditor().cancelCellEditing();
+ }
+ }
+
+ break;
+ }
+
+ c = c.getParent();
+ }
+ }
+ }
+
+ private static void initAttribNameToTypeMap(final DataObjectType objectType, final String columnName,
+ final Map<String, Class> attribNameToTypeMap)
+ {
+ final CyAttributes cyAttribs;
+ switch (objectType) {
+ case NODES:
+ cyAttribs = Cytoscape.getNodeAttributes();
+ break;
+ case EDGES:
+ cyAttribs = Cytoscape.getEdgeAttributes();
+ break;
+ case NETWORK:
+ cyAttribs = Cytoscape.getNetworkAttributes();
+ break;
+ default:
+ throw new IllegalStateException("unknown DataObjectType: " + objectType + "!");
+ }
+
+ Util.initAttribNameToTypeMap(cyAttribs, columnName, attribNameToTypeMap);
+ }
+
+ /**
+ * @returns the column index of the ID column or -1 if there is no ID column
+ */
+ private int getIdColumn() {
+ final int columnCount = getColumnCount();
+ for (int idx = 0; idx < columnCount; idx++) {
+ if (getColumnName(idx).equals(AttributeBrowser.ID))
+ return idx;
+ }
+
+ return -1;
+ }
+}
diff --git a/coreplugins/browser/src/main/java/browser/ui/DeletionDialog.java b/coreplugins/browser/src/main/java/browser/ui/DeletionDialog.java
new file mode 100644
index 0000000..a3839c2
--- /dev/null
+++ b/coreplugins/browser/src/main/java/browser/ui/DeletionDialog.java
@@ -0,0 +1,162 @@
+/*
+ * DeletionDialog.java
+ *
+ * Created on 2006/03/20, 10:46
+ */
+package browser.ui;
+
+import browser.DataTableModel;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.data.CyAttributes;
+
+import org.jdesktop.layout.GroupLayout;
+
+import java.awt.Frame;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import javax.swing.AbstractListModel;
+import javax.swing.JDialog;
+
+
+/**
+ *
+ * @author kono
+ */
+public class DeletionDialog extends JDialog {
+ private String[] attributes = null;
+ private String type;
+ private DataTableModel model;
+
+ /** Creates new form DeletionDialog */
+ protected DeletionDialog(Frame parent, boolean modal, String[] attributes, String type,
+ DataTableModel model) {
+ super(parent, modal);
+
+ this.type = type;
+ this.attributes = attributes;
+ this.model = model;
+
+ String title = "Delete " + type + " Attributes";
+ this.setTitle(title);
+ initComponents();
+ }
+
+ /**
+ * This method is called from within the constructor to initialize the form.
+ * WARNING: Do NOT modify this code. The content of this method is always
+ * regenerated by the Form Editor.
+ */
+
+ // <editor-fold defaultstate="collapsed" desc=" Generated Code ">
+ private void initComponents() {
+ deletionPane = new javax.swing.JScrollPane();
+ attributeList = new javax.swing.JList();
+ deleteButton = new javax.swing.JButton();
+ cancelButton = new javax.swing.JButton();
+ descriptionLabel = new javax.swing.JLabel();
+
+ setDefaultCloseOperation(javax.swing.WindowConstants.DISPOSE_ON_CLOSE);
+ attributeList.setModel(new AbstractListModel() {
+ public int getSize() {
+ return attributes.length;
+ }
+
+ public Object getElementAt(int i) {
+ return attributes[i];
+ }
+ });
+ deletionPane.setViewportView(attributeList);
+
+ deleteButton.setText("Delete");
+ deleteButton.addActionListener(new ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ deleteButtonActionPerformed(evt);
+ }
+ });
+
+ cancelButton.setText("Cancel");
+ cancelButton.addActionListener(new ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ cancelButtonActionPerformed(evt);
+ ;
+ }
+ });
+
+ descriptionLabel.setText("Please select attributes to be deleted:");
+
+ GroupLayout layout = new org.jdesktop.layout.GroupLayout(getContentPane());
+ getContentPane().setLayout(layout);
+ layout.setHorizontalGroup(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(layout.createSequentialGroup().addContainerGap()
+ .add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(org.jdesktop.layout.GroupLayout.TRAILING,
+ layout.createSequentialGroup()
+ .add(deleteButton)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(cancelButton)
+ .addContainerGap())
+ .add(org.jdesktop.layout.GroupLayout.TRAILING,
+ layout.createSequentialGroup()
+ .add(deletionPane,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 229, Short.MAX_VALUE)
+ .add(12, 12, 12))
+ .add(layout.createSequentialGroup()
+ .add(descriptionLabel)
+ .addContainerGap(26,
+ Short.MAX_VALUE)))));
+ layout.setVerticalGroup(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+ .add(org.jdesktop.layout.GroupLayout.TRAILING,
+ layout.createSequentialGroup().addContainerGap()
+ .add(descriptionLabel).add(12, 12, 12)
+ .add(deletionPane,
+ org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+ 200, Short.MAX_VALUE)
+ .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE)
+ .add(deleteButton).add(cancelButton))
+ .addContainerGap()));
+ pack();
+ } // </editor-fold>
+
+ private void deleteButtonActionPerformed(ActionEvent evt) {
+ CyAttributes attr = null;
+
+ if (type.equalsIgnoreCase("node")) {
+ attr = Cytoscape.getNodeAttributes();
+ } else if (type.equalsIgnoreCase("edge")) {
+ attr = Cytoscape.getEdgeAttributes();
+ } else {
+ attr = Cytoscape.getNetworkAttributes();
+ }
+
+ Object[] selected = attributeList.getSelectedValues();
+
+ for (int i = 0; i < selected.length; i++)
+ attr.deleteAttribute(selected[i].toString());
+
+ Cytoscape.getSwingPropertyChangeSupport()
+ .firePropertyChange(Cytoscape.ATTRIBUTES_CHANGED, null, null);
+ Cytoscape.getPropertyChangeSupport()
+ .firePropertyChange(Cytoscape.ATTRIBUTES_CHANGED, null, null);
+
+ model.setTableData();
+ dispose();
+ }
+
+ private void cancelButtonActionPerformed(ActionEvent evt) {
+ this.dispose();
+ }
+
+ // Variables declaration - do not modify
+ private javax.swing.JList attributeList;
+ private javax.swing.JButton cancelButton;
+ private javax.swing.JButton deleteButton;
+ private javax.swing.JScrollPane deletionPane;
+ private javax.swing.JLabel descriptionLabel;
+
+ // End of variables declaration
+}
diff --git a/coreplugins/browser/src/main/java/browser/ui/FormulaBuilderDialog.java b/coreplugins/browser/src/main/java/browser/ui/FormulaBuilderDialog.java
new file mode 100644
index 0000000..e647a12
--- /dev/null
+++ b/coreplugins/browser/src/main/java/browser/ui/FormulaBuilderDialog.java
@@ -0,0 +1,699 @@
+/*
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package browser.ui;
+
+
+import browser.DataObjectType;
+import browser.DataTableModel;
+
+import cytoscape.data.CyAttributes;
+import cytoscape.data.attr.MultiHashMapDefinition;
+
+import giny.model.GraphObject;
+
+import java.awt.Container;
+import java.awt.Dimension;
+import java.awt.FlowLayout;
+import java.awt.FontMetrics;
+import java.awt.Frame;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import javax.swing.BorderFactory;
+import javax.swing.JButton;
+import javax.swing.JComboBox;
+import javax.swing.JDialog;
+import javax.swing.JFrame;
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JTable;
+import javax.swing.JTextField;
+import javax.swing.SwingUtilities;
+
+import java.text.BreakIterator;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.Stack;
+
+import org.cytoscape.equations.BooleanList;
+import org.cytoscape.equations.DoubleList;
+import org.cytoscape.equations.EqnCompiler;
+import org.cytoscape.equations.EqnParser;
+import org.cytoscape.equations.Equation;
+import org.cytoscape.equations.EquationUtil;
+import org.cytoscape.equations.Function;
+import org.cytoscape.equations.LongList;
+import org.cytoscape.equations.Parser;
+import org.cytoscape.equations.StringList;
+
+import org.jdesktop.layout.GroupLayout;
+
+
+enum ApplicationDomain {
+ CURRENT_CELL("Current cell only"), // The currently selected cell in the browser.
+ CURRENT_SELECTION("Current selection"), // All entries in the browser.
+ ENTIRE_ATTRIBUTE("Entire attribute"); // All values of the current attribute.
+
+ private final String asString;
+ ApplicationDomain(final String asString) { this.asString = asString; }
+ @Override public String toString() { return asString; }
+}
+
+
+public class FormulaBuilderDialog extends JDialog {
+ private String targetAttrName;
+ private JComboBox functionComboBox = null;
+ private JLabel usageLabel = null;
+ private JTextField formulaTextField = null;
+ private JPanel argumentPanel = null;
+ private JButton addButton = null;
+ private JButton undoButton = null;
+ private JComboBox attribNamesComboBox = null;
+ private JTextField constantValuesTextField = null;
+ private JLabel applyToLabel = null;
+ private JComboBox applyToComboBox = null;
+ private JButton okButton = null;
+ private JButton cancelButton = null;
+ private Function function = null;
+ private Map<String, Function> stringToFunctionMap;
+ private Map<String, Class> attribNamesAndTypes;
+ private ArrayList<Class> leadingArgs;
+ private ApplicationDomain applicationDomain;
+ private Stack<Integer> undoStack;
+ private DataTableModel tableModel;
+ private DataObjectType tableObjectType;
+ private final JTable table;
+ private static final String FUNC_SELECTION_MESSAGE = "Please select a function...";
+
+
+ public FormulaBuilderDialog(final DataTableModel tableModel, final JTable table,
+ final DataObjectType tableObjectType, final Frame parent,
+ final Map<String, Class> attribNamesAndTypes,
+ final String targetAttrName)
+ {
+ super(parent);
+ this.setTitle("Creating a formula for: " + targetAttrName);
+
+ this.targetAttrName = targetAttrName;
+ this.stringToFunctionMap = new HashMap<String, Function>();
+ this.attribNamesAndTypes = attribNamesAndTypes;
+ this.leadingArgs = new ArrayList<Class>();
+ this.applicationDomain = ApplicationDomain.CURRENT_CELL;
+ this.tableModel = tableModel;
+ this.tableObjectType = tableObjectType;
+ this.table = table;
+ this.undoStack = new Stack<Integer>();
+
+ final Container contentPane = getContentPane();
+ final GroupLayout groupLayout = new GroupLayout(contentPane);
+ contentPane.setLayout(groupLayout);
+
+ initFunctionComboBox(contentPane);
+ initUsageLabel(contentPane);
+ initArgumentPanel(contentPane);
+ initApplyToLabel(contentPane);
+ initApplyToComboBox(contentPane);
+ initFormulaTextField(contentPane);
+ initOkButton(contentPane);
+ initCancelButton(contentPane);
+
+ setSize(614, 342);
+
+ initLayout(groupLayout);
+ setResizable(false);
+ }
+
+ private void initFunctionComboBox(final Container contentPane) {
+ functionComboBox = new JComboBox();
+ final Dimension desiredWidthAndHeight = new Dimension(600, 30);
+ functionComboBox.setPreferredSize(desiredWidthAndHeight);
+ contentPane.add(functionComboBox);
+ functionComboBox.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent arg0) {
+ functionSelected();
+ }
+ });
+
+ final EqnParser parser = Parser.getParser();
+ final Set<Function> functions = parser.getRegisteredFunctions();
+ final String[] functionNames = new String[functions.size()];
+ int index = 0;
+ for (final Function function : functions) {
+ functionNames[index] = function.getName() + ": " + function.getFunctionSummary();
+ stringToFunctionMap.put(functionNames[index], function);
+ ++index;
+ }
+
+ Arrays.sort(functionNames);
+
+ final Class requestedReturnType = getAttributeType(targetAttrName);
+ functionComboBox.addItem(FUNC_SELECTION_MESSAGE);
+ for (final String functionName : functionNames) {
+ if (returnTypeIsCompatible(requestedReturnType, stringToFunctionMap.get(functionName).getReturnType()))
+ functionComboBox.addItem(functionName);
+ }
+
+ functionComboBox.setEditable(false);
+ functionComboBox.setSelectedIndex(0);
+ }
+
+ /**
+ * @returns the type of the attribute "attribName" translated into the language of attribute equations or null
+ */
+ private Class getAttributeType(final String attribName) {
+ final byte type = tableObjectType.getAssociatedAttributes().getType(attribName);
+ switch (type) {
+ case CyAttributes.TYPE_BOOLEAN:
+ return Boolean.class;
+ case CyAttributes.TYPE_FLOATING:
+ return Double.class;
+ case CyAttributes.TYPE_INTEGER:
+ return Long.class;
+ case CyAttributes.TYPE_STRING:
+ return String.class;
+ case CyAttributes.TYPE_SIMPLE_LIST:
+ return List.class;
+ default:
+ return null;
+ }
+ }
+
+ private boolean returnTypeIsCompatible(final Class requiredType, final Class returnType) {
+ if (returnType == requiredType)
+ return true;
+
+ if (requiredType == String.class)
+ return true;
+
+ if (requiredType == Boolean.class
+ && (returnType == Double.class || returnType == Long.class || returnType == Object.class))
+ return true;
+
+ if (requiredType == Double.class
+ && (returnType == Long.class || returnType == Boolean.class || returnType == String.class || returnType == Object.class))
+ return true;
+
+ if (requiredType == Long.class
+ && (returnType == Double.class || returnType == Boolean.class || returnType == String.class || returnType == Object.class))
+ return true;
+
+ if (requiredType == List.class
+ && (returnType == DoubleList.class || returnType == BooleanList.class
+ || returnType == LongList.class || returnType == StringList.class))
+ return true;
+
+ return false;
+ }
+
+ private void initUsageLabel(final Container contentPane) {
+ usageLabel = new JLabel();
+ contentPane.add(usageLabel);
+ if (function != null)
+ wrapLabelText(usageLabel, function.getUsageDescription());
+ }
+
+ private void initFormulaTextField(final Container contentPane) {
+ formulaTextField = new JTextField(50);
+ formulaTextField.setPreferredSize(new Dimension(600, 120));
+ contentPane.add(formulaTextField);
+ formulaTextField.setEditable(false);
+ if (function != null)
+ formulaTextField.setText("=" + function.getName() + "(");
+ }
+
+ private void initArgumentPanel(final Container contentPane) {
+ argumentPanel = new JPanel();
+ contentPane.add(argumentPanel);
+ argumentPanel.setBorder(BorderFactory.createTitledBorder("Next Argument"));
+
+ attribNamesComboBox = new JComboBox();
+ attribNamesComboBox.setPreferredSize(new Dimension(160, 30));
+ argumentPanel.add(attribNamesComboBox);
+ attribNamesComboBox.setEnabled(false);
+
+ final JLabel orLabel = new JLabel();
+ orLabel.setText("or");
+ argumentPanel.add(orLabel);
+
+ constantValuesTextField = new JTextField(15);
+ argumentPanel.add(constantValuesTextField);
+ constantValuesTextField.setEnabled(false);
+
+ addButton = new JButton("Add");
+ addButton.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ final int oldLength = formulaTextField.getText().length();
+ if (addNewArg()) {
+ undoStack.push(oldLength);
+ undoButton.setEnabled(true);
+ updateButtonsAndArgumentDropdown();
+ }
+ }
+ });
+ argumentPanel.add(addButton);
+ addButton.setEnabled(false);
+
+ undoButton = new JButton("Undo");
+ undoButton.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ final String formula = formulaTextField.getText();
+ final int previousLength = undoStack.pop();
+ formulaTextField.setText(formula.substring(0, previousLength));
+ addButton.setEnabled(true);
+ leadingArgs.remove(leadingArgs.size() - 1);
+ if (undoStack.empty())
+ undoButton.setEnabled(false);
+ updateButtonsAndArgumentDropdown();
+ }
+ });
+ argumentPanel.add(undoButton);
+ undoButton.setEnabled(false);
+ }
+
+ private void initApplyToLabel(final Container contentPane) {
+ applyToLabel = new JLabel("Apply to: ");
+ contentPane.add(applyToLabel);
+ }
+
+ private void initApplyToComboBox(final Container contentPane) {
+ applyToComboBox = new JComboBox();
+
+ final int selectedCellRow = table.getSelectedRow();
+ if (selectedCellRow >= 0)
+ applyToComboBox.addItem(ApplicationDomain.CURRENT_CELL);
+ final List<GraphObject> selectedGraphObjects = tableModel.getObjects();
+ if (selectedGraphObjects != null && !selectedGraphObjects.isEmpty())
+ applyToComboBox.addItem(ApplicationDomain.CURRENT_SELECTION);
+ applyToComboBox.addItem(ApplicationDomain.ENTIRE_ATTRIBUTE);
+
+ final Dimension widthAndHeight = applyToComboBox.getPreferredSize();
+ final Dimension desiredWidthAndHeight = new Dimension(180, 30);
+ applyToComboBox.setPreferredSize(desiredWidthAndHeight);
+ applyToComboBox.setMinimumSize(desiredWidthAndHeight);
+ applyToComboBox.setSize(desiredWidthAndHeight);
+ applyToComboBox.setMaximumSize(desiredWidthAndHeight);
+
+ contentPane.add(applyToComboBox);
+ applyToComboBox.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent arg0) {
+ applicationDomain = (ApplicationDomain)applyToComboBox.getSelectedItem();
+ }
+ });
+ applyToComboBox.setEditable(false);
+ applyToComboBox.setEnabled(false);
+ }
+
+ /**
+ * Tests whether "expression" is valid given the possible argument types are "validArgTypes".
+ * @returns null, if "expression" is invalid, or, the type of "expression" if it was valid
+ */
+ private Class expressionIsValid(final List<Class> validArgTypes, final String expression) {
+ final EqnParser parser = Parser.getParser();
+ if (!parser.parse("=" + expression, attribNamesAndTypes)) {
+ displayErrorMessage(parser.getErrorMsg());
+ return null;
+ }
+
+ final Class expressionType = parser.getType();
+ if (validArgTypes.contains(expressionType))
+ return expressionType;
+
+ final StringBuilder errorMessage = new StringBuilder("Expression is of an incompatible data type (");
+ errorMessage.append(getLastDotComponent(expressionType.toString()));
+ errorMessage.append(") valid types are: ");
+ for (int i = 0; i < validArgTypes.size(); ++i) {
+ if (validArgTypes.get(i) == null)
+ continue;
+
+ errorMessage.append(getLastDotComponent(validArgTypes.get(i).toString()));
+ if (i < validArgTypes.size() - 1)
+ errorMessage.append(',');
+ }
+ displayErrorMessage(errorMessage.toString());
+
+ return null;
+ }
+
+ /**
+ * Assumes that "s" consists of components separated by dots.
+ * @returns the last component of "s" or all of "s" if there are no dots
+ */
+ private static String getLastDotComponent(final String s) {
+ final int lastDotPos = s.lastIndexOf('.');
+ if (lastDotPos == -1)
+ return s;
+
+ return s.substring(lastDotPos + 1);
+ }
+
+ /**
+ * Fills the attribute names combox box with the subset of valid (as in potential current function
+ * arguments) attribute names.
+ */
+ private void updateAttribNamesComboBox() {
+ if (function == null)
+ return;
+
+ attribNamesComboBox.removeAllItems();
+ final List<Class> possibleArgTypes = getPossibleNextArgumentTypes();
+ final ArrayList<String> possibleAttribNames = new ArrayList<String>(20);
+ for (final String attribName : attribNamesAndTypes.keySet()) {
+ final Class attribType = attribNamesAndTypes.get(attribName);
+ if (isTypeCompatible(possibleArgTypes, attribType))
+ possibleAttribNames.add(attribName);
+ }
+
+ Collections.sort(possibleAttribNames);
+
+ for (final String attribName : possibleAttribNames)
+ attribNamesComboBox.addItem(attribName);
+ }
+
+ /**
+ * @returns the set of allowed types for the next argument or null if no additional argument is valid
+ */
+ private List<Class> getPossibleNextArgumentTypes() {
+ final Class[] leadingArgsAsArray = new Class[leadingArgs.size()];
+ leadingArgs.toArray(leadingArgsAsArray);
+ return function.getPossibleArgTypes(leadingArgsAsArray);
+ }
+
+ private boolean isTypeCompatible(final List<Class> allowedArgumentTypes, final Class attribType) {
+ if (allowedArgumentTypes == null)
+ return false;
+ if (allowedArgumentTypes.contains(Object.class))
+ return true;
+ return allowedArgumentTypes.contains(attribType);
+ }
+
+ private void initOkButton(final Container contentPane) {
+ okButton = new JButton("Ok");
+ contentPane.add(okButton);
+ okButton.setEnabled(false);
+ okButton.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ final StringBuilder errorMessage = new StringBuilder(30);
+ if (updateCells(errorMessage))
+ dispose();
+ else
+ displayErrorMessage(errorMessage.toString());
+ }
+ });
+ }
+
+ /**
+ * Updates the appearance and status of various GUI components based on what is currently in the formula field.
+ */
+ private void updateButtonsAndArgumentDropdown() {
+ final List<Class> possibleNextArgTypes = getPossibleNextArgumentTypes();
+ if (possibleNextArgTypes == null) {
+ final String currentFormula = formulaTextField.getText();
+ formulaTextField.setText(currentFormula + ")");
+
+ addButton.setEnabled(false);
+ okButton.setEnabled(true);
+ } else if (possibleNextArgTypes.contains(null))
+ okButton.setEnabled(true);
+ else {
+ addButton.setEnabled(true);
+ okButton.setEnabled(false);
+ }
+
+ updateAttribNamesComboBox();
+ }
+
+ /**
+ * Attempts to add a new argument.
+ * @return if we succeeded in adding the new argument
+ */
+ private boolean addNewArg() {
+ boolean successFullyAddedANewArg = false;
+
+ final StringBuilder formula = new StringBuilder(formulaTextField.getText());
+
+ if (!leadingArgs.isEmpty()) // Not the first argument => we need a comma!
+ formula.append(',');
+
+ final String constExpr = constantValuesTextField.getText();
+ if (constExpr != null && constExpr.length() > 0) {
+ final List<Class> possibleArgTypes = getPossibleNextArgumentTypes();
+ final Class exprType;
+ if ((exprType = expressionIsValid(possibleArgTypes, constExpr)) == null)
+ return false;
+
+ formula.append(constExpr);
+ constantValuesTextField.setText("");
+ leadingArgs.add(exprType);
+ successFullyAddedANewArg = true;
+ } else {
+ final String attribName = (String)attribNamesComboBox.getSelectedItem();
+ if (attribName != null) {
+ formula.append(EquationUtil.attribNameAsReference(attribName));
+ leadingArgs.add(attribNamesAndTypes.get(attribName));
+ successFullyAddedANewArg = true;
+ }
+ }
+
+ if (successFullyAddedANewArg) {
+ formulaTextField.setText(formula.toString());
+ return true;
+ } else
+ return false;
+ }
+
+ private boolean updateCells(final StringBuilder errorMessage) {
+ String formula = formulaTextField.getText();
+ if (formula.charAt(formula.length() - 1) != ')')
+ formula = formula + ")";
+
+ final int cellColum = table.getSelectedColumn();
+ final String attribName = tableModel.getColumnName(cellColum);
+ final CyAttributes attribs = tableModel.getCyAttributes();
+
+ final Equation equation = compileEquation(attribs, attribName, formula, errorMessage);
+ if (equation == null)
+ return false;
+
+ switch (applicationDomain) {
+ case CURRENT_CELL:
+ final int cellRow = table.getSelectedRow();
+ tableModel.setValueAt(formula, cellRow, cellColum);
+ break;
+ case CURRENT_SELECTION:
+ final List<GraphObject> selectedGraphObjects = tableModel.getObjects();
+ for (final GraphObject graphObject : selectedGraphObjects) {
+ if (!setAttribute(attribs, graphObject.getIdentifier(), attribName,
+ equation, errorMessage))
+ return false;
+ }
+ tableModel.updateColumn(equation, cellColum, /* skipRowIdx = */-1);
+ break;
+ case ENTIRE_ATTRIBUTE:
+ final Iterable<String> ids = tableObjectType.getAssociatedIdentifiers();
+ for (final String id : ids) {
+ if (!setAttribute(attribs, id, attribName, equation, errorMessage))
+ return false;
+ }
+ tableModel.updateColumn(equation, cellColum, /* skipRowIdx = */-1);
+ break;
+ default:
+ throw new IllegalStateException("unknown application domain: "
+ + applicationDomain + "!");
+ }
+
+ return true;
+ }
+
+ /**
+ * @returns the compiled equation upon success or null if an error occurred
+ */
+ private Equation compileEquation(final CyAttributes attribs, final String attribName,
+ final String formula, final StringBuilder errorMessage)
+ {
+ final Map<String, Class> attribNameToTypeMap = new HashMap<String, Class>();
+ initAttribNameToTypeMap(attribs, attribName, attribNameToTypeMap);
+ final EqnCompiler compiler = new EqnCompiler();
+ if (compiler.compile(formula, attribNameToTypeMap))
+ return compiler.getEquation();
+
+ errorMessage.append(compiler.getLastErrorMsg());
+ return null;
+ }
+
+ /**
+ * @returns true if the attribute value has been successfully updated, else false
+ */
+ private boolean setAttribute(final CyAttributes attribs, final String id,
+ final String attribName, final Equation newValue,
+ final StringBuilder errorMessage)
+ {
+ try {
+ attribs.setAttribute(id, attribName, newValue);
+ return true;
+ } catch (final Exception e) {
+ errorMessage.append(e.getMessage());
+ return false;
+ }
+ }
+
+ private void initCancelButton(final Container contentPane) {
+ cancelButton = new JButton("Cancel");
+ contentPane.add(okButton);
+ cancelButton.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ dispose();
+ }
+ });
+ }
+
+ private void functionSelected() {
+ final String funcName = (String)functionComboBox.getSelectedItem();
+ if (funcName == null || formulaTextField == null || usageLabel == null
+ || funcName.equals(FUNC_SELECTION_MESSAGE))
+ return;
+
+ functionComboBox.removeItem(FUNC_SELECTION_MESSAGE);
+
+ attribNamesComboBox.setEnabled(true);
+ constantValuesTextField.setEnabled(true);
+ applyToComboBox.setEnabled(true);
+
+ leadingArgs.clear();
+ function = stringToFunctionMap.get(funcName);
+ final boolean zeroArgumentFunction = getPossibleNextArgumentTypes() == null;
+ formulaTextField.setText("=" + function.getName() + (zeroArgumentFunction ? "()" : "("));
+ wrapLabelText(usageLabel, function.getUsageDescription());
+ updateAttribNamesComboBox();
+ addButton.setEnabled(zeroArgumentFunction ? false : true);
+ okButton.setEnabled(zeroArgumentFunction);
+ }
+
+ private void initLayout(final GroupLayout groupLayout) {
+ // 1. vertical layout
+ groupLayout.setVerticalGroup(groupLayout.createSequentialGroup()
+ .add(functionComboBox, GroupLayout.PREFERRED_SIZE, GroupLayout.DEFAULT_SIZE, GroupLayout.PREFERRED_SIZE)
+ .add(usageLabel, GroupLayout.PREFERRED_SIZE, GroupLayout.DEFAULT_SIZE, GroupLayout.PREFERRED_SIZE)
+ .add(argumentPanel, GroupLayout.PREFERRED_SIZE, GroupLayout.DEFAULT_SIZE, GroupLayout.PREFERRED_SIZE)
+ .add(formulaTextField, GroupLayout.PREFERRED_SIZE, GroupLayout.DEFAULT_SIZE, GroupLayout.PREFERRED_SIZE)
+ .add(groupLayout.createParallelGroup(GroupLayout.BASELINE)
+ .add(applyToLabel, GroupLayout.PREFERRED_SIZE, GroupLayout.DEFAULT_SIZE, GroupLayout.PREFERRED_SIZE)
+ .add(applyToComboBox, GroupLayout.PREFERRED_SIZE, GroupLayout.DEFAULT_SIZE, GroupLayout.PREFERRED_SIZE))
+ .add(groupLayout.createParallelGroup(GroupLayout.BASELINE)
+ .add(okButton, GroupLayout.PREFERRED_SIZE, GroupLayout.DEFAULT_SIZE, GroupLayout.PREFERRED_SIZE)
+ .add(cancelButton, GroupLayout.PREFERRED_SIZE, GroupLayout.DEFAULT_SIZE, GroupLayout.PREFERRED_SIZE)));
+
+ // 2. horizontal layout
+ groupLayout.setHorizontalGroup(groupLayout.createParallelGroup(GroupLayout.CENTER)
+ .add(functionComboBox, GroupLayout.PREFERRED_SIZE, GroupLayout.DEFAULT_SIZE, GroupLayout.PREFERRED_SIZE)
+ .add(usageLabel, GroupLayout.PREFERRED_SIZE, GroupLayout.DEFAULT_SIZE, GroupLayout.PREFERRED_SIZE)
+ .add(argumentPanel, GroupLayout.PREFERRED_SIZE, GroupLayout.DEFAULT_SIZE, GroupLayout.PREFERRED_SIZE)
+ .add(groupLayout.createSequentialGroup()
+ .add(applyToLabel, GroupLayout.PREFERRED_SIZE, GroupLayout.DEFAULT_SIZE, GroupLayout.PREFERRED_SIZE)
+ .add(applyToComboBox, GroupLayout.PREFERRED_SIZE, GroupLayout.DEFAULT_SIZE, GroupLayout.PREFERRED_SIZE))
+ .add(formulaTextField, GroupLayout.PREFERRED_SIZE, GroupLayout.DEFAULT_SIZE, GroupLayout.PREFERRED_SIZE)
+ .add(groupLayout.createSequentialGroup()
+ .add(okButton, GroupLayout.PREFERRED_SIZE, GroupLayout.DEFAULT_SIZE, GroupLayout.PREFERRED_SIZE)
+ .add(cancelButton, GroupLayout.PREFERRED_SIZE, GroupLayout.DEFAULT_SIZE, GroupLayout.PREFERRED_SIZE)));
+ }
+
+ private static void displayErrorMessage(final String errorMessage) {
+ JOptionPane.showMessageDialog(new JFrame(), errorMessage, "Error",
+ JOptionPane.ERROR_MESSAGE);
+ }
+
+ /**
+ * Populates "attribNameToTypeMap" with the names from "cyAttribs" and their types as mapped
+ * to the types used by attribute equations. Types (and associated names) not used by
+ * attribute equations are ommitted.
+ *
+ * @param cyAttribs the attributes to map
+ * @param ignore if not null, skip the attribute with this name
+ * @param attribNameToTypeMap the result of the translation from attribute types to
+ * attribute equation types
+ */
+ private static void initAttribNameToTypeMap(final CyAttributes cyAttribs, final String ignore,
+ final Map<String, Class> attribNameToTypeMap)
+ {
+ for (final String attribName : cyAttribs.getAttributeNames()) {
+ if (ignore == null || ignore.equals(attribName))
+ continue;
+ if (!cyAttribs.getUserVisible(attribName))
+ continue;
+
+ final byte type = cyAttribs.getType(attribName);
+ if (type == CyAttributes.TYPE_BOOLEAN)
+ attribNameToTypeMap.put(attribName, Boolean.class);
+ else if (type == CyAttributes.TYPE_INTEGER)
+ attribNameToTypeMap.put(attribName, Long.class);
+ else if (type == CyAttributes.TYPE_FLOATING)
+ attribNameToTypeMap.put(attribName, Double.class);
+ else if (type == CyAttributes.TYPE_STRING)
+ attribNameToTypeMap.put(attribName, String.class);
+ else if (type == CyAttributes.TYPE_SIMPLE_LIST)
+ attribNameToTypeMap.put(attribName, List.class);
+ else
+ /* We intentionally ignore everything else! */;
+ }
+ }
+
+ private void wrapLabelText(final JLabel label, final String text) {
+ final FontMetrics fm = label.getFontMetrics(label.getFont());
+ final Container container = label.getParent();
+ final int containerWidth = container.getWidth();
+
+ final BreakIterator boundary = BreakIterator.getWordInstance();
+ boundary.setText(text);
+
+ final StringBuilder trial = new StringBuilder();
+ final StringBuilder real = new StringBuilder("<html>");
+
+ int start = boundary.first();
+ for (int end = boundary.next(); end != BreakIterator.DONE; start = end, end = boundary.next()) {
+ final String word = text.substring(start, end);
+ trial.append(word);
+ int trialWidth = SwingUtilities.computeStringWidth(fm, trial.toString());
+ if (trialWidth > containerWidth) {
+ trial.setLength(0);
+ trial.append(word);
+ real.append("<br>");
+ }
+ real.append(word);
+ }
+
+ real.append("</html>");
+
+ label.setText(real.toString());
+ }
+}
diff --git a/coreplugins/browser/src/main/java/browser/ui/ModDialog.java b/coreplugins/browser/src/main/java/browser/ui/ModDialog.java
new file mode 100644
index 0000000..285d775
--- /dev/null
+++ b/coreplugins/browser/src/main/java/browser/ui/ModDialog.java
@@ -0,0 +1,90 @@
+/*
+ Copyright (c) 2006, 2007, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package browser.ui;
+
+import java.awt.Dimension;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.Frame;
+
+import javax.swing.JButton;
+import javax.swing.JDialog;
+
+import browser.DataObjectType;
+import browser.DataTableModel;
+
+
+public class ModDialog extends JDialog {
+ public JButton okButton;
+
+ /**
+ * Creates a new AttrSelectModPanel object.
+ *
+ * @param dataTable DOCUMENT ME!
+ * @param data DOCUMENT ME!
+ * @param tableModel DOCUMENT ME!
+ * @param tableObjectType DOCUMENT ME!
+ */
+ public ModDialog(final DataTableModel tableModel, final DataObjectType tableObjectType,
+ final Frame parent)
+ {
+ super(parent);
+ final ModPanel modPanel = new ModPanel(tableModel, tableObjectType);
+ this.setTitle(tableObjectType.getDisplayName() + " Attribute Batch Editor");
+ this.setAlwaysOnTop(true);
+
+ setLayout(new GridBagLayout());
+
+ okButton = new JButton("OK");
+ okButton.setPreferredSize(new Dimension(70, 20));
+
+ GridBagConstraints gridBagConstraints = new GridBagConstraints();
+
+ gridBagConstraints = new GridBagConstraints();
+ gridBagConstraints.gridx = 0;
+ gridBagConstraints.gridy = 0;
+ gridBagConstraints.fill = GridBagConstraints.BOTH;
+ gridBagConstraints.weightx = 1.0;
+ gridBagConstraints.weighty = 1.0;
+ gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
+ add(modPanel, gridBagConstraints);
+
+
+ pack();
+ this.setModal(false);
+
+ okButton.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ dispose();
+ }
+ });
+ }
+}
diff --git a/coreplugins/browser/src/main/java/browser/ui/ModPanel.java b/coreplugins/browser/src/main/java/browser/ui/ModPanel.java
new file mode 100644
index 0000000..0de7281
--- /dev/null
+++ b/coreplugins/browser/src/main/java/browser/ui/ModPanel.java
@@ -0,0 +1,408 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package browser.ui;
+
+import java.awt.Dimension;
+import java.awt.GridBagLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.util.Arrays;
+import java.util.List;
+import java.util.TreeSet;
+import java.util.Set;
+
+import javax.swing.JButton;
+import javax.swing.JComboBox;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JTabbedPane;
+import javax.swing.JTextField;
+
+import browser.AttributeModel;
+import browser.DataObjectType;
+import browser.DataTableModel;
+import browser.MultiDataEditAction;
+import cytoscape.Cytoscape;
+import cytoscape.data.CyAttributes;
+
+
+/**
+ *
+ */
+public class ModPanel extends JPanel implements ActionListener {
+ // Backend data objects
+ private CyAttributes data;
+ private DataTableModel tableModel;
+ private DataObjectType objectType;
+
+ private CyAttributes attrData;
+ private byte currentAttributeCopyToType = CyAttributes.TYPE_UNDEFINED;
+ private final AttributeModel defaultAttrModel;
+
+ // Set/Modify
+ JComboBox attributeModifyBox;
+ JTextField field1;
+ JTextField field2;
+ JComboBox actionBox;
+ JButton applyModify;
+ JLabel between;
+ JLabel field2Label;
+
+ // Copy
+ JComboBox attributeCopyFromBox;
+ JComboBox attributeCopyToBox;
+ JButton copyGo;
+
+ // Delete
+ JComboBox attributeClearBox;
+ JButton clearGo;
+
+ /**
+ * Creates a new ModPanel object.
+ *
+ * @param data DOCUMENT ME!
+ * @param tableModel DOCUMENT ME!
+ * @param graphObjectType DOCUMENT ME!
+ */
+ public ModPanel(final DataTableModel tableModel, final DataObjectType graphObjectType) {
+ // get proper Global CytoscapeData object
+ this.attrData = graphObjectType.getAssociatedAttributes();
+
+ this.data = graphObjectType.getAssociatedAttributes();
+ this.tableModel = tableModel;
+ this.objectType = graphObjectType;
+
+ this.defaultAttrModel = new AttributeModel(this.data, null);
+
+ setLayout(new GridBagLayout());
+
+ java.awt.GridBagConstraints gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.weightx = 1.0;
+
+ gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
+
+ JTabbedPane tabs = new JTabbedPane();
+ add(tabs, gridBagConstraints);
+
+ // create Operation panel
+ JPanel operation = new JPanel();
+ operation.setLayout(new java.awt.GridBagLayout());
+
+ tabs.add("Operation", operation);
+ attributeModifyBox = createAttributeBox();
+ attributeModifyBox.setEditable(false);
+
+ if (attributeModifyBox.getItemCount() != 0) {
+ attributeModifyBox.setSelectedIndex(0);
+ }
+
+ attributeModifyBox.setToolTipText("Select attribute name.");
+
+ field1 = new JTextField(18);
+ field2 = new JTextField(18);
+ field2.setVisible(false);
+
+ actionBox = new JComboBox();
+ actionBox.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent arg0) {
+ actionChanged();
+ }
+ });
+
+ for (ActionName action : ActionName.values()) {
+ if ((action.equals(ActionName.COPY) == false)
+ && (action.equals(ActionName.CLEAR) == false)) {
+ actionBox.addItem(action.getDisplayName());
+ }
+ }
+
+ actionBox.setEditable(false);
+
+ if (actionBox.getItemCount() != 0) {
+ actionBox.setSelectedIndex(0);
+ }
+
+ applyModify = new JButton("GO");
+
+ applyModify.addActionListener(this);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 0;
+ gridBagConstraints.gridy = 0;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.weightx = 0.1;
+ gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
+
+ operation.add(actionBox, gridBagConstraints);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 1;
+ gridBagConstraints.gridy = 0;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.weightx = 0.2;
+ gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
+
+ operation.add(attributeModifyBox, gridBagConstraints);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 2;
+ gridBagConstraints.gridy = 0;
+ gridBagConstraints.insets = new java.awt.Insets(10, 0, 10, 0);
+ between = new JLabel("by/to");
+ operation.add(between, gridBagConstraints);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 4;
+ gridBagConstraints.gridy = 0;
+ gridBagConstraints.insets = new java.awt.Insets(10, 0, 10, 0);
+ field2Label = new JLabel("to");
+ operation.add(field2Label, gridBagConstraints);
+ field2Label.setVisible(false);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 3;
+ gridBagConstraints.gridy = 0;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.weightx = 0.5;
+ gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
+
+ operation.add(field1, gridBagConstraints);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 5;
+ gridBagConstraints.gridy = 0;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.weightx = 0.5;
+ gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
+
+ operation.add(field2, gridBagConstraints);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 6;
+ gridBagConstraints.gridy = 0;
+ gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
+
+ operation.add(applyModify, gridBagConstraints);
+
+ // create Copy Panel
+ JPanel copy = new JPanel(new java.awt.GridBagLayout());
+ tabs.add("Copy", copy);
+ attributeCopyFromBox = createAttributeBox();
+ attributeCopyFromBox.addActionListener(this);
+ attributeCopyToBox = createAttributeBox();
+ attributeCopyToBox.setEditable(true);
+ copyGo = new JButton("GO");
+
+ copyGo.addActionListener(this);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 0;
+ gridBagConstraints.gridy = 0;
+ gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
+
+ copy.add(new JLabel("Copy From:"), gridBagConstraints);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 1;
+ gridBagConstraints.gridy = 0;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.weightx = 0.5;
+
+ copy.add(attributeCopyFromBox, gridBagConstraints);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 2;
+ gridBagConstraints.gridy = 0;
+ gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
+
+ copy.add(new JLabel("To:"), gridBagConstraints);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 3;
+ gridBagConstraints.gridy = 0;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.weightx = 0.5;
+ gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
+
+ copy.add(attributeCopyToBox, gridBagConstraints);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 4;
+ gridBagConstraints.gridy = 0;
+ gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
+
+ copy.add(copyGo, gridBagConstraints);
+
+ // create Delete Panel
+ JPanel clear = new JPanel(new java.awt.GridBagLayout());
+ tabs.add("Clear", clear);
+ attributeClearBox = createAttributeBox();
+ clearGo = new JButton("GO");
+
+ clearGo.addActionListener(this);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 0;
+ gridBagConstraints.gridy = 0;
+ gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
+
+ clear.add(new JLabel("Clear"), gridBagConstraints);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 1;
+ gridBagConstraints.gridy = 0;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.weightx = 1.0;
+ gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
+
+ clear.add(attributeClearBox, gridBagConstraints);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 2;
+ gridBagConstraints.gridy = 0;
+ gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
+
+ clear.add(clearGo, gridBagConstraints);
+ }
+
+ protected void actionChanged() {
+ final ActionName action = ActionName.getValueOf(actionBox.getSelectedItem().toString());
+
+ if (between == null)
+ return;
+
+ if (action.equals(ActionName.REPLACE)) {
+ between.setText("From: ");
+ field2Label.setVisible(true);
+ field2.setVisible(true);
+ field1.setVisible(true);
+ } else if (action.equals(ActionName.TO_LOWER) || action.equals(ActionName.TO_UPPER)) {
+ between.setText("Convert to upper/lower case ");
+ field2Label.setVisible(false);
+ field1.setVisible(false);
+ field2.setVisible(false);
+ } else if (action.equals(ActionName.REMOVE)) {
+ between.setText("Pattern: ");
+ field2Label.setVisible(false);
+ field1.setVisible(true);
+ field2.setVisible(false);
+ } else if (action.equals(ActionName.MUL) || action.equals(ActionName.DIV)) {
+ between.setText("by ");
+ field1.setVisible(true);
+ field2Label.setVisible(false);
+ field2.setVisible(false);
+ } else {
+ between.setText("to ");
+ field1.setVisible(true);
+ field2Label.setVisible(false);
+ field2.setVisible(false);
+ }
+ }
+
+ private JComboBox createAttributeBox() {
+ JComboBox box = new JComboBox(defaultAttrModel);
+ Dimension newSize = new Dimension(100, (int) box.getPreferredSize().getHeight());
+ box.setMaximumSize(newSize);
+ box.setPreferredSize(newSize);
+
+ return box;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ final MultiDataEditAction edit;
+
+ //
+ // Operations
+ //
+
+ // 1. Set, Add, Mul and Div operations
+ if (e.getSource() == applyModify) {
+ String input = field1.getText();
+
+ if (ActionName.getValueOf(actionBox.getSelectedItem().toString())
+ .equals(ActionName.REPLACE)) {
+ input = field1.getText() + "\t" + field2.getText();
+ }
+
+ edit = new MultiDataEditAction(input,
+ ActionName.getValueOf(actionBox.getSelectedItem()
+ .toString()),
+ tableModel.getObjects(),
+ (String) attributeModifyBox.getSelectedItem(), null,
+ null, objectType, tableModel);
+ }
+ // 2. Copy operation
+ else if (e.getSource() == copyGo) {
+ edit = new MultiDataEditAction(null, ActionName.COPY, tableModel.getObjects(),
+ (String) attributeCopyToBox.getSelectedItem(),
+ (String) attributeCopyFromBox.getSelectedItem(), null,
+ objectType, tableModel);
+ }
+ // 3. The copy source combobox fired an event
+ else if (e.getSource() == attributeCopyFromBox) {
+ final String selectedItem = (String)attributeCopyFromBox.getSelectedItem();
+ if (selectedItem != null) {
+ final byte fromType = attrData.getType(selectedItem);
+ if (fromType != currentAttributeCopyToType) {
+ final Set<Byte> attrTypes = new TreeSet<Byte>();
+ attrTypes.add(fromType);
+ if (fromType == CyAttributes.TYPE_INTEGER) // Allow copying from int to float.
+ attrTypes.add(CyAttributes.TYPE_FLOATING);
+ attributeCopyToBox.setModel(new AttributeModel(data, null, attrTypes));
+ }
+ }
+ return;
+ }
+ // 4. Delete (Clear?) operation
+ else {
+ edit = new MultiDataEditAction(null, ActionName.CLEAR, tableModel.getObjects(),
+ (String) attributeClearBox.getSelectedItem(), null,
+ null, objectType, tableModel);
+ }
+
+ cytoscape.util.undo.CyUndo.getUndoableEditSupport().postEdit(edit);
+
+ Cytoscape.getSwingPropertyChangeSupport().firePropertyChange(Cytoscape.ATTRIBUTES_CHANGED, null, null);
+ Cytoscape.getPropertyChangeSupport().firePropertyChange(Cytoscape.ATTRIBUTES_CHANGED, null, null);
+
+ }
+}
+
diff --git a/coreplugins/browser/src/main/java/browser/ui/MultiLineTableCellEditor.java b/coreplugins/browser/src/main/java/browser/ui/MultiLineTableCellEditor.java
new file mode 100644
index 0000000..87e3edb
--- /dev/null
+++ b/coreplugins/browser/src/main/java/browser/ui/MultiLineTableCellEditor.java
@@ -0,0 +1,194 @@
+package browser.ui;
+
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Dimension;
+import java.awt.Rectangle;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.InputEvent;
+import java.awt.event.KeyEvent;
+import java.awt.event.KeyListener;
+import java.awt.event.MouseEvent;
+
+import javax.swing.AbstractCellEditor;
+import javax.swing.Action;
+import javax.swing.BorderFactory;
+import javax.swing.JComponent;
+import javax.swing.JTable;
+import javax.swing.JTextArea;
+import javax.swing.KeyStroke;
+import javax.swing.text.Keymap;
+import javax.swing.SwingUtilities;
+import javax.swing.text.BadLocationException;
+import javax.swing.text.SimpleAttributeSet;
+import javax.swing.text.Document;
+import javax.swing.text.Keymap;
+import javax.swing.text.TextAction;
+import javax.swing.text.JTextComponent;
+
+import javax.swing.event.DocumentEvent;
+import javax.swing.event.DocumentListener;
+import javax.swing.table.TableCellEditor;
+import javax.swing.table.TableColumn;
+
+import java.util.EventObject;
+
+import browser.ValidatedObjectAndEditString;
+
+
+public class MultiLineTableCellEditor extends AbstractCellEditor implements TableCellEditor,
+ ActionListener
+{
+ private ResizableTextArea textArea;
+
+ /**
+ * Creates a new MultiLineTableCellEditor object.
+ */
+ public MultiLineTableCellEditor() {
+ textArea = new ResizableTextArea(this);
+ textArea.setBorder(BorderFactory.createLineBorder(Color.GRAY));
+ textArea.setLineWrap(true);
+ textArea.setWrapStyleWord(true);
+ }
+
+ public Object getCellEditorValue() {
+ return textArea.getText();
+ }
+
+ protected int clickCountToStart = 2;
+
+ public int getClickCountToStart() {
+ return clickCountToStart;
+ }
+
+ public void setClickCountToStart(int clickCountToStart) {
+ this.clickCountToStart = clickCountToStart;
+ }
+
+ public boolean isCellEditable(EventObject e) {
+ return !(e instanceof MouseEvent)
+ || (((MouseEvent) e).getClickCount() >= clickCountToStart);
+ }
+
+ public void actionPerformed(ActionEvent ae) {
+ stopCellEditing();
+ }
+
+ public Component getTableCellEditorComponent(final JTable table, final Object value, final boolean isSelected,
+ final int row, final int column)
+ {
+ final String text = (value != null) ? ((ValidatedObjectAndEditString)value).getEditString() : "";
+ textArea.setTable(table);
+ textArea.setText(text);
+
+ return textArea;
+ }
+
+ public static final String UPDATE_BOUNDS = "UpdateBounds";
+
+ class ResizableTextArea extends JTextArea implements KeyListener {
+ private JTable table;
+ private MultiLineTableCellEditor parent;
+
+ ResizableTextArea(final MultiLineTableCellEditor parent) {
+ super();
+ this.parent = parent;
+ addKeyListener(this);
+ }
+
+ public void setTable(JTable t) {
+ table = t;
+ }
+
+ public void setText(String text) {
+ super.setText(text);
+ updateBounds();
+ }
+
+ public void setBounds(int x, int y, int width, int height) {
+ if (Boolean.TRUE.equals(getClientProperty(UPDATE_BOUNDS)))
+ super.setBounds(x, y, width, height);
+ }
+
+ public void addNotify() {
+ super.addNotify();
+ getDocument().addDocumentListener(listener);
+ }
+
+ public void removeNotify() {
+ getDocument().removeDocumentListener(listener);
+ super.removeNotify();
+ }
+
+ DocumentListener listener = new DocumentListener() {
+ public void insertUpdate(DocumentEvent e) {
+ updateBounds();
+ }
+
+ public void removeUpdate(DocumentEvent e) {
+ updateBounds();
+ }
+
+ public void changedUpdate(DocumentEvent e) {
+ updateBounds();
+ }
+ };
+
+ private void updateBounds() {
+ if (table == null) {
+ System.err.println("table is null");
+ return;
+ }
+
+ if (table.isEditing()) {
+ Rectangle cellRect = table.getCellRect(table.getEditingRow(),
+ table.getEditingColumn(), false);
+ Dimension prefSize = getPreferredSize();
+ putClientProperty(UPDATE_BOUNDS, Boolean.TRUE);
+ setBounds(getX(), getY(), Math.min(cellRect.width, prefSize.width),
+ Math.max(cellRect.height + prefSize.height, prefSize.height));
+ putClientProperty(UPDATE_BOUNDS, Boolean.FALSE);
+ validate();
+ }
+ }
+
+ //
+ // KeyListener Interface
+ //
+
+ public void keyTyped(KeyEvent e) {}
+
+ public void keyReleased(KeyEvent e) {}
+
+ public void keyPressed(final KeyEvent event) {
+ if (event.getKeyCode() != KeyEvent.VK_ENTER)
+ return;
+
+ final int modifiers = event.getModifiers();
+
+ // We want to move to the next cell if Enter and no modifiers have been pressed:
+ if (modifiers == 0) {
+ parent.stopCellEditing();
+ this.transferFocus();
+ return;
+ }
+
+ // We want to move to the previous cell if Shift+Enter have been pressed:
+ if (modifiers == KeyEvent.VK_SHIFT) {
+ parent.stopCellEditing();
+ this.transferFocusBackward();
+ return;
+ }
+
+ // We want to insert a newline if Enter+Alt or Enter+Alt+Meta have been pressed:
+ final int OPTION_AND_COMMAND = 12; // On Mac to emulate Excel.
+ if (modifiers == KeyEvent.VK_ALT || modifiers == OPTION_AND_COMMAND) {
+ final int caretPosition = this.getCaretPosition();
+ final StringBuilder text = new StringBuilder(this.getText());
+ this.setText(text.insert(caretPosition, '\n').toString());
+ this.setCaretPosition(caretPosition + 1);
+ }
+ }
+ }
+}
diff --git a/coreplugins/browser/src/main/java/browser/ui/SortArrowIcon.java b/coreplugins/browser/src/main/java/browser/ui/SortArrowIcon.java
new file mode 100644
index 0000000..8bf606d
--- /dev/null
+++ b/coreplugins/browser/src/main/java/browser/ui/SortArrowIcon.java
@@ -0,0 +1,115 @@
+/*
+ * $Archive: SourceJammer$
+ * $FileName: SortArrowIcon.java$
+ * $FileID: 3986$
+ *
+ * Last change:
+ * $AuthorName: Timo Haberkern$
+ * $Date: 2007-12-08 03:57:59 +0100 (Sat, 08 Dec 2007) $
+ * $Comment: $
+ *
+ * $KeyWordsOff: $
+ */
+
+/*
+ =====================================================================
+
+ SortArrowIcon.java
+
+ Created by Claude Duguay
+ Copyright (c) 2002
+
+ =====================================================================
+ */
+package browser.ui;
+
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Graphics;
+
+import javax.swing.Icon;
+
+
+/**
+ *
+ */
+public class SortArrowIcon implements Icon {
+ /**
+ *
+ */
+ public static final int NONE = 0;
+
+ /**
+ *
+ */
+ public static final int DECENDING = 1;
+
+ /**
+ *
+ */
+ public static final int ASCENDING = 2;
+ protected int direction;
+ protected int width = 8;
+ protected int height = 8;
+
+ /**
+ * Creates a new SortArrowIcon object.
+ *
+ * @param direction DOCUMENT ME!
+ */
+ public SortArrowIcon(int direction) {
+ this.direction = direction;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getIconWidth() {
+ return width;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getIconHeight() {
+ return height;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param c DOCUMENT ME!
+ * @param g DOCUMENT ME!
+ * @param x DOCUMENT ME!
+ * @param y DOCUMENT ME!
+ */
+ public void paintIcon(Component c, Graphics g, int x, int y) {
+ Color bg = c.getBackground();
+ Color light = bg.brighter();
+ Color shade = bg.darker();
+
+ int w = width;
+ int h = height;
+ int m = w / 2;
+
+ if (direction == ASCENDING) {
+ g.setColor(shade);
+ g.drawLine(x, y, x + w, y);
+ g.drawLine(x, y, x + m, y + h);
+ g.setColor(light);
+ g.drawLine(x + w, y, x + m, y + h);
+ }
+
+ if (direction == DECENDING) {
+ g.setColor(shade);
+ g.drawLine(x + m, y, x, y + h);
+ g.setColor(light);
+ g.drawLine(x, y + h, x + w, y + h);
+ g.drawLine(x + m, y, x + w, y + h);
+ }
+ }
+}
diff --git a/coreplugins/browser/src/main/java/browser/ui/SortHeaderRenderer.java b/coreplugins/browser/src/main/java/browser/ui/SortHeaderRenderer.java
new file mode 100644
index 0000000..45507f6
--- /dev/null
+++ b/coreplugins/browser/src/main/java/browser/ui/SortHeaderRenderer.java
@@ -0,0 +1,103 @@
+/*
+ * $Archive: SourceJammer$
+ * $FileName: SortHeaderRenderer.java$
+ * $FileID: 3985$
+ *
+ * Last change:
+ * $AuthorName: Timo Haberkern$
+ * $Date: 2007-12-08 03:57:59 +0100 (Sat, 08 Dec 2007) $
+ * $Comment: $
+ *
+ * $KeyWordsOff: $
+ */
+
+/*
+=====================================================================
+
+ SortHeaderRenderer.java
+
+ Created by Claude Duguay
+ Copyright (c) 2002
+
+=====================================================================
+*/
+package browser.ui;
+
+import java.awt.Component;
+
+import javax.swing.Icon;
+import javax.swing.JTable;
+import javax.swing.UIManager;
+import javax.swing.table.DefaultTableCellRenderer;
+import javax.swing.table.JTableHeader;
+
+
+
+/**
+ *
+ */
+public class SortHeaderRenderer extends DefaultTableCellRenderer {
+ /**
+ *
+ */
+ public static Icon NONSORTED = new SortArrowIcon(SortArrowIcon.NONE);
+
+ /**
+ *
+ */
+ public static Icon ASCENDING = new SortArrowIcon(SortArrowIcon.ASCENDING);
+
+ /**
+ *
+ */
+ public static Icon DECENDING = new SortArrowIcon(SortArrowIcon.DECENDING);
+
+ /**
+ * Creates a new SortHeaderRenderer object.
+ */
+ public SortHeaderRenderer() {
+ setHorizontalTextPosition(LEFT);
+ setHorizontalAlignment(CENTER);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param table DOCUMENT ME!
+ * @param value DOCUMENT ME!
+ * @param isSelected DOCUMENT ME!
+ * @param hasFocus DOCUMENT ME!
+ * @param row DOCUMENT ME!
+ * @param col DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected,
+ boolean hasFocus, int row, int col) {
+ int index = -1;
+ boolean ascending = true;
+
+ if (table instanceof CyAttributeBrowserTable) {
+ CyAttributeBrowserTable sortTable = (CyAttributeBrowserTable) table;
+ index = sortTable.getSortedColumnIndex();
+ ascending = sortTable.isSortedColumnAscending();
+ }
+
+ if (table != null) {
+ JTableHeader header = table.getTableHeader();
+
+ if (header != null) {
+ setForeground(header.getForeground());
+ setBackground(header.getBackground());
+ setFont(header.getFont());
+ }
+ }
+
+ Icon icon = ascending ? ASCENDING : DECENDING;
+ setIcon((col == index) ? icon : NONSORTED);
+ setText((value == null) ? "" : value.toString());
+ setBorder(UIManager.getBorder("TableHeader.cellBorder"));
+
+ return this;
+ }
+}
diff --git a/coreplugins/browser/src/main/java/browser/ui/Util.java b/coreplugins/browser/src/main/java/browser/ui/Util.java
new file mode 100644
index 0000000..e877910
--- /dev/null
+++ b/coreplugins/browser/src/main/java/browser/ui/Util.java
@@ -0,0 +1,96 @@
+/*
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package browser.ui;
+
+
+import browser.DataObjectType;
+import cytoscape.Cytoscape;
+import cytoscape.data.CyAttributes;
+import org.cytoscape.equations.EquationUtil;
+
+import java.util.List;
+import java.util.Map;
+
+
+public class Util {
+ /**
+ * Populates "attribNameToTypeMap" with the names from "cyAttribs" and their types as mapped
+ * to the types used by attribute equations. Types (and associated names) not used by
+ * attribute equations are ommitted.
+ *
+ * @param cyAttribs the attributes to map
+ * @param ignore if not null, skip the attribute with this name
+ * @param attribNameToTypeMap the result of the translation from attribute types to
+ * attribute equation types
+ */
+ public static void initAttribNameToTypeMap(final CyAttributes cyAttribs, final String ignore,
+ final Map<String, Class> attribNameToTypeMap)
+ {
+ for (final String attribName : cyAttribs.getAttributeNames()) {
+ if (ignore == null || ignore.equals(attribName))
+ continue;
+ if (!cyAttribs.getUserVisible(attribName))
+ continue;
+
+ final byte type = cyAttribs.getType(attribName);
+ if (type == CyAttributes.TYPE_BOOLEAN)
+ attribNameToTypeMap.put(attribName, Boolean.class);
+ else if (type == CyAttributes.TYPE_INTEGER)
+ attribNameToTypeMap.put(attribName, Long.class);
+ else if (type == CyAttributes.TYPE_FLOATING)
+ attribNameToTypeMap.put(attribName, Double.class);
+ else if (type == CyAttributes.TYPE_STRING)
+ attribNameToTypeMap.put(attribName, String.class);
+ else if (type == CyAttributes.TYPE_SIMPLE_LIST)
+ attribNameToTypeMap.put(attribName, List.class);
+ else
+ /* We intentionally ignore everything else! */;
+ }
+ }
+
+ public static void initAttribNameToTypeMap(final DataObjectType objectType, final String columnName,
+ final Map<String, Class> attribNameToTypeMap)
+ {
+ final CyAttributes cyAttribs;
+ switch (objectType) {
+ case NODES:
+ cyAttribs = Cytoscape.getNodeAttributes();
+ break;
+ case EDGES:
+ cyAttribs = Cytoscape.getEdgeAttributes();
+ break;
+ case NETWORK:
+ cyAttribs = Cytoscape.getNetworkAttributes();
+ break;
+ default:
+ throw new IllegalStateException("unknown DataObjectType: " + objectType + "!");
+ }
+
+ initAttribNameToTypeMap(cyAttribs, columnName, attribNameToTypeMap);
+ }
+}
diff --git a/coreplugins/browser/src/main/java/browser/util/AttrUtil.java b/coreplugins/browser/src/main/java/browser/util/AttrUtil.java
new file mode 100644
index 0000000..a9c5bb7
--- /dev/null
+++ b/coreplugins/browser/src/main/java/browser/util/AttrUtil.java
@@ -0,0 +1,60 @@
+/*
+ Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package browser.util;
+
+
+import java.util.List;
+import java.util.Map;
+import java.util.TreeMap;
+import cytoscape.data.CyAttributes;
+
+
+public class AttrUtil {
+ /**
+ * @returns a map of attribute names and Java types corresponding to the types internally used by attribute equations
+ */
+ public static Map<String, Class> getAttrNamesAndTypes(final CyAttributes attribs) {
+ final String[] attrNames = attribs.getAttributeNames();
+ final Map<String, Class> attribNameToTypeMap = new TreeMap<String, Class>();
+ for (final String attrName : attrNames) {
+ final byte type = attribs.getType(attrName);
+ if (type == CyAttributes.TYPE_INTEGER)
+ attribNameToTypeMap.put(attrName, Long.class);
+ if (type == CyAttributes.TYPE_BOOLEAN)
+ attribNameToTypeMap.put(attrName, Boolean.class);
+ if (type == CyAttributes.TYPE_FLOATING)
+ attribNameToTypeMap.put(attrName, Double.class);
+ if (type == CyAttributes.TYPE_SIMPLE_LIST)
+ attribNameToTypeMap.put(attrName, List.class);
+ if (type == CyAttributes.TYPE_STRING)
+ attribNameToTypeMap.put(attrName, String.class);
+ }
+
+ return attribNameToTypeMap;
+ }
+}
\ No newline at end of file
diff --git a/coreplugins/browser/src/main/java/browser/util/CopyToExcel.java b/coreplugins/browser/src/main/java/browser/util/CopyToExcel.java
new file mode 100644
index 0000000..2a7fd6e
--- /dev/null
+++ b/coreplugins/browser/src/main/java/browser/util/CopyToExcel.java
@@ -0,0 +1,179 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package browser.util;
+
+import browser.ui.CyAttributeBrowserTable;
+import cytoscape.Cytoscape;
+
+import java.awt.*;
+import java.awt.datatransfer.*;
+import java.awt.event.*;
+
+import java.util.*;
+
+import javax.swing.*;
+
+
+/**
+ * ExcelAdapter enables Copy-Paste Clipboard functionality on JTables. The
+ * clipboard data format used by the adapter is compatible with the clipboard
+ * format used by Excel. This provides for clipboard interoperability between
+ * enabled JTables and Excel.
+ */
+public class CopyToExcel implements ActionListener {
+ private String rowstring;
+ private String value;
+ private Clipboard system;
+ private StringSelection stsel;
+ private CyAttributeBrowserTable jTable1;
+
+ /**
+ * The Excel Adapter is constructed with a JTable on which it enables
+ * Copy-Paste and acts as a Clipboard listener.
+ */
+ public CopyToExcel(CyAttributeBrowserTable myJSortTable) {
+ jTable1 = myJSortTable;
+
+ KeyStroke copy = KeyStroke.getKeyStroke(KeyEvent.VK_C, ActionEvent.CTRL_MASK, false);
+
+ // Identifying the copy KeyStroke user can modify this
+ // to copy on some other Key combination.
+ KeyStroke paste = KeyStroke.getKeyStroke(KeyEvent.VK_V, ActionEvent.CTRL_MASK, false);
+ // Identifying the Paste KeyStroke user can modify this
+ // to copy on some other Key combination.
+ jTable1.registerKeyboardAction(this, "Copy", copy, JComponent.WHEN_FOCUSED);
+
+ jTable1.registerKeyboardAction(this, "Paste", paste, JComponent.WHEN_FOCUSED);
+ system = Toolkit.getDefaultToolkit().getSystemClipboard();
+ }
+
+ /**
+ * Public Accessor methods for the Table on which this adapter acts.
+ */
+ public CyAttributeBrowserTable getJTable() {
+ return jTable1;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param jSortTable1 DOCUMENT ME!
+ */
+ public void setJTable(CyAttributeBrowserTable jSortTable1) {
+ this.jTable1 = jSortTable1;
+ }
+
+ /**
+ * This method is activated on the Keystrokes we are listening to in this
+ * implementation. Here it listens for Copy and Paste ActionCommands.
+ * Selections comprising non-adjacent cells result in invalid selection and
+ * then copy action cannot be performed. Paste is done by aligning the upper
+ * left corner of the selection with the 1st element in the current
+ * selection of the JTable.
+ */
+ public void actionPerformed(ActionEvent e) {
+ if (e.getActionCommand().compareTo("Copy") == 0) {
+ StringBuffer sbf = new StringBuffer();
+
+ // Check to ensure we have selected only a contiguous block of
+ // cells
+ int numcols = jTable1.getSelectedColumnCount();
+ int numrows = jTable1.getSelectedRowCount();
+ int[] rowsselected = jTable1.getSelectedRows();
+ int[] colsselected = jTable1.getSelectedColumns();
+
+ if (!((((numrows - 1) == (rowsselected[rowsselected.length - 1] - rowsselected[0]))
+ && (numrows == rowsselected.length))
+ && (((numcols - 1) == (colsselected[colsselected.length - 1] - colsselected[0]))
+ && (numcols == colsselected.length)))) {
+ JOptionPane.showMessageDialog(Cytoscape.getDesktop(), "Invalid Copy Selection",
+ "Invalid Copy Selection", JOptionPane.ERROR_MESSAGE);
+
+ return;
+ }
+
+ for (int i = 0; i < numrows; i++) {
+ for (int j = 0; j < numcols; j++) {
+ sbf.append(jTable1.getValueAt(rowsselected[i], colsselected[j]));
+
+ if (j < (numcols - 1))
+ sbf.append("\t");
+ }
+
+ sbf.append("\n");
+ }
+
+ stsel = new StringSelection(sbf.toString());
+ system = Toolkit.getDefaultToolkit().getSystemClipboard();
+ system.setContents(stsel, stsel);
+ }
+
+ if (e.getActionCommand().compareTo("Paste") == 0) {
+ // System.out.println("Trying to Paste");
+
+ int startRow = (jTable1.getSelectedRows())[0];
+ int startCol = (jTable1.getSelectedColumns())[0];
+
+ try {
+ String trstring = (String) (system.getContents(this)
+ .getTransferData(DataFlavor.stringFlavor));
+ // System.out.println("String is:" + trstring);
+
+ StringTokenizer st1 = new StringTokenizer(trstring, "\n");
+
+ for (int i = 0; st1.hasMoreTokens(); i++) {
+ rowstring = st1.nextToken();
+
+ StringTokenizer st2 = new StringTokenizer(rowstring, "\t");
+
+ for (int j = 0; st2.hasMoreTokens(); j++) {
+ value = (String) st2.nextToken();
+
+ if (((startRow + i) < jTable1.getRowCount())
+ && ((startCol + j) < jTable1.getColumnCount()))
+ jTable1.setValueAt(value, startRow + i, startCol + j);
+
+ // System.out.println("Putting " + value + "at row=" + startRow + i
+ // + "column=" + startCol + j);
+ }
+ }
+ } catch (Exception ex) {
+ ex.printStackTrace();
+ }
+ }
+ }
+}
diff --git a/coreplugins/browser/src/main/java/browser/util/HyperLinkOut.java b/coreplugins/browser/src/main/java/browser/util/HyperLinkOut.java
new file mode 100644
index 0000000..9447114
--- /dev/null
+++ b/coreplugins/browser/src/main/java/browser/util/HyperLinkOut.java
@@ -0,0 +1,143 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package browser.util;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.data.ontology.DBCrossReferences;
+
+import cytoscape.util.OpenBrowser;
+
+import java.awt.Color;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import java.net.MalformedURLException;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+
+
+/**
+ *
+ */
+public class HyperLinkOut extends JMenu {
+ private static final String TITLE = "Search";
+ private final String value;
+ private final Map<String, Map<String, String>> structure;
+
+ /**
+ * Creates a new HyperLinkOut object.
+ *
+ * @param value DOCUMENT ME!
+ * @param menuStructure DOCUMENT ME!
+ */
+ public HyperLinkOut(String value, final Map<String, Map<String, String>> menuStructure) {
+ this.value = value;
+ this.structure = menuStructure;
+
+ setBackground(Color.white);
+
+ String dispStr = null;
+
+ if (value.length() > 30) {
+ dispStr = value.substring(0, 29) + " ... ";
+ } else
+ dispStr = value;
+
+ setText("<html>Search <strong text=\"#DC143C\">" + dispStr + "</strong> on the web</html>");
+ buildLinks();
+ }
+
+ private Map<String, List> getDefaultMenu() {
+ Map<String, List> def = new HashMap<String, List>();
+
+ List<String> se = new ArrayList<String>();
+ se.add("Google");
+ se.add("Ask");
+ def.put("Search Engines", se);
+
+ List<String> bio = new ArrayList<String>();
+ bio.add("SGD");
+ bio.add("GO");
+ bio.add("MGD");
+ bio.add("Reactome");
+ def.put("Biological Databases", bio);
+
+ return def;
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void search() {
+ }
+
+ private void buildLinks() {
+ // Set<String> dbNames = xref.getDBNames();
+ String fullName;
+
+ JMenu cat;
+
+ for (final String category : structure.keySet()) {
+ cat = new JMenu(category);
+
+ Map<String, String> children = structure.get(category);
+
+ for (final String name : children.keySet()) {
+ JMenuItem dbLink = new JMenuItem(name);
+ dbLink.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ openBrowser(structure.get(category).get(name).replace("%ID%", value));
+ }
+ });
+ cat.add(dbLink);
+ }
+
+ this.add(cat);
+ }
+ }
+
+ private void openBrowser(String url) {
+ // System.out.println("URL ==== " + url);
+ OpenBrowser.openURL(url);
+ }
+}
diff --git a/coreplugins/browser/src/main/java/browser/util/StringUtil.java b/coreplugins/browser/src/main/java/browser/util/StringUtil.java
new file mode 100644
index 0000000..e3bae32
--- /dev/null
+++ b/coreplugins/browser/src/main/java/browser/util/StringUtil.java
@@ -0,0 +1,257 @@
+/*
+ * Copyright (C) 2001, 2002 Robert MacGrogan
+ *
+ * This library is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation; either
+ * version 2.1 of the License, or (at your option) any later version.
+ *
+ * This library is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this library; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+ *
+ *
+ * $Archive: SourceJammer$
+ * $FileName: StringUtil.java$
+ * $FileID: 4337$
+ *
+ * Last change:
+ * $AuthorName: Rob MacGrogan$
+ * $Date: 2007-12-08 03:58:10 +0100 (Sat, 08 Dec 2007) $
+ * $Comment: Replaced GPL header with LGPL header.$
+ */
+package browser.util;
+
+import java.text.DateFormat;
+import java.text.SimpleDateFormat;
+
+import java.util.Date;
+import java.util.Vector;
+import java.util.regex.*;
+
+
+/**
+ * Title: $FileName: StringUtil.java$
+ * @author $AuthorName: Rob MacGrogan$
+ * @version $VerNum: 2$<br><br>
+ *
+ * $Description: $
+ * $KeyWordsOff: $
+ */
+public class StringUtil {
+ public static final class DateFormats {
+ public static final int LONG_WITH_TIME = 1;
+ public static final int SHORT_WITH_TIME = 2;
+ public static final int MEDIUM = 3;
+ }
+
+ private static SimpleDateFormat moLongWithTimeFormat = new SimpleDateFormat("MMMM d, yyyy h:mm:ss a");
+ private static DateFormat moShortWithTimeFormat = DateFormat.getDateTimeInstance(DateFormat.SHORT,
+ DateFormat.SHORT);
+ private static DateFormat medium = DateFormat.getDateInstance(DateFormat.MEDIUM);
+
+ private StringUtil() {
+ }
+
+ /**
+ * Returns sTarget with all instances of sSubstring replaced with sReplaceWith.
+ */
+ public static String replaceSubstring(String sTarget, String sSubstring, String sReplaceWith) {
+ // If there is a taget and a substring...
+ if ((sTarget != null) && (sSubstring != null)) {
+ // If there is no replace with string, make it an empty string.
+ if (sReplaceWith == null) {
+ sReplaceWith = "";
+ }
+
+ // Get the lengths of all of the strings (so that the function is only called once).
+ int len = sTarget.length();
+ int searchlen = sSubstring.length();
+ int replacelen = sReplaceWith.length();
+
+ // Holds the result of replacing the string.
+ StringBuffer result = null;
+
+ // Keeps track of where the start of a match is.
+ int pos = 0;
+
+ // Keeps track of the last good position (used as a starting position).
+ int lastPos = 0;
+
+ // Search the substring for the text.
+ while ((pos = sTarget.indexOf(sSubstring, lastPos)) > -1) {
+ // If the buffer has not been created, create it.
+ if (result == null) {
+ result = new StringBuffer(len);
+ }
+
+ // Append the first part of the string on before the match.
+ result.append(sTarget.substring(lastPos, pos));
+
+ // If there is text to replace the matched text, add that.
+ if (replacelen > 0) {
+ result.append(sReplaceWith);
+ }
+
+ // Set the last position to one position beyond the matched text.
+ lastPos = pos + searchlen;
+ }
+
+ // If there was at least one match, append the remainder of the string onto the buffer
+ // and return it.
+ if (result != null) {
+ // Add in what is left over.
+ if (lastPos < len) {
+ result.append(sTarget.substring(lastPos));
+ }
+
+ return result.toString();
+ }
+ }
+
+ // Else, return the original string.
+ return sTarget;
+ } //end replaceSubstring
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param d DOCUMENT ME!
+ * @param format DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static String dateString(Date d, int format) {
+ String sReturn = null;
+
+ DateFormat oFormatter = null;
+
+ if (format == DateFormats.LONG_WITH_TIME) {
+ oFormatter = moLongWithTimeFormat;
+ } else if (format == DateFormats.SHORT_WITH_TIME) {
+ oFormatter = moShortWithTimeFormat;
+ } else if (format == DateFormats.MEDIUM) {
+ oFormatter = medium;
+ }
+
+ if (d != null) {
+ sReturn = oFormatter.format(d);
+ }
+
+ return sReturn;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param source DOCUMENT ME!
+ * @param length DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static String fixedLength(String source, int length) {
+ String sReturn = null;
+
+ if (source.length() >= length) {
+ sReturn = source.substring(0, length);
+ } else {
+ int iFillLength = length - source.length();
+ char[] fill = new char[iFillLength];
+ java.util.Arrays.fill(fill, ' ');
+ sReturn = source + new String(fill);
+ }
+
+ return sReturn;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ */
+ public static void main(String[] args) {
+ try {
+ String test = "testtesttesttest";
+ String result = fixedLength(test, 8);
+ System.out.println("before: |" + test + "|");
+ System.out.println("after: |" + result + "|" + " length=" + result.length());
+ } catch (Throwable thr) {
+ thr.printStackTrace();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param sOne DOCUMENT ME!
+ * @param sTwo DOCUMENT ME!
+ * @param invert DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static boolean firstStringSortsBeforeSecond(String sOne, String sTwo, boolean invert) {
+ boolean bReturn = false;
+
+ try {
+ double dblOne = Double.parseDouble(sOne);
+ double dblTwo = Double.parseDouble(sTwo);
+
+ if (dblOne <= dblTwo) {
+ bReturn = true;
+ } else {
+ bReturn = false;
+ }
+ } catch (NumberFormatException ex) {
+ Pattern p = Pattern.compile("([a-zA-Z]+)([0-9]+)");
+ Matcher m1 = p.matcher(sOne);
+ Matcher m2 = p.matcher(sTwo);
+
+ if (m1.matches() && m2.matches() && m1.group(1).equals(m2.group(1))) {
+ double d1 = (new Double(m1.group(2))).doubleValue();
+ double d2 = (new Double(m2.group(2))).doubleValue();
+
+ if (d1 > d2) {
+ bReturn = true;
+ }
+ } else {
+ int iComp = sOne.compareToIgnoreCase(sTwo);
+
+ if (iComp <= 0) {
+ bReturn = true;
+ } else {
+ bReturn = false;
+ }
+ }
+ }
+
+ if (invert) {
+ bReturn = !bReturn;
+ }
+
+ return bReturn;
+ }
+
+ /**
+ * Checks if the string is numeric.
+ */
+ public static boolean isNumeric(String sCheck) {
+ boolean bReturn = false;
+
+ try {
+ if (sCheck != null) {
+ double dblCheck = Double.parseDouble(sCheck);
+ bReturn = true;
+ }
+ } //end try
+ catch (NumberFormatException ex) {
+ //this means sCheck is not numeric
+ } //end catch
+
+ return bReturn;
+ } //end isNumeric(String)
+}
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diff --git a/coreplugins/browser/src/main/resources/browser/images/stock_select-row.png b/coreplugins/browser/src/main/resources/browser/images/stock_select-row.png
new file mode 100644
index 0000000..873aeb6
Binary files /dev/null and b/coreplugins/browser/src/main/resources/browser/images/stock_select-row.png differ
diff --git a/coreplugins/browser/src/main/resources/browser/images/unselect_all.png b/coreplugins/browser/src/main/resources/browser/images/unselect_all.png
new file mode 100644
index 0000000..78f1281
Binary files /dev/null and b/coreplugins/browser/src/main/resources/browser/images/unselect_all.png differ
diff --git a/coreplugins/browser/src/main/resources/browser/plugin.props b/coreplugins/browser/src/main/resources/browser/plugin.props
new file mode 100644
index 0000000..0af77bd
--- /dev/null
+++ b/coreplugins/browser/src/main/resources/browser/plugin.props
@@ -0,0 +1,31 @@
+# This props file would be filled out and included in the plugin jar file. This props file will be used
+# to put information into the Plugin Manager about the plugin
+
+# -- The following properties are REQUIRED -- #
+
+# The plugin name that will be displayed to users
+pluginName=Browser
+
+# Description used to give users information about the plugin such as what it does.
+# Html tags are encouraged for formatting purposes.
+pluginDescription=Attribute browser
+
+# Plugin version number, this must be two numbers separated by a decimlal. Ex. 0.2, 14.03
+pluginVersion=0.8
+
+# Compatible Cytoscape version
+cytoscapeVersion=2.5,2.6,2.7,2.8
+
+# Category, use one of the categories listed on the website or create your own
+pluginCategory=Core
+
+
+# List of authors. Note each author and institution pair are separated by a : (colon)
+# each additional author institution pair must be separated from other pairs bye a ; (semicolon)
+pluginAuthorsIntstiutions=Kei Ono:UCSD;Rowan Christmas:Institute for Systems Biology;Dr. Johannes Ruscheinski:UCSD
+
+# -- The following properties should be set ONLY BY CORE PLUGINS -- #
+downloadURL=http://cytoscape.org/plugins/plugins.xml
+uniqueID=3
+
+
diff --git a/coreplugins/browser/src/test/java/browser/tests/DefaultSortTableModel.java b/coreplugins/browser/src/test/java/browser/tests/DefaultSortTableModel.java
new file mode 100644
index 0000000..00502eb
--- /dev/null
+++ b/coreplugins/browser/src/test/java/browser/tests/DefaultSortTableModel.java
@@ -0,0 +1,131 @@
+/*
+ * $Archive: SourceJammer$
+ * $FileName: DefaultSortTableModel.java$
+ * $FileID: 3982$
+ *
+ * Last change:
+ * $AuthorName: Timo Haberkern$
+ * $Date: 2008-08-16 20:01:50 -0700 (Sat, 16 Aug 2008) $
+ * $Comment: $
+ *
+ * $KeyWordsOff: $
+ */
+
+/*
+=====================================================================
+
+ DefaultSortTableModel.java
+
+ Created by Claude Duguay
+ Copyright (c) 2002
+
+=====================================================================
+*/
+package browser.tests;
+
+import java.util.Collections;
+import java.util.Vector;
+
+import javax.swing.table.DefaultTableModel;
+
+import cytoscape.data.CyAttributes;
+
+import browser.ColumnComparator;
+import browser.SortTableModel;
+
+
+/**
+ *
+ */
+public class DefaultSortTableModel extends DefaultTableModel implements SortTableModel {
+ /**
+ * Creates a new DefaultSortTableModel object.
+ */
+ public DefaultSortTableModel() {
+ }
+
+ /**
+ * Creates a new DefaultSortTableModel object.
+ *
+ * @param rows DOCUMENT ME!
+ * @param cols DOCUMENT ME!
+ */
+ public DefaultSortTableModel(int rows, int cols) {
+ super(rows, cols);
+ }
+
+ /**
+ * Creates a new DefaultSortTableModel object.
+ *
+ * @param data DOCUMENT ME!
+ * @param names DOCUMENT ME!
+ */
+ public DefaultSortTableModel(Object[][] data, Object[] names) {
+ super(data, names);
+ }
+
+ /**
+ * Creates a new DefaultSortTableModel object.
+ *
+ * @param names DOCUMENT ME!
+ * @param rows DOCUMENT ME!
+ */
+ public DefaultSortTableModel(Object[] names, int rows) {
+ super(names, rows);
+ }
+
+ /**
+ * Creates a new DefaultSortTableModel object.
+ *
+ * @param names DOCUMENT ME!
+ * @param rows DOCUMENT ME!
+ */
+ public DefaultSortTableModel(Vector names, int rows) {
+ super(names, rows);
+ }
+
+ /**
+ * Creates a new DefaultSortTableModel object.
+ *
+ * @param data DOCUMENT ME!
+ * @param names DOCUMENT ME!
+ */
+ public DefaultSortTableModel(Vector data, Vector names) {
+ super(data, names);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param col DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isSortable(int col) {
+ return true;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param col DOCUMENT ME!
+ * @param ascending DOCUMENT ME!
+ */
+ public void sortColumn(int col, boolean ascending) {
+ // All of our test data is Integer
+ Collections.sort(getDataVector(),
+ new ColumnComparator(col, CyAttributes.TYPE_INTEGER, ascending));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param aValue DOCUMENT ME!
+ * @param rowIndex DOCUMENT ME!
+ * @param columnIndex DOCUMENT ME!
+ */
+ public void setValueAt(Object aValue, int rowIndex, int columnIndex) {
+ // System.out.println("SetValueAt: " + aValue + " " + rowIndex + " " + columnIndex);
+ super.setValueAt(aValue, rowIndex, columnIndex);
+ }
+}
diff --git a/coreplugins/browser/src/test/java/browser/tests/JSortTableTest.java b/coreplugins/browser/src/test/java/browser/tests/JSortTableTest.java
new file mode 100644
index 0000000..178a5c8
--- /dev/null
+++ b/coreplugins/browser/src/test/java/browser/tests/JSortTableTest.java
@@ -0,0 +1,86 @@
+/*
+ * $Archive: SourceJammer$
+ * $FileName: JSortTableTest.java$
+ * $FileID: 3987$
+ *
+ * Last change:
+ * $AuthorName: Timo Haberkern$
+ * $Date: 2007-02-13 12:13:13 -0800 (火, 13 2 2007) $
+ * $Comment: $
+ *
+ * $KeyWordsOff: $
+ */
+
+/*
+=====================================================================
+
+ JSortTableTest.java
+
+ Created by Claude Duguay
+ Copyright (c) 2002
+
+=====================================================================
+*/
+package browser.tests;
+
+import java.awt.Dimension;
+import java.awt.GridLayout;
+import java.util.Vector;
+
+import javax.swing.BorderFactory;
+import javax.swing.JFrame;
+import javax.swing.JPanel;
+
+import browser.SortTableModel;
+
+
+/**
+ *
+ */
+public class JSortTableTest extends JPanel {
+ /**
+ * Creates a new JSortTableTest object.
+ */
+ public JSortTableTest() {
+ setLayout(new GridLayout());
+ setBorder(BorderFactory.createEmptyBorder(4, 4, 4, 4));
+ setPreferredSize(new Dimension(400, 400));
+ //add(new JScrollPane(new JSortTable(makeModel())));
+ }
+
+ protected SortTableModel makeModel() {
+ Vector data = new Vector();
+
+ for (int i = 0; i < 3; i++) {
+ Vector row = new Vector();
+
+ for (int j = 0; j < 5; j++) {
+ row.add(new Integer((int) (Math.random() * 256)));
+ }
+
+ data.add(row);
+ }
+
+ Vector names = new Vector();
+ names.add("One");
+ names.add("Two");
+ names.add("Three");
+ names.add("Four");
+ names.add("Five");
+
+ return new DefaultSortTableModel(data, names);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ */
+ public static void main(String[] args) {
+ JFrame frame = new JFrame("JSortTable Test");
+ frame.getContentPane().setLayout(new GridLayout());
+ frame.getContentPane().add(new JSortTableTest());
+ frame.pack();
+ frame.setVisible(true);
+ }
+}
diff --git a/coreplugins/cPath/docs/CPATH_README.txt b/coreplugins/cPath/docs/CPATH_README.txt
new file mode 100644
index 0000000..1c1c229
--- /dev/null
+++ b/coreplugins/cPath/docs/CPATH_README.txt
@@ -0,0 +1,168 @@
+Cytoscape cPath PlugIn
+--------------------------------
+
+Table of Contents
+=================
+1. Introduction
+2. About cPath
+3. PlugIn Installation Instructions
+4. Using the cPath PlugIn
+5. Configuring the cPath PlugIn
+6. Bugs / Feature Requests
+7. Contacts
+8. Release Notes
+
+1. Introduction
+=======================================
+This directory contains a copy of the Cytoscape cPath PlugIn.
+
+The cPath PlugIn enables Cytoscape users to query, retrieve and visualize
+protein-protein interactions stored in the cPath database.
+
+2. About cPath
+=======================================
+
+cPath aims to be a freely available cancer pathway database. Currently, only
+information about protein-protein interactions collected from major interaction
+databases that support the PSI-MI format is available. cPath is open-source
+and is easy to locally install for private management of protein-protein
+interactions. Future directions include support for the BioPAX format so that
+entire pathways can be stored, queried and presented.
+
+cPath is currently available at: http://www.cbio.mskcc.org/cpath
+
+3. PlugIn Installation Instructions
+=======================================
+
+To use the cPath Plugin, you must first obtain a copy of Cytoscape,
+Version 2.0. You can download a copy from: http://cytoscape.org/.
+
+(Important Note: You must be using Cytoscape 2.0. The cPath PlugIn does
+*not* work with earlier versions of Cytoscape.)
+
+Once you have downloaded Cytoscape and verified that it works, install the
+cPath PlugIn:
+
+1. Copy all the .jar files in the /plugin directory to your
+[Cytoscape_Home]/plugins directory.
+
+2. Restart Cytoscape from the command line. For example, run:
+ cytoscape.sh or cytoscape.bat.
+
+-------------------------------------------------------------------------------
+| Warning: The cPath PlugIn *cannot* be loaded dynamically from Cytoscape |
+| via the PlugIns menu. It can only be loaded by following the instructions |
+| above. |
+-------------------------------------------------------------------------------
+
+
+4. Using the cPath PlugIn
+=======================================
+
+To use the cPath PlugIn:
+
+1. Start Cytoscape. For example, on Unix/Linux or MacOS X, run:
+
+cytoscape.sh
+
+On Windows, run:
+
+cytoscape.bat
+
+2. From the Main Menu, Select "PlugIns" --> "Search cPath..."
+
+2. A new cPath query window will appear. Enter your search terms, and click
+the "Search" button.
+
+Your search results will be automatically downloaded and displayed in the
+main Cytoscape desktop window.
+
+5. Configuring the cPath PlugIn
+=======================================
+If you have a local installation of cPath, and want to point your plugin
+to this local installation, you can do so my modifying the central Cytoscape
+properties file: cytoscape.props.
+
+The property name is: dataservice.cpath_read_location.
+
+For example, the following line points the cPath PlugIn to a local copy
+of cPath
+
+dataservice.cpath_read_location=http://localhost:8080/cpath/webservice.do
+
+6. Bugs / Feature Requests
+=======================================
+
+If you encounter a bug with this plugin, or have a feature suggestion, we
+encourage you to use the Cytoscape Bug Tracker:
+http://www.cbio.mskcc.org/cytoscape/bugs/.
+
+If you log a bug, we will automatically email you when the bug is resolved.
+
+Updates regarding this plugin will be posted to the Cytoscape-announce
+mailing list. You can subscribe to the mailing list or browse the archives
+at: http://groups-beta.google.com/group/cytoscape-announce.
+
+7. Contacts
+=======================================
+
+Sander Group, Computational Biology Center
+Memorial Sloan-Kettering Cancer Center, New York City
+http://www.cbio.mskcc.org/
+
+For any questions concerning this plugin, please contact:
+
+Gary Bader: baderg AT mskcc.org
+Ethan Cerami: cerami AT cbio.mskcc.org
+
+This software is made available under the LGPL (Lesser General Public License).
+
+This product includes software developed by the Apache Software Foundation
+(http://www.apache.org).
+
+VIII. Release Notes
+=======================================
+
+Beta1: August, 2004
+ -- Initial Release of plugin.
+
+Beta2: October, 2004
+ -- PlugIn now supports retrieval of arbitrarily large data sets. For
+ example, you can now download all human records from cPath. This
+ functionality is provided by connecting to the newly revised
+ cPath XML Web Services API.
+ -- PlugIn refactored to use the new csplugins Task Framework, and common
+ Progress Bar component. Progress of data retrieval and time remaining
+ estimates are therefore presented to the end user. Users can now also
+ cancel long-running queries.
+ -- Because very large data sets can now be downloaded, the TreeView
+ for viewing / navigating Interactions/Interactors is no longer practical.
+ The TreeView is therefore no longer available.
+ -- In place of the TreeView, users can now select nodes/edges in the main
+ Cytoscape window and view full Interaction/Interactor details.
+ -- If number of interactors < the Cytoscape View Threshold (default=500), a
+ Cytoscape view is automatically created. Otherwise, a view is not
+ automatically created.
+ -- PlugIn Console now provides more informative log messages to the user.
+ For example, it reports progress of each call to cPath, and reports
+ status of and warnings associated with mapping of cPath data to
+ Cytoscape.
+ -- Quick Reference Manual is updated and now available via a more prominent
+ Help button, instead of via the cPath PlugIn Menu.
+ -- About Dialog box is now available via a more prominent About button,
+ instead of via the cPath PlugIn Menu.
+ -- Added details regarding configuration of cPath PlugIn, so that
+ users can point to local installations of cPath (see README.txt file).
+ This feature was available in beta1, but was undocumented.
+ -- Bug Fix: Beta1 PlugIn attempted to map interactions to Cytoscape Edges
+ via a matrix view (by default.) However, if the number of interactors is
+ large, this can result in a huge number of edges
+ (where # of edges = n(n+1) / 2). The Beta2 PlugIn now only maps
+ interactions with 5 or fewer interactors. Those interactions with more
+ than 5 interactors are reported to the end user as warnings.
+
+Beta 3: June, 2006
+ -- Updated to Work with Cytoscape 2.3 (remains backward compatible to earlier
+ Cytoscape versions).
+
+
diff --git a/coreplugins/cPath/pom.xml b/coreplugins/cPath/pom.xml
new file mode 100644
index 0000000..b3aee1e
--- /dev/null
+++ b/coreplugins/cPath/pom.xml
@@ -0,0 +1,56 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>parent</artifactId>
+ <version>2.8.4-SNAPSHOT</version>
+ </parent>
+
+ <artifactId>cpath</artifactId>
+ <packaging>jar</packaging>
+
+ <name>cPath</name>
+
+ <!-- bootstrap for cytoscape dependencies, namely the parent POM snapshots -->
+ <repositories>
+ <repository>
+ <id>cytoscape_snapshots</id>
+ <snapshots>
+ <enabled>true</enabled>
+ </snapshots>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <name>Cytoscape Snapshots</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/</url>
+ </repository>
+ <repository>
+ <id>cytoscape_releases</id>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ <name>Cytoscape Releases</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/releases/</url>
+ </repository>
+ </repositories>
+
+ <build>
+ <plugins>
+ <plugin>
+ <artifactId>maven-assembly-plugin</artifactId>
+ <configuration>
+ <archive>
+ <manifestEntries>
+ <Cytoscape-Plugin>org.cytoscape.coreplugin.cpath2.plugin.CPathPlugIn2</Cytoscape-Plugin>
+ </manifestEntries>
+ </archive>
+ </configuration>
+ </plugin>
+ </plugins>
+ </build>
+
+</project>
+
diff --git a/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/action/ExecuteQuery.java b/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/action/ExecuteQuery.java
new file mode 100644
index 0000000..efe74d0
--- /dev/null
+++ b/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/action/ExecuteQuery.java
@@ -0,0 +1,144 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.cpath.action;
+
+import cytoscape.task.ui.JTaskConfig;
+
+import cytoscape.task.util.TaskManager;
+
+import org.cytoscape.coreplugin.cpath.model.OrganismOption;
+import org.cytoscape.coreplugin.cpath.model.SearchBundleList;
+import org.cytoscape.coreplugin.cpath.model.SearchRequest;
+import org.cytoscape.coreplugin.cpath.task.QueryCPathTask;
+import org.cytoscape.coreplugin.cpath.ui.Console;
+
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.KeyAdapter;
+import java.awt.event.KeyEvent;
+
+import java.util.HashMap;
+
+import javax.swing.*;
+
+
+/**
+ * Executes cPath Searches.
+ *
+ * @author Ethan Cerami
+ */
+public class ExecuteQuery extends KeyAdapter implements ActionListener {
+ private HashMap cyMap;
+ private SearchRequest searchRequest;
+ private JFrame parent;
+ private QueryCPathTask task;
+ private SearchBundleList searchBundleList;
+ private JButton searchButton;
+ private Console console;
+
+ /**
+ * Constructor.
+ *
+ * @param cyMap CyMap Object.
+ * @param request SearchRequest Object.
+ * @param searchList List of Searches.
+ * @param console Console Panel.
+ * @param searchButton Search Button.
+ * @param parent Parent Component.
+ */
+ public ExecuteQuery(HashMap cyMap, SearchRequest request, SearchBundleList searchList,
+ Console console, JButton searchButton, JFrame parent) {
+ this.cyMap = cyMap;
+ this.searchRequest = request;
+ this.parent = parent;
+ this.searchBundleList = searchList;
+ this.searchButton = searchButton;
+ this.console = console;
+ }
+
+ /**
+ * Execute cPath Query.
+ *
+ * @param e ActionEvent Object.
+ */
+ public void actionPerformed(ActionEvent e) {
+ executeQuery();
+ }
+
+ /**
+ * Listen to Key Press Events in Search Box.
+ *
+ * @param e Key Event.
+ */
+ public void keyPressed(KeyEvent e) {
+ int keyCode = e.getKeyCode();
+
+ if (keyCode == 10) {
+ JTextField textField = (JTextField) e.getSource();
+ searchRequest.setQuery(textField.getText());
+ executeQuery();
+ }
+ }
+
+ /**
+ * Execute Query Against cPath.
+ */
+ private void executeQuery() {
+ if ((searchRequest.getQuery().length() == 0)
+ && searchRequest.getOrganism().equals(OrganismOption.ALL_ORGANISMS)) {
+ JOptionPane.showMessageDialog(parent,
+ "Please Specify a Keyword and/or an Organism, and "
+ + "try again.", "cPath PlugIn",
+ JOptionPane.INFORMATION_MESSAGE);
+ } else {
+ // Disable search button so that user cannot initiate
+ // multiple concurrent searches.
+ searchButton.setEnabled(false);
+ console.clear();
+ // Instantiate QueryCPathTask
+ // Task runs in a new thread, so that GUI remains responsive.
+ task = new QueryCPathTask(cyMap, searchRequest, searchBundleList, console);
+
+ JTaskConfig config = new JTaskConfig();
+ config.setAutoDispose(true);
+ config.displayCancelButton(true);
+ config.displayTimeElapsed(true);
+ config.displayTimeRemaining(true);
+ config.displayStatus(true);
+ config.setOwner(parent);
+ TaskManager.executeTask(task, config);
+ }
+ }
+}
diff --git a/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/action/UpdateSearchRequest.java b/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/action/UpdateSearchRequest.java
new file mode 100644
index 0000000..1a6ab2d
--- /dev/null
+++ b/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/action/UpdateSearchRequest.java
@@ -0,0 +1,97 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.cpath.action;
+
+import org.cytoscape.coreplugin.cpath.model.MaxHitsOption;
+import org.cytoscape.coreplugin.cpath.model.OrganismOption;
+import org.cytoscape.coreplugin.cpath.model.SearchRequest;
+
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.FocusAdapter;
+import java.awt.event.FocusEvent;
+
+import javax.swing.*;
+
+
+/**
+ * Updates the SearchRequest Object based on User Input.
+ *
+ * @author Ethan Cerami
+ */
+public class UpdateSearchRequest extends FocusAdapter implements ActionListener {
+ /**
+ * Search Request Object.
+ */
+ private SearchRequest searchRequest;
+
+ /**
+ * Constructor.
+ *
+ * @param searchRequest Search Request Object.
+ */
+ public UpdateSearchRequest(SearchRequest searchRequest) {
+ this.searchRequest = searchRequest;
+ }
+
+ /**
+ * User has selected an item from the pull-down menu.
+ *
+ * @param e ActionEvent.
+ */
+ public void actionPerformed(ActionEvent e) {
+ JComboBox cb = (JComboBox) e.getSource();
+
+ Object object = cb.getSelectedItem();
+
+ if (object instanceof MaxHitsOption) {
+ MaxHitsOption maxHitsOption = (MaxHitsOption) object;
+ searchRequest.setMaxHits(maxHitsOption);
+ } else if (object instanceof OrganismOption) {
+ OrganismOption organismOption = (OrganismOption) object;
+ searchRequest.setOrganism(organismOption);
+ }
+ }
+
+ /**
+ * Users has Entered New Text in the Search Text Box.
+ *
+ * @param e Focus Event.
+ */
+ public void focusLost(FocusEvent e) {
+ JTextField textField = (JTextField) e.getSource();
+ searchRequest.setQuery(textField.getText());
+ }
+}
diff --git a/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/action/package.html b/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/action/package.html
new file mode 100644
index 0000000..8404e74
--- /dev/null
+++ b/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/action/package.html
@@ -0,0 +1,8 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+<html>
+<head></head>
+
+<body bgcolor="white">
+cPath PlugIn Action Classes.
+</body>
+</html>
diff --git a/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/model/CPathException.java b/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/model/CPathException.java
new file mode 100644
index 0000000..fd61afd
--- /dev/null
+++ b/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/model/CPathException.java
@@ -0,0 +1,60 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.cpath.model;
+
+
+/**
+ * Indicates Error Connecting to cPath.
+ *
+ * @author Ethan Cerami.
+ */
+public class CPathException extends Exception {
+ /**
+ * Constructor.
+ * @param msg Error message.
+ */
+ public CPathException(String msg) {
+ super(msg);
+ }
+
+ /**
+ * Constructor.
+ * @param msg Error message.
+ * @param t Root throwable.
+ */
+ public CPathException(String msg, Throwable t) {
+ super(msg, t);
+ }
+}
diff --git a/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/model/EmptySetException.java b/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/model/EmptySetException.java
new file mode 100644
index 0000000..24ea9cf
--- /dev/null
+++ b/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/model/EmptySetException.java
@@ -0,0 +1,44 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.cpath.model;
+
+
+/**
+ * Empty Set Exception.
+ *
+ * @author Ethan Cerami
+ */
+public class EmptySetException extends Exception {
+}
diff --git a/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/model/MaxHitsOption.java b/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/model/MaxHitsOption.java
new file mode 100644
index 0000000..6c7eab1
--- /dev/null
+++ b/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/model/MaxHitsOption.java
@@ -0,0 +1,137 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.cpath.model;
+
+import java.util.Vector;
+
+
+/**
+ * Contains a Single Option for the MaxHits Pull-Down Menu.
+ *
+ * @author Ethan Cerami
+ */
+public class MaxHitsOption {
+ /**
+ * Get All Description.
+ */
+ public static final String GET_ALL_DESCRIPTION = "No Limit";
+
+ /**
+ * Default Number of Hits.
+ */
+ public static final MaxHitsOption DEFAULT_NUM_HITS = new MaxHitsOption(10);
+
+ /**
+ * Max Number of Hits.
+ */
+ private int maxHits;
+
+ /**
+ * Description of Option (as displayed in pull-down menu).
+ */
+ private String description;
+
+ /**
+ * Constructor.
+ *
+ * @param maxHits MaxHits int value.
+ */
+ public MaxHitsOption(int maxHits) {
+ this.maxHits = maxHits;
+
+ if (maxHits == Integer.MAX_VALUE) {
+ this.description = GET_ALL_DESCRIPTION;
+ } else {
+ this.description = "Limit to " + maxHits;
+ }
+ }
+
+ /**
+ * Gets Max Number of Hits.
+ *
+ * @return max hits integer value.
+ */
+ public int getMaxHits() {
+ return maxHits;
+ }
+
+ /**
+ * Gets Description of Option (as displayed in pull-down menu).
+ *
+ * @return Option description.
+ */
+ public String getDescription() {
+ return description;
+ }
+
+ /**
+ * Gets Description of Option (as displayed in pull-down menu).
+ *
+ * @return Option description.
+ */
+ public String toString() {
+ return this.description;
+ }
+
+ /**
+ * Gets All Options for the Pull-Down Menu.
+ *
+ * @return Vector of MaxHitsOption Objects.
+ */
+ public static Vector getAllOptions() {
+ Vector allOptions = new Vector();
+ allOptions.add(MaxHitsOption.DEFAULT_NUM_HITS);
+ allOptions.add(new MaxHitsOption(20));
+ allOptions.add(new MaxHitsOption(50));
+ allOptions.add(new MaxHitsOption(100));
+ allOptions.add(new MaxHitsOption(500));
+ allOptions.add(new MaxHitsOption(1000));
+ allOptions.add(new MaxHitsOption(5000));
+ allOptions.add(new MaxHitsOption(Integer.MAX_VALUE));
+
+ return allOptions;
+ }
+
+ /**
+ * Clone Object.
+ *
+ * @return Cloned Object.
+ */
+ public Object clone() {
+ MaxHitsOption option = new MaxHitsOption(maxHits);
+
+ return option;
+ }
+}
diff --git a/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/model/OrganismOption.java b/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/model/OrganismOption.java
new file mode 100644
index 0000000..64bd357
--- /dev/null
+++ b/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/model/OrganismOption.java
@@ -0,0 +1,129 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.cpath.model;
+
+import java.util.Vector;
+
+
+/**
+ * Contains a Single Option for the Organism Pull-Down Menu.
+ *
+ * @author Ethan Cerami
+ */
+public class OrganismOption {
+ /**
+ * All Organisms Option.
+ */
+ public static final OrganismOption ALL_ORGANISMS = new OrganismOption(-9999, "All Organisms");
+
+ /**
+ * NCBI Taxonomy ID.
+ */
+ private int taxonomyId;
+
+ /**
+ * Organism Species Name.
+ */
+ private String speciesName;
+
+ /**
+ * Constructor.
+ *
+ * @param taxonomyId NCBI Taxonomy ID.
+ * @param speciesName Organism Species Name.
+ */
+ public OrganismOption(int taxonomyId, String speciesName) {
+ this.taxonomyId = taxonomyId;
+ this.speciesName = speciesName;
+ }
+
+ /**
+ * Gets NCBI Taxonomy ID.
+ *
+ * @return NCBI Taxonomy ID.
+ */
+ public int getTaxonomyId() {
+ return taxonomyId;
+ }
+
+ /**
+ * Gets Organism Species Name.
+ *
+ * @return Organism Species Name.
+ */
+ public String getSpeciesName() {
+ return speciesName;
+ }
+
+ /**
+ * Gets Description of Option (as displayed in pull-down menu).
+ *
+ * @return Option description.
+ */
+ public String toString() {
+ return this.speciesName;
+ }
+
+ /**
+ * Gets All Options for the Pull-Down Menu.
+ *
+ * @return Vector of OrganismOption Objects.
+ */
+ public static Vector getAllOptions() {
+ Vector items = new Vector();
+ items.add(ALL_ORGANISMS);
+ items.add(new OrganismOption(6239, "Caenorhabditis elegans"));
+ items.add(new OrganismOption(7227, "Drosophila melanogaster"));
+ items.add(new OrganismOption(562, "Escherichia coli"));
+ items.add(new OrganismOption(9606, "Homo Sapiens"));
+ items.add(new OrganismOption(85962, "Helicobacter pylori 26695"));
+ items.add(new OrganismOption(10090, "Mus Musculus"));
+ items.add(new OrganismOption(4932, "Saccharomyces cerevisiae"));
+ items.add(new OrganismOption(10116, "Rattus norvegicus"));
+
+ return items;
+ }
+
+ /**
+ * Clone Object.
+ *
+ * @return Cloned Object.
+ */
+ public Object clone() {
+ OrganismOption option = new OrganismOption(taxonomyId, speciesName);
+
+ return option;
+ }
+}
diff --git a/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/model/SearchBundle.java b/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/model/SearchBundle.java
new file mode 100644
index 0000000..fa7cd7e
--- /dev/null
+++ b/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/model/SearchBundle.java
@@ -0,0 +1,112 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.cpath.model;
+
+
+/**
+ * Encapsulates a Search Request and its corresponding Search Response.
+ * Each SearchBundle is identified with a unique integer ID value.
+ *
+ * @author Ethan Cerami
+ */
+public class SearchBundle {
+ /**
+ * The Search Request Object.
+ */
+ private SearchRequest request;
+
+ /**
+ * The Search Respone Object.
+ */
+ private SearchResponse response;
+
+ /**
+ * A Unique Identifier
+ */
+ private int id;
+
+ /**
+ * Stores the Next Bundle ID.
+ */
+ private static int nextId = 0;
+
+ /**
+ * Constructor.
+ *
+ * @param request SearchRequest.
+ * @param response SearchResponse.
+ */
+ public SearchBundle(SearchRequest request, SearchResponse response) {
+ this.id = generateId();
+ this.request = request;
+ this.response = response;
+ }
+
+ /**
+ * Gets Unique Identifier.
+ *
+ * @return Unique Identifier.
+ */
+ public int getId() {
+ return id;
+ }
+
+ /**
+ * Gets Search Request Object.
+ *
+ * @return Search Request.
+ */
+ public SearchRequest getRequest() {
+ return request;
+ }
+
+ /**
+ * Gets Search Response Object.
+ *
+ * @return Search Response.
+ */
+ public SearchResponse getResponse() {
+ return response;
+ }
+
+ /**
+ * Generates a Unique ID based on Static next_id variable.
+ *
+ * @return
+ */
+ private synchronized int generateId() {
+ return nextId++;
+ }
+}
diff --git a/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/model/SearchBundleList.java b/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/model/SearchBundleList.java
new file mode 100644
index 0000000..9599e7f
--- /dev/null
+++ b/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/model/SearchBundleList.java
@@ -0,0 +1,127 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.cpath.model;
+
+import cytoscape.CyNetwork;
+
+import java.util.ArrayList;
+import java.util.Observable;
+
+
+/**
+ * Encapsulates a Complete History of All Search Requests and Search
+ * Responses executed by a user.
+ *
+ * @author Ethan Cerami
+ */
+public class SearchBundleList extends Observable {
+ /**
+ * List of All Search Buncldes.
+ */
+ private ArrayList searchBundles = new ArrayList();
+
+ /**
+ * Adds a new Search Request / Response Pair.
+ *
+ * @param bundle SearchBundle Object.
+ */
+ public void add(SearchBundle bundle) {
+ searchBundles.add(bundle);
+ this.setChanged();
+ this.notifyObservers();
+ }
+
+ /**
+ * Gets Total Number of Search Bundles.
+ *
+ * @return Number of Search Bundles.
+ */
+ public int getNumSearchBundles() {
+ return searchBundles.size();
+ }
+
+ /**
+ * Gets the Search Bundle at the Specified Index.
+ *
+ * @param index Index Value.
+ * @return SearchBundle Object.
+ */
+ public SearchBundle getSearchBundleByIndex(int index) {
+ return (SearchBundle) searchBundles.get(index);
+ }
+
+ /**
+ * Gets the Search Bundle with the Specified Bundle ID.
+ *
+ * @param bundleId Unique Bundle Identifier.
+ * @return SearchBundle Object.
+ */
+ public SearchBundle getSearchBundleByBundleId(int bundleId) {
+ for (int i = 0; i < searchBundles.size(); i++) {
+ SearchBundle bundle = (SearchBundle) searchBundles.get(i);
+ int id = bundle.getId();
+
+ if (bundleId == id) {
+ return bundle;
+ }
+ }
+
+ return null;
+ }
+
+ /**
+ * Gets the Search Bundle with the Specified CyNewtork ID.
+ *
+ * @param networkId Unique CyNetwork Identifier.
+ * @return SearchBundle Object.
+ */
+ public SearchBundle getSearchBundleByCynetworkId(int networkId) {
+ for (int i = 0; i < searchBundles.size(); i++) {
+ SearchBundle bundle = (SearchBundle) searchBundles.get(i);
+ SearchResponse response = bundle.getResponse();
+ CyNetwork network = response.getCyNetwork();
+
+ if (network != null) {
+ int id = Integer.parseInt(network.getIdentifier());
+
+ if (networkId == id) {
+ return bundle;
+ }
+ }
+ }
+
+ return null;
+ }
+}
diff --git a/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/model/SearchRequest.java b/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/model/SearchRequest.java
new file mode 100644
index 0000000..3b7bab9
--- /dev/null
+++ b/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/model/SearchRequest.java
@@ -0,0 +1,156 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.cpath.model;
+
+
+/**
+ * Encapsulates a Search Request which will be sent to cPath.
+ *
+ * @author Ethan Cerami
+ */
+public class SearchRequest {
+ /**
+ * Search Query Terms.
+ */
+ private String query;
+
+ /**
+ * Organism Selection.
+ */
+ private OrganismOption organism;
+
+ /**
+ * MaxHits Selection.
+ */
+ private MaxHitsOption maxHits;
+
+ /**
+ * Constructor.
+ * By default, MaxHits is set to the default value,
+ * and we search all organisms.
+ */
+ public SearchRequest() {
+ this.query = null;
+ this.organism = OrganismOption.ALL_ORGANISMS;
+ this.maxHits = MaxHitsOption.DEFAULT_NUM_HITS;
+ }
+
+ /**
+ * Gets Search Query.
+ *
+ * @return Search Query Terms.
+ */
+ public String getQuery() {
+ return query;
+ }
+
+ /**
+ * Sets Search Query.
+ *
+ * @param query Search Query Terms.
+ */
+ public void setQuery(String query) {
+ this.query = query;
+ }
+
+ /**
+ * Gets Organism Option.
+ *
+ * @return Organism Option.
+ */
+ public OrganismOption getOrganism() {
+ return organism;
+ }
+
+ /**
+ * Sets Organism Option.
+ *
+ * @param organism Organism Option.
+ */
+ public void setOrganism(OrganismOption organism) {
+ this.organism = organism;
+ }
+
+ /**
+ * Gets Max Hits Option.
+ *
+ * @return MaxHits Option.
+ */
+ public MaxHitsOption getMaxHitsOption() {
+ return maxHits;
+ }
+
+ /**
+ * Set Max Hits Option.
+ *
+ * @param maxHits MaxHits Option.
+ */
+ public void setMaxHits(MaxHitsOption maxHits) {
+ this.maxHits = maxHits;
+ }
+
+ /**
+ * Clone the Search Query Object.
+ *
+ * @return Cloned object.
+ */
+ public Object clone() {
+ SearchRequest clone = new SearchRequest();
+ clone.setMaxHits((MaxHitsOption) maxHits.clone());
+ clone.setOrganism((OrganismOption) organism.clone());
+ clone.setQuery(new String(query));
+
+ return clone;
+ }
+
+ /**
+ * Gets Search Query Description.
+ *
+ * @return Query Description.
+ */
+ public String toString() {
+ if ((query != null) && (query.length() > 0)) {
+ StringBuffer text = new StringBuffer(query);
+ String species = organism.getSpeciesName();
+ text.append(" [" + species + "]");
+
+ return text.toString();
+ } else if (organism != null) {
+ return organism.getSpeciesName();
+ } else {
+ return "Query not specified";
+ }
+ }
+}
diff --git a/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/model/SearchResponse.java b/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/model/SearchResponse.java
new file mode 100644
index 0000000..2bc7c28
--- /dev/null
+++ b/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/model/SearchResponse.java
@@ -0,0 +1,142 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.cpath.model;
+
+import cytoscape.CyNetwork;
+
+import cytoscape.view.CyNetworkView;
+
+import java.util.ArrayList;
+
+
+/**
+ * Encapsulates a Search Response received by cPath.
+ *
+ * @author Ethan Cerami
+ */
+public class SearchResponse {
+ /**
+ * Array List of DataService Interaction Objects.
+ */
+ private ArrayList interactions;
+
+ /**
+ * An Exception Object (if one has occurred).
+ */
+ private Throwable exception;
+
+ /**
+ * The Corresponding CyNetwork in Cytoscape.
+ */
+ private CyNetwork cyNetwork;
+
+ /**
+ * The Corresponding CyNetworkView in Cytoscape.
+ */
+ private CyNetworkView cyNetworkView;
+
+ /**
+ * Gets List of Interaction Objects.
+ *
+ * @return ArrayList of Data Service Interaction Object.
+ */
+ public ArrayList getInteractions() {
+ return interactions;
+ }
+
+ /**
+ * Sets List of Interaction Objects.
+ *
+ * @param interactions ArrayList of Data Service Interaction Object.
+ */
+ public void setInteractions(ArrayList interactions) {
+ this.interactions = interactions;
+ }
+
+ /**
+ * Gets Exception (if one has occurred).
+ * If no exception has occurred, this method will return null.
+ *
+ * @return exception or null.
+ */
+ public Throwable getException() {
+ return exception;
+ }
+
+ /**
+ * Sets the Exception.
+ *
+ * @param exception Exception Object.
+ */
+ public void setException(Throwable exception) {
+ this.exception = exception;
+ }
+
+ /**
+ * Gets the CyNetwork Corresponding to this list of interactions.
+ *
+ * @return Cytoscape CyNetwork Object.
+ */
+ public CyNetwork getCyNetwork() {
+ return cyNetwork;
+ }
+
+ /**
+ * Sets the CyNetwork Corresponding to this list of interactions.
+ *
+ * @param cyNetwork Cytoscape CyNetwork Object.
+ */
+ public void setCyNetwork(CyNetwork cyNetwork) {
+ this.cyNetwork = cyNetwork;
+ }
+
+ /**
+ * Gets the CyNetworkView Corresponding to this list of interactions.
+ *
+ * @return Cytoscape CyNetworkView Object.
+ */
+ public CyNetworkView getCyNetworkView() {
+ return cyNetworkView;
+ }
+
+ /**
+ * Sets the CyNetworkView Corresponding to this list of interactions.
+ *
+ * @param cyNetworkView Cytoscape CyNetworkView Object.
+ */
+ public void setCyNetworkView(CyNetworkView cyNetworkView) {
+ this.cyNetworkView = cyNetworkView;
+ }
+}
diff --git a/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/model/UserSelection.java b/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/model/UserSelection.java
new file mode 100644
index 0000000..84d7815
--- /dev/null
+++ b/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/model/UserSelection.java
@@ -0,0 +1,138 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.cpath.model;
+
+import java.util.Observable;
+
+
+/**
+ * Encapsulates Current Selections of the User.
+ * For example, this class stores which Search Request/Response has the
+ * current focus, and which Interactor / Interaction has the current focus.
+ *
+ * @author Ethan Cerami
+ */
+public class UserSelection extends Observable {
+ /**
+ * Property Change: Interactor Focus Has Changed.
+ */
+ public static final Integer INTERACTOR_CHANGED = new Integer(1);
+
+ /**
+ * Property Change: Interaction Focus Has Changed.
+ */
+ public static final Integer INTERACTION_CHANGED = new Integer(2);
+
+ /**
+ * The Currently Selected Interactor.
+ */
+
+ // private Interactor selectedInteractor;
+
+ /**
+ * Selected Node ID.
+ */
+ private String selectedNodeId;
+
+ /**
+ * The Currently Selected Interaction.
+ */
+
+ // private Interaction selectedInteraction;
+
+ /**
+ * Current Search Request / Response that is in Focus.
+ */
+ private int currentSearchIndex;
+
+ /**
+ * Gets the Currently Selected Interactor.
+ *
+ * @return Interactor Object.
+ */
+
+ // public Interactor getSelectedInteractor() {
+ // return selectedInteractor;
+ // }
+
+ /**
+ * Gets the ID of the Currently Selected Node.
+ *
+ * @return Node ID.
+ */
+ public String getSelectedNodeId() {
+ return this.selectedNodeId;
+ }
+
+ /**
+ * Gets the Currently Selected Interaction.
+ *
+ * @return Interaction Object.
+ */
+
+ // public Interaction getSelectedInteraction() {
+ // return selectedInteraction;
+ // }
+
+ /**
+ * Sets the Currently Selected Interactor.
+ *
+ * @param nodeId Node Identifier.
+ * @param selectedInteractor Interactor Object.
+ */
+
+ // public void setSelectedInteractor(String nodeId,
+ // Interactor selectedInteractor) {
+ // this.selectedInteractor = selectedInteractor;
+ // this.selectedNodeId = nodeId;
+ // this.selectedInteraction = null;
+ // this.setChanged();
+ // this.notifyObservers(INTERACTOR_CHANGED);
+ // }
+
+ /**
+ * Sets the Currently Selected Interaction.
+ *
+ * @param selectedInteraction Interaction Object.
+ */
+
+ // public void setSelectedInteraction(Interaction selectedInteraction) {
+ // this.selectedInteraction = selectedInteraction;
+ // this.selectedInteractor = null;
+ // this.selectedNodeId = null;
+ // this.setChanged();
+ // this.notifyObservers(INTERACTION_CHANGED);
+ // }
+}
diff --git a/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/model/package.html b/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/model/package.html
new file mode 100644
index 0000000..98db5d4
--- /dev/null
+++ b/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/model/package.html
@@ -0,0 +1,8 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+<html>
+<head></head>
+
+<body bgcolor="white">
+Core cPath Data Model Objects.
+</body>
+</html>
diff --git a/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/plugin/CPathPlugIn.java b/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/plugin/CPathPlugIn.java
new file mode 100644
index 0000000..dbcf714
--- /dev/null
+++ b/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/plugin/CPathPlugIn.java
@@ -0,0 +1,86 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.cpath.plugin;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.plugin.CytoscapePlugin;
+
+import cytoscape.view.CyMenus;
+import cytoscape.view.CytoscapeDesktop;
+
+import org.cytoscape.coreplugin.cpath.ui.CPathDesktop;
+
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import javax.swing.*;
+
+
+/**
+ * PlugIn For exchanging Data with CPath.
+ *
+ * @author Robert Sheridan, Ethan Cerami
+ */
+public class CPathPlugIn extends CytoscapePlugin implements ActionListener {
+ private CPathDesktop cPathDesktop;
+
+ /**
+ * Constructor.
+ * This method is called by the main Cytoscape Application upon startup.
+ */
+ public CPathPlugIn() {
+ CytoscapeDesktop desktop = Cytoscape.getDesktop();
+ CyMenus cyMenus = desktop.getCyMenus();
+ JMenu plugInMenu = cyMenus.getNewNetworkMenu();
+ JMenuItem menuItem = new JMenuItem("Construct Network Using cPath...");
+ plugInMenu.add(menuItem);
+ menuItem.addActionListener(this);
+ }
+
+ /**
+ * User Has Selected the cPath Plug from the PlugIn Menu.
+ *
+ * @param e ActionEvent Object.
+ */
+ public void actionPerformed(ActionEvent e) {
+ if (cPathDesktop == null) {
+ CytoscapeDesktop desktop = Cytoscape.getDesktop();
+ cPathDesktop = new CPathDesktop(desktop);
+ }
+
+ cPathDesktop.setVisible(true);
+ }
+}
diff --git a/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/plugin/package.html b/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/plugin/package.html
new file mode 100644
index 0000000..0499ba5
--- /dev/null
+++ b/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/plugin/package.html
@@ -0,0 +1,8 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+<html>
+<head></head>
+
+<body bgcolor="white">
+cPath Cytoscape PlugIn Classes.
+</body>
+</html>
diff --git a/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/protocol/CPathProtocol.java b/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/protocol/CPathProtocol.java
new file mode 100644
index 0000000..7793d7b
--- /dev/null
+++ b/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/protocol/CPathProtocol.java
@@ -0,0 +1,427 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.cpath.protocol;
+
+import org.cytoscape.coreplugin.cpath.model.CPathException;
+import org.cytoscape.coreplugin.cpath.model.EmptySetException;
+import org.cytoscape.coreplugin.cpath.util.CPathProperties;
+import org.jdom.Document;
+import org.jdom.Element;
+import org.jdom.JDOMException;
+import org.jdom.input.SAXBuilder;
+
+import java.io.*;
+import java.net.HttpURLConnection;
+import java.net.URL;
+import java.net.UnknownHostException;
+import java.net.URLEncoder;
+
+/**
+ * Utility Class for Connecting to the cPath Web Service API.
+ *
+ * @author Ethan Cerami
+ */
+public class CPathProtocol {
+
+ /**
+ * The CPath Web Service Path.
+ */
+ public static final String WEB_SERVICE_PATH = "webservice.do";
+
+ /**
+ * Command Argument.
+ */
+ public static final String ARG_COMMAND = "cmd";
+
+ /**
+ * Query Argument.
+ */
+ public static final String ARG_QUERY = "q";
+
+ /**
+ * Format Argument.
+ */
+ public static final String ARG_FORMAT = "format";
+
+ /**
+ * Organism Argument.
+ */
+ public static final String ARG_ORGANISM = "organism";
+
+ /**
+ * Max Hits Argument.
+ */
+ public static final String ARG_MAX_HITS = "maxHits";
+
+ /**
+ * Start Index Argument.
+ */
+ public static final String ARG_START_INDEX = "startIndex";
+
+ /**
+ * Version Argument.
+ */
+ public static final String ARG_VERSION = "version";
+
+ /**
+ * PSI-MI XML Format.
+ */
+ public static final String FORMAT_XML = "xml";
+
+ /**
+ * BIOXPAX XML Format.
+ */
+ public static final String FORMAT_BIOPAX = "biopax";
+
+ /**
+ * Count Only Format.
+ */
+ public static final String FORMAT_COUNT_ONLY = "count_only";
+
+ /**
+ * Currently Supported Version.
+ */
+ public static final String CURRENT_VERSION = "1.0";
+
+ /**
+ * Get Interactions By Keyword.
+ */
+ public static final String COMMAND_GET_BY_KEYWORD =
+ "get_by_keyword";
+
+ /**
+ * Get Interactions By Interactor Name / Xref.
+ */
+ public static final String COMMAND_GET_BY_INTERACTOR_XREF =
+ "get_by_interactor_name_xref";
+
+ /**
+ * Get Interactions By Organism.
+ */
+ public static final String COMMAND_GET_BY_ORGANISM =
+ "get_by_organism";
+
+ /**
+ * Get Interactions By Experiment Type.
+ */
+ public static final String COMMAND_GET_BY_EXPERIMENT_TYPE =
+ "get_by_experiment_type";
+
+ /**
+ * Get Interactions by PMID.
+ */
+ public static final String COMMAND_GET_BY_PMID =
+ "get_by_pmid";
+
+ /**
+ * Get Interactions By Database.
+ */
+ public static final String COMMAND_GET_BY_DATABASE =
+ "get_by_database";
+
+ /**
+ * Get Top Level Pathway List.
+ */
+ public static final String COMMAND_GET_TOP_LEVEL_PATHWAY_LIST =
+ "get_top_level_pathway_list";
+
+ /**
+ * Get Patheway record by CPath ID.
+ */
+ public static final String COMMAND_GET_RECORD_BY_CPATH_ID =
+ "get_record_by_cpath_id";
+
+ /**
+ * Default for Max Hits.
+ */
+ public static final int DEFAULT_MAX_HITS = 10;
+
+ /**
+ * Not Specified
+ */
+ public static final int NOT_SPECIFIED = -1;
+
+ /**
+ * XML Tag.
+ */
+ private static final String XML_TAG = "xml";
+
+ private String command;
+ private String query;
+ private int taxonomyId;
+ private int maxHits;
+ private int startIndex;
+ private String format;
+ private String baseUrl;
+
+ /**
+ * Constructor.
+ */
+ public CPathProtocol () {
+ this.baseUrl = CPathProperties.getCPathUrl();
+ this.maxHits = DEFAULT_MAX_HITS;
+ this.taxonomyId = NOT_SPECIFIED;
+ }
+
+ /**
+ * Sets the Command Argument.
+ *
+ * @param command Command Argument.
+ */
+ public void setCommand (String command) {
+ this.command = command;
+ }
+
+ /**
+ * Sets the Query Argument.
+ *
+ * @param query Query Argument.
+ */
+ public void setQuery (String query) {
+ this.query = query;
+ }
+
+ /**
+ * Sets the Format Argument.
+ *
+ * @param format Format Argument.
+ */
+ public void setFormat (String format) {
+ this.format = format;
+ }
+
+ /**
+ * Sets the Organism Argument.
+ *
+ * @param taxonomyId NCBI TaxonomyID
+ */
+ public void setOrganism (int taxonomyId) {
+ this.taxonomyId = taxonomyId;
+ }
+
+ /**
+ * Sets the MaxHits Argument.
+ *
+ * @param maxHits Max Number of Hits.
+ */
+ public void setMaxHits (int maxHits) {
+ this.maxHits = maxHits;
+ }
+
+ /**
+ * Sets the StartIndex Argument.
+ *
+ * @param startIndex StartIndex Argument.
+ */
+ public void setStartIndex (int startIndex) {
+ this.startIndex = startIndex;
+ }
+
+ /**
+ * Connects to cPath Web Service API.
+ *
+ * @return XML Document.
+ * @throws CPathException Indicates Error connecting.
+ * @throws EmptySetException All went all, but no results found.
+ */
+ public String connect () throws CPathException, EmptySetException {
+ try {
+ NameValuePair[] nvps = createNameValuePairs();
+ String liveUrl = createURI(baseUrl, nvps);
+ URL cPathUrl = new URL(liveUrl);
+ HttpURLConnection cPathConnection = (HttpURLConnection) cPathUrl.openConnection();
+
+ // Check status code
+ int statusCode = cPathConnection.getResponseCode();
+ checkHttpStatusCode(statusCode);
+
+ // Read all the text returned by the server
+ BufferedReader in = new BufferedReader(new InputStreamReader(cPathUrl.openStream()));
+ StringBuffer buf = new StringBuffer();
+ String str;
+ while ((str = in.readLine()) != null) {
+ buf.append(str + "\n");
+ }
+ in.close();
+
+ // Check for errors
+ String content = buf.toString();
+ if (content.toLowerCase().indexOf(XML_TAG) >= 0) {
+ // Check for protocol errors.
+ if (content.indexOf("<error>") >=0) {
+ StringReader reader = new StringReader(content);
+ SAXBuilder builder = new SAXBuilder();
+ Document document = builder.build(reader);
+ checkForErrors(document);
+ }
+ return content;
+ } else {
+ return content.trim();
+ }
+ } catch (UnknownHostException e) {
+ String msg = "Network error occurred while tring to connect to "
+ + "the cPath Web Service. Could not find server: "
+ + e.getMessage()
+ + ". Please check your server and network settings, "
+ + "and try again.";
+ throw new CPathException(msg, e);
+ } catch (IOException e) {
+ String msg = "Network error occurred while trying to "
+ + "connect to the cPath Web Service. "
+ + "Please check your server and network settings, "
+ + "and try again.";
+ throw new CPathException(msg, e);
+ } catch (JDOMException e) {
+ String msg = "Error occurred while trying to parse XML results "
+ + "retrieved from the cPath Web Service. "
+ + "Please check your server and network settings, "
+ + "and try again.";
+ throw new CPathException(msg, e);
+ }
+ }
+
+ /**
+ * Gets URI
+ *
+ * @return URI.
+ */
+ public String getURI () {
+ NameValuePair[] nvps = createNameValuePairs();
+ return createURI(baseUrl, nvps);
+ }
+
+ /**
+ * Gets URI of cPath Call.
+ *
+ * @return URI for cPath Call.
+ */
+ private String createURI (String url, NameValuePair[] nvps) {
+ StringBuffer buf = new StringBuffer(url);
+ buf.append("?");
+ for (int i = 0; i < nvps.length; i++) {
+ buf.append(nvps[i].getName() + "=" + nvps[i].getValue() + "&");
+ }
+ return buf.toString();
+ }
+
+ private NameValuePair[] createNameValuePairs () {
+ NameValuePair nvps[] = null;
+ if (taxonomyId == NOT_SPECIFIED) {
+ nvps = new NameValuePair[6];
+ } else {
+ nvps = new NameValuePair[7];
+ nvps[6] = new NameValuePair(ARG_ORGANISM,
+ Integer.toString(taxonomyId));
+ }
+ nvps[0] = new NameValuePair(ARG_COMMAND, command);
+ nvps[1] = new NameValuePair(ARG_QUERY, query);
+ nvps[2] = new NameValuePair(ARG_FORMAT, format);
+ nvps[3] = new NameValuePair(ARG_VERSION, CPathProtocol.CURRENT_VERSION);
+ nvps[4] = new NameValuePair(ARG_MAX_HITS, Integer.toString(maxHits));
+ nvps[5] = new NameValuePair(ARG_START_INDEX,
+ Integer.toString(startIndex));
+ return nvps;
+ }
+
+ private void checkHttpStatusCode (int statusCode)
+ throws CPathException {
+ if (statusCode != 200) {
+ String msg = new String("Error Connecting to cPath "
+ + "Web Service (Details: HTTP Status Code: "
+ + statusCode + ")");
+ throw new CPathException(msg);
+ }
+ }
+
+ private void checkForErrors (Document document)
+ throws CPathException, EmptySetException {
+ Element element = document.getRootElement();
+ String name = element.getName();
+ if (name.equals("error")) {
+ String errorCode = element.getChild("error_code").getText();
+ String errorMsg = element.getChild("error_msg").getText();
+ if (errorCode.equals("460")) {
+ throw new EmptySetException();
+ } else {
+ String msg = new String("Error Connecting to cPath "
+ + "Web Service (Error Code: " + errorCode
+ + ", Error Message: " + errorMsg
+ + ")");
+ throw new CPathException(msg);
+ }
+ }
+ }
+}
+
+/**
+ * Name Value Pair.
+ *
+ * @author Ethan Cerami.
+ */
+class NameValuePair {
+ private String name;
+ private String value;
+
+ /**
+ * Constructor.
+ * @param name name.
+ * @param value value.
+ */
+ public NameValuePair (String name, String value) {
+ this.name = name;
+ try {
+ this.value = URLEncoder.encode(value, "UTF-8");
+ } catch (UnsupportedEncodingException e) {
+ e.printStackTrace();
+ this.value = value;
+ }
+ }
+
+ /**
+ * Gets name.
+ * @return name.
+ */
+ public String getName () {
+ return name;
+ }
+
+ /**
+ * Gets value.
+ * @return value.
+ */
+ public String getValue () {
+ return value;
+ }
+}
diff --git a/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/protocol/package.html b/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/protocol/package.html
new file mode 100644
index 0000000..710c475
--- /dev/null
+++ b/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/protocol/package.html
@@ -0,0 +1,8 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+<html>
+<head></head>
+
+<body bgcolor="white">
+cPath Protocol for Web Service API.
+</body>
+</html>
diff --git a/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/task/CPathTimeEstimator.java b/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/task/CPathTimeEstimator.java
new file mode 100644
index 0000000..bee2b2b
--- /dev/null
+++ b/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/task/CPathTimeEstimator.java
@@ -0,0 +1,67 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.cpath.task;
+
+
+/**
+ * Estimates Time Remaining for a Long-Running cPath Query.
+ *
+ * @author Ethan Cerami.
+ */
+public class CPathTimeEstimator {
+ /**
+ * Calculates Estimated Time Remaining.
+ *
+ * @param lastRequestTime Time Interval for Last Request.
+ * @param startIndex Start Index for just completed request.
+ * @param increment Number of Interactions retrieved per request.
+ * @param totalNumInteractions Total Number of Interactions to Retrieve.
+ * @return estimated time, in milliseconds.
+ */
+ public static long calculateEsimatedTimeRemaining(long lastRequestTime, int startIndex,
+ int increment, int totalNumInteractions) {
+ // How Many more interactions do we need to donwload?
+ int numInteractionsRemaining = totalNumInteractions - startIndex - increment;
+ numInteractionsRemaining = Math.max(numInteractionsRemaining, 0);
+
+ // How Many more network request do we need to make?
+ int numRequestsRemaining = (int) Math.ceil(numInteractionsRemaining / (double) increment);
+
+ // Based on last request, approximate time remaining.
+ long totalTimeRemaining = lastRequestTime * numRequestsRemaining;
+
+ return totalTimeRemaining;
+ }
+}
diff --git a/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/task/QueryCPathTask.java b/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/task/QueryCPathTask.java
new file mode 100644
index 0000000..95a6001
--- /dev/null
+++ b/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/task/QueryCPathTask.java
@@ -0,0 +1,309 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.cpath.task;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import cytoscape.CytoscapeInit;
+import cytoscape.layout.CyLayoutAlgorithm;
+import cytoscape.data.readers.GraphReader;
+import cytoscape.task.Task;
+import cytoscape.task.TaskMonitor;
+import cytoscape.view.CyNetworkView;
+import org.cytoscape.coreplugin.cpath.model.*;
+import org.cytoscape.coreplugin.cpath.protocol.CPathProtocol;
+import org.cytoscape.coreplugin.cpath.ui.Console;
+import org.cytoscape.coreplugin.cpath.util.CPathProperties;
+
+import javax.swing.*;
+import java.io.IOException;
+import java.util.Date;
+import java.util.HashMap;
+
+/**
+ * Task to Query cPath.
+ *
+ * @author Ethan Cerami.
+ */
+public class QueryCPathTask implements Task {
+ private HashMap cyMap;
+ private SearchRequest searchRequest;
+ private SearchResponse searchResponse;
+ private SearchBundle searchBundle;
+ private SearchBundleList searchList;
+ private Console console;
+ private static final int DEFAULT_INCREMENT = 10;
+ private static final int LARGER_INCREMENT = 100;
+ private TaskMonitor taskMonitor;
+ private boolean isInterrupted;
+
+ /**
+ * Constructor.
+ *
+ * @param cyMap HashMap
+ * @param searchRequest SearchRequest Object.
+ * @param searchList List of Search Bundles.
+ * @param console Console Object.
+ */
+ public QueryCPathTask (HashMap cyMap, SearchRequest searchRequest,
+ SearchBundleList searchList, Console console) {
+ this.logToConsole("Retrieving Data from cPath: "
+ + searchRequest.toString() + "...", "bold");
+
+ String url = CPathProperties.getCPathUrl();
+ logToConsole("Connecting to cPath: " + url);
+
+ this.cyMap = cyMap;
+ this.searchRequest = searchRequest;
+ this.searchList = searchList;
+ this.console = console;
+ }
+
+ /**
+ * Halts cPath Task.
+ */
+ public void halt () {
+ isInterrupted = true;
+ }
+
+ /**
+ * Sets Task Monitor.
+ *
+ * @param taskMonitor TaskMonitor Object.
+ * @throws IllegalThreadStateException Illegal Thread State.
+ */
+ public void setTaskMonitor (TaskMonitor taskMonitor) throws IllegalThreadStateException {
+ this.taskMonitor = taskMonitor;
+ }
+
+ /**
+ * Gets Task Title.
+ *
+ * @return task title.
+ */
+ public String getTitle () {
+ return "Connecting to cPath: " + searchRequest.toString();
+ }
+
+ /**
+ * Executes Task
+ */
+ public void run () {
+ // Set Initial Messages
+ taskMonitor.setPercentCompleted(-1);
+ taskMonitor.setStatus("Connecting to cPath...");
+ searchResponse = new SearchResponse();
+ try {
+ OrganismOption organism = searchRequest.getOrganism();
+ int taxonomyId = organism.getTaxonomyId();
+ if (organism == OrganismOption.ALL_ORGANISMS) {
+ taxonomyId = CPathProtocol.NOT_SPECIFIED;
+ }
+ int maxHits = searchRequest.getMaxHitsOption().getMaxHits();
+ getAllInteractions(taxonomyId, maxHits);
+ taskMonitor.setPercentCompleted(100);
+ } catch (EmptySetException e) {
+ this.logToConsole ("No Matching Results Found for: "
+ + searchRequest.getQuery() + ". Please Try Again.", "red");
+ taskMonitor.setPercentCompleted(100);
+ } catch (RuntimeException e) {
+ searchResponse.setException(e);
+ } catch (Exception e) {
+ searchResponse.setException(e);
+ } catch (Throwable e) {
+ searchResponse.setException(e);
+ } finally {
+ searchBundle = new SearchBundle
+ ((SearchRequest) searchRequest.clone(), searchResponse);
+ searchList.add(searchBundle);
+ if (isInterrupted) {
+ logToConsole("Data Retrieval Cancelled by User.");
+ }
+ }
+ }
+
+ /**
+ * Gets All Interactions.
+ */
+ private void getAllInteractions (int taxonomyId, int maxHits)
+ throws InterruptedException, CPathException, EmptySetException, IOException {
+ searchResponse = new SearchResponse();
+
+ // First, determine how many interactions we have in total
+ ReadPsiFromCPath reader = new ReadPsiFromCPath();
+ int totalNumInteractions = reader.getInteractionsCount
+ (searchRequest.getQuery(), taxonomyId);
+ logToConsole("Total Number of Matching Interactions: "
+ + totalNumInteractions);
+
+ // 0% Complete
+ taskMonitor.setPercentCompleted(0);
+
+ // Retrieve the interactions
+ int index = 0;
+ int endIndex = Math.min(maxHits, totalNumInteractions);
+ int increment = DEFAULT_INCREMENT;
+ if (maxHits > 100) {
+ increment = LARGER_INCREMENT;
+ }
+
+ // Create CyNetwork
+ String title = searchRequest.toString();
+
+ if (title.length() > 25) {
+ title = title.substring(0,24) + "...";
+ }
+
+ // Create Network w/o view
+ CyNetwork cyNetwork = Cytoscape.createNetwork(title, false);
+
+ GraphReader graphReader = null;
+ while (index < endIndex && !isInterrupted) {
+ graphReader = getInteractions(taxonomyId, index, increment, endIndex);
+ graphReader.read();
+ addToCyNetwork(graphReader, cyNetwork);
+ index += increment;
+ if (isInterrupted) {
+ throw new InterruptedException();
+ }
+
+ }
+
+ CyNetworkView networkView = createNetworkView(cyNetwork);
+ if (networkView != null) {
+ CyLayoutAlgorithm layoutAlgorithm = graphReader.getLayoutAlgorithm();
+ if (layoutAlgorithm != null) {
+ layoutAlgorithm.doLayout(networkView);
+ }
+ }
+ }
+
+ /**
+ * Iteratively Get Interactions from cPath.
+ */
+ private GraphReader getInteractions (int taxonomyId, int startIndex, int increment,
+ int totalNumInteractions) throws CPathException, EmptySetException {
+
+ ReadPsiFromCPath reader = new ReadPsiFromCPath();
+ int endIndex = Math.min(startIndex + increment, totalNumInteractions);
+ taskMonitor.setStatus("Getting Interactions: " + startIndex
+ + " - " + endIndex + " of "
+ + totalNumInteractions);
+
+ GraphReader graphReader = reader.getInteractionsByKeyword
+ (searchRequest.getQuery(), taxonomyId,
+ startIndex, increment);
+
+ //logToConsole("Getting Interactions: " + startIndex
+ // + " - " + endIndex + " of "
+ // + totalNumInteractions + " [OK]");
+
+ double percentCompleted = (startIndex + increment) / (double) totalNumInteractions;
+ int percent = (int) (percentCompleted * 100.0);
+ if (percent > 100) {
+ percent = 100;
+ }
+ taskMonitor.setPercentCompleted(percent);
+ return graphReader;
+ }
+
+ private void addToCyNetwork (GraphReader reader, CyNetwork cyNetwork) {
+ // Add new nodes/edges to network
+ int nodeIndices[] = reader.getNodeIndicesArray();
+ int edgeIndices[] = reader.getEdgeIndicesArray();
+ for (int i = 0; i < nodeIndices.length; i++) {
+ cyNetwork.addNode(nodeIndices[i]);
+ }
+ for (int i = 0; i < edgeIndices.length; i++) {
+ cyNetwork.addEdge(edgeIndices[i]);
+ }
+ }
+
+ private CyNetworkView createNetworkView (CyNetwork cyNetwork) {
+ // Conditionally Create a View, based on Number of Nodes.
+ // GetViewThreshold is settable by the End User.
+ logToConsole("Total Number of Nodes in Network: "
+ + cyNetwork.getNodeCount());
+ logToConsole("Total Number of Edges in Network: "
+ + cyNetwork.getEdgeCount());
+ int threshold = Integer.parseInt(CytoscapeInit.getProperties().getProperty
+ ("viewThreshold", "5000"));
+ CyNetworkView view = null;
+ if (cyNetwork.getNodeCount() < threshold) {
+ logToConsole("Your Network is Under "
+ + threshold
+ + " nodes --> a Cytoscape View will be "
+ + "automatically created.");
+ taskMonitor.setStatus("Creating Network View. Please wait.");
+ view = Cytoscape.createNetworkView(cyNetwork);
+ searchResponse.setCyNetworkView(view);
+ taskMonitor.setStatus("Applying Visual Styles.");
+ Cytoscape.getVisualMappingManager().applyAppearances();
+ } else {
+ logToConsole("Your Network is Over " + threshold
+ + " nodes --> a Cytoscape View will not be "
+ + "automatically created.");
+ }
+ return view;
+ }
+
+ /**
+ * Logs to Console by queing an event to the Event-Dispatch Thread.
+ *
+ * @param msg Message to Log.
+ */
+ private void logToConsole (final String msg) {
+ Runnable runnable = new Runnable() {
+ public void run () {
+ console.logMessage(msg);
+ }
+ };
+ SwingUtilities.invokeLater(runnable);
+ }
+
+ /**
+ * Logs to Console by queing an event to the Event-Dispatch Thread.
+ *
+ * @param msg Message to Log.
+ */
+ private void logToConsole (final String msg, final String style) {
+ Runnable runnable = new Runnable() {
+ public void run () {
+ console.logMessage(msg, style);
+ }
+ };
+ SwingUtilities.invokeLater(runnable);
+ }
+}
diff --git a/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/task/ReadPsiFromCPath.java b/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/task/ReadPsiFromCPath.java
new file mode 100644
index 0000000..47a76f6
--- /dev/null
+++ b/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/task/ReadPsiFromCPath.java
@@ -0,0 +1,181 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.cpath.task;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.data.ImportHandler;
+
+import cytoscape.data.readers.GraphReader;
+
+import org.cytoscape.coreplugin.cpath.model.CPathException;
+import org.cytoscape.coreplugin.cpath.model.EmptySetException;
+import org.cytoscape.coreplugin.cpath.protocol.CPathProtocol;
+
+import java.net.MalformedURLException;
+import java.net.URL;
+
+
+/**
+ * Reads PSI Interactions from cPath.
+ *
+ * @author Ethan Cerami
+ */
+public class ReadPsiFromCPath {
+ /**
+ * Parameter Not Specified.
+ */
+ public static final int NOT_SPECIFIED = -1;
+ private String uri;
+
+ /**
+ * Gets ArrayList of Interactions by Keyword
+ *
+ * @param keyword Keyword String.
+ * @param taxonomyId TaxonomyID.
+ * @param maxHits MaxHits.
+ * @return ArrayList of Interactions.
+ * @throws CPathException cPath Connection Error.
+ * @throws EmptySetException No Matching Interactions Found.
+ */
+ public GraphReader getInteractionsByKeyword(String keyword, int taxonomyId, int maxHits)
+ throws CPathException, EmptySetException {
+ return process(CPathProtocol.COMMAND_GET_BY_KEYWORD, keyword, taxonomyId, 0, maxHits);
+ }
+
+ /**
+ * Gets ArrayList of Interactions by Keyword
+ *
+ * @param keyword Keyword String.
+ * @param taxonomyId TaxonomyID.
+ * @param startIndex StartIndex.
+ * @param maxHits MaxHits.
+ * @return GraphReader Object.
+ * @throws CPathException cPath Connection Error.
+ * @throws EmptySetException No Matching Interactions Found.
+ */
+ public GraphReader getInteractionsByKeyword(String keyword, int taxonomyId, int startIndex,
+ int maxHits)
+ throws CPathException, EmptySetException {
+ return process(CPathProtocol.COMMAND_GET_BY_KEYWORD, keyword, taxonomyId, startIndex,
+ maxHits);
+ }
+
+ /**
+ * Gets Total Number of Interactions for specified search parameters.
+ *
+ * @param keyword Search Keyword.
+ * @param taxonomyId Taxonomy ID.
+ * @return number of interactions.
+ * @throws CPathException Data Service Error.
+ * @throws EmptySetException No Results Found.
+ */
+ public int getInteractionsCount(String keyword, int taxonomyId)
+ throws CPathException, EmptySetException {
+ CPathProtocol cpath = new CPathProtocol();
+ cpath.setCommand(CPathProtocol.COMMAND_GET_BY_KEYWORD);
+ cpath.setFormat(CPathProtocol.FORMAT_COUNT_ONLY);
+ cpath.setQuery(keyword);
+
+ if (taxonomyId != NOT_SPECIFIED) {
+ cpath.setOrganism(taxonomyId);
+ }
+
+ uri = cpath.getURI();
+
+ String value = cpath.connect();
+ int count;
+
+ try {
+ count = Integer.parseInt(value);
+ } catch (NumberFormatException e) {
+ throw new CPathException("Error Occurred while connecting "
+ + "to the cPath Web Service (Details: Invalid data "
+ + "returned. Double check that you are using the correct "
+ + "cPath URL.)");
+ }
+
+ return count;
+ }
+
+ /**
+ * Gets ArrayList of Interactions by Keyword
+ *
+ * @param keyword Keyword String.
+ * @param maxHits MaxHits.
+ * @return ArrayList of Interactions.
+ * @throws CPathException Indicates error connecting to data service.
+ * @throws EmptySetException No Matching Interactions Found.
+ */
+ public GraphReader getInteractionsByKeyword(String keyword, int maxHits)
+ throws CPathException, EmptySetException {
+ return process(CPathProtocol.COMMAND_GET_BY_KEYWORD, keyword, NOT_SPECIFIED, 0, maxHits);
+ }
+
+ /**
+ * Gets URI of Last Query.
+ *
+ * @return URI String.
+ */
+ public String getLastQueryURI() {
+ return uri;
+ }
+
+ /**
+ * Process Service.
+ */
+ private GraphReader process(String command, String query, int taxonomyId, int startIndex,
+ int maxHits) throws CPathException {
+ CPathProtocol cpath = new CPathProtocol();
+ cpath.setCommand(command);
+ cpath.setFormat(CPathProtocol.FORMAT_XML);
+ cpath.setQuery(query);
+ cpath.setStartIndex(startIndex);
+ cpath.setMaxHits(maxHits);
+
+ if (taxonomyId != NOT_SPECIFIED) {
+ cpath.setOrganism(taxonomyId);
+ }
+
+ try {
+ URL url = new URL(cpath.getURI());
+ GraphReader reader = Cytoscape.getImportHandler().getReader(url);
+
+ return reader;
+ } catch (MalformedURLException e) {
+ throw new CPathException("Could not parse URL", e);
+ }
+ }
+}
diff --git a/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/task/package.html b/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/task/package.html
new file mode 100644
index 0000000..1d59e0a
--- /dev/null
+++ b/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/task/package.html
@@ -0,0 +1,8 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+<html>
+<head></head>
+
+<body bgcolor="white">
+Long term cPath tasks.
+</body>
+</html>
diff --git a/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/ui/AboutDialog.java b/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/ui/AboutDialog.java
new file mode 100644
index 0000000..a2f5a43
--- /dev/null
+++ b/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/ui/AboutDialog.java
@@ -0,0 +1,152 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.cpath.ui;
+
+import java.awt.*;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+
+import javax.swing.*;
+import javax.swing.border.EmptyBorder;
+
+
+/**
+ * Displays Information About the cPath PlugIn.
+ *
+ * @author Ethan Cerami.
+ */
+public class AboutDialog extends MouseAdapter implements ActionListener {
+ /**
+ * Current Version Number.
+ */
+ public static final String VERSION = "Beta 3";
+
+ /**
+ * Current Release Date.
+ */
+ public static final String RELEASE_DATE = "June, 2006";
+ private JFrame parent;
+ private JDialog dialog;
+ private static final int WIDTH = 400;
+ private static final int HEIGHT = 450;
+
+ /**
+ * Constructor.
+ *
+ * @param parent Parent Frame.
+ */
+ public AboutDialog(JFrame parent) {
+ this.parent = parent;
+ }
+
+ /**
+ * User has requested that we shows the About Dialog.
+ *
+ * @param event ActionEvent Object.
+ */
+ public void actionPerformed(ActionEvent event) {
+ dialog = new JDialog(parent, "About the cPath PlugIn", true);
+
+ Container contentPane = dialog.getContentPane();
+ contentPane.setLayout(new BorderLayout());
+
+ JEditorPane htmlPane = new JEditorPane();
+ htmlPane.addMouseListener(this);
+
+ EmptyBorder border = new EmptyBorder(5, 5, 5, 5);
+ htmlPane.setBorder(border);
+ htmlPane.setContentType("text/html");
+ htmlPane.setEditable(false);
+ htmlPane.setPreferredSize(new Dimension(WIDTH, HEIGHT));
+
+ String html = this.getAboutHtml();
+ htmlPane.setText(html);
+
+ JScrollPane scrollPane = new JScrollPane(htmlPane);
+ contentPane.add(scrollPane, BorderLayout.CENTER);
+
+ Point point = parent.getLocation();
+ Dimension size = parent.getSize();
+ int x = (int) ((point.getX() + (size.getWidth() / 2)) - (WIDTH / 2));
+ int y = (int) ((point.getY() + (size.getHeight() / 2)) - (HEIGHT / 2));
+ dialog.setLocation(x, y);
+ dialog.pack();
+ dialog.setVisible(true);
+ }
+
+ private String getAboutHtml() {
+ StringBuffer html = new StringBuffer();
+ html.append("<FONT FACE=ARIAL>");
+ html.append("<IMG SRC='http://www.mskcc.org/mskcc_resources/" + "images/logos/336699.gif'>");
+ html.append("<BR>cPath PlugIn Version: " + VERSION);
+ html.append("<BR>Release Date: " + RELEASE_DATE);
+
+ // PropertyManager pManager = PropertyManager.getInstance();
+ // String url = pManager.getProperty(PropertyManager.CPATH_READ_LOCATION);
+ // html.append("<P>Your PlugIn is currently configured to retrieve "
+ // + "data from: " + url);
+ html.append("<P>The Cytoscape cPath Plugin is maintained by ");
+ html.append("the Sander group at the Computational Biology Center ");
+ html.append("of Memorial Sloan-Kettering Cancer Center.");
+ html.append("<P>");
+ html.append("cPath is available at: " + "http://cbio.mskcc.org/cpath.");
+ html.append("<P>");
+ html.append("For scientific questions regarding cPath or the cPath"
+ + " PlugIn, please contact Gary Bader: <" + "bader at cbio.mskcc.org>.");
+ html.append("<P>");
+ html.append("For technical / programming questions regarding cPath or"
+ + " the cPath PlugIn, please contact Ethan Cerami: "
+ + " <cerami at cbio.mskcc.org>");
+ html.append("</FONT>");
+ html.append("<P><HR><FONT FACE=ARIAL SIZE=-1>");
+ html.append("Copyright � 2004 Memorial Sloan-Kettering Cancer Center.");
+ html.append("</FONT>");
+
+ return html.toString();
+ }
+
+ /**
+ * Mouse Clicked. Dialog if Disposed.
+ *
+ * @param e MouseEvent.
+ */
+ public void mouseClicked(MouseEvent e) {
+ if (dialog != null) {
+ dialog.dispose();
+ }
+ }
+}
diff --git a/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/ui/CPathDesktop.java b/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/ui/CPathDesktop.java
new file mode 100644
index 0000000..601563e
--- /dev/null
+++ b/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/ui/CPathDesktop.java
@@ -0,0 +1,287 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.cpath.ui;
+
+import org.cytoscape.coreplugin.cpath.action.ExecuteQuery;
+import org.cytoscape.coreplugin.cpath.action.UpdateSearchRequest;
+import org.cytoscape.coreplugin.cpath.model.*;
+import org.cytoscape.coreplugin.cpath.util.CPathProperties;
+
+import javax.swing.*;
+import javax.swing.border.EmptyBorder;
+import javax.swing.border.TitledBorder;
+import javax.swing.border.LineBorder;
+import java.awt.*;
+import java.util.HashMap;
+import java.util.Observable;
+import java.util.Observer;
+import java.util.Vector;
+
+/**
+ * cPath Frame with Search Box and Search Results.
+ *
+ * @author Ethan Cerami
+ */
+public class CPathDesktop extends JFrame implements Observer {
+
+ /**
+ * The Current Search Query (Data Model Object)
+ */
+ private SearchRequest searchRequest;
+
+ /**
+ * List of All Searches (Data Model Object)
+ */
+ private static SearchBundleList searchList = new SearchBundleList();
+
+ /**
+ * Console Panel.
+ */
+ private ConsolePanel consolePanel;
+
+ /**
+ * Current User Node / Edge Selection.
+ */
+ private UserSelection userSelection;
+
+ /**
+ * CyMap of all Interactors/Interactions Index by Node/Edge Id.
+ */
+ private HashMap cyMap;
+
+ /**
+ * Search Button.
+ */
+ private JButton searchButton;
+
+ /**
+ * Preferred Width of Component.
+ */
+ private static final int WIDTH = 400;
+
+ /**
+ * Preferred Height of Component.
+ */
+ private static final int HEIGHT = 400;
+
+ /**
+ * Constructor.
+ *
+ * @param parent Parent Frame.3
+ */
+ public CPathDesktop (JFrame parent) {
+ super("cPath PlugIn");
+
+ // Initialize User Selection Object and CyMap
+ userSelection = new UserSelection();
+ cyMap = new HashMap();
+
+ // Create Empty Search Query Object
+ searchRequest = new SearchRequest();
+
+ // Register to Listen to changes to SearchList
+ searchList.addObserver(this);
+
+ // Use Border Layout
+ Container cPane = getContentPane();
+ cPane.setLayout(new BorderLayout());
+
+ // Create Center Panel (Console plus Details)
+ consolePanel = new ConsolePanel();
+ String url = CPathProperties.getCPathUrl();
+ consolePanel.logMessage("Plugin is currently set to retrieve data "
+ + "from: " + url);
+ cPane.add(consolePanel, BorderLayout.CENTER);
+
+ // Create Northern Panel (cPath Search)
+ JPanel northPanel = createPanelNorth();
+ cPane.add(northPanel, BorderLayout.NORTH);
+
+ // Pack it, Size it, Center it.
+ pack();
+ setLocationRelativeTo(parent);
+ }
+
+ /**
+ * Creates Nothern Panel with cPath Search Box.
+ */
+ private JPanel createPanelNorth () {
+ int hspace = 5;
+ JPanel northPanel = new JPanel();
+ northPanel.setLayout(new GridLayout(2, 1));
+
+ // Create Titled Border
+ TitledBorder border = new TitledBorder("Search cPath");
+ northPanel.setBorder(border);
+
+ JPanel buttonBar = new JPanel();
+ buttonBar.setLayout(new BoxLayout(buttonBar, BoxLayout.X_AXIS));
+
+ // Create Listener
+ searchButton = new JButton("Search");
+ searchButton.setAlignmentX(Component.LEFT_ALIGNMENT);
+ ExecuteQuery queryListener = new ExecuteQuery(cyMap, searchRequest,
+ searchList, consolePanel, searchButton, this);
+ buttonBar.add(Box.createRigidArea(new Dimension(hspace, 0)));
+
+ // Create Search Text Field
+ JTextField textField = new JTextField("", 20);
+ Font font = textField.getFont();
+ textField.setFont(new Font(font.getName(), Font.PLAIN, 11));
+ textField.setToolTipText("Enter Search Term(s)");
+ UpdateSearchRequest textListener =
+ new UpdateSearchRequest(searchRequest);
+ textField.addFocusListener(textListener);
+ textField.addKeyListener(queryListener);
+ textField.setAlignmentY(Component.BOTTOM_ALIGNMENT);
+ textField.setMinimumSize(new Dimension(100, 50));
+ buttonBar.add(Box.createRigidArea(new Dimension(hspace, 0)));
+ buttonBar.add(textField);
+ buttonBar.add(Box.createRigidArea(new Dimension(hspace, 0)));
+
+ // Create Organism Combo Box
+ JComboBox orgCombo = createOrganismComboBox();
+ orgCombo.setFont(new Font(font.getName(), Font.PLAIN, 11));
+ orgCombo.setToolTipText("Filter by Organism");
+ // Used to specify a default size for pull down menu
+ orgCombo.setPrototypeDisplayValue
+ (new String("Saccharomyces cerevisiae"));
+ orgCombo.setAlignmentY(Component.BOTTOM_ALIGNMENT);
+ buttonBar.add(orgCombo);
+ buttonBar.add(Box.createRigidArea(new Dimension(hspace, 0)));
+
+ // Create Result Limit Combo Box
+ JComboBox limitCombo = createResultLimitComboBox();
+ limitCombo.setFont(new Font(font.getName(), Font.PLAIN, 11));
+ limitCombo.setToolTipText("Limit Result Set or Get All");
+ limitCombo.setAlignmentY(Component.BOTTOM_ALIGNMENT);
+
+ // Used to specify a default size for pull down menu;
+ // Particularly important for Windows, see Bug #520.
+ limitCombo.setPrototypeDisplayValue
+ (new String("Get All --- Get All"));
+ buttonBar.add(limitCombo);
+ buttonBar.add(Box.createRigidArea(new Dimension(hspace, 0)));
+
+ // Create Search Button
+ searchButton.setToolTipText("Execute Search Query");
+ searchButton.setAlignmentY(Component.BOTTOM_ALIGNMENT);
+ buttonBar.add(searchButton);
+ buttonBar.add(Box.createRigidArea(new Dimension(hspace, 0)));
+ searchButton.addActionListener(queryListener);
+
+ JButton helpButton = new JButton("Help");
+ helpButton.setToolTipText("View Quick Reference Manual");
+ helpButton.addActionListener(new QuickReferenceDialog((JFrame) this));
+ helpButton.setAlignmentY(Component.BOTTOM_ALIGNMENT);
+ buttonBar.add(helpButton);
+ buttonBar.add(Box.createRigidArea(new Dimension(hspace, 0)));
+
+ JButton aboutButton = new JButton("About");
+ aboutButton.setToolTipText("About the cPath PlugIn");
+ aboutButton.addActionListener(new AboutDialog((JFrame) this));
+ aboutButton.setAlignmentY(Component.BOTTOM_ALIGNMENT);
+ buttonBar.add(aboutButton);
+ buttonBar.add(Box.createHorizontalGlue());
+
+ northPanel.add(buttonBar);
+
+ // Create Search Examples Label
+ JLabel examples = new JLabel("Examples: p53 | rad51");
+ examples.setBorder(new EmptyBorder(hspace, 10, 5, 5));
+ northPanel.add(examples);
+ return northPanel;
+ }
+
+ /**
+ * Creates Result Set Limit Pull-Down Menu.
+ */
+ private JComboBox createResultLimitComboBox () {
+ Vector options = MaxHitsOption.getAllOptions();
+ JComboBox limitCombo = new JComboBox(options);
+ UpdateSearchRequest maxHitsListener =
+ new UpdateSearchRequest(searchRequest);
+ limitCombo.addActionListener(maxHitsListener);
+
+ return limitCombo;
+ }
+
+ /**
+ * Creates Organism Pull-Down Menu.
+ */
+ private JComboBox createOrganismComboBox () {
+ Vector options = OrganismOption.getAllOptions();
+ JComboBox orgCombo = new JComboBox(options);
+ UpdateSearchRequest organismListener =
+ new UpdateSearchRequest(searchRequest);
+ orgCombo.addActionListener(organismListener);
+ return orgCombo;
+ }
+
+ /**
+ * Receive Notification of Changes to the Search List.
+ *
+ * @param o Observable Object.
+ * @param arg Observable Arguments.
+ */
+ public void update (Observable o, Object arg) {
+ this.setVisible(true);
+ int numSearches = searchList.getNumSearchBundles();
+ SearchBundle bundle = searchList.getSearchBundleByIndex
+ (numSearches - 1);
+ SearchResponse searchResponse = bundle.getResponse();
+ Throwable exception = searchResponse.getException();
+ if (exception != null) {
+ if (exception instanceof InterruptedException) {
+ // Do Nothing
+ } else {
+ showError(exception);
+ }
+ }
+
+ // Re-enable search button.
+ searchButton.setEnabled(true);
+ }
+
+ /**
+ * Show Error Message.
+ *
+ * @param exception Exception.
+ */
+ private void showError (Throwable exception) {
+ ErrorDisplay errorDisplay = new ErrorDisplay(this);
+ errorDisplay.displayError(exception, consolePanel);
+ }
+}
diff --git a/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/ui/Console.java b/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/ui/Console.java
new file mode 100644
index 0000000..486c2d7
--- /dev/null
+++ b/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/ui/Console.java
@@ -0,0 +1,62 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.cpath.ui;
+
+/**
+ * Console Interface.
+ *
+ * @author Ethan Cerami.
+ */
+public interface Console {
+
+ /**
+ * Logs Message to the Console.
+ *
+ * @param msg Message
+ */
+ void logMessage (String msg);
+
+ /**
+ * Logs Message in Bold.
+ *
+ * @param msg Message
+ */
+ void logMessage (String msg, String style);
+
+ /**
+ * Clears the Console.
+ */
+ void clear ();
+}
\ No newline at end of file
diff --git a/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/ui/ConsolePanel.java b/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/ui/ConsolePanel.java
new file mode 100644
index 0000000..3b17a48
--- /dev/null
+++ b/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/ui/ConsolePanel.java
@@ -0,0 +1,164 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.cpath.ui;
+
+import javax.swing.*;
+import javax.swing.text.*;
+import java.awt.*;
+
+/**
+ * Console Panel Component.
+ *
+ * @author Ethan Cerami
+ */
+public class ConsolePanel extends JPanel implements Console {
+ private JTextPane ta;
+ private JScrollPane scrollPane;
+
+ /**
+ * No Arg Constructor.
+ */
+ public ConsolePanel () {
+ this.setLayout(new BorderLayout());
+ ta = new JTextPane();
+ ta.setMargin(new Insets(5, 7, 5, 7));
+ ta.setEditable(false);
+ ta.setBackground(Color.WHITE);
+ ta.setForeground(Color.BLACK);
+ addStylesToDocument(ta.getStyledDocument());
+ Font font = new Font("Courier", Font.PLAIN, 12);
+ ta.setFont(font);
+ scrollPane = new JScrollPane(ta);
+
+ StyledDocument doc = ta.getStyledDocument();
+ try {
+ doc.insertString(doc.getLength(), "Note: As of January 1, 2008, the " +
+ "cPath plugin will continue to operate, but will no longer be maintained. "
+ + "Users are advised to use the Pathway Commons plugin instead. "
+ + "\n\nTo access the Pathway Commons plugin, select File -> Import -> "
+ + "Network from Web Services, and select the Pathway Commons Web Service."
+ + "\n\n", doc.getStyle("red-bold"));
+ } catch (BadLocationException e) {
+ }
+ add(scrollPane, BorderLayout.CENTER);
+ }
+
+ /**
+ * Sets the Main Status Message.
+ *
+ * @param msg Status Message.
+ */
+ public void logMessage (String msg) {
+ logMessage(msg, "regular");
+ }
+
+ /**
+ * Sets the Main Status Message in Bold.
+ *
+ * @param msg Status Message.
+ * @param style Style.
+ */
+ public void logMessage (String msg, String style) {
+ logMessageWithStyle(msg, style);
+ }
+
+ /**
+ * Clears the Console.
+ */
+ public void clear () {
+ ta.setText("");
+ }
+
+ /**
+ * Sets the Main Status Message in the Specified Style.
+ *
+ * @param msg Status Message.
+ * @param style Style, e.g. "regular", "bold".
+ */
+ private void logMessageWithStyle (String msg, String style) {
+ StyledDocument doc = ta.getStyledDocument();
+ try {
+ doc.insertString(doc.getLength(), msg + "\n", doc.getStyle(style));
+ } catch (BadLocationException e) {
+ }
+
+ // Causes the ScrollPane to automatically scroll down.
+ // The line below used to use this code: ta.getText().length()
+ // However, it resulted in error when running on Windows
+ // (see bug #509). To fix the bug, use ta.getDocument().getLength().
+ ta.setCaretPosition(ta.getDocument().getLength());
+ }
+
+ /**
+ * Adds Styles to the JTextArea.
+ *
+ * @param doc StyledDocument Object.
+ */
+ protected void addStylesToDocument (StyledDocument doc) {
+ Style def = StyleContext.getDefaultStyleContext().
+ getStyle(StyleContext.DEFAULT_STYLE);
+
+ Style regular = doc.addStyle("regular", def);
+ StyleConstants.setFontFamily(def, "SansSerif");
+
+ Style s = doc.addStyle("italic", regular);
+ StyleConstants.setItalic(s, true);
+
+ s = doc.addStyle("bold", regular);
+ StyleConstants.setBold(s, true);
+
+ s = doc.addStyle("small", regular);
+ StyleConstants.setFontSize(s, 10);
+
+ s = doc.addStyle("large", regular);
+ StyleConstants.setFontSize(s, 16);
+
+ s = doc.addStyle("red", regular);
+ StyleConstants.setForeground(s, Color.RED);
+
+ s = doc.addStyle("red-bold", regular);
+ StyleConstants.setBold(s, true);
+ StyleConstants.setForeground(s, Color.RED);
+ }
+
+ /**
+ * Gets te Preferred Size.
+ *
+ * @return Dimension Object.CP
+ */
+ public Dimension getPreferredSize () {
+ return new Dimension(2, 150);
+ }
+}
\ No newline at end of file
diff --git a/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/ui/ErrorDisplay.java b/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/ui/ErrorDisplay.java
new file mode 100644
index 0000000..42cadfd
--- /dev/null
+++ b/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/ui/ErrorDisplay.java
@@ -0,0 +1,147 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.cpath.ui;
+
+import javax.swing.*;
+import java.awt.*;
+
+/**
+ * Error Display Widget.
+ *
+ * @author Ethan Cerami
+ */
+public class ErrorDisplay {
+ private Frame parent;
+ private static final int WIDTH = 50;
+ private static final char SPACE = ' ';
+ private static final String NEW_LINE = "\n";
+
+ /**
+ * Constructor.
+ *
+ * @param frame Frame object.
+ */
+ public ErrorDisplay (Frame frame) {
+ this.parent = frame;
+ }
+
+ /**
+ * Displays the Error Dialog Box.
+ *
+ * @param e Exception.
+ */
+ public void displayError (Throwable e) {
+ showError(e);
+ }
+
+ /**
+ * Displays the Error Dialog Box.
+ *
+ * @param e Exception.
+ * @param cPanel ConsolePanel Object.
+ */
+ public void displayError (Throwable e, ConsolePanel cPanel) {
+ String msg = showError(e);
+ cPanel.logMessage(msg);
+ }
+
+ /**
+ * Displays the Error Dialog Box.
+ *
+ * @param errorMsg Error Message String.
+ */
+ public void displayError (String errorMsg) {
+ String msg = wrapText(errorMsg);
+ JOptionPane.showMessageDialog(parent, msg,
+ "Error", JOptionPane.ERROR_MESSAGE);
+ }
+
+ /**
+ * Displays the Error Dialog Box.
+ *
+ * @param e Exception.
+ */
+ private String showError (Throwable e) {
+ e.printStackTrace();
+ String msg = null;
+// if (e instanceof DataServiceException) {
+// DataServiceException dse = (DataServiceException) e;
+// msg = new String("An Error Has Occurred: "
+// + dse.getHumanReadableErrorMessage());
+// } else if (e instanceof MapperException) {
+// MapperException me = (MapperException) e;
+// msg = new String("An Error Has Occurred: "
+// + me.getHumanReadableErrorMessage());
+// } else {
+// Throwable t = e.getCause();
+// if (t == null) {
+// t = e;
+// }
+// msg = new String("An Error Has Occurred: " + e.toString());
+// }
+ msg = wrapText(msg);
+ JOptionPane.showMessageDialog(parent, msg,
+ "Error", JOptionPane.ERROR_MESSAGE);
+ return msg;
+ }
+
+ /**
+ * Wraps text to WIDTH characters long.
+ *
+ * @param msg Message.
+ * @return Wrapped Text message.
+ */
+ public String wrapText (String msg) {
+ StringBuffer newMessage = new StringBuffer();
+ if (msg != null) {
+ String strs[] = msg.split("\\s+");
+ int lineIndex = 0;
+ for (int i = 0; i < strs.length; i++) {
+ newMessage.append(strs[i] + SPACE);
+ lineIndex += strs[i].length();
+ if (lineIndex > WIDTH) {
+ newMessage.append(NEW_LINE);
+ lineIndex = 0;
+ }
+ }
+ if (newMessage.length() > 500) {
+ return newMessage.substring(0, 500) + "...";
+ }
+ return newMessage.toString();
+ } else {
+ return msg;
+ }
+ }
+}
\ No newline at end of file
diff --git a/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/ui/QuickReferenceDialog.java b/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/ui/QuickReferenceDialog.java
new file mode 100644
index 0000000..49b86ef
--- /dev/null
+++ b/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/ui/QuickReferenceDialog.java
@@ -0,0 +1,162 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.cpath.ui;
+
+import javax.swing.*;
+import javax.swing.border.EmptyBorder;
+import java.awt.*;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+/**
+ * Displays a Quick Reference Search Help Page.
+ *
+ * @author Ethan Cerami.
+ */
+public class QuickReferenceDialog implements ActionListener {
+ private static final int WIDTH = 400;
+ private static final int HEIGHT = 450;
+ private JFrame parent;
+ private JFrame helpFrame;
+
+ /**
+ * Constructor.
+ *
+ * @param parent Parent Frame.
+ */
+ public QuickReferenceDialog (JFrame parent) {
+ this.parent = parent;
+ init();
+ }
+
+ /**
+ * Users has requested that we show the Quick Reference Dialog.
+ *
+ * @param e ActionEvent Object.
+ */
+ public void actionPerformed (ActionEvent e) {
+ if (parent != null) {
+ Point point = parent.getLocation();
+ Dimension size = parent.getSize();
+ int x = (int) (point.getX() + size.getWidth() / 2 - WIDTH / 2);
+ int y = (int) (point.getY() + size.getHeight() / 2 - HEIGHT / 2);
+ helpFrame.setLocation(x, y);
+ }
+ helpFrame.setVisible(true);
+ }
+
+ private void init () {
+ helpFrame = new JFrame("Quick Reference Manual");
+ Container contentPane = helpFrame.getContentPane();
+ contentPane.setLayout(new BorderLayout());
+
+ JEditorPane htmlPane = new JEditorPane();
+ EmptyBorder border = new EmptyBorder(5, 5, 5, 5);
+ htmlPane.setBorder(border);
+ htmlPane.setContentType("text/html");
+ htmlPane.setEditable(false);
+ htmlPane.setPreferredSize(new Dimension(WIDTH, HEIGHT));
+
+ String html = this.getAboutHtml();
+ htmlPane.setText(html);
+ htmlPane.setCaretPosition(0);
+
+ JScrollPane scrollPane = new JScrollPane(htmlPane);
+ contentPane.add(scrollPane, BorderLayout.CENTER);
+
+ // Pack it, but don't show it yet.
+ helpFrame.pack();
+ }
+
+ private String getAboutHtml () {
+ StringBuffer html = new StringBuffer();
+ html.append("<TABLE WIDTH=100%><TR BGCOLOR=#DDDDDD><TD>");
+ html.append("<FONT FACE=ARIAL SIZE=+1>");
+ html.append("Quick Reference Manual");
+ html.append("</FONT>");
+ html.append("</TD></TR></TABLE>");
+ html.append("<FONT FACE=ARIAL>");
+
+ html.append("<P><U>About cPath</U>");
+ html.append("<P>cPath is a database and software suite for storing, visualizing, and "
+ + "analyzing biological pathways."
+ + "<P>A demo version of cPath is currently available at "
+ + "http://www.cbio.mskcc.org/cpath/."
+ + "<P>The demo site contains all public data from IntACT "
+ + "and MINT.");
+
+ html.append("<P><U>About the cPath PlugIn</U>");
+ html.append("<P>The cPath PlugIn provides interactive access to the "
+ + "the cPath demo site. Cytoscape users can query cPath, download "
+ + "matching interactions and view them within Cytoscape.");
+
+ html.append("<P><U>Search Examples:</U>");
+ html.append("<P>dna repair");
+ html.append("<BR>-- Finds all records that contains the words "
+ + " dna or repair.");
+ html.append("<P>dna AND repair");
+ html.append("<BR>-- Finds all records the contain the words "
+ + " dna AND repair.");
+
+ html.append("<P>dna NOT repair");
+ html.append("<BR>-- Finds all records that contain the word "
+ + "dna, but do not contain the word repair.");
+
+ html.append("<P>\"dna repair\"");
+ html.append("<BR>-- Finds all records containing the exact "
+ + " text: \"dna repair\".");
+
+ html.append("<P>regulat*");
+ html.append("<BR>-- Finds all records begin with the wildcard: "
+ + "\"regulat\". This will match against records, such as "
+ + "regulate, regulatory, etc.");
+
+ html.append("</FONT>");
+
+ html.append("<P><HR><FONT FACE=ARIAL SIZE=-1>");
+ html.append("Copyright 2004-2007 Memorial Sloan-Kettering Cancer Center.");
+ html.append("</FONT>");
+ return html.toString();
+ }
+
+ /**
+ * Main Method (used to testing purposes).
+ *
+ * @param args Command Line Arguments.
+ */
+ public static void main (String args[]) {
+ QuickReferenceDialog frame = new QuickReferenceDialog(null);
+ }
+}
diff --git a/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/ui/package.html b/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/ui/package.html
new file mode 100644
index 0000000..2da2c8a
--- /dev/null
+++ b/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/ui/package.html
@@ -0,0 +1,8 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+<html>
+<head></head>
+
+<body bgcolor="white">
+Graphical User Interface (GUI) widgets, panels, and components.
+</body>
+</html>
diff --git a/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/ui/resources/Loading1.gif b/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/ui/resources/Loading1.gif
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diff --git a/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/ui/resources/run_tool.gif b/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/ui/resources/run_tool.gif
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diff --git a/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/util/CPathProperties.java b/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/util/CPathProperties.java
new file mode 100644
index 0000000..b1e8bf3
--- /dev/null
+++ b/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/util/CPathProperties.java
@@ -0,0 +1,69 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.cpath.util;
+
+import cytoscape.CytoscapeInit;
+
+import java.util.Properties;
+
+
+/**
+ * Contains cPath Specific Properties
+ *
+ * @author Ethan Cerami.
+ */
+public class CPathProperties {
+ /**
+ * Property: CPath Read Location.
+ */
+ private static final String CPATH_URL = new String("cpath.url");
+
+ /**
+ * Gets URL for cPath Web Service API.
+ *
+ * @return cPath URL.
+ */
+ public static String getCPathUrl() {
+ Properties properties = CytoscapeInit.getProperties();
+ String url = properties.getProperty(CPATH_URL);
+
+ if (url != null) {
+ return url;
+ } else {
+ // hard-coded default
+ return "http://cbio.mskcc.org/cpath/webservice.do";
+ }
+ }
+}
diff --git a/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/util/package.html b/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/util/package.html
new file mode 100644
index 0000000..336170b
--- /dev/null
+++ b/coreplugins/cPath/src/main/java/org/cytoscape/coreplugin/cpath/util/package.html
@@ -0,0 +1,8 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+<html>
+<head></head>
+
+<body bgcolor="white">
+Misc Utility Classes.
+</body>
+</html>
diff --git a/coreplugins/cPath/src/main/resources/org/cytoscape/coreplugin/cpath/plugin/plugin.props b/coreplugins/cPath/src/main/resources/org/cytoscape/coreplugin/cpath/plugin/plugin.props
new file mode 100644
index 0000000..97f000d
--- /dev/null
+++ b/coreplugins/cPath/src/main/resources/org/cytoscape/coreplugin/cpath/plugin/plugin.props
@@ -0,0 +1,30 @@
+# This props file would be filled out and included in the plugin jar file. This props file will be used
+# to put information into the Plugin Manager about the plugin
+
+# -- The following properties are REQUIRED -- #
+
+# The plugin name that will be displayed to users
+pluginName=cPath
+
+# Description used to give users information about the plugin such as what it does.
+# Html tags are encouraged for formatting purposes.
+pluginDescription=A plugin that queries the cPath database for specified terms and returns interaction networks.
+
+# Plugin version number, this must be two numbers separated by a decimlal. Ex. 0.2, 14.03
+pluginVersion=1.0
+
+# Compatible Cytoscape version
+cytoscapeVersion=2.5,2.6,2.7,2.8
+
+# Category, use one of the categories listed on the website or create your own
+pluginCategory=Core
+
+
+# List of authors. Note each author and institution pair are separated by a : (colon)
+# each additional author institution pair must be separated from other pairs bye a ; (semicolon)
+pluginAuthorsIntsitutions=Ethan Cerami:Memorial Sloan-Kettering Cancer Center
+
+# -- The following properties should be set ONLY BY CORE PLUGINS -- #
+downloadURL=http://cytoscape.org/plugins/plugins.xml
+uniqueID=4
+
diff --git a/coreplugins/cPath/src/test/java/org/cytoscape/coreplugin/cpath/test/AllTests.java b/coreplugins/cPath/src/test/java/org/cytoscape/coreplugin/cpath/test/AllTests.java
new file mode 100644
index 0000000..98a6294
--- /dev/null
+++ b/coreplugins/cPath/src/test/java/org/cytoscape/coreplugin/cpath/test/AllTests.java
@@ -0,0 +1,83 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.cpath.test;
+
+import junit.framework.Test;
+import junit.framework.TestCase;
+import junit.framework.TestSuite;
+
+import org.cytoscape.coreplugin.cpath.test.task.TaskSuite;
+
+
+/**
+ * Runs All JUnit Tests.
+ *
+ * @author Ethan Cerami
+ */
+public class AllTests extends TestCase {
+ /**
+ * The suite method kicks off all of the tests.
+ *
+ * @return junit.framework.Test
+ */
+ public static Test suite() {
+ // Organize all suites into one master suite.
+ TestSuite suite = new TestSuite();
+ suite.addTest(TaskSuite.suite());
+ /*
+ * Commenting out test of webservice since it's not testing
+ * code, but rather an external service
+ */
+// suite.addTest(ProtocolSuite.suite());
+ suite.setName("Cytoscape cPath Plugin Tests");
+
+ return suite;
+ }
+
+ /**
+ * Runs all Cytoscape Unit Tests.
+ *
+ * @param args Command Line Arguments. use -ui to run the JUnit Graphical
+ * interface.
+ */
+ public static void main(String[] args) {
+ if ((args.length > 0) && (args[0] != null) && args[0].equals("-ui")) {
+ String[] newargs = { "org.cytoscape.coreplugin.cpath.test.AllTests", "-noloading" };
+ junit.swingui.TestRunner.main(newargs);
+ } else {
+ junit.textui.TestRunner.run(suite());
+ }
+ }
+}
diff --git a/coreplugins/cPath/src/test/java/org/cytoscape/coreplugin/cpath/test/package.html b/coreplugins/cPath/src/test/java/org/cytoscape/coreplugin/cpath/test/package.html
new file mode 100644
index 0000000..3199df4
--- /dev/null
+++ b/coreplugins/cPath/src/test/java/org/cytoscape/coreplugin/cpath/test/package.html
@@ -0,0 +1,8 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+<html>
+<head></head>
+
+<body bgcolor="white">
+JUnit Tests.
+</body>
+</html>
diff --git a/coreplugins/cPath/src/test/java/org/cytoscape/coreplugin/cpath/test/protocol/ProtocolSuite.java b/coreplugins/cPath/src/test/java/org/cytoscape/coreplugin/cpath/test/protocol/ProtocolSuite.java
new file mode 100644
index 0000000..7a71d8d
--- /dev/null
+++ b/coreplugins/cPath/src/test/java/org/cytoscape/coreplugin/cpath/test/protocol/ProtocolSuite.java
@@ -0,0 +1,60 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.cpath.test.protocol;
+
+import junit.framework.Test;
+import junit.framework.TestCase;
+import junit.framework.TestSuite;
+
+
+/**
+ * Suite of Mapper JUnit Tests.
+ *
+ * @author Ethan Cerami.
+ */
+public class ProtocolSuite extends TestCase {
+ /**
+ * The suite method runs all the tests.
+ *
+ * @return Suite of JUnit tests.
+ */
+ public static Test suite() {
+ TestSuite suite = new TestSuite();
+ suite.addTestSuite(TestCPathProtocol.class);
+ suite.setName("Test cPath Protocol");
+
+ return suite;
+ }
+}
diff --git a/coreplugins/cPath/src/test/java/org/cytoscape/coreplugin/cpath/test/protocol/TestCPathProtocol.java b/coreplugins/cPath/src/test/java/org/cytoscape/coreplugin/cpath/test/protocol/TestCPathProtocol.java
new file mode 100644
index 0000000..7828403
--- /dev/null
+++ b/coreplugins/cPath/src/test/java/org/cytoscape/coreplugin/cpath/test/protocol/TestCPathProtocol.java
@@ -0,0 +1,104 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.cpath.test.protocol;
+
+import junit.framework.TestCase;
+import org.cytoscape.coreplugin.cpath.model.EmptySetException;
+import org.cytoscape.coreplugin.cpath.model.CPathException;
+import org.cytoscape.coreplugin.cpath.protocol.CPathProtocol;
+
+/**
+ * Tests the CPath Protocol.
+ * <p/>
+ * Requires network access to cPath Web Service API.
+ *
+ * @author Ethan Cerami
+ */
+public class TestCPathProtocol extends TestCase {
+
+ public void testDummy () {
+ }
+
+ /**
+ * Tests the Get Counter Query.
+ *
+ * @throws Exception All Errors.
+ public void testGetCounter () throws Exception {
+ CPathProtocol cpath = new CPathProtocol();
+
+ // This query should get some hits
+ cpath.setCommand(CPathProtocol.COMMAND_GET_BY_KEYWORD);
+ cpath.setFormat(CPathProtocol.FORMAT_COUNT_ONLY);
+ cpath.setQuery("p53");
+
+ String url = cpath.getURI();
+ assertEquals("http://cbio.mskcc.org/cpath/webservice.do?cmd=get_by_keyword&q=p53"
+ + "&format=count_only&version=1.0&maxHits=10&startIndex=0&", url);
+
+ String response = cpath.connect();
+ int count = Integer.parseInt(response);
+ assertTrue(count > 1);
+
+ // This query should trigger an empty set exception
+ cpath.setQuery("blahblahboogy");
+ try {
+ cpath.connect();
+ fail("Empty Set Exception should have been thrown");
+ } catch (EmptySetException e) {
+ }
+
+ // Test that the query is URL Encoded.
+ // When not encoded, users cannot enter more than one search term.
+ // Bug was discovered by Melissa, during creation of the Nature Cytoscape
+ // Protocol paper
+ cpath.setQuery("p53 rad51");
+ String uri = cpath.getURI();
+ int index = uri.indexOf("p53+rad51");
+ assertTrue ("cPath URL is not URL Encoded", index > 0);
+
+ // Try sending an invalid format, and verify that we trigger a cPath Exception
+ cpath.setFormat("SMBL");
+ try {
+ String content = cpath.connect();
+ System.out.println(content);
+ } catch (CPathException e) {
+ String msg = e.getMessage();
+ assertEquals ("Error Connecting to cPath Web Service "
+ + "(Error Code: 451, Error Message: Bad Data Format "
+ + "(data format not recognized))", msg);
+ }
+ }
+ */
+}
diff --git a/coreplugins/cPath/src/test/java/org/cytoscape/coreplugin/cpath/test/protocol/package.html b/coreplugins/cPath/src/test/java/org/cytoscape/coreplugin/cpath/test/protocol/package.html
new file mode 100644
index 0000000..5154e94
--- /dev/null
+++ b/coreplugins/cPath/src/test/java/org/cytoscape/coreplugin/cpath/test/protocol/package.html
@@ -0,0 +1,8 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+<html>
+<head></head>
+
+<body bgcolor="white">
+JUnit Tests for cPath Protocol classes.
+</body>
+</html>
diff --git a/coreplugins/cPath/src/test/java/org/cytoscape/coreplugin/cpath/test/task/TaskSuite.java b/coreplugins/cPath/src/test/java/org/cytoscape/coreplugin/cpath/test/task/TaskSuite.java
new file mode 100644
index 0000000..3d86905
--- /dev/null
+++ b/coreplugins/cPath/src/test/java/org/cytoscape/coreplugin/cpath/test/task/TaskSuite.java
@@ -0,0 +1,60 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.cpath.test.task;
+
+import junit.framework.Test;
+import junit.framework.TestCase;
+import junit.framework.TestSuite;
+
+
+/**
+ * Suite of Mapper JUnit Tests.
+ *
+ * @author Ethan Cerami.
+ */
+public class TaskSuite extends TestCase {
+ /**
+ * The suite method runs all the tests.
+ *
+ * @return Suite of JUnit tests.
+ */
+ public static Test suite() {
+ TestSuite suite = new TestSuite();
+ suite.addTestSuite(TestCPathTimeEstimator.class);
+ suite.setName("Test cPath Tasks");
+
+ return suite;
+ }
+}
diff --git a/coreplugins/cPath/src/test/java/org/cytoscape/coreplugin/cpath/test/task/TestCPathTimeEstimator.java b/coreplugins/cPath/src/test/java/org/cytoscape/coreplugin/cpath/test/task/TestCPathTimeEstimator.java
new file mode 100644
index 0000000..f260bb3
--- /dev/null
+++ b/coreplugins/cPath/src/test/java/org/cytoscape/coreplugin/cpath/test/task/TestCPathTimeEstimator.java
@@ -0,0 +1,64 @@
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.coreplugin.cpath.test.task;
+
+import junit.framework.TestCase;
+
+import org.cytoscape.coreplugin.cpath.task.CPathTimeEstimator;
+
+
+/**
+ * Tests the CPathTimeEstimator.
+ *
+ * @author Ethan Cerami.
+ */
+public class TestCPathTimeEstimator extends TestCase {
+ /**
+ * Tests the Time Estimator.
+ */
+ public void testEstimator() {
+ // Last Request took 1 sec, and we have just retrieved the firt
+ // 100 of 1000 interactions, in 100 value increments.
+ // Time Remaining Should be: 9 seconds
+ long timeRemaining = CPathTimeEstimator.calculateEsimatedTimeRemaining(1000, 0, 100, 1000);
+ assertEquals(9000, timeRemaining);
+
+ // Last Request took 100 ms, and we have just retrieved
+ // 900 of 1000 interactions, in 100 value increments.
+ // Time Remaining Should be: 100 ms
+ timeRemaining = CPathTimeEstimator.calculateEsimatedTimeRemaining(100, 800, 100, 1000);
+ assertEquals(100, timeRemaining);
+ }
+}
diff --git a/coreplugins/cPath/src/test/java/org/cytoscape/coreplugin/cpath/test/task/package.html b/coreplugins/cPath/src/test/java/org/cytoscape/coreplugin/cpath/test/task/package.html
new file mode 100644
index 0000000..c7ea2aa
--- /dev/null
+++ b/coreplugins/cPath/src/test/java/org/cytoscape/coreplugin/cpath/test/task/package.html
@@ -0,0 +1,8 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+<html>
+<head></head>
+
+<body bgcolor="white">
+JUnit Tests for All Tasks.
+</body>
+</html>
diff --git a/coreplugins/cPath2/README.txt b/coreplugins/cPath2/README.txt
new file mode 100644
index 0000000..68a9db5
--- /dev/null
+++ b/coreplugins/cPath2/README.txt
@@ -0,0 +1,25 @@
+Modifying the Plugin to Point to a Different cPath Server
+=========================================================
+
+The cPath2 Plugin provides direct access to any cPath server. By default, however,
+it provides access to PathwayCommons.org.
+
+If you want to point the plugin to a different instance of cPath:
+
+1. Modify plugin.props (in this directory). You can change any of the following three properties:
+
+#cpath2.server_name=Mouse Interaction Database
+#cpath2.server_url=http://awabi.cbio.mskcc.org/pc-demo/webservice.do
+#cpath2.server_blurb=The Mouse Interaction Database is... blah, blah, blah....
+
+Feel free to update the following other properties:
+
+pluginName=PathwayCommons
+pluginDescription=Provides connectivity to the Pathway Commons repository (http://www.pathwaycommons.org).
+projectURL=http://www.pathwaycommons.org
+
+2. recreate the jar
+
+ant jar
+
+3. That's it. You are Done!
\ No newline at end of file
diff --git a/coreplugins/cPath2/pom.xml b/coreplugins/cPath2/pom.xml
new file mode 100644
index 0000000..36d5ccf
--- /dev/null
+++ b/coreplugins/cPath2/pom.xml
@@ -0,0 +1,129 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>parent</artifactId>
+ <version>2.8.4-SNAPSHOT</version>
+ </parent>
+
+ <artifactId>cpath2</artifactId>
+ <packaging>jar</packaging>
+
+ <name>Pathway Commons plugin</name>
+
+ <!-- bootstrap for cytoscape dependencies, namely the parent POM snapshots -->
+ <repositories>
+ <repository>
+ <id>cytoscape_snapshots</id>
+ <snapshots>
+ <enabled>true</enabled>
+ </snapshots>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <name>Cytoscape Snapshots</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/</url>
+ </repository>
+ <repository>
+ <id>cytoscape_releases</id>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ <name>Cytoscape Releases</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/releases/</url>
+ </repository>
+ </repositories>
+
+ <dependencies>
+ <dependency>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>biopax</artifactId>
+ <version>${project.version}</version>
+ <scope>provided</scope> <!-- don't include biopax in jar-with-dependencies -->
+ </dependency>
+ <dependency>
+ <groupId>commons-logging</groupId>
+ <artifactId>commons-logging</artifactId>
+ <version>1.1.1</version>
+ <scope>provided</scope> <!-- also used by biopax, so rely on that one -->
+ </dependency>
+ <dependency>
+ <groupId>commons-codec</groupId>
+ <artifactId>commons-codec</artifactId>
+ <version>1.3</version>
+ </dependency>
+ <dependency>
+ <groupId>commons-httpclient</groupId>
+ <artifactId>commons-httpclient</artifactId>
+ <version>3.1</version>
+ </dependency>
+ </dependencies>
+
+
+ <build>
+ <plugins>
+ <plugin>
+ <artifactId>maven-assembly-plugin</artifactId>
+ <configuration>
+ <archive>
+ <manifestEntries>
+ <Cytoscape-Plugin>org.cytoscape.coreplugin.cpath2.plugin.CPathPlugIn2</Cytoscape-Plugin>
+ </manifestEntries>
+ </archive>
+ </configuration>
+ </plugin>
+ <plugin>
+ <groupId>org.jvnet.jaxb2.maven2</groupId>
+ <artifactId>maven-jaxb2-plugin</artifactId>
+ <version>0.7.4</version>
+ <executions>
+ <execution>
+ <id>SearchResponse</id>
+ <goals>
+ <goal>generate</goal>
+ </goals>
+ <configuration>
+ <schemaDirectory>src/main/resources/xsd</schemaDirectory>
+ <schemaIncludes>
+ <include>SearchResponse.xsd</include>
+ </schemaIncludes>
+ <generatePackage>org.cytoscape.coreplugin.cpath2.schemas.search_response</generatePackage>
+ <verbose>true</verbose>
+ <removeOldOutput>false</removeOldOutput>
+ <forceRegenerate>true</forceRegenerate>
+ </configuration>
+ </execution>
+ <execution>
+ <id>SummaryResponse</id>
+ <goals>
+ <goal>generate</goal>
+ </goals>
+ <configuration>
+ <schemaDirectory>src/main/resources/xsd</schemaDirectory>
+ <schemaIncludes>
+ <include>SummaryResponse.xsd</include>
+ </schemaIncludes>
+ <generatePackage>org.cytoscape.coreplugin.cpath2.schemas.summary_response</generatePackage>
+ <verbose>true</verbose>
+ <removeOldOutput>false</removeOldOutput>
+ <forceRegenerate>true</forceRegenerate>
+ </configuration>
+ </execution>
+ </executions>
+ </plugin>
+ </plugins>
+ </build>
+
+ <pluginRepositories>
+ <pluginRepository>
+ <id>maven2-repository.dev.java.net</id>
+ <name>Java.net Maven 2 Repository</name>
+ <url>http://download.java.net/maven/2</url>
+ </pluginRepository>
+ </pluginRepositories>
+
+</project>
+
diff --git a/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/cytoscape/BinarySifVisualStyleUtil.java b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/cytoscape/BinarySifVisualStyleUtil.java
new file mode 100644
index 0000000..3ba590e
--- /dev/null
+++ b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/cytoscape/BinarySifVisualStyleUtil.java
@@ -0,0 +1,169 @@
+package org.cytoscape.coreplugin.cpath2.cytoscape;
+
+import cytoscape.visual.*;
+import cytoscape.visual.calculators.Calculator;
+import cytoscape.visual.calculators.BasicCalculator;
+import cytoscape.visual.mappings.DiscreteMapping;
+import cytoscape.visual.mappings.ObjectMapping;
+import cytoscape.visual.mappings.PassThroughMapping;
+import cytoscape.Cytoscape;
+import cytoscape.data.Semantics;
+import java.awt.*;
+
+import cytoscape.coreplugins.biopax.util.BioPaxVisualStyleUtil;
+import cytoscape.coreplugins.biopax.MapBioPaxToCytoscape;
+
+/**
+ * Binary SIF Visual Style.
+ *
+ * @author Ethan Cerami.
+ */
+public class BinarySifVisualStyleUtil {
+ public final static String BINARY_SIF_VISUAL_STYLE = "Binary_SIF_Version_1";
+ public final static String BINARY_NETWORK = "BINARY_NETWORK";
+ public final static String COMPONENT_OF = "COMPONENT_OF";
+ public final static String COMPONENT_IN_SAME = "IN_SAME_COMPONENT";
+ public final static String SEQUENTIAL_CATALYSIS = "SEQUENTIAL_CATALYSIS";
+ public final static String CONTROLS_STATE_CHANGE = "STATE_CHANGE";
+ public final static String CONTROLS_METABOLIC_CHANGE = "METABOLIC_CATALYSIS";
+ public final static String PARTICIPATES_CONVERSION = "REACTS_WITH";
+ public final static String PARTICIPATES_INTERACTION = "INTERACTS_WITH";
+ public final static String CO_CONTROL_INDEPENDENT_SIMILAR = "CO_CONTROL_INDEPENDENT_SIMILAR";
+ public final static String CO_CONTROL_INDEPENDENT_ANTI = "CO_CONTROL_INDEPENDENT_ANTI";
+ public final static String CO_CONTROL_DEPENDENT_SIMILAR = "CO_CONTROL_DEPENDENT_SIMILAR";
+ public final static String CO_CONTROL_DEPENDENT_ANTI = "CO_CONTROL_DEPENDENT_ANTI";
+ private final static String COMPLEX = "Complex";
+
+ /**
+ * Constructor.
+ * If an existing BioPAX Viz Mapper already exists, we use it.
+ * Otherwise, we create a new one.
+ *
+ * @return VisualStyle Object.
+ */
+ public static VisualStyle getVisualStyle() {
+ VisualMappingManager manager = Cytoscape.getVisualMappingManager();
+ CalculatorCatalog catalog = manager.getCalculatorCatalog();
+
+ VisualStyle visualStyle = catalog.getVisualStyle(BINARY_SIF_VISUAL_STYLE);
+ if (visualStyle == null) {
+ visualStyle = new VisualStyle(BINARY_SIF_VISUAL_STYLE);
+
+ NodeAppearanceCalculator nac = visualStyle.getNodeAppearanceCalculator();
+
+ // set node opacity
+ nac.getDefaultAppearance().set(cytoscape.visual.VisualPropertyType.NODE_OPACITY, 125);
+ // unlock node size
+ visualStyle.getDependency().set(VisualPropertyDependency.Definition.NODE_SIZE_LOCKED,false);
+
+ createNodeShapes(nac);
+ createNodeColors(nac);
+ createNodeLabel(nac);
+
+ EdgeAppearanceCalculator eac = visualStyle.getEdgeAppearanceCalculator();
+ eac.getDefaultAppearance().set(cytoscape.visual.VisualPropertyType.EDGE_LINE_WIDTH,4.0);
+ createEdgeColor (eac);
+ createDirectedEdges (eac);
+
+ visualStyle.setNodeAppearanceCalculator(nac);
+ visualStyle.setEdgeAppearanceCalculator(eac);
+ GlobalAppearanceCalculator gac = new GlobalAppearanceCalculator();
+ gac.setDefaultBackgroundColor(Color.WHITE);
+ visualStyle.setGlobalAppearanceCalculator(gac);
+
+ // The visual style must be added to the Global Catalog
+ // in order for it to be written out to vizmap.props upon user exit
+ catalog.addVisualStyle(visualStyle);
+ }
+ return visualStyle;
+ }
+
+ private static void createNodeShapes(NodeAppearanceCalculator nac) {
+ // Default shape is an ellipse.
+ nac.getDefaultAppearance().set(VisualPropertyType.NODE_SHAPE, NodeShape.ELLIPSE);
+
+ // Complexes are Hexagons.
+ DiscreteMapping discreteMapping = new DiscreteMapping(NodeShape.ELLIPSE,
+ MapBioPaxToCytoscape.BIOPAX_ENTITY_TYPE, ObjectMapping.NODE_MAPPING);
+ discreteMapping.putMapValue(COMPLEX, NodeShape.HEXAGON);
+ Calculator nodeShapeCalculator = new BasicCalculator("Node Shape",
+ discreteMapping, VisualPropertyType.NODE_SHAPE);
+ nac.setCalculator(nodeShapeCalculator);
+ }
+
+ private static void createNodeColors(NodeAppearanceCalculator nac) {
+ Color color = new Color (255, 153, 153);
+ nac.getDefaultAppearance().set(VisualPropertyType.NODE_FILL_COLOR, color);
+
+ // Complexes are a Different Color.
+ Color lightBlue = new Color (153, 153, 255);
+ DiscreteMapping discreteMapping = new DiscreteMapping(color,
+ MapBioPaxToCytoscape.BIOPAX_ENTITY_TYPE, ObjectMapping.NODE_MAPPING);
+ discreteMapping.putMapValue(COMPLEX, lightBlue);
+
+ Calculator nodeShapeCalculator = new BasicCalculator("Node Color",
+ discreteMapping, VisualPropertyType.NODE_FILL_COLOR);
+ nac.setCalculator(nodeShapeCalculator);
+ }
+
+ private static void createEdgeColor(EdgeAppearanceCalculator eac) {
+ // create a discrete mapper, for mapping biopax node type
+ // to a particular node color
+ DiscreteMapping discreteMapping = new DiscreteMapping(Color.BLACK,
+ Semantics.INTERACTION, ObjectMapping.EDGE_MAPPING);
+
+ discreteMapping.putMapValue(PARTICIPATES_CONVERSION, Color.decode("#ccc1da"));
+ discreteMapping.putMapValue(PARTICIPATES_INTERACTION, Color.decode("#7030a0"));
+ discreteMapping.putMapValue(CONTROLS_STATE_CHANGE, Color.decode("#0070c0"));
+ discreteMapping.putMapValue(CONTROLS_METABOLIC_CHANGE, Color.decode("#00b0f0"));
+ discreteMapping.putMapValue(SEQUENTIAL_CATALYSIS, Color.decode("#7f7f7f"));
+ discreteMapping.putMapValue(CO_CONTROL_DEPENDENT_ANTI, Color.decode("#ff0000"));
+ discreteMapping.putMapValue(CO_CONTROL_INDEPENDENT_ANTI, Color.decode("#fd95a6"));
+ discreteMapping.putMapValue(CO_CONTROL_DEPENDENT_SIMILAR, Color.decode("#00b050"));
+ discreteMapping.putMapValue(CO_CONTROL_INDEPENDENT_SIMILAR, Color.decode("#92d050"));
+ discreteMapping.putMapValue(COMPONENT_IN_SAME, Color.decode("#ffff00"));
+ discreteMapping.putMapValue(COMPONENT_OF, Color.decode("#ffc000"));
+
+ // create and set edge label calculator in edge appearance calculator
+ Calculator edgeColorCalculator = new BasicCalculator("Edge Color",
+ discreteMapping, VisualPropertyType.EDGE_COLOR);
+ eac.setCalculator(edgeColorCalculator);
+
+ // set default color
+ eac.getDefaultAppearance().set(cytoscape.visual.VisualPropertyType.EDGE_COLOR,
+ Color.BLACK);
+ }
+
+ private static void createDirectedEdges(EdgeAppearanceCalculator eac) {
+ DiscreteMapping discreteMapping = new DiscreteMapping(ArrowShape.NONE,
+ Semantics.INTERACTION, ObjectMapping.EDGE_MAPPING);
+
+ discreteMapping.putMapValue(COMPONENT_OF, ArrowShape.ARROW);
+ discreteMapping.putMapValue(CONTROLS_STATE_CHANGE, ArrowShape.ARROW);
+ discreteMapping.putMapValue(CONTROLS_METABOLIC_CHANGE, ArrowShape.ARROW);
+ discreteMapping.putMapValue(SEQUENTIAL_CATALYSIS, ArrowShape.ARROW);
+
+ // create and set edge label calculator in edge appearance calculator
+ Calculator edgeColorCalculator = new BasicCalculator("Edge Source Arrow Shape",
+ discreteMapping, VisualPropertyType.EDGE_TGTARROW_SHAPE);
+ eac.setCalculator(edgeColorCalculator);
+
+ // set default color
+ eac.getDefaultAppearance().set(cytoscape.visual.VisualPropertyType.EDGE_TGTARROW_SHAPE,
+ ArrowShape.NONE);
+ }
+
+ private static void createNodeLabel(NodeAppearanceCalculator nac) {
+ // create pass through mapper for node labels
+ PassThroughMapping passThroughMapping = new PassThroughMapping("",
+ ObjectMapping.NODE_MAPPING);
+ passThroughMapping.setControllingAttributeName(BioPaxVisualStyleUtil.BIOPAX_NODE_LABEL,
+ null, false);
+
+ // create and set node label calculator in node appearance calculator
+ Calculator nodeLabelCalculator = new BasicCalculator("BioPAX Node Label",
+ passThroughMapping,
+ VisualPropertyType.NODE_LABEL);
+ nac.setCalculator(nodeLabelCalculator);
+ }
+}
diff --git a/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/cytoscape/MergeNetworkEdit.java b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/cytoscape/MergeNetworkEdit.java
new file mode 100644
index 0000000..d064bb5
--- /dev/null
+++ b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/cytoscape/MergeNetworkEdit.java
@@ -0,0 +1,150 @@
+// $Id: MergeNetworkEdit.java,v 1.1 2007/06/22 16:02:34 grossb Exp $
+//------------------------------------------------------------------------------
+/** Copyright (c) 2007 Memorial Sloan-Kettering Cancer Center.
+ **
+ ** Code written by: Ethan Cerami, Benjamin Gross
+ ** Authors: Ethan Cerami, Gary Bader, Chris Sander, Benjamin Gross
+ **
+ ** This library is free software; you can redistribute it and/or modify it
+ ** under the terms of the GNU Lesser General Public License as published
+ ** by the Free Software Foundation; either version 2.1 of the License, or
+ ** any later version.
+ **
+ ** This library is distributed in the hope that it will be useful, but
+ ** WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ ** MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ ** documentation provided hereunder is on an "as is" basis, and
+ ** Memorial Sloan-Kettering Cancer Center
+ ** has no obligations to provide maintenance, support,
+ ** updates, enhancements or modifications. In no event shall
+ ** Memorial Sloan-Kettering Cancer Center
+ ** be liable to any party for direct, indirect, special,
+ ** incidental or consequential damages, including lost profits, arising
+ ** out of the use of this software and its documentation, even if
+ ** Memorial Sloan-Kettering Cancer Center
+ ** has been advised of the possibility of such damage. See
+ ** the GNU Lesser General Public License for more details.
+ **
+ ** You should have received a copy of the GNU Lesser General Public License
+ ** along with this library; if not, write to the Free Software Foundation,
+ ** Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ **/
+package org.cytoscape.coreplugin.cpath2.cytoscape;
+
+// imports
+
+import cytoscape.CyEdge;
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+import cytoscape.util.undo.CyAbstractEdit;
+import cytoscape.view.CyNetworkView;
+import giny.view.NodeView;
+
+import java.awt.geom.Point2D;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Set;
+
+/**
+ * An undoable edit used by MergeNetworkTask
+ * to provide undo/redo support. Code based on cytoscape.editor.AddNodeEdit
+ */
+public class MergeNetworkEdit extends CyAbstractEdit {
+
+ /**
+ * ref to CyNetwork that we are modifying
+ */
+ private CyNetwork cyNetwork;
+
+ /**
+ * ref to map: node is key, value is node position
+ */
+ private Map<CyNode, Point2D.Double> cyNodes;
+
+ /**
+ * ref to edge set
+ */
+ private Set<CyEdge> cyEdges;
+
+ /**
+ * Constructor.
+ *
+ * @param cyNetwork CyNetwork
+ * @param cyNodes Set<CyNode>
+ * @param cyEdges Set<CyEdge>
+ */
+ public MergeNetworkEdit(CyNetwork cyNetwork, Set<CyNode> cyNodes, Set<CyEdge> cyEdges) {
+ super("Merge Network");
+
+ // check args
+ if (cyNetwork == null || cyNodes == null || cyEdges == null)
+ throw new IllegalArgumentException("network, nodes, or edges is null");
+
+ // init args
+ this.cyNetwork = cyNetwork;
+ this.cyEdges = cyEdges;
+
+ this.cyNodes = new HashMap<CyNode, Point2D.Double>();
+ CyNetworkView view = Cytoscape.getNetworkView(cyNetwork.getIdentifier());
+ if (view != null || view != Cytoscape.getNullNetworkView()) {
+ for (CyNode cyNode : cyNodes) {
+ NodeView nv = view.getNodeView(cyNode);
+ Point2D.Double point = new Point2D.Double(nv.getXPosition(), nv.getYPosition());
+ this.cyNodes.put(cyNode, point);
+ }
+ }
+ }
+
+ /**
+ * Method to undo this network merge
+ */
+ public void undo() {
+ super.undo();
+
+ // iterate through nodes and hide each one
+ for (CyNode cyNode : cyNodes.keySet()) {
+ cyNetwork.hideNode(cyNode);
+ }
+
+ // iteracte through edges and hide each one
+ for (CyEdge cyEdge : cyEdges) {
+ cyNetwork.hideEdge(cyEdge);
+ }
+
+ // fire Cytoscape.NETWORK_MODIFIED
+ Cytoscape.firePropertyChange(Cytoscape.NETWORK_MODIFIED, null, cyNetwork);
+ }
+
+ /**
+ * Method to redo this network merge
+ */
+ public void redo() {
+ super.redo();
+
+ // get ref to view
+ CyNetworkView view = Cytoscape.getNetworkView(cyNetwork.getIdentifier());
+
+ if (view != null || view != Cytoscape.getNullNetworkView()) {
+
+ // iterate through nodes and restore each one (also set proper position)
+ for (CyNode cyNode : cyNodes.keySet()) {
+ cyNetwork.restoreNode(cyNode);
+ Point2D.Double point = cyNodes.get(cyNode);
+ NodeView nv = view.getNodeView(cyNode);
+ nv.setXPosition(point.getX());
+ nv.setYPosition(point.getY());
+ }
+
+ // interate through edges and restore each one...
+ for (CyEdge cyEdge : cyEdges) {
+ cyNetwork.restoreEdge(cyEdge);
+ }
+
+ // do we perform layout here ?
+ }
+
+ // fire Cytoscape.NETWORK_MODIFIED
+ Cytoscape.firePropertyChange(Cytoscape.NETWORK_MODIFIED, null, cyNetwork);
+ }
+}
diff --git a/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/driver/Driver.java b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/driver/Driver.java
new file mode 100644
index 0000000..3e2e73c
--- /dev/null
+++ b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/driver/Driver.java
@@ -0,0 +1,71 @@
+// $Id: Driver.java,v 1.3 2007/04/26 21:56:42 grossb Exp $
+//------------------------------------------------------------------------------
+/** Copyright (c) 2007 Memorial Sloan-Kettering Cancer Center.
+ **
+ ** Code written by: Ethan Cerami, Benjamin Gross
+ ** Authors: Ethan Cerami, Gary Bader, Chris Sander, Benjamin Gross
+ **
+ ** This library is free software; you can redistribute it and/or modify it
+ ** under the terms of the GNU Lesser General Public License as published
+ ** by the Free Software Foundation; either version 2.1 of the License, or
+ ** any later version.
+ **
+ ** This library is distributed in the hope that it will be useful, but
+ ** WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ ** MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ ** documentation provided hereunder is on an "as is" basis, and
+ ** Memorial Sloan-Kettering Cancer Center
+ ** has no obligations to provide maintenance, support,
+ ** updates, enhancements or modifications. In no event shall
+ ** Memorial Sloan-Kettering Cancer Center
+ ** be liable to any party for direct, indirect, special,
+ ** incidental or consequential damages, including lost profits, arising
+ ** out of the use of this software and its documentation, even if
+ ** Memorial Sloan-Kettering Cancer Center
+ ** has been advised of the possibility of such damage. See
+ ** the GNU Lesser General Public License for more details.
+ **
+ ** You should have received a copy of the GNU Lesser General Public License
+ ** along with this library; if not, write to the Free Software Foundation,
+ ** Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ **/
+package org.cytoscape.coreplugin.cpath2.driver;
+
+// imports
+import cytoscape.logger.CyLogger;
+
+import org.cytoscape.coreplugin.cpath2.http.HTTPEvent;
+import org.cytoscape.coreplugin.cpath2.http.HTTPServer;
+import org.cytoscape.coreplugin.cpath2.http.HTTPServerListener;
+
+/**
+ * Driver class for cPath Plugin components.
+ *
+ * @author Benjamin Gross
+ */
+public class Driver implements HTTPServerListener {
+ CyLogger logger = CyLogger.getLogger(HTTPServerListener.class);
+
+ /**
+ * Our implementation of HTTPServerListener.
+ *
+ * @param event HTTPEvent
+ */
+ public void httpEvent(HTTPEvent event) {
+
+ logger.debug("request received: " + event.getRequest());
+ }
+
+ public static void main(String[] args) {
+
+ // create instance of driver
+ Driver driver = new Driver();
+
+ String debugProperty = System.getProperty("DEBUG");
+ Boolean debug = (debugProperty != null && debugProperty.length() > 0) &&
+ new Boolean(debugProperty.toLowerCase());
+
+ // create server
+ new HTTPServer(HTTPServer.DEFAULT_PORT, driver, debug).start();
+ }
+}
diff --git a/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/driver/index.html b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/driver/index.html
new file mode 100644
index 0000000..568bb05
--- /dev/null
+++ b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/driver/index.html
@@ -0,0 +1,11 @@
+<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML//EN">
+<html>
+<head>
+ <title>cpath plugin driver page</title>
+</head>
+<body>
+<h1>cpath plugin driver page</h1>
+<a href="http://127.0.0.1:27182/www.pathwaycommons.org/pc/webservice.do?version=1.0&cmd=get_record_by_cpath_id&format=biopax&q=23911">click
+ me</a>
+</body>
+</html>
diff --git a/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/filters/ChainedFilter.java b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/filters/ChainedFilter.java
new file mode 100644
index 0000000..cd1ad6b
--- /dev/null
+++ b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/filters/ChainedFilter.java
@@ -0,0 +1,37 @@
+package org.cytoscape.coreplugin.cpath2.filters;
+
+import org.cytoscape.coreplugin.cpath2.schemas.summary_response.BasicRecordType;
+
+import java.util.List;
+import java.util.ArrayList;
+
+/**
+ * Chained Filter.
+ *
+ * @author Ethan Cerami
+ */
+public class ChainedFilter implements Filter {
+ private ArrayList<Filter> filterList = new ArrayList<Filter>();
+
+ /**
+ * Adds a new filter.
+ * @param filter Filter Object.
+ */
+ public void addFilter (Filter filter) {
+ filterList.add(filter);
+ }
+
+ /**
+ * Filters the record list. Those items which pass the filter
+ * are included in the returned list.
+ *
+ * @param recordList List of RecordType Objects.
+ * @return List of RecordType Objects.
+ */
+ public List<BasicRecordType> filter(List<BasicRecordType> recordList) {
+ for (Filter filter: filterList) {
+ recordList = filter.filter(recordList);
+ }
+ return recordList;
+ }
+}
\ No newline at end of file
diff --git a/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/filters/DataSourceFilter.java b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/filters/DataSourceFilter.java
new file mode 100644
index 0000000..4735f46
--- /dev/null
+++ b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/filters/DataSourceFilter.java
@@ -0,0 +1,49 @@
+package org.cytoscape.coreplugin.cpath2.filters;
+
+import org.cytoscape.coreplugin.cpath2.schemas.summary_response.BasicRecordType;
+import org.cytoscape.coreplugin.cpath2.schemas.summary_response.DataSourceType;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Set;
+
+/**
+ * Data Source Filter.
+ *
+ * @author Ethan Cerami
+ */
+public class DataSourceFilter implements Filter {
+ Set<String> dataSourceSet;
+
+ /**
+ * Constructor.
+ *
+ * @param dataSourceSet Set of Data Sources we want to keep.
+ */
+ public DataSourceFilter(Set<String> dataSourceSet) {
+ this.dataSourceSet = dataSourceSet;
+ }
+
+ /**
+ * Filters the record list. Those items which pass the filter
+ * are included in the returned list.
+ *
+ * @param recordList List of RecordType Objects.
+ * @return List of RecordType Objects.
+ */
+ public List<BasicRecordType> filter(List<BasicRecordType> recordList) {
+ ArrayList<BasicRecordType> passedList = new ArrayList<BasicRecordType>();
+ for (BasicRecordType record : recordList) {
+ DataSourceType dataSource = record.getDataSource();
+ if (dataSource != null) {
+ String dataSourceName = dataSource.getName();
+ if (dataSourceName != null) {
+ if (dataSourceSet.contains(dataSourceName)) {
+ passedList.add(record);
+ }
+ }
+ }
+ }
+ return passedList;
+ }
+}
diff --git a/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/filters/EntityTypeFilter.java b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/filters/EntityTypeFilter.java
new file mode 100644
index 0000000..327dac8
--- /dev/null
+++ b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/filters/EntityTypeFilter.java
@@ -0,0 +1,50 @@
+package org.cytoscape.coreplugin.cpath2.filters;
+
+import org.cytoscape.coreplugin.cpath2.util.BioPaxEntityTypeMap;
+import org.cytoscape.coreplugin.cpath2.schemas.summary_response.BasicRecordType;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Set;
+
+/**
+ * EntityType Filter.
+ *
+ * @author Ethan Cerami
+ */
+public class EntityTypeFilter implements Filter {
+ Set<String> entityTypeSet;
+
+ /**
+ * Constructor.
+ *
+ * @param entityTypeSet Set of Entity Types we want to keep.
+ */
+ public EntityTypeFilter(Set<String> entityTypeSet) {
+ this.entityTypeSet = entityTypeSet;
+ }
+
+ /**
+ * Filters the record list. Those items which pass the filter
+ * are included in the returned list.
+ *
+ * @param recordList List of RecordType Objects.
+ * @return List of RecordType Objects.
+ */
+ public List<BasicRecordType> filter(List<BasicRecordType> recordList) {
+ BioPaxEntityTypeMap bpMap = BioPaxEntityTypeMap.getInstance();
+ ArrayList<BasicRecordType> passedList = new ArrayList<BasicRecordType>();
+ for (BasicRecordType record : recordList) {
+ String type = record.getEntityType();
+ if (type != null) {
+ if (bpMap.containsKey(type)) {
+ type = (String) bpMap.get(type);
+ }
+ if (entityTypeSet.contains(type)) {
+ passedList.add(record);
+ }
+ }
+ }
+ return passedList;
+ }
+}
\ No newline at end of file
diff --git a/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/filters/Filter.java b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/filters/Filter.java
new file mode 100644
index 0000000..a3ad3a1
--- /dev/null
+++ b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/filters/Filter.java
@@ -0,0 +1,22 @@
+package org.cytoscape.coreplugin.cpath2.filters;
+
+import org.cytoscape.coreplugin.cpath2.schemas.summary_response.BasicRecordType;
+
+import java.util.List;
+
+/**
+ * Filter interface.
+ *
+ * @author Ethan Cerami
+ */
+public interface Filter {
+
+ /**
+ * Filters the record list. Those items which pass the filter
+ * are included in the returned list.
+ *
+ * @param recordList List of RecordType Objects.
+ * @return List of RecordType Objects.
+ */
+ public List<BasicRecordType> filter (List<BasicRecordType> recordList);
+}
\ No newline at end of file
diff --git a/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/http/HTTPConnectionHandler.java b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/http/HTTPConnectionHandler.java
new file mode 100644
index 0000000..0fdfd58
--- /dev/null
+++ b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/http/HTTPConnectionHandler.java
@@ -0,0 +1,126 @@
+// $Id$
+//------------------------------------------------------------------------------
+/** Copyright (c) 2007 Memorial Sloan-Kettering Cancer Center.
+ **
+ ** Code written by: Ethan Cerami, Benjamin Gross
+ ** Authors: Ethan Cerami, Gary Bader, Chris Sander, Benjamin Gross
+ **
+ ** This library is free software; you can redistribute it and/or modify it
+ ** under the terms of the GNU Lesser General Public License as published
+ ** by the Free Software Foundation; either version 2.1 of the License, or
+ ** any later version.
+ **
+ ** This library is distributed in the hope that it will be useful, but
+ ** WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ ** MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ ** documentation provided hereunder is on an "as is" basis, and
+ ** Memorial Sloan-Kettering Cancer Center
+ ** has no obligations to provide maintenance, support,
+ ** updates, enhancements or modifications. In no event shall
+ ** Memorial Sloan-Kettering Cancer Center
+ ** be liable to any party for direct, indirect, special,
+ ** incidental or consequential damages, including lost profits, arising
+ ** out of the use of this software and its documentation, even if
+ ** Memorial Sloan-Kettering Cancer Center
+ ** has been advised of the possibility of such damage. See
+ ** the GNU Lesser General Public License for more details.
+ **
+ ** You should have received a copy of the GNU Lesser General Public License
+ ** along with this library; if not, write to the Free Software Foundation,
+ ** Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ **/
+package org.cytoscape.coreplugin.cpath2.http;
+
+// import
+
+import java.io.IOException;
+import java.net.Socket;
+
+/**
+ * Class which handles connections.
+ *
+ * @author Benjamin Gross.
+ */
+public class HTTPConnectionHandler extends Thread {
+
+ /**
+ * web service url string constant
+ */
+ public static final String WEB_SERVICE_URL = "webservice.do";
+
+ /**
+ * ref to socket
+ */
+ private Socket sock;
+
+ /**
+ * ref to server listener
+ */
+ private HTTPServerListener listener;
+
+ /**
+ * debug flag
+ */
+ private boolean debug;
+
+ /**
+ * Constructor.
+ *
+ * @param sock Socket
+ * @param listener HTTServerListener
+ * @param debug boolean
+ */
+ public HTTPConnectionHandler(Socket sock, HTTPServerListener listener, boolean debug) {
+
+ // init our members
+ this.sock = sock;
+ this.listener = listener;
+ this.debug = debug;
+ }
+
+ /**
+ * Our implementation of run
+ */
+ public void run() {
+
+ try {
+
+ // get the event object to pass on
+ String uri = HTTPReader.processRequest(sock);
+ HTTPEvent request = new HTTPEvent(this, uri, null);
+ if (debug)
+ System.out.println("HTTPConnectionHandler, request received: " + request.getRequest());
+
+ // only interested in cpath web service urls
+ if (request.getRequest().indexOf(WEB_SERVICE_URL) != -1) {
+
+ // send response back to client - before we process here
+ // note: callBack() is a javascript routine in webstart.js
+ // which will be execute immediately after web browser receives this request
+ HTTPEvent response = new HTTPEvent(this, null, "callBack();");
+ if (debug)
+ System.out.println("HTTPConnectionHandler, sending response to web browser: " + response.getResponse());
+ HTTPWriter.processResponse(sock, response);
+ if (debug) System.out.println("HTTPConnectionHandler, closing socket...");
+ sock.close();
+
+ // pass on the event to our listener
+ if (debug)
+ System.out.println("HTTPConnectionHandler, sending request to listener.");
+ listener.httpEvent(request);
+ if (debug) System.out.println("HTTPConnectionHandler, listener complete");
+ }
+ // nothing we are interested in, just close socket
+ else {
+ // outta here
+ if (debug)
+ System.out.println("HTTPConnectionHandler, no work to be done, closing socket...");
+ sock.close();
+ }
+
+ }
+ catch (IOException e) {
+ e.printStackTrace();
+ }
+ }
+}
diff --git a/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/http/HTTPEvent.java b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/http/HTTPEvent.java
new file mode 100644
index 0000000..4779b93
--- /dev/null
+++ b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/http/HTTPEvent.java
@@ -0,0 +1,85 @@
+// $Id: HTTPEvent.java,v 1.2 2007/04/20 15:50:40 grossb Exp $
+//------------------------------------------------------------------------------
+/** Copyright (c) 2007 Memorial Sloan-Kettering Cancer Center.
+ **
+ ** Code written by: Ethan Cerami, Benjamin Gross
+ ** Authors: Ethan Cerami, Gary Bader, Chris Sander, Benjamin Gross
+ **
+ ** This library is free software; you can redistribute it and/or modify it
+ ** under the terms of the GNU Lesser General Public License as published
+ ** by the Free Software Foundation; either version 2.1 of the License, or
+ ** any later version.
+ **
+ ** This library is distributed in the hope that it will be useful, but
+ ** WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ ** MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ ** documentation provided hereunder is on an "as is" basis, and
+ ** Memorial Sloan-Kettering Cancer Center
+ ** has no obligations to provide maintenance, support,
+ ** updates, enhancements or modifications. In no event shall
+ ** Memorial Sloan-Kettering Cancer Center
+ ** be liable to any party for direct, indirect, special,
+ ** incidental or consequential damages, including lost profits, arising
+ ** out of the use of this software and its documentation, even if
+ ** Memorial Sloan-Kettering Cancer Center
+ ** has been advised of the possibility of such damage. See
+ ** the GNU Lesser General Public License for more details.
+ **
+ ** You should have received a copy of the GNU Lesser General Public License
+ ** along with this library; if not, write to the Free Software Foundation,
+ ** Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ **/
+package org.cytoscape.coreplugin.cpath2.http;
+
+// imports
+
+import java.util.EventObject;
+
+/**
+ * A proxy event object.
+ */
+public class HTTPEvent extends EventObject {
+
+ /**
+ * the request
+ */
+ private String request;
+
+ /**
+ * the response
+ */
+ private String response;
+
+ /**
+ * Constructor.
+ *
+ * @param source Object
+ * @param request String
+ * @param response String
+ */
+ public HTTPEvent(Object source, String request, String response) {
+ super(source);
+
+ // init members
+ this.request = request;
+ this.response = response;
+ }
+
+ /**
+ * Method to get the request.
+ *
+ * @return String
+ */
+ public String getRequest() {
+ return request;
+ }
+
+ /**
+ * Method to get the response.
+ *
+ * @return String
+ */
+ public String getResponse() {
+ return response;
+ }
+}
diff --git a/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/http/HTTPReader.java b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/http/HTTPReader.java
new file mode 100644
index 0000000..9d12e92
--- /dev/null
+++ b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/http/HTTPReader.java
@@ -0,0 +1,92 @@
+// $Id: HTTPReader.java,v 1.5 2007/04/25 15:28:34 grossb Exp $
+//------------------------------------------------------------------------------
+/** Copyright (c) 2007 Memorial Sloan-Kettering Cancer Center.
+ **
+ ** Code written by: Ethan Cerami, Benjamin Gross
+ ** Authors: Ethan Cerami, Gary Bader, Chris Sander, Benjamin Gross
+ **
+ ** This library is free software; you can redistribute it and/or modify it
+ ** under the terms of the GNU Lesser General Public License as published
+ ** by the Free Software Foundation; either version 2.1 of the License, or
+ ** any later version.
+ **
+ ** This library is distributed in the hope that it will be useful, but
+ ** WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ ** MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ ** documentation provided hereunder is on an "as is" basis, and
+ ** Memorial Sloan-Kettering Cancer Center
+ ** has no obligations to provide maintenance, support,
+ ** updates, enhancements or modifications. In no event shall
+ ** Memorial Sloan-Kettering Cancer Center
+ ** be liable to any party for direct, indirect, special,
+ ** incidental or consequential damages, including lost profits, arising
+ ** out of the use of this software and its documentation, even if
+ ** Memorial Sloan-Kettering Cancer Center
+ ** has been advised of the possibility of such damage. See
+ ** the GNU Lesser General Public License for more details.
+ **
+ ** You should have received a copy of the GNU Lesser General Public License
+ ** along with this library; if not, write to the Free Software Foundation,
+ ** Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ **/
+package org.cytoscape.coreplugin.cpath2.http;
+
+// imports
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.net.Socket;
+import java.util.ArrayList;
+
+/**
+ * This class reads incoming http requests.
+ *
+ * @author Benjamin Gross.
+ */
+public class HTTPReader {
+
+ // some string constants
+ private static final String SPACE = " ";
+ private static final String HTTP_PREFIX = "http://";
+
+ /**
+ * Called to handle incoming request.
+ *
+ * @param sock Socket
+ */
+ public static String processRequest(Socket sock) throws IOException {
+
+ // create buffered reader from socket
+ BufferedReader in =
+ new BufferedReader(new InputStreamReader(sock.getInputStream()));
+
+ // init some vars
+ String s;
+ ArrayList<String> request = new ArrayList<String>();
+
+ // grab the entire request
+ while ((s = in.readLine()) != null && s.length() > 0) {
+ request.add(s);
+ }
+
+ // outta here - at this point we only care about the request line
+ return parseRequestLine(request.get(0));
+ }
+
+ /**
+ * Parse request line from client browser.
+ *
+ * @param requestLine String
+ */
+ private static String parseRequestLine(String requestLine) {
+
+ // per rfc2616, request line in following format:
+ // request-line: Method SP Request-URI SP HTTP-Version CRLF
+
+ // replace w/regex if we need to parse arguments
+ String uri =
+ requestLine.substring(requestLine.indexOf(SPACE) + 2, requestLine.lastIndexOf(SPACE));
+ return HTTP_PREFIX + uri;
+ }
+}
diff --git a/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/http/HTTPServer.java b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/http/HTTPServer.java
new file mode 100644
index 0000000..1a1123c
--- /dev/null
+++ b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/http/HTTPServer.java
@@ -0,0 +1,123 @@
+// $Id: HTTPServer.java,v 1.9 2007/04/26 21:56:24 grossb Exp $
+//------------------------------------------------------------------------------
+/** Copyright (c) 2007 Memorial Sloan-Kettering Cancer Center.
+ **
+ ** Code written by: Ethan Cerami, Benjamin Gross
+ ** Authors: Ethan Cerami, Gary Bader, Chris Sander, Benjamin Gross
+ **
+ ** This library is free software; you can redistribute it and/or modify it
+ ** under the terms of the GNU Lesser General Public License as published
+ ** by the Free Software Foundation; either version 2.1 of the License, or
+ ** any later version.
+ **
+ ** This library is distributed in the hope that it will be useful, but
+ ** WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ ** MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ ** documentation provided hereunder is on an "as is" basis, and
+ ** Memorial Sloan-Kettering Cancer Center
+ ** has no obligations to provide maintenance, support,
+ ** updates, enhancements or modifications. In no event shall
+ ** Memorial Sloan-Kettering Cancer Center
+ ** be liable to any party for direct, indirect, special,
+ ** incidental or consequential damages, including lost profits, arising
+ ** out of the use of this software and its documentation, even if
+ ** Memorial Sloan-Kettering Cancer Center
+ ** has been advised of the possibility of such damage. See
+ ** the GNU Lesser General Public License for more details.
+ **
+ ** You should have received a copy of the GNU Lesser General Public License
+ ** along with this library; if not, write to the Free Software Foundation,
+ ** Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ **/
+package org.cytoscape.coreplugin.cpath2.http;
+
+// import
+
+import java.io.IOException;
+import java.net.ServerSocket;
+import java.net.Socket;
+import cytoscape.logger.CyLogger;
+
+/**
+ * HTTPServer class provides a bare-bones
+ * server to listen for requests from cPath instance.
+ * web pages.
+ * <p/>
+ * First version will be single-thread since
+ * we assume only one browser w/pc is running.
+ *
+ * @author Benjamin Gross.
+ */
+public class HTTPServer extends Thread {
+
+ /**
+ * default port
+ */
+ public static final int DEFAULT_PORT = 27182;
+
+ /**
+ * ref to port
+ */
+ private int port;
+
+ /**
+ * debug flag
+ */
+ private boolean debug;
+
+ /**
+ * ref to server listener
+ */
+ private HTTPServerListener listener;
+
+ /**
+ * Constructor.
+ *
+ * @param port int
+ * @param listener HTTServerListener
+ * @param debug boolean
+ */
+ public HTTPServer(int port, HTTPServerListener listener, boolean debug) {
+
+ // init members
+ this.port = port;
+ this.listener = listener;
+ this.debug = debug;
+ }
+
+ /**
+ * Our implementation of run.
+ */
+ public void run() {
+
+ // create new server socket
+ ServerSocket ssocket;
+ try {
+ if (debug) System.out.println("HTTPServer, creating server socket...");
+ ssocket = new ServerSocket(port);
+ } catch (Exception e) {
+ CyLogger.getLogger(HTTPServer.class).warn("HTTPServer couldn't create socket.",e);
+ return;
+ }
+
+ // run indefinitely
+ while (true) {
+
+ try {
+
+ // block until connection is made
+ if (debug) System.out.println("HTTPServer, waiting for connection...");
+ Socket sock = ssocket.accept();
+
+ // connection made, create an new connection handler
+ if (debug)
+ System.out.println("HTTPServer, instantiating new HTTPConnectionHandler");
+ new HTTPConnectionHandler(sock, listener, debug).start();
+
+ } catch (IOException e) {
+ CyLogger.getLogger(HTTPServer.class).warn("HTTPServer couldn't create connection handler.",e);
+ break;
+ }
+ }
+ }
+}
diff --git a/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/http/HTTPServerListener.java b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/http/HTTPServerListener.java
new file mode 100644
index 0000000..b1c7059
--- /dev/null
+++ b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/http/HTTPServerListener.java
@@ -0,0 +1,49 @@
+// $Id: HTTPServerListener.java,v 1.4 2007/04/20 15:50:13 grossb Exp $
+//------------------------------------------------------------------------------
+/** Copyright (c) 2007 Memorial Sloan-Kettering Cancer Center.
+ **
+ ** Code written by: Ethan Cerami, Benjamin Gross
+ ** Authors: Ethan Cerami, Gary Bader, Chris Sander, Benjamin Gross
+ **
+ ** This library is free software; you can redistribute it and/or modify it
+ ** under the terms of the GNU Lesser General Public License as published
+ ** by the Free Software Foundation; either version 2.1 of the License, or
+ ** any later version.
+ **
+ ** This library is distributed in the hope that it will be useful, but
+ ** WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ ** MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ ** documentation provided hereunder is on an "as is" basis, and
+ ** Memorial Sloan-Kettering Cancer Center
+ ** has no obligations to provide maintenance, support,
+ ** updates, enhancements or modifications. In no event shall
+ ** Memorial Sloan-Kettering Cancer Center
+ ** be liable to any party for direct, indirect, special,
+ ** incidental or consequential damages, including lost profits, arising
+ ** out of the use of this software and its documentation, even if
+ ** Memorial Sloan-Kettering Cancer Center
+ ** has been advised of the possibility of such damage. See
+ ** the GNU Lesser General Public License for more details.
+ **
+ ** You should have received a copy of the GNU Lesser General Public License
+ ** along with this library; if not, write to the Free Software Foundation,
+ ** Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ **/
+package org.cytoscape.coreplugin.cpath2.http;
+
+// imports
+
+import java.util.EventListener;
+
+/**
+ * Interface implemented by class which is interested in cPath instance events.
+ */
+public interface HTTPServerListener extends EventListener {
+
+ /**
+ * Method called when a ProxyEvent has been received.
+ *
+ * @param event HTTPEvent
+ */
+ public void httpEvent(HTTPEvent event);
+}
diff --git a/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/http/HTTPWriter.java b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/http/HTTPWriter.java
new file mode 100644
index 0000000..d3b5827
--- /dev/null
+++ b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/http/HTTPWriter.java
@@ -0,0 +1,75 @@
+// $Id: HTTPWriter.java,v 1.4 2007/04/20 15:49:36 grossb Exp $
+//------------------------------------------------------------------------------
+/** Copyright (c) 2007 Memorial Sloan-Kettering Cancer Center.
+ **
+ ** Code written by: Ethan Cerami, Benjamin Gross
+ ** Authors: Ethan Cerami, Gary Bader, Chris Sander, Benjamin Gross
+ **
+ ** This library is free software; you can redistribute it and/or modify it
+ ** under the terms of the GNU Lesser General Public License as published
+ ** by the Free Software Foundation; either version 2.1 of the License, or
+ ** any later version.
+ **
+ ** This library is distributed in the hope that it will be useful, but
+ ** WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ ** MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ ** documentation provided hereunder is on an "as is" basis, and
+ ** Memorial Sloan-Kettering Cancer Center
+ ** has no obligations to provide maintenance, support,
+ ** updates, enhancements or modifications. In no event shall
+ ** Memorial Sloan-Kettering Cancer Center
+ ** be liable to any party for direct, indirect, special,
+ ** incidental or consequential damages, including lost profits, arising
+ ** out of the use of this software and its documentation, even if
+ ** Memorial Sloan-Kettering Cancer Center
+ ** has been advised of the possibility of such damage. See
+ ** the GNU Lesser General Public License for more details.
+ **
+ ** You should have received a copy of the GNU Lesser General Public License
+ ** along with this library; if not, write to the Free Software Foundation,
+ ** Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ **/
+package org.cytoscape.coreplugin.cpath2.http;
+
+// imports
+
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.net.Socket;
+
+/**
+ * This class writes to the http client.
+ *
+ * @author Benjamin Gross.
+ */
+public class HTTPWriter {
+
+ // some string constants
+ private static final String CRNL = "\r\n";
+ private static final String CONTENT_TYPE = "Content-Type: ";
+ private static final String HTTP_RESPONSE = "HTTP/1.1 200 OK";
+ private static final String CONTENT_LENGTH = "Content-Length: ";
+ private static final String CONTENT_TYPE_TEXT_HTML = "text/html";
+
+ /**
+ * Called to write client respones
+ *
+ * @param sock Socket
+ * @param event HTTPEvent
+ */
+ public static void processResponse(Socket sock, HTTPEvent event) throws IOException {
+
+ // setup print writer
+ PrintWriter printWriter = new PrintWriter(sock.getOutputStream());
+
+ String response = event.getResponse();
+
+ // write out the contents
+ printWriter.print(HTTP_RESPONSE + CRNL);
+ printWriter.print(CONTENT_TYPE + CONTENT_TYPE_TEXT_HTML + CRNL);
+ printWriter.print(CONTENT_LENGTH + response.length() + CRNL);
+ printWriter.print(CRNL);
+ printWriter.print(response);
+ printWriter.flush();
+ }
+}
\ No newline at end of file
diff --git a/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/mapping/MapCPathToCytoscape.java b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/mapping/MapCPathToCytoscape.java
new file mode 100644
index 0000000..5716e4b
--- /dev/null
+++ b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/mapping/MapCPathToCytoscape.java
@@ -0,0 +1,127 @@
+// $Id: MapCPathToCytoscape.java,v 1.3 2007/04/20 15:48:50 grossb Exp $
+//------------------------------------------------------------------------------
+/** Copyright (c) 2007 Memorial Sloan-Kettering Cancer Center.
+ **
+ ** Code written by: Ethan Cerami, Benjamin Gross
+ ** Authors: Ethan Cerami, Gary Bader, Chris Sander, Benjamin Gross
+ **
+ ** This library is free software; you can redistribute it and/or modify it
+ ** under the terms of the GNU Lesser General Public License as published
+ ** by the Free Software Foundation; either version 2.1 of the License, or
+ ** any later version.
+ **
+ ** This library is distributed in the hope that it will be useful, but
+ ** WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ ** MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ ** documentation provided hereunder is on an "as is" basis, and
+ ** Memorial Sloan-Kettering Cancer Center
+ ** has no obligations to provide maintenance, support,
+ ** updates, enhancements or modifications. In no event shall
+ ** Memorial Sloan-Kettering Cancer Center
+ ** be liable to any party for direct, indirect, special,
+ ** incidental or consequential damages, including lost profits, arising
+ ** out of the use of this software and its documentation, even if
+ ** Memorial Sloan-Kettering Cancer Center
+ ** has been advised of the possibility of such damage. See
+ ** the GNU Lesser General Public License for more details.
+ **
+ ** You should have received a copy of the GNU Lesser General Public License
+ ** along with this library; if not, write to the Free Software Foundation,
+ ** Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ **/
+package org.cytoscape.coreplugin.cpath2.mapping;
+
+// imports
+
+import cytoscape.util.ProxyHandler;
+import ding.view.NodeContextMenuListener;
+import org.cytoscape.coreplugin.cpath2.http.HTTPConnectionHandler;
+import org.cytoscape.coreplugin.cpath2.http.HTTPEvent;
+import org.cytoscape.coreplugin.cpath2.http.HTTPServerListener;
+import org.cytoscape.coreplugin.cpath2.util.NetworkUtil;
+import org.cytoscape.coreplugin.cpath2.util.NetworkMergeUtil;
+import org.cytoscape.coreplugin.cpath2.view.model.NetworkWrapper;
+import org.cytoscape.coreplugin.cpath2.web_service.CPathProperties;
+
+import java.net.Proxy;
+
+/**
+ * This class listens for requests from cPath instance
+ * and maps the requests into Cytoscape tasks.
+ *
+ * @author Benjamin Gross.
+ */
+public class MapCPathToCytoscape implements HTTPServerListener {
+
+ /*
+ * ref to network listener - for context menus
+ */
+ NodeContextMenuListener nodeContextMenuListener;
+
+ /**
+ * Constructor
+ *
+ * @param nodeContextMenuListener NodeContextMenuListener
+ */
+ public MapCPathToCytoscape(NodeContextMenuListener nodeContextMenuListener) {
+
+ // init member vars
+ this.nodeContextMenuListener = nodeContextMenuListener;
+ }
+
+ /**
+ * Our implementation of HTTPServerListener.
+ *
+ * @param event HTTPEvent
+ */
+ public void httpEvent(HTTPEvent event) {
+
+ // get the request/url
+ String cpathRequest = event.getRequest();
+
+ // swap in proxy server if necessary
+ Proxy proxyServer = ProxyHandler.getProxyServer();
+ if (proxyServer != null) {
+ String proxyAddress = proxyServer.toString();
+ if (proxyAddress != null) {
+ // parse protocol from ip/port address
+ String[] addressComponents = proxyAddress.split("@");
+ // do we have valid components ?
+ if (addressComponents[0] != null && addressComponents[0].length() > 0 &&
+ addressComponents[1] != null && addressComponents[1].length() > 0) {
+ String newURL = addressComponents[0].trim() + ":/" + addressComponents[1].trim();
+ int indexOfWebService = cpathRequest.indexOf(HTTPConnectionHandler.WEB_SERVICE_URL);
+ if (indexOfWebService > -1) {
+ cpathRequest = newURL + cpathRequest.substring(indexOfWebService);
+ }
+ }
+ }
+ }
+ // System.out.println("CPATH REQUEST: " + cpathRequest.toString());
+ loadMergeDialog(cpathRequest);
+ }
+
+ /**
+ * Loads the merge dialog.
+ *
+ * @param cpathRequest String
+ */
+ private void loadMergeDialog(String cpathRequest) {
+ CPathProperties cPathProperties = CPathProperties.getInstance();
+ int downloadMode = cPathProperties.getDownloadMode();
+ cPathProperties.setDownloadMode(CPathProperties.DOWNLOAD_FULL_BIOPAX);
+ NetworkMergeUtil mergeUtil = new NetworkMergeUtil();
+ if (mergeUtil.mergeNetworksExist()) {
+ NetworkWrapper networkWrapper = mergeUtil.promptForNetworkToMerge();
+ if (networkWrapper != null && networkWrapper.getNetwork() != null) {
+ new NetworkUtil(cpathRequest, networkWrapper.getNetwork(),
+ true, nodeContextMenuListener).start();
+ } else {
+ new NetworkUtil(cpathRequest, null, false, nodeContextMenuListener).start();
+ }
+ } else {
+ new NetworkUtil(cpathRequest, null, false, nodeContextMenuListener).start();
+ }
+ cPathProperties.setDownloadMode(downloadMode);
+ }
+}
diff --git a/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/plugin/CPathPlugIn2.java b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/plugin/CPathPlugIn2.java
new file mode 100644
index 0000000..7b5b842
--- /dev/null
+++ b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/plugin/CPathPlugIn2.java
@@ -0,0 +1,163 @@
+// $Id: CPathPlugIn2.java,v 1.8 2007/04/27 19:18:48 grossb Exp $
+//------------------------------------------------------------------------------
+/** Copyright (c) 2007 Memorial Sloan-Kettering Cancer Center.
+ **
+ ** Code written by: Ethan Cerami, Benjamin Gross
+ ** Authors: Ethan Cerami, Gary Bader, Chris Sander, Benjamin Gross
+ **
+ ** This library is free software; you can redistribute it and/or modify it
+ ** under the terms of the GNU Lesser General Public License as published
+ ** by the Free Software Foundation; either version 2.1 of the License, or
+ ** any later version.
+ **
+ ** This library is distributed in the hope that it will be useful, but
+ ** WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ ** MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ ** documentation provided hereunder is on an "as is" basis, and
+ ** Memorial Sloan-Kettering Cancer Center
+ ** has no obligations to provide maintenance, support,
+ ** updates, enhancements or modifications. In no event shall
+ ** Memorial Sloan-Kettering Cancer Center
+ ** be liable to any party for direct, indirect, special,
+ ** incidental or consequential damages, including lost profits, arising
+ ** out of the use of this software and its documentation, even if
+ ** Memorial Sloan-Kettering Cancer Center
+ ** has been advised of the possibility of such damage. See
+ ** the GNU Lesser General Public License for more details.
+ **
+ ** You should have received a copy of the GNU Lesser General Public License
+ ** along with this library; if not, write to the Free Software Foundation,
+ ** Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ **/
+package org.cytoscape.coreplugin.cpath2.plugin;
+
+// imports
+
+import cytoscape.data.webservice.WebServiceClientManager;
+import cytoscape.plugin.CytoscapePlugin;
+import cytoscape.plugin.PluginProperties;
+import org.cytoscape.coreplugin.cpath2.http.HTTPServer;
+import org.cytoscape.coreplugin.cpath2.mapping.MapCPathToCytoscape;
+import org.cytoscape.coreplugin.cpath2.util.NetworkListener;
+import org.cytoscape.coreplugin.cpath2.web_service.CPathProperties;
+import org.cytoscape.coreplugin.cpath2.web_service.CytoscapeCPathWebService;
+
+import javax.swing.*;
+import javax.swing.border.EmptyBorder;
+import javax.swing.border.TitledBorder;
+import java.awt.*;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.io.IOException;
+
+/**
+ * The cPath plugin class. It gets called by Cytoscape's plugin manager
+ * to install inself. The main job of this guy is to instantiate our http server.
+ *
+ * @author Benjamin Gross.
+ */
+public class CPathPlugIn2 extends CytoscapePlugin {
+
+ /**
+ * Constructor.
+ */
+ public CPathPlugIn2() throws IOException {
+
+ String debugProperty = System.getProperty("DEBUG");
+ Boolean debug = (debugProperty != null && debugProperty.length() > 0) &&
+ new Boolean(debugProperty.toLowerCase());
+ initProperties();
+
+ // to catch network creation events - to setup context menu
+ NetworkListener networkListener = new NetworkListener();
+
+ // create our http server and start its thread
+ new HTTPServer(HTTPServer.DEFAULT_PORT,
+ new MapCPathToCytoscape(networkListener), debug).start();
+
+ // Register Web Service
+ WebServiceClientManager.registerClient(CytoscapeCPathWebService.getClient());
+ }
+
+ private void initProperties() throws IOException {
+ PluginProperties pluginProperties = new PluginProperties(this);
+ CPathProperties cpathProperties = CPathProperties.getInstance();
+ cpathProperties.initProperties(pluginProperties);
+ }
+
+ public static JScrollPane createConfigPanel() {
+ JPanel configPanel = new JPanel();
+ configPanel.setBorder(new TitledBorder("Retrieval Options"));
+ configPanel.setLayout(new GridBagLayout());
+ GridBagConstraints c = new GridBagConstraints();
+ final JRadioButton button1 = new JRadioButton("Full Model");
+
+ JTextArea textArea1 = new JTextArea();
+ textArea1.setLineWrap(true);
+ textArea1.setWrapStyleWord(true);
+ textArea1.setEditable(false);
+ textArea1.setOpaque(false);
+ Font font = textArea1.getFont();
+ Font smallerFont = new Font(font.getFamily(), font.getStyle(), font.getSize() - 2);
+ textArea1.setFont(smallerFont);
+ textArea1.setText("Retrieve the full model, as stored in the original BioPAX "
+ + "representation. In this representation, nodes within a network can "
+ + "refer to physical entities and interactions.");
+ textArea1.setBorder(new EmptyBorder(5, 20, 0, 0));
+
+ JTextArea textArea2 = new JTextArea(3, 20);
+ textArea2.setLineWrap(true);
+ textArea2.setWrapStyleWord(true);
+ textArea2.setEditable(false);
+ textArea2.setOpaque(false);
+ textArea2.setFont(smallerFont);
+ textArea2.setText("Retrieve a simplified binary network, as inferred from the original "
+ + "BioPAX representation. In this representation, nodes within a network refer "
+ + "to physical entities only, and edges refer to inferred interactions.");
+ textArea2.setBorder(new EmptyBorder(5, 20, 0, 0));
+
+
+ final JRadioButton button2 = new JRadioButton("Simplified Binary Model");
+ button2.setSelected(true);
+ ButtonGroup group = new ButtonGroup();
+ group.add(button1);
+ group.add(button2);
+
+ c.fill = GridBagConstraints.HORIZONTAL;
+ c.weightx = 1.0;
+
+ c.gridx = 0;
+ c.gridy = 0;
+ configPanel.add(button2, c);
+
+ c.gridy = 1;
+ configPanel.add(textArea2, c);
+
+ c.gridy = 2;
+ configPanel.add(button1, c);
+
+ c.gridy = 3;
+ configPanel.add(textArea1, c);
+
+ // Add invisible filler to take up all remaining space
+ c.gridy = 4;
+ c.weighty = 1.0;
+ JPanel panel = new JPanel();
+ configPanel.add(panel, c);
+
+ button1.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent actionEvent) {
+ CPathProperties config = CPathProperties.getInstance();
+ config.setDownloadMode(CPathProperties.DOWNLOAD_FULL_BIOPAX);
+ }
+ });
+ button2.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent actionEvent) {
+ CPathProperties config = CPathProperties.getInstance();
+ config.setDownloadMode(CPathProperties.DOWNLOAD_REDUCED_BINARY_SIF);
+ }
+ });
+ JScrollPane scrollPane = new JScrollPane(configPanel);
+ return scrollPane;
+ }
+}
diff --git a/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/task/ExecuteGetRecordByCPathId.java b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/task/ExecuteGetRecordByCPathId.java
new file mode 100644
index 0000000..a0d6764
--- /dev/null
+++ b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/task/ExecuteGetRecordByCPathId.java
@@ -0,0 +1,544 @@
+package org.cytoscape.coreplugin.cpath2.task;
+
+import cytoscape.*;
+import cytoscape.util.CyNetworkNaming;
+import cytoscape.ding.DingNetworkView;
+import cytoscape.ding.CyGraphLOD;
+import cytoscape.layout.CyLayoutAlgorithm;
+import cytoscape.layout.CyLayouts;
+import cytoscape.logger.CyLogger;
+import cytoscape.view.CyNetworkView;
+import cytoscape.data.CyAttributes;
+import cytoscape.data.readers.GraphReader;
+import cytoscape.task.Task;
+import cytoscape.task.TaskMonitor;
+import cytoscape.visual.VisualStyle;
+import cytoscape.visual.VisualMappingManager;
+
+import org.biopax.paxtools.converter.OneTwoThree;
+import org.biopax.paxtools.io.SimpleIOHandler;
+import org.biopax.paxtools.model.BioPAXElement;
+import org.biopax.paxtools.model.BioPAXLevel;
+import org.biopax.paxtools.model.Model;
+import org.biopax.paxtools.model.level3.Complex;
+import org.biopax.paxtools.model.level3.EntityReference;
+import org.biopax.paxtools.model.level3.PhysicalEntity;
+import org.cytoscape.coreplugin.cpath2.cytoscape.BinarySifVisualStyleUtil;
+import org.cytoscape.coreplugin.cpath2.web_service.*;
+//import org.mskcc.biopax_plugin.mapping.MapNodeAttributes;
+import cytoscape.coreplugins.biopax.MapBioPaxToCytoscape;
+import cytoscape.coreplugins.biopax.util.BioPaxUtil;
+import cytoscape.coreplugins.biopax.util.CytoscapeWrapper;
+import cytoscape.coreplugins.biopax.action.NetworkListener;
+import cytoscape.coreplugins.biopax.view.BioPaxContainer;
+import cytoscape.coreplugins.biopax.util.BioPaxVisualStyleUtil;
+
+import javax.swing.*;
+
+import java.io.ByteArrayInputStream;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+
+/**
+ * Controller for Executing a Get Record(s) by CPath ID(s) command.
+ *
+ * @author Ethan Cerami.
+ */
+public class ExecuteGetRecordByCPathId implements Task {
+ private CPathWebService webApi;
+ private TaskMonitor taskMonitor;
+ private long ids[];
+ private String networkTitle;
+ private boolean haltFlag = false;
+ private CyNetwork mergedNetwork;
+ private CPathResponseFormat format;
+ private final static String CPATH_SERVER_NAME_ATTRIBUTE = "CPATH_SERVER_NAME";
+ private final static String CPATH_SERVER_DETAILS_URL = "CPATH_SERVER_DETAILS_URL";
+ private CyLogger logger = CyLogger.getLogger(ExecuteGetRecordByCPathId.class);
+
+ /**
+ * Constructor.
+ *
+ * @param webApi cPath Web API.
+ * @param ids Array of cPath IDs.
+ * @param format CPathResponseFormat Object.
+ * @param networkTitle Tentative Network Title.
+ */
+ public ExecuteGetRecordByCPathId(CPathWebService webApi, long ids[], CPathResponseFormat format,
+ String networkTitle) {
+ this.webApi = webApi;
+ this.ids = ids;
+ this.format = format;
+ this.networkTitle = networkTitle;
+ }
+
+ /**
+ * Constructor.
+ *
+ * @param webApi cPath Web API.
+ * @param ids Array of cPath IDs.
+ * @param format CPathResponseFormat Object.
+ * @param networkTitle Tentative Network Title.
+ * @param mergedNetwork Network to merge into.
+ */
+ public ExecuteGetRecordByCPathId(CPathWebService webApi, long ids[], CPathResponseFormat format,
+ String networkTitle, CyNetwork mergedNetwork) {
+ this.webApi = webApi;
+ this.ids = ids;
+ this.format = format;
+ this.networkTitle = networkTitle;
+ this.mergedNetwork = mergedNetwork;
+ }
+
+ /**
+ * Our implementation of Task.abort()
+ */
+ public void halt() {
+ webApi.abort();
+ haltFlag = true;
+ }
+
+ /**
+ * Our implementation of Task.setTaskMonitor().
+ *
+ * @param taskMonitor TaskMonitor
+ */
+ public void setTaskMonitor(TaskMonitor taskMonitor) throws IllegalThreadStateException {
+ this.taskMonitor = taskMonitor;
+ }
+
+ /**
+ * Our implementation of Task.getTitle.
+ *
+ * @return Task Title.
+ */
+ public String getTitle() {
+ return "Retrieving " + networkTitle + " from "
+ + CPathProperties.getInstance().getCPathServerName() + "...";
+ }
+
+ /**
+ * Our implementation of Task.run().
+ */
+ public void run() {
+ try {
+ // read the network from cpath instance
+ if (taskMonitor != null) {
+ taskMonitor.setPercentCompleted(-1);
+ taskMonitor.setStatus("Retrieving " + networkTitle + ".");
+ }
+
+ // Store BioPAX to Temp File
+ String tmpDir = System.getProperty("java.io.tmpdir");
+ // Branch based on download mode setting.
+ File tmpFile;
+ if (format == CPathResponseFormat.BIOPAX) {
+ tmpFile = File.createTempFile("temp", ".xml", new File(tmpDir));
+ } else {
+ tmpFile = File.createTempFile("temp", ".sif", new File(tmpDir));
+ }
+ tmpFile.deleteOnExit();
+
+ // Get Data, and write to temp file.
+ String data = webApi.getRecordsByIds(ids, format, taskMonitor);
+ FileWriter writer = new FileWriter(tmpFile);
+ writer.write(data);
+ writer.close();
+
+ // Load up File via ImportHandler Framework
+ // the biopax graph reader is going to be called
+ // it will look for the network view title
+ // via system properties, so lets set it now
+ if (networkTitle != null && networkTitle.length() > 0) {
+ System.setProperty("biopax.network_view_title", networkTitle);
+ }
+ GraphReader reader = Cytoscape.getImportHandler().getReader(tmpFile.getAbsolutePath());
+ if (taskMonitor != null) {
+ taskMonitor.setStatus("Creating Cytoscape Network...");
+ taskMonitor.setPercentCompleted(-1);
+ }
+
+ CyNetwork cyNetwork = null;
+ // Branch, based on download mode.
+ if (format == CPathResponseFormat.BINARY_SIF) {
+ // create network, without the view.
+ cyNetwork = Cytoscape.createNetwork(reader, false, null);
+ postProcessingBinarySif(cyNetwork);
+ } else {
+ // create network, without the view.
+ cyNetwork = Cytoscape.createNetwork(reader, false, null);
+ postProcessingBioPAX(cyNetwork);
+ }
+
+ // Fire appropriate network event.
+ if (mergedNetwork == null) {
+ // Fire a Network Loaded Event
+ Object[] ret_val = new Object[2];
+ ret_val[0] = cyNetwork;
+ ret_val[1] = networkTitle;
+ Cytoscape.firePropertyChange(Cytoscape.NETWORK_LOADED, null, ret_val);
+ } else {
+ // Fire a Network Modified Event; causes Quick Find to Re-Index.
+ Object[] ret_val = new Object[2];
+ ret_val[0] = mergedNetwork;
+ ret_val[1] = networkTitle;
+ Cytoscape.firePropertyChange(Cytoscape.NETWORK_MODIFIED, null,
+ ret_val);
+ }
+
+ // Add Links Back to cPath Instance
+ addLinksToCPathInstance (cyNetwork);
+
+ if (taskMonitor != null) {
+ taskMonitor.setStatus("Done");
+ taskMonitor.setPercentCompleted(100);
+ }
+ } catch (IOException e) {
+ taskMonitor.setException(e, "Failed to retrieve records.",
+ "Please try again.");
+ } catch (EmptySetException e) {
+ taskMonitor.setException(e, "No matches found for your request. ",
+ "Please try again.");
+ } catch (CPathException e) {
+ if (e.getErrorCode() != CPathException.ERROR_CANCELED_BY_USER) {
+ taskMonitor.setException(e, e.getMessage(), e.getRecoveryTip());
+ }
+ }
+ }
+
+ /**
+ * Add Node Links Back to cPath Instance.
+ * @param cyNetwork CyNetwork.
+ */
+ private void addLinksToCPathInstance(CyNetwork cyNetwork) {
+ CyAttributes networkAttributes = Cytoscape.getNetworkAttributes();
+ CPathProperties props = CPathProperties.getInstance();
+ String serverName = props.getCPathServerName();
+ String serverURL = props.getCPathUrl();
+ String cPathServerDetailsUrl = networkAttributes.getStringAttribute
+ (cyNetwork.getIdentifier(), ExecuteGetRecordByCPathId.CPATH_SERVER_DETAILS_URL);
+ if (cPathServerDetailsUrl == null) {
+ networkAttributes.setAttribute(cyNetwork.getIdentifier(),
+ ExecuteGetRecordByCPathId.CPATH_SERVER_NAME_ATTRIBUTE,
+ serverName);
+ String url = serverURL.replaceFirst("webservice.do", "record2.do?id=");
+ networkAttributes.setAttribute(cyNetwork.getIdentifier(),
+ ExecuteGetRecordByCPathId.CPATH_SERVER_DETAILS_URL,
+ url);
+ }
+ }
+
+ /**
+ * Execute Post-Processing on BINARY SIF Network.
+ *
+ * @param cyNetwork Cytoscape Network Object.
+ */
+ private void postProcessingBinarySif(final CyNetwork cyNetwork) {
+ CyAttributes nodeAttributes = Cytoscape.getNodeAttributes();
+
+ // Init the node attribute meta data, e.g. description, visibility, etc.
+ MapBioPaxToCytoscape.initAttributes(nodeAttributes);
+
+ // Set the Quick Find Default Index
+ Cytoscape.getNetworkAttributes().setAttribute(cyNetwork.getIdentifier(),
+ "quickfind.default_index", BioPaxVisualStyleUtil.BIOPAX_NODE_LABEL);
+
+ // Specify that this is a BINARY_NETWORK
+ Cytoscape.getNetworkAttributes().setAttribute(cyNetwork.getIdentifier(),
+ BinarySifVisualStyleUtil.BINARY_NETWORK, Boolean.TRUE);
+ Cytoscape.getNetworkAttributes().setAttribute(cyNetwork.getIdentifier(),
+ MapBioPaxToCytoscape.BIOPAX_NETWORK, Boolean.TRUE);
+
+ // Get all node details.
+ getNodeDetails(cyNetwork, nodeAttributes);
+
+ if (haltFlag == false) {
+ if (mergedNetwork != null) {
+ mergeNetworks(cyNetwork);
+ } else if (cyNetwork.getNodeCount() < Integer.parseInt(CytoscapeInit.getProperties()
+ .getProperty("viewThreshold"))) {
+ if (taskMonitor != null) {
+ taskMonitor.setStatus("Creating Network View...");
+ taskMonitor.setPercentCompleted(-1);
+ }
+
+ // Set up the right visual style
+ VisualStyle visualStyle = BinarySifVisualStyleUtil.getVisualStyle();
+
+ // Set up the right layout algorithm.
+ CyLayoutAlgorithm layoutAlgorithm = CyLayouts.getLayout("force-directed");
+
+ // Now, create the view.
+ // Use local create view option, so that we don't mess up the visual style.
+ CyNetworkView view = createNetworkView
+ (cyNetwork, cyNetwork.getTitle(), layoutAlgorithm, null);
+
+ // Now apply the visual style;
+ // Doing this as a separate step ensures that the visual style appears
+ // in the visual style drop-down menu.
+ view.applyVizmapper(visualStyle);
+
+ // Set up clickable node details.
+ CytoscapeWrapper.initBioPaxPlugInUI();
+ final BioPaxContainer bpContainer = BioPaxContainer.getInstance();
+ NetworkListener networkListener = bpContainer.getNetworkListener();
+ networkListener.registerNetwork(cyNetwork);
+
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ CytoscapeWrapper.activateBioPaxPlugInTab(bpContainer);
+ bpContainer.showLegend();
+ Cytoscape.getCurrentNetworkView().fitContent();
+ String networkTitleWithUnderscores = networkTitle.replaceAll(": ", "");
+ networkTitleWithUnderscores = networkTitleWithUnderscores.replaceAll(" ", "_");
+ networkTitleWithUnderscores = CyNetworkNaming.getSuggestedNetworkTitle
+ (networkTitleWithUnderscores);
+ cyNetwork.setTitle(networkTitleWithUnderscores);
+ }
+ });
+ }
+ } else {
+ // If we have requested a halt, and we have a network, destroy it.
+ if (cyNetwork != null) {
+ Cytoscape.destroyNetwork(cyNetwork);
+ }
+ }
+ }
+
+ /**
+ * Execute Post-Processing on BioPAX Network.
+ *
+ * @param cyNetwork Cytoscape Network Object.
+ */
+ private void postProcessingBioPAX(final CyNetwork cyNetwork) {
+ if (haltFlag == false) {
+ if (mergedNetwork != null) {
+ mergeNetworks(cyNetwork);
+ } else if (cyNetwork.getNodeCount() < Integer.parseInt(CytoscapeInit.getProperties()
+ .getProperty("viewThreshold"))) {
+ if (taskMonitor != null) {
+ taskMonitor.setStatus("Creating Network View...");
+ taskMonitor.setPercentCompleted(-1);
+ }
+
+ // Set up the right visual style
+ VisualStyle visualStyle = BioPaxVisualStyleUtil.getBioPaxVisualStyle();
+
+ // Set up the right layout algorithm.
+ CyLayoutAlgorithm layoutAlgorithm = CyLayouts.getLayout("force-directed");
+
+ // Now, create the view.
+ // Use local create view option, so that we don't mess up the visual style.
+ CyNetworkView view = createNetworkView(cyNetwork,
+ cyNetwork.getTitle(), layoutAlgorithm, null);
+
+ // Now apply the visual style;
+ // Doing this as a separate step ensures that the visual style appears
+ // in the visual style drop-down menu.
+ view.applyVizmapper(visualStyle);
+ }
+ } else {
+ // If we have requested a halt, and we have a network, destroy it.
+ if (cyNetwork != null) {
+ Cytoscape.destroyNetwork(cyNetwork);
+ }
+ }
+ }
+
+
+ private void mergeNetworks(CyNetwork cyNetwork) {
+ taskMonitor.setStatus("Merging Network...");
+ List<CyNode> nodeList = cyNetwork.nodesList();
+ for (int i = 0; i < nodeList.size(); i++) {
+ CyNode node = (CyNode) nodeList.get(i);
+ mergedNetwork.addNode(node);
+ }
+ List<CyEdge> edgeList = cyNetwork.edgesList();
+ for (int i = 0; i < edgeList.size(); i++) {
+ CyEdge edge = (CyEdge) edgeList.get(i);
+ mergedNetwork.addEdge(edge);
+ }
+
+ // Select this view
+ final CyNetworkView networkView = Cytoscape.getNetworkView
+ (mergedNetwork.getIdentifier());
+ Cytoscape.setCurrentNetwork(mergedNetwork.getIdentifier());
+ Cytoscape.setCurrentNetworkView(mergedNetwork.getIdentifier());
+
+ final BioPaxContainer bpContainer = BioPaxContainer.getInstance();
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ CytoscapeWrapper.activateBioPaxPlugInTab(bpContainer);
+ bpContainer.showLegend();
+ VisualMappingManager vizmapper = Cytoscape.getVisualMappingManager();
+ vizmapper.applyAppearances();
+ }
+ });
+
+ // Select only the new nodes
+ mergedNetwork.unselectAllEdges();
+ mergedNetwork.unselectAllNodes();
+ mergedNetwork.setSelectedNodeState(nodeList, true);
+ mergedNetwork.setSelectedEdgeState(edgeList, true);
+
+ // Delete the temp network.
+ Cytoscape.destroyNetwork(cyNetwork);
+
+ // Apply Layout
+ Object[] options = {"Yes", "No"};
+ int n = JOptionPane.showOptionDialog(Cytoscape.getDesktop(),
+ "Would you like to layout the modified network?",
+ "Adjust Layout?",
+ JOptionPane.YES_NO_CANCEL_OPTION,
+ JOptionPane.QUESTION_MESSAGE,
+ null,
+ options, options[0]);
+ if (n==0) {
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ CyLayoutAlgorithm layoutAlgorithm = CyLayouts.getLayout("force-directed");
+ networkView.applyLayout(layoutAlgorithm);
+ Cytoscape.getCurrentNetworkView().fitContent();
+ }
+ });
+ }
+ }
+
+ /**
+ * Gets Details for Each Node from Web Service API.
+ */
+ private void getNodeDetails (CyNetwork cyNetwork, CyAttributes nodeAttributes) {
+ if (taskMonitor != null) {
+ taskMonitor.setStatus("Retrieving node details...");
+ taskMonitor.setPercentCompleted(0);
+ }
+ List<List<CyNode>> batchList = createBatchArray(cyNetwork);
+ if (batchList.size()==0) {
+ logger.info ("Skipping node details. Already have all the details new need.");
+ }
+ for (int i=0; i<batchList.size(); i++) {
+ if (haltFlag == true) {
+ break;
+ }
+ List<CyNode> currentList = (List<CyNode>) batchList.get(i);
+ logger.debug ("Getting node details, batch: " + i);
+ long ids[] = new long [currentList.size()];
+ for (int j=0; j<currentList.size(); j++) {
+ CyNode node = (CyNode) currentList.get(j);
+ ids[j] = Long.valueOf(node.getIdentifier());
+ }
+ try {
+ String xml = webApi.getRecordsByIds(ids, CPathResponseFormat.BIOPAX, new NullTaskMonitor());
+ Model model = (new SimpleIOHandler())
+ .convertFromOWL(new ByteArrayInputStream(xml.getBytes()));
+ if(model != null && BioPAXLevel.L2.equals(model.getLevel())) {
+ model = new OneTwoThree().filter(model);
+ }
+ for(BioPAXElement e: model.getObjects()) {
+ if(e instanceof EntityReference
+ || e instanceof Complex
+ || e.getModelInterface().equals(PhysicalEntity.class)) {
+ String cpathId = e.getRDFId()
+ .replaceFirst(model.getXmlBase()+"CPATH-", "");
+ MapBioPaxToCytoscape.mapNodeAttribute(e, model, cpathId);
+ }
+ }
+ int percentComplete = (int) (100.0 * (i / (double) batchList.size()));
+ if (taskMonitor != null) {
+ taskMonitor.setPercentCompleted(percentComplete);
+ }
+ } catch (EmptySetException e) {
+ e.printStackTrace();
+ } catch (CPathException e) {
+ e.printStackTrace();
+ }
+ }
+ }
+
+ private List<List<CyNode>> createBatchArray(CyNetwork cyNetwork) {
+ CyAttributes nodeAttributes = Cytoscape.getNodeAttributes();
+ int max_ids_per_request = 50;
+ List<List<CyNode>> masterList = new ArrayList<List<CyNode>>();
+ List<CyNode> currentList = new ArrayList<CyNode>();
+ Iterator<CyNode> nodeIterator = cyNetwork.nodesIterator();
+ int counter = 0;
+ while (nodeIterator.hasNext()) {
+ CyNode node = nodeIterator.next();
+ String label = nodeAttributes.getStringAttribute(node.getIdentifier(),
+ BioPaxVisualStyleUtil.BIOPAX_NODE_LABEL);
+
+ // If we already have details on this node, skip it.
+ if (label == null) {
+ currentList.add(node);
+ counter++;
+ }
+ if (counter > max_ids_per_request) {
+ masterList.add(currentList);
+ currentList = new ArrayList<CyNode>();
+ counter = 0;
+ }
+ }
+ if (currentList.size() > 0) {
+ masterList.add(currentList);
+ }
+
+ return masterList;
+ }
+
+ private CyNetworkView createNetworkView (CyNetwork network, String title, CyLayoutAlgorithm
+ layout, VisualStyle vs) {
+
+ if (Cytoscape.viewExists(network.getIdentifier())) {
+ return Cytoscape.getNetworkView(network.getIdentifier());
+ }
+
+ final DingNetworkView view = new DingNetworkView(network, title);
+ view.setGraphLOD(new CyGraphLOD());
+ view.setIdentifier(network.getIdentifier());
+ view.setTitle(network.getTitle());
+ Cytoscape.getNetworkViewMap().put(network.getIdentifier(), view);
+ Cytoscape.setSelectionMode(Cytoscape.getSelectionMode(), view);
+
+ VisualMappingManager VMM = Cytoscape.getVisualMappingManager();
+ if (vs != null) {
+ view.setVisualStyle(vs.getName());
+ VMM.setVisualStyle(vs);
+ VMM.setNetworkView(view);
+ }
+
+ if (layout == null) {
+ layout = CyLayouts.getDefaultLayout();
+ }
+
+ Cytoscape.firePropertyChange(cytoscape.view.CytoscapeDesktop.NETWORK_VIEW_CREATED,
+ null, view);
+ layout.doLayout(view);
+ view.fitContent();
+ view.redrawGraph(false, true);
+ return view;
+ }
+}
+
+class NullTaskMonitor implements TaskMonitor {
+
+ public void setPercentCompleted(int i) throws IllegalArgumentException {
+ }
+
+ public void setEstimatedTimeRemaining(long l) throws IllegalThreadStateException {
+ }
+
+ public void setException(Throwable throwable, String string)
+ throws IllegalThreadStateException {
+ }
+
+ public void setException(Throwable throwable, String string, String string1)
+ throws IllegalThreadStateException {
+ }
+
+ public void setStatus(String string) throws IllegalThreadStateException, NullPointerException {
+ }
+}
diff --git a/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/task/ExecutePhysicalEntitySearch.java b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/task/ExecutePhysicalEntitySearch.java
new file mode 100644
index 0000000..217b912
--- /dev/null
+++ b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/task/ExecutePhysicalEntitySearch.java
@@ -0,0 +1,113 @@
+package org.cytoscape.coreplugin.cpath2.task;
+
+import cytoscape.task.Task;
+import cytoscape.task.TaskMonitor;
+import cytoscape.Cytoscape;
+import org.cytoscape.coreplugin.cpath2.web_service.CPathWebService;
+import org.cytoscape.coreplugin.cpath2.web_service.EmptySetException;
+import org.cytoscape.coreplugin.cpath2.web_service.CPathException;
+import org.cytoscape.coreplugin.cpath2.web_service.CPathProperties;
+import org.cytoscape.coreplugin.cpath2.schemas.search_response.SearchResponseType;
+import org.cytoscape.coreplugin.cpath2.schemas.search_response.ExtendedRecordType;
+
+import javax.swing.*;
+import java.util.List;
+
+/**
+ * Controller for Executing a Physical Entity Search.
+ *
+ * @author Ethan Cerami.
+ */
+public class ExecutePhysicalEntitySearch implements Task {
+ private CPathWebService webApi;
+ private String keyword;
+ private int ncbiTaxonomyId;
+ private TaskMonitor taskMonitor;
+ private int numMatchesFound = 0;
+
+ /**
+ * Constructor.
+ *
+ * @param webApi cPath Web Api.
+ * @param keyword Keyword
+ * @param ncbiTaxonomyId NCBI Taxonomy ID.
+ */
+ public ExecutePhysicalEntitySearch(CPathWebService webApi, String keyword,
+ int ncbiTaxonomyId) {
+ this.webApi = webApi;
+ this.keyword = keyword;
+ this.ncbiTaxonomyId = ncbiTaxonomyId;
+ }
+
+ /**
+ * Our implementation of Task.abort()
+ */
+ public void halt() {
+ webApi.abort();
+ }
+
+ /**
+ * Our implementation of Task.setTaskMonitor().
+ *
+ * @param taskMonitor TaskMonitor
+ */
+ public void setTaskMonitor(TaskMonitor taskMonitor) throws IllegalThreadStateException {
+ this.taskMonitor = taskMonitor;
+ }
+
+ /**
+ * Gets Number of Matches Found.
+ * @return Number of Matches Found.
+ */
+ public int getNumMatchesFound() {
+ return this.numMatchesFound;
+ }
+
+ /**
+ * Our implementation of Task.getTitle.
+ *
+ * @return Task Title.
+ */
+ public String getTitle() {
+ return "Searching " + CPathProperties.getInstance().getCPathServerName() + "...";
+ }
+
+ /**
+ * Our implementation of Task.run().
+ */
+ public void run() {
+ try {
+ // read the network from cpath instance
+ taskMonitor.setPercentCompleted(-1);
+ taskMonitor.setStatus("Executing Search");
+
+ // Execute the Search
+ SearchResponseType searchResponse = webApi.searchPhysicalEntities(keyword,
+ ncbiTaxonomyId, taskMonitor);
+ List<ExtendedRecordType> searchHits = searchResponse.getSearchHit();
+
+ int numHits = searchHits.size();
+ int numRetrieved = 1;
+ taskMonitor.setPercentCompleted(1);
+ for (ExtendedRecordType hit: searchHits) {
+ taskMonitor.setStatus("Retrieving interaction details for: " +
+ hit.getName());
+ try {
+ webApi.getParentSummaries(hit.getPrimaryId(), taskMonitor);
+ } catch (EmptySetException e) {
+ }
+ int percentComplete = (int) (100 * (numRetrieved++ / (float) numHits));
+ taskMonitor.setPercentCompleted(percentComplete);
+ }
+ this.numMatchesFound = numHits;
+ } catch (EmptySetException e) {
+ } catch (CPathException e) {
+ if (e.getErrorCode() != CPathException.ERROR_CANCELED_BY_USER) {
+ taskMonitor.setException(e, e.getMessage(), e.getRecoveryTip());
+ }
+ } finally {
+ taskMonitor.setStatus("Done");
+ taskMonitor.setPercentCompleted(100);
+ }
+ }
+}
\ No newline at end of file
diff --git a/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/task/ExpandNode.java b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/task/ExpandNode.java
new file mode 100644
index 0000000..6b15910
--- /dev/null
+++ b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/task/ExpandNode.java
@@ -0,0 +1,52 @@
+package org.cytoscape.coreplugin.cpath2.task;
+
+import ding.view.NodeContextMenuListener;
+import giny.view.NodeView;
+
+import javax.swing.*;
+import java.net.URL;
+import java.awt.event.ActionListener;
+import java.awt.event.ActionEvent;
+
+import org.cytoscape.coreplugin.cpath2.view.SearchHitsPanel;
+import org.cytoscape.coreplugin.cpath2.view.InteractionBundlePanel;
+import org.cytoscape.coreplugin.cpath2.view.model.InteractionBundleModel;
+import org.cytoscape.coreplugin.cpath2.web_service.CPathProperties;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+import cytoscape.task.ui.JTaskConfig;
+import cytoscape.task.util.TaskManager;
+
+/**
+ * Expand a Node Feature.
+ */
+public class ExpandNode implements NodeContextMenuListener, ActionListener {
+ private NodeView nodeView;
+
+ public ExpandNode (NodeView nodeView) {
+ this.nodeView = nodeView;
+ }
+
+ public void addNodeContextMenuItems(NodeView nodeView, JPopupMenu jPopupMenu) {
+ this.nodeView = nodeView;
+ CPathProperties cpathProperties = CPathProperties.getInstance();
+ JMenuItem menuItem = new JMenuItem ("Get Neighbors from: "
+ + cpathProperties.getCPathServerName());
+ menuItem.addActionListener(this);
+ jPopupMenu.add(menuItem);
+ }
+
+ public void actionPerformed(ActionEvent actionEvent) {
+ GetParentInteractions task = new GetParentInteractions((CyNode) nodeView.getNode());
+
+ // Configure JTask Dialog Pop-Up Box
+ JTaskConfig jTaskConfig = new JTaskConfig();
+ jTaskConfig.setOwner(Cytoscape.getDesktop());
+ jTaskConfig.displayCloseButton(true);
+ jTaskConfig.displayStatus(true);
+ jTaskConfig.setAutoDispose(true);
+
+ // Execute Task in New Thread; pops open JTask Dialog Box.
+ TaskManager.executeTask(task, jTaskConfig);
+ }
+}
diff --git a/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/task/GetParentInteractions.java b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/task/GetParentInteractions.java
new file mode 100644
index 0000000..e1263ca
--- /dev/null
+++ b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/task/GetParentInteractions.java
@@ -0,0 +1,84 @@
+package org.cytoscape.coreplugin.cpath2.task;
+
+import cytoscape.task.Task;
+import cytoscape.task.TaskMonitor;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+import cytoscape.data.CyAttributes;
+import org.cytoscape.coreplugin.cpath2.web_service.CPathWebService;
+import org.cytoscape.coreplugin.cpath2.web_service.CPathException;
+import org.cytoscape.coreplugin.cpath2.web_service.EmptySetException;
+import org.cytoscape.coreplugin.cpath2.web_service.CPathWebServiceImpl;
+import org.cytoscape.coreplugin.cpath2.schemas.summary_response.SummaryResponseType;
+import org.cytoscape.coreplugin.cpath2.view.model.InteractionBundleModel;
+import org.cytoscape.coreplugin.cpath2.view.model.RecordList;
+import org.cytoscape.coreplugin.cpath2.view.InteractionBundlePanel;
+import cytoscape.coreplugins.biopax.util.BioPaxVisualStyleUtil;
+
+import javax.swing.*;
+
+public class GetParentInteractions implements Task {
+ private long cpathId;
+ private TaskMonitor taskMonitor;
+ private CPathWebService webApi = CPathWebServiceImpl.getInstance();
+ private InteractionBundleModel interactionBundleModel;
+ private CyNode node;
+
+ public GetParentInteractions (CyNode node) {
+ this.cpathId = Long.parseLong(node.getIdentifier());
+ this.node = node;
+ }
+
+ public void run() {
+ try {
+ taskMonitor.setStatus("Retrieving neighborhood summary.");
+ SummaryResponseType response = webApi.getParentSummaries(cpathId, taskMonitor);
+ RecordList recordList = new RecordList(response);
+ interactionBundleModel = new InteractionBundleModel();
+ interactionBundleModel.setRecordList(recordList);
+ interactionBundleModel.setPhysicalEntityName("Network Neighborhood");
+
+ JDialog dialog = new JDialog(Cytoscape.getDesktop());
+
+ CyAttributes nodeAttributes = Cytoscape.getNodeAttributes();
+ String nodeLabel = nodeAttributes.getStringAttribute(node.getIdentifier(),
+ BioPaxVisualStyleUtil.BIOPAX_NODE_LABEL);
+ if (nodeLabel != null) {
+ dialog.setTitle(nodeLabel);
+ } else {
+ dialog.setTitle("Neighborhood");
+ }
+ InteractionBundlePanel interactionBundlePanel =
+ new InteractionBundlePanel(interactionBundleModel,
+ Cytoscape.getCurrentNetwork(), dialog);
+ dialog.getContentPane().add(interactionBundlePanel);
+ interactionBundleModel.setRecordList(recordList);
+ interactionBundlePanel.expandAllNodes();
+ dialog.pack();
+ dialog.setLocationRelativeTo(Cytoscape.getDesktop());
+ dialog.setVisible(true);
+ } catch (CPathException e) {
+ if (e.getErrorCode() != CPathException.ERROR_CANCELED_BY_USER) {
+ taskMonitor.setException(e, e.getMessage(), e.getRecoveryTip());
+ }
+ } catch (EmptySetException e) {
+ taskMonitor.setException(e, "No neighbors found for selected node.");
+ }
+ }
+
+ public void halt() {
+ webApi.abort();
+ }
+
+ public void setTaskMonitor(TaskMonitor taskMonitor) throws IllegalThreadStateException {
+ this.taskMonitor = taskMonitor;
+ }
+
+ public String getTitle() {
+ return "Getting neighbors...";
+ }
+
+ public InteractionBundleModel getInteractionBundle() {
+ return this.interactionBundleModel;
+ }
+}
diff --git a/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/task/LoadNetworkFromUrlTask.java b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/task/LoadNetworkFromUrlTask.java
new file mode 100644
index 0000000..f150d19
--- /dev/null
+++ b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/task/LoadNetworkFromUrlTask.java
@@ -0,0 +1,196 @@
+/*
+ File: LoadNetworkFromUrlTask.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+// $Revision: 8703 $
+// $Date: 2006-11-06 23:17:02 -0800 (Mon, 06 Nov 2006) $
+// $Author: pwang $
+package org.cytoscape.coreplugin.cpath2.task;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import cytoscape.CytoscapeInit;
+
+import cytoscape.data.readers.GraphReader;
+
+import cytoscape.task.Task;
+import cytoscape.task.TaskMonitor;
+
+import cytoscape.task.ui.JTaskConfig;
+
+import cytoscape.task.util.TaskManager;
+
+import java.io.IOException;
+
+import java.net.URL;
+
+import java.text.DecimalFormat;
+import java.text.NumberFormat;
+
+import javax.swing.JOptionPane;
+
+/**
+ * Task to load a new network from a URL.
+ *
+ * Modified version of the original LoadNetworkTask from cytoscape code.
+ */
+public class LoadNetworkFromUrlTask implements Task {
+ private URL url;
+ private TaskMonitor taskMonitor;
+ private GraphReader reader;
+
+ /**
+ * Loads a Network from the specified URL.
+ *
+ * @param url URL.
+ * @param skipMessage Show result of download or skip it.
+ */
+ public static void loadURL(URL url, boolean skipMessage) {
+ LoadNetworkFromUrlTask task = new LoadNetworkFromUrlTask(url);
+ setupTask(task, skipMessage);
+ }
+
+ private static void setupTask(LoadNetworkFromUrlTask task, boolean skipMessage) {
+ // Configure JTask Dialog Pop-Up Box
+ JTaskConfig jTaskConfig = new JTaskConfig();
+ jTaskConfig.setOwner(Cytoscape.getDesktop());
+ jTaskConfig.displayCloseButton(true);
+ jTaskConfig.displayStatus(true);
+ jTaskConfig.setAutoDispose(skipMessage);
+
+ // Execute Task in New Thread; pops open JTask Dialog Box.
+ TaskManager.executeTask(task, jTaskConfig);
+ }
+
+ private LoadNetworkFromUrlTask(URL url) {
+ this.url = url;
+ }
+
+ /**
+ * Executes Task.
+ */
+ public void run() {
+ taskMonitor.setPercentCompleted(-1);
+ taskMonitor.setStatus("Reading in Network Data...");
+
+ try {
+ reader = Cytoscape.getImportHandler().getReader(url);
+
+ if (reader == null) {
+ JOptionPane.showMessageDialog(Cytoscape.getDesktop(),
+ "Unable to connect to URL "+ url ,
+ "URL Connect Error", JOptionPane.ERROR_MESSAGE);
+ return;
+ }
+ taskMonitor.setStatus("Creating Cytoscape Network...");
+ CyNetwork cyNetwork = Cytoscape.createNetwork(reader, true, null);
+
+ Object[] ret_val = new Object[2];
+ ret_val[0] = cyNetwork;
+ ret_val[1] = url.toString();
+
+ Cytoscape.firePropertyChange(Cytoscape.NETWORK_LOADED, null, ret_val);
+
+ if (cyNetwork != null) {
+ informUserOfGraphStats(cyNetwork);
+ } else {
+ StringBuffer sb = new StringBuffer();
+ sb.append("Could not read network from: ");
+ sb.append(url);
+ sb.append("\nThis file may not be a valid file format.");
+ taskMonitor.setException(new IOException(sb.toString()), sb.toString());
+ }
+ taskMonitor.setPercentCompleted(100);
+ } catch (Exception e) {
+ taskMonitor.setException(e, "Unable to load network.");
+ }
+ }
+
+ /**
+ * Inform User of Network Stats.
+ */
+ private void informUserOfGraphStats(CyNetwork newNetwork) {
+ NumberFormat formatter = new DecimalFormat("#,###,###");
+ StringBuffer sb = new StringBuffer();
+
+ // Give the user some confirmation
+ sb.append("Successfully loaded network from: ");
+ sb.append(url);
+ sb.append("\n\nNetwork contains " + formatter.format(newNetwork.getNodeCount()));
+ sb.append(" nodes and " + formatter.format(newNetwork.getEdgeCount()));
+ sb.append(" edges.\n\n");
+
+ if (newNetwork.getNodeCount() < Integer.parseInt(CytoscapeInit.getProperties()
+ .getProperty("viewThreshold"))) {
+ sb.append("Network is under "
+ + CytoscapeInit.getProperties().getProperty("viewThreshold")
+ + " nodes. A view will be automatically created.");
+ } else {
+ sb.append("Network is over "
+ + CytoscapeInit.getProperties().getProperty("viewThreshold")
+ + " nodes. A view has not been created."
+ + " If you wish to view this network, use "
+ + "\"Create View\" from the \"Edit\" menu.");
+ }
+ taskMonitor.setStatus(sb.toString());
+ }
+
+ /**
+ * Halts the Task: Not Currently Implemented.
+ */
+ public void halt() {
+ // Task can not currently be halted.
+ }
+
+ /**
+ * Sets the Task Monitor.
+ *
+ * @param taskMonitor
+ * TaskMonitor Object.
+ */
+ public void setTaskMonitor(TaskMonitor taskMonitor) throws IllegalThreadStateException {
+ this.taskMonitor = taskMonitor;
+ }
+
+ /**
+ * Gets the Task Title.
+ *
+ * @return Task Title.
+ */
+ public String getTitle() {
+ return new String("Loading Network");
+ }
+}
diff --git a/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/task/MergeNetworkTask.java b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/task/MergeNetworkTask.java
new file mode 100644
index 0000000..4fc119e
--- /dev/null
+++ b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/task/MergeNetworkTask.java
@@ -0,0 +1,200 @@
+// $Id: MergeNetworkTask.java,v 1.3 2007/04/20 15:49:12 grossb Exp $
+//------------------------------------------------------------------------------
+/** Copyright (c) 2007 Memorial Sloan-Kettering Cancer Center.
+ **
+ ** Code written by: Ethan Cerami, Benjamin Gross
+ ** Authors: Ethan Cerami, Gary Bader, Chris Sander, Benjamin Gross
+ **
+ ** This library is free software; you can redistribute it and/or modify it
+ ** under the terms of the GNU Lesser General Public License as published
+ ** by the Free Software Foundation; either version 2.1 of the License, or
+ ** any later version.
+ **
+ ** This library is distributed in the hope that it will be useful, but
+ ** WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ ** MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ ** documentation provided hereunder is on an "as is" basis, and
+ ** Memorial Sloan-Kettering Cancer Center
+ ** has no obligations to provide maintenance, support,
+ ** updates, enhancements or modifications. In no event shall
+ ** Memorial Sloan-Kettering Cancer Center
+ ** be liable to any party for direct, indirect, special,
+ ** incidental or consequential damages, including lost profits, arising
+ ** out of the use of this software and its documentation, even if
+ ** Memorial Sloan-Kettering Cancer Center
+ ** has been advised of the possibility of such damage. See
+ ** the GNU Lesser General Public License for more details.
+ **
+ ** You should have received a copy of the GNU Lesser General Public License
+ ** along with this library; if not, write to the Free Software Foundation,
+ ** Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ **/
+package org.cytoscape.coreplugin.cpath2.task;
+
+// imports
+
+import cytoscape.CyEdge;
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+import cytoscape.data.readers.GraphReader;
+import cytoscape.task.Task;
+import cytoscape.task.TaskMonitor;
+import cytoscape.util.undo.CyUndo;
+import org.cytoscape.coreplugin.cpath2.cytoscape.MergeNetworkEdit;
+import org.cytoscape.coreplugin.cpath2.web_service.CPathProperties;
+
+import java.net.URL;
+import java.text.DecimalFormat;
+import java.text.NumberFormat;
+import java.util.HashSet;
+import java.util.Set;
+
+/**
+ * Task to merge a network.
+ *
+ * @author Benjamin Gross
+ */
+public class MergeNetworkTask implements Task {
+
+ /**
+ * ref to cpathInstanceURL
+ */
+ private URL cpathInstanceURL;
+
+ /**
+ * ref to cyNetwork
+ */
+ private CyNetwork cyNetwork;
+
+ /**
+ * ref to our graph reader
+ */
+ private GraphReader reader;
+
+ /**
+ * ref to the task monitor
+ */
+ private TaskMonitor taskMonitor;
+
+ /**
+ * Constructor.
+ *
+ * @param cpathURL URL
+ * @param cyNetwork CyNetwork
+ */
+ public MergeNetworkTask(URL cpathURL, CyNetwork cyNetwork) {
+
+ // init member vars
+ this.cpathInstanceURL = cpathURL;
+ this.cyNetwork = cyNetwork;
+ reader = Cytoscape.getImportHandler().getReader(cpathURL);
+ }
+
+ /**
+ * Our implementation of Task.halt()
+ */
+ public void halt() {
+ // Task can not currently be halted.
+ }
+
+ /**
+ * Our implementation of Task.setTaskMonitor().
+ *
+ * @param taskMonitor TaskMonitor
+ */
+ public void setTaskMonitor(TaskMonitor taskMonitor) throws IllegalThreadStateException {
+ this.taskMonitor = taskMonitor;
+ }
+
+ /**
+ * Our implementation of Task.getTitle.
+ *
+ * @return Task Title.
+ */
+ public String getTitle() {
+ return CPathProperties.getInstance().getCPathServerName() + " Plugin - Merge Network";
+ }
+
+ /**
+ * Our implementation of Task.run().
+ */
+ public void run() {
+
+ try {
+
+ // read the network from cpath instance
+ taskMonitor.setPercentCompleted(-1);
+ taskMonitor.setStatus("Reading in Network Data from "
+ + CPathProperties.getInstance().getCPathServerName() + "...");
+ reader.read();
+
+ // unselect all nodes / edges
+ cyNetwork.unselectAllNodes();
+ cyNetwork.unselectAllEdges();
+
+ // refs to capture new nodes and edgets
+ Set<CyNode> newNodes = new HashSet<CyNode>();
+ Set<CyEdge> newEdges = new HashSet<CyEdge>();
+
+ // add new nodes and edges to existing network
+ // tbd: worry about networks that exceed # node/edge threshold
+ final int[] nodes = reader.getNodeIndicesArray();
+ final int[] edges = reader.getEdgeIndicesArray();
+ for (int node : nodes) {
+ cyNetwork.addNode(node);
+ newNodes.add((CyNode) Cytoscape.getRootGraph().getNode(node));
+ }
+ for (int edge : edges) {
+ cyNetwork.addEdge(edge);
+ newEdges.add((CyEdge) Cytoscape.getRootGraph().getEdge(edge));
+ }
+
+ // execute any post processing -
+ // in this case, biopax style is applied, network attributes set, etc
+ reader.doPostProcessing(cyNetwork);
+
+ // select nodes / edges
+ cyNetwork.setSelectedNodeState(newNodes, true);
+ cyNetwork.setSelectedEdgeState(newEdges, true);
+
+ // setup undo
+ CyUndo.getUndoableEditSupport().postEdit(new MergeNetworkEdit(cyNetwork, newNodes, newEdges));
+
+ // fire Cytoscape.NETWORK_MODIFIED - should be removed when undo support is back in
+ Cytoscape.firePropertyChange(Cytoscape.NETWORK_MODIFIED, null, cyNetwork);
+
+ // update the task monitor
+ taskMonitor.setStatus(getMergeStatus(cyNetwork, nodes.length, edges.length));
+ taskMonitor.setPercentCompleted(100);
+
+ } catch (Exception e) {
+ taskMonitor.setException(e, "Unable to merge networks.");
+ }
+ }
+
+ /**
+ * Constructs merge status string.
+ * (based on cytoscape.action.LoadNetworkFromUrlTask.informUserOfGraphStats)
+ *
+ * @param cyNetwork CyNetwork
+ * @param nodeCount int
+ * @param edgeCount int
+ * @return String
+ */
+ private String getMergeStatus(CyNetwork cyNetwork, int nodeCount, int edgeCount) {
+
+ NumberFormat formatter = new DecimalFormat("#,###,###");
+ StringBuffer sb = new StringBuffer();
+
+ // construct status string
+ sb.append("Succesfully merged network from: ");
+ sb.append(cpathInstanceURL.toString() + ".\n");
+ sb.append(formatter.format(nodeCount) + " nodes and " + formatter.format(edgeCount) + " edges have been merged.");
+ sb.append(" The merged network contains a total of " + formatter.format(cyNetwork.getNodeCount()));
+ sb.append(" nodes and " + formatter.format(cyNetwork.getEdgeCount()) + " edges.");
+
+ // outta here
+ return sb.toString();
+ }
+}
diff --git a/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/task/SelectPhysicalEntity.java b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/task/SelectPhysicalEntity.java
new file mode 100644
index 0000000..286657e
--- /dev/null
+++ b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/task/SelectPhysicalEntity.java
@@ -0,0 +1,182 @@
+package org.cytoscape.coreplugin.cpath2.task;
+
+import org.cytoscape.coreplugin.cpath2.view.model.InteractionBundleModel;
+import org.cytoscape.coreplugin.cpath2.view.model.RecordList;
+import org.cytoscape.coreplugin.cpath2.view.model.PathwayTableModel;
+import org.cytoscape.coreplugin.cpath2.schemas.search_response.*;
+import org.cytoscape.coreplugin.cpath2.schemas.summary_response.SummaryResponseType;
+
+import javax.swing.text.Document;
+import javax.swing.*;
+import java.util.List;
+import java.util.Vector;
+import java.util.HashMap;
+
+/**
+ * Indicates that the user has selected a physical entity from the list of search results.
+ *
+ * @author Ethan Cerami.
+ */
+public class SelectPhysicalEntity {
+ private HashMap<Long, RecordList> parentRecordsMap;
+
+ /**
+ * Constructor.
+ *
+ * @param parentRecordsMap RecordList.
+ */
+ public SelectPhysicalEntity (HashMap<Long, RecordList> parentRecordsMap) {
+ this.parentRecordsMap = parentRecordsMap;
+ }
+
+ /**
+ * Select the Phsyical Entity specified by the selected index.
+ *
+ * @param peSearchResponse SearchResponseType peSearchResponse.
+ * @param selectedIndex Selected Index.
+ * @param interactionBundleModel Interaction Table Model.
+ * @param pathwayTableModel Pathway Table Model.
+ * @param summaryDocumentModel Summary Document Model.
+ */
+ public void selectPhysicalEntity(SearchResponseType peSearchResponse,
+ int selectedIndex, InteractionBundleModel interactionBundleModel, PathwayTableModel
+ pathwayTableModel, Document summaryDocumentModel,
+ JTextPane textPane, JComponent textPaneOwner) {
+ if (peSearchResponse != null) {
+ java.util.List<ExtendedRecordType> searchHits = peSearchResponse.getSearchHit();
+ ExtendedRecordType searchHit = searchHits.get(selectedIndex);
+
+ StringBuffer html = new StringBuffer();
+ html.append("<html>");
+
+ html.append ("<h2>" + searchHit.getName() + "</h2>");
+
+ OrganismType organism = searchHit.getOrganism();
+ if (organism != null) {
+ String speciesName = organism.getSpeciesName();
+ html.append ("<H3>" + speciesName + "</H3>");
+ }
+
+ // Next, add synonyms
+ List <String> synList = searchHit.getSynonym();
+ StringBuffer synBuffer = new StringBuffer();
+ if (synList != null && synList.size() > 0) {
+ for (String synonym: synList) {
+ if (!synonym.equalsIgnoreCase(searchHit.getName())) {
+ synBuffer.append("<LI>- " + synonym + "</LI>");
+ }
+ }
+ if (synBuffer.length() > 0) {
+ html.append("<h4>Synonyms:</h4>");
+ html.append("<UL>");
+ html.append(synBuffer.toString());
+ html.append("</UL>");
+ }
+ }
+
+ // Next, add XRefs
+ List <XRefType> xrefList = searchHit.getXref();
+ if (xrefList != null && xrefList.size() > 0) {
+ html.append("<H4>Links:</H4>");
+ html.append("<UL>");
+ for (XRefType xref: xrefList) {
+ String url = xref.getUrl();
+ if (url != null && url.length() > 0) {
+ html.append("<LI>- <a class=\"link\" href=\"" + url + "\">"
+ + xref.getDb() + ": "
+ + xref.getId() + "</a></LI>") ;
+ } else {
+ html.append("<LI>- " + xref.getDb() + ": " + xref.getId() + "</LI>");
+ }
+ }
+ html.append("</UL>");
+ }
+
+ List <String> excerptList = searchHit.getExcerpt();
+ if (excerptList != null && excerptList.size() > 0) {
+ String primeExcerpt = null;
+ for (String excerpt: excerptList) {
+ if (primeExcerpt == null || excerpt.length() > primeExcerpt.length()) {
+ if (!excerpt.equalsIgnoreCase(searchHit.getName())) {
+ primeExcerpt = excerpt;
+ }
+ }
+ }
+ if (primeExcerpt != null) {
+ html.append("<H4>Matching Excerpt(s):</H4>");
+ html.append("<span class='excerpt'>" + primeExcerpt + "</span><BR>") ;
+ }
+ }
+
+ // Temporarily removed comments.
+ //java.util.List<String> commentList = searchHit.getComment();
+ //if (commentList != null) {
+ // html.append("<BR><B>Description:</B>");
+ // for (int i = commentList.size() - 1; i >= 0; i--) {
+ // html.append("<BR>" + commentList.get(i) + "<BR>");
+ // }
+ //}
+
+ html.append ("</html>");
+ textPane.setText(html.toString());
+ textPane.setCaretPosition(0);
+ updatePathwayData(searchHit, pathwayTableModel);
+ updateInteractionData(searchHit, interactionBundleModel);
+ textPaneOwner.repaint();
+ }
+ }
+
+ /**
+ * Updates Interaction Data.
+ *
+ * @param searchHit Search Hit Object.
+ * @param interactionBundleModel Interaction Bundle Model.
+ */
+ private void updateInteractionData(ExtendedRecordType searchHit, InteractionBundleModel
+ interactionBundleModel) {
+ RecordList recordList = parentRecordsMap.get(searchHit.getPrimaryId());
+ if (recordList != null) {
+ interactionBundleModel.setRecordList(recordList);
+ } else {
+ SummaryResponseType summaryResponseType = new SummaryResponseType();
+ recordList = new RecordList(summaryResponseType);
+ interactionBundleModel.setRecordList(recordList);
+ }
+ interactionBundleModel.setPhysicalEntityName(searchHit.getName());
+ }
+
+ /**
+ * Updates Pathway Data.
+ *
+ * @param searchHit SearchHit Object.
+ * @param pathwayTableModel Pathway Table Model.
+ */
+ private void updatePathwayData(ExtendedRecordType searchHit, PathwayTableModel
+ pathwayTableModel) {
+ List<PathwayType> pathwayList = searchHit.getPathwayList().getPathway();
+
+ Vector dataVector = pathwayTableModel.getDataVector();
+ dataVector.removeAllElements();
+
+ if (pathwayList != null) {
+ pathwayTableModel.setRowCount(pathwayList.size());
+ pathwayTableModel.resetInternalIds(pathwayList.size());
+ // Only set the column count, if it is not already set.
+ // If we reset the column count, the user-modified column widths are lost.
+ if (pathwayTableModel.getColumnCount() != 2) {
+ pathwayTableModel.setColumnCount(2);
+ }
+ if (pathwayList.size() == 0) {
+ pathwayTableModel.setRowCount(1);
+ pathwayTableModel.setValueAt("No pathways found.", 0, 0);
+ } else {
+ for (int i = 0; i < pathwayList.size(); i++) {
+ PathwayType pathway = pathwayList.get(i);
+ pathwayTableModel.setValueAt(pathway.getName(), i, 0);
+ pathwayTableModel.setValueAt(pathway.getDataSource().getName(), i, 1);
+ pathwayTableModel.setInternalId(i, pathway.getPrimaryId());
+ }
+ }
+ }
+ }
+}
\ No newline at end of file
diff --git a/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/util/BioPaxEntityTypeMap.java b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/util/BioPaxEntityTypeMap.java
new file mode 100644
index 0000000..c104670
--- /dev/null
+++ b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/util/BioPaxEntityTypeMap.java
@@ -0,0 +1,42 @@
+package org.cytoscape.coreplugin.cpath2.util;
+
+import java.util.HashMap;
+
+public class BioPaxEntityTypeMap extends HashMap{
+ private static BioPaxEntityTypeMap map;
+
+ /**
+ * Gets Singleton Instance.
+ * @return Singleton Instance.
+ */
+ public static BioPaxEntityTypeMap getInstance() {
+ if (map == null) {
+ map = new BioPaxEntityTypeMap();
+ }
+ return map;
+ }
+
+ /**
+ * Gets the complete HashMap of all BioPAX Entity Types.
+ * @return HashMap Object.
+ */
+ private BioPaxEntityTypeMap () {
+ put("pathway", "Pathway");
+ put("protein", "Protein");
+ put("smallMolecule", "Small Molecule");
+ put("physicalEntity", "Physical Entity");
+ put("complex", "Complex");
+ put("rna", "RNA");
+ put("dna", "DNA");
+ put("transportWithBiochemicalReaction", "Transport with Biochemical Reaction");
+ put("transport", "Transport Reaction");
+ put("complexAssembly", "Complex Assembly");
+ put("biochemicalReaction", "Biochemical Reaction");
+ put("conversion", "Conversion Reaction");
+ put("modulation", "Modulation Reaction");
+ put("catalysis", "Catalysis Reaction");
+ put("control", "Control Reaction");
+ put("physicalInteraction", "Physical Interaction");
+ put("interaction", "Interaction");
+ }
+}
diff --git a/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/util/NetworkGroupUtil.java b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/util/NetworkGroupUtil.java
new file mode 100644
index 0000000..6a3ad05
--- /dev/null
+++ b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/util/NetworkGroupUtil.java
@@ -0,0 +1,52 @@
+package org.cytoscape.coreplugin.cpath2.util;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import cytoscape.data.CyAttributes;
+
+import java.util.Set;
+import java.util.HashSet;
+
+import cytoscape.coreplugins.biopax.MapBioPaxToCytoscape;
+import org.cytoscape.coreplugin.cpath2.web_service.CPathProperties;
+import org.cytoscape.coreplugin.cpath2.cytoscape.BinarySifVisualStyleUtil;
+
+/**
+ * Utility for Finding Groups of Networks.
+ *
+ * @author Ethan Cerami.
+ */
+public class NetworkGroupUtil {
+
+ /**
+ * Constructs a set of X networks.
+ *
+ * @return Set<CyNetwork>
+ */
+ public static Set<CyNetwork> getNetworkSet(int type) {
+
+ // set to return
+ Set<CyNetwork> networkSet = new HashSet<CyNetwork>();
+
+ // get set of cynetworks
+ Set<CyNetwork> cyNetworks = (Set<CyNetwork>) Cytoscape.getNetworkSet();
+ if (cyNetworks.size() == 0) return cyNetworks;
+
+ CyAttributes networkAttributes = Cytoscape.getNetworkAttributes();
+ for (CyNetwork net : cyNetworks) {
+ String networkID = net.getIdentifier();
+
+ String attribute = MapBioPaxToCytoscape.BIOPAX_NETWORK;
+ if (type == CPathProperties.DOWNLOAD_REDUCED_BINARY_SIF) {
+ attribute = BinarySifVisualStyleUtil.BINARY_NETWORK;
+ }
+ Boolean b = networkAttributes.getBooleanAttribute(networkID, attribute);
+ if (b != null && b) {
+ networkSet.add(net);
+ }
+ }
+
+ // outta here
+ return networkSet;
+ }
+}
diff --git a/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/util/NetworkListener.java b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/util/NetworkListener.java
new file mode 100644
index 0000000..5e66822
--- /dev/null
+++ b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/util/NetworkListener.java
@@ -0,0 +1,174 @@
+// $Id: NetworkUtil.java,v 1.12 2007/05/01 15:56:45 grossb Exp $
+//------------------------------------------------------------------------------
+/** Copyright (c) 2007 Memorial Sloan-Kettering Cancer Center.
+ **
+ ** Code written by: Ethan Cerami, Benjamin Gross
+ ** Authors: Ethan Cerami, Gary Bader, Chris Sander, Benjamin Gross
+ **
+ ** This library is free software; you can redistribute it and/or modify it
+ ** under the terms of the GNU Lesser General Public License as published
+ ** by the Free Software Foundation; either version 2.1 of the License, or
+ ** any later version.
+ **
+ ** This library is distributed in the hope that it will be useful, but
+ ** WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ ** MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ ** documentation provided hereunder is on an "as is" basis, and
+ ** Memorial Sloan-Kettering Cancer Center
+ ** has no obligations to provide maintenance, support,
+ ** updates, enhancements or modifications. In no event shall
+ ** Memorial Sloan-Kettering Cancer Center
+ ** be liable to any party for direct, indirect, special,
+ ** incidental or consequential damages, including lost profits, arising
+ ** out of the use of this software and its documentation, even if
+ ** Memorial Sloan-Kettering Cancer Center
+ ** has been advised of the possibility of such damage. See
+ ** the GNU Lesser General Public License for more details.
+ **
+ ** You should have received a copy of the GNU Lesser General Public License
+ ** along with this library; if not, write to the Free Software Foundation,
+ ** Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ **/
+package org.cytoscape.coreplugin.cpath2.util;
+
+// imports
+
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+import cytoscape.data.CyAttributes;
+import cytoscape.view.CyNetworkView;
+import ding.view.NodeContextMenuListener;
+import giny.view.NodeView;
+import cytoscape.coreplugins.biopax.MapBioPaxToCytoscape;
+import cytoscape.coreplugins.biopax.util.BioPaxUtil;
+import cytoscape.coreplugins.biopax.util.BioPaxVisualStyleUtil;
+
+import javax.swing.*;
+import java.awt.*;
+import java.awt.event.ActionEvent;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.io.UnsupportedEncodingException;
+import java.net.URL;
+import java.net.URLEncoder;
+
+/**
+ * Manages network neighborhood map - node context menus
+ *
+ * @author Benjamin Gross.
+ */
+public class NetworkListener implements PropertyChangeListener, NodeContextMenuListener {
+
+ /**
+ * Context menu title.
+ */
+ private static final String CONTEXT_MENU_TITLE = "View network neighborhood map";
+
+ /**
+ * Context menu item command.
+ */
+ private static final String PC_WEB_SERVICE_URL = "/webservice.do?version=3.0&cmd=get_neighbors&q=";
+
+ /**
+ * Property change listener - to get network/network view destroy events.
+ *
+ * @param event PropertyChangeEvent
+ */
+ public void propertyChange(PropertyChangeEvent event) {
+
+ if (event.getPropertyName().equals(Cytoscape.NETWORK_LOADED)) {
+ CyNetwork cyNetwork = (CyNetwork) ((Object[]) event.getNewValue())[0];
+ if (cyNetwork != null && BioPaxUtil.isBioPaxNetwork(cyNetwork)) {
+ // setup the context menu
+ CyNetworkView view = Cytoscape.getNetworkView(cyNetwork.getIdentifier());
+ if (view != null) view.addNodeContextMenuListener(this);
+ }
+ }
+ }
+
+ /**
+ * Our implementation of NodeContextMenuListener.addNodeContextMenuItems(..).
+ */
+ public void addNodeContextMenuItems(NodeView nodeView, JPopupMenu menu) {
+
+ // check if we have already added menu item
+ if (contextMenuExists(menu)) return;
+
+ // setup refs to get network attributes
+ CyAttributes networkAttributes = Cytoscape.getNetworkAttributes();
+ CyNetworkView view = Cytoscape.getCurrentNetworkView();
+
+ // grab web services url from network attributes
+ String webServicesURL = networkAttributes.getStringAttribute(view.getNetwork().getIdentifier(),
+ "biopax.web_services_url");
+ if (webServicesURL.startsWith("http://")) {
+ webServicesURL = webServicesURL.substring(7);
+ }
+
+ // grab data sources from network attributes - already encoded
+ String dataSources = networkAttributes.getStringAttribute(view.getNetwork().getIdentifier(),
+ "biopax.data_sources");
+
+ // generate menu url
+ CyAttributes nodeAttributes = Cytoscape.getNodeAttributes();
+ CyNode cyNode = (CyNode) nodeView.getNode();
+ String biopaxID = nodeAttributes.getStringAttribute(cyNode.getIdentifier(), MapBioPaxToCytoscape.BIOPAX_RDF_ID);
+ biopaxID = biopaxID.replace("CPATH-", "");
+ String neighborhoodParam = "Neighborhood: " + nodeAttributes.getStringAttribute(cyNode.getIdentifier(), BioPaxVisualStyleUtil.BIOPAX_NODE_LABEL);
+
+ // encode some parts of the url
+ try {
+ neighborhoodParam = URLEncoder.encode(neighborhoodParam, "UTF-8");
+ }
+ catch (UnsupportedEncodingException e) {
+ // if exception occurs leave encoded string, but cmon, utf-8 not supported ??
+ // anyway, at least encode spaces, and commas (data sources)
+ neighborhoodParam = neighborhoodParam.replaceAll(" ", "%20");
+ }
+
+ final String urlString = "http://127.0.0.1:27182/" + webServicesURL +
+ PC_WEB_SERVICE_URL + biopaxID + "&neighborhood_title=" + neighborhoodParam +
+ "&data_source=" + dataSources;
+
+ // add new menu item
+ JMenuItem item = new JMenuItem(new AbstractAction(CONTEXT_MENU_TITLE) {
+ public void actionPerformed(ActionEvent e) {
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ try {
+ URL url = new URL(urlString);
+ url.getContent();
+ }
+ catch (Exception e) {
+ e.printStackTrace();
+ }
+ }
+ });
+ }
+ });
+ menu.add(item);
+ }
+
+ /**
+ * Method checks if we have already added a neighborhood map context menu
+ * to given menu.
+ *
+ * @param menu JPopupMenu
+ * @return boolean
+ */
+ private boolean contextMenuExists(JPopupMenu menu) {
+
+ for (MenuElement element : menu.getSubElements()) {
+ Component component = element.getComponent();
+ if (component instanceof JMenuItem) {
+ String text = ((JMenuItem) component).getText();
+ if (text != null && text.equals(CONTEXT_MENU_TITLE)) return true;
+ }
+ }
+
+ // outta here
+ return false;
+ }
+
+}
\ No newline at end of file
diff --git a/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/util/NetworkMergeUtil.java b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/util/NetworkMergeUtil.java
new file mode 100644
index 0000000..a628aca
--- /dev/null
+++ b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/util/NetworkMergeUtil.java
@@ -0,0 +1,86 @@
+package org.cytoscape.coreplugin.cpath2.util;
+
+import org.cytoscape.coreplugin.cpath2.web_service.CPathProperties;
+import org.cytoscape.coreplugin.cpath2.view.model.NetworkWrapper;
+import org.cytoscape.coreplugin.cpath2.view.SearchDetailsPanel;
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+
+import javax.swing.*;
+import java.util.Set;
+import java.util.Vector;
+import java.net.URL;
+
+/**
+ * Network Merge Utility.
+ */
+public class NetworkMergeUtil {
+ private Vector networkVector;
+
+ /**
+ * Constructor.
+ */
+ public NetworkMergeUtil() {
+ CPathProperties cPathProperties = CPathProperties.getInstance();
+ int downloadMode = cPathProperties.getDownloadMode();
+
+ // Get networks which we could merge with.
+ Set<CyNetwork> networkSet = NetworkGroupUtil.getNetworkSet(downloadMode);
+
+ networkVector = new Vector();
+ networkVector.add(new NetworkWrapper(null));
+ if (networkSet != null && networkSet.size() > 0) {
+ for (CyNetwork net : networkSet) {
+ NetworkWrapper netWrapper = new NetworkWrapper (net);
+ networkVector.add(netWrapper);
+ }
+ }
+ }
+
+ /**
+ * Prompt User for Network to Merge.
+ * @return NetworkWrapper Object.
+ */
+ public NetworkWrapper promptForNetworkToMerge() {
+ if (mergeNetworksExist()) {
+ NetworkWrapper[] networks = (NetworkWrapper[]) getMergeNetworks().toArray
+ (new NetworkWrapper[getMergeNetworks().size()]);
+ URL iconURL = SearchDetailsPanel.class.getResource("resources/question.png");
+ Icon icon = null;
+ if (iconURL != null) {
+ icon = new ImageIcon(iconURL);
+ }
+ NetworkWrapper mergeNetwork = (NetworkWrapper)
+ JOptionPane.showInputDialog(Cytoscape.getDesktop(),
+ "Create new network or merge with existing network?", "Create / Merge",
+ JOptionPane.PLAIN_MESSAGE, icon,
+ networks, networks[0]);
+ if (mergeNetwork == null) {
+ return null;
+ } else {
+ return mergeNetwork;
+ }
+ }
+ return null;
+ }
+
+ /**
+ * Do mergeable network exist?
+ * @return true or false.
+ */
+ public boolean mergeNetworksExist() {
+ if (networkVector != null && networkVector.size() >1) {
+ return true;
+ } else {
+ return false;
+ }
+ }
+
+ /**
+ * Candidate networks for merging.
+ * @return Vector of NetworkWrapper Objects.
+ */
+ public Vector getMergeNetworks() {
+ return networkVector;
+ }
+}
diff --git a/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/util/NetworkUtil.java b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/util/NetworkUtil.java
new file mode 100644
index 0000000..fffa172
--- /dev/null
+++ b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/util/NetworkUtil.java
@@ -0,0 +1,266 @@
+// $Id: NetworkUtil.java,v 1.12 2007/05/01 15:56:45 grossb Exp $
+//------------------------------------------------------------------------------
+/** Copyright (c) 2007 Memorial Sloan-Kettering Cancer Center.
+ **
+ ** Code written by: Ethan Cerami, Benjamin Gross
+ ** Authors: Ethan Cerami, Gary Bader, Chris Sander, Benjamin Gross
+ **
+ ** This library is free software; you can redistribute it and/or modify it
+ ** under the terms of the GNU Lesser General Public License as published
+ ** by the Free Software Foundation; either version 2.1 of the License, or
+ ** any later version.
+ **
+ ** This library is distributed in the hope that it will be useful, but
+ ** WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ ** MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ ** documentation provided hereunder is on an "as is" basis, and
+ ** Memorial Sloan-Kettering Cancer Center
+ ** has no obligations to provide maintenance, support,
+ ** updates, enhancements or modifications. In no event shall
+ ** Memorial Sloan-Kettering Cancer Center
+ ** be liable to any party for direct, indirect, special,
+ ** incidental or consequential damages, including lost profits, arising
+ ** out of the use of this software and its documentation, even if
+ ** Memorial Sloan-Kettering Cancer Center
+ ** has been advised of the possibility of such damage. See
+ ** the GNU Lesser General Public License for more details.
+ **
+ ** You should have received a copy of the GNU Lesser General Public License
+ ** along with this library; if not, write to the Free Software Foundation,
+ ** Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ **/
+package org.cytoscape.coreplugin.cpath2.util;
+
+// imports
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import cytoscape.data.CyAttributes;
+import cytoscape.layout.CyLayoutAlgorithm;
+import cytoscape.layout.CyLayouts;
+import cytoscape.task.ui.JTaskConfig;
+import cytoscape.task.util.TaskManager;
+import cytoscape.view.CyNetworkView;
+import cytoscape.view.CytoscapeDesktop;
+import ding.view.NodeContextMenuListener;
+import org.cytoscape.coreplugin.cpath2.task.MergeNetworkTask;
+import org.cytoscape.coreplugin.cpath2.task.LoadNetworkFromUrlTask;
+
+import java.net.MalformedURLException;
+import java.net.URL;
+
+/**
+ * This is a network utilities class.
+ *
+ * @author Benjamin Gross.
+ */
+public class NetworkUtil extends Thread {
+
+ /**
+ * ref to NodeContextMenuListener
+ */
+ NodeContextMenuListener nodeContextMenuListener;
+
+ /**
+ * Stores web services url
+ */
+ private String webServicesURL;
+
+ /**
+ * ref to cPathRequst
+ */
+ private String cPathRequest;
+
+ /**
+ * ref to cyNetwork
+ */
+ private CyNetwork cyNetwork;
+
+ /**
+ * ref to cyNetworkTitle
+ */
+ private String networkTitle;
+
+ /**
+ * ref to data source set
+ */
+ private String dataSources;
+
+ /**
+ * boolean indicated if we are merging
+ */
+ private boolean merging;
+
+ /**
+ * Neighborhood title parameter.
+ */
+ private static final String NEIGHBORHOOD_TITLE_ARG = "&neighborhood_title=";
+
+ /**
+ * Data Source Arg
+ */
+ private static final String DATA_SOURCE_ARG = "&data_source=";
+
+ /**
+ * Constructor.
+ *
+ * @param cpathRequest String
+ * @param cyNetwork CyNetwork
+ * @param merging boolean
+ * @param nodeContextMenuListener NodeContextMenuListener
+ */
+ public NetworkUtil(String cpathRequest, CyNetwork cyNetwork,
+ boolean merging, NodeContextMenuListener nodeContextMenuListener) {
+
+ // init member vars
+ parseRequest(cpathRequest);
+ this.cyNetwork = cyNetwork;
+ this.merging = merging;
+ this.nodeContextMenuListener = nodeContextMenuListener;
+ }
+
+ /**
+ * Our implementation of run.
+ */
+ public void run() {
+
+ try {
+ URL cpathURL = new URL(cPathRequest);
+
+ // are we merging ?
+ if (merging) {
+ // start merge network task
+ TaskManager.executeTask(new MergeNetworkTask(cpathURL, cyNetwork),
+ setupTask());
+ postProcess(cyNetwork, true);
+ } else {
+ // the biopax graph reader is going to be called
+ // it will look for the network view title
+ // via system properties, so lets set it now
+ if (networkTitle != null && networkTitle.length() > 0) {
+ System.setProperty("biopax.network_view_title", networkTitle);
+ }
+ LoadNetworkFromUrlTask.loadURL(cpathURL, true);
+ postProcess(Cytoscape.getCurrentNetwork(), false);
+ }
+ }
+ catch (MalformedURLException e) {
+ e.printStackTrace();
+ }
+ }
+
+ /**
+ * Method to process/parse the cpath request and
+ * set proper member variables.
+ *
+ * @param cpathRequest String
+ */
+ private void parseRequest(String cpathRequest) {
+
+ // web services url
+ int indexToStartOfPC = cpathRequest.indexOf("/pc");
+ if (indexToStartOfPC > 0) {
+ this.webServicesURL = cpathRequest.substring(7, indexToStartOfPC + 3);
+ }
+
+ // extract title
+ this.networkTitle = extractRequestArg(NEIGHBORHOOD_TITLE_ARG,
+ cpathRequest);
+
+ // extract data sources
+ dataSources = extractRequestArg(DATA_SOURCE_ARG,
+ cpathRequest);
+
+ // set request member
+ this.cPathRequest = cpathRequest;
+ }
+
+ /**
+ * Extracts argument from cpath request (url).
+ * Method removes argument from cPathRequest arg,
+ * and returns it as String.
+ *
+ * @param arg String - the argument to extract
+ * @param cpathRequest String
+ * @return String
+ */
+ private String extractRequestArg(String arg, String cpathRequest) {
+
+ // get index of argument
+ int indexOfArg = cpathRequest.indexOf(arg);
+
+ // if arg is not in list, bail
+ if (indexOfArg == -1) return null;
+
+ int startIndexOfValue = indexOfArg + arg.length();
+ int endIndexOfValue = cpathRequest.indexOf("&", startIndexOfValue);
+ String value = (endIndexOfValue == -1) ?
+ cpathRequest.substring(startIndexOfValue) :
+ cpathRequest.substring(startIndexOfValue, endIndexOfValue);
+
+ // remove arg from request
+ cpathRequest = (endIndexOfValue == -1) ?
+ cpathRequest.substring(0, indexOfArg) :
+ cpathRequest.substring(0, indexOfArg) +
+ cpathRequest.substring(endIndexOfValue);
+
+ // outta here
+ return value;
+ }
+
+ /**
+ * Method to setup cytoscape task
+ */
+ private JTaskConfig setupTask() {
+
+ // configure JTask Dialog Pop-Up Box
+ JTaskConfig jTaskConfig = new JTaskConfig();
+ jTaskConfig.setOwner(Cytoscape.getDesktop());
+ jTaskConfig.displayStatus(true);
+ jTaskConfig.setAutoDispose(true);
+
+ // outta here
+ return jTaskConfig;
+ }
+
+ /**
+ * Method for any post processing of recently loaded network.
+ *
+ * @param cyNetwork CyNetwork
+ * @param doLayout boolean
+ */
+ private void postProcess(final CyNetwork cyNetwork, boolean doLayout) {
+
+ // ref to view used below
+ CyNetworkView view = Cytoscape.getNetworkView(cyNetwork.getIdentifier());
+
+ // if do layout, do it
+ if (doLayout) {
+ CyLayoutAlgorithm layout = CyLayouts.getLayout("force-directed");
+ view.applyLayout(layout);
+ view.fitContent();
+ }
+
+ // setup web services url to pc attribute - used by nodeContextMenuListener
+ CyAttributes networkAttributes = Cytoscape.getNetworkAttributes();
+ if (webServicesURL != null) {
+ networkAttributes.setAttribute(cyNetwork.getIdentifier(),
+ "biopax.web_services_url",
+ webServicesURL);
+ }
+
+ // setup data sources attribute - used by nodeContextMenuListener - remains encoded
+ if (dataSources != null) {
+ networkAttributes.setAttribute(cyNetwork.getIdentifier(),
+ "biopax.data_sources",
+ dataSources);
+ }
+
+ // setup the context menu
+ //view.addNodeContextMenuListener(nodeContextMenuListener);
+
+ // set focus current
+ Cytoscape.firePropertyChange(CytoscapeDesktop.NETWORK_VIEW_FOCUS,
+ null, cyNetwork.getIdentifier());
+ }
+}
diff --git a/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/util/NullTaskMonitor.java b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/util/NullTaskMonitor.java
new file mode 100644
index 0000000..9cccca4
--- /dev/null
+++ b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/util/NullTaskMonitor.java
@@ -0,0 +1,23 @@
+package org.cytoscape.coreplugin.cpath2.util;
+
+import cytoscape.task.TaskMonitor;
+
+public class NullTaskMonitor implements TaskMonitor {
+
+ public void setPercentCompleted(int i) throws IllegalArgumentException {
+ }
+
+ public void setEstimatedTimeRemaining(long l) throws IllegalThreadStateException {
+ }
+
+ public void setException(Throwable throwable, String string)
+ throws IllegalThreadStateException {
+ }
+
+ public void setException(Throwable throwable, String string, String string1)
+ throws IllegalThreadStateException {
+ }
+
+ public void setStatus(String string) throws IllegalThreadStateException, NullPointerException {
+ }
+}
\ No newline at end of file
diff --git a/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/CategoryCount.java b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/CategoryCount.java
new file mode 100644
index 0000000..d0e6545
--- /dev/null
+++ b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/CategoryCount.java
@@ -0,0 +1,30 @@
+package org.cytoscape.coreplugin.cpath2.view;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: cerami
+ * Date: Nov 20, 2007
+ * Time: 10:33:26 AM
+ * To change this template use File | Settings | File Templates.
+ */
+class CategoryCount {
+ private String categoryName;
+ private int count;
+
+ public CategoryCount (String categoryName, int count) {
+ this.categoryName = categoryName;
+ this.count = count;
+ }
+
+ public String getCategoryName() {
+ return categoryName;
+ }
+
+ public int getCount() {
+ return count;
+ }
+
+ public String toString() {
+ return categoryName + ": " + count;
+ }
+}
diff --git a/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/CollapsablePanel.java b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/CollapsablePanel.java
new file mode 100644
index 0000000..5366f45
--- /dev/null
+++ b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/CollapsablePanel.java
@@ -0,0 +1,381 @@
+package org.cytoscape.coreplugin.cpath2.view;
+
+import javax.swing.*;
+import javax.swing.border.Border;
+import javax.swing.border.TitledBorder;
+import java.awt.*;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemListener;
+import java.awt.event.ActionEvent;
+import java.awt.event.ItemEvent;
+import java.net.URL;
+
+/**
+ * The user-triggered collapsable panel containing the component (trigger) in the titled border
+ */
+public class CollapsablePanel extends JPanel {
+ //Border
+ CollapsableTitledBorder border; // includes upper left component and line type
+ Border collapsedBorderLine = BorderFactory.createEmptyBorder(2, 2, 2, 2); // no border
+ Border expandedBorderLine = null; // because this is null, default is used,
+ // etched lowered border on MAC
+
+ //Title
+ AbstractButton titleComponent; // displayed in the titled border
+
+ //Expand/Collapse button
+ final static int COLLAPSED = 0, EXPANDED = 1; // image States
+ ImageIcon[] iconArrow = createExpandAndCollapseIcon();
+ JButton arrow = createArrowButton();
+
+ //Content Pane
+ JPanel panel;
+
+ //Container State
+ boolean collapsed; // stores curent state of the collapsable panel
+
+ /**
+ * Constructor for an option button controlled collapsable panel.
+ * This is useful when a group of options each have unique sub contents. The radio buttons
+ * should be created, grouped, and then used to construct their own collapsable panels. This
+ * way choosing a different option in the same option group will collapse all unselected
+ * options. Expanded panels draw a border around the contents and through the radio button
+ * in the fashion of a titled border.
+ *
+ * @param component Radio button that expands and collapses the panel based on if it is
+ * selected or not
+ */
+ public CollapsablePanel(JRadioButton component) {
+ component.addItemListener(new CollapsablePanel.ExpandAndCollapseAction());
+ titleComponent = component;
+ collapsed = !component.isSelected();
+ commonConstructor();
+ }
+
+ /**
+ * Constructor for a label/button controlled collapsable panel. Displays a clickable title
+ * that resembles a native titled border except for an arrow on the right side indicating an
+ * expandable panel. The actual border only appears when the panel is expanded.
+ *
+ * @param text Title of the collapsable panel in string format, used to create a button with
+ * text and an arrow icon
+ */
+ public CollapsablePanel(String text) {
+ arrow.setText(text);
+ titleComponent = arrow;
+ collapsed = true;
+ commonConstructor();
+ }
+
+ /**
+ * Sets layout, creates the content panel and adds it and the title component to the container,
+ * all constructors have this procedure in common.
+ */
+ private void commonConstructor() {
+ setLayout(new BorderLayout());
+
+ panel = new JPanel();
+ panel.setLayout(new BorderLayout());
+
+ add(titleComponent, BorderLayout.CENTER);
+ add(panel, BorderLayout.CENTER);
+ setCollapsed(collapsed);
+
+ placeTitleComponent();
+ }
+
+ /**
+ * Sets the bounds of the border title component so that it is properly positioned.
+ */
+ private void placeTitleComponent() {
+ Insets insets = this.getInsets();
+ Rectangle containerRectangle = this.getBounds();
+ Rectangle componentRectangle = border.getComponentRect(containerRectangle, insets);
+ titleComponent.setBounds(componentRectangle);
+ }
+
+ public void setTitleComponentText(String text) {
+ if (titleComponent instanceof JButton) {
+ titleComponent.setText(text);
+ }
+ placeTitleComponent();
+ }
+
+ /**
+ * This class requires that all content be placed within a designated panel, this method
+ * returns that panel.
+ *
+ * @return panel The content panel
+ */
+ public JPanel getContentPane() {
+ return panel;
+ }
+
+ /**
+ * Collapses or expands the panel. This is done by adding or removing the content pane,
+ * alternating between a frame and empty border, and changing the title arrow.
+ * Also, the current state is stored in the collapsed boolean.
+ *
+ * @param collapse When set to true, the panel is collapsed, else it is expanded
+ */
+ public void setCollapsed(boolean collapse) {
+ if (collapse) {
+ //collapse the panel, remove content and set border to empty border
+ remove(panel);
+ arrow.setIcon(iconArrow[COLLAPSED]);
+ border = new CollapsableTitledBorder(collapsedBorderLine, titleComponent);
+ } else {
+ //expand the panel, add content and set border to titled border
+ add(panel, BorderLayout.NORTH);
+ arrow.setIcon(iconArrow[EXPANDED]);
+ border = new CollapsableTitledBorder(expandedBorderLine, titleComponent);
+ }
+ setBorder(border);
+ collapsed = collapse;
+ updateUI();
+ }
+
+ /**
+ * Returns the current state of the panel, collapsed (true) or expanded (false).
+ *
+ * @return collapsed Returns true if the panel is collapsed and false if it is expanded
+ */
+ public boolean isCollapsed() {
+ return collapsed;
+ }
+
+ /**
+ * Returns an ImageIcon array with arrow images used for the different states of the panel.
+ *
+ * @return iconArrow An ImageIcon array holding the collapse and expanded versions of the
+ * right hand side arrow
+ */
+ private ImageIcon[] createExpandAndCollapseIcon() {
+ ImageIcon[] iconArrow = new ImageIcon[2];
+ URL iconURL;
+
+ iconURL = CollapsablePanel.class.getResource("resources/arrow_collapsed.gif");
+ if (iconURL != null) {
+ iconArrow[COLLAPSED] = new ImageIcon(iconURL);
+ }
+ iconURL = CollapsablePanel.class.getResource("resources/arrow_expanded.gif");
+ if (iconURL != null) {
+ iconArrow[EXPANDED] = new ImageIcon(iconURL);
+ }
+ return iconArrow;
+ }
+
+ /**
+ * Returns a button with an arrow icon and a collapse/expand action listener.
+ *
+ * @return button Button which is used in the titled border component
+ */
+ private JButton createArrowButton() {
+ JButton button = new JButton("arrow", iconArrow[COLLAPSED]);
+ button.setBorder(BorderFactory.createEmptyBorder(0, 1, 5, 1));
+ button.setVerticalTextPosition(AbstractButton.CENTER);
+ button.setHorizontalTextPosition(AbstractButton.LEFT);
+ button.setMargin(new Insets(0, 0, 3, 0));
+
+ //We want to use the same font as those in the titled border font
+ Font font = BorderFactory.createTitledBorder("Sample").getTitleFont();
+ Color color = BorderFactory.createTitledBorder("Sample").getTitleColor();
+ button.setFont(font);
+ button.setForeground(color);
+ button.setFocusable(false);
+ button.setContentAreaFilled(false);
+
+ button.addActionListener(new CollapsablePanel.ExpandAndCollapseAction());
+
+ return button;
+ }
+
+ /**
+ * Handles expanding and collapsing of extra content on the user's click of the
+ * titledBorder component.
+ */
+ private class ExpandAndCollapseAction extends AbstractAction implements ActionListener,
+ ItemListener {
+ public void actionPerformed(ActionEvent e) {
+ setCollapsed(!isCollapsed());
+ }
+
+ public void itemStateChanged(ItemEvent e) {
+ setCollapsed(!isCollapsed());
+ }
+ }
+
+ /**
+ * Special titled border that includes a component in the title area
+ */
+ private class CollapsableTitledBorder extends TitledBorder {
+ JComponent component;
+ //Border border;
+
+ public CollapsableTitledBorder(JComponent component) {
+ this(null, component, LEFT, TOP);
+ }
+
+ public CollapsableTitledBorder(Border border) {
+ this(border, null, LEFT, TOP);
+ }
+
+ public CollapsableTitledBorder(Border border, JComponent component) {
+ this(border, component, LEFT, TOP);
+ }
+
+ public CollapsableTitledBorder(Border border, JComponent component,
+ int titleJustification, int titlePosition) {
+ //TitledBorder needs border, title, justification, position, font, and color
+ super(border, null, titleJustification, titlePosition, null, null);
+ this.component = component;
+ if (border == null) {
+ this.border = super.getBorder();
+ }
+ }
+
+ public void paintBorder(Component c, Graphics g, int x, int y, int width, int height) {
+ Rectangle borderR = new Rectangle(x + EDGE_SPACING, y + EDGE_SPACING, width
+ - (EDGE_SPACING * 2), height - (EDGE_SPACING * 2));
+ Insets borderInsets;
+ if (border != null) {
+ borderInsets = border.getBorderInsets(c);
+ } else {
+ borderInsets = new Insets(0, 0, 0, 0);
+ }
+
+ Rectangle rect = new Rectangle(x, y, width, height);
+ Insets insets = getBorderInsets(c);
+ Rectangle compR = getComponentRect(rect, insets);
+ int diff;
+ switch (titlePosition) {
+ case ABOVE_TOP:
+ diff = compR.height + TEXT_SPACING;
+ borderR.y += diff;
+ borderR.height -= diff;
+ break;
+ case TOP:
+ case DEFAULT_POSITION:
+ diff = insets.top / 2 - borderInsets.top - EDGE_SPACING;
+ borderR.y += diff;
+ borderR.height -= diff;
+ break;
+ case BELOW_TOP:
+ case ABOVE_BOTTOM:
+ break;
+ case BOTTOM:
+ diff = insets.bottom / 2 - borderInsets.bottom - EDGE_SPACING;
+ borderR.height -= diff;
+ break;
+ case BELOW_BOTTOM:
+ diff = compR.height + TEXT_SPACING;
+ borderR.height -= diff;
+ break;
+ }
+ border.paintBorder(c, g, borderR.x, borderR.y, borderR.width, borderR.height);
+ Color col = g.getColor();
+ g.setColor(c.getBackground());
+ g.fillRect(compR.x, compR.y, compR.width, compR.height);
+ g.setColor(col);
+ }
+
+ public Insets getBorderInsets(Component c, Insets insets) {
+ Insets borderInsets;
+ if (border != null) {
+ borderInsets = border.getBorderInsets(c);
+ } else {
+ borderInsets = new Insets(0, 0, 0, 0);
+ }
+ insets.top = EDGE_SPACING + TEXT_SPACING + borderInsets.top;
+ insets.right = EDGE_SPACING + TEXT_SPACING + borderInsets.right;
+ insets.bottom = EDGE_SPACING + TEXT_SPACING + borderInsets.bottom;
+ insets.left = EDGE_SPACING + TEXT_SPACING + borderInsets.left;
+
+ if (c == null || component == null) {
+ return insets;
+ }
+
+ int compHeight = component.getPreferredSize().height;
+
+ switch (titlePosition) {
+ case ABOVE_TOP:
+ insets.top += compHeight + TEXT_SPACING;
+ break;
+ case TOP:
+ case DEFAULT_POSITION:
+ insets.top += Math.max(compHeight, borderInsets.top) - borderInsets.top;
+ break;
+ case BELOW_TOP:
+ insets.top += compHeight + TEXT_SPACING;
+ break;
+ case ABOVE_BOTTOM:
+ insets.bottom += compHeight + TEXT_SPACING;
+ break;
+ case BOTTOM:
+ insets.bottom += Math.max(compHeight, borderInsets.bottom)
+ - borderInsets.bottom;
+ break;
+ case BELOW_BOTTOM:
+ insets.bottom += compHeight + TEXT_SPACING;
+ break;
+ }
+ return insets;
+ }
+
+ public JComponent getTitleComponent() {
+ return component;
+ }
+
+ public void setTitleComponent(JComponent component) {
+ this.component = component;
+ }
+
+ public Rectangle getComponentRect(Rectangle rect, Insets borderInsets) {
+ Dimension compD = component.getPreferredSize();
+ Rectangle compR = new Rectangle(0, 0, compD.width, compD.height);
+ switch (titlePosition) {
+ case ABOVE_TOP:
+ compR.y = EDGE_SPACING;
+ break;
+ case TOP:
+ case DEFAULT_POSITION:
+ if (titleComponent instanceof JButton) {
+ compR.y = EDGE_SPACING + (borderInsets.top - EDGE_SPACING
+ - TEXT_SPACING - compD.height) / 2;
+ } else if (titleComponent instanceof JRadioButton) {
+ compR.y = (borderInsets.top - EDGE_SPACING
+ - TEXT_SPACING - compD.height) / 2;
+ }
+ break;
+ case BELOW_TOP:
+ compR.y = borderInsets.top - compD.height - TEXT_SPACING;
+ break;
+ case ABOVE_BOTTOM:
+ compR.y = rect.height - borderInsets.bottom + TEXT_SPACING;
+ break;
+ case BOTTOM:
+ compR.y = rect.height - borderInsets.bottom + TEXT_SPACING
+ + (borderInsets.bottom - EDGE_SPACING
+ - TEXT_SPACING - compD.height) / 2;
+ break;
+ case BELOW_BOTTOM:
+ compR.y = rect.height - compD.height - EDGE_SPACING;
+ break;
+ }
+ switch (titleJustification) {
+ case LEFT:
+ case DEFAULT_JUSTIFICATION:
+ //compR.x = TEXT_INSET_H + borderInsets.left;
+ compR.x = TEXT_INSET_H + borderInsets.left - EDGE_SPACING;
+ break;
+ case RIGHT:
+ compR.x = rect.width - borderInsets.right - TEXT_INSET_H - compR.width;
+ break;
+ case CENTER:
+ compR.x = (rect.width - compR.width) / 2;
+ break;
+ }
+ return compR;
+ }
+ }
+}
\ No newline at end of file
diff --git a/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/DownloadDetails.java b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/DownloadDetails.java
new file mode 100644
index 0000000..91a503a
--- /dev/null
+++ b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/DownloadDetails.java
@@ -0,0 +1,193 @@
+package org.cytoscape.coreplugin.cpath2.view;
+
+import org.cytoscape.coreplugin.cpath2.task.ExecuteGetRecordByCPathId;
+import org.cytoscape.coreplugin.cpath2.schemas.summary_response.BasicRecordType;
+import org.cytoscape.coreplugin.cpath2.web_service.CPathWebService;
+import org.cytoscape.coreplugin.cpath2.web_service.CPathProperties;
+import org.cytoscape.coreplugin.cpath2.web_service.CPathWebServiceImpl;
+import org.cytoscape.coreplugin.cpath2.web_service.CPathResponseFormat;
+import org.cytoscape.coreplugin.cpath2.util.NetworkGroupUtil;
+import org.cytoscape.coreplugin.cpath2.view.model.NetworkWrapper;
+
+import javax.swing.*;
+import javax.swing.border.EmptyBorder;
+import javax.swing.table.DefaultTableModel;
+import java.awt.*;
+import java.awt.event.ActionListener;
+import java.awt.event.ActionEvent;
+import java.util.Vector;
+import java.util.Set;
+import java.util.HashMap;
+
+import cytoscape.Cytoscape;
+import cytoscape.CyNetwork;
+import cytoscape.task.ui.JTaskConfig;
+import cytoscape.task.util.TaskManager;
+
+/**
+ * Download Details Frame.
+ *
+ * @author Ethan Cerami
+ */
+public class DownloadDetails extends JDialog {
+ private MergePanel mergePanel;
+ private long ids[];
+ private String peName;
+
+ /**
+ * Constructor.
+ * @param passedRecordList List of Records that Passed over Filter.
+ * @param peName Name of Physical Entity.
+ */
+ public DownloadDetails(java.util.List<BasicRecordType> passedRecordList,
+ String peName) {
+ super();
+ this.peName = peName;
+ this.setTitle("Retrieval Confirmation");
+ this.setModal(true);
+ Container contentPane = getContentPane();
+ contentPane.setLayout(new BorderLayout());
+ GradientHeader header = new GradientHeader("Confirm Retrieval: "+ passedRecordList.size()
+ + " records");
+ contentPane.add(header, BorderLayout.NORTH);
+
+ DefaultTableModel tableModel = new NonEditableTableModel();
+ Vector headerList = new Vector();
+ headerList.add("Name (if available)");
+ headerList.add("Type");
+ headerList.add("Data Source");
+ tableModel.setColumnIdentifiers(headerList);
+ tableModel.setRowCount(passedRecordList.size());
+ JTable table = new JTable(tableModel);
+
+ // Adjust width / height of viewport; fixes bug #1620.
+ Dimension d = table.getPreferredSize();
+ d.width = d.width * 2;
+ if (d.height > 200) {
+ d.height = 200;
+ }
+ table.setPreferredScrollableViewportSize(d);
+ table.setAutoCreateColumnsFromModel(true);
+ table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
+
+ ids = new long[passedRecordList.size()];
+ int i = 0;
+ for (BasicRecordType record : passedRecordList) {
+ if (record.getName().equalsIgnoreCase("N/A")) {
+ record.setName("---");
+ }
+ tableModel.setValueAt(record.getName(), i, 0);
+ tableModel.setValueAt(record.getEntityType(), i, 1);
+ if (record.getDataSource() != null) {
+ tableModel.setValueAt(record.getDataSource().getName(), i, 2);
+ } else {
+ tableModel.setValueAt("---", i, 3);
+ }
+ ids[i++] = record.getPrimaryId();
+ }
+ JScrollPane scrollPane = new JScrollPane(table);
+ scrollPane.setBorder(new EmptyBorder(5, 5, 5, 5));
+ contentPane.add(scrollPane, BorderLayout.CENTER);
+
+ JPanel buttonPanel = createButtonPanel(this);
+ mergePanel = new MergePanel();
+ JPanel panel = new JPanel();
+ panel.setLayout(new BoxLayout(panel, BoxLayout.Y_AXIS));
+ if (mergePanel != null) {
+ panel.add(mergePanel);
+ }
+ panel.add(buttonPanel);
+ contentPane.add(panel, BorderLayout.SOUTH);
+ pack();
+ setLocationRelativeTo(Cytoscape.getDesktop());
+ }
+
+ /**
+ * Button Panel.
+ */
+ private JPanel createButtonPanel(final JDialog dialog) {
+ JButton okButton = new JButton("OK");
+ okButton.addActionListener(new ActionListener() {
+
+ public void actionPerformed(ActionEvent actionEvent) {
+ dialog.setVisible(false);
+ dialog.dispose();
+ downloadInteractions();
+ }
+ });
+
+ JButton cancelButton = new JButton("Cancel");
+ cancelButton.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent actionEvent) {
+ dialog.setVisible(false);
+ dialog.dispose();
+ }
+ });
+
+ JPanel buttonPanel = new JPanel();
+ buttonPanel.setLayout(new FlowLayout(FlowLayout.LEFT));
+ buttonPanel.add(okButton);
+ buttonPanel.add(cancelButton);
+ return buttonPanel;
+ }
+
+ /**
+ * Downloads interaction bundles in a new thread.
+ */
+ private void downloadInteractions() {
+ CyNetwork networkToMerge = null;
+ JComboBox networkComboBox = mergePanel.getNetworkComboBox();
+ if (networkComboBox != null) {
+ NetworkWrapper netWrapper = (NetworkWrapper) networkComboBox.getSelectedItem();
+ if (netWrapper != null) {
+ networkToMerge = netWrapper.getNetwork();
+ }
+ }
+ downloadInteractions(networkToMerge);
+ }
+
+ public void downloadInteractions(CyNetwork networkToMerge) {
+ String networkTitle = peName + ": Network";
+ CPathWebService webApi = CPathWebServiceImpl.getInstance();
+
+ CPathResponseFormat format;
+ CPathProperties config = CPathProperties.getInstance();
+ if (config.getDownloadMode() == CPathProperties.DOWNLOAD_FULL_BIOPAX) {
+ format = CPathResponseFormat.BIOPAX;
+ } else {
+ format = CPathResponseFormat.BINARY_SIF;
+ }
+
+ ExecuteGetRecordByCPathId task = new ExecuteGetRecordByCPathId(webApi, ids, format,
+ networkTitle, networkToMerge);
+
+ JTaskConfig jTaskConfig = new JTaskConfig();
+ jTaskConfig.setOwner(Cytoscape.getDesktop());
+ jTaskConfig.displayStatus(true);
+ jTaskConfig.setAutoDispose(true);
+ jTaskConfig.displayCancelButton(true);
+ TaskManager.executeTask(task, jTaskConfig);
+ }
+}
+
+class NonEditableTableModel extends DefaultTableModel {
+
+ /**
+ * Constructor.
+ */
+ public NonEditableTableModel() {
+ super();
+ }
+
+ /**
+ * Is the specified cell editable? Never!
+ *
+ * @param row row index.
+ * @param col col index.
+ * @return false.
+ */
+ public boolean isCellEditable(int row, int col) {
+ return false;
+ }
+}
+
diff --git a/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/GradientHeader.java b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/GradientHeader.java
new file mode 100644
index 0000000..0bf8410
--- /dev/null
+++ b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/GradientHeader.java
@@ -0,0 +1,73 @@
+package org.cytoscape.coreplugin.cpath2.view;
+
+import javax.swing.*;
+import javax.swing.border.EmptyBorder;
+import java.awt.*;
+import java.net.URL;
+
+/**
+ * Gradient Header Panel.
+ *
+ * @author Ethan Cerami
+ */
+public class GradientHeader extends JPanel {
+
+ /**
+ * Constructor.
+ * @param header Header Title.
+ */
+ public GradientHeader(String header) {
+ this.setLayout(new BorderLayout());
+ JLabel label = new JLabel(header);
+ label.setBorder(new EmptyBorder(0,0,0,0));
+ Font font = label.getFont();
+ Font newFont = new Font (font.getFamily(), Font.BOLD, font.getSize()-1);
+ label.setFont(newFont);
+ label.setForeground(new Color(102,51,51));
+ label.setOpaque(false);
+ this.add (label, BorderLayout.WEST);
+ this.setBorder (new EmptyBorder(2,2,2,2));
+ }
+
+ /**
+ * Constructor.
+ * @param header Header Title.
+ */
+ public GradientHeader(String header, JButton button) {
+ button.setBorder(new EmptyBorder (0,0,0,0));
+ this.setLayout(new BorderLayout());
+ JLabel label = new JLabel(header);
+ label.setBorder(new EmptyBorder(0,0,0,0));
+ Font font = label.getFont();
+ Font newFont = new Font (font.getFamily(), Font.BOLD, font.getSize()-1);
+ label.setFont(newFont);
+ label.setForeground(new Color(102,51,51));
+ label.setOpaque(false);
+ this.add (label, BorderLayout.WEST);
+ this.add (button, BorderLayout.EAST);
+ this.setBorder (new EmptyBorder(2,2,2,2));
+ }
+
+ /**
+ * Override paintComponent() with gradient painting code.
+ * @param graphics Graphics Object.
+ */
+ protected void paintComponent(Graphics graphics) {
+ super.paintComponent(graphics);
+ Graphics2D g2 = (Graphics2D) graphics;
+
+ // Create the gradient
+ GradientPaint p = new GradientPaint (0,0, new Color (0xFFFFFF),
+ 0, getHeight(), new Color (0xC8D2DE));
+
+ // Save the state
+ Paint oldPaint = g2.getPaint();
+
+ // Paint the background
+ g2.setPaint(p);
+ g2.fillRect(0, 0, getWidth(), getHeight());
+
+ // Restore the state
+ g2.setPaint(oldPaint);
+ }
+}
diff --git a/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/GuiUtils.java b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/GuiUtils.java
new file mode 100644
index 0000000..6cdafd0
--- /dev/null
+++ b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/GuiUtils.java
@@ -0,0 +1,26 @@
+package org.cytoscape.coreplugin.cpath2.view;
+
+import javax.swing.border.TitledBorder;
+import java.awt.*;
+
+/**
+ * Graphical User Interface (GUI) Utiltities.
+ *
+ * @author Ethan Cerami
+ */
+public class GuiUtils {
+
+ /**
+ * Creates a Titled Border with appropriate font settings.
+ * @param title Title.
+ * @return TitledBorder Object.
+ */
+ public static TitledBorder createTitledBorder (String title) {
+ TitledBorder border = new TitledBorder(title);
+ Font font = border.getTitleFont();
+ Font newFont = new Font (font.getFamily(), Font.BOLD, font.getSize()+2);
+ border.setTitleFont(newFont);
+ border.setTitleColor(new Color(102,51,51));
+ return border;
+ }
+}
diff --git a/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/InteractionBundlePanel.java b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/InteractionBundlePanel.java
new file mode 100644
index 0000000..f77c317
--- /dev/null
+++ b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/InteractionBundlePanel.java
@@ -0,0 +1,279 @@
+package org.cytoscape.coreplugin.cpath2.view;
+
+import cytoscape.Cytoscape;
+import cytoscape.CyNetwork;
+import org.cytoscape.coreplugin.cpath2.filters.ChainedFilter;
+import org.cytoscape.coreplugin.cpath2.filters.DataSourceFilter;
+import org.cytoscape.coreplugin.cpath2.filters.EntityTypeFilter;
+import org.cytoscape.coreplugin.cpath2.schemas.summary_response.BasicRecordType;
+import org.cytoscape.coreplugin.cpath2.view.model.InteractionBundleModel;
+import org.cytoscape.coreplugin.cpath2.view.model.RecordList;
+import org.cytoscape.coreplugin.cpath2.view.tree.CheckNode;
+import org.cytoscape.coreplugin.cpath2.view.tree.JTreeWithCheckNodes;
+
+import javax.swing.*;
+import javax.swing.border.EmptyBorder;
+import javax.swing.event.TreeModelEvent;
+import javax.swing.event.TreeModelListener;
+import javax.swing.tree.DefaultTreeModel;
+import javax.swing.tree.TreePath;
+import java.awt.*;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.util.*;
+import java.util.List;
+import java.lang.reflect.InvocationTargetException;
+
+/**
+ * Interaction Bundle Panel.
+ *
+ * @author Ethan Cerami
+ */
+public class InteractionBundlePanel extends JPanel {
+ private JLabel matchingInteractionsLabel;
+ private InteractionBundleModel interactionBundleModel;
+ private CheckNode dataSourceFilter;
+ private CheckNode interactionTypeFilter;
+ private JButton retrieveButton;
+ private JTreeWithCheckNodes tree;
+ private CollapsablePanel filterPanel;
+ private JDialog dialog;
+ private CyNetwork mergeNetwork;
+
+ public InteractionBundlePanel(InteractionBundleModel
+ interactionBundleModel, JDialog dialog) {
+ this(interactionBundleModel);
+ this.dialog = dialog;
+ }
+
+ public InteractionBundlePanel(InteractionBundleModel
+ interactionBundleModel, CyNetwork mergeNetwork, JDialog dialog) {
+ this(interactionBundleModel);
+ this.dialog = dialog;
+ this.mergeNetwork = mergeNetwork;
+ }
+
+ public InteractionBundlePanel(InteractionBundleModel
+ interactionBundleModel) {
+ this.interactionBundleModel = interactionBundleModel;
+ JPanel panel = new JPanel();
+ panel.setLayout(new BoxLayout(panel, BoxLayout.Y_AXIS));
+
+ matchingInteractionsLabel = new JLabel("Matching Interactions: N/A");
+ matchingInteractionsLabel.setAlignmentX(Component.LEFT_ALIGNMENT);
+ Font font = matchingInteractionsLabel.getFont();
+ Font newFont = new Font(font.getFamily(), Font.BOLD, font.getSize());
+ matchingInteractionsLabel.setFont(newFont);
+ matchingInteractionsLabel.setBorder(new EmptyBorder(5, 10, 5, 5));
+ panel.add(matchingInteractionsLabel);
+
+ final CheckNode rootNode = new CheckNode("All Filters");
+ tree = new JTreeWithCheckNodes(rootNode);
+ tree.setOpaque(false);
+
+ filterPanel = new CollapsablePanel("Filters (Optional)");
+ filterPanel.setAlignmentX(Component.LEFT_ALIGNMENT);
+ filterPanel.getContentPane().add(tree);
+
+ panel.add(filterPanel);
+ addObserver(interactionBundleModel, matchingInteractionsLabel, tree, rootNode);
+
+ JPanel footer = new JPanel();
+ footer.setAlignmentX(Component.LEFT_ALIGNMENT);
+ footer.setLayout(new FlowLayout(FlowLayout.LEFT));
+ createInteractionDownloadButton(footer);
+ panel.add(footer);
+ JScrollPane scrollPane = new JScrollPane(panel);
+
+ this.setLayout(new BorderLayout());
+ this.add(scrollPane, BorderLayout.CENTER);
+ }
+
+ /**
+ * Expands all Nodes.
+ */
+ public void expandAllNodes() {
+ filterPanel.setCollapsed(false);
+ dataSourceFilter.setSelected(true);
+ interactionTypeFilter.setSelected(true);
+ TreePath path = new TreePath(dataSourceFilter.getPath());
+ tree.expandPath(path);
+ path = new TreePath(interactionTypeFilter.getPath());
+ tree.expandPath(path);
+ }
+
+ private void addObserver(final InteractionBundleModel interactionBundleModel,
+ final JLabel matchingInteractionsLabel, final JTreeWithCheckNodes tree,
+ final CheckNode rootNode) {
+ interactionBundleModel.addObserver(new Observer() {
+ public void update(Observable observable, Object object) {
+ RecordList recordList = interactionBundleModel.getRecordList();
+ matchingInteractionsLabel.setText("Matching Interactions: "
+ + recordList.getNumRecords());
+
+ if (recordList.getNumRecords() == 0) {
+ filterPanel.setVisible(false);
+ retrieveButton.setVisible(false);
+ } else {
+ filterPanel.setVisible(true);
+ retrieveButton.setVisible(true);
+ }
+
+ TreeMap<String, Integer> dataSourceMap = recordList.getDataSourceMap();
+ TreeMap<String, Integer> entityTypeMap = recordList.getEntityTypeMap();
+
+ // Store current expansion states
+ boolean dataSourceFilterExpanded = false;
+ if (dataSourceFilter != null) {
+ TreePath path = new TreePath(dataSourceFilter.getPath());
+ dataSourceFilterExpanded = tree.isExpanded(path);
+ }
+ boolean interactionTypeFilterExpanded = false;
+ if (interactionTypeFilter != null) {
+ TreePath path = new TreePath(interactionTypeFilter.getPath());
+ interactionTypeFilterExpanded = tree.isExpanded(path);
+ }
+
+ // Remove all children
+ rootNode.removeAllChildren();
+
+ // Create Data Source Filter
+ if (dataSourceMap.size() > 0) {
+ dataSourceFilter = new CheckNode("Filter by Data Source");
+ rootNode.add(dataSourceFilter);
+ for (String key : dataSourceMap.keySet()) {
+ CategoryCount categoryCount = new CategoryCount(key,
+ dataSourceMap.get(key));
+ CheckNode dataSourceNode = new CheckNode(categoryCount, false, true);
+ dataSourceFilter.add(dataSourceNode);
+ }
+ dataSourceFilter.setSelected(true);
+ }
+
+ // Create Entity Type Filter
+ if (entityTypeMap.size() > 0) {
+ interactionTypeFilter = new CheckNode("Filter by Interaction Type");
+ rootNode.add(interactionTypeFilter);
+ for (String key : entityTypeMap.keySet()) {
+ CategoryCount categoryCount = new CategoryCount(key,
+ entityTypeMap.get(key));
+ CheckNode dataSourceNode = new CheckNode(categoryCount, false, true);
+ interactionTypeFilter.add(dataSourceNode);
+ }
+ }
+ DefaultTreeModel treeModel = new DefaultTreeModel(rootNode);
+ tree.setModel(treeModel);
+ treeModel.addTreeModelListener(new TreeModelListener() {
+
+ /**
+ * Respond to user check node selections.
+ *
+ * @param treeModelEvent Tree Model Event Object.
+ */
+ public void treeNodesChanged(TreeModelEvent treeModelEvent) {
+ java.util.List<BasicRecordType> passedRecordList = executeFilter();
+ if (passedRecordList != null) {
+ matchingInteractionsLabel.setText("Matching Interactions: "
+ + passedRecordList.size());
+ if (passedRecordList.size() > 0) {
+ retrieveButton.setEnabled(true);
+ } else {
+ retrieveButton.setEnabled(false);
+ }
+ }
+ }
+
+ public void treeNodesInserted(TreeModelEvent treeModelEvent) {
+ // no-op
+ }
+
+ public void treeNodesRemoved(TreeModelEvent treeModelEvent) {
+ // no-op
+ }
+
+ public void treeStructureChanged(TreeModelEvent treeModelEvent) {
+ // no-op
+ }
+ });
+
+ // Restore expansion state.
+ if (dataSourceFilterExpanded) {
+ TreePath path = new TreePath(dataSourceFilter.getPath());
+ tree.expandPath(path);
+ }
+ if (interactionTypeFilterExpanded) {
+ TreePath path = new TreePath(interactionTypeFilter.getPath());
+ tree.expandPath(path);
+ }
+ }
+ });
+ }
+
+ private void createInteractionDownloadButton(JPanel footer) {
+ retrieveButton = new JButton("Retrieve Interactions");
+ retrieveButton.addActionListener(new ActionListener() {
+
+ public void actionPerformed(ActionEvent actionEvent) {
+ List<BasicRecordType> passedRecordList = executeFilter();
+ if (passedRecordList.size() == 0) {
+ JOptionPane.showMessageDialog(Cytoscape.getDesktop(),
+ "Your current filter settings result in 0 matching interactions. "
+ + "\nPlease check your filter settings and try again.",
+ "No matches.", JOptionPane.INFORMATION_MESSAGE);
+ } else {
+ DownloadDetails detailsFrame = new DownloadDetails(passedRecordList,
+ interactionBundleModel.getPhysicalEntityName());
+ if (dialog != null) {
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ dialog.dispose();
+ }
+ });
+ }
+ if (mergeNetwork == null) {
+ detailsFrame.setVisible(true);
+ } else {
+ detailsFrame.downloadInteractions(mergeNetwork);
+ }
+ }
+ }
+ });
+ footer.add(retrieveButton);
+ }
+
+ private List<BasicRecordType> executeFilter() {
+ Set<String> dataSourceSet = new HashSet<String>();
+ Set<String> entityTypeSet = new HashSet<String>();
+ int childCount = dataSourceFilter.getChildCount();
+ for (int i = 0; i < childCount; i++) {
+ CheckNode checkNode = (CheckNode) dataSourceFilter.getChildAt(i);
+ CategoryCount categoryCount = (CategoryCount) checkNode.getUserObject();
+ String dataSource = categoryCount.getCategoryName();
+ if (checkNode.isSelected()) {
+ dataSourceSet.add(dataSource);
+ }
+ }
+ childCount = interactionTypeFilter.getChildCount();
+ for (int i = 0; i < childCount; i++) {
+ CheckNode checkNode = (CheckNode) interactionTypeFilter.getChildAt(i);
+ CategoryCount categoryCount = (CategoryCount) checkNode.getUserObject();
+ String entityType = categoryCount.getCategoryName();
+ if (checkNode.isSelected()) {
+ entityTypeSet.add(entityType);
+ }
+ }
+ ChainedFilter chainedFilter = new ChainedFilter();
+ DataSourceFilter dataSourceFilter = new DataSourceFilter(dataSourceSet);
+ EntityTypeFilter entityTypeFilter = new EntityTypeFilter(entityTypeSet);
+ chainedFilter.addFilter(dataSourceFilter);
+ chainedFilter.addFilter(entityTypeFilter);
+ List<BasicRecordType> passedRecordList;
+ try {
+ passedRecordList = chainedFilter.filter(interactionBundleModel.getRecordList().
+ getSummaryResponse().getRecord());
+ } catch (NullPointerException e) {
+ passedRecordList = null;
+ }
+ return passedRecordList;
+ }
+}
diff --git a/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/JListWithToolTips.java b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/JListWithToolTips.java
new file mode 100644
index 0000000..99f82a1
--- /dev/null
+++ b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/JListWithToolTips.java
@@ -0,0 +1,72 @@
+package org.cytoscape.coreplugin.cpath2.view;
+
+import org.cytoscape.coreplugin.cpath2.schemas.search_response.ExtendedRecordType;
+import org.cytoscape.coreplugin.cpath2.schemas.search_response.OrganismType;
+import org.cytoscape.coreplugin.cpath2.schemas.search_response.XRefType;
+import org.cytoscape.coreplugin.cpath2.view.model.ExtendedRecordWrapper;
+
+import javax.swing.*;
+import java.awt.event.MouseEvent;
+import java.util.List;
+
+/**
+ * Extension to JList to Support Tool Tips.
+ * <p/>
+ * Based on sample code from:
+ * http://www.roseindia.net/java/example/java/swing/TooltipTextOfList.shtml
+ *
+ * @author Ethan Cerami
+ */
+public class JListWithToolTips extends JList {
+
+ public JListWithToolTips(ListModel listModel) {
+ super(listModel);
+ }
+
+ /**
+ * Impelement Tool Tip Functionality.
+ *
+ * @param mouseEvent Mouse Event.
+ * @return Tool Tip.
+ */
+ public String getToolTipText(MouseEvent mouseEvent) {
+ int index = locationToIndex(mouseEvent.getPoint());
+ if (-1 < index) {
+ ExtendedRecordWrapper wrapper = (ExtendedRecordWrapper) getModel().getElementAt(index);
+ ExtendedRecordType record = wrapper.getRecord();
+ StringBuffer html = new StringBuffer();
+ html.append("<html>");
+ html.append("<table cellpadding=10><tr><td>");
+ html.append ("<B>" + record.getName() + "</B> ");
+
+ OrganismType organism = record.getOrganism();
+ if (organism != null) {
+ String speciesName = organism.getSpeciesName();
+ html.append ("[" + speciesName + "]");
+ }
+
+ // Next, add synonyms
+ List<String> synList = record.getSynonym();
+ StringBuffer synBuffer = new StringBuffer();
+ if (synList != null && synList.size() > 0) {
+ for (String synonym: synList) {
+ if (!synonym.equalsIgnoreCase(record.getName())) {
+ synBuffer.append("- " + synonym + "<BR>");
+ }
+ }
+ if (synBuffer.length() > 0) {
+ html.append("<BR><BR>");
+ html.append(synBuffer.toString());
+ }
+ }
+
+ html.append ("</td></tr></table>");
+ html.append ("</html>");
+ return html.toString();
+ } else {
+ return null;
+ }
+ }
+
+
+}
diff --git a/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/MergePanel.java b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/MergePanel.java
new file mode 100644
index 0000000..fc18429
--- /dev/null
+++ b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/MergePanel.java
@@ -0,0 +1,33 @@
+package org.cytoscape.coreplugin.cpath2.view;
+
+import org.cytoscape.coreplugin.cpath2.util.NetworkMergeUtil;
+
+import javax.swing.*;
+import java.awt.*;
+import java.util.Vector;
+
+/**
+ * Merge Panel
+ *
+ * @author Ethan Cerami.
+ */
+public class MergePanel extends JPanel {
+ private JComboBox networkComboBox;
+
+ public MergePanel() {
+ this.setLayout(new FlowLayout(FlowLayout.LEFT));
+ NetworkMergeUtil mergeUtil = new NetworkMergeUtil();
+ if (mergeUtil.mergeNetworksExist()) {
+ Vector networkVector = mergeUtil.getMergeNetworks();
+ networkComboBox = new JComboBox(networkVector);
+ JLabel label = new JLabel("Create / Merge: ");
+ this.add(label);
+ this.add(networkComboBox);
+ networkComboBox.setSelectedIndex(0);
+ }
+ }
+
+ public JComboBox getNetworkComboBox() {
+ return this.networkComboBox;
+ }
+}
\ No newline at end of file
diff --git a/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/ModalPanel.java b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/ModalPanel.java
new file mode 100644
index 0000000..b9f0777
--- /dev/null
+++ b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/ModalPanel.java
@@ -0,0 +1,130 @@
+// $Id$
+//------------------------------------------------------------------------------
+/** Copyright (c) 2007 Memorial Sloan-Kettering Cancer Center.
+ **
+ ** Code written by: Ethan Cerami, Benjamin Gross
+ ** Authors: Ethan Cerami, Gary Bader, Chris Sander, Benjamin Gross
+ **
+ ** This library is free software; you can redistribute it and/or modify it
+ ** under the terms of the GNU Lesser General Public License as published
+ ** by the Free Software Foundation; either version 2.1 of the License, or
+ ** any later version.
+ **
+ ** This library is distributed in the hope that it will be useful, but
+ ** WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ ** MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ ** documentation provided hereunder is on an "as is" basis, and
+ ** Memorial Sloan-Kettering Cancer Center
+ ** has no obligations to provide maintenance, support,
+ ** updates, enhancements or modifications. In no event shall
+ ** Memorial Sloan-Kettering Cancer Center
+ ** be liable to any party for direct, indirect, special,
+ ** incidental or consequential damages, including lost profits, arising
+ ** out of the use of this software and its documentation, even if
+ ** Memorial Sloan-Kettering Cancer Center
+ ** has been advised of the possibility of such damage. See
+ ** the GNU Lesser General Public License for more details.
+ **
+ ** You should have received a copy of the GNU Lesser General Public License
+ ** along with this library; if not, write to the Free Software Foundation,
+ ** Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ **/
+package org.cytoscape.coreplugin.cpath2.view;
+
+// imports
+import java.awt.Color;
+import java.awt.Graphics;
+import java.awt.Composite;
+import java.awt.Graphics2D;
+import java.awt.AlphaComposite;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.image.BufferedImage;
+import javax.swing.JPanel;
+import javax.swing.JComponent;
+
+/**
+ * Modal Panel provides modal support for popup panel.
+ *
+ * @author Benjamin Gross
+ */
+public class ModalPanel extends JPanel implements MouseListener {
+
+ /**
+ * ref to color
+ */
+ private static Color m_backgroundColor = Color.DARK_GRAY;
+
+ /**
+ * image that we used to draw into.
+ */
+ private BufferedImage m_img;
+
+ /**
+ * Constructor.
+ */
+ public ModalPanel() {
+ addMouseListener(this);
+ setVisible(false);
+ }
+
+ /**
+ * Our implementation of set bounds.
+ */
+ public void setBounds(int x, int y, int width, int height) {
+ super.setBounds(x, y, width, height);
+ m_img = new BufferedImage(width, height, BufferedImage.TYPE_INT_ARGB);
+ }
+
+ /**
+ * Our implementation of paint component.
+ */
+ public void paintComponent(Graphics g) {
+
+ // only paint if we have an image
+ if (m_img != null) {
+
+ // we need a g2d ref
+ Graphics2D g2d = (Graphics2D)g;
+
+ // clear our image
+ clearImage(((BufferedImage) m_img).createGraphics());
+
+ // setup composite
+ Composite origComposite = g2d.getComposite();
+ Composite newComposite = AlphaComposite.getInstance(AlphaComposite.SRC_OVER, (float)0.050);
+
+ // draw
+ g2d.setComposite(newComposite);
+ g2d.drawImage(m_img, 0, 0, null);
+
+ // restore composite
+ g2d.setComposite(origComposite);
+ }
+ }
+
+ // kill mouse events - fixes bug where user can
+ // click on gradient header and select things underneath
+ public void mouseClicked(MouseEvent e) {}
+ public void mouseEntered(MouseEvent e) {}
+ public void mouseExited(MouseEvent e) {}
+ public void mousePressed(MouseEvent e) {}
+ public void mouseReleased(MouseEvent e) {}
+
+ /**
+ * Utility function to clean the background of the image,
+ * using m_backgroundColor
+ *
+ * image2D Graphics2D
+ */
+ private void clearImage(Graphics2D image2D) {
+
+ // set the alpha composite on the image, and clear its area
+ Composite origComposite = image2D.getComposite();
+ image2D.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC));
+ image2D.setPaint(m_backgroundColor);
+ image2D.fillRect(0, 0, m_img.getWidth(null), m_img.getHeight(null));
+ image2D.setComposite(origComposite);
+ }
+
+}
\ No newline at end of file
diff --git a/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/PhysicalEntityDetailsPanel.java b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/PhysicalEntityDetailsPanel.java
new file mode 100644
index 0000000..606f1ef
--- /dev/null
+++ b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/PhysicalEntityDetailsPanel.java
@@ -0,0 +1,114 @@
+package org.cytoscape.coreplugin.cpath2.view;
+
+import javax.swing.*;
+import javax.swing.event.HyperlinkListener;
+import javax.swing.event.HyperlinkEvent;
+import javax.swing.text.Document;
+import javax.swing.text.html.StyleSheet;
+import javax.swing.text.html.HTMLEditorKit;
+import javax.swing.text.html.HTMLDocument;
+import javax.swing.border.EmptyBorder;
+import java.awt.*;
+import java.awt.event.*;
+import java.net.URL;
+
+import cytoscape.util.OpenBrowser;
+
+/**
+ * Summary Panel.
+ *
+ * @author Ethan Cerami.
+ */
+public class PhysicalEntityDetailsPanel extends JPanel implements MouseListener {
+ private Document doc;
+ private JTextPane textPane;
+ private SearchHitsPanel searchHitsPanel; // ref to parent
+
+ /**
+ * Constructor.
+ */
+ public PhysicalEntityDetailsPanel(SearchHitsPanel searchHitsPanel) {
+ this.setLayout(new BorderLayout());
+ this.searchHitsPanel = searchHitsPanel;
+ textPane = createHtmlTextPane();
+ doc = textPane.getDocument();
+ JScrollPane scrollPane = encloseInJScrollPane (textPane);
+
+ GradientHeader header = new GradientHeader("Details");
+ // we become gradient header mouse listener - see comment below
+ header.addMouseListener(this);
+
+ add (header, BorderLayout.NORTH);
+ add(scrollPane, BorderLayout.CENTER);
+ }
+
+ // kill mouse events - fixes bug where user can
+ // click on gradient header and select things underneath
+ public void mouseClicked(MouseEvent e) {}
+ public void mouseEntered(MouseEvent e) {}
+ public void mouseExited(MouseEvent e) {}
+ public void mousePressed(MouseEvent e) {}
+ public void mouseReleased(MouseEvent e) {}
+
+ /**
+ * Gets the summary document model.
+ * @return Document object.
+ */
+ public Document getDocument() {
+ return doc;
+ }
+
+ /**
+ * Gets the summary text pane object.
+ * @return JTextPane Object.
+ */
+ public JTextPane getTextPane() {
+ return textPane;
+ }
+
+ /**
+ * Encloses the specified JTextPane in a JScrollPane.
+ *
+ * @param textPane JTextPane Object.
+ * @return JScrollPane Object.
+ */
+ private JScrollPane encloseInJScrollPane(JTextPane textPane) {
+ JScrollPane scrollPane = new JScrollPane(textPane);
+ return scrollPane;
+ }
+
+ /**
+ * Creates a JTextPane with correct line wrap settings.
+ *
+ * @return JTextPane Object.
+ */
+ public static JTextPane createHtmlTextPane() {
+ JTextPane textPane = new JTextPane();
+ textPane.setEditable(false);
+ textPane.setBorder(new EmptyBorder(7,7,7,7));
+ textPane.setContentType("text/html");
+ textPane.putClientProperty(JEditorPane.HONOR_DISPLAY_PROPERTIES, Boolean.TRUE);
+ textPane.addHyperlinkListener(new HyperlinkListener() {
+ public void hyperlinkUpdate(HyperlinkEvent hyperlinkEvent) {
+ if (hyperlinkEvent.getEventType() == HyperlinkEvent.EventType.ACTIVATED) {
+ OpenBrowser.openURL(hyperlinkEvent.getURL().toString());
+ }
+ }
+ });
+
+ HTMLDocument htmlDoc = (HTMLDocument) textPane.getDocument();
+ StyleSheet styleSheet = htmlDoc.getStyleSheet();
+ styleSheet.addRule("h2 {color: #663333; font-size: 102%; font-weight: bold; "
+ + "margin-bottom:3px}");
+ styleSheet.addRule("h3 {color: #663333; font-size: 95%; font-weight: bold;"
+ + "margin-bottom:7px}");
+ styleSheet.addRule("ul { list-style-type: none; margin-left: 5px; "
+ + "padding-left: 1em; text-indent: -1em;}");
+ styleSheet.addRule("h4 {color: #66333; font-weight: bold; margin-bottom:3px;}");
+ styleSheet.addRule("b {background-color: #FFFF00;}");
+ styleSheet.addRule(".bold {font-weight:bold;}");
+ styleSheet.addRule(".link {color:blue; text-decoration: underline;}");
+ styleSheet.addRule(".excerpt {font-size: 90%;}");
+ return textPane;
+ }
+}
\ No newline at end of file
diff --git a/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/PulsatingBorder.java b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/PulsatingBorder.java
new file mode 100644
index 0000000..3d911b1
--- /dev/null
+++ b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/PulsatingBorder.java
@@ -0,0 +1,47 @@
+package org.cytoscape.coreplugin.cpath2.view;
+
+import javax.swing.border.Border;
+import javax.swing.*;
+import java.awt.*;
+import java.awt.geom.Rectangle2D;
+
+public class PulsatingBorder implements Border {
+ private float thickness = 0.5f;
+ private JComponent c;
+
+ public PulsatingBorder(JComponent c) {
+ this.c = c;
+ }
+
+ public void paintBorder(Component c1, Graphics g,
+ int x, int y, int width, int height) {
+ Graphics2D g2 = (Graphics2D) g.create();
+ g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+ RenderingHints.VALUE_ANTIALIAS_ON);
+
+ Rectangle2D r = new Rectangle2D.Double(x, y, width - 1, height - 1);
+ g2.setStroke(new BasicStroke(2.0f * getThickness()));
+
+ AlphaComposite ac = AlphaComposite.getInstance(AlphaComposite.SRC_OVER, getThickness());
+ g2.setComposite(ac);
+ g2.setColor(new Color(0x54A4DE));
+ g2.draw(r);
+ }
+
+ public Insets getBorderInsets(Component c) {
+ return new Insets(2, 2, 2, 2);
+ }
+
+ public boolean isBorderOpaque() {
+ return false;
+ }
+
+ public float getThickness() {
+ return thickness;
+ }
+
+ public void setThickness(float thickness) {
+ this.thickness = thickness;
+ c.repaint();
+ }
+}
diff --git a/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/SearchBoxPanel.java b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/SearchBoxPanel.java
new file mode 100644
index 0000000..4982f9d
--- /dev/null
+++ b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/SearchBoxPanel.java
@@ -0,0 +1,200 @@
+package org.cytoscape.coreplugin.cpath2.view;
+
+import cytoscape.task.ui.JTaskConfig;
+import cytoscape.task.util.TaskManager;
+import cytoscape.Cytoscape;
+import org.cytoscape.coreplugin.cpath2.task.ExecutePhysicalEntitySearch;
+import org.cytoscape.coreplugin.cpath2.web_service.CPathWebService;
+import org.cytoscape.coreplugin.cpath2.web_service.CPathProperties;
+import org.cytoscape.coreplugin.cpath2.view.model.Organism;
+
+import javax.swing.*;
+import javax.swing.event.HyperlinkListener;
+import javax.swing.event.HyperlinkEvent;
+import javax.swing.border.EmptyBorder;
+import java.awt.*;
+import java.awt.event.*;
+import java.util.Vector;
+import java.util.ArrayList;
+import java.net.URL;
+
+/**
+ * Search Box Panel.
+ *
+ * @author Ethan Cerami.
+ */
+public class SearchBoxPanel extends JPanel {
+ private JButton searchButton;
+ private CPathWebService webApi;
+ private static final String ENTER_TEXT = "Enter Gene Name or ID";
+ private PulsatingBorder pulsatingBorder;
+ private JComboBox organismComboBox;
+
+ /**
+ * Constructor.
+ *
+ * @param webApi CPath Web Service Object.
+ */
+ public SearchBoxPanel(CPathWebService webApi) {
+ this.webApi = webApi;
+ GradientHeader header = new GradientHeader("Step 1: Search");
+ header.setAlignmentX(Component.LEFT_ALIGNMENT);
+ BoxLayout boxLayout = new BoxLayout(this, BoxLayout.Y_AXIS);
+ setLayout(boxLayout);
+ add (header);
+ add (Box.createVerticalStrut(5));
+
+ JPanel centerPanel = new JPanel();
+ BoxLayout boxLayoutMain = new BoxLayout(centerPanel, BoxLayout.X_AXIS);
+ centerPanel.setLayout(boxLayoutMain);
+ centerPanel.setAlignmentX(Component.LEFT_ALIGNMENT);
+
+ final JTextField searchField = createSearchField();
+
+ pulsatingBorder = new PulsatingBorder (searchField);
+ searchField.setBorder (BorderFactory.createCompoundBorder(searchField.getBorder(),
+ pulsatingBorder));
+
+ organismComboBox = createOrganismComboBox();
+ searchButton = createSearchButton(searchField);
+
+ searchField.setAlignmentX(Component.LEFT_ALIGNMENT);
+
+ JEditorPane label = new JEditorPane ("text/html", "Examples: <a href='TP53'>TP53</a>, " +
+ "<a href='BRCA1'>BRCA1</a>, or <a href='SRY'>SRY</a>.");
+ label.setEditable(false);
+ label.setOpaque(false);
+ label.putClientProperty(JEditorPane.HONOR_DISPLAY_PROPERTIES, Boolean.TRUE);
+ label.addHyperlinkListener(new HyperlinkListener() {
+
+ // Update search box with activated example.
+ public void hyperlinkUpdate(HyperlinkEvent hyperlinkEvent) {
+ if (hyperlinkEvent.getEventType() == HyperlinkEvent.EventType.ACTIVATED) {
+ searchField.setText(hyperlinkEvent.getDescription());
+ }
+ }
+ });
+
+ label.setAlignmentX(Component.LEFT_ALIGNMENT);
+ Font font = label.getFont();
+ Font newFont = new Font (font.getFamily(), font.getStyle(), font.getSize()-2);
+ label.setFont(newFont);
+ label.setBorder(new EmptyBorder(5,3,3,3));
+ label.setAlignmentX(Component.LEFT_ALIGNMENT);
+
+ centerPanel.add(searchField);
+
+ organismComboBox.setAlignmentX(Component.LEFT_ALIGNMENT);
+ searchButton.setAlignmentX(Component.LEFT_ALIGNMENT);
+ centerPanel.add(organismComboBox);
+ centerPanel.add(searchButton);
+
+ add(centerPanel);
+ add(label);
+ }
+
+ /**
+ * Creates the Organism Combo Box.
+ *
+ * @return JComboBox Object.
+ */
+ private JComboBox createOrganismComboBox() {
+ // Organism List is currently hard-coded.
+ Vector organismList = new Vector();
+ organismList.add(new Organism("All Organisms", -1));
+ CPathProperties props = CPathProperties.getInstance();
+ organismList.addAll(props.getOrganismList());
+ DefaultComboBoxModel organismComboBoxModel = new DefaultComboBoxModel(organismList);
+ JComboBox organismComboBox = new JComboBox(organismComboBoxModel);
+ organismComboBox.setToolTipText("Select Organism");
+ organismComboBox.setMaximumSize(new Dimension(200, 9999));
+ organismComboBox.setPrototypeDisplayValue("12345678901234567");
+ return organismComboBox;
+ }
+
+ /**
+ * Creates the Search Field and associated listener(s)
+ *
+ * @return JTextField Object.
+ */
+ private JTextField createSearchField() {
+ final JTextField searchField = new JTextField(ENTER_TEXT.length());
+ searchField.setText(ENTER_TEXT);
+ searchField.setToolTipText(ENTER_TEXT);
+ searchField.setMaximumSize(new Dimension(200, 9999));
+ searchField.addFocusListener(new FocusAdapter() {
+ public void focusGained(FocusEvent focusEvent) {
+ if (searchField.getText() != null
+ && searchField.getText().startsWith("Enter")) {
+ searchField.setText("");
+ }
+ }
+ });
+ searchField.addKeyListener(new KeyAdapter() {
+ public void keyPressed(KeyEvent e) {
+ int keyCode = e.getKeyCode();
+ if (keyCode == 10) {
+ Organism organism = (Organism) organismComboBox.getSelectedItem();
+ executeSearch(searchField.getText(), organism.getNcbiTaxonomyId(),
+ organism.getSpeciesName());
+ }
+ }
+ });
+ return searchField;
+ }
+
+ /**
+ * Creates the Search Button and associated action listener.
+ *
+ * @param searchField JTextField searchField
+ * @return
+ */
+ private JButton createSearchButton(final JTextField searchField) {
+ URL url = GradientHeader.class.getResource("resources/run_tool.gif");
+ ImageIcon icon = new ImageIcon(url);
+ //searchButton = new JButton(icon);
+ searchButton = new JButton("Search");
+ searchButton.setToolTipText("Execute Search");
+ searchButton.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent actionEvent) {
+ Organism organism = (Organism) organismComboBox.getSelectedItem();
+ executeSearch(searchField.getText(), organism.getNcbiTaxonomyId(),
+ organism.getSpeciesName());
+ }
+ });
+ return searchButton;
+ }
+
+ private void executeSearch(String keyword, int ncbiTaxonomyId, String speciesName) {
+ Window window = Cytoscape.getDesktop();
+ if (keyword == null || keyword.trim().length() == 0
+ || keyword.startsWith(ENTER_TEXT)) {
+ JOptionPane.showMessageDialog(window, "Please enter a Gene Name or ID.",
+ "Search Error", JOptionPane.ERROR_MESSAGE);
+ } else {
+ ExecutePhysicalEntitySearch search = new ExecutePhysicalEntitySearch
+ (webApi, keyword.trim(), ncbiTaxonomyId);
+ JTaskConfig jTaskConfig = new JTaskConfig();
+ jTaskConfig.setAutoDispose(true);
+ jTaskConfig.displayStatus(true);
+ jTaskConfig.displayCancelButton(true);
+ jTaskConfig.displayCloseButton(false);
+ jTaskConfig.setOwner(window);
+ TaskManager.executeTask(search, jTaskConfig);
+ if (search.getNumMatchesFound() == 0) {
+ JOptionPane.showMessageDialog(Cytoscape.getDesktop(),
+ "No matches found for: " + keyword + " [" + speciesName + "]" +
+ "\nPlease try a different search term and/or organism filter.",
+ "No matches found.",
+ JOptionPane.WARNING_MESSAGE);
+ }
+ }
+ }
+
+ /**
+ * Initializes Focus to the Search Button.
+ */
+ public void initFocus() {
+ searchButton.requestFocusInWindow();
+ }
+}
diff --git a/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/SearchDetailsPanel.java b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/SearchDetailsPanel.java
new file mode 100644
index 0000000..f6e178e
--- /dev/null
+++ b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/SearchDetailsPanel.java
@@ -0,0 +1,132 @@
+package org.cytoscape.coreplugin.cpath2.view;
+
+import javax.swing.*;
+import java.awt.*;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+
+import org.cytoscape.coreplugin.cpath2.view.model.InteractionBundleModel;
+import org.cytoscape.coreplugin.cpath2.view.model.PathwayTableModel;
+import org.cytoscape.coreplugin.cpath2.view.model.NetworkWrapper;
+import org.cytoscape.coreplugin.cpath2.task.ExecuteGetRecordByCPathId;
+import org.cytoscape.coreplugin.cpath2.web_service.CPathWebService;
+import org.cytoscape.coreplugin.cpath2.web_service.CPathWebServiceImpl;
+import org.cytoscape.coreplugin.cpath2.web_service.CPathProperties;
+import org.cytoscape.coreplugin.cpath2.web_service.CPathResponseFormat;
+import org.cytoscape.coreplugin.cpath2.util.NetworkMergeUtil;
+import cytoscape.Cytoscape;
+import cytoscape.task.ui.JTaskConfig;
+import cytoscape.task.util.TaskManager;
+
+/**
+ * Search Details Panel.
+ *
+ * @author Ethan Cerami.
+ */
+public class SearchDetailsPanel extends JPanel {
+ private InteractionBundleModel interactionBundleModel;
+
+ /**
+ * Constructor.
+ *
+ * @param interactionBundleModel InteractionBundleModel Object.
+ * @param pathwayTableModel PathwayTableModel Object.
+ */
+ public SearchDetailsPanel(InteractionBundleModel interactionBundleModel,
+ PathwayTableModel pathwayTableModel) {
+ this.interactionBundleModel = interactionBundleModel;
+ GradientHeader header = new GradientHeader("Step 3: Select Network(s)");
+ setLayout(new BorderLayout());
+ this.add(header, BorderLayout.NORTH);
+
+ JTabbedPane tabbedPane = new JTabbedPane();
+ JPanel interactionPanel = new InteractionBundlePanel(interactionBundleModel);
+ JPanel pathwayPane = createPathwayPane(pathwayTableModel);
+ Font font = tabbedPane.getFont();
+ Font newFont = new Font (font.getFamily(), Font.PLAIN, font.getSize()-2);
+ tabbedPane.setFont(newFont);
+
+ tabbedPane.add("Pathways", pathwayPane);
+ tabbedPane.add("Interaction Networks", interactionPanel);
+ add(tabbedPane, BorderLayout.CENTER);
+ }
+
+ private JPanel createPathwayPane(PathwayTableModel pathwayTableModel) {
+ JPanel pathwayPane = new JPanel(new BorderLayout());
+ JScrollPane pathwayTable = createPathwayTable(pathwayTableModel);
+ pathwayPane.add(pathwayTable, BorderLayout.CENTER);
+ JLabel label = new JLabel ("> Double-click pathway to retrieve.");
+ label.setForeground(Color.BLUE);
+ Font font = label.getFont();
+ Font newFont = new Font(font.getFamily(), Font.PLAIN, font.getSize()-2);
+ label.setFont(newFont);
+ pathwayPane.add(label, BorderLayout.SOUTH);
+ return pathwayPane;
+ }
+ /**
+ * Creates the Pathway Table.
+ *
+ * @return JScrollPane Object.
+ */
+ private JScrollPane createPathwayTable(final PathwayTableModel pathwayTableModel) {
+ final JTable pathwayTable = new JTable(pathwayTableModel);
+ pathwayTable.setAutoCreateColumnsFromModel(true);
+ pathwayTable.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
+
+ pathwayTable.addMouseListener(new MouseAdapter() {
+ public void mouseClicked(MouseEvent e) {
+ if (e.getClickCount() == 2) {
+ int rows[] = pathwayTable.getSelectedRows();
+ if (rows.length > 0) {
+ long id = pathwayTableModel.getInternalId(rows[0]);
+ String title = pathwayTableModel.getValueAt(rows[0], 0) + " ("
+ + pathwayTableModel.getValueAt(rows[0], 1) + ")";
+ downloadPathway(id, title);
+ }
+ }
+ }
+ });
+ JScrollPane scrollPane = new JScrollPane(pathwayTable);
+ return scrollPane;
+ }
+
+ /*
+ * Downloads a single pathway in a new thread.
+ */
+ private void downloadPathway(long pathwayId, String title) {
+ NetworkWrapper mergeNetwork = null;
+ NetworkMergeUtil mergeUtil = new NetworkMergeUtil();
+ if (mergeUtil.mergeNetworksExist()) {
+ mergeNetwork = mergeUtil.promptForNetworkToMerge();
+ if (mergeNetwork == null) {
+ return;
+ }
+ }
+
+ CPathWebService webApi = CPathWebServiceImpl.getInstance();
+ ExecuteGetRecordByCPathId task;
+
+ CPathResponseFormat format;
+ CPathProperties config = CPathProperties.getInstance();
+ if (config.getDownloadMode() == CPathProperties.DOWNLOAD_FULL_BIOPAX) {
+ format = CPathResponseFormat.BIOPAX;
+ } else {
+ format = CPathResponseFormat.BINARY_SIF;
+ }
+
+ if (mergeNetwork != null && mergeNetwork.getNetwork() != null) {
+ task = new ExecuteGetRecordByCPathId(webApi, new long[]{pathwayId}, format, title,
+ mergeNetwork.getNetwork());
+ } else {
+ task = new ExecuteGetRecordByCPathId(webApi, new long[]{pathwayId}, format, title);
+ }
+
+ JTaskConfig jTaskConfig = new JTaskConfig();
+ jTaskConfig.setOwner(Cytoscape.getDesktop());
+ jTaskConfig.displayStatus(true);
+ jTaskConfig.setAutoDispose(true);
+ jTaskConfig.displayCancelButton(true);
+ TaskManager.executeTask(task, jTaskConfig);
+ }
+}
+
diff --git a/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/SearchHitsPanel.java b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/SearchHitsPanel.java
new file mode 100644
index 0000000..e598a00
--- /dev/null
+++ b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/SearchHitsPanel.java
@@ -0,0 +1,244 @@
+package org.cytoscape.coreplugin.cpath2.view;
+
+import cytoscape.Cytoscape;
+import cytoscape.view.cytopanels.*;
+import cytoscape.view.CytoscapeDesktop;
+
+import org.cytoscape.coreplugin.cpath2.task.SelectPhysicalEntity;
+import org.cytoscape.coreplugin.cpath2.view.model.PathwayTableModel;
+import org.cytoscape.coreplugin.cpath2.view.model.InteractionBundleModel;
+import org.cytoscape.coreplugin.cpath2.view.model.RecordList;
+import org.cytoscape.coreplugin.cpath2.view.model.ExtendedRecordWrapper;
+import org.cytoscape.coreplugin.cpath2.web_service.CPathWebServiceListener;
+import org.cytoscape.coreplugin.cpath2.web_service.CPathWebService;
+import org.cytoscape.coreplugin.cpath2.schemas.search_response.SearchResponseType;
+import org.cytoscape.coreplugin.cpath2.schemas.search_response.ExtendedRecordType;
+import org.cytoscape.coreplugin.cpath2.schemas.summary_response.SummaryResponseType;
+
+import javax.swing.*;
+import javax.swing.event.ListSelectionEvent;
+import javax.swing.event.ListSelectionListener;
+import javax.swing.text.Document;
+import java.util.List;
+import java.util.HashMap;
+import java.awt.*;
+import java.awt.event.ActionListener;
+import java.awt.event.ActionEvent;
+import java.net.URL;
+
+/**
+ * Search Hits Panel.
+ *
+ * @author Ethan Cerami.
+ */
+public class SearchHitsPanel extends JPanel implements CPathWebServiceListener, CytoPanelListener {
+ private DefaultListModel peListModel;
+ private JList peList;
+ private SearchResponseType peSearchResponse;
+ private Document summaryDocument;
+ private String currentKeyword;
+ private InteractionBundleModel interactionBundleModel;
+ private PathwayTableModel pathwayTableModel;
+ private JTextPane summaryTextPane;
+ private PhysicalEntityDetailsPanel peDetailsPanel;
+ private JLayeredPane appLayeredPane;
+ private HashMap <Long, RecordList> parentRecordsMap;
+ private CytoPanelState cytoPanelState;
+ private JFrame detailsFrame;
+
+ /**
+ * Constructor.
+ * @param interactionBundleModel Interaction Table Model.
+ * @param pathwayTableModel Pathway Table Model.
+ * @param webApi cPath Web API.
+ */
+ public SearchHitsPanel(InteractionBundleModel interactionBundleModel, PathwayTableModel
+ pathwayTableModel, CPathWebService webApi) {
+ this.interactionBundleModel = interactionBundleModel;
+ this.pathwayTableModel = pathwayTableModel;
+ appLayeredPane = Cytoscape.getDesktop().getRootPane().getLayeredPane();
+ webApi.addApiListener(this);
+ setLayout(new BoxLayout(this, BoxLayout.Y_AXIS));
+
+ // Create the Summary Panel, but don't show it yet
+ peDetailsPanel = new PhysicalEntityDetailsPanel(this);
+ summaryDocument = peDetailsPanel.getDocument();
+ summaryTextPane = peDetailsPanel.getTextPane();
+
+ // create popup window
+// modalPanel = new ModalPanel();
+// popup = new PopupPanel(appLayeredPane, peDetailsPanel, modalPanel);
+// appLayeredPane.add(modalPanel, 1000);
+// appLayeredPane.add(popup, 1000);
+
+ // Create the Hit List
+ peListModel = new DefaultListModel();
+ peList = createHitJList(peListModel);
+
+ JPanel hitListPane = new JPanel();
+ hitListPane.setLayout(new BorderLayout());
+ JScrollPane hitListScrollPane = new JScrollPane(peList);
+ hitListScrollPane.setAlignmentX(Component.LEFT_ALIGNMENT);
+ GradientHeader header = new GradientHeader("Step 2: Select");
+ header.setAlignmentX(Component.LEFT_ALIGNMENT);
+ hitListPane.add(header, BorderLayout.NORTH);
+ JSplitPane internalPanel = new JSplitPane(JSplitPane.VERTICAL_SPLIT, hitListScrollPane,
+ peDetailsPanel);
+ internalPanel.setDividerLocation(100);
+ hitListPane.add(internalPanel, BorderLayout.CENTER);
+
+ // Create Search Details Panel
+ SearchDetailsPanel detailsPanel = new SearchDetailsPanel(interactionBundleModel,
+ pathwayTableModel);
+
+ // Create the Split Pane
+ JSplitPane splitPane = new JSplitPane (JSplitPane.HORIZONTAL_SPLIT, hitListPane,
+ detailsPanel);
+ splitPane.setDividerLocation(200);
+ splitPane.setAlignmentX(Component.LEFT_ALIGNMENT);
+ this.add(splitPane);
+ createListener(interactionBundleModel, pathwayTableModel, summaryTextPane);
+
+ // listener for cytopanel events
+ CytoPanel cytoPanel = Cytoscape.getDesktop().getCytoPanel(SwingConstants.EAST);
+ cytoPanel.addCytoPanelListener(this);
+ cytoPanelState = cytoPanel.getState();
+ }
+
+ private JList createHitJList(DefaultListModel peListModel) {
+ JList peList = new JListWithToolTips(peListModel);
+ peList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
+ peList.setPrototypeCellValue("12345678901234567890");
+ return peList;
+ }
+
+ /**
+ * Indicates that user has initiated a phsyical entity search.
+ *
+ * @param keyword Keyword.
+ * @param ncbiTaxonomyId NCBI Taxonomy ID.
+ */
+ public void searchInitiatedForPhysicalEntities(String keyword, int ncbiTaxonomyId) {
+ this.currentKeyword = keyword;
+ }
+
+ /**
+ * Indicates that a search for physical entities has just completed.
+ *
+ * @param peSearchResponse PhysicalEntitySearchResponse Object.
+ */
+ public void searchCompletedForPhysicalEntities(final SearchResponseType peSearchResponse) {
+
+ if (peSearchResponse.getTotalNumHits() > 0) {
+
+ // Reset parent summary map
+ parentRecordsMap = new HashMap<Long, RecordList>();
+
+ // store for later reference
+ this.peSearchResponse = peSearchResponse;
+
+ // Populate the hit list
+ List<ExtendedRecordType> searchHits = peSearchResponse.getSearchHit();
+ peListModel.setSize(searchHits.size());
+ int i = 0;
+ for (ExtendedRecordType searchHit : searchHits) {
+ ExtendedRecordWrapper wrapper = new ExtendedRecordWrapper (searchHit);
+ peListModel.setElementAt(wrapper, i++);
+ }
+ } else {
+ SwingUtilities.invokeLater(new Runnable(){
+ public void run() {
+ Window window = SwingUtilities.getWindowAncestor(SearchHitsPanel.this);
+ JOptionPane.showMessageDialog(window, "No matches found for: "
+ + currentKeyword + ". Please try again.", "Search Results",
+ JOptionPane.INFORMATION_MESSAGE);
+ }
+ });
+ }
+ }
+
+ public void requestInitiatedForParentSummaries(long primaryId) {
+ // Currently no-op
+ }
+
+ public void requestCompletedForParentSummaries(long primaryId,
+ SummaryResponseType summaryResponse) {
+ // Store parent summaries for later reference
+
+ RecordList recordList = new RecordList(summaryResponse);
+ parentRecordsMap.put(primaryId, recordList);
+
+ // If we have just received parent summaries for the first search hit, select it.
+ if (peSearchResponse != null) {
+ List <ExtendedRecordType> searchHits = peSearchResponse.getSearchHit();
+ if (searchHits.size() > 0) {
+ ExtendedRecordType searchHit = searchHits.get(0);
+ if (primaryId == searchHit.getPrimaryId()) {
+ peList.setSelectedIndex(0);
+ SelectPhysicalEntity selectTask = new SelectPhysicalEntity(parentRecordsMap);
+ selectTask.selectPhysicalEntity(peSearchResponse, 0,
+ interactionBundleModel, pathwayTableModel, summaryDocument,
+ summaryTextPane, appLayeredPane);
+ }
+ }
+ }
+ }
+
+ /**
+ * Listen for list selection events.
+ *
+ * @param interactionBundleModel InteractionBundleModel.
+ * @param pathwayTableModel PathwayTableModel.
+ */
+ private void createListener(final InteractionBundleModel interactionBundleModel,
+ final PathwayTableModel pathwayTableModel, final JTextPane textPane) {
+ peList.addListSelectionListener(new ListSelectionListener() {
+ public void valueChanged(ListSelectionEvent listSelectionEvent) {
+ int selectedIndex = peList.getSelectedIndex();
+ // Ignore the "unselect" event.
+ if (!listSelectionEvent.getValueIsAdjusting()) {
+ if (selectedIndex >=0) {
+ SelectPhysicalEntity selectTask = new SelectPhysicalEntity(parentRecordsMap);
+ selectTask.selectPhysicalEntity(peSearchResponse, selectedIndex,
+ interactionBundleModel, pathwayTableModel, summaryDocument,
+ textPane, appLayeredPane);
+ }
+ }
+ }
+ });
+ }
+
+ //
+ // cytopanel listener implementation
+ //
+
+ /**
+ * Notifies the listener on a change in the CytoPanel state.
+ *
+ * @param newState The new CytoPanel state - see CytoPanelState class.
+ */
+ public void onStateChange(CytoPanelState newState) {
+ cytoPanelState = newState;
+ }
+
+ /**
+ * Notifies the listener when a new component on the CytoPanel is selected.
+ *
+ * @param componentIndex The index of the component selected.
+ */
+ public void onComponentSelected(int componentIndex) {}
+
+ /**
+ * Notifies the listener when a component is added to the CytoPanel.
+ *
+ * @param count The number of components on the CytoPanel after the add.
+ */
+ public void onComponentAdded(int count) {}
+
+ /**
+ * Notifies the listener when a component is removed from the CytoPanel.
+ *
+ * @param count The number of components on the CytoPanel after the remove.
+ */
+ public void onComponentRemoved(int count) {}
+}
\ No newline at end of file
diff --git a/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/TabUi.java b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/TabUi.java
new file mode 100644
index 0000000..017e1bc
--- /dev/null
+++ b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/TabUi.java
@@ -0,0 +1,29 @@
+package org.cytoscape.coreplugin.cpath2.view;
+
+import javax.swing.*;
+
+/**
+ * TabUI Singleton.
+ *
+ */
+public class TabUi extends JTabbedPane {
+ private static TabUi tabs;
+
+ /**
+ * Gets Instance of TabUI Object.
+ * @return TabUI Object.
+ */
+ public static TabUi getInstance() {
+ if (tabs == null) {
+ tabs = new TabUi();
+ }
+ return tabs;
+ }
+
+ /**
+ * Private Constructor.
+ * Enforces Singelton Pattern.
+ */
+ private TabUi() {
+ }
+}
diff --git a/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/cPathSearchPanel.java b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/cPathSearchPanel.java
new file mode 100644
index 0000000..f098a4d
--- /dev/null
+++ b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/cPathSearchPanel.java
@@ -0,0 +1,134 @@
+package org.cytoscape.coreplugin.cpath2.view;
+
+import org.cytoscape.coreplugin.cpath2.view.model.InteractionBundleModel;
+import org.cytoscape.coreplugin.cpath2.view.model.PathwayTableModel;
+import org.cytoscape.coreplugin.cpath2.web_service.CPathWebService;
+import org.cytoscape.coreplugin.cpath2.web_service.CPathWebServiceListener;
+import org.cytoscape.coreplugin.cpath2.web_service.CPathProperties;
+import org.cytoscape.coreplugin.cpath2.web_service.CPathWebServiceImpl;
+import org.cytoscape.coreplugin.cpath2.schemas.search_response.SearchResponseType;
+import org.cytoscape.coreplugin.cpath2.schemas.summary_response.SummaryResponseType;
+
+import javax.swing.*;
+import java.awt.*;
+
+/**
+ * Main GUI Panel for Searching a cPath Instance.
+ *
+ * @author Ethan Cerami.
+ */
+public class cPathSearchPanel extends JPanel implements CPathWebServiceListener {
+ protected InteractionBundleModel interactionBundleModel;
+ protected PathwayTableModel pathwayTableModel;
+ protected CPathWebService webApi;
+ private JPanel searchBoxPanel;
+ private JPanel searchHitsPanel = null;
+ private JPanel cards;
+
+ /**
+ * Constructor.
+ *
+ * @param webApi CPathWebService API.
+ */
+ public cPathSearchPanel(CPathWebService webApi) {
+
+ // Store the web API model
+ this.webApi = webApi;
+
+ // Create shared model classes
+ interactionBundleModel = new InteractionBundleModel();
+ pathwayTableModel = new PathwayTableModel();
+
+ // Create main Border Layout
+ setLayout(new BorderLayout());
+
+ // Create North Panel: Search Box
+ searchBoxPanel = new SearchBoxPanel(webApi);
+ add(searchBoxPanel, BorderLayout.NORTH);
+
+ cards = new JPanel(new CardLayout());
+ searchHitsPanel = createSearchResultsPanel();
+
+ JPanel aboutPanel = createAboutPanel();
+ cards.add (aboutPanel, "ABOUT");
+ cards.add(searchHitsPanel, "HITS");
+ add(cards, BorderLayout.CENTER);
+ webApi.addApiListener(this);
+ this.setMinimumSize(new Dimension (300,40));
+ }
+
+ public void showAboutPanel() {
+ CardLayout cl = (CardLayout)(cards.getLayout());
+ cl.show(cards, "ABOUT");
+ }
+
+ private JPanel createAboutPanel() {
+ JPanel aboutPanel = new JPanel();
+ aboutPanel.setLayout(new BorderLayout());
+ GradientHeader header = new GradientHeader("About");
+
+ aboutPanel.add(header, BorderLayout.NORTH);
+ JTextPane textPane = PhysicalEntityDetailsPanel.createHtmlTextPane();
+ textPane.setText(CPathProperties.getInstance().getCPathBlurb());
+ aboutPanel.add(textPane, BorderLayout.CENTER);
+ return aboutPanel;
+ }
+
+ public void searchInitiatedForPhysicalEntities(String keyword, int ncbiTaxonomyId) {
+ }
+
+ public void searchCompletedForPhysicalEntities(SearchResponseType peSearchResponse) {
+ if (peSearchResponse.getTotalNumHits() > 0) {
+ if (!searchHitsPanel.isVisible()) {
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ CardLayout cl = (CardLayout)(cards.getLayout());
+ cl.show(cards, "HITS"); }
+ });
+ }
+ }
+ }
+
+ public void requestInitiatedForParentSummaries(long primaryId) {
+ // Currently no-op
+ }
+
+ public void requestCompletedForParentSummaries(long primaryId,
+ SummaryResponseType summaryResponse) {
+ // Currently no-op
+ }
+
+ /**
+ * Initialize the Focus. Can only be called after component has been
+ * packed and displayed.
+ */
+ public void initFocus() {
+ searchBoxPanel.requestFocusInWindow();
+ }
+
+ /**
+ * Creates the Search Results Split Pane.
+ *
+ * @return JSplitPane Object.
+ */
+ private JPanel createSearchResultsPanel() {
+ JPanel hitListPanel = new SearchHitsPanel(this.interactionBundleModel,
+ this.pathwayTableModel, webApi);
+ return hitListPanel;
+ }
+
+ /**
+ * Main Method. Used for debugging purposes only.
+ *
+ * @param args Command Line Arguments.
+ */
+ public static void main(String[] args) {
+ JFrame frame = new JFrame();
+ cPathSearchPanel form = new cPathSearchPanel(
+ CPathWebServiceImpl.getInstance());
+ frame.getContentPane().add(form);
+ frame.pack();
+ form.initFocus();
+ frame.setVisible(true);
+ }
+}
\ No newline at end of file
diff --git a/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/model/ExtendedRecordWrapper.java b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/model/ExtendedRecordWrapper.java
new file mode 100644
index 0000000..8b11f1d
--- /dev/null
+++ b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/model/ExtendedRecordWrapper.java
@@ -0,0 +1,24 @@
+package org.cytoscape.coreplugin.cpath2.view.model;
+
+import org.cytoscape.coreplugin.cpath2.schemas.search_response.ExtendedRecordType;
+
+/**
+ * Wrapper for ExtendedRecordType.
+ *
+ * @author Ethan Cerami.
+ */
+public class ExtendedRecordWrapper {
+ private ExtendedRecordType record;
+
+ public ExtendedRecordWrapper (ExtendedRecordType record) {
+ this.record = record;
+ }
+
+ public ExtendedRecordType getRecord() {
+ return this.record;
+ }
+
+ public String toString() {
+ return record.getName();
+ }
+}
diff --git a/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/model/InteractionBundleModel.java b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/model/InteractionBundleModel.java
new file mode 100644
index 0000000..ed0ee75
--- /dev/null
+++ b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/model/InteractionBundleModel.java
@@ -0,0 +1,47 @@
+package org.cytoscape.coreplugin.cpath2.view.model;
+
+import java.util.Observable;
+
+/**
+ * Contains information regarding the currently selected set of interaction bundles.
+ *
+ * @author Ethan Cerami
+ */
+public class InteractionBundleModel extends Observable {
+ private RecordList recordList;
+ private String physicalEntityName;
+
+ /**
+ * Sets the SummaryResponse Object.
+ * @param recordList Record List.
+ */
+ public void setRecordList (RecordList recordList) {
+ this.recordList = recordList;
+ this.setChanged();
+ this.notifyObservers();
+ }
+
+ /**
+ * Gets the Record List.
+ * @return RecordList Object.
+ */
+ public RecordList getRecordList() {
+ return recordList;
+ }
+
+ /**
+ * Gets the Physical Entity Name.
+ * @return PE Name.
+ */
+ public String getPhysicalEntityName() {
+ return physicalEntityName;
+ }
+
+ /**
+ * Sets the Physical Entity Name.
+ * @param physicalEntityName PE Name.
+ */
+ public void setPhysicalEntityName(String physicalEntityName) {
+ this.physicalEntityName = physicalEntityName;
+ }
+}
\ No newline at end of file
diff --git a/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/model/NetworkWrapper.java b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/model/NetworkWrapper.java
new file mode 100644
index 0000000..460347a
--- /dev/null
+++ b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/model/NetworkWrapper.java
@@ -0,0 +1,27 @@
+package org.cytoscape.coreplugin.cpath2.view.model;
+
+import cytoscape.CyNetwork;
+
+public class NetworkWrapper {
+ private CyNetwork network;
+
+ public NetworkWrapper (CyNetwork network) {
+ this.network = network;
+ }
+
+ public CyNetwork getNetwork() {
+ return network;
+ }
+
+ public String toString() {
+ if (network != null) {
+ String title = network.getTitle();
+ if (title != null && title.length() > 40) {
+ title = title.substring(0, 38) + "...";
+ }
+ return "Merge with: " + title;
+ } else {
+ return "Create New Network";
+ }
+ }
+}
diff --git a/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/model/Organism.java b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/model/Organism.java
new file mode 100644
index 0000000..a4a2212
--- /dev/null
+++ b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/model/Organism.java
@@ -0,0 +1,84 @@
+package org.cytoscape.coreplugin.cpath2.view.model;
+
+/**
+ * Encapsulates Organism Information.
+ *
+ * @author Ethan Cerami
+ */
+public class Organism {
+ private String commonName;
+ private String speciesName;
+ private int ncbiTaxonomyId;
+
+ /**
+ * Constructor.
+ * @param speciesName Organism Species Name.
+ * @param ncbiTaxonomyId NCBI Taxonomy ID.
+ */
+ public Organism (String speciesName, int ncbiTaxonomyId) {
+ this.speciesName = speciesName;
+ this.ncbiTaxonomyId = ncbiTaxonomyId;
+ }
+
+ /**
+ * Empty-Arg Constructor.
+ */
+ public Organism() {
+ }
+
+ /**
+ * Gets Organism Common Name.
+ * @return organism common name.
+ */
+ public String getCommonName() {
+ return commonName;
+ }
+
+ /**
+ * Sets Organism Common Name.
+ * @param commonName organism common name.
+ */
+ public void setCommonName(String commonName) {
+ this.commonName = commonName;
+ }
+
+ /**
+ * Gets the Species Name.
+ * @return species name.
+ */
+ public String getSpeciesName() {
+ return speciesName;
+ }
+
+ /**
+ * Sets the Species Name.
+ * @param speciesName species name.
+ */
+ public void setSpeciesName(String speciesName) {
+ this.speciesName = speciesName;
+ }
+
+ /**
+ * Gets Organism NCBI Taxonomy ID.
+ * @return NCBI Taxonomy ID.
+ */
+ public int getNcbiTaxonomyId() {
+ return ncbiTaxonomyId;
+ }
+
+ /**
+ * Sets Organism NCBI Taxonomy ID.
+ * @param ncbiTaxonomyId NCBI Taxonomy ID.
+ */
+ public void setNcbiTaxonomyId(int ncbiTaxonomyId) {
+ this.ncbiTaxonomyId = ncbiTaxonomyId;
+ }
+
+ /**
+ * Over-rides toString() to return common name.
+ * @return Organism common name.
+ */
+ public String toString() {
+ return speciesName;
+ }
+}
diff --git a/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/model/PathwayTableModel.java b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/model/PathwayTableModel.java
new file mode 100644
index 0000000..ee72e2d
--- /dev/null
+++ b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/model/PathwayTableModel.java
@@ -0,0 +1,69 @@
+package org.cytoscape.coreplugin.cpath2.view.model;
+
+import javax.swing.table.DefaultTableModel;
+import java.util.Vector;
+import java.util.ArrayList;
+
+/**
+ * Pathway Table Model.
+ *
+ * @author Ethan Cerami
+ */
+public class PathwayTableModel extends DefaultTableModel {
+ ArrayList internalIdList = new ArrayList();
+
+ /**
+ * Constructor.
+ */
+ public PathwayTableModel() {
+ super();
+ Vector columnNames = new Vector();
+ columnNames.add("Pathway");
+ columnNames.add("Data Source");
+ //columnNames.add("Select");
+ this.setColumnIdentifiers(columnNames);
+ }
+
+ /**
+ * Is the specified cell editable?
+ *
+ * @param row row index.
+ * @param col col index.
+ * @return true or false.
+ */
+ public boolean isCellEditable(int row, int col) {
+ return false;
+// if (col == 2) {
+// return true;
+// } else {
+// return false;
+// }
+ }
+
+ /**
+ * Gets the column class.
+ *
+ * @param columnIndex column index.
+ * @return Class.
+ */
+ public Class getColumnClass(int columnIndex) {
+ return String.class;
+// if (columnIndex == 2) {
+// return Boolean.class;
+// } else {
+// return String.class;
+// }
+ }
+
+ public void resetInternalIds (int size) {
+ internalIdList = new ArrayList(size);
+ }
+
+ public void setInternalId (int index, long internalId) {
+ internalIdList.add(index, internalId);
+ }
+
+ public long getInternalId (int index) {
+ return (Long) internalIdList.get(index);
+ }
+}
\ No newline at end of file
diff --git a/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/model/RecordList.java b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/model/RecordList.java
new file mode 100644
index 0000000..eedaae0
--- /dev/null
+++ b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/model/RecordList.java
@@ -0,0 +1,103 @@
+package org.cytoscape.coreplugin.cpath2.view.model;
+
+import org.cytoscape.coreplugin.cpath2.schemas.summary_response.SummaryResponseType;
+import org.cytoscape.coreplugin.cpath2.schemas.summary_response.BasicRecordType;
+import org.cytoscape.coreplugin.cpath2.schemas.summary_response.DataSourceType;
+import org.cytoscape.coreplugin.cpath2.util.BioPaxEntityTypeMap;
+
+import java.util.List;
+import java.util.TreeMap;
+
+/**
+ * List of BioPAX Records.
+ *
+ * @author Ethan Cerami.
+ */
+public class RecordList {
+ private SummaryResponseType summaryResponse;
+ TreeMap<String, Integer> dataSourceMap = new TreeMap<String, Integer>();
+ TreeMap<String, Integer> interactionTypeMap = new TreeMap<String, Integer>();
+
+ /**
+ * Constructor.
+ * @param summaryResponse SummaryResponseType Object.
+ */
+ public RecordList (SummaryResponseType summaryResponse) {
+ this.summaryResponse = summaryResponse;
+ catalogInteractions();
+ }
+
+ /**
+ * Gets number of records.
+ * @return number of records.
+ */
+ public int getNumRecords() {
+ if (summaryResponse != null && summaryResponse.getRecord() != null) {
+ return summaryResponse.getRecord().size();
+ } else {
+ return -1;
+ }
+ }
+
+ /**
+ * Gets the Summary Response XML.
+ * @return SummaryResponse Object.
+ */
+ public SummaryResponseType getSummaryResponse() {
+ return summaryResponse;
+ }
+
+ /**
+ * Gets catalog of data sources.
+ * @return Map<Data Source Name, # Records>
+ */
+ public TreeMap<String, Integer> getDataSourceMap() {
+ return dataSourceMap;
+ }
+
+ /**
+ * Gets catalog of entity sources.
+ * @return Map<Entity Type, # Records>
+ */
+ public TreeMap<String, Integer> getEntityTypeMap() {
+ return interactionTypeMap;
+ }
+
+ private void catalogInteractions() {
+ List<BasicRecordType> recordList = summaryResponse.getRecord();
+ if (recordList != null) {
+ for (BasicRecordType record: recordList) {
+ catalogDataSource(record.getDataSource());
+ catalogInteractionType(record);
+ // TODO: additional catalogs, as needed.
+ }
+ }
+ }
+
+ private void catalogDataSource(DataSourceType dataSource) {
+ String name = dataSource.getName();
+ Integer count = dataSourceMap.get(name);
+ if (count != null) {
+ count = count + 1;
+ } else {
+ count = 1;
+ }
+ dataSourceMap.put(name, count);
+ }
+
+ private void catalogInteractionType(BasicRecordType record) {
+ String type = record.getEntityType();
+ BioPaxEntityTypeMap map = BioPaxEntityTypeMap.getInstance();
+ if (map.containsKey(type)) {
+ type = (String) map.get(type);
+ record.setEntityType(type);
+ }
+ Integer count = interactionTypeMap.get(type);
+ if (count != null) {
+ count = count + 1;
+ } else {
+ count = 1;
+ }
+ interactionTypeMap.put(type, count);
+ }
+}
\ No newline at end of file
diff --git a/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/tree/CheckNode.java b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/tree/CheckNode.java
new file mode 100644
index 0000000..5ab1418
--- /dev/null
+++ b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/tree/CheckNode.java
@@ -0,0 +1,87 @@
+package org.cytoscape.coreplugin.cpath2.view.tree;
+
+import javax.swing.tree.DefaultMutableTreeNode;
+import java.util.Enumeration;
+
+
+/**
+ * Model for selectable nodes.
+ *
+ * Code was originally obtained from:
+ * http://www.javaresearch.org/source/javaresearch/jrlib0.6/org/jr/swing/tree/
+ *
+ * and, has since been modified.
+ *
+ */
+public class CheckNode extends DefaultMutableTreeNode {
+ public final static int SINGLE_SELECTION = 0;
+ public final static int DIG_IN_SELECTION = 4;
+ protected int selectionMode;
+ protected boolean isSelected;
+
+ /**
+ * Constructor.
+ *
+ * @param userObject User Object.
+ */
+ public CheckNode(Object userObject) {
+ this(userObject, true, false);
+ }
+
+ /**
+ * Constructor.
+ *
+ * @param userObject User Object.
+ * @param allowsChildren Node allows children.
+ * @param isSelected Node is currently selected.
+ */
+ public CheckNode(Object userObject, boolean allowsChildren, boolean isSelected) {
+ super(userObject, allowsChildren);
+ this.isSelected = isSelected;
+ setSelectionMode(DIG_IN_SELECTION);
+ }
+
+ /**
+ * Sets the selection mode.
+ *
+ * @param mode Selection mode.
+ */
+ public void setSelectionMode(int mode) {
+ selectionMode = mode;
+ }
+
+ /**
+ * Gets the selection mode.
+ * @return selection mode.
+ */
+ public int getSelectionMode() {
+ return selectionMode;
+ }
+
+ /**
+ * Sets selected / unselected.
+ *
+ * @param isSelected selected/uncselected.
+ */
+ public void setSelected(boolean isSelected) {
+ this.isSelected = isSelected;
+
+ // DIG_IN Option
+ if ((selectionMode == DIG_IN_SELECTION)
+ && (children != null)) {
+ Enumeration enum1 = children.elements();
+ while (enum1.hasMoreElements()) {
+ CheckNode node = (CheckNode) enum1.nextElement();
+ node.setSelected(isSelected);
+ }
+ }
+ }
+
+ /**
+ * Node is selected.
+ * @return true or false.
+ */
+ public boolean isSelected() {
+ return isSelected;
+ }
+}
\ No newline at end of file
diff --git a/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/tree/CheckNodeRenderer.java b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/tree/CheckNodeRenderer.java
new file mode 100644
index 0000000..5a189f8
--- /dev/null
+++ b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/tree/CheckNodeRenderer.java
@@ -0,0 +1,88 @@
+package org.cytoscape.coreplugin.cpath2.view.tree;
+
+import org.cytoscape.coreplugin.cpath2.view.GradientHeader;
+
+import javax.swing.tree.TreeCellRenderer;
+import javax.swing.*;
+import java.awt.*;
+import java.net.URL;
+
+/**
+ * Node with CheckBox Renderer.
+ *
+ * Code was originally obtained from:
+ * http://www.javaresearch.org/source/javaresearch/jrlib0.6/org/jr/swing/tree/
+ *
+ * and, has since been modified.
+*/
+public class CheckNodeRenderer implements TreeCellRenderer {
+
+ /**
+ * Gets the Tree Cell Renderer.
+ * @param tree JTree Object.
+ * @param value Object value.
+ * @param isSelected Node is selected.
+ * @param expanded Node is expanded.
+ * @param leaf Node is a leaf.
+ * @param row Row number.
+ * @param hasFocus Node has focus.
+ * @return Custom Component.
+ */
+ public Component getTreeCellRendererComponent(JTree tree, Object value,
+ boolean isSelected, boolean expanded,
+ boolean leaf, int row, boolean hasFocus) {
+ String stringValue = tree.convertValueToText(value, isSelected,
+ expanded, leaf, row, hasFocus);
+ CustomNodePanel customNodePanel = new CustomNodePanel(tree, value,
+ expanded, leaf, stringValue);
+ customNodePanel.setEnabled(tree.isEnabled());
+ return customNodePanel;
+ }
+}
+
+/**
+ * Custom Node Panel.
+ *
+ * Code was originally obtained from:
+ * http://www.javaresearch.org/source/javaresearch/jrlib0.6/org/jr/swing/tree/
+ *
+ */
+class CustomNodePanel extends JPanel {
+ private JCheckBox check;
+ private JLabel label;
+ private static URL url = GradientHeader.class.getResource("resources/stock_autofilter.png");
+ private static ImageIcon filterIcon = new ImageIcon(url);
+
+ /**
+ * Constructor.
+ * @param tree JTree Object.
+ * @param value Object value.
+ * @param expanded Node is expanded.
+ * @param leaf Node is a leaf.
+ * @param stringValue String value.
+ */
+ public CustomNodePanel(JTree tree, Object value,
+ boolean expanded, boolean leaf, String stringValue) {
+ setLayout(new BorderLayout());
+ if (leaf) {
+ add(check = new JCheckBox(), BorderLayout.WEST);
+ check.setBackground(UIManager.getColor("Tree.textBackground"));
+ check.setSelected(((CheckNode) value).isSelected());
+ check.setOpaque(false);
+ }
+ add(label = new JLabel(), BorderLayout.EAST);
+ label.setOpaque(false);
+ label.setFont(tree.getFont());
+ label.setText(stringValue);
+ if (leaf) {
+ //label.setIcon(UIManager.getIcon("Tree.leafIcon"));
+ } else if (expanded) {
+ label.setIcon(filterIcon);
+ //label.setIcon(UIManager.getIcon("Tree.openIcon"));
+ } else {
+ label.setIcon(filterIcon);
+ //label.setIcon(UIManager.getIcon("Tree.closedIcon"));
+ }
+ setOpaque(false);
+ }
+}
diff --git a/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/tree/JTreeWithCheckNodes.java b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/tree/JTreeWithCheckNodes.java
new file mode 100644
index 0000000..ef403d5
--- /dev/null
+++ b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/tree/JTreeWithCheckNodes.java
@@ -0,0 +1,80 @@
+package org.cytoscape.coreplugin.cpath2.view.tree;
+
+import javax.swing.*;
+import javax.swing.tree.TreeNode;
+import javax.swing.tree.TreeSelectionModel;
+import javax.swing.tree.TreePath;
+import javax.swing.tree.DefaultTreeModel;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+
+/**
+ * JTree with selectable leaves.
+ *
+ * Code was originally obtained from:
+ * http://www.javaresearch.org/source/javaresearch/jrlib0.6/org/jr/swing/tree/
+ *
+ * and, has since been modified.
+ */
+public class JTreeWithCheckNodes extends JTree {
+
+ /**
+ * Constructor.
+ *
+ * @param rootNode Root Node.
+ */
+ public JTreeWithCheckNodes(TreeNode rootNode) {
+ super(rootNode);
+ setCellRenderer(new CheckNodeRenderer());
+ getSelectionModel().setSelectionMode(
+ TreeSelectionModel.SINGLE_TREE_SELECTION
+ );
+ putClientProperty("JTree.lineStyle", "Angled");
+ addMouseListener(new NodeSelectionListener(this));
+ }
+}
+
+/**
+ * Listens for node selection events.
+ */
+class NodeSelectionListener extends MouseAdapter {
+ JTree tree;
+
+ /**
+ * Constructor.
+ *
+ * @param tree JTree Object.
+ */
+ NodeSelectionListener(JTree tree) {
+ this.tree = tree;
+ }
+
+ /**
+ * Mouse Click Event.
+ *
+ * @param e MouseEvent Object.
+ */
+ public void mouseClicked(MouseEvent e) {
+ int x = e.getX();
+ int y = e.getY();
+ int row = tree.getRowForLocation(x, y);
+ TreePath path = tree.getPathForRow(row);
+ if (path != null) {
+ CheckNode node = (CheckNode) path.getLastPathComponent();
+ boolean isSelected = !(node.isSelected());
+ node.setSelected(isSelected);
+ if (node.getSelectionMode() == CheckNode.DIG_IN_SELECTION) {
+ if (isSelected) {
+ tree.expandPath(path);
+ } else {
+ tree.collapsePath(path);
+ }
+ }
+ ((DefaultTreeModel) tree.getModel()).nodeChanged(node);
+ if (row == 0) {
+ tree.revalidate();
+ tree.repaint();
+ }
+ }
+ }
+}
diff --git a/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/tree/TreeDemo.java b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/tree/TreeDemo.java
new file mode 100644
index 0000000..8bfbbfe
--- /dev/null
+++ b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/view/tree/TreeDemo.java
@@ -0,0 +1,94 @@
+package org.cytoscape.coreplugin.cpath2.view.tree;
+
+import org.cytoscape.coreplugin.cpath2.view.CollapsablePanel;
+
+import java.util.*;
+import java.awt.*;
+import java.awt.event.*;
+import javax.swing.*;
+import javax.swing.tree.*;
+
+/**
+ * Tree Demo. Used to debug JTreeWithCheckNodes.
+ *
+ * Code was originally obtained from:
+ * http://www.javaresearch.org/source/javaresearch/jrlib0.6/org/jr/swing/tree/
+ *
+ * and, has since been modified.
+ */
+public class TreeDemo extends JFrame {
+
+ public TreeDemo() {
+ super("CheckNode TreeExample");
+ String[] strs = {"Filters (optional)", // 0
+ "Filter by Data Source", // 1
+ "Reactome (4)", // 2
+ "Cancer Cell Map (5)", // 3
+ "Filter by Interaction Type", // 4
+ "Protein-Protein Interactions (43)", // 5
+ "Other (52)"}; // 6
+
+ CheckNode[] nodes = new CheckNode[strs.length];
+ for (int i=0;i<strs.length;i++) {
+ nodes[i] = new CheckNode(strs[i]);
+ }
+ nodes[0].add(nodes[1]);
+ nodes[1].add(nodes[2]);
+ nodes[1].add(nodes[3]);
+ nodes[0].add(nodes[4]);
+ nodes[3].setSelected(true);
+ nodes[4].add(nodes[5]);
+ nodes[4].add(nodes[6]);
+ JTreeWithCheckNodes tree = new JTreeWithCheckNodes( nodes[0] );
+ JScrollPane sp = new JScrollPane(tree);
+
+ JTextArea textArea = new JTextArea(3,10);
+ JScrollPane textPanel = new JScrollPane(textArea);
+ JButton button = new JButton("print");
+ button.addActionListener(
+ new ButtonActionListener(nodes[0], textArea));
+ JPanel panel = new JPanel(new BorderLayout());
+ panel.add(button, BorderLayout.SOUTH);
+
+ CollapsablePanel filterPanel = new CollapsablePanel("Filters (Optional)");
+ filterPanel.getContentPane().add(sp);
+
+ getContentPane().add(filterPanel, BorderLayout.CENTER);
+ getContentPane().add(panel, BorderLayout.EAST);
+ getContentPane().add(textPanel, BorderLayout.SOUTH);
+ }
+
+ class ButtonActionListener implements ActionListener {
+ CheckNode root;
+ JTextArea textArea;
+
+ ButtonActionListener(final CheckNode root,
+ final JTextArea textArea) {
+ this.root = root;
+ this.textArea = textArea;
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ Enumeration enum1 = root.breadthFirstEnumeration();
+ while (enum1.hasMoreElements()) {
+ CheckNode node = (CheckNode)enum1.nextElement();
+ if (node.isSelected()) {
+ TreeNode[] nodes = node.getPath();
+ textArea.append("\n" + nodes[0].toString());
+ for (int i=1;i<nodes.length;i++) {
+ textArea.append("/" + nodes[i].toString());
+ }
+ }
+ }
+ }
+ }
+
+ public static void main(String args[]) {
+ TreeDemo frame = new TreeDemo();
+ frame.addWindowListener(new WindowAdapter() {
+ public void windowClosing(WindowEvent e) {System.exit(0);}
+ });
+ frame.setSize(300, 200);
+ frame.setVisible(true);
+ }
+}
\ No newline at end of file
diff --git a/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/web_service/CPathException.java b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/web_service/CPathException.java
new file mode 100644
index 0000000..f0b506f
--- /dev/null
+++ b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/web_service/CPathException.java
@@ -0,0 +1,127 @@
+package org.cytoscape.coreplugin.cpath2.web_service;
+
+/**
+ * Indicates Error Connecting to cPath.
+ *
+ * @author Ethan Cerami.
+ */
+public class CPathException extends Exception {
+ /**
+ * Error: Canceled by User.
+ */
+ public final static int ERROR_CANCELED_BY_USER = 1;
+
+ /**
+ * Error: Unknown Host.
+ */
+ public final static int ERROR_UNKNOWN_HOST = 2;
+
+ /**
+ * Error: Network IO.
+ */
+ public final static int ERROR_NETWORK_IO = 3;
+
+ /**
+ * Error: XML Parsing.
+ */
+ public final static int ERROR_XML_PARSING = 4;
+
+ /**
+ * Error: Web Service API.
+ */
+ public final static int ERROR_WEB_SERVICE_API = 5;
+
+ /**
+ * Error HTTP
+ */
+ public final static int ERROR_HTTP = 6;
+
+ private int errorCode;
+ private String errorMessage;
+ private String errorDetail;
+ private String recoveryTip;
+
+ private final static String NETWORK_RECOVERY_TIP
+ = "Please check your network settings and try again.";
+
+ private final static String SERVER_ERROR_RECOVERY_TIP
+ = "Please try a different search term, or try again later.";
+
+ /**
+ * Constructor.
+ * @param errorCode Error Code.
+ * @param t Root throwable.
+ */
+ public CPathException(int errorCode, Throwable t) {
+ super(t);
+ this.errorCode = errorCode;
+ setErrorMessages(errorCode);
+ if (t != null) {
+ errorMessage = errorMessage + " " + t.getMessage();
+ }
+ }
+
+ public CPathException(int errorCode, String errorDetail) {
+ this.errorDetail = errorDetail;
+ this.errorCode = errorCode;
+ setErrorMessages(errorCode);
+ if (errorDetail != null) {
+ errorMessage = errorMessage + " " + errorDetail;
+ }
+ }
+
+ /**
+ * Gets the Error Code.
+ * @return Error Code.
+ */
+ public int getErrorCode() {
+ return errorCode;
+ }
+
+ /**
+ * Gets Error Message.
+ * @return Error Message.
+ */
+ public String getMessage() {
+ return errorMessage;
+ }
+
+ /**
+ * Gets the Recovery Tip.
+ * @return Recovery Tip.
+ */
+ public String getRecoveryTip() {
+ return recoveryTip;
+ }
+
+ private void setErrorMessages(int errorCode) {
+ switch (errorCode) {
+ case ERROR_CANCELED_BY_USER:
+ errorMessage = "Canceled by user.";
+ break;
+ case ERROR_UNKNOWN_HOST:
+ errorMessage = "Network error occurred while tring to connect to "
+ + "remote web service.";
+ recoveryTip = NETWORK_RECOVERY_TIP;
+ break;
+ case ERROR_NETWORK_IO:
+ errorMessage = "Network error occurred while tring to connect to "
+ + "remote web service.";
+ recoveryTip = NETWORK_RECOVERY_TIP;
+ break;
+ case ERROR_XML_PARSING:
+ errorMessage = "Error occurred while trying to parse XML results "
+ + "retrieved from remote web service.";
+ break;
+ case ERROR_HTTP:
+ errorMessage = "Network error occurred while trying to connect to "
+ + "remote web service.";
+ recoveryTip = SERVER_ERROR_RECOVERY_TIP;
+ break;
+ case ERROR_WEB_SERVICE_API:
+ errorMessage = "Error occurred while trying to connect to remote web service. ";
+ recoveryTip = SERVER_ERROR_RECOVERY_TIP;
+ break;
+ }
+ }
+}
diff --git a/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/web_service/CPathProperties.java b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/web_service/CPathProperties.java
new file mode 100644
index 0000000..f06401d
--- /dev/null
+++ b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/web_service/CPathProperties.java
@@ -0,0 +1,209 @@
+package org.cytoscape.coreplugin.cpath2.web_service;
+
+import cytoscape.CytoscapeInit;
+import cytoscape.plugin.PluginProperties;
+
+import java.util.Properties;
+import java.util.ArrayList;
+
+import org.cytoscape.coreplugin.cpath2.view.model.Organism;
+
+/**
+ * Contains cPath Specific Properties
+ *
+ * @author Ethan Cerami.
+ */
+public class CPathProperties {
+ /**
+ * Property: CPath2 Read Location.
+ */
+ public static final String CPATH_URL = new String("cpath2.server_url");
+
+ /**
+ * Property: CPath2 Server Name.
+ */
+ public static final String CPATH_INSTANCE_BNAME = new String("cpath2.server_name");
+
+ /**
+ * Property: CPath2 Server Blurb
+ */
+ public static final String CPATH_INSTANCE_BLURB = new String ("cpath2.server_blurb");
+
+ /**
+ * Property: Icon Tool Tip
+ */
+ public static final String ICON_TOOL_TIP = new String ("cpath2.icon_tool_tip");
+
+ /**
+ * Property: Icon File
+ */
+ public static final String ICON_FILE_NAME = new String ("cpath2.icon_file_name");
+
+ /**
+ * Property: Organism.
+ */
+ public static final String ORGANISM_PREFIX = new String ("cpath2.organism");
+
+ /**
+ * Download Networks in Full BioPAX Mode.
+ */
+ public final static int DOWNLOAD_FULL_BIOPAX = 1;
+
+ /**
+ * Download Networks in Binary SIF Reduced Mode
+ */
+ public final static int DOWNLOAD_REDUCED_BINARY_SIF = 2;
+
+
+ private static CPathProperties cpathProperties;
+ private static String cPathUrl;
+ private static String serverName;
+ private static String blurb;
+ private static String iconToolTip;
+ private static String iconFileName;
+ private static ArrayList<Organism> organismList = new ArrayList<Organism>();
+ private int downloadMode = DOWNLOAD_REDUCED_BINARY_SIF;
+
+ /**
+ * Gets singleton instance of cPath Properties.
+ * @return CPathProperties class.
+ */
+ public static CPathProperties getInstance() {
+ if (cpathProperties == null) {
+ cpathProperties = new CPathProperties();
+ cpathProperties.initProperties (new Properties());
+ }
+ return cpathProperties;
+ }
+
+ private CPathProperties () {
+ // no-op; private constructor;
+ }
+
+ public void initProperties (Properties pluginProperties) {
+ cPathUrl = pluginProperties.getProperty(CPATH_URL);
+
+ if (cPathUrl == null) {
+ cPathUrl = "http://www.pathwaycommons.org/pc/webservice.do";
+ }
+
+ serverName = pluginProperties.getProperty(CPATH_INSTANCE_BNAME);
+ if (serverName == null) {
+ serverName = "Pathway Commons";
+ }
+
+ iconToolTip = pluginProperties.getProperty(ICON_TOOL_TIP);
+ if (iconToolTip == null) {
+ iconToolTip = "Retrieve Pathway Data from PathwayCommons.org";
+ }
+
+ iconFileName = pluginProperties.getProperty(ICON_FILE_NAME);
+ if (iconFileName == null) {
+ iconFileName = "pc.png";
+ }
+
+ blurb = pluginProperties.getProperty(CPATH_INSTANCE_BLURB);
+ if (blurb == null) {
+ blurb = "<span class='bold'>Pathway Commons</span> is a convenient point of access " +
+ "to biological pathway " +
+ "information collected from public pathway databases, which you can " +
+ "browse or search. <BR><BR>Pathways include biochemical reactions, complex " +
+ "assembly, transport and catalysis events, and physical interactions " +
+ "involving proteins, DNA, RNA, small molecules and complexes.";
+ }
+
+ int index = 0;
+ String orgField = pluginProperties.getProperty(ORGANISM_PREFIX + index);
+ while (orgField != null) {
+ String parts[] = orgField.split(":");
+ Organism organism = new Organism();
+ if (parts != null && parts.length == 2) {
+ organism.setSpeciesName(parts[0]);
+ try {
+ organism.setNcbiTaxonomyId(Integer.parseInt(parts[1]));
+ organismList.add(organism);
+ } catch(NumberFormatException e) {
+ }
+ }
+ index++;
+ orgField = pluginProperties.getProperty(ORGANISM_PREFIX + index);
+ }
+
+ }
+
+ /**
+ * Gets URL for cPath Web Service API.
+ *
+ * @return cPath URL.
+ */
+ public String getCPathUrl() {
+ return cPathUrl;
+ }
+
+ /**
+ * Gets Name of cPath Instance.
+ *
+ * @return cPath URL.
+ */
+ public String getCPathServerName() {
+ return serverName;
+ }
+
+ /**
+ * Gets the Web Services ID.
+ * @return Web Service ID.
+ */
+ public String getWebServicesId() {
+ String temp = serverName.toLowerCase();
+ return temp.replaceAll(" ", "_");
+ }
+
+ /**
+ * Gets Text Blurb for cPath Instance
+ *
+ * @return cPath URL.
+ */
+ public String getCPathBlurb() {
+ return blurb;
+ }
+
+ /**
+ * Gets the Icon Tool Tip.
+ * @return Gets the Icon Tool Tip.
+ */
+ public String getIconToolTip() {
+ return iconToolTip;
+ }
+
+ /**
+ * Gets the Icon File Name.
+ * @return Icon File Name.
+ */
+ public String getIconFileName() {
+ return iconFileName;
+ }
+
+ /**
+ * Gets Download Mode.
+ * @return DOWNLOAD_FULL_BIOPAX or DOWNLOAD_REDUCED_BINARY_SIF.
+ */
+ public int getDownloadMode() {
+ return downloadMode;
+ }
+
+ /**
+ * Sets Download Mode.
+ * @param downloadMode DOWNLOAD_FULL_BIOPAX or DOWNLOAD_REDUCED_BINARY_SIF.
+ */
+ public void setDownloadMode(int downloadMode) {
+ this.downloadMode = downloadMode;
+ }
+
+ /**
+ * Gets the Organism List.
+ * @return ArrayList of <Organism> Objects.
+ */
+ public ArrayList<Organism> getOrganismList() {
+ return organismList;
+ }
+}
\ No newline at end of file
diff --git a/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/web_service/CPathProtocol.java b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/web_service/CPathProtocol.java
new file mode 100644
index 0000000..8316cc7
--- /dev/null
+++ b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/web_service/CPathProtocol.java
@@ -0,0 +1,447 @@
+package org.cytoscape.coreplugin.cpath2.web_service;
+
+import org.apache.commons.httpclient.methods.GetMethod;
+import org.apache.commons.httpclient.methods.PostMethod;
+import org.apache.commons.httpclient.HttpClient;
+import org.apache.commons.httpclient.HttpStatus;
+import org.apache.commons.httpclient.NameValuePair;
+import org.apache.commons.httpclient.HttpMethodBase;
+import org.jdom.input.SAXBuilder;
+import org.jdom.Document;
+import org.jdom.JDOMException;
+import org.jdom.Element;
+import cytoscape.logger.CyLogger;
+import cytoscape.task.TaskMonitor;
+import cytoscape.util.ProxyHandler;
+
+import java.io.*;
+import java.net.UnknownHostException;
+import java.net.SocketException;
+import java.net.Proxy;
+import java.net.URLEncoder;
+
+/**
+ * Utility Class for Connecting to the cPath Web Service API.
+ *
+ * @author Ethan Cerami
+ */
+public class CPathProtocol {
+
+ /**
+ * The CPath Web Service Path.
+ */
+ public static final String WEB_SERVICE_PATH = "webservice.do";
+
+ /**
+ * Command Argument.
+ */
+ public static final String ARG_COMMAND = "cmd";
+
+ /**
+ * Query Argument.
+ */
+ public static final String ARG_QUERY = "q";
+
+ /**
+ * Format Argument.
+ */
+ public static final String ARG_FORMAT = "output";
+
+ /**
+ * Organism Argument.
+ */
+ public static final String ARG_ORGANISM = "organism";
+
+ /**
+ * Max Hits Argument.
+ */
+ public static final String ARG_MAX_HITS = "maxHits";
+
+ /**
+ * Start Index Argument.
+ */
+ public static final String ARG_START_INDEX = "startIndex";
+
+ /**
+ * Version Argument.
+ */
+ public static final String ARG_VERSION = "version";
+
+ /**
+ * Count Only Format.
+ */
+ public static final String FORMAT_COUNT_ONLY = "count_only";
+
+ /**
+ * Currently Supported Version.
+ */
+ public static final String CURRENT_VERSION = "3.0";
+
+ /**
+ * Get Records By Keyword.
+ */
+ public static final String COMMAND_SEARCH ="search";
+
+ /**
+ * Gets Parent Summaries.
+ */
+ public static final String COMMAND_GET_PARENTS = "get_parents";
+
+ /**
+ * Get Interactions By Interactor Name / Xref.
+ */
+ public static final String COMMAND_GET_BY_INTERACTOR_XREF =
+ "get_by_interactor_name_xref";
+
+ /**
+ * Get Interactions By Organism.
+ */
+ public static final String COMMAND_GET_BY_ORGANISM =
+ "get_by_organism";
+
+ /**
+ * Get Interactions By Experiment Type.
+ */
+ public static final String COMMAND_GET_BY_EXPERIMENT_TYPE =
+ "get_by_experiment_type";
+
+ /**
+ * Get Interactions by PMID.
+ */
+ public static final String COMMAND_GET_BY_PMID =
+ "get_by_pmid";
+
+ /**
+ * Get Interactions By Database.
+ */
+ public static final String COMMAND_GET_BY_DATABASE =
+ "get_by_database";
+
+ /**
+ * Get Top Level Pathway List.
+ */
+ public static final String COMMAND_GET_TOP_LEVEL_PATHWAY_LIST =
+ "get_top_level_pathway_list";
+
+ /**
+ * Get Patheway record by CPath ID.
+ */
+ public static final String COMMAND_GET_RECORD_BY_CPATH_ID =
+ "get_record_by_cpath_id";
+
+ /**
+ * Default for Max Hits.
+ */
+ public static final int DEFAULT_MAX_HITS = 10;
+
+ /**
+ * Not Specified
+ */
+ public static final int NOT_SPECIFIED = -1;
+
+ /**
+ * XML Tag.
+ */
+ private static final String XML_TAG = "xml";
+
+ /*** Default initial size of the response buffer if content length is unknown. */
+ private static final int DEFAULT_INITIAL_BUFFER_SIZE = 4*1024; // 4 kB
+
+ private String command;
+ private String query;
+ private int taxonomyId;
+ private int maxHits;
+ private int startIndex;
+ private String format;
+ private String baseUrl;
+ private volatile HttpMethodBase method;
+ private boolean cancelledByUser = false;
+ private static boolean debug = false;
+ private CyLogger logger = CyLogger.getLogger(CPathProtocol.class);
+
+ /**
+ * Constructor.
+ */
+ public CPathProtocol() {
+ this.baseUrl = CPathProperties.getInstance().getCPathUrl();
+ this.maxHits = DEFAULT_MAX_HITS;
+ this.taxonomyId = NOT_SPECIFIED;
+ }
+
+ /**
+ * Sets the Command Argument.
+ *
+ * @param command Command Argument.
+ */
+ public void setCommand (String command) {
+ this.command = command;
+ }
+
+ /**
+ * Sets the Query Argument.
+ *
+ * @param query Query Argument.
+ */
+ public void setQuery (String query) {
+ this.query = query;
+ }
+
+ /**
+ * Sets the Format Argument.
+ *
+ * @param format Format Argument.
+ */
+ public void setFormat (CPathResponseFormat format) {
+ this.format = format.getFormatString();
+ }
+
+ /**
+ * Sets the Organism Argument.
+ *
+ * @param taxonomyId NCBI TaxonomyID
+ */
+ public void setOrganism (int taxonomyId) {
+ this.taxonomyId = taxonomyId;
+ }
+
+ /**
+ * Sets the MaxHits Argument.
+ *
+ * @param maxHits Max Number of Hits.
+ */
+ public void setMaxHits (int maxHits) {
+ this.maxHits = maxHits;
+ }
+
+ /**
+ * Sets the StartIndex Argument.
+ *
+ * @param startIndex StartIndex Argument.
+ */
+ public void setStartIndex (int startIndex) {
+ this.startIndex = startIndex;
+ }
+
+ /**
+ * Abort the Request.
+ */
+ public void abort() {
+ if (method != null) {
+ cancelledByUser = true;
+ method.abort();
+ }
+ }
+
+ /**
+ * Connects to cPath Web Service API.
+ *
+ * @return XML Document.
+ * @throws CPathException Indicates Error connecting.
+ * @throws EmptySetException All went all, but no results found.
+ */
+ public String connect (TaskMonitor taskMonitor) throws CPathException, EmptySetException {
+ try {
+ NameValuePair[] nvps;
+
+ // Create an instance of HttpClient.
+ HttpClient client = new HttpClient();
+ setProxyInfo(client);
+
+ // Create a method instance.
+ // If the query string is long, use POST. Otherwise, use GET.
+ if (query != null && query.length() > 100) {
+ nvps = createNameValuePairs(true);
+ method = new PostMethod(baseUrl);
+ ((PostMethod)(method)).addParameters(nvps);
+ logger.info("Connect: " + method.getURI() + " (via POST)");
+ } else {
+ nvps = createNameValuePairs(false);
+ String liveUrl = createURI(baseUrl, nvps);
+ method = new GetMethod(liveUrl);
+ logger.info("Connect: " + liveUrl);
+ }
+
+ int statusCode = client.executeMethod(method);
+
+ // Check status code
+ checkHttpStatusCode(statusCode);
+
+ // Read in Content
+ InputStream instream = method.getResponseBodyAsStream();
+ long contentLength = method.getResponseContentLength();
+ if (contentLength > 0) {
+ if (taskMonitor != null) {
+ taskMonitor.setPercentCompleted(0);
+ }
+ }
+
+ ByteArrayOutputStream outstream = new ByteArrayOutputStream(
+ contentLength > 0 ? (int) contentLength : DEFAULT_INITIAL_BUFFER_SIZE);
+ byte[] buffer = new byte[4096];
+ int len;
+ int totalBytes = 0;
+ while ((len = instream.read(buffer)) > 0) {
+ outstream.write(buffer, 0, len);
+ totalBytes = updatePercentComplete(contentLength, len, totalBytes, taskMonitor);
+ }
+ instream.close();
+
+ String content = new String(outstream.toByteArray());
+ if (content.toLowerCase().indexOf(XML_TAG) >= 0) {
+ // Check for protocol errors.
+ if (content.indexOf("<error>") >=0) {
+ StringReader reader = new StringReader(content);
+ SAXBuilder builder = new SAXBuilder();
+ Document document = builder.build(reader);
+ checkForErrors(document);
+ }
+ return content.trim();
+ } else {
+ return content.trim();
+ }
+ } catch (UnknownHostException e) {
+ throw new CPathException(CPathException.ERROR_UNKNOWN_HOST, e);
+ } catch (SocketException e) {
+ if (cancelledByUser) {
+ throw new CPathException(CPathException.ERROR_CANCELED_BY_USER, e);
+ } else {
+ throw new CPathException(CPathException.ERROR_NETWORK_IO, e);
+ }
+ } catch (IOException e) {
+ throw new CPathException(CPathException.ERROR_NETWORK_IO, e);
+ } catch (JDOMException e) {
+ throw new CPathException(CPathException.ERROR_XML_PARSING, e);
+ }
+ }
+
+ /**
+ * Sets Proxy Information (if set).
+ */
+ private void setProxyInfo(HttpClient client) {
+ Proxy proxyServer = ProxyHandler.getProxyServer();
+
+ // The java.net.Proxy object does not provide getters for host and port.
+ // So, we have to hack it by using the toString() method.
+
+ // Note to self for future reference: I was able to test all this code
+ // by downloading and installing Privoxy, a local HTTP proxy,
+ // available at: http://www.privoxy.org/. Once it was running, I used the
+ // following props in ~/.cytoscape/cytoscape.props:
+ // proxy.server=127.0.0.1
+ // proxy.server.port=8118
+ // proxy.server.type=HTTP
+ if (proxyServer != null) {
+ String proxyAddress = proxyServer.toString();
+ if (debug) logger.debug("full proxy string: " + proxyAddress);
+ String[] addressComponents = proxyAddress.split("@");
+ if (addressComponents.length == 2) {
+ String parts[] = addressComponents[1].split(":");
+ if (parts.length == 2) {
+ String hostString = parts[0].trim();
+ String hostParts[] = hostString.split("/");
+ if (hostParts.length > 0) {
+ String host = hostParts[0].trim();
+ String port = parts[1].trim();
+ if (debug) logger.debug("proxy host: " + host);
+ if (debug) logger.debug("proxy port: " + port);
+ client.getHostConfiguration().setProxy(host, Integer.parseInt(port));
+ }
+ }
+ }
+ }
+ }
+
+ private int updatePercentComplete(long contentLength, int len, int totalBytes,
+ TaskMonitor taskMonitor) {
+ if (contentLength > 0) {
+ totalBytes += len;
+ int percentComplete = (int) (100.0 * (totalBytes / (double) contentLength));
+ if (taskMonitor != null) {
+ taskMonitor.setPercentCompleted(percentComplete);
+ }
+ if (debug) {
+ try {
+ Thread.sleep(200);
+ } catch (InterruptedException e) {
+ e.printStackTrace();
+ }
+ }
+ }
+ return totalBytes;
+ }
+
+ /**
+ * Gets URI
+ *
+ * @return URI.
+ */
+ public String getURI () {
+ NameValuePair[] nvps = createNameValuePairs(false);
+ return createURI(baseUrl, nvps);
+ }
+
+ /**
+ * Gets URI of cPath Call.
+ *
+ * @return URI for cPath Call.
+ */
+ private String createURI (String url, NameValuePair[] nvps) {
+ StringBuffer buf = new StringBuffer(url);
+ buf.append("?");
+ for (int i = 0; i < nvps.length; i++) {
+ buf.append(nvps[i].getName() + "=" + nvps[i].getValue() + "&");
+ }
+ return buf.toString();
+ }
+
+ private NameValuePair[] createNameValuePairs (boolean post) {
+ NameValuePair nvps[] = null;
+ if (taxonomyId == NOT_SPECIFIED) {
+ nvps = new NameValuePair[6];
+ } else {
+ nvps = new NameValuePair[7];
+ nvps[6] = new NameValuePair(ARG_ORGANISM,
+ Integer.toString(taxonomyId));
+ }
+ nvps[0] = new NameValuePair(ARG_COMMAND, command);
+ try {
+ if (!post) {
+ nvps[1] = new NameValuePair(ARG_QUERY, URLEncoder.encode(query, "UTF-8"));
+ } else {
+ nvps[1] = new NameValuePair(ARG_QUERY, query);
+ }
+ } catch (UnsupportedEncodingException e) {
+ e.printStackTrace();
+ }
+ nvps[2] = new NameValuePair(ARG_FORMAT, format);
+ nvps[3] = new NameValuePair(ARG_VERSION, CURRENT_VERSION);
+ nvps[4] = new NameValuePair(ARG_MAX_HITS, Integer.toString(maxHits));
+ nvps[5] = new NameValuePair(ARG_START_INDEX,
+ Integer.toString(startIndex));
+ return nvps;
+ }
+
+ private void checkHttpStatusCode (int statusCode)
+ throws CPathException {
+ if (statusCode != 200) {
+ throw new CPathException(CPathException.ERROR_HTTP, "HTTP Status Code: " + statusCode
+ + ": " + HttpStatus.getStatusText(statusCode) + ".");
+ }
+ }
+
+ private void checkForErrors (Document document)
+ throws CPathException, EmptySetException {
+ Element element = document.getRootElement();
+ String name = element.getName();
+ if (name.equals("error")) {
+ String errorCode = element.getChild("error_code").getText();
+ String errorMsg = element.getChild("error_msg").getText();
+ if (errorCode.equals("460")) {
+ throw new EmptySetException();
+ } else {
+ throw new CPathException(CPathException.ERROR_WEB_SERVICE_API,
+ "Error Code: " + errorCode + ", " + errorMsg + ".");
+ }
+ }
+ }
+}
diff --git a/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/web_service/CPathResponseFormat.java b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/web_service/CPathResponseFormat.java
new file mode 100644
index 0000000..6f824b5
--- /dev/null
+++ b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/web_service/CPathResponseFormat.java
@@ -0,0 +1,57 @@
+package org.cytoscape.coreplugin.cpath2.web_service;
+
+/**
+ * CPath Response Format.
+ */
+public class CPathResponseFormat {
+ private String format;
+
+ /**
+ * BioPAX Format.
+ */
+ public static CPathResponseFormat BIOPAX = new CPathResponseFormat ("biopax");
+
+ /**
+ * Simplified Binary SIF Format.
+ */
+ public static CPathResponseFormat BINARY_SIF = new CPathResponseFormat ("binary_sif");
+
+ /**
+ * Generic XML Format.
+ */
+ public static CPathResponseFormat GENERIC_XML = new CPathResponseFormat ("xml");
+
+ /**
+ * Gets the Proper cPath Response Format.
+ * @param format Format String.
+ * @return CPathResponseFormat Object.
+ */
+ public static CPathResponseFormat getResponseFormat (String format) {
+ if (format.equals(BIOPAX.getFormatString())) {
+ return BIOPAX;
+ } else if (format.equals(BINARY_SIF.getFormatString())) {
+ return BINARY_SIF;
+ } else if (format.equals(GENERIC_XML.getFormatString())) {
+ return GENERIC_XML;
+ }
+ else {
+ throw new IllegalArgumentException ("Format: " + format + " is not valid.");
+ }
+ }
+
+ /**
+ * Private Constructor.
+ * @param format Format String.
+ */
+ private CPathResponseFormat(String format) {
+ this.format = format;
+ }
+
+ /**
+ * Gets the format string.
+ * @return format string.
+ */
+ public String getFormatString() {
+ return this.format;
+ }
+}
diff --git a/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/web_service/CPathWebService.java b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/web_service/CPathWebService.java
new file mode 100644
index 0000000..bfe4650
--- /dev/null
+++ b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/web_service/CPathWebService.java
@@ -0,0 +1,103 @@
+package org.cytoscape.coreplugin.cpath2.web_service;
+
+import javax.xml.bind.Unmarshaller;
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBElement;
+import java.util.ArrayList;
+import java.util.List;
+import java.io.StringReader;
+import java.io.File;
+
+import cytoscape.task.TaskMonitor;
+import org.cytoscape.coreplugin.cpath2.schemas.search_response.*;
+import org.cytoscape.coreplugin.cpath2.schemas.summary_response.SummaryResponseType;
+
+/**
+ * Interface for accessing the cPath Web API.
+ *
+ * @author Ethan Cerami
+ */
+public interface CPathWebService {
+
+ /**
+ * Searches for Physical Entities in cPath Instance.
+ * Given a keyword, such as "BRCA1", this method returns the first 10 physical entities
+ * which contain this keyword. For each matching physical entity, you will receive
+ * entity details, such as name, synonyms, external links, and list of all pathways in
+ * which this entity participates.
+ *
+ * @param keyword Keyword to search for.
+ * @param ncbiTaxonomyId Organism filter (-1 to to search all organisms).
+ * @param taskMonitor TaskMonitor Object (can be null);
+ * @return SearchResponseType Object.
+ * @throws CPathException CPath Connect Error.
+ * @throws EmptySetException No matches found to specified query.
+ */
+ public SearchResponseType searchPhysicalEntities(String keyword, int ncbiTaxonomyId,
+ TaskMonitor taskMonitor) throws CPathException, EmptySetException;
+
+ /**
+ * Gets parent summaries for specified record.
+ * For example, if primaryId refers to protein A, the "parent" records are all
+ * interactions in which protein A participates. If primaryId refers to interaction X,
+ * the "parent" records are all parent interactions which control or modulate X.
+ * To retrieve the full record (instead of just the summary), you must extract the primary
+ * ID, and follow-up with a call to getRecordsByIds().
+ *
+ * @param primaryId Primary ID of Record.
+ * @param taskMonitor Task Monitor Object.
+ * @return SummaryResponse Object.
+ * @throws CPathException CPath Error.
+ * @throws EmptySetException Empty Set Error.
+ */
+ public SummaryResponseType getParentSummaries (long primaryId, TaskMonitor taskMonitor)
+ throws CPathException, EmptySetException;
+
+ /**
+ * Gets One or more records by primary ID.
+ * You can obtain primary IDs for physical entities and/or pathways via the
+ * searchPhysicalEntities() method.
+ *
+ * @param ids Array of Primary IDs.
+ * @param format CPathResponseFormat.BIOPAX or CPathResponseFormat.BINARY_SIF.
+ * @param taskMonitor Task Monitor Object.
+ * @return BioPAX XML String or SIF String.
+ * @throws CPathException CPath Error.
+ * @throws EmptySetException Empty Set Error.
+ */
+ public String getRecordsByIds(long[] ids, CPathResponseFormat format, TaskMonitor taskMonitor)
+ throws CPathException, EmptySetException;
+
+ /**
+ * Gets a list of all Organisms currently available within the cPath instance.
+ *
+ * @return ArrayList of Organism Type Objects.
+ */
+ public ArrayList<OrganismType> getOrganismList();
+
+ /**
+ * Abort the Request.
+ */
+ public void abort();
+
+ /**
+ * Registers a new listener.
+ *
+ * @param listener CPathWebService Listener.
+ */
+ public void addApiListener(CPathWebServiceListener listener);
+
+ /**
+ * Removes the specified listener.
+ *
+ * @param listener CPathWebService Listener.
+ */
+ public void removeApiListener(CPathWebServiceListener listener);
+
+ /**
+ * Gets the list of all registered listeners.
+ *
+ * @return ArrayList of CPathWebServiceListener Objects.
+ */
+ public ArrayList<CPathWebServiceListener> getListeners();
+}
\ No newline at end of file
diff --git a/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/web_service/CPathWebServiceImpl.java b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/web_service/CPathWebServiceImpl.java
new file mode 100644
index 0000000..bc249d6
--- /dev/null
+++ b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/web_service/CPathWebServiceImpl.java
@@ -0,0 +1,261 @@
+package org.cytoscape.coreplugin.cpath2.web_service;
+
+import org.cytoscape.coreplugin.cpath2.schemas.search_response.*;
+import org.cytoscape.coreplugin.cpath2.schemas.summary_response.SummaryResponseType;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.io.StringReader;
+
+import cytoscape.task.TaskMonitor;
+
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.Unmarshaller;
+import javax.xml.bind.JAXBElement;
+
+/**
+ * Class for accessing the cPath Web API.
+ *
+ * @author Ethan Cerami
+ */
+public class CPathWebServiceImpl implements CPathWebService {
+ private static ArrayList<CPathWebServiceListener> listeners =
+ new ArrayList<CPathWebServiceListener>();
+ private volatile CPathProtocol protocol;
+ private static CPathWebService webApi;
+
+ /**
+ * Gets Singelton instance of CPath Web API.
+ * @return CPathWebService Object.
+ */
+ public static CPathWebService getInstance() {
+ if (webApi == null) {
+ webApi = new CPathWebServiceImpl();
+ }
+ return webApi;
+ }
+
+ /**
+ * Private Constructor.
+ */
+ private CPathWebServiceImpl() {
+ }
+
+ /**
+ * Searches Physical Entities in cPath Instance.
+ *
+ * @param keyword Keyword to search for.
+ * @param ncbiTaxonomyId Organism filter (-1 to to search all organisms)
+ * @return SearchResponseType Object.
+ */
+ public SearchResponseType searchPhysicalEntities(String keyword, int ncbiTaxonomyId,
+ TaskMonitor taskMonitor) throws CPathException, EmptySetException {
+
+ // Notify all listeners of start
+ for (int i = listeners.size() - 1; i >= 0; i--) {
+ CPathWebServiceListener listener = listeners.get(i);
+ listener.searchInitiatedForPhysicalEntities(keyword, ncbiTaxonomyId);
+ }
+
+ protocol = new CPathProtocol();
+ protocol.setCommand(CPathProtocol.COMMAND_SEARCH);
+ protocol.setOrganism(ncbiTaxonomyId);
+ protocol.setFormat(CPathResponseFormat.GENERIC_XML);
+ protocol.setQuery(keyword);
+
+ SearchResponseType searchResponse;
+ if (keyword.equalsIgnoreCase("dummy")) {
+ searchResponse = this.createDummySearchResults();
+ searchResponse.setTotalNumHits(10L);
+ } else {
+ String responseXml = protocol.connect(taskMonitor);
+ StringReader reader = new StringReader(responseXml);
+
+ Class[] classes = new Class[2];
+ classes[0] = org.cytoscape.coreplugin.cpath2.schemas.search_response.SearchResponseType.class;
+ classes[1] = org.cytoscape.coreplugin.cpath2.schemas.search_response.ObjectFactory.class;
+ try {
+ JAXBContext jc = JAXBContext.newInstance(classes);
+ Unmarshaller u = jc.createUnmarshaller();
+ JAXBElement element = (JAXBElement) u.unmarshal(reader);
+ searchResponse = (SearchResponseType) element.getValue();
+ } catch(Throwable e){
+ throw new CPathException(CPathException.ERROR_XML_PARSING, e);
+ }
+ }
+
+ //SearchResponseType searchResponse = createDummySearchResults();
+ // Notify all listeners of end
+ for (int i = listeners.size() - 1; i >= 0; i--) {
+ CPathWebServiceListener listener = listeners.get(i);
+ listener.searchCompletedForPhysicalEntities(searchResponse);
+ }
+ return searchResponse;
+ }
+
+ /**
+ * Gets parent summaries for specified record.
+ *
+ * @param primaryId Primary ID of Record.
+ * @param taskMonitor Task Monitor Object.
+ * @return SummaryResponse Object.
+ * @throws CPathException CPath Error.
+ * @throws EmptySetException Empty Set Error.
+ */
+ public SummaryResponseType getParentSummaries (long primaryId, TaskMonitor taskMonitor)
+ throws CPathException, EmptySetException {
+ // Notify all listeners of start
+ for (int i = listeners.size() - 1; i >= 0; i--) {
+ CPathWebServiceListener listener = listeners.get(i);
+ listener.requestInitiatedForParentSummaries(primaryId);
+ }
+
+ protocol = new CPathProtocol();
+ protocol.setCommand(CPathProtocol.COMMAND_GET_PARENTS);
+ protocol.setFormat(CPathResponseFormat.GENERIC_XML);
+
+ protocol.setQuery(Long.toString(primaryId));
+
+ SummaryResponseType summaryResponse;
+ String responseXml = protocol.connect(taskMonitor);
+ StringReader reader = new StringReader(responseXml);
+
+ Class[] classes = new Class[2];
+ classes[0] = org.cytoscape.coreplugin.cpath2.schemas.summary_response.SummaryResponseType.class;
+ classes[1] = org.cytoscape.coreplugin.cpath2.schemas.summary_response.ObjectFactory.class;
+ try {
+ JAXBContext jc = JAXBContext.newInstance(classes);
+ Unmarshaller u = jc.createUnmarshaller();
+ JAXBElement element = (JAXBElement) u.unmarshal(reader);
+ summaryResponse = (SummaryResponseType) element.getValue();
+ } catch(Throwable e){
+ throw new CPathException(CPathException.ERROR_XML_PARSING, e);
+ }
+
+ // Notify all listeners of end
+ for (int i = listeners.size() - 1; i >= 0; i--) {
+ CPathWebServiceListener listener = listeners.get(i);
+ listener.requestCompletedForParentSummaries(primaryId, summaryResponse);
+ }
+ return summaryResponse;
+ }
+
+ /**
+ * Gets One or more records by Primary ID.
+ * @param ids Array of Primary IDs.
+ * @param format CPathResponseFormat Object.
+ * @param taskMonitor Task Monitor Object.
+ * @return BioPAX XML String.
+ * @throws CPathException CPath Error.
+ * @throws EmptySetException Empty Set Error.
+ */
+ public String getRecordsByIds(long[] ids, CPathResponseFormat format,
+ TaskMonitor taskMonitor) throws CPathException, EmptySetException {
+ protocol = new CPathProtocol();
+ protocol.setCommand(CPathProtocol.COMMAND_GET_RECORD_BY_CPATH_ID);
+ protocol.setFormat(format);
+ StringBuffer q = new StringBuffer();
+ for (int i=0; i<ids.length; i++) {
+ q.append (Long.toString(ids[i])+",");
+ }
+ protocol.setQuery(q.toString());
+ String xml = protocol.connect(taskMonitor);
+ return xml;
+ }
+
+ /**
+ * Abort the Request.
+ */
+ public void abort() {
+ protocol.abort();
+ }
+
+ private SearchResponseType createDummySearchResults() {
+ SearchResponseType searchResponse = new SearchResponseType();
+ List<ExtendedRecordType> searchHits = searchResponse.getSearchHit();
+ for (int i = 0; i < 10; i++) {
+ ExtendedRecordType searchHit = new ExtendedRecordType();
+ searchHit.setName("Protein " + i);
+
+ OrganismType organism = new OrganismType();
+ organism.setCommonName("Human");
+ organism.setSpeciesName("Homo Sapiens");
+ searchHit.setOrganism(organism);
+
+ List synList = new ArrayList();
+ synList.add("Synonym 1");
+ synList.add("Synonym 2");
+ synList.add("Synonym 3");
+ synList.add("Synonym 4");
+ searchHit.getSynonym().addAll(synList);
+
+ List <XRefType> xrefList = new ArrayList();
+ for (int j=0; j<3; j++) {
+ XRefType xref = new XRefType();
+ xref.setDb("Database_" + j);
+ xref.setId("ID_" + j);
+ xref.setUrl("http://www.yahoo.com");
+ xrefList.add(xref);
+ }
+ searchHit.getXref().addAll(xrefList);
+
+ List extracts = searchHit.getExcerpt();
+ extracts.add ("Vestibulum pharetra <B>laoreet ante</B> dictum dolor sed, "
+ + "elementum egestas nunc nullam, pede mauris mattis, eros nam, elit "
+ + "aliquam lorem vestibulum duis a tortor. Adipiscing elit habitant justo, "
+ + "nonummy nunc wisi eros, dictum eget orci placerat metus vehicula eu.");
+
+ ObjectFactory factory = new ObjectFactory();
+ PathwayListType pathwayListType = factory.createPathwayListType();
+ List <PathwayType> pathwayList = pathwayListType.getPathway();
+ searchHit.setPathwayList(pathwayListType);
+ for (int j = 0; j < 10; j++) {
+ PathwayType pathwaySummary = new PathwayType();
+ pathwaySummary.setName("Pathway " + j + "[" + i + "]");
+ pathwaySummary.setPrimaryId((long) j);
+ DataSourceType dataSource = new DataSourceType();
+ dataSource.setName("Data Source " + j);
+ pathwaySummary.setDataSource(dataSource);
+ pathwayList.add(pathwaySummary);
+ }
+ searchHits.add(searchHit);
+ }
+ return searchResponse;
+ }
+
+ /**
+ * Gets a list of all Organisms currently available within cPath instance.
+ *
+ * @return ArrayList of Organism Type Objects.
+ */
+ public ArrayList<OrganismType> getOrganismList() {
+ throw new UnsupportedOperationException("getOrganismList() is not yet implemented.");
+ }
+
+ /**
+ * Registers a new listener.
+ *
+ * @param listener CPathWebService Listener.
+ */
+ public void addApiListener(CPathWebServiceListener listener) {
+ listeners.add(listener);
+ }
+
+ /**
+ * Removes the specified listener.
+ *
+ * @param listener CPathWebService Listener.
+ */
+ public void removeApiListener(CPathWebServiceListener listener) {
+ listeners.remove(listener);
+ }
+
+ /**
+ * Gets the list of all registered listeners.
+ *
+ * @return ArrayList of CPathWebServiceListener Objects.
+ */
+ public ArrayList<CPathWebServiceListener> getListeners() {
+ return listeners;
+ }
+}
diff --git a/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/web_service/CPathWebServiceListener.java b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/web_service/CPathWebServiceListener.java
new file mode 100644
index 0000000..0e715b4
--- /dev/null
+++ b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/web_service/CPathWebServiceListener.java
@@ -0,0 +1,43 @@
+package org.cytoscape.coreplugin.cpath2.web_service;
+
+import org.cytoscape.coreplugin.cpath2.schemas.search_response.SearchResponseType;
+import org.cytoscape.coreplugin.cpath2.schemas.summary_response.SummaryResponseType;
+
+/**
+ * Listener for listener to Requests made to the cPath Web API.
+ *
+ * @author Ethan Cerami
+ */
+public interface CPathWebServiceListener {
+
+ /**
+ * Indicates that someone has initiated a search for physical entities.
+ *
+ * @param keyword Keyword Term(s)
+ * @param ncbiTaxonomyId NCBI Texonomy ID.
+ */
+ public void searchInitiatedForPhysicalEntities(String keyword, int ncbiTaxonomyId);
+
+ /**
+ * Indicates that a search for physical entities has completed.
+ *
+ * @param peSearchResponse Search Response Object.
+ */
+ public void searchCompletedForPhysicalEntities(SearchResponseType peSearchResponse);
+
+ /**
+ * Indicates that someone has initiated a request for parent summaries.
+ *
+ * @param primaryId Primary ID of Child.
+ */
+ public void requestInitiatedForParentSummaries (long primaryId);
+
+ /**
+ * Indicates that a request for parent summaries has completed.
+ *
+ * @param primaryId Primary ID of Child.
+ * @param summaryResponse Summary Response Object.
+ */
+ public void requestCompletedForParentSummaries (long primaryId,
+ SummaryResponseType summaryResponse);
+}
diff --git a/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/web_service/CytoscapeCPathWebService.java b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/web_service/CytoscapeCPathWebService.java
new file mode 100644
index 0000000..1009152
--- /dev/null
+++ b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/web_service/CytoscapeCPathWebService.java
@@ -0,0 +1,226 @@
+package org.cytoscape.coreplugin.cpath2.web_service;
+
+import cytoscape.Cytoscape;
+import cytoscape.CyNode;
+import cytoscape.CyNetwork;
+import cytoscape.view.CyNetworkView;
+import cytoscape.visual.VisualStyle;
+import cytoscape.data.webservice.*;
+import cytoscape.data.webservice.ui.WebServiceClientGUI;
+import cytoscape.data.CyAttributes;
+import cytoscape.layout.Tunable;
+import cytoscape.util.ModuleProperties;
+import cytoscape.util.ModulePropertiesImpl;
+import org.cytoscape.coreplugin.cpath2.schemas.search_response.SearchResponseType;
+import org.cytoscape.coreplugin.cpath2.task.ExecuteGetRecordByCPathId;
+import org.cytoscape.coreplugin.cpath2.task.ExpandNode;
+import org.cytoscape.coreplugin.cpath2.util.NullTaskMonitor;
+import org.cytoscape.coreplugin.cpath2.view.cPathSearchPanel;
+import org.cytoscape.coreplugin.cpath2.view.TabUi;
+import org.cytoscape.coreplugin.cpath2.view.SearchHitsPanel;
+import org.cytoscape.coreplugin.cpath2.plugin.CPathPlugIn2;
+import org.cytoscape.coreplugin.cpath2.cytoscape.BinarySifVisualStyleUtil;
+
+import javax.swing.*;
+import java.awt.*;
+import java.net.URL;
+import java.util.*;
+import java.util.List;
+
+import giny.view.NodeView;
+import giny.view.EdgeView;
+import giny.model.Node;
+
+/**
+ * CPath Web Service, integrated into the Cytoscape Web Services Framework.
+ */
+public class CytoscapeCPathWebService extends WebServiceClientImpl implements WebServiceClientGUI,
+ NetworkImportWebServiceClient {
+ // Display name of this client.
+ private static final String DISPLAY_NAME = CPathProperties.getInstance().getCPathServerName() +
+ " Web Service Client";
+
+ // Client ID. This should be unique.
+ private static final String CLIENT_ID = CPathProperties.getInstance().getWebServicesId();
+
+ // Instance of this client. This is a singleton.
+ private static final WebServiceClient client = new CytoscapeCPathWebService();
+
+ /**
+ * NCBI Taxonomy ID Filter.
+ */
+ public static final String NCBI_TAXONOMY_ID_FILTER = "ncbi_taxonomy_id_filter";
+
+ /**
+ * Response Format.
+ */
+ public static final String RESPONSE_FORMAT = "response_format";
+
+ private JPanel mainPanel;
+
+ /**
+ * Return instance of this client.
+ *
+ * @return WebServiceClient Object.
+ */
+ public static WebServiceClient getClient() {
+ return client;
+ }
+
+ /**
+ * Execute Request Service.
+ * @param e CyWebService Object.
+ * @throws Exception All Errors.
+ */
+ public void executeService(CyWebServiceEvent e) throws CyWebServiceException{
+ if (e.getSource().equals(CLIENT_ID)) {
+ if (e.getEventType().equals(CyWebServiceEvent.WSEventType.IMPORT_NETWORK)) {
+ importNetwork(e);
+ } else if (e.getEventType().equals(CyWebServiceEvent.WSEventType.EXPAND_NETWORK)) {
+
+ } else if (e.getEventType().equals(CyWebServiceEvent.WSEventType.SEARCH_DATABASE)) {
+ try {
+ searchDatabase(e);
+ } catch (CPathException e1) {
+ throw new CyWebServiceException
+ (CyWebServiceException.WSErrorCode.REMOTE_EXEC_FAILED);
+ } catch (EmptySetException e1) {
+ throw new CyWebServiceException
+ (CyWebServiceException.WSErrorCode.NO_RESULT);
+ }
+ }
+ }
+ }
+
+ public List<JMenuItem> getNodeContextMenuItems(NodeView nodeView) {
+ CyNetworkView networkView = (CyNetworkView) nodeView.getGraphView();
+ CyNetwork cyNetwork = networkView.getNetwork();
+ CyAttributes networkAttributes = Cytoscape.getNetworkAttributes();
+ Boolean b = networkAttributes.getBooleanAttribute(cyNetwork.getIdentifier(),
+ BinarySifVisualStyleUtil.BINARY_NETWORK);
+ if (b != null) {
+ List<JMenuItem> menuList = new ArrayList<JMenuItem>();
+ JMenuItem menuItem = new JMenuItem ("Get Neighbors");
+ menuItem.addActionListener(new ExpandNode(nodeView));
+ menuList.add(menuItem);
+ return menuList;
+ }
+ return null;
+ }
+
+ public List getEdgeContextMenuItems(EdgeView edgeView) {
+ return null;
+ }
+
+ public Container getGUI() {
+ return mainPanel;
+ }
+
+ public void setGUI(Container container) {
+ //
+ }
+
+ public VisualStyle getDefaultVisualStyle() {
+ return null;
+ }
+
+ public String getDescription() {
+ String desc = CPathProperties.getInstance().getCPathBlurb();
+ desc = desc.replaceAll("<span class='bold'>", "<B>");
+ desc = desc.replaceAll("</span>", "</B>");
+ return "<html><body>" + desc + "</body></html>";
+ }
+
+ public Icon getIcon(IconSize iconSize) {
+ URL iconURL = SearchHitsPanel.class.getResource("resources/"
+ + CPathProperties.getInstance().getIconFileName());
+ return new ImageIcon(iconURL);
+ }
+
+ /**
+ * Creates a new Web Services client.
+ */
+ private CytoscapeCPathWebService() {
+ super(CLIENT_ID, DISPLAY_NAME, new WebServiceClientManager.ClientType[]
+ {WebServiceClientManager.ClientType.NETWORK});
+ // Set properties for this client.
+ this.setClientStub(CPathWebServiceImpl.getInstance());
+ setProperty();
+
+ mainPanel = new JPanel();
+ mainPanel.setPreferredSize(new Dimension (500,400));
+ mainPanel.setLayout (new BorderLayout());
+
+ CPathWebService webApi = CPathWebServiceImpl.getInstance();
+ cPathSearchPanel cpathPanel = new cPathSearchPanel(webApi);
+
+ TabUi tabbedPane = TabUi.getInstance();
+ tabbedPane.add("Search", cpathPanel);
+
+ JScrollPane configPanel = CPathPlugIn2.createConfigPanel();
+ tabbedPane.add("Options", configPanel);
+ mainPanel.add(tabbedPane, BorderLayout.CENTER);
+
+ }
+
+ /**
+ * Set props for this client.
+ */
+ private void setProperty() {
+ props = new ModulePropertiesImpl(clientID, "wsc");
+ props.add(new Tunable(NCBI_TAXONOMY_ID_FILTER, "Filter by Organism - NCBI Taxonomy ID",
+ Tunable.INTEGER, new Integer(-1)));
+ props.add(new Tunable(RESPONSE_FORMAT, "Response Format",
+ Tunable.INTEGER, CPathResponseFormat.BINARY_SIF.getFormatString()));
+ }
+
+ private void importNetwork(CyWebServiceEvent e) {
+ CPathWebService webApi = CPathWebServiceImpl.getInstance();
+ String q = e.getParameter().toString();
+
+ String idStrs[] = q.split(" ");
+ long ids[] = new long[idStrs.length];
+ for (int i = 0; i < ids.length; i++) {
+ ids[i] = Long.parseLong(idStrs[i]);
+ }
+
+ ModuleProperties properties = this.getProps();
+ Tunable tunable = properties.get(RESPONSE_FORMAT);
+ CPathResponseFormat format = CPathResponseFormat.BINARY_SIF;
+ if (tunable != null) {
+ format = CPathResponseFormat.getResponseFormat((String) tunable.getValue());
+ }
+
+ // Create the task
+ ExecuteGetRecordByCPathId task = new ExecuteGetRecordByCPathId(webApi,
+ ids, format, CPathProperties.getInstance().getCPathServerName());
+ // Run right here in this thread.
+ task.run();
+ }
+
+ private void searchDatabase(CyWebServiceEvent e) throws CPathException, EmptySetException {
+ String q = e.getParameter().toString();
+ CPathWebService webApi = CPathWebServiceImpl.getInstance();
+ ModuleProperties properties = this.getProps();
+ Tunable tunable = properties.get(NCBI_TAXONOMY_ID_FILTER);
+ Integer taxonomyId = -1;
+ if (tunable != null) {
+ taxonomyId = (Integer) tunable.getValue();
+ }
+ SearchResponseType response = webApi.searchPhysicalEntities(q, taxonomyId,
+ new NullTaskMonitor());
+ Integer totalNumHits = response.getTotalNumHits().intValue();
+
+ // Fire appropriate events.
+ if (e.getNextMove() != null) {
+ Cytoscape.firePropertyChange("SEARCH_RESULT", this.clientID,
+ new DatabaseSearchResult(totalNumHits, response,
+ e.getNextMove()));
+ } else {
+ Cytoscape.firePropertyChange("SEARCH_RESULT", this.clientID,
+ new DatabaseSearchResult(totalNumHits, response,
+ CyWebServiceEvent.WSEventType.IMPORT_NETWORK));
+ }
+ }
+}
+
diff --git a/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/web_service/EmptySetException.java b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/web_service/EmptySetException.java
new file mode 100644
index 0000000..dc8eb94
--- /dev/null
+++ b/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/web_service/EmptySetException.java
@@ -0,0 +1,9 @@
+package org.cytoscape.coreplugin.cpath2.web_service;
+
+/**
+ * Empty Set Exception.
+ *
+ * @author Ethan Cerami
+ */
+public class EmptySetException extends Exception {
+}
diff --git a/coreplugins/cPath2/src/main/resources/org/cytoscape/coreplugin/cpath2/plugin/plugin.props b/coreplugins/cPath2/src/main/resources/org/cytoscape/coreplugin/cpath2/plugin/plugin.props
new file mode 100644
index 0000000..3ed0b16
--- /dev/null
+++ b/coreplugins/cPath2/src/main/resources/org/cytoscape/coreplugin/cpath2/plugin/plugin.props
@@ -0,0 +1,43 @@
+# This props file should be filled out and included in the plugin jar file. This props file will be used
+# to put information into the Plugin Manager about the plugin
+
+# The plugin name that will be displayed to users, white space within name is not allowed
+pluginName=PathwayCommons
+
+# Description used to give users information about the plugin such as what it does.
+# Html tags are encouraged for formatting purposes.
+pluginDescription=Provides connectivity to the Pathway Commons repository (http://www.pathwaycommons.org).
+
+# Plugin version number, this must be two numbers separated by a decimal. Ex. 0.2, 14.03
+pluginVersion=2.2
+
+# Compatible Cytoscape version. If there are more than one version, seperate by ",".
+cytoscapeVersion=2.7,2.8
+
+# Category, use one of the categories listed on the http://cytoscape.org/plugins2.php site
+pluginCategory=Core
+
+# URL to a website that gives more information about your plugin, Ex. http://my-lab-site.org
+projectURL=http://www.pathwaycommons.org
+
+# List of authors. Note each author and institution pair are separated by a : (colon)
+# each additional author institution pair must be separated from other pairs by a ; (semicolon)
+pluginAuthorsIntsitutions=Ethan Cerami, Benjamin Gross and Chris Sander:Memorial Sloan-Kettering Cancer Center;Igor Rodchenkov and Gary Bader:University of Toronto
+
+# Date this plugin/plugin version was released
+releaseDate=October 16, 2012
+
+cpath2.organism0=Human:9606
+cpath2.organism1=Fruit Fly:7227
+cpath2.organism2=Mouse:10090
+cpath2.organism3=Rat:10116
+cpath2.organism4=C. elegans:6239
+cpath2.organism5=S. cerevisiae:4932
+
+# Change these properties if you want to point the plugin to a different cPath server.
+#cpath2.server_name=Mouse Interaction Database
+#cpath2.server_url=http://awabi.cbio.mskcc.org/pc-demo/webservice.do
+#cpath2.server_url=http://awabi.cbio.mskcc.org/pc/webservice.do
+#cpath2.server_url=http://localhost:8080/cpath/webservice.do
+cpath2.server_url=http://www.pathwaycommons.org/pc/webservice.do
+#cpath2.server_blurb=The Mouse Interaction Database is... blah, blah, blah....
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diff --git a/coreplugins/cPath2/src/main/resources/org/cytoscape/coreplugin/cpath2/view/resources/stock_zoom-16.png b/coreplugins/cPath2/src/main/resources/org/cytoscape/coreplugin/cpath2/view/resources/stock_zoom-16.png
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diff --git a/coreplugins/cPath2/src/main/resources/xsd/RecordBase.xsd b/coreplugins/cPath2/src/main/resources/xsd/RecordBase.xsd
new file mode 100644
index 0000000..0c787f6
--- /dev/null
+++ b/coreplugins/cPath2/src/main/resources/xsd/RecordBase.xsd
@@ -0,0 +1,144 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema">
+
+ <xsd:complexType name="BasicRecordType">
+ <xsd:annotation>
+ <xsd:documentation xml:lang="en">
+ Summarizes a single BioPAX Record.
+ </xsd:documentation>
+ </xsd:annotation>
+ <xsd:sequence>
+ <xsd:element name="name" type="xsd:string" minOccurs="0" maxOccurs="1">
+ <xsd:annotation>
+ <xsd:documentation xml:lang="en">
+ Record name.
+ </xsd:documentation>
+ </xsd:annotation>
+ </xsd:element>
+ <xsd:element name="description" type="xsd:string" minOccurs="0" maxOccurs="1">
+ <xsd:annotation>
+ <xsd:documentation xml:lang="en">
+ Record description.
+ </xsd:documentation>
+ </xsd:annotation>
+ </xsd:element>
+ <xsd:element name="entity_type" type="xsd:string">
+ <xsd:annotation>
+ <xsd:documentation xml:lang="en">
+ BioPAX Record type. For example: pathway, biochemicalReaction, or physicalEntity.
+ </xsd:documentation>
+ </xsd:annotation>
+ </xsd:element>
+ <xsd:element name="data_source" type="DataSourceType"/>
+ </xsd:sequence>
+ <xsd:attribute name="primary_id" type="xsd:long">
+ <xsd:annotation>
+ <xsd:documentation xml:lang="en">
+ Internal ID. Use this ID to request additional information regarding the record.
+ </xsd:documentation>
+ </xsd:annotation>
+ </xsd:attribute>
+ </xsd:complexType>
+
+ <xsd:complexType name="ExtendedRecordType">
+ <xsd:annotation>
+ <xsd:documentation xml:lang="en">
+ Extended BioPAX Record Type.
+ </xsd:documentation>
+ </xsd:annotation>
+ <xsd:complexContent>
+ <xsd:extension base="BasicRecordType">
+ <xsd:sequence>
+ <xsd:element name="synonym" type="xsd:string" minOccurs="0" maxOccurs="unbounded"/>
+ <xsd:element name="xref" type="XRefType" minOccurs="0" maxOccurs="unbounded"/>
+ <xsd:element name="excerpt" type="xsd:string" minOccurs="0" maxOccurs="unbounded"/>
+ <xsd:element name="organism" type="OrganismType"/>
+ <xsd:element name="pathway_list" type="PathwayListType"/>
+ </xsd:sequence>
+ </xsd:extension>
+ </xsd:complexContent>
+ </xsd:complexType>
+
+ <xsd:complexType name="DataSourceType">
+ <xsd:annotation>
+ <xsd:documentation xml:lang="en">
+ Encapsulates data source information.
+ </xsd:documentation>
+ </xsd:annotation>
+ <xsd:sequence>
+ <xsd:element name="name" type="xsd:string"/>
+ </xsd:sequence>
+ <xsd:attribute name="primary_id" type="xsd:string">
+ <xsd:annotation>
+ <xsd:documentation xml:lang="en">
+ Internal ID.
+ </xsd:documentation>
+ </xsd:annotation>
+ </xsd:attribute>
+ </xsd:complexType>
+
+ <xsd:complexType name="OrganismType">
+ <xsd:annotation>
+ <xsd:documentation xml:lang="en">
+ Encapsulates organism data.
+ </xsd:documentation>
+ </xsd:annotation>
+ <xsd:sequence>
+ <xsd:element name="common_name" type="xsd:string"/>
+ <xsd:element name="species_name" type="xsd:string"/>
+ </xsd:sequence>
+ <xsd:attribute name="ncbi_organism_id" type="xsd:integer"/>
+ </xsd:complexType>
+
+ <xsd:complexType name="XRefType">
+ <xsd:annotation>
+ <xsd:documentation xml:lang="en">
+ Encapsulates an XREF.
+ </xsd:documentation>
+ </xsd:annotation>
+ <xsd:sequence>
+ <xsd:element name="db" type="xsd:string" minOccurs="1" maxOccurs="1"/>
+ <xsd:element name="id" type="xsd:string" minOccurs="1" maxOccurs="1"/>
+ <xsd:element name="url" type="xsd:string" minOccurs="0" maxOccurs="1"/>
+ </xsd:sequence>
+ </xsd:complexType>
+
+
+ <xsd:complexType name="ErrorType">
+ <xsd:annotation>
+ <xsd:documentation xml:lang="en">
+ Encapsulates error information.s
+ </xsd:documentation>
+ </xsd:annotation>
+ <xsd:sequence>
+ <xsd:element name="error_code" type="xsd:integer"/>
+ <xsd:element name="error_msg" type="xsd:integer"/>
+ <xsd:element name="error_details" type="xsd:integer"/>
+ </xsd:sequence>
+ </xsd:complexType>
+
+ <xsd:complexType name="PathwayListType">
+ <xsd:annotation>
+ <xsd:documentation xml:lang="en">
+ Encapsulates lists of pathways.
+ </xsd:documentation>
+ </xsd:annotation>
+ <xsd:sequence>
+ <xsd:element name="pathway" type="PathwayType" minOccurs="0" maxOccurs="unbounded"/>
+ </xsd:sequence>
+ </xsd:complexType>
+
+ <xsd:complexType name="PathwayType">
+ <xsd:annotation>
+ <xsd:documentation xml:lang="en">
+ Encapsulates pathway data.
+ </xsd:documentation>
+ </xsd:annotation>
+ <xsd:sequence>
+ <xsd:element name="name" type="xsd:string"/>
+ <xsd:element name="data_source" type="DataSourceType"/>
+ </xsd:sequence>
+ <xsd:attribute name="primary_id" type="xsd:long"/>
+ </xsd:complexType>
+
+</xsd:schema>
\ No newline at end of file
diff --git a/coreplugins/cPath2/src/main/resources/xsd/SearchResponse.xsd b/coreplugins/cPath2/src/main/resources/xsd/SearchResponse.xsd
new file mode 100644
index 0000000..9c7005e
--- /dev/null
+++ b/coreplugins/cPath2/src/main/resources/xsd/SearchResponse.xsd
@@ -0,0 +1,25 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema">
+ <xsd:include schemaLocation="RecordBase.xsd"/>
+ <xsd:annotation>
+ <xsd:documentation xml:lang="en">
+ Pathway Commons Web API: Search Response.
+ </xsd:documentation>
+ </xsd:annotation>
+
+ <xsd:element name="search_response" type="SearchResponseType"/>
+ <xsd:element name="error" type="ErrorType"/>
+
+ <xsd:complexType name="SearchResponseType">
+ <xsd:annotation>
+ <xsd:documentation xml:lang="en">
+ Encapsulates search response.
+ </xsd:documentation>
+ </xsd:annotation>
+ <xsd:sequence>
+ <xsd:element name="search_hit" type="ExtendedRecordType" minOccurs="0" maxOccurs="unbounded"/>
+ </xsd:sequence>
+ <xsd:attribute name="total_num_hits" type="xsd:long"/>
+ </xsd:complexType>
+
+ </xsd:schema>
\ No newline at end of file
diff --git a/coreplugins/cPath2/src/main/resources/xsd/SummaryResponse.xsd b/coreplugins/cPath2/src/main/resources/xsd/SummaryResponse.xsd
new file mode 100644
index 0000000..81026df
--- /dev/null
+++ b/coreplugins/cPath2/src/main/resources/xsd/SummaryResponse.xsd
@@ -0,0 +1,23 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema">
+ <xsd:include schemaLocation="RecordBase.xsd"/>
+ <xsd:annotation>
+ <xsd:documentation xml:lang="en">
+ Pathway Commons Web API: Summary Response.
+ </xsd:documentation>
+ </xsd:annotation>
+
+ <xsd:element name="summary_response" type="SummaryResponseType"/>
+ <xsd:element name="error" type="ErrorType"/>
+
+ <xsd:complexType name="SummaryResponseType">
+ <xsd:annotation>
+ <xsd:documentation xml:lang="en">
+ Encapsulates summaries of BioPAX Records.
+ </xsd:documentation>
+ </xsd:annotation>
+ <xsd:sequence>
+ <xsd:element name="record" type="BasicRecordType" minOccurs="0" maxOccurs="unbounded"/>
+ </xsd:sequence>
+ </xsd:complexType>
+ </xsd:schema>
\ No newline at end of file
diff --git a/coreplugins/cPath2/src/test/java/org/cytoscape/coreplugin/cpath2/test/TestCytoscapeCPathWebService.java b/coreplugins/cPath2/src/test/java/org/cytoscape/coreplugin/cpath2/test/TestCytoscapeCPathWebService.java
new file mode 100644
index 0000000..b6775d3
--- /dev/null
+++ b/coreplugins/cPath2/src/test/java/org/cytoscape/coreplugin/cpath2/test/TestCytoscapeCPathWebService.java
@@ -0,0 +1,128 @@
+package org.cytoscape.coreplugin.cpath2.test;
+
+import junit.framework.TestCase;
+import cytoscape.data.webservice.*;
+import cytoscape.util.ModuleProperties;
+import cytoscape.layout.Tunable;
+import cytoscape.Cytoscape;
+import cytoscape.CyMain;
+import org.cytoscape.coreplugin.cpath2.web_service.*;
+import org.cytoscape.coreplugin.cpath2.schemas.search_response.SearchResponseType;
+import org.cytoscape.coreplugin.cpath2.schemas.summary_response.SummaryResponseType;
+import org.cytoscape.coreplugin.cpath2.schemas.summary_response.BasicRecordType;
+
+import java.util.List;
+import java.beans.PropertyChangeListener;
+import java.beans.PropertyChangeEvent;
+import java.io.InputStreamReader;
+import java.io.BufferedReader;
+import java.io.IOException;
+
+/**
+ * Test Harness for the CytosacpeCPathWebService.
+ *
+ * NB: The test below connect to the live instance of Pathway Commons.
+ * As such, the data is likely to change, and these tests are likely to break.
+ *
+ */
+public class TestCytoscapeCPathWebService extends TestCase {
+
+ public void testWebService() { assertTrue(true); }
+ public void DO_NOT_testWebService() throws EmptySetException, CPathException {
+ try {
+ CyMain.main(new String[0]);
+ } catch (Exception e) {
+ e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
+ }
+ // First, create the client and register it.
+ WebServiceClient wsClient = CytoscapeCPathWebService.getClient();
+ WebServiceClientManager.registerClient(wsClient);
+
+ // Get the client back from the manager
+ wsClient = WebServiceClientManager.getClient(wsClient.getClientID());
+ //validateStub(wsClient);
+
+ CyWebServiceEventSupport eventManager =
+ WebServiceClientManager.getCyWebServiceEventSupport();
+ validateSearchEvent(wsClient, eventManager);
+ validateImportEvent(eventManager);
+
+ System.out.println("Press <ENTER> to exit: ");
+ InputStreamReader converter = new InputStreamReader(System.in);
+ BufferedReader in = new BufferedReader(converter);
+ try {
+ in.readLine();
+ } catch (IOException e) {
+ }
+ }
+
+ private void validateImportEvent(CyWebServiceEventSupport eventManager) {
+ CyWebServiceEvent wsEvent = new CyWebServiceEvent
+ (CPathProperties.getInstance().getWebServicesId(),
+ CyWebServiceEvent.WSEventType.IMPORT_NETWORK, "1");
+ try {
+ eventManager.fireCyWebServiceEvent(wsEvent);
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+ }
+
+ private void validateSearchEvent(WebServiceClient wsClient, CyWebServiceEventSupport eventManager) {
+ // Set Organism Filter
+ ModuleProperties props = wsClient.getProps();
+ props.add(new Tunable(CytoscapeCPathWebService.NCBI_TAXONOMY_ID_FILTER,
+ "Filter by Organism - NCBI Taxonomy ID",
+ Tunable.INTEGER, new Integer(9606)));
+ CyWebServiceEvent wsEvent = new CyWebServiceEvent
+ (CPathProperties.getInstance().getWebServicesId(),
+ CyWebServiceEvent.WSEventType.SEARCH_DATABASE, "brca1");
+
+ // TODO: Recmd: fire should throw something narrower than Exception
+ Cytoscape.getPropertyChangeSupport().addPropertyChangeListener(new MiniListener());
+ try {
+ eventManager.fireCyWebServiceEvent(wsEvent);
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+ }
+
+ private void validateStub(WebServiceClient wsClient) throws CPathException, EmptySetException {
+ // 1. try getting the stub and executing calls that way.
+ CPathWebService webApi = (CPathWebService) wsClient.getClientStub();
+
+ // a. Search Physical Entities
+ SearchResponseType responseType =
+ webApi.searchPhysicalEntities("brca1", -1, null);
+ assertTrue (responseType.getTotalNumHits() > 0);
+
+ // b. Get Records by ID
+ long ids[] = new long[1];
+ ids[0] = 1;
+ String response = webApi.getRecordsByIds(ids, CPathResponseFormat.BIOPAX, null);
+ assertTrue (response.length() > 100);
+ response = webApi.getRecordsByIds(ids, CPathResponseFormat.BINARY_SIF, null);
+ assertTrue (response.length() > 100);
+
+ // c. Get Organism List, which is not (yet) implemented.
+ try {
+ webApi.getOrganismList();
+ fail ("UnsupportedOperationException should have been thrown.");
+ } catch (UnsupportedOperationException e) {
+ }
+
+ // d. Get Parent Summaries.
+ SummaryResponseType summaryResponseType = webApi.getParentSummaries(100, null);
+ List<BasicRecordType> list = summaryResponseType.getRecord();
+ assertTrue (list.size() > 1) ;
+ }
+}
+
+class MiniListener implements PropertyChangeListener {
+
+ public void propertyChange(PropertyChangeEvent propertyChangeEvent) {
+ if (propertyChangeEvent.getPropertyName().equals("SEARCH_RESULT")) {
+ DatabaseSearchResult result = (DatabaseSearchResult) propertyChangeEvent.getNewValue();
+ System.out.println(result.getResultSize());
+ }
+ }
+}
diff --git a/coreplugins/filters/pom.xml b/coreplugins/filters/pom.xml
new file mode 100644
index 0000000..2be547f
--- /dev/null
+++ b/coreplugins/filters/pom.xml
@@ -0,0 +1,65 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>parent</artifactId>
+ <version>2.8.4-SNAPSHOT</version>
+ </parent>
+
+ <artifactId>filters</artifactId>
+ <packaging>jar</packaging>
+
+ <name>Filters</name>
+
+ <!-- bootstrap for cytoscape dependencies, namely the parent POM snapshots -->
+ <repositories>
+ <repository>
+ <id>cytoscape_snapshots</id>
+ <snapshots>
+ <enabled>true</enabled>
+ </snapshots>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <name>Cytoscape Snapshots</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/</url>
+ </repository>
+ <repository>
+ <id>cytoscape_releases</id>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ <name>Cytoscape Releases</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/releases/</url>
+ </repository>
+ </repositories>
+
+ <build>
+ <plugins>
+ <plugin>
+ <artifactId>maven-assembly-plugin</artifactId>
+ <configuration>
+ <archive>
+ <manifestEntries>
+ <Cytoscape-Plugin>cytoscape.filters.FilterPlugin</Cytoscape-Plugin>
+ </manifestEntries>
+ </archive>
+ </configuration>
+ </plugin>
+ </plugins>
+ </build>
+
+ <dependencies>
+ <dependency>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>quickfind</artifactId>
+ <version>2.8.4-SNAPSHOT</version>
+ <scope>provided</scope>
+ </dependency>
+ </dependencies>
+
+</project>
+
diff --git a/coreplugins/filters/src/main/java/cytoscape/filters/AdvancedSetting.java b/coreplugins/filters/src/main/java/cytoscape/filters/AdvancedSetting.java
new file mode 100644
index 0000000..1be97cc
--- /dev/null
+++ b/coreplugins/filters/src/main/java/cytoscape/filters/AdvancedSetting.java
@@ -0,0 +1,126 @@
+package cytoscape.filters;
+
+
+//Advanced settings
+public class AdvancedSetting {
+ // default settings
+ private boolean session = true, global=false; //scope
+ private boolean node=false, edge=false; // selectionType
+ private boolean source=true, target=true; // EdgeType
+ private Relation relation = Relation.AND;
+
+ public String toString() {
+ String retStr = "<AdvancedSetting>\n";
+ retStr += "scope.global=";
+ if (global) {
+ retStr += "true\n";
+ }
+ else {
+ retStr += "false\n";
+ }
+ retStr += "scope.session=";
+ if (session) {
+ retStr += "true\n";
+ }
+ else {
+ retStr += "false\n";
+ }
+ retStr += "selection.node=";
+ if (node) {
+ retStr += "true\n";
+ }
+ else {
+ retStr += "false\n";
+ }
+ retStr += "selection.edge=";
+ if (edge) {
+ retStr += "true\n";
+ }
+ else {
+ retStr += "false\n";
+ }
+
+ retStr += "edge.source=";
+ if (source) {
+ retStr += "true\n";
+ }
+ else {
+ retStr += "false\n";
+ }
+ retStr += "edge.target=";
+ if (target) {
+ retStr += "true\n";
+ }
+ else {
+ retStr += "false\n";
+ }
+
+ retStr += "Relation="+relation+ "\n";
+ retStr += "</AdvancedSetting>";
+ return retStr;
+ }
+
+ public Relation getRelation()
+ {
+ return relation;
+ }
+
+ public void setRelation(Relation pRelation)
+ {
+ relation = pRelation;
+ }
+
+ public boolean isSessionChecked()
+ {
+ return session;
+ }
+ public void setSession(boolean pSession)
+ {
+ session = pSession;
+ }
+
+ public boolean isGlobalChecked()
+ {
+ return global;
+ }
+ public void setGlobal(boolean pGlobal)
+ {
+ global = pGlobal;
+ }
+
+ public boolean isNodeChecked()
+ {
+ return node;
+ }
+ public void setNode(boolean pNode)
+ {
+ node = pNode;
+ }
+ public boolean isEdgeChecked()
+ {
+ return edge;
+ }
+ public void setEdge(boolean pEdge)
+ {
+ edge = pEdge;
+ }
+ public void setSource(boolean pSource)
+ {
+ source = pSource;
+ }
+ public void setTarget(boolean pTarget)
+ {
+ target = pTarget;
+ }
+
+ public boolean isSourceChecked()
+ {
+ return source;
+ }
+ public boolean isTargetChecked()
+ {
+ return target;
+ }
+
+
+}//End of Advanced settings
diff --git a/coreplugins/filters/src/main/java/cytoscape/filters/AtomicFilter.java b/coreplugins/filters/src/main/java/cytoscape/filters/AtomicFilter.java
new file mode 100644
index 0000000..39526bc
--- /dev/null
+++ b/coreplugins/filters/src/main/java/cytoscape/filters/AtomicFilter.java
@@ -0,0 +1,165 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.filters;
+
+import giny.model.Edge;
+import giny.model.Node;
+
+import java.util.*;
+
+import cytoscape.CyNetwork;
+import csplugins.quickfind.util.QuickFind;
+import csplugins.widgets.autocomplete.index.GenericIndex;
+
+
+public abstract class AtomicFilter implements CyFilter {
+
+ protected BitSet node_bits = null;
+ protected BitSet edge_bits = null;
+
+ protected CyFilter parent;
+
+ protected String name; // Name of the filter
+ protected String controllingAttribute = null;
+ protected boolean negation = false;
+ protected CyNetwork network = null;
+
+ protected int index_type = QuickFind.INDEX_NODES;
+
+ protected GenericIndex quickFind_index = null;
+
+ public AtomicFilter() {
+ }
+
+ public void setNetwork(CyNetwork pNetwork) {
+ network = pNetwork;
+ }
+
+ public CyNetwork getNetwork() {
+ return network;
+ }
+
+
+ public GenericIndex getIndex() {
+ return quickFind_index;
+ }
+
+ public void setIndex(GenericIndex pIndex) {
+ quickFind_index = pIndex;
+ }
+
+ public void setIndexType(int pIndexType) {
+ index_type = pIndexType;
+ }
+
+ public int getIndexType() {
+ return index_type;
+ }
+
+ public BitSet getNodeBits() {
+ apply();
+ return node_bits;
+ }
+
+ public BitSet getEdgeBits(){
+ apply();
+ return edge_bits;
+ }
+
+ public boolean passesFilter(Object obj) {
+
+ int index = -1;
+ if (obj instanceof Node) {
+ List<Node> nodes_list = network.nodesList();
+ index = nodes_list.indexOf((Node) obj);
+ return node_bits.get(index);
+ }
+
+ if (obj instanceof Edge) {
+ List<Edge> edges_list = network.edgesList();
+ index = edges_list.indexOf((Edge) obj);
+ return edge_bits.get(index);
+ }
+
+ return false;
+ }
+
+ public void setNodeBits(BitSet b) {
+ node_bits = b;
+ parent.childChanged();
+ }
+
+ public void setEdgeBits(BitSet b) {
+ edge_bits = b;
+ parent.childChanged();
+ }
+
+ public void setParent(CyFilter p) {
+ parent = p;
+ }
+ public CyFilter getParent() {
+ return parent;
+ }
+
+ // an atomic filter can't have any children, so this is a no-op
+ public void childChanged() {};
+
+ public void setNegation(boolean pNot) {
+ negation = pNot;
+ if (getParent() != null) {
+ getParent().childChanged();
+ }
+ }
+ public boolean getNegation() {
+ return negation;
+ }
+
+ public String getName(){
+ return name;
+ }
+ public void setName(String pName){
+ name = pName;
+ }
+
+ public String getControllingAttribute() {
+ return controllingAttribute;
+ }
+
+ public void setControllingAttribute(String pAttributeName) {
+ controllingAttribute = pAttributeName;
+ }
+}
diff --git a/coreplugins/filters/src/main/java/cytoscape/filters/CompositeFilter.java b/coreplugins/filters/src/main/java/cytoscape/filters/CompositeFilter.java
new file mode 100644
index 0000000..427306f
--- /dev/null
+++ b/coreplugins/filters/src/main/java/cytoscape/filters/CompositeFilter.java
@@ -0,0 +1,487 @@
+/*
+ Copyright (c) 2006, 2007, 2009 The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.filters;
+
+import giny.model.Edge;
+import giny.model.Node;
+
+import java.util.List;
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import cytoscape.logger.CyLogger;
+
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.BitSet;
+import java.util.LinkedList;
+
+import csplugins.quickfind.util.QuickFind;
+
+public class CompositeFilter implements CyFilter {
+
+ protected List<CyFilter> children;
+ protected boolean negation;
+ //Relation relation;
+ protected String name;
+ protected BitSet node_bits, edge_bits;
+ protected boolean childChanged = true;// so we calculate the first time through
+ protected CyFilter parent;
+ protected String description;
+ protected AdvancedSetting advancedSetting = null;
+ //private int indexType = -1; //QuickFind.INDEX_NODES //QuickFind.INDEX_EDGES
+ protected CyNetwork network;
+ private CyLogger logger = null;
+
+ protected Hashtable compositeNotTab = new Hashtable<CompositeFilter, Boolean>();
+
+ public CompositeFilter() {
+ logger = CyLogger.getLogger(FilterPlugin.class);
+ advancedSetting = new AdvancedSetting();
+ children = new LinkedList<CyFilter>();
+ }
+
+ public CompositeFilter(String pName) {
+ name = pName;
+ logger = CyLogger.getLogger(FilterPlugin.class);
+ advancedSetting = new AdvancedSetting();
+ children = new LinkedList<CyFilter>();
+ }
+
+ public void setNetwork(CyNetwork pNetwork) {
+ if (network != null && network == pNetwork) {
+ return;
+ }
+ network = pNetwork;
+ // Set network for all the children
+ if (children == null || children.size() == 0){
+ return;
+ }
+ for (int i=0; i< children.size(); i++) {
+ children.get(i).setNetwork(pNetwork);
+ children.get(i).childChanged();
+ }
+ childChanged();
+ }
+
+ public CyNetwork getNetwork(){
+ return network;
+ }
+
+ public Hashtable getNotTable() {
+ return compositeNotTab;
+ }
+
+ public void setNotTable(CompositeFilter pFilter, boolean pNot) {
+ compositeNotTab.put(pFilter, new Boolean(pNot));
+ childChanged();
+ }
+
+ public boolean passesFilter(Object obj) {
+
+ List<Node> nodes_list = null;
+ List<Edge> edges_list=null;
+
+ int index = -1;
+ if (obj instanceof Node) {
+ nodes_list = network.nodesList();
+ index = nodes_list.lastIndexOf((Node) obj);
+ return node_bits.get(index);
+ }
+
+ if (obj instanceof Edge) {
+ edges_list = network.edgesList();
+ index = edges_list.lastIndexOf((Edge) obj);
+ return edge_bits.get(index);
+ }
+
+ return false;
+ }
+
+ public void setNegation(boolean pNegation) {
+ negation = pNegation;
+ }
+ public boolean getNegation() {
+ return negation;
+ }
+
+ private void calculateNodeBitSet() {
+ //System.out.println("Entering CompositeFilter.calculatNodeBits() ... ");
+
+ // set the initial bits to a clone of the first child
+ if (children.get(0).getNodeBits() == null) {
+ node_bits = new BitSet(network.getNodeCount());
+ }
+ else {
+ node_bits = (BitSet) children.get(0).getNodeBits().clone();
+ }
+
+ // now perform the requested relation with each subsequent child
+ for ( int i = 1; i < children.size(); i++ ) {
+ CyFilter n = children.get(i);
+ if ( advancedSetting.getRelation() == Relation.AND ) {
+ if (n.getNodeBits() == null) {
+ node_bits = new BitSet();//all set to false
+ return;
+ }
+ if ((n instanceof CompositeFilter)&&(((Boolean)compositeNotTab.get(n)).booleanValue()==true)) {
+ BitSet tmpBitSet = (BitSet) n.getNodeBits().clone();
+ tmpBitSet.flip(0, network.getNodeCount());
+ node_bits.and(tmpBitSet);
+ }
+ else {
+ node_bits.and(n.getNodeBits());
+ }
+
+ } else if ( advancedSetting.getRelation() == Relation.OR ) {
+ if (n.getNodeBits() != null) {
+ if ((n instanceof CompositeFilter)&&(((Boolean)compositeNotTab.get(n)).booleanValue()==true)) {
+ BitSet tmpBitSet = (BitSet) n.getNodeBits().clone();
+ tmpBitSet.flip(0, network.getNodeCount());
+ node_bits.or(tmpBitSet);
+ }
+ else {
+ node_bits.or(n.getNodeBits());
+ }
+ }
+ }
+ else { //advancedSetting.getRelation() == Relation.XOR|NOR
+ logger.warn("CompositeFilter: Relation.XOR|NOR: not implemented yet");
+ }
+ }
+
+ if (negation) {
+ node_bits.flip(0, network.getNodeCount());
+ }
+ }
+
+
+ private void calculateEdgeBitSet() {
+ //System.out.println("Entering CompositeFilter.calculatEdgeBits() ... ");
+
+ // if there are no children, just return an empty bitset
+ if ( children.size() <= 0 ) {
+ edge_bits = new BitSet();
+ return;
+ }
+
+ // set the initial bits to a clone of the first child
+ if (children.get(0).getEdgeBits() == null) {
+ edge_bits = new BitSet();
+ }
+ else {
+ edge_bits = (BitSet) children.get(0).getEdgeBits().clone();
+ }
+
+ // now perform the requested relation with each subsequent child
+ for ( int i = 1; i < children.size(); i++ ) {
+ CyFilter n = children.get(i);
+ if ( advancedSetting.getRelation() == Relation.AND ) {
+ if (n.getEdgeBits() == null) {
+ edge_bits = new BitSet();
+ return;//all set to false
+ }
+ if ((n instanceof CompositeFilter)&&(((Boolean)compositeNotTab.get(n)).booleanValue()==true)) {
+ BitSet tmpBitSet = (BitSet) n.getEdgeBits().clone();
+ tmpBitSet.flip(0, network.getEdgeCount());
+ edge_bits.and(tmpBitSet);
+ }
+ else {
+ edge_bits.and(n.getEdgeBits());
+ }
+ } else if ( advancedSetting.getRelation() == Relation.OR ) {
+ if (n.getEdgeBits() != null) {
+ if ((n instanceof CompositeFilter)&&(((Boolean)compositeNotTab.get(n)).booleanValue()==true)) {
+ BitSet tmpBitSet = (BitSet) n.getEdgeBits().clone();
+ tmpBitSet.flip(0, network.getEdgeCount());
+ edge_bits.or(tmpBitSet);
+ }
+ else {
+ edge_bits.or(n.getEdgeBits());
+ }
+ }
+ }
+ else { //advancedSetting.getRelation() == Relation.XOR|NOR
+ logger.warn("CompositeFilter: Relation.XOR|NOR: not implemented yet");
+ }
+ }
+
+ if (negation) {
+ edge_bits.flip(0, network.getEdgeCount());
+ }
+ }
+
+ public void apply() {
+ if (network == null) {
+ setNetwork(Cytoscape.getCurrentNetwork());
+ }
+
+ //System.out.println("CompositeFilter.apply() ....");
+ //System.out.println("\tNetwork.getIdentifier() = " + network.getIdentifier());
+
+ // only recalculate the bits if the child has actually changed
+ if ( !childChanged )
+ return;
+
+ // if there are no children, just create empty bitSet
+ if ( children.size() <= 0 ) {
+ node_bits = new BitSet(network.getNodeCount());
+ edge_bits = new BitSet(network.getEdgeCount());
+ return;
+ }
+
+ updateSelectionType();
+
+ if (advancedSetting.isNodeChecked()) {
+ calculateNodeBitSet();
+ }
+ if (advancedSetting.isEdgeChecked()) {
+ calculateEdgeBitSet();
+ }
+
+ // record that we've calculated the bits
+ childChanged = false;
+ }
+
+
+ private void updateSelectionType() {
+ boolean selectNode = false;
+ boolean selectEdge = false;
+ //List<CyFilter> childFilters = theFilter.getChildren();
+ for (int i=0; i< children.size(); i++) {
+ CyFilter child = children.get(i);
+ if (child instanceof AtomicFilter) {
+ AtomicFilter tmp = (AtomicFilter) child;
+ if (tmp.getIndexType() == QuickFind.INDEX_NODES) {
+ selectNode = true;
+ }
+ if (tmp.getIndexType() == QuickFind.INDEX_EDGES) {
+ selectEdge = true;
+ }
+ }
+ else if (child instanceof CompositeFilter) {
+ CompositeFilter tmp = (CompositeFilter) child;
+ if (tmp.getAdvancedSetting().isNodeChecked()) {
+ selectNode = true;
+ }
+ if (tmp.getAdvancedSetting().isEdgeChecked()) {
+ selectEdge = true;
+ }
+ }
+ }//end of for loop
+
+ advancedSetting.setNode(selectNode);
+ advancedSetting.setEdge(selectEdge);
+ }
+
+ public BitSet getEdgeBits() {
+ apply();
+ return edge_bits;
+ }
+
+ public BitSet getNodeBits() {
+ apply();
+ return node_bits;
+ }
+
+
+ public void removeChild( CyFilter pChild ) {
+ if (pChild instanceof CompositeFilter) {
+ compositeNotTab.remove(pChild);
+ }
+ children.remove(pChild);
+ childChanged();
+ }
+
+ public void removeChildAt( int pChildIndex ) {
+ if (children.get(pChildIndex) instanceof CompositeFilter) {
+ compositeNotTab.remove(children.get(pChildIndex));
+ }
+ children.remove(pChildIndex);
+ childChanged();
+ }
+
+ public void addChild( AtomicFilter pChild ) {
+ pChild.setNetwork(network);
+ children.add( pChild );
+
+ // so the the child can communicate with us
+ // (i.e. so we know when the child changes)
+ pChild.setParent(this);
+
+ // to force this class to recalculate and to
+ // notify parents
+ childChanged();
+ }
+
+ public void addChild( CompositeFilter pChild, boolean pNot ) {
+ pChild.setNetwork(network);
+ children.add( pChild );
+ compositeNotTab.put(pChild, new Boolean(pNot));
+
+ // so the the child can communicate with us
+ // (i.e. so we know when the child changes)
+ pChild.setParent(this);
+
+ // to force this class to recalculate and to
+ // notify parents
+ childChanged();
+ }
+
+
+ // called by any children
+ public void childChanged() {
+ childChanged = true;
+ // pass the message on to the parent
+ if ( parent != null )
+ parent.childChanged();
+ }
+
+ public CyFilter getParent() {
+ return parent;
+ }
+
+ public void setParent(CyFilter f) {
+ parent = f;
+ }
+
+ public List<CyFilter> getChildren() {
+ return children;
+ }
+
+ public String getName() {
+ return name;
+ }
+
+ public void setName(String pName) {
+ name = pName;
+ }
+
+
+ public String getDescription() {
+ return description;
+ }
+
+ public void setDescription(String pDescription) {
+ description = pDescription;
+ }
+
+ public Relation getRelation() {
+ return advancedSetting.getRelation();
+ }
+
+ public void setRelation(Relation pRelation) {
+ advancedSetting.setRelation(pRelation);
+ }
+
+ public AdvancedSetting getAdvancedSetting() {
+ return advancedSetting;
+ }
+
+ public void setAdvancedSetting(AdvancedSetting pAdvancedSetting) {
+ advancedSetting = pAdvancedSetting;
+ }
+
+ /**
+ * Returns the display String used by the filter panel combobox.
+ * Required as toString is used to provide the persistable representation
+ * of the filter state.
+ *
+ * @return
+ */
+ public String getLabel() {
+ AdvancedSetting as = getAdvancedSetting();
+ String prefix = "";
+ if (as.isGlobalChecked()) {
+ prefix = "global: ";
+ }
+ if (as.isSessionChecked()) {
+ prefix += "session: ";
+ }
+
+ return prefix + getName();
+ }
+
+ /**
+ * @return the string represention of this Filter.
+ */
+ public String toString()
+ {
+ String retStr = "<Composite>\n";
+
+ retStr = retStr + "name=" + name + "\n";
+ retStr = retStr + advancedSetting.toString() + "\n";
+ retStr = retStr + "Negation=" + negation + "\n";
+
+ for (int i=0; i< children.size(); i++) {
+
+ if (children.get(i) instanceof AtomicFilter) {
+ AtomicFilter atomicFilter = (AtomicFilter)children.get(i);
+ retStr = retStr + atomicFilter.toString()+"\n";
+ }
+ else {// it is a CompositeFilter
+ CompositeFilter tmpFilter = (CompositeFilter)children.get(i);
+ retStr = retStr + "CompositeFilter=" + tmpFilter.getName()+ ":" + compositeNotTab.get(tmpFilter)+"\n";
+ }
+ }
+ retStr += "</Composite>";
+
+ return retStr;
+ }
+
+ /**
+ */
+ public boolean equals(Object other_object) {
+ if (!(other_object instanceof CompositeFilter)) {
+ return false;
+ }
+ CompositeFilter theOtherFilter = (CompositeFilter) other_object;
+
+ if (theOtherFilter.toString().equalsIgnoreCase(this.toString())) {
+ return true;
+ }
+ return false;
+ }
+
+ /**
+ * CompositeFilter may be cloned.
+ */
+ public Object clone() {
+ logger.warn("CompositeFilter.clone() not implemented yet");
+
+ return null;
+ }
+
+}
diff --git a/coreplugins/filters/src/main/java/cytoscape/filters/CyFilter.java b/coreplugins/filters/src/main/java/cytoscape/filters/CyFilter.java
new file mode 100644
index 0000000..7863381
--- /dev/null
+++ b/coreplugins/filters/src/main/java/cytoscape/filters/CyFilter.java
@@ -0,0 +1,62 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.filters;
+
+import java.util.*;
+import cytoscape.CyNetwork;
+
+import giny.filter.Filter;
+
+public interface CyFilter extends Filter{
+ public BitSet getNodeBits();
+ public BitSet getEdgeBits();
+
+ public void setNegation(boolean pNot);
+ public boolean getNegation();
+ public String getName();
+ public void setName(String pName);
+
+ public void setNetwork(CyNetwork pNetwork);
+ public CyNetwork getNetwork();
+
+ public void childChanged();
+ public CyFilter getParent();
+ public void setParent(CyFilter f);
+
+ public void apply();
+ public String toString();
+}
diff --git a/coreplugins/filters/src/main/java/cytoscape/filters/EdgeInteractionFilter.java b/coreplugins/filters/src/main/java/cytoscape/filters/EdgeInteractionFilter.java
new file mode 100644
index 0000000..70909d2
--- /dev/null
+++ b/coreplugins/filters/src/main/java/cytoscape/filters/EdgeInteractionFilter.java
@@ -0,0 +1,142 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.filters;
+
+import giny.model.Edge;
+import giny.model.Node;
+
+import java.util.*;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import csplugins.quickfind.util.QuickFind;
+import csplugins.widgets.autocomplete.index.GenericIndex;
+
+
+public class EdgeInteractionFilter extends InteractionFilter {
+
+ public EdgeInteractionFilter() {
+ //Set selection for edge
+ advancedSetting.setNode(false);
+ advancedSetting.setEdge(true);
+ }
+
+
+ public EdgeInteractionFilter(String pName) {
+ name = pName;
+ //Set selection for edge
+ advancedSetting.setNode(false);
+ advancedSetting.setEdge(true);
+ }
+
+
+ public void apply() {
+ if ( !childChanged )
+ return;
+
+ if (network == null) {
+ setNetwork(Cytoscape.getCurrentNetwork());
+ }
+
+ if (network == null) {
+ return;
+ }
+
+ //Make sure the pass filter is current
+ if (passFilter == null) {
+ passFilter = new CompositeFilter("None");
+ }
+
+ if (!passFilter.getName().equalsIgnoreCase("None")) {
+ passFilter.setNetwork(network);
+ passFilter.apply();
+ }
+ BitSet passFilter_nodeBits = passFilter.getNodeBits();
+
+ List<Edge> edges_list = null;
+
+ // EdgeInteractionFilter will select edge only
+ edges_list = network.edgesList();
+ int objectCount = edges_list.size();
+ edge_bits = new BitSet(objectCount); // all the bits are false at very beginning
+
+ if (nodeType != NODE_UNDEFINED) {
+ for (int i=0; i<objectCount; i++) {
+ if (isHit((Edge)edges_list.get(i), passFilter_nodeBits)) {
+ edge_bits.set(i);
+ }
+ }
+ }
+
+ if (negation) {
+ edge_bits.flip(0, objectCount);
+ }
+
+ childChanged = false;
+ }
+
+
+ private boolean isHit(Edge pEdge, BitSet pPassFilter_nodeBits) {
+
+ // Get the list of relevant nodes for this edge
+ List<Node> adjacentNodes = new ArrayList<Node>();
+
+ if (nodeType == NODE_SOURCE) {
+ adjacentNodes.add(pEdge.getSource());
+ }
+ else if (nodeType == NODE_TARGET) {
+ adjacentNodes.add(pEdge.getTarget());
+ }
+ else if (nodeType == NODE_SOURCE_TARGET) {
+ adjacentNodes.add(pEdge.getSource());
+ adjacentNodes.add(pEdge.getTarget()); }
+ else { //nodeType == NODE_UNDEFINED --Neither source or target is selected
+ return false;
+ }
+
+ int nodeIndex = -1;
+ for (int i=0; i < adjacentNodes.size(); i++) {
+ nodeIndex = network.nodesList().indexOf(adjacentNodes.get(i));
+
+ if (pPassFilter_nodeBits.get(nodeIndex) == true) {
+ return true;
+ }
+ }
+
+ return false;
+ }
+}
diff --git a/coreplugins/filters/src/main/java/cytoscape/filters/FilterIO.java b/coreplugins/filters/src/main/java/cytoscape/filters/FilterIO.java
new file mode 100644
index 0000000..5a8bd47
--- /dev/null
+++ b/coreplugins/filters/src/main/java/cytoscape/filters/FilterIO.java
@@ -0,0 +1,679 @@
+/*
+ Copyright (c) 2006, 2007, 2009, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.filters;
+
+import java.io.BufferedReader;
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.FileWriter;
+import java.io.InputStreamReader;
+import java.util.List;
+import java.util.Vector;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Comparator;
+
+import cytoscape.CytoscapeInit;
+import cytoscape.logger.CyLogger;
+import cytoscape.filters.util.FilterUtil;
+import cytoscape.filters.FilterPlugin;
+
+
+public class FilterIO {
+ private CyLogger logger = null;
+
+ public FilterIO () {
+ logger = CyLogger.getLogger(FilterIO.class);
+ }
+
+ /**
+ * Construct the filter objects based on the string representation of each filter.
+ */
+ public int[] getFilterVectFromPropFile(final InputStreamReader reader) {
+ int addCount = 0;
+ int totalCount = 0;
+ int retValue[] = new int[2];
+ retValue[0] = totalCount;
+ retValue[1] = addCount;
+
+ try {
+ BufferedReader in = new BufferedReader(reader);
+
+ try {
+ String oneLine = in.readLine();
+
+ if (oneLine == null) {
+ return retValue;
+ }
+ double filterVersion = 0.0;
+ if (oneLine.trim().startsWith("FilterVersion")) {
+ String versionStr = oneLine.trim().substring(14);
+ filterVersion = Double.valueOf(versionStr);
+ }
+
+ // Ignore filters from the old version
+ if (filterVersion <0.2) {
+ return retValue;
+ }
+
+ while (oneLine != null) {
+ // ignore comment, empty line or the version line
+ if (oneLine.startsWith("#") || oneLine.trim().equals("")||oneLine.startsWith("FilterVersion")) {
+ oneLine = in.readLine();
+ continue;
+ }
+
+ if (oneLine.trim().startsWith("<Composite>")||oneLine.trim().startsWith("<TopologyFilter>")
+ ||oneLine.trim().startsWith("<InteractionFilter>")) {
+ Vector<String> filterStrVect = new Vector<String>();
+ filterStrVect.add(oneLine);
+ while ((oneLine = in.readLine()) != null) {
+ if (oneLine.trim().startsWith("</Composite>")||oneLine.trim().startsWith("</TopologyFilter>")
+ ||oneLine.trim().startsWith("</InteractionFilter>")) {
+ filterStrVect.add(oneLine);
+ break;
+ }
+ filterStrVect.add(oneLine);
+ } // inner while loop
+
+ totalCount++;
+
+ CompositeFilter aFilter = getFilterFromStrVect(filterStrVect);
+ if (aFilter != null && !FilterUtil.isFilterNameDuplicated(aFilter.getName())) {
+ FilterPlugin.getAllFilterVect().add(aFilter);
+ addCount++;
+ }
+ }
+
+ oneLine = in.readLine();
+ } // while loop
+ }
+ finally {
+ if (in != null) {
+ in.close();
+ }
+ }
+ } catch (Exception ex) {
+ logger.error("Filter Read error", ex);
+ }
+
+ retValue[0] = totalCount;
+ retValue[1] = addCount;
+ return retValue;
+ }
+
+ /**
+ * Construct the filter objects based on the string representation of each filter.
+ */
+ public int[] getFilterVectFromPropFile(final File input) {
+ try {
+ return getFilterVectFromPropFile(new FileReader(input));
+ }
+ catch (final FileNotFoundException e) {
+ logger.error("Filter Read error", e);
+ final int[] retval = { 0, 0 };
+ return retval;
+ }
+ }
+
+ private AdvancedSetting getAdvancedSettingFromStrVect(Vector<String> pAdvSettingStrVect) {
+ AdvancedSetting advSetting = new AdvancedSetting();
+ String line = null;
+ for (int i=0; i<pAdvSettingStrVect.size(); i++ ) {
+ line = pAdvSettingStrVect.elementAt(i);
+ if (line.startsWith("scope.global=true")) {
+ advSetting.setGlobal(true);
+ }
+ if (line.startsWith("scope.global=false")) {
+ advSetting.setGlobal(false);
+ }
+ if (line.startsWith("scope.session=true")) {
+ advSetting.setSession(true);
+ }
+ if (line.startsWith("scope.session=false")) {
+ advSetting.setSession(false);
+ }
+ if (line.startsWith("selection.node=true")) {
+ advSetting.setNode(true);
+ }
+ if (line.startsWith("selection.node=false")) {
+ advSetting.setNode(false);
+ }
+ if (line.startsWith("selection.edge=true")) {
+ advSetting.setEdge(true);
+ }
+ if (line.startsWith("selection.edge=false")) {
+ advSetting.setEdge(false);
+ }
+ if (line.startsWith("edge.source=true")) {
+ advSetting.setSource(true);
+ }
+ if (line.startsWith("edge.source=false")) {
+ advSetting.setSource(false);
+ }
+ if (line.startsWith("edge.target=true")) {
+ advSetting.setTarget(true);
+ }
+ if (line.startsWith("edge.target=false")) {
+ advSetting.setTarget(false);
+ }
+ if (line.startsWith("Relation=AND")) {
+ advSetting.setRelation(Relation.AND);
+ }
+ if (line.startsWith("Relation=OR")) {
+ advSetting.setRelation(Relation.OR);
+ }
+ }
+
+ return advSetting;
+ }
+
+
+ private CompositeFilter getFilterFromStrVect(Vector<String> pFilterStrVect){
+
+ boolean isTopologyFilter = false;
+ boolean isInteractionFilter = false;
+
+ if (((String)pFilterStrVect.elementAt(0)).startsWith("<TopologyFilter>")) {
+ isTopologyFilter = true;
+ }
+ if (((String)pFilterStrVect.elementAt(0)).startsWith("<InteractionFilter>")) {
+ isInteractionFilter = true;
+ }
+
+ Vector<String> advSettingStrVect = new Vector<String>();
+ Vector<String> filterStrVect = new Vector<String>();
+
+ String line = null;
+ // Seperate AdvancedSetting from the rest
+ int startIndex = -1, endIndex = -1;
+ for (int i=0; i< pFilterStrVect.size(); i++) {
+ line = (String) pFilterStrVect.elementAt(i);
+
+ if (line.startsWith("<AdvancedSetting>")) {
+ startIndex = i;
+ }
+ if (line.startsWith("</AdvancedSetting>")) {
+ endIndex = i;
+ break;
+ }
+ }
+ advSettingStrVect.addAll(pFilterStrVect.subList(startIndex+1, endIndex));
+
+ filterStrVect.addAll(pFilterStrVect.subList(1, startIndex));
+ filterStrVect.addAll(pFilterStrVect.subList(endIndex+1, pFilterStrVect.size()));
+
+ CompositeFilter retFilter = new CompositeFilter();
+ retFilter.setAdvancedSetting(getAdvancedSettingFromStrVect(advSettingStrVect));
+
+ if (isTopologyFilter) {
+ retFilter = new TopologyFilter();
+ retFilter.setAdvancedSetting(getAdvancedSettingFromStrVect(advSettingStrVect));
+ getTopologyFilterFromStrVect((TopologyFilter)retFilter, filterStrVect);
+ return retFilter;
+ }
+
+ if (isInteractionFilter) {
+ AdvancedSetting advSetting = getAdvancedSettingFromStrVect(advSettingStrVect);
+ if (advSetting.isNodeChecked()) {
+ retFilter = new NodeInteractionFilter();
+ }
+ else {//advSetting.isEdgeChecked() == true
+ retFilter = new EdgeInteractionFilter();
+ }
+
+ retFilter.setAdvancedSetting(advSetting);
+ getInteractionFilterFromStrVect((InteractionFilter)retFilter, filterStrVect);
+ return retFilter;
+ }
+
+
+ for (int i=0; i<filterStrVect.size(); i++ ) {
+ line = filterStrVect.elementAt(i) ;
+
+ if (line.startsWith("name=")) {
+ String name =line.substring(5);
+ retFilter.setName(name);
+ }
+ if (line.startsWith("Negation=true")) {
+ retFilter.setNegation(true);
+ }
+ if (line.startsWith("Negation=false")) {
+ retFilter.setNegation(false);
+ }
+ if (line.startsWith("StringFilter=")) {
+ String _stringFilterValue = line.substring(13);
+ String[] _values = _stringFilterValue.split(":");
+ //controllingAttribute+":" + negation+ ":"+searchStr+":"+index_type;
+ StringFilter _strFilter = new StringFilter();
+ _strFilter.setParent(retFilter);
+ _strFilter.setControllingAttribute(_values[0]);
+ _strFilter.setNegation((new Boolean(_values[1])).booleanValue());
+
+ // handle the case where ':' is part of the search string
+ String _searchStr = _stringFilterValue.substring(_values[0].length()+_values[1].length()+2, _stringFilterValue.length()-_values[_values.length-1].length()-1);
+ _strFilter.setSearchStr(_searchStr);
+
+ _strFilter.setIndexType((new Integer(_values[_values.length-1])).intValue());
+ retFilter.addChild(_strFilter);
+ }
+ if (line.startsWith("NumericFilter=")) {
+ String[] _values = line.substring(14).split(":");
+ //controllingAttribute + ":" + negation+ ":"+lowBound+":" + highBound+ ":"+index_type;
+
+ // Determine data type of the attribute
+ String dataType = "int";
+ if (_values[2].indexOf(".")>=0 ||_values[2].indexOf("E")>=0 ||
+ _values[3].indexOf(".")>=0 ||_values[3].indexOf("E")>=0) {
+ dataType = "double";
+ }
+
+ if (dataType.equalsIgnoreCase("double")) {
+ NumericFilter<Double> _numFilter = new NumericFilter<Double>();
+ _numFilter.setParent(retFilter);
+ _numFilter.setControllingAttribute(_values[0]);
+ _numFilter.setNegation((new Boolean(_values[1])).booleanValue());
+ _numFilter.setLowBound(Double.valueOf(_values[2]));
+ _numFilter.setHighBound(Double.valueOf(_values[3]));
+ _numFilter.setIndexType((new Integer(_values[4])).intValue());
+ retFilter.addChild(_numFilter);
+ }
+ else { // dataType = "int"
+ NumericFilter<Integer> _numFilter = new NumericFilter<Integer>();
+ _numFilter.setParent(retFilter);
+ _numFilter.setControllingAttribute(_values[0]);
+ _numFilter.setNegation((new Boolean(_values[1])).booleanValue());
+ _numFilter.setLowBound(Integer.valueOf(_values[2]));
+ _numFilter.setHighBound(Integer.valueOf(_values[3]));
+ _numFilter.setIndexType((new Integer(_values[4])).intValue());
+ retFilter.addChild(_numFilter);
+ }
+ }
+ if (line.startsWith("CompositeFilter=")) {
+ //e.g. CompositeFilter=AAA:true
+ String[] _values = line.substring(16).split(":");
+
+ String name = _values[0].trim();
+ String notValue = _values[1].trim();
+
+ // get the reference CompositeFilter
+ CompositeFilter cmpFilter = null;
+
+ for (int j=0; j< FilterPlugin.getAllFilterVect().size(); j++) {
+ if (FilterPlugin.getAllFilterVect().elementAt(j).getName().equalsIgnoreCase(name)) {
+ cmpFilter = FilterPlugin.getAllFilterVect().elementAt(j);
+ break;
+ }
+ }
+ if (cmpFilter !=null) {
+ retFilter.addChild(cmpFilter, (new Boolean(notValue)).booleanValue());
+ }
+ }
+ if (line.startsWith("TopologyFilter=")) {
+ //e.g. TopologyFilter=AAA:true
+ String[] _values = line.substring(15).split(":");
+
+ String name = _values[0].trim();
+ String notValue = _values[1].trim();
+
+ // get the reference TopologyFilter
+ TopologyFilter topoFilter = null;
+ for (int j=0; j< FilterPlugin.getAllFilterVect().size(); j++) {
+ if (FilterPlugin.getAllFilterVect().elementAt(j).getName().equalsIgnoreCase(name)) {
+ topoFilter = (TopologyFilter) FilterPlugin.getAllFilterVect().elementAt(j);
+ break;
+ }
+ }
+ if (topoFilter !=null) {
+ retFilter.addChild(topoFilter, (new Boolean(notValue)).booleanValue());
+ }
+ }
+ if (line.startsWith("InteractionFilter=")) {
+ //e.g. InteractionFilter=AAA:true
+ String[] _values = line.substring(15).split(":");
+
+ String name = _values[0].trim();
+ String notValue = _values[1].trim();
+
+ // get the reference InteractionFilter
+ InteractionFilter interactionFilter = null;
+ for (int j=0; j< FilterPlugin.getAllFilterVect().size(); j++) {
+ if (FilterPlugin.getAllFilterVect().elementAt(j).getName().equalsIgnoreCase(name)) {
+ interactionFilter = (InteractionFilter) FilterPlugin.getAllFilterVect().elementAt(j);
+ break;
+ }
+ }
+ if (interactionFilter !=null) {
+ retFilter.addChild(interactionFilter, (new Boolean(notValue)).booleanValue());
+ }
+ }
+ }
+
+ return retFilter;
+ }
+
+
+ private void getTopologyFilterFromStrVect(TopologyFilter pFilter, Vector<String> pFilterStrVect){
+ //logger.debug("\nFilterIO.getTopologyFilterFromStrVect() ...\n");
+
+ String line = null;
+ for (int i=0; i<pFilterStrVect.size(); i++ ) {
+ line = pFilterStrVect.elementAt(i) ;
+
+ if (line.startsWith("name=")) {
+ String name =line.substring(5).trim();
+ pFilter.setName(name);
+ }
+ if (line.startsWith("Negation=true")) {
+ pFilter.setNegation(true);
+ }
+ if (line.startsWith("Negation=false")) {
+ pFilter.setNegation(false);
+ }
+
+ if (line.startsWith("minNeighbors=")) {
+ String minNeighbors = line.substring(13);
+ int minN = new Integer(minNeighbors).intValue();
+ pFilter.setMinNeighbors(minN);
+ }
+ if (line.startsWith("withinDistance=")) {
+ String withinDistance = line.substring(15);
+ int distance = new Integer(withinDistance).intValue();
+ pFilter.setDistance(distance);
+ }
+ if (line.startsWith("passFilter=")) {
+ String name = line.substring(11).trim();
+ // get the reference CompositeFilter
+ CompositeFilter cmpFilter = null;
+
+ for (int j=0; j< FilterPlugin.getAllFilterVect().size(); j++) {
+ if (FilterPlugin.getAllFilterVect().elementAt(j).getName().equalsIgnoreCase(name)) {
+ cmpFilter = FilterPlugin.getAllFilterVect().elementAt(j);
+ break;
+ }
+ }
+ if (cmpFilter !=null) {
+ pFilter.setPassFilter(cmpFilter);
+ }
+ }
+ }
+ //logger.debug("\n\nLeaving FilterIO.getTopologyFilterFromStrVect() ...\n");
+ //logger.debug("\nRecovered topo filter is :" + pFilter.toString()+ "\n\n");
+ }
+
+
+ private void getInteractionFilterFromStrVect(InteractionFilter pFilter, Vector<String> pFilterStrVect){
+
+ String line = null;
+ for (int i=0; i<pFilterStrVect.size(); i++ ) {
+ line = pFilterStrVect.elementAt(i) ;
+
+ if (line.startsWith("name=")) {
+ String name =line.substring(5).trim();
+ pFilter.setName(name);
+ }
+ if (line.startsWith("Negation=true")) {
+ pFilter.setNegation(true);
+ }
+ if (line.startsWith("Negation=false")) {
+ pFilter.setNegation(false);
+ }
+
+ if (line.startsWith("nodeType=")) {
+ String nodeTypeStr = line.substring(9);
+ int nodeType = new Integer(nodeTypeStr).intValue();
+ pFilter.setNodeType(nodeType);
+ }
+ if (line.startsWith("passFilter=")) {
+ String name = line.substring(11).trim();
+ // get the reference CompositeFilter
+ CompositeFilter cmpFilter = null;
+
+ for (int j=0; j< FilterPlugin.getAllFilterVect().size(); j++) {
+ if (FilterPlugin.getAllFilterVect().elementAt(j).getName().equalsIgnoreCase(name)) {
+ cmpFilter = FilterPlugin.getAllFilterVect().elementAt(j);
+ break;
+ }
+ }
+ if (cmpFilter !=null) {
+ pFilter.setPassFilter(cmpFilter);
+ }
+ }
+ }
+ }
+
+
+ public void saveGlobalPropFile(File pPropFile) {
+
+ // Because one filter may depend on the other, CompositeFilters must
+ // be sorted in the order of depthLevel before save
+ Object [] sortedFilters = getSortedCompositeFilter(FilterPlugin.getAllFilterVect());
+ Object[] globalFilters = getFiltersByScope(sortedFilters, "global");
+
+ try {
+ BufferedWriter writer = new BufferedWriter(new FileWriter(pPropFile));
+
+ try {
+ // Need to allow writing of header only so that when the last
+ // global filter is deleted, the props file is updated to reflect this
+ writer.write("FilterVersion=0.2\n");
+
+ if (globalFilters != null) {
+ for (int i = 0; i < globalFilters.length; i++) {
+ CompositeFilter theFilter = (CompositeFilter) globalFilters[i];
+ writer.write(theFilter.toString());
+ writer.newLine();
+ }
+ }
+ }
+ finally {
+ if (writer != null) {
+ writer.close();
+ }
+ }
+ } catch (Exception ex) {
+ logger.error("Global filter Write error",ex);
+ }
+ }
+
+
+ private Object[] getFiltersByScope(Object[] pFilters, String pScope) {
+ if (pFilters == null || pFilters.length == 0) {
+ return null;
+ }
+ ArrayList<CompositeFilter> retFilterList = new ArrayList<CompositeFilter>();
+ for (int i = 0; i < pFilters.length; i++) {
+ CompositeFilter theFilter = (CompositeFilter) pFilters[i];
+ AdvancedSetting advSetting = theFilter.getAdvancedSetting();
+
+ if (pScope.equalsIgnoreCase("global")) {
+ if (advSetting.isGlobalChecked()) {
+ retFilterList.add(theFilter);
+ }
+ }
+ if (pScope.equalsIgnoreCase("session")) {
+ if (advSetting.isSessionChecked()) {
+ retFilterList.add(theFilter);
+ }
+ }
+ }
+ return retFilterList.toArray();
+ }
+
+ public void saveSessionStateFiles(List<File> pFileList){
+
+ // Because one filter may depend on the other, CompositeFilters must
+ // be sorted in the order of depthLevel before save
+ Object [] sortedFilters = getSortedCompositeFilter(FilterPlugin.getAllFilterVect());
+ Object[] sessionFilters = getFiltersByScope(sortedFilters, "session");
+
+ if (sessionFilters == null || sessionFilters.length == 0) {
+ return;
+ }
+
+ // Create an empty file on system temp directory
+ String tmpDir = System.getProperty("java.io.tmpdir");
+ // logger.debug("java.io.tmpdir: [" + tmpDir + "]");
+
+ File session_filter_file = new File(tmpDir, "session_filters.props");
+
+ //
+ try {
+ BufferedWriter writer = new BufferedWriter(new FileWriter(session_filter_file));
+
+ try {
+ writer.write("FilterVersion=0.2\n");
+
+ for (int i = 0; i < sessionFilters.length; i++) {
+ CompositeFilter theFilter = (CompositeFilter) sessionFilters[i];
+ writer.write(theFilter.toString());
+ writer.newLine();
+ }
+ }
+ finally {
+ if ( writer != null) {
+ writer.close();
+ }
+ }
+ } catch (Exception ex) {
+ logger.error("Session filter Write error",ex);
+ }
+
+ if ((session_filter_file != null) && (session_filter_file.exists())) {
+ pFileList.add(session_filter_file);
+ }
+ }
+
+
+ public void restoreSessionState(List<File> pStateFileList) {
+ if ((pStateFileList == null) || (pStateFileList.size() == 0)) {
+ logger.warn("\tNo previous filter state to restore.");
+ return;
+ }
+
+ try {
+ File session_filter_file = pStateFileList.get(0);
+
+ int[] loadCounts = getFilterVectFromPropFile(session_filter_file);
+ logger.info("\tLoad " + loadCounts[1] + " session filters");
+ logger.info("\t\t" + (loadCounts[0]-loadCounts[1]) + " duplicated filters are not loaded");
+ } catch (Throwable ee) {
+ logger.error("Failed to restore Filters from session!");
+ }
+ }
+
+
+ // Determine the nest level of the given CompositeFilter
+ private int getTreeDepth(CompositeFilter pFilter, int pDepthLevel){
+ List<CyFilter> childrenList = pFilter.getChildren();
+ List<CompositeFilter> theList = new ArrayList<CompositeFilter>();
+
+ // Find all the child compositeFilter
+ for (int i=0; i<childrenList.size(); i++) {
+ if (childrenList.get(i) instanceof CompositeFilter) {
+ theList.add((CompositeFilter)childrenList.get(i));
+ }
+ }
+
+ if (theList.size() == 0) {
+ return pDepthLevel;
+ }
+
+ int [] depths = new int[theList.size()];
+ for (int j=0; j<theList.size(); j++) {
+ depths[j] = getTreeDepth((CompositeFilter)theList.get(j), pDepthLevel+1);
+ }
+
+ java.util.Arrays.sort(depths);
+
+ return depths[depths.length-1];
+ }
+
+ public Object [] getSortedCompositeFilter(Vector pAllFilterVect) {
+ if (pAllFilterVect == null || pAllFilterVect.size() == 0) {
+ return null;
+ }
+
+ //Seperate TopologyFilter from other CompositeFilter
+ Vector<TopologyFilter> topoFilterVect = new Vector<TopologyFilter>();
+ Vector<CompositeFilter> otherFilterVect = new Vector<CompositeFilter>();
+ for (int i=0; i<pAllFilterVect.size(); i++ ) {
+ if (pAllFilterVect.elementAt(i) instanceof TopologyFilter) {
+ topoFilterVect.add((TopologyFilter)pAllFilterVect.elementAt(i));
+ }
+ else {
+ otherFilterVect.add((CompositeFilter)pAllFilterVect.elementAt(i));
+ }
+ }
+
+ //TopologyFilters depend on other compositeFilter, they should follow other compositeFilter
+ Object[] sortedFilters = otherFilterVect.toArray();
+ Arrays.sort(sortedFilters, (new CompositeFilterCmp<CompositeFilter>()));
+
+ Vector<CompositeFilter> sortedFilterVect = new Vector<CompositeFilter>();
+ for (int i=0; i<sortedFilters.length; i++) {
+ sortedFilterVect.add((CompositeFilter)sortedFilters[i]);
+ }
+
+ sortedFilterVect.addAll(topoFilterVect);
+
+ return sortedFilterVect.toArray();
+ }
+
+ class CompositeFilterCmp<T> implements Comparator {
+
+ public int compare(Object o1, Object o2){
+ int depth1 = getTreeDepth((CompositeFilter) o1, 0);
+ int depth2 = getTreeDepth((CompositeFilter) o2, 0);
+
+ if (depth1 > depth2) {
+ return 1;
+ }
+ if (depth1 == depth2) {
+ return 0;
+ }
+ return -1;//depth1 < depth2
+ }
+
+ public boolean equals(Object obj) {
+ return false;
+ }
+
+ }
+}
+
diff --git a/coreplugins/filters/src/main/java/cytoscape/filters/FilterMenuItemAction.java b/coreplugins/filters/src/main/java/cytoscape/filters/FilterMenuItemAction.java
new file mode 100644
index 0000000..6e135ec
--- /dev/null
+++ b/coreplugins/filters/src/main/java/cytoscape/filters/FilterMenuItemAction.java
@@ -0,0 +1,110 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.filters;
+
+import cytoscape.*;
+
+import cytoscape.data.*;
+
+import cytoscape.util.*;
+
+import cytoscape.view.*;
+import cytoscape.view.cytopanels.CytoPanelImp;
+import cytoscape.view.cytopanels.CytoPanelState;
+
+import java.awt.event.*;
+
+import javax.swing.*;
+
+
+/**
+ *
+ */
+public class FilterMenuItemAction extends CytoscapeAction {
+ //protected JFrame frame;
+ protected FilterPlugin theFilter;
+ private CytoPanelImp cytoPanelWest = (CytoPanelImp) Cytoscape.getDesktop().getCytoPanel(SwingConstants.WEST);
+
+ /**
+ * Creates a new FilterMenuItem object.
+ *
+ * @param icon DOCUMENT ME!
+ * @param csfilter DOCUMENT ME!
+ */
+ public FilterMenuItemAction(ImageIcon icon, FilterPlugin pFilter) {
+ super("Use Filters", icon);
+ theFilter = pFilter;
+ setPreferredMenu("Select");
+ setAcceleratorCombo(java.awt.event.KeyEvent.VK_F7, 0);
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+
+ // If the state of the cytoPanelEast is HIDE, show it
+ if (cytoPanelWest.getState() == CytoPanelState.HIDE) {
+ cytoPanelWest.setState(CytoPanelState.DOCK);
+ }
+
+ // Select the filter panel
+ int index = cytoPanelWest.indexOfComponent("Filters");
+ cytoPanelWest.setSelectedIndex(index);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isInToolBar() {
+ return false;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isInMenuBar() {
+ return true;
+ }
+}
diff --git a/coreplugins/filters/src/main/java/cytoscape/filters/FilterPlugin.java b/coreplugins/filters/src/main/java/cytoscape/filters/FilterPlugin.java
new file mode 100644
index 0000000..b7d14de
--- /dev/null
+++ b/coreplugins/filters/src/main/java/cytoscape/filters/FilterPlugin.java
@@ -0,0 +1,164 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.filters;
+
+import cytoscape.Cytoscape;
+import cytoscape.CytoscapeInit;
+import cytoscape.filters.view.FilterMainPanel;
+import cytoscape.logger.CyLogger;
+import cytoscape.plugin.CytoscapePlugin;
+import cytoscape.util.*;
+import cytoscape.view.cytopanels.CytoPanelImp;
+import java.io.File;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.util.List;
+import java.util.Vector;
+import javax.swing.ImageIcon;
+import javax.swing.SwingConstants;
+
+/**
+ *
+ */
+public class FilterPlugin extends CytoscapePlugin {
+
+ private static Vector<CompositeFilter> allFilterVect = null;
+ private FilterIO filterIO = new FilterIO();
+ private CyLogger logger = null;
+
+ public static final String DYNAMIC_FILTER_THRESHOLD = "dynamicFilterThreshold";
+ public static final int DEFAULT_DYNAMIC_FILTER_THRESHOLD = 1000;
+
+ // Other plugin can turn on/off the FilterEvent
+ public static boolean shouldFireFilterEvent = false;
+
+ protected ImageIcon icon = new ImageIcon(getClass().getResource("/stock_filter-data-by-criteria.png"));
+ protected ImageIcon icon2 = new ImageIcon(getClass().getResource("/stock_filter-data-by-criteria-16.png"));
+
+ // Other plugin can get a handler to all the filters defined
+ public static Vector<CompositeFilter> getAllFilterVect() {
+ if (allFilterVect == null) {
+ allFilterVect = new Vector<CompositeFilter>();
+ }
+ return allFilterVect;
+ }
+
+ /**
+ * Creates a new FilterPlugin object.
+ *
+ * @param icon
+ * DOCUMENT ME!
+ * @param csfilter
+ * DOCUMENT ME!
+ */
+ public FilterPlugin() {
+
+ // Add a menuItem on "select" menu
+ FilterMenuItemAction menuAction = new FilterMenuItemAction(icon2, this);
+ Cytoscape.getDesktop().getCyMenus().addCytoscapeAction(
+ (CytoscapeAction) menuAction);
+
+ // Add an icon to tool-bar
+ FilterPluginToolBarAction toolbarAction = new FilterPluginToolBarAction(
+ icon, this);
+ Cytoscape.getDesktop().getCyMenus().addCytoscapeAction(
+ (CytoscapeAction) toolbarAction);
+
+ if (allFilterVect == null) {
+ allFilterVect = new Vector<CompositeFilter>();
+ }
+
+ logger = CyLogger.getLogger(FilterPlugin.class);
+
+ restoreInitState();
+
+ // initialize the filterMainPanel and add it to the control panel
+ CytoPanelImp cytoPanelWest = (CytoPanelImp) Cytoscape.getDesktop()
+ .getCytoPanel(SwingConstants.WEST);
+
+ cytoPanelWest.add("Filters", new FilterMainPanel(allFilterVect));
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void onCytoscapeExit() {
+ // Save global filter to "filters.prop"
+ filterIO.saveGlobalPropFile(CytoscapeInit.getConfigFile("filters.props"));
+ }
+
+ public void restoreInitState() {
+ final File globalFilterFile = CytoscapeInit.getConfigFile("filters.props");
+ int[] loadCount = filterIO.getFilterVectFromPropFile(globalFilterFile);
+ logger.debug("FilterPlugin: load " + loadCount[1] + " of " + loadCount[0] + " filters from filters.prop");
+
+ if (loadCount[1] == 0) {
+ final String DEFAULT_FILTERS_FILENAME = "/default_filters.props";
+ final InputStream inputStream = FilterPlugin.class.getResourceAsStream(DEFAULT_FILTERS_FILENAME);
+ if (inputStream == null) {
+ System.err.println("FilterPlugin: Failed to read default filters from \""
+ + DEFAULT_FILTERS_FILENAME + "\" in the plugin's jar file!");
+ return;
+ }
+
+ final InputStreamReader inputStreamReader = new InputStreamReader(inputStream);
+ loadCount = filterIO.getFilterVectFromPropFile(inputStreamReader);
+ logger.debug("FilterPlugin: load " + loadCount[1] + " of " + loadCount[0]
+ + " filters from " + DEFAULT_FILTERS_FILENAME);
+ }
+ }
+
+ // override the following two methods to save state.
+ /**
+ * DOCUMENT ME!
+ *
+ * @param pStateFileList
+ * DOCUMENT ME!
+ */
+ public void restoreSessionState(List<File> pStateFileList) {
+ filterIO.restoreSessionState(pStateFileList);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param pFileList
+ * DOCUMENT ME!
+ */
+ public void saveSessionStateFiles(List<File> pFileList) {
+ filterIO.saveSessionStateFiles(pFileList);
+ }
+}
diff --git a/coreplugins/filters/src/main/java/cytoscape/filters/FilterPluginToolBarAction.java b/coreplugins/filters/src/main/java/cytoscape/filters/FilterPluginToolBarAction.java
new file mode 100644
index 0000000..d4a294e
--- /dev/null
+++ b/coreplugins/filters/src/main/java/cytoscape/filters/FilterPluginToolBarAction.java
@@ -0,0 +1,115 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.filters;
+
+import cytoscape.*;
+
+import cytoscape.data.*;
+
+import cytoscape.util.*;
+
+import cytoscape.view.*;
+import cytoscape.view.cytopanels.CytoPanelImp;
+import cytoscape.view.cytopanels.CytoPanelState;
+
+import java.awt.event.*;
+
+import javax.swing.*;
+
+import cytoscape.filters.FilterPlugin;
+
+
+/**
+ *
+ */
+public class FilterPluginToolBarAction extends CytoscapeAction {
+ //protected JFrame frame;
+ protected FilterPlugin theFilter;
+ private CytoPanelImp cytoPanelWest = (CytoPanelImp) Cytoscape.getDesktop().getCytoPanel(SwingConstants.WEST);
+
+ /**
+ * Creates a new FilterPlugin object.
+ *
+ * @param icon DOCUMENT ME!
+ * @param csfilter DOCUMENT ME!
+ */
+ public FilterPluginToolBarAction(ImageIcon icon, FilterPlugin pFilter) {
+ super("", icon);
+ // Set SHORT_DESCRIPTION; used to create tool-tip
+ this.putValue(Action.SHORT_DESCRIPTION, "Use Filters");
+ theFilter = pFilter;
+ setPreferredMenu("Select");
+ //setAcceleratorCombo(java.awt.event.KeyEvent.VK_A,
+ // ActionEvent.CTRL_MASK | ActionEvent.SHIFT_MASK);
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+
+ // If the state of the cytoPanel is HIDE, show it
+ if (cytoPanelWest.getState() == CytoPanelState.HIDE) {
+ cytoPanelWest.setState(CytoPanelState.DOCK);
+ }
+
+ // Select the filter panel on CytoPanelWEST
+ int index = cytoPanelWest.indexOfComponent("Filters");
+ cytoPanelWest.setSelectedIndex(index);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isInToolBar() {
+ return true;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isInMenuBar() {
+ return false;
+ }
+}
diff --git a/coreplugins/filters/src/main/java/cytoscape/filters/InteractionFilter.java b/coreplugins/filters/src/main/java/cytoscape/filters/InteractionFilter.java
new file mode 100644
index 0000000..0e9ae2e
--- /dev/null
+++ b/coreplugins/filters/src/main/java/cytoscape/filters/InteractionFilter.java
@@ -0,0 +1,162 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.filters;
+
+import cytoscape.CyNetwork;
+
+
+public class InteractionFilter extends CompositeFilter {
+ public static int NODE_UNDEFINED = -1;
+ public static int NODE_SOURCE = 0;
+ public static int NODE_TARGET = 1;
+ public static int NODE_SOURCE_TARGET = 3;
+
+ protected int nodeType = NODE_UNDEFINED;
+
+ protected boolean isSourceChecked = true;
+ protected boolean isTargetChecked = true;
+
+ protected CompositeFilter passFilter = new CompositeFilter("None");
+
+ public InteractionFilter() {
+ }
+
+ public InteractionFilter(String pName) {
+ name = pName;
+ }
+
+ public void setPassFilter(CompositeFilter pFilter) {
+ passFilter = pFilter;
+ childChanged = true;
+ }
+
+ public CompositeFilter getPassFilter() {
+ return passFilter;
+ }
+
+ public int getNodeType() {
+ return nodeType;
+ }
+
+ public void setNodeType(int pNodeType) {
+ if (nodeType == pNodeType) {
+ return;
+ }
+ nodeType = pNodeType;
+ if (nodeType == NODE_SOURCE) {
+ isSourceChecked = true;
+ isTargetChecked = false;
+ }
+ else if (nodeType == NODE_TARGET) {
+ isSourceChecked = false;
+ isTargetChecked = true;
+ }
+ else if (nodeType == NODE_SOURCE_TARGET) {
+ isSourceChecked = true;
+ isTargetChecked = true;
+ }
+ childChanged = true;
+ }
+
+ public boolean isSourceChecked() {
+ return isSourceChecked;
+ }
+
+ public boolean isTargetChecked() {
+ return isTargetChecked;
+ }
+
+ public void setSourceChecked(boolean pIsChecked) {
+ isSourceChecked =pIsChecked;
+ updateNodeType();
+ }
+
+ public void setTargetChecked(boolean pIsChecked) {
+ isTargetChecked =pIsChecked;
+ updateNodeType();
+ }
+
+ private void updateNodeType() {
+ //update nodeType
+ if (isSourceChecked && isTargetChecked) {
+ nodeType = NODE_SOURCE_TARGET;
+ }
+ else if (isSourceChecked) {
+ nodeType = NODE_SOURCE;
+ }
+ else if (isTargetChecked) {
+ nodeType = NODE_TARGET;
+ }
+ else {
+ nodeType = NODE_UNDEFINED;
+ }
+ }
+
+
+ public void setNetwork(CyNetwork pNetwork) {
+ if (network != null && network == pNetwork) {
+ return;
+ }
+ network = pNetwork;
+ if (passFilter != null) {
+ passFilter.setNetwork(network);
+ }
+
+ childChanged();
+ }
+
+
+ public String toString() {
+ String retStr = "<InteractionFilter>\n";
+
+ retStr = retStr + "name=" + name + "\n";
+ retStr = retStr + advancedSetting.toString() + "\n";
+ retStr = retStr + "Negation=" + negation + "\n";
+ retStr = retStr + "nodeType=" + nodeType + "\n";
+
+ if (passFilter == null) {
+ retStr += "passFilter=null\n";
+ }
+ else {
+ retStr += "passFilter=" + passFilter.getName()+"\n";
+ }
+
+ retStr += "</InteractionFilter>";
+
+ return retStr;
+ }
+}
diff --git a/coreplugins/filters/src/main/java/cytoscape/filters/NodeInteractionFilter.java b/coreplugins/filters/src/main/java/cytoscape/filters/NodeInteractionFilter.java
new file mode 100644
index 0000000..e4929a5
--- /dev/null
+++ b/coreplugins/filters/src/main/java/cytoscape/filters/NodeInteractionFilter.java
@@ -0,0 +1,140 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.filters;
+
+import giny.model.Node;
+import java.util.*;
+import cytoscape.Cytoscape;
+
+
+public class NodeInteractionFilter extends InteractionFilter {
+
+ public NodeInteractionFilter() {
+ //Set selection for node
+ advancedSetting.setNode(true);
+ advancedSetting.setEdge(false);
+ }
+
+ public NodeInteractionFilter(String pName) {
+ name = pName;
+ // Set selection for node
+ advancedSetting.setNode(true);
+ advancedSetting.setEdge(false);
+ }
+
+
+ public void apply() {
+ if ( !childChanged )
+ return;
+
+ if (network == null) {
+ setNetwork(Cytoscape.getCurrentNetwork());
+ }
+
+ if (network == null) {
+ return;
+ }
+
+ //Make sure the pass filter is current
+ if (passFilter == null) {
+ passFilter = new CompositeFilter("None");
+ }
+
+ if (!passFilter.getName().equalsIgnoreCase("None")) {
+ passFilter.setNetwork(network);
+ passFilter.apply();
+ }
+
+ List<Node> nodes_list = null;
+
+ // NodeInteractionFilter will select node only
+ nodes_list = network.nodesList();
+ int objectCount = nodes_list.size();
+ node_bits = new BitSet(objectCount); // all the bits are false at very beginning
+
+ if ((nodeType != NODE_UNDEFINED)&&(!passFilter.getName().equalsIgnoreCase("None"))) {
+ for (int i=0; i<objectCount; i++) {
+ if (isHit((Node)nodes_list.get(i))) {
+ node_bits.set(i);
+ }
+ }
+ }
+
+ if (negation) {
+ node_bits.flip(0, objectCount);
+ }
+
+ childChanged = false;
+ }
+
+
+ private boolean isHit(Node pNode) {
+
+ // Get the list of relevant edges for this node
+ List adjacentEdges = null;
+
+ if (nodeType == NODE_SOURCE) {
+ adjacentEdges = network.getAdjacentEdgesList(pNode, true, false, true);
+ }
+ else if (nodeType == NODE_TARGET) {
+ adjacentEdges = network.getAdjacentEdgesList(pNode, true, true, false);
+ }
+ else if (nodeType == NODE_SOURCE_TARGET) {
+ adjacentEdges = network.getAdjacentEdgesList(pNode, true, true, true);
+ }
+ else { //nodeType == NODE_UNDEFINED --Neither source or target is selected
+ return false;
+ }
+
+ if (adjacentEdges == null || adjacentEdges.size() == 0) {
+ return false;
+ }
+
+ BitSet passFilter_edgeBits = passFilter.getEdgeBits();
+
+ int edgeIndex = -1;
+ for (int i=0; i < adjacentEdges.size(); i++) {
+ edgeIndex = network.edgesList().indexOf(adjacentEdges.get(i));
+
+ if (passFilter_edgeBits.get(edgeIndex) == true) {
+ return true;
+ }
+ }
+
+ return false;
+ }
+}
diff --git a/coreplugins/filters/src/main/java/cytoscape/filters/NumericFilter.java b/coreplugins/filters/src/main/java/cytoscape/filters/NumericFilter.java
new file mode 100644
index 0000000..5438d5a
--- /dev/null
+++ b/coreplugins/filters/src/main/java/cytoscape/filters/NumericFilter.java
@@ -0,0 +1,168 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.filters;
+
+import giny.model.Edge;
+import giny.model.Node;
+
+import java.util.*;
+
+import csplugins.quickfind.util.QuickFind;
+import csplugins.widgets.autocomplete.index.TextIndex;
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import cytoscape.logger.CyLogger;
+import cytoscape.filters.util.FilterUtil;
+import csplugins.widgets.autocomplete.index.Hit;
+import csplugins.widgets.autocomplete.index.NumberIndex;
+
+
+/**
+ * This is a Cytoscape specific filter that will pass nodes if
+ * a selected attribute matches a specific value.
+ */
+
+public class NumericFilter<T extends Number> extends AtomicFilter {
+
+ private T lowBound, highBound;
+
+ public NumericFilter() {
+ }
+
+ public NumericFilter(String pCtrlAttri, int pIndexType, NumberIndex pIndex) {
+ controllingAttribute = pCtrlAttri;
+ index_type = pIndexType;
+ quickFind_index = pIndex;
+ }
+
+ public boolean passesFilter(Object obj) {
+ return false;
+ }
+ public T getLowBound(){
+ return lowBound;
+ }
+
+ public T getHighBound(){
+ return highBound;
+ }
+
+ public void setLowBound(T pLowBound){
+ lowBound = pLowBound;
+ }
+
+ public void setHighBound(T pHighBound){
+ highBound = pHighBound;
+ }
+
+ public void setRange(T pLowBound, T pUpBound){
+ lowBound = pLowBound;
+ highBound = pUpBound;
+ }
+
+ public void apply() {
+
+ List<Node> nodes_list = null;
+ List<Edge> edges_list=null;
+
+ int objectCount = -1;
+ if (index_type == QuickFind.INDEX_NODES) {
+ nodes_list = network.nodesList();
+ objectCount = nodes_list.size();
+ node_bits = new BitSet(objectCount); // all the bits are false initially
+ }
+ else if (index_type == QuickFind.INDEX_EDGES) {
+ edges_list = network.edgesList();
+ objectCount = edges_list.size();
+ edge_bits = new BitSet(objectCount); // all the bits are false initially
+ }
+ else {
+ CyLogger.getLogger(NumericFilter.class).error("StringFilter: Index_type is undefined.");
+ return;
+ }
+
+ if (lowBound == null || highBound == null || network == null || !FilterUtil.hasSuchAttribute(controllingAttribute,index_type)) {
+ return;
+ }
+
+ //If quickFind_index does not exist, build the Index
+ //if (quickFind_index == null) {
+ quickFind_index = FilterUtil.getQuickFindIndex(controllingAttribute, network, index_type);
+ //}
+
+ //System.out.println(" NumberFilter.apply(): objectCount = " + objectCount);
+ NumberIndex numberIndex = (NumberIndex) quickFind_index;
+ List list = numberIndex.getRange(lowBound, highBound);
+
+ if (list.size() == 0) {
+ return;
+ }
+
+ int index;
+ if (index_type == QuickFind.INDEX_NODES) {
+ for (Object obj : list) {
+ index = nodes_list.lastIndexOf((Node) obj);
+ node_bits.set(index, true);
+ }
+ } else if (index_type == QuickFind.INDEX_EDGES) {
+ for (Object obj : list) {
+ index = edges_list.lastIndexOf((Edge) obj);
+ edge_bits.set(index, true);
+ }
+ }
+
+ if (negation) {
+ if (index_type == QuickFind.INDEX_NODES) {
+ node_bits.flip(0, objectCount);
+ }
+ if (index_type == QuickFind.INDEX_EDGES) {
+ edge_bits.flip(0, objectCount);
+ }
+ }
+ }
+
+ /**
+ *
+ */
+ public String toString() {
+ return "NumericFilter="+controllingAttribute + ":" + negation+ ":"+lowBound+":" + highBound+ ":"+index_type;
+ }
+
+ //public NumericFilter clone() {
+ // return new NumericFilter(attributeName, searchValues);
+ //}
+
+}
diff --git a/coreplugins/filters/src/main/java/cytoscape/filters/Relation.java b/coreplugins/filters/src/main/java/cytoscape/filters/Relation.java
new file mode 100644
index 0000000..cac53fb
--- /dev/null
+++ b/coreplugins/filters/src/main/java/cytoscape/filters/Relation.java
@@ -0,0 +1,8 @@
+package cytoscape.filters;
+
+public enum Relation {
+ AND,
+ OR,
+ XOR,
+ NAND,
+}
diff --git a/coreplugins/filters/src/main/java/cytoscape/filters/StringFilter.java b/coreplugins/filters/src/main/java/cytoscape/filters/StringFilter.java
new file mode 100644
index 0000000..5cad185
--- /dev/null
+++ b/coreplugins/filters/src/main/java/cytoscape/filters/StringFilter.java
@@ -0,0 +1,175 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.filters;
+
+import giny.model.Node;
+import giny.model.Edge;
+import java.util.*;
+import csplugins.widgets.autocomplete.index.Hit;
+import csplugins.widgets.autocomplete.index.TextIndex;
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import cytoscape.logger.CyLogger;
+import csplugins.quickfind.util.QuickFind;
+import cytoscape.filters.util.FilterUtil;
+
+/**
+ * This is a Cytoscape specific filter that will pass nodes if
+ * a selected attribute matches a specific value.
+ */
+public class StringFilter extends AtomicFilter {
+
+ private String searchStr = null;
+
+ //---------------------------------------//
+ // Constructor
+ //----------------------------------------//
+
+ /**
+ * Creates a new StringPatternFilter object.
+ *
+ * @param desc DOCUMENT ME!
+ */
+
+ public StringFilter() {
+ super();
+ }
+
+ public StringFilter(String pCtrlAttri, int pIndexType, TextIndex pIndex) {
+ controllingAttribute = pCtrlAttri;
+ index_type = pIndexType;
+ quickFind_index = pIndex;
+ }
+
+ public String getSearchStr() {
+ return searchStr;
+ }
+
+ public void setSearchStr(String pSearchStr) {
+ searchStr = pSearchStr;
+ if (getParent() != null) {
+ getParent().childChanged();
+ }
+ }
+
+ /**
+ * Caculate the bitSet based on the existing TextIndex and search string.
+ * The size of the bitSet is the number of nodes/edges in the given network,
+ * All bits are initially set to false, those with hits are set to true.
+ * @param none.
+ * @return none.
+ */
+
+ public void apply() {
+
+ List<Node> nodes_list = null;
+ List<Edge> edges_list=null;
+
+ // Initialize the bitset
+ int objectCount = -1;
+ if (index_type == QuickFind.INDEX_NODES) {
+ nodes_list = network.nodesList();
+ objectCount = nodes_list.size();
+ node_bits = new BitSet(objectCount); // all the bits are false at very beginning
+ }
+ else if (index_type == QuickFind.INDEX_EDGES) {
+ edges_list = network.edgesList();
+ objectCount = edges_list.size();
+ edge_bits = new BitSet(objectCount); // all the bits are false at very beginning
+ }
+ else {
+ CyLogger.getLogger(StringFilter.class).error("StringFilter: Index_type is undefined.");
+ return;
+ }
+
+ if (searchStr == null || network == null || !FilterUtil.hasSuchAttribute(controllingAttribute,index_type)) {
+ return;
+ }
+
+ //If quickFind_index does not exist, build the Index
+ //if (quickFind_index == null) {
+ quickFind_index = FilterUtil.getQuickFindIndex(controllingAttribute, network, index_type);
+ //}
+
+ TextIndex theIndex = (TextIndex) quickFind_index;
+ Hit[] hits = theIndex.getHits(searchStr, Integer.MAX_VALUE);
+
+ if (hits.length == 0) {
+ return;
+ }
+ Hit hit0 = hits[0];
+
+ Object[] hit_objs = hit0.getAssociatedObjects();
+
+ int index=-1;
+ if (index_type == QuickFind.INDEX_NODES) {
+ for (Object obj : hit_objs) {
+ index = nodes_list.indexOf((Node) obj);
+ node_bits.set(index, true);
+ }
+ } else if (index_type == QuickFind.INDEX_EDGES){
+ for (Object obj : hit_objs) {
+ index = edges_list.indexOf((Edge) obj);
+ edge_bits.set(index, true);
+ }
+ }
+
+ if (negation) {
+ if (index_type == QuickFind.INDEX_NODES) {
+ node_bits.flip(0, objectCount);
+ }
+ if (index_type == QuickFind.INDEX_EDGES) {
+ edge_bits.flip(0, objectCount);
+ }
+ }
+ }
+
+ /**
+ * @return the name of this Filter and the search string (keyword).
+ */
+ public String toString() {
+ return "StringFilter="+controllingAttribute+":" + negation+ ":"+searchStr+":"+index_type;
+ }
+/*
+ public StringFilter clone() {
+ StringFilter newStringFilter = new StringFilter("copy_of_"+name, controllingAttribute, searchStr);
+ newStringFilter.setNegation(negation);
+ return newStringFilter;
+ }
+*/
+
+}
diff --git a/coreplugins/filters/src/main/java/cytoscape/filters/TopologyFilter.java b/coreplugins/filters/src/main/java/cytoscape/filters/TopologyFilter.java
new file mode 100644
index 0000000..171ffab
--- /dev/null
+++ b/coreplugins/filters/src/main/java/cytoscape/filters/TopologyFilter.java
@@ -0,0 +1,288 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.filters;
+
+import giny.model.Edge;
+import giny.model.Node;
+
+import java.util.*;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import cytoscape.logger.CyLogger;
+import csplugins.quickfind.util.QuickFind;
+import csplugins.widgets.autocomplete.index.GenericIndex;
+
+
+public class TopologyFilter extends CompositeFilter {
+
+ private int minNeighbors = 1;
+ private int withinDistance = 1;
+ private CompositeFilter passFilter = null;
+
+ public TopologyFilter() {
+ super.advancedSetting.setNode(true);
+ }
+
+ public TopologyFilter(String pName) {
+ name = pName;
+ super.advancedSetting.setNode(true);
+ }
+
+ public void setPassFilter(CompositeFilter pFilter) {
+ passFilter = pFilter;
+ childChanged = true;
+ }
+
+ public CompositeFilter getPassFilter() {
+ return passFilter;
+ }
+
+ public void setMinNeighbors(int pNeighbors) {
+ minNeighbors = pNeighbors;
+ childChanged = true;
+ }
+
+ public int getMinNeighbors() {
+ return minNeighbors;
+ }
+
+ public void setDistance(int pDistance) {
+ withinDistance = pDistance;
+ childChanged = true;
+ }
+
+ public int getDistance() {
+ return withinDistance;
+ }
+
+ public BitSet getNodeBits() {
+ apply();
+ return node_bits;
+ }
+
+ public BitSet getEdgeBits(){
+ apply();
+ return edge_bits;
+ }
+
+
+ public void apply() {
+ if ( !childChanged )
+ return;
+
+ if (network == null) {
+ return;
+ }
+
+ //Make sure the pass filter is current
+ if (passFilter == null) {
+ passFilter = new TopologyFilter("None");
+ }
+
+ if (!passFilter.getName().equalsIgnoreCase("None")) {
+ passFilter.setNetwork(network);
+ passFilter.apply();
+ }
+
+ List<Node> nodes_list = null;
+ List<Edge> edges_list=null;
+
+ int objectCount = -1;
+
+ if (advancedSetting.isNodeChecked()) {
+ nodes_list = network.nodesList();
+ objectCount = nodes_list.size();
+
+ //Create an index mapping between RootGraphIndex and index in current network
+ HashMap<Integer, Integer> indexMap = new HashMap<Integer, Integer>();
+ Object [] nodeArray = network.nodesList().toArray();
+ int rootgraphIndex = -1;
+ for (int i=0; i<objectCount; i++) {
+ rootgraphIndex = network.getIndex((Node)nodeArray[i]);
+ indexMap.put(new Integer(rootgraphIndex), new Integer(i));
+ }
+
+ //
+ node_bits = new BitSet(objectCount); // all the bits are false at very beginning
+
+ for (int i=0; i<objectCount; i++) {
+ if (isHit(nodes_list.get(i), indexMap)) {
+ node_bits.set(i);
+ }
+ }
+ }
+ else {
+ CyLogger.getLogger(TopologyFilter.class).error("objectType is undefined.");
+ return;
+ }
+
+ if (negation) {
+ if (advancedSetting.isNodeChecked()) {
+ node_bits.flip(0, objectCount);
+ }
+ }
+
+ childChanged = false;
+ }
+
+
+ private boolean isHit(Object pObj, HashMap<Integer, Integer> pIndexMap) {
+ // Get all the neighbors for pNode that pass the given filter
+ HashSet neighborSet = new HashSet();
+ getNeighbors(pObj, neighborSet, withinDistance);
+
+ //Exclude self from the neighbor
+ if (neighborSet.contains(pObj)) {
+ neighborSet.remove(pObj);
+ }
+
+ // Obviously, this does not meet the criteria, don't do extra work
+ if (neighborSet.size() < minNeighbors) {
+ return false;
+ }
+
+ // remove all the neighbors that do not pass the given filter
+ if (!passFilter.getName().equalsIgnoreCase("None")) {
+ Object [] nodeArray = neighborSet.toArray();
+ for (int i=0; i< nodeArray.length; i++) {
+ //int nodeIndex = network.nodesList().indexOf(nodeArray[i]); //This works, but very slow
+ int rootgraphIndex = network.getIndex((Node)nodeArray[i]);
+ int nodeIndex = pIndexMap.get(new Integer(rootgraphIndex)).intValue();
+
+ if (!passFilter.getNodeBits().get(nodeIndex)) {
+ neighborSet.remove(nodeArray[i]);
+ }
+ }
+ }
+
+ if (neighborSet.size() < minNeighbors) {
+ return false;
+ }
+
+ return true;
+ }
+
+ // Get all the neighbors for pNode within pDistance
+ private void getNeighbors(Object pObj, HashSet pNeighborSet, int pDistance) {
+ if (pDistance == 0) {
+ if (!pNeighborSet.contains(pObj)) {
+ pNeighborSet.add(pObj);
+ }
+ return;
+ }
+
+ List neighbors = network.neighborsList((Node)pObj);
+
+ Iterator nodeIt = neighbors.iterator();
+ while (nodeIt.hasNext()) {
+ Node nextNode = (Node) nodeIt.next();
+
+ if (!pNeighborSet.contains(nextNode)) {
+ pNeighborSet.add(nextNode);
+ }
+ getNeighbors(nextNode, pNeighborSet, pDistance-1);
+ }
+ }
+
+
+ public String toString() {
+ String retStr = "<TopologyFilter>\n";
+
+ retStr = retStr + "name=" + name + "\n";
+ retStr = retStr + advancedSetting.toString() + "\n";
+ retStr = retStr + "Negation=" + negation + "\n";
+ retStr = retStr + "minNeighbors=" + minNeighbors + "\n";
+ retStr = retStr + "withinDistance=" + withinDistance + "\n";
+
+ if (passFilter == null) {
+ retStr += "passFilter=null\n";
+ }
+ else {
+ retStr += "passFilter=" + passFilter.getName()+"\n";
+ }
+
+ retStr += "</TopologyFiler>";
+
+ return retStr;
+
+ }
+
+ public void setNodeBits(BitSet b) {
+ node_bits = b;
+ //parent.childChanged();
+ }
+
+ public void setEdgeBits(BitSet b) {
+ edge_bits = b;
+ //parent.childChanged();
+ }
+
+ public void setParent(CyFilter p) {
+ parent = p;
+ }
+ public CyFilter getParent() {
+ return parent;
+ }
+
+ public void setNegation(boolean pNot) {
+ negation = pNot;
+ //getParent().childChanged();
+ }
+ public boolean getNegation() {
+ return negation;
+ }
+
+ public String getName(){
+ return name;
+ }
+ public void setName(String pName){
+ name = pName;
+ }
+
+ public void setNetwork(CyNetwork pNetwork) {
+ if (network != null && network == pNetwork) {
+ return;
+ }
+ network = pNetwork;
+ if (passFilter != null) {
+ passFilter.setNetwork(network);
+ }
+
+ childChanged();
+ }
+}
diff --git a/coreplugins/filters/src/main/java/cytoscape/filters/util/ApplyFilterThread.java b/coreplugins/filters/src/main/java/cytoscape/filters/util/ApplyFilterThread.java
new file mode 100644
index 0000000..83b0730
--- /dev/null
+++ b/coreplugins/filters/src/main/java/cytoscape/filters/util/ApplyFilterThread.java
@@ -0,0 +1,263 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.filters.util;
+
+import ViolinStrings.Strings;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import cytoscape.CytoscapeInit;
+
+import cytoscape.data.CyAttributes;
+
+import cytoscape.filters.AdvancedSetting;
+import cytoscape.filters.AtomicFilter;
+import cytoscape.filters.CompositeFilter;
+import cytoscape.filters.NumericFilter;
+import cytoscape.filters.StringFilter;
+
+import cytoscape.filters.view.FilterMainPanel;
+
+import csplugins.quickfind.util.QuickFind;
+import cytoscape.util.CytoscapeAction;
+
+import giny.model.Edge;
+import giny.model.Node;
+
+import java.beans.PropertyChangeEvent;
+
+import java.io.BufferedReader;
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileReader;
+import java.io.FileWriter;
+
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+import java.util.StringTokenizer;
+import java.util.Vector;
+
+import javax.swing.ImageIcon;
+
+
+class ApplyFilterThread extends Thread {
+ CompositeFilter theFilter = null;
+
+ /**
+ * Creates a new ApplyFilterThread object.
+ *
+ * @param pFilter DOCUMENT ME!
+ */
+ public ApplyFilterThread(CompositeFilter pFilter) {
+ theFilter = pFilter;
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void run() {
+ Cytoscape.getCurrentNetwork().unselectAllNodes();
+ Cytoscape.getCurrentNetwork().unselectAllEdges();
+
+ testObjects(theFilter);
+ Cytoscape.getCurrentNetworkView().updateView();
+ }
+
+ private boolean passAtomicFilter(Object pObject, AtomicFilter pAtomicFilter) {
+ CyAttributes data = null;
+ String name = "";
+
+ if (pObject instanceof Node) {
+ data = Cytoscape.getNodeAttributes();
+ name = ((Node) pObject).getIdentifier();
+ } else {
+ data = Cytoscape.getEdgeAttributes();
+ name = ((Edge) pObject).getIdentifier();
+ }
+
+ if (name == null) {
+ return false;
+ }
+
+ if (pAtomicFilter instanceof StringFilter) {
+ StringFilter theStringFilter = (StringFilter) pAtomicFilter;
+
+ String value = data.getStringAttribute(name,
+ theStringFilter.getControllingAttribute().substring(5));
+
+ if (value == null) {
+ return false;
+ }
+
+ if (theStringFilter == null) {
+ return false;
+ }
+
+ if (theStringFilter.getSearchStr() == null) {
+ return false;
+ }
+
+ String[] pattern = theStringFilter.getSearchStr().split("\\s");
+
+ for (int p = 0; p < pattern.length; ++p) {
+ if (!Strings.isLike((String) value, pattern[p], 0, true)) {
+ // this is an OR function
+ return false;
+ }
+ }
+ } else if (pAtomicFilter instanceof NumericFilter) {
+ NumericFilter theNumericFilter = (NumericFilter) pAtomicFilter;
+
+ Number value;
+
+ if (data.getType(theNumericFilter.getControllingAttribute().substring(5)) == CyAttributes.TYPE_FLOATING)
+ value = (Number) data.getDoubleAttribute(name,
+ theNumericFilter.getControllingAttribute()
+ .substring(5));
+ else
+ value = (Number) data.getIntegerAttribute(name,
+ theNumericFilter.getControllingAttribute()
+ .substring(5));
+
+ if (value == null) {
+ return false;
+ }
+
+ Double lowValue = (Double) theNumericFilter.getLowBound();
+ Double highValue = (Double) theNumericFilter.getHighBound();
+
+ //To correct the boundary values for lowValue and highValue
+ if (lowValue.doubleValue()>0.0) {
+ lowValue = lowValue*0.99999;
+ }
+ else {
+ lowValue = lowValue*1.00001;
+ }
+
+ if (highValue.doubleValue()>0.0) {
+ highValue = highValue*1.00001;
+ }
+ else {
+ highValue = highValue*0.99999;
+ }
+
+ //if (!(value.doubleValue() >= lowValue.doubleValue() && value.doubleValue()<= highValue.doubleValue())) {
+ if (!((Double.compare(value.doubleValue(), lowValue.doubleValue()) >= 0)
+ && (Double.compare(value.doubleValue(), highValue.doubleValue())) <= 0)) {
+ return false;
+ }
+ }
+
+ return true;
+ }
+
+ private boolean passesCompositeFilter(Object pObject, CompositeFilter pFilter) {
+ /*
+ Vector<AtomicFilter> atomicFilterVect = pFilter.getAtomicFilterVect();
+
+ for (int i = 0; i < atomicFilterVect.size(); i++) {
+ boolean passTheAtomicFilter = passAtomicFilter(pObject,
+ (AtomicFilter) atomicFilterVect.elementAt(i));
+
+ if (pFilter.getAdvancedSetting().isANDSelected() && !passTheAtomicFilter) {
+ return false;
+ }
+
+ if (pFilter.getAdvancedSetting().isORSelected() && passTheAtomicFilter) {
+ return true;
+ }
+ }
+
+ if (pFilter.getAdvancedSetting().isANDSelected()) {
+ return true;
+ } else { // pFilter.getAdvancedSetting().isORSelected()
+
+ return false;
+ }
+ */
+ return false;
+ }
+
+ protected void testObjects(CompositeFilter pCompositeFilter) {
+ final CyNetwork network = Cytoscape.getCurrentNetwork();
+
+ final List<Node> nodes_list = network.nodesList();
+ final List<Edge> edges_list = network.edgesList();
+
+ if (pCompositeFilter == null)
+ return;
+
+ if (pCompositeFilter.getAdvancedSetting().isNodeChecked()) {
+ final List<Node> passedNodes = new ArrayList<Node>();
+
+ for (Node node : nodes_list) {
+ try {
+ if (passesCompositeFilter(node, pCompositeFilter)) {
+ passedNodes.add(node);
+ }
+ } catch (StackOverflowError soe) {
+ soe.printStackTrace();
+
+ return;
+ }
+ }
+
+ //System.out.println("\tpassedNodes.size() ="+passedNodes.size());
+ Cytoscape.getCurrentNetwork().setSelectedNodeState(passedNodes, true);
+ }
+
+ if (pCompositeFilter.getAdvancedSetting().isEdgeChecked()) {
+ final List<Edge> passedEdges = new ArrayList<Edge>();
+
+ for (Edge edge : edges_list) {
+ try {
+ if (passesCompositeFilter(edge, pCompositeFilter)) {
+ passedEdges.add(edge);
+ }
+ } catch (StackOverflowError soe) {
+ soe.printStackTrace();
+
+ return;
+ }
+ }
+
+ //System.out.println("\tpassedEdges.size() ="+passedEdges.size());
+ Cytoscape.getCurrentNetwork().setSelectedEdgeState(passedEdges, true);
+ }
+ } //testObjects
+}
diff --git a/coreplugins/filters/src/main/java/cytoscape/filters/util/FilterUtil.java b/coreplugins/filters/src/main/java/cytoscape/filters/util/FilterUtil.java
new file mode 100644
index 0000000..243bda1
--- /dev/null
+++ b/coreplugins/filters/src/main/java/cytoscape/filters/util/FilterUtil.java
@@ -0,0 +1,185 @@
+package cytoscape.filters.util;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import cytoscape.CytoscapeInit;
+import cytoscape.filters.CompositeFilter;
+import giny.model.Edge;
+import giny.model.Node;
+
+import java.awt.Cursor;
+import java.util.ArrayList;
+import java.util.List;
+import csplugins.quickfind.util.QuickFind;
+import csplugins.quickfind.util.QuickFindFactory;
+import csplugins.quickfind.util.TaskMonitorBase;
+import cytoscape.data.CyAttributes;
+import cytoscape.filters.FilterPlugin;
+import cytoscape.init.CyInitParams;
+import csplugins.widgets.autocomplete.index.GenericIndex;
+
+public class FilterUtil {
+
+ // do selection on given network
+ public static void doSelection(CompositeFilter pFilter) {
+ //System.out.println("Entering FilterUtil.doSelection() ...");
+
+ CyInitParams init = CytoscapeInit.getCyInitParams();
+
+ if (init == null)
+ return;
+
+ if (pFilter.getNetwork() == null)
+ return;
+
+ // Set wait cursor
+ if ((init.getMode() == CyInitParams.GUI)
+ || (init.getMode() == CyInitParams.EMBEDDED_WINDOW)) {
+ // set the wait cursor
+ Cytoscape.getDesktop().setCursor(
+ Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR));
+ }
+
+ pFilter.apply();
+
+ CyNetwork network = pFilter.getNetwork();
+
+ network.unselectAllNodes();
+ network.unselectAllEdges();
+
+ final List<Node> nodes_list = network.nodesList();
+ final List<Edge> edges_list = network.edgesList();
+
+ if (pFilter.getAdvancedSetting().isNodeChecked()&& (pFilter.getNodeBits() != null)) {
+ // Select nodes
+ final List<Node> passedNodes = new ArrayList<Node>();
+
+ Node node = null;
+
+ for (int i=0; i< pFilter.getNodeBits().length(); i++) {
+ int next_set_bit = pFilter.getNodeBits().nextSetBit(i);
+
+ node = nodes_list.get(next_set_bit);
+
+ passedNodes.add(node);
+ i = next_set_bit;
+ }
+ network.setSelectedNodeState(passedNodes, true);
+ }
+ if (pFilter.getAdvancedSetting().isEdgeChecked()&& (pFilter.getEdgeBits() != null)) {
+ // Select edges
+ final List<Edge> passedEdges = new ArrayList<Edge>();
+
+ Edge edge = null;
+ for (int i=0; i< edges_list.size(); i++) {
+ int next_set_bit = pFilter.getEdgeBits().nextSetBit(i);
+ if (next_set_bit == -1) {
+ break;
+ }
+ edge = edges_list.get(next_set_bit);
+ passedEdges.add(edge);
+ i = next_set_bit;
+ }
+ network.setSelectedEdgeState(passedEdges, true);
+ }
+ Cytoscape.getCurrentNetworkView().updateView();
+
+ //Restore cursor
+ if ((init.getMode() == CyInitParams.GUI)
+ || (init.getMode() == CyInitParams.EMBEDDED_WINDOW)) {
+ // set the wait cursor
+ Cytoscape.getDesktop().setCursor(
+ Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR));
+ }
+
+ }
+
+
+ public static boolean isFilterNameDuplicated(String pFilterName) {
+ if (FilterPlugin.getAllFilterVect() == null || FilterPlugin.getAllFilterVect().size() == 0)
+ return false;
+
+ for (int i=0; i<FilterPlugin.getAllFilterVect().size(); i++) {
+ CompositeFilter theFilter = (CompositeFilter) FilterPlugin.getAllFilterVect().elementAt(i);
+ if (pFilterName.equalsIgnoreCase(theFilter.getName().trim())) {
+ return true;
+ }
+ }
+ return false;
+ }
+
+
+ public static GenericIndex getQuickFindIndex(String pCtrlAttribute, CyNetwork pNetwork, int pIndexType) {
+ final QuickFind quickFind = QuickFindFactory.getGlobalQuickFindInstance();
+ quickFind.reindexNetwork(pNetwork, pIndexType, pCtrlAttribute, new TaskMonitorBase());
+
+ return quickFind.getIndex(pNetwork);
+ }
+
+
+ public static boolean hasSuchAttribute(String pAttribute, int pType) {
+ int attributeType = CyAttributes.TYPE_UNDEFINED;
+ if (pType == QuickFind.INDEX_NODES) {
+ attributeType = Cytoscape.getNodeAttributes().getType(pAttribute);
+ }
+ else if (pType == QuickFind.INDEX_EDGES) {
+ attributeType = Cytoscape.getEdgeAttributes().getType(pAttribute);
+ }
+
+ if (attributeType == CyAttributes.TYPE_UNDEFINED) {
+ return false;
+ }
+ return true;
+ }
+
+ // This is used in old version, for backward compatible
+ public static void applyFilter(CompositeFilter pFilter) {
+ doSelection(pFilter);
+ }
+
+ // If a network size (node count and edge count) is less than DYNAMIC_FILTER_THRESHOLD, return true
+ // Otherwise, return false
+ public static boolean isDynamicFilter(CompositeFilter pFilter) {
+ CyNetwork theNetwork = pFilter.getNetwork();
+
+ if (theNetwork == null) {
+ return false;
+ }
+
+ int nodeCount = theNetwork.getNodeCount();
+ int edgeCount = theNetwork.getEdgeCount();
+
+ int dynamicFilterThresholdValue = -1;
+ String dynamicFilterThreshold = CytoscapeInit.getProperties().getProperty(FilterPlugin.DYNAMIC_FILTER_THRESHOLD);
+ if (dynamicFilterThreshold == null) { // threshold not defined, use the default value
+ dynamicFilterThresholdValue = FilterPlugin.DEFAULT_DYNAMIC_FILTER_THRESHOLD;
+ }
+ else {
+ dynamicFilterThresholdValue = (new Integer(dynamicFilterThreshold)).intValue();
+ }
+
+ if (pFilter.getAdvancedSetting().isNodeChecked() && pFilter.getAdvancedSetting().isEdgeChecked()) {
+ // Select both nodes and edges
+ if (nodeCount > dynamicFilterThresholdValue || edgeCount > dynamicFilterThresholdValue) {
+ return false;
+ }
+ return true;
+ }
+ else if (pFilter.getAdvancedSetting().isNodeChecked()) {
+ //Select node only
+ if (nodeCount < dynamicFilterThresholdValue) {
+ return true;
+ }
+ }
+ else if (pFilter.getAdvancedSetting().isEdgeChecked()){
+ // select edge only
+ if (edgeCount < dynamicFilterThresholdValue) {
+ return true;
+ }
+ }
+
+ return false;
+ }
+}
+
+
diff --git a/coreplugins/filters/src/main/java/cytoscape/filters/view/EditNameDialog.java b/coreplugins/filters/src/main/java/cytoscape/filters/view/EditNameDialog.java
new file mode 100644
index 0000000..ca98893
--- /dev/null
+++ b/coreplugins/filters/src/main/java/cytoscape/filters/view/EditNameDialog.java
@@ -0,0 +1,136 @@
+package cytoscape.filters.view;
+
+import java.awt.Dimension;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.Insets;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import javax.swing.JButton;
+import javax.swing.JDialog;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JTextField;
+import java.util.Vector;
+
+public class EditNameDialog extends JDialog implements ActionListener {
+
+ /**
+ * Creates a new EditNetworkTitleDialog object.
+ *
+ * @param parent DOCUMENT ME!
+ * @param modal DOCUMENT ME!
+ * @param pName DOCUMENT ME!
+ */
+ public EditNameDialog(String pTitle, String pMsg, Vector pNameVect, int pWinX, int pWinY) {
+ //super(parent, modal);
+ initComponents();
+
+ setModal(true);
+ nameVect = pNameVect;
+ String oldName = (String) pNameVect.elementAt(0);
+ tfName.setText(oldName);
+ tfName.setSelectionStart(0);
+ tfName.setSelectionEnd(oldName.length());
+
+ setSize(new java.awt.Dimension(pWinX, pWinY));
+ setTitle(pTitle);
+ jLabel1.setText(pMsg);
+
+ btnOK.addActionListener(this);
+ btnCancel.addActionListener(this);
+
+ tfName.addActionListener(this);
+ }
+
+ private Vector<String> nameVect;
+
+ /** This method is called from within the constructor to
+ * initialize the form.
+ * WARNING: Do NOT modify this code. The content of this method is
+ * always regenerated by the Form Editor.
+ */
+
+ // <editor-fold defaultstate="collapsed" desc=" Generated Code ">
+ private void initComponents() {
+ GridBagConstraints gridBagConstraints;
+
+ jLabel1 = new JLabel();
+ tfName = new JTextField();
+ jPanel1 = new JPanel();
+ btnOK = new JButton();
+ btnCancel = new JButton();
+
+ getContentPane().setLayout(new GridBagLayout());
+
+ setDefaultCloseOperation(javax.swing.WindowConstants.DISPOSE_ON_CLOSE);
+ //setTitle("Edit Network Title");
+ //jLabel1.setText("Please enter new network title:");
+ gridBagConstraints = new GridBagConstraints();
+ gridBagConstraints.anchor = GridBagConstraints.WEST;
+ gridBagConstraints.insets = new Insets(15, 10, 0, 0);
+ getContentPane().add(jLabel1, gridBagConstraints);
+
+ gridBagConstraints = new GridBagConstraints();
+ gridBagConstraints.gridy = 1;
+ gridBagConstraints.fill = GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.weightx = 1.0;
+ gridBagConstraints.insets = new Insets(10, 10, 10, 10);
+ getContentPane().add(tfName, gridBagConstraints);
+
+ btnOK.setText("OK");
+ btnOK.setPreferredSize(new Dimension(65, 23));
+ //btnCancel.setPreferredSize(new Dimension(65, 23));
+
+ jPanel1.add(btnOK);
+
+ btnCancel.setText("Cancel");
+ jPanel1.add(btnCancel);
+
+ gridBagConstraints = new GridBagConstraints();
+ gridBagConstraints.gridy = 2;
+ gridBagConstraints.insets = new Insets(10, 0, 10, 0);
+ getContentPane().add(jPanel1, gridBagConstraints);
+
+ pack();
+ } // </editor-fold>
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ Object _actionObject = e.getSource();
+
+ // handle Button events
+ if (_actionObject instanceof JButton) {
+ JButton _btn = (JButton) _actionObject;
+
+ if (_btn == btnOK) {
+ nameVect.set(0, tfName.getText().trim());
+ }
+ else if (_btn == btnCancel) {
+ nameVect.set(0, null);
+ }
+ }
+ else if (_actionObject instanceof JTextField) {
+ JTextField _tf = (JTextField) _actionObject;
+ if (_tf == tfName) {
+ nameVect.set(0, tfName.getText().trim());
+ }
+ }
+ this.dispose();
+ }
+
+
+ // Variables declaration - do not modify
+ private JButton btnCancel;
+ private JButton btnOK;
+ private JLabel jLabel1;
+ private JPanel jPanel1;
+ private JTextField tfName;
+
+ // End of variables declaration
+}
diff --git a/coreplugins/filters/src/main/java/cytoscape/filters/view/EditRangeDialog.java b/coreplugins/filters/src/main/java/cytoscape/filters/view/EditRangeDialog.java
new file mode 100644
index 0000000..96b4122
--- /dev/null
+++ b/coreplugins/filters/src/main/java/cytoscape/filters/view/EditRangeDialog.java
@@ -0,0 +1,214 @@
+package cytoscape.filters.view;
+
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.util.Vector;
+
+import javax.swing.JButton;
+import javax.swing.JDialog;
+import javax.swing.JTextField;
+import javax.swing.JOptionPane;
+
+public class EditRangeDialog extends JDialog implements ActionListener {
+
+ private Vector<String> boundValueVect;
+ private String dataType = "int";
+
+ /** Creates new form EditRangeDialog */
+ public EditRangeDialog(javax.swing.JFrame parent, boolean modal, String pCtrlAttribute, Vector<String> pBoundsVect, String pDataType) {
+ super(parent, modal);
+ initComponents();
+ setTitle("Edit range for "+ pCtrlAttribute);
+
+ dataType = pDataType;
+
+ String message = lbPleaseEnterBoundValues.getText()+ " (" + pBoundsVect.elementAt(2).toString()+ " ~ " +pBoundsVect.elementAt(3).toString() + "):";
+ lbPleaseEnterBoundValues.setText(message);
+
+ boundValueVect = pBoundsVect;
+ tfLowBound.setText(pBoundsVect.elementAt(0).toString());
+ tfHighBound.setText(pBoundsVect.elementAt(1).toString());
+
+ tfLowBound.setSelectionStart(0);
+ tfLowBound.setSelectionEnd(pBoundsVect.elementAt(0).toString().length());
+
+ setSize(new java.awt.Dimension(300, 170));
+
+ btnOK.addActionListener(this);
+ btnCancel.addActionListener(this);
+
+ }
+
+ private boolean isUserInputValid() {
+
+ // User inputs must be (1) numbers (2) lowBound < highBound
+ String lowBoundStr = tfLowBound.getText().trim();
+ String highBoundStr = tfHighBound.getText().trim();
+
+ if (dataType.equalsIgnoreCase("int")) {
+ try {
+ int lowBound = Integer.parseInt(lowBoundStr);
+ int highBound = Integer.parseInt(highBoundStr);
+ if (lowBound > highBound) {
+ return false;
+ }
+
+ int minValue = Integer.parseInt(this.boundValueVect.elementAt(2));
+ int maxValue = Integer.parseInt(this.boundValueVect.elementAt(3));
+ if (lowBound > maxValue || highBound < minValue){
+ return false;
+ }
+ }
+ catch (NumberFormatException nfe) {
+ return false;
+ }
+ }
+ else {
+ try {
+ double lowBound = Double.parseDouble(lowBoundStr);
+ double highBound = Double.parseDouble(highBoundStr);
+ if (lowBound > highBound) {
+ return false;
+ }
+
+ double minValue = Double.parseDouble(this.boundValueVect.elementAt(2));
+ double maxValue = Double.parseDouble(this.boundValueVect.elementAt(3));
+ if (lowBound > maxValue || highBound < minValue){
+ return false;
+ }
+ }
+ catch (NumberFormatException nfe) {
+ return false;
+ }
+ }
+
+ return true;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ Object _actionObject = e.getSource();
+
+ // handle Button events
+ if (_actionObject instanceof JButton) {
+ JButton _btn = (JButton) _actionObject;
+
+ if (_btn == btnOK) {
+ if (!isUserInputValid()) {
+ JOptionPane.showMessageDialog(this, "Invalid bound values", "Warning", JOptionPane.ERROR_MESSAGE);
+ return;
+ }
+ boundValueVect.set(0, tfLowBound.getText().trim());
+ boundValueVect.set(1, tfHighBound.getText().trim());
+ }
+ else if (_btn == btnCancel) {
+ // do nothing
+ }
+ }
+ this.dispose();
+ }
+
+ /** This method is called from within the constructor to
+ * initialize the form.
+ * WARNING: Do NOT modify this code. The content of this method is
+ * always regenerated by the Form Editor.
+ */
+ // <editor-fold defaultstate="collapsed" desc=" Generated Code ">
+ private void initComponents() {
+ java.awt.GridBagConstraints gridBagConstraints;
+
+ lbPleaseEnterBoundValues = new javax.swing.JLabel();
+ lbLowBound = new javax.swing.JLabel();
+ tfLowBound = new javax.swing.JTextField();
+ lbHighBound = new javax.swing.JLabel();
+ tfHighBound = new javax.swing.JTextField();
+ jPanel1 = new javax.swing.JPanel();
+ btnOK = new javax.swing.JButton();
+ btnCancel = new javax.swing.JButton();
+
+ getContentPane().setLayout(new java.awt.GridBagLayout());
+
+ setDefaultCloseOperation(javax.swing.WindowConstants.DISPOSE_ON_CLOSE);
+ lbPleaseEnterBoundValues.setText("Please enter the bound values");
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridwidth = 2;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
+ gridBagConstraints.insets = new java.awt.Insets(20, 10, 10, 0);
+ getContentPane().add(lbPleaseEnterBoundValues, gridBagConstraints);
+
+ lbLowBound.setText("Low bound");
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = 1;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.EAST;
+ gridBagConstraints.insets = new java.awt.Insets(0, 20, 10, 10);
+ getContentPane().add(lbLowBound, gridBagConstraints);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = 1;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.insets = new java.awt.Insets(0, 0, 5, 20);
+ getContentPane().add(tfLowBound, gridBagConstraints);
+
+ lbHighBound.setText("High bound");
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = 2;
+ gridBagConstraints.insets = new java.awt.Insets(0, 20, 0, 10);
+ getContentPane().add(lbHighBound, gridBagConstraints);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = 2;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.insets = new java.awt.Insets(0, 0, 0, 20);
+ getContentPane().add(tfHighBound, gridBagConstraints);
+
+ btnOK.setText("OK");
+ jPanel1.add(btnOK);
+
+ btnCancel.setText("Cancel");
+ jPanel1.add(btnCancel);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = 3;
+ gridBagConstraints.gridwidth = 2;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.weightx = 1.0;
+ gridBagConstraints.insets = new java.awt.Insets(20, 0, 20, 0);
+ getContentPane().add(jPanel1, gridBagConstraints);
+
+ pack();
+ }// </editor-fold>
+
+ /**
+ * @param args the command line arguments
+ */
+ public static void main(String args[]) {
+ java.awt.EventQueue.invokeLater(new Runnable() {
+ public void run() {
+ Vector<String> _boundsVect = new Vector<String>();
+ _boundsVect.add("0.51");
+ _boundsVect.add("1.08");
+ _boundsVect.add("-0.1");
+ _boundsVect.add("2.0");
+
+ EditRangeDialog theDialog =new EditRangeDialog(new javax.swing.JFrame(), true, "Degree", _boundsVect, "int");
+
+ theDialog.setVisible(true);
+ }
+ });
+ }
+
+ // Variables declaration - do not modify
+ private javax.swing.JButton btnCancel;
+ private javax.swing.JButton btnOK;
+ private javax.swing.JPanel jPanel1;
+ private javax.swing.JLabel lbHighBound;
+ private javax.swing.JLabel lbLowBound;
+ private javax.swing.JLabel lbPleaseEnterBoundValues;
+ private javax.swing.JTextField tfHighBound;
+ private javax.swing.JTextField tfLowBound;
+ // End of variables declaration
+}
diff --git a/coreplugins/filters/src/main/java/cytoscape/filters/view/FilterMainPanel.java b/coreplugins/filters/src/main/java/cytoscape/filters/view/FilterMainPanel.java
new file mode 100644
index 0000000..d0c1693
--- /dev/null
+++ b/coreplugins/filters/src/main/java/cytoscape/filters/view/FilterMainPanel.java
@@ -0,0 +1,1368 @@
+/*
+ Copyright (c) 2006, 2007, 2009, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.filters.view;
+
+import javax.swing.ImageIcon;
+import javax.swing.JButton;
+import javax.swing.JLabel;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JPopupMenu;
+import javax.swing.ListCellRenderer;
+import javax.swing.SwingConstants;
+
+import java.awt.Component;
+import javax.swing.JList;
+import javax.swing.JComboBox;
+import javax.swing.DefaultComboBoxModel;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import cytoscape.view.CytoscapeDesktop;
+import cytoscape.util.swing.DropDownMenuButton;
+import cytoscape.view.cytopanels.CytoPanelImp;
+import cytoscape.view.cytopanels.CytoPanelState;
+import cytoscape.data.SelectEventListener;
+import cytoscape.data.SelectEvent;
+
+import java.awt.event.ActionListener;
+import java.awt.event.ActionEvent;
+import java.awt.event.ComponentAdapter;
+import java.awt.event.ComponentEvent;
+
+import javax.swing.AbstractAction;
+
+import cytoscape.filters.FilterPlugin;
+import cytoscape.filters.util.FilterUtil;
+import cytoscape.filters.AdvancedSetting;
+import cytoscape.filters.CompositeFilter;
+import cytoscape.filters.TopologyFilter;
+import cytoscape.filters.InteractionFilter;
+import cytoscape.filters.NodeInteractionFilter;
+import cytoscape.filters.EdgeInteractionFilter;
+
+import java.util.Collections;
+import java.util.Vector;
+import java.awt.event.ItemListener;
+import java.awt.event.ItemEvent;
+import java.awt.GridBagConstraints;
+import java.util.HashMap;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import cytoscape.data.CyAttributes;
+import cytoscape.view.cytopanels.CytoPanelListener;
+import cytoscape.util.swing.WidestStringComboBoxModel;
+import cytoscape.util.swing.WidestStringComboBoxPopupMenuListener;
+import cytoscape.util.swing.WidestStringProvider;
+import javax.swing.ComboBoxModel;
+import javax.swing.table.DefaultTableModel;
+import javax.swing.tree.DefaultMutableTreeNode;
+import cytoscape.data.CyAttributesUtils;
+
+/**
+ *
+ */
+public class FilterMainPanel extends JPanel implements ActionListener,
+ ItemListener,SelectEventListener, PropertyChangeListener, CytoPanelListener {
+
+ // String constants used for seperator entries in the attribute combobox
+ private static final String filtersSeperator = "-- Filters --";
+ private static final String attributesSeperator = "-- Attributes --";
+
+ private static JPopupMenu optionMenu;
+
+ private static JMenuItem newFilterMenuItem;
+ private static JMenuItem newTopologyFilterMenuItem;
+ private static JMenuItem newNodeInteractionFilterMenuItem;
+ private static JMenuItem newEdgeInteractionFilterMenuItem;
+
+ private static JMenuItem renameFilterMenuItem;
+
+ private static JMenuItem deleteFilterMenuItem;
+
+ private static JMenuItem duplicateFilterMenuItem;
+
+ private DropDownMenuButton optionButton;
+
+ private FilterSettingPanel currentFilterSettingPanel = null;
+ private HashMap<CompositeFilter,FilterSettingPanel> filter2SettingPanelMap = new HashMap<CompositeFilter,FilterSettingPanel>();
+
+ private Vector<CompositeFilter> allFilterVect = null;
+ /*
+ * Icons used in this panel.
+ */
+ private static final ImageIcon optionIcon = new ImageIcon(Cytoscape.class
+ .getResource("/cytoscape/images/ximian/stock_form-properties.png"));
+
+ private static final ImageIcon delIcon = new ImageIcon(Cytoscape.class
+ .getResource("/cytoscape/images/ximian/stock_delete-16.png"));
+
+ private static final ImageIcon addIcon = new ImageIcon(
+ Cytoscape.class
+ .getResource("/cytoscape/images/ximian/stock_data-new-table-16.png"));
+
+ private static final ImageIcon renameIcon = new ImageIcon(Cytoscape.class
+ .getResource("/cytoscape/images/ximian/stock_redo-16.png"));
+
+ private static final ImageIcon duplicateIcon = new ImageIcon(
+ Cytoscape.class
+ .getResource("/cytoscape/images/ximian/stock_slide-duplicate.png"));
+
+ private CytoPanelImp cytoPanelWest = (CytoPanelImp) Cytoscape.getDesktop().getCytoPanel(SwingConstants.WEST);
+
+
+ public FilterMainPanel(Vector<CompositeFilter> pAllFilterVect) {
+ allFilterVect = pAllFilterVect;
+ //Initialize the option menu with menuItems
+ setupOptionMenu();
+
+ optionButton = new DropDownMenuButton(new AbstractAction() {
+ public void actionPerformed(ActionEvent ae) {
+ DropDownMenuButton b = (DropDownMenuButton) ae.getSource();
+ optionMenu.show(b, 0, b.getHeight());
+ }
+ });
+
+ optionButton.setToolTipText("Options...");
+ optionButton.setIcon(optionIcon);
+ optionButton.setMargin(new java.awt.Insets(2, 2, 2, 2));
+ optionButton.setComponentPopupMenu(optionMenu);
+
+ //Initialize the UI components
+ initComponents();
+
+ this.btnSelectAll.setEnabled(false);
+ this.btnDeSelect.setEnabled(false);
+
+ // reduce the text font to fit three buttons within visible window
+ this.btnSelectAll.setFont(new java.awt.Font("Tahoma", 0, 9));
+ this.btnDeSelect.setFont(new java.awt.Font("Tahoma", 0, 9));
+ this.btnApplyFilter.setFont(new java.awt.Font("Tahoma", 0, 9));
+ //
+ String[][] data = {{"","",""}};
+ String[] col = {"Network","Nodes","Edges"};
+ DefaultTableModel model = new DefaultTableModel(data,col);
+
+ tblFeedBack.setModel(model);
+
+ addEventListeners();
+
+ //btnApplyFilter.setVisible(false);
+
+ //Update the status of interactionMenuItems if this panel become visible
+ MyComponentAdapter cmpAdpt = new MyComponentAdapter();
+ addComponentListener(cmpAdpt);
+ }
+
+
+ // Listen to ATTRIBUTES_CHNAGED and NETWORK_VIEW_FOCUSED event
+ public void propertyChange(PropertyChangeEvent e) {
+
+ if (e.getPropertyName().equalsIgnoreCase(Cytoscape.ATTRIBUTES_CHANGED))
+ {
+ refreshAttributeCMB();
+ replaceFilterSettingPanel((CompositeFilter)cmbSelectFilter.getSelectedItem());
+
+ FilterSettingPanel theSettingPanel= filter2SettingPanelMap.get((CompositeFilter)cmbSelectFilter.getSelectedItem());
+ if (theSettingPanel != null) {
+ theSettingPanel.refreshIndicesForWidgets();
+ }
+ }
+ if (e.getPropertyName().equalsIgnoreCase(CytoscapeDesktop.NETWORK_VIEW_FOCUSED))
+ {
+ // If FilterPanel is not selected, do nothing
+ if (cmbSelectFilter.getSelectedItem() == null) {
+ return;
+ }
+
+ //Refresh indices for UI widgets after network switch
+ CompositeFilter selectedFilter = (CompositeFilter) cmbSelectFilter.getSelectedItem();
+ selectedFilter.setNetwork(Cytoscape.getCurrentNetwork());
+ FilterSettingPanel theSettingPanel= filter2SettingPanelMap.get(selectedFilter);
+ theSettingPanel.refreshIndicesForWidgets();
+ }
+
+ //Enable/disable select/deselect buttons
+ if (e.getPropertyName().equalsIgnoreCase(Cytoscape.NETWORK_CREATED)
+ || e.getPropertyName().equalsIgnoreCase(Cytoscape.NETWORK_DESTROYED)
+ ||e.getPropertyName().equalsIgnoreCase(Cytoscape.NETWORK_LOADED)){
+ enableForNetwork();
+ }
+
+ // For turning off listener during session loading
+ if(e.getPropertyName().equals(Integer.toString(Cytoscape.SESSION_OPENED))) {
+ return; //ignore = true;
+ }
+
+ if (e.getPropertyName().equals(Cytoscape.NETWORK_CREATED)
+ || e.getPropertyName().equals(Cytoscape.NETWORK_DESTROYED)
+ || e.getPropertyName().equals(Cytoscape.NETWORK_TITLE_MODIFIED)) {
+ updateFeedbackTableModel();
+ }
+
+ if ( e.getPropertyName().equalsIgnoreCase(CytoscapeDesktop.NETWORK_VIEW_FOCUSED)
+ || e.getPropertyName().equals(Cytoscape.SESSION_LOADED)
+ || e.getPropertyName().equals(Cytoscape.CYTOSCAPE_INITIALIZED)
+ || e.getPropertyName().equals(CytoscapeDesktop.NETWORK_VIEWS_SELECTED)) {
+
+ if (currentNetwork != null) {
+ currentNetwork.removeSelectEventListener(this);
+ }
+
+ // Change the target network
+ currentNetwork = Cytoscape.getCurrentNetwork();
+
+ if (currentNetwork != null) {
+ currentNetwork.addSelectEventListener(this);
+ updateFeedbackTableModel();
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param arg0 DOCUMENT ME!
+ */
+ public void onSelectEvent(SelectEvent event) {
+ if (((event.getTargetType() == SelectEvent.SINGLE_NODE)
+ || (event.getTargetType() == SelectEvent.NODE_SET))) {
+ updateFeedbackTableModel();
+ }
+ if (((event.getTargetType() == SelectEvent.SINGLE_EDGE)
+ || (event.getTargetType() == SelectEvent.EDGE_SET))) {
+ updateFeedbackTableModel();
+ }
+ }
+
+ private void updateFeedbackTableModel(){
+ CyNetwork cyNetwork = Cytoscape.getCurrentNetwork();
+ tblFeedBack.getModel().setValueAt(cyNetwork.getTitle(), 0, 0);
+
+ String nodeStr = "" + cyNetwork.getNodeCount() + "(" + cyNetwork.getSelectedNodes().size() + ")";
+ tblFeedBack.getModel().setValueAt(nodeStr, 0, 1);
+
+ String edgeStr = "" + cyNetwork.getEdgeCount() + "(" + cyNetwork.getSelectedEdges().size() + ")";
+ tblFeedBack.getModel().setValueAt(edgeStr, 0, 2);
+ }
+
+ /**
+ * Enable select/deselect buttons if the current network exists and is not null.
+ */
+ protected void enableForNetwork() {
+
+ CyNetwork n = Cytoscape.getCurrentNetwork();
+
+ if ( n == null || n == Cytoscape.getNullNetwork() ) {
+ this.btnSelectAll.setEnabled(false);
+ this.btnDeSelect.setEnabled(false);
+ }
+ else {
+ this.btnSelectAll.setEnabled(true);
+ this.btnDeSelect.setEnabled(true);
+ }
+ }
+
+
+ // Target network to watch selection
+ private CyNetwork currentNetwork;
+
+
+ public void refreshFilterSelectCMB() {
+ ComboBoxModel cbm;
+
+ // Whatever change caused the refresh may have altered the longest display String
+ // so need to have the model recalculate it.
+ cbm = cmbSelectFilter.getModel();
+ if (cbm instanceof WidestStringProvider) {
+ ((WidestStringProvider)cbm).resetWidest();
+ }
+
+ this.cmbSelectFilter.repaint();
+ }
+
+ private void refreshAttributeCMB() {
+ updateCMBAttributes();
+ cmbAttributes.repaint();
+ }
+
+ /*
+ * Get the list of attribute names for either "node" or "edge". The attribute names will be
+ * prefixed either with "node." or "edge.". Those attributes whose data type is neither
+ * "String" nor "numeric" will be excluded
+ */
+ private Vector<Object> getCyAttributesList(String pType) {
+ Vector<String> attributeList = new Vector<String>();
+ CyAttributes attributes = null;
+
+ if (pType.equalsIgnoreCase("node")) {
+ attributes = Cytoscape.getNodeAttributes();
+
+ }
+ else if (pType.equalsIgnoreCase("edge")){
+ attributes = Cytoscape.getEdgeAttributes();
+ }
+
+ String[] attributeNames = attributes.getAttributeNames();
+
+ if (attributeNames != null) {
+ // Show all attributes, with type of String or Number
+ for (int i = 0; i < attributeNames.length; i++) {
+ int type = attributes.getType(attributeNames[i]);
+
+ // only show user visible attributes,with type = Number/String/List
+ if (!attributes.getUserVisible(attributeNames[i])) {
+ continue;
+ }
+ if ((type == CyAttributes.TYPE_INTEGER)||(type == CyAttributes.TYPE_FLOATING)||(type == CyAttributes.TYPE_BOOLEAN)||(type == CyAttributes.TYPE_STRING)||(type == CyAttributes.TYPE_SIMPLE_LIST)) {
+ attributeList.add(pType+"."+attributeNames[i]);
+ }
+ } //for loop
+
+ // Alphabetical sort
+ Collections.sort(attributeList);
+ }
+
+ // type conversion
+ Vector<Object> retList = new Vector<Object>();
+
+ for (int i=0; i<attributeList.size(); i++) {
+ retList.add(attributeList.elementAt(i));
+ }
+ return retList;
+ }
+
+
+ /*
+ * Hide the visible filterSettingPanel, if any, and show the new FilterSettingPanel for
+ * the given filter.
+ */
+ private void replaceFilterSettingPanel(CompositeFilter pNewFilter) {
+ if (pNewFilter == null) {
+ pnlFilterDefinition.setVisible(false);
+ lbPlaceHolder_pnlFilterDefinition.setVisible(true);
+ return;
+ }
+
+ FilterSettingPanel next;
+ next = filter2SettingPanelMap.get(pNewFilter);
+
+ // When the next panel exists and is the same as the current one,
+ // we can exit now and avoid hiding and showing the same panel.
+ //
+ if ((next != null) && (next == currentFilterSettingPanel)) {
+ return;
+ }
+
+ //Hide the existing FilterSettingPanel, if any
+ if (currentFilterSettingPanel != null) {
+ currentFilterSettingPanel.setVisible(false);
+ }
+
+ currentFilterSettingPanel = next;
+
+ if (currentFilterSettingPanel == null || currentFilterSettingPanel.hasNullIndexChildFilter()) {
+ currentFilterSettingPanel = new FilterSettingPanel(this, pNewFilter);
+ //Update the HashMap
+ filter2SettingPanelMap.put(pNewFilter, currentFilterSettingPanel);
+ }
+
+ GridBagConstraints gridBagConstraints = new GridBagConstraints();
+ gridBagConstraints.gridx = 0;
+ gridBagConstraints.gridy = 1;
+ gridBagConstraints.gridwidth = 3;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.BOTH;
+ gridBagConstraints.weightx = 1.0;
+ gridBagConstraints.weighty = 1.0;
+ gridBagConstraints.insets = new java.awt.Insets(7, 0, 0, 0);
+
+ if (pNewFilter instanceof TopologyFilter) {
+ btnAddFilterWidget.setVisible(false);
+ cmbAttributes.setVisible(false);
+ pnlFilterDefinition.setBorder(javax.swing.BorderFactory
+ .createTitledBorder("Topology Filter Definition"));
+ }
+ else if (pNewFilter instanceof InteractionFilter) {
+ btnAddFilterWidget.setVisible(false);
+ cmbAttributes.setVisible(false);
+ pnlFilterDefinition.setBorder(javax.swing.BorderFactory
+ .createTitledBorder("Interaction Filter Definition"));
+ }
+ else {
+ btnAddFilterWidget.setVisible(true);
+ cmbAttributes.setVisible(true);
+ pnlFilterDefinition.setBorder(javax.swing.BorderFactory
+ .createTitledBorder("Filter Definition"));
+
+ }
+ pnlFilterDefinition.add(currentFilterSettingPanel, gridBagConstraints);
+
+ pnlFilterDefinition.setVisible(true);
+ currentFilterSettingPanel.setVisible(true);
+ lbPlaceHolder_pnlFilterDefinition.setVisible(false);
+
+ this.repaint();
+ }
+
+
+
+ private void addEventListeners() {
+ btnApplyFilter.addActionListener(this);
+
+ btnAddFilterWidget.addActionListener(this);
+
+ newFilterMenuItem.addActionListener(this);
+ newTopologyFilterMenuItem.addActionListener(this);
+ newNodeInteractionFilterMenuItem.addActionListener(this);
+ newEdgeInteractionFilterMenuItem.addActionListener(this);
+
+ deleteFilterMenuItem.addActionListener(this);
+ renameFilterMenuItem.addActionListener(this);
+ duplicateFilterMenuItem.addActionListener(this);
+
+ cmbSelectFilter.addItemListener(this);
+ cmbAttributes.addItemListener(this);
+
+ CytoPanelListener l = new MyCytoPanelListener();
+ cytoPanelWest.addCytoPanelListener(l);
+
+ Cytoscape.getPropertyChangeSupport().addPropertyChangeListener(Cytoscape.ATTRIBUTES_CHANGED, this);
+
+ // SelectEvent -- used to update feedback Panel
+ Cytoscape.getDesktop().getSwingPropertyChangeSupport().addPropertyChangeListener(CytoscapeDesktop.NETWORK_VIEWS_SELECTED,this);
+
+ Cytoscape.getDesktop().getSwingPropertyChangeSupport().addPropertyChangeListener(CytoscapeDesktop.NETWORK_VIEW_FOCUSED, this);
+
+ Cytoscape.getPropertyChangeSupport().addPropertyChangeListener(Cytoscape.NETWORK_CREATED, this);
+ Cytoscape.getPropertyChangeSupport().addPropertyChangeListener(Cytoscape.NETWORK_DESTROYED, this);
+ Cytoscape.getPropertyChangeSupport().addPropertyChangeListener(Cytoscape.NETWORK_LOADED, this);
+ Cytoscape.getPropertyChangeSupport().addPropertyChangeListener(Cytoscape.NETWORK_TITLE_MODIFIED, this);
+
+ btnSelectAll.addActionListener(this);
+ btnDeSelect.addActionListener(this);
+
+ // This is used for syn of feednack panel
+ CytoPanelImp cytoPanelWest = (CytoPanelImp) Cytoscape.getDesktop()
+ .getCytoPanel(SwingConstants.WEST);
+ cytoPanelWest.addCytoPanelListener(this);
+
+ }
+
+ //CytoPanelListener
+ public void onComponentAdded(int count){}
+ public void onComponentRemoved(int count) {}
+ public void onComponentSelected(int componentIndex){
+ // Add selection listener for the feedback table
+
+ CytoPanelImp cytoPanelWest = (CytoPanelImp) Cytoscape.getDesktop()
+ .getCytoPanel(SwingConstants.WEST);
+ int _index = cytoPanelWest.indexOfComponent("Filters");
+ if (_index != componentIndex)
+ return;
+
+ //FiltersPanel is selected
+ if (Cytoscape.getCurrentNetwork() == null)
+ return;
+
+ Cytoscape.getCurrentNetwork().addSelectEventListener(this);
+ }
+ public void onStateChange(CytoPanelState newState){}
+ //////End of CytoPanelListener///////
+
+ public void initCMBSelectFilter(){
+ ComboBoxModel theModel = new FilterSelectWidestStringComboBoxModel(allFilterVect);
+ cmbSelectFilter.setModel(theModel);
+ cmbSelectFilter.setRenderer(new FilterRenderer());
+
+ if (allFilterVect.size() == 0) {
+ this.btnApplyFilter.setEnabled(false);
+ this.btnAddFilterWidget.setEnabled(false);
+ }
+ for (int i=0; i<allFilterVect.size(); i++) {
+ filter2SettingPanelMap.put(allFilterVect.elementAt(i), null);
+ }
+
+ // Force the first filter in the model to be selected, so that it's panel will be shown
+ if (theModel.getSize() > 0) {
+ cmbSelectFilter.setSelectedIndex(0);
+ }
+
+ replaceFilterSettingPanel((CompositeFilter)cmbSelectFilter.getSelectedItem());
+ }
+
+ class MyCytoPanelListener implements CytoPanelListener{
+ public void onStateChange(CytoPanelState newState) {}
+ public void onComponentSelected(int componentIndex){
+
+ if (componentIndex == cytoPanelWest.indexOfComponent("Filters")) {
+ //if (cmbSelectFilter.getModel().getSize() == 0 && allFilterVect.size()>0) {
+ if (cmbSelectFilter.getModel().getSize() == 0) {
+ // CMBSelectFilter will not be initialize until the Filer Panel is selected
+ initCMBSelectFilter();
+ }
+
+ updateCMBAttributes();
+ }
+ }
+ public void onComponentAdded(int count){}
+ public void onComponentRemoved(int count){}
+ }
+
+ /*
+ * Update the attribute list in the attribute combobox based on the settings in the
+ * current selected filter
+ */
+ private void updateCMBAttributes() {
+ DefaultComboBoxModel cbm;
+
+ cbm = ((DefaultComboBoxModel)cmbAttributes.getModel());
+ cbm.removeAllElements();
+
+ cbm.addElement(attributesSeperator);
+ CompositeFilter selectedFilter = (CompositeFilter)cmbSelectFilter.getSelectedItem();
+
+ if (selectedFilter == null) {
+ return;
+ }
+
+ Vector<Object> av;
+
+ av = getCyAttributesList("node");
+ for (int i = 0; i < av.size(); i++) {
+ cbm.addElement(av.elementAt(i));
+ }
+
+ av = getCyAttributesList("edge");
+ for (int i = 0; i < av.size(); i++) {
+ cbm.addElement(av.elementAt(i));
+ }
+
+ cbm.addElement(filtersSeperator);
+ if (allFilterVect != null) {
+ for (int i = 0; i < allFilterVect.size(); i++) {
+ Object fi;
+
+ fi = allFilterVect.elementAt(i);
+ if (fi != selectedFilter) {
+ cbm.addElement(fi);
+ }
+ }
+ }
+ }
+
+
+ /**
+ * Setup menu items.
+ *
+ */
+ private void setupOptionMenu() {
+ /*
+ * Option Menu
+ */
+ newFilterMenuItem = new JMenuItem("Create new filter...");
+ newFilterMenuItem.setIcon(addIcon);
+
+ newTopologyFilterMenuItem = new JMenuItem("Create new topology filter...");
+ newTopologyFilterMenuItem.setIcon(addIcon);
+
+ newNodeInteractionFilterMenuItem = new JMenuItem("Create new NodeInteraction filter...");
+ newNodeInteractionFilterMenuItem.setIcon(addIcon);
+ newNodeInteractionFilterMenuItem.setEnabled(false);
+
+ newEdgeInteractionFilterMenuItem = new JMenuItem("Create new EdgeInteraction filter...");
+ newEdgeInteractionFilterMenuItem.setIcon(addIcon);
+ newEdgeInteractionFilterMenuItem.setEnabled(false);
+
+ deleteFilterMenuItem = new JMenuItem("Delete filter...");
+ deleteFilterMenuItem.setIcon(delIcon);
+
+ renameFilterMenuItem = new JMenuItem("Rename filter...");
+ renameFilterMenuItem.setIcon(renameIcon);
+
+ duplicateFilterMenuItem = new JMenuItem("Copy existing filter...");
+ duplicateFilterMenuItem.setIcon(duplicateIcon);
+ // Hide copy icon for now, we may need it in the future
+ duplicateFilterMenuItem.setVisible(false);
+
+ optionMenu = new JPopupMenu();
+ optionMenu.add(newFilterMenuItem);
+ optionMenu.add(newTopologyFilterMenuItem);
+ optionMenu.add(newNodeInteractionFilterMenuItem);
+ optionMenu.add(newEdgeInteractionFilterMenuItem);
+ optionMenu.add(deleteFilterMenuItem);
+ optionMenu.add(renameFilterMenuItem);
+ optionMenu.add(duplicateFilterMenuItem);
+ }
+
+ /**
+ * This method is called from within the constructor to initialize the form.
+ * WARNING: Do NOT modify this code. The content of this method is always
+ * regenerated by the Form Editor.
+ */
+ // <editor-fold defaultstate="collapsed" desc=" Generated Code ">
+ private void initComponents() {
+ java.awt.GridBagConstraints gridBagConstraints;
+
+ pnlCurrentFilter = new javax.swing.JPanel();
+ cmbSelectFilter = new JComboBox();
+ cmbSelectFilter.addPopupMenuListener(new WidestStringComboBoxPopupMenuListener());
+ // optionButton = new javax.swing.JButton();
+ pnlFilterDefinition = new javax.swing.JPanel();
+
+ WidestStringComboBoxModel wscbm = new AttributeSelectWidestStringComboBoxModel();
+ cmbAttributes = new JComboBox(wscbm);
+ cmbAttributes.addPopupMenuListener(new WidestStringComboBoxPopupMenuListener());
+
+ btnAddFilterWidget = new javax.swing.JButton();
+ lbPlaceHolder = new javax.swing.JLabel();
+ pnlButton = new javax.swing.JPanel();
+ btnApplyFilter = new javax.swing.JButton();
+ lbPlaceHolder_pnlFilterDefinition = new javax.swing.JLabel();
+
+ pnlFeedBack = new javax.swing.JPanel();
+ tblFeedBack = new javax.swing.JTable();
+
+ pnlSelectButtons = new javax.swing.JPanel();
+ btnSelectAll = new javax.swing.JButton();
+ btnDeSelect = new javax.swing.JButton();
+ pnlScroll = new javax.swing.JScrollPane();
+
+ setLayout(new java.awt.GridBagLayout());
+
+ pnlCurrentFilter.setLayout(new java.awt.GridBagLayout());
+
+ pnlCurrentFilter.setBorder(javax.swing.BorderFactory
+ .createTitledBorder("Current Filter"));
+ // cmbSelectFilter.setModel(new javax.swing.DefaultComboBoxModel(new
+ // String[] { "My First filter", "My second Filter" }));
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
+ gridBagConstraints.weightx = 0.5;
+ gridBagConstraints.insets = new java.awt.Insets(5, 10, 5, 10);
+ pnlCurrentFilter.add(cmbSelectFilter, gridBagConstraints);
+
+ optionButton.setText("Option");
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.insets = new java.awt.Insets(0, 0, 0, 5);
+ pnlCurrentFilter.add(optionButton, gridBagConstraints);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 0;
+ gridBagConstraints.gridy = 0;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.ipady = 4;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
+ gridBagConstraints.weightx = 1.0;
+ add(pnlCurrentFilter, gridBagConstraints);
+
+ pnlFilterDefinition.setLayout(new java.awt.GridBagLayout());
+
+ pnlFilterDefinition.setBorder(javax.swing.BorderFactory
+ .createTitledBorder("Filter Definition"));
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 1;
+ gridBagConstraints.gridy = 0;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.weightx = 1.0;
+ gridBagConstraints.insets = new java.awt.Insets(10, 10, 0, 10);
+ pnlFilterDefinition.add(cmbAttributes, gridBagConstraints);
+
+ btnAddFilterWidget.setText("Add");
+ btnAddFilterWidget.setEnabled(false);
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = 0;
+ gridBagConstraints.insets = new java.awt.Insets(10, 0, 0, 5);
+ pnlFilterDefinition.add(btnAddFilterWidget, gridBagConstraints);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = 1;
+ gridBagConstraints.gridwidth = 3;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.BOTH;
+ gridBagConstraints.weightx = 1.0;
+ gridBagConstraints.weighty = 1.0;
+ pnlFilterDefinition.add(lbPlaceHolder, gridBagConstraints);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 0;
+ gridBagConstraints.gridy = 1;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.BOTH;
+ gridBagConstraints.weightx = 1.0;
+ gridBagConstraints.weighty = 1.0;
+ add(pnlFilterDefinition, gridBagConstraints);
+
+ ///
+ pnlButton.setLayout(new java.awt.FlowLayout());
+
+ btnApplyFilter.setText("Apply Filter");
+ pnlButton.add(btnApplyFilter);
+
+ btnSelectAll.setText("Select All");
+ pnlButton.add(btnSelectAll);
+
+ btnDeSelect.setText("Deselect All");
+ pnlButton.add(btnDeSelect);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 0;
+ gridBagConstraints.gridy = 2;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.weightx = 1.0;
+ gridBagConstraints.insets = new java.awt.Insets(10, 0, 10, 0);
+ add(pnlButton, gridBagConstraints);
+
+ // lbPlaceHolder_pnlFilterDefinition.setText("jLabel1");
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 0;
+ gridBagConstraints.gridy = 1;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.BOTH;
+ gridBagConstraints.weightx = 1.0;
+ gridBagConstraints.weighty = 1.0;
+ add(lbPlaceHolder_pnlFilterDefinition, gridBagConstraints);
+
+ // feedback panel
+ pnlFeedBack.setLayout(new java.awt.GridBagLayout());
+ pnlFeedBack.setBorder(javax.swing.BorderFactory.createTitledBorder(""));
+ pnlFeedBack.setMinimumSize(new java.awt.Dimension(pnlFeedBack.getWidth(),52));
+ //pnlFeedBack.setMinimumSize(new java.awt.Dimension(300,52));
+
+ pnlScroll.setViewportView(tblFeedBack);
+
+ //tblFeedBack.setAutoCreateColumnsFromModel(true);
+ //tblFeedBack.setAutoResizeMode(javax.swing.JTable.AUTO_RESIZE_OFF);
+ tblFeedBack.setEnabled(false);
+ tblFeedBack.setFocusable(false);
+ //tblFeedBack.setRequestFocusEnabled(false);
+ //tblFeedBack.setRowSelectionAllowed(false);
+ //tblFeedBack.setTableHeader(null);
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.fill = java.awt.GridBagConstraints.BOTH; //.HORIZONTAL;
+ gridBagConstraints.weightx = 1.0;
+ gridBagConstraints.weighty = 1.0;
+ //gridBagConstraints.insets = new java.awt.Insets(0, 0, 1, 1);
+ pnlFeedBack.add(pnlScroll, gridBagConstraints);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = 3;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.weightx = 1.0;
+ gridBagConstraints.insets = new java.awt.Insets(1, 1, 2, 1);
+
+ add(pnlFeedBack, gridBagConstraints);
+ // Set customized renderer for attributes/filter combobox
+ cmbAttributes.setRenderer(new AttributeFilterRenderer());
+
+ }// </editor-fold>
+
+ // Variables declaration - do not modify
+ private javax.swing.JButton btnAddFilterWidget;
+
+ private javax.swing.JButton btnApplyFilter;
+
+ private javax.swing.JComboBox cmbAttributes;
+
+ private javax.swing.JComboBox cmbSelectFilter;
+
+ private javax.swing.JLabel lbPlaceHolder;
+
+ private javax.swing.JLabel lbPlaceHolder_pnlFilterDefinition;
+
+ // private javax.swing.JButton optionButton;
+ private javax.swing.JPanel pnlButton;
+
+ private javax.swing.JPanel pnlCurrentFilter;
+
+ private javax.swing.JPanel pnlFilterDefinition;
+
+ private javax.swing.JPanel pnlFeedBack;
+ private javax.swing.JTable tblFeedBack;
+
+ private javax.swing.JPanel pnlSelectButtons;
+ private javax.swing.JButton btnDeSelect;
+ private javax.swing.JButton btnSelectAll;
+ private javax.swing.JScrollPane pnlScroll;
+ // End of variables declaration
+
+
+ public JComboBox getCMBAttributes()
+ {
+ return cmbAttributes;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+
+ public void itemStateChanged(ItemEvent e) {
+ Object source = e.getSource();
+
+ //System.out.println("Entering FilterMainPanel.itemStateChnaged() ...");
+
+ if (source instanceof JComboBox) {
+ JComboBox cmb = (JComboBox) source;
+ if (cmb == cmbSelectFilter) {
+ CompositeFilter selectedFilter = (CompositeFilter)cmbSelectFilter.getSelectedItem();
+ if (selectedFilter == null) {
+ this.btnApplyFilter.setEnabled(false);
+ this.btnAddFilterWidget.setEnabled(false);
+ return;
+ }
+ else {
+ this.btnAddFilterWidget.setEnabled(true);
+ this.btnApplyFilter.setEnabled(true);
+ }
+ replaceFilterSettingPanel(selectedFilter);
+
+ if (Cytoscape.getCurrentNetwork() != null) {
+ Cytoscape.getCurrentNetwork().unselectAllNodes();
+ }
+
+ if (cmbSelectFilter.getSelectedItem() instanceof TopologyFilter || cmbSelectFilter.getSelectedItem() instanceof InteractionFilter) {
+ // do not apply TopologyFilter or InteractionFilter automatically
+ return;
+ }
+
+ // If network size is greater than pre-defined threshold, don't apply it automatically
+ if (FilterUtil.isDynamicFilter(selectedFilter)) {
+ FilterUtil.doSelection(selectedFilter);
+ }
+
+ refreshAttributeCMB();
+ }
+ else if (cmb == cmbAttributes) {
+ Object selectObject = cmbAttributes.getSelectedItem();
+ if (selectObject != null) {
+ String selectItem = selectObject.toString();
+ // Disable the Add button if "--Attribute--" or "-- Filter ---" is selected
+ if (selectItem.equalsIgnoreCase(filtersSeperator) ||selectItem.equalsIgnoreCase(attributesSeperator)) {
+ btnAddFilterWidget.setEnabled(false);
+ }
+ else {
+ btnAddFilterWidget.setEnabled(true);
+ }
+ }
+ }
+ }
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+
+ public void actionPerformed(ActionEvent e) {
+ Object _actionObject = e.getSource();
+
+ // handle Button events
+ if (_actionObject instanceof JButton) {
+ JButton _btn = (JButton) _actionObject;
+
+ if (_btn == btnApplyFilter) {
+ //System.out.println("\nApplyButton is clicked!");
+ //System.out.println("\tThe Filter to apply is \n" + cmbSelectFilter.getSelectedItem().toString()+"\n");
+ CompositeFilter theFilterToApply = (CompositeFilter) cmbSelectFilter.getSelectedItem();
+ theFilterToApply.setNetwork(Cytoscape.getCurrentNetwork());
+ FilterUtil.doSelection(theFilterToApply);
+ }
+ if (_btn == btnAddFilterWidget) {
+ //btnAddFilterWidget is clicked!
+ CompositeFilter selectedFilter = (CompositeFilter) cmbSelectFilter.getSelectedItem();
+ FilterSettingPanel theSettingPanel = filter2SettingPanelMap.get(selectedFilter);
+
+ if (cmbAttributes.getSelectedItem() instanceof String) {
+ String selectItem = (String) cmbAttributes.getSelectedItem();
+ if (selectItem.equalsIgnoreCase(filtersSeperator) ||selectItem.equalsIgnoreCase(attributesSeperator)) {
+ return;
+ }
+ }
+
+ if (cmbAttributes.getSelectedItem().toString().startsWith("node.")||
+ cmbAttributes.getSelectedItem().toString().startsWith("edge.")){
+ String attributeType = cmbAttributes.getSelectedItem().toString().substring(0,4);// "node" or "edge"
+ String attributeName = cmbAttributes.getSelectedItem().toString().substring(5);
+
+ if(CyAttributesUtils.isNullAttribute(attributeType, attributeName)){
+ JOptionPane.showMessageDialog(this, "All the values for this attribute are NULL!", "Can not create filter", JOptionPane.ERROR_MESSAGE);
+ return;
+ }
+ }
+ theSettingPanel.addNewWidget((Object)cmbAttributes.getSelectedItem());
+ }
+ if (_btn == btnSelectAll){
+ Cytoscape.getCurrentNetwork().selectAllNodes();
+
+ Cytoscape.getCurrentNetwork().selectAllEdges();
+
+ if (Cytoscape.getCurrentNetworkView() != null) {
+ Cytoscape.getCurrentNetworkView().updateView();
+ }
+ }
+ if (_btn == btnDeSelect){
+ Cytoscape.getCurrentNetwork().unselectAllNodes();
+ Cytoscape.getCurrentNetwork().unselectAllEdges();
+ Cytoscape.getCurrentNetworkView().updateView();
+ }
+
+ } // JButton event
+
+ if (_actionObject instanceof JMenuItem) {
+ JMenuItem _menuItem = (JMenuItem) _actionObject;
+ if (_menuItem == newFilterMenuItem || _menuItem == newTopologyFilterMenuItem
+ || _menuItem == newNodeInteractionFilterMenuItem || _menuItem == newEdgeInteractionFilterMenuItem) {
+ String filterType = "Composite";
+ //boolean isTopoFilter = false;
+ //boolean isInteractionFilter = false;
+ if (_menuItem == newTopologyFilterMenuItem) {
+ filterType = "Topology";
+ if (Cytoscape.getCurrentNetwork() != null) {
+ Cytoscape.getCurrentNetwork().unselectAllNodes();
+ }
+ }
+ if (_menuItem == newNodeInteractionFilterMenuItem) {
+ filterType = "NodeInteraction";
+ if (Cytoscape.getCurrentNetwork() != null) {
+ Cytoscape.getCurrentNetwork().unselectAllNodes();
+ }
+ }
+ if (_menuItem == newEdgeInteractionFilterMenuItem) {
+ filterType = "EdgeInteraction";
+ if (Cytoscape.getCurrentNetwork() != null) {
+ Cytoscape.getCurrentNetwork().unselectAllNodes();
+ }
+ }
+
+ String newFilterName = "";
+ while (true) {
+ newFilterName = javax.swing.JOptionPane.showInputDialog(
+ this, "New filter name", "New Filter Name",
+ JOptionPane.INFORMATION_MESSAGE);
+
+ if (newFilterName == null) { // user clicked "cancel"
+ break;
+ }
+ if (newFilterName.trim().equals("")) {
+ Object[] options = { "OK" };
+ JOptionPane.showOptionDialog(this,
+ "Filter name is empty!", "Warning",
+ JOptionPane.DEFAULT_OPTION,
+ JOptionPane.WARNING_MESSAGE, null, options,
+ options[0]);
+ continue;
+ }
+
+ if (cytoscape.filters.util.FilterUtil
+ .isFilterNameDuplicated(newFilterName)) {
+ Object[] options = { "OK" };
+ JOptionPane.showOptionDialog(this,
+ "Filter name already existed!", "Warning",
+ JOptionPane.DEFAULT_OPTION,
+ JOptionPane.WARNING_MESSAGE, null, options,
+ options[0]);
+ continue;
+ }
+ break;
+ }// while loop
+
+ if ((newFilterName != null)
+ && (!newFilterName.trim().equals(""))) {
+ createNewFilter(newFilterName, filterType);
+
+ //System.out.println("FilterMainPanel.firePropertyChange() -- NEW_FILTER_CREATED");
+ //pcs.firePropertyChange("NEW_FILTER_CREATED", "", "");
+ if (FilterPlugin.shouldFireFilterEvent) {
+ PropertyChangeEvent evt = new PropertyChangeEvent(this, "NEW_FILTER_CREATED", null, null);
+ Cytoscape.getPropertyChangeSupport().firePropertyChange(evt);
+ }
+ }
+ } else if (_menuItem == deleteFilterMenuItem) {
+ CompositeFilter theSelectedFilter = (CompositeFilter)cmbSelectFilter.getSelectedItem();
+ if (theSelectedFilter == null) {
+ return;
+ }
+
+ Object[] options = { "YES", "CANCEL" };
+ int userChoice = JOptionPane.showOptionDialog(this,
+ "Are you sure you want to delete " + theSelectedFilter.getName()
+ + "?", "Warning", JOptionPane.DEFAULT_OPTION,
+ JOptionPane.WARNING_MESSAGE, null, options, options[0]);
+
+ if (userChoice == 1) { // user clicked CANCEL
+ return;
+ }
+ deleteFilter(theSelectedFilter);
+ if (FilterPlugin.shouldFireFilterEvent) {
+ PropertyChangeEvent evt = new PropertyChangeEvent(this, "FILTER_DELETED", null, null);
+ Cytoscape.getPropertyChangeSupport().firePropertyChange(evt);
+ }
+ } else if (_menuItem == renameFilterMenuItem) {
+ CompositeFilter theSelectedFilter = (CompositeFilter)cmbSelectFilter.getSelectedItem();
+ if (theSelectedFilter == null) {
+ return;
+ }
+ renameFilter();
+ if (FilterPlugin.shouldFireFilterEvent) {
+ PropertyChangeEvent evt = new PropertyChangeEvent(this, "FILTER_RENAMED", null, null);
+ Cytoscape.getPropertyChangeSupport().firePropertyChange(evt);
+ }
+ } else if (_menuItem == duplicateFilterMenuItem) {
+ CompositeFilter theSelectedFilter = (CompositeFilter)cmbSelectFilter.getSelectedItem();
+ if (theSelectedFilter == null) {
+ return;
+ }
+ duplicateFilter();
+ if (FilterPlugin.shouldFireFilterEvent) {
+ PropertyChangeEvent evt = new PropertyChangeEvent(this, "FILTER_DUPLICATED", null, null);
+ Cytoscape.getPropertyChangeSupport().firePropertyChange(evt);
+ }
+ }
+ } // JMenuItem event
+
+ updateInteractionMenuItemStatus();
+ }
+
+ private void updateInteractionMenuItemStatus() {
+ //Disable interactionMenuItem if there is no other filters to depend on
+ if (FilterPlugin.getAllFilterVect() == null || FilterPlugin.getAllFilterVect().size() == 0) {
+ newNodeInteractionFilterMenuItem.setEnabled(false);
+ newEdgeInteractionFilterMenuItem.setEnabled(false);
+ return;
+ }
+
+ // Set newEdgeInteractionFilterMenuItem on only if there are at least one
+ // Node Filter
+ if (hasNodeFilter(FilterPlugin.getAllFilterVect())) {
+ newEdgeInteractionFilterMenuItem.setEnabled(true);
+ }
+ else {
+ newEdgeInteractionFilterMenuItem.setEnabled(false);
+ }
+
+ // Set newNodeInteractionFilterMenuItem on only if there are at least one
+ // Edge Filter
+ if (hasEdgeFilter(FilterPlugin.getAllFilterVect())) {
+ newNodeInteractionFilterMenuItem.setEnabled(true);
+ }
+ else {
+ newNodeInteractionFilterMenuItem.setEnabled(false);
+ }
+ }
+
+ // Check if there are any NodeFilter in the AllFilterVect
+ private boolean hasNodeFilter(Vector<CompositeFilter> pAllFilterVect) {
+ boolean selectNode = false;
+
+ for (int i=0; i< pAllFilterVect.size(); i++) {
+ CompositeFilter curFilter = (CompositeFilter) pAllFilterVect.elementAt(i);
+ if (curFilter.getAdvancedSetting().isNodeChecked()) {
+ selectNode = true;
+ }
+ }//end of for loop
+
+ return selectNode;
+ }
+
+ // Check if there are any NodeFilter in the AllFilterVect
+ private boolean hasEdgeFilter(Vector<CompositeFilter> pAllFilterVect) {
+ boolean selectEdge = false;
+
+ for (int i=0; i< pAllFilterVect.size(); i++) {
+ CompositeFilter curFilter = (CompositeFilter) pAllFilterVect.elementAt(i);
+ if (curFilter.getAdvancedSetting().isEdgeChecked()) {
+ selectEdge = true;
+ }
+ }//end of for loop
+
+ return selectEdge;
+ }
+
+ //Each time, the FilterMainPanel become visible, update the status of InteractionMaenuItems
+ class MyComponentAdapter extends ComponentAdapter {
+ public void componentShown(ComponentEvent e) {
+ updateInteractionMenuItemStatus();
+ }
+ }
+
+ private void duplicateFilter(){
+ CompositeFilter theFilter = (CompositeFilter)cmbSelectFilter.getSelectedItem();
+
+ String tmpName = "Copy of " + theFilter.getName();
+ String newFilterName = null;
+
+ while (true) {
+ Vector<String> nameVect = new Vector<String>();
+ nameVect.add(tmpName);
+
+ EditNameDialog theDialog = new EditNameDialog("Copy Filter", "Please enter a new Filter name:", nameVect, 300,170);
+ theDialog.setLocationRelativeTo(this);
+ theDialog.setVisible(true);
+
+ newFilterName = (String) nameVect.elementAt(0);
+
+ if ((newFilterName == null)) { // cancel buton is clicked
+ return;
+ }
+
+ if (cytoscape.filters.util.FilterUtil
+ .isFilterNameDuplicated(newFilterName)) {
+ Object[] options = { "OK" };
+ JOptionPane.showOptionDialog(this,
+ "Filter name already existed!", "Warning",
+ JOptionPane.DEFAULT_OPTION,
+ JOptionPane.WARNING_MESSAGE, null, options,
+ options[0]);
+ continue;
+ }
+
+ break;
+ }// while loop
+
+ CompositeFilter newFilter = (CompositeFilter) theFilter.clone();
+ newFilter.setName(newFilterName);
+
+ allFilterVect.add(newFilter);
+ FilterSettingPanel newFilterSettingPanel = new FilterSettingPanel(this, newFilter);
+ filter2SettingPanelMap.put(newFilter, newFilterSettingPanel);
+
+ // set the new filter in the combobox selected
+ cmbSelectFilter.setSelectedItem(newFilter);
+ }
+
+
+ private void renameFilter(){
+ CompositeFilter theFilter = (CompositeFilter)cmbSelectFilter.getSelectedItem();
+
+ String oldFilterName = theFilter.getName();
+ String newFilterName = "";
+ while (true) {
+ Vector<String> nameVect = new Vector<String>();
+ nameVect.add(oldFilterName);
+
+ EditNameDialog theDialog = new EditNameDialog("Edit Filter Name", "Please enter a new Filter name:", nameVect, 300,170);
+ theDialog.setLocationRelativeTo(this);
+ theDialog.setVisible(true);
+
+ newFilterName = (String) nameVect.elementAt(0);
+
+ if ((newFilterName == null) || newFilterName.trim().equals("")
+ ||newFilterName.equals(oldFilterName)) {
+ return;
+ }
+
+ if (cytoscape.filters.util.FilterUtil
+ .isFilterNameDuplicated(newFilterName)) {
+ Object[] options = { "OK" };
+ JOptionPane.showOptionDialog(this,
+ "Filter name already existed!", "Warning",
+ JOptionPane.DEFAULT_OPTION,
+ JOptionPane.WARNING_MESSAGE, null, options,
+ options[0]);
+ continue;
+ }
+
+ break;
+ }// while loop
+
+ theFilter.setName(newFilterName);
+
+ cmbSelectFilter.setSelectedItem(theFilter);
+ refreshFilterSelectCMB();
+ }
+
+ private void deleteFilter(CompositeFilter pFilter) {
+
+ filter2SettingPanelMap.remove(pFilter);
+ cmbSelectFilter.removeItem(pFilter);
+
+ if (allFilterVect == null || allFilterVect.size() == 0) {
+ replaceFilterSettingPanel(null);
+ }
+ this.validate();
+ this.repaint();
+ }
+
+ private void createNewFilter(String pFilterName, String pFilterType) {
+ // Create an empty filter, add it to the current filter list
+
+ CompositeFilter newFilter = null;
+
+ if (pFilterType.equalsIgnoreCase("Topology")) {
+ newFilter = new TopologyFilter();
+ newFilter.getAdvancedSetting().setEdge(false);
+ newFilter.setName(pFilterName);
+ }
+ else if (pFilterType.equalsIgnoreCase("NodeInteraction")) {
+ newFilter = new NodeInteractionFilter();
+ //newFilter.getAdvancedSetting().setEdge(false);
+ newFilter.setName(pFilterName);
+ }
+ else if (pFilterType.equalsIgnoreCase("EdgeInteraction")) {
+ newFilter = new EdgeInteractionFilter();
+ //newFilter.getAdvancedSetting().setEdge(false);
+ newFilter.setName(pFilterName);
+ }
+ else {
+ newFilter = new CompositeFilter(pFilterName);
+ }
+
+ newFilter.setNetwork(Cytoscape.getCurrentNetwork());
+
+ allFilterVect.add(newFilter);
+ FilterSettingPanel newFilterSettingPanel = new FilterSettingPanel(this,newFilter);
+ filter2SettingPanelMap.put(newFilter, newFilterSettingPanel);
+
+ // set the new filter in the combobox selected
+ cmbSelectFilter.setSelectedItem(newFilter);
+ refreshFilterSelectCMB();
+
+ if (pFilterType.equalsIgnoreCase("Composite")) {
+ updateCMBAttributes();
+ }
+ }
+
+ class AttributeFilterRenderer extends JLabel implements ListCellRenderer {
+ public AttributeFilterRenderer() {
+ setOpaque(true);
+ }
+
+ public Component getListCellRendererComponent(JList list, Object value,
+ int index, boolean isSelected, boolean cellHasFocus) {
+ if (value != null) {
+ if (value instanceof String) {
+ setText((String)value);
+ }
+ else if (value instanceof CompositeFilter) {
+ CompositeFilter theFilter = (CompositeFilter) value;
+ setText(theFilter.getName());
+ }
+ }
+ else { // value == null
+ setText("");
+ }
+
+ if (isSelected) {
+ setBackground(list.getSelectionBackground());
+ setForeground(list.getSelectionForeground());
+ } else {
+ setBackground(list.getBackground());
+ setForeground(list.getForeground());
+ }
+ return this;
+ }
+ }// AttributeRenderer
+
+ class FilterRenderer extends JLabel implements ListCellRenderer {
+ public FilterRenderer() {
+ setOpaque(true);
+ }
+
+ public Component getListCellRendererComponent(JList list, Object value,
+ int index, boolean isSelected, boolean cellHasFocus) {
+ if (value != null) {
+ CompositeFilter theFilter = (CompositeFilter) value;
+ setText(theFilter.getLabel());
+ }
+ else { // value == null
+ setText("");
+ }
+
+ if (isSelected) {
+ setBackground(list.getSelectionBackground());
+ setForeground(list.getSelectionForeground());
+ } else {
+ setBackground(list.getBackground());
+ setForeground(list.getForeground());
+ }
+
+ return this;
+ }
+ }// FilterRenderer
+
+ class FilterSelectWidestStringComboBoxModel extends WidestStringComboBoxModel {
+ public FilterSelectWidestStringComboBoxModel() {
+ super();
+ }
+
+ public FilterSelectWidestStringComboBoxModel(Object[] items) {
+ super(items);
+ }
+
+ public FilterSelectWidestStringComboBoxModel(Vector<?> v) {
+ super(v);
+ }
+
+ @Override
+ protected String getLabel(Object anObject) {
+ return (anObject != null) ? ((CompositeFilter)anObject).getLabel() : "";
+ }
+ }
+
+ class AttributeSelectWidestStringComboBoxModel extends WidestStringComboBoxModel {
+ public AttributeSelectWidestStringComboBoxModel() {
+ super();
+ }
+
+ public AttributeSelectWidestStringComboBoxModel(Object[] items) {
+ super(items);
+ }
+
+ public AttributeSelectWidestStringComboBoxModel(Vector<?> v) {
+ super(v);
+ }
+
+ @Override
+ protected String getLabel(Object anObject) {
+ String rv = "";
+
+ if (anObject != null) {
+ if (anObject instanceof CompositeFilter) {
+ rv = ((CompositeFilter)anObject).getLabel();
+ }
+ else {
+ rv = anObject.toString();
+ }
+ }
+
+ return rv;
+ }
+ }
+}
diff --git a/coreplugins/filters/src/main/java/cytoscape/filters/view/FilterSettingPanel.java b/coreplugins/filters/src/main/java/cytoscape/filters/view/FilterSettingPanel.java
new file mode 100644
index 0000000..1d4b2ea
--- /dev/null
+++ b/coreplugins/filters/src/main/java/cytoscape/filters/view/FilterSettingPanel.java
@@ -0,0 +1,1377 @@
+/*
+ Copyright (c) 2006, 2007, 2009, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.filters.view;
+
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import javax.swing.ImageIcon;
+
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import cytoscape.data.CyAttributes;
+import cytoscape.filters.AtomicFilter;
+import cytoscape.filters.CompositeFilter;
+import cytoscape.filters.CyFilter;
+import cytoscape.filters.TopologyFilter;
+import cytoscape.filters.InteractionFilter;
+import cytoscape.filters.StringFilter;
+import cytoscape.filters.NumericFilter;
+import cytoscape.filters.AdvancedSetting;
+import cytoscape.filters.Relation;
+import cytoscape.filters.util.FilterUtil;
+import cytoscape.filters.FilterPlugin;
+import cytoscape.filters.view.EditRangeDialog;
+
+import java.util.List;
+import java.util.Vector;
+import java.awt.Dimension;
+import java.awt.GridBagConstraints;
+import javax.swing.JTextField;
+import javax.swing.JSlider;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.ItemEvent;
+import javax.swing.JCheckBox;
+import javax.swing.JComboBox;
+import javax.swing.event.ChangeListener;
+import javax.swing.event.MouseInputAdapter;
+//import java.awt.event.FocusAdapter;
+import java.awt.event.FocusListener;
+import java.awt.event.FocusEvent;
+
+//import java.awt.event.KeyAdapter;
+//import java.awt.event.KeyEvent;
+
+import csplugins.quickfind.util.QuickFind;
+import csplugins.quickfind.util.QuickFindFactory;
+import csplugins.widgets.autocomplete.view.TextIndexComboBox;
+import csplugins.widgets.autocomplete.index.GenericIndex;
+import csplugins.widgets.autocomplete.index.IndexFactory;
+import csplugins.widgets.autocomplete.index.NumberIndex;
+import csplugins.widgets.autocomplete.index.TextIndex;
+import csplugins.widgets.autocomplete.view.ComboBoxFactory;
+import csplugins.widgets.autocomplete.view.TextIndexComboBox;
+import csplugins.widgets.autocomplete.index.Hit;
+import csplugins.widgets.slider.JRangeSliderExtended;
+import prefuse.data.query.NumberRangeModel;
+import prefuse.util.ui.JRangeSlider;
+import csplugins.quickfind.util.TaskMonitorBase;
+import cytoscape.logger.CyLogger;
+import cytoscape.task.Task;
+import cytoscape.task.TaskMonitor;
+import cytoscape.task.ui.JTaskConfig;
+import cytoscape.task.util.TaskManager;
+import cytoscape.view.CyNetworkView;
+
+import java.awt.AWTEvent;
+import javax.swing.event.ChangeEvent;
+import javax.swing.text.JTextComponent;
+
+import java.awt.Component;
+import javax.swing.JRadioButton;
+
+public class FilterSettingPanel extends JPanel {
+
+ private static final ImageIcon plusIcon = new ImageIcon(
+ Cytoscape.class.getResource("/cytoscape/images/ximian/plus.gif"));
+ private static final ImageIcon minusIcon = new ImageIcon(
+ Cytoscape.class.getResource("/cytoscape/images/ximian/minus.gif"));
+ private static final ImageIcon delIcon = new ImageIcon(Cytoscape.class
+ .getResource("/cytoscape/images/ximian/stock_delete-16.png"));
+
+ private CompositeFilter theFilter;
+ private FilterMainPanel parentPanel;
+ private CyNetwork currentNetwork = null;
+ private TopoFilterPanel topoPanel = null;
+ private InteractionFilterPanel interactionPanel = null;
+ private CyLogger logger = null;
+
+ public FilterSettingPanel(FilterMainPanel pParent, Object pFilterObj) {
+ logger = CyLogger.getLogger(FilterSettingPanel.class);
+ theFilter = (CompositeFilter) pFilterObj;
+ setName(theFilter.getName());
+ parentPanel = pParent;
+ initComponents();
+
+ initAdvancedSetting();
+
+ // Select "node/edge" will be determined automatically through the attribute selected
+ lbSelect.setVisible(false);
+ chkEdge.setVisible(false);
+ chkNode.setVisible(false);
+
+ initCustomSetting();
+
+ if (pFilterObj instanceof TopologyFilter) {
+
+ java.awt.GridBagConstraints gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = 2;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.weightx = 1.0;
+
+ pnlCustomSettings.removeAll();
+ topoPanel = new TopoFilterPanel((TopologyFilter)theFilter);
+ pnlCustomSettings.add(topoPanel, gridBagConstraints);
+ //topoPanel.addParentPanelListener(); // Update passFilterCOM when shown
+ topoPanel.addParentPanelListener(this); // Update passFilterCOM when shown
+
+ addBlankLabelToCustomPanel();
+
+ // Hide un-used components in AdvancedPanel
+ lbRelation.setVisible(false);
+ rbtAND.setVisible(false);
+ rbtOR.setVisible(false);
+ chkEdge.setVisible(false);
+ chkNode.setEnabled(false);
+
+ this.validate();
+ }
+
+ if (pFilterObj instanceof InteractionFilter) {
+
+ java.awt.GridBagConstraints gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = 2;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.weightx = 1.0;
+
+ pnlCustomSettings.removeAll();
+ interactionPanel = new InteractionFilterPanel((InteractionFilter)theFilter);
+ pnlCustomSettings.add(interactionPanel, gridBagConstraints);
+ //interactionPanel.addParentPanelListener(); // Update passFilterCOM when shown
+ interactionPanel.addParentPanelListener(this); // Update passFilterCOM when shown
+
+ addBlankLabelToCustomPanel();
+
+ // Hide un-used components in AdvancedPanel
+ lbRelation.setVisible(false);
+ rbtAND.setVisible(false);
+ rbtOR.setVisible(false);
+ lbSelect.setVisible(false);
+ chkEdge.setVisible(false);
+ chkNode.setVisible(false);
+
+ this.validate();
+ }
+ }
+
+ private void initCustomSetting() {
+ List<CyFilter> theCustomFilterList = theFilter.getChildren();
+
+ for (int i=0; i <theCustomFilterList.size();i++) {
+ addWidgetRow((CyFilter)theCustomFilterList.get(i),i*2);
+ }
+ addBlankLabelToCustomPanel();
+
+ this.validate();
+ this.repaint();
+ }
+
+
+ private int getAttributeDataType(String pAttribute, int pType) {
+ int attributeType = CyAttributes.TYPE_UNDEFINED;
+ if (pType == QuickFind.INDEX_NODES) {
+ attributeType = Cytoscape.getNodeAttributes().getType(pAttribute);
+ }
+ else if (pType == QuickFind.INDEX_EDGES) {
+ attributeType = Cytoscape.getEdgeAttributes().getType(pAttribute);
+ }
+ return attributeType;
+ }
+
+
+ private JComboBox getTextIndexComboBox(StringFilter pFilter){
+ TextIndexComboBox comboBox = null;
+
+ try {
+ // If index doesnot exist, check if there is such attribute or
+ if (!FilterUtil.hasSuchAttribute(pFilter.getControllingAttribute(), pFilter.getIndexType())) {
+ // no such attribute
+ JComboBox tmpCombo;
+ if (pFilter.getSearchStr() != null) {
+ Object[] objList = {pFilter.getSearchStr()};
+ tmpCombo = new JComboBox(objList);
+ }
+ else {
+ tmpCombo = new JComboBox();
+ }
+ tmpCombo.setEnabled(false);
+ return tmpCombo;
+ }
+ // The attribute exists, create an index
+ //final QuickFind quickFind = QuickFindFactory.getGlobalQuickFindInstance();
+ //quickFind.reindexNetwork(Cytoscape.getCurrentNetwork(), pFilter.getIndexType(),
+ // pFilter.getControllingAttribute(), new TaskMonitorBase());
+ //TextIndex index_by_thisAttr = (TextIndex) quickFind.getIndex(Cytoscape.getCurrentNetwork());
+
+ pFilter.setIndex(createTextIndex(pFilter));
+
+ comboBox = ComboBoxFactory.createTextIndexComboBox((TextIndex)pFilter.getIndex(), 2.0);
+
+ // Set Size of ComboBox Display, based on # of specific chars
+ comboBox.setPrototypeDisplayValue("01234567");
+
+ // Set Max Size of ComboBox to match preferred size
+ comboBox.setMaximumSize(comboBox.getPreferredSize());
+ comboBox.setName(pFilter.getControllingAttribute());
+
+ if (pFilter.getSearchStr() != null) {
+ comboBox.setSelectedItem(pFilter.getSearchStr());
+ }
+
+ ActionListener listener = new UserSelectionListener(comboBox);
+ comboBox.addFinalSelectionListener(listener);
+
+ final JTextComponent editor = (JTextComponent) comboBox.getEditor().getEditorComponent();
+ ComboBoxFocusListener focuslistener = new ComboBoxFocusListener(comboBox);
+ editor.addFocusListener(focuslistener);
+
+ } catch (Exception e) {
+ logger.error("Exception in FilterSettingpanel.getTextIndexComboBox()");
+ }
+
+ return comboBox;
+ }
+
+
+ private JRangeSliderExtended getRangerSlider(NumericFilter pFilter) {
+ //System.out.println("Entering FilterSettingPanel.getRangerSlider()...");
+
+ NumberIndex theIndex = createNumberIndex(pFilter);
+
+ if (theIndex != null) {
+ //System.out.println("theIndex != null");
+ pFilter.setIndex(theIndex);
+ }
+ else {
+ //System.out.println("theIndex == null");
+ }
+
+ NumberRangeModel rangeModel = null;
+ if (theIndex == null) {
+ rangeModel = new NumberRangeModel(0,0,0,0);
+ }
+ else {
+
+ int dataType = getAttributeDataType(pFilter.getControllingAttribute(), pFilter.getIndexType());
+ //Initialize the search values, lowBound and highBound
+
+ if (pFilter.getLowBound() == null) {
+ pFilter.setLowBound(theIndex.getMinimumValue());
+ }
+ if (pFilter.getHighBound() == null) {
+ pFilter.setHighBound(theIndex.getMaximumValue());
+ }
+
+ if (dataType == CyAttributes.TYPE_FLOATING) {
+ Double lowB = (Double)pFilter.getLowBound();
+ Double highB = (Double)pFilter.getHighBound();
+ Double min = (Double)theIndex.getMinimumValue();
+ Double max = (Double)theIndex.getMaximumValue();
+
+ rangeModel = new NumberRangeModel(lowB.doubleValue(),highB.doubleValue(),min.doubleValue(),max.doubleValue());
+ }
+ else if (dataType == CyAttributes.TYPE_INTEGER) {
+ rangeModel = new NumberRangeModel(pFilter.getLowBound(),pFilter.getHighBound(),
+ theIndex.getMinimumValue(),theIndex.getMaximumValue());
+ }
+ }
+
+ JRangeSliderExtended rangeSlider = new JRangeSliderExtended(rangeModel, JRangeSlider.HORIZONTAL,
+ JRangeSlider.LEFTRIGHT_TOPBOTTOM);
+
+ rangeSlider.setMinimumSize(new Dimension(100,20));
+ rangeSlider.setPreferredSize(new Dimension(100,20));
+
+ RangeSelectionListener rangeSelectionListener = new RangeSelectionListener(rangeSlider);
+ rangeSlider.addChangeListener(rangeSelectionListener);
+ rangeSlider.setName(pFilter.getControllingAttribute());
+
+ RangeSlideMouseAdapter l = new RangeSlideMouseAdapter();
+ rangeSlider.addMouseListener(l);
+
+ MyMouseInputAdapter myMouseInputAdapter = new MyMouseInputAdapter();
+ rangeSlider.addMouseMotionListener(myMouseInputAdapter);
+
+ return rangeSlider;
+ }
+
+ private class MyMouseInputAdapter extends MouseInputAdapter {
+ public void mouseMoved(MouseEvent e) {
+ String toolTipText = "";
+ JRangeSliderExtended _range = null;
+ NumberRangeModel _model = null;
+ Object _obj = e.getSource();
+ if (_obj instanceof JRangeSliderExtended) {
+ _range = (JRangeSliderExtended) _obj;
+ _model = (NumberRangeModel) _range.getModel();
+ toolTipText = _model.getLowValue() + " ~ " + _model.getHighValue() + " Double-click to edit";
+ _range.setToolTipText(toolTipText);
+ }
+ }
+ }
+
+ public boolean hasNullIndexChildFilter() {
+ List<CyFilter> children = theFilter.getChildren();
+ if ((children == null)||(children.size() == 0)) {
+ return false;
+ }
+ for (int i=0; i<children.size(); i++) {
+ CyFilter child = children.get(i);
+ if (child instanceof AtomicFilter) {
+ AtomicFilter aFilter = (AtomicFilter) child;
+ if (aFilter.getIndex() == null)
+ return true;
+ }
+ }
+
+ return false;
+ }
+
+
+ // Refresh indices for widget after network switch or Cytoscape.ATTRIBUTES_CHANGED event is received
+ // The method may be triggered by event of NETWORK_VIEW_FOCUSED
+ public void refreshIndicesForWidgets(){
+ // Check if each widget has associatd index, if not, try to create one
+ //System.out.println("FilterSettingpanel:refreshIndicesForWidgets()...\n");
+ List<CyFilter> children = theFilter.getChildren();
+ if ((children == null)||(children.size() == 0)) {
+ return;
+ }
+
+ CyNetwork network = Cytoscape.getCurrentNetwork();
+
+ for (int i=0; i<children.size(); i++) {
+ CyFilter child = children.get(i);
+ if (child instanceof StringFilter) {
+ if (pnlCustomSettings.getComponent(i*5+3) instanceof TextIndexComboBox) {
+ TextIndexComboBox theBox = (TextIndexComboBox) pnlCustomSettings.getComponent(i*5+3);
+ if (network != null) {
+ CyNetworkView networkView = Cytoscape.getNetworkView(network.getIdentifier());
+ if (networkView != Cytoscape.getNullNetworkView()) {
+ TextIndex textIndex = createTextIndex((StringFilter) child);;
+ if (textIndex != null) {
+ theBox.setTextIndex(textIndex);
+ StringFilter aFilter = (StringFilter) child;
+ aFilter.setIndex(textIndex);
+ }
+ }
+ }
+ }
+ }
+ if (child instanceof NumericFilter) {
+ if (pnlCustomSettings.getComponent(i*5+3) instanceof JRangeSliderExtended) {
+ JRangeSliderExtended theSlider = (JRangeSliderExtended) pnlCustomSettings.getComponent(i*5+3);
+ if (network != null) {
+ CyNetworkView networkView = Cytoscape.getNetworkView(network.getIdentifier());
+
+ if (networkView != Cytoscape.getNullNetworkView()) {
+ NumberIndex numIndex = createNumberIndex((NumericFilter) child);;
+ if (numIndex != null) {
+ NumberRangeModel rangeModel = (NumberRangeModel) theSlider.getModel();
+ rangeModel.setMinValue(numIndex.getMinimumValue());
+ rangeModel.setMaxValue(numIndex.getMaximumValue());
+
+ NumericFilter aFilter = (NumericFilter) child;
+ aFilter.setIndex(numIndex);
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+
+ /**
+ * Inner class Mouse listener for double click events on rangeSlider.
+ */
+ public class RangeSlideMouseAdapter extends MouseAdapter
+ {
+ public void mouseClicked(MouseEvent pMouseEvent)
+ {
+ if (pMouseEvent.getClickCount() >= 2)
+ {
+ Object srcObj = pMouseEvent.getSource();
+ if (srcObj instanceof JRangeSliderExtended) {
+ JRangeSliderExtended theSlider = (JRangeSliderExtended) srcObj;
+ NumberRangeModel model = (NumberRangeModel) theSlider.getModel();
+
+ Vector<String> boundVect = new Vector<String>();
+ boundVect.add(model.getLowValue().toString());
+ boundVect.add(model.getHighValue().toString());
+ boundVect.add(model.getMinValue().toString());
+ boundVect.add(model.getMaxValue().toString());
+
+ if (model.getLowValue().getClass().getName().equalsIgnoreCase("java.lang.Integer")) {
+ EditRangeDialog theDialog = new EditRangeDialog(new javax.swing.JFrame(), true, theSlider.getName(), boundVect, "int");
+ theDialog.setLocation(theSlider.getLocationOnScreen());
+ theDialog.setVisible(true);
+ //if lowBound < min, set it to min
+ //if highBound > max, set it to max
+ adjustBoundValues(boundVect, "int");
+
+ model.setValueRange(new Integer(boundVect.elementAt(0)),new Integer(boundVect.elementAt(1)), (Integer) model.getMinValue(), (Integer) model.getMaxValue());
+ }
+ else {
+ EditRangeDialog theDialog = new EditRangeDialog(new javax.swing.JFrame(), true, theSlider.getName(), boundVect, "double");
+ theDialog.setLocation(theSlider.getLocationOnScreen());
+ theDialog.setVisible(true);
+ adjustBoundValues(boundVect, "double");
+ model.setValueRange(new Double(boundVect.elementAt(0)),new Double(boundVect.elementAt(1)), (Double) model.getMinValue(), (Double) model.getMaxValue());
+ }
+
+ //Update the selection on screen
+ theFilter.setNetwork(Cytoscape.getCurrentNetwork());
+ FilterUtil.doSelection(theFilter);
+ }
+ }
+ }
+ }
+
+ private void adjustBoundValues(Vector<String> pBoundVect, String pDataType){
+ if (pDataType.equalsIgnoreCase("int")) {
+ int lowBound = new Integer(pBoundVect.elementAt(0)).intValue();
+ int highBound = new Integer(pBoundVect.elementAt(1)).intValue();
+ int min = new Integer(pBoundVect.elementAt(2)).intValue();
+ int max = new Integer(pBoundVect.elementAt(3)).intValue();
+ if (lowBound < min) {
+ lowBound = min;
+ pBoundVect.setElementAt(new Integer(lowBound).toString(),0);
+ }
+ if (highBound > max) {
+ highBound = max;
+ pBoundVect.setElementAt(new Integer(highBound).toString(),1);
+ }
+ }
+ else if (pDataType.equalsIgnoreCase("double")) {
+ double lowBound = new Double(pBoundVect.elementAt(0)).doubleValue();
+ double highBound = new Double(pBoundVect.elementAt(1)).doubleValue();
+ double min = new Double(pBoundVect.elementAt(2)).doubleValue();
+ double max = new Double(pBoundVect.elementAt(3)).doubleValue();
+ if (lowBound < min) {
+ lowBound = min;
+ pBoundVect.setElementAt(new Double(lowBound).toString(),0);
+ }
+ if (highBound > max) {
+ highBound = max;
+ pBoundVect.setElementAt(new Double(highBound).toString(),1);
+ }
+ }
+ }
+
+ private AtomicFilter getAtomicFilterFromStr(String pCtrlAttribute, int pIndexType) {
+ AtomicFilter retFilter = null;
+
+ final QuickFind quickFind = QuickFindFactory.getGlobalQuickFindInstance();
+ //quickFind.addNetwork(cyNetwork, new TaskMonitorBase());
+ //index_by_UniqueIdentification = (TextIndex) quickFind.getIndex(cyNetwork);
+
+ quickFind.reindexNetwork(Cytoscape.getCurrentNetwork(), pIndexType, pCtrlAttribute, new TaskMonitorBase());
+
+ int attributeType = -1;
+
+ if (pIndexType == QuickFind.INDEX_NODES) {
+ attributeType = Cytoscape.getNodeAttributes().getType(pCtrlAttribute);
+ }
+ else if (pIndexType == QuickFind.INDEX_EDGES) {
+ attributeType = Cytoscape.getEdgeAttributes().getType(pCtrlAttribute);
+ }
+ //
+ if ((attributeType == CyAttributes.TYPE_INTEGER)
+ ||(attributeType == CyAttributes.TYPE_FLOATING)) {
+ retFilter = new NumericFilter();
+ retFilter.setControllingAttribute(pCtrlAttribute);
+ retFilter.setIndexType(pIndexType);
+
+ //NumberIndex index_by_thisAttr = (NumberIndex) quickFind.getIndex(Cytoscape.getCurrentNetwork());
+
+ retFilter.setIndex(quickFind.getIndex(Cytoscape.getCurrentNetwork()));
+
+ }
+ else if ((attributeType == CyAttributes.TYPE_STRING)||(attributeType == CyAttributes.TYPE_SIMPLE_LIST)||(attributeType == CyAttributes.TYPE_BOOLEAN)) {
+ retFilter = new StringFilter();
+ retFilter.setControllingAttribute(pCtrlAttribute);
+ retFilter.setIndexType(pIndexType);
+
+ //TextIndex index_by_thisAttr = (TextIndex) quickFind.getIndex(Cytoscape.getCurrentNetwork());
+
+ retFilter.setIndex(quickFind.getIndex(Cytoscape.getCurrentNetwork()));
+ }
+ else {
+ logger.error("AttributeType is not numeric/string/list/boolean!");
+ }
+
+ return retFilter;
+ }
+
+ // Update the relation label after user click radio button "AND" or "OR" in AdvancedPanel
+ private void updateRelationLabel(){
+ Component[] allComponents = pnlCustomSettings.getComponents();
+
+ String relationStr = "AND";
+ if (theFilter.getAdvancedSetting().getRelation()== Relation.OR) {
+ relationStr = "OR";
+ }
+
+ for (int i=0; i<allComponents.length; i++) {
+ if (allComponents[i] instanceof JLabel) {
+ JLabel theLabel = (JLabel) allComponents[i];
+ String labelName = theLabel.getName();
+ if ((labelName != null) &&(labelName.equalsIgnoreCase("RelationLabel"))) {
+ theLabel.setText(relationStr);
+ theLabel.repaint();
+ }
+ }
+ }
+ }
+
+ //user Clicked CheckBox_Not left-side of the child filter
+ private void updateNegationStatus(MouseEvent e) {
+ // Determine the child index in theFilter,
+ // then update the negation value for that child filter
+ Object _actionObject = e.getSource();
+
+ if (_actionObject instanceof JCheckBox) {
+ JCheckBox _chk = (JCheckBox) _actionObject;
+ int widgetGridY = (new Integer(_chk.getName())).intValue();
+ int childIndex =widgetGridY/2;
+
+ CyFilter childFilter = theFilter.getChildren().get(childIndex);
+ if (childFilter instanceof CompositeFilter) {
+ CompositeFilter tmpFilter = (CompositeFilter)childFilter;
+ theFilter.setNotTable(tmpFilter, new Boolean(_chk.isSelected()));
+ }
+ else { // it is an AtomiCFilter
+ childFilter.setNegation(_chk.isSelected());
+ }
+ //Update the selection on screen
+ doSelection();
+ }
+ }
+
+
+ private void addWidgetRow(CyFilter pFilter, int pGridY) {
+
+ GridBagConstraints gridBagConstraints = new GridBagConstraints();
+
+ if (pGridY > 0) {
+ // add a row to indicate the relationship between the widgets
+ String relationStr = "AND";
+ if (theFilter.getAdvancedSetting().getRelation()== Relation.OR) {
+ relationStr = "OR";
+ }
+
+ //Col 2 ---> Label to indicate relationship between widgets
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 2;
+ gridBagConstraints.gridy = pGridY-1;
+ JLabel lbRelation = new JLabel(relationStr);
+ lbRelation.setName("RelationLabel");
+ pnlCustomSettings.add(lbRelation, gridBagConstraints);
+ }
+
+ // Col 0 -- label with attributeName/Filter
+ JLabel theLabel_col0 = new JLabel();
+
+ if (pFilter instanceof AtomicFilter) {
+ AtomicFilter atomicFilter = (AtomicFilter) pFilter;
+ theLabel_col0.setText(atomicFilter.getControllingAttribute());
+ }
+ else {
+ theLabel_col0.setText("Filter");
+ }
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = pGridY;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
+ //gridBagConstraints.insets = new java.awt.Insets(0, 10, 0, 10);
+ pnlCustomSettings.add(theLabel_col0, gridBagConstraints);
+
+ //Col 1 ---> chk box -- NOT
+ JCheckBox chkNot = new JCheckBox("Not");
+ chkNot.setName(Integer.toString(pGridY));
+ chkNot.setSelected(pFilter.getNegation());
+ chkNot.addMouseListener(
+ new MouseAdapter() {
+ public void mouseClicked(MouseEvent e) {
+ updateNegationStatus(e);
+ }
+ }
+ );
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = pGridY;
+ //gridBagConstraints.insets = new java.awt.Insets(0, 10, 0, 0);
+ pnlCustomSettings.add(chkNot, gridBagConstraints);
+
+ gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.weightx = 1.0;
+ //Col 2 ---> Widget if atomicFilter
+ if (pFilter instanceof StringFilter) {
+ JComboBox aBox = getTextIndexComboBox((StringFilter)pFilter);
+ pnlCustomSettings.add(aBox, gridBagConstraints);
+ }
+ else if (pFilter instanceof NumericFilter) {
+ JRangeSliderExtended theSlider = getRangerSlider((NumericFilter) pFilter);
+ pnlCustomSettings.add(theSlider, gridBagConstraints);
+ }
+ else {// CompositeFilter
+ gridBagConstraints.fill = java.awt.GridBagConstraints.NONE;
+ //gridBagConstraints.weightx = 0.0;
+ //gridBagConstraints.anchor = java.awt.GridBagConstraints.
+ pnlCustomSettings.add(new JLabel(pFilter.getName()), gridBagConstraints);
+ }
+ gridBagConstraints.weightx = 0.0;
+ //Col 3 ---> label (a trash can) for delete of the row
+ JLabel theDelLabel = new JLabel();
+
+ theDelLabel.setIcon(delIcon);
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = pGridY;
+ //gridBagConstraints.insets = new java.awt.Insets(0, 5, 0, 0);
+ pnlCustomSettings.add(theDelLabel, gridBagConstraints);
+
+ theDelLabel.setName(Integer.toString(pGridY));
+ theDelLabel.addMouseListener(
+ new MouseAdapter() {
+ public void mouseClicked(MouseEvent e) {
+ removeFilterWidget(e);
+ }
+ }
+ );
+
+ this.validate();
+
+ }
+
+ public void addNewWidget(Object pObj) {
+ // The parameter pObj is the object selected from Attribute/Filter combobox
+ // It can be either (1) a string with prefix "node."/"edge." (2) a CompositeFilter object
+ if (pObj instanceof CompositeFilter) {
+ if (pObj == theFilter) {
+ return; // Ignore if try to add self
+ }
+
+ CompositeFilter theCompositeFilter = (CompositeFilter) pObj;
+ addWidgetRow(theCompositeFilter, theFilter.getChildren().size()*2);
+ // Update theFilter object
+ theFilter.addChild(theCompositeFilter, new Boolean(false));
+
+ //determine the filter selection type
+ if (theCompositeFilter.getAdvancedSetting().isNodeChecked()) {
+ theFilter.getAdvancedSetting().setNode(true);
+ }
+ if (theCompositeFilter.getAdvancedSetting().isEdgeChecked()) {
+ theFilter.getAdvancedSetting().setEdge(true);
+ }
+ }
+ else { //(pObj instanceof String)
+ String tmpObj = (String)pObj;
+ String ctrlAttribute = tmpObj.substring(5);
+
+ int indexType = QuickFind.INDEX_NODES;
+ if (tmpObj.startsWith("edge.")) {
+ indexType = QuickFind.INDEX_EDGES;
+ // determine the filter selection type
+ theFilter.getAdvancedSetting().setEdge(true);
+ }
+ else {
+ theFilter.getAdvancedSetting().setNode(true);
+ }
+ AtomicFilter newChildFilter = getAtomicFilterFromStr(ctrlAttribute, indexType);
+ addWidgetRow(newChildFilter, theFilter.getChildren().size()*2);
+ // Update theFilter object
+ theFilter.addChild(newChildFilter);
+ }
+ // Update selection type of the filter setting
+ updateSelectionType();
+
+ //Update the selection on screen
+ doSelection();
+ }
+
+
+ private void updateSelectionType() {
+ boolean selectNode = false;
+ boolean selectEdge = false;
+ List<CyFilter> childFilters = theFilter.getChildren();
+ for (int i=0; i< childFilters.size(); i++) {
+ CyFilter child = childFilters.get(i);
+ if (child instanceof AtomicFilter) {
+ AtomicFilter tmp = (AtomicFilter) child;
+ if (tmp.getIndexType() == QuickFind.INDEX_NODES) {
+ selectNode = true;
+ }
+ if (tmp.getIndexType() == QuickFind.INDEX_EDGES) {
+ selectEdge = true;
+ }
+ }
+ else if (child instanceof CompositeFilter) {
+ CompositeFilter tmp = (CompositeFilter) child;
+ if (tmp.getAdvancedSetting().isNodeChecked()) {
+ selectNode = true;
+ }
+ if (tmp.getAdvancedSetting().isEdgeChecked()) {
+ selectEdge = true;
+ }
+ }
+ }//end of for loop
+
+ theFilter.getAdvancedSetting().setNode(selectNode);
+ theFilter.getAdvancedSetting().setEdge(selectEdge);
+ }
+
+ // Determine the child index in filter based on the row index of a component
+ // (TextIndexComboBox or RangeSlider) in the customSetting panel
+ private int getChildIndexFromComponent(Component pComponent) {
+ int childIndex = -1;
+ int componentCount = pnlCustomSettings.getComponentCount();
+ for (int i = 0; i<componentCount; i++ ) {
+ Component theComponent = pnlCustomSettings.getComponent(i);
+ if (theComponent == pComponent){
+ if (i<5) {
+ childIndex =0;
+ }
+ else {
+ childIndex = (i-2)/5;
+ }
+ break;
+ }
+ }
+ return childIndex;
+ }
+
+ private void doSelection() {
+ // If network size is greater than pre-defined threshold, don't apply theFilter automatically
+ if (FilterUtil.isDynamicFilter(theFilter)) {
+ FilterUtil.doSelection(theFilter);
+ }
+ }
+
+ // remove a GUI widget from the customeSetting panel
+ private void removeFilterWidget(MouseEvent e)
+ {
+ Object _actionObject = e.getSource();
+
+ if (_actionObject instanceof JLabel) {
+ JLabel _lbl = (JLabel) _actionObject;
+ int widgetGridY = (new Integer(_lbl.getName())).intValue();
+ int childIndex =widgetGridY /2;
+
+ theFilter.removeChildAt(childIndex);
+ hidePopupForRangeSlider();
+ pnlCustomSettings.removeAll();
+ initCustomSetting();
+ }
+
+ updateSelectionType();
+
+ doSelection();
+ }
+
+
+ private void hidePopupForRangeSlider() {
+ if (pnlCustomSettings.getComponentCount() == 0) {
+ return;
+ }
+
+ int cmpCount = pnlCustomSettings.getComponentCount();
+ for (int i=0; i< cmpCount; i++) {
+ Component theCmp = pnlCustomSettings.getComponent(i);
+ if (theCmp instanceof JRangeSliderExtended) {
+ JRangeSliderExtended theSlider = (JRangeSliderExtended) theCmp;
+ theSlider.resetPopup();
+ }
+ }
+
+ }
+
+ // Fix Bug #0001940
+ class ComboBoxFocusListener implements FocusListener {
+ private TextIndexComboBox comboBox = null;
+ public ComboBoxFocusListener (TextIndexComboBox comboBox) {
+ this.comboBox = comboBox;
+ }
+
+ public void focusLost(FocusEvent e) {
+ // sync the StringFilter with the UI
+ final JTextComponent editor = (JTextComponent) comboBox.getEditor().getEditorComponent();
+ String userInput = editor.getText();
+
+ // Determine the row index of the TextIndexCombobox in the customSetting panel
+ int widgetIndex = getChildIndexFromComponent(comboBox);
+
+ //Update theFilter Object
+ List<CyFilter> theFilterlist = theFilter.getChildren();
+
+ StringFilter theStringFilter = (StringFilter) theFilterlist.get(widgetIndex);
+ theStringFilter.setSearchStr(userInput);
+ }
+ public void focusGained(FocusEvent e) {
+ // do nothing
+ }
+ }
+
+
+ /**
+ * Listens for Final Selection from User.
+ *
+ * @author Ethan Cerami.
+ */
+ class UserSelectionListener implements ActionListener {
+ private TextIndexComboBox comboBox;
+
+ /**
+ * Constructor.
+ *
+ * @param comboBox TextIndexComboBox.
+ */
+ public UserSelectionListener(TextIndexComboBox comboBox) {
+ this.comboBox = comboBox;
+ }
+
+ /**
+ * User has made final selection.
+ *
+ * @param e ActionEvent Object.
+ */
+ public void actionPerformed(ActionEvent e) {
+ //Update the StringFilter after user made a selection in the TextIndexCombobox
+
+ // Get Current User Selection
+ Object o = comboBox.getSelectedItem();
+
+ if ((o != null) && o instanceof Hit) {
+ Hit hit = (Hit) comboBox.getSelectedItem();
+
+ // Determine the row index of the TextIndexCombobox in the customSetting panel
+ int widgetIndex = getChildIndexFromComponent(comboBox);
+
+ //Update theFilter Object
+ List<CyFilter> theFilterlist = theFilter.getChildren();
+
+ StringFilter theStringFilter = (StringFilter) theFilterlist.get(widgetIndex);
+ theStringFilter.setSearchStr(hit.getKeyword());
+ }
+
+ //Update the selection on screen
+ doSelection();
+ }
+ }
+
+
+ /**
+ * Action to select a range of nodes.
+ *
+ * @author Ethan Cerami.
+ */
+ class RangeSelectionListener implements ChangeListener {
+ private JRangeSliderExtended slider;
+
+ /**
+ * Constructor.
+ *
+ * @param slider JRangeSliderExtended Object.
+ */
+ public RangeSelectionListener(JRangeSliderExtended slider) {
+ this.slider = slider;
+ }
+
+ /**
+ * State Change Event.
+ *
+ * @param e ChangeEvent Object.
+ */
+ public void stateChanged(ChangeEvent e) {
+
+ //Update theFilter object if the slider is adjusted
+ List<CyFilter> theFilterList = theFilter.getChildren();
+
+ try {
+ NumberRangeModel model = (NumberRangeModel) slider.getModel();
+ NumericFilter theNumericFilter = (NumericFilter) theFilterList.get(getChildIndexFromComponent(slider));
+
+ theNumericFilter.setRange((Number)model.getLowValue(), (Number)model.getHighValue());
+ }
+ catch (Exception ex) {
+ //NullPointerException caught -- the slider is not initialized yet
+ logger.error("FilterSettingPanel.stateChanged():NullPointerException caught -- the slider is not initialized yet");
+ }
+
+ theFilter.childChanged();
+ //Update the selection on screen
+ doSelection();
+ }
+ }
+
+
+ private TextIndex createTextIndex(StringFilter pFilter) {
+ final QuickFind quickFind = QuickFindFactory.getGlobalQuickFindInstance();
+ quickFind.reindexNetwork(Cytoscape.getCurrentNetwork(), pFilter.getIndexType(),
+ pFilter.getControllingAttribute(), new TaskMonitorBase());
+ return (TextIndex) quickFind.getIndex(Cytoscape.getCurrentNetwork());
+ }
+
+
+ private NumberIndex createNumberIndex(NumericFilter pNumericFilter) {
+ final QuickFind quickFind = QuickFindFactory.getGlobalQuickFindInstance();
+ currentNetwork = Cytoscape.getCurrentNetwork();
+
+ int indexType = pNumericFilter.getIndexType();
+ quickFind.reindexNetwork(currentNetwork, indexType,
+ pNumericFilter.getControllingAttribute(), new TaskMonitorBase());
+
+ GenericIndex currentIndex = quickFind.getIndex(currentNetwork);
+ if (currentIndex == null|| !(currentIndex instanceof NumberIndex)) {
+ return null;
+ }
+ return (NumberIndex) currentIndex;
+ }
+
+ // Add a label to take up the extra space at the custom setting panel
+ private void addBlankLabelToCustomPanel(){
+ GridBagConstraints gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = 99;
+ gridBagConstraints.gridwidth = 3;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.BOTH;
+ gridBagConstraints.weightx = 1.0;
+ gridBagConstraints.weighty = 1.0;
+ pnlCustomSettings.add(new JLabel(), gridBagConstraints);
+ }
+
+ private void initAdvancedSetting() {
+ chkSession.setSelected(theFilter.getAdvancedSetting().isSessionChecked());
+ chkGlobal.setSelected(theFilter.getAdvancedSetting().isGlobalChecked());
+ chkNode.setSelected(theFilter.getAdvancedSetting().isNodeChecked());
+ chkEdge.setSelected(theFilter.getAdvancedSetting().isEdgeChecked());
+ chkNegation.setSelected(theFilter.getNegation());
+
+ if (theFilter.getAdvancedSetting().getRelation() == Relation.AND) {
+ rbtAND.setSelected(true);
+ rbtOR.setSelected(false);
+ }
+ else { // Relation.OR
+ rbtAND.setSelected(false);
+ rbtOR.setSelected(true);
+ }
+
+ lbAdvancedIcon.setIcon(plusIcon);
+ lbAdvancedIcon.addMouseListener( new MouseAdapter() {
+ //Inner class Mouse listener for click on the plus/minus sign.
+ public void mouseClicked(MouseEvent e) {
+ Object _actionObject = e.getSource();
+ // click on the plus/minus sign to hide/show advancedPanel
+ if (_actionObject instanceof JLabel) {
+ JLabel _lbl = (JLabel) _actionObject;
+
+ if (_lbl == lbAdvancedIcon) {
+ if (pnlAdvancedOptions.isVisible()) {
+ pnlAdvancedOptions.setVisible(false);
+ lbAdvancedIcon.setIcon(plusIcon);
+ }
+ else {
+ pnlAdvancedOptions.setVisible(true);
+ lbAdvancedIcon.setIcon(minusIcon);
+ }
+ }
+ }
+ }
+ });
+
+ ItemListener l = new MyItemListener();
+ chkSession.addItemListener(l);
+ chkGlobal.addItemListener(l);
+
+ //The following no longer needed
+ //chkNode.addItemListener(l);
+ //chkEdge.addItemListener(l);
+
+ chkSource.addItemListener(l);
+ chkTarget.addItemListener(l);
+ rbtAND.addItemListener(l);
+ rbtOR.addItemListener(l);
+ chkNegation.addItemListener(l);
+ //By default, the AdvancedPanel is invisible
+ pnlAdvancedOptions.setVisible(false);
+
+ }
+
+ //To sync the filter object with the setting Panel
+ public class MyItemListener implements ItemListener{
+
+ public void itemStateChanged(ItemEvent e) {
+ Object soureObj= e.getSource();
+ if (soureObj instanceof javax.swing.JCheckBox) {
+ JCheckBox theCheckBox = (JCheckBox) soureObj;
+
+ if (theCheckBox == chkSession) {
+ theFilter.getAdvancedSetting().setSession(chkSession.isSelected());
+ // filter name has a prefix "global." or "session.", refresh CMB to update
+ parentPanel.refreshFilterSelectCMB();
+ }
+ else if (theCheckBox == chkGlobal)
+ {
+ theFilter.getAdvancedSetting().setGlobal(chkGlobal.isSelected());
+ parentPanel.refreshFilterSelectCMB();
+ }
+ /*
+ * "select Node/Edge" will be determined automatically through selection of attribute in attributeComboBox
+ else if (theCheckBox == chkNode)
+ {
+ theFilter.getAdvancedSetting().setNode(chkNode.isSelected());
+ parentPanel.refreshAttributeCMB();
+ }
+ else if (theCheckBox == chkEdge)
+ {
+ theFilter.getAdvancedSetting().setEdge(chkEdge.isSelected());
+ parentPanel.refreshAttributeCMB();
+ }
+ */
+ else if (theCheckBox == chkSource)
+ {
+ theFilter.getAdvancedSetting().setSource(chkSource.isSelected());
+ //parentPanel.refreshAttributeCMB();
+ }
+ else if (theCheckBox == chkTarget)
+ {
+ theFilter.getAdvancedSetting().setTarget(chkTarget.isSelected());
+ //parentPanel.refreshAttributeCMB();
+ }
+ else if (theCheckBox == chkNegation)
+ {
+ theFilter.setNegation(chkNegation.isSelected());
+ }
+ //Update the selection on screen
+ if ((theCheckBox == chkNegation)) { //||(theCheckBox == chkEdge)||(theCheckBox == chkNode)) {
+ theFilter.childChanged();//The setting has changed
+ doSelection();
+ }
+ }
+ if (soureObj instanceof javax.swing.JRadioButton) {
+ JRadioButton theRadioButton = (JRadioButton) soureObj;
+
+ if (theRadioButton == rbtAND) {
+ theFilter.getAdvancedSetting().setRelation(Relation.AND);
+ }
+ if (theRadioButton == rbtOR) {
+ theFilter.getAdvancedSetting().setRelation(Relation.OR);
+ }
+ updateRelationLabel();
+
+ //Update the selection on screen
+ //System.out.println("FilterSettingPanel. rbtAND/rbtOR is clicked");
+ theFilter.childChanged();
+ doSelection();
+ }
+ }
+ }
+
+
+ /** This method is called from within the constructor to
+ * initialize the form.
+ * WARNING: Do NOT modify this code. The content of this method is
+ * always regenerated by the Form Editor.
+ */
+ // <editor-fold defaultstate="collapsed" desc=" Generated Code ">
+ private void initComponents() {
+ java.awt.GridBagConstraints gridBagConstraints;
+
+ buttonGroup1 = new javax.swing.ButtonGroup();
+ pnlAdvancedSettings = new javax.swing.JPanel();
+ pnlAdvancedIcon = new javax.swing.JPanel();
+ lbAdvanced = new javax.swing.JLabel();
+ lbAdvancedIcon = new javax.swing.JLabel();
+ pnlAdvancedOptions = new javax.swing.JPanel();
+ jLabel6 = new javax.swing.JLabel();
+ chkSession = new javax.swing.JCheckBox();
+ chkGlobal = new javax.swing.JCheckBox();
+ lbSelect = new javax.swing.JLabel();
+ chkNode = new javax.swing.JCheckBox();
+ chkEdge = new javax.swing.JCheckBox();
+
+ jLabel8 = new javax.swing.JLabel();
+ chkSource = new javax.swing.JCheckBox();
+ chkTarget = new javax.swing.JCheckBox();
+
+ // hide source/target row
+ jLabel8.setVisible(false);
+ chkSource.setVisible(false);
+ chkTarget.setVisible(false);
+
+ lbRelation = new javax.swing.JLabel();
+ rbtAND = new javax.swing.JRadioButton();
+ rbtOR = new javax.swing.JRadioButton();
+ lbNegation = new javax.swing.JLabel();
+ chkNegation = new javax.swing.JCheckBox();
+
+ pnlCustomSettings = new javax.swing.JPanel();
+ //lbSpaceHolder = new javax.swing.JLabel();
+ jPanel1 = new javax.swing.JPanel();
+ btnAdd = new javax.swing.JButton();
+ btnClose = new javax.swing.JButton();
+
+ setLayout(new java.awt.GridBagLayout());
+
+ pnlAdvancedSettings.setLayout(new java.awt.GridBagLayout());
+
+ pnlAdvancedIcon.setLayout(new java.awt.GridBagLayout());
+
+ lbAdvanced.setText(" Advanced ");
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 1;
+ gridBagConstraints.gridy = 0;
+ pnlAdvancedIcon.add(lbAdvanced, gridBagConstraints);
+
+ lbAdvancedIcon.setIcon(plusIcon);
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 0;
+ pnlAdvancedIcon.add(lbAdvancedIcon, gridBagConstraints);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 0;
+ gridBagConstraints.gridy = 0;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.FIRST_LINE_START;
+ pnlAdvancedSettings.add(pnlAdvancedIcon, gridBagConstraints);
+
+ pnlAdvancedOptions.setLayout(new java.awt.GridBagLayout());
+
+ pnlAdvancedOptions.setBorder(javax.swing.BorderFactory.createTitledBorder(""));
+ jLabel6.setText("Save");
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
+ gridBagConstraints.insets = new java.awt.Insets(0, 0, 5, 0);
+ pnlAdvancedOptions.add(jLabel6, gridBagConstraints);
+
+ chkSession.setSelected(true);
+ chkSession.setText("Session");
+ chkSession.setBorder(javax.swing.BorderFactory.createEmptyBorder(0, 0, 0, 0));
+ chkSession.setMargin(new java.awt.Insets(0, 0, 0, 0));
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
+ gridBagConstraints.insets = new java.awt.Insets(0, 5, 5, 0);
+ pnlAdvancedOptions.add(chkSession, gridBagConstraints);
+
+ chkGlobal.setText("Global");
+ chkGlobal.setBorder(javax.swing.BorderFactory.createEmptyBorder(0, 0, 0, 0));
+ chkGlobal.setMargin(new java.awt.Insets(0, 0, 0, 0));
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
+ gridBagConstraints.insets = new java.awt.Insets(0, 5, 5, 0);
+ pnlAdvancedOptions.add(chkGlobal, gridBagConstraints);
+
+ lbSelect.setText("Select");
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = 1;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
+ pnlAdvancedOptions.add(lbSelect, gridBagConstraints);
+
+ chkNode.setSelected(true);
+ chkNode.setText("Node");
+ chkNode.setBorder(javax.swing.BorderFactory.createEmptyBorder(0, 0, 0, 0));
+ chkNode.setMargin(new java.awt.Insets(0, 0, 0, 0));
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = 1;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
+ gridBagConstraints.insets = new java.awt.Insets(0, 5, 0, 0);
+ pnlAdvancedOptions.add(chkNode, gridBagConstraints);
+
+ chkEdge.setSelected(true);
+ chkEdge.setText("Edge");
+ chkEdge.setBorder(javax.swing.BorderFactory.createEmptyBorder(0, 0, 0, 0));
+ chkEdge.setMargin(new java.awt.Insets(0, 0, 0, 0));
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = 1;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
+ gridBagConstraints.insets = new java.awt.Insets(0, 5, 0, 0);
+ pnlAdvancedOptions.add(chkEdge, gridBagConstraints);
+
+ jLabel8.setText("Edge");
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = 2;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
+ gridBagConstraints.insets = new java.awt.Insets(5, 0, 0, 0);
+ pnlAdvancedOptions.add(jLabel8, gridBagConstraints);
+
+
+ chkSource.setSelected(true);
+ chkSource.setText("Source");
+ chkSource.setBorder(javax.swing.BorderFactory.createEmptyBorder(0, 0, 0, 0));
+ chkSource.setMargin(new java.awt.Insets(0, 0, 0, 0));
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = 2;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
+ gridBagConstraints.insets = new java.awt.Insets(5, 5, 0, 0);
+ pnlAdvancedOptions.add(chkSource, gridBagConstraints);
+
+ chkTarget.setSelected(true);
+ chkTarget.setText("Target");
+ chkTarget.setBorder(javax.swing.BorderFactory.createEmptyBorder(0, 0, 0, 0));
+ chkTarget.setMargin(new java.awt.Insets(0, 0, 0, 0));
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = 2;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
+ gridBagConstraints.insets = new java.awt.Insets(5, 5, 0, 0);
+ pnlAdvancedOptions.add(chkTarget, gridBagConstraints);
+
+
+ lbRelation.setText("Relation");
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
+ gridBagConstraints.gridy = 3;
+ gridBagConstraints.insets = new java.awt.Insets(0, 0, 0, 0);
+ pnlAdvancedOptions.add(lbRelation, gridBagConstraints);
+
+ rbtAND.setSelected(true);
+ rbtAND.setText("AND");
+ rbtAND.setBorder(javax.swing.BorderFactory.createEmptyBorder(0, 0, 0, 0));
+ rbtAND.setMargin(new java.awt.Insets(0, 0, 0, 0));
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = 3;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
+ gridBagConstraints.insets = new java.awt.Insets(5, 5, 0, 0);
+ pnlAdvancedOptions.add(rbtAND, gridBagConstraints);
+
+ rbtOR.setText("OR");
+ rbtOR.setBorder(javax.swing.BorderFactory.createEmptyBorder(0, 0, 0, 0));
+ rbtOR.setMargin(new java.awt.Insets(0, 0, 0, 0));
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = 3;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
+ gridBagConstraints.insets = new java.awt.Insets(5, 5, 0, 0);
+ pnlAdvancedOptions.add(rbtOR, gridBagConstraints);
+
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 1;
+ gridBagConstraints.gridy = 0;
+ gridBagConstraints.gridwidth = 3;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
+ gridBagConstraints.insets = new java.awt.Insets(0, 0, 3, 0);
+ pnlAdvancedSettings.add(pnlAdvancedOptions, gridBagConstraints);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
+ add(pnlAdvancedSettings, gridBagConstraints);
+
+
+ lbNegation.setText("Negation");
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = 4;
+ pnlAdvancedOptions.add(lbNegation, gridBagConstraints);
+
+ chkNegation.setBorder(javax.swing.BorderFactory.createEmptyBorder(0, 0, 0, 0));
+ chkNegation.setMargin(new java.awt.Insets(0, 0, 0, 0));
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = 4;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
+ gridBagConstraints.insets = new java.awt.Insets(5, 5, 0, 0);
+ pnlAdvancedOptions.add(chkNegation, gridBagConstraints);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 1;
+ gridBagConstraints.gridy = 0;
+ gridBagConstraints.gridwidth = 3;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
+ gridBagConstraints.insets = new java.awt.Insets(0, 0, 5, 0);
+ pnlAdvancedSettings.add(pnlAdvancedOptions, gridBagConstraints);
+
+ pnlCustomSettings.setLayout(new java.awt.GridBagLayout());
+
+ pnlCustomSettings.setBorder(javax.swing.BorderFactory.createTitledBorder(""));
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = 1;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.BOTH;
+ gridBagConstraints.weightx = 1.0;
+ gridBagConstraints.weighty = 1.0;
+ gridBagConstraints.insets = new java.awt.Insets(1, 2, 0, 2);
+ add(new JScrollPane(pnlCustomSettings), gridBagConstraints);
+ //add(pnlCustomSettings, gridBagConstraints);
+
+ btnAdd.setText("Add Widgets");
+ jPanel1.add(btnAdd);
+
+ btnClose.setText("Close");
+ jPanel1.add(btnClose);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = 2;
+
+ //Unomment the following line for test
+ //add(jPanel1, gridBagConstraints);
+
+
+ buttonGroup1.add(rbtAND);
+ buttonGroup1.add(rbtOR);
+
+ }// </editor-fold>
+
+
+ // Variables declaration - do not modify
+
+ private javax.swing.JButton btnAdd;
+ private javax.swing.JButton btnClose;
+ private javax.swing.ButtonGroup buttonGroup1;
+ private javax.swing.JCheckBox chkEdge;
+ private javax.swing.JCheckBox chkGlobal;
+ private javax.swing.JCheckBox chkNegation;
+ private javax.swing.JCheckBox chkNode;
+ private javax.swing.JCheckBox chkSession;
+ private javax.swing.JCheckBox chkSource;
+ private javax.swing.JCheckBox chkTarget;
+ private javax.swing.JLabel lbRelation;
+ private javax.swing.JLabel jLabel6;
+ private javax.swing.JLabel lbSelect;
+ private javax.swing.JLabel jLabel8;
+ private javax.swing.JPanel jPanel1;
+ private javax.swing.JLabel lbAdvanced;
+ private javax.swing.JLabel lbAdvancedIcon;
+ //private javax.swing.JLabel lbSpaceHolder;
+ private javax.swing.JPanel pnlAdvancedIcon;
+ private javax.swing.JPanel pnlAdvancedOptions;
+ private javax.swing.JPanel pnlAdvancedSettings;
+ private javax.swing.JPanel pnlCustomSettings;
+ private javax.swing.JRadioButton rbtAND;
+ private javax.swing.JRadioButton rbtOR;
+ private javax.swing.JLabel lbNegation;
+ // End of variables declaration
+
+}
diff --git a/coreplugins/filters/src/main/java/cytoscape/filters/view/InteractionFilterPanel.java b/coreplugins/filters/src/main/java/cytoscape/filters/view/InteractionFilterPanel.java
new file mode 100644
index 0000000..2a988e5
--- /dev/null
+++ b/coreplugins/filters/src/main/java/cytoscape/filters/view/InteractionFilterPanel.java
@@ -0,0 +1,331 @@
+/*
+ Copyright (c) 2006, 2007, 2009, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.filters.view;
+
+import java.awt.Component;
+import java.awt.event.ComponentAdapter;
+import java.awt.event.ComponentEvent;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.util.Vector;
+
+import javax.swing.JCheckBox;
+import javax.swing.JComboBox;
+import javax.swing.JLabel;
+import javax.swing.JList;
+import javax.swing.JPanel;
+import javax.swing.ListCellRenderer;
+
+import cytoscape.filters.CompositeFilter;
+import cytoscape.filters.FilterPlugin;
+import cytoscape.filters.InteractionFilter;
+import cytoscape.filters.EdgeInteractionFilter;
+import cytoscape.filters.NodeInteractionFilter;
+import cytoscape.filters.util.FilterUtil;
+import cytoscape.util.swing.WidestStringComboBoxPopupMenuListener;
+
+public class InteractionFilterPanel extends JPanel implements ItemListener{
+
+ private InteractionFilter theFilter;
+
+ /** Creates new form InteractionFilterPanel */
+ public InteractionFilterPanel(InteractionFilter pFilter) {
+ theFilter = pFilter;
+ setName(theFilter.getName());
+
+ initComponents();
+ if (pFilter instanceof EdgeInteractionFilter) {
+ changeLabelText();
+ }
+
+ buildCMBmodel();
+
+ cmbPassFilter.setRenderer(new FilterRenderer());
+
+ //add EventListeners
+ chkSource.addItemListener(this);
+ chkTarget.addItemListener(this);
+
+ cmbPassFilter.addItemListener(this);
+
+ //Make sure bits will be calculated for the first time
+ pFilter.childChanged();
+
+ // Recovery initial values
+ chkSource.setSelected(pFilter.isSourceChecked());
+ chkTarget.setSelected(pFilter.isTargetChecked());
+
+ //Initialize the passFilter, if it is a new fIlter
+ if (theFilter.getPassFilter().getName().equalsIgnoreCase("None")) {
+ // thePassFilter name == "None", it's a brand new filter
+ // Set the passFilter the first appropriate filter in the comboBox
+ int index = 0;
+ CompositeFilter curFilter = null;
+ for (int i=0; i< cmbPassFilter.getModel().getSize(); i++) {
+ curFilter = (CompositeFilter)cmbPassFilter.getModel().getElementAt(i);
+ if ((theFilter instanceof EdgeInteractionFilter && curFilter.getAdvancedSetting().isNodeChecked())||
+ theFilter instanceof NodeInteractionFilter && curFilter.getAdvancedSetting().isEdgeChecked()) {
+ index = i;
+ break;
+ }
+ }
+ theFilter.setPassFilter((CompositeFilter)cmbPassFilter.getModel().getElementAt(index));
+ }
+ cmbPassFilter.setSelectedItem(theFilter.getPassFilter());
+
+ MyComponentAdapter cmpAdpt = new MyComponentAdapter();
+ addComponentListener(cmpAdpt);
+ }
+
+ private void changeLabelText() {
+ lbSelectionType.setText("Select Edges");
+ lbNodeType.setText("with a node");
+ lbAboveFilter.setText("which pass the filter");
+ }
+
+ /**
+ * @deprecated
+ * If nothing else calls this, then it's more sensible to just pass the panel
+ * to listen to directly.
+ */
+ public void addParentPanelListener() {
+ // Listen to the visible event from FilterSettingPanel
+ // To syn Filters in cmbPassFilter
+ MyComponentAdapter cmpAdpt = new MyComponentAdapter();
+ Component comp;
+
+ comp = this;
+ while (comp != null) {
+ if (comp instanceof FilterSettingPanel) {
+ comp.addComponentListener(cmpAdpt);
+ break;
+ }
+ else {
+ comp = comp.getParent();
+ }
+ }
+ }
+
+ public void addParentPanelListener(Component comp) {
+ // Listen to the visible event from FilterSettingPanel
+ // To syn Filters in cmbPassFilter
+ MyComponentAdapter cmpAdpt = new MyComponentAdapter();
+ comp.addComponentListener(cmpAdpt);
+ }
+
+ //Each time, the FilterSettingPanel become visible, rebuild the model for the cmbPassFilter
+ class MyComponentAdapter extends ComponentAdapter {
+ public void componentShown(ComponentEvent e) {
+ buildCMBmodel();
+ }
+ }
+
+ private void buildCMBmodel() {
+ // Create an empty filter, add to the top of the filter list in the combobox
+ //CompositeFilter emptyFilter = new CompositeFilter("None");
+
+ Vector<CompositeFilter> tmpVect = new Vector<CompositeFilter>();
+ //tmpVect.add(emptyFilter);
+ tmpVect.addAll(FilterPlugin.getAllFilterVect());
+
+ PassFilterWidestStringComboBoxModel pfwscbm = new PassFilterWidestStringComboBoxModel(tmpVect);
+ cmbPassFilter.setModel(pfwscbm);
+ if (theFilter.getPassFilter() != null) {
+ cmbPassFilter.setSelectedIndex(0);
+ cmbPassFilter.setSelectedItem(theFilter.getPassFilter());
+ }
+ }
+
+
+ public void itemStateChanged(ItemEvent e) {
+ Object source = e.getSource();
+ //System.out.println("Entering InteractionFilterPanel.itemStateChanged() ...");
+
+ Object soureObj= e.getSource();
+ if (soureObj instanceof JCheckBox) {
+ JCheckBox theCheckBox = (JCheckBox) soureObj;
+
+ if (theCheckBox == chkSource) {
+ theFilter.setSourceChecked(chkSource.isSelected());
+ }
+ if (theCheckBox == chkTarget) {
+ theFilter.setTargetChecked(chkTarget.isSelected());
+ }
+ }
+
+ if (source instanceof JComboBox) {
+ theFilter.setPassFilter((CompositeFilter) cmbPassFilter.getSelectedItem());
+ }
+ theFilter.childChanged();
+
+ // If network size is less than pre-defined threshold, apply theFilter automatically
+ if (FilterUtil.isDynamicFilter(theFilter)) {
+ FilterUtil.doSelection(theFilter);
+ }
+ }
+
+
+ /** This method is called from within the constructor to
+ * initialize the form.
+ * WARNING: Do NOT modify this code. The content of this method is
+ * always regenerated by the Form Editor.
+ */
+ // <editor-fold defaultstate="collapsed" desc=" Generated Code ">
+ private void initComponents() {
+ java.awt.GridBagConstraints gridBagConstraints;
+
+ lbSelectionType = new javax.swing.JLabel();
+ lbNodeType = new javax.swing.JLabel();
+ chkSource = new javax.swing.JCheckBox();
+ chkTarget = new javax.swing.JCheckBox();
+ lbAboveFilter = new javax.swing.JLabel();
+ cmbPassFilter = new javax.swing.JComboBox();
+ cmbPassFilter.setModel(new PassFilterWidestStringComboBoxModel());
+ cmbPassFilter.addPopupMenuListener(new WidestStringComboBoxPopupMenuListener());
+ lbPlaceHolder = new javax.swing.JLabel();
+
+ setLayout(new java.awt.GridBagLayout());
+
+ lbSelectionType.setText("Select Nodes");
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
+ gridBagConstraints.insets = new java.awt.Insets(10, 10, 0, 0);
+ add(lbSelectionType, gridBagConstraints);
+
+ lbNodeType.setText("which are the");
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = 1;
+ gridBagConstraints.insets = new java.awt.Insets(10, 10, 0, 0);
+ add(lbNodeType, gridBagConstraints);
+
+ chkSource.setText("Source");
+ chkSource.setBorder(javax.swing.BorderFactory.createEmptyBorder(0, 0, 0, 0));
+ chkSource.setMargin(new java.awt.Insets(0, 0, 0, 0));
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = 1;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
+ gridBagConstraints.insets = new java.awt.Insets(10, 10, 0, 0);
+ add(chkSource, gridBagConstraints);
+
+ chkTarget.setText("Target");
+ chkTarget.setBorder(javax.swing.BorderFactory.createEmptyBorder(0, 0, 0, 0));
+ chkTarget.setMargin(new java.awt.Insets(0, 0, 0, 0));
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = 1;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
+ gridBagConstraints.insets = new java.awt.Insets(10, 10, 0, 0);
+ add(chkTarget, gridBagConstraints);
+
+ lbAboveFilter.setText("of at least one edge which pass the filter");
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = 2;
+ gridBagConstraints.gridwidth = 3;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
+ gridBagConstraints.insets = new java.awt.Insets(10, 10, 0, 0);
+ add(lbAboveFilter, gridBagConstraints);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 0;
+ gridBagConstraints.gridy = 3;
+ gridBagConstraints.gridwidth = 3;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.weightx = 1.0;
+ gridBagConstraints.insets = new java.awt.Insets(10, 10, 0, 10);
+ add(cmbPassFilter, gridBagConstraints);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = 10;
+ gridBagConstraints.gridwidth = 3;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.BOTH;
+ gridBagConstraints.weightx = 1.0;
+ gridBagConstraints.weighty = 1.0;
+ add(lbPlaceHolder, gridBagConstraints);
+
+ }// </editor-fold>
+
+
+ // Variables declaration - do not modify
+ private javax.swing.JCheckBox chkSource;
+ private javax.swing.JCheckBox chkTarget;
+ private javax.swing.JComboBox cmbPassFilter;
+ private javax.swing.JLabel lbAboveFilter;
+ private javax.swing.JLabel lbNodeType;
+ private javax.swing.JLabel lbPlaceHolder;
+ private javax.swing.JLabel lbSelectionType;
+ // End of variables declaration
+
+ class FilterRenderer extends JLabel implements ListCellRenderer {
+ public FilterRenderer() {
+ setOpaque(true);
+ }
+
+ public Component getListCellRendererComponent(JList list, Object value,
+ int index, boolean isSelected, boolean cellHasFocus) {
+
+ if (value == null) {
+ setText("");
+ return this;
+ }
+
+ if (isSelected) {
+ setBackground(list.getSelectionBackground());
+ setForeground(list.getSelectionForeground());
+ } else {
+ setBackground(list.getBackground());
+ setForeground(list.getForeground());
+ }
+
+ //Ignore self
+ if (value == theFilter) {
+ setText("");
+
+ return this;
+ }
+
+ //Display related filters only
+ CompositeFilter tmpFilter = (CompositeFilter) value;
+ if ((theFilter instanceof EdgeInteractionFilter && tmpFilter.getAdvancedSetting().isNodeChecked()) ||
+ (theFilter instanceof NodeInteractionFilter && tmpFilter.getAdvancedSetting().isEdgeChecked())) {
+ setText(tmpFilter.getName());
+ }
+ else {
+ setText("");
+ }
+
+ return this;
+ }
+ }// FilterRenderer
+}
diff --git a/coreplugins/filters/src/main/java/cytoscape/filters/view/PassFilterWidestStringComboBoxModel.java b/coreplugins/filters/src/main/java/cytoscape/filters/view/PassFilterWidestStringComboBoxModel.java
new file mode 100644
index 0000000..0e1c340
--- /dev/null
+++ b/coreplugins/filters/src/main/java/cytoscape/filters/view/PassFilterWidestStringComboBoxModel.java
@@ -0,0 +1,64 @@
+/*
+ Copyright (c) 2009, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.filters.view;
+
+import cytoscape.filters.CompositeFilter;
+import cytoscape.util.swing.WidestStringComboBoxModel;
+import java.util.Vector;
+
+/**
+ *
+ * @author Noel Ruddock
+ */
+public class PassFilterWidestStringComboBoxModel extends WidestStringComboBoxModel {
+ public PassFilterWidestStringComboBoxModel() {
+ super();
+ }
+
+ public PassFilterWidestStringComboBoxModel(Object[] items) {
+ super(items);
+ }
+
+ public PassFilterWidestStringComboBoxModel(Vector<?> v) {
+ super(v);
+ }
+
+ @Override
+ protected String getLabel(Object anObject) {
+ return (anObject != null) ? ((CompositeFilter)anObject).getName() : "";
+ }
+}
+
diff --git a/coreplugins/filters/src/main/java/cytoscape/filters/view/TopoFilterPanel.java b/coreplugins/filters/src/main/java/cytoscape/filters/view/TopoFilterPanel.java
new file mode 100644
index 0000000..e2236cc
--- /dev/null
+++ b/coreplugins/filters/src/main/java/cytoscape/filters/view/TopoFilterPanel.java
@@ -0,0 +1,365 @@
+/*
+ Copyright (c) 2006, 2007, 2009, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.filters.view;
+
+import java.awt.event.ActionListener;
+import java.awt.event.ActionEvent;
+
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.KeyAdapter;
+import java.awt.event.KeyEvent;
+import java.awt.event.ComponentAdapter;
+import java.awt.event.ComponentEvent;
+import java.awt.Component;
+import java.awt.event.ActionEvent;
+import java.util.Vector;
+
+import javax.swing.JButton;
+import javax.swing.JComboBox;
+import javax.swing.JLabel;
+import javax.swing.JList;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.ListCellRenderer;
+import javax.swing.JTextField;
+import cytoscape.Cytoscape;
+import cytoscape.filters.AdvancedSetting;
+import cytoscape.filters.CompositeFilter;
+import cytoscape.filters.TopologyFilter;
+import cytoscape.filters.util.FilterUtil;
+import cytoscape.filters.view.FilterMainPanel.FilterRenderer;
+import cytoscape.filters.view.FilterMainPanel.MyCytoPanelListener;
+import cytoscape.view.cytopanels.CytoPanelListener;
+import cytoscape.filters.FilterPlugin;
+import cytoscape.util.swing.WidestStringComboBoxPopupMenuListener;
+
+
+/**
+ * @author Peng
+ *
+ */
+public class TopoFilterPanel extends JPanel implements ActionListener, ItemListener {
+
+ //private Vector<CompositeFilter> allFilterVect = null;
+ private TopologyFilter theFilter;
+
+ /** Creates new form TopoFilterPanel */
+ public TopoFilterPanel(TopologyFilter pFilter) {
+ theFilter = pFilter;
+ setName(theFilter.getName());
+ initComponents();
+
+ buildCMBmodel();
+
+ cmbPassFilter.setRenderer(new FilterRenderer());
+
+ //add EventListeners
+ tfDistance.addActionListener(this);
+ tfMinNeighbors.addActionListener(this);
+
+ MyKeyListener l = new MyKeyListener();
+ tfDistance.addKeyListener(l);
+ tfMinNeighbors.addKeyListener(l);
+
+ cmbPassFilter.addItemListener(this);
+
+ //Make sure bits will be calculated for the first time
+ pFilter.childChanged();
+
+ // Recovery initial values if any
+ tfMinNeighbors.setText(new Integer(pFilter.getMinNeighbors()).toString());
+ tfDistance.setText(new Integer(pFilter.getDistance()).toString());
+
+ MyComponentAdapter cmpAdpt = new MyComponentAdapter();
+ addComponentListener(cmpAdpt);
+ }
+
+ /**
+ * @deprecated
+ * If nothing else calls this, then it's more sensible to just pass the panel
+ * to listen to directly.
+ */
+ public void addParentPanelListener() {
+ // Listen to the visible event from FilterSettingPanel
+ // To syn Filters in cmbPassFilter
+ MyComponentAdapter cmpAdpt = new MyComponentAdapter();
+ Component comp;
+
+ comp = this;
+ while (comp != null) {
+ if (comp instanceof FilterSettingPanel) {
+ comp.addComponentListener(cmpAdpt);
+ break;
+ }
+ else {
+ comp = comp.getParent();
+ }
+ }
+ }
+
+ public void addParentPanelListener(Component comp) {
+ // Listen to the visible event from FilterSettingPanel
+ // To syn Filters in cmbPassFilter
+ MyComponentAdapter cmpAdpt = new MyComponentAdapter();
+ comp.addComponentListener(cmpAdpt);
+ }
+
+ //Each time, the FilterSettingPanel become visible, rebuild the model for the cmbPassFilter
+ class MyComponentAdapter extends ComponentAdapter {
+ public void componentShown(ComponentEvent e) {
+ buildCMBmodel();
+ }
+ }
+
+ private void buildCMBmodel() {
+ // Create an empty filter, add to the top of the filter list in the combobox
+ CompositeFilter emptyFilter = new CompositeFilter("None");
+
+ Vector<CompositeFilter> tmpVect = new Vector<CompositeFilter>();
+ tmpVect.add(emptyFilter);
+ tmpVect.addAll(FilterPlugin.getAllFilterVect());
+
+ PassFilterWidestStringComboBoxModel pfwscbm = new PassFilterWidestStringComboBoxModel(tmpVect);
+ cmbPassFilter.setModel(pfwscbm);
+ if (theFilter.getPassFilter() != null) {
+ cmbPassFilter.setSelectedIndex(0);
+ cmbPassFilter.setSelectedItem(theFilter.getPassFilter());
+ }
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ Object _actionObject = e.getSource();
+
+ // System.out.println("Entering TopoFIlterPanel.actionPerformed() ...");
+
+ // handle Button events
+ if (_actionObject instanceof JTextField) {
+ JTextField _tfObj = (JTextField) _actionObject;
+ if (_tfObj == tfMinNeighbors) {
+ int _neighbors = (new Integer(tfMinNeighbors.getText())).intValue();
+ theFilter.setMinNeighbors(_neighbors);
+ }
+ else if (_tfObj == tfDistance) {
+ int _distance = (new Integer(tfDistance.getText())).intValue();
+ theFilter.setDistance(_distance);
+ }
+ }
+ // System.out.println(theFilter.getName());
+
+ }
+
+ public void itemStateChanged(ItemEvent e) {
+ Object source = e.getSource();
+
+ //System.out.println("Entering TopoFilterPanel.itemStateChanged() ...");
+
+ if (source instanceof JComboBox) {
+ theFilter.setPassFilter((CompositeFilter) cmbPassFilter.getSelectedItem());
+ theFilter.childChanged();
+
+ // If network size is less than pre-defined threshold, apply theFilter automatically
+ if (FilterUtil.isDynamicFilter(theFilter)) {
+ FilterUtil.doSelection(theFilter);
+ }
+ }
+ }
+
+ /** This method is called from within the constructor to
+ * initialize the form.
+ * WARNING: Do NOT modify this code. The content of this method is
+ * always regenerated by the Form Editor.
+ */
+ // <editor-fold defaultstate="collapsed" desc=" Generated Code ">
+ private void initComponents() {
+ java.awt.GridBagConstraints gridBagConstraints;
+
+ lbSelectNodeEdge = new javax.swing.JLabel();
+ lbWithAtLeast = new javax.swing.JLabel();
+ tfMinNeighbors = new javax.swing.JTextField();
+ lbNeighbors = new javax.swing.JLabel();
+ lbWithinDistance = new javax.swing.JLabel();
+ tfDistance = new javax.swing.JTextField();
+ lbThatPassTheFilter = new javax.swing.JLabel();
+ cmbPassFilter = new javax.swing.JComboBox();
+ cmbPassFilter.setModel(new PassFilterWidestStringComboBoxModel());
+ cmbPassFilter.addPopupMenuListener(new WidestStringComboBoxPopupMenuListener());
+ lbPlaceHolder = new javax.swing.JLabel();
+
+ setLayout(new java.awt.GridBagLayout());
+
+ lbSelectNodeEdge.setText("Select nodes");
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 0);
+ add(lbSelectNodeEdge, gridBagConstraints);
+
+ lbWithAtLeast.setText("with at least");
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = 1;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.EAST;
+ gridBagConstraints.insets = new java.awt.Insets(0, 0, 10, 10);
+ add(lbWithAtLeast, gridBagConstraints);
+
+ tfMinNeighbors.setText("1");
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = 1;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.weightx = 0.5;
+ gridBagConstraints.insets = new java.awt.Insets(0, 0, 10, 10);
+ add(tfMinNeighbors, gridBagConstraints);
+
+ lbNeighbors.setText("neighbors");
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = 1;
+ gridBagConstraints.insets = new java.awt.Insets(0, 0, 10, 10);
+ add(lbNeighbors, gridBagConstraints);
+
+ lbWithinDistance.setText("within distance");
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = 2;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.EAST;
+ gridBagConstraints.insets = new java.awt.Insets(0, 0, 10, 10);
+ add(lbWithinDistance, gridBagConstraints);
+
+ tfDistance.setText("1");
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = 2;
+ gridBagConstraints.gridwidth = 2;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.insets = new java.awt.Insets(0, 0, 10, 10);
+ add(tfDistance, gridBagConstraints);
+
+ lbThatPassTheFilter.setText("and the nodes pass the filter");
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = 3;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.EAST;
+ gridBagConstraints.insets = new java.awt.Insets(0, 10, 0, 10);
+ add(lbThatPassTheFilter, gridBagConstraints);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = 3;
+ gridBagConstraints.gridwidth = 2;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.insets = new java.awt.Insets(0, 0, 0, 10);
+ add(cmbPassFilter, gridBagConstraints);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridy = 10;
+ gridBagConstraints.gridwidth = 3;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.BOTH;
+ gridBagConstraints.weightx = 1.0;
+ gridBagConstraints.weighty = 1.0;
+ add(lbPlaceHolder, gridBagConstraints);
+
+ }// </editor-fold>
+
+ // Variables declaration - do not modify
+ private javax.swing.JComboBox cmbPassFilter;
+ private javax.swing.JLabel lbNeighbors;
+ private javax.swing.JLabel lbPlaceHolder;
+ private javax.swing.JLabel lbSelectNodeEdge;
+ private javax.swing.JLabel lbThatPassTheFilter;
+ private javax.swing.JLabel lbWithAtLeast;
+ private javax.swing.JLabel lbWithinDistance;
+ private javax.swing.JTextField tfDistance;
+ private javax.swing.JTextField tfMinNeighbors;
+ // End of variables declaration
+
+ class FilterRenderer extends JLabel implements ListCellRenderer {
+ public FilterRenderer() {
+ setOpaque(true);
+ }
+
+ public Component getListCellRendererComponent(JList list, Object value,
+ int index, boolean isSelected, boolean cellHasFocus) {
+ if (value != null) {
+ if (value == theFilter) {
+ setText("");
+ }
+ else {
+ CompositeFilter tmpFilter = (CompositeFilter) value;
+ setText(tmpFilter.getName());
+ }
+ }
+ else { // value == null
+ setText("");
+ }
+
+ if (isSelected) {
+ setBackground(list.getSelectionBackground());
+ setForeground(list.getSelectionForeground());
+ } else {
+ setBackground(list.getBackground());
+ setForeground(list.getForeground());
+ }
+
+ return this;
+ }
+ }
+
+class MyKeyListener extends KeyAdapter {
+
+ public void keyReleased(KeyEvent e) {
+ Object _actionObject = e.getSource();
+
+ if (tfMinNeighbors.getText().trim().equalsIgnoreCase("") ||
+ tfDistance.getText().trim().equalsIgnoreCase("")) {
+ return;
+ }
+ if (_actionObject instanceof JTextField) {
+ JTextField _tfObj = (JTextField) _actionObject;
+ if (_tfObj == tfMinNeighbors) {
+
+ //Validate the data
+ //try {
+ // Integer.parseInt(tfMinNeighbors.getText());
+ //}
+ //catch (NumberFormatException nfe) {
+ // JOptionPane.showMessageDialog((Component)e.getSource(), "Invalid values", "Warning", JOptionPane.ERROR_MESSAGE);
+ // return;
+ //}
+
+ int _neighbors = (new Integer(tfMinNeighbors.getText())).intValue();
+ theFilter.setMinNeighbors(_neighbors);
+ }
+ else if (_tfObj == tfDistance) {
+ int _distance = (new Integer(tfDistance.getText())).intValue();
+ theFilter.setDistance(_distance);
+ }
+ }
+ }
+ }
+}
diff --git a/coreplugins/filters/src/main/java/cytoscape/quickfind/test/package.html b/coreplugins/filters/src/main/java/cytoscape/quickfind/test/package.html
new file mode 100644
index 0000000..2299ebb
--- /dev/null
+++ b/coreplugins/filters/src/main/java/cytoscape/quickfind/test/package.html
@@ -0,0 +1,8 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+<html>
+<head></head>
+
+<body bgcolor="white">
+Master JUnit Suite for running all Unit Tests.
+</body>
+</html>
diff --git a/coreplugins/filters/src/main/java/cytoscape/quickfind/test/widgets/test/package.html b/coreplugins/filters/src/main/java/cytoscape/quickfind/test/widgets/test/package.html
new file mode 100644
index 0000000..ab74cb3
--- /dev/null
+++ b/coreplugins/filters/src/main/java/cytoscape/quickfind/test/widgets/test/package.html
@@ -0,0 +1,8 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+<html>
+<head></head>
+
+<body bgcolor="white">
+Test Package.
+</body>
+</html>
diff --git a/coreplugins/filters/src/main/java/cytoscape/quickfind/test/widgets/test/uiTests/package.html b/coreplugins/filters/src/main/java/cytoscape/quickfind/test/widgets/test/uiTests/package.html
new file mode 100644
index 0000000..1d7ae2e
--- /dev/null
+++ b/coreplugins/filters/src/main/java/cytoscape/quickfind/test/widgets/test/uiTests/package.html
@@ -0,0 +1,8 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+<html>
+<head></head>
+
+<body bgcolor="white">
+Usability / UI Tests.
+</body>
+</html>
diff --git a/coreplugins/filters/src/main/java/cytoscape/quickfind/test/widgets/test/unitTests/package.html b/coreplugins/filters/src/main/java/cytoscape/quickfind/test/widgets/test/unitTests/package.html
new file mode 100644
index 0000000..3199df4
--- /dev/null
+++ b/coreplugins/filters/src/main/java/cytoscape/quickfind/test/widgets/test/unitTests/package.html
@@ -0,0 +1,8 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+<html>
+<head></head>
+
+<body bgcolor="white">
+JUnit Tests.
+</body>
+</html>
diff --git a/coreplugins/filters/src/main/resources/cytoscape/filters/plugin.props b/coreplugins/filters/src/main/resources/cytoscape/filters/plugin.props
new file mode 100644
index 0000000..e2c6dd8
--- /dev/null
+++ b/coreplugins/filters/src/main/resources/cytoscape/filters/plugin.props
@@ -0,0 +1,30 @@
+# This props file would be filled out and included in the plugin jar file. This props file will be used
+# to put information into the Plugin Manager about the plugin
+
+
+# -- The following properties are REQUIRED -- #
+
+# The plugin name that will be displayed to users
+pluginName=Filters
+
+# Description used to give users information about the plugin such as what it does.
+# Html tags are encouraged for formatting purposes.
+pluginDescription=Select nodes and edges based on specific attributes
+
+# Plugin version number, this must be two numbers separated by a decimlal. Ex. 0.2, 14.03
+pluginVersion=0.3
+
+# Compatible Cytoscape version
+cytoscapeVersion=2.5,2.6,2.7,2.8
+
+# Category, use one of the categories listed on the website or create your own
+pluginCategory=Core
+
+
+# List of authors. Note each author and institution pair are separated by a : (colon)
+# each additional author institution pair must be separated from other pairs bye a ; (semicolon)
+pluginAuthorsIntsitutions=Peng-Liang Wang:UCSD
+
+# -- The following properties should be set ONLY BY CORE PLUGINS -- #
+downloadURL=http://cytoscape.org/plugins/plugins.xml
+uniqueID=8
diff --git a/coreplugins/filters/src/main/resources/default_filters.props b/coreplugins/filters/src/main/resources/default_filters.props
new file mode 100644
index 0000000..d9986cc
--- /dev/null
+++ b/coreplugins/filters/src/main/resources/default_filters.props
@@ -0,0 +1,14 @@
+FilterVersion=0.2
+<Composite>
+name=Default
+<AdvancedSetting>
+scope.global=false
+scope.session=true
+selection.node=false
+selection.edge=false
+edge.source=true
+edge.target=true
+Relation=AND
+</AdvancedSetting>
+Negation=false
+</Composite>
diff --git a/coreplugins/filters/src/main/resources/stock_filter-data-by-criteria-16.png b/coreplugins/filters/src/main/resources/stock_filter-data-by-criteria-16.png
new file mode 100644
index 0000000..ba4d92e
Binary files /dev/null and b/coreplugins/filters/src/main/resources/stock_filter-data-by-criteria-16.png differ
diff --git a/coreplugins/filters/src/main/resources/stock_filter-data-by-criteria.png b/coreplugins/filters/src/main/resources/stock_filter-data-by-criteria.png
new file mode 100644
index 0000000..bcf0fbb
Binary files /dev/null and b/coreplugins/filters/src/main/resources/stock_filter-data-by-criteria.png differ
diff --git a/coreplugins/filters/src/test/java/cytoscape/filters/CompositeFilterTest.java b/coreplugins/filters/src/test/java/cytoscape/filters/CompositeFilterTest.java
new file mode 100644
index 0000000..a352578
--- /dev/null
+++ b/coreplugins/filters/src/test/java/cytoscape/filters/CompositeFilterTest.java
@@ -0,0 +1,238 @@
+package cytoscape.filters;
+
+import cytoscape.filters.Relation;
+import cytoscape.filters.StringFilter;
+import cytoscape.filters.NumericFilter;
+import cytoscape.filters.CompositeFilter;
+
+import java.io.File;
+import java.util.BitSet;
+
+import csplugins.quickfind.util.QuickFind;
+import csplugins.quickfind.util.QuickFindFactory;
+import csplugins.quickfind.util.TaskMonitorBase;
+import csplugins.widgets.autocomplete.index.NumberIndex;
+import csplugins.widgets.autocomplete.index.TextIndex;
+
+public class CompositeFilterTest extends FilterTest {
+
+ private StringFilter locationFilter, pmidFilter;
+ private NumericFilter rankFilter, scoreFilter;
+
+ private CompositeFilter compositeFilter1, compositeFilter2;
+ public void setUp() {
+ // Create a sample network and add sample node/edge attributes
+ initNetwork();
+
+ // Index this network by all the related Node attributes
+ TaskMonitorBase monitor = new TaskMonitorBase();
+ QuickFind quickFind = QuickFindFactory.getGlobalQuickFindInstance();
+ quickFind.addNetwork(cyNetwork, monitor);
+
+ // Try indexing all attributes
+ //quickFind.reindexNetwork(cyNetwork, QuickFind.INDEX_NODES, LOCATION, new TaskMonitorBase());
+ //TextIndex index_by_location = (TextIndex) quickFind.getIndex(cyNetwork);
+
+ //quickFind.reindexNetwork(cyNetwork, QuickFind.INDEX_NODES, RANK, new TaskMonitorBase());
+ //NumberIndex integerIndex_rank = (NumberIndex) quickFind.getIndex(cyNetwork);
+
+ //quickFind.reindexNetwork(cyNetwork, QuickFind.INDEX_NODES, SCORE, new TaskMonitorBase());
+ //NumberIndex doubleIndex_score = (NumberIndex) quickFind.getIndex(cyNetwork);
+
+ //quickFind.reindexNetwork(cyNetwork, QuickFind.INDEX_EDGES, PMID, new TaskMonitorBase());
+ //TextIndex textIndex_pmid = (TextIndex) quickFind.getIndex(cyNetwork);
+
+ // Create a list of atomic filters
+ locationFilter = new StringFilter();
+ locationFilter.setName("locationFilter");
+ locationFilter.setControllingAttribute(LOCATION);
+ locationFilter.setSearchStr("cy*");
+ locationFilter.setIndexType(QuickFind.INDEX_NODES);
+
+ locationFilter.setNetwork(cyNetwork);
+
+ rankFilter = new NumericFilter<Integer>();
+ rankFilter.setName("rankFilter");
+ rankFilter.setControllingAttribute(RANK);
+ rankFilter.setLowBound(2);
+ rankFilter.setHighBound(3);
+ rankFilter.setIndexType(QuickFind.INDEX_NODES);
+ rankFilter.setNetwork(cyNetwork);
+
+ scoreFilter = new NumericFilter<Double>();
+ scoreFilter.setName("scoreFilter");
+ scoreFilter.setControllingAttribute(SCORE);
+ scoreFilter.setLowBound(1.0);
+ scoreFilter.setHighBound(5.0);
+ scoreFilter.setIndexType(QuickFind.INDEX_NODES);
+ scoreFilter.setNetwork(cyNetwork);
+
+ pmidFilter = new StringFilter();
+ pmidFilter.setName("edgeFilter");
+ pmidFilter.setControllingAttribute(PMID);
+ pmidFilter.setSearchStr("123");
+ pmidFilter.setIndexType(QuickFind.INDEX_EDGES);
+ pmidFilter.setNetwork(cyNetwork);
+
+ // Create a composite filter 1
+ compositeFilter1 = new CompositeFilter("firstCompositeFilter");
+ compositeFilter1.addChild(locationFilter);
+ compositeFilter1.addChild(rankFilter);
+ compositeFilter1.setRelation(Relation.AND);
+
+ // Create a composite filter 2
+ compositeFilter2 = new CompositeFilter("secondCompositeFilter");
+ compositeFilter2.addChild(locationFilter);
+ compositeFilter2.addChild(pmidFilter);
+ compositeFilter2.setRelation(Relation.AND);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+
+ public void testAND1() {
+ CompositeFilter testCmpFilter = new CompositeFilter("testCmpFilter1");
+ testCmpFilter.addChild(locationFilter);
+ testCmpFilter.addChild(rankFilter);
+ testCmpFilter.setRelation(Relation.AND);
+ testCmpFilter.setNetwork(cyNetwork);
+ testCmpFilter.apply();
+
+ BitSet expectedNodeBitSet = new BitSet(4);
+ expectedNodeBitSet.set(2, true);
+
+ assertEquals(expectedNodeBitSet.toString(), testCmpFilter.getNodeBits().toString());
+ }
+
+ public void testAND2() {
+ // (node filter) AND (edge filter) ==> return empty bitSet -- false for all bits
+ CompositeFilter testCmpFilter = new CompositeFilter("testCmpFilter2");
+ testCmpFilter.addChild(locationFilter); // node filter
+ testCmpFilter.addChild(pmidFilter); // edge filter
+ testCmpFilter.setRelation(Relation.AND);
+ testCmpFilter.setNetwork(cyNetwork);
+ testCmpFilter.apply();
+
+ BitSet expectedBitSet = new BitSet(4);
+
+ assertEquals(expectedBitSet.toString(), testCmpFilter.getNodeBits().toString());
+ assertEquals(expectedBitSet.toString(), testCmpFilter.getEdgeBits().toString());
+ }
+
+ public void testOR1() {
+ CompositeFilter testCmpFilter = new CompositeFilter("testCmpFilter3");
+ testCmpFilter.addChild(locationFilter);
+ testCmpFilter.addChild(rankFilter);
+ testCmpFilter.setRelation(Relation.OR);
+ testCmpFilter.setNetwork(cyNetwork);
+
+ testCmpFilter.apply();
+ //System.out.println("testCmpFilter.toString() ="+ testCmpFilter.toString());
+
+ BitSet expectedNodeBitSet = new BitSet(4);
+ expectedNodeBitSet.set(0, true);
+ expectedNodeBitSet.set(2, true);
+ expectedNodeBitSet.set(3, true);
+
+ assertEquals(expectedNodeBitSet.toString(), testCmpFilter.getNodeBits().toString());
+ }
+
+ public void testChildDeletion() {
+ // Test child deletion
+ CompositeFilter testCmpFilter = new CompositeFilter("testCmpFilter4");
+ testCmpFilter.addChild(locationFilter);
+ testCmpFilter.addChild(rankFilter);
+ testCmpFilter.setRelation(Relation.AND);
+ testCmpFilter.setNetwork(cyNetwork);
+
+ testCmpFilter.apply();
+
+ // Before deletion
+ BitSet expectedBitSet4 = new BitSet();
+ expectedBitSet4.set(2, true);
+
+ assertEquals(expectedBitSet4.toString(), testCmpFilter.getNodeBits().toString());
+
+ testCmpFilter.removeChild(locationFilter);
+ testCmpFilter.apply();
+
+ // after deletion
+ expectedBitSet4.set(0, true);
+ expectedBitSet4.set(1, false);
+ expectedBitSet4.set(2, true);
+ expectedBitSet4.set(3, false);
+
+ assertEquals(expectedBitSet4.toString(), testCmpFilter.getNodeBits().toString());
+ }
+
+ public void testChildAddition() {
+ // Test child addition
+ CompositeFilter testCmpFilter = new CompositeFilter("testCmpFilter5");
+ testCmpFilter.addChild(locationFilter);
+ testCmpFilter.setRelation(Relation.AND);
+ testCmpFilter.setNetwork(cyNetwork);
+
+ testCmpFilter.apply();
+
+ BitSet expectedNodeBitSet = new BitSet(4);
+ expectedNodeBitSet.set(0, false);
+ expectedNodeBitSet.set(1, false);
+ expectedNodeBitSet.set(2, true);
+ expectedNodeBitSet.set(3, true);
+
+ assertEquals(expectedNodeBitSet.toString(), testCmpFilter.getNodeBits().toString());
+
+ // Add new child
+ testCmpFilter.addChild(rankFilter);
+
+ testCmpFilter.apply();
+
+ expectedNodeBitSet.set(0, false);
+ expectedNodeBitSet.set(1, false);
+ expectedNodeBitSet.set(2, true);
+ expectedNodeBitSet.set(3, false);
+
+ assertEquals(expectedNodeBitSet.toString(), testCmpFilter.getNodeBits().toString());
+ }
+
+ // String representation of a filter
+ public void test_toString() {
+ String compositeFilter1_expectStr = "<Composite>" +
+ "\nname=firstCompositeFilter" +
+ "\n<AdvancedSetting>" +
+ "\nscope.global=false" +
+ "\nscope.session=true" +
+ "\nselection.node=false" +
+ "\nselection.edge=false" +
+ "\nedge.source=true" +
+ "\nedge.target=true" +
+ "\nRelation=AND" +
+ "\n</AdvancedSetting>" +
+ "\nNegation=false" +
+ "\nStringFilter=location:false:cy*:0" +
+ "\nNumericFilter=rank:false:2:3:0" +
+ "\n</Composite>";
+
+ assertEquals(compositeFilter1.toString(), compositeFilter1_expectStr);
+
+ String compositeFilter2_expectStr = "<Composite>" +
+ "\nname=secondCompositeFilter" +
+ "\n<AdvancedSetting>" +
+ "\nscope.global=false" +
+ "\nscope.session=true" +
+ "\nselection.node=false" +
+ "\nselection.edge=false" +
+ "\nedge.source=true" +
+ "\nedge.target=true" +
+ "\nRelation=AND" +
+ "\n</AdvancedSetting>" +
+ "\nNegation=false" +
+ "\nStringFilter=location:false:cy*:0" +
+ "\nStringFilter=pmid:false:123:1" +
+ "\n</Composite>";
+ assertEquals(compositeFilter2.toString(), compositeFilter2_expectStr);
+ }
+}
diff --git a/coreplugins/filters/src/test/java/cytoscape/filters/EdgeInteractionFilterTest.java b/coreplugins/filters/src/test/java/cytoscape/filters/EdgeInteractionFilterTest.java
new file mode 100644
index 0000000..6d13bc9
--- /dev/null
+++ b/coreplugins/filters/src/test/java/cytoscape/filters/EdgeInteractionFilterTest.java
@@ -0,0 +1,159 @@
+package cytoscape.filters;
+
+import cytoscape.filters.Relation;
+import cytoscape.filters.StringFilter;
+import cytoscape.filters.NumericFilter;
+import cytoscape.filters.CompositeFilter;
+
+import java.io.File;
+import java.util.BitSet;
+
+import csplugins.quickfind.util.QuickFind;
+import csplugins.quickfind.util.QuickFindFactory;
+import csplugins.quickfind.util.TaskMonitorBase;
+import csplugins.widgets.autocomplete.index.NumberIndex;
+import csplugins.widgets.autocomplete.index.TextIndex;
+
+public class EdgeInteractionFilterTest extends FilterTest {
+
+ private StringFilter locationFilter;
+
+ public void setUp() {
+ // Create a sample network and add sample node/edge attributes
+ initNetwork();
+
+ // node filter
+ locationFilter = new StringFilter();
+ locationFilter.setName("locationFilter");
+ locationFilter.setControllingAttribute(LOCATION);
+ locationFilter.setSearchStr("cy*");
+ locationFilter.setIndexType(QuickFind.INDEX_NODES);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testNodeSource() {
+ // Test selection source nodes only
+ CompositeFilter testCmpFilter = new CompositeFilter("testCmpFilter");
+ testCmpFilter.addChild(locationFilter);
+
+ EdgeInteractionFilter edgeInteractionFilter = new EdgeInteractionFilter();
+ edgeInteractionFilter.setPassFilter(testCmpFilter);
+ edgeInteractionFilter.setName("myEdgeInteractionFilter");
+ edgeInteractionFilter.setNetwork(cyNetwork);
+ edgeInteractionFilter.setSourceChecked(true);
+ edgeInteractionFilter.setTargetChecked(false);
+
+ edgeInteractionFilter.apply();
+
+ BitSet expectedEdgeBitSet = new BitSet(3);
+ expectedEdgeBitSet.set(0, true);
+ expectedEdgeBitSet.set(1, true);
+ expectedEdgeBitSet.set(2, true);
+
+ assertEquals(expectedEdgeBitSet.toString(), edgeInteractionFilter.getEdgeBits().toString());
+ }
+
+ public void testNodeTarget() {
+ // Test selection source nodes only
+ CompositeFilter testCmpFilter = new CompositeFilter("testCmpFilter");
+ testCmpFilter.addChild(locationFilter);
+
+ EdgeInteractionFilter edgeInteractionFilter = new EdgeInteractionFilter();
+ edgeInteractionFilter.setPassFilter(testCmpFilter);
+ edgeInteractionFilter.setName("myEdgeInteractionFilter");
+ edgeInteractionFilter.setNetwork(cyNetwork);
+ edgeInteractionFilter.setSourceChecked(false);
+ edgeInteractionFilter.setTargetChecked(true);
+
+ edgeInteractionFilter.apply();
+
+ BitSet expectedEdgeBitSet = new BitSet(3);
+ expectedEdgeBitSet.set(2, true);
+
+ assertEquals(expectedEdgeBitSet.toString(), edgeInteractionFilter.getEdgeBits().toString());
+ }
+
+ public void testNodeSourceTarget() {
+ // Test selection source nodes only
+ CompositeFilter testCmpFilter = new CompositeFilter("testCmpFilter");
+ testCmpFilter.addChild(locationFilter);
+
+ EdgeInteractionFilter edgeInteractionFilter = new EdgeInteractionFilter();
+ edgeInteractionFilter.setPassFilter(testCmpFilter);
+ edgeInteractionFilter.setName("myEdgeInteractionFilter");
+ edgeInteractionFilter.setNetwork(cyNetwork);
+ edgeInteractionFilter.setSourceChecked(true);
+ edgeInteractionFilter.setTargetChecked(true);
+
+ edgeInteractionFilter.apply();
+
+ BitSet expectedEdgeBitSet = new BitSet(3);
+ expectedEdgeBitSet.set(0, true);
+ expectedEdgeBitSet.set(1, true);
+ expectedEdgeBitSet.set(2, true);
+
+ assertEquals(expectedEdgeBitSet.toString(), edgeInteractionFilter.getEdgeBits().toString());
+ }
+
+
+
+ public void testNegation() {
+ CompositeFilter testCmpFilter = new CompositeFilter("testCmpFilter");
+ testCmpFilter.addChild(locationFilter);
+
+ EdgeInteractionFilter edgeInteractionFilter = new EdgeInteractionFilter();
+ edgeInteractionFilter.setPassFilter(testCmpFilter);
+ edgeInteractionFilter.setName("myEdgeInteractionFilter");
+ edgeInteractionFilter.setNetwork(cyNetwork);
+ edgeInteractionFilter.setSourceChecked(false);
+ edgeInteractionFilter.setTargetChecked(true);
+ edgeInteractionFilter.setNegation(true);
+
+ edgeInteractionFilter.apply();
+
+ BitSet expectedEdgeBitSet = new BitSet(3);
+ expectedEdgeBitSet.set(0, true);
+ expectedEdgeBitSet.set(1, true);
+
+ assertEquals(expectedEdgeBitSet.toString(), edgeInteractionFilter.getEdgeBits().toString());
+ }
+
+
+
+ // String representation of a filter
+ public void test_toString() {
+ CompositeFilter testCmpFilter = new CompositeFilter("testCmpFilter");
+ testCmpFilter.addChild(locationFilter);
+
+ EdgeInteractionFilter edgeInteractionFilter = new EdgeInteractionFilter();
+ edgeInteractionFilter.setPassFilter(testCmpFilter);
+ edgeInteractionFilter.setName("myEdgeInteractionFilter");
+ edgeInteractionFilter.setNetwork(cyNetwork);
+ edgeInteractionFilter.setSourceChecked(false);
+ edgeInteractionFilter.setTargetChecked(true);
+
+ edgeInteractionFilter.apply();
+
+ String edgeInteractionFilter_expectStr = "<InteractionFilter>" +
+ "\nname=myEdgeInteractionFilter" +
+ "\n<AdvancedSetting>" +
+ "\nscope.global=false" +
+ "\nscope.session=true" +
+ "\nselection.node=false" +
+ "\nselection.edge=true" +
+ "\nedge.source=true" +
+ "\nedge.target=true" +
+ "\nRelation=AND" +
+ "\n</AdvancedSetting>" +
+ "\nNegation=false" +
+ "\nnodeType=1" +
+ "\npassFilter=testCmpFilter" +
+ "\n</InteractionFilter>";
+
+ assertEquals(edgeInteractionFilter.toString(), edgeInteractionFilter_expectStr);
+ }
+}
diff --git a/coreplugins/filters/src/test/java/cytoscape/filters/FilterTest.java b/coreplugins/filters/src/test/java/cytoscape/filters/FilterTest.java
new file mode 100644
index 0000000..2e2f66c
--- /dev/null
+++ b/coreplugins/filters/src/test/java/cytoscape/filters/FilterTest.java
@@ -0,0 +1,73 @@
+package cytoscape.filters;
+
+import cytoscape.CyEdge;
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+import junit.framework.TestCase;
+import cytoscape.data.CyAttributes;
+import cytoscape.data.Semantics;
+
+public class FilterTest extends TestCase {
+
+ protected void initNetwork() {
+ cyNetwork = Cytoscape.createNetwork("network1");
+ CyNode node0 = Cytoscape.getCyNode("rain", true);
+ CyNode node1 = Cytoscape.getCyNode("rainbow", true);
+ CyNode node2 = Cytoscape.getCyNode("rabbit", true);
+ CyNode node3 = Cytoscape.getCyNode("yellow", true);
+
+ cyNetwork.addNode(node0);
+ cyNetwork.addNode(node1);
+ cyNetwork.addNode(node2);
+ cyNetwork.addNode(node3);
+
+ CyEdge edge0 = Cytoscape.getCyEdge(node0, node1, Semantics.INTERACTION, "pp", true);
+ CyEdge edge1 = Cytoscape.getCyEdge(node0, node2, Semantics.INTERACTION, "pp", true);
+ CyEdge edge2 = Cytoscape.getCyEdge(node0, node3, Semantics.INTERACTION, "pp", true);
+ cyNetwork.addEdge(edge0);
+ cyNetwork.addEdge(edge1);
+ cyNetwork.addEdge(edge2);
+
+ // Create Sample String Attributes
+ CyAttributes nodeAttributes = Cytoscape.getNodeAttributes();
+ nodeAttributes.setAttribute(node0.getIdentifier(), LOCATION, CYTOPLASM);
+ nodeAttributes.setAttribute(node1.getIdentifier(), LOCATION, CYTOPLASM);
+ nodeAttributes.setAttribute(node2.getIdentifier(), LOCATION, NUCLEUS);
+ nodeAttributes.setAttribute(node3.getIdentifier(), LOCATION, NUCLEUS);
+
+ // Create Sample Integer Attributes
+ nodeAttributes.setAttribute(node0.getIdentifier(), RANK, 4);
+ nodeAttributes.setAttribute(node1.getIdentifier(), RANK, 3);
+ nodeAttributes.setAttribute(node2.getIdentifier(), RANK, 1);
+ nodeAttributes.setAttribute(node3.getIdentifier(), RANK, 2);
+
+ // Create Sample Double Attributes
+ nodeAttributes.setAttribute(node0.getIdentifier(), SCORE, 45.2);
+ nodeAttributes.setAttribute(node1.getIdentifier(), SCORE, 3.211);
+ nodeAttributes.setAttribute(node2.getIdentifier(), SCORE, 22.2);
+ nodeAttributes.setAttribute(node3.getIdentifier(), SCORE, 2.1);
+
+ // Create Sample String Attributes
+ CyAttributes edgeAttributes = Cytoscape.getEdgeAttributes();
+ edgeAttributes.setAttribute(edge0.getIdentifier(), PMID, "12345");
+ edgeAttributes.setAttribute(edge1.getIdentifier(), PMID, "12345");
+ edgeAttributes.setAttribute(edge2.getIdentifier(), PMID, "12666");
+
+ Cytoscape.setCurrentNetwork(cyNetwork.getIdentifier());
+ }
+
+ protected static final String LOCATION = "location";
+ protected static final String NUCLEUS = "nucleus";
+ protected static final String CYTOPLASM = "cytoplasm";
+ protected static final String RANK = "rank";
+ protected static final String SCORE = "score";
+ protected static final String PMID = "pmid";
+ protected CyNetwork cyNetwork;
+
+ public void testDumb() {
+ //No test for FilterTest. It holds test data only!
+ // Without this dumb test-case, a warning message will be printed out
+ }
+
+}
diff --git a/coreplugins/filters/src/test/java/cytoscape/filters/NodeInteractionFilterTest.java b/coreplugins/filters/src/test/java/cytoscape/filters/NodeInteractionFilterTest.java
new file mode 100644
index 0000000..b9e61c2
--- /dev/null
+++ b/coreplugins/filters/src/test/java/cytoscape/filters/NodeInteractionFilterTest.java
@@ -0,0 +1,156 @@
+package cytoscape.filters;
+
+import cytoscape.filters.Relation;
+import cytoscape.filters.StringFilter;
+import cytoscape.filters.NumericFilter;
+import cytoscape.filters.CompositeFilter;
+
+import java.io.File;
+import java.util.BitSet;
+
+import csplugins.quickfind.util.QuickFind;
+import csplugins.quickfind.util.QuickFindFactory;
+import csplugins.quickfind.util.TaskMonitorBase;
+import csplugins.widgets.autocomplete.index.NumberIndex;
+import csplugins.widgets.autocomplete.index.TextIndex;
+
+public class NodeInteractionFilterTest extends FilterTest {
+
+ private StringFilter pmidFilter;
+
+ public void setUp() {
+ // Create a sample network and add sample node/edge attributes
+ initNetwork();
+
+ // edge filter
+ pmidFilter = new StringFilter();
+ pmidFilter.setName("edgeFilter");
+ pmidFilter.setControllingAttribute(PMID);
+ pmidFilter.setSearchStr("123*");
+ pmidFilter.setIndexType(QuickFind.INDEX_EDGES);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testNodeSource() {
+ // Test selection source nodes only
+ CompositeFilter testCmpFilter = new CompositeFilter("testCmpFilter");
+ testCmpFilter.addChild(pmidFilter);
+
+ NodeInteractionFilter nodeInteractionFilter = new NodeInteractionFilter();
+ nodeInteractionFilter.setPassFilter(testCmpFilter);
+ nodeInteractionFilter.setName("myNodeInteractionFilter");
+ nodeInteractionFilter.setNetwork(cyNetwork);
+ nodeInteractionFilter.setSourceChecked(true);
+ nodeInteractionFilter.setTargetChecked(false);
+
+ nodeInteractionFilter.apply();
+
+ BitSet expectedNodeBitSet = new BitSet(4);
+ expectedNodeBitSet.set(3, true);
+
+ assertEquals(expectedNodeBitSet.toString(), nodeInteractionFilter.getNodeBits().toString());
+ }
+
+ public void testNodeTarget() {
+ // Test selection Target nodes only
+ CompositeFilter testCmpFilter = new CompositeFilter("testCmpFilter");
+ testCmpFilter.addChild(pmidFilter);
+
+ NodeInteractionFilter nodeInteractionFilter = new NodeInteractionFilter();
+ nodeInteractionFilter.setPassFilter(testCmpFilter);
+ nodeInteractionFilter.setName("myNodeInteractionFilter");
+ nodeInteractionFilter.setNetwork(cyNetwork);
+ nodeInteractionFilter.setSourceChecked(false);
+ nodeInteractionFilter.setTargetChecked(true);
+
+ nodeInteractionFilter.apply();
+
+ BitSet expectedNodeBitSet = new BitSet(4);
+ expectedNodeBitSet.set(1, true);
+ expectedNodeBitSet.set(2, true);
+
+ assertEquals(expectedNodeBitSet.toString(), nodeInteractionFilter.getNodeBits().toString());
+ }
+
+
+ public void testNegation() {
+ CompositeFilter testCmpFilter = new CompositeFilter("testCmpFilter");
+ testCmpFilter.addChild(pmidFilter);
+
+ NodeInteractionFilter nodeInteractionFilter = new NodeInteractionFilter();
+ nodeInteractionFilter.setPassFilter(testCmpFilter);
+ nodeInteractionFilter.setName("myNodeInteractionFilter");
+ nodeInteractionFilter.setNetwork(cyNetwork);
+ nodeInteractionFilter.setSourceChecked(false);
+ nodeInteractionFilter.setTargetChecked(true);
+ nodeInteractionFilter.setNegation(true);
+
+ nodeInteractionFilter.apply();
+
+ BitSet expectedNodeBitSet = new BitSet(4);
+ expectedNodeBitSet.set(0, true);
+ expectedNodeBitSet.set(3, true);
+
+ assertEquals(expectedNodeBitSet.toString(), nodeInteractionFilter.getNodeBits().toString());
+ }
+
+
+ public void testNodeSourceTarget() {
+ // Test selection Target nodes only
+ CompositeFilter testCmpFilter = new CompositeFilter("testCmpFilter");
+ testCmpFilter.addChild(pmidFilter);
+
+ NodeInteractionFilter nodeInteractionFilter = new NodeInteractionFilter();
+ nodeInteractionFilter.setPassFilter(testCmpFilter);
+ nodeInteractionFilter.setName("myNodeInteractionFilter");
+ nodeInteractionFilter.setNetwork(cyNetwork);
+ nodeInteractionFilter.setSourceChecked(true);
+ nodeInteractionFilter.setTargetChecked(true);
+
+ nodeInteractionFilter.apply();
+
+ BitSet expectedNodeBitSet = new BitSet(4);
+ expectedNodeBitSet.set(1, true);
+ expectedNodeBitSet.set(2, true);
+ expectedNodeBitSet.set(3, true);
+
+ assertEquals(expectedNodeBitSet.toString(), nodeInteractionFilter.getNodeBits().toString());
+ }
+
+ // String representation of a filter
+ public void test_toString() {
+ CompositeFilter testCmpFilter = new CompositeFilter("testCmpFilter");
+ testCmpFilter.addChild(pmidFilter);
+
+ NodeInteractionFilter nodeInteractionFilter = new NodeInteractionFilter();
+ nodeInteractionFilter.setPassFilter(testCmpFilter);
+ nodeInteractionFilter.setName("myNodeInteractionFilter");
+ nodeInteractionFilter.setNetwork(cyNetwork);
+ nodeInteractionFilter.setSourceChecked(false);
+ nodeInteractionFilter.setTargetChecked(true);
+
+ nodeInteractionFilter.apply();
+
+ String nodeInteractionFilter_expectStr = "<InteractionFilter>" +
+ "\nname=myNodeInteractionFilter" +
+ "\n<AdvancedSetting>" +
+ "\nscope.global=false" +
+ "\nscope.session=true" +
+ "\nselection.node=true" +
+ "\nselection.edge=false" +
+ "\nedge.source=true" +
+ "\nedge.target=true" +
+ "\nRelation=AND" +
+ "\n</AdvancedSetting>" +
+ "\nNegation=false" +
+ "\nnodeType=1" +
+ "\npassFilter=testCmpFilter" +
+ "\n</InteractionFilter>";
+
+ assertEquals(nodeInteractionFilter.toString(), nodeInteractionFilter_expectStr);
+ }
+}
diff --git a/coreplugins/filters/src/test/java/cytoscape/filters/NumericFilterTest.java b/coreplugins/filters/src/test/java/cytoscape/filters/NumericFilterTest.java
new file mode 100644
index 0000000..35e4573
--- /dev/null
+++ b/coreplugins/filters/src/test/java/cytoscape/filters/NumericFilterTest.java
@@ -0,0 +1,115 @@
+package cytoscape.filters;
+
+
+import java.util.BitSet;
+import csplugins.quickfind.util.QuickFind;
+import csplugins.quickfind.util.QuickFindFactory;
+import csplugins.quickfind.util.TaskMonitorBase;
+import csplugins.widgets.autocomplete.index.NumberIndex;
+//import java.util.List;
+
+public class NumericFilterTest extends FilterTest {
+
+ private NumericFilter<Integer> theIntegerFilter;
+ private NumericFilter<Double> theDoubleFilter;
+ private BitSet expectedBitSet1, expectedBitSet1_not, expectedBitSet2, expectedBitSet2_not;
+
+ public void setUp() {
+ // Crerate a sample network and add sample node/edge attributes
+ initNetwork();
+
+ //1. Index network by rank (Integer type)
+ final QuickFind quickFind = QuickFindFactory.getGlobalQuickFindInstance();
+ quickFind.addNetwork(cyNetwork, new TaskMonitorBase());
+
+ //NumberIndex integerIndex = (NumberIndex) quickFind.getIndex(cyNetwork);
+
+ quickFind.reindexNetwork(cyNetwork, QuickFind.INDEX_NODES, RANK, new TaskMonitorBase());
+ NumberIndex integetIndex = (NumberIndex) quickFind.getIndex(cyNetwork);
+
+ quickFind.reindexNetwork(cyNetwork, QuickFind.INDEX_NODES, SCORE, new TaskMonitorBase());
+ NumberIndex doubleIndex = (NumberIndex) quickFind.getIndex(cyNetwork);
+
+ //Create two numericFilter objects -- Integer or Double
+ theIntegerFilter = new NumericFilter<Integer>();
+ theIntegerFilter.setName("integerFilter");
+ theIntegerFilter.setControllingAttribute(RANK);
+ theIntegerFilter.setLowBound(2);
+ theIntegerFilter.setHighBound(3);
+ theIntegerFilter.setIndex(integetIndex);
+ theIntegerFilter.setNetwork(cyNetwork);
+
+ theDoubleFilter = new NumericFilter<Double>();
+ theDoubleFilter.setName("doubleFilter");
+ theDoubleFilter.setControllingAttribute(SCORE);
+ theDoubleFilter.setLowBound(3.0);
+ theDoubleFilter.setHighBound(25.0);
+ theDoubleFilter.setIndex(doubleIndex);
+ theDoubleFilter.setNetwork(cyNetwork);
+
+ //Expected values
+ expectedBitSet1 = new BitSet(4);
+ expectedBitSet1.set(0, true);
+ expectedBitSet1.set(2, true);
+
+ expectedBitSet2 = new BitSet(4);
+ expectedBitSet2.set(1, true);
+ expectedBitSet2.set(2, true);
+
+ expectedBitSet1_not = (BitSet) expectedBitSet1.clone();
+ expectedBitSet1_not.flip(0,4);
+
+ expectedBitSet2_not = (BitSet) expectedBitSet2.clone();
+ expectedBitSet2_not.flip(0,4);
+
+ }
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testIntegerFilter_getNodeBits() {
+ // test NumericFilter<Integer>
+ theIntegerFilter.setNegation(false);
+ theIntegerFilter.apply();
+
+ assertEquals(expectedBitSet1.toString(), theIntegerFilter.getNodeBits().toString());
+ }
+
+ public void testIntegerFilter_getNodeBits_not() {
+ theIntegerFilter.setNegation(true);
+ theIntegerFilter.apply();
+
+ assertEquals(expectedBitSet1_not.toString(), theIntegerFilter.getNodeBits().toString());
+ }
+
+ public void testDoubleFilter_getNodeBits() {
+ //test NumericFilter<Double>
+ theDoubleFilter.setNegation(false);
+ theDoubleFilter.apply();
+
+ assertEquals(expectedBitSet2.toString(), theDoubleFilter.getNodeBits().toString());
+ }
+
+ public void testDoubleFilter_getNodeBits_not() {
+ theDoubleFilter.setNegation(true);
+ theDoubleFilter.apply();
+
+ assertEquals(expectedBitSet2_not.toString(), theDoubleFilter.getNodeBits().toString());
+ }
+
+ // String representation of a filter
+ public void test_toString() {
+ String theFirstFilter_expectStr = "NumericFilter=rank:false:2:3:"+ QuickFind.INDEX_NODES;
+ theIntegerFilter.setNegation(false);
+ theDoubleFilter.apply();
+
+ assertEquals(theFirstFilter_expectStr, theIntegerFilter.toString());
+
+ String theSecondFilter_expectStr = "NumericFilter=score:false:3.0:25.0:"+QuickFind.INDEX_NODES;
+ theDoubleFilter.setNegation(false);
+ theDoubleFilter.apply();
+
+ assertEquals(theSecondFilter_expectStr, theDoubleFilter.toString());
+ }
+}
diff --git a/coreplugins/filters/src/test/java/cytoscape/filters/StringFilterTest.java b/coreplugins/filters/src/test/java/cytoscape/filters/StringFilterTest.java
new file mode 100644
index 0000000..d9e996b
--- /dev/null
+++ b/coreplugins/filters/src/test/java/cytoscape/filters/StringFilterTest.java
@@ -0,0 +1,108 @@
+package cytoscape.filters;
+
+import cytoscape.filters.StringFilter;
+import java.util.BitSet;
+
+import csplugins.quickfind.util.QuickFind;
+import csplugins.quickfind.util.QuickFindFactory;
+import csplugins.quickfind.util.TaskMonitorBase;
+import csplugins.widgets.autocomplete.index.TextIndex;
+
+public class StringFilterTest extends FilterTest {
+
+ private BitSet expectedBitSet1, expectedBitSet1_not;
+ private BitSet expectedBitSet2, expectedBitSet2_not;
+ private TextIndex index_by_UniqueIdentification, index_by_location;
+ private StringFilter theFirstFilter, theSecondFilter;
+
+ public void setUp() {
+ // Crerate a sample network and add sample node/edge attributes
+ initNetwork();
+
+ // Set expected values
+ expectedBitSet1 = new BitSet(4);
+ expectedBitSet1.set(2, true);
+ expectedBitSet1.set(3, true);
+
+ expectedBitSet2 = new BitSet(4);
+ expectedBitSet2.set(0, true);
+ expectedBitSet2.set(1, true);
+
+ expectedBitSet1_not = (BitSet) expectedBitSet1.clone();
+ expectedBitSet1_not.flip(0,4);
+
+ expectedBitSet2_not = (BitSet) expectedBitSet2.clone();
+ expectedBitSet2_not.flip(0,4);
+
+ //Create two indices (1) by default "Unique Identifier" and (2) "location"
+ final QuickFind quickFind = QuickFindFactory.getGlobalQuickFindInstance();
+ quickFind.addNetwork(cyNetwork, new TaskMonitorBase());
+ index_by_UniqueIdentification = (TextIndex) quickFind.getIndex(cyNetwork);
+
+ quickFind.reindexNetwork(cyNetwork, QuickFind.INDEX_NODES, LOCATION, new TaskMonitorBase());
+ index_by_location = (TextIndex) quickFind.getIndex(cyNetwork);
+
+ // Created two StringFilter objects
+ theFirstFilter = new StringFilter();
+ theFirstFilter.setName("firstStringFilter");
+ //theFirstFilter.setControllingAttribute(QuickFind.UNIQUE_IDENTIFIER);
+ theFirstFilter.setControllingAttribute("canonicalName");
+
+ theFirstFilter.setSearchStr("rai*");
+ theFirstFilter.setIndex(index_by_UniqueIdentification);
+ theFirstFilter.setNetwork(cyNetwork);
+
+ theSecondFilter = new StringFilter();
+ theSecondFilter.setName("secondStringFilter");
+ theSecondFilter.setControllingAttribute(LOCATION);
+ theSecondFilter.setSearchStr("nu*");
+ theSecondFilter.setIndex(index_by_location);
+ theSecondFilter.setNetwork(cyNetwork);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+
+ public void testGetBits() { // Indexing Node
+
+ // Test case 1: indexed by "Unique Identifier"
+ theFirstFilter.setNegation(false);
+ theFirstFilter.apply();
+ assertEquals(expectedBitSet1.toString(), theFirstFilter.getNodeBits().toString());
+
+ //Test case 2: indexed by "location"
+ theSecondFilter.setNegation(false);
+ theSecondFilter.apply();
+
+ assertEquals(expectedBitSet2.toString(), theSecondFilter.getNodeBits().toString());
+ }
+
+ public void testGetBits_not() {
+ //Test case 1: indexed by "Unique Identifier"
+ theFirstFilter.setNegation(true);
+ theFirstFilter.apply();
+
+ assertEquals(expectedBitSet1_not.toString(), theFirstFilter.getNodeBits().toString());
+
+ //Test case 2: indexed by "location"
+ theSecondFilter.setNegation(true);
+ theSecondFilter.apply();
+
+ assertEquals(expectedBitSet2_not.toString(), theSecondFilter.getNodeBits().toString());
+ }
+
+ // String representation of a filter
+ public void test_toString() {
+ String theFirstFilter_expectStr = "StringFilter=canonicalName:false:rai*:"+QuickFind.INDEX_NODES;
+
+ assertEquals(theFirstFilter_expectStr, theFirstFilter.toString());
+
+ String theSecondFilter_expectStr = "StringFilter=location:false:nu*:"+QuickFind.INDEX_NODES;
+ assertEquals(theSecondFilter_expectStr, theSecondFilter.toString());
+ }
+
+ // May also need to test Indexing Edge?
+}
diff --git a/coreplugins/filters/src/test/java/cytoscape/filters/TopologyFilterTest.java b/coreplugins/filters/src/test/java/cytoscape/filters/TopologyFilterTest.java
new file mode 100644
index 0000000..dda09d0
--- /dev/null
+++ b/coreplugins/filters/src/test/java/cytoscape/filters/TopologyFilterTest.java
@@ -0,0 +1,115 @@
+package cytoscape.filters;
+
+import cytoscape.filters.Relation;
+import cytoscape.filters.StringFilter;
+import cytoscape.filters.NumericFilter;
+import cytoscape.filters.CompositeFilter;
+import cytoscape.filters.TopologyFilter;
+
+import java.io.File;
+import java.util.BitSet;
+
+import csplugins.quickfind.util.QuickFind;
+import csplugins.quickfind.util.QuickFindFactory;
+import csplugins.quickfind.util.TaskMonitorBase;
+import csplugins.widgets.autocomplete.index.NumberIndex;
+import csplugins.widgets.autocomplete.index.TextIndex;
+
+public class TopologyFilterTest extends FilterTest {
+
+ //private CompositeFilter compositeFilter1, compositeFilter2;
+ public void setUp() {
+ // Create a sample network and add sample node/edge attributes
+ initNetwork();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ public void testPassFilterNone() {
+ TopologyFilter topoFilter = new TopologyFilter("testTopoFilter1");
+ topoFilter.setNetwork(cyNetwork);
+ topoFilter.setMinNeighbors(1);
+ topoFilter.setDistance(1);
+ topoFilter.apply();
+
+ BitSet expectedNodeBitSet = new BitSet(4);
+ expectedNodeBitSet.set(0, true);
+ expectedNodeBitSet.set(1, true);
+ expectedNodeBitSet.set(2, true);
+ expectedNodeBitSet.set(3, true);
+
+ assertEquals(expectedNodeBitSet.toString(), topoFilter.getNodeBits().toString());
+ topoFilter.setMinNeighbors(3);
+ topoFilter.apply();
+
+ expectedNodeBitSet.set(0, false);
+ expectedNodeBitSet.set(1, false);
+ expectedNodeBitSet.set(2, false);
+ expectedNodeBitSet.set(3, true);
+ assertEquals(expectedNodeBitSet.toString(), topoFilter.getNodeBits().toString());
+ }
+
+ public void testPassFilter() {
+ // Define a compositeFilter
+ CompositeFilter compositeFilter1 = new CompositeFilter("firstCompositeFilter");
+ NumericFilter scoreFilter = new NumericFilter();
+ scoreFilter.setControllingAttribute(SCORE);
+ scoreFilter.setLowBound(20.0);
+ scoreFilter.setHighBound(30.0);
+ scoreFilter.setIndexType(QuickFind.INDEX_NODES);
+ compositeFilter1.addChild(scoreFilter);
+
+ TopologyFilter topoFilter = new TopologyFilter("testTopoFilter2");
+ topoFilter.setNetwork(cyNetwork);
+ topoFilter.setPassFilter(compositeFilter1);
+ topoFilter.setMinNeighbors(1);
+ topoFilter.setDistance(1);
+ topoFilter.apply();
+
+ BitSet expectedNodeBitSet = new BitSet(4);
+ expectedNodeBitSet.set(3, true);
+
+ assertEquals(expectedNodeBitSet.toString(), topoFilter.getNodeBits().toString());
+ }
+
+ // String representation of a filter
+ public void test_toString() {
+
+ CompositeFilter compositeFilter1 = new CompositeFilter("firstCompositeFilter");
+ NumericFilter scoreFilter = new NumericFilter();
+ scoreFilter.setControllingAttribute(SCORE);
+ scoreFilter.setLowBound(20.0);
+ scoreFilter.setHighBound(30.0);
+ scoreFilter.setIndexType(QuickFind.INDEX_NODES);
+ compositeFilter1.addChild(scoreFilter);
+
+ TopologyFilter topoFilter = new TopologyFilter("testTopoFilter2");
+ topoFilter.setNetwork(cyNetwork);
+ topoFilter.setPassFilter(compositeFilter1);
+ topoFilter.setMinNeighbors(1);
+ topoFilter.setDistance(1);
+ topoFilter.apply();
+
+ String topoFilter_expectStr = "<TopologyFilter>" +
+ "\nname=testTopoFilter2" +
+ "\n<AdvancedSetting>" +
+ "\nscope.global=false" +
+ "\nscope.session=true" +
+ "\nselection.node=true" +
+ "\nselection.edge=false" +
+ "\nedge.source=true" +
+ "\nedge.target=true" +
+ "\nRelation=AND" +
+ "\n</AdvancedSetting>" +
+ "\nNegation=false" +
+ "\nminNeighbors=1" +
+ "\nwithinDistance=1" +
+ "\npassFilter=firstCompositeFilter" +
+ "\n</TopologyFiler>";
+
+ assertEquals(topoFilter.toString(), topoFilter_expectStr);
+ }
+}
diff --git a/coreplugins/linkout/pom.xml b/coreplugins/linkout/pom.xml
new file mode 100644
index 0000000..1f5c1fe
--- /dev/null
+++ b/coreplugins/linkout/pom.xml
@@ -0,0 +1,56 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>parent</artifactId>
+ <version>2.8.4-SNAPSHOT</version>
+ </parent>
+
+ <artifactId>linkout</artifactId>
+ <packaging>jar</packaging>
+
+ <name>Linkout</name>
+
+ <!-- bootstrap for cytoscape dependencies, namely the parent POM snapshots -->
+ <repositories>
+ <repository>
+ <id>cytoscape_snapshots</id>
+ <snapshots>
+ <enabled>true</enabled>
+ </snapshots>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <name>Cytoscape Snapshots</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/</url>
+ </repository>
+ <repository>
+ <id>cytoscape_releases</id>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ <name>Cytoscape Releases</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/releases/</url>
+ </repository>
+ </repositories>
+
+ <build>
+ <plugins>
+ <plugin>
+ <artifactId>maven-assembly-plugin</artifactId>
+ <configuration>
+ <archive>
+ <manifestEntries>
+ <Cytoscape-Plugin>linkout.LinkOutPlugin</Cytoscape-Plugin>
+ </manifestEntries>
+ </archive>
+ </configuration>
+ </plugin>
+ </plugins>
+ </build>
+
+</project>
+
diff --git a/coreplugins/linkout/src/main/java/linkout/LinkOut.java b/coreplugins/linkout/src/main/java/linkout/LinkOut.java
new file mode 100644
index 0000000..9dc51ae
--- /dev/null
+++ b/coreplugins/linkout/src/main/java/linkout/LinkOut.java
@@ -0,0 +1,523 @@
+/*$Id: LinkOut.java 24812 2011-04-22 16:22:41Z mcreech $*/
+package linkout;
+
+import cytoscape.Cytoscape;
+import cytoscape.CytoscapeInit;
+
+import cytoscape.data.CyAttributes;
+import cytoscape.logger.CyLogger;
+
+import cytoscape.util.OpenBrowser;
+
+import giny.model.Edge;
+import giny.model.Node;
+
+import giny.view.EdgeView;
+import giny.view.NodeView;
+
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.event.ActionEvent;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Enumeration;
+import java.util.HashSet;
+import java.util.Properties;
+import java.util.Set;
+import java.util.List;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+import javax.swing.AbstractAction;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.SwingUtilities;
+
+
+/**
+* Generates links to external web pages specified in the cytoscape.props file.
+* Nodes can be linked to external web pages by specifying web resources in the linkout.properties file
+* The format for a weblink is in the form of a <key> = <value> pair where <key> is the name of the
+* website (e.g. NCBI, E!, PubMed, SGD,etc) and <value> is the URL. The key name must be preceded by the keyword "url." to distinguish
+* this property from other properties.
+* In the URL string the placeholder %ID% will be replaced with the node label that is visible on the node.
+* If no label is visible, the node identifier (far left of attribute browser) will be used.
+* It is the users responsibility
+* to ensure that the URL is correct and the node's name will match the required query value.
+* Examples:
+* url.NCBI=http\://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd\=Search&db\=Protein&term\=%ID%&doptcmdl\=GenPept
+* url.SGD=http\://db.yeastgenome.org/cgi-bin/locus.pl?locus\=%ID%
+* url.E\!Ensamble=http\://www.ensembl.org/Homo_sapiens/textview?species\=all&idx\=All&q\=%ID%
+* url.Pubmed=http\://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd\=Search&db\=PubMed&term\=%ID%
+*
+*/
+public class LinkOut {
+ //keyword that marks properties that should be added to LinkOut
+ private static final String nodeMarker = "nodelinkouturl.";
+ private static final String edgeMarker = "edgelinkouturl.";
+ private static final String linkMarker = "Linkout.externalLinkName";
+ private static String externalLinksAttribute = "Linkout.ExternalLinks";
+ private Properties props;
+ private static final Font TITLE_FONT = new Font("sans-serif", Font.BOLD, 14);
+ private static CyLogger logger = null;
+
+ //null constractor
+ /**
+ * Creates a new LinkOut object.
+ */
+ public LinkOut() {
+ if (LinkOut.logger == null)
+ LinkOut.logger = CyLogger.getLogger(LinkOut.class);
+ }
+
+ /**
+ * Generates URL links with node name and places them in hierarchical JMenu list
+ * @param node the NodeView.
+ * @return JMenuItem
+ */
+ public JMenuItem addLinks(NodeView node) {
+ // System.out.println("linkout.addLinks called with node "
+ // + ((NodeView) node).getLabel().getText());
+ readProperties();
+
+ final JMenu top_menu = new JMenu("LinkOut");
+ final JMenuItem source = new JMenuItem("Database");
+ source.setBackground(Color.white);
+ source.setFont(TITLE_FONT);
+ source.setEnabled(false);
+ top_menu.add(source);
+
+ //iterate through properties list
+ try {
+ CyAttributes na = Cytoscape.getNodeAttributes();
+ final NodeView mynode = (NodeView) node;
+
+ // Get the set of attribute names for this node
+ Node n = mynode.getNode();
+ String nodeId = n.getIdentifier();
+
+ for (Enumeration e = props.propertyNames(); e.hasMoreElements();) {
+ String propKey = (String) e.nextElement();
+ int p = propKey.lastIndexOf(nodeMarker);
+
+ if (p == -1)
+ continue;
+
+ p = p + nodeMarker.length();
+
+ //the URL
+ String url = props.getProperty(propKey);
+
+ if (url == null) {
+ url = "<html><small><i>empty- no links<br> See documentation</i></small></html>"
+ + "http://www.cytoscape.org/";
+ }
+
+ String fUrl = subsAttrs(url, na, nodeId, "ID", "");
+
+ //the link name
+ String[] temp = ((String) propKey.substring(p)).split("\\.");
+ ArrayList keys = new ArrayList(Arrays.asList(temp));
+
+ //Generate the menu path
+ generateLinks(keys, top_menu, fUrl);
+ }
+
+ // Now, see if the user has specified their own URL to add to linkout
+ generateExternalLinks(na, nodeId, top_menu);
+
+ //if no links specified insert a default message
+ if (top_menu.getMenuComponentCount() == 0) {
+ String url = "<html><small><i>empty- no links<br> See documentation</i></small></html>"
+ + "http://www.cytoscape.org/";
+ top_menu.add(new JMenuItem(url));
+ }
+
+ // For debugging
+ // printMenu(top_menu);
+ } catch (NullPointerException e) {
+ String url = "<html><small><i>empty- no links<br> See documentation</i></small></html>"
+ + "http://www.cytoscape.org/";
+ top_menu.add(new JMenuItem(url));
+ logger.error("NullPointerException: " + e.getMessage());
+ }
+
+ return top_menu;
+ }
+
+ /**
+ * Perform variable substitution on a url using attribute values.
+ *
+ * Given a url, look for attribute names within that url specified by %AttributeName%
+ * If our current node or edge (as specified by graphObjId) has an attribute name that
+ * matches the string in the URL, replace the string with the value of the attribute.
+ *
+ * Special cases:
+ * 1. For backwards compatibility, if the attribute name given by idKeyword is found
+ * substitute the value of the attribute id as given by graphObjId.
+ * 2. When looking for attribute names, we can specify that they must have a prefix added
+ * to the beginning. This allows us to specify a "from" or "to" prefix in edge attributes
+ * so that from.AttributeName and to.AttributeName can select different properties.
+ *
+ * @param url the url to perform replacements on.
+ * @param attrs a set of node or edge attributes.
+ * @param graphObjId the id of the node or edge that is selected.
+ * @param idKeyword a special attribute keyword, that if found, should be replaced by graphObjId
+ * @param prefix a prefix to prepend to attribute names.
+ * @return modified url after variable substitution
+ */
+ private String subsAttrs(String url, CyAttributes attrs, String graphObjId, String idKeyword,
+ String prefix) {
+ Set<String> validAttrs = new HashSet<String>();
+
+ for (String attrName : attrs.getAttributeNames()) {
+ if (attrs.hasAttribute(graphObjId, attrName)) {
+ validAttrs.add(prefix + attrName);
+ }
+ }
+
+ // Replace %ATTRIBUTE.NAME% mark with the value of the attribute
+ final String REGEX = "%.*?%";
+ Pattern pat = Pattern.compile(REGEX);
+ Matcher mat = pat.matcher(url);
+
+ while (mat.find()) {
+ String attrName = url.substring(mat.start() + 1, mat.end() - 1);
+ // backwards compatibility, old keywords were %ID%, %ID1%, %ID2%.
+ if (attrName.equals(idKeyword)) {
+ String attrValue = graphObjId;
+ url = url.replace("%" + idKeyword + "%", attrValue);
+ mat = pat.matcher(url);
+ } else if (validAttrs.contains(attrName)) {
+ String prefixlessAttrName = attrName.substring(prefix.length());
+ String attrValue = attrToString(attrs, graphObjId, prefixlessAttrName);
+ url = url.replace("%" + attrName + "%", attrValue);
+ mat = pat.matcher(url);
+ }
+ }
+
+ return url;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param attributes DOCUMENT ME!
+ * @param id DOCUMENT ME!
+ * @param attributeName DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ private String attrToString(CyAttributes attributes, String id, String attributeName) {
+ Object value = null;
+ byte attrType = attributes.getType(attributeName);
+
+ if (attrType == CyAttributes.TYPE_BOOLEAN) {
+ value = attributes.getBooleanAttribute(id, attributeName);
+ } else if (attrType == CyAttributes.TYPE_FLOATING) {
+ value = attributes.getDoubleAttribute(id, attributeName);
+ } else if (attrType == CyAttributes.TYPE_INTEGER) {
+ value = attributes.getIntegerAttribute(id, attributeName);
+ } else if (attrType == CyAttributes.TYPE_STRING) {
+ value = attributes.getStringAttribute(id, attributeName);
+ }
+
+ if (value != null)
+ return value.toString();
+ else
+
+ return "N/A";
+ }
+
+ /**
+ * Generate URL links with edge property and places them in hierarchical JMenu list
+ * @param edge edgeView object
+ * @return JMenuItem
+ */
+ public JMenuItem addLinks(EdgeView edge) {
+ readProperties();
+
+ JMenu top_menu = new JMenu("LinkOut");
+
+ //iterate through properties list
+ try {
+ final EdgeView myedge = (EdgeView) edge;
+
+ // Replace edge attributes with values
+ Edge ed = myedge.getEdge();
+
+ for (Enumeration e = props.propertyNames(); e.hasMoreElements();) {
+ String propKey = (String) e.nextElement();
+
+ int p = propKey.lastIndexOf(edgeMarker);
+
+ if (p == -1)
+ continue;
+
+ p = p + edgeMarker.length();
+
+ //the URL
+ String url = props.getProperty(propKey);
+
+ if (url == null) {
+ url = "<html><small><i>empty- no links<br> See documentation</i></small></html>"
+ + "http://www.cytoscape.org/";
+ }
+
+ //add edge label to the URL
+ String edgelabel;
+
+ CyAttributes nodeAtts = Cytoscape.getNodeAttributes();
+ CyAttributes edgeAtts = Cytoscape.getEdgeAttributes();
+ String sourceId = ed.getSource().getIdentifier();
+ String targetId = ed.getTarget().getIdentifier();
+ String edgeId = ed.getIdentifier();
+// String fUrl = subsAttrs(url, attrs, sourceId, "ID%1", "source.");
+// fUrl = subsAttrs(fUrl, attrs, targetId, "ID%2", "target.");
+ String fUrl = subsAttrs(url, nodeAtts, sourceId, "ID1", "source.");
+ fUrl = subsAttrs(fUrl, nodeAtts, targetId, "ID2", "target.");
+ fUrl = subsAttrs(fUrl, edgeAtts, edgeId, "ID", "");
+
+ // System.out.println(fUrl);
+
+ //the link name
+ String[] temp = ((String) propKey.substring(p)).split("\\.");
+ ArrayList keys = new ArrayList(Arrays.asList(temp));
+
+ //Generate the menu path
+ generateLinks(keys, top_menu, fUrl);
+ }
+
+ CyAttributes edgeAttributes = Cytoscape.getEdgeAttributes();
+
+ // Now, see if the user has specified their own URL to add to linkout
+ generateExternalLinks(edgeAttributes, ed.getIdentifier(), top_menu);
+
+ //if no links specified insert a default message
+ if (top_menu.getMenuComponentCount() == 0) {
+ String url = "<html><small><i>empty- no links<br> See documentation</i></small></html>"
+ + "http://www.cytoscape.org/";
+ top_menu.add(new JMenuItem(url));
+ }
+
+ // For debugging
+ // printMenu(top_menu);
+ } catch (NullPointerException e) {
+ String url = "<html><small><i>empty- no links<br> See documentation</i></small></html>"
+ + "http://www.cytoscape.org/";
+ top_menu.add(new JMenuItem(url));
+ logger.error("NullPointerException: " + e.getMessage());
+ }
+
+ return top_menu;
+ }
+
+ /**
+ * Recursive method that expands the current menu list
+ * The list of keys mark the current path of sub-menus
+ * @param keys ArrayList
+ * @param j JMenu the curren JMenu object
+ * @param url String the url to link the node
+ */
+ private void generateLinks(ArrayList keys, JMenu j, final String url) {
+ //Get the sub-menu
+ JMenuItem jmi = getMenuItem((String) keys.get(0), j);
+
+ //if its null and this is the last key generate a new JMenuItem
+ if ((jmi == null) && (keys.size() == 1)) {
+ final String s = (String) keys.get(0);
+ JMenuItem new_jmi = new JMenuItem(new AbstractAction((String) keys.get(0)) {
+ public void actionPerformed(ActionEvent e) {
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ // System.out.println("Opening link: "+url);
+ OpenBrowser.openURL(url);
+ }
+ });
+ }
+ }); //end of AbstractAction class
+
+ j.add(new_jmi);
+
+ return;
+
+ //if its a JMenuItem and this is the last key then there
+ //is a duplicate of keys in the file. i.e two url with the exact same manu path
+ } else if (jmi instanceof JMenuItem && (keys.size() == 1)) {
+ logger.error("Duplicate URL specified for " + (String) keys.get(0));
+
+ return;
+
+ //if not null create a new JMenu with current key
+ // remove key from the keys ArrayList and call generateLinks
+ } else if (jmi == null) {
+ JMenu new_jm = new JMenu((String) keys.get(0));
+
+ keys.remove(0);
+ generateLinks(keys, new_jm, url);
+ j.add(new_jm);
+
+ return;
+
+ //Remove key from top of the list and call generateLinks with new JMenu
+ } else {
+ keys.remove(0);
+
+ generateLinks(keys, (JMenu) jmi, url);
+ }
+
+ return;
+ }
+
+ /**
+ * Search for an existing JmenuItem that is nested within a higher level JMenu
+ * @param name String the name of the jmenu item
+ * @param menu JMenu the parent JMenu to search in
+ * @return JMenuItem if found, null otherwise
+ */
+ private JMenuItem getMenuItem(String name, JMenu menu) {
+ int count = menu.getMenuComponentCount();
+
+ if (count == 0) {
+ return null;
+ }
+
+ //Skip over all JMenu components that are not JMenu or JMenuItem
+ for (int i = 0; i < count; i++) {
+ if (!menu.getItem(i).getClass().getName().equals("javax.swing.JMenu")
+ && !menu.getItem(i).getClass().getName().equals("javax.swing.JMenuItem")) {
+ continue;
+ }
+
+ JMenuItem jmi = menu.getItem(i);
+
+ if (jmi.getText().equalsIgnoreCase(name)) {
+ return jmi;
+ }
+ }
+
+ return null;
+ }
+
+ /**
+ * Print menu items - for debugging
+ */
+ private void printMenu(JMenu jm) {
+ int count = jm.getMenuComponentCount();
+
+ for (int i = 0; i < count; i++) {
+ if (jm.getItem(i).getClass().getName().equals("javax.swing.JMenuItem")) {
+ logger.debug(jm.getItem(i).getText());
+
+ continue;
+ } else {
+ logger.debug(jm.getItem(i).getText() + "--");
+ printMenu((JMenu) jm.getItem(i));
+ }
+ }
+ }
+
+ /**
+ * Read properties values from linkout.props file included in the
+ * linkout.jar file and apply those properties to the base Cytoscape
+ * properties. Only apply the properties from the jar file if
+ * NO linkout properties already exist.
+ * This allows linkout properties to be specified on the command line,
+ * editted in the preferences dialog, and to be saved with other
+ * properties.
+ */
+ private void readProperties() {
+ // Set the properties to be Cytoscape's properties.
+ // This allows the linkout properties to be edited in
+ // the preferences editor.
+ //System.out.println(CytoscapeInit.getPropertiesLocation());
+ props = CytoscapeInit.getProperties();
+
+ // Loop over the default props and see if any
+ // linkout urls have been specified. We don't want to
+ // override or even supplement what was set from the
+ // command line. Only use the defaults if nothing
+ // else can be found.
+ boolean linkoutFound = false;
+ boolean externalLinkNameFound = false;
+ Enumeration names = props.propertyNames();
+
+ while (names.hasMoreElements()) {
+ String name = (String) names.nextElement();
+ if (name.compareToIgnoreCase(linkMarker) == 0) {
+ externalLinkNameFound = true;
+ externalLinksAttribute = props.getProperty(linkMarker);
+ continue;
+ }
+ int p = name.lastIndexOf(nodeMarker);
+ int q = name.lastIndexOf(edgeMarker);
+
+ if (p != -1 || q != -1) {
+ linkoutFound = true;
+
+ break;
+ }
+ }
+
+ // If we don't have any linkout properties, load the defaults.
+ if (!linkoutFound) {
+ try {
+ logger.info("loading defaults");
+
+ ClassLoader cl = LinkOut.class.getClassLoader();
+ props.load(cl.getResource("linkout.props").openStream());
+ if (!externalLinkNameFound) {
+ externalLinksAttribute = props.getProperty(linkMarker);
+ }
+ } catch (Exception e) {
+ logger.error("Couldn't load default linkout props", e);
+ }
+ }
+ }
+
+ /**
+ * If we have an ExternalLinks attribute, see if it's formatted as a LinkOut,
+ * and if so, add that to the menu. A LinkOut may be one of:
+ * String: name=URL
+ * List: [name1=URL1,name2=URL2,etc.]
+ * where the name will be used as the menu label and the URL will be what we
+ * actually hand off to the browser.
+ *
+ * @param attributes the attribute map we are currently using
+ * @param id the ID of the object we are currently linking out from
+ * @param menu the menu to add links to
+ */
+ private void generateExternalLinks(CyAttributes attributes, String id, JMenu menu) {
+ if (attributes.hasAttribute(id, externalLinksAttribute)) {
+ // Maybe.....
+ byte attrType = attributes.getType(externalLinksAttribute);
+ if (attrType == CyAttributes.TYPE_STRING) {
+ // Single title=url pair
+ String attr = attributes.getStringAttribute(id, externalLinksAttribute);
+ addExternalLink(attr, menu);
+ } else if (attrType == CyAttributes.TYPE_SIMPLE_LIST) {
+ // List of title=url pairs
+ List attrList = attributes.getListAttribute(id, externalLinksAttribute);
+ for (String attr: (List<String>)attrList) {
+ addExternalLink(attr, menu);
+ }
+ }
+ }
+ return;
+ }
+
+ private void addExternalLink(String attr, JMenu menu) {
+ if (attr == null || attr.length() < 9)
+ return;
+ String[] pair = attr.split("=",2);
+ if (pair.length != 2) return;
+ if (!pair[1].startsWith("http://")) {
+ return;
+ }
+ ArrayList<String>key = new ArrayList();
+ key.add("ExternalLinks");
+ key.add(pair[0]);
+ generateLinks(key, menu, pair[1]);
+ }
+}
diff --git a/coreplugins/linkout/src/main/java/linkout/LinkOutEdgeContextMenuListener.java b/coreplugins/linkout/src/main/java/linkout/LinkOutEdgeContextMenuListener.java
new file mode 100644
index 0000000..c87d5ce
--- /dev/null
+++ b/coreplugins/linkout/src/main/java/linkout/LinkOutEdgeContextMenuListener.java
@@ -0,0 +1,43 @@
+/*$Id$*/
+package linkout;
+
+import ding.view.EdgeContextMenuListener;
+
+import giny.view.EdgeView;
+
+import javax.swing.JPopupMenu;
+import javax.swing.JSeparator;
+
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: doron
+ * Date: Oct 12, 2006
+ * Time: 4:47:00 PM
+ * To change this template use File | Settings | File Templates.
+ */
+public class LinkOutEdgeContextMenuListener implements EdgeContextMenuListener {
+ /**
+ * Creates a new LinkOutEdgeContextMenuListener object.
+ */
+ public LinkOutEdgeContextMenuListener() {
+ //System.out.println("[LinkOutContextMenuListener]: Constructor called");
+ }
+
+ /**
+ * @param edgeView The clicked NodeView
+ * @param menu popup menu to add the LinkOut menu
+ */
+ public void addEdgeContextMenuItems(EdgeView edgeView, JPopupMenu menu) {
+ //System.out.println("[LinkOutContextMenuListener]: addNodeContextMenuItem called");
+ LinkOut lo = new LinkOut();
+
+ if (menu == null) {
+ menu = new JPopupMenu();
+ }
+
+ menu.add(new JSeparator());
+ menu.add(lo.addLinks(edgeView));
+ menu.add(new JSeparator());
+ }
+}
diff --git a/coreplugins/linkout/src/main/java/linkout/LinkOutNetworkListener.java b/coreplugins/linkout/src/main/java/linkout/LinkOutNetworkListener.java
new file mode 100644
index 0000000..56cf19b
--- /dev/null
+++ b/coreplugins/linkout/src/main/java/linkout/LinkOutNetworkListener.java
@@ -0,0 +1,54 @@
+/*$Id: LinkOutNetworkListener.java 9566 2007-02-13 20:13:13Z mes $*/
+package linkout;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.view.CytoscapeDesktop;
+
+import ding.view.*;
+
+import java.beans.*;
+
+
+/**
+ * LinkOutNetworkListener implements PropertyChangeListener for new Network instances
+ * When a new cytoscape network view is created it registers the LinkOutContextMenuListener
+ * with the new DGraphView.
+**/
+public class LinkOutNetworkListener implements PropertyChangeListener {
+ /**
+ * DOCUMENT ME!
+ */
+ public void LinkOutNetworkListener() {
+ //System.out.println("[LinkOutNetworkListener]: constructor called");
+ }
+
+ /**
+ * Register a LinkOut[Node/Edge]ContextMenuListener for all new DGraphView
+ * objects (ie new network instances).
+ * @param evnt PropertyChangeEvent
+ */
+ public void propertyChange(PropertyChangeEvent evnt) {
+ if (evnt.getPropertyName() == CytoscapeDesktop.NETWORK_VIEW_CREATED) {
+ //System.out.println("[LinkOutNetworkListener]: propertyChange called");
+
+ //Register NodeContext...
+ LinkOutNodeContextMenuListener nodeMenuListener = new LinkOutNodeContextMenuListener();
+ ((DGraphView) Cytoscape.getCurrentNetworkView()).addNodeContextMenuListener(nodeMenuListener);
+
+ //Register EdgeContext...
+ LinkOutEdgeContextMenuListener edgeMenuListener = new LinkOutEdgeContextMenuListener();
+ ((DGraphView) Cytoscape.getCurrentNetworkView()).addEdgeContextMenuListener(edgeMenuListener);
+ }
+ }
+}
+/*$Log: LinkOutNetworkListener.java,v $
+/*Revision 1.1 2006/06/14 18:12:46 mes
+/*updated project to actually compile and work with ant
+/*
+/*Revision 1.2 2006/06/12 19:27:44 betel
+/*Fixes to bug reports 346-links to missing labels, 637-linkout fix for command line mode
+/*
+/*Revision 1.1 2006/05/19 21:51:29 betel
+/*New implementation of LinkOut with network-view listener
+/**/
diff --git a/coreplugins/linkout/src/main/java/linkout/LinkOutNodeContextMenuListener.java b/coreplugins/linkout/src/main/java/linkout/LinkOutNodeContextMenuListener.java
new file mode 100644
index 0000000..9b781e5
--- /dev/null
+++ b/coreplugins/linkout/src/main/java/linkout/LinkOutNodeContextMenuListener.java
@@ -0,0 +1,40 @@
+/*$Id: LinkOutContextMenuListener.java,v 1.1 2006/06/14 18:12:46 mes Exp $*/
+package linkout;
+
+import ding.view.NodeContextMenuListener;
+
+import giny.view.NodeView;
+
+import javax.swing.JPopupMenu;
+import javax.swing.JSeparator;
+
+
+/**
+ * LinkOutContextMenuListener implements NodeContextMenuListener
+ * When a node is selected it calls LinkOut that adds the linkout menu to the node's popup menu
+ */
+public class LinkOutNodeContextMenuListener implements NodeContextMenuListener {
+ /**
+ * Creates a new LinkOutNodeContextMenuListener object.
+ */
+ public LinkOutNodeContextMenuListener() {
+ //System.out.println("[LinkOutContextMenuListener]: Constructor called");
+ }
+
+ /**
+ * @param nodeView The clicked NodeView
+ * @param menu popup menu to add the LinkOut menu
+ */
+ public void addNodeContextMenuItems(NodeView nodeView, JPopupMenu menu) {
+ //System.out.println("[LinkOutContextMenuListener]: addNodeContextMenuItem called");
+ LinkOut lo = new LinkOut();
+
+ if (menu == null) {
+ menu = new JPopupMenu();
+ }
+
+ menu.add(new JSeparator());
+ menu.add(lo.addLinks(nodeView));
+ menu.add(new JSeparator());
+ }
+}
diff --git a/coreplugins/linkout/src/main/java/linkout/LinkOutPlugin.java b/coreplugins/linkout/src/main/java/linkout/LinkOutPlugin.java
new file mode 100644
index 0000000..eb70f4c
--- /dev/null
+++ b/coreplugins/linkout/src/main/java/linkout/LinkOutPlugin.java
@@ -0,0 +1,125 @@
+/*$Id: LinkOutPlugin.java 14701 2008-08-17 03:01:50Z scooter $*/
+package linkout;
+
+import cytoscape.*;
+
+import cytoscape.plugin.*;
+
+import ding.view.*;
+
+import java.util.*;
+
+
+/**
+ * Linkout plugin for customized url links
+ * this is the old implementation of the plugin using previous node context menu
+ **
+public class LinkOutPlugin
+ extends
+ CytoscapePlugin
+ implements
+ PropertyChangeListener {
+
+ public LinkOutPlugin () {
+ Cytoscape.getDesktop().getSwingPropertyChangeSupport().addPropertyChangeListener( CytoscapeDesktop.NETWORK_VIEW_CREATED, this );
+ System.out.println("Initialized LinkOutPlugin");
+ }
+
+ //Note - This implementation does not work with the cytoscape-2.3
+ //see 'TooltipsAndContextMenusForRender' on Cytoscape wiki for future implementation
+ //
+ public void propertyChange ( PropertyChangeEvent e ) {
+
+ if ( e.getPropertyName() == CytoscapeDesktop.NETWORK_VIEW_CREATED ) {
+ CyNetworkView view = ( CyNetworkView )e.getNewValue();
+
+
+ //Add LinkOut Menu
+ //TODO- check the bool return value
+ view.addContextMethod("class phoebe.PNodeView",//phoebe class is part of the GINY graph library
+ // the package name
+ "csplugins.mskcc.doron.LinkOut",
+ "AddLinks", //method name
+ new Object[] {view}, // arguments
+ CytoscapeInit.getClassLoader() ); // the class load
+
+ }
+
+ }
+
+}
+
+*************************/
+
+/**
+ * LinkOut plugin for customized URL links
+ * **/
+public class LinkOutPlugin extends CytoscapePlugin {
+ /**
+ * Creates a new LinkOutPlugin object.
+ */
+ public LinkOutPlugin() {
+ try {
+ //Create a Network create event listener
+ LinkOutNetworkListener m_listener = new LinkOutNetworkListener();
+ Cytoscape.getSwingPropertyChangeSupport().addPropertyChangeListener(m_listener);
+
+ // Create a new ContextMenuListener and register with the pre-loaded networks.
+ // Cases where networks are loaded before the plugins. For example, when running Cytoscape
+ // from the command line.
+ //Todo - To be tested
+ Set networkSet = Cytoscape.getNetworkSet();
+
+ for (Iterator it = networkSet.iterator(); it.hasNext();) {
+ CyNetwork cyNetwork = (CyNetwork) it.next();
+
+ LinkOutNodeContextMenuListener nodeMenuListener = new LinkOutNodeContextMenuListener();
+ ((DGraphView) Cytoscape.getNetworkView(cyNetwork.getIdentifier()))
+ .addNodeContextMenuListener(nodeMenuListener);
+
+ LinkOutEdgeContextMenuListener edgeMenuListener = new LinkOutEdgeContextMenuListener();
+ ((DGraphView) Cytoscape.getNetworkView(cyNetwork.getIdentifier()))
+ .addEdgeContextMenuListener(edgeMenuListener);
+ }
+
+ /*
+ DGraphView currentNetwork=((DGraphView)Cytoscape.getCurrentNetworkView());
+
+ if(currentNetwork!=null){
+
+ LinkOutNodeContextMenuListener nodeMenuListener=new LinkOutNodeContextMenuListener();
+ currentNetwork.addNodeContextMenuListener(nodeMenuListener);
+
+ LinkOutEdgeContextMenuListener edgeMenuListener=new LinkOutEdgeContextMenuListener();
+ currentNetwork.addEdgeContextMenuListener(edgeMenuListener);
+
+ }
+ */
+ } catch (ClassCastException e) {
+ cytoscape.logger.CyLogger.getLogger(LinkOutPlugin.class).error(e.getMessage());
+
+ return;
+ }
+ }
+}
+/*
+$Log: LinkOutPlugin.java,v $
+Revision 1.1 2006/06/14 18:12:46 mes
+updated project to actually compile and work with ant
+
+Revision 1.4 2006/06/12 19:27:44 betel
+Fixes to bug reports 346-links to missing labels, 637-linkout fix for command line mode
+
+Revision 1.3 2006/05/19 21:51:29 betel
+New implementation of LinkOut with network-view listener
+
+Revision 1.1 2006/05/11 22:42:28 betel
+Initial deposit of linkout to pre-coreplugins
+
+Revision 1.2 2006/05/09 22:32:47 betel
+New implementation of LinkOutPlugin with new context menu interface and addition of linkout.props
+
+Revision 1.1 2006/05/08 17:15:22 betel
+Initial deposit of linkout source code
+
+*/
diff --git a/coreplugins/linkout/src/main/resources/linkout.props b/coreplugins/linkout/src/main/resources/linkout.props
new file mode 100644
index 0000000..eb5cae6
--- /dev/null
+++ b/coreplugins/linkout/src/main/resources/linkout.props
@@ -0,0 +1,93 @@
+#Linkout Property File
+#12/5/2007 Links re-organized by Keiichiro Ono (kono at ucsd.edu)
+
+#nodelinkouturl.yeast.BioGRID=http://www.thebiogrid.org/search.php?keywords=%ID%&searchbutton=GO&organismid=4932
+#nodelinkouturl.Biological\ resources.iHOP=http://www.ihop-net.org/UniPub/iHOP/in?syns_1=%ID%
+
+nodelinkouturl.Entrez.All\ Databases\ (Global\ search\ by\ free\ keyword)=http://www.ncbi.nlm.nih.gov/sites/gquery?GlobalQuery.GQueryCluster.GQuerySearchBox.Term=%ID%
+nodelinkouturl.Entrez.Pubmed=http\://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd\=Search&db\=PubMed&term\=%ID%&doptcmdl\=Abstract
+nodelinkouturl.Entrez.Protein=http\://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd\=Search&db\=Protein&term\=%ID%&doptcmdl\=GenPept
+nodelinkouturl.Entrez.Nucleotide=http\://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd\=Search&db\=nucleotide&term\=%ID%&doptcmdl\=GenBank
+nodelinkouturl.Entrez.OMIM=http\://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd\=Search&db\=omim&term\=%ID%&doptcmdl\=Synopsis
+nodelinkouturl.Entrez.Structure=http\://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd\=Search&db\=structure&term\=%ID%&doptcmdl\=Brief
+nodelinkouturl.Entrez.Gene=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Search&term=%ID%
+
+nodelinkouturl.iHOP.yeast=http\://www.ihop-net.org/UniPub/iHOP/?search\=%ID%&field\=all&ncbi_tax_id\=4932
+nodelinkouturl.iHOP.human=http\://www.ihop-net.org/UniPub/iHOP/?search\=%ID%&field\=all&ncbi_tax_id\=9606
+
+nodelinkouturl.Search\ Engines.Google=http://www.google.com/search?hl=en&q=%ID%&btnG=Google+Search
+nodelinkouturl.Search\ Engines.Ask=http://www.ask.com/web?q=%ID%&qsrc=0&o=0
+
+nodelinkouturl.UniProt.PIR=http://www.pir.uniprot.org/cgi-bin/upEntry?id=%ID%
+nodelinkouturl.UniProt.KB\ Beta=http://beta.uniprot.org/uniprot/%ID%
+
+nodelinkouturl.Other\ Biological\ DB.GeneCards=http://www.genecards.org/cgi-bin/carddisp.pl?gene=%ID%&alias=yes
+nodelinkouturl.Other\ Biological\ DB.Pfam=http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?%ID%
+nodelinkouturl.Other\ Biological\ DB.InterPro=http://www.ebi.ac.uk/interpro/IEntry?ac=%ID%
+
+
+nodelinkouturl.Model\ Organism\ DB.MGI\ (mouse)=http://www.informatics.jax.org/javawi2/servlet/WIFetch?page=searchTool&query=%ID%&selectedQuery=Genes+and+Markers
+nodelinkouturl.Model\ Organism\ DB.WormBase\ (worm)=http://www.wormbase.org/db/gene/gene?name=%ID%
+nodelinkouturl.Model\ Organism\ DB.SGD\ (yeast)=http\://db.yeastgenome.org/cgi-bin/locus.pl?locus\=%ID%
+nodelinkouturl.Model\ Organism\ DB.FlyBase\ (fly)=http://flybase.bio.indiana.edu/.bin/fbidq.html?%ID%
+nodelinkouturl.Model\ Organism\ DB.HGNC\ (human)=http://www.genenames.org/data/hgnc_data.php?hgnc_id=%ID%
+
+#Ontology
+nodelinkouturl.Ontology.Gene\ Ontology\ (QuickGO\ by\ ID)=http://www.ebi.ac.uk/ego/DisplayGoTerm?id=%ID%
+nodelinkouturl.Ontology.Gene\ Ontology\ (QuickGO\ by\ name)=http://www.ebi.ac.uk/ego/GSearch?query=%ID%&mode=name&ontology=all_ont
+
+#Ensembl
+nodelinkouturl.Ensembl\ Gene\ View.yeast=http://www.ensembl.org/Saccharomyces_cerevisiae/geneview?gene=%ID%
+nodelinkouturl.Ensembl\ Gene\ View.human=http://www.ensembl.org/Homo_sapiens/geneview?gene=%ID%
+nodelinkouturl.Ensembl\ Gene\ View.fly=http://www.ensembl.org/Drosophila_melanogaster/geneview?gene=%ID%
+nodelinkouturl.Ensembl\ Gene\ View.mouse=http://www.ensembl.org/Mus_musculus/geneview?gene=%ID%
+nodelinkouturl.Ensembl\ Gene\ View.worm=http://www.ensembl.org/Caenorhabditis_elegans/geneview?gene=%ID%
+
+#EB-eye
+nodelinkouturl.EBI\ Tools.All\ the\ EBI\ (Global\ search\ by\ free\ keyword)=http://www.ebi.ac.uk/ebisearch/search.ebi?query=%ID%&db=allebi
+nodelinkouturl.EBI\ Tools.Dasty2\ (Visualize\ protein\ sequence\ feature\ information)=http://www.ebi.ac.uk/dasty/display.html?q=%ID%&label=BIOSAPIENS&t=3
+nodelinkouturl.EBI\ Tools.PRIDE\ (PRoteomics\ IDEntifications\ database)=http://www.ebi.ac.uk/pride/simpleSearch.do?simpleSearchValue=%ID%
+
+#Reactome links
+nodelinkouturl.Reactome.ReactomeID=http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=%ID%
+nodelinkouturl.Reactome.Entrez=http://www.reactome.org/cgi-bin/link?SOURCE=Entrez+Gene&ID=%ID%
+nodelinkouturl.Reactome.UniProt=http://www.reactome.org/cgi-bin/link?SOURCE=UNIPROT&ID=%ID%
+nodelinkouturl.Reactome.SGD=http://www.reactome.org/cgi-bin/link?SOURCE=SGD&ID=%ID%&FOCUS_SPECIES=Saccharomyces+cerevisiae
+nodelinkouturl.Reactome.RefSeq=http://www.reactome.org/cgi-bin/link?SOURCE=RefSeq&ID=%ID%
+nodelinkouturl.Reactome.Wormbase=http://www.reactome.org/cgi-bin/link?SOURCE=Wormbase&ID=%ID%&FOCUS_SPECIES=Caenorhabditis+elegans
+
+#Network/Pathway databases
+nodelinkouturl.Interaction\ Databases.HPRD=http://www.hprd.org/resultsQuery?multiplefound=&prot_name=%ID%&external=Ref_seq&accession_id=&hprd=&gene_symbol=&chromo_locus=&function=&ptm_type=&localization=&domain=&motif=&expression=&prot_start=&prot_end=&limit=0&mole_start=&mole_end=&disease=&query_submit=Search
+nodelinkouturl.Interaction\ Databases.IntAct=http://www.ebi.ac.uk/intact/search/do/search?searchString=%ID%&filter=ac
+nodelinkouturl.Interaction\ Databases.BioGRID=http://www.thebiogrid.org/search.php?keywords=%ID%&searchbutton=GO&organismid=0
+
+#EBI Links
+nodelinkouturl.Array\ Express.All\ Species=http://www.ebi.ac.uk/microarray-as/aew/DW?queryFor=gene&gene_query=%ID%&species=&displayInsitu=on&exp_query=
+nodelinkouturl.Array\ Express.human=http://www.ebi.ac.uk/microarray-as/aew/DW?queryFor=gene&gene_query=%ID%&species=Homo+sapiens&displayInsitu=on&exp_query=
+nodelinkouturl.Array\ Express.yeast=http://www.ebi.ac.uk/microarray-as/aew/DW?queryFor=gene&gene_query=%ID%&species=Saccharomyces+cerevisiae&displayInsitu=on&exp_query=
+
+#KEGG Links
+nodelinkouturl.KEGG.All\ Species\ (use\ KEGG\ ID)=http://www.kegg.jp/dbget-bin/www_bget?%ID%
+nodelinkouturl.KEGG.human\ (use\ NCBI\ GeneID)=http://www.kegg.jp/dbget-bin/www_bget?hsa:%ID%
+nodelinkouturl.KEGG.yeast\ (use\ ORF\ name)=http://www.kegg.jp/dbget-bin/www_bget?sce:%ID%
+nodelinkouturl.KEGG.mouse\ (use\ NCBI\ GeneID)=http://www.genome.jp/dbget-bin/www_bget?mmu:%ID%
+
+#BindingDB Links
+nodelinkouturl.BindingDB.BindingDB\ (UniProt)= http://www.bindingdb.org/uniprot/%biopax.xref.UNIPROT%
+nodelinkouturl.BindingDB.BindingDB\ (canonical\ name)= http://www.bindingdb.org/bind/searchby_tw.jsp?constrain=0&target1=%biopax.entity.NAME%&submit=Search
+
+#Edge Links
+edgelinkouturl.iHop.yeast=http://www.ihop-net.org/UniPub/iHOP/in?syns_1=%ID1%&ncbi_tax_id_1=4932&syns_2=%ID2%&ncbi_tax_id_2=4932
+edgelinkouturl.iHop.human=http://www.ihop-net.org/UniPub/iHOP/in?syns_1=%ID1%&ncbi_tax_id_1=9606&syns_2=%ID2%&ncbi_tax_id_2=9606
+
+edgelinkouturl.Entrez.Pubmed=http\://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd\=Search&db\=PubMed&term\=%ID%&doptcmdl\=Abstract
+
+edgelinkouturl.Ontology.Molecular\ Interaction\ (PSI-MI)=http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI&termId=MI%3A%ID%
+
+
+#Interaction Database Links
+edgelinkouturl.Network\ Database.IntAct=http://www.ebi.ac.uk/intact/search/do/search?searchString=%ID%&filter=ac
+edgelinkouturl.Network\ Database.BioGRID=http://www.thebiogrid.org/SearchResults/summary/%ID%
+
+#Attribute name for user-embedded URLs
+Linkout.externalLinkName=Linkout.ExternalLinks
diff --git a/coreplugins/linkout/src/main/resources/linkout/plugin.props b/coreplugins/linkout/src/main/resources/linkout/plugin.props
new file mode 100644
index 0000000..db62040
--- /dev/null
+++ b/coreplugins/linkout/src/main/resources/linkout/plugin.props
@@ -0,0 +1,30 @@
+# This props file would be filled out and included in the plugin jar file. This props file will be used
+# to put information into the Plugin Manager about the plugin
+
+# -- The following properties are REQUIRED -- #
+
+# The plugin name that will be displayed to users
+pluginName=LinkOut
+
+# Description used to give users information about the plugin such as what it does.
+# Html tags are encouraged for formatting purposes.
+pluginDescription=Provides URLs that link to various biological databases based on query terms.
+
+# Plugin version number, this must be two numbers separated by a decimlal. Ex. 0.2, 14.03
+pluginVersion=2.01
+
+# Compatible Cytoscape version
+cytoscapeVersion=2.6,2.7,2.8
+
+# Category, use one of the categories listed on the website or create your own
+pluginCategory=Core
+
+
+# List of authors. Note each author and institution pair are separated by a : (colon)
+# each additional author institution pair must be separated from other pairs bye a ; (semicolon)
+pluginAuthorsIntsitutions=Doron Betel:MSKCC
+
+# -- The following properties should be set ONLY BY CORE PLUGINS -- #
+downloadURL=http://cytoscape.org/plugins/plugins.xml
+uniqueID=10
+
diff --git a/coreplugins/pom.xml b/coreplugins/pom.xml
new file mode 100644
index 0000000..2fd2d0e
--- /dev/null
+++ b/coreplugins/pom.xml
@@ -0,0 +1,135 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>cytoscape</groupId>
+ <artifactId>parent</artifactId>
+ <version>2.8.4-SNAPSHOT</version>
+ </parent>
+
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>parent</artifactId>
+ <packaging>pom</packaging>
+ <name>Cytoscape Core Plugins Parent POM</name>
+
+ <modules>
+ <module>AdvancedNetworkMerge</module>
+ <module>AutomaticLayout</module>
+ <module>BioMartClient</module>
+ <module>BioPAX</module>
+ <module>CytoscapeEditor2</module>
+ <module>EquationFunctions</module>
+ <module>ManualLayout</module>
+ <module>NCBIClient</module>
+ <module>PSI-MI</module>
+ <module>QuickFind</module>
+ <module>RFilters</module>
+ <module>SBMLReader</module>
+ <module>TableImport</module>
+ <module>browser</module>
+ <module>cPath</module>
+ <module>cPath2</module>
+ <module>filters</module>
+ <module>linkout</module>
+ <module>CoreCommands</module>
+ <module>NetworkAnalyzer</module>
+ </modules>
+
+ <build>
+ <pluginManagement>
+ <plugins>
+ <plugin>
+ <artifactId>maven-assembly-plugin</artifactId>
+ <version>2.2-beta-5</version>
+ <configuration>
+ <descriptorRefs>
+ <descriptorRef>jar-with-dependencies</descriptorRef>
+ </descriptorRefs>
+ </configuration>
+ <executions>
+ <execution>
+ <id>make-assembly</id>
+ <phase>package</phase>
+ <goals>
+ <goal>single</goal>
+ </goals>
+ </execution>
+ </executions>
+ </plugin>
+ </plugins>
+ </pluginManagement>
+ </build>
+
+ <!--
+ Don't add additional repositories!
+ We want everything coming from either Maven Central or our repository.
+ Remember, it's easy to add third party jars to our repository.
+ -->
+ <repositories>
+ <repository>
+ <id>cytoscape_snapshots</id>
+ <snapshots>
+ <enabled>true</enabled>
+ </snapshots>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <name>Cytoscape Snapshots</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/</url>
+ </repository>
+ <repository>
+ <id>cytoscape_releases</id>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ <name>Cytoscape Releases</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/releases/</url>
+ </repository>
+ <repository>
+ <id>cytoscape_thirdparty</id>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ <name>Cytoscape Third Party</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/thirdparty/</url>
+ </repository>
+ <repository>
+ <id>cytoscape_biopax_release</id>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ <name>Cytoscape BioPAX Release Mirror</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/biopax-release/</url>
+ </repository>
+ <repository>
+ <id>cytoscape_biopax_snapshot</id>
+ <snapshots>
+ <enabled>true</enabled>
+ </snapshots>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <name>Cytoscape BioPAX Snapshot Mirror</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/biopax-snapshot/</url>
+ </repository>
+ </repositories>
+
+ <dependencies>
+ <dependency>
+ <groupId>cytoscape</groupId>
+ <artifactId>application</artifactId>
+ <version>${project.version}</version>
+ <scope>provided</scope>
+ </dependency>
+ </dependencies>
+
+</project>
+
diff --git a/debian/changelog b/debian/changelog
deleted file mode 100644
index c158c4c..0000000
--- a/debian/changelog
+++ /dev/null
@@ -1,5 +0,0 @@
-cytoscape (3.1.0-1) UNRELEASED; urgency=low
-
- * Initial release (Closes: #465331).
-
- -- Ivo Maintz <ivo at maintz.de> Sat, 23 Feb 2013 22:06:02 +0100
diff --git a/debian/compat b/debian/compat
deleted file mode 100644
index ec63514..0000000
--- a/debian/compat
+++ /dev/null
@@ -1 +0,0 @@
-9
diff --git a/debian/control b/debian/control
deleted file mode 100644
index e37d534..0000000
--- a/debian/control
+++ /dev/null
@@ -1,22 +0,0 @@
-Source: cytoscape
-Section: science
-Priority: extra
-Maintainer: Ivo Maintz <ivo at maintz.de>
-Build-Depends: debhelper (>= 9.0.0),
- maven,
- default-jdk
-Standards-Version: 3.9.3
-Homepage: http://www.cytoscape.org
-
-Package: cytoscape
-Architecture: all
-Depends: ${misc:Depends},
- default-jre, jarwrapper
-Description: visualizing molecular interaction networks
- Cytoscape is an open source bioinformatics software platform for visualizing
- molecular interaction networks and biological pathways and integrating these
- networks with annotations, gene expression profiles and other state data.
- Although Cytoscape was originally designed for biological research, now it is
- a general platform for complex network analysis and visualization.
- Cytoscape core distribution provides a basic set of features for data
- integration and visualization.
diff --git a/debian/copyright b/debian/copyright
deleted file mode 100644
index 11c5675..0000000
--- a/debian/copyright
+++ /dev/null
@@ -1,19 +0,0 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
-Upstream-Name: Cytoscape
-Source: http://chianti.ucsd.edu/svn/cytoscape/trunk
-
-Files: *
-Copyright: 2001-2012 Cytoscape Consortium
-License: LGPL-2.1
-
-Files: debian/*
-Copyright: 2012 Ivo Maintz <ivo at maintz.de>
-License: GPL-2.0+
-
-License: GPL-2.0+
- On Debian systems, the complete text of the GNU General
- Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
-
-License: LGPL-2.1
- On Debian systems, the complete text of the GNU Lesser General
- Public License version 2.1 can be found in "/usr/share/common-licenses/LGPL-2.1".
diff --git a/debian/cytoscape.1 b/debian/cytoscape.1
deleted file mode 100644
index 4038f24..0000000
--- a/debian/cytoscape.1
+++ /dev/null
@@ -1,60 +0,0 @@
-.TH cytoscape 1 "Februar 23, 2013" "" "cytoscape"
-
-.SH NAME
-cytoscape
-
-.SH SYNOPSIS
-.B cytoscape
-.RI [ OPTIONS ]
-.br
-
-.SH DESCRIPTION
- Cytoscape is an open source bioinformatics software platform for visualizing
- molecular interaction networks and biological pathways and integrating these
- networks with annotations, gene expression profiles and other state data.
- Although Cytoscape was originally designed for biological research, now it is
- a general platform for complex network analysis and visualization.
- Cytoscape core distribution provides a basic set of features for data
- integration and visualization.
-.PP
-\fBcytoscape\fP is a software application for visualizing molecular interaction networks
-
-.SH OPTIONS
-.B
-.IP
-.B \-h, \-\-help
- Print the help
-.IP
-.B \-v, \-\-version
- Print the version number
-.IP
-.B \-s, \-\-session <file>
- Load a cytoscape session (.cys) file
-.IP
-.B \-n,\-\-network <file>
- Load a network file (any format)
-.IP
-.B \-s, \-\-edge-attrs <file>
- Load an edge attributes file (edge attribute format)
-.IP
-.B \-n, \-\--node-attrs <file>
- Load a node attributes file (node attribute format)
-.IP
-.B \-m, \-\-matrix <file>
- Load a node attribute matrix file (table)
-.IP
-.B \-p, \-\-plugin <file>
- Load a plugin jar file, directory of jar files, plugin class name, or plugin jar URL
-.IP
-.B \-P, \-\-props <file>
- Load cytoscape properties file (Java properties format) or individual property: -P name=value
-.IP
-.B \-\-validate
- Only validate the given input file (COPASI, Gepasi, or SBML) without performing any calculations.
-.IP
-.B \-V, \-\-vizmap <file>
- Load vizmap properties file (Java properties format)
-
-.PP
-This manual page was written by Ivo Maintz <ivo at maintz.de>,
-for the Debian project (and may be used by others).
diff --git a/debian/cytoscape.desktop b/debian/cytoscape.desktop
deleted file mode 100644
index 8cd34d3..0000000
--- a/debian/cytoscape.desktop
+++ /dev/null
@@ -1,9 +0,0 @@
-[Desktop Entry]
-Name=Cytoscape
-Comment=visualizing molecular interaction networks
-Exec=/usr/bin/cytoscape
-Icon=/usr/share/icons/CytoscapeLogo.svg
-Terminal=false
-Type=Application
-Categories=Development;Science;Biology
-StartupNotify=true
diff --git a/debian/cytoscape.docs b/debian/cytoscape.docs
deleted file mode 100644
index 1f0354d..0000000
--- a/debian/cytoscape.docs
+++ /dev/null
@@ -1,2 +0,0 @@
-distribution/target/cytoscape-*/cytoscape-*/sampleData
-distribution/target/cytoscape-*/cytoscape-*/docs/*
diff --git a/debian/cytoscape.install b/debian/cytoscape.install
deleted file mode 100644
index 72b1668..0000000
--- a/debian/cytoscape.install
+++ /dev/null
@@ -1,7 +0,0 @@
-distribution/target/cytoscape-*/cytoscape-*/plugins /usr/share/cytoscape
-distribution/target/cytoscape-*/cytoscape-*/Cytoscape.vmoptions /usr/share/cytoscape
-distribution/target/cytoscape-*/cytoscape-*/cytoscape.sh /usr/share/cytoscape
-distribution/target/cytoscape-*/cytoscape-*/gen_vmoptions.sh /usr/share/cytoscape
-distribution/target/cytoscape-*/cytoscape-*/cytoscape.jar /usr/share/cytoscape
-debian/cytoscape.desktop /usr/share/applications
-application/src/main/resources/cytoscape/images/CytoscapeLogo.svg /usr/share/icons/
diff --git a/debian/cytoscape.links b/debian/cytoscape.links
deleted file mode 100644
index fcedecf..0000000
--- a/debian/cytoscape.links
+++ /dev/null
@@ -1,2 +0,0 @@
-/usr/share/doc/cytoscape/sampleData /usr/share/cytoscape/sampleData
-/usr/share/cytoscape/cytoscape.sh /usr/bin/cytoscape
diff --git a/debian/cytoscape.manpages b/debian/cytoscape.manpages
deleted file mode 100644
index 810e732..0000000
--- a/debian/cytoscape.manpages
+++ /dev/null
@@ -1 +0,0 @@
-debian/cytoscape.1
diff --git a/debian/dirs b/debian/dirs
deleted file mode 100644
index 0988f3a..0000000
--- a/debian/dirs
+++ /dev/null
@@ -1 +0,0 @@
-usr/share/cytoscape
diff --git a/debian/docs b/debian/docs
deleted file mode 100644
index 35252fd..0000000
--- a/debian/docs
+++ /dev/null
@@ -1 +0,0 @@
-LICENSE.txt
diff --git a/debian/get-orig-source b/debian/get-orig-source
deleted file mode 100755
index 38f3393..0000000
--- a/debian/get-orig-source
+++ /dev/null
@@ -1,30 +0,0 @@
-#!/bin/sh
-# get source for cytoscape from SVN because there is no source tarball distribution
-
-set -e
-NAME=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'`
-ORIGNAME=cytoscape
-COMPRESSION=xz
-
-if ! echo $@ | grep -q upstream-version ; then
- VERSION=`dpkg-parsechangelog | awk '/^Version:/ { print $2 }' | sed 's/\([0-9\.]\+\)-[0-9]\+$/\1/'`
-else
- VERSION=`echo $@ | sed "s?^.*--upstream-version \([0-9.]\+\) .*${ORIGNAME}_release.*?\1?"`
- if echo "$VERSION" | grep -q "upstream-version" ; then
- echo "Unable to parse version number"
- exit
- fi
-fi
-
-SVNTAG=`echo ${VERSION} | sed 's/\./_/g'`
-rm -f ../${ORIGNAME}_release_${SVNTAG}
-RELEASE=${ORIGNAME}_release_${SVNTAG}
-TARDIR=${NAME}-${VERSION}
-
-mkdir -p ../tarballs
-cd ../tarballs
-# svn export conserves time stamps of the files, checkout does not
-LC_ALL=C svn --quiet export http://chianti.ucsd.edu/svn/cytoscape/trunk ${TARDIR}
-
-GZIP="--best --no-name" XZ_OPT="-6v" tar --owner=root --group=root --mode=a+rX -caf "$NAME"_"$VERSION".orig.tar.${COMPRESSION} "${TARDIR}"
-rm -rf "${NAME}"-"$VERSION"
diff --git a/debian/patches/MPL.patch b/debian/patches/MPL.patch
deleted file mode 100644
index 199cb78..0000000
--- a/debian/patches/MPL.patch
+++ /dev/null
@@ -1,380 +0,0 @@
-Description: added the text for the Mozilla Public License
-Author: Ivo Maintz <ivo at maintz.de>
-Last-Update: 2013-02-01
-
---- /dev/null
-+++ b/src/main/licenses/MOZILLA_PUBLIC_LICENSE.txt
-@@ -0,0 +1,373 @@
-+Mozilla Public License Version 2.0
-+==================================
-+
-+1. Definitions
-+--------------
-+
-+1.1. "Contributor"
-+ means each individual or legal entity that creates, contributes to
-+ the creation of, or owns Covered Software.
-+
-+1.2. "Contributor Version"
-+ means the combination of the Contributions of others (if any) used
-+ by a Contributor and that particular Contributor's Contribution.
-+
-+1.3. "Contribution"
-+ means Covered Software of a particular Contributor.
-+
-+1.4. "Covered Software"
-+ means Source Code Form to which the initial Contributor has attached
-+ the notice in Exhibit A, the Executable Form of such Source Code
-+ Form, and Modifications of such Source Code Form, in each case
-+ including portions thereof.
-+
-+1.5. "Incompatible With Secondary Licenses"
-+ means
-+
-+ (a) that the initial Contributor has attached the notice described
-+ in Exhibit B to the Covered Software; or
-+
-+ (b) that the Covered Software was made available under the terms of
-+ version 1.1 or earlier of the License, but not also under the
-+ terms of a Secondary License.
-+
-+1.6. "Executable Form"
-+ means any form of the work other than Source Code Form.
-+
-+1.7. "Larger Work"
-+ means a work that combines Covered Software with other material, in
-+ a separate file or files, that is not Covered Software.
-+
-+1.8. "License"
-+ means this document.
-+
-+1.9. "Licensable"
-+ means having the right to grant, to the maximum extent possible,
-+ whether at the time of the initial grant or subsequently, any and
-+ all of the rights conveyed by this License.
-+
-+1.10. "Modifications"
-+ means any of the following:
-+
-+ (a) any file in Source Code Form that results from an addition to,
-+ deletion from, or modification of the contents of Covered
-+ Software; or
-+
-+ (b) any new file in Source Code Form that contains any Covered
-+ Software.
-+
-+1.11. "Patent Claims" of a Contributor
-+ means any patent claim(s), including without limitation, method,
-+ process, and apparatus claims, in any patent Licensable by such
-+ Contributor that would be infringed, but for the grant of the
-+ License, by the making, using, selling, offering for sale, having
-+ made, import, or transfer of either its Contributions or its
-+ Contributor Version.
-+
-+1.12. "Secondary License"
-+ means either the GNU General Public License, Version 2.0, the GNU
-+ Lesser General Public License, Version 2.1, the GNU Affero General
-+ Public License, Version 3.0, or any later versions of those
-+ licenses.
-+
-+1.13. "Source Code Form"
-+ means the form of the work preferred for making modifications.
-+
-+1.14. "You" (or "Your")
-+ means an individual or a legal entity exercising rights under this
-+ License. For legal entities, "You" includes any entity that
-+ controls, is controlled by, or is under common control with You. For
-+ purposes of this definition, "control" means (a) the power, direct
-+ or indirect, to cause the direction or management of such entity,
-+ whether by contract or otherwise, or (b) ownership of more than
-+ fifty percent (50%) of the outstanding shares or beneficial
-+ ownership of such entity.
-+
-+2. License Grants and Conditions
-+--------------------------------
-+
-+2.1. Grants
-+
-+Each Contributor hereby grants You a world-wide, royalty-free,
-+non-exclusive license:
-+
-+(a) under intellectual property rights (other than patent or trademark)
-+ Licensable by such Contributor to use, reproduce, make available,
-+ modify, display, perform, distribute, and otherwise exploit its
-+ Contributions, either on an unmodified basis, with Modifications, or
-+ as part of a Larger Work; and
-+
-+(b) under Patent Claims of such Contributor to make, use, sell, offer
-+ for sale, have made, import, and otherwise transfer either its
-+ Contributions or its Contributor Version.
-+
-+2.2. Effective Date
-+
-+The licenses granted in Section 2.1 with respect to any Contribution
-+become effective for each Contribution on the date the Contributor first
-+distributes such Contribution.
-+
-+2.3. Limitations on Grant Scope
-+
-+The licenses granted in this Section 2 are the only rights granted under
-+this License. No additional rights or licenses will be implied from the
-+distribution or licensing of Covered Software under this License.
-+Notwithstanding Section 2.1(b) above, no patent license is granted by a
-+Contributor:
-+
-+(a) for any code that a Contributor has removed from Covered Software;
-+ or
-+
-+(b) for infringements caused by: (i) Your and any other third party's
-+ modifications of Covered Software, or (ii) the combination of its
-+ Contributions with other software (except as part of its Contributor
-+ Version); or
-+
-+(c) under Patent Claims infringed by Covered Software in the absence of
-+ its Contributions.
-+
-+This License does not grant any rights in the trademarks, service marks,
-+or logos of any Contributor (except as may be necessary to comply with
-+the notice requirements in Section 3.4).
-+
-+2.4. Subsequent Licenses
-+
-+No Contributor makes additional grants as a result of Your choice to
-+distribute the Covered Software under a subsequent version of this
-+License (see Section 10.2) or under the terms of a Secondary License (if
-+permitted under the terms of Section 3.3).
-+
-+2.5. Representation
-+
-+Each Contributor represents that the Contributor believes its
-+Contributions are its original creation(s) or it has sufficient rights
-+to grant the rights to its Contributions conveyed by this License.
-+
-+2.6. Fair Use
-+
-+This License is not intended to limit any rights You have under
-+applicable copyright doctrines of fair use, fair dealing, or other
-+equivalents.
-+
-+2.7. Conditions
-+
-+Sections 3.1, 3.2, 3.3, and 3.4 are conditions of the licenses granted
-+in Section 2.1.
-+
-+3. Responsibilities
-+-------------------
-+
-+3.1. Distribution of Source Form
-+
-+All distribution of Covered Software in Source Code Form, including any
-+Modifications that You create or to which You contribute, must be under
-+the terms of this License. You must inform recipients that the Source
-+Code Form of the Covered Software is governed by the terms of this
-+License, and how they can obtain a copy of this License. You may not
-+attempt to alter or restrict the recipients' rights in the Source Code
-+Form.
-+
-+3.2. Distribution of Executable Form
-+
-+If You distribute Covered Software in Executable Form then:
-+
-+(a) such Covered Software must also be made available in Source Code
-+ Form, as described in Section 3.1, and You must inform recipients of
-+ the Executable Form how they can obtain a copy of such Source Code
-+ Form by reasonable means in a timely manner, at a charge no more
-+ than the cost of distribution to the recipient; and
-+
-+(b) You may distribute such Executable Form under the terms of this
-+ License, or sublicense it under different terms, provided that the
-+ license for the Executable Form does not attempt to limit or alter
-+ the recipients' rights in the Source Code Form under this License.
-+
-+3.3. Distribution of a Larger Work
-+
-+You may create and distribute a Larger Work under terms of Your choice,
-+provided that You also comply with the requirements of this License for
-+the Covered Software. If the Larger Work is a combination of Covered
-+Software with a work governed by one or more Secondary Licenses, and the
-+Covered Software is not Incompatible With Secondary Licenses, this
-+License permits You to additionally distribute such Covered Software
-+under the terms of such Secondary License(s), so that the recipient of
-+the Larger Work may, at their option, further distribute the Covered
-+Software under the terms of either this License or such Secondary
-+License(s).
-+
-+3.4. Notices
-+
-+You may not remove or alter the substance of any license notices
-+(including copyright notices, patent notices, disclaimers of warranty,
-+or limitations of liability) contained within the Source Code Form of
-+the Covered Software, except that You may alter any license notices to
-+the extent required to remedy known factual inaccuracies.
-+
-+3.5. Application of Additional Terms
-+
-+You may choose to offer, and to charge a fee for, warranty, support,
-+indemnity or liability obligations to one or more recipients of Covered
-+Software. However, You may do so only on Your own behalf, and not on
-+behalf of any Contributor. You must make it absolutely clear that any
-+such warranty, support, indemnity, or liability obligation is offered by
-+You alone, and You hereby agree to indemnify every Contributor for any
-+liability incurred by such Contributor as a result of warranty, support,
-+indemnity or liability terms You offer. You may include additional
-+disclaimers of warranty and limitations of liability specific to any
-+jurisdiction.
-+
-+4. Inability to Comply Due to Statute or Regulation
-+---------------------------------------------------
-+
-+If it is impossible for You to comply with any of the terms of this
-+License with respect to some or all of the Covered Software due to
-+statute, judicial order, or regulation then You must: (a) comply with
-+the terms of this License to the maximum extent possible; and (b)
-+describe the limitations and the code they affect. Such description must
-+be placed in a text file included with all distributions of the Covered
-+Software under this License. Except to the extent prohibited by statute
-+or regulation, such description must be sufficiently detailed for a
-+recipient of ordinary skill to be able to understand it.
-+
-+5. Termination
-+--------------
-+
-+5.1. The rights granted under this License will terminate automatically
-+if You fail to comply with any of its terms. However, if You become
-+compliant, then the rights granted under this License from a particular
-+Contributor are reinstated (a) provisionally, unless and until such
-+Contributor explicitly and finally terminates Your grants, and (b) on an
-+ongoing basis, if such Contributor fails to notify You of the
-+non-compliance by some reasonable means prior to 60 days after You have
-+come back into compliance. Moreover, Your grants from a particular
-+Contributor are reinstated on an ongoing basis if such Contributor
-+notifies You of the non-compliance by some reasonable means, this is the
-+first time You have received notice of non-compliance with this License
-+from such Contributor, and You become compliant prior to 30 days after
-+Your receipt of the notice.
-+
-+5.2. If You initiate litigation against any entity by asserting a patent
-+infringement claim (excluding declaratory judgment actions,
-+counter-claims, and cross-claims) alleging that a Contributor Version
-+directly or indirectly infringes any patent, then the rights granted to
-+You by any and all Contributors for the Covered Software under Section
-+2.1 of this License shall terminate.
-+
-+5.3. In the event of termination under Sections 5.1 or 5.2 above, all
-+end user license agreements (excluding distributors and resellers) which
-+have been validly granted by You or Your distributors under this License
-+prior to termination shall survive termination.
-+
-+************************************************************************
-+* *
-+* 6. Disclaimer of Warranty *
-+* ------------------------- *
-+* *
-+* Covered Software is provided under this License on an "as is" *
-+* basis, without warranty of any kind, either expressed, implied, or *
-+* statutory, including, without limitation, warranties that the *
-+* Covered Software is free of defects, merchantable, fit for a *
-+* particular purpose or non-infringing. The entire risk as to the *
-+* quality and performance of the Covered Software is with You. *
-+* Should any Covered Software prove defective in any respect, You *
-+* (not any Contributor) assume the cost of any necessary servicing, *
-+* repair, or correction. This disclaimer of warranty constitutes an *
-+* essential part of this License. No use of any Covered Software is *
-+* authorized under this License except under this disclaimer. *
-+* *
-+************************************************************************
-+
-+************************************************************************
-+* *
-+* 7. Limitation of Liability *
-+* -------------------------- *
-+* *
-+* Under no circumstances and under no legal theory, whether tort *
-+* (including negligence), contract, or otherwise, shall any *
-+* Contributor, or anyone who distributes Covered Software as *
-+* permitted above, be liable to You for any direct, indirect, *
-+* special, incidental, or consequential damages of any character *
-+* including, without limitation, damages for lost profits, loss of *
-+* goodwill, work stoppage, computer failure or malfunction, or any *
-+* and all other commercial damages or losses, even if such party *
-+* shall have been informed of the possibility of such damages. This *
-+* limitation of liability shall not apply to liability for death or *
-+* personal injury resulting from such party's negligence to the *
-+* extent applicable law prohibits such limitation. Some *
-+* jurisdictions do not allow the exclusion or limitation of *
-+* incidental or consequential damages, so this exclusion and *
-+* limitation may not apply to You. *
-+* *
-+************************************************************************
-+
-+8. Litigation
-+-------------
-+
-+Any litigation relating to this License may be brought only in the
-+courts of a jurisdiction where the defendant maintains its principal
-+place of business and such litigation shall be governed by laws of that
-+jurisdiction, without reference to its conflict-of-law provisions.
-+Nothing in this Section shall prevent a party's ability to bring
-+cross-claims or counter-claims.
-+
-+9. Miscellaneous
-+----------------
-+
-+This License represents the complete agreement concerning the subject
-+matter hereof. If any provision of this License is held to be
-+unenforceable, such provision shall be reformed only to the extent
-+necessary to make it enforceable. Any law or regulation which provides
-+that the language of a contract shall be construed against the drafter
-+shall not be used to construe this License against a Contributor.
-+
-+10. Versions of the License
-+---------------------------
-+
-+10.1. New Versions
-+
-+Mozilla Foundation is the license steward. Except as provided in Section
-+10.3, no one other than the license steward has the right to modify or
-+publish new versions of this License. Each version will be given a
-+distinguishing version number.
-+
-+10.2. Effect of New Versions
-+
-+You may distribute the Covered Software under the terms of the version
-+of the License under which You originally received the Covered Software,
-+or under the terms of any subsequent version published by the license
-+steward.
-+
-+10.3. Modified Versions
-+
-+If you create software not governed by this License, and you want to
-+create a new license for such software, you may create and use a
-+modified version of this License if you rename the license and remove
-+any references to the name of the license steward (except to note that
-+such modified license differs from this License).
-+
-+10.4. Distributing Source Code Form that is Incompatible With Secondary
-+Licenses
-+
-+If You choose to distribute Source Code Form that is Incompatible With
-+Secondary Licenses under the terms of this version of the License, the
-+notice described in Exhibit B of this License must be attached.
-+
-+Exhibit A - Source Code Form License Notice
-+-------------------------------------------
-+
-+ This Source Code Form is subject to the terms of the Mozilla Public
-+ License, v. 2.0. If a copy of the MPL was not distributed with this
-+ file, You can obtain one at http://mozilla.org/MPL/2.0/.
-+
-+If it is not possible or desirable to put the notice in a particular
-+file, then You may include the notice in a location (such as a LICENSE
-+file in a relevant directory) where a recipient would be likely to look
-+for such a notice.
-+
-+You may add additional accurate notices of copyright ownership.
-+
-+Exhibit B - "Incompatible With Secondary Licenses" Notice
-+---------------------------------------------------------
-+
-+ This Source Code Form is "Incompatible With Secondary Licenses", as
-+ defined by the Mozilla Public License, v. 2.0.
diff --git a/debian/patches/series b/debian/patches/series
deleted file mode 100644
index 582d173..0000000
--- a/debian/patches/series
+++ /dev/null
@@ -1,2 +0,0 @@
-MPL.patch
-shell.patch
diff --git a/debian/patches/shell.patch b/debian/patches/shell.patch
deleted file mode 100644
index 667b61e..0000000
--- a/debian/patches/shell.patch
+++ /dev/null
@@ -1,18 +0,0 @@
-Description: repaired the handling of a softlinked startup script
-Author: Ivo Maintz <ivo at maintz.de>
-Last-Update: 2013-02-01
-
---- a/distribution/src/main/bin/cytoscape.sh
-+++ b/distribution/src/main/bin/cytoscape.sh
-@@ -4,10 +4,7 @@
- # This script is a UNIX-only (i.e. Linux, Mac OS, etc.) version
- #-------------------------------------------------------------------------------
-
--script_path="$(dirname -- $0)"
--if [ -h $script_path ]; then
-- script_path="$(readlink $script_path)"
--fi
-+script_path="$(dirname $(readlink -f $0))"
-
- #vm_options_path=$HOME/.cytoscape
- vm_options_path=$script_path
diff --git a/debian/postinst b/debian/postinst
deleted file mode 100644
index 2f584cc..0000000
--- a/debian/postinst
+++ /dev/null
@@ -1,28 +0,0 @@
-#!/bin/bash
-# postinst script for cytoscape
-#
-# see: dh_installdeb(1)
-
-set -e
-
-case "$1" in
- configure)
- cd /usr/share/cytoscape
- ./gen_vmoptions.sh
-
- ;;
- abort-upgrade|abort-remove|abort-deconfigure)
- ;;
-
- *)
- echo "postinst called with unknown argument \`$1'" >&2
- exit 1
- ;;
-esac
-
-# dh_installdeb will replace this with shell code automatically
-# generated by other debhelper scripts.
-
-#DEBHELPER#
-
-exit 0
diff --git a/debian/prerm b/debian/prerm
deleted file mode 100644
index 1590bf6..0000000
--- a/debian/prerm
+++ /dev/null
@@ -1,33 +0,0 @@
-#!/bin/sh
-# prerm script for cytoscape
-#
-# see: dh_installdeb(1)
-
-set -e
-
-case "$1" in
- remove)
- rm -f /usr/share/cytoscape/*ytoscape.vmoptions
- ;;
-
- purge)
- ;;
-
- upgrade|failed-upgrade|disappear)
- ;;
-
- abort-install|abort-upgrade)
- ;;
-
- *)
- echo "$0 called with unknown argument \`$1'" 1>&2
- exit 1
- ;;
-esac
-
-# dh_installdeb will replace this with shell code automatically
-# generated by other debhelper scripts.
-
-#DEBHELPER#
-
-exit 0
diff --git a/debian/rules b/debian/rules
deleted file mode 100755
index 74a3b02..0000000
--- a/debian/rules
+++ /dev/null
@@ -1,25 +0,0 @@
-#!/usr/bin/make -f
-# -*- makefile -*-
-# Sample debian/rules that uses debhelper.
-# This file was originally written by Joey Hess and Craig Small.
-# As a special exception, when this file is copied by dh-make into a
-# dh-make output file, you may use that output file without restriction.
-# This special exception was added by Craig Small in version 0.37 of dh-make.
-
-# Uncomment this to turn on verbose mode.
-#export DH_VERBOSE=1
-
-%:
- dh $@
-
-override_dh_auto_clean:
- mvn clean -Dmaven.repo.local=${CURDIR}/../mvntmp
- rm -f pwMexVersion.p
-
-override_dh_auto_build:
- mvn install -Dmaven.test.skip=true -Dmaven.repo.local=${CURDIR}/../mvntmp
- chmod -x distribution/target/cytoscape*/cytoscape*/Cytoscape.vmoptions
- find distribution/target/cytoscape-*/cytoscape-* -name "*.jar" -exec chmod -x {} +
-
-get-orig-source:
- debian/get-orig-source
diff --git a/debian/source/format b/debian/source/format
deleted file mode 100644
index 163aaf8..0000000
--- a/debian/source/format
+++ /dev/null
@@ -1 +0,0 @@
-3.0 (quilt)
diff --git a/distribution/pom.xml b/distribution/pom.xml
new file mode 100644
index 0000000..8da2809
--- /dev/null
+++ b/distribution/pom.xml
@@ -0,0 +1,225 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+
+ <parent>
+ <groupId>cytoscape</groupId>
+ <artifactId>parent</artifactId>
+ <version>2.8.4-SNAPSHOT</version>
+ </parent>
+
+ <groupId>cytoscape</groupId>
+ <artifactId>cytoscape</artifactId>
+ <packaging>jar</packaging>
+ <name>Cytoscape Distribution</name>
+
+
+ <build>
+ <plugins>
+ <plugin>
+ <artifactId>maven-assembly-plugin</artifactId>
+ <configuration>
+ <descriptors>
+ <descriptor>src/main/assembly/src.xml</descriptor>
+ </descriptors>
+ </configuration>
+ <executions>
+ <execution>
+ <id>directory-assembly</id>
+ <phase>compile</phase>
+ <goals>
+ <goal>directory-single</goal>
+ </goals>
+ </execution>
+ <execution>
+ <id>zip-assembly</id>
+ <phase>package</phase>
+ <goals>
+ <goal>single</goal>
+ </goals>
+ </execution>
+ </executions>
+ </plugin>
+ </plugins>
+ </build>
+
+ <!-- bootstrap for cytoscape dependencies, namely the parent POM snapshots -->
+ <repositories>
+ <repository>
+ <id>cytoscape_snapshots</id>
+ <snapshots>
+ <enabled>true</enabled>
+ </snapshots>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <name>Cytoscape Snapshots</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/</url>
+ </repository>
+ <repository>
+ <id>cytoscape_releases</id>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ <name>Cytoscape Releases</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/releases/</url>
+ </repository>
+ </repositories>
+
+ <dependencies>
+ <!-- the application -->
+ <dependency>
+ <groupId>cytoscape</groupId>
+ <artifactId>application</artifactId>
+ <version>${project.version}</version>
+ <classifier>jar-with-dependencies</classifier>
+ </dependency>
+
+ <!-- documentation -->
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>docs</artifactId>
+ <version>${project.version}</version>
+ <classifier>html</classifier>
+ <type>zip</type>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>docs</artifactId>
+ <version>${project.version}</version>
+ <classifier>pdf</classifier>
+ <type>zip</type>
+ </dependency>
+
+ <!-- coreplugins -->
+ <dependency>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>advanced-network-merge</artifactId>
+ <version>${project.version}</version>
+ <classifier>jar-with-dependencies</classifier>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>automatic-layout</artifactId>
+ <version>${project.version}</version>
+ <classifier>jar-with-dependencies</classifier>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>biomart-client</artifactId>
+ <version>${project.version}</version>
+ <classifier>jar-with-dependencies</classifier>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>biopax</artifactId>
+ <version>${project.version}</version>
+ <classifier>jar-with-dependencies</classifier>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>editor</artifactId>
+ <version>${project.version}</version>
+ <classifier>jar-with-dependencies</classifier>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>equation-functions</artifactId>
+ <version>${project.version}</version>
+ <classifier>jar-with-dependencies</classifier>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>manual-layout</artifactId>
+ <version>${project.version}</version>
+ <classifier>jar-with-dependencies</classifier>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>ncbi-client</artifactId>
+ <version>${project.version}</version>
+ <classifier>jar-with-dependencies</classifier>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>psi-mi</artifactId>
+ <version>${project.version}</version>
+ <classifier>jar-with-dependencies</classifier>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>rfilters</artifactId>
+ <version>${project.version}</version>
+ <classifier>jar-with-dependencies</classifier>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>sbml-reader</artifactId>
+ <version>${project.version}</version>
+ <classifier>jar-with-dependencies</classifier>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>table-import</artifactId>
+ <version>${project.version}</version>
+ <classifier>jar-with-dependencies</classifier>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>attribute-browser</artifactId>
+ <version>${project.version}</version>
+ <classifier>jar-with-dependencies</classifier>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>cpath</artifactId>
+ <version>${project.version}</version>
+ <classifier>jar-with-dependencies</classifier>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>cpath2</artifactId>
+ <version>${project.version}</version>
+ <classifier>jar-with-dependencies</classifier>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>linkout</artifactId>
+ <version>${project.version}</version>
+ <classifier>jar-with-dependencies</classifier>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>quickfind</artifactId>
+ <version>${project.version}</version>
+ <classifier>jar-with-dependencies</classifier>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>filters</artifactId>
+ <version>${project.version}</version>
+ <classifier>jar-with-dependencies</classifier>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>core-commands</artifactId>
+ <version>${project.version}</version>
+ <classifier>jar-with-dependencies</classifier>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>network-analyzer</artifactId>
+ <version>${project.version}</version>
+ <classifier>jar-with-dependencies</classifier>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape-temp</groupId>
+ <artifactId>y-layouts</artifactId>
+ <version>1.0.1</version>
+ </dependency>
+ </dependencies>
+
+</project>
+
diff --git a/distribution/src/main/assembly/src.xml b/distribution/src/main/assembly/src.xml
new file mode 100644
index 0000000..8e00e5a
--- /dev/null
+++ b/distribution/src/main/assembly/src.xml
@@ -0,0 +1,59 @@
+<assembly xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0 http://maven.apache.org/xsd/assembly-1.1.0.xsd">
+ <formats>
+ <format>zip</format>
+ <format>tar.gz</format>
+ </formats>
+ <fileSets>
+ <fileSet>
+ <directory>${basedir}/src/main/bin</directory>
+ <outputDirectory>/</outputDirectory>
+ <fileMode>0755</fileMode>
+ </fileSet>
+ <fileSet>
+ <directory>${basedir}/src/main/licenses</directory>
+ <outputDirectory>licenses</outputDirectory>
+ <fileMode>0644</fileMode>
+ </fileSet>
+ <fileSet>
+ <directory>${basedir}/src/main/sampleData</directory>
+ <outputDirectory>sampleData</outputDirectory>
+ <fileMode>0644</fileMode>
+ </fileSet>
+ </fileSets>
+ <dependencySets>
+ <dependencySet>
+ <includes>
+ <include>cytoscape.coreplugins:*:jar:jar-with-dependencies</include>
+ </includes>
+ <excludes>
+ <exclude>cytoscape:application:jar:jar-with-dependencies</exclude>
+ </excludes>
+ <outputDirectory>plugins</outputDirectory>
+ <unpack>false</unpack>
+ </dependencySet>
+ <dependencySet>
+ <includes>
+ <include>cytoscape-temp:y-layouts:jar</include>
+ </includes>
+ <outputDirectory>plugins</outputDirectory>
+ <unpack>false</unpack>
+ </dependencySet>
+ <dependencySet>
+ <includes>
+ <include>cytoscape:application:jar:jar-with-dependencies</include>
+ </includes>
+ <outputFileNameMapping>cytoscape.jar</outputFileNameMapping>
+ <unpack>false</unpack>
+ </dependencySet>
+ <dependencySet>
+ <includes>
+ <include>cytoscape.corelibs:docs:zip:html</include>
+ <include>cytoscape.corelibs:docs:zip:pdf</include>
+ </includes>
+ <unpack>true</unpack>
+ <outputDirectory>docs</outputDirectory>
+ </dependencySet>
+ </dependencySets>
+</assembly>
diff --git a/distribution/src/main/bin/Cytoscape.vmoptions b/distribution/src/main/bin/Cytoscape.vmoptions
new file mode 100644
index 0000000..1941927
--- /dev/null
+++ b/distribution/src/main/bin/Cytoscape.vmoptions
@@ -0,0 +1,5 @@
+-Xms10m
+-Xmx768m
+-Xss10m
+-Dswing.aatext=true
+-Dawt.useSystemAAFontSettings=lcd
diff --git a/distribution/src/main/bin/INSTALL.txt b/distribution/src/main/bin/INSTALL.txt
new file mode 100644
index 0000000..fab51c7
--- /dev/null
+++ b/distribution/src/main/bin/INSTALL.txt
@@ -0,0 +1,105 @@
+################################################
+# CYTOSCAPE INSTALLATION INSTRUCTIONS #
+# Cytoscape version @version@, June., 2006 #
+# http://www.cytoscape.org #
+# #
+# (c) The Cytoscape Collaboration #
+# #
+################################################
+
+######################################################################
+LICENSE AGREEMENT AND DISCLAIMER #####################################
+######################################################################
+
+Cytoscape is a collaborative effort between the Institute for Systems
+Biology, the University of California at San Diego, Memorial Sloan-
+Kettering Cancer Center, the Institut Pasteur, and Agilent Technologies.
+It is available at http://www.cytoscape.org and provided to all users
+free of charge.
+
+Users of Cytoscape must first agree to the license agreement provided
+in the file "LICENSE.txt".
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+######################################################################
+INSTALLATION AND STARTUP #############################################
+######################################################################
+
+Currently, Cytoscape runs under Java on Linux, Windows, and MacOSX
+platforms. Although Cytoscape handles arbitrary types and sizes
+of interaction network, it is most powerful when used in conjunction
+with large interaction data sets such as are currently available for
+species such as the yeast S. cerevisiae.
+
+(1) Download and unpack the distribution. Cytoscape is distributed as
+a compressed archive containing the following files and directories:
+
+INSTALL.txt ............ Quick-start installation instructions (this file)
+manual.pdf.............. Overview and details of Cytoscape functionality
+LICENSE.txt ............ The license agreement
+LICENSE.html............ The license agreement in a different format
+
+cytoscape.jar .......... Main Cytoscape application (Java archive)
+
+cytoscape.sh ........... Shell script used to run Cytoscape (Linux)*
+cytoscape.bat .......... Shell script used to run Cytoscape (Windows)
+
+*Note: the cytoscape.sh shell script can be used to start Cytoscape on
+Mac OS X, although the default use for Mac OS X is to double-click on
+the Cytoscape application.
+
+sampleData/
+ galFiltered.gml ..... Sample molecular interaction network file *
+ galFiltered.sif ..... Identical network in Simple Interaction Format *
+ galFiltered.cys ..... Cytoscape session file containing galFiltered
+ data.
+ galExpData.pvals .... Sample gene expression matrix file *
+ galFiltered.*attr*... Various sample attribute files for the
+ galFiltered data.
+ BINDyeast.sif ....... Network of all yeast protein-protein
+ interactions in the BIND database as of
+ July, 2004 **
+ BINDhuman.sif ....... Network of all human protein-protein
+ interactions in the BIND database as of
+ July, 2004 **
+ yeastHighQuality.sif Set of high-quality yeast interactions as
+ determined by:
+ von Mering et al., Nature p.399,2002
+ Lee et al., Science p.799,2002
+
+annotation/ ............ Directory containing Gene Ontology database
+ and KEGG ontology entries (currently for
+ yeast only). Info in this directory is used
+ to associate gene names with synonyms as well
+ as process, function, and and cellular location data.
+
+* Sample data sets taken from Ideker et al, Science 292:929 (2001)
+** Obtained from data hosted at http://www.bind.ca/
+
+(2) If not already installed on your computer, download and install
+the Java 2 Runtime Environment, version 1.4.2 or higher. It can be
+found at:
+
+http://java.sun.com/j2se/1.4.2/download.html.
+
+(3) Launch the application by running "cytoscape.sh" from the command
+line (Linux) or double-clicking "cytoscape.bat" (Windows) or double-
+clicking on the Cytoscape icon under Mac OS X.
+Alternatively, you can pass the .jar file to Java directly using the
+command "java -jar cytoscape". In Windows, it is also possible to
+directly double-click the .jar file to launch it. However, this does
+not allow specification of command-line arguments (such as the
+location of the annotation data directory, see MANUAL.txt for details).
+
+!!!!IMPORTANT NOTE!!!! For the application to work properly, ALL
+FILES MUST BE LEFT IN THE DIRECTORY IN WHICH THEY ARE UNPACKED. [The
+core Cytoscape application assumes this directory structure when
+looking for plugins.
+
diff --git a/distribution/src/main/bin/LICENSE.html b/distribution/src/main/bin/LICENSE.html
new file mode 100644
index 0000000..ab2c8e0
--- /dev/null
+++ b/distribution/src/main/bin/LICENSE.html
@@ -0,0 +1,530 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html><head>
+
+
+<h1>GNU Lesser General Public License</h1>
+
+<tt><!-- Insert License text here -->
+
+
+
+</tt><p><tt>Version 2.1, February 1999</tt></p>
+
+<blockquote>
+<p><tt>Copyright (C) 1991, 1999 Free Software Foundation, Inc.
+59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+Everyone is permitted to copy and distribute verbatim copies
+of this license document, but changing it is not allowed.</tt></p>
+
+<p><tt>[This is the first released version of the Lesser GPL. It also counts
+ as the successor of the GNU Library Public License, version 2, hence
+ the version number 2.1.]</tt></p></blockquote>
+
+<h3><tt>Preamble</tt></h3>
+
+<p><tt> The licenses for most software are designed to take away your
+freedom to share and change it. By contrast, the GNU General Public
+Licenses are intended to guarantee your freedom to share and change
+free software--to make sure the software is free for all its users. </tt></p>
+
+<tt> </tt><p><tt>This license, the Lesser General Public License,
+applies to some specially designated software packages--typically
+libraries--of the Free Software Foundation and other authors who decide
+to use it. You can use it too, but we suggest you first think carefully
+about whether this license or the ordinary General Public License is
+the better strategy to use in any particular case, based on the
+explanations below.
+</tt></p>
+<p><tt> When we speak of free software, we are referring to freedom of
+use, not price. Our General Public Licenses are designed to make sure
+that you have the freedom to distribute copies of free software (and
+charge for this service if you wish); that you receive source code or
+can get it if you want it; that you can change the software and use
+pieces of it in new free programs; and that you are informed that you
+can do these things.</tt></p>
+
+<tt> </tt><p><tt>To protect your rights, we need to make restrictions
+that forbid distributors to deny you these rights or to ask you to
+surrender these rights. These restrictions translate to certain
+responsibilities for you if you distribute copies of the library or if
+you modify it.
+</tt></p>
+<p><tt> For example, if you distribute copies of the library, whether
+gratis or for a fee, you must give the recipients all the rights that
+we gave you. You must make sure that they, too, receive or can get the
+source code. If you link other code with the library, you must provide
+complete object files to the recipients, so that they can relink them
+with the library after making changes to the library and recompiling
+it. And you must show them these terms so they know their rights. </tt></p>
+
+<tt> </tt><p><tt>We protect your rights with a two-step method: (1) we
+copyright the library, and (2) we offer you this license, which gives
+you legal permission to copy, distribute and/or modify the library. </tt></p>
+
+<tt> </tt><p><tt>To protect each distributor, we want to make it very
+clear that there is no warranty for the free library. Also, if the
+library is modified by someone else and passed on, the recipients
+should know that what they have is not the original version, so that
+the original author's reputation will not be affected by problems that
+might be introduced by others. </tt></p>
+<p>
+<tt> Finally, software patents pose a constant threat to the existence
+of any free program. We wish to make sure that a company cannot
+effectively restrict the users of a free program by obtaining a
+restrictive license from a patent holder. Therefore, we insist that any
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+<!--END OF BODY-->
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diff --git a/distribution/src/main/bin/LICENSE.txt b/distribution/src/main/bin/LICENSE.txt
new file mode 100644
index 0000000..5be1362
--- /dev/null
+++ b/distribution/src/main/bin/LICENSE.txt
@@ -0,0 +1,467 @@
+################################################
+# CYTOSCAPE LICENSE AGREEMENT : GNU LGPL #
+# Cytoscape v. 2.1; February 2005 #
+# http://www.cytoscape.org #
+# #
+# (c) The Cytoscape Collaboration #
+################################################
+
+ GNU LESSER GENERAL PUBLIC LICENSE
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+
diff --git a/distribution/src/main/bin/README.txt b/distribution/src/main/bin/README.txt
new file mode 100644
index 0000000..16ee4a4
--- /dev/null
+++ b/distribution/src/main/bin/README.txt
@@ -0,0 +1,7 @@
+This directory contains scripts for running Cytoscape from the command line prompt.
+
+These scripts are bundled with the official Cytoscape release.
+
+cytoscape.sh: Used for running Cytoscape from Unix (including Mac OS X) and Linux.
+cytoscape.bat Used for running Cytoscape from Window.
+
diff --git a/distribution/src/main/bin/cytoscape.bat b/distribution/src/main/bin/cytoscape.bat
new file mode 100755
index 0000000..47b8d27
--- /dev/null
+++ b/distribution/src/main/bin/cytoscape.bat
@@ -0,0 +1,31 @@
+:: Simple Cytoscape batch script for windows/dos
+:: (c) Trey Ideker June 21, 2002; Owen Ozier March 06, 2003
+::
+:: Runs Cytoscape from its jar file with GO data loaded
+
+ at echo off
+
+:: Create the Cytoscape.vmoptions file, if it doesn't exist.
+IF EXIST "Cytoscape.vmoptions" GOTO vmoptionsFileExists
+CALL gen_vmoptions.bat
+:vmoptionsFileExists
+
+IF EXIST "Cytoscape.vmoptions" GOTO itIsThere
+; Run with defaults:
+echo "*** Missing Cytoscape.vmoptions, falling back to using defaults!"
+java -Dswing.aatext=true -Dawt.useSystemAAFontSettings=lcd -Xss10M -Xmx768M -jar cytoscape.jar -p plugins %*
+GOTO end
+
+:: We end up here if we have a Cytoscape.vmoptions file:
+:itIsThere
+:: Read vmoptions, one per line.
+setLocal EnableDelayedExpansion
+for /f "tokens=* delims= " %%a in (Cytoscape.vmoptions) do (
+set /a N+=1
+set opt!N!=%%a
+)
+
+java !opt1! !opt2! !opt3! !opt4! !opt5! !opt6! !opt7! !opt8! !opt9! -jar cytoscape.jar -p plugins %*
+
+
+:end
diff --git a/distribution/src/main/bin/cytoscape.sh b/distribution/src/main/bin/cytoscape.sh
new file mode 100755
index 0000000..bb4295e
--- /dev/null
+++ b/distribution/src/main/bin/cytoscape.sh
@@ -0,0 +1,27 @@
+#!/bin/sh
+#
+# Run cytoscape from a jar file
+# This script is a UNIX-only (i.e. Linux, Mac OS, etc.) version
+#-------------------------------------------------------------------------------
+
+script_path="$(dirname -- $0)"
+if [ -h $script_path ]; then
+ script_path="$(readlink $script_path)"
+fi
+
+#vm_options_path=$HOME/.cytoscape
+vm_options_path=$script_path
+
+# Attempt to generate Cytoscape.vmoptions if it doesn't exist!
+if [ ! -e "$vm_options_path/Cytoscape.vmoptions" -a -x "$script_path/gen_vmoptions.sh" ]; then
+ "$script_path/gen_vmoptions.sh"
+fi
+
+if [ -r $vm_options_path/Cytoscape.vmoptions ]; then
+ java `cat "$vm_options_path/Cytoscape.vmoptions"` -jar "$script_path/cytoscape.jar" -p "$script_path/plugins" "$@"
+else # Just use sensible defaults.
+ echo '*** Missing Cytoscape.vmoptions, falling back to using defaults!'
+ java -Dswing.aatext=true -Dawt.useSystemAAFontSettings=lcd -Xss10M -Xmx1550M \
+ -jar "$script_path/cytoscape.jar" -p "$script_path/plugins" "$@"
+fi
+
diff --git a/distribution/src/main/bin/gen_vmoptions.bat b/distribution/src/main/bin/gen_vmoptions.bat
new file mode 100644
index 0000000..db71e1f
--- /dev/null
+++ b/distribution/src/main/bin/gen_vmoptions.bat
@@ -0,0 +1,56 @@
+ at echo off
+
+:: Generates the Cytoscape.vmoptions file based on whether
+:: we're dealing with a 32 bit or 64 bit JVM.
+
+:: Create the .cytoscape directory if it doesn't already exist
+;if exist "%HOMEPATH%\.cytoscape" goto dot_cytoscape_exists
+;mkdir "%HOMEPATH%\.cytoscape"
+;:dot_cytoscape_exists
+
+set physmem=768
+set mem=768
+if exist findmem.out del findmem.out
+systeminfo | find "Total Physical Memory" > findmem.out
+if %ERRORLEVEL% NEQ 0 GOTO Javatest
+for /f "tokens=4" %%i in (findmem.out) do set physmem=%%i
+set physmem=%physmem:,=%
+
+if %physmem% GTR 1536 set mem=1024
+if %physmem% GTR 2048 set mem=1536
+if %physmem% GTR 3072 set /a mem=%physmem%-1024
+REM if %physmem% GTR 4096 set mem=3072
+REM if %physmem% GTR 9216 set mem=4096
+
+:Javatest
+ if exist findstr.out del findstr.out
+ java -version 2>&1 | findstr /I 64-Bit > findstr.out
+ if %ERRORLEVEL% NEQ 0 GOTO Nojava
+ for /f %%i in ('dir /b findstr.out') do if %%~zi equ 0 goto 32bit
+
+:64bit
+ REM echo "64 bit %mem% MB"
+ echo -Xms20m > Cytoscape.vmoptions
+ echo -Xmx%mem%m >>Cytoscape.vmoptions
+ echo -Xss10m >>Cytoscape.vmoptions
+ goto Shared
+
+:32bit
+ REM echo "32 bit %mem% MB"
+ REM Some java versions can only support 1400MB
+ if %mem% GTR 1400 set mem=1400
+ echo -Xms10m > Cytoscape.vmoptions
+ echo -Xmx%mem%m >>Cytoscape.vmoptions
+ echo -Xss10m >>Cytoscape.vmoptions
+
+:Shared
+ echo -Dswing.aatext=true >>Cytoscape.vmoptions
+ echo -Dawt.useSystemAAFontSettings=lcd >>Cytoscape.vmoptions
+ goto End
+
+:Nojava
+ echo ERROR: Can't find java executable
+
+:End
+ del findstr.out
+ del findmem.out
diff --git a/distribution/src/main/bin/gen_vmoptions.sh b/distribution/src/main/bin/gen_vmoptions.sh
new file mode 100755
index 0000000..e5797de
--- /dev/null
+++ b/distribution/src/main/bin/gen_vmoptions.sh
@@ -0,0 +1,52 @@
+#!/bin/sh
+# Generates the Cytoscape.vmoptions file
+
+script_path="$(dirname -- $0)"
+
+#vm_options_path="$HOME/.cytoscape"
+vm_options_path=$script_path
+
+if [ ! -e $vm_options_path ]; then
+ /bin/mkdir $vm_options_path
+fi
+
+# Determine amount of physical memory present:
+if [ `uname` = "Darwin" ]; then
+ phys_mem=`sysctl -a | grep 'hw.memsize =' | sed 's/[ ][ ][ ]*/ /g' | cut -f 3 -d ' '`
+ phys_mem=$((phys_mem / 1024 / 1024)) # Convert from B to MiB
+else # We assume Linux
+ phys_mem=`cat /proc/meminfo | grep 'MemTotal:' | sed 's/[ ][ ][ ]*/ /g' | cut -f 2 -d ' '`
+ phys_mem=$((phys_mem / 1024)) # Convert from KiB to MiB
+fi
+
+# Now we know the amount of physical memory, but we don't want to try to use it all
+mem=768
+if [ $phys_mem -gt 3071 ]; then
+ mem=$((phys_mem-1024))
+elif [ $phys_mem -gt 2047 ]; then
+ mem=1536
+elif [ $phys_mem -gt 1535 ]; then
+ mem=1024
+fi
+
+if `java -version 2>&1 | grep -- 64-Bit > /dev/null`; then # We have a 64 bit JVM.
+ echo -Xms20m > "$vm_options_path/Cytoscape.vmoptions"
+ echo -Xmx${mem}m >> "$vm_options_path/Cytoscape.vmoptions"
+ echo -Xss10m >> "$vm_options_path/Cytoscape.vmoptions"
+ echo -d64 >> "$vm_options_path/Cytoscape.vmoptions"
+else # Assume a 32 bit JVM.
+ # Truncate memory setting at 1550 MiB:
+ if [ $mem -gt 1550 ]; then
+ mem=1550
+ fi
+
+ echo -Xms10m > "$vm_options_path/Cytoscape.vmoptions"
+ echo -Xmx${mem}m >> "$vm_options_path/Cytoscape.vmoptions"
+ echo -Xss10m >> "$vm_options_path/Cytoscape.vmoptions"
+fi
+
+# Shared JVM options
+echo -Dswing.aatext=true >> "$vm_options_path/Cytoscape.vmoptions"
+echo -Dawt.useSystemAAFontSettings=lcd >> "$vm_options_path/Cytoscape.vmoptions"
+
+exit 0
diff --git a/distribution/src/main/licenses/APACHE_LICENSE.txt b/distribution/src/main/licenses/APACHE_LICENSE.txt
new file mode 100644
index 0000000..70cb54a
--- /dev/null
+++ b/distribution/src/main/licenses/APACHE_LICENSE.txt
@@ -0,0 +1,56 @@
+/*
+ * The Apache Software License, Version 1.1
+ *
+ *
+ * Copyright (c) 1999-2002 The Apache Software Foundation. All rights
+ * reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ *
+ * 1. Redistributions of source code must retain the above copyright
+ * notice, this list of conditions and the following disclaimer.
+ *
+ * 2. Redistributions in binary form must reproduce the above copyright
+ * notice, this list of conditions and the following disclaimer in
+ * the documentation and/or other materials provided with the
+ * distribution.
+ *
+ * 3. The end-user documentation included with the redistribution,
+ * if any, must include the following acknowledgment:
+ * "This product includes software developed by the
+ * Apache Software Foundation (http://www.apache.org/)."
+ * Alternately, this acknowledgment may appear in the software itself,
+ * if and wherever such third-party acknowledgments normally appear.
+ *
+ * 4. The names "Xerces" and "Apache Software Foundation" must
+ * not be used to endorse or promote products derived from this
+ * software without prior written permission. For written
+ * permission, please contact apache at apache.org.
+ *
+ * 5. Products derived from this software may not be called "Apache",
+ * nor may "Apache" appear in their name, without prior written
+ * permission of the Apache Software Foundation.
+ *
+ * THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED
+ * WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ * DISCLAIMED. IN NO EVENT SHALL THE APACHE SOFTWARE FOUNDATION OR
+ * ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+ * USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ * OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+ * OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ * SUCH DAMAGE.
+ * ====================================================================
+ *
+ * This software consists of voluntary contributions made by many
+ * individuals on behalf of the Apache Software Foundation and was
+ * originally based on software copyright (c) 1999, International
+ * Business Machines, Inc., http://www.ibm.com. For more
+ * information on the Apache Software Foundation, please see
+ * <http://www.apache.org/>.
+ */
diff --git a/distribution/src/main/licenses/COLT_LICENCES.html b/distribution/src/main/licenses/COLT_LICENCES.html
new file mode 100644
index 0000000..b76194b
--- /dev/null
+++ b/distribution/src/main/licenses/COLT_LICENCES.html
@@ -0,0 +1,558 @@
+<html>
+
+<head>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../stylesheet.css" TITLE="Style">
+</head>
+<body text="#000000" bgcolor="#BFABFA" link="#0000FF" vlink="#6255FD" alink="#FF0000">
+<h2 align="center">License Agreements and Copyrights for Colt Distribution Version
+ 1.2.0</h2>
+<p></p>
+<p>These are the copyright and licence statements for the Colt Distribution, Version
+ 1.2.0. Do not use this software if you do not accept the terms of the licenses
+ described below. In alphabetic order:</p>
+<p>
+Packages cern.colt* , cern.jet*, cern.clhep
+<blockquote>
+ Copyright (c) 1999 CERN - European Organization for Nuclear Research.
+<p>
+ Permission to use, copy, modify, distribute and sell this software and
+ its documentation for any purpose is hereby granted without fee, provided
+ that the above copyright notice appear in all copies and that both that
+ copyright notice and this permission notice appear in supporting documentation.
+ CERN makes no representations about the suitability of this software for
+ any purpose. It is provided "as is" without expressed or implied
+ warranty.
+</p>
+</blockquote>
+</p>
+
+<p>
+Packages hep.aida.*
+<blockquote>
+ Written by Pavel Binko, Dino Ferrero Merlino, Wolfgang Hoschek, Tony Johnson, Andreas Pfeiffer, and others. Check the FreeHEP home page for more info.
+ Permission to use and/or redistribute this work is granted under the terms of the LGPL License, with the exception that any usage related to military applications is expressly forbidden. The software and documentation made available under the terms of this license are provided with no warranty.
+</blockquote>
+<p>
+corejava
+<blockquote>
+<pre>
+
+ GNU LESSER GENERAL PUBLIC LICENSE
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+
+That's all there is to it!
+</pre>
+</blockquote>
+</p>
+
+<p>
+concurrent
+</p>
+
+<p>
+<blockquote>
+All classes are released to the public domain and may be used for any purpose whatsoever without permission or acknowledgment.
+Portions of the CopyOnWriteArrayList and ConcurrentReaderHashMap classes are adapted from Sun JDK source code.
+These are copyright of Sun Microsystems, Inc, and are used with their kind permission.
+</blockquote>
+</p>
+
+ </body></html>
diff --git a/distribution/src/main/licenses/GLF_SUN_LICENSE.txt b/distribution/src/main/licenses/GLF_SUN_LICENSE.txt
new file mode 100644
index 0000000..084ef4d
--- /dev/null
+++ b/distribution/src/main/licenses/GLF_SUN_LICENSE.txt
@@ -0,0 +1,30 @@
+Copyright 1994-2004 Sun Microsystems, Inc. All Rights Reserved.
+Redistribution and use in source and binary forms, with or without modification, are
+permitted provided that the following conditions are met:
+
+
+ * Redistribution of source code must retain the above copyright notice, this
+list of conditions and the following disclaimer.
+
+ * Redistribution in binary form must reproduce the above copyright notice, this
+list of conditions and the following disclaimer in the documentation and/or other
+materials provided with the distribution.
+
+Neither the name of Sun Microsystems, Inc. or the names of contributors may be used
+to endorse or promote products derived from this software without specific prior
+written permission.
+
+This software is provided "AS IS," without a warranty of any kind. ALL EXPRESS
+OR IMPLIED CONDITIONS, REPRESENTATIONS AND WARRANTIES, INCLUDING ANY
+IMPLIED WARRANTY OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE
+OR NON-INFRINGEMENT, ARE HEREBY EXCLUDED. SUN MICROSYSTEMS, INC. ("SUN")
+AND ITS LICENSORS SHALL NOT BE LIABLE FOR ANY DAMAGES SUFFERED BY LICENSEE
+AS A RESULT OF USING, MODIFYING OR DISTRIBUTING THIS SOFTWARE OR ITS
+DERIVATIVES. IN NO EVENT WILL SUN OR ITS LICENSORS BE LIABLE FOR ANY LOST
+REVENUE, PROFIT OR DATA, OR FOR DIRECT, INDIRECT, SPECIAL, CONSEQUENTIAL,
+INCIDENTAL OR PUNITIVE DAMAGES, HOWEVER CAUSED AND REGARDLESS OF THE
+THEORY OF LIABILITY, ARISING OUT OF THE USE OF OR INABILITY TO USE THIS
+SOFTWARE, EVEN IF SUN HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
+
+You acknowledge that this software is not designed, licensed or intended for use in
+the design, construction, operation or maintenance of any nuclear facility.
\ No newline at end of file
diff --git a/distribution/src/main/licenses/JDOM_LICENSE.txt b/distribution/src/main/licenses/JDOM_LICENSE.txt
new file mode 100644
index 0000000..2be5e35
--- /dev/null
+++ b/distribution/src/main/licenses/JDOM_LICENSE.txt
@@ -0,0 +1,56 @@
+/*--
+
+ $Id: JDOM_LICENSE.txt 5721 2004-03-25 15:11:22Z cerami $
+
+ Copyright (C) 2000-2003 Jason Hunter & Brett McLaughlin.
+ All rights reserved.
+
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions, and the following disclaimer.
+
+ 2. Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions, and the disclaimer that follows
+ these conditions in the documentation and/or other materials
+ provided with the distribution.
+
+ 3. The name "JDOM" must not be used to endorse or promote products
+ derived from this software without prior written permission. For
+ written permission, please contact <license AT jdom DOT org>.
+
+ 4. Products derived from this software may not be called "JDOM", nor
+ may "JDOM" appear in their name, without prior written permission
+ from the JDOM Project Management <pm AT jdom DOT org>.
+
+ In addition, we request (but do not require) that you include in the
+ end-user documentation provided with the redistribution and/or in the
+ software itself an acknowledgement equivalent to the following:
+ "This product includes software developed by the
+ JDOM Project (http://www.jdom.org/)."
+ Alternatively, the acknowledgment may be graphical using the logos
+ available at http://www.jdom.org/images/logos.
+
+ THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED
+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL THE JDOM AUTHORS OR THE PROJECT
+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ SUCH DAMAGE.
+
+ This software consists of voluntary contributions made by many
+ individuals on behalf of the JDOM Project and was originally
+ created by Jason Hunter <jhunter AT jdom DOT org> and
+ Brett McLaughlin <brett AT jdom DOT org>. For more information on
+ the JDOM Project, please see <http://www.jdom.org/>.
+
+ */
+
diff --git a/distribution/src/main/licenses/JGOODIES_LICENSE.txt b/distribution/src/main/licenses/JGOODIES_LICENSE.txt
new file mode 100644
index 0000000..2988562
--- /dev/null
+++ b/distribution/src/main/licenses/JGOODIES_LICENSE.txt
@@ -0,0 +1,31 @@
+
+ The BSD License for the JGoodies Looks
+ ======================================
+
+Copyright (c) 2001-2004 JGoodies Karsten Lentzsch. All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+ o Redistributions of source code must retain the above copyright notice,
+ this list of conditions and the following disclaimer.
+
+ o Redistributions in binary form must reproduce the above copyright notice,
+ this list of conditions and the following disclaimer in the documentation
+ and/or other materials provided with the distribution.
+
+ o Neither the name of JGoodies Karsten Lentzsch nor the names of
+ its contributors may be used to endorse or promote products derived
+ from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
+EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
diff --git a/distribution/src/main/licenses/README.doc b/distribution/src/main/licenses/README.doc
new file mode 100644
index 0000000..35b70c7
Binary files /dev/null and b/distribution/src/main/licenses/README.doc differ
diff --git a/distribution/src/main/sampleData/Apoptosis_BioPAX.xml b/distribution/src/main/sampleData/Apoptosis_BioPAX.xml
new file mode 100644
index 0000000..750bff8
--- /dev/null
+++ b/distribution/src/main/sampleData/Apoptosis_BioPAX.xml
@@ -0,0 +1,4999 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns="http://www.biopax.org/release/biopax-level2.owl#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:owl="http://www.w3.org/2002/07/owl#" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xml:base="http://www.biopax.org/release/biopax-level2.owl#">
+ <owl:Ontology rdf:about="">
+ <owl:imports rdf:resource="http://www.biopax.org/Downloads/Level2v0.9/biopax-level2.owl" />
+ <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BioPAX pathway converted from "Apoptosis" in the Reactome database.</rdfs:comment>
+ </owl:Ontology>
+ <pathway rdf:ID="Apoptosis">
+ <PATHWAY-COMPONENTS rdf:resource="#Extrinsic_Pathway_for_ApoptosisStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#Activation_of__Effector_CaspasesStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#Apoptotic_execution__phaseStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#Intrinsic_Pathway_for_ApoptosisStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#Activation__myristolyation_of_BID_and_translocation_to_mitochondriaStep" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Apoptosis</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Apoptosis</SHORT-NAME>
+ <XREF rdf:resource="#Reactome109581" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Apoptosis is a distinct form of cell death that is functionally and morphologically different from necrosis. Nuclear chromatin condensation, cytoplasmic shrinking, dilated endoplasmic reticulum, and membrane blebbing characterize apoptosis in general. Mitochondria remain morphologically unchanged. In 1972 Kerr et al introduced the concept of apoptosis as a distinct form of "cell-death", and the mechanisms of various apop [...]
+ <EVIDENCE rdf:resource="#Summation_109577" />
+ <XREF rdf:resource="#apoptosis" />
+ <CELLULAR-LOCATION rdf:resource="#cell" />
+ </pathway>
+ <pathway rdf:ID="Extrinsic_Pathway_for_Apoptosis">
+ <PATHWAY-COMPONENTS rdf:resource="#Caspase_8_is_formed_from_procaspase_8Step" />
+ <PATHWAY-COMPONENTS rdf:resource="#Death_Receptor__SignallingStep" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Extrinsic Pathway for Apoptosis</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Extrinsic Pathway for Apoptosis</SHORT-NAME>
+ <XREF rdf:resource="#Reactome109607" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Known as the "death receptor pathway" the extrinsic or caspase 8/10 dependent pathway is activated by ligand binding. The "death receptors" are specialized cell-surface receptors including Fas/CD95, tumor necrosis factor-alpha (TNF-alpha) receptor 1, and two receptors, DR4 and DR5, that bind to the TNF-alpha related apoptosis-inducing ligand (TRAIL). The extrinsic and intrinsic pathways unite in the activation of Caspase [...]
+ <EVIDENCE rdf:resource="#Summation_139959" />
+ <XREF rdf:resource="#induction_of_apoptosis_by_extracellular_signals" />
+ <CELLULAR-LOCATION rdf:resource="#cell" />
+ </pathway>
+ <pathway rdf:ID="Death_Receptor__Signalling">
+ <PATHWAY-COMPONENTS rdf:resource="#FasL__CD95L_signalingStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#TRAIL__signalingStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#TNF_signalingStep" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Death Receptor Signalling</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Death Receptor Signalling</SHORT-NAME>
+ <XREF rdf:resource="#Reactome73887" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The death receptors, all cell-surface receptors, begin the process of caspase activation. The common feature of these type 1 transmembrane proteins is the "death-domain" a conserved cytoplasmic motif found on all of the three receptors (FAS/CD95, TNF-receptor, and TRAIL-receptor) that binds the Fas-associated protein with death domain (FADD)</COMMENT>
+ <EVIDENCE rdf:resource="#Summation_139958" />
+ <XREF rdf:resource="#induction_of_apoptosis_by_extracellular_signals" />
+ <CELLULAR-LOCATION rdf:resource="#cell" />
+ </pathway>
+ <pathway rdf:ID="FasL__CD95L_signaling">
+ <PATHWAY-COMPONENTS rdf:resource="#FasL_Fas_binds_FADDStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#FASL_binds_FAS_ReceptorStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#FASL_FAS_Receptor_Trimer_FADD_complex_binds_pro_Caspase_10Step" />
+ <PATHWAY-COMPONENTS rdf:resource="#FASL_FAS_Receptor_Trimer_FADD_complex_binds_pro_Caspase_8Step" />
+ <PATHWAY-COMPONENTS rdf:resource="#Trimerization_of_the_FASL_FAS_receptor_complexStep" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FasL/ CD95L signaling</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FasL/ CD95L signaling</SHORT-NAME>
+ <XREF rdf:resource="#Reactome75157" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The Fas family of cell surface receptors initiate the apototic pathway through interaction with the external ligand, FasL. The cytoplasmic domain of Fas interacts with a number of molecules in the transduction of the external signal to the cytoplasmic side of the cell membrane. The most notable cytoplasmic domain is the Death Domain (DD) that is involved in recruiting the FAS-associating death domain-containing protein [...]
+ <EVIDENCE rdf:resource="#Summation_140481" />
+ <XREF rdf:resource="#Pubmed_11048727" />
+ <XREF rdf:resource="#induction_of_apoptosis_by_extracellular_signals" />
+ <CELLULAR-LOCATION rdf:resource="#cell" />
+ </pathway>
+ <biochemicalReaction rdf:ID="FASL_binds_FAS_Receptor">
+ <LEFT rdf:resource="#FASL__extracellular_region_" />
+ <LEFT rdf:resource="#FAS_Receptor__plasma_membrane_" />
+ <RIGHT rdf:resource="#FASL_FAS_Receptor_monomer__plasma_membrane_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FASL binds FAS Receptor</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FASL binds FAS Receptor</SHORT-NAME>
+ <XREF rdf:resource="#Reactome75244" />
+ <XREF rdf:resource="#Pubmed_7530336" />
+ <XREF rdf:resource="#induction_of_apoptosis_by_extracellular_signals" />
+ </biochemicalReaction>
+ <proteinParticipant rdf:ID="FASL__extracellular_region_">
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P48023_1_Tumor_necrosis_factor_ligand_superfamily_member_6__FAS_antigen_ligand___Apoptosis_antigen_ligand___APTL___CD178_antigen_" />
+ </proteinParticipant>
+ <openControlledVocabulary rdf:ID="extracellular_region">
+ <TERM rdf:datatype="http://www.w3.org/2001/XMLSchema#string">extracellular region</TERM>
+ <XREF rdf:resource="#GO_0005576" />
+ </openControlledVocabulary>
+ <xref rdf:ID="GO_0005576">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GO</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0005576</ID>
+ </xref>
+ <protein rdf:ID="UniProt_P48023_1_Tumor_necrosis_factor_ligand_superfamily_member_6__FAS_antigen_ligand___Apoptosis_antigen_ligand___APTL___CD178_antigen_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P48023-1 Tumor necrosis factor ligand superfamily member 6 (FAS antigen ligand) (Apoptosis antigen ligand) (APTL) (CD178 antigen)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FASL</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TNFSF6</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">APT1LG1</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P48023" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Cytokine that binds to TNFRSF6/FAS, a receptor that transduces the apoptotic signal into cells. May be involved in cytotoxic T cell mediated apoptosis and in T cell development. TNFRSF6/FAS-mediated apoptosis may have a role in the induction of peripheral tolerance, in the antigen-stimulated suicide of mature T cells, or both. Binding to the decoy receptor TNFRSF6B/DcR3 modulates its effects. SUBUNIT: Homotrime [...]
+ </protein>
+ <bioSource rdf:ID="Homo_sapiens">
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Homo sapiens</NAME>
+ <TAXON-XREF rdf:resource="#NCBI_taxonomy_9606" />
+ </bioSource>
+ <xref rdf:ID="NCBI_taxonomy_9606">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">NCBI_taxonomy</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">9606</ID>
+ </xref>
+ <unificationXref rdf:ID="UniProt_P48023">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P48023</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="FAS_Receptor__plasma_membrane_">
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P25445_1_Tumor_necrosis_factor_receptor_superfamily_member_6_precursor__FASL_receptor___Apoptosis_mediating_surface_antigen_FAS___Apo_1_antigen___CD95_antigen_" />
+ </proteinParticipant>
+ <openControlledVocabulary rdf:ID="plasma_membrane">
+ <TERM rdf:datatype="http://www.w3.org/2001/XMLSchema#string">plasma membrane</TERM>
+ <XREF rdf:resource="#GO_0005886" />
+ </openControlledVocabulary>
+ <xref rdf:ID="GO_0005886">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GO</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0005886</ID>
+ </xref>
+ <protein rdf:ID="UniProt_P25445_1_Tumor_necrosis_factor_receptor_superfamily_member_6_precursor__FASL_receptor___Apoptosis_mediating_surface_antigen_FAS___Apo_1_antigen___CD95_antigen_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P25445-1 Tumor necrosis factor receptor superfamily member 6 precursor (FASL receptor) (Apoptosis-mediating surface antigen FAS) (Apo-1 antigen) (CD95 antigen)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FAS</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TNFRSF6</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">APT1</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FAS1</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P25445" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Receptor for TNFSF6/FASL. The adapter molecule FADD recruits caspase-8 to the activated receptor. The resulting death- inducing signaling complex (DISC) performs caspase-8 proteolytic activation which initiates the subsequent cascade of caspases (aspartate-specific cysteine proteases) mediating apoptosis. FAS- mediated apoptosis may have a role in the induction of peripheral tolerance, in the antigen-stimulated [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_P25445">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P25445</ID>
+ </unificationXref>
+ <complexParticipant rdf:ID="FASL_FAS_Receptor_monomer__plasma_membrane_">
+ <CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#FASL_FAS_Receptor_monomer__plasma_membrane_1" />
+ </complexParticipant>
+ <complex rdf:ID="FASL_FAS_Receptor_monomer__plasma_membrane_1">
+ <COMPONENTS rdf:resource="#FASL__extracellular_region_1" />
+ <COMPONENTS rdf:resource="#FAS_Receptor__plasma_membrane_1" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FASL:FAS Receptor monomer [plasma membrane]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FASL:FAS Receptor monomer</SHORT-NAME>
+ </complex>
+ <proteinParticipant rdf:ID="FASL__extracellular_region_1">
+ <CELLULAR-LOCATION rdf:resource="#extracellular_region" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P48023_1_Tumor_necrosis_factor_ligand_superfamily_member_6__FAS_antigen_ligand___Apoptosis_antigen_ligand___APTL___CD178_antigen_" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="FAS_Receptor__plasma_membrane_1">
+ <CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P25445_1_Tumor_necrosis_factor_receptor_superfamily_member_6_precursor__FASL_receptor___Apoptosis_mediating_surface_antigen_FAS___Apo_1_antigen___CD95_antigen_" />
+ </proteinParticipant>
+ <unificationXref rdf:ID="Reactome75244">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">75244</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <publicationXref rdf:ID="Pubmed_7530336">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">7530336</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1995</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cell-autonomous Fas (CD95)/Fas-ligand interaction mediates activation-induced apoptosis in T-cell hybridomas</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Brunner, T</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mogil, RJ</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">LaFace, D</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Yoo, NJ</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mahboubi, A</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Echeverri, F</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Martin, SJ</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Force, WR</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Lynch, DH</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Ware, CF</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Nature 373:441-4</SOURCE>
+ </publicationXref>
+ <relationshipXref rdf:ID="induction_of_apoptosis_by_extracellular_signals">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GO</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0008624</ID>
+ </relationshipXref>
+ <openControlledVocabulary rdf:ID="cell">
+ <TERM rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cell</TERM>
+ <XREF rdf:resource="#GO_0005623" />
+ </openControlledVocabulary>
+ <xref rdf:ID="GO_0005623">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GO</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0005623</ID>
+ </xref>
+ <pathwayStep rdf:ID="FASL_binds_FAS_ReceptorStep">
+ <STEP-INTERACTIONS rdf:resource="#FASL_binds_FAS_Receptor" />
+ <NEXT-STEP rdf:resource="#Trimerization_of_the_FASL_FAS_receptor_complexStep" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="Trimerization_of_the_FASL_FAS_receptor_complex">
+ <LEFT rdf:resource="#FASL_FAS_Receptor_monomer__plasma_membrane_2" />
+ <RIGHT rdf:resource="#FASL_FAS_Receptor_Trimer__plasma_membrane_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Trimerization of the FASL:FAS receptor complex</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Trimerization of the FASL:FAS receptor complex</SHORT-NAME>
+ <XREF rdf:resource="#Reactome71050" />
+ <XREF rdf:resource="#Pubmed_8521815" />
+ <CELLULAR-LOCATION rdf:resource="#cell" />
+ </biochemicalReaction>
+ <complexParticipant rdf:ID="FASL_FAS_Receptor_monomer__plasma_membrane_2">
+ <CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#FASL_FAS_Receptor_monomer__plasma_membrane_1" />
+ </complexParticipant>
+ <complexParticipant rdf:ID="FASL_FAS_Receptor_Trimer__plasma_membrane_">
+ <CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#FASL_FAS_Receptor_Trimer__plasma_membrane_1" />
+ </complexParticipant>
+ <complex rdf:ID="FASL_FAS_Receptor_Trimer__plasma_membrane_1">
+ <COMPONENTS rdf:resource="#FASL_FAS_Receptor_monomer__plasma_membrane_3" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FASL:FAS Receptor Trimer [plasma membrane]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FASL:FAS Receptor Trimer</SHORT-NAME>
+ </complex>
+ <complexParticipant rdf:ID="FASL_FAS_Receptor_monomer__plasma_membrane_3">
+ <CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#FASL_FAS_Receptor_monomer__plasma_membrane_1" />
+ <STOICHIOMETRIC-COEFFICIENT rdf:datatype="http://www.w3.org/2001/XMLSchema#int">3</STOICHIOMETRIC-COEFFICIENT>
+ </complexParticipant>
+ <unificationXref rdf:ID="Reactome71050">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">71050</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <publicationXref rdf:ID="Pubmed_8521815">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">8521815</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1995</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cytotoxicity-dependent APO-1 (Fas/CD95)-associated proteins form a death-inducing signaling complex (DISC) with the receptor</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Kischkel, FC</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Hellbardt, S</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Behrmann, I</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Germer, M</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pawlita, M</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Krammer, PH</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Peter, ME</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">EMBO J 14:5579-88</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="Trimerization_of_the_FASL_FAS_receptor_complexStep">
+ <STEP-INTERACTIONS rdf:resource="#Trimerization_of_the_FASL_FAS_receptor_complex" />
+ <NEXT-STEP rdf:resource="#FasL_Fas_binds_FADDStep" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="FasL_Fas_binds_FADD">
+ <LEFT rdf:resource="#FASL_FAS_Receptor_Trimer__plasma_membrane_2" />
+ <LEFT rdf:resource="#FADD__cytosol_" />
+ <RIGHT rdf:resource="#FASL_FAS_Receptor_Trimer_FADD_complex__plasma_membrane_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FasL:Fas binds FADD</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FasL:Fas binds FADD</SHORT-NAME>
+ <XREF rdf:resource="#Reactome83650" />
+ <XREF rdf:resource="#Pubmed_7536190" />
+ <CELLULAR-LOCATION rdf:resource="#cell" />
+ </biochemicalReaction>
+ <complexParticipant rdf:ID="FASL_FAS_Receptor_Trimer__plasma_membrane_2">
+ <CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#FASL_FAS_Receptor_Trimer__plasma_membrane_1" />
+ </complexParticipant>
+ <proteinParticipant rdf:ID="FADD__cytosol_">
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q13158_FADD_protein__FAS_associating_death_domain_containing_protein___Mediator_of_receptor_induced_toxicity_" />
+ </proteinParticipant>
+ <openControlledVocabulary rdf:ID="cytosol">
+ <TERM rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cytosol</TERM>
+ <XREF rdf:resource="#GO_0005829" />
+ </openControlledVocabulary>
+ <xref rdf:ID="GO_0005829">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GO</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0005829</ID>
+ </xref>
+ <protein rdf:ID="UniProt_Q13158_FADD_protein__FAS_associating_death_domain_containing_protein___Mediator_of_receptor_induced_toxicity_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:Q13158 FADD protein (FAS-associating death domain-containing protein) (Mediator of receptor induced toxicity)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">MORT1</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FADD</SYNONYMS>
+ <XREF rdf:resource="#UniProt_Q13158" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Apoptotic adaptor molecule that recruits caspase-8 or caspase-10 to the activated Fas (CD95) or TNFR-1 receptors. The resulting aggregate called the death-inducing signaling complex (DISC) performs caspase-8 proteolytic activation. Active caspase-8 initiates the subsequent cascade of caspases (aspartate-specific cysteine proteases) mediating apoptosis. SUBUNIT: Interacts with CFLAR, PEA15 and MBD4. TISSUE SPECI [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_Q13158">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Q13158</ID>
+ </unificationXref>
+ <complexParticipant rdf:ID="FASL_FAS_Receptor_Trimer_FADD_complex__plasma_membrane_">
+ <CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#FASL_FAS_Receptor_Trimer_FADD_complex__plasma_membrane_1" />
+ </complexParticipant>
+ <complex rdf:ID="FASL_FAS_Receptor_Trimer_FADD_complex__plasma_membrane_1">
+ <COMPONENTS rdf:resource="#FASL_FAS_Receptor_Trimer__plasma_membrane_3" />
+ <COMPONENTS rdf:resource="#FADD__cytosol_1" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FASL:FAS Receptor Trimer:FADD complex [plasma membrane]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FASL:FAS Receptor Trimer:FADD complex</SHORT-NAME>
+ </complex>
+ <complexParticipant rdf:ID="FASL_FAS_Receptor_Trimer__plasma_membrane_3">
+ <CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#FASL_FAS_Receptor_Trimer__plasma_membrane_1" />
+ </complexParticipant>
+ <proteinParticipant rdf:ID="FADD__cytosol_1">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q13158_FADD_protein__FAS_associating_death_domain_containing_protein___Mediator_of_receptor_induced_toxicity_" />
+ </proteinParticipant>
+ <unificationXref rdf:ID="Reactome83650">
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+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <publicationXref rdf:ID="Pubmed_7536190">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">7536190</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1995</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A novel protein that interacts with the death domain of Fas/APO1 contains a sequence motif related to the death domain</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Boldin, MP</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Varfolomeev, EE</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pancer, Z</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mett, IL</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Camonis, JH</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Wallach, D</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Biol Chem 270:7795-8</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="FasL_Fas_binds_FADDStep">
+ <STEP-INTERACTIONS rdf:resource="#FasL_Fas_binds_FADD" />
+ <NEXT-STEP rdf:resource="#FASL_FAS_Receptor_Trimer_FADD_complex_binds_pro_Caspase_8Step" />
+ <NEXT-STEP rdf:resource="#FASL_FAS_Receptor_Trimer_FADD_complex_binds_pro_Caspase_10Step" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="FASL_FAS_Receptor_Trimer_FADD_complex_binds_pro_Caspase_8">
+ <LEFT rdf:resource="#FASL_FAS_Receptor_Trimer_FADD_complex__plasma_membrane_2" />
+ <LEFT rdf:resource="#Caspase_8_precursor___cytosol_" />
+ <RIGHT rdf:resource="#FASL_FAS_Receptor_Trimer_FADD_pro_Caspase_8_DISC__plasma_membrane_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FASL:FAS Receptor Trimer:FADD complex binds pro-Caspase-8</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FASL:FAS Receptor Trimer:FADD complex binds pro-Caspase-8</SHORT-NAME>
+ <XREF rdf:resource="#Reactome83586" />
+ <XREF rdf:resource="#Pubmed_8681376" />
+ <CELLULAR-LOCATION rdf:resource="#cell" />
+ </biochemicalReaction>
+ <complexParticipant rdf:ID="FASL_FAS_Receptor_Trimer_FADD_complex__plasma_membrane_2">
+ <CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#FASL_FAS_Receptor_Trimer_FADD_complex__plasma_membrane_1" />
+ </complexParticipant>
+ <proteinParticipant rdf:ID="Caspase_8_precursor___cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q14790_1_Caspase_8_precursor__EC_3_4_22_____CASP_8___ICE_like_apoptotic_protease_5___MORT1_associated_CED_3_homolog___MACH___FADD_homologous_ICE_CED_3_like_protease___FADD_like_ICE___FLICE___Apoptotic_cysteine_protease___Apoptotic_protease_Mch_5___CAP4_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_Q14790_1_Caspase_8_precursor__EC_3_4_22_____CASP_8___ICE_like_apoptotic_protease_5___MORT1_associated_CED_3_homolog___MACH___FADD_homologous_ICE_CED_3_like_protease___FADD_like_ICE___FLICE___Apoptotic_cysteine_protease___Apoptotic_protease_Mch_5___CAP4_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:Q14790-1 Caspase-8 precursor (EC 3.4.22.-) (CASP-8) (ICE-like apoptotic protease 5) (MORT1-associated CED-3 homolog) (MACH) (FADD-homologous ICE/CED-3-like protease) (FADD-like ICE) (FLICE) (Apoptotic cysteine protease) (Apoptotic protease Mch-5) (CAP4)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CASP8</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">MCH5</SYNONYMS>
+ <XREF rdf:resource="#UniProt_Q14790" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Most upstream protease of the activation cascade of caspases responsible for the TNFRSF6/FAS mediated and TNFRSF1A induced cell death. Binding to the adapter molecule FADD recruits it to either receptor. The resulting aggregate called death- inducing signaling complex (DISC) performs CASP8 proteolytic activation. The active dimeric enzyme is then liberated from the DISC and free to activate downstream apoptotic [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_Q14790">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Q14790</ID>
+ </unificationXref>
+ <complexParticipant rdf:ID="FASL_FAS_Receptor_Trimer_FADD_pro_Caspase_8_DISC__plasma_membrane_">
+ <CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#FASL_FAS_Receptor_Trimer_FADD_pro_Caspase_8_DISC__plasma_membrane_1" />
+ </complexParticipant>
+ <complex rdf:ID="FASL_FAS_Receptor_Trimer_FADD_pro_Caspase_8_DISC__plasma_membrane_1">
+ <COMPONENTS rdf:resource="#FASL_FAS_Receptor_Trimer_FADD_complex__plasma_membrane_3" />
+ <COMPONENTS rdf:resource="#Caspase_8_precursor___cytosol_1" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FASL:FAS Receptor Trimer:FADD:pro-Caspase-8 DISC [plasma membrane]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FASL:FAS Receptor Trimer:FADD:pro-Caspase-8 DISC</SHORT-NAME>
+ </complex>
+ <complexParticipant rdf:ID="FASL_FAS_Receptor_Trimer_FADD_complex__plasma_membrane_3">
+ <CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#FASL_FAS_Receptor_Trimer_FADD_complex__plasma_membrane_1" />
+ </complexParticipant>
+ <proteinParticipant rdf:ID="Caspase_8_precursor___cytosol_1">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q14790_1_Caspase_8_precursor__EC_3_4_22_____CASP_8___ICE_like_apoptotic_protease_5___MORT1_associated_CED_3_homolog___MACH___FADD_homologous_ICE_CED_3_like_protease___FADD_like_ICE___FLICE___Apoptotic_cysteine_protease___Apoptotic_protease_Mch_5___CAP4_" />
+ </proteinParticipant>
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+ </unificationXref>
+ <publicationXref rdf:ID="Pubmed_8681376">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">8681376</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1996</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Involvement of MACH, a novel MORT1/FADD-interacting protease, in Fas/APO-1- and TNF receptor-induced cell death</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Boldin, MP</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Goncharov, TM</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Goltsev, YV</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Wallach, D</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cell 85:803-15</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="FASL_FAS_Receptor_Trimer_FADD_complex_binds_pro_Caspase_8Step">
+ <STEP-INTERACTIONS rdf:resource="#FASL_FAS_Receptor_Trimer_FADD_complex_binds_pro_Caspase_8" />
+ <NEXT-STEP rdf:resource="#FAS_Mediated_Activation_of_Pro_caspase_8Step" />
+ <NEXT-STEP rdf:resource="#TRAIL_Mediated_Activation_of_Pro_caspase_8Step" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="FASL_FAS_Receptor_Trimer_FADD_complex_binds_pro_Caspase_10">
+ <LEFT rdf:resource="#FASL_FAS_Receptor_Trimer_FADD_complex__plasma_membrane_4" />
+ <LEFT rdf:resource="#Caspase_10_precursor___plasma_membrane_" />
+ <RIGHT rdf:resource="#FASL_FAS_Receptor_Trimer_FADD_pro_Caspase_10__plasma_membrane_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FASL:FAS Receptor Trimer:FADD complex binds pro-Caspase-10</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FASL:FAS Receptor Trimer:FADD complex binds pro-Caspase-10</SHORT-NAME>
+ <XREF rdf:resource="#Reactome141310" />
+ <XREF rdf:resource="#Pubmed_11717445" />
+ <XREF rdf:resource="#Pubmed_12198154" />
+ <CELLULAR-LOCATION rdf:resource="#cell" />
+ </biochemicalReaction>
+ <complexParticipant rdf:ID="FASL_FAS_Receptor_Trimer_FADD_complex__plasma_membrane_4">
+ <CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#FASL_FAS_Receptor_Trimer_FADD_complex__plasma_membrane_1" />
+ </complexParticipant>
+ <proteinParticipant rdf:ID="Caspase_10_precursor___plasma_membrane_">
+ <CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q92851_1_Caspase_10_precursor__EC_3_4_22_____CASP_10___ICE_like_apoptotic_protease_4___Apoptotic_protease_Mch_4___FAS_associated_death_domain_protein_interleukin_1B_converting_enzyme_2___FLICE2_" />
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+ <protein rdf:ID="UniProt_Q92851_1_Caspase_10_precursor__EC_3_4_22_____CASP_10___ICE_like_apoptotic_protease_4___Apoptotic_protease_Mch_4___FAS_associated_death_domain_protein_interleukin_1B_converting_enzyme_2___FLICE2_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:Q92851-1 Caspase-10 precursor (EC 3.4.22.-) (CASP-10) (ICE-like apoptotic protease 4) (Apoptotic protease Mch-4) (FAS-associated death domain protein interleukin-1B-converting enzyme 2) (FLICE2)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">MCH4</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CASP10</SYNONYMS>
+ <XREF rdf:resource="#UniProt_Q92851" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Involved in the activation cascade of caspases responsible for apoptosis execution. Recruited to both Fas- and TNFR-1 receptors in a FADD dependent manner. May participate in the granzyme B apoptotic pathways. Cleaves and activates caspase- 3, -4, -6, -7, -8, and -9. Hydrolyzes the small- molecule substrates, Tyr-Val-Ala-Asp-|-AMC and Asp-Glu-Val-Asp-|-AMC. FUNCTION: Isoform C is proteolytically inactive. SUBUN [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_Q92851">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Q92851</ID>
+ </unificationXref>
+ <complexParticipant rdf:ID="FASL_FAS_Receptor_Trimer_FADD_pro_Caspase_10__plasma_membrane_">
+ <CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#FASL_FAS_Receptor_Trimer_FADD_pro_Caspase_10__plasma_membrane_1" />
+ </complexParticipant>
+ <complex rdf:ID="FASL_FAS_Receptor_Trimer_FADD_pro_Caspase_10__plasma_membrane_1">
+ <COMPONENTS rdf:resource="#FASL_FAS_Receptor_Trimer_FADD_complex__plasma_membrane_5" />
+ <COMPONENTS rdf:resource="#Caspase_10_precursor___plasma_membrane_1" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FASL:FAS Receptor Trimer:FADD:pro-Caspase-10 [plasma membrane]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FASL:FAS Receptor Trimer:FADD:pro-Caspase-10</SHORT-NAME>
+ </complex>
+ <complexParticipant rdf:ID="FASL_FAS_Receptor_Trimer_FADD_complex__plasma_membrane_5">
+ <CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#FASL_FAS_Receptor_Trimer_FADD_complex__plasma_membrane_1" />
+ </complexParticipant>
+ <proteinParticipant rdf:ID="Caspase_10_precursor___plasma_membrane_1">
+ <CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q92851_1_Caspase_10_precursor__EC_3_4_22_____CASP_10___ICE_like_apoptotic_protease_4___Apoptotic_protease_Mch_4___FAS_associated_death_domain_protein_interleukin_1B_converting_enzyme_2___FLICE2_" />
+ </proteinParticipant>
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+ </unificationXref>
+ <publicationXref rdf:ID="Pubmed_11717445">
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+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2001</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Caspase-10 is an initiator caspase in death receptor signaling</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Wang, J</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Chun, HJ</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Wong, W</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Spencer, DM</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Lenardo, MJ</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Proc Natl Acad Sci U S A 98:13884-8</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_12198154">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">12198154</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2002</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Caspase-10 is recruited to and activated at the native TRAIL and CD95 death-inducing signalling complexes in a FADD-dependent manner but can not functionally substitute caspase-8</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Sprick, MR</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Rieser, E</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Stahl, H</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Grosse-Wilde, A</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Weigand, MA</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Walczak, H</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">EMBO J 21:4520-30</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="FASL_FAS_Receptor_Trimer_FADD_complex_binds_pro_Caspase_10Step">
+ <STEP-INTERACTIONS rdf:resource="#FASL_FAS_Receptor_Trimer_FADD_complex_binds_pro_Caspase_10" />
+ </pathwayStep>
+ <unificationXref rdf:ID="Reactome75157">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">75157</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <evidence rdf:ID="Summation_140481">
+ <XREF rdf:resource="#Pubmed_1713127" />
+ <XREF rdf:resource="#Pubmed_2469768" />
+ <XREF rdf:resource="#Pubmed_7538907" />
+ </evidence>
+ <publicationXref rdf:ID="Pubmed_1713127">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">1713127</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1991</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The polypeptide encoded by the cDNA for human cell surface antigen Fas can mediate apoptosis</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Itoh, N</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Yonehara, S</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Ishii, A</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Yonehara, M</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mizushima, S</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Sameshima, M</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Hase, A</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Seto, Y</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Nagata, S</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cell 66:233-43</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_2469768">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2469768</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1989</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A cell-killing monoclonal antibody (anti-Fas) to a cell surface antigen co-downregulated with the receptor of tumor necrosis factor</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Yonehara, S</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Ishii, A</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Yonehara, M</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Exp Med 169:1747-56</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_7538907">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">7538907</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1995</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FADD, a novel death domain-containing protein, interacts with the death domain of Fas and initiates apoptosis</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Chinnaiyan, AM</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">O'Rourke, K</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Tewari, M</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Dixit, VM</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cell 81:505-12</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_11048727">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">11048727</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2000</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The biochemistry of apoptosis.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Hengartner, MO</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Nature 407:770-6</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="FasL__CD95L_signalingStep">
+ <STEP-INTERACTIONS rdf:resource="#FasL__CD95L_signaling" />
+ </pathwayStep>
+ <pathway rdf:ID="TNF_signaling">
+ <PATHWAY-COMPONENTS rdf:resource="#TRADD_TRAF2_RIP1_complex_binds_FADDStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#TRADD_TRAF2_RIP1_complex_dissociates_from_the_TNF_alpha_TNF_R1_complex_Step" />
+ <PATHWAY-COMPONENTS rdf:resource="#TNF_Binds_TNF_R1Step" />
+ <PATHWAY-COMPONENTS rdf:resource="#TRADD_TRAF2_RIP1_FADD_complex_binds_Pro_Caspase_8__Step" />
+ <PATHWAY-COMPONENTS rdf:resource="#TNF_TNF_R1_binds_TRADD__TRAF2_and_RIP_ComplexStep" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TNF signaling</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TNF signaling</SHORT-NAME>
+ <XREF rdf:resource="#Reactome75893" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The Tumor Necrosis Factor alpha (TNF-alpha) mediated apoptosis pathway has been implicated in the pathogenesis of a number of diseases including sepsis, diabetes, cancer, osteoporosis, multiple sclerosis, rheumatoid arthritis, and inflammatory bowel diseases. The TNF signaling network provides extensive cross talk between the apoptotic pathway, and the other NF-B, and JNK pathways that also emanate from TNF-R.</COMMENT>
+ <EVIDENCE rdf:resource="#Summation_140942" />
+ <CELLULAR-LOCATION rdf:resource="#cell" />
+ </pathway>
+ <biochemicalReaction rdf:ID="TNF_Binds_TNF_R1">
+ <LEFT rdf:resource="#TNF_alpha__plasma_membrane_" />
+ <LEFT rdf:resource="#TNF_RI__plasma_membrane_" />
+ <RIGHT rdf:resource="#TNF_alpha_TNF_R1_complex__plasma_membrane_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TNF Binds TNF-R1</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TNF Binds TNF-R1</SHORT-NAME>
+ <XREF rdf:resource="#Reactome83660" />
+ <XREF rdf:resource="#Pubmed_2848815" />
+ <CELLULAR-LOCATION rdf:resource="#cell" />
+ </biochemicalReaction>
+ <proteinParticipant rdf:ID="TNF_alpha__plasma_membrane_">
+ <CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P01375_Tumor_necrosis_factor_precursor__TNF_alpha___Tumor_necrosis_factor_ligand_superfamily_member_2___TNF_a___Cachectin_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_P01375_Tumor_necrosis_factor_precursor__TNF_alpha___Tumor_necrosis_factor_ligand_superfamily_member_2___TNF_a___Cachectin_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P01375 Tumor necrosis factor precursor (TNF-alpha) (Tumor necrosis factor ligand superfamily member 2) (TNF-a) (Cachectin)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TNF</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TNFA</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TNFSF2</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P01375" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Cytokine that binds to TNFRSF1A/TNFR1 and TNFRSF1B/TNFBR. It is mainly secreted by macrophages and can induce cell death of certain tumor cell lines. It is potent pyrogen causing fever by direct action or by stimulation of interleukin 1 secretion and is implicated in the induction of cachexia, Under certain conditions it can stimulate cell proliferation and induce cell differentiation. SUBUNIT: Homotrimer. SUBC [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_P01375">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P01375</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="TNF_RI__plasma_membrane_">
+ <CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P19438_Tumor_necrosis_factor_receptor_superfamily_member_1A_precursor__p60___TNF_R1___TNF_RI___p55___CD120a___Contains__Tumor_necrosis_factor_binding_protein_1__TBPI__" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_P19438_Tumor_necrosis_factor_receptor_superfamily_member_1A_precursor__p60___TNF_R1___TNF_RI___p55___CD120a___Contains__Tumor_necrosis_factor_binding_protein_1__TBPI__">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P19438 Tumor necrosis factor receptor superfamily member 1A precursor (p60) (TNF-R1) (TNF-RI) (p55) (CD120a) [Contains: Tumor necrosis factor binding protein 1 (TBPI)]</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TNFRSF1A</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TNFR1</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TNFAR</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P19438" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Receptor for TNFSF2/TNF-alpha and homotrimeric TNFSF1/lymphotoxin-alpha. The adaptor molecule FADD recruits caspase-8 to the activated receptor. The resulting death-inducing signaling complex (DISC) performs caspase-8 proteolytic activation which initiates the subsequent cascade of caspases (aspartate- specific cysteine proteases) mediating apoptosis. Contributes to the induction of noncytocidal TNF effects inc [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_P19438">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P19438</ID>
+ </unificationXref>
+ <complexParticipant rdf:ID="TNF_alpha_TNF_R1_complex__plasma_membrane_">
+ <CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#TNF_alpha_TNF_R1_complex__plasma_membrane_1" />
+ </complexParticipant>
+ <complex rdf:ID="TNF_alpha_TNF_R1_complex__plasma_membrane_1">
+ <COMPONENTS rdf:resource="#TNF_alpha__plasma_membrane_1" />
+ <COMPONENTS rdf:resource="#TNF_RI__plasma_membrane_1" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TNF-alpha:TNF-R1 complex [plasma membrane]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TNF-alpha:TNF-R1 complex</SHORT-NAME>
+ </complex>
+ <proteinParticipant rdf:ID="TNF_alpha__plasma_membrane_1">
+ <CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P01375_Tumor_necrosis_factor_precursor__TNF_alpha___Tumor_necrosis_factor_ligand_superfamily_member_2___TNF_a___Cachectin_" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="TNF_RI__plasma_membrane_1">
+ <CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P19438_Tumor_necrosis_factor_receptor_superfamily_member_1A_precursor__p60___TNF_R1___TNF_RI___p55___CD120a___Contains__Tumor_necrosis_factor_binding_protein_1__TBPI__" />
+ </proteinParticipant>
+ <unificationXref rdf:ID="Reactome83660">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">83660</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <publicationXref rdf:ID="Pubmed_2848815">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2848815</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1988</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Human tumor necrosis factor-alpha receptor. Purification by immunoaffinity chromatography and initial characterization.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Stauber, GB</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Aiyer, RA</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Aggarwal, BB</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Biol Chem 263:19098-104</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="TNF_Binds_TNF_R1Step">
+ <STEP-INTERACTIONS rdf:resource="#TNF_Binds_TNF_R1" />
+ <NEXT-STEP rdf:resource="#TNF_TNF_R1_binds_TRADD__TRAF2_and_RIP_ComplexStep" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="TNF_TNF_R1_binds_TRADD__TRAF2_and_RIP_Complex">
+ <LEFT rdf:resource="#TNF_receptor_associated_factor_2__cytosol_" />
+ <LEFT rdf:resource="#RIP__cytosol_" />
+ <LEFT rdf:resource="#TNF_alpha_TNF_R1_complex__plasma_membrane_2" />
+ <LEFT rdf:resource="#Tumor_necrosis_factor_receptor_type_1_associated_DEATH_domain_protein__cytosol_" />
+ <RIGHT rdf:resource="#TNF_alpha_TNF_R1_TRAPP_RIP1_TRAF2_Complex__plasma_membrane_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TNF:TNF-R1 binds TRADD, TRAF2 and RIP Complex</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TNF:TNF-R1 binds TRADD, TRAF2 and RIP Complex</SHORT-NAME>
+ <XREF rdf:resource="#Reactome83656" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Once the TNF-aplha:TNF-R1:TRADD complex is formed the two TNF-alpha mediated pathways are possible. The variable is the recruitment of FADD to the larger complex formed by the TNF-aplha:TNF-R1 platform via the interaction of the Death Domains. The steps leading to the Jun, NF kappaB, or apoptotic pathways are rife with modulation.</COMMENT>
+ <EVIDENCE rdf:resource="#Summation_74302" />
+ <XREF rdf:resource="#Pubmed_7758105" />
+ <CELLULAR-LOCATION rdf:resource="#cell" />
+ </biochemicalReaction>
+ <proteinParticipant rdf:ID="TNF_receptor_associated_factor_2__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q12933_1_TNF_receptor_associated_factor_2__Tumor_necrosis_factor_type_2_receptor_associated_protein_3_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_Q12933_1_TNF_receptor_associated_factor_2__Tumor_necrosis_factor_type_2_receptor_associated_protein_3_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:Q12933-1 TNF receptor associated factor 2 (Tumor necrosis factor type 2 receptor associated protein 3)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRAP3</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRAF2</SYNONYMS>
+ <XREF rdf:resource="#UniProt_Q12933" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Adapter protein and signal transducer that links members of the tumor necrosis factor receptor family to different signaling pathways by association with the receptor cytoplasmic domain and kinases. Association to the receptor is also mediated by the interaction with TRADD. Mediates activation of NF-kappa-B and JNK and is involved in apoptosis. The TRAF1/TRAF2 complex recruits the apoptotic suppressors BIRC2 an [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_Q12933">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Q12933</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="RIP__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q13546_Receptor_interacting_serine_threonine_protein_kinase_2__EC_2_7_1_37___Serine_threonine_protein_kinase_RIP___Cell_death_protein_RIP___Receptor_interacting_protein_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_Q13546_Receptor_interacting_serine_threonine_protein_kinase_2__EC_2_7_1_37___Serine_threonine_protein_kinase_RIP___Cell_death_protein_RIP___Receptor_interacting_protein_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:Q13546 Receptor-interacting serine/threonine-protein kinase 2 (EC 2.7.1.37) (Serine/threonine-protein kinase RIP) (Cell death protein RIP) (Receptor interacting protein)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RIP</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RIPK1</SYNONYMS>
+ <XREF rdf:resource="#UniProt_Q13546" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Promotes apoptosis and activation of NF-kappa-B. Required for TNFRSF1A mediated activation of NF-kappa-B. CATALYTIC ACTIVITY: ATP + a protein = ADP + a phosphoprotein. SUBUNIT: Binds to the death domain of TNFRSF6 and TRADD. Is recruited by TRADD to TNFRSF1A in a TNF-dependent process. Binds RIPK3, UBCE7IP1, EGFR, IKBKG, TRAF1, TRAF2 and TRAF3. Interacts with BNLF1. SUBCELLULAR LOCATION: Cytoplasmic. PTM: Prote [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_Q13546">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Q13546</ID>
+ </unificationXref>
+ <complexParticipant rdf:ID="TNF_alpha_TNF_R1_complex__plasma_membrane_2">
+ <CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#TNF_alpha_TNF_R1_complex__plasma_membrane_1" />
+ </complexParticipant>
+ <proteinParticipant rdf:ID="Tumor_necrosis_factor_receptor_type_1_associated_DEATH_domain_protein__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q15628_Tumor_necrosis_factor_receptor_type_1_associated_DEATH_domain_protein__TNFR1_associated_DEATH_domain_protein___TNFRSF1A_associated_via_death_domain_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_Q15628_Tumor_necrosis_factor_receptor_type_1_associated_DEATH_domain_protein__TNFR1_associated_DEATH_domain_protein___TNFRSF1A_associated_via_death_domain_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:Q15628 Tumor necrosis factor receptor type 1 associated DEATH domain protein (TNFR1-associated DEATH domain protein) (TNFRSF1A-associated via death domain)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRADD</SYNONYMS>
+ <XREF rdf:resource="#UniProt_Q15628" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Adapter molecule for TNFRSF1A/TNFR1 that specifically associates with the cytoplasmic domain of activated TNFRSF1A/TNFR1 mediating its interaction with FADD. Overexpression of TRADD leads to two major TNF-induced responses, apoptosis and activation of NF-kappa-B. SUBUNIT: Heterodimer with TNFRSF1A/TNFR1. Binds to TRAF2. Interacts with TRAF1, FADD, RIPK1 and TRPC4AP (By similarity). TISSUE SPECIFICITY: Found in [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_Q15628">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Q15628</ID>
+ </unificationXref>
+ <complexParticipant rdf:ID="TNF_alpha_TNF_R1_TRAPP_RIP1_TRAF2_Complex__plasma_membrane_">
+ <CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#TNF_alpha_TNF_R1_TRAPP_RIP1_TRAF2_Complex__plasma_membrane_1" />
+ </complexParticipant>
+ <complex rdf:ID="TNF_alpha_TNF_R1_TRAPP_RIP1_TRAF2_Complex__plasma_membrane_1">
+ <COMPONENTS rdf:resource="#TNF_receptor_associated_factor_2__cytosol_1" />
+ <COMPONENTS rdf:resource="#RIP__cytosol_1" />
+ <COMPONENTS rdf:resource="#TNF_alpha_TNF_R1_complex__plasma_membrane_3" />
+ <COMPONENTS rdf:resource="#Tumor_necrosis_factor_receptor_type_1_associated_DEATH_domain_protein__cytosol_1" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TNF-alpha:TNF-R1:TRAPP:RIP1:TRAF2 Complex [plasma membrane]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TNF-alpha:TNF-R1:TRAPP:RIP1:TRAF2 Complex</SHORT-NAME>
+ </complex>
+ <proteinParticipant rdf:ID="TNF_receptor_associated_factor_2__cytosol_1">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q12933_1_TNF_receptor_associated_factor_2__Tumor_necrosis_factor_type_2_receptor_associated_protein_3_" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="RIP__cytosol_1">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q13546_Receptor_interacting_serine_threonine_protein_kinase_2__EC_2_7_1_37___Serine_threonine_protein_kinase_RIP___Cell_death_protein_RIP___Receptor_interacting_protein_" />
+ </proteinParticipant>
+ <complexParticipant rdf:ID="TNF_alpha_TNF_R1_complex__plasma_membrane_3">
+ <CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#TNF_alpha_TNF_R1_complex__plasma_membrane_1" />
+ </complexParticipant>
+ <proteinParticipant rdf:ID="Tumor_necrosis_factor_receptor_type_1_associated_DEATH_domain_protein__cytosol_1">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q15628_Tumor_necrosis_factor_receptor_type_1_associated_DEATH_domain_protein__TNFR1_associated_DEATH_domain_protein___TNFRSF1A_associated_via_death_domain_" />
+ </proteinParticipant>
+ <unificationXref rdf:ID="Reactome83656">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">83656</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <evidence rdf:ID="Summation_74302" />
+ <publicationXref rdf:ID="Pubmed_7758105">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">7758105</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1995</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The TNF receptor 1-associated protein TRADD signals cell death and NF-kappa B activation</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Hsu, H</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Xiong, J</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Goeddel, DV</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cell 81:495-504</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="TNF_TNF_R1_binds_TRADD__TRAF2_and_RIP_ComplexStep">
+ <STEP-INTERACTIONS rdf:resource="#TNF_TNF_R1_binds_TRADD__TRAF2_and_RIP_Complex" />
+ <NEXT-STEP rdf:resource="#TRADD_TRAF2_RIP1_complex_dissociates_from_the_TNF_alpha_TNF_R1_complex_Step" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="TRADD_TRAF2_RIP1_complex_dissociates_from_the_TNF_alpha_TNF_R1_complex_">
+ <LEFT rdf:resource="#TNF_alpha_TNF_R1_TRAPP_RIP1_TRAF2_Complex__plasma_membrane_2" />
+ <RIGHT rdf:resource="#TRAF2_TRADD_RIP1_Complex__cytosol_" />
+ <RIGHT rdf:resource="#TNF_alpha_TNF_R1_complex__plasma_membrane_4" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRADD:TRAF2:RIP1 complex dissociates from the TNF-alpha:TNF-R1 complex.</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRADD:TRAF2:RIP1 complex dissociates from the TNF-alpha:TNF-R1 complex.</SHORT-NAME>
+ <XREF rdf:resource="#Reactome83582" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Once formed the TRADD:TRAF2:RIP1 complex may dissociate from the TNF:TNF-R1 platform and become cytosolic. If this complex recruits FADD then the cell will be pushed along the apoptotic pathway.</COMMENT>
+ <EVIDENCE rdf:resource="#Summation_74353" />
+ <XREF rdf:resource="#Pubmed_12887920" />
+ <CELLULAR-LOCATION rdf:resource="#cell" />
+ </biochemicalReaction>
+ <complexParticipant rdf:ID="TNF_alpha_TNF_R1_TRAPP_RIP1_TRAF2_Complex__plasma_membrane_2">
+ <CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#TNF_alpha_TNF_R1_TRAPP_RIP1_TRAF2_Complex__plasma_membrane_1" />
+ </complexParticipant>
+ <complexParticipant rdf:ID="TRAF2_TRADD_RIP1_Complex__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#TRAF2_TRADD_RIP1_Complex__cytosol_1" />
+ </complexParticipant>
+ <complex rdf:ID="TRAF2_TRADD_RIP1_Complex__cytosol_1">
+ <COMPONENTS rdf:resource="#TNF_receptor_associated_factor_2__cytosol_2" />
+ <COMPONENTS rdf:resource="#RIP__cytosol_2" />
+ <COMPONENTS rdf:resource="#Tumor_necrosis_factor_receptor_type_1_associated_DEATH_domain_protein__cytosol_2" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRAF2:TRADD:RIP1 Complex [cytosol]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRAF2:TRADD:RIP1 Complex</SHORT-NAME>
+ </complex>
+ <proteinParticipant rdf:ID="TNF_receptor_associated_factor_2__cytosol_2">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q12933_1_TNF_receptor_associated_factor_2__Tumor_necrosis_factor_type_2_receptor_associated_protein_3_" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="RIP__cytosol_2">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q13546_Receptor_interacting_serine_threonine_protein_kinase_2__EC_2_7_1_37___Serine_threonine_protein_kinase_RIP___Cell_death_protein_RIP___Receptor_interacting_protein_" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="Tumor_necrosis_factor_receptor_type_1_associated_DEATH_domain_protein__cytosol_2">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q15628_Tumor_necrosis_factor_receptor_type_1_associated_DEATH_domain_protein__TNFR1_associated_DEATH_domain_protein___TNFRSF1A_associated_via_death_domain_" />
+ </proteinParticipant>
+ <complexParticipant rdf:ID="TNF_alpha_TNF_R1_complex__plasma_membrane_4">
+ <CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#TNF_alpha_TNF_R1_complex__plasma_membrane_1" />
+ </complexParticipant>
+ <unificationXref rdf:ID="Reactome83582">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">83582</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <evidence rdf:ID="Summation_74353" />
+ <publicationXref rdf:ID="Pubmed_12887920">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">12887920</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2003</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Induction of TNF receptor I-mediated apoptosis via two sequential signaling complexes</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Micheau, O</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Tschopp, J</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cell 114:181-90</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="TRADD_TRAF2_RIP1_complex_dissociates_from_the_TNF_alpha_TNF_R1_complex_Step">
+ <STEP-INTERACTIONS rdf:resource="#TRADD_TRAF2_RIP1_complex_dissociates_from_the_TNF_alpha_TNF_R1_complex_" />
+ <NEXT-STEP rdf:resource="#TRADD_TRAF2_RIP1_complex_binds_FADDStep" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="TRADD_TRAF2_RIP1_complex_binds_FADD">
+ <LEFT rdf:resource="#TRAF2_TRADD_RIP1_Complex__cytosol_2" />
+ <LEFT rdf:resource="#FADD__cytosol_2" />
+ <RIGHT rdf:resource="#TRAF2_TRADD_RIP1_FADD__cytosol_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRADD:TRAF2:RIP1 complex binds FADD</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRADD:TRAF2:RIP1 complex binds FADD</SHORT-NAME>
+ <XREF rdf:resource="#Reactome140978" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Once formed the TRADD:TRAF2:RIP1 complex may dissociate from the TNF:TNF-R1 platform and become cytosolic. If this complex recruits FADD then the cell will be pushed along the apoptotic pathway.</COMMENT>
+ <EVIDENCE rdf:resource="#Summation_74353" />
+ <XREF rdf:resource="#Pubmed_12887920" />
+ <CELLULAR-LOCATION rdf:resource="#cell" />
+ </biochemicalReaction>
+ <complexParticipant rdf:ID="TRAF2_TRADD_RIP1_Complex__cytosol_2">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#TRAF2_TRADD_RIP1_Complex__cytosol_1" />
+ </complexParticipant>
+ <proteinParticipant rdf:ID="FADD__cytosol_2">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q13158_FADD_protein__FAS_associating_death_domain_containing_protein___Mediator_of_receptor_induced_toxicity_" />
+ </proteinParticipant>
+ <complexParticipant rdf:ID="TRAF2_TRADD_RIP1_FADD__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#TRAF2_TRADD_RIP1_FADD__cytosol_1" />
+ </complexParticipant>
+ <complex rdf:ID="TRAF2_TRADD_RIP1_FADD__cytosol_1">
+ <COMPONENTS rdf:resource="#TRAF2_TRADD_RIP1_Complex__cytosol_3" />
+ <COMPONENTS rdf:resource="#FADD__cytosol_3" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRAF2:TRADD:RIP1:FADD [cytosol]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRAF2:TRADD:RIP1:FADD</SHORT-NAME>
+ </complex>
+ <complexParticipant rdf:ID="TRAF2_TRADD_RIP1_Complex__cytosol_3">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#TRAF2_TRADD_RIP1_Complex__cytosol_1" />
+ </complexParticipant>
+ <proteinParticipant rdf:ID="FADD__cytosol_3">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q13158_FADD_protein__FAS_associating_death_domain_containing_protein___Mediator_of_receptor_induced_toxicity_" />
+ </proteinParticipant>
+ <unificationXref rdf:ID="Reactome140978">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">140978</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <pathwayStep rdf:ID="TRADD_TRAF2_RIP1_complex_binds_FADDStep">
+ <STEP-INTERACTIONS rdf:resource="#TRADD_TRAF2_RIP1_complex_binds_FADD" />
+ <NEXT-STEP rdf:resource="#TRADD_TRAF2_RIP1_FADD_complex_binds_Pro_Caspase_8__Step" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="TRADD_TRAF2_RIP1_FADD_complex_binds_Pro_Caspase_8__">
+ <LEFT rdf:resource="#TRAF2_TRADD_RIP1_FADD__cytosol_2" />
+ <LEFT rdf:resource="#Caspase_8_precursor___cytosol_2" />
+ <RIGHT rdf:resource="#TRADD_TRAF2_RIP1_FADD_Capase_8_Complex__cytosol_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRADD:TRAF2:RIP1:FADD complex binds Pro-Caspase 8</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRADD:TRAF2:RIP1:FADD complex binds Pro-Caspase 8</SHORT-NAME>
+ <XREF rdf:resource="#Reactome75240" />
+ <XREF rdf:resource="#Pubmed_12887920" />
+ <CELLULAR-LOCATION rdf:resource="#cell" />
+ </biochemicalReaction>
+ <complexParticipant rdf:ID="TRAF2_TRADD_RIP1_FADD__cytosol_2">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#TRAF2_TRADD_RIP1_FADD__cytosol_1" />
+ </complexParticipant>
+ <proteinParticipant rdf:ID="Caspase_8_precursor___cytosol_2">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q14790_1_Caspase_8_precursor__EC_3_4_22_____CASP_8___ICE_like_apoptotic_protease_5___MORT1_associated_CED_3_homolog___MACH___FADD_homologous_ICE_CED_3_like_protease___FADD_like_ICE___FLICE___Apoptotic_cysteine_protease___Apoptotic_protease_Mch_5___CAP4_" />
+ </proteinParticipant>
+ <complexParticipant rdf:ID="TRADD_TRAF2_RIP1_FADD_Capase_8_Complex__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#TRADD_TRAF2_RIP1_FADD_Capase_8_Complex__cytosol_1" />
+ </complexParticipant>
+ <complex rdf:ID="TRADD_TRAF2_RIP1_FADD_Capase_8_Complex__cytosol_1">
+ <COMPONENTS rdf:resource="#TRAF2_TRADD_RIP1_FADD__cytosol_3" />
+ <COMPONENTS rdf:resource="#Caspase_8_precursor___cytosol_3" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRADD:TRAF2:RIP1:FADD:Capase-8 Complex [cytosol]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRADD:TRAF2:RIP1:FADD:Capase-8 Complex</SHORT-NAME>
+ </complex>
+ <complexParticipant rdf:ID="TRAF2_TRADD_RIP1_FADD__cytosol_3">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#TRAF2_TRADD_RIP1_FADD__cytosol_1" />
+ </complexParticipant>
+ <proteinParticipant rdf:ID="Caspase_8_precursor___cytosol_3">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q14790_1_Caspase_8_precursor__EC_3_4_22_____CASP_8___ICE_like_apoptotic_protease_5___MORT1_associated_CED_3_homolog___MACH___FADD_homologous_ICE_CED_3_like_protease___FADD_like_ICE___FLICE___Apoptotic_cysteine_protease___Apoptotic_protease_Mch_5___CAP4_" />
+ </proteinParticipant>
+ <unificationXref rdf:ID="Reactome75240">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">75240</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <pathwayStep rdf:ID="TRADD_TRAF2_RIP1_FADD_complex_binds_Pro_Caspase_8__Step">
+ <STEP-INTERACTIONS rdf:resource="#TRADD_TRAF2_RIP1_FADD_complex_binds_Pro_Caspase_8__" />
+ <NEXT-STEP rdf:resource="#TNF_Mediated_Activation_of_Pro_caspase_8Step" />
+ </pathwayStep>
+ <unificationXref rdf:ID="Reactome75893">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">75893</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <evidence rdf:ID="Summation_140942">
+ <XREF rdf:resource="#Pubmed_12040173" />
+ </evidence>
+ <publicationXref rdf:ID="Pubmed_12040173">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">12040173</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2002</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TNF-R1 signaling: a beautiful pathway</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Chen, G</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Goeddel, DV</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Science 296:1634-5</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="TNF_signalingStep">
+ <STEP-INTERACTIONS rdf:resource="#TNF_signaling" />
+ </pathwayStep>
+ <pathway rdf:ID="TRAIL__signaling">
+ <PATHWAY-COMPONENTS rdf:resource="#TRAIL_TRAIL_Receptor2_Trimer_FADD_complex_binds_Caspase_10Step" />
+ <PATHWAY-COMPONENTS rdf:resource="#TRAIL_TRAIL_Receptor2_Trimer_FADD_complex_binds_Caspase_8Step" />
+ <PATHWAY-COMPONENTS rdf:resource="#TRAIL_TRAIL_receptor_2_Trimer_Binds_FADDStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#Trimerization_of_TRAIL__TRAIL_receptor_2_complexStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#TRAIL_Binds_TRAIL_Receptor2Step" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRAIL signaling</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRAIL signaling</SHORT-NAME>
+ <XREF rdf:resource="#Reactome75158" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Tumor necrosis factor-related apoptosis-inducing ligand or Apo 2 ligand (TRAIL/Apo2L) is a member of the tumor necrosis factor (TNF) family. This group of apoptosis induction pathways all work through protein interactions mediated by the intracellular death domain (DD), encoded within the cytoplasmic domain of the receptor. TRAIL selectively induces apoptosis through its interaction with the Fas-associated death domain p [...]
+ <EVIDENCE rdf:resource="#Summation_141083" />
+ <XREF rdf:resource="#Pubmed_14634624" />
+ <CELLULAR-LOCATION rdf:resource="#cell" />
+ </pathway>
+ <biochemicalReaction rdf:ID="TRAIL_Binds_TRAIL_Receptor2">
+ <LEFT rdf:resource="#TRAIL_receptor_2__plasma_membrane_" />
+ <LEFT rdf:resource="#TRAIL__extracellular_region_" />
+ <RIGHT rdf:resource="#TRAIL_receptor_2_TRAIL_complex__plasma_membrane_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRAIL Binds TRAIL-Receptor2</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRAIL Binds TRAIL-Receptor2</SHORT-NAME>
+ <XREF rdf:resource="#Reactome75238" />
+ <XREF rdf:resource="#Pubmed_8777713" />
+ <CELLULAR-LOCATION rdf:resource="#cell" />
+ </biochemicalReaction>
+ <proteinParticipant rdf:ID="TRAIL_receptor_2__plasma_membrane_">
+ <CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_O14763_1_Tumor_necrosis_factor_receptor_superfamily_member_10B_precursor__Death_receptor_5___TNF_related_apoptosis_inducing_ligand_receptor_2___TRAIL_receptor_2___TRAIL_R2_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_O14763_1_Tumor_necrosis_factor_receptor_superfamily_member_10B_precursor__Death_receptor_5___TNF_related_apoptosis_inducing_ligand_receptor_2___TRAIL_receptor_2___TRAIL_R2_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:O14763-1 Tumor necrosis factor receptor superfamily member 10B precursor (Death receptor 5) (TNF-related apoptosis-inducing ligand receptor 2) (TRAIL receptor-2) (TRAIL-R2)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">KILLER</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ZTNFR9</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRICK2</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DR5</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRAILR2</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TNFRSF10B</SYNONYMS>
+ <XREF rdf:resource="#UniProt_O14763" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Receptor for the cytotoxic ligand TNFSF10/TRAIL. The adaptor molecule FADD recruits caspase-8 to the activated receptor. The resulting death-inducing signaling complex (DISC) performs caspase-8 proteolytic activation which initiates the subsequent cascade of caspases (aspartate-specific cysteine proteases) mediating apoptosis. Promotes the activation of NF- kappa-B. SUBUNIT: Homotrimer. Can interact with TRADD [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_O14763">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">O14763</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="TRAIL__extracellular_region_">
+ <CELLULAR-LOCATION rdf:resource="#extracellular_region" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P50591_Tumor_necrosis_factor_ligand_superfamily_member_10__TNF_related_apoptosis_inducing_ligand___TRAIL_protein___Apo_2_ligand___Apo_2L_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_P50591_Tumor_necrosis_factor_ligand_superfamily_member_10__TNF_related_apoptosis_inducing_ligand___TRAIL_protein___Apo_2_ligand___Apo_2L_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P50591 Tumor necrosis factor ligand superfamily member 10 (TNF-related apoptosis inducing ligand) (TRAIL protein) (Apo-2 ligand) (Apo-2L)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">APO2L</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TNFSF10</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRAIL</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P50591" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Cytokine that binds to TNFRSF10A/TRAILR1, TNFRSF10B/TRAILR2, TNFRSF10C/TRAILR3, TNFRSF10D/TRAILR4 and possibly also to TNFRSF11B/OPG. Induces apoptosis. Its activity may be modulated by binding to the decoy receptors TNFRSF10C/TRAILR3, TNFRSF10D/TRAILR4 and TNFRSF11B/OPG that cannot induce apoptosis. COFACTOR: Binds 1 zinc ion and one anionic solvent molecule per trimer. SUBUNIT: Homotrimer. SUBCELLULAR LOCATIO [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_P50591">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P50591</ID>
+ </unificationXref>
+ <complexParticipant rdf:ID="TRAIL_receptor_2_TRAIL_complex__plasma_membrane_">
+ <CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#TRAIL_receptor_2_TRAIL_complex__plasma_membrane_1" />
+ </complexParticipant>
+ <complex rdf:ID="TRAIL_receptor_2_TRAIL_complex__plasma_membrane_1">
+ <COMPONENTS rdf:resource="#TRAIL_receptor_2__plasma_membrane_1" />
+ <COMPONENTS rdf:resource="#TRAIL__extracellular_region_1" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRAIL receptor-2:TRAIL complex [plasma membrane]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRAIL receptor-2:TRAIL complex</SHORT-NAME>
+ </complex>
+ <proteinParticipant rdf:ID="TRAIL_receptor_2__plasma_membrane_1">
+ <CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_O14763_1_Tumor_necrosis_factor_receptor_superfamily_member_10B_precursor__Death_receptor_5___TNF_related_apoptosis_inducing_ligand_receptor_2___TRAIL_receptor_2___TRAIL_R2_" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="TRAIL__extracellular_region_1">
+ <CELLULAR-LOCATION rdf:resource="#extracellular_region" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P50591_Tumor_necrosis_factor_ligand_superfamily_member_10__TNF_related_apoptosis_inducing_ligand___TRAIL_protein___Apo_2_ligand___Apo_2L_" />
+ </proteinParticipant>
+ <unificationXref rdf:ID="Reactome75238">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">75238</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <publicationXref rdf:ID="Pubmed_8777713">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">8777713</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1995</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Identification and characterization of a new member of the TNF family that induces apoptosis</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Wiley, SR</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Schooley, K</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Smolak, PJ</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Din, WS</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Huang, CP</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Nicholl, JK</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Sutherland, GR</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Smith, TD</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Rauch, C</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Smith, CA</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Immunity 3:673-82</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="TRAIL_Binds_TRAIL_Receptor2Step">
+ <STEP-INTERACTIONS rdf:resource="#TRAIL_Binds_TRAIL_Receptor2" />
+ <NEXT-STEP rdf:resource="#Trimerization_of_TRAIL__TRAIL_receptor_2_complexStep" />
+ <NEXT-STEP rdf:resource="#TRAIL_TRAIL_receptor_2_Trimer_Binds_FADDStep" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="Trimerization_of_TRAIL__TRAIL_receptor_2_complex">
+ <LEFT rdf:resource="#TRAIL_receptor_2_TRAIL_complex__plasma_membrane_2" />
+ <RIGHT rdf:resource="#TRAIL_receptor_2_TRAIL_Trimer__plasma_membrane_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Trimerization of TRAIL: TRAIL receptor-2 complex</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Trimerization of TRAIL: TRAIL receptor-2 complex</SHORT-NAME>
+ <XREF rdf:resource="#Reactome141139" />
+ <XREF rdf:resource="#Pubmed_10894160" />
+ <CELLULAR-LOCATION rdf:resource="#cell" />
+ </biochemicalReaction>
+ <complexParticipant rdf:ID="TRAIL_receptor_2_TRAIL_complex__plasma_membrane_2">
+ <CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#TRAIL_receptor_2_TRAIL_complex__plasma_membrane_1" />
+ <STOICHIOMETRIC-COEFFICIENT rdf:datatype="http://www.w3.org/2001/XMLSchema#int">3</STOICHIOMETRIC-COEFFICIENT>
+ </complexParticipant>
+ <complexParticipant rdf:ID="TRAIL_receptor_2_TRAIL_Trimer__plasma_membrane_">
+ <CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#TRAIL_receptor_2_TRAIL_Trimer__plasma_membrane_1" />
+ </complexParticipant>
+ <complex rdf:ID="TRAIL_receptor_2_TRAIL_Trimer__plasma_membrane_1">
+ <COMPONENTS rdf:resource="#TRAIL_receptor_2_TRAIL_complex__plasma_membrane_3" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRAIL receptor-2:TRAIL Trimer [plasma membrane]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRAIL receptor-2:TRAIL Trimer</SHORT-NAME>
+ </complex>
+ <complexParticipant rdf:ID="TRAIL_receptor_2_TRAIL_complex__plasma_membrane_3">
+ <CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#TRAIL_receptor_2_TRAIL_complex__plasma_membrane_1" />
+ <STOICHIOMETRIC-COEFFICIENT rdf:datatype="http://www.w3.org/2001/XMLSchema#int">3</STOICHIOMETRIC-COEFFICIENT>
+ </complexParticipant>
+ <unificationXref rdf:ID="Reactome141139">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">141139</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <publicationXref rdf:ID="Pubmed_10894160">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">10894160</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2000</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FADD/MORT1 and caspase-8 are recruited to TRAIL receptors 1 and 2 and are essential for apoptosis mediated by TRAIL receptor 2</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Sprick, MR</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Weigand, MA</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Rieser, E</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Rauch, CT</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Juo, P</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Blenis, J</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Krammer, PH</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Walczak, H</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Immunity 12:599-609</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="Trimerization_of_TRAIL__TRAIL_receptor_2_complexStep">
+ <STEP-INTERACTIONS rdf:resource="#Trimerization_of_TRAIL__TRAIL_receptor_2_complex" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="TRAIL_TRAIL_receptor_2_Trimer_Binds_FADD">
+ <LEFT rdf:resource="#FADD__cytosol_4" />
+ <LEFT rdf:resource="#TRAIL_receptor_2_TRAIL_Trimer__plasma_membrane_2" />
+ <RIGHT rdf:resource="#TRAIL_TRAIL_receptor_2_FADD_complex__plasma_membrane_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRAIL:TRAIL receptor-2 Trimer Binds FADD</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRAIL:TRAIL receptor-2 Trimer Binds FADD</SHORT-NAME>
+ <XREF rdf:resource="#Reactome75187" />
+ <XREF rdf:resource="#Pubmed_10894160" />
+ <CELLULAR-LOCATION rdf:resource="#cell" />
+ </biochemicalReaction>
+ <proteinParticipant rdf:ID="FADD__cytosol_4">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q13158_FADD_protein__FAS_associating_death_domain_containing_protein___Mediator_of_receptor_induced_toxicity_" />
+ </proteinParticipant>
+ <complexParticipant rdf:ID="TRAIL_receptor_2_TRAIL_Trimer__plasma_membrane_2">
+ <CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#TRAIL_receptor_2_TRAIL_Trimer__plasma_membrane_1" />
+ </complexParticipant>
+ <complexParticipant rdf:ID="TRAIL_TRAIL_receptor_2_FADD_complex__plasma_membrane_">
+ <CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#TRAIL_TRAIL_receptor_2_FADD_complex__plasma_membrane_1" />
+ </complexParticipant>
+ <complex rdf:ID="TRAIL_TRAIL_receptor_2_FADD_complex__plasma_membrane_1">
+ <COMPONENTS rdf:resource="#FADD__cytosol_5" />
+ <COMPONENTS rdf:resource="#TRAIL_receptor_2_TRAIL_Trimer__plasma_membrane_3" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRAIL:TRAIL receptor-2:FADD complex [plasma membrane]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRAIL:TRAIL receptor-2:FADD complex</SHORT-NAME>
+ </complex>
+ <proteinParticipant rdf:ID="FADD__cytosol_5">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q13158_FADD_protein__FAS_associating_death_domain_containing_protein___Mediator_of_receptor_induced_toxicity_" />
+ </proteinParticipant>
+ <complexParticipant rdf:ID="TRAIL_receptor_2_TRAIL_Trimer__plasma_membrane_3">
+ <CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#TRAIL_receptor_2_TRAIL_Trimer__plasma_membrane_1" />
+ </complexParticipant>
+ <unificationXref rdf:ID="Reactome75187">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">75187</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <modulation rdf:ID="_CASP8_and_FADD_like_apoptosis_regulator_precursor__negatively_regulates__TRAIL_TRAIL_receptor_2_Trimer_Binds_FADD_">
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">'CASP8 and FADD-like apoptosis regulator precursor' negatively regulates 'TRAIL:TRAIL receptor-2 Trimer Binds FADD'</NAME>
+ <CONTROL-TYPE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">INHIBITION</CONTROL-TYPE>
+ <CONTROLLER rdf:resource="#CASP8_and_FADD_like_apoptosis_regulator_precursor__cytosol_" />
+ <CONTROLLED rdf:resource="#TRAIL_TRAIL_receptor_2_Trimer_Binds_FADD" />
+ </modulation>
+ <proteinParticipant rdf:ID="CASP8_and_FADD_like_apoptosis_regulator_precursor__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_O15519_1_CASP8_and_FADD_like_apoptosis_regulator_precursor__Cellular_FLICE_like_inhibitory_protein___c_FLIP___Caspase_eight_related_protein___Casper___Caspase_like_apoptosis_regulatory_protein___CLARP___MACH_related_inducer_of_toxicity___MRIT___Caspase_homolog___CASH___Inhibitor_of_FLICE___I_FLICE___FADD_like_antiapoptotic_molecule_1___Flame_1___Usurpin_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_O15519_1_CASP8_and_FADD_like_apoptosis_regulator_precursor__Cellular_FLICE_like_inhibitory_protein___c_FLIP___Caspase_eight_related_protein___Casper___Caspase_like_apoptosis_regulatory_protein___CLARP___MACH_related_inducer_of_toxicity___MRIT___Caspase_homolog___CASH___Inhibitor_of_FLICE___I_FLICE___FADD_like_antiapoptotic_molecule_1___Flame_1___Usurpin_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:O15519-1 CASP8 and FADD-like apoptosis regulator precursor (Cellular FLICE-like inhibitory protein) (c-FLIP) (Caspase-eight-related protein) (Casper) (Caspase-like apoptosis regulatory protein) (CLARP) (MACH-related inducer of toxicity) (MRIT) (Caspase homolog) (CASH) (Inhibitor of FLICE) (I-FLICE) (FADD-like antiapoptotic molecule 1) (Flame-1) (Usurpin)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CASH</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CFLAR</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">MRIT</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CLARP</SYNONYMS>
+ <XREF rdf:resource="#UniProt_O15519" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Apoptosis regulator protein which may function as a crucial link between cell survival and cell death pathways in mammalian cells. Acts as an inhibitor of TNFRSF6 mediated apoptosis. A proteolytic fragment (p43) is likely retained in the death-inducing signaling complex (DISC) thereby blocking further recruitment and processing of caspase-8 at the complex. Full length and shorter isoforms have been shown either [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_O15519">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">O15519</ID>
+ </unificationXref>
+ <pathwayStep rdf:ID="TRAIL_TRAIL_receptor_2_Trimer_Binds_FADDStep">
+ <STEP-INTERACTIONS rdf:resource="#TRAIL_TRAIL_receptor_2_Trimer_Binds_FADD" />
+ <NEXT-STEP rdf:resource="#TRAIL_TRAIL_Receptor2_Trimer_FADD_complex_binds_Caspase_8Step" />
+ <NEXT-STEP rdf:resource="#TRAIL_TRAIL_Receptor2_Trimer_FADD_complex_binds_Caspase_10Step" />
+ <STEP-INTERACTIONS rdf:resource="#_CASP8_and_FADD_like_apoptosis_regulator_precursor__negatively_regulates__TRAIL_TRAIL_receptor_2_Trimer_Binds_FADD_" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="TRAIL_TRAIL_Receptor2_Trimer_FADD_complex_binds_Caspase_8">
+ <LEFT rdf:resource="#TRAIL_TRAIL_receptor_2_FADD_complex__plasma_membrane_2" />
+ <LEFT rdf:resource="#Caspase_8_precursor___cytosol_4" />
+ <RIGHT rdf:resource="#TRAIL_TRAIL_receptor_2_Trimer_FADD_Caspase_8_precursor_complex__plasma_membrane_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRAIL:TRAIL-Receptor2 Trimer:FADD complex binds Caspase-8</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRAIL:TRAIL-Receptor2 Trimer:FADD complex binds Caspase-8</SHORT-NAME>
+ <XREF rdf:resource="#Reactome75146" />
+ <XREF rdf:resource="#Pubmed_10894160" />
+ <CELLULAR-LOCATION rdf:resource="#cell" />
+ </biochemicalReaction>
+ <complexParticipant rdf:ID="TRAIL_TRAIL_receptor_2_FADD_complex__plasma_membrane_2">
+ <CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#TRAIL_TRAIL_receptor_2_FADD_complex__plasma_membrane_1" />
+ </complexParticipant>
+ <proteinParticipant rdf:ID="Caspase_8_precursor___cytosol_4">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q14790_1_Caspase_8_precursor__EC_3_4_22_____CASP_8___ICE_like_apoptotic_protease_5___MORT1_associated_CED_3_homolog___MACH___FADD_homologous_ICE_CED_3_like_protease___FADD_like_ICE___FLICE___Apoptotic_cysteine_protease___Apoptotic_protease_Mch_5___CAP4_" />
+ </proteinParticipant>
+ <complexParticipant rdf:ID="TRAIL_TRAIL_receptor_2_Trimer_FADD_Caspase_8_precursor_complex__plasma_membrane_">
+ <CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#TRAIL_TRAIL_receptor_2_Trimer_FADD_Caspase_8_precursor_complex__plasma_membrane_1" />
+ </complexParticipant>
+ <complex rdf:ID="TRAIL_TRAIL_receptor_2_Trimer_FADD_Caspase_8_precursor_complex__plasma_membrane_1">
+ <COMPONENTS rdf:resource="#TRAIL_TRAIL_receptor_2_FADD_complex__plasma_membrane_3" />
+ <COMPONENTS rdf:resource="#Caspase_8_precursor___cytosol_5" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRAIL:TRAIL receptor-2 Trimer:FADD:Caspase-8 precursor complex [plasma membrane]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRAIL:TRAIL receptor-2 Trimer:FADD:Caspase-8 precursor complex</SHORT-NAME>
+ </complex>
+ <complexParticipant rdf:ID="TRAIL_TRAIL_receptor_2_FADD_complex__plasma_membrane_3">
+ <CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#TRAIL_TRAIL_receptor_2_FADD_complex__plasma_membrane_1" />
+ </complexParticipant>
+ <proteinParticipant rdf:ID="Caspase_8_precursor___cytosol_5">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q14790_1_Caspase_8_precursor__EC_3_4_22_____CASP_8___ICE_like_apoptotic_protease_5___MORT1_associated_CED_3_homolog___MACH___FADD_homologous_ICE_CED_3_like_protease___FADD_like_ICE___FLICE___Apoptotic_cysteine_protease___Apoptotic_protease_Mch_5___CAP4_" />
+ </proteinParticipant>
+ <unificationXref rdf:ID="Reactome75146">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">75146</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <pathwayStep rdf:ID="TRAIL_TRAIL_Receptor2_Trimer_FADD_complex_binds_Caspase_8Step">
+ <STEP-INTERACTIONS rdf:resource="#TRAIL_TRAIL_Receptor2_Trimer_FADD_complex_binds_Caspase_8" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="TRAIL_TRAIL_Receptor2_Trimer_FADD_complex_binds_Caspase_10">
+ <LEFT rdf:resource="#TRAIL_TRAIL_receptor_2_FADD_complex__plasma_membrane_4" />
+ <LEFT rdf:resource="#Caspase_10_precursor___plasma_membrane_2" />
+ <RIGHT rdf:resource="#TRAIL_TRAIL_receptor_2_Trimer_FADD_Caspase_10_precursor_complex__plasma_membrane_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRAIL:TRAIL-Receptor2 Trimer:FADD complex binds Caspase-10</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TRAIL:TRAIL-Receptor2 Trimer:FADD complex binds Caspase-10</SHORT-NAME>
+ <XREF rdf:resource="#Reactome141316" />
+ <XREF rdf:resource="#Pubmed_11717445" />
+ <XREF rdf:resource="#Pubmed_12198154" />
+ <CELLULAR-LOCATION rdf:resource="#cell" />
+ </biochemicalReaction>
+ <complexParticipant rdf:ID="TRAIL_TRAIL_receptor_2_FADD_complex__plasma_membrane_4">
+ <CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#TRAIL_TRAIL_receptor_2_FADD_complex__plasma_membrane_1" />
+ </complexParticipant>
+ <proteinParticipant rdf:ID="Caspase_10_precursor___plasma_membrane_2">
+ <CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q92851_1_Caspase_10_precursor__EC_3_4_22_____CASP_10___ICE_like_apoptotic_protease_4___Apoptotic_protease_Mch_4___FAS_associated_death_domain_protein_interleukin_1B_converting_enzyme_2___FLICE2_" />
+ </proteinParticipant>
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+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0008633</ID>
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+ <pathwayStep rdf:ID="Caspase_8_is_formed_from_procaspase_8Step">
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+ </pathwayStep>
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+ </unificationXref>
+ <evidence rdf:ID="Summation_139959">
+ <XREF rdf:resource="#Pubmed_11048727" />
+ </evidence>
+ <pathwayStep rdf:ID="Extrinsic_Pathway_for_ApoptosisStep">
+ <STEP-INTERACTIONS rdf:resource="#Extrinsic_Pathway_for_Apoptosis" />
+ </pathwayStep>
+ <pathway rdf:ID="Activation__myristolyation_of_BID_and_translocation_to_mitochondria">
+ <PATHWAY-COMPONENTS rdf:resource="#Translocation_of_tBID_to_mitochondriaStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#Caspase_8_activates_BID_by_cleavageStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#Myristoylation_of_tBID_by_NMT1Step" />
+ <PATHWAY-COMPONENTS rdf:resource="#Granzyme_B_activates_BID_by_cleavageStep" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Activation, myristolyation of BID and translocation to mitochondria</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Activation, myristolyation of BID and translocation to mitochondria</SHORT-NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Activation of BID and translocation to mitochondria</SYNONYMS>
+ <XREF rdf:resource="#Reactome75108" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BID may promote cell death by activating BAX and BAK while inactivating anti-apoptotic proteins. The engagement of cell surface receptors activates the caspase-8, a heterodimer, that cleaves BID in its amino terminal region. This particular event may act as a link between Extrinsic (caspase 8/10 dependent) and Intrinsic (Bcl-2 inhibitable) pathways although some evidences from mouse genetic experiments suggest the contra [...]
+ <EVIDENCE rdf:resource="#Summation_140549" />
+ <XREF rdf:resource="#activation_of_pro_apoptotic_gene_products" />
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ </pathway>
+ <biochemicalReaction rdf:ID="Caspase_8_activates_BID_by_cleavage">
+ <LEFT rdf:resource="#BID__cytosol_" />
+ <RIGHT rdf:resource="#tBID_p15__cytosol_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Caspase-8 activates BID by cleavage</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Caspase-8 activates BID by cleavage</SHORT-NAME>
+ <XREF rdf:resource="#Reactome139898" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The caspase 8 -mediated cleavage of cytosolic, inactive p22 BID at internal Asp sites yields a major p15 and minor p13 and p11 fragments. After myristoylation, tBID translocates to mitochondria as an integral membrane protein.</COMMENT>
+ <EVIDENCE rdf:resource="#Summation_163355" />
+ <XREF rdf:resource="#Pubmed_12804595" />
+ <XREF rdf:resource="#activation_of_pro_apoptotic_gene_products" />
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ </biochemicalReaction>
+ <proteinParticipant rdf:ID="BID__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P55957_BH3_interacting_domain_death_agonist__BID_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_P55957_BH3_interacting_domain_death_agonist__BID_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P55957 BH3 interacting domain death agonist (BID)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BID</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P55957" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Induces ICE-like proteases and apoptosis. Counters the protective effect of Bcl-2 (By similarity). SUBUNIT: Forms heterodimers either with the pro-apoptotic protein BAX or the anti-apoptotic protein Bcl-2 (By similarity). SUBCELLULAR LOCATION: Predominantly cytoplasmic (By similarity). DOMAIN: Intact BH3 domain is required by BIK, BID, BAK, BAD and BAX for their pro-apoptotic activity and for their interaction [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_P55957">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P55957</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="tBID_p15__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P55957_BH3_interacting_domain_death_agonist__BID_" />
+ </proteinParticipant>
+ <catalysis rdf:ID="caspase_activity_of_Caspase_8_dimer__cytosol_">
+ <CONTROLLER rdf:resource="#Caspase_8_dimer__cytosol_2" />
+ <CONTROLLED rdf:resource="#Caspase_8_activates_BID_by_cleavage" />
+ <DIRECTION rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PHYSIOL-LEFT-TO-RIGHT</DIRECTION>
+ <XREF rdf:resource="#caspase_activity" />
+ </catalysis>
+ <complexParticipant rdf:ID="Caspase_8_dimer__cytosol_2">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#Caspase_8_dimer__cytosol_1" />
+ </complexParticipant>
+ <relationshipXref rdf:ID="caspase_activity">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GO</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0030693</ID>
+ </relationshipXref>
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+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <evidence rdf:ID="Summation_163355">
+ <XREF rdf:resource="#Pubmed_9873064" />
+ </evidence>
+ <publicationXref rdf:ID="Pubmed_9873064">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">9873064</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1999</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Caspase cleaved BID targets mitochondria and is required for cytochrome c release, while BCL-XL prevents this release but not tumor necrosis factor-R1/Fas death</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Gross, A</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Yin, XM</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Wang, K</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Wei, MC</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Jockel, J</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Milliman, C</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Erdjument-Bromage, H</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Tempst, P</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Korsmeyer, SJ</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Biol Chem 274:1156-63</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_12804595">
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+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2003</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Caspase 8-mediated cleavage of the pro-apoptotic BCL-2 family member BID in p53-dependent apoptosis</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Fischer, B</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Coelho, D</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Dufour, P</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bergerat, JP</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Denis, JM</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Gueulette, J</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bischoff, P</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Biochem Biophys Res Commun 306:516-22</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="Caspase_8_activates_BID_by_cleavageStep">
+ <STEP-INTERACTIONS rdf:resource="#Caspase_8_activates_BID_by_cleavage" />
+ <NEXT-STEP rdf:resource="#tBID_activates_BAX_proteinStep" />
+ <NEXT-STEP rdf:resource="#Myristoylation_of_tBID_by_NMT1Step" />
+ <STEP-INTERACTIONS rdf:resource="#caspase_activity_of_Caspase_8_dimer__cytosol_" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="Granzyme_B_activates_BID_by_cleavage">
+ <LEFT rdf:resource="#BID__cytosol_1" />
+ <RIGHT rdf:resource="#tBID_p15__cytosol_1" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Granzyme-B activates BID by cleavage</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Granzyme-B activates BID by cleavage</SHORT-NAME>
+ <XREF rdf:resource="#Reactome139893" />
+ <XREF rdf:resource="#Pubmed_11114298" />
+ <XREF rdf:resource="#activation_of_pro_apoptotic_gene_products" />
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ </biochemicalReaction>
+ <proteinParticipant rdf:ID="BID__cytosol_1">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P55957_BH3_interacting_domain_death_agonist__BID_" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="tBID_p15__cytosol_1">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P55957_BH3_interacting_domain_death_agonist__BID_" />
+ </proteinParticipant>
+ <catalysis rdf:ID="granzyme_B_activity_of_Granzyme_B__cytosol_">
+ <CONTROLLER rdf:resource="#Granzyme_B__cytosol_" />
+ <CONTROLLED rdf:resource="#Granzyme_B_activates_BID_by_cleavage" />
+ <DIRECTION rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PHYSIOL-LEFT-TO-RIGHT</DIRECTION>
+ <XREF rdf:resource="#granzyme_B_activity" />
+ </catalysis>
+ <proteinParticipant rdf:ID="Granzyme_B__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P10144_Granzyme_B_precursor__EC_3_4_21_79___T_cell_serine_protease_1_3E___Cytotoxic_T_lymphocyte_proteinase_2___Lymphocyte_protease___SECT___Granzyme_2___Cathepsin_G_like_1___CTSGL1___CTLA_1___Fragmentin_2___Human_lymphocyte_protein___HLP___C11_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_P10144_Granzyme_B_precursor__EC_3_4_21_79___T_cell_serine_protease_1_3E___Cytotoxic_T_lymphocyte_proteinase_2___Lymphocyte_protease___SECT___Granzyme_2___Cathepsin_G_like_1___CTSGL1___CTLA_1___Fragmentin_2___Human_lymphocyte_protein___HLP___C11_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P10144 Granzyme B precursor (EC 3.4.21.79) (T-cell serine protease 1-3E) (Cytotoxic T-lymphocyte proteinase 2) (Lymphocyte protease) (SECT) (Granzyme 2) (Cathepsin G-like 1) (CTSGL1) (CTLA-1) (Fragmentin 2) (Human lymphocyte protein) (HLP) (C11)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GZMB</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CGL1</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GRB</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CSPB</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CTLA1</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P10144" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: This enzyme is necessary for target cell lysis in cell- mediated immune responses. It cleaves after Asp. Seems to be linked to an activation cascade of caspases (aspartate-specific cysteine proteases) responsible for apoptosis execution. Cleaves caspase-3, -7, -9 and 10 to give rise to active enzymes mediating apoptosis. CATALYTIC ACTIVITY: Preferential cleavage: Asp-|-Xaa >> Asn-|-Xaa > Met-|-Xaa, Ser [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_P10144">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P10144</ID>
+ </unificationXref>
+ <relationshipXref rdf:ID="granzyme_B_activity">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GO</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0004278</ID>
+ </relationshipXref>
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+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <publicationXref rdf:ID="Pubmed_11114298">
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+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2001</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Granzyme B induces BID-mediated cytochrome c release and mitochondrial permeability transition</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Alimonti, JB</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Shi, L</AUTHORS>
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+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Greenberg, AH</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Biol Chem 276:6974-82</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="Granzyme_B_activates_BID_by_cleavageStep">
+ <STEP-INTERACTIONS rdf:resource="#Granzyme_B_activates_BID_by_cleavage" />
+ <NEXT-STEP rdf:resource="#tBID_activates_BAX_proteinStep" />
+ <NEXT-STEP rdf:resource="#Myristoylation_of_tBID_by_NMT1Step" />
+ <STEP-INTERACTIONS rdf:resource="#granzyme_B_activity_of_Granzyme_B__cytosol_" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="Myristoylation_of_tBID_by_NMT1">
+ <LEFT rdf:resource="#tBID_p15__cytosol_2" />
+ <RIGHT rdf:resource="#tBID__cytosol_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Myristoylation of tBID by NMT1</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Myristoylation of tBID by NMT1</SHORT-NAME>
+ <XREF rdf:resource="#Reactome141367" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">After proteolytic activation, tBID is myristoylated by NMT-1 at an exposed glycine. N-myristoylation may enable the activated tBID to associate with the lipid components of the mitochondrial membrane.</COMMENT>
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+ <XREF rdf:resource="#Pubmed_11099414" />
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ </biochemicalReaction>
+ <proteinParticipant rdf:ID="tBID_p15__cytosol_2">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P55957_BH3_interacting_domain_death_agonist__BID_" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="tBID__cytosol_">
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+ </proteinParticipant>
+ <catalysis rdf:ID="myristoyltransferase_activity_of_NMT_1__cytosol_">
+ <CONTROLLER rdf:resource="#NMT_1__cytosol_" />
+ <CONTROLLED rdf:resource="#Myristoylation_of_tBID_by_NMT1" />
+ <DIRECTION rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PHYSIOL-LEFT-TO-RIGHT</DIRECTION>
+ <XREF rdf:resource="#myristoyltransferase_activity" />
+ </catalysis>
+ <proteinParticipant rdf:ID="NMT_1__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P30419_1_Glycylpeptide_N_tetradecanoyltransferase_1__EC_2_3_1_97___Peptide_N__myristoyltransferase_1___Myristoyl_CoA_protein_N_myristoyltransferase_1___NMT_1___Type_I_N_myristoyltransferase_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_P30419_1_Glycylpeptide_N_tetradecanoyltransferase_1__EC_2_3_1_97___Peptide_N__myristoyltransferase_1___Myristoyl_CoA_protein_N_myristoyltransferase_1___NMT_1___Type_I_N_myristoyltransferase_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P30419-1 Glycylpeptide N-tetradecanoyltransferase 1 (EC 2.3.1.97) (Peptide N- myristoyltransferase 1) (Myristoyl-CoA:protein N-myristoyltransferase 1) (NMT 1) (Type I N-myristoyltransferase)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">NMT</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">NMT1</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P30419" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Adds a myristoyl group to the N-terminal glycine residue of certain cellular and viral proteins. CATALYTIC ACTIVITY: Tetradecanoyl-CoA + glycyl-peptide = CoA + N- tetradecanoylglycyl-peptide. SUBCELLULAR LOCATION: Cytoplasmic. ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=Long; IsoId=P30419-1; Sequence=Displayed; Name=Short; IsoId=P30419-2; Sequence=VSP_003570; TISSUE SPECIFICITY: Hea [...]
+ </protein>
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+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P30419</ID>
+ </unificationXref>
+ <relationshipXref rdf:ID="myristoyltransferase_activity">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GO</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0019107</ID>
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+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <evidence rdf:ID="Summation_142108" />
+ <publicationXref rdf:ID="Pubmed_11099414">
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+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2000</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Posttranslational N-myristoylation of BID as a molecular switch for targeting mitochondria and apoptosis</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Zha, J</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Weiler, S</AUTHORS>
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+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Science 290:1761-5</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="Myristoylation_of_tBID_by_NMT1Step">
+ <STEP-INTERACTIONS rdf:resource="#Myristoylation_of_tBID_by_NMT1" />
+ <NEXT-STEP rdf:resource="#Translocation_of_tBID_to_mitochondriaStep" />
+ <NEXT-STEP rdf:resource="#tBID_activates_BAK_proteinStep" />
+ <STEP-INTERACTIONS rdf:resource="#myristoyltransferase_activity_of_NMT_1__cytosol_" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="Translocation_of_tBID_to_mitochondria">
+ <LEFT rdf:resource="#tBID__cytosol_1" />
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+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Translocation of tBID to mitochondria</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Translocation of tBID to mitochondria</SHORT-NAME>
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+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ </biochemicalReaction>
+ <proteinParticipant rdf:ID="tBID__cytosol_1">
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+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P55957_BH3_interacting_domain_death_agonist__BID_" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="tBID__mitochondrial_outer_membrane_">
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P55957_BH3_interacting_domain_death_agonist__BID_" />
+ </proteinParticipant>
+ <openControlledVocabulary rdf:ID="mitochondrial_outer_membrane">
+ <TERM rdf:datatype="http://www.w3.org/2001/XMLSchema#string">mitochondrial outer membrane</TERM>
+ <XREF rdf:resource="#GO_0005741" />
+ </openControlledVocabulary>
+ <xref rdf:ID="GO_0005741">
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+ </xref>
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+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <pathwayStep rdf:ID="Translocation_of_tBID_to_mitochondriaStep">
+ <STEP-INTERACTIONS rdf:resource="#Translocation_of_tBID_to_mitochondria" />
+ <NEXT-STEP rdf:resource="#Sequestration_of_tBID_by_BCL_2Step" />
+ <NEXT-STEP rdf:resource="#Permeabilization_of_mitochondriaStep" />
+ <NEXT-STEP rdf:resource="#Interaction_of_tBID_with_BCL_xlStep" />
+ <NEXT-STEP rdf:resource="#Release_of_Cytochrome_c_from_mitochondriaStep" />
+ </pathwayStep>
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+ <evidence rdf:ID="Summation_140549">
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+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2003</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The Bcl-2 family: roles in cell survival and oncogenesis.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cory, S</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Huang, DC</AUTHORS>
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+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Oncogene 22:8590-607</SOURCE>
+ </publicationXref>
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+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1998</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cleavage of BID by caspase 8 mediates the mitochondrial damage in the Fas pathway of apoptosis</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Li, H</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Zhu, H</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Xu, CJ</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Yuan, J</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cell 94:491-501</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="Activation__myristolyation_of_BID_and_translocation_to_mitochondriaStep">
+ <STEP-INTERACTIONS rdf:resource="#Activation__myristolyation_of_BID_and_translocation_to_mitochondria" />
+ <NEXT-STEP rdf:resource="#Intrinsic_Pathway_for_ApoptosisStep" />
+ </pathwayStep>
+ <pathway rdf:ID="Intrinsic_Pathway_for_Apoptosis">
+ <PATHWAY-COMPONENTS rdf:resource="#Activation__translocation_and_oligomerization_of_BAXStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#BH3_only_proteins_associate_with_and_inactivate_anti_apoptotic_BCL_2_membersStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#Apoptotic_factor_mediated_responseStep" />
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+ <PATHWAY-COMPONENTS rdf:resource="#Activation_of_BH3_only_proteinsStep" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Intrinsic Pathway for Apoptosis</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Intrinsic Pathway for Apoptosis</SHORT-NAME>
+ <XREF rdf:resource="#Reactome109606" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The intrinsic (Bcl-2 inhibitable or mitochondrial) pathway of apoptosis functions in response to various types of intracellular stress including growth factor withdrawal, DNA damage, unfolding stresses in the endoplasmic reticulum and death receptor stimulation. Following the reception of stress signals, proapoptotic BCL-2 family proteins are activated and subsequently interact with and inactivate antiapoptotic BCL-2 pro [...]
+ <EVIDENCE rdf:resource="#Summation_140375" />
+ <XREF rdf:resource="#Pubmed_15077149" />
+ <XREF rdf:resource="#Pubmed_11711427" />
+ <XREF rdf:resource="#Pubmed_12042762" />
+ <XREF rdf:resource="#induction_of_apoptosis_by_intracellular_signals" />
+ </pathway>
+ <pathway rdf:ID="Activation_of_BH3_only_proteins">
+ <PATHWAY-COMPONENTS rdf:resource="#Activation_of_NOXA_and_translocation_to_mitochondriaStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#Activation_of_PUMA_and_translocation_to_mitochondriaStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#Activation_of_BAD_and_translocation_to_mitochondria_Step" />
+ <PATHWAY-COMPONENTS rdf:resource="#Activation_of_BIM_and_translocation_to_mitochondria_Step" />
+ <PATHWAY-COMPONENTS rdf:resource="#Activation_of_BMF_and_translocation_to_mitochondriaStep" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Activation of BH3-only proteins</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Activation of BH3-only proteins</SHORT-NAME>
+ <XREF rdf:resource="#Reactome114452" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The BH3-only members act as sentinels that selectively trigger apoptosis in response to developmental cues or stress-signals like DNA damages. Widely expressed mammalian BH3-only proteins are thought to act by binding to and neutralizing their pro-survival counterparts. Activation of BH3-only proteins directly or indirectly results in the activation of proapoptotic BAX and BAK to trigger cell death. Anti-apoptotic BCL-2 [...]
+ <EVIDENCE rdf:resource="#Summation_140552" />
+ <XREF rdf:resource="#activation_of_pro_apoptotic_gene_products" />
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ </pathway>
+ <pathway rdf:ID="Activation_of_BAD_and_translocation_to_mitochondria_">
+ <PATHWAY-COMPONENTS rdf:resource="#BAD_displaces_tBID_from_BCL_2_sequestrationStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#Akt1_phosphorylates_BAD_proteinStep" />
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+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Activation of BAD and translocation to mitochondria</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Activation of BAD and translocation to mitochondria</SHORT-NAME>
+ <XREF rdf:resource="#Reactome111447" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The switching on/off of its phosphorylation by growth/survival factors regulates BAD activity. BAD remains sequestered by 14-3-3 scaffold proteins after phosphorylation by Akt1. Calcineurin activates BAD by dephosphorylation.</COMMENT>
+ <EVIDENCE rdf:resource="#Summation_140545" />
+ <XREF rdf:resource="#Pubmed_15231831" />
+ <XREF rdf:resource="#activation_of_pro_apoptotic_gene_products" />
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ </pathway>
+ <biochemicalReaction rdf:ID="Akt1_phosphorylates_BAD_protein">
+ <LEFT rdf:resource="#BAD_protein__cytosol_" />
+ <RIGHT rdf:resource="#Phospho_BAD__cytosol_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Akt1 phosphorylates BAD protein</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Akt1 phosphorylates BAD protein</SHORT-NAME>
+ <XREF rdf:resource="#Reactome139903" />
+ <XREF rdf:resource="#Pubmed_15183529" />
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
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+ <proteinParticipant rdf:ID="BAD_protein__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q92934_Bcl2_antagonist_of_cell_death__BAD___Bcl_2_binding_component_6___Bcl__XL_Bcl_2_associated_death_promoter___Bcl_2_like_8_protein_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_Q92934_Bcl2_antagonist_of_cell_death__BAD___Bcl_2_binding_component_6___Bcl__XL_Bcl_2_associated_death_promoter___Bcl_2_like_8_protein_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:Q92934 Bcl2-antagonist of cell death (BAD) (Bcl-2 binding component 6) (Bcl- XL/Bcl-2 associated death promoter) (Bcl-2-like 8 protein)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BCL2L8</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BAD</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BBC6</SYNONYMS>
+ <XREF rdf:resource="#UniProt_Q92934" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Promotes cell death. Successfully competes for the binding to Bcl-X(L), Bcl-2 and Bcl-W, thereby affecting the level of heterodimerization of these proteins with BAX. Can reverse the death repressor activity of Bcl-X(L), but not that of Bcl-2 (By similarity). Appears to act as a link between growth factor receptor signaling and the apoptotic pathways. SUBUNIT: Forms heterodimers with the anti-apoptotic proteins [...]
+ </protein>
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+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Q92934</ID>
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+ <proteinParticipant rdf:ID="Phospho_BAD__cytosol_">
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+ </proteinParticipant>
+ <catalysis rdf:ID="kinase_activity_of_AKT1__cytosol_">
+ <CONTROLLER rdf:resource="#AKT1__cytosol_" />
+ <CONTROLLED rdf:resource="#Akt1_phosphorylates_BAD_protein" />
+ <DIRECTION rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PHYSIOL-LEFT-TO-RIGHT</DIRECTION>
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+ </catalysis>
+ <proteinParticipant rdf:ID="AKT1__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P31749_RAC_alpha_serine_threonine_protein_kinase__EC_2_7_1_37___RAC_PK_alpha___Protein_kinase_B___PKB___C_AKT_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_P31749_RAC_alpha_serine_threonine_protein_kinase__EC_2_7_1_37___RAC_PK_alpha___Protein_kinase_B___PKB___C_AKT_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P31749 RAC-alpha serine/threonine-protein kinase (EC 2.7.1.37) (RAC-PK-alpha) (Protein kinase B) (PKB) (C-AKT)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PKB</SYNONYMS>
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+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">AKT1</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P31749" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: General protein kinase capable of phosphorylating several known proteins. CATALYTIC ACTIVITY: ATP + a protein = ADP + a phosphoprotein. SUBCELLULAR LOCATION: Cytoplasmic and nuclear after activation by integrin-linked protein kinase 1 (ILK1). TISSUE SPECIFICITY: In all human cell types so far analyzed. DOMAIN: Binding of the PH domain to the phosphatidylinositol 3- kinase alpha (PI(3)K) results in its targeting [...]
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+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Positive correlation between overexpression of phospho-BAD with phosphorylated Akt at serine 15183529</TITLE>
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+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cancer Lett 210:139-50</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="Akt1_phosphorylates_BAD_proteinStep">
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+ <NEXT-STEP rdf:resource="#Sequesteration_of_BAD_protein_by_14_3_3Step" />
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+ <biochemicalReaction rdf:ID="Sequesteration_of_BAD_protein_by_14_3_3">
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+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P31946 14-3-3 protein beta/alpha (Protein kinase C inhibitor protein-1) (KCIP-1) (Protein 1054)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">YWHAB</SYNONYMS>
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+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Activates tyrosine and tryptophan hydroxylases in the presence of Ca(2+)/calmodulin-dependent protein kinase II, and strongly activates protein kinase C. Is probably a multifunctional regulator of the cell signaling processes mediated by both kinases. SUBUNIT: Homodimer. SUBCELLULAR LOCATION: Cytoplasmic. ALTERNATIVE PRODUCTS: Event=Alternative initiation; Comment=2 isoforms, Long (shown here) and Short, are pr [...]
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+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P31946</ID>
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+ </proteinParticipant>
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+ <complex rdf:ID="_143B_phospo_BAD_complex__cytosol_1">
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+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">143B:phospo-BAD complex [cytosol]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">143B:phospo-BAD complex</SHORT-NAME>
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+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cleavage of 14-3-3 protein by caspase-3 facilitates bad interaction with Bcl-x(L) during apoptosis</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Won, J</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Kim, DY</AUTHORS>
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+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Biol Chem 278:19347-51</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="Sequesteration_of_BAD_protein_by_14_3_3Step">
+ <STEP-INTERACTIONS rdf:resource="#Sequesteration_of_BAD_protein_by_14_3_3" />
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+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Activation of BAD by calcineurin</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Activation of BAD by calcineurin</SHORT-NAME>
+ <XREF rdf:resource="#Reactome139906" />
+ <XREF rdf:resource="#Pubmed_10195903" />
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ </biochemicalReaction>
+ <complexParticipant rdf:ID="_143B_phospo_BAD_complex__cytosol_2">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#_143B_phospo_BAD_complex__cytosol_1" />
+ </complexParticipant>
+ <proteinParticipant rdf:ID="BAD_protein__cytosol_1">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q92934_Bcl2_antagonist_of_cell_death__BAD___Bcl_2_binding_component_6___Bcl__XL_Bcl_2_associated_death_promoter___Bcl_2_like_8_protein_" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="_143B_protein__cytosol_2">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P31946_14_3_3_protein_beta_alpha__Protein_kinase_C_inhibitor_protein_1___KCIP_1___Protein_1054_" />
+ </proteinParticipant>
+ <catalysis rdf:ID="calcium_dependent_protein_serine_threonine_phosphatase_regulator_activity_of_Calcineurin_B_complex__cytosol_">
+ <CONTROLLER rdf:resource="#Calcineurin_B_complex__cytosol_" />
+ <CONTROLLED rdf:resource="#Activation_of_BAD_by_calcineurin" />
+ <DIRECTION rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PHYSIOL-LEFT-TO-RIGHT</DIRECTION>
+ <XREF rdf:resource="#calcium_dependent_protein_serine_threonine_phosphatase_regulator_activity" />
+ </catalysis>
+ <complexParticipant rdf:ID="Calcineurin_B_complex__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#Calcineurin_B_complex__cytosol_1" />
+ </complexParticipant>
+ <complex rdf:ID="Calcineurin_B_complex__cytosol_1">
+ <COMPONENTS rdf:resource="#Calcineurin_B_gamma__catalytic__cytosol_" />
+ <COMPONENTS rdf:resource="#Calcineurin_B__alpha_regulatory__cytosol_" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Calcineurin B complex [cytosol]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Calcineurin B complex</SHORT-NAME>
+ </complex>
+ <proteinParticipant rdf:ID="Calcineurin_B_gamma__catalytic__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P48454_Serine_threonine_protein_phosphatase_2B_catalytic_subunit__gamma_isoform__EC_3_1_3_16___Calmodulin_dependent_calcineurin_A_subunit__gamma_isoform___Calcineurin__testis_specific_catalytic_subunit___CAM__PRP_catalytic_subunit_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_P48454_Serine_threonine_protein_phosphatase_2B_catalytic_subunit__gamma_isoform__EC_3_1_3_16___Calmodulin_dependent_calcineurin_A_subunit__gamma_isoform___Calcineurin__testis_specific_catalytic_subunit___CAM__PRP_catalytic_subunit_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P48454 Serine/threonine protein phosphatase 2B catalytic subunit, gamma isoform (EC 3.1.3.16) (Calmodulin-dependent calcineurin A subunit, gamma isoform) (Calcineurin, testis-specific catalytic subunit) (CAM- PRP catalytic subunit)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CALNA3</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PPP3CC</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CNA3</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P48454" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Calcium-dependent, calmodulin-stimulated protein phosphatase. This subunit may have a role in the calmodulin activation of calcineurin. CATALYTIC ACTIVITY: A phosphoprotein + H(2)O = a protein + phosphate. COFACTOR: Binds 1 iron(III) ion and 1 zinc ion per subunit (By similarity). SUBUNIT: Composed of two components (A and B), the A component is the catalytic subunit and the B component confers calcium sensitiv [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_P48454">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P48454</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="Calcineurin_B__alpha_regulatory__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P63098_Calcineurin_B_subunit_isoform_1__Protein_phosphatase_2B_regulatory_subunit_1___Protein_phosphatase_3_regulatory_subunit_B_alpha_isoform_1_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_P63098_Calcineurin_B_subunit_isoform_1__Protein_phosphatase_2B_regulatory_subunit_1___Protein_phosphatase_3_regulatory_subunit_B_alpha_isoform_1_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P63098 Calcineurin B subunit isoform 1 (Protein phosphatase 2B regulatory subunit 1) (Protein phosphatase 3 regulatory subunit B alpha isoform 1)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CNA2</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CNB</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PPP3R1</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P63098" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Regulatory subunit of calcineurin, a calcium-dependent, calmodulin stimulated protein phosphatase. Confers calcium sensitivity. SUBUNIT: Composed of a catalytic subunit (A) and a regulatory subunit (B). MISCELLANEOUS: This protein has four functional calcium-binding sites. SIMILARITY: Contains 4 EF-hand calcium-binding domains.</COMMENT>
+ </protein>
+ <unificationXref rdf:ID="UniProt_P63098">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P63098</ID>
+ </unificationXref>
+ <relationshipXref rdf:ID="calcium_dependent_protein_serine_threonine_phosphatase_regulator_activity">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GO</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0008597</ID>
+ </relationshipXref>
+ <unificationXref rdf:ID="Reactome139906">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">139906</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <publicationXref rdf:ID="Pubmed_10195903">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">10195903</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1999</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Ca2+-induced apoptosis through calcineurin dephosphorylation of BAD.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Wang, HG</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pathan, N</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Ethell, IM</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Krajewski, S</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Yamaguchi, Y</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Shibasaki, F</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">McKeon, F</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bobo, T</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Franke, TF</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reed, JC</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Science 284:339-43</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="Activation_of_BAD_by_calcineurinStep">
+ <STEP-INTERACTIONS rdf:resource="#Activation_of_BAD_by_calcineurin" />
+ <NEXT-STEP rdf:resource="#Interaction__of_BAD_with_BCL_xl___Step" />
+ <NEXT-STEP rdf:resource="#Interaction_of_BAD_with_BCL2__Step" />
+ <NEXT-STEP rdf:resource="#Translocation_of_activated_BAD_protein_to_mitochondriaStep" />
+ <STEP-INTERACTIONS rdf:resource="#calcium_dependent_protein_serine_threonine_phosphatase_regulator_activity_of_Calcineurin_B_complex__cytosol_" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="Translocation_of_activated_BAD_protein_to_mitochondria">
+ <LEFT rdf:resource="#BAD_protein__cytosol_2" />
+ <RIGHT rdf:resource="#BAD_protein__mitochondrial_outer_membrane_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Translocation of activated BAD protein to mitochondria</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Translocation of activated BAD protein to mitochondria</SHORT-NAME>
+ <XREF rdf:resource="#Reactome139905" />
+ <XREF rdf:resource="#protein_insertion_into_mitochondrial_membrane_during_induction_of_apoptosis" />
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ </biochemicalReaction>
+ <proteinParticipant rdf:ID="BAD_protein__cytosol_2">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q92934_Bcl2_antagonist_of_cell_death__BAD___Bcl_2_binding_component_6___Bcl__XL_Bcl_2_associated_death_promoter___Bcl_2_like_8_protein_" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="BAD_protein__mitochondrial_outer_membrane_">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q92934_Bcl2_antagonist_of_cell_death__BAD___Bcl_2_binding_component_6___Bcl__XL_Bcl_2_associated_death_promoter___Bcl_2_like_8_protein_" />
+ </proteinParticipant>
+ <unificationXref rdf:ID="Reactome139905">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">139905</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <relationshipXref rdf:ID="protein_insertion_into_mitochondrial_membrane_during_induction_of_apoptosis">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GO</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0001844</ID>
+ </relationshipXref>
+ <pathwayStep rdf:ID="Translocation_of_activated_BAD_protein_to_mitochondriaStep">
+ <STEP-INTERACTIONS rdf:resource="#Translocation_of_activated_BAD_protein_to_mitochondria" />
+ <NEXT-STEP rdf:resource="#BAD_displaces_tBID_from_BCL_2_sequestrationStep" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="BAD_displaces_tBID_from_BCL_2_sequestration">
+ <LEFT rdf:resource="#BAD_protein__mitochondrial_outer_membrane_1" />
+ <LEFT rdf:resource="#tBID_BCL_2__mitochondrial_outer_membrane_" />
+ <RIGHT rdf:resource="#tBID__mitochondrial_outer_membrane_2" />
+ <RIGHT rdf:resource="#BAD_BCL_2__mitochondrial_outer_membrane_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BAD displaces tBID from BCL-2 sequestration</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BAD displaces tBID from BCL-2 sequestration</SHORT-NAME>
+ <XREF rdf:resource="#Reactome139897" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Short peptides representing BAD and BIX were found to bind BCL-2 displacing BID-like BH3 domains that initiate mitochondrial dysfunction.</COMMENT>
+ <EVIDENCE rdf:resource="#Summation_140378" />
+ </biochemicalReaction>
+ <proteinParticipant rdf:ID="BAD_protein__mitochondrial_outer_membrane_1">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q92934_Bcl2_antagonist_of_cell_death__BAD___Bcl_2_binding_component_6___Bcl__XL_Bcl_2_associated_death_promoter___Bcl_2_like_8_protein_" />
+ </proteinParticipant>
+ <complexParticipant rdf:ID="tBID_BCL_2__mitochondrial_outer_membrane_">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#tBID_BCL_2__mitochondrial_outer_membrane_1" />
+ </complexParticipant>
+ <complex rdf:ID="tBID_BCL_2__mitochondrial_outer_membrane_1">
+ <COMPONENTS rdf:resource="#tBID__mitochondrial_outer_membrane_1" />
+ <COMPONENTS rdf:resource="#Bcl_2_protein__mitochondrial_outer_membrane_" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">tBID:BCL-2 [mitochondrial outer membrane]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">tBID:BCL-2</SHORT-NAME>
+ </complex>
+ <proteinParticipant rdf:ID="tBID__mitochondrial_outer_membrane_1">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P55957_BH3_interacting_domain_death_agonist__BID_" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="Bcl_2_protein__mitochondrial_outer_membrane_">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P10415_1_Apoptosis_regulator_Bcl_2" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_P10415_1_Apoptosis_regulator_Bcl_2">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P10415-1 Apoptosis regulator Bcl-2</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BCL2</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P10415" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Suppresses apoptosis in a variety of cell systems including factor-dependent lymphohematopoietic and neural cells. Regulates cell death by controlling the mitochondrial membrane permeability. Appears to function in a feedback loop system with caspases. Inhibits caspase activity either by preventing the release of cytochrome c from the mitochondria and/or by binding to the apoptosis-activating factor (APAF-1). S [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_P10415">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P10415</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="tBID__mitochondrial_outer_membrane_2">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P55957_BH3_interacting_domain_death_agonist__BID_" />
+ </proteinParticipant>
+ <complexParticipant rdf:ID="BAD_BCL_2__mitochondrial_outer_membrane_">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#BAD_BCL_2__mitochondrial_outer_membrane_1" />
+ </complexParticipant>
+ <complex rdf:ID="BAD_BCL_2__mitochondrial_outer_membrane_1">
+ <COMPONENTS rdf:resource="#BAD_protein__mitochondrial_outer_membrane_2" />
+ <COMPONENTS rdf:resource="#Bcl_2_protein__mitochondrial_outer_membrane_1" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BAD:BCL-2 [mitochondrial outer membrane]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BAD:BCL-2</SHORT-NAME>
+ </complex>
+ <proteinParticipant rdf:ID="BAD_protein__mitochondrial_outer_membrane_2">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q92934_Bcl2_antagonist_of_cell_death__BAD___Bcl_2_binding_component_6___Bcl__XL_Bcl_2_associated_death_promoter___Bcl_2_like_8_protein_" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="Bcl_2_protein__mitochondrial_outer_membrane_1">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P10415_1_Apoptosis_regulator_Bcl_2" />
+ </proteinParticipant>
+ <unificationXref rdf:ID="Reactome139897">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">139897</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <evidence rdf:ID="Summation_140378">
+ <XREF rdf:resource="#Pubmed_12242151" />
+ </evidence>
+ <publicationXref rdf:ID="Pubmed_12242151">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">12242151</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2002</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Distinct BH3 domains either sensitize or activate mitochondrial apoptosis, serving as prototype cancer therapeutics</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Letai, A</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bassik, MC</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Walensky, LD</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Sorcinelli, MD</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Weiler, S</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Korsmeyer, SJ</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cancer Cell 2:183-92</SOURCE>
+ </publicationXref>
+ <openControlledVocabulary rdf:ID="mitochondrial_membrane">
+ <TERM rdf:datatype="http://www.w3.org/2001/XMLSchema#string">mitochondrial membrane</TERM>
+ <XREF rdf:resource="#GO_0005740" />
+ </openControlledVocabulary>
+ <xref rdf:ID="GO_0005740">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GO</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0005740</ID>
+ </xref>
+ <pathwayStep rdf:ID="BAD_displaces_tBID_from_BCL_2_sequestrationStep">
+ <STEP-INTERACTIONS rdf:resource="#BAD_displaces_tBID_from_BCL_2_sequestration" />
+ </pathwayStep>
+ <unificationXref rdf:ID="Reactome111447">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">111447</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <evidence rdf:ID="Summation_140545">
+ <XREF rdf:resource="#Pubmed_12209154" />
+ </evidence>
+ <publicationXref rdf:ID="Pubmed_12209154">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">12209154</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2002</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The Bcl2 family: regulators of the cellular life-or-death switch</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cory, S</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Adams, JM</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Nat Rev Cancer 2:647-56</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_15231831">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">15231831</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2004</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BAD Is a Pro-survival Factor Prior to Activation of Its Pro-apoptotic Function.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Seo, SY</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Chen, YB</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Ivanovska, I</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Ranger, AM</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Hong, SJ</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Dawson, VL</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Korsmeyer, SJ</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bellows, DS</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Fannjiang, Y</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Hardwick, JM</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Biol Chem 279:42240-9</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="Activation_of_BAD_and_translocation_to_mitochondria_Step">
+ <STEP-INTERACTIONS rdf:resource="#Activation_of_BAD_and_translocation_to_mitochondria_" />
+ </pathwayStep>
+ <pathway rdf:ID="Activation_of_NOXA_and_translocation_to_mitochondria">
+ <PATHWAY-COMPONENTS rdf:resource="#Transactivation_of_NOXA_by_E2F1Step" />
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+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q13794_Phorbol_12_myristate_13_acetate_induced_protein_1__PMA_induced_protein_1___Immediate_early_response_protein_APR_" />
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+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:Q13794 Phorbol-12-myristate-13-acetate-induced protein 1 (PMA-induced protein 1) (Immediate-early-response protein APR)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PMAIP1</SYNONYMS>
+ <XREF rdf:resource="#UniProt_Q13794" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TISSUE SPECIFICITY: Highly expressed in adult T-cell leukemia cell line.</COMMENT>
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+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Apoptotic signaling pathways induced by nitric oxide in human lymphoblastoid cells expressing wild-type or mutant p53</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Li, CQ</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Robles, AI</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Hanigan, CL</AUTHORS>
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+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cancer Res 64:3022-9</SOURCE>
+ </publicationXref>
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+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Transactivation of NOXA by E2F1</NAME>
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+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q13794_Phorbol_12_myristate_13_acetate_induced_protein_1__PMA_induced_protein_1___Immediate_early_response_protein_APR_" />
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+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Up-regulation of Bcl-2 homology 3 (BH3)-only proteins by E2F1 mediates apoptosis</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Hershko, T</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Ginsberg, D</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Biol Chem 279:8627-34</SOURCE>
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+ <LEFT rdf:resource="#NOXA_protein__cytosol_2" />
+ <RIGHT rdf:resource="#NOXA_protein__mitochondrial_outer_membrane_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Translocation of NOXA to mitochondria</NAME>
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+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">It was observed that cytosolic Noxa underwent BH3 motif-dependent localization to mitochondria and interacted with anti-apoptotic Bcl-2 family members, resulting in the activation of caspase-9.</COMMENT>
+ <EVIDENCE rdf:resource="#Summation_140386" />
+ <XREF rdf:resource="#protein_insertion_into_mitochondrial_membrane_during_induction_of_apoptosis" />
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+ </proteinParticipant>
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+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2000</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Noxa, a BH3-only member of the Bcl-2 family and candidate mediator of p53-induced apoptosis</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Oda, E</AUTHORS>
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+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Science 288:1053-8</SOURCE>
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+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Activation of PUMA and translocation to mitochondria</NAME>
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+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2001</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PUMA, a novel proapoptotic gene, is induced by p53</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Nakano, K</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Vousden, KH</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mol Cell 7:683-94</SOURCE>
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+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">'transcriptional activator activity of E2F1 [nucleoplasm]' positively regulates 'Transactivation of PUMA by E2F1'</NAME>
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+ <biochemicalReaction rdf:ID="Translocation_of_PUMA_protein_to_mitochondria">
+ <LEFT rdf:resource="#PUMA_protein__cytosol_2" />
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+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Translocation of PUMA protein to mitochondria</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Translocation of PUMA protein to mitochondria</SHORT-NAME>
+ <XREF rdf:resource="#Reactome139914" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">It is thought that due to its p53 dependence for expression, PUMA could function as a mediator of p53-induced apoptosis. Newly synthesized PUMA protein translocates to mitochondria and binds to BCL-2 and Bcl-X(L) through a BH3 domain.</COMMENT>
+ <EVIDENCE rdf:resource="#Summation_140403" />
+ <XREF rdf:resource="#protein_insertion_into_mitochondrial_membrane_during_induction_of_apoptosis" />
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
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+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2001</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PUMA induces the rapid apoptosis of colorectal cancer cells</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Yu, J</AUTHORS>
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+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <pathwayStep rdf:ID="Activation_of_PUMA_and_translocation_to_mitochondriaStep">
+ <STEP-INTERACTIONS rdf:resource="#Activation_of_PUMA_and_translocation_to_mitochondria" />
+ </pathwayStep>
+ <pathway rdf:ID="Activation_of_BIM_and_translocation_to_mitochondria_">
+ <PATHWAY-COMPONENTS rdf:resource="#Phosphorylation_of_DLC1_by_MAPK_8Step" />
+ <PATHWAY-COMPONENTS rdf:resource="#Translocation_of_BIM_to_mitochondriaStep" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Activation of BIM and translocation to mitochondria</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Activation of BIM and translocation to mitochondria</SHORT-NAME>
+ <XREF rdf:resource="#Reactome111446" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BIM acts as a sentinel to check the integrity of the cytoskeleton. It exists as two variant proteins: BIM-EL and BIM-L. In healthy cells, these two isoforms are sequestered to the dynein motor complex on microtubules via the dynein light chain DLC1. JNK or MAPK8 releases BIM in response to UV irradiation by phosphorylation.</COMMENT>
+ <EVIDENCE rdf:resource="#Summation_140550" />
+ <XREF rdf:resource="#Pubmed_14764673" />
+ <XREF rdf:resource="#activation_of_pro_apoptotic_gene_products" />
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ </pathway>
+ <biochemicalReaction rdf:ID="Phosphorylation_of_DLC1_by_MAPK_8">
+ <LEFT rdf:resource="#BIM_sequestered_to_dynein__DLC1___plasma_membrane_" />
+ <RIGHT rdf:resource="#BIM__cytosol_" />
+ <RIGHT rdf:resource="#phospho_dynein_DLC1__on_microtubules__plasma_membrane_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Phosphorylation of DLC1 by MAPK 8</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Phosphorylation of DLC1 by MAPK 8</SHORT-NAME>
+ <XREF rdf:resource="#Reactome139918" />
+ <XREF rdf:resource="#Pubmed_12591950" />
+ <CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ </biochemicalReaction>
+ <complexParticipant rdf:ID="BIM_sequestered_to_dynein__DLC1___plasma_membrane_">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#BIM_sequestered_to_dynein__DLC1___plasma_membrane_1" />
+ </complexParticipant>
+ <complex rdf:ID="BIM_sequestered_to_dynein__DLC1___plasma_membrane_1">
+ <COMPONENTS rdf:resource="#BIM_protein__plasma_membrane_" />
+ <COMPONENTS rdf:resource="#DLC1__plasma_membrane_" />
+ <COMPONENTS rdf:resource="#microtubules__plasma_membrane_" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BIM sequestered to dynein (DLC1) [plasma membrane]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BIM sequestered to dynein (DLC1)</SHORT-NAME>
+ </complex>
+ <proteinParticipant rdf:ID="BIM_protein__plasma_membrane_">
+ <CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_O43521_1_Bcl_2_like_protein_11__Bcl2_interacting_mediator_of_cell_death_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_O43521_1_Bcl_2_like_protein_11__Bcl2_interacting_mediator_of_cell_death_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:O43521-1 Bcl-2-like protein 11 (Bcl2 interacting mediator of cell death)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BCL2L11</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BIM</SYNONYMS>
+ <XREF rdf:resource="#UniProt_O43521" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Induces apoptosis. Isoform BimL is more potent than isoform BimEL. SUBUNIT: Forms heterodimers with a number of antiapoptotic Bcl-2 proteins including Mcl-1, Bcl-2, Bcl-X(L), BFL-1, and BHRF1. Does not heterodimerize with proapoptotic proteins such as BAD, BOK, BAX or BAK (By similarity). SUBCELLULAR LOCATION: Associated with intracytoplasmic membranes (By similarity). ALTERNATIVE PRODUCTS: Event=Alternative sp [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_O43521">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">O43521</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="DLC1__plasma_membrane_">
+ <CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P63167_Dynein_light_chain_1__cytoplasmic__8_kDa_dynein_light_chain___DLC8___Protein_inhibitor_of_neuronal_nitric_oxide_synthase___PIN_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_P63167_Dynein_light_chain_1__cytoplasmic__8_kDa_dynein_light_chain___DLC8___Protein_inhibitor_of_neuronal_nitric_oxide_synthase___PIN_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P63167 Dynein light chain 1, cytoplasmic (8 kDa dynein light chain) (DLC8) (Protein inhibitor of neuronal nitric oxide synthase) (PIN)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DNCL1</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DNCLC1</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DLC1</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">HDLC1</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P63167" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: May be involved in some aspects of dynein-related intracellular transport and motility. May play a role in changing or maintaining the spatial distribution of cytoskeletal structures. FUNCTION: Binds and inhibits the catalytic activity of neuronal nitric oxide synthase. SUBUNIT: Consists of at least two heavy chains and a number of intermediate and light chains. SUBCELLULAR LOCATION: Cytoplasmic. TISSUE SPECIFI [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_P63167">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P63167</ID>
+ </unificationXref>
+ <physicalEntityParticipant rdf:ID="microtubules__plasma_membrane_">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#microtubules__plasma_membrane_1" />
+ </physicalEntityParticipant>
+ <physicalEntity rdf:ID="microtubules__plasma_membrane_1">
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">microtubules [plasma membrane]</NAME>
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome. Each synonym is a name of a ConcreteEntity, and each XREF points to one ConcreteEntity</COMMENT>
+ </physicalEntity>
+ <proteinParticipant rdf:ID="BIM__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_O43521_1_Bcl_2_like_protein_11__Bcl2_interacting_mediator_of_cell_death_" />
+ </proteinParticipant>
+ <complexParticipant rdf:ID="phospho_dynein_DLC1__on_microtubules__plasma_membrane_">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#phospho_dynein_DLC1__on_microtubules__plasma_membrane_1" />
+ </complexParticipant>
+ <complex rdf:ID="phospho_dynein_DLC1__on_microtubules__plasma_membrane_1">
+ <COMPONENTS rdf:resource="#Phospho_DLC1__cytosol_" />
+ <COMPONENTS rdf:resource="#microtubules__plasma_membrane_2" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">phospho-dynein(DLC1) on microtubules [plasma membrane]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">phospho-dynein(DLC1) on microtubules</SHORT-NAME>
+ </complex>
+ <proteinParticipant rdf:ID="Phospho_DLC1__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P63167_Dynein_light_chain_1__cytoplasmic__8_kDa_dynein_light_chain___DLC8___Protein_inhibitor_of_neuronal_nitric_oxide_synthase___PIN_" />
+ </proteinParticipant>
+ <physicalEntityParticipant rdf:ID="microtubules__plasma_membrane_2">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#microtubules__plasma_membrane_1" />
+ </physicalEntityParticipant>
+ <catalysis rdf:ID="kinase_activity_of_Mitogen_activated_protein_kinase_8___cytosol_">
+ <CONTROLLER rdf:resource="#Mitogen_activated_protein_kinase_8___cytosol_" />
+ <CONTROLLED rdf:resource="#Phosphorylation_of_DLC1_by_MAPK_8" />
+ <DIRECTION rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PHYSIOL-LEFT-TO-RIGHT</DIRECTION>
+ <XREF rdf:resource="#kinase_activity" />
+ </catalysis>
+ <proteinParticipant rdf:ID="Mitogen_activated_protein_kinase_8___cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P45983_1_Mitogen_activated_protein_kinase_8__EC_2_7_1_37___Stress_activated_protein_kinase_JNK1___c_Jun_N_terminal_kinase_1___JNK_46_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_P45983_1_Mitogen_activated_protein_kinase_8__EC_2_7_1_37___Stress_activated_protein_kinase_JNK1___c_Jun_N_terminal_kinase_1___JNK_46_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P45983-1 Mitogen-activated protein kinase 8 (EC 2.7.1.37) (Stress-activated protein kinase JNK1) (c-Jun N-terminal kinase 1) (JNK-46)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PRKM8</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">JNK1</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">MAPK8</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P45983" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Responds to activation by environmental stress and pro- inflammatory cytokines by phosphorylating a number of transcription factors, primarily components of AP-1 such as c-Jun and ATF2 and thus regulates AP-1 transcriptional activity. In T- cells, JNK1 and JNK2 are required for polarized differentiation of T-helper cells into Th1 cells (By similarity). FUNCTION: JNK1 isoforms display different binding patterns: [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_P45983">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P45983</ID>
+ </unificationXref>
+ <unificationXref rdf:ID="Reactome139918">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">139918</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <publicationXref rdf:ID="Pubmed_12591950">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">12591950</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2003</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">JNK phosphorylation of Bim-related members of the Bcl2 family induces Bax-dependent apoptosis</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Lei, K</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Davis, RJ</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Proc Natl Acad Sci U S A 100:2432-7</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="Phosphorylation_of_DLC1_by_MAPK_8Step">
+ <STEP-INTERACTIONS rdf:resource="#Phosphorylation_of_DLC1_by_MAPK_8" />
+ <STEP-INTERACTIONS rdf:resource="#kinase_activity_of_Mitogen_activated_protein_kinase_8___cytosol_" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="Translocation_of_BIM_to_mitochondria">
+ <LEFT rdf:resource="#BIM__cytosol_1" />
+ <RIGHT rdf:resource="#BIM__mitochondrial_outer_membrane_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Translocation of BIM to mitochondria</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Translocation of BIM to mitochondria</SHORT-NAME>
+ <XREF rdf:resource="#Reactome139919" />
+ <XREF rdf:resource="#protein_insertion_into_mitochondrial_membrane_during_induction_of_apoptosis" />
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ </biochemicalReaction>
+ <proteinParticipant rdf:ID="BIM__cytosol_1">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_O43521_1_Bcl_2_like_protein_11__Bcl2_interacting_mediator_of_cell_death_" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="BIM__mitochondrial_outer_membrane_">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_O43521_1_Bcl_2_like_protein_11__Bcl2_interacting_mediator_of_cell_death_" />
+ </proteinParticipant>
+ <unificationXref rdf:ID="Reactome139919">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">139919</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <pathwayStep rdf:ID="Translocation_of_BIM_to_mitochondriaStep">
+ <STEP-INTERACTIONS rdf:resource="#Translocation_of_BIM_to_mitochondria" />
+ <NEXT-STEP rdf:resource="#Interaction_of_BIM_with_BCL2_Step" />
+ </pathwayStep>
+ <unificationXref rdf:ID="Reactome111446">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">111446</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <evidence rdf:ID="Summation_140550">
+ <XREF rdf:resource="#Pubmed_14634621" />
+ </evidence>
+ <publicationXref rdf:ID="Pubmed_14764673">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">14764673</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2004</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">B cell receptor-mediated apoptosis of human lymphocytes is associated with a new regulatory pathway of Bim isoform expression.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mouhamad, S</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Besnault, L</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Auffredou, MT</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Leprince, C</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bourgeade, MF</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Leca, G</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Vazquez, A</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Immunol 172:2084-91</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="Activation_of_BIM_and_translocation_to_mitochondria_Step">
+ <STEP-INTERACTIONS rdf:resource="#Activation_of_BIM_and_translocation_to_mitochondria_" />
+ </pathwayStep>
+ <pathway rdf:ID="Activation_of_BMF_and_translocation_to_mitochondria">
+ <PATHWAY-COMPONENTS rdf:resource="#Translocation_of_BMF_to_mitochondriaStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#Phosphorylation_of_DLC2_by_MAPK_8Step" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Activation of BMF and translocation to mitochondria</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Activation of BMF and translocation to mitochondria</SHORT-NAME>
+ <XREF rdf:resource="#Reactome139910" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">In healthy cells, BMF is bound to the myosin V motor complex through its interaction with DLC2. UV irradiation or anoikis induces MAPK8 (JNK) to phosphorylate Dynein Light Chain 2 (DLC2) to release BMF.</COMMENT>
+ <EVIDENCE rdf:resource="#Summation_140551" />
+ <XREF rdf:resource="#activation_of_pro_apoptotic_gene_products" />
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ </pathway>
+ <biochemicalReaction rdf:ID="Phosphorylation_of_DLC2_by_MAPK_8">
+ <LEFT rdf:resource="#BMF_sequestered_to_dynein__DLC2___plasma_membrane_" />
+ <RIGHT rdf:resource="#BMF__cytosol_" />
+ <RIGHT rdf:resource="#phospho_dynein_DLC2__on_microtubules__plasma_membrane_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Phosphorylation of DLC2 by MAPK-8</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Phosphorylation of DLC2 by MAPK-8</SHORT-NAME>
+ <XREF rdf:resource="#Reactome139908" />
+ <XREF rdf:resource="#Pubmed_12591950" />
+ <CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ </biochemicalReaction>
+ <complexParticipant rdf:ID="BMF_sequestered_to_dynein__DLC2___plasma_membrane_">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#BMF_sequestered_to_dynein__DLC2___plasma_membrane_1" />
+ </complexParticipant>
+ <complex rdf:ID="BMF_sequestered_to_dynein__DLC2___plasma_membrane_1">
+ <COMPONENTS rdf:resource="#DLC2__plasma_membrane_" />
+ <COMPONENTS rdf:resource="#BMF_protein__plasma_membrane_" />
+ <COMPONENTS rdf:resource="#microtubules__plasma_membrane_3" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BMF sequestered to dynein (DLC2) [plasma membrane]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BMF sequestered to dynein (DLC2)</SHORT-NAME>
+ </complex>
+ <proteinParticipant rdf:ID="DLC2__plasma_membrane_">
+ <CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q96FJ2" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_Q96FJ2">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:Q96FJ2</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DLC1</SHORT-NAME>
+ <XREF rdf:resource="#UniProt_Q96FJ21" />
+ </protein>
+ <unificationXref rdf:ID="UniProt_Q96FJ21">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Q96FJ2</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="BMF_protein__plasma_membrane_">
+ <CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q96LC9_BMF_protein" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_Q96LC9_BMF_protein">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:Q96LC9 BMF protein</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BMF protein</SHORT-NAME>
+ <XREF rdf:resource="#UniProt_Q96LC9" />
+ </protein>
+ <unificationXref rdf:ID="UniProt_Q96LC9">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Q96LC9</ID>
+ </unificationXref>
+ <physicalEntityParticipant rdf:ID="microtubules__plasma_membrane_3">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#microtubules__plasma_membrane_1" />
+ </physicalEntityParticipant>
+ <proteinParticipant rdf:ID="BMF__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q96LC9_BMF_protein" />
+ </proteinParticipant>
+ <complexParticipant rdf:ID="phospho_dynein_DLC2__on_microtubules__plasma_membrane_">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#phospho_dynein_DLC2__on_microtubules__plasma_membrane_1" />
+ </complexParticipant>
+ <complex rdf:ID="phospho_dynein_DLC2__on_microtubules__plasma_membrane_1">
+ <COMPONENTS rdf:resource="#Phospho_DLC2__cytosol_" />
+ <COMPONENTS rdf:resource="#microtubules__plasma_membrane_4" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">phospho-dynein(DLC2) on microtubules [plasma membrane]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">phospho-dynein(DLC2) on microtubules</SHORT-NAME>
+ </complex>
+ <proteinParticipant rdf:ID="Phospho_DLC2__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q96FJ2" />
+ </proteinParticipant>
+ <physicalEntityParticipant rdf:ID="microtubules__plasma_membrane_4">
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Converted from GenericEntity in Reactome</COMMENT>
+ <CELLULAR-LOCATION rdf:resource="#plasma_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#microtubules__plasma_membrane_1" />
+ </physicalEntityParticipant>
+ <catalysis rdf:ID="kinase_activity_of_Mitogen_activated_protein_kinase_8___cytosol_1">
+ <CONTROLLER rdf:resource="#Mitogen_activated_protein_kinase_8___cytosol_1" />
+ <CONTROLLED rdf:resource="#Phosphorylation_of_DLC2_by_MAPK_8" />
+ <DIRECTION rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PHYSIOL-LEFT-TO-RIGHT</DIRECTION>
+ <XREF rdf:resource="#kinase_activity" />
+ </catalysis>
+ <proteinParticipant rdf:ID="Mitogen_activated_protein_kinase_8___cytosol_1">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P45983_1_Mitogen_activated_protein_kinase_8__EC_2_7_1_37___Stress_activated_protein_kinase_JNK1___c_Jun_N_terminal_kinase_1___JNK_46_" />
+ </proteinParticipant>
+ <unificationXref rdf:ID="Reactome139908">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">139908</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <pathwayStep rdf:ID="Phosphorylation_of_DLC2_by_MAPK_8Step">
+ <STEP-INTERACTIONS rdf:resource="#Phosphorylation_of_DLC2_by_MAPK_8" />
+ <STEP-INTERACTIONS rdf:resource="#kinase_activity_of_Mitogen_activated_protein_kinase_8___cytosol_1" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="Translocation_of_BMF_to_mitochondria">
+ <LEFT rdf:resource="#BMF__cytosol_1" />
+ <RIGHT rdf:resource="#BMF__mitochondrial_outer_membrane_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Translocation of BMF to mitochondria</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Translocation of BMF to mitochondria</SHORT-NAME>
+ <XREF rdf:resource="#Reactome139909" />
+ <XREF rdf:resource="#protein_insertion_into_mitochondrial_membrane_during_induction_of_apoptosis" />
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ </biochemicalReaction>
+ <proteinParticipant rdf:ID="BMF__cytosol_1">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q96LC9_BMF_protein" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="BMF__mitochondrial_outer_membrane_">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q96LC9_BMF_protein" />
+ </proteinParticipant>
+ <unificationXref rdf:ID="Reactome139909">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">139909</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <pathwayStep rdf:ID="Translocation_of_BMF_to_mitochondriaStep">
+ <STEP-INTERACTIONS rdf:resource="#Translocation_of_BMF_to_mitochondria" />
+ </pathwayStep>
+ <unificationXref rdf:ID="Reactome139910">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">139910</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <evidence rdf:ID="Summation_140551">
+ <XREF rdf:resource="#Pubmed_14634621" />
+ </evidence>
+ <pathwayStep rdf:ID="Activation_of_BMF_and_translocation_to_mitochondriaStep">
+ <STEP-INTERACTIONS rdf:resource="#Activation_of_BMF_and_translocation_to_mitochondria" />
+ </pathwayStep>
+ <unificationXref rdf:ID="Reactome114452">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">114452</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <evidence rdf:ID="Summation_140552">
+ <XREF rdf:resource="#Pubmed_12209154" />
+ <XREF rdf:resource="#Pubmed_14634621" />
+ </evidence>
+ <pathwayStep rdf:ID="Activation_of_BH3_only_proteinsStep">
+ <STEP-INTERACTIONS rdf:resource="#Activation_of_BH3_only_proteins" />
+ </pathwayStep>
+ <pathway rdf:ID="BH3_only_proteins_associate_with_and_inactivate_anti_apoptotic_BCL_2_members">
+ <PATHWAY-COMPONENTS rdf:resource="#Interaction_of_PUMA_and_Bcl_XLStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#Interaction_of_NOXA_with_BCL2Step" />
+ <PATHWAY-COMPONENTS rdf:resource="#Interaction_of_BIM_with_BCL2_Step" />
+ <PATHWAY-COMPONENTS rdf:resource="#Sequestration_of_tBID_by_BCL_2Step" />
+ <PATHWAY-COMPONENTS rdf:resource="#Interaction__of_BAD_with_BCL_xl___Step" />
+ <PATHWAY-COMPONENTS rdf:resource="#Interaction_of_BAD_with_BCL2__Step" />
+ <PATHWAY-COMPONENTS rdf:resource="#Interaction_of_BIM_with_BCL_xlStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#Interaction_of_NOXA_with_BCL_xlStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#Interaction_of_PUMA_and_Bcl_2Step" />
+ <PATHWAY-COMPONENTS rdf:resource="#Interaction_of_tBID_with_BCL_xlStep" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members</SHORT-NAME>
+ <XREF rdf:resource="#Reactome111453" />
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ </pathway>
+ <biochemicalReaction rdf:ID="Interaction_of_BAD_with_BCL2__">
+ <LEFT rdf:resource="#Bcl_2_protein__mitochondrial_outer_membrane_2" />
+ <LEFT rdf:resource="#BAD_protein__cytosol_3" />
+ <RIGHT rdf:resource="#BAD_BCL_2__mitochondrial_outer_membrane_2" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Interaction of BAD with BCL2</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Interaction of BAD with BCL2</SHORT-NAME>
+ <XREF rdf:resource="#Reactome114277" />
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <EVIDENCE rdf:resource="#InferredFrom_Interaction_of_BAD_with_Bcl_2" />
+ </biochemicalReaction>
+ <proteinParticipant rdf:ID="Bcl_2_protein__mitochondrial_outer_membrane_2">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P10415_1_Apoptosis_regulator_Bcl_2" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="BAD_protein__cytosol_3">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q92934_Bcl2_antagonist_of_cell_death__BAD___Bcl_2_binding_component_6___Bcl__XL_Bcl_2_associated_death_promoter___Bcl_2_like_8_protein_" />
+ </proteinParticipant>
+ <complexParticipant rdf:ID="BAD_BCL_2__mitochondrial_outer_membrane_2">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#BAD_BCL_2__mitochondrial_outer_membrane_1" />
+ </complexParticipant>
+ <unificationXref rdf:ID="Reactome114277">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">114277</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <evidence rdf:ID="InferredFrom_Interaction_of_BAD_with_Bcl_2">
+ <XREF rdf:resource="#Pubmed_7834748" />
+ </evidence>
+ <publicationXref rdf:ID="Pubmed_7834748">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">7834748</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1995</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bad, a heterodimeric partner for Bcl-XL and Bcl-2, displaces Bax and promotes cell death</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Yang, E</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Zha, J</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Jockel, J</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Boise, LH</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Thompson, CB</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Korsmeyer, SJ</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cell 80:285-91</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="Interaction_of_BAD_with_BCL2__Step">
+ <STEP-INTERACTIONS rdf:resource="#Interaction_of_BAD_with_BCL2__" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="Interaction__of_BAD_with_BCL_xl___">
+ <LEFT rdf:resource="#Apoptosis_regulator_Bcl_X__mitochondrial_outer_membrane_" />
+ <LEFT rdf:resource="#BAD_protein__cytosol_4" />
+ <RIGHT rdf:resource="#BAD_BCL_xl__mitochondrial_outer_membrane_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Interaction of BAD with BCL-xl</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Interaction of BAD with BCL-xl</SHORT-NAME>
+ <XREF rdf:resource="#Reactome114276" />
+ <XREF rdf:resource="#Pubmed_10195903" />
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ </biochemicalReaction>
+ <proteinParticipant rdf:ID="Apoptosis_regulator_Bcl_X__mitochondrial_outer_membrane_">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q07817_1_Apoptosis_regulator_Bcl_X__Bcl_2_like_1_protein_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_Q07817_1_Apoptosis_regulator_Bcl_X__Bcl_2_like_1_protein_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:Q07817-1 Apoptosis regulator Bcl-X (Bcl-2-like 1 protein)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BCL2L</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BCLX</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BCL2L1</SYNONYMS>
+ <XREF rdf:resource="#UniProt_Q07817" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Potent inhibitor of cell death. Isoform Bcl-X(L) anti- apoptotic activity is inhibited by association with SIVA isoform 1. Inhibits activation of caspases (By similarity). Appears to regulate cell death by blocking the voltage-dependent anion channnel (VDAC) by binding to it and preventing the release of the caspase activator, cytochrome c, from the mitochondrial membrane. The Bcl-X(S) isoform promotes apoptosi [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_Q07817">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Q07817</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="BAD_protein__cytosol_4">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q92934_Bcl2_antagonist_of_cell_death__BAD___Bcl_2_binding_component_6___Bcl__XL_Bcl_2_associated_death_promoter___Bcl_2_like_8_protein_" />
+ </proteinParticipant>
+ <complexParticipant rdf:ID="BAD_BCL_xl__mitochondrial_outer_membrane_">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#BAD_BCL_xl__mitochondrial_outer_membrane_1" />
+ </complexParticipant>
+ <complex rdf:ID="BAD_BCL_xl__mitochondrial_outer_membrane_1">
+ <COMPONENTS rdf:resource="#Apoptosis_regulator_Bcl_X__mitochondrial_outer_membrane_1" />
+ <COMPONENTS rdf:resource="#BAD_protein__mitochondrial_outer_membrane_3" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BAD:BCL-xl [mitochondrial outer membrane]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BAD:BCL-xl</SHORT-NAME>
+ </complex>
+ <proteinParticipant rdf:ID="Apoptosis_regulator_Bcl_X__mitochondrial_outer_membrane_1">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q07817_1_Apoptosis_regulator_Bcl_X__Bcl_2_like_1_protein_" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="BAD_protein__mitochondrial_outer_membrane_3">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q92934_Bcl2_antagonist_of_cell_death__BAD___Bcl_2_binding_component_6___Bcl__XL_Bcl_2_associated_death_promoter___Bcl_2_like_8_protein_" />
+ </proteinParticipant>
+ <unificationXref rdf:ID="Reactome114276">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">114276</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <pathwayStep rdf:ID="Interaction__of_BAD_with_BCL_xl___Step">
+ <STEP-INTERACTIONS rdf:resource="#Interaction__of_BAD_with_BCL_xl___" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="Sequestration_of_tBID_by_BCL_2">
+ <LEFT rdf:resource="#tBID__mitochondrial_outer_membrane_3" />
+ <LEFT rdf:resource="#Bcl_2_protein__mitochondrial_outer_membrane_3" />
+ <RIGHT rdf:resource="#tBID_BCL_2__mitochondrial_outer_membrane_2" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Sequestration of tBID by BCL-2</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Sequestration of tBID by BCL-2</SHORT-NAME>
+ <XREF rdf:resource="#Reactome114352" />
+ <XREF rdf:resource="#Pubmed_12624108" />
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ </biochemicalReaction>
+ <proteinParticipant rdf:ID="tBID__mitochondrial_outer_membrane_3">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P55957_BH3_interacting_domain_death_agonist__BID_" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="Bcl_2_protein__mitochondrial_outer_membrane_3">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P10415_1_Apoptosis_regulator_Bcl_2" />
+ </proteinParticipant>
+ <complexParticipant rdf:ID="tBID_BCL_2__mitochondrial_outer_membrane_2">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#tBID_BCL_2__mitochondrial_outer_membrane_1" />
+ </complexParticipant>
+ <unificationXref rdf:ID="Reactome114352">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">114352</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <publicationXref rdf:ID="Pubmed_12624108">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">12624108</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2003</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Inhibition of Bid-induced apoptosis by Bcl-2. tBid insertion, Bax translocation, and Bax/Bak oligomerization suppressed.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Yi, X</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Yin, XM</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Dong, Z</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Biol Chem 278:16992-9</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="Sequestration_of_tBID_by_BCL_2Step">
+ <STEP-INTERACTIONS rdf:resource="#Sequestration_of_tBID_by_BCL_2" />
+ <NEXT-STEP rdf:resource="#BAD_displaces_tBID_from_BCL_2_sequestrationStep" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="Interaction_of_tBID_with_BCL_xl">
+ <LEFT rdf:resource="#Apoptosis_regulator_Bcl_X__mitochondrial_outer_membrane_2" />
+ <LEFT rdf:resource="#tBID__mitochondrial_outer_membrane_4" />
+ <RIGHT rdf:resource="#tBID_BCL_xl__mitochondrial_outer_membrane_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Interaction of tBID with BCL-xl</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Interaction of tBID with BCL-xl</SHORT-NAME>
+ <XREF rdf:resource="#Reactome114365" />
+ <XREF rdf:resource="#Pubmed_9727492" />
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ </biochemicalReaction>
+ <proteinParticipant rdf:ID="Apoptosis_regulator_Bcl_X__mitochondrial_outer_membrane_2">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q07817_1_Apoptosis_regulator_Bcl_X__Bcl_2_like_1_protein_" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="tBID__mitochondrial_outer_membrane_4">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P55957_BH3_interacting_domain_death_agonist__BID_" />
+ </proteinParticipant>
+ <complexParticipant rdf:ID="tBID_BCL_xl__mitochondrial_outer_membrane_">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#tBID_BCL_xl__mitochondrial_outer_membrane_1" />
+ </complexParticipant>
+ <complex rdf:ID="tBID_BCL_xl__mitochondrial_outer_membrane_1">
+ <COMPONENTS rdf:resource="#tBID__mitochondrial_outer_membrane_5" />
+ <COMPONENTS rdf:resource="#Apoptosis_regulator_Bcl_X__mitochondrial_outer_membrane_3" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">tBID:BCL-xl [mitochondrial outer membrane]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">tBID:BCL-xl</SHORT-NAME>
+ </complex>
+ <proteinParticipant rdf:ID="tBID__mitochondrial_outer_membrane_5">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P55957_BH3_interacting_domain_death_agonist__BID_" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="Apoptosis_regulator_Bcl_X__mitochondrial_outer_membrane_3">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q07817_1_Apoptosis_regulator_Bcl_X__Bcl_2_like_1_protein_" />
+ </proteinParticipant>
+ <unificationXref rdf:ID="Reactome114365">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">114365</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <pathwayStep rdf:ID="Interaction_of_tBID_with_BCL_xlStep">
+ <STEP-INTERACTIONS rdf:resource="#Interaction_of_tBID_with_BCL_xl" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="Interaction_of_BIM_with_BCL2_">
+ <LEFT rdf:resource="#BIM__mitochondrial_outer_membrane_1" />
+ <LEFT rdf:resource="#Bcl_2_protein__mitochondrial_outer_membrane_4" />
+ <RIGHT rdf:resource="#BIM_BCL2__mitochondrial_outer_membrane_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Interaction of BIM with BCL2</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Interaction of BIM with BCL2</SHORT-NAME>
+ <XREF rdf:resource="#Reactome114279" />
+ <XREF rdf:resource="#Pubmed_10198631" />
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ </biochemicalReaction>
+ <proteinParticipant rdf:ID="BIM__mitochondrial_outer_membrane_1">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_O43521_1_Bcl_2_like_protein_11__Bcl2_interacting_mediator_of_cell_death_" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="Bcl_2_protein__mitochondrial_outer_membrane_4">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P10415_1_Apoptosis_regulator_Bcl_2" />
+ </proteinParticipant>
+ <complexParticipant rdf:ID="BIM_BCL2__mitochondrial_outer_membrane_">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#BIM_BCL2__mitochondrial_outer_membrane_1" />
+ </complexParticipant>
+ <complex rdf:ID="BIM_BCL2__mitochondrial_outer_membrane_1">
+ <COMPONENTS rdf:resource="#BIM__mitochondrial_outer_membrane_2" />
+ <COMPONENTS rdf:resource="#Bcl_2_protein__mitochondrial_outer_membrane_5" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BIM:BCL2 [mitochondrial outer membrane]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BIM:BCL2</SHORT-NAME>
+ </complex>
+ <proteinParticipant rdf:ID="BIM__mitochondrial_outer_membrane_2">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_O43521_1_Bcl_2_like_protein_11__Bcl2_interacting_mediator_of_cell_death_" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="Bcl_2_protein__mitochondrial_outer_membrane_5">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P10415_1_Apoptosis_regulator_Bcl_2" />
+ </proteinParticipant>
+ <unificationXref rdf:ID="Reactome114279">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">114279</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <publicationXref rdf:ID="Pubmed_10198631">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">10198631</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1999</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The proapoptotic activity of the Bcl-2 family member Bim is regulated by interaction with the dynein motor complex</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Puthalakath, H</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Huang, DC</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">O'Reilly, LA</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">King, SM</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Strasser, A</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mol Cell 3:287-96</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="Interaction_of_BIM_with_BCL2_Step">
+ <STEP-INTERACTIONS rdf:resource="#Interaction_of_BIM_with_BCL2_" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="Interaction_of_BIM_with_BCL_xl">
+ <LEFT rdf:resource="#Apoptosis_regulator_Bcl_X__mitochondrial_outer_membrane_4" />
+ <LEFT rdf:resource="#BIM__mitochondrial_outer_membrane_3" />
+ <RIGHT rdf:resource="#BIM_BCL_xl__mitochondrial_outer_membrane_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Interaction of BIM with BCL-xl</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Interaction of BIM with BCL-xl</SHORT-NAME>
+ <XREF rdf:resource="#Reactome114278" />
+ <XREF rdf:resource="#Pubmed_10198631" />
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ </biochemicalReaction>
+ <proteinParticipant rdf:ID="Apoptosis_regulator_Bcl_X__mitochondrial_outer_membrane_4">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q07817_1_Apoptosis_regulator_Bcl_X__Bcl_2_like_1_protein_" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="BIM__mitochondrial_outer_membrane_3">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_O43521_1_Bcl_2_like_protein_11__Bcl2_interacting_mediator_of_cell_death_" />
+ </proteinParticipant>
+ <complexParticipant rdf:ID="BIM_BCL_xl__mitochondrial_outer_membrane_">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#BIM_BCL_xl__mitochondrial_outer_membrane_1" />
+ </complexParticipant>
+ <complex rdf:ID="BIM_BCL_xl__mitochondrial_outer_membrane_1">
+ <COMPONENTS rdf:resource="#Apoptosis_regulator_Bcl_X__mitochondrial_outer_membrane_5" />
+ <COMPONENTS rdf:resource="#BIM__mitochondrial_outer_membrane_4" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BIM:BCL-xl [mitochondrial outer membrane]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BIM:BCL-xl</SHORT-NAME>
+ </complex>
+ <proteinParticipant rdf:ID="Apoptosis_regulator_Bcl_X__mitochondrial_outer_membrane_5">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q07817_1_Apoptosis_regulator_Bcl_X__Bcl_2_like_1_protein_" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="BIM__mitochondrial_outer_membrane_4">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_O43521_1_Bcl_2_like_protein_11__Bcl2_interacting_mediator_of_cell_death_" />
+ </proteinParticipant>
+ <unificationXref rdf:ID="Reactome114278">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">114278</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <pathwayStep rdf:ID="Interaction_of_BIM_with_BCL_xlStep">
+ <STEP-INTERACTIONS rdf:resource="#Interaction_of_BIM_with_BCL_xl" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="Interaction_of_NOXA_with_BCL2">
+ <LEFT rdf:resource="#Bcl_2_protein__mitochondrial_outer_membrane_6" />
+ <LEFT rdf:resource="#NOXA_protein__mitochondrial_outer_membrane_1" />
+ <RIGHT rdf:resource="#NOXA_BCL2__mitochondrial_outer_membrane_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Interaction of NOXA with BCL2</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Interaction of NOXA with BCL2</SHORT-NAME>
+ <XREF rdf:resource="#Reactome114241" />
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <EVIDENCE rdf:resource="#InferredFrom_Interaction_of_NOXA_and_Bcl_2" />
+ </biochemicalReaction>
+ <proteinParticipant rdf:ID="Bcl_2_protein__mitochondrial_outer_membrane_6">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P10415_1_Apoptosis_regulator_Bcl_2" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="NOXA_protein__mitochondrial_outer_membrane_1">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q13794_Phorbol_12_myristate_13_acetate_induced_protein_1__PMA_induced_protein_1___Immediate_early_response_protein_APR_" />
+ </proteinParticipant>
+ <complexParticipant rdf:ID="NOXA_BCL2__mitochondrial_outer_membrane_">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#NOXA_BCL2__mitochondrial_outer_membrane_1" />
+ </complexParticipant>
+ <complex rdf:ID="NOXA_BCL2__mitochondrial_outer_membrane_1">
+ <COMPONENTS rdf:resource="#Bcl_2_protein__mitochondrial_outer_membrane_7" />
+ <COMPONENTS rdf:resource="#NOXA_protein__mitochondrial_outer_membrane_2" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">NOXA:BCL2 [mitochondrial outer membrane]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">NOXA:BCL2</SHORT-NAME>
+ </complex>
+ <proteinParticipant rdf:ID="Bcl_2_protein__mitochondrial_outer_membrane_7">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P10415_1_Apoptosis_regulator_Bcl_2" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="NOXA_protein__mitochondrial_outer_membrane_2">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q13794_Phorbol_12_myristate_13_acetate_induced_protein_1__PMA_induced_protein_1___Immediate_early_response_protein_APR_" />
+ </proteinParticipant>
+ <unificationXref rdf:ID="Reactome114241">
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+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">114241</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <evidence rdf:ID="InferredFrom_Interaction_of_NOXA_and_Bcl_2">
+ <XREF rdf:resource="#Pubmed_10807576" />
+ </evidence>
+ <pathwayStep rdf:ID="Interaction_of_NOXA_with_BCL2Step">
+ <STEP-INTERACTIONS rdf:resource="#Interaction_of_NOXA_with_BCL2" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="Interaction_of_PUMA_and_Bcl_2">
+ <LEFT rdf:resource="#Bcl_2_protein__mitochondrial_outer_membrane_8" />
+ <LEFT rdf:resource="#PUMA_protein__mitochondrial_outer_membrane_1" />
+ <RIGHT rdf:resource="#PUMA_Bcl_2_complex__mitochondrial_outer_membrane_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Interaction of PUMA and Bcl-2</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Interaction of PUMA and Bcl-2</SHORT-NAME>
+ <XREF rdf:resource="#Reactome140230" />
+ <XREF rdf:resource="#Pubmed_11463392" />
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_membrane" />
+ </biochemicalReaction>
+ <proteinParticipant rdf:ID="Bcl_2_protein__mitochondrial_outer_membrane_8">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P10415_1_Apoptosis_regulator_Bcl_2" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="PUMA_protein__mitochondrial_outer_membrane_1">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q9BXH1_PUMA_protein" />
+ </proteinParticipant>
+ <complexParticipant rdf:ID="PUMA_Bcl_2_complex__mitochondrial_outer_membrane_">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#PUMA_Bcl_2_complex__mitochondrial_outer_membrane_1" />
+ </complexParticipant>
+ <complex rdf:ID="PUMA_Bcl_2_complex__mitochondrial_outer_membrane_1">
+ <COMPONENTS rdf:resource="#Bcl_2_protein__mitochondrial_outer_membrane_9" />
+ <COMPONENTS rdf:resource="#PUMA_protein__mitochondrial_outer_membrane_2" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PUMA:Bcl-2 complex [mitochondrial outer membrane]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PUMA:Bcl-2 complex</SHORT-NAME>
+ </complex>
+ <proteinParticipant rdf:ID="Bcl_2_protein__mitochondrial_outer_membrane_9">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P10415_1_Apoptosis_regulator_Bcl_2" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="PUMA_protein__mitochondrial_outer_membrane_2">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q9BXH1_PUMA_protein" />
+ </proteinParticipant>
+ <unificationXref rdf:ID="Reactome140230">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">140230</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <pathwayStep rdf:ID="Interaction_of_PUMA_and_Bcl_2Step">
+ <STEP-INTERACTIONS rdf:resource="#Interaction_of_PUMA_and_Bcl_2" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="Interaction_of_PUMA_and_Bcl_XL">
+ <LEFT rdf:resource="#Apoptosis_regulator_Bcl_X__mitochondrial_outer_membrane_6" />
+ <LEFT rdf:resource="#PUMA_protein__mitochondrial_outer_membrane_3" />
+ <RIGHT rdf:resource="#PUMA_Bcl_XL_complex__mitochondrial_outer_membrane_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Interaction of PUMA and Bcl-XL</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Interaction of PUMA and Bcl-XL</SHORT-NAME>
+ <XREF rdf:resource="#Reactome140232" />
+ <XREF rdf:resource="#Pubmed_11463392" />
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_membrane" />
+ </biochemicalReaction>
+ <proteinParticipant rdf:ID="Apoptosis_regulator_Bcl_X__mitochondrial_outer_membrane_6">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q07817_1_Apoptosis_regulator_Bcl_X__Bcl_2_like_1_protein_" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="PUMA_protein__mitochondrial_outer_membrane_3">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q9BXH1_PUMA_protein" />
+ </proteinParticipant>
+ <complexParticipant rdf:ID="PUMA_Bcl_XL_complex__mitochondrial_outer_membrane_">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#PUMA_Bcl_XL_complex__mitochondrial_outer_membrane_1" />
+ </complexParticipant>
+ <complex rdf:ID="PUMA_Bcl_XL_complex__mitochondrial_outer_membrane_1">
+ <COMPONENTS rdf:resource="#Apoptosis_regulator_Bcl_X__mitochondrial_outer_membrane_7" />
+ <COMPONENTS rdf:resource="#PUMA_protein__mitochondrial_outer_membrane_4" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PUMA:Bcl-XL complex [mitochondrial outer membrane]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PUMA:Bcl-XL complex</SHORT-NAME>
+ </complex>
+ <proteinParticipant rdf:ID="Apoptosis_regulator_Bcl_X__mitochondrial_outer_membrane_7">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q07817_1_Apoptosis_regulator_Bcl_X__Bcl_2_like_1_protein_" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="PUMA_protein__mitochondrial_outer_membrane_4">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q9BXH1_PUMA_protein" />
+ </proteinParticipant>
+ <unificationXref rdf:ID="Reactome140232">
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+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">140232</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <pathwayStep rdf:ID="Interaction_of_PUMA_and_Bcl_XLStep">
+ <STEP-INTERACTIONS rdf:resource="#Interaction_of_PUMA_and_Bcl_XL" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="Interaction_of_NOXA_with_BCL_xl">
+ <LEFT rdf:resource="#Apoptosis_regulator_Bcl_X__mitochondrial_outer_membrane_8" />
+ <LEFT rdf:resource="#NOXA_protein__mitochondrial_outer_membrane_3" />
+ <RIGHT rdf:resource="#NOXA_BCL_xl__mitochondrial_outer_membrane_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Interaction of NOXA with BCL-xl</NAME>
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+ <XREF rdf:resource="#Reactome114281" />
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <EVIDENCE rdf:resource="#InferredFrom_Interaction_of_NOXA_and_Bcl_XL" />
+ </biochemicalReaction>
+ <proteinParticipant rdf:ID="Apoptosis_regulator_Bcl_X__mitochondrial_outer_membrane_8">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q07817_1_Apoptosis_regulator_Bcl_X__Bcl_2_like_1_protein_" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="NOXA_protein__mitochondrial_outer_membrane_3">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q13794_Phorbol_12_myristate_13_acetate_induced_protein_1__PMA_induced_protein_1___Immediate_early_response_protein_APR_" />
+ </proteinParticipant>
+ <complexParticipant rdf:ID="NOXA_BCL_xl__mitochondrial_outer_membrane_">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#NOXA_BCL_xl__mitochondrial_outer_membrane_1" />
+ </complexParticipant>
+ <complex rdf:ID="NOXA_BCL_xl__mitochondrial_outer_membrane_1">
+ <COMPONENTS rdf:resource="#Apoptosis_regulator_Bcl_X__mitochondrial_outer_membrane_9" />
+ <COMPONENTS rdf:resource="#NOXA_protein__mitochondrial_outer_membrane_4" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">NOXA:BCL-xl [mitochondrial outer membrane]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">NOXA:BCL-xl</SHORT-NAME>
+ </complex>
+ <proteinParticipant rdf:ID="Apoptosis_regulator_Bcl_X__mitochondrial_outer_membrane_9">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q07817_1_Apoptosis_regulator_Bcl_X__Bcl_2_like_1_protein_" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="NOXA_protein__mitochondrial_outer_membrane_4">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q13794_Phorbol_12_myristate_13_acetate_induced_protein_1__PMA_induced_protein_1___Immediate_early_response_protein_APR_" />
+ </proteinParticipant>
+ <unificationXref rdf:ID="Reactome114281">
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+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">114281</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <evidence rdf:ID="InferredFrom_Interaction_of_NOXA_and_Bcl_XL">
+ <XREF rdf:resource="#Pubmed_10807576" />
+ </evidence>
+ <pathwayStep rdf:ID="Interaction_of_NOXA_with_BCL_xlStep">
+ <STEP-INTERACTIONS rdf:resource="#Interaction_of_NOXA_with_BCL_xl" />
+ </pathwayStep>
+ <unificationXref rdf:ID="Reactome111453">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">111453</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <pathwayStep rdf:ID="BH3_only_proteins_associate_with_and_inactivate_anti_apoptotic_BCL_2_membersStep">
+ <STEP-INTERACTIONS rdf:resource="#BH3_only_proteins_associate_with_and_inactivate_anti_apoptotic_BCL_2_members" />
+ </pathwayStep>
+ <pathway rdf:ID="Activation__translocation_and_oligomerization_of_BAX">
+ <PATHWAY-COMPONENTS rdf:resource="#tBID_activates_BAX_proteinStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#Oligomerization_of_BAX_at_the_mitochondrial_membraneStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#Translocation_of_activated_BAX_to_the_mitochondriaStep" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Activation, translocation and oligomerization of BAX</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Activation, translocation and oligomerization of BAX</SHORT-NAME>
+ <XREF rdf:resource="#Reactome114294" />
+ <XREF rdf:resource="#Pubmed_11136736" />
+ <XREF rdf:resource="#activation_of_pro_apoptotic_gene_products" />
+ </pathway>
+ <biochemicalReaction rdf:ID="tBID_activates_BAX_protein">
+ <LEFT rdf:resource="#tBID_p15__cytosol_3" />
+ <LEFT rdf:resource="#Bax_alpha_protein__cytosol_" />
+ <RIGHT rdf:resource="#tBID_p15__cytosol_4" />
+ <RIGHT rdf:resource="#Activated_BAX__cytosol_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">tBID activates BAX protein</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">tBID activates BAX protein</SHORT-NAME>
+ <XREF rdf:resource="#Reactome139917" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">During certain types of apoptosis, activated tBID (p15) induces a change in conformation of Bax which leads to the unmasking of its NH2-terminal domain. This change in confirmation usually results in the release of cytochrome c from mitochondria.</COMMENT>
+ <EVIDENCE rdf:resource="#Summation_163347" />
+ <XREF rdf:resource="#Pubmed_10629050" />
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ </biochemicalReaction>
+ <proteinParticipant rdf:ID="tBID_p15__cytosol_3">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P55957_BH3_interacting_domain_death_agonist__BID_" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="Bax_alpha_protein__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q07812_1_Apoptosis_regulator_BAX__membrane_isoform_alpha" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_Q07812_1_Apoptosis_regulator_BAX__membrane_isoform_alpha">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:Q07812-1 Apoptosis regulator BAX, membrane isoform alpha</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BAX</SYNONYMS>
+ <XREF rdf:resource="#UniProt_Q07812" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Accelerates programmed cell death by binding to, and antagonizing the apoptosis repressor BCL2 or its adenovirus homolog E1B 19k protein. Induces the release of cytochrome c, activation of CASP3, and thereby apoptosis. SUBUNIT: Homodimers and heterodimers with BCL2, E1B 19K protein, BCL2L1 isoform Bcl-X(L), MCL1 and A1. Interacts with SH3GLB1 and HN. SUBCELLULAR LOCATION: Membrane-bound. ALTERNATIVE PRODUCTS: E [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_Q07812">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Q07812</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="tBID_p15__cytosol_4">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P55957_BH3_interacting_domain_death_agonist__BID_" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="Activated_BAX__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q07812_1_Apoptosis_regulator_BAX__membrane_isoform_alpha" />
+ </proteinParticipant>
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+ </unificationXref>
+ <evidence rdf:ID="Summation_163347">
+ <XREF rdf:resource="#Pubmed_10085289" />
+ </evidence>
+ <publicationXref rdf:ID="Pubmed_10085289">
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+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1999</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bid-induced conformational change of Bax is responsible for mitochondrial cytochrome c release during apoptosis</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Desagher, S</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Osen-Sand, A</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Nichols, A</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Eskes, R</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Montessuit, S</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Lauper, S</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Maundrell, K</AUTHORS>
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+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Martinou, JC</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Cell Biol 144:891-901</SOURCE>
+ </publicationXref>
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+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2000</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bid induces the oligomerization and insertion of Bax into the outer mitochondrial membrane</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Eskes, R</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Desagher, S</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Antonsson, B</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Martinou, JC</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mol Cell Biol 20:929-35</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="tBID_activates_BAX_proteinStep">
+ <STEP-INTERACTIONS rdf:resource="#tBID_activates_BAX_protein" />
+ <NEXT-STEP rdf:resource="#Translocation_of_activated_BAX_to_the_mitochondriaStep" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="Translocation_of_activated_BAX_to_the_mitochondria">
+ <LEFT rdf:resource="#Activated_BAX__cytosol_1" />
+ <RIGHT rdf:resource="#Activated_BAX_inserted_into_mitochondrial_membrane__mitochondrial_outer_membrane_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Translocation of activated BAX to the mitochondria</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Translocation of activated BAX to the mitochondria</SHORT-NAME>
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+ <XREF rdf:resource="#Pubmed_12624108" />
+ <XREF rdf:resource="#protein_insertion_into_mitochondrial_membrane_during_induction_of_apoptosis" />
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ </biochemicalReaction>
+ <proteinParticipant rdf:ID="Activated_BAX__cytosol_1">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q07812_1_Apoptosis_regulator_BAX__membrane_isoform_alpha" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="Activated_BAX_inserted_into_mitochondrial_membrane__mitochondrial_outer_membrane_">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q07812_1_Apoptosis_regulator_BAX__membrane_isoform_alpha" />
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+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2001</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bax is present as a high molecular weight oligomer/complex in the mitochondrial membrane of apoptotic cells.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Antonsson, B</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Montessuit, S</AUTHORS>
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+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Biol Chem 276:11615-23</SOURCE>
+ </publicationXref>
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+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2002</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Spontaneous and drug-induced apoptosis is mediated by conformational changes of Bax and Bak in B-cell chronic lymphocytic leukemia.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bellosillo, B</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Villamor, N</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">López-Guillermo, A</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Marcé, S</AUTHORS>
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+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Colomer, D</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Blood 100:1810-6</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="Translocation_of_activated_BAX_to_the_mitochondriaStep">
+ <STEP-INTERACTIONS rdf:resource="#Translocation_of_activated_BAX_to_the_mitochondria" />
+ <NEXT-STEP rdf:resource="#Oligomerization_of_BAX_at_the_mitochondrial_membraneStep" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="Oligomerization_of_BAX_at_the_mitochondrial_membrane">
+ <LEFT rdf:resource="#Activated_BAX_inserted_into_mitochondrial_membrane__mitochondrial_outer_membrane_1" />
+ <RIGHT rdf:resource="#Activated_BAX__mitochondrial_outer_membrane_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Oligomerization of BAX at the mitochondrial membrane</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Oligomerization of BAX at the mitochondrial membrane</SHORT-NAME>
+ <XREF rdf:resource="#Reactome114275" />
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+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_membrane" />
+ </biochemicalReaction>
+ <proteinParticipant rdf:ID="Activated_BAX_inserted_into_mitochondrial_membrane__mitochondrial_outer_membrane_1">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q07812_1_Apoptosis_regulator_BAX__membrane_isoform_alpha" />
+ <STOICHIOMETRIC-COEFFICIENT rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2</STOICHIOMETRIC-COEFFICIENT>
+ </proteinParticipant>
+ <complexParticipant rdf:ID="Activated_BAX__mitochondrial_outer_membrane_">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#Activated_BAX__mitochondrial_outer_membrane_1" />
+ </complexParticipant>
+ <complex rdf:ID="Activated_BAX__mitochondrial_outer_membrane_1">
+ <COMPONENTS rdf:resource="#BAX_alpha_protein__mitochondrial_outer_membrane_" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Activated BAX [mitochondrial outer membrane]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Activated BAX</SHORT-NAME>
+ </complex>
+ <proteinParticipant rdf:ID="BAX_alpha_protein__mitochondrial_outer_membrane_">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
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+ <pathway rdf:ID="Activation_and_oligomerization_of_BAK_protein">
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+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_membrane" />
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+ <proteinParticipant rdf:ID="tBID__mitochondrial_outer_membrane_6">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P55957_BH3_interacting_domain_death_agonist__BID_" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="Inactive_BAK_protein__mitochondrial_outer_membrane_">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q16611_Bcl_2_homologous_antagonist_killer__Apoptosis_regulator_BAK___BCL2__like_7_protein_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_Q16611_Bcl_2_homologous_antagonist_killer__Apoptosis_regulator_BAK___BCL2__like_7_protein_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:Q16611 Bcl-2 homologous antagonist/killer (Apoptosis regulator BAK) (BCL2- like 7 protein)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BCL2L7</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BAK</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BAK1</SYNONYMS>
+ <XREF rdf:resource="#UniProt_Q16611" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: In the presence of an appropriate stimulus, accelerates programmed cell death by binding to, and antagonizing the a repressor Bcl-2 or its adenovirus homolog E1B 19k protein. SUBUNIT: Forms heterodimers with Bcl-2, E1B 19k protein, and Bcl- X(L). SUBCELLULAR LOCATION: Membrane-bound (Potential). TISSUE SPECIFICITY: Expressed in a wide variety of tissues, with highest levels in the heart and skeletal muscle. DOM [...]
+ </protein>
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+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Q16611</ID>
+ </unificationXref>
+ <proteinParticipant rdf:ID="tBID__mitochondrial_outer_membrane_7">
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+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P55957_BH3_interacting_domain_death_agonist__BID_" />
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+ <proteinParticipant rdf:ID="Activated_BAK_protein__mitochondrial_outer_membrane_">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q16611_Bcl_2_homologous_antagonist_killer__Apoptosis_regulator_BAK___BCL2__like_7_protein_" />
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+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Genes Dev 14:2060-71</SOURCE>
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+ <biochemicalReaction rdf:ID="Oligomerization__of_BAK_at_the_mitochondrial_membrane">
+ <LEFT rdf:resource="#Activated_BAK_protein__mitochondrial_outer_membrane_1" />
+ <RIGHT rdf:resource="#Active_BAK__mitochondrial_outer_membrane_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Oligomerization of BAK at the mitochondrial membrane</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Oligomerization of BAK at the mitochondrial membrane</SHORT-NAME>
+ <XREF rdf:resource="#Reactome114263" />
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+ <proteinParticipant rdf:ID="Activated_BAK_protein__mitochondrial_outer_membrane_1">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q16611_Bcl_2_homologous_antagonist_killer__Apoptosis_regulator_BAK___BCL2__like_7_protein_" />
+ <STOICHIOMETRIC-COEFFICIENT rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2</STOICHIOMETRIC-COEFFICIENT>
+ </proteinParticipant>
+ <complexParticipant rdf:ID="Active_BAK__mitochondrial_outer_membrane_">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#Active_BAK__mitochondrial_outer_membrane_1" />
+ </complexParticipant>
+ <complex rdf:ID="Active_BAK__mitochondrial_outer_membrane_1">
+ <COMPONENTS rdf:resource="#Activated_BAK_protein__mitochondrial_outer_membrane_2" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Active BAK [mitochondrial outer membrane]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Active BAK</SHORT-NAME>
+ </complex>
+ <proteinParticipant rdf:ID="Activated_BAK_protein__mitochondrial_outer_membrane_2">
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q16611_Bcl_2_homologous_antagonist_killer__Apoptosis_regulator_BAK___BCL2__like_7_protein_" />
+ <STOICHIOMETRIC-COEFFICIENT rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2</STOICHIOMETRIC-COEFFICIENT>
+ </proteinParticipant>
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+ </unificationXref>
+ <publicationXref rdf:ID="Pubmed_12721291">
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+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2003</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BCL-2 selectively interacts with the BID-induced open conformer of BAK, inhibiting BAK auto-oligomerization.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Ruffolo, SC</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Shore, GC</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Biol Chem 278:25039-45</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="Oligomerization__of_BAK_at_the_mitochondrial_membraneStep">
+ <STEP-INTERACTIONS rdf:resource="#Oligomerization__of_BAK_at_the_mitochondrial_membrane" />
+ <NEXT-STEP rdf:resource="#Release_of_Cytochrome_c_from_mitochondriaStep" />
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+ </unificationXref>
+ <pathwayStep rdf:ID="Activation_and_oligomerization_of_BAK_proteinStep">
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+ <NEXT-STEP rdf:resource="#Permeabilization_of_mitochondriaStep" />
+ </pathwayStep>
+ <pathway rdf:ID="Permeabilization_of_mitochondria">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Permeabilization of mitochondria</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Permeabilization of mitochondria</SHORT-NAME>
+ <XREF rdf:resource="#Reactome111455" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Activation and oligomerization of Bax and Bak result in the destabilization of the outer mitochondrial membrane. This results in the release of the apoptotic factors Cytochrome c and SMAC from the intermembrane space.</COMMENT>
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+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
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+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The expanding role of mitochondria in apoptosis.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Wang, X</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Genes Dev 15:2922-33</SOURCE>
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+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2003</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mitochondrial release of AIF and EndoG requires caspase activation downstream of Bax/Bak-mediated permeabilization.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Arnoult, D</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Gaume, B</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Karbowski, M</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Sharpe, JC</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cecconi, F</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Youle, RJ</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">EMBO J 22:4385-99</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="Permeabilization_of_mitochondriaStep">
+ <STEP-INTERACTIONS rdf:resource="#Permeabilization_of_mitochondria" />
+ <NEXT-STEP rdf:resource="#Release_of_apoptotic_factors_from_the_mitochondriaStep" />
+ </pathwayStep>
+ <pathway rdf:ID="Release_of_apoptotic_factors_from_the_mitochondria">
+ <PATHWAY-COMPONENTS rdf:resource="#Release_of_Cytochrome_c_from_mitochondriaStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#Release_of_SMAC_from_mitochondriaStep" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Release of apoptotic factors from the mitochondria</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Release of apoptotic factors from the mitochondria</SHORT-NAME>
+ <XREF rdf:resource="#Reactome111457" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Apoptotic factors released from the mitochondria promote apoptosis through several different mechanisms. Cytochrome C participates in Apoptosome driven effector caspase activation while SMAC relieves IAP mediated caspase inhibition.</COMMENT>
+ <EVIDENCE rdf:resource="#Summation_140366" />
+ <XREF rdf:resource="#Pubmed_10913597" />
+ <XREF rdf:resource="#Pubmed_12941691" />
+ <XREF rdf:resource="#Pubmed_12660240" />
+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
+ </pathway>
+ <biochemicalReaction rdf:ID="Release_of_Cytochrome_c_from_mitochondria">
+ <LEFT rdf:resource="#Cytochrome_c__mitochondrial_intermembrane_space_" />
+ <RIGHT rdf:resource="#Cytochrome_c__cytosol_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Release of Cytochrome c from mitochondria</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Release of Cytochrome c from mitochondria</SHORT-NAME>
+ <XREF rdf:resource="#Reactome114284" />
+ <XREF rdf:resource="#Pubmed_12941691" />
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+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_outer_membrane" />
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+ <proteinParticipant rdf:ID="Cytochrome_c__mitochondrial_intermembrane_space_">
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P99999_Cytochrome_c" />
+ </proteinParticipant>
+ <openControlledVocabulary rdf:ID="mitochondrial_intermembrane_space">
+ <TERM rdf:datatype="http://www.w3.org/2001/XMLSchema#string">mitochondrial intermembrane space</TERM>
+ <XREF rdf:resource="#GO_0005758" />
+ </openControlledVocabulary>
+ <xref rdf:ID="GO_0005758">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GO</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0005758</ID>
+ </xref>
+ <protein rdf:ID="UniProt_P99999_Cytochrome_c">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P99999 Cytochrome c</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CYCS</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CYC</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P99999" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Electron carrier protein. The oxidized form of the cytochrome c heme group can accept an electron from the heme group of the cytochrome c1 subunit of cytochrome reductase. Cytochrome c then transfers this electron to the cytochrome oxidase complex, the final protein carrier in the mitochondrial electron-transport chain. FUNCTION: Plays a role in apoptosis. Suppression of the anti- apoptotic members or activatio [...]
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+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2003</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Direct interaction between survivin and Smac/DIABLO is essential for the anti-apoptotic activity of survivin during taxol-induced apoptosis.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Song, Z</AUTHORS>
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+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Wu, M</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Biol Chem 278:23130-40</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="Release_of_Cytochrome_c_from_mitochondriaStep">
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+ <NEXT-STEP rdf:resource="#Cytochrome_c_mediated_apoptotic_responseStep" />
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+ <biochemicalReaction rdf:ID="Release_of_SMAC_from_mitochondria">
+ <LEFT rdf:resource="#Smac_protein__mitochondrial_precursor__mitochondrial_intermembrane_space_" />
+ <RIGHT rdf:resource="#SMAC__cytosol_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Release of SMAC from mitochondria</NAME>
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+ <CELLULAR-LOCATION rdf:resource="#mitochondrial_intermembrane_space" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q9NR28_1_Diablo_homolog__mitochondrial_precursor__Second_mitochondria_derived_activator_of_caspase___Smac_protein___Direct_IAP_binding_protein_with_low_pI_" />
+ </proteinParticipant>
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+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:Q9NR28-1 Diablo homolog, mitochondrial precursor (Second mitochondria-derived activator of caspase) (Smac protein) (Direct IAP binding protein with low pI)</NAME>
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+ <XREF rdf:resource="#UniProt_Q9NR28" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Promotes apoptosis by activating caspases in the cytochrome c/Apaf-1/caspase-9 pathway. Acts by opposing the inhibitory activity of inhibitor of apoptosis proteins (IAP). SUBUNIT: Homodimer. Interacts with BIRC2, BIRC3, BIRC4/XIAP and BIRC7. SUBCELLULAR LOCATION: Mitochondrial but released into the cytosol when cells undergo apoptosis. ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; [...]
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+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q9NR28_1_Diablo_homolog__mitochondrial_precursor__Second_mitochondria_derived_activator_of_caspase___Smac_protein___Direct_IAP_binding_protein_with_low_pI_" />
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+ <NEXT-STEP rdf:resource="#SMAC_binds_XIAP_Caspase_3Step" />
+ <NEXT-STEP rdf:resource="#SMAC_binds_XIAP_Caspase_7Step" />
+ <NEXT-STEP rdf:resource="#SMAC_binds_XIAP_Caspase_9Step" />
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+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2004</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Toxic proteins released from mitochondria in cell death.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Saelens, X</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Festjens, N</AUTHORS>
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+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Vandenabeele, P</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Oncogene 23:2861-74</SOURCE>
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+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2000</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Apoptosis-inducing factor (AIF): a ubiquitous mitochondrial oxidoreductase involved in apoptosis.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Daugas, E</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Nochy, D</AUTHORS>
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+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FEBS Lett 476:118-23</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="Release_of_apoptotic_factors_from_the_mitochondriaStep">
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+ <pathway rdf:ID="Apoptotic_factor_mediated_response">
+ <PATHWAY-COMPONENTS rdf:resource="#SMAC_mediated_apoptotic_responseStep" />
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+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Apoptotic factor-mediated response</NAME>
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+ <pathway rdf:ID="Cytochrome_c_mediated_apoptotic_response">
+ <PATHWAY-COMPONENTS rdf:resource="#Activation_of_caspases_through_apoptosome_mediated_cleavageStep" />
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+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cytochrome c-mediated apoptotic response</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cytochrome c-mediated apoptotic response</SHORT-NAME>
+ <XREF rdf:resource="#Reactome111461" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Upon its release from the mitochondrial intermembrane space, Cytochrome c binds to and causes a conformational change in the cytoplasmic protein Apaf1. This conformational change allows the Cytochrome c:Apaf1 complex to associate with ATP triggering oligomerization of the Apaf1:Cytochrome c:ATP complex. The apoptosome then associates with Procaspase-9 resulting in the formation of the active caspase-9 holoenzyme which f [...]
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+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ </pathway>
+ <pathway rdf:ID="Formation_of_apoptosome">
+ <PATHWAY-COMPONENTS rdf:resource="#Cleavage_of_Procaspase_9_to_Caspase_9Step" />
+ <PATHWAY-COMPONENTS rdf:resource="#Cytochrome_C_Apaf_1_binds_Procaspase_9Step" />
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+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Formation of apoptosome</NAME>
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+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ </pathway>
+ <biochemicalReaction rdf:ID="Cytochrome_C_Binds_to_Apaf_1">
+ <LEFT rdf:resource="#Cytochrome_c__cytosol_1" />
+ <LEFT rdf:resource="#Apaf_1__cytosol_" />
+ <RIGHT rdf:resource="#Apaf_1_Cytochrome_C__cytosol_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cytochrome C Binds to Apaf-1</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cytochrome C Binds to Apaf-1</SHORT-NAME>
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+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
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+ <proteinParticipant rdf:ID="Cytochrome_c__cytosol_1">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P99999_Cytochrome_c" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="Apaf_1__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_O14727_1_Apoptotic_protease_activating_factor_1__Apaf_1_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_O14727_1_Apoptotic_protease_activating_factor_1__Apaf_1_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:O14727-1 Apoptotic protease activating factor 1 (Apaf-1)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">KIAA0413</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">APAF1</SYNONYMS>
+ <XREF rdf:resource="#UniProt_O14727" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Oligomeric Apaf-1 mediates the cytochrome c-dependent autocatalytic activation of pro-caspase-9 (Apaf-3), leading to the activation of caspase-3 and apoptosis. This activation requires ATP. Isoform 6 is less effective in inducing apoptosis. SUBUNIT: Monomer. Oligomerizes upon binding of cytochrome c and dATP. Oligomeric Apaf-1 and pro-caspase-9 bind to each other via their respective NH2-terminal CARD domains a [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_O14727">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">O14727</ID>
+ </unificationXref>
+ <complexParticipant rdf:ID="Apaf_1_Cytochrome_C__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#Apaf_1_Cytochrome_C__cytosol_1" />
+ </complexParticipant>
+ <complex rdf:ID="Apaf_1_Cytochrome_C__cytosol_1">
+ <COMPONENTS rdf:resource="#Cytochrome_c__cytosol_2" />
+ <COMPONENTS rdf:resource="#Apaf_1__cytosol_1" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Apaf-1:Cytochrome C [cytosol]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Apaf-1:Cytochrome C</SHORT-NAME>
+ </complex>
+ <proteinParticipant rdf:ID="Cytochrome_c__cytosol_2">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P99999_Cytochrome_c" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="Apaf_1__cytosol_1">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_O14727_1_Apoptotic_protease_activating_factor_1__Apaf_1_" />
+ </proteinParticipant>
+ <unificationXref rdf:ID="Reactome114254">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">114254</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <publicationXref rdf:ID="Pubmed_9267021">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">9267021</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1997</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Apaf-1, a human protein homologous to C. elegans CED-4, participates in cytochrome c-dependent activation of caspase-3.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Zou, H</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Henzel, WJ</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Liu, X</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Lutschg, A</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Wang, X</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cell 90:405-13</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="Cytochrome_C_Binds_to_Apaf_1Step">
+ <STEP-INTERACTIONS rdf:resource="#Cytochrome_C_Binds_to_Apaf_1" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="Cytochrome_C_Apaf_1_binds_Procaspase_9">
+ <LEFT rdf:resource="#Caspase_9_precursor___cytosol_" />
+ <LEFT rdf:resource="#Apaf_1_Cytochrome_C__cytosol_2" />
+ <RIGHT rdf:resource="#Cytochrome_C_Apaf_1_Procaspase_9__cytosol_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cytochrome C:Apaf-1 binds Procaspase-9</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cytochrome C:Apaf-1 binds Procaspase-9</SHORT-NAME>
+ <XREF rdf:resource="#Reactome114256" />
+ <XREF rdf:resource="#Pubmed_9390557" />
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ </biochemicalReaction>
+ <proteinParticipant rdf:ID="Caspase_9_precursor___cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P55211_1_Caspase_9_precursor__EC_3_4_22_____CASP_9___ICE_like_apoptotic_protease_6___ICE_LAP6___Apoptotic_protease_Mch_6___Apoptotic_protease_activating_factor_3___APAF_3_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_P55211_1_Caspase_9_precursor__EC_3_4_22_____CASP_9___ICE_like_apoptotic_protease_6___ICE_LAP6___Apoptotic_protease_Mch_6___Apoptotic_protease_activating_factor_3___APAF_3_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P55211-1 Caspase-9 precursor (EC 3.4.22.-) (CASP-9) (ICE-like apoptotic protease 6) (ICE-LAP6) (Apoptotic protease Mch-6) (Apoptotic protease activating factor 3) (APAF-3)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CASP9</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">MCH6</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P55211" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Involved in the activation cascade of caspases responsible for apoptosis execution. Binding of caspase-9 to Apaf- 1 leads to activation of the protease which then cleaves and activates caspase-3. Proteolytically cleaves poly(ADP-ribose) polymerase (PARP). FUNCTION: Isoform 2 lacks activity is an dominant-negative inhibitor of caspase-9. SUBUNIT: Heterodimer of a 35 kDa (P35) and a 10 kDa (P10) subunit. Caspase- [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_P55211">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P55211</ID>
+ </unificationXref>
+ <complexParticipant rdf:ID="Apaf_1_Cytochrome_C__cytosol_2">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#Apaf_1_Cytochrome_C__cytosol_1" />
+ </complexParticipant>
+ <complexParticipant rdf:ID="Cytochrome_C_Apaf_1_Procaspase_9__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#Cytochrome_C_Apaf_1_Procaspase_9__cytosol_1" />
+ </complexParticipant>
+ <complex rdf:ID="Cytochrome_C_Apaf_1_Procaspase_9__cytosol_1">
+ <COMPONENTS rdf:resource="#Caspase_9_precursor___cytosol_1" />
+ <COMPONENTS rdf:resource="#Apaf_1_Cytochrome_C__cytosol_3" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cytochrome C:Apaf-1:Procaspase-9 [cytosol]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cytochrome C:Apaf-1:Procaspase-9</SHORT-NAME>
+ </complex>
+ <proteinParticipant rdf:ID="Caspase_9_precursor___cytosol_1">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P55211_1_Caspase_9_precursor__EC_3_4_22_____CASP_9___ICE_like_apoptotic_protease_6___ICE_LAP6___Apoptotic_protease_Mch_6___Apoptotic_protease_activating_factor_3___APAF_3_" />
+ </proteinParticipant>
+ <complexParticipant rdf:ID="Apaf_1_Cytochrome_C__cytosol_3">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#Apaf_1_Cytochrome_C__cytosol_1" />
+ </complexParticipant>
+ <unificationXref rdf:ID="Reactome114256">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">114256</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <publicationXref rdf:ID="Pubmed_9390557">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">9390557</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1997</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cytochrome c and dATP-dependent formation of Apaf-1/caspase-9 complex initiates an apoptotic protease cascade.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Li, P</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Nijhawan, D</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Budihardjo, I</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Srinivasula, SM</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Ahmad, M</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Alnemri, ES</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Wang, X</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cell 91:479-89</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="Cytochrome_C_Apaf_1_binds_Procaspase_9Step">
+ <STEP-INTERACTIONS rdf:resource="#Cytochrome_C_Apaf_1_binds_Procaspase_9" />
+ <NEXT-STEP rdf:resource="#Cleavage_of_Procaspase_9_to_Caspase_9Step" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="Cleavage_of_Procaspase_9_to_Caspase_9">
+ <LEFT rdf:resource="#Cytochrome_C_Apaf_1_Procaspase_9__cytosol_2" />
+ <RIGHT rdf:resource="#Apoptosome__cytosol_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cleavage of Procaspase-9 to Caspase-9</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cleavage of Procaspase-9 to Caspase-9</SHORT-NAME>
+ <XREF rdf:resource="#Reactome114259" />
+ <XREF rdf:resource="#Pubmed_9390557" />
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ </biochemicalReaction>
+ <complexParticipant rdf:ID="Cytochrome_C_Apaf_1_Procaspase_9__cytosol_2">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#Cytochrome_C_Apaf_1_Procaspase_9__cytosol_1" />
+ </complexParticipant>
+ <complexParticipant rdf:ID="Apoptosome__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#Apoptosome__cytosol_1" />
+ </complexParticipant>
+ <complex rdf:ID="Apoptosome__cytosol_1">
+ <COMPONENTS rdf:resource="#Apaf_1_Cytochrome_C__cytosol_4" />
+ <COMPONENTS rdf:resource="#Cleaved_Caspase_9__cytosol_" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Apoptosome [cytosol]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Apoptosome</SHORT-NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cytochrome C:Apaf-1:Caspase-9</SYNONYMS>
+ </complex>
+ <complexParticipant rdf:ID="Apaf_1_Cytochrome_C__cytosol_4">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#Apaf_1_Cytochrome_C__cytosol_1" />
+ </complexParticipant>
+ <complexParticipant rdf:ID="Cleaved_Caspase_9__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#Cleaved_Caspase_9__cytosol_1" />
+ </complexParticipant>
+ <complex rdf:ID="Cleaved_Caspase_9__cytosol_1">
+ <COMPONENTS rdf:resource="#Caspase_9__large_subunit___cytosol_" />
+ <COMPONENTS rdf:resource="#Caspase_9__small_subunit___cytosol_" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cleaved Caspase-9 [cytosol]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cleaved Caspase-9</SHORT-NAME>
+ </complex>
+ <proteinParticipant rdf:ID="Caspase_9__large_subunit___cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P55211_1_Caspase_9_precursor__EC_3_4_22_____CASP_9___ICE_like_apoptotic_protease_6___ICE_LAP6___Apoptotic_protease_Mch_6___Apoptotic_protease_activating_factor_3___APAF_3_" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="Caspase_9__small_subunit___cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P55211_1_Caspase_9_precursor__EC_3_4_22_____CASP_9___ICE_like_apoptotic_protease_6___ICE_LAP6___Apoptotic_protease_Mch_6___Apoptotic_protease_activating_factor_3___APAF_3_" />
+ </proteinParticipant>
+ <catalysis rdf:ID="caspase_activity_of_Apoptosome__cytosol_">
+ <CONTROLLER rdf:resource="#Apoptosome__cytosol_2" />
+ <CONTROLLED rdf:resource="#Cleavage_of_Procaspase_9_to_Caspase_9" />
+ <DIRECTION rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PHYSIOL-LEFT-TO-RIGHT</DIRECTION>
+ <XREF rdf:resource="#caspase_activity" />
+ </catalysis>
+ <complexParticipant rdf:ID="Apoptosome__cytosol_2">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#Apoptosome__cytosol_1" />
+ </complexParticipant>
+ <unificationXref rdf:ID="Reactome114259">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">114259</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <pathwayStep rdf:ID="Cleavage_of_Procaspase_9_to_Caspase_9Step">
+ <STEP-INTERACTIONS rdf:resource="#Cleavage_of_Procaspase_9_to_Caspase_9" />
+ <STEP-INTERACTIONS rdf:resource="#caspase_activity_of_Apoptosome__cytosol_" />
+ </pathwayStep>
+ <unificationXref rdf:ID="Reactome111458">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">111458</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <publicationXref rdf:ID="Pubmed_15184073">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">15184073</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2004</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Apo cytochrome c inhibits caspases by preventing apoptosome formation.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Martin, AG</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Nguyen, J</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Wells, JA</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Fearnhead, HO</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Biochem Biophys Res Commun 319:944-50</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="Formation_of_apoptosomeStep">
+ <STEP-INTERACTIONS rdf:resource="#Formation_of_apoptosome" />
+ <NEXT-STEP rdf:resource="#Cleavage_of__Procaspase_3_by_the_apoptosomeStep" />
+ <NEXT-STEP rdf:resource="#Activation_of_caspases_through_apoptosome_mediated_cleavageStep" />
+ <NEXT-STEP rdf:resource="#Cleavage_of_Procaspase_7_by_the_apoptosomeStep" />
+ </pathwayStep>
+ <pathway rdf:ID="Activation_of_caspases_through_apoptosome_mediated_cleavage">
+ <PATHWAY-COMPONENTS rdf:resource="#Cleavage_of_Procaspase_7_by_the_apoptosomeStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#Cleavage_of__Procaspase_3_by_the_apoptosomeStep" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Activation of caspases through apoptosome-mediated cleavage</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Activation of caspases through apoptosome-mediated cleavage</SHORT-NAME>
+ <XREF rdf:resource="#Reactome111459" />
+ <XREF rdf:resource="#Pubmed_9390557" />
+ <XREF rdf:resource="#Pubmed_9922454" />
+ <XREF rdf:resource="#caspase_activation_via_cytochrome_c" />
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ </pathway>
+ <biochemicalReaction rdf:ID="Cleavage_of__Procaspase_3_by_the_apoptosome">
+ <LEFT rdf:resource="#Apopain_precursor___cytosol_" />
+ <RIGHT rdf:resource="#Active_caspase_3__cytosol_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cleavage of Procaspase-3 by the apoptosome</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cleavage of Procaspase-3 by the apoptosome</SHORT-NAME>
+ <XREF rdf:resource="#Reactome114252" />
+ <XREF rdf:resource="#Pubmed_9390557" />
+ <XREF rdf:resource="#Pubmed_10206961" />
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ </biochemicalReaction>
+ <proteinParticipant rdf:ID="Apopain_precursor___cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P42574_Caspase_3_precursor__EC_3_4_22_____CASP_3___Apopain___Cysteine_protease_CPP32___Yama_protein___CPP_32___SREBP_cleavage_activity_1___SCA_1_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_P42574_Caspase_3_precursor__EC_3_4_22_____CASP_3___Apopain___Cysteine_protease_CPP32___Yama_protein___CPP_32___SREBP_cleavage_activity_1___SCA_1_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P42574 Caspase-3 precursor (EC 3.4.22.-) (CASP-3) (Apopain) (Cysteine protease CPP32) (Yama protein) (CPP-32) (SREBP cleavage activity 1) (SCA-1)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CASP3</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CPP32</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P42574" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Involved in the activation cascade of caspases responsible for apoptosis execution. At the onset of apoptosis it proteolytically cleaves poly(ADP-ribose) polymerase (PARP) at a 216-Asp-|-Gly-217 bond. Cleaves and activates sterol regulatory element binding proteins (SREBPs) between the basic helix-loop- helix leucine zipper domain and the membrane attachment domain. Cleaves and activates caspase-6, -7 and -9. I [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_P42574">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P42574</ID>
+ </unificationXref>
+ <complexParticipant rdf:ID="Active_caspase_3__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#Active_caspase_3__cytosol_1" />
+ </complexParticipant>
+ <complex rdf:ID="Active_caspase_3__cytosol_1">
+ <COMPONENTS rdf:resource="#Caspase_3__small_subunit___cytosol_" />
+ <COMPONENTS rdf:resource="#Caspase_3__large_subunit___cytosol_" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Active caspase-3 [cytosol]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Active caspase-3</SHORT-NAME>
+ </complex>
+ <proteinParticipant rdf:ID="Caspase_3__small_subunit___cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P42574_Caspase_3_precursor__EC_3_4_22_____CASP_3___Apopain___Cysteine_protease_CPP32___Yama_protein___CPP_32___SREBP_cleavage_activity_1___SCA_1_" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="Caspase_3__large_subunit___cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P42574_Caspase_3_precursor__EC_3_4_22_____CASP_3___Apopain___Cysteine_protease_CPP32___Yama_protein___CPP_32___SREBP_cleavage_activity_1___SCA_1_" />
+ </proteinParticipant>
+ <catalysis rdf:ID="caspase_activity_of_Apoptosome__cytosol_1">
+ <CONTROLLER rdf:resource="#Apoptosome__cytosol_3" />
+ <CONTROLLED rdf:resource="#Cleavage_of__Procaspase_3_by_the_apoptosome" />
+ <DIRECTION rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PHYSIOL-LEFT-TO-RIGHT</DIRECTION>
+ <XREF rdf:resource="#caspase_activity" />
+ </catalysis>
+ <complexParticipant rdf:ID="Apoptosome__cytosol_3">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#Apoptosome__cytosol_1" />
+ </complexParticipant>
+ <unificationXref rdf:ID="Reactome114252">
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+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <publicationXref rdf:ID="Pubmed_10206961">
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+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1999</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An APAF-1.cytochrome c multimeric complex is a functional apoptosome that activates procaspase-9.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Zou, H</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Li, Y</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Liu, X</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Wang, X</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Biol Chem 274:11549-56</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="Cleavage_of__Procaspase_3_by_the_apoptosomeStep">
+ <STEP-INTERACTIONS rdf:resource="#Cleavage_of__Procaspase_3_by_the_apoptosome" />
+ <NEXT-STEP rdf:resource="#Cleavage_of_cellular_proteins_by_active_caspasesStep" />
+ <NEXT-STEP rdf:resource="#Activation_of__Effector_CaspasesStep" />
+ <STEP-INTERACTIONS rdf:resource="#caspase_activity_of_Apoptosome__cytosol_1" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="Cleavage_of_Procaspase_7_by_the_apoptosome">
+ <LEFT rdf:resource="#Caspase_7_precursor___cytosol_" />
+ <RIGHT rdf:resource="#Active_Caspase_7__cytosol_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cleavage of Procaspase-7 by the apoptosome</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cleavage of Procaspase-7 by the apoptosome</SHORT-NAME>
+ <XREF rdf:resource="#Reactome114261" />
+ <XREF rdf:resource="#Pubmed_9922454" />
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ </biochemicalReaction>
+ <proteinParticipant rdf:ID="Caspase_7_precursor___cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P55210_1_Caspase_7_precursor__EC_3_4_22_____CASP_7___ICE_like_apoptotic_protease_3___ICE_LAP3___Apoptotic_protease_Mch_3___CMH_1_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_P55210_1_Caspase_7_precursor__EC_3_4_22_____CASP_7___ICE_like_apoptotic_protease_3___ICE_LAP3___Apoptotic_protease_Mch_3___CMH_1_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P55210-1 Caspase-7 precursor (EC 3.4.22.-) (CASP-7) (ICE-like apoptotic protease 3) (ICE-LAP3) (Apoptotic protease Mch-3) (CMH-1)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">MCH3</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CASP7</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P55210" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Involved in the activation cascade of caspases responsible for apoptosis execution. Cleaves and activates sterol regulatory element binding proteins (SREBPs). Proteolytically cleaves poly(ADP-ribose) polymerase (PARP) at a 216-Asp-|-Gly-217 bond. Overexpression promotes programmed cell death. ENZYME REGULATION: Inhibited by isatin sulfonamides. SUBUNIT: Heterodimer of a 20 kDa (p20) and a 11 kDa (p11) subunit. [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_P55210">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P55210</ID>
+ </unificationXref>
+ <complexParticipant rdf:ID="Active_Caspase_7__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#Active_Caspase_7__cytosol_1" />
+ </complexParticipant>
+ <complex rdf:ID="Active_Caspase_7__cytosol_1">
+ <COMPONENTS rdf:resource="#Caspase_7__large_subunit___cytosol_" />
+ <COMPONENTS rdf:resource="#Caspase_7__small_subunit___cytosol_" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Active Caspase-7 [cytosol]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Active Caspase-7</SHORT-NAME>
+ </complex>
+ <proteinParticipant rdf:ID="Caspase_7__large_subunit___cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P55210_1_Caspase_7_precursor__EC_3_4_22_____CASP_7___ICE_like_apoptotic_protease_3___ICE_LAP3___Apoptotic_protease_Mch_3___CMH_1_" />
+ </proteinParticipant>
+ <proteinParticipant rdf:ID="Caspase_7__small_subunit___cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P55210_1_Caspase_7_precursor__EC_3_4_22_____CASP_7___ICE_like_apoptotic_protease_3___ICE_LAP3___Apoptotic_protease_Mch_3___CMH_1_" />
+ </proteinParticipant>
+ <catalysis rdf:ID="caspase_activity_of_Apoptosome__cytosol_2">
+ <CONTROLLER rdf:resource="#Apoptosome__cytosol_4" />
+ <CONTROLLED rdf:resource="#Cleavage_of_Procaspase_7_by_the_apoptosome" />
+ <DIRECTION rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PHYSIOL-LEFT-TO-RIGHT</DIRECTION>
+ <XREF rdf:resource="#caspase_activity" />
+ </catalysis>
+ <complexParticipant rdf:ID="Apoptosome__cytosol_4">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#Apoptosome__cytosol_1" />
+ </complexParticipant>
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+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <publicationXref rdf:ID="Pubmed_9922454">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">9922454</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1999</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Ordering the cytochrome c-initiated caspase cascade: hierarchical activation of caspases-2, -3, -6, -7, -8, and -10 in a caspase-9-dependent manner.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Slee, EA</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Harte, MT</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Kluck, RM</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Wolf, BB</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Casiano, CA</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Newmeyer, DD</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Wang, HG</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reed, JC</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Nicholson, DW</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Alnemri, ES</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Green, DR</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Martin, SJ</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Cell Biol 144:281-92</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="Cleavage_of_Procaspase_7_by_the_apoptosomeStep">
+ <STEP-INTERACTIONS rdf:resource="#Cleavage_of_Procaspase_7_by_the_apoptosome" />
+ <NEXT-STEP rdf:resource="#Cleavage_of_cellular_proteins_by_active_caspasesStep" />
+ <NEXT-STEP rdf:resource="#Activation_of__Effector_CaspasesStep" />
+ <STEP-INTERACTIONS rdf:resource="#caspase_activity_of_Apoptosome__cytosol_2" />
+ </pathwayStep>
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+ </unificationXref>
+ <relationshipXref rdf:ID="caspase_activation_via_cytochrome_c">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GO</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0008635</ID>
+ </relationshipXref>
+ <pathwayStep rdf:ID="Activation_of_caspases_through_apoptosome_mediated_cleavageStep">
+ <STEP-INTERACTIONS rdf:resource="#Activation_of_caspases_through_apoptosome_mediated_cleavage" />
+ </pathwayStep>
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+ </unificationXref>
+ <evidence rdf:ID="Summation_140362">
+ <XREF rdf:resource="#Pubmed_11711427" />
+ </evidence>
+ <pathwayStep rdf:ID="Cytochrome_c_mediated_apoptotic_responseStep">
+ <STEP-INTERACTIONS rdf:resource="#Cytochrome_c_mediated_apoptotic_response" />
+ </pathwayStep>
+ <pathway rdf:ID="SMAC_mediated_apoptotic_response">
+ <PATHWAY-COMPONENTS rdf:resource="#SMAC_mediated_dissociation_of_IAP_caspase_complexes_Step" />
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+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SMAC-mediated apoptotic response</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SMAC-mediated apoptotic response</SHORT-NAME>
+ <XREF rdf:resource="#Reactome111469" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Once released from the mitochondria, SMAC binds to IAP family proteins displacing them from Caspase:IAP complexes liberating the active caspases.</COMMENT>
+ <EVIDENCE rdf:resource="#Summation_140376" />
+ <XREF rdf:resource="#Pubmed_15077149" />
+ </pathway>
+ <pathway rdf:ID="SMAC_binds_to_IAPs_">
+ <PATHWAY-COMPONENTS rdf:resource="#SMAC_binds_XIAP_Caspase_3Step" />
+ <PATHWAY-COMPONENTS rdf:resource="#SMAC_binds_XIAP_Caspase_7Step" />
+ <PATHWAY-COMPONENTS rdf:resource="#SMAC_binds_XIAP_Caspase_9Step" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SMAC binds to IAPs</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SMAC binds to IAPs</SHORT-NAME>
+ <XREF rdf:resource="#Reactome111463" />
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ </pathway>
+ <biochemicalReaction rdf:ID="SMAC_binds_XIAP_Caspase_3">
+ <LEFT rdf:resource="#SMAC__cytosol_1" />
+ <LEFT rdf:resource="#XIAP_Caspase_3__cytosol_" />
+ <RIGHT rdf:resource="#SMAC_XIAP_Caspase_3__cytosol_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SMAC binds XIAP:Caspase-3</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SMAC binds XIAP:Caspase-3</SHORT-NAME>
+ <XREF rdf:resource="#Reactome114306" />
+ <XREF rdf:resource="#Pubmed_11257231" />
+ <XREF rdf:resource="#Pubmed_9230442" />
+ <XREF rdf:resource="#Pubmed_14960576" />
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <EVIDENCE rdf:resource="#InferredFrom_SMAC_binds_XIAP_Caspase_7" />
+ </biochemicalReaction>
+ <proteinParticipant rdf:ID="SMAC__cytosol_1">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q9NR28_1_Diablo_homolog__mitochondrial_precursor__Second_mitochondria_derived_activator_of_caspase___Smac_protein___Direct_IAP_binding_protein_with_low_pI_" />
+ </proteinParticipant>
+ <complexParticipant rdf:ID="XIAP_Caspase_3__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#XIAP_Caspase_3__cytosol_1" />
+ </complexParticipant>
+ <complex rdf:ID="XIAP_Caspase_3__cytosol_1">
+ <COMPONENTS rdf:resource="#XIAP__cytosol_" />
+ <COMPONENTS rdf:resource="#Active_caspase_3__cytosol_2" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">XIAP:Caspase-3 [cytosol]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">XIAP:Caspase-3</SHORT-NAME>
+ </complex>
+ <proteinParticipant rdf:ID="XIAP__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P98170_Baculoviral_IAP_repeat_containing_protein_4__Inhibitor_of_apoptosis_protein_3___X_linked_inhibitor_of_apoptosis_protein___X_linked_IAP___IAP_like_protein___HILP_" />
+ </proteinParticipant>
+ <protein rdf:ID="UniProt_P98170_Baculoviral_IAP_repeat_containing_protein_4__Inhibitor_of_apoptosis_protein_3___X_linked_inhibitor_of_apoptosis_protein___X_linked_IAP___IAP_like_protein___HILP_">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt:P98170 Baculoviral IAP repeat-containing protein 4 (Inhibitor of apoptosis protein 3) (X-linked inhibitor of apoptosis protein) (X-linked IAP) (IAP-like protein) (HILP)</NAME>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">XIAP</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BIRC4</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">IAP3</SYNONYMS>
+ <SYNONYMS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">API3</SYNONYMS>
+ <XREF rdf:resource="#UniProt_P98170" />
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FUNCTION: Apoptotic suppressor. Inhibitor of caspase-3, -7 and -9. SUBUNIT: Interacts with SMAC and with PRSS25; these interactions inhibit apoptotic suppressor activity. SUBCELLULAR LOCATION: Cytoplasmic. TISSUE SPECIFICITY: Ubiquitous, except peripheral blood leukocytes. DOMAIN: The second BIR domain is sufficient to inhibit caspase-3 and -7, while the third BIR is involved in caspase-9 inhibition. The interactions wit [...]
+ </protein>
+ <unificationXref rdf:ID="UniProt_P98170">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P98170</ID>
+ </unificationXref>
+ <complexParticipant rdf:ID="Active_caspase_3__cytosol_2">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#Active_caspase_3__cytosol_1" />
+ </complexParticipant>
+ <complexParticipant rdf:ID="SMAC_XIAP_Caspase_3__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#SMAC_XIAP_Caspase_3__cytosol_1" />
+ </complexParticipant>
+ <complex rdf:ID="SMAC_XIAP_Caspase_3__cytosol_1">
+ <COMPONENTS rdf:resource="#SMAC__cytosol_2" />
+ <COMPONENTS rdf:resource="#XIAP_Caspase_3__cytosol_2" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SMAC:XIAP:Caspase-3 [cytosol]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SMAC:XIAP:Caspase-3</SHORT-NAME>
+ </complex>
+ <proteinParticipant rdf:ID="SMAC__cytosol_2">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q9NR28_1_Diablo_homolog__mitochondrial_precursor__Second_mitochondria_derived_activator_of_caspase___Smac_protein___Direct_IAP_binding_protein_with_low_pI_" />
+ </proteinParticipant>
+ <complexParticipant rdf:ID="XIAP_Caspase_3__cytosol_2">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#XIAP_Caspase_3__cytosol_1" />
+ </complexParticipant>
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+ </unificationXref>
+ <publicationXref rdf:ID="Pubmed_11257231">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">11257231</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2001</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Structural basis of caspase inhibition by XIAP: differential roles of the linker versus the BIR domain.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Huang, Y</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Park, YC</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Rich, RL</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Segal, D</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Myszka, DG</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Wu, H</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cell 104:781-90</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_9230442">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">9230442</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1997</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">X-linked IAP is a direct inhibitor of cell-death proteases.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Deveraux, QL</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Takahashi, R</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Salvesen, GS</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reed, JC</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Nature 388:300-4</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_14960576">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">14960576</ID>
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+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2004</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Smac/DIABLO selectively reduces the levels of c-IAP1 and c-IAP2 but not that of XIAP and livin in HeLa cells.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Yang, QH</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Du, C</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Biol Chem 279:16963-70</SOURCE>
+ </publicationXref>
+ <evidence rdf:ID="InferredFrom_SMAC_binds_XIAP_Caspase_7">
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+ <pathwayStep rdf:ID="SMAC_binds_XIAP_Caspase_3Step">
+ <STEP-INTERACTIONS rdf:resource="#SMAC_binds_XIAP_Caspase_3" />
+ <NEXT-STEP rdf:resource="#Dissociation_of_Caspase_3_from_SMAC_XIAP_Caspase_3Step" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="SMAC_binds_XIAP_Caspase_7">
+ <LEFT rdf:resource="#SMAC__cytosol_3" />
+ <LEFT rdf:resource="#XIAP_Caspase_7__cytosol_" />
+ <RIGHT rdf:resource="#SMAC_XIAP_Caspase_7__cytosol_" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SMAC binds XIAP:Caspase-7</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SMAC binds XIAP:Caspase-7</SHORT-NAME>
+ <XREF rdf:resource="#Reactome114354" />
+ <XREF rdf:resource="#Pubmed_11257231" />
+ <XREF rdf:resource="#Pubmed_9230442" />
+ <XREF rdf:resource="#Pubmed_14960576" />
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ </biochemicalReaction>
+ <proteinParticipant rdf:ID="SMAC__cytosol_3">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q9NR28_1_Diablo_homolog__mitochondrial_precursor__Second_mitochondria_derived_activator_of_caspase___Smac_protein___Direct_IAP_binding_protein_with_low_pI_" />
+ </proteinParticipant>
+ <complexParticipant rdf:ID="XIAP_Caspase_7__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#XIAP_Caspase_7__cytosol_1" />
+ </complexParticipant>
+ <complex rdf:ID="XIAP_Caspase_7__cytosol_1">
+ <COMPONENTS rdf:resource="#XIAP__cytosol_1" />
+ <COMPONENTS rdf:resource="#Active_Caspase_7__cytosol_2" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">XIAP:Caspase-7 [cytosol]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">XIAP:Caspase-7</SHORT-NAME>
+ </complex>
+ <proteinParticipant rdf:ID="XIAP__cytosol_1">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P98170_Baculoviral_IAP_repeat_containing_protein_4__Inhibitor_of_apoptosis_protein_3___X_linked_inhibitor_of_apoptosis_protein___X_linked_IAP___IAP_like_protein___HILP_" />
+ </proteinParticipant>
+ <complexParticipant rdf:ID="Active_Caspase_7__cytosol_2">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#Active_Caspase_7__cytosol_1" />
+ </complexParticipant>
+ <complexParticipant rdf:ID="SMAC_XIAP_Caspase_7__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#SMAC_XIAP_Caspase_7__cytosol_1" />
+ </complexParticipant>
+ <complex rdf:ID="SMAC_XIAP_Caspase_7__cytosol_1">
+ <COMPONENTS rdf:resource="#SMAC__cytosol_4" />
+ <COMPONENTS rdf:resource="#XIAP_Caspase_7__cytosol_2" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SMAC:XIAP:Caspase-7 [cytosol]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SMAC:XIAP:Caspase-7</SHORT-NAME>
+ </complex>
+ <proteinParticipant rdf:ID="SMAC__cytosol_4">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q9NR28_1_Diablo_homolog__mitochondrial_precursor__Second_mitochondria_derived_activator_of_caspase___Smac_protein___Direct_IAP_binding_protein_with_low_pI_" />
+ </proteinParticipant>
+ <complexParticipant rdf:ID="XIAP_Caspase_7__cytosol_2">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#XIAP_Caspase_7__cytosol_1" />
+ </complexParticipant>
+ <unificationXref rdf:ID="Reactome114354">
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+ </unificationXref>
+ <pathwayStep rdf:ID="SMAC_binds_XIAP_Caspase_7Step">
+ <STEP-INTERACTIONS rdf:resource="#SMAC_binds_XIAP_Caspase_7" />
+ <NEXT-STEP rdf:resource="#Dissociation_of_Caspase_7_from_SMAC_XIAP_Caspase_7Step" />
+ </pathwayStep>
+ <biochemicalReaction rdf:ID="SMAC_binds_XIAP_Caspase_9">
+ <LEFT rdf:resource="#SMAC__cytosol_5" />
+ <LEFT rdf:resource="#XIAP_Caspase_9__cytosol_" />
+ <RIGHT rdf:resource="#SMAC_XIAP_Caspase_9__cytosol_" />
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+ <XREF rdf:resource="#Pubmed_11084335" />
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+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <EVIDENCE rdf:resource="#InferredFrom_SMAC_binds_XIAP_Caspase_7" />
+ </biochemicalReaction>
+ <proteinParticipant rdf:ID="SMAC__cytosol_5">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q9NR28_1_Diablo_homolog__mitochondrial_precursor__Second_mitochondria_derived_activator_of_caspase___Smac_protein___Direct_IAP_binding_protein_with_low_pI_" />
+ </proteinParticipant>
+ <complexParticipant rdf:ID="XIAP_Caspase_9__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#XIAP_Caspase_9__cytosol_1" />
+ </complexParticipant>
+ <complex rdf:ID="XIAP_Caspase_9__cytosol_1">
+ <COMPONENTS rdf:resource="#XIAP__cytosol_2" />
+ <COMPONENTS rdf:resource="#Cleaved_Caspase_9__cytosol_2" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">XIAP:Caspase-9 [cytosol]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">XIAP:Caspase-9</SHORT-NAME>
+ </complex>
+ <proteinParticipant rdf:ID="XIAP__cytosol_2">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_P98170_Baculoviral_IAP_repeat_containing_protein_4__Inhibitor_of_apoptosis_protein_3___X_linked_inhibitor_of_apoptosis_protein___X_linked_IAP___IAP_like_protein___HILP_" />
+ </proteinParticipant>
+ <complexParticipant rdf:ID="Cleaved_Caspase_9__cytosol_2">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#Cleaved_Caspase_9__cytosol_1" />
+ </complexParticipant>
+ <complexParticipant rdf:ID="SMAC_XIAP_Caspase_9__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#SMAC_XIAP_Caspase_9__cytosol_1" />
+ </complexParticipant>
+ <complex rdf:ID="SMAC_XIAP_Caspase_9__cytosol_1">
+ <COMPONENTS rdf:resource="#SMAC__cytosol_6" />
+ <COMPONENTS rdf:resource="#XIAP_Caspase_9__cytosol_2" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SMAC:XIAP:Caspase-9 [cytosol]</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SMAC:XIAP:Caspase-9</SHORT-NAME>
+ </complex>
+ <proteinParticipant rdf:ID="SMAC__cytosol_6">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q9NR28_1_Diablo_homolog__mitochondrial_precursor__Second_mitochondria_derived_activator_of_caspase___Smac_protein___Direct_IAP_binding_protein_with_low_pI_" />
+ </proteinParticipant>
+ <complexParticipant rdf:ID="XIAP_Caspase_9__cytosol_2">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#XIAP_Caspase_9__cytosol_1" />
+ </complexParticipant>
+ <unificationXref rdf:ID="Reactome114361">
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+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <publicationXref rdf:ID="Pubmed_11084335">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">11084335</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2000</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ML-IAP, a novel inhibitor of apoptosis that is preferentially expressed in human melanomas.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Vucic, D</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Stennicke, HR</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pisabarro, MT</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Salvesen, GS</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Dixit, VM</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Curr Biol 10:1359-66</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="SMAC_binds_XIAP_Caspase_9Step">
+ <STEP-INTERACTIONS rdf:resource="#SMAC_binds_XIAP_Caspase_9" />
+ <NEXT-STEP rdf:resource="#Dissociation_of_Caspase_9_from_SMAC_XIAP_Caspase_9Step" />
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+ </unificationXref>
+ <pathwayStep rdf:ID="SMAC_binds_to_IAPs_Step">
+ <STEP-INTERACTIONS rdf:resource="#SMAC_binds_to_IAPs_" />
+ <NEXT-STEP rdf:resource="#SMAC_mediated_dissociation_of_IAP_caspase_complexes_Step" />
+ </pathwayStep>
+ <pathway rdf:ID="SMAC_mediated_dissociation_of_IAP_caspase_complexes_">
+ <PATHWAY-COMPONENTS rdf:resource="#Dissociation_of_Caspase_3_from_SMAC_XIAP_Caspase_3Step" />
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+ <PATHWAY-COMPONENTS rdf:resource="#Dissociation_of_Caspase_7_from_SMAC_XIAP_Caspase_7Step" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
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+ <XREF rdf:resource="#Reactome111464" />
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
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+ <biochemicalReaction rdf:ID="Dissociation_of_Caspase_3_from_SMAC_XIAP_Caspase_3">
+ <LEFT rdf:resource="#SMAC_XIAP_Caspase_3__cytosol_2" />
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+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
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+ </biochemicalReaction>
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+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#SMAC_XIAP_Caspase_3__cytosol_1" />
+ </complexParticipant>
+ <complexParticipant rdf:ID="Active_caspase_3__cytosol_3">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#Active_caspase_3__cytosol_1" />
+ </complexParticipant>
+ <complexParticipant rdf:ID="SMAC_XIAP__cytosol_">
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ <PHYSICAL-ENTITY rdf:resource="#SMAC_XIAP__cytosol_1" />
+ </complexParticipant>
+ <complex rdf:ID="SMAC_XIAP__cytosol_1">
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+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SMAC:XIAP</SHORT-NAME>
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+ <proteinParticipant rdf:ID="SMAC__cytosol_7">
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+ <PHYSICAL-ENTITY rdf:resource="#UniProt_Q9NR28_1_Diablo_homolog__mitochondrial_precursor__Second_mitochondria_derived_activator_of_caspase___Smac_protein___Direct_IAP_binding_protein_with_low_pI_" />
+ </proteinParticipant>
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+ <biochemicalReaction rdf:ID="Dissociation_of_Caspase_7_from_SMAC_XIAP_Caspase_7">
+ <LEFT rdf:resource="#SMAC_XIAP_Caspase_7__cytosol_2" />
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+ <biochemicalReaction rdf:ID="Dissociation_of_Caspase_9_from_SMAC_XIAP_Caspase_9">
+ <LEFT rdf:resource="#SMAC_XIAP_Caspase_9__cytosol_2" />
+ <RIGHT rdf:resource="#Cleaved_Caspase_9__cytosol_3" />
+ <RIGHT rdf:resource="#SMAC_XIAP__cytosol_3" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Dissociation of Caspase-9 from SMAC:XIAP:Caspase-9</NAME>
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+ </biochemicalReaction>
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+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2002</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">IAP proteins: blocking the road to death's door.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Salvesen, GS</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Duckett, CS</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Nat Rev Mol Cell Biol 3:401-10</SOURCE>
+ </publicationXref>
+ <pathwayStep rdf:ID="SMAC_mediated_apoptotic_responseStep">
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+ </evidence>
+ <publicationXref rdf:ID="Pubmed_14561771">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">14561771</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2003</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Ways of dying: multiple pathways to apoptosis.</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Adams, JM</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Genes Dev 17:2481-95</SOURCE>
+ </publicationXref>
+ <relationshipXref rdf:ID="induction_of_apoptosis_by_intracellular_signals">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GO</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0008629</ID>
+ </relationshipXref>
+ <pathwayStep rdf:ID="Intrinsic_Pathway_for_ApoptosisStep">
+ <STEP-INTERACTIONS rdf:resource="#Intrinsic_Pathway_for_Apoptosis" />
+ </pathwayStep>
+ <pathway rdf:ID="Activation_of__Effector_Caspases">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Activation of Effector Caspases</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Activation of Effector Caspases</SHORT-NAME>
+ <XREF rdf:resource="#Reactome75142" />
+ </pathway>
+ <unificationXref rdf:ID="Reactome75142">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">75142</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <pathwayStep rdf:ID="Activation_of__Effector_CaspasesStep">
+ <STEP-INTERACTIONS rdf:resource="#Activation_of__Effector_Caspases" />
+ <NEXT-STEP rdf:resource="#Apoptotic_execution__phaseStep" />
+ </pathwayStep>
+ <pathway rdf:ID="Apoptotic_execution__phase">
+ <PATHWAY-COMPONENTS rdf:resource="#Cleavage_of_cellular_proteins_by_active_caspasesStep" />
+ <PATHWAY-COMPONENTS rdf:resource="#Apoptosis_induced_DNA_fragmentationStep" />
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Apoptotic execution phase</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Apoptotic execution phase</SHORT-NAME>
+ <XREF rdf:resource="#Reactome75153" />
+ <CELLULAR-LOCATION rdf:resource="#cell" />
+ </pathway>
+ <pathway rdf:ID="Cleavage_of_cellular_proteins_by_active_caspases">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cleavage of cellular proteins by active caspases</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cleavage of cellular proteins by active caspases</SHORT-NAME>
+ <XREF rdf:resource="#Reactome111465" />
+ <CELLULAR-LOCATION rdf:resource="#cytosol" />
+ </pathway>
+ <unificationXref rdf:ID="Reactome111465">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">111465</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <pathwayStep rdf:ID="Cleavage_of_cellular_proteins_by_active_caspasesStep">
+ <STEP-INTERACTIONS rdf:resource="#Cleavage_of_cellular_proteins_by_active_caspases" />
+ </pathwayStep>
+ <pathway rdf:ID="Apoptosis_induced_DNA_fragmentation">
+ <ORGANISM rdf:resource="#Homo_sapiens" />
+ <NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Apoptosis induced DNA fragmentation</NAME>
+ <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Apoptosis induced DNA fragmentation</SHORT-NAME>
+ <XREF rdf:resource="#Reactome140342" />
+ <XREF rdf:resource="#DNA_fragmentation_during_apoptosis" />
+ </pathway>
+ <unificationXref rdf:ID="Reactome140342">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">140342</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <relationshipXref rdf:ID="DNA_fragmentation_during_apoptosis">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GO</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0006309</ID>
+ </relationshipXref>
+ <openControlledVocabulary rdf:ID="nucleus">
+ <TERM rdf:datatype="http://www.w3.org/2001/XMLSchema#string">nucleus</TERM>
+ <XREF rdf:resource="#GO_0005634" />
+ </openControlledVocabulary>
+ <xref rdf:ID="GO_0005634">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GO</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0005634</ID>
+ </xref>
+ <pathwayStep rdf:ID="Apoptosis_induced_DNA_fragmentationStep">
+ <STEP-INTERACTIONS rdf:resource="#Apoptosis_induced_DNA_fragmentation" />
+ </pathwayStep>
+ <unificationXref rdf:ID="Reactome75153">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">75153</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <pathwayStep rdf:ID="Apoptotic_execution__phaseStep">
+ <STEP-INTERACTIONS rdf:resource="#Apoptotic_execution__phase" />
+ </pathwayStep>
+ <unificationXref rdf:ID="Reactome109581">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reactome</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">109581</ID>
+ <COMMENT rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://www.reactome.org</COMMENT>
+ </unificationXref>
+ <evidence rdf:ID="Summation_109577">
+ <XREF rdf:resource="#Pubmed_12505355" />
+ <XREF rdf:resource="#Pubmed_4561027" />
+ <XREF rdf:resource="#Pubmed_15218528" />
+ <XREF rdf:resource="#Pubmed_14634621" />
+ <XREF rdf:resource="#Pubmed_14561771" />
+ <XREF rdf:resource="#Pubmed_12189384" />
+ <XREF rdf:resource="#Pubmed_12209154" />
+ </evidence>
+ <publicationXref rdf:ID="Pubmed_12505355">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">12505355</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2002</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">History of the events leading to the formulation of the apoptosis concept</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Kerr, JF</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Toxicology 181:471-4</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_4561027">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">4561027</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1972</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Apoptosis: a basic biological phenomenon with wide-ranging implications in tissue kinetics</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Kerr, JF</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Wyllie, AH</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Currie, AR</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Br J Cancer 26:239-57</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_15218528">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">15218528</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2004</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Apoptosis and disease: a life or death decision</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">MacFarlane, M</AUTHORS>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Williams, AC</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">EMBO Rep 5:674-8</SOURCE>
+ </publicationXref>
+ <publicationXref rdf:ID="Pubmed_12189384">
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">12189384</ID>
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pubmed</DB>
+ <YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2002</YEAR>
+ <TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Targeting death and decoy receptors of the tumour-necrosis factor superfamily</TITLE>
+ <AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Ashkenazi, A</AUTHORS>
+ <SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Nat Rev Cancer 2:420-30</SOURCE>
+ </publicationXref>
+ <relationshipXref rdf:ID="apoptosis">
+ <DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GO</DB>
+ <ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0006915</ID>
+ </relationshipXref>
+</rdf:RDF>
+
diff --git a/distribution/src/main/sampleData/BINDhuman.sif b/distribution/src/main/sampleData/BINDhuman.sif
new file mode 100644
index 0000000..e71afa7
--- /dev/null
+++ b/distribution/src/main/sampleData/BINDhuman.sif
@@ -0,0 +1,38715 @@
+LAT pp Grb2
+LAT pp PI3K_p85-alpha
+LAT pp PLC-gamma
+LAT pp Grap
+LAT pp Gads
+SLP-76 pp Vav
+SLP-76 pp Nck
+SLP-76 pp SLAP-130
+SLP-76 pp Gads
+SLP-76 pp Shc
+SLP-76 pp Cbl
+SLP-76 pp Lyn
+SLP-76 pp PLC-gamma2
+CD28 pp Grb2
+CD28 pp PI3K_p85-beta
+CD28 pp CD80
+CD28 pp CD86
+CD28 pp Itk
+Cbl pp Fyn
+Cbl pp Grb2
+Cbl pp PI3K_p85-beta
+Cbl pp CD19
+Cbl pp Syk
+Cbl-b pp Syk
+Cbl-b pp Grb2
+Cbl pp Tyk2
+Cbl pp Btk
+Cbl pp 14-3-3tau
+Cbl pp Lyn
+Cbl pp CrkL
+Cbl-b pp CrkL
+Cbl pp Crk
+Cbl pp EGFR
+Fyn pp CD2
+Fyn pp Fc-epsilon-RII
+SKAP55 pp SLAP-130
+Fyn pp SKAP55
+Fyn pp PI3K_p85-alpha
+Fyn pp IL-7R_alpha
+Fyn pp CD3-zeta
+EGF pp EGFR
+EGF-EGFR interactsWith EGF-EGFR
+EphB3 pp RasGAP
+EphB3 pp fyn
+EphB3 pp Crk
+EphB1 pp Grb10
+PDGF-B pp PDGF-B
+PDGF-BB interactsWith PDGFR-{beta}
+PDGF-BB/PDGF-(beta)-R/ATP interactsWith PDGF-(beta)-R
+(EGF-EGFR)_dimer_complex interactsWith ATP
+(EGF-EGFR)_dimer-ATP interactsWith (EGF-EGFR)_dimer_complex
+EphB1 pp Grb2
+EphB1 pp Nck
+EphB1 pp LMW-PTP
+EphB2 pp LMW-PTP
+EphB2 pp EphB2
+PI3K_p85-alpha pp PI3K_p110-alpha
+PDGF-BB/PDGF-beta-R_dimer interactsWith PI3K-alpha
+PI3K-alpha* interactsWith PIP2
+Grb2 pp Sos1
+(EGF-EGFR)_dimer_P-Tyr1068 interactsWith Grb2-Sos1
+PIP3 interactsWith PDK1
+PIP3 interactsWith PKB-alpha_multimer
+PKB interactsWith BAD
+PIP3-PDK1-ATP_complex interactsWith PIP3-PKB-alpha
+15.5kD interactsWith U4_snRNA
+15.5kD interactsWith U4atac_snRNA
+PI3K_p110-alpha pp Ha-Ras
+PI3K_p110-alpha interactsWith PI-4,5-P2
+MEK pp Raf-1
+PDGF-BB/PDGF-beta-R interactsWith ATP
+PKB-alpha pp PKB-alpha
+PI3K-alpha*-PIP2 interactsWith ATP
+PDGF-BB/PDGF-beta-R_dimer/PI3K-alpha interactsWith ATP
+PDK1-PIP3 interactsWith ATP
+PDK1-PIP3-ATP interactsWith PRK2
+Grb2 pp Frs2
+Grb2 pp Gab1
+PIP3-PKB-alpha interactsWith ATP
+H-Ras interactsWith GDP
+Grb2-Sos interactsWith H-Ras-GDP
+Grb2-Sos-H-Ras_complex interactsWith GTP
+Ras-GTP interactsWith Raf
+ITK pp LAT
+ITK pp SLP-76
+ITK pp PLC
+PP5 pp GR
+NF-YB pp NF-YC
+NF-YB/_NF-YC interactsWith NF-YA
+XL-alpha-s interactsWith GDP
+NF-Y interactsWith p-MDR1
+Sp1 pd p-MDR1
+G-beta3 pp G-gamma_3
+G-alpha interactsWith GDP
+XL-alpha-GDP interactsWith G-beta-gamma
+G-alpha-GDP interactsWith G-beta-gamma
+p53 pd p-MDR1
+Bcl-XL pp Bak1
+Bcl-XL pp BaxB
+Bcl-XL pp BCL2L12
+Bcl-XL pp BimL
+CCX-CKR pp ELC
+CCX_CKR pp SLC
+CCX_CKR pp TECK
+CCX_CKR pp BLC
+TBP pp ER
+SHP pp LRH-1
+SHP-LRH1 interactsWith p-SHP
+ShcA pp Grb2
+Gab1 pp PI3K_p85-alpha
+Gab1 interactsWith PIP3
+hSos1 interactsWith Ras-GDP
+PKCa pp Cdc42
+WAVE_1 pp WRP
+Unknown interactsWith Abi_1
+Unknown interactsWith Abi_2
+Unknown interactsWith SNIP
+Unknown interactsWith alpha-tubulin
+Unknown interactsWith Spectrin_aII
+Unknown interactsWith Spectrin_bIII
+KIAA0319 pp KIAA0396
+KIAA0319 pp KIAA1299
+KIAA0343 pp KIAA0417
+KIAA0343 pp KIAA1251
+KIAA0343 pp KIAA1634
+KIAA0348 pp KIAA1256
+KIAA0358 pp KIAA0453
+KIAA0364 pp KIAA1131
+KIAA0364 pp KIAA1464
+KIAA0387 pp KIAA0097
+KIAA0463 pp KIAA0144
+KIAA0463 pp KIAA1014
+KIAA0463 pp KIAA1199
+KIAA0463 pp KIAA1374
+KIAA0543 pp KIAA1043
+KIAA0543 pp KIAA1218
+KIAA0578 pp KIAA0300
+KIAA0578 pp KIAA0440
+KIAA0578 pp KIAA0865
+KIAA0578 pp KIAA1251
+KIAA0603 pp KIAA0332
+KIAA0603 pp KIAA0765
+KIAA0603 pp KIAA1498
+KIAA0603 pp KIAA1546
+KIAA0620 pp KIAA1251
+KIAA0690 pp KIAA0109
+KIAA0812 pp KIAA0640
+KIAA0812 pp KIAA0728
+KIAA0816 pp KIAA1526
+KIAA0868 pp KIAA0155
+KIAA0868 pp KIAA1224
+KIAA0868 pp KIAA1251
+KIAA0911 pp KIAA0045
+KIAA0911 pp KIAA0067
+KIAA0911 pp KIAA0204
+KIAA0911 pp KIAA0572
+KIAA0911 pp KIAA1447
+KIAA0921 pp KIAA1251
+KIAA0960 pp KIAA0400
+KIAA0987 pp KIAA0912
+KIAA0987 pp KIAA1032
+KIAA1062 pp KIAA1633
+KIAA1132 pp KIAA0705
+KIAA1132 pp KIAA1092
+KIAA1132 pp KIAA1634
+KIAA1206 pp KIAA0076
+KIAA1206 pp KIAA0275
+KIAA1206 pp KIAA0380
+KIAA1206 pp KIAA0705
+KIAA1206 pp KIAA0708
+KIAA1206 pp KIAA0952
+KIAA1206 pp KIAA1634
+KIAA1216 pp KIAA0235
+KIAA1216 pp KIAA0593
+KIAA1216 pp KIAA1037
+KIAA1216 pp KIAA1041
+KIAA1278 pp KIAA0316
+KIAA1278 pp KIAA0807
+KIAA1278 pp KIAA1633
+KIAA1368 pp KIAA0777_
+KIAA1368 pp KIAA1256
+KIAA1368 pp KIAA1296
+KIAA1368 pp KIAA1494
+KIAA1394 pp KIAA0045
+KIAA1549 pp KIAA0728
+KIAA1549 pp KIAA1119
+KIAA1549 pp KIAA1121
+KIAA1549 pp KIAA1256
+KIAA1549 pp KIAA1461
+KIAA1573 pp KIAA0240
+KIAA1573 pp KIAA1177
+KIAA1573 pp KIAA1224
+KIAA1573 pp KIAA1464
+KIAA1679 pp KIAA1464
+KIAA1746 pp KIAA0465
+KIAA1763 pp KIAA0561
+KIAA1763 pp KIAA0875
+KIAA1763 pp KIAA1251_
+KIAA1763 pp KIAA1464
+KIAA1780 pp KIAA0109
+KIAA1780 pp KIAA0207
+KIAA1780 pp KIAA0577
+KIAA1780 pp KIAA0788
+KIAA1780 pp KIAA1464
+BRCA1 pp BACH1
+BRCA1 pp ER-alpha
+BRCA1 pp BRG1
+BRCA1 pp ATM
+BRCA1 pp ATF1
+BRCA1 pp RAD50
+BRCA1 pp hCds1
+BRCA1 pp FANCD2
+BRCA1 pp JnB
+BRCA1 pp c-Jun
+BRCA1 pp JunD
+BRCA1 pp CK2beta
+BRCA1 pp FANCA
+BRCA1 pp CtIP
+BRCA1 pp ATR
+BRCA1 pp BRCA2
+BRCA1 pp Rad51
+BRCA2 pp RAD51
+BRCA2 pp hsFLNa
+BRCA1 pp MYC
+BRCA1 pp Nmi
+MYC pp Nmi
+BRCA1 pp CDC2
+BRCA1 pp CDK2
+BRCA1 pp CDK4
+BRCA1 pp Cyclin_B1
+BRCA1 pp Cyclin_A
+BRCA1 pp Cyclin_D1
+BRCA1 pp E2F-1
+BRCA1 pp E2F-4
+BRCA1 pp Rb
+BRCA1 pp RbAp46_
+BRCA1 pp RbAp48
+BRCA1 pp HDAC1
+BRCA1 pp HDAC2
+Rb pp RbAp46_
+Rb pp RbAp48
+Rb pp HDAC1
+RbAp48_ pp HDAC1
+Elongin_B pp Elongin_C
+ElonginB-ElonginC interactsWith Muf1
+ElonginB-ElonginC interactsWith VHL
+ElonginB-ElonginC interactsWith VHL/VDU1
+pVHL pp hVDU1
+Elongin_BC interactsWith SOCS-1
+Elongin_BC interactsWith SOCS-3
+Elongin_BC interactsWith WSB-1
+Elongin_BC interactsWith ASB-2_
+Elongin_BC interactsWith Rar-1__
+Stat5b pp Nmi
+Stat1 pp Nmi
+Stat3 pp Nmi
+Stat4 pp Nmi
+Stat5a pp Nmi
+Stat6 pp Nmi
+IFP_35 pp Nmi
+BRCA1 pp Oct-1
+BRCA1 pp NF-YA
+Oct-1 pp NF-YA
+VBC interactsWith CUL2
+Elongin_BC interactsWith mMED8
+mMED8-Elongin_BC_ interactsWith Cul2
+mMED8-Elongin_BC_ interactsWith RBX1__________________
+SOCS1 pp Kit
+SOCS1 pp Flt3__
+SOCS1 pp PDGF-R__
+SOCS1 pp CSF1-R_
+SOCS1 pp TEK
+SOCS1 pp Vav
+SOCS1 pp Vav2
+SOCS-1 pp Grb2_
+SOCS1 pp p85-beta
+BRCA1 pp CBP
+BRCA1 pp p300
+BRCA1 pp p53
+BRCA1 pp LMO4
+LMO4 pp CtIP
+LMO2 pp CtIP
+LMO4,_BRCA1,_and_CtIP interactsWith LDB1
+SOCS1 pp Nck
+SOCS1 pp Itk
+SOCS-1 pp Fyn
+D52 pp D52
+D52 pp D53
+D52 pp D54
+TPD52 pp MAL2
+D54 pp D54
+D53 pp D53
+D53 pp D54
+IGF-IR pp SOCS-2
+IGF-IR pp SOCS-1
+IGFIR pp SOCS-3
+BRCA1 pp ACCA
+Tuberin pp 14-3-3-epsilon
+Tuberin_ pp 14-3-3-eta__
+Tuberin pp 14-3-3-zeta__
+Tuberin pp 14-3-3-theta
+Tuberin pp 14-3-3-beta__
+Tuberin pp 14-3-3-gamma__
+IGFIR pp 14-3-3-epsilon__
+IRS-1 pp 14-3-3-epsilon__
+IGFIR pp 14-3-3-beta_
+IGFIR pp 14-3-3-zeta_
+IGF-IR pp SHC-1
+IGF-IR pp p85_beta
+IRS-1 pp SHC-1
+IGF-IR_beta pp IRS-2
+IR pp IRS-1
+IR pp IRS-2
+IR pp SOCS-1
+IR pp SOCS-6
+MLH1_ pp BLM
+MSH2 pp BRCA1
+MSH6 pp BRCA1
+MSH6_ pp MSH2
+hPMS1 pp hMLH1
+hMLH1 pp hMLH3
+hMLH1 pp hPMS2
+HEX1 pp hMLH1
+hEXO1b pp hMLH1
+hEXO1b pp hMSH2
+hExoI pp PMS2
+ExoI pp MSH3
+MLH1 pp MED1
+MLH1 pp MSH4
+hPMS1 interactsWith hMutS-alpha
+hPMS2 interactsWith hMutS-alpha
+hMLH1 interactsWith hMutS-alpha
+hMutL-beta interactsWith hMutS-alpha
+hMutL-alpha interactsWith hMutS-alpha
+MEK1 pp ERK1
+MEK2 pp ERK1
+MEK1 pp ERK2
+MEK2 pp ERK2
+vav pp ERK2
+vav pp gp130
+Vav pp Grb2
+K14_ pp TRADD
+K18 pp TRADD
+TNFR1 pp TRADD_
+PCNA pp MSH6
+HEX1 pp hMSH2
+PCNA pp POLD1_
+PCNA pp LIG1
+PCNA interactsWith MSH2/MSH6_Heterodimer
+PCNA pp KIAA0039
+PCNA pp FEN1
+PCNA pp DDX17
+PCNA pp NONO
+PCNA pp MGC5528
+PCNA pp RFC2
+PCNA pp RFC5
+PCNA pp RFC3
+Unknown interactsWith RFC5
+Unknown interactsWith RFC4
+Unknown interactsWith RFC3
+Unknown interactsWith RFC2
+MEK1 pp c-Raf
+MEK1 pp B-Raf
+MEK1 pp A-Raf
+PCNA pp p50
+PCNA pp POLB
+MUTYH pp APE1
+PCNA pp MUTYH
+MUTYH pp RPA
+PCNA pp APE2
+Naf1-alpha pp ERK2
+MEK2 pp A-Raf
+hMSH2 pp hMSH3
+SHIP1_ pp DOK1
+SHC pp SHIP1_
+SHIP1_ pp Dok2
+Dok2 pp RASGAP
+DOK1 pp RASGAP
+c-Raf-1 pp 14-3-3-zeta
+PCNA pp UNG
+PCNA pp TCOF1
+PCNA pp PRKDC
+PCNA interactsWith CHL12/RFCs2-5_complex_
+PCNA pp POLE
+PCNA pp DNMT1
+PCNA pp MYBBP1A
+CCND2 pp CDK4
+Sab pp JNK1-alpha-1
+Sab pp JNK1-alpha-2
+Sab pp JNK1-beta-1
+Sab pp JNK1-beta-2
+Sab pp JNK2-alpha-1
+Sab pp JNK2-alpha-2
+Sab pp JNK2-beta-1
+Sab pp JNK2-beta-2
+Sab pp JNK3-alpha-1
+Sab pp JNK3-alpha-2
+Pax6 pp HoxB1
+Pax6 pp Pbx1
+pVhl pp FN1
+pVHL pp HIF-1-alpha
+HIF-1-alpha interactsWith VBC
+Crx pp Nrl
+pVHL pp HIF-2-alpha
+SOX18 pp MEF2C
+Vhl pp Jade-1_
+Vhl pp VBP1
+Vhl pp FLNA_
+MDM2 pp p14ARF
+CDKN2A pp CDK4
+p14ARF pp HIF-1alpha
+p53 pp PP2AC
+HIPK2 pp RanBPM
+HIPK2 pp p53
+AIRE pp AIRE
+AIRE pp CBP
+ALDP_ pp ALDP_
+ALDP pp ALDRP
+ALDRP pp ALDRP
+PMP70_ pp PMP70_
+ALDP_ pp PMP70_
+PMP70_ pp ALDRP_
+Nod1 pp Nod1
+Nod1 pp Caspase-9
+Nod2 pp RICK
+Nod1 pp RICK
+HIRA pp Cyclin-A_
+ALDP_ pp PEX19_
+PEX19 pp ALDRP
+PEX19 pp PMP70_
+PhLP pp TCP-1-alpha
+apoE3 pp CNTF
+p-eNOS_ pd GATA-2_
+p-eNOS_ pd Sp1_
+mSin3A pp HDAC1
+mSin3A pp HDAC2
+PDE4A interactsWith Mg++
+Rabin8 pp Rab8
+Grap2 pp HPK1
+CrkL pp HPK1
+D5 pp NCS-1
+D3 pp NCS-1
+D2 pp NCS-1
+GAP-43 pp CaM
+Crk pp HPK1
+Grb2 pp HPK1
+CFTR pp CANX
+D53 pp D53+5
+CD_155 pp VTN
+Rac1 pp TIAM1
+PKB/Akt pp IMPDH
+Cdc42 pp Dbs
+Cdc42 pp ITSN1
+RhoA__ pp Dbs
+CTSH pp CSTA
+Cdc42 interactsWith GTP
+Cdc42 interactsWith Mg2+
+Mg2+ interactsWith GTP
+Cdc42-GTP-Mg2+ interactsWith Par6
+Stat3 pp Nmi
+Stat1 pp Nmi
+GAIP pp GIPC
+APP-BP1 pp APP
+YB-1 pp Pur-alpha
+TSHR pp CANX
+TSHR pp CALR
+TSHR pp BiP
+S100A7 pp EFABP
+Jab1 pp HIF-1-alpha
+APP-BP1 pp hUba3
+APP-BP1 pp ASPP2
+Zn2+__ interactsWith UBA3
+Kit pp Grb2
+Kit pp PLC-gamma
+Kit pp p85-alpha
+Kit pp p85-beta
+AANAT pp 14-3-3-zeta_
+Rabin8 pp Rab8b
+CRABP-I interactsWith RA
+S100A4 pp S100A1
+CAPL pp CAPL
+Akt pp 14-3-3_zeta
+DDX1 pp hnRNP-K
+apoE4 pp CNTF
+MAPKAPK2 pp 14-3-3-zeta
+Akt pp p47(phox)
+p34 pp p20
+14-3-3zeta pp 14-3-3zeta
+p41 pp p16
+CRABP-II interactsWith RA
+APPBP1 interactsWith UBA3-Zn2+
+Grb2 pp Bcr-Abl
+Grb2 pp Sam68
+p41 pp p34
+p41 pp p20
+p41 pp Arp2
+p20 pp p16
+p20 pp Arp2
+p20 pp Arp3
+Calcyclin pp Calcyclin
+p16 pp Arp2
+p21 pp Arp3
+CaCY-CaCY interactsWith Ca2+
+Arp2 pp Arp3
+p34 pp Arp3
+MAPKAPK2 interactsWith Arp2/3
+MAPKAPK2 pp p16-Arc
+Egr1 pp Sp1
+5LO pp CLP
+5LO pp TRAP-1
+MAPKAPK2 pp 14-3-3-zeta
+14-3-3zeta pp 14-3-3zeta
+hnRNP_L pp hnRNP_K
+Ku70 pp Ku80
+SRp20 pp hnRNP_K
+D2L pp FLN-A
+D2S pp FLN-A
+D3 pp FLN-A
+Hamartin pp 14-3-3-epsilon
+Hamartin pp 14-3-3-eta_
+Hamartin pp 14-3-3-theta
+Smad3 pp CAN/Nup214
+VLA3-alpha3 pp VLA3-beta
+VLA6-alpha6 pp VLA-beta1
+VLA6-alpha6 pp Integrin-beta4
+Integrin-alpha11 pp Integrin-beta1
+VLA2-alpha2 pp VLA2-beta
+VLA1-alpha1 pp VLA1-beta
+Integrin-alphaV pp Integrin-beta3
+Integrin-alphaV pp Integrin-beta_1
+VLA4-alpha4 pp VLA4-beta
+Integrin-alpha4 pp Integrin-beta7
+VLA5-alpha5 pp VLA5-beta
+Integrin-alpha8 pp Integrin-beta1
+Integrin-alpha9 pp Integrin-beta1
+Integrin-alphaIIb pp Integrin-beta3
+Integrin-alphaV pp Integrin-beta5
+Integrin-alphaV pp Integrin-beta6
+Integrin-alphaV pp Integrin-beta8
+VLA3-alpha3 pp VLA3-beta
+VLA6-alpha6 pp VLA-beta1
+CD151 interactsWith Integrin_alpha-3_beta-1
+CD151 interactsWith Integrin_alpha-6_beta-1
+CD151 interactsWith Integrin_alpha-3_beta-1
+CD151 interactsWith Integrin_alpha-6_beta-1
+CD151 interactsWith Integrin_alpha-6_beta-4
+FN interactsWith Integrin_alpha-4_beta-1
+FN interactsWith Integrin_alpha-5_beta-1
+FN interactsWith Integrin_alpha-8_beta-1
+FN interactsWith Integrin_alpha-9_beta-1
+FN interactsWith Integrin_alpha-IIb_beta-3
+FN interactsWith Integrin_alpha-v_beta-1
+FN interactsWith Integrin_alpha-v_beta-3
+FN interactsWith Integrin_alpha-v_beta-6
+tenascin interactsWith Integrin_alpha-2_beta-1
+14-3-3-zeta_ pp Tau
+COX-1 pp COX-1
+Hamartin pp Tuberin
+tenascin interactsWith Integrin_alpha-8_beta-1
+D3 pp FLN-A
+tenascin interactsWith Integrin_alpha-9_beta-1
+tenascin interactsWith Integrin_alpha-v_beta-3
+tenascin interactsWith Integrin_alpha-v_beta-6
+hamartin pp ezrin
+hamartin pp radixin
+hamartin pp moesin
+PPAR-delta pp BCL-6
+Akt pp 14-3-3_zeta
+PPAR-delta pp HDAC7
+PPAR-delta pp SMRT
+Hamartin pp NF-L
+p53 interactsWith Zn2+
+53BP1 interactsWith p53-Zn2+
+Hamartin pp merlin_
+BRCA1a pp p53
+Nut2 interactsWith Unknown
+Med25 interactsWith Unknown
+Intersex interactsWith Unknown
+LCMR1 interactsWith Unknown
+Med28 interactsWith Unknown
+CRSP70 interactsWith Unknown
+YY1 pp Hdm2
+YY1 pp p53
+YY1 pp p14ARF
+Bcl-2 pp Bax
+Bcl-2 pp Bik
+Bcl-2 pp Rheb
+LATS1 pp LIMK1
+PCNA pp EXO1b
+hCNK1 pp rhophilin
+Htt pp Htt
+Htt pp CBP
+Htt pp TBP
+alpha-DG pp LARGE
+Unknown interactsWith POT1
+Unknown interactsWith TRF2
+TIN2 interactsWith Unknown
+Unknown interactsWith PTOP
+PTOP pp POT1
+PTOP pp TIN2
+A-beta_subunit pp C-alpha_subunit
+Htt pp Htt
+SIX3 pp TLE1
+SIX3 pp AES
+SIX3 pp TLE3
+SIX6 pp TLE1
+SIX6 pp AES
+SIX1 pp TLE1
+SIX1 pp AES
+SIX2 pp TLE1
+SIX2 pp AES
+SIX4 pp TLE1
+SIX4 pp TLE3
+IGF-II pp IGFBP-5
+IGF-I pp IGFBP-2
+IGF-I pp IGFBP-3
+IGF-I pp IGFBP-5
+IGF-I pp IGFBP-6
+IGF-I pp IGFBP-1
+IGF-I pp IGFBP-4
+IGF-II pp IGFBP-6
+merlin pp ezrin
+merlin pp HRS
+Stat2 pp p300
+JIP1 pp APP
+B-Raf interactsWith unknown
+unknown interactsWith MLK3
+MEK1 pp MLK3
+Stat1-alpha pp CBP
+Stat1-beta pp CBP
+Smad3 pp CDK4
+Smad3 pp CDK2
+Rb pp CDK4
+Rb pp CDK2
+Smad2 pp CDK4
+Smad2 pp CDK2
+A-alpha_subunit pp C-alpha_subunit
+IGF-II pp IGFBP-4
+PML pp Mdm2
+PML pp L11
+ATR pp PML
+Stat1-beta pp p300
+alpha-DG pp Laminin_alpha_2
+A-alpha/C-alpha_complex interactsWith B"/PR72_subunit
+hREV1 pp POLK
+hREV1 pp POLI
+hREV1 pp POLH
+Pak1 pp RhoGDI
+Pak1 pp P47
+p300_promoter pd Egr1
+p300 pp Egr1
+p300_promoter interactsWith Egr1-p300_complex
+p300 pd Egr1_promoter
+CBP_promoter pd Egr1
+ApoJ pp TGFBR2
+ApoJ pp TGFBR1
+cyclin_A1 pp p21
+cyclin_A1 pp p27
+YB-1 pp CTCF
+CBP pd Egr1_promoter
+STAT1-alpha pp c-kit
+cyclin_A1 pp GPS2
+cyclin_A1 pp INCA1
+cyclin_A1 pp PROCA1
+EZH2 pp EED
+EED pp SUZ12
+EED pp AEBP2
+RbAp48 pp SUZ12
+SUZ12 pp AEBP2
+RbAp48 pp AEBP2
+p73_alpha pp c-Myc
+Dicer interactsWith dsRNA
+Dicer interactsWith pre-miRNA
+cyclin_A1 pp RACK1
+STRA13 pp STAT3-beta
+Stat2 pp p48
+SUZ12 pd HoxA9_upstream_region
+IGF-II pp IGFBP-1
+IGF-II pp IGFBP-2
+IGF-II pp IGFBP-3
+SUZ12 pd HoxA9_promoter
+cyclin_A1 pp DKFZ
+cyclin_A1 pp Ku70
+Plexin-B1 pp Rnd1
+R-Ras interactsWith Plexin-B1-Rnd1_Complex
+c-Raf1 interactsWith Unknown
+Unknown interactsWith R-Ras
+Rhotekin interactsWith Unknown
+Unknown interactsWith RhoA
+D2S pp D2S
+ACTR pp E2F1
+ArgBP2-A pp Cbl
+cyclin_A1 pp RBM4
+cyclin_A1 pp KARCA1
+htt pp HIP14
+hRAD51-ATP interactsWith DNA
+hRAD51-ADP interactsWith DNA
+hRAD51 interactsWith Unknown
+Unknown interactsWith hXRCC2
+BRCA1 pp MEKK3
+FANCG pp FANCG
+FANCA pp FANCG
+FANCA pp FANCA
+CXCR1 pp IL-8
+CXCR1 pp MGSA
+Alpha-1_PI pp Neutrophil_elastase
+Alpha-1_PI pp Cathepsin_G
+Alpha-1_ACT pp Cathepsin_G
+LRP pp alpha-1-ACT
+LRP pp alpha-1-PI
+LRP pp Cathepsin_G
+LRP pp Elastase_2
+Cbf-beta pp AML1a
+Cbf-beta pp AML1b
+Cbf-beta pp AML2
+Alpha-1_PI/neutrophil_elastase interactsWith LRP
+Alpha-1_PI/cathepsin_G interactsWith LRP
+Alpha-1_ACT/cathepsin_G interactsWith LRP
+Unknown interactsWith RPB1
+Unknown interactsWith RPB2
+Unknown interactsWith RPB3
+Unknown interactsWith RPB4
+Unknown interactsWith RPB5
+Unknown interactsWith RPB6
+Unknown interactsWith RPB7
+Unknown interactsWith RPB8
+RPB9 interactsWith Unknown
+Unknown interactsWith RPB10-alpha
+Unknown interactsWith RPB10-beta
+Unknown interactsWith RPB11
+hRAD51-hXRCC2-ATP interactsWith DNA
+hRAD51-hXRCC2-ADP interactsWith DNA
+CGI-99 pp NIN
+CGI-99 pp CGI-99
+CRP2 pp PIAS1
+ErbB-4 pp PSD-95
+ErbB-4 pp Beta2-Syntropin
+ErbB-4 pp CHAPSYN-110
+ErbB-4 pp SAP-102
+HIP1 pp Clathrin-HC
+KIAA1196 pp PTPN3
+KIAA1196 pp ZNF198
+KIAA1196 pp PPP1R15A
+KIAA1196 pp RN3
+KIAA1196 pp ZF
+KIAA1196 pp PLCG2
+KIAA1196 pp FLJ10884
+KIAA1196 pp APPH
+KIAA1196 pp TRX2
+KIAA1196 pp HTATSF1
+KIAA1196 pp PEG10
+KIAA1196 pp XPC
+KIAA1196 pp PIASY
+KIAA1196 pp RPS27A
+KIAA1196 pp LOC89272
+KIAA1196 pp BTBD2
+KIAA1196 pp VPS41
+KIAA1196 pp tankyraseII
+KIAA1196 pp PTPRF
+KIAA1196 pp ATRX
+KIAA1196 pp TIEG
+KIAA1196 pp DCTN1
+KIAA1196 pp BRD1
+KIAA1196 pp KIAA1082
+KIAA1196 pp Ku70
+KIAA1196 pp VHL
+KIAA1196 pp SUPT5H
+KIAA1196 pp YES1
+KIAA1196 pp PLAC3
+KIAA1196 pp IL1HY1
+KIAA1196 pp OS-9
+KIAA1196 pp FBXL11
+KIAA1196 pp KIAA0737
+KIAA1196 pp DDX27
+KIAA1196 pp CTBP2
+KIAA1196 pp TRAF4
+KIAA1196 pp SPTBN1
+KIAA1196 pp PAPPE
+KIAA1196 pp MBD1
+KIAA1196 pp MEG3
+KIAA1196 pp Cab45
+KIAA1196 pp MYH10
+KIAA1196 pp LAMB2
+KIAA1196 pp INVS
+KIAA1196 pp PB1
+KIAA1196 pp BAT8
+KIAA1196 pp DDX3
+KIAA1196 pp KIAA0692
+KIAA1196 pp VWF
+KIAA1196 pp KIAA1813
+KIAA1196 pp KIAA0379
+KIAA1196 pp PDE4DIP
+KIAA1196 pp HEY-L
+KIAA1196 pp TOM1
+KIAA1196 pp VPS35
+KIAA1196 pp D123
+KIAA1196 pp AP1G1
+KIAA1196 pp Smad1
+KIAA1196 pp TXNL2
+KIAA1196 pp DVL3
+KIAA1196 pp TGM2
+RNF11 pp ENDOFIN
+RNF11 pp RPS27A
+RNF11 pp UBC
+RNF11 pp LOC133957
+RNF11 pp USP5
+RNF11 pp FLJ12392
+RNF11 pp FLJ21588
+RNF11 pp UBB
+RNF11 pp SMURF1
+RNF11 pp FLJ32746
+RNF11 pp UBQLN2
+RNF11 pp GGA3
+RNF11 pp cbl-b
+RNF11 pp RABEX5
+RNF11 pp UBE2N
+RNF11 pp NAF1
+RNF11 pp PDCD6IP
+RNF11 pp OPTN
+RNF11 pp KIAA0323
+RNF11 pp SDCBP
+RNF11 pp NDP52
+RNF11 pp ERCC6
+RNF11 pp QARS
+RNF11 pp DKFZP547N043
+RNF11 pp WWP2
+RNF11 pp TRIAD3
+RNF11 pp UBE2D2
+RNF11 pp STAM2
+RNF11 pp NEMO
+RNF11 pp A1U
+RNF11 pp MYO6
+RNF11 pp HERC2
+RNF11 pp LOC51619
+RNF11 pp POLI
+RNF11 pp PTPRC
+RNF11 pp GGA1
+RNF11 pp TAX1BP1
+RNF11 pp AUP1
+RNF11 pp HERC1
+RNF11 pp SMURF2
+RNF11 pp GDBR1
+RNF11 pp RP42protein
+RNF11 pp SNRP70
+RNF11 pp NY-REN-25
+RNF11 pp EPN3
+RNF11 pp UBA52
+RNF11 pp TNFAIP3
+RNF11 pp WWP1
+RNF11 pp FLJ35794
+RNF11 pp NEDD4
+RNF11 pp EPSIN
+RNF11 pp UREB1
+RNF11 pp EPN2
+RNF11 pp NEDD4L
+ZNF8 pp DCTN1
+ZNF8 pp FBN2
+ZNF8 pp LRP1
+ZNF8 pp NOTCH2
+ZNF8 pp THBS1
+ZNF8 pp KIAA1042
+ZNF8 pp CCND1
+ZNF8 pp RES4-22
+ZNF8 pp DLK1
+ZNF8 pp fibulin-1A
+ZNF8 pp MGC11256
+ZNF8 pp MTMR4
+ZNF8 pp Smad8a
+ZNF8 pp Smad1
+LMO4 pp PITPNB
+LMO4 pp LDB1
+LMO4 pp TCF21
+LMO4 pp IMAGE_4824025
+LMO4 pp KIF3B
+LMO4 pp LIECG3
+LMO4 pp MERTK
+LMO4 pp ITSN1
+LMO4 pp KPNA1
+LMO4 pp LDB2
+LMO4 pp SEC24D
+LMO4 pp TIZ
+LMO4 pp DDB1
+FLJ20037 pp SPINT1
+FLJ20037 pp NR2F2
+FLJ20037 pp TBX4
+FLJ20037 pp PSG1
+FLJ20037 pp LOC121133
+FLJ20037 pp COL4A2
+FLJ20037 pp HDLBP
+FLJ20037 pp RNF14
+FLJ20037 pp PRSS11
+FLJ20037 pp DNCH1
+FLJ20037 pp EGLN2
+FLJ20037 pp KEAP1
+FLJ20037 pp BCCIP
+FLJ20037 pp MESDC2
+FLJ20037 pp BAT3
+Smad2 pp RPS27A
+Smad2 pp BTBD2
+Smad2 pp OS-9
+Smad2 pp PSG11
+Smad2 pp CSH1
+Smad2 pp SMURF1
+Smad2 pp PPP2R1A
+Smad2 pp FBN2
+Smad2 pp SnoN
+Smad2 pp PRKAR1A
+Smad2 pp AP1B1
+Smad2 pp PAPPA
+Smad2 pp LAMA5
+Smad2 pp SMURF2
+Smad2 pp SIP1
+Smad2 pp FLJ10759
+Smad2 pp PSAP
+Smad2 pp HSA242910
+Smad2 pp STAG1
+Smad2 pp FLJ12565
+Smad2 pp ABTB1
+Smad2 pp PSMD8
+Smad2 pp ANK3
+Smad2 pp RANBP9
+Smad2 pp BAZ1A
+Smad2 pp RP42protein
+Smad2 pp MLLT4/AF6
+Smad2 pp TTC2
+Smad2 pp ROCK1
+Smad2 pp CYP11A
+Smad2 pp CBP
+Smad2 pp PSMD11
+Smad2 pp EEF1A1
+Smad2 pp IMAGE_3831740
+Smad2 pp RXRA
+Smad2 pp AIB3
+Smad2 pp LOC157909
+Smad2 pp DD5
+Smad2 pp p66
+Smad2 pp COPS5
+Smad2 pp SRI
+Smad2 pp KPNB1
+Smad2 pp ST13
+Smad2 pp TIP47
+Smad2 pp SNAPAP
+Smad2 pp RPS14
+Smad2 pp LOC145483
+Smad2 pp capillary_morphogenes
+Smad2 pp FLJ00026
+Smad2 pp APC2
+Smad2 pp FLJ20729
+Smad2 pp BS69
+Smad2 pp PAXIP1L
+Smad2 pp ZNF41
+Smad2 pp IMAGE_5271668
+Smad2 pp SAM68
+Smad2 pp RARB
+Smad2 pp PIG7
+Smad2 pp HSPC025
+Smad2 pp CISH
+Smad2 pp FLJ32109
+Smad2 pp FLJ23584
+Smad2 pp RanBP6
+Smad2 pp ST5
+Smad2 pp TBC1D1
+Smad2 pp PXF
+Smad2 pp KIAA1839
+Smad2 pp KIAA1033
+Smad2 pp CUL5
+Smad2 pp dynein
+Smad2 pp SNRP70
+Smad2 pp UBA52
+Smad2 pp TGM2
+SnoN pp ZNF198
+SnoN pp PIAS1
+SnoN pp PIAS3
+SnoN pp FN1
+SnoN pp PIASY
+SnoN pp PTPRF
+SnoN pp Ku70
+SnoN pp IL1HY1
+SnoN pp HEY-L
+SnoN pp Smad2
+SnoN pp LRP1
+SnoN pp KIAA1042
+SnoN pp HSPC195
+SnoN pp Smad3
+SnoN pp HIPK3
+SnoN pp FBLC-1C
+SnoN pp zid
+SnoN pp ACF7
+SnoN pp PAPPA
+SnoN pp FLJ90754
+SnoN pp PPL
+SnoN pp KRTHB1
+SnoN pp LOC168451
+SnoN pp GOLGB1
+SnoN pp EIF4G2
+SnoN pp LOC221088
+SnoN pp TTF2
+SnoN pp Ubc9
+SnoN pp DDX30
+SnoN pp FAF1
+SnoN pp IMAGE_5277162
+SnoN pp LOC139547
+SnoN pp FLJ11565
+SnoN pp KIAA0790
+SnoN pp RNAH
+SnoN pp TDG
+SnoN pp ZNF237
+SnoN pp GLUL
+SnoN pp NCOR1
+SnoN pp SETDB1
+SnoN pp FLJ10759
+SnoN pp LOC157922
+SnoN pp CHD3
+SnoN pp E2IG4
+SnoN pp FLJ23392
+SnoN pp MAST_9
+SnoN pp SRP72
+SnoN pp RAP80
+SnoN pp SNX17
+SnoN pp USP25
+SnoN pp IMAGE_4856728
+SnoN pp KIAA0399
+SnoN pp Nbak2
+SnoN pp MYG1
+SnoN pp EEF1G
+SnoN pp PSMC2
+SnoN pp NID
+SnoN pp TTRAP
+SnoN pp TFPI2
+SnoN pp KIAA0960
+SnoN pp ZFP106
+SnoN pp LOC168388
+SnoN pp FLJ14964
+SnoN pp IMAGE_4128192
+SnoN pp NID2
+SnoN pp P5CR2
+SnoN pp TPM2
+SnoN pp LOC113026
+SnoN pp NCOR2
+SnoN pp Smad4
+SnoN pp SNRP70
+SnoN pp HEY1
+SnoN pp PSG1
+SnoN pp COL4A2
+Smad3 pp TRX2
+Smad3 pp Ku70
+Smad3 pp FBXL11
+Smad3 pp MBD1
+Smad3 pp HEY-L
+Smad3 pp SMURF1
+Smad3 pp PPP2R1A
+Smad3 pp GGA1
+Smad3 pp HSPC195
+Smad3 pp GMEB1
+Smad3 pp PAPPA
+Smad3 pp PCDH1
+Smad3 pp FLJ90754
+Smad3 pp KIAA0256
+Smad3 pp SIP1
+Smad3 pp Smad8a
+Smad3 pp Smad4
+Smad3 pp ANK3
+Smad3 pp RANBP9
+Smad3 pp GAMP
+Smad3 pp SARA
+Smad3 pp CYP11A
+Smad3 pp ZNF83
+Smad3 pp PSMD11
+Smad3 pp LOC90987
+Smad3 pp M96
+Smad3 pp IMAGE_3831740
+Smad3 pp CFDP1
+Smad3 pp IMAGE_5260671
+Smad3 pp EBI3
+Smad3 pp KIAA1095
+Smad3 pp FLJ12761
+Smad3 pp AIB3
+Smad3 pp EPAS1
+Smad3 pp KIAA1522
+Smad3 pp DKFZP727C091
+Smad3 pp FLJ12586
+Smad3 pp ZNF145
+Smad3 pp HIVEP1
+Smad3 pp PLAGL1
+Smad3 pp IL1RL1LG
+Smad3 pp PLAG1
+Smad3 pp CSH2
+Smad3 pp PRDM4
+Smad3 pp IMAGE_4158410
+Smad3 pp FLNA
+Smad3 pp RPLP0
+Smad3 pp SNRP70
+Smad3 pp HEY1
+Smad3 pp TGM2
+HIPK3 pp NR2F2
+HIPK3 pp KIAA0737
+HIPK3 pp MBD1
+HIPK3 pp HEY-L
+HIPK3 pp MTMR4
+HIPK3 pp TGFB1I1
+HIPK3 pp ZYX
+HIPK3 pp AIM1
+HIPK3 pp LIMK2
+HIPK3 pp C1QA
+HIPK3 pp FLNC
+HIPK3 pp RGS3
+HIPK3 pp SIAH1
+HIPK3 pp PINCH-2
+HIPK3 pp ARRB2
+HIPK3 pp ZFD25
+HIPK3 pp LIMD1
+HIPK3 pp SIAH2
+HIPK3 pp FLJ23443
+PKD2 pp PTPN3
+PKD2 pp LNPEP
+PKD2 pp TRAD
+PKD2 pp M96
+PKD2 pp CASK
+PKD2 pp ENIGMA
+PKD2 pp GRIP1
+PKD2 pp RXRA
+PKD2 pp FLJ10980
+PKD2 pp BPAG1
+PKD2 pp FLJ23443
+PKD2 pp RARB
+PKD2 pp TXNL2
+PKD2 pp RRBP1
+PKD2 pp MYLK
+PKD2 pp SNRP70
+PKD2 pp HEY1
+PKD2 pp LOC255969
+PKD2 pp PSG1
+PTPN12 pp PSG11
+PTPN12 pp IMAGE_5500261
+PTPN12 pp IMAGE_3915000
+PTPN12 pp CGA
+PTPN12 pp FLJ20287
+PTPN12 pp KIAA0682
+PTPN12 pp FLJ21628
+PTPN12 pp LOC150208
+PTPN12 pp STX16
+PTPN12 pp UTRN
+PTPN12 pp CSH1
+PTPN12 pp KIAA0916
+PTPN12 pp LOC90410
+PTPN12 pp BAT3
+SMURF2 pp RNF11
+SMURF2 pp TRAF4
+SMURF2 pp Smad2
+SMURF2 pp DAZAP2
+SMURF2 pp FLNB
+SMURF2 pp TRN-SR
+SMURF2 pp Smad5
+SMURF2 pp HSPC063
+SMURF2 pp TAHCCP1
+SMURF2 pp TFPI2
+SMURF2 pp CANX
+SMURF2 pp N4BP3
+SMURF2 pp IMAGE_4717000
+SMURF2 pp FLJ20739
+SMURF2 pp ARHGAP5
+SMURF2 pp VDUP1
+SMURF2 pp DAB2
+SMURF2 pp Smad6
+SMURF2 pp IDD
+SMURF2 pp KIAA0157
+SMURF2 pp GOLPH1
+SMURF2 pp SF3A2
+SMURF2 pp ACOX3
+SMURF2 pp ARK
+SMURF2 pp FLJ90586
+SMURF2 pp LAPTm5
+SMURF2 pp SNRP70
+Smad7 pp PIAS1
+Smad7 pp PIASY
+Smad7 pp Ku70
+Smad7 pp FBXL11
+Smad7 pp MBD1
+Smad7 pp HEY-L
+Smad7 pp HSPC195
+Smad7 pp SOX7
+Smad7 pp ZFD25
+Smad7 pp HSPC063
+Smad7 pp TTF2
+Smad7 pp MYOD1
+Smad7 pp SOX5
+Smad7 pp LOC91999
+Smad7 pp ASH1
+Smad7 pp ZNF-U69274
+Smad7 pp SOX13
+Smad7 pp KIAA1243
+Smad7 pp TTF1
+Smad5 pp ZNF8
+Smad5 pp MBD1
+Smad5 pp SMURF1
+Smad5 pp HSPC195
+Smad5 pp SOX7
+Smad5 pp PTPN12
+Smad5 pp SF3B1
+Smad5 pp FLJ20313
+Smad5 pp PNKP
+Smad5 pp SFPQ
+Smad5 pp SNRPA
+Smad5 pp PSMD11
+Smad5 pp sim._to_HSPC063
+Smad5 pp U2AF65
+Smad5 pp SOX5
+Smad5 pp LOC90987
+Smad5 pp HBG2
+Smad5 pp RBM4
+Smad5 pp RYR2
+Smad5 pp LOC51652
+Smad5 pp BCAT1
+Smad5 pp PPIL4
+Smad5 pp SNRP70
+Smad5 pp NY-REN-25
+Smad5 pp WWP1
+Smad5 pp NEDD4
+HYPA pp ZAP3
+HYPA pp PIAS1
+HYPA pp PIAS3
+HYPA pp FN1
+HYPA pp PTPRF
+HYPA pp UBQLN2
+HYPA pp A1U
+HYPA pp PFKL
+HYPA pp KIAA1076
+HYPA pp FMNL
+HYPA pp LOC221935
+HYPA pp RBAF600
+HYPA pp FNBP4
+HYPA pp PSG5
+HYPA pp CDC2L5
+HYPA pp FLJ10898
+HYPA pp SON
+HYPA pp IMAGE_4991985
+HYPA pp HDIA1
+HYPA pp COASTER
+HYPA pp FLJ90157
+HYPA pp KIAA2014
+HYPA pp FLJ11393
+HYPA pp UBQLN1
+HYPA pp CrkRS
+HYPA pp FLJ39436
+HYPA pp PECAM1
+HYPA pp KIAA1902
+HYPA pp PDCD7
+HYPA pp CAP2
+HYPA pp KIAA0630
+HYPA pp STIM2
+HYPA pp DKFZp434E2220
+HYPA pp PCBP2
+HYPA pp BRD4
+HYPA pp IL1RAP
+HYPA pp VCL
+HYPA pp UBE2I
+HYPA pp RLF
+HYPA pp HSPG2
+HYPA pp PRKAR1A
+HYPA pp MMP11
+HYPA pp LTBP3
+HYPA pp BIG2
+HYPA pp SNRP70
+HYPA pp BAT3
+p621 pp PIAS3
+p621 pp SPTBN1
+p621 pp PAPPE
+p621 pp HEY-L
+p621 pp HSPG2
+p621 pp STRN
+p621 pp KIAA0335
+p621 pp genethonin_1
+p621 pp CEP2
+p621 pp FLJ20783
+p621 pp ZBRK1
+p621 pp zid
+p621 pp PEX6
+p621 pp FLJ13755
+p621 pp PKD1
+p621 pp CDH11
+p621 pp GMEB1
+p621 pp A2M
+p621 pp AP1B1
+p621 pp SLC12A4
+p621 pp DKFZP761E1824
+p621 pp HSPC126
+p621 pp ACF7
+p621 pp TTC3
+p621 pp CSPG4
+p621 pp MCAM
+p621 pp HLA-B13
+p621 pp LAMC1
+p621 pp RBKIN
+p621 pp DNM2
+p621 pp PM5
+p621 pp FLT4/VEGFR3
+p621 pp PAPPA
+p621 pp SENP3
+p621 pp NPR1
+p621 pp PCDH1
+p621 pp DMTF
+p621 pp LOC51631
+p621 pp FLJ20259
+p621 pp ACTG1
+p621 pp FLJ90754
+p621 pp LOC136579
+p621 pp IGSF4
+p621 pp FLNB
+p621 pp PRSS8
+p621 pp LAMA5
+p621 pp RPS3A
+p621 pp KIAA0256
+p621 pp LAMA4
+p621 pp TRIP12
+p621 pp MGC3207
+p621 pp ACTB
+p621 pp RRBP1
+p621 pp PSG1
+p621 pp KRT7
+p621 pp COL4A2
+Smad8a pp ZNF8
+Smad8a pp LMO4
+Smad8a pp MBD1
+Smad8a pp HEY-L
+Smad8a pp MGC4054
+Smad8a pp DSTN
+Smad8a pp FLI1
+Smad8a pp FLJ21832
+Smad8a pp SIP1
+Smad8a pp TERF1
+Smad8a pp SNRP70
+Smad8a pp HEY1
+Smad4 pp ZNF198
+Smad4 pp PIAS1
+Smad4 pp FN1
+Smad4 pp PAPPE
+Smad4 pp Smad2
+Smad4 pp CSH1
+Smad4 pp fibulin-1A
+Smad4 pp SnoN
+Smad4 pp Smad3
+Smad4 pp UBE2I
+Smad4 pp Smad5
+Smad4 pp MYOD1
+Smad4 pp TDG
+Smad4 pp Ski
+Smad4 pp HYPA
+Smad4 pp KIAA1455
+Smad4 pp p621
+Smad4 pp RFX1
+Smad4 pp Smad8a
+Smad4 pp PSMD11
+Smad4 pp sim._to_HSPC063
+Smad4 pp HSJ1
+Smad4 pp SMIF
+Smad4 pp FLJ31638
+Smad4 pp EFEMP1
+Smad4 pp HMG20A
+Smad4 pp exportin_5
+Smad4 pp RPL28
+Smad4 pp TCTA
+Smad4 pp prey224058_-_Human
+Smad4 pp CD59_antigen_p18-20
+Smad4 pp RALA
+Smad4 pp prey216512_-_Human
+Smad4 pp GPNMB
+Smad4 pp PSG9
+Smad4 pp TH1L
+Smad4 pp MAPK13
+Smad4 pp TM9SF2
+Smad4 pp EEF1A1
+Smad4 pp LOC58486
+Smad4 pp CNK1
+Smad4 pp FLJ22318
+Smad4 pp URF2
+Smad4 pp PSG2
+Smad4 pp JUNB
+Smad4 pp FLJ13154
+Smad4 pp SNRP70
+Smad1 pp KIAA1196
+Smad1 pp ZNF8
+Smad1 pp PIAS1
+Smad1 pp XPC
+Smad1 pp PIASY
+Smad1 pp MBD1
+Smad1 pp SMURF1
+Smad1 pp NOTCH2
+Smad1 pp PKD2
+Smad1 pp GMEB1
+Smad1 pp SMURF2
+Smad1 pp SIP1
+Smad1 pp Smad5
+Smad1 pp HSPC063
+Smad1 pp TTF2
+Smad1 pp LOC157922
+Smad1 pp KIAA0960
+Smad1 pp MLL2
+Smad1 pp SF3B1
+Smad1 pp RFX1
+Smad1 pp MAN1
+Smad1 pp FLJ35105
+Smad1 pp Smad4
+Smad1 pp Smad1
+Smad1 pp PSMD11
+Smad1 pp SOX5
+Smad1 pp LOC90987
+Smad1 pp LOC51652
+Smad1 pp KIAA1243
+Smad1 pp TTF1
+Smad1 pp KIAA0899
+Smad1 pp CBX4
+Smad1 pp HEF1
+Smad1 pp EWSR1
+Smad1 pp GT650
+Smad1 pp INPP4A
+Smad1 pp AKR1B1
+Smad1 pp PIGQ
+Smad1 pp PUM1
+Smad1 pp PSMB4
+Smad1 pp DKFZP434L0718
+Smad1 pp IMAGE_5740090
+Smad1 pp FLJ32368
+Smad1 pp KIAA0936
+Smad1 pp LOC51304
+Smad1 pp TCF20
+Smad1 pp SMARCE1
+Smad1 pp KIAA0972
+Smad1 pp KIAA0303
+Smad1 pp PSMD1
+Smad1 pp IMAGE_3831740
+Smad1 pp IMAGE_3948563
+Smad1 pp ZNF76
+Smad1 pp LOC152903
+Smad1 pp HBP1
+Smad1 pp KIAA1301
+Smad1 pp GCN1L1
+Smad1 pp SNRP70
+Smad1 pp NEDD4
+SARA pp RNF11
+SARA pp SUPT5H
+SARA pp beta_catenin
+SARA pp FLJ20037
+SARA pp PPP1CB
+SARA pp Smad2
+SARA pp PPP1CC
+SARA pp DAZAP2
+SARA pp PPP2R1A
+SARA pp Erbin
+SARA pp FLJ90754
+SARA pp NUP155
+SARA pp DKFZP566I1024
+SARA pp ETS2
+SARA pp IMAGE_5269682
+SARA pp RNPEP
+SARA pp IMAGE_3510047
+SARA pp FHL2
+SARA pp EIF4G1
+SARA pp PRKCBP1
+SARA pp FLJ22369
+SARA pp RBQ-1
+SARA pp MIRO-2
+SARA pp ZNF36
+SARA pp TAHCCP1
+SARA pp BMP4
+SARA pp IMAGE_3882729
+SARA pp JUP
+SARA pp NIT1
+SARA pp PPP1CA
+SARA pp BAT3
+Smad8 pp ZNF8
+Smad8 pp LIECG3
+Smad8 pp FN1
+Smad8 pp LMO4
+Smad8 pp SPTBN1
+Smad8 pp Smad2
+Smad8 pp CSH1
+Smad8 pp QARS
+Smad8 pp A1U
+Smad8 pp HSPC195
+Smad8 pp UBQLN1
+Smad8 pp PKD2
+Smad8 pp PAPPA
+Smad8 pp TRIP12
+Smad8 pp ACTB
+Smad8 pp FLI1
+Smad8 pp SIP1
+Smad8 pp TERF1
+Smad8 pp LOC157922
+Smad8 pp FLJ14964
+Smad8 pp PIR
+Smad8 pp LRP5
+Smad8 pp MLL2
+Smad8 pp FLJ32214
+Smad8 pp SF3B1
+Smad8 pp IMAGE_5752707
+Smad8 pp exophilin_5
+Smad8 pp RFX1
+Smad8 pp MAN1
+Smad8 pp LOC161828
+Smad8 pp FLJ35105
+Smad8 pp E4F1
+Smad8 pp LOC163172
+Smad8 pp KIAA0226
+Smad8 pp SBP2
+Smad8 pp ARNT
+Smad8 pp KIAA1377
+Smad8 pp EUROIMAGE_1654781
+Smad8 pp FLJ20765
+Smad8 pp ZF6
+Smad8 pp ARHGAP9
+Smad8 pp PKP2
+Smad8 pp MNAR
+Smad8 pp GRN
+Smad8 pp FLJ10747
+Smad8 pp ASH2L1
+Smad8 pp METAP1
+Smad8 pp PSAP
+Smad8 pp KIAA0372
+Smad8 pp HSA242910
+Smad8 pp SIL1
+Smad8 pp TID1
+Smad8 pp FLJ23132
+Smad8 pp DKK1
+Smad8 pp PABPC4
+Smad8 pp PLEC1
+Smad8 pp STAG1
+Smad8 pp FLJ13621
+Smad8 pp LBN
+Smad8 pp ELD/OSA1
+Smad8 pp HMIC
+Smad8 pp EIF3S6
+Smad8 pp FLJ22678
+Smad8 pp FLJ12565
+Smad8 pp ABTB1
+Smad8 pp PSMD8
+Smad8 pp UTX
+Smad8 pp EIF3S8
+Smad8 pp PPP2R5E
+Smad8 pp KIAA0804
+Smad8 pp RANBP9
+Smad8 pp KIAA0155
+Smad8 pp MLLT2
+Smad8 pp HCNP
+Smad8 pp TRIM29
+Smad8 pp GAMP
+Smad8 pp PPARD
+Smad8 pp EIF3S5
+Smad8 pp BAZ1A
+Smad8 pp KIAA0211
+Smad8 pp FLJ20313
+Smad8 pp MAN1A2
+Smad8 pp FLJ20113
+Smad8 pp mop-4
+Smad8 pp FLJ13910
+Smad8 pp PHKA2
+Smad8 pp TTC2
+Smad8 pp TBCD
+Smad8 pp YWHAQ
+Smad8 pp FTL
+Smad8 pp IMAGE_4875483
+Smad8 pp LOC92216
+Smad8 pp FLJ39681
+Smad8 pp SMG1
+Smad8 pp UBE3A
+Smad8 pp DKFZP434C0931
+Smad8 pp CYP11A
+Smad8 pp FLJ13152
+Smad8 pp ZNF83
+Smad8 pp MGAT1
+Smad8 pp AP2A1
+Smad8 pp ASB2
+Smad8 pp MAN2B1
+Smad8 pp SMAP-1b
+Smad8 pp LNPEP
+Smad8 pp BPAG1
+Smad8 pp RRBP1
+Smad8 pp SNRP70
+Smad8 pp UREB1
+SNIP1 pp ZNF198
+SNIP1 pp PIAS1
+SNIP1 pp PIASY
+SNIP1 pp SON
+SNIP1 pp COASTER
+SNIP1 pp HIPK3
+SNIP1 pp GMEB1
+SNIP1 pp hPIASX-BETA
+SNIP1 pp Ubc9
+SNIP1 pp FAF1
+SNIP1 pp TDG
+SNIP1 pp ZNF237
+SNIP1 pp SETDB1
+SNIP1 pp Nbak2
+SNIP1 pp SF3B1
+SNIP1 pp EIF3S8
+SNIP1 pp FLJ22611
+SNIP1 pp TP53BPL
+SNIP1 pp SP100
+LAPTm5 pp HEY-L
+LAPTm5 pp HERC1
+LAPTm5 pp SMURF2
+LAPTm5 pp GDBR1
+LAPTm5 pp RP42protein
+LAPTm5 pp HEY1
+LAPTm5 pp KRT7
+LAPTm5 pp NY-REN-25
+LAPTm5 pp IMAGE_4830174
+LAPTm5 pp EPN3
+LAPTm5 pp UBA52
+LAPTm5 pp USP13
+LAPTm5 pp TNFAIP3
+LAPTm5 pp WWP1
+LAPTm5 pp FLJ35794
+LAPTm5 pp NEDD4
+LAPTm5 pp EPS15
+LAPTm5 pp EPSIN
+LAPTm5 pp UREB1
+LAPTm5 pp EPN2
+LAPTm5 pp NEDD4L
+LAPTm5 pp TOM1L2
+PPP1CA pp LOC201522
+PPP1CA pp AF107455
+PPP1CA pp PPP1R8
+PPP1CA pp KIAA1949
+PPP1CA pp KIAA1571
+PPP1CA pp ZAP3
+PPP1CA pp PPP1R10
+PPP1CA pp FLJ33903
+PPP1CA pp PPP1R15B
+PPP1CA pp IMAGE_4303927
+PPP1CA pp LAP1B
+PPP1CA pp STAU
+PPP1CA pp TP53BP2
+PPP1CA pp STAM
+PPP1CA pp PPP1R15A
+PPP1CA pp LOC144871
+PPP1CA pp DKFZP434G2226
+PPP1CA pp KANK
+PPP1CA pp PPP1R3B
+PPP1CA pp LOC84687
+PPP1CA pp H17739
+PPP1CA pp PLCL2
+PPP1CA pp AF15Q14
+PPP1CA pp LOC57821
+PPP1CA pp PPP1R13B
+PPP1CA pp LOC256602
+PPP1CA pp MPP10
+PPP1CA pp DKFZP434D193
+PPP1CA pp ENDOFIN
+PPP1CA pp TP53
+PPP1CA pp RAI
+PPP1CA pp KIAA0649
+PPP1CA pp C12orf22
+PPP1CA pp SYTL2
+PPP1CA pp N33
+PPP1CA pp HEY-L
+PPP1CA pp SARA
+Unknown interactsWith ATP5A1
+Unknown interactsWith BRAF
+Unknown interactsWith C1QBP
+Unknown interactsWith CSNK2A1
+Unknown interactsWith DHX15
+Unknown interactsWith HSPA1B
+Unknown interactsWith HSPA5
+Unknown interactsWith HSPCB
+Unknown interactsWith KIF5B
+Unknown interactsWith KNS2
+Unknown interactsWith MARK3
+Unknown interactsWith MLLT4
+Unknown interactsWith NTHL1
+Unknown interactsWith PIK4CB
+Unknown interactsWith SFRS3
+Unknown interactsWith SON
+Unknown interactsWith TSC1
+Unknown interactsWith UBC
+Unknown interactsWith WEE1
+Unknown interactsWith IRS2
+Unknown interactsWith USP8
+Unknown interactsWith TJP2
+Unknown interactsWith KIF23
+Unknown interactsWith SLC4A7
+Unknown interactsWith DOCK4
+Unknown interactsWith IFI30
+Unknown interactsWith MAP3K2
+Unknown interactsWith FUSIP1
+Unknown interactsWith NCKAP1
+Unknown interactsWith RNPS1
+Unknown interactsWith AKAP13
+Unknown interactsWith STK38
+Unknown interactsWith Tuba2
+Unknown interactsWith STK38L
+Unknown interactsWith U5-200KD
+Unknown interactsWith KIAA0826
+Unknown interactsWith MYCBP2
+Unknown interactsWith EPB41L3
+Unknown interactsWith M-RIP
+Unknown interactsWith C22orf9
+Unknown interactsWith LARP
+Unknown interactsWith SRRM2
+Unknown interactsWith OSBPL3
+Unknown interactsWith RAI14
+Unknown interactsWith DKFZP434C212
+Unknown interactsWith RABGEF1
+Unknown interactsWith RACGAP1
+Unknown interactsWith PIK3R4
+Unknown interactsWith LISCH7
+Unknown interactsWith FLJ10211
+Unknown interactsWith RALGPS2
+Unknown interactsWith FLJ10579
+Unknown interactsWith FLJ10324
+Unknown interactsWith PARD3
+Unknown interactsWith ALS2
+Unknown interactsWith MEP50
+Unknown interactsWith FLJ21128
+Unknown interactsWith RIOK1
+Unknown interactsWith MIRAB13
+Unknown interactsWith C14orf31
+Unknown interactsWith TORC2
+Unknown interactsWith OK/SW-cl.56
+Unknown interactsWith SRPK1
+Unknown interactsWith LBR
+Unknown interactsWith LOC256165
+Unknown interactsWith DDX48
+Unknown interactsWith PRKDC
+Unknown interactsWith MYCPBP_
+Unknown interactsWith ACIN1
+Unknown interactsWith SKB1Hs
+Unknown interactsWith KIAA0415
+Unknown interactsWith ALB
+Unknown interactsWith ARAF1
+Unknown interactsWith ATP5A1
+Unknown interactsWith BRAF
+Unknown interactsWith C1QBP
+Unknown interactsWith CDC5L
+Unknown interactsWith CLK1
+Unknown interactsWith CLK2
+Unknown interactsWith CLK3
+Unknown interactsWith DHX15
+Unknown interactsWith DFFA
+Unknown interactsWith DYRK1A
+Unknown interactsWith EEF1G
+Unknown interactsWith GSK3A
+Unknown interactsWith HNRPH1
+Unknown interactsWith HSPA1A
+Unknown interactsWith HSPA9B
+Unknown interactsWith IGF1R
+Unknown interactsWith KIF5B
+Unknown interactsWith MFAP1
+Unknown interactsWith MLLT4
+Unknown interactsWith NEFL
+Unknown interactsWith PCTK2
+Unknown interactsWith PIK3C3
+Unknown interactsWith PIK3R1
+Unknown interactsWith PIK4CB
+Unknown interactsWith SFRS3
+Unknown interactsWith SFRS10
+Unknown interactsWith SON
+Unknown interactsWith SSA1
+Unknown interactsWith TIAM1
+Unknown interactsWith TSC1
+Unknown interactsWith UBC
+Unknown interactsWith VIM
+Unknown interactsWith BAT1
+Unknown interactsWith PPFIBP1
+Unknown interactsWith IRS2
+Unknown interactsWith GBF1
+Unknown interactsWith ARHGEF7
+Unknown interactsWith USP8
+Unknown interactsWith RABEP1
+Unknown interactsWith ARHGEF2
+Unknown interactsWith NOLC1
+Unknown interactsWith PPIG
+Unknown interactsWith TJP2
+Unknown interactsWith RASAL2
+Unknown interactsWith KIF23
+Unknown interactsWith HDAC4
+Unknown interactsWith BCLAF1
+Unknown interactsWith THRAP3
+Unknown interactsWith HAN11
+Unknown interactsWith SRRM1
+Unknown interactsWith PAK4
+Unknown interactsWith YAP1
+Unknown interactsWith MAP3K2
+Unknown interactsWith RNPS1
+Unknown interactsWith AKAP13
+Unknown interactsWith C12orf2
+Unknown interactsWith Tuba2
+Unknown interactsWith SIAHBP1
+Unknown interactsWith Rab11-FIP2
+Unknown interactsWith U5-200KD
+Unknown interactsWith SAMD4
+Unknown interactsWith MYCBP2
+Unknown interactsWith ELKS
+Unknown interactsWith KIF1B
+Unknown interactsWith EPB41L3
+Unknown interactsWith M-RIP
+Unknown interactsWith ANKS1
+Unknown interactsWith C22orf9
+Unknown interactsWith CLASP1
+Unknown interactsWith LARP
+Unknown interactsWith SF3B3
+Unknown interactsWith SRRM2
+Unknown interactsWith SH3BP4
+Unknown interactsWith OSBPL3
+Unknown interactsWith RAI14
+Unknown interactsWith PABPC1
+Unknown interactsWith PRP19
+Unknown interactsWith RABGEF1
+Unknown interactsWith IGKV1-12
+Unknown interactsWith GTL3
+Unknown interactsWith RACGAP1
+Unknown interactsWith TRA2A
+Unknown interactsWith ZNF295
+Unknown interactsWith HDAC7A
+Unknown interactsWith LISCH7
+Unknown interactsWith LUC7L2
+Unknown interactsWith FLJ20232
+Unknown interactsWith FLJ10211
+Unknown interactsWith RALGPS2
+Unknown interactsWith FLJ10292
+Unknown interactsWith FLJ10330
+Unknown interactsWith FLJ10579
+Unknown interactsWith FNBP3
+Unknown interactsWith PARD3
+Unknown interactsWith CGN
+Unknown interactsWith KLC2
+Unknown interactsWith FLJ13052
+Unknown interactsWith SHCBP1
+Unknown interactsWith FLJ21128
+Unknown interactsWith KIAA1720
+Unknown interactsWith MIRAB13
+Unknown interactsWith C14orf31
+Unknown interactsWith SNAP23P
+Unknown interactsWith TORC2
+Unknown interactsWith OK/SW-cl.56
+Unknown interactsWith C10orf9
+Unknown interactsWith FLJ35827
+Unknown interactsWith FLJ36878
+Unknown interactsWith FNBP2
+Unknown interactsWith SRPK1
+Unknown interactsWith LBR
+Unknown interactsWith LOC256165
+Unknown interactsWith CTAK75a
+Unknown interactsWith DDX48
+Unknown interactsWith PRKDC
+Unknown interactsWith MYCPBP
+Unknown interactsWith ACIN1
+Unknown interactsWith KIAA0826
+Unknown interactsWith dJ1013A10.1
+Unknown interactsWith BAIAP2
+Unknown interactsWith LUC7A
+Unknown interactsWith PNN
+Unknown interactsWith DOCK7
+Unknown interactsWith TASR-2
+Unknown interactsWith TBC1D1
+Unknown interactsWith HSPA8
+Unknown interactsWith KIF5B
+Unknown interactsWith KRT1
+Unknown interactsWith KRT9
+Unknown interactsWith MAGOH
+Unknown interactsWith PIK4CB
+Unknown interactsWith SFRS3
+Unknown interactsWith USP8
+Unknown interactsWith DDX48
+Unknown interactsWith Tuba2
+Unknown interactsWith M-RIP
+Unknown interactsWith LARP
+Unknown interactsWith RAI14
+Unknown interactsWith FLJ10211
+Unknown interactsWith AD026
+Unknown interactsWith KLC2
+Unknown interactsWith ADCK2
+Unknown interactsWith SKB1Hs
+Unknown interactsWith HSPA1A
+Unknown interactsWith ATP5A1
+Unknown interactsWith BRAF
+Unknown interactsWith DFFA
+Unknown interactsWith ENO1
+Unknown interactsWith HSPA1B
+Unknown interactsWith KIF5B
+Unknown interactsWith SFRS10
+Unknown interactsWith SSA1
+Unknown interactsWith UBC
+Unknown interactsWith USP8
+Unknown interactsWith TJP2
+Unknown interactsWith PAK4
+Unknown interactsWith STK38
+Unknown interactsWith Tuba2
+Unknown interactsWith EPB41L3
+Unknown interactsWith C22orf9
+Unknown interactsWith LARP
+Unknown interactsWith FLJ10211
+Unknown interactsWith RALGPS2
+Unknown interactsWith AD026
+Unknown interactsWith KLC2
+Unknown interactsWith KNSL8
+Unknown interactsWith OK/SW-cl.56
+Unknown interactsWith SKB1Hs
+Unknown interactsWith DDX48
+Unknown interactsWith LOC119358
+AML1b pp TLE1
+AML2 pp TLE1
+FANCD2 pp BRCA2
+FANCG pp BRCA2
+EGFR pp EGFR
+ETO pp HEBa
+ETO pp HEBb
+AML1-ETO pp HEBa
+AML1-ETO pp HEBb
+HEBa pp p300
+HEBb pp p300
+HEBa pp CBP
+HEBb pp CBP
+ETO pp E2A
+ETO pp E2-2
+ETO pp N-CoR
+ETO pp HDAC3
+ETO pp Sin3A
+ETO pp HDAC1
+ETO pp MTGR1
+Unknown interactsWith TAF4
+Unknown interactsWith TBP
+Unknown interactsWith HDAC1
+Unknown interactsWith HDAC3
+Unknown interactsWith E2A
+PIAS1 pd A/T-rich_dsDNA
+PIAS1 pp p53
+14-3-3-alpha-beta interactsWith unknown
+14-3-3-gamma interactsWith unknown
+14-3-3-tau-theta interactsWith unknown
+14-3-3-zeta-delta interactsWith unknown
+CT pp CTR
+BCL-XL pp BID
+BCL-XL pp BID-EL
+hRrp4p pp hRrp41p
+hRrp40p pp hRrp46p
+hRrp4p pp hRrp42p
+hRrp41p pp hRrp41p
+Apollon pp SMAC
+hRrp42p pp hRrp41p
+hRrp42p pp hCsl4p
+Apollon pp Caspase-9
+Apollon pp HtrA2
+XIAP pp SMAC
+XIAP pp Caspase-9
+XIAP pp HtrA2
+hRrp42p pp hMtr3p
+hRrp46p pp hCsl4p
+hRrp46p pp OIP2
+hCsl4p pp hRrp41p
+hCsl4p pp PM/Scl-75
+hCsl4p pp hMtr3p
+OIP2 pp hMtr3p
+VPS37B pp TSG101
+VPS28 pp TSG101
+VPS37A pp TSG101
+AML1a pp TLE1
+LEF-1 pp TLE1
+NEIL1 interactsWith Unknown
+unknown interactsWith Tat-SF1
+unknown interactsWith Pol_II
+unknown interactsWith TBP
+unknown interactsWith RAP30
+unknown interactsWith ERCC3
+PGRP-I-alpha pp PGRP-I-alpha
+Unknown interactsWith XRCC1
+Unknown interactsWith pol-beta
+Unknown interactsWith PNK
+Unknown interactsWith Ligase_III-alpha
+Lamin_C pp Lco1
+Lamin_A pp Lco1
+Lamin_B1 pp Lco1
+TR pp CTCF
+YB-1 pp SRp30c
+Htt pp Caspase_8
+Htt pp Caspase_7
+Htt pp Caspase_6
+SRC-1 pp p50
+Syk pp moesin
+Syk pp ezrin
+CDK7 interactsWith Unknown
+Unknown interactsWith Cyclin_H
+Unknown interactsWith p36
+YB-1 pp IRP2
+N-Myc pd EAAT2_promoter
+JAK2 pp Tid-1S
+hSiah1 pp Ubc9
+p300 pp p65
+p300 pp MyoD
+p300 pp TBP
+p300 pp TFIIB
+Unknown interactsWith VPS28
+Unknown interactsWith TSG101
+VPS37B interactsWith Unknown
+MTA1 pp MAT1
+Geminin/Geminin interactsWith HoxA11
+Geminin/Geminin interactsWith Cdt1
+Toca-1 pp N-WASP
+Geminin pp Geminin
+Chk1 pp Cdc25A-a
+Chk1 pp Cdc25A-b
+CBP pp TRAM-1
+hDasra_B interactsWith Unknown
+Unknown interactsWith hAurora_B
+Unknown interactsWith hSurvivin
+S100A11 pp S100A11
+S100A10 pp S100A10
+Pol_beta pp Neil1
+Ligase_III-alpha pp Neil1
+XRCC1 pp Neil1
+PKD2 pp DRF1
+HGF pp Met
+DEAF-1 pd TTCG_containing_DNA
+DEAF-1 pp DEAF-1
+Tctex-1 pp hVDAC1
+PBP74 pp hVDAC1
+Itk pp Rch1-alpha
+E2F4 pd TTK
+E2F4 pd TYMS
+E2F4 pd FLJ10287
+E2F4 pd FLJ11029
+E2F4 pd RECQL
+E2F4 pd CpG12B10
+SKIP pp Smad2
+VDR pp Smad3
+SKIP pp Smad3
+p72 pp p68
+DISC1 pp kendrin
+P/CAF pp TRAM-1
+Neil1 pd DNA_with_oxidized_base_lesion
+PNK pd DNA_with_3'_phosphate
+Pol_Beta pd DNA_with_3'_OH
+Nth1 pd DNA_with_oxidized_base_lesion
+NEIL1/PNK/XRCC1/pol-beta/Ligase_III-alpha_complex interactsWith DNA_with_oxidized_base_lesion
+Ligase_III-alpha pd DNA_with_3'OH
+Htt pp Caspase_2
+Nek2A pp Nek11L
+TRAM-1 pp ER
+TRAM-1 pp THR-beta
+c-Kit pp p56Lyn
+Huntingtin pp caspase_3
+ACTR pp ER81
+ACTR pp TR
+ACTR pp RXR
+ACTR pp VDR
+ACTR pp CBP
+Unknown interactsWith HDAC2
+Unknown interactsWith ER
+Unknown interactsWith MTA1
+CAK interactsWith Unknown
+hSiah2 pp Ubc9
+hSiah2 pp DCC
+Huntingtin pp caspase_1
+Atrophin-1 pp caspase_3
+Atrophin-1 pp caspase_1
+Atrophin-1 pp caspase_7
+Atrophin-1 pp caspase_8
+NEK1 pp ZBRK1
+c-Kit pp p53Lyn
+hSiah1 pp DCC
+unknown interactsWith ELL
+unknown interactsWith IIB
+unknown interactsWith Elongin_B
+unknown interactsWith CDK9
+Ataxin-3 pp caspase_1
+Ataxin-3 pp caspase_3
+A20 pp RIP
+Androgen_Receptor pp caspase_1
+Androgen_Receptor pp caspase_3
+Androgen_Receptor pp caspase_8
+c-Jun pp Jun_B
+hPop1 pp hPop1
+hPop1 pp hPop4
+hPop4 pp hPop5
+hPop1 pp Rpp38
+hPop1 pp Rpp40
+hPop4 pp hPop4
+hPop4 pp Rpp38
+hPop5 pp Rpp14
+Rpp14 pp Rpp30
+Rpp14 pp Rpp40
+Rpp20 pp Rpp25
+Rpp21 pp Rpp40
+Rpp25 pp hPop1
+Rpp25 pp hPop4
+hPop1 interactsWith RNase_MRP_RNA
+hPop4 interactsWith RNase_MRP_RNA
+Rpp20 interactsWith RNase_MRP_RNA
+Rpp21 interactsWith RNase_MRP_RNA
+Rpp25 interactsWith RNase_MRP_RNA
+Rpp38 interactsWith RNase_MRP_RNA
+hPop1 interactsWith RNase_P_RNA
+hPop4 interactsWith RNase_P_RNA
+Rpp20 interactsWith RNase_P_RNA
+Rpp21 interactsWith RNase_P_RNA
+Rpp25 interactsWith RNase_P_RNA
+Rpp38 interactsWith RNase_P_RNA
+U2AF65 pp SF1
+Androgen_Receptor pp caspase_7
+TRAF2 pp RIP
+TR-alpha pp hSrb7
+E2F4 pd CpG32C1
+E2F4 pd CpG18G8
+E2F4 pd CYP27B1
+E2F4 pd HP1-alpha
+E2F4 pd MFAP1
+BRCA1 pp TRAP220
+TRAM-1 pp RXR-beta
+SRC-1 pp THR-beta
+JAK1 pp IL4R-alpha
+PKR interactsWith huntingtin
+SETA pp Grb2
+CD2 pp SETA
+TR-beta pp hSrb7
+IL4R-alpha pp IL4
+TR-alpha pp hMo15
+TR-alpha pp SRC-1
+Neogenin pp Caspase_3
+RAR-alpha pp hMo15
+IL-4R pp IRS-1
+VDR pp hMo15
+THR-beta pp RXR-beta
+TRAM-1 interactsWith THR-beta-RXR-beta
+SRC-1 interactsWith THR-beta-RXR-beta
+IL-4_receptor-alpha pp Stat_6
+ER-alpha pp MICoA
+Nop132 pp RRAGA
+Nop132 pp RRAGC
+Nop132 pp Nip7
+p75NTR pp NGF
+p75NTR pp NT-4
+MTA1 pp MICoA
+hSMC1 interactsWith unknown
+Unknown interactsWith hSMC3
+SMYD3 pp HELZ
+HELZ interactsWith RNA_Polymerase_II
+PRB pp PCAF
+RAC3 pp RAR-alpha
+IL-4 pp gamma-C
+Activin_Dimer interactsWith ActRIIb
+VDR pp SRC-1
+alpha-synuclein pp lamp2a
+RAR-alpha pp SRC-1
+VDR pp hTFIIB
+Tax interactsWith Unknown
+Unknown interactsWith HSP70
+Unknown interactsWith hTid-1
+p50 pp p50
+Stat1-alpha pp Stat1-alpha
+Stat1-alpha-Stat1-alpha interactsWith p300
+Stat1-alpha-Stat1-alpha interactsWith CBP
+KIP pp hTERT
+TRAF4 pp UBC9
+Skp1 pp Fbw2
+Skp1 pp Fbx5
+Skp1 pp Fbx7
+Skp1 pp Fbl3a
+Skp1 pp Fbw1a
+Skp1 pp Fbx4
+TRAF4 pp PLSCR1
+TRAF4 pp Hic-5
+TRAF4 pp TARBP2
+Skp1 pp Fbx6a
+TRAF4 pp ArgBP2
+Tsg101 pp Tsg101
+CEM15 pp CEM15
+UAP56 pp Aly
+RAC3 pp PPAR-alpha
+E2F-1 pd MAD2_promoter_and_5-prime_UTR
+E2F-1 pd CycA_promoter_and_5-prime_UTR
+Beta-catenin pp LGS1
+Beta-catenin pp APC
+Beta-catenin pp Alpha-catenin
+IL-1_NTP pp HAX-1
+IQGAP2 pp HAX-1
+MSH4 pp MSH5
+hCAP-C interactsWith unknown
+Unknown interactsWith hCAP-E
+SA-1 interactsWith Unknown
+Unknown interactsWith Scc1
+Unknown interactsWith Smc1
+Unknown interactsWith Smc3
+NEK1 pp MRE11
+NEK1 pp 53BP1
+CAK interactsWith Unknown
+Unknown interactsWith ERCC2
+GRIP1 pp TR
+GRIP1 pp AR
+SRC-1a pp AR
+SRC-1e pp AR
+TRAF4 pp NRAGE
+Mcm2 pp Mcm3
+Pin1 pp Myt1
+Ngb pp Flotillin-1
+Pin1 pp PLK1
+Sp1 pd Homo_sapiens_chromosome_21[12063493-12063666]
+Sp1 pd Homo_sapiens_chromosome_21[12418957-12420612]
+Sp1 pd Homo_sapiens_chromosome_21[15649361-15649780]
+Sp1 pd Homo_sapiens_chromosome_21[23685167-23686559]
+Sp1 pd Homo_sapiens_chromosome_21[26943655-26944402]
+Sp1 pd Homo_sapiens_chromosome_21[29608642-29609557]
+Sp1 pd Homo_sapiens_chromosome_21[29620887-29621622]
+Sp1 pd Homo_sapiens_chromosome_21[29868601-29868805]
+Sp1 pd Homo_sapiens_chromosome_21[30341890-30343162]
+Sp1 pd Homo_sapiens_chromosome_21[30550504-30550946]
+Sp1 pd Homo_sapiens_chromosome_21[30677925-30678701]
+Sp1 pd Homo_sapiens_chromosome_21[30889970-30889972]
+Sp1 pd Homo_sapiens_chromosome_21[31215428-31216725]
+Sp1 pd Homo_sapiens_chromosome_21[31273950-31274999]
+Sp1 pd Homo_sapiens_chromosome_21[31330307-31330684]
+Sp1 pd Homo_sapiens_chromosome_21[31440625-31441968]
+Sp1 pd Homo_sapiens_chromosome_21[31491579-31493417]
+Sp1 pd Homo_sapiens_chromosome_21[31590861-31592288]
+Sp1 pd Homo_sapiens_chromosome_21[31864800-31865788]
+Sp1 pd Homo_sapiens_chromosome_21[31881305-31881402]
+Sp1 pd Homo_sapiens_chromosome_21[32193567-32193601]
+Sp1 pd Homo_sapiens_chromosome_21[32377098-32377100]
+Sp1 pd Homo_sapiens_chromosome_21[32896210-32896212]
+Sp1 pd Homo_sapiens_chromosome_21[32896456-32896925]
+Sp1 pd Homo_sapiens_chromosome_21[33000728-33001595]
+Sp1 pd Homo_sapiens_chromosome_21[33088319-33088618]
+Sp1 pd Homo_sapiens_chromosome_21[33979012-33979376]
+Sp1 pd Homo_sapiens_chromosome_21[34080170-34080485]
+Sp1 pd Homo_sapiens_chromosome_21[34105955-34105957]
+Sp1 pd Homo_sapiens_chromosome_21[34123429-34123881]
+Sp1 pd Homo_sapiens_chromosome_21[34269437-34269949]
+Sp1 pd Homo_sapiens_chromosome_21[34270452-34270776]
+Sp1 pd Homo_sapiens_chromosome_21[34334439-34334968]
+Sp1 pd Homo_sapiens_chromosome_21[34915798-34915800]
+Sp1 pd Homo_sapiens_chromosome_21[35012919-35013259]
+Sp1 pd Homo_sapiens_chromosome_21[35170781-35170956]
+Sp1 pd Homo_sapiens_chromosome_21[35188125-35188834]
+Sp1 pd Homo_sapiens_chromosome_21[35216495-35217403]
+Sp1 pd Homo_sapiens_chromosome_21[35496726-35497383]
+Sp1 pd Homo_sapiens_chromosome_21[36424703-36425112]
+Sp1 pd Homo_sapiens_chromosome_21[36805871-36806249]
+Sp1 pd Homo_sapiens_chromosome_21[36812390-36813827]
+Sp1 pd Homo_sapiens_chromosome_21[36955189-36956266]
+Sp1 pd Homo_sapiens_chromosome_21[36992600-36993294]
+Sp1 pd Homo_sapiens_chromosome_21[37133132-37133388]
+Sp1 pd Homo_sapiens_chromosome_21[37297285-37297287]
+Sp1 pd Homo_sapiens_chromosome_21[37297719-37297891]
+Sp1 pd Homo_sapiens_chromosome_21[37334189-37334637]
+Sp1 pd Homo_sapiens_chromosome_21[37392221-37392974]
+Sp1 pd Homo_sapiens_chromosome_21[39059442-39059969]
+Sp1 pd Homo_sapiens_chromosome_21[39863884-39864227]
+Sp1 pd Homo_sapiens_chromosome_21[39966400-39966949]
+Sp1 pd Homo_sapiens_chromosome_21[40023965-40024472]
+Sp1 pd Homo_sapiens_chromosome_21[40030637-40030719]
+Sp1 pd Homo_sapiens_chromosome_21[40190997-40191173]
+Sp1 pd Homo_sapiens_chromosome_21[40417168-40417982]
+Sp1 pd Homo_sapiens_chromosome_21[40529832-40530104]
+Sp1 pd Homo_sapiens_chromosome_21[40634272-40634320]
+Sp1 pd Homo_sapiens_chromosome_21[40657609-40658429]
+Sp1 pd Homo_sapiens_chromosome_21[40860751-40860836]
+Sp1 pd Homo_sapiens_chromosome_21[40941499-40942001]
+Sp1 pd Homo_sapiens_chromosome_21[41144592-41145295]
+Sp1 pd Homo_sapiens_chromosome_21[41234257-41234391]
+Sp1 pd Homo_sapiens_chromosome_21[41512474-41513261]
+Sp1 pd Homo_sapiens_chromosome_21[41647876-41647878]
+Sp1 pd Homo_sapiens_chromosome_21[41708305-41708307]
+Sp1 pd Homo_sapiens_chromosome_21[41781603-41782545]
+Sp1 pd Homo_sapiens_chromosome_21[42036729-42036781]
+Sp1 pd Homo_sapiens_chromosome_21[42062791-42063061]
+Sp1 pd Homo_sapiens_chromosome_21[42093890-42094451]
+Sp1 pd Homo_sapiens_chromosome_21[42111162-42111164]
+Sp1 pd Homo_sapiens_chromosome_21[42267249-42268382]
+Sp1 pd Homo_sapiens_chromosome_21[42269507-42269567]
+Sp1 pd Homo_sapiens_chromosome_21[42384596-42384725]
+Sp1 pd Homo_sapiens_chromosome_21[42505232-42505572]
+Sp1 pd Homo_sapiens_chromosome_21[42746265-42746363]
+Sp1 pd Homo_sapiens_chromosome_21[42799330-42801132]
+Sp1 pd Homo_sapiens_chromosome_21[42814146-42815199]
+Sp1 pd Homo_sapiens_chromosome_21[42944189-42944620]
+Sp1 pd Homo_sapiens_chromosome_21[43222001-43222003]
+Sp1 pd Homo_sapiens_chromosome_21[43274537-43275783]
+Sp1 pd Homo_sapiens_chromosome_21[43403765-43403807]
+Sp1 pd Homo_sapiens_chromosome_21[43407685-43408666]
+Sp1 pd Homo_sapiens_chromosome_21[43428782-43428870]
+Sp1 pd Homo_sapiens_chromosome_21[43456897-43457557]
+Sp1 pd Homo_sapiens_chromosome_21[43485152-43486030]
+Sp1 pd Homo_sapiens_chromosome_21[43541426-43542373]
+Sp1 pd Homo_sapiens_chromosome_21[43561881-43563309]
+Sp1 pd Homo_sapiens_chromosome_21[43563830-43564567]
+Sp1 pd Homo_sapiens_chromosome_21[43844676-43845421]
+Sp1 pd Homo_sapiens_chromosome_21[43850478-43851470]
+Sp1 pd Homo_sapiens_chromosome_21[43858256-43859809]
+Sp1 pd Homo_sapiens_chromosome_21[43864833-43865790]
+Sp1 pd Homo_sapiens_chromosome_21[43907653-43908264]
+Sp1 pd Homo_sapiens_chromosome_21[43914279-43914917]
+Sp1 pd Homo_sapiens_chromosome_21[43973868-43975143]
+Sp1 pd Homo_sapiens_chromosome_21[43988813-43989765]
+Sp1 pd Homo_sapiens_chromosome_21[44110204-44111711]
+Sp1 pd Homo_sapiens_chromosome_21[44127491-44128289]
+Sp1 pd Homo_sapiens_chromosome_21[44154581-44154861]
+Sp1 pd Homo_sapiens_chromosome_21[44156387-44156790]
+Sp1 pd Homo_sapiens_chromosome_21[44213158-44213672]
+Sp1 pd Homo_sapiens_chromosome_21[44248963-44249873]
+Sp1 pd Homo_sapiens_chromosome_21[44309554-44311107]
+Sp1 pd Homo_sapiens_chromosome_21[44329408-44330948]
+Sp1 pd Homo_sapiens_chromosome_21[44350635-44350897]
+Sp1 pd Homo_sapiens_chromosome_21[44351334-44352055]
+Sp1 pd Homo_sapiens_chromosome_21[44479875-44479877]
+Sp1 pd Homo_sapiens_chromosome_21[44562721-44562723]
+Sp1 pd Homo_sapiens_chromosome_22[13142716-13142856]
+Sp1 pd Homo_sapiens_chromosome_22[14524017-14524331]
+Sp1 pd Homo_sapiens_chromosome_22[14584706-14584809]
+Sp1 pd Homo_sapiens_chromosome_22[15051492-15052046]
+Sp1 pd Homo_sapiens_chromosome_22[15061856-15062725]
+Sp1 pd Homo_sapiens_chromosome_22[15200224-15200453]
+Sp1 pd Homo_sapiens_chromosome_22[15202560-15203130]
+Sp1 pd Homo_sapiens_chromosome_22[15419542-15420082]
+Sp1 pd Homo_sapiens_chromosome_22[15580349-15580385]
+Sp1 pd Homo_sapiens_chromosome_22[15580902-15580904]
+Sp1 pd Homo_sapiens_chromosome_22[15611467-15611803]
+Sp1 pd Homo_sapiens_chromosome_22[15615903-15616389]
+Sp1 pd Homo_sapiens_chromosome_22[15619785-15620532]
+Sp1 pd Homo_sapiens_chromosome_22[15632404-15632946]
+Sp1 pd Homo_sapiens_chromosome_22[15653101-15653814]
+Sp1 pd Homo_sapiens_chromosome_22[15666003-15666593]
+Sp1 pd Homo_sapiens_chromosome_22[15670162-15670610]
+Sp1 pd Homo_sapiens_chromosome_22[15698268-15698463]
+Sp1 pd Homo_sapiens_chromosome_22[15723086-15723088]
+Sp1 pd Homo_sapiens_chromosome_22[15739687-15740405]
+Sp1 pd Homo_sapiens_chromosome_22[15758422-15758877]
+Sp1 pd Homo_sapiens_chromosome_22[15779720-15782822]
+Sp1 pd Homo_sapiens_chromosome_22[15784768-15785210]
+Sp1 pd Homo_sapiens_chromosome_22[15787376-15787913]
+Sp1 pd Homo_sapiens_chromosome_22[15807897-15808322]
+Sp1 pd Homo_sapiens_chromosome_22[15811888-15812476]
+Sp1 pd Homo_sapiens_chromosome_22[15813497-15813579]
+Sp1 pd Homo_sapiens_chromosome_22[15833574-15833607]
+Sp1 pd Homo_sapiens_chromosome_22[15953258-15953316]
+Sp1 pd Homo_sapiens_chromosome_22[16007556-16007808]
+Sp1 pd Homo_sapiens_chromosome_22[16050833-16050915]
+Sp1 pd Homo_sapiens_chromosome_22[16072005-16072795]
+Sp1 pd Homo_sapiens_chromosome_22[16106750-16107557]
+Sp1 pd Homo_sapiens_chromosome_22[16219417-16219903]
+Sp1 pd Homo_sapiens_chromosome_22[16360283-16360640]
+Sp1 pd Homo_sapiens_chromosome_22[16375349-16376144]
+Sp1 pd Homo_sapiens_chromosome_22[16376473-16377123]
+Sp1 pd Homo_sapiens_chromosome_22[16395867-16396368]
+Sp1 pd Homo_sapiens_chromosome_22[16406860-16407942]
+Sp1 pd Homo_sapiens_chromosome_22[16819976-16820537]
+Sp1 pd Homo_sapiens_chromosome_22[16820573-16820575]
+Sp1 pd Homo_sapiens_chromosome_22[16834703-16835205]
+Sp1 pd Homo_sapiens_chromosome_22[16835573-16835701]
+Sp1 pd Homo_sapiens_chromosome_22[17047298-17047300]
+Sp1 pd Homo_sapiens_chromosome_22[17055010-17055043]
+Sp1 pd Homo_sapiens_chromosome_22[17402886-17402903]
+Sp1 pd Homo_sapiens_chromosome_22[17403553-17404031]
+Sp1 pd Homo_sapiens_chromosome_22[17408075-17408289]
+Sp1 pd Homo_sapiens_chromosome_22[17512605-17513332]
+Sp1 pd Homo_sapiens_chromosome_22[17748182-17751254]
+Sp1 pd Homo_sapiens_chromosome_22[17755624-17756908]
+Sp1 pd Homo_sapiens_chromosome_22[17868462-17868944]
+Sp1 pd Homo_sapiens_chromosome_22[17912562-17912628]
+Sp1 pd Homo_sapiens_chromosome_22[17921148-17921276]
+Sp1 pd Homo_sapiens_chromosome_22[18032341-18032532]
+Sp1 pd Homo_sapiens_chromosome_22[18055112-18055490]
+Sp1 pd Homo_sapiens_chromosome_22[18066766-18067066]
+Sp1 pd Homo_sapiens_chromosome_22[18167373-18167887]
+Sp1 pd Homo_sapiens_chromosome_22[18170075-18170574]
+Sp1 pd Homo_sapiens_chromosome_22[18172464-18175543]
+Sp1 pd Homo_sapiens_chromosome_22[18197914-18198369]
+Sp1 pd Homo_sapiens_chromosome_22[18214623-18214657]
+Sp1 pd Homo_sapiens_chromosome_22[18225132-18225883]
+Sp1 pd Homo_sapiens_chromosome_22[18229264-18229754]
+Sp1 pd Homo_sapiens_chromosome_22[18257745-18257928]
+Sp1 pd Homo_sapiens_chromosome_22[18282649-18282651]
+Sp1 pd Homo_sapiens_chromosome_22[18299228-18300071]
+Sp1 pd Homo_sapiens_chromosome_22[18318104-18318559]
+Sp1 pd Homo_sapiens_chromosome_22[18340913-18343992]
+Sp1 pd Homo_sapiens_chromosome_22[18345846-18346381]
+Sp1 pd Homo_sapiens_chromosome_22[18348507-18348987]
+Sp1 pd Homo_sapiens_chromosome_22[18368983-18369469]
+Sp1 pd Homo_sapiens_chromosome_22[18372915-18373609]
+Sp1 pd Homo_sapiens_chromosome_22[18383396-18383938]
+Sp1 pd Homo_sapiens_chromosome_22[18418154-18418773]
+Sp1 pd Homo_sapiens_chromosome_22[18472599-18472632]
+Sp1 pd Homo_sapiens_chromosome_22[18520946-18522163]
+Sp1 pd Homo_sapiens_chromosome_22[18568195-18568263]
+Sp1 pd Homo_sapiens_chromosome_22[18694281-18695242]
+Sp1 pd Homo_sapiens_chromosome_22[18790024-18790081]
+Sp1 pd Homo_sapiens_chromosome_22[18938325-18938930]
+Sp1 pd Homo_sapiens_chromosome_22[19038630-19038632]
+Sp1 pd Homo_sapiens_chromosome_22[19374562-19375758]
+Sp1 pd Homo_sapiens_chromosome_22[19456297-19457272]
+Sp1 pd Homo_sapiens_chromosome_22[19674683-19675086]
+Sp1 pd Homo_sapiens_chromosome_22[19677034-19680070]
+Sp1 pd Homo_sapiens_chromosome_22[19692011-19692206]
+Sp1 pd Homo_sapiens_chromosome_22[19708712-19709080]
+Sp1 pd Homo_sapiens_chromosome_22[19924121-19925100]
+Sp1 pd Homo_sapiens_chromosome_22[20185586-20186147]
+Sp1 pd Homo_sapiens_chromosome_22[20257943-20258635]
+Sp1 pd Homo_sapiens_chromosome_22[20291078-20291203]
+Sp1 pd Homo_sapiens_chromosome_22[20353790-20354012]
+Sp1 pd Homo_sapiens_chromosome_22[20356323-20359231]
+Sp1 pd Homo_sapiens_chromosome_22[20359828-20359887]
+Sp1 pd Homo_sapiens_chromosome_22[20429416-20430317]
+Sp1 pd Homo_sapiens_chromosome_22[20466857-20467024]
+Sp1 pd Homo_sapiens_chromosome_22[20518105-20518554]
+Sp1 pd Homo_sapiens_chromosome_22[20809391-20809470]
+Sp1 pd Homo_sapiens_chromosome_22[20825487-20826343]
+Sp1 pd Homo_sapiens_chromosome_22[20877174-20877993]
+Sp1 pd Homo_sapiens_chromosome_22[21004190-21005551]
+Sp1 pd Homo_sapiens_chromosome_22[21012419-21013780]
+Sp1 pd Homo_sapiens_chromosome_22[21068475-21069555]
+Sp1 pd Homo_sapiens_chromosome_22[21069662-21069828]
+Sp1 pd Homo_sapiens_chromosome_22[21124185-21124304]
+Sp1 pd Homo_sapiens_chromosome_22[21246226-21246553]
+Sp1 pd Homo_sapiens_chromosome_22[21338023-21338126]
+Sp1 pd Homo_sapiens_chromosome_22[21349212-21352249]
+Sp1 pd Homo_sapiens_chromosome_22[21356947-21357572]
+Sp1 pd Homo_sapiens_chromosome_22[21724057-21724186]
+Sp1 pd Homo_sapiens_chromosome_22[21727294-21727463]
+Sp1 pd Homo_sapiens_chromosome_22[21740296-21740656]
+Sp1 pd Homo_sapiens_chromosome_22[21742645-21745788]
+Sp1 pd Homo_sapiens_chromosome_22[22328122-22328447]
+Sp1 pd Homo_sapiens_chromosome_22[22497826-22498125]
+Sp1 pd Homo_sapiens_chromosome_22[22526372-22526374]
+Sp1 pd Homo_sapiens_chromosome_22[22782574-22783250]
+Sp1 pd Homo_sapiens_chromosome_22[22849682-22849958]
+Sp1 pd Homo_sapiens_chromosome_22[23079953-23080127]
+Sp1 pd Homo_sapiens_chromosome_22[23469468-23470019]
+Sp1 pd Homo_sapiens_chromosome_22[23520852-23521079]
+Sp1 pd Homo_sapiens_chromosome_22[23595083-23595227]
+Sp1 pd Homo_sapiens_chromosome_22[23682288-23682648]
+Sp1 pd Homo_sapiens_chromosome_22[23740571-23740920]
+Sp1 pd Homo_sapiens_chromosome_22[23763994-23765376]
+Sp1 pd Homo_sapiens_chromosome_22[24694550-24694552]
+Sp1 pd Homo_sapiens_chromosome_22[25011508-25012001]
+Sp1 pd Homo_sapiens_chromosome_22[25092630-25092743]
+Sp1 pd Homo_sapiens_chromosome_22[25834007-25834816]
+Sp1 pd Homo_sapiens_chromosome_22[25892538-25893342]
+Sp1 pd Homo_sapiens_chromosome_22[25894192-25894414]
+Sp1 pd Homo_sapiens_chromosome_22[25902797-25903722]
+Sp1 pd Homo_sapiens_chromosome_22[25974356-25975242]
+Sp1 pd Homo_sapiens_chromosome_22[26295834-26295964]
+Sp1 pd Homo_sapiens_chromosome_22[26395792-26395815]
+Sp1 pd Homo_sapiens_chromosome_22[26480729-26480758]
+Sp1 pd Homo_sapiens_chromosome_22[26673144-26673201]
+Sp1 pd Homo_sapiens_chromosome_22[26695076-26695640]
+Sp1 pd Homo_sapiens_chromosome_22[26858878-26859667]
+Sp1 pd Homo_sapiens_chromosome_22[27398141-27399082]
+Sp1 pd Homo_sapiens_chromosome_22[27416154-27416425]
+Sp1 pd Homo_sapiens_chromosome_22[27420385-27420975]
+Sp1 pd Homo_sapiens_chromosome_22[27515606-27516573]
+Sp1 pd Homo_sapiens_chromosome_22[27683637-27684506]
+Sp1 pd Homo_sapiens_chromosome_22[28172510-28174205]
+Sp1 pd Homo_sapiens_chromosome_22[28199509-28200318]
+Sp1 pd Homo_sapiens_chromosome_22[28241115-28241242]
+Sp1 pd Homo_sapiens_chromosome_22[28339944-28340189]
+Sp1 pd Homo_sapiens_chromosome_22[28378274-28378948]
+Sp1 pd Homo_sapiens_chromosome_22[28491277-28491532]
+Sp1 pd Homo_sapiens_chromosome_22[28753300-28754838]
+Sp1 pd Homo_sapiens_chromosome_22[28841963-28842246]
+Sp1 pd Homo_sapiens_chromosome_22[29037259-29037558]
+Sp1 pd Homo_sapiens_chromosome_22[29062459-29062461]
+Sp1 pd Homo_sapiens_chromosome_22[29421929-29422895]
+Sp1 pd Homo_sapiens_chromosome_22[32391321-32392756]
+Sp1 pd Homo_sapiens_chromosome_22[32491484-32492399]
+Sp1 pd Homo_sapiens_chromosome_22[32591318-32592293]
+Sp1 pd Homo_sapiens_chromosome_22[32773936-32774626]
+Sp1 pd Homo_sapiens_chromosome_22[33348276-33348762]
+Sp1 pd Homo_sapiens_chromosome_22[33368546-33368895]
+Sp1 pd Homo_sapiens_chromosome_22[33539526-33540135]
+Sp1 pd Homo_sapiens_chromosome_22[33786246-33787428]
+Sp1 pd Homo_sapiens_chromosome_22[33988215-33988217]
+Sp1 pd Homo_sapiens_chromosome_22[34197396-34197467]
+Sp1 pd Homo_sapiens_chromosome_22[34566513-34566579]
+Sp1 pd Homo_sapiens_chromosome_22[34617491-34619432]
+Sp1 pd Homo_sapiens_chromosome_22[34668495-34669329]
+Sp1 pd Homo_sapiens_chromosome_22[34688151-34688184]
+Sp1 pd Homo_sapiens_chromosome_22[34696696-34697443]
+Sp1 pd Homo_sapiens_chromosome_22[34813585-34814137]
+Sp1 pd Homo_sapiens_chromosome_22[34854022-34855101]
+Sp1 pd Homo_sapiens_chromosome_22[34860568-34860719]
+Sp1 pd Homo_sapiens_chromosome_22[35191542-35192758]
+Sp1 pd Homo_sapiens_chromosome_22[35212289-35212759]
+Sp1 pd Homo_sapiens_chromosome_22[35579883-35581144]
+Sp1 pd Homo_sapiens_chromosome_22[35666583-35667484]
+Sp1 pd Homo_sapiens_chromosome_22[35691888-35692208]
+Sp1 pd Homo_sapiens_chromosome_22[35715569-35716721]
+Sp1 pd Homo_sapiens_chromosome_22[35717701-35717798]
+Sp1 pd Homo_sapiens_chromosome_22[35764196-35765317]
+Sp1 pd Homo_sapiens_chromosome_22[35804282-35805397]
+Sp1 pd Homo_sapiens_chromosome_22[36001295-36001326]
+Sp1 pd Homo_sapiens_chromosome_22[36025855-36025895]
+Sp1 pd Homo_sapiens_chromosome_22[36030884-36032046]
+Sp1 pd Homo_sapiens_chromosome_22[36050684-36051690]
+Sp1 pd Homo_sapiens_chromosome_22[36087044-36087895]
+Sp1 pd Homo_sapiens_chromosome_22[36100167-36100715]
+Sp1 pd Homo_sapiens_chromosome_22[36160571-36160998]
+Sp1 pd Homo_sapiens_chromosome_22[36329804-36330757]
+Sp1 pd Homo_sapiens_chromosome_22[36513229-36513231]
+Sp1 pd Homo_sapiens_chromosome_22[36530464-36531175]
+Sp1 pd Homo_sapiens_chromosome_22[36544381-36544740]
+Sp1 pd Homo_sapiens_chromosome_22[37054266-37055527]
+Sp1 pd Homo_sapiens_chromosome_22[37647099-37648068]
+Sp1 pd Homo_sapiens_chromosome_22[37829674-37829931]
+Sp1 pd Homo_sapiens_chromosome_22[37867013-37867015]
+Sp1 pd Homo_sapiens_chromosome_22[37961727-37963045]
+Sp1 pd Homo_sapiens_chromosome_22[38101239-38101968]
+Sp1 pd Homo_sapiens_chromosome_22[38207254-38207723]
+Sp1 pd Homo_sapiens_chromosome_22[38215439-38216278]
+Sp1 pd Homo_sapiens_chromosome_22[38296713-38297177]
+Sp1 pd Homo_sapiens_chromosome_22[38478792-38480461]
+Sp1 pd Homo_sapiens_chromosome_22[38600273-38600812]
+Sp1 pd Homo_sapiens_chromosome_22[38631543-38632479]
+Sp1 pd Homo_sapiens_chromosome_22[38692484-38693197]
+Sp1 pd Homo_sapiens_chromosome_22[38884356-38884572]
+Sp1 pd Homo_sapiens_chromosome_22[39090164-39091338]
+Sp1 pd Homo_sapiens_chromosome_22[39100876-39101343]
+Sp1 pd Homo_sapiens_chromosome_22[39367536-39367830]
+Sp1 pd Homo_sapiens_chromosome_22[39442855-39442857]
+Sp1 pd Homo_sapiens_chromosome_22[39493950-39494311]
+Sp1 pd Homo_sapiens_chromosome_22[39535578-39537956]
+Sp1 pd Homo_sapiens_chromosome_22[39613199-39614236]
+Sp1 pd Homo_sapiens_chromosome_22[40112075-40112077]
+Sp1 pd Homo_sapiens_chromosome_22[40261854-40262340]
+Sp1 pd Homo_sapiens_chromosome_22[40824779-40825306]
+Sp1 pd Homo_sapiens_chromosome_22[41125708-41125974]
+Sp1 pd Homo_sapiens_chromosome_22[42006387-42006560]
+Sp1 pd Homo_sapiens_chromosome_22[42272447-42272920]
+Sp1 pd Homo_sapiens_chromosome_22[42299928-42300419]
+Sp1 pd Homo_sapiens_chromosome_22[43057451-43058094]
+Sp1 pd Homo_sapiens_chromosome_22[43566875-43567348]
+Sp1 pd Homo_sapiens_chromosome_22[43983327-43983582]
+Sp1 pd Homo_sapiens_chromosome_22[43990507-43991000]
+Sp1 pd Homo_sapiens_chromosome_22[44079323-44079325]
+Sp1 pd Homo_sapiens_chromosome_22[46141067-46141082]
+Sp1 pd Homo_sapiens_chromosome_22[46250418-46251415]
+Sp1 pd Homo_sapiens_chromosome_22[46315784-46316316]
+Sp1 pd Homo_sapiens_chromosome_22[46368979-46371305]
+Sp1 pd Homo_sapiens_chromosome_22[46445561-46445600]
+Sp1 pd Homo_sapiens_chromosome_22[46567158-46567513]
+Sp1 pd Homo_sapiens_chromosome_22[47029559-47030132]
+Sp1 pd Homo_sapiens_chromosome_22[47136940-47137817]
+Sp1 pd Homo_sapiens_chromosome_22[47158375-47158439]
+Sp1 pd Homo_sapiens_chromosome_22[47234071-47234073]
+Sp1 pd Homo_sapiens_chromosome_22[47415936-47415938]
+Sp1 pd Homo_sapiens_chromosome_22[47450701-47451321]
+Sp1 pd Homo_sapiens_chromosome_22[47554643-47555463]
+Sp1 pd Homo_sapiens_chromosome_22[47570534-47571009]
+Sp1 pd Homo_sapiens_chromosome_22[47580618-47580852]
+Sp1 pd Homo_sapiens_chromosome_22[47689083-47689243]
+Sp1 pd Homo_sapiens_chromosome_22[47690793-47691599]
+c-Myc pd Homo_sapiens_chromosome_21[7906577-7907511]
+c-Myc pd Homo_sapiens_chromosome_21[11236108-11236110]
+c-Myc pd Homo_sapiens_chromosome_21[11661703-11661705]
+c-Myc pd Homo_sapiens_chromosome_21[11703565-11704067]
+c-Myc pd Homo_sapiens_chromosome_21[11776786-11776839]
+c-Myc pd Homo_sapiens_chromosome_21[11860584-11860652]
+c-Myc pd Homo_sapiens_chromosome_21[11861692-11862436]
+c-Myc pd Homo_sapiens_chromosome_21[11882008-11882491]
+c-Myc pd Homo_sapiens_chromosome_21[11884009-11884562]
+c-Myc pd Homo_sapiens_chromosome_21[12063493-12063666]
+c-Myc pd Homo_sapiens_chromosome_21[12419071-12420767]
+c-Myc pd Homo_sapiens_chromosome_21[12578525-12579031]
+c-Myc pd Homo_sapiens_chromosome_21[15164544-15165158]
+c-Myc pd Homo_sapiens_chromosome_21[15490950-15491864]
+c-Myc pd Homo_sapiens_chromosome_21[15550052-15550150]
+c-Myc pd Homo_sapiens_chromosome_21[15648396-15648640]
+c-Myc pd Homo_sapiens_chromosome_21[15856184-15856777]
+c-Myc pd Homo_sapiens_chromosome_21[21526322-21526490]
+c-Myc pd Homo_sapiens_chromosome_21[23591257-23591835]
+c-Myc pd Homo_sapiens_chromosome_21[23685136-23687581]
+c-Myc pd Homo_sapiens_chromosome_21[23752450-23752713]
+c-Myc pd Homo_sapiens_chromosome_21[24138759-24138851]
+c-Myc pd Homo_sapiens_chromosome_21[24793045-24796248]
+c-Myc pd Homo_sapiens_chromosome_21[26836295-26836626]
+c-Myc pd Homo_sapiens_chromosome_21[26943560-26944233]
+c-Myc pd Homo_sapiens_chromosome_21[26953777-26954477]
+c-Myc pd Homo_sapiens_chromosome_21[26969803-26971068]
+c-Myc pd Homo_sapiens_chromosome_21[26975407-26977137]
+c-Myc pd Homo_sapiens_chromosome_21[27022390-27023090]
+c-Myc pd Homo_sapiens_chromosome_21[27080209-27080772]
+c-Myc pd Homo_sapiens_chromosome_21[27098159-27099108]
+c-Myc pd Homo_sapiens_chromosome_21[27171757-27171790]
+c-Myc pd Homo_sapiens_chromosome_21[27249215-27250586]
+c-Myc pd Homo_sapiens_chromosome_21[29083859-29084104]
+c-Myc pd Homo_sapiens_chromosome_21[29085326-29087176]
+c-Myc pd Homo_sapiens_chromosome_21[29369834-29370465]
+c-Myc pd Homo_sapiens_chromosome_21[29428443-29428918]
+c-Myc pd Homo_sapiens_chromosome_21[29464462-29464464]
+c-Myc pd Homo_sapiens_chromosome_21[29479738-29479986]
+c-Myc pd Homo_sapiens_chromosome_21[29509779-29510003]
+c-Myc pd Homo_sapiens_chromosome_21[29606494-29606566]
+c-Myc pd Homo_sapiens_chromosome_21[29608579-29609854]
+c-Myc pd Homo_sapiens_chromosome_21[29620835-29621973]
+c-Myc pd Homo_sapiens_chromosome_21[29682413-29683645]
+c-Myc pd Homo_sapiens_chromosome_21[29844589-29845482]
+c-Myc pd Homo_sapiens_chromosome_21[29868601-29868863]
+c-Myc pd Homo_sapiens_chromosome_21[29903481-29903483]
+c-Myc pd Homo_sapiens_chromosome_21[29924739-29924741]
+c-Myc pd Homo_sapiens_chromosome_21[30014221-30014542]
+c-Myc pd Homo_sapiens_chromosome_21[30086624-30086626]
+c-Myc pd Homo_sapiens_chromosome_21[30138377-30138723]
+c-Myc pd Homo_sapiens_chromosome_21[30139946-30140778]
+c-Myc pd Homo_sapiens_chromosome_21[30332896-30333629]
+c-Myc pd Homo_sapiens_chromosome_21[30341742-30342853]
+c-Myc pd Homo_sapiens_chromosome_21[30476311-30476697]
+c-Myc pd Homo_sapiens_chromosome_21[30550328-30550946]
+c-Myc pd Homo_sapiens_chromosome_21[30574482-30574873]
+c-Myc pd Homo_sapiens_chromosome_21[30677997-30677999]
+c-Myc pd Homo_sapiens_chromosome_21[30882205-30883193]
+c-Myc pd Homo_sapiens_chromosome_21[30889970-30890095]
+c-Myc pd Homo_sapiens_chromosome_21[31066126-31066573]
+c-Myc pd Homo_sapiens_chromosome_21[31164962-31166279]
+c-Myc pd Homo_sapiens_chromosome_21[31189034-31189722]
+c-Myc pd Homo_sapiens_chromosome_21[31194577-31195749]
+c-Myc pd Homo_sapiens_chromosome_21[31218647-31219081]
+c-Myc pd Homo_sapiens_chromosome_21[31250726-31250762]
+c-Myc pd Homo_sapiens_chromosome_21[31273789-31275256]
+c-Myc pd Homo_sapiens_chromosome_21[31330307-31330684]
+c-Myc pd Homo_sapiens_chromosome_21[31332863-31333271]
+c-Myc pd Homo_sapiens_chromosome_21[31394313-31394315]
+c-Myc pd Homo_sapiens_chromosome_21[31441612-31441834]
+c-Myc pd Homo_sapiens_chromosome_21[31491193-31493541]
+c-Myc pd Homo_sapiens_chromosome_21[31500886-31501770]
+c-Myc pd Homo_sapiens_chromosome_21[31864746-31865896]
+c-Myc pd Homo_sapiens_chromosome_21[31881305-31881802]
+c-Myc pd Homo_sapiens_chromosome_21[31890611-31891111]
+c-Myc pd Homo_sapiens_chromosome_21[31898218-31900351]
+c-Myc pd Homo_sapiens_chromosome_21[32078340-32079856]
+c-Myc pd Homo_sapiens_chromosome_21[32193472-32193664]
+c-Myc pd Homo_sapiens_chromosome_21[32276145-32276400]
+c-Myc pd Homo_sapiens_chromosome_21[32324601-32324727]
+c-Myc pd Homo_sapiens_chromosome_21[32325884-32326158]
+c-Myc pd Homo_sapiens_chromosome_21[32377098-32377100]
+c-Myc pd Homo_sapiens_chromosome_21[32416649-32417399]
+c-Myc pd Homo_sapiens_chromosome_21[32637993-32638622]
+c-Myc pd Homo_sapiens_chromosome_21[32771853-32771940]
+c-Myc pd Homo_sapiens_chromosome_21[32811453-32811694]
+c-Myc pd Homo_sapiens_chromosome_21[32814913-32815492]
+c-Myc pd Homo_sapiens_chromosome_21[32858516-32858827]
+c-Myc pd Homo_sapiens_chromosome_21[32860227-32860463]
+c-Myc pd Homo_sapiens_chromosome_21[32876186-32876407]
+c-Myc pd Homo_sapiens_chromosome_21[32883989-32884066]
+c-Myc pd Homo_sapiens_chromosome_21[32896210-32896781]
+c-Myc pd Homo_sapiens_chromosome_21[32936608-32937212]
+c-Myc pd Homo_sapiens_chromosome_21[32948541-32949906]
+c-Myc pd Homo_sapiens_chromosome_21[32955431-32955433]
+c-Myc pd Homo_sapiens_chromosome_21[32976715-32976717]
+c-Myc pd Homo_sapiens_chromosome_21[32978184-32978522]
+c-Myc pd Homo_sapiens_chromosome_21[32995395-32996750]
+c-Myc pd Homo_sapiens_chromosome_21[33000058-33001716]
+c-Myc pd Homo_sapiens_chromosome_21[33088319-33088969]
+c-Myc pd Homo_sapiens_chromosome_21[33177508-33177839]
+c-Myc pd Homo_sapiens_chromosome_21[33377981-33378533]
+c-Myc pd Homo_sapiens_chromosome_21[33453237-33453411]
+c-Myc pd Homo_sapiens_chromosome_21[33582788-33583743]
+c-Myc pd Homo_sapiens_chromosome_21[33774628-33775174]
+c-Myc pd Homo_sapiens_chromosome_21[33978984-33979910]
+c-Myc pd Homo_sapiens_chromosome_21[34079948-34080839]
+c-Myc pd Homo_sapiens_chromosome_21[34099063-34099469]
+c-Myc pd Homo_sapiens_chromosome_21[34123429-34123881]
+c-Myc pd Homo_sapiens_chromosome_21[34226577-34226970]
+c-Myc pd Homo_sapiens_chromosome_21[34269437-34269949]
+c-Myc pd Homo_sapiens_chromosome_21[34270199-34270745]
+c-Myc pd Homo_sapiens_chromosome_21[34371950-34372010]
+c-Myc pd Homo_sapiens_chromosome_21[34461262-34462002]
+c-Myc pd Homo_sapiens_chromosome_21[34915773-34915800]
+c-Myc pd Homo_sapiens_chromosome_21[35021923-35022110]
+c-Myc pd Homo_sapiens_chromosome_21[35023336-35024223]
+c-Myc pd Homo_sapiens_chromosome_21[35148319-35148359]
+c-Myc pd Homo_sapiens_chromosome_21[35170608-35171132]
+c-Myc pd Homo_sapiens_chromosome_21[35187344-35188155]
+c-Myc pd Homo_sapiens_chromosome_21[35206879-35208818]
+c-Myc pd Homo_sapiens_chromosome_21[35216045-35217319]
+c-Myc pd Homo_sapiens_chromosome_21[35328255-35328782]
+c-Myc pd Homo_sapiens_chromosome_21[35496726-35498396]
+c-Myc pd Homo_sapiens_chromosome_21[35792305-35792929]
+c-Myc pd Homo_sapiens_chromosome_21[36423565-36424103]
+c-Myc pd Homo_sapiens_chromosome_21[36424759-36425177]
+c-Myc pd Homo_sapiens_chromosome_21[36577584-36577895]
+c-Myc pd Homo_sapiens_chromosome_21[36627173-36627863]
+c-Myc pd Homo_sapiens_chromosome_21[36714879-36715382]
+c-Myc pd Homo_sapiens_chromosome_21[36753348-36753538]
+c-Myc pd Homo_sapiens_chromosome_21[36805871-36805981]
+c-Myc pd Homo_sapiens_chromosome_21[36811514-36812494]
+c-Myc pd Homo_sapiens_chromosome_21[36918402-36919181]
+c-Myc pd Homo_sapiens_chromosome_21[36922572-36923479]
+c-Myc pd Homo_sapiens_chromosome_21[36925752-36926956]
+c-Myc pd Homo_sapiens_chromosome_21[36937269-36937304]
+c-Myc pd Homo_sapiens_chromosome_21[36955316-36956445]
+c-Myc pd Homo_sapiens_chromosome_21[37010433-37010435]
+c-Myc pd Homo_sapiens_chromosome_21[37031779-37031920]
+c-Myc pd Homo_sapiens_chromosome_21[37131993-37132435]
+c-Myc pd Homo_sapiens_chromosome_21[37262530-37262958]
+c-Myc pd Homo_sapiens_chromosome_21[37320219-37320750]
+c-Myc pd Homo_sapiens_chromosome_21[37392085-37392974]
+c-Myc pd Homo_sapiens_chromosome_21[37448802-37449584]
+c-Myc pd Homo_sapiens_chromosome_21[37611862-37612137]
+c-Myc pd Homo_sapiens_chromosome_21[38189497-38190002]
+c-Myc pd Homo_sapiens_chromosome_21[38940951-38941374]
+c-Myc pd Homo_sapiens_chromosome_21[39059170-39060088]
+c-Myc pd Homo_sapiens_chromosome_21[39159832-39160534]
+c-Myc pd Homo_sapiens_chromosome_21[39187400-39188031]
+c-Myc pd Homo_sapiens_chromosome_21[39255187-39256024]
+c-Myc pd Homo_sapiens_chromosome_21[39712993-39713454]
+c-Myc pd Homo_sapiens_chromosome_21[39729862-39729864]
+c-Myc pd Homo_sapiens_chromosome_21[39846127-39846349]
+c-Myc pd Homo_sapiens_chromosome_21[39847402-39847912]
+c-Myc pd Homo_sapiens_chromosome_21[39863837-39864000]
+c-Myc pd Homo_sapiens_chromosome_21[39895900-39896511]
+c-Myc pd Homo_sapiens_chromosome_21[39960840-39960936]
+c-Myc pd Homo_sapiens_chromosome_21[39966400-39966949]
+c-Myc pd Homo_sapiens_chromosome_21[39976751-39977364]
+c-Myc pd Homo_sapiens_chromosome_21[39979083-39979563]
+c-Myc pd Homo_sapiens_chromosome_21[39996961-39997862]
+c-Myc pd Homo_sapiens_chromosome_21[40024777-40024779]
+c-Myc pd Homo_sapiens_chromosome_21[40030261-40030719]
+c-Myc pd Homo_sapiens_chromosome_21[40057253-40057285]
+c-Myc pd Homo_sapiens_chromosome_21[40086663-40087098]
+c-Myc pd Homo_sapiens_chromosome_21[40089322-40089846]
+c-Myc pd Homo_sapiens_chromosome_21[40117628-40117896]
+c-Myc pd Homo_sapiens_chromosome_21[40160916-40161313]
+c-Myc pd Homo_sapiens_chromosome_21[40183101-40183178]
+c-Myc pd Homo_sapiens_chromosome_21[40190242-40191277]
+c-Myc pd Homo_sapiens_chromosome_21[40199825-40202041]
+c-Myc pd Homo_sapiens_chromosome_21[40203849-40204894]
+c-Myc pd Homo_sapiens_chromosome_21[40264508-40265405]
+c-Myc pd Homo_sapiens_chromosome_21[40272349-40272461]
+c-Myc pd Homo_sapiens_chromosome_21[40291318-40291320]
+c-Myc pd Homo_sapiens_chromosome_21[40328712-40329500]
+c-Myc pd Homo_sapiens_chromosome_21[40362274-40363171]
+c-Myc pd Homo_sapiens_chromosome_21[40372373-40373266]
+c-Myc pd Homo_sapiens_chromosome_21[40391538-40392588]
+c-Myc pd Homo_sapiens_chromosome_21[40394387-40394389]
+c-Myc pd Homo_sapiens_chromosome_21[40415006-40415574]
+c-Myc pd Homo_sapiens_chromosome_21[40416526-40416528]
+c-Myc pd Homo_sapiens_chromosome_21[40417545-40418096]
+c-Myc pd Homo_sapiens_chromosome_21[40429674-40430322]
+c-Myc pd Homo_sapiens_chromosome_21[40432080-40432489]
+c-Myc pd Homo_sapiens_chromosome_21[40557180-40557744]
+c-Myc pd Homo_sapiens_chromosome_21[40582512-40583073]
+c-Myc pd Homo_sapiens_chromosome_21[40622405-40622440]
+c-Myc pd Homo_sapiens_chromosome_21[40651717-40652347]
+c-Myc pd Homo_sapiens_chromosome_21[40776788-40777290]
+c-Myc pd Homo_sapiens_chromosome_21[40800794-40801489]
+c-Myc pd Homo_sapiens_chromosome_21[40817944-40817946]
+c-Myc pd Homo_sapiens_chromosome_21[40846149-40848113]
+c-Myc pd Homo_sapiens_chromosome_21[40860187-40860871]
+c-Myc pd Homo_sapiens_chromosome_21[40941179-40942001]
+c-Myc pd Homo_sapiens_chromosome_21[40960120-40960149]
+c-Myc pd Homo_sapiens_chromosome_21[41043339-41043620]
+c-Myc pd Homo_sapiens_chromosome_21[41070770-41070851]
+c-Myc pd Homo_sapiens_chromosome_21[41074766-41075279]
+c-Myc pd Homo_sapiens_chromosome_21[41144642-41145295]
+c-Myc pd Homo_sapiens_chromosome_21[41236690-41236967]
+c-Myc pd Homo_sapiens_chromosome_21[41318281-41318863]
+c-Myc pd Homo_sapiens_chromosome_21[41361123-41361125]
+c-Myc pd Homo_sapiens_chromosome_21[41395828-41396678]
+c-Myc pd Homo_sapiens_chromosome_21[41589066-41589615]
+c-Myc pd Homo_sapiens_chromosome_21[41620114-41620116]
+c-Myc pd Homo_sapiens_chromosome_21[41851224-41851538]
+c-Myc pd Homo_sapiens_chromosome_21[41948447-41948769]
+c-Myc pd Homo_sapiens_chromosome_21[42011633-42012947]
+c-Myc pd Homo_sapiens_chromosome_21[42013219-42014236]
+c-Myc pd Homo_sapiens_chromosome_21[42062791-42063354]
+c-Myc pd Homo_sapiens_chromosome_21[42085804-42086071]
+c-Myc pd Homo_sapiens_chromosome_21[42228969-42229090]
+c-Myc pd Homo_sapiens_chromosome_21[42269565-42269567]
+c-Myc pd Homo_sapiens_chromosome_21[42282925-42284591]
+c-Myc pd Homo_sapiens_chromosome_21[42295199-42295201]
+c-Myc pd Homo_sapiens_chromosome_21[42403441-42404077]
+c-Myc pd Homo_sapiens_chromosome_21[42543246-42543248]
+c-Myc pd Homo_sapiens_chromosome_21[42585934-42585966]
+c-Myc pd Homo_sapiens_chromosome_21[42614624-42614626]
+c-Myc pd Homo_sapiens_chromosome_21[42625046-42625127]
+c-Myc pd Homo_sapiens_chromosome_21[42777901-42779744]
+c-Myc pd Homo_sapiens_chromosome_21[42784097-42785418]
+c-Myc pd Homo_sapiens_chromosome_21[42793695-42793729]
+c-Myc pd Homo_sapiens_chromosome_21[42799330-42801821]
+c-Myc pd Homo_sapiens_chromosome_21[42814241-42814955]
+c-Myc pd Homo_sapiens_chromosome_21[42849484-42849486]
+c-Myc pd Homo_sapiens_chromosome_21[42868208-42869026]
+c-Myc pd Homo_sapiens_chromosome_21[42985562-42985604]
+c-Myc pd Homo_sapiens_chromosome_21[43000873-43000875]
+c-Myc pd Homo_sapiens_chromosome_21[43015082-43015868]
+c-Myc pd Homo_sapiens_chromosome_21[43058860-43059296]
+c-Myc pd Homo_sapiens_chromosome_21[43067896-43068435]
+c-Myc pd Homo_sapiens_chromosome_21[43081371-43082184]
+c-Myc pd Homo_sapiens_chromosome_21[43152472-43153005]
+c-Myc pd Homo_sapiens_chromosome_21[43156058-43156385]
+c-Myc pd Homo_sapiens_chromosome_21[43225085-43225129]
+c-Myc pd Homo_sapiens_chromosome_21[43305194-43306011]
+c-Myc pd Homo_sapiens_chromosome_21[43404182-43404281]
+c-Myc pd Homo_sapiens_chromosome_21[43407602-43408635]
+c-Myc pd Homo_sapiens_chromosome_21[43428611-43429355]
+c-Myc pd Homo_sapiens_chromosome_21[43479968-43480726]
+c-Myc pd Homo_sapiens_chromosome_21[43485456-43485838]
+c-Myc pd Homo_sapiens_chromosome_21[43545262-43545403]
+c-Myc pd Homo_sapiens_chromosome_21[43561881-43563309]
+c-Myc pd Homo_sapiens_chromosome_21[43563830-43564567]
+c-Myc pd Homo_sapiens_chromosome_21[43857905-43860022]
+c-Myc pd Homo_sapiens_chromosome_21[43871437-43871572]
+c-Myc pd Homo_sapiens_chromosome_21[43974120-43974914]
+c-Myc pd Homo_sapiens_chromosome_21[43985494-43986849]
+c-Myc pd Homo_sapiens_chromosome_21[43988782-43989765]
+c-Myc pd Homo_sapiens_chromosome_21[44097038-44097040]
+c-Myc pd Homo_sapiens_chromosome_21[44127491-44128289]
+c-Myc pd Homo_sapiens_chromosome_21[44129443-44129445]
+c-Myc pd Homo_sapiens_chromosome_21[44154859-44154861]
+c-Myc pd Homo_sapiens_chromosome_21[44248823-44249873]
+c-Myc pd Homo_sapiens_chromosome_21[44309076-44311228]
+c-Myc pd Homo_sapiens_chromosome_21[44351085-44352457]
+c-Myc pd Homo_sapiens_chromosome_21[44485970-44486447]
+c-Myc pd Homo_sapiens_chromosome_21[44489929-44490081]
+c-Myc pd Homo_sapiens_chromosome_21[44586997-44587249]
+c-Myc pd Homo_sapiens_chromosome_22[13142586-13142856]
+c-Myc pd Homo_sapiens_chromosome_22[13326498-13326639]
+c-Myc pd Homo_sapiens_chromosome_22[13327153-13327155]
+c-Myc pd Homo_sapiens_chromosome_22[13411928-13412229]
+c-Myc pd Homo_sapiens_chromosome_22[13928075-13928764]
+c-Myc pd Homo_sapiens_chromosome_22[14028137-14028297]
+c-Myc pd Homo_sapiens_chromosome_22[14336042-14336407]
+c-Myc pd Homo_sapiens_chromosome_22[14399101-14399677]
+c-Myc pd Homo_sapiens_chromosome_22[14512219-14512906]
+c-Myc pd Homo_sapiens_chromosome_22[14523859-14524294]
+c-Myc pd Homo_sapiens_chromosome_22[14584184-14585174]
+c-Myc pd Homo_sapiens_chromosome_22[15046319-15046474]
+c-Myc pd Homo_sapiens_chromosome_22[15061631-15062763]
+c-Myc pd Homo_sapiens_chromosome_22[15149958-15150226]
+c-Myc pd Homo_sapiens_chromosome_22[15169578-15169614]
+c-Myc pd Homo_sapiens_chromosome_22[15186631-15186695]
+c-Myc pd Homo_sapiens_chromosome_22[15196430-15196571]
+c-Myc pd Homo_sapiens_chromosome_22[15200224-15200453]
+c-Myc pd Homo_sapiens_chromosome_22[15201488-15203462]
+c-Myc pd Homo_sapiens_chromosome_22[15209640-15211741]
+c-Myc pd Homo_sapiens_chromosome_22[15221640-15221670]
+c-Myc pd Homo_sapiens_chromosome_22[15321604-15321826]
+c-Myc pd Homo_sapiens_chromosome_22[15326269-15326984]
+c-Myc pd Homo_sapiens_chromosome_22[15406058-15406890]
+c-Myc pd Homo_sapiens_chromosome_22[15419542-15420082]
+c-Myc pd Homo_sapiens_chromosome_22[15444667-15445068]
+c-Myc pd Homo_sapiens_chromosome_22[15446897-15447341]
+c-Myc pd Homo_sapiens_chromosome_22[15501378-15501815]
+c-Myc pd Homo_sapiens_chromosome_22[15572583-15572585]
+c-Myc pd Homo_sapiens_chromosome_22[15595860-15596690]
+c-Myc pd Homo_sapiens_chromosome_22[15606277-15606889]
+c-Myc pd Homo_sapiens_chromosome_22[15610573-15610644]
+c-Myc pd Homo_sapiens_chromosome_22[15613030-15613163]
+c-Myc pd Homo_sapiens_chromosome_22[15615903-15617237]
+c-Myc pd Homo_sapiens_chromosome_22[15619721-15621124]
+c-Myc pd Homo_sapiens_chromosome_22[15665373-15667036]
+c-Myc pd Homo_sapiens_chromosome_22[15669282-15670610]
+c-Myc pd Homo_sapiens_chromosome_22[15673358-15673542]
+c-Myc pd Homo_sapiens_chromosome_22[15675874-15675881]
+c-Myc pd Homo_sapiens_chromosome_22[15679829-15680418]
+c-Myc pd Homo_sapiens_chromosome_22[15694843-15695638]
+c-Myc pd Homo_sapiens_chromosome_22[15698268-15698396]
+c-Myc pd Homo_sapiens_chromosome_22[15705141-15705633]
+c-Myc pd Homo_sapiens_chromosome_22[15706490-15707325]
+c-Myc pd Homo_sapiens_chromosome_22[15722951-15723516]
+c-Myc pd Homo_sapiens_chromosome_22[15737676-15738228]
+c-Myc pd Homo_sapiens_chromosome_22[15739557-15740431]
+c-Myc pd Homo_sapiens_chromosome_22[15753129-15754920]
+c-Myc pd Homo_sapiens_chromosome_22[15758507-15758774]
+c-Myc pd Homo_sapiens_chromosome_22[15761787-15762517]
+c-Myc pd Homo_sapiens_chromosome_22[15766489-15766959]
+c-Myc pd Homo_sapiens_chromosome_22[15778268-15778390]
+c-Myc pd Homo_sapiens_chromosome_22[15779942-15780989]
+c-Myc pd Homo_sapiens_chromosome_22[15782077-15782744]
+c-Myc pd Homo_sapiens_chromosome_22[15784612-15785210]
+c-Myc pd Homo_sapiens_chromosome_22[15786610-15787406]
+c-Myc pd Homo_sapiens_chromosome_22[15798068-15798473]
+c-Myc pd Homo_sapiens_chromosome_22[15802570-15802641]
+c-Myc pd Homo_sapiens_chromosome_22[15804939-15805157]
+c-Myc pd Homo_sapiens_chromosome_22[15807897-15809230]
+c-Myc pd Homo_sapiens_chromosome_22[15811514-15813118]
+c-Myc pd Homo_sapiens_chromosome_22[15952743-15953438]
+c-Myc pd Homo_sapiens_chromosome_22[16046407-16047028]
+c-Myc pd Homo_sapiens_chromosome_22[16071819-16072650]
+c-Myc pd Homo_sapiens_chromosome_22[16098124-16098340]
+c-Myc pd Homo_sapiens_chromosome_22[16100031-16100885]
+c-Myc pd Homo_sapiens_chromosome_22[16119002-16119004]
+c-Myc pd Homo_sapiens_chromosome_22[16143751-16143927]
+c-Myc pd Homo_sapiens_chromosome_22[16144441-16144443]
+c-Myc pd Homo_sapiens_chromosome_22[16186122-16186440]
+c-Myc pd Homo_sapiens_chromosome_22[16219729-16220254]
+c-Myc pd Homo_sapiens_chromosome_22[16278965-16279021]
+c-Myc pd Homo_sapiens_chromosome_22[16347483-16347907]
+c-Myc pd Homo_sapiens_chromosome_22[16352260-16353407]
+c-Myc pd Homo_sapiens_chromosome_22[16358367-16358636]
+c-Myc pd Homo_sapiens_chromosome_22[16360483-16360640]
+c-Myc pd Homo_sapiens_chromosome_22[16375205-16376475]
+c-Myc pd Homo_sapiens_chromosome_22[16407052-16407942]
+c-Myc pd Homo_sapiens_chromosome_22[16639550-16640152]
+c-Myc pd Homo_sapiens_chromosome_22[16814536-16814538]
+c-Myc pd Homo_sapiens_chromosome_22[16818880-16820631]
+c-Myc pd Homo_sapiens_chromosome_22[16822952-16823568]
+c-Myc pd Homo_sapiens_chromosome_22[16869857-16870553]
+c-Myc pd Homo_sapiens_chromosome_22[16883987-16883989]
+c-Myc pd Homo_sapiens_chromosome_22[16885327-16885686]
+c-Myc pd Homo_sapiens_chromosome_22[17028191-17028567]
+c-Myc pd Homo_sapiens_chromosome_22[17046631-17047135]
+c-Myc pd Homo_sapiens_chromosome_22[17054113-17055069]
+c-Myc pd Homo_sapiens_chromosome_22[17121257-17121664]
+c-Myc pd Homo_sapiens_chromosome_22[17172816-17173520]
+c-Myc pd Homo_sapiens_chromosome_22[17399748-17400225]
+c-Myc pd Homo_sapiens_chromosome_22[17402705-17403728]
+c-Myc pd Homo_sapiens_chromosome_22[17406780-17406970]
+c-Myc pd Homo_sapiens_chromosome_22[17419986-17420821]
+c-Myc pd Homo_sapiens_chromosome_22[17449897-17450316]
+c-Myc pd Homo_sapiens_chromosome_22[17450686-17450688]
+c-Myc pd Homo_sapiens_chromosome_22[17512605-17512607]
+c-Myc pd Homo_sapiens_chromosome_22[17588698-17589211]
+c-Myc pd Homo_sapiens_chromosome_22[17605642-17605769]
+c-Myc pd Homo_sapiens_chromosome_22[17624948-17626126]
+c-Myc pd Homo_sapiens_chromosome_22[17634689-17635050]
+c-Myc pd Homo_sapiens_chromosome_22[17746758-17746822]
+c-Myc pd Homo_sapiens_chromosome_22[17748374-17749266]
+c-Myc pd Homo_sapiens_chromosome_22[17750551-17751056]
+c-Myc pd Homo_sapiens_chromosome_22[17860185-17860187]
+c-Myc pd Homo_sapiens_chromosome_22[17860692-17860694]
+c-Myc pd Homo_sapiens_chromosome_22[17912531-17912533]
+c-Myc pd Homo_sapiens_chromosome_22[17920316-17921564]
+c-Myc pd Homo_sapiens_chromosome_22[17971074-17971572]
+c-Myc pd Homo_sapiens_chromosome_22[18156004-18156081]
+c-Myc pd Homo_sapiens_chromosome_22[18167880-18168669]
+c-Myc pd Homo_sapiens_chromosome_22[18170075-18170673]
+c-Myc pd Homo_sapiens_chromosome_22[18172542-18173124]
+c-Myc pd Homo_sapiens_chromosome_22[18174334-18175347]
+c-Myc pd Homo_sapiens_chromosome_22[18176898-18177019]
+c-Myc pd Homo_sapiens_chromosome_22[18189751-18190342]
+c-Myc pd Homo_sapiens_chromosome_22[18194351-18194974]
+c-Myc pd Homo_sapiens_chromosome_22[18198017-18198284]
+c-Myc pd Homo_sapiens_chromosome_22[18201902-18203725]
+c-Myc pd Homo_sapiens_chromosome_22[18224568-18225883]
+c-Myc pd Homo_sapiens_chromosome_22[18228416-18229754]
+c-Myc pd Homo_sapiens_chromosome_22[18232494-18232712]
+c-Myc pd Homo_sapiens_chromosome_22[18235012-18235079]
+c-Myc pd Homo_sapiens_chromosome_22[18239321-18239855]
+c-Myc pd Homo_sapiens_chromosome_22[18254303-18255107]
+c-Myc pd Homo_sapiens_chromosome_22[18257745-18257861]
+c-Myc pd Homo_sapiens_chromosome_22[18264694-18264726]
+c-Myc pd Homo_sapiens_chromosome_22[18266043-18267039]
+c-Myc pd Homo_sapiens_chromosome_22[18270262-18270359]
+c-Myc pd Homo_sapiens_chromosome_22[18282514-18283079]
+c-Myc pd Homo_sapiens_chromosome_22[18297381-18297861]
+c-Myc pd Homo_sapiens_chromosome_22[18299223-18300097]
+c-Myc pd Homo_sapiens_chromosome_22[18312790-18314571]
+c-Myc pd Homo_sapiens_chromosome_22[18318189-18318484]
+c-Myc pd Homo_sapiens_chromosome_22[18321499-18322122]
+c-Myc pd Homo_sapiens_chromosome_22[18326128-18326719]
+c-Myc pd Homo_sapiens_chromosome_22[18339437-18339558]
+c-Myc pd Homo_sapiens_chromosome_22[18341109-18342156]
+c-Myc pd Homo_sapiens_chromosome_22[18343236-18343914]
+c-Myc pd Homo_sapiens_chromosome_22[18345783-18346381]
+c-Myc pd Homo_sapiens_chromosome_22[18347787-18348576]
+c-Myc pd Homo_sapiens_chromosome_22[18359199-18359766]
+c-Myc pd Homo_sapiens_chromosome_22[18363654-18363725]
+c-Myc pd Homo_sapiens_chromosome_22[18366025-18366243]
+c-Myc pd Homo_sapiens_chromosome_22[18369295-18370317]
+c-Myc pd Homo_sapiens_chromosome_22[18372625-18373714]
+c-Myc pd Homo_sapiens_chromosome_22[18418117-18418773]
+c-Myc pd Homo_sapiens_chromosome_22[18458149-18458426]
+c-Myc pd Homo_sapiens_chromosome_22[18472131-18472570]
+c-Myc pd Homo_sapiens_chromosome_22[18568598-18568700]
+c-Myc pd Homo_sapiens_chromosome_22[18582386-18582663]
+c-Myc pd Homo_sapiens_chromosome_22[18682345-18682703]
+c-Myc pd Homo_sapiens_chromosome_22[18693993-18695095]
+c-Myc pd Homo_sapiens_chromosome_22[18699396-18699578]
+c-Myc pd Homo_sapiens_chromosome_22[18756879-18756905]
+c-Myc pd Homo_sapiens_chromosome_22[18819535-18820884]
+c-Myc pd Homo_sapiens_chromosome_22[18837688-18837719]
+c-Myc pd Homo_sapiens_chromosome_22[18869814-18870298]
+c-Myc pd Homo_sapiens_chromosome_22[18919523-18919949]
+c-Myc pd Homo_sapiens_chromosome_22[18920567-18921204]
+c-Myc pd Homo_sapiens_chromosome_22[18938325-18938930]
+c-Myc pd Homo_sapiens_chromosome_22[18973540-18974336]
+c-Myc pd Homo_sapiens_chromosome_22[19028519-19028916]
+c-Myc pd Homo_sapiens_chromosome_22[19249297-19249358]
+c-Myc pd Homo_sapiens_chromosome_22[19263812-19264505]
+c-Myc pd Homo_sapiens_chromosome_22[19363203-19363659]
+c-Myc pd Homo_sapiens_chromosome_22[19374343-19375490]
+c-Myc pd Homo_sapiens_chromosome_22[19406480-19407043]
+c-Myc pd Homo_sapiens_chromosome_22[19429422-19430314]
+c-Myc pd Homo_sapiens_chromosome_22[19456297-19457218]
+c-Myc pd Homo_sapiens_chromosome_22[19481152-19481808]
+c-Myc pd Homo_sapiens_chromosome_22[19566945-19567352]
+c-Myc pd Homo_sapiens_chromosome_22[19574007-19574009]
+c-Myc pd Homo_sapiens_chromosome_22[19597723-19598010]
+c-Myc pd Homo_sapiens_chromosome_22[19646210-19646472]
+c-Myc pd Homo_sapiens_chromosome_22[19661217-19661540]
+c-Myc pd Homo_sapiens_chromosome_22[19672601-19673207]
+c-Myc pd Homo_sapiens_chromosome_22[19674657-19675202]
+c-Myc pd Homo_sapiens_chromosome_22[19677145-19677886]
+c-Myc pd Homo_sapiens_chromosome_22[19678871-19679918]
+c-Myc pd Homo_sapiens_chromosome_22[19681472-19681536]
+c-Myc pd Homo_sapiens_chromosome_22[19692615-19693479]
+c-Myc pd Homo_sapiens_chromosome_22[19694677-19695584]
+c-Myc pd Homo_sapiens_chromosome_22[19707506-19709080]
+c-Myc pd Homo_sapiens_chromosome_22[19726827-19727131]
+c-Myc pd Homo_sapiens_chromosome_22[19787573-19787668]
+c-Myc pd Homo_sapiens_chromosome_22[19890138-19890824]
+c-Myc pd Homo_sapiens_chromosome_22[19899244-19899855]
+c-Myc pd Homo_sapiens_chromosome_22[19942151-19942153]
+c-Myc pd Homo_sapiens_chromosome_22[20000005-20000655]
+c-Myc pd Homo_sapiens_chromosome_22[20076663-20077161]
+c-Myc pd Homo_sapiens_chromosome_22[20160508-20161205]
+c-Myc pd Homo_sapiens_chromosome_22[20245040-20245518]
+c-Myc pd Homo_sapiens_chromosome_22[20257943-20258920]
+c-Myc pd Homo_sapiens_chromosome_22[20260646-20260860]
+c-Myc pd Homo_sapiens_chromosome_22[20262274-20262276]
+c-Myc pd Homo_sapiens_chromosome_22[20266041-20266445]
+c-Myc pd Homo_sapiens_chromosome_22[20331038-20331427]
+c-Myc pd Homo_sapiens_chromosome_22[20351654-20352394]
+c-Myc pd Homo_sapiens_chromosome_22[20353746-20354703]
+c-Myc pd Homo_sapiens_chromosome_22[20356354-20356436]
+c-Myc pd Homo_sapiens_chromosome_22[20358002-20359008]
+c-Myc pd Homo_sapiens_chromosome_22[20360516-20360580]
+c-Myc pd Homo_sapiens_chromosome_22[20429497-20430260]
+c-Myc pd Homo_sapiens_chromosome_22[20467022-20467024]
+c-Myc pd Homo_sapiens_chromosome_22[20472684-20473209]
+c-Myc pd Homo_sapiens_chromosome_22[20492126-20492881]
+c-Myc pd Homo_sapiens_chromosome_22[20497371-20497947]
+c-Myc pd Homo_sapiens_chromosome_22[20498087-20498166]
+c-Myc pd Homo_sapiens_chromosome_22[20510129-20510908]
+c-Myc pd Homo_sapiens_chromosome_22[20515660-20515749]
+c-Myc pd Homo_sapiens_chromosome_22[20518105-20519337]
+c-Myc pd Homo_sapiens_chromosome_22[20521891-20522450]
+c-Myc pd Homo_sapiens_chromosome_22[20614466-20614563]
+c-Myc pd Homo_sapiens_chromosome_22[20619533-20619658]
+c-Myc pd Homo_sapiens_chromosome_22[20622822-20622964]
+c-Myc pd Homo_sapiens_chromosome_22[20629515-20630360]
+c-Myc pd Homo_sapiens_chromosome_22[20710728-20711548]
+c-Myc pd Homo_sapiens_chromosome_22[20752233-20752551]
+c-Myc pd Homo_sapiens_chromosome_22[20825718-20826019]
+c-Myc pd Homo_sapiens_chromosome_22[20933583-20934084]
+c-Myc pd Homo_sapiens_chromosome_22[21004553-21005551]
+c-Myc pd Homo_sapiens_chromosome_22[21012419-21013417]
+c-Myc pd Homo_sapiens_chromosome_22[21036719-21037240]
+c-Myc pd Homo_sapiens_chromosome_22[21068475-21070113]
+c-Myc pd Homo_sapiens_chromosome_22[21246029-21246805]
+c-Myc pd Homo_sapiens_chromosome_22[21254654-21255416]
+c-Myc pd Homo_sapiens_chromosome_22[21334839-21335518]
+c-Myc pd Homo_sapiens_chromosome_22[21336688-21337266]
+c-Myc pd Homo_sapiens_chromosome_22[21337956-21338227]
+c-Myc pd Homo_sapiens_chromosome_22[21347826-21347850]
+c-Myc pd Homo_sapiens_chromosome_22[21349404-21350387]
+c-Myc pd Homo_sapiens_chromosome_22[21351656-21352178]
+c-Myc pd Homo_sapiens_chromosome_22[21354119-21354594]
+c-Myc pd Homo_sapiens_chromosome_22[21356118-21356881]
+c-Myc pd Homo_sapiens_chromosome_22[21363605-21364100]
+c-Myc pd Homo_sapiens_chromosome_22[21500558-21501013]
+c-Myc pd Homo_sapiens_chromosome_22[21646493-21646994]
+c-Myc pd Homo_sapiens_chromosome_22[21655602-21656077]
+c-Myc pd Homo_sapiens_chromosome_22[21696123-21697084]
+c-Myc pd Homo_sapiens_chromosome_22[21715421-21715699]
+c-Myc pd Homo_sapiens_chromosome_22[21724741-21725494]
+c-Myc pd Homo_sapiens_chromosome_22[21726707-21727669]
+c-Myc pd Homo_sapiens_chromosome_22[21736918-21737008]
+c-Myc pd Homo_sapiens_chromosome_22[21738205-21738820]
+c-Myc pd Homo_sapiens_chromosome_22[21740296-21740814]
+c-Myc pd Homo_sapiens_chromosome_22[21742756-21743391]
+c-Myc pd Homo_sapiens_chromosome_22[21744516-21745534]
+c-Myc pd Homo_sapiens_chromosome_22[21747083-21747204]
+c-Myc pd Homo_sapiens_chromosome_22[21963785-21964261]
+c-Myc pd Homo_sapiens_chromosome_22[22372305-22372307]
+c-Myc pd Homo_sapiens_chromosome_22[22372984-22373807]
+c-Myc pd Homo_sapiens_chromosome_22[22409107-22409315]
+c-Myc pd Homo_sapiens_chromosome_22[22496001-22496331]
+c-Myc pd Homo_sapiens_chromosome_22[22497826-22498125]
+c-Myc pd Homo_sapiens_chromosome_22[22510618-22511598]
+c-Myc pd Homo_sapiens_chromosome_22[22528247-22528993]
+c-Myc pd Homo_sapiens_chromosome_22[22655043-22656500]
+c-Myc pd Homo_sapiens_chromosome_22[22747522-22747524]
+c-Myc pd Homo_sapiens_chromosome_22[22782833-22783121]
+c-Myc pd Homo_sapiens_chromosome_22[22842499-22842909]
+c-Myc pd Homo_sapiens_chromosome_22[22945739-22946430]
+c-Myc pd Homo_sapiens_chromosome_22[22966356-22967069]
+c-Myc pd Homo_sapiens_chromosome_22[23469445-23469509]
+c-Myc pd Homo_sapiens_chromosome_22[23520852-23520888]
+c-Myc pd Homo_sapiens_chromosome_22[23571268-23572214]
+c-Myc pd Homo_sapiens_chromosome_22[23671315-23671743]
+c-Myc pd Homo_sapiens_chromosome_22[23682288-23682529]
+c-Myc pd Homo_sapiens_chromosome_22[23740190-23741536]
+c-Myc pd Homo_sapiens_chromosome_22[23763854-23765813]
+c-Myc pd Homo_sapiens_chromosome_22[23917514-23917624]
+c-Myc pd Homo_sapiens_chromosome_22[24358995-24359028]
+c-Myc pd Homo_sapiens_chromosome_22[24840650-24841126]
+c-Myc pd Homo_sapiens_chromosome_22[25010318-25010942]
+c-Myc pd Homo_sapiens_chromosome_22[25011508-25012001]
+c-Myc pd Homo_sapiens_chromosome_22[25197253-25197716]
+c-Myc pd Homo_sapiens_chromosome_22[25204473-25205022]
+c-Myc pd Homo_sapiens_chromosome_22[25534073-25534180]
+c-Myc pd Homo_sapiens_chromosome_22[25786040-25786697]
+c-Myc pd Homo_sapiens_chromosome_22[25834038-25834229]
+c-Myc pd Homo_sapiens_chromosome_22[25836678-25836680]
+c-Myc pd Homo_sapiens_chromosome_22[25892538-25893342]
+c-Myc pd Homo_sapiens_chromosome_22[25894036-25895308]
+c-Myc pd Homo_sapiens_chromosome_22[25902392-25903722]
+c-Myc pd Homo_sapiens_chromosome_22[25913624-25914071]
+c-Myc pd Homo_sapiens_chromosome_22[25974449-25975138]
+c-Myc pd Homo_sapiens_chromosome_22[25989948-25990908]
+c-Myc pd Homo_sapiens_chromosome_22[26012654-26013153]
+c-Myc pd Homo_sapiens_chromosome_22[26061392-26061503]
+c-Myc pd Homo_sapiens_chromosome_22[26118767-26119130]
+c-Myc pd Homo_sapiens_chromosome_22[26259236-26260055]
+c-Myc pd Homo_sapiens_chromosome_22[26295220-26295222]
+c-Myc pd Homo_sapiens_chromosome_22[26295834-26296367]
+c-Myc pd Homo_sapiens_chromosome_22[26360792-26361313]
+c-Myc pd Homo_sapiens_chromosome_22[26395571-26395815]
+c-Myc pd Homo_sapiens_chromosome_22[26454788-26455297]
+c-Myc pd Homo_sapiens_chromosome_22[26672241-26672416]
+c-Myc pd Homo_sapiens_chromosome_22[26724714-26725477]
+c-Myc pd Homo_sapiens_chromosome_22[26834132-26834795]
+c-Myc pd Homo_sapiens_chromosome_22[26859665-26859667]
+c-Myc pd Homo_sapiens_chromosome_22[27099716-27099747]
+c-Myc pd Homo_sapiens_chromosome_22[27354719-27355647]
+c-Myc pd Homo_sapiens_chromosome_22[27357817-27358071]
+c-Myc pd Homo_sapiens_chromosome_22[27367312-27368532]
+c-Myc pd Homo_sapiens_chromosome_22[27369725-27370352]
+c-Myc pd Homo_sapiens_chromosome_22[27398141-27399173]
+c-Myc pd Homo_sapiens_chromosome_22[27420385-27420975]
+c-Myc pd Homo_sapiens_chromosome_22[27499636-27499694]
+c-Myc pd Homo_sapiens_chromosome_22[27515813-27516091]
+c-Myc pd Homo_sapiens_chromosome_22[27516258-27516290]
+c-Myc pd Homo_sapiens_chromosome_22[27517667-27518364]
+c-Myc pd Homo_sapiens_chromosome_22[27683502-27684506]
+c-Myc pd Homo_sapiens_chromosome_22[27797630-27798740]
+c-Myc pd Homo_sapiens_chromosome_22[28241204-28241242]
+c-Myc pd Homo_sapiens_chromosome_22[28378274-28378948]
+c-Myc pd Homo_sapiens_chromosome_22[28445541-28445943]
+c-Myc pd Homo_sapiens_chromosome_22[28491277-28492207]
+c-Myc pd Homo_sapiens_chromosome_22[28582048-28583010]
+c-Myc pd Homo_sapiens_chromosome_22[28711306-28711505]
+c-Myc pd Homo_sapiens_chromosome_22[28753333-28754838]
+c-Myc pd Homo_sapiens_chromosome_22[28841317-28841965]
+c-Myc pd Homo_sapiens_chromosome_22[29037158-29037965]
+c-Myc pd Homo_sapiens_chromosome_22[29143966-29144392]
+c-Myc pd Homo_sapiens_chromosome_22[29503621-29504157]
+c-Myc pd Homo_sapiens_chromosome_22[29752517-29752911]
+c-Myc pd Homo_sapiens_chromosome_22[29853641-29853760]
+c-Myc pd Homo_sapiens_chromosome_22[30422896-30423382]
+c-Myc pd Homo_sapiens_chromosome_22[30696121-30696853]
+c-Myc pd Homo_sapiens_chromosome_22[30941219-30941484]
+c-Myc pd Homo_sapiens_chromosome_22[31506680-31507231]
+c-Myc pd Homo_sapiens_chromosome_22[31691216-31691932]
+c-Myc pd Homo_sapiens_chromosome_22[32115922-32116068]
+c-Myc pd Homo_sapiens_chromosome_22[32206078-32206540]
+c-Myc pd Homo_sapiens_chromosome_22[32391522-32392421]
+c-Myc pd Homo_sapiens_chromosome_22[32402669-32403523]
+c-Myc pd Homo_sapiens_chromosome_22[32422010-32422981]
+c-Myc pd Homo_sapiens_chromosome_22[32491303-32492033]
+c-Myc pd Homo_sapiens_chromosome_22[32654944-32654946]
+c-Myc pd Homo_sapiens_chromosome_22[33105307-33105839]
+c-Myc pd Homo_sapiens_chromosome_22[33170869-33170898]
+c-Myc pd Homo_sapiens_chromosome_22[33200494-33200522]
+c-Myc pd Homo_sapiens_chromosome_22[33277944-33279432]
+c-Myc pd Homo_sapiens_chromosome_22[33368109-33369216]
+c-Myc pd Homo_sapiens_chromosome_22[33370666-33373208]
+c-Myc pd Homo_sapiens_chromosome_22[33445033-33445455]
+c-Myc pd Homo_sapiens_chromosome_22[33462426-33462462]
+c-Myc pd Homo_sapiens_chromosome_22[33462990-33463077]
+c-Myc pd Homo_sapiens_chromosome_22[33490760-33491674]
+c-Myc pd Homo_sapiens_chromosome_22[33539195-33540135]
+c-Myc pd Homo_sapiens_chromosome_22[33704861-33705485]
+c-Myc pd Homo_sapiens_chromosome_22[34007569-34007709]
+c-Myc pd Homo_sapiens_chromosome_22[34495165-34495712]
+c-Myc pd Homo_sapiens_chromosome_22[34572259-34572586]
+c-Myc pd Homo_sapiens_chromosome_22[34617459-34618140]
+c-Myc pd Homo_sapiens_chromosome_22[34668528-34669388]
+c-Myc pd Homo_sapiens_chromosome_22[34696760-34697835]
+c-Myc pd Homo_sapiens_chromosome_22[34778821-34778848]
+c-Myc pd Homo_sapiens_chromosome_22[34813446-34814312]
+c-Myc pd Homo_sapiens_chromosome_22[34854157-34854920]
+c-Myc pd Homo_sapiens_chromosome_22[34859987-34860831]
+c-Myc pd Homo_sapiens_chromosome_22[35191372-35192691]
+c-Myc pd Homo_sapiens_chromosome_22[35276231-35277164]
+c-Myc pd Homo_sapiens_chromosome_22[35280247-35280487]
+c-Myc pd Homo_sapiens_chromosome_22[35326212-35326277]
+c-Myc pd Homo_sapiens_chromosome_22[35491559-35492266]
+c-Myc pd Homo_sapiens_chromosome_22[35515747-35516144]
+c-Myc pd Homo_sapiens_chromosome_22[35523632-35524075]
+c-Myc pd Homo_sapiens_chromosome_22[35579914-35581032]
+c-Myc pd Homo_sapiens_chromosome_22[35666583-35667813]
+c-Myc pd Homo_sapiens_chromosome_22[35715784-35716488]
+c-Myc pd Homo_sapiens_chromosome_22[35763179-35763693]
+c-Myc pd Homo_sapiens_chromosome_22[35764437-35765249]
+c-Myc pd Homo_sapiens_chromosome_22[35879189-35879800]
+c-Myc pd Homo_sapiens_chromosome_22[35971288-35971352]
+c-Myc pd Homo_sapiens_chromosome_22[36001060-36001326]
+c-Myc pd Homo_sapiens_chromosome_22[36031091-36031585]
+c-Myc pd Homo_sapiens_chromosome_22[36051271-36051494]
+c-Myc pd Homo_sapiens_chromosome_22[36087643-36087810]
+c-Myc pd Homo_sapiens_chromosome_22[36323782-36323955]
+c-Myc pd Homo_sapiens_chromosome_22[36328518-36331212]
+c-Myc pd Homo_sapiens_chromosome_22[36399503-36399627]
+c-Myc pd Homo_sapiens_chromosome_22[36530464-36531371]
+c-Myc pd Homo_sapiens_chromosome_22[36544381-36544975]
+c-Myc pd Homo_sapiens_chromosome_22[36629830-36630396]
+c-Myc pd Homo_sapiens_chromosome_22[36937661-36938172]
+c-Myc pd Homo_sapiens_chromosome_22[36947566-36947763]
+c-Myc pd Homo_sapiens_chromosome_22[37020267-37021363]
+c-Myc pd Homo_sapiens_chromosome_22[37046863-37047436]
+c-Myc pd Homo_sapiens_chromosome_22[37054606-37055400]
+c-Myc pd Homo_sapiens_chromosome_22[37055907-37056280]
+c-Myc pd Homo_sapiens_chromosome_22[37259411-37259982]
+c-Myc pd Homo_sapiens_chromosome_22[37275892-37276580]
+c-Myc pd Homo_sapiens_chromosome_22[37335684-37336413]
+c-Myc pd Homo_sapiens_chromosome_22[37355543-37355545]
+c-Myc pd Homo_sapiens_chromosome_22[37473793-37473795]
+c-Myc pd Homo_sapiens_chromosome_22[37659551-37659821]
+c-Myc pd Homo_sapiens_chromosome_22[37725352-37725354]
+c-Myc pd Homo_sapiens_chromosome_22[37742160-37742373]
+c-Myc pd Homo_sapiens_chromosome_22[37829324-37829326]
+c-Myc pd Homo_sapiens_chromosome_22[37867602-37867694]
+c-Myc pd Homo_sapiens_chromosome_22[37962096-37962955]
+c-Myc pd Homo_sapiens_chromosome_22[38101208-38101816]
+c-Myc pd Homo_sapiens_chromosome_22[38215649-38216278]
+c-Myc pd Homo_sapiens_chromosome_22[38296713-38297177]
+c-Myc pd Homo_sapiens_chromosome_22[38390467-38390990]
+c-Myc pd Homo_sapiens_chromosome_22[38412347-38412349]
+c-Myc pd Homo_sapiens_chromosome_22[38478963-38480135]
+c-Myc pd Homo_sapiens_chromosome_22[38631689-38632677]
+c-Myc pd Homo_sapiens_chromosome_22[38692422-38693197]
+c-Myc pd Homo_sapiens_chromosome_22[38698423-38699590]
+c-Myc pd Homo_sapiens_chromosome_22[38884082-38884628]
+c-Myc pd Homo_sapiens_chromosome_22[39090360-39091096]
+c-Myc pd Homo_sapiens_chromosome_22[39101198-39101415]
+c-Myc pd Homo_sapiens_chromosome_22[39167221-39167370]
+c-Myc pd Homo_sapiens_chromosome_22[39177911-39178666]
+c-Myc pd Homo_sapiens_chromosome_22[39284591-39284593]
+c-Myc pd Homo_sapiens_chromosome_22[39322680-39323502]
+c-Myc pd Homo_sapiens_chromosome_22[39442713-39442993]
+c-Myc pd Homo_sapiens_chromosome_22[39479561-39479711]
+c-Myc pd Homo_sapiens_chromosome_22[39493950-39494311]
+c-Myc pd Homo_sapiens_chromosome_22[39535578-39535947]
+c-Myc pd Homo_sapiens_chromosome_22[39613260-39614272]
+c-Myc pd Homo_sapiens_chromosome_22[40002833-40003148]
+c-Myc pd Homo_sapiens_chromosome_22[40051665-40051870]
+c-Myc pd Homo_sapiens_chromosome_22[40261733-40262381]
+c-Myc pd Homo_sapiens_chromosome_22[40344966-40344993]
+c-Myc pd Homo_sapiens_chromosome_22[40346050-40346606]
+c-Myc pd Homo_sapiens_chromosome_22[40563323-40563853]
+c-Myc pd Homo_sapiens_chromosome_22[40627219-40627673]
+c-Myc pd Homo_sapiens_chromosome_22[40731504-40731962]
+c-Myc pd Homo_sapiens_chromosome_22[40967305-40968080]
+c-Myc pd Homo_sapiens_chromosome_22[40988314-40988575]
+c-Myc pd Homo_sapiens_chromosome_22[41125341-41128387]
+c-Myc pd Homo_sapiens_chromosome_22[41171282-41171947]
+c-Myc pd Homo_sapiens_chromosome_22[41486883-41487161]
+c-Myc pd Homo_sapiens_chromosome_22[41902562-41903327]
+c-Myc pd Homo_sapiens_chromosome_22[41962445-41962648]
+c-Myc pd Homo_sapiens_chromosome_22[42004478-42004480]
+c-Myc pd Homo_sapiens_chromosome_22[42029201-42029460]
+c-Myc pd Homo_sapiens_chromosome_22[42115050-42115461]
+c-Myc pd Homo_sapiens_chromosome_22[42132981-42133121]
+c-Myc pd Homo_sapiens_chromosome_22[42272447-42272920]
+c-Myc pd Homo_sapiens_chromosome_22[42324192-42324708]
+c-Myc pd Homo_sapiens_chromosome_22[42443962-42444179]
+c-Myc pd Homo_sapiens_chromosome_22[43057492-43058094]
+c-Myc pd Homo_sapiens_chromosome_22[43200263-43200756]
+c-Myc pd Homo_sapiens_chromosome_22[43201929-43202632]
+c-Myc pd Homo_sapiens_chromosome_22[43205761-43205763]
+c-Myc pd Homo_sapiens_chromosome_22[43216336-43217023]
+c-Myc pd Homo_sapiens_chromosome_22[43276231-43276727]
+c-Myc pd Homo_sapiens_chromosome_22[43426309-43426499]
+c-Myc pd Homo_sapiens_chromosome_22[43528968-43529177]
+c-Myc pd Homo_sapiens_chromosome_22[43554310-43555488]
+c-Myc pd Homo_sapiens_chromosome_22[43566875-43567348]
+c-Myc pd Homo_sapiens_chromosome_22[43593227-43594484]
+c-Myc pd Homo_sapiens_chromosome_22[43724243-43724980]
+c-Myc pd Homo_sapiens_chromosome_22[43793185-43793187]
+c-Myc pd Homo_sapiens_chromosome_22[43894260-43894568]
+c-Myc pd Homo_sapiens_chromosome_22[43913554-43914306]
+c-Myc pd Homo_sapiens_chromosome_22[43968236-43968271]
+c-Myc pd Homo_sapiens_chromosome_22[43975849-43975851]
+c-Myc pd Homo_sapiens_chromosome_22[44007799-44007919]
+c-Myc pd Homo_sapiens_chromosome_22[44085509-44086093]
+c-Myc pd Homo_sapiens_chromosome_22[44102171-44102173]
+c-Myc pd Homo_sapiens_chromosome_22[44173094-44175664]
+c-Myc pd Homo_sapiens_chromosome_22[44367176-44367949]
+c-Myc pd Homo_sapiens_chromosome_22[44723129-44723825]
+c-Myc pd Homo_sapiens_chromosome_22[46141067-46141107]
+c-Myc pd Homo_sapiens_chromosome_22[46177089-46177510]
+c-Myc pd Homo_sapiens_chromosome_22[46315784-46316785]
+c-Myc pd Homo_sapiens_chromosome_22[46369073-46371305]
+c-Myc pd Homo_sapiens_chromosome_22[46484640-46485476]
+c-Myc pd Homo_sapiens_chromosome_22[46486336-46486978]
+c-Myc pd Homo_sapiens_chromosome_22[46566790-46567713]
+c-Myc pd Homo_sapiens_chromosome_22[46638522-46638977]
+c-Myc pd Homo_sapiens_chromosome_22[46708591-46709009]
+c-Myc pd Homo_sapiens_chromosome_22[46772741-46773764]
+c-Myc pd Homo_sapiens_chromosome_22[46775547-46775549]
+c-Myc pd Homo_sapiens_chromosome_22[46808582-46809040]
+c-Myc pd Homo_sapiens_chromosome_22[46837054-46837894]
+c-Myc pd Homo_sapiens_chromosome_22[47017755-47019005]
+c-Myc pd Homo_sapiens_chromosome_22[47029559-47030132]
+c-Myc pd Homo_sapiens_chromosome_22[47079299-47079462]
+c-Myc pd Homo_sapiens_chromosome_22[47180996-47181653]
+c-Myc pd Homo_sapiens_chromosome_22[47233589-47234978]
+c-Myc pd Homo_sapiens_chromosome_22[47415878-47415938]
+c-Myc pd Homo_sapiens_chromosome_22[47440340-47440419]
+c-Myc pd Homo_sapiens_chromosome_22[47450831-47451321]
+c-Myc pd Homo_sapiens_chromosome_22[47524763-47524765]
+c-Myc pd Homo_sapiens_chromosome_22[47563774-47564256]
+c-Myc pd Homo_sapiens_chromosome_22[47627721-47629326]
+c-Myc pd Homo_sapiens_chromosome_22[47725948-47726565]
+p53 pd Homo_sapiens_chromosome_21[7777422-7778164]
+p53 pd Homo_sapiens_chromosome_21[13095905-13095907]
+p53 pd Homo_sapiens_chromosome_21[13201179-13201342]
+p53 pd Homo_sapiens_chromosome_21[15644161-15644444]
+p53 pd Homo_sapiens_chromosome_21[15704123-15704534]
+p53 pd Homo_sapiens_chromosome_21[24341113-24341795]
+p53 pd Homo_sapiens_chromosome_21[32624413-32625308]
+p53 pd Homo_sapiens_chromosome_21[32757889-32757891]
+p53 pd Homo_sapiens_chromosome_21[35012919-35013259]
+p53 pd Homo_sapiens_chromosome_21[36955421-36955516]
+p53 pd Homo_sapiens_chromosome_21[42029224-42029541]
+p53 pd Homo_sapiens_chromosome_21[42479100-42479412]
+p53 pd Homo_sapiens_chromosome_21[42639820-42639937]
+p53 pd Homo_sapiens_chromosome_21[43456807-43457267]
+p53 pd Homo_sapiens_chromosome_21[43561881-43563309]
+p53 pd Homo_sapiens_chromosome_21[43850963-43851338]
+p53 pd Homo_sapiens_chromosome_21[43985672-43987006]
+p53 pd Homo_sapiens_chromosome_22[14149990-14150718]
+p53 pd Homo_sapiens_chromosome_22[17412277-17412957]
+p53 pd Homo_sapiens_chromosome_22[17413900-17413953]
+p53 pd Homo_sapiens_chromosome_22[17414716-17414804]
+p53 pd Homo_sapiens_chromosome_22[17415717-17416832]
+p53 pd Homo_sapiens_chromosome_22[20466384-20466386]
+p53 pd Homo_sapiens_chromosome_22[20863952-20865398]
+p53 pd Homo_sapiens_chromosome_22[23585627-23585629]
+p53 pd Homo_sapiens_chromosome_22[24185870-24186236]
+p53 pd Homo_sapiens_chromosome_22[24812030-24812055]
+p53 pd Homo_sapiens_chromosome_22[25990340-25990939]
+p53 pd Homo_sapiens_chromosome_22[26074667-26076071]
+p53 pd Homo_sapiens_chromosome_22[27168976-27169138]
+p53 pd Homo_sapiens_chromosome_22[28269273-28270199]
+p53 pd Homo_sapiens_chromosome_22[28345907-28346383]
+p53 pd Homo_sapiens_chromosome_22[28775095-28775763]
+p53 pd Homo_sapiens_chromosome_22[30674064-30674066]
+p53 pd Homo_sapiens_chromosome_22[31339698-31339700]
+p53 pd Homo_sapiens_chromosome_22[34442232-34442990]
+p53 pd Homo_sapiens_chromosome_22[34909224-34909744]
+p53 pd Homo_sapiens_chromosome_22[35222332-35222485]
+p53 pd Homo_sapiens_chromosome_22[39803538-39803540]
+p53 pd Homo_sapiens_chromosome_22[41393135-41393724]
+p53 pd Homo_sapiens_chromosome_22[43543244-43543382]
+p53 pd Homo_sapiens_chromosome_22[43593599-43594246]
+p53 pd Homo_sapiens_chromosome_22[43983327-43984008]
+p53 pd Homo_sapiens_chromosome_22[44092024-44092143]
+p53 pd Homo_sapiens_chromosome_22[44367757-44367804]
+p53 pd Homo_sapiens_chromosome_22[47136975-47137715]
+p53 pd Homo_sapiens_chromosome_22[47580618-47580852]
+p53 pd Homo_sapiens_chromosome_22[47690635-47691379]
+cFos pp cJun
+pRB pp E2F1
+cJun pp cJun
+p107 pp E2F4
+E2F1 pp DP1
+IRF3 pd p-IP-10
+SA2 interactsWith Unknown
+Unknown interactsWith Smc1
+Unknown interactsWith Smc3
+Unknown interactsWith Scc1
+SSBP1 pp SSBP1
+HBE1 pp HBA2
+HBA2 pp HBE1
+HBE1 pp HBA2
+F2 pp Alpha_Thrombin
+ITGA2 pp ITGA2
+p300 pd p-IP-10
+p65 pd p-IP-10
+MYD118 pp PCNA
+GADD45 pp PCNA
+RRAGA pp RRAGC
+RRAGA pp RRAGD
+hMSH4-hMSH5 interactsWith Holliday_Junction
+hMSH2-hMSH6 interactsWith Holliday_Junction
+hMSH2-hMSH6 interactsWith DNA_with_G/T_mismatch
+hMSH2-hMSH6 interactsWith Y_Junction_DNA
+TRAF4 pp HCR
+TRAF4 pp VRP
+TRAF4 pp MAGE
+TRAF4 pp BCKDK
+IR-beta pp JAK-1
+IGF-1R-beta pp JAK-1
+Annexin_VI pp GAP
+Cdc27 interactsWith Unknown
+Unknown interactsWith APC1
+Unknown interactsWith APC4
+DCC pp Siah-2
+DCC pp Siah-1
+Ubc9 pp Siah-1
+Ubc9 pp Siah-2
+Unknown interactsWith APC7
+Unknown interactsWith APC2
+Unknown interactsWith APC5
+Unknown interactsWith CDC16
+Unknown interactsWith CDC23
+PrPc pp HSPD1
+YY1 pp ATFa2
+ST-2-beta pp ST-2-beta
+YY1 pp ATFa3
+YY1 pp CREB
+ASC-2 pp C/EBP_alpha
+TC10 pp WASP
+Cdc42 pp WASP
+CHIP pp Hsc70
+Hsp40 pp Hsc70
+YY1 pp ATF-2
+MBD1 pp SETDB1
+MBD1 pp CAF-1
+SETDB1 pp CAF-1
+hPop1 pp Rpp25
+hPop1 pp hPop1
+hPop4 pp hPop4
+Rpp38 pp hPop1
+Rpp38 pp hPop4
+hPop4 pp Rpp25
+hPop5 pp hPop4
+hPop1 pp hPop4
+PDS5 interactsWith 14S_cohesin_complex
+PDS5 interactsWith 14S_cohesin_complex
+E2F-4 pp p130
+E2F-4 pp DP-1
+E2F-5 pp p130
+E2F-5 pp DP-1
+E2F-1 pp p130
+E2F-1 pd MYC_P2_promoter
+E2F-4 pd MYC_P2_promoter
+E2F-5 pd MYC_P2_promoter
+Mcm2 pp Mcm5
+Mcm2 pp Mcm6
+Mcm3 pp Mcm5
+Mcm3 pp Mcm7
+Mcm4 pp Mcm6
+Mcm4 pp Mcm7
+Mcm6 pp Mcm6
+Mcm7 pp Mcm7
+beta-catenin pp LRH-1
+TRPC3 pp VAMP2
+TRPC3 pp alpha-SNAP
+DNMT1 pp HDAC2
+DNMT1 pp DMAP1
+Bax pp MAP-1
+MAP-1 pp MAP-1
+MAP-1 pp Bcl-XL
+MAP-1 pp Bcl-2
+Bax pp Bcl-XL
+C/EBP-alpha pp C/EBP-alpha
+C/EBP-alpha pp C/EBP-beta
+C/EBP-alpha pp C/EBP-gamma
+C/EBP-alpha pp C/EBP-delta
+C/EBP-epsilon pp C/EBP-alpha
+C/EBP-alpha pp CHOP
+ATF-7 pp C/EBP-alpha
+CREBPA pp C/EBP-alpha
+C/EBP-alpha pp ATF-4
+C/EBP-alpha pp ATF-5
+B-ATF pp C/EBP-alpha
+p21SNFT pp C/EBP-alpha
+C/EBP-beta pp C/EBP-beta
+C/EBP-beta pp C/EBP-gamma
+C/EBP-beta pp C/EBP-delta
+C/EBP-beta pp C/EBP-epsilon
+C/EBP-beta pp CHOP
+C/EBP-beta pp HP8
+C/EBP-beta pp ATF-7
+CREBPA pp C/EBP-beta
+C/EBP-beta pp ATF-4
+C/EBP-beta pp ATF-5
+C/EBP-beta pp B-ATF
+C/EBP-beta pp p21SNFT
+C/EBP-beta pp DBP
+C/EBP-gamma pp C/EBP-delta
+C/EBP-gamma pp C/EBP-epsilon
+C/EBP-gamma pp CHOP
+C/EBP-gamma pp HP8
+C/EBP-gamma pp OASIS
+C/EBP-gamma pp CREB-H
+C/EBP-gamma pp CREB3
+C/EBP-gamma pp CREB4
+C/EBP-gamma pp E4BP4
+C/EBP-gamma pp ATF-2
+C/EBP-gamma pp ATF-7
+C/EBP-gamma pp CREBPA
+C/EBP-gamma pp Fos
+C/EBP-gamma pp Fra1
+C/EBP-gamma pp Fra2
+C/EBP-gamma pp ATF-3
+C/EBP-gamma pp ATF-4
+C/EBP-gamma pp ATF-4L1
+C/EBP-gamma pp ATF-5
+C/EBP-gamma pp B-ATF
+C/EBP-gamma pp p21SNFT
+C/EBP-gamma pp DBP
+C/EBP-gamma pp HLF
+C/EBP-gamma pp TEF
+C/EBP-gamma pp MafK
+C/EBP-delta pp C/EBP-delta
+C/EBP-delta pp C/EBP-epsilon
+C/EBP-delta pp CHOP
+C/EBP-delta pp HP8
+C/EBP-delta pp ATF-4
+C/EBP-delta pp ATF-5
+C/EBP-delta pp B-ATF
+p21SNFT pp C/EBP-delta
+C/EBP-epsilon pp C/EBP-epsilon
+C/EBP-epsilon pp CHOP
+CREBPA pp C/EBP-epsilon
+cJun pp C/EBP-epsilon
+C/EBP-epsilon pp ATF-4
+B-ATF pp C/EBP-epsilon
+p21SNFT pp C/EBP-epsilon
+CHOP pp CHOP
+CHOP pp HP8
+CHOP pp CREB3
+CHOP pp E4BP4
+CHOP pp ATF-2
+CHOP pp ATF-7
+CHOP pp CREBPA
+CHOP pp Fos
+CHOP pp FosB
+CHOP pp Fra1
+CHOP pp Fra2
+CHOP pp ATF-3
+CHOP pp ATF-4
+CHOP pp B-ATF
+CHOP pp p21SNFT
+CHOP pp DBP
+CHOP pp HLF
+CHOP pp TEF
+CHOP pp MafG
+CHOP pp MafK
+CREBPA pp HP8
+HP8 pp ATF-4
+p21SNFT pp HP8
+ATF-1 pp ATF-1
+ATF-1 pp CREM-Ia
+ATF-1 pp CREM-Ia(K324R)
+ATF-1 pp CREM-Ib
+ATF-1 pp CREB-delta
+ATF-1 pp E4BP4
+BACH1 pp ATF-1
+CREM-Ia pp CREM-Ia
+CREM-Ia pp CREM-Ia(K324R)
+CREM-Ia pp CREM-Ib
+CREM-Ia pp CREB-delta
+CREM-Ia pp OASIS
+CREM-Ia pp CREB-H
+CREM-Ia pp E4BP4
+BACH1 pp CREM-Ia
+CREM-Ia(K324R) pp CREM-Ia(K324R)
+CREM-Ia(K324R) pp CREM-Ib
+CREM-Ia(K324R) pp CREB-delta
+CREM-Ia(K324R) pp OASIS
+CREM-Ia(K324R) pp CREB-H
+CREM-Ia(K324R) pp E4BP4
+CREM-Ib pp CREM-Ib
+CREM-Ib pp CREB-delta
+cJun pp CREM-Ib
+BACH1 pp CREM-Ib
+CREB-delta pp CREB-delta
+CREB-delta pp E4BP4
+OASIS pp OASIS
+OASIS pp CREB-H
+OASIS pp CREB3
+OASIS pp CREB4
+OASIS pp E4BP4
+p21SNFT pp OASIS
+OASIS pp NFE2-p45
+CREB-H pp CREB-H
+CREB3 pp CREB-H
+CREB-H pp CREB4
+CREB-H pp E4BP4
+p21SNFT pp CREB-H
+CREB3 pp CREB3
+CREB3 pp CREB4
+CREB3 pp E4BP4
+CREBPA pp CREB3
+p21SNFT pp CREB3
+CREB3 pp MafK
+CREB4 pp CREB4
+p21SNFT pp CREB4
+ATF-6 pp ATF-6
+ZF pp ATF-6
+ATF-6 pp XBP-1
+ZF pp ZF
+ZF pp XBP-1
+CREBPA pp ZF
+cJun pp ZF
+ZF pp ATF-4
+ZF pp NFE2-p45
+NFE2L1 pp ZF
+XBP-1 pp XBP-1
+E4BP4 pp E4BP4
+B-ATF pp E4BP4
+p21SNFT pp E4BP4
+ATF-2 pp ATF-7
+CREBPA pp ATF-2
+ATF-2 pp cJun
+ATF-2 pp JunB
+ATF-2 pp JunD
+ATF-2 pp Fos
+ATF-2 pp FosB
+Fra1 pp ATF-2
+ATF-2 pp Fra2
+ATF-2 pp ATF-3
+B-ATF pp ATF-2
+p21SNFT pp ATF-2
+BACH1 pp ATF-2
+ATF-7 pp ATF-7
+ATF-7 pp CREBPA
+ATF-7 pp cJun
+ATF-7 pp JunB
+ATF-7 pp JunD
+ATF-7 pp Fos
+ATF-7 pp FosB
+ATF-7 pp Fra1
+ATF-7 pp Fra2
+ATF-7 pp ATF-3
+ATF-7 pp ATF-4
+ATF-7 pp p21SNFT
+ATF-7 pp MafG
+ATF-7 pp MafK
+BACH1 pp ATF-7
+ATF-7 pp BACH2
+CREBPA pp CREBPA
+CREBPA pp cJun
+CREBPA pp JunB
+CREBPA pp JunD
+CREBPA pp Fos
+CREBPA pp FosB
+CREBPA pp Fra1
+CREBPA pp Fra2
+CREBPA pp ATF-3
+CREBPA pp ATF-4
+CREBPA pp B-ATF
+CREBPA pp p21SNFT
+CREBPA pp MafG
+CREBPA pp MafK
+CREBPA pp NFE2-p45
+CREBPA pp NFE2L1
+CREBPA pp BACH1
+CREBPA pp BACH2
+cJun pp cJun
+cJun pp JunD
+cJun pp Fos
+cJun pp FosB
+cJun pp Fra1
+cJun pp Fra2
+cJun pp ATF-3
+cJun pp B-ATF
+cJun pp p21SNFT
+cJun pp DBP
+cJun pp HLF
+MafG pp cJun
+cJun pp MafK
+cJun pp NFE2L2
+cJun pp BACH2
+JunB pp Fos
+JunB pp FosB
+JunB pp Fra1
+JunB pp Fra2
+JunB pp ATF-3
+JunB pp B-ATF
+JunB pp p21SNFT
+MafG pp JunB
+JunB pp MafK
+JunD pp Fos
+JunD pp FosB
+JunD pp Fra1
+JunD pp Fra2
+JunD pp ATF-3
+JunD pp B-ATF
+JunD pp p21SNFT
+JunD pp HLF
+JunD pp MafK
+Fra2 pp Fos
+Fos pp ATF-4
+Fos pp MafB
+Fra1 pp FosB
+FosB pp ATF-4
+FosB pp MafB
+Fra1 pp MafB
+TEF pp Fra2
+Fra2 pp MafB
+ATF-3 pp ATF-4
+p21SNFT pp ATF-3
+ATF-4 pp B-ATF
+ATF-4 pp p21SNFT
+ATF-4 pp HLF
+ATF-4 pp cMaf
+ATF-4 pp NFE2L1
+ATF-5 pp B-ATF
+p21SNFT pp ATF-5
+p21SNFT pp B-ATF
+B-ATF pp DBP
+B-ATF pp HLF
+B-ATF pp TEF
+p21SNFT pp p21SNFT
+p21SNFT pp DBP
+p21SNFT pp HLF
+p21SNFT pp TEF
+p21SNFT pp MafG
+p21SNFT pp MafK
+DBP pp DBP
+DBP pp HLF
+DBP pp TEF
+HLF pp HLF
+HLF pp TEF
+TEF pp TEF
+MafG pp MafG
+MafG pp MafK
+MafG pp NFE2-p45
+MafG pp NFE2L1
+MafG pp NFE2L2
+MafG pp NFE2L3
+MafG pp BACH1
+MafG pp BACH2
+MafK pp NFE2-p45
+MafK pp NFE2L1
+MafK pp NFE2L2
+MafK pp NFE2L3
+MafK pp BACH1
+MafK pp BACH2
+cMaf pp cMaf
+cMaf pp MafB
+cMaf pp BACH1
+MafB pp MafB
+NFE2L1 pp MafB
+MafB pp BACH1
+MafB pp BACH2
+NFE2-p45 pp NFE2-p45
+NFE2-p45 pp NFE2L2
+NFE2-p45 pp NFE2L3
+DDB1 pp CDT1
+DDB1 pp CUL4A
+ROC1 pp Cul4A
+HSF1 pp CBP
+ASC-2 pp HSF1
+Pin1 pp Cdc27
+p230 pp MACF1
+EphA7 pp ST-1
+Neurexin_I-alpha pp ST-1
+PAD4 pd p-pS2
+YY1 pp RPD3
+YY1 pp Sp1
+TRAF1 pp CD30
+CRAF1 pp CD30
+PAD4 pp H3
+PAD4 pp H4
+H4 pd p-pS2
+E2F-1 pp pRb
+E2F-2 pp pRb
+LC8 pp LC8
+DIC pp LC8
+DIC pp RP3
+DIC pp Tctex1
+LIG4 pp XRCC4
+LIG4-XRCC4_complex interactsWith DNA-PK
+E2F4 pd H2A
+E2F4 pd H2B
+PADI4 pd pS2
+TNF-alpha pp TNFR-1
+TRAF2 pp TNF-R2
+TRAF2 pp TRAF1
+TRAF2 pp TRADD
+p50 pp p65
+TRAF2 pp RIP
+TAB3 pp NEMO
+TAB3 pp TRAF6
+PPM1D pp UNG2
+NEK1 pp alpha-catulin
+NEK1 pp Tuberin
+ER-alpha pp STAT5a
+snail pp GSK-3beta
+GRIP1 pp VDR
+GRIP1 pp RXR
+GRIP1 pp RAR
+GRIP1 pp p300
+TR-beta pp pp32
+RAR-alpha pp pp32
+E2F-1/DP-1 interactsWith MYC_P2_promoter
+E2F-4/DP-1 interactsWith MYC_P2_promoter
+E2F-5/DP-1 interactsWith MYC_P2_promoter
+SMYD3 pp HSP90A
+F13A1 pp F13A1
+Translin pp Translin
+Translin pp Translin
+Translin pp Translin
+Translin pp Translin
+HBA2 pp HBA2
+HBB pp HBB
+CCNA1 pp CDK2
+Ala-Ala-Aba-Arg-Ser-Leu-Ile-Pff-Nh2 pp CCNA1
+CCNA1 pp CDK2
+h-Arg-Arg-Leu-Ile-Phe-Nh2 pp CCNA1
+CCNA1 pp CDK2
+CCNA1 pp CDK2
+CDK2 pp CCNA1
+CCNA1 pp CDK2
+CCNA1 pp CDK2
+CCNA1 pp CDK2
+CCNA1 pp CDK2
+9-Residue_Influenza_Virus_Hemagglutinin_Related_Peptide_Fvkqna(Maa)al pp HLA-DRB4
+Bit1 pp Bit1
+TREM1 pp TREM1
+TREM1 pp TREM1
+TREM1 pp TREM1
+SOS1 pp SOS1
+SOS1 pp SOS1
+SOS1 pp SOS1
+SOS1 pp SOS1
+SOS1 pp SOS1
+SOS1 pp SOS1
+SOS1 pp SOS1
+SOS1 pp SOS1
+SOS1 pp SOS1
+SOS1 pp SOS1
+SOS1 pp SOS1
+BCL6 pp BCL6
+BCL6 pp BCL6
+Nuclear_Receptor_Co-Repressor_2 pp BCL6
+Nuclear_Receptor_Co-Repressor_2 pp BCL6
+Nuclear_Receptor_Co-Repressor_2 pp BCL6
+UBE1C pp APPBP1
+Ubiquitin-Like_Protein_Nedd8 pp UBE1C
+Ubiquitin-Like_Protein_Nedd8 pp APPBP1
+UBE1C pp APPBP1
+Ubiquitin-Like_Protein_Nedd8 pp UBE1C
+Ubiquitin-Like_Protein_Nedd8 pp APPBP1
+WARS pp WARS
+WARS pp WARS
+GBF1 pp ARF6
+EDA pp EDA
+EDA pp EDA
+EDA pp EDA
+EDA pp EDA
+EDA pp EDA
+PDE4C pp PDE4C
+PDE4C pp PDE4C
+PDE4C pp PDE4C
+PDE4C pp PDE4C
+PDE4C pp PDE4C
+Sterol_Regulatory_Element_Binding_Protein-2 pp KPNB1
+Sterol_Regulatory_Element_Binding_Protein-2 pp KPNB1
+Sterol_Regulatory_Element_Binding_Protein-2 pp Sterol_Regulatory_Element_Binding_Protein-2
+Galectin-1 pp LGALS2
+SUFU pp SUFU
+SUFU pp SUFU
+Anti-Factor_Ix_Antibody,_10c12,_Chain_H pp IGLL1
+Factor_Ix pp IGLL1
+Factor_Ix pp Anti-Factor_Ix_Antibody,_10c12,_Chain_H
+PVR pp PVR
+PVR pp PVR
+PVR pp PVR
+SOX2 pp POU2F1
+Immunoglobulin_E pp Thioredoxin_1
+Immunoglobulin_E pp Thioredoxin_1
+Vasoactive_Intestinal_Polypeptide_Receptor_1 pp HLA-A
+B2M pp HLA-A
+RAB11A pp RAB11A
+DAF pp DAF
+DAF pp DAF
+DAF pp DAF
+DAF pp DAF
+DAF pp DAF
+CRYBB1 pp CRYBB1
+TMPRSS3 pp HPN
+Mad1 pp Sin3b_Protein
+Collagen_Alfa_1(I)_Chain_Peptide_Gpogpogfogergpogpogpo pp Collagen_Alfa_1(I)_Chain_Peptide_Gpogpogfogergpogpogpo
+Collagen_Alfa_1(I)_Chain_Peptide_Gpogpogfogergpogpogpo pp Collagen_Alfa_1(I)_Chain_Peptide_Gpogpogfogergpogpogpo
+Collagen_Alfa_1(I)_Chain_Peptide_Gpogpogfogergpogpogpo pp Collagen_Alfa_1(I)_Chain_Peptide_Gpogpogfogergpogpogpo
+ACY1 pp ACY1
+ACY1 pp ACY1
+ACY1 pp ACY1
+ACY1 pp ACY1
+ACY1 pp ACY1
+Golgi_Autoantigen,_Golgin_Subfamily_A_Member_4 pp ARL1
+Golgi_Autoantigen,_Golgin_Subfamily_A_Member_4 pp Golgi_Autoantigen,_Golgin_Subfamily_A_Member_4
+Golgi_Autoantigen,_Golgin_Subfamily_A_Member_4 pp Golgi_Autoantigen,_Golgin_Subfamily_A_Member_4
+Golgi_Autoantigen,_Golgin_Subfamily_A_Member_4 pp Golgi_Autoantigen,_Golgin_Subfamily_A_Member_4
+PSCD2 pp ARF6
+Vcl_Protein pp VCL
+VEGF pp VEGF
+FLT1 pp VEGF
+FLT1 pp VEGF
+FLT1 pp VEGF
+FLT1 pp VEGF
+RAC2 pp RAC2
+RAC2 pp RAC2
+Fab_48d_Heavy_Chain pp Fab_48d_Light_Chain
+Fab_17b_Heavy_Chain pp Fab_17b_Light_Chain
+Fab_E51_Heavy_Chain pp IGLL1
+Fab_412d_Heavy_Chain pp Fab_412d_Light_Chain
+Fab_412d_Light_Chain pp Fab_412d_Light_Chain
+Fab_412d_Heavy_Chain pp Fab_412d_Light_Chain
+Fab_412d_Heavy_Chain pp Fab_412d_Light_Chain
+Fab_47e_Heavy_Chain pp Fab_47e_Light_Chain
+Antibody_17b,_Heavy_Chain pp Antibody_17b,_Light_Chain
+WARS pp WARS
+Ste-20_Related_Adaptor pp Mo25_Protein
+CDC37L1 pp HSPCA
+1GTW_C pd CEBPB
+1GTW_C pd CEBPB
+1GTW_D pd CEBPB
+1GTW_D pd CEBPB
+ETS1 pp ETS1
+1M3Q_B pd OGG1
+1M3Q_C pd OGG1
+HBB pp HBB
+NFATC2 pp NFATC2
+1OWR_B pd NFATC2
+ATIC pp ATIC
+SORD pp SORD
+SORD pp SORD
+SORD pp SORD
+SORD pp SORD
+SORD pp SORD
+SORD pp SORD
+Fab_447-52d,_Heavy_Chain pp IGLL1
+F2 pp Thrombin_Light_Chain
+F2 pp Thrombin_Light_Chain
+Fibrin_Alpha-E_Chain pp F2
+Fibrin_Beta_Chain pp Fibrin_Alpha-E_Chain
+Fibrin_Beta_Chain pp F2
+Fibrinogen_Gamma_Chain pp Fibrin_Beta_Chain
+Fibrinogen_Gamma_Chain pp Fibrin_Alpha-E_Chain
+Fibrin_Alpha-E_Chain pp Fibrin_Beta_Chain
+Fibrin_Alpha-E_Chain pp F2
+Fibrin_Beta_Chain pp Fibrin_Alpha-E_Chain
+Fibrin_Beta_Chain pp Fibrin_Alpha-E_Chain
+Fibrinogen_Gamma_Chain pp Fibrinogen_Gamma_Chain
+Fibrinogen_Gamma_Chain pp Fibrin_Beta_Chain
+Fibrinogen_Gamma_Chain pp Fibrin_Beta_Chain
+Fibrinogen_Gamma_Chain pp Fibrin_Alpha-E_Chain
+TDP1 pp TDP1
+Topoisomerase_I-Derived_Peptide pp TDP1
+FGFR3 pp FGF1
+POLL pp POLL
+Rho-Associated,_Coiled-Coil_Containing_Protein_Kinase_1 pp RHOA
+Rho-Associated,_Coiled-Coil_Containing_Protein_Kinase_1 pp RHOA
+Rho-Associated,_Coiled-Coil_Containing_Protein_Kinase_1 pp Rho-Associated,_Coiled-Coil_Containing_Protein_Kinase_1
+PSCD2 pp ARF6
+HLA-DQB1 pp HLA-DOA
+26s_Proteasome_Non-Atpase_Regulatory_Subunit_4 pp RAD23B
+CENPB pp CENPB
+Thrombopoietin pp Monoclonal_Tn1_Fab_Light_Chain
+Thrombopoietin pp Monoclonal_Tn1_Fab_Light_Chain
+Thrombopoietin pp Monoclonal_Tn1_Fab_Heavy_Chain
+HLA-DQB1 pp HLA-DQA1
+Orexin pp HLA-DQA1
+Orexin pp HLA-DQB1
+Hla_Dpa0201_Peptide pp AZGP1
+Immunoglobulin pp Immunoglobulin
+Splicing_Factor_Sf1 pp Splicing_Factor_U2af_65_Kda_Subunit
+ATIC pp ATIC
+TFF3 pp TFF3
+MMP10 pp MMP10
+MMP10 pp MMP10
+MMP10 pp MMP10
+Beta-2-Microglobulin pp Mhc_H2-Tl-T10-129
+Alpha-Galactosidase_A pp Alpha-Galactosidase_A
+Alpha-Galactosidase_A pp Alpha-Galactosidase_A
+HLA-DRB4 pp HLA-DOA
+EP300 pp CbpP300-Interacting_Transactivator_2
+SMYD3 pd Nkx2.8
+KCND3 pp KCND3
+Insulin pp Insulin_A_Chain
+UPF2 pp UPF3B
+BRAF pp BRAF
+BRAF pp BRAF
+Immunoglobulin_Heavy_Chain pp Immunoglobulin_Light_Chain
+Immunoglobulin_Light_Chain pp Immunoglobulin_Light_Chain
+Immunoglobulin_Heavy_Chain pp Immunoglobulin_Light_Chain
+S100P pp S100P
+ICAM3 pp ICAM3
+ATIC pp ATIC
+F2 pp Prothrombin
+BMP4 pp BMP4
+BMPR1A pp BMP4
+BMPR1A pp BMP4
+BMPR1A pp BMP4
+ACAD8 pp ACAD8
+ACAD8 pp ACAD8
+ACAD8 pp ACAD8
+ACAD8 pp ACAD8
+Signal_Recognition_Particle_14_Kda_Protein pp SRP9
+UBA52 pp Tumor_Susceptibility_Gene_101_Protein
+EGFR pp EGFR
+Pertuzumab_Fab_Light_Chain pp ERBB2
+Pertuzumab_Fab_Heavy_Chain pp EGFR
+Pertuzumab_Fab_Heavy_Chain pp EGFR
+DCPS pp DCPS
+DCPS pp DCPS
+TFRC pp TFRC
+TF pp TFRC
+TF pp TF
+TF pp TFRC
+UCK2 pp UCK2
+UCK2 pp UCK2
+UCK2 pp UCK2
+UCK2 pp UCK2
+UCK2 pp UCK2
+UCK2 pp UCK2
+Pals1-Associated_Tight_Junction_Protein pp Pals1-Associated_Tight_Junction_Protein
+Steroid_Receptor_Coactivator-1 pp HNF4A
+B2M pp HLA-A
+HLA-A pp HLA-A
+B2M pp HLA-A
+B2M pp HLA-A
+CASP3 pp Caspase-3
+Caspase-3 pp CASP3
+Caspase-3 pp Caspase-3
+CASP3 pp CASP3
+CASP3 pp Caspase-3
+Casp-3 pp Casp-3
+Caspase-3 pp Caspase-3
+Casp-3 pp Casp-3
+Casp-3 pp Casp-3
+Caspase-3 pp Caspase-3
+Caspase-3 pp Caspase-3
+Caspase-3 pp Caspase-3
+Caspase-3 pp Caspase-3
+Caspase-3 pp Caspase-3
+F2 pp Prothrombin
+F2 pp Thrombin
+BDNF pp BDNF
+NGFR pp BDNF
+NGFR pp BDNF
+MAPBPIP pp Mitogen-Activated_Protein_Kinase_Kinase_1_Interacting_Protein_1
+PDE3A pp PDE3A
+PDE3A pp PDE3A
+RAP1GA1 pp RAP1GA1
+CD3E pp Okt3_Fab_Heavy_Chain
+CD3E pp Okt3_Fab_Light_Chain
+Bach1_Phosphorylated_Peptide pp BRCA1
+GMDS pp GMDS
+GMDS pp GMDS
+GMDS pp GMDS
+LDHB pp LDHB
+LDHB pp LDHB
+LDHB pp LDHB
+LDHB pp LDHB
+LDHB pp LDHB
+LDHB pp LDHB
+ACADS pp ACADS
+ACADS pp ACADS
+ETFB pp ETFA
+ETFB pp ACADS
+NR1H3 pp RXRG
+GGA1 pp GGA1
+Potential_Transcriptional_Repressor_Not4hp pp UBE2D2
+DMC1 pp DMC1
+Orf2_Contains_A_Reverse_Transcriptase_Domain pp Orf2_Contains_A_Reverse_Transcriptase_Domain
+FKBP4 pp FKBP4
+FKBP4 pp FKBP4
+FKBP4 pp FKBP4
+5-Mer_Peptide_From_Heat_Shock_Protein_Hsp_90 pp FKBP4
+5-Mer_Peptide_From_Heat_Shock_Protein_Hsp_90 pp FKBP4
+HIP1 pp HIP1
+24-Residue_Peptide_From_Lymphotoxin-B_Receptor pp TRAF3
+1RR8_A pd TOP1
+1RR8_B pd TOP1
+1RRJ_B pd TOP1
+1RRJ_C pd TOP1
+Single-Stranded_Dna-Binding_Protein,_Mitochondrial pp Single-Stranded_Dna-Binding_Protein,_Mitochondrial
+Sin3a_Protein pp Mad_Protein
+PPP1R12A pp PPP1CB
+Ezrin-Radixin-Moesin_Binding_Phosphoprotein_50 pp MSN
+MET pp HGF
+CD209L pp CD209L
+CD209L pp CD209L
+CD209L pp CD209L
+CD209L pp CD209L
+Camp-Dependent_Protein_Kinase_Inhibitor,_Alpha_Form pp PRKACA
+MASP2 pp MASP2
+IDH1 pp IDH1
+Voltage-Dependent_L-Type_Calcium_Channel_Alpha-_1c_Subunit pp CACNB2
+IDH1 pp IDH1
+Factor_Viia_Light_Chain pp Tissue_Factor
+Factor_Viia_Heavy_Chain pp Factor_Viia_Light_Chain
+Cyclin_A2 pp Cell_Division_Protein_Kinase_2
+Jto2,_A_Lambda-6_Type_Immunoglobulin_Light_Chain,_Variable_Domain pp Jto2,_A_Lambda-6_Type_Immunoglobulin_Light_Chain,_Variable_Domain
+Adaptor_Protein_With_Pleckstrin_Homology_And_Src_Homology_2_Domains pp Adaptor_Protein_With_Pleckstrin_Homology_And_Src_Homology_2_Domains
+Adaptor_Protein_With_Pleckstrin_Homology_And_Src_Homology_2_Domains pp Adaptor_Protein_With_Pleckstrin_Homology_And_Src_Homology_2_Domains
+Deoxyhypusine_Synthase pp Deoxyhypusine_Synthase
+High_Affinity_Immunoglobulin_Epsilon_Receptor_Alpha-Subunit_Precursor pp High_Affinity_Immunoglobulin_Epsilon_Receptor_Alpha-Subunit_Precursor
+High_Affinity_Immunoglobulin_Epsilon_Receptor_Alpha-Subunit_Precursor pp High_Affinity_Immunoglobulin_Epsilon_Receptor_Alpha-Subunit_Precursor
+Peptide_E131 pp High_Affinity_Immunoglobulin_Epsilon_Receptor_Alpha-Subunit_Precursor
+Peptide_E131 pp High_Affinity_Immunoglobulin_Epsilon_Receptor_Alpha-Subunit_Precursor
+Deoxyhypusine_Synthase pp Deoxyhypusine_Synthase
+Hu3s193_Fab_Fragment,_Heavy_Chain pp Hu3s193_Fab_Fragment,_Light_Chain
+Heme_Oxygenase_1 pp Heme_Oxygenase_1
+11-Peptide_Hirudin_Fragment pp Thrombin
+Talin_1 pp Vinculin_Isoform_Vcl
+Polymerase_(Dna_Directed)_Iota pp Polymerase_(Dna_Directed)_Iota
+Geminin pp Geminin
+Camp-Specific_3',5'-Cyclic_Phosphodiesterase_4b pp Camp-Specific_3',5'-Cyclic_Phosphodiesterase_4b
+Camp-Specific_3',5'-Cyclic_Phosphodiesterase_4d pp Camp-Specific_3',5'-Cyclic_Phosphodiesterase_4d
+Camp-Specific_3',5'-Cyclic_Phosphodiesterase_4d pp Camp-Specific_3',5'-Cyclic_Phosphodiesterase_4d
+Estrogen-Related_Receptor_Gamma pp Estrogen-Related_Receptor_Gamma
+Prothrombin pp Prothrombin
+Prothrombin pp Prothrombin
+Geminin pp Geminin
+Igg_Fab_Heavy_Chain pp Igg_Fab_Light_Chain
+Tissue_Factor pp Igg_Fab_Light_Chain
+Tissue_Factor pp Igg_Fab_Heavy_Chain
+RB pp HDAC1
+Unknown interactsWith ORC1
+Unknown interactsWith BRCA1-IRIS
+CDC6 interactsWith Unknown
+Unknown interactsWith Geminin
+ORC5 interactsWith Unknown
+MCM6 interactsWith Unknown
+Unknown interactsWith MCM2
+Unknown interactsWith MCM7
+BRCA1-IRIS-interacting_complex interactsWith Unknown
+Unknown interactsWith rDNA_origin
+Unknown interactsWith Beta-globin_origin
+MCM2 interactsWith Unknown
+Lbc pp nm23-H2
+SAP155 pp U2AF65
+SAP155 pp U2AF35
+S100A1 pp S100B
+S100A6 pp S100B
+S100A11 pp S100B
+S100B pp S100B
+Histone_H3 pd E-cadherin_promoter
+Histone_H3 pd erbB2_promoter
+TRAF4 pp NADP-ME
+ICAP-1-alpha pp nm23-H2
+TRAF4 pp alpha-actinin
+TRAF4 pp p47phox
+Unknown interactsWith SF2A-p32
+Unknown interactsWith Tubulin_beta-1
+Unknown interactsWith Tubulin_alpha-3
+Unknown interactsWith PRMT5
+Unknown interactsWith PRMT1
+FIB interactsWith Unknown
+L-selectin pp PKC-theta
+L-selectin pp PKC-alpha
+L-selectin pp PKC-iota
+ER-alpha pp pp32
+Amyloid-beta interactsWith FKBP12-SLF-CR_complex
+Amyloid-beta interactsWith FKBP12-SLF-CR_complex
+Amyloid-beta interactsWith FKBP12-SLF-CR_complex
+cPML pp SARA
+cPML pp Smad2
+cPML pp Smad3
+cPML pp T-beta-RI
+cPML pp T-beta-RII
+TRF1 pp nm23-H2
+nm23-H2 interactsWith Telomeric_DNA
+ER-alpha pp HDAC1
+CBP pd pS2
+p300 pd pS2
+ER-alpha pd pS2
+HS1 pp HAX-1
+12-LOX pp K5
+E2F1 pp pRB
+NEK1 pp FEZ-1
+HKIII pp leptin
+HKIII pp PGDS
+HKIII pp granulin_precursor
+HKIII pp IGFBP-4
+HKIII pp Miz-1
+HKII pp IGFBP-4
+HKII pp PGDS
+HKII pp Miz-1
+KRIT1 pp ICAP-1
+NEK1 pp FEZ-2
+Syndecan-3 pp ST-1
+CNX pp ERp57
+CRT pp ERp57
+NEK1 pp 14-3-3
+CD40 pp TRAF2
+CD40 pp TRAF3
+CD40 pp TRAF3
+Ephrin-B2 pp ST-1
+Pro-TGF-alpha pp ST-1
+TCP10L pp MAD4
+EPOR pp EPO
+EPOR pp EPO
+NEK1 pp ATRX
+NEK1 pp KIF3A
+NEK1 pp PP2A
+PFN_IIa pp FHOS
+KRIT1 pp ICAP-1
+KRIT1 pp ICAP-1
+KRIT1 pp ICAP-1
+PS1 pp Syntaxin_1A
+Flt-1 pp Nck
+BLM pp WRN
+Flt-1 pp p85
+U2AF65 pp UAP56
+Lamin_B1 pp Lamin_B1
+Lamin_A pp Lamin_B1
+IRAP pp FHOS
+PFN_IIa pp FHOS78
+PS1 pp APP
+E2F4 pd GAR22
+E2F4 pd DBPA
+E2F4 pd RAD51
+E2F4 pd H4F2
+IKK-alpha interactsWith Unknown
+Unknown interactsWith IKK-gamma
+Unknown interactsWith IKK-beta
+c-IAP1 pp TRAF2
+c-IAP2 pp TRAF2
+c-IAP2 pp TRAF1
+c-IAP1 pp TRAF1
+Prelamin_A pp Prelamin_A
+GASP-1 pp DOR
+PS1 pp Syx5
+GASP-1 pp ORL1
+GASP-1 pp MOR
+GASP-1 pp KOR
+PLCG1 pp ACTB
+TRP3 pp IP3R-3
+TRP3 pp IP3R-3
+ARG pp ArgBP1A
+hnRNP_K pp TBP
+hnRNP_K pp TBP
+MPB-1 pp MIP-2A
+MPB-1 pp MIP-2A
+MPB-1 pp MIP-2A
+PQBP-1 pp NPWBP
+PQBP-1 pp NPWBP
+PQBP-1 pp NPWBP
+RB1 pp BRF
+RBL1 pp BRF
+RB2 pp BRF
+RB1 pp BRF
+RB2 pp BRF
+RBL1 pp BRF
+BRF pp RB2
+BRF pp RBL1
+SLC2A1 pp EPB72
+surface_glycoprotein_CD100 pp surface_glycoprotein_CD100
+PEX12 pp PXR1
+PEX12 pp PXR1
+PEX12 pp PEX10
+PEX12 pp PEX10
+BTK pp PRKCM
+BTK pp PRKCM
+POU3F2 pp PQBP-1
+POU3F2 pp PQBP-1
+IGF1R pp IGF1R
+ATOX1 pp ATP7B
+ATOX1 pp ATP7B
+ATP7A pp ATOX1
+FZD1 pp WNT3A
+FZD1 pp WNT5A
+NCF2 pp NCF4
+PTK2 pp PXN
+PTK2 pp VCL
+RB1 pp p50_protein
+RB1 pp p50_protein
+PTK2 pp BCAR1
+PLAUR pp IL6ST
+ARNT pp ARNT
+ARNT pp ARNT2
+ARNT2 pp ARNT2
+PKD1 pp PKD2
+PKD1 pp PKD2
+HIF1A pp ARNT
+HIF1A pp ARNT2
+GNAI2 pp IL8RA
+FBN1 pp FBN2
+GR pp HNRPU
+GR pp HNRPU
+ARNT pp HIF1A
+MLL pp SET
+MLL pp SET
+MLL pp SET
+SET pp PPP2R1B
+SET pp PPP2CA
+MLL pp GADD34
+MLL pp GADD34
+LYN pp GADD34
+LYN pp GADD34
+GADD34 pp LYN
+RAP pp LRP1
+LRP1 pp LRP1
+IL-9R pp HTATIP
+IL-9R pp HTATIP
+HTATIP pp IL-9R
+ZNF74 pp POLR2A
+ZNF74 pp POLR2A
+MAP4K3 pp TRAF2
+GP1BB pp GP1BA
+MST1 pp MST1
+MST1 pp MST1
+MST1 pp MST1
+CTNNA1 pp ACTN1
+CDH1 pp CTNNA1
+SP1 pp NFYA
+GRB2 pp ADA
+ADA pp GRB2
+ADA pp GRB2
+LINE-1_retrotransposon_protein_(ORF1) pp LINE-1_retrotransposon_protein_(ORF1)
+APOH pp LPA
+TUBG pp KRT18
+TUBG pp KRT19
+SGF3G pp STAT2
+SGF3G pp STAT2
+LBP pp APOA1
+PLCG1 pp ACTB
+LBP pp FHR1
+FHR1 pp LBP
+PICALM pp CLTC
+PICALM pp CLTC
+PEX3 pp PXF
+PEX3 pp PXF
+APP pp APOE
+CTLA4 pp AP2M1
+CTLA4 pp AP2M1
+DDIT3 pp CEBPB
+E2F1 pp SP1
+E2F2 pp SP1
+E2F3 pp SP1
+WRN pp RPA1
+CYC pp BCL2L1
+CYC pp BCL2L1
+CD45 pp PTPRCAP
+RB1 pp GTF3C2
+RB1 pp BRF
+PLCG1 pp AXL
+PLCG1 pp AXL
+AXL pp PLCG1
+AXL pp PIK3R1
+PIK3R1 pp AXL
+PIK3R1 pp AXL
+PIK3R2 pp AXL
+PIK3R2 pp AXL
+AXL pp PIK3R2
+CSK pp AXL
+CSK pp AXL
+AXL pp CSK
+AXL pp LCK
+LCK pp AXL
+LCK pp AXL
+GRB2 pp AXL
+GRB2 pp AXL
+AXL pp GRB2
+INSR pp ARF1
+BRCA2 pp SHFDG1
+SHFDG1 pp BRCA2
+BRCA2 pp RAD51
+SERPINA1 pp UDP-glucose:glycoprotein_glucosyltransferase_1_(UGTR)
+PSEN2 pp CIB1
+CIB1 pp PSEN2
+CIB1 pp PSEN2
+PSEN1 pp CIB1
+RARA pp SP1
+RARA pp SP1
+RARA pp SP1
+ESR1 pp HSPCA
+ESR1 pp HSPCA
+MADH3 pp MADH4
+MADH3 pp MADH3
+MADH4 pp MADH4
+MADH4 pp MADH4
+MADH3 pp MADH3
+ITGB3 pp ITGA2B
+CIB1 pp ITGA2B
+AHR pp ARNTL
+HSPCA pp ARNTL
+HIF1A pp ARNT
+ARNT pp HIF1A
+ARNT pp EPAS1
+EPAS1 pp ARNT
+HSPCA pp HIF1A
+HSPCA pp NPAS2
+AR pp NCOA4
+AR pp NCOA4
+CAP2 pp CAP
+CAP2 pp CAP
+HS1BP1 pp YWHAQ
+HS1BP1 pp YWHAQ
+RXRA pp NCOA4
+RXRA pp NCOA4
+CAP pp CAP
+CAP pp CAP
+CAP pp CAP
+PLP2 pp PLP2
+HDAC4 pp RBBP4
+HDAC4 pp HDAC3
+HDAC5 pp HDAC3
+AP2A1 pp EPS15
+CRKL pp BCR-ABL_fusion_protein
+BCR-ABL_fusion_protein pp CRKL
+CRKL pp BCR-ABL_fusion_protein
+CRKL pp BCR-ABL_fusion_protein
+TYK2 pp IFNAR1
+IFNAR1 pp TYK2
+ACVR2 pp ACVR1B
+ACVR2 pp ACVRL1
+MAPK8 pp REL
+CSF2RB pp CSF2RB
+REL pp MAPK8
+CDK2 pp CDKN1A
+TOP1 pp NCL
+NCL pp TOP1
+HSPA1A pp TP53
+RAC1 pp RASGRF1
+ARHA pp RASGRF1
+SLBP pp LSM10
+E2F1 pp DDB2
+E2F1 pp DDB2
+DDB2 pp DDB1
+THRA pp ALIEN
+THRA pp ALIEN
+ALIEN pp THRA
+THRB pp ALIEN
+THRB pp ALIEN
+RARA pp ALIEN
+ALIEN pp NR2F1
+RAD9 pp BCL2
+EIF-4G2 pp EIF-4E
+EIF-4E pp EIF-4G2
+EIF-4E pp EIF-4G1
+EIF-4G2 pp EIF-4A
+EIF-4G2 pp EIF-3
+EIF-4G1 pp EIF-4A
+EIF-4G1 pp EIF-3
+EIF-4G1 pp EIF-4E
+EIF-4G2 pp EIF-4E
+PAX5 pp TBP
+PAX5 pp RB1
+TNFRSF6 pp CASP8
+TNFRSF6 pp FADD
+STAT5A pp MAPK3
+MAPK3 pp STAT5A
+EPB41 pp NUMA1
+EPB41 pp NUMA1
+EPB41 pp NUMA1
+KCNJ11 pp ABCC9
+KCNJ11 pp ABCC8
+PURA pp NSEP1
+NSEP1 pp PURA
+VHL pp CUL2
+VHL pp TCEB2
+VHL pp TCEB1
+VHL pp VHL
+VHL pp CUL2
+VHL pp TCEB2
+VHL pp TCEB1
+Elongin_C_(RNA_polymerase_II_elongation_factor_SIII,_p15_subunit_(Transcription_elongation_factor_B_(SIII),_polypeptide_1) pp CUL2
+Elongin_C_(RNA_polymerase_II_elongation_factor_SIII,_p15_subunit_(Transcription_elongation_factor_B_(SIII),_polypeptide_1) pp Elongin_B_(RNA_polymerase_II_transcription_factor_SIII_P18_subunit)
+PSEN2 pp APP
+PSEN1 pp APP
+APP pp APBA3
+APP pp APBA3
+APP pp APBA3
+PSEN1 pp CTNND2
+PSEN1 pp CTNND2
+PSEN1 pp PKP4
+PSEN1 pp CTNNB1
+PSEN2 pp CTNND2
+PSEN2 pp CTNNB1
+STAT1 pp PLAUR
+PLAUR pp TYK2
+PLAUR pp JAK1
+CTNND2 pp CDH2
+EPB41 pp CLNS1A
+EPB41 pp CLNS1A
+NOLC1 pp COIL
+NOLC1 pp COIL
+PSEN2 pp PSEN2
+TEGT pp BCL2
+TEGT pp BCL2
+TEGT pp BAD
+TEGT pp BAD
+SCAMP1 pp EGFR
+SCAMP3 pp EGFR
+ARHA pp KCNA2
+CAV1 pp ARHA
+SGCD pp SGCA
+SGCD pp SGCG
+GNB2L1 pp SRC
+SRC pp GNB2L1
+GNB2L1 pp SRC
+FANCC pp TRA1
+FANCC pp TRA1
+POL pp CDK2
+CD47 pp ITGA2
+CD47 pp ITGB1
+USA-CYP pp PRPF4
+GRB2 pp HNRPC
+AR pp CBP
+LHCGR pp CANX
+FSHR pp CANX
+TGFBR1 pp TGFBR1
+TGFBR1 pp TGFBR1
+TGFBR2 pp TGFBR2
+IRF3 pp CITED1
+HGCN5 pp G22P1
+G22P1 pp HGCN5
+HGCN5 pp G22P1
+G22P1 pp XRCC5
+HGCN5 pp XRCC5
+PTK2B pp Hic-5
+NMI pp MYC
+NMI pp MYC
+NMI pp MYCN
+NMI pp MAX
+NMI pp FOS
+TNFRSF1A pp TRADD
+MAD1 pp MAX
+MYC pp MAX
+RANK pp TRAF2
+RANK pp TNF_receptor_associated_factor_5
+RANK pp TRAF6
+CRKL pp STAT5A
+CRKL pp STAT5A
+GRB2 pp RET/PTC2
+RET/PTC2 pp GRB2
+RET pp GRB2
+GRB2 pp RET
+BAK pp VDAC
+BAX pp VDAC
+TOP1 pp PSF
+TOP1 pp PSF
+TOP1 pp PSF
+VHL pp TCEB2
+VHL pp TCEB1
+VHL pp CUL2
+STAT1 pp PIAS1
+GNA11 pp RGS3
+PIAS1 pp STAT1
+PIAS3 pp STAT3
+HIRA pp HIRIP1
+HIRIP1 pp HIRA
+HIRA pp HIRIP1
+H4F2 pp HIRA
+HIRA pp HIRIP3
+HIRIP3 pp HIRA
+HIRIP3 pp HIRIP1
+HIRIP3 pp Histone_H3
+HIRIP5 pp HIRA
+HIRA pp HIRIP5
+PURA pp RB1
+SP1 pp PLZF
+SP1 pp PLZF
+PLZF pp SP1
+TAF4 pp TAF12
+TAF12 pp TAF4
+TAF4 pp TAF12
+TCF21 pp TCF12
+TITF1 pp RARA
+TITF1 pp NCOA2
+POR1 pp ARF1
+PRKCABP pp ARF1
+PRKCABP pp ARF3
+ATM pp AP1B1
+BCL2L1 pp CFLAR
+BCL2 pp RAD9
+BCL2L1 pp RAD9
+BCL2L1 pp RAD9
+BAX pp BCL2
+BAD pp BCL2L1
+HSCDC6 pp PR48
+HSCDC6 pp PR48
+HSCDC6 pp PR48
+PPP2R1A pp PR48
+PPP2R1A pp PPP2R3A
+HSCDC6 pp PPP2R3A
+CD9 pp ITGA5
+CD9 pp ITGA3
+CD9 pp ITGA2
+CD9 pp ITGB1
+TRAF3 pp TNFRSF7
+SGCG pp ABPL
+ABPL pp SGCG
+SGCG pp ABPL
+SGCD pp ABPL
+ABPL pp SGCD
+ABPL pp SGCD
+PRKCQ pp PICOT
+PICOT pp PRKCQ
+CD38 pp LCK
+PICOT pp PRKCQ
+PICOT pp PRKCZ
+NOT1 pp NOT2
+NOT1 pp NOT4-N
+NOT1 pp CNOT8
+NOT3 pp CNOT8
+CNOT8 pp NOT3
+Dvl2 pp TCTEL1
+NPM pp PLCG2
+PLCG2 pp PLCG2
+Dvl2 pp PPM1A
+DVL1 pp PPM1A
+DVL1 pp TCTEL1
+PPM1A pp DVL3
+PPM1A pp CTNNB1
+DVL3 pp CTNNB1
+DVL3 pp DVL1
+DVL3 pp DVL1
+DVL1 pp DVL1
+AHR pp RB1
+APCL pp MAPRE1
+MAPRE3 pp APCL
+APCL pp MAPRE3
+APCL pp MAPRE3
+VIL2 pp ICAM-2
+ICAM-2 pp VIL2
+ICAM-2 pp VIL2
+ICAM-2 pp VIL2
+ICAM-1 pp VIL2
+ICAM-1 pp VIL2
+PTEN pp hdlg-1
+hdlg-1 pp PTEN
+CHUK pp PRKR
+FHL2 pp MCM7
+IRE1b pp TRAF2
+TRAF2 pp IRE1b
+TRAF2 pp IRE1a
+FHL2 pp MCM7
+PTPN11 pp SNT-1
+SNT-1 pp PTPN11
+TP73 pp EP300
+EP300 pp TP73
+EP300 pp TP53
+TP73 pp EP300
+CBP pp TP53
+CBP pp TP73
+TP73 pp CBP
+ITGB1 pp CD9
+CD9 pp ITGA2
+CD9 pp ITGA3
+CD9 pp ITGA5
+FANCF pp FANCG
+FANCC pp FANCE
+FANCE pp FANCA
+FANCE pp FANCG
+FANCG pp FANCG
+FANCA pp FANCG
+FANCA pp FANCG
+FANCG pp FANCF
+FANCE pp FANCC
+REV3L pp MAD2L2
+REV3L pp MAD2L2
+MAD2L1 pp MAD2L2
+MAD2L1 pp REV3L
+MAD2L1 pp MAD1
+PTPN6 pp PILRA
+PTPN6 pp PILRA
+PILRA pp PTPN6
+BMX pp RUFY1
+RUFY1 pp BMX
+BMX pp RUFY2
+MAGOH pp RBM8B
+MAGOH pp RBM8B
+FRAP1 pp YWHAQ
+FRAP1 pp YWHAQ
+VAV1 pp RHGDIB
+RHGDIB pp VAV1
+VAV1 pp RHGDIB
+ARHGDIA pp VAV1
+VAV1 pp ARHGDIA
+RAD51 pp UBL1
+RAD51 pp UBE2I
+RAD51 pp UBE2I
+RAD51 pp RAD52
+RAD51 pp UBL1
+UBL1 pp RAD52
+RAD52 pp UBE2I
+UBL1 pp UBE2I
+PML pp DAXX
+PML_and_RARA pp DAXX
+PML pp DAXX
+HDAC1 pp DAXX
+HDAC1 pp DAXX
+DAXX pp HDAC1
+HDAC2 pp DAXX
+HDAC3 pp DAXX
+KDR pp PLCG1
+KDR pp PLCG1
+NFKBIA pp Kappa_B-ras_1
+NFKBIB pp Kappa_B-ras_1
+NFKBIB pp Kappa_B-ras_2
+SP1 pp ESR2
+CD45 pp CD45
+ARNT pp HEY2
+ARNT pp HEY1
+DRD2 pp FLNA
+DRD2 pp FLNA
+DRD3 pp FLNA
+DRD3 pp FLNA
+MITF pp UBE2I
+UBE2I pp MITF
+DRD1 pp D1_dopamine_receptor-interacting_protein_calcyon
+HSPG2 pp FGF7
+FGF7 pp HSPG2
+ETS1 pp DAXX
+DAXX pp ETS1
+ESR1 pp HET
+HET pp ESR1
+SHC pp NPM
+IRS1 pp NPM
+GRB2 pp NPM
+BMPR2 pp BMPR2
+BMPR2 pp BMPR1A
+BMPR1A pp BMPR1A
+ALIEN pp NR0B1
+ALIEN pp NR0B1
+ALIEN pp NR0B1
+ALIEN pp THRB
+RNF4 pp PATZ
+RNF4 pp PATZ
+RNF4 pp HMGA1
+HMGA1 pp RNF4
+THRB pp NR2F6
+THRB pp NR2F6
+NR2F6 pp THRB
+NR2F6 pp GR
+Skiip pp CBF1
+CDC25B pp YWHAZ
+CDC25B pp YWHAH
+CDC25B pp YWHAB
+CDC25B pp YWHAH
+CBF1 pp Skiip
+YWHAH pp CDC25B
+YWHAZ pp CDC25B
+NCOR2,_SMRT pp Skiip
+CDKN2A pp CDK4
+ERBB4 pp DLG4
+ERBB4 pp DLG2
+ERBB4 pp DLG3
+ERBB4 pp SNTB2
+FALZ pp MAZ
+FALZ pp MAZ
+FALZ pp MAZ
+ALAS2 pp SUCLA2
+ALAS2 pp SUCLA2
+ALOX12 pp KRT5
+ALOX12 pp KRT5
+KRT5 pp ALOX12
+JUN_activation_domain-binding_protein-1_(JAB1) pp Steroid_receptor_coactivator-1_(SRC-1)
+JUN_activation_domain-binding_protein-1_(JAB1) pp Steroid_receptor_coactivator-1_(SRC-1)
+Steroid_receptor_coactivator-1_(SRC-1) pp ESR1
+Steroid_receptor_coactivator-1_(SRC-1) pp ESR2
+Steroid_receptor_coactivator-1_(SRC-1) pp GR
+Steroid_receptor_coactivator-1_(SRC-1) pp AR
+Steroid_receptor_coactivator-1_(SRC-1) pp PPARA
+Steroid_receptor_coactivator-1_(SRC-1) pp PPARG
+HDAC4 pp MEF2A
+HDAC4 pp MEF2A
+HDAC9 pp MEF2A
+PSEN1 pp BACE1
+KCNMA1 interactsWith Unknown
+Unknown interactsWith ALS2
+Unknown interactsWith FCER2
+Unknown interactsWith GDAP1L1
+Unknown interactsWith GP2
+Unknown interactsWith HMOX2
+Unknown interactsWith TGM2
+Unknown interactsWith CALU
+Unknown interactsWith CAMK1
+Unknown interactsWith MFAP3
+Unknown interactsWith SELPLG
+Unknown interactsWith ANXA5
+Unknown interactsWith CCND2
+Unknown interactsWith FSTL1
+Unknown interactsWith PALM
+Unknown interactsWith RABGGTB
+Unknown interactsWith PNMA1
+Unknown interactsWith PPP6C
+Unknown interactsWith HNRPC
+Unknown interactsWith HNRPC
+Unknown interactsWith SAE1
+Unknown interactsWith TNFRSF10B
+Unknown interactsWith CRTAP
+Unknown interactsWith CIAO1
+Unknown interactsWith PP
+Unknown interactsWith ALDRL6
+Unknown interactsWith SYND3
+Unknown interactsWith SYND3
+Unknown interactsWith SNX16
+Unknown interactsWith TXNDC5
+Unknown interactsWith KRT19
+Unknown interactsWith RAD51L1
+Unknown interactsWith SERTAD2
+Unknown interactsWith KIAA0652
+mTOR interactsWith Unknown
+Unknown interactsWith mLST8
+Unknown interactsWith raptor
+Unknown interactsWith mAVO3
+mTOR pp FKBP12
+mTORC1 interactsWith 4E-bp1
+mTOR pp mTOR
+mTOR pp mAVO3
+mTORC2 interactsWith 4E-bp1
+Rhotekin pp RhoA
+GASP-1 pp M1
+GASP-1 pp M2
+Prelamin_A pp Lamin_A
+Prelamin_A pp Lamin_B1
+BPGAP1 pp Cdc42GAP
+BPGAP1 pp BPGAP1
+HDAC1 interactsWith Unknown
+Unknown interactsWith MBD3
+Unknown interactsWith MBD2b
+Unknown interactsWith MBD2a
+Unknown interactsWith RbAp46
+Unknown interactsWith RbAp48
+Unknown interactsWith Kiaa0071
+unknown interactsWith Kiaa0601
+Unknown interactsWith Mta-L1
+unknown interactsWith Mi-2
+emerin pp BAF
+PARP-1 pp Topo_I
+GASP-1 pp H2
+GASP-1 pp 5-HT7
+TAFI48 pp TAFI110
+TBP pp TAFI110
+TBP pp TAFI48
+TBP pp TAFI63
+TBP pp TAFII150
+TAFI110 pp TAFI63
+TAFI48 pp TAFI63
+GASP-1 pp TXA2-alpha
+CYLD pp TRIP
+GASP-1 pp beta-1-AR
+GASP-1 pp CALCR
+AKAP-Lbc pp PKC-alpha
+AKAP-Lbc pp PKC-eta
+AKAP-Lbc pp PKD
+pKi-67 pp HP1-gamma
+GASP-2 pp M1
+GASP-2 pp M2
+TIRP pp TRIF
+TIRP pp TIRAP
+TIRP pp IL-1RAcP
+GASP-2 pp 5-HT7
+CYLD pp NEMO
+CYLD pp TRAF2
+GASP-2 pp beta-1-AR
+GASP-2 pp CALCR
+GASP-2 pp H2
+IKK-beta pp I-kappa-B-alpha
+IKK-beta pp NIK
+IKK-beta pp IKK-beta
+IKK-alpha pp IKK-beta
+IKK-alpha pp NIK
+IKK-alpha pp I-kappa-B-alpha
+IKK-beta pp I-kappa-B-beta
+Flt-1 pp SHP-2
+12-LOX pp C8FW
+E2F4 pd UXT
+E2F3 pd UXT
+E2F2 pd UXT
+E2F1 pd UXT
+ARC pp ARC
+Fas interactsWith Unknown
+Unknown interactsWith FADD
+Unknown interactsWith procaspase-8
+Fas pp FADD
+hMis12 interactsWith Unknown
+Unknown interactsWith KIAA1570
+Unknown interactsWith PMF1
+Unknown interactsWith HEC1
+hMis12 pp c20orf172
+hMis12 pp Zwint-1
+hMis12 pp DC8
+hMis12 pp HP1-alpha
+hMis12 pp HP1-gamma
+c20orf172 pp HP1-alpha
+c20orf172 pp HP1-gamma
+c20orf172 pp DC8
+c20orf172 pp Zwint-1
+HP1-alpha pp DC8
+pro-IL-16 pp MYPT1
+pro-IL-16 pp MYPT2
+pro-IL-16 pp MBS85
+npro-IL-16 pp MYPT2
+beta-actin pd p-MHC2TA
+Pol_II pd p-MHC2TA
+H4 pd p-MHC2TA
+beta-actin pd p-G1P3
+Pol_II pd p-G1P3
+H4 pd p-G1P3
+beta-actin interactsWith Unknown
+Unknown interactsWith RNAPII
+Unknown interactsWith TBP
+pKi-67 pp HP1-beta
+pKi-67 pp HP1-alpha
+Amphiphysin1 pp Hypothetical_protein_FLJ10100
+Amphiphysin1 pp NPAS2
+Amphiphysin1 pp Hypothetical_protein_[Fragment]
+Amphiphysin1 pp HT019
+Endophilin1 pp PHF2
+Endophilin1 pp CABIN1
+Endophilin1 pp NAG-5_protein
+Endophilin1 pp FLJ00179_protein_[Fragment]
+Endophilin1 pp Hypothetical_protein_[Fragment]
+Endophilin1 pp C8G
+Endophilin1 pp DNM2
+Endophilin1 pp WBSCR20C
+Endophilin1 pp REPS2
+Endophilin1 pp ITCH
+Endophilin1 pp CBLB
+Endophilin1 pp HT019
+Met pp Met
+Flt-1 pp PLC-gamma
+BCL6 pp MTA3
+npro-IL-16 pp NR2A
+Unknown interactsWith MTA2
+CRT pp HLA-A2
+CK2B pp Synphilin-1
+p32 pp CBF-B
+CRT pp CRT
+NTH1 pp p53
+Unknown interactsWith SMRT
+Unknown interactsWith N-CoR
+BCL6 interactsWith HDAC1
+BCL6 pp Mi2
+BCL6 pp MBD3
+PS1 pp APP
+NP-2 pp VEGF165
+SRC-3 pp ER
+SRC-3 pp NF-kappa-B
+SRC-3 pp CBP
+SRC-3 pp CARM1
+SRC-3 pp GSK3-beta
+NP-2 pp VEGF145
+PlexinD1 pp Npn-1
+Rb pp AR
+URH49 pp Aly
+IRF7 pp TRAF6
+IRF7 pp MyD88
+nucleolin pp hTERT
+PS2 pp APP
+TIRP pp IRAK-2
+TIRP pp IRAK-M
+TIRP pp IL-1R
+NIK pp TRAF1
+NIK pp TRAF2
+NIK pp TRAF3
+TRAF2 pp GCK
+GCK pp MEKK1
+Rb pp ASC-2
+SF3b155 interactsWith Unknown
+Unknown interactsWith SF3b145
+Unknown interactsWith SF3b130
+Unknown interactsWith SF3b125
+Unknown interactsWith SF3b49
+Unknown interactsWith SF3b14a
+Unknown interactsWith SF3b14b
+Unknown interactsWith SF3b10
+SAP145 pp SAP49
+p14 pp SF3b155
+BCL6-MTA3_complex interactsWith CCL3
+CyclinT1 pp Cdk9
+TIN2 pp TRF2
+TIN2 pp TRF1
+p14ARF pp c-Myc
+RanBP2 pp Ubc9
+Unknown interactsWith TIN2
+Unknown interactsWith Rad50
+Unknown interactsWith PIP1
+Unknown interactsWith POT1
+hRap1 pp TRF1
+hRap1 interactsWith Unknown
+actin pp actin
+hRap1 pp TRF2
+BRUCE pp Casp-3
+BRUCE pp Casp-3
+BRUCE pp Casp-6
+BRUCE pp Casp-7
+BRUCE pp Casp-9
+BRUCE pp SMAC
+BRUCE pp HtrA2
+Ryk pp Wnt-1
+Ryk pp Wnt-3a
+Frizzled-8 pp Ryk
+Frizzled-8 pp Wnt-1
+CBP pp Daxx
+CBP pp Pax5
+beta-APP pp X11
+EGF-R pp Grb2
+EGF-R pp Shc
+PPEF1 pp PPEF1
+CASP7 pp CASP7
+CASP7 pp CASP7
+Gag_Polyprotein pp HLA-DRB1
+Gag_Polyprotein pp HLA-DRA
+Gag_Polyprotein pp HLA-DRB1
+Gag_Polyprotein pp HLA-DRA
+F2 pp Prothrombin
+F2 pp SERPINB4
+Insulin pp Insulin
+15-Mer_Peptide_Fragment_Of_Regulatory_Protein_Mig1 pp HLA-DRB1
+15-Mer_Peptide_Fragment_Of_Regulatory_Protein_Mig1 pp HLA-DRA
+15-Mer_Peptide_Fragment_Of_Regulatory_Protein_Mig1 pp HLA-DRA
+PGAM1 pp PGAM1
+HS3ST3B1 pp HS3ST3B1
+F2 pp Thrombin
+SERPINB4 pp F2
+1U6B_B interactsWith SNRPA
+1U6B_C interactsWith 1U6B_B
+1U6B_D interactsWith 1U6B_B
+11-Mer_Peptide_From_C-Jun-Amino-Terminal_Kinase_Interacting_Protein_1 pp MAPK8
+11-Mer_Peptide_From_C-Jun-Amino-Terminal_Kinase_Interacting_Protein_1 pp MAPK8
+eIF4GI pp CBP20
+eIF4GI pp eIF4E
+CBP20 pp CBP80
+eIF4GI pp CBP80
+eIF4GII pp CBP80
+Fn14 pp Rac1
+Egr1 pp c/EBP-beta
+Ptc1 pp Cyclin_B1
+p85 pp Grb2
+p85 pp Shc
+ASC pp Bax
+TORC2 pp SIK2
+TORC2 pp 14-3-3-beta
+TORC2 pp CnA
+TORC1 pp CREB
+CBP pp CREB
+ATBF1 pp PIAS3
+NIK pp TRAF5
+NIK pp TRAF6
+h-beta-TrCP pp I-kappa-B-alpha
+Unknown interactsWith p65
+I-kappa-B-alpha interactsWith Unknown
+Unknown interactsWith Skp1
+Unknown interactsWith h-beta-TrCP
+hepcidin pp ferroportin
+SNCAIP pp SNCA
+APPswe pp X11-alpha
+PID pp p53
+Notch1 pp X11-alpha
+APPswe pp PS-1delta-9
+p53 interactsWith PID_complex
+alpha-synuclein pp hDAT
+Cdc2 interactsWith Unknown
+Cdc2 interactsWith Unknown
+RNF11 pp UbcH5a
+RNF11 pp UbcH5b
+RNF11 pp UbcH5c
+ARNT pp HIF-1-alpha
+BNIPL pp MIF
+BNIPL-2 pp Cdc42GAP
+LT-betaR pp LT-betaR
+SirT1 interactsWith Unknown
+CyclinT2b pp Cdk9
+CyclinT2a pp Cdk9
+XIAP pp Casp-3
+XIAP pp Casp-7
+XIAP pp Casp-6
+GSK3-beta pp BCL-3
+Erk1 pp BCL-3
+GSK3-alpha pp BCL-3
+p50 pp BCL-3
+p52 pp BCL-3
+HDAC1 pp BCL-3
+HDAC3 pp BCL-3
+HDAC6 pp BCL-3
+htt pp CA150
+htt pp HYPA
+htt pp HZFH
+htt pp IKAP
+htt pp Ku70
+htt pp PIASy
+htt pp HIP1
+htt pp PFN2
+htt pp SH3GL3
+htt pp FEZ1
+htt pp GIT1
+htt pp DRP-1
+htt pp CGI-125
+htt pp HIP5
+htt pp HIP11
+htt pp HIP13
+htt pp HIP16
+htt pp IKAP
+htt pp FEZ1
+htt pp GIT1
+htt pp HZFH
+htt pp IKAP
+htt pp Ku70
+htt pp PIASy
+htt pp CA150
+htt pp HYPA
+htt pp PFN2
+htt pp SH3GL3
+htt pp CGI-125
+htt pp HIP13
+htt pp CA150
+htt pp HYPA
+htt pp HP28
+htt pp PFN2
+htt pp SH3GL3
+htt pp CGI-125
+htt pp HIP13
+htt pp HIP15
+BARD1 pp CA150
+BARD1 pp HBO1
+BARD1 pp HZFH
+BARD1 pp IKAP
+BARD1 pp NAG4
+BARD1 pp PIASy
+BARD1 pp PLIP
+BARD1 pp SETDB1
+BARD1 pp ZHX1
+BARD1 pp mHAP1
+BARD1 pp PTN
+BARD1 pp FEZ1
+BARD1 pp GIT1
+BARD1 pp BAIP1
+BARD1 pp BAIP2
+BARD1 pp BAIP3
+BARD1 pp HIP5
+BARD1 pp HIP15
+CA150 pp HZFH
+CA150 pp PIASy
+CA150 pp SETDB1
+CA150 pp LUC7B1
+GADD45G pp PIASy
+GADD45G pp PLIP
+GADD45G pp PTN
+GADD45G pp GDF9
+GADD45G pp PTPK
+GADD45G pp EF1A
+GADD45G pp EF1G
+GADD45G pp BAIP3
+GADD45G pp CGI-74
+GADD45G pp CGI-125
+GADD45G pp G45IP1
+GADD45G pp G45IP2
+GADD45G pp G45IP3
+GADD45G pp HIP5
+GADD45G pp HIP16
+GADD45G pp LUC7B1
+hADA3 pp Ku70
+hADA3 pp PIASy
+hADA3 pp BAIP1
+hADA3 pp MAGEH1
+HYPA pp HZFH
+HYPA pp PIASy
+HYPA pp ZHX1
+HYPA pp MAP1lc3
+HZFH pp HZFH
+HZFH pp PIASy
+HZFH pp VIMc
+HZFH pp GIT1
+mp53 pp HZFH
+mp53 pp PIASy
+mp53 pp ZHX1
+PIASy pp SUMO-2
+PIASy pp SUMO-3
+PIASy pp MAP1lc3
+SUMO-3 pp HZFH
+SUMO-3 pp PIASy
+SUMO-3 pp SETDB1
+ZHX1 pp HZFH
+ZHX1 pp PIASy
+ZHX1 pp VIMc
+ZNF33B pp ZHX1
+ZNF33B pp mHAP1
+APP1 pp SETDB1
+APP1 pp GDF9
+APP1 pp EF1A
+APP1 pp BAIP1
+APP1 pp G45IP1
+APP1 pp HIP16
+CLH-17 pp Ku70
+HMP pp HZFH
+HMP pp PIASy
+HMP pp HMP
+HMP pp FEZ1
+KPNB1 pp HZFH
+KPNB1 pp PIASy
+KPNB1 pp PTN
+NEFL pp HZFH
+NEFL pp NAG4
+NEFL pp PIASy
+NEFL pp VIMc
+PTN pp HZFH
+PTN pp PIASy
+PTN pp PTN
+PTN pp FEZ1
+PTN pp HIP15
+VIM pp HBO1
+VIM pp HZFH
+VIM pp PIASy
+VIM pp SETDB1
+VIM pp NEFL
+VIM pp SH3GL3
+VIM pp VIMc
+VIM pp ALEX2
+VIM pp DRP-1
+VIM pp MOV34
+VIM pp BAIP1
+VIM pp G45IP1
+VIM pp HSPC232
+VIM pp HIP16
+ALEX2 pp ALEX2
+CLK1 pp PIASy
+GAPD pp PLIP
+IMPD2 pp PIASy
+TAL1 pp HZFH
+TAL1 pp ZHX1
+EF1G pp EF1G
+EF1G pp HIP11
+htt pp PIASy
+TCPG pp Ku70
+BAIP3 pp HBO1
+BAIP3 pp HZFH
+BAIP3 pp NAG4
+BAIP3 pp PIASy
+BAIP3 pp PLIP
+BAIP3 pp SETDB1
+BAIP3 pp APP1
+BAIP3 pp mHAP1
+BAIP3 pp HMP
+BAIP3 pp FEZ1
+BAIP3 pp GIT1
+BAIP3 pp BAIP2
+BAIP3 pp BAIP3
+BAIP3 pp HIP5
+BAIP3 pp HIP15
+G45IP3 pp SH3GL3
+G45IP3 pp KPNA2
+G45IP3 pp FEZ1
+G45IP3 pp GIT1
+G45IP3 pp BAIP1
+HIP5 pp HBO1
+HIP5 pp NAG4
+HIP5 pp PLIP
+HIP5 pp APP1
+HIP5 pp mHAP1
+HIP5 pp HMP
+HIP5 pp KPNA2
+HIP5 pp VIMc
+HIP5 pp FEZ1
+HIP5 pp GIT1
+HIP5 pp BAIP1
+HIP5 pp BAIP2
+HIP5 pp CGI-74
+HIP5 pp HIP15
+MAGEH1 pp PIASy
+MAGEH1 pp KPNA2
+E2F1 pp FHL2
+E2F4 pp FHL2
+E2F2 pp FHL2
+E2F3 pp FHL2
+E2F2 pp RYBP
+E2F3 pp RYBP
+DEF6 pp Rac2
+SirT1 pp H1b
+hEAAT2 pp hEAAT2
+hEAAT2_dimer interactsWith hEAAT2
+hSac1 pp alpha-COP
+hSac1 pp gamma-COP
+hSac1 pp beta-COP
+CDC2 pp cyclin_A2
+CDC2 pp cyclin_B2
+CDC2 pp cyclin_B1
+CDC2/cyclin_B1 interactsWith CDKN1A
+CK2alpha pp Bdp1
+ROMK pp NHERF-1
+IL2 pp IL2RA
+SirT1 pp H4
+SirT1 pp H3
+C/EBP-epsilon pp PU.1
+C/EBP-epsilon pp GATA-1
+PU.1 pp GATA-1
+Bdp1 pd U6_promoter
+KIAA1536 pp MAPK1
+RB1 pp MAPK1
+ROMK pp NHERF-2
+C-RAF pp OIP5
+p107 pd UXT
+p130 pd UXT
+TIP47 pp CI-MPR
+IL2 pp IL2RB
+PUM2 pp NOS1
+PUM2 pp PUM2
+Skp2 pp Rb
+Skp2 pp Skp1
+Skp2 pp p27
+p27 pp Cyc_A
+p27 pp Cyc_E
+Ub pp p27
+Unknown interactsWith HPH2
+Unknown interactsWith Bmi1
+Unknown interactsWith Ring2
+Ring1 interactsWith Unknown
+MBP-P2_promoter pd GATA-1
+M33 interactsWith Unknown
+p53 pp ERCC3
+Unknown interactsWith HPH3
+Unknown interactsWith HPH1
+p65 pd EAAT2_promoter
+Cdk2 pp p27
+RNF11 pp AMSH
+RNF11 pp Smurf2
+RNF11 pp AIP4
+RNF11 pp ZBRK1
+RNF11 pp EPS15
+RNF11 pp RPS27A
+RNF11 pp UbC
+FATZ pp ACTN2
+FATZ pp TELE
+FATZ pp FLNC
+BRCA1 pp NUFIP
+PM/Scl-75c-alpha pp hRrp41p
+Unknown interactsWith Snf2H
+Unknown interactsWith SCMH1
+Unknown interactsWith HPC2
+NP-2(a17) pp PlGF-2
+NP-2(a22) pp PlGF-2
+C-RAF pp CCT3
+E2F2 pp SET_07
+ADAM10 pp Eve-1c
+ADAM9 pp Eve-1c
+hMip130/TWIT pp p107
+hMip130/TWIT pp p130
+ADAM17 pp Eve-1c
+KPC1 pp KPC2
+KPC interactsWith p27Kip1
+DEF6 pp RhoA
+DEF6 pp Cdc42
+DEF6 pp Rac1
+BNIPL pp GFER
+ARC pp Fas
+ARC pp FADD
+ARC pp Bax
+ARC pp procaspase-8
+PCNA pp WSTF
+Gemin2 interactsWith Unknown
+Unknown interactsWith Gemin3
+Unknown interactsWith Gemin5
+Unknown interactsWith Gemin4
+Unknown interactsWith U1A
+Unknown interactsWith SmB'
+Unknown interactsWith SmD3
+Unknown interactsWith SmD2
+Unknown interactsWith SmG
+GAIT_element interactsWith GluProRS
+p38 pp GluProRS
+NSAP-1 pp GluProRS
+NSAP-1 pp GAPDH
+I-kappa-B-alpha interactsWith Unknown
+Unknown interactsWith RelA
+IKAP pp IKK-beta
+IKAP pp NIK
+IKAP pp IKK-alpha
+p38 pp LysRS
+MBP-P2_promoter pd PU.1
+NSAP-1 pp L13a
+Unknown interactsWith HSP70
+HDAC1 pp I-kappa-B-alpha
+HDAC3 pp I-kappa-B-alpha
+Unknown interactsWith p50
+Unknown interactsWith p65
+I-kappa-B-alpha interactsWith Unknown
+Unknown interactsWith RING1A
+Unknown interactsWith HPC3
+Raf-1 pp Rb
+Unknown interactsWith BMI1
+Unknown interactsWith HPH2
+Unknown interactsWith RING1B
+Gab2 pp GC-GAP
+Gab1 pp GC-GAP
+Nck pp GC-GAP
+Grap pp GC-GAP
+Src pp GC-GAP
+pRb pp hMip40
+pRb pp hMip120
+pRb pp hMip130/TWIT
+Cyclin_F pp Cyclin_B1
+MBP-P2_promoter pd C/EBP-epsilon
+MBP-P2_promoter pd C/EBP-beta
+SMN pp SmB'
+CD99 pp CypA
+CD99 pp ANXA2
+CD99 pp UBE2H
+CD99 pp KPNB1
+CD99 pp FTH1
+CD99 pp TRIP13
+CD99 pp SDCCAG3
+STAT1 pp STAT2
+Syk pp STAT1-alpha
+Syk pp STAT1-beta
+PS1 pp APP751
+12-LOX pp Integrin-beta4
+12-LOX pp Lamin_A
+SMN interactsWith Unknown
+p27Kip1 pp CRM1
+Unknown interactsWith Gemin5
+Unknown interactsWith Gemin3
+Unknown interactsWith Gemin4
+c-FLIP pp FADD
+caspase-8 pp FADD
+delta pp sigma-3A
+gamma-1 pp sigma-1A
+delta pp sigma-3B
+MM1 pp p73-alpha
+MEKK1 pp ERK2
+MEKK1 pp Raf-1
+MEKK1 pp MEK4
+MEKK1 pp MEK1
+MEKK1 pp MEK7
+ASIC3 pp PIST
+ASIC3 pp LIN-7B
+ASIC3 pp MAGI-1B
+ASIC3 pp DLG4
+Raf-1 pp p130
+p53 pp Sp1
+Crk pp GC-GAP
+IL-8_Promoter pd p65
+IL-8_Promoter pd p50
+IL-8_Promoter pd IKK-alpha
+IL-8_Promoter pd IKK-beta
+IL-8_Promoter pd p300
+IL-8 pd Pol_II
+IL-8_Promoter pd SMRT
+IL-8_Promoter pd HDAC3
+PS1 pp APP695
+IL-8_Promoter pd H3
+cIAP-2_Promoter pd p65
+cIAP-2_Promoter pd p50
+cIAP-2_Promoter pd IKK-alpha
+cIAP-2_Promoter pd IKK-beta
+cIAP-2_Promoter pd p300
+cIAP-2_Promoter pd SMRT
+cIAP-2_Promoter pd HDAC3
+cIAP-2_Promoter pd H3
+cIAP-2_Promoter pd Ubc5
+cIAP-2_Promoter pd 14-3-3-epsilon
+IKK-alpha pp SMRT
+14-3-3-epsilon pp SMRT
+LEMD3 pp Smad1
+LEMD3 pp Smad2
+CyclinT1 pp NUFIP
+Unknown interactsWith Gemin6
+Unknown interactsWith SMN
+Unknown interactsWith SmF
+Unknown interactsWith SmE
+Unknown interactsWith SmD1
+Unknown interactsWith Sip3
+Gemin6 pp SmD2
+Gemin6 pp SmD3
+Gemin6 pp SmE
+Unknown interactsWith Unrip/STRAP
+Gemin6 pp SmB
+Unknown interactsWith Gemin2
+Unknown interactsWith U1A
+Unknown interactsWith SmB/B'
+Unknown interactsWith Gemin6
+Unknown interactsWith Gemin7
+Unknown interactsWith TBL1
+Unknown interactsWith TBLR1
+Unknown interactsWith GPS2
+Unknown interactsWith HDAC3
+N-CoR pp HDAC3
+Unknown interactsWith IR10
+SMRT interactsWith Unknown
+N-CoR pp TBLR1
+N-CoR pp GPS2
+N-CoR pp TBL1
+RB pp c-Jun
+PBEF pp IR
+PBEF pp IGF-IR
+Insulin pp IGF-IR
+IGF-I pp IGF-IR
+Arp2/3 interactsWith Cortactin
+Arp2/3 interactsWith Scar
+Arp2/3 interactsWith WASP
+I-kappa-B-alpha interactsWith Unknown
+I-kappa-B-beta interactsWith Unknown
+I-kappa-B-epsilon interactsWith Unknown
+Unknown interactsWith cRel
+Unknown interactsWith RelA
+Unknown interactsWith Actin
+TRF1 interactsWith Telomeric_DNA
+TRF2 interactsWith Telomeric_DNA
+hSRY pp KRAB-O
+hRap1 interactsWith Telomeric_DNA
+Mre11 interactsWith Telomeric_DNA
+Beta-arr2 pp Smo
+Raf-1 pp MST2
+Raf-1 pp Hsp90
+MST2 pp MST2
+Actin interactsWith Arp2/3_Complex
+KCNMA1 pp HO-2
+DCC pp FAK
+Arf1-GTP interactsWith delta-sigma-3A_hemicomplex
+Arf1-GTP interactsWith delta-sigma-3B_hemicomplex
+CHFR pp PML
+Delta1 pp MAGI-1
+IL7 pp IL-7R-alpha
+RACK-1 pp STAT1-alpha
+RACK-1 pp STAT1-beta
+RACK-1 pp Jak1
+RACK-1 pp Tyk2
+IFNR-beta-L pp Jak1
+IFNR-beta-L pp Tyk2
+IFNR-beta-L pp RACK-1
+IL-4R-alpha pp RACK-1
+IL-2R-beta pp RACK-1
+EPOR pp RACK-1
+myosin_VIIa pp MyRIP
+Sp1 pd PgRA_promoter
+Sp1 pd PgRB_promoter
+ER-alpha pd PgRB_promoter
+ER-alpha pd PgRA_promoter
+ADAM12 pp Eve-1c
+ADAM12 pp Eve-1d
+FAK pp DCC
+TIRP pp TRAF6
+IL-10R-alpha pp Jak1
+IL-2R-beta pp Jak1
+FAK pp RIP
+Prelamin_A pp Lamin_C
+ErbB-2 pd p-PRPK
+ErbB-2 pd MMP16_locus
+ErbB-2 pd DDX10_locus
+Kaiso pd matrilysin_promoter
+Kaiso pd metastasin_promoter
+ADAM10 pp Eve-1d
+ADAM17 pp Eve-1d
+IL7 pp IL-2R-gamma
+IL7 interactsWith IL-2R-gamma-IL-7R
+Bub1/Bub3_complex interactsWith Cdc20
+Bub1 pp Bub3
+Mad2 pp Cdc20
+BubR1 pp Cdc20
+Bub1 pp Cdc20
+MeCP2 pd clone_RP11-403I13
+MeCP2 pd clone_RP11-9017
+MeCP2 pd DKFZp686D16148
+MeCP2 pd enpp4
+MeCP2 pd FLJ00132
+MBD1 pd shoygo(ax09h10)
+MBD1 pd Bing4
+MBD1 pd clone_RP11_576P10
+MBD2 pd pak2
+MBD2 pd cloneRP1-77N19
+MBD2 pd tbx19
+MBD2 pd atp5i
+MBD3 pd cox6c
+MBD3 pd LOC199704
+MBD3 pd leng6
+MBD3 pd clone_CTC-454I21
+MBD3 pd stearoyl-CoA_desaturase
+MBD3 pd Paired_box_protein_pax-6
+MBD2 pd mps-1
+MBD3 pd mps-1
+MBD2 pd cox6c
+MBD3 pd cox6c
+MBD2 pd ptpn4
+MBD3 pd ptpn4
+MBD1 pd efna5
+MBD2 pd efna5
+MBD3 pd efna5
+MBD1 pd bact2
+MBD2 pd bact2
+MBD3 pd bact2
+MBD1 pd dppiv
+MBD2 pd dppiv
+MBD3 pd dppiv
+MeCP2 pd clone:IMAGE:4550691
+MeCP2 pd pip5k
+MeCP2 pd FLJ32618
+MeCP2 pd FLJ32760
+MeCP2 pd CS0DJ015YH07
+MBD1 pd oatp-d
+MBD1 pd clone_YB67A06
+MBD1 pd ptprm
+MBD2 pd clone_RP1-207F6
+MBD2 pd kcnk10
+MBD2 pd prlr
+MBD2 pd clone_RP5-947L8
+MBD3 pd clone_RP13-202B6
+MBD3 pd bat5
+MBD2 pd DKFZp564E1878(hspc228)
+MBD3 pd DKFZp564E1878(hspc228)
+MBD2 pd HSPC228
+MBD3 pd HSPC228
+MBD2 pd mef2a
+MBD3 pd mef2a
+MBD1 pd alox12b
+MBD2 pd alox12b
+MBD3 pd alox12b
+MBD1 pd Apo-E
+MBD2 pd Apo-E
+MBD3 pd Apo-E
+MBD1 pd clone:IMAGE:3086912
+MBD2 pd clone:IMAGE:3086912
+MBD3 pd clone:IMAGE:3086912
+MBD1 pd crybb2
+MBD2 pd crybb2
+MBD3 pd crybb2
+MBD1 pd FLJ14146
+MBD2 pd FLJ14146
+MBD3 pd FLJ14146
+sorcin pp sorcin
+sorcin pp grancalcin
+hSGT pp myostatin
+p0071 pp VE-cadherin
+p0071 pp desmoplakin
+plakoglobin pp desmoplakin
+Kaiso pd Wnt11_promoter
+Nrg-1 pd PSD-95
+Nrg-1 pp Eos
+Nrg-1/Eos interactsWith PSD-95
+DDX3 pp CRM1
+AT1 pp AT1
+ELMO1 pp Dock180
+ELMO1/Dock180_complex interactsWith Rac
+FANCA interactsWith Unknown
+Unknown interactsWith FAAP250
+Unknown interactsWith FAAP100
+Unknown interactsWith FANCB
+Unknown interactsWith FANCG
+Unknown interactsWith FANCC
+Unknown interactsWith FANCE
+Unknown interactsWith FANCL
+Unknown interactsWith FANCF
+N-CoR interactsWith Unknown
+N-CoR-1 interactsWith BRG-1
+Unknown interactsWith BAF170
+Unknown interactsWith BAF155
+Unknown interactsWith BAF47
+FAK pp Neogenin
+DCC pp Fyn
+IRAK pp IRAK
+IRAK-M pp IRAK-M
+IRAK-2 pp IRAK-2
+IRAK pp IRAK-M
+IRAK pp IRAK-2
+IRAK-2 pp IRAK-M
+H3 pp RbAp48
+H4 pp RbAp48
+H2A pp RbAp48
+H2B pp TBLR1
+H4 pp TBLR1
+H4 pp TBL1
+H2B pp TBL1
+HDAC3 pp TBL1
+DDX3 pp Nup62
+PELP1 pp pRb
+PLP2/A4 pp CCR1
+ANCO-1 pp RAC3
+ANCO-1 pp HDAC3
+MCM7 pp Rb
+IRAK-2 pp MyD88
+IRAK-M pp MyD88
+IRAK-2 pp TRAF6
+IRAK-M pp TRAF6
+IL4R pp IL4
+IL4-IL4R interactsWith gamma-C
+Rac pp Dock180
+H3 pd PgRA_promoter
+H4 pd PgRA_promoter
+H3 pd PgRB_promoter
+H4 pd PgRB_promoter
+TRFP pp hIntersex
+Nut2 interactsWith Unknown
+Unknown interactsWith LCMR1
+Unknown interactsWith TRAP240
+Unknown interactsWith KIAA1025
+Unknown interactsWith TRAP230
+Unknown interactsWith TRAP220
+Unknown interactsWith RGR1
+Unknown interactsWith SUR2
+Unknown interactsWith TRAP100
+Unknown interactsWith TRAP95
+Unknown interactsWith PC2
+Unknown interactsWith ARC92
+Unknown interactsWith TRAP80
+Unknown interactsWith CRSP70
+Unknown interactsWith TRAP37
+Unknown interactsWith TRAP36
+Unknown interactsWith Med6
+Unknown interactsWith Med7
+Unknown interactsWith Med8
+Unknown interactsWith TRAP25
+Unknown interactsWith Srb7
+Unknown interactsWith Surf5
+Unknown interactsWith Soh1
+Unknown interactsWith HSPC296
+Sema3A pp Npn-1
+Sema3F pp Npn-2
+STAT5a pp STAT5a
+Cdk1 pp Gadd45a
+Cdk1 pp Gadd45b
+Cyclin_B1 pp Gadd45a
+Cdk1 pp Gadd45g
+Cyclin_B1 pp Gadd45b
+Cyclin_B1 pp Gadd45g
+Unknown interactsWith SF3a120
+Unknown interactsWith SAP130
+p14ARF pp E2F-1
+MCM7 pp p107
+TRFP pp p28b
+MCM7 pp p130
+CycH interactsWith Unknown
+Unknown interactsWith XPB
+Unknown interactsWith XPD
+Unknown interactsWith p62
+Unknown interactsWith p44
+Unknown interactsWith Cdk7
+ADAM9 pp Eve-1d
+ADAM15 pp Eve-1d
+ADAM15 pp Eve-1c
+ZNF216 pp A20
+ZNF216 pp ZNF216
+ZNF216 pp RIP
+ZNF216 pp TRAF6
+ZNF216 pp IKK-gamma
+ABIN-2 pp BAF60a
+LTC4S interactsWith Unknown
+Pol_I pp TIF-IA
+NMI pp TIF-IA
+Pol_I pp actin
+TIF-IA pp actin
+Pol_I pd rDNA
+TIF-IA pd rDNA
+actin pd rDNA
+NMI pd rDNA
+EED pp YY1
+Unknown interactsWith EZH2
+ANCO-1 pp TIF2
+ANCO-1 pp SRC-1
+menin pp ASK
+FBP pd FUSE
+IRAK pp MyD88
+IRF-3 pp CBP
+IRF-3 pd p-P56
+Drosha pp DGCR8
+Unknown interactsWith hnRNP_RALY
+Unknown interactsWith hnRNPM4
+Unknown interactsWith hnRNPUb
+Unknown interactsWith hnRNPU-like
+Unknown interactsWith hnRNPH1
+Unknown interactsWith hnRNPD-L
+HtrA2 pp APP
+Tpr2 pp Rad9
+TNF-R55 pp FAN
+TNF-R55 pp RACK1
+FAN pp RACK1
+Unknown interactsWith DDX1
+Unknown interactsWith DDX3X
+Unknown interactsWith DDX5
+Unknown interactsWith DDX15
+Unknown interactsWith 90kDa_NFAR
+Unknown interactsWith NF-AT_45K
+Unknown interactsWith FUS/TLS
+Unknown interactsWith TAF15
+Unknown interactsWith TDP-43
+Unknown interactsWith SRPK1a
+Unknown interactsWith EWS
+Unknown interactsWith DDX17
+Drosha/DGCR8_complex interactsWith Unknown
+TRAP36 pp TRAP25
+Surf5 pp TRAP25
+Surf5 pp HSPC296
+TRAP80 pp TRAP25
+TRAP37 pp TRAP25
+TRAP80 pp Surf5
+TRAP37 pp Surf5
+TRAP80 pp LCMR1
+TRAP37 pp LCMR1
+PYPAF1 pp ASC
+AR pd p-PSA
+AR pd p-KLK-2
+Pol_II pd p-PSA
+Pol_II pd p-KLK-2
+ACAP1 pp TfR
+ACAP1 pp Cbv
+TNFR1 interactsWith Unknown
+Unknown interactsWith TRADD
+Unknown interactsWith TRAF2
+Unknown interactsWith IKK-beta
+FAK pp integrin_beta_5
+CD95L pp Grb2
+Tf pp TfR
+CK2-beta_subunit pp CK2-alpha_subunit
+CtBP pp APC
+APC pp Beta-catenin
+LEF-1 pp Beta-catenin
+CtBP pp TCF-4
+CK2-beta_subunit pp CK2-alpha_subunit
+CK2-beta_subunit pp CK2-alpha_subunit
+CK2-beta_subunit pp CK2-beta_subunit
+CK2-beta_subunit pp CK2-alpha_subunit
+CD95L pp FBP17
+CD95L pp PACSIN2
+Skp1 pp Fbx3
+Skp1 pp Fbw2
+Skp1 pp Fbl2
+Skp1 pp Fbl4
+Skp1 pp Fbl5
+Skp1 pp Fbx7
+SIM2 pd EPO_enhancer
+p53 pd hdm2_promoter
+p53 interactsWith CKII
+p53 interactsWith CyclinA/Cdk2_complex
+STIP1 pp Hsp70
+STIP1 pp Hsp90
+TRPM4 pp TRPM4
+MBD2 pd BRCA1_promoter
+MBD2 pd GSTP1_promoter
+MBD2 pd MGMT_promoter
+MeCP2 pd GSTP1_promoter
+MeCP2 pd RASSF1_promoter
+MeCP2 pd RARB2_promoter
+Stat5b pp Stat5b
+STAT5a_dimer interactsWith STAT5a_dimer
+STAT5a_tetramer interactsWith IL2RA_promoter
+IL5R-alpha pp IL5
+Grb10 pp IR
+Grb10 pp IGFIR
+Grb10 pp EGFR
+TRIF pp TRAF6
+TRIF pp A20
+I-kappa-B-beta pp p65
+I-kappa-B-gamma interactsWith p50/p50
+PARP pp Caspase-7
+c-IAP1 pp caspase-7
+XIAP pp caspase-7
+hGBP3 pp HGK
+Stat3 pp CBP
+Stat3 pp p300
+Stat3 pp HDAC1
+Stat3 pp HDAC2
+Stat3 pp HDAC3
+Stat3 pp Stat3
+Mdm2 pp H3
+Mdm2 pp H4
+Miz1 pd p-P57KIP2
+Miz1 pd p-P21CIP1
+Miz1 pp Akt
+Miz1 pd p-p15Ink4b
+Miz1 pp 14-3-3_eta
+Mdm2 pd p21_promoter
+Miz1 pd p-H41
+ER-alpha pp c-Jun
+ASG3 pp ASG3
+LGN pp LGN
+NuMA pp Galphai1
+LGN pp Galphai1
+LGN pp NuMA
+TRADD pp FADD
+TRADD pp TRAF2
+ER-alpha pp JunB
+PICK1 pp BNC1a
+PICK1 pp BNC1b
+PICK1 pp ASIC
+PICK1 pp PICK1
+ER-alpha-c-Jun_complex interactsWith GRIP1
+SARA1 pp DCTN1
+DCTN2 pp DCTN1
+SEC24D pp DCTN1
+SEC23A pp DCTN1
+HES1_Promoter pd CBF1
+HES1_Promoter pd FACT
+HES1_Promoter pd HES1
+H3 pd pS2_promoter
+H4 pd pS2_promoter
+PS1 pp Bcl-2
+AIPL1 pp NUB1
+HRG4 pp ARL2
+Tie2 pp Ang2
+Tie2 pp Ang1
+Tie2 pp Ang4
+Tie2 pp Ang3
+VEGF pp KDR
+PUM2 pp DAZ
+Unknown interactsWith Notch
+HES1_Promoter pd RNAPII
+Unknown interactsWith MAM
+ARA55 pp AR
+Rab5 pp Rab5
+EGFR pp Grb2
+Grb2 pp Cbl
+Unknown interactsWith SKIP
+Unknown interactsWith CDK8
+PUM2 interactsWith NRE
+Unknown interactsWith Med220
+Unknown interactsWith p300
+Unknown interactsWith CDK7
+Unknown interactsWith Spt6
+Unknown interactsWith CDK9-CycT1_complex
+PUM2-NRE_complex interactsWith DAZL
+Unknown interactsWith SRCAP
+Arnt pp HIF1-alpha
+Arnt pp HLF
+Arnt pp AhR
+Arnt pp Arnt
+polycystin-1 pp FAK
+polycystin-1 pp beta-catenin
+FAK pp paxillin
+Wrch-1 pp Grb2
+CLUAP1 pp nCLU
+PINCH pp ILK
+PINCH pp Thymosin_Beta-4
+ILK pp Thymosin_Beta-4
+Calsarcin-1 pp gamma-filamin
+Calsarcin-3 pp gamma-filamin
+Calsarcin-2 pp gamma-filamin
+ZASP pp alpha-Actinin_2
+Wrch-1 pp PAK
+TIF-IA pp RPA43
+TIF-IA pp PAF67
+TIF-IA pp TAFI68
+TIF-IA pp TAFI95
+IL5-IL5R-alpha interactsWith IL5R-beta
+IL5R-beta interactsWith Unknown
+Unknown interactsWith PKC-beta_II
+SAE2 pp SUMO-1
+UBC9 pp RanGAP1
+SENP1 pp SP3
+SAE1 pp SAE2
+CK2-alpha_subunit pp CK2-beta_subunit
+CK2-beta_subunit pp CK2-beta_subunit
+CK2-alpha'_subunit pp CK2-beta_subunit
+Wrch-1 pp Nck
+Unknown interactsWith KAP-1
+Wrch-1 pp PLC-gamma
+Unknown interactsWith CBP
+CycT1 pp CDK9
+IKK-beta/NIK interactsWith I-kappa-B-alpha
+IKK-alpha/IKK-beta interactsWith I-kappa-B-alpha
+IKK-alpha/IKK-beta/NIK interactsWith I-kappa-B-alpha
+TRADD pp TRADD
+CDK8 pp MAM
+CGI-55 pp CHD-3
+Ki-1/57 pp CHD-3
+SP1 pd MDM2_intronic_promoter
+integrin_beta-7 pp WAIT-1
+integrin_alpha-4 pp WAIT-1
+integrin_alpha-E pp WAIT-1
+integrin_beta-2 pp cytohesin-1
+SKIP pp Notch
+Brn-2 pp p300
+beta-globin pd pol_II
+Brn-2 pp TBP
+FAK pp integrin_beta_1
+FAK pp integrin_beta_3
+Brn-2 pp Sox10
+SNRPD3 pp SNRPG
+SNRPN pp SNRPD1
+SNRPD3 pp SNRPN
+SNRPD2 pp SNRPF
+SNRPD2 pp SNRPD1
+SNRPE pp SNRPF
+SNRPE pp SNRPE
+Ras pp RalGDS
+SNRPD2 pp SNRPE
+SNRPD3 pp SNRPE
+Sox10 pp Sox10
+p300 pp MAML1
+E2F1 pd TTK
+E2F1 pd H2A
+E2F1 pd H2B
+E2F1 pd TYMS
+E2F1 pd FLJ10287
+E2F1 pd GAR22
+E2F1 pd FLJ11029
+E2F1 pd RECQL
+E2F1 pd CpG12B10
+E2F1 pd CpG32C1
+E2F1 pd CpG18G8
+E2F1 pd DBPA
+E2F1 pd RAD51
+E2F1 pd H4F2
+E2F1 pd HP1-alpha
+E2F1 pd MFAP1
+Unknown interactsWith Sin3A
+Unknown interactsWith HDAC1
+Unknown interactsWith HDAC2
+Unknown interactsWith HDAC3
+Unknown interactsWith SAP30
+N-CoR interactsWith Unknown
+Brn-2 pp Pax3
+Pax3 pp Sox10
+Integrin-alpha-1 pp TCPTP
+Integrin-alpha-1_/_beta-1 interactsWith TCPTP
+Brn-2 pp TFIIB
+FIG pp Syntaxin_6
+Psor pp Jab1
+TNFR1 interactsWith Unknown
+N-CoR-1 interactsWith HDAC3
+KChIP1 pp Kv4.2
+STRA13 pp STAT3-alpha
+MBD3 pp HDAC1
+MBD3 pp MTA2
+RLIP76 pp mu-2
+hMYH pp hMSH6
+RLIP76 pp alpha-adaptin
+STAT6 pp STAT6
+hMYH interactsWith hMutS-alpha
+HDAC3 pp TFII-I
+HDAC3 pp hMusTRD1
+p8 pp PTIP
+ZASP/Cypher-2 pp Calsarcin-3
+ZASP/Cypher-2 pp Calsarcin-2
+ZASP/Cypher-2 pp Calsarcin-1
+ZASP/Cypher-1 pp Calsarcin-3
+ZASP/Cypher-1 pp Calsarcin-2
+ZASP/Cypher-1 pp Calsarcin-1
+tTG pp importin-alpha3
+Tpr2 pp Tpr2
+Tpr2 pp Rad1
+Tpr2 pp Hus1
+hMusTRD1 pp PIASx-beta
+SCP1 pp REST
+AUF1p45 pp SAF-B
+AUF1p42 pp SAF-B
+SCP1-REST_complex interactsWith GRIN2A_RE-1
+SCP1-REST_complex interactsWith SCN2A2_RE-1
+SCP1-REST_complex interactsWith GAD1_RE-1
+Nox1 pp p22phox
+RIAM pp Profilin
+RIAM pp Rap1
+RIAM pp Ras
+RIAM pp VASP
+EGFR pp 14-3-3-zeta
+SNRPD2 pp SNRPE
+SNRPE pp SNRPG
+SNRPF pp SNRPG
+Artemis pp 53BP1
+IRS5/DOK4 pp RasGAP
+IRS5/DOK4 pp Crk
+IRS5/DOK4 pp Src
+IRS5/DOK4 pp Fyn
+RIAM pp Evl
+Cyclin_A interactsWith APC_complex
+UbcH10 pp UbcH10
+HalphaA-crystallin pp Bcl-Xs
+HalphaA-crystallin pp Bax
+HalphaB-crystallin pp Bax
+HalphaB-crystallin pp Bcl-Xs
+Geminin interactsWith APC_complex
+BCL6 pd p53_promoter
+SNAP19 pp SNAP190
+BCL6 pp SMRT
+BCL6 pd p-CCL3
+SMRT pd p-CCL3
+NcoR pd p-CCL3
+BCL6 pd p-CCND2
+SMRT pd p-CCND2
+NcoR pd p-CCND2
+CCS pp SOD1
+X11alpha pp APP
+X11alpha pp CCS
+SNAP43 pp SNAP50
+SNAP45 pp SNAP190
+LYPLA1 pp LYPLA1
+SKP2 pp SKP2
+SKP2 pp SKP2
+SKP2 pp SKP2
+SKP1A pp Cyclin_ACDK2-Associated_P19
+SKP1A pp SKP1A
+SKP1A pp Cyclin_ACDK2-Associated_P19
+SKP1A pp SKP2
+SKP2 pp SKP1A
+SKP2 pp SKP2
+SKP1A pp SKP2
+SKP1A pp SKP2
+MADH4 pp MADH4
+HIST1H2BD pp H2AFZ
+HIST1H3A pp H2AFZ
+HIST1H4A pp H2AFZ
+H2AFZ pp H2AFZ
+H2AFZ pp HIST1H3A
+H2AFZ pp HIST1H4A
+HIST1H2BD pp H2AFZ
+Mad_Protein_(Max_Dimerizer) pp Paired_Amphipathic_Helix_Protein_Sin3b
+FGFR2 pp FGF1
+FGFR2 pp FGFR2
+FGFR2 pp FGF1
+Uracil_Dna_Glycosylase_(Ung2) pp RPA2
+SRP14 pp SRP9
+SRP14 pp SRP9
+1E8O_E interactsWith SRP9
+1E8O_E interactsWith SRP14
+1E8O_E interactsWith SRP14
+1E8O_E interactsWith SRP9
+CXADR pp CXADR
+T-Cell_Receptor_Alpha_Chain pp HLA-DRB1
+T-Cell_Receptor_Beta_Chain pp T-Cell_Receptor_Alpha_Chain
+ALDOB pp ALDOB
+ALDOB pp ALDOB
+ALDOB pp ALDOB
+ALDOB pp ALDOB
+ALDOB pp ALDOB
+ALDOB pp ALDOB
+ALDOB pp ALDOB
+ALDOB pp ALDOB
+ALDOB pp ALDOB
+ALDOB pp ALDOB
+ALDOB pp ALDOB
+ALDOB pp ALDOB
+ALDOB pp ALDOB
+ALDOB pp ALDOB
+ALDOB pp ALDOB
+ALDOB pp ALDOB
+ALDOB pp ALDOB
+Liver_Glycogen_Phosphorylase pp Liver_Glycogen_Phosphorylase
+Liver_Glycogen_Phosphorylase pp Liver_Glycogen_Phosphorylase
+Beta-Defensin_2 pp Beta-Defensin_2
+Beta-Defensin_2 pp Beta-Defensin_2
+Beta-Defensin_2 pp Beta-Defensin_2
+Beta-Defensin_2 pp Beta-Defensin_2
+Beta-Defensin_2 pp Beta-Defensin_2
+Beta-Defensin_2 pp Beta-Defensin_2
+Beta-Defensin_2 pp Beta-Defensin_2
+Beta-Defensin_2 pp Beta-Defensin_2
+Beta-Defensin_2 pp Beta-Defensin_2
+Beta-Defensin_2 pp Beta-Defensin_2
+Beta-Defensin_2 pp Beta-Defensin_2
+Beta-Defensin_2 pp Beta-Defensin_2
+Beta-Defensin_2 pp Beta-Defensin_2
+ODC1 pp ODC1
+MMP3 pp MMP3
+MMP3 pp MMP3
+B-Cell_Surface_Antigen_Cd40 pp TRAF3
+B-Cell_Surface_Antigen_Cd40 pp TRAF3
+Insulin,_B_Chain pp Insulin,_A_Chain
+Insulin,_B_Chain pp Insulin,_A_Chain
+Insulin,_B_Chain pp Insulin,_B_Chain
+Insulin,_A_Chain pp Insulin,_B_Chain
+Insulin,_B_Chain pp Insulin,_A_Chain
+Insulin,_B_Chain pp Insulin,_B_Chain
+Insulin,_B_Chain pp Insulin,_A_Chain
+Insulin,_B_Chain pp Insulin,_B_Chain
+Insulin,_B_Chain pp Insulin,_A_Chain
+Insulin,_B_Chain pp Insulin,_A_Chain
+Insulin,_B_Chain pp Insulin,_B_Chain
+GTF2F1 pp GTF2F2
+IFNGR1 pp Interferon-Gamma
+Bone_Morphogenetic_Protein_Receptor_Ia pp BMP2
+BMP2 pp BMP2
+BMP2 pp Bone_Morphogenetic_Protein_Receptor_Ia
+Bone_Morphogenetic_Protein_Receptor_Ia pp BMP2
+CD69 pp CD69
+Myelin_Basic_Protein pp HLA-DRB5
+Antibody_17b,_Heavy_Chain pp Antibody_17b,_Light_Chain
+Antibody_17b,_Heavy_Chain pp Antibody_17b,_Light_Chain
+CCS pp CCS
+CCS pp CCS
+CCS pp CCS
+CCS pp CCS
+CCS pp CCS
+Antibody_M3c65_(Heavy_Chain) pp Antibody_M3c65_(Light_Chain)
+NXF1 pp NXF1
+NXF1 pp NXF1
+NXF1 pp NXF1
+NXF1 pp NXF1
+NXF1 pp NXF1
+NXF1 pp NXF1
+NXF1 pp NXF1
+XRCC4 pp XRCC4
+GCH1 pp GCH1
+GCH1 pp GCH1
+GCH1 pp GCH1
+GCH1 pp GCH1
+GCH1 pp GCH1
+PXR1 pp PXR1
+Hepatocyte_Growth_Factor_Receptor_Peptide pp GRB2
+SIN3A pp Mad1_Protein
+CEBPB pp Transcription_Factor_Atf-4
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Kappa-4_Immunoglobulin_(Light_Chain) pp Kappa-4_Immunoglobulin_(Light_Chain)
+B3GAT3 pp B3GAT3
+GZMB pp GZMB
+TYMS pp TYMS
+Igm-Kappa_Cold_Agglutinin_(Heavy_Chain) pp Igm-Kappa_Cold_Agglutinin_(Light_Chain)
+ATOX1 pp ATOX1
+ATOX1 pp ATOX1
+RAC1 pp TIAM1
+CDKN2C pp CDK6
+CDK6 pp CDK6
+DIABLO pp DIABLO
+BIRC4 pp DIABLO
+BIRC4 pp DIABLO
+BIRC4 pp DIABLO
+Cellular_Tumor_Antigen_P53 pp Cellular_Tumor_Antigen_P53
+ADH1C pp ADH1C
+ADH1C pp ADH1C
+ADH1C pp ADH1C
+S100A12 pp S100A12
+Transforming_Protein_P21H-Ras-1 pp PIK3CG
+TFF1 pp TFF1
+Syndecan-4 pp Syndecan-4
+Peptide_Py469 pp PTPN6
+FGF9 pp FGF9
+FGF9 pp FGF9
+FGF9 pp FGF9
+BAG1 pp HSPA8
+Kappa-4_Immunoglobulin_Light_Chain_Vl pp Kappa-4_Immunoglobulin_Light_Chain_Vl
+Bcl2-Like_11_(Apoptosis_Facilitator) pp DNCL1
+Bcl2-Like_11_(Apoptosis_Facilitator) pp DNCL1
+Bcl2-Like_11_(Apoptosis_Facilitator) pp DNCL1
+Bcl2-Like_11_(Apoptosis_Facilitator) pp DNCL1
+Nnos,_Neuronal_Nitric_Oxide_Synthase pp DNCL1
+Nnos,_Neuronal_Nitric_Oxide_Synthase pp DNCL1
+Nnos,_Neuronal_Nitric_Oxide_Synthase pp DNCL1
+Nnos,_Neuronal_Nitric_Oxide_Synthase pp DNCL1
+CXCL12 pp CXCL12
+CD81 pp CD81
+MIF pp MIF
+MIF pp MIF
+1E7K_C interactsWith NHP2L1
+RNASE1 pp RNASE1
+PPARG pp RXRA
+RXRA pp RXRA
+PPARG pp RXRA
+PPARG pp RXRA
+Steroid_Receptor_Coactivator pp RXRA
+Steroid_Receptor_Coactivator pp PPARG
+Antibody_(Heavy_Chain) pp CSF2RB
+F2 pp Thrombin
+UBE2C pp UBE2C
+CTLA4 pp CTLA4
+CD80 pp CD80
+CTLA4 pp CD80
+CTLA4 pp CD80
+LDHB pp LDHB
+LDHA pp LDHA
+LDHA pp LDHA
+LDHA pp LDHA
+LDHA pp LDHA
+LDHA pp LDHA
+LDHA pp LDHA
+Viral_Il-6 pp IL6ST
+FSHB pp CGA
+CGA pp FSHB
+CGA pp CGA
+FSHB pp CGA
+FSHB pp FSHB
+FSHB pp CGA
+CASP3 pp CASP3
+CASP3 pp CASP3
+CASP3 pp CASP3
+CASP3 pp CASP3
+CASP3 pp CASP3
+BIRC4 pp CASP3
+BIRC4 pp CASP3
+BIRC4 pp CASP3
+BIRC4 pp CASP3
+CASP7 pp CASP7
+Three_Residue_Peptide_Inhibitor pp MMP8
+Beta-Platelet-Derived_Growth_Factor_Receptor pp PIK3R1
+CEBPB pp CEBPB
+1IO4_E pd CEBPB
+1IO4_E pd CEBPB
+1IO4_F pd CEBPB
+1IO4_F pd CEBPB
+1HJB_G pd RUNX1
+1HJB_H pd RUNX1
+SLC4A1 pp SLC4A1
+ARFIP2 pp ARFIP2
+ARFIP2 pp ARFIP2
+RAC1 pp ARFIP2
+RAC1 pp ARFIP2
+ARFIP2 pp ARFIP2
+RAC1 pp ARFIP2
+RAC2 pp ARFIP2
+ARFIP2 pp ARFIP2
+RAC2 pp ARFIP2
+Ig_Gamma-1_Chain_C_Region pp Ig_Gamma-1_Chain_C_Region
+Ig_Gamma-1_Chain_C_Region pp Ig_Gamma-1_Chain_C_Region
+CDK2 pp CDKN3
+PGF pp PGF
+FGFR2 pp Heparin-Binding_Growth_Factor_2
+FGFR2 pp Heparin-Binding_Growth_Factor_2
+GSN pp ACTB
+ARHGDIA pp ARHGDIA
+ARHGDIA pp ARHGDIA
+ARHGDIA pp ARHGDIA
+RXRA pp RXRA
+RXRA pp RXRA
+RXRA pp RXRA
+RXRA pp RXRA
+CHC1 pp RAN
+RAN pp CHC1
+CHC1 pp RAN
+CHC1 pp CHC1
+YWHAZ pp YWHAZ
+AANAT pp YWHAZ
+AANAT pp YWHAZ
+RXRA pp RXRA
+RXRA pp RXRA
+RXRA pp RXRA
+Cr2CD121C3DEPSTEIN-Barr_Virus_Receptor pp C3
+Cr2CD121C3DEPSTEIN-Barr_Virus_Receptor pp Cr2CD121C3DEPSTEIN-Barr_Virus_Receptor
+Cr2CD121C3DEPSTEIN-Barr_Virus_Receptor pp C3
+P-Selectin_Peptide pp AP1M1
+B2M pp Hla_Class_I_Histocompatibility_Antigen,_Cw-4_Cw0401_Alpha_Chain
+Hla-Cw4-Specific_Peptide pp Hla_Class_I_Histocompatibility_Antigen,_Cw-4_Cw0401_Alpha_Chain
+Hla_Class_I_Histocompatibility_Antigen,_Cw-4_Cw0401_Alpha_Chain pp B2M
+B2M pp Hla_Class_I_Histocompatibility_Antigen,_Cw-4_Cw0401_Alpha_Chain
+Hla-Cw4-Specific_Peptide pp Hla_Class_I_Histocompatibility_Antigen,_Cw-4_Cw0401_Alpha_Chain
+Hla-Cw4-Specific_Peptide pp Hla_Class_I_Histocompatibility_Antigen,_Cw-4_Cw0401_Alpha_Chain
+Insulin_B pp Insulin_A
+Insulin_B pp Insulin_B
+Insulin_B pp Insulin_A
+CASP7 pp CASP7
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+KLRK1 pp KLRK1
+MICA pp KLRK1
+MICA pp KLRK1
+SRF pp SRF
+ELK4 pp SRF
+ELK4 pp SRF
+1HBX_W pd ELK4
+1HBX_W pd SRF
+1HBX_W pd SRF
+1HBX_C pd SRF
+1HBX_C pd ELK4
+1HBX_C pd SRF
+ACTN1 pp ACTN1
+IL12A pp IL12B
+Gamma-Delta_T-Cell_Receptor pp Gamma-Delta_T-Cell_Receptor
+Insulin_B pp Insulin_A
+Insulin_B pp Insulin_A
+Insulin_B pp Insulin_B
+Insulin_B pp Insulin_A
+Immunoglobulin_Heavy_Chain pp Immunoglobulin_Heavy_Chain
+Immunoglobulin_Light_Chain pp Immunoglobulin_Heavy_Chain
+Immunoglobulin_Light_Chain pp Immunoglobulin_Heavy_Chain
+Human_Monoclonal_Bo2c11_Fab_Heavy_Chain pp Human_Monoclonal_Bo2c11_Fab_Light_Chain
+F8 pp Human_Monoclonal_Bo2c11_Fab_Light_Chain
+F8 pp Human_Monoclonal_Bo2c11_Fab_Heavy_Chain
+XRCC5 pp G22P1
+CBS pp CBS
+Heavy_Chain_Of_Ig pp Kappa_Light_Chain_Of_Ig
+Heavy_Chain_Of_Ig pp Kappa_Light_Chain_Of_Ig
+Protein_L pp Kappa_Light_Chain_Of_Ig
+Protein_L pp Kappa_Light_Chain_Of_Ig
+XRCC5 pp G22P1
+F2 pp Thrombin,_Light_Chain
+Vav_Proto-Oncogene pp GRB2
+Vav_Proto-Oncogene pp GRB2
+UBE2N pp UBE2V2
+Insulin_B-Chain pp Insulin_A-Chain
+Insulin_B-Chain pp Insulin_A-Chain
+Insulin_B-Chain pp Insulin_B-Chain
+Melanoma-Associated_Antigen_4 pp HLA-A
+KIF11 pp KIF11
+CBFB pp RUNX1
+ALAD pp ALAD
+F7 pp F7
+DR1 pp DRAP1
+TBP pp DRAP1
+TBP pp DR1
+CASP8 pp CASP8
+CASP8 pp CASP8
+CASP8 pp CASP8
+CASP8 pp CASP8
+CASP8 pp CASP8
+SIRT2 pp SIRT2
+SIRT2 pp SIRT2
+NPR3 pp NPR3
+C-Type_Natriuretic_Peptide pp NPR3
+C-Type_Natriuretic_Peptide pp NPR3
+FCER1A pp FCER1A
+FCER1A pp FCER1A
+FCER1A pp FCER1A
+FCER1A pp FCER1A
+FCER1A pp FCER1A
+ARHGDIA pp RAC2
+ARHGDIA pp RAC2
+HLA-DQB1 pp HLA-DQA2
+Insulin_B_Peptide pp HLA-DQB1
+Insulin_B_Peptide pp HLA-DQA2
+CA12 pp CA12
+KPNB1 pp RAN
+TGFBR1 pp TGFBR1
+TGFBR1 pp TGFBR1
+TGFBR1 pp TGFBR1
+AKR1C2 pp AKR1C2
+Insulin_B_Chain pp Insulin_A_Chain
+BARD1 pp BRCA1
+IL17F pp IL17F
+IL17F pp IL17F
+IL17F pp IL17F
+IL17F pp IL17F
+IL17F pp IL17F
+Plasminogen_Activator_Inhibitor-2 pp SERPINB2
+GPHN pp GPHN
+GPHN pp GPHN
+GPHN pp GPHN
+Syndecan-4 pp Syndecan-4
+CD4 pp HLA-DQB1
+CD4 pp HLA-DQA2
+Splicing_Factor_U2af_65_Kda_Subunit pp U2AF1
+TYMS pp TYMS
+TYMS pp TYMS
+HBG2 pp HBG2
+HBG2 pp HBG2
+TERF2 pp TERF2
+F2 pp Thrombin
+PLAU pp Urokinase-Type_Plasminogen_Activator
+TRAF2 pp TRAF2
+TRAF2 pp TRAF2
+Cd_40_Peptide pp TRAF2
+Cd_40_Peptide pp TRAF2
+Myc_Proto-Oncogene_Protein pp KPNA5
+Myc_Proto-Oncogene_Protein pp KPNA5
+Mitogen-Activated_Protein_Kinase_Kinase_2 pp Lethal_Factor
+UROS pp UROS
+1K1G_B interactsWith Sf1-Bo_Isoform
+Peptide_N-Py pp SH2D1A
+Peptide_N-Y-C pp SH2D1A
+FNTB pp FNTA
+Fragment_Of_Wbp-1 pp 65_Kda_Yes-Associated_Protein
+9_Residue_Peptide pp HLA-A
+9_Residue_Peptide pp HLA-A
+9_Residue_Peptide pp HLA-A
+EGF pp EGF
+Hirudin_Iib pp F2
+1JID_B interactsWith SRP19
+NXF1 pp NXT1
+NXF1 pp NXT1
+Fg-Repeat pp NXF1
+ITGB5 pp ITGAV
+Insulin pp Insulin
+SELP pp SELP
+SELP pp SELP
+SELP pp SELP
+Psgl-1_Peptide pp SELP
+TNFRSF1A pp TNFRSF1A
+HGF pp HGF
+HGF pp HGF
+TRAF2 pp TRAF2
+TRAF2 pp TRAF2
+POU2F2 pp POU2F2
+Antibody_Germline_Precursor_To_28b4 pp Antibody_Germline_Precursor_To_28b4
+Antibody_Germline_Precursor_To_Antibody_28b4 pp Antibody_Germline_Precursor_To_Antibody_28b4
+NR1D1 pp NR1D1
+HGF pp HGF
+CRYGS pp CRYGS
+CASP7 pp CASP7
+CASP7 pp CASP7
+Cytotoxic_T-Lymphocyte_Protein_4 pp AP1M1
+CSF2RB pp CSF2RB
+Steroid_Receptor_Coactivator pp PPARA
+Steroid_Receptor_Coactivator pp RXRA
+Insulin_Receptor_Substrate_1 pp IGF1R
+Transcription_Factor_7-Like_2 pp JUP
+Htcf-4 pp CTNNB1
+DGUOK pp DGUOK
+XRCC4 pp XRCC4
+Dna_Ligase_Iv pp XRCC4
+Dna_Ligase_Iv pp XRCC4
+NTF5 pp NTF5
+NTRK2 pp NTF5
+NTRK2 pp NTF5
+NTRK2 pp NTF5
+NTRK2 pp NTF5
+CAPNS1 pp CAPN2
+CAPNS1 pp CAPN2
+GCA pp GCA
+MADH1 pp MADH1
+MADH1 pp MADH1
+MADH1 pp MADH1
+MADH1 pp MADH1
+MADH1 pp MADH1
+AUH pp AUH
+AUH pp AUH
+AUH pp AUH
+AUH pp AUH
+AUH pp AUH
+Ig_Chain_Heavy_Chain_Precursor_V_Region pp Ig_Kappa_Chain_Precursor_V_Region
+KLRK1 pp KLRK1
+ULBP3 pp KLRK1
+ULBP3 pp KLRK1
+Insulin pp Insulin
+CASP7 pp CASP7
+ETS1 pp PAX5
+ETS1 pp PAX5
+PAX5 pp ETS1
+EEA1 pp EEA1
+CD209 pp CD209
+CD209 pp CD209
+CD209 pp CD209
+CD209 pp CD209
+CD209 pp CD209
+CD209 pp CD209
+CD209 pp CD209
+CD209 pp CD209
+CD209 pp CD209
+CD209 pp CD209
+CD209 pp CD209
+FKBP1A pp FKBP1A
+FKBP1A pp FKBP1A
+FKBP1A pp FKBP1A
+FGF1 pp FGF1
+Ubiquitin pp Ubiquitin
+ESR1 pp ESR1
+GC pp GC
+GC pp GC
+Immunoglobulin_Fab_D3h44,_Heavy_Chain pp Immunoglobulin_Fab_D3h44,_Light_Chain
+F3 pp Immunoglobulin_Fab_D3h44,_Heavy_Chain
+F3 pp Immunoglobulin_Fab_D3h44,_Light_Chain
+NFAT5 pp NFAT5
+ASL pp ASL
+SRI pp SRI
+PTK2 pp PTK2
+PTK2 pp PTK2
+ST14 pp ST14
+CEBPB pp CEBPB
+CEBPB pp CEBPB
+CEBPB pp CEBPB
+HBB pp HBZ
+HBZ pp HBB
+HBZ pp HBZ
+HBB pp HBZ
+HBB pp HBZ
+F2 pp Thrombin
+SRF pp SRF
+NF2 pp NF2
+Adenomatous_Polyposis_Coli_Protein pp JUP
+CASP7 pp CASP7
+BIRC4 pp CASP7
+F2 pp Thrombin_Light_Chain
+VIM pp VIM
+S100A12 pp S100A12
+S100A12 pp S100A12
+S100A12 pp S100A12
+S100A12 pp S100A12
+S100A12 pp S100A12
+S100A12 pp S100A12
+S100A12 pp S100A12
+S100A12 pp S100A12
+S100A12 pp S100A12
+Insulin pp Insulin
+Insulin pp Insulin
+RNASE1 pp RNASE1
+CASP7 pp CASP7
+CASP7 pp CASP7
+CASP7 pp CASP7
+CASP7 pp CASP7
+CASP7 pp CASP7
+CASP7 pp CASP7
+BIRC4 pp CASP7
+BIRC4 pp CASP7
+BIRC4 pp CASP7
+TNFSF5 pp TNFSF5
+TNFSF5 pp TNFSF5
+Immunoglobulin_H pp TNFSF5
+Immunoglobulin_L pp TNFSF5
+Immunoglobulin_L pp Immunoglobulin_H
+Immunoglobulin_L pp TNFSF5
+S100A9 pp S100A9
+S100A9 pp S100A9
+S100A9 pp S100A9
+BST1 pp BST1
+BST1 pp BST1
+BST1 pp BST1
+1J4W_B pd FUBP1
+Hemagglutinin_Ha1_Peptide_Chain pp HLA-DRB1
+T-Cell_Receptor_Alpha_Chain pp HLA-DRB1
+T-Cell_Receptor_Alpha_Chain pp Hemagglutinin_Ha1_Peptide_Chain
+T-Cell_Receptor_Beta_Chain pp Hemagglutinin_Ha1_Peptide_Chain
+T-Cell_Receptor_Beta_Chain pp T-Cell_Receptor_Alpha_Chain
+T-Cell_Receptor_Beta_Chain pp HLA-DRB1
+TNFSF13B pp TNFSF13B
+TNFSF13B pp TNFSF13B
+TNFSF13B pp TNFSF13B
+TNFSF13B pp TNFSF13B
+TNFSF13B pp TNFSF13B
+TNFSF13B pp TNFSF13B
+GGA3 pp GGA3
+Cation-Dependent_Mannose-6-Phosphate_Receptor pp GGA3
+GGA3 pp GGA3
+Cation-Dependent_Mannose-6-Phosphate_Receptor pp GGA3
+GGA3 pp GGA3
+GGA3 pp GGA3
+Cation-Dependent_Mannose-6-Phosphate_Receptor pp GGA3
+Cation-Independent_Mannose-6-Phosphate_Receptor pp GGA1
+HBA2 pp HBA2
+HBB pp HBB
+CTSC pp CTSC
+CTSC pp CTSC
+CTSC pp CTSC
+RANBP1 pp RAN
+RANBP1 pp RAN
+Ran_Gtpase_Activating_Protein_1 pp RAN
+Ran_Gtpase_Activating_Protein_1 pp Ran_Gtpase_Activating_Protein_1
+Protein_Kinase_Byr2 pp Transforming_Protein_P21H-Ras-1
+PPARA pp PPARA
+Nuclear_Receptor_Co-Repressor_2 pp PPARA
+NXF1 pp NXF1
+NXF1 pp NXF1
+NXF1 pp NXF1
+NXF1 pp NXF1
+NXF1 pp NXF1
+NXF1 pp NXF1
+NXF1 pp NXF1
+NXF1 pp NXF1
+NXF1 pp NXF1
+NXF1 pp NXF1
+RANGAP1 pp UBE2I
+UBE2I pp RANGAP1
+RANGAP1 pp UBE2I
+RANGAP1 pp RANGAP1
+RANGAP1 pp UBE2I
+TGM2 pp TGM2
+GLUD2 pp GLUD2
+GLUD2 pp GLUD2
+GLUD2 pp GLUD2
+GLUD2 pp GLUD2
+NCBP2 pp NCBP1
+F2 pp Thrombin
+TBX3 pp TBX3
+RXRB pp RXRB
+RXRB pp RXRB
+RXRB pp RXRB
+RXRB pp RXRB
+RXRB pp RXRB
+1IV6_B pd TERF1
+1IV6_C pd TERF1
+IGF1R pp IGF1R
+IGF1R pp IGF1R
+IGF1R pp IGF1R
+NME1 pp NME1
+NME1 pp NME1
+NME1 pp NME1
+NME1 pp NME1
+NME1 pp NME1
+Steroid_Receptor_Coactivator-1 pp RORB
+S100A6 pp S100A6
+Traf_Family_Member-Associated_Nf-Kappa-B_Activator pp TRAF3
+Traf_Family_Member-Associated_Nf-Kappa-B_Activator pp TRAF3
+ESR1 pp ESR1
+ITGB5 pp ITGAV
+Hypoxia-Inducible_Factor_1_Alpha pp CREBBP
+GGH pp GGH
+SNRPA pp SNRPA
+1DZ5_C interactsWith SNRPA
+1DZ5_C interactsWith SNRPA
+1DZ5_D interactsWith 1DZ5_C
+MAD2L1 pp MAD2L1
+MAD2L1 pp MAD2L1
+MAD1L1 pp MAD2L1
+MAD1L1 pp MAD2L1
+MAD1L1 pp MAD1L1
+MAD1L1 pp MAD2L1
+MAD1L1 pp MAD2L1
+MAD1L1 pp MAD2L1
+MAD1L1 pp MAD2L1
+MAD1L1 pp MAD1L1
+MAD1L1 pp MAD1L1
+MAD1L1 pp MAD1L1
+MAD1L1 pp MAD2L1
+MAD1L1 pp MAD2L1
+Insulin-Like_Growth_Factor_Binding_Protein_5 pp IGF1
+GPI pp GPI
+AKR1C1 pp AKR1C1
+IGLL1 pp IGLL1
+VDR pp VDR
+ITSN1 pp CDC42
+PDE6D pp ARL2
+PDE6D pp ARL2
+Integrin_Beta-3 pp Integrin_Alpha-Iib
+Integrin_Beta-3 pp Integrin_Alpha-Iib
+RPA2 pp RPA3
+RPA1 pp RPA2
+RPA1 pp RPA3
+RPA3 pp RPA3
+RPA2 pp RPA3
+RPA1 pp RPA2
+RPA1 pp RPA3
+RPA1 pp RPA1
+ARHA pp MCF2L
+MCF2L pp ARHA
+RBX1 pp CUL1
+CUL1 pp CUL1
+RBX1 pp CUL1
+SKP1A pp CUL1
+Skp2-Like_Protein_Type_Gamma pp SKP1A
+Skp2-Like_Protein_Type_Gamma pp CUL1
+CHFR pp CHFR
+COL4A1 pp COL4A1
+COL4A2 pp COL4A1
+COL4A2 pp COL4A1
+COL4A1 pp COL4A1
+COL4A1 pp COL4A1
+COL4A1 pp COL4A2
+COL4A1 pp COL4A1
+COL4A2 pp COL4A1
+COL4A2 pp COL4A2
+Insulin pp Insulin
+Insulin_B_Chain pp Insulin_A_Chain
+TLE1 pp TLE1
+NUTF2 pp NUTF2
+TP53BP1 pp TP53
+ETV6 pp ETV6
+ETV6 pp ETV6
+GPI pp GPI
+BTK pp BTK
+GC pp GC
+GC pp ACTA1
+GGA3 pp GGA3
+GGA3 pp GGA3
+GGA3 pp GGA3
+ETV6 pp ETV6
+TCEB1 pp TCEB2
+VHL pp TCEB1
+VHL pp TCEB2
+Hypoxia-Inducible_Factor_1_Alpha pp VHL
+TCEB1 pp TCEB2
+VHL pp TCEB2
+Hypoxia-Inducible_Factor_1_Alpha pp VHL
+C1R pp C1R
+TIMP2 pp MMP2
+ME2 pp ME2
+ME2 pp ME2
+ME2 pp ME2
+B2M pp CD1B
+NMNAT1 pp NMNAT1
+NMNAT1 pp NMNAT1
+S100A3 pp S100A3
+Chimera_Of_Fab2c4:_"humanized"_Murine_Monoclonal_Antibody pp Chimera_Of_Fab2c4:_"humanized"_Murine_Monoclonal_Antibody
+Receptor_Activator_Of_Nuclear_Factor-Kappa_B pp TRAF6
+Cd40_Antigen pp TRAF6
+9d7_Light_Chain pp IL10
+DSP pp DSP
+ACTA1 pp GC
+IL2 pp IL2
+IL2 pp IL2
+NOS3 pp NOS3
+AP2B1 pp AP2A2
+AP1M2 pp AP2B1
+AP2S1 pp AP2B1
+CBFB pp RUNX1
+CBFB pp CBFB
+MMP2 pp MMP2
+Inhibitor_Peptide pp MMP2
+Inhibitor_Peptide pp MMP2
+ESR1 pp ESR1
+Nuclear_Receptor_Coactivator_2 pp ESR1
+Nuclear_Receptor_Coactivator_2 pp ESR1
+ESR1 pp ESR1
+ELA2 pp ELA2
+CDK5 pp CDK5
+CDK5R1 pp CDK5
+CDK5R1 pp CDK5
+DPEP1 pp DPEP1
+DPEP1 pp DPEP1
+F2 pp Thrombin,_Light_Chain
+CREBBP pp Tumor_Protein_P53
+UAP1 pp UAP1
+UAP1 pp UAP1
+UAP1 pp UAP1
+RAD52 pp RAD52
+RAD52 pp RAD52
+RAD52 pp RAD52
+RAD52 pp RAD52
+RAD52 pp RAD52
+1LPQ_B pd TOP1
+1LPQ_C pd TOP1
+GP1BA pp GP1BA
+GP1BA pp VWF
+ITGB5 pp ITGAV
+Beta-Secretase_Inhibitor_Om00-3 pp BACE
+CBS pp CBS
+NOS3 pp NOS3
+NOS3 pp NOS3
+Transcription_Initiation_Factor_Tfiid_2015_Kda_Subunits pp TAF4
+TAF4 pp Transcription_Initiation_Factor_Tfiid_2015_Kda_Subunits
+Transcription_Initiation_Factor_Tfiid_2015_Kda_Subunits pp TAF4
+Transcription_Initiation_Factor_Tfiid_2015_Kda_Subunits pp TAF4
+Transcription_Initiation_Factor_Tfiid_2015_Kda_Subunits pp Transcription_Initiation_Factor_Tfiid_2015_Kda_Subunits
+BRCA2 pp SHFM1
+Monoclonal_Antibody_Heavy_Chain pp Monoclonal_Antibody_Light_Chain
+F7 pp F7
+MAPKAPK2 pp MAPKAPK2
+PKM2 pp PKM2
+PKM2 pp PKM2
+PKM2 pp PKM2
+PKM2 pp PKM2
+PKM2 pp PKM2
+PKM2 pp PKM2
+PKM2 pp PKM2
+BHMT pp BHMT
+BHMT pp BHMT
+PPP3R1 pp PPP3CA
+PPIA pp PPP3CA
+PPIA pp PPP3R1
+PPP3CA pp PPIA
+PPP3R1 pp PPP3CA
+PPIA pp PPP3CA
+PPIA pp PPP3CA
+PPIA pp PPP3R1
+Platele_Integrin_Beta3_Subunit:__Cytoplasmic_Domain pp Platelet_Integrin_Alfaiib_Subunit:__Cytoplasmic_Domain
+1M8W_C interactsWith PUM2
+1M8W_E interactsWith 1M8W_C
+1M8W_E interactsWith PUM2
+1M8X_D interactsWith PUM2
+1M8Y_D interactsWith PUM2
+SRP19 interactsWith 1MFQ_A
+SRP54 interactsWith 1MFQ_A
+SRP54 pp SRP19
+BRCA2 pp SHFM1
+BRCA2 pp SHFM1
+1MJE_C pd BRCA2
+HBA2 pp HBA2
+HBB pp HBB
+Immunoglobulin_Heavy_Chain_Epsilon-1 pp Immunoglobulin_Heavy_Chain_Epsilon-1
+Frattide pp GSK3B
+NCBP2 pp NCBP1
+NCBP2 pp NCBP1
+NCBP2 pp NCBP1
+EGF pp EGFR
+ABL2 pp Crk
+B2M pp HLA-A
+F7 pp F7
+Farnesylated_K-Ras4b_Peptide_Product pp FNTA
+Farnesylated_K-Ras4b_Peptide_Product pp FNTB
+Farnesylated_K-Ras4b_Peptide_Product pp FNTB
+Farnesylated_K-Ras4b_Peptide_Product pp FNTA
+APOA2 pp APOA2
+APOA2 pp APOA2
+APOA2 pp APOA2
+APOA2 pp APOA2
+APOA2 pp APOA2
+APOA2 pp APOA2
+APOA2 pp APOA2
+APOA2 pp APOA2
+APOA2 pp APOA2
+APOA2 pp APOA2
+APOA2 pp APOA2
+APOA2 pp APOA2
+APOA2 pp APOA2
+APOA2 pp APOA2
+APOA2 pp APOA2
+APOA2 pp APOA2
+APOA2 pp APOA2
+APOA2 pp APOA2
+APOA2 pp APOA2
+APOA2 pp APOA2
+APOA2 pp APOA2
+APOA2 pp APOA2
+APOA2 pp APOA2
+APOA2 pp APOA2
+APOA2 pp APOA2
+APOA2 pp APOA2
+APOA2 pp APOA2
+APOA2 pp APOA2
+APOA2 pp APOA2
+APOA2 pp APOA2
+APOA2 pp APOA2
+APOA2 pp APOA2
+APOA2 pp APOA2
+APOA2 pp APOA2
+APOA2 pp APOA2
+APOA2 pp APOA2
+RUNX1 pp RUNX1
+CTNNBIP1 pp CTNNB1
+CTNNBIP1 pp JUP
+S100A4 pp S100A4
+PPP3R1 pp PPP3CA
+PPIA pp PPP3CA
+PPIA pp PPP3R1
+Madh-Interacting_Protein pp MADH3
+Nuclear_Receptor_Coactivator_2 pp RXRA
+Nuclear_Receptor_Coactivator_2 pp RXRA
+Nuclear_Receptor_Coactivator_2 pp RXRA
+RXRA pp RXRA
+Nuclear_Receptor_Coactivator_2 pp RXRA
+HADHSC pp HADHSC
+Hypoxia-Inducible_Factor_1_Alpha pp HIF1AN
+Hypoxia-Inducible_Factor_1_Alpha pp HIF1AN
+Histone_H3_Lysine_4_Specific_Methyltransferase pp Histone_H3_Lysine_4_Specific_Methyltransferase
+TCF1 pp TCF1
+TNFSF13B pp TNFSF13B
+TNFSF13B pp TNFSF13B
+GHR pp GH1
+GHR pp GH1
+T-Cell_Surface_Antigen_Cd2 pp CD2BP2
+Glycogen_Phosphorylase,_Liver_Form pp Glycogen_Phosphorylase,_Liver_Form
+Glycogen_Phosphorylase,_Liver_Form pp Glycogen_Phosphorylase,_Liver_Form
+APOA2 pp APOA2
+APOA2 pp APOA2
+APOA2 pp APOA2
+APOA2 pp APOA2
+APOA2 pp APOA2
+APOA2 pp APOA2
+APOA2 pp APOA2
+APOA2 pp APOA2
+APOA2 pp APOA2
+APOA2 pp APOA2
+APOA2 pp APOA2
+APOA2 pp APOA2
+APOA2 pp APOA2
+APOA2 pp APOA2
+Glycogen_Phosphorylase,_Liver_Form pp Glycogen_Phosphorylase,_Liver_Form
+Pulmonary_Surfactant-Associated_Protein_D pp Pulmonary_Surfactant-Associated_Protein_D
+Pulmonary_Surfactant-Associated_Protein_D pp Pulmonary_Surfactant-Associated_Protein_D
+Breast_Cancer_Type_2_Susceptibility_Protein pp RAD51
+Glycogen_Synthase_Kinase-3_Beta pp AKT2
+T-Cell_Receptor_Beta_Chain pp T-Cell_Receptor_Alpha_Chain
+PPARG pp PPARG
+Troponin_I,_Cardiac_Muscle pp TNNC1
+NOG pp BMP7
+ETS1 pp PAX5
+Cathepsin_L pp CTSL
+CTSL pp CTSL
+CTSL pp Cathepsin_L
+Cathepsin_L pp CTSL
+S100B pp S100B
+F-Actin_Capping_Protein_Alpha-1_Subunit pp S100B
+FKBP4 pp FKBP4
+ACPP pp ACPP
+ACPP pp ACPP
+ACPP pp ACPP
+ACPP pp ACPP
+ACPP pp ACPP
+ACPP pp ACPP
+ACPP pp ACPP
+ACPP pp ACPP
+ACPP pp ACPP
+ACPP pp ACPP
+HBB pp Hemoglobin_Alpha_Chain
+GSN pp ACTA1
+Transcription_Factor_E2f1 pp CCNA2
+Retinoblastoma-Associated_Protein pp CCNA2
+Cellular_Tumor_Antigen_P53 pp CCNA2
+Cyclin-Dependent_Kinase_Inhibitor_1b pp CCNA2
+Retinoblastoma-Like_Protein_1 pp CCNA2
+Ig_Gamma-1_Chain_C_Region pp Ig_Gamma-1_Chain_C_Region
+Ig_Gamma-1_Chain_C_Region pp Ig_Gamma-1_Chain_C_Region
+Ig_Gamma-1_Chain_C_Region pp Ig_Gamma-1_Chain_C_Region
+CD81 pp CD81
+Rna_Polymerase_Ii_Ctd_Phosphatase pp GTF2F1
+NMNAT1 pp NMNAT1
+NMNAT1 pp NMNAT1
+NMNAT1 pp NMNAT1
+NMNAT1 pp NMNAT1
+NMNAT1 pp NMNAT1
+NMNAT1 pp NMNAT1
+NMNAT1 pp NMNAT1
+NMNAT1 pp NMNAT1
+NMNAT1 pp NMNAT1
+NMNAT1 pp NMNAT1
+ESRRG pp ESRRG
+Steroid_Receptor_Coactivator_1 pp ESRRG
+Steroid_Receptor_Coactivator_1 pp ESRRG
+Parathyroid_Hormone-Related_Protein pp KPNB1
+IGF1R pp IGF1R
+ACTA1 pp GC
+ACTA1 pp GSN
+ACTA1 pp GSN
+ACTA1 pp GSN
+B2M pp HLA-B
+Tcr_Alpha_Chain pp HLA-B
+Tcr_Beta_Chain pp Tcr_Alpha_Chain
+Tcr_Beta_Chain pp HLA-B
+TLN1 pp Integrin_Beta3
+TLN1 pp Integrin_Beta3
+Integrin_Beta3 pp TLN1
+TLN1 pp Integrin_Beta3
+TLN1 pp Integrin_Beta3
+TLN1 pp Integrin_Beta3
+ITGAL pp ICAM1
+ICAM1 pp ICAM1
+SKI pp MADH4
+PSAP pp PSAP
+PSAP pp PSAP
+PSAP pp PSAP
+USP7 pp USP7
+UBA52 pp USP7
+UBA52 pp USP7
+UBA52 pp USP7
+UBA52 pp UBA52
+USP7 pp USP7
+USP7 pp USP7
+MAX pp MAD
+MAD pp MAD
+MAX pp MAX
+MAX pp MAD
+GP1BA pp GP1BA
+GPI pp GPI
+B2M pp HLA-E
+Peptide_Vmaprtvll pp HLA-E
+Peptide_Vtaprtlll pp HLA-E
+Plasma_Serine_Protease_Inhibitor pp SERPINA5
+1N3C_B pd OGG1
+1LWY_E pd OGG1
+Insulin_B-Chain pp Insulin_A-Chain
+NFYC pp NFYB
+1N39_C pd OGG1
+1N3A_C pd OGG1
+1N3C_C pd OGG1
+NCBP2 pp NCBP1
+NCBP2 pp NCBP1
+CSTA pp CSTA
+CSTA pp CTSH
+CSTA pp Cathepsin_H_Mini_Chain
+CSTA pp CTSH
+CSTA pp Cathepsin_H_Mini_Chain
+CSTA pp CTSH
+CSTA pp CTSH
+CSTA pp CTSH
+CSTA pp CTSH
+CTSH pp CSTA
+CSTA pp CTSH
+PARD6G pp CDC42
+1NH3_B interactsWith TOP1
+1NH3_C interactsWith TOP1
+1NH3_D interactsWith 1NH3_C
+1NH3_D interactsWith TOP1
+1NH3_D interactsWith 1NH3_B
+SNRPA pp SNRPA
+FGFR2 pp FGF10
+F2 pp Thrombin_Light_Chain
+Gene_Fragment_For_Histone_H3 pp Histone-Lysine_N-Methyltransferase,_H3_Lysine-4_Specific
+Fxfg_Nucleoporin_Peptide pp NXF1
+DAF pp DAF
+Lymphocyte_Cytosolic_Protein_2 pp GRAP2
+CHI3L1 pp CHI3L1
+CHI3L1 pp CHI3L1
+CHI3L1 pp CHI3L1
+CHI3L1 pp CHI3L1
+CHI3L1 pp CHI3L1
+CHI3L1 pp CHI3L1
+CHI3L1 pp CHI3L1
+CHI3L1 pp CHI3L1
+Marcks pp CALM2
+PLA2G2A pp PLA2G2A
+PSPH pp PSPH
+ACVR2 pp BMP7
+UBE1C pp APPBP1
+CASP3 pp CASP3
+CASP3 pp CASP3
+CASP3 pp CASP3
+TDP1 pp TDP1
+Topoisomerase_I-Derived_Peptide pp TDP1
+1NOP_D pd TDP1
+1NOP_D pd Topoisomerase_I-Derived_Peptide
+1NOP_F pd TDP1
+EGF pp EGFR
+SOS2 pp Transforming_Protein_P21H-Ras-1
+SOS2 pp Transforming_Protein_P21H-Ras-1
+SOS2 pp Transforming_Protein_P21H-Ras-1
+SOS2 pp Transforming_Protein_P21H-Ras-1
+SOS2 pp Transforming_Protein_P21H-Ras-1
+SOS2 pp Transforming_Protein_P21H-Ras-1
+SOS2 pp Transforming_Protein_P21H-Ras-1
+CASP9 pp BIRC4
+Immunoglobulin_Gamma-1_Heavy_Chain_Constant_Region pp Immunoglobulin_Gamma-1_Heavy_Chain_Constant_Region
+Immunoglobulin_Gamma-1_Heavy_Chain_Constant_Region pp Immunoglobulin_Gamma-1_Heavy_Chain_Constant_Region
+Hematopoietic_Prostagladin_D_Synthase pp Hematopoietic_Prostagladin_D_Synthase
+Signaling_Lymphocytic_Activation_Molecule pp SH2D1A
+FYN pp SH2D1A
+Thyroid_Hormone_Receptor_Beta-1 pp Thyroid_Hormone_Receptor_Beta-1
+GLUD1 pp GLUD1
+GLUD1 pp GLUD1
+GLUD1 pp GLUD1
+GLUD1 pp GLUD1
+GLUD1 pp GLUD1
+GLUD1 pp GLUD1
+GLUD1 pp GLUD1
+GLUD1 pp GLUD1
+GLUD1 pp GLUD1
+GLUD1 pp GLUD1
+Protein-Glutamine_Glutamyltransferase_E pp Protein-Glutamine_Glutamyltransferase_E
+Protein-Glutamine_Glutamyltransferase_E pp Protein-Glutamine_Glutamyltransferase_E
+INHBA pp ACVR2B
+INHBA pp ACVR2B
+Splicing_Factor_Sf1 pp U2AF2
+TNFSF13B pp TNFSF13B
+ARHA pp ARHGAP1
+TNFRSF13C pp TNFRSF13C
+IGF1R pp IGF1R
+ME2 pp ME2
+ME2 pp ME2
+ME2 pp ME2
+ME2 pp ME2
+ME2 pp ME2
+ME2 pp ME2
+Proto-Oncogene_C-Jun pp Proto-Oncogene_C-Jun
+1JNM_C pd Proto-Oncogene_C-Jun
+1JNM_C pd Proto-Oncogene_C-Jun
+1JNM_D pd Proto-Oncogene_C-Jun
+1JNM_D pd Proto-Oncogene_C-Jun
+P14-P8_Reactive_Loop_Peptide pp SERPINC1
+Antithrombin_P14-P9_Peptide pp SERPINC1
+Hiv-1_Capsid pp PPIA
+Hiv-1_Capsid pp PPIA
+NMNAT1 pp NMNAT1
+NMNAT1 pp NMNAT1
+NMNAT1 pp NMNAT1
+NMNAT1 pp NMNAT1
+NMNAT1 pp NMNAT1
+NMNAT1 pp NMNAT1
+CXCL10 pp CXCL10
+CXCL10 pp CXCL10
+CXCL10 pp CXCL10
+CXCL10 pp CXCL10
+CXCL10 pp CXCL10
+CXCL10 pp CXCL10
+CXCL10 pp CXCL10
+Serine_Phosphatase_Fcp1a pp GTF2F1
+Tumor_Necrosis_Factor_Receptor_Superfamily_Member_17 pp TNFSF13B
+Tumor_Necrosis_Factor_Receptor_Superfamily_Member_17 pp TNFSF13B
+Tumor_Necrosis_Factor_Receptor_Superfamily_Member_17 pp TNFSF13B
+Tumor_Necrosis_Factor_Receptor_Superfamily_Member_17 pp TNFSF13B
+Tumor_Necrosis_Factor_Receptor_Superfamily_Member_17 pp TNFSF13B
+Tumor_Necrosis_Factor_Receptor_Superfamily_Member_13c pp TNFSF13B
+Tumor_Necrosis_Factor_Receptor_Superfamily_Member_13c pp TNFSF13B
+Tumor_Necrosis_Factor_Receptor_Superfamily_Member_13c pp TNFSF13B
+TNFSF13B pp TNFSF13B
+TNFSF13B pp TNFSF13B
+TNFSF13B pp TNFSF13B
+TNFSF13B pp TNFSF13B
+TNFSF13B pp TNFSF13B
+TNFSF13B pp TNFSF13B
+TNFSF13B pp TNFSF13B
+FCAR pp FCAR
+Ig_Alpha-1_Chain_C_Region pp Ig_Alpha-1_Chain_C_Region
+FCAR pp Ig_Alpha-1_Chain_C_Region
+14.5_Kda_Translational_Inhibitor_Protein pp 14.5_Kda_Translational_Inhibitor_Protein
+14.5_Kda_Translational_Inhibitor_Protein pp 14.5_Kda_Translational_Inhibitor_Protein
+CEBPB pp CEBPB
+CEBPB pp CEBPB
+Polyadenylate-Binding_Protein-Interacting_Protein_2 pp PABPC3
+Polyadenylate-Binding_Protein-Interacting_Protein-1 pp PABPC3
+CAP1 pp CAP1
+IGLL1 pp IGLL1
+IGLL1 pp IGLL1
+PDHB pp PDHA1
+PDHA1 pp PDHB
+PDHA1 pp PDHA1
+PDHB pp PDHA1
+PDHB pp PDHB
+C1S pp C1S
+Vitronectin pp SERPINE1
+S100A12 pp S100A12
+T-Cell_Receptor_Alpha_Chain_V_Region pp HLA-A
+T-Cell_Receptor_Beta_Chain_C_Region pp T-Cell_Receptor_Alpha_Chain_V_Region
+T-Cell_Receptor_Beta_Chain_C_Region pp HLA-A
+SKP1A pp BTRC
+Beta-Catenin pp BTRC
+DCK pp DCK
+NR1H2 pp NR1H2
+NR3C1 pp NR3C1
+IL6 pp IL6ST
+IL6R pp IL6ST
+PARK7 pp PARK7
+PARK7 pp PARK7
+ME2 pp ME2
+ME2 pp ME2
+ME2 pp ME2
+ME2 pp ME2
+ME2 pp ME2
+ME2 pp ME2
+Antibody_2f5_(Heavy_Chain) pp Antibody_2f5_(Light_Chain)
+NR1H2 pp NR1H2
+NR1H2 pp NR1H2
+NR1H2 pp NR1H2
+ALAD pp ALAD
+B2M pp HLA-B
+Ebna-3_Nuclear_Protein pp HLA-B
+B2M pp HLA-A
+Hla_Dpa0201_Peptide pp HLA-A
+U4U6_SNRNP_60KDA_PROTEIN pp PPIH
+Phosphopantothenoylcysteine_Synthetase pp Phosphopantothenoylcysteine_Synthetase
+PF4 pp PF4
+PF4 pp PF4
+PF4 pp PF4
+PF4 pp PF4
+PF4 pp PF4
+PF4 pp PF4
+PF4 pp PF4
+PF4 pp PF4
+PF4 pp PF4
+PF4 pp PF4
+PF4 pp PF4
+PF4 pp PF4
+PF4 pp PF4
+PF4 pp PF4
+F2 pp Alpha_Thrombin
+BIRC7 pp BIRC7
+BIRC7 pp BIRC7
+CASP2 pp CASP2
+Acetyl-Leu-Asp-Glu-Ser-Asp-Cho pp CASP2
+Acetyl-Leu-Asp-Glu-Ser-Asp-Cho pp CASP2
+CASP2 pp CASP2
+CASP2 pp CASP2
+CASP2 pp CASP2
+CASP2 pp CASP2
+NR1I2 pp NR1I2
+RBM8A pp MAGOH
+MAGOH pp MAGOH
+RBM8A pp MAGOH
+KPNA2 pp Retinoblastoma-Associated_Protein
+Camp-Dependent_Protein_Kinase_Inhibitor,_Alpha_Form pp PRKACA
+DUT pp DUT
+DUT pp DUT
+DUT pp DUT
+DUT pp DUT
+Axin_Peptide pp GSK3B
+HBA2 pp HBA2
+HBB pp HBB
+MBL2 pp MBL2
+MBL2 pp MBL2
+MBL2 pp MBL2
+CCL17 pp CCL17
+MBL2 pp MBL2
+MBL2 pp MBL2
+GGA1 pp GGA1
+GGA1 pp GGA1
+TIMP1 pp MMP3
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Peptide_Ligand pp CDC14B
+F2 pp Human_Alpha_Thrombin
+Phe-Pro-Arg-Chloromethylketone pp F2
+GP1BA pp F2
+F2 pp Prothrombin
+F2 pp GP1BA
+TNNI3 pp TNNC1
+TNNI3 pp TNNC1
+Nuclear_Receptor_Coactivator_2 pp NR3C1
+NR3C1 pp NR3C1
+Nuclear_Receptor_Coactivator_2 pp NR3C1
+PPARG pp PPARG
+Fab_2g12,_Heavy_Chain pp Fab_2g12,_Heavy_Chain
+Fab_2g12,_Heavy_Chain pp Fab_2g12,_Heavy_Chain
+Fab_2g12,_Heavy_Chain pp Fab_2g12,_Heavy_Chain
+RALA pp RALA
+SEC5L1 pp RALA
+SEC5L1 pp RALA
+SEC5L1 pp RALA
+SEC5L1 pp RALA
+Antibody_2f5_(Heavy_Chain) pp Antibody_2f5_(Light_Chain)
+Thrombin pp Thrombin
+F2 pp Thrombin
+F2 pp Thrombin
+F2 pp Thrombin
+Haemadin pp F2
+Haemadin pp F2
+Haemadin pp F2
+Haemadin pp F2
+Ig_Gamma-1_Chain_C_Region pp Ig_Gamma-1_Chain_C_Region
+YWHAZ pp YWHAZ
+Phosphopeptide pp YWHAZ
+Transforming_Growth_Factor_Alpha pp EGFR
+BIN1 pp Myc_Box_Dependent_Interacting_Protein_1
+Steroid_Receptor_Coactivator-1 pp RORB
+GNPDA1 pp GNPDA1
+GNPDA1 pp GNPDA1
+GNPDA1 pp GNPDA1
+GNPDA1 pp GNPDA1
+GNPDA1 pp GNPDA1
+Myosin_Light_Chain_1,_Slow-Twitch_Muscle_A_Isoform pp MYO5A
+SEMA4D pp SEMA4D
+Troponin_I,_Cardiac_Muscle pp TNNC1
+NFATC2 pp NFATC2
+RAD23A pp 26s_Proteasome_Non-Atpase_Regulatory_Subunit_4
+ME2 pp ME2
+ME2 pp ME2
+Camp-Dependent_Protein_Kinase_Inhibitor,_Alpha_Form pp PRKACB
+Camp-Dependent_Protein_Kinase_Inhibitor,_Alpha_Form pp PRKACA
+HBA2 pp HBA2
+NME1 pp NME1
+Peptidyl-Prolyl_Cis-Trans_Isomerase_Nima-_Interacting_1 pp Microtubule-Associated_Protein_Tau
+CDA pp CDA
+GTF2A1 pp TBP
+GTF2A1 pp Transcription_Initiation_Factor_Iia_Alpha_Chain
+GTF2A2 pp GTF2A1
+GTF2A2 pp Transcription_Initiation_Factor_Iia_Alpha_Chain
+GTF2A2 pp TBP
+MAPKAPK2 pp MAPKAPK2
+MAPKAPK2 pp MAPKAPK2
+MAPKAPK2 pp MAPKAPK2
+MAPKAPK2 pp MAPKAPK2
+MAPKAPK2 pp MAPKAPK2
+HEXB pp HEXB
+HEXB pp HEXB
+HEXB pp HEXB
+HEXB pp HEXB
+HEXB pp HEXB
+Restricted_Expression_Proliferation_Associated_Protein_100 pp STK6
+PTK2 pp PTK2
+PTK2 pp PTK2
+PTK2 pp PTK2
+PTK2 pp PTK2
+PTK2 pp PTK2
+LILRB1 pp B2M
+LILRB1 pp HLA-A
+ACTA1 pp GSN
+ESR1 pp ESR1
+C1QG pp C1QA
+LIF pp IL6ST
+GGA1 pp GGA1
+MAX pp MAX
+NR1H4 pp RXRA
+B2M pp CD1B
+F2 pp Prothrombin
+F2 pp Prothrombin
+B2M pp HLA-B
+Tumor_Necrosis_Factor_Receptor_Associated_Factor_2 pp Tumor_Necrosis_Factor_Receptor_Associated_Factor_2
+Cd30_Peptide pp Tumor_Necrosis_Factor_Receptor_Associated_Factor_2
+Ig_Gamma-1_Chain_C_Region pp Ig_Gamma-1_Chain_C_Region
+Self-Peptide_P1049 pp HLA-A
+T-Cell_Receptor_Alpha_Chain pp HLA-A
+T-Cell_Receptor_Alpha_Chain pp Self-Peptide_P1049
+T-Cell_Receptor_Beta_Chain pp HLA-A
+T-Cell_Receptor_Beta_Chain pp Self-Peptide_P1049
+MEF2B pp MEF2B
+Calcineurin-Binding_Protein_Cabin_1 pp MEF2B
+Calcineurin-Binding_Protein_Cabin_1 pp MEF2B
+GMEB1 pp GMEB1
+Proto-Oncogene_Tyrosine-Protein_Kinase_Lck pp T-Cell_Surface_Glycoprotein_Cd4
+Proto-Oncogene_Tyrosine-Protein_Kinase_Lck pp T-Cell_Surface_Glycoprotein_Cd8_Alpha_Chain
+Melanoma-Associated_Antigen_3 pp HLA-A
+CLIC1 pp CLIC1
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Golgi_Autoantigen,_Golgin_Subfamily_A_Member_4 pp ARL1
+Golgi_Autoantigen,_Golgin_Subfamily_A_Member_4 pp ARL1
+Golgi_Autoantigen,_Golgin_Subfamily_A_Member_4 pp Golgi_Autoantigen,_Golgin_Subfamily_A_Member_4
+EGFR pp Hsp90
+PAK1 pp Grb2
+Rsk3 pp ERK2
+EphB6 pp AF6
+EphB3 pp AF6
+CD150 pp SHP-2
+SH2D1A pp CD150
+EphA7 pp AF6
+EphB2 pp AF6
+EGFR pp PAK1
+EGFR pp Vav2
+PDGFR pp SHC
+PDGFR pp Syp
+PDGFR pp Nck
+Unknown interactsWith RAG2
+RAG1 interactsWith Unknown
+hCDC4 pp cyclin_E
+PDGFR pp GAP
+PDGFR pp PLC-gamma
+RAG interactsWith Bcl2_Mbr
+Grb2 pp RN-tre
+EGFR interactsWith Grb2-RN-tre
+HNF1-alpha pd AADAC
+HNF1-alpha pd APOH
+HNF1-alpha pd ARHGAP11A
+HNF1-alpha pd BIKE
+HNF1-alpha pd C4BPA
+HNF1-alpha pd CTSZ
+HNF1-alpha pd CYB5-M
+HNF1-alpha pd DLEU1
+HNF1-alpha pd ELF3
+HNF1-alpha pd FE65L2
+HNF1-alpha pd FLJ10242
+HNF1-alpha pd FLJ10650
+HNF1-alpha pd FLJ13448
+HNF1-alpha pd FLJ21272
+HNF1-alpha pd FNTB
+HNF1-alpha pd GIOT-2
+HNF1-alpha pd HNF4a7
+HNF1-alpha pd KIAA0844
+HNF1-alpha pd MGC10500
+HNF1-alpha pd MIA2
+HNF1-alpha pd MRPL15
+HNF1-alpha pd NR0B2
+HNF1-alpha pd NR5A2
+HNF1-alpha pd PAFAH2
+HNF1-alpha pd PAX8
+HNF1-alpha pd PS-PLA1
+HNF1-alpha pd RAB33B
+HNF1-alpha pd SEL1L
+HNF1-alpha pd SGK2
+HNF1-alpha pd SRI
+HNF1-alpha pd SSTR1
+HNF1-alpha pd TM4SF4
+HNF1-alpha pd UQCRC2
+HNF1-alpha pd VNN3
+HNF1-alpha pd WBP4
+HNF1-alpha pd ABCC2
+HNF1-alpha pd ACF
+HNF1-alpha pd ADH1A
+HNF1-alpha pd ADH1B
+HNF1-alpha pd ADH6
+HNF1-alpha pd AGT
+HNF1-alpha pd AHSG
+HNF1-alpha pd AK2
+HNF1-alpha pd AKR1C2
+HNF1-alpha pd AKR1C3
+HNF1-alpha pd AKR1C4
+HNF1-alpha pd ALB
+HNF1-alpha pd ALDH3A2
+HNF1-alpha pd ALS2
+HNF1-alpha pd AMBP
+HNF1-alpha pd ANGPTL3
+HNF1-alpha pd ANPEP
+HNF1-alpha pd AP3M1
+HNF1-alpha pd APCS
+HNF1-alpha pd APG3
+HNF1-alpha pd APOA2
+HNF1-alpha pd AQP3
+HNF1-alpha pd AQP9
+HNF1-alpha pd ASGR1
+HNF1-alpha pd ASGR2
+HNF1-alpha pd ATF2
+HNF1-alpha pd AUTL1
+HNF1-alpha pd BAT3
+HNF1-alpha pd BTN2A1
+HNF1-alpha pd C1S
+HNF1-alpha pd C2
+HNF1-alpha pd C8B
+HNF1-alpha pd CCNE1
+HNF1-alpha pd CDCA1
+HNF1-alpha pd CISH
+HNF1-alpha pd CLYBL
+HNF1-alpha pd CNTNAP2
+HNF1-alpha pd CPB2
+HNF1-alpha pd CREBL2
+HNF1-alpha pd CRP
+HNF1-alpha pd CYB5
+HNF1-alpha pd CYP2E
+HNF1-alpha pd CYP3A43
+HNF1-alpha pd DAF
+HNF1-alpha pd DC13
+HNF1-alpha pd DKFZP564O0463
+HNF1-alpha pd DKFZP586A0522
+HNF1-alpha pd DKFZP586M0122
+HNF1-alpha pd DUSP6
+HNF1-alpha pd EIF4EBP2
+HNF1-alpha pd ENPEP
+HNF1-alpha pd F11
+HNF1-alpha pd FH
+HNF1-alpha pd FKSG87
+HNF1-alpha pd FLJ10276
+HNF1-alpha pd FLJ10525
+HNF1-alpha pd FLJ10583
+HNF1-alpha pd FLJ10774
+HNF1-alpha pd FLJ11000
+HNF1-alpha pd FLJ11838
+HNF1-alpha pd FLJ12788
+HNF1-alpha pd FLJ13611
+HNF1-alpha pd FLJ14356
+HNF1-alpha pd FLJ20080
+HNF1-alpha pd FLJ20718
+HNF1-alpha pd FLJ21934
+HNF1-alpha pd FLJ22551
+HNF1-alpha pd FLJ23259
+HNF1-alpha pd G0S2
+HNF1-alpha pd G3A
+HNF1-alpha pd G6PT1
+HNF1-alpha pd GARS
+HNF1-alpha pd GBE1
+HNF1-alpha pd GCKR
+HNF1-alpha pd GDI2
+HNF1-alpha pd GJB1
+HNF1-alpha pd GOT1
+HNF1-alpha pd GPR39
+HNF1-alpha pd GPX2
+HNF1-alpha pd GRHPR
+HNF1-alpha pd GTF2B
+HNF1-alpha pd GTF2E1
+HNF1-alpha pd GTPBG3
+HNF1-alpha pd HABP2
+HNF1-alpha pd HAL
+HNF1-alpha pd HAO1
+HNF1-alpha pd HCAP-G
+HNF1-alpha pd HGD
+HNF1-alpha pd HGFAC
+HNF1-alpha pd HNF4A
+HNF1-alpha pd HNMT
+HNF1-alpha pd HPCL2
+HNF1-alpha pd HPX
+HNF1-alpha pd HSD11B1
+HNF1-alpha pd HSD17B2
+HNF1-alpha pd HSPC111
+HNF1-alpha pd HSPC129
+HNF1-alpha pd IFNAR1
+HNF1-alpha pd IGF1R
+HNF1-alpha pd IGFBP1
+HNF1-alpha pd INADL
+HNF1-alpha pd ITIH3
+HNF1-alpha pd ITIH4
+HNF1-alpha pd ITM2B
+HNF1-alpha pd KIAA0022
+HNF1-alpha pd KIAA0669
+HNF1-alpha pd KIAA0872
+HNF1-alpha pd KIAA1041
+HNF1-alpha pd KNG
+HNF1-alpha pd LBP
+HNF1-alpha pd LOC51060
+HNF1-alpha pd LOC51096
+HNF1-alpha pd LOC51326
+HNF1-alpha pd LOC54518
+HNF1-alpha pd LOC56902
+HNF1-alpha pd LOC58486
+HNF1-alpha pd LY6E
+HNF1-alpha pd M17S2
+HNF1-alpha pd M96
+HNF1-alpha pd MAGEA9
+HNF1-alpha pd MGC11034
+HNF1-alpha pd MGC11266
+HNF1-alpha pd MGC13010
+HNF1-alpha pd MGC15435
+HNF1-alpha pd MGC955
+HNF1-alpha pd MRPS18B
+HNF1-alpha pd MSH6
+HNF1-alpha pd MT1H
+HNF1-alpha pd MT1L
+HNF1-alpha pd MT1X
+HNF1-alpha pd MTHFD1
+HNF1-alpha pd MTP
+HNF1-alpha pd NAPA
+HNF1-alpha pd NET-2
+HNF1-alpha pd NFKBIB
+HNF1-alpha pd NPC1L1
+HNF1-alpha pd NR1D1
+HNF1-alpha pd NRD1
+HNF1-alpha pd PCK1
+HNF1-alpha pd PHF2
+HNF1-alpha pd PIST
+HNF1-alpha pd PLCB1
+HNF1-alpha pd PLG
+HNF1-alpha pd PLGL
+HNF1-alpha pd PZP
+HNF1-alpha pd RAMP
+HNF1-alpha pd RARB
+HNF1-alpha pd RBP5
+HNF1-alpha pd RNGTT
+HNF1-alpha pd RPL37AP1
+HNF1-alpha pd SAC
+HNF1-alpha pd SCYE1
+HNF1-alpha pd SERPINA1
+HNF1-alpha pd SERPINA10
+HNF1-alpha pd SERPINA6
+HNF1-alpha pd SERPINC1
+HNF1-alpha pd SERPINE1
+HNF1-alpha pd SERPING1
+HNF1-alpha pd SLC17A2
+HNF1-alpha pd SLC22A11
+HNF1-alpha pd SLPI
+HNF1-alpha pd SNX17
+HNF1-alpha pd SSA2
+HNF1-alpha pd SSTR4
+HNF1-alpha pd STRAIT11499
+HNF1-alpha pd SUPV3L1
+HNF1-alpha pd SYN3
+HNF1-alpha pd TARS
+HNF1-alpha pd TBPL1
+HNF1-alpha pd TEF
+HNF1-alpha pd TFRC
+HNF1-alpha pd TIEG2
+HNF1-alpha pd TMEM1
+HNF1-alpha pd TNFRSF6
+HNF1-alpha pd UGT1A1
+HNF1-alpha pd UGT2B11
+HNF1-alpha pd UGT2B15
+HNF1-alpha pd VTN
+HNF1-alpha pd WDF2
+HNF1-alpha pd WDR12
+HNF1-alpha pd XDH
+HNF1-alpha pd XPC
+HNF1-alpha pd ZK1
+HNF1-alpha pd ZNF288
+HNF1-alpha pd ZNF361
+HNF1-alpha pd ABCC9
+HNF1-alpha pd ADH4
+HNF1-alpha pd B29
+HNF1-alpha pd BCL6
+HNF1-alpha pd C6orf11
+HNF1-alpha pd CDC45L
+HNF1-alpha pd COL3A1
+HNF1-alpha pd COQ7
+HNF1-alpha pd CPXCR1
+HNF1-alpha pd CRH
+HNF1-alpha pd DKFZP564J157
+HNF1-alpha pd DOCK1
+HNF1-alpha pd DSC1
+HNF1-alpha pd EIF3S6
+HNF1-alpha pd FBXO8
+HNF1-alpha pd FIL1(EPSILON)
+HNF1-alpha pd FLJ10252
+HNF1-alpha pd FLJ10474
+HNF1-alpha pd FLJ11301
+HNF1-alpha pd FLJ13273
+HNF1-alpha pd FLJ13385
+HNF1-alpha pd FLJ14855
+HNF1-alpha pd FLJ20156
+HNF1-alpha pd FLJ20225
+HNF1-alpha pd FLJ20234
+HNF1-alpha pd FLJ20298
+HNF1-alpha pd FLJ20643
+HNF1-alpha pd FLJ20731
+HNF1-alpha pd FLJ22559
+HNF1-alpha pd GCNT3
+HNF1-alpha pd GLA
+HNF1-alpha pd GNB2L1
+HNF1-alpha pd GPR74
+HNF1-alpha pd H4F2
+HNF1-alpha pd HAVCR-1
+HNF1-alpha pd HHLA2
+HNF1-alpha pd IFNA10
+HNF1-alpha pd INSR
+HNF1-alpha pd KIAA0101
+HNF1-alpha pd KIAA0399
+HNF1-alpha pd KIF13A
+HNF1-alpha pd KIR-023GB
+HNF1-alpha pd KIR2DS2
+HNF1-alpha pd KIR3DL1
+HNF1-alpha pd KRTAP1.1
+HNF1-alpha pd KRTHA3A
+HNF1-alpha pd LIPA
+HNF1-alpha pd LOC113201
+HNF1-alpha pd LOC113220
+HNF1-alpha pd LOC51092
+HNF1-alpha pd LOC56906
+HNF1-alpha pd MCCC1
+HNF1-alpha pd MGC15677
+HNF1-alpha pd Nod1(-)6kb
+HNF1-alpha pd NPY2R
+HNF1-alpha pd NR2C2
+HNF1-alpha pd pcnp
+HNF1-alpha pd PEX13
+HNF1-alpha pd PGCP
+HNF1-alpha pd PRO2032
+HNF1-alpha pd PSMA5
+HNF1-alpha pd RAB6KIFL
+HNF1-alpha pd SDCCAG10
+HNF1-alpha pd SLC26A7
+HNF1-alpha pd SPO11
+HNF1-alpha pd TACR3
+HNF1-alpha pd TMOD2
+HNF1-alpha pd TMP21
+HNF1-alpha pd UROD
+HNF1-alpha pd ZNF155
+HNF1-alpha pd ZNF300
+HNF4-alpha pd AK2
+HNF4-alpha pd ALS2
+HNF4-alpha pd AP3M1
+HNF4-alpha pd APG3
+HNF4-alpha pd AQP3
+HNF4-alpha pd ARHGAP11A
+HNF4-alpha pd AUTL1
+HNF4-alpha pd BAT3
+HNF4-alpha pd CDCA1
+HNF4-alpha pd CREBL2
+HNF4-alpha pd CYB5-M
+HNF4-alpha pd DC13
+HNF4-alpha pd DKFZP564O0463
+HNF4-alpha pd FE65L2
+HNF4-alpha pd FH
+HNF4-alpha pd FLJ10276
+HNF4-alpha pd FLJ10525
+HNF4-alpha pd FLJ10583
+HNF4-alpha pd FLJ10774
+HNF4-alpha pd FLJ11000
+HNF4-alpha pd FLJ11838
+HNF4-alpha pd FLJ12788
+HNF4-alpha pd FLJ13611
+HNF4-alpha pd FLJ20080
+HNF4-alpha pd FLJ21272
+HNF4-alpha pd FLJ21934
+HNF4-alpha pd FLJ22551
+HNF4-alpha pd FNTB
+HNF4-alpha pd GOT1
+HNF4-alpha pd GTF2E1
+HNF4-alpha pd HGD
+HNF4-alpha pd HPCL2
+HNF4-alpha pd HSPC111
+HNF4-alpha pd HSPC129
+HNF4-alpha pd KIAA0872
+HNF4-alpha pd KIAA1041
+HNF4-alpha pd LOC51060
+HNF4-alpha pd LOC51096
+HNF4-alpha pd LOC51326
+HNF4-alpha pd LOC56902
+HNF4-alpha pd M17S2
+HNF4-alpha pd M96
+HNF4-alpha pd MGC11266
+HNF4-alpha pd MRPS18B
+HNF4-alpha pd MTHFD1
+HNF4-alpha pd NAPA
+HNF4-alpha pd NFKBIB
+HNF4-alpha pd NRD1
+HNF4-alpha pd PAFAH2
+HNF4-alpha pd PIST
+HNF4-alpha pd RAMP
+HNF4-alpha pd RNGTT
+HNF4-alpha pd SCYE1
+HNF4-alpha pd SEL1L
+HNF4-alpha pd SNX17
+HNF4-alpha pd SSA2
+HNF4-alpha pd SUPV3L1
+HNF4-alpha pd UQCRC2
+HNF4-alpha pd WBP4
+HNF4-alpha pd WDF2
+HNF4-alpha pd WDR12
+HNF4-alpha pd XPC
+HNF4-alpha pd ZNF361
+HNF4-alpha pd C6orf11
+HNF4-alpha pd FBXO8
+HNF4-alpha pd FLJ13273
+HNF4-alpha pd H4F2
+HNF4-alpha pd MGC15677
+HNF4-alpha pd PEX13
+HNF4-alpha pd PSMA5
+HNF4-alpha pd RAB6KIFL
+HNF4-alpha pd SDCCAG10
+HNF4-alpha pd TMOD2
+HNF4-alpha pd TMP21
+HNF4-alpha pd UROD
+HNF4-alpha pd ZNF155
+HNF4-alpha pd C20orf188
+HNF4-alpha pd CDC25A
+HNF4-alpha pd COPB2
+HNF4-alpha pd CYP51
+HNF4-alpha pd D13S106E
+HNF4-alpha pd DKFZP564O0523
+HNF4-alpha pd FACTP140
+HNF4-alpha pd FLJ10407
+HNF4-alpha pd FLJ10415
+HNF4-alpha pd FLJ11029
+HNF4-alpha pd FLJ12770
+HNF4-alpha pd FLJ12910
+HNF4-alpha pd FLJ13798
+HNF4-alpha pd FLJ20084
+HNF4-alpha pd FLJ20627
+HNF4-alpha pd FLJ20671
+HNF4-alpha pd FLJ22169
+HNF4-alpha pd FLJ23263
+HNF4-alpha pd FLJ23499
+HNF4-alpha pd GABPA
+HNF4-alpha pd GSS
+HNF4-alpha pd HBP1
+HNF4-alpha pd KIAA0806
+HNF4-alpha pd LOC51287
+HNF4-alpha pd LOC51633
+HNF4-alpha pd LOC81558
+HNF4-alpha pd MGC4189
+HNF4-alpha pd MGST3
+HNF4-alpha pd NOLC1
+HNF4-alpha pd PSMA1
+HNF4-alpha pd REA
+HNF4-alpha pd RPS6KA5
+HNF4-alpha pd SAS10
+HNF4-alpha pd SEC10L1
+HNF4-alpha pd SERPINI1
+HNF4-alpha pd SLC7A9
+HNF4-alpha pd SNW1
+HNF4-alpha pd TOMM70A
+HNF4-alpha pd TSG101
+HNF4-alpha pd URKL1
+HNF4-alpha pd AF15Q14
+HNF4-alpha pd ARL1
+HNF4-alpha pd C2F
+HNF4-alpha pd CLONE24922
+HNF4-alpha pd COX7A2L
+HNF4-alpha pd MDH1
+HNF4-alpha pd MGC19595
+HNF4-alpha pd NUDT2
+HNF4-alpha pd TEGT
+HNF4-alpha pd ABCB10
+HNF4-alpha pd ABCG1
+HNF4-alpha pd ABS
+HNF4-alpha pd ABT1
+HNF4-alpha pd ACADSB
+HNF4-alpha pd ACO2
+HNF4-alpha pd ACOX1
+HNF4-alpha pd ACOX3
+HNF4-alpha pd ACP2
+HNF4-alpha pd AD022
+HNF4-alpha pd AD034
+HNF4-alpha pd AD158
+HNF4-alpha pd AD24
+HNF4-alpha pd AF093680
+HNF4-alpha pd AF140225
+HNF4-alpha pd AGA
+HNF4-alpha pd ANKRA2
+HNF4-alpha pd AP1M1
+HNF4-alpha pd AP2A1
+HNF4-alpha pd AP4B1
+HNF4-alpha pd APC10
+HNF4-alpha pd APMCF1
+HNF4-alpha pd GTF2H1
+HNF4-alpha pd H326
+HNF4-alpha pd HAAO
+HNF4-alpha pd HAX1
+HNF4-alpha pd HBQ1
+HNF4-alpha pd HBXIP
+HNF4-alpha pd HCDI
+HNF4-alpha pd HEL308
+HNF4-alpha pd HEXA
+HNF4-alpha pd HKE2
+HNF4-alpha pd HKE4
+HNF4-alpha pd HMG1
+HNF4-alpha pd HNRPA1
+HNF4-alpha pd HPRP4P
+HNF4-alpha pd HSPA5
+HNF4-alpha pd HSPC051
+HNF4-alpha pd HSPC052
+HNF4-alpha pd HSPC117
+HNF4-alpha pd HSPC141
+HNF4-alpha pd HSPC157
+HNF4-alpha pd HSPC166
+HNF4-alpha pd HSU79274
+HNF4-alpha pd HSU84971
+HNF4-alpha pd HT010
+HNF4-alpha pd IER5
+HNF4-alpha pd IFRD1
+HNF4-alpha pd RNPC2
+HNF4-alpha pd RPL18
+HNF4-alpha pd RPL31
+HNF4-alpha pd RPL7
+HNF4-alpha pd RPS16
+HNF4-alpha pd RPS19
+HNF4-alpha pd RPS27A
+HNF4-alpha pd RPS3A
+HNF4-alpha pd RPS6KB1
+HNF4-alpha pd RSU1
+HNF4-alpha pd RXRB
+HNF4-alpha pd SAD1
+HNF4-alpha pd SAP18
+HNF4-alpha pd SDCCAG28
+HNF4-alpha pd SDFR1
+HNF4-alpha pd SEC61B
+HNF4-alpha pd SENP1
+HNF4-alpha pd SES2
+HNF4-alpha pd SF3A3
+HNF4-alpha pd SF3B2
+HNF4-alpha pd SFRS11
+HNF4-alpha pd SFRS5
+HNF4-alpha pd SFRS8
+HNF4-alpha pd SGT1
+HNF4-alpha pd SH3BGRL2
+HNF4-alpha pd SKB1
+HNF4-alpha pd SKD1
+HNF4-alpha pd AQP6
+HNF4-alpha pd ARF1GAP
+HNF4-alpha pd ARFD1
+HNF4-alpha pd ARS2
+HNF4-alpha pd ASB3
+HNF4-alpha pd ATF4
+HNF4-alpha pd ATF7
+HNF4-alpha pd ATP5F1
+HNF4-alpha pd ATP5G3
+HNF4-alpha pd ATP6M
+HNF4-alpha pd ATP6S14
+HNF4-alpha pd AUP1
+HNF4-alpha pd BAT1
+HNF4-alpha pd BAT4
+HNF4-alpha pd BAZ1B
+HNF4-alpha pd BCCIP
+HNF4-alpha pd BCS1L
+HNF4-alpha pd BET1
+HNF4-alpha pd BRCA1
+HNF4-alpha pd BTD
+HNF4-alpha pd BYSL
+HNF4-alpha pd C14orf3
+HNF4-alpha pd C1orf8
+HNF4-alpha pd C20orf13
+HNF4-alpha pd C20orf154
+HNF4-alpha pd C20orf164
+HNF4-alpha pd C20orf4
+HNF4-alpha pd C20orf64
+HNF4-alpha pd C20orf72
+HNF4-alpha pd C20orf77
+HNF4-alpha pd C21orf18
+HNF4-alpha pd IMMT
+HNF4-alpha pd INVS
+HNF4-alpha pd ITGA6
+HNF4-alpha pd ITM1
+HNF4-alpha pd KBRAS1
+HNF4-alpha pd KEO4
+HNF4-alpha pd KIAA0092
+HNF4-alpha pd KIAA0102
+HNF4-alpha pd KIAA0105
+HNF4-alpha pd KIAA0255
+HNF4-alpha pd KIAA0258
+HNF4-alpha pd KIAA0391
+HNF4-alpha pd KIAA0433
+HNF4-alpha pd KIAA0438
+HNF4-alpha pd KIAA0670
+HNF4-alpha pd KIAA0795
+HNF4-alpha pd KIAA1017
+HNF4-alpha pd KIF9
+HNF4-alpha pd KRT10
+HNF4-alpha pd LAPTM4A
+HNF4-alpha pd LEPR
+HNF4-alpha pd LISCH7
+HNF4-alpha pd LIV-1
+HNF4-alpha pd LOC129401
+HNF4-alpha pd LOC151534
+HNF4-alpha pd LOC51004
+HNF4-alpha pd SLC2A8
+HNF4-alpha pd SLC31A1
+HNF4-alpha pd SLC35A2
+HNF4-alpha pd SMAC
+HNF4-alpha pd SMAP
+HNF4-alpha pd SMARCA5
+HNF4-alpha pd SMARCE1
+HNF4-alpha pd SMC2L1
+HNF4-alpha pd SNRPA
+HNF4-alpha pd SNRPD3
+HNF4-alpha pd SNRPF
+HNF4-alpha pd SNX1
+HNF4-alpha pd SNX5
+HNF4-alpha pd SP2
+HNF4-alpha pd SPATA2
+HNF4-alpha pd SPC18
+HNF4-alpha pd SQRDL
+HNF4-alpha pd SRP54
+HNF4-alpha pd SRP68
+HNF4-alpha pd SSSCA1
+HNF4-alpha pd STAF42
+HNF4-alpha pd STAF65(gamma)
+HNF4-alpha pd STAM
+HNF4-alpha pd STAM2
+HNF4-alpha pd STCH
+HNF4-alpha pd STK19
+HNF4-alpha pd STOML1
+HNF4-alpha pd STX18
+HNF4-alpha pd SUCLG1
+HNF4-alpha pd SUPT5H
+HNF4-alpha pd TADA3L
+HNF4-alpha pd TCF1
+HNF4-alpha pd TCOF1
+HNF4-alpha pd TCP1
+HNF4-alpha pd C6orf35
+HNF4-alpha pd C7orf10
+HNF4-alpha pd CAT56
+HNF4-alpha pd CBARA1
+HNF4-alpha pd CBX5
+HNF4-alpha pd CDC42BPB
+HNF4-alpha pd CDC5L
+HNF4-alpha pd CDKN1B
+HNF4-alpha pd CETN2
+HNF4-alpha pd CG005
+HNF4-alpha pd CGBP
+HNF4-alpha pd CGI-01
+HNF4-alpha pd CGI-51
+HNF4-alpha pd CHIC2
+HNF4-alpha pd CHM
+HNF4-alpha pd CIAO1
+HNF4-alpha pd CITED2
+HNF4-alpha pd CKAP1
+HNF4-alpha pd CKS2
+HNF4-alpha pd CLPTM1
+HNF4-alpha pd CLPX
+HNF4-alpha pd CLTA
+HNF4-alpha pd CLTCL1
+HNF4-alpha pd CNOT4
+HNF4-alpha pd COASTER
+HNF4-alpha pd COPB
+HNF4-alpha pd COPS7B
+HNF4-alpha pd COX7A2
+HNF4-alpha pd CPSF5
+HNF4-alpha pd LOC51016
+HNF4-alpha pd LOC51026
+HNF4-alpha pd LOC51027
+HNF4-alpha pd LOC51104
+HNF4-alpha pd LOC51107
+HNF4-alpha pd LOC51142
+HNF4-alpha pd LOC51174
+HNF4-alpha pd LOC51187
+HNF4-alpha pd LOC51205
+HNF4-alpha pd LOC51231
+HNF4-alpha pd LOC51246
+HNF4-alpha pd LOC51292
+HNF4-alpha pd LOC51596
+HNF4-alpha pd LOC51644
+HNF4-alpha pd LOC51651
+HNF4-alpha pd LOC54516
+HNF4-alpha pd LOC55815
+HNF4-alpha pd LOC55954
+HNF4-alpha pd LOC57019
+HNF4-alpha pd LOC57107
+HNF4-alpha pd LOC81034
+HNF4-alpha pd LOC89953
+HNF4-alpha pd LOC90799
+HNF4-alpha pd LSM3
+HNF4-alpha pd LTA4H
+HNF4-alpha pd LZTR1
+HNF4-alpha pd MAGOH
+HNF4-alpha pd MAP3K11
+HNF4-alpha pd MAP3K7
+HNF4-alpha pd MAPK7
+HNF4-alpha pd MAT2A
+HNF4-alpha pd MBD4
+HNF4-alpha pd MCEE
+HNF4-alpha pd MDFI
+HNF4-alpha pd MDS025
+HNF4-alpha pd MEF2B
+HNF4-alpha pd MEP50
+HNF4-alpha pd TDRKH
+HNF4-alpha pd TESK2
+HNF4-alpha pd TIMM23
+HNF4-alpha pd TIMM9
+HNF4-alpha pd TLN1
+HNF4-alpha pd TM9SF2
+HNF4-alpha pd TNFAIP1
+HNF4-alpha pd TPT
+HNF4-alpha pd TRA1
+HNF4-alpha pd TRAP150
+HNF4-alpha pd TRIM4
+HNF4-alpha pd TRIP11
+HNF4-alpha pd TRN-SR
+HNF4-alpha pd TRPS1
+HNF4-alpha pd TSLRP
+HNF4-alpha pd TXNL
+HNF4-alpha pd U2AF1
+HNF4-alpha pd U5-116KD
+HNF4-alpha pd UBE2M
+HNF4-alpha pd UBQLN1
+HNF4-alpha pd UCH37
+HNF4-alpha pd UGTREL1
+HNF4-alpha pd UROS
+HNF4-alpha pd UXT
+HNF4-alpha pd VEGFC
+HNF4-alpha pd VMP1
+HNF4-alpha pd CPT1B
+HNF4-alpha pd CRFG
+HNF4-alpha pd CRSP3
+HNF4-alpha pd CRYZ
+HNF4-alpha pd CS
+HNF4-alpha pd CSNK2A1
+HNF4-alpha pd CSTF1
+HNF4-alpha pd CSTF3
+HNF4-alpha pd CTMP
+HNF4-alpha pd CUL2
+HNF4-alpha pd D123
+HNF4-alpha pd DBT
+HNF4-alpha pd DC11
+HNF4-alpha pd DC8
+HNF4-alpha pd DCLRE1B
+HNF4-alpha pd DDX28
+HNF4-alpha pd DDX38
+HNF4-alpha pd DDX8
+HNF4-alpha pd DED
+HNF4-alpha pd DJ37E16.5
+HNF4-alpha pd DKFZP564G2022
+HNF4-alpha pd DKFZP564L2423
+HNF4-alpha pd DKFZP566C243
+HNF4-alpha pd DKFZP586A011
+HNF4-alpha pd DKFZP586J0119
+HNF4-alpha pd METAP2
+HNF4-alpha pd MGC10433
+HNF4-alpha pd MGC10702
+HNF4-alpha pd MGC10924
+HNF4-alpha pd MGC10974
+HNF4-alpha pd MGC10999
+HNF4-alpha pd MGC1127
+HNF4-alpha pd MGC11279
+HNF4-alpha pd MGC12943
+HNF4-alpha pd MGC12981
+HNF4-alpha pd MGC13102
+HNF4-alpha pd MGC13138
+HNF4-alpha pd MGC13159
+HNF4-alpha pd MGC1346
+HNF4-alpha pd MGC14151
+HNF4-alpha pd MGC14421
+HNF4-alpha pd MGC16733
+HNF4-alpha pd MGC17347
+HNF4-alpha pd MGC2404
+HNF4-alpha pd MGC2474
+HNF4-alpha pd MGC2477
+HNF4-alpha pd MGC2488
+HNF4-alpha pd MGC2560
+HNF4-alpha pd MGC2650
+HNF4-alpha pd MGC2747
+HNF4-alpha pd MGC3180
+HNF4-alpha pd MGC3222
+HNF4-alpha pd MGC3248
+HNF4-alpha pd MGC4161
+HNF4-alpha pd MGC4606
+HNF4-alpha pd MGC4767
+HNF4-alpha pd MGC5302
+HNF4-alpha pd MGC5509
+HNF4-alpha pd MGC9084
+HNF4-alpha pd MPPE1
+HNF4-alpha pd MRE11A
+HNF4-alpha pd MRPL18
+HNF4-alpha pd MRPL2
+HNF4-alpha pd MRPL24
+HNF4-alpha pd MRPL33
+HNF4-alpha pd MRPL44
+HNF4-alpha pd MRPL46
+HNF4-alpha pd MRPL48
+HNF4-alpha pd WDR13
+HNF4-alpha pd XRCC5
+HNF4-alpha pd YWHAB
+HNF4-alpha pd ZBRK1
+HNF4-alpha pd ZF5128
+HNF4-alpha pd ZFP95
+HNF4-alpha pd ZNF133
+HNF4-alpha pd ZNF146
+HNF4-alpha pd ZNF183
+HNF4-alpha pd ZNF192
+HNF4-alpha pd ZNF207
+HNF4-alpha pd ZNF214
+HNF4-alpha pd ZNF221
+HNF4-alpha pd ZNF222
+HNF4-alpha pd ZNF224
+HNF4-alpha pd ZNF225
+HNF4-alpha pd ZNF226
+HNF4-alpha pd ZNF230
+HNF4-alpha pd ZNF302
+HNF4-alpha pd ZNF-U69274
+HNF4-alpha pd ZNRD1
+HNF4-alpha pd DNAJB11
+HNF4-alpha pd DNAJB4
+HNF4-alpha pd DPAGT1
+HNF4-alpha pd DPM1
+HNF4-alpha pd DSCR3
+HNF4-alpha pd DYRK1B
+HNF4-alpha pd EEF1B2
+HNF4-alpha pd EFG1
+HNF4-alpha pd EHD3
+HNF4-alpha pd EIF2S1
+HNF4-alpha pd EIF2S3
+HNF4-alpha pd EIF5
+HNF4-alpha pd ERCC5
+HNF4-alpha pd EWSR1
+HNF4-alpha pd F12
+HNF4-alpha pd FBXO24
+HNF4-alpha pd FBXW2
+HNF4-alpha pd FDX1
+HNF4-alpha pd FDXR
+HNF4-alpha pd FHIT
+HNF4-alpha pd FLJ10038
+HNF4-alpha pd FLJ10116
+HNF4-alpha pd FLJ10287
+HNF4-alpha pd FLJ10330
+HNF4-alpha pd FLJ10422
+HNF4-alpha pd FLJ10432
+HNF4-alpha pd FLJ10511
+HNF4-alpha pd FLJ10535
+HNF4-alpha pd FLJ10581
+HNF4-alpha pd FLJ10604
+HNF4-alpha pd FLJ10637
+HNF4-alpha pd FLJ10640
+HNF4-alpha pd FLJ10661
+HNF4-alpha pd FLJ10856
+HNF4-alpha pd FLJ10871
+HNF4-alpha pd FLJ10891
+HNF4-alpha pd FLJ11046
+HNF4-alpha pd FLJ11159
+HNF4-alpha pd MRPL51
+HNF4-alpha pd MRPS11
+HNF4-alpha pd MRPS14
+HNF4-alpha pd MRPS16
+HNF4-alpha pd MRPS18C
+HNF4-alpha pd MRPS21
+HNF4-alpha pd MRPS30
+HNF4-alpha pd MRPS35
+HNF4-alpha pd MRPS7
+HNF4-alpha pd MSTP028
+HNF4-alpha pd MTMR4
+HNF4-alpha pd mtTFB
+HNF4-alpha pd MUT
+HNF4-alpha pd NAGK
+HNF4-alpha pd NBP
+HNF4-alpha pd NCBP1
+HNF4-alpha pd NCBP2
+HNF4-alpha pd NDUFA4
+HNF4-alpha pd NDUFA6
+HNF4-alpha pd NDUFB5
+HNF4-alpha pd NDUFS1
+HNF4-alpha pd NDUFS4
+HNF4-alpha pd NEDD8
+HNF4-alpha pd NFE2L1
+HNF4-alpha pd NFYA
+HNF4-alpha pd NKTR
+HNF4-alpha pd NME1
+HNF4-alpha pd NPAS2
+HNF4-alpha pd NPC1
+HNF4-alpha pd NR1H3
+HNF4-alpha pd NRAS
+HNF4-alpha pd NRCAM
+HNF4-alpha pd NS1-BP
+HNF4-alpha pd NT5C3
+HNF4-alpha pd NUDT5
+HNF4-alpha pd NUP107
+HNF4-alpha pd NUP62
+HNF4-alpha pd OPA3
+HNF4-alpha pd ORC3L
+HNF4-alpha pd FLJ11186
+HNF4-alpha pd FLJ11274
+HNF4-alpha pd FLJ11848
+HNF4-alpha pd FLJ12707
+HNF4-alpha pd FLJ12888
+HNF4-alpha pd FLJ13102
+HNF4-alpha pd FLJ13158
+HNF4-alpha pd FLJ13194
+HNF4-alpha pd FLJ13195
+HNF4-alpha pd FLJ13291
+HNF4-alpha pd FLJ13491
+HNF4-alpha pd FLJ13615
+HNF4-alpha pd FLJ13949
+HNF4-alpha pd FLJ13962
+HNF4-alpha pd FLJ14431
+HNF4-alpha pd FLJ14511
+HNF4-alpha pd FLJ14697
+HNF4-alpha pd FLJ14840
+HNF4-alpha pd FLJ20010
+HNF4-alpha pd FLJ20081
+HNF4-alpha pd FLJ20125
+HNF4-alpha pd FLJ20511
+HNF4-alpha pd FLJ20628
+HNF4-alpha pd FLJ20729
+HNF4-alpha pd FLJ20730
+HNF4-alpha pd FLJ21820
+HNF4-alpha pd FLJ21939
+HNF4-alpha pd OSGEP
+HNF4-alpha pd P29
+HNF4-alpha pd PAI-RBP1
+HNF4-alpha pd PARVB
+HNF4-alpha pd PCYT1A
+HNF4-alpha pd PDE4DIP
+HNF4-alpha pd PDE6D
+HNF4-alpha pd PEMT
+HNF4-alpha pd PEX11B
+HNF4-alpha pd PEX16
+HNF4-alpha pd PHACS
+HNF4-alpha pd PIGPC1
+HNF4-alpha pd PINK1
+HNF4-alpha pd PIP5K1A
+HNF4-alpha pd PME-1
+HNF4-alpha pd PMS2
+HNF4-alpha pd PMS2L8
+HNF4-alpha pd PNAS-131
+HNF4-alpha pd PNKP
+HNF4-alpha pd POLE3
+HNF4-alpha pd POLR2A
+HNF4-alpha pd POLR2K
+HNF4-alpha pd POP5
+HNF4-alpha pd PPP1R11
+HNF4-alpha pd FLJ22028
+HNF4-alpha pd FLJ22191
+HNF4-alpha pd FLJ22501
+HNF4-alpha pd FLJ22555
+HNF4-alpha pd FLJ22637
+HNF4-alpha pd FLJ22729
+HNF4-alpha pd FLJ22865
+HNF4-alpha pd FLJ22875
+HNF4-alpha pd FLJ23109
+HNF4-alpha pd FLJ23251
+HNF4-alpha pd FLJ23468
+HNF4-alpha pd FRG1
+HNF4-alpha pd FTSJ1
+HNF4-alpha pd FUBP1
+HNF4-alpha pd G10
+HNF4-alpha pd GABPB2
+HNF4-alpha pd GDAP2
+HNF4-alpha pd GJA4
+HNF4-alpha pd GK001
+HNF4-alpha pd GNS
+HNF4-alpha pd GOSR2
+HNF4-alpha pd GRIK3
+HNF4-alpha pd GSPT1
+HNF4-alpha pd PPP1R12B
+HNF4-alpha pd PPP1R15B
+HNF4-alpha pd PPP2R5B
+HNF4-alpha pd PRCC
+HNF4-alpha pd PRKCABP
+HNF4-alpha pd PRO2389
+HNF4-alpha pd PRPF31
+HNF4-alpha pd PRSS25
+HNF4-alpha pd PSMA2
+HNF4-alpha pd PSMD10
+HNF4-alpha pd PSMD7
+HNF4-alpha pd PSME3
+HNF4-alpha pd PTD012
+HNF4-alpha pd PTD013
+HNF4-alpha pd PTD015
+HNF4-alpha pd PWP1
+HNF4-alpha pd R3HDM
+HNF4-alpha pd RA410
+HNF4-alpha pd RAB11A
+HNF4-alpha pd RAB18
+HNF4-alpha pd RAB2
+HNF4-alpha pd RAB30
+HNF4-alpha pd RAGA
+HNF4-alpha pd RANBP8
+HNF4-alpha pd RANGAP1
+HNF4-alpha pd RASSF1
+HNF4-alpha pd RBBP4
+HNF4-alpha pd RBM15
+HNF4-alpha pd RBM6
+HNF4-alpha pd RBM7
+HNF4-alpha pd RDBP
+HNF4-alpha pd RDH5
+HNF4-alpha pd RECQL5
+HNF4-alpha pd RENT1
+HNF4-alpha pd RFC3
+HNF4-alpha pd RNF5
+HNF4-alpha pd ABCC2
+HNF4-alpha pd ACF
+HNF4-alpha pd ADH1B
+HNF4-alpha pd ADH6
+HNF4-alpha pd AGT
+HNF4-alpha pd AHSG
+HNF4-alpha pd AKR1C2
+HNF4-alpha pd AKR1C3
+HNF4-alpha pd AKR1C4
+HNF4-alpha pd AMBP
+HNF4-alpha pd ANPEP
+HNF4-alpha pd APCS
+HNF4-alpha pd APOA2
+HNF4-alpha pd APOH
+HNF4-alpha pd AQP9
+HNF4-alpha pd ASGR1
+HNF4-alpha pd ASGR2
+HNF4-alpha pd ATF2
+HNF4-alpha pd BIKE
+HNF4-alpha pd BTN2A1
+HNF4-alpha pd C1S
+HNF4-alpha pd C2
+HNF4-alpha pd C4BPA
+HNF4-alpha pd C8B
+HNF4-alpha pd CISH
+HNF4-alpha pd CLYBL
+HNF4-alpha pd CPB2
+HNF4-alpha pd CRP
+HNF4-alpha pd CTSZ
+HNF4-alpha pd CYB5
+HNF4-alpha pd CYP2E
+HNF4-alpha pd CYP3A43
+HNF4-alpha pd DAF
+HNF4-alpha pd DKFZP586A0522
+HNF4-alpha pd DLEU1
+HNF4-alpha pd DUSP6
+HNF4-alpha pd EIF4EBP2
+HNF4-alpha pd ELF3
+HNF4-alpha pd FKSG87
+HNF4-alpha pd FLJ13448
+HNF4-alpha pd FLJ20718
+HNF4-alpha pd G0S2
+HNF4-alpha pd G3A
+HNF4-alpha pd G6PT1
+HNF4-alpha pd GBE1
+HNF4-alpha pd GCKR
+HNF4-alpha pd GIOT-2
+HNF4-alpha pd GJB1
+HNF4-alpha pd GPR39
+HNF4-alpha pd GPX2
+HNF4-alpha pd GRHPR
+HNF4-alpha pd GTPBG3
+HNF4-alpha pd HAL
+HNF4-alpha pd HAO1
+HNF4-alpha pd HNF4a7
+HNF4-alpha pd HNMT
+HNF4-alpha pd HPX
+HNF4-alpha pd HSD11B1
+HNF4-alpha pd HSD17B2
+HNF4-alpha pd IFNAR1
+HNF4-alpha pd IGFBP1
+HNF4-alpha pd INADL
+HNF4-alpha pd ITIH3
+HNF4-alpha pd ITIH4
+HNF4-alpha pd KNG
+HNF4-alpha pd LBP
+HNF4-alpha pd LOC54518
+HNF4-alpha pd MGC11034
+HNF4-alpha pd MGC15435
+HNF4-alpha pd MRPL15
+HNF4-alpha pd MT1H
+HNF4-alpha pd MT1L
+HNF4-alpha pd MT1X
+HNF4-alpha pd MTP
+HNF4-alpha pd NET-2
+HNF4-alpha pd NR0B2
+HNF4-alpha pd NR5A2
+HNF4-alpha pd PAX8
+HNF4-alpha pd PCK1
+HNF4-alpha pd PLGL
+HNF4-alpha pd PZP
+HNF4-alpha pd RAB33B
+HNF4-alpha pd RBP5
+HNF4-alpha pd RPL37AP1
+HNF4-alpha pd SAC
+HNF4-alpha pd SERPINA1
+HNF4-alpha pd SERPINA10
+HNF4-alpha pd SERPINA6
+HNF4-alpha pd SERPINC1
+HNF4-alpha pd SERPINE1
+HNF4-alpha pd SERPING1
+HNF4-alpha pd SGK2
+HNF4-alpha pd SLC17A2
+HNF4-alpha pd SLPI
+HNF4-alpha pd SSTR1
+HNF4-alpha pd STRAIT11499
+HNF4-alpha pd SYN3
+HNF4-alpha pd TARS
+HNF4-alpha pd TEF
+HNF4-alpha pd TM4SF4
+HNF4-alpha pd TNFRSF6
+HNF4-alpha pd UGT2B11
+HNF4-alpha pd UGT2B15
+HNF4-alpha pd VTN
+HNF4-alpha pd XDH
+HNF4-alpha pd ZK1
+HNF4-alpha pd B29
+HNF4-alpha pd BCL6
+HNF4-alpha pd MCCC1
+HNF4-alpha pd A1BG
+HNF4-alpha pd AASS
+HNF4-alpha pd ABCB11
+HNF4-alpha pd ACVR1
+HNF4-alpha pd ALDH3A1
+HNF4-alpha pd ALDH5A1
+HNF4-alpha pd AMT
+HNF4-alpha pd BF
+HNF4-alpha pd C8G
+HNF4-alpha pd CASP2
+HNF4-alpha pd CDK2
+HNF4-alpha pd CDSN
+HNF4-alpha pd CLCN3
+HNF4-alpha pd CLDN2
+HNF4-alpha pd CRADD
+HNF4-alpha pd CRI1
+HNF4-alpha pd DKFZP434J037
+HNF4-alpha pd EIF4E
+HNF4-alpha pd F9
+HNF4-alpha pd FLJ11726
+HNF4-alpha pd FLJ12552
+HNF4-alpha pd FLJ14153
+HNF4-alpha pd FLJ21963
+HNF4-alpha pd FLJ22557
+HNF4-alpha pd FLJ23071
+HNF4-alpha pd FXYD7
+HNF4-alpha pd G6PC
+HNF4-alpha pd GRO3
+HNF4-alpha pd HNRPR
+HNF4-alpha pd HSD17B4
+HNF4-alpha pd IRF6
+HNF4-alpha pd JIK
+HNF4-alpha pd LOC51074
+HNF4-alpha pd NR1I2
+HNF4-alpha pd OAZ2
+HNF4-alpha pd PABPC1
+HNF4-alpha pd PHTF1
+HNF4-alpha pd PIK4CB
+HNF4-alpha pd POLS
+HNF4-alpha pd PON1
+HNF4-alpha pd RPLP1
+HNF4-alpha pd SILV
+HNF4-alpha pd SLC25A13
+HNF4-alpha pd SNX3
+HNF4-alpha pd SPP2
+HNF4-alpha pd TAF2GL
+HNF4-alpha pd TAT
+HNF4-alpha pd TMF1
+HNF4-alpha pd 24432
+HNF4-alpha pd C8orf4
+HNF4-alpha pd FLJ10482
+HNF4-alpha pd GSTA4
+HNF4-alpha pd HT007
+HNF4-alpha pd humNRDR
+HNF4-alpha pd KIAA0660
+HNF4-alpha pd MDS029
+HNF4-alpha pd MGC3413
+HNF4-alpha pd PPFIBP1
+HNF4-alpha pd PPP1R3D
+HNF4-alpha pd RIG-I
+HNF4-alpha pd RPC32
+HNF4-alpha pd SAMHD1
+HNF4-alpha pd 384D8-2
+HNF4-alpha pd 54TM
+HNF4-alpha pd AB026190
+HNF4-alpha pd ABCA6
+HNF4-alpha pd ABCC3
+HNF4-alpha pd ABCC6
+HNF4-alpha pd ABCE1
+HNF4-alpha pd ABCG8
+HNF4-alpha pd ABLIM
+HNF4-alpha pd ACAA2
+HNF4-alpha pd ACADVL
+HNF4-alpha pd ACLY
+HNF4-alpha pd ACTA2
+HNF4-alpha pd ACTN1
+HNF4-alpha pd ACTR3
+HNF4-alpha pd ACY1
+HNF4-alpha pd ADPRH
+HNF4-alpha pd ADPRTL1
+HNF4-alpha pd ADPRTL3
+HNF4-alpha pd ADRB2
+HNF4-alpha pd AGM1
+HNF4-alpha pd AGPAT1
+HNF4-alpha pd AGXT2
+HNF4-alpha pd AGXT2L1
+HNF4-alpha pd AKAP13
+HNF4-alpha pd ALCAM
+HNF4-alpha pd ALDH1A1
+HNF4-alpha pd ALDH2
+HNF4-alpha pd ALDH3B1
+HNF4-alpha pd ALDH8A1
+HNF4-alpha pd ALDOC
+HNF4-alpha pd ALS2CR19
+HNF4-alpha pd AMACR
+HNF4-alpha pd AMOT
+HNF4-alpha pd ANG
+HNF4-alpha pd ANXA5
+HNF4-alpha pd ANXA6
+HNF4-alpha pd ANXA9
+HNF4-alpha pd AP3B1
+HNF4-alpha pd APEH
+HNF4-alpha pd APG-1
+HNF4-alpha pd APOA1
+HNF4-alpha pd GYS2
+HNF4-alpha pd H2A/S
+HNF4-alpha pd H2AFG
+HNF4-alpha pd H2AFO
+HNF4-alpha pd H2BFA
+HNF4-alpha pd H2BFB
+HNF4-alpha pd H2BFF
+HNF4-alpha pd H2BFG
+HNF4-alpha pd H4FD
+HNF4-alpha pd H6PD
+HNF4-alpha pd HADH2
+HNF4-alpha pd HADHA
+HNF4-alpha pd HADHB
+HNF4-alpha pd HADHSC
+HNF4-alpha pd HARC
+HNF4-alpha pd HBS1L
+HNF4-alpha pd HCA112
+HNF4-alpha pd HDAC6
+HNF4-alpha pd HEY1
+HNF4-alpha pd HFL3
+HNF4-alpha pd HGC6.2
+HNF4-alpha pd HIF1A
+HNF4-alpha pd HINT2
+HNF4-alpha pd HLA-B
+HNF4-alpha pd HLA-F
+HNF4-alpha pd HMCS
+HNF4-alpha pd HMG17L3
+HNF4-alpha pd HMOX2
+HNF4-alpha pd HOOK3
+HNF4-alpha pd HOXA1
+HNF4-alpha pd HOXC8
+HNF4-alpha pd HPN
+HNF4-alpha pd HRIHFB2436
+HNF4-alpha pd HSA011916
+HNF4-alpha pd HSD17B7
+HNF4-alpha pd HSPC002
+HNF4-alpha pd HSPC048
+HNF4-alpha pd HSPC154
+HNF4-alpha pd HSPC213
+HNF4-alpha pd HT002
+HNF4-alpha pd HT012
+HNF4-alpha pd HYAL3
+HNF4-alpha pd IFITM2
+HNF4-alpha pd IFNGR1
+HNF4-alpha pd RNPEPL1
+HNF4-alpha pd ROCK1
+HNF4-alpha pd RORC
+HNF4-alpha pd RPL5
+HNF4-alpha pd RQCD1
+HNF4-alpha pd RSHL1
+HNF4-alpha pd RSP3
+HNF4-alpha pd RTCD1
+HNF4-alpha pd RTP801
+HNF4-alpha pd RUVBL2
+HNF4-alpha pd S100A9
+HNF4-alpha pd SAA1
+HNF4-alpha pd SAA2
+HNF4-alpha pd SC4MOL
+HNF4-alpha pd SCA2
+HNF4-alpha pd SCAND1
+HNF4-alpha pd SCD
+HNF4-alpha pd SCYA14
+HNF4-alpha pd SCYA15
+HNF4-alpha pd SCYA16
+HNF4-alpha pd SDC1
+HNF4-alpha pd SEC23A
+HNF4-alpha pd SEC24D
+HNF4-alpha pd SEMA3C
+HNF4-alpha pd SEMA6C
+HNF4-alpha pd SEMA7A
+HNF4-alpha pd SEPX1
+HNF4-alpha pd SERPINA5
+HNF4-alpha pd SERPIND1
+HNF4-alpha pd SGK
+HNF4-alpha pd SH2D3C
+HNF4-alpha pd SIX2
+HNF4-alpha pd SKRP1
+HNF4-alpha pd SLC10A1
+HNF4-alpha pd SLC17A5
+HNF4-alpha pd SLC19A3
+HNF4-alpha pd SLC22A1LS
+HNF4-alpha pd SLC22A3
+HNF4-alpha pd SLC22A7
+HNF4-alpha pd APOA5
+HNF4-alpha pd APOB
+HNF4-alpha pd APOC2
+HNF4-alpha pd APOC3
+HNF4-alpha pd ARG2
+HNF4-alpha pd ARHI
+HNF4-alpha pd ARL5
+HNF4-alpha pd ARL7
+HNF4-alpha pd ARPC5
+HNF4-alpha pd ATM
+HNF4-alpha pd ATP5C1
+HNF4-alpha pd ATP6D
+HNF4-alpha pd ATP6G1
+HNF4-alpha pd ATP6L
+HNF4-alpha pd ATP7B
+HNF4-alpha pd ATPW
+HNF4-alpha pd B3GAT1
+HNF4-alpha pd b5&b5R
+HNF4-alpha pd BACE
+HNF4-alpha pd BAI2
+HNF4-alpha pd BAL
+HNF4-alpha pd BAZ1A
+HNF4-alpha pd BCAT2
+HNF4-alpha pd BCDO2
+HNF4-alpha pd BHMT
+HNF4-alpha pd BIRC6
+HNF4-alpha pd BLOV1
+HNF4-alpha pd BPHL
+HNF4-alpha pd BRD4
+HNF4-alpha pd BRIP1
+HNF4-alpha pd BTF3
+HNF4-alpha pd BTG1
+HNF4-alpha pd C12orf8
+HNF4-alpha pd C14orf1
+HNF4-alpha pd C20orf163
+HNF4-alpha pd C20orf172
+HNF4-alpha pd C20orf32
+HNF4-alpha pd C20orf7
+HNF4-alpha pd C21orf33
+HNF4-alpha pd C3
+HNF4-alpha pd IGF1
+HNF4-alpha pd IL11RA
+HNF4-alpha pd IL15
+HNF4-alpha pd IL1RAP
+HNF4-alpha pd IL22R
+HNF4-alpha pd IL2RB
+HNF4-alpha pd IL6ST
+HNF4-alpha pd INHBC
+HNF4-alpha pd ITGAL
+HNF4-alpha pd ITPR2
+HNF4-alpha pd JRKL
+HNF4-alpha pd JUN
+HNF4-alpha pd JunB(-)1kb
+HNF4-alpha pd JunB(-)2kb
+HNF4-alpha pd JunB(-)3kb
+HNF4-alpha pd KAP3A
+HNF4-alpha pd KCNC3
+HNF4-alpha pd KCNJ12
+HNF4-alpha pd KCNN2
+HNF4-alpha pd KHDRBS1
+HNF4-alpha pd KIAA0103
+HNF4-alpha pd KIAA0141
+HNF4-alpha pd KIAA0205
+HNF4-alpha pd KIAA0266
+HNF4-alpha pd KIAA0409
+HNF4-alpha pd KIAA0618
+HNF4-alpha pd KIAA0645
+HNF4-alpha pd KIAA0747
+HNF4-alpha pd KIAA0792
+HNF4-alpha pd KIAA0905
+HNF4-alpha pd KIAA0914
+HNF4-alpha pd KIAA1116
+HNF4-alpha pd KIAA1169
+HNF4-alpha pd KIAA1453
+HNF4-alpha pd KIAA1638
+HNF4-alpha pd KIF1B
+HNF4-alpha pd KLF15
+HNF4-alpha pd KLHL6
+HNF4-alpha pd KNSL4
+HNF4-alpha pd KPNB1
+HNF4-alpha pd LAD1
+HNF4-alpha pd LALP1
+HNF4-alpha pd LATS1
+HNF4-alpha pd LC27
+HNF4-alpha pd LCN2
+HNF4-alpha pd LENG5
+HNF4-alpha pd LGALS1
+HNF4-alpha pd LIMK2
+HNF4-alpha pd LNPEP
+HNF4-alpha pd LOC115330
+HNF4-alpha pd LOC151636
+HNF4-alpha pd LOC51011
+HNF4-alpha pd SLC25A18
+HNF4-alpha pd SLC25A5
+HNF4-alpha pd SLC26A1
+HNF4-alpha pd SLC35A3
+HNF4-alpha pd SLC38A1
+HNF4-alpha pd SLC38A4
+HNF4-alpha pd SLC39A1
+HNF4-alpha pd SLC5A3
+HNF4-alpha pd SLC7A2
+HNF4-alpha pd SMPD1
+HNF4-alpha pd SNAI2
+HNF4-alpha pd SNAP23
+HNF4-alpha pd SNAPC1
+HNF4-alpha pd SNK
+HNF4-alpha pd SOD1
+HNF4-alpha pd SORCS3
+HNF4-alpha pd SOX10
+HNF4-alpha pd SPATA6
+HNF4-alpha pd SPOCK
+HNF4-alpha pd SREBF2
+HNF4-alpha pd SRPR
+HNF4-alpha pd SSAT2
+HNF4-alpha pd STARD7
+HNF4-alpha pd STAT1
+HNF4-alpha pd STAU2
+HNF4-alpha pd STIM1
+HNF4-alpha pd STK2
+HNF4-alpha pd SUCLA2
+HNF4-alpha pd SUDD
+HNF4-alpha pd SULT1A1
+HNF4-alpha pd SULT2A1
+HNF4-alpha pd SUOX
+HNF4-alpha pd SUPT3H
+HNF4-alpha pd SYTL4
+HNF4-alpha pd SZF1
+HNF4-alpha pd TAGLN2
+HNF4-alpha pd TCF12
+HNF4-alpha pd TCF19
+HNF4-alpha pd TCF21
+HNF4-alpha pd TCF7L2
+HNF4-alpha pd TCIRG1
+HNF4-alpha pd C3F
+HNF4-alpha pd C40
+HNF4-alpha pd C4A
+HNF4-alpha pd C4B
+HNF4-alpha pd CABC1
+HNF4-alpha pd CACNA2D2
+HNF4-alpha pd CAMK2D
+HNF4-alpha pd CARD15
+HNF4-alpha pd CASP6
+HNF4-alpha pd CATSPER
+HNF4-alpha pd CBS
+HNF4-alpha pd CBX3
+HNF4-alpha pd CCNG1
+HNF4-alpha pd CCNG2
+HNF4-alpha pd CCNH
+HNF4-alpha pd CCT6A
+HNF4-alpha pd CD1D
+HNF4-alpha pd CD68
+HNF4-alpha pd CDA
+HNF4-alpha pd CDC14A
+HNF4-alpha pd CDKL3
+HNF4-alpha pd CDW92
+HNF4-alpha pd CEACAM1
+HNF4-alpha pd CEP3
+HNF4-alpha pd CERD4
+HNF4-alpha pd CEZANNE
+HNF4-alpha pd CFL2
+HNF4-alpha pd CGI-11
+HNF4-alpha pd CHD1L
+HNF4-alpha pd CHI3L1
+HNF4-alpha pd CHP
+HNF4-alpha pd CKN1
+HNF4-alpha pd CL683
+HNF4-alpha pd CLCN6
+HNF4-alpha pd CLCNKA
+HNF4-alpha pd CLDN3
+HNF4-alpha pd CNOT2
+HNF4-alpha pd COQ3
+HNF4-alpha pd COX11
+HNF4-alpha pd LOC51015
+HNF4-alpha pd LOC51054
+HNF4-alpha pd LOC51064
+HNF4-alpha pd LOC51091
+HNF4-alpha pd LOC51134
+HNF4-alpha pd LOC51143
+HNF4-alpha pd LOC51175
+HNF4-alpha pd LOC51240
+HNF4-alpha pd LOC51285
+HNF4-alpha pd LOC51601
+HNF4-alpha pd LOC51611
+HNF4-alpha pd LOC51659
+HNF4-alpha pd LOC55580
+HNF4-alpha pd LOC56834
+HNF4-alpha pd LOC57018
+HNF4-alpha pd LOC57228
+HNF4-alpha pd LOC57406
+HNF4-alpha pd LOC57826
+HNF4-alpha pd LOC57862
+HNF4-alpha pd LOC64182
+HNF4-alpha pd LOC84518
+HNF4-alpha pd LOC84661
+HNF4-alpha pd LOC91689
+HNF4-alpha pd LR8
+HNF4-alpha pd LSR7
+HNF4-alpha pd MADCAM1
+HNF4-alpha pd MADH4
+HNF4-alpha pd MAF
+HNF4-alpha pd MAL2
+HNF4-alpha pd MANBA
+HNF4-alpha pd MAOA
+HNF4-alpha pd MAP3K4
+HNF4-alpha pd MAP7
+HNF4-alpha pd MAT1A
+HNF4-alpha pd MCP
+HNF4-alpha pd MDM2UAS6
+HNF4-alpha pd MDM2UAS8
+HNF4-alpha pd MDS009
+HNF4-alpha pd MEA
+HNF4-alpha pd TEAD3
+HNF4-alpha pd TED
+HNF4-alpha pd TF
+HNF4-alpha pd THPO
+HNF4-alpha pd THTP
+HNF4-alpha pd TIA1
+HNF4-alpha pd TIMM17A
+HNF4-alpha pd TIMM17B
+HNF4-alpha pd TLH29
+HNF4-alpha pd TMEM7
+HNF4-alpha pd TNFRSF11B
+HNF4-alpha pd TNFSF13
+HNF4-alpha pd TNS
+HNF4-alpha pd TOM1
+HNF4-alpha pd TP53TG1
+HNF4-alpha pd TPP2
+HNF4-alpha pd TRAF6
+HNF4-alpha pd TRIM15
+HNF4-alpha pd TRIM26
+HNF4-alpha pd TRIM31
+HNF4-alpha pd TRIM34
+HNF4-alpha pd TRPC5
+HNF4-alpha pd TTY14
+HNF4-alpha pd TUBB5
+HNF4-alpha pd TUFT1
+HNF4-alpha pd TXNIP
+HNF4-alpha pd TXNRD1
+HNF4-alpha pd TYMS
+HNF4-alpha pd U3-55K
+HNF4-alpha pd UBE2B
+HNF4-alpha pd UBE2D3
+HNF4-alpha pd UBP1
+HNF4-alpha pd UBQLN2
+HNF4-alpha pd UCHL3
+HNF4-alpha pd UGDH
+HNF4-alpha pd UGTREL7
+HNF4-alpha pd ULBP3
+HNF4-alpha pd UPB1
+HNF4-alpha pd USP1
+HNF4-alpha pd USP15
+HNF4-alpha pd USP2
+HNF4-alpha pd VAMP1
+HNF4-alpha pd VAMP5
+HNF4-alpha pd VDAC1
+HNF4-alpha pd VDAC2
+HNF4-alpha pd VEZATIN
+HNF4-alpha pd VPS29
+HNF4-alpha pd CPT2
+HNF4-alpha pd CRIPT
+HNF4-alpha pd CRKL
+HNF4-alpha pd CROT
+HNF4-alpha pd CRSP9
+HNF4-alpha pd CRY1
+HNF4-alpha pd CSDUFD1
+HNF4-alpha pd CSPG6
+HNF4-alpha pd CYP1A2
+HNF4-alpha pd CYP1B1
+HNF4-alpha pd CYP21A2
+HNF4-alpha pd CYP2B6
+HNF4-alpha pd CYP2C8
+HNF4-alpha pd CYP2D6
+HNF4-alpha pd CYP2D7AP
+HNF4-alpha pd CYP2J2
+HNF4-alpha pd CYP3A5
+HNF4-alpha pd CYP4F11
+HNF4-alpha pd CYP4F2
+HNF4-alpha pd CYP4F3
+HNF4-alpha pd CYP8B1
+HNF4-alpha pd Cyt19
+HNF4-alpha pd D6S2654E
+HNF4-alpha pd DAG1
+HNF4-alpha pd DBI
+HNF4-alpha pd DBP
+HNF4-alpha pd DCK
+HNF4-alpha pd DCLRE1C
+HNF4-alpha pd DDA3
+HNF4-alpha pd DDX18
+HNF4-alpha pd DDX27
+HNF4-alpha pd DDX35
+HNF4-alpha pd DEDD2
+HNF4-alpha pd DEPP
+HNF4-alpha pd DGKD
+HNF4-alpha pd DJ726C3.2
+HNF4-alpha pd DKFZP434C245
+HNF4-alpha pd DKFZp434D177
+HNF4-alpha pd DKFZP434H0115
+HNF4-alpha pd DKFZP434L0117
+HNF4-alpha pd DKFZP564A2416
+HNF4-alpha pd DKFZP566M1046
+HNF4-alpha pd DKFZp566O084
+HNF4-alpha pd DKFZp762L0311
+HNF4-alpha pd DLST
+HNF4-alpha pd DMC1
+HNF4-alpha pd DNAJA2
+HNF4-alpha pd MGAT4B
+HNF4-alpha pd MGC:13379
+HNF4-alpha pd MGC10823
+HNF4-alpha pd MGC10940
+HNF4-alpha pd MGC10960
+HNF4-alpha pd MGC12435
+HNF4-alpha pd MGC13008
+HNF4-alpha pd MGC13017
+HNF4-alpha pd MGC13033
+HNF4-alpha pd MGC14433
+HNF4-alpha pd MGC14839
+HNF4-alpha pd MGC14844
+HNF4-alpha pd MGC15504
+HNF4-alpha pd MGC15523
+HNF4-alpha pd MGC15563
+HNF4-alpha pd MGC15737
+HNF4-alpha pd MGC15906
+HNF4-alpha pd MGC16943
+HNF4-alpha pd MGC2629
+HNF4-alpha pd MGC2734
+HNF4-alpha pd MGC2835
+HNF4-alpha pd MGC3067
+HNF4-alpha pd MGC4400
+HNF4-alpha pd MGC4638
+HNF4-alpha pd MGC4663
+HNF4-alpha pd MGC4677
+HNF4-alpha pd MGEA5
+HNF4-alpha pd MGST1
+HNF4-alpha pd MGST2
+HNF4-alpha pd MIPEP
+HNF4-alpha pd MLC1SA
+HNF4-alpha pd MNAT1
+HNF4-alpha pd MOV10
+HNF4-alpha pd MPP1
+HNF4-alpha pd MRP63
+HNF4-alpha pd MRPL34
+HNF4-alpha pd MRPL37
+HNF4-alpha pd MRPL4
+HNF4-alpha pd VPS45A
+HNF4-alpha pd WASF3
+HNF4-alpha pd WASL
+HNF4-alpha pd WDR10
+HNF4-alpha pd XPA
+HNF4-alpha pd XPR1
+HNF4-alpha pd YKT6
+HNF4-alpha pd ZAN
+HNF4-alpha pd ZNF144
+HNF4-alpha pd ZNF147
+HNF4-alpha pd ZNF22
+HNF4-alpha pd ZNF237
+HNF4-alpha pd ZNF281
+HNF4-alpha pd ZNF9
+HNF4-alpha pd ZnTL2
+HNF4-alpha pd DNAJA3
+HNF4-alpha pd DNAJB9
+HNF4-alpha pd DOC-1R
+HNF4-alpha pd DUSP11
+HNF4-alpha pd DUSP3
+HNF4-alpha pd EHHADH
+HNF4-alpha pd EHM2
+HNF4-alpha pd ELP2
+HNF4-alpha pd ENC1
+HNF4-alpha pd EPB72
+HNF4-alpha pd EPHA2
+HNF4-alpha pd EPI64
+HNF4-alpha pd ERBB2IP
+HNF4-alpha pd ERBB3
+HNF4-alpha pd ERCC6
+HNF4-alpha pd ERO1L
+HNF4-alpha pd EVA1
+HNF4-alpha pd EVC
+HNF4-alpha pd EVG1
+HNF4-alpha pd F10
+HNF4-alpha pd F7
+HNF4-alpha pd FAP48
+HNF4-alpha pd FAPP2
+HNF4-alpha pd FBXL7
+HNF4-alpha pd FBXO4
+HNF4-alpha pd FEM1A
+HNF4-alpha pd FEM1B
+HNF4-alpha pd FETUB
+HNF4-alpha pd FIGF
+HNF4-alpha pd FLJ10111
+HNF4-alpha pd FLJ10143
+HNF4-alpha pd FLJ10761
+HNF4-alpha pd FLJ11011
+HNF4-alpha pd MRPL49
+HNF4-alpha pd MRPS36
+HNF4-alpha pd MRS2L
+HNF4-alpha pd MST1
+HNF4-alpha pd MT2A
+HNF4-alpha pd MTHFR
+HNF4-alpha pd MTHFS
+HNF4-alpha pd MTMR2
+HNF4-alpha pd MYO1A
+HNF4-alpha pd N6AMT1
+HNF4-alpha pd NAGA
+HNF4-alpha pd NAT8
+HNF4-alpha pd NCALD
+HNF4-alpha pd NCF1
+HNF4-alpha pd NCK1
+HNF4-alpha pd NCOA3
+HNF4-alpha pd NCOA5
+HNF4-alpha pd NCOR1
+HNF4-alpha pd NDRG1
+HNF4-alpha pd NDUFB1
+HNF4-alpha pd NEK2
+HNF4-alpha pd NONO
+HNF4-alpha pd NPAT
+HNF4-alpha pd NR3C1
+HNF4-alpha pd NTHL1
+HNF4-alpha pd NTN4
+HNF4-alpha pd NUFIP1
+HNF4-alpha pd NUP98
+HNF4-alpha pd OAS1
+HNF4-alpha pd OAS3
+HNF4-alpha pd ORM1
+HNF4-alpha pd ORM2
+HNF4-alpha pd FLJ11184
+HNF4-alpha pd FLJ11198
+HNF4-alpha pd FLJ11286
+HNF4-alpha pd FLJ11342
+HNF4-alpha pd FLJ11526
+HNF4-alpha pd FLJ11767
+HNF4-alpha pd FLJ12171
+HNF4-alpha pd FLJ12377
+HNF4-alpha pd FLJ12439
+HNF4-alpha pd FLJ12618
+HNF4-alpha pd FLJ12886
+HNF4-alpha pd FLJ13162
+HNF4-alpha pd FLJ13181
+HNF4-alpha pd FLJ13262
+HNF4-alpha pd FLJ13340
+HNF4-alpha pd FLJ13660
+HNF4-alpha pd FLJ13769
+HNF4-alpha pd FLJ13952
+HNF4-alpha pd FLJ13964
+HNF4-alpha pd FLJ14393
+HNF4-alpha pd FLJ14621
+HNF4-alpha pd FLJ14624
+HNF4-alpha pd FLJ14642
+HNF4-alpha pd FLJ14681
+HNF4-alpha pd FLJ14827
+HNF4-alpha pd FLJ20014
+HNF4-alpha pd FLJ20037
+HNF4-alpha pd FLJ20123
+HNF4-alpha pd FLJ20130
+HNF4-alpha pd FLJ20202
+HNF4-alpha pd FLJ20287
+HNF4-alpha pd FLJ20331
+HNF4-alpha pd FLJ20442
+HNF4-alpha pd FLJ20452
+HNF4-alpha pd FLJ20534
+HNF4-alpha pd FLJ20580
+HNF4-alpha pd FLJ20595
+HNF4-alpha pd FLJ20619
+HNF4-alpha pd FLJ20699
+HNF4-alpha pd FLJ20707
+HNF4-alpha pd FLJ21007
+HNF4-alpha pd FLJ21144
+HNF4-alpha pd FLJ21415
+HNF4-alpha pd FLJ21908
+HNF4-alpha pd OSMR
+HNF4-alpha pd OTC
+HNF4-alpha pd p100
+HNF4-alpha pd P115
+HNF4-alpha pd p21UAS11
+HNF4-alpha pd p21UAS8
+HNF4-alpha pd p21UAS9
+HNF4-alpha pd P23
+HNF4-alpha pd P2RY2
+HNF4-alpha pd PABPN1
+HNF4-alpha pd PAK4
+HNF4-alpha pd PALMD
+HNF4-alpha pd PANK
+HNF4-alpha pd PBEF
+HNF4-alpha pd PCDH20
+HNF4-alpha pd PCK2
+HNF4-alpha pd PCMT1
+HNF4-alpha pd PDCD4
+HNF4-alpha pd PDE11A
+HNF4-alpha pd PDIR
+HNF4-alpha pd PDK2
+HNF4-alpha pd PDK4
+HNF4-alpha pd PDZK1
+HNF4-alpha pd PECI
+HNF4-alpha pd PELO
+HNF4-alpha pd PEPD
+HNF4-alpha pd PEX3
+HNF4-alpha pd PFKFB4
+HNF4-alpha pd PGM1
+HNF4-alpha pd PHLDA1
+HNF4-alpha pd PIGS
+HNF4-alpha pd PIK3R3
+HNF4-alpha pd PILB
+HNF4-alpha pd PIPOX
+HNF4-alpha pd PIR
+HNF4-alpha pd PITPNB
+HNF4-alpha pd PKM2
+HNF4-alpha pd PLA2G13
+HNF4-alpha pd PLAB
+HNF4-alpha pd PLAGL2
+HNF4-alpha pd PLD2
+HNF4-alpha pd PLSCR1
+HNF4-alpha pd PMS1
+HNF4-alpha pd PNLIPRP1
+HNF4-alpha pd POLB
+HNF4-alpha pd POLD4
+HNF4-alpha pd PORIMIN
+HNF4-alpha pd POV1
+HNF4-alpha pd PP5395
+HNF4-alpha pd PPGB
+HNF4-alpha pd PPM1D
+HNF4-alpha pd FLJ22353
+HNF4-alpha pd FLJ22477
+HNF4-alpha pd FLJ22578
+HNF4-alpha pd FLJ22649
+HNF4-alpha pd FLJ22692
+HNF4-alpha pd FLJ23093
+HNF4-alpha pd FLJ23305
+HNF4-alpha pd FLJ23441
+HNF4-alpha pd FLJ23518
+HNF4-alpha pd FLOT1
+HNF4-alpha pd FMR1
+HNF4-alpha pd FNTA
+HNF4-alpha pd FOSL2
+HNF4-alpha pd FRK
+HNF4-alpha pd FSTL3
+HNF4-alpha pd FTHFD
+HNF4-alpha pd FZD1
+HNF4-alpha pd FZD3
+HNF4-alpha pd GAB1
+HNF4-alpha pd GADD45G
+HNF4-alpha pd GAPD
+HNF4-alpha pd GC20
+HNF4-alpha pd GCHFR
+HNF4-alpha pd GFER
+HNF4-alpha pd GGCX
+HNF4-alpha pd GIPC2
+HNF4-alpha pd GLYAT
+HNF4-alpha pd GMDS
+HNF4-alpha pd GNB1L
+HNF4-alpha pd GNG5
+HNF4-alpha pd GNMT
+HNF4-alpha pd GOLGA2
+HNF4-alpha pd GOLGA4
+HNF4-alpha pd GOLPH4
+HNF4-alpha pd GPC6
+HNF4-alpha pd GPHN
+HNF4-alpha pd GPT
+HNF4-alpha pd GPX1
+HNF4-alpha pd GRIN2D
+HNF4-alpha pd GSK3B
+HNF4-alpha pd GSTM4
+HNF4-alpha pd GSTTLp28
+HNF4-alpha pd PPP1R3B
+HNF4-alpha pd PPP1R3C
+HNF4-alpha pd PPP2CA
+HNF4-alpha pd PPP4R1
+HNF4-alpha pd PPP5C
+HNF4-alpha pd PQBP1
+HNF4-alpha pd PRCP
+HNF4-alpha pd PRKAB2
+HNF4-alpha pd PRKCL2
+HNF4-alpha pd PRLR
+HNF4-alpha pd PRO1728
+HNF4-alpha pd PRO2831
+HNF4-alpha pd PROZ
+HNF4-alpha pd PRPS1
+HNF4-alpha pd PSA
+HNF4-alpha pd PTK2
+HNF4-alpha pd PTPN18
+HNF4-alpha pd PTPN4
+HNF4-alpha pd PTPRE
+HNF4-alpha pd PTPRG
+HNF4-alpha pd PURG
+HNF4-alpha pd PYGL
+HNF4-alpha pd QP-C
+HNF4-alpha pd RAB10
+HNF4-alpha pd RAB4B
+HNF4-alpha pd RAB9P40
+HNF4-alpha pd RABEX5
+HNF4-alpha pd RAD17
+HNF4-alpha pd RAD23B
+HNF4-alpha pd RAD50
+HNF4-alpha pd RA-GEF-2
+HNF4-alpha pd RAP1GA1
+HNF4-alpha pd RASA1
+HNF4-alpha pd RBSK
+HNF4-alpha pd RBT1
+HNF4-alpha pd RCL
+HNF4-alpha pd RFC5
+HNF4-alpha pd RGL
+HNF4-alpha pd RIP60
+HNF4-alpha pd RNASE2
+HNF4-alpha pd RNASE3
+HNF4-alpha pd RNASE4
+HNF4-alpha pd RNF29
+HNF4-alpha pd CCNE1
+HNF4-alpha pd GTF2B
+HNF4-alpha pd HCAP-G
+HNF4-alpha pd MGC10500
+HNF4-alpha pd NR1D1
+HNF4-alpha pd SSTR4
+HNF4-alpha pd CDC45L
+HNF4-alpha pd EIF3S6
+HNF4-alpha pd FLJ11301
+HNF4-alpha pd FLJ14855
+HNF4-alpha pd FLJ20643
+HNF4-alpha pd FLJ20731
+HNF4-alpha pd GLA
+HNF4-alpha pd GNB2L1
+HNF4-alpha pd HHLA2
+HNF4-alpha pd pcnp
+HNF4-alpha pd ZNF300
+HNF4-alpha pd BCAR1
+HNF4-alpha pd BCKDHA
+HNF4-alpha pd CCT8
+HNF4-alpha pd CFL1
+HNF4-alpha pd CLLD8
+HNF4-alpha pd COPS7A
+HNF4-alpha pd EPHA1
+HNF4-alpha pd FLJ20422
+HNF4-alpha pd FLJ20772
+HNF4-alpha pd GBF1
+HNF4-alpha pd HSP105B
+HNF4-alpha pd MAP2K5
+HNF4-alpha pd MGC16169
+HNF4-alpha pd MGC16386
+HNF4-alpha pd MN1
+HNF4-alpha pd NTF2
+HNF4-alpha pd OGFR
+HNF4-alpha pd ORC1L
+HNF4-alpha pd PSMB1
+HNF4-alpha pd RRP46
+HNF4-alpha pd SART3
+HNF4-alpha pd SNRPD2
+HNF4-alpha pd SPG4
+HNF4-alpha pd ABCB8
+HNF4-alpha pd CIR
+HNF4-alpha pd DKFZp761J139
+HNF4-alpha pd EED
+HNF4-alpha pd FLJ10342
+HNF4-alpha pd FLJ11271
+HNF4-alpha pd FLJ13220
+HNF4-alpha pd FLJ14486
+HNF4-alpha pd HASJ4442
+HNF4-alpha pd HBOA
+HNF4-alpha pd HMG2
+HNF4-alpha pd MTERF
+HNF4-alpha pd PAPA-1
+HNF4-alpha pd PEX6
+HNF4-alpha pd SERPINB8
+HNF4-alpha pd ZNF317
+HNF4-alpha pd 101F6
+HNF4-alpha pd 4E-T
+HNF4-alpha pd AAMP
+HNF4-alpha pd ABCB9
+HNF4-alpha pd ABCC5
+HNF4-alpha pd ABH
+HNF4-alpha pd ACAD8
+HNF4-alpha pd ACATN
+HNF4-alpha pd ACTR1A
+HNF4-alpha pd AD-017
+HNF4-alpha pd ADAT1
+HNF4-alpha pd ADCY7
+HNF4-alpha pd ADD2
+HNF4-alpha pd ADSS
+HNF4-alpha pd AGTPBP1
+HNF4-alpha pd AIP
+HNF4-alpha pd AKR1B1
+HNF4-alpha pd AMSH
+HNF4-alpha pd AP2B1
+HNF4-alpha pd AP2M1
+HNF4-alpha pd AP2S1
+HNF4-alpha pd APACD
+HNF4-alpha pd ARD1
+HNF4-alpha pd ARSDR1
+HNF4-alpha pd ASE-1
+HNF4-alpha pd ATF6
+HNF4-alpha pd ATP10C
+HNF4-alpha pd ATP5B
+HNF4-alpha pd ATP5J2
+HNF4-alpha pd ATP6E
+HNF4-alpha pd B3GNT6
+HNF4-alpha pd BAD
+HNF4-alpha pd BAG4
+HNF4-alpha pd BARD1
+HNF4-alpha pd BAT2
+HNF4-alpha pd BCL2L1
+HNF4-alpha pd BET3
+HNF4-alpha pd IGSF8
+HNF4-alpha pd IMAGE145052
+HNF4-alpha pd IMAGE3455200
+HNF4-alpha pd IMP13
+HNF4-alpha pd INCENP
+HNF4-alpha pd ING3
+HNF4-alpha pd ING4
+HNF4-alpha pd IRS4
+HNF4-alpha pd ITGA9
+HNF4-alpha pd ITGB3BP
+HNF4-alpha pd JM4
+HNF4-alpha pd JTB
+HNF4-alpha pd KARS
+HNF4-alpha pd KCNQ5
+HNF4-alpha pd KIAA0028
+HNF4-alpha pd KIAA0057
+HNF4-alpha pd KIAA0164
+HNF4-alpha pd KIAA0196
+HNF4-alpha pd KIAA0274
+HNF4-alpha pd KIAA0317
+HNF4-alpha pd KIAA0372
+HNF4-alpha pd KIAA0416
+HNF4-alpha pd KIAA0419
+HNF4-alpha pd KIAA0426
+HNF4-alpha pd KIAA0537
+HNF4-alpha pd KIAA0547
+HNF4-alpha pd KIAA0682
+HNF4-alpha pd KIAA0710
+HNF4-alpha pd KIAA0766
+HNF4-alpha pd KIAA0907
+HNF4-alpha pd KIAA0950
+HNF4-alpha pd KIAA0971
+HNF4-alpha pd KIAA1012
+HNF4-alpha pd KIAA1068
+HNF4-alpha pd KIAA1100
+HNF4-alpha pd KIAA1608
+HNF4-alpha pd KIAA1775
+HNF4-alpha pd KIF3B
+HNF4-alpha pd KLRF1
+HNF4-alpha pd KNSL7
+HNF4-alpha pd KPTN
+HNF4-alpha pd LCMT
+HNF4-alpha pd LCP
+HNF4-alpha pd LDB1
+HNF4-alpha pd LGMN
+HNF4-alpha pd LHX6
+HNF4-alpha pd LIM
+HNF4-alpha pd LIMS1
+HNF4-alpha pd LIN-7-C
+HNF4-alpha pd LOC113251
+HNF4-alpha pd LOC113444
+HNF4-alpha pd LOC113622
+HNF4-alpha pd LOC115827
+HNF4-alpha pd LOC153768
+HNF4-alpha pd LOC51002
+HNF4-alpha pd LOC51019
+HNF4-alpha pd LOC51067
+HNF4-alpha pd SNX11
+HNF4-alpha pd SON
+HNF4-alpha pd SOX17
+HNF4-alpha pd SOX9
+HNF4-alpha pd SPK
+HNF4-alpha pd SRP19
+HNF4-alpha pd SSBP1
+HNF4-alpha pd SSFA2
+HNF4-alpha pd SSR2
+HNF4-alpha pd SSR3
+HNF4-alpha pd SSTK
+HNF4-alpha pd ST13
+HNF4-alpha pd STK24
+HNF4-alpha pd STOML2
+HNF4-alpha pd SULT1A3
+HNF4-alpha pd SULT1C1
+HNF4-alpha pd T54
+HNF4-alpha pd TAF11
+HNF4-alpha pd TAF6
+HNF4-alpha pd TARBP2
+HNF4-alpha pd TAX1BP1
+HNF4-alpha pd TCERG1
+HNF4-alpha pd TCF2
+HNF4-alpha pd TFAP4
+HNF4-alpha pd TFPT
+HNF4-alpha pd TG737
+HNF4-alpha pd TIP39
+HNF4-alpha pd TLE3
+HNF4-alpha pd TM9SF1
+HNF4-alpha pd TMSB10
+HNF4-alpha pd TOR2A
+HNF4-alpha pd TRAF5
+HNF4-alpha pd TRFP
+HNF4-alpha pd TRIP
+HNF4-alpha pd TSN
+HNF4-alpha pd TSNAX
+HNF4-alpha pd TUBB4
+HNF4-alpha pd BIG1
+HNF4-alpha pd BLTR2
+HNF4-alpha pd BLZF1
+HNF4-alpha pd BM-002
+HNF4-alpha pd BMI1
+HNF4-alpha pd BMP5
+HNF4-alpha pd BNC
+HNF4-alpha pd BNIP1
+HNF4-alpha pd BPGM
+HNF4-alpha pd BRAP
+HNF4-alpha pd BRF2
+HNF4-alpha pd BRIX
+HNF4-alpha pd BST1
+HNF4-alpha pd BTRC
+HNF4-alpha pd BUB1B
+HNF4-alpha pd BUB3
+HNF4-alpha pd C11orf10
+HNF4-alpha pd C11orf2
+HNF4-alpha pd C1D
+HNF4-alpha pd C1orf22
+HNF4-alpha pd C1orf25
+HNF4-alpha pd C20orf1
+HNF4-alpha pd C20orf10
+HNF4-alpha pd C20orf111
+HNF4-alpha pd C20orf12
+HNF4-alpha pd C20orf14
+HNF4-alpha pd C20orf28
+HNF4-alpha pd C20orf30
+HNF4-alpha pd C20orf33
+HNF4-alpha pd C20orf43
+HNF4-alpha pd C20orf44
+HNF4-alpha pd C20orf45
+HNF4-alpha pd C21orf55
+HNF4-alpha pd C21orf59
+HNF4-alpha pd C2orf9
+HNF4-alpha pd C3orf4
+HNF4-alpha pd C4orf1
+HNF4-alpha pd C5orf6
+HNF4-alpha pd C9orf12
+HNF4-alpha pd C9orf5
+HNF4-alpha pd CAP
+HNF4-alpha pd CAPZA2
+HNF4-alpha pd CAV1
+HNF4-alpha pd CCNT1
+HNF4-alpha pd CCT6B
+HNF4-alpha pd CCT7
+HNF4-alpha pd CDC10
+HNF4-alpha pd CDC23
+HNF4-alpha pd CDC6
+HNF4-alpha pd CDIPT
+HNF4-alpha pd CDK5
+HNF4-alpha pd CDK8
+HNF4-alpha pd CEBPA
+HNF4-alpha pd CEBPB
+HNF4-alpha pd CEP2
+HNF4-alpha pd CES2
+HNF4-alpha pd CETN3
+HNF4-alpha pd CG1I
+HNF4-alpha pd LOC51075
+HNF4-alpha pd LOC51076
+HNF4-alpha pd LOC51077
+HNF4-alpha pd LOC51094
+HNF4-alpha pd LOC51117
+HNF4-alpha pd LOC51118
+HNF4-alpha pd LOC51202
+HNF4-alpha pd LOC51204
+HNF4-alpha pd LOC51290
+HNF4-alpha pd LOC51300
+HNF4-alpha pd LOC51329
+HNF4-alpha pd LOC51604
+HNF4-alpha pd LOC51605
+HNF4-alpha pd LOC51626
+HNF4-alpha pd LOC51631
+HNF4-alpha pd LOC51657
+HNF4-alpha pd LOC51691
+HNF4-alpha pd LOC54543
+HNF4-alpha pd LOC56851
+HNF4-alpha pd LOC56993
+HNF4-alpha pd LOC57109
+HNF4-alpha pd LOC57147
+HNF4-alpha pd LOC63929
+HNF4-alpha pd LOC90346
+HNF4-alpha pd LOC90678
+HNF4-alpha pd LOC90701
+HNF4-alpha pd LOC92106
+HNF4-alpha pd LRP5
+HNF4-alpha pd LRRN1
+HNF4-alpha pd LSM4
+HNF4-alpha pd LSM5
+HNF4-alpha pd LYPLA2
+HNF4-alpha pd LZTFL1
+HNF4-alpha pd M6A
+HNF4-alpha pd M9
+HNF4-alpha pd MAP3K3
+HNF4-alpha pd MAPK8IP2
+HNF4-alpha pd MAPK8IP3
+HNF4-alpha pd MCFP
+HNF4-alpha pd MCM3
+HNF4-alpha pd MDH2
+HNF4-alpha pd MDS032
+HNF4-alpha pd MDS033
+HNF4-alpha pd MEN1
+HNF4-alpha pd METL
+HNF4-alpha pd U5-100K
+HNF4-alpha pd UBE2N
+HNF4-alpha pd UBE2V1
+HNF4-alpha pd UMPS
+HNF4-alpha pd UNRIP
+HNF4-alpha pd UPF3B
+HNF4-alpha pd UQCRH
+HNF4-alpha pd USF1
+HNF4-alpha pd USP5
+HNF4-alpha pd V1RL1
+HNF4-alpha pd VPS33A
+HNF4-alpha pd WARS2
+HNF4-alpha pd WHIP
+HNF4-alpha pd XPO1
+HNF4-alpha pd XRCC4
+HNF4-alpha pd XRN2
+HNF4-alpha pd YR-29
+HNF4-alpha pd ZFP37
+HNF4-alpha pd ZFP93
+HNF4-alpha pd ZNF134
+HNF4-alpha pd ZNF142
+HNF4-alpha pd ZNF175
+HNF4-alpha pd ZNF189
+HNF4-alpha pd ZNF193
+HNF4-alpha pd ZNF264
+HNF4-alpha pd ZNF265
+HNF4-alpha pd ZNF277
+HNF4-alpha pd ZNF304
+HNF4-alpha pd ZNF338
+HNF4-alpha pd ZNF345
+HNF4-alpha pd CGI-203
+HNF4-alpha pd CHEK2
+HNF4-alpha pd CHERP
+HNF4-alpha pd CHMP1.5
+HNF4-alpha pd CHRNB2
+HNF4-alpha pd CIP29
+HNF4-alpha pd CNAP1
+HNF4-alpha pd CNOT3
+HNF4-alpha pd COP9
+HNF4-alpha pd COX7C
+HNF4-alpha pd COX8
+HNF4-alpha pd CPA2
+HNF4-alpha pd CREBL1
+HNF4-alpha pd CrkRS
+HNF4-alpha pd CRYZL1
+HNF4-alpha pd CSK
+HNF4-alpha pd CSTF2T
+HNF4-alpha pd CTAG1
+HNF4-alpha pd CTNNA1
+HNF4-alpha pd CXorf12
+HNF4-alpha pd CYLD
+HNF4-alpha pd D1S155E
+HNF4-alpha pd DACH2
+HNF4-alpha pd DAD1
+HNF4-alpha pd DC50
+HNF4-alpha pd DCTN4
+HNF4-alpha pd DDOST
+HNF4-alpha pd DDX10
+HNF4-alpha pd DDX21
+HNF4-alpha pd DEDD
+HNF4-alpha pd DESC1
+HNF4-alpha pd DGUOK
+HNF4-alpha pd DIS3
+HNF4-alpha pd DKFZP434B168NM_015434
+HNF4-alpha pd DKFZP434C245NM_015426
+HNF4-alpha pd DKFZp434E2220
+HNF4-alpha pd DKFZP434E2318
+HNF4-alpha pd DKFZP434L1123
+HNF4-alpha pd DKFZp434N0650
+HNF4-alpha pd DKFZp434N1415
+HNF4-alpha pd MFAP1
+HNF4-alpha pd MGC11102
+HNF4-alpha pd MGC11115
+HNF4-alpha pd MGC11296
+HNF4-alpha pd MGC11352
+HNF4-alpha pd MGC13114
+HNF4-alpha pd MGC14126
+HNF4-alpha pd MGC14288
+HNF4-alpha pd MGC14595
+HNF4-alpha pd MGC14697
+HNF4-alpha pd MGC14798
+HNF4-alpha pd MGC14836
+HNF4-alpha pd MGC20486
+HNF4-alpha pd MGC2408
+HNF4-alpha pd MGC24447
+HNF4-alpha pd MGC2508
+HNF4-alpha pd MGC2655
+HNF4-alpha pd MGC2840
+HNF4-alpha pd MGC3121
+HNF4-alpha pd MGC3123
+HNF4-alpha pd MGC3133
+HNF4-alpha pd MGC4054
+HNF4-alpha pd MGC4093
+HNF4-alpha pd MGC4251
+HNF4-alpha pd MGC4308
+HNF4-alpha pd MGC4771
+HNF4-alpha pd MGC5347
+HNF4-alpha pd MGC5378
+HNF4-alpha pd MGC5469
+HNF4-alpha pd MGC5521
+HNF4-alpha pd MGC9740
+HNF4-alpha pd MID1
+HNF4-alpha pd MKRN1
+HNF4-alpha pd MLH1
+HNF4-alpha pd MLN
+HNF4-alpha pd MOCS3
+HNF4-alpha pd MRPL11
+HNF4-alpha pd MRPL19
+HNF4-alpha pd MRPL22
+HNF4-alpha pd MRPL27
+HNF4-alpha pd MRPL3
+HNF4-alpha pd MRPL30
+HNF4-alpha pd MRPL32
+HNF4-alpha pd DKFZP547N043
+HNF4-alpha pd DKFZP564I0422
+HNF4-alpha pd DKFZP564M082
+HNF4-alpha pd DKFZP566B183
+HNF4-alpha pd DKFZP566D1346
+HNF4-alpha pd DKFZP566E144
+HNF4-alpha pd DKFZP761E2110
+HNF4-alpha pd DKFZP762I166
+HNF4-alpha pd DLG4
+HNF4-alpha pd DMAP1
+HNF4-alpha pd DMP1
+HNF4-alpha pd DNAJB12
+HNF4-alpha pd DPH2L2
+HNF4-alpha pd DPM2
+HNF4-alpha pd DSCR5
+HNF4-alpha pd DSS1
+HNF4-alpha pd E2F4
+HNF4-alpha pd E2F5
+HNF4-alpha pd E2IG3
+HNF4-alpha pd EAF1
+HNF4-alpha pd EGLN2
+HNF4-alpha pd EIF1A
+HNF4-alpha pd EIF2B1
+HNF4-alpha pd EIF2S2
+HNF4-alpha pd EIF3S2
+HNF4-alpha pd EIF4G1
+HNF4-alpha pd ELL
+HNF4-alpha pd EXO1
+HNF4-alpha pd EZFIT
+HNF4-alpha pd F23149_1
+HNF4-alpha pd FANCF
+HNF4-alpha pd FDPS
+HNF4-alpha pd FEN1
+HNF4-alpha pd FGF13
+HNF4-alpha pd FGF7
+HNF4-alpha pd FKBP10
+HNF4-alpha pd FKBP3
+HNF4-alpha pd FKBPL
+HNF4-alpha pd FKSG32
+HNF4-alpha pd FLJ10052
+HNF4-alpha pd FLJ10142
+HNF4-alpha pd FLJ10374
+HNF4-alpha pd FLJ10377
+HNF4-alpha pd FLJ10450
+HNF4-alpha pd FLJ10468
+HNF4-alpha pd MRPL43
+HNF4-alpha pd MRPL53
+HNF4-alpha pd MRPS12
+HNF4-alpha pd MRPS15
+HNF4-alpha pd MRPS23
+HNF4-alpha pd MRPS27
+HNF4-alpha pd MRPS28
+HNF4-alpha pd MSMB
+HNF4-alpha pd MTF1
+HNF4-alpha pd MTR
+HNF4-alpha pd MTRF1
+HNF4-alpha pd MUTYH
+HNF4-alpha pd MXI1
+HNF4-alpha pd MYCBP
+HNF4-alpha pd MYL6
+HNF4-alpha pd NAG
+HNF4-alpha pd NAKAP95
+HNF4-alpha pd NBR2
+HNF4-alpha pd NCOA4
+HNF4-alpha pd NDUFA1
+HNF4-alpha pd NDUFA3
+HNF4-alpha pd NDUFA5
+HNF4-alpha pd NDUFA7
+HNF4-alpha pd NDUFB3
+HNF4-alpha pd NDUFS3
+HNF4-alpha pd NDUFV1
+HNF4-alpha pd NEK7
+HNF4-alpha pd NFATC2
+HNF4-alpha pd NFE2L3
+HNF4-alpha pd NFKBIL1
+HNF4-alpha pd NIMP
+HNF4-alpha pd NLN
+HNF4-alpha pd NMA
+HNF4-alpha pd NME7
+HNF4-alpha pd NOH61
+HNF4-alpha pd NOLA1
+HNF4-alpha pd NOSIP
+HNF4-alpha pd NOT56L
+HNF4-alpha pd NPR2L
+HNF4-alpha pd NSEP1
+HNF4-alpha pd NSF
+HNF4-alpha pd FLJ10477
+HNF4-alpha pd FLJ10509
+HNF4-alpha pd FLJ10628
+HNF4-alpha pd FLJ10634
+HNF4-alpha pd FLJ10803
+HNF4-alpha pd FLJ10826
+HNF4-alpha pd FLJ10853
+HNF4-alpha pd FLJ10989
+HNF4-alpha pd FLJ10998
+HNF4-alpha pd FLJ11016
+HNF4-alpha pd FLJ11017
+HNF4-alpha pd FLJ11193
+HNF4-alpha pd FLJ11220
+HNF4-alpha pd FLJ11292
+HNF4-alpha pd FLJ12085
+HNF4-alpha pd FLJ12168
+HNF4-alpha pd FLJ12455
+HNF4-alpha pd FLJ12525
+HNF4-alpha pd FLJ12571
+HNF4-alpha pd FLJ12735
+HNF4-alpha pd FLJ12785
+HNF4-alpha pd FLJ12879
+HNF4-alpha pd FLJ12895
+HNF4-alpha pd FLJ12960
+HNF4-alpha pd FLJ13315
+HNF4-alpha pd FLJ13912
+HNF4-alpha pd FLJ14451
+HNF4-alpha pd FLJ14547
+HNF4-alpha pd FLJ14803
+HNF4-alpha pd FLJ20045
+HNF4-alpha pd FLJ20070
+HNF4-alpha pd FLJ20189
+HNF4-alpha pd FLJ20190
+HNF4-alpha pd FLJ20257
+HNF4-alpha pd FLJ20288
+HNF4-alpha pd FLJ20291
+HNF4-alpha pd FLJ20342
+HNF4-alpha pd FLJ20343
+HNF4-alpha pd NTE
+HNF4-alpha pd NUCB1
+HNF4-alpha pd NUDT6
+HNF4-alpha pd NUP54
+HNF4-alpha pd NVL
+HNF4-alpha pd NYD-SP11
+HNF4-alpha pd NY-REN-41
+HNF4-alpha pd OBTP
+HNF4-alpha pd OPA1
+HNF4-alpha pd OSBP
+HNF4-alpha pd OSBPL11
+HNF4-alpha pd OSCAR
+HNF4-alpha pd P125
+HNF4-alpha pd P15-2
+HNF4-alpha pd P5326
+HNF4-alpha pd PACE
+HNF4-alpha pd PACE4
+HNF4-alpha pd PANX2
+HNF4-alpha pd PAWR
+HNF4-alpha pd PAX1
+HNF4-alpha pd PCQAP
+HNF4-alpha pd PDCD10
+HNF4-alpha pd PDE9A
+HNF4-alpha pd PEAS
+HNF4-alpha pd PEF
+HNF4-alpha pd PET112L
+HNF4-alpha pd PEX12
+HNF4-alpha pd PFDN5
+HNF4-alpha pd PHB
+HNF4-alpha pd PHKB
+HNF4-alpha pd PIGN
+HNF4-alpha pd PIK3C3
+HNF4-alpha pd PL6
+HNF4-alpha pd PLA2G2D
+HNF4-alpha pd PLA2G4B
+HNF4-alpha pd PLAA
+HNF4-alpha pd PLDN
+HNF4-alpha pd PNMA1
+HNF4-alpha pd PODXL
+HNF4-alpha pd POLL
+HNF4-alpha pd POLR3F
+HNF4-alpha pd POLRMT
+HNF4-alpha pd POR1
+HNF4-alpha pd POU5F1
+HNF4-alpha pd PPIL1
+HNF4-alpha pd PPIL2
+HNF4-alpha pd PPP1CA
+HNF4-alpha pd PPP1R10
+HNF4-alpha pd FLJ20420
+HNF4-alpha pd FLJ20450
+HNF4-alpha pd FLJ20498
+HNF4-alpha pd FLJ20508
+HNF4-alpha pd FLJ20546
+HNF4-alpha pd FLJ20558
+HNF4-alpha pd FLJ20624
+HNF4-alpha pd FLJ20644
+HNF4-alpha pd FLJ20651
+HNF4-alpha pd FLJ20695
+HNF4-alpha pd FLJ20748
+HNF4-alpha pd FLJ20859
+HNF4-alpha pd FLJ21613
+HNF4-alpha pd FLJ21742
+HNF4-alpha pd FLJ21945
+HNF4-alpha pd FLJ21952
+HNF4-alpha pd FLJ21977
+HNF4-alpha pd FLJ21986
+HNF4-alpha pd FLJ22184
+HNF4-alpha pd FLJ22347
+HNF4-alpha pd FLJ22688
+HNF4-alpha pd FLJ23182
+HNF4-alpha pd FLJ23469
+HNF4-alpha pd FLNA
+HNF4-alpha pd FOXO1A
+HNF4-alpha pd FRSB
+HNF4-alpha pd FTL
+HNF4-alpha pd FXC1
+HNF4-alpha pd FYCO1
+HNF4-alpha pd G22P1
+HNF4-alpha pd G6PD
+HNF4-alpha pd GABRE
+HNF4-alpha pd GALNAC4ST-2
+HNF4-alpha pd GAS1
+HNF4-alpha pd GCN5L1
+HNF4-alpha pd GHITM
+HNF4-alpha pd GIOT-3
+HNF4-alpha pd GLTSCR2
+HNF4-alpha pd GNAI3
+HNF4-alpha pd GOSR1
+HNF4-alpha pd GPCR150
+HNF4-alpha pd GPR105
+HNF4-alpha pd GPR37
+HNF4-alpha pd GPR52
+HNF4-alpha pd PPP6C
+HNF4-alpha pd PRDM5
+HNF4-alpha pd PRDX5
+HNF4-alpha pd PRKAB1
+HNF4-alpha pd PRKCE
+HNF4-alpha pd PRP18
+HNF4-alpha pd PRRG2
+HNF4-alpha pd PSCD2
+HNF4-alpha pd PSMA3
+HNF4-alpha pd PSMB5
+HNF4-alpha pd PSMB7
+HNF4-alpha pd PSMC4
+HNF4-alpha pd PSMD1
+HNF4-alpha pd PSMD4
+HNF4-alpha pd PSMD8
+HNF4-alpha pd PTD009
+HNF4-alpha pd PTK7
+HNF4-alpha pd PTPN13
+HNF4-alpha pd RAB1B
+HNF4-alpha pd RAB7
+HNF4-alpha pd RABAC1
+HNF4-alpha pd Rabip4R
+HNF4-alpha pd RAD51
+HNF4-alpha pd RAI2
+HNF4-alpha pd RAP1
+HNF4-alpha pd RARG-1
+HNF4-alpha pd RBAK
+HNF4-alpha pd RBL1
+HNF4-alpha pd RBL2
+HNF4-alpha pd RECQL
+HNF4-alpha pd REG1A
+HNF4-alpha pd REG1B
+HNF4-alpha pd RFPL2
+HNF4-alpha pd RNF40
+HNF4-alpha pd RPA2
+HNF4-alpha pd RPA40
+HNF4-alpha pd RPL10
+HNF4-alpha pd RPL12
+HNF4-alpha pd RPL18A
+HNF4-alpha pd RPL26
+HNF4-alpha pd RPL27
+HNF4-alpha pd RPL32
+HNF4-alpha pd RPL37
+HNF4-alpha pd RPL37A
+HNF4-alpha pd RPL41
+HNF4-alpha pd GPRK2L
+HNF4-alpha pd GRTH
+HNF4-alpha pd GRWD
+HNF4-alpha pd GSTZ1
+HNF4-alpha pd GTF2H3
+HNF4-alpha pd GTF2H4
+HNF4-alpha pd GTF2I
+HNF4-alpha pd GTF3C5
+HNF4-alpha pd GUSB
+HNF4-alpha pd H_GS165L15.1
+HNF4-alpha pd H17
+HNF4-alpha pd H3FM
+HNF4-alpha pd H4FI
+HNF4-alpha pd HCNGP
+HNF4-alpha pd HD
+HNF4-alpha pd HDAC8
+HNF4-alpha pd HEC
+HNF4-alpha pd HHEX
+HNF4-alpha pd HIF1AN
+HNF4-alpha pd HIRIP3
+HNF4-alpha pd HLF
+HNF4-alpha pd HNRPA0
+HNF4-alpha pd HNRPC
+HNF4-alpha pd HRB2
+HNF4-alpha pd HRMT1L2
+HNF4-alpha pd HSGT1
+HNF4-alpha pd HSPC003
+HNF4-alpha pd HSPC016
+HNF4-alpha pd HSPC031
+HNF4-alpha pd HSPC056
+HNF4-alpha pd HSPC072
+HNF4-alpha pd HSPC128
+HNF4-alpha pd HSPC134
+HNF4-alpha pd HSPC138
+HNF4-alpha pd HSPC142
+HNF4-alpha pd HSPC144
+HNF4-alpha pd HSPC148
+HNF4-alpha pd HSPC152
+HNF4-alpha pd HSPC160
+HNF4-alpha pd HSPC171
+HNF4-alpha pd HSPC182
+HNF4-alpha pd HSPC189
+HNF4-alpha pd HSPE1
+HNF4-alpha pd HT011
+HNF4-alpha pd HUNK
+HNF4-alpha pd IFRD2
+HNF4-alpha pd IGBP1
+HNF4-alpha pd RPLP0L
+HNF4-alpha pd Rpo1-2
+HNF4-alpha pd RPS14
+HNF4-alpha pd RPS18
+HNF4-alpha pd RPS20
+HNF4-alpha pd RPS21
+HNF4-alpha pd RPS25
+HNF4-alpha pd RPS28
+HNF4-alpha pd RPS3
+HNF4-alpha pd RPS5
+HNF4-alpha pd RPS6
+HNF4-alpha pd RPS6KC1
+HNF4-alpha pd RRM1
+HNF4-alpha pd RRP4
+HNF4-alpha pd SACM2L
+HNF4-alpha pd SBP2
+HNF4-alpha pd SCDGF-B
+HNF4-alpha pd SCML1
+HNF4-alpha pd SDF2
+HNF4-alpha pd SDHC
+HNF4-alpha pd SEC22L1
+HNF4-alpha pd SEC3
+HNF4-alpha pd SEC8
+HNF4-alpha pd SEDLP
+HNF4-alpha pd SERPINA4
+HNF4-alpha pd SERPINB3
+HNF4-alpha pd SETDB1
+HNF4-alpha pd SF3B1
+HNF4-alpha pd SF3B4
+HNF4-alpha pd SFRS1
+HNF4-alpha pd SFRS2
+HNF4-alpha pd SGCE
+HNF4-alpha pd SHH
+HNF4-alpha pd SIP
+HNF4-alpha pd SIRT2
+HNF4-alpha pd SKD3
+HNF4-alpha pd SKI
+HNF4-alpha pd SKP2
+HNF4-alpha pd SLC16A6
+HNF4-alpha pd SLC25A19
+HNF4-alpha pd SLC35A1
+HNF4-alpha pd SMC1L1
+HNF4-alpha pd SMC4L1
+HNF4-alpha pd SMCX
+HNF4-alpha pd SMPD2
+HNF6 pd ADH1A
+HNF6 pd AMBP
+HNF6 pd APCS
+HNF6 pd APOH
+HNF6 pd C1S
+HNF6 pd CYP3A43
+HNF6 pd F11
+HNF6 pd FLJ10650
+HNF6 pd FLJ21934
+HNF6 pd GJB1
+HNF6 pd HABP2
+HNF6 pd HNF4a7
+HNF6 pd KIAA0872
+HNF6 pd LOC51060
+HNF6 pd SERPING1
+HNF6 pd TNFRSF6
+HNF6 pd UGT2B15
+HNF6 pd VTN
+HNF6 pd WDR12
+HNF6 pd FLJ11301
+HNF6 pd FLJ20156
+HNF6 pd LOC56906
+HNF6 pd AASS
+HNF6 pd ACVR1
+HNF6 pd AF038169
+HNF6 pd AMT
+HNF6 pd BCKDHA
+HNF6 pd BF
+HNF6 pd BTN3A2
+HNF6 pd C20orf188
+HNF6 pd CCT8
+HNF6 pd CDC2L5
+HNF6 pd CH25H
+HNF6 pd CLDN2
+HNF6 pd CLLD8
+HNF6 pd COPB2
+HNF6 pd COPS7A
+HNF6 pd CRI1
+HNF6 pd CSN2
+HNF6 pd EIF4E
+HNF6 pd FABP5
+HNF6 pd FLJ10407
+HNF6 pd FLJ10415
+HNF6 pd FLJ11029
+HNF6 pd FLJ11773
+HNF6 pd FLJ12770
+HNF6 pd FLJ12910
+HNF6 pd FLJ13798
+HNF6 pd FLJ14153
+HNF6 pd FLJ20084
+HNF6 pd FLJ20422
+HNF6 pd FLJ20627
+HNF6 pd FLJ20671
+HNF6 pd FLJ20772
+HNF6 pd FLJ21963
+HNF6 pd FLJ22169
+HNF6 pd FLJ23263
+HNF6 pd FLJ23375
+HNF6 pd GABPA
+HNF6 pd GRB2
+HNF6 pd GRO1
+HNF6 pd GRO3
+HNF6 pd GSS
+HNF6 pd HBP1
+HNF6 pd HNRPR
+HNF6 pd HSD17B4
+HNF6 pd HSP105B
+HNF6 pd HSPA1B
+HNF6 pd HTR2B
+HNF6 pd IRF3
+HNF6 pd JIK
+HNF6 pd KIAA0806
+HNF6 pd KIAA1056
+HNF6 pd LOC51287
+HNF6 pd LOC51633
+HNF6 pd LOC81558
+HNF6 pd LOH11CR2A
+HNF6 pd MGC13053
+HNF6 pd MGC4189
+HNF6 pd MGST3
+HNF6 pd NOLC1
+HNF6 pd OGFR
+HNF6 pd ORC1L
+HNF6 pd PPFIA1
+HNF6 pd PSMA1
+HNF6 pd PSMB1
+HNF6 pd REA
+HNF6 pd RPS6KA5
+HNF6 pd RRP46
+HNF6 pd SART3
+HNF6 pd SAS10
+HNF6 pd SEC10L1
+HNF6 pd SERPINI1
+HNF6 pd SLC1A3
+HNF6 pd SNRPD2
+HNF6 pd SNW1
+HNF6 pd SPG4
+HNF6 pd SPINK1
+HNF6 pd TMF1
+HNF6 pd TNFSF10
+HNF6 pd TOMM70A
+HNF6 pd VCP
+HNF6 pd ABCC2
+HNF6 pd ADH1B
+HNF6 pd AKR1C4
+HNF6 pd C2
+HNF6 pd C8B
+HNF6 pd CRP
+HNF6 pd DKFZP586A0522
+HNF6 pd HCAP-G
+HNF6 pd HNMT
+HNF6 pd M17S2
+HNF6 pd MGC10500
+HNF6 pd PCK1
+HNF6 pd PLGL
+HNF6 pd RPL37AP1
+HNF6 pd TM4SF4
+HNF6 pd UGT1A1
+HNF6 pd UGT2B11
+HNF6 pd TMOD2
+HNF6 pd A1BG
+HNF6 pd ABCA8
+HNF6 pd ABCB11
+HNF6 pd ABL2
+HNF6 pd AGTR1
+HNF6 pd ALDH3A1
+HNF6 pd ALDH5A1
+HNF6 pd ASPA
+HNF6 pd BCAR1
+HNF6 pd BM039
+HNF6 pd BNIP3L
+HNF6 pd C8G
+HNF6 pd CACNA1D
+HNF6 pd CASP2
+HNF6 pd CDC25A
+HNF6 pd CDK2
+HNF6 pd CDSN
+HNF6 pd CFL1
+HNF6 pd CLCN3
+HNF6 pd COL5A1
+HNF6 pd COL5A3
+HNF6 pd CRADD
+HNF6 pd CYGB
+HNF6 pd CYP51
+HNF6 pd D13S106E
+HNF6 pd DDB2
+HNF6 pd DHFR
+HNF6 pd DKFZP434J037
+HNF6 pd DKFZP564O0523
+HNF6 pd DXF68S1E
+HNF6 pd E2F1
+HNF6 pd EIF4A1
+HNF6 pd ELOVL1
+HNF6 pd EPHA1
+HNF6 pd F9
+HNF6 pd FACTP140
+HNF6 pd FADS3
+HNF6 pd FLJ10209
+HNF6 pd FLJ10578
+HNF6 pd FLJ11105
+HNF6 pd FLJ11726
+HNF6 pd FLJ12552
+HNF6 pd FLJ22557
+HNF6 pd FLJ23071
+HNF6 pd FLJ23499
+HNF6 pd FLJ23598
+HNF6 pd FXYD7
+HNF6 pd G6PC
+HNF6 pd GAL3ST2
+HNF6 pd GBF1
+HNF6 pd H3FF
+HNF6 pd H4FK
+HNF6 pd HESX1
+HNF6 pd HIVEP3
+HNF6 pd HMGCR
+HNF6 pd IF
+HNF6 pd INSM2
+HNF6 pd IRF6
+HNF6 pd ITGAV
+HNF6 pd ITIH1
+HNF6 pd KLF3
+HNF6 pd LIMK1
+HNF6 pd LOC51074
+HNF6 pd LOC51646
+HNF6 pd MAP2K5
+HNF6 pd MGC16169
+HNF6 pd MGC16386
+HNF6 pd MN1
+HNF6 pd NEK6
+HNF6 pd NFKBIA
+HNF6 pd NR1I2
+HNF6 pd NTF2
+HNF6 pd OAT
+HNF6 pd OAZ2
+HNF6 pd PABPC1
+HNF6 pd PCDHA12
+HNF6 pd PHTF1
+HNF6 pd PIK4CB
+HNF6 pd POLR2D
+HNF6 pd POLS
+HNF6 pd PON1
+HNF6 pd PPP2R5A
+HNF6 pd PRO1855
+HNF6 pd PTPRR
+HNF6 pd RING1
+HNF6 pd RNF20
+HNF6 pd RPL35
+HNF6 pd RPLP1
+HNF6 pd SCYB13
+HNF6 pd SILV
+HNF6 pd SLC25A13
+HNF6 pd SLC7A9
+HNF6 pd SMARCC1
+HNF6 pd SMCY
+HNF6 pd SNX3
+HNF6 pd SPP2
+HNF6 pd SRF
+HNF6 pd STMN2
+HNF6 pd TAF2GL
+HNF6 pd TAT
+HNF6 pd TBX2
+HNF6 pd TCEB3
+HNF6 pd TSG101
+HNF6 pd URKL1
+HNF6 pd WDR5B
+HNF6 pd AGT
+HNF6 pd FLJ21272
+HNF6 pd GTF2E1
+HNF6 pd NR0B2
+HNF6 pd FLJ20643
+HNF6 pd GLA
+HNF6 pd KRTAP1.1
+HNF6 pd ABCB8
+HNF6 pd ACPP
+HNF6 pd AF15Q14
+HNF6 pd ARL1
+HNF6 pd BBP
+HNF6 pd C2F
+HNF6 pd C8orf4
+HNF6 pd CIR
+HNF6 pd CLCN4
+HNF6 pd CLNS1A
+HNF6 pd CLONE24922
+HNF6 pd CMG1
+HNF6 pd COX4I1
+HNF6 pd COX7A2L
+HNF6 pd DKFZp761D221
+HNF6 pd DKFZp761J139
+HNF6 pd EED
+HNF6 pd EGR2
+HNF6 pd EHD4
+HNF6 pd EHF
+HNF6 pd F2RL2
+HNF6 pd FER1L3
+HNF6 pd FLJ10342
+HNF6 pd FLJ10482
+HNF6 pd FLJ11271
+HNF6 pd FLJ13220
+HNF6 pd FLJ13955
+HNF6 pd FLJ14486
+HNF6 pd GABARAPL1
+HNF6 pd GCP3
+HNF6 pd GSTA4
+HNF6 pd H4FA
+HNF6 pd H4FH
+HNF6 pd HASJ4442
+HNF6 pd HBOA
+HNF6 pd HLA-G
+HNF6 pd HMG2
+HNF6 pd HNRPA2B1
+HNF6 pd HSN44A4A
+HNF6 pd HSPC125
+HNF6 pd HT007
+HNF6 pd humNRDR
+HNF6 pd IGSF3
+HNF6 pd KIAA0660
+HNF6 pd KIAA0712
+HNF6 pd LAMC2
+HNF6 pd LBC
+HNF6 pd LUC7A
+HNF6 pd MDH1
+HNF6 pd MDS029
+HNF6 pd MEIS1
+HNF6 pd MGC13040
+HNF6 pd MGC19595
+HNF6 pd MGC3020
+HNF6 pd MGC3413
+HNF6 pd MTERF
+HNF6 pd NET-6
+HNF6 pd NOVA1
+HNF6 pd NUDT2
+HNF6 pd PAPA-1
+HNF6 pd PEX6
+HNF6 pd PMAIP1
+HNF6 pd PPFIBP1
+HNF6 pd PPP1R3D
+HNF6 pd PTPRN2
+HNF6 pd RECK
+HNF6 pd RIG-I
+HNF6 pd RPC32
+HNF6 pd RPL36P1
+HNF6 pd SAMHD1
+HNF6 pd SCYA28
+HNF6 pd SEMA6A
+HNF6 pd SERPINB8
+HNF6 pd SH3BGRL
+HNF6 pd TEGT
+HNF6 pd UGT2B17
+HNF6 pd ZNF317
+Shc pp Grb2
+SHC pp EGFR
+Bit1 pp AES
+p120RNP pp CR2
+p68 pp CR2
+p53 pp CR2
+ER-alpha pp hdm2
+p53 pp ER-alpha
+Beta-PDGFR pp PLC-gamma
+Beta-PDGFR pp p85-alpha
+HTK-L pp ELK
+ELK-L pp NUK
+HTK-L pp NUK
+B61 pp EHK1
+LERK4 pp EHK1
+EHK1-L pp ECK
+EHK1-L pp EHK1
+AL-1 pp EHK1
+ELK-L pp ELK
+Grb2 pp Syp
+Grb2 pp c-Kit
+Syp pp c-Kit
+Raf pp Ras
+p210bcr-abl pp Syp
+GSK3beta pp Ftau
+Grb2 pp Sos1
+AKT2 pp IKK-alpha
+Cdh1 interactsWith Unknown
+Unknown interactsWith Cks1
+Unknown interactsWith Skp2
+Cdh1 interactsWith Unknown
+Cdh1 pp Skp2
+PDGFR pp p66Shc
+PDGFR pp p52Shc
+PDGFR pp GAP
+B61 pp ECK
+Ku_antigen interactsWith DNA-PKcs
+p75 pp NgR1
+LINGO-1 pp p75
+LINGO-1 pp NgR1
+PDGFR pp p55-gamma
+PDGFR pp p85-beta
+Pax5 pp Daxx
+p73-beta pp HMGB1
+p73-alpha pp HMGB1
+Shc pp Trk
+IRS-1 pp p85-beta
+EGFR pp PLD2
+Topors pp p53
+EGFR pp p85-beta
+APPL pp p110-alpha
+APPL pp Akt1
+Raf pp Ras
+Akt pp PED
+Sck pp KDR
+NRP1 pp VEGF165
+ING4 pp p65
+Unknown interactsWith p53
+FOXO3 interactsWith Unknown
+Unknown interactsWith PCAF
+FOXO3 interactsWith Unknown
+NRP1 pp PlGF-2
+FOXO3 pp SIRT1
+NRSF/REST pd mGluR2_promoter
+Sm pp PACT
+MAD2 pp CMT2
+Ub pp Lyn
+Ub pp Syk
+MAD2 pp p55CDC
+NRSF/REST pd SCG10_promoter
+BRG1 pd mGluR2_promoter
+BRG1 pd SCG10_promoter
+BAF170 pd mGluR2_promoter
+BAF170 pd SCG10_promoter
+AKT2 pp APPL
+Akt pp AR
+p53 pp GSK3-beta
+p210_Bcr-Abl pp p160_Bcr
+Bcr-Abl interactsWith Grb2-Sos1
+Bcr-Abl pp Grb2
+NDF-alpha pp Her3
+eIF2B-alpha pp beta-2-AR
+c-Src pp Sam68
+Unknown interactsWith Rap1
+Raf1 interactsWith Unknown
+Rap1-GTP interactsWith RalGDS
+B-RAF pp C-RAF
+mSin3A pp PLZF
+HDAC1 pp PLZF
+SMRT pp PLZF
+huntingtin pp PACSIN1
+Smad3 pp ZNF198
+Smad3 pp 4-ET
+Smad3 pp SF3b2
+Smad3 pp Pex6
+IR pp Shc
+mSin3A pp htt
+p53 pp htt
+CBP pp htt
+p53 pp mSin3A
+p53 pp CBP
+TPST pp PSGL-1
+Huntingtin pp HAP1
+Htt pp tTG
+HIP1 pp HIP1
+HIP1 pp HIP12
+HIP1 pp HD
+Huntingtin pp Sp1
+HD pp SH3GL3
+MLK2 pp Huntingtin
+p52Shc interactsWith Unknown
+p66Shc interactsWith Unknown
+FIP-2 pp Rab8
+FIP-2 pp Huntingtin
+Unknown interactsWith GM-CSF_receptor-beta_subunit
+Shb pp Eps8
+Shb pp Src
+Shb pp p85-alpha_PI3_kinase
+Shb pp PDGF-beta_receptor
+Shb pp FGFR-1
+X11-ALPHA pp Lin-2
+Huntingtin pp CTBP
+Mre11 pp NBS1
+Mre11 pp Rad50
+p300 pp p28ING5
+p300 pp p29ING4
+HD pp N-CoR
+Daxx pp p51-ETS1
+Daxx pp p42-ETS1
+D4.7 pp Nck
+D3 pp Nck
+D3 pp Grb2
+ATM pp Chk2
+ATM pp p53
+ATM pp H2AX
+D4.4 pp Nck
+D4.2 pp Nck
+ATM interactsWith MRN
+TXBP181 pp TXBP181
+TXBP181 pp HsMAD2
+Htt pp SUMO-1
+Unknown interactsWith Ubiquitin
+Akt pp Tuberin
+XRCC1 pp PNK
+Dnmt3b pp SUMO-1
+Dnmt3b pp Ubc9
+p12DOC-1/CDK2AP1 pp p14DOC-1R
+Gab1 pp Sos1
+beta-1-AR pp Grb2
+M4 pp Grb2
+D4.4 pp Grb2
+D4.2 pp Grb2
+D4.7 pp Grb2
+D4.4 pp c-Src
+CHMP4C pp Alix
+CHMP4B pp Alix
+CHMP4A pp Alix
+MAD2B pp MAD2B
+EGFR pp p85
+TAFII250 pp Cyclin_D1
+Rb pp Cyclin_D1
+TAFII250 pp Rb
+CRIF1 pp Gadd45gamma
+Huntingtin pp PSD-95
+mDia3 pp CENP-A
+mDia1 pp CENP-A
+HD pp hE2-25K
+FOXO3a pd p27Kip1_promoter
+IKK-beta pp I-kappa-Ba
+IKK-alpha pp FOXO3a
+IKK-beta pp FOXO3a
+htt pp CIP4
+Cyclin_C pp Cdk3
+HDP pp RasGAP
+HDP pp Grb2
+hDNMT3a pp hDNMT1
+hMAD2 pp hREV3
+TAFII130 pp htt
+ABL pp CRK
+Sp1 pd D2R_promoter
+Smad3 pp p300
+CD44 pp EGFR
+hDNMT3b pp hDNMT1
+EIF2beta pp CK2beta
+EIF2beta pp CK2alpha
+CFTR pp CANX
+htt pp CA150
+WAVE_1 pp Abl
+PS1 pp caspase_1
+PS1 pp caspase_4
+WAVE_1 pp G-actin
+p53 pp SUMO-1
+Calmodulin interactsWith Htt-tTG
+CRIF1 pp Gadd45alpha
+ER-alpha pp REA
+ER-alpha pp SRC-1
+PrxI pp PA26
+PrxI pp Hi95
+FoxO3 pd p21Cip1_promoter
+Smad4 pd p21Cip1_promoter
+FoxO4 pp FoxG1
+FoxH1 pp Smad2
+FoxO3 pp FoxG1
+FoxO1 pp FoxG1
+FoxH1 pp Smad3
+FoxO4 pd p21Cip1promoter
+FoxO1 pd p21Cip1promoter
+FoxO4 pp Smad4
+FoxO1 pp Smad3
+FoxO4 pp Smad3
+FoxO1 pp Smad4
+FoxO3 pp Smad3
+c-Myc pd p21Cip1promoter
+FoxO3 pp Smad4
+CD28 interactsWith Unknown
+Unknown interactsWith NSF
+Unknown interactsWith P85-PI3-Kinase
+Unknown interactsWith VP41
+CD28 pp NSF
+Unknown interactsWith Vps33a
+Unknown interactsWith Vps16
+TRAF2 pp LTBR
+Smac pp LTBR
+cIAP1 pp LTBR
+TRAF3 pp LTBR
+CD4 pp CD4
+WAVE-1 pp PKA
+Cdk5 pp p35
+PBX2 pp IKBKAP
+PBX2 pp GCN5L1
+PBX2 pp FLJ21080
+PBX2 pp ZDHHC7
+PBX2 pp MGC16385
+PBX2 pp MCRS1
+PBX2 pp KIAA0052
+PBX2 pp NUP62
+PBX2 pp COPS6
+PBX2 pp BAIAP2
+PBX2 pp RPS6KC1
+PBX2 pp CS0DH004YA13
+PBX2 pp RPL4
+PBX2 pp DKFZp434G0920
+PBX2 pp Dynactin3
+RNF5 pp E2E_1
+RNF5 pp E2E_3
+RNF5 pp E2D_2
+RNF5 pp E2D_3
+RNF5 pp FHOD1
+STK19 pp POLE
+STK19 pp POLR2G
+STK19 pp SF3B_su4
+STK19 pp SP3
+STK19 pp SLC29A1
+STK19 pp PRAME
+DOM3Z pp Flotillin_2
+DOM3Z pp IMAGE:2161292
+DOM3Z pp LOC128127
+NELF-E pp COBRA1
+NELF-E pp NCOR1
+NELF-E pp NY-REN-24
+LSM2 pp LSM8
+LSM2 pp LSM3
+LSM2 pp LSM7
+LSM2 pp SNRPE
+LSM2 pp SNRPD2
+LSM2 pp PR-zinc_finger_17
+LSM2 pp DNAJ-like-2
+CLIC1 pp LSM1
+CLIC1 pp IMAGE:5804540
+BAT5 pp IFITM1
+BAT5 pp HNRPA1
+BAT5 pp RNF5
+BAT5 pp SPP
+BAT5 pp NIFIE14
+BAT5 pp DKFZP564D0478
+BAT5 pp DNAJL1
+BAT5 pp GPRC5C
+BAT5 pp PILRBeta
+BAT5 pp SPAG7
+BAT5 pp SAFB
+BAT5 pp ATP5G3
+BAT5 pp NAD3
+BAT5 pp NAD4
+BAT5 pp COXII
+CSNK2B pp CSNK2A2
+CSNK2B pp LYN
+CSNK2B pp CSNK2A1
+CSNK2B pp CSNK2B
+CSNK2B pp RPL5
+CSNK2B pp CG1I
+CSNK2B pp MBD4
+CSNK2B pp GIOT-2
+C6orf47 pp FGFR3
+Scythe pp SGT1
+Scythe pp MGC14421
+Scythe pp FLJ20552
+BAT2 pp HNRPA1
+BAT2 pp EIF3S6
+BAT2 pp DDX20
+BAT2 pp FGA
+BAT2 pp P4HA2
+BAT2 pp HRMT1L1
+BAT2 pp MAN2C1
+BAT2 pp CPSF1
+BAT2 pp IMMT
+BAT2 pp GPR2
+BAT2 pp G2AN
+BAT2 pp SSR3
+BAT2 pp TG737
+BAT2 pp MAD2L2
+BAT2 pp HNRPM
+BAT2 pp KIAA0144
+BAT2 pp QARS
+BAT2 pp PSMA3
+BAT2 pp GRB2
+BAT2 pp C1QBP
+LST1/f pp KIAA1333
+LST1/f pp NY-REN-24
+ATP6G2 pp ATP6E
+UAP56 pp DDX39
+UAP56 pp UAP56
+UAP56 pp CIP29
+UAP56 pp DKFZP547E1010
+UAP56 pp HIPK2
+UAP56 pp ZHX1
+UAP56 pp PMSCL1
+UAP56 pp PIASX-BETA
+UAP56 pp TDG
+UAP56 pp RPS15A
+UAP56 pp ALY
+UAP56 pp MGC:15775
+HsSen2 interactsWith Unknown
+Unknown interactsWith HsSen54
+Unknown interactsWith HsSen34
+Unknown interactsWith HsSen15
+Unknown interactsWith HsClp1
+BNIP-2 pp BNIP-2
+Cdc42GAP pp Cdc42GAP
+BNIP-2 pp Cdc42GAP
+Unknown interactsWith HsSen54
+Unknown interactsWith HsClp1
+tRNA_splicing_endonuclease_complex interactsWith pre-tRNA
+HsSen2-delta-Ex8 interactsWith Unknown
+huntingtin pp Akt
+PKA pp PKA
+Casp2 pp RAIDD
+PIDD pp RAIDD
+p53 pp p28ING5
+CRIF1 pp Gadd45beta
+PKA interactsWith Pericentrin
+p53 pp p29ING4
+Rb pp hDnmt1
+Che-1 pp hHRPB11
+p53 pp Ubc9
+hHR23A pp p300
+HDS pp NPC2
+PAPIN pp p0071
+PAPIN pp NPRAP
+amphiphysin_1 pp p35
+amphiphysin_1 interactsWith p35/Cdk5
+Tf pp Cubilin
+LTA pp galectin-2
+Che-1 pp Rb
+COP1 pp p53
+Unknown interactsWith SAP130
+Unknown interactsWith TAF5L
+Unknown interactsWith TAF6L
+Unknown interactsWith hSPT7
+Unknown interactsWith TRRAP
+Unknown interactsWith GNC5L
+Unknown interactsWith hADA1
+Unknown interactsWith TAF9
+Unknown interactsWith TAF10
+Unknown interactsWith TAF12
+Unknown interactsWith hADA2
+Unknown interactsWith hADA2
+L11 pp Hdm2
+NGF pp NGF
+NGF_homodimer interactsWith p75
+Unknown interactsWith hADA3
+hSPT3 interactsWith Unknown
+DMPK pp MYPT1
+BLM pp RAD51
+TCL-GTP interactsWith PAK-1
+TES pp mena
+TES pp Talin_1
+p53 pp BLM
+Hck pp Sam68
+Lck pp Sam68
+Rbp2 pp GR
+Endofin pp TOM1
+Sp100 pp ETS-1
+EAPII pp ETS1
+EAPII pp p42-ETS1
+Rrp41 pp PM_Scl_100
+Rrp41 pp Rrp40
+Rrp41 pp Dom3
+Rrp41 pp Ski2
+Rrp42 pp PM_Scl_100
+Rrp42 pp Dom3
+Rrp46 pp Rrp40
+Rrp46 pp Oip2
+Rrp46 pp Csl4
+Rrp46 pp PM_Scl_100
+Mtr3 pp Rrp42
+Mtr3 pp Oip2
+Mtr3 pp Csl4
+Mtr3 pp Mtr3
+Mtr3 pp PM_Scl_100
+Mtr3 pp Dcp1B
+Mtr3 pp Kiaa0052
+Mtr3 pp TTP
+Oip2 pp Rrp46
+Oip2 pp Oip2
+Oip2 pp TTP
+Rrp4 pp Rrp42
+Rrp4 pp Znf408
+Rrp40 pp Rrp46
+Rrp40 pp Oip2
+Csl4 pp Rrp46
+Csl4 pp Rrp41
+Csl4 pp Oip2
+PM_Scl_100 pp PM_Scl_100
+PM_Scl_100 pp Dom3
+PM_Scl_100 pp Ski2
+PM_Scl_100 pp Rrp44
+PM_Scl_100 pp Mtr3
+PM_Scl_100 pp Oip2
+Mpp6 pp Kiaa0052
+Mpp6 pp PARN
+Mpp6 pp PM_Scl_100
+Rrp44 pp Oip2
+Lsm1 pp Lsm3
+Lsm1 pp Lsm2
+Lsm1 pp Lsm4
+Lsm1 pp Mtr3
+Lsm1 pp Oip2
+Lsm2 pp Lsm3
+Lsm2 pp Lsm8
+Lsm2 pp Znf408
+Lsm2 pp PM_Scl_100
+Lsm2 pp Lsm1
+Lsm2 pp Lsm7
+Lsm3 pp Lsm1
+Lsm3 pp Lsm2
+Lsm3 pp Lsm5
+Lsm3 pp Lsm6
+Lsm3 pp Lsm7
+Lsm3 pp Lsm8
+Lsm3 pp Xrn2
+Lsm4 pp Lsm7
+Lsm4 pp Lsm8
+Lsm5 pp Lsm3
+Lsm5 pp Lsm6
+Lsm5 pp Lsm7
+Lsm6 pp Lsm3
+Lsm6 pp Lsm5
+Lsm6 pp Lsm7
+Lsm6 pp Lsm1
+Lsm6 pp Lsm8
+Lsm7 pp Lsm3
+Lsm7 pp Lsm5
+Lsm7 pp Mtr3
+Lsm7 pp Lsm2
+Lsm7 pp Lsm4
+Lsm7 pp Lsm6
+Lsm7 pp Oip2
+Lsm8 pp Lsm2
+Lsm8 pp Lsm3
+Lsm8 pp Lsm6
+Lsm8 pp PM_Scl_100
+Lsm8 pp Lsm4
+Lsm8 pp Lsm7
+Lsm8 pp Mtr3
+Lsm8 pp Dcp1A
+Lsm8 pp Upf1
+Dcp2 pp Dcp1A
+Dcp2 pp Dcp1B
+Xrn1 pp Dcp1A
+Xrn1 pp Dom3
+Xrn1 pp Ski2
+Xrn1 pp PM_Scl_100
+Xrn1 pp Lsm4
+Xrn1 pp Oip2
+Xrn1 pp Csl4
+Xrn1 pp Mtr3
+Xrn1 pp Dcp1B
+Xrn1 pp TTP
+Xrn1 pp Kiaa0052
+Xrn2 pp Dom3
+Xrn2 pp PM_Scl_100
+Xrn2 pp Oip2
+Dom3 pp Dom3
+Dom3 pp PM_Scl_100
+HuR pp HuR
+Upf1 pp Dom3
+Upf2 pp Oip2
+Upf2 pp Mtr3
+Upf2 pp TTP
+Upf2 pp Dcp1B
+Upf2 pp Csl4
+Upf2 pp Kiaa0052
+Upf2 pp Upf2
+Upf2 pp Dcp2
+Upf2 pp Xrn2
+Upf2 pp PM_Scl_100
+Upf2 pp Znf408
+Upf2 pp Lsm1
+Upf3B pp Upf2
+Znf408 pp Znf408
+Znf408 pp Upf2
+Znf408 pp Rrp4
+Rrp41 pp PM_Scl_75
+Rrp41 pp FLJ20297
+Rrp41 pp C1orf19
+Rrp41 pp DKFZp566J2046
+Rrp41 pp FLJ33418
+Rrp41 pp EEF1A1
+Rrp41 pp NEK1
+Rrp41 pp BM770606
+Rrp41 pp AKR1A1
+Rrp41 pp GTF2IRD1
+Rrp41 pp LRRC5
+Rrp41 pp FLJ21047
+Rrp41 pp PLINP
+Rrp41 pp BC006102
+Rrp46 pp OIP2
+Rrp46 pp POLR2L
+Rrp46 pp Lsm5
+Rrp46 pp Rrp40
+Rrp46 pp EBP1
+Rrp46 pp NUP210
+Rrp46 pp Csl4
+Rrp46 pp PKM2
+Rrp46 pp SFPQ
+Rrp46 pp FLJ30932
+Rrp46 pp CDK5RAP1
+Mtr3 pp EIF3S2
+Mtr3 pp Rrp42
+Mtr3 pp GRIM19
+Mtr3 pp SF2p32
+Mtr3 pp SFRS3
+Mtr3 pp CPSF5
+Mtr3 pp RAB3_GAP150
+Mtr3 pp PSMB1
+Mtr3 pp ERRalpha
+Mtr3 pp AD023
+Mtr3 pp MOCS3
+Mtr3 pp FLJ22678
+Mtr3 pp WBSCR18
+Mtr3 pp KIAA0182
+Oip2 pp FHOD1
+Oip2 pp RASSF1
+Oip2 pp MKRN1
+Oip2 pp KIAA1604
+Oip2 pp AI685517
+Oip2 pp FOXN3
+Rrp4 pp Rrp42
+Rrp4 pp Znf408
+Rrp4 pp RNF8
+Rrp4 pp FLJ40491
+Rrp40 pp Rrp46
+Rrp40 pp CDK5RAP1
+Csl4 pp NUP160
+Csl4 pp Rrp41
+Csl4 pp AV753896
+PM_Scl_100_Rrp6 pp CIB1
+PM_Scl_100_Rrp6 pp C14orf92
+PM_Scl_100_Rrp6 pp SCRIB
+PM_Scl_100_Rrp6 pp PTGES2
+PM_Scl_100_Rrp6 pp BM451300
+PM_Scl_100_Rrp6 pp AL512687
+PM_Scl_100_Rrp6 pp GA17
+PM_Scl_100_Rrp6 pp FACT_80
+PM_Scl_100_Rrp6 pp USP16
+PM_Scl_100_Rrp6 pp EPPB9
+PM_Scl_100_Rrp6 pp H17
+PM_Scl_100_Rrp6 pp FLJ22678
+PM_Scl_100_Rrp6 pp FLJ23784
+PM_Scl_100_Rrp6 pp AL110135
+PM_Scl_100_Rrp6 pp AL512687
+PM_Scl_100_Rrp6 pp FLJ11934
+PM_Scl_100_Rrp6 pp TARDBP
+PM_Scl_100_Rrp6 pp RPE
+PM_Scl_100_Rrp6 pp URP2
+PM_Scl_100_Rrp6 pp RUVBL2
+PM_Scl_100_Rrp6 pp AJ431196
+PM_Scl_100_Rrp6 pp AI620703
+Mpp6 pp EIF3S4
+Mpp6 pp FTL
+Mpp6 pp SNX9
+Mpp6 pp THOP1
+Mpp6 pp FLJ14502
+Mpp6 pp DNLC2A
+Mpp6 pp MT2P1
+Mpp6 pp BM806939
+Mpp6 pp RPS20
+Mpp6 pp BRG1
+Mpp6 pp DYN2
+Mpp6 pp AATF
+Mpp6 pp MacGAP
+Rrp44 pp AD_003
+Rrp44 pp ZNF151
+Ski2 pp SmB
+Ski2 pp AL517440
+Ski2 pp FLJ34136
+Ski2 pp GALNT13
+Ski2 pp AI580336
+Ski2 pp WDR1
+Ski2 pp CDC2L2
+Ski2 pp U80752
+Lsm1 pp VPS11
+Lsm1 pp Lsm2
+Lsm1 pp NARS
+Lsm1 pp PSMB8
+Lsm1 pp Lsm3
+Lsm1 pp PSMB5
+Lsm1 pp FLJ20254
+Lsm1 pp UXT
+Lsm1 pp N4BP1
+Lsm1 pp GRHPR
+Lsm1 pp HSPC1
+Lsm1 pp DKFZP564J0123
+Lsm1 pp AW27564
+Lsm1 pp AW974116
+Lsm1 pp KIAA0179
+Lsm1 pp AF090094
+Lsm1 pp AW975586
+Lsm2 pp Lsm8
+Lsm2 pp Lsm3
+Lsm2 pp SmE
+Lsm2 pp Znf408
+Lsm2 pp DNAJL2
+Lsm2 pp Lsm7
+Lsm2 pp SmD2
+Lsm3 pp Lsm2
+Lsm3 pp Lsm8
+Lsm3 pp Lsm10
+Lsm3 pp SmD3
+Lsm3 pp SmE
+Lsm3 pp Lsm7
+Lsm3 pp XPC
+Lsm3 pp BC009518
+LSM4 pp Lsm8
+LSM4 pp Lsm7
+LSM4 pp FLJ13289
+LSM4 pp SmE
+LSM4 pp Nmi
+LSM4 pp PEPP2
+Lsm5 pp Lsm7
+Lsm5 pp SmF
+Lsm5 pp SmE
+Lsm5 pp Lsm3
+Lsm6 pp Lsm5
+Lsm6 pp SmD2
+Lsm6 pp Lsm7
+Lsm6 pp Lsm3
+Lsm6 pp MCRS1
+Lsm6 pp POLD2
+Lsm7 pp Lsm5
+Lsm7 pp SmD3
+Lsm7 pp LSM4
+Lsm7 pp RAB7L1
+Lsm7 pp NPY1R
+Lsm7 pp MYH13
+Lsm8 pp Lsm2
+Lsm8 pp NY_REN_45
+Lsm8 pp LSM4
+Lsm8 pp TALDO1
+Lsm8 pp SmD1
+Lsm8 pp PGD
+Lsm8 pp ASK
+Lsm8 pp FLJ23469
+Lsm8 pp RPL24
+Lsm8 pp SMBP2
+Lsm8 pp PNUTL1
+Lsm8 pp MTHFR
+Lsm8 pp DKFZP434F091
+Lsm8 pp MGC10966
+Lsm8 pp GTF2I
+Lsm8 pp ITSN2
+Lsm8 pp DKFZp565A176
+Dcp2 pp POLA2
+Dcp2 pp NAGK
+Dcp2 pp PSMB1
+Dcp2 pp RCD_8
+Xrn1_Sep1 pp BAT3
+Xrn1_Sep1 pp LDHA
+Xrn1_Sep1 pp PABPC4
+Xrn1_Sep1 pp BC001200
+Xrn1_Sep1 pp ALDOA
+Xrn1_Sep1 pp MGC13198
+Xrn1_Sep1 pp AP1G2
+Xrn1_Sep1 pp STAM2A
+Xrn1_Sep1 pp CHD4
+Xrn1_Sep1 pp SMARCD2
+Xrn1_Sep1 pp CCT5
+Xrn1_Sep1 pp GRIM19
+Xrn1_Sep1 pp FLJ10359
+Xrn1_Sep1 pp FLJ21347
+Xrn1_Sep1 pp AI821928
+Xrn1_Sep1 pp HnRNPA1
+Xrn1_Sep1 pp KIAA0261
+Xrn1_Sep1 pp DPP2
+Xrn2_Rat1 pp PSMA3
+Xrn2_Rat1 pp EIF3S6IP
+Xrn2_Rat1 pp AW977134
+Xrn2_Rat1 pp EEF1A1
+Xrn2_Rat1 pp EIF6
+Xrn2_Rat1 pp EIF5A
+Xrn2_Rat1 pp DKFZP434J214
+Xrn2_Rat1 pp COMT
+Xrn2_Rat1 pp MOCS3
+Xrn2_Rat1 pp TOLLIP
+Xrn2_Rat1 pp TARDBP
+Dom3c pp AI580336
+PARN pp DKFZp434N0650
+Auf1_hnRNPD pp Rrp41
+Auf1_hnRNPD pp SF2p32
+Auf1_hnRNPD pp Lsm5
+Upf1 pp HIRA
+Upf1 pp BC040175
+Upf1 pp N21259
+Upf1 pp PLEKHB2
+Upf1 pp FLJ10631
+Upf1 pp ACAS2
+Upf1 pp BAT5
+Upf1 pp PEPP2
+Upf1 pp KIAA0460
+Upf1 pp GNPTAG
+Upf2 pp RPS15
+Upf2 pp RPL5
+Upf2 pp REA
+Upf2 pp MAP1A
+Upf2 pp RPS25
+Upf2 pp ART4
+Upf2 pp UPF3B
+Upf3A pp GSK3B
+Upf3A pp IFITM2
+Upf3A pp BM310104
+Upf3B pp MCRS1
+Upf3B pp FLJ20343
+Znf408 pp RGS19IP1
+Znf408 pp RIL
+Znf408 pp NOH61
+Znf408 pp Lsm2
+Znf408 pp Znf408
+Znf408 pp NOA36
+Znf408 pp DKFZP434G156
+Znf408 pp BG403593
+Znf408 pp BQ069192
+Znf408 pp MIF
+Znf408 pp TOP3B
+Znf408 pp CAF1B
+Lsm8 pp FLJ23534
+Lsm8 pp PDCD2
+Lsm8 pp IFNLR1
+Lsm8 pp FLJ11280
+Lsm8 pp DKFZp434K0621
+Rbp2 pp RAR
+Rbp2 pp ER
+MAGE-A4 pp gankyrin
+Beta-Arr2 pp I-kappa-B-alpha
+Beta-Arr1 pp I-kappa-B-alpha
+KPNB1 pp RAN
+RANBP1 pp RAN
+TrkA pp NGF
+TrkA pp NGF
+NGF pp NGF
+TrkA pp NGF
+TrkA pp NGF
+RET pp FRS2
+LKB1 pp AMPK-alpha
+Rap1GAP pp Rap1
+Bcl10 interactsWith Unknown
+Bcl10 pp Bcl10
+TRAF2 pp MALT1
+TRAF6 pp Ub
+TRAF6 interactsWith Unknown
+TRAF6 pp TRAF6
+TRAF6 pp MALT1
+GATA-6 pd I-BRE
+Rbp2 pp VDR
+Smad1 pd BRE-1
+Smad1 pd I-BRE
+HDM2 pp Akt
+HSP22 pp cvHSP
+HSP22 pp MKBP
+HSP22 pp HSP27
+HSP22 pp HSP22
+JNK3alpha1 pp c-Jun
+JNK2beta2 pp c-Jun
+JNK2beta1 pp c-Jun
+JNK2alpha2 pp c-Jun
+JNK1alpha2 pp c-Jun
+JNK1beta1 pp c-Jun
+JNK2alpha1 pp c-Jun
+JNK1beta2 pp c-Jun
+c-Myc pp GNC5L
+c-Myc pp TRRAP
+MTMR2 pp MTMR5
+MTMR2 pp MTMR2
+TGF-beta-1 pp Amyloid-beta
+Nir2 pp Cdk1
+MUC1 pp beta-catenin
+Nir2 pp Plk1
+Nir2 pp RhoA
+MUC1 pp c-Src
+MUC1 pp EGFR
+RANBP1 pp RAN
+TES pp GRIP1
+TES pp TES
+TES pp VASP
+RecQ5-beta pp Top3-beta
+RecQ5-beta pp Top3-alpha
+liprin-alpha4 pp GIT1
+liprin-alpha4 pp ERC2
+liprin-alpha3 pp ERC2
+liprin-alpha2 pp ERC2
+liprin-alpha2 pp GIT1
+liprin-alpha3 pp GIT1
+liprin-alpha1 pp ERC2
+liprin-alpha1 pp GIT1
+hCNK1 pp RhoA
+Rpp20 pp SMN
+CDT1 pp GEMININ
+ORC6 pp MCM2
+CDC6 pp ORC1
+CDC5 pp ORC1
+MCM5 pp ORC1
+MCM3 pp MCM2
+MCM7 pp ORC4
+MCM3 pp MCM5
+MCM6 pp ORC6
+ORC4 pp ORC6
+ORC4 pp MCM10
+ORC5 pp ORC3
+MCM4 pp ORC6
+CDC45 pp MCM10
+MCM2 pp MCM10
+ORC2 pp MCM2
+CDT1 pp ORC1
+MCM6 pp MCM10
+MCM5 pp MCM2
+ORC2 pp MCM10
+CDC45 pp ORC5
+CDK6 pp MCM2
+ORC5 pp ORC1
+ORC2 pp ORC1
+CDC7 pp ORC6
+CYCD1 pp ORC4
+CDC45 pp ORC3
+CDC7 pp MCM10
+ORC5 pp MCM3
+CDC5 pp MCM3
+MCM3 pp MCM10
+MCM3 pp ORC4
+CDC5 pp ORC2
+CYCD3 pp MCM10
+CDC5 pp MCM4
+CDC6 pp ORC2
+CDC5 pp MCM10
+CYCB2 pp MCM2
+MCM6 pp MCM6
+CDC6 pp MCM10
+CYCD1 pp MCM10
+ORC3 pp ORC6
+MCM7 pp MCM10
+CYCE2 pp ORC3
+MCM7 pp MCM2
+ORC3 pp MCM7
+ORC5 pp MCM2
+ORC4 pp ORC5
+ORC3 pp ORC1
+CDC6 pp MCM2
+P16 pp CDK6
+P16 pp CDK4
+CYCA1 pp MCM6
+GEMININ pp P16
+MCM5 pp ORC3
+P16 pp ORC4
+ORC3 pp ORC4
+MCM5 pp CDC5
+ORC5 pp ORC2
+CDK6 pp MCM10
+CYCD3 pp P21
+GEMININ pp MCM6
+ORC5 pp CDC6
+CDC6 pp ORC3
+ORC5 pp CDC5
+ORC6 pp CDC6
+MCM10 pp ORC3
+MCM7 pp ORC6
+CYCE2 pp CDK2
+CDC6 pp P16
+CDK4 pp MCM2
+CYCE2 pp P21
+CDC5 pp P16
+CYCD1 pp CDK4
+CDC45 pp P21
+CDC6 pp P21
+CDC7 pp P21
+ORC5 pp CDC7
+CDC45 pp P16
+CYCD1 pp P21
+CDC7 pp P16
+P16 pp MCM2
+MCM5 pp MCM7
+MCM10 pp P16
+CDT1 pp CDC5
+CDC7 pp MCM3
+CDC5 pp P21
+CDK6 pp P21
+ORC4 pp ORC2
+CYCB2 pp P21
+CDK2 pp ORC2
+MCM5 pp P16
+CDT1 pp CDC6
+MCM5 pp ORC5
+CDK4 pp P21
+MCM7 pp MCM4
+CDC6 pp MCM3
+CYCB2 pp CDK2
+CYCA1 pp P21
+CYCA1 pp MCM4
+CDT1 pp ORC2
+CDK2 pp MCM3
+CDK2 pp P21
+GEMININ pp P21
+MCM10 pp P21
+CDK4 pp CDC7
+MCM6 pp MCM3
+FOS pp JUN
+CDK4 pp P16
+CDK6 pp P16
+eIF2c1 interactsWith siRNA
+Unknown interactsWith TAB1
+TAB2 interactsWith Unknown
+Smad3 pp APC10
+Smad2 pp APC10
+Unknown interactsWith TAK1
+STAGA_complex interactsWith DDB1
+Unknown interactsWith TAK1
+STAGA_complex interactsWith DDB2
+TAB3 interactsWith Unknown
+Unknown interactsWith TAB1
+NTF5 pp NTF5
+CTIP2 pp HP1-alpha
+Sua1 pp hUba2
+Rbp2 pp Rb
+hUbc9 pp SUMO-1
+RanGAP1 pp SUMO-1
+REV1 pp REV7
+BLM pp TOPO_III-alpha
+REV7 pp REV7
+Sua1/hUBa2_complex interactsWith SUMO-1
+Synphilin-1 pp Ubiquitin
+Synphilin-1 pp Parkin
+Parkin pp Ubiquitin
+PKC-lambda/iota pp LIP
+TES pp Actin-like_7A
+G-alpha-s-Short pp TPR1
+MIF pp CD74
+G-alpha-16 pp TPR1
+G-alpha-s-Long pp TPR1
+G-alpha-q pp TPR1
+Merlin pp TRBP
+Srm160 interactsWith Unknown
+Unknown interactsWith DEK
+Unknown interactsWith Y14
+Unknown interactsWith REF
+Unknown interactsWith RNPS1
+eIF4AIII interactsWith EJC_complex
+hDmc1 pp Rad54B
+p45 pp NEDD4
+p45 pp NEDD4
+p45 pp hYAP
+PCNA interactsWith Unknown
+PCNA_homotrimer interactsWith Ubiquitin
+Ubiquitin-PCNA_homotrimer interactsWith Pol-eta
+TRKB pp NTF4
+TRKB pp NTF4
+TRKB pp NTF4
+TRKB pp NTF4
+CDH1 pp HEF1
+Par-4 pp Par-4
+Smad3 pp HEF1
+Lamin_C pp Lamin_A
+Lamin_C pp Lamin_C
+Lamin_C pp Lamin_B1
+TNFR1 pp TNFR1
+NTF4 pp NTF4
+CIP4 pp WASP
+CrkL pp Syk
+CrkL pp WASP
+PSTPIP1 pp WASP
+Par-4 pp PKC-zeta
+Par-4 pp PKC-lambda/iota
+Eps15 pp ehb21a
+Eps15 pp ehb21b
+p53-R72 pp Bak
+p53-P72 pp Bak
+Eps15 pp ehb10
+Eps15 pp ehb3
+Eps15 pp NUMB-R
+Eps15 pp RAB-R
+Eps15 pp RAB
+Eps15 pp NUMB
+RGS6S pp DMAP1
+PD-1 pp B7-H1
+PD-1 pp B7-DC
+SF3a66 pp SF3a120
+SF3a60 pp SF3a120
+integrin-alpha-V-beta-3 interactsWith Myo10
+CDC5L pp PLRG1
+ZAP-70 pp Crk-I
+TGF-beta-2 pp Amyloid-beta
+KSRP interactsWith IL-2_3'UTR
+KSRP interactsWith AREfos
+KSRP interactsWith AREjun
+KSRP interactsWith AREtnf
+KSRP pp hRrp40p
+KSRP pp hRrp4p
+Shc interactsWith Unknown
+Unknown interactsWith Memo
+Unknown interactsWith ErbB2
+ErbB2 interactsWith Unknown
+Unknown interactsWith Shc
+Unknown interactsWith Memo
+integrin-beta-3 pp Myo10
+integrin-beta-5 pp Myo10
+integrin-beta-1 pp Myo10
+integrin-alpha-V-beta-5 interactsWith Myo10
+CIRL1 pp SSTRIP
+WRN pp RAD52
+Med150 interactsWith Unknown
+Med130 interactsWith Unknown
+Med78 interactsWith Unknown
+Med105 interactsWith Unknown
+KLF6 pp Cyclin_D1
+Unknown interactsWith Smad3
+Unknown interactsWith CDH1
+HEF1 interactsWith Unknown
+Unknown interactsWith APC10
+RanBPM pp beta-2-LFA-1
+PDIP38 pp PCNA
+PDIP46 pp p50
+PDIP38 pp p50
+Waf1 pp p50
+ATM pp hUpf1
+WIP pp WASP
+WIP pp CrkL
+hSMG-1 pp hUpf1
+hSMG-1 pp p53
+ATM pp p53
+gamma-SNAP pp Gaf-1
+PT-alpha pp REA
+Rab11 pp Gaf-1
+CASK pp Ca-alpha-1B
+ERK5 pp MKK5
+E2F-1 pp MDMX
+p73-alpha pp p300
+Pin1 pp p73-alpha
+Pin1 pp p73-beta
+pRb pp MDMX
+Rb pp E2F-1
+Unknown interactsWith Arp2/3_Complex
+Unknown interactsWith WASP
+Unknown interactsWith Actin
+Unknown interactsWith Arp2/3_Complex
+PARP pp caspase-3
+CXCR4 interactsWith CD4/HIV-1_gp120_complex
+NDUFS1 pp caspase-3
+CXCR4 pp SDF-1-alpha
+p73-alpha pd p53_AIP1_promoter
+Unknown interactsWith Nut2
+Unknown interactsWith MED28
+Unknown interactsWith ARC92
+Unknown interactsWith Rpb3
+Unknown interactsWith TRAP25
+Unknown interactsWith Srb7
+Unknown interactsWith MED8
+Unknown interactsWith ARC105
+Unknown interactsWith LCMR1
+Unknown interactsWith Sur2
+Unknown interactsWith Rgr1
+Unknown interactsWith TRAP80
+Unknown interactsWith CRSP70
+Unknown interactsWith TRAP37
+Unknown interactsWith TRAP220
+Unknown interactsWith MED7
+Unknown interactsWith TRFP
+Unknown interactsWith MED6
+Unknown interactsWith CDK11
+Unknown interactsWith Surf5
+Unknown interactsWith TRAP240L
+Unknown interactsWith Intersex
+Unknown interactsWith TRAP95
+Unknown interactsWith SOH1
+Unknown interactsWith TRAP100
+Unknown interactsWith HSPC296
+Unknown interactsWith CDK8
+Unknown interactsWith Rpb1
+Unknown interactsWith Rpb2
+Unknown interactsWith Rpb7
+Unknown interactsWith Rpb4
+Unknown interactsWith TRAP230
+Unknown interactsWith TRAP240
+Unknown interactsWith Rpb11
+Unknown interactsWith TRAP36
+Unknown interactsWith Med25
+Unknown interactsWith p28b
+Unknown interactsWith Rpb10
+Unknown interactsWith Rpb6
+Unknown interactsWith Rpb5
+Unknown interactsWith HSPA1L
+Unknown interactsWith Rpb8
+Unknown interactsWith TTN
+Unknown interactsWith Rpb9
+Unknown interactsWith EIF4A1
+Unknown interactsWith cyclin_C
+Unknown interactsWith NPM1
+Unknown interactsWith NONO
+Unknown interactsWith EEF1A1
+Unknown interactsWith ELL2
+Unknown interactsWith AF5Q31
+Unknown interactsWith LOC390814
+Unknown interactsWith DDX3X
+Unknown interactsWith PTBP1
+Unknown interactsWith RNPC2
+Unknown interactsWith TARDBP
+Unknown interactsWith HDAC6
+Unknown interactsWith E2F7
+Unknown interactsWith UBB
+Unknown interactsWith TMLHE
+Unknown interactsWith FLJ10081
+Unknown interactsWith RECQL5
+Unknown interactsWith CCAR1
+Unknown interactsWith DKFZP586J0619
+Unknown interactsWith LOC391392
+Unknown interactsWith UREB1
+Unknown interactsWith Rpb12
+Unknown interactsWith Nut2
+Unknown interactsWith MED28
+Unknown interactsWith ARC92
+Unknown interactsWith Rpb3
+Unknown interactsWith TRAP25
+Unknown interactsWith Srb7
+Unknown interactsWith MED8
+Unknown interactsWith ARC105
+Unknown interactsWith LCMR1
+Unknown interactsWith Sur2
+Unknown interactsWith Rgr1
+Unknown interactsWith TRAP80
+Unknown interactsWith CRSP70
+Unknown interactsWith TRAP37
+Unknown interactsWith TRAP220
+Unknown interactsWith MED7
+Unknown interactsWith TRFP
+Unknown interactsWith MED6
+Unknown interactsWith CDK11
+Unknown interactsWith Surf5
+Unknown interactsWith TRAP240L
+Unknown interactsWith Intersex
+Unknown interactsWith TRAP95
+Unknown interactsWith SOH1
+Unknown interactsWith TRAP100
+Unknown interactsWith HSPC296
+Unknown interactsWith CDK8
+Unknown interactsWith Rpb1
+Unknown interactsWith Rpb2
+Unknown interactsWith Rpb7
+Unknown interactsWith Rpb4
+Unknown interactsWith TRAP230
+Unknown interactsWith TRAP240
+Unknown interactsWith Rpb11
+Unknown interactsWith TRAP36
+Unknown interactsWith Med25
+Unknown interactsWith p28b
+Unknown interactsWith Rpb6
+Unknown interactsWith Rpb5
+Unknown interactsWith HSPA1L
+Unknown interactsWith TMPO
+Unknown interactsWith EIF4A1
+Unknown interactsWith GCN1L1
+Unknown interactsWith NPM1
+Unknown interactsWith NONO
+Unknown interactsWith EEF1A1
+Unknown interactsWith SMN2
+Unknown interactsWith SR140
+Unknown interactsWith DDX52
+Unknown interactsWith BAG2
+Unknown interactsWith SNRPD1
+Unknown interactsWith NOP5
+Unknown interactsWith HDAC6
+Unknown interactsWith E2F7
+Unknown interactsWith UBB
+Unknown interactsWith TMLHE
+Unknown interactsWith DCD
+Unknown interactsWith MGC14560
+Unknown interactsWith DSP
+Unknown interactsWith HSPA9B
+Unknown interactsWith HSPD1
+Unknown interactsWith KPNA2
+Unknown interactsWith NUMA1
+Unknown interactsWith DICER1
+Unknown interactsWith CCT3
+Unknown interactsWith ELAVL1
+Unknown interactsWith UREB1
+Unknown interactsWith CCT4
+Unknown interactsWith MSH6
+Unknown interactsWith CRSP3
+Unknown interactsWith USP49
+Unknown interactsWith Nut2
+Unknown interactsWith MED28
+Unknown interactsWith ARC92
+Unknown interactsWith Rpb3
+Unknown interactsWith TRAP25
+Unknown interactsWith Srb7
+Unknown interactsWith MED8
+Unknown interactsWith ARC105
+Unknown interactsWith LCMR1
+Unknown interactsWith Sur2
+Unknown interactsWith Rgr1
+Unknown interactsWith TRAP80
+Unknown interactsWith CRSP70
+Unknown interactsWith TRAP37
+Unknown interactsWith TRAP220
+Unknown interactsWith MED7
+Unknown interactsWith TRFP
+Unknown interactsWith MED6
+Unknown interactsWith CDK11
+Unknown interactsWith Surf5
+Unknown interactsWith TRAP240L
+Unknown interactsWith Intersex
+Unknown interactsWith TRAP95
+Unknown interactsWith SOH1
+Unknown interactsWith TRAP100
+Unknown interactsWith HSPC296
+Unknown interactsWith CDK8
+Unknown interactsWith Rpb1
+Unknown interactsWith Rpb2
+Unknown interactsWith Rpb7
+Unknown interactsWith Rpb4
+Unknown interactsWith TRAP230
+Unknown interactsWith TRAP240
+Unknown interactsWith Rpb11
+Unknown interactsWith TRAP36
+Unknown interactsWith Med25
+Unknown interactsWith p28b
+Unknown interactsWith Rpb10
+Unknown interactsWith Rpb6
+Unknown interactsWith Rpb5
+Unknown interactsWith HSPA1L
+Unknown interactsWith TMPO
+Unknown interactsWith Rpb8
+Unknown interactsWith TTN
+Unknown interactsWith Rpb9
+Unknown interactsWith GCN1L1
+Unknown interactsWith cyclin_C
+Unknown interactsWith NPM1
+Unknown interactsWith NONO
+Unknown interactsWith EEF1A1
+Unknown interactsWith HNRPM
+Unknown interactsWith SR140
+Unknown interactsWith DDX52
+Unknown interactsWith BAG2
+Unknown interactsWith SNRPD1
+Unknown interactsWith NOP5
+Unknown interactsWith DDX3X
+Unknown interactsWith PTBP1
+Unknown interactsWith RNPC2
+Unknown interactsWith TARDBP
+Unknown interactsWith UBB
+Unknown interactsWith TMLHE
+Unknown interactsWith PRKDC
+Unknown interactsWith MGC4308
+Unknown interactsWith DDX20
+Unknown interactsWith DDX31
+Unknown interactsWith BAT1
+Unknown interactsWith LUC7A
+Unknown interactsWith ZBTB9
+Unknown interactsWith DNAJA1
+Unknown interactsWith SFRS3
+Unknown interactsWith DNM2
+Unknown interactsWith MYBBP1A
+Unknown interactsWith DICER1
+Unknown interactsWith CCT3
+Unknown interactsWith ELAVL1
+Unknown interactsWith LOC391392
+Unknown interactsWith TREX2
+Unknown interactsWith MGC20533
+Unknown interactsWith PDCD8
+Unknown interactsWith SEC8L1
+Unknown interactsWith BCAS2
+Unknown interactsWith HSA9761
+Unknown interactsWith PRP19
+Unknown interactsWith HSPC152
+Unknown interactsWith Nut2
+Unknown interactsWith MED28
+Unknown interactsWith ARC92
+Unknown interactsWith Rpb3
+Unknown interactsWith TRAP25
+Unknown interactsWith Srb7
+Unknown interactsWith MED8
+Unknown interactsWith ARC105
+Unknown interactsWith LCMR1
+Unknown interactsWith Sur2
+Unknown interactsWith Rgr1
+Unknown interactsWith TRAP80
+Unknown interactsWith CRSP70
+Unknown interactsWith TRAP37
+Unknown interactsWith TRAP220
+Unknown interactsWith MED7
+Unknown interactsWith TRFP
+Unknown interactsWith MED6
+Unknown interactsWith CDK11
+Unknown interactsWith Surf5
+Unknown interactsWith TRAP240L
+Unknown interactsWith Intersex
+Unknown interactsWith TRAP95
+Unknown interactsWith SOH1
+Unknown interactsWith TRAP100
+Unknown interactsWith HSPC296
+Unknown interactsWith CDK8
+Unknown interactsWith Rpb1
+Unknown interactsWith Rpb2
+Unknown interactsWith Rpb7
+Unknown interactsWith Rpb4
+Unknown interactsWith TRAP230
+Unknown interactsWith TRAP240
+Unknown interactsWith Rpb11
+Unknown interactsWith TRAP36
+Unknown interactsWith Med25
+Unknown interactsWith p28b
+Unknown interactsWith Rpb10
+Unknown interactsWith Rpb6
+Unknown interactsWith Rpb5
+Unknown interactsWith HSPA1L
+Unknown interactsWith TMPO
+Unknown interactsWith Rpb8
+Unknown interactsWith TTN
+Unknown interactsWith Rpb9
+Unknown interactsWith EIF4A1
+Unknown interactsWith GCN1L1
+Unknown interactsWith cyclin_C
+Unknown interactsWith NPM1
+Unknown interactsWith NONO
+Unknown interactsWith EEF1A1
+Unknown interactsWith DNALI1
+Unknown interactsWith HNRPM
+Unknown interactsWith SMN2
+Unknown interactsWith ELL2
+Unknown interactsWith AF5Q31
+Unknown interactsWith LOC390814
+Unknown interactsWith SR140
+Unknown interactsWith DDX52
+Unknown interactsWith BAG2
+Unknown interactsWith SNRPD1
+Unknown interactsWith NOP5
+Unknown interactsWith DDX3X
+Unknown interactsWith PTBP1
+Unknown interactsWith RNPC2
+Unknown interactsWith TARDBP
+Unknown interactsWith HDAC6
+Unknown interactsWith E2F7
+Unknown interactsWith DDX50
+Unknown interactsWith FLJ13150
+Unknown interactsWith DD5
+Unknown interactsWith PRKDC
+Unknown interactsWith MGC4308
+Unknown interactsWith DDX20
+Unknown interactsWith DDX31
+Unknown interactsWith BAT1
+Unknown interactsWith LUC7A
+Unknown interactsWith ZBTB9
+Unknown interactsWith DNAJA1
+Unknown interactsWith SFRS3
+Unknown interactsWith DNM2
+Unknown interactsWith MYBBP1A
+Unknown interactsWith HSPA9B
+Unknown interactsWith HSPD1
+Unknown interactsWith KPNA2
+Unknown interactsWith NUMA1
+Unknown interactsWith DKFZP586J0619
+Unknown interactsWith FBL
+Unknown interactsWith ANAPC1
+Unknown interactsWith MGC3162
+Unknown interactsWith DDB1
+Unknown interactsWith DDX21
+Unknown interactsWith PRPF4B
+Unknown interactsWith RNPS1
+Unknown interactsWith IPO4
+Unknown interactsWith RFX1
+Unknown interactsWith ANAPC5
+Unknown interactsWith SMC4L1
+Unknown interactsWith ELYS
+Unknown interactsWith LMNA
+Unknown interactsWith C10orf104
+Unknown interactsWith NOL5A
+Unknown interactsWith PNN
+Unknown interactsWith DKFZP564M182
+Unknown interactsWith ZCCHC8
+Unknown interactsWith FLJ12178
+Unknown interactsWith NOL8
+Unknown interactsWith PPIG
+Unknown interactsWith RANGAP1
+Unknown interactsWith RUVBL1
+Unknown interactsWith TCOF1
+Unknown interactsWith USP7
+Unknown interactsWith CDC23
+Unknown interactsWith NOLC1
+Unknown interactsWith HCFC1
+Unknown interactsWith SAP18
+Unknown interactsWith RUVBL2
+Unknown interactsWith ZNF281
+Unknown interactsWith ANAPC2
+Unknown interactsWith UBTF
+Unknown interactsWith ACIN1
+Unknown interactsWith ZCCHC10
+Unknown interactsWith Nut2
+Unknown interactsWith MED28
+Unknown interactsWith ARC92
+Unknown interactsWith Rpb3
+Unknown interactsWith TRAP25
+Unknown interactsWith Srb7
+Unknown interactsWith MED8
+Unknown interactsWith ARC105
+Unknown interactsWith LCMR1
+Unknown interactsWith Sur2
+Unknown interactsWith Rgr1
+Unknown interactsWith TRAP80
+Unknown interactsWith CRSP70
+Unknown interactsWith TRAP37
+Unknown interactsWith TRAP220
+Unknown interactsWith MED7
+Unknown interactsWith TRFP
+Unknown interactsWith MED6
+Unknown interactsWith CDK11
+Unknown interactsWith Surf5
+Unknown interactsWith TRAP240L
+Unknown interactsWith Intersex
+Unknown interactsWith TRAP95
+Unknown interactsWith SOH1
+Unknown interactsWith TRAP100
+Unknown interactsWith HSPC296
+Unknown interactsWith CDK8
+Unknown interactsWith Rpb1
+Unknown interactsWith Rpb2
+Unknown interactsWith Rpb7
+Unknown interactsWith Rpb4
+Unknown interactsWith TRAP230
+Unknown interactsWith TRAP240
+Unknown interactsWith Rpb11
+Unknown interactsWith TRAP36
+Unknown interactsWith Med25
+Unknown interactsWith p28b
+Unknown interactsWith Rpb10
+Unknown interactsWith GCN1L1
+Unknown interactsWith cyclin_C
+Unknown interactsWith DNALI1
+Unknown interactsWith LOC390814
+Unknown interactsWith CCAR1
+Unknown interactsWith Nut2
+Unknown interactsWith MED28
+Unknown interactsWith ARC92
+Unknown interactsWith Rpb3
+Unknown interactsWith TRAP25
+Unknown interactsWith Srb7
+Unknown interactsWith MED8
+Unknown interactsWith ARC105
+Unknown interactsWith LCMR1
+Unknown interactsWith Sur2
+Unknown interactsWith Rgr1
+Unknown interactsWith TRAP80
+Unknown interactsWith CRSP70
+Unknown interactsWith TRAP37
+Unknown interactsWith TRAP220
+Unknown interactsWith MED7
+Unknown interactsWith TRFP
+Unknown interactsWith MED6
+Unknown interactsWith CDK11
+Unknown interactsWith Surf5
+Unknown interactsWith TRAP240L
+Unknown interactsWith Intersex
+Unknown interactsWith TRAP95
+Unknown interactsWith SOH1
+Unknown interactsWith TRAP100
+Unknown interactsWith HSPC296
+Unknown interactsWith CDK8
+Unknown interactsWith Rpb1
+Unknown interactsWith Rpb2
+Unknown interactsWith Rpb7
+Unknown interactsWith Rpb4
+Unknown interactsWith TRAP230
+Unknown interactsWith TRAP240
+Unknown interactsWith Rpb11
+Unknown interactsWith TRAP36
+Unknown interactsWith Med25
+Unknown interactsWith p28b
+Unknown interactsWith Rpb10
+Unknown interactsWith Rpb6
+Unknown interactsWith Rpb5
+Unknown interactsWith HSPA1L
+Unknown interactsWith TMPO
+Unknown interactsWith Rpb8
+Unknown interactsWith TTN
+Unknown interactsWith Rpb9
+Unknown interactsWith EIF4A1
+Unknown interactsWith DNALI1
+Unknown interactsWith HNRPM
+Unknown interactsWith SMN2
+Unknown interactsWith ELL2
+Unknown interactsWith AF5Q31
+Unknown interactsWith DDX50
+Unknown interactsWith FLJ13150
+Unknown interactsWith DD5
+Unknown interactsWith DCD
+Unknown interactsWith MGC14560
+Unknown interactsWith DSP
+Unknown interactsWith FLJ10081
+Unknown interactsWith RECQL5
+Unknown interactsWith P4HB
+Unknown interactsWith LEPRE1
+Unknown interactsWith GRINL1A
+Unknown interactsWith KPNA4
+Fibrillin-1 pp Fibulin-2
+Cingulin pp ZO-1
+ZAP-70 pp CrkL
+p300 pp p53
+CARM1 pp p53
+pRb pp P/CAF
+RasGAP pp HsAIRK-1
+RasGAP pp HsAIRK-2
+HsAIRK-2 pp Survivin
+ZAP-70 pp Crk-II
+Survivin pp INCENP
+HP1 pp INCENP
+PRMT1 pp p53
+DNMT3L pp Dnmt3a
+N-WASP interactsWith Arp2/3_complex
+DNMT3L pp Dnmt3b
+5S_rDNA interactsWith DNMT3L/Dnmt3a_complex
+p14ARF pp TBP-1
+Mad2 pp CSF2RB
+CAV1 pp PP1-C
+Ubc9 pp CHD3
+Ubc9 pp HIPK2
+Ubc9 pp PIASx-beta
+Antibody_17B,_Heavy_Chain pp Antibody_17B,_Light_Chain
+Lamin_A pp Lamin_A
+PDIP1 pp PCNA
+PDIP1 pp p50
+c-Jun pp c-Jun
+c-Jun pp c-Fos
+NF-kappa-B pp c-Fos
+NF-kappa-B pp c-Jun
+Sirt1 pp NcoR
+Sirt1 pp SMRT
+hSMN pp hSMN
+Unknown interactsWith p130Cas
+Ku70 pp HP1-alpha
+p50/p65 interactsWith EAAT2_promoter
+p53 pd GADD45_p53RE
+p300-p53_complex interactsWith GADD45_p53RE
+CARM1-p53_complex interactsWith GADD45_p53RE
+PRMT1-p53_complex interactsWith GADD45_p53RE
+AES pp AES
+AES pp p65
+TLE1 pp p65
+hVPS28 pp TSG101
+HRS pp TSG101
+5S_rDNA interactsWith DNMT3L/Dnmt3b_complex
+paxillin pp MAP4
+paxillin pp LOC146053
+paxillin pp RRBP1
+paxillin pp A39045
+paxillin pp NALP12
+paxillin pp FAAH
+paxillin pp LOC220294
+paxillin pp LOC255381
+paxillin pp TM7SF2
+paxillin pp NARS
+paxillin pp HIST1H2BK
+paxillin pp BANF1
+paxillin pp ARID3B
+paxillin pp HIST1H4A
+paxillin pp COL1A1
+paxillin pp COL4A1
+paxillin pp LMNA
+paxillin pp ACTG1
+paxillin pp FN1
+paxillin pp GAPD
+paxillin pp SLC25A5
+paxillin pp TUBB2
+paxillin pp OK/SW-cl.56
+paxillin pp RPLP2
+paxillin pp COL5A2
+paxillin pp ENO1
+paxillin pp P4HB
+paxillin pp ANXA2
+paxillin pp COL1A2
+paxillin pp SLC3A2
+paxillin pp RPL27
+paxillin pp VIM
+paxillin pp LAMR1
+paxillin pp LGALS1
+paxillin pp RPS6
+paxillin pp HSPA5
+paxillin pp HSPA8
+paxillin pp DBT
+paxillin pp COL6A1
+paxillin pp COL6A2
+paxillin pp COL6A3
+paxillin pp G22P1
+paxillin pp XRCC5
+paxillin pp P4HA1
+paxillin pp RPL19
+paxillin pp PKM2
+paxillin pp MYL6
+paxillin pp RPS24
+paxillin pp NSEP1
+paxillin pp RPL7
+paxillin pp RPL17
+paxillin pp HIST1H2AD
+paxillin pp COL5A1
+paxillin pp FLNA
+paxillin pp TGM2
+paxillin pp HIST1H1T
+paxillin pp RPL23
+paxillin pp SFRS3
+paxillin pp SFPQ
+paxillin pp PRRG2
+paxillin pp RPL38
+paxillin pp RPS7
+paxillin pp TNC
+paxillin pp RPL8
+paxillin pp RPL13
+paxillin pp PTBP1
+paxillin pp COL8A1
+paxillin pp YWHAZ
+paxillin pp GRP58
+paxillin pp LRPAP1
+paxillin pp RPL9
+paxillin pp RPL22
+paxillin pp MYH9
+paxillin pp RPL4
+paxillin pp RPL3
+paxillin pp RPL11
+paxillin pp RPS23
+paxillin pp TMPO
+paxillin pp TMPO
+paxillin pp RPS27
+paxillin pp RPL21
+paxillin pp RPL28
+paxillin pp CAPZA2
+paxillin pp RPL29
+paxillin pp PXN
+paxillin pp EMD
+paxillin pp SERPINH1
+paxillin pp RPL14
+paxillin pp HMGA2
+paxillin pp EWSR1
+paxillin pp RPL26
+paxillin pp RPL6
+paxillin pp SSBP1
+paxillin pp PRDX1
+paxillin pp LRP1
+paxillin pp TFCP2
+paxillin pp G3BP
+paxillin pp MVP
+paxillin pp PCOLCE
+paxillin pp NONO
+paxillin pp LIP8
+paxillin pp ZFYVE27
+paxillin pp RPL15
+paxillin pp URB
+paxillin pp CKAP4
+paxillin pp DNAH3
+paxillin pp RPL10
+paxillin pp NICAL
+paxillin pp DDX1
+paxillin pp KIAA1893
+paxillin pp COL12A1
+paxillin pp TGFB1I1
+paxillin pp TUBA3
+paxillin pp M11S1
+paxillin pp HNRPM
+paxillin pp RPL5
+paxillin pp FAU
+paxillin pp FLJ11292
+paxillin pp AASS
+paxillin pp DCTN4
+paxillin pp RPLP0
+paxillin pp COG5
+paxillin pp TLN1
+paxillin pp WASP-family_protein_member_2
+talin pp FRMPD1
+talin pp MAP4
+talin pp LOC119995
+talin pp HNRPH1
+talin pp OR51B6
+talin pp LOC150128
+talin pp LOC222143
+talin pp LOC220078
+talin pp LOC204026
+talin pp LOC204121
+talin pp BAI2
+talin pp BUB1B
+talin pp HIST1H2BK
+talin pp PDE4DIP
+talin pp CLASP1
+talin pp TIP120B
+talin pp SCFD1
+talin pp FMNL1
+talin pp ACTG1
+talin pp FN1
+talin pp TFRC
+talin pp ACTC
+talin pp GAPD
+talin pp COL5A2
+talin pp SNRPE
+talin pp VIM
+talin pp PABPC1
+talin pp C2orf3
+talin pp NSEP1
+talin pp FLNA
+talin pp RPL23
+talin pp SFRS3
+talin pp SFPQ
+talin pp GNB2L1
+talin pp GRP58
+talin pp LRPAP1
+talin pp FMO4
+talin pp ARF1
+talin pp FUS
+talin pp SNRPD3
+talin pp RGS7
+talin pp TPMT
+talin pp BASP1
+talin pp RBM3
+talin pp EWSR1
+talin pp PTPN11
+talin pp HNRPK
+talin pp LRP1
+talin pp STX3A
+talin pp G3BP
+talin pp CIRBP
+talin pp NICE-4
+talin pp BCLAF1
+talin pp SNRPF
+talin pp NBEA
+talin pp ZNF618
+talin pp PFKL
+talin pp KIAA0746
+talin pp PTPRE
+talin pp AAK69721
+talin pp VAT1
+talin pp COL12A1
+talin pp KHDRBS1
+talin pp SMYD3
+talin pp BAB14693
+talin pp HNRPH3
+talin pp HMG20A
+talin pp AVEN
+talin pp HNYA
+talin pp THSD1
+talin pp HSPC117
+talin pp KIAA1411
+talin pp NET1
+talin pp ADAM28
+talin pp G3BP2
+talin pp SCFD1
+talin pp ZNF510
+talin pp TLN1
+talin pp KIAA0423
+talin pp ZFR
+talin pp BIG1
+talin pp LOC284058
+vinculin pp CYCS
+vinculin pp HNRPH1
+vinculin pp CALML5
+vinculin pp LOC170356
+vinculin pp FUCA1
+vinculin pp RIT2
+vinculin pp TAF15
+vinculin pp MGC10561
+vinculin pp EIF3S5
+vinculin pp DDX3X
+vinculin pp HNRPDL
+vinculin pp SLC16A5
+vinculin pp CPSF5
+vinculin pp PRMT3
+vinculin pp HIST1H2BK
+vinculin pp DDX46
+vinculin pp SCFD1
+vinculin pp ABCC6
+vinculin pp BAG4
+vinculin pp SEC24A
+vinculin pp LOC391306
+vinculin pp CYCS
+vinculin pp B2M
+vinculin pp ACTG1
+vinculin pp FN1
+vinculin pp TFRC
+vinculin pp ACTC
+vinculin pp GAPD
+vinculin pp EEF1A1
+vinculin pp SLC25A5
+vinculin pp TUBB2
+vinculin pp ATP5B
+vinculin pp EIF4E
+vinculin pp ANXA2
+vinculin pp PFN1
+vinculin pp SNRPE
+vinculin pp VIM
+vinculin pp LAMR1
+vinculin pp SNRPA
+vinculin pp LGALS1
+vinculin pp PABPC1
+vinculin pp MIF
+vinculin pp PGAM2
+vinculin pp HIVEP1
+vinculin pp MYL6
+vinculin pp RPS24
+vinculin pp RPS20
+vinculin pp PSMB1
+vinculin pp NME2
+vinculin pp SFPQ
+vinculin pp PRRG2
+vinculin pp GNB2L1
+vinculin pp PSMA2
+vinculin pp U2AF2
+vinculin pp COL8A1
+vinculin pp LAP3
+vinculin pp GRP58
+vinculin pp LRPAP1
+vinculin pp RPS21
+vinculin pp MYH9
+vinculin pp FUS
+vinculin pp RPS19
+vinculin pp FEN1
+vinculin pp DCT
+vinculin pp SERPINH1
+vinculin pp FXR1
+vinculin pp SLC25A1
+vinculin pp HADHB
+vinculin pp RBM3
+vinculin pp U2AF1
+vinculin pp HSPE1
+vinculin pp CKAP4
+vinculin pp HNRPK
+vinculin pp LRP1
+vinculin pp LGALS3BP
+vinculin pp STX3A
+vinculin pp G3BP
+vinculin pp CIRBP
+vinculin pp NICE-4
+vinculin pp NONO
+vinculin pp SNRPF
+vinculin pp SNRPG
+vinculin pp VCL
+vinculin pp LRRN5
+vinculin pp NBEA
+vinculin pp PARK2
+vinculin pp DDX1
+vinculin pp PRO1855
+vinculin pp LOC201158
+vinculin pp KIAA0746
+vinculin pp KIAA1797
+vinculin pp hnRNP_Q2
+vinculin pp IKIP
+vinculin pp OLFM3
+vinculin pp ALS2CR11
+vinculin pp S100A13
+vinculin pp KHDRBS1
+vinculin pp AAH06380
+vinculin pp HSPA8
+vinculin pp HNRPH3
+vinculin pp AVEN
+vinculin pp WDTC
+vinculin pp HSPC117
+vinculin pp UBC
+vinculin pp SNRPB
+vinculin pp C14orf166
+vinculin pp KIAA0423
+vinculin pp MORC
+vinculin pp BIG1
+vinculin pp P62
+vinculin pp LDHA
+vinculin pp BIRC6
+vinculin pp LOC284058
+vinculin pp KIAA1728
+vinculin pp SYNE1
+vinculin pp MGC42174
+vinculin pp FLJ25409
+vinculin pp LOC128158
+vinculin pp LOC118660
+vinculin pp LOC124695
+vinculin pp LOC126505
+vinculin pp LOC132623
+vinculin pp LOC151484
+vinculin pp LOC163718
+vinculin pp LOC161927
+vinculin pp LOC151099
+vinculin pp LOC165524
+vinculin pp LOC167821
+vinculin pp LOC169497
+vinculin pp LOC163939
+vinculin pp LOC165578
+vinculin pp LOC153872
+vinculin pp TLN1
+RACK1 pp PDE4D5
+unknown interactsWith TFIIHp89
+Unknown interactsWith TFIIEp34
+Unknown interactsWith TFIIEp57
+Unknown interactsWith TBP
+PDE4D4 pp Lyn
+PDE4D4 pp Fyn
+PDE4D4 pp Src
+PDE4D4 pp Abl
+PDE4D4 pp Fodrin
+PDE4D4 pp PI3K
+PDE4D4 pp Grb2
+hU2AF(65) pp hU2AF(35)
+ER-alpha interactsWith Unknown
+Unknown interactsWith c-Src
+Unknown interactsWith p85
+Eed pp EZH1
+SIRT1 pp Ku70
+SIRT1 pp p53
+cyclin_A1 pp E2F-1
+PDE4D5 pp Beta-Arrestin_1
+PDE4D5 pp Beta-Arrestin_2
+Unknown interactsWith Derlin-1
+Unknown interactsWith p97
+VIMP interactsWith Unknown
+VIMP pp p97
+VIMP pp VIMP
+PLC-gamma1 pp PLD2
+VIMP interactsWith Unknown
+Unknown interactsWith p97
+Unknown interactsWith Ufd1
+p150 pp hPrt1
+Unknown interactsWith IKK1
+Unknown interactsWith NEMO
+ELKS interactsWith Unknown
+Unknown interactsWith IKK2
+p150 pp K7
+UbcH8 pp E6AP
+UbcH7 pp E6AP
+CBP pp p21
+ELKS pp I-kappa-B-alpha
+MAPKAP-K2 pp hnRNPA0
+NRSF pp G9a
+caveolin-1 pp AR
+Hrk pp Bcl-2
+Hrk pp Bcl-XL
+Bcl-2 pp Bad
+COX-2 pp COX-2
+COX-2 interactsWith Prostaglandin
+IGFIR pp IRS-1
+HIF-1alpha pp HIF-1beta
+Sam68 pp p85
+HIF-1alpha pp HIF-1beta
+HIF-1alpha pp HIF-1beta
+HIF-1alpha pp HIF-1beta
+Sam68 interactsWith Grb2-Sos
+Sam68 pp p120GAP
+HIF-1alpha pp p53
+Nmi pp Nmi
+BRCA1 interactsWith Nmi_homodimer
+p73_delta_N_alpha pp p73_alpha
+p73_delta_N_alpha pp p73_beta_
+Hamartin pp 14-3-3-beta
+Hamartin pp 14-3-3-gamma_
+p73_delta_N_gamma pp p73_beta
+hamartin-tuberin interactsWith NF-L
+DNA-PKcs pp RPA2
+IR pp p85-alpha
+p65 pd HS.22.q.33
+p65 pd HS.22.q.171
+p65 pd HS.22.q.240
+p65 pd HS.22.q.248
+p65 pd HS.22.q.433
+p65 pd HS.22.q.586
+p65 pd HS.22.q.1112
+p65 pd HS.22.q.1233
+p65 pd HS.22.q.1273
+p65 pd HS.22.q.1348
+p65 pd HS.22.q.1392
+p65 pd HS.22.q.1660
+p65 pd HS.22.q.1724
+p65 pd HS.22.q.1941
+p65 pd HS.22.q.1959
+p65 pd HS.22.q.1992
+p65 pd HS.22.q.2084
+p65 pd HS.22.q.2094
+p65 pd HS.22.q.2105
+p65 pd HS.22.q.2146
+p65 pd HS.22.q.2156
+p65 pd HS.22.q.2210
+p65 pd HS.22.q.2220
+p65 pd HS.22.q.2282
+p65 pd HS.22.q.2341
+p65 pd HS.22.q.2363
+p65 pd HS.22.q.2365
+p65 pd HS.22.q.2394
+p65 pd HS.22.q.2419
+p65 pd HS.22.q.2425
+p65 pd HS.22.q.2443
+p65 pd HS.22.q.2449
+p65 pd HS.22.q.2450
+p65 pd HS.22.q.2452
+p65 pd HS.22.q.2454
+p65 pd HS.22.q.2469
+p65 pd HS.22.q.2536
+p65 pd HS.22.q.2554
+p65 pd HS.22.q.2584
+p65 pd HS.22.q.2601
+p65 pd HS.22.q.2623
+p65 pd HS.22.q.2704
+p65 pd HS.22.q.2714
+p65 pd HS.22.q.2717
+p65 pd HS.22.q.2721
+p65 pd HS.22.q.2726
+p65 pd HS.22.q.2749
+p65 pd HS.22.q.2761
+p65 pd HS.22.q.2797
+p65 pd HS.22.q.2827
+p65 pd HS.22.q.2829
+p65 pd HS.22.q.2833
+p65 pd HS.22.q.2839
+p65 pd HS.22.q.2865
+p65 pd HS.22.q.2869
+p65 pd HS.22.q.2980
+p65 pd HS.22.q.3009
+p65 pd HS.22.q.3018
+p65 pd HS.22.q.3022
+p65 pd HS.22.q.3072
+p65 pd HS.22.q.3089
+p65 pd HS.22.q.3112
+p65 pd HS.22.q.3113
+p65 pd HS.22.q.3119
+p65 pd HS.22.q.3136
+p65 pd HS.22.q.3478
+p65 pd HS.22.q.3702
+p65 pd HS.22.q.3703
+p65 pd HS.22.q.4017
+p65 pd HS.22.q.4137
+p65 pd HS.22.q.5263
+p65 pd HS.22.q.5959
+p65 pd HS.22.q.6753
+p65 pd HS.22.q.6762
+p65 pd HS.22.q.6827
+p65 pd HS.22.q.6829
+p65 pd HS.22.q.7468
+p65 pd HS.22.q.7468
+p65 pd HS.22.q.7698
+p65 pd HS.22.q.7824
+p65 pd HS.22.q.7880
+p65 pd HS.22.q.8061
+p65 pd HS.22.q.8256
+p65 pd HS.22.q.8555
+p65 pd HS.22.q.8578
+p65 pd HS.22.q.8584
+p65 pd HS.22.q.8925
+p65 pd HS.22.q.8942
+p65 pd HS.22.q.9038
+p65 pd HS.22.q.9100
+p65 pd HS.22.q.9169
+p65 pd HS.22.q.9175
+p65 pd HS.22.q.9224
+p65 pd HS.22.q.9226
+p65 pd HS.22.q.9231
+p65 pd HS.22.q.9303
+p65 pd HS.22.q.9345
+p65 pd HS.22.q.9615
+p65 pd HS.22.q.9960
+p65 pd HS.22.q.9991
+p65 pd HS.22.q.9993
+p65 pd HS.22.q.10039
+p65 pd HS.22.q.10881
+p65 pd HS.22.q.10950
+p65 pd HS.22.q.10957
+p65 pd HS.22.q.11037
+p65 pd HS.22.q.11074
+p65 pd HS.22.q.11175
+p65 pd HS.22.q.11208
+p65 pd HS.22.q.11224
+p65 pd HS.22.q.11561
+p65 pd HS.22.q.11563
+p65 pd HS.22.q.12001
+p65 pd HS.22.q.12251
+p65 pd HS.22.q.12820
+p65 pd HS.22.q.12830
+p65 pd HS.22.q.13110
+p65 pd HS.22.q.13903
+p65 pd HS.22.q.14221
+p65 pd HS.22.q.14927
+p65 pd HS.22.q.14939
+p65 pd HS.22.q.14945
+p65 pd HS.22.q.15075
+p65 pd HS.22.q.15121
+p65 pd HS.22.q.15231
+p65 pd HS.22.q.15579
+p65 pd HS.22.q.15621
+p65 pd HS.22.q.15639
+p65 pd HS.22.q.15643
+p65 pd HS.22.q.15859
+p65 pd HS.22.q.15996
+p65 pd HS.22.q.16134
+p65 pd HS.22.q.16194
+p65 pd HS.22.q.16220
+p65 pd HS.22.q.16230
+p65 pd HS.22.q.16328
+p65 pd HS.22.q.16494
+p65 pd HS.22.q.16497
+p65 pd HS.22.q.16576
+p65 pd HS.22.q.16657
+p65 pd HS.22.q.16660
+p65 pd HS.22.q.16662
+p65 pd HS.22.q.16745
+p65 pd HS.22.q.16747
+p65 pd HS.22.q.16754
+p65 pd HS.22.q.16792
+p65 pd HS.22.q.16793
+p65 pd HS.22.q.16836
+p65 pd HS.22.q.16980
+p65 pd HS.22.q.17173
+p65 pd HS.22.q.17179
+p65 pd HS.22.q.17193
+p65 pd HS.22.q.17201
+p65 pd HS.22.q.17241
+p65 pd HS.22.q.17257
+p65 pd HS.22.q.17262
+p65 pd HS.22.q.17281
+p65 pd HS.22.q.17338
+p65 pd HS.22.q.17428
+p65 pd HS.22.q.17474
+p65 pd HS.22.q.17495
+p65 pd HS.22.q.17514
+p65 pd HS.22.q.17517
+p65 pd HS.22.q.17535
+p65 pd HS.22.q.17601
+p65 pd HS.22.q.17603
+p65 pd HS.22.q.17604
+p65 pd HS.22.q.17683
+p65 pd HS.22.q.17684
+p65 pd HS.22.q.17690
+p65 pd HS.22.q.17692
+p65 pd HS.22.q.17774
+p65 pd HS.22.q.17776
+p65 pd HS.22.q.17819
+p65 pd HS.22.q.17839
+p65 pd HS.22.q.17861
+p65 pd HS.22.q.17864
+p65 pd HS.22.q.17886
+p65 pd HS.22.q.18040
+p65 pd HS.22.q.18047
+p65 pd HS.22.q.18048
+p65 pd HS.22.q.18113
+p65 pd HS.22.q.18169
+p65 pd HS.22.q.18170
+p65 pd HS.22.q.18174
+p65 pd HS.22.q.18204
+p65 pd HS.22.q.18452
+p65 pd HS.22.q.18514
+p65 pd HS.22.q.18538
+p65 pd HS.22.q.18616
+p65 pd HS.22.q.18641
+p65 pd HS.22.q.18673
+p65 pd HS.22.q.18737
+p65 pd HS.22.q.18739
+p65 pd HS.22.q.18796
+p65 pd HS.22.q.18863
+p65 pd HS.22.q.19024
+p65 pd HS.22.q.19215
+p65 pd HS.22.q.20022
+p65 pd HS.22.q.20067
+p65 pd HS.22.q.20551
+p65 pd HS.22.q.20568
+p65 pd HS.22.q.20572
+p65 pd HS.22.q.20582
+p65 pd HS.22.q.20587
+p65 pd HS.22.q.20590
+p65 pd HS.22.q.20779
+p65 pd HS.22.q.20807
+p65 pd HS.22.q.20983
+Rbx1 pp Cul5
+EBP50 pp CFTR
+NHERF pp beta2-AR
+Ub pp APOBEC3G
+MLH1 pp Myc
+Myc pp Max
+MSH2 pp Max
+Myc pp Sp1
+Myc pp NF-YB
+Myc pp NF-YC
+NHERF-2 pp beta2-AR
+Myc interactsWith NF-Y_complex
+NHERF pp P2Y1R
+CIA pp TAFII250
+YB-1 pp hnRNP_K
+SAFB pp hnRNP_K
+syn1A pp CFTR
+URI pp RPB5
+URI pp STAP1
+BRCA1 pp Rad51
+STAP1 pp SKP2
+STAP1 interactsWith Unknown
+URI interactsWith Unknown
+Unknown interactsWith TIP49
+TIP48 interactsWith Unknown
+Unknown interactsWith RPB5
+Unknown interactsWith PFD2
+Unknown interactsWith PFD4r
+Unknown interactsWith SKP2
+Unknown interactsWith CUL1
+Unknown interactsWith SKP1
+BRCA2 pp RAD51
+Csp1 pp CFTR
+Csp2 pp CFTR
+E3KARP pp CFTR
+TCL1 pp AKT1
+TCL1B_ pp AKT1
+MTCP1 pp AKT1
+TCL1 pp AKT2
+TCL1 pp Akt3
+alpha1-H pp BKCA-alpha
+GIPC pp TRKA
+FBH1 pp SKP1
+Unknown interactsWith CUL1
+Sam68 pp hnRNP_K
+CUL1 pp ROC1
+E3KARP pp ezrin
+PKA_II pp ezrin
+PSR interactsWith PS
+PKA_II pp CFTR
+Rb pp TFIIIC2
+Cul1_[15-410] pp Cul1_[411-776]
+RBX1 pp Cul1_[411-776]
+SKP1A pp Cul1_[15-410]
+Skp2-Fbox pp SKP1A
+Skp2-Fbox pp Cul1_[15-410]
+Rb pp TFIIIB90
+PMCA2b pp NHERF2
+Rb pp p55gamma
+Huntingtin pp HYPA
+Rb pp p55alpha
+PSR pp DOCK180
+PSR pp ELMO1
+Huntingtin pp HYPB
+Huntingtin pp HYPC
+HYPA pp HYPA
+HYPB pp HYPB
+SAP97 pp TACE
+CDKN2A pp CDK6
+TPD52L1 pp MAL2
+TPD52L2 pp MAL2
+Rb pp SNAP43
+Rb pp SNAP50
+Rb pp TBP
+eIF6 pp RACK1
+PMCA2b pp SAP97
+RACK1 pp p73alpha
+RACK1 pp Rb
+RACK1 pp p120GAP
+PMCA2b pp SAP93
+PMCA2b pp SAP90
+Top1 pp Nucleolin
+RKIP pp GRK-2
+RKIP pp Raf-1
+PKCalpha pp RKIP
+PKCdelta pp RKIP
+PCNA pp MSH3
+Top1 pp Top1
+PMCA4b pp SAP97
+Top1 interactsWith Unknown
+Rb pp LAP2alpha
+beta-COP pp delta-COP
+Rb pp lamin_C
+PMCA4b pp SAP93
+PMCA4b pp SAP102
+gamma-COP pp zeta-COP
+alpha-COP pp epsilon-COP
+Arf1 interactsWith GTP
+Arf1-GTP interactsWith Coatomer
+PSF pp p54nrb
+Arf1-GTP interactsWith ArfGAP1
+SPINO pp p14ARF
+PMCA2b pp PISP
+PMCA4b pd PISP
+PS1 pp caspase_7
+PMCA4b pp PSD-95
+merlin pp hNHE-RF
+moesin pp hNHE-RF
+radixin pp hNHE-RF
+hDLG pp DAP-1alpha
+hDLG pp DAP-1beta
+HDAC2 pp Ebp1
+GLUR1 pp GluR-delta-2
+GluR6 pp GluR-delta-2
+Mac25/AGM pp SLC
+Rb pp PAI-2
+PSD-95 pp DAP-1alpha
+CHL12 interactsWith RFCs2-5_complex
+CDK4 pp Cyclin_D1
+Rb pp E2F
+hDLG pp DAP-2
+Rb pp c-Abl
+NR1a pp NR2A
+Mac25/AGM pp IP-10
+Mac25/AGM pp RANTES
+RasGRP3 pp PKC-theta
+RasGRP3 pp PKC-beta2
+Top1 interactsWith PSF-p54nrb
+ErbB-3 pp Ebp1
+Sam68 pp hnRNP_K
+Smad3 pp c-Ski
+Rb pp CypA
+Smad2 pp c-Ski
+Prohibitin pp Brg-1
+Prohibitin pp Brm
+Top1 pp PSF
+ZHX2 pp ZHX3
+Murr1 pp I-kappaB-alpha
+PCNA pp p21
+Daxx pp Sentrin
+FADD pp TRADD
+Fas pp Sentrin
+hRev3 pp hRev7
+Exp5 interactsWith Pre-miR-31
+SALL1 pp SUMO-1
+SALL1 pp UBE2I
+Murr1 pp Cul1
+Rb pp ATF2
+RelA pp I-kappaB-beta
+Daxx pp Ubc9
+Sentrin pp Sentrin
+Rb pp JNK2
+PS1 pp NPRAP
+PS1 pp beta-catenin
+Bcl10 pp paracaspase
+Bcl10 pp NEMO
+Bcl10 pp UBC13
+Bcl10 pp MMS2
+Ub pp paracaspase
+Ub pp NEMO
+paracaspase pp paracaspase
+Wrn pp TRF2
+Max pp Mxi1
+Max pp Mad1
+BLM pp TRF2
+IMP pp Ras
+WRN pp p53
+BLM pp p53
+Raf pp MEK1
+E2F-1 pp C/EBPepsilon
+Rb pp C/EBPepsilon
+Raf pp Mek2
+IMP pp IMP
+DMPK interactsWith Sp1
+DMPK interactsWith RAR-gamma
+p-CLCN1 pd Sp1
+DMPK interactsWith CUGBP1
+Smad3 pp SnoN
+Smad2 pp SnoN
+Smad1 pp SnoN
+p73_beta pp p73_beta
+p73_alpha pp p73_beta
+p73_alpha pp p73_alpha
+p73_delta_N_beta pp p73_beta
+M4 pp eEf1A
+beta-1-AR pp GIPC
+alpha-2A-AR pp beta-1-AR
+Unknown interactsWith RFC1
+menin pp JunD
+menin pp vimentin
+TNFR1 pp Sentrin
+BRCA1 pp Sp1
+AMF1 pp AMF1
+p53 pp securin
+p53 pp STK15
+p53 pp HMG-1
+PS1 pp caspase_3
+TALL-1 interactsWith Unknown
+TALL-1 interactsWith Unknown
+PTB pp hnRNP_L
+Beta-PDGFR pp p85
+Beta-PDGFR pp PLC-gamma
+merlin pp merlin
+p300 pp c-Maf
+Smad4 pp c-Ski
+p300 pp Prox-1
+c-Ski pp c-Ski
+RET51 pp GRB2
+RET9 pp Shc
+RET51 pp Shc
+RET51 pp PLC-gamma
+RET9 pp PLC-gamma
+p53 pp AMF1
+p53 pp GR
+p53 pp ING1b
+GAP pp EGFR
+CBP pp c-Maf
+Cdc42 pp Borg1
+TC10 pp Borg1
+GAP pp PDGFR
+hDET1 pp hCOP1
+hDET1 pp DDB1
+DDB1 pp CUL4A
+hCOP1-hDET1-DDB1-CUL4A interactsWith Unknown
+ROC1 interactsWith Unknown
+SRp38 pp Tra2-alpha
+SRp38 pp U1-70K
+cycE pp Fbw7
+DCX-hDET1-hCOP1 interactsWith c-jun
+hCOP1 pp c-jun
+Rac1 pp RhoGDI
+ShcA pp EGFR
+Shc pp NGFR
+MAD2 pp TACE
+TC10 pp Borg2
+Cdc42 pp Borg2
+FBP17 pp SNX2
+ER_alpha pp ER_beta
+ER_alpha pp TIF2
+ER_alpha pp TRIP1
+MAD2 pp ER_beta
+MAD2B pp MDC9
+MAD2 pp FAT10
+p53 pp AP2gamma
+p53 pp AP2alpha
+Itk pp hnRNPK
+p85 pp hnRNPK
+Fyn pp hnRNPK
+Src pp hnRNPK
+merlin pp Pak1
+DDR1b pp Shc
+DDR1b pp DDR1b
+VG5Q pp TWEAK
+Src pp FAK
+Grb2 pp Shc
+schwannomin pp syntenin
+EGFR pp E-cadherin
+SHP2 pp Gab1
+SUMO-1 pp PIAS1
+Ubc9 pp PIAS1
+Src pp Src
+p85-alpha interactsWith PI_3'-kinase
+Elk pp beta-PDGFR
+ShcA pp EGFR
+ShcA pp TrkA
+ShcA pp Axl
+geminin pp Six3
+SLAM pp SAP
+SH2D1A pp CD229
+SH2D1A pp CD84
+SH2D1A pp CD244
+Src pp Shc
+EGFR pp calmodulin
+Robo1 pp Abl1
+GAP pp p190
+Pnn pp SRp75
+Pnn pp SRm300
+Pnn pp SRrp130
+c-FLIP(L) pp Daxx
+p75NTR pp Sortilin
+Clk pp CARS-Cyp
+NGF pp TrkA
+NGF pp p75NTR
+proNGF interactsWith p75NTR/Sortilin
+EGFR pp EGF
+FAK pp Grb2
+c-Abl pp ARG
+c-Abl pp GAP
+c-Abl pp c-Abl
+c-Abl pp Src
+c-Abl pp PLCgamma1
+EGFR pp STAT3
+B61 pp SEK1
+EHK1-L pp SEK1
+LERK4 pp SEK1
+AL-1 pp SEK1
+HTK-L pp SEK1
+B61 pp EHK2
+EHK1-L pp EHK2
+LERK4 pp EHK2
+AL-1 pp EHK2
+B61 pp EHK3
+EHK1-L pp EHK3
+LERK4 pp EHK3
+AL-1 pp EHK3
+LERK4 pp ECK
+AL-1 pp ECK
+B61 pp EPH
+c-Abl pp p85
+BCR pp GAP
+BCR pp PLCgamma1
+BCR pp Src
+BCR pp ARG
+BCR pp c-Abl
+Ubc9 pp TTRAP
+SUMO-1 pp PIASxbeta
+SUMO-1 pp HIPK2
+SUMO-1 pp CHD3
+SUMO-1 pp TTRAP
+PDGFR pp Syp
+EGFR pp PLC-gamma
+PDGFR pp Src
+PDGFR pp Crk
+103D_B interactsWith 103D_A
+APP pp APP
+F2 pp 1ABI_L
+F2 pp Thrombin_Light_Chain
+HBA2 pp HBA2
+HBA2 pp HBA2
+HBB pp HBB
+1BBR_F pp F2
+1BBR_F pp F2
+1BBR_G pp F2
+1BBR_I pp F2
+APP pp PRSS1
+HBB pp HBB
+HBB pp HBB
+HBB pp HBB
+HBB pp HBB
+HBB pp HBB
+MMP1 pp MMP1
+CKS2 pp CKS2
+CKS2 pp CKS2
+CKS2 pp CKS2
+1CMK_I pp PRKACA
+HBA2 pp HBA2
+HBB pp HBB
+CSF2 pp CSF2
+1DFB_H pp 1DFB_L
+1DFN_B pp 1DFN_A
+DHFR pp DHFR
+HLA-DRB1 pp HLA-DRB1
+1FC1_B pp 1FC1_A
+HBG2 pp HBA2
+1FGV_H pp 1FGV_L
+FKBP1A pp FKBP1A
+F2 pp 1FPH_L
+1FPH_F pp F2
+1FVC_B pp 1FVC_A
+1FVD_D pp 1FVD_C
+1FVE_D pp 1FVE_C
+F2 pp Thrombin:short_Chain
+CGB pp CGA
+ADH1C pp ADH1C
+ADH1B pp ADH1B
+ADH1B pp ADH1B
+1HIQ_B pp 1HIQ_A
+1HIS_B pp 1HIS_A
+1HIT_B pp 1HIT_A
+LGALS2 pp LGALS2
+1HLT_R pp F2
+1HLT_R pp F2
+CGB pp CGA
+HLA-A pp HLA-A
+B2M pp HLA-A
+TPI1 pp TPI1
+PGC pp 1HTR_P
+CTSB pp 1HUC_C
+CCL4 pp CCL4
+CCL4 pp CCL4
+F2 pp 1HUT_L
+1IGM_H pp 1IGM_L
+IL8 pp IL8
+IL1RN pp IL1RN
+IMPA1 pp IMPA1
+IMPA1 pp IMPA1
+IMPA1 pp IMPA1
+PNLIP pp CLPS
+PNLIP pp CLPS
+CTSD pp CTSD
+CTSD pp CTSD
+CTSD pp CTSD
+IGLL1 pp IGLL1
+IGLL1 pp IGLL1
+IGLL1 pp IGLL1
+IGLL1 pp IGLL1
+IGLL1 pp IGLL1
+IGLL1 pp IGLL1
+IGLL1 pp IGLL1
+IGLL1 pp IGLL1
+IGLL1 pp IGLL1
+IGLL1 pp IGLL1
+IGLL1 pp IGLL1
+1MCO_H pp IGLL1
+IGLL1 pp IGLL1
+IGLL1 pp IGLL1
+IGLL1 pp IGLL1
+IGLL1 pp IGLL1
+CXCL1 pp CXCL1
+CXCL1 pp CXCL1
+MPO pp MPO
+MPO pp MPO
+MPO pp MPO
+MPO pp MPO
+MPO pp MPO
+MPO pp MPO
+F2 pp 1NRN_L
+1NRN_R pp F2
+F2 pp 1NRO_L
+1NRO_R pp F2
+F2 pp 1NRP_L
+1NRP_R pp F2
+F2 pp 1NRQ_L
+1NRQ_R pp F2
+1NRR_R pp F2
+1NRS_R pp F2
+1OLH_D pp 1OLH_C
+1OLH_D pp 1OLH_B
+PDGFB pp PDGFB
+1PET_D pp 1PET_C
+1PET_D pp 1PET_B
+1PES_C pp 1PES_B
+1PET_C pp 1PET_B
+PLA2G2A pp PLA2G2A
+F2 pp 1PPB_L
+1REI_B pp 1REI_A
+CSF3 pp CSF3
+CSF3 pp CSF3
+PF4 pp PF4
+PF4 pp PF4
+PF4 pp PF4
+PF4 pp PF4
+PF4 pp PF4
+FYN pp FYN
+UBA52 pp UBA52
+F2 pp 1THS_L
+B2M pp HLA-A
+F2 pp 1TMU_L
+TNF pp TNF
+TNF pp TNF
+TNF pp TNF
+TNFRSF1A pp LTA
+1TRZ_B pp 1TRZ_A
+1TRZ_D pp 1TRZ_C
+1TRZ_D pp 1TRZ_B
+Human_Insulin pp Human_Insulin
+1TYL_B pp 1TYL_A
+Fatty_Acid_Acylated_Insulin pp Fatty_Acid_Acylated_Insulin
+1TYL_D pp 1TYL_B
+1TYM_B pp 1TYM_A
+1TYM_D pp 1TYM_B
+1WTL_B pp 1WTL_A
+2CLR_C pp HLA-A
+2CLR_F pp HLA-A
+DHFR pp DHFR
+2FB4_H pp IGLL1
+F2 pp 2HNT_L
+F2 pp 2HNT_L
+F2 pp 2HNT_L
+F2 pp 2HPP_L
+F2 pp 2HPQ_L
+2IG2_H pp IGLL1
+IGLL1 pp IGLL1
+PPIA pp PPIA
+PPIA pp PPIA
+PPIA pp PPIA
+PPIA pp PPIA
+PPIA pp PPIA
+PPIA pp PPIA
+TNF pp TNF
+TNF pp TNF
+TNF pp TNF
+TNF pp TNF
+TNF pp TNF
+TNF pp TNF
+TNF pp TNF
+F2 pp 3HAT_L
+GHR pp GH1
+GHR pp GH1
+ADH1C pp ADH1C
+IL2 pp IL2
+IGLL1 pp IGLL1
+F2 pp 4HTC_L
+6Q21_B pp 6Q21_A
+6Q21_C pp 6Q21_A
+6Q21_D pp 6Q21_C
+6Q21_D pp 6Q21_B
+6RLX_B pp 6RLX_A
+6RLX_C pp 6RLX_A
+6RLX_C pp 6RLX_B
+6RLX_D pp 6RLX_A
+6RLX_D pp 6RLX_B
+7FAB_H pp IGLL1
+8FAB_D pp IGLL1
+ARF1 pp ARF1
+1FOS_F pp 1FOS_E
+1FOS_G pp 1FOS_F
+1FOS_H pp 1FOS_E
+1FOS_H pp 1FOS_G
+CCL5 pp CCL5
+CCL5 pp CCL5
+REN pp REN
+Insulin pp Insulin
+CASP1 pp CASP1
+PLA2G2A pp PLA2G2A
+PF4 pp PF4
+PF4 pp PF4
+PF4 pp PF4
+PF4 pp PF4
+PF4 pp PF4
+PF4 pp PF4
+PF4 pp PF4
+PF4 pp PF4
+PLAU pp Urokinase-Type_Plasminogen_Activator
+PLAU pp PLAU
+ITGAL pp ITGAL
+REN pp REN
+REN pp REN
+MPO pp MPO
+MPO pp MPO
+MPO pp MPO
+PPBP pp PPBP
+PPBP pp PPBP
+PPBP pp PPBP
+PPBP pp PPBP
+PPBP pp PPBP
+PPBP pp PPBP
+IGLL1 pp IGLL1
+IGLL1 pp IGLL1
+TNFRSF1A pp TNFRSF1A
+IL5 pp IL5
+ADH1C pp ADH1C
+IGLL1 pp IGLL1
+ESR2 pp ESR2
+ESR2 pp ESR2
+FBP1 pp FBP1
+FBP1 pp FBP1
+FBP1 pp FBP1
+FBP1 pp FBP1
+FBP1 pp FBP1
+FBP1 pp FBP1
+FGF1 pp FGF1
+FGF1 pp FGF1
+FGF1 pp FGF1
+FGF1 pp FGF1
+Tumor_Suppressor_P53 pp Tumor_Suppressor_P53
+Tumor_Suppressor_P53 pp Tumor_Suppressor_P53
+Tumor_Suppressor_P53 pp Tumor_Suppressor_P53
+Tumor_Suppressor_P53 pp Tumor_Suppressor_P53
+Tumor_Suppressor_P53 pp Tumor_Suppressor_P53
+Tumor_Suppressor_P53 pp Tumor_Suppressor_P53
+Tumor_Suppressor_P53 pp Tumor_Suppressor_P53
+NME2 pp NME2
+NME2 pp NME2
+NME2 pp NME2
+NME2 pp NME2
+Insulin pp Insulin
+Insulin pp Insulin
+F2 pp Alpha-Thrombin
+Bence-Jones_Kappa_I_Protein_Bre pp Bence-Jones_Kappa_I_Protein_Bre
+Bence-Jones_Kappa_I_Protein_Bre pp Bence-Jones_Kappa_I_Protein_Bre
+Bence-Jones_Kappa_I_Protein_Bre pp Bence-Jones_Kappa_I_Protein_Bre
+Bence-Jones_Kappa_I_Protein_Bre pp Bence-Jones_Kappa_I_Protein_Bre
+Bence-Jones_Kappa_I_Protein_Bre pp Bence-Jones_Kappa_I_Protein_Bre
+TTR pp TTR
+TTR pp TTR
+TTR pp TTR
+TTR pp TTR
+NTF3 pp BDNF
+NME2 pp NME2
+F2 pp Alpha-Thrombin
+CTSB pp Cathepsin_B
+SNRPA pp SNRPA
+SNRPA pp SNRPA
+SNRPA pp SNRPA
+CKS1B pp CKS1B
+CKS1B pp CKS1B
+ADH1C pp ADH1C
+HINT1 pp HINT1
+Insulin_B-Chain pp Insulin_A-Chain
+Human_Insulin pp Human_Insulin
+Insulin_B-Chain pp Insulin_B-Chain
+VCAM1 pp VCAM1
+HLA-DRB1 pp HLA-DRB1
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+C-Jun_Homodimer pp C-Jun_Homodimer
+Tr1.9_Fab pp Tr1.9_Fab
+SRF pp SRF
+PPIA pp PPIA
+CCL5 pp CCL5
+Factor_Ix pp Factor_Ix
+CCL2 pp CCL2
+TGFB1 pp TGFB1
+GZMM pp GZMM
+HBA2 pp HBA2
+HBB pp HBB
+CXCL1 pp CXCL1
+THRA pp Retinoic_Acid_Receptor
+2NLL_C pd Retinoic_Acid_Receptor
+2NLL_C pd THRA
+2NLL_D pd THRA
+2NLL_D pd Retinoic_Acid_Receptor
+CCL2 pp CCL2
+1FKZ_B interactsWith 1FKZ_A
+MIF pp MIF
+MIF pp MIF
+Insulin pp Insulin
+IL8 pp IL8
+FKBP1A pp PPP3CA
+FKBP1A pp PPP3R1
+F13A1 pp F13A1
+PPBP pp PPBP
+PPBP pp PPBP
+PPBP pp PPBP
+PPBP pp PPBP
+PPBP pp PPBP
+PPBP pp PPBP
+PLAT pp Two_Chain_Tissue_Plasminogen_Activator
+RAF1 pp RAP1A
+CDK2 pp CDK2
+TNFRSF1A pp TNFRSF1A
+AGA pp AGA
+AGA pp AGA
+AGA pp AGA
+AGA pp AGA
+AGA pp AGA
+AGA pp AGA
+AGA pp AGA
+AGA pp AGA
+AGA pp AGA
+1CDW_B pd TBP
+1CDW_C pd TBP
+ITGAL pp ITGAL
+MIF pp MIF
+MIF pp MIF
+MIF pp MIF
+LCK pp LCK
+F2 pp Alpha-Thrombin
+F2 pp Alpha-Thrombin
+F2 pp Thrombin
+Acetyl-Thr-Ptr-Glu-Thr-Leu-Nh2 pp SYK
+Acetyl-Thr-Ptr-Glu-Thr-Leu-Nh2 pp SYK
+PPGB pp PPGB
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+1FKY_B interactsWith 1FKY_A
+CNTF pp CNTF
+Phosphopeptide_Of_The_Zeta_Chain_Of_T_Cell_Receptor pp SHC1
+Trka_Receptor_Phosphopeptide pp SHC1
+IGLL1 pp IGLL1
+Il-4_Receptor_Phosphopeptide pp IRS1
+IGLL1 pp IGLL1
+Fatty_Acid_Acylated_Insulin pp Fatty_Acid_Acylated_Insulin
+Fatty_Acid_Acylated_Insulin pp Fatty_Acid_Acylated_Insulin
+CASP3 pp CASP3
+PLA2G2A pp PLA2G2A
+APP pp PRSS1
+GLO1 pp GLO1
+B2M pp HLA-B
+CDKN1B pp CCNA2
+CDKN1B pp CDK2
+2GLI_C pd GLI
+2GLI_D pd GLI
+FGFR1 pp FGFR1
+FRAP1 pp FKBP1A
+HCK pp HCK
+PROC pp PROC
+Beta-Platelet-Derived_Growth_Factor_Receptor pp PIK3R1
+Synthetic_N-Terminal_Tail pp C5
+GUSB pp GUSB
+BTK pp BTK
+USF1 pp USF1
+T_Cell_Receptor_Alpha pp HLA-A
+T_Cell_Receptor_Beta pp T_Cell_Receptor_Alpha
+T_Cell_Receptor_Beta pp HLA-A
+CD8A pp HLA-A
+CD8A pp B2M
+CD8A pp CD8A
+CD8A pp HLA-A
+Glycophorin_A pp Glycophorin_A
+F7 pp F7
+F3 pp F3
+HBA2 pp HBA2
+HBA2 pp HBA2
+R6_Insulin_Hexamer pp R6_Insulin_Hexamer
+R6_Insulin_Hexamer pp R6_Insulin_Hexamer
+Insulin pp Insulin
+Insulin pp Insulin
+R6_Insulin_Hexamer pp R6_Insulin_Hexamer
+R6_Insulin_Hexamer pp R6_Insulin_Hexamer
+Insulin pp Insulin
+Insulin pp Insulin
+R6_Insulin_Hexamer pp R6_Insulin_Hexamer
+R6_Insulin_Hexamer pp R6_Insulin_Hexamer
+R6_Insulin_Hexamer pp R6_Insulin_Hexamer
+Insulin pp Insulin
+R6_Insulin_Hexamer pp R6_Insulin_Hexamer
+R6_Insulin_Hexamer pp R6_Insulin_Hexamer
+1JMC_B pd RPA1
+CCL7 pp CCL7
+ARHGDIA pp ARHGDIA
+ARHGDIA pp ARHGDIA
+2EZD_B pd Hmg-I(Y)
+2EZD_C pd Hmg-I(Y)
+2EZE_B pd Hmg-I(Y)
+2EZF_B pd Hmg-I(Y)
+2EZF_C pd Hmg-I(Y)
+SPARC pp SPARC
+PSME1 pp PSME1
+PSME1 pp PSME1
+PSME1 pp PSME1
+PSME1 pp PSME1
+PSME1 pp PSME1
+PSME1 pp PSME1
+PSME1 pp PSME1
+PSME1 pp PSME1
+APBA1 pp APBA1
+Peptide pp APBA1
+Peptide pp APBA1
+CASP3 pp CASP3
+ETFB pp ETFA
+MAX pp MAX
+F2 pp Thrombin
+TP53BP2 pp TP53
+GHR pp GH1
+GHR pp GH1
+GHR pp GH1
+PPP3R1 pp PPP3CA
+CASP1 pp CASP1
+Fab_B7-15a2 pp IGLL1
+APOA1 pp APOA1
+APOA1 pp APOA1
+APOA1 pp APOA1
+APOA1 pp APOA1
+APOA1 pp APOA1
+IL1R1 pp IL1B
+Peptide_From_Collagen_Ii pp HLA-DRB1
+Insulin pp Insulin
+Insulin_A-Chain pp Insulin_B-Chain
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+P21WAF1 pp PCNA
+PCNA pp PCNA
+PCNA pp PCNA
+PCNA pp PCNA
+GHR pp GH1
+Hla-A2 pp HLA-DRB1
+F2 pp Alpha-Thrombin
+TFPI pp PRSS3
+13-Mer_Peptide pp APBA1
+ASL pp ASL
+Transcriptional_Coactivator_Pc4 pp Transcriptional_Coactivator_Pc4
+Proinsulin pp Proinsulin
+FYN pp Pro-Pro-Arg-Pro-Leu-Pro-Val-Ala-Pro-Gly-Ser-Ser-_Lys-Thr
+Fab_Fragment,_Antibody_A5b7 pp Fab_Fragment,_Antibody_A5b7
+Fab_Fragment_Ctm01 pp Fab_Fragment_Ctm01
+F3 pp Immunoglobulin_Fab_5g9
+Antichymotrypsin pp SERPINA3
+1AUD_B interactsWith SNRPA
+PGC pp Gastricsin
+GZMM pp GZMM
+Antichymotrypsin pp SERPINA3
+Antichymotrypsin pp SERPINA3
+T_Cell_Receptor pp T_Cell_Receptor
+SRC pp SRC
+SRC pp SRC
+SRC pp SRC
+SRC pp SRC
+B2M pp HLA-B
+P53 pp P53
+IFNGR1 pp Antibody_A6
+IFNGR1 pp Antibody_A6
+PLG pp PLG
+HINT1 pp HINT1
+HSD17B1 pp HSD17B1
+HSD17B1 pp HSD17B1
+CASK pp CASK
+Clip pp HLA-DRB3
+C-Fos pp NFATC2
+C-Jun pp NFATC2
+C-Jun pp C-Fos
+NFKB2 pp NFKB2
+S100A10 pp S100A10
+IVD pp IVD
+IVD pp IVD
+IVD pp IVD
+IVD pp IVD
+IVD pp IVD
+GHR pp GH1
+CRABP2 pp CRABP2
+SREBF1 pp SREBF1
+1AM9_E pd SREBF1
+1AM9_E pd SREBF1
+1AM9_F pd SREBF1
+1AM9_F pd SREBF1
+1AM9_G interactsWith 1AM9_F
+1AM9_H interactsWith 1AM9_F
+1AM9_H interactsWith 1AM9_E
+F2 pp Alpha-Thrombin
+PRDX6 pp PRDX6
+IL1R1 pp IL1RN
+FKBP1A pp FKBP1A
+IGLL1 pp IGLL1
+TNF pp TNF
+TNF pp TNF
+TNF pp TNF
+IFNB1 pp IFNB1
+S100B pp S100B
+Antibody_17b pp Antibody_17b
+CASP1 pp CASP1
+Insulin pp Insulin
+CDC42 pp ARHGAP1
+RASA1 pp H-Ras
+Insulin pp Insulin
+Insulin pp Insulin
+T_Cell_Receptor_Alpha pp HLA-A
+T_Cell_Receptor_Beta pp T_Cell_Receptor_Alpha
+F13A1 pp F13A1
+CXCL12 pp CXCL12
+SNRPB2 interactsWith 1A9N_Q
+ARHA pp ARHGAP1
+ACPP pp ACPP
+ESR1 pp ESR1
+Rf-An_IgmLAMBDA pp Igg4_Rea
+IGLL1 pp Rf-An_IgmLAMBDA
+IGLL1 pp Igg4_Rea
+PBP pp PBP
+FGA pp FGA
+FGA pp FGA
+FGA pp FGA
+FGA pp FGA
+FGA pp FGA
+FGA pp FGA
+FGA pp FGA
+FGA pp FGA
+FGA pp FGA
+Ig_Kappa_Chain_V-I_Region_Rei pp Ig_Kappa_Chain_V-I_Region_Rei
+LGALS7 pp LGALS7
+LGALS7 pp LGALS7
+LGALS7 pp LGALS7
+LGALS7 pp LGALS7
+GLO1 pp GLO1
+HGF pp HGF
+F2 pp Alpha_Thrombin
+F2 pp Alpha_Thrombin
+Alpha_Thrombin pp F2
+PFN1 pp PFN1
+LCK pp LCK
+NR1D1 pp NR1D1
+C-Myc-Max pp C-Myc-Max
+B2M pp HLA-B
+B2M pp HLA-B
+ANG pp RNH
+ESR1 pp ESR1
+ESR1 pp ESR1
+SPARC pp SPARC
+Insulin pp Insulin
+TIMP1 pp MMP3
+T-Cell_Surface_Glycoprotein_Cd3_Epsilon_Chain pp SYK
+SYK pp SYK
+T-Cell_Surface_Glycoprotein_Cd3_Epsilon_Chain pp SYK
+SYK pp SYK
+SYK pp SYK
+T-Cell_Surface_Glycoprotein_Cd3_Epsilon_Chain pp SYK
+GSTM1 pp GSTM1
+C-Myc-Max_Heterodimeric_Leucine_Zipper pp C-Myc-Max_Heterodimeric_Leucine_Zipper
+Immunoglobulin pp Immunoglobulin
+Campath-1h_Antibody pp Campath-1h_Antibody
+S-Nonyl-Glutathione pp GSTP1
+Sulfasalazine pp GSTP1
+PPIA pp PPIA
+S100A7 pp S100A7
+SOS1 pp H-Ras
+CDKN2D pp CDK6
+CDKN2A pp CDK6
+CHC1 pp CHC1
+CHC1 pp CHC1
+CHC1 pp CHC1
+PBX1 pp HOXB1
+CD74 pp CD74
+CD74 pp CD74
+MTHFD1 pp MTHFD1
+NTF5 pp BDNF
+NFKB1 pp RELA
+NFKBIA pp RELA
+NFKBIA pp NFKB1
+B2M pp HLA-A
+B2M pp HFE
+GSTT2 pp GSTT2
+B2M pp HLA-E
+HLA-E pp HLA-E
+GSTT2 pp GSTT2
+GSTT2 pp GSTT2
+PLAT pp Tissue_Plasminogen_Activator
+AHCY pp AHCY
+CCL5 pp CCL5
+Hirugen,_Cvs1695 pp F2
+Tumor_Necrosis_Factor_Receptor_Associated_Protein_2 pp Tumor_Necrosis_Factor_Receptor_Associated_Protein_2
+Tumor_Necrosis_Factor_Receptor_Associated_Protein_2 pp Tumor_Necrosis_Factor_Receptor_Associated_Protein_2
+TRAF2 pp TRAF2
+TRAF2 pp TRAF2
+TRAF2 pp TRAF2
+TRAF2 pp TRAF2
+TRAF2 pp TRAF2
+TRAF2 pp TRAF2
+TRAF2 pp TRAF2
+NFKBIA pp NFKB1
+Ras pp RALGDS
+C1QBP pp C1QBP
+C1QBP pp C1QBP
+CD58 pp CD2
+ESR1 pp ESR1
+CDC42 pp CDC42
+EPHB2 pp EPHB2
+EPHB2 pp EPHB2
+EPHB2 pp EPHB2
+EPHB2 pp EPHB2
+EPHB2 pp EPHB2
+EPHB2 pp EPHB2
+EPHB2 pp EPHB2
+EPHB2 pp EPHB2
+S100A10 pp S100A10
+CDKN2D pp CDK6
+RAN pp TNPO1
+Importin_Alpha-2_Subunit pp KPNB1
+Importin_Alpha-2_Subunit pp KPNB1
+RANBP2 pp RAN
+RANBP2 pp RAN
+Len pp Len
+PPARG pp PPARG
+TNF pp TNF
+TNF pp TNF
+TNF pp TNF
+TNF pp TNF
+TNF pp TNF
+TNF pp TNF
+TNF pp TNF
+TNF pp TNF
+Antibody_(Heavy_Chain) pp Antibody_(Light_Chain)
+BTK pp BTK
+TGFBR1 pp FKBP1A
+TAF11 pp Tafii18
+TAF11 pp Tafii18
+BTK pp BTK
+Wiskott-Aldrich_Syndrome_Protein_Wasp pp CDC42
+L-Pro10-Iodotyrosine pp PFN1
+L-Pro10-Iodotyrosine pp PFN1
+Activated_P21cdc42hs_Kinase pp CDC42
+MCP pp MCP
+MCP pp MCP
+MCP pp MCP
+MCP pp MCP
+MCP pp MCP
+MCP pp MCP
+MCP pp MCP
+MCP pp MCP
+MCP pp MCP
+MCP pp MCP
+MCP pp MCP
+Troponin_I pp TNNC1
+MIF pp MIF
+Hbv_Capsid_Protein pp Hbv_Capsid_Protein
+Hbv_Capsid_Protein pp Hbv_Capsid_Protein
+Hbv_Capsid_Protein pp Hbv_Capsid_Protein
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Bence-Jones_Kappa_I_Antibody_Bre_(Light_Chain) pp Bence-Jones_Kappa_I_Antibody_Bre_(Light_Chain)
+Bence-Jones_Kappa_I_Antibody_Bre_(Light_Chain) pp Bence-Jones_Kappa_I_Antibody_Bre_(Light_Chain)
+CAT pp CAT
+CAT pp CAT
+CAT pp CAT
+CAT pp CAT
+F13A1 pp F13A1
+Metal_Chelatase_Catalytic_Antibody pp Metal_Chelatase_Catalytic_Antibody
+Metal_Chelatase_Catalytic_Antibody pp Metal_Chelatase_Catalytic_Antibody
+S100A7 pp S100A7
+F2 pp Alpha-Thrombin
+CCL3 pp CCL3
+CCL3 pp CCL3
+PLG pp PLG
+MMP3 pp MMP3
+TIMP2 pp MMP14
+RAF1 pp RAP1A
+EPO pp EPOR
+EPO pp EPOR
+CTSD pp CTSD
+CTSD pp CTSD
+CTSD pp CTSD
+CTSD pp CTSD
+CTSD pp CTSD
+CTSD pp CTSD
+CTSD pp CTSD
+CTSD pp CTSD
+CTSD pp CTSD
+CTSD pp CTSD
+CTSD pp CTSD
+CTSD pp CTSD
+F7 pp F7
+FKBP1A pp FKBP1A
+IRS1 pp IRS1
+Tnf_Receptor_Associated_Factor_2 pp Tnf_Receptor_Associated_Factor_2
+Tnf_Receptor_Associated_Factor_2 pp Tnf_Receptor_Associated_Factor_2
+Tnf_Receptor_Associated_Factor_2 pp Tnf_Receptor_Associated_Factor_2
+RPA3 pp RPA2
+F9 pp F9
+NTRK1 pp NTRK1
+PPARG pp PPARG
+NCOA1 pp PPARG
+NCOA1 pp PPARG
+GSTM3 pp GSTM2
+Insulin pp Insulin
+Insulin pp Insulin
+PAH pp PAH
+EPOR pp EPO
+EPOR pp EPO
+YWHAZ pp YWHAZ
+Phosphopeptide pp YWHAZ
+Phosphopeptide pp YWHAZ
+HLA-DMB pp HLA-DMA
+TFRC pp TFRC
+PLG pp PLG
+ACPP pp ACPP
+ACPP pp ACPP
+ACPP pp ACPP
+ACPP pp ACPP
+ACPP pp ACPP
+F7 pp F7
+Calcium_Pump pp CALM2
+TNFRSF10B pp TNFSF10
+CTSK pp CTSK
+TNFSF10 pp TNFRSF10B
+TNFSF10 pp TNFRSF10B
+TNFSF10 pp TNFSF10
+TNFSF10 pp TNFRSF10B
+TNFSF10 pp TNFRSF10B
+TNFSF10 pp TNFRSF10B
+TNFSF10 pp TNFSF10
+NQO1 pp NQO1
+Pkn pp ARHA
+Signaling_Lymphocytic_Activation_Molecule pp SH2D1A
+T-Cell_Receptor,_Alpha_Chain pp HLA-A
+T-Cell_Receptor,_Beta_Chain pp T-Cell_Receptor,_Alpha_Chain
+T-Cell_Receptor,_Beta_Chain pp HLA-A
+SH2D1A pp SH2D1A
+SH2D1A pp SH2D1A
+SH2D1A pp SH2D1A
+SRP54 pp SRP54
+GSN pp ACTA1
+MBL2 pp MBL2
+MBL2 pp MBL2
+MBL2 pp MBL2
+MADH4 pp MADH4
+MADH4 pp MADH4
+MADH4 pp MADH4
+GLO1 pp GLO1
+Insulin pp Insulin
+Insulin pp Insulin
+UBE3A pp UBE3A
+UBE3A pp UBE3A
+UBE3A pp UBE3A
+UBE2L3 pp UBE3A
+UBE3A pp UBE3A
+UBE3A pp UBE3A
+UBE3A pp UBE3A
+Cholecystokinin-8 pp Cholecystokinin_Type_A_Receptor
+SERPINE1 pp SERPINE1
+RNASE4 pp RNASE4
+PABPC1 pp PABPC1
+PABPC1 pp PABPC1
+PABPC1 pp PABPC1
+PABPC1 pp PABPC1
+PABPC1 pp PABPC1
+PFN2 pp PFN2
+PFN2 pp PFN2
+PFN2 pp PFN2
+PFN2 pp PFN2
+PFN2 pp PFN2
+SNRPB pp SNRPD3
+SNRPD3 pp SNRPB
+SNRPD3 pp SNRPB
+SNRPB pp SNRPD3
+SNRPB pp SNRPD3
+Hman_T-Cell_Receptor pp HLA-A
+Hla-A_0201 pp Hman_T-Cell_Receptor
+Hla-A_0201 pp HLA-A
+Hman_T-Cell_Receptor pp HLA-A
+Hla-A_0201 pp Hman_T-Cell_Receptor
+Hla-A_0201 pp HLA-A
+Substrate_Peptide pp CDK2
+Substrate_Peptide pp CCNA2
+B2M pp Histocompatibility_Leukocyte_Antigen_(Hla)-Cw4_(Heavy_Chain)
+F7 pp F7
+1D4R_B interactsWith 1D4R_A
+1D4R_C interactsWith 1D4R_B
+PRLR pp GH1
+TF pp TF
+CKS1B pp CDK2
+Ubiquitin-Like_Protein_Nedd8 pp Ubiquitin-Like_Protein_Nedd8
+Ubiquitin-Like_Protein_Nedd8 pp Ubiquitin-Like_Protein_Nedd8
+Ubiquitin-Like_Protein_Nedd8 pp Ubiquitin-Like_Protein_Nedd8
+Ubiquitin-Like_Protein_Nedd8 pp Ubiquitin-Like_Protein_Nedd8
+HGF pp HGF
+Plasminogen_Activator_Inhibitor-1 pp F2
+ARHGAP1 pp CDC42
+Hla-Dr2 pp HLA-DRB1
+HLA-DRB1 pp HLA-DRB1
+Hla-Dr2 pp HLA-DRB1
+F13A1 pp F13A1
+F13A1 pp F13A1
+ARHGAP1 pp CDC42
+Interleukin-8_Receptor pp IL8
+Interleukin-8_Receptor_A pp IL8
+Insulin_Precursor pp Insulin_Precursor
+Insulin_Precursor pp Insulin_Precursor
+HSD17B1 pp HSD17B1
+B2M pp HLA-G
+B2M pp HLA-G
+Smad_Anchor_For_Receptor_Activation pp MADH2
+B2M pp HFE
+TFRC pp HFE
+TFRC pp TFRC
+TFRC pp HFE
+HFE pp HFE
+B2M pp HFE
+GSTM4 pp GSTM4
+SNRPD2 pp SNRPD1
+Cathepsin_L:_Light_Chain pp CTSL
+Invariant_Chain pp CTSL
+Invariant_Chain pp Cathepsin_L:_Light_Chain
+FLT1 pp FLT1
+TBP pp GTF2B
+TBP pp GTF2B
+TBP pp GTF2B
+ARHGDIA pp ARHA
+ARHA pp ARHA
+ARHGDIA pp ARHA
+NOS2A pp NOS2A
+NOS2A pp NOS2A
+PPARG pp PPARG
+Inhibitor pp F2
+PIP5K2B pp PIP5K2B
+NTF5 pp NTF5
+FGFR1 pp Fibroblast_Growth_Factor_2
+FGFR1 pp Fibroblast_Growth_Factor_2
+FGFR1 pp Fibroblast_Growth_Factor_2
+FGFR1 pp FGFR1
+FGFR1 pp Fibroblast_Growth_Factor_2
+CSF3R pp CSF3
+CSF3 pp CSF3R
+CSF3R pp CSF3
+CSF3R pp CSF3
+Latent_Membrane_Protein_1 pp Tumor_Necrosis_Factor_Receptor_Associated_Protein_2
+HMGCR pp HMGCR
+HMGCR pp HMGCR
+HMGCR pp HMGCR
+HMGCR pp HMGCR
+HMGCR pp HMGCR
+HMGCR pp HMGCR
+ME2 pp ME2
+ME2 pp ME2
+CSF3R pp CSF3
+CSF3 pp CSF3R
+CSF3R pp CSF3
+CSF3R pp CSF3
+Bence-Jones_Protein_Wil,_A_Variable_Domain_From_Lambda-6_Type_Immunoglobulin_Light_Chain pp Bence-Jones_Protein_Wil,_A_Variable_Domain_From_Lambda-6_Type_Immunoglobulin_Light_Chain
+Jto,_A_Variable_Domain_From_Lambda-6_Type_Immunoglobulin_Light_Chain pp Jto,_A_Variable_Domain_From_Lambda-6_Type_Immunoglobulin_Light_Chain
+ME2 pp ME2
+IL4R pp IL4
+DNCL1 pp DNCL1
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Insulin pp Insulin
+Annexin_I pp S100A11
+Immunoglobulin_Light_Chain_Variable_Domain pp Immunoglobulin_Light_Chain_Variable_Domain
+CAT pp CAT
+CAT pp CAT
+CAT pp CAT
+CAT pp CAT
+CAT pp CAT
+K-Ras4b_Peptide_Substrate pp FNTB
+K-Ras4b_Peptide_Substrate pp FNTA
+ARHGDIA pp CDC42
+CXCL2 pp CXCL2
+NOS3 pp NOS3
+NOS2A pp NOS2A
+FGF1 pp FGFR2
+AZGP1 pp AZGP1
+K-Ras4b_Peptide_Substrate pp FNTB
+K-Ras4b_Peptide_Substrate pp FNTA
+MEF2C pp MEF2C
+BCKDHB pp BCKDHA
+GSN pp ACTA1
+IL8 pp IL8
+MMP3 pp MMP3
+1EGW_F interactsWith 1EGW_E
+1EGW_H interactsWith 1EGW_G
+PPARD pp PPARD
+CTSZ pp CTSZ
+Eukaryotic_Translation_Initiation_Factor_4e_Binding_Protein_1 pp EIF4E
+Eukaryotic_Initiation_Factor_4gii pp EIF4E
+F2 pp Mutant_Alpha_Thrombin:light_Chain
+BLMH pp BLMH
+BLMH pp BLMH
+BLMH pp BLMH
+TCEB1 pp TCEB2
+VHL pp TCEB1
+ACTA1 pp GSN
+RARA pp RXRA
+CGB pp CGA
+Antibody_(Anti_Alpha_Subunit)_(Light_Chain) pp CGB
+Antibody_(Anti_Alpha_Subunit)_(Light_Chain) pp CGA
+Antibody_(Anti_Alpha_Subunit)_(Heavy_Chain) pp CGA
+Antibody_(Anti_Beta_Subunit)_(Light_Chain) pp CGA
+Antibody_(Anti_Beta_Subunit)_(Light_Chain) pp CGB
+Antibody_(Anti_Beta_Subunit)_(Heavy_Chain) pp CGB
+MPO pp MPO
+Casein_Kinase_Ii pp Casein_Kinase_Ii
+CASP9 pp APAF1
+ELK1 pp ELK1
+CKMT1 pp CKMT1
+CKMT1 pp CKMT1
+CKMT1 pp CKMT1
+CKMT1 pp CKMT1
+CKMT1 pp CKMT1
+CKMT1 pp CKMT1
+CKMT1 pp CKMT1
+CKMT1 pp CKMT1
+CKMT1 pp CKMT1
+CKMT1 pp CKMT1
+CKMT1 pp CKMT1
+CKMT1 pp CKMT1
+CKMT1 pp CKMT1
+F2 pp Thrombin_Light_Chain
+F2 pp Thrombin_Light_Chain
+THBD pp F2
+THBD pp F2
+ME2 pp ME2
+GSTA4 pp GSTA4
+GSTA4 pp GSTA4
+TFDP2 pp E2F4
+FGFR2 pp Fibroblast_Growth_Factor_2
+FGFR2 pp Fibroblast_Growth_Factor_2
+FGFR2 pp Fibroblast_Growth_Factor_2
+FGFR1 pp FGF1
+FGFR1 pp FGF1
+FGFR1 pp FGFR1
+Igm_Rf_2a2 pp Igm_Rf_2a2
+Igm_Rf_2a2 pp Igm_Rf_2a2
+Igm_Rf_2a2 pp Igm_Rf_2a2
+Igm_Rf_2a2 pp Igm_Rf_2a2
+Immunoglobulin_Lambda_Heavy_Chain pp Immunoglobulin_Lambda_Heavy_Chain
+NME4 pp NME4
+ITGA1 pp ITGA1
+DMD pp DMD
+DMD pp DMD
+F7 pp F7
+F7 pp F7
+F7 pp F7
+F7 pp F7
+MSN pp MSN
+MSN pp MSN
+MSN pp MSN
+MSN pp MSN
+MSN pp MSN
+MSN pp MSN
+F13A1 pp F13A1
+MMP3 pp MMP3
+Adenomatous_Polyposis_Coli_Protein pp AXIN1
+HBB pp Hemoglobin_Alpha_Chain
+HBB pp Hemoglobin_Alpha_Chain
+SerineTHREONINE-Protein_Kinase_Pak-Alpha pp SerineTHREONINE-Protein_Kinase_Pak-Alpha
+SerineTHREONINE-Protein_Kinase_Pak-Alpha pp SerineTHREONINE-Protein_Kinase_Pak-Alpha
+SerineTHREONINE-Protein_Kinase_Pak-Alpha pp SerineTHREONINE-Protein_Kinase_Pak-Alpha
+CASP3 pp CASP3
+CAT pp CAT
+CAT pp CAT
+CAT pp CAT
+B2M pp HLA-C
+Peptide_From_Importin_Alpha-2 pp HLA-C
+KIR2DL2 pp HLA-C
+KIR2DL2 pp Peptide_From_Importin_Alpha-2
+KIR2DL2 pp KIR2DL2
+FLT3LG pp FLT3LG
+1CX0_B interactsWith SNRPA
+T3-785 pp T3-785
+T3-785 pp T3-785
+PRDX2 pp PRDX2
+PRDX2 pp PRDX2
+MMP3 pp MMP3
+Ig_Epsilon_Chain_C_Region pp FCER1A
+Ig_Epsilon_Chain_C_Region pp Ig_Epsilon_Chain_C_Region
+Ig_Epsilon_Chain_C_Region pp FCER1A
+MMP3 pp MMP3
+ACTA1 pp GSN
+TALDO1 pp TALDO1
+RXRA pp RARA
+CASP8 pp CASP8
+CASP8 pp CASP8
+CASP8 pp CASP8
+CASP8 pp CASP8
+CASP8 pp CASP8
+CASP8 pp CASP8
+KITLG pp KITLG
+KITLG pp KITLG
+KITLG pp KITLG
+KITLG pp KITLG
+KITLG pp KITLG
+KITLG pp KITLG
+Cellular_Tumor_Antigen_P53 pp S100B
+SULT2A1 pp SULT2A1
+Parathyroid_Hormone pp Parathyroid_Hormone
+SCYE1 pp SCYE1
+CX3CL1 pp CX3CL1
+CX3CL1 pp CX3CL1
+CX3CL1 pp CX3CL1
+CX3CL1 pp CX3CL1
+CX3CL1 pp CX3CL1
+Tumor_Necrosis_Factor_Receptor-Associated_Protein pp TRADD
+Adenomatous_Polyposis_Coli_Protein pp Adenomatous_Polyposis_Coli_Protein
+Interferon_Gamma pp Interferon_Gamma
+PYGM pp PYGM
+DMD pp Beta-Dystroglycan
+ESR1 pp ESR1
+Synaptobrevin-Ii pp Synaptobrevin-Ii
+IFNG pp IFNG
+IFNGR1 pp IFNG
+IFNGR1 pp IFNG
+IFNGR1 pp IFNG
+IFNGR1 pp IFNG
+IFNGR1 pp IFNGR1
+B2M pp FCGRT
+FKBP1A pp FKBP1A
+ITGAL pp ITGAL
+Fc_Fragment_Of_Human_Igg1 pp Fc_Fragment_Of_Human_Igg1
+RXRA pp RXRA
+Igm_Mez_Immunoglobulin pp Igm_Mez_Immunoglobulin
+TNFSF10 pp TNFRSF10B
+TNFSF10 pp TNFRSF10B
+TNFSF10 pp TNFSF10
+TNFSF10 pp TNFRSF10B
+TNFSF10 pp TNFRSF10B
+TNFSF10 pp TNFSF10
+TNFSF10 pp TNFRSF10B
+TNFSF10 pp TNFRSF10B
+TNFSF10 pp TNFSF10
+GCA pp GCA
+GCA pp GCA
+FGFR1 pp Fibroblast_Growth_Factor_2
+FGFR1 pp Fibroblast_Growth_Factor_2
+FGFR1 pp Fibroblast_Growth_Factor_2
+FGFR1 pp FGFR1
+FGFR1 pp Fibroblast_Growth_Factor_2
+CASP8 pp CASP8
+Igm_Fab_Region_Iv-J(H4)-C_(Kau_Cold_Agglutinin) pp Igm_Kappa_Chain_V-Iii_(Kau_Cold_Agglutinin)
+Igm_Kappa_Chain_V-Iii_(Kau_Cold_Agglutinin) pp Igm_Kappa_Chain_V-Iii_(Kau_Cold_Agglutinin)
+Igm_Fab_Region_Iv-J(H4)-C_(Kau_Cold_Agglutinin) pp Igm_Kappa_Chain_V-Iii_(Kau_Cold_Agglutinin)
+Monoclonal_Antibody_Mak33 pp Monoclonal_Antibody_Mak33
+B2M pp HLA-A
+B2M pp HLA-A
+MPG pp THRB
+MPG pp PPARG
+MPG pp RXRA
+EP300 pp ESR1
+EP300 pp EP300
+PRKCD pd TNFRSF10B
+RARA pd TNFRSF10B
+SIRT1/NAD+ interactsWith p53
+Myc pd MSH6_promoter
+Sp1 pd MSH6_promoter
+HIF-1alpha pd MSH6_promoter
+Myc pd MSH2_promoter
+Sp1 pd MSH2_promoter
+HIF-1alpha pd MSH2_promoter
+Sp3 pd MSH2_promoter
+Sp1 pp HIF-1alpha
+Sp1 pp Myc
+AR pd FGF8_promoter
+UBE2I pp TP53
+DLG1 pp MRPS34
+MAPK8 pp DUSP10
+MAPK14 pp DUSP10
+DLC8 pp GKAP
+DLC8 pp AIBC1
+DLC8 pp Myosin_V
+DLC8 pp KIAA0710
+titin pp titin
+titin pp nbr1
+titin pp p62
+titin pp telethonin
+HCAP1 pp NDP52
+HCAP1 pp SQSTM1
+HCAP1 pp PIAS3
+HCAP1 pp ARS2
+HCAP1 pp SPRY1
+DDIT3/CEBPB interactsWith TRIB3
+DDIT3 pp CEBPB
+TRIB3 pp DDIT3
+BTRC pp CTNNB1
+BTRC pp SKP1A
+E2F1 pd MT1G_promoter
+E2F2 pd MT1G_promoter
+E2F3 pd MT1G_promoter
+E2F4 pd MT1G_promoter
+E2F5 pd MT1G_promoter
+RB1 pd MT1G_promoter
+RBL1 pd MT1G_promoter
+MYC pp PML
+RBL2 pd MT1G_promoter
+RUVBL1 pd KLK3_promoter
+HDAC1 pd MT1G_promoter
+CAV1 pp CAV1
+PGRMC1 pp INSIG1
+SCAP pp SCAP
+INSIG1 interactsWith SCAP_homodimer
+PGRMC1 pp SCAP
+CDK7 pp CDK2
+CDK6 pp Rb
+CDK2 pp H1
+MTF1 pd MT1G_promoter
+E2F1 pd TP53INP1_promoter
+E2F1 pd PPP1R13B_promoter
+E2F1 pd TP53BP2_promoter
+E2F1 pd JMY_promoter
+MBP pp MAPK1
+RAF1 interactsWith GTP-HRAS
+SHC1-P pp GRB2
+ZAP70 pp SHC1
+JUND pd CYP19A1_promoter
+JUN pd CYP19A1_promoter
+CREB1 pd CYP19A1_promoter
+NCOR1 pp PML/RAR-alpha
+NCOR1 pp AML1/ETO
+PML/RAR-alpha pp SIN3A
+AML1/ETO pp SIN3A
+NCOR2 pp PML/RAR-alpha
+NCOR2 pp AML1/ETO
+NCOR1 pd p-p14(ARF)
+NCOR2 pd p-p14(ARF)
+NCOR1 pd p-RAR-alpha2
+NCOR2 pd p-RAR-alpha2
+GNA13 interactsWith G-beta-1-gamma-2_dimer
+GNAQ interactsWith G-beta-1-gamma-2_dimer
+GNA13 pp PPP5C
+GNA13 pp ARHGEF1
+ZAP70 pp ZAP70
+STAT1 pp STAT1
+PKP3 pp Dsc2a
+PKP3 pp Dsc3a
+PEX3 pp PEX19
+PEX10 pp PEX19
+PEX11B pp PEX19
+PEX12 pp PEX19
+PEX13 pp PEX19
+PEX14 pp PEX19
+PEX14 pp PEX14
+PEX14 pp PEX5
+PEX16 pp PEX19
+RELA pp CHEK1
+BRCA1 pp Smad4
+BRCA1 pp Smad3
+BRCA1 pp Smad2
+ATR pp TP53
+ATR pp CHEK1
+FoxO3a pd BCL2L11_promoter
+CSNK1D pp PER3
+CSNK1D pp PER2
+CSNK1D pp PER1
+UNC5C pp DAPK1
+UNC5B pp DAPK1
+UNC5A pp DAPK1
+Vps11 pp Stx6
+CDKN1A pp CCNE1
+CDKN1A pp CCND1
+CDKN1A pp PCNA
+CDKN1A pp CCNB1
+Erk1 pp Elk-1
+beta-catenin pp FOXO3a
+beta-catenin pp FOXO1
+beta-catenin pp FOXO4
+NTKL-BP1 pp RCHY1
+ETS2 pd BRCA1
+KLF9 pp PGR
+ESR1 pp NCOR1
+ESR1 pp NCOR2
+ESR1 pp DDX17
+ESR1 pp DDX5
+ESR1 pp PPARBP
+ESR1 pp TRRAP
+POLR2E pp POLR2A
+POLR2C pp POLR2A
+E2F2 pd JMY_promoter
+E2F2 pd TP53INP1_promoter
+E2F2 pd PPP1R13B_promoter
+E2F2 pd TP53BP2_promoter
+E2F3 pd TP53BP2_promoter
+E2F3 pd PPP1R13B_promoter
+E2F3 pd TP53INP1_promoter
+E2F3 pd JMY_promoter
+E2F4 pd TP53BP2_promoter
+E2F4 pd PPP1R13B_promoter
+E2F4 pd TP53INP1_promoter
+E2F4 pd JMY_promoter
+CAK pp CDK6
+HIST4H4 pd CDKN1A_promoter
+HIST4H4 pd PRDM2_promoter
+HIST4H4 pd MGMT_promoter
+HIST4H4 pd GSTP1_promoter
+HIST4H4 pd LAGE-1_promoter
+HIST4H4 pd PSCA_promoter
+CASK pp DLG1
+PBK pp DLG1
+DLGAP1 pp DLG1
+HDAC3 pp CSNK2A1
+MYH6 pp MYL7
+CSNK2A1 pp CSNK2A1
+HDAC3 pp PPP4R1
+HDAC3 pp PPP4C
+CDK2/CCNA2 interactsWith BRCA2
+BRCA2 pp RAD51
+LYN pp LYN
+ABL1 pp ABL1
+CSK pp CSK
+SRC pp RGS16
+CSK pp RGS16
+LYN pp RGS16
+Unknown interactsWith SMARCB1
+ETS2 pp SMARCA4
+C4orf16 pp AP1G1
+C4orf16 pp GGA1
+p53 pd CHEK1_promoter
+p53 pd PTTG1_promoter
+MCAF1 pp SETDB1
+MCAF2 pp SETDB1
+MCAF1 pp Sp1
+MCAF2 pp Sp1
+TCF8 pd CDH1_promoter
+ROCK2 pp MBP
+ROCK1 pp MBP
+CEBPB pp SMAD4
+NBS1 pp ATM
+TREX1 pp ATR
+XRCC5 pp PRKDC
+ATM pp MRE11A
+NBS1 pp MRE11A
+NBS1 pp RAD50
+TREX1 pp PRKDC
+NBS1 pp PRKDC
+XRCC5 pp ATR
+NBS1 pp XRCC5
+NBS1 pp ATR
+TREX1 pp ATM
+NBS1 pp TREX1
+XRCC5 pp ATM
+NCOA3 pp ETS1
+PARG1 pp Rap2
+Raf-1 pp Rap2
+Smad4 pp CHIP
+NCOA3 pp ETS2
+SRC pp ETS1
+SRC pp ETS2
+EGR2 pd p-FasL
+EGR3 pd p-FasL
+NCOR1 pp ETS1
+NCOR1 pp ETS2
+SRC pd ERBB2_promoter
+WEE1 interactsWith CDK2/CCNA2_complex
+WEE1 interactsWith CDC2/CCNB1_complex
+WEE1 interactsWith CDC2/CCNB1_complex
+EIF4E pp EIF4EBP1
+NCOA3 pd ERBB2_promoter
+NCOR1 pd ERBB2_promoter
+PDCD6IP pp Tsg101
+PDCD6IP pp CHMP4A
+Vps4A pp CHMP4A
+STK6 pp CHFR
+TSHR pp SCRIB
+E2F1 pp EAPP
+E2F2 pp EAPP
+E2F3 pp EAPP
+ABL2 pp CRK
+ABL1 pp ABL2
+ABL2 pp ABL2
+POLR2G pp POLR2E
+POLR2F pp POLR2E
+POLR2F pp POLR2C
+POLR2E pp POLR2E
+POLR2L pp POLR2B
+POLR2H pp POLR2B
+POLR2E pp POLR2C
+POLR2C pp POLR2C
+POLR2C pp POLR2B
+POLR2J pp POLR2C
+POLR2L pp POLR2C
+POLR2K pp POLR2C
+POLR2H pp POLR2C
+POLR2G pp POLR2C
+POLR2G pp POLR2A
+VPS18 pp STX8
+VPS18 pp STX7
+VPS18 pp STX6
+VPS18 pp STX1A
+VPS11 pp STX1A
+VPS11 pp STX7
+VPS11 pp STX8
+CAMK2B pp ACTN4
+CAMK2A pp ACTN4
+LRRC7 pp ACTN4
+LRRC7 pp CAMK2A
+HABP4 pp GNB2L1
+CDC2 pp CCNB1
+CDC2 pp CCNB2
+PARP-1 pp TR-alpha
+Cdk8 interactsWith Unknown
+Unknown interactsWith CycC
+Unknown interactsWith Med6
+Unknown interactsWith Med7
+Unknown interactsWith Trap220
+PARP-1 pp RAR-alpha
+Med6 pp RAR-alpha
+Unknown interactsWith Med6
+Cdk8 interactsWith Unknown
+PARP-1 pp Med6
+MCM8 pp cdc6
+MCM8 pp ORC2
+CAPN1 pp SYNE1
+CAPN1 pp GPT
+CAPN1 pp FLJ11200
+CAPN1 pp LCN7
+Unknown interactsWith Top3A
+Unknown interactsWith RPA2
+Unknown interactsWith RPA3
+Unknown interactsWith RPA1
+BLM interactsWith Unknown
+Unknown interactsWith BLAP75
+BLM pp Top3A
+CDKN1B pp SKP2
+Nop56p interactsWith Unknown
+Unknown interactsWith TCOF1
+Unknown interactsWith ILF3
+Unknown interactsWith EEF2
+Unknown interactsWith SRPK1
+Unknown interactsWith TOP1
+Unknown interactsWith SCYL2
+Unknown interactsWith HNRPM
+Unknown interactsWith IMP-1
+Unknown interactsWith PWP1
+Unknown interactsWith U2AF2
+Unknown interactsWith TUBA3
+Unknown interactsWith EEF1A1
+Unknown interactsWith TUBB1
+Unknown interactsWith TUFM
+Unknown interactsWith LUC7L2
+Unknown interactsWith NAP1L1
+Unknown interactsWith ILF2
+Unknown interactsWith LYAR
+Unknown interactsWith ACTA2
+Unknown interactsWith HNRPA1
+Unknown interactsWith NSEP1
+Unknown interactsWith SLC25A5
+Unknown interactsWith U2AF1
+Unknown interactsWith ACTG2
+Unknown interactsWith H1FX
+Unknown interactsWith HIST1H1D
+Unknown interactsWith SRP14
+Unknown interactsWith HIST1H2BM
+Unknown interactsWith MYBBP1A
+Unknown interactsWith NOP5/NOP58
+Unknown interactsWith CAPZB
+Unknown interactsWith NHP2L1
+Unknown interactsWith DHX9
+Unknown interactsWith DDX21
+Unknown interactsWith RBM28
+Unknown interactsWith PPAN
+Unknown interactsWith EBNA1BP2
+Unknown interactsWith BRIX
+Unknown interactsWith RSL1D1
+Unknown interactsWith GNL3
+Unknown interactsWith NCL
+Unknown interactsWith NPM1
+Unknown interactsWith NOLC1
+Unknown interactsWith HNRPU
+CDC2 pp MDM4
+Med6 pd p-dio1
+PARP-1 pd p-dio1
+TR-alpha pd p-dio1
+ER-alpha pd c-myc_promoter
+AIB1 pd c-myc_promoter
+Pol_II pd c-myc_promoter
+IKK-alpha pd c-myc_promoter
+ER-alpha pd EBAG9_promoter
+AIB1 pd EBAG9_promoter
+Pol_II pd EBAG9_promoter
+IKK-alpha pd EBAG9_promoter
+ER-alpha pd cyclin_D1_promoter
+AIB1 pd cyclin_D1_promoter
+Pol_II pd cyclin_D1_promoter
+CBP pd cyclin_D1_promoter
+IKK-alpha pd cyclin_D1_promoter
+IKK-alpha interactsWith Unknown
+Unknown interactsWith AIB1
+IKK-alpha pp ER-alpha
+IKK-beta pp I-kappa-B-alpha
+EGFR pp CBL
+GRB2 pp SHC3
+GRB2 pp PTPRA
+Bcl-2 pp BAG-3
+Bcl-2 pp BAG-4
+K2P1 pp Ubc-9
+K2P1 pp SENP-1
+BMP4 pp BMP4
+BGN interactsWith BMP4/BMP4
+TWSG1 interactsWith BMP4/BMP4
+BGN pp CHRD
+BMP4 pp CHRD
+BMP4 pp BMPR1B
+CLU pp G22P1
+PGR pp PGR
+TRADD pp NGFR
+EWS-FLI1 pd ACCN1_promoter
+EWS-FLI1 pd ASNS_promoter
+EWS-FLI1 pd CDC14B_promoter
+EWS-FLI1 pd CLASP2_promoter
+EWS-FLI1 pd CNTNAP2_promoter
+EWS-FLI1 pd DLG2_promoter
+EWS-FLI1 pd GTF2E2_promoter
+EWS-FLI1 pd IDH3B_promoter
+EWS-FLI1 pd LRBA_promoter
+EWS-FLI1 pd MK-STYX_promoter
+EWS-FLI1 pd NOL5A_promoter
+EWS-FLI1 pd PCCA_promoter
+EWS-FLI1 pd PFTK1_promoter
+EWS-FLI1 pd POT1_promoter
+EWS-FLI1 pd RFC1_promoter
+EWS-FLI1 pd SLC2A5_promoter
+EWS-FLI1 pd SSR3_promoter
+EWS-FLI1 pd TBL1X_promoter
+EWS-FLI1 pd ATP1B1_promoter
+EWS-FLI1 pd CDK7_promoter
+EWS-FLI1 pd FLJ21613_promoter
+EWS-FLI1 pd KIAA1026_promoter
+EWS-FLI1 pd KIAA1361_promoter
+EWS-FLI1 pd KIAA1432_promoter
+EWS-FLI1 pd LIMS1_promoter
+EWS-FLI1 pd LIPA_promoter
+EWS-FLI1 pd MDH2_promoter
+EWS-FLI1 pd NPY_promoter
+EWS-FLI1 pd NCAM1_promoter
+EWS-FLI1 pd PCLO_promoter
+EWS-FLI1 pd RHOBTB3_promoter
+EWS-FLI1 pd TCF12_promoter
+EWS-FLI1 pd VGF_promoter
+EWS-FLI1 pd ARNT2_promoter
+EWS-FLI1 pd BIA2_promoter
+EWS-FLI1 pd CDH13_promoter
+EWS-FLI1 pd CHL1_promoter
+EWS-FLI1 pd CNGB3_promoter
+EWS-FLI1 pd CYP4A11_promoter
+EWS-FLI1 pd DPP9_promoter
+EWS-FLI1 pd EB-1_promoter
+EWS-FLI1 pd FHIT_promoter
+EWS-FLI1 pd FLJ23049_promoter
+EWS-FLI1 pd GRIA3_promoter
+EWS-FLI1 pd HCMOGT-1_promoter
+EWS-FLI1 pd HESX1_promoter
+EWS-FLI1 pd KCNAB1_promoter
+EWS-FLI1 pd KIAA1680_promoter
+EWS-FLI1 pd LRP1B_promoter
+EWS-FLI1 pd LTF_promoter
+EWS-FLI1 pd NR5A2_promoter
+EWS-FLI1 pd PDE10A_promoter
+EWS-FLI1 pd POPDC2_promoter
+EWS-FLI1 pd PTPRD_promoter
+EWS-FLI1 pd RIT2_promoter
+EWS-FLI1 pd XPR1_promoter
+EWS-FLI1 pd ADCY1_promoter
+EWS-FLI1 pd ELKS_promoter
+EWS-FLI1 pd GALNT10_promoter
+EWS-FLI1 pd HEY1_promoter
+EWS-FLI1 pd ME1_promoter
+EWS-FLI1 pd NEK1_promoter
+EWS-FLI1 pd NEO1_promoter
+EWS-FLI1 pd NFIL3_promoter
+EWS-FLI1 pd PAPPA_promoter
+EWS-FLI1 pd PIP5K1B_promoter
+EWS-FLI1 pd PTPN4_promoter
+EWS-FLI1 pd PVT1_promoter
+EWS-FLI1 pd TNFRSF10B_promoter
+EWS-FLI1 pd WWP2_promoter
+EWS-FLI1 pd CCRL2_promoter
+EWS-FLI1 pd COP1_promoter
+EWS-FLI1 pd FLJ32440_promoter
+EWS-FLI1 pd GOR_promoter
+EWS-FLI1 pd GRID1_promoter
+EWS-FLI1 pd HS6ST3_promoter
+EWS-FLI1 pd LYRIC_promoter
+EWS-FLI1 pd Raptor_promoter
+EWS-FLI1 pd SYTL5_promoter
+EWS-FLI1 pd TNRC6_promoter
+EWS-FLI1 pd UVRAG_promoter
+EWS-FLI1 pd ZFYVE20_promoter
+EWS-FLI1 pd ZNF406_promoter
+MME pp Abeta40
+RUSC2 pp RAB1B
+G-beta1-gamma2_complex interactsWith STX1A
+G-beta1-gamma2_complex interactsWith SNAP25
+MME pp Abeta42
+RUSC2 pp GOLGA2
+CCND1-CDK4_complex interactsWith RB1
+MICAL1 pp RAB1B
+M6PRBP1 pp RAB9A
+M6PRBP1 pp IGF2R
+M6PRBP1 pp IGF2R
+M6PRBP1 pp RAB9A
+M6PRBP1 pp RAB9A
+TP53 pp Sp1
+UBC9-SUMO1 interactsWith TDG
+CTNNB1 pd KLK3_promoter
+MAP3K1 pd CD82_promoter
+POLR2A pd CD82_promoter
+NFKB1 pp NFKB1
+NFKB1 pp RELA
+Smad7 pp Smurf1
+Smad1 pp Smurf1
+DISC1 pp ARHGEF11
+DISC1 pp TENC1
+DISC1 pp SPTAN1
+DISC1 pp MGC2599
+DISC1 pp HAPIP
+DISC1 pp DMT
+DISC1 pp APLP1
+DISC1 pp SMARCE1
+DISC1 pp PPFIA4
+DISC1 pp MGAT3
+DISC1 pp KIAA0373
+DISC1 pp IMMT
+DISC1 pp GM130
+DISC1 pp NUDE
+DISC1 pp GRIPAP1
+DISC1 pp ATF4
+DISC1 pp AKAP9
+Axl pp p85-beta
+Axl pp p85-alpha
+Axl pp Nck2
+Axl pp SOCS-1
+Axl pp Grb2
+Smad4 pp Ecto
+FGFR1 pp NCK2
+FGFR1 pp SH3BP2
+FGFR1 pp PLC-gamma
+FGFR1 pp KIAA1075
+FGFR1 pp SLAP
+FGFR1 pp p85-beta
+FGFR1 pp RTN3
+FGFR1 pp RTN1
+MxA pp TRPC6
+MxA pp TRPC1
+MxA pp TRPC4
+MxA pp TRPC3
+MxA pp TRPC5
+MxA pp TRPC7
+DYRK1A pp PAHX-AP1
+DYRK1A pp CREB
+KyoT pp RBP-J
+KyoT pp RING1
+RPK118 pp PRDX3
+PHLPP pp Akt
+PKP3 pp DSP
+PKP3 pp KRT18
+CDH1 pp P120ctn_3AC
+PKP3 pp Dsc3b
+PKP3 pp Dsc1a
+PKP3 pp Dsg3
+PKP3 pp Dsg2
+PKP3 pp JUP
+PKP3 pp Dsg1
+MDM2 pp MDM4
+TAF9 pp TAF6
+TAF4B pd TNFAIP3_promoter
+TAF4B pp GTF2A1
+PrPc pp CSNK2B
+PrPc pp CSNK2A2
+PrPc pp CSNK2A1
+PrPc interactsWith CK2_holoenzyme
+PEX12 pp PEX5
+PEX14 pp PEX13
+PEX13 pp PEX13
+PEX10 pp PEX12
+PrPSc pp PLG
+RNPS1 pp DKFZp586K0717
+RNPS1 pp NKTR
+RNPS1 pp Zfr
+RNPS1 pp CIF150
+pRB pp Rak
+FCP1 pp RPB2
+FCP1 pp NDR1
+FCP1 pp ERH
+unknown interactsWith MEP50
+FCP1 pp PRMT5
+Axl pp Axl
+Axl pp RanBPM
+GTF2B pp THRA
+HTATIP pd FAS_promoter
+CTNNB1 pd FAS_promoter
+RUVBL2 pd FAS_promoter
+CREBBP pd ICAM1_promoter
+RUVBL2 pp HDAC1
+RUVBL2 pp HDAC4
+RUVBL2 pp HDAC5
+NCOR1 pd CD82_promoter
+MAP3K7IP2 pd CD82_promoter
+HDAC3 pd CD82_promoter
+NFKB1 pp BCL3
+NFKB1 pp RUVBL2
+NFKB1 pp CTNNB1
+NFKB1 pd CD82_promoter
+BCL3 pd CD82_promoter
+RAB6A pp RAB6IP2
+RUVBL2 pp BCL3
+POLR2K pp POLR2K
+POLR2H pp POLR2K
+POLR2E pp POLR2K
+POLR2H pp POLR2H
+POLR2H pp POLR2G
+POLR2G pp POLR2G
+POLR2L pp POLR2E
+POLR2L pp POLR2A
+POLR2H pp POLR2E
+POLR2H pp POLR2A
+VPS11 pp VPS45A
+VPS18 pp VPS45A
+TNF pp TNF
+TNF pp TNF
+TNF pp TNF
+BNIP-2 pp Cdc42
+p35 interactsWith Unknown
+Unknown interactsWith hRad21
+Unknown interactsWith Smc3
+p35 interactsWith Unknown
+Unknown interactsWith hRad21
+Unknown interactsWith Smc3
+Unknown interactsWith Pds5B
+Unknown interactsWith Pds5A
+Unknown interactsWith Smc1
+CAPN1 pp FHL2
+CAPN1 pp CREG1
+CAPN1 pp VIM
+CAPN1 pp FLJ20625
+CAPN1 pp ECHS1
+CAPN1 pp COL3A1
+CAPN1 pp CTSC
+C5 pp C5R1
+SEC10 interactsWith ARF1-GTP
+SEC10 interactsWith ARF6-GTP
+APAF1 pp CASP9
+APAF1 pp CASP9
+ER-alpha pd NRIP1_ERE
+ER-alpha pd GREB1_ERE
+ER-alpha pd ABCA3_ERE
+GIPC pp CD93
+Moesin pp CD93
+CCNA2 pp CDC2
+EWS-FLI1 pd PTPN13_promoter
+VDR pp RXRA
+VDR-RXRA_heterodimer interactsWith PDGFA_promoter
+FMR1 pp RANBP9
+RUVBL2 interactsWith HTATIP-CD82_promoter
+CTNNB1 interactsWith HTATIP-CD82_promoter
+HTATIP pd CD82_promoter
+RUVBL2 pd CD82_promoter
+CTNNB1 pd CD82_promoter
+HTATIP pd KLK3_promoter
+RUVBL1 pd CD82_promoter
+CTNNB1 pp RUVBL2
+CTNNB1 pp BCL3
+HTATIP pp NFKB1
+HTATIP pp RUVBL1
+HTATIP pp BCL3
+RNAPII interactsWith Sp1
+RNAPII interactsWith FBP21
+SMARCA5 pp HDAC2
+JAK3S pp JAK3S
+JAK3B pp JAK3S
+E2F4 pd CDC2_promoter
+E2F4 pd CCNA2_promoter
+E2F4 pd SNRPD2_promoter
+E2F4 pd ACR_promoter
+E2F4 pd PSMA4_promoter
+E2F4 pd SRC_enhancer
+E2F4 pd PPIA_enhancer
+E2F4 pd C21orf32_promoter
+E2F4 pd MGC45922_promoter
+E2F4 pd FLJ20712_promoter
+E2F4 pd ARHGAP11A_promoter
+E2F4 pd MAP3K7_promoter
+E2F4 pd METAP2_promoter
+E2F4 pd JPH2_promoter
+E2F4 pd HOXA3_promoter
+E2F4 pd CSTF3_promoter
+E2F4 pd BTRC_promoter
+E2F4 pd SOAT2_promoter
+E2F4 pd SLC3A2_promoter
+E2F4 pd LMO7_promoter
+E2F4 pd DRF1_promoter
+E2F4 pd TOPK_promoter
+E2F4 pd RNF29_promoter
+E2F4 pd RAD54L_promoter
+E2F4 pd QPCTL_promoter
+FMR1 interactsWith MAP1B
+FLI1 pd DUSP24
+Axl pp p55-gamma
+Axl pp C1-TEN
+c-Cbl pp hSpry2
+UbcH7 pp Ari-1
+UbcH7 pp hAri-2
+c-Cbl pp UbcH7
+c-Cbl pp EGFR
+PrPc pp HSPA5
+FLI1 pd TGFBR2_promoter
+M6PRBP1 pp M6PR
+M6PRBP1 pp IGF2R
+M6PRBP1 pp IGF2R
+M6PRBP1 pp M6PR
+M6PRBP1 pp IGF2R
+CASK pp Id1
+CASK pp Id1'
+beta-Arr2 pp NHE5
+beta-Arr1 pp NHE5
+IGFBP-5 pp TS-1
+alpha-V-beta3 pp TS-1
+IAP pp TS-1
+SPRY2 pp c-Cbl
+SPRY2 pp Cbl-b
+c-Cbl pp Grb2
+TSG101 pp TSG101
+TSG101 pp VPS28
+TSG101 pp PDCD6IP
+TSG101 pp HGS
+CARD11 pp BCL10
+CARD14 pp BCL10
+PRKCQ pp CARD11
+PRKCQ pp VAV1
+SYK pp SYK
+PI3K interactsWith NFKBIA
+GLRX pp MAP3K5
+TXN pp MAP3K5
+PRKCE pp PRKD1
+PDPK1 pp PDPK1
+PRKCH pp PRKD1
+PRKCE pp PRKCE
+PDPK1 pp PRKCZ
+PRKCH pp PRKCH
+PDPK1 pp PRKCH
+PDPK1 pp PRKCE
+CLU pp CLU
+CSN4 pp CSN6
+CSN2 pp CSN6
+CSN5 pp CSN6
+CSN6 pp CSN3
+CSN6 pp CSN6
+CSN4 pp CSN4
+CSN4 pp CSN8
+CSN4 pp CSN7
+CSN4 pp CSN3
+CSN2 pp CSN4
+BAK1 pp BAK1
+INSIG-1 pp SCAP
+INSIG-2 pp SCAP
+SEC10 interactsWith ARF6-GDP
+caveolin-1 pp PTP1B
+caveolin-1 pp PTP-1C
+caveolin-1 pp SH-PTP2
+caveolin-1 pp PTEN
+caveolin-1 pp LAR
+TGFBR2 pp TGFBR2
+BACE1 pp PSAP
+BACE1 pp PDIA3
+BACE1 pp UMP-CMPK
+BACE1 pp ATP1B1
+BACE1 pp KHSRP
+BACE1 pp RANBP9
+TRADD pp FADD
+GCM1 pd ERVWE1_promoter
+TGM1 pp RARRES3
+TYROBP pp TYROBP
+MAPK8 pp ATF2
+MAPK8 pp TP53
+IKK_complex interactsWith NFKBIA
+p50/p65 interactsWith PTGS2
+Rb pp E2F-1
+RFP pp EID-1
+Rb pp RFP
+Flg pp Flg
+BNIP-2 pp Flg
+BNIP-2 pp Cdc42
+BNIP-2 pp Cdc42GAP
+Cdc42GAP pp Cdc42
+Cdc42GAP pp Cdc42
+Cdc42GAP pp Cdc42GAP
+BNIP-2 pp BNIP-2
+BNIP-S-alpha pp Cdc42GAP
+BNIP-S-alpha pp BNIP-2
+BNIP-2 pp Cdc42GAP
+BNIP-S-alpha pp BNIP-S-alpha
+TSC1 pp TSC2
+Erk2 pp TSC2
+ERBB2 pp CBL
+PLK1 pp CCNB1
+HMGB1 pp HNRPK
+HMGB1 pp MECP2
+HMGB1 pp RB1
+Src pp CDCP1
+PKC-delta pp CDCP1
+Rb pp RFP-beta
+ER-alpha pp Ubc9
+ER-alpha pp FHL2
+ER-alpha pp PIAS1
+CDK2-CCNE1_complex interactsWith CDKN1A
+CDK4-CCND1_complex interactsWith CDKN1A
+CDK4 pp CCND1
+RB1 pp JARID1B
+RELA pp CHUK
+OIP106 pp KIF5B
+PKC-lambda pp MBP
+PKC-delta pp MBP
+PKC-alpha pp MBP
+PKC-zeta pp hnRNPA1
+PKC-zeta pp MBP
+SNT2 pp PKC-lambda
+CSN1 pp CSN4
+CSN1 pp CSN2
+CSN2 pp CSN2
+CSN8 pp CSN3
+CSN8 pp CSN8
+Cdc42-GTP interactsWith BNIP-2
+RAC1 pp PAK1B
+CDC42 pp WAS
+GEMIN7 pp SNRPD2
+GEMIN7 pp SNRPB
+GEMIN7 pp SNRPE
+GEMIN7 pp SNRPD3
+EGF pp EGFR
+ZAK pp ZNF33A
+Cdc42-GTP interactsWith BNIP-2
+SEPT5 pp SEPT8
+SEPT5 pp SEPT5
+SEPT4 pp SEPT8
+SEPT4 pp SEPT5
+SEPT8 pp SEPT8
+SEPT4 pp SEPT4
+BNIP-2 pp Cdc42GAP
+BNIP-2 pp Cdc42
+DOT1L pp AF10
+WRS pp EF-1-alpha
+FRS-alpha pp EF-1-delta
+GRS pp EF-1-delta
+AlaRS pp EF-1-beta
+E2F4 pd AAMP_promoter
+E2F4 pd ABC1_promoter
+E2F4 pd ABHD2_promoter
+E2F4 pd ACR_promoter
+E2F4 pd ADAMTS6_promoter
+E2F4 pd APM1_promoter
+E2F4 pd ARHGAP11A_promoter
+E2F4 pd ARHGEF5_promoter
+E2F4 pd ARNT2_first_intron
+E2F4 pd BLVRB_promoter
+E2F4 pd BTRC_promoter
+E2F4 pd C14ORF80_promoter
+E2F4 pd C1QTNF2_first_intron
+E2F4 pd C20ORF141_promoter
+E2F4 pd C20ORF186_promoter
+E2F4 pd CAMK2A_promoter
+E2F4 pd CCL27_promoter
+E2F4 pd CCRL2_promoter
+E2F4 pd COX5B_promoter
+E2F4 pd CRIP1_promoter
+E2F4 pd CSTF3_promoter
+E2F4 pd CTAG3_promoter
+E2F4 pd CYP24A1_promoter
+E2F4 pd DC2_promoter
+E2F4 pd DNALI1_promoter
+E2F4 pd DRF1_promoter
+E2F4 pd EPHA3_promoter
+E2F4 pd FHIT_promoter
+E2F4 pd FIBL-6_promoter
+E2F4 pd FLJ12168_promoter
+E2F4 pd FLJ12892_promoter
+E2F4 pd FLJ13912_promoter
+E2F4 pd FLJ22353_promoter
+E2F4 pd FLJ23074_promoter
+E2F4 pd FLJ25416_promoter
+E2F4 pd FLJ32000_promoter
+E2F4 pd FLJ33387_promoter
+E2F4 pd FLJ33962_first_intron
+E2F4 pd FLJ37927_promoter
+E2F4 pd FLJ40296_promoter
+E2F4 pd FLJ90834_promoter
+E2F4 pd FLRT1_first_intron
+E2F4 pd FS_first_intron
+E2F4 pd FUT3_promoter
+E2F4 pd GAJ_promoter
+E2F4 pd GAL3ST1_promoter
+E2F4 pd GSG1_promoter
+E2F4 pd GYPC_promoter
+E2F4 pd HAVCR1_promoter
+E2F4 pd HIST1H2BL_promoter
+E2F4 pd HIST2H2AC_promoter
+E2F4 pd HOXA3_promoter
+E2F4 pd IFNW1_promoter
+E2F4 pd IGF2AS_promoter
+E2F4 pd IPO8_first_intron
+E2F4 pd JPH2_promoter
+E2F4 pd KCNJ12_promoter
+E2F4 pd KCNJ15_promoter
+E2F4 pd KIAA0440_promoter
+E2F4 pd KIAA1579_first_intron
+E2F4 pd KRTAP6-3_promoter
+E2F4 pd LHX4_promoter
+E2F4 pd LMO1_first_intron
+E2F4 pd LMO7_promoter
+E2F4 pd LOC115509_promoter
+E2F4 pd LOC57795_promoter
+E2F4 pd LSM5_promoter
+E2F4 pd MAP3K7_promoter
+E2F4 pd METAP2_promoter
+E2F4 pd MGC10940_promoter
+E2F4 pd MGC15523_promoter
+E2F4 pd MGC2865_first_intron
+E2F4 pd MGC39650_promoter
+E2F4 pd MGC43690_first_intron
+E2F4 pd MGC45780_first_intron
+E2F4 pd MPV17_promoter
+E2F4 pd MSX2_promoter
+E2F4 pd MTMR1_promoter
+E2F4 pd MTUS1_promoter
+E2F4 pd NCOR2_promoter
+E2F4 pd NDUFB6_promoter
+E2F4 pd NEK8_promoter
+E2F4 pd OCA2_promoter
+E2F4 pd PAG_promoter
+E2F4 pd PC_promoter
+E2F4 pd PDGFA_promoter
+E2F4 pd PDGFC_promoter
+E2F4 pd PFDN5_promoter
+E2F4 pd PIK3AP1_promoter
+E2F4 pd PKD1L1_first_intron
+E2F4 pd PLCB1_promoter
+E2F4 pd PNKP_promoter
+E2F4 pd POU4F3_promoter
+E2F4 pd PRCP_promoter
+E2F4 pd PSMA4_promoter
+E2F4 pd PSMD5_promoter
+E2F4 pd PXK_promoter
+E2F4 pd QPCTL_promoter
+E2F4 pd RAB34_promoter
+E2F4 pd RAD54L_promoter
+E2F4 pd RAP2C_promoter
+E2F4 pd RBMS3_promoter
+E2F4 pd RFXAP_first_intron
+E2F4 pd RGS19IP1_promoter
+E2F4 pd RIOK1_promoter
+E2F4 pd RNF29_promoter
+E2F4 pd RNGTT_promoter
+E2F4 pd RPL23A_promoter
+E2F4 pd SERPINA1_first_intron
+E2F4 pd SIGLECL1_promoter
+E2F4 pd SLC1A2_promoter
+E2F4 pd SLC3A2_promoter
+E2F4 pd SLC6A5_promoter
+E2F4 pd SMAP-1_promoter
+E2F4 pd SNIP1_promoter
+E2F4 pd SNRPD2_promoter
+E2F4 pd SOAT2_promoter
+E2F4 pd SP110_promoter
+E2F4 pd SPATA13_promoter
+E2F4 pd SPTBN4_promoter
+E2F4 pd TBC1D1_promoter
+E2F4 pd TBC1D3_first_intron
+E2F4 pd TBX3_promoter
+E2F4 pd TBXAS1_promoter
+E2F4 pd TM4SF4_first_intron
+E2F4 pd TNFSF18_first_intron
+E2F4 pd TNS_promoter
+E2F4 pd TOPK_promoter
+E2F4 pd TRAF5_promoter
+E2F4 pd TREP-132_promoter
+E2F4 pd TSGA10_promoter
+E2F4 pd ULBP3_promoter
+E2F4 pd UNQ2492_promoter
+E2F4 pd VMP1_promoter
+E2F4 pd ZIC3_promoter
+E2F4 pd ZNF219_promoter
+E2F4 pd ZNF366_promoter
+CTNNB1 pd IGFBP2_promoter
+CTNNB1 pd SGK_promoter
+PTK2 pp DNM2
+WASL pp HSPCA
+CASP8 pp FADD
+CASP8 pp PIAS-1
+CASP8 pp SUMO1
+MKK6 pp MTK1
+MKK4 pp MTK1
+MEK1 pp Raf-1
+MKK7 pp MEKK1
+MKK4 pp MEKK1
+MKK6 pp ASK1
+MKK3 pp MTK1
+IEX-1 pp BAT3
+IEX-1 pp MCL1
+IEX-1 pp TNFSF10
+IEX-1 pp CAML
+ADAM19 pp ubiquitin
+ADAM19 pp beta-COP
+ADAM19 pp HEP18272
+ADAM19 pp ArgBP1
+MICAL-2 pp rab1b
+MICAL-3 pp rab1b
+MCAF2 pp MBD1
+MCAF1 pp MBD1
+Mdm2 pp p53
+WASL pp HSPCB
+CASP9 pp RB1
+CASP10 pp RB1
+CASP6 pp RB1
+CASP8 pp RB1
+CASP7 pp RB1
+CASP2 pp RB1
+CASP3 pp RB1
+WEE1 pp CDC2
+CHEK1 pp CDC25C
+BPGAP1 pp Cortactin
+EIF2C1 pp EIF2C2
+CTBP1 pp CTBP1
+CTBP1 pp CREBBP
+CTBP1 pp PCAF
+EP300 pp HIST4H4
+Sp1 pd CD209_promoter
+EP300 pp H3F3A
+NCR3 interactsWith Unknown
+Unknown interactsWith CD3z
+CDH5 pp CSK
+ARHGEF2 pp CGN
+Vav1 interactsWith EZH2-SUZ12-EED_complex
+Unknown interactsWith EED
+Unknown interactsWith SUZ12
+EZH2 interactsWith Unknown
+DRS pp EF-1-delta
+CyPA pp HAb18G/CD147
+DDB1 pp DDB2
+DDB2 pp XPC
+Rbp4 pd IRF-1_promoter
+Rbp4 pd IRF-1
+CTD pd IRF-1_promoter
+MLF1 pp COPS3
+APP pp APP
+AIDA-1c pp COIL
+MET pp INPPL1
+MET pp PIK3R1
+MET pp INPP5D
+INSR pp PIK3R1
+CSF1R pp INPPL1
+CSF1R pp PIK3R1
+CSF1R pp INPP5D
+TBP pd IRF-1_promoter
+AIDA-1a pp COIL
+Mdm2 pp Mdm2
+Mdm2 pp p53
+RhoA pp Rhotekin
+FRAP1 pp Rheb
+TAF12/ATF7_complex interactsWith SELE_promoter
+TAF4 pp ATF7
+TAF12 pp ATF7
+mTOR-Rheb interactsWith EIF4EBP1
+mTOR-Rheb interactsWith RPS6KB1
+raptor pp Rheb
+lamdaPKC pp p62
+p62 pp p62
+zetaPKC pp p62
+MEK5 pp p62
+GBL pp Rheb
+RAF1 pp Rheb
+ATM pp Rheb
+ATR pp Rheb
+TSC2 pp Rheb
+EGFR interactsWith alphavbeta3_complex
+alphavbeta3-EGFR_complex interactsWith Unknown
+Unknown interactsWith PIK3R2
+Unknown interactsWith PIK3R1
+Unknown interactsWith SRC
+Mettl1 interactsWith pre-tRNA
+Mettl1 pp RSK
+Mettl1 pp PKB-alpha
+alphaII-spectrin pp Tes
+alphaII-spectrin pp EVL
+Tes pp EVL
+I-kappa-B-alpha pp beta-TrCP
+I-kappa-B-alpha pp RelA
+Dr1 pd IRF-1_promoter
+DRAP1 pd IRF-1_promoter
+MED23 pd IRF-1_promoter
+TFIIH pd Cyclin_D1_promoter
+CK2-beta pd TAF7_promoter
+CK2-alpha pd TAF7_promoter
+PC4 pd TAF7_promoter
+TFIIH pd TAF7_promoter
+CK2-beta pd IRF-1_promoter
+CK2-alpha pd IRF-1_promoter
+PC4 pd IRF-1_promoter
+TFIIF pd IRF-1_promoter
+TFIIH pd IRF-1_promoter
+Mettl1 pp WDR4
+Survivin pp Hsp90
+p300 pd p53AIP1_promoter
+p73-alpha pd p53AIP1_promoter
+p73-alpha pp YAP
+p73-alpha pd BAX_promoter
+PCNA pp p21
+PCNA pp Gadd45
+PCNA pp Fen1
+PCNA pp Tigger
+Unknown interactsWith Survivin_promoter
+Unknown interactsWith CTNNB1
+TCF7L2 interactsWith Unknown
+Survivin_promoter/TCF/beta-catenin_complex interactsWith Ep300
+Survivin_promoter/TCF/beta-catenin_complex interactsWith CREBBP
+p53 pp Mdm2
+TGN38 pp Mu2
+Survivin_promoter/TCF/beta-catenin/p300_complex interactsWith Unknown
+Unknown interactsWith HDAC6
+Unknown interactsWith PML
+Unknown interactsWith SUMO1
+Src pp GJP1
+ABL2 pp CRK
+ABL2-RIN1 interactsWith HRAS
+ABL1 pp RIN1
+ABL2 pp RIN1
+KPNB1 pp SOX9
+Jamip1 pp Jak1
+Jamip1 pp Jamip1
+Jamip1 pp Tyk2
+BCAS2 pp PPAR-gamma
+BCAS2 pp PR
+BCAS2 pp TR-beta
+BCAS2 pp ER-beta
+BCAS2 pp ER-alpha
+Mdm2 pp p14ARF
+hdm2 pp p53
+YB-1 pd MVP_promoter
+HNRPA1 interactsWith PTMA_mRNA
+ELAVL1 interactsWith PTMA_mRNA
+CD22 pp CD22
+p14 pp MDM2
+p14 pp WRN
+p18 pp cdk6
+p18 pp cdk4
+p16 pp cdk6
+p16 pp cdk4
+GAD interactsWith Unknown
+Unknown interactsWith Lamp-2
+Unknown interactsWith Hsc70
+TRAF6 pp IRAK1
+Ang2 pp Tie2
+EIF2C1 pp DCP1A
+EIF2C1 pp DCP2
+EIF2C2 pp DCP2
+PDK3 pp PDHA1
+SHBG pp A2M
+SHBG pp ACTA2
+SHBG pp EIF3S5
+SHBG pp PLP2
+SHBG pp DSTN
+SHBG pp FLOT1
+SHBG pp PRV1
+SHBG pp SNAPAP
+SHBG pp ACTG2
+SHBG pp MPDU1
+SHBG pp MCPIP
+SHBG pp MT2A
+SHBG pp ACPP
+SHBG pp UBE3A
+SHBG pp ACTB
+SHBG pp FLNA
+SHBG pp AP2A1
+SHBG pp MT1G
+SHBG pp EEF1A1
+SHBG pp AP1B1
+SHBG pp C9orf24
+SHBG pp APOBEC3C
+SHBG pp CTSD
+SHBG pp APEH
+SHBG pp KLK4
+SHBG pp PSTPIP2
+SHBG pp AK2
+SHBG pp ATP5A1
+SHBG pp PTGDS
+SHBG pp MT1F
+SHBG pp DKFZp762C2414
+SHBG pp SEMA3F
+SHBG pp PLA2G4B
+SHBG pp PKM2
+SHBG pp SORD
+SHBG pp DDX3Y
+SHBG pp MXD4
+SHBG pp CLDN4
+SHBG pp FLJ22318
+SHBG pp E2-230K
+SHBG pp SRI
+SHBG pp dJ222E13.2
+SHBG pp FYTTD1
+SHBG pp SHBG
+SHBG pp COL1A2
+SHBG pp SLC37A1
+SHBG pp Cep192
+SHBG pp CECR5
+SHBG pp NOMO1
+SHBG pp DES
+BARD1 pp XRCC6
+TP53 pp XRCC6
+TP53 pp BARD1
+HIF1A pp VHL
+MAPK3 pp ELK1
+MAPK1 pp ELK1
+E2F4 pd E2F2_promoter
+RBL2 pd E2F2_promoter
+BPGAP1 pp BNIP-2
+RBL2 pd CDC6_promoter
+PDGFRB pp PDGFRB
+CTBP1 pp EP300
+PLAUR pp PDGFRB
+RhoA pp RTKN
+p53 pp Hsc70
+beta-APP pd rNEPP1
+CK2 pp c-Myc
+DAP-1 pp DLC-2
+I-kappa-B-alpha pp Dlc-1
+TRAF2 interactsWith UBE2J1-BIRC2
+RB1 pp CRI1
+RB1 pp UBE2I
+UBE2J1 pp BIRC2
+Hsc70 pp p53
+ATF2 pp ATM
+ATF2 pp Nbs1
+ATM pp p53
+Vav2 pp Nek3
+Vav2 pp PRLr
+Nek3 pp PRLr
+Nek3 pp Casein
+Cdk4 pp p21
+cyclin_D1 pp p21
+Hdmx pp HAUSP
+p53 pp HAUSP
+Mdm2 pp HAUSP
+Mdm2 pp Hdmx
+p53 pp mdm2
+Cdh1 pp Cdc27
+Cdh1 interactsWith APC/C_complex
+Cyclin_B pp Cdh1
+Cyclin_B pp Cdc20
+Securin pp Cdc20
+Unknown interactsWith Cdc16
+Unknown interactsWith Apc7
+Cdc27 interactsWith Unknown
+PCNA pp p21
+PCNA pp Fen1
+PCNA pp Gadd45
+Unknown interactsWith CUL5
+Unknown interactsWith RBX1
+Unknown interactsWith TCEB1
+Unknown interactsWith TCEB2
+DIO2 interactsWith Unknown
+WSB1 pp DIO2
+Unknown interactsWith p50
+Unknown interactsWith RelA
+Unknown interactsWith RelB
+Unknown interactsWith c-Rel
+Unknown interactsWith p52
+IKK-alpha pp I-kappa-B-alpha
+RNAP pd SFI1_promoter
+RNAP pd ZNF687_promoter
+RNAP pd POGZ_promoter
+RNAP pd APXL2_promoter
+RNAP pd MCF2L_promoter
+RNAP pd MAP3K1_promoter
+RNAP pd C21ORF4_promoter
+RNAP pd SERF2_promoter
+RNAP pd IKBKG_promoter
+RNAP pd AF116626_promoter
+RNAP pd PFTK1_promoter
+RNAP pd HSPC117_promoter
+RNAP pd LENG9_promoter
+RNAP pd C6ORF49_promoter
+RNAP pd C21ORF108_promoter
+RNAP pd C21ORF59_promoter
+RNAP pd LOC85865_promoter
+RNAP pd TFEB_promoter
+RNAP pd THOC2_promoter
+RNAP pd AK056230_promoter
+RNAP pd AK056734_promoter
+RNAP pd C16ORF9_promoter
+RNAP pd MGC13125_promoter
+RNAP pd AK057926_promoter
+RNAP pd C9ORF54_promoter
+RNAP pd DKFZP762E1312_promoter
+RNAP pd MGAT2_promoter
+RNAP pd C6ORF147_promoter
+RNAP pd AK092192_promoter
+RNAP pd C9ORF106_promoter
+RNAP pd AK093147_promoter
+RNAP pd ST7_promoter
+RNAP pd LOC439914_promoter
+RNAP pd C6ORF150_promoter
+RNAP pd AK098583_promoter
+RNAP pd IER5L_promoter
+RNAP pd AK126581_promoter
+RNAP pd C20ORF44_promoter
+RNAP pd AK128432_promoter
+RNAP pd SLC22A5_promoter
+RNAP pd AK130600_promoter
+RNAP pd CNOT3_promoter
+RNAP pd PISD_promoter
+RNAP pd AL833465_promoter
+RNAP pd KATNAL1_promoter
+RNAP pd HOXA10_promoter
+RNAP pd HBE1_promoter
+RNAP pd BC017846_promoter
+RNAP pd SF1_promoter
+RNAP pd PPP2R4_promoter
+RNAP pd TKTL1_promoter
+RNAP pd C21ORF13_promoter
+RNAP pd C21ORF55_promoter
+RNAP pd BC029951_promoter
+RNAP pd BC041619_promoter
+RNAP pd DEPDC5_promoter
+RNAP pd FGF1_promoter
+RNAP pd HOXA10_promoter
+RNAP pd APOA1_promoter
+RNAP pd EMD_promoter
+RNAP pd EXT1_promoter
+RNAP pd MEN1_promoter
+RNAP pd MET_promoter
+RNAP pd TIMP3_promoter
+RNAP pd RFX5_promoter
+RNAP pd HOXA13_promoter
+RNAP pd IL10RB_promoter
+RNAP pd IFNAR1_promoter
+RNAP pd CRAT_promoter
+RNAP pd GART_promoter
+RNAP pd RPS9_promoter
+RNAP pd BIRC4_promoter
+RNAP pd CAV2_promoter
+RNAP pd DKC1_promoter
+RNAP pd EEF1A1_promoter
+RNAP pd FLNA_promoter
+RNAP pd GDI1_promoter
+RNAP pd IRAK1_promoter
+RNAP pd ARHGAP4_promoter
+RNAP pd ATP5O_promoter
+RNAP pd CAV1_promoter
+RNAP pd CTGF_promoter
+RNAP pd HOXA9_promoter
+RNAP pd IRF1_promoter
+RNAP pd ITGB4BP_promoter
+RNAP pd MAP1A_promoter
+RNAP pd MPG_promoter
+RNAP pd SERPINB8_promoter
+RNAP pd PIK4CB_promoter
+RNAP pd PSMB4_promoter
+RNAP pd PSMD4_promoter
+RNAP pd SLC22A4_promoter
+RNAP pd SLC22A5_promoter
+RNAP pd SPAG4_promoter
+RNAP pd YWHAH_promoter
+RNAP pd CXORF12_promoter
+RNAP pd FZD1_promoter
+RNAP pd PIP5K1A_promoter
+RNAP pd IKBKG_promoter
+RNAP pd PDLIM4_promoter
+RNAP pd DSCR2_promoter
+RNAP pd SNX3_promoter
+RNAP pd SYNJ1_promoter
+RNAP pd ZNF259_promoter
+RNAP pd CPNE1_promoter
+RNAP pd SELENBP1_promoter
+RNAP pd NDUFA3_promoter
+RNAP pd WRB_promoter
+RNAP pd RNPC2_promoter
+RNAP pd HMGN1_promoter
+RNAP pd MECP2_promoter
+RNAP pd CRYZL1_promoter
+RNAP pd HOXA1_promoter
+RNAP pd HOXA11_promoter
+RNAP pd IFNGR2_promoter
+RNAP pd MDFI_promoter
+RNAP pd TP53BP1_promoter
+RNAP pd PHEMX_promoter
+RNAP pd RAD50_promoter
+RNAP pd RASGRP2_promoter
+RNAP pd MFAP1_promoter
+RNAP pd TCFL1_promoter
+RNAP pd RPL10_promoter
+RNAP pd STAG2_promoter
+RNAP pd DNASE1L1_promoter
+RNAP pd DDX18_promoter
+RNAP pd EHD1_promoter
+RNAP pd HOXA7_promoter
+RNAP pd TFEB_promoter
+RNAP pd CEP2_promoter
+RNAP pd SEC63_promoter
+RNAP pd C16ORF35_promoter
+RNAP pd MTO1_promoter
+RNAP pd CLDN12_promoter
+RNAP pd FBXO7_promoter
+RNAP pd C21ORF66_promoter
+RNAP pd GMPPA_promoter
+RNAP pd TFPT_promoter
+RNAP pd OSTM1_promoter
+RNAP pd MTCP1_promoter
+RNAP pd QP-C_promoter
+RNAP pd TMEM15_promoter
+RNAP pd TES_promoter
+RNAP pd SDBCAG84_promoter
+RNAP pd POLR3K_promoter
+RNAP pd HYPK_promoter
+RNAP pd LUC7L_promoter
+RNAP pd C20ORF44_promoter
+RNAP pd ST7_promoter
+RNAP pd BRWD1_promoter
+RNAP pd EIF4ENIF1_promoter
+RNAP pd SLC10A3_promoter
+RNAP pd TUFT1_promoter
+RNAP pd DOLPP1_promoter
+RNAP pd DECR2_promoter
+RNAP pd NFS1_promoter
+RNAP pd TMEM8_promoter
+RNAP pd FAM3A_promoter
+RNAP pd RHBDF1_promoter
+RNAP pd HOXA6_promoter
+RNAP pd TSEN34_promoter
+RNAP pd LENG1_promoter
+RNAP pd GCC1_promoter
+RNAP pd SNX27_promoter
+RNAP pd TRIM5_promoter
+RNAP pd STK11IP_promoter
+RNAP pd LENG8_promoter
+RNAP pd TRIM6_promoter
+RNAP pd C21ORF63_promoter
+RNAP pd MYADM_promoter
+RNAP pd FOXP4_promoter
+RNAP pd SYT8_promoter
+RNAP pd LACE1_promoter
+RNAP pd STEAP2_promoter
+RNAP pd LOC168850_promoter
+RNAP pd MDFIC_promoter
+RNAP pd APEG1_promoter
+TAF1 pd SFI1_promoter
+TAF1 pd ZNF687_promoter
+TAF1 pd POGZ_promoter
+TAF1 pd APXL2_promoter
+TAF1 pd MCF2L_promoter
+TAF1 pd MAP3K1_promoter
+TAF1 pd C21ORF4_promoter
+TAF1 pd SERF2_promoter
+TAF1 pd IKBKG_promoter
+TAF1 pd AF116626_promoter
+TAF1 pd PFTK1_promoter
+TAF1 pd HSPC117_promoter
+TAF1 pd LENG9_promoter
+TAF1 pd C6ORF49_promoter
+TAF1 pd C21ORF108_promoter
+TAF1 pd C21ORF59_promoter
+TAF1 pd LOC85865_promoter
+TAF1 pd TFEB_promoter
+TAF1 pd THOC2_promoter
+TAF1 pd AK056230_promoter
+TAF1 pd AK056734_promoter
+TAF1 pd C16ORF9_promoter
+TAF1 pd MGC13125_promoter
+TAF1 pd AK057926_promoter
+TAF1 pd C9ORF54_promoter
+TAF1 pd DKFZP762E1312_promoter
+TAF1 pd MGAT2_promoter
+TAF1 pd C6ORF147_promoter
+TAF1 pd AK092192_promoter
+TAF1 pd C9ORF106_promoter
+TAF1 pd AK093147_promoter
+TAF1 pd ST7_promoter
+TAF1 pd LOC439914_promoter
+TAF1 pd C6ORF150_promoter
+TAF1 pd AK098583_promoter
+TAF1 pd IER5L_promoter
+TAF1 pd AK126581_promoter
+TAF1 pd C20ORF44_promoter
+TAF1 pd AK128432_promoter
+TAF1 pd SLC22A5_promoter
+TAF1 pd AK130600_promoter
+TAF1 pd CNOT3_promoter
+TAF1 pd PISD_promoter
+TAF1 pd AL833465_promoter
+TAF1 pd KATNAL1_promoter
+TAF1 pd HOXA10_promoter
+TAF1 pd HBE1_promoter
+TAF1 pd BC017846_promoter
+TAF1 pd SF1_promoter
+TAF1 pd PPP2R4_promoter
+TAF1 pd TKTL1_promoter
+TAF1 pd C21ORF13_promoter
+TAF1 pd C21ORF55_promoter
+TAF1 pd BC029951_promoter
+TAF1 pd BC041619_promoter
+TAF1 pd DEPDC5_promoter
+TAF1 pd FGF1_promoter
+TAF1 pd HOXA10_promoter
+TAF1 pd APOA1_promoter
+TAF1 pd EMD_promoter
+TAF1 pd EXT1_promoter
+TAF1 pd MEN1_promoter
+TAF1 pd MET_promoter
+TAF1 pd TIMP3_promoter
+TAF1 pd RFX5_promoter
+TAF1 pd HOXA13_promoter
+TAF1 pd IL10RB_promoter
+TAF1 pd IFNAR1_promoter
+TAF1 pd CRAT_promoter
+TAF1 pd GART_promoter
+TAF1 pd RPS9_promoter
+TAF1 pd BIRC4_promoter
+TAF1 pd CAV2_promoter
+TAF1 pd DKC1_promoter
+TAF1 pd EEF1A1_promoter
+TAF1 pd FLNA_promoter
+TAF1 pd GDI1_promoter
+TAF1 pd IRAK1_promoter
+TAF1 pd ARHGAP4_promoter
+TAF1 pd ATP5O_promoter
+TAF1 pd CAV1_promoter
+TAF1 pd CTGF_promoter
+TAF1 pd HOXA9_promoter
+TAF1 pd IRF1_promoter
+TAF1 pd ITGB4BP_promoter
+TAF1 pd MAP1A_promoter
+TAF1 pd MPG_promoter
+TAF1 pd SERPINB8_promoter
+TAF1 pd PIK4CB_promoter
+TAF1 pd PSMB4_promoter
+TAF1 pd PSMD4_promoter
+TAF1 pd SLC22A4_promoter
+TAF1 pd SLC22A5_promoter
+TAF1 pd SPAG4_promoter
+TAF1 pd YWHAH_promoter
+TAF1 pd CXORF12_promoter
+TAF1 pd FZD1_promoter
+TAF1 pd PIP5K1A_promoter
+TAF1 pd IKBKG_promoter
+TAF1 pd PDLIM4_promoter
+TAF1 pd DSCR2_promoter
+TAF1 pd SNX3_promoter
+TAF1 pd SYNJ1_promoter
+TAF1 pd ZNF259_promoter
+TAF1 pd CPNE1_promoter
+TAF1 pd SELENBP1_promoter
+TAF1 pd NDUFA3_promoter
+TAF1 pd WRB_promoter
+TAF1 pd RNPC2_promoter
+TAF1 pd HMGN1_promoter
+TAF1 pd MECP2_promoter
+TAF1 pd CRYZL1_promoter
+TAF1 pd HOXA1_promoter
+TAF1 pd HOXA11_promoter
+TAF1 pd IFNGR2_promoter
+TAF1 pd MDFI_promoter
+TAF1 pd TP53BP1_promoter
+TAF1 pd PHEMX_promoter
+TAF1 pd RAD50_promoter
+TAF1 pd RASGRP2_promoter
+TAF1 pd MFAP1_promoter
+TAF1 pd TCFL1_promoter
+TAF1 pd RPL10_promoter
+TAF1 pd STAG2_promoter
+TAF1 pd DNASE1L1_promoter
+TAF1 pd DDX18_promoter
+TAF1 pd EHD1_promoter
+TAF1 pd HOXA7_promoter
+TAF1 pd TFEB_promoter
+TAF1 pd CEP2_promoter
+TAF1 pd SEC63_promoter
+TAF1 pd C16ORF35_promoter
+TAF1 pd MTO1_promoter
+TAF1 pd CLDN12_promoter
+TAF1 pd FBXO7_promoter
+TAF1 pd C21ORF66_promoter
+TAF1 pd GMPPA_promoter
+TAF1 pd TFPT_promoter
+TAF1 pd OSTM1_promoter
+TAF1 pd MTCP1_promoter
+TAF1 pd QP-C_promoter
+TAF1 pd TMEM15_promoter
+TAF1 pd TES_promoter
+TAF1 pd SDBCAG84_promoter
+TAF1 pd POLR3K_promoter
+TAF1 pd HYPK_promoter
+TAF1 pd LUC7L_promoter
+TAF1 pd C20ORF44_promoter
+TAF1 pd ST7_promoter
+TAF1 pd BRWD1_promoter
+TAF1 pd EIF4ENIF1_promoter
+TAF1 pd SLC10A3_promoter
+TAF1 pd TUFT1_promoter
+TAF1 pd DOLPP1_promoter
+TAF1 pd DECR2_promoter
+TAF1 pd NFS1_promoter
+TAF1 pd TMEM8_promoter
+TAF1 pd FAM3A_promoter
+TAF1 pd RHBDF1_promoter
+TAF1 pd HOXA6_promoter
+TAF1 pd TSEN34_promoter
+TAF1 pd LENG1_promoter
+TAF1 pd GCC1_promoter
+TAF1 pd SNX27_promoter
+TAF1 pd TRIM5_promoter
+TAF1 pd STK11IP_promoter
+TAF1 pd LENG8_promoter
+TAF1 pd TRIM6_promoter
+TAF1 pd C21ORF63_promoter
+TAF1 pd MYADM_promoter
+TAF1 pd FOXP4_promoter
+TAF1 pd SYT8_promoter
+TAF1 pd LACE1_promoter
+TAF1 pd STEAP2_promoter
+TAF1 pd LOC168850_promoter
+TAF1 pd MDFIC_promoter
+TAF1 pd APEG1_promoter
+RNAP pd MRPL23_regulatory_element
+RNAP pd PYGM_regulatory_element
+RNAP pd HYPK_regulatory_element
+RNAP pd MFAP1_regulatory_element
+RNAP pd MYADM_regulatory_element
+RNAP pd LENG1_regulatory_element
+RNAP pd LENG8_regulatory_element
+RNAP pd PIK4CB_regulatory_element
+RNAP pd PSMB4_regulatory_element
+RNAP pd RNPC2_regulatory_element
+RNAP pd SYNJ1_regulatory_element
+RNAP pd C21ORF66_regulatory_element
+RNAP pd CRYZL1_regulatory_element
+RNAP pd DSCR2_regulatory_element
+RNAP pd BRWD1_regulatory_element
+RNAP pd EIF4ENIF1_regulatory_element
+RNAP pd PISD_regulatory_element
+RNAP pd YWHAH_regulatory_element
+RNAP pd ACCN4_regulatory_element
+RNAP pd P4HA2_regulatory_element
+RNAP pd IRF1_regulatory_element
+RNAP pd RAD50_regulatory_element
+RNAP pd QP-C_regulatory_element
+RNAP pd SEC63_regulatory_element
+RNAP pd SNX3_regulatory_element
+RNAP pd LACE1_regulatory_element
+RNAP pd EEF1A1_regulatory_element
+RNAP pd ST7_regulatory_element
+RNAP pd LOC168850_regulatory_element
+RNAP pd FZD1_regulatory_element
+RNAP pd CRAT_regulatory_element
+RNAP pd STAG2_regulatory_element
+RNAP pd ARHGAP4_regulatory_element
+RNAP pd CXORF12_regulatory_element
+RNAP pd FLNA_regulatory_element
+RNAP pd EMD_regulatory_element
+RNAP pd RPL10_regulatory_element
+RNAP pd FAM3A_regulatory_element
+RNAP pd CTAG1B_regulatory_element
+RNAP pd BC041619_regulatory_element
+RNAP pd C16ORF9_regulatory_element
+RNAP pd BC070227_regulatory_element
+RNAP pd MGC52000_regulatory_element
+RNAP pd MPG_regulatory_element
+RNAP pd AK125420_regulatory_element
+RNAP pd MYADM_regulatory_element
+RNAP pd CNOT3_regulatory_element
+RNAP pd RPS9_regulatory_element
+RNAP pd TTYH1_regulatory_element
+RNAP pd LENG8_regulatory_element
+RNAP pd LENG9_regulatory_element
+RNAP pd ZNF687_regulatory_element
+RNAP pd ZNF687_regulatory_element
+RNAP pd AK128432_regulatory_element
+RNAP pd C21ORF119_regulatory_element
+RNAP pd C21ORF59_regulatory_element
+RNAP pd C21ORF13_regulatory_element
+RNAP pd PISD_regulatory_element
+RNAP pd DEPDC5_regulatory_element
+RNAP pd AB051444_regulatory_element
+RNAP pd KIAA0657_regulatory_element
+RNAP pd DKFZP762E1312_regulatory_element
+RNAP pd AK129632_regulatory_element
+RNAP pd AK093147_regulatory_element
+RNAP pd AF127918_regulatory_element
+RNAP pd AF118091_regulatory_element
+RNAP pd PPP2R4_regulatory_element
+RNAP pd FLNA_regulatory_element
+RNAP pd FLNA_regulatory_element
+TAF1 pd MRPL23_regulatory_element
+TAF1 pd LUC7L_regulatory_element
+TAF1 pd MYADM_regulatory_element
+TAF1 pd TFPT_regulatory_element
+TAF1 pd RPS9_regulatory_element
+TAF1 pd CDC42EP5_regulatory_element
+TAF1 pd C21ORF66_regulatory_element
+TAF1 pd IL10RB_regulatory_element
+TAF1 pd GART_regulatory_element
+TAF1 pd ITSN1_regulatory_element
+TAF1 pd DSCR2_regulatory_element
+TAF1 pd BRWD1_regulatory_element
+TAF1 pd HMGN1_regulatory_element
+TAF1 pd WRB_regulatory_element
+TAF1 pd EIF4ENIF1_regulatory_element
+TAF1 pd YWHAH_regulatory_element
+TAF1 pd GMPPA_regulatory_element
+TAF1 pd P4HA2_regulatory_element
+TAF1 pd RAD50_regulatory_element
+TAF1 pd IL4_regulatory_element
+TAF1 pd SEC63_regulatory_element
+TAF1 pd OSTM1_regulatory_element
+TAF1 pd SNX3_regulatory_element
+TAF1 pd EEF1A1_regulatory_element
+TAF1 pd CAV2_regulatory_element
+TAF1 pd MET_regulatory_element
+TAF1 pd LOC168850_regulatory_element
+TAF1 pd HOXA1_regulatory_element
+TAF1 pd HOXA5_regulatory_element
+TAF1 pd FZD1_regulatory_element
+TAF1 pd EXT1_regulatory_element
+TAF1 pd STAG2_regulatory_element
+TAF1 pd DKC1_regulatory_element
+TAF1 pd CXORF53_regulatory_element
+TAF1 pd BC017846_regulatory_element
+TAF1 pd C16ORF9_regulatory_element
+TAF1 pd CNOT3_regulatory_element
+TAF1 pd POGZ_regulatory_element
+TAF1 pd C20ORF44_regulatory_element
+TAF1 pd C21ORF119_regulatory_element
+TAF1 pd C21ORF63_regulatory_element
+TAF1 pd C21ORF59_regulatory_element
+TAF1 pd PISD_regulatory_element
+TAF1 pd DEPDC5_regulatory_element
+TAF1 pd BC040870_regulatory_element
+TAF1 pd C6ORF49_regulatory_element
+TAF1 pd RPL39_regulatory_element
+TAF1 pd AK056230_regulatory_element
+TAF1 pd LOC285943_regulatory_element
+TAF1 pd AK096334_regulatory_element
+TAF1 pd PPP2R4_regulatory_element
+TAF1 pd IER5L_regulatory_element
+TAF1 pd THOC2_regulatory_element
+DAP-1 pp DLC-1
+FoxH1 pp Smad3
+FoxH1 pp Smad2
+CBP pp Smad3
+CBP pp Smad2
+Lef1 pp Smad3
+DAP-1 pp Chapsyn-110
+Nck pp PAK1
+CHRNA4 pp CHRNB2
+p21WAF1 pp PCNA
+ARHGEF6 pp PARVB
+C1D pp TRAX
+p53 pp Ref-1
+p53 pp Trx
+p14ARF pp Mdm2
+p53 pd p53con
+KLF2 pd WEE1_promoter
+p16 pp cdk6
+p16 pp cdk4
+KPNB1 interactsWith Ran-GTP
+Unknown interactsWith Orc3
+Unknown interactsWith Orc2
+Orc2 pd C-Myc_origin
+Orc2 pd beta-globin_origin
+Unknown interactsWith Orc6
+Unknown interactsWith Ku70
+Unknown interactsWith Ku80
+Orc4 interactsWith Unknown
+Ku80 pd beta-globin_origin
+Ku80 pd C-Myc_origin
+Ku80 pd Lamin_B2_origin
+BPGAP1 pp Rac1
+c-Cbl pp Keratin_18
+c-Cbl pp huncM_IC
+ECRG2 pp EPB42
+ECRG2 pp MRPS12
+ECRG2 pp AAN27916
+ECRG2 pp FLJ10101
+ECRG2 pp MT1G
+ECRG2 pp MT1H
+ECRG2 pp MT2A
+TRAX pp Translin
+C1D pp C1D
+MAFB pp MAFB
+CD11a pp CD45
+CDK11-p110 pp 14-3-3-beta
+CDK11-p110 pp 14-3-3-epsilon
+CDK11-p110 pp 14-3-3-gamma
+CDK11-p110 pp 14-3-3-theta
+C1D-C1D interactsWith TRAX
+ARHGEF6 pp ARHGEF7
+YY1 pd HLJ1_YY1-binding_site
+Substance_P pp TACR1
+PIN pp PKIA
+PIN pp PKIB
+TNF-R1 pp RASSF1A
+MAP-1 pp Bax
+MAP-1 pp RASSF1A
+TNF-R1 pp MAP-1
+TRAIL-R1 pp RASSF1A
+TRAIL-R1 pp MAP-1
+Nck-2 pp PINCH
+hnRNP_L interactsWith SLC2A2
+hnRNP_L interactsWith GSTZ1
+G-gamma-2 pp G-beta-1
+PhLP pp G-beta-1
+PhLP pp CCT-epsilon
+PAK1 pp H4
+PAK1 pp Cdc42
+LH/CGr pp LH/CGr
+TSHr pp TSHr
+STAT3 pd APRE
+EGFR pd Cyclin_D1_promoter
+EGFR-STAT3_complex interactsWith iNOS_promoter
+EGFR pd iNOS_promoter
+EGFR pp STAT3
+EGFR pp EGF
+STAT3 pd iNOS_promoter
+STAT3 pd Cyclin_D1_promoter
+EGFR pd c-fos_promoter
+STAT3 pd c-fos_promoter
+Myc pd mir-17_cluster
+Myc pd NPM1
+Gemin6 pp SNRPG
+Gemin6 pp SNRPF
+Gemin6 pp SNRPE
+Gemin6 pp SNRPD3
+Gemin6 pp SNRPB
+Gemin6 pp SNRPD2
+BIG2 pp Exo70
+GRIM-19 pp Stat3
+c-Cbl pp 14-3-3-beta
+c-Cbl pp 14-3-3-zeta
+14-3-3-epsilon pp cdc25A
+14-3-3-beta pp cdc25A
+14-3-3-beta pp cdc25B
+14-3-3-epsilon pp cdc25B
+14-3-3-epsilon pp Raf-1
+FBW7 pp SREBP1a
+FBW7 pp SREBP2
+FBW7 pp SREBP1c
+GSK3B pp SREBP1a
+NCK pp SOS
+GRB2 pp SOS
+PKC-delta pp gp130
+gp130 pp Stat3
+HDM2 pp p53
+Siah1 pp Siah1
+NEDD4 pp NEDD4
+HDM2 pp HDM2
+Crk pp Vav
+Crk-L pp C3G
+Grb2 pp C3G
+PIN pp PKIG
+PITX1 pd RASAL1_promoter
+PKC-delta pp Stat3
+PKC-zeta pp Stat3
+PKC-beta pp Stat3
+RalA pp Sec5
+HSJ1b pp Uba52
+HSJ1b pp Uba80
+HSJ1a pp Htt-Q103
+HSJ1a interactsWith Unknown
+Unknown interactsWith C8
+Unknown interactsWith Hsc70
+caspase-3 pp cten
+pRB pp BAA90908
+pRB pp PLZF
+pRB pp RBP2
+pRB pp E2F-2
+RBP2 pd OC_promoter
+pRB pd BRD8_promoter
+pRB pd BRD2_promoter
+p130 pd BRD8_promoter
+p130 pd BRD2_promoter
+RBP2 pd BRD2_promoter
+RBP2 pd BRD8_promoter
+Grb7 pp CaM
+WDR5 interactsWith Unknown
+Unknown interactsWith MGA
+Unknown interactsWith CHD8
+Unknown interactsWith TAF1
+Unknown interactsWith PELP1
+Unknown interactsWith TAF4
+Unknown interactsWith PHF20
+Unknown interactsWith LOC284058
+Unknown interactsWith HCF1
+Unknown interactsWith FLJ12525
+Unknown interactsWith TEX10
+Unknown interactsWith ASH2L
+Unknown interactsWith TAF6
+Unknown interactsWith HSP70
+Unknown interactsWith SENP3
+Unknown interactsWith CAB43677
+Unknown interactsWith MCRS2
+Unknown interactsWith TAF7
+Unknown interactsWith E2F6_isoform_1
+Unknown interactsWith TAF9
+Unknown interactsWith C18orf37
+Unknown interactsWith MAX_protein_isoform_b
+Unknown interactsWith MGC49942
+pRB pp EID-1
+pRB pp E2F-1
+Akt-1 pp YB-1
+PLCB1 pp PARD6A
+PLCB1 pp PARD3
+PLCB3 pp PARD6A
+PLCB3 pp PARD3
+Elk1 pd FRA-1_promoter
+c-Jun pd FRA-1_promoter
+ATF1 pd FRA-1_promoter
+CREB pd FRA-1_promoter
+SRF pd FRA-1_promoter
+unknown interactsWith WDR5
+p53 interactsWith unknown
+Casp-3 pp Trx
+Cdc42 pp Pak1
+BPGAP1 pp RhoA
+BPGAP1 pp Cdc42
+L-endoglin pp S-endoglin
+p21WAF1 pp PCNA
+p53 pp Mdm2
+p21WAF1 pp Cdk2
+Cav2.2 pp Cav2.2
+Cav2.1 pp G-beta-1
+Cav2.2 pp G-beta-1
+Cav1.2 pp G-beta-1
+Unknown interactsWith MLL2
+Unknown interactsWith RbBP5
+WDR5 interactsWith Unknown
+Unknown interactsWith Ash2
+MLL1 pd HOXA9
+MLL1 pd HOXA9_promoter
+MLL1 pd HOXC8_promoter
+MLL1 pd HOXC8
+Ski pp alpha-tubulin
+Mre11 pp p53
+BLM pp p53
+p21 pp Cdk2
+p21 pp PCNA
+Ring2 pp MLL
+Ring2 pp MOF
+MOF pp MLL
+ATF2 pd CDK4_promoter
+ATF2 pd ERCC3_promoter
+ATF2 pd GJA1_promoter
+ATF2 pd MLH1_promoter
+ATF2 pd PKD1_promoter
+ATF2 pd TIMP3_promoter
+ATF2 pd EGR2_promoter
+ATF2 pd G6PD_promoter
+ATF2 pd CYP1A1_promoter
+ATF2 pd PMS2_promoter
+ATF2 pd VHL_promoter
+ATF2 pd IL4_promoter
+ATF2 pd TNF_promoter
+ATF2 pd SERPINE1_promoter
+ATF2 pd IGF2_promoter
+ATF2 pd BCL2_promoter
+ATF2 pd TNFSF6_promoter
+ATF2 pd IL11_promoter
+ATF2 pd TGFB1_promoter
+ATF2 pd BGLAP_promoter
+ATF2 pd GSTP1_promoter
+ATF2 pd RRM1_promoter
+ATF2 pd ATP6IP1_promoter
+ATF2 pd BID_promoter
+ATF2 pd CCNA2_promoter
+ATF2 pd CDC20_promoter
+ATF2 pd FAAH_promoter
+ATF2 pd FOXO3A_promoter
+ATF2 pd HIF1A_promoter
+ATF2 pd ALOX5AP_promoter
+ATF2 pd KLK3_promoter
+ATF2 pd CCND2_promoter
+ATF2 pd CENPE_promoter
+ATF2 pd CLU_promoter
+ATF2 pd CTSD_promoter
+ATF2 pd EGR1_promoter
+ATF2 pd ENO2_promoter
+ATF2 pd ERCC1_promoter
+ATF2 pd FGF2_promoter
+ATF2 pd FLI1_promoter
+ATF2 pd GAP43_promoter
+ATF2 pd HMOX1_promoter
+ATF2 pd IGFBP6_promoter
+ATF2 pd JUN_promoter
+ATF2 pd LAMA4_promoter
+ATF2 pd MEIS1_promoter
+ATF2 pd MKI67_promoter
+ATF2 pd MMP1_promoter
+ATF2 pd MTAP_promoter
+ATF2 pd MYBL2_promoter
+ATF2 pd MYC_promoter
+ATF2 pd NFKB2_promoter
+ATF2 pd TCF7_promoter
+ATF2 pd VIL2_promoter
+ATF2 pd ZNF267_promoter
+ATF2 pd HIST1H2AC_promoter
+ATF2 pd PPAP2B_promoter
+ATF2 pd HDAC3_promoter
+ATF2 pd CDKN1B_promoter
+ATF2 pd CSRP1_promoter
+ATF2 pd DAZ_promoter
+ATF2 pd CITED1_promoter
+ATF2 pd SREBF1_promoter
+ATF2 pd DUSP1_promoter
+ATF2 pd FOXD1_promoter
+ATF2 pd MMP2_promoter
+ATF2 pd PLAB_promoter
+ATF2 pd DAPK1_promoter
+ATF2 pd PPARA_promoter
+ATF2 pd AKT1_promoter
+ATF2 pd CHES1_promoter
+ATF2 pd NR2F6_promoter
+ATF2 pd FOS_promoter
+ATF2 pd JUND_promoter
+ATF2 pd MAGEA12_promoter
+ATF2 pd BMP15_promoter
+ATF2 pd KRT6B_promoter
+ATF2 pd RGS4_promoter
+ATF2 pd RAD50_promoter
+ATF2 pd TOPORS_promoter
+ATF2 pd C3ORF8_promoter
+ATF2 pd MFGE8_promoter
+ATF2 pd MT3_promoter
+ATF2 pd SPRR1A_promoter
+ATF2 pd PCBP1_promoter
+ATF2 pd TNFAIP3_promoter
+ATF2 pd LGALS8_promoter
+ATF2 pd IMP-2_promoter
+ATF2 pd GADD45G_promoter
+ATF2 pd FOSB_promoter
+ATF2 pd TTF1_promoter
+ATF2 pd BNIP1_promoter
+ATF2 pd BBC3_promoter
+ATF2 pd SCHIP1_promoter
+ATF2 pd KIAA0087_promoter
+ATF2 pd CAP350_promoter
+ATF2 pd FGFR1_promoter
+ATF2 pd WIT-1_promoter
+ATF2 pd BK65A6.2_promoter
+ATF2 pd REPRIMO_promoter
+ATF2 pd WRNIP1_promoter
+ATF2 pd APS_promoter
+ATF2 pd HIST1H2BJ_promoter
+ATF2 pd PLEKHB1_promoter
+ATF2 pd PELI2_promoter
+ATF2 pd HPSE2_promoter
+ATF2 pd MCL1_promoter
+ATF2 pd HIPK2_promoter
+ATF2 pd FLJ23584_promoter
+ATF2 pd TCF7L2_promoter
+ATF2 pd CCNB1_promoter
+ATF2 pd DKFZP434K1421_promoter
+ATF2 pd PINK1_promoter
+ATF2 pd CREB1_promoter
+ATF2 pd APOA1_promoter
+ATF2 pd CDKN2A_promoter
+ATF2 pd CKN1_promoter
+ATF2 pd MSH6_promoter
+ATF2 pd LIG1_promoter
+ATF2 pd MSH2_promoter
+ATF2 pd STAR_promoter
+ATF2 pd XPA_promoter
+ATF2 pd PSEN2_promoter
+ATF2 pd IL1B_promoter
+ATF2 pd IGFBP2_promoter
+ATF2 pd CACNB3_promoter
+ATF2 pd RARB_promoter
+ATF2 pd TCN1_promoter
+ATF2 pd BIRC2_promoter
+ATF2 pd G22P1_promoter
+ATF2 pd FGFR4_promoter
+ATF2 pd JUNB_promoter
+ATF2 pd TGM3_promoter
+ATF2 pd TIMP1_promoter
+ATF2 pd KCNAB2_promoter
+ATF2 pd TMEFF1_promoter
+ATF2 pd AURKB_promoter
+ATF2 pd TOM1_promoter
+ATF2 pd NBR2_promoter
+ATF2 pd P37NB_promoter
+ATF2 pd MXI1_promoter
+ATF2 pd NTS_promoter
+ATF2 pd PENK_promoter
+ATF2 pd ABHD2_promoter
+ATF2 pd DMC1_promoter
+ATF2 pd KCNJ14_promoter
+ATF2 pd MKRN2_promoter
+ATF2 pd P101-PI3K_promoter
+ATF2 pd KIAA0852_promoter
+ATF2 pd PEG10_promoter
+ATF2 pd DKFZP564B167_promoter
+ATF2 pd HDAC7A_promoter
+ATF2 pd HOXC10_promoter
+ATF2 pd C9ORF7_promoter
+ATF2 pd FLJ20641_promoter
+ATF2 pd FLJ10815_promoter
+ATF2 pd FLJ11046_promoter
+ATF2 pd FLJ11078_promoter
+ATF2 pd BM045_promoter
+ATF2 pd LOC55924_promoter
+ATF2 pd LTB4R2_promoter
+ATF2 pd UNG2_promoter
+ATF2 pd ST7_promoter
+ATF2 pd RELA_promoter
+ATF2 pd 24432_promoter
+ATF2 pd FGFR1_promoter
+ATF2 pd FLJ13590_promoter
+ATF2 pd PWDMP_promoter
+ATF2 pd EMILIN2_promoter
+c-Jun pd APC_promoter
+c-Jun pd AR_promoter
+c-Jun pd ATM_promoter
+c-Jun pd CDK4_promoter
+c-Jun pd ERCC3_promoter
+c-Jun pd GJA1_promoter
+c-Jun pd GPI_promoter
+c-Jun pd LAMA3_promoter
+c-Jun pd MLH1_promoter
+c-Jun pd NP_promoter
+c-Jun pd PKD1_promoter
+c-Jun pd PKD2_promoter
+c-Jun pd TIMP3_promoter
+c-Jun pd ERCC2_promoter
+c-Jun pd G6PD_promoter
+c-Jun pd CYP1A1_promoter
+c-Jun pd ELN_promoter
+c-Jun pd PMS2_promoter
+c-Jun pd VHL_promoter
+c-Jun pd IL3_promoter
+c-Jun pd IL4_promoter
+c-Jun pd TNF_promoter
+c-Jun pd SERPINE1_promoter
+c-Jun pd IGF2_promoter
+c-Jun pd BCL2_promoter
+c-Jun pd TNFSF6_promoter
+c-Jun pd IL11_promoter
+c-Jun pd TGFB1_promoter
+c-Jun pd BGLAP_promoter
+c-Jun pd GSTP1_promoter
+c-Jun pd ITGAX_promoter
+c-Jun pd MME_promoter
+c-Jun pd RRM1_promoter
+c-Jun pd TBXA2R_promoter
+c-Jun pd AMELX_promoter
+c-Jun pd BIRC5_promoter
+c-Jun pd ATP6IP1_promoter
+c-Jun pd BID_promoter
+c-Jun pd BIK_promoter
+c-Jun pd BNIP1_promoter
+c-Jun pd CCNA2_promoter
+c-Jun pd CDC20_promoter
+c-Jun pd DDX3X_promoter
+c-Jun pd EEF1A1_promoter
+c-Jun pd EP300_promoter
+c-Jun pd FAAH_promoter
+c-Jun pd FOXO3A_promoter
+c-Jun pd HIF1A_promoter
+c-Jun pd ADPRT_promoter
+c-Jun pd ALOX5AP_promoter
+c-Jun pd KLK3_promoter
+c-Jun pd KLF5_promoter
+c-Jun pd CAV1_promoter
+c-Jun pd CCND2_promoter
+c-Jun pd CENPE_promoter
+c-Jun pd CKS2_promoter
+c-Jun pd CLU_promoter
+c-Jun pd CSNK2A1_promoter
+c-Jun pd CTSD_promoter
+c-Jun pd DCN_promoter
+c-Jun pd EGR1_promoter
+c-Jun pd ENO2_promoter
+c-Jun pd ERCC1_promoter
+c-Jun pd FGF2_promoter
+c-Jun pd FGF4_promoter
+c-Jun pd FLI1_promoter
+c-Jun pd GAP43_promoter
+c-Jun pd GLRX_promoter
+c-Jun pd HLA-A_promoter
+c-Jun pd HMOX1_promoter
+c-Jun pd TNC_promoter
+c-Jun pd IGFBP6_promoter
+c-Jun pd ITPR3_promoter
+c-Jun pd JUN_promoter
+c-Jun pd KRT8_promoter
+c-Jun pd LAMA4_promoter
+c-Jun pd MEIS1_promoter
+c-Jun pd MMP1_promoter
+c-Jun pd MTAP_promoter
+c-Jun pd MYBL2_promoter
+c-Jun pd MYC_promoter
+c-Jun pd SERPINB5_promoter
+c-Jun pd PRSS8_promoter
+c-Jun pd PTPN1_promoter
+c-Jun pd PTPRG_promoter
+c-Jun pd CCL2_promoter
+c-Jun pd SHC1_promoter
+c-Jun pd SNRPF_promoter
+c-Jun pd SPI1_promoter
+c-Jun pd SYK_promoter
+c-Jun pd TCF7_promoter
+c-Jun pd TGFBR2_promoter
+c-Jun pd TRAF3_promoter
+c-Jun pd VIL2_promoter
+c-Jun pd ZNF267_promoter
+c-Jun pd TRRAP_promoter
+c-Jun pd HIST1H2AC_promoter
+c-Jun pd PPAP2B_promoter
+c-Jun pd HDAC3_promoter
+c-Jun pd CDKN1B_promoter
+c-Jun pd CSRP1_promoter
+c-Jun pd DAZ_promoter
+c-Jun pd CITED1_promoter
+c-Jun pd OAZ1_promoter
+c-Jun pd SREBF1_promoter
+c-Jun pd BAX_promoter
+c-Jun pd CREB1_promoter
+c-Jun pd DUSP1_promoter
+c-Jun pd FOXD1_promoter
+c-Jun pd MMP2_promoter
+c-Jun pd SNRPA_promoter
+c-Jun pd MAPKAPK3_promoter
+c-Jun pd PLAB_promoter
+c-Jun pd ETR101_promoter
+c-Jun pd DAPK1_promoter
+c-Jun pd MMP14_promoter
+c-Jun pd PPARA_promoter
+c-Jun pd AKAP12_promoter
+c-Jun pd TRAP240_promoter
+c-Jun pd AKT1_promoter
+c-Jun pd CEBPB_promoter
+c-Jun pd CHES1_promoter
+c-Jun pd ELK1_promoter
+c-Jun pd NR2F6_promoter
+c-Jun pd FOS_promoter
+c-Jun pd GTF2H1_promoter
+c-Jun pd JUND_promoter
+c-Jun pd MAGEA12_promoter
+c-Jun pd BMP15_promoter
+c-Jun pd ING1_promoter
+c-Jun pd KRT6B_promoter
+c-Jun pd RGS4_promoter
+c-Jun pd ARPC4_promoter
+c-Jun pd RAD50_promoter
+c-Jun pd RFP2_promoter
+c-Jun pd TOPORS_promoter
+c-Jun pd C3ORF8_promoter
+c-Jun pd MFGE8_promoter
+c-Jun pd MT3_promoter
+c-Jun pd NAB2_promoter
+c-Jun pd SPRR1A_promoter
+c-Jun pd ARMET_promoter
+c-Jun pd CITED2_promoter
+c-Jun pd PCBP1_promoter
+c-Jun pd PIN1_promoter
+c-Jun pd TNFAIP3_promoter
+c-Jun pd FST_promoter
+c-Jun pd TADA3L_promoter
+c-Jun pd PRDX4_promoter
+c-Jun pd CLN5_promoter
+c-Jun pd LGALS8_promoter
+c-Jun pd BCL2L11_promoter
+c-Jun pd IMP-2_promoter
+c-Jun pd GADD45G_promoter
+c-Jun pd FOSB_promoter
+c-Jun pd EBNA1BP2_promoter
+c-Jun pd BZRP_promoter
+c-Jun pd TTF1_promoter
+c-Jun pd PSEN2_promoter
+c-Jun pd BNIP1_promoter
+c-Jun pd BBC3_promoter
+c-Jun pd SCHIP1_promoter
+c-Jun pd ERO1L_promoter
+c-Jun pd KIAA0087_promoter
+c-Jun pd CAP350_promoter
+c-Jun pd PAM_promoter
+c-Jun pd FGFR1_promoter
+c-Jun pd WIT-1_promoter
+c-Jun pd GAL_promoter
+c-Jun pd MAGEE1_promoter
+c-Jun pd SLC21A12_promoter
+c-Jun pd HSD17B7_promoter
+c-Jun pd TREX1_promoter
+c-Jun pd COPZ2_promoter
+c-Jun pd SARS2_promoter
+c-Jun pd FLJ20721_promoter
+c-Jun pd FLJ10539_promoter
+c-Jun pd ZNF302_promoter
+c-Jun pd BK65A6.2_promoter
+c-Jun pd F7_promoter
+c-Jun pd REPRIMO_promoter
+c-Jun pd WRNIP1_promoter
+c-Jun pd APS_promoter
+c-Jun pd HIST1H2BJ_promoter
+c-Jun pd PLEKHB1_promoter
+c-Jun pd PELI2_promoter
+c-Jun pd MCL1_promoter
+c-Jun pd GALNT11_promoter
+c-Jun pd LOC64172_promoter
+c-Jun pd HIPK2_promoter
+c-Jun pd C1ORF35_promoter
+c-Jun pd FLJ23584_promoter
+c-Jun pd CCNB1_promoter
+c-Jun pd PCDHGA7_promoter
+c-Jun pd DKFZP434K1421_promoter
+c-Jun pd PINK1_promoter
+c-Jun pd SCIN_promoter
+c-Jun pd HIST3H2A_promoter
+c-Jun pd CREB1_promoter
+P75 pp NgR
+RbBP5 pp MLL
+WDR5 pp MLL
+PCNA_trimer interactsWith p21
+PCNA pp PCNA
+ELK1 pp PIAS2a
+hLHR pp EBP50
+GIPC pp hLHR
+CAMK4 pp CABIN1
+MEF2D pp CABIN1
+YWHAQ pp CABIN1
+BNIP-2 pp Cdc42
+CALM1 pp CABIN1
+F7 pp F7
+Transthyretin pp Transthyretin
+Glycine_N-Methyltransferase pp Glycine_N-Methyltransferase
+CALM1 interactsWith Unknown
+Huzaf_Antibody_Heavy_Chain pp Huzaf_Antibody_Light_Chain
+Huzaf_Antibody_Heavy_Chain pp Huzaf_Antibody_Light_Chain
+ACTA1 pp GSN
+Igg1 pp Igg1
+FCGR3B pp Igg1
+FCGR3B pp Igg1
+ENO2 pp ENO2
+SUMO1 pp SENP2
+APC pp CTNNB1
+Anti-Hiv-1_Antibody_2f5_Heavy_Chain pp Anti-Hiv-1_Antibody_2f5_Light_Chain
+UBE1C pp APPBP1
+Ubiquitin-Conjugating_Enzyme_E2_M pp UBE1C
+RAB5A pp RAB5A
+RAB5A pp RAB5A
+RABEP1 pp RAB5A
+RABEP1 pp RAB5A
+RABEP1 pp RABEP1
+RABEP1 pp RAB5A
+RABEP1 pp RAB5A
+RABEP1 pp RAB5A
+RABEP1 pp RAB5A
+RABEP1 pp RAB5A
+RABEP1 pp RAB5A
+RABEP1 pp RABEP1
+RABEP1 pp RAB5A
+CTSK pp CTSK
+1U1L_B pd HNRPA1
+1U1Q_B pd HNRPA1
+1U1R_B pd HNRPA1
+1U1P_B pd HNRPA1
+SMAD4 pp SMAD3
+SMAD3 pp SMAD3
+SMAD3 pp SMAD4
+HADH2 pp HADH2
+HADH2 pp HADH2
+HADH2 pp HADH2
+HADH2 pp HADH2
+SMAD2 pp SMAD2
+SMAD4 pp SMAD2
+SMAD4 pp SMAD2
+Gp41_Peptide pp Antibody_2f5_(Light_Chain)
+Gp41_Peptide pp Antibody_2f5_(Heavy_Chain)
+Antibody_2f5_(Heavy_Chain) pp Antibody_2f5_(Light_Chain)
+Antibody_2f5_(Heavy_Chain) pp Antibody_2f5_(Light_Chain)
+CYGB pp CYGB
+Unknown interactsWith YWHAQ
+DPP4 pp DPP4
+OGT pp OGT
+RAB9B pp RAB9B
+RHOA pp ARHGEF12
+Arpg836 pp Arpg836
+Arpg836 pp Arpg836
+Arpg836 pp Arpg836
+FAHD1 pp FAHD1
+HBD pp Hemoglobin_Alpha_Chain
+Hemoglobin_Alpha_Chain pp Hemoglobin_Alpha_Chain
+Hemoglobin_Alpha_Chain pp HBD
+HBD pp Hemoglobin_Alpha_Chain
+HBD pp HBD
+Hemoglobin_Alpha_Chain pp Hemoglobin_Alpha_Chain
+HBD pp Hemoglobin_Alpha_Chain
+HBD pp HBD
+B2M pp Leukocyte_Antigen_(Hla)_Class_I_Molecule
+B2M pp Mhc_Class_I_Antigen
+Beta-Catenin-Interacting_Protein_1 pp CTNNB1
+Adenomatous_Polyposis_Coli_Protein pp CTNNB1
+FNTB pp FNTA
+Diablo_Homolog,_Mitochondrial pp BIRC7
+ADH1A pp ADH1A
+ADH1B pp ADH1B
+LGALS1 pp LGALS1
+LGALS1 pp LGALS1
+LGALS1 pp LGALS1
+RABEP1 pp GGA1
+RABEP1 pp RABEP1
+RABEP1 pp GGA1
+Baculoviral_Iap_Repeat-Containing_Protein_8 pp Baculoviral_Iap_Repeat-Containing_Protein_8
+Baculoviral_Iap_Repeat-Containing_Protein_8 pp Baculoviral_Iap_Repeat-Containing_Protein_8
+Baculoviral_Iap_Repeat-Containing_Protein_8 pp Baculoviral_Iap_Repeat-Containing_Protein_8
+Baculoviral_Iap_Repeat-Containing_Protein_8 pp Baculoviral_Iap_Repeat-Containing_Protein_8
+Baculoviral_Iap_Repeat-Containing_Protein_8 pp Baculoviral_Iap_Repeat-Containing_Protein_8
+Baculoviral_Iap_Repeat-Containing_Protein_8 pp Baculoviral_Iap_Repeat-Containing_Protein_8
+Baculoviral_Iap_Repeat-Containing_Protein_8 pp Baculoviral_Iap_Repeat-Containing_Protein_8
+Baculoviral_Iap_Repeat-Containing_Protein_8 pp Baculoviral_Iap_Repeat-Containing_Protein_8
+Baculoviral_Iap_Repeat-Containing_Protein_8 pp Baculoviral_Iap_Repeat-Containing_Protein_8
+SOS1 pp HRAS
+DPP6 pp DPP6
+C6orf82 pp C6orf82
+C6orf82 pp C6orf82
+C6orf82 pp C6orf82
+FASN pp FASN
+HSD11B1 pp HSD11B1
+HSD11B1 pp HSD11B1
+HSD11B1 pp HSD11B1
+HSD11B1 pp HSD11B1
+HSD11B1 pp HSD11B1
+ESR1 pp ESR1
+ESR1 pp ESR1
+Lxxll_Motif_Coactivator pp RXRA
+PPARG pp RXRA
+Lxxll_Motif_Coactivator pp PPARG
+F2 pp Thrombin_Light_Chain
+F2 pp Thrombin_Light_Chain
+MAP2K2 pp MAP2K2
+Cyclic-Amp-Dependent_Transcription_Factor_Atf-2 pp IRF3
+Cyclic-Amp-Dependent_Transcription_Factor_Atf-2 pp Transcription_Factor_Ap-1
+1T2K_E pd Cyclic-Amp-Dependent_Transcription_Factor_Atf-2
+1T2K_E pd IRF3
+1T2K_E pd IRF3
+1T2K_F pd IRF3
+1T2K_F pd IRF3
+1T2K_F pd Cyclic-Amp-Dependent_Transcription_Factor_Atf-2
+CCL5 pp CCL5
+CCL5 pp CCL5
+CCL5 pp CCL5
+CCL5 pp CCL5
+CDK5R1 pp CDK5
+CDK5 pp CDK5
+CDK5R1 pp CDK5
+CDK5R1 pp CDK5
+Gene_Terminal_Protein_(Membrane_Protein_Lmp-2aLMP-2b) pp Hla_Class_I_Histocompatibility_Antigen_B-27_Alpha_Chain
+B2M pp Hla_Class_I_Histocompatibility_Antigen
+Melanoma-Associated_Antigen_1 pp Hla_Class_I_Histocompatibility_Antigen
+Hyb3_Light_Chain pp Hyb3_Heavy_Chain
+BCKDHB pp BCKDHA
+RPS27A pp UCHL3
+PIGR pp PIGR
+Aa_4-17_(Lpavvglspgeqey)_Of_Alternative_Reading_Frame_Of_M-Csf pp Hla_Class_I_Histocompatibility_Antigen,_B-35_Alpha_Chain
+CD3D pp CD3E
+Immunoglobulin_Light_Chain_Variable_Region pp CD3E
+Immunoglobulin_Heavy_Chain_Variable_Region pp CD3E
+CD3D pp CD3E
+CD3D pp Immunoglobulin_Light_Chain_Variable_Region
+Immunoglobulin_Light_Chain_Variable_Region pp CD3D
+F2 pp Thrombin_Light_Chain
+Decamer_Fragment_Of_Androgen_Receptor pp AR
+14-Mer_Fragment_Of_Nuclear_Receptor_Coactivator_2 pp AR
+9-Mer_Peptide_From_Tumor_Protein_P53 pp SET7
+SET7 pp SET7
+Tumor_Necrosis_Factor_Receptor_Superfamily_Member_13b pp TNFSF13
+Tumor_Necrosis_Factor_Receptor_Superfamily_Member_13b pp TNFSF13
+Tumor_Necrosis_Factor_Receptor_Superfamily_Member_13b pp TNFSF13
+Tumor_Necrosis_Factor_Receptor_Superfamily_Member_17 pp TNFSF13
+Tumor_Necrosis_Factor_Receptor_Superfamily_Member_17 pp TNFSF13
+Tumor_Necrosis_Factor_Receptor_Superfamily_Member_17 pp TNFSF13
+Ecotin pp F11
+Ecotin pp F11
+Ecotin pp Ecotin
+Ecotin pp F11
+Ecotin pp F11
+Ecotin pp Ecotin
+Ecotin pp F11
+Ecotin pp F11
+Ecotin pp Ecotin
+Ecotin pp F11
+Hemoglobin_Beta_Chain pp Hemoglobin_Alpha_Chain
+Hemoglobin_Beta_Chain pp Hemoglobin_Alpha_Chain
+Hemoglobin_Beta_Chain pp HBA2
+HBA2 pp Hemoglobin_Beta_Chain
+HBA2 pp Hemoglobin_Beta_Chain
+Hemoglobin_Beta_Chain pp HBA2
+Hemoglobin_Alpha_Chain pp Hemoglobin_Alpha_Chain
+HBA2 pp Hemoglobin_Beta_Chain
+Hemoglobin_Beta_Chain pp Hemoglobin_Alpha_Chain
+DPP4 pp DPP4
+PTP4A1 pp PTP4A1
+PTP4A1 pp PTP4A1
+LRBA pp LRBA
+LRBA pp LRBA
+Endothelin-1 pp Endothelin-1
+GM2A pp GM2A
+GM2A pp GM2A
+MEF2B pp MEF2B
+RBX1 pp CUL1
+CAND1 pp RBX1
+CAND1 pp CUL1
+Kanrqvsitgffqrk_Peptide_From_Dna_Polymerase_Delta_Subunit_3 pp PCNA
+Srqgstqgrlddffkvtgsl_Peptide_Of_Flap_Endonuclease-1 pp PCNA
+ITGB3 pp ITGAV
+XPO1 pp XPO1
+TK1 pp TK1
+TK1 pp TK1
+TK1 pp TK1
+RHOA pp ARHGEF11
+NR1I3 pp RXRA
+NR1I3 pp RXRA
+NR1I3 pp NR1I3
+NR1I3 pp RXRA
+NR1I3 pp RXRA
+PDE4B pp PDE4B
+PDE4B pp PDE4B
+PDE4B pp PDE4B
+DHRS8 pp DHRS8
+CRYZ pp CRYZ
+Hemoglobin_Beta_Chain pp HBA2
+Hemoglobin_Beta_Chain pp Hemoglobin_Alpha_Chain
+Hemoglobin_Alpha_Chain pp Hemoglobin_Beta_Chain
+Hemoglobin_Beta_Chain pp Hemoglobin_Alpha_Chain
+Hemoglobin_Alpha_Chain pp Hemoglobin_Beta_Chain
+Hemoglobin_Beta_Chain pp Hemoglobin_Alpha_Chain
+Hemoglobin_Beta_Chain pp Hemoglobin_Alpha_Chain
+Hemoglobin_Beta_Chain pp Hemoglobin_Alpha_Chain
+DCI pp DCI
+DCI pp DCI
+ARHGEF1 pp ARHGEF1
+Nuclear_Receptor_Coactivator_4 pp AR
+Nuclear_Receptor_Coactivator_2 pp AR
+Nuclear_Receptor_Coactivator_2 pp AR
+GSTA3 pp GSTA3
+Adenomatous_Polyposis_Coli pp CTNNB1
+PCNA pp PCNA
+PCNA pp PCNA
+PCNA pp PCNA
+PCNA pp PCNA
+PCNA pp PCNA
+PCNA pp PCNA
+Acetylcholinesterase pp Acetylcholinesterase
+Acetylcholinesterase pp Acetylcholinesterase
+Acetylcholinesterase pp Acetylcholinesterase
+Acetylcholinesterase pp Acetylcholinesterase
+Acetylcholinesterase_Collagenic_Tail_Peptide pp Acetylcholinesterase
+Acetylcholinesterase_Collagenic_Tail_Peptide pp Acetylcholinesterase
+Acetylcholinesterase_Collagenic_Tail_Peptide pp Acetylcholinesterase
+Acetylcholinesterase_Collagenic_Tail_Peptide pp Acetylcholinesterase
+F7 pp F7
+Neutrophil_Cytosol_Factor_1 pp NCF4
+F2 pp Thrombin_Light_Chain
+SCO1 pp SCO1
+MAPRE1 pp MAPRE1
+PTP4A1 pp PTP4A1
+PTP4A1 pp PTP4A1
+PTP4A1 pp PTP4A1
+PTP4A1 pp PTP4A1
+PTP4A1 pp PTP4A1
+PTP4A1 pp PTP4A1
+PTP4A1 pp PTP4A1
+PTP4A1 pp PTP4A1
+PTP4A1 pp PTP4A1
+ESR1 pp ESR1
+FSHB pp CGA
+FSHR pp FSHB
+FSHR pp CGA
+Decamer_Fragment_Of_Phospholipid_Scramblase_1 pp KPNA2
+ZNF174 pp ZNF174
+UBA2 pp SAE1
+UBA2 pp SAE1
+SUMO1 pp UBA2
+TREX2 pp TREX2
+Retinal_DehydrogenaseREDUCTASE_3 pp Retinal_DehydrogenaseREDUCTASE_3
+Retinal_DehydrogenaseREDUCTASE_3 pp Retinal_DehydrogenaseREDUCTASE_3
+Retinal_DehydrogenaseREDUCTASE_3 pp Retinal_DehydrogenaseREDUCTASE_3
+Retinal_DehydrogenaseREDUCTASE_3 pp Retinal_DehydrogenaseREDUCTASE_3
+Retinal_DehydrogenaseREDUCTASE_3 pp Retinal_DehydrogenaseREDUCTASE_3
+Retinal_DehydrogenaseREDUCTASE_3 pp Retinal_DehydrogenaseREDUCTASE_3
+Retinal_DehydrogenaseREDUCTASE_3 pp Retinal_DehydrogenaseREDUCTASE_3
+Retinal_DehydrogenaseREDUCTASE_3 pp Retinal_DehydrogenaseREDUCTASE_3
+Retinal_DehydrogenaseREDUCTASE_3 pp Retinal_DehydrogenaseREDUCTASE_3
+Retinal_DehydrogenaseREDUCTASE_3 pp Retinal_DehydrogenaseREDUCTASE_3
+Retinal_DehydrogenaseREDUCTASE_3 pp Retinal_DehydrogenaseREDUCTASE_3
+Retinal_DehydrogenaseREDUCTASE_3 pp Retinal_DehydrogenaseREDUCTASE_3
+Retinal_DehydrogenaseREDUCTASE_3 pp Retinal_DehydrogenaseREDUCTASE_3
+Retinal_DehydrogenaseREDUCTASE_3 pp Retinal_DehydrogenaseREDUCTASE_3
+Retinal_DehydrogenaseREDUCTASE_3 pp Retinal_DehydrogenaseREDUCTASE_3
+Retinal_DehydrogenaseREDUCTASE_3 pp Retinal_DehydrogenaseREDUCTASE_3
+Retinal_DehydrogenaseREDUCTASE_3 pp Retinal_DehydrogenaseREDUCTASE_3
+Retinal_DehydrogenaseREDUCTASE_3 pp Retinal_DehydrogenaseREDUCTASE_3
+Retinal_DehydrogenaseREDUCTASE_3 pp Retinal_DehydrogenaseREDUCTASE_3
+Retinal_DehydrogenaseREDUCTASE_3 pp Retinal_DehydrogenaseREDUCTASE_3
+Retinal_DehydrogenaseREDUCTASE_3 pp Retinal_DehydrogenaseREDUCTASE_3
+Retinal_DehydrogenaseREDUCTASE_3 pp Retinal_DehydrogenaseREDUCTASE_3
+Hemoglobin_Beta_Chain pp Hemoglobin_Alpha_Chain
+Hemoglobin_Beta_Chain pp Hemoglobin_Alpha_Chain
+Hemoglobin_Alpha_Chain pp Hemoglobin_Beta_Chain
+Hemoglobin_Beta_Chain pp Hemoglobin_Alpha_Chain
+Hemoglobin_Beta_Chain pp Hemoglobin_Alpha_Chain
+Hemoglobin_Beta_Chain pp Hemoglobin_Alpha_Chain
+Hemoglobin_Alpha_Chain pp Hemoglobin_Beta_Chain
+Hemoglobin_Beta_Chain pp Hemoglobin_Alpha_Chain
+Hemoglobin_Beta_Chain pp Hemoglobin_Alpha_Chain
+Hemoglobin_Alpha_Chain pp Hemoglobin_Alpha_Chain
+Hemoglobin_Beta_Chain pp Hemoglobin_Alpha_Chain
+Hemoglobin_Alpha_Chain pp Hemoglobin_Beta_Chain
+Hemoglobin_Beta_Chain pp Hemoglobin_Alpha_Chain
+F7 pp F7
+Hemoglobin_Beta_Chain pp Hemoglobin_Alpha_Chain
+Hemoglobin_Beta_Chain pp Hemoglobin_Alpha_Chain
+Hemoglobin_Alpha_Chain pp Hemoglobin_Beta_Chain
+Hemoglobin_Beta_Chain pp Hemoglobin_Alpha_Chain
+Hemoglobin_Beta_Chain pp Hemoglobin_Alpha_Chain
+Hemoglobin_Beta_Chain pp Hemoglobin_Alpha_Chain
+Hemoglobin_Beta_Chain pp Hemoglobin_Alpha_Chain
+Hemoglobin_Alpha_Chain pp Hemoglobin_Beta_Chain
+Hemoglobin_Beta_Chain pp Hemoglobin_Alpha_Chain
+GSTM1 pp GSTM1
+GSTM1 pp GSTM1
+HIP2 pp HIP2
+DPP4 pp DPP4
+DPP4 pp DPP4
+ADA pp DPP4
+Hemoglobin_Beta_Chain pp HBA2
+HBA2 pp Hemoglobin_Beta_Chain
+Hemoglobin_Beta_Chain pp HBA2
+Hemoglobin_Beta_Chain pp HBA2
+NR1I3 pp RXRA
+RXRA pp RXRA
+NR1I3 pp RXRA
+NR1I3 pp RXRA
+RXRA pp RXRA
+NR1I3 pp RXRA
+NEDD8 pp Sentrin-Specific_Protease_8
+GSTM1 pp GSTM1
+HBA2 pp ERAF
+Hemoglobin_Beta_Chain pp Hemoglobin_Alpha_Chain
+Hemoglobin_Alpha_Chain pp Hemoglobin_Beta_Chain
+Hemoglobin_Beta_Chain pp Hemoglobin_Alpha_Chain
+Hemoglobin_Alpha_Chain pp Hemoglobin_Beta_Chain
+Hemoglobin_Beta_Chain pp Hemoglobin_Alpha_Chain
+Hemoglobin_Alpha_Chain pp Hemoglobin_Beta_Chain
+Hemoglobin_Beta_Chain pp Hemoglobin_Alpha_Chain
+Hemoglobin_Beta_Chain pp Hemoglobin_Alpha_Chain
+Hemoglobin_Alpha_Chain pp Hemoglobin_Beta_Chain
+Hemoglobin_Alpha_Chain pp Hemoglobin_Beta_Chain
+HBA2 pp Hemoglobin_Beta_Chain
+Hemoglobin_Beta_Chain pp HBA2
+Hemoglobin_Beta_Chain pp HBA2
+HBA2 pp Hemoglobin_Beta_Chain
+Hemoglobin_Alpha_Chain pp Hemoglobin_Beta_Chain
+Hemoglobin_Beta_Chain pp Hemoglobin_Alpha_Chain
+Hemoglobin_Beta_Chain pp Hemoglobin_Alpha_Chain
+Hemoglobin_Beta_Chain pp Hemoglobin_Alpha_Chain
+Hemoglobin_Beta_Chain pp Hemoglobin_Alpha_Chain
+Hemoglobin_Beta_Chain pp Hemoglobin_Alpha_Chain
+Hemoglobin_Beta_Chain pp Hemoglobin_Alpha_Chain
+HSD17B4 pp HSD17B4
+IL1RAPL1 pp IL1RAPL1
+Fab_4e10 pp Fab_4e10
+PCNA pp FEN1
+AOC3 pp AOC3
+TK1 pp TK1
+TK1 pp TK1
+TK1 pp TK1
+MLC1SA pp MYO5A
+Insulin_B-Chain pp Insulin_A-Chain
+Insulin_B-Chain pp Insulin_A-Chain
+Insulin_B-Chain pp Insulin_B-Chain
+Insulin_B-Chain pp Insulin_A-Chain
+Insulin_B-Chain pp Insulin_B-Chain
+Insulin_B-Chain pp Insulin_A-Chain
+Insulin_A-Chain pp Insulin_B-Chain
+Insulin_A-Chain pp Insulin_B-Chain
+Insulin_B-Chain pp Insulin_A-Chain
+Insulin_B-Chain pp Insulin_B-Chain
+Insulin_B-Chain pp Insulin_B-Chain
+Insulin_A-Chain pp Insulin_B-Chain
+Insulin_B-Chain pp Insulin_A-Chain
+Insulin_B-Chain pp Insulin_A-Chain
+Insulin_B-Chain pp Insulin_A-Chain
+Insulin_B-Chain pp Insulin_B-Chain
+Insulin_B-Chain pp Insulin_B-Chain
+Insulin_B-Chain pp Insulin_B-Chain
+CCNE1 pp CDK2
+IGF1 pp IGFBP4
+ESR1 pp ESR1
+ALDOC pp ALDOC
+ALDOC pp ALDOC
+ALDOC pp ALDOC
+ALDOC pp ALDOC
+ALDOC pp ALDOC
+ALDOC pp ALDOC
+ALDOC pp ALDOC
+HSPA1B pp HSPBP1
+PDE4B pp PDE4B
+BAIAP2 pp BAIAP2
+SUMF2 pp SUMF2
+UBE1C pp UBE2M
+SPINT1 pp HGFAC
+GGA3 pp Ubiquin
+CD28 pp Fab_Fragment_Of_5.11a1_Antibody_Heavy_Chain
+CD28 pp Fab_Fragment_Of_5.11a1_Antibody_Light_Chain
+OLR1 pp OLR1
+OLR1 pp OLR1
+NR5A2 pp NR5A2
+SFN pp SFN
+SUMO1 pp HIP2
+PIM1 pp Consensus_Pim1_Peptide_Pimtide
+ESR1 pp ESR1
+SENP8 pp SENP8
+Interleukin-2 pp Interleukin-2
+DPP4 pp DPP4
+DPP4 pp DPP4
+DPP4 pp DPP4
+Camp-Dependent_Protein_Kinase_Inhibitor,_Alpha_Form pp PRKACA
+ICAM3 pp ITGAL
+F2 pp Prothrombin
+CLPP pp CLPP
+CLPP pp CLPP
+CLPP pp CLPP
+CLPP pp CLPP
+CLPP pp CLPP
+CLPP pp CLPP
+CLPP pp CLPP
+LIMS1 pp NCK2
+Insulin pp Insulin
+Camp-Dependent_Protein_Kinase_Inhibitor,_Alpha_Form pp PRKACA
+Butyrate_Response_Factor_2 pp Hla_Class_I_Histocompatibility_Antigen
+Butyrate_Response_Factor_2 pp Hla_Class_I_Histocompatibility_Antigen
+PARP1 pp PARP1
+PARP1 pp PARP1
+PARP1 pp PARP1
+PARP1 pp PARP1
+ALDOB pp ALDOB
+ALDOB pp ALDOB
+DCPS pp DCPS
+DCPS pp DCPS
+BACE1 pp BACE1
+BACE1 pp BACE1
+BACE1 pp BACE1
+BACE1 pp BACE1
+UCK2 pp UCK2
+C1orf16 pp C1orf16
+B2M pp HLA-G
+MAPRE1 pp MAPRE1
+PPIA pp PPIA
+UBE1C pp APPBP1
+STAT1 pp STAT1
+5-Residue_Peptide pp STAT1
+PECR pp PECR
+PECR pp PECR
+PECR pp PECR
+PECR pp PECR
+PECR pp PECR
+SFN pp SFN
+SPR pp SPR
+STK6 pp STK6
+Ig_Gamma-1_Chain_C_Region pp Ig_Gamma-1_Chain_C_Region
+9_Residue_Peptide pp Hla_Class_I_Histocompatibility_Antigen,_A-2_Alpha_Chain
+F2 pp Prothrombin
+Maguk_P55_Subfamily_Member_5 pp Maguk_P55_Subfamily_Member_5
+Hla_Class_Ii_Histocompatibility_Antigen,_Dr_Beta_Chain pp HLA-DRA
+T_Cell_Receptor_Alpha_Chain pp Hla_Class_Ii_Histocompatibility_Antigen,_Dr_Beta_Chain
+T-Cell_Receptor_Beta_Chain pp HLA-DRA
+T-Cell_Receptor_Beta_Chain pp T_Cell_Receptor_Alpha_Chain
+B2M pp HLA-E
+RPS27A pp PSMD4
+RPS27A pp PSMD4
+Antibody_17b_Heavy_Chain pp Antibody_17b_Light_Chain
+Antibody_17b_Heavy_Chain pp Antibody_17b_Light_Chain
+FAP pp FAP
+F7 pp F7
+F3 pp F7
+UHRF2 pp UHRF2
+Glutamate_Carboxypeptidase_Ii pp Glutamate_Carboxypeptidase_Ii
+HSD17B4 pp HSD17B4
+UBE2S pp UBE2S
+SRM pp SRM
+11-Mer_Peptide_From_C-Jun-Amino-Terminal_Kinase_Interacting_Protein_1 pp MAPK8
+11-Mer_Peptide_From_C-Jun-Amino-Terminal_Kinase_Interacting_Protein_1 pp MAPK8
+RNASE2 pp RNH1
+LXN pp CPA4
+CPA4 pp CPA4
+LXN pp CPA4
+F2 pp Thrombin_Light_Chain
+MURF-2 pp Nebulin
+MURF-2 pp Myotilin
+MURF-2 pp T-cap
+MURF-2 pp MLC-2
+MURF-2 pp TnI
+MURF-1 pp MLC-2
+MURF-1 pp MURF-1
+Rap1A pp Epac2
+Rap1A pp Repac
+Rap1A pp C3G
+Rap1A pp Epac1
+Miz1 pd DDB2_promoter
+c-Myc pd p53R2_promoter
+Miz1 pd p53R2_promoter
+c-Myc pd p21WAF1_promoter
+Miz1 pd NOXA_promoter
+c-Myc pd NOXA_promoter
+c-Myc pd DDB2_promoter
+BPGAP1 pp EEN
+L1-CAM pp TAG-1
+RALT pp ERBB2
+RALT interactsWith Unknown
+Unknown interactsWith ERBB3
+IKKbeta pp IKKalpha
+IKKbeta-IKKalpha_complex interactsWith IkappaBalpha
+Thy-1 interactsWith alphavbeta3_integrin
+APRIL pp BCMA
+CK2 pp Akt
+ARF-BP1 pp P53
+ARF-BP1 pp ARF-BP1
+ARF pp ARF-BP1
+Unknown interactsWith B23
+ARF interactsWith Unknown
+CK2_holoenzyme interactsWith Akt
+E2F4 pd RBL1_promoter
+E2F4 pd RB1_promoter
+E2F4 pd CDC2_promoter
+E2F4 pd CDC25A_promoter
+E2F4 pd CCNA2_promoter
+E2F4 pd E2F3_promoter
+E2F4 pd E2F2_promoter
+E2F4 pd CDK2_promoter
+E2F4 pd CKS1_promoter
+E2F4 pd POLA_promoter
+E2F4 pd ORC1L_promoter
+E2F4 pd MCM3_promoter
+E2F4 pd CDC6_promoter
+E2F4 pd RFC4_promoter
+E2F4 pd RFC3_promoter
+E2F4 pd PRIM2A_promoter
+E2F4 pd DUT_promoter
+E2F4 pd RRM1_promoter
+E2F4 pd MCM5_promoter
+E2F4 pd PCNA_promoter
+E2F4 pd TOP2A_promoter
+E2F4 pd RPA3_promoter
+E2F4 pd RFC2_promoter
+E2F4 pd POLA2_promoter
+E2F4 pd TK1_promoter
+E2F4 pd UMPS_promoter
+E2F4 pd MCM6_promoter
+E2F4 pd ASK_promoter
+E2F4 pd CHEK1_promoter
+E2F4 pd MAD2L1_promoter
+E2F4 pd BUB3_promoter
+E2F4 pd TP53_promoter
+E2F4 pd CENPE_promoter
+E2F4 pd TTK_promoter
+E2F4 pd UNG_promoter
+E2F4 pd CSTF1_promoter
+E2F4 pd RAD54L_promoter
+E2F4 pd PRKDC_promoter
+E2F4 pd MSH2_promoter
+E2F4 pd RAD51_promoter
+E2F4 pd POLD1_promoter
+E2F4 pd BARD1_promoter
+E2F4 pd MLH1_promoter
+E2F4 pd FEN1_promoter
+E2F4 pd SMC2L1_promoter
+E2F4 pd PTTG1_promoter
+E2F4 pd CENPA_promoter
+E2F4 pd SMC4L1_promoter
+E2F4 pd HMG1_promoter
+E2F4 pd H3FB_promoter
+E2F4 pd NAP1L4_promoter
+E2F4 pd H2AFX_promoter
+E2F4 pd H2AFZ_promoter
+E2F4 pd HEC_promoter
+E2F4 pd HMG4_promoter
+E2F4 pd SMARCA3_promoter
+E2F4 pd CBX5_promoter
+E2F4 pd SUPT4H1_promoter
+E2F4 pd H2BFQ_promoter
+E2F4 pd H2AFO_promoter
+E2F4 pd BRD2_promoter
+E2F4 pd H2AFL_promoter
+E2F4 pd PLK_promoter
+E2F4 pd PRC1_promoter
+E2F4 pd STK12_promoter
+E2F4 pd KNSL4_promoter
+E2F4 pd NEK2_promoter
+E2F4 pd KIF4A_promoter
+E2F4 pd HMMR_promoter
+E2F4 pd KIAA0101_promoter
+E2F4 pd MTHFD1_promoter
+E2F4 pd KIAA0186_promoter
+E2F4 pd SFPQ_promoter
+E2F4 pd TRA1_promoter
+E2F4 pd FLJ10287_promoter
+E2F4 pd MAP3K7_promoter
+E2F4 pd KIAA0923_promoter
+E2F4 pd ZNF267_promoter
+E2F4 pd PLSCR1_promoter
+E2F4 pd KIAA0092_promoter
+E2F4 pd PSA_promoter
+E2F4 pd LOC51154_promoter
+E2F4 pd LOC51278_promoter
+E2F4 pd FLJ10604_promoter
+E2F4 pd TMPO_promoter
+E2F4 pd PMSCL1_promoter
+E2F4 pd CALR_promoter
+E2F4 pd PRKCSH_promoter
+E2F4 pd TERA_promoter
+E2F4 pd NFE2L1_promoter
+E2F4 pd STAM_promoter
+E2F4 pd ANLN_promoter
+E2F4 pd LOC51234_promoter
+E2F4 pd MKI67_promoter
+E2F4 pd TRAF2_promoter
+E2F4 pd CALM2_promoter
+E2F4 pd SFRS2_promoter
+E2F4 pd CKS2_promoter
+E2F4 pd SAM68_promoter
+E2F4 pd ID3_promoter
+E2F4 pd TEAD4_promoter
+E2F4 pd OSR1_promoter
+E2F4 pd SRPR_promoter
+E2F4 pd PRKCL2_promoter
+E2F4 pd NCL_promoter
+E2F4 pd SLC3A2_promoter
+E2F4 pd TCEB1L_promoter
+E2F4 pd RABIF_promoter
+E2F4 pd HSPC150_promoter
+E2F4 pd EIF2B2_promoter
+E2F4 pd COX7C_promoter
+E2F4 pd FGF7_promoter
+E2F4 pd ZNF91_promoter
+E2F4 pd KIAA0426_promoter
+E2F4 pd FPGT_promoter
+E2F4 pd MYC_promoter
+E2F4 pd FDFT1_promoter
+E2F4 pd PPP2R2B_promoter
+E2F4 pd SRM300_promoter
+E2F4 pd PRPSAP1_promoter
+E2F4 pd AF093680_promoter
+E2F4 pd Jun_promoter
+E2F1 pd RBL1_promoter
+E2F1 pd RB1_promoter
+E2F1 pd CDC2_promoter
+E2F1 pd CDC25A_promoter
+E2F1 pd E2F3_promoter
+E2F1 pd POLA_promoter
+E2F1 pd MCM3_promoter
+E2F1 pd RFC4_promoter
+E2F1 pd RFC3_promoter
+E2F1 pd PRIM2A_promoter
+E2F1 pd DUT_promoter
+E2F1 pd RRM1_promoter
+E2F1 pd MCM5_promoter
+E2F1 pd PCNA_promoter
+E2F1 pd TOP2A_promoter
+E2F1 pd RPA3_promoter
+E2F1 pd RFC2_promoter
+E2F1 pd POLA2_promoter
+E2F1 pd UMPS_promoter
+E2F1 pd ASK_promoter
+E2F1 pd UNG_promoter
+E2F1 pd RAD54L_promoter
+E2F1 pd PRKDC_promoter
+E2F1 pd MSH2_promoter
+E2F1 pd MLH1_promoter
+E2F1 pd FEN1_promoter
+E2F1 pd SMC4L1_promoter
+E2F1 pd HMG1_promoter
+E2F1 pd HEC_promoter
+E2F1 pd SMARCA3_promoter
+E2F1 pd CBX5_promoter
+E2F1 pd H2AFO_promoter
+E2F1 pd H2AFL_promoter
+E2F1 pd KIAA0101_promoter
+E2F1 pd MTHFD1_promoter
+E2F1 pd KIAA0186_promoter
+E2F1 pd FLJ10287_promoter
+E2F1 pd PSA_promoter
+E2F1 pd PMSCL1_promoter
+E2F1 pd TERA_promoter
+E2F1 pd STAM_promoter
+E2F1 pd CALM2_promoter
+E2F1 pd SFRS2_promoter
+E2F1 pd ID3_promoter
+E2F1 pd OSR1_promoter
+E2F1 pd NCL_promoter
+E2F1 pd SLC3A2_promoter
+E2F1 pd MYC_promoter
+E2F1 pd PRPSAP1_promoter
+hNMT1 pp PRKACA
+p53 pp Mdm2
+Seladin-1 pp Mdm2
+Seladin-1 pp p53
+p8 pp p300
+TNF-R1 interactsWith Unknown
+Unknown interactsWith TRADD
+Unknown interactsWith TRAF2
+Unknown interactsWith cIAP1
+BMI1 pp BMI1
+RING1 pp BMI1
+RING1 pp RING1
+RING1 pp HPC2
+IKK-alpha pp TANK
+IKK-epsilon pp TANK
+IKK-alpha pp Cdc37
+IKK-beta pp Cdc37
+IQGAP1 pp CLIP-170
+APC pp Asef
+C-RAF pp PyK
+C-RAF pp Ha-Ras
+C-RAF pp 14-3-3-beta
+HLF pp Arnt
+HIF1-alpha pp Arnt
+Bax pp Bid
+Bid pp Bcl-2
+Bid pp Bcl-xL
+Bax pp Bcl-2
+Bax pp Bcl-xL
+Bax pp PUMA
+PUMA pp Bcl-2
+HIF1-alpha/Arnt interactsWith Epo_enhancer
+HLF/Arnt interactsWith Epo_enhancer
+A-RAF pp SGN3
+A-RAF pp TOPK/PBK
+A-RAF pp ASS
+A-RAF pp R-RAS
+A-RAF pp CPS1
+A-RAF pp TIMM44
+A-RAF pp TH1
+A-RAF pp RABGGT-beta
+Kap13 pp Pax3
+Kap13 pp Crx
+CLP-36 pp alpha-actinin_1
+CLP-36 pp alpha-actinin_4
+VEGF165 pp KDR
+VEGF165 pp Flt-1
+VEGF165 pp neuropilin-1
+CIN85 pp Cbl
+CIN85 pp endophilin_A1
+SNAP43 interactsWith Unknown
+MKK7 pp JNK1
+MKK4 pp JNK1
+Importin-beta interactsWith Unknown
+Unknown interactsWith RAN
+Unknown interactsWith RANBP1
+Unknown interactsWith SNAP190
+Unknown interactsWith SNAP19
+HIRA pp ASF1a
+IKK-gamma pp TANK
+DNMT3B pp hSNF2H
+DNMT3B pp HDAC2
+DNMT3B pp HDAC1
+DNMT3B pp DNMT1
+DNMT3B pp HP1-alpha
+DNMT3B pp HP1-beta
+DNMT3B pp HP1-gamma
+Gab2_promoter pd E2F3
+Gab2_promoter pd E2F2
+Gab2_promoter pd E2F1
+CLP-36 pp CLIK1
+CLIK1 pp CLIK1
+Parc pp p53
+iASPP pp p53
+HDM-2 pp p53
+Endophilin_A3 pp CIN85
+Endophilin_A2 pp CIN85
+E2F4 pd ABCB6_promoter
+E2F4 pd ACTA2_promoter
+E2F4 pd ADSS_promoter
+E2F4 pd AF15Q14_promoter
+E2F4 pd AK2_promoter
+E2F4 pd NUSAP1_promoter
+E2F4 pd ANLN_promoter
+E2F4 pd ANP32E_promoter
+E2F4 pd AP4B1_promoter
+E2F4 pd ARHGAP11A_promoter
+E2F4 pd ASF1B_promoter
+E2F4 pd ASH2L_promoter
+E2F4 pd ATF2_promoter
+E2F4 pd ATM_promoter
+E2F4 pd BAZ1B_promoter
+E2F4 pd BIRC5_promoter
+E2F4 pd BLM_promoter
+E2F4 pd BMI1_promoter
+E2F4 pd BRCA1_promoter
+E2F4 pd BRIP1_promoter
+E2F4 pd BRIX_promoter
+E2F4 pd BUB1B_promoter
+E2F4 pd C11orf10_promoter
+E2F4 pd C14orf106_promoter
+E2F4 pd C20orf172_promoter
+E2F4 pd C20orf77_promoter
+E2F4 pd C21orf45_promoter
+E2F4 pd C6orf166_promoter
+E2F4 pd C6orf18_promoter
+E2F4 pd C9orf5_promoter
+E2F4 pd CASP8AP2_promoter
+E2F4 pd CBX3_promoter
+E2F4 pd CBX5_promoter
+E2F4 pd CCNA2_promoter
+E2F4 pd CCNB1_promoter
+E2F4 pd CCNB2_promoter
+E2F4 pd CCNG2_promoter
+E2F4 pd CDC23_promoter
+E2F4 pd CDC25A_promoter
+E2F4 pd CDC25B_promoter
+E2F4 pd CDC25C_promoter
+E2F4 pd CDC45L_promoter
+E2F4 pd CDC6_promoter
+E2F4 pd CDC7_promoter
+E2F4 pd CDCA1_promoter
+E2F4 pd CDCA3_promoter
+E2F4 pd CDCA7_promoter
+E2F4 pd CDCA8_promoter
+E2F4 pd CENPA_promoter
+E2F4 pd CENPE_promoter
+E2F4 pd CENPF_promoter
+E2F4 pd CENPH_promoter
+E2F4 pd CETN1_promoter
+E2F4 pd CGI-09_promoter
+E2F4 pd CGI-100_promoter
+E2F4 pd CGI-121_promoter
+E2F4 pd CGI-141_promoter
+E2F4 pd CHEK2_promoter
+E2F4 pd CKS2_promoter
+E2F4 pd CLSPN_promoter
+E2F4 pd CNOT3_promoter
+E2F4 pd CNOT4_promoter
+E2F4 pd COPS7B_promoter
+E2F4 pd COX8_promoter
+E2F4 pd CSPG6_promoter
+E2F4 pd CSTF1_promoter
+E2F4 pd CSTF2T_promoter
+E2F4 pd CSTF3_promoter
+E2F4 pd CYB5-M_promoter
+E2F4 pd DC13_promoter
+E2F4 pd DCLRE1B_promoter
+E2F4 pd DCLRE1C_promoter
+E2F4 pd DDA3_promoter
+E2F4 pd DDX10_promoter
+E2F4 pd DDX21_promoter
+E2F4 pd DHX35_promoter
+E2F4 pd DKFZP434B168_promoter
+E2F4 pd DKFZP434C245_promoter
+E2F4 pd DKFZP434G2226_promoter
+E2F4 pd DKFZp566O084_promoter
+E2F4 pd DLG7_promoter
+E2F4 pd DMTF1_promoter
+E2F4 pd E2F3_promoter
+E2F4 pd E2IG2_promoter
+E2F4 pd ELP4_promoter
+E2F4 pd EPM2AIP1_promoter
+E2F4 pd EXO1_promoter
+E2F4 pd F12_promoter
+E2F4 pd FANCD2_promoter
+E2F4 pd FBXO8_promoter
+E2F4 pd FEN1_promoter
+E2F4 pd FGF22_promoter
+E2F4 pd FLJ10156_promoter
+E2F4 pd FLJ10287_promoter
+E2F4 pd FLJ10407_promoter
+E2F4 pd FLJ10539_promoter
+E2F4 pd FLJ10853_promoter
+E2F4 pd FLJ10922_promoter
+E2F4 pd FLJ10998_promoter
+E2F4 pd FLJ11029_promoter
+E2F4 pd C18orf9_promoter
+E2F4 pd FLJ12606_promoter
+E2F4 pd FLJ12735_promoter
+E2F4 pd FLJ13215_promoter
+E2F4 pd FLJ13912_promoter
+E2F4 pd MASTL_promoter
+E2F4 pd FLJ20084_promoter
+E2F4 pd FLJ20156_promoter
+E2F4 pd FGIF_promoter
+E2F4 pd DEPDC1_promoter
+E2F4 pd FLJ20508_promoter
+E2F4 pd FLJ20641_promoter
+E2F4 pd FLJ22688_promoter
+E2F4 pd C15orf20_promoter
+E2F4 pd FLJ22875_promoter
+E2F4 pd KLIP1_promoter
+E2F4 pd FNTB_promoter
+E2F4 pd FTSJ2_promoter
+E2F4 pd GAJ_promoter
+E2F4 pd GALNACT-2_promoter
+E2F4 pd GRIN2D_promoter
+E2F4 pd GTL3_promoter
+E2F4 pd GTSE1_promoter
+E2F4 pd GZMA_promoter
+E2F4 pd HCAP-G_promoter
+E2F4 pd KNTC2_promoter
+E2F4 pd HIST1H2AG_promoter
+E2F4 pd HIST1H2AI_promoter
+E2F4 pd HIST1H2AJ_promoter
+E2F4 pd HIST1H2AL_promoter
+E2F4 pd HIST1H2BJ_promoter
+E2F4 pd HIST1H2BK_promoter
+E2F4 pd HIST1H2BL_promoter
+E2F4 pd HIST1H2BM_promoter
+E2F4 pd HIST1H2BN_promoter
+E2F4 pd HIST1H3B_promoter
+E2F4 pd HIST1H3C_promoter
+E2F4 pd HIST1H3D_promoter
+E2F4 pd HIST1H3F_promoter
+E2F4 pd HIST1H3G_promoter
+E2F4 pd HIST2H4_promoter
+E2F4 pd HNRPA2B1_promoter
+E2F4 pd HSPC129_promoter
+E2F4 pd HSPC148_promoter
+E2F4 pd HSPC150_promoter
+E2F4 pd HSU79274_promoter
+E2F4 pd HUMGT198A_promoter
+E2F4 pd IER5_promoter
+E2F4 pd INCENP_promoter
+E2F4 pd IRF3_promoter
+E2F4 pd ITGB3BP_promoter
+E2F4 pd KIAA0092_promoter
+E2F4 pd KIAA0101_promoter
+E2F4 pd KIAA0186_promoter
+E2F4 pd USP52_promoter
+E2F4 pd KIF14_promoter
+E2F4 pd KIF20A_promoter
+E2F4 pd KIF22_promoter
+E2F4 pd KIF2C_promoter
+E2F4 pd KIF4A_promoter
+E2F4 pd KNSL7_promoter
+E2F4 pd KPNB1_promoter
+E2F4 pd LOC115648_promoter
+E2F4 pd UCHL5_promoter
+E2F4 pd CHCHD2_promoter
+E2F4 pd LOC51248_promoter
+E2F4 pd LOC56902_promoter
+E2F4 pd THAP10_promoter
+E2F4 pd OSGEPL1_promoter
+E2F4 pd LOC81691_promoter
+E2F4 pd LSM3_promoter
+E2F4 pd LSM4_promoter
+E2F4 pd LSM5_promoter
+E2F4 pd M17S2_promoter
+E2F4 pd M96_promoter
+E2F4 pd MAD2L1_promoter
+E2F4 pd MAP3K7_promoter
+E2F4 pd MBC2_promoter
+E2F4 pd MCM3_promoter
+E2F4 pd MCM6_promoter
+E2F4 pd MCM8_promoter
+E2F4 pd MDH1_promoter
+E2F4 pd MELK_promoter
+E2F4 pd METTL2_promoter
+E2F4 pd MGC13183_promoter
+E2F4 pd MGC14386_promoter
+E2F4 pd BMSC-UbP_promoter
+E2F4 pd MGC16733_promoter
+E2F4 pd MGC16943_promoter
+E2F4 pd ZNF486_promoter
+E2F4 pd ALG8_promoter
+E2F4 pd MGC4308_promoter
+E2F4 pd MGC4771_promoter
+E2F4 pd MGC5528_promoter
+E2F4 pd MGC9084_promoter
+E2F4 pd MIS12_promoter
+E2F4 pd MNS1_promoter
+E2F4 pd MPHOSPH1_promoter
+E2F4 pd MRE11A_promoter
+E2F4 pd MRP63_promoter
+E2F4 pd MRPL27_promoter
+E2F4 pd MRPL37_promoter
+E2F4 pd MRPL46_promoter
+E2F4 pd MRPS11_promoter
+E2F4 pd MSH2_promoter
+E2F4 pd MTAP_promoter
+E2F4 pd NUDT15_promoter
+E2F4 pd MTHFD1_promoter
+E2F4 pd MUT_promoter
+E2F4 pd MYC_promoter
+E2F4 pd NBR2_promoter
+E2F4 pd NEK2_promoter
+E2F4 pd NEK7_promoter
+E2F4 pd NOLC1_promoter
+E2F4 pd NUDT2_promoter
+E2F4 pd NUDT6_promoter
+E2F4 pd NUP107_promoter
+E2F4 pd ORC3L_promoter
+E2F4 pd ORC6L_promoter
+E2F4 pd ORMDL2_promoter
+E2F4 pd CTDSP2_promoter
+E2F4 pd PCNA_promoter
+E2F4 pd PCNT2_promoter
+E2F4 pd PCSK1N_promoter
+E2F4 pd FANCL_promoter
+E2F4 pd PIGN_promoter
+E2F4 pd PIR51_promoter
+E2F4 pd PLAA_promoter
+E2F4 pd PLK1_promoter
+E2F4 pd POLA_promoter
+E2F4 pd POLR2J_promoter
+E2F4 pd POLR2K_promoter
+E2F4 pd PRC1_promoter
+E2F4 pd PRIM2A_promoter
+E2F4 pd PTTG1_promoter
+E2F4 pd PXF_promoter
+E2F4 pd RAD51_promoter
+E2F4 pd RAD54B_promoter
+E2F4 pd RAM2_promoter
+E2F4 pd RAMP_promoter
+E2F4 pd RBL1_promoter
+E2F4 pd RBM15_promoter
+E2F4 pd RECQL_promoter
+E2F4 pd RFC3_promoter
+E2F4 pd RFC5_promoter
+E2F4 pd RNF26_promoter
+E2F4 pd RNF5_promoter
+E2F4 pd RPS20_promoter
+E2F4 pd RQCD1_promoter
+E2F4 pd RRM1_promoter
+E2F4 pd SFPQ_promoter
+E2F4 pd SFRS1_promoter
+E2F4 pd SFRS2_promoter
+E2F4 pd SIL_promoter
+E2F4 pd SLC25A14_promoter
+E2F4 pd SMAP_promoter
+E2F4 pd SMC4L1_promoter
+E2F4 pd SNIP1_promoter
+E2F4 pd SNRPA_promoter
+E2F4 pd SNRPD2_promoter
+E2F4 pd SNX1_promoter
+E2F4 pd SNX5_promoter
+E2F4 pd SRPR_promoter
+E2F4 pd SSA2_promoter
+E2F4 pd SAT2_promoter
+E2F4 pd STCH_promoter
+E2F4 pd PLK4_promoter
+E2F4 pd STOML2_promoter
+E2F4 pd SUCLG1_promoter
+E2F4 pd SULT1A3_promoter
+E2F4 pd TAF11_promoter
+E2F4 pd TCERG1_promoter
+E2F4 pd TCF19_promoter
+E2F4 pd TCP1_promoter
+E2F4 pd TERF1_promoter
+E2F4 pd TIMELESS_promoter
+E2F4 pd TIMM23_promoter
+E2F4 pd TIMM8A_promoter
+E2F4 pd TMPO_promoter
+E2F4 pd TOE1_promoter
+E2F4 pd TOP1_promoter
+E2F4 pd TOP2A_promoter
+E2F4 pd TOPBP1_promoter
+E2F4 pd TOPK_promoter
+E2F4 pd TRA1_promoter
+E2F4 pd TRIP_promoter
+E2F4 pd TROAP_promoter
+E2F4 pd TTF2_promoter
+E2F4 pd TYMS_promoter
+E2F4 pd UBL1_promoter
+E2F4 pd USP1_promoter
+E2F4 pd USP5_promoter
+E2F4 pd VPS35_promoter
+E2F4 pd VPS45A_promoter
+E2F4 pd VRK3_promoter
+E2F4 pd XRCC2_promoter
+E2F4 pd XRCC4_promoter
+E2F4 pd ZNF254_promoter
+E2F4 pd ZNF300_promoter
+E2F4 pd ZNF85_promoter
+E2F4 pd ZWINT_promoter
+p130 pd ABCB6_promoter
+p130 pd ACTA2_promoter
+p130 pd ADSS_promoter
+p130 pd AF15Q14_promoter
+p130 pd AGA_promoter
+p130 pd AK2_promoter
+p130 pd AKR1B1_promoter
+p130 pd WDHD1_promoter
+p130 pd NUSAP1_promoter
+p130 pd ANP32E_promoter
+p130 pd AP4B1_promoter
+p130 pd ARHGAP11A_promoter
+p130 pd ASF1B_promoter
+p130 pd ASH2L_promoter
+p130 pd ATF2_promoter
+p130 pd ATM_promoter
+p130 pd BAZ1B_promoter
+p130 pd BIRC5_promoter
+p130 pd BLM_promoter
+p130 pd BMI1_promoter
+p130 pd BRCA1_promoter
+p130 pd BRIP1_promoter
+p130 pd BRIX_promoter
+p130 pd BUB1B_promoter
+p130 pd BUB3_promoter
+p130 pd C11orf10_promoter
+p130 pd C14orf106_promoter
+p130 pd C20orf172_promoter
+p130 pd C20orf72_promoter
+p130 pd C20orf77_promoter
+p130 pd C21orf45_promoter
+p130 pd C6orf166_promoter
+p130 pd C6orf18_promoter
+p130 pd C9orf5_promoter
+p130 pd CBX3_promoter
+p130 pd CBX5_promoter
+p130 pd CCNA2_promoter
+p130 pd CCNB1_promoter
+p130 pd CCNB2_promoter
+p130 pd CCNG2_promoter
+p130 pd CDC2_promoter
+p130 pd CDC23_promoter
+p130 pd CDC25A_promoter
+p130 pd CDC25B_promoter
+p130 pd CDC25C_promoter
+p130 pd CDC45L_promoter
+p130 pd CDC6_promoter
+p130 pd CDC7_promoter
+p130 pd CDCA1_promoter
+p130 pd CDCA3_promoter
+p130 pd CDCA7_promoter
+p130 pd CDCA8_promoter
+p130 pd CENPA_promoter
+p130 pd CENPE_promoter
+p130 pd CENPF_promoter
+p130 pd CENPH_promoter
+p130 pd CETN1_promoter
+p130 pd CGI-09_promoter
+p130 pd CGI-100_promoter
+p130 pd CGI-121_promoter
+p130 pd CGI-141_promoter
+p130 pd CHEK2_promoter
+p130 pd CIP29_promoter
+p130 pd CKS2_promoter
+p130 pd CLSPN_promoter
+p130 pd CNOT4_promoter
+p130 pd COPS7B_promoter
+p130 pd COX8_promoter
+p130 pd CSPG6_promoter
+p130 pd CSTF1_promoter
+p130 pd CSTF3_promoter
+p130 pd CYB5-M_promoter
+p130 pd DC13_promoter
+p130 pd DC8_promoter
+p130 pd DCK_promoter
+p130 pd DCLRE1B_promoter
+p130 pd DCLRE1C_promoter
+p130 pd DCPS_promoter
+p130 pd DDA3_promoter
+p130 pd DDX10_promoter
+p130 pd DDX21_promoter
+p130 pd DHPS_promoter
+p130 pd DHX35_promoter
+p130 pd DKFZP434B168_promoter
+p130 pd DKFZP434C245_promoter
+p130 pd DKFZP434G2226_promoter
+p130 pd DKFZP547N043_promoter
+p130 pd DKFZP564M082_promoter
+p130 pd DKFZp566O084_promoter
+p130 pd DLG7_promoter
+p130 pd DMTF1_promoter
+p130 pd E2F2_promoter
+p130 pd E2F3_promoter
+p130 pd E2IG2_promoter
+p130 pd EED_promoter
+p130 pd ELP4_promoter
+p130 pd EPM2AIP1_promoter
+p130 pd EXO1_promoter
+p130 pd FANCD2_promoter
+p130 pd FBXO8_promoter
+p130 pd FEN1_promoter
+p130 pd FGF22_promoter
+p130 pd FLJ10156_promoter
+p130 pd FLJ10287_promoter
+p130 pd FLJ10407_promoter
+p130 pd FLJ10539_promoter
+p130 pd FLJ10581_promoter
+p130 pd FLJ10853_promoter
+p130 pd FLJ10858_promoter
+p130 pd FLJ10922_promoter
+p130 pd FLJ10998_promoter
+p130 pd FLJ11029_promoter
+p130 pd FLJ11193_promoter
+p130 pd FLJ11526_promoter
+p130 pd FLJ11848_promoter
+p130 pd C18orf9_promoter
+p130 pd FLJ12606_promoter
+p130 pd FLJ12735_promoter
+p130 pd FLJ12788_promoter
+p130 pd FLJ12886_promoter
+p130 pd C9orf76_promoter
+p130 pd FLJ13215_promoter
+p130 pd FLJ13621_promoter
+p130 pd FLJ13912_promoter
+p130 pd FLJ14451_promoter
+p130 pd MASTL_promoter
+p130 pd FLJ20084_promoter
+p130 pd FLJ20156_promoter
+p130 pd FGIF_promoter
+p130 pd DEPDC1_promoter
+p130 pd FLJ20508_promoter
+p130 pd FLJ20641_promoter
+p130 pd FLJ22688_promoter
+p130 pd C15orf20_promoter
+p130 pd KLIP1_promoter
+p130 pd FTSJ2_promoter
+p130 pd GAJ_promoter
+p130 pd GAPD_promoter
+p130 pd GBF1_promoter
+p130 pd GRIN2D_promoter
+p130 pd GSG2_promoter
+p130 pd GTL3_promoter
+p130 pd GTSE1_promoter
+p130 pd GZMA_promoter
+p130 pd H17_promoter
+p130 pd HCAP-G_promoter
+p130 pd KNTC2_promoter
+p130 pd HIST1H2AD_promoter
+p130 pd HIST1H2AE_promoter
+p130 pd HIST1H2AG_promoter
+p130 pd HIST1H2AH_promoter
+p130 pd HIST1H2AI_promoter
+p130 pd HIST1H2AJ_promoter
+p130 pd HIST1H2AK_promoter
+p130 pd HIST1H2AL_promoter
+p130 pd HIST1H2AM_promoter
+p130 pd HIST1H2BF_promoter
+p130 pd HIST1H2BG_promoter
+p130 pd HIST1H2BJ_promoter
+p130 pd HIST1H2BK_promoter
+p130 pd HIST1H2BL_promoter
+p130 pd HIST1H2BM_promoter
+p130 pd HIST1H2BN_promoter
+p130 pd HIST1H2BO_promoter
+p130 pd HIST1H3B_promoter
+p130 pd HIST1H3C_promoter
+p130 pd HIST1H3D_promoter
+p130 pd HIST1H3F_promoter
+p130 pd HIST1H3G_promoter
+p130 pd HIST1H3H_promoter
+p130 pd HIST1H3I_promoter
+p130 pd HIST2H2AA_promoter
+p130 pd HIST2H4_promoter
+p130 pd HIST3H2A_promoter
+p130 pd HNRPA2B1_promoter
+p130 pd HPCL2_promoter
+p130 pd PRPF3_promoter
+p130 pd HSPC129_promoter
+p130 pd HSPC148_promoter
+p130 pd HSPC150_promoter
+p130 pd HSU79274_promoter
+p130 pd HUMGT198A_promoter
+p130 pd IER5_promoter
+p130 pd INCENP_promoter
+p130 pd IRF3_promoter
+p130 pd ITGB3BP_promoter
+p130 pd KIAA0092_promoter
+p130 pd KIAA0101_promoter
+p130 pd KIAA0186_promoter
+p130 pd KIAA0907_promoter
+p130 pd KIF14_promoter
+p130 pd KIF20A_promoter
+p130 pd KIF22_promoter
+p130 pd KIF2C_promoter
+p130 pd KIF4A_promoter
+p130 pd KNSL7_promoter
+p130 pd KPNB1_promoter
+p130 pd LOC115648_promoter
+p130 pd UCHL5_promoter
+p130 pd CHCHD2_promoter
+p130 pd LOC51248_promoter
+p130 pd LOC56902_promoter
+p130 pd THAP10_promoter
+p130 pd OSGEPL1_promoter
+p130 pd LOC81691_promoter
+p130 pd LSM3_promoter
+p130 pd LSM4_promoter
+p130 pd LSM5_promoter
+p130 pd M17S2_promoter
+p130 pd M96_promoter
+p130 pd MAD2L1_promoter
+p130 pd MAP3K7_promoter
+p130 pd MCM3_promoter
+p130 pd MCM6_promoter
+p130 pd MCM8_promoter
+p130 pd MDH1_promoter
+p130 pd MELK_promoter
+p130 pd METTL2_promoter
+p130 pd MFAP1_promoter
+p130 pd MGC11266_promoter
+p130 pd MGC13017_promoter
+p130 pd MGC13183_promoter
+p130 pd MGC14386_promoter
+p130 pd BMSC-UbP_promoter
+p130 pd MGC14799_promoter
+p130 pd MGC16943_promoter
+p130 pd ZNF486_promoter
+p130 pd MGC2603_promoter
+p130 pd MGC2731_promoter
+p130 pd ALG8_promoter
+p130 pd MGC3248_promoter
+p130 pd MGC4308_promoter
+p130 pd MGC4771_promoter
+p130 pd MGC5528_promoter
+p130 pd MGC9084_promoter
+p130 pd MIS12_promoter
+p130 pd MLH1_promoter
+p130 pd MNS1_promoter
+p130 pd MPHOSPH1_promoter
+p130 pd MRE11A_promoter
+p130 pd MRP63_promoter
+p130 pd MRPL18_promoter
+p130 pd MRPL27_promoter
+p130 pd MRPL37_promoter
+p130 pd MRPL46_promoter
+p130 pd MRPL51_promoter
+p130 pd MRPS11_promoter
+p130 pd MSH2_promoter
+p130 pd MTAP_promoter
+p130 pd NUDT15_promoter
+p130 pd MTHFD1_promoter
+p130 pd MTR_promoter
+p130 pd MUT_promoter
+p130 pd NBR2_promoter
+p130 pd NEK2_promoter
+p130 pd NOLC1_promoter
+p130 pd NPAT_promoter
+p130 pd NUDT2_promoter
+p130 pd NUDT6_promoter
+p130 pd NUP107_promoter
+p130 pd ORC1L_promoter
+p130 pd ORC3L_promoter
+p130 pd ORC6L_promoter
+p130 pd CTDSP2_promoter
+p130 pd PAF53_promoter
+p130 pd PAI-RBP1_promoter
+p130 pd PAK4_promoter
+p130 pd PCNA_promoter
+p130 pd PCNT1_promoter
+p130 pd PCNT2_promoter
+p130 pd PCSK1N_promoter
+p130 pd PDE6D_promoter
+p130 pd PELO_promoter
+p130 pd FANCL_promoter
+p130 pd PIGN_promoter
+p130 pd PIR51_promoter
+p130 pd PLAA_promoter
+p130 pd PLK1_promoter
+p130 pd POLA_promoter
+p130 pd POLR2J_promoter
+p130 pd POLR2K_promoter
+p130 pd POLR3K_promoter
+p130 pd PPP5C_promoter
+p130 pd PRC1_promoter
+p130 pd PRIM2A_promoter
+p130 pd PTTG1_promoter
+p130 pd PXF_promoter
+p130 pd RAD51_promoter
+p130 pd RAD54B_promoter
+p130 pd RAM2_promoter
+p130 pd RAMP_promoter
+p130 pd RANGAP1_promoter
+p130 pd RBL1_promoter
+p130 pd RBM15_promoter
+p130 pd RECQL_promoter
+p130 pd RFC3_promoter
+p130 pd RFC5_promoter
+p130 pd RNF26_promoter
+p130 pd RNF5_promoter
+p130 pd RNPC2_promoter
+p130 pd RPA2_promoter
+p130 pd RPS20_promoter
+p130 pd RQCD1_promoter
+p130 pd RRM1_promoter
+p130 pd SDCCAG10_promoter
+p130 pd SFPQ_promoter
+p130 pd SFRS1_promoter
+p130 pd SFRS11_promoter
+p130 pd SFRS2_promoter
+p130 pd SIL_promoter
+p130 pd SLC25A14_promoter
+p130 pd SLC31A1_promoter
+p130 pd SMAP_promoter
+p130 pd SMC2L1_promoter
+p130 pd SMC4L1_promoter
+p130 pd SMC6L1_promoter
+p130 pd SNRPA_promoter
+p130 pd SNRPD2_promoter
+p130 pd SRPR_promoter
+p130 pd SSA2_promoter
+p130 pd SAT2_promoter
+p130 pd STCH_promoter
+p130 pd PLK4_promoter
+p130 pd STOML2_promoter
+p130 pd SUCLG1_promoter
+p130 pd SULT1A3_promoter
+p130 pd TAF11_promoter
+p130 pd TCERG1_promoter
+p130 pd TCF19_promoter
+p130 pd TCP1_promoter
+p130 pd TERF1_promoter
+p130 pd THOC1_promoter
+p130 pd THOC3_promoter
+p130 pd TIMELESS_promoter
+p130 pd TIMM23_promoter
+p130 pd TIMM8A_promoter
+p130 pd TMPO_promoter
+p130 pd TOE1_promoter
+p130 pd TOP1_promoter
+p130 pd TOP2A_promoter
+p130 pd TOPBP1_promoter
+p130 pd TOPK_promoter
+p130 pd TRA1_promoter
+p130 pd TRIM4_promoter
+p130 pd TRIP_promoter
+p130 pd TROAP_promoter
+p130 pd TTF2_promoter
+p130 pd TYMS_promoter
+p130 pd UBL1_promoter
+p130 pd UMPS_promoter
+p130 pd USP1_promoter
+p130 pd USP5_promoter
+p130 pd VPS29_promoter
+p130 pd VPS35_promoter
+p130 pd VPS45A_promoter
+p130 pd VRK3_promoter
+p130 pd XRCC4_promoter
+p130 pd ZDHHC12_promoter
+p130 pd ZNF254_promoter
+p130 pd ZNF300_promoter
+p130 pd ZNF443_promoter
+p130 pd ZNF331_promoter
+p130 pd ZNF85_promoter
+p130 pd ZWINT_promoter
+E2F4 pd BUB3_promoter
+E2F4 pd C12orf8_promoter
+E2F4 pd DHPS_promoter
+E2F4 pd DKFZP564M082_promoter
+E2F4 pd DNAJB11_promoter
+E2F4 pd E2F2_promoter
+E2F4 pd EBP_promoter
+E2F4 pd FDXR_promoter
+E2F4 pd FLJ12525_promoter
+E2F4 pd C9orf76_promoter
+E2F4 pd HINT3_promoter
+E2F4 pd HIST1H2AD_promoter
+E2F4 pd HIST1H2AH_promoter
+E2F4 pd HIST1H2AK_promoter
+E2F4 pd HIST1H2AM_promoter
+E2F4 pd HIST1H2BF_promoter
+E2F4 pd HIST1H2BO_promoter
+E2F4 pd HIST1H3H_promoter
+E2F4 pd HIST1H3I_promoter
+E2F4 pd HIST2H2AA_promoter
+E2F4 pd HNRPA1_promoter
+E2F4 pd HT007_promoter
+E2F4 pd KIAA0433_promoter
+E2F4 pd HSRG1_promoter
+E2F4 pd LOC81558_promoter
+E2F4 pd MGC11266_promoter
+E2F4 pd MGC14799_promoter
+E2F4 pd MGST3_promoter
+E2F4 pd MLH1_promoter
+E2F4 pd NFYA_promoter
+E2F4 pd NPAT_promoter
+E2F4 pd ORC1L_promoter
+E2F4 pd PDE6D_promoter
+E2F4 pd POLR3K_promoter
+E2F4 pd PSMA1_promoter
+E2F4 pd RANGAP1_promoter
+E2F4 pd SMC2L1_promoter
+E2F4 pd THRAP6_promoter
+E2F4 pd VPS29_promoter
+E2F4 pd ZHX2_promoter
+E2F4 pd ZNF267_promoter
+E2F4 pd ZNF331_promoter
+p130 pd Spc25_promoter
+p130 pd APBB3_promoter
+p130 pd CNOT3_promoter
+p130 pd CSTF2T_promoter
+p130 pd DBN1_promoter
+p130 pd AATF_promoter
+p130 pd DKFZP434F0318_promoter
+p130 pd F12_promoter
+p130 pd FLJ11712_promoter
+p130 pd FLJ13273_promoter
+p130 pd FLJ14803_promoter
+p130 pd FLJ22875_promoter
+p130 pd FNTB_promoter
+p130 pd GALNACT-2_promoter
+p130 pd HINT3_promoter
+p130 pd HIST1H2AC_promoter
+p130 pd HIST1H2BB_promoter
+p130 pd HIST1H2BD_promoter
+p130 pd HIST1H2BE_promoter
+p130 pd HIST1H2BH_promoter
+p130 pd HIST1H3A_promoter
+p130 pd HIST1H3E_promoter
+p130 pd HIST1H4D_promoter
+p130 pd HIST1H4K_promoter
+p130 pd HIST1H4L_promoter
+p130 pd HIST3H3_promoter
+p130 pd KCNA10_promoter
+p130 pd HSRG1_promoter
+p130 pd LOC81558_promoter
+p130 pd MGC16733_promoter
+p130 pd MGC19595_promoter
+p130 pd MGST3_promoter
+p130 pd MYC_promoter
+p130 pd NEK7_promoter
+p130 pd NFYA_promoter
+p130 pd ORMDL2_promoter
+p130 pd PLSCR1_promoter
+p130 pd PRKDC_promoter
+p130 pd PRKWNK1_promoter
+p130 pd PSMA1_promoter
+p130 pd SUV39H1_promoter
+p130 pd UBE2C_promoter
+p130 pd XPC_promoter
+E2F4 pd Spc25_promoter
+E2F4 pd WDHD1_promoter
+E2F4 pd C20orf72_promoter
+E2F4 pd CYP51A1_promoter
+E2F4 pd DCK_promoter
+E2F4 pd FANCG_promoter
+E2F4 pd C9orf40_promoter
+E2F4 pd FLJ10858_promoter
+E2F4 pd FLJ11193_promoter
+E2F4 pd FLJ11712_promoter
+E2F4 pd FLJ12788_promoter
+E2F4 pd FLJ12886_promoter
+E2F4 pd FLJ13273_promoter
+E2F4 pd FLJ13621_promoter
+E2F4 pd FLJ14642_promoter
+E2F4 pd FLJ20628_promoter
+E2F4 pd FLJ20701_promoter
+E2F4 pd FTHL17_promoter
+E2F4 pd GAPD_promoter
+E2F4 pd GPHN_promoter
+E2F4 pd HRB2_promoter
+E2F4 pd LOC129401_promoter
+E2F4 pd LRP6_promoter
+E2F4 pd MFAP1_promoter
+E2F4 pd MGC10433_promoter
+E2F4 pd MGC2603_promoter
+E2F4 pd MGC3130_promoter
+E2F4 pd MRPL18_promoter
+E2F4 pd MSH5_promoter
+E2F4 pd MTR_promoter
+E2F4 pd NEU1_promoter
+E2F4 pd PAF53_promoter
+E2F4 pd PC-LKC_promoter
+E2F4 pd PCNT1_promoter
+E2F4 pd PLSCR1_promoter
+E2F4 pd PPM1D_promoter
+E2F4 pd PPP5C_promoter
+E2F4 pd PTK7_promoter
+E2F4 pd RIN3_promoter
+E2F4 pd RPA2_promoter
+E2F4 pd RPL39L_promoter
+E2F4 pd SBZF3_promoter
+E2F4 pd SDCCAG10_promoter
+E2F4 pd SFRP5_promoter
+E2F4 pd SMC6L1_promoter
+E2F4 pd THOC1_promoter
+E2F4 pd TUBA2_promoter
+E2F4 pd UMPS_promoter
+E2F4 pd ZDHHC12_promoter
+E2F4 pd ZNF214_promoter
+E2F4 pd ZNF215_promoter
+p130 pd APEX1_promoter
+p130 pd BCAS2_promoter
+p130 pd CASP8AP2_promoter
+p130 pd CTSL2_promoter
+p130 pd CYP51A1_promoter
+p130 pd EBP_promoter
+p130 pd FANCG_promoter
+p130 pd C9orf40_promoter
+p130 pd FLJ14642_promoter
+p130 pd FLJ20628_promoter
+p130 pd NES_promoter
+p130 pd FLJ21977_promoter
+p130 pd FGFR1OP_promoter
+p130 pd GMPPB_promoter
+p130 pd USP52_promoter
+p130 pd KIF23_promoter
+p130 pd LSM8_promoter
+p130 pd MCM5_promoter
+p130 pd PSMD14_promoter
+p130 pd ROD1_promoter
+p130 pd RPL39L_promoter
+p130 pd SBZF3_promoter
+p130 pd SIRT1_promoter
+p130 pd SLC35A3_promoter
+p130 pd SNIP1_promoter
+p130 pd SNX1_promoter
+p130 pd THRAP6_promoter
+p130 pd TUBA2_promoter
+p130 pd ZNF215_promoter
+alpha-1A-AR pp BMP-1
+Nap1 pp hNap1BP
+hNap1BP pp c-Abl
+laforin pp EPM2AIP1
+Ataxin-3 pp HHR23A
+Ataxin-3 pp HHR23B
+APC pp IQGAP1
+Rac1 interactsWith IQGAP1-APC
+Cdc42 interactsWith IQGAP1-APC
+pRb pp E2F1
+Cdk2 pp Bcl-2
+5'_MSH2_promoter pd E2F1
+Cdk2 pp p27kip1
+TGF-beta-1 pp TGF-beta-R-II
+TGF-beta-3 pp TGF-beta-R-II
+TGF-beta-3 pp TGF-beta-R-I
+TGF-beta-1 pp TGF-beta-R-I
+TGF-beta-2 pp TGF-beta-R-III
+TGF-beta-R-I pp TGF-beta-R-I
+VEGF-A pp VEGFR-1
+VEGF-A pp VEGFR-2
+VEGF-C pp VEGFR-2
+VEGF-C pp VEGFR-3
+PEN-2 pp PS1
+PEN-2 pp APH-1
+PEN-2 pp NCT
+Endophilin_A3/CIN85 interactsWith Cbl
+Endophilin_A3 pp Dynamin
+Met pp Cbl
+Met pp Gab1
+SKB1 pp SKB1
+Unknown interactsWith HRMT1L2
+CIN85/endophilin_A1 interactsWith Unknown
+Unknown interactsWith EGFR
+Tropoelastin pp Nidogen-2
+NOP56 interactsWith U3_snoRNA
+hU3-55K interactsWith U3_snoRNA
+NOP58 interactsWith U3_snoRNA
+Fibrillarin interactsWith U3_snoRNA
+La interactsWith U3_snoRNA
+Phax interactsWith U3_snoRNA
+TGS1 interactsWith U3_snoRNA
+Crm1 interactsWith U3_snoRNA
+p53 pd cdc25c_promoter
+p53 pd SFN_promoter
+p53 pp Sp1
+Sp1 pd cdc25c_promoter
+p53 pd CDKN1A_promoter
+p38 pp Elk-1
+IGF-IR pp RACK1
+PKC-delta pp IGF-IR
+beta-1_integrin pp RACK1
+beta-1_integrin pp IGF-IR
+PKC-delta pp RACK1
+PKC-mu pp IGF-IR
+PKC-mu pp RACK1
+T-beta-R1 pp T-beta-R2
+Mnk1 pp eIF4G1
+eIF4E pp Mnk1
+eIF4E pp eIF4G1
+E2F4 pd MAD2_promoter
+E2F4 pd RAD54_promoter
+E2F4 pd TopoII_promoter
+E2F4 pd MLH1_promoter
+E2F4 pd Chk1_promoter
+E2F4 pd BARD1_promoter
+E2F4 pd p107_promoter
+E2F4 pd E2F1_promoter
+E2F4 pd Cyclin_A_promoter
+ARPC1B interactsWith p20-Arc/p16-Arc
+ERK1 pp ATF2
+JNK2 pp ATF2
+ERK1 pp Elk-1
+JNK2 pp Elk-1
+Unknown interactsWith TAF4
+Unknown interactsWith TAF5
+Unknown interactsWith TAF6
+Unknown interactsWith TAF9
+Unknown interactsWith TAF12
+A-RAF pp FBNL
+A-RAF pp TIMM50
+B-RAF pp TIMM50
+C-RAF pp TIMM50
+C-RAF pp CPS1
+B-RAF pp 14-3-3-beta
+B-RAF pp OIP5
+C-RAF pp SGN3
+hCsl4p pp hRrp42p
+HIP14 pp PSD-95
+HIP14 pp Synaptotagmin_I
+HIP14 pp GAD65
+HIP14 pp htt
+hCsl4p pp hRrp46p
+p38 pp ATF2
+MRIT-beta-1 pp FADD
+MRIT-beta-1 pp YAMA
+MRIT-beta-1 pp FLICE
+Foxo3a pp p53
+FoxM1 pd p-Cyclin_B1
+FoxM1 pd p-CENP-F
+Sap-1a pp JNK-1
+Sap-1a pp ERK-1
+Elk-1 pp JNK-1
+Elk-1 pp ERK-1
+p38 pp ATF2
+MK2 pp Hsp27
+hDrosha pp DGCR8
+p53 pd Bnip3L
+TORC1 pp calcineurin
+NRF1 pd p-TFAM
+NRF1 pd p-MRP63
+NRF1 pd p-CDC2
+Unknown interactsWith karyopherin_alpha
+Unknown interactsWith karyopherin_beta
+TLE1 interactsWith Unknown
+Unknown interactsWith MYH10
+Unknown interactsWith NPM1
+Unknown interactsWith ACTB
+Unknown interactsWith NONO
+Unknown interactsWith HSPA4
+Unknown interactsWith NCL
+Unknown interactsWith RAD50
+Unknown interactsWith TOP2B
+Unknown interactsWith PARP1
+p38 pp c-Jun
+p38 pp MNK1
+CARD-8 pp Casp-1
+MRIT-alpha-1 pp BclXL
+MRIT-alpha-1 pp FLICE
+MRIT-alpha-1 pp YAMA
+mTOR pp rictor
+mTOR pp raptor
+mTOR-rictor interactsWith Akt1
+PDK1 pp Akt1
+Sap-1a pp ERK-1
+Elk-1 pp ERK-1
+Sap-1a pp p38_MAPK
+Elk-1 pp p38_MAPK
+Sap-1a pd c-fos_SRE
+ADAMTS1 pp VEGF165
+BAG5 pp Hsp70
+BAG5 pp BAG5
+BAG1 pp Hsp70
+BAG5 pp parkin
+Hsp70 pp parkin
+synphilin pp parkin
+CD80 pp CD28
+p21 pp CDC2
+p21 pp CDK2
+p21 interactsWith Unknown
+Unknown interactsWith CDK4
+Unknown interactsWith Cyclin_D1
+p21 pp PCNA
+golgin-84 pp CASP
+giantin pp p115
+Galpha12 pp Aalpha
+MD-1 pp RP105
+Cx43 pp v-Src
+T-beta-R1/T-beta-R2 interactsWith Smad2
+E2F4 pd p-CDC2
+hMAD-3 interactsWith TGF-beta-RI/TGF-beta-RII
+IKK-gamma pp IKK-gamma
+LSD1 pp H3
+Unknown interactsWith IKKalpha
+Unknown interactsWith MALT1
+Unknown interactsWith MALT1
+Unknown interactsWith Bcl10
+Unknown interactsWith IKKbeta
+Unknown interactsWith Casp8
+Unknown interactsWith Bcl10
+FADD interactsWith Unknown
+Casp8 interactsWith unknown
+PUMA-alpha pp Bcl-2
+PUMA-beta pp Bcl-2
+CTLA-4 pp Jak2
+SRF pd c-fos_promoter_CArG_box
+SRF pp ACT
+SRF pp FHL2
+SRF pp FHL3
+SRF pp FHL1
+HDS pp LO
+Unknown interactsWith IKK-beta
+Unknown interactsWith IKK-alpha
+Unknown interactsWith Bcl10
+Casp8 interactsWith Unknown
+IKK-alpha-IKK-beta-IKK-gamma interactsWith I-kappa-B-alpha
+ELMO1 pp RhoG
+ELMO1/Dock180 interactsWith RhoG
+E2F4 pd Cdc25A_promoter
+E2F4 pd Cdc6_promoter
+E2F4 pd Cdc2_promoter
+E2F1 pd MAD2_promoter
+E2F1 pd RAD54_promoter
+TSG101 pp HRS
+TSG101 pp TSG101
+TSG101 pp VPS28
+VPS4B pp CHMP1A
+CHMP2A pp VPS4B
+TSG101 pp AIP1
+AIP1 pp AIP1
+AIP1 pp CHMP4A
+AIP1 pp CHMP4B
+AIP1 pp CHMP4C
+EAP20 pp CHMP6
+CHMP6 pp EAP30
+CHMP6 pp EAP45
+EAP30 pp EAP20
+EAP45 pp EAP30
+EAP45 pp EAP20
+EAP30 pp EAP30
+TSG101 pp EAP30
+TSG101 pp EAP45
+VPS4A pp CHMP1A
+CHMP1A pp CHMP1A
+CHMP1B pp CHMP1A
+CHMP1B pp VPS4A
+CHMP1B pp VPS4B
+CHMP2A pp VPS4A
+CHMP3 pp CHMP4A
+VPS4A pp CHMP4A
+CHMP4A pp CHMP4C
+CHMP4B pp CHMP6
+CHMP4B pp CHMP4C
+CHMP4C pp CHMP4C
+VPS4A pp CHMP4C
+E2F1 pd MLH1_promoter
+E2F1 pd BARD1_promoter
+E2F1 pd Chk1_promoter
+E2F1 pd MSH2_promoter
+E2F4 pd MSH2_promoter
+E2F3 pd MSH2_promoter
+p35 pp Cdk5
+E2F3 pd Cdc2_promoter
+E2F3 pd Cdc6_promoter
+E2F3 pd Cdc25A_promoter
+ERK1 pp MNK1
+MD-2 pp TLR4
+hPAK65 pp hPAK65
+Nck pp WASp
+Nck pp SLP-76
+CD80 pp CTLA-4
+FAK pp FAK
+Sos1 pp Grb2
+FAK pp Grb2
+hRPB3 pp hRPB5
+hRPB1 pp hRPB8
+hRPB4 pp hRPB3
+hRPB4 pp hRPB1
+hRPB4 pp hRPB2
+hRPB4 pp hRPB4
+hRPB4 pp hRPB5
+hRPB4 pp hRPB10-beta
+hRPB4 pp hRPB7
+SART-1 pp UBL5
+MITF pd CDK2_promoter
+ERK1 pp p90-RSK2
+ERK1 pp ZNF7
+ERK1 pp HSF-1
+ERK1 pp c-Myc
+ERK1 pp Topoisomerase_II-beta
+ERK1 pp RalGDS
+p38-2 pp c-Jun
+TNFR1 pp TRADD
+p53 pd puma
+p53 pd DR5
+CBP pd Bnip3L
+p53 pd Bax
+T-beta-R2 pp hMAD-3
+T-beta-R1 pp hMAD-3
+p38-2 pp Elk1
+JNK1 pp Elk1
+ERK1 pp Elk1
+amyloid-beta pp amyloid-beta
+amyloid-beta interactsWith Unknown
+BNIPL-2 pp Bcl-2
+BNIPL-2 pp BNIPL-2
+p38 pp ATF2
+hNMT1 pp MARCKS
+HDAC1 pd p-TNFSF10
+HDAC2 pd p-TNFSF10
+HDAC3 pd p-TNFSF10
+HDAC4 pd p-TNFSF10
+HDAC5 pd p-TNFSF10
+SP1 pd p-TNFSF10
+SP3 pd p-TNFSF10
+CBP pd p-TNFSF10
+RNA_Pol_II interactsWith p-TNFSF10
+NF-YA pp ZHX1
+NF-YA pp SRF
+DAT pp RACK1
+DAT pp Syn1A
+DAT pp DAT
+HuF2 pp AIP1
+CIDE-B pp CIDE-B
+RalB pp RLIP76
+Rac1 pp RLIP76
+p40 pp p40
+YY1 pp EED
+EED pp EZH2
+E2F2 pd p107_promoter
+c-Cbl pp Ubc4
+c-Cbl pp PDGF-R-beta
+E2F1 pd E2F1_promoter
+E2F1 pd Cdc25A_promoter
+p35 pp p35
+Pin2 pp TRF1
+Pin2 pp Pin2
+E2F1 pd Cdc2_promoter
+E2F1 pd p107_promoter
+E2F1 pd Cdc6_promoter
+E2F2 pd E2F1_promoter
+E2F2 pd Cdc6_promoter
+E2F2 pd Cdc25A_promoter
+FBP17 pp TNKS
+IRAK4 pp PELI2
+IRAK1 pp PELI2
+HuF2 pp NAF1
+HuF2 pp TACC3
+HuF2 pp CDC5L
+MT1_receptor pp MT1_receptor
+MT2_receptor pp MT2_receptor
+MT1_receptor pp MT2_receptor
+ARTS-1 pp TNFR1
+ELD/OSA1 pp BRG1
+HSPRY4 pp TESK1
+IL12A-IL12B interactsWith IL12RB1
+p53_dimer interactsWith HIF-1_alpha
+Ubc9 pp SUMO1
+hRPB8 pp hRPB10-beta
+hRPB7 pp hRPB5
+hRPB10-beta pp hRPB3
+hRPB3 pp hRPB3
+hRPB2 pp hRPB8
+hRPB4 pp hRPB8
+hRPB4 pp hRPB10-alpha
+p53 pp HIF-1_alpha
+TACC2 pp hGCN5L2
+TACC1 pp hGCN5L2
+TACC3 pp hGCN5L2
+TACC2 pp pCAF
+TACC2 pp p300
+TACC2 pp CBP
+TRAF2 pp CD30
+Ubc9 pp Pc2
+Pc2 pp SUMO1
+c-Src pp CAS
+c-Src pp FAK
+Grb2 pp Shc
+Grb2 pp FAK
+Shc pp FAK
+CAS pp FAK
+Pc2 pp CtBP
+Chk1 pp RAD51
+p38-alpha pp p47phox
+p38-alpha pp Cdc25B
+MAPKAP_kinase-2 pp Cdc25B
+14-3-3-zeta pp Cdc25B
+p38-2 pp Sap-1a
+p38 pp Sap-1a
+p38-2 pp ATF2
+CTCF pd EIF2S3_5'_end
+H3 pd EIF2S3_5'_end
+FLI1 pp EAPII
+ETS2 pp EAPII
+Rb pp MDM2
+JMJ pp GATA4
+JMJ pp Nkx2.5
+Nkx2.5 pp GATA4
+Ubc9 pp RanBP2
+SUMO-1 pp RanBP2
+p21 interactsWith CycA/Cdk2_complex
+p21 pp PCNA
+p21 pp Cdk2
+PEA-15 pp RSK2
+SKIP3 pp ATF4
+Runx2 pp pRb
+p53_dimer interactsWith HIF-1_alpha
+p53 pp HIF-1_alpha
+p53_dimer interactsWith p53_dimer
+ARHGEF7 pp Cdc42
+ARHGEF6 pp Cdc42
+ARHGEF6 pp Rac1
+SMAD4 pp SUMO1
+Pc2 pp Pc2
+hSpry2 pp c-Cbl
+Hsp70 pp K-alpha
+STAT1 pp K-alpha
+PEA-15 pp ERK_1
+IL12RB1 pp IL12RB1
+IL12RB1 interactsWith IL12RB1_homodimer
+PICK1 pp mGluR7b
+Syntenin pp mGluR7b
+GRIP pp mGluR7b
+p53_tetramer interactsWith Mdm2_promoter
+p53_tetramer interactsWith p21_promoter
+IL12A-IL12B interactsWith IL12RB1_homodimer
+IL12A-IL12B interactsWith IL12RB1_oligomer
+p130 pd Cdc6_promoter
+p130 pd p107_promoter
+p130 pd E2F1_promoter
+APTX pp XRCC1
+p130 pd Cyclin_A_promoter
+p130 pd B-myb_promoter
+EGFR pp ErbB2
+RalA pp ZONAB
+CTNNB1 pd CCND1_promoter
+CTNNB1 pd DKK1_promoter
+CTNNB1 pd FGF20_promoter
+E2F1 pd B-myb_promoter
+hnRNPA2 pp RBM3
+hnRNPA2 pp hnRNPA2
+Rb pp Mdm2
+p21 pp Cyclin_D
+p21 pp Cyclin_E
+p27 pp Cyclin_E
+p27 pp Cyclin_D
+p21 pp PCNA
+Cyclin_E_/_cdk2 interactsWith p21
+p27 pp Cyclin_A
+Cyclin_E_/_cdk2 interactsWith p27
+TAFI48 pp c-Myc
+TAFI63 pp c-Myc
+TBP pp c-Myc
+TAFI110 pp c-Myc
+c-Myc pd rDNA
+UBF pd rDNA
+TBP pd rDNA
+p300 pp Smad2
+CBP pp Smad2
+p300 pp Smad4_fragment
+CSK pp IGF-IR
+CSK pp IR
+IRS-1 pp IGF-IR
+IRS-1 pp IR
+p27 pp Stathmin
+p27 pp CDK2
+p27 pp Cyclin_A
+SNAP29 pp SNAP29
+EHD3 pp SNAP29
+EHD1 pp SNAP29
+EHD1 pp IGF-1R
+CARM1 pp p65
+p300 pp p65
+CARM1 pp p300
+Egr-1 pd Gadd45a_promoter
+Egr-1 pd Gadd45b_promoter
+RelA pd Egr-1_promoter
+p107 pp Mdm2
+E2F2 pd B-myb_promoter
+E2F4 pd B-myb_promoter
+E2F3 pd B-myb_promoter
+p130 pp Mdm2
+p53 pp Mdm2
+Plexin-B1 pp Rac1
+Kap13 pp Pax6
+HsCdc7 pp HsDbf4
+HsCdc7-HsDbf4 interactsWith HsCdc7-HsDbf4
+HsCdc7-HsDbf4 interactsWith MCM2
+JMJ pd ANF_promoter
+CD93 pp GIPC
+NSP-C pp Bcl-XL
+RTN-XS pp Bcl-XL
+RTN-XS pp Bcl-2
+Unknown interactsWith TACC3
+HSF2 pp CAP-G
+HSF2 pd hsp70i_promoter
+Smad3 pp Smad4
+Smad2 pp Smad4
+Smad2 pp Smad3
+T-beta-RII pp T-beta-RII
+T-beta-RII pp hMAD-4
+T-beta-RI pp hMAD-4
+pCAF interactsWith Unknown
+CLASP1-alpha pp EB3
+CLASP1-alpha pp EB1
+TrkA pp FRS2-beta
+TrkA pp FRS2-alpha
+FGFR1 pp FRS2-beta
+Unknown interactsWith IL12RB2
+IL12RB1 interactsWith Unknown
+IL12A-IL12B interactsWith IL12RB2
+IL12A-IL12B interactsWith IL12RB2_homodimer
+IL12RB2 pp IL12RB2
+Cdk6 pp Rb
+Cyclin_A-Cdk2 interactsWith Rb
+Cyclin_B1-Cdc2 interactsWith Rb
+Cyclin_E-Cdk2 interactsWith Rb
+Cyclin_E-Cdk2 interactsWith HsCdc6
+Cyclin_A-Cdk2 interactsWith HsCdc6
+NCSTN pp BACE1
+MNK1 pp cPLA2
+MSK1 pp cPLA2
+PRAK1 pp cPLA2
+TBP pp GLI-2
+NPAS1 pp Arnt
+XIAP pp TAB1
+TGF-beta-RI pp XIAP
+ALK4 pp XIAP
+ALK1 pp XIAP
+c-Abl pp Crk
+JNK pp 14-3-3-eta
+c-Abl pp 14-3-3-eta
+c-Abl pp 14-3-3-delta
+H3 pp Asf1a
+H3.1 pp Asf1b
+H3.1 pp Asf1a
+H3.3 pp Asf1b
+H3.3 pp Asf1a
+CAF-1_p150 pp H3.1
+CAF-1_p60 pp H3.1
+Asf1a pp NASP
+Asf1a pp p48
+BRCA1 pp Ub
+BRCA1 pp BRCA1
+C/EBP-epsilon pp CHOP
+C/EBP-epsilon pp C/EBP-delta
+C/EBP-epsilon pp E6TP1
+C/EBP-epsilon pp AF17
+C/EBP-epsilon pp LDOC1
+C/EBP-epsilon pp ZNF198
+C/EBP-epsilon pp PIAS1
+C/EBP-epsilon pp UBE2I
+C/EBP-alpha pp PIAS1
+CMS pp Cbl
+CAP pp Cbl
+ArgBP2 pp Cbl
+ArgBP2 pp Pyk2
+CAP pp flotillin-1
+nArgBP2 pp flotillin-1
+ArgBP2 pp flotillin-1
+RhoA pp RTKN
+CDC42 pp WASP
+RELA pd CCND1_promoter
+KLF5_promoter pd C/EBP-beta
+KLF5_promoter pd C/EBP-gamma
+ARF3 pp GGA1
+Rpp20 pp Hsp27
+Rpp14 pp LIMD1
+Rpp14 pp OIP2
+Unknown interactsWith Chk2
+H3.1 interactsWith Unknown
+Unknown interactsWith p48
+Unknown interactsWith NASP
+BACE1 pp ITM2C_(BRI3)
+E2F1 pd CYP27B1
+E2F1 pd H2AFM
+E2F1 pd similar_to_FLJ10891
+E2F4 pd ALG5
+E2F4 pd BM037
+E2F4 pd CDC25C
+E2F4 pd CGI-141
+E2F4 pd CpG66E11
+E2F4 pd DDX11
+E2F4 pd DHPS
+E2F4 pd DKFZp564C0482
+E2F4 pd DKFZP564M082
+E2F4 pd DKFZp586C1942
+E2F4 pd DLEU1
+E2F4 pd DLEU2
+E2F4 pd EPAS1
+E2F4 pd ESTs
+E2F4 pd ESTs
+E2F4 pd ESTs
+E2F4 pd ESTs
+E2F4 pd ESTs
+E2F4 pd ESTs
+E2F4 pd ESTs
+E2F4 pd ESTs
+E2F4 pd FANCD2
+E2F4 pd FLJ10466
+E2F4 pd FLJ11193
+E2F4 pd FLJ12190
+E2F4 pd FLJ12758
+E2F4 pd FLJ12973
+E2F4 pd fls353
+E2F4 pd FOXD3
+E2F4 pd GTF2H4
+E2F4 pd H2AFM
+E2F4 pd H3FL
+E2F4 pd HNRPA1
+E2F4 pd HPR6.6
+E2F4 pd HT007
+E2F4 pd MCM10_homolog
+E2F4 pd MGC11266
+E2F4 pd MTHFD1
+E2F4 pd N-Ras_related_gene
+E2F4 pd NASP
+E2F4 pd OIP5
+E2F4 pd RBBP5
+E2F4 pd RN3
+E2F4 pd RPA3
+E2F4 pd RPS16
+E2F4 pd SAAS
+E2F4 pd similar_to_FLJ10891
+E2F4 pd SMARCA5
+E2F4 pd SNRPC
+E2F4 pd THOX2
+E2F4 pd UBCH10
+RNAP interactsWith CpG12B10
+RNAP interactsWith CpG18G8
+RNAP interactsWith CpG32C1
+RNAP interactsWith CYP27B1
+RNAP interactsWith DBPA
+RNAP interactsWith FLJ10287
+RNAP interactsWith FLJ11029
+RNAP interactsWith Gar22
+RNAP interactsWith H2AFM
+RNAP interactsWith H2AFP
+RNAP interactsWith H2BFR
+RNAP interactsWith H4F2
+RNAP interactsWith HP1
+RNAP interactsWith MFAP1
+RNAP interactsWith RAD51
+RNAP interactsWith RECQL
+RNAP interactsWith similar_to_FLJ10891
+RNAP interactsWith TTK
+RNAP interactsWith TYMS
+RNAP interactsWith UXT
+EBAG9 pp Snapin
+H3F3A pp SMARCA5
+H3F3A pp SMARCA4
+H3F3A pp PCAF
+H3F3A pp CREBBP
+FAK pp EGFR
+FAK pp FAK
+SNAP25 pp Snapin
+SNAP23 pp Snapin
+Calmodulin pp CRF1R
+Calmodulin pp CALTR
+Calmodulin pp GLP2R
+Calmodulin pp GLP1R
+Calmodulin pp SECRR
+Calmodulin pp PACPR
+Calmodulin pp PTH2R
+Calmodulin pp VIP1R
+Asf1a pp H4AcK12
+Beta-1-AR pp SH3p13
+Beta-1-AR pp SH3p4
+UCP2 pp 14.3.3-gamma
+UCP2 pp 14.3.3-beta
+UCP2 pp 14.3.3-zeta
+UCP2 pp 14.3.3-theta
+UCP3 pp 14.3.3-gamma
+UCP3 pp 14.3.3-beta
+Hsp90 pp PP5
+p18 pp ATM
+p18 pp ATR
+UCP3 pp 14.3.3-zeta
+UCP3 pp 14.3.3-theta
+p300 pd p21
+RPTP-alpha pp RPTP-alpha
+p40 interactsWith IL12R
+IL12A-IL12B interactsWith IL12R
+p40_homodimer interactsWith IL12R
+IL12RB1 pp Tyk2
+TIMP2 pp ITGA3
+furin pp ADAMTS4
+NCSTN interactsWith unknown
+SMAD3 pp BRCA2
+PRKACA pp NPR1
+DISC-1 pp ITSN
+DISC-1 pp ATF4
+GRAP2 pp CD28
+GRAP2 pp GNB2L1
+GRAP2 pp Sos2
+GRAP2 pp KHDRBS1
+SMAD3 pp SREBPF2
+FAK pp v-Src
+NMU pp FM-4/TGR-1
+NMU pp FM-3/GPR66
+NMS pp FM-4/TGR-1
+NMS pp FM-3/GPR66
+Miz-1 pp Dmnt3a
+Myc pp Dmnt3a
+Miz-1-Myc-Dnmt3a_complex interactsWith p21Cip1promoter
+H3 pd Chromosome_21
+H3 pd Chromosome_22
+Raf-1 pp Ras
+Raf-1 pp ERK2
+Raf-1 pp Pin1
+Raf-1 interactsWith Unknown
+Unknown interactsWith PP2AA-alpha
+Unknown interactsWith PP2AB-alpha
+Unknown interactsWith PP2AC-beta
+DAPK pp Erk1
+DAPK pp Erk2
+CBP pd HNF-4_gene
+MKK3 pp p38
+MKK7 pp MKK7
+MKK6 pp MKK6
+MKK6 pp p38
+TAK1 pp TAB1
+TAK1 pp MKK3
+TAK1 pp MAPKK6
+TAB1 pp p38
+H3F3A pp SUPT16H
+Cat pp Shp-2
+atrophin-1 pp AIP2
+atrophin-1 pp AIP1
+atrophin-1 pp AIP4
+atrophin-1 pp AIP5
+atrophin-1 pp AIP3
+c-Myb pp p300
+Elp3 pd HNF-4_gene
+Brg-1 pd HNF-4_gene
+CBP pd HNF-1_gene
+Cdc2 pp Myt1
+Elp3 pd HNF-1_gene
+Brg-1 pd HNF-1_gene
+SNF2H pd HNF-1_gene
+FACT pd HNF-1_gene
+PCAF pd Albumin_gene
+Elp3 pd Albumin_gene
+PDK1 pp PKC-theta
+PKC-theta pp NEMO
+PKC-theta pp IKK-alpha
+PKC-theta pp IKK-beta
+NEMO pp IKK-beta
+PDK1 pp CARD11
+CD93 pp BM046
+CD93 pp RanBP
+CD93 pp p105
+RBM23 pd pS2
+RNPC2 pp PR
+RBM23 pp PR
+RBM23 pp ESR1
+DISC-1 pp NUDEL
+DISC-1 pp alpha-actinin_2
+DISC-1 pp EIF3
+DISC-1 pp B4_Spectrin
+DISC-1 pp APAP2
+DISC-1 pp RanBPM
+DISC-1 pp MAP1A
+DISC-1 pp ATF7ip
+MCM2 pp MCM3
+MCM2 pp MCM5
+MCM2 pp MCM6
+MCM3 pp MCM5
+MCM3 pp MCM7
+MCM4 pp MCM4
+MCM4 pp MCM6
+MCM4 pp MCM7
+Pin1 pp Myt1
+Brg-1 pd Albumin_gene
+H3F3A pd TCF1_gene
+H3F3A pd HNF4A_gene
+SNF2H pd Albumin_gene
+PKR pp PACT
+DNA-PK interactsWith Sp1
+CARD9 pp BCL10
+CARD9 pp CARD9
+CREBBP pp NAP1L1
+CARD12 pp Bcl10
+H3F3A pd ALB_gene
+CARD10 pp BCL10
+HIST4H4 pd ALB_gene
+HIST4H4 pd TCF1_gene
+RAD51 pp RAD51
+Bax pp SH3GLB1
+SH3GLB1 pp SH3GLB1
+SH3GLB1 pp SH3GLB2
+SH3GLB2 pp SH3GLB2
+APH-1A pp PSEN1
+unknown interactsWith PSEN2
+unknown interactsWith APH-1A
+JAK2 pp IL12RB2
+Stat4 interactsWith Unknown
+Unknown interactsWith Fc-gammaRI_promoter
+Stau1 pp CBP80
+Stau1 pp Barentsz
+Upf1 pp Stau1
+Upf1 pp Upf3X
+Stau1 interactsWith PAICS
+Stau1 interactsWith Arf1
+Htt pp HAP1
+Htt pp HSP70
+Htt pp Tpr
+TNFR1 pp TRADD
+MEKK1 pp ERK1
+ERBB2 pp HSC70
+ERBB2 pp P50CDC37
+ERBB2 pp HSP90
+USP1 pp FANCD2
+Rac1 pp TCF4
+USP1 pp Ubiquitin
+Cyclin_T1 pp GRIP1
+GR-alpha pp GRIP1
+LDOC1 pp MZF-1
+integrin-beta-1 pp ILK
+integrin-beta-3 pp ILK
+affixin pp ILK
+integrin-beta-3 pp Shc
+integrin-alpha-6-beta-4 interactsWith Shc
+integrin-alpha-5-beta-1 interactsWith Shc
+integrin-alpha-V-beta-3 interactsWith Shc
+integrin-alpha-6-beta-1 interactsWith Shc
+TAJ pp Lingo-1
+TAJ pp NgR1
+Gadd45a pp PCNA
+Gadd45b pp PCNA
+Gadd45g pp PCNA
+Bmf pp Bcl-2
+SSH-2S pp LIMK1
+SSH-3S pp LIMK1
+PKC-zeta pp PKC-zeta
+PAK4 pp LIMK1
+Htt pp HAP1
+Bad pp Bcl-w
+Bmf pp Bcl-w
+Puma pp Bcl-w
+Bid pp Bcl-XL
+Hrk pp Bcl-XL
+Bmf pp Bcl-XL
+Bid pp Bcl-2
+Hrk pp Bcl-2
+HHEX pp TLE1
+Bik pp Bcl-w
+Hrk pp Bcl-w
+Bid pp Bcl-w
+Bid pp Mcl-1
+Bik pp A1
+Bad pp A1
+SMG7 pp UPF1
+UPF1 pp SMG6
+DISC-1 pp MIP-T3
+DISC-1 pp ATF5
+MCC pp NFKBIB
+Rb-NeuroD1_complex interactsWith NGFI-B
+TRAF7 pp TRAF7
+FKBP5 pp CHUK
+NFKB1 pp SPAG9
+MAD2L1 pp Cdc20
+MAD1L1 pp MAD2L1
+MAD2L1 interactsWith MAD1L1-MAD2L1_tetramer
+TRAF7 pp MAP3K3
+TNFR1 pp RIP1
+p68 pp p53
+hLRH-1 pp hSHP
+TROY pp NgR
+Nogo-66 pp NgR
+p75 pp NgR
+Rhotekin pp NgR
+Rhotekin interactsWith Nogo_Receptor_complex
+Bad pp Bcl-2
+Puma pp Bcl-2
+Bim pp Bcl-2
+Bim pp Bcl-w
+Bik pp Bcl-XL
+Bik pp Bcl-2
+Bim pp Bcl-XL
+Smac pp XIAP
+GraB pp Caspase-7
+CatG pp Caspase-7
+Caspase-7 pp XIAP
+Caspase-3 pp XIAP
+Puma pp Mcl-1
+Bik pp Mcl-1
+Hrk pp Mcl-1
+Puma pp A1
+Hrk pp A1
+Bid pp A1
+Noxa pp A1
+TAFII250 pd CHM_promoter
+Max pd HMBS_promoter
+Pol_II interactsWith RPL9_promoter
+Max pd RPL9_promoter
+TAFII250 pd RPL9_promoter
+c-Myc pd RPL9_promoter
+Pol_II interactsWith FANCF_promoter
+Max pd FANCF_promoter
+TAFII250 pd FANCF_promoter
+c-Myc pd FANCF_promoter
+Pol_II interactsWith PHKB_promoter
+TAFII250 pd PHKB_promoter
+Max pd RPL13_promoter
+TAFII250 pd RPL13_promoter
+c-Myc pd RPL13_promoter
+Pol_II interactsWith RPS6_promoter
+Max pd RPS6_promoter
+TAFII250 pd RPS6_promoter
+c-Myc pd RPS6_promoter
+Pol_II interactsWith LSP1_promoter
+Max pd LSP1_promoter
+TAFII250 pd LSP1_promoter
+c-Myc pd LSP1_promoter
+Max pd MDH1_promoter
+TAFII250 pd MDH1_promoter
+c-Myc pd MDH1_promoter
+E2F1 pd RPL18_promoter
+Pol_II interactsWith RPL18_promoter
+Max pd RPL18_promoter
+TAFII250 pd RPL18_promoter
+c-Myc pd RPL18_promoter
+Max pd RPS6KB1_promoter
+TAFII250 pd RPS6KB1_promoter
+c-Myc pd RPS6KB1_promoter
+Max pd LTA4H_promoter
+c-Myc pd LTA4H_promoter
+TAFII250 pd MDM4_promoter
+c-Myc pd MDM4_promoter
+Pol_II interactsWith RPL19_promoter
+Max pd RPL19_promoter
+TAFII250 pd RPL19_promoter
+c-Myc pd RPL19_promoter
+Pol_II interactsWith H3F3B_promoter
+Max pd HIP2_promoter
+c-Myc pd HIP2_promoter
+E2F1 pd ABCE1_promoter
+Pol_II interactsWith ABCE1_promoter
+Max pd ABCE1_promoter
+TAFII250 pd ABCE1_promoter
+c-Myc pd ABCE1_promoter
+Pol_II interactsWith CTSC_promoter
+Max pd CTSC_promoter
+TAFII250 pd CTSC_promoter
+c-Myc pd CTSC_promoter
+E2F1 pd HNRPA1_promoter
+Pol_II interactsWith HNRPA1_promoter
+Max pd HNRPA1_promoter
+TAFII250 pd HNRPA1_promoter
+c-Myc pd HNRPA1_promoter
+TAFII250 pd MARK3_promoter
+Pol_II interactsWith PFKFB3_promoter
+Max pd PFKFB3_promoter
+TAFII250 pd ERCC4_promoter
+Max pd PDK1_promoter
+c-Myc pd PDK1_promoter
+Pol_II interactsWith PFN1_promoter
+Max pd PFN1_promoter
+TAFII250 pd PFN1_promoter
+c-Myc pd PFN1_promoter
+Pol_II interactsWith HRMT1L1_promoter
+TAFII250 pd HRMT1L1_promoter
+Pol_II interactsWith PLD2_promoter
+Pol_II interactsWith PP_promoter
+Max pd PP_promoter
+TAFII250 pd PP_promoter
+c-Myc pd PP_promoter
+Max pd CLCN2_promoter
+c-Myc pd CLCN2_promoter
+TAFII250 pd HSBP1_promoter
+Max pd RSU1_promoter
+TAFII250 pd RSU1_promoter
+Pol_II interactsWith COX15_promoter
+Max pd COX15_promoter
+c-Myc pd COX15_promoter
+Pol_II interactsWith SFRS8_promoter
+TAFII250 pd SFRS8_promoter
+c-Myc pd SFRS8_promoter
+Max pd ARRB2_promoter
+c-Myc pd ARRB2_promoter
+Max pd UBL3_promoter
+c-Myc pd UBL3_promoter
+Max pd FLOT2_promoter
+c-Myc pd FLOT2_promoter
+Max pd KITLG_promoter
+Pol_II interactsWith MMP8_promoter
+Max pd MMP8_promoter
+TAFII250 pd MMP8_promoter
+c-Myc pd MMP8_promoter
+Pol_II interactsWith RXRB_promoter
+Max pd RXRB_promoter
+TAFII250 pd RXRB_promoter
+c-Myc pd RXRB_promoter
+Pol_II interactsWith DNAJA1_promoter
+TAFII250 pd DNAJA1_promoter
+Max pd MMP13_promoter
+Pol_II interactsWith SDF2_promoter
+Max pd SDF2_promoter
+TAFII250 pd SDF2_promoter
+c-Myc pd SDF2_promoter
+Max pd MMP15_promoter
+TAFII250 pd MMP15_promoter
+c-Myc pd MMP15_promoter
+Pol_II interactsWith POLH_promoter
+Max pd POLH_promoter
+TAFII250 pd POLH_promoter
+c-Myc pd POLH_promoter
+Pol_II interactsWith SDHD_promoter
+TAFII250 pd SDHD_promoter
+c-Myc pd SDHD_promoter
+E2F1 pd PDE6A_promoter
+Pol_II interactsWith AGL_promoter
+TAFII250 pd AGL_promoter
+E2F1 pd MCM3_promoter
+Max pd MCM3_promoter
+c-Myc pd MCM3_promoter
+TAFII250 pd RPL11_promoter
+E2F1 pd PDE6D_promoter
+Pol_II interactsWith PDE6D_promoter
+Max pd PDE6D_promoter
+TAFII250 pd PDE6D_promoter
+c-Myc pd PDE6D_promoter
+E2F1 pd RNF4_promoter
+Pol_II interactsWith RNF4_promoter
+Max pd RNF4_promoter
+c-Myc pd RNF4_promoter
+Pol_II interactsWith RPL15_promoter
+Max pd RPL15_promoter
+TAFII250 pd RPL15_promoter
+c-Myc pd RPL15_promoter
+Max pd RPS6KA2_promoter
+c-Myc pd RPS6KA2_promoter
+c-Myc pd EMD_promoter
+TAFII250 pd ABCB7_promoter
+Pol_II interactsWith PCDH7_promoter
+E2F1 pd CFL1_promoter
+Pol_II interactsWith CFL1_promoter
+TAFII250 pd CFL1_promoter
+Pol_II interactsWith FAU_promoter
+TAFII250 pd FAU_promoter
+c-Myc pd MAPT_promoter
+Pol_II interactsWith SERPINB9_promoter
+Max pd RPS13_promoter
+TAFII250 pd RPS13_promoter
+c-Myc pd RPS13_promoter
+Pol_II interactsWith CD68_promoter
+E2F1 pd H4F2_promoter
+Pol_II interactsWith H4F2_promoter
+TAFII250 pd H4F2_promoter
+c-Myc pd H4F2_promoter
+Pol_II interactsWith ADPRTL1_promoter
+TAFII250 pd ADPRTL1_promoter
+Pol_II interactsWith HNRPA2B1_promoter
+TAFII250 pd HNRPA2B1_promoter
+c-Myc pd HNRPA2B1_promoter
+Max pd PFKFB4_promoter
+c-Myc pd PFKFB4_promoter
+Max pd SERPINI1_promoter
+TAFII250 pd SERPINI1_promoter
+E2F1 pd RPS15_promoter
+Pol_II interactsWith RPS15_promoter
+TAFII250 pd RPS15_promoter
+Pol_II interactsWith ERCC6_promoter
+Max pd ERCC6_promoter
+TAFII250 pd ERCC6_promoter
+c-Myc pd ERCC6_promoter
+E2F1 pd PCM1_promoter
+Pol_II interactsWith PCM1_promoter
+Max pd PCM1_promoter
+TAFII250 pd PCM1_promoter
+c-Myc pd PCM1_promoter
+Max pd PDK2_promoter
+c-Myc pd PDK2_promoter
+TAFII250 pd RPL24_promoter
+TAFII250 pd RPS16_promoter
+c-Myc pd RPS16_promoter
+Pol_II interactsWith FRAP1_promoter
+Max pd FRAP1_promoter
+TAFII250 pd FRAP1_promoter
+c-Myc pd FRAP1_promoter
+Max pd SFRS5_promoter
+TAFII250 pd SFRS5_promoter
+c-Myc pd SFRS5_promoter
+Pol_II interactsWith GABPA_promoter
+Max pd GABPA_promoter
+TAFII250 pd GABPA_promoter
+c-Myc pd GABPA_promoter
+Max pd CLCN6_promoter
+c-Myc pd CLCN6_promoter
+E2F1 pd HUS1_promoter
+Pol_II interactsWith HUS1_promoter
+Max pd HUS1_promoter
+TAFII250 pd HUS1_promoter
+Max pd CLN3_promoter
+TAFII250 pd CLN3_promoter
+c-Myc pd CLN3_promoter
+Max pd SGT_promoter
+E2F1 pd MYPT1_promoter
+Pol_II interactsWith MYPT1_promoter
+Max pd MYPT1_promoter
+TAFII250 pd MYPT1_promoter
+c-Myc pd MYPT1_promoter
+Max pd PKIA_promoter
+TAFII250 pd PKIA_promoter
+TAFII250 pd BPGM_promoter
+Max pd JMJ_promoter
+TAFII250 pd JMJ_promoter
+c-Myc pd JMJ_promoter
+Pol_II interactsWith PSMA5_promoter
+Max pd PSMA5_promoter
+TAFII250 pd PSMA5_promoter
+c-Myc pd PSMA5_promoter
+TAFII250 pd IMPA1_promoter
+Pol_II interactsWith PSMB1_promoter
+Max pd PSMB1_promoter
+TAFII250 pd PSMB1_promoter
+c-Myc pd PSMB1_promoter
+Max pd NDUFB2_promoter
+c-Myc pd NDUFB2_promoter
+c-Myc pd SLC6A2_promoter
+Max pd PRPS2_promoter
+c-Myc pd PRPS2_promoter
+c-Myc pd SMOH_promoter
+Pol_II interactsWith NDUFB4_promoter
+Max pd NDUFB4_promoter
+TAFII250 pd NDUFB4_promoter
+c-Myc pd NDUFB4_promoter
+Pol_II interactsWith PPT1_promoter
+TAFII250 pd PPT1_promoter
+Pol_II interactsWith NDUFB6_promoter
+Max pd NDUFB6_promoter
+TAFII250 pd NDUFB6_promoter
+c-Myc pd NDUFB6_promoter
+Pol_II interactsWith BSG_promoter
+Max pd BSG_promoter
+Max pd DDX1_promoter
+TAFII250 pd DDX1_promoter
+c-Myc pd DDX1_promoter
+Max pd GNL1_promoter
+c-Myc pd GNL1_promoter
+Max pd NME2_promoter
+Max pd PSMC4_promoter
+TAFII250 pd PSMC4_promoter
+c-Myc pd PSMC4_promoter
+Max pd NDUFB8_promoter
+TAFII250 pd NDUFB8_promoter
+TAFII250 pd SKIV2L_promoter
+TAFII250 pd BST2_promoter
+Pol_II interactsWith KCNN3_promoter
+TAFII250 pd KCNN3_promoter
+c-Myc pd PTGER3_promoter
+TAFII250 pd CCNG2_promoter
+Pol_II interactsWith LIG3_promoter
+TAFII250 pd LIG3_promoter
+Pol_II interactsWith SSB_promoter
+Max pd SSB_promoter
+TAFII250 pd SSB_promoter
+c-Myc pd SSB_promoter
+E2F1 pd GPRK2L_promoter
+Max pd GPRK2L_promoter
+TAFII250 pd GPRK2L_promoter
+c-Myc pd GPRK2L_promoter
+E2F1 pd NPAT_promoter
+Pol_II interactsWith NPAT_promoter
+TAFII250 pd NPAT_promoter
+Pol_II interactsWith SOD1_promoter
+Max pd SOD1_promoter
+TAFII250 pd SOD1_promoter
+c-Myc pd SOD1_promoter
+Max pd LAMP1_promoter
+c-Myc pd LAMP1_promoter
+E2F1 pd RBBP2_promoter
+Pol_II interactsWith RBBP2_promoter
+Max pd RBBP2_promoter
+TAFII250 pd RBBP2_promoter
+c-Myc pd RBBP2_promoter
+TAFII250 pd DNMT2_promoter
+Max pd GPRK6_promoter
+TAFII250 pd PTHR2_promoter
+c-Myc pd PTHR2_promoter
+TAFII250 pd ORC1L_promoter
+Max pd RAC2_promoter
+TAFII250 pd RAC2_promoter
+c-Myc pd RAC2_promoter
+Pol_II interactsWith NPM1_promoter
+TAFII250 pd NPM1_promoter
+TAFII250 pd LIPA_promoter
+c-Myc pd LIPA_promoter
+TAFII250 pd ORC5L_promoter
+E2F1 pd RBL1_promoter
+Max pd RBL1_promoter
+TAFII250 pd RBL1_promoter
+c-Myc pd RBL1_promoter
+Pol_II interactsWith PAFAH1B2_promoter
+TAFII250 pd PAFAH1B2_promoter
+E2F1 pd RBM4_promoter
+Pol_II interactsWith RBM4_promoter
+Max pd RBM4_promoter
+TAFII250 pd RBM4_promoter
+c-Myc pd RBM4_promoter
+Pol_II interactsWith NRAS_promoter
+Max pd SRD5A1_promoter
+TAFII250 pd SRD5A1_promoter
+c-Myc pd SRD5A1_promoter
+Max pd FADS3_promoter
+c-Myc pd FADS3_promoter
+TAFII250 pd PAFAH2_promoter
+Pol_II interactsWith STRN_promoter
+TAFII250 pd STRN_promoter
+Pol_II interactsWith GALT_promoter
+TAFII250 pd GALT_promoter
+Pol_II interactsWith ILK_promoter
+Max pd ILK_promoter
+TAFII250 pd ILK_promoter
+c-Myc pd ILK_promoter
+Pol_II interactsWith GLA_promoter
+TAFII250 pd GLA_promoter
+Max pd NID_promoter
+E2F1 pd ATM_promoter
+Pol_II interactsWith ATM_promoter
+Max pd ATM_promoter
+TAFII250 pd ATM_promoter
+c-Myc pd ATM_promoter
+Max pd NAGA_promoter
+c-Myc pd NAGA_promoter
+Pol_II interactsWith BRCA1_promoter
+TAFII250 pd BRCA1_promoter
+Max pd GCLC_promoter
+TAFII250 pd GCLC_promoter
+c-Myc pd GCLC_promoter
+TAFII250 pd GNB3_promoter
+Pol_II interactsWith NKTR_promoter
+TAFII250 pd NKTR_promoter
+Pol_II interactsWith ING1_promoter
+Max pd ING1_promoter
+TAFII250 pd ING1_promoter
+c-Myc pd ING1_promoter
+Pol_II interactsWith NDUFB3_promoter
+Max pd NDUFB3_promoter
+TAFII250 pd NDUFB3_promoter
+c-Myc pd NDUFB3_promoter
+Pol_II interactsWith PPP5C_promoter
+TAFII250 pd PPP5C_promoter
+c-Myc pd PPP5C_promoter
+TAFII250 pd BICD1_promoter
+Pol_II interactsWith BRCA2_promoter
+TAFII250 pd BRCA2_promoter
+c-Myc pd BRCA2_promoter
+Pol_II interactsWith PSMB5_promoter
+Max pd PSMB5_promoter
+TAFII250 pd PSMB5_promoter
+c-Myc pd PSMB5_promoter
+Pol_II interactsWith NDUFB5_promoter
+Max pd NDUFB5_promoter
+TAFII250 pd NDUFB5_promoter
+c-Myc pd NDUFB5_promoter
+Pol_II interactsWith PRKCL1_promoter
+Max pd PRKCL1_promoter
+Max pd NME1_promoter
+TAFII250 pd NME1_promoter
+c-Myc pd NME1_promoter
+Pol_II interactsWith PSMB10_promoter
+TAFII250 pd PSMB10_promoter
+Max pd NUBP1_promoter
+TAFII250 pd NUBP1_promoter
+c-Myc pd NUBP1_promoter
+Pol_II interactsWith DDX5_promoter
+Max pd DDX5_promoter
+TAFII250 pd DDX5_promoter
+c-Myc pd DDX5_promoter
+c-Myc pd KCNN2_promoter
+E2F1 pd PSMC5_promoter
+Pol_II interactsWith PSMC5_promoter
+Max pd PSMC5_promoter
+TAFII250 pd PSMC5_promoter
+c-Myc pd PSMC5_promoter
+TAFII250 pd CSTF2_promoter
+Pol_II interactsWith CYBA_promoter
+Max pd CYBA_promoter
+TAFII250 pd CYBA_promoter
+c-Myc pd CYBA_promoter
+Max pd BTD_promoter
+TAFII250 pd BTD_promoter
+Pol_II interactsWith DAF_promoter
+TAFII250 pd DAF_promoter
+Pol_II interactsWith GLS_promoter
+TAFII250 pd GLS_promoter
+Pol_II interactsWith GNS_promoter
+Max pd GNS_promoter
+TAFII250 pd GNS_promoter
+c-Myc pd GNS_promoter
+Pol_II interactsWith PSMD3_promoter
+Max pd PSMD3_promoter
+TAFII250 pd PSMD3_promoter
+c-Myc pd PSMD3_promoter
+Max pd NUP88_promoter
+TAFII250 pd NUP88_promoter
+c-Myc pd NUP88_promoter
+Pol_II interactsWith PTS_promoter
+Max pd PTS_promoter
+TAFII250 pd PTS_promoter
+Max pd RBBP1_promoter
+TAFII250 pd RBBP1_promoter
+c-Myc pd RBBP1_promoter
+Pol_II interactsWith STK2_promoter
+TAFII250 pd STK2_promoter
+E2F1 pd RAD9_promoter
+Max pd RAD9_promoter
+c-Myc pd RAD9_promoter
+E2F1 pd RBBP8_promoter
+Pol_II interactsWith RBBP8_promoter
+Max pd RBBP8_promoter
+TAFII250 pd RBBP8_promoter
+c-Myc pd RBBP8_promoter
+E2F1 pd CAD_promoter
+Max pd CAD_promoter
+TAFII250 pd CAD_promoter
+c-Myc pd CAD_promoter
+Pol_II interactsWith OAZ1_promoter
+Max pd OAZ1_promoter
+TAFII250 pd OAZ1_promoter
+c-Myc pd OAZ1_promoter
+Max pd PTPN1_promoter
+TAFII250 pd PTPN1_promoter
+c-Myc pd PTPN1_promoter
+Max pd PYCR1_promoter
+c-Myc pd PYCR1_promoter
+Max pd SOX22_promoter
+c-Myc pd SOX22_promoter
+Pol_II interactsWith LDHA_promoter
+Max pd LDHA_promoter
+TAFII250 pd LDHA_promoter
+c-Myc pd LDHA_promoter
+TAFII250 pd LLGL1_promoter
+TAFII250 pd CD72_promoter
+Max pd CDK6_promoter
+c-Myc pd CDK6_promoter
+TAFII250 pd HADH2_promoter
+E2F1 pd HKR3_promoter
+Pol_II interactsWith HKR3_promoter
+Max pd HKR3_promoter
+TAFII250 pd HKR3_promoter
+Pol_II interactsWith PDK3_promoter
+Max pd PDK3_promoter
+TAFII250 pd PDK3_promoter
+c-Myc pd PDK3_promoter
+Max pd MAP3K5_promoter
+c-Myc pd MAP3K5_promoter
+E2F1 pd CD79B_promoter
+Pol_II interactsWith CD79B_promoter
+Max pd CD79B_promoter
+TAFII250 pd CD79B_promoter
+c-Myc pd CD79B_promoter
+Pol_II interactsWith RPL27A_promoter
+Max pd RPL27A_promoter
+TAFII250 pd RPL27A_promoter
+c-Myc pd RPL27A_promoter
+E2F1 pd RPS20_promoter
+Pol_II interactsWith RPS20_promoter
+Max pd RPS20_promoter
+TAFII250 pd RPS20_promoter
+c-Myc pd RPS20_promoter
+Pol_II interactsWith ETFA_promoter
+Max pd ETFA_promoter
+TAFII250 pd ETFA_promoter
+c-Myc pd ETFA_promoter
+Max pd PCTK1_promoter
+TAFII250 pd PCTK1_promoter
+c-Myc pd PCTK1_promoter
+E2F1 pd MBNL_promoter
+Max pd MBNL_promoter
+TAFII250 pd MBNL_promoter
+c-Myc pd MBNL_promoter
+E2F1 pd RPL32_promoter
+Pol_II interactsWith RPL32_promoter
+Max pd RPL32_promoter
+TAFII250 pd RPL32_promoter
+c-Myc pd RPL32_promoter
+c-Myc pd PENK_promoter
+Pol_II interactsWith METTL1_promoter
+Max pd METTL1_promoter
+TAFII250 pd METTL1_promoter
+c-Myc pd METTL1_promoter
+Pol_II interactsWith RPS25_promoter
+Max pd RPS25_promoter
+TAFII250 pd RPS25_promoter
+c-Myc pd RPS25_promoter
+E2F1 pd CDC6_promoter
+Pol_II interactsWith CDC6_promoter
+Max pd CDC6_promoter
+TAFII250 pd CDC6_promoter
+c-Myc pd CDC6_promoter
+Pol_II interactsWith HLA-G_promoter
+TAFII250 pd HLA-G_promoter
+E2F1 pd M17S2_promoter
+Max pd M17S2_promoter
+TAFII250 pd M17S2_promoter
+c-Myc pd M17S2_promoter
+Max pd PER1_promoter
+c-Myc pd PER1_promoter
+E2F1 pd RLN2_promoter
+Max pd RLN2_promoter
+TAFII250 pd RPL6_promoter
+c-Myc pd RPL6_promoter
+Pol_II interactsWith RPS27A_promoter
+Max pd RPS27A_promoter
+TAFII250 pd RPS27A_promoter
+c-Myc pd RPS27A_promoter
+E2F1 pd CDC25B_promoter
+Pol_II interactsWith CDC25B_promoter
+Max pd CDC25B_promoter
+TAFII250 pd CDC25B_promoter
+c-Myc pd CDC25B_promoter
+Max pd PEX1_promoter
+Max pd APEH_promoter
+Max pd HSPA9B_promoter
+TAFII250 pd HSPA9B_promoter
+c-Myc pd HSPA9B_promoter
+TAFII250 pd ARFD1_promoter
+c-Myc pd ARFD1_promoter
+Max pd MST1R_promoter
+c-Myc pd MST1R_promoter
+TAFII250 pd COPA_promoter
+Pol_II interactsWith ICSBP1_promoter
+TAFII250 pd ICSBP1_promoter
+c-Myc pd PLAGL2_promoter
+Max pd ASAH_promoter
+TAFII250 pd ASAH_promoter
+c-Myc pd ASAH_promoter
+c-Myc pd GAD1_promoter
+Pol_II interactsWith IFNB1_promoter
+Max pd MT3_promoter
+TAFII250 pd MT3_promoter
+c-Myc pd MT3_promoter
+E2F1 pd POLR2K_promoter
+Pol_II interactsWith POLR2K_promoter
+TAFII250 pd POLR2K_promoter
+c-Myc pd POLR2K_promoter
+Pol_II interactsWith SLC31A1_promoter
+Max pd SLC31A1_promoter
+TAFII250 pd SLC31A1_promoter
+c-Myc pd SLC31A1_promoter
+E2F1 pd HSPE1_promoter
+Pol_II interactsWith HSPE1_promoter
+Max pd HSPE1_promoter
+TAFII250 pd HSPE1_promoter
+c-Myc pd HSPE1_promoter
+Pol_II interactsWith SACM2L_promoter
+Max pd SACM2L_promoter
+TAFII250 pd SACM2L_promoter
+c-Myc pd SACM2L_promoter
+Pol_II interactsWith CSE1L_promoter
+TAFII250 pd CSE1L_promoter
+E2F1 pd GAK_promoter
+Pol_II interactsWith GAK_promoter
+Max pd GAK_promoter
+TAFII250 pd GAK_promoter
+c-Myc pd GAK_promoter
+E2F1 pd IFNGR1_promoter
+Pol_II interactsWith IFNGR1_promoter
+Max pd IFNGR1_promoter
+TAFII250 pd IFNGR1_promoter
+c-Myc pd IFNGR1_promoter
+E2F1 pd PPP1R6_promoter
+Pol_II interactsWith PPP1R6_promoter
+Max pd PPP1R6_promoter
+TAFII250 pd PPP1R6_promoter
+c-Myc pd PPP1R6_promoter
+Pol_II interactsWith CNGB1_promoter
+TAFII250 pd CNGB1_promoter
+Pol_II interactsWith COX4_promoter
+Max pd COX4_promoter
+TAFII250 pd COX4_promoter
+c-Myc pd COX4_promoter
+E2F1 pd FNTB_promoter
+TAFII250 pd FNTB_promoter
+Pol_II interactsWith PMS1_promoter
+Max pd PMS1_promoter
+TAFII250 pd PMS1_promoter
+c-Myc pd PMS1_promoter
+Pol_II interactsWith CREBL2_promoter
+Max pd CREBL2_promoter
+TAFII250 pd CREBL2_promoter
+c-Myc pd CREBL2_promoter
+Max pd CSF2RB_promoter
+c-Myc pd CSF2RB_promoter
+Pol_II interactsWith POU2F1_promoter
+Max pd POU2F1_promoter
+TAFII250 pd POU2F1_promoter
+c-Myc pd POU2F1_promoter
+E2F1 pd COX6A1_promoter
+Pol_II interactsWith COX6A1_promoter
+TAFII250 pd COX6A1_promoter
+TAFII250 pd IDH3G_promoter
+Pol_II interactsWith PMS2L9_promoter
+Max pd PMS2L9_promoter
+TAFII250 pd PMS2L9_promoter
+c-Myc pd PMS2L9_promoter
+TAFII250 pd CRHBP_promoter
+Pol_II interactsWith IGF2R_promoter
+TAFII250 pd IGF2R_promoter
+Pol_II interactsWith MTP_promoter
+TAFII250 pd MTP_promoter
+c-Myc pd MTP_promoter
+Max pd PPP2CA_promoter
+TAFII250 pd PPP2CA_promoter
+c-Myc pd PPP2CA_promoter
+Max pd FPGS_promoter
+TAFII250 pd FPGS_promoter
+c-Myc pd HTR1B_promoter
+TAFII250 pd IGFBP1_promoter
+c-Myc pd IGFBP1_promoter
+TAFII250 pd POU4F2_promoter
+c-Myc pd POU4F2_promoter
+Pol_II interactsWith PPP2R1B_promoter
+Max pd PPP2R1B_promoter
+TAFII250 pd PPP2R1B_promoter
+c-Myc pd PPP2R1B_promoter
+Max pd ENO2_promoter
+TAFII250 pd ENO2_promoter
+c-Myc pd ENO2_promoter
+Max pd HADHB_promoter
+TAFII250 pd HADHB_promoter
+c-Myc pd HADHB_promoter
+E2F1 pd RHEB2_promoter
+Pol_II interactsWith RHEB2_promoter
+Max pd RHEB2_promoter
+TAFII250 pd RHEB2_promoter
+c-Myc pd RHEB2_promoter
+E2F1 pd MEL_promoter
+Max pd MEL_promoter
+TAFII250 pd MEL_promoter
+c-Myc pd MEL_promoter
+Pol_II interactsWith PIGF_promoter
+Max pd PIGF_promoter
+TAFII250 pd PIGF_promoter
+c-Myc pd PIGF_promoter
+Max pd RPS19_promoter
+c-Myc pd RPS19_promoter
+TAFII250 pd ENSA_promoter
+Pol_II interactsWith HARS_promoter
+Max pd HARS_promoter
+TAFII250 pd HARS_promoter
+c-Myc pd HARS_promoter
+TAFII250 pd HLA-DNA_promoter
+Max pd SLC26A4_promoter
+c-Myc pd SLC26A4_promoter
+E2F1 pd RLN1_promoter
+Max pd RLN1_promoter
+c-Myc pd RLN1_promoter
+Max pd HOXA1_promoter
+Pol_II interactsWith RPL31_promoter
+Max pd RPL31_promoter
+TAFII250 pd RPL31_promoter
+c-Myc pd RPL31_promoter
+Pol_II interactsWith RPS21_promoter
+Max pd RPS21_promoter
+TAFII250 pd RPS21_promoter
+c-Myc pd RPS21_promoter
+E2F1 pd CDC2_promoter
+Pol_II interactsWith PCYT1A_promoter
+Max pd PCYT1A_promoter
+TAFII250 pd PCYT1A_promoter
+c-Myc pd PCYT1A_promoter
+Pol_II interactsWith CHD2_promoter
+TAFII250 pd CHD2_promoter
+TAFII250 pd CDC5L_promoter
+Pol_II interactsWith HLA-F_promoter
+Max pd HLA-F_promoter
+TAFII250 pd HLA-F_promoter
+c-Myc pd HLA-F_promoter
+Pol_II interactsWith M6PR_promoter
+Max pd M6PR_promoter
+TAFII250 pd M6PR_promoter
+c-Myc pd M6PR_promoter
+Pol_II interactsWith MAGOH_promoter
+Max pd MAGOH_promoter
+c-Myc pd MAGOH_promoter
+Max pd CISH_promoter
+c-Myc pd CISH_promoter
+Max pd MFAP1_promoter
+c-Myc pd MFAP1_promoter
+Pol_II interactsWith RPL37_promoter
+Max pd RPL37_promoter
+TAFII250 pd RPL37_promoter
+c-Myc pd RPL37_promoter
+Pol_II interactsWith CDC25A_promoter
+Max pd CDC25A_promoter
+TAFII250 pd CDC25A_promoter
+TAFII250 pd HLALS_promoter
+Pol_II interactsWith PET112L_promoter
+Max pd PET112L_promoter
+TAFII250 pd PET112L_promoter
+c-Myc pd PET112L_promoter
+Pol_II interactsWith SLC25A3_promoter
+TAFII250 pd SLC25A3_promoter
+Pol_II interactsWith RPL41_promoter
+Max pd RPS29_promoter
+TAFII250 pd RPS29_promoter
+c-Myc pd RPS29_promoter
+c-Myc pd CLGN_promoter
+Max pd MADH3_promoter
+c-Myc pd MADH3_promoter
+Max pd MAN2A1_promoter
+c-Myc pd MAN2A1_promoter
+Max pd PDE4C_promoter
+c-Myc pd PDE4C_promoter
+Pol_II interactsWith PEX6_promoter
+Max pd PEX6_promoter
+TAFII250 pd PEX6_promoter
+c-Myc pd PEX6_promoter
+Pol_II interactsWith RPL8_promoter
+Max pd RPL8_promoter
+TAFII250 pd RPL8_promoter
+c-Myc pd RPL8_promoter
+Max pd MFNG_promoter
+c-Myc pd MFNG_promoter
+Pol_II interactsWith MRPS12_promoter
+Max pd MRPS12_promoter
+TAFII250 pd MRPS12_promoter
+Pol_II interactsWith APEX_promoter
+Max pd APEX_promoter
+TAFII250 pd APEX_promoter
+Pol_II interactsWith ICAM4_promoter
+E2F1 pd SCO1_promoter
+Pol_II interactsWith SCO1_promoter
+Max pd SCO1_promoter
+TAFII250 pd SCO1_promoter
+c-Myc pd SCO1_promoter
+TAFII250 pd ARF1_promoter
+Pol_II interactsWith GABRR2_promoter
+Pol_II interactsWith IFNAR1_promoter
+Max pd IFNAR1_promoter
+TAFII250 pd IFNAR1_promoter
+c-Myc pd IFNAR1_promoter
+Max pd SEDL_promoter
+TAFII250 pd SH3BGRL_promoter
+Pol_II interactsWith CR2_promoter
+Max pd CR2_promoter
+TAFII250 pd CR2_promoter
+c-Myc pd CR2_promoter
+Pol_II interactsWith FKBP2_promoter
+Max pd FKBP2_promoter
+TAFII250 pd FKBP2_promoter
+c-Myc pd FKBP2_promoter
+Max pd MKLN1_promoter
+TAFII250 pd MKLN1_promoter
+c-Myc pd MKLN1_promoter
+Max pd MOCS2_promoter
+c-Myc pd MOCS2_promoter
+Pol_II interactsWith CREBL1_promoter
+Max pd CREBL1_promoter
+TAFII250 pd CREBL1_promoter
+E2F1 pd GALC_promoter
+Max pd GALC_promoter
+TAFII250 pd GALC_promoter
+c-Myc pd GALC_promoter
+Max pd IL10RB_promoter
+Max pd PPP1R7_promoter
+c-Myc pd PPP1R7_promoter
+E2F1 pd IDH3B_promoter
+Max pd IDH3B_promoter
+TAFII250 pd IDH3B_promoter
+c-Myc pd IDH3B_promoter
+E2F1 pd IGBP1_promoter
+Max pd IGBP1_promoter
+c-Myc pd IGBP1_promoter
+Pol_II interactsWith PPP1R10_promoter
+TAFII250 pd PPP1R10_promoter
+Max pd SARS_promoter
+c-Myc pd SARS_promoter
+Max pd GALNS_promoter
+c-Myc pd IL15_promoter
+Max pd PPP2R1A_promoter
+TAFII250 pd PPP2R1A_promoter
+E2F1 pd G22P1_promoter
+Pol_II interactsWith G22P1_promoter
+Max pd G22P1_promoter
+TAFII250 pd G22P1_promoter
+c-Myc pd G22P1_promoter
+Max pd MYOD1_promoter
+Max pd PPP2R4_promoter
+TAFII250 pd PPP2R4_promoter
+c-Myc pd PPP2R4_promoter
+Max pd CSTF3_promoter
+c-Myc pd CSTF3_promoter
+Max pd NCBP1_promoter
+TAFII250 pd NCBP1_promoter
+c-Myc pd NCBP1_promoter
+Max pd NDUFC1_promoter
+TAFII250 pd NDUFC1_promoter
+TAFII250 pd PRCP_promoter
+Max pd BLVRB_promoter
+Max pd DDX10_promoter
+TAFII250 pd DDX10_promoter
+c-Myc pd DDX10_promoter
+Pol_II interactsWith GOLGA1_promoter
+TAFII250 pd GOLGA1_promoter
+Max pd PSMD4_promoter
+TAFII250 pd PSMD4_promoter
+Max pd SNAPC3_promoter
+TAFII250 pd SNAPC3_promoter
+c-Myc pd SNAPC3_promoter
+E2F1 pd NDUFS3_promoter
+Pol_II interactsWith NDUFS3_promoter
+TAFII250 pd NDUFS3_promoter
+E2F1 pd PREP_promoter
+Max pd PREP_promoter
+c-Myc pd PREP_promoter
+TAFII250 pd GM2A_promoter
+E2F1 pd PSMD7_promoter
+Pol_II interactsWith PSMD7_promoter
+Max pd PSMD7_promoter
+TAFII250 pd PSMD7_promoter
+c-Myc pd PSMD7_promoter
+TAFII250 pd ATP5G3_promoter
+Max pd BCKDHA_promoter
+c-Myc pd BCKDHA_promoter
+Pol_II interactsWith NDUFS4_promoter
+TAFII250 pd NDUFS4_promoter
+Max pd MAP2K5_promoter
+c-Myc pd MAP2K5_promoter
+E2F1 pd SLC1A5_promoter
+Pol_II interactsWith SLC1A5_promoter
+TAFII250 pd SLC1A5_promoter
+Pol_II interactsWith DAXX_promoter
+Max pd DAXX_promoter
+TAFII250 pd DAXX_promoter
+c-Myc pd DAXX_promoter
+E2F1 pd NFKBIL1_promoter
+TAFII250 pd PSMD9_promoter
+E2F1 pd SNRPA_promoter
+Pol_II interactsWith SNRPA_promoter
+Max pd SNRPA_promoter
+TAFII250 pd SNRPA_promoter
+c-Myc pd SNRPA_promoter
+TAFII250 pd GIPR_promoter
+Pol_II interactsWith IRF3_promoter
+Max pd IRF3_promoter
+TAFII250 pd IRF3_promoter
+c-Myc pd IRF3_promoter
+Pol_II interactsWith NDUFA2_promoter
+Max pd NDUFA2_promoter
+TAFII250 pd NDUFA2_promoter
+c-Myc pd NDUFA2_promoter
+E2F1 pd NDUFS6_promoter
+Pol_II interactsWith NDUFS6_promoter
+Max pd NDUFS6_promoter
+TAFII250 pd NDUFS6_promoter
+c-Myc pd NDUFS6_promoter
+E2F1 pd MAP2K7_promoter
+Pol_II interactsWith MAP2K7_promoter
+Max pd MAP2K7_promoter
+TAFII250 pd MAP2K7_promoter
+c-Myc pd MAP2K7_promoter
+Max pd GNA12_promoter
+c-Myc pd GNA12_promoter
+c-Myc pd KCNJ2_promoter
+Max pd KHK_promoter
+c-Myc pd KHK_promoter
+Pol_II interactsWith CNOT4_promoter
+Max pd CNOT4_promoter
+TAFII250 pd CNOT4_promoter
+c-Myc pd CNOT4_promoter
+TAFII250 pd PSMD11_promoter
+c-Myc pd ITPR3_promoter
+TAFII250 pd NDUFV2_promoter
+Max pd DBI_promoter
+TAFII250 pd DBI_promoter
+c-Myc pd DBI_promoter
+Max pd KIF3C_promoter
+E2F1 pd SLPI_promoter
+TAFII250 pd NDUFA8_promoter
+Pol_II interactsWith DRG1_promoter
+Max pd DRG1_promoter
+TAFII250 pd DRG1_promoter
+c-Myc pd DRG1_promoter
+Pol_II interactsWith PRKAB2_promoter
+Max pd PRKAB2_promoter
+TAFII250 pd PRKAB2_promoter
+c-Myc pd PRKAB2_promoter
+TAFII250 pd DBT_promoter
+E2F1 pd NFYC_promoter
+Pol_II interactsWith NFYC_promoter
+TAFII250 pd NFYC_promoter
+Pol_II interactsWith PSMA3_promoter
+TAFII250 pd PSMA3_promoter
+E2F1 pd NRD1_promoter
+Pol_II interactsWith NRD1_promoter
+TAFII250 pd NRD1_promoter
+TAFII250 pd ODF2_promoter
+TAFII250 pd PTPN4_promoter
+E2F1 pd SP4_promoter
+Pol_II interactsWith SP4_promoter
+Max pd SP4_promoter
+TAFII250 pd SP4_promoter
+c-Myc pd SP4_promoter
+Pol_II interactsWith SRI_promoter
+Max pd SRI_promoter
+TAFII250 pd SRI_promoter
+c-Myc pd SRI_promoter
+TAFII250 pd LMAN1_promoter
+Pol_II interactsWith DR1_promoter
+Max pd DR1_promoter
+TAFII250 pd DR1_promoter
+TAFII250 pd PTPN11_promoter
+Pol_II interactsWith SREBF2_promoter
+Max pd SREBF2_promoter
+TAFII250 pd SREBF2_promoter
+c-Myc pd SREBF2_promoter
+TAFII250 pd CD80_promoter
+E2F1 pd E2F3_promoter
+Pol_II interactsWith E2F3_promoter
+TAFII250 pd E2F3_promoter
+Max pd LGALS1_promoter
+c-Myc pd ST14_promoter
+Pol_II interactsWith KPNA3_promoter
+Max pd KPNA3_promoter
+TAFII250 pd KPNA3_promoter
+c-Myc pd KPNA3_promoter
+TAFII250 pd TNFSF8_promoter
+Pol_II interactsWith STXBP2_promoter
+Max pd STXBP2_promoter
+TAFII250 pd STXBP2_promoter
+E2F1 pd KPNB2_promoter
+Pol_II interactsWith KPNB2_promoter
+Max pd KPNB2_promoter
+TAFII250 pd KPNB2_promoter
+Pol_II interactsWith SRP19_promoter
+TAFII250 pd SRP19_promoter
+TAFII250 pd ECH1_promoter
+Pol_II interactsWith RARS_promoter
+TAFII250 pd RARS_promoter
+Pol_II interactsWith STAT2_promoter
+TAFII250 pd STAT2_promoter
+Pol_II interactsWith PTPRF_promoter
+Max pd PTPRF_promoter
+TAFII250 pd PTPRF_promoter
+c-Myc pd PTPRF_promoter
+Max pd RAB3A_promoter
+TAFII250 pd RAB3A_promoter
+c-Myc pd RAB3A_promoter
+Pol_II interactsWith SPIB_promoter
+Max pd SPIB_promoter
+TAFII250 pd SPIB_promoter
+c-Myc pd SPIB_promoter
+Pol_II interactsWith SRP68_promoter
+Max pd SRP68_promoter
+TAFII250 pd SRP68_promoter
+c-Myc pd SRP68_promoter
+E2F1 pd RECQL_promoter
+Pol_II interactsWith RECQL_promoter
+Max pd RECQL_promoter
+TAFII250 pd RECQL_promoter
+c-Myc pd RECQL_promoter
+E2F1 pd CAPZA1_promoter
+Pol_II interactsWith CAPZA1_promoter
+Max pd CAPZA1_promoter
+TAFII250 pd CAPZA1_promoter
+c-Myc pd CAPZA1_promoter
+E2F1 pd CCNA2_promoter
+TAFII250 pd CCNA2_promoter
+E2F1 pd LRN_promoter
+Pol_II interactsWith LRN_promoter
+Max pd LRN_promoter
+TAFII250 pd LRN_promoter
+Max pd SLC7A1_promoter
+c-Myc pd SLC7A1_promoter
+Pol_II interactsWith GLUL_promoter
+TAFII250 pd GLUL_promoter
+c-Myc pd GLUL_promoter
+Max pd PSD_promoter
+Pol_II interactsWith PSMD5_promoter
+Max pd PSMD5_promoter
+TAFII250 pd PSMD5_promoter
+c-Myc pd PSMD5_promoter
+Max pd SLC22A3_promoter
+c-Myc pd SLC22A3_promoter
+Max pd ATP5G2_promoter
+TAFII250 pd ATP5G2_promoter
+c-Myc pd ATP5G2_promoter
+E2F1 pd EIF3S6_promoter
+Pol_II interactsWith EIF3S6_promoter
+TAFII250 pd EIF3S6_promoter
+TAFII250 pd ITM1_promoter
+Max pd NDUFV1_promoter
+c-Myc pd NDUFV1_promoter
+Max pd SLC1A4_promoter
+c-Myc pd SLC1A4_promoter
+Max pd GMDS_promoter
+TAFII250 pd GMDS_promoter
+c-Myc pd GMDS_promoter
+Max pd NFKBIB_promoter
+c-Myc pd NFKBIB_promoter
+Pol_II interactsWith PSMD8_promoter
+Max pd PSMD8_promoter
+TAFII250 pd PSMD8_promoter
+c-Myc pd PSMD8_promoter
+Max pd SLC22A4_promoter
+c-Myc pd SLC22A4_promoter
+TAFII250 pd SNRP70_promoter
+E2F1 pd BCKDHB_promoter
+Pol_II interactsWith BCKDHB_promoter
+Max pd BCKDHB_promoter
+TAFII250 pd BCKDHB_promoter
+c-Myc pd BCKDHB_promoter
+Pol_II interactsWith NDUFA1_promoter
+Max pd NDUFA1_promoter
+TAFII250 pd NDUFA1_promoter
+c-Myc pd NDUFA1_promoter
+Max pd PSMD10_promoter
+c-Myc pd PSMD10_promoter
+Max pd PRKRIR_promoter
+c-Myc pd PRKRIR_promoter
+Pol_II interactsWith SLC2A1_promoter
+TAFII250 pd SLC2A1_promoter
+c-Myc pd SLC2A1_promoter
+TAFII250 pd BNIP1_promoter
+E2F1 pd GCN5L1_promoter
+E2F1 pd NDUFA6_promoter
+Pol_II interactsWith NDUFA6_promoter
+Max pd NDUFA6_promoter
+TAFII250 pd NDUFA6_promoter
+c-Myc pd NDUFA6_promoter
+Pol_II interactsWith PRKAB1_promoter
+Max pd PRKAB1_promoter
+TAFII250 pd PRKAB1_promoter
+c-Myc pd PRKAB1_promoter
+Max pd SLC2A4_promoter
+c-Myc pd SLC2A4_promoter
+E2F1 pd SLC12A2_promoter
+Max pd SLC12A2_promoter
+TAFII250 pd SLC12A2_promoter
+c-Myc pd SLC12A2_promoter
+E2F1 pd PSMA1_promoter
+Pol_II interactsWith PSMA1_promoter
+Max pd PSMA1_promoter
+TAFII250 pd PSMA1_promoter
+c-Myc pd PSMA1_promoter
+E2F1 pd SNRPD3_promoter
+Pol_II interactsWith SNRPD3_promoter
+Max pd SNRPD3_promoter
+TAFII250 pd SNRPD3_promoter
+c-Myc pd SNRPD3_promoter
+Max pd NR6A1_promoter
+c-Myc pd NR6A1_promoter
+Pol_II interactsWith TIMM8A_promoter
+Max pd TIMM8A_promoter
+TAFII250 pd SNX1_promoter
+E2F1 pd CALU_promoter
+TAFII250 pd CALU_promoter
+E2F1 pd KNSL1_promoter
+Pol_II interactsWith KNSL1_promoter
+Max pd KNSL1_promoter
+TAFII250 pd KNSL1_promoter
+c-Myc pd KNSL1_promoter
+Max pd PTPN6_promoter
+c-Myc pd PTPN6_promoter
+Max pd SREBF1_promoter
+Max pd ST13_promoter
+Max pd SRM_promoter
+Pol_II interactsWith CD86_promoter
+TAFII250 pd CD86_promoter
+Pol_II interactsWith LNPEP_promoter
+Max pd LNPEP_promoter
+TAFII250 pd LNPEP_promoter
+c-Myc pd LNPEP_promoter
+Max pd RAP2B_promoter
+c-Myc pd RAP2B_promoter
+TAFII250 pd CA9_promoter
+Max pd KPNA5_promoter
+Max pd RAB1_promoter
+TAFII250 pd RAB1_promoter
+c-Myc pd RAB1_promoter
+Max pd RAB2L_promoter
+c-Myc pd RAB2L_promoter
+Max pd SRP54_promoter
+TAFII250 pd SRP54_promoter
+c-Myc pd SRP54_promoter
+Pol_II interactsWith EIF4EBP2_promoter
+TAFII250 pd EIF4EBP2_promoter
+c-Myc pd EIF4EBP2_promoter
+Pol_II interactsWith EIF4G2_promoter
+TAFII250 pd EIF4G2_promoter
+TAFII250 pd GSS_promoter
+TAFII250 pd LRMP_promoter
+TAFII250 pd CAPZA2_promoter
+TAFII250 pd TAF2D_promoter
+E2F1 pd ITGB3BP_promoter
+Pol_II interactsWith ITGB3BP_promoter
+Max pd ITGB3BP_promoter
+TAFII250 pd ITGB3BP_promoter
+c-Myc pd ITGB3BP_promoter
+E2F1 pd H2BFE_promoter
+Pol_II interactsWith H2BFE_promoter
+Max pd H2BFE_promoter
+TAFII250 pd H2BFE_promoter
+c-Myc pd H2BFE_promoter
+E2F1 pd ARPP-19_promoter
+Max pd ARPP-19_promoter
+TAFII250 pd ARPP-19_promoter
+c-Myc pd ARPP-19_promoter
+Max pd HS3ST2_promoter
+c-Myc pd HS3ST2_promoter
+Max pd PTE1_promoter
+TAFII250 pd PTE1_promoter
+E2F1 pd H2BFH_promoter
+Pol_II interactsWith H2BFH_promoter
+Max pd H2BFH_promoter
+TAFII250 pd H2BFH_promoter
+c-Myc pd H2BFH_promoter
+E2F1 pd RQCD1_promoter
+Pol_II interactsWith RQCD1_promoter
+Max pd RQCD1_promoter
+TAFII250 pd RQCD1_promoter
+c-Myc pd RQCD1_promoter
+TAFII250 pd YME1L1_promoter
+Max pd ZNF274_promoter
+c-Myc pd ZNF274_promoter
+Max pd NGB_promoter
+TAFII250 pd NGB_promoter
+c-Myc pd NGB_promoter
+Pol_II interactsWith LZTR1_promoter
+Max pd LZTR1_promoter
+TAFII250 pd LZTR1_promoter
+c-Myc pd LZTR1_promoter
+TAFII250 pd AIP_promoter
+Pol_II interactsWith NPR2L_promoter
+Max pd NPR2L_promoter
+TAFII250 pd NPR2L_promoter
+c-Myc pd NPR2L_promoter
+Pol_II interactsWith AP4E1_promoter
+Max pd AP4E1_promoter
+TAFII250 pd AP4E1_promoter
+c-Myc pd AP4E1_promoter
+Pol_II interactsWith M9_promoter
+Max pd M9_promoter
+TAFII250 pd M9_promoter
+c-Myc pd M9_promoter
+Pol_II interactsWith NXT1_promoter
+Max pd NXT1_promoter
+TAFII250 pd NXT1_promoter
+c-Myc pd NXT1_promoter
+E2F1 pd H2BFK_promoter
+Pol_II interactsWith H2BFK_promoter
+Max pd H2BFK_promoter
+TAFII250 pd H2BFK_promoter
+c-Myc pd H2BFK_promoter
+E2F1 pd SAE1_promoter
+Pol_II interactsWith SAE1_promoter
+Max pd SAE1_promoter
+TAFII250 pd SAE1_promoter
+c-Myc pd SAE1_promoter
+Max pd STAG3_promoter
+Max pd WDR4_promoter
+TAFII250 pd WDR4_promoter
+c-Myc pd WDR4_promoter
+c-Myc pd UBN1_promoter
+E2F1 pd HIG2_promoter
+Pol_II interactsWith HIG2_promoter
+TAFII250 pd HIG2_promoter
+E2F1 pd TRAP150_promoter
+Pol_II interactsWith TRAP150_promoter
+Max pd TRAP150_promoter
+TAFII250 pd TRAP150_promoter
+c-Myc pd TRAP150_promoter
+E2F1 pd EBP_promoter
+Pol_II interactsWith EBP_promoter
+TAFII250 pd EBP_promoter
+Max pd FHOS_promoter
+E2F1 pd H2BFN_promoter
+Pol_II interactsWith H2BFN_promoter
+Max pd H2BFN_promoter
+TAFII250 pd H2BFN_promoter
+c-Myc pd H2BFN_promoter
+E2F1 pd ABCB6_promoter
+Max pd ABCB6_promoter
+TAFII250 pd ABCB6_promoter
+c-Myc pd ABCB6_promoter
+Max pd GMPPB_promoter
+TAFII250 pd GMPPB_promoter
+Max pd SYK_promoter
+TAFII250 pd SYK_promoter
+c-Myc pd SYK_promoter
+Pol_II interactsWith DXF68S1E_promoter
+Max pd DXF68S1E_promoter
+TAFII250 pd DXF68S1E_promoter
+c-Myc pd DXF68S1E_promoter
+E2F1 pd CDC7L1_promoter
+TAFII250 pd CDC7L1_promoter
+Max pd NIFS_promoter
+TAFII250 pd NIFS_promoter
+c-Myc pd NIFS_promoter
+E2F1 pd NUP153_promoter
+Pol_II interactsWith NUP153_promoter
+Max pd NUP153_promoter
+TAFII250 pd NUP153_promoter
+c-Myc pd NUP153_promoter
+Pol_II interactsWith RABEX5_promoter
+Max pd RABEX5_promoter
+TAFII250 pd RABEX5_promoter
+c-Myc pd RABEX5_promoter
+Pol_II interactsWith H3FC_promoter
+E2F1 pd PLA2G6_promoter
+Pol_II interactsWith PLA2G6_promoter
+Max pd PLA2G6_promoter
+TAFII250 pd PLA2G6_promoter
+c-Myc pd PLA2G6_promoter
+Max pd PDCD8_promoter
+TAFII250 pd PDCD8_promoter
+c-Myc pd PDCD8_promoter
+Max pd USP11_promoter
+TAFII250 pd USP11_promoter
+c-Myc pd USP11_promoter
+E2F1 pd TDG_promoter
+Pol_II interactsWith TDG_promoter
+TAFII250 pd TDG_promoter
+Pol_II interactsWith H3FF_promoter
+TAFII250 pd H3FF_promoter
+Pol_II interactsWith SLC25A11_promoter
+Max pd SLC25A11_promoter
+TAFII250 pd SLC25A11_promoter
+c-Myc pd SLC25A11_promoter
+Pol_II interactsWith SCAMP3_promoter
+Max pd SCAMP3_promoter
+TAFII250 pd SCAMP3_promoter
+c-Myc pd SCAMP3_promoter
+Max pd ACTR1A_promoter
+TAFII250 pd ZNF261_promoter
+TAFII250 pd MBLL_promoter
+Pol_II interactsWith SEI1_promoter
+Max pd SEI1_promoter
+TAFII250 pd SEI1_promoter
+c-Myc pd SEI1_promoter
+Max pd TSC2_promoter
+TAFII250 pd TSC2_promoter
+c-Myc pd TSC2_promoter
+Pol_II interactsWith U2AF1_promoter
+Max pd U2AF1_promoter
+TAFII250 pd U2AF1_promoter
+c-Myc pd U2AF1_promoter
+E2F1 pd RPS6KA5_promoter
+Pol_II interactsWith RPS6KA5_promoter
+Max pd RPS6KA5_promoter
+TAFII250 pd RPS6KA5_promoter
+c-Myc pd RPS6KA5_promoter
+Max pd ABCC4_promoter
+c-Myc pd ABCC4_promoter
+TAFII250 pd MOV34-34KD_promoter
+Max pd LIV-1_promoter
+TAFII250 pd LIV-1_promoter
+c-Myc pd LIV-1_promoter
+Max pd TPD52L2_promoter
+TAFII250 pd TPD52L2_promoter
+E2F1 pd EXO1_promoter
+Max pd EXO1_promoter
+TAFII250 pd EXO1_promoter
+c-Myc pd EXO1_promoter
+Max pd POMT2_promoter
+c-Myc pd POMT2_promoter
+TAFII250 pd TSHB_promoter
+Pol_II interactsWith SCYE1_promoter
+TAFII250 pd SCYE1_promoter
+Pol_II interactsWith SF3B4_promoter
+TAFII250 pd SF3B4_promoter
+Pol_II interactsWith MAPRE2_promoter
+Max pd MAPRE2_promoter
+TAFII250 pd MAPRE2_promoter
+c-Myc pd MAPRE2_promoter
+E2F1 pd CD2AP_promoter
+Pol_II interactsWith CD2AP_promoter
+Max pd CD2AP_promoter
+TAFII250 pd CD2AP_promoter
+c-Myc pd CD2AP_promoter
+Max pd LLPL_promoter
+c-Myc pd LLPL_promoter
+Max pd TSPY_promoter
+c-Myc pd TSPY_promoter
+E2F1 pd DDXBP1_promoter
+Pol_II interactsWith DDXBP1_promoter
+Max pd DDXBP1_promoter
+TAFII250 pd DDXBP1_promoter
+c-Myc pd DDXBP1_promoter
+Pol_II interactsWith TRIP15_promoter
+Max pd TRIP15_promoter
+TAFII250 pd TRIP15_promoter
+c-Myc pd TRIP15_promoter
+E2F1 pd NBR2_promoter
+Pol_II interactsWith NBR2_promoter
+Max pd NBR2_promoter
+TAFII250 pd NBR2_promoter
+c-Myc pd NBR2_promoter
+Pol_II interactsWith COPS5_promoter
+TAFII250 pd COPS5_promoter
+Max pd JM23_promoter
+c-Myc pd JM23_promoter
+Max pd TMF1_promoter
+TAFII250 pd TMF1_promoter
+c-Myc pd TMF1_promoter
+E2F1 pd SIP1_promoter
+Pol_II interactsWith SIP1_promoter
+Max pd SIP1_promoter
+TAFII250 pd SIP1_promoter
+c-Myc pd SIP1_promoter
+Pol_II interactsWith COX7A2L_promoter
+Max pd COX7A2L_promoter
+TAFII250 pd COX7A2L_promoter
+c-Myc pd COX7A2L_promoter
+TAFII250 pd NRBP_promoter
+E2F1 pd UBE2D3_promoter
+Pol_II interactsWith UBE2D3_promoter
+Max pd UBE2D3_promoter
+TAFII250 pd UBE2D3_promoter
+c-Myc pd UBE2D3_promoter
+Pol_II interactsWith STK17B_promoter
+Max pd STK17B_promoter
+TAFII250 pd STK17B_promoter
+E2F1 pd GTF3C5_promoter
+Pol_II interactsWith GTF3C5_promoter
+Max pd GTF3C5_promoter
+TAFII250 pd GTF3C5_promoter
+c-Myc pd GTF3C5_promoter
+Pol_II interactsWith TMSB4X_promoter
+Max pd TMSB4X_promoter
+TAFII250 pd TMSB4X_promoter
+c-Myc pd TMSB4X_promoter
+E2F1 pd VAPB_promoter
+TAFII250 pd HPR6.6_promoter
+Pol_II interactsWith 54TM_promoter
+Max pd 54TM_promoter
+TAFII250 pd 54TM_promoter
+c-Myc pd 54TM_promoter
+Pol_II interactsWith TTC4_promoter
+Max pd TTC4_promoter
+TAFII250 pd TTC4_promoter
+c-Myc pd TTC4_promoter
+E2F1 pd DEGS_promoter
+Pol_II interactsWith DEGS_promoter
+Max pd DEGS_promoter
+TAFII250 pd DEGS_promoter
+c-Myc pd DEGS_promoter
+Max pd RASGRP2_promoter
+TAFII250 pd RASGRP2_promoter
+E2F1 pd RANBP3_promoter
+Pol_II interactsWith RANBP3_promoter
+Max pd RANBP3_promoter
+TAFII250 pd RANBP3_promoter
+c-Myc pd RANBP3_promoter
+Pol_II interactsWith UGTREL1_promoter
+Max pd SEC61B_promoter
+TAFII250 pd SEC61B_promoter
+c-Myc pd SEC61B_promoter
+TAFII250 pd SURF2_promoter
+Pol_II interactsWith TAF2F_promoter
+TAFII250 pd TAF2F_promoter
+E2F1 pd H4FM_promoter
+Pol_II interactsWith H4FM_promoter
+Max pd H4FM_promoter
+TAFII250 pd H4FM_promoter
+c-Myc pd H4FM_promoter
+Max pd RAGA_promoter
+TAFII250 pd RAGA_promoter
+c-Myc pd RAGA_promoter
+c-Myc pd DKK1_promoter
+Max pd TCF12_promoter
+TAFII250 pd TCF12_promoter
+c-Myc pd TCF12_promoter
+E2F1 pd H2BFG_promoter
+Pol_II interactsWith H2BFG_promoter
+Max pd H2BFG_promoter
+TAFII250 pd H2BFG_promoter
+c-Myc pd H2BFG_promoter
+Pol_II interactsWith SLC16A4_promoter
+E2F1 pd ACTR3_promoter
+Pol_II interactsWith ACTR3_promoter
+Max pd ACTR3_promoter
+TAFII250 pd ACTR3_promoter
+c-Myc pd ACTR3_promoter
+E2F1 pd P23_promoter
+Pol_II interactsWith P23_promoter
+Max pd P23_promoter
+TAFII250 pd P23_promoter
+c-Myc pd P23_promoter
+Pol_II interactsWith P5CR2_promoter
+Max pd P5CR2_promoter
+TAFII250 pd P5CR2_promoter
+c-Myc pd P5CR2_promoter
+Max pd SUV39H1_promoter
+TAFII250 pd SUV39H1_promoter
+Pol_II interactsWith TAF2I_promoter
+TAFII250 pd TAF2I_promoter
+Max pd DGCR6_promoter
+c-Myc pd DGCR6_promoter
+TAFII250 pd SEC10L1_promoter
+Pol_II interactsWith H2BFJ_promoter
+Max pd H2BFJ_promoter
+TAFII250 pd H2BFJ_promoter
+c-Myc pd H2BFJ_promoter
+E2F1 pd CSPG6_promoter
+E2F1 pd UBA2_promoter
+TAFII250 pd UBA2_promoter
+E2F1 pd NUBP2_promoter
+Pol_II interactsWith NUBP2_promoter
+Max pd NUBP2_promoter
+c-Myc pd NUBP2_promoter
+c-Myc pd NME7_promoter
+E2F1 pd VAMP1_promoter
+Pol_II interactsWith VAMP1_promoter
+Max pd VAMP1_promoter
+TAFII250 pd VAMP1_promoter
+c-Myc pd VAMP1_promoter
+Pol_II interactsWith ACOX3_promoter
+Max pd ACOX3_promoter
+TAFII250 pd ACOX3_promoter
+c-Myc pd ACOX3_promoter
+c-Myc pd AKR7A3_promoter
+Max pd ASC_promoter
+c-Myc pd ASC_promoter
+E2F1 pd H2BFL_promoter
+Pol_II interactsWith H2BFL_promoter
+Max pd H2BFL_promoter
+TAFII250 pd H2BFL_promoter
+c-Myc pd H2BFL_promoter
+Max pd HPRP4P_promoter
+TAFII250 pd HPRP4P_promoter
+Pol_II interactsWith SLC17A3_promoter
+TAFII250 pd SLC17A3_promoter
+Pol_II interactsWith ALG5_promoter
+TAFII250 pd ALG5_promoter
+E2F1 pd HDAC6_promoter
+Pol_II interactsWith HDAC6_promoter
+Max pd HDAC6_promoter
+TAFII250 pd HDAC6_promoter
+c-Myc pd HDAC6_promoter
+Pol_II interactsWith H3FA_promoter
+TAFII250 pd H3FA_promoter
+Pol_II interactsWith RAB6KIFL_promoter
+Max pd RAB6KIFL_promoter
+TAFII250 pd RAB6KIFL_promoter
+c-Myc pd RAB6KIFL_promoter
+E2F1 pd JAZ_promoter
+Pol_II interactsWith JAZ_promoter
+TAFII250 pd JAZ_promoter
+Max pd TIM22_promoter
+TAFII250 pd TIM22_promoter
+c-Myc pd TIM22_promoter
+E2F1 pd H3FD_promoter
+Pol_II interactsWith H3FD_promoter
+TAFII250 pd H3FD_promoter
+Pol_II interactsWith SYPL_promoter
+Max pd SYPL_promoter
+TAFII250 pd SYPL_promoter
+c-Myc pd SYPL_promoter
+Max pd CNTN2_promoter
+c-Myc pd CNTN2_promoter
+c-Myc pd BCL2L11_promoter
+E2F1 pd ABCB10_promoter
+Max pd ABCB10_promoter
+TAFII250 pd ABCB10_promoter
+c-Myc pd ABCB10_promoter
+Pol_II interactsWith H3FH_promoter
+TAFII250 pd H3FH_promoter
+Max pd HUMAGCGB_promoter
+c-Myc pd HUMAGCGB_promoter
+TAFII250 pd UTF1_promoter
+Max pd POR1_promoter
+c-Myc pd POR1_promoter
+Pol_II interactsWith TSG101_promoter
+TAFII250 pd TSG101_promoter
+Max pd BLZF1_promoter
+c-Myc pd BLZF1_promoter
+Max pd CBF2_promoter
+TAFII250 pd CBF2_promoter
+c-Myc pd CBF2_promoter
+Max pd CORO1C_promoter
+c-Myc pd CORO1C_promoter
+Max pd MLX_promoter
+c-Myc pd MLX_promoter
+Max pd IKBKAP_promoter
+TAFII250 pd IKBKAP_promoter
+Pol_II interactsWith PRAX-1_promoter
+Max pd COPS7A_promoter
+Pol_II interactsWith PSME3_promoter
+Max pd PSME3_promoter
+TAFII250 pd PSME3_promoter
+c-Myc pd PSME3_promoter
+Max pd MKRN1_promoter
+TAFII250 pd MKRN1_promoter
+c-Myc pd MKRN1_promoter
+Max pd ZFP95_promoter
+TAFII250 pd ZFP95_promoter
+c-Myc pd ZFP95_promoter
+Max pd ENIGMA_promoter
+Pol_II interactsWith MNPEP_promoter
+TAFII250 pd MNPEP_promoter
+Max pd TPR_promoter
+TAFII250 pd TPR_promoter
+c-Myc pd TPR_promoter
+E2F1 pd GNPAT_promoter
+Pol_II interactsWith GNPAT_promoter
+Max pd GNPAT_promoter
+TAFII250 pd GNPAT_promoter
+c-Myc pd GNPAT_promoter
+E2F1 pd MPHOSPH6_promoter
+Pol_II interactsWith MPHOSPH6_promoter
+Max pd MPHOSPH6_promoter
+c-Myc pd MPHOSPH6_promoter
+Max pd RUVBL2_promoter
+TAFII250 pd RUVBL2_promoter
+Pol_II interactsWith GTF3C4_promoter
+Max pd GTF3C4_promoter
+TAFII250 pd GTF3C4_promoter
+c-Myc pd GTF3C4_promoter
+E2F1 pd ZMPSTE24_promoter
+Pol_II interactsWith ZMPSTE24_promoter
+Max pd ZMPSTE24_promoter
+TAFII250 pd ZMPSTE24_promoter
+c-Myc pd ZMPSTE24_promoter
+Max pd E46L_promoter
+c-Myc pd E46L_promoter
+Pol_II interactsWith DUSP11_promoter
+TAFII250 pd DUSP11_promoter
+c-Myc pd DUSP11_promoter
+Max pd VAPA_promoter
+c-Myc pd VAPA_promoter
+E2F1 pd UBE2G2_promoter
+Pol_II interactsWith UBE2G2_promoter
+Max pd UBE2G2_promoter
+TAFII250 pd UBE2G2_promoter
+c-Myc pd UBE2G2_promoter
+Max pd PSCD2_promoter
+TAFII250 pd PSCD2_promoter
+c-Myc pd PSCD2_promoter
+E2F1 pd STUB1_promoter
+Max pd STUB1_promoter
+c-Myc pd STUB1_promoter
+Max pd TNFAIP1_promoter
+c-Myc pd TNFAIP1_promoter
+Max pd EMR2_promoter
+Pol_II interactsWith MADD_promoter
+Max pd MADD_promoter
+TAFII250 pd MADD_promoter
+c-Myc pd MADD_promoter
+TAFII250 pd CNOT8_promoter
+Max pd HPCL2_promoter
+TAFII250 pd HPCL2_promoter
+Max pd JRKL_promoter
+c-Myc pd JRKL_promoter
+TAFII250 pd STX8_promoter
+Pol_II interactsWith CEPT1_promoter
+Max pd CEPT1_promoter
+TAFII250 pd CEPT1_promoter
+c-Myc pd CEPT1_promoter
+Pol_II interactsWith TIM23_promoter
+Max pd TIM23_promoter
+TAFII250 pd TIM23_promoter
+c-Myc pd TIM23_promoter
+E2F1 pd NUDT6_promoter
+Max pd NUDT6_promoter
+TAFII250 pd NUDT6_promoter
+c-Myc pd NUDT6_promoter
+TAFII250 pd ZNF265_promoter
+Pol_II interactsWith DNAJA2_promoter
+Max pd DNAJA2_promoter
+c-Myc pd DNAJA2_promoter
+Max pd HSF2BP_promoter
+c-Myc pd HSF2BP_promoter
+TAFII250 pd PA_promoter
+Pol_II interactsWith CRADD_promoter
+Max pd CRADD_promoter
+TAFII250 pd CRADD_promoter
+c-Myc pd CRADD_promoter
+E2F1 pd GSTTLP28_promoter
+Max pd GSTTLP28_promoter
+TAFII250 pd GSTTLP28_promoter
+c-Myc pd GSTTLP28_promoter
+E2F1 pd APC10_promoter
+Pol_II interactsWith APC10_promoter
+Max pd APC10_promoter
+TAFII250 pd APC10_promoter
+c-Myc pd APC10_promoter
+Max pd RPC155_promoter
+TAFII250 pd RPC155_promoter
+c-Myc pd RPC155_promoter
+Pol_II interactsWith E2IG3_promoter
+Max pd E2IG3_promoter
+TAFII250 pd E2IG3_promoter
+Pol_II interactsWith HN1_promoter
+TAFII250 pd HN1_promoter
+Max pd PEX16_promoter
+TAFII250 pd PEX16_promoter
+c-Myc pd PEX16_promoter
+Max pd CSL4_promoter
+TAFII250 pd CSL4_promoter
+Pol_II interactsWith ZNF35_promoter
+Max pd ZNF35_promoter
+TAFII250 pd ZNF35_promoter
+c-Myc pd ZNF35_promoter
+E2F1 pd CDC23_promoter
+Pol_II interactsWith CDC23_promoter
+TAFII250 pd CDC23_promoter
+TAFII250 pd PSMF1_promoter
+Pol_II interactsWith IFI30_promoter
+Max pd IFI30_promoter
+TAFII250 pd IFI30_promoter
+c-Myc pd IFI30_promoter
+c-Myc pd SOX21_promoter
+E2F1 pd DED_promoter
+E2F1 pd EIF3S7_promoter
+Pol_II interactsWith EIF3S7_promoter
+TAFII250 pd EIF3S7_promoter
+Pol_II interactsWith NLVCF_promoter
+Max pd NLVCF_promoter
+TAFII250 pd NLVCF_promoter
+c-Myc pd NLVCF_promoter
+Pol_II interactsWith UNRIP_promoter
+Max pd UNRIP_promoter
+TAFII250 pd UNRIP_promoter
+Pol_II interactsWith FE65L2_promoter
+Max pd FE65L2_promoter
+TAFII250 pd FE65L2_promoter
+TAFII250 pd ADAMTS6_promoter
+c-Myc pd CNNM1_promoter
+Pol_II interactsWith DCTN4_promoter
+Max pd DCTN4_promoter
+TAFII250 pd DCTN4_promoter
+c-Myc pd DCTN4_promoter
+E2F1 pd USP1_promoter
+Pol_II interactsWith USP1_promoter
+Max pd USP1_promoter
+TAFII250 pd USP1_promoter
+c-Myc pd USP1_promoter
+E2F1 pd DSCR2_promoter
+Pol_II interactsWith DSCR2_promoter
+Max pd DSCR2_promoter
+TAFII250 pd DSCR2_promoter
+c-Myc pd DSCR2_promoter
+Max pd EIF3S2_promoter
+c-Myc pd EIF3S2_promoter
+Max pd PPT2_promoter
+c-Myc pd PPT2_promoter
+TAFII250 pd LOC51133_promoter
+E2F1 pd CD164_promoter
+Pol_II interactsWith CD164_promoter
+Max pd CD164_promoter
+TAFII250 pd CD164_promoter
+c-Myc pd CD164_promoter
+Max pd NUFIP1_promoter
+c-Myc pd NUFIP1_promoter
+E2F1 pd ZNF147_promoter
+Pol_II interactsWith ZNF147_promoter
+Max pd ZNF147_promoter
+TAFII250 pd ZNF147_promoter
+c-Myc pd ZNF147_promoter
+Pol_II interactsWith ZNF225_promoter
+Max pd ZNF225_promoter
+TAFII250 pd ZNF225_promoter
+c-Myc pd ZNF225_promoter
+Pol_II interactsWith CD84_promoter
+Pol_II interactsWith BAG4_promoter
+TAFII250 pd BAG4_promoter
+Max pd SPAG6_promoter
+c-Myc pd SPAG6_promoter
+E2F1 pd TIM44_promoter
+Pol_II interactsWith TIM44_promoter
+Max pd TIM44_promoter
+TAFII250 pd TIM44_promoter
+c-Myc pd TIM44_promoter
+E2F1 pd FACTP140_promoter
+Pol_II interactsWith FACTP140_promoter
+Max pd FACTP140_promoter
+TAFII250 pd FACTP140_promoter
+c-Myc pd FACTP140_promoter
+Max pd BET3_promoter
+c-Myc pd BET3_promoter
+Pol_II interactsWith CUL5_promoter
+Max pd CUL5_promoter
+TAFII250 pd CUL5_promoter
+c-Myc pd CUL5_promoter
+Pol_II interactsWith CDC16_promoter
+Max pd CDC16_promoter
+TAFII250 pd CDC16_promoter
+c-Myc pd CDC16_promoter
+Max pd HERC3_promoter
+TAFII250 pd HERC3_promoter
+Max pd ZNF230_promoter
+TAFII250 pd ZNF230_promoter
+TAFII250 pd SCEL_promoter
+Pol_II interactsWith BAG2_promoter
+Max pd DNAI1_promoter
+c-Myc pd DNAI1_promoter
+Pol_II interactsWith APPBP1_promoter
+TAFII250 pd APPBP1_promoter
+Pol_II interactsWith PEX11B_promoter
+Max pd PEX11B_promoter
+TAFII250 pd PEX11B_promoter
+c-Myc pd PEX11B_promoter
+Max pd HRH3_promoter
+Max pd HKE4_promoter
+TAFII250 pd HKE4_promoter
+c-Myc pd HKE4_promoter
+E2F1 pd SUCLG1_promoter
+Pol_II interactsWith SUCLG1_promoter
+Max pd SUCLG1_promoter
+TAFII250 pd SUCLG1_promoter
+c-Myc pd SUCLG1_promoter
+E2F1 pd SLC25A17_promoter
+Pol_II interactsWith DCTN3_promoter
+Max pd DCTN3_promoter
+TAFII250 pd DCTN3_promoter
+c-Myc pd DCTN3_promoter
+Pol_II interactsWith LOC51275_promoter
+TAFII250 pd LOC51275_promoter
+Pol_II interactsWith LY117_promoter
+E2F1 pd GAS41_promoter
+Pol_II interactsWith GAS41_promoter
+TAFII250 pd GAS41_promoter
+TAFII250 pd RABAC1_promoter
+E2F1 pd KEO4_promoter
+Pol_II interactsWith KEO4_promoter
+Max pd KEO4_promoter
+TAFII250 pd KEO4_promoter
+c-Myc pd KEO4_promoter
+Max pd IL17C_promoter
+c-Myc pd IL17C_promoter
+Pol_II interactsWith PTP4A1_promoter
+Max pd PTP4A1_promoter
+TAFII250 pd PTP4A1_promoter
+c-Myc pd PTP4A1_promoter
+E2F1 pd CREG_promoter
+Pol_II interactsWith CREG_promoter
+TAFII250 pd CREG_promoter
+Pol_II interactsWith ABH_promoter
+Max pd ABH_promoter
+TAFII250 pd ABH_promoter
+c-Myc pd ABH_promoter
+Pol_II interactsWith PSCDBP_promoter
+Max pd PSCDBP_promoter
+TAFII250 pd PSCDBP_promoter
+c-Myc pd PSCDBP_promoter
+Pol_II interactsWith EPM2A_promoter
+Max pd EPM2A_promoter
+TAFII250 pd EPM2A_promoter
+c-Myc pd EPM2A_promoter
+Pol_II interactsWith DEEPEST_promoter
+Max pd DEEPEST_promoter
+TAFII250 pd DEEPEST_promoter
+c-Myc pd DEEPEST_promoter
+Pol_II interactsWith M96_promoter
+Max pd M96_promoter
+TAFII250 pd M96_promoter
+c-Myc pd M96_promoter
+Max pd MIR16_promoter
+TAFII250 pd MIR16_promoter
+c-Myc pd MIR16_promoter
+TAFII250 pd ZNF189_promoter
+Pol_II interactsWith LAPTM5_promoter
+TAFII250 pd LAPTM5_promoter
+Pol_II interactsWith PCF11_promoter
+Max pd PCF11_promoter
+TAFII250 pd PCF11_promoter
+c-Myc pd PCF11_promoter
+Pol_II interactsWith LPXN_promoter
+TAFII250 pd LPXN_promoter
+Max pd SSTRIP_promoter
+TAFII250 pd VIM_promoter
+E2F1 pd MAEA_promoter
+Pol_II interactsWith MAEA_promoter
+Max pd MAEA_promoter
+TAFII250 pd MAEA_promoter
+c-Myc pd MAEA_promoter
+TAFII250 pd GGA1_promoter
+E2F1 pd FBXO24_promoter
+TAFII250 pd FBXO24_promoter
+TAFII250 pd RRP40_promoter
+E2F1 pd WNT2B_promoter
+Pol_II interactsWith AIM2_promoter
+TAFII250 pd AIM2_promoter
+Pol_II interactsWith UQCRB_promoter
+TAFII250 pd UQCRB_promoter
+E2F1 pd HPRP8BP_promoter
+Pol_II interactsWith HPRP8BP_promoter
+Max pd HPRP8BP_promoter
+TAFII250 pd HPRP8BP_promoter
+c-Myc pd HPRP8BP_promoter
+TAFII250 pd PAK4_promoter
+c-Myc pd PAK4_promoter
+Pol_II interactsWith LOC51035_promoter
+Max pd LOC51035_promoter
+TAFII250 pd LOC51035_promoter
+c-Myc pd LOC51035_promoter
+Pol_II interactsWith MD-1_promoter
+Max pd MD-1_promoter
+TAFII250 pd MD-1_promoter
+c-Myc pd MD-1_promoter
+Max pd UQCRC2_promoter
+TAFII250 pd UQCRC2_promoter
+c-Myc pd UQCRC2_promoter
+E2F1 pd DLEU1_promoter
+Pol_II interactsWith DLEU1_promoter
+Max pd DLEU1_promoter
+TAFII250 pd DLEU1_promoter
+c-Myc pd DLEU1_promoter
+Pol_II interactsWith PIM2_promoter
+TAFII250 pd PIM2_promoter
+E2F1 pd FBXO5_promoter
+Pol_II interactsWith FBXO5_promoter
+Max pd FBXO5_promoter
+TAFII250 pd FBXO5_promoter
+c-Myc pd FBXO5_promoter
+Max pd LOC51042_promoter
+TAFII250 pd LOC51042_promoter
+c-Myc pd LOC51042_promoter
+E2F1 pd XK_promoter
+Pol_II interactsWith XK_promoter
+Max pd XK_promoter
+TAFII250 pd XK_promoter
+c-Myc pd XK_promoter
+Max pd TIM17_promoter
+TAFII250 pd TIM17_promoter
+c-Myc pd TIM17_promoter
+Pol_II interactsWith CRIPT_promoter
+Max pd CRIPT_promoter
+TAFII250 pd CRIPT_promoter
+TAFII250 pd HIBCH_promoter
+Pol_II interactsWith PWP1_promoter
+Max pd PWP1_promoter
+TAFII250 pd PWP1_promoter
+c-Myc pd PWP1_promoter
+TAFII250 pd VRK2_promoter
+Max pd HMG20A_promoter
+TAFII250 pd HMG20A_promoter
+c-Myc pd HMG20A_promoter
+Max pd LOC51134_promoter
+TAFII250 pd LOC51134_promoter
+c-Myc pd LOC51134_promoter
+Max pd YY1_promoter
+c-Myc pd YY1_promoter
+c-Myc pd ZNF221_promoter
+TAFII250 pd TNFRSF14_promoter
+Pol_II interactsWith PMPCB_promoter
+Max pd PMPCB_promoter
+TAFII250 pd PMPCB_promoter
+c-Myc pd PMPCB_promoter
+Pol_II interactsWith ZNF151_promoter
+TAFII250 pd ZNF151_promoter
+Pol_II interactsWith BAG3_promoter
+Max pd HKE2_promoter
+TAFII250 pd HKE2_promoter
+Max pd SIP2-28_promoter
+c-Myc pd SIP2-28_promoter
+Pol_II interactsWith SIAT8D_promoter
+TAFII250 pd SIAT8D_promoter
+Pol_II interactsWith ZNF259_promoter
+Max pd ZNF259_promoter
+TAFII250 pd ZNF259_promoter
+c-Myc pd ZNF259_promoter
+TAFII250 pd HERC2_promoter
+c-Myc pd HERC2_promoter
+E2F1 pd GGH_promoter
+Max pd GGH_promoter
+TAFII250 pd GGH_promoter
+c-Myc pd GGH_promoter
+E2F1 pd RPA40_promoter
+Pol_II interactsWith RPA40_promoter
+Max pd RPA40_promoter
+TAFII250 pd RPA40_promoter
+c-Myc pd RPA40_promoter
+E2F1 pd MPHOSPH1_promoter
+Pol_II interactsWith MPHOSPH1_promoter
+Max pd MPHOSPH1_promoter
+TAFII250 pd MPHOSPH1_promoter
+c-Myc pd MPHOSPH1_promoter
+E2F1 pd CACYBP_promoter
+Pol_II interactsWith CACYBP_promoter
+Max pd CACYBP_promoter
+TAFII250 pd CACYBP_promoter
+c-Myc pd CACYBP_promoter
+Pol_II interactsWith ALDH5A1_promoter
+Pol_II interactsWith SLC5A6_promoter
+Max pd SLC5A6_promoter
+TAFII250 pd SLC5A6_promoter
+c-Myc pd SLC5A6_promoter
+E2F1 pd PTDSS1_promoter
+Pol_II interactsWith PTDSS1_promoter
+Max pd PTDSS1_promoter
+TAFII250 pd PTDSS1_promoter
+c-Myc pd PTDSS1_promoter
+Max pd ABS_promoter
+c-Myc pd ABS_promoter
+Pol_II interactsWith ZNF174_promoter
+Max pd ZNF174_promoter
+TAFII250 pd ZNF174_promoter
+c-Myc pd ZNF174_promoter
+c-Myc pd SLC30A4_promoter
+Max pd RANBP8_promoter
+TAFII250 pd RANBP8_promoter
+Max pd ATP2C1_promoter
+Max pd FXR1_promoter
+TAFII250 pd FXR1_promoter
+E2F1 pd MBD4_promoter
+Pol_II interactsWith MBD4_promoter
+Max pd MBD4_promoter
+TAFII250 pd MBD4_promoter
+c-Myc pd MBD4_promoter
+Max pd HSA9761_promoter
+E2F1 pd SUCLA2_promoter
+Pol_II interactsWith SUCLA2_promoter
+TAFII250 pd SUCLA2_promoter
+Max pd AKAP10_promoter
+TAFII250 pd AKAP10_promoter
+c-Myc pd AKAP10_promoter
+Max pd ACAD8_promoter
+TAFII250 pd ACAD8_promoter
+c-Myc pd ACAD8_promoter
+Pol_II interactsWith SCAND1_promoter
+Max pd SCAND1_promoter
+TAFII250 pd SCAND1_promoter
+c-Myc pd SCAND1_promoter
+TAFII250 pd EIF2S2_promoter
+E2F1 pd KIAA0132_promoter
+Max pd KIAA0132_promoter
+TAFII250 pd KIAA0132_promoter
+c-Myc pd KIAA0132_promoter
+Pol_II interactsWith HIS1_promoter
+TAFII250 pd HIS1_promoter
+E2F1 pd TIF1_promoter
+Pol_II interactsWith TIF1_promoter
+Max pd TIF1_promoter
+TAFII250 pd TIF1_promoter
+c-Myc pd TIF1_promoter
+E2F1 pd DLEU2_promoter
+Pol_II interactsWith DLEU2_promoter
+Max pd DLEU2_promoter
+TAFII250 pd DLEU2_promoter
+c-Myc pd DLEU2_promoter
+E2F1 pd JTV1_promoter
+Pol_II interactsWith JTV1_promoter
+Max pd JTV1_promoter
+TAFII250 pd JTV1_promoter
+c-Myc pd JTV1_promoter
+Pol_II interactsWith CERD4_promoter
+Max pd CERD4_promoter
+TAFII250 pd CERD4_promoter
+Pol_II interactsWith KIAA0905_promoter
+Max pd KIAA0905_promoter
+TAFII250 pd KIAA0905_promoter
+Pol_II interactsWith SERP1_promoter
+Max pd SERP1_promoter
+TAFII250 pd SERP1_promoter
+c-Myc pd SERP1_promoter
+E2F1 pd LOC51582_promoter
+Pol_II interactsWith LOC51582_promoter
+Max pd LOC51582_promoter
+TAFII250 pd LOC51582_promoter
+c-Myc pd LOC51582_promoter
+Pol_II interactsWith ZNF192_promoter
+Max pd ZNF192_promoter
+TAFII250 pd ZNF192_promoter
+c-Myc pd ZNF192_promoter
+Pol_II interactsWith D1S155E_promoter
+Max pd D1S155E_promoter
+TAFII250 pd D1S155E_promoter
+c-Myc pd D1S155E_promoter
+Max pd APBA3_promoter
+c-Myc pd APBA3_promoter
+Pol_II interactsWith MTERF_promoter
+TAFII250 pd MTERF_promoter
+E2F1 pd TGN51_promoter
+Pol_II interactsWith TGN51_promoter
+TAFII250 pd TGN51_promoter
+E2F1 pd REA_promoter
+Pol_II interactsWith REA_promoter
+Max pd REA_promoter
+TAFII250 pd REA_promoter
+c-Myc pd REA_promoter
+Pol_II interactsWith SMCX_promoter
+Max pd SMCX_promoter
+TAFII250 pd SMCX_promoter
+c-Myc pd SMCX_promoter
+TAFII250 pd PAPSS2_promoter
+Pol_II interactsWith PMVK_promoter
+Max pd PMVK_promoter
+TAFII250 pd PMVK_promoter
+c-Myc pd PMVK_promoter
+TAFII250 pd CCT6B_promoter
+Max pd ABCB9_promoter
+Max pd OMI_promoter
+TAFII250 pd OMI_promoter
+c-Myc pd OMI_promoter
+Pol_II interactsWith H3FJ_promoter
+TAFII250 pd RAB5EP_promoter
+Pol_II interactsWith DPP3_promoter
+Max pd DPP3_promoter
+TAFII250 pd DPP3_promoter
+Pol_II interactsWith GRAP_promoter
+TAFII250 pd GRAP_promoter
+E2F1 pd HUMGT198A_promoter
+Max pd G2A_promoter
+TAFII250 pd G2A_promoter
+c-Myc pd G2A_promoter
+Pol_II interactsWith TBCE_promoter
+Max pd TBCE_promoter
+TAFII250 pd TBCE_promoter
+Pol_II interactsWith GFI1B_promoter
+E2F1 pd SLP65_promoter
+Pol_II interactsWith SLP65_promoter
+TAFII250 pd SLP65_promoter
+E2F1 pd H3FL_promoter
+Pol_II interactsWith H3FL_promoter
+TAFII250 pd H3FL_promoter
+c-Myc pd H3FL_promoter
+Pol_II interactsWith TAGLN2_promoter
+Max pd TAGLN2_promoter
+TAFII250 pd TAGLN2_promoter
+c-Myc pd TAGLN2_promoter
+E2F1 pd DXS9879E_promoter
+Pol_II interactsWith DXS9879E_promoter
+Max pd DXS9879E_promoter
+TAFII250 pd DXS9879E_promoter
+c-Myc pd DXS9879E_promoter
+E2F1 pd H2AFD_promoter
+Pol_II interactsWith H2AFD_promoter
+Max pd H2AFD_promoter
+TAFII250 pd H2AFD_promoter
+c-Myc pd H2AFD_promoter
+Max pd TROAP_promoter
+TAFII250 pd TROAP_promoter
+Pol_II interactsWith EEA1_promoter
+Max pd EEA1_promoter
+TAFII250 pd EEA1_promoter
+c-Myc pd EEA1_promoter
+E2F1 pd NUP50_promoter
+TAFII250 pd NUP50_promoter
+Pol_II interactsWith SDCCAG16_promoter
+Max pd SDCCAG16_promoter
+TAFII250 pd SDCCAG16_promoter
+Max pd RIG-I_promoter
+TAFII250 pd RIG-I_promoter
+c-Myc pd RIG-I_promoter
+E2F1 pd H2AFI_promoter
+Pol_II interactsWith H2AFI_promoter
+TAFII250 pd H2AFI_promoter
+E2F1 pd BAZ1B_promoter
+Max pd BAZ1B_promoter
+c-Myc pd BAZ1B_promoter
+Max pd TMOD2_promoter
+c-Myc pd TMOD2_promoter
+E2F1 pd H4FG_promoter
+Pol_II interactsWith H4FG_promoter
+TAFII250 pd H4FG_promoter
+Max pd ARFRP1_promoter
+c-Myc pd ARFRP1_promoter
+Max pd AHCYL1_promoter
+c-Myc pd AHCYL1_promoter
+E2F1 pd OSRF_promoter
+Max pd OSRF_promoter
+c-Myc pd OSRF_promoter
+Pol_II interactsWith TPT_promoter
+Max pd TPT_promoter
+TAFII250 pd TPT_promoter
+c-Myc pd TPT_promoter
+E2F1 pd H2AFN_promoter
+Pol_II interactsWith H2AFN_promoter
+Max pd H2AFN_promoter
+TAFII250 pd H2AFN_promoter
+c-Myc pd H2AFN_promoter
+E2F1 pd CASP8AP2_promoter
+Pol_II interactsWith CASP8AP2_promoter
+Max pd CASP8AP2_promoter
+TAFII250 pd CASP8AP2_promoter
+Pol_II interactsWith ADPRTL3_promoter
+Max pd ADPRTL3_promoter
+TAFII250 pd ADPRTL3_promoter
+c-Myc pd ADPRTL3_promoter
+Pol_II interactsWith ABT1_promoter
+Max pd ABT1_promoter
+TAFII250 pd ABT1_promoter
+c-Myc pd ABT1_promoter
+Max pd TLL2_promoter
+c-Myc pd TLL2_promoter
+E2F1 pd H4FI_promoter
+Pol_II interactsWith H4FI_promoter
+Max pd H4FI_promoter
+TAFII250 pd H4FI_promoter
+c-Myc pd H4FI_promoter
+E2F1 pd LATS1_promoter
+Pol_II interactsWith LATS1_promoter
+Max pd LATS1_promoter
+TAFII250 pd LATS1_promoter
+c-Myc pd LATS1_promoter
+E2F1 pd HOOK2_promoter
+Max pd HOOK2_promoter
+c-Myc pd HOOK2_promoter
+E2F1 pd RBT1_promoter
+TAFII250 pd RBT1_promoter
+Pol_II interactsWith NSP3_promoter
+Max pd NSP3_promoter
+TAFII250 pd NSP3_promoter
+c-Myc pd NSP3_promoter
+Pol_II interactsWith MGEA5_promoter
+Max pd MGEA5_promoter
+TAFII250 pd MGEA5_promoter
+c-Myc pd MGEA5_promoter
+Pol_II interactsWith HSPC051_promoter
+Max pd HSPC051_promoter
+TAFII250 pd HSPC051_promoter
+c-Myc pd HSPC051_promoter
+E2F1 pd H4FK_promoter
+Pol_II interactsWith H4FK_promoter
+Max pd H4FK_promoter
+TAFII250 pd H4FK_promoter
+c-Myc pd H4FK_promoter
+Max pd HCF-2_promoter
+TAFII250 pd HCF-2_promoter
+c-Myc pd HCF-2_promoter
+Pol_II interactsWith CARKL_promoter
+Max pd CARKL_promoter
+TAFII250 pd CARKL_promoter
+c-Myc pd CARKL_promoter
+E2F1 pd UBQLN1_promoter
+Pol_II interactsWith UBQLN1_promoter
+Max pd UBQLN1_promoter
+TAFII250 pd UBQLN1_promoter
+c-Myc pd UBQLN1_promoter
+E2F1 pd TUBG1_promoter
+Pol_II interactsWith TUBG1_promoter
+Max pd TUBG1_promoter
+TAFII250 pd TUBG1_promoter
+c-Myc pd TUBG1_promoter
+Max pd CSDA_promoter
+TAFII250 pd CSDA_promoter
+c-Myc pd CSDA_promoter
+Max pd C6ORF11_promoter
+TAFII250 pd C6ORF11_promoter
+c-Myc pd C6ORF11_promoter
+c-Myc pd PDIR_promoter
+TAFII250 pd CUL2_promoter
+TAFII250 pd OSMR_promoter
+c-Myc pd OSMR_promoter
+Pol_II interactsWith P5-1_promoter
+TAFII250 pd P5-1_promoter
+Pol_II interactsWith SDF2L1_promoter
+Max pd SDF2L1_promoter
+TAFII250 pd SDF2L1_promoter
+c-Myc pd SDF2L1_promoter
+Max pd SLC2A8_promoter
+Pol_II interactsWith CGBP_promoter
+Max pd CGBP_promoter
+TAFII250 pd CGBP_promoter
+c-Myc pd CGBP_promoter
+E2F1 pd COPS3_promoter
+Pol_II interactsWith COPS3_promoter
+Max pd COPS3_promoter
+TAFII250 pd COPS3_promoter
+c-Myc pd COPS3_promoter
+E2F1 pd KHSRP_promoter
+Max pd KHSRP_promoter
+c-Myc pd KHSRP_promoter
+Pol_II interactsWith NPIP_promoter
+E2F1 pd PEX3_promoter
+Pol_II interactsWith PEX3_promoter
+Max pd PEX3_promoter
+TAFII250 pd PEX3_promoter
+c-Myc pd PEX3_promoter
+Pol_II interactsWith POH1_promoter
+Max pd POH1_promoter
+TAFII250 pd POH1_promoter
+c-Myc pd POH1_promoter
+Max pd ZNRD1_promoter
+TAFII250 pd ZNRD1_promoter
+c-Myc pd ZNRD1_promoter
+E2F1 pd TULP3_promoter
+Pol_II interactsWith TULP3_promoter
+Max pd TULP3_promoter
+TAFII250 pd TULP3_promoter
+c-Myc pd TULP3_promoter
+E2F1 pd UCHL1_promoter
+Pol_II interactsWith UCHL1_promoter
+Max pd UCHL1_promoter
+TAFII250 pd UCHL1_promoter
+c-Myc pd UCHL1_promoter
+Max pd AKR7A2_promoter
+c-Myc pd AKR7A2_promoter
+Max pd SDCCAG10_promoter
+TAFII250 pd SDCCAG10_promoter
+c-Myc pd SDCCAG10_promoter
+c-Myc pd NOG_promoter
+c-Myc pd EHD3_promoter
+Pol_II interactsWith UK114_promoter
+Max pd UK114_promoter
+TAFII250 pd UK114_promoter
+c-Myc pd UK114_promoter
+E2F1 pd GEMIN4_promoter
+Pol_II interactsWith GEMIN4_promoter
+TAFII250 pd GEMIN4_promoter
+c-Myc pd GEMIN4_promoter
+Pol_II interactsWith CNIL_promoter
+Max pd CNIL_promoter
+TAFII250 pd CNIL_promoter
+E2F1 pd RNPS1_promoter
+Pol_II interactsWith RNPS1_promoter
+Max pd RNPS1_promoter
+TAFII250 pd RNPS1_promoter
+c-Myc pd RNPS1_promoter
+E2F1 pd NUP62_promoter
+Pol_II interactsWith NUP62_promoter
+Max pd NUP62_promoter
+TAFII250 pd NUP62_promoter
+c-Myc pd NUP62_promoter
+Pol_II interactsWith CTAG2_promoter
+Max pd TYK2_promoter
+TAFII250 pd TYK2_promoter
+c-Myc pd TYK2_promoter
+TAFII250 pd UBE4A_promoter
+TAFII250 pd SRM160_promoter
+E2F1 pd TMP21_promoter
+Pol_II interactsWith TMP21_promoter
+Max pd TMP21_promoter
+TAFII250 pd TMP21_promoter
+c-Myc pd TMP21_promoter
+c-Myc pd RAB35_promoter
+Pol_II interactsWith ZFP26_promoter
+Max pd ZFP26_promoter
+c-Myc pd ZFP26_promoter
+Pol_II interactsWith RBM7_promoter
+TAFII250 pd RBM7_promoter
+c-Myc pd RBM7_promoter
+Max pd ERO1L_promoter
+TAFII250 pd ERO1L_promoter
+c-Myc pd ERO1L_promoter
+Max pd STOML2_promoter
+TAFII250 pd STOML2_promoter
+c-Myc pd QPCT_promoter
+E2F1 pd SMC1L1_promoter
+Pol_II interactsWith SMC1L1_promoter
+Max pd SMC1L1_promoter
+c-Myc pd SMC1L1_promoter
+Pol_II interactsWith P84_promoter
+Max pd P84_promoter
+TAFII250 pd P84_promoter
+c-Myc pd P84_promoter
+Pol_II interactsWith CCT8_promoter
+Max pd CCT8_promoter
+TAFII250 pd CCT8_promoter
+c-Myc pd CCT8_promoter
+Pol_II interactsWith MAT2B_promoter
+Max pd MAT2B_promoter
+TAFII250 pd MAT2B_promoter
+c-Myc pd MAT2B_promoter
+Pol_II interactsWith H3FK_promoter
+TAFII250 pd H3FK_promoter
+Pol_II interactsWith U3-55K_promoter
+Max pd U3-55K_promoter
+TAFII250 pd U3-55K_promoter
+c-Myc pd U3-55K_promoter
+Max pd 13CDNA73_promoter
+TAFII250 pd 13CDNA73_promoter
+c-Myc pd 13CDNA73_promoter
+Max pd CPSF1_promoter
+c-Myc pd CPSF1_promoter
+Max pd CXORF12_promoter
+c-Myc pd CXORF12_promoter
+E2F1 pd H2AFC_promoter
+Pol_II interactsWith H2AFC_promoter
+Max pd H2AFC_promoter
+TAFII250 pd H2AFC_promoter
+c-Myc pd H2AFC_promoter
+E2F1 pd CH25H_promoter
+Max pd CH25H_promoter
+c-Myc pd CH25H_promoter
+E2F1 pd DMTF1_promoter
+Pol_II interactsWith DMTF1_promoter
+Max pd DMTF1_promoter
+TAFII250 pd DMTF1_promoter
+c-Myc pd DMTF1_promoter
+E2F1 pd H4FA_promoter
+Pol_II interactsWith H4FA_promoter
+TAFII250 pd H4FA_promoter
+Pol_II interactsWith UXT_promoter
+Max pd UXT_promoter
+TAFII250 pd UXT_promoter
+c-Myc pd UXT_promoter
+E2F1 pd APG12L_promoter
+Pol_II interactsWith APG12L_promoter
+Max pd APG12L_promoter
+TAFII250 pd APG12L_promoter
+c-Myc pd APG12L_promoter
+Pol_II interactsWith TRAP1_promoter
+Max pd TRAP1_promoter
+c-Myc pd TRAP1_promoter
+E2F1 pd H2AFE_promoter
+Pol_II interactsWith H2AFE_promoter
+Max pd H2AFE_promoter
+TAFII250 pd H2AFE_promoter
+c-Myc pd H2AFE_promoter
+E2F1 pd ASH2L_promoter
+Pol_II interactsWith ASH2L_promoter
+Max pd ASH2L_promoter
+TAFII250 pd ASH2L_promoter
+c-Myc pd ASH2L_promoter
+E2F1 pd AP4B1_promoter
+Max pd AP4B1_promoter
+TAFII250 pd AP4B1_promoter
+c-Myc pd AP4B1_promoter
+Pol_II interactsWith CAPN7_promoter
+Pol_II interactsWith PQBP1_promoter
+Pol_II interactsWith H2AFM_promoter
+E2F1 pd ADPRTL2_promoter
+Pol_II interactsWith ADPRTL2_promoter
+Max pd ADPRTL2_promoter
+TAFII250 pd ADPRTL2_promoter
+c-Myc pd ADPRTL2_promoter
+Max pd TLE3_promoter
+TAFII250 pd TLE3_promoter
+c-Myc pd TLE3_promoter
+E2F1 pd H4FH_promoter
+Pol_II interactsWith HHLA1_promoter
+Pol_II interactsWith AKAP9_promoter
+Max pd AKAP9_promoter
+TAFII250 pd AKAP9_promoter
+c-Myc pd AKAP9_promoter
+E2F1 pd TAF2B_promoter
+Pol_II interactsWith TAF2B_promoter
+TAFII250 pd TAF2B_promoter
+c-Myc pd TAF2B_promoter
+Pol_II interactsWith TCEB3_promoter
+Max pd TCEB3_promoter
+TAFII250 pd TCEB3_promoter
+c-Myc pd TCEB3_promoter
+E2F1 pd H2BFA_promoter
+Pol_II interactsWith H2BFA_promoter
+Max pd H2BFA_promoter
+TAFII250 pd H2BFA_promoter
+c-Myc pd H2BFA_promoter
+E2F1 pd KCNH4_promoter
+Max pd KCNH4_promoter
+c-Myc pd KCNH4_promoter
+E2F1 pd TLOC1_promoter
+Pol_II interactsWith TLOC1_promoter
+Max pd TLOC1_promoter
+TAFII250 pd TLOC1_promoter
+c-Myc pd TLOC1_promoter
+E2F1 pd H2BFD_promoter
+Pol_II interactsWith H2BFD_promoter
+Max pd H2BFD_promoter
+TAFII250 pd H2BFD_promoter
+c-Myc pd H2BFD_promoter
+Pol_II interactsWith NFAT5_promoter
+Max pd NFAT5_promoter
+TAFII250 pd NFAT5_promoter
+c-Myc pd NFAT5_promoter
+Pol_II interactsWith H4FL_promoter
+Pol_II interactsWith ARPC4_promoter
+Max pd ARPC4_promoter
+TAFII250 pd ARPC4_promoter
+c-Myc pd ARPC4_promoter
+Pol_II interactsWith POP4_promoter
+TAFII250 pd POP4_promoter
+Pol_II interactsWith POV1_promoter
+Max pd POV1_promoter
+TAFII250 pd POV1_promoter
+c-Myc pd POV1_promoter
+E2F1 pd AP4M1_promoter
+Pol_II interactsWith AP4M1_promoter
+Max pd AP4M1_promoter
+TAFII250 pd AP4M1_promoter
+c-Myc pd AP4M1_promoter
+E2F1 pd D13S106E_promoter
+Pol_II interactsWith D13S106E_promoter
+Max pd D13S106E_promoter
+TAFII250 pd D13S106E_promoter
+c-Myc pd D13S106E_promoter
+TAFII250 pd TUFT1_promoter
+E2F1 pd MKNK1_promoter
+Pol_II interactsWith MKNK1_promoter
+Max pd MKNK1_promoter
+TAFII250 pd MKNK1_promoter
+c-Myc pd MKNK1_promoter
+Max pd SR-BP1_promoter
+TAFII250 pd SR-BP1_promoter
+c-Myc pd SR-BP1_promoter
+Pol_II interactsWith PRDX5_promoter
+Max pd PRDX5_promoter
+TAFII250 pd PRDX5_promoter
+c-Myc pd PRDX5_promoter
+Max pd PPIL2_promoter
+Pol_II interactsWith RAB9P40_promoter
+TAFII250 pd RAB9P40_promoter
+Pol_II interactsWith RAB3-GAP150_promoter
+Max pd RAB3-GAP150_promoter
+TAFII250 pd RAB3-GAP150_promoter
+c-Myc pd RAB3-GAP150_promoter
+Max pd JAM1_promoter
+Pol_II interactsWith PARG_promoter
+Max pd PARG_promoter
+TAFII250 pd PARG_promoter
+c-Myc pd PARG_promoter
+c-Myc pd PNMA1_promoter
+Max pd RNAC_promoter
+c-Myc pd RNAC_promoter
+Pol_II interactsWith SGT1_promoter
+Max pd SGT1_promoter
+TAFII250 pd SGT1_promoter
+c-Myc pd SGT1_promoter
+Max pd MAFF_promoter
+c-Myc pd MAFF_promoter
+TAFII250 pd HSU15552_promoter
+Pol_II interactsWith PRKRA_promoter
+Max pd PRKRA_promoter
+TAFII250 pd PRKRA_promoter
+c-Myc pd PRKRA_promoter
+Pol_II interactsWith SAP18_promoter
+Max pd SAP18_promoter
+TAFII250 pd SAP18_promoter
+c-Myc pd SAP18_promoter
+Max pd DEF6_promoter
+c-Myc pd DEF6_promoter
+Max pd SUPT3H_promoter
+TAFII250 pd MSC_promoter
+E2F1 pd AGPS_promoter
+Pol_II interactsWith AGPS_promoter
+Max pd AGPS_promoter
+TAFII250 pd AGPS_promoter
+c-Myc pd AGPS_promoter
+E2F1 pd RPP20_promoter
+Pol_II interactsWith C8FW_promoter
+Max pd C8FW_promoter
+TAFII250 pd C8FW_promoter
+c-Myc pd C8FW_promoter
+TAFII250 pd TIP-1_promoter
+E2F1 pd SFRS11_promoter
+Max pd SFRS11_promoter
+TAFII250 pd SFRS11_promoter
+c-Myc pd SFRS11_promoter
+Pol_II interactsWith GC20_promoter
+TAFII250 pd GC20_promoter
+Max pd HEBP_promoter
+c-Myc pd HEBP_promoter
+Pol_II interactsWith UGDH_promoter
+Max pd UGDH_promoter
+TAFII250 pd ZFP93_promoter
+Max pd SF3A1_promoter
+Pol_II interactsWith APPL_promoter
+Max pd APPL_promoter
+TAFII250 pd APPL_promoter
+c-Myc pd APPL_promoter
+Max pd H326_promoter
+TAFII250 pd H326_promoter
+c-Myc pd H326_promoter
+Pol_II interactsWith GRHPR_promoter
+Max pd GRHPR_promoter
+TAFII250 pd GRHPR_promoter
+E2F1 pd RTN3_promoter
+Pol_II interactsWith RTN3_promoter
+Max pd RTN3_promoter
+TAFII250 pd RTN3_promoter
+E2F1 pd E1B-AP5_promoter
+Max pd E1B-AP5_promoter
+TAFII250 pd E1B-AP5_promoter
+c-Myc pd E1B-AP5_promoter
+E2F1 pd B3GAT3_promoter
+Pol_II interactsWith ZNF85_promoter
+Max pd ZNF85_promoter
+TAFII250 pd ZNF85_promoter
+c-Myc pd ZNF85_promoter
+E2F1 pd RAB11A_promoter
+Pol_II interactsWith RAB11A_promoter
+Max pd RAB11A_promoter
+TAFII250 pd RAB11A_promoter
+c-Myc pd RAB11A_promoter
+E2F1 pd FXR2_promoter
+Max pd FXR2_promoter
+TAFII250 pd FXR2_promoter
+c-Myc pd FXR2_promoter
+Pol_II interactsWith DDX26_promoter
+TAFII250 pd DDX26_promoter
+E2F1 pd LOC51172_promoter
+Max pd LOC51172_promoter
+TAFII250 pd LOC51172_promoter
+c-Myc pd LOC51172_promoter
+TAFII250 pd RPC_promoter
+TAFII250 pd VAMP4_promoter
+TAFII250 pd CBARA1_promoter
+Max pd EIF4EL3_promoter
+TAFII250 pd EIF4EL3_promoter
+c-Myc pd EIF4EL3_promoter
+Max pd SLC2A6_promoter
+TAFII250 pd SLC2A6_promoter
+Max pd WBSCR1_promoter
+c-Myc pd WBSCR1_promoter
+Max pd CIAO1_promoter
+c-Myc pd CIAO1_promoter
+Pol_II interactsWith LOC51065_promoter
+Max pd LOC51065_promoter
+TAFII250 pd LOC51065_promoter
+c-Myc pd LOC51065_promoter
+E2F1 pd LOC51143_promoter
+Pol_II interactsWith LOC51143_promoter
+Max pd LOC51143_promoter
+TAFII250 pd LOC51143_promoter
+c-Myc pd LOC51143_promoter
+E2F1 pd ZFPL1_promoter
+Max pd ZFPL1_promoter
+TAFII250 pd ZFPL1_promoter
+c-Myc pd ZFPL1_promoter
+Pol_II interactsWith ZNF134_promoter
+Max pd ZNF134_promoter
+TAFII250 pd ZNF134_promoter
+c-Myc pd ZNF134_promoter
+E2F1 pd SKB1_promoter
+Pol_II interactsWith SKB1_promoter
+Max pd SKB1_promoter
+TAFII250 pd SKB1_promoter
+c-Myc pd SKB1_promoter
+E2F1 pd HAX1_promoter
+Pol_II interactsWith HAX1_promoter
+Max pd HAX1_promoter
+TAFII250 pd HAX1_promoter
+c-Myc pd HAX1_promoter
+Pol_II interactsWith TIMM9_promoter
+Max pd TIMM9_promoter
+TAFII250 pd TIMM9_promoter
+c-Myc pd TIMM9_promoter
+Max pd NESH_promoter
+c-Myc pd NESH_promoter
+Pol_II interactsWith LOC51082_promoter
+Max pd LOC51082_promoter
+c-Myc pd LOC51082_promoter
+Pol_II interactsWith ZNF136_promoter
+Max pd ZNF136_promoter
+TAFII250 pd ZNF136_promoter
+c-Myc pd ZNF136_promoter
+E2F1 pd SNX3_promoter
+Pol_II interactsWith SNX3_promoter
+Max pd SNX3_promoter
+TAFII250 pd SNX3_promoter
+c-Myc pd SNX3_promoter
+E2F1 pd EEF1E1_promoter
+Pol_II interactsWith EEF1E1_promoter
+Max pd EEF1E1_promoter
+TAFII250 pd EEF1E1_promoter
+c-Myc pd EEF1E1_promoter
+Max pd GDBR1_promoter
+TAFII250 pd GDBR1_promoter
+c-Myc pd GDBR1_promoter
+E2F1 pd MAD2L2_promoter
+TAFII250 pd LOC51185_promoter
+Max pd DSCR5_promoter
+c-Myc pd DSCR5_promoter
+Pol_II interactsWith VDAC2_promoter
+Max pd VDAC2_promoter
+TAFII250 pd VDAC2_promoter
+c-Myc pd VDAC2_promoter
+TAFII250 pd CRSP3_promoter
+Pol_II interactsWith 101F6_promoter
+Max pd 101F6_promoter
+TAFII250 pd 101F6_promoter
+c-Myc pd 101F6_promoter
+c-Myc pd ZNF140_promoter
+Max pd GPSN2_promoter
+E2F1 pd GCP3_promoter
+Pol_II interactsWith LOC51187_promoter
+Max pd LOC51187_promoter
+TAFII250 pd LOC51187_promoter
+c-Myc pd LOC51187_promoter
+E2F1 pd TMEM5_promoter
+Max pd TMEM5_promoter
+c-Myc pd TMEM5_promoter
+Max pd ZNF7_promoter
+c-Myc pd ZNF7_promoter
+E2F1 pd ZNF142_promoter
+Pol_II interactsWith ZNF142_promoter
+Max pd ZNF142_promoter
+TAFII250 pd ZNF142_promoter
+c-Myc pd ZNF142_promoter
+Pol_II interactsWith MPDU1_promoter
+TAFII250 pd MPDU1_promoter
+Pol_II interactsWith GOLTC1_promoter
+Max pd GOLTC1_promoter
+TAFII250 pd GOLTC1_promoter
+c-Myc pd GOLTC1_promoter
+E2F1 pd LOC51192_promoter
+Pol_II interactsWith LOC51192_promoter
+TAFII250 pd LOC51192_promoter
+c-Myc pd ZNF193_promoter
+Pol_II interactsWith DAP3_promoter
+Max pd DAP3_promoter
+TAFII250 pd DAP3_promoter
+c-Myc pd DAP3_promoter
+Pol_II interactsWith SSSCA1_promoter
+Max pd SSSCA1_promoter
+TAFII250 pd SSSCA1_promoter
+Max pd PSCD4_promoter
+Pol_II interactsWith LOC51291_promoter
+Max pd LOC51291_promoter
+c-Myc pd LOC51291_promoter
+Pol_II interactsWith DSS1_promoter
+TAFII250 pd DSS1_promoter
+Pol_II interactsWith CGTHBA_promoter
+Max pd CGTHBA_promoter
+TAFII250 pd CGTHBA_promoter
+Pol_II interactsWith AF020591_promoter
+Max pd AF020591_promoter
+TAFII250 pd AF020591_promoter
+c-Myc pd AF020591_promoter
+c-Myc pd ZNF200_promoter
+Pol_II interactsWith SPAG7_promoter
+TAFII250 pd SPAG7_promoter
+TAFII250 pd VPS41_promoter
+E2F1 pd SNX5_promoter
+Max pd SNX5_promoter
+TAFII250 pd SNX5_promoter
+c-Myc pd SNX5_promoter
+E2F1 pd H2AFP_promoter
+Pol_II interactsWith H2AFP_promoter
+Max pd H2AFP_promoter
+TAFII250 pd H2AFP_promoter
+c-Myc pd H2AFP_promoter
+TAFII250 pd KIAA0274_promoter
+E2F1 pd RPC32_promoter
+Pol_II interactsWith RPC32_promoter
+Max pd RPC32_promoter
+TAFII250 pd RPC32_promoter
+c-Myc pd RPC32_promoter
+Pol_II interactsWith FUS1_promoter
+Max pd FUS1_promoter
+TAFII250 pd FUS1_promoter
+c-Myc pd FUS1_promoter
+Pol_II interactsWith NCBP2_promoter
+Max pd NCBP2_promoter
+TAFII250 pd NCBP2_promoter
+c-Myc pd NCBP2_promoter
+Max pd DR6_promoter
+c-Myc pd DR6_promoter
+TAFII250 pd SYNJ1_promoter
+Pol_II interactsWith CHD1L_promoter
+Max pd CHD1L_promoter
+TAFII250 pd CHD1L_promoter
+c-Myc pd CHD1L_promoter
+Pol_II interactsWith XIP_promoter
+Max pd XIP_promoter
+TAFII250 pd XIP_promoter
+c-Myc pd XIP_promoter
+E2F1 pd GLRA3_promoter
+Max pd GLRA3_promoter
+c-Myc pd GLRA3_promoter
+E2F1 pd COIL_promoter
+Pol_II interactsWith COIL_promoter
+Max pd COIL_promoter
+TAFII250 pd COIL_promoter
+c-Myc pd COIL_promoter
+Pol_II interactsWith NS1-BP_promoter
+Max pd NS1-BP_promoter
+TAFII250 pd NS1-BP_promoter
+c-Myc pd NS1-BP_promoter
+Max pd MAPRE1_promoter
+c-Myc pd MAPRE1_promoter
+TAFII250 pd PA26_promoter
+E2F1 pd MOCS3_promoter
+Pol_II interactsWith MOCS3_promoter
+Max pd MOCS3_promoter
+TAFII250 pd MOCS3_promoter
+c-Myc pd MOCS3_promoter
+Max pd LOC51596_promoter
+TAFII250 pd LOC51596_promoter
+c-Myc pd LOC51596_promoter
+Max pd FZD5_promoter
+c-Myc pd FZD5_promoter
+E2F1 pd SAP30_promoter
+Pol_II interactsWith SAP30_promoter
+Max pd SAP30_promoter
+TAFII250 pd SAP30_promoter
+c-Myc pd SAP30_promoter
+E2F1 pd P85SPR_promoter
+Pol_II interactsWith P85SPR_promoter
+Max pd P85SPR_promoter
+TAFII250 pd P85SPR_promoter
+c-Myc pd P85SPR_promoter
+Pol_II interactsWith RNF7_promoter
+Max pd RNF7_promoter
+TAFII250 pd RNF7_promoter
+c-Myc pd RNF7_promoter
+Max pd KIAA1017_promoter
+Pol_II interactsWith QP-C_promoter
+TAFII250 pd QP-C_promoter
+Pol_II interactsWith LOC51304_promoter
+Max pd LOC51304_promoter
+TAFII250 pd LOC51304_promoter
+c-Myc pd LOC51304_promoter
+Max pd VATD_promoter
+TAFII250 pd VATD_promoter
+c-Myc pd VATD_promoter
+Max pd ATF6_promoter
+TAFII250 pd ATF6_promoter
+c-Myc pd ATF6_promoter
+Pol_II interactsWith LOC51601_promoter
+Max pd LOC51601_promoter
+TAFII250 pd LOC51601_promoter
+c-Myc pd LOC51601_promoter
+Max pd ZNF215_promoter
+E2F1 pd GTPBP1_promoter
+Pol_II interactsWith D10S170_promoter
+Max pd D10S170_promoter
+TAFII250 pd D10S170_promoter
+c-Myc pd D10S170_promoter
+Max pd ELL_promoter
+TAFII250 pd ELL_promoter
+c-Myc pd ELL_promoter
+E2F1 pd PLOD3_promoter
+Max pd PLOD3_promoter
+TAFII250 pd PLOD3_promoter
+c-Myc pd PLOD3_promoter
+E2F1 pd MBNT_promoter
+Pol_II interactsWith MBNT_promoter
+TAFII250 pd MBNT_promoter
+E2F1 pd LSM1_promoter
+Pol_II interactsWith LSM1_promoter
+Max pd LSM1_promoter
+TAFII250 pd LSM1_promoter
+c-Myc pd LSM1_promoter
+Pol_II interactsWith LOC51603_promoter
+Max pd LOC51603_promoter
+TAFII250 pd LOC51603_promoter
+c-Myc pd LOC51603_promoter
+Pol_II interactsWith ARMET_promoter
+Max pd ARMET_promoter
+TAFII250 pd ARMET_promoter
+c-Myc pd ARMET_promoter
+Max pd CES2_promoter
+Max pd SGPL1_promoter
+c-Myc pd SGPL1_promoter
+Pol_II interactsWith GOSR2_promoter
+TAFII250 pd GOSR2_promoter
+Pol_II interactsWith MYBBP1A_promoter
+Max pd MYBBP1A_promoter
+TAFII250 pd MYBBP1A_promoter
+c-Myc pd MYBBP1A_promoter
+E2F1 pd TIP30_promoter
+Max pd B4GALT7_promoter
+Pol_II interactsWith RARG-1_promoter
+Max pd RARG-1_promoter
+TAFII250 pd RARG-1_promoter
+c-Myc pd RARG-1_promoter
+Max pd AMMECR1_promoter
+TAFII250 pd AMMECR1_promoter
+c-Myc pd AMMECR1_promoter
+Max pd SCLY_promoter
+TAFII250 pd SCLY_promoter
+c-Myc pd SCLY_promoter
+Pol_II interactsWith LOC51605_promoter
+Max pd LOC51605_promoter
+TAFII250 pd LOC51605_promoter
+c-Myc pd LOC51605_promoter
+c-Myc pd CDYL_promoter
+Pol_II interactsWith LANCL1_promoter
+Max pd LANCL1_promoter
+TAFII250 pd LANCL1_promoter
+c-Myc pd LANCL1_promoter
+Max pd LOC51136_promoter
+c-Myc pd LOC51136_promoter
+E2F1 pd YWHAH_promoter
+Pol_II interactsWith YWHAH_promoter
+Max pd YWHAH_promoter
+TAFII250 pd YWHAH_promoter
+c-Myc pd YWHAH_promoter
+Pol_II interactsWith RIPK2_promoter
+Max pd RIPK2_promoter
+TAFII250 pd RIPK2_promoter
+c-Myc pd RIPK2_promoter
+TAFII250 pd FXC1_promoter
+Pol_II interactsWith VASP_promoter
+Max pd VASP_promoter
+TAFII250 pd VASP_promoter
+c-Myc pd VASP_promoter
+Pol_II interactsWith RNASE6PL_promoter
+Max pd RNASE6PL_promoter
+c-Myc pd RNASE6PL_promoter
+Max pd STX16_promoter
+TAFII250 pd STX16_promoter
+c-Myc pd STX16_promoter
+Max pd CACNG3_promoter
+c-Myc pd CACNG3_promoter
+Pol_II interactsWith PP35_promoter
+Max pd PP35_promoter
+TAFII250 pd PP35_promoter
+Pol_II interactsWith LOC51064_promoter
+TAFII250 pd LOC51064_promoter
+Pol_II interactsWith ZFP37_promoter
+TAFII250 pd ZFP37_promoter
+c-Myc pd ZFP37_promoter
+E2F1 pd SPTLC2_promoter
+Max pd SPTLC2_promoter
+TAFII250 pd SPTLC2_promoter
+c-Myc pd SPTLC2_promoter
+E2F1 pd MAP4K5_promoter
+Pol_II interactsWith MAP4K5_promoter
+Max pd MAP4K5_promoter
+TAFII250 pd MAP4K5_promoter
+c-Myc pd MAP4K5_promoter
+Max pd TIMM10_promoter
+TAFII250 pd TIMM10_promoter
+Max pd STX10_promoter
+c-Myc pd STX10_promoter
+c-Myc pd CHST2_promoter
+Pol_II interactsWith K-ALPHA-1_promoter
+Max pd K-ALPHA-1_promoter
+c-Myc pd K-ALPHA-1_promoter
+Pol_II interactsWith LOC51144_promoter
+Max pd LOC51144_promoter
+TAFII250 pd LOC51144_promoter
+Pol_II interactsWith APG5L_promoter
+TAFII250 pd APG5L_promoter
+Pol_II interactsWith TBPL1_promoter
+TAFII250 pd TBPL1_promoter
+E2F1 pd TESK2_promoter
+Max pd TESK2_promoter
+TAFII250 pd TESK2_promoter
+c-Myc pd TESK2_promoter
+Pol_II interactsWith TIMM8B_promoter
+Max pd TIMM8B_promoter
+TAFII250 pd TIMM8B_promoter
+c-Myc pd TIMM8B_promoter
+Pol_II interactsWith NAKAP95_promoter
+TAFII250 pd NAKAP95_promoter
+Pol_II interactsWith LOC51184_promoter
+Max pd LOC51184_promoter
+TAFII250 pd LOC51184_promoter
+c-Myc pd LOC51184_promoter
+Pol_II interactsWith VCP_promoter
+Max pd VCP_promoter
+TAFII250 pd VCP_promoter
+c-Myc pd VCP_promoter
+Max pd PLA2G4B_promoter
+c-Myc pd PLA2G4B_promoter
+TAFII250 pd BTN3A2_promoter
+Pol_II interactsWith TRFP_promoter
+Max pd TRFP_promoter
+TAFII250 pd TRFP_promoter
+c-Myc pd TRFP_promoter
+Max pd VDAC3_promoter
+TAFII250 pd VDAC3_promoter
+c-Myc pd VDAC3_promoter
+Pol_II interactsWith RECQL5_promoter
+Max pd RECQL5_promoter
+c-Myc pd RECQL5_promoter
+Pol_II interactsWith CRSP6_promoter
+Max pd CRSP6_promoter
+TAFII250 pd CRSP6_promoter
+c-Myc pd CRSP6_promoter
+Pol_II interactsWith NOC4_promoter
+Max pd NOC4_promoter
+TAFII250 pd NOC4_promoter
+c-Myc pd NOC4_promoter
+Max pd BTN2A1_promoter
+c-Myc pd BTN2A1_promoter
+Pol_II interactsWith MYCBP_promoter
+Max pd MYCBP_promoter
+TAFII250 pd MYCBP_promoter
+c-Myc pd MYCBP_promoter
+Pol_II interactsWith SKD1_promoter
+TAFII250 pd SKD1_promoter
+Max pd VGF_promoter
+c-Myc pd VGF_promoter
+E2F1 pd TMEM4_promoter
+Pol_II interactsWith TMEM4_promoter
+Max pd TMEM4_promoter
+TAFII250 pd TMEM4_promoter
+c-Myc pd TMEM4_promoter
+E2F1 pd SCML2_promoter
+Max pd SCML2_promoter
+TAFII250 pd SCML2_promoter
+c-Myc pd SCML2_promoter
+E2F1 pd TOPBP1_promoter
+Pol_II interactsWith TOPBP1_promoter
+Max pd TOPBP1_promoter
+TAFII250 pd TOPBP1_promoter
+c-Myc pd TOPBP1_promoter
+Max pd BAG5_promoter
+TAFII250 pd CG1I_promoter
+c-Myc pd CG1I_promoter
+E2F1 pd CDKL3_promoter
+Pol_II interactsWith CDKL3_promoter
+Max pd CDKL3_promoter
+TAFII250 pd CDKL3_promoter
+c-Myc pd CDKL3_promoter
+Pol_II interactsWith ZNF195_promoter
+TAFII250 pd ZNF195_promoter
+E2F1 pd STK19_promoter
+Pol_II interactsWith STK19_promoter
+TAFII250 pd RNASEHI_promoter
+Pol_II interactsWith GAN_promoter
+TAFII250 pd GAN_promoter
+Pol_II interactsWith H3FI_promoter
+TAFII250 pd H3FI_promoter
+Pol_II interactsWith APEXL2_promoter
+E2F1 pd TIF1GAMMA_promoter
+Pol_II interactsWith TIF1GAMMA_promoter
+Max pd TIF1GAMMA_promoter
+TAFII250 pd TIF1GAMMA_promoter
+c-Myc pd TIF1GAMMA_promoter
+E2F1 pd DPM1_promoter
+Pol_II interactsWith DPM1_promoter
+Max pd DPM1_promoter
+TAFII250 pd DPM1_promoter
+c-Myc pd DPM1_promoter
+Max pd H2AFY_promoter
+c-Myc pd H2AFY_promoter
+Pol_II interactsWith D8S2298E_promoter
+Max pd D8S2298E_promoter
+TAFII250 pd D8S2298E_promoter
+c-Myc pd D8S2298E_promoter
+Pol_II interactsWith AP1G2_promoter
+TAFII250 pd AP1G2_promoter
+E2F1 pd H2BFR_promoter
+Pol_II interactsWith H2BFR_promoter
+Max pd H2BFR_promoter
+TAFII250 pd H2BFR_promoter
+c-Myc pd H2BFR_promoter
+Max pd GABARAP_promoter
+c-Myc pd GABARAP_promoter
+Pol_II interactsWith ZNF207_promoter
+TAFII250 pd ZNF207_promoter
+Pol_II interactsWith DPM2_promoter
+Max pd DPM2_promoter
+c-Myc pd DPM2_promoter
+Max pd VPS26_promoter
+Pol_II interactsWith LOC51303_promoter
+Max pd LOC51303_promoter
+TAFII250 pd LOC51303_promoter
+c-Myc pd LOC51303_promoter
+Pol_II interactsWith AKAP1_promoter
+TAFII250 pd AKAP1_promoter
+TAFII250 pd MTHFS_promoter
+Max pd LISCH7_promoter
+TAFII250 pd LISCH7_promoter
+c-Myc pd LISCH7_promoter
+Max pd H6PD_promoter
+c-Myc pd H6PD_promoter
+TAFII250 pd MTRF1_promoter
+Pol_II interactsWith JWA_promoter
+Max pd JWA_promoter
+TAFII250 pd JWA_promoter
+c-Myc pd JWA_promoter
+Max pd PDCD10_promoter
+c-Myc pd PDCD10_promoter
+Max pd ST6GALNACIV_promoter
+c-Myc pd ST6GALNACIV_promoter
+TAFII250 pd WASL_promoter
+c-Myc pd WASL_promoter
+Pol_II interactsWith ZNF216_promoter
+Max pd ZNF216_promoter
+TAFII250 pd ZNF216_promoter
+Max pd ABCG1_promoter
+TAFII250 pd ABCG1_promoter
+Pol_II interactsWith LOC51307_promoter
+TAFII250 pd LOC51307_promoter
+Max pd PME-1_promoter
+TAFII250 pd PME-1_promoter
+c-Myc pd PME-1_promoter
+Pol_II interactsWith SPK_promoter
+Max pd SPK_promoter
+TAFII250 pd SPK_promoter
+c-Myc pd SPK_promoter
+Pol_II interactsWith WDR1_promoter
+Pol_II interactsWith LSM3_promoter
+Max pd LSM3_promoter
+TAFII250 pd LSM3_promoter
+Pol_II interactsWith LOC51604_promoter
+TAFII250 pd LOC51604_promoter
+Pol_II interactsWith PDX1_promoter
+TAFII250 pd PDX1_promoter
+Max pd GOLGA5_promoter
+c-Myc pd GOLGA5_promoter
+Max pd PIR51_promoter
+TAFII250 pd PIR51_promoter
+c-Myc pd PIR51_promoter
+Pol_II interactsWith AICDA_promoter
+TAFII250 pd AICDA_promoter
+E2F1 pd LOC57862_promoter
+Max pd LOC57862_promoter
+TAFII250 pd LOC57862_promoter
+c-Myc pd LOC57862_promoter
+Pol_II interactsWith ATP5B_promoter
+Max pd ATP5B_promoter
+TAFII250 pd ATP5B_promoter
+c-Myc pd ATP5B_promoter
+E2F1 pd TOP2A_promoter
+Pol_II interactsWith TOP2A_promoter
+TAFII250 pd TOP2A_promoter
+TAFII250 pd TSN_promoter
+c-Myc pd TSN_promoter
+TAFII250 pd LOC51654_promoter
+E2F1 pd GIOT-3_promoter
+Pol_II interactsWith GIOT-3_promoter
+Max pd GIOT-3_promoter
+TAFII250 pd GIOT-3_promoter
+c-Myc pd GIOT-3_promoter
+Max pd NLI-IF_promoter
+c-Myc pd NLI-IF_promoter
+TAFII250 pd PRIM2A_promoter
+TAFII250 pd LOC51762_promoter
+E2F1 pd PTOV1_promoter
+Max pd PTOV1_promoter
+c-Myc pd PTOV1_promoter
+E2F1 pd BUB3_promoter
+Max pd BUB3_promoter
+TAFII250 pd BUB3_promoter
+Pol_II interactsWith LCP1_promoter
+Pol_II interactsWith LOC51278_promoter
+Max pd LOC51278_promoter
+TAFII250 pd LOC51278_promoter
+c-Myc pd LOC51278_promoter
+Pol_II interactsWith TP53_promoter
+Max pd TP53_promoter
+TAFII250 pd TP53_promoter
+c-Myc pd TP53_promoter
+E2F1 pd LOC51659_promoter
+Max pd LOC51659_promoter
+c-Myc pd LOC51659_promoter
+TAFII250 pd KIAA0426_promoter
+TAFII250 pd PPAP2B_promoter
+E2F1 pd TM9SF2_promoter
+Pol_II interactsWith TM9SF2_promoter
+TAFII250 pd TM9SF2_promoter
+Pol_II interactsWith FXYD7_promoter
+TAFII250 pd FXYD7_promoter
+Pol_II interactsWith PTPRCAP_promoter
+Max pd PTPRCAP_promoter
+TAFII250 pd PTPRCAP_promoter
+TAFII250 pd PPIE_promoter
+TAFII250 pd PRKCABP_promoter
+Max pd TM7SF3_promoter
+Pol_II interactsWith MDS024_promoter
+TAFII250 pd MDS024_promoter
+E2F1 pd PSA_promoter
+Max pd PSA_promoter
+TAFII250 pd PSA_promoter
+c-Myc pd PSA_promoter
+E2F1 pd POLR3K_promoter
+Pol_II interactsWith POLR3K_promoter
+Max pd POLR3K_promoter
+TAFII250 pd POLR3K_promoter
+c-Myc pd POLR3K_promoter
+E2F1 pd TMPO_promoter
+Pol_II interactsWith TMPO_promoter
+Max pd TMPO_promoter
+TAFII250 pd TMPO_promoter
+c-Myc pd TMPO_promoter
+E2F1 pd ZF_promoter
+Pol_II interactsWith ZF_promoter
+TAFII250 pd ZF_promoter
+E2F1 pd ASK_promoter
+TAFII250 pd ASK_promoter
+E2F1 pd FLJ10287_promoter
+Max pd FLJ10287_promoter
+TAFII250 pd FLJ10287_promoter
+c-Myc pd FLJ10287_promoter
+Pol_II interactsWith PPP1CB_promoter
+Max pd PPP1CB_promoter
+TAFII250 pd PPP1CB_promoter
+c-Myc pd PPP1CB_promoter
+Max pd AASDHPPT_promoter
+TAFII250 pd AASDHPPT_promoter
+TAFII250 pd LOC55967_promoter
+E2F1 pd PSMB8_promoter
+Pol_II interactsWith PSMB8_promoter
+TAFII250 pd PSMB8_promoter
+E2F1 pd TRA1_promoter
+Max pd TRA1_promoter
+c-Myc pd TRA1_promoter
+Max pd U5-116KD_promoter
+TAFII250 pd U5-116KD_promoter
+c-Myc pd U5-116KD_promoter
+E2F1 pd CHRAC17_promoter
+Pol_II interactsWith CHRAC17_promoter
+Max pd CHRAC17_promoter
+TAFII250 pd CHRAC17_promoter
+c-Myc pd CHRAC17_promoter
+TAFII250 pd RAYL_promoter
+Max pd HSA249128_promoter
+TAFII250 pd HSA249128_promoter
+c-Myc pd HSA249128_promoter
+Max pd RFX5_promoter
+TAFII250 pd RFX5_promoter
+c-Myc pd RFX5_promoter
+E2F1 pd CDC6:500_promoter
+Pol_II interactsWith CDC6:500_promoter
+Max pd CDC6:500_promoter
+TAFII250 pd CDC6:500_promoter
+c-Myc pd CDC6:500_promoter
+TAFII250 pd LOC54518_promoter
+E2F1 pd MAPK7_promoter
+Max pd MAPK7_promoter
+TAFII250 pd MAPK7_promoter
+c-Myc pd MAPK7_promoter
+Pol_II interactsWith WW45_promoter
+Max pd WW45_promoter
+TAFII250 pd WW45_promoter
+c-Myc pd WW45_promoter
+E2F1 pd IPT_promoter
+TAFII250 pd CDK2_promoter
+c-Myc pd CDK2_promoter
+TAFII250 pd GTF2A2_promoter
+TAFII250 pd RPL36_promoter
+Pol_II interactsWith ZNF76_promoter
+TAFII250 pd ZNF76_promoter
+c-Myc pd ZNF76_promoter
+E2F1 pd RBL1:500_promoter
+TAFII250 pd RBL1:500_promoter
+c-Myc pd RBL1:500_promoter
+E2F1 pd HCR_promoter
+Max pd HCR_promoter
+TAFII250 pd HCR_promoter
+c-Myc pd HCR_promoter
+Pol_II interactsWith RABIF_promoter
+TAFII250 pd RABIF_promoter
+E2F1 pd USP4_promoter
+Pol_II interactsWith USP4_promoter
+Max pd USP4_promoter
+TAFII250 pd USP4_promoter
+c-Myc pd USP4_promoter
+Pol_II interactsWith XBP1_promoter
+TAFII250 pd XBP1_promoter
+c-Myc pd XBP1_promoter
+Max pd OCIA_promoter
+TAFII250 pd OCIA_promoter
+c-Myc pd OCIA_promoter
+Pol_II interactsWith MPV17_promoter
+TAFII250 pd MPV17_promoter
+E2F1 pd RGS16_promoter
+Pol_II interactsWith RGS16_promoter
+Max pd RGS16_promoter
+TAFII250 pd RGS16_promoter
+c-Myc pd RGS16_promoter
+E2F1 pd LOC54543_promoter
+Pol_II interactsWith LOC54543_promoter
+TAFII250 pd LOC54543_promoter
+E2F1 pd FIGNL1_promoter
+TAFII250 pd FIGNL1_promoter
+E2F1 pd MAGEF1_promoter
+Pol_II interactsWith MAGEF1_promoter
+Max pd MAGEF1_promoter
+TAFII250 pd MAGEF1_promoter
+c-Myc pd MAGEF1_promoter
+E2F1 pd MAD2L1_promoter
+Pol_II interactsWith MAD2L1_promoter
+Max pd MAD2L1_promoter
+TAFII250 pd MAD2L1_promoter
+c-Myc pd MAD2L1_promoter
+Max pd MARS_promoter
+TAFII250 pd MARS_promoter
+c-Myc pd MARS_promoter
+Pol_II interactsWith LIN-7-C_promoter
+Max pd LIN-7-C_promoter
+TAFII250 pd LIN-7-C_promoter
+E2F1 pd HSA242910_promoter
+Pol_II interactsWith HSA242910_promoter
+Max pd HSA242910_promoter
+TAFII250 pd HSA242910_promoter
+Pol_II interactsWith GROS1_promoter
+Max pd GROS1_promoter
+TAFII250 pd GROS1_promoter
+c-Myc pd GROS1_promoter
+Max pd CDKN1B_promoter
+TAFII250 pd CDKN1B_promoter
+c-Myc pd CDKN1B_promoter
+Max pd CIR_promoter
+c-Myc pd CIR_promoter
+TAFII250 pd MGC2835_promoter
+E2F1 pd MSH2_promoter
+Pol_II interactsWith MSH2_promoter
+Max pd MSH2_promoter
+TAFII250 pd MSH2_promoter
+c-Myc pd MSH2_promoter
+Max pd RPL5_promoter
+c-Myc pd RPL5_promoter
+E2F1 pd CDC25A:950_promoter
+TAFII250 pd CDC25A:950_promoter
+Max pd MAP-1_promoter
+TAFII250 pd CAT_promoter
+E2F1 pd XRCC5_promoter
+Pol_II interactsWith XRCC5_promoter
+TAFII250 pd XRCC5_promoter
+Pol_II interactsWith LUC7L_promoter
+TAFII250 pd LUC7L_promoter
+E2F1 pd DHFR:950_promoter
+TAFII250 pd DHFR:950_promoter
+E2F1 pd LOC64116_promoter
+Max pd LOC64116_promoter
+TAFII250 pd LOC64116_promoter
+c-Myc pd LOC64116_promoter
+E2F1 pd MAT2A_promoter
+Pol_II interactsWith MAT2A_promoter
+Max pd MAT2A_promoter
+TAFII250 pd MAT2A_promoter
+c-Myc pd MAT2A_promoter
+E2F1 pd RAD54L_promoter
+Max pd RAD54L_promoter
+TAFII250 pd RAD54L_promoter
+c-Myc pd RAD54L_promoter
+Max pd MT2A_promoter
+c-Myc pd MT2A_promoter
+E2F1 pd RPS17_promoter
+Pol_II interactsWith RPS17_promoter
+Max pd RPS17_promoter
+TAFII250 pd RPS17_promoter
+c-Myc pd RPS17_promoter
+E2F1 pd MCM3:950_promoter
+Max pd MCM3:950_promoter
+c-Myc pd MCM3:950_promoter
+TAFII250 pd GIOT-2_promoter
+TAFII250 pd MRS2L_promoter
+Max pd ATP5C1_promoter
+c-Myc pd ATP5C1_promoter
+Pol_II interactsWith KIF5B_promoter
+TAFII250 pd KIF5B_promoter
+E2F1 pd TFRC_promoter
+Pol_II interactsWith TFRC_promoter
+TAFII250 pd TFRC_promoter
+Max pd TGIF2_promoter
+c-Myc pd TGIF2_promoter
+Pol_II interactsWith BTK_promoter
+TAFII250 pd BTK_promoter
+c-Myc pd TOP2B_promoter
+Pol_II interactsWith LOC51657_promoter
+Max pd LOC51657_promoter
+TAFII250 pd LOC51657_promoter
+c-Myc pd LOC51657_promoter
+Max pd LOC57404_promoter
+Max pd ARL1_promoter
+TAFII250 pd ARL1_promoter
+c-Myc pd ARL1_promoter
+Max pd ATP5E_promoter
+TAFII250 pd ATP5E_promoter
+c-Myc pd ATP5E_promoter
+Max pd TM7SF2_promoter
+Max pd DSCR6_promoter
+c-Myc pd DSCR6_promoter
+Pol_II interactsWith LOC51292_promoter
+c-Myc pd TUBA8_promoter
+Pol_II interactsWith ASB1_promoter
+Max pd ASB1_promoter
+TAFII250 pd ASB1_promoter
+c-Myc pd ASB1_promoter
+E2F1 pd LOC51723_promoter
+Pol_II interactsWith LOC51723_promoter
+Max pd LOC51723_promoter
+TAFII250 pd LOC51723_promoter
+c-Myc pd LOC51723_promoter
+Pol_II interactsWith BIRC6_promoter
+Max pd BIRC6_promoter
+TAFII250 pd BIRC6_promoter
+c-Myc pd BIRC6_promoter
+TAFII250 pd ARL5_promoter
+c-Myc pd FKBP1A_promoter
+E2F1 pd PPIA_promoter
+Pol_II interactsWith PPIA_promoter
+Max pd PPIA_promoter
+TAFII250 pd PPIA_promoter
+c-Myc pd PPIA_promoter
+Max pd LOC51765_promoter
+TAFII250 pd LOC51765_promoter
+c-Myc pd LOC51765_promoter
+Max pd UBL5_promoter
+TAFII250 pd UBL5_promoter
+Max pd FLJ11126_promoter
+Max pd LOC51660_promoter
+c-Myc pd LOC51660_promoter
+c-Myc pd TPM2_promoter
+E2F1 pd MASA_promoter
+Pol_II interactsWith MASA_promoter
+Max pd MASA_promoter
+TAFII250 pd MASA_promoter
+c-Myc pd MASA_promoter
+Pol_II interactsWith MDS023_promoter
+TAFII250 pd MDS023_promoter
+c-Myc pd MDS023_promoter
+Max pd C2ORF3_promoter
+TAFII250 pd C2ORF3_promoter
+c-Myc pd C2ORF3_promoter
+Pol_II interactsWith TPP2_promoter
+Max pd TPP2_promoter
+TAFII250 pd TPP2_promoter
+c-Myc pd TPP2_promoter
+Pol_II interactsWith TXNRD1_promoter
+TAFII250 pd TXNRD1_promoter
+E2F1 pd LOC51729_promoter
+Pol_II interactsWith LOC51729_promoter
+TAFII250 pd LOC51729_promoter
+E2F1 pd KNSL4_promoter
+Pol_II interactsWith KNSL4_promoter
+TAFII250 pd KNSL4_promoter
+c-Myc pd KNSL4_promoter
+TAFII250 pd PPM1G_promoter
+Pol_II interactsWith PRKCL2_promoter
+Max pd PRKCL2_promoter
+TAFII250 pd PRKCL2_promoter
+c-Myc pd PRKCL2_promoter
+Pol_II interactsWith TNF_promoter
+Max pd ZAK_promoter
+c-Myc pd ZAK_promoter
+Pol_II interactsWith PSMB7_promoter
+Max pd PSMB7_promoter
+TAFII250 pd PSMB7_promoter
+c-Myc pd PSMB7_promoter
+Pol_II interactsWith TPT1_promoter
+Max pd TPT1_promoter
+c-Myc pd TPT1_promoter
+Max pd LOC51678_promoter
+TAFII250 pd LOC51678_promoter
+c-Myc pd LOC51678_promoter
+E2F1 pd PRKCSH_promoter
+Max pd PRKCSH_promoter
+c-Myc pd PRKCSH_promoter
+Pol_II interactsWith BLK_promoter
+Max pd BLK_promoter
+TAFII250 pd BLK_promoter
+c-Myc pd BLK_promoter
+Pol_II interactsWith C6ORF9_promoter
+Max pd C6ORF9_promoter
+TAFII250 pd C6ORF9_promoter
+c-Myc pd C6ORF9_promoter
+Pol_II interactsWith PSMB9_promoter
+TAFII250 pd PSMB9_promoter
+Max pd CHRAC1_promoter
+c-Myc pd CARS_promoter
+E2F1 pd HCAP-G_promoter
+Pol_II interactsWith HCAP-G_promoter
+Max pd HCAP-G_promoter
+TAFII250 pd HCAP-G_promoter
+c-Myc pd HCAP-G_promoter
+Pol_II interactsWith H2BFS_promoter
+Max pd H2BFS_promoter
+TAFII250 pd H2BFS_promoter
+c-Myc pd H2BFS_promoter
+Pol_II interactsWith CD22_promoter
+Pol_II interactsWith RABGGTA_promoter
+TAFII250 pd GNB2L1_promoter
+Pol_II interactsWith GTF2B_promoter
+TAFII250 pd GTF2B_promoter
+TAFII250 pd RPL37A_promoter
+Pol_II interactsWith FLJ20494_promoter
+TAFII250 pd FLJ20494_promoter
+Max pd MAD_promoter
+Pol_II interactsWith XPA_promoter
+TAFII250 pd XPA_promoter
+Pol_II interactsWith GTF2F2_promoter
+TAFII250 pd GTF2F2_promoter
+Pol_II interactsWith MGAT2_promoter
+Max pd MGAT2_promoter
+TAFII250 pd MGAT2_promoter
+c-Myc pd MGAT2_promoter
+TAFII250 pd RPL44_promoter
+TAFII250 pd ORC1L:950_promoter
+Pol_II interactsWith RAD50_promoter
+Max pd RAD50_promoter
+TAFII250 pd RAD50_promoter
+c-Myc pd RAD50_promoter
+Pol_II interactsWith RPLP1_promoter
+Max pd RPLP1_promoter
+TAFII250 pd RPLP1_promoter
+c-Myc pd RPLP1_promoter
+E2F1 pd CCNA2:950_promoter
+TAFII250 pd WDR11_promoter
+E2F1 pd E2F3:950_promoter
+Pol_II interactsWith E2F3:950_promoter
+TAFII250 pd E2F3:950_promoter
+Max pd GDAP1_promoter
+TAFII250 pd GDAP1_promoter
+c-Myc pd GDAP1_promoter
+Pol_II interactsWith G1P3_promoter
+TAFII250 pd MIF_promoter
+Pol_II interactsWith RPS2_promoter
+TAFII250 pd RPS2_promoter
+c-Myc pd RPS2_promoter
+Pol_II interactsWith LOC55830_promoter
+Max pd LOC55830_promoter
+TAFII250 pd LOC55830_promoter
+c-Myc pd LOC55830_promoter
+E2F1 pd H2BFQ_promoter
+Pol_II interactsWith H2BFQ_promoter
+Max pd H2BFQ_promoter
+TAFII250 pd H2BFQ_promoter
+c-Myc pd H2BFQ_promoter
+TAFII250 pd ATA1_promoter
+E2F1 pd DDB2_promoter
+E2F1 pd SFRS2_promoter
+Pol_II interactsWith SFRS2_promoter
+Max pd SFRS2_promoter
+TAFII250 pd SFRS2_promoter
+c-Myc pd SFRS2_promoter
+c-Myc pd TMG4_promoter
+Pol_II interactsWith CREB1_promoter
+Max pd CREB1_promoter
+TAFII250 pd CREB1_promoter
+c-Myc pd CREB1_promoter
+Pol_II interactsWith MYC_promoter
+TAFII250 pd MYC_promoter
+TAFII250 pd NR4A1_promoter
+Max pd PRO2389_promoter
+c-Myc pd PRO2389_promoter
+TAFII250 pd MYD88_promoter
+TAFII250 pd SEC23B_promoter
+Pol_II interactsWith ERO1-L(BETA)_promoter
+Max pd ERO1-L(BETA)_promoter
+TAFII250 pd ERO1-L(BETA)_promoter
+c-Myc pd ERO1-L(BETA)_promoter
+E2F1 pd NR4A3_promoter
+Max pd NR4A3_promoter
+E2F1 pd LOC55871_promoter
+Pol_II interactsWith LOC55871_promoter
+Max pd LOC55871_promoter
+TAFII250 pd LOC55871_promoter
+c-Myc pd LOC55871_promoter
+E2F1 pd SMAC_promoter
+Max pd SMAC_promoter
+TAFII250 pd SMAC_promoter
+c-Myc pd SMAC_promoter
+E2F1 pd DDX3_promoter
+Max pd DDX3_promoter
+TAFII250 pd DDX3_promoter
+c-Myc pd DDX3_promoter
+E2F1 pd HNRPDL_promoter
+Max pd HNRPDL_promoter
+TAFII250 pd HNRPDL_promoter
+E2F1 pd TOPK_promoter
+E2F1 pd LOC55972_promoter
+Max pd LOC55972_promoter
+TAFII250 pd LOC55972_promoter
+c-Myc pd LOC55972_promoter
+Pol_II interactsWith SAT_promoter
+TAFII250 pd SAT_promoter
+E2F1 pd HNRPK_promoter
+Pol_II interactsWith HNRPK_promoter
+TAFII250 pd HNRPK_promoter
+E2F1 pd HSPA8_promoter
+Pol_II interactsWith HSPA8_promoter
+Max pd HSPA8_promoter
+TAFII250 pd HSPA8_promoter
+c-Myc pd NNAT_promoter
+E2F1 pd NUCB2_promoter
+TAFII250 pd NUCB2_promoter
+E2F1 pd SCD_promoter
+Pol_II interactsWith SCD_promoter
+Max pd SCD_promoter
+TAFII250 pd SCD_promoter
+c-Myc pd SCD_promoter
+E2F1 pd CYP3A7_promoter
+Pol_II interactsWith DKFZP564B167_promoter
+TAFII250 pd DKFZP564B167_promoter
+Pol_II interactsWith NOH61_promoter
+TAFII250 pd NOH61_promoter
+E2F1 pd ACYP1_promoter
+TAFII250 pd ACYP1_promoter
+Pol_II interactsWith JUN_promoter
+TAFII250 pd JUN_promoter
+Pol_II interactsWith PHAP1_promoter
+TAFII250 pd PHAP1_promoter
+E2F1 pd MDM1_promoter
+Pol_II interactsWith ABCC5_promoter
+TAFII250 pd ABCC5_promoter
+TAFII250 pd KIAA0203_promoter
+Pol_II interactsWith P115_promoter
+Max pd P115_promoter
+TAFII250 pd P115_promoter
+c-Myc pd P115_promoter
+Max pd PCMT1_promoter
+TAFII250 pd PCMT1_promoter
+c-Myc pd PCMT1_promoter
+Max pd SNAPC1_promoter
+TAFII250 pd SNAPC1_promoter
+c-Myc pd SNAPC1_promoter
+E2F1 pd EIF2S1_promoter
+Max pd EIF2S1_promoter
+TAFII250 pd EIF2S1_promoter
+c-Myc pd EIF2S1_promoter
+E2F1 pd SUPT5H_promoter
+Max pd SUPT5H_promoter
+TAFII250 pd SUPT5H_promoter
+c-Myc pd SUPT5H_promoter
+E2F1 pd KIAA0186_promoter
+Pol_II interactsWith KIAA0186_promoter
+Max pd KIAA0186_promoter
+TAFII250 pd KIAA0186_promoter
+c-Myc pd KIAA0186_promoter
+E2F1 pd SQSTM1_promoter
+Max pd SQSTM1_promoter
+TAFII250 pd SQSTM1_promoter
+c-Myc pd SQSTM1_promoter
+Pol_II interactsWith ALDOC_promoter
+TAFII250 pd ALDOC_promoter
+E2F1 pd EIF3S10_promoter
+Pol_II interactsWith EIF3S10_promoter
+TAFII250 pd EIF3S10_promoter
+E2F1 pd PHKG2_promoter
+Pol_II interactsWith PHKG2_promoter
+TAFII250 pd PHKG2_promoter
+E2F1 pd PMI_promoter
+TAFII250 pd PMI_promoter
+E2F1 pd MDS003_promoter
+Pol_II interactsWith MDS003_promoter
+Max pd MDS003_promoter
+TAFII250 pd MDS003_promoter
+Pol_II interactsWith SRM300_promoter
+Max pd SRM300_promoter
+TAFII250 pd SRM300_promoter
+c-Myc pd SRM300_promoter
+Max pd LOC56902_promoter
+TAFII250 pd LOC56902_promoter
+c-Myc pd LOC56902_promoter
+E2F1 pd IL1RL1LG_promoter
+TAFII250 pd IL1RL1LG_promoter
+E2F1 pd HKLP2_promoter
+Pol_II interactsWith HKLP2_promoter
+Max pd HKLP2_promoter
+TAFII250 pd HKLP2_promoter
+c-Myc pd HKLP2_promoter
+TAFII250 pd ACLY_promoter
+Max pd DPYSL3_promoter
+c-Myc pd DPYSL3_promoter
+Pol_II interactsWith ERCC5_promoter
+TAFII250 pd ERCC5_promoter
+E2F1 pd IDI1_promoter
+Pol_II interactsWith IDI1_promoter
+TAFII250 pd IDI1_promoter
+E2F1 pd TDO2_promoter
+Pol_II interactsWith TDO2_promoter
+E2F1 pd LOC55831_promoter
+Max pd DMAP1_promoter
+TAFII250 pd DMAP1_promoter
+c-Myc pd DMAP1_promoter
+Max pd LENG5_promoter
+TAFII250 pd LENG5_promoter
+c-Myc pd LENG5_promoter
+E2F1 pd ULBP1_promoter
+Pol_II interactsWith ULBP1_promoter
+Max pd ULBP1_promoter
+TAFII250 pd ULBP1_promoter
+c-Myc pd ULBP1_promoter
+Pol_II interactsWith H3FB_promoter
+TAFII250 pd H3FB_promoter
+Pol_II interactsWith NCL_promoter
+Max pd NCL_promoter
+TAFII250 pd NCL_promoter
+c-Myc pd NCL_promoter
+c-Myc pd CHST7_promoter
+Pol_II interactsWith HMMR_promoter
+Max pd HMMR_promoter
+TAFII250 pd HMMR_promoter
+c-Myc pd HMMR_promoter
+E2F1 pd HSD17B4_promoter
+Pol_II interactsWith SFRS7_promoter
+Max pd SFRS7_promoter
+TAFII250 pd SFRS7_promoter
+c-Myc pd SFRS7_promoter
+Pol_II interactsWith LOC55969_promoter
+Max pd LOC55969_promoter
+TAFII250 pd LOC55969_promoter
+c-Myc pd LOC55969_promoter
+TAFII250 pd CRKL_promoter
+TAFII250 pd CYB5-M_promoter
+Pol_II interactsWith DDX17_promoter
+Max pd DDX17_promoter
+TAFII250 pd DDX17_promoter
+c-Myc pd DDX17_promoter
+TAFII250 pd HSF2_promoter
+Max pd NDUFS1_promoter
+TAFII250 pd NDUFS1_promoter
+c-Myc pd NDUFS1_promoter
+Pol_II interactsWith SERF1B_promoter
+Max pd SERF1B_promoter
+TAFII250 pd SERF1B_promoter
+c-Myc pd SERF1B_promoter
+TAFII250 pd FYCO1_promoter
+TAFII250 pd COL4A5_promoter
+TAFII250 pd P12_promoter
+Max pd HSPBP1_promoter
+TAFII250 pd HSPBP1_promoter
+E2F1 pd NONO_promoter
+Pol_II interactsWith NONO_promoter
+TAFII250 pd NONO_promoter
+Max pd EPB72_promoter
+TAFII250 pd EPB72_promoter
+c-Myc pd EPB72_promoter
+TAFII250 pd PHB_promoter
+Pol_II interactsWith DVL2_promoter
+c-Myc pd DVL2_promoter
+Pol_II interactsWith PCNA_promoter
+Max pd PCNA_promoter
+TAFII250 pd PCNA_promoter
+c-Myc pd PCNA_promoter
+Max pd SQLE_promoter
+E2F1 pd LALP1_promoter
+Pol_II interactsWith LALP1_promoter
+Max pd LALP1_promoter
+c-Myc pd LALP1_promoter
+c-Myc pd ALDH3A2_promoter
+Pol_II interactsWith EIF2S3_promoter
+Max pd EIF2S3_promoter
+TAFII250 pd EIF2S3_promoter
+c-Myc pd EIF2S3_promoter
+TAFII250 pd ADAR_promoter
+Pol_II interactsWith PCNP_promoter
+Max pd PCNP_promoter
+TAFII250 pd PCNP_promoter
+c-Myc pd PCNP_promoter
+Max pd PMM2_promoter
+TAFII250 pd PMM2_promoter
+c-Myc pd PMM2_promoter
+Pol_II interactsWith DPAGT1_promoter
+Max pd DPAGT1_promoter
+TAFII250 pd DPAGT1_promoter
+c-Myc pd DPAGT1_promoter
+TAFII250 pd SNRPB2_promoter
+Pol_II interactsWith SRPR_promoter
+Max pd SRPR_promoter
+TAFII250 pd SRPR_promoter
+c-Myc pd SRPR_promoter
+Pol_II interactsWith AMD1_promoter
+Max pd AMD1_promoter
+TAFII250 pd AMD1_promoter
+c-Myc pd AMD1_promoter
+E2F1 pd KIAA0101_promoter
+Pol_II interactsWith KIAA0101_promoter
+TAFII250 pd KIAA0101_promoter
+TAFII250 pd LOC56993_promoter
+TAFII250 pd IDE_promoter
+TAFII250 pd POLA2_promoter
+Max pd LOC51684_promoter
+TAFII250 pd LOC51684_promoter
+Max pd LOC51735_promoter
+TAFII250 pd LOC51735_promoter
+c-Myc pd LOC51735_promoter
+Pol_II interactsWith FARSL_promoter
+TAFII250 pd FARSL_promoter
+TAFII250 pd PPP1R2_promoter
+TAFII250 pd BM-002_promoter
+E2F1 pd PELO_promoter
+TAFII250 pd PELO_promoter
+E2F1 pd UBE2N_promoter
+Pol_II interactsWith UBE2N_promoter
+TAFII250 pd UBE2N_promoter
+c-Myc pd UBE2N_promoter
+TAFII250 pd BCAA_promoter
+E2F1 pd ATF4_promoter
+Pol_II interactsWith ATF4_promoter
+Max pd ATF4_promoter
+TAFII250 pd ATF4_promoter
+c-Myc pd ATF4_promoter
+E2F1 pd TIAM1_promoter
+Pol_II interactsWith TNFSF10_promoter
+TAFII250 pd TNFSF10_promoter
+Max pd TM6SF1_promoter
+E2F1 pd TRAM_promoter
+Pol_II interactsWith TRAM_promoter
+TAFII250 pd TRAM_promoter
+TAFII250 pd LOC57823_promoter
+Pol_II interactsWith PPP2R5D_promoter
+TAFII250 pd PPP2R5D_promoter
+Pol_II interactsWith G4_promoter
+E2F1 pd FLJ10816_promoter
+Max pd FLJ10816_promoter
+TAFII250 pd FLJ10816_promoter
+c-Myc pd FLJ10816_promoter
+E2F1 pd BRF1_promoter
+Pol_II interactsWith BRF1_promoter
+TAFII250 pd BRF1_promoter
+E2F1 pd LOC51154_promoter
+Pol_II interactsWith LOC51154_promoter
+Max pd LOC51154_promoter
+TAFII250 pd LOC51154_promoter
+c-Myc pd LOC51154_promoter
+Max pd LSR7_promoter
+TAFII250 pd LSR7_promoter
+TAFII250 pd RAB18_promoter
+TAFII250 pd FACL5_promoter
+TAFII250 pd FEM1B_promoter
+Max pd FPGT_promoter
+TAFII250 pd TRIP4_promoter
+E2F1 pd UMPS_promoter
+Pol_II interactsWith UMPS_promoter
+TAFII250 pd UMPS_promoter
+TAFII250 pd SCAND2_promoter
+E2F1 pd CBX5_promoter
+Pol_II interactsWith CBX5_promoter
+Max pd CBX5_promoter
+TAFII250 pd CBX5_promoter
+c-Myc pd CBX5_promoter
+E2F1 pd CD6_promoter
+Max pd CD6_promoter
+TAFII250 pd CD6_promoter
+TAFII250 pd RAGB_promoter
+TAFII250 pd REL_promoter
+Max pd MMS19L_promoter
+TAFII250 pd MMS19L_promoter
+Pol_II interactsWith RPS26_promoter
+Max pd RPS26_promoter
+TAFII250 pd RPS26_promoter
+c-Myc pd RPS26_promoter
+E2F1 pd E2F2:500_promoter
+Max pd LZTFL1_promoter
+TAFII250 pd LZTFL1_promoter
+c-Myc pd LZTFL1_promoter
+Pol_II interactsWith GADD45A_promoter
+Max pd GADD45A_promoter
+TAFII250 pd GADD45A_promoter
+Pol_II interactsWith MCL1_promoter
+TAFII250 pd MCL1_promoter
+Pol_II interactsWith ZFP36_promoter
+Pol_II interactsWith HSA275986_promoter
+TAFII250 pd HSA275986_promoter
+E2F1 pd ADIR_promoter
+TAFII250 pd ADIR_promoter
+E2F1 pd CENPA_promoter
+TAFII250 pd CENPA_promoter
+Pol_II interactsWith CKS2_promoter
+Max pd CKS2_promoter
+TAFII250 pd CKS2_promoter
+c-Myc pd CKS2_promoter
+E2F1 pd MLH1_promoter
+Pol_II interactsWith MLH1_promoter
+TAFII250 pd MLH1_promoter
+E2F1 pd MTHFD1_promoter
+Pol_II interactsWith MTHFD1_promoter
+Max pd MTHFD1_promoter
+TAFII250 pd MTHFD1_promoter
+c-Myc pd MTHFD1_promoter
+E2F1 pd CDC25A:500_promoter
+Pol_II interactsWith CROT_promoter
+TAFII250 pd CROT_promoter
+E2F1 pd MCM5_promoter
+Pol_II interactsWith MCM5_promoter
+Max pd MCM5_promoter
+TAFII250 pd MCM5_promoter
+c-Myc pd MCM5_promoter
+E2F1 pd LOC55810_promoter
+E2F1 pd H1F2_promoter
+Pol_II interactsWith H1F2_promoter
+E2F1 pd RPS5_promoter
+Pol_II interactsWith RPS5_promoter
+Max pd RPS5_promoter
+TAFII250 pd RPS5_promoter
+c-Myc pd RPS5_promoter
+E2F1 pd RFC1_promoter
+Pol_II interactsWith BLOV1_promoter
+TAFII250 pd BLOV1_promoter
+c-Myc pd BLOV1_promoter
+Pol_II interactsWith CLCN3_promoter
+Max pd CLCN3_promoter
+TAFII250 pd CLCN3_promoter
+c-Myc pd CLCN3_promoter
+E2F1 pd RRAS_promoter
+Max pd RRAS_promoter
+c-Myc pd RRAS_promoter
+E2F1 pd MCM3:500_promoter
+Max pd MCM3:500_promoter
+c-Myc pd MCM3:500_promoter
+TAFII250 pd ETAA16_promoter
+TAFII250 pd MAP3K7_promoter
+E2F1 pd RFC3_promoter
+TAFII250 pd RFC3_promoter
+Pol_II interactsWith PEGASUS_promoter
+TAFII250 pd PEGASUS_promoter
+E2F1 pd H2AFL_promoter
+Pol_II interactsWith H2AFL_promoter
+Max pd H2AFL_promoter
+TAFII250 pd H2AFL_promoter
+c-Myc pd H2AFL_promoter
+Pol_II interactsWith RPL17_promoter
+TAFII250 pd RPL17_promoter
+c-Myc pd RPL17_promoter
+E2F1 pd CDC2:500_promoter
+TAFII250 pd ZNF263_promoter
+Pol_II interactsWith GSPT1_promoter
+TAFII250 pd GSPT1_promoter
+E2F1 pd H2AFX_promoter
+Pol_II interactsWith H2AFX_promoter
+Max pd H2AFX_promoter
+TAFII250 pd H2AFX_promoter
+c-Myc pd H2AFX_promoter
+Pol_II interactsWith RPL27_promoter
+Max pd RPL27_promoter
+TAFII250 pd RPL27_promoter
+c-Myc pd RPL27_promoter
+TAFII250 pd RXRG_promoter
+c-Myc pd RXRG_promoter
+Pol_II interactsWith POLD4_promoter
+Max pd POLD4_promoter
+TAFII250 pd POLD4_promoter
+c-Myc pd POLD4_promoter
+Pol_II interactsWith B2M_promoter
+TAFII250 pd B2M_promoter
+c-Myc pd B2M_promoter
+TAFII250 pd FBL_promoter
+c-Myc pd FBL_promoter
+TAFII250 pd KIAA0737_promoter
+E2F1 pd PRKDC_promoter
+Pol_II interactsWith PRKDC_promoter
+Max pd PRKDC_promoter
+TAFII250 pd PRKDC_promoter
+c-Myc pd PRKDC_promoter
+c-Myc pd DUOX1_promoter
+Max pd ALOXE3_promoter
+c-Myc pd ALOXE3_promoter
+Pol_II interactsWith LMNA_promoter
+TAFII250 pd LOC58486_promoter
+TAFII250 pd PTTG1_promoter
+Pol_II interactsWith LOC51691_promoter
+Max pd LOC51691_promoter
+TAFII250 pd LOC51691_promoter
+c-Myc pd LOC51691_promoter
+Pol_II interactsWith BTBD1_promoter
+Max pd BTBD1_promoter
+TAFII250 pd BTBD1_promoter
+c-Myc pd BTBD1_promoter
+Pol_II interactsWith LOC59346_promoter
+TAFII250 pd LOC59346_promoter
+c-Myc pd LOC59346_promoter
+TAFII250 pd SRR_promoter
+c-Myc pd SRR_promoter
+Pol_II interactsWith CACNB1_promoter
+Max pd CACNB1_promoter
+TAFII250 pd CACNB1_promoter
+c-Myc pd CACNB1_promoter
+E2F1 pd ATF5_promoter
+Pol_II interactsWith ATF5_promoter
+TAFII250 pd ATF5_promoter
+Pol_II interactsWith FBXW2_promoter
+TAFII250 pd FBXW2_promoter
+E2F1 pd FLJ10604_promoter
+Pol_II interactsWith FLJ10604_promoter
+Max pd FLJ10604_promoter
+TAFII250 pd FLJ10604_promoter
+c-Myc pd KIAA0923_promoter
+E2F1 pd CALM2_promoter
+Pol_II interactsWith CALM2_promoter
+Max pd CALM2_promoter
+TAFII250 pd CALM2_promoter
+c-Myc pd CALM2_promoter
+TAFII250 pd PTB_promoter
+TAFII250 pd UBTF_promoter
+c-Myc pd UBTF_promoter
+E2F1 pd VPS29_promoter
+Max pd VPS29_promoter
+TAFII250 pd VPS29_promoter
+c-Myc pd VPS29_promoter
+E2F1 pd BARD1_promoter
+Max pd BARD1_promoter
+c-Myc pd BARD1_promoter
+Pol_II interactsWith FDFT1_promoter
+TAFII250 pd FDFT1_promoter
+Pol_II interactsWith PPP3CA_promoter
+Max pd PPP3CA_promoter
+TAFII250 pd PPP3CA_promoter
+c-Myc pd PPP3CA_promoter
+TAFII250 pd PRP18_promoter
+E2F1 pd NUP54_promoter
+Pol_II interactsWith NUP54_promoter
+Max pd NUP54_promoter
+TAFII250 pd NUP54_promoter
+c-Myc pd NUP54_promoter
+E2F1 pd BRD2_promoter
+TAFII250 pd BRD2_promoter
+Pol_II interactsWith CALR_promoter
+Max pd CALR_promoter
+TAFII250 pd CALR_promoter
+c-Myc pd CALR_promoter
+TAFII250 pd LRPAP1_promoter
+Pol_II interactsWith RAB10_promoter
+TAFII250 pd RAB10_promoter
+TAFII250 pd SNX6_promoter
+Pol_II interactsWith FDX1_promoter
+TAFII250 pd FDX1_promoter
+Pol_II interactsWith FLJ10830_promoter
+Max pd FLJ10830_promoter
+TAFII250 pd FLJ10830_promoter
+c-Myc pd FLJ10830_promoter
+Pol_II interactsWith PRPSAP1_promoter
+Max pd PRPSAP1_promoter
+TAFII250 pd PRPSAP1_promoter
+c-Myc pd PRPSAP1_promoter
+Max pd LOC51182_promoter
+TAFII250 pd LOC51182_promoter
+c-Myc pd LOC51182_promoter
+Pol_II interactsWith LTB_promoter
+TAFII250 pd LTB_promoter
+Max pd TRIP13_promoter
+c-Myc pd TRIP13_promoter
+Pol_II interactsWith LOC51759_promoter
+TAFII250 pd LOC51759_promoter
+TAFII250 pd ATP5A1_promoter
+E2F1 pd FEN1_promoter
+Pol_II interactsWith FEN1_promoter
+TAFII250 pd FEN1_promoter
+c-Myc pd PRC1_promoter
+Pol_II interactsWith TK1_promoter
+TAFII250 pd TK1_promoter
+E2F1 pd ADAM22_promoter
+Max pd ADAM22_promoter
+TAFII250 pd ADAM22_promoter
+c-Myc pd ADAM22_promoter
+Max pd TLR9_promoter
+Pol_II interactsWith BTF3_promoter
+TAFII250 pd BTF3_promoter
+TAFII250 pd LOC51202_promoter
+Max pd RAB4B_promoter
+TAFII250 pd TSC22_promoter
+Max pd GNB1L_promoter
+TAFII250 pd GNB1L_promoter
+c-Myc pd GNB1L_promoter
+Pol_II interactsWith CC1.3_promoter
+Max pd CC1.3_promoter
+TAFII250 pd CC1.3_promoter
+c-Myc pd CC1.3_promoter
+TAFII250 pd CD74_promoter
+c-Myc pd CD74_promoter
+Max pd ELOVL1_promoter
+c-Myc pd ELOVL1_promoter
+TAFII250 pd RPS3_promoter
+Max pd CD97_promoter
+c-Myc pd CD97_promoter
+Pol_II interactsWith GADD45B_promoter
+Max pd GADD45B_promoter
+TAFII250 pd GADD45B_promoter
+Pol_II interactsWith GBL_promoter
+TAFII250 pd BCL11B_promoter
+c-Myc pd BCL11B_promoter
+Pol_II interactsWith MCCC2_promoter
+Max pd MCCC2_promoter
+TAFII250 pd MCCC2_promoter
+c-Myc pd MCCC2_promoter
+Pol_II interactsWith REV3L_promoter
+Pol_II interactsWith RPL10_promoter
+TAFII250 pd RPL10_promoter
+c-Myc pd RPL10_promoter
+Max pd GARS_promoter
+TAFII250 pd GARS_promoter
+Pol_II interactsWith MAP3K4_promoter
+TAFII250 pd MAP3K4_promoter
+c-Myc pd MAP3K4_promoter
+Pol_II interactsWith H1F5_promoter
+Pol_II interactsWith RFC4_promoter
+E2F1 pd H2AFO_promoter
+Pol_II interactsWith H2AFO_promoter
+Max pd H2AFO_promoter
+TAFII250 pd H2AFO_promoter
+c-Myc pd H2AFO_promoter
+Pol_II interactsWith HASJ4442_promoter
+Max pd HASJ4442_promoter
+TAFII250 pd HASJ4442_promoter
+c-Myc pd HASJ4442_promoter
+Pol_II interactsWith CCT7_promoter
+Max pd CCT7_promoter
+TAFII250 pd CCT7_promoter
+c-Myc pd CCT7_promoter
+TAFII250 pd ZNF267_promoter
+TAFII250 pd CHEK1_promoter
+Pol_II interactsWith CLNS1A_promoter
+TAFII250 pd CLNS1A_promoter
+Pol_II interactsWith H2AFZ_promoter
+Max pd H2AFZ_promoter
+TAFII250 pd H2AFZ_promoter
+c-Myc pd H2AFZ_promoter
+Pol_II interactsWith RPL28_promoter
+TAFII250 pd RPL28_promoter
+TAFII250 pd HBS1L_promoter
+Pol_II interactsWith CYP51_promoter
+TAFII250 pd CYP51_promoter
+TAFII250 pd NOP56_promoter
+TAFII250 pd OAS2_promoter
+TAFII250 pd SCYA4_promoter
+Pol_II interactsWith SIRT1_promoter
+E2F1 pd SMARCA3_promoter
+E2F1 pd EPC1_promoter
+Pol_II interactsWith EPC1_promoter
+Max pd EPC1_promoter
+TAFII250 pd EPC1_promoter
+c-Myc pd EPC1_promoter
+E2F1 pd CSTF1_promoter
+Max pd CSTF1_promoter
+TAFII250 pd HDAC2_promoter
+E2F1 pd HMG1_promoter
+Pol_II interactsWith HMG1_promoter
+Max pd HMG1_promoter
+TAFII250 pd HMG1_promoter
+E2F1 pd NAP1L4_promoter
+TAFII250 pd NAP1L4_promoter
+E2F1 pd DARS_promoter
+Max pd DARS_promoter
+TAFII250 pd DARS_promoter
+TAFII250 pd HSU53209_promoter
+E2F1 pd SFPQ_promoter
+Pol_II interactsWith SFPQ_promoter
+TAFII250 pd SFPQ_promoter
+Max pd DNAJB9_promoter
+TAFII250 pd DNAJB9_promoter
+TAFII250 pd SMC2L1_promoter
+Pol_II interactsWith ACP2_promoter
+TAFII250 pd ACP2_promoter
+E2F1 pd PA2G4_promoter
+Pol_II interactsWith PA2G4_promoter
+Max pd PA2G4_promoter
+TAFII250 pd PA2G4_promoter
+c-Myc pd PA2G4_promoter
+TAFII250 pd PDE4B_promoter
+E2F1 pd SSR3_promoter
+TAFII250 pd SSR3_promoter
+E2F1 pd C12ORF4_promoter
+TAFII250 pd C12ORF4_promoter
+Pol_II interactsWith ID3_promoter
+TAFII250 pd ID3_promoter
+E2F1 pd PIN1_promoter
+TAFII250 pd PIN1_promoter
+E2F1 pd POLD1_promoter
+Pol_II interactsWith POLD1_promoter
+E2F1 pd RRP46_promoter
+Max pd RRP46_promoter
+TAFII250 pd RRP46_promoter
+Pol_II interactsWith PDHA1_promoter
+TAFII250 pd PDHA1_promoter
+E2F1 pd ERPROT213-21_promoter
+Pol_II interactsWith ERPROT213-21_promoter
+Max pd ERPROT213-21_promoter
+TAFII250 pd ERPROT213-21_promoter
+c-Myc pd ERPROT213-21_promoter
+E2F1 pd PIST_promoter
+Pol_II interactsWith PIST_promoter
+TAFII250 pd PIST_promoter
+Max pd TEF_promoter
+Pol_II interactsWith MCCC1_promoter
+TAFII250 pd MCCC1_promoter
+TAFII250 pd AKL3L_promoter
+E2F1 pd STAM_promoter
+Pol_II interactsWith STAM_promoter
+Max pd STAM_promoter
+TAFII250 pd STAM_promoter
+Pol_II interactsWith ETF1_promoter
+Max pd ETF1_promoter
+TAFII250 pd ETF1_promoter
+c-Myc pd ETF1_promoter
+E2F1 pd AKR1D1_promoter
+Pol_II interactsWith AKR1D1_promoter
+E2F1 pd EEF1G_promoter
+Pol_II interactsWith ETR101_promoter
+Max pd ETR101_promoter
+TAFII250 pd ETR101_promoter
+c-Myc pd ETR101_promoter
+Pol_II interactsWith ICAM1_promoter
+TAFII250 pd ICAM1_promoter
+Pol_II interactsWith DDX24_promoter
+TAFII250 pd DDX24_promoter
+E2F1 pd STK12_promoter
+TAFII250 pd STK12_promoter
+Pol_II interactsWith AP4S1_promoter
+Max pd AP4S1_promoter
+TAFII250 pd AP4S1_promoter
+c-Myc pd AP4S1_promoter
+Pol_II interactsWith ARHGDIB_promoter
+TAFII250 pd ARHGDIB_promoter
+Max pd DLX2_promoter
+Pol_II interactsWith CSNK2B_promoter
+Max pd CSNK2B_promoter
+TAFII250 pd CSNK2B_promoter
+Pol_II interactsWith HCNGP_promoter
+TAFII250 pd HCNGP_promoter
+c-Myc pd HCNGP_promoter
+Pol_II interactsWith HLA-E_promoter
+Pol_II interactsWith NACA_promoter
+Max pd NACA_promoter
+TAFII250 pd NACA_promoter
+c-Myc pd NACA_promoter
+TAFII250 pd SERPINB8_promoter
+Max pd LOC55902_promoter
+c-Myc pd LOC55902_promoter
+TAFII250 pd SCDGF-B_promoter
+E2F1 pd CAT56_promoter
+Pol_II interactsWith CAT56_promoter
+Max pd CAT56_promoter
+TAFII250 pd CAT56_promoter
+c-Myc pd CAT56_promoter
+Max pd COX7C_promoter
+TAFII250 pd COX7C_promoter
+c-Myc pd COX7C_promoter
+TAFII250 pd CSRP1_promoter
+TAFII250 pd NAP1L1_promoter
+Max pd NAPA_promoter
+TAFII250 pd NFKBIA_promoter
+Max pd DBP_promoter
+c-Myc pd DBP_promoter
+Pol_II interactsWith DNAJB1_promoter
+TAFII250 pd CPSF4_promoter
+E2F1 pd HEC_promoter
+TAFII250 pd HEC_promoter
+Pol_II interactsWith 4E-T_promoter
+Max pd 4E-T_promoter
+TAFII250 pd 4E-T_promoter
+Pol_II interactsWith LOC56851_promoter
+TAFII250 pd LOC56851_promoter
+Pol_II interactsWith HSU79253_promoter
+Max pd HSU79253_promoter
+TAFII250 pd HSU79253_promoter
+c-Myc pd HSU79253_promoter
+Max pd NR1D1_promoter
+c-Myc pd NR1D1_promoter
+TAFII250 pd NCF1_promoter
+E2F1 pd SFRS1_promoter
+Pol_II interactsWith SFRS1_promoter
+TAFII250 pd SFRS1_promoter
+Pol_II interactsWith DDB1_promoter
+Max pd DDB1_promoter
+TAFII250 pd DDB1_promoter
+c-Myc pd DDB1_promoter
+TAFII250 pd DNAJC3_promoter
+TAFII250 pd SMC4L1_promoter
+TAFII250 pd PDK4_promoter
+Pol_II interactsWith TERA_promoter
+Max pd TERA_promoter
+TAFII250 pd TERA_promoter
+Pol_II interactsWith IRF1_promoter
+Pol_II interactsWith PKM2_promoter
+Max pd PKM2_promoter
+TAFII250 pd PKM2_promoter
+c-Myc pd PKM2_promoter
+Pol_II interactsWith INHBC_promoter
+Pol_II interactsWith SP140_promoter
+TAFII250 pd AP2B1_promoter
+TAFII250 pd ZNF304_promoter
+TAFII250 pd IGHMBP2_promoter
+Pol_II interactsWith JUNB_promoter
+LKB1 pp PAPK
+MARK4 pp LKB1
+cIAP2 pp Casp3
+cIAP2 pp Casp7
+PIN1 pp Cyclin_D1
+GB1 pp GB2
+MAGI3 pp PTEN/MMAC
+MAGI3 pp BAI-1
+MAGI3 pp NMDA_receptor_2B
+p68 pd p21_promoter
+SNAP23 pp VAMP2
+CAP350 pp LXR-alpha
+CAP350 pp PPAR-alpha
+CAP350 pp PPAR-gamma-2
+CAP350 pp PPAR-delta
+SNAP23 pp VAMP7
+SNAP23 pp VAMP3
+Csp1 pp VAMP2
+Csp1 pp VAMP7
+ARA55 pp Smad4
+ARA55 pp Smad3
+PAK4 pp SSH-1L
+SSH-3S pp 14-3-3-zeta
+SSH-1S pp 14-3-3-zeta
+SSH-1L pp 14-3-3-zeta
+SSH-2S pp 14-3-3-zeta
+SSH-1S pp LIMK1
+SSH-1L pp LIMK1
+unknown interactsWith XRCC5
+WRN pp PARP1
+WRN pp G22P1
+unknown interactsWith G22P1
+SMG7 pp SMG5
+NUPL2 pp XPO1
+MMP-1 pp PAR1
+Thrombin pp PAR1
+5-HT1A pp 5-HT1A
+SSH-1L pp cofilin
+PTEN pp ROCK1
+SSH-1L pp LIMK2
+Mitf pp Rb
+Rb pd p107_promoter
+Rb pd TYR_promoter
+Rb pd p21_promoter
+Mitf pd p21_promoter
+E2F1 pd ALG5_promoter
+E2F1 pd Beta_lactamase_promoter
+E2F1 pd BMP4_promoter
+E2F1 pd CBX5_promoter
+E2F1 pd CYP27B1_promoter
+E2F1 pd DCC_promoter
+E2F1 pd Diacylglycerol_kinase,_iota_promoter
+E2F1 pd DLEU1/2_promoter
+E2F1 pd EIF3S8_promoter
+E2F1 pd EYA2_promoter
+E2F1 pd EYA4_promoter
+E2F1 pd GMPS_promoter
+E2F1 pd GPS2_promoter
+E2F1 pd GRAP_promoter
+E2F1 pd GTF2H4_promoter
+E2F1 pd H2BFR_promoter
+E2F1 pd H4FH_promoter
+E2F1 pd H4FR_promoter
+E2F1 pd HN1_promoter
+E2F1 pd KCNA3_promoter
+E2F1 pd MAGEF1_promoter
+E2F1 pd Meis1_promoter
+E2F1 pd MFAP1_promoter
+E2F1 pd Myc_promoter
+E2F1 pd NEDD8_promoter
+E2F1 pd NKX6A_promoter
+E2F1 pd OAZ2_promoter
+E2F1 pd PPT2_promoter
+E2F1 pd PTPN4_promoter
+E2F1 pd RAD51_promoter
+E2F1 pd SAFB_promoter
+E2F1 pd SDCCAG10_promoter
+E2F1 pd SLC22A1L_promoter
+E2F1 pd SMARCA5_promoter
+E2F1 pd SNRPC_promoter
+E2F1 pd Sox7_promoter
+E2F1 pd SRPR_promoter
+E2F1 pd TCP10_promoter
+E2F1 pd UXT_promoter
+E2F1 pd YWHAE_promoter
+E2F4 pd ALG5_promoter
+E2F4 pd Beta_lactamase_promoter
+E2F4 pd Myc_promoter
+E2F4 pd UXT_promoter
+p107 pd ALG5_promoter
+p107 pd Beta_lactamase_promoter
+p107 pd Myc_promoter
+p130 pd ALG5_promoter
+p130 pd Beta_lactamase_promoter
+p130 pd Myc_promoter
+p130 pd UXT_promoter
+pRb pd ALG5_promoter
+pRb pd Beta_lactamase_promoter
+pRb pd CYP27B1_promoter
+pRb pd GMPS_promoter
+pRb pd GPS2_promoter
+pRb pd GTF2H4_promoter
+pRb pd H2BFR_promoter
+pRb pd HN1_promoter
+pRb pd KPNA4_promoter
+pRb pd MAGEF1_promoter
+pRb pd Myc_promoter
+pRb pd NP220_promoter
+pRb pd OAZ2_promoter
+pRb pd PPT2_promoter
+pRb pd PTPN4_promoter
+pRb pd SAFB_promoter
+pRb pd SDCCAG10_promoter
+pRb pd SLC22A1L_promoter
+pRb pd Sox7_promoter
+pRb pd SRPR_promoter
+pRb pd TCP10_promoter
+pRb pd UXT_promoter
+pRb pd YWHAE_promoter
+RNAP interactsWith ALG5
+RNAP interactsWith Beta_lactamase
+RNAP interactsWith Myc
+RNAP interactsWith UXT
+beta-catenin pd Axin2_promoter
+ER-alpha pd Axin2_promoter
+beta-catenin pd pS2_promoter
+ER-alpha pd pS2_promoter
+beta-catenin pp ER-alpha
+MUC1_C-ter pp p53
+MUC1_C-ter pd p21_promoter
+CREBBP pd p21_promoter
+HDAC1 pd p21_promoter
+HIST4H4 pd p21_promoter
+MUC1_C-ter pd Bax_promoter
+p53 pd Bax_promoter
+TBP pd Bax_promoter
+GTF2B pd Bax_promoter
+TAF1 pd Bax_promoter
+FGFR1 pp RSK1
+MTA1 pp NRIF3
+BAP31 pp PTPLB
+PMCA4b pp RASSF1E
+PRMT2 pp PRMT2
+PRMT2 pp ER-alpha
+PRMT2 pp ER-beta
+PRMT2 pp PR
+PRMT2 pp TR-beta
+PRMT2 pp RAR
+PRMT2 pp RXR-alpha
+PRMT2 pp PPAR-gamma
+PRMT2 pp SRC-1
+PRMT2 pp PRIP
+cyclin_T1 pp granulin
+cyclin_T1 pp CDK9
+P-TEFb interactsWith granulin
+Fas pp FADD
+Fas pp caspase-8
+RB1 pp Suv4-20h1
+CKIP-1 pp CASP3
+CKIP-1 pp c-Jun
+CKIP-1 pp CKIP-1
+CKIP-1 pp JunD
+c-Jun pp c-Jun
+C/EBP-delta pp E2F1
+C/EBP-delta pp Rb
+Raf-1 interactsWith CASP9_dimer
+Unknown interactsWith HEC/hNdc80
+Unknown interactsWith CDCA1
+Unknown interactsWith PMF1
+Unknown interactsWith C1orf48
+Unknown interactsWith C20orf172
+Unknown interactsWith AF15Q14
+Unknown interactsWith ZWINT
+Unknown interactsWith SPBC25
+Unknown interactsWith SPBC24
+SNSR-4 interactsWith G-beta-1-gamma-2_dimer
+Alpha-2A-AR interactsWith G-beta-1-gamma-2_dimer
+TP-alpha-R interactsWith G-beta-1-gamma-2_dimer
+TP-alpha-R interactsWith Trimeric_G_protein
+V2R interactsWith Trimeric_G_protein
+G-beta-1 pp G-alpha-s
+G-beta-1 pp G-gamma-2
+RB1 pp Suv4-20h2
+PMCA4b pp RASSF1A
+PMCA4b pp RASSF1C
+RNPS1 pp p54
+RNPS1 pp hTra2-beta
+Mpp11 pp Hsc70
+CIKS pp IKK-gamma
+MEKK2 pp MEKK2
+MEKK2 pp MEK5
+MEKK2 pp MKK7
+ERK5 pp MEF2C
+Rnf2 pp HPc2
+3pK pp HPc2
+HPH1 pp HPc2
+HPH1 pp Bmi1
+Rnf2 pp Bmi1
+3pK pp Bmi1
+3pK pp HPH2
+CAR pp PGC-1
+CAR pp TRAP
+CAR pp SRC-1
+ARHGAP4 interactsWith Rac1-GTP
+NADE pp Smac
+Tiam1-NR1 interactsWith NR2B
+Tiam1 pp NR1
+RBL1 pp Suv4-20h2
+CypA pp CypA
+Col-2 interactsWith alpha-2-beta-1_integrin
+5-HT1A pp 5-HT1B
+5-HT1A pp 5-HT1D
+5-HT1D pp 5-HT1D
+5-HT1B pp 5-HT1B
+Vigilin interactsWith Unknown
+Unknown interactsWith DNA-PKcs
+Vigilin interactsWith Ku_complex
+RHA interactsWith Ku_complex
+Nuclear_Vigilin_Complex interactsWith RHA
+Nuclear_Vigilin_Complex interactsWith ADAR1
+Nuclear_Vigilin_Complex interactsWith HP1-alpha
+Nuclear_Vigilin_Complex interactsWith H2AX
+RBL1 pp Suv4-20h1
+SKP1 pp FBL7
+RBL2 pp Suv4-20h1
+RBL2 pp Suv4-20h2
+CBX1 pp Suv4-20h1
+RNPS1 pp pinin
+COX-2 pp p53
+Beta-2AR interactsWith G-beta-1-gamma-2_dimer
+Beta-2AR interactsWith Trimeric_G_protein
+AK023923 pp LXRalpha
+AK023923 pp LXRbeta
+AK023923 pp KIFF22
+AK023923 pp RORalpha
+CAMK2B pp CAMK2B
+TRIP1 pp Troponin_1
+TRIP1 pp HARS
+TRIP1 pp Troponin_1s
+TRIP1 pp Vimentin
+TRIP1 pp ERRalpha
+TRIP1 pp RORgamma
+TRIP1 pp PHLP
+TRIP1 pp TBP7/MIP224
+TRIP1 pp ST18
+TRIP1 pp RORalpha
+TRIP1 pp NM_144705
+RIP140 pp Actinin_alpha2
+RIP140 pp ERRalpha
+RIP140 pp calmyrin
+RIP140 pp LXRbeta
+SRC1 pp Actinin_alpha1
+SRC1 pp Actinin_alpha2
+SRC1 pp RXRalpha
+SRC1 pp ERRalpha
+SRC1 pp RORgamma
+SRC1 pp CAR1
+SRC1 pp LXRalpha
+SRC1 pp JAB1/COP9S5
+SRC1 pp LXRbeta
+SRC1 pp RXRbeta
+SRC1 pp RORalpha
+SRC1 pp PPARgamma
+SRC1 pp PPARgamma
+SRC1 pp AY495330
+pCAF pp Actinin_alpha1
+pCAF pp Actinin_alpha2
+pCAF pp RAB11A
+pCAF pp LXRalpha
+pCAF pp PNMA1
+pCAF pp ARA160/TMF1
+pCAF pp CEP2
+pCAF pp PAI-RBP1
+pCAF pp GLP
+pCAF pp PGR1
+pCAF pp SSAT2
+DRIP150 pp Actinin_alpha1
+DRIP150 pp Actinin_alpha2
+DRIP150 pp Dynactin1
+DRIP150 pp uveal_autoantigen
+DRIP150 pp EFCBP2
+DRIP150 pp uveal_autoantigen
+TRAP220 pp LXRbeta
+TRAP220 pp KIF1a
+TRAP220 pp PPARgamma
+TRAP220 pp PPARgamma
+PHLP pp TRIP1
+PHLP pp BF668725
+TSG101 pp Troponin_T3f
+TSG101 pp HCRP1
+NCoR1 pp Actinin_alpha2
+NCoR1 pp Ferritin_hc
+NCoR1 pp LXRbeta
+NCoR1 pp RevErbAalpha
+NCoR1 pp PPARgamma
+SMRT pp RARalpha
+SMRT pp RARbeta
+SMRT pp RARgamma
+SMRT pp RXRalpha
+SMRT pp AP2M1
+SMRT pp RANBP9
+SMRT pp RXRgamma
+SMRT pp LXRbeta
+SMRT pp SHARP
+SMRT pp RevErbAalpha
+SMRT pp ABIN-2
+SMRT pp PPARgamma
+MIF1 pp NM_017822
+TBP7/MIP224 pp TRIP1
+TBP7/MIP224 pp BF668725
+NCoA3 pp RARalpha
+NCoA3 pp RARgamma
+NCoA3 pp ERRalpha
+NCoA3 pp LXRalpha
+NCoA3 pp LXRbeta
+NCoA3 pp PPARgamma
+NCoA62 pp DAX
+NCoA62 pp Actinin_alpha2
+NCoA62 pp SHP
+NCoA62 pp NM_138421
+RAP250 pp PPARgamma
+RAP250 pp RORgamma
+RAP250 pp RANBP9
+RAP250 pp LXRalpha
+RAP250 pp LXRbeta
+RAP250 pp FHOD1
+RAP250 pp PPARgamma
+RAP250 pp PPARgamma
+NRIF3 pp Actinin_alpha2
+PNRC2 pp SMIF
+Sherc pp PAR-4
+NR0B1 pp ERRalpha
+NR0B1 pp NCoA62
+NR0B1 pp PPARgamma
+NR0B1 pp PPARgamma
+NR1A1 pp RXRalpha
+NR1A1 pp Cul1
+NR1A1 pp RGN
+NR1A1 pp NCoR1
+NR1A2 pp CAMK2B
+NR1A2 pp TRIP1
+NR1A2 pp RXRalpha
+NR1A2 pp RIP140
+NR1A2 pp SRC1
+NR1A2 pp TRIP7/HMGN3
+NR1A2 pp NCoA3
+NR1A2 pp RXRgamma
+NR1A2 pp RXRbeta
+NR1B1 pp TRIP1
+NR1B1 pp RXRalpha
+NR1B1 pp PRDX6
+NR1B1 pp NCoR1
+NR1B1 pp RXRgamma
+NR1B1 pp LXRbeta
+NR1B1 pp Melusin
+NR1B1 pp RXRbeta
+NR1B2 pp TRIP1
+NR1B2 pp SRC1
+NR1B2 pp PNRC1
+NR1B2 pp RXRgamma
+NR1B2 pp RXRbeta
+NR1B2 pp MAP6
+NR1B3 pp TRIP1
+NR1B3 pp RXRalpha
+NR1B3 pp SRC1
+NR1B3 pp PNRC1
+NR1B3 pp RXRgamma
+NR1B3 pp Melusin
+NR1B3 pp PNRC2
+NR1B3 pp SHP
+NR1B3 pp RXRbeta
+NR1B3 pp MAP6
+NR1C2 pp GLUL
+NR1C2 pp Integrin_beta5
+NR1C2 pp PROX1
+NR1C2 pp TRIP1
+NR1C2 pp RXRalpha
+NR1C2 pp SRC1
+NR1C2 pp PRDX6
+NR1C2 pp RANBP9
+NR1C2 pp RXRgamma
+NR1C2 pp KCTD9
+NR1C2 pp SHP
+NR1C2 pp RXRbeta
+NR1C3 pp RANBP9
+NR1C3 pp JAB1/COP9S5
+NR1C3 pp FHOD1
+NR1C3 pp KIF1a
+NR1D1 pp NCoR1
+NR1D1 pp KIFF22
+NR1D2 pp hUBC9
+NR1D2 pp Cul1
+NR1D2 pp RGN
+NR1D2 pp RevErbAalpha
+NR1F1 pp PROX1
+NR1F1 pp TRIP1
+NR1F1 pp SRC1
+NR1F1 pp PNRC1
+NR1F1 pp JAB1/COP9S5
+NR1F1 pp PNRC2
+NR1F2 pp TRIP1
+NR1F2 pp Troponin_1f
+NR1F2 pp hUBC9
+NR1F2 pp RIP140
+NR1F2 pp SRC1
+NR1F2 pp TBP7/MIP224
+NR1F2 pp PNRC1
+NR1F2 pp RAP250
+NR1F2 pp PNRC2
+NR1F2 pp MAP6
+NR1H2 pp FOXO3A
+NR1H2 pp RXRalpha
+NR1H2 pp hUBC9
+NR1H2 pp SRC1
+NR1H2 pp NCoR1
+NR1H2 pp SMRT
+NR1H2 pp NCoA3
+NR1H2 pp RXRgamma
+NR1H2 pp NM_017814
+NR1H2 pp ING3
+NR1H2 pp RXRbeta
+NR1H2 pp AL137505
+NR1H2 pp BF981716
+NR1H3 pp Actinin_alpha1
+NR1H3 pp FOXO3A
+NR1H3 pp TRIP1
+NR1H3 pp RIP140
+NR1H3 pp SRC1
+NR1H3 pp NCoR1
+NR1H3 pp NCoA3
+NR1H3 pp RXRgamma
+NR1H3 pp NM_017814
+NR1H3 pp ING3
+NR1H3 pp RXRbeta
+NR1H3 pp AK023923.1
+NR1H3 pp AW292937
+NR1H4 pp GAPDH
+NR1H4 pp RXRgamma
+NR1I1 pp TRIP1
+NR1I1 pp RXRalpha
+NR1I1 pp RIP140
+NR1I1 pp SRC1
+NR1I1 pp TRIP7/HMGN3
+NR1I1 pp RXRgamma
+NR1I1 pp SWAP2
+NR1I1 pp LXRbeta
+NR1I1 pp GABARAPL2
+NR1I1 pp GNPAT
+NR1I1 pp SHP
+NR1I1 pp RXRbeta
+NR1I1 pp GABARAPL1
+NR1I1 pp NM_138423
+NR1I2 pp Actinin_alpha2
+NR1I2 pp TRIP1
+NR1I2 pp RXRalpha
+NR1I2 pp SRC1
+NR1I2 pp NUCB2
+NR1I2 pp RXRgamma
+NR1I2 pp PGC1
+NR1I2 pp RXRbeta
+NR1I3 pp Ferritin_hc
+NR1I3 pp TRIP1
+NR1I3 pp SRC1
+NR1I3 pp MAP4
+NR2A1 pp HNF4a
+NR2A1 pp PROX1
+NR2A1 pp hUBC9
+NR2A1 pp RIP140
+NR2A1 pp NPPA
+NR2A1 pp PNRC1
+NR2A1 pp JAB1/COP9S5
+NR2A1 pp RAP250
+NR2A1 pp PNRC2
+NR2A1 pp SHP
+NR2A2 pp GAPDH
+NR2A2 pp TRIP1
+NR2A2 pp Troponin_1f
+NR2A2 pp SRC1
+NR2A2 pp PRDX6
+NR2A2 pp RANBP9
+NR2A2 pp HAX1
+NR2A2 pp PNRC1
+NR2A2 pp JAB1/COP9S5
+NR2A2 pp PNRC2
+NR2A2 pp SHP
+NR2B1 pp KIF1a
+NR2B1 pp R38818
+NR2B2 pp SRC1
+NR2B2 pp LXRalpha
+NR2B2 pp LXRbeta
+NR2B2 pp MAP4
+NR2B2 pp PPARgamma
+NR2B2 pp PPARgamma
+NR2B3 pp CAMK2B
+NR2B3 pp MAP4
+NR2C2 pp RXRbeta
+NR2F1 pp NR2FBP1
+NR2F1 pp NR2FBP2
+NR2F1 pp EEF1D
+NR2F1 pp MAP6
+NR2F6 pp NR2FBP1
+NR2F6 pp NR2FBP2
+NR2F6 pp COUP-TFII
+NR3A1 pp DUT
+NR3A1 pp SRC1
+NR3A1 pp MTCH2
+NR3A1 pp GEF15
+NR3A1 pp PNRC2
+NR3A1 pp Sherc
+NR3A1 pp KIF1a
+NR3A2 pp TRIP1
+NR3A2 pp RIP140
+NR3A2 pp SRC1
+NR3A2 pp PNRC1
+NR3A2 pp PGC1
+NR3A2 pp RAP250
+NR3A2 pp PNRC2
+NR3B1 pp ERRgamma
+NR3B1 pp DUT
+NR3B1 pp PROX1
+NR3B1 pp TRIP1
+NR3B1 pp Troponin_1f
+NR3B1 pp SRC1
+NR3B1 pp MACF1
+NR3B1 pp SHP
+NR3B3 pp DAX
+NR3B3 pp DUT
+NR3B3 pp PROX1
+NR3B3 pp TRIP1
+NR3B3 pp RIP140
+NR3B3 pp SRC1
+NR3B3 pp ERRalpha
+NR3B3 pp EBP
+NR3B3 pp PNRC1
+NR3B3 pp GEF15
+NR3B3 pp PNRC2
+NR3C1 pp Ferritin_hc
+NR3C1 pp HNRNPA1
+NR3C1 pp AY495330
+NR3C2 pp PROX1
+NR3C2 pp TRIP1
+NR3C2 pp SRC1
+NR3C4 pp Gelsolin
+NR3C4 pp ARA54
+NR3C4 pp POB1/REPS2
+NR3C4 pp ARA70
+NR3C4 pp KIF1a
+NR4A2 pp RXRalpha
+NR4A2 pp JAB1/COP9S5
+NR4A2 pp RXRbeta
+NR4A3 pp JAB1/COP9S5
+NR4A3 pp AL134489
+NR5A2 pp Ferritin_hc
+NR5A2 pp RIP140
+NR5A2 pp SRC1
+NR5A2 pp NPPA
+NR5A2 pp PNRC1
+NR5A2 pp PNRC2
+NR5A2 pp Sherc
+HIF-1_alpha pp PHD3
+HIF-1_alpha pp PHD2
+HIF-1_alpha pp OS-9
+OS-9 pp PHD2
+OS-9 pp PHD3
+Hydroxylated_HIF-1_alpha pp VHL
+LKB1 pp LKB1
+BCR-ABL pp BCR-ABL
+p53_dimer interactsWith p21_promoter
+Ref-1 pd p21_promoter
+p53_tetramer interactsWith p21_promoter
+GRB2 pp EGFR
+Snapin pp Cappuccino
+Snapin pp BLOS1
+Snapin pp Dysbindin
+Pallidin pp Dysbindin
+Pallidin pp Cappuccino
+Pallidin pp Pallidin
+Pallidin pp BLOS1
+Muted pp Dysbindin
+RXRB interactsWith THRA-PCSK2_promoter
+THRA pd PCSK2_promoter
+PACS2 pp BID
+E-cadherin pp caveolin-1
+Bcl-XL pp Bid
+Bcl-XL pp Bim
+Bcl-XL pp Bik
+Bcl-XL pp Bad
+Bcl-XL pp Bmf
+Bcl-XL pp Hrk
+RSK2 pp RSK2
+OIP106 pp KIF5C
+ATM interactsWith MRN
+ATM pp p53
+ATM_dimer interactsWith MRN
+ATM pp Chk2
+ATM pp ATM
+Mcl-1 pp Bim
+Mcl-1 pp Bmf
+Mcl-1 pp Puma
+A-Raf pp RABGGT-beta
+A-Raf pp TH1
+A-Raf pp TOM
+A-Raf pp FBNL
+A-Raf pp TIMM44
+A-Raf pp CPS1
+A-Raf pp R-Ras
+A-Raf pp ASS
+A-Raf pp TOPK
+p73-alpha pp Itch
+p73-alpha pp Nedd4
+p53_dimer interactsWith p53_dimer
+Wee1A interactsWith CyclinB1-Cdc2
+Wee1A pp Plk1
+Wee1A pp beta-TrCP2
+Wee1A pp beta-TrCP1
+Wee1A pp SKP2
+SKP1 pp SKP2
+SKP1 pp beta-TrCP2
+SKP1 pp beta-TrCP1
+SKP1 pp FBW5
+SKP1 pp FBW3
+SKP1 pp FBW2
+SKP1 pp FBW6
+SKP1 pp FBW7
+SKP1 pp KIAA1940
+SKP1 pp FBL11
+MeCP2_corepressor interactsWith THBS1_promoter
+MeCP2_corepressor interactsWith FMR1_promoter
+MeCP2_corepressor interactsWith ABCB1_promoter
+Unknown interactsWith Sin3a
+Unknown interactsWith HDAC1
+MeCP2 interactsWith Unknown
+MeCP2 pp Brm
+Unknown interactsWith BAF57
+PTPN2 pp TRAF2
+PTPN2 pp Src
+BLOS3 pp BLOS2
+BLOS1 pp BLOS2
+Snapin pp BLOS2
+BLOS2 pp Cappuccino
+Muted pp BLOS2
+Cbl pp Src
+Cbl pp SH3P2
+SH3P2 pp beta-actin
+Zap70 pp TCR-zeta
+Dyn2 pp p85-alpha
+Dyn2 pp Grb2
+Dyn2 pp Nck
+Dyn2 pp Cortactin
+Dyn2 pp Abi-1
+Dyn2 pp Gads
+Dyn2 pp Lck
+Dyn2 pp CrkL
+Dyn2 pp Vav1
+LAT pp PLC-gamma-1
+LAT interactsWith Gads/SLP-76
+LAT interactsWith Grb2/Sos1
+5-HT1D pp 5-HT1B
+5-HT1D pp EDG1
+5-HT1A pp GABAB2
+5-HT1A pp GPR26
+5-HT1A pp EDG3
+5-HT1A pp EDG1
+RAD51B pp RAD51C
+RAD51B pp H4
+RAD51B pp H3
+RAD51B pp H2B
+RAD51B pp H1
+RAD51B/RAD51C interactsWith H4
+RAD51B/RAD51C interactsWith H3
+RAD51B/RAD51C interactsWith H2B
+RAD51B/RAD51C interactsWith H1
+hPEBP4 pp MEK1
+hPEBP4 pp Raf-1
+PTEN pp PICT-1
+hMINK-beta pp Nck
+HOXA5 pp Twist
+p27 pp importin-alpha
+integrin-beta-1 pp RACK1
+RB1 pp HIF1A
+HIF1A pd EPO_gene_3(prime)_enhancer
+HIF1A pd VEGF_promoter
+RB1 pd EPO_gene_3(prime)_enhancer
+RB1 pd VEGF_promoter
+CARD12 pp CARD12
+CARD12 pp CARD15
+CARD12 pp NALP1
+CARD12 pp NALP4
+CARD12 pp CARD4
+CARD12 pp BIRC1
+CARD12 pp CIAS1
+CARD12 pp CASP1
+CARD15 pp CASP1
+NALP1 pp CASP1
+Dock180 pp ELMO
+Dock180 pp Dock180
+C/EBP-epsilon pd p-lactoferrin
+C/EBP-alpha pd p-lactoferrin
+C/EBP-delta pd p-lactoferrin
+C/EBP-epsilon_-_C/EBP-delta_heterodimer interactsWith p-lactoferrin
+NEMO pp CIKS
+TANK pp IKK-alpha
+ABI-1 pp p47phox
+c-Abl pp p47phox
+DNA-PK interactsWith Akt1
+DNA-PK interactsWith Akt2
+DNA-PK interactsWith Akt3
+PDK1 pp Akt1
+DNA-PKcs pp Akt1
+Dock180-ELMO interactsWith Rac1
+Dock2 pp ELMO
+Dock2-ELMO interactsWith Rac1
+Nogo-A pp UQCRC2
+Nogo-A pp UQCRC1
+PACS-1 pp CLC-7
+Nogo-A pp NIMP
+PLCG1 pp TRPC3
+SKIP pp kinesin_HC
+PACS-1 pp TRPV4
+PML3 pp Aurora_A
+EPRS pp EF-1-gamma
+HRS pp EF-1-beta
+LRS pp EF-1-gamma
+HRS pp EF-1-gamma
+PLG pp ACTG1
+PRKCSH pp STXBP3
+PRKCZ pp PRKCSH
+BTG1 pp THRA
+BTG1 pp THRB
+BTG1 pp RARA
+BTG1 pp MYOD1
+BTG1 pp JUN
+BTG1 pp MYOG
+BTG1 pp HRMT1L2
+PACS-1 pp PKD2
+B-beta(15-42) pp CDH5
+PKD2 interactsWith Unknown
+Unknown interactsWith GGA1
+PKD1 pp PKD2
+UCH37 pp UIP1
+UCH37 pp S14
+PACS-2 pp PKD2
+HDAC1 pd CDKN1A_promoter
+RNA_polymerase_II interactsWith CDKN1A_promoter
+TP53 pp SP1
+AHR pp TBP
+AHR pp TAF4
+NR5A2 pp NCOA3
+AHR pp TAF6
+AHR pp NCOA1
+HDAC1 pd RECQL4_promoter
+RNA_polymerase_II interactsWith RECQL4_promoter
+SP1 pd RECQL4_promoter
+TP53 pd RECQL4_promoter
+AHR pp NCOA2
+Daxx pp SUMO1
+PML pp SUMO1
+Daxx pp MCRS1
+PRKCD pp PDPK1
+PRKCZ pp PDPK1
+PKN2 pp PDPK1
+KY pp MYBPC1
+KY pp TTN
+KY pp DKFZp434B1231
+KY pp FLNC
+hTR interactsWith hTR
+ARAF pp COPS3
+ARAF pp NUDT14
+RAF1 pp YWHAB
+RAF1 pp TIMM50
+RAF1 pp HRAS
+RAF1 pp OIP5
+RAF1 pp PKM2
+RAF1 pp CCT3
+CDC2/CCNB1_complex interactsWith CDC25B
+CDK2/CCNA2_complex interactsWith CDC25B
+Unknown interactsWith PNKP
+Unknown interactsWith XRCC1
+TDP1 pp LIG3-alpha
+TDP1 pp LIG3-beta
+FOXO1A pp FHL2
+IQCB1 pp CALM2
+IRX2 pp MAPK3
+CNKSR1 pp ARHGEF1
+GPS2 pp TBL1X
+Unknown interactsWith NCOR
+HDAC5 interactsWith Unknown
+Unknown interactsWith HDAC3
+HDAC1 interactsWith Unknown
+Unknown interactsWith SIN3A
+TXNIP pp TXN
+TXNIP pp KPNA2
+CTSD pp IGF2R
+NRP1 pp FGF4
+RPS6KB1 pp RPS6
+CDC2-CCNB1 interactsWith RPS6KB1
+INVS pp CALM2
+MIS12 interactsWith Unknown
+ITGAV pp ITGB5
+cyclin_E-CDK2 interactsWith RB1
+CDKN1B interactsWith cyclin_E-CDK2
+CDKN1A interactsWith cyclin_E-CDK2
+NRP1 pp FGF1
+ESR1 pp NRIP1
+ESR1 pp TIF1
+TRIF pp TRAF6
+TRIF pp TBK1
+NRP1 pp FGF2
+NRP1 pp FGF7
+HuF2 pp SMIF_TF
+HuF2 pp B-myb
+HuF2 pp Peroxiredoxin_4
+HuF2 pp NC2
+FOXO1A pp SIRT1
+FHL2 pp SIRT1
+ER-alpha pd TFF1/pS2_ERE
+BRAF pp YWHAB
+RAF1 pp CPS1
+RAF1 pp RRAS2
+RAF1 pp PBK
+RAF1 pp COPS3
+RAF1 pp NUDT14
+RAF1 pp EFEMP1
+ARAF pp HRAS
+ARAF pp PKM2
+ARAF pp TIMM50
+DNASE1 pp ACTB
+ACTB pp HNRPU
+PC4 pp CSTF2
+AKT1 pp GSK3B
+COPS5 pp CDKN1B
+AKT1 pp MLLT7
+MLLT7 pd CCND1_promoter
+POLR2A interactsWith unknown
+unknown interactsWith HNRPU
+unknown interactsWith GTF2F1
+ARHGAP21 interactsWith ARF6-GTP
+ARHGAP21 interactsWith ARF1-GTP
+SMAD3 pp EP300
+NCOA1 pp EP300
+MSX1 pp TP53
+EPB41L3 pp PLA2G2A
+EPB41L3 pp SPTBN1
+EPB41L3 pp CD44
+NRP1 pp HGF
+FHL2 pp TTN
+FHL2 pp AK1
+FHL2 pp CKM
+HDAC9 pp HDAC1
+HDAC9 pp HDAC3
+CNKSR1 pp MAP2K7
+CNKSR1 pp MAP3K10
+MYOM1 pp MYOM1
+ESR1 pp ABC1
+GIT1 pp PXN
+PXN pp ITGA4
+ARHGAP21 interactsWith Cdc42-GTP
+ARHGAP21 interactsWith Rac1-GTP
+ARHGAP21 pp RhoA
+HIST4H4 pd CNR1_promoter
+PAX3 pd CNR1_promoter
+Pax3/FKHR pd EPHA2_promoter
+Pax3/FKHR pd EPHA4_promoter
+RNA_polymerase_II interactsWith EPHA4_promoter
+Smad1 pp CHIP
+T-beta-R1/T-beta-R2 interactsWith Par6
+T-beta-R1/T-beta-R2 interactsWith Smad2
+T-beta-R1/T-beta-R2/Par6 interactsWith PKC_zeta
+T-beta-R1 pp T-beta-R1
+T-beta-R1 pp FKBP12
+T-beta-R1 pp STRAP
+ANG pp ACTN2
+Pax3/FKHR pd CNR1_promoter
+Plk1 pp CDC25C
+TGFB1I1 pp ITGA4
+LXN pp ITGA4
+RB1 pd BIRC5
+DDEF1 pp CTTN
+DDEF1 pp CRK
+DDEF1 pp SH3KBP1
+DDEF1 pp ITSN1
+DDEF1 pp PACSIN3
+DDEF2 pp SH3KBP1
+DDEF2 pp ITSN1
+DDEF2 pp PACSIN3
+PXN pp CTTN
+ILK1 pp caveolin-1
+T-beta-RII pp CRIB
+T-beta-RI pp CRIB
+T-beta-RI/T-beta-RII interactsWith OCLN
+T-beta-RI/T-beta-RII interactsWith Cdc42
+T-beta-RI/T-beta-RII interactsWith Beta-PIX
+T-beta-RII pp Beta-PIX
+KyoT1 pp HPC2
+T-beta-RI pp TRIK
+T-beta-RII pp TRIK
+T-beta-RII pp alpha-PIX
+T-beta-RI pp alpha-PIX
+T-beta-RI pp OSR1
+T-beta-RII pp OSR1
+T-beta-RII pp PAK1
+T-beta-RI pp STK22D
+T-beta-RII pp STK22D
+T-beta-RI pp PPP1C
+T-beta-RII pp PPP1C
+p16 pp CDK4
+p16 pp CDK6
+Rak pp Rak
+miR16 interactsWith Cox2
+TTP interactsWith Cox2
+Unknown interactsWith miR16
+TTP interactsWith Unknown
+Unknown interactsWith eiF2C4
+TTP interactsWith Unknown
+Unknown interactsWith eiF2C2
+TTP interactsWith Unknown
+Myc pp Pam
+Smad4 pp Smad2
+T-beta-RI pp Smad2
+Smad4 pp Smad3
+Smad4 pp Ski
+Smad4 pp Smad1
+Smad4 pp SnoN
+HIST4H4 pd RARB
+DNMT3B pd RARB
+DNMT3A pd RARB
+DNMT1 pd RARB
+HDAC1 pd RARB
+RBL2 pd BIRC5
+CTTN pp ITSN1
+E2F4 pd BIRC5
+E2F5 pd BIRC5
+E2F1 pd BIRC5
+E2F3 pd BIRC5
+Survivin pp Survivin-deltaEx3
+Survivin pp Survivin-2B
+E2F1 pd TP53BP2_promoter
+E2F1 pd PPP1R13B_promoter
+MSH2 pp MSH6
+PRKACA pp AKIP1a
+MYC pd CDK4
+USF1 pd IGF2R
+USF2 pd IGF2R
+EP300 pp MPG
+TERT pp RELA
+LCK pp NFKBIA
+TP53 pd TNFRSF10C
+SFRP2 pp FN1
+MAP3K11 pp MAP2K7
+Unknown interactsWith CDC37
+Unknown interactsWith HSPCB
+Unknown interactsWith HSPCA
+MAP3K11 interactsWith Unknown
+TNFSF10 pp TNFRSF10B
+TAF4B pp TAF1
+TAF4B pp TAF12
+ESR1 pp MPG
+RTKN pp RhoA
+SMURF2 pp RAN
+TGF-beta-RI pp KBRAS1
+ACVR1 pp KBRAS1
+BMPR1B pp KBRAS1
+SMURF2 pp KBRAS1
+SMAD4 pp ARHG
+TGF-beta-RI pp ARHG
+SMAD1 pp ARHG
+SMAD2 pp RIT1
+SMAD3 pp RIT1
+SMURF1 pp RIT1
+SMURF2 pp RAB22A
+SMAD2 pp RIS
+SMAD3 pp RIS
+SMAD4 pp RIS
+TGF-beta-RI pp RIS
+SMAD1 pp RIS
+ACVR1 pp RIS
+BMPR1B pp RIS
+SMURF2 pp RIS
+SMAD2 pp RASD2
+SMAD3 pp RASD2
+SMAD4 pp RASD2
+TGF-beta-RI pp RASD2
+SMAD1 pp RASD2
+ACVR1 pp RASD2
+BMPR1B pp RASD2
+SMURF1 pp RASD2
+SMURF2 pp RASD2
+SMAD4 pp RAB13
+TGF-beta-RI pp RAB13
+SMURF2 pp RAB13
+ACVR1 pp RAB17
+SMURF2 pp RAB17
+SMURF2 pp RAB14
+TGF-beta-RI pp ARHA
+SMAD1 pp RAB30
+TGF-beta-RI pp ARHH
+SMAD4 pp RAB25
+TGF-beta-RI pp RAB25
+ACVR1 pp RAB25
+BMPR1B pp RAB25
+SMURF2 pp RAB25
+SMAD2 pp ARHJ
+SMAD4 pp ARHJ
+TGF-beta-RI pp ARHJ
+ACVR1 pp ARHJ
+BMPR1B pp ARHJ
+TGF-beta-RI pp RAB33B
+ACVR1 pp RAB33B
+SMAD4 pp RAB2B
+SMAD1 pp RAB2B
+TGF-beta-RI pp RAP2A
+SMAD1 pp RAP2A
+ACVR1 pp RAP2A
+BMPR1B pp RAP2A
+SMAD2 pp RAB34
+SMAD4 pp RAB34
+TGF-beta-RI pp RAB34
+SMAD1 pp RAB34
+SMAD2 pp RHEBL1
+SMAD4 pp RHEBL1
+TGF-beta-RI pp RHEBL1
+SMAD1 pp RHEBL1
+ACVR1 pp RHEBL1
+BMPR1B pp RHEBL1
+SMAD2 pp ARHD
+SMAD4 pp ARHD
+TGF-beta-RI pp ARHD
+ACVR1 pp ARHD
+BMPR1B pp ARHD
+SMURF2 pp ARHD
+TGF-beta-RI pp RAB6B
+SMAD1 pp RAB6B
+ACVR1 pp RAB6B
+BMPR1B pp RAB6B
+SMAD4 pp RAC2
+SMAD1 pp RAC2
+SMAD4 pp NRAS
+ACVR1 pp NRAS
+SMURF2 pp NRAS
+SMURF2 pp RAC1
+SMAD4 pp RAB3B
+TGF-beta-RI pp RAB3B
+SMAD1 pp RAB3B
+ACVR1 pp RAB3B
+SMAD2 pp RAB38
+SMAD3 pp RAB38
+SMAD4 pp RAB38
+TGF-beta-RI pp RAB38
+SMAD1 pp RAB38
+BMPR1B pp RAB38
+SMAD3 pp RRAS2
+SMAD4 pp RRAS2
+ACVR1 pp RRAS2
+BMPR1B pp RRAS2
+SMURF2 pp RRAS2
+SMAD2 pp RHOBTB1
+TGF-beta-RI pp RHOBTB1
+SMAD1 pp RHOBTB1
+ACVR1 pp RHOBTB1
+BMPR1B pp RHOBTB1
+SMURF1 pp RHOBTB1
+SMAD2 pp RAN
+TGF-beta-RI pp DKFZP761H079
+SMAD1 pp DKFZP761H079
+ACVR1 pp DKFZP761H079
+BMPR1B pp DKFZP761H079
+SMURF1 pp FLJ22595
+SMAD4 pp ARL5
+TGF-beta-RI pp ARL5
+SMAD1 pp ARL5
+SMAD4 pp ARFRP1
+SMAD4 pp ARL8
+TGF-beta-RI pp FLJ10702
+SMAD2 pp ARF4L
+TGF-beta-RI pp ARF4L
+SMAD1 pp ARF4L
+SMURF1 pp ARF4L
+TGF-beta-RI pp GIT2
+SMURF2 pp SMAP1
+SMAD2 pp ARFGAP3-V1
+TGF-beta-RI pp GNA13
+SMURF1 pp GNG11
+SMURF2 pp GNG2
+TGF-beta-RI pp CDGAP
+SMURF1 pp CDGAP
+TGF-beta-RI pp CHN2
+SMURF1 pp INPP5B
+TGF-beta-RI pp BCR
+BMPR1B pp BCR
+TGF-beta-RI pp CHN1
+ACVR1 pp CHN1
+BMPR1B pp CHN1
+SMAD2 pp ARHGEF1
+SMURF1 pp ARHGEF1
+SMURF2 pp ARHGEF1
+SMAD4 pp ARHGEF11
+SMURF1 pp ARHGEF11
+SMAD2 pp ARHGEF7
+SMAD3 pp ARHGEF7
+SMAD4 pp ARHGEF7
+SMAD1 pp ARHGEF7
+SMURF1 pp ARHGEF7
+SMAD1 pp SMURF1
+TGF-beta-RI pp LOC51035
+SMAD1 pp LOC51035
+ACVR1 pp LOC51035
+BMPR1B pp LOC51035
+SMURF1 pp LOC51035
+SMAD4 pp UBB
+TGF-beta-RI pp UBB
+SMURF1 pp UBB
+SMAD2 pp RPS27A
+SMAD4 pp RPS27A
+TGF-beta-RI pp RPS27A
+SMAD1 pp RPS27A
+ACVR1 pp RPS27A
+BMPR1B pp RPS27A
+SMURF1 pp RPS27A
+SMURF1 pp SF3A1
+TGF-beta-RI pp UBD
+SMAD2 pp UBA52
+SMAD4 pp UBA52
+TGF-beta-RI pp UBA52
+SMAD1 pp UBA52
+ACVR1 pp UBA52
+BMPR1B pp UBA52
+SMURF1 pp UBA52
+TGF-beta-RI pp USP45
+SMAD1 pp USP45
+BMPR1B pp USP45
+SMURF1 pp USP45
+ACVR1 pp USP39
+TGF-beta-RI pp USP21
+ACVR1 pp USP21
+SMAD4 pp FLJ13855
+TGF-beta-RI pp FLJ13855
+SMAD1 pp FLJ13855
+BMPR1B pp FLJ13855
+SMURF2 pp UBE2G1
+TGF-beta-RI pp UBE2E3
+ACVR1 pp UBE2E3
+TGF-beta-RI pp FBX30
+SMAD1 pp FBX30
+ACVR1 pp FBX30
+BMPR1B pp FBX30
+SMURF1 pp FBX30
+TGF-beta-RI pp FBXL12
+SMAD1 pp FBXL12
+SMAD4 pp FBXO30
+SMAD1 pp FBXO30
+ACVR1 pp FBXO30
+SMURF1 pp FBXO30
+SMAD2 pp FBXO3
+SMAD3 pp FBXO3
+TGF-beta-RI pp FBXO3
+SMAD1 pp FBXO3
+BMPR1B pp FBXO3
+SMURF1 pp FBXO3
+SMAD4 pp FBXO34
+TGF-beta-RI pp FBXO34
+TGF-beta-RI pp FBXO24
+SMAD1 pp FBXO24
+BMPR1B pp FBXO24
+SMURF1 pp FBXO24
+TGF-beta-RI pp CUL5
+SMURF1 pp CUL5
+SMAD2 pp SQSTM1
+SMAD3 pp SQSTM1
+SMAD4 pp SQSTM1
+TGF-beta-RI pp SQSTM1
+SMAD1 pp SQSTM1
+ACVR1 pp SQSTM1
+BMPR1B pp SQSTM1
+SMURF1 pp SQSTM1
+SMAD2 pp PC326
+TGF-beta-RI pp PC326
+ACVR1 pp PC326
+BMPR1B pp PC326
+SMAD2 pp PPP2R2D
+SMAD3 pp PPP2R2D
+SMURF1 pp PPP2R2D
+TGF-beta-RI pp KIAA1892
+BMPR1B pp KIAA1892
+TGF-beta-RI pp APG16L
+BMPR1B pp APG16L
+TGF-beta-RI pp PRPF4
+BMPR1B pp HAN11
+TGF-beta-RI pp CDC20
+TGF-beta-RI pp KATNB1
+TGF-beta-RI pp NUP37
+TGF-beta-RI pp GNB3
+SMURF1 pp TBL2
+TGF-beta-RI pp WSB1
+SMAD1 pp WSB1
+TGF-beta-RI pp PREB
+SMAD1 pp PREB
+TGF-beta-RI pp WDR13
+SMAD2 pp CDC40
+SMURF1 pp CDC40
+TGF-beta-RI pp REC14
+ACVR1 pp REC14
+SMURF1 pp REC14
+TGF-beta-RI pp GNB2
+SMURF1 pp PAK1IP1
+SMURF1 pp PWP1
+SMURF1 pp RNU3IP2
+SMAD2 pp PPP2R2B-V2
+SMAD3 pp PPP2R2B-V2
+SMURF1 pp PPP2R2B-V2
+TGF-beta-RI pp FBXW5
+SMAD1 pp FBXW5
+BMPR1B pp FBXW5
+SMURF1 pp UNRIP
+TGF-beta-RI pp CSNK2A2
+SMURF1 pp CSNK2A2
+SMURF1 pp DKFZP434E1822
+TGF-beta-RI pp CDKL1
+SMURF1 pp CDKL1
+TGF-beta-RI pp C14ORF20
+SMURF2 pp C14ORF20
+SMAD4 pp NEK6
+TGF-beta-RI pp NEK6
+SMURF2 pp NEK6
+SMAD4 pp STK35
+TGF-beta-RI pp STK35
+BMPR1B pp STK35
+SMURF1 pp STK35
+TGF-beta-RI pp MKNK2
+BMPR1B pp MKNK2
+SMAD4 pp RIPK2
+SMURF1 pp RIPK2
+TGF-beta-RI pp AURKB
+SMAD2 pp MAP2K3
+SMAD3 pp MAP2K3
+SMAD4 pp MAP2K3
+TGF-beta-RI pp MAP2K3
+SMAD1 pp MAP2K3
+BMPR1B pp MAP2K3
+SMURF1 pp MAP2K3
+SMAD3 pp WEE1
+SMURF1 pp WEE1
+SMAD4 pp CHEK1
+TGF-beta-RI pp IKBKB
+ACVR1 pp IKBKB
+SMAD4 pp LYK5
+TGF-beta-RI pp CDK4
+BMPR1B pp CDK4
+SMAD4 pp EIF2AK4
+TGF-beta-RI pp EIF2AK4
+SMAD1 pp EIF2AK4
+TGF-beta-RI pp DAPK2
+TGF-beta-RI pp CSNK1D
+SMAD2 pp SNARK
+SMAD4 pp SNARK
+TGF-beta-RI pp SNARK
+ACVR1 pp SNARK
+TGF-beta-RI pp STK22D
+TGF-beta-RI pp FANCL
+ACVR1 pp FANCL
+BMPR1B pp FANCL
+SMAD4 pp TOPK
+SMAD2 pp KIS
+SMAD4 pp KIS
+TGF-beta-RI pp KIS
+SMAD1 pp KIS
+ACVR1 pp KIS
+BMPR1B pp KIS
+SMURF1 pp KIS
+TGF-beta-RI pp OSR1
+BMPR1B pp OSR1
+SMURF1 pp OSR1
+SMAD4 pp CAMK2D
+TGF-beta-RI pp NEK8
+ACVR1 pp NEK8
+TGF-beta-RI pp CSNK1A1
+TGF-beta-RI pp HRI
+TGF-beta-RI pp FLJ23356
+BMPR1B pp FLJ23356
+TGF-beta-RI pp PFTK1
+ACVR1 pp PFTK1
+BMPR1B pp PFTK1
+SMURF1 pp PFTK1
+SMAD2 pp PAK1
+SMAD4 pp PAK1
+TGF-beta-RI pp PAK1
+SMAD1 pp PAK1
+ACVR1 pp PAK1
+BMPR1B pp PAK1
+SMURF1 pp PAK1
+SMAD2 pp IRAK2
+SMURF1 pp IRAK2
+TGF-beta-RI pp PCTK2
+TGF-beta-RI pp MYO3A
+TGF-beta-RI pp CHUK
+TGF-beta-RI pp CDK6
+TGF-beta-RI pp TGFBR1
+ACVR1 pp TGFBR1
+BMPR1B pp TGFBR1
+TGF-beta-RI pp BMPR2
+BMPR1B pp BMPR2
+SMAD4 pp STK18
+TGF-beta-RI pp STK18
+SMURF1 pp MAP3K7
+SMURF2 pp PPID
+TGF-beta-RI pp STUB1
+SMAD1 pp STUB1
+BMPR1B pp STUB1
+SMURF1 pp STUB1
+TGF-beta-RI pp TTC1
+SMURF1 pp DNAJC7
+TGF-beta-RI pp ANAPC5
+SMURF1 pp ANAPC5
+SMURF2 pp ANAPC5
+ACVR1 pp FLJ10890
+BMPR1B pp FLJ10890
+SMURF1 pp FLJ10890
+SMURF1 pp FLJ22054
+TGF-beta-RI pp FLJ21908
+TGF-beta-RI pp FLJ20272
+ACVR1 pp FLJ20272
+BMPR1B pp FLJ20272
+SMAD1 pp RAPSN
+SMURF1 pp RAPSN
+SMURF1 pp RNF127
+SMURF1 pp ZBTB8
+TGF-beta-RI pp ENC1
+TGF-beta-RI pp BTBD2
+SMAD1 pp BTBD2
+TGF-beta-RI pp FLJ33790
+ACVR1 pp FLJ33790
+TGF-beta-RI pp KLHL1
+BMPR1B pp KLHL1
+BMPR1B pp LZTR1
+TGF-beta-RI pp SCAP2
+SMAD4 pp ITK
+TGF-beta-RI pp ITK
+TGF-beta-RI pp SNTG1
+TGF-beta-RI pp PLEK
+ACVR1 pp PLEK
+TGF-beta-RI pp PLEKHB1
+SMAD1 pp PLEKHB1
+ACVR1 pp PLEKHB1
+BMPR1B pp PLEKHB1
+SMAD1 pp OSBPL3
+SMURF1 pp OSBPL3
+TGF-beta-RI pp POLR2J2
+SMAD1 pp POLR2J2
+TGF-beta-RI pp FLJ12604
+SMAD1 pp FLJ12604
+ACVR1 pp FLJ12604
+BMPR1B pp FLJ12604
+TGF-beta-RI pp GNRPX
+ACVR1 pp GNRPX
+TGF-beta-RI pp FLJ12987
+ACVR1 pp FGD6
+TGF-beta-RI pp FLJ10244
+SMAD1 pp FLJ10244
+BMPR1B pp FLJ10244
+SMURF1 pp FLJ10244
+TGF-beta-RI pp ARHGAP15
+SMURF1 pp ARHGAP15
+SMAD1 pp GEFT
+SMURF1 pp CKIP-1
+SMAD2 pp ARHGEF6
+SMAD3 pp ARHGEF6
+TGF-beta-RI pp ARHGEF6
+SMAD1 pp ARHGEF6
+BMPR1B pp ARHGEF6
+TGF-beta-RI pp PARD6A
+SMAD2 pp RGS3
+SMAD3 pp RGS3
+SMAD1 pp RGS3
+SMAD2 pp GRIP1
+SMURF1 pp GRIP1
+SMURF1 pp ALS2CR19-V1
+TGF-beta-RI pp MK-STYX
+TGF-beta-RI pp DUSP10
+TGF-beta-RI pp DUSP13-LIKE
+ACVR1 pp DUSP13-LIKE
+SMURF1 pp DUSP13-LIKE
+TGF-beta-RI pp DUSP6
+SMAD4 pp ILKAP
+TGF-beta-RI pp ILKAP
+ACVR1 pp ILKAP
+BMPR1B pp ILKAP
+TGF-beta-RI pp PPP3CC
+BMPR1B pp PPP3CC
+TGF-beta-RI pp PPP1CA
+BMPR1B pp PPP2CA
+TGF-beta-RI pp PPP6C
+SMURF1 pp PPP1CB
+SMAD2 pp LMO2
+TGF-beta-RI pp LIMS1-V1
+SMURF1 pp LIMS1-V1
+SMAD2 pp LHX9
+SMURF1 pp LHX9
+ACVR1 pp JUB
+SMAD1 pp FHL5
+SMAD1 pp TRIP6
+SMAD4 pp DKFZP434J0617
+SMAD2 pp TRIM35
+SMAD3 pp TRIM35
+SMAD4 pp TRIM35
+SMAD1 pp TRIM35
+SMURF1 pp TRIM35
+TGF-beta-RI pp RNF146
+SMAD4 pp RNF14
+SMAD1 pp RNF14
+SMURF1 pp RNF14
+SMURF2 pp RNF14
+SMURF2 pp RNF2
+TGF-beta-RI pp RNF130
+SMURF1 pp RNF141
+SMURF1 pp RNF12
+SMAD4 pp RNF138
+TGF-beta-RI pp RNF138
+SMAD1 pp RNF138
+SMURF1 pp RNF138
+SMAD2 pp FLJ23360
+SMAD1 pp FLJ23360
+SMURF1 pp FLJ23360
+TGF-beta-RI pp RNF5
+BMPR1B pp SH3KBP1
+BMPR1B pp SRGAP1
+TGF-beta-RI pp NOXO1
+SMAD4 pp CXORF9
+SMAD8 pp CXORF9
+BMPR1B pp CXORF9
+SMURF1 pp CXORF9
+SMAD2 pp TNNT1-V1
+TGF-beta-RI pp TNNT1-V1
+SMAD1 pp TNNT1-V1
+BMPR1B pp TNNT1-V1
+SMURF1 pp TNNT1-V1
+TGF-beta-RI pp SAT2
+SMAD4 pp NAT8
+TGF-beta-RI pp NAT8
+SMAD1 pp ELP3
+SMURF1 pp ELP3
+TGF-beta-RI pp NAT5
+SMAD1 pp NAT5
+ACVR1 pp NAT5
+BMPR1B pp NAT5
+SMURF1 pp NAT5
+SMAD1 pp DKFZP564C103
+SMAD1 pp ING1L
+SMURF1 pp ING1L
+SMURF2 pp ING1L
+SMURF1 pp DKFZP727G051
+SMURF1 pp CGBP
+SMAD4 pp AP2B1
+ACVR1 pp AP2B1
+SMURF1 pp AP2B1
+SMAD4 pp RTDR1
+SMAD1 pp WWOX-V2
+TGF-beta-RI pp HYPB
+SMAD2 pp WWP2
+SMAD3 pp WWP2
+SMAD7 pp WWP2
+TGF-beta-RI pp WWP2
+SMAD1 pp WWP2
+SMURF1 pp NOLA1
+SMURF2 pp NOLA1
+SMAD3 pp SFRS16
+SMAD4 pp SMAD1
+SMAD2 pp SMAD2
+SMAD4 pp SMAD2
+SMAD3 pp SMAD3
+SMAD4 pp SMAD3
+SMAD1 pp SMAD3
+SMURF1 pp SMAD3
+BMPR1B pp SMAD6
+SMURF1 pp SMAD6
+SMURF2 pp SMAD6
+TGF-beta-RI pp SMAD7
+BMPR1B pp SMAD7
+SMURF1 pp SMAD7
+TGF-beta-RI pp SOCS4
+ACVR1 pp SOCS4
+BMPR1B pp SOCS4
+SMURF2 pp SOCS4
+SMAD4 pp STAT1
+TGF-beta-RI pp STAT1
+ACVR1 pp STAT1
+SMURF1 pp STAT1
+SMURF2 pp SLA2
+SMURF2 pp EPHA1
+SMURF1 pp ETV6
+TGF-beta-RI pp SAMD8
+ACVR1 pp FKBP4
+SMURF2 pp FKBP4
+TGF-beta-RI pp FKBP1B
+BMPR1B pp FKBP1B
+TGF-beta-RI pp FKBP1A
+BMPR1B pp FKBP1A
+SMAD2 pp GSC
+SMAD3 pp GSC
+SMAD1 pp GSC
+TGF-beta-RI pp IRF7
+BMPR1B pp IRF7
+SMURF2 pp IRF3
+SMURF2 pp ICSBP1
+SMURF1 pp SFRS5
+TGF-beta-RI pp EFNA1
+SMURF1 pp SFRS4
+SMURF2 pp SFRS4
+TGF-beta-RI pp RHPN2
+SMURF1 pp RHPN2
+TGF-beta-RI pp RTKN
+SMURF1 pp RTKN
+TGF-beta-RI pp CDC42EP4
+TGF-beta-RI pp STX8
+ACVR1 pp STX8
+ACVR1 pp KIAA0290
+SMURF1 pp KIAA0290
+SMURF1 pp UBTF
+SMURF1 pp AVEN
+TGF-beta-RI pp ASH2L
+SMURF1 pp ASH2L
+SMURF2 pp ASH2L
+TGF-beta-RI pp C20ORF121
+TGF-beta-RI pp RGS19
+TGF-beta-RI pp RRH
+SMAD4 pp OCLN
+TGF-beta-RI pp OCLN
+SMURF1 pp OCLN
+SMAD4 pp HDGF
+SMURF1 pp HDGFRP3
+SMURF2 pp HDGFRP3
+SMAD4 pp APBB2
+SMURF1 pp APBB2
+SMURF1 pp SITPEC
+TGF-beta-RI pp RAN
+SMAD1 pp RAN
+BMPR1B pp RAN
+SMAD2 pp SMURF2
+SMAD3 pp SMURF2
+SMAD1 pp SMURF2
+TGF-beta-RI pp FLJ11294
+TGF-beta-RI pp PPP2R2B
+SMAD4 pp STK22C
+TGF-beta-RI pp WWOX
+SMAD3 pp SMAD2
+Hras pp Raf
+Nras pp Raf
+Collagen_VII pp laminin_5
+Myc pd CDKN1A_promoter
+Miz-1 pd CDKN1A_promoter
+Sp1 pd CDKN1A_promoter
+HIF-1alpha pd CDKN1A_promoter
+Lats1 pp Lats1
+STK4 pp STK4
+Mst4 pp Mst4
+STK3 pp STK3
+STK4 pp Lats1
+Lats2 pp Lats2
+STK3 pp Lats2
+STK3 pp Lats1
+STK3 pp SAV1
+STARD13 pp SMARCD3
+STARD13 pp TAX1BP1
+STARD13 pp K-ALPHA-1
+STARD13 pp HMGCR
+STARD13 pp ITPR1
+STARD13 pp HSPCB
+STARD13 pp BAI2
+CAPN1 pp ACTC
+CAPN1 pp ACTN2
+CAPN1 pp CAPNS1
+CAPN1 pp COL1A1
+CAPN1 pp DES
+CAPN1 pp MYBPC3
+CAPN1 pp NFE2L1
+CAPN1 pp PTGDS
+CAPN1 pp SH3BGR
+CAPN1 pp SLIT3
+CAPN1 pp SKB1
+STARD13 pp EPB41L1
+STARD13 pp KIF1B
+SNF2H pp hACF1
+Unknown interactsWith BAF170
+Unknown interactsWith BAF155
+Unknown interactsWith INI1
+Unknown interactsWith BAF57
+Unknown interactsWith BAF60a
+BRG1 interactsWith Unknown
+BRG1 pd p21_promoter
+BRG1 pd CSF1_promoter
+CDK9 pp POLR2A
+PPP1CC pp POLR2A
+MDM2 pp MAPKAPK2
+PARP10 pp HIST4H4
+PARP10 pp H3F3A
+Ncl pp Myc
+PARP10 pp Myc
+MDM2 pp TP53
+CCNA1 pp HIST1H1A
+CCNA1 pp CDC2
+CCNB1 pp CDC2
+CCNA1 pp CDK2
+CCND1 pp CDK4
+Homer_3 pp GRM5
+MDM2 pp MAPKAPK2
+pRB pd OC_promoter
+HMGA1 pd INSR_locus
+STAT5A pd Cyclin_D2_promoter
+STAT5A pd IL-5_promoter
+STAT5A pd IL-9_promoter
+Rad9 pp RPA70
+Rad9 pp Hus1
+Rad9 pp Hus1
+Rad1 pp RPA32
+Hus1 pp RPA32
+Rad9 pp RPA32
+Separase pp Cdk1
+Separase pp Cyclin_B1
+Cyclin_B1 pp Cdk1
+CCNB1 pp CDC2
+CDC2 pp CCNB1
+Cks2 pp Cyclin_B1
+Separase pp Cks2
+EGFR pp SH3BGRL3
+ERBB2 pp GRB2
+EGFR pp STAT5B
+ERBB3 pp PIK3R2
+EGFR pp GRB2
+EGFR pp GRB2
+ERBB2 pp PTPN11
+ERBB2 pp SH3BGRL3
+EGFR pp SHC1
+EGFR pp CBL
+EGFR pp CRK
+ERBB2 pp SHC1
+ERBB3 pp GRB2
+ERBB4 pp PTPN11
+ERBB4 pp NCK2
+ERBB4 pp GRB2
+ERBB4 pp CRK
+ERBB4 pp PIK3R2
+ERBB4 pp SHC1
+ERBB4 pp STAT5B
+ERBB3 pp CSK
+ERBB3 pp SHC1
+EGFR pp PTPN11
+EGFR pp CSK
+Mule pp Mcl-1
+eIF-4E interactsWith Unknown
+Unknown interactsWith 4E-BP1
+L1CAM pp ankyrin
+L1CAM pp AP-2_mu2_chain
+eIF-4E pp eIF-4G
+CDKN2A pp MAPK8
+CK2 interactsWith USP15
+p63 pd CD95
+Tctex-1 pp DIC
+ATF3 pp ATF3
+ATF3 pp p53
+p300 pp p53
+p300 pp p53
+PCAF pp H4
+ASCIZ pp CHK2
+ATR pp ASCIZ
+MAPK8 pp JUN
+JNK1alpha1 pp c-Jun
+MAPK10 pp JUN
+JNK3alpha2 pp c-Jun
+CDKN2A pp MAPK10
+TOP2A pp BRCA1
+ESPL1 pp PTTG1
+Separase pp Securin
+IL6 pp IL6R
+IL6R pp IL6
+IL6-IL6R interactsWith IL6ST
+VCAM1 pp SEC61B
+Unknown interactsWith ELMO1
+Unknown interactsWith DOCK1
+CRKII interactsWith Unknown
+PAK1 interactsWith GTP-RAC1
+PAK interactsWith Rac1-GTP
+PAK1 interactsWith GTP-RAC1
+PAK1 interactsWith GTP-RAC1
+H1 pp alpha1-integrin
+Nav1.4 pp CaM
+c-Fos pd Jagged1_promoter
+c-Jun pd Jagged1_promoter
+Htt pp TP53
+Pak1 pp SHARP
+MED21 pd p21_promoter
+MED1 pd p21_promoter
+MED1 pd pS2_promoter
+MED11 pd pS2_promoter
+MED21 pd pS2_promoter
+MED25 pd pS2_promoter
+MED19 pd pS2_promoter
+MED1 pd Cathepsin-D_promoter
+PAK1 pp Rac
+PAK1 pp Rac
+Rac1 pp Pak1
+Rac1 pp Pak1
+CREB pd Nurr1_promoter
+Glut4 pp Sortilin
+CCR2b pp FROUNT
+CD8-Beta pp CD3-Zeta
+CD8-Beta pp Lck
+RELA pp CREBBP
+CBP pp p65
+CREB1 pp CREBBP
+Mdm2 pp Mdm2
+Mdm2 pp Mdm2
+Hdm2 pp Hdm2
+MDM2 pp MDM2
+gankyrin pp S6
+gankyrin pp Mdm2
+proteasome-alpha2_subunit interactsWith Unknown
+Unknown interactsWith Mdm2
+Unknown interactsWith proteasome-beta6_subunit
+Mdm2 pp p53
+Mdm2 pp p53
+Hdm2 pp p53
+Mdm2 pp p53
+Mdm2 pp p53
+Mdm2 pp p53
+Mdm2 pp p53
+Mdm2 pp p53
+MDM2 pp p53
+ER pd XBP-1_enhancer
+ER pd CELSR1
+ER pd Chromosome_22
+ER pd SNAP29
+ER pd AP1B1
+ER pd C22orf19
+ER pd ASC1p100
+ER pd SFI1
+ER pd CSNK1E
+ER pd CYB5R3
+AIB-1 pd XBP-1_enhancer
+Pol_II pd XBP-1_enhancer
+FOXA1 pd XBP-1_enhancer
+FOXA1 pd DSCAM-1_enhancer
+FOXA1 pd NRIP-1_enhancer
+FOXA1 pd TFF-1_promoter
+Pol_II pd DSCAM-1_enhancer
+Pol_II pd SOD-1_enhancer
+Pol_II pd NRIP-1_enhancer
+Pol_II pd TFF-1_enhancer
+Pol_II pd TFF-1_promoter
+AIB-1 pd DSCAM-1_enhancer
+AIB-1 pd SOD-1_Enhancer
+AIB-1 pd NRIP-1_enhancer
+AIB-1 pd TFF-1_enhancer
+AIB-1 pd TFF-1_promoter
+ER pd DSCAM-1_enhancer
+ER pd NRIP-1_enhancer
+ER pd SOD-1_Enhancer
+ER pd TFF-1_enhancer
+ER pd TFF-1_promoter
+ER pd BAGE3
+ER pd NCAM2
+ER pd C21orf129
+ER pd SLC37A1
+ER pd LOC441967
+ER pd Chromosome_21
+Unknown interactsWith Roc1
+Unknown interactsWith Cul1
+NIPA interactsWith Unknown
+Fbw7-beta pp c-Jun
+Fbw7-alpha pp c-Jun
+Fbw7-gamma pp c-Jun
+Fbw7-alpha pp c-Myc
+Fbw7-beta pp c-Myc
+NIPA pp Cyclin_B1
+PKC-delta pp GSK3-beta
+cyclin_A pp p21
+p21 pp Cyclin_A
+CDKN1A pp CCNA2
+cyclin_A interactsWith unknown
+unknown interactsWith Cdk2
+unknown interactsWith Cdk1
+p53 pd 14-3-3-sigma_promoter
+p53 pd bax_promoter
+p53 pd PIG3_promoter
+p53 pd MSH6_promoter
+p53 pd MSH2_promoter
+p53 pp p53
+TP53 pp TP53
+TP53 pp TP53
+mp53 pp p53
+p53 pp p53
+p53 pp p53
+SCF_complex interactsWith Cyclin_B1
+RAF1 pp PPP2R2A
+RAF1 pp PHB
+RAF1 pp PPP2R2B
+RAF1 pp PPP2R2C
+NPM1 pp XPO1
+RNASEL pp GSPT1
+alpha-actinin-2 pp NR1A
+NIPA pp Skp1
+CREB pd CRE
+AP-1 interactsWith AP-1_consensus_sequence
+Bcl-xL pp TCTP
+ERAP1 pp ERAP2
+Cnx pp RNase
+MeCP2 pd ER-alpha_promoter
+Dnmt1 pd pS2_promoter
+MeCP2 pd pS2_promoter
+Dnmt1 pd ER-alpha_promoter
+Dnmt1 pd cycD1_promoter
+MeCP2 pd cycD1_promoter
+HDAC1 pd pS2_promoter
+HDAC3 pd pS2_promoter
+HDAC7 pd pS2_promoter
+MTA1 pd pS2_promoter
+2ACH_B pp SERPINA3
+RBP4 pp TTR
+RBP4 pp TTR
+RBP4 pp TTR
+1MDK_B pp TXN
+9API_C pp SERPINA1
+1CGJ_I pp 1CGJ_E
+1CGI_I pp 1CGI_E
+SNRPB2 pp SNRPA1
+CBL pp CBL
+CBL pp CBL
+Double-Stranded_Rna_Specific_Adenosine_Deaminase_(Adar1) pp Double-Stranded_Rna_Specific_Adenosine_Deaminase_(Adar1)
+Zap-70 pp CBL
+APP pp Bovine_Chymotrypsin
+APP pp Bovine_Chymotrypsin
+Ref-1_Peptide pp TXN
+PI3 pp ELA1
+DNM1 pp DNM1
+DNM1 pp DNM1
+Clip pp HLA-DRA
+HLA-DRB3 pp HLA-DRA
+Hla-A2 pp HLA-DRA
+Peptide_From_Collagen_Ii pp HLA-DRA
+FAP pp FAP
+FAP pp FAP
+TNNT2 pp TNNC1
+TNNT2 pp TNNC1
+TNNI3 pp TNNT2
+TNNI3 pp TNNT2
+NCF4 pp NCF2
+Enterotoxin_Type_C-3 pp HLA-DRA
+Enterotoxin_Type_C-3 pp HLA-DRA
+Enterotoxin_Type_C-3 pp HLA-DRA
+Enterotoxin_Type_C-3 pp HLA-DRA
+Enterotoxin_Type_C-3 pp HLA-DRA
+EP300 pp CbpP300-Interacting_Transactivator_2
+ATXN1 pp ATXN1
+ATXN1 pp ATXN1
+ATXN1 pp ATXN1
+1OBZ_P pp SDCBP
+1OBX_B pp SDCBP
+Syndecan-4 pp SDCBP
+Syndecan-4 pp SDCBP
+Liver_Carboxylesterase_I pp Liver_Carboxylesterase_I
+Liver_Carboxylesterase_I pp Liver_Carboxylesterase_I
+Liver_Carboxylesterase_I pp Liver_Carboxylesterase_I
+Liver_Carboxylesterase_I pp Liver_Carboxylesterase_I
+Liver_Carboxylesterase_I pp Liver_Carboxylesterase_I
+Liver_Carboxylesterase_I pp Liver_Carboxylesterase_I
+Liver_Carboxylesterase_I pp Liver_Carboxylesterase_I
+Liver_Carboxylesterase_I pp Liver_Carboxylesterase_I
+Liver_Carboxylesterase_I pp Liver_Carboxylesterase_I
+Liver_Carboxylesterase_I pp Liver_Carboxylesterase_I
+Liver_Carboxylesterase_I pp Liver_Carboxylesterase_I
+Liver_Carboxylesterase_I pp Liver_Carboxylesterase_I
+Liver_Carboxylesterase_I pp Liver_Carboxylesterase_I
+Liver_Carboxylesterase_I pp Liver_Carboxylesterase_I
+Liver_Carboxylesterase_I pp Liver_Carboxylesterase_I
+Liver_Carboxylesterase_I pp Liver_Carboxylesterase_I
+SDCBP pp SDCBP
+SDCBP pp SDCBP
+SDCBP pp SDCBP
+ERBB2 pp Herceptin_Fab_(Antibody)_-_Light_Chain
+9-Residue_Influenza_Virus_Hemagglutinin_Related_Peptide_Fvkqna(Maa)al pp HLA-DRA
+BF pp BF
+FDFT1 pp FDFT1
+FDFT1 pp FDFT1
+FDFT1 pp FDFT1
+PRSS3 pp SERPINA1
+PRSS3 pp SERPINA1
+Myelin_Basic_Protein pp HLA-DRA
+BIRC5 pp BIRC5
+survivin pp survivin
+BIRC5 pp BIRC5
+Alpha-1-Antitrypsin pp SERPINA1
+7API_B pp SERPINA1
+8API_B pp SERPINA1
+9API_B pp SERPINA1
+T-Cell_Receptor_Beta_Chain pp HLA-DRA
+NCF2 pp RAC1
+Apoptosis_Inhibitor_Survivin pp Apoptosis_Inhibitor_Survivin
+BCAT2 pp BCAT2
+BCAT2 pp BCAT2
+Hla-Dr2 pp HLA-DRA
+Hla-Dr2 pp HLA-DRA
+HLA-DRB1 pp HLA-DRA
+HLA-DRB1 pp HLA-DRA
+HLA-DRA pp HLA-DRB1
+NOVA2 pp NOVA2
+NOVA2 pp NOVA2
+NOVA2 pp NOVA2
+ELA1 pp Beta-Casomorphin-7
+ARHGDIB pp RAC2
+FCGR3A pp Fc_Fragment_Of_Human_Igg1
+FCGR3A pp Fc_Fragment_Of_Human_Igg1
+FCGR3A pp Ig_Gamma-1_Chain_C_Region
+FCGR3A pp Ig_Gamma-1_Chain_C_Region
+FCGR3A pp Ig_Gamma-1_Chain_C_Region
+FCGR3A pp Ig_Gamma-1_Chain_C_Region
+UBE2L3 pp CBL
+Alpha-1-Antitrypsin pp SERPINA1
+P1-Arg_Antitrypsin pp SERPINA1
+GALE pp GALE
+Phagocyte_Nadph_Oxidase_Subunit_P47phox pp Phagocyte_Nadph_Oxidase_Subunit_P67phox
+EP300 pp Hypoxia_Inducible_Factor-1_Alpha_Subunit
+CRP pp CRP
+CRP pp CRP
+CRP pp CRP
+CRP pp CRP
+CRP pp CRP
+CRP pp CRP
+CRP pp CRP
+CRP pp CRP
+CRP pp CRP
+Hemagglutinin_Ha1_Peptide_Chain pp HLA-DRA
+HLA-DRB1 pp HLA-DRA
+HLA-DRB1 pp HLA-DRA
+HLA-DRB1 pp HLA-DRA
+HLA-DRB1 pp HLA-DRA
+HLA-DRB1 pp HLA-DRA
+HLA-DRB1 pp HLA-DRA
+NUP98 pp NUP98
+NUP98 pp NUP98
+NUP98 pp NUP98
+NUP98 pp NUP98
+SOD2 pp SOD2
+SOD2 pp SOD2
+SOD2 pp SOD2
+SOD2 pp SOD2
+SOD2 pp SOD2
+SOD2 pp SOD2
+SOD2 pp SOD2
+SOD2 pp SOD2
+SOD2 pp SOD2
+SOD2 pp SOD2
+SOD2 pp SOD2
+SOD2 pp SOD2
+SOD2 pp SOD2
+SOD2 pp SOD2
+SOD2 pp SOD2
+ERBB3 pp ERBB3
+DSP pp DSP
+HLA-DRB1 pp HLA-DRA
+HLA-DRB1 pp HLA-DRA
+HLA-DRB1 pp HLA-DRA
+HLA-DRB1 pp HLA-DRA
+HLA-DRB1 pp HLA-DRA
+HLA-DRB1 pp HLA-DRA
+HLA-DRB1 pp HLA-DRA
+HLA-DRB1 pp HLA-DRA
+HLA-DRB1 pp HLA-DRA
+HLA-DRA pp HLA-DRB1
+HLA-DRA pp HLA-DRB1
+RBP4 pp TTR
+RBP4 pp TTR
+RBP4 pp TTR
+RBP4 pp TTR
+RBP4 pp TTR
+RBP4 pp TTR
+FECH pp FECH
+Beta-Casomorphin-7 pp ELA1
+ELA1 pp Beta-Casomorphin-7
+PAFAH1B1 pp PAFAH1B2
+PAFAH1B1 pp PAFAH1B2
+PAFAH1B1 pp PAFAH1B2
+PAFAH1B2 pp PAFAH1B2
+B2M pp Hla_Class_I_Histocompatibility_Antigen,_B-27_Alpha_Chain_Precursor
+B2M pp Hla_Class_I_Histocompatibility_Antigen_B-27_Alpha_Chain
+DLAT pp PDK3
+YWHAB pp YWHAB
+AKR7A2 pp AKR7A2
+Anti_Egfr_Antibody_Fv_Region pp Anti_Egfr_Antibody_Fv_Region
+Igg_Heavy_Chain pp Igg_Heavy_Chain
+Igg_Heavy_Chain pp Igg_Light_Chain
+Igg_Heavy_Chain pp Igg_Light_Chain
+Igg_Heavy_Chain pp Igg_Light_Chain
+Igg_Light_Chain pp Igg_Heavy_Chain
+DIAPH1 pp RHOC
+ACTN3 pp ACTN3
+T-Cell_Receptor_Beta_Chain_C_Region pp Hla_Class_I_Histocompatibility_Antigen
+T-Cell_Receptor_Alpha_Chain_V_Region pp Hla_Class_I_Histocompatibility_Antigen
+T-Cell_Receptor_Alpha_Chain_V_Region pp Hla_Class_I_Histocompatibility_Antigen
+PLAUR pp PLAUR
+PLAUR pp PLAUR
+PLAUR pp PLAUR
+PLAUR pp PLAUR
+PDE4D pp PDE4D
+PDE4D pp PDE4D
+PDE4D pp PDE4D
+PDE4D pp PDE4D
+PDE4D pp PDE4D
+PDE4D pp PDE4D
+PDE4D pp PDE4D
+PDE4D pp PDE4D
+PDE4D pp PDE4D
+PDE4D pp PDE4D
+PDE4D pp PDE4D
+PDE4D pp PDE4D
+PDE4D pp PDE4D
+PDE4D pp PDE4D
+PDE4D pp PDE4D
+PDE4D pp PDE4D
+PGAM1 pp PGAM1
+ZFYVE20 pp RAB24
+ZFYVE20 pp RAB14
+ZFYVE20 pp RAB5C
+Unknown interactsWith p120
+Unknown interactsWith SHC
+Unknown interactsWith C-CBL
+Unknown interactsWith Vav
+Grb2 interactsWith Unknown
+Unknown pp ZAP-70
+Unknown interactsWith SLP76
+Unknown interactsWith ADAP
+Unknown interactsWith LAT
+Unknown interactsWith Gads
+Unknown interactsWith SHP-2
+Unknown interactsWith PLCG1
+TSAd pp Src
+VEGFR-2 pp TSAd
+GABARAP pp Tubulin
+GABARAP pp GABA(A)-gamma-2S
+GABARAP pp GABA(A)-gamma-2L
+p63-gamma pd p21_promoter
+p63-alpha pd p21_promoter
+Tip60 pp CBP
+Tip60 pp p300
+p73-alpha pd PEDF
+p73-beta pd PEDF
+p63-gamma pd PEDF
+p63-alpha pd PEDF
+p73-beta pd p21_promoter
+p73-beta pd p21_promoter
+p73-alpha pd p21_promoter
+p73-alpha pd p21_promoter
+GSK-3-beta pp beta-catenin
+GSK3B pp CTNNB1
+GSK-3-beta pp Erk2
+GSK-3-beta pp GSK-3-beta
+GSK3B pp GSK3B
+GSK3B pp GSK3B
+GSK3B pp GSK3B
+GSK3B pp GSK3B
+GSK3B pp GSK3B
+GSK3B pp GSK3B
+GSK3B pp GSK3B
+SLC26A6 pp CAII
+IPR2 pp HOIL-1
+NFAT1 pd autotaxin_promoter
+H4 pd TrkA_promoter
+H3 pd TrkA_promoter
+D2i3 pp Par-4
+D2i3 pp CaM
+CALM1 pp FKBP8
+BCL2 pp BAD
+Bad pp Bcl-2
+CARMIL pp CP_beta2
+Shc3 pp c-Ret
+Foxo4 pd IGFBP-1_gene
+Myc pp PAK2
+p53 pd PTEN_promoter
+beta-Arr2 pp Akt1
+beta-Arr1 pp Akt1
+p66 pp cyt_c
+TACI pp BAFF
+SpRNAP-IV pd ALDH8A1
+BCL2 interactsWith CALM1-FKBP8
+Dicer pp TRBP
+CA150 pp DIAPH1
+KIAA0144 pp NEDD4-1
+WWOX pp p68
+NEDD4-1 pp p68
+CA150 pp p68
+FE65 pp p68
+KIAA0144 pp AIP4
+AIP4 pp p68
+Unknown interactsWith SMARCE1
+Unknown interactsWith p25
+Unknown interactsWith EWS
+AIP4 interactsWith Unknown
+Unknown interactsWith p25
+AIP4 interactsWith Unknown
+AIP4 interactsWith Unknown
+Unknown interactsWith p25
+Unknown interactsWith SMARCC2
+Unknown interactsWith SMARCC1
+Unknown interactsWith POLR2E
+Unknown interactsWith POLR2C
+Unknown interactsWith POLR2B
+Unknown interactsWith POLR2A
+Unknown interactsWith EWS
+Unknown interactsWith C19orf2
+Unknown interactsWith ARID1A
+AIP4 interactsWith Unknown
+AIP4 interactsWith Unknown
+AIP4 pp POLR2A
+Unknown interactsWith p25
+Unknown interactsWith FMNL1
+Unknown interactsWith DDX46
+Unknown interactsWith NSEP1
+Unknown interactsWith CRKRS
+FBP11 interactsWith Unknown
+Unknown interactsWith WIRE
+Unknown interactsWith WASF2
+Unknown interactsWith WAS
+Unknown interactsWith FMNL1
+Unknown interactsWith EVL
+Unknown interactsWith DIAPH2
+Unknown interactsWith DIAPH1
+Unknown interactsWith CYFIP2
+Unknown interactsWith CYFIP1
+Unknown interactsWith DHX15
+Unknown interactsWith HNRPF
+Unknown interactsWith NONO
+Unknown interactsWith EVL
+Unknown interactsWith DIAPH1
+Unknown interactsWith RPL4
+Unknown interactsWith U2AF2
+Unknown interactsWith SFPQ
+Unknown interactsWith SF3B4
+Unknown interactsWith SF3B3
+Unknown interactsWith SF3B2
+Unknown interactsWith SF3B1
+Unknown interactsWith SF3A3
+Unknown interactsWith SF3A2
+Unknown interactsWith SF3A1
+Unknown interactsWith SF1
+Unknown interactsWith ABI1
+Unknown interactsWith BRD4
+Unknown interactsWith U2AF2
+Unknown interactsWith UBAP2
+Unknown interactsWith KIAA0144
+Unknown interactsWith FLJ21908
+Unknown interactsWith SPG20
+Unknown interactsWith ITCH
+Unknown interactsWith SF1
+Unknown interactsWith PABPC1
+Unknown interactsWith MGC9315
+Unknown interactsWith HNRPUL1
+Unknown interactsWith HNRPL
+Unknown interactsWith FLJ13150
+Unknown interactsWith DAZAP1
+Unknown interactsWith p68
+Unknown interactsWith WBP2
+CA150 interactsWith Unknown
+Unknown interactsWith p25
+Unknown interactsWith SFPQ
+Unknown interactsWith SF3B3
+Unknown interactsWith SF3B2
+Unknown interactsWith SF3B1
+Unknown interactsWith SF3A3
+Unknown interactsWith SF3A2
+Unknown interactsWith SF3A1
+Unknown interactsWith SF1
+Unknown interactsWith PSPC1
+Unknown interactsWith NONO
+Unknown interactsWith HNRPU
+Unknown interactsWith HNRPK
+Unknown interactsWith p68
+Unknown interactsWith p25
+Unknown interactsWith PPARBP
+Unknown interactsWith PRPF8
+Unknown interactsWith HNRPUL1
+Unknown interactsWith HNRPU
+Unknown interactsWith HNRPL
+Unknown interactsWith HNRPK
+Unknown interactsWith FLJ13150
+Unknown interactsWith DHX30
+Unknown interactsWith DDX3X
+Unknown interactsWith p68
+Unknown interactsWith p25
+Unknown interactsWith CPSF1
+Unknown interactsWith THRAP3
+Unknown interactsWith SMARCF1
+Unknown interactsWith SFRS7
+Unknown interactsWith EPRS
+Unknown interactsWith RPS3A
+Unknown interactsWith ETV6
+Unknown interactsWith CRKRS
+Unknown interactsWith CCNK
+Unknown interactsWith BCLAF1
+PIN1 interactsWith Unknown
+Unknown interactsWith CAD
+Unknown interactsWith WBP2
+Unknown interactsWith FLJ21908
+Unknown interactsWith GRINL1A
+Unknown interactsWith NEDD4-1
+Unknown interactsWith PDZ-GEF2
+Unknown interactsWith AMOTL1
+Unknown interactsWith DIAPH1
+Unknown interactsWith SMARCC1
+Unknown interactsWith RUVBL1
+Unknown interactsWith RPC155
+Unknown interactsWith GAPD
+Unknown interactsWith ABI1
+Unknown interactsWith WAS
+Unknown interactsWith FMNL1
+Unknown interactsWith CYFIP2
+Unknown interactsWith CYFIP1
+Unknown interactsWith WASF2
+Unknown interactsWith DIAPH1
+GAS7 interactsWith Unknown
+Unknown interactsWith MGC20255
+Unknown interactsWith C14orf170
+Unknown interactsWith CHERP
+Unknown interactsWith WASPIP
+Unknown interactsWith SF1
+Unknown interactsWith HNRPU
+Unknown interactsWith SFPQ
+Unknown interactsWith POLR2E
+Unknown interactsWith POLR2C
+Unknown interactsWith POLR2B
+Unknown interactsWith POLR2A
+Unknown interactsWith NSEP1
+Unknown interactsWith C19orf2
+NEDD4-1 interactsWith Unknown
+Unknown interactsWith HEM1
+Unknown interactsWith RPLP0
+Unknown interactsWith APBB1IP
+Unknown interactsWith NCKAP1
+Unknown interactsWith KHDRBS1
+Unknown interactsWith SF3A1
+Unknown interactsWith WASL
+Unknown interactsWith WBP2
+Unknown interactsWith CPSF1
+Unknown interactsWith TCERG1
+Unknown interactsWith SMARCC1
+Unknown interactsWith POLR2B
+Unknown interactsWith POLR2A
+WWOX interactsWith Unknown
+Unknown interactsWith PKM2
+Unknown interactsWith HADHA
+Unknown interactsWith TFG
+Unknown interactsWith TBC1D4
+Unknown interactsWith M11S1
+Unknown interactsWith LLID133619
+Unknown interactsWith C13orf8
+Unknown interactsWith CPSF2
+Unknown interactsWith CPSF3
+Unknown interactsWith p25
+Unknown interactsWith LLID55339
+Unknown interactsWith FLJ23260
+Unknown interactsWith SPK
+Unknown interactsWith SFPQ
+Unknown interactsWith SF3B3
+Unknown interactsWith SF3B1
+Unknown interactsWith SF3A1
+Unknown interactsWith PABPC1
+Unknown interactsWith KIAA0460
+Unknown interactsWith HNRPK
+Unknown interactsWith FLJ12529
+Unknown interactsWith FIP1L1
+Unknown interactsWith p68
+Unknown interactsWith REPS1
+Unknown interactsWith AP2A1
+Unknown interactsWith VCY2IP1
+Unknown interactsWith KIAA0031
+Unknown interactsWith HNRPU
+Unknown interactsWith HNRPK
+Unknown interactsWith HNRPH1
+Unknown interactsWith HDH_VIII
+Unknown interactsWith G3BP2
+Unknown interactsWith FLJ21850
+Unknown interactsWith DKFZP434I116
+Unknown interactsWith DHX15
+Unknown interactsWith DDX5
+Unknown interactsWith DDX3X
+Unknown interactsWith DDX17
+Unknown interactsWith TLE3
+Unknown interactsWith NONO
+Unknown interactsWith PABPC1
+Unknown interactsWith PRPF8
+Unknown interactsWith G22P1
+Unknown interactsWith CDC2L2
+Unknown interactsWith CDC2L1
+Unknown interactsWith WRNIP1
+Unknown interactsWith DDB1
+Unknown interactsWith RPL4
+Unknown interactsWith U5-200KD
+Unknown interactsWith U2AF2
+Unknown interactsWith SRRM2
+Unknown interactsWith SRRM1
+Unknown interactsWith SFRS11
+Unknown interactsWith SFPQ
+Unknown interactsWith RNPS1
+Unknown interactsWith THRAP3
+Unknown interactsWith WASF2
+Unknown interactsWith SF1
+Unknown interactsWith SMARCA3
+Unknown interactsWith HTATSF1
+Unknown interactsWith FUS
+Unknown interactsWith EWS
+FBP21 interactsWith Unknown
+Unknown interactsWith CCT7
+Unknown interactsWith CCT4
+Unknown interactsWith CCT2
+Unknown interactsWith GAPD
+Unknown interactsWith HEM1
+Unknown interactsWith C14orf170
+Unknown interactsWith APBB1IP
+Unknown interactsWith WASPIP
+Unknown interactsWith TCERG1
+Unknown interactsWith ZNF207
+Unknown interactsWith p68
+Unknown interactsWith SART1
+Unknown interactsWith PSPC1
+Unknown interactsWith PRPF4
+Unknown interactsWith PRP3
+Unknown interactsWith PABPC1
+Unknown interactsWith NONO
+Unknown interactsWith MGC9315
+Unknown interactsWith KHDRBS1
+Unknown interactsWith HNRPU
+Unknown interactsWith HNRPK
+Unknown interactsWith DHX15
+Unknown interactsWith DDX3X
+Unknown interactsWith DDX23
+Unknown interactsWith WASL
+Unknown interactsWith WASF2
+Unknown interactsWith WAS
+Unknown interactsWith NONO
+Unknown interactsWith HNRPU
+Unknown interactsWith HNRPK
+Unknown interactsWith HNRPF
+Unknown interactsWith DHX9
+Unknown interactsWith p68
+FBP11 interactsWith Unknown
+Unknown interactsWith HEM1
+Unknown interactsWith ATAD3A
+Unknown interactsWith WASPIP
+Unknown interactsWith WASL
+Unknown interactsWith WAS
+Unknown interactsWith VASP
+Unknown interactsWith SF1
+Unknown interactsWith SF3A1
+Unknown interactsWith SF3A2
+Unknown interactsWith SSH3BP1
+Unknown interactsWith FMNL1
+Unknown interactsWith EVL
+Unknown interactsWith DIAPH1
+Unknown interactsWith CYFIP2
+Unknown interactsWith CYFIP1
+Unknown interactsWith KIAA1470
+Unknown interactsWith G22P1
+Unknown interactsWith RPLP0
+Unknown interactsWith U2AF2
+Unknown interactsWith SFPQ
+Unknown interactsWith SF3B3
+Unknown interactsWith SF3B1
+Unknown interactsWith SSH3BP1
+Unknown interactsWith WAS
+Unknown interactsWith SF3B1
+Unknown interactsWith SF3A3
+Unknown interactsWith SF3A2
+Unknown interactsWith SF3A1
+Unknown interactsWith SF1
+Unknown interactsWith PTBP1
+Unknown interactsWith PABPC1
+Unknown interactsWith NONO
+Unknown interactsWith MGC9315
+Unknown interactsWith MGC14439
+Unknown interactsWith KHSRP
+Unknown interactsWith KHDRBS1
+Unknown interactsWith HNRPK
+Unknown interactsWith SF3B2
+Unknown interactsWith SF3B3
+Unknown interactsWith SF3B4
+Unknown interactsWith VASP
+Unknown interactsWith SSH3BP1
+Unknown interactsWith FLJ23260
+Unknown interactsWith EVL
+Unknown interactsWith ENAH
+Unknown interactsWith DIAPH2
+Unknown interactsWith DIAPH1
+Unknown interactsWith CYFIP2
+Unknown interactsWith CYFIP1
+Unknown interactsWith RPL4
+Unknown interactsWith WBP11
+Unknown interactsWith U2AF2
+Unknown interactsWith SFPQ
+Unknown interactsWith HNRPH1
+Unknown interactsWith DHX9
+Unknown interactsWith DHX15
+Unknown interactsWith CTF8
+Unknown interactsWith BUB3
+Unknown interactsWith WBP11
+Unknown interactsWith U5-116KD
+Unknown interactsWith SNRPA
+Unknown interactsWith SNRP70
+Unknown interactsWith SFRS15
+Unknown interactsWith SFPQ
+Unknown interactsWith SF3B4
+Unknown interactsWith SF3B3
+Unknown interactsWith SF3B1
+Unknown interactsWith SF3A3
+Unknown interactsWith SF3A2
+Unknown interactsWith G22P1
+Unknown interactsWith DIAPH1
+Unknown interactsWith DNM2
+Unknown interactsWith DDX46
+Unknown interactsWith DDX3X
+Unknown interactsWith DDX17
+Unknown interactsWith p68
+Unknown interactsWith THRAP3
+Unknown interactsWith PQBP1
+Unknown interactsWith NSEP1
+Unknown interactsWith HTATSF1
+FE65 interactsWith Unknown
+Unknown interactsWith M11S1
+Unknown interactsWith CHERP
+Unknown interactsWith WASPIP
+Unknown interactsWith WAS
+Unknown interactsWith SF3A1
+Dicer-TRBP_complex interactsWith Ago2
+Unknown interactsWith MED4
+Unknown interactsWith SIP25
+Unknown interactsWith SIP24
+Unknown interactsWith SIP22
+Unknown interactsWith SIP21
+Unknown interactsWith SIP20
+Unknown interactsWith SIP19
+Unknown interactsWith SIP18
+Unknown interactsWith SIP17
+Unknown interactsWith SIP16
+Unknown interactsWith SIP15
+Unknown interactsWith SIP14
+Unknown interactsWith SIP13
+Unknown interactsWith SIP12
+Unknown interactsWith SIP26
+MED1 interactsWith Unknown
+Unknown interactsWith MED13L
+Unknown interactsWith MED19
+Unknown interactsWith MED27
+Unknown interactsWith CDK8
+Unknown interactsWith MED26
+Unknown interactsWith MED17
+Unknown interactsWith MED16
+Unknown interactsWith MED25
+Unknown interactsWith MED15
+Unknown interactsWith MED24
+Unknown interactsWith MED23
+Unknown interactsWith MED14
+Unknown interactsWith MED12
+Unknown interactsWith MED13
+Unknown interactsWith SIP11
+Unknown interactsWith SIP10
+Unknown interactsWith SIP9
+Unknown interactsWith SYNJ2
+Unknown interactsWith RAE1
+Unknown interactsWith PSCD2
+Unknown interactsWith KNS2
+Unknown interactsWith KLC2
+Unknown interactsWith KIF5b
+Unknown interactsWith TRIM32
+Unknown interactsWith PAM
+Unknown interactsWith NP220
+Unknown interactsWith LISCH7
+Unknown interactsWith HDAC7
+Unknown interactsWith HDAC4
+Unknown interactsWith USP8
+Unknown interactsWith FUSIP1
+Unknown interactsWith HNRPU
+Unknown interactsWith SRRM2
+Unknown interactsWith SIP8
+Unknown interactsWith SIP7
+Unknown interactsWith SIP6
+Unknown interactsWith SIP5
+Unknown interactsWith SIP4
+Unknown interactsWith SIP3
+Unknown interactsWith SIP2
+Unknown interactsWith SAV1
+Unknown interactsWith LMO7
+Unknown interactsWith KLHDC2
+Unknown interactsWith HAN11
+Unknown interactsWith ANKS1
+Unknown interactsWith ISCU
+Unknown interactsWith NEDD4L
+Unknown interactsWith RPB5
+Unknown interactsWith RPB4
+Unknown interactsWith RPB3
+Unknown interactsWith RPB2
+Unknown interactsWith RPB1
+Unknown interactsWith MED11
+Unknown interactsWith MED31
+Unknown interactsWith MED21
+Unknown interactsWith MED22
+Unknown interactsWith MED30
+Unknown interactsWith MED18
+Unknown interactsWith MED20
+Unknown interactsWith Cyclin_C
+Unknown interactsWith RPB6
+Unknown interactsWith RPB7
+Unknown interactsWith RPB8
+JNK1 interactsWith unknown
+JNK2 pp RACK1
+JNK1 pp RACK1
+unknown interactsWith PKCbeta2
+JNK2 pp c-Jun
+JNK2 pp c-Jun
+Unknown interactsWith RPB11
+Unknown interactsWith RPB10-beta
+Unknown interactsWith RPB10-alpha
+Unknown interactsWith RPB9
+Unknown interactsWith MED8
+Unknown interactsWith MED7
+Unknown interactsWith MED6
+Unknown interactsWith MED10
+Unknown interactsWith MED31
+Unknown interactsWith MED21
+Unknown interactsWith MED22
+Unknown interactsWith MED9
+Unknown interactsWith MED28
+Unknown interactsWith MED30
+Unknown interactsWith MED29
+Unknown interactsWith MED18
+Unknown interactsWith MED20
+Unknown interactsWith Cyclin_C
+Unknown interactsWith MED8
+Unknown interactsWith MED7
+Unknown interactsWith MED11
+MED10 interactsWith Unknown
+Unknown interactsWith MED13
+Unknown interactsWith MED4
+Unknown interactsWith MED19
+Unknown interactsWith MED27
+Unknown interactsWith CDK8
+Unknown interactsWith MED26
+Unknown interactsWith MED17
+Unknown interactsWith MED16
+Unknown interactsWith MED15
+Unknown interactsWith MED24
+Unknown interactsWith MED23
+Unknown interactsWith MED14
+Unknown interactsWith MED1
+Unknown interactsWith MED12
+Unknown interactsWith MED6
+Unknown interactsWith ITCH
+Unknown interactsWith ABLIM
+Unknown interactsWith YWHAG
+Unknown interactsWith 14-3-3-sigma
+14-3-3-sigma interactsWith Unknown
+Unknown interactsWith ARGBP2
+Unknown interactsWith MAPKAP1
+Unknown interactsWith MAP3K2
+Unknown interactsWith IRS2
+Unknown interactsWith IRS1
+Unknown interactsWith DYRK1A
+Unknown interactsWith DTX2
+Unknown interactsWith CSNK2A1
+Unknown interactsWith c-RAF
+Unknown interactsWith B-RAF
+Unknown interactsWith A-RAF1
+Unknown interactsWith APC
+Unknown interactsWith TJP2
+Unknown interactsWith Spir-1
+Unknown interactsWith OSBPL3
+Unknown interactsWith PIK3C2B
+Unknown interactsWith PIK4CB
+Unknown interactsWith ZAK
+Unknown interactsWith WEE1
+Unknown interactsWith PTOV1
+Unknown interactsWith MARK3
+Unknown interactsWith MKLP1
+Unknown interactsWith TNK1
+Unknown interactsWith ST5
+Unknown interactsWith SHCBP1
+Unknown interactsWith SH3BP4
+Unknown interactsWith SH2D3A
+Unknown interactsWith SASH1
+Unknown interactsWith PTPN2
+Unknown interactsWith PPP1R3D
+Unknown interactsWith SIPA1L3
+Unknown interactsWith SIPA1L1
+Unknown interactsWith SHRML
+Unknown interactsWith LAD1
+Unknown interactsWith GRB7
+Unknown interactsWith GAN
+Unknown interactsWith CTEN
+Unknown interactsWith CGN
+Unknown interactsWith BCAR1
+Unknown interactsWith BAIAP1
+Unknown interactsWith ARHGEF16
+Unknown interactsWith ARHGEF17
+Unknown interactsWith ARHGEF5
+Unknown interactsWith ARHGAP21
+Unknown interactsWith ARHGAP11A
+Unknown interactsWith ARHE
+Unknown interactsWith MARK1
+Unknown interactsWith MARK2
+Unknown interactsWith M-RIP
+Unknown interactsWith SCEL
+Unknown interactsWith RICS
+Unknown interactsWith RHPN2
+Unknown interactsWith RALGPS2
+Unknown interactsWith RACGAP1
+Unknown interactsWith PTPN3
+Unknown interactsWith PPFIBP2
+Unknown interactsWith PPFIBP1
+Unknown interactsWith PKP3
+Unknown interactsWith PKP2
+Unknown interactsWith PAR3
+Unknown interactsWith PAR3L
+Unknown interactsWith PAK4
+Unknown interactsWith APXL2
+JNK1 pp c-Jun
+JNK1 pp c-Jun
+c-Jun pp JNK-1
+PTB interactsWith ESS1
+hnRNP-L interactsWith ESS1
+hnRNP-E2 interactsWith ESS1
+14-3-3-sigma pp AJUBA
+14-3-3-sigma pp MIG-6
+MED1/TRAP220-containing_complex interactsWith RNA_Polymerase_II
+CKI-alpha pp FADD
+TIP5 pp SNF2h
+FGF-BP pp FGF-10
+FGF-BP pp FGF-2
+FGF-BP pp FGF-7
+FGF-BP pp FGF-22
+H3 pd MLH1_promoter
+H3 pd p-TNFSF10
+H3 pd CDH1_promoter
+H3 pd GAPDH_promoter
+CFTR pp CFTR
+CFTR pp CFTR
+CFTR pp CFTR
+Smad7 pp Smurf2
+SMAD7 pp SMURF2
+SMURF2 pp Smad7
+Smurf2 pp UbcH7
+Unknown interactsWith T-beta-RI
+Unknown interactsWith T-beta-RII
+Smad7 pp UbcH7
+Smurf2 pp Smurf2
+SMURF2 pp SMURF2
+MR pp SRC2
+p53 pd p21_promoter
+p53 pd p21_promoter
+p53 pd p21
+p53 pd p21_promoter
+p53 pp E2F1
+WARTS pp Omi
+APC pp NE-dlg
+Merlin pp RalGDS
+RalBP1 pp RalA
+RalA pp RLIP76
+RalA pp RalBP1
+Runx1 pd c-fms_gene
+Trask pp N-cadherin
+Trask pp MT-SP1
+Trask pp syndecans-4
+Trask pp P-cadherin
+Trask pp Src
+Trask pp yes
+Trask pp syndecans-1
+mu-calpain pp Bax
+mu-calpain pp Bfl-1
+HIF-1alpha pp VHL
+HIF-1alpha pp pVHL
+HPH-2 pp HIF-1alpha
+Notch pp Nct
+53BP1 interactsWith Unknown
+53BP1 pp RPA2
+Unknown interactsWith RPA1
+Unknown interactsWith Ku80
+Unknown interactsWith Ku70
+APP pp Nct
+PS1 pp Nct
+PS1 pp Nct
+Brd4 interactsWith Unknown
+Brd4 pp Cyclin_T1
+Nav1.7 pp CaM
+Fli1 pd Id2_promoter
+Human_Sigma_Alcohol_Dehydrogenase pp Human_Sigma_Alcohol_Dehydrogenase
+Pr3 pp Pr3
+Pr3 pp Pr3
+Pr3 pp Pr3
+Pr3 pp Pr3
+Nerve_Growth_Factor pp Nerve_Growth_Factor
+Alcohol_Dehydrogenase_Class_Iv_Sigma_Chain pp Alcohol_Dehydrogenase_Class_Iv_Sigma_Chain
+NTRK1 pp Nerve_Growth_Factor
+NTRK1 pp Nerve_Growth_Factor
+NTRK1 pp Nerve_Growth_Factor
+NTRK1 pp Nerve_Growth_Factor
+ALDH2 pp ALDH2
+ALDH2 pp ALDH2
+ALDH2 pp ALDH2
+ALDH2 pp ALDH2
+ALDH2 pp ALDH2
+Receptor_Protein-Tyrosine_Kinase_Erbb-2 pp Growth_Factor_Receptor-Bound_Protein_7
+GART pp GART
+GART pp GART
+GART pp GART
+Fibrinogen_Gamma_Chain pp FGA
+Fibrinogen_Gamma_Chain pp FGA
+Fibrinogen_Gamma_Chain pp FGA
+Fibrinogen_Beta_Chain pp FGA
+Fibrinogen_Beta_Chain pp FGA
+Fibrinogen_Beta_Chain pp FGA
+HMOX1 pp HMOX1
+HMOX1 pp HMOX1
+HMOX1 pp HMOX1
+HMOX1 pp HMOX1
+HMOX1 pp HMOX1
+MAX pp Myc_Proto-Oncogene_Protein
+MAX pp Myc_Proto-Oncogene_Protein
+MAX pp Myc_Proto-Oncogene_Protein
+Myc_Proto-Oncogene_Protein pp MAX
+Fibrin_Gamma_Chain pp Fibrin_Gamma_Chain
+Gamma_Fibrinogen pp Gamma_Fibrinogen
+Fibrinogen pp Fibrinogen
+Fibrin pp Fibrin
+Fibrinogen pp Fibrinogen
+Fibrinogen pp Fibrinogen
+Fibrin_Gamma_Chain pp FGA
+Fibrinogen pp FGA
+Fibrinogen pp FGA
+Fibrin pp FGA
+Fibrinogen pp FGA
+Fibrinogen pp FGA
+Fibrinogen pp FGA
+Fibrinogen_Gamma_Chain pp FGA
+Fibrinogen_Gamma_Chain pp FGA
+Fibrin_Gamma_Chain pp Fibrin_Beta_Chain
+Fibrinogen pp Fibrinogen
+Fibrinogen pp Fibrinogen
+Fibrin pp Fibrin
+Fibrin pp Fibrin
+Fibrinogen pp Fibrinogen
+Fibrinogen pp Fibrinogen
+Fibrinogen pp Fibrinogen
+Fibrinogen pp Fibrinogen
+Fibrinogen pp Fibrinogen
+Fibrinogen_Gamma_Chain pp Fibrinogen_Beta_Chain
+Fibrin_Gamma_Chain pp Fibrin_Beta_Chain
+Fibrinogen_Gamma_Chain pp Fibrinogen_Beta_Chain
+Fibrinogen_Gamma_Chain pp Fibrinogen_Beta_Chain
+Fibrinogen_Gamma_Chain pp Fibrinogen_Beta_Chain
+Fibrinogen_Gamma_Chain pp Fibrinogen_Beta_Chain
+Fibrin_Beta_Chain pp FGA
+Fibrinogen pp FGA
+Fibrinogen pp FGA
+Fibrin pp FGA
+Fibrinogen pp FGA
+Fibrinogen pp FGA
+Fibrinogen pp FGA
+Fibrinogen_Beta_Chain pp FGA
+Fibrinogen_Beta_Chain pp FGA
+Fibrinogen_Beta_Chain pp FGA
+Fibrin_Beta_Chain pp FGA
+Alcohol_Dehydrogenase_Class_Iii_Chi_Chain pp Alcohol_Dehydrogenase_Class_Iii_Chi_Chain
+Gamma1-Adaptin pp Gamma1-Adaptin
+Proto-Oncogene_Protein_C-Fos pp Nuclear_Factor_Of_Activated_T-Cells,_Cytoplasmic_2
+Oxidised_Low_Density_Lipoprotein_(Lectin-Like)_Receptor_1 pp Oxidised_Low_Density_Lipoprotein_(Lectin-Like)_Receptor_1
+Aldo-Keto_Reductase_Family_1_Member_C2 pp Aldo-Keto_Reductase_Family_1_Member_C2
+Gem-Associated_Protein_7 pp Gem-Associated_Protein_6
+Ran-Binding_Protein_2 pp Ubiquitin-Conjugating_Enzyme_E2_I
+Ran-Binding_Protein_2 pp Ubiquitin-Like_Protein_Smt3c
+Hemoglobin_Alpha_Chain pp Alpha-Hemoglobin_Stabilizing_Protein
+Ribonuclease_Inhibitor pp Ribonuclease_Inhibitor
+RNH pp RNH
+Ran_Gtpase-Activating_Protein_1 pp Ubiquitin-Conjugating_Enzyme_E2_I
+Ubiquitin-Like_Protein_Smt3c pp Ubiquitin-Conjugating_Enzyme_E2_I
+Heterogeneous_Nuclear_Ribonucleoprotein_C_Protein pp Heterogeneous_Nuclear_Ribonucleoprotein_C_Protein
+Heterogeneous_Nuclear_Ribonucleoprotein_C_Protein pp Heterogeneous_Nuclear_Ribonucleoprotein_C_Protein
+Heterogeneous_Nuclear_Ribonucleoprotein_C_Protein pp Heterogeneous_Nuclear_Ribonucleoprotein_C_Protein
+Heterogeneous_Nuclear_Ribonucleoprotein_C_Protein pp Heterogeneous_Nuclear_Ribonucleoprotein_C_Protein
+Thioredoxin pp Thioredoxin
+Transthyretin pp Transthyretin
+17-Mer_Peptide_P1-Xpc_From_Xeroderma_Pigmentosum,_Complementation_Group_C pp Centrin_2
+Transcription_Factor_Ap-1 pp Proto-Oncogene_Protein_C-Fos
+Transcription_Factor_Ap-1 pp Nuclear_Factor_Of_Activated_T-Cells,_Cytoplasmic_2
+Eukaryotic_Translation_Initiation_Factor_4e_Binding_Protein_1 pp Eukaryotic_Translation_Initiation_Factor_4e
+Insulin_Receptor_Substrate_P53 pp Insulin_Receptor_Substrate_P53
+Adp-Ribosylation_Factor_Binding_Protein_Gga3 pp Adp-Ribosylation_Factor_Binding_Protein_Gga3
+Adp-Ribosylation_Factor_Binding_Protein_Gga3 pp Adp-Ribosylation_Factor_Binding_Protein_Gga3
+Adp-Ribosylation_Factor_Binding_Protein_Gga3 pp Adp-Ribosylation_Factor_Binding_Protein_Gga3
+Ubiquitin-Like_Protein_Smt3c pp GT_MISMATCH-Specific_Thymine_Dna_Glycosylase
+Tissue_Factor pp Blood_Coagulation_Factor_Viia
+Factor_Viia_Heavy_Chain pp Tissue_Factor
+Blood_Coagulation_Factor_Viia pp Blood_Coagulation_Factor_Viia
+Thrombin_Light pp Thrombin_Heavy
+Syntenin_1 pp Syntenin_1
+Acyl-Coa_Dehydrogenase,_Medium-Chain_Specific,_Mitochondrial_Precursor pp Acyl-Coa_Dehydrogenase,_Medium-Chain_Specific,_Mitochondrial_Precursor
+ACADM pp ACADM
+ACADM pp ACADM
+ACADM pp ACADM
+ACADM pp ACADM
+ACADM pp ACADM
+ACADM pp ACADM
+ACADM pp ACADM
+ACADM pp ACADM
+ACADM pp ACADM
+ACADM pp ACADM
+Acyl-Coa_Dehydrogenase,_Medium-Chain_Specific,_Mitochondrial_Precursor pp Acyl-Coa_Dehydrogenase,_Medium-Chain_Specific,_Mitochondrial_Precursor
+Acyl-Coa_Dehydrogenase,_Medium-Chain_Specific,_Mitochondrial_Precursor pp Acyl-Coa_Dehydrogenase,_Medium-Chain_Specific,_Mitochondrial_Precursor
+Acyl-Coa_Dehydrogenase,_Medium-Chain_Specific,_Mitochondrial_Precursor pp Acyl-Coa_Dehydrogenase,_Medium-Chain_Specific,_Mitochondrial_Precursor
+Electron_Transfer_Flavoprotein_Beta-Subunit pp Acyl-Coa_Dehydrogenase,_Medium-Chain_Specific,_Mitochondrial_Precursor
+Electron_Transfer_Flavoprotein_Beta-Subunit pp Electron_Transfer_Flavoprotein_Alpha-Subunit,_Mitochondrial_Precursor
+Electron_Transfer_Flavoprotein_Beta-Subunit pp Electron_Transfer_Flavoprotein_Alpha-Subunit,_Mitochondrial_Precursor
+Electron_Transfer_Flavoprotein_Alpha-Subunit,_Mitochondrial_Precursor pp Acyl-Coa_Dehydrogenase,_Medium-Chain_Specific,_Mitochondrial_Precursor
+Electron_Transfer_Flavoprotein_Alpha-Subunit,_Mitochondrial_Precursor pp Acyl-Coa_Dehydrogenase,_Medium-Chain_Specific,_Mitochondrial_Precursor
+14-3-3_Protein_Tau pp 14-3-3_Protein_Tau
+Coagulation_Factor_X_Synonym:_Factor_Xa,_Stuart_Factor pp Coagulation_Factor_X_Synonym:_Factor_Xa,_Stuart_Factor
+Tumor_Necrosis_Factor_Receptor_Superfamily_Member_10b pp Fab-Ysd1_Light_Chain
+Tumor_Necrosis_Factor_Receptor_Superfamily_Member_10b pp Fab-Ysd1_Heavy_Chain
+Fab-Ysd1_Heavy_Chain pp Fab-Ysd1_Light_Chain
+Aldehyde_Dehydrogenase pp Aldehyde_Dehydrogenase
+Aldehyde_Dehydrogenase pp Aldehyde_Dehydrogenase
+Aldehyde_Dehydrogenase pp Aldehyde_Dehydrogenase
+Nadp-Dependent_Leukotriene_B4_12-_Hydroxydehydrogenase pp Nadp-Dependent_Leukotriene_B4_12-_Hydroxydehydrogenase
+Nucleoside_Diphosphate_Kinase_3 pp Nucleoside_Diphosphate_Kinase_3
+Nucleoside_Diphosphate_Kinase_3 pp Nucleoside_Diphosphate_Kinase_3
+Nucleoside_Diphosphate_Kinase_3 pp Nucleoside_Diphosphate_Kinase_3
+Dihydrolipoyl_Dehydrogenase pp Dihydrolipoyl_Dehydrogenase
+Dihydrolipoyl_Dehydrogenase pp Dihydrolipoyl_Dehydrogenase
+Dihydrolipoyl_Dehydrogenase pp Dihydrolipoyl_Dehydrogenase
+Dihydrolipoyl_Dehydrogenase pp Dihydrolipoyl_Dehydrogenase
+Dihydrolipoyl_Dehydrogenase pp Dihydrolipoyl_Dehydrogenase
+Dihydrolipoyl_Dehydrogenase pp Dihydrolipoyl_Dehydrogenase
+Dihydrolipoyl_Dehydrogenase pp Dihydrolipoyl_Dehydrogenase
+Dihydrolipoyl_Dehydrogenase pp Dihydrolipoyl_Dehydrogenase
+Histone_H3.1 pp Histone_H3.1
+Histone_H2b_K pp Histone_H2a.A
+Histone_H2b_K pp Histone_H2a.A
+Histone_H2a.A pp Histone_H3.1
+Histone_H2a.A pp Histone_H3.1
+Histone_H3.1 pp Histone_H2a.A
+Histone_H2a.A pp Histone_H2a.A
+Histone_H4 pp Histone_H2b_K
+Histone_H2b_K pp Histone_H4
+Histone_H2b_K pp Histone_H4
+Histone_H4 pp Histone_H2a.A
+Histone_H2a.A pp Histone_H4
+Histone_H4 pp Histone_H3.1
+Histone_H4 pp Histone_H3.1
+Unknown interactsWith FANCF
+Unknown interactsWith FANCL
+Unknown interactsWith FANCG
+Unknown interactsWith FANCE
+Unknown interactsWith FANCC
+Unknown interactsWith FANCM
+Unknown interactsWith FANCB
+FANCA interactsWith Unknown
+PML pp SUMO-3
+Orc1 pd GM-CSF
+Orc2 pd GM-CSF
+Orc4 pd GM-CSF
+Cdc6 pd GM-CSF
+Mcm5 pd GM-CSF
+Orc1 pd Lamin_B2
+Orc2 pd Lamin_B2
+Orc2 pd Lamin_B2_origin
+Orc4 pd Lamin_B2
+Cdc6 pd Lamin_B2
+Mcm5 pd Lamin_B2
+RENT1 pp Upf2
+Upf1 pp Upf2
+p53 pd p21_promoter
+TP53 pd CDKN1A_promoter
+p53 pd p21_promoter
+p53 pd p21_promoter
+p53 pd p21_promoter
+p53 pd GAPDH_promoter
+TP53 pd MDM2-promoter
+p53 pd mdm2_promoter
+HIPK2 pp MBP
+PIK3CG pp TPM2
+PIK3CG pp ADRBK1
+ADRB2 pp AP2B1
+Bax pp Bax
+Bax pp Bax
+Bax pp Bax
+BAX pp BAX
+Bax pp Bax
+BAX pp BAX
+Clu pp Bax
+PKD2 pp PI4KIII-beta
+PKD1 pp PI4KIII-beta
+PKD3 pp PI4KIII-beta
+PKD1 pp PKD1
+PRKD1 pp PRKD1
+PKD2 pp PKD2
+PKD3 pp PKD3
+CAML pp p56Lck
+VHL pp HIF-1-alpha
+JunB pd Clusterin_promoter
+ENL pp AF5q31
+ENL pp H1
+ENL pp H3
+ENL pp AF4
+ENL pp PC3
+ENL pp AF10
+c-Abl pp CRM1
+GHR pp GHR
+GHR pp GHR
+GHR pp GHR
+GHR pp GHR
+GHR pp GHR
+OBR pp OBR
+LEPR pp LEPR
+EPOR pp EPOR
+EPOR pp EPOR
+EPOR pp EPOR
+Unknown interactsWith FANCF
+Unknown interactsWith Hef
+FANCC interactsWith Unknown
+Beta-arrestin2 pp V1aR
+Beta-arrestin2 pp V2R
+beta-arrestin pp V2R
+Beta-arrestin2 pp CCR5
+Beta-arrestin2 pp PAF-R
+Beta-arrestin2 pp Beta-2AR
+Beta-arrestin2 pp CXCR4
+p65 pp I-kappa-B-alpha
+RelA pp I-kappaB-alpha
+RELA pp NFKBIA
+I-kappa-B-alpha pp NF-kappa-B-p65
+Unknown interactsWith TRAP220
+P-TEFb_complex interactsWith Brd4
+Unknown interactsWith 7SK
+P-TEFb_complex interactsWith pol_II_CTD
+P-TEFb interactsWith POLR2A
+P-TEFb_complex interactsWith HXM1
+P-TEFb_complex interactsWith Unknown
+Brd4 interactsWith Unknown
+GluR6b pp PP2B-alpha
+GluR6b pp PP2B-beta
+GluR6a pp GluR6b
+Stat3 pd Akt1_promoter
+p53 pd p21_promoter
+p53 pd p53AIP1_promoter
+PCAF pd p21_promoter
+p53 pd Tk_promoter
+Brk pp IRS-1
+IRS-4 pp Grb2
+Brk pp IRS-4
+Brk pp Brk
+EDG1 pp ER-alpha
+EDG1 pp Cyclin_T1
+Cyclin_T1 pp ER-alpha
+ERE pd ER-alpha
+Coagulation_Factor_X_Synonym:_Factor_Xa,_Stuart_Factor pp F10
+AK5 pp AK5
+GMPR pp GMPR
+GMPR pp GMPR
+DCXR pp DCXR
+DCXR pp DCXR
+DCXR pp DCXR
+DCXR pp DCXR
+DCXR pp DCXR
+DCXR pp DCXR
+Kb752_Peptide pp GNAI1
+Kb752_Peptide pp GNAI1
+Kb752_Peptide pp GNAI1
+Kb752_Peptide pp GNAI1
+GNAI1 pp GNAI1
+GNAI1 pp GNAI1
+ESR2 pp ESR2
+ESR2 pp ESR2
+ESR2 pp ESR2
+ESR2 pp ESR2
+ESR2 pp ESR2
+LILRB1 pp LILRB1
+IL22 pp IL22
+IL22 pp IL22
+Alpha-Actinin_4 pp VCL
+DNCL2A pp DNCL2A
+CES1 pp CES1
+CES1 pp CES1
+CES1 pp CES1
+CES1 pp CES1
+CES1 pp CES1
+CES1 pp CES1
+CES1 pp CES1
+CES1 pp CES1
+CES1 pp CES1
+CES1 pp CES1
+CES1 pp CES1
+CES1 pp CES1
+Activation_Peptide_From_Cathepsin_E pp CTSE
+CST3 pp CST3
+CST3 pp CST3
+CST3 pp CST3
+CST3 pp CST3
+CST3 pp CST3
+CST3 pp CST3
+CST3 pp CST3
+CST3 pp CST3
+CST3 pp CST3
+CST3 pp CST3
+CST3 pp CST3
+CST3 pp CST3
+CST3 pp CST3
+CST3 pp CST3
+PKM2 pp PKM2
+PKM2 pp PKM2
+PKM2 pp PKM2
+PKM2 pp PKM2
+PKM2 pp PKM2
+PKM2 pp PKM2
+PKM2 pp PKM2
+PKM2 pp PKM2
+ERCC1 pp ERCC4
+F2 pp F2
+F2 pp F2
+F2 pp F2
+F2 pp F2
+F2 pp F2
+F2 pp F2
+F2 pp F2
+F2 pp F2
+F2 pp F2
+F2 pp F2
+F2 pp F2
+F2 pp F2
+F2 pp F2
+F2 pp F2
+F2 pp F2
+F2 pp F2
+F2 pp F2
+F2 pp Thrombin,_Light_Chain
+F2 pp Thrombin,_Light_Chain
+CD1D pp CD1D
+B2M pp CD1D
+B2M pp CD1D
+CD1D pp B2M
+B2M pp HLA-A
+B2M pp HLA-A
+Trafficking_Protein_Particle_Complex_Subunit_6b pp Trafficking_Protein_Particle_Complex_Subunit_6b
+NR3C2 pp NR3C2
+APCS pp APCS
+APCS pp APCS
+APCS pp APCS
+APCS pp APCS
+APCS pp APCS
+APCS pp APCS
+APCS pp APCS
+APCS pp APCS
+APCS pp APCS
+APCS pp APCS
+APCS pp APCS
+APCS pp APCS
+APCS pp APCS
+APCS pp APCS
+APCS pp APCS
+APCS pp APCS
+RGS7 pp RGS7
+HPRT1 pp HPRT1
+HPRT1 pp HPRT1
+HPRT1 pp HPRT1
+HPRT1 pp HPRT1
+HPRT1 pp HPRT1
+HPRT1 pp HPRT1
+HPRT1 pp HPRT1
+ZFYVE20 pp RAB4A
+RAB2 pp RAB2
+RAB2 pp RAB2
+RAB2 pp RAB2
+RAB2 pp RAB2
+RAB2 pp RAB2
+Rac1 pp TIAM1
+Synthetic_Peptide pp Hla_Class_I_Histocompatibility_Antigen
+T-Cell_Receptor_Beta_Chain_C_Region pp T-Cell_Receptor_Alpha_Chain_V_Region
+T-Cell_Receptor_Beta_Chain_C_Region pp Synthetic_Peptide
+T-Cell_Receptor_Alpha_Chain_V_Region pp Synthetic_Peptide
+Synthetic_Peptide pp Hla_Class_I_Histocompatibility_Antigen
+T-Cell_Receptor_Beta_Chain_C_Region pp T-Cell_Receptor_Alpha_Chain_C_Region
+Nuclear_Receptor_Coactivator_2 pp NR5A2
+Nuclear_Receptor_Coactivator_2 pp NR5A2
+Nuclear_Receptor_Coactivator_2 pp NR5A1
+Tif2_Peptide pp NR5A1
+1VFC_C pd Telomeric_Repeat_Binding_Factor_2
+1VFC_B pd Telomeric_Repeat_Binding_Factor_2
+Consensus_Peptide_For_14-3-3_Proteins pp YWHAE
+F2 pp Prothrombin
+SPDEF pd 1YO5_A
+SPDEF pd 1YO5_B
+Rab_Interacting_Lysosomal_Protein pp RAB7
+IPS-1 pp FADD
+IPS-1 pp RIP1
+IPS-1 pp Mda5
+IPS-1 pp RIG1
+HOX11 pp PP2A
+RALGDS pp RAP1A
+Rap1A pp RalGDS
+SIPA1 pp AQP2
+Fbx29 pp Skp1
+CUL7 pp ROC1
+p300 pd p21_promoter
+SP1 pd p21_promoter
+SP1 pd CDKN1A_promoter
+SP3 pd p21_promoter
+RB pd Bcl-2_promoter
+SRC-2 pd alpha-1-AT_promoter
+Rb pp HNF-4
+Rb pd alpha-1-AT_promoter
+HNF-4 pd alpha-1-AT_promoter
+ATR pp BID
+ATR pp BID
+ATM pp BID
+ATM pp BID
+TFIIB pd REK
+ESXR1 pd REK
+PKD1 pp Rap1
+Unknown interactsWith Beta-1_integrin
+PKD1 interactsWith Unknown
+PKD1 pp C3G
+TIA-1 interactsWith Fas_pre-mRNA
+PTB interactsWith Fas_pre-mRNA
+U2AF65 interactsWith Fas_pre-mRNA
+Cul7 interactsWith Fbx29-Skp1_complex
+CDKN1A_promoter pd Miz-1
+Miz1 pd p21WAF1_promoter
+BCL6 pp Miz-1
+Bcl-XL pp Bad
+Bad pp Bcl-xL
+Bad pp Bcl-XL
+TNF-alpha_mRNA interactsWith hnRNP_A1
+TNF-alpha_mRNA interactsWith Unknown
+Unknown interactsWith hnRNP_A0
+Mnk1 pp hnRNP_A1
+Mnk1 pp eIF4E
+UbcH7 pp E6AP
+UbE1 pp UbcH5b
+E1 pp UbcH7
+L1CAM pp RanBPM
+L1CAM pp ezrin
+L1CAM interactsWith CKII
+L1-CAM pp ankyrin
+L1cam pp p90rsk
+Gfi-1 pp Atx-1
+Ago2 pp Xrn1
+Ago2 pp Dcp1a
+EIF2C2 pp DCP1A
+NRON interactsWith KPNB1
+NRON interactsWith CSE1L
+NRON interactsWith PSMD11
+NRON interactsWith IQGAP1
+NRON interactsWith PPP2R1A
+NRON interactsWith TNPO1
+NRON interactsWith CUL4B
+NRON interactsWith DDX3X
+NRON interactsWith SPAG9
+NRON interactsWith EIF3S6
+NRON interactsWith UREB1
+BAF pp BAF
+BANF1 pp BANF1
+BANF1 pp BANF1
+BANF1 pp BANF1
+BANF1 pp BANF1
+BANF1 pp BANF1
+BAF pp BAF
+Unknown interactsWith Cul4A
+Chk1 interactsWith Unknown
+Unknown interactsWith Cul1
+TRAP220 pd PSA_regulatory_region
+p300 pd PSA_regulatory_region
+AIB1 pd PSA_regulatory_region
+GRIP1 pd PSA_regulatory_region
+SRC1 pd PSA_regulatory_region
+TBP pd PSA_regulatory_region
+AR pd PSA_regulatory_region
+CARM1 pd PSA_enhancer
+Bcl-xL pp PUMA
+Bcl-XL pp Puma
+PUMA pp Bcl-xL
+Puma pp Bcl-XL
+Bcl-xL pp BAX
+Bax pp Bcl-XL
+Bcl-xL pp p53
+Bcl-xl pp p53
+JUN pp TCF7L2
+CTNNB1 pp TCF7L2
+Beta-catenin pp TCF4
+TCF-4 pp Beta-catenin
+TCF7L2 pd MYC_promoter
+JUN pd CDC2_promoter
+c-Jun pd RET_promoter
+c-Jun pd EGR2_promoter
+c-Jun pd MKI67_promoter
+c-Jun pd NFKB2_promoter
+c-Jun pd VIM_promoter
+c-Jun pd NCOA4_promoter
+c-Jun pd ACF_promoter
+c-Jun pd BCCIP_promoter
+c-Jun pd FLJ20360_promoter
+c-Jun pd HPSE2_promoter
+c-Jun pd TCF7L2_promoter
+c-Jun pd FZD8_promoter
+JUN-TCF7L2-CTNNB1 interactsWith JUN_promoter
+CtBP pp Evi-1a
+Smad3 pp Evi-1a
+PrP pp PrP
+Chk2 pp CK2-beta
+Chk2 pp p53
+DNCL1 pp BS69
+DNCL1 pp Bim
+IRF-3 pp IRF-3
+IRF-3 pp IRF-3
+MAVS pp TRAF6
+eIF4AIII interactsWith Magoh-Y14
+eIF4AIII pp MLN51
+Cdk2 pp N-myc
+Cyclin_B1 pp N-myc
+CyclinA pp N-myc
+Cdk1 pp N-myc
+Cdk5 pp N-myc
+Rab5 pp EEA1
+Rab5 pp EEA.1
+Rab5 interactsWith Unknown
+Unknown interactsWith hVps39
+Unknown interactsWith hVps18
+Unknown interactsWith hVps16
+Unknown interactsWith hVps11
+65K interactsWith U12_snRNA
+65K pp 59K
+AOF2 pp AR
+AOF2 pp H3F3A
+AOF2-AR interactsWith KLK3_upstream_region
+SHBG pp megalin
+Evi-1a pp Evi-1a
+Girdin pp Girdin
+Akt1 pp Girdin
+Cyclin_D3 pp cdk6
+CYCD3 pp CDK6
+cdk6 pp Cyclin_D1
+CYCD1 pp CDK6
+CCND1 pp CDK6
+Cyclin_A pp cdk2
+Cyclin_A pp Cdk2
+CCNA2 pp Cdk2
+Cdk2 pp Cyc_A
+CDK2 pp CCNA2
+Cyclin_E pp cdk2
+Cyclin_E pp Cdk2
+CCNE1 pp CDK2
+CCNE1 pp Cdk2
+Cdk2 pp Cyc_E
+CDK2 pp CCNE1
+Skp1 pp Fbxo7
+Cyclin_D3 pp cdk4
+CYCD3 pp CDK4
+p27 pp Fbxo7
+cdk6 pp Fbxo7
+Rbx1 pp Fbxo7
+Cyclin_D3 pp Fbxo7
+Cyclin_D1 pp Fbxo7
+MDC1 pp Rad51
+CBP80 pp Upf1
+Upf1 pp Stau1
+Heparin_Cofactor_Ii pp F2
+Heparin_Cofactor_Ii pp Heparin_Cofactor_Ii
+MMP9 pp MMP9
+Fab_2g12,_Light_Chain pp Fab_2g12,_Light_Chain
+Fab_2g12,_Light_Chain pp Fab_2g12,_Light_Chain
+Fab_2g12,_Heavy_Chain pp Fab_2g12,_Light_Chain
+Fab_2g12,_Heavy_Chain pp Fab_2g12,_Light_Chain
+Fab_2g12,_Heavy_Chain pp Fab_2g12,_Light_Chain
+Fab_2g12,_Light_Chain pp Fab_2g12,_Heavy_Chain
+Fab_2g12,_Light_Chain pp Fab_2g12,_Heavy_Chain
+Fab_2g12,_Light_Chain pp Fab_2g12,_Heavy_Chain
+Fab_2g12,_Heavy_Chain pp Fab_2g12,_Light_Chain
+Fab_2g12,_Heavy_Chain pp Fab_2g12,_Light_Chain
+Fab_2g12,_Heavy_Chain pp Fab_2g12,_Light_Chain
+Fab_2g12,_Heavy_Chain pp Fab_2g12,_Light_Chain
+Fab_2g12,_Heavy_Chain pp Fab_2g12,_Light_Chain
+Fab_2g12,_Heavy_Chain pp Fab_2g12,_Light_Chain
+AMD1 pp AMD1
+AMD1 pp AMD1
+AMD1 pp AMD1
+AMD1 pp AMD1
+AMD1 pp AMD1
+AMD1 pp AMD1
+AMD1 pp AMD1
+AMD1 pp AMD1
+MMP12 pp MMP12
+Beta-2-Microglobulin pp Hla_Class_I_Histocompatibility_Antigen,_A-2_Alpha_Chain
+PAPSS1 pp PAPSS1
+Branched_Chain_Aminotransferase_1,_Cytosolic pp Branched_Chain_Aminotransferase_1,_Cytosolic
+Di-Ubiquitin pp Di-Ubiquitin
+Fab_2g12,_Light_Chain pp Fab_2g12,_Light_Chain
+PLN pp PLN
+PLN pp PLN
+PLN pp PLN
+PLN pp PLN
+PLN pp PLN
+Neutrophil_Defensin_2 pp Neutrophil_Defensin_2
+Neutrophil_Defensin_2 pp Neutrophil_Defensin_2
+Fab_2g12,_Heavy_Chain pp Fab_2g12,_Light_Chain
+Fab_2g12,_Heavy_Chain pp Fab_2g12,_Light_Chain
+Fab_2g12,_Heavy_Chain pp Fab_2g12,_Light_Chain
+Fab_2g12,_Heavy_Chain pp Fab_2g12,_Light_Chain
+Fab_2g12,_Heavy_Chain pp Fab_2g12,_Light_Chain
+Fab_2g12,_Heavy_Chain pp Fab_2g12,_Light_Chain
+Fab_2g12,_Light_Chain pp Fab_2g12,_Heavy_Chain
+Fab_2g12,_Heavy_Chain pp Fab_2g12,_Heavy_Chain
+Fab_2g12,_Heavy_Chain pp Fab_2g12,_Heavy_Chain
+Fab_2g12,_Heavy_Chain pp Fab_2g12,_Heavy_Chain
+Kunitz_Protease_Inhibitory_Domain_Of_Protease_Nexin_Ii pp Catalytic_Domain_Of_Coagulation_Factor_Xi
+GAPDH pp GAPDH
+GAPD pp GAPD
+GAPDH pp GAPDH
+GAPDH pp GAPDH
+GAPDH pp GAPDH
+GAPDH pp GAPDH
+GAPDH pp GAPDH
+F105_Heavy_Chain pp F105_Light_Chain
+Ctip_Phosphorylated_Peptide pp Breast_Cancer_Type_1_Susceptibility_Protein
+DehydrogenaseREDUCTASE_(SDR_FAMILY)_MEMBER_6 pp DehydrogenaseREDUCTASE_(SDR_FAMILY)_MEMBER_6
+DehydrogenaseREDUCTASE_(SDR_FAMILY)_MEMBER_6 pp DehydrogenaseREDUCTASE_(SDR_FAMILY)_MEMBER_6
+DehydrogenaseREDUCTASE_(SDR_FAMILY)_MEMBER_6 pp DehydrogenaseREDUCTASE_(SDR_FAMILY)_MEMBER_6
+DehydrogenaseREDUCTASE_(SDR_FAMILY)_MEMBER_6 pp DehydrogenaseREDUCTASE_(SDR_FAMILY)_MEMBER_6
+Glutaminyl-Peptide_Cyclotransferase pp Glutaminyl-Peptide_Cyclotransferase
+Glutaminyl-Peptide_Cyclotransferase pp Glutaminyl-Peptide_Cyclotransferase
+Glutaminyl-Peptide_Cyclotransferase pp Glutaminyl-Peptide_Cyclotransferase
+Glutaminyl-Peptide_Cyclotransferase pp Glutaminyl-Peptide_Cyclotransferase
+Pyridoxal_Kinase pp Pyridoxal_Kinase
+SerineTHREONINE-Protein_Kinase_Pak_1 pp Rho_Guanine_Nucleotide_Exchange_Factor_7
+Heterogeneous_Nuclear_Ribonucleoprotein_K pp Heterogeneous_Nuclear_Ribonucleoprotein_K
+Dna_Topoisomerase_Ii,_Alpha_Isozyme pp Dna_Topoisomerase_Ii,_Alpha_Isozyme
+Dna_Topoisomerase_Ii,_Alpha_Isozyme pp Dna_Topoisomerase_Ii,_Alpha_Isozyme
+Ubiquitin_Carboxyl-Terminal_Hydrolase_8 pp Ubiquitin_Carboxyl-Terminal_Hydrolase_8
+Calcyclin-Binding_Protein pp Calcyclin-Binding_Protein
+Calcyclin-Binding_Protein pp Calcyclin-Binding_Protein
+Calcyclin-Binding_Protein pp Calcyclin-Binding_Protein
+Calcyclin-Binding_Protein_Peptide pp Ubiquitin_Ligase_Siah1
+Branched_Chain_Aminotransferase pp Branched_Chain_Aminotransferase
+TNF-alpha pp TNFR_II
+TNF-alpha pp TNFR-2
+Cdk5/p35 interactsWith alpha-1C
+AR interactsWith unknown
+unknown interactsWith Hop
+unknown interactsWith p23
+Bcl-XL pp Ins(1,4,5)P3R-1
+Bcl-XL pp Ins(1,4,5)P3R-2
+Bcl-2 pp Ins(1,4,5)P3R-1
+Bcl-XL pp Ins(1,4,5)P3R-3
+KCNK3 pp 14-3-3-beta
+GPR15 pp 14-3-3-beta
+Abi1 pp WAVE2
+Abi1 pp N-WASP
+BHC110 pp CoREST
+Unknown interactsWith ZnF516
+Unknown interactsWith BRAF35
+Unknown interactsWith BHC80
+Unknown interactsWith ZnF217
+Unknown interactsWith KIAA0182
+Unknown interactsWith FIM
+BHC110 interactsWith unknown
+GNPTAG pp MGC4170
+GNPTAG pp CMT1A
+GNPTAG pp Fibulin_4
+beta-catenin pp E-cadherin
+Beta-catenin pp E-cadherin
+beta-catenin pp E-cadherin
+CDH1 pp CTNNB1
+E-cadherin pp beta-catenin
+ARHGAP10 pp alpha-catenin
+beta-catenin pp alpha-catenin
+Nek2 pp HEF1
+AurA pp HEF1
+Nek2 pp MBP
+TAF1 pd DCLRE1B_promoter
+TAF1 pd RBM15_promoter
+TAF1 pd FAM40A_promoter
+TAF1 pd AHCYL1_promoter
+TAF1 pd CSF1_promoter
+TAF1 pd GSTM4_promoter
+TAF1 pd AMPD2_promoter
+TAF1 pd GNAI3_promoter
+TAF1 pd CYB561D1_promoter
+TAF1 pd ATXN7L2_promoter
+TAF1 pd PSMA5_promoter
+TAF1 pd PSRC1_promoter
+TAF1 pd SARS_promoter
+TAF1 pd CLCC1_promoter
+TAF1 pd STXBP3_promoter
+TAF1 pd HBXIP_promoter
+TAF1 pd C1orf103_promoter
+TAF1 pd AP4B1_promoter
+TAF1 pd RSBN1_promoter
+TAF1 pd PHTF1_promoter
+TAF1 pd MAGI3_promoter
+TAF1 pd LRIG2_promoter
+TAF1 pd SLC16A1_promoter
+TAF1 pd RHOC_promoter
+TAF1 pd MOV10_promoter
+TAF1 pd CAPZA1_promoter
+TAF1 pd ST7L_promoter
+TAF1 pd CTTNBP2NL_promoter
+TAF1 pd C1orf183_promoter
+TAF1 pd ATP5F1_promoter
+TAF1 pd CEPT1_promoter
+TAF1 pd PRPF38B_promoter
+TAF1 pd SLC25A24_promoter
+TAF1 pd ALG14_promoter
+TAF1 pd CNN3_promoter
+TAF1 pd F3_promoter
+TAF1 pd ABCD3_promoter
+TAF1 pd GCLM_promoter
+TAF1 pd ERBP_promoter
+TAF1 pd BCAR3_promoter
+TAF1 pd DR1_promoter
+TAF1 pd TMED5_promoter
+TAF1 pd MTF2_promoter
+TAF1 pd RPL5_promoter
+TAF1 pd C1orf82_promoter
+TAF1 pd BTBD8_promoter
+TAF1 pd TGFBR3_promoter
+TAF1 pd RWDD3_promoter
+TAF1 pd PTBP2_promoter
+TAF1 pd RNPC3_promoter
+TAF1 pd EDG1_promoter
+TAF1 pd SLC30A7_promoter
+TAF1 pd EXTL2_promoter
+TAF1 pd CDC14A_promoter
+TAF1 pd RTCD1_promoter
+TAF1 pd DBT_promoter
+TAF1 pd FLJ10287_promoter
+TAF1 pd HIAT1_promoter
+TAF1 pd SLC35A3_promoter
+TAF1 pd AGL_promoter
+TAF1 pd LPPR4_promoter
+TAF1 pd SNX7_promoter
+TAF1 pd DPYD_promoter
+TAF1 pd CDC7_promoter
+TAF1 pd HIPK1_promoter
+TAF1 pd LYSMD1_promoter
+TAF1 pd MRPS21_promoter
+TAF1 pd APH1A_promoter
+TAF1 pd ANP32E_promoter
+TAF1 pd CKIP-1_promoter
+TAF1 pd VPS45A_promoter
+TAF1 pd ZA20D1_promoter
+TAF1 pd SF3B4_promoter
+TAF1 pd BOLA1_promoter
+TAF1 pd HIST2H2BE_promoter
+TAF1 pd HIST2H2AA_promoter
+TAF1 pd HIST2H3C_promoter
+TAF1 pd HIST2H4_promoter
+TAF1 pd KIAA0493_promoter
+TAF1 pd DJ328E19.C1.1_promoter
+TAF1 pd PRPF3_promoter
+TAF1 pd KIAA0460_promoter
+TAF1 pd SEMA6C_promoter
+TAF1 pd MGC29891_promoter
+TAF1 pd MLLT11_promoter
+TAF1 pd C1orf56_promoter
+TAF1 pd PRUNE_promoter
+TAF1 pd FAM63A_promoter
+TAF1 pd LASS2_promoter
+TAF1 pd SETDB1_promoter
+TAF1 pd ARNT_promoter
+TAF1 pd ENSA_promoter
+TAF1 pd MCL1_promoter
+TAF1 pd C1orf138_promoter
+TAF1 pd ECM1_promoter
+TAF1 pd TARSL1_promoter
+TAF1 pd BCL9_promoter
+TAF1 pd CHD1L_promoter
+TAF1 pd WARS2_promoter
+TAF1 pd WDR3_promoter
+TAF1 pd GDAP2_promoter
+TAF1 pd FAM46C_promoter
+TAF1 pd MAN1A2_promoter
+TAF1 pd TRIM45_promoter
+TAF1 pd TTF2_promoter
+TAF1 pd CD58_promoter
+TAF1 pd MGC16179_promoter
+TAF1 pd NGFB_promoter
+TAF1 pd FLJ21168_promoter
+TAF1 pd CSDE1_promoter
+TAF1 pd NRAS_promoter
+TAF1 pd BCAS2_promoter
+TAF1 pd PHGDH_promoter
+TAF1 pd NOTCH2_promoter
+TAF1 pd PRKAB2_promoter
+TAF1 pd LOC200030_promoter
+TAF1 pd PIAS3_promoter
+TAF1 pd ANKRD35_promoter
+TAF1 pd PEX11B_promoter
+TAF1 pd GNRHR2_promoter
+TAF1 pd RBM8A_promoter
+TAF1 pd ANKRD34_promoter
+TAF1 pd TXNIP_promoter
+TAF1 pd NOTCH2NL_promoter
+TAF1 pd PDE4DIP_promoter
+TAF1 pd SEC22L1_promoter
+TAF1 pd FLJ39739_promoter
+TAF1 pd FLJ44253_promoter
+TAF1 pd OLFML3_promoter
+TAF1 pd ZNF326_promoter
+TAF1 pd C1orf41_promoter
+TAF1 pd NRD1_promoter
+TAF1 pd OSBPL9_promoter
+TAF1 pd RNF11_promoter
+TAF1 pd CDKN2C_promoter
+TAF1 pd FAF1_promoter
+TAF1 pd FOXD2_promoter
+TAF1 pd MGC12982_promoter
+TAF1 pd CMPK_promoter
+TAF1 pd SIL_promoter
+TAF1 pd KIAA0494_promoter
+TAF1 pd MOBKL2C_promoter
+TAF1 pd NSUN4_promoter
+TAF1 pd LRRC41_promoter
+TAF1 pd RAD54L_promoter
+TAF1 pd KTI12_promoter
+TAF1 pd TXNDC12_promoter
+TAF1 pd YIPF1_promoter
+TAF1 pd TMEM48_promoter
+TAF1 pd LRP8_promoter
+TAF1 pd MAGOH_promoter
+TAF1 pd C1orf123_promoter
+TAF1 pd CPT2_promoter
+TAF1 pd SCP2_promoter
+TAF1 pd ZYG11A_promoter
+TAF1 pd C1orf163_promoter
+TAF1 pd ZCCHC11_promoter
+TAF1 pd PRPF38A_promoter
+TAF1 pd ORC1L_promoter
+TAF1 pd CC2D1B_promoter
+TAF1 pd BTF3L4_promoter
+TAF1 pd PIK3R3_promoter
+TAF1 pd MAST2_promoter
+TAF1 pd B4GALT2_promoter
+TAF1 pd ATP6V0B_promoter
+TAF1 pd IPO13_promoter
+TAF1 pd ST3GAL3_promoter
+TAF1 pd JMJD2A_promoter
+TAF1 pd PTPRF_promoter
+TAF1 pd MED8_promoter
+TAF1 pd EBNA1BP2_promoter
+TAF1 pd SLC2A1_promoter
+TAF1 pd ZNF691_promoter
+TAF1 pd ERMAP_promoter
+TAF1 pd C1orf50_promoter
+TAF1 pd LEPRE1_promoter
+TAF1 pd YBX1_promoter
+TAF1 pd DMAP1_promoter
+TAF1 pd C1orf164_promoter
+TAF1 pd TMEM69_promoter
+TAF1 pd GPBP1L1_promoter
+TAF1 pd NASP_promoter
+TAF1 pd AKR1A1_promoter
+TAF1 pd PRDX1_promoter
+TAF1 pd LOC126661_promoter
+TAF1 pd TESK2_promoter
+TAF1 pd TOE1_promoter
+TAF1 pd UROD_promoter
+TAF1 pd EIF2B3_promoter
+TAF1 pd LOC149478_promoter
+TAF1 pd PLK3_promoter
+TAF1 pd RPS8_promoter
+TAF1 pd KIF2C_promoter
+TAF1 pd PPIH_promoter
+TAF1 pd TMEM59_promoter
+TAF1 pd LOC492303_promoter
+TAF1 pd SAMD13_promoter
+TAF1 pd PRKACB_promoter
+TAF1 pd TTLL7_promoter
+TAF1 pd LPHN2_promoter
+TAF1 pd PTGFR_promoter
+TAF1 pd FUBP1_promoter
+TAF1 pd NEXN_promoter
+TAF1 pd USP33_promoter
+TAF1 pd ZZZ3_promoter
+TAF1 pd AK5_promoter
+TAF1 pd PIGK_promoter
+TAF1 pd RABGGTB_promoter
+TAF1 pd ACADM_promoter
+TAF1 pd C1orf171_promoter
+TAF1 pd BXDC5_promoter
+TAF1 pd GNG5_promoter
+TAF1 pd LRRC8C_promoter
+TAF1 pd GBP1_promoter
+TAF1 pd RBMXL1_promoter
+TAF1 pd GTF2B_promoter
+TAF1 pd PKN2_promoter
+TAF1 pd LMO4_promoter
+TAF1 pd SEP15_promoter
+TAF1 pd SH3GLB1_promoter
+TAF1 pd ODF2L_promoter
+TAF1 pd C1orf181_promoter
+TAF1 pd CYR61_promoter
+TAF1 pd DDAH1_promoter
+TAF1 pd BCL10_promoter
+TAF1 pd C1orf52_promoter
+TAF1 pd CRYZ_promoter
+TAF1 pd FPGT_promoter
+TAF1 pd ITGB3BP_promoter
+TAF1 pd ALG6_promoter
+TAF1 pd ATG4C_promoter
+TAF1 pd LOC400756_promoter
+TAF1 pd USP1_promoter
+TAF1 pd INADL_promoter
+TAF1 pd TM2D1_promoter
+TAF1 pd FLJ10986_promoter
+TAF1 pd JUN_promoter
+TAF1 pd OMA1_promoter
+TAF1 pd PPAP2B_promoter
+TAF1 pd LOC148987_promoter
+TAF1 pd PARS2_promoter
+TAF1 pd TTC4_promoter
+TAF1 pd PGM1_promoter
+TAF1 pd JAK1_promoter
+TAF1 pd NEGR1_promoter
+TAF1 pd ZNF265_promoter
+TAF1 pd CTH_promoter
+TAF1 pd ANKRD13C_promoter
+TAF1 pd SFRS11_promoter
+TAF1 pd LRRC40_promoter
+TAF1 pd DEPDC1_promoter
+TAF1 pd C1orf139_promoter
+TAF1 pd GADD45A_promoter
+TAF1 pd PAI-RBP1_promoter
+TAF1 pd SLC35D1_promoter
+TAF1 pd MIER1_promoter
+TAF1 pd SGIP1_promoter
+TAF1 pd LEPROT_promoter
+TAF1 pd MRPL37_promoter
+TAF1 pd RNPEP_promoter
+TAF1 pd CCDC7_promoter
+TAF1 pd ANKRD26_promoter
+TAF1 pd ABI1_promoter
+TAF1 pd C10orf63_promoter
+TAF1 pd PRTFDC1_promoter
+TAF1 pd ARHGAP21_promoter
+TAF1 pd OTUD1_promoter
+TAF1 pd PCGF4_promoter
+TAF1 pd COMMD3_promoter
+TAF1 pd FLJ45187_promoter
+TAF1 pd PLXDC2_promoter
+TAF1 pd ARL8_promoter
+TAF1 pd STAM_promoter
+TAF1 pd VIM_promoter
+TAF1 pd RSU1_promoter
+TAF1 pd YME1L1_promoter
+TAF1 pd ACBD5_promoter
+TAF1 pd EPC1_promoter
+TAF1 pd KIF5B_promoter
+TAF1 pd ARHGAP12_promoter
+TAF1 pd TCF8_promoter
+TAF1 pd LOC220930_promoter
+TAF1 pd LOC220929_promoter
+TAF1 pd MAP3K8_promoter
+TAF1 pd PAPD1_promoter
+TAF1 pd SVIL_promoter
+TAF1 pd LOC387647_promoter
+TAF1 pd BAMBI_promoter
+TAF1 pd WAC_promoter
+TAF1 pd LOC220906_promoter
+TAF1 pd RAB18_promoter
+TAF1 pd PTER_promoter
+TAF1 pd C10orf97_promoter
+TAF1 pd PFKFB3_promoter
+TAF1 pd RBM17_promoter
+TAF1 pd GDI2_promoter
+TAF1 pd KLF6_promoter
+TAF1 pd PITRM1_promoter
+TAF1 pd PFKP_promoter
+TAF1 pd KIN_promoter
+TAF1 pd ATP5C1_promoter
+TAF1 pd RPP38_promoter
+TAF1 pd C10orf111_promoter
+TAF1 pd DCLRE1C_promoter
+TAF1 pd ARMETL1_promoter
+TAF1 pd HSPA14_promoter
+TAF1 pd C10orf45_promoter
+TAF1 pd FRMD4A_promoter
+TAF1 pd PRPF18_promoter
+TAF1 pd PHYH_promoter
+TAF1 pd C10orf7_promoter
+TAF1 pd NUDT5_promoter
+TAF1 pd UPF2_promoter
+TAF1 pd LOC439951_promoter
+TAF1 pd TAF3_promoter
+TAF1 pd ITGB1_promoter
+TAF1 pd ADAMTS14_promoter
+TAF1 pd HNRPH3_promoter
+TAF1 pd SIRT1_promoter
+TAF1 pd C10orf74_promoter
+TAF1 pd JMJD1C_promoter
+TAF1 pd NRBF2_promoter
+TAF1 pd C10orf22_promoter
+TAF1 pd ARID5B_promoter
+TAF1 pd RHOBTB1_promoter
+TAF1 pd CDC2_promoter
+TAF1 pd CCDC6_promoter
+TAF1 pd TFAM_promoter
+TAF1 pd UBE2D1_promoter
+TAF1 pd C10orf70_promoter
+TAF1 pd ZWINT_promoter
+TAF1 pd MAWBP_promoter
+TAF1 pd RUFY2_promoter
+TAF1 pd EIF4EBP2_promoter
+TAF1 pd PP_promoter
+TAF1 pd SARA1_promoter
+TAF1 pd TYSND1_promoter
+TAF1 pd AMID_promoter
+TAF1 pd HK1_promoter
+TAF1 pd VPS26_promoter
+TAF1 pd KIAA1279_promoter
+TAF1 pd DDX21_promoter
+TAF1 pd DDX50_promoter
+TAF1 pd CCAR1_promoter
+TAF1 pd CXXC6_promoter
+TAF1 pd SLC25A16_promoter
+TAF1 pd DNA2L_promoter
+TAF1 pd DKK1_promoter
+TAF1 pd CSTF2T_promoter
+TAF1 pd ZNF485_promoter
+TAF1 pd HNRPF_promoter
+TAF1 pd GALNACT-2_promoter
+TAF1 pd BMS1L_promoter
+TAF1 pd ZNF11B_promoter
+TAF1 pd LOC285961_promoter
+TAF1 pd LOC158160_promoter
+TAF1 pd ZNF37A_promoter
+TAF1 pd ZNF33A_promoter
+TAF1 pd ZNF25_promoter
+TAF1 pd ZNF248_promoter
+TAF1 pd FZD8_promoter
+TAF1 pd C10orf9_promoter
+TAF1 pd CREM_promoter
+TAF1 pd LOC220980_promoter
+TAF1 pd C10orf10_promoter
+TAF1 pd PRKG1_promoter
+TAF1 pd FLJ31958_promoter
+TAF1 pd TMEM23_promoter
+TAF1 pd FLJ31813_promoter
+TAF1 pd TIMM23_promoter
+TAF1 pd NCOA4_promoter
+TAF1 pd PARG_promoter
+TAF1 pd ERCC6_promoter
+TAF1 pd C10orf72_promoter
+TAF1 pd ARHGAP22_promoter
+TAF1 pd LOC255326_promoter
+TAF1 pd LOC387680_promoter
+TAF1 pd FAM21C_promoter
+TAF1 pd ZNF22_promoter
+TAF1 pd NRP1_promoter
+IQGAP1 pp Caspase_8
+FUS pp Caspase_3
+PSME3 pp Caspase_7
+PSME3 pp Caspase_3
+HNRPA0 pp Caspase_7
+HNRPA0 pp Caspase_3
+BCAP31 pp Caspase_7
+BCAP31 pp Caspase_3
+ACIN1 pp Caspase_8
+ACIN1 pp Caspase_7
+ACIN1 pp Caspase_6
+ACIN1 pp Caspase_3
+U2AF2 pp Caspase_3
+FUS pp Caspase_7
+IQGAP1 pp Caspase_7
+IQGAP1 pp Caspase_6
+IQGAP1 pp Caspase_3
+CBPIN pp Caspase_8
+CBPIN pp Caspase_6
+CBPIN pp Caspase_3
+DNAJC7 pp Caspase_8
+KARS pp Caspase_8
+KARS pp Caspase_6
+KARS pp Caspase_3
+TRIM28 pp Caspase_8
+TRIM28 pp Caspase_3
+TARDBP pp Caspase_7
+TARDBP pp Caspase_3
+TAF1 pd COMTD1_promoter
+TAF1 pd DDIT4_promoter
+TAF1 pd ASCC1_promoter
+TAF1 pd CHST3_promoter
+TAF1 pd PSAP_promoter
+TAF1 pd CDH23_promoter
+TAF1 pd SGPL1_promoter
+TAF1 pd DNAJB12_promoter
+TAF1 pd CBARA1_promoter
+TAF1 pd SAMD8_promoter
+TAF1 pd ADK_promoter
+TAF1 pd AP3M1_promoter
+TAF1 pd VCL_promoter
+TAF1 pd CHCHD1_promoter
+TAF1 pd FLJ44715_promoter
+TAF1 pd FUT11_promoter
+TAF1 pd SEC24C_promoter
+TAF1 pd PPP3CB_promoter
+TAF1 pd ANXA7_promoter
+TAF1 pd DNAJC9_promoter
+TAF1 pd HSGT1_promoter
+TAF1 pd P4HA1_promoter
+TAF1 pd C10orf42_promoter
+TAF1 pd LOC439985_promoter
+TAF1 pd ZNF143_promoter
+TAF1 pd SMPD1_promoter
+TAF1 pd PRKCDBP_promoter
+TAF1 pd CNGA4_promoter
+TAF1 pd DKFZP566M1046_promoter
+TAF1 pd TRIM5_promoter
+TAF1 pd TRIM68_promoter
+TAF1 pd RRM1_promoter
+TAF1 pd STIM1_promoter
+TAF1 pd FRAG1_promoter
+TAF1 pd NUP98_promoter
+TAF1 pd CARS_promoter
+TAF1 pd NAP1L4_promoter
+TAF1 pd PHLDA2_promoter
+TAF1 pd CDKN1C_promoter
+TAF1 pd ARFIP2_promoter
+TAF1 pd FXC1_promoter
+TAF1 pd IPO7_promoter
+TAF1 pd TMEM41B_promoter
+TAF1 pd RAB6IP1_promoter
+TAF1 pd ST5_promoter
+TAF1 pd MGC10850_promoter
+TAF1 pd EIF3S5_promoter
+TAF1 pd NALP10_promoter
+TAF1 pd ZNF214_promoter
+TAF1 pd ZNF215_promoter
+TAF1 pd MRPL17_promoter
+TAF1 pd TPP1_promoter
+TAF1 pd TAF10_promoter
+TAF1 pd ILK_promoter
+TAF1 pd KIAA0409_promoter
+TAF1 pd TSSC4_promoter
+TAF1 pd MRPL23_promoter
+TAF1 pd BNIP3_promoter
+TAF1 pd TXNL2_promoter
+TAF1 pd MKI67_promoter
+TAF1 pd BCCIP_promoter
+TAF1 pd C10orf137_promoter
+TAF1 pd KIAA0157_promoter
+TAF1 pd LOC399818_promoter
+TAF1 pd OAT_promoter
+TAF1 pd BUB3_promoter
+TAF1 pd ACADSB_promoter
+TAF1 pd ZNFN1A5_promoter
+TAF1 pd C10orf89_promoter
+TAF1 pd C10orf88_promoter
+TAF1 pd FAM24B_promoter
+TAF1 pd TUBGCP2_promoter
+TAF1 pd PAOX_promoter
+TAF1 pd LOC255512_promoter
+TAF1 pd MGC3234_promoter
+TAF1 pd RPLP2_promoter
+TAF1 pd TALDO1_promoter
+TAF1 pd LOC283232_promoter
+TAF1 pd DEAF1_promoter
+TAF1 pd KIAA1542_promoter
+TAF1 pd RNH1_promoter
+TAF1 pd IFITM3_promoter
+TAF1 pd PSMD13_promoter
+TAF1 pd SIRT3_promoter
+TAF1 pd RIC8A_promoter
+TAF1 pd BET1L_promoter
+TAF1 pd GTPBP7_promoter
+TAF1 pd HTRA1_promoter
+TAF1 pd WEE1_promoter
+TAF1 pd TRAF6_promoter
+TAF1 pd RCN1_promoter
+TAF1 pd ELP4_promoter
+TAF1 pd ZCSL3_promoter
+TAF1 pd FLJ38968_promoter
+TAF1 pd METT5D1_promoter
+TAF1 pd KIF18A_promoter
+TAF1 pd BDNF_promoter
+TAF1 pd LIN7C_promoter
+TAF1 pd NY-REN-41_promoter
+TAF1 pd LOC387758_promoter
+TAF1 pd DKFZp313A2432_promoter
+TAF1 pd FANCF_promoter
+TAF1 pd HRMT1L3_promoter
+TAF1 pd HTATIP2_promoter
+TAF1 pd hfl-B5_promoter
+TAF1 pd FLJ11336_promoter
+TAF1 pd FLJ14213_promoter
+TAF1 pd COMMD9_promoter
+TAF1 pd LOC143458_promoter
+TAF1 pd TRIM44_promoter
+TAF1 pd FJX1_promoter
+TAF1 pd CD44_promoter
+TAF1 pd CAT_promoter
+TAF1 pd ABTB2_promoter
+TAF1 pd FLJ10774_promoter
+TAF1 pd M11S1_promoter
+TAF1 pd FBXO3_promoter
+TAF1 pd CD59_promoter
+TAF1 pd HIPK3_promoter
+TAF1 pd CSTF3_promoter
+TAF1 pd NAV2_promoter
+TAF1 pd ZDHHC13_promoter
+TAF1 pd BTBD10_promoter
+TAF1 pd TEAD1_promoter
+TAF1 pd PARVA_promoter
+TAF1 pd FLJ14966_promoter
+TAF1 pd MICAL2_promoter
+TAF1 pd USP47_promoter
+TAF1 pd GALNTL4_promoter
+TAF1 pd LOC58486_promoter
+TAF1 pd EIF4G2_promoter
+TAF1 pd SH2BP1_promoter
+TAF1 pd MRVI1_promoter
+TAF1 pd AMPD3_promoter
+TAF1 pd ADM_promoter
+TAF1 pd LOC283104_promoter
+TAF1 pd MLSTD2_promoter
+TAF1 pd RRAS2_promoter
+TAF1 pd FLJ39441_promoter
+TAF1 pd UEV3_promoter
+TAF1 pd TSG101_promoter
+TAF1 pd LDHA_promoter
+TAF1 pd LOC113174_promoter
+TAF1 pd DKFZp686O24166_promoter
+TAF1 pd NUCB2_promoter
+TAF1 pd PIK3C2A_promoter
+TAF1 pd RPS13_promoter
+TAF1 pd SMAP_promoter
+TAF1 pd SOX6_promoter
+TAF1 pd CYP2R1_promoter
+TAF1 pd PSMA1_promoter
+TAF1 pd COPB_promoter
+TAF1 pd SWAP70_promoter
+TAF1 pd TACC2_promoter
+TAF1 pd COX15_promoter
+TAF1 pd ARHGAP19_promoter
+TAF1 pd SMBP_promoter
+TAF1 pd TLL2_promoter
+TAF1 pd FLJ34077_promoter
+TAF1 pd CCNJ_promoter
+TAF1 pd C10orf61_promoter
+TAF1 pd ALDH18A1_promoter
+TAF1 pd PDLIM1_promoter
+TAF1 pd HELLS_promoter
+TAF1 pd NOC3L_promoter
+TAF1 pd PSMD4P2_promoter
+TAF1 pd C10orf4_promoter
+TAF1 pd FER1L3_promoter
+TAF1 pd HHEX_promoter
+TAF1 pd FRAT1_promoter
+TAF1 pd FRAT2_promoter
+TAF1 pd ENTPD7_promoter
+TAF1 pd SLC25A28_promoter
+TAF1 pd GOT1_promoter
+TAF1 pd HPS1_promoter
+TAF1 pd C10orf33_promoter
+TAF1 pd C10orf28_promoter
+TAF1 pd ZFYVE27_promoter
+TAF1 pd MARVELD1_promoter
+TAF1 pd AVPI1_promoter
+TAF1 pd MMS19L_promoter
+TAF1 pd ZDHHC16_promoter
+TAF1 pd EXOSC1_promoter
+TAF1 pd PGAM1_promoter
+TAF1 pd KIAA0690_promoter
+TAF1 pd FAM35A_promoter
+TAF1 pd GLUD1_promoter
+TAF1 pd BMPR1A_promoter
+TAF1 pd LOC439990_promoter
+TAF1 pd BTAF1_promoter
+TAF1 pd C10orf13_promoter
+TAF1 pd PPP1R3C_promoter
+TAF1 pd HECTD2_promoter
+TAF1 pd PCGF5_promoter
+TAF1 pd RPP30_promoter
+TAF1 pd MPHOSPH1_promoter
+TAF1 pd PANK1_promoter
+TAF1 pd LIPA_promoter
+TAF1 pd FAS_promoter
+TAF1 pd AMSH-LP_promoter
+TAF1 pd C10orf59_promoter
+TAF1 pd ZNF503_promoter
+TAF1 pd SPFH1_promoter
+TAF1 pd ATE1_promoter
+TAF1 pd C10orf118_promoter
+TAF1 pd CASP7_promoter
+TAF1 pd TCF7L2_promoter
+TAF1 pd VTI1A_promoter
+TAF1 pd ZDHHC6_promoter
+TAF1 pd GPAM_promoter
+TAF1 pd LOC92482_promoter
+TAF1 pd PDCD4_promoter
+TAF1 pd CSPG6_promoter
+TAF1 pd DUSP5_promoter
+TAF1 pd MXI1_promoter
+TAF1 pd XPNPEP1_promoter
+TAF1 pd KIAA1754_promoter
+TAF1 pd GSTO2_promoter
+TAF1 pd KIAA1600_promoter
+TAF1 pd TRUB1_promoter
+TAF1 pd BRWD2_promoter
+TAF1 pd SEC23IP_promoter
+TAF1 pd INPP5F_promoter
+TAF1 pd BAG3_promoter
+TAF1 pd TIAL1_promoter
+TAF1 pd GRK5_promoter
+TAF1 pd PRDX3_promoter
+TAF1 pd EIF3S10_promoter
+TAF1 pd C10orf46_promoter
+TAF1 pd C10orf84_promoter
+TAF1 pd CASC2_promoter
+TAF1 pd PDZK8_promoter
+TAF1 pd KIAA1598_promoter
+TAF1 pd HSPA12A_promoter
+TAF1 pd GSTO1_promoter
+TAF1 pd C10orf78_promoter
+TAF1 pd LDB1_promoter
+TAF1 pd MGEA5_promoter
+TAF1 pd FBXW4_promoter
+TAF1 pd RP11-529I10.4_promoter
+TAF1 pd BTRC_promoter
+TAF1 pd KAZALD1_promoter
+TAF1 pd SFXN3_promoter
+TAF1 pd LZTS2_promoter
+TAF1 pd C10orf6_promoter
+TAF1 pd HIF1AN_promoter
+TAF1 pd NDUFB8_promoter
+TAF1 pd C10orf75_promoter
+TAF1 pd SCD_promoter
+TAF1 pd CWF19L1_promoter
+TAF1 pd PPRC1_promoter
+TAF1 pd NOLC1_promoter
+TAF1 pd SLK_promoter
+TAF1 pd USMG5_promoter
+TAF1 pd C10orf32_promoter
+TAF1 pd ACTR1A_promoter
+TAF1 pd CHUK_promoter
+TAF1 pd TIMM44_promoter
+TAF1 pd FLJ10374_promoter
+TAF1 pd EEF2_promoter
+TAF1 pd DAPK3_promoter
+TAF1 pd HLRC1_promoter
+TAF1 pd GADD45B_promoter
+TAF1 pd LSM7_promoter
+TAF1 pd OAZ1_promoter
+TAF1 pd SF3A2_promoter
+TAF1 pd REXO1_promoter
+TAF1 pd UQCR_promoter
+TAF1 pd C19orf25_promoter
+TAF1 pd RPS15_promoter
+TAF1 pd DAZAP1_promoter
+TAF1 pd MUM1_promoter
+TAF1 pd STAP2_promoter
+TAF1 pd C19orf10_promoter
+TAF1 pd FEM1A_promoter
+TAF1 pd LOC554363_promoter
+TAF1 pd XAB2_promoter
+TAF1 pd NTE_promoter
+TAF1 pd ZNF557_promoter
+TAF1 pd TNFSF9_promoter
+TAF1 pd GTF2F1_promoter
+TAF1 pd RANBP3_promoter
+TAF1 pd NDUFA11_promoter
+TAF1 pd DUS3L_promoter
+TAF1 pd PRSS15_promoter
+TAF1 pd RPL36_promoter
+TAF1 pd SAFB_promoter
+TAF1 pd SAFB2_promoter
+TAF1 pd UHRF1_promoter
+TAF1 pd C19orf23_promoter
+TAF1 pd CIRBP_promoter
+TAF1 pd FVT1_promoter
+TAF1 pd KIAA1468_promoter
+TAF1 pd PIGN_promoter
+TAF1 pd PMAIP1_promoter
+TAF1 pd LMAN1_promoter
+TAF1 pd ZNF532_promoter
+TAF1 pd NARS_promoter
+TAF1 pd WDR7_promoter
+TAF1 pd TXNL1_promoter
+TAF1 pd TCF4_promoter
+TAF1 pd C18orf54_promoter
+TAF1 pd POLI_promoter
+TAF1 pd RKHD2_promoter
+TAF1 pd SMAD4_promoter
+TAF1 pd VPS4B_promoter
+TAF1 pd DOK6_promoter
+TAF1 pd RTTN_promoter
+TAF1 pd STK11_promoter
+TAF1 pd POLR2E_promoter
+TAF1 pd C19orf6_promoter
+TAF1 pd WDR18_promoter
+TAF1 pd ARID3A_promoter
+TAF1 pd PTBP1_promoter
+TAF1 pd FLJ00038_promoter
+TAF1 pd C18orf22_promoter
+TAF1 pd TXNL4A_promoter
+TAF1 pd ZNF516_promoter
+TAF1 pd SDCCAG33_promoter
+TAF1 pd ZADH2_promoter
+TAF1 pd LOC400657_promoter
+TAF1 pd CYB5_promoter
+TAF1 pd MBD1_promoter
+TAF1 pd NDUFA7_promoter
+TAF1 pd ZNF507_promoter
+TAF1 pd CRSP7_promoter
+TAF1 pd RAB8A_promoter
+TAF1 pd WIZ_promoter
+TAF1 pd AKAP8L_promoter
+TAF1 pd GPSN2_promoter
+TAF1 pd DNAJB1_promoter
+TAF1 pd DDX39_promoter
+TAF1 pd ZSWIM4_promoter
+TAF1 pd MGC10471_promoter
+TAF1 pd IER2_promoter
+TAF1 pd TRMT1_promoter
+TAF1 pd NFIX_promoter
+TAF1 pd RAD23A_promoter
+TAF1 pd CALR_promoter
+TAF1 pd NY-SAR-48_promoter
+TAF1 pd MDS032_promoter
+TAF1 pd HSPC142_promoter
+TAF1 pd MGC39821_promoter
+TAF1 pd NDUFA13_promoter
+TAF1 pd TSSK6_promoter
+TAF1 pd KIAA0892_promoter
+TAF1 pd SF4_promoter
+TAF1 pd RFXANK_promoter
+TAF1 pd MEF2B_promoter
+TAF1 pd DDX49_promoter
+TAF1 pd COPE_promoter
+TAF1 pd ELL_promoter
+TAF1 pd GDF15_promoter
+TAF1 pd JUND_promoter
+TAF1 pd RPL18A_promoter
+TAF1 pd GTPBP3_promoter
+TAF1 pd PRDX2_promoter
+TAF1 pd JUNB_promoter
+TAF1 pd SLC44A2_promoter
+TAF1 pd CDKN2D_promoter
+TAF1 pd KEAP1_promoter
+TAF1 pd CDC37_promoter
+TAF1 pd TYK2_promoter
+TAF1 pd EDG5_promoter
+TAF1 pd EIF3S4_promoter
+TAF1 pd UBL5_promoter
+TAF1 pd ZNF562_promoter
+TAF1 pd ZNF426_promoter
+TAF1 pd ZNF266_promoter
+TAF1 pd ZNF317_promoter
+TAF1 pd ZNF414_promoter
+TAF1 pd HNRPM_promoter
+TAF1 pd LOC147727_promoter
+TAF1 pd ILF3_promoter
+TAF1 pd QTRT1_promoter
+TAF1 pd ASNA1_promoter
+TAF1 pd TNPO2_promoter
+TAF1 pd FBXW9_promoter
+TAF1 pd DHPS_promoter
+TAF1 pd PTD008_promoter
+TAF1 pd FLJ90396_promoter
+TAF1 pd ZNF490_promoter
+TAF1 pd FLJ14959_promoter
+TAF1 pd SITPEC_promoter
+TAF1 pd PRKCSH_promoter
+TAF1 pd FLJ35119_promoter
+TAF1 pd LDLR_promoter
+TAF1 pd LOC90580_promoter
+TAF1 pd TMED1_promoter
+TAF1 pd RPS28_promoter
+TAF1 pd RPL17_promoter
+TAF1 pd USP36_promoter
+TAF1 pd ZC3H5_promoter
+TAF1 pd H3F3B_promoter
+TAF1 pd GALK1_promoter
+TAF1 pd KIAA0195_promoter
+TAF1 pd GRB2_promoter
+TAF1 pd SLC25A19_promoter
+TAF1 pd MRPS7_promoter
+TAF1 pd GGA3_promoter
+TAF1 pd PCNT1_promoter
+TAF1 pd SUMO2_promoter
+TAF1 pd HN1_promoter
+TAF1 pd ICT1_promoter
+TAF1 pd HUMPPA_promoter
+TAF1 pd FDXR_promoter
+TAF1 pd WBP2_promoter
+TAF1 pd FBF1_promoter
+TAF1 pd ACOX1_promoter
+TAF1 pd PGS1_promoter
+TAF1 pd SOCS3_promoter
+TAF1 pd SEPT9_promoter
+TAF1 pd SEC14L1_promoter
+TAF1 pd SFRS2_promoter
+TAF1 pd ET_promoter
+TAF1 pd PTDSR_promoter
+TAF1 pd MXRA7_promoter
+TAF1 pd SPHK1_promoter
+TAF1 pd PRPSAP1_promoter
+TAF1 pd MGC29814_promoter
+TAF1 pd RNF157_promoter
+TAF1 pd EXOC7_promoter
+TAF1 pd SRP68_promoter
+TAF1 pd SLC9A3R1_promoter
+TAF1 pd CDC42EP4_promoter
+TAF1 pd POLG2_promoter
+TAF1 pd HT008_promoter
+TAF1 pd ERN1_promoter
+TAF1 pd FTSJ3_promoter
+TAF1 pd DDX42_promoter
+TAF1 pd GK001_promoter
+TAF1 pd LYK5_promoter
+TAF1 pd LOC51204_promoter
+TAF1 pd WDR68_promoter
+TAF1 pd TLK2_promoter
+TAF1 pd FLJ12760_promoter
+TAF1 pd THRAP1_promoter
+TAF1 pd KIAA1287_promoter
+TAF1 pd BRIP1_promoter
+TAF1 pd DDX5_promoter
+TAF1 pd LOC90799_promoter
+TAF1 pd SMURF2_promoter
+TAF1 pd FLJ14775_promoter
+TAF1 pd COG1_promoter
+TAF1 pd SOX9_promoter
+TAF1 pd KCNJ2_promoter
+TAF1 pd FLJ36644_promoter
+TAF1 pd PRKAR1A_promoter
+TAF1 pd WIPI49_promoter
+TAF1 pd AMZ2_promoter
+TAF1 pd KPNA2_promoter
+TAF1 pd LOC284018_promoter
+TAF1 pd FALZ_promoter
+TAF1 pd PSMD12_promoter
+TAF1 pd FLJ32065_promoter
+TAF1 pd LOC440456_promoter
+TAF1 pd TBX2_promoter
+TAF1 pd FLJ20753_promoter
+TAF1 pd BC022357_promoter
+TAF1 pd LOC284242_promoter
+TAF1 pd ZNF521_promoter
+TAF1 pd OSBPL1A_promoter
+TAF1 pd CABYR_promoter
+TAF1 pd C18orf17_promoter
+TAF1 pd NPC1_promoter
+TAF1 pd RIOK3_promoter
+TAF1 pd C18orf45_promoter
+TAF1 pd GATA6_promoter
+TAF1 pd MIB1_promoter
+TAF1 pd SNRPD1_promoter
+TAF1 pd ESCO1_promoter
+TAF1 pd ROCK1_promoter
+TAF1 pd RNMT_promoter
+TAF1 pd KIAA1012_promoter
+TAF1 pd MAPRE2_promoter
+TAF1 pd ZNF397_promoter
+TAF1 pd KIAA0427_promoter
+TAF1 pd IER3IP1_promoter
+TAF1 pd HDHD2_promoter
+TAF1 pd C18orf25_promoter
+TAF1 pd CCDC5_promoter
+TAF1 pd ATP5A1_promoter
+TAF1 pd PIK3C3_promoter
+TAF1 pd C18orf10_promoter
+TAF1 pd STATIP1_promoter
+TAF1 pd SLC39A6_promoter
+TAF1 pd P15RS_promoter
+TAF1 pd C18orf37_promoter
+TAF1 pd ZNF24_promoter
+TAF1 pd ZNF271_promoter
+TAF1 pd C18orf19_promoter
+TAF1 pd Cep192_promoter
+TAF1 pd KNTC2_promoter
+TAF1 pd METTL4_promoter
+TAF1 pd YES1_promoter
+TAF1 pd C18orf56_promoter
+TAF1 pd COLEC12_promoter
+TAF1 pd USP14_promoter
+TAF1 pd NARF_promoter
+TAF1 pd CSNK1D_promoter
+TAF1 pd P4HB_promoter
+TAF1 pd HGS_promoter
+TAF1 pd LOC339231_promoter
+TAF1 pd ACTG1_promoter
+TAF1 pd raptor_promoter
+TAF1 pd FLJ35220_promoter
+TAF1 pd MRCL3_promoter
+TAF1 pd MRLC2_promoter
+TAF1 pd TGIF_promoter
+TAF1 pd SEH1L_promoter
+TAF1 pd PTPN2_promoter
+TAF1 pd TNFSF5IP1_promoter
+TAF1 pd AFG3L2_promoter
+TAF1 pd TUBB6_promoter
+TAF1 pd CHMP1B_promoter
+TAF1 pd GNAL_promoter
+TAF1 pd VAPA_promoter
+TAF1 pd PPP4R1_promoter
+TAF1 pd RALBP1_promoter
+TAF1 pd ANKRD12_promoter
+TAF1 pd C18orf18_promoter
+TAF1 pd LOC339290_promoter
+TAF1 pd MGC11082_promoter
+TAF1 pd DDX48_promoter
+TAF1 pd LAPTM4A_promoter
+TAF1 pd DDEF2_promoter
+TAF1 pd OACT2_promoter
+TAF1 pd KIDINS220_promoter
+TAF1 pd ID2_promoter
+TAF1 pd SOX11_promoter
+TAF1 pd MTCBP-1_promoter
+TAF1 pd TTC15_promoter
+TAF1 pd TSSC1_promoter
+TAF1 pd RNASEH1_promoter
+TAF1 pd PXDN_promoter
+TAF1 pd TMEM18_promoter
+TAF1 pd ACP1_promoter
+TAF1 pd ZNF499_promoter
+TAF1 pd ZNF584_promoter
+TAF1 pd CPSF3_promoter
+TAF1 pd ADAM17_promoter
+TAF1 pd YWHAQ_promoter
+TAF1 pd WDR35_promoter
+TAF1 pd LOC130502_promoter
+TAF1 pd OSR1_promoter
+TAF1 pd RDH14_promoter
+TAF1 pd LOC284952_promoter
+TAF1 pd SMC6L1_promoter
+TAF1 pd NAG_promoter
+TAF1 pd TRIB2_promoter
+TAF1 pd LPIN1_promoter
+TAF1 pd E2F6_promoter
+TAF1 pd ROCK2_promoter
+TAF1 pd PQLC3_promoter
+TAF1 pd NOL10_promoter
+TAF1 pd RRM2_promoter
+TAF1 pd RPS5_promoter
+TAF1 pd ZNF274_promoter
+TAF1 pd EPN1_promoter
+TAF1 pd FLJ14768_promoter
+TAF1 pd ISOC2_promoter
+TAF1 pd RPL28_promoter
+TAF1 pd LENG9_promoter
+TAF1 pd LENG8_promoter
+TAF1 pd RPS9_promoter
+TAF1 pd LENG1_promoter
+TAF1 pd CNOT3_promoter
+TAF1 pd PRPF31_promoter
+TAF1 pd NDUFA3_promoter
+TAF1 pd MYADM_promoter
+TAF1 pd LOC91661_promoter
+TAF1 pd ZNF677_promoter
+TAF1 pd ZNF542_promoter
+TAF1 pd MGC9913_promoter
+TAF1 pd ZNF264_promoter
+TAF1 pd ZNF329_promoter
+TAF1 pd ZNF256_promoter
+TAF1 pd ZNF417_promoter
+TAF1 pd ZNF587_promoter
+TAF1 pd FLJ38288_promoter
+TAF1 pd ZNF551_promoter
+TAF1 pd ZIK1_promoter
+TAF1 pd ZNF550_promoter
+TAF1 pd MGC4728_promoter
+TAF1 pd FLJ16360_promoter
+TAF1 pd ZNF548_promoter
+TAF1 pd SEDLP_promoter
+TAF1 pd ZNF304_promoter
+TAF1 pd ZNF272_promoter
+TAF1 pd ZNF665_promoter
+TAF1 pd PUM2_promoter
+TAF1 pd HNRPLL_promoter
+TAF1 pd SPAST_promoter
+TAF1 pd LOC84661_promoter
+TAF1 pd C2orf4_promoter
+TAF1 pd EHD3_promoter
+TAF1 pd LYCAT_promoter
+TAF1 pd LBH_promoter
+TAF1 pd YPEL5_promoter
+TAF1 pd RSNL2_promoter
+TAF1 pd WDR43_promoter
+TAF1 pd FLJ20628_promoter
+TAF1 pd PPP1CB_promoter
+TAF1 pd FLJ31356_promoter
+TAF1 pd FOSL2_promoter
+TAF1 pd BRE_promoter
+TAF1 pd SLC30A6_promoter
+TAF1 pd YIPF4_promoter
+TAF1 pd BIRC6_promoter
+TAF1 pd ARL6IP2_promoter
+TAF1 pd FAM82A_promoter
+TAF1 pd CDC42EP3_promoter
+TAF1 pd PRO1853_promoter
+TAF1 pd CEBPZ_promoter
+TAF1 pd SULT6B1_promoter
+TAF1 pd EIF2AK2_promoter
+TAF1 pd KIAA1414_promoter
+TAF1 pd STRN_promoter
+TAF1 pd CRIM1_promoter
+TAF1 pd DKFZP564F0522_promoter
+TAF1 pd RASGRP3_promoter
+TAF1 pd LTBP1_promoter
+TAF1 pd FLJ20272_promoter
+TAF1 pd RBKS_promoter
+TAF1 pd MRPL33_promoter
+TAF1 pd HADHB_promoter
+TAF1 pd HADHA_promoter
+TAF1 pd RAB10_promoter
+TAF1 pd KIF3C_promoter
+TAF1 pd ASXL2_promoter
+TAF1 pd RBJ_promoter
+TAF1 pd MGC11266_promoter
+TAF1 pd TP53I3_promoter
+TAF1 pd SF3B14_promoter
+TAF1 pd FLJ21945_promoter
+TAF1 pd UBXD4_promoter
+TAF1 pd KIAA1240_promoter
+TAF1 pd FLJ21820_promoter
+TAF1 pd HS1BP3_promoter
+TAF1 pd C2orf18_promoter
+TAF1 pd CENPA_promoter
+TAF1 pd FLJ20254_promoter
+TAF1 pd SLC4A1AP_promoter
+TAF1 pd XAB1_promoter
+TAF1 pd FLJ13646_promoter
+TAF1 pd ZNF512_promoter
+TAF1 pd PPM1G_promoter
+TAF1 pd ZNF513_promoter
+TAF1 pd SNX17_promoter
+TAF1 pd EIF2B4_promoter
+TAF1 pd GTF3C2_promoter
+TAF1 pd MPV17_promoter
+TAF1 pd CAD_promoter
+TAF1 pd C2orf28_promoter
+TAF1 pd EMILIN1_promoter
+TAF1 pd FLJ21839_promoter
+TAF1 pd RHOB_promoter
+TAF1 pd ZNF347_promoter
+TAF1 pd ZNF224_promoter
+TAF1 pd SNRPA_promoter
+TAF1 pd FLJ41131_promoter
+TAF1 pd ADCK4_promoter
+TAF1 pd LTBP4_promoter
+TAF1 pd SERTAD3_promoter
+TAF1 pd LOC284323_promoter
+TAF1 pd ZNF546_promoter
+TAF1 pd PSMC4_promoter
+TAF1 pd CRI2_promoter
+TAF1 pd TIMM50_promoter
+TAF1 pd SUPT5H_promoter
+TAF1 pd RPS16_promoter
+TAF1 pd IXL_promoter
+TAF1 pd FLJ10211_promoter
+TAF1 pd RAB4B_promoter
+TAF1 pd EGLN2_promoter
+TAF1 pd HNRPUL1_promoter
+TAF1 pd ZNF223_promoter
+TAF1 pd ZNF222_promoter
+TAF1 pd ZNF155_promoter
+TAF1 pd ZNF221_promoter
+TAF1 pd FLJ12886_promoter
+TAF1 pd ZNF576_promoter
+TAF1 pd IRGQ1_promoter
+TAF1 pd RABAC1_promoter
+TAF1 pd ARHGEF1_promoter
+TAF1 pd RPS19_promoter
+TAF1 pd FLJ10241_promoter
+TAF1 pd BCKDHA_promoter
+TAF1 pd EXOSC5_promoter
+TAF1 pd MGC20255_promoter
+TAF1 pd PAK4_promoter
+TAF1 pd MRPS12_promoter
+TAF1 pd ZNF565_promoter
+TAF1 pd CAPNS1_promoter
+TAF1 pd POLR2I_promoter
+TAF1 pd THAP8_promoter
+TAF1 pd MGC15677_promoter
+TAF1 pd LOC148137_promoter
+TAF1 pd COX6B1_promoter
+TAF1 pd KIAA0841_promoter
+TAF1 pd ZNF181_promoter
+TAF1 pd ZNF302_promoter
+TAF1 pd UBA2_promoter
+TAF1 pd FAM61A_promoter
+TAF1 pd PEPD_promoter
+TAF1 pd MGC32020_promoter
+TAF1 pd ZNF146_promoter
+TAF1 pd ZNF566_promoter
+TAF1 pd ZFP260_promoter
+TAF1 pd SARS2_promoter
+TAF1 pd ECH1_promoter
+TAF1 pd ACTN4_promoter
+TAF1 pd EIF3S12_promoter
+TAF1 pd PSMD8_promoter
+TAF1 pd ZNF573_promoter
+TAF1 pd LOC390927_promoter
+TAF1 pd ZNF569_promoter
+TAF1 pd HKR1_promoter
+TAF1 pd ZNF383_promoter
+TAF1 pd ZNF585A_promoter
+TAF1 pd ZNF345_promoter
+TAF1 pd GIOT-1_promoter
+TAF1 pd ZNF529_promoter
+TAF1 pd LOC400684_promoter
+TAF1 pd ZNF225_promoter
+TAF1 pd ZNF160_promoter
+TAF1 pd LOC284361_promoter
+TAF1 pd NUP62_promoter
+TAF1 pd TBC1D17_promoter
+TAF1 pd AKT1S1_promoter
+TAF1 pd PTOV1_promoter
+TAF1 pd FLJ22688_promoter
+TAF1 pd CPT1C_promoter
+TAF1 pd HRMT1L2_promoter
+TAF1 pd SR-A1_promoter
+TAF1 pd RRAS_promoter
+TAF1 pd NOSIP_promoter
+TAF1 pd RPS11_promoter
+TAF1 pd RPL13A_promoter
+TAF1 pd ALDH16A1_promoter
+TAF1 pd ETFB_promoter
+TAF1 pd ZNF175_promoter
+TAF1 pd ZNF577_promoter
+TAF1 pd MGC35402_promoter
+TAF1 pd ZNF611_promoter
+TAF1 pd ZNF701_promoter
+TAF1 pd ZNF528_promoter
+TAF1 pd LOC400713_promoter
+TAF1 pd ZNF610_promoter
+TAF1 pd ZNF480_promoter
+TAF1 pd LOC90321_promoter
+TAF1 pd PPP2R1A_promoter
+TAF1 pd LOC284371_promoter
+TAF1 pd ZNF432_promoter
+TAF1 pd ZNF614_promoter
+TAF1 pd ZNF615_promoter
+TAF1 pd ZNF613_promoter
+TAF1 pd FLJ20643_promoter
+TAF1 pd TEAD2_promoter
+TAF1 pd QPCTL_promoter
+TAF1 pd SNRPD2_promoter
+TAF1 pd VASP_promoter
+TAF1 pd FOSB_promoter
+TAF1 pd ERCC1_promoter
+TAF1 pd BLOC1S3_promoter
+TAF1 pd GEMIN7_promoter
+TAF1 pd SFRS16_promoter
+TAF1 pd RELB_promoter
+TAF1 pd CLPTM1_promoter
+TAF1 pd PVRL2_promoter
+TAF1 pd ZNF229_promoter
+TAF1 pd ZNF228_promoter
+TAF1 pd ZNF226_promoter
+TAF1 pd PPP5C_promoter
+TAF1 pd SLC1A5_promoter
+TAF1 pd C19orf7_promoter
+TAF1 pd SNRP70_promoter
+TAF1 pd GYS1_promoter
+TAF1 pd FTL_promoter
+TAF1 pd PPP1R15A_promoter
+TAF1 pd SPHK2_promoter
+TAF1 pd RPL18_promoter
+TAF1 pd PSCD2_promoter
+TAF1 pd FLJ32926_promoter
+TAF1 pd CARD8_promoter
+TAF1 pd PLA2G4C_promoter
+TAF1 pd SEPW1_promoter
+TAF1 pd NAPA_promoter
+TAF1 pd CCDC9_promoter
+TAF1 pd SAE1_promoter
+TAF1 pd ZNF234_promoter
+TAF1 pd ARL2BP_promoter
+TAF1 pd VPS35_promoter
+TAF1 pd SHCBP1_promoter
+TAF1 pd FLJ13868_promoter
+TAF1 pd ARMC5_promoter
+TAF1 pd FUS_promoter
+TAF1 pd MYST1_promoter
+TAF1 pd VKORC1_promoter
+TAF1 pd ZNF668_promoter
+TAF1 pd STX4A_promoter
+TAF1 pd KIAA0339_promoter
+TAF1 pd FBXL19_promoter
+TAF1 pd LOC283932_promoter
+TAF1 pd CTF1_promoter
+TAF1 pd ZNF629_promoter
+TAF1 pd ORC6L_promoter
+TAF1 pd DNAJA2_promoter
+TAF1 pd CDA08_promoter
+TAF1 pd KIAA1972_promoter
+TAF1 pd NIP30_promoter
+TAF1 pd HERPUD1_promoter
+TAF1 pd MT1X_promoter
+TAF1 pd MT1E_promoter
+TAF1 pd MT2A_promoter
+TAF1 pd FLJ10826_promoter
+TAF1 pd NUDT21_promoter
+TAF1 pd MMP2_promoter
+TAF1 pd FTO_promoter
+TAF1 pd RBL2_promoter
+TAF1 pd CHD9_promoter
+TAF1 pd SIAH1_promoter
+TAF1 pd PHKB_promoter
+TAF1 pd RNF40_promoter
+TAF1 pd LOC90835_promoter
+TAF1 pd KIF22_promoter
+TAF1 pd LAT1-3TM_promoter
+TAF1 pd GIYD2_promoter
+TAF1 pd SPIN1_promoter
+TAF1 pd RABEP2_promoter
+TAF1 pd SH2B_promoter
+TAF1 pd ATXN2L_promoter
+TAF1 pd EIF3S8_promoter
+TAF1 pd CLN3_promoter
+TAF1 pd P8_promoter
+TAF1 pd LOC112869_promoter
+TAF1 pd FLJ13798_promoter
+TAF1 pd ZNF694_promoter
+TAF1 pd LCMT1_promoter
+TAF1 pd LOC440356_promoter
+TAF1 pd LOC124446_promoter
+TAF1 pd HIRIP3_promoter
+TAF1 pd PHKG2_promoter
+TAF1 pd SRCAP_promoter
+TAF1 pd FBS1_promoter
+TAF1 pd MGC3121_promoter
+TAF1 pd ZNF689_promoter
+TAF1 pd FLJ32130_promoter
+TAF1 pd ZNF688_promoter
+TAF1 pd MGC13138_promoter
+TAF1 pd MGC2474_promoter
+TAF1 pd SEPHS2_promoter
+TAF1 pd ZNF553_promoter
+TAF1 pd CD2BP2_promoter
+TAF1 pd BOLA2_promoter
+TAF1 pd ALDOA_promoter
+TAF1 pd ARHGAP17_promoter
+TAF1 pd CIAPIN1_promoter
+TAF1 pd OKL38_promoter
+TAF1 pd ATBF1_promoter
+TAF1 pd DHX38_promoter
+TAF1 pd TXNL4B_promoter
+TAF1 pd KIAA0174_promoter
+TAF1 pd AP1G1_promoter
+TAF1 pd ZNF19_promoter
+TAF1 pd ZNF23_promoter
+TAF1 pd FLJ11171_promoter
+TAF1 pd SF3B3_promoter
+TAF1 pd COG4_promoter
+TAF1 pd DDX19A_promoter
+TAF1 pd DDX19B_promoter
+TAF1 pd AARS_promoter
+TAF1 pd PDPR_promoter
+TAF1 pd PSMD7_promoter
+TAF1 pd LOC283922_promoter
+TAF1 pd GLG1_promoter
+TAF1 pd CDH13_promoter
+TAF1 pd MPHOSPH6_promoter
+TAF1 pd CMIP_promoter
+TAF1 pd ASCIZ_promoter
+TAF1 pd BM039_promoter
+TAF1 pd DC13_promoter
+TAF1 pd WWOX_promoter
+TAF1 pd MON1B_promoter
+TAF1 pd TERF2IP_promoter
+TAF1 pd KARS_promoter
+TAF1 pd ADAT1_promoter
+TAF1 pd CFDP1_promoter
+TAF1 pd BCAR1_promoter
+TAF1 pd RFWD3_promoter
+TAF1 pd LOC283970_promoter
+TAF1 pd NOB1P_promoter
+TAF1 pd ACD_promoter
+TAF1 pd CTCF_promoter
+TAF1 pd ATP6V0D1_promoter
+TAF1 pd FHOD1_promoter
+TAF1 pd MGC4655_promoter
+TAF1 pd CBFB_promoter
+TAF1 pd CKLF_promoter
+TAF1 pd CDH11_promoter
+TAF1 pd FLJ10815_promoter
+TAF1 pd CNOT1_promoter
+TAF1 pd FLJ13912_promoter
+TAF1 pd GTL3_promoter
+TAF1 pd KIFC3_promoter
+TAF1 pd KATNB1_promoter
+TAF1 pd MGC11335_promoter
+TAF1 pd RANBP10_promoter
+TAF1 pd TSNAXIP1_promoter
+TAF1 pd NQO1_promoter
+TAF1 pd CYB5-M_promoter
+TAF1 pd CGI-37_promoter
+TAF1 pd COG8_promoter
+TAF1 pd SNTB2_promoter
+TAF1 pd FLJ12688_promoter
+TAF1 pd SLC7A6OS_promoter
+TAF1 pd SLC7A6_promoter
+TAF1 pd LYPLA3_promoter
+TAF1 pd FLJ21918_promoter
+TAF1 pd DDX28_promoter
+TAF1 pd PSMB10_promoter
+TAF1 pd RCD-8_promoter
+TAF1 pd FLJ13111_promoter
+TAF1 pd POLR2C_promoter
+TAF1 pd RBBP6_promoter
+TAF1 pd WDTC2_promoter
+TAF1 pd ASB7_promoter
+TAF1 pd LINS1_promoter
+TAF1 pd LRRC28_promoter
+TAF1 pd TTC23_promoter
+TAF1 pd IGF1R_promoter
+TAF1 pd NR2F2_promoter
+TAF1 pd MCTP2_promoter
+TAF1 pd VPS33B_promoter
+TAF1 pd SMAP-1_promoter
+TAF1 pd BLM_promoter
+TAF1 pd NGRN_promoter
+TAF1 pd AP3S2_promoter
+TAF1 pd LOC254571_promoter
+TAF1 pd POLG_promoter
+TAF1 pd CHSY1_promoter
+TAF1 pd SELS_promoter
+TAF1 pd SNRPA1_promoter
+TAF1 pd C16orf30_promoter
+TAF1 pd KIAA0683_promoter
+TAF1 pd UBE2I_promoter
+TAF1 pd CHTF18_promoter
+TAF1 pd WDR24_promoter
+TAF1 pd RHOT2_promoter
+TAF1 pd MGC13114_promoter
+TAF1 pd SOLH_promoter
+TAF1 pd TMEM8_promoter
+TAF1 pd C16orf9_promoter
+TAF1 pd LUC7L_promoter
+TAF1 pd LOC349338_promoter
+TAF1 pd TARSL2_promoter
+TAF1 pd TM2D3_promoter
+TAF1 pd FLJ10719_promoter
+TAF1 pd ABHD2_promoter
+TAF1 pd RKHD3_promoter
+TAF1 pd STARD5_promoter
+TAF1 pd MESDC2_promoter
+TAF1 pd KIAA1199_promoter
+TAF1 pd FAH_promoter
+TAF1 pd ZA20D3_promoter
+TAF1 pd LOC283687_promoter
+TAF1 pd MTHFS_promoter
+TAF1 pd TMED3_promoter
+TAF1 pd MORF4L1_promoter
+TAF1 pd PSMA4_promoter
+TAF1 pd WDR61_promoter
+TAF1 pd KIAA1055_promoter
+TAF1 pd HMG20A_promoter
+TAF1 pd EFTUD1_promoter
+TAF1 pd LOC388152_promoter
+TAF1 pd RPS17_promoter
+TAF1 pd MFGE8_promoter
+TAF1 pd ISG20_promoter
+TAF1 pd ISG20L1_promoter
+TAF1 pd ZNF592_promoter
+TAF1 pd SEC11L1_promoter
+TAF1 pd WDR73_promoter
+TAF1 pd ZSCAN2_promoter
+TAF1 pd FLJ43276_promoter
+TAF1 pd BNC1_promoter
+TAF1 pd HDGFRP3_promoter
+TAF1 pd BTBD1_promoter
+TAF1 pd MGC29937_promoter
+TAF1 pd MGC2560_promoter
+TAF1 pd KIAA1971_promoter
+TAF1 pd TSPAN3_promoter
+TAF1 pd FAHD1_promoter
+TAF1 pd DCTN5_promoter
+TAF1 pd RPS15A_promoter
+TAF1 pd FLJ31153_promoter
+TAF1 pd RRN3_promoter
+TAF1 pd KIAA0251_promoter
+TAF1 pd BFAR_promoter
+TAF1 pd ERCC4_promoter
+TAF1 pd FLJ11151_promoter
+TAF1 pd GSPT1_promoter
+TAF1 pd RSL1D1_promoter
+TAF1 pd ZC3H7A_promoter
+TAF1 pd SOCS1_promoter
+TAF1 pd KIAA0350_promoter
+TAF1 pd NUBP1_promoter
+TAF1 pd PRO0149_promoter
+TAF1 pd ARL6IP_promoter
+TAF1 pd SMG1_promoter
+TAF1 pd COQ7_promoter
+TAF1 pd FLJ21816_promoter
+TAF1 pd NDUFAB1_promoter
+TAF1 pd COG7_promoter
+TAF1 pd LOC440346_promoter
+TAF1 pd CDR2_promoter
+TAF1 pd UQCRC2_promoter
+TAF1 pd DREV1_promoter
+TAF1 pd IMAA_promoter
+TAF1 pd FLJ41766_promoter
+TAF1 pd MGC16943_promoter
+TAF1 pd THUMPD1_promoter
+TAF1 pd MGC35048_promoter
+TAF1 pd MGC16824_promoter
+TAF1 pd MIR16_promoter
+TAF1 pd CARHSP1_promoter
+TAF1 pd PMM2_promoter
+TAF1 pd TNFRSF12A_promoter
+TAF1 pd PKMYT1_promoter
+TAF1 pd TCEB2_promoter
+TAF1 pd SRRM2_promoter
+TAF1 pd KCTD5_promoter
+TAF1 pd FLJ39075_promoter
+TAF1 pd RNPS1_promoter
+TAF1 pd DCI_promoter
+TAF1 pd E4F1_promoter
+TAF1 pd TRAF7_promoter
+TAF1 pd RNU60_promoter
+TAF1 pd PKD1_promoter
+TAF1 pd TBL3_promoter
+TAF1 pd RPS2_promoter
+TAF1 pd HCFC1R1_promoter
+TAF1 pd ZNF213_promoter
+TAF1 pd ZNF200_promoter
+TAF1 pd MGC2654_promoter
+TAF1 pd SB153_promoter
+TAF1 pd ALG1_promoter
+TAF1 pd N-PAC_promoter
+TAF1 pd ZNF500_promoter
+TAF1 pd LOC146562_promoter
+TAF1 pd LOC124402_promoter
+TAF1 pd DNAJA3_promoter
+TAF1 pd ADCY9_promoter
+TAF1 pd TRAP1_promoter
+TAF1 pd FLJ14154_promoter
+TAF1 pd ZNF597_promoter
+TAF1 pd ZNF263_promoter
+TAF1 pd FLJ39639_promoter
+TAF1 pd SEPX1_promoter
+TAF1 pd FZD2_promoter
+TAF1 pd COASY_promoter
+TAF1 pd HSD17B1_promoter
+TAF1 pd ATP6V0A1_promoter
+TAF1 pd PTRF_promoter
+TAF1 pd STAT3_promoter
+TAF1 pd RAB5C_promoter
+TAF1 pd NKIRAS2_promoter
+TAF1 pd DNAJC7_promoter
+TAF1 pd DKFZP434H0115_promoter
+TAF1 pd ACLY_promoter
+TAF1 pd KLHL11_promoter
+TAF1 pd FKBP10_promoter
+TAF1 pd HAP1_promoter
+TAF1 pd SUI1_promoter
+TAF1 pd TBPIP_promoter
+TAF1 pd LOC162427_promoter
+TAF1 pd VPS25_promoter
+TAF1 pd KIAA0553_promoter
+TAF1 pd GRN_promoter
+TAF1 pd DKFZp762C2414_promoter
+TAF1 pd MGC3130_promoter
+TAF1 pd HDAC5_promoter
+TAF1 pd G6PC3_promoter
+TAF1 pd DHX8_promoter
+TAF1 pd ARF4L_promoter
+TAF1 pd MGC20235_promoter
+TAF1 pd NBR1_promoter
+TAF1 pd RPL27_promoter
+TAF1 pd PSME3_promoter
+TAF1 pd BECN1_promoter
+TAF1 pd HSPC009_promoter
+TAF1 pd SMARCE1_promoter
+TAF1 pd TOP2A_promoter
+TAF1 pd PSMB3_promoter
+TAF1 pd SOCS7_promoter
+TAF1 pd MRPL45_promoter
+TAF1 pd DDX52_promoter
+TAF1 pd AP1GBP1_promoter
+TAF1 pd AATF_promoter
+TAF1 pd FLJ22578_promoter
+TAF1 pd ZNF403_promoter
+TAF1 pd DKFZp564H213_promoter
+TAF1 pd PIGW_promoter
+TAF1 pd TAF15_promoter
+TAF1 pd AP2B1_promoter
+TAF1 pd PEX12_promoter
+TAF1 pd FLJ10260_promoter
+TAF1 pd PIP5K2B_promoter
+TAF1 pd FLJ20291_promoter
+TAF1 pd RPL23_promoter
+TAF1 pd RARA_promoter
+TAF1 pd CDC6_promoter
+TAF1 pd CASC3_promoter
+TAF1 pd LOC339287_promoter
+TAF1 pd NR1D1_promoter
+TAF1 pd THRAP4_promoter
+TAF1 pd PSMD3_promoter
+TAF1 pd ORMDL3_promoter
+TAF1 pd ERBB2_promoter
+TAF1 pd STARD3_promoter
+TAF1 pd CRK7_promoter
+TAF1 pd PPARBP_promoter
+TAF1 pd RPL19_promoter
+TAF1 pd LASP1_promoter
+TAF1 pd FLJ34922_promoter
+TAF1 pd FLJ31795_promoter
+TAF1 pd PPM1D_promoter
+TAF1 pd MRPS23_promoter
+TAF1 pd AKAP1_promoter
+TAF1 pd WDR50_promoter
+TAF1 pd NME2_promoter
+TAF1 pd NME1_promoter
+TAF1 pd SPAG9_promoter
+TAF1 pd TOB1_promoter
+TAF1 pd CROP_promoter
+TAF1 pd ANKRD40_promoter
+TAF1 pd SFRS1_promoter
+TAF1 pd FLJ20345_promoter
+TAF1 pd SUPT4H1_promoter
+TAF1 pd APPBP2_promoter
+TAF1 pd USP32_promoter
+TAF1 pd ABC1_promoter
+TAF1 pd LOC51136_promoter
+TAF1 pd RPS6KB1_promoter
+TAF1 pd TMEM49_promoter
+TAF1 pd BIT1_promoter
+TAF1 pd CLTC_promoter
+TAF1 pd DHX40_promoter
+TAF1 pd FLJ10587_promoter
+TAF1 pd FLJ11029_promoter
+TAF1 pd FAM33A_promoter
+TAF1 pd TRIM37_promoter
+TAF1 pd MTMR4_promoter
+TAF1 pd PRO1855_promoter
+TAF1 pd MRPL27_promoter
+TAF1 pd CDK5RAP3_promoter
+TAF1 pd SP2_promoter
+TAF1 pd MRPL10_promoter
+TAF1 pd OSBPL7_promoter
+TAF1 pd KPNB1_promoter
+TAF1 pd CDC27_promoter
+TAF1 pd GOSR2_promoter
+TAF1 pd NSF_promoter
+TAF1 pd LOC51326_promoter
+TAF1 pd LOC284058_promoter
+TAF1 pd HEXIM1_promoter
+LEF1 pp Nrarp
+Unknown interactsWith FLJ31741
+Unknown interactsWith KIAA0889
+Unknown interactsWith USP9X
+Unknown interactsWith PPP2R1A
+Unknown interactsWith C6orf69
+Unknown interactsWith KIAA0802
+Unknown interactsWith ARHGEF2
+Unknown interactsWith CYFIP2
+Unknown interactsWith Gamma-TUBULIN
+Unknown interactsWith KIAA1771
+Unknown interactsWith PNMA1
+Unknown interactsWith CYFIP1
+Unknown interactsWith MARK1
+Unknown interactsWith KIF23
+Unknown interactsWith PNMA2
+Unknown interactsWith RNF41
+Unknown interactsWith TIAF1
+Unknown interactsWith MYBBP1a
+Unknown interactsWith FLJ20643
+Unknown interactsWith LLGL2
+Unknown interactsWith PKC-zeta
+Unknown interactsWith C20ORF126
+Unknown interactsWith FLJ21908_("mSPAGHETTI")
+Unknown interactsWith LGL1
+Unknown interactsWith CYFIP1
+Unknown interactsWith USP7
+Unknown interactsWith KIAA1771
+Unknown interactsWith LOC342684
+Unknown interactsWith PNMA2
+Unknown interactsWith Gamma-TUBULIN
+Unknown interactsWith BRG1/SMARCA4
+Unknown interactsWith PPP2CB
+Unknown interactsWith AN11
+Unknown interactsWith MARK2
+MARK4 interactsWith Unknown
+LKB1 interactsWith Unknown
+14-3-3-zeta interactsWith Unknown
+14-3-3-eta interactsWith Unknown
+Par-3 interactsWith Unknown
+Par-6A interactsWith Unknown
+Par-6B interactsWith Unknown
+Unknown interactsWith MARK3
+Unknown interactsWith Par-6A
+Unknown interactsWith similar_to_PNMA3
+Unknown interactsWith FLJ10781
+Unknown interactsWith DBC-1
+Unknown interactsWith PNMA2
+Unknown interactsWith Hensin
+Unknown interactsWith Par-6C
+Unknown interactsWith LLGL2
+Unknown interactsWith LGL1
+Unknown interactsWith PKC-zeta
+PNMA1 interactsWith Unknown
+PKC-lambda interactsWith Unknown
+Par-6C interactsWith Unknown
+Unknown interactsWith SUGT1
+Par-3 pp Par-6A
+MARK4 pp PNMA1
+14-3-3-zeta pp Par-3
+PNMA1 pp PKC-lambda
+Unknown interactsWith LGL1
+Unknown interactsWith PNMA2
+Unknown interactsWith LOC55580
+Unknown interactsWith HOJ-1
+Unknown interactsWith AN11
+Unknown interactsWith Myosin_X
+Unknown interactsWith PDZ-GEF
+Unknown interactsWith NIPSNAP1
+Unknown interactsWith CDC37
+Unknown interactsWith LLGL2
+Unknown interactsWith HSP90alpha
+MARK4 pp CDC42
+MARK4 pp PKC-lambda
+14-3-3-eta pp PKC-lambda
+Par-3 pp Par-6B
+Par-3 pp PKC-lambda
+PKC-lambda pp Par-6A
+PKC-lambda pp Par-6B
+LKB1 pp Mo25
+Par-6A pp CDC42
+Par-6C pp Par-3
+Par-6C pp CDC42
+Par-6C pp PKC-lambda
+PARD6A pp PRKCI
+PNMA1 pp Par-3
+Par-6B pp CDC42
+Par-6A pp MARK2
+Par-6A pp 14-3-3
+14-3-3-eta pp MARK4
+Unknown interactsWith LGL1
+Unknown interactsWith NIPSNAP2
+Unknown interactsWith Gamma-TUBULIN
+Unknown interactsWith CYFIP2
+Unknown interactsWith MARK1
+Unknown interactsWith Par-6C
+Unknown interactsWith Par-6A
+Unknown interactsWith CYFIP1
+Unknown interactsWith Par-3
+Unknown interactsWith Par-6B
+Unknown interactsWith KIF23
+Unknown interactsWith KIAA1771
+Unknown interactsWith HOJ-1
+Unknown interactsWith ARHGEF2
+Unknown interactsWith MARK3
+Unknown interactsWith MARK2
+Unknown interactsWith LOC55580
+Unknown interactsWith LGL1
+Unknown interactsWith PKC-zeta
+Unknown interactsWith SQSTM1
+Unknown interactsWith BRG1/SMARCA4
+Unknown interactsWith SMARCC1
+Unknown interactsWith KIF23
+Unknown interactsWith LIMS1/PINCH
+Unknown interactsWith USP11
+Unknown interactsWith FLJ21908_("mSPAGHETTI")
+Unknown interactsWith FKBP51
+Unknown interactsWith HSP90beta
+Unknown interactsWith CDC37
+Unknown interactsWith STRADa
+Unknown interactsWith HSP90alpha
+Unknown interactsWith Par-6B
+Unknown interactsWith LLGL2
+Unknown interactsWith AN11
+CDK1 pp NIFK
+KLF4 pd PE21
+AUF1 interactsWith CSF2_mRNA
+Pin1 interactsWith Unknown
+Pin1 pp p40
+Pin1 pp p45
+Unknown interactsWith p37
+Unknown interactsWith p42
+hnRNP_C interactsWith CSF2_mRNA
+Breakpoint_Cluster_Region_Protein pp Breakpoint_Cluster_Region_Protein
+Breakpoint_Cluster_Region_Protein pp Breakpoint_Cluster_Region_Protein
+Breakpoint_Cluster_Region_Protein pp Breakpoint_Cluster_Region_Protein
+Breakpoint_Cluster_Region_Protein pp Breakpoint_Cluster_Region_Protein
+Breakpoint_Cluster_Region_Protein pp Breakpoint_Cluster_Region_Protein
+Breakpoint_Cluster_Region_Protein pp Breakpoint_Cluster_Region_Protein
+Adp-Ribosylation_Factor_Binding_Protein_Gga2 pp Adp-Ribosylation_Factor_Binding_Protein_Gga2
+Vascular_Endothelial_Growth_Factor pp Fab_Fragment
+Light_Chain_Of_Neutralizing_Antibody pp Vascular_Endothelial_Growth_Factor
+FLT1 pp Vascular_Endothelial_Growth_Factor
+FLT1 pp Vascular_Endothelial_Growth_Factor
+FLT1 pp Vascular_Endothelial_Growth_Factor
+FLT1 pp Vascular_Endothelial_Growth_Factor
+FLT1 pp Vascular_Endothelial_Growth_Factor
+FLT1 pp Vascular_Endothelial_Growth_Factor
+FLT1 pp Vascular_Endothelial_Growth_Factor
+FLT1 pp Vascular_Endothelial_Growth_Factor
+FLT1 pp Vascular_Endothelial_Growth_Factor
+Vascular_Endothelial_Growth_Factor pp Vascular_Endothelial_Growth_Factor
+Vascular_Endothelial_Growth_Factor pp Vascular_Endothelial_Growth_Factor
+Vascular_Endothelial_Growth_Factor pp Vascular_Endothelial_Growth_Factor
+Vascular_Endothelial_Growth_Factor pp Vascular_Endothelial_Growth_Factor
+Vascular_Endothelial_Growth_Factor pp Vascular_Endothelial_Growth_Factor
+Vascular_Endothelial_Growth_Factor pp Vascular_Endothelial_Growth_Factor
+Vascular_Endothelial_Growth_Factor pp Vascular_Endothelial_Growth_Factor
+Vascular_Endothelial_Growth_Factor pp Vascular_Endothelial_Growth_Factor
+Vascular_Endothelial_Growth_Factor pp Vascular_Endothelial_Growth_Factor
+Vascular_Endothelial_Growth_Factor pp Vascular_Endothelial_Growth_Factor
+Vascular_Endothelial_Growth_Factor_A pp Vascular_Endothelial_Growth_Factor_A
+Vascular_Endothelial_Growth_Factor_A pp Vascular_Endothelial_Growth_Factor_A
+Vascular_Endothelial_Growth_Factor_A pp Vascular_Endothelial_Growth_Factor_A
+B3GAT1 pp B3GAT1
+S100A13 pp S100A13
+S100A13 pp S100A13
+S100A13 pp S100A13
+S100A13 pp S100A13
+Ubiquitin pp TOM1
+GSTA1 pp GSTA1
+GSTA1 pp GSTA1
+GSTA1 pp GSTA1
+GSTA1 pp GSTA1
+GSTA1 pp GSTA1
+GSTA1 pp GSTA1
+GSTA1 pp GSTA1
+GSTA1 pp GSTA1
+S100A9 pp S100A8
+S100A9 pp S100A8
+S100A9 pp S100A8
+S100A8 pp S100A8
+S100A8 pp S100A8
+F7 pp Blood_Coagulation_Factor_Viia
+T_Cell_Receptor_Beta_Chain pp T_Cell_Receptor_Alpha_Chain
+T_Cell_Receptor_Beta_Chain pp T_Cell_Receptor_Alpha_Chain
+T_Cell_Receptor_Beta_Chain pp T_Cell_Receptor_Alpha_Chain
+T_Cell_Receptor_Beta_Chain pp T_Cell_Receptor_Alpha_Chain
+T_Cell_Receptor_Alpha_Chain pp HLA-DRA
+T_Cell_Receptor_Beta_Chain pp T_Cell_Receptor_Beta_Chain
+T_Cell_Receptor_Beta_Chain pp HLA-DRA
+T_Cell_Receptor_Beta_Chain pp HLA-DRA
+T_Cell_Receptor_Beta_Chain pp HLA-DRA
+T_Cell_Receptor_Beta_Chain pp HLA-DRA
+T_Cell_Receptor_Beta_Chain pp HLA-DRA
+T_Cell_Receptor_Beta_Chain pp HLA-DRA
+HLA-DRA pp T_Cell_Receptor_Beta_Chain
+HLA-DRA pp T_Cell_Receptor_Beta_Chain
+T_Cell_Receptor_Beta_Chain pp HLA-DRB5
+T_Cell_Receptor_Beta_Chain pp HLA-DRB5
+T_Cell_Receptor_Beta_Chain pp HLA-DRB5
+T_Cell_Receptor_Beta_Chain pp HLA-DRB5
+HLA-DRB5 pp T_Cell_Receptor_Beta_Chain
+HLA-DRB5 pp T_Cell_Receptor_Beta_Chain
+T_Cell_Receptor_Beta_Chain pp HLA-DRB5
+T_Cell_Receptor_Beta_Chain pp HLA-DRB5
+T_Cell_Receptor_Beta_Chain pp HLA-DRB5
+T_Cell_Receptor_Beta_Chain pp HLA-DRB5
+HLA-DRB5 pp T_Cell_Receptor_Alpha_Chain
+T_Cell_Receptor_Alpha_Chain pp HLA-DRB5
+T_Cell_Receptor_Alpha_Chain pp HLA-DRB5
+HLA-DRA pp HLA-DRB5
+HLA-DRB5 pp HLA-DRA
+HLA-DRB5 pp HLA-DRA
+HLA-DRB5 pp HLA-DRA
+HLA-DRB5 pp HLA-DRA
+HLA-DRB5 pp HLA-DRA
+HLA-DRB5 pp HLA-DRA
+HLA-DRB5 pp HLA-DRA
+HLA-DRB5 pp HLA-DRA
+HLA-DRA pp HLA-DRA
+HLA-DRA pp HLA-DRA
+Blood_Coagulation_Factor_Viia pp Blood_Coagulation_Factor_Viia
+SUMO3 pp SENP1
+NEDD8 pp Sentrin-Specific_Protease_8
+FLJ20628 pp FLJ20628
+Gmp_Reductase_2 pp Gmp_Reductase_2
+Gmp_Reductase_2 pp Gmp_Reductase_2
+Gmp_Reductase_2 pp Gmp_Reductase_2
+B2M pp Hla_Class_I_Histocompatibility_Antigen,_B-57_Alpha_Chain
+B2M pp Hla_Class_I_Histocompatibility_Antigen,_B-57_Alpha_Chain
+PCBP2 pp PCBP2
+PCBP2 pp PCBP2
+PCBP2 pp PCBP2
+Sf4_T_Cell_Receptor_Beta_Chain pp Sf4_T_Cell_Receptor_Beta_Chain
+T_Cell_Receptor_Beta_Chain pp T_Cell_Receptor_Beta_Chain
+PAPSS2 pp PAPSS2
+DDEFL1 pp DDEFL1
+ME1 pp ME1
+NQO2 pp NQO2
+NQO2 pp NQO2
+NQO2 pp NQO2
+TXN2 pp TXN2
+C11orf30 pp C11orf30
+C11orf30 pp C11orf30
+CD2BP2 pp TXNL4A
+SAT2 pp SAT2
+SERPINC1 pp SERPINC1
+SERPINC1 pp SERPINC1
+SERPINC1 pp SERPINC1
+SERPINC1 pp SERPINC1
+SERPINC1 pp SERPINC1
+SERPINC1 pp SERPINC1
+SERPINC1 pp SERPINC1
+SERPINC1 pp SERPINC1
+SERPINC1 pp SERPINC1
+SERPINC1 pp SERPINC1
+Dynein_Light_Chain_2a pp Dynein_Light_Chain_2a
+DIRAS2 pp DIRAS2
+ADAR pp ADAR
+ADAR pp ADAR
+Sb27_T_Cell_Receptor_Alpha_Chain pp Hla-B35_Variant
+Sb27_T_Cell_Receptor_Beta_Chain pp Hla-B35_Variant
+Sb27_T_Cell_Receptor_Beta_Chain pp Hla-B35_Variant
+Sb27_T_Cell_Receptor_Beta_Chain pp Hla-B35_Variant
+Sb27_T_Cell_Receptor_Alpha_Chain pp Hla-B35_Variant
+Sb27_T_Cell_Receptor_Alpha_Chain pp Hla-B35_Variant
+2A9N_I pp 2A9N_H
+2A9N_H pp Anti-Glycoprotein_Vi_Immunoglobulin_Lambda_Light_Chain_Variable_Region_Antibody
+2A9N_I pp Anti-Glycoprotein_Vi_Immunoglobulin_Lambda_Light_Chain_Variable_Region_Antibody
+2A9M_I pp 2A9M_H
+Anti-Glycoprotein_Vi_Immunoglobulin_Lambda_Light_Chain_Variable_Region_Antibody pp 2A9M_H
+2A9M_H pp Anti-Glycoprotein_Vi_Immunoglobulin_Lambda_Light_Chain_Variable_Region_Antibody
+2A9M_I pp Anti-Glycoprotein_Vi_Immunoglobulin_Lambda_Light_Chain_Variable_Region_Antibody
+2A9M_I pp Anti-Glycoprotein_Vi_Immunoglobulin_Lambda_Light_Chain_Variable_Region_Antibody
+Growth_Factor_Receptor-Bound_Protein_14 pp Insulin_Receptor
+GRB14 pp GRB14
+RPS27A pp USP14
+FST pp FST
+FST pp Inhibin_Beta_A_Chain
+FST pp Inhibin_Beta_A_Chain
+FST pp Inhibin_Beta_A_Chain
+FST pp Inhibin_Beta_A_Chain
+Inhibin_Beta_A_Chain pp Inhibin_Beta_A_Chain
+Activin_A pp Activin_A
+YWHAG pp YWHAG
+YWHAG pp YWHAG
+YWHAG pp YWHAG
+YWHAG pp YWHAG
+CKS1B pp SKP2
+CKS1B pp SKP2
+Sb27_T_Cell_Receptor_Beta_Chain pp Sb27_T_Cell_Receptor_Alpha_Chain
+Sb27_T_Cell_Receptor_Beta_Chain pp Sb27_T_Cell_Receptor_Alpha_Chain
+Sb27_T_Cell_Receptor_Beta_Chain pp Sb27_T_Cell_Receptor_Alpha_Chain
+Sb27_T_Cell_Receptor_Beta_Chain pp Sb27_T_Cell_Receptor_Alpha_Chain
+SKP2 pp SKP1A
+SKP2 pp SKP1A
+SKP2 pp SKP1A
+SKP1A pp SKP2
+SKP1A pp SKP2
+SKP1A pp SKP2
+SKP1A pp SKP2
+SKP1A pp SKP2
+Protein_Inhibitor_Of_Activated_Stat2 pp SUMO1
+Hla-B35_Variant pp Hla-B35_Variant
+Hla-B35_Variant pp Hla-B35_Variant
+Hla-B35_Variant pp Hla-B35_Variant
+EIF2AK2 pp EIF2AK2
+EIF2AK2 pp EIF2S1
+PKR pp eIF2-alpha
+Cgmp-Dependent_Protein_Kinase_1,_Alpha_Isozyme pp Cgmp-Dependent_Protein_Kinase_1,_Alpha_Isozyme
+TNFRSF14 pp BTLA
+COMTD1 pp COMTD1
+Small_Gtp_Binding_Protein_Tc10 pp Small_Gtp_Binding_Protein_Tc10
+GRB2 pp GRB2
+GRB2 pp GRB2
+GRB2 pp GRB2
+GRB2 pp GRB2
+GRB2 pp GRB2
+GRB2 pp GRB2
+GRB2 pp GRB2
+GRB2 pp GRB2
+GRB2 pp GRB2
+GRB2 pp GRB2
+GRB2 pp GRB2
+C3 pp C3
+C3 pp C3
+C3 pp C3
+C3 pp C3
+NR1H3 pp RXRA
+NR1H3 pp RXRalpha
+B4GALT1 pp B4GALT1
+B4GALT1 pp B4GALT1
+Tissue_Factor pp Coagulation_Factor_Vii
+CR2 pp C3
+Coagulation_Factor_Vii pp Coagulation_Factor_Vii
+RUNX1T1 pp RUNX1T1
+Hirudin pp F2
+MMP13 pp MMP13
+MMP13 pp MMP13
+MMP13 pp MMP13
+MMP13 pp MMP13
+CASP9 pp CASP9
+CASP9 pp CASP9
+CASP9 pp CASP9
+CASP9 pp CASP9
+CASP9 pp CASP9
+CASP9 pp CASP9
+B2M pp Hla_Class_I_Histocompatibility_Antigen,_B-35_Alpha_Chain
+GSTM2 pp GSTM2
+GSTM2 pp GSTM2
+GSTM2 pp GSTM2
+GSTM2 pp GSTM2
+GSTM2 pp GSTM2
+GSTM2 pp GSTM2
+B2M pp Hla_Class_I_Histocompatibility_Antigen,_B-15_Alpha_Chain
+B2M pp Hla_Class_I_Histocompatibility_Antigen,_B-15_Alpha_Chain
+B2M pp Hla_Class_I_Histocompatibility_Antigen,_A-2_Alpha_Chain
+B2M pp Hla_Class_I_Histocompatibility_Antigen,_A-2_Alpha_Chain
+B2M pp Hla_Class_I_Histocompatibility_Antigen,_A-2_Alpha_Chain
+B2M pp Hla_Class_I_Histocompatibility_Antigen,_A-2_Alpha_Chain
+B2M pp Hla_Class_I_Histocompatibility_Antigen
+B2M pp Hla_Class_I_Histocompatibility_Antigen
+B2M pp HLA-A
+B2M pp HLA-A
+B2M pp HLA-A
+B2M pp HLA-A
+B2M pp HLA-A
+B2M pp HLA-A
+B2M pp HLA-A
+B2M pp HLA-A
+B2M pp HLA-A
+B2M pp HLA-A
+B2M pp HLA-A
+B2M pp HLA-A
+B2M pp HLA-A
+B2M pp HLA-A
+B2M pp HLA-A
+B2M pp HLA-A
+B2M pp HLA-A
+HLA-A pp B2M
+OAT pp OAT
+OAT pp OAT
+OAT pp OAT
+OAT pp OAT
+OAT pp OAT
+OAT pp OAT
+OAT pp OAT
+OAT pp OAT
+OAT pp OAT
+OAT pp OAT
+OAT pp OAT
+F3 pp F7
+F3 pp F7
+F3 pp F7
+F3 pp F7
+F3 pp F7
+F3 pp F7
+F3 pp F7
+F3 pp F7
+F3 pp F7
+B2M pp HLA-A
+B2M pp HLA-A
+TTR pp TTR
+TTR pp TTR
+TTR pp TTR
+TTR pp TTR
+TTR pp TTR
+TTR pp TTR
+TTR pp TTR
+TTR pp TTR
+TTR pp TTR
+TTR pp TTR
+TTR pp TTR
+TTR pp TTR
+TTR pp TTR
+TTR pp TTR
+TTR pp TTR
+TTR pp TTR
+TTR pp TTR
+TTR pp TTR
+TTR pp TTR
+TTR pp TTR
+TTR pp TTR
+TTR pp TTR
+TTR pp TTR
+F7 pp F7
+Methylated-Dna--Protein-Cysteine_Methyltransferase pp Methylated-Dna--Protein-Cysteine_Methyltransferase
+IL10RA pp Interleukin-10
+IL10RA pp IL10
+Acetyl-Coa_Acetyltransferase,_Mitochondrial pp Acetyl-Coa_Acetyltransferase,_Mitochondrial
+Acetyl-Coa_Acetyltransferase,_Mitochondrial pp Acetyl-Coa_Acetyltransferase,_Mitochondrial
+Acetyl-Coa_Acetyltransferase,_Mitochondrial pp Acetyl-Coa_Acetyltransferase,_Mitochondrial
+DECR1 pp DECR1
+DECR1 pp DECR1
+DECR1 pp DECR1
+DECR1 pp DECR1
+DECR1 pp DECR1
+DECR1 pp DECR1
+DECR1 pp DECR1
+DECR1 pp DECR1
+DECR1 pp DECR1
+DECR1 pp DECR1
+DECR1 pp DECR1
+DECR1 pp DECR1
+DECR1 pp DECR1
+DECR1 pp DECR1
+Diamine_Acetyltransferase_1 pp Diamine_Acetyltransferase_1
+Acetyl-Coa_Acetyltransferase,_Mitochondrial pp Acetyl-Coa_Acetyltransferase,_Mitochondrial
+Dna_Repair_Endonuclease_Xpf pp Dna_Excision_Repair_Protein_Ercc-1
+PARN pp PARN
+PARN pp PARN
+The_Glucagon_Receptor_(Gr)_Peptide pp Hla_Class_I_Histocompatibility_Antigen,_B-27_Alpha_Chain
+Mrna_Capping_Enzyme pp Mrna_Capping_Enzyme
+Mrna_Capping_Enzyme pp Mrna_Capping_Enzyme
+Mrna_Capping_Enzyme pp Mrna_Capping_Enzyme
+Glutathione_S-Transferase_Theta_1 pp Glutathione_S-Transferase_Theta_1
+Glutathione_S-Transferase_Theta_1 pp Glutathione_S-Transferase_Theta_1
+PIM1 pp Pimtide
+Ctp_Synthase pp Ctp_Synthase
+Ctp_Synthase pp Ctp_Synthase
+Ctp_Synthase pp Ctp_Synthase
+Ctp_Synthase pp Ctp_Synthase
+Ctp_Synthase pp Ctp_Synthase
+Ctp_Synthase pp Ctp_Synthase
+Ubiquitin-Conjugating_Enzyme_E2_Variant_1 pp Ubiquitin-Conjugating_Enzyme_E2_N
+Ubiquitin-Conjugating_Enzyme_E2_N pp Ubiquitin-Conjugating_Enzyme_E2_N
+Ubiquitin-Conjugating_Enzyme_E2_Variant_1 pp Ubiquitin-Conjugating_Enzyme_E2_N
+Ubiquitin-Conjugating_Enzyme_E2_Variant_1 pp Ubiquitin-Conjugating_Enzyme_E2_Variant_1
+POLR2G pp Dna-Directed_Rna_Polymerase_Ii_16_Kda_Polypeptide
+Ubiquitin-Conjugating_Enzyme_E2_Variant_1 pp Ubiquitin-Conjugating_Enzyme_E2_N
+Alpha-1-Antitrypsin pp Alpha-1-Antitrypsin
+Rho-Associated_Protein_Kinase_1 pp Rho-Associated_Protein_Kinase_1
+Rho-Associated_Protein_Kinase_1 pp Rho-Associated_Protein_Kinase_1
+Rho-Associated_Protein_Kinase_1 pp Rho-Associated_Protein_Kinase_1
+Rho-Associated_Protein_Kinase_1 pp Rho-Associated_Protein_Kinase_1
+14-3-3_Protein_Eta pp 14-3-3_Protein_Eta
+Gmp_Reductase_2 pp Gmp_Reductase_2
+Gmp_Reductase_2 pp Gmp_Reductase_2
+Gmp_Reductase_2 pp Gmp_Reductase_2
+14-3-3_Protein_Eta pp 14-3-3_Protein_Eta
+14-3-3_Protein_Eta pp 14-3-3_Protein_Eta
+14-3-3_Protein_Eta pp 14-3-3_Protein_Eta
+14-3-3_Protein_Eta pp 14-3-3_Protein_Eta
+Hydroxymethylglutaryl-Coa_Lyase,_Mitochondrial pp Hydroxymethylglutaryl-Coa_Lyase,_Mitochondrial
+CAMTA1 pp CAMTA1
+CAMTA1 pp CAMTA1
+CAMTA1 pp CAMTA1
+CDY1 pp CDY1
+CDY1 pp CDY1
+CDY1 pp CDY1
+UHRF1 pp UHRF1
+Fab_Fragment,_Light_Chain pp Fab_Fragment,_Heavy_Chain
+Fab_Fragment,_Light_Chain pp Fab_Fragment,_Heavy_Chain
+Fab_Fragment,_Light_Chain pp Fab_Fragment,_Heavy_Chain
+Fab_Fragment,_Light_Chain pp Fab_Fragment,_Heavy_Chain
+Fab_Fragment,_Light_Chain pp Fab_Fragment,_Heavy_Chain
+Fab_Fragment,_Light_Chain pp Fab_Fragment,_Heavy_Chain
+PPIC pp PPIC
+PPIC pp PPIC
+PPIC pp PPIC
+CYP2D6 pp CYP2D6
+CYP2D6 pp CYP2D6
+CYP2D6 pp CYP2D6
+CYP2D6 pp CYP2D6
+CYP2D6 pp CYP2D6
+CYP2D6 pp CYP2D6
+GPX1 pp GPX1
+RAB27B pp RAB27B
+PECI pp PECI
+PECI pp PECI
+PECI pp PECI
+Histone_H3 pp CHD1
+Histone_H3 pp CHD1
+Histone_H3 pp CHD1
+CHD1 pp CHD1
+CHD1 pp CHD1
+CHD1 pp CHD1
+CHD1 pp CHD1
+CHD1 pp CHD1
+CHD1 pp CHD1
+CHD1 pp CHD1
+CHD1 pp CHD1
+CHD1 pp CHD1
+CHD1 pp CHD1
+Histone_H3_Tail pp CHD1
+AXL pp GAS6
+AXL pp GAS6
+SOD1 pp SOD1
+SOD1 pp SOD1
+SOD1 pp SOD1
+SOD1 pp SOD1
+SOD1 pp SOD1
+SOD1 pp SOD1
+SOD1 pp SOD1
+SOD1 pp SOD1
+SOD1 pp SOD1
+SOD1 pp SOD1
+SOD1 pp SOD1
+SOD1 pp SOD1
+SOD1 pp SOD1
+SOD1 pp SOD1
+SOD1 pp SOD1
+SOD1 pp SOD1
+SOD1 pp SOD1
+SOD1 pp SOD1
+CCNA2 pp CDK2
+CCNA2 pp CDK2
+CCNA2 pp CDK2
+CCNA2 pp CDK2
+CCNA2 pp CDK2
+CCNA2 pp CDK2
+CCNA2 pp CDK2
+CCNA2 pp CDK2
+CCNA2 pp CDK2
+CCNA2 pp CDK2
+CCNA2 pp CDK2
+CCNA2 pp CDK2
+CCNA2 pp CDK2
+CCNA2 pp CDK2
+CCNA2 pp CDK2
+CCNA2 pp CDK2
+CCNA2 pp CDK2
+CCNA2 pp CDK2
+CCNA2 pp CDK2
+CCNA2 pp CDK2
+CCNA2 pp CDK2
+CCNA2 pp CDK2
+CCNA2 pp CDK2
+CCNA2 pp CDK2
+Cyclin_A2 pp CDK2
+Cyclin_A2 pp CDK2
+CCNA2 pp CDK2
+CCNA2 pp CDK2
+CCNA2 pp CDK2
+CDK2 pp CCNA2
+CDK2 pp CCNA2
+CDK2 pp CCNA2
+CDK2 pp CCNA2
+CDK2 pp CCNA2
+CDK2 pp Cyclin_A2
+14-3-3_Protein_ZetaDELTA pp 14-3-3_Protein_ZetaDELTA
+Pyruvate_Dehydrogenase_Protein_X_Component,_Mitochondrial pp Dihydrolipoyl_Dehydrogenase,_Mitochondrial
+Pyruvate_Dehydrogenase_Protein_X_Component,_Mitochondrial pp Dihydrolipoyl_Dehydrogenase,_Mitochondrial
+Dihydrolipoyl_Dehydrogenase,_Mitochondrial pp Dihydrolipoyl_Dehydrogenase,_Mitochondrial
+2A66_C pd Orphan_Nuclear_Receptor_Nr5a2
+2A66_B pd Orphan_Nuclear_Receptor_Nr5a2
+Herv-Frd_6p24.1_Provirus_Ancestral_Env_Polyprotein pp Herv-Frd_6p24.1_Provirus_Ancestral_Env_Polyprotein
+Herv-Frd_6p24.1_Provirus_Ancestral_Env_Polyprotein pp Herv-Frd_6p24.1_Provirus_Ancestral_Env_Polyprotein
+GSTK1 pp GSTK1
+Complement_C1q_Subcomponent,_B_Chain_Precursor pp C1QA
+C1QG pp Complement_C1q_Subcomponent,_B_Chain_Precursor
+MAOB pp MAOB
+MAOB pp MAOB
+MAOB pp MAOB
+MAOB pp MAOB
+MAOB pp MAOB
+F2 pp 1HLT_L
+F2 pp 1HLT_J
+Troponin_C,_Slow_Skeletal_And_Cardiac_Muscles pp Troponin_C,_Slow_Skeletal_And_Cardiac_Muscles
+Troponin_C,_Slow_Skeletal_And_Cardiac_Muscles pp Troponin_C,_Slow_Skeletal_And_Cardiac_Muscles
+Mucin-1 pp Mucin-1
+Ubiquitin-Protein_Ligase_E3_Mdm2 pp Ubiquitin-Protein_Ligase_E3_Mdm2
+Ubiquitin-Protein_Ligase_E3_Mdm2 pp Ubiquitin-Protein_Ligase_E3_Mdm2
+GP1BA pp Von_Willebrand_Factor_(Vwf)_[contains:_Von_Willebrand_Antigen_Ii]
+Neutrophil_Cytosol_Factor_1 pp Neutrophil_Cytosol_Factor_1
+CTLA4 pp T_Lymphocyte_Activation_Antigen_Cd86
+T_Lymphocyte_Activation_Antigen_Cd86 pp T_Lymphocyte_Activation_Antigen_Cd86
+Immunoglobulin_Igg_Ru5 pp Von_Willebrand_Factor
+Immunoglobulin_Igg_Ru5 pp Von_Willebrand_Factor
+Von_Willebrand_Factor pp Immunoglobulin_Igg_Ru5
+Immunoglobulin_Igg_Ru5 pp Von_Willebrand_Factor
+Immunoglobulin_Igg_Ru5 pp Von_Willebrand_Factor
+L-3-Hydroxyacyl-Coa_Dehydrogenase pp L-3-Hydroxyacyl-Coa_Dehydrogenase
+3-Hydroxyacyl-Coa_Dehydrogenase pp 3-Hydroxyacyl-Coa_Dehydrogenase
+3-Hydroxyacyl-Coa_Dehydrogenase pp 3-Hydroxyacyl-Coa_Dehydrogenase
+3-Hydroxyacyl-Coa_Dehydrogenase pp 3-Hydroxyacyl-Coa_Dehydrogenase
+3-Hydroxyacyl-Coa_Dehydrogenase pp 3-Hydroxyacyl-Coa_Dehydrogenase
+3-Hydroxyacyl-Coa_Dehydrogenase pp 3-Hydroxyacyl-Coa_Dehydrogenase
+L-3-Hydroxyacyl-Coa_Dehydrogenase pp L-3-Hydroxyacyl-Coa_Dehydrogenase
+Neutrophil_Cytosol_Factor_1 pp Neutrophil_Cytosol_Factor_1
+Neutrophil_Cytosol_Factor_1 pp Neutrophil_Cytosol_Factor_1
+Neutrophil_Cytosol_Factor_1 pp Neutrophil_Cytosol_Factor_1
+Death-Associated_Protein_Kinase pp Death-Associated_Protein_Kinase
+ITGB2 pp ITGB2
+Von_Willebrand_Factor pp Nmc-4_Igg1
+Von_Willebrand_Factor pp Von_Willebrand_Factor
+P53 pp Mdm2
+P53 pp Mdm2
+Neutrophil_Cytosol_Factor_1 pp Cytochrome_B-245_Light_Chain
+1U35_J pd H2AFY
+1U35_J pd H2AFY
+1U35_I pd H2AFY
+Monoclonal_Antibody_10e5_Heavy_Chain pp Integrin_Alpha-Iib
+Monoclonal_Antibody_10e5_Light_Chain pp Integrin_Alpha-Iib
+H2AFY pp H2AFY
+HIST1H4A pp H2AFY
+H2AFY pp HIST1H4A
+HIST1H3A pp H2AFY
+H2AFY pp HIST1H3A
+HIST1H2BB pp H2AFY
+HIST1H2BB pp H2AFY
+Cystic_Fibrosis_Transmembrane_Conductance_Regulator pp Cystic_Fibrosis_Transmembrane_Conductance_Regulator
+Cystic_Fibrosis_Transmembrane_Conductance_Regulator pp Cystic_Fibrosis_Transmembrane_Conductance_Regulator
+Cystic_Fibrosis_Transmembrane_Conductance_Regulator pp Cystic_Fibrosis_Transmembrane_Conductance_Regulator
+Cystic_Fibrosis_Transmembrane_Conductance_Regulator pp Cystic_Fibrosis_Transmembrane_Conductance_Regulator
+CFTR pp Cystic_Fibrosis_Transmembrane_Conductance_Regulator
+CFTR pp Cystic_Fibrosis_Transmembrane_Conductance_Regulator
+ITGB3 pp Integrin_Alpha-Iib
+ITGB3 pp Integrin_Alpha-Iib
+ITGB3 pp Integrin_Alpha-Iib
+ITGB3 pp Integrin_Alpha-Iib
+ITGB3 pp Integrin_Alpha-Iib
+ITGB3 pp Integrin_Alpha-Iib
+PO3F2_HUMAN pp PO3F2_HUMAN
+Brn-2 pp Brn-2
+PKNX2_HUMAN pp HXB1_HUMAN
+PKNX2_HUMAN pp PBX1_HUMAN
+PBX1_HUMAN pp IPF1_HUMAN
+PKNX1_HUMAN pp IPF1_HUMAN
+PKNX1_HUMAN pp PO2F1_HUMAN
+PBX1_HUMAN pp PO2F1_HUMAN
+HXA10_HUMAN pp PBX2_HUMAN
+HXA10_HUMAN pp PBX1_HUMAN
+HXB1_HUMAN pp PKNX1_HUMAN
+HXB1_HUMAN pp PBX2_HUMAN
+HXB1_HUMAN pp PBX1_HUMAN
+PBX1_HUMAN pp HXB1_HUMAN
+PO3F2_HUMAN pp PAX3_HUMAN
+PO3F2_HUMAN pp PAX3_HUMAN
+PBX1_HUMAN pp PKNX1_HUMAN
+PBX1_HUMAN pp PKNX1_HUMAN
+PBX1_HUMAN pp PKNX1_HUMAN
+MEIS1_HUMAN pp PBX3_HUMAN
+PBX2_HUMAN pp HXA9_HUMAN
+MEIS1_HUMAN pp PBX2_HUMAN
+PBX1_HUMAN pp HXA9_HUMAN
+MEIS1_HUMAN pp PBX1_HUMAN
+PBX1_HUMAN pp MEIS1_HUMAN
+HBB pp HBA2
+HBB pp HBA2
+HBB pp HBA2
+HBB pp HBA2
+HBB pp HBA2
+HBB pp HBA2
+HBB pp HBA2
+HBB pp HBA2
+HBA2 pp HBB
+HBA2 pp HBB
+HBA2 pp HBB
+HBA2 pp HBB
+HBA2 pp HBA2
+HBA2 pp HBA2
+HBA2 pp HBA2
+F10 pp F10
+F10 pp F10
+F10 pp F10
+F10 pp F10
+F10 pp F10
+F10 pp F10
+F10 pp F10
+F10 pp F10
+F10 pp F10
+F10 pp F10
+F10 pp F10
+F10 pp F10
+F10 pp F10
+F10 pp F10
+F10 pp F10
+F10 pp F10
+F10 pp F10
+F10 pp F10
+Transcription_Factor_E2f2 pp Retinoblastoma_Pocket
+Transcription_Factor_E2f2 pp Retinoblastoma_Pocket
+Transcription_Factor_E2f2 pp Retinoblastoma_Pocket
+Poly(Rc)-Binding_Protein_1 pp Poly(Rc)-Binding_Protein_1
+Collagenase_3 pp Collagenase_3
+Nuclear_Receptor_Coactivator_2 pp Estrogen_Receptor
+Thrombin pp Thrombin
+Nuclear_Receptor_Coactivator_2 pp Estrogen_Receptor
+Estrogen_Receptor pp Estrogen_Receptor
+Phosphatidylinositol-4-Phosphate_5-Kinase,_Type_Ii,_Gamma pp Phosphatidylinositol-4-Phosphate_5-Kinase,_Type_Ii,_Gamma
+Phosphatidylinositol-4-Phosphate_5-Kinase,_Type_Ii,_Gamma pp Phosphatidylinositol-4-Phosphate_5-Kinase,_Type_Ii,_Gamma
+Phosphatidylinositol-4-Phosphate_5-Kinase,_Type_Ii,_Gamma pp Phosphatidylinositol-4-Phosphate_5-Kinase,_Type_Ii,_Gamma
+Phosphatidylinositol-4-Phosphate_5-Kinase,_Type_Ii,_Gamma pp Phosphatidylinositol-4-Phosphate_5-Kinase,_Type_Ii,_Gamma
+Glutathione_S-Transferase_P pp Glutathione_S-Transferase_P
+Cyclin_A2 pp Cell_Division_Protein_Kinase_2
+Cell_Division_Control_Protein_6_Homolog pp Cyclin_A2
+Cyclin_A2 pp Cell_Division_Protein_Kinase_2
+Cell_Division_Control_Protein_6_Homolog pp Cell_Division_Protein_Kinase_2
+Cell_Division_Control_Protein_6_Homolog pp Cyclin_A2
+Estrogen_Receptor pp Estrogen_Receptor
+Hla_Class_Ii_Histocompatibility_Antigen,_Dm_Beta_Chain pp Hla_Class_Ii_Histocompatibility_Antigen,_Dm_Alpha_Chain
+GSTP1 pp GSTP1
+GSTP1 pp GSTP1
+GSTP1 pp GSTP1
+GSTP1 pp GSTP1
+GSTP1 pp GSTP1
+GSTP1 pp GSTP1
+GSTP1 pp GSTP1
+GSTP1 pp GSTP1
+GSTP1 pp GSTP1
+GSTP1 pp GSTP1
+GSTP1 pp GSTP1
+1XJV_B pd POT1
+CASP1 pp CASP1
+CASP1 pp CASP1
+CASP1 pp CASP1
+CASP1 pp CASP1
+Glucose-6-Phosphate_1-Dehydrogenase pp Glucose-6-Phosphate_1-Dehydrogenase
+Glucose-6-Phosphate_1-Dehydrogenase pp Glucose-6-Phosphate_1-Dehydrogenase
+Glucose-6-Phosphate_1-Dehydrogenase pp Glucose-6-Phosphate_1-Dehydrogenase
+Glucose-6-Phosphate_1-Dehydrogenase pp Glucose-6-Phosphate_1-Dehydrogenase
+Glucose-6-Phosphate_1-Dehydrogenase pp Glucose-6-Phosphate_1-Dehydrogenase
+Glucose-6-Phosphate_1-Dehydrogenase pp Glucose-6-Phosphate_1-Dehydrogenase
+Glucose-6-Phosphate_1-Dehydrogenase pp Glucose-6-Phosphate_1-Dehydrogenase
+F5 pp F5
+B2M pp HLA-A
+TPSAB1 pp TPSAB1
+TPSAB1 pp TPSAB1
+TPSAB1 pp TPSAB1
+TPSAB1 pp TPSAB1
+Retinoblastoma_Protein pp Retinoblastoma_Protein
+Retinoblastoma_Pocket pp Retinoblastoma_Pocket
+Retinoblastoma_Tumour_Suppressor_Protein pp Retinoblastoma_Tumour_Suppressor_Protein
+Retinoblastoma_Tumour_Suppressor_Protein pp Retinoblastoma_Tumour_Suppressor_Protein
+HBB pp HBA2
+HBB pp HBA2
+HBB pp HBA2
+HBB pp HBA2
+HBB pp HBA2
+HBB pp HBA2
+HBB pp HBA2
+HBB pp HBA2
+HBB pp HBA2
+HBB pp HBA2
+HBB pp HBA2
+HBB pp HBA2
+HBB pp HBA2
+HBB pp HBA2
+HBB pp HBA2
+HBB pp HBA2
+HBB pp HBA2
+HBB pp HBA2
+HBB pp HBA2
+HBB pp HBA2
+HBB pp HBA2
+HBB pp HBA2
+HBB pp HBA2
+HBB pp HBA2
+HBB pp HBA2
+HBB pp HBA2
+HBB pp HBA2
+HBB pp HBA2
+HBB pp HBA2
+HBB pp HBA2
+HBB pp HBA2
+HBB pp HBA2
+HBB pp HBA2
+HBB pp HBA2
+HBB pp HBA2
+HBB pp Hemoglobin_Alpha_Chain
+HBA2 pp HBB
+HBA2 pp HBB
+HBA2 pp HBB
+HBA2 pp HBB
+HBA2 pp HBB
+HBA2 pp HBB
+HBA2 pp HBB
+HBA2 pp HBB
+HBA2 pp HBB
+HBA2 pp HBB
+HBA2 pp HBB
+HBA2 pp HBB
+HBA2 pp HBB
+HBA2 pp HBB
+HBA2 pp HBB
+HBA2 pp HBB
+HBA2 pp HBB
+Hemoglobin_Alpha_Chain pp HBB
+Hemoglobin_Alpha_Chain pp HBB
+Dna_Polymerase_Gamma_Subunit_2 pp Dna_Polymerase_Gamma_Subunit_2
+Peptide pp Jumonji_Domain-Containing_Protein_2a
+Tryptase_Beta-2 pp Tryptase_Beta-2
+Tryptase_Beta-2 pp Tryptase_Beta-2
+Tryptase_Beta-2 pp Tryptase_Beta-2
+TASP1 pp TASP1
+Threonine_Aspartase_1 pp Threonine_Aspartase_1
+TASP1 pp TASP1
+TASP1 pp TASP1
+Beta-Hexosaminidase_Alpha_Chain pp Beta-Hexosaminidase_Alpha_Chain
+Beta-Hexosaminidase_Beta_Chain pp Beta-Hexosaminidase_Alpha_Chain
+Ig_Gamma-1_Chain_C_Region pp Ig_Gamma-1_Chain_C_Region
+Beta-Hexosaminidase_Alpha_Chain pp Beta-Hexosaminidase_Beta_Chain
+Beta-Hexosaminidase_Beta_Chain pp Beta-Hexosaminidase_Beta_Chain
+Beta-Hexosaminidase_Beta_Chain pp Beta-Hexosaminidase_Alpha_Chain
+Beta-Hexosaminidase_Beta_Chain pp Beta-Hexosaminidase_Alpha_Chain
+Beta-Hexosaminidase_Beta_Chain pp Beta-Hexosaminidase_Alpha_Chain
+Beta-Hexosaminidase_Alpha_Chain pp Beta-Hexosaminidase_Beta_Chain
+Nuclear_Receptor_Coactivator_1 pp Peroxisome_Proliferator-Activated_Receptor_Gamma
+Caspase-1 pp Caspase-1
+Caspase-1 pp Caspase-1
+Caspase-1 pp Caspase-1
+Caspase-1 pp Caspase-1
+Proto-Oncogene_Tyrosine-Protein_Kinase_Abl1 pp Proto-Oncogene_Tyrosine-Protein_Kinase_Abl1
+Antithrombin-Iii pp Coagulation_Factor,_Stuart_Factor,_Stuart-Prower_Factor,_Contains:_Factor_X_Light_Chain
+Coagulation_Factor,_Stuart_Factor,_Stuart-Prower_Factor,_Contains:_Factor_X_Light_Chain pp Coagulation_Factor_X,_Stuart_Factor,_Stuart-_Prower_Factor,_Contains:_Factor_X_Light_Chain
+Ubiquitin pp Ubiquitin
+Ubiquitin pp Ubiquitin
+Abl_Tyrosine_Kinase pp Abl_Tyrosine_Kinase
+Trna-Splicing_Endonuclease_Subunit_Sen15 pp Trna-Splicing_Endonuclease_Subunit_Sen15
+Chromodomain_Y-Like_Protein pp Chromodomain_Y-Like_Protein
+Chromodomain_Y-Like_Protein pp Chromodomain_Y-Like_Protein
+Chromodomain_Y-Like_Protein pp Chromodomain_Y-Like_Protein
+Regulator_Of_G-Protein_Signaling_1 pp Guanine_Nucleotide-Binding_Protein_G(I),_Alpha-1_Subunit
+Dihydropyrimidinase-Related_Protein_2 pp Dihydropyrimidinase-Related_Protein_2
+Dihydropyrimidinase-Related_Protein_2 pp Dihydropyrimidinase-Related_Protein_2
+Dihydropyrimidinase-Related_Protein_2 pp Dihydropyrimidinase-Related_Protein_2
+Bone_Morphogenetic_Protein_Receptor_Type_Ia pp Bone_Morphogenetic_Protein_2
+Bone_Morphogenetic_Protein_Receptor_Type_Ia pp Bone_Morphogenetic_Protein_Receptor_Type_Ia
+Bone_Morphogenetic_Protein_Receptor_Type_Ia pp Bone_Morphogenetic_Protein_2
+Dihydropyrimidinase-Related_Protein_2 pp Dihydropyrimidinase-Related_Protein_2
+Ran_Gtpase-Activating_Protein_1 pp Ubiquitin-Conjugating_Enzyme_E2_I
+Ran_Gtpase-Activating_Protein_1 pp Ubiquitin-Conjugating_Enzyme_E2_I
+Estrogen-Related_Receptor_Gamma pp Estrogen-Related_Receptor_Gamma
+Estrogen-Related_Receptor_Gamma pp Estrogen-Related_Receptor_Gamma
+Estrogen-Related_Receptor_Gamma pp Estrogen-Related_Receptor_Gamma
+Hemoglobin_Beta_Subunit pp Hemoglobin_Alpha_Subunit
+Nad(P)h_Dehydrogenase_[quinone]_1 pp Nad(P)h_Dehydrogenase_[quinone]_1
+Fop pp Fop
+Ubiquitin-Like_Protein_Smt3b pp GT_MISMATCH-Specific_Thymine_Dna_Glycosylase
+Aflatoxin_B1_Aldehyde_Reductase_Member_3 pp Aflatoxin_B1_Aldehyde_Reductase_Member_3
+Aflatoxin_B1_Aldehyde_Reductase_Member_3 pp Aflatoxin_B1_Aldehyde_Reductase_Member_3
+Aflatoxin_B1_Aldehyde_Reductase_Member_3 pp Aflatoxin_B1_Aldehyde_Reductase_Member_3
+Aflatoxin_B1_Aldehyde_Reductase_Member_3 pp Aflatoxin_B1_Aldehyde_Reductase_Member_3
+Aflatoxin_B1_Aldehyde_Reductase_Member_3 pp Aflatoxin_B1_Aldehyde_Reductase_Member_3
+Aflatoxin_B1_Aldehyde_Reductase_Member_3 pp Aflatoxin_B1_Aldehyde_Reductase_Member_3
+Aflatoxin_B1_Aldehyde_Reductase_Member_3 pp Aflatoxin_B1_Aldehyde_Reductase_Member_3
+Aflatoxin_B1_Aldehyde_Reductase_Member_3 pp Aflatoxin_B1_Aldehyde_Reductase_Member_3
+Aflatoxin_B1_Aldehyde_Reductase_Member_3 pp Aflatoxin_B1_Aldehyde_Reductase_Member_3
+Thrombin_Heavy_Chain pp Thrombin_Light_Chain
+Low-Density_Lipoprotein_Receptor pp Alpha-2-Macroglobulin_Receptor-Associated_Protein
+Estrogen_Receptor pp Estrogen_Receptor
+Chromobox_Protein_Homolog_1 pp Chromobox_Protein_Homolog_1
+Chromobox_Protein_Homolog_1 pp Chromobox_Protein_Homolog_1
+Chromobox_Protein_Homolog_1 pp Protein_Emsy
+Chromobox_Protein_Homolog_1 pp Chromobox_Protein_Homolog_1
+Chromobox_Protein_Homolog_1 pp Protein_Emsy
+Chromobox_Protein_Homolog_1 pp Chromobox_Protein_Homolog_1
+Chromobox_Protein_Homolog_1 pp Chromobox_Protein_Homolog_1
+Chromobox_Protein_Homolog_1 pp Protein_Emsy
+Chromobox_Protein_Homolog_1 pp Protein_Emsy
+Histone_H3.1 pp Histone_H3.1
+2F8N_I pd Histone_H3.1
+2F8N_I pd Histone_H3.1
+2F8N_J pd Histone_H3.1
+Ring_Finger_Protein_41 pp Ubiquitin_Carboxyl-Terminal_Hydrolase_8
+Ubiquitin_Ligase_Protein_Ring2 pp B_Lymphoma_Mo-Mlv_Insertion_Region
+Angiopoietin-1_Receptor pp Angiopoietin-2
+Caspase_1,_Isoform_Gamma pp Caspase_1,_Isoform_Gamma
+Adaptor_Protein_Aps pp INSR
+KIR2DL1 pp Hla_Class_I_Histocompatibility_Antigen,_Cw-4_Cw0401_Alpha_Chain
+Telethonin pp N2b-Titin_Isoform
+Telethonin pp N2b-Titin_Isoform
+B2M pp CD1A
+B2M pp CD1A
+FRS2 pp Basic_Fibroblast_Growth_Factor_Receptor_1
+DMD pp DMD
+Fyn pp mTAg
+Grb2 interactsWith -
+Sos1 interactsWith -
+H-Ras interactsWith -
+H-Ras interactsWith -
+GTP interactsWith -
+SRF pp GATA4
+SRF pp Nkx2-5
+ShcA pp PymT
+GRK6 interactsWith palmitate
+E1B-AP5 pp E1B-55kDa
+E1B-AP5 pp E1B-55kDa
+Cdc42 pp SopE
+YB-1 pp T-antigen
+Pur-alpha pp T-antigen
+p53 pp Large_T-antigen
+COX-1 interactsWith Ibuprofen
+COX-1 interactsWith Flurbiprofen
+COX-1 interactsWith Alclofenac
+COX-1 interactsWith Methyl_flurbiprofen
+SRF pd vSRE
+hIF2 pp p17
+D2 interactsWith LSD-25
+D2 interactsWith Dopamine
+D2 interactsWith PCP
+NSEP1 pp Tat
+MAD2B pp TCS
+P0 pp TCS
+P1 pp TCS
+D2S interactsWith Raclopride
+D2S interactsWith Spiperone
+hRAD51 pd ssDNA
+hRAD51 interactsWith ATP
+hRAD51 interactsWith ADP
+hRAD51-hXRCC2 interactsWith ATP
+hRAD51-hXRCC2 interactsWith ADP
+PGRP-I-alpha interactsWith PGN
+Ini1 pp HIV-1_IN
+HGF interactsWith Copper(II)
+HLA-A pp Nef
+PACS1 pp Nef
+PKA-RII-alpha pp E1A
+PKA-RI-alpha pp E1A
+PrPC interactsWith CuCl2.2H2O
+CD81 pp E2
+GSTZ1c-1c interactsWith GSH
+GSTZ1c-1c interactsWith DCA
+GSTZ1-GSH interactsWith DCA
+GSTZ1-DCA interactsWith GSH
+Nucleolin pp Intimin-gamma
+Nucleolin pp Intimin-beta
+Nucleolin pp Intimin-alpha
+PKR pp Tat-2
+PKR pp Tat
+CYP2D6 interactsWith MMDA-2
+CYP2D6 interactsWith MDMA
+CYP2D6 interactsWith MDA
+CYP2D6 interactsWith MMDA
+CYP2D6 interactsWith (d,l)-2-Methoxyamphetamine
+CYP2D6 interactsWith (d,l)-3-Methoxyamphetamine
+IRF-3 pp HPV16_E6
+IRF-1 pp HPV16_E6
+hMSH4-hMSH5 interactsWith ATP
+hMSH4-hMSH5 interactsWith ADP
+hMSH4-hMSH5 interactsWith Holliday_Junction_Progenitor
+CYP2D6.10 interactsWith Paroxetine
+CYP2D6 interactsWith (+)-4-Hydroxyamphetamine
+CYP2D6 interactsWith 3,4,5-TMA
+CYP2D6 interactsWith 2,4,6-TMA
+CYP2D6 interactsWith (+)-Amphetamine
+CYP2D6 interactsWith (+)-Methamphetamine
+CYP2D6 interactsWith PMA
+CYP2D6 interactsWith (d,l)-Cathinone
+CYP2D6 interactsWith (d,l)-4-Hydroxymethamphetamine
+PrPc pp groEL
+CYP2D6 interactsWith PEPAP
+CYP2D6 interactsWith MPPP
+CYP2D6 interactsWith Dextromethorphan
+hCE-1 interactsWith R-(-)Cocaine
+hCE-1 interactsWith 3-Beta-(Methylphenylphosphonodithionyloxy)-8-azabicyclo[_3.2.1]octane-2-Beta-carboxylic_acid_methyl_ester
+hCE-1 interactsWith 3-Beta-(Methyl_phenylphosphonothionyloxy)-8-azabicyclo[3.2.1]octane-2-Beta-carboxylic_acid_methyl_ester
+hCE-1 interactsWith 3-Beta-(Diphenylphosphonyloxy)-8-azabicyclo[3.2.1]octane-2-Beta-carboxylic_acid_methyl_ester
+hCE-1 interactsWith 3-beta-(Methylphenylphosphonothionyloxy)-8-azabicyclo[3.2.1]octane-2-beta-carboxylic_acid_methyl_ester
+E2F-2 pd E2F_site
+E2F-1 pd E2F_site
+E2F-3 pd E2F_site
+CCR5 interactsWith gp120-CD4
+Antibody_17b,_Heavy_Chain pp env
+Antibody_17b,_Heavy_Chain pp env
+C4BPA pp Echovirus_11_Coat_Protein_Vp2
+C4BPA pp Echovirus_11_Coat_Protein_Vp1
+1P34_I pd Histone_H3
+1P34_I pd Histone_H2a
+1P3B_I pd Histone_H2b
+1P3A_I pd Histone_H4
+1P34_I pd Histone_H3
+1P34_I pd Histone_H4
+1P34_I pd Histone_H2a
+1P34_I pd Histone_H2b
+1P34_J pd Histone_H3
+1P34_J pd Histone_H2b
+1P34_J pd Histone_H2a
+1P34_J pd Histone_H3
+1P34_J pd Histone_H4
+1P34_J pd Histone_H4
+1P3A_J pd Histone_H2b
+1P3A_I pd Histone_H3
+1P3B_J pd Histone_H2b
+1P3B_I pd Histone_H2a
+1P3A_I pd Histone_H3
+1P3A_I pd Histone_H4
+1P3B_I pd Histone_H2b
+1P3A_J pd Histone_H3
+1P3A_J pd Histone_H2b
+1P3B_J pd Histone_H2a
+1P3A_J pd Histone_H3
+1P3B_J pd Histone_H4
+1P3A_J pd Histone_H4
+1P3B_I pd Histone_H3
+1P3B_I pd Histone_H3
+1P3B_I pd Histone_H4
+1P3B_J pd Histone_H3
+1P3B_J pd Histone_H3
+1P3B_J pd Histone_H4
+1P3L_I pd Histone_H3
+1P3P_I pd Histone_H2b
+1P3I_I pd Histone_H2a
+1P3K_I pd Histone_H4
+1P3P_I pd Histone_H2b
+1P3I_I pd Histone_H3
+1P3F_I pd Histone_H4
+1P3F_I pd Histone_H2a
+1P3K_J pd Histone_H3
+1P3M_J pd Histone_H2a
+1P3F_J pd Histone_H3
+1P3O_J pd Histone_H4
+1P3F_J pd Histone_H4
+1P3G_I pd Histone_H2b
+1P3K_J pd Histone_H2a
+1P3G_I pd Histone_H4
+1P3G_J pd Histone_H2b
+1P3G_J pd Histone_H2a
+1P3O_J pd Histone_H3
+1P3G_J pd Histone_H4
+1P3G_J pd Histone_H4
+1P3I_I pd Histone_H3
+1P3I_I pd Histone_H4
+1P3I_J pd Histone_H3
+1P3I_J pd Histone_H4
+1P3K_I pd Histone_H2a
+1P3K_I pd Histone_H3
+1P3L_I pd Histone_H4
+1P3K_J pd Histone_H3
+1P3P_J pd Histone_H4
+1P3L_I pd Histone_H3
+1P3L_J pd Histone_H3
+1P3L_J pd Histone_H2b
+1P3L_J pd Histone_H3
+1P3M_I pd Histone_H2a
+1P3M_I pd Histone_H3
+1P3M_J pd Histone_H3
+1P3M_J pd Histone_H2b
+1P3M_J pd Histone_H3
+1P3P_I pd Histone_H2a
+1P3P_J pd Histone_H2b
+1P3P_J pd Histone_H2a
+Thrombopoietin pp Monoclonal_Tn1_Fab_Heavy_Chain
+Thrombopoietin pp Monoclonal_Tn1_Fab_Heavy_Chain
+F2 pp Thrombin
+UBA52 pp Homolog_Of_Yeast_Nuclear_Protein_Localization_4
+SRP19 interactsWith 1RY1_A
+Calmodulin pp Calmodulin-Sensitive_Adenylate_Cyclase
+Ldl-Receptor_Class_A_3 pp Coat_Protein_Vp1
+CXADR pp Fiber_Protein
+HLA-A pp Pol_Polyprotein
+Calmodulin pp Calmodulin-Sensitive_Adenylate_Cyclase
+hCE-1 interactsWith 3-beta-(Methylphenylphosphonothionyloxy)-8-azabicyclo[3.2.1]octane-2-beta-carboxylic_acid_methyl_ester
+hCE-1 interactsWith 3-beta-(Methanesulfonyloxy)-8-azabicyclo[3.2.1]octane-2-beta-carboxylic_acid_methyl_ester
+hCE-1 interactsWith 3-beta-(Phenylphosphonic_acid)-8-azabicyclo[3.2.1]octane-2-beta-carboxylic_acid_methyl_ester
+La interactsWith DEN4_3'UTR
+La pp NS5
+La pp NS3
+La interactsWith DEN4_5'UTR
+hGBP3 interactsWith GTP
+p42MAPK pp Tat
+p42MAPK pp Rev
+Amyloid-beta interactsWith CR
+Amyloid-beta interactsWith CR
+Amyloid-beta interactsWith CR
+FKBP12 interactsWith CR
+FKBP12 interactsWith SLF
+FKBP12 interactsWith SLF-CR
+p42MAPK pp p17gag
+p42MAPK pp Nef
+p42MAPK pp Vif
+AP1G2 pp L
+HuR interactsWith HCV_3'UTR
+hnRNP_C interactsWith HCV_3'UTR
+HuR interactsWith Antisense_HCV_5'_UTR
+hnRNP_C1 interactsWith Antisense_HCV_5'_UTR
+SERPINA1 pp CANX
+SP1 pp HDAC1
+SP1 pp HDAC1
+SMN pp PFN2
+SMN pp PFN1
+SMN pp PFN1
+SMN pp PFN2
+JIP-1 pp RGNEF
+JIP-1 pp RGNEF
+JIP-1 pp RGNEF
+IGF1R pp PIK3R3
+IGF1R pp PIK3R3
+ALL-1 pp UNR
+ALL-1 pp UNR
+SHANK1 pp SSTR2
+ARNT pp SIM1
+ARNT pp SIM2
+ARNT2 pp SIM1
+ARNT pp AHR
+ARNT pp dioxin-activated_dioxin_receptor_(ligand-activated_transcription_factor)
+ACTA1 pp P50
+LYN pp MYD116
+YWHAZ pp TLK2
+YWHAZ pp TLK2
+YWHAZ pp TLK2
+YWHAB pp TLK2
+DSG2 pp DSC1
+IGF1R pp PIK3R3
+SERPINA1 pp CANX
+CAP pp BAT3
+AHR pp SP1
+ACVR2 pp ACVR1
+ACVR2 pp BMPR1B
+IGF1R pp PIK3R3
+IGF1R pp PIK3R3
+GTF2B pp RXRB
+GTF2B pp RXRB
+GTF2B pp RXRB
+GHR pp JAK2
+GHR pp GHR
+GHR pp JAK2
+GNG10 pp KSR
+GNG3 pp KSR
+CTNND2 pp E-cadherin
+CITED1 pp STAT5A
+CITED1 pp STAT5A
+STAT1 pp PIAS1
+AR pp RNF4
+PGR pp RNF4
+GABRR1 pp SLC6A9
+GABRR1 pp SLC6A9
+Dvl2 pp FLNB
+NPM pp PLCG1
+DVL1 pp FLNB
+PPM1A pp AXIN1
+DVL1 pp DVL3
+DVL1 pp AXIN1
+DVL1 pp AXIN1
+PTEN pp MTSSK
+CBX3 pp PIM1
+GRB7 pp RND1
+GRB7 pp RND1
+CBP pp ZAC1
+EP300 pp ZAC1
+EP300 pp ZAC1
+NTRK1 pp PLCG1
+NTRK1 pp ABL1
+NTRK1 pp SH2BPSM1
+BMPR2 pp BMPR1B
+RNF4 pp PATZ
+GRB14 pp FGFR1
+GRB14 pp FGFR1
+NR2F6 pp SRC1
+CCNB1 pp CCNF
+ERBB4 pp DLG4
+JUN_activation_domain-binding_protein-1_(JAB1) pp PGR
+MAP3K pp ADRBK1
+JUN_activation_domain-binding_protein-1_(JAB1) pp PGR
+Steroid_receptor_coactivator-1_(SRC-1) pp ESR2
+NGFR pp RANBPM
+NGFR pp RANBPM
+MAPBPIP pp MAP2K1IP1
+MAPBPIP pp MAP2K1IP1
+MAPBPIP pp MAP2K1IP1
+PARP-1 interactsWith NAD+
+hCE-1 interactsWith WIN_36,065-2
+hCE-1 interactsWith WIN_35,428
+hCE-1 interactsWith RTI_55
+hCE-1 interactsWith RTI_31
+hCE-1 interactsWith (+/-)-allopseudococaine
+hCE-1 interactsWith S-(-)-pseudococaine
+hCE-1 interactsWith R-(+)-pseudococaine
+hCE-1 interactsWith Cocaethylene
+hCE-1 interactsWith S-(+)cocaine
+beta-actin-RNAPII-TBP_complex interactsWith p-AdML
+hCE-1 interactsWith Heroin
+hCE-1 interactsWith Atropine
+hCE-1 interactsWith Tropacocaine
+hCE-1 interactsWith Ecgonine
+hCE-1 interactsWith benzoylecgonine_propyl_ester
+hCE-1 interactsWith Morphine
+hCE-1 interactsWith ecgonine_methyl_ester
+hCE-1 interactsWith 6-Acetylmorphine
+hCE-1 interactsWith Benzoylecgonine
+PTBP1 interactsWith DEN4_3'UTR
+CYP1A1 interactsWith Meperidine
+CYP1A2 interactsWith Meperidine
+CYP2B6 interactsWith Meperidine
+CYP2C8 interactsWith Meperidine
+CYP2C18 interactsWith Meperidine
+CYP2C19 interactsWith Meperidine
+Nucleolin pp NS5B
+CYP2D6.17 interactsWith Codeine
+CYP2D6.2 interactsWith Codeine
+La interactsWith HCV_5'_UTR
+La interactsWith HCV_3'_UTR
+PID interactsWith unknown
+CYP2D6 interactsWith Meperidine
+CYP19 interactsWith Meperidine
+CYP4A11 interactsWith Meperidine
+CYP3A4 interactsWith Meperidine
+CYP3A5 interactsWith Meperidine
+CYP3A7 interactsWith Meperidine
+DAPP1 interactsWith PtdIns3,4,5P3.
+Importin-alpha pp Rep68
+Importin-alpha pp Rep78
+Importin-alpha interactsWith ITR-Rep68
+Importin-alpha interactsWith ITR-Rep78
+CYP2D6 interactsWith (R)-methadone
+CYP2C8 interactsWith (R)-methadone
+CYP3A4 interactsWith (R)-methadone
+CYP3A4 interactsWith (S)-methadone
+CYP2D6 interactsWith (S)-methadone
+CYP2C8 interactsWith (S)-methadone
+hSac1 interactsWith PI(3,5)P2
+hSac1 interactsWith PI(3,4,5)P3
+LL5-alpha interactsWith PtdIns3P
+LL5-alpha interactsWith PtdIns4P
+LL5-alpha interactsWith PtdIns5P
+LL5-alpha interactsWith PtdIns3,5P2
+LL5-alpha interactsWith PtdIns4,5P2
+LL5-alpha interactsWith PtdIns3,4P2
+LL5-alpha interactsWith PtdIns3,4,5P3
+PCAF pp Bel1
+p300 pp Bel1
+Arp2/3 interactsWith ATP
+Unknown interactsWith ActA
+p50 pp I-kappa-B-alpha
+p52 pp I-kappa-B-epsilon
+Grb2 pp B19_11-kDa
+Arp2/3 interactsWith ADP
+hCX5.36 interactsWith Cannabidiol
+hCX5.36 interactsWith Cannabinol
+hCX5.36 interactsWith THC
+hCX5.36 interactsWith Anandamide
+hCX5.36 interactsWith 11OH-THC
+CYP2D6.10 interactsWith PMA
+CYP2D6.10 interactsWith Dextromethorphan
+CYP2D6.10 interactsWith MDMA
+CYP2D6.10 interactsWith MPTP
+CYP2D6.10 interactsWith Amitriptyline
+CYP2D6.10 interactsWith (+)Methamphetamine
+LL5-beta interactsWith PtdIns3P
+LL5-beta interactsWith PtdIns4P
+LL5-beta interactsWith PtdIns5P
+LL5-beta interactsWith PtdIns(3,5)P2
+LL5-beta interactsWith PtdIns3,4,5P3
+LL5-beta interactsWith PtdIns(3,4)P2
+LL5-beta interactsWith PtdIns(4,5)P2
+Evectin-2 interactsWith PtdIns4P
+Evectin-2 interactsWith PtdIns(3,5)P2
+Evectin-2 interactsWith PtdIns(3,4)P2
+Evectin-2 interactsWith PtdIns3,4,5P3
+hnRNP_C1 interactsWith Antisense_HCV_3'_UTR
+G-alpha-q11 interactsWith GTP-gamma-S
+DDX3 pp Rev
+NSAP1 interactsWith HCV_IRES
+heIF4AII pp NS5B
+SERCA2 interactsWith GSH
+CYP2D6.10 interactsWith (-)Methamphetamine
+CYP2D6.10 interactsWith Sparteine
+CYP2D6.10 interactsWith Debrisoquine
+CYP2D6.10 interactsWith Budipine
+CYP2D6.10 interactsWith (+/-)fluoxetine
+CYP2D6.10 interactsWith (+/-)norfluoxetine
+CYP2D6.1 interactsWith Paroxetine
+CYP2D6.1 interactsWith (-)Methamphetamine
+CYP2D6.1 interactsWith MPTP
+CYP2D6.1 interactsWith Amitriptyline
+CYP2D6.1 interactsWith Sparteine
+CYP2D6.1 interactsWith Debrisoquine
+CYP2D6.1 interactsWith Budipine
+Unknown interactsWith NS5A
+CYP2D6.1 interactsWith (+/-)norfluoxetine
+CYP2D6.10 interactsWith MMDA-2
+CYP2D6.1 interactsWith (+/-)fluoxetine
+caveolin-1 pp gp41
+ATGL interactsWith NBD-HEHP
+CD81 pp E2
+TF pp E2
+ApoE pp NS5A
+ApoE pp NS5A
+SmD1 interactsWith HCV_3'UTR
+SmD1 interactsWith JEV_3'UTR
+hVAP-33 pp NS5B
+hVAP-33 pp NS5A
+LF pp E2
+TNFR1 pp Core
+C1-Inh pp NS3
+Alpha-2AP pp NS3
+Unknown interactsWith Calnexin
+T-Cell_Receptor_Alpha_Chain pp Hemagglutinin_Ha1_Peptide_Chain
+T-Cell_Receptor_Beta_Chain pp Hemagglutinin_Ha1_Peptide_Chain
+CD4 pp env
+Antibody_17b,_Light_Chain pp env
+Antibody_17b,_Heavy_Chain pp env
+CD4 pp env
+Antibody_17b,_Light_Chain pp env
+Antibody_17b,_Heavy_Chain pp env
+RAC3 pp stpA
+Casein_Kinase,_Beta_Chain pp Casein_Kinase,_Alpha_Chain
+Casein_Kinase,_Beta_Chain pp Casein_Kinase,_Alpha_Chain
+RAC1 pp exoS
+F2 pp Hirudin_I
+CASP8 pp Early_35_Kda_Protein
+1IO4_E pd Runx1
+1IO4_F pd Runx1
+POU2F2 pd 1E3O_B
+POU2F2 pd 1E3O_A
+PAX5 pd 1K78_D
+PAX5 pd 1K78_C
+NFAT5 pd 1IMH_A
+NFAT5 pd 1IMH_B
+NFAT5 pd 1IMH_B
+NFAT5 pd 1IMH_A
+CALM2 pp Calmodulin-Sensitive_Adenylate_Cyclase
+CALM2 pp Calmodulin-Sensitive_Adenylate_Cyclase
+CALM2 pp Calmodulin-Sensitive_Adenylate_Cyclase
+CALM2 pp Calmodulin-Sensitive_Adenylate_Cyclase
+RAN pp Ran_Gtpase_Activating_Protein_1
+T-Cell_Receptor_Beta_Chain pp Exotoxin_Type_C
+T-Cell_Receptor_Beta_Chain pp Exotoxin_Type_C
+1L9A_B interactsWith Signal_Recognition_Particle_19_Kda_Protein
+P300CBP-Associated_Factor pp Hiv-1_Tat_Peptide
+Eukaryotic_Protein_Synthesis_Initiation_Factor pp Nonstructural_Rna-Binding_Protein_34
+Eukaryotic_Protein_Synthesis_Initiation_Factor pp Nonstructural_Rna-Binding_Protein_34
+Eukaryotic_Protein_Synthesis_Initiation_Factor pp Nonstructural_Rna-Binding_Protein_34
+Eukaryotic_Protein_Synthesis_Initiation_Factor pp Nonstructural_Rna-Binding_Protein_34
+SNRPA interactsWith 1M5P_E
+Cellular_Tumor_Antigen_P53 pp Transcriptional_Regulatory_Protein,_Sir2_Family
+CALM2 pp Calmodulin-Sensitive_Adenylate_Cyclase
+CCL2 pp M3_Protein
+CDH1 pp Internalin_A
+POU2F2 pd 1GT0_A
+POU2F2 pd 1GT0_B
+Tcr_Alpha_Chain pp Epstein_Barr_Virus_Peptide
+Tcr_Beta_Chain pp Epstein_Barr_Virus_Peptide
+GSN pp Actin
+ANG pp Antibody_Fab_Fragment,_Light_Chain
+ANG pp Antibody_Fab_Fragment,_Heavy_Chain
+T-Cell_Receptor_Alpha_Chain_V_Region pp Gilgfvftl
+T-Cell_Receptor_Beta_Chain_C_Region pp Gilgfvftl
+VWF pp Bitiscetin_Alpha_Chain
+VWF pp Bitiscetin_Beta_Chain
+LYZ pp Hl6_Camel_Vhh_Fragment
+Topors pp Rep78
+Topors pp Rep68
+APOBEC3G pp HBcAg
+H-ras interactsWith GDP
+H-ras interactsWith GTP
+Nedd4 pp LMP2A
+AIP4 pp LMP2A
+KIAA0439 pp LMP2A
+Syk pp LMP2A
+WWP2 pp LMP2A
+COP-beta pp Nef
+Rap1 interactsWith GTP
+Ras interactsWith GTP
+Ras interactsWith GDP
+N-WASP interactsWith Unknown
+Nck pp Tir
+ER-alpha interactsWith estrogen
+Shb pp v-Src
+TXBP181 pp Tax
+Htt interactsWith Unknown
+Rac1 interactsWith GTP
+p53 pp NS5A
+hTAFII32 pp NS5A
+D4.7 interactsWith GTP-gamma-S
+D4.4 interactsWith GTP-gamma-S
+D4.4 interactsWith Dopamine
+D4.7 interactsWith Dopamine
+D4.7 interactsWith Spiperone
+D4.4 interactsWith Spiperone
+Hck pp Vif
+TCL interactsWith GDP
+TC10 interactsWith GDP
+Casp2 interactsWith VAD-fmk
+Brd4 pp HPV16_E2
+Brd4 pp BPV-1_E2
+TC10 interactsWith GTP
+TCL interactsWith GTP
+Nrk1 interactsWith Tiazofurin
+Nrk2 interactsWith Nicotinamide_Riboside
+Nrk2 interactsWith Tiazofurin
+Nrk2 interactsWith Uridine
+Nrk1 interactsWith Nicotinamide_Riboside
+CTIP2 pp Tat
+Parkin interactsWith NO
+CD4 pp Gp120
+HT2A pp Tat
+HT2A pp Tat
+Antibody_17B,_Heavy_Chain pp Gp120
+Antibody_17B,_Light_Chain pp Gp120
+EED pp HIV-1_IN
+PARP1 interactsWith ADP-ribose
+H1 interactsWith ADP-ribose
+PDE4D5 interactsWith Rolipram
+c-Jun-c-Fos interactsWith HIV-1
+IMPDH_II interactsWith K+
+IMPDH_II interactsWith IMP
+IMPDH_II interactsWith MPA
+LC8 pp Pmok
+LC8 pp P
+ACE2 pp S_protein
+alpha-COP interactsWith Unknown
+epsilon-COP interactsWith Unknown
+beta-prime-COP interactsWith Unknown
+alpha/beta-prime/epsilon-COP interactsWith Unknown
+CERT interactsWith ceramide
+CERTL interactsWith ceramide
+CERT interactsWith PtdIns4P
+CERTL interactsWith PtdIns4P
+CERT interactsWith PtdIns5P
+CERTL interactsWith PtdIns5P
+CERT interactsWith PtdIns3P
+CERTL interactsWith PtdIns3P
+CERT interactsWith PtdIns3,5P
+CERTL interactsWith PtdIns3,5P
+1FC2_D pp 1FC2_C
+POU2F2 pd 1OCT_A
+POU2F2 pd 1OCT_B
+CSTB pp 1STF_E
+1FOS_E pd 1FOS_A
+1FOS_E pd 1FOS_B
+1FOS_F pd 1FOS_B
+1FOS_F pd 1FOS_A
+1FOS_G pd 1FOS_D
+1FOS_G pd 1FOS_C
+1FOS_H pd 1FOS_C
+1FOS_H pd 1FOS_D
+1CKB_B pp 1CKB_A
+SRC pp Acetyl-Pyeeie-Oh
+SRC pp Acetyl-Pyeeie-Oh
+CASP1 pp 1ICE_T
+TBP pd 1TGH_C
+TBP pd 1TGH_B
+T_Cell_Receptor_Alpha pp Tax_Peptide
+T_Cell_Receptor_Beta pp Tax_Peptide
+HBB pp Hemoglobin
+HBB pp Hemoglobin
+F3 pp Immunoglobulin_Fab_5g9
+DTR pp Diphtheria_Toxin
+Fyn_Tyrosine_Kinase pp Negative_Factor
+HBB pp Hemoglobin-Based_Blood_Substitute
+HBB pp Hemoglobin-Based_Blood_Substitute
+T_Cell_Receptor_Alpha pp Tax_Peptide
+T_Cell_Receptor_Beta pp Tax_Peptide
+ELK4 pd 1BC7_B
+ELK4 pd 1BC7_A
+ELK4 pd 1BC8_B
+ELK4 pd 1BC8_A
+NFKBIA pp Nf-Kappa-B_P65_Subunit
+T-Cell_Receptor,_Alpha_Chain pp Tax_Peptide_P6a
+T-Cell_Receptor,_Beta_Chain pp Tax_Peptide_P6a
+CXADR pp Fiber_Knob_Protein
+Hman_T-Cell_Receptor pp Tax_Peptide_V7r
+Hla-A_0201 pp Tax_Peptide_V7r
+Hman_T-Cell_Receptor pp Tax_Peptide_Y8a
+Hla-A_0201 pp Tax_Peptide_Y8a
+APEX1 pd 1DE8_V
+APEX1 pd 1DE8_U
+APEX1 pd 1DE9_W
+APEX1 pd 1DE9_U
+APEX1 pd 1DE9_V
+APEX1 pd 1DEW_Y
+APEX1 pd 1DEW_X
+ELK1 pd 1DUX_B
+ELK1 pd 1DUX_A
+GSTA4 pp Glutathione_Ligand
+EIF1A pp N-Terminal_Histidine_Tag
+Synaptobrevin-Ii pp Botulinum_Neurotoxin_Type_B
+Synaptobrevin-Ii pp Botulinum_Neurotoxin_Type_B
+C1QBP interactsWith Rev-RRE_complex
+DLG1 pp E6
+DLG1 pp Tax
+SIRT1 interactsWith NAD+
+SGPP1 interactsWith dihydro-S1P
+SGPP1 interactsWith S1P
+ESR2 interactsWith 17beta-estradiol
+RHEB interactsWith GTP
+RHEB interactsWith GDP
+PKN2 interactsWith Rockout
+RPS6KA5 interactsWith Rockout
+PRKACA interactsWith Rockout
+ROCK2 interactsWith Rockout
+ROCK2 interactsWith Y-27632
+ROCK1 interactsWith Y-27632
+ROCK1 interactsWith Rockout
+CEBPB pd HIV-1_LTR
+GSTP1 interactsWith GLU-BCS-PGY
+NSEP1 pd HTLV-1_promoter
+RAD54L interactsWith ATP
+APAF1 interactsWith ATP
+APAF1 interactsWith ATP
+CTBP1 pp E1a
+MCM3 pd OriP
+SMARCA5-HDAC2 interactsWith OriP
+HDAC1 pd OriP
+CASP9 interactsWith bVAD-FMK
+CASP9 interactsWith bEVD-AOMK
+CASP8 interactsWith bVAD-FMK
+CASP8 interactsWith bEVD-AOMK
+CASP8 interactsWith Asp-AOMK
+CASP7 interactsWith bVAD-FMK
+CASP7 interactsWith bEVD-AOMK
+CASP7 interactsWith Asp-AOMK
+CASP6 interactsWith Asp-AOMK
+CASP6 interactsWith bVAD-FMK
+CASP3 interactsWith bVAD-FMK
+CASP3 interactsWith bEVD-AOMK
+CASP3 interactsWith Asp-AOMK
+CTSL interactsWith JPM-OEt
+CTSL interactsWith Leu-AOMK
+CTSL interactsWith Gly-AOMK
+CTSL interactsWith Lys-AOMK
+CTSL interactsWith Arg-AOMK
+LGMN interactsWith Asn-AOMK
+LGMN interactsWith Asp-AOMK
+CYP2C9 interactsWith OXY
+CYP2C8 interactsWith OXY
+CYP2C19 interactsWith OXY
+CYP2D6 interactsWith OXY
+CYP2B6 interactsWith OXY
+CYP2A6 interactsWith OXY
+CYP1A2 interactsWith OXY
+CYP1A1 interactsWith OXY
+CYP2D6 interactsWith NOC
+CYP3A4 interactsWith OXY
+OPRK1 interactsWith Salvinorinyl-2-heptanoate
+OPRK1 interactsWith Salvinorinyl-2-propionate
+OPRK1 interactsWith Salvinorin_A
+p50/p65 interactsWith HIV-1_LTR
+ACE2 pp S_protein_(TOR2)
+ACE2 pp S_protein_(GD03T0013)
+ACE2 pp S_protein_(SZ3)
+ATP5O interactsWith Bz-423
+PTEN interactsWith Unknown
+WASL pp v-Src
+CTBP1 pp E1A
+NCR3-CD3z interactsWith HHV5gp078
+KIF16B interactsWith PI(3,4,5)P3
+KIF16B interactsWith PI(3,4)P2
+KIF16B interactsWith PI(3)P
+CyPA pp nucleocapsid
+PI3K_p110beta interactsWith PI(4,5)P2
+PI3K_p110alpha interactsWith PI(4,5)P2
+HRH1 interactsWith [3H]mepyramine
+PTX3 pp KpOmpA
+HDAC3 pp E7
+HSPCA interactsWith Geldanamycin
+FCGR3B interactsWith Ligand_5/9
+FCGR3B interactsWith Ligand_12/3
+CtBP pp EBNA3C
+RB1 pp E1A
+p53 interactsWith Zn2+
+SHP-2 pp CagA
+GZMB interactsWith Ac-IEPD-pNA
+GZMA interactsWith Z-K-SBzl
+PARP9 interactsWith ADP-ribose
+CHD1L interactsWith ADP-ribose
+PARP9 interactsWith PAR
+GZMA interactsWith Suc-AAPR-pNA
+Grb7 interactsWith PA
+Grb7 interactsWith PI(3,5)P2
+Grb7 interactsWith PI(3,4,5)P3
+Grb7 interactsWith PI(4,5)P2
+Grb7 interactsWith PI(3)P
+Grb7 interactsWith PI(5)P
+Grb7 interactsWith PI(3,4)P2
+Grb7 interactsWith PI(4)P
+pRB pp SV40_T_antigen
+MOF interactsWith unknown
+Unknown interactsWith Tax
+CBP interactsWith Unknown
+p53 pp SV40_large_T_antigen
+ITGA2 pp Ems16_A_Chain
+ITGA2 pp Ems16_B_Chain
+ARHGEF1 pp Guanine_Nucleotide-Binding_Protein_Galpha(13)_:galpha(I1)_Chimera
+ARHGEF1 pp Guanine_Nucleotide-Binding_Protein_Galpha(13)_:galpha(I1)_Chimera
+ARHGEF1 pp Guanine_Nucleotide-Binding_Protein_Galpha(13)_:galpha(I1)_Chimera
+CDK4 pp SaHV2gp73
+Calmodulin_2 pp pxo1_122
+Calmodulin_2 pp pxo1_122
+CALM2 pp pxo1_122
+Calmodulin_2 pp pxo1_122
+Calmodulin_2 pp pxo1_122
+Maguk_P55_Subfamily_Member_5 pp Protein_Associated_To_Tight_Junctions
+Maguk_P55_Subfamily_Member_5 pp Protein_Associated_To_Tight_Junctions
+T_Cell_Receptor_Alpha_Chain pp Mbp_Peptide
+T-Cell_Receptor_Beta_Chain pp Mbp_Peptide
+AVPR1A pp Maltose-Binding_Periplasmic_Protein
+SKB1 pp NS3
+Mu-2 interactsWith Ketamine
+TTR interactsWith Compound_1
+TTR interactsWith Compound_22
+TTR interactsWith Compound_21
+TTR interactsWith Compound_20
+TTR interactsWith Compound_19
+TTR interactsWith Compound_15
+TTR interactsWith Compound_14
+TTR interactsWith Compound_13
+TTR interactsWith Compound_11
+TTR interactsWith Compound_3
+TTR interactsWith Compound_9
+TTR interactsWith Compound_10
+CD80 interactsWith Compound_2
+CYP2D6 interactsWith Nor-BUP
+CYP2D6 interactsWith BUP
+CYP3A4 interactsWith BUP
+TTR interactsWith Compound_18
+TTR interactsWith Compound_17
+TTR interactsWith Compound_16
+TTR interactsWith Compound_12
+hNMT1 pp mu-1
+MT1/MT2_heterodimer interactsWith melatonin
+MT1_receptor interactsWith melatonin
+MT2_receptor interactsWith melatonin
+p38-2 interactsWith ATP
+CRM1 interactsWith unknown
+p27 pp E1A
+Unknown interactsWith Gag-Pol
+Unknown interactsWith Vif
+Unknown interactsWith Gag
+ABCE1 interactsWith Unknown
+CYP1A2 interactsWith Caffeine
+CYP1A1 interactsWith Caffeine
+B2 interactsWith HOE_140
+CYP1A1 interactsWith Progesterone
+CYP1A1 interactsWith Phenacetin
+CYP1A2 interactsWith Phenacetin
+CYP1A2 interactsWith 17beta-estradiol
+CYP1A1 interactsWith 17beta-estradiol
+Calmodulin interactsWith BN2
+Calmodulin interactsWith BN1
+Calmodulin interactsWith BT2
+Calmodulin interactsWith MT2
+Calmodulin interactsWith BT1
+Calmodulin interactsWith MT5
+Calmodulin interactsWith Tryptamine
+Calmodulin interactsWith MT7
+Calmodulin interactsWith MT3
+PChE interactsWith Heroin
+hCE-2 interactsWith 6-MAM
+PChE interactsWith 6-MAM
+hCE-2 interactsWith Cocaine_HCl
+PChE interactsWith Cocaine_HCl
+hCE-2 interactsWith Heroin
+CYP3A4 interactsWith NorLAAM
+CYP3A4 interactsWith Methadone
+CYP3A4 interactsWith LAAM
+TNFR1 pp protein_A
+CYP2D6.17 interactsWith Dextromethorphan
+CYP2D6.17 interactsWith Fluoxetine
+CYP2D6.2 interactsWith Fluoxetine
+CYP2D6.2 interactsWith Dextromethorphan
+CYP2D6.1 interactsWith Codeine
+c-Rel interactsWith Unknown
+c-Rel interactsWith Unknown
+Cot/Tpl2 interactsWith Unknown
+I-TRAF interactsWith Unknown
+IkBalpha interactsWith Unknown
+IkBalpha interactsWith Unknown
+IkBbeta interactsWith Unknown
+IkBbeta interactsWith Unknown
+IkBepsilon interactsWith Unknown
+IkBepsilon interactsWith Unknown
+IKKalpha interactsWith Unknown
+IKKalpha interactsWith Unknown
+IKKbeta interactsWith Unknown
+IKKepsilon interactsWith Unknown
+IKKepsilon interactsWith Unknown
+IKKgamma interactsWith Unknown
+MEKK1 interactsWith Unknown
+MEKK3 interactsWith Unknown
+MEKK3 interactsWith Unknown
+NF-kB1/p105 interactsWith Unknown
+NF-kB1/p50 interactsWith Unknown
+NF-kB1/p50 interactsWith Unknown
+NF-kB2/p100 interactsWith Unknown
+NF-kB2/p100 interactsWith Unknown
+NF-kB2/p52 interactsWith Unknown
+NF-kB2/p52 interactsWith Unknown
+NIK interactsWith Unknown
+RelA interactsWith Unknown
+RelB interactsWith Unknown
+RelB interactsWith Unknown
+TAB1 interactsWith Unknown
+TAB2 interactsWith Unknown
+TAK1 interactsWith Unknown
+TBK1 interactsWith Unknown
+TNFR1 interactsWith Unknown
+TNFR1 interactsWith Unknown
+TNFR2 interactsWith Unknown
+TNFR2 interactsWith Unknown
+TRADD interactsWith Unknown
+TRAF1 interactsWith Unknown
+TRAF6 interactsWith Unknown
+hPPAR-gamma interactsWith P3,4I
+hPPAR-gamma interactsWith P3,5I
+hPPAR-gamma interactsWith P5I
+hPPAR-gamma interactsWith P4,5I
+hPPAR-gamma interactsWith P3,4,5I
+hLRH-1 interactsWith P5I
+hLRH-1 interactsWith P4I
+hLRH-1 interactsWith P3I
+hLRH-1 interactsWith P4,5I
+hLRH-1 interactsWith P3,5I
+hLRH-1 interactsWith P3,4,5I
+hLRH-1 interactsWith P3,4I
+MCM8 interactsWith ATP
+Caspase-7 interactsWith Ac-DEVD-afc
+ARTS-1 interactsWith Ile
+ARTS-1 interactsWith Phe
+ARTS-1 interactsWith Gly
+ARTS-1 interactsWith Cys
+ARTS-1 interactsWith Leu
+ARTS-1 interactsWith Met
+ARTS-1 interactsWith Ala
+ARTS-1 interactsWith Pro
+ARTS-1 interactsWith Val
+PRMT1 interactsWith SAM
+PRMT2 interactsWith SAM
+p53 pp large_T_antigen
+GRB2 interactsWith Unknown
+UGT1A1 interactsWith 5-hydroxyrofecoxib
+UGT1A4 interactsWith 5-hydroxyrofecoxib
+Beta-Glucuronidase interactsWith 5-hydroxyrofecoxib_O-glucuronide
+UGT2B7 interactsWith 5-hydroxyrofecoxib
+UGT2B15 interactsWith 5-hydroxyrofecoxib
+UGT1A9 interactsWith 5-hydroxyrofecoxib
+UGT1A8 interactsWith 5-hydroxyrofecoxib
+UGT1A6 interactsWith 5-hydroxyrofecoxib
+UGT1A3 interactsWith 5-hydroxyrofecoxib
+GRB2 interactsWith Unknown
+PLCG1-TRPC3 interactsWith PtdIns(3,5)P2
+PLCG1-TRPC3 interactsWith PtdIns(4,5)P2
+PLCG1-TRPC3 interactsWith PtdIns(3,4,5)P3
+FKBP1A interactsWith 2-(2-pyridyl)benz-imidazole
+FKBP1A interactsWith N-cyclohexyl-p_toluenesulphonamide
+INDO interactsWith 1MT
+INDO interactsWith MTH-trp
+INDO interactsWith N-Formylkynurenine
+ARF6 interactsWith GTP
+ARF6 interactsWith GDP
+MBD2 pd HTLV-1_5'_LTR
+HIST3H3 pd HTLV-1_5'_LTR
+MKP-3 interactsWith pNPP
+NSEP1 interactsWith TAR
+BRG1 interactsWith ATP
+SNF2H interactsWith ATP
+PARP10 interactsWith NAD+
+RAN interactsWith GTP
+CyPB pp NS5B
+CyPB pp Gag
+CyPB pp Pr55gag
+CyPA pp Gag
+CyPB interactsWith NS5B-HCV
+Arf1 interactsWith GTP
+H2AFY interactsWith OAADPR
+H2AFY interactsWith ADPR
+BMX interactsWith PtdIns(3,4,5)P3
+DOCK1 interactsWith PtdIns(3,5)P2
+AKT1 interactsWith PtdIns(3,4,5)P3
+DOCK1 interactsWith PtdIns(3,4,5)P3
+EFNB2 pp G
+E2F-7 pd E2A_promoter
+E2F-8 pd E2A_promoter
+eIF-4E interactsWith 7-methyl-GTP
+Midkine interactsWith heparin
+LTF pp 1LGB_A
+ERBB2 pp Herceptin_Fab_(Antibody)_-_Heavy_Chain
+CALM2 pp Calmodulin-Sensitive_Adenylate_Cyclase
+Galphai2 interactsWith GTP
+Galphai3 interactsWith GTP
+Galphao interactsWith GTP
+Galphai1 interactsWith GTP
+IPR2 interactsWith Heme
+IPR2 interactsWith ferrous-CO_heme
+IPR2 interactsWith Hemin
+Syntenin-1 interactsWith PtdIns(4,5)P2
+PLC-delta-1 interactsWith PtdIns(3,4,5)P3
+PLC-delta-1 interactsWith PtdIns(3,5)P2
+PLC-delta-1 interactsWith PtdIns(3,4)P2
+Magi-3 interactsWith PtdIns(4,5)P2
+PAR-6 interactsWith PtdIns(4,5)P2
+EBP50 interactsWith PtdIns(4,5)P2
+PLC-delta-1 interactsWith PtdIns(4,5)P2
+PLCD1 interactsWith PtdIns(4,5)P2
+OSBP interactsWith PtdIns4P
+DAPP1 interactsWith PtdIns(3,4)P2
+DAPP1 interactsWith PtdIns3,4P2.
+cyt_c interactsWith TOCL
+Bb pp SCIN
+WARTS interactsWith Unknown
+AcP interactsWith Benzoylphosphate
+Beta-2-Microglobulin pp H-2_Class_I_Histocompatibility_Antigen,_K-D_Alpha_Chain
+Ras-Related_Protein_Ral-A pp Exocyst_Complex_Protein_Exo84
+Ras-Related_Protein_Ral-A pp Exocyst_Complex_Protein_Exo84
+Tissue_Factor_Pathway_Inhibitor_2 pp Cationic_Trypsin
+PIK3CG interactsWith PtdIns(4,5)P2
+Rab5a interactsWith GTP
+Rab41 interactsWith GTP
+Rab5c interactsWith GTP
+Rab5b interactsWith GTP
+PI4KIII-beta interactsWith PtdIns
+Hef interactsWith ATP
+AP-2 pd SV40_lntergenic_Control_Region
+Sp1 pd hMT_IIA_promoter
+Sp1 pd SV40_lntergenic_Control_Region
+AP-2 pd hMT_IIA_promoter
+PI3K-beta interactsWith LY294002
+PI3K-alpha interactsWith LY294002
+PI3K-gamma interactsWith Wortmannin
+PI3K-delta interactsWith Wortmannin
+PI3K-alpha interactsWith Wortmannin
+PI3K-delta interactsWith AS-605240
+PI3K-alpha interactsWith AS-605240
+PI3K-alpha interactsWith AS-604850
+PI3K-gamma interactsWith AS-604850
+PI3K-gamma interactsWith AS-605240
+PI3K-beta interactsWith Wortmannin
+PI3K-delta interactsWith LY294002
+PI3K-beta interactsWith AS-605240
+PI3K-delta interactsWith ATP
+PI3K-beta interactsWith ATP
+PI3K-gamma interactsWith ATP
+PI3K-alpha interactsWith ATP
+PI3K-delta interactsWith PtdIns
+PI3K-beta interactsWith PtdIns
+PI3K-alpha interactsWith PtdIns
+PIK3CA interactsWith PtdIns
+PI3K-gamma interactsWith PtdIns
+PIK3CG interactsWith PtdIns
+PI3K-gamma interactsWith LY294002
+GluR6b interactsWith Unknown
+GluR6a interactsWith Unknown
+GluR6a interactsWith Unknown
+mPGES-1 interactsWith PGH2
+PLAUR pp Antagonist_Peptide
+PLAUR pp Antagonist_Peptide
+beta-parvin interactsWith Unknown
+eIF4AIII interactsWith ATP
+RC2 interactsWith Chitobiose
+CDK6 pp Cyclin_Homolog
+Girdin interactsWith PI(4)P
+Girdin interactsWith PI(3)P
+Calmodulin pp Cyaa_With_C-Terminal_Calmodulin
+Lymphocyte_Cytosolic_Protein_2 pp 1-Phosphatidylinositol-4,5-Bisphosphate_Phosphodiesterase_Gamma_1
+RhoA interactsWith GTP
+RhoA interactsWith GTP
+RhoA interactsWith GTP
+Rac1 interactsWith GTP
+Rac1 interactsWith GTP
+Rac1 interactsWith GTP
+Cdc42 interactsWith GTP
+Cdc42 interactsWith GTP
+Cdc42 interactsWith GTP
+IDO interactsWith L-tryptophan
+Vascular_Endothelial_Growth_Factor pp Fab_Fragment
+IL10RA pp Viral_Interleukin-10_Homolog
+T_Cell_Receptor_Alpha_Chain pp Myelin_Basic_Protein
+T_Cell_Receptor_Beta_Chain pp Myelin_Basic_Protein
+T_Cell_Receptor_Beta_Chain pp Myelin_Basic_Protein
+T_Cell_Receptor_Beta_Chain pp Myelin_Basic_Protein
+T_Cell_Receptor_Beta_Chain pp Myelin_Basic_Protein
+PSIP1 pp gag-pol
+PSIP1 pp gag-pol
+PSIP1 pp gag-pol
+PSIP1 pp gag-pol
+Sb27_T_Cell_Receptor_Beta_Chain pp Ebv_Peptide_Lpeplpqgqltay
+Sb27_T_Cell_Receptor_Beta_Chain pp Ebv_Peptide_Lpeplpqgqltay
+Sb27_T_Cell_Receptor_Alpha_Chain pp Ebv_Peptide_Lpeplpqgqltay
+1U35_J pd Hist2h4
+1U35_J pd Hist1h3g
+1U35_I pd Hist2h4
+1U35_I pd Hist2h4
+1U35_I pd Hist1h3g
+1U35_I pd Hist1h3g
+Calmodulin pp Bifunctional_Hemolysin-Adenylate_Cyclase
+Peripheral_Plasma_Membrane_Protein_Cask pp Lin-7
+PPIA interactsWith BMT-ABA-SAR-MLE-VAL-MLE-ALA-ALA-MLE-MLE-MVA
+PPIA interactsWith BMT-ABA-SAR-MLE-VAL-MLE-ALA-ALA-MLE-MLE-MVA
+PPIA interactsWith DMT-ABA-SAR-MLE-VAL-MLE-ALA-ALA-MLE-MLE-MVA
+PPIA interactsWith DMT-ABA-SAR-MLE-VAL-MLE-ALA-ALA-MLE-MLE-MVA
+CRABP-II interactsWith RA
+CFTR interactsWith ATP
+Fab_Fragment,_Heavy_Chain pp H(+)CL(-)_Exchange_Transporter_Clca
+Fab_Fragment,_Light_Chain pp H(+)CL(-)_Exchange_Transporter_Clca
+Fab_Fragment,_Heavy_Chain pp H(+)CL(-)_Exchange_Transporter_Clca
+Von_Willebrand_Factor pp Nmc-4_Igg1
+MEIS1_HUMAN pp HXA9_MOUSE
+Retinoblastoma-Associated_Protein pp Large_T_Antigen
+1U35_J pd Hist3h2ba
+1U35_J pd Hist3h2ba
+1U35_I pd Hist3h2ba
+1U35_I pd Hist3h2ba
+Cell_Division_Cycle_42_Isoform_1 pp Collybistin_Ii
+Cell_Division_Cycle_42_Isoform_1 pp Collybistin_Ii
+Nuclear_Receptor_Coactivator_1 pp Creb-Binding_Protein
+2F8N_I pd Histone_H2a_Type_1
+2F8N_J pd Histone_H2a_Type_1
+2F8N_J pd Histone_H4
+2F8N_J pd Core_Histone_Macro-H2a.1
+2F8N_J pd Histone_H2b.1
+2F8N_I pd Histone_H2b.1
+2F8N_I pd Core_Histone_Macro-H2a.1
+2F8N_I pd Histone_H4
+2F8N_I pd Histone_H4
+Cdc4 pp Cyclin_E1
+VV-35kDa pp hMCP-1
+Taxol interactsWith TUBB
+Synstab_A interactsWith TUBB
+Nocodazole interactsWith Tubulin-beta
+PymT pp PI3K_p85-alpha
+Unknown interactsWith MLH1
+Unknown interactsWith MRE11
+Unknown interactsWith RFC-p140
+Unknown interactsWith NBS1
+Unknown interactsWith RFC-p37
+Unknown interactsWith RFC-p40
+Unknown interactsWith BLM
+PorB pp VDAC
+HA pp CANX
+Protein_F pp CANX
+HA pp CALR
+HA pp GRP_78
+Protein_F pp GRP_78
+HCV_core pp p73
+STI-571 interactsWith BCR-ABL
+HA pp CD46
+NS5A pp KPNB3
+NS5A pp apoA1
+gH pp CD46
+HCV_core pp hnRNPK
+IE63 pp hnRNPK
+Tat pp Egr2
+Tat pp Egr1
+Tat pp Egr3
+IE62 pp Sp1
+NS5A pp apoA1
+E3L pp SUMO-1
+E3L pp L23a
+MA pp EF1-alpha
+Gag pp EF1-alpha
+Gag pp KIF-4
+Vif pp CypA
+Nef pp CypA
+VacA pp VIP54
+Unknown interactsWith TFIIHp62
+Unknown interactsWith RNA_polymerase_II
+Unknown interactsWith TAF250
+NS3 pp NRBP
+IE2_86 pp Rb
+IN pp UNG2
+IN pp UNG2
+Gag interactsWith BAF/BAF
+MA interactsWith BAF/BAF
+E1E2_heterodimer interactsWith CD81
+Compound_3 interactsWith cIAP2
+Compound_3 interactsWith cIAP_1
+Compound_3 interactsWith XIAP
+EICP27 pp TBP
+Tat interactsWith RNAPII
+Tat interactsWith unknown
+Gag pp APOBEC3G
+A36R pp Nck
+A36R pp TPR
+HPV16_E1 pp 16E1-BP
+HPV16_E1 pp hUBC9
+Phosphonate_Inhibitor_Suc-Val-Pro-Lysp-(Oph)2 pp CTSG
+Tax pp TTP
+Tax pp TIP-1
+Tax pp GLUT
+Tax pp P5CD
+Tax pp MSX2
+Tax pp GNB2
+Tax pp KIAA0184_protein
+Tax-1 pp TTP
+E7 pp hTid-1
+E7 pp hTid-1
+TAg pp p70
+Integrase pp Rad18
+JlpA pp Hsp90-alpha
+DEN4_3'UTR(-) interactsWith La
+Unknown interactsWith CALR
+Unknown interactsWith PDI
+VP26 pp RP3
+VP26 pp Tctex1
+VP11/12 pp RP3
+VP11/12 pp Tctex1
+Vpr pp TFIIB
+AfaE pp DAF
+EBNA-3C pp J-kappa-1
+EBNA-3C pp RBP-2N
+EBNA-3A pp J-kappa-1
+1R49_B pd TOP1MT
+1R49_C pd TOP1MT
+Bisubstrate_Inhibitor pp INSR
+Bisubstrate_Inhibitor pp INSR
+Coat_Protein_Vp1 pp PVR
+1O4X_C pd SOX2
+1O4X_C pd POU2F1
+1O4X_D pd POU2F1
+1O4X_D pd SOX2
+Talin pp VCL
+Gp120_V3_Peptide pp Fab_447-52d,_Heavy_Chain
+Gp120_V3_Peptide pp IGLL1
+1RG1_F pd TDP1
+1RGT_F pd TDP1
+1RGO_D interactsWith ZFP36L1
+1RGU_D pd TDP1
+1RZT_B pd POLL
+1RZT_D pd POLL
+Alpha-I_Gliadin pp HLA-DOA
+Alpha-I_Gliadin pp HLA-DQB1
+Hirudin_Iib pp F2
+Hirudin_Iib pp F2
+1OZJ_C pd SMAD3
+1OZJ_C pd SMAD3
+1OZJ_D pd SMAD3
+1OZJ_D pd SMAD3
+1Q3F_B pd UNG
+Hemagglutinin_Peptide pp HLA-DOA
+Superantigen pp HLA-DRB4
+Superantigen pp HLA-DOA
+1M3H_C pd OGG1
+1M3H_D pd OGG1
+B2.1_Peptide pp Immunoglobulin_Heavy_Chain
+B2.1_Peptide pp Immunoglobulin_Light_Chain
+B2.1_Peptide pp Immunoglobulin_Heavy_Chain
+B2.1_Peptide pp Immunoglobulin_Light_Chain
+B2.1_Peptide pp Immunoglobulin_Heavy_Chain
+1RY1_E interactsWith Signal_Recognition_Particle_14_Kda_Protein
+1RY1_E interactsWith SRP9
+1RY1_M interactsWith SRP9
+Maguk_P55_Subfamily_Member_5 pp Pals1-Associated_Tight_Junction_Protein
+Maguk_P55_Subfamily_Member_5 pp Pals1-Associated_Tight_Junction_Protein
+Maguk_P55_Subfamily_Member_5 pp Pals1-Associated_Tight_Junction_Protein
+Maguk_P55_Subfamily_Member_5 pp Pals1-Associated_Tight_Junction_Protein
+Pol_Polyprotein pp HLA-A
+Pol_Polyprotein pp HLA-A
+Negative_Factor pp HLA-A
+Acetyl-Asp-Glu-Val-Asp pp Caspase-3
+Acetyl-Asp-Glu-Val-Asp pp Caspase-3
+Ace-Val-Asp pp Caspase-3
+Ace-Val-Asp pp Caspase-3
+Hirugen pp F2
+1SI2_B interactsWith EIF2C1
+1SI3_B interactsWith EIF2C1
+1VBY_B interactsWith SNRPA
+Brca1_Interacting_Protein_C-Terminal_Helicase_1 pp BRCA1
+Brctide-7ps pp BRCA1
+1T42_B interactsWith SNRPA
+10-Mer_Peptide_From_Nuclear_Receptor_Coactivator_2 pp RXRG
+10-Mer_Peptide_From_Nuclear_Receptor_Coactivator_2 pp NR1H3
+C-Terminal_Peptide_From_Beta-Secretase pp GGA1
+C-Terminal_Peptide_From_Beta-Secretase pp GGA1
+Acetyl_Hirudin pp PROC
+1T38_B pd Methylated-Dna--Protein-Cysteine_Methyltransferase
+1T38_C pd Methylated-Dna--Protein-Cysteine_Methyltransferase
+1T39_C pd Methylated-Dna--Protein-Cysteine_Methyltransferase
+1T39_D pd Methylated-Dna--Protein-Cysteine_Methyltransferase
+1T3N_T pd Polymerase_(Dna_Directed)_Iota
+1T3N_T pd Polymerase_(Dna_Directed)_Iota
+1T3N_P pd Polymerase_(Dna_Directed)_Iota
+1T3N_P pd Polymerase_(Dna_Directed)_Iota
+Steroid_Receptor_Coactivator-1 pp Estrogen-Related_Receptor_Gamma
+Steroid_Receptor_Coactivator-1 pp Estrogen-Related_Receptor_Gamma
+Inhibitor pp Prothrombin
+EBNA-3C pp Nm23-H1
+EBNA-3C pp SUMO-1
+EBNA-3C pp SUMO-3
+A73 pp RACK1
+RPMS1 pp CBF1
+NSP4 pp Laminin-beta-3
+NSP4 pp Fibronectin
+NS5A pp Hck
+NS5A pp Lck
+NS5A pp Lyn
+NS5A pp Fyn
+NS5A pp Grb2
+P4ha2 pp P4HB
+Tank pp TRAF2
+Prkcsh pp PRKCSH
+Psmc5 pp ERCC3
+Nrg3 pp ERBB4
+Anp32a pp SCA1
+Bap1 pp BRCA1
+Hif3a pp AHR
+Shcbp1 pp SHC1
+Casp8ap2 pp CASP8
+Casp8ap2 pp TNFRSF6
+Tiam2 pp RAC1
+Rybp pp YY1
+Cdc42ep5 pp CDC42
+Rhoq pp CDC42EP4
+Actr10 pp ACTR1A
+Gng13 pp GNB1
+Gtn pp GNB1
+AW742319 pp RAC1
+Txnip pp TXN
+Cdc42ep5 pp CDC42
+Pdcd1lg2 pp PDCD1
+Dusp16 pp MAPK8
+Dusp16 pp MAPK1
+Tirap pp TLR4
+Cd22 pp PTPNS1
+Cd22 pp GRB2
+Hdac6 pp UBC
+Myod1 pp MADH3
+Mx1 pp SP100
+Cotl1 pp ALOX5
+Rpl12 pp IPO11
+Adprtl2 pp LIG3
+Adprtl2 pp POLB
+Adprtl2 pp XRCC1
+Adprtl2 pp ADPRT
+Tada3l pp TADA2L
+Cdkn2a pp ALS2CR8
+Rgs13 pp GNAI2
+Rgs13 pp GNAQ
+Nid1 pp COL4A2
+Nid1 pp COL4A1
+Nid2 pp COL4A1
+Nid2 pp COL4A2
+Nid2 pp ITGB3
+Nid2 pp ITGA5
+Hod pp SRF
+Card11 pp BCL10
+Vgll2 pp TEAD1
+Stk4 pp PRKRIR
+Prkwnk4 pp SLC12A3
+Sin3a pp MAD
+Sin3b pp MAD
+Prkrip1 pp PRKR
+Myh10 pp PBX1
+Jam4 pp BAIAP1
+Nr1i3 pp PPP2CB
+Nr3c1 pp PPP2CB
+Robo4 pp SLIT2
+DEN_core pp hnRNP_E2
+Tat pp CBP
+Tat pp Notch1
+Tat pp Notch2
+MA pp HO3
+Xpac interactsWith XPA
+PPARG pp NCOA4
+PPARG pp NCOA4
+SYK pp CBL
+SSTR2 pp SHANK1
+SSTR2 pp SHANK1
+SIM1 pp ARNT
+SIM2 pp ARNT
+SIM2 pp ARNT2
+HSP90 pp HIF1A
+P50 pp ACTA1
+P50 pp ACTA1
+P50 pp ACTA1
+P50 pp ACTA1
+IL4R pp HTATIP
+DSC1 pp DSG2
+IR-A pp ARF1
+RXRA pp SP1
+RXRA pp SP1
+ACT pp CAP
+ACT pp CAP
+ACT pp CAP2
+GRIN2B pp KARS
+GRIN2B pp SSR4
+UBTF pp TATA_box_binding_protein_(TBP)-associated_factor
+PIK3R3 pp IGF1R
+IRS1 pp INSR
+MAPK1 pp TOP2A
+MAPK1 pp TOP2A
+TNFRSF9 pp TRAF2
+TNFRSF4 pp TRAF2
+TNFRSF9 pp TRAF2
+TNFRSF4 pp TRAF2
+TNFRSF9 pp TRAF1
+TNFRSF4 pp TRAF3
+TNFRSF4 pp TRAF1
+RXRB pp GTF2B
+PTPN11 pp GHR
+PTPN11 pp GHR
+KSR pp GNB1/GNG3
+KSR pp GNB1/GNG3
+GP49B pp PTPN6
+GP49B pp PTPN11
+SHC pp GRB2
+STAT6 pp NFKBIA
+MLLT4 pp EPHB3
+MLLT4 pp EPHB6
+MLLT4 pp EPHB3
+SYK pp EPOR
+SYK pp EPOR
+STAT5A pp CITED1
+PRKAR1A pp COX5B
+PRKAR1A pp COX5B
+GNAI3 pp RGS3
+SHC pp GRB2
+SLC6A9 pp GABRR1
+SLC6A9 pp GABRR1
+NCF2 pp PRKCABP
+AP3B2 pp ATM
+TRAF2 pp TNFRSF7
+AXIN1 pp DVL1
+AXIN1 pp GSK3B
+AXIN1 pp CTNNB1
+AHR pp RB1
+AHR pp RB1
+PIM1 pp CBX3
+PIM1 pp CBX3
+CCT6 pp STIP1
+RND1 pp GRB7
+EPAS1 pp APEX1
+ZAC1 pp AR
+ZAC1 pp ESR1
+ZAC1 pp THRB
+NCOA2 pp AR
+NCOA2 pp ESR1
+NCOA2 pp THRB
+NR1I2 pp NRIP1
+STX1A pp SNPH
+STX1A pp SNPH
+STX1A pp SNPH
+ABL1 pp NTRK1
+PLCG1 pp NTRK1
+SH2BPSM1 pp NTRK1
+BMPR1B pp BMPR1A
+ARHE pp ARHGAP5
+RND1 pp ARHGAP5
+ARHN pp ARHGAP5
+PAPOLA pp YWHAE
+NS5A pp hVAP-33
+NS5B pp hVAP-33
+NS5B pp Hydroxyacid_oxidase_1
+NS5B pp Tetratricopeptide_repeat_protein_4
+NS3 pp LMP7
+NS5B pp Alpha-actinin
+HCV_core pp DBX
+Rev pp ACTB
+Rev pp CSNK2B
+Rev pp CDC2
+Rev pp C1QBP
+Rev pp XPO1
+Rev pp EIF5A
+Rev pp LGALS3
+Rev pp KHDRBS1
+Rev pp HNRPA1
+Rev pp HRB
+Rev pp NFKBIA
+Rev pp IFITM1
+Rev pp KPNB1
+Rev pp LMNA
+Rev pp MAPK1
+Rev pp NPM1
+Rev pp NUP153
+Rev pp NUP214
+Rev pp NUP62
+Rev pp NUP98
+Rev pp NUPL2
+Rev pp ITPA
+Rev pp PABPC1
+Rev pp PTBP1
+Rev pp PRKCA
+Rev pp PTMA
+Rev pp RANBP1
+Rev pp RAN
+Rev pp HRBL
+Rev pp RPL5
+Rev pp DHX9
+Rev pp SNRPA1
+Rev pp SFRS1
+Rev pp SFRS2
+Rev pp TGM2
+Rev pp K-ALPHA-1
+Rev pp HNRPK
+Vif pp CD4
+Vif pp APOBEC3G
+Vif pp PPIA
+Vif pp VIM
+Vif pp PLEC1
+Vif pp HCK
+Vif pp ABCE1
+Vif pp MAPK1
+Vif pp G22P1
+Vif pp SP140
+Vpu pp CSNK2B
+Vpu pp SGTA
+Vpu pp TNFRSF6
+Vpu pp BTRC
+Vpu pp NFKBIA
+Vpu pp NFKB1
+Vpu pp CASP3
+Vpu pp BCL2L1
+Vpu pp BCL2A1
+Vpu pp TRAF1
+Vpu pp HLA-A
+Vpu pp HLA-B
+Vpu pp HLA-C
+Vpu pp CD4
+Vpr pp SLC25A4
+Vpr pp VDAC1
+Vpr pp BAX
+Vpr pp BCL2
+Vpr pp CYC1
+Vpr pp TNF
+Vpr pp BCL2L1
+Vpr pp CDH1
+Vpr pp ITGA5
+Vpr pp ITGA6
+Vpr pp ACTG1
+Vpr pp VIL2
+Vpr pp RHOA
+Vpr pp RHOB
+Vpr pp RHOG
+Vpr pp ARHGDIA
+Vpr pp CASP1
+Vpr pp CASP8
+Vpr pp CASP9
+Vpr pp CASP3
+Vpr pp CD4
+Vpr pp CCL5
+Vpr pp CCL3
+Vpr pp CCL4
+Vpr pp CCL1
+Vpr pp IL8
+Vpr pp IL10
+Vpr pp CCNT1
+Vpr pp CDK9
+Vpr pp NR3C1
+Vpr pp GTF2B
+Vpr pp TBP
+Vpr pp NCOA1
+Vpr pp NUPL2
+Vpr pp HSPA1A
+Vpr pp NUP54
+Vpr pp XPO1
+Vpr pp LMNA
+Vpr pp LMNB1
+Vpr pp KPNB1
+Vpr pp KPNA1
+Vpr pp KPNA2
+Vpr pp KARS
+Vpr pp BIRC5
+Vpr pp WEE1
+Vpr pp VprBP
+Rev pp HRB2
+Vpr pp SP1
+Vpr pp TP53
+Vpr pp UNG
+Vpr pp RAD23A
+Vpr pp PAPOLA
+Vpr pp GTF2H1
+Vpr pp CDK7
+Vpr pp CCNH
+Vpr pp MNAT1
+Vpr pp COPS6
+Vpr pp NFKBIA
+Vpr pp IFNG
+Vpr pp IL6
+Vpr pp CEBPB
+Vpr pp IL2
+Vpr pp IL4
+Vpr pp IL12A
+Vpr pp NFKB1
+Vpr pp CD44
+Vpr pp TLR4
+Vpr pp INDO
+Vpr pp MARCO
+Vpr pp THBS1
+Vpr pp ATF1
+Vpr pp RELA
+Vpr pp EP300
+Vpr pp CREBBP
+Vpr pp POLR2A
+Vpr pp POLR2B
+Vpr pp POLR2C
+Vpr pp POLR2D
+Vpr pp POLR2E
+Vpr pp POLR2F
+Vpr pp POLR2G
+Vpr pp POLR2H
+Vpr pp POLR2I
+Vpr pp POLR2J
+Vpr pp POLR2K
+Vpr pp POLR2L
+Vpr pp PPP2R2A
+Vpr pp PPP2R2B
+Vpr pp PPP2R2C
+Vpr pp PPP2R3A
+Vpr pp PPP2R4
+Vpr pp PPP2R5A
+Vpr pp PPP2R5B
+Vpr pp PPP2R5C
+Vpr pp PPP2R5D
+Vpr pp PPP2R5E
+Vpr pp YWHAB
+Vpr pp YWHAE
+Vpr pp YWHAG
+Vpr pp YWHAH
+Vpr pp YWHAZ
+Vpr pp TEBP
+Vpr pp CDC2
+Vpr pp CCNB1
+Vpr pp CCNB2
+Vpr pp CCNB3
+Vpr pp CDC25C
+Matrix pp CALM1
+Matrix pp CALM2
+Matrix pp CALM3
+Matrix pp PPIA
+Matrix pp EEF1A1
+Matrix pp EED
+Matrix pp EIF5B
+Matrix pp HARSL
+Matrix pp HSPA1A
+Matrix pp ICAM1
+Matrix pp IFNG
+Matrix pp TNF
+Matrix pp IL4
+Matrix pp IL2
+Matrix pp IL12A
+Matrix pp IL12B
+Matrix pp IL15
+Matrix pp IL6
+Matrix pp TNIP1
+Matrix pp PRKCA
+Matrix pp PRKACA
+Matrix pp PRKACB
+Matrix pp PRKACG
+Matrix pp PRKAG1
+Matrix pp PRKAR1A
+Matrix pp PRKAR1B
+Matrix pp PRKAR2A
+Matrix pp EP300
+Matrix pp PAK2
+Vpu pp CSNK2A1
+Vpu pp CSNK2A2
+Rev pp CSNK2A1
+Rev pp CSNK2A2
+Matrix pp CSNK2A1
+Matrix pp CSNK2A2
+Matrix pp CSNK2B
+Matrix pp NMT1
+Matrix pp NMT2
+Matrix pp XPO1
+Matrix pp THY1
+Matrix pp CD59
+Matrix pp FBP1
+Matrix pp FBP2
+Matrix pp CYP27B1
+Matrix pp NCL
+Matrix pp MAPK1
+Matrix pp MAPK3
+Matrix pp KPNA1
+Matrix pp KPNA2
+Matrix pp KPNA3
+Matrix pp KPNA4
+Matrix pp KPNA5
+Matrix pp KPNA6
+Matrix pp KPNB1
+Matrix pp TNPO1
+Matrix pp RANBP5
+Matrix pp NUTF2
+Matrix pp RAN
+Matrix pp HMGA1
+Vpr pp CDKN1A
+Rev pp MAPK3
+Vif pp MAPK3
+Vpr pp TNPO1
+Vpr pp RANBP5
+Rev pp TNPO1
+Rev pp RANBP5
+Vif pp SAT
+Vif pp TRIAD3
+Capsid pp IFNG
+Capsid pp HLA-DRB1
+Capsid pp HLA-DRB3
+Capsid pp HLA-DRB4
+Capsid pp HLA-DRB5
+Capsid pp HLA-DRA
+Capsid pp CYBB
+Capsid pp CD63
+Capsid pp LAMP1
+Capsid pp PLAUR
+Capsid pp PPIA
+Capsid pp PPIB
+Capsid pp CD2
+Capsid pp CD3D
+Capsid pp CD3E
+Capsid pp CD3G
+Capsid pp CD3Z
+Capsid pp IL10
+Capsid pp PTGES
+Nucleocapsid pp ACTB
+Nucleocapsid pp ACTG1
+Nucleocapsid pp NFKB1
+Nucleocapsid pp SP1
+Nucleocapsid pp GTF2B
+Nucleocapsid pp TOP1
+Nucleocapsid pp PPP2R2A
+Nucleocapsid pp PPP2R2B
+Nucleocapsid pp PPP2R2C
+Nucleocapsid pp PPP2R3A
+Nucleocapsid pp PPP2R4
+Nucleocapsid pp PPP2R5A
+Nucleocapsid pp PPP2R5B
+Nucleocapsid pp PPP2R5C
+Nucleocapsid pp PPP2R5D
+Nucleocapsid pp PPP2R5E
+P6 pp MAPK3
+P6 pp MAPK1
+P6 pp NEDD4
+P6 pp TSG101
+Gag pp VIL2
+Gag pp MSN
+Gag pp CFL1
+Gag pp APOH
+Gag pp PLAU
+Gag pp HSPA1A
+Gag pp HSPD1
+Gag pp HSPA8
+Gag pp STAU
+Gag pp IFNA1
+Gag pp KARS
+Gag pp HLA-DRA
+Gag pp HLA-DRB1
+Gag pp HLA-DRB3
+Gag pp HLA-DRB4
+Gag pp HLA-DRB5
+Gag pp ABCE1
+Gag pp KIF4A
+Gag pp SGTA
+Gag pp PPIA
+Integrase pp FEN1
+Integrase pp ATR
+Integrase pp HMGA1
+Integrase pp RAD18
+Integrase pp ATM
+Integrase pp XRCC5
+Integrase pp BANF1
+Integrase pp PRKDC
+Integrase pp G22P1
+Integrase pp PARP1
+Integrase pp HSPD1
+Integrase pp HSPE1
+Integrase pp PCK1
+Integrase pp CCT4
+Integrase pp EEF1A1
+Integrase pp KPNA1
+Integrase pp KPNA2
+Integrase pp KPNA3
+Integrase pp KPNA4
+Integrase pp KPNA5
+Integrase pp KPNA6
+Integrase pp KPNB1
+Integrase pp TNPO1
+Integrase pp RANBP5
+Integrase pp SMARCB1
+Integrase pp PML
+Integrase pp PSIP1
+Integrase pp UNG
+Integrase pp EED
+P6 pp PDCD6IP
+Vpr pp UNG2
+Integrase pp UNG2
+P6 pp CUL5
+P6 pp C20orf178
+P6 pp Shax3
+Vif pp C14orf123
+Vif pp TCEB2
+Vif pp TCEB1
+Vif pp RBX1
+Matrix pp BANF1
+Gag pp BANF1
+Vpu pp CTNNB1
+Vpu pp ATF4
+Rev pp KIF22
+Vpr pp NFATC1
+Vpr pp NFATC2
+Vpr pp NFATC3
+Vpr pp NFATC4
+Vpr pp ATR
+Vpr pp CHEK1
+Vpr pp PPIA
+Capsid pp PRKACA
+Capsid pp PRKACB
+Capsid pp PRKACG
+Rev pp TUBB5
+Rev pp TUBB4
+Rev pp TUBB2
+Rev pp TUBB1
+Rev pp TUBB
+Rev pp TUBA8
+Rev pp TUBA6
+Rev pp TUBA4
+Rev pp TUBA3
+Rev pp TUBA2
+Rev pp TUBA1
+Tat pp K-ALPHA-1
+Tat pp TUBB5
+Tat pp TUBB4
+Tat pp TUBB2
+Tat pp TUBB1
+Tat pp TUBB
+Tat pp TUBA8
+Tat pp TUBA6
+Tat pp TUBA4
+Tat pp TUBA3
+Tat pp TUBA2
+Tat pp TUBA1
+Tat pp BCL2L11
+Tat pp BTEB1
+Tat pp TCERG1
+Tat pp CAMK2A
+Tat pp CAMK2B
+Tat pp CREM
+Tat pp TJP2
+Tat pp CLDN5
+Tat pp CLDN1
+Tat pp MYC
+Tat pp COL1A1
+Tat pp COL1A2
+Tat pp NR2F1
+Tat pp CREB1
+Tat pp CTDP1
+Tat pp ADCY1
+Tat pp ADCY2
+Tat pp ADCY3
+Tat pp ADCY4
+Tat pp ADCY5
+Tat pp ADCY6
+Tat pp ADCY7
+Tat pp ADCY8
+Tat pp ADCY9
+Tat pp E2F1
+Tat pp E2F4
+Tat pp EDF1
+Tat pp EEF1D
+Tat pp EGR1
+Tat pp EGR2
+Tat pp EGR3
+Tat pp EIF2S1
+Tat pp EIF2S2
+Tat pp EIF2S3
+Tat pp NOS3
+Tat pp GRN
+Tat pp ZBTB7
+Tat pp COL3A1
+Tat pp CX3CL1
+Tat pp LGALS3
+Tat pp GATA2
+Tat pp GLI2
+Tat pp G6PD
+Tat pp GSK3B
+Tat pp MDM2
+Tat pp UBE1
+Tat pp UBE2D1
+Tat pp UBB
+Tat pp UBC
+Tat pp UBD
+P6 pp UBB
+P6 pp UBC
+P6 pp UBD
+Tat pp BCL11B
+Tat pp CBX5
+Tat pp TRIM32
+Tat pp SDHB
+Tat pp IGFBP4
+Tat pp C1QBP
+Tat pp PAWR
+Tat pp PC4
+Tat pp PSMC2
+Tat pp PPP1CA
+Tat pp PPP1CB
+Tat pp PPP1CC
+Tat pp PPP1R8
+Tat pp NOTCH2
+Tat pp NCOA2
+Tat pp NCOA1
+Tat pp NCOA3
+Tat pp SLC22A1
+Tat pp SLC22A2
+Tat pp WHSC2
+Tat pp NSEP1
+Tat pp YY1
+Tat pp HDAC1
+Tat pp TFCP2
+Tat pp NPM1
+Tat pp BCL2
+Tat pp BAX
+Tat pp POLB
+Tat pp MME
+Tat pp FOS
+Tat pp PML
+Tat pp KPNB1
+Tat pp TNPO1
+Tat pp RANBP5
+Tat pp NOS2A
+Tat pp SSB
+Tat pp UBP1
+Tat pp G22P1
+Tat pp XRCC5
+Tat pp LRP1
+Tat pp A2M
+Tat pp APOE
+Tat pp APP
+Tat pp MRC1
+Tat pp MRC2
+Tat pp HIS1
+Tat pp ENO1
+Tat pp RNGTT
+Tat pp NGFB
+Tat pp PDE4A
+Tat pp PDE4B
+Tat pp PARP1
+Tat pp PAPOLA
+Tat pp PAPOLB
+Tat pp PAPOLG
+Tat pp RBL2
+Tat pp HIVEP1
+Tat pp REL
+Tat pp PRNP
+Tat pp RB1
+Tat pp GPX1
+Tat pp GPX2
+Tat pp GPX3
+Tat pp GPX4
+Tat pp GPX5
+Tat pp GPX6
+Tat pp GSS
+Tat pp TCF7L2
+Tat pp TARDBP
+Tat pp THBS1
+Tat pp THRA
+Tat pp TH
+Tat pp PLAU
+Tat pp SERPINE1
+Nucleocapsid pp PPP2CA
+Vpr pp PPP2CA
+Nucleocapsid pp PPP2CB
+Vpr pp PPP2CB
+Nucleocapsid pp PPP2R1A
+Vpr pp PPP2R1A
+Nucleocapsid pp PPP2R1B
+Vpr pp PPP2R1B
+Tat pp PPP2CA
+Tat pp PPP2CB
+Tat pp PPP2R1A
+Tat pp PPP2R1B
+Tat pp PPP2R2A
+Tat pp PPP2R2B
+Tat pp PPP2R2C
+Tat pp PPP2R3A
+Tat pp PPP2R4
+Tat pp PPP2R5A
+Tat pp PPP2R5B
+Tat pp PPP2R5C
+Tat pp PPP2R5D
+Tat pp PPP2R5E
+Tat pp B2M
+Tat pp CASP8
+Tat pp CASP3
+Tat pp CD4
+Tat pp CCR1
+Tat pp CXCR3
+Tat pp CXCL10
+Tat pp CCL1
+Tat pp CCR2
+Tat pp CCR5
+Tat pp CCR3
+Tat pp CXCR4
+Tat pp CXCL12
+Tat pp ITGB2
+Tat pp ITGA3
+Tat pp ITGA5
+Tat pp ITGB1
+Tat pp ITGAV
+Tat pp ITGB3
+Tat pp ITGB5
+Tat pp ITGB4
+Tat pp IGF1
+Tat pp TGFA
+Tat pp EGF
+Tat pp TGFB1
+Tat pp SMAD3
+Tat pp SMAD4
+Tat pp TNF
+Tat pp LTA
+Tat pp TNFRSF1A
+Tat pp TNFRSF1B
+Tat pp SOD2
+Tat pp MMP9
+Tat pp MMP2
+Tat pp MMP7
+Tat pp MMP1
+Tat pp TIMP2
+Tat pp TIMP1
+Tat pp IFNA1
+Tat pp IFNB1
+Tat pp IFNG
+Tat pp CCL2
+Tat pp CCL5
+Tat pp CCL3
+Tat pp CCL4
+Tat pp CCL8
+Tat pp CCL7
+Tat pp IL1B
+Tat pp IL1A
+Tat pp IL1R1
+Tat pp IL2
+Tat pp IL2RA
+Tat pp IL2RB
+Tat pp IL4
+Tat pp IL4R
+Tat pp IL6
+Tat pp CEBPB
+Tat pp IL8
+Tat pp IL10
+Tat pp IL12A
+Tat pp IL12B
+Tat pp IL13
+Tat pp IL16
+Tat pp CSF2
+Tat pp NFATC2
+Tat pp NFATC1
+Tat pp NFATC3
+Tat pp NFATC4
+Tat pp IRF7
+Tat pp STAT1
+Tat pp TRIM22
+Tat pp CXCL9
+Tat pp TNFSF10
+Tat pp MX1
+Tat pp MT1A
+Tat pp MT1B
+Tat pp MT1E
+Tat pp MT1F
+Tat pp MT1G
+Tat pp MT1H
+Tat pp MT1J
+Tat pp MT1K
+Tat pp MT1X
+Tat pp MT2A
+Tat pp MT3
+Tat pp MT4
+Tat pp PRKR
+Tat pp TAP1
+Tat pp IFIT3
+Tat pp G1P2
+Tat pp SP110
+Tat pp IFI16
+Tat pp IFI35
+Tat pp IFI27
+Tat pp BIRC3
+Tat pp SEMA4D
+Tat pp SERPING1
+Tat pp NCF1
+Tat pp SAT
+Tat pp IFI44
+Tat pp APOBEC3A
+Tat pp SCGB2A1
+Tat pp SCGB2A2
+Tat pp ISG20
+Tat pp PRRX1
+Tat pp LY64
+Tat pp CCND1
+Tat pp METTL1
+Tat pp CAMK1
+Tat pp PPM1F
+Tat pp FGF1
+Tat pp FGF2
+Tat pp SDC1
+Tat pp SDC2
+Tat pp SDC3
+Tat pp SDC4
+Tat pp CDK2
+Tat pp CCNE1
+Tat pp CDC2
+Tat pp FN1
+Tat pp VTN
+Tat pp LAMA1
+Tat pp LAMA2
+Tat pp LAMA3
+Tat pp LAMA4
+Tat pp LAMA5
+Tat pp LAMB1
+Tat pp LAMB2
+Tat pp LAMB3
+Tat pp LAMC1
+Tat pp LAMC2
+Tat pp LAMC3
+Tat pp SELE
+Tat pp VCAM1
+Tat pp ICAM1
+Tat pp SART3
+Tat pp RPL3
+Tat pp TARBP1
+Tat pp TARBP2
+Tat pp EEF1A1
+Tat pp EEF1A2
+Tat pp PTBP1
+Tat pp PTBP2
+Tat pp CCT4
+Tat pp HTATIP2
+Tat pp HTATIP
+Tat pp HTATSF1
+Tat pp SNRPA1
+Tat pp SNRPB
+Tat pp SNRPB2
+Tat pp SNRPD1
+Tat pp SNRPD2
+Tat pp SNRPD3
+Tat pp HUMGT198A
+Tat pp PSMC3
+Tat pp PSMC5
+Tat pp PSMC4
+Tat pp TRAF4
+Tat pp ITGAL
+Tat pp FCGR3A
+Tat pp FCGR3B
+Tat pp CD69
+Vpr pp LMNB2
+Tat pp LMNA
+Tat pp LMNB1
+Tat pp LMNB2
+Tat pp MAP3K14
+Tat pp NFKBIA
+Tat pp NFKBIB
+Tat pp HLA-A
+Tat pp HLA-B
+Tat pp HLA-C
+Tat pp HLA-E
+Tat pp HLA-F
+Tat pp HLA-G
+Tat pp HLA-DRA
+Tat pp HLA-DRB1
+Tat pp HLA-DRB3
+Tat pp HLA-DRB4
+Tat pp HLA-DRB5
+Tat pp TNFRSF5
+Tat pp CD80
+Tat pp CD86
+Tat pp CD83
+Tat pp MHC2TA
+Tat pp GRIN1
+Tat pp GRIN2A
+Tat pp GRIN2B
+Tat pp GRIN2C
+Tat pp GRIN2D
+Tat pp GRIN3A
+Tat pp DPP4
+Tat pp IL1RN
+Tat pp TNFRSF6
+Tat pp TNFSF6
+Tat pp FLT1
+Tat pp KDR
+Tat pp VEGF
+Tat pp ALB
+Tat pp PTK2B
+Tat pp PXN
+Tat pp BCAR1
+Tat pp SRC
+Tat pp CSK
+Tat pp OAS1
+Tat pp OAS2
+Tat pp OAS3
+Tat pp TP53
+Tat pp GH1
+Tat pp PRKCA
+Tat pp PRKCB1
+Tat pp PRKCD
+Tat pp PRKCE
+Tat pp PRKCG
+Tat pp PRKCH
+Tat pp PRKCI
+Tat pp PRKCM
+Tat pp PRKCQ
+Tat pp PRKCZ
+Tat pp PRKCN
+Tat pp PIK3C2A
+Tat pp PIK3C2B
+Tat pp PIK3C2G
+Tat pp PIK3C3
+Tat pp PIK3CA
+Tat pp PIK3CB
+Tat pp PIK3CD
+Tat pp PIK3CG
+Tat pp PIK3R1
+Tat pp PIK3R2
+Tat pp PTK2
+Tat pp PTEN
+Tat pp PDE10A
+Tat pp PDE11A
+Tat pp PDE1A
+Tat pp PDE1B
+Tat pp PDE1C
+Tat pp PDE2A
+Tat pp PDE3A
+Tat pp PDE3B
+Tat pp PDE4C
+Tat pp PDE4D
+Tat pp PDE7A
+Tat pp PDE8A
+Tat pp CNP
+Tat pp AKT1
+Tat pp AKT2
+Tat pp AKT3
+Tat pp BCL2L1
+Tat pp IL3
+Tat pp BAD
+Tat pp BAG1
+Tat pp BCL6
+Tat pp LCK
+Tat pp RELA
+Tat pp SHC1
+Tat pp MAPK3
+Tat pp MAPK1
+Tat pp MAP2K1
+Tat pp MAP2K2
+Tat pp PPP3CA
+Tat pp PPP3CB
+Tat pp PPP3CC
+Tat pp PPP3R1
+Tat pp PPP3R2
+Tat pp MAPK8
+Tat pp JUN
+Tat pp CD28
+Tat pp CD3D
+Tat pp CD3E
+Tat pp CD3G
+Tat pp CD3Z
+Tat pp ITPR1
+Tat pp ITPR2
+Tat pp ITPR3
+Tat pp PRKACA
+Tat pp PRKACB
+Tat pp PRKACG
+Tat pp PRKAG1
+Tat pp PRKAG2
+Tat pp PRKAR1A
+Tat pp PRKAR1B
+Tat pp PRKAR2A
+Tat pp EP300
+Matrix pp PRKAG2
+Tat pp PLCB1
+Tat pp PLCB2
+Tat pp PLCB3
+Tat pp PLCB4
+Tat pp PLCD1
+Tat pp PLCD3
+Tat pp PLCD4
+Tat pp PLCE1
+Tat pp PLCG1
+Tat pp PLCG2
+Tat pp HSPA1A
+Tat pp HSPA1B
+Tat pp HSPA2
+Tat pp HSPA4
+Tat pp HSPA5
+Tat pp HSPA6
+Tat pp HSPA8
+Tat pp HSPA9B
+Tat pp HSPCA
+Tat pp CDC37
+Tat pp CDK5R1
+Tat pp CDK5
+Tat pp HLA-DMA
+Tat pp HLA-DMB
+Tat pp HLA-DOA
+Tat pp HLA-DOB
+Tat pp HLA-DPA1
+Tat pp HLA-DPB1
+Tat pp HLA-DQA1
+Tat pp HLA-DQA2
+Tat pp HLA-DQB1
+Tat pp HLA-DQB2
+Vpr pp HSPA1B
+Vpr pp HSPA2
+Vpr pp HSPA4
+Vpr pp HSPA5
+Vpr pp HSPA6
+Vpr pp HSPA8
+Vpr pp HSPA9B
+Matrix pp HSPA1B
+Matrix pp HSPA2
+Matrix pp HSPA4
+Matrix pp HSPA5
+Matrix pp HSPA6
+Matrix pp HSPA8
+Matrix pp HSPA9B
+Gag pp HSPA1B
+Gag pp HSPA2
+Gag pp HSPA4
+Gag pp HSPA5
+Gag pp HSPA6
+Gag pp HSPA9B
+Tat pp PURA
+Tat pp PSMA1
+Tat pp PSMA2
+Tat pp PSMA3
+Tat pp PSMA4
+Tat pp PSMA5
+Tat pp PSMA6
+Tat pp PSMA7
+Tat pp PSMB1
+Tat pp PSMB2
+Tat pp PSMB3
+Tat pp PSMB4
+Tat pp PSMB5
+Tat pp PSMB6
+Tat pp PSMB7
+Tat pp PSMB8
+Tat pp PSMB9
+Tat pp PSMB10
+Tat pp PSMC1
+Tat pp PSMC6
+Tat pp PSMD1
+Tat pp PSMD2
+Tat pp PSMD3
+Tat pp PSMD4
+Tat pp PSMD5
+Tat pp PSMD7
+Tat pp PSMD8
+Tat pp PSMD9
+Tat pp PSMD10
+Tat pp PSMD11
+Tat pp PSMD12
+Tat pp PSMD13
+Tat pp PSME1
+Tat pp PSME2
+Tat pp PSME3
+Tat pp PSMF1
+Integrase pp PSMA1
+Integrase pp PSMA2
+Integrase pp PSMA3
+Integrase pp PSMA4
+Integrase pp PSMA5
+Integrase pp PSMA6
+Integrase pp PSMA7
+Integrase pp PSMB1
+Integrase pp PSMB2
+Integrase pp PSMB3
+Integrase pp PSMB4
+Integrase pp PSMB5
+Integrase pp PSMB6
+Integrase pp PSMB7
+Integrase pp PSMB8
+Integrase pp PSMB9
+Integrase pp PSMB10
+Integrase pp PSMC1
+Integrase pp PSMC2
+Integrase pp PSMC3
+Integrase pp PSMC4
+Integrase pp PSMC5
+Integrase pp PSMC6
+Integrase pp PSMD1
+Integrase pp PSMD2
+Integrase pp PSMD3
+Integrase pp PSMD4
+Integrase pp PSMD5
+Integrase pp PSMD7
+Integrase pp PSMD8
+Integrase pp PSMD9
+Integrase pp PSMD10
+Integrase pp PSMD11
+Integrase pp PSMD12
+Integrase pp PSMD13
+Integrase pp PSME1
+Integrase pp PSME2
+Integrase pp PSME3
+Integrase pp PSMF1
+Vif pp PSMA1
+Vif pp PSMA2
+Vif pp PSMA3
+Vif pp PSMA4
+Vif pp PSMA5
+Vif pp PSMA6
+Vif pp PSMA7
+Vif pp PSMB1
+Vif pp PSMB2
+Vif pp PSMB3
+Vif pp PSMB4
+Vif pp PSMB5
+Vif pp PSMB6
+Vif pp PSMB7
+Vif pp PSMB8
+Vif pp PSMB9
+Vif pp PSMB10
+Vif pp PSMC1
+Vif pp PSMC2
+Vif pp PSMC3
+Vif pp PSMC4
+Vif pp PSMC5
+Vif pp PSMC6
+Vif pp PSMD1
+Vif pp PSMD2
+Vif pp PSMD3
+Vif pp PSMD4
+Vif pp PSMD5
+Vif pp PSMD7
+Vif pp PSMD8
+Vif pp PSMD9
+Vif pp PSMD10
+Vif pp PSMD11
+Vif pp PSMD12
+Vif pp PSMD13
+Vif pp PSME1
+Vif pp PSME2
+Vif pp PSME3
+Vif pp PSMF1
+Tat pp EP300
+Tat pp GCN5L2
+Tat pp CREBBP
+Tat pp PCAF
+Tat pp H3F3A
+Tat pp H3F3B
+Tat pp HIST1H3A
+Tat pp HIST1H3B
+Tat pp HIST1H3C
+Tat pp HIST1H3D
+Tat pp HIST1H3E
+Tat pp HIST1H3F
+Tat pp HIST1H3G
+Tat pp HIST1H3H
+Tat pp HIST1H3I
+Tat pp HIST1H3J
+Tat pp HIST2H3C
+Tat pp HIST3H3
+Tat pp HIST1H4A
+Tat pp HIST1H4B
+Tat pp HIST1H4C
+Tat pp HIST1H4D
+Tat pp HIST1H4E
+Tat pp HIST1H4F
+Tat pp HIST1H4G
+Tat pp HIST1H4H
+Tat pp HIST1H4I
+Tat pp HIST1H4J
+Tat pp HIST1H4K
+Tat pp HIST1H4L
+Tat pp HIST2H4
+Tat pp HIST4H4
+Tat pp HIST1H2AE
+Tat pp HIST1H2AI
+Tat pp HIST1H2AK
+Tat pp HIST1H2AJ
+Tat pp H2AFV
+Tat pp HIST1H2AD
+Tat pp HIST1H2AL
+Tat pp H2AFJ
+Tat pp HIST1H2AC
+Tat pp HIST1H2AB
+Tat pp HIST1H2AM
+Tat pp HIST2H2AA
+Tat pp HIST1H2AG
+Tat pp HIST2H2AC
+Tat pp HIST1H2AA
+Tat pp HIST1H2AH
+Tat pp H2AFX
+Tat pp H2AFY
+Tat pp H2AFZ
+Tat pp H2AFY2
+Tat pp HIST2H2AB
+Tat pp HIST3H2A
+Tat pp HIST1H2BA
+Tat pp HIST1H2BB
+Tat pp HIST3H2BB
+Tat pp HIST1H2BC
+Tat pp HIST1H2BD
+Tat pp HIST1H2BE
+Tat pp HIST2H2BE
+Tat pp HIST1H2BF
+Tat pp HIST1H2BG
+Tat pp HIST1H2BH
+Tat pp HIST1H2BI
+Tat pp HIST1H2BJ
+Tat pp HIST1H2BK
+Tat pp HIST1H2BL
+Tat pp HIST1H2BM
+Tat pp HIST1H2BN
+Tat pp HIST1H2BO
+Tat pp H2BFS
+Tat pp GTF3C1
+Tat pp GTF3C2
+Tat pp GTF3C3
+Tat pp GTF3C4
+Tat pp GTF3C5
+Tat pp POLR3D
+Tat pp POLR3F
+Tat pp POLR3K
+Tat pp POLR3C
+Tat pp RPC155
+Tat pp POLR3B
+Tat pp POLR3G
+Tat pp POLR3E
+Tat pp POLR3H
+Tat pp POLR2H
+Tat pp POLR2K
+Tat pp POLR2L
+Tat pp GTF2A1
+Tat pp GTF2A2
+Tat pp DR1
+Tat pp GTF2B
+Tat pp TAF1
+Tat pp TCF3
+Tat pp TFAP4
+Tat pp BTAF1
+Tat pp TAF12
+Tat pp TAF9
+Tat pp TAF4
+Tat pp TAF2
+Tat pp TAF5
+Tat pp TAF7
+Tat pp TAF10
+Tat pp TAF6
+Tat pp TBN
+Tat pp TAF11
+Tat pp TAF13
+Tat pp TAF15
+Tat pp GTF2E1
+Tat pp GTF2E2
+Tat pp GTF2F1
+Tat pp GTF2F2
+Tat pp ELL
+Tat pp TCEB2
+Tat pp GTF2H1
+Tat pp GTF2H2
+Tat pp GTF2H3
+Tat pp GTF2H4
+Tat pp ERCC2
+Tat pp ERCC3
+Tat pp MNAT1
+Tat pp CDK7
+Tat pp CCNH
+Tat pp CDK4
+Tat pp TCEA1
+Tat pp TCEA2
+Tat pp CDK8
+Tat pp CCNC
+Tat pp SURB7
+Tat pp POLE
+Tat pp RPA1
+Tat pp RFC1
+Tat pp RFC2
+Tat pp RFC3
+Tat pp RFC4
+Tat pp RFC5
+Tat pp RAD51
+Tat pp TBP
+Tat pp SUPT5H
+Tat pp SUPT4H1
+Tat pp COBRA1
+Tat pp NELF
+Tat pp RDBP
+Tat pp TH1L
+Tat pp SP3
+Tat pp SP4
+Tat pp NFIC
+Tat pp SFRS1
+Tat pp SFRS7
+Tat pp POU2F1
+Tat pp PRKDC
+Tat pp SP1
+Tat pp ABCB1
+Tat pp CCNT1
+Tat pp CDK9
+Tat pp CCNT2
+Tat pp POLR2A
+Tat pp POLR2B
+Tat pp POLR2C
+Tat pp POLR2D
+Tat pp POLR2E
+Tat pp POLR2F
+Tat pp POLR2G
+Tat pp POLR2I
+Tat pp POLR2J
+Tat pp NFKB1
+Tat pp NFKB2
+Tat pp RELB
+NS5A pp Amph_II2
+NS5A pp Amph_II2_short
+E1 pp DC-SIGN
+E2 pp DC-SIGN
+E1 pp DC-SIGNR
+E2 pp DC-SIGNR
+NS5A pp SRCAP
+NS5B pp p68
+E2 pp DC-SIGN
+E2 pp DC-SIGNR
+Core pp p21
+Core pp p53
+E2 pp CD81
+HCV_core pp CBP
+HCV_core pp ASPP2
+HCV_core pp p300
+NS3 pp PRMT1
+unknown interactsWith CHD4
+unknown interactsWith HDAC1
+unknown interactsWith RbAp48
+unknown interactsWith MBD3
+Tat pp LRP
+NS3 pp PRMT1
+NS5A pp p53
+NS5A pp TBP
+HCV_core pp LT-betaR
+HCV_core interactsWith LT-betaR_dimer
+E2 pp CD81
+NS5A pp p53
+HCV_core pp p300
+HCV_core pp CBP
+SEA0400 interactsWith NCX1.7
+SEA0400 interactsWith NCX1.3
+E1 pp LTF
+NS5A pp hVAP-A
+IRAK[Lys239Ser] pp TRAF6
+Core pp DDX3
+IRAK[Lys239Ser] pp MyD88
+R-ibuprofen interactsWith HSA
+S-lorazepam_acetate interactsWith R-ibuprofen/HSA
+S-oxazepam_hemisuccinate interactsWith HSA
+NS3 pp TSG101
+NS5A pp TRAF2
+Phenytoin interactsWith HSA
+L-tryptophan interactsWith HSA
+S-ibuprofen interactsWith HSA
+S-lorazepam_acetate interactsWith S-ibuprofen/HSA
+NS5A pp La
+E2 pp CD81
+Unknown interactsWith talin
+Unknown interactsWith E-cadherin
+Unknown interactsWith vinculin
+Unknown interactsWith p130Cas
+Unknown interactsWith alpha-actinin
+Unknown interactsWith gamma-catenin
+Unknown interactsWith pp60c-src
+HCV_core pp translin
+E2 pp LTF
+NS3 pp SmD1
+E1/E2_heterodimer interactsWith DC-SIGN
+E2 pp DC-SIGN
+E1 pp DC-SIGN
+NS5B pp hPLIC1
+Unknown interactsWith TRADD
+Unknown interactsWith TRAF2
+CTX3 pp KChIP1
+CTX3 pp KChIP2.2
+CTX3 pp KChIP3
+CTX3 pp KChIP4.1
+LANA pp MNDA
+Rifampicin interactsWith alpha-synuclein
+RITA interactsWith p53
+HCV_core pp Smad3
+NS3 pp Smad3
+IpaC pp RanBPM
+Antagonist_Peptide_Af10847 pp IL1R1
+1F66_I pd H2AFZ
+1F66_I pd H2AFZ
+1F66_J pd H2AFZ
+Hemagglutinin_Ha1_Peptide_Chain pp HLA-DRB1
+Hirugen pp F2
+Ptgssstnpfr pp EPS15
+Ptgssstnpfl_Peptide pp EPS15
+Peptide_Inhibitor_Om99-2 pp BACE
+Decapeptide_Inhibitor pp F2
+Hirugen pp F2
+Bivalent_Inhibitor_(Bza-2_Hirulog) pp F2
+Streptococcal_Pyrogenic_Exotoxin_C pp HLA-DRB5
+Streptococcal_Pyrogenic_Exotoxin_C pp Myelin_Basic_Protein
+Gamma_Herpesvirus_Cyclin pp CDK2
+Factor_Xiii_Activation_Peptide_(28-37) pp F2
+1EWN_D pd MPG
+1EWN_E pd MPG
+1F6O_D pd MPG
+Pts1-Containing_Peptide pp PXR1
+Pts1-Containing_Peptide pp PXR1
+Pts1-Containing_Peptide pp PXR1
+Bad_Protein pp BCL2L1
+1FXL_B interactsWith ELAVL4
+1G2E_B interactsWith ELAVL4
+Ala-Asp-Pbf-Ptr-Leu-Ile-Pro pp PTPN1
+Leu-Glu-Phe-Ptr-Met-Asp-Tyr-Glu pp PTPN1
+Bisubstrate_Peptide_Inhibitor pp INSR
+Fasciculin-2 pp ACHE
+Fasciculin_Ii pp ACHE
+Tri-Phosphorylated_Peptide_From_The_Insulin_Receptor_Kinase pp PTPN1
+Mono-Phosphorylated_Peptide_From_The_Insulin_Receptor_Kinase pp PTPN1
+Bi-Phosphorylated_Peptide_From_The_Insulin_Receptor_Kinase pp PTPN1
+Smac pp BIRC4
+V-Cyclin pp CDK6
+V-Cyclin pp CDK6
+Tcf3-Cbd_(Catenin_Binding_Domain) pp JUP
+Antibody_(Light_Chain) pp CSF2RB
+A_Ligand_Peptide pp GRB2
+Collagen pp ITGA2
+Collagen pp ITGA2
+Acetyl-Isoleucyl-Glutamyl-Prolyl-Aspartyl-_Aldehyde pp GZMB
+Chimera_Of_Igg_Binding_Protein_G_And_Dna_Fragmentation_Factor_45 pp DFFB
+1FN7_C pd OGG1
+1FN7_D pd OGG1
+Thrombin_Nonapeptide_Inhibitor pp F2
+Cytomegalovirus_Protein_Us2 pp HLA-A
+1IG4_B pd MBD1
+1IG4_C pd MBD1
+Ace-Asp-Glu-Val-Asp-Cho pp CASP7
+Hemagglutinin_Ha_Peptide pp HLA-DRB1
+MW0051 pp HLA-DRB1
+1JEY_C pd G22P1
+1JEY_C pd XRCC5
+1JEY_D pd XRCC5
+1JEY_D pd G22P1
+Peptide_Exosite_Inhibitor_A-183 pp F7
+1JFI_D pd DRAP1
+1JFI_D pd TBP
+1JFI_D pd DR1
+1JFI_E pd DR1
+1JFI_E pd TBP
+(Phq)devd pp CASP8
+(Phq)devd pp CASP8
+(Phq)devd pp CASP8
+1J46_B pd SRY
+1J46_C pd SRY
+1J47_B pd SRY
+1J47_C pd SRY
+Coxsackievirus_Capsid,_Coat_Protein_Vp1 pp CXADR
+Coxsackievirus_Capsid,_Coat_Protein_Vp2 pp CXADR
+Glycoprotein_D pp TNFRSF14
+Decameric_Peptide_Ligand_From_The_Mart-1MELAN-A pp HLA-A
+Nonameric_Peptide_Ligand_From_The_Mart-1MELAN-A pp HLA-A
+Acetyl_Hirudin pp F2
+Acetyl_Hirudin pp F2
+1C5N_I pp F2
+Acetyl_Hirudin pp F2
+4-1bb_Ligand_Receptor pp TRAF2
+4-1bb_Ligand_Receptor pp TRAF2
+1HF0_M pd POU2F2
+1HF0_M pd POU2F2
+1HF0_N pd POU2F2
+1HF0_N pd POU2F2
+1HLZ_C pd NR1D1
+1HLZ_C pd NR1D1
+1HLZ_D pd NR1D1
+1HLZ_D pd NR1D1
+Glu-Val-Dehydroxymethylaspartic_Acid_Inhibitor pp CASP9
+Titin pp ACTN2
+1K78_C pd PAX5
+1K78_D pd PAX5
+1K78_H pd PAX5
+Ww_Domain_Binding_Protein-1 pp 65_Kda_Yes-Associated_Protein
+Ww_Domain_Binding_Protein-1 pp 65_Kda_Yes-Associated_Protein
+Ww_Domain_Binding_Protein-1 pp 65_Kda_Yes-Associated_Protein
+Dde(Ahp)(Tpo)g(Ptr)vatr pp DUSP3
+Creb-Binding_Protein pp Nuclear_Receptor_Coactivator
+Hirudin_Iib pp F2
+Hirudin_Iib pp F2
+Pancreatic_Trypsin_Inhibitor pp ST14
+Pancreatic_Trypsin_Inhibitor pp ST14
+1H88_D pd CEBPB
+1H88_D pd CEBPB
+1H88_E pd CEBPB
+1H88_E pd CEBPB
+1H89_D pd CEBPB
+1H89_D pd CEBPB
+1H89_E pd CEBPB
+1H89_E pd CEBPB
+1H8A_D pd CEBPB
+1H8A_E pd CEBPB
+1H8A_E pd CEBPB
+Mad2-Binding_Peptide pp MAD2L1
+Acetyl_Hirudin pp F2
+1K6O_D pd ELK4
+1K6O_D pd SRF
+1K6O_D pd SRF
+1K6O_E pd SRF
+1K6O_E pd SRF
+1K6O_E pd ELK4
+1HLV_B pd CENPB
+1HLV_C pd CENPB
+Peptide_Inhibitor pp F2
+Peptide:_Pspyvnvqn pp GRB2
+Ran_Gtpase_Activating_Protein_1 pp RAN
+1H6F_C pd TBX3
+1H6F_C pd TBX3
+Glucocorticoid_Receptor-Interacting_Protein_1 pp ESR1
+Glucocorticoid_Receptor-Interacting_Protein_1 pp ESR1
+Cyclic_Arg-Gly-Asp_Peptide pp ITGAV
+Cyclic_Arg-Gly-Asp_Peptide pp ITGB5
+Minimized_B-Domain_Of_Protein_A_Z34c pp Immunoglobulin_Gamma-1_Heavy_Chain_Constant_Region
+Substrate_Peptide pp CDK2
+Substrate_Peptide pp CDK2
+Substrate_Peptide pp CCNA2
+Hirudin_Variant-2 pp F2
+1KB2_C pd VDR
+1KB2_C pd VDR
+1KB2_D pd VDR
+1KB2_D pd VDR
+1KB4_C pd VDR
+1KB4_C pd VDR
+1KB4_D pd VDR
+1KB4_D pd VDR
+1KB6_C pd VDR
+1KB6_C pd VDR
+1KB6_D pd VDR
+1KB6_D pd VDR
+Regulator_Of_G-Protein_Signaling_14 pp GNAI3
+Synthetic_Phosphopeptide pp CHEK2
+Cation-Independent_Mannose-6-Phosphate_Receptor pp GGA3
+Cation-Independent_Mannose-6-Phosphate_Receptor pp GGA3
+Cation-Independent_Mannose-6-Phosphate_Receptor pp GGA3
+Cation-Independent_Mannose-6-Phosphate_Receptor pp GGA3
+Vitamin-K_Dependent_Protein_C pp PROCR
+Peptide_Fadseadeneqvsav pp PTPN13
+1J5K_B pd Heterogeneous_Nuclear_Ribonucleoprotein_K
+Triosephosphate_Isomerase_Peptide pp HLA-DRB1
+Triosephosphate_Isomerase_Peptide pp HLA-DRB1
+9d7_Heavy_Chain pp IL10
+Interleukin-10-Like_Protein pp IL10RA
+Interleukin-10-Like_Protein pp IL10RA
+Interleukin-10-Like_Protein pp IL10RA
+Dna_Polymerase pp HLA-DRB5
+Peptide_M9 pp HLA-A
+Crk pp Crk
+Nonameric_Model_Peptide_M9 pp HLA-A
+Gag_Polyprotein pp TSG101
+1IC8_E pd TCF1
+1IC8_E pd TCF1
+1IC8_F pd TCF1
+1IC8_F pd TCF1
+1K4S_B pd TOP1
+1K4S_C pd TOP1
+1K4S_D pd TOP1
+1K4T_C pd TOP1
+1K4T_D pd TOP1
+Peptide_Linker pp Breast_Cancer_Type_2_Susceptibility_Protein
+Streptokinase pp PLG
+Streptokinase pp PLG
+Hemagglutinin_Peptide pp HLA-DRB1
+1MDM_C pd PAX5
+1MDM_D pd PAX5
+F-Actin_Capping_Protein_Alpha-1_Subunit pp S100B
+Erb-B2_Carboxyl-Terminal_Fragment pp ERBB2IP
+Phosphorylated_Erb-B2_Carboxyl-Terminal_Fragment. pp ERBB2IP
+Epstein_Barr_Virus_Peptide pp HLA-B
+1MQ2_T pd POLB
+1MQ3_T pd POLB
+Phage-Derived_Peptide pp ERBB2IP
+1HU0_D pd OGG1
+1HU0_E pd OGG1
+Herceptin_Fab_(Antibody)_-_Heavy_Chain pp Herceptin_Fab_(Antibody)_-_Light_Chain
+Hirugen pp F2
+Inhibitor_(Sequence_Rppgf) pp F2
+Protein_A_Z34c pp Immunoglobulin_Gamma-1_Heavy_Chain_Constant_Region
+1LO1_B pd ESRRB
+1LO1_C pd ESRRB
+Peptide_Asvsa pp CHEK1
+Synthetic_Glfg_Peptide pp KPNB1
+Synthetic_Glfg_Peptide pp KPNB1
+Exogenous_Tripeptide_Formyl-Mlf pp SERPINC1
+pol pp PPIA
+pol pp PPIA
+pol pp PPIA
+Fibronectin_Binding_Protein pp FN1
+Gp2_Peptide pp HLA-A
+Gp2_Peptide pp HLA-A
+1GU4_C pd CEBPB
+1GU4_C pd CEBPB
+1GU4_D pd CEBPB
+1GU4_D pd CEBPB
+1GU5_C pd CEBPB
+1GU5_C pd CEBPB
+1GU5_D pd CEBPB
+1GU5_D pd CEBPB
+Peptide_S10r pp HLA-A
+Ha_Peptide pp HLA-DRB1
+Ha_Peptide pp HLA-DRB1
+Gilgfvftl pp HLA-A
+Hirudin_Iib pp F2
+Gp41_Epitope pp Antibody_2f5_(Heavy_Chain)
+Gp41_Epitope pp Antibody_2f5_(Light_Chain)
+Nuclear_Factor_Of_Activated_T-Cells,_Cytoplasmic_2 pp NFATC2
+1PZU_X pd NFATC2
+1PZU_Y pd NFATC2
+Hirugen pp F2
+Hirugen pp F2
+Hirugen pp F2
+3-Mer_Peptide pp FAP
+eco pp F10
+Rabaptin-5 pp GGA3
+Hirugen pp F2
+Hirugen pp F2
+Cap-23NAP-22 pp CALM2
+1P7H_A pd NFATC2
+1P7H_A pd NFATC2
+1P7H_C pd NFATC2
+1P7H_C pd NFATC2
+1P7H_B pd NFATC2
+1P7H_B pd NFATC2
+1P7H_D pd NFATC2
+1NVP_E pd GTF2A1
+1NVP_E pd TBP
+1NVP_F pd TBP
+1NVP_F pd GTF2A1
+Decapeptide_Hirudin_Analogue pp F2
+Decapeptide_Hirudin_Analogue pp F2
+Nucleoporin_Nsp1 pp KPNB1
+Paxillin pp PTK2
+Paxillin pp PTK2
+Paxillin pp PTK2
+Paxillin pp PTK2
+Paxillin pp PTK2
+Paxillin pp PTK2
+Pol_Polyprotein pp HLA-A
+Igf-1_Antagonist_F1-1 pp IGF1
+Beta-Secretase pp GGA1
+1R0N_C pd RXRA
+1R0N_D pd RXRA
+Peptide pp PLK1
+coa pp F2
+coa pp F2
+coa pp F2
+Ebna-6_Nuclear_Protein_(Ebna-3c)_(Ebna-4b) pp HLA-B
+1N6J_C pd MEF2B
+1N6J_C pd MEF2B
+1N6J_D pd MEF2B
+1N6J_D pd MEF2B
+1PGZ_B pd HNRPA1
+1PO6_B pd HNRPA1
+Phospho-Peptide_Sequence_Met.Gln.Ser.Pthr.Pro.Leu pp PLK1
+Axin pp JUP
+HTNV_NP pp CHD3
+HTNV_NP pp TTRAP
+HTNV_NP pp HIPK2
+HTNV_NP pp PIASxbeta
+HTNV_NP pp PIAS1
+HTNV_NP pp Ubc9
+Ad2_E1B pp Daxx
+Ad12_E1B pp Daxx
+SEOV_NP pp TTRAP
+SEOV_NP pp HIPK2
+v-Src pp Sam68
+HBV_X pp XAP-1
+IE63 pp CK2beta
+X pp XIP
+X pp XAP2
+ADP pp MAD2B
+E1A pp p300
+NS5A pp Jak1
+Rb interactsWith Cyclin_C/Cdk3-complex
+Crk_Phosphopeptide pp CRK
+E1A pp Smad2
+E1A pp Smad1
+E1A pp Smad3
+Mg++ interactsWith Hi95
+ATP interactsWith Hi95
+Tat pp hNotch2
+Tat pp E2F-4
+Apoptin pp Hippi
+Ad5_fiber interactsWith CAR
+Ad3_fiber interactsWith CD80
+Ad3_fiber interactsWith CD86
+HCV_core pp LTBR
+Matrix pp VAN
+ORF-K13 pp RIP
+MC159L pp RIP
+E8 pp RIP
+Unknown interactsWith MALT1
+SV40_T pp Imp-alpha
+Rev pp Imp-beta
+Tat pp Imp-beta
+Nef pp p53
+Nef pp p53
+Vpr pp cyclin_T1
+Tat pp cyclin_T1
+Tat pp granulin
+HIV-2_Tat pp granulin
+p24gag pp CypA
+p26gag pp CypA
+p17gag pp CypA
+Gp120env pp CypA
+YopM pp RSK1
+YopM pp PRK2
+HCV_core pp 14-3-3_beta
+HCV_core pp 14-3-3_zeta
+Tat pp PCAF
+HCV_core pp 14-3-3E
+YopT pp RhoA
+YopT pp Rac1
+YopT pp Cdc42
+Tat pp p300
+Tat pp PSM_beta-3
+Tat pp PSM_beta-7
+Tat pp PSM_beta-6
+Tat pp PSM_beta-5
+Tat pp PSM_beta-2
+Tat pp PSM_beta-1
+Tat pp PSM_alpha-4
+Tat pp PSM_alpha-7
+Tat pp PSM_beta-2i
+Integrase pp PCK1
+Integrase pp CCT4
+Integrase pp EEF1A1
+Gag pp Tsg101
+US11 pp Derlin-1
+US11 pp Derlin-1
+HCV_core pp p73
+HCV_core pp p53
+HCV_core pp p73
+HCV_core pp p73
+Vif pp Cul5
+Unknown interactsWith Elongin_B
+Unknown interactsWith Elongin_C
+Vif pp APOBEC3G
+L pp GRP78__
+Rev pp REBP
+NS4B pp CREB-RP
+N_protein pp SUMO-1
+ZN interactsWith RBX1
+ZN interactsWith RBX1
+ZN interactsWith RBX1
+Tat-2 pp Sp1
+PUUV-N pp Daxx
+PUUV-N pp SUMO-1
+v-Src pp GAP
+SEOV_NP pp Ubc9
+SEOV_NP pp PIAS1
+v-Src interactsWith PI_3'-kinase
+1ABI_I pp F2
+1ABJ_I pp F2
+1CDL_F pp CALM2
+1DLH_C pp HLA-DRB1
+1DWC_I pp F2
+1DWE_P pp F2
+1FPC_I pp F2
+1FPH_I pp F2
+1GSS_I pp GSTP1
+1HAG_I pp F2
+Hirudin_I pp F2
+1HLT_I pp F2
+1HGT_I pp F2
+1HHG_C pp HLA-A
+1HHH_C pp HLA-A
+1HHI_C pp HLA-A
+1HHJ_C pp HLA-A
+1HHK_F pp HLA-A
+2HPP_I pp F2
+1HNE_I pp ELA2
+1HSA_C pp HLA-A
+1HSB_C pp HLA-A
+1HSB_D pp HLA-A
+1HUT_I pp F2
+1HUT_D pd F2
+1IHS_I pp F2
+1IHT_I pp F2
+1LYB_I pp CTSD
+1LYB_I pp CTSD
+1LYB_J pp CTSD
+1LYB_J pp CTSD
+1MCB_P pp IGLL1
+1MCB_P pp IGLL1
+1MCC_P pp IGLL1
+1MCC_P pp IGLL1
+1MCD_P pp IGLL1
+1MCD_P pp IGLL1
+1MCE_P pp IGLL1
+1MCE_P pp IGLL1
+1MCF_P pp IGLL1
+1MCF_P pp IGLL1
+1MCH_P pp IGLL1
+1MCH_P pp IGLL1
+1MCI_P pp IGLL1
+1MCI_P pp IGLL1
+1MCJ_P pp IGLL1
+1MCJ_P pp IGLL1
+1MCK_P pp IGLL1
+1MCK_P pp IGLL1
+1MCL_P pp IGLL1
+1MCL_P pp IGLL1
+1MCN_P pp IGLL1
+1MCN_P pp IGLL1
+1MCQ_P pp IGLL1
+1MCR_P pp IGLL1
+1MCR_P pp IGLL1
+1MCS_P pp IGLL1
+1MCS_P pp IGLL1
+1NRR_P pp F2
+1NRS_I pp F2
+D-Phe-Pro-Arg-Chloromethylketone_(Ppack)_With_Chloromethylketone_Replaced_By_A_Methylene_Group pp F2
+1PPF_I pp ELA2
+1PPG_I pp ELA2
+1SHD_B pp SRC
+1THR_I pp F2
+1THS_I pp F2
+1TMB_I pp F2
+1TMB_T pp F2
+1TMC_C pp HLA-A
+1TMT_I pp F2
+1TMT_J pp F2
+1TMU_I pp F2
+Inhibitor pp F2
+2HGT_J pp F2
+3HAT_I pp F2
+3HAT_T pp F2
+4HTC_I pp F2
+1HBT_I pp F2
+1PSO_I pp PGA5
+1FCC_C pp 1FCC_A
+1HRZ_B pd SRY
+1HRY_B pd SRY
+1ICE_T pp CASP1
+1TSR_E pd TP53
+1TSR_E pd TP53
+1TSR_E pd TP53
+1TSR_F pd TP53
+1TSR_F pd TP53
+Glu-Gly-Arg_Chloromethyl_Ketone pp PLAU
+Glu-Gly-Arg_Chloromethyl_Ketone pp PLAU
+1TUP_F pd TP53
+1HCQ_C pd ESR2
+1HCQ_C pd ESR2
+1HCQ_D pd ESR2
+1HCQ_D pd ESR2
+1HCQ_G pd ESR2
+Tail_Phosphopeptide_Tegq(Phospho)yqpqpa pp LCK
+Phosphopeptide_Epq(Phospho)yeeipiyl pp LCK
+Hirugen_Peptide pp F2
+N-[n-[n-[4-(Aminoiminomethyl)amino]-1-Oxobutyl]-L_-Phenylalanyl]-L-Allo-Threonyl-L-Phenylalanine,_Methyl_Ester_(Bms-183507) pp F2
+1HAP_D pd F2
+1HAO_D pd F2
+Cathepsin_B pp Cathepsin_B
+Cathepsin_B pp CTSB
+Hirugen pp F2
+1URN_P interactsWith SNRPA
+1URN_R interactsWith SNRPA
+Phosphotyrosyl_Peptide_Ac-Ptyr-Glu-Glu-Gly pp LCK
+Phosphotyrosyl_Peptide_Ac-Ptyr-Glu-Glu-Ile pp LCK
+Dipeptide_Gly-Pro pp PPIA
+Dipeptide_His-Pro pp PPIA
+Dipeptide_Ser-Pro pp PPIA
+Dipeptide_Ala-Pro pp PPIA
+Pro-Leu-Gly-Hydroxylamine pp MMP8
+1SVC_D pd NFKB1
+Peptide_Inhibitor_Cvs995 pp F2
+Cysteine pp LYZ
+Cysteine pp LYZ
+1SRS_W pd SRF
+1SRS_W pd SRF
+1SRS_C pd SRF
+1SRS_C pd SRF
+Aapf_Peptide_Substrate pp PPIA
+Aapf_Peptide_Substrate pp PPIA
+Phosphotyrosine pp PTPN1
+Phosphotyrosine-Containing_Hexa-Peptide pp PTPN1
+Phosphotyrosine-Containing_Tetra-Peptide pp PTPN1
+2STT_B pd ETS1
+2STW_B pd ETS1
+Hirugen pp F2
+Hirudin_Variant pp F2
+Hiv-1_Nef_Protein pp FYN
+Hiv-1_Nef_Protein pp FYN
+1UBD_A pd YY1
+1UBD_B pd YY1
+Aspartate pp AGA
+Phosphonopeptide_Pro-Glu-Gly-Asp-Pmp-Glu-Glu-Val-Leu,_Where_Pmp_Is_(Phosphonomethyl)phenylalanine pp LCK
+Phosphonopeptide_Acq-Pmp-Glu-Glu-Ile-Pro_Where_Acq_Is_N-Acetyl_Glutamine_And_Pmp_Is_(Phosphonomethyl)phenylalanine pp LCK
+Phosphonopeptide_Acq-Pmp-Glu-Glu-Ile-Pro_Where_Acq_Is_N-Acetyl_Glutamine_And_Pmp_Is_(Phosphonomethyl)phenylalanine pp LCK
+Hirudin_I pp F2
+Hirudin_I pp F2
+1ZQP_T pd POLB
+1ZQP_P pd POLB
+9ICI_P pd POLB
+7ICV_T pd POLB
+7ICV_P pd POLB
+9ICF_P pd POLB
+8ICE_P pd POLB
+8ICU_P pd POLB
+8ICV_P pd POLB
+8ICW_P pd POLB
+8ICY_P pd POLB
+1ZQH_P pd POLB
+1ZQJ_P pd POLB
+At3g13445 pp GTF2B
+1VOL_C pd GTF2B
+1VOL_D pd GTF2B
+Hirudin pp F2
+Hirudin pp F2
+Hirudin pp F2
+Hirudin_Variant-1 pp F2
+3bp-2 pp FYN
+Hiv-1_Gag_Protein pp PPIA
+1TZE_I pp GRB2
+Ace-Asp-Glu-Val-Asp-Cho pp CASP3
+Ace-Asp-Glu-Val-Asp-Cho pp CASP3
+Phosphonate_Inhibitor_Suc-Val-Pro-Phep-(Oph)2 pp CTSG
+1BPX_T pd POLB
+1BPX_P pd POLB
+1BPY_T pd POLB
+1BPY_P pd POLB
+1BPZ_T pd POLB
+1BPZ_P pd POLB
+Hiv-1_Gag_Peptide_(Ggkkrykl_-_5r_Mutation) pp HLA-B
+Hiv-1_Gag_Peptide_(Ggkkkykl_-_Index_Peptide) pp HLA-B
+Hiv-1_Gag_Peptide_(Ggkkkyql_-_7q_Mutation) pp HLA-B
+Hiv-1_Gag_Peptide_(Ggrkkykl_-_3r_Mutation) pp HLA-B
+Hiv-1_Gag_Peptide_(Ggkkkyrl_-_7r_Mutation) pp HLA-B
+Epo_Mimetics_Peptide_1 pp EPOR
+Epo_Mimetics_Peptide_1 pp EPOR
+Epo_Mimetics_Peptide_1 pp EPOR
+1AN4_C pd USF1
+1AN4_C pd USF1
+1AN4_D pd USF1
+1AN4_D pd USF1
+Tax_Peptide pp HLA-A
+Hiv_Reverse_Transcriptase_Epitope pp HLA-A
+(Dpn)-Phe-Arg pp F7
+Hirudin53-65_Peptide pp F2
+Hirudin_Iiib pp F2
+Hirugen pp F2
+pol pp PPIA
+Peptide_Substrate pp INSR
+Bovine_Pancreatic_Trypsin_Inhibitor pp F2
+Acetyl-Asp-Val-Ala-Asp-Fluoromethylketone pp CASP3
+Acetyl-Asp-Val-Ala-Asp-Fluoromethylketone pp CASP3
+1HLO_C pd MAX
+1HLO_C pd MAX
+Sel2711 pp F2
+Peptide_Ace-Trp-Glu-His-Asp pp CASP1
+Peptide_Ace-Trp-Glu-His-Asp pp CASP1
+Arginine pp GATM
+Hirunorm_V pp F2
+Phosphotyrosyl_Peptide pp FYN
+Phosphotyrosyl_Peptide pp FYN
+Peptide_From_The_Hiv-1_Capsid_Protein pp PPIA
+Peptide_From_The_Hiv-1_Capsid_Protein pp PPIA
+Peptide_From_The_Hiv-1_Capsid_Protein pp PPIA
+Peptide_From_The_Hiv-1_Capsid_Protein pp PPIA
+Peptide_From_The_Hiv-1_Capsid_Protein pp PPIA
+Peptide_From_The_Hiv-1_Capsid_Protein pp PPIA
+Peptide_From_The_Hiv-1_Capsid_Protein pp PPIA
+Peptide_From_The_Hiv-1_Capsid_Protein pp PPIA
+Peptide_From_The_Hiv-1_Capsid_Protein pp PPIA
+Peptide_From_The_Hiv-1_Capsid_Protein pp PPIA
+Peptide_From_The_Hiv-1_Capsid_Protein pp PPIA
+Peptide_From_The_Hiv-1_Capsid_Protein pp PPIA
+Peptide_From_The_Hiv-1_Capsid_Protein pp PPIA
+Peptide_From_The_Hiv-1_Capsid_Protein pp PPIA
+Peptide_From_The_Hiv-1_Capsid_Protein pp PPIA
+Hirugen pp F2
+Hirugen pp F2
+Peptide_Typdinqml pp HLA-B
+Peptide_Vplrpmty pp HLA-B
+Peptide_Ls6_(Kpivqydnf) pp HLA-A
+Hirugen pp F2
+Hirugen pp F2
+1A02_A pd NFATC2
+1A02_A pd C-Jun
+1A02_A pd C-Fos
+1A02_B pd C-Fos
+1A02_B pd C-Jun
+1A02_B pd NFATC2
+1A3Q_C pd NFKB2
+1A3Q_C pd NFKB2
+1A3Q_D pd NFKB2
+1A3Q_D pd NFKB2
+Hirugen pp F2
+D-Phe-Pro-Arg-Chloromethylketone_(Ppack)_With_Chloromethylketone_Replaced_By_A_Methylene_Group pp PRSS1
+Hirugen pp F2
+1A66_B pd NFATC1
+1A66_C pd NFATC1
+Boronate_Inhibitor_Borolog1 pp F2
+Boronate_Inhibitor_Borolog2 pp F2
+1A35_C pd TOP1
+1A35_D pd TOP1
+1A31_C pd TOP1
+1A31_D pd TOP1
+Tax_Peptide pp HLA-A
+1BF5_B pd STAT1
+1BF5_C pd STAT1
+1A36_B pd TOP1
+1A36_C pd TOP1
+L-Pro10 pp PFN1
+L-Pro10 pp PFN1
+Inhibitor_Ace-Ipa-Glu-Glu-Ile pp LCK
+1A6Y_C pd NR1D1
+1A6Y_C pd NR1D1
+1A6Y_D pd NR1D1
+1A6Y_D pd NR1D1
+Peptide_Lpplditpy pp HLA-B
+Peptide_Lpplditpy pp HLA-B
+Hirugen pp F2
+Peptide_P41 pp Abl_Tyrosine_Kinase
+Peptide_P1049_(Alwgffpvl) pp HLA-A
+Ala-Pro_Dipeptide pp PIN1
+Tetrapeptide pp PPIA
+Sulfur-Substituted_Tetrapeptide pp PPIA
+4SKN_A pd UNG
+4SKN_B pd UNG
+1B72_D pd PBX1
+1B72_D pd HOXB1
+1B72_E pd HOXB1
+1B72_E pd PBX1
+Uracil-Dna_Glycosylase_Inhibitor pp UNG
+Epidermal_Growth_Factor_Receptor-Derived_Peptide pp GRB2
+N-Acetylhirudin pp F2
+Pentapeptide pp SERPINE1
+Pentapeptide pp SERPINE1
+Peptide_(Vmaprtvll) pp HLA-E
+Peptide_(Vmaprtvll) pp HLA-E
+Peptide_(Vmaprtvll) pp HLA-E
+Peptide_(Vmaprtvll) pp HLA-E
+Hirugen,_Cvs1578 pp F2
+Hirugen,_Cvs1578 pp F2
+Tnf-R2 pp TRAF2
+Tnf-R2 pp TRAF2
+Tnf-R2 pp TRAF2
+Annexin_Ii pp S100A10
+Annexin_Ii pp S100A10
+Annexin_Ii pp S100A10
+Sos pp Grb2
+Dansyl-Glu-Gly-Arg_Chloromethyl_Ketone pp PLAT
+Insulin pp Insulin
+1SSP_A pd UNG
+1SSP_B pd UNG
+2SSP_A pd UNG
+2SSP_B pd UNG
+2UP1_B pd HNRPA1
+Hirunorm_Iv pp F2
+Shc-Derived_Peptide pp GRB2
+Streptokinase pp PLG
+Streptokinase pp PLG
+Grip1 pp Thyroid_Hormone_Receptor_Beta
+Proline_Peptide pp PFN1
+1MHD_C pd MADH3
+1MHD_C pd MADH3
+1MHD_D pd MADH3
+1MHD_D pd MADH3
+Tripeptidyl_Inhibitor pp F7
+Cd40_Receptor pp Tnf_Receptor_Associated_Factor_2
+6PAX_B pd PAX6
+6PAX_C pd PAX6
+Staphylokinase_Sak-C-Phi-C pp PLG
+Staphylokinase_Sak-C-Phi-C pp PLG
+Inhibitor pp PLG
+Degr-Ck_Inhibitor_(Glu-Gly-Arm) pp F7
+Sulfated_Hirudin_(53_-65) pp F2
+Signaling_Lymphocytic_Activation_Molecule pp SH2D1A
+Tax_Peptide_P6a pp HLA-A
+Hirugen pp F2
+1CVJ_M interactsWith PABPC1
+1CVJ_M interactsWith PABPC1
+1CVJ_R interactsWith PABPC1
+1CVJ_O interactsWith PABPC1
+1CVJ_Q interactsWith PABPC1
+Gp2_Peptide pp HLA-A
+Tax_Peptide_V7r pp HLA-A
+Tax_Peptide_Y8a pp HLA-A
+Hla-Cw4_Specific_Peptide pp Histocompatibility_Leukocyte_Antigen_(Hla)-Cw4_(Heavy_Chain)
+5l15 pp F7
+Pkf273-791 pp GRB2
+Pkf270-974 pp GRB2
+1BNK_D pd MPG
+1F6O_E pd MPG
+Peptide pp SERPINC1
+Protein-Tyrosine-Phosphatase_1b_Inhibitor pp PTPN1
+Epo_Mimetics_Peptide_33 pp EPOR
+Epo_Mimetics_Peptide_33 pp EPOR
+Epo_Mimetics_Peptide_33 pp EPOR
+Epo_Mimetics_Peptide_33 pp EPOR
+Peptidic_Inhibitor pp CMA1
+Influenza_Matrix_Peptide_With_The_C-Terminal_Group_Replaced_By_A_Methyl_Group pp HLA-A
+Hiv-Rt_Variant_Peptide_I1y_(Ylkepvhgv) pp HLA-A
+Hiv-Rt_Variant_Peptide_I1f_(Flkepvhgv) pp HLA-A
+1C9B_C pd GTF2B
+1C9B_O pd GTF2B
+1C9B_O pd TBP
+1C9B_C pd GTF2B
+1C9B_T pd GTF2B
+1C9B_T pd TBP
+1C9B_G pd GTF2B
+1C9B_G pd GTF2B
+1C9B_L pd TBP
+1C9B_P pd TBP
+1C9B_S pd TBP
+Actin pp GSN
+Chimeric_Actin pp GSN
+Neuronal_Nitric_Oxide_Synthase pp DNCL1
+Htlv-1_Octameric_Tax_Peptide pp HLA-A
+Iva-Val-Val-Leu(P)-(O)phe-Ala-Ala-Ome pp PGA5
+P21-Activated_Kinase pp CDC42
+1C7U_C pd MEF2C
+1C7U_C pd MEF2C
+1EBM_C pd OGG1
+1EBM_D pd OGG1
+Fibrinopeptide pp F2
+Thrombin_Inhibitor_P798 pp F2
+Thrombin_Inhibitor_P628 pp F2
+Hsp90-Peptide_Meevd pp STIP1
+Hsc70-Peptide pp STIP1
+SerineTHREONINE-Protein_Kinase_Pak-Alpha pp CDC42
+Thrombin_Inhibitor_L-Glu-L-Gly-L-Arm pp F2
+Glutathione_Ligand pp GSTA4
+Glutathione_Ligand pp GSTA4
+1CF7_C pd TFDP2
+1CF7_C pd E2F4
+1CF7_D pd E2F4
+1CF7_D pd TFDP2
+Hirugen pp F2
+Immunoglobulin_G_Binding_Protein_A pp Igm_Rf_2a2
+Engineered_Peptide pp Immunoglobulin_Lambda_Heavy_Chain
+1EMH_B pd UNG
+1EMJ_B pd UNG
+1EMJ_C pd UNG
+Peptide_E-76 pp F7
+1DRZ_B interactsWith SNRPA
+Peptide_Inhibitor pp HLA-DRB1
+Peptidomimetic_Inhibitor pp HLA-DRB1
+1EJ9_C pd TOP1
+1EJ9_D pd TOP1
+Metallocarboxypeptidase_Inhibitor pp CPA2
+1DSZ_C pd RARA
+1DSZ_C pd RXRA
+1DSZ_D pd RXRA
+1DSZ_D pd RARA
+Z-Evd-Dcbmk_(Tripeptide_Ketone_Inhibitor_(Glu-_Val-Ask)) pp CASP8
+Z-Evd-Dcbmk_(Tripeptide_Ketone_Inhibitor_(Glu-_Val-Ask)) pp CASP8
+Z-Evd-Dcbmk_(Tripeptide_Ketone_Inhibitor_(Glu-_Val-Ask)) pp CASP8
+Y(Sep)pt(Sep)s_Peptide pp PIN1
+Fxfg_Nucleoporin_Repeats pp KPNB1
+Hirugen pp F2
+Myelin_Basic_Protein pp HLA-DRB5
+Acetyl-Ile-Glu-Thr-Asp-Aldehyde pp CASP8
+Acetyl-Ile-Glu-Thr-Asp-Aldehyde pp CASP8
+Hiv-1_Peptide_(Lppvvakei) pp HLA-A
+Peptide pp HLA-A
+diethylstilbestrol interactsWith ESR1
+OHT interactsWith ESR1
+Epinephrine interactsWith TPH1
+NAR interactsWith TPH1
+dopamine interactsWith TPH1
+DAH interactsWith TPH1
+GNH interactsWith CDC42
+AL5 interactsWith CA2
+AL6 interactsWith CA2
+AL9 interactsWith CA2
+AL8 interactsWith CA2
+AL1 interactsWith CA2
+NAG interactsWith LGALS3BP
+DBG interactsWith HRAS
+Mg2+ interactsWith RAN
+GNP interactsWith RAN
+GAL-(1-4)NAG-(1-1)GOL interactsWith LYZ
+DBG interactsWith HRAS
+Uracil interactsWith UNG
+RAD interactsWith FKBP1A
+RAD interactsWith FRAP1
+aminocaproic_acid interactsWith LPAL2
+072 interactsWith PPARG
+072 interactsWith PPARG
+072 interactsWith PPARG
+072 interactsWith PPARG
+BSP interactsWith GSTP1
+ITS interactsWith BTK
+I10 interactsWith CTSL2
+PMB interactsWith TAF11
+SOA interactsWith KLK6
+ITS interactsWith BTK
+IMU interactsWith HPRT1
+Mg2+ interactsWith HPRT1
+4-Hydroxyphenyl_pyruvate interactsWith MIF
+4-Hydroxyphenyl_pyruvate interactsWith MIF
+Adenine interactsWith MTAP
+GTO interactsWith CDC42
+GNP interactsWith CDC42
+GNP interactsWith Activated_P21cdc42hs_Kinase
+MTA interactsWith MTAP
+NAG-(4-1)NAG-(3-1)MAN-(6-1)MAN-(3-1)MAN-(2-1)MAN-(3,3-1)MAN-(2-1)MAN interactsWith MCP
+NAG-(4-1)NAG-(3-1)MAN-(3-1)MAN interactsWith MCP
+NAG-(4-1)NAG-(4-1)MAN interactsWith MCP
+NAG-(4-1)NAG-(4-1)MAN interactsWith MCP
+NAG-(4-1)NAG interactsWith MCP
+NAG-(4-1)NAG interactsWith MCP
+NAG-(4-1)NAG-(4-1)BMA-(6-1)BMA-(3,3-1)BMA interactsWith MCP
+NAG-(4-1)NAG-(4-1)MAN interactsWith MCP
+NAG-(4-1)NAG-(4-1)MAN-(6-1)MAN-(6-1)MAN-(2-1)MAN-(3,3-1)MAN-(4,3-1)MAN interactsWith MCP
+NAG-(4-1)NAG-(4-1)MAN-(6-1)MAN-(3-1)MAN-(4,6-1)MAN interactsWith MCP
+NAG-(4-1)NAG-(4-1)MAN-(6-1)MAN-(3-1)MAN-(4,6-1)MAN interactsWith MCP
+NAG-(4-1)NAG-(4-1)BMA-(6-1)BMA-(3,3-1)BMA interactsWith MCP
+Ca2+ interactsWith MCP
+CoA interactsWith GCN5L2
+GLC-(4-1)AGL-(4-1)HMC-(4-1)GLC-(4-1)GLC interactsWith AMY1A
+NAG interactsWith Fibrinogen
+NAG-(3-2)(4-1)NAG interactsWith Fibrinogen
+AMP-PNP interactsWith MAPK10
+Mg2+ interactsWith MAPK10
+577 interactsWith MAPK1
+PP1 interactsWith LCK
+IPH interactsWith Insulin
+IPH interactsWith Insulin
+heme interactsWith CAT
+HEG interactsWith HBB
+Mg2+ interactsWith GSS
+Mg2+ interactsWith GSS
+ADP interactsWith GSS
+GSH interactsWith GSS
+Ca2+ interactsWith S100A7
+Ca2+ interactsWith MMP3
+CGS interactsWith MMP3
+Mg2+ interactsWith Metal_Chelatase_Catalytic_Antibody
+Na+ interactsWith Metal_Chelatase_Catalytic_Antibody
+MMP interactsWith Metal_Chelatase_Catalytic_Antibody
+MMP interactsWith Metal_Chelatase_Catalytic_Antibody
+Zn2+ interactsWith S100A7
+Ca2+ interactsWith MMP3
+AL7 interactsWith CA2
+AL4 interactsWith CA2
+AL2 interactsWith CA2
+AL3 interactsWith CA2
+TPS interactsWith CA2
+NAG-(4-1)NAG interactsWith MICB
+PLP interactsWith SHMT2
+sb216995 interactsWith MAPK14
+sb_220025 interactsWith MAPK14
+Zn2+ interactsWith MMP27
+3MP-HAV-MSB interactsWith MMP27
+sb218655 interactsWith MAPK14
+TBU interactsWith 1BN5
+TBU interactsWith Methionine_Aminopeptidase_2
+FUM interactsWith 1BOA
+mmp_inhibitor_ii interactsWith MMP3
+Zn2+ interactsWith MMP14
+Zn2+ interactsWith MMP14
+Ca2+ interactsWith MMP14
+NAG interactsWith MADCAM1
+Triiodothyronine interactsWith THRB
+3-(prop-2-ene-1-sulfinyl)-propene-1-thiol interactsWith Glutathione_Reductase
+GTP interactsWith RAP1A
+OC2 interactsWith MMP20
+OC1 interactsWith MMP20
+DPS interactsWith MMP20
+HOM interactsWith PFN1
+Zn2+ interactsWith MMP2
+Zn2+ interactsWith MMP2
+Ca2+ interactsWith MMP2
+Ca2+ interactsWith MMP2
+O-DIC-O interactsWith KLK6
+Ca2+ interactsWith EPS15L1
+NAG-(1-4)NAG-(6-1)FUC interactsWith F7
+heme interactsWith HBB
+858 interactsWith FKBP1A
+B7G interactsWith FKBP1A
+587 interactsWith FKBP1A
+587 interactsWith FKBP1A
+587 interactsWith FKBP1A
+Ca2+ interactsWith F9
+PBZ interactsWith F9
+TBU interactsWith F9
+Zn2+ interactsWith 1XPA
+Menadione interactsWith NQO2
+Menadione interactsWith NQO2
+AMP-PNP interactsWith SRC
+GBX interactsWith GSTP1
+GBX interactsWith GSTP1
+rs-113456 interactsWith MMP13
+RS1 interactsWith MMP13
+RS2 interactsWith MMP3
+RCO interactsWith Insulin
+RCO interactsWith Insulin
+RCO interactsWith Insulin
+2FP interactsWith ALDOC
+PAO interactsWith Ornithine_Transcarbamoylase
+Fe3+ interactsWith PAH
+Stanolone interactsWith Estrogenic_17-Beta_Hydroxysteroid_Dehydrogenase
+3',5'-ADP interactsWith NDST2
+PD1 interactsWith FGFR1
+PD1 interactsWith FGFR1
+Zn2+ interactsWith Apoptotic_Protease_Activating_Factor_1
+Zn2+ interactsWith Apoptotic_Protease_Activating_Factor_1
+Zn2+ interactsWith Apoptotic_Protease_Activating_Factor_1
+NAG interactsWith TFRC
+NAG interactsWith TFRC
+NAG interactsWith TFRC
+NAG interactsWith TFRC
+DPS interactsWith MMP20
+IN7 interactsWith MMP20
+NAG-(4-1)NAG-(4-1)MAN interactsWith ACPP
+NAG-(4-1)NAG-(4-1)MAN-(6-1)MAN interactsWith ACPP
+FUC-(1-6)NAG-(4-1)NAG-(4-1)MAN-(3-1)MAN-(2-1)NAG-(4,6-1)MAN-(2-1)NAG interactsWith ACPP
+NAG-(4-1)NAG-(4-1)MAN-(6-1)MAN interactsWith ACPP
+NAG-(4-1)NAG-(4-1)MAN interactsWith ACPP
+NAG-(4-1)NAG-(4-1)MAN-(3-1)MAN interactsWith ACPP
+NAG-(4-1)NAG-(4-1)MAN-(6-1)MAN-(6-1)MAN-(3,3-1)MAN interactsWith ACPP
+glycine interactsWith ACPP
+ANS interactsWith F7
+PPX interactsWith F2
+DSS interactsWith FKBP1A
+BUQ interactsWith FKBP1A
+Zn2+ interactsWith BIRC2
+Zn2+ interactsWith Nucleotide_Excision_Repair_Protein_Xpa_(Xpa-Mbd)
+staurosporine interactsWith MATK
+NAG interactsWith APOH
+NAG interactsWith APOH
+NAG-(4-1)NAG-(4-1)MAN interactsWith APOH
+NAG-(4-1)NAG interactsWith APOH
+MO6 interactsWith ADK
+MO4 interactsWith ADK
+MO4 interactsWith ADK
+ADN interactsWith ADK
+ADN interactsWith ADK
+BPP interactsWith F2
+Ca2+ interactsWith GSN
+Palmitate interactsWith FABP5
+NAG interactsWith IGF1R
+FUC-(1-6)NAG-(4-1)NAG interactsWith IGF1R
+NAG interactsWith IGF1R
+FUC-(1-6)NAG-(4-1)NAG-(4-1)MAN-(3-1)MAN interactsWith IGF1R
+Ca2+ interactsWith MBL2
+Ca2+ interactsWith MBL2
+PHG interactsWith Coagulation_Factor_V
+FMN interactsWith Nadph-Cytochrome_P450_Reductase
+GIP interactsWith GLO1
+GIP interactsWith GLO1
+ZNO interactsWith GLO1
+ZNO interactsWith GLO1
+GNB interactsWith GLO1
+GNB interactsWith GLO1
+GNB interactsWith GLO1
+GNB interactsWith GLO1
+tranexamic_acid interactsWith Plasminogen
+NAG-(4-1)NAG-(4-1)BMA-(6-1)BMA-(3,3-1)BMA interactsWith Beta2-Glycoprotein-I
+NAG-(4-1)NAG-(4-1)MAN interactsWith Beta2-Glycoprotein-I
+I3N interactsWith PLA2G2D
+Zn2+ interactsWith MMP2
+Zn2+ interactsWith MMP2
+Ca2+ interactsWith MMP2
+Ca2+ interactsWith MMP2
+Ca2+ interactsWith MMP2
+indole_8 interactsWith PLA2G2D
+indole_6 interactsWith PLA2G2D
+Mg2+ interactsWith HK3
+Mg2+ interactsWith HK3
+AMP-PNP interactsWith HK3
+AMP-PNP interactsWith HK3
+UM3 interactsWith RNASE4
+UM3 interactsWith RNASE4
+A interactsWith PABPC1
+A interactsWith PABPC1
+A interactsWith PABPC1
+MO2 interactsWith HPRT1
+MO2 interactsWith HPRT1
+PPO interactsWith HPRT1
+PRPP interactsWith HPRT1
+PRPP interactsWith HPRT1
+GTT interactsWith GLRX
+PG6 interactsWith PFN2
+PG5 interactsWith PFN2
+Citiric_acid interactsWith SNRPB
+Citiric_acid interactsWith SNRPD3
+Citiric_acid interactsWith SNRPB
+Citiric_acid interactsWith SNRPD3
+R13 interactsWith CRABP1
+R12 interactsWith CRABP1
+ATP interactsWith Substrate_Peptide
+ATP interactsWith Substrate_Peptide
+S27 interactsWith MMP3
+MO4 interactsWith 1D4R_B
+MO3 interactsWith 1D4R_B
+MO3 interactsWith 1D4R_A
+MO3 interactsWith 1D4R_A
+FUC-(1-6)NAG-(4-1)NAG interactsWith PRSSL1
+SEI interactsWith PRSSL1
+flufenamic_acid interactsWith TTR
+NDP interactsWith DHFR
+PRD interactsWith DHFR
+Zn2+ interactsWith GH1
+TPI interactsWith PTPN1
+Ca2+ interactsWith Low_Density_Lipoprotein_Receptor_Related_Protein
+NAG interactsWith CMA1
+NAG interactsWith CMA1
+Mg2+ interactsWith HSPCB
+ADP interactsWith HSPCB
+PIC interactsWith PTPN9
+PVB interactsWith CDK2
+ADP interactsWith Heat-Shock_70kd_Protein
+2PI interactsWith L-Arginine:glycine_Amidinotransferase
+glycine interactsWith L-Arginine:glycine_Amidinotransferase
+ABU interactsWith L-Arginine:glycine_Amidinotransferase
+DAV interactsWith L-Arginine:glycine_Amidinotransferase
+ALA interactsWith L-Arginine:glycine_Amidinotransferase
+ABA interactsWith L-Arginine:glycine_Amidinotransferase
+NADP+ interactsWith HSD17B1
+Equilin interactsWith HSD17B1
+DCY interactsWith F8
+GAL-(1-4)NAG-(1-1)GOL interactsWith LYZ
+Fe3+ interactsWith TF
+NAG interactsWith HFE
+Ca2+ interactsWith TFRC
+BMA interactsWith CLC
+OVA interactsWith Methionine_Aminopeptidase
+Ca2+ interactsWith Lipoprotein_Receptor_Related_Protein
+Rev pp C1QBP
+NAG interactsWith Invariant_Chain
+Zn2+ interactsWith NOS2A
+heme interactsWith NOS2A
+BH4 interactsWith NOS2A
+BH4 interactsWith NOS2A
+ARG interactsWith NOS2A
+s-ethylisothiourea interactsWith NOS2A
+SIA-(2-6)NAG-(3-1)GAL interactsWith REG1B
+Mg2+ interactsWith ALDH2
+NAD+ interactsWith ALDH2
+TNP interactsWith METAP2
+Mn2+ interactsWith APEX1
+ADP interactsWith HK1
+ADP interactsWith HK1
+CoA interactsWith HMGCR
+CoA interactsWith HMGCR
+3-hydroxy-3-methyl-glutaric_acid interactsWith HMGCR
+3-hydroxy-3-methyl-glutaric_acid interactsWith HMGCR
+HMG interactsWith HMGCR
+HMG interactsWith HMGCR
+NADP+ interactsWith HMGCR
+NADP+ interactsWith HMGCR
+MO1 interactsWith ME2
+NAD+ interactsWith ME2
+NAD+ interactsWith ME2
+NAD+ interactsWith ME2
+MAK interactsWith ME2
+Mg2+ interactsWith ME2
+TTN interactsWith ME2
+NAG interactsWith LCN2
+NAG-(4-1)NAG interactsWith LCN2
+OXL interactsWith ME2
+Mn2+ interactsWith ME2
+OXL interactsWith ME2
+NAG interactsWith Thrombomodulin
+NAG interactsWith Thrombomodulin
+NMY interactsWith 1EI2_A
+IPH interactsWith Insulin
+heme interactsWith CAT
+heme interactsWith CAT
+NDP interactsWith CAT
+heme interactsWith CAT
+PCA interactsWith AMY1A
+G6D-(1-4)GLC-(1-4)AC1-(1-4)GLC interactsWith AMY1A
+FII interactsWith K-Ras4b_Peptide_Substrate
+GER interactsWith CDC42
+Zn2+ interactsWith NOS3
+HAR interactsWith NOS3
+heme interactsWith NOS3
+BH4 interactsWith NOS3
+BH4 interactsWith NOS3
+VDX interactsWith VDR
+NAG interactsWith AZGP1
+NAG interactsWith AZGP1
+NAG-(4-1)NAG-(4-1)MAN-(6-1)MAN-(2-1)NAG-(3,3-1)MAN-(2-1)NAG interactsWith AZGP1
+NAG-(4-1)NAG-(4-1)MAN-(6-1)MAN-(2-1)NAG-(4-1)GAL-(6-2)SIA-(3,3-1)MAN-(2-1)NAG interactsWith AZGP1
+NAG-(4-1)NAG interactsWith AZGP1
+NAG-(4-1)NAG-(4-1)MAN interactsWith AZGP1
+BNN-CHG-PRR interactsWith F2
+Na+ interactsWith LYZ
+FII interactsWith K-Ras4b_Peptide_Substrate
+Mg2+ interactsWith BCKDHA
+K+ interactsWith BCKDHA
+K+ interactsWith BCKDHB
+TDP interactsWith BCKDHA
+HBI interactsWith TPH1
+Ca2+ interactsWith Low-Density_Lipoprotein_Receptor
+433 interactsWith PPARD
+433 interactsWith PPARD
+5-iodo-2-(oxalyl-amino)-benzoic_acid interactsWith PTPN1
+NAG interactsWith LIPF
+NAG interactsWith LIPF
+NAG-(4-1)NAG interactsWith LIPF
+NAG interactsWith LIPF
+NAG-(4-1)NAG interactsWith LIPF
+C78 interactsWith GRB2
+OAI interactsWith PTPN1
+761 interactsWith PTPN1
+OBA interactsWith PTPN1
+OPA interactsWith PTPN1
+OTA interactsWith PTPN1
+BBS interactsWith F2
+TAR interactsWith Mln64_Protein
+BMS interactsWith RARA
+cis-5,8,11,14,17-Eicosapentaenoic_acid interactsWith PPARD
+cis-5,8,11,14,17-Eicosapentaenoic_acid interactsWith PPARD
+DQN interactsWith NQO1
+DQN interactsWith NQO1
+DQN interactsWith NQO1
+DQN interactsWith NQO1
+DQN interactsWith NQO1
+NAG-(4-1)NAG-(4-1)MAN interactsWith Neutrophil_Gelatinase
+decanoate interactsWith Neutrophil_Gelatinase
+Ca2+ interactsWith PLA2G4A
+Ca2+ interactsWith PLA2G4A
+Zn2+ interactsWith Casein_Kinase_Ii
+GNP interactsWith CDC42
+GDP interactsWith ARL5
+Zn2+ interactsWith MGMT
+Ca2+ interactsWith THBD
+s-(2-iodobenzyl)_glutathione interactsWith GSTA4
+2PI interactsWith Ornithine_Carbamoyltransferase
+CP interactsWith Ornithine_Transcarbamylase
+BSI interactsWith MMP1
+HMD interactsWith CDK2
+157 interactsWith F2
+PP2 interactsWith SRC
+NAG-(4-1)NAG interactsWith SERPINC1
+NAG-(4-1)NAG interactsWith SERPINC1
+NAG-(4-1)NAG interactsWith SERPINC1
+AMP-PNP interactsWith SRC
+staurosporine interactsWith LCK
+GAL-(1-4)NAG-(1-2)MAN-(1-6)MAN-(1-4)NAG-(1-4)NAG-(6-1)FUC-(4,3-1)MAN interactsWith Immunoglobulin_Lambda_Heavy_Chain
+n-(1-adamantyl)-n'-(4-guanidinobenzyl)urea interactsWith PLAU
+OC1 interactsWith S100A8
+OC1 interactsWith S100A8
+Mg2+ interactsWith ITGA1
+GLC-(4-1)GAL interactsWith F7
+I84 interactsWith AKR1B1
+PGO interactsWith F13A1
+S80 interactsWith MMP3
+NADP+ interactsWith MTHFD1
+L24 interactsWith MTHFD1
+L34 interactsWith MTHFD1
+L37 interactsWith MTHFD1
+COL interactsWith PTPN1
+heme interactsWith Hemoglobin_Alpha_Chain
+heme interactsWith Hemoglobin_Alpha_Chain
+Ca2+ interactsWith Sex_Hormone-Binding_Globulin
+Stanolone interactsWith Sex_Hormone-Binding_Globulin
+ACE-HAC-ARG-MAA-HAQ-SEL interactsWith HLA-DRB1
+ACE-HAC-ARG-ALA-ODA-SER-CLE interactsWith HLA-DRB1
+MSI interactsWith CASP3
+MSI interactsWith CASP3
+166 interactsWith F2
+GDP interactsWith RAC1
+PC2 interactsWith BPI
+PC2 interactsWith BPI
+heme interactsWith CAT
+Zn2+ interactsWith FLT3LG
+Zn2+ interactsWith FLT3LG
+394 interactsWith RARB
+LMU interactsWith RARB
+395 interactsWith RARB
+LMU interactsWith RARB
+NAG interactsWith High_Affinity_Immunoglobulin_Epsilon_Receptor_Alpha-Subunit_Precursor
+NAG-(4-1)NAG-(4-1)MAN interactsWith High_Affinity_Immunoglobulin_Epsilon_Receptor_Alpha-Subunit_Precursor
+Mg2+ interactsWith 1CX0_B
+Mg2+ interactsWith 1CX0_B
+Mg2+ interactsWith 1CX0_B
+Mg2+ interactsWith 1CX0_B
+Rapamycin interactsWith FKBP1B
+GEN interactsWith ESRRA
+TR1 interactsWith MMP3
+Ca2+ interactsWith CLEC10A
+Ca2+ interactsWith CLEC10A
+Ca2+ interactsWith CLEC10A
+Zn2+ interactsWith Camp-Specific_3',5'-Cyclic_Phosphodiesterase_4b
+Mg2+ interactsWith Camp-Specific_3',5'-Cyclic_Phosphodiesterase_4b
+NAG-(4-1)NAG-(4-1)BMA-(6-1)BMA-(3,3-1)BMA interactsWith FCER1A
+NAG-(4-1)NAG-(4-1)MAN-(6-1)MAN-(2-1)MAN-(3,3-1)MAN interactsWith Ig_Epsilon_Chain_C_Region
+NAG-(4-1)NAG-(4-1)MAN interactsWith Ig_Epsilon_Chain_C_Region
+ITS interactsWith Dual_Adaptor_Of_Phosphotyrosine_And_3-_Phosphoinositides
+Ca2+ interactsWith Epidermal_Growth_Factor_Receptor_Pathway_Substrate_15
+TR1 interactsWith MMP3
+TR1 interactsWith MMP3
+Mg2+ interactsWith RAC2
+GDP interactsWith RAC2
+Zn2+ interactsWith CPA2
+Glu interactsWith CPA2
+Zn2+ interactsWith RARA
+Zn2+ interactsWith RARA
+CBZ interactsWith CASP8
+Ca2+ interactsWith KITLG
+Ca2+ interactsWith KITLG
+Ca2+ interactsWith KITLG
+3',5'-ADP interactsWith SULT2A1
+Na+ interactsWith Parathyroid_Hormone
+Zn2+ interactsWith Sex_Hormone-Binding_Globulin
+Zn2+ interactsWith Sex_Hormone-Binding_Globulin
+Stanolone interactsWith Sex_Hormone-Binding_Globulin
+Ca2+ interactsWith MRC1
+Ca2+ interactsWith LDLR
+Ca2+ interactsWith LDLR
+PBR interactsWith TTR
+TBP interactsWith TTR
+NBG interactsWith Liver_Glycogen_Phosphorylase
+PLP interactsWith Liver_Glycogen_Phosphorylase
+CC1 interactsWith LCK
+CC1 interactsWith LCK
+MO5 interactsWith AP2B1
+MO5 interactsWith AP2B1
+MO5 interactsWith AP2B1
+NIK interactsWith AP2B1
+NIK interactsWith AP2B1
+17beta-estradiol interactsWith ESR1
+Zn2+ interactsWith Synaptobrevin-Ii
+GSH interactsWith GSTO1
+Zn2+ interactsWith BIRC4
+Lovastatin interactsWith ITGAL
+Lovastatin interactsWith ITGAL
+FUC-(1-6)NAG-(4-1)NAG-(4-1)MAN-(6-1)MAN-(2-1)NAG-(4-1)GAL-(4,3-1)MAN-(2-1)NAG interactsWith Fc_Fragment_Of_Human_Igg1
+REA interactsWith RXRA
+BZT interactsWith F2
+BT3 interactsWith F2
+BT2 interactsWith F2
+Z34 interactsWith F10
+Zn2+ interactsWith RABIF
+IH1 interactsWith F2
+IH2 interactsWith F2
+Ca2+ interactsWith GCA
+Mg2+ interactsWith GBP1
+GNP interactsWith GBP1
+UAP-(1-4)SGN-(1-4)IDU interactsWith FGFR1
+UAP-(1-4)SGN-(1-4)IDU interactsWith FGFR1
+UAP-(1-4)SGN-(1-4)IDU interactsWith FGF2
+SGN-(1-4)IDU interactsWith FGF2
+SGN-(1-4)IDU interactsWith FGF2
+UAP-(1-4)SGN-(1-4)IDU interactsWith FGFR1
+UAP-(1-4)SGN-(1-4)IDU interactsWith FGFR1
+SGN interactsWith FGF2
+RPR interactsWith F10
+815 interactsWith F10
+PR2 interactsWith F10
+DTD interactsWith CASP8
+DTD interactsWith CASP8
+DTD interactsWith CASP8
+NAG-(6-1)FUC interactsWith Igm_Fab_Region_Iv-J(H4)-C_(Kau_Cold_Agglutinin)
+BRE interactsWith Dihydroorotate_Dehydrogenase
+FMN interactsWith Dihydroorotate_Dehydrogenase
+Orotic_acid interactsWith Dihydroorotate_Dehydrogenase
+DDQ interactsWith Dihydroorotate_Dehydrogenase
+A26 interactsWith Dihydroorotate_Dehydrogenase
+ARD interactsWith FKBP1A
+ARD interactsWith FRAP1
+ARD interactsWith FRAP1
+184 interactsWith RARB
+564 interactsWith RARB
+156 interactsWith RARB
+NAG-(4-1)NAG interactsWith SERPINC1
+NAG-(4-1)NAG-(4-1)MAN-(6-1)MAN-(3,3-1)MAN interactsWith SERPINC1
+whi-p180 interactsWith CDK2
+MSQ interactsWith MAPK14
+Mn2+ interactsWith H2AFZ
+staurosporine interactsWith PIK3CG
+GTP interactsWith RAC1
+SGN-(4-1)2SI-(4-1)SGN-(4-1)2SI-(4-1)SGN-(4-1)2SI-(4-1)SGN-(4-1)2SI-(4-1)SGN-(4-1)2SI interactsWith FGF1
+SGN-(4-1)2SI-(4-1)SGN-(4-1)2SI-(4-1)SGN-(4-1)2SI-(4-1)SGN-(4-1)2SI-(4-1)SGN-(4-1)2SI interactsWith FGF1
+SGN-(4-1)2SI-(4-1)SGN-(4-1)2SI-(4-1)SGN-(4-1)2SI-(4-1)SGN-(4-1)2SI-(4-1)SGN-(4-1)2SI interactsWith FGFR2
+GPI interactsWith FKBP1B
+n-(2-flouro-benzyl)-4-sulfamoyl-benzamide interactsWith CA2
+n-(2-flouro-benzyl)-4-sulfamoyl-benzamide interactsWith CA2
+F2B interactsWith CA2
+n-(2,6-diflouro-benzyl)-4-sulfamoyl-benzamide interactsWith CA2
+FFB interactsWith CA2
+FFB interactsWith CA2
+BSB interactsWith CA2
+n-(2,6-diflouro-benzyl)-4-sulfamoyl-benzamide interactsWith CA2
+FFB interactsWith CA2
+decanoate interactsWith AFP
+decanoate interactsWith AFP
+decanoate interactsWith AFP
+decanoate interactsWith AFP
+decanoate interactsWith AFP
+decanoate interactsWith AFP
+decanoate interactsWith AFP
+decanoate interactsWith AFP
+decanoate interactsWith AFP
+decanoate interactsWith AFP
+lauric_acid interactsWith AFP
+lauric_acid interactsWith AFP
+lauric_acid interactsWith AFP
+lauric_acid interactsWith AFP
+lauric_acid interactsWith AFP
+lauric_acid interactsWith AFP
+lauric_acid interactsWith AFP
+lauric_acid interactsWith AFP
+MYR interactsWith AFP
+MYR interactsWith AFP
+MYR interactsWith AFP
+STE interactsWith AFP
+STE interactsWith AFP
+STE interactsWith AFP
+STE interactsWith AFP
+STE interactsWith AFP
+STE interactsWith AFP
+STE interactsWith AFP
+Fe2+ interactsWith HGD
+CH3-DPN-PRO-AR2 interactsWith F2
+CP4 interactsWith Liver_Glycogen_Phosphorylase
+700 interactsWith Liver_Glycogen_Phosphorylase
+700 interactsWith Liver_Glycogen_Phosphorylase
+Ca2+ interactsWith EPS15
+DPR interactsWith EPS15
+Zn2+ interactsWith Cdk-Activating_Kinase_Assembly_Factor_Mat1
+Zn2+ interactsWith Cdk-Activating_Kinase_Assembly_Factor_Mat1
+CHN-HMM-SML interactsWith F2
+AIM-HMM-SML interactsWith F2
+BBH interactsWith MMP3
+Zn2+ interactsWith Tfiih_P44_Subunit
+Zn2+ interactsWith Tfiih_P44_Subunit
+SPC interactsWith MMP3
+SPC interactsWith MMP3
+SPC interactsWith MMP3
+SPI interactsWith MMP3
+Zn2+ interactsWith Transcription_Factor_Ii_B_(Tfiib)
+Ca2+ interactsWith Low-Density_Lipoprotein_Receptor
+172 interactsWith PLAU
+4MZ interactsWith CA2
+NAG interactsWith MMP2
+IH3 interactsWith F2
+MM3 interactsWith MMP3
+MM3 interactsWith MMP3
+APH-PIP interactsWith F2
+NADP+ interactsWith NNT
+Zn2+ interactsWith Transcription_Factor_Wstf
+Zn2+ interactsWith Transcription_Factor_Wstf
+RDF interactsWith Neutral_Endopeptidase
+Zn2+ interactsWith CCS
+NCH interactsWith Antibody_M3c65_(Light_Chain)
+NCH interactsWith Antibody_M3c65_(Heavy_Chain)
+Na+ interactsWith MPG
+Palmitate interactsWith AFP
+Palmitate interactsWith AFP
+Palmitate interactsWith AFP
+Palmitate interactsWith AFP
+Palmitate interactsWith AFP
+Palmitate interactsWith AFP
+Palmitate interactsWith AFP
+Zn2+ interactsWith GCH1
+CSN interactsWith ARSA
+RQ3 interactsWith HBA2
+RQ3 interactsWith HBB
+RQ3 interactsWith HBA2
+CRS interactsWith Insulin
+CRS interactsWith Insulin
+CRS interactsWith Insulin
+CRS interactsWith Insulin
+CRS interactsWith Insulin
+CRS interactsWith Insulin
+CRS interactsWith Insulin
+CRS interactsWith Insulin
+CRS interactsWith Insulin
+CRS interactsWith Insulin
+CRS interactsWith Insulin
+CRS interactsWith Insulin
+CRS interactsWith Insulin
+CRS interactsWith Insulin
+CRS interactsWith Insulin
+CRS interactsWith Insulin
+CRS interactsWith Insulin
+CRS interactsWith Insulin
+CRS interactsWith Insulin
+CRS interactsWith Insulin
+CRS interactsWith Insulin
+CRS interactsWith Insulin
+Na+ interactsWith Insulin
+RCO interactsWith Insulin
+RCO interactsWith Insulin
+RCO interactsWith Insulin
+RCO interactsWith Insulin
+RCO interactsWith Insulin
+RCO interactsWith Insulin
+RCO interactsWith Insulin
+RCO interactsWith Insulin
+RCO interactsWith Insulin
+RCO interactsWith Insulin
+RCO interactsWith Insulin
+RCO interactsWith Insulin
+RCO interactsWith Insulin
+RCO interactsWith Insulin
+RCO interactsWith Insulin
+RCO interactsWith Insulin
+RCO interactsWith Insulin
+RCO interactsWith Insulin
+RCO interactsWith Insulin
+RCO interactsWith Insulin
+RCO interactsWith Insulin
+RCO interactsWith Insulin
+RCO interactsWith Insulin
+FID interactsWith AKR1B1
+GAL-(1-3)GAL interactsWith B3GAT3
+Mn2+ interactsWith B3GAT3
+UDP interactsWith B3GAT3
+NAG-(4-1)NAG-(4-1)MAN interactsWith GZMB
+NAG-(4-1)NAG-(4-1)MAN interactsWith GZMB
+NAG-(4-1)NAG-(4-1)MAN interactsWith GZMB
+D16 interactsWith TYMS
+dUMP interactsWith TYMS
+dUMP interactsWith TYMS
+SUC interactsWith ATOX1
+Zn2+ interactsWith TRIM28
+Zn2+ interactsWith TRIM28
+GDP interactsWith RAC1
+112 interactsWith INSR
+diclofenac interactsWith TTR
+BPD interactsWith TTR
+OFL interactsWith TTR
+resveratrol interactsWith TTR
+Flurbiprofen interactsWith TTR
+dibenzofuran-4,6-dicarboxylic_acid interactsWith TTR
+SUC interactsWith ATOX1
+Cu1+ interactsWith ATOX1
+SUC interactsWith ATOX1
+FUC-(1-6)NAG-(4-1)NAG interactsWith ACHE
+NAG interactsWith ACHE
+PFL interactsWith AFP
+PFL interactsWith AFP
+PFL interactsWith AFP
+HLT interactsWith AFP
+HLT interactsWith AFP
+HLT interactsWith AFP
+HLT interactsWith AFP
+HLT interactsWith AFP
+HLT interactsWith AFP
+HLT interactsWith AFP
+HLT interactsWith AFP
+HLT interactsWith AFP
+HLT interactsWith AFP
+HLT interactsWith AFP
+HLT interactsWith AFP
+NAG-(4-1)NAG interactsWith ACHE
+Ca2+ interactsWith MAN1B1
+DMJ interactsWith MAN1B1
+KIF interactsWith MAN1B1
+106 interactsWith CDK2
+107 interactsWith CDK2
+S-Adenosylhomocysteine interactsWith DNMT2
+NAG interactsWith CD80
+NAG interactsWith CD80
+NAG interactsWith CD80
+Zn2+ interactsWith BIRC4
+Zn2+ interactsWith ADH1C
+Zn2+ interactsWith ADH1C
+NAD+ interactsWith ADH1C
+PYZ interactsWith ADH1C
+PYZ interactsWith ADH1C
+Zn2+ interactsWith ADH1C
+Zn2+ interactsWith ADH1C
+NAD+ interactsWith ADH1C
+Ca2+ interactsWith S100A12
+Ca2+ interactsWith S100A12
+NAG-(1-4)NAG-(6-1)FUC interactsWith FGF9
+NAG interactsWith FGF9
+ACP interactsWith INSR
+Ca2+ interactsWith Kappa-4_Immunoglobulin_Light_Chain_Vl
+PHW interactsWith F2
+NADP+ interactsWith BLVRB
+BLA interactsWith BLVRB
+MBV interactsWith BLVRB
+FMN interactsWith BLVRB
+LUM interactsWith BLVRB
+Ca2+ interactsWith LYZ
+Zn2+ interactsWith LIMS2
+Zn2+ interactsWith LIMS2
+Citiric_acid interactsWith MIF
+Citiric_acid interactsWith MIF
+YZ9 interactsWith MIF
+YZ9 interactsWith MIF
+REA interactsWith RXRA
+GI262570 interactsWith PPARG
+GSP interactsWith ARF6
+GSP interactsWith ARF6
+Citric_acid interactsWith RNASE3
+Citric_acid interactsWith RNASE3
+Citric_acid interactsWith RNASE3
+PHW interactsWith F2
+NAG interactsWith CD80
+NAG interactsWith CD80
+NAG interactsWith CD80
+NAG interactsWith CTLA4
+NAG interactsWith CTLA4
+NAG interactsWith ALPI
+Zn2+ interactsWith ALPI
+Zn2+ interactsWith ALPI
+Mg2+ interactsWith ALPI
+Mg2+ interactsWith ALPI
+NADH interactsWith LDHB
+OXM interactsWith LDHB
+NADH interactsWith LDHA
+OXM interactsWith LDHA
+INL interactsWith CA2
+INM interactsWith CA2
+INQ interactsWith CA2
+INV interactsWith CA2
+INV interactsWith CA2
+INW interactsWith CA2
+INW interactsWith CA2
+IOA interactsWith CA2
+IOC interactsWith CA2
+IOC interactsWith CA2
+IOE interactsWith CA2
+IOF interactsWith CA2
+IOF interactsWith CA2
+NAG-(4-1)NAG-(4-1)MAN interactsWith CGA
+NAG-(4-1)NAG interactsWith FSHB
+NAG-(4-1)NAG interactsWith FSHB
+NAG-(4-1)NAG interactsWith FSHB
+NAG-(1-4)NAG-(6-1)FUC interactsWith MASP2
+NES interactsWith MASP2
+Zn2+ interactsWith SERPINA1
+Zn2+ interactsWith SERPINA1
+K+ interactsWith TF
+GNP interactsWith RAC2
+KH1 interactsWith VDR
+MAN-(1-6)NAG-(1-2)MAN-(1-6)MAN-(1-4)NAG-(1-4)NAG-(6-1)MAN-(4,3-1)MAN interactsWith Ig_Gamma-1_Chain_C_Region
+MAN-(1-6)MAN-(1-6)MAN-(1-4)NAG-(1-4)NAG-(6-1)FUC-(3,3-1)MAN-(6-1)MAN interactsWith Ig_Gamma-1_Chain_C_Region
+MAN-(1-6)MAN-(1-6)MAN-(1-4)NAG-(1-4)NAG-(6-1)FUC-(3,3-1)MAN-(6-1)MAN interactsWith Ig_Gamma-1_Chain_C_Region
+114 interactsWith HMGCR
+114 interactsWith HMGCR
+114 interactsWith HMGCR
+114 interactsWith HMGCR
+ADP interactsWith HMGCR
+ADP interactsWith HMGCR
+ADP interactsWith HMGCR
+SIM interactsWith HMGCR
+SIM interactsWith HMGCR
+ADP interactsWith HMGCR
+115 interactsWith HMGCR
+115 interactsWith HMGCR
+116 interactsWith HMGCR
+116 interactsWith HMGCR
+ADP interactsWith HMGCR
+117 interactsWith HMGCR
+117 interactsWith HMGCR
+Ca2+ interactsWith FREQ
+Ca2+ interactsWith FREQ
+Ca2+ interactsWith FREQ
+REA interactsWith RXRA
+REA interactsWith RXRA
+NAG interactsWith GZMB
+FUC-(1-6)NAG-(4-1)NAG-(4-1)MAN-(4-1)NAG-(4,6-1)MAN interactsWith GZMB
+Zn2+ interactsWith GZMB
+Zn2+ interactsWith GZMB
+COT interactsWith AANAT
+COT interactsWith AANAT
+FBS interactsWith CA2
+FBT interactsWith CA2
+FBU interactsWith CA2
+SBR interactsWith CA2
+SBS interactsWith CA2
+SBB interactsWith CA2
+HQQ interactsWith MMP3
+110 interactsWith F2
+HAV interactsWith MMP3
+3MP interactsWith MMP3
+MSB interactsWith MMP3
+INZ interactsWith PTPN9
+INX interactsWith PTPN9
+NAG interactsWith Cr2CD121C3DEPSTEIN-Barr_Virus_Receptor
+NAG interactsWith C3
+A2P interactsWith RNASE3
+3',5'-ADP interactsWith RNASE3
+ADP interactsWith RNASE3
+5'-TMP interactsWith Thymidylate_Kinase
+ADP interactsWith Similar_To_Thymidylate_Kinase_(Dtmp_Kinase)
+AMP-PNP interactsWith Similar_To_Thymidylate_Kinase_(Dtmp_Kinase)
+5'-TMP interactsWith Thymidylate_Kinase
+dTDP interactsWith Thymidylate_Kinase
+Mg2+ interactsWith Thymidylate_Kinase
+ATP interactsWith Thymidylate_Kinase
+GLC-(1-4)GLC interactsWith AMY2A
+L-Thyroxine interactsWith TTR
+L-Thyroxine interactsWith TTR
+SRL interactsWith NR1I3
+Ca2+ interactsWith REPS1
+Zn2+ interactsWith LTA4H
+BES interactsWith LTA4H
+IMD interactsWith LTA4H
+NAG-(4-1)NAG-(4-1)MAN interactsWith IL12B
+MYR interactsWith AFP
+MYR interactsWith AFP
+RWF interactsWith AFP
+MYR interactsWith AFP
+SWF interactsWith AFP
+BAM interactsWith PLAU
+AMR interactsWith PLAU
+MNB interactsWith IL12B
+MNB interactsWith IL12B
+NAG interactsWith SERPINB4
+NAG-(4-1)NAG-(4-1)MAN interactsWith SERPINC1
+NAG-(4-1)NAG-(4-1)MAN interactsWith SERPINC1
+NAG-(4-1)NAG interactsWith SERPINC1
+NAG-(4-1)NAG-(4-1)MAN-(6-1)MAN-(2-1)NAG-(4-1)GAL-(3,3-1)MAN-(2-1)MAN interactsWith SERPINC1
+WAY interactsWith MMP3
+Ca2+ interactsWith LDLR
+Ca2+ interactsWith LDLR
+GAL-(1-4)NAG-(1-2)MAN-(1-6)MAN-(3-1)MAN-(2-1)NAG-(4-1)GAL-(4,1-4)NAG-(1-4)NAG interactsWith Immunoglobulin_Heavy_Chain
+GAL-(1-4)NAG-(1-2)MAN-(1-6)MAN-(1-4)NAG-(1-4)NAG-(6-1)FUC-(4,3-1)MAN-(2-1)NAG interactsWith Immunoglobulin_Heavy_Chain
+OKA interactsWith PPP1CC
+heme interactsWith CBS
+PLP interactsWith CBS
+IMD interactsWith Heavy_Chain_Of_Ig
+IMD interactsWith Kappa_Light_Chain_Of_Ig
+GGP interactsWith Bradykinin
+BBT interactsWith MMP1
+ODS-PHE-NFP interactsWith CTSL2
+BNS interactsWith CTSL2
+BNS interactsWith CTSL2
+HXA interactsWith FABP7
+HXA interactsWith FABP7
+Oleic_Acid interactsWith FABP3
+PBG interactsWith ALAD
+Zn2+ interactsWith ALAD
+Ca2+ interactsWith LDLR
+Benzamidine interactsWith F7
+UKP interactsWith PLAU
+Zn2+ interactsWith SIRT2
+CPQ interactsWith Insulin-Like_Growth_Factor_1a
+NAG interactsWith FCER1A
+NAG interactsWith FCER1A
+NAG interactsWith FCER1A
+NAG interactsWith High_Affinity_Immunoglobulin_Epsilon_Receptor_Alpha-Subunit_Precursor
+NAG-(4-1)NAG-(4-1)MAN-(4-1)MAN-(4-1)MAN-(3,6-1)MAN interactsWith NPR2
+FUC-(1-6)NAG-(4-1)NAG-(4-1)MAN-(4-1)MAN interactsWith NPR2
+NAG interactsWith NPR3
+NAG interactsWith NPR3
+NAG-(4-1)NAG interactsWith NPR3
+NAG-(4-1)NAG interactsWith FCER1A
+NAG-(4-1)NAG-(4-1)MAN-(6-1)MAN interactsWith FCER1A
+FUC-(1-3)NAG-(4-1)NAG interactsWith FCER1A
+NAG interactsWith High_Affinity_Immunoglobulin_Epsilon_Receptor_Alpha-Subunit_Precursor
+NAG-(4-1)NAG-(4-1)MAN-(3-1)MAN interactsWith High_Affinity_Immunoglobulin_Epsilon_Receptor_Alpha-Subunit_Precursor
+NAG-(1-4)NAG-(6-1)FUC interactsWith FCER1A
+NAG-(4-1)NAG interactsWith FCER1A
+NAG-(4-1)NAG-(4-1)BMA-(6-1)BMA-(3,3-1)BMA interactsWith FCER1A
+NAG-(1-4)NAG-(6-1)FUC interactsWith FCER1A
+NAG-(4-1)NAG interactsWith FCER1A
+NAG-(4-1)NAG-(4-1)MAN interactsWith FCER1A
+NAG-(4-1)NAG interactsWith FCER1A
+NAG interactsWith FCER1A
+NAG-(4-1)NAG-(4-1)MAN interactsWith FCER1A
+NAG-(4-1)NAG interactsWith FCER1A
+NAG interactsWith FCER1A
+NAG-(4-1)NAG-(4-1)MAN interactsWith FCER1A
+NAG-(4-1)NAG-(4-1)MAN-(6-1)MAN interactsWith FCER1A
+NAG-(4-1)NAG-(4-1)MAN-(6-1)MAN interactsWith FCER1A
+U55 interactsWith CDK2
+benzoate interactsWith PRDX5
+GER interactsWith ARHGDIA
+GER interactsWith RAC2
+Zn2+ interactsWith CA12
+acetazolamide interactsWith CA12
+IU5 interactsWith AKR1C2
+IU5 interactsWith AKR1C2
+NAG interactsWith SERPINF1
+Zn2+ interactsWith BRCA1
+Zn2+ interactsWith BRCA1
+Zn2+ interactsWith BARD1
+Zn2+ interactsWith BARD1
+CNO interactsWith HBB
+CNO interactsWith HBA2
+CNO interactsWith HBA2
+CNO interactsWith HBB
+CNO interactsWith HBA2
+NAG interactsWith Heparin-Binding_Protein
+NAG interactsWith IL17F
+NAG-(4-1)NAG interactsWith IL17F
+NAG interactsWith IL17F
+GSH interactsWith Glutathione_Transferase_Zeta
+dUMP interactsWith TYMS
+dUMP interactsWith TYMS
+LYA interactsWith TYMS
+Zn2+ interactsWith CA1
+E09 interactsWith NQO1
+E09 interactsWith NQO1
+ADP interactsWith ABCB9
+RH1 interactsWith NQO1
+RH1 interactsWith NQO1
+ARH interactsWith NQO1
+ARH interactsWith NQO1
+Zn2+ interactsWith F2
+BAI interactsWith F2
+BAB interactsWith F2
+Zn2+ interactsWith Thrombin
+Zn2+ interactsWith F2
+bis(5-amidino-2-benzimidazolyl)methane_ketone_hydrate interactsWith F2
+BAM interactsWith F2
+Citrate interactsWith PLAU
+Citrate interactsWith PLAU
+Citrate interactsWith PLAU
+4-iodobenzo[b]thiophene-2-carboxamidine interactsWith PLAU
+thieno[2,3-b]pyridine-2-carboxamidine interactsWith PLAU
+Citrate interactsWith PLAU
+BAM interactsWith PLAU
+BT1 interactsWith F2
+Ca2+ interactsWith Calmodulin
+Ca2+ interactsWith Calmodulin
+Ca2+ interactsWith Calmodulin
+Ca2+ interactsWith Calmodulin
+h717 interactsWith CDK2
+SUC interactsWith FNTB
+SUC interactsWith FNTA
+Zn2+ interactsWith FNTB
+Farnesyl-PP interactsWith FNTB
+Farnesyl-PP interactsWith FNTA
+739 interactsWith FNTB
+739 interactsWith FNTA
+PIB interactsWith NCF4
+111 interactsWith MMP3
+T87 interactsWith F2
+R11 interactsWith F2
+benzoate interactsWith PRDX5
+T87 interactsWith F10
+R11 interactsWith F10
+MO3 interactsWith 1JID_B
+MO3 interactsWith 1JID_B
+heme interactsWith HBB
+Fe3+ interactsWith TF
+NAG-(4-1)NAG interactsWith ITGAV
+NAG interactsWith ITGAV
+NAG-(4-1)NAG interactsWith ITGAV
+NAG interactsWith ITGAV
+NAG-(4-1)NAG interactsWith ITGAV
+NAG-(4-1)NAG interactsWith ITGAV
+NAG-(4-1)NAG interactsWith ITGAV
+NAG interactsWith ITGB5
+NAG interactsWith ITGAV
+NAG interactsWith ITGB5
+NAG-(4-1)NAG interactsWith ITGB5
+NAG-(4-1)NAG interactsWith ITGB5
+Ca2+ interactsWith ITGB5
+Ca2+ interactsWith ITGAV
+Ca2+ interactsWith ITGAV
+Ca2+ interactsWith ITGAV
+Ca2+ interactsWith ITGAV
+Ca2+ interactsWith ITGAV
+Ca2+ interactsWith SELP
+SIA-(2-3)GAL-(1-4)1NA-(3-1)FUC interactsWith SELP
+SIA-(2-3)GAL-(1-4)NAG-(1-6)NGA-(3-1)GAL-(3,3-1)FUC interactsWith SELP
+SIA-(2-3)GAL-(1-4)NAG-(1-6)NGA-(3-1)GAL-(3,3-1)FUC interactsWith Psgl-1_Peptide
+SIA-(2-3)GAL-(1-4)1NA-(3-1)FUC interactsWith SELL
+703 interactsWith TNFRSF1A
+5'-TMP interactsWith Thymidylate_Kinase
+ATM interactsWith Thymidylate_Kinase
+5'-TMP interactsWith Thymidylate_Kinase
+INR interactsWith CDK2
+INR interactsWith CDK2
+Ca2+ interactsWith TNNC1
+Ca2+ interactsWith TNNC1
+EMD interactsWith TNNC1
+ADP interactsWith Thymidylate_Kinase
+ATM interactsWith Thymidylate_Kinase
+ATM interactsWith Thymidylate_Kinase
+Z5A interactsWith Thymidylate_Kinase
+SGN-(4-1)IDS interactsWith HGF
+SGN-(4-1)IDS interactsWith HGF
+IDS interactsWith HGF
+IDS interactsWith HGF
+SGN-(4-1)IDS interactsWith HGF
+SGN interactsWith HGF
+SGN-(4-1)IDS interactsWith HGF
+AAH interactsWith Antibody_Germline_Precursor_To_28b4
+PMB interactsWith CLC
+PMB interactsWith CLC
+Zn2+ interactsWith NR1D1
+Zn2+ interactsWith NR1D1
+ADP interactsWith PMS2
+Mg2+ interactsWith PMS2
+AGS interactsWith PMS2
+AGS interactsWith PMS2
+NAG-(4-1)NAG-(4-1)MAN interactsWith CSF2RB
+FAD-NYP interactsWith MAOB
+544 interactsWith PPARA
+544 interactsWith PPARA
+544 interactsWith PPARA
+544 interactsWith PPARG
+ACP interactsWith IGF1R
+ATP interactsWith DGUOK
+Ca2+ interactsWith GCA
+S-Adenosylhomocysteine interactsWith PNMT
+sk&f_29661 interactsWith PNMT
+CBZ interactsWith CASP9
+I52 interactsWith MMP13
+GSH interactsWith ULBP3
+Oleic_Acid interactsWith AFP
+Oleic_Acid interactsWith AFP
+Oleic_Acid interactsWith AFP
+Oleic_Acid interactsWith AFP
+Oleic_Acid interactsWith AFP
+Oleic_Acid interactsWith AFP
+Oleic_Acid interactsWith AFP
+Arachidonic_acid interactsWith AFP
+Arachidonic_acid interactsWith AFP
+Arachidonic_acid interactsWith AFP
+Arachidonic_acid interactsWith AFP
+Arachidonic_acid interactsWith AFP
+Arachidonic_acid interactsWith AFP
+Arachidonic_acid interactsWith AFP
+Arachidonic_acid interactsWith AFP
+JST interactsWith MMP1
+LIG interactsWith CDK2
+NAG-(1-2)MAN-(1-3)MAN-(6-1)MAN-(2-1)NAG interactsWith CD209
+NAG-(1-2)MAN-(1-3)MAN-(6-1)MAN-(2-1)NAG interactsWith CD209
+Ca2+ interactsWith CD209
+Ca2+ interactsWith CD209
+Ca2+ interactsWith CD209
+NAG-(1-2)MAN-(1-3)MAN-(6-1)MAN-(2-1)NAG interactsWith CD209
+Ca2+ interactsWith CD209
+Ca2+ interactsWith CD209
+001 interactsWith FKBP1A
+Ca2+ interactsWith Low-Density_Lipoprotein_Receptor-Related_Protein_1
+1PU interactsWith CDK2
+1PU interactsWith CDK2
+2PU interactsWith CDK2
+Oleic_Acid interactsWith GC
+Oleic_Acid interactsWith GC
+VDY interactsWith GC
+JY interactsWith GC
+JY interactsWith GC
+Oleic_Acid interactsWith GC
+C24 interactsWith F2
+C02 interactsWith F2
+Benzamidine interactsWith PRSS7
+heme interactsWith HBZ
+120 interactsWith F2
+BMZ interactsWith F2
+121 interactsWith F2
+120 interactsWith PLAU
+Citric_acid interactsWith PLAU
+Citric_acid interactsWith PLAU
+CIT-CIT interactsWith PLAU
+BMZ interactsWith PLAU
+123 interactsWith PLAU
+MBS interactsWith MMP3
+340 interactsWith NQO1
+340 interactsWith NQO1
+936 interactsWith NQO1
+936 interactsWith NQO1
+ALC-PRO-MMO interactsWith F2
+SMS interactsWith CA2
+Ca2+ interactsWith S100A12
+Ca2+ interactsWith S100A12
+Ca2+ interactsWith COL8A1
+Benzamidine interactsWith PRSS3
+Ca2+ interactsWith PRSS3
+S-Adenosylhomocysteine interactsWith Protein-L-Isoaspartate_O-Methyltransferase
+AZ2 interactsWith PPARA
+CPQ interactsWith PPARA
+AZ2 interactsWith PPARG
+AZ2 interactsWith PPARG
+L-Thyroxine interactsWith TTR
+L-Thyroxine interactsWith TTR
+L-Thyroxine interactsWith TTR
+Ca2+ interactsWith S100A9
+Ca2+ interactsWith S100A9
+NAG-(4-1)NAG interactsWith BST1
+SAP interactsWith BST1
+ENP interactsWith BST1
+Nicotinamide interactsWith BST1
+Nicotinamide interactsWith BST1
+ENA interactsWith BST1
+ENA interactsWith BST1
+NMN interactsWith BST1
+NMN interactsWith BST1
+Nicotinamide interactsWith BST1
+Nicotinamide interactsWith BST1
+NAG interactsWith HLA-DRB1
+TBH interactsWith PTPN1
+TBH interactsWith PTPN1
+Zn2+ interactsWith CSNK2B
+AMP-PNP interactsWith CSNK2A1
+BLI interactsWith F2
+MAZ-PTR-PTM-ASN interactsWith GRB2
+NAG interactsWith CTSC
+NAG interactsWith CTSC
+Citiric_acid interactsWith Angiogenin
+GNP interactsWith RAN
+GDP interactsWith RAN
+Mn2+ interactsWith Phosphoenolpyruvate_Carboxykinase,_Cytosolic_(Gtp)
+GTO interactsWith Phosphoenolpyruvate_Carboxykinase,_Cytosolic_(Gtp)
+phosphoenolpyruvate interactsWith Phosphoenolpyruvate_Carboxykinase,_Cytosolic
+471 interactsWith PPARA
+471 interactsWith PPARA
+471 interactsWith PPARA
+471 interactsWith PPARA
+Zn2+ interactsWith Zinc_Finger_Y-Chromosomal_Protein
+Zn2+ interactsWith Zinc_Finger_Y-Chromosomal_Protein
+NBS interactsWith SRC
+BMU interactsWith MAPK14
+B96 interactsWith MAPK14
+GDP interactsWith TGM2
+Mg2+ interactsWith TNFSF13B
+Citiric_acid interactsWith TNFSF13B
+Citiric_acid interactsWith TNFSF13B
+A2G interactsWith Leukosialin_(Cd43)_Fragment
+A2G interactsWith Leukosialin_(Cd43)_Fragment
+A2G interactsWith Leukosialin_(Cd43)_Fragment
+Zn2+ interactsWith Transcriptional_Repressor_Not4
+Zn2+ interactsWith Transcriptional_Repressor_Not4
+132 interactsWith F2
+130 interactsWith F2
+132 interactsWith PLAU
+133 interactsWith PLAU
+134 interactsWith PLAU
+135 interactsWith PLAU
+130 interactsWith PLAU
+MO6 interactsWith TBX3
+LG2 interactsWith RXRB
+Zenarestat interactsWith AKR1B1
+CC0 interactsWith LCK
+AMP-PNP interactsWith IGF1R
+Ca2+ interactsWith S100A6
+Ca2+ interactsWith S100A6
+KTP interactsWith CTSG
+KTP interactsWith CTSG
+ETC interactsWith ESR1
+ETC interactsWith ESR2
+NAG-(4-1)NAG interactsWith ITGAV
+NAG-(4-1)NAG interactsWith ITGAV
+NAG-(4-1)NAG interactsWith ITGB5
+Mn2+ interactsWith ITGB5
+Mn2+ interactsWith ITGB5
+Mn2+ interactsWith ITGB5
+Mn2+ interactsWith ITGAV
+Mn2+ interactsWith ITGAV
+Mn2+ interactsWith ITGAV
+Mn2+ interactsWith ITGAV
+Mn2+ interactsWith ITGAV
+GAL-(1-4)NAG-(1-2)MAN-(1-6)MAN-(1-4)NAG-(1-4)NAG-(6-1)FUC-(4,3-1)MAN-(2-1)NAG-(4-1)GAL interactsWith Immunoglobulin_Gamma-1_Heavy_Chain_Constant_Region
+Ca2+ interactsWith CETN1
+Ca2+ interactsWith CETN1
+Ca2+ interactsWith CETN1
+Ca2+ interactsWith CETN1
+136 interactsWith PLAU
+ATP interactsWith CDK2
+GTA interactsWith EIF4E
+MGP interactsWith EIF4E
+E4P interactsWith GPI
+E4P interactsWith GPI
+CYU interactsWith PPP1CC
+Fe2+ interactsWith TPH1
+BH4 interactsWith TPH1
+Testosterone interactsWith AKR1C1
+Testosterone interactsWith AKR1C1
+AND interactsWith SULT2B1
+IGN interactsWith F2
+NAG-(4-1)NAG interactsWith F2
+MEL interactsWith F2
+Zn2+ interactsWith VDR
+Zn2+ interactsWith VDR
+Stanolone interactsWith Sex_Hormone-Binding_Globulin
+Stanolone interactsWith Sex_Hormone-Binding_Globulin
+LS1 interactsWith CDK2
+LS2 interactsWith CDK2
+LS3 interactsWith CDK2
+LS4 interactsWith CDK2
+LS5 interactsWith CDK2
+K+ interactsWith 1KF1_A
+K+ interactsWith 1KF1_A
+K+ interactsWith 1KF1_A
+BCN interactsWith HGF
+BCN interactsWith HGF
+BCN interactsWith HGF
+Mg2+ interactsWith GNAI3
+Zn2+ interactsWith CPB1
+Citiric_acid interactsWith CPB1
+Zn2+ interactsWith RPA1
+Benzamidine interactsWith KLK6
+DBD interactsWith PTPN1
+Ca2+ interactsWith TGM6
+Ca2+ interactsWith TGM6
+Ca2+ interactsWith TGM6
+Ca2+ interactsWith TGM6
+Zn2+ interactsWith RBX1
+Zn2+ interactsWith RBX1
+Zn2+ interactsWith RBX1
+Zn2+ interactsWith Creb_Binding_Protein
+N-ethylmaleimide interactsWith CLC
+N-ethylmaleimide interactsWith CLC
+PAPS interactsWith SULT1E1
+FNP interactsWith PTPN9
+FEP interactsWith PTPN9
+FXV interactsWith F10
+UDPGA interactsWith B3GAT3
+NAG-(4-1)NAG interactsWith PROCR
+NAG interactsWith PROCR
+NAG-(4-1)NAG interactsWith PROCR
+PTY interactsWith PROCR
+Mg2+ interactsWith 1L9A_B
+Mg2+ interactsWith 1L9A_B
+Mg2+ interactsWith 1L9A_B
+Mg2+ interactsWith 1L9A_B
+Mg2+ interactsWith 1L9A_B
+Mg2+ interactsWith 1L9A_B
+Mg2+ interactsWith 1L9A_B
+Mg2+ interactsWith 1L9A_B
+Mg2+ interactsWith 1L9A_B
+Mg2+ interactsWith 1L9A_B
+U66 interactsWith FNTB
+U66 interactsWith FNTA
+U49 interactsWith FNTB
+U49 interactsWith FNTA
+Citiric_acid interactsWith C8G
+DLP interactsWith PCTP
+DLP interactsWith Phosphatidylcholine_Transfer_Protein
+CPL interactsWith Phosphatidylcholine_Transfer_Protein
+CPL interactsWith Phosphatidylcholine_Transfer_Protein
+NAG interactsWith PROCR
+NAG interactsWith PROCR
+NAG interactsWith PROCR
+NAG interactsWith PROCR
+PTY interactsWith PROCR
+HBI interactsWith TPH1
+FUC-(1-6)NAG-(4-1)NAG-(4-1)BMA interactsWith C1R
+NAG-(1-4)NAG-(6-1)FUC interactsWith C1R
+NAG interactsWith C1R
+ATP interactsWith ME2
+ATP interactsWith ME2
+TTN interactsWith ME2
+FUM interactsWith ME2
+FUM interactsWith ME2
+GM2 interactsWith CD1B
+D12 interactsWith CD1B
+TWT interactsWith CD1B
+PII interactsWith CD1B
+TWT interactsWith CD1B
+C15 interactsWith Insulin-Like_Growth_Factor_I
+NMN interactsWith NMNAT1
+NMN interactsWith NMNAT1
+NMN interactsWith NMNAT1
+S-Adenosylhomocysteine interactsWith HNMT
+HSM interactsWith HNMT
+HSM interactsWith HNMT
+QUN interactsWith HNMT
+LIH interactsWith Dihydrofolate_Reductase
+LII interactsWith Dihydrofolate_Reductase
+Na+ interactsWith Beta-2-Microglobulin
+BGD interactsWith PTPN1
+BGD interactsWith PTPN1
+NAG interactsWith CR2
+NAG interactsWith CR2
+FRG interactsWith IL2
+CMM interactsWith IL2
+MPE interactsWith Interleukin-2
+NMP interactsWith Interleukin-2
+Mg2+ interactsWith RND2
+GTP interactsWith RND2
+Na+ interactsWith NOS3
+6NI interactsWith NOS3
+6NI interactsWith NOS3
+5NI interactsWith NOS3
+Zn2+ interactsWith MMP2
+Zn2+ interactsWith MMP2
+Ca2+ interactsWith MMP2
+Citiric_acid interactsWith Angiogenin
+ZTW interactsWith ESR1
+17beta-estradiol interactsWith ESR1
+151 interactsWith ELA2
+NAG-(6-1)FUC interactsWith ELA2
+NAG-(6-1)FUC interactsWith ELA2
+NAG-(6-1)FUC interactsWith ELA2
+NAG interactsWith DPEP1
+NAG interactsWith DPEP1
+Zn2+ interactsWith DPEP1
+Zn2+ interactsWith DPEP1
+NAG interactsWith DPEP1
+CIL interactsWith DPEP1
+UD1 interactsWith UAP1
+UD1 interactsWith UAP1
+UD1 interactsWith UAP1
+Ca2+ interactsWith PLA2G10
+BHG-(2-1)FUC interactsWith GBGT1
+AQ4 interactsWith EGFR
+NAG-(4-1)NAG interactsWith ITGAV
+NAG-(4-1)NAG interactsWith ITGB5
+Mn2+ interactsWith ITGB5
+Mn2+ interactsWith ITGAV
+PLP interactsWith CBS
+heme interactsWith CBS
+heme interactsWith CBS
+FAD interactsWith Programmed_Cell_Death_Protein_8
+CLW interactsWith NOS3
+7NI interactsWith NOS3
+INE interactsWith NOS3
+INE interactsWith NOS3
+INE interactsWith NOS3
+INE interactsWith NOS3
+254 interactsWith RARB
+AEM-APD-DFA interactsWith CTSB
+AEM-APD-DFA interactsWith CTSB
+2A6 interactsWith CDK2
+6CP interactsWith CDK2
+4SP interactsWith CDK2
+4SP interactsWith CDK2
+GA4 interactsWith Monoclonal_Antibody_Heavy_Chain
+GA4 interactsWith Monoclonal_Antibody_Heavy_Chain
+Benzamidine interactsWith F7
+NAG-(1-4)NAG interactsWith CHI3L2
+B-D-Fructose-1,6-DP interactsWith PKM2
+Phosphoglycolate interactsWith PKM2
+K+ interactsWith PKM2
+Mn2+ interactsWith PKM2
+Citiric_acid interactsWith BHMT
+Citiric_acid interactsWith BHMT
+Citiric_acid interactsWith BHMT
+Zn2+ interactsWith BHMT
+CBH interactsWith BHMT
+CBH interactsWith BHMT
+BMT-ABA-SAR-MLE-VAL-MLE-ALA-DAL-MLE-MLE-MVA interactsWith PPP3R1
+BMT-ABA-SAR-MLE-VAL-MLE-ALA-DAL-MLE-MLE-MVA interactsWith PPP3CA
+Zn2+ interactsWith PPP3CA
+Fe3+ interactsWith PPP3CA
+Mg2+ interactsWith 1MFQ_A
+Mg2+ interactsWith 1MFQ_A
+Mg2+ interactsWith 1MFQ_A
+heme interactsWith Sulfite_Oxidase
+4MZ interactsWith CA2
+4MZ interactsWith CA2
+NAG-(4-1)NAG-(4-1)MAN-(6-1)MAN-(3-1)MAN-(3,3-1)MAN-(4,6-1)MAN interactsWith Immunoglobulin_Heavy_Chain_Epsilon-1
+NAG-(4-1)NAG-(4-1)MAN-(6-1)MAN-(3-1)MAN-(3,3-1)MAN-(4,6-1)MAN interactsWith Immunoglobulin_Heavy_Chain_Epsilon-1
+NAG-(4-1)NAG-(4-1)MAN-(6-1)MAN-(3-1)MAN-(3,3-1)MAN-(4,6-1)MAN interactsWith Immunoglobulin_Heavy_Chain_Epsilon-1
+A2P interactsWith RNASE3
+GDP-7MG interactsWith NCBP2
+Na+ interactsWith LYZ
+NAG interactsWith EGFR
+NAG interactsWith EGFR
+NAG interactsWith EGFR
+NAG interactsWith EGFR
+NAG interactsWith EGFR
+NAG-(4-1)NAG interactsWith EGFR
+NAG interactsWith EGFR
+FAR interactsWith Farnesylated_K-Ras4b_Peptide_Product
+Farnesyl-PP interactsWith Farnesylated_K-Ras4b_Peptide_Product
+FAR interactsWith Farnesylated_K-Ras4b_Peptide_Product
+Zn2+ interactsWith Sex_Hormone-Binding_Globulin
+AND interactsWith Sex_Hormone-Binding_Globulin
+AOM interactsWith Sex_Hormone-Binding_Globulin
+17beta-estradiol interactsWith Sex_Hormone-Binding_Globulin
+NOG interactsWith Sex_Hormone-Binding_Globulin
+2-Methoxyestradiol interactsWith Sex_Hormone-Binding_Globulin
+Ca2+ interactsWith SNRPA
+BMT-ABA-SAR-MLE-VAL-MLE-ALA-DAL-MLE-MLE-MVA interactsWith PPP3CA
+Mg2+ interactsWith Deoxyribonucleotidase
+Mg2+ interactsWith KIF5A
+ADP interactsWith KIF5A
+S-Adenosylhomocysteine interactsWith Set9
+HXA interactsWith RXRA
+BM6 interactsWith RXRA
+heme interactsWith HMOX1
+NAD+ interactsWith HADHSC
+OGA interactsWith HIF1AN
+2-Oxoglutaric_acid interactsWith Factor_Inhibiting_Hif1
+Zn2+ interactsWith HIF1AN
+TTC interactsWith TOP1
+TTG interactsWith TOP1
+T4A interactsWith TTR
+Caffeine interactsWith Glycogen_Phosphorylase,_Liver_Form
+Caffeine interactsWith Glycogen_Phosphorylase,_Liver_Form
+riboflavin interactsWith Glycogen_Phosphorylase,_Liver_Form
+Uric_acid interactsWith Glycogen_Phosphorylase,_Liver_Form
+HDI interactsWith MIF
+HDI interactsWith MIF
+DAF-(1-4)GLC-(1-4)DAF-(1-4)GLC-(1-4)GLC interactsWith AMY1A
+ACI-(1-4)GLD-(1-4)GLC-(1-4)GLB interactsWith AMY1A
+GLC-(1-4)GLC interactsWith AMY1A
+ACI-(1-4)GLD-(1-4)GLC-(1-4)GLB interactsWith AMY1A
+alpha-D-Glucose interactsWith AMY1A
+HMC-(1-4)AGL-(1-4)GLC-(1-4)HMC-(1-4)AGL-(1-4)GLC interactsWith Alpha-Amylase,_Salivary
+AGL-(1-4)GLC-(1-4)GLC interactsWith Alpha-Amylase,_Salivary
+TAR interactsWith Factor_Inhibiting_Hif1
+Mg2+ interactsWith RAD51
+Mg2+ interactsWith RAB5B
+GNP interactsWith RAB5B
+GDP interactsWith RAB5B
+GNP interactsWith RAB5B
+GNP interactsWith RAB5B
+GNP interactsWith RAB5B
+GNP interactsWith RAB5B
+AMP-PNP interactsWith Glycogen_Synthase_Kinase-3_Beta
+AMP-PNP interactsWith AKT2
+Mn2+ interactsWith AKT2
+AMP-PNP interactsWith Glycogen_Synthase_Kinase-3_Beta
+AGS interactsWith PFKFB1
+YPA interactsWith PPARG
+Palmitate interactsWith HNF4A
+BEP interactsWith Troponin_I,_Cardiac_Muscle
+BEP interactsWith TNNC1
+NAG-(4-1)NAG interactsWith BMP7
+DQO interactsWith MAPK14
+GAR interactsWith GART
+BP4-CYS-DAR-TYR-PEA interactsWith Cathepsin_L
+BP4-CYS-DAR-TYR-PEA interactsWith CTSL
+BP4-CYS-DAR-TYR-PEA interactsWith CTSL
+BP4-CYS-DAR-TYR-PEA interactsWith CTSL
+Fe3+ interactsWith TPH1
+HBI interactsWith TPH1
+NAD+ interactsWith CTBP2
+FUC-(1-6)NAG-(4-1)NAG interactsWith DPP4
+FUC-(1-6)NAG-(4-1)NAG interactsWith DPP4
+NAG-(4-1)NAG-(4-1)MAN interactsWith FAP
+NAG-(4-1)NAG-(4-1)MAN interactsWith FAP
+A3M interactsWith FAP
+NAG-(4-1)NAG-(4-1)MAN-(6-1)MAN-(4-1)NAG interactsWith IL6R
+NAG interactsWith IL6R
+NAG-(4-1)NAG interactsWith IL6R
+NAG interactsWith IL6R
+DCY interactsWith IL6R
+Cholesterol interactsWith RORA
+MHC interactsWith Interleukin-2
+NAG interactsWith ACPP
+2BF interactsWith ACPP
+glycine interactsWith ACPP
+MON interactsWith ESR2
+heme interactsWith Hemoglobin_Alpha_Chain
+heme interactsWith Hemoglobin_Alpha_Chain
+Fluoro-Hydrocortisone interactsWith AR
+Ca2+ interactsWith GSN
+Ca2+ interactsWith GSN
+Ca2+ interactsWith GSN
+AFL-(1-6)NAG-(4-1)NAG-(4-1)BMA interactsWith Ig_Gamma-1_Chain_C_Region
+BMA interactsWith Ig_Gamma-1_Chain_C_Region
+AFL-(1-6)NAG-(4-1)NAG-(4-1)BMA-(6-1)MAN-(4,3-1)MAN interactsWith Ig_Gamma-1_Chain_C_Region
+AFL-(1-6)NAG-(4-1)NAG-(4-1)BMA-(6-1)MAN-(4,3-1)BMA interactsWith Ig_Gamma-1_Chain_C_Region
+FUC-(1-6)NAG-(4-1)NAG-(4-1)BMA-(6-1)BMA-(2-1)NAG interactsWith Ig_Gamma-1_Chain_C_Region
+AFL-(1-6)NAG-(4-1)NAG-(4-1)MAN-(6-1)MAN-(2-1)NDG-(4-1)GLA-(4,3-1)MAN-(2-1)NAG interactsWith Ig_Gamma-1_Chain_C_Region
+AFL-(1-6)NAG-(4-1)NAG-(4-1)BMA-(6-1)MAN-(2-1)NAG-(4-1)GLA-(4,3-1)MAN-(2-1)NAG interactsWith Ig_Gamma-1_Chain_C_Region
+Zn2+ interactsWith GTF2F1
+Ca2+ interactsWith S100P
+Ca2+ interactsWith S100P
+NAD+ interactsWith NMNAT1
+DND interactsWith NMNAT1
+TAD interactsWith NMNAT1
+BH4 interactsWith TPH1
+TIH interactsWith TPH1
+SG1 interactsWith CA2
+SG2 interactsWith CA2
+dCTP interactsWith POLB
+XLC interactsWith F10
+XLD interactsWith F10
+NAG interactsWith ICAM1
+NAG-(4-1)NAG interactsWith ICAM1
+NAG interactsWith ICAM1
+NAG-(4-1)NAG interactsWith ICAM1
+NAG-(4-1)NAG interactsWith ICAM1
+Mn2+ interactsWith ITGAL
+Zn2+ interactsWith SKI
+NAG interactsWith IL19
+PEH interactsWith PSAP
+PEH interactsWith PSAP
+SAM interactsWith Set_Domain-Containing_Protein_7
+SAM interactsWith Set_Domain-Containing_Protein_7
+NAG-(4-1)NAG-(4-1)MAN-(6-1)MAN-(3,3-1)MAN interactsWith LDLR
+NAG-(4-1)NAG-(4-1)MAN-(6-1)MAN interactsWith LDLR
+Ca2+ interactsWith LDLR
+Ca2+ interactsWith LDLR
+Ca2+ interactsWith LDLR
+Ca2+ interactsWith LDLR
+Ca2+ interactsWith LDLR
+Ca2+ interactsWith LDLR
+Ca2+ interactsWith LDLR
+Ca2+ interactsWith LDLR
+750 interactsWith CTSL2
+2CA interactsWith CTSK
+2CA interactsWith CTSK
+NAG interactsWith GP1BA
+NDG interactsWith GP1BA
+OXG interactsWith OGG1
+SUM interactsWith SERPINA1
+RUP interactsWith F10
+NAG-(4-1)NAG interactsWith SERPINA5
+NAG interactsWith SERPINA5
+NAG interactsWith SERPINA5
+MAN-(1-3)MAN-(6-1)MAN interactsWith SERPINA5
+NAG-(4-1)NAG interactsWith SERPINA5
+NAG interactsWith SERPINA5
+ANG interactsWith OGG1
+ANG interactsWith 1LWV_E
+BRG interactsWith OGG1
+HYF interactsWith NR1I3
+ZAR interactsWith PDE4D
+GTG interactsWith NCBP2
+Na+ interactsWith LTF
+GNP interactsWith CDC42
+RRP interactsWith F10
+RRR interactsWith F10
+RDR interactsWith F10
+RTR interactsWith F10
+NAG-(4-1)NAG interactsWith GZMA
+FMN interactsWith PNPO
+PLP interactsWith PNPO
+Malonic_acid interactsWith SNRPA
+Malonic_acid interactsWith SNRPA
+Malonic_acid interactsWith SNRPA
+Malonic_acid interactsWith SNRPA
+Malonic_acid interactsWith SNRPA
+Malonic_acid interactsWith SNRPA
+Malonic_acid interactsWith SNRPA
+Malonic_acid interactsWith SNRPA
+Malonic_acid interactsWith SNRPA
+Malonic_acid interactsWith SNRPA
+Malonic_acid interactsWith SNRPA
+PA5 interactsWith GPI
+Taurocholic_acid interactsWith Gastrotropin
+NAG interactsWith ACE
+NAG interactsWith ACE
+NAG interactsWith ACE
+NAG interactsWith ACE
+NDG interactsWith ACE
+NAG interactsWith ACE
+Zn2+ interactsWith ACE
+NXA interactsWith ACE
+S-Adenosylhomocysteine interactsWith SET7
+S-Adenosylhomocysteine interactsWith Gene_Fragment_For_Histone_H3
+S-Adenosylhomocysteine interactsWith Gene_Fragment_For_Histone_H3
+LPR interactsWith ACE
+glycine interactsWith ACE
+NAG-(1-4)NAG-(1-4)NAG interactsWith CHI3L1
+NAG-(1-4)NAG-(1-4)NAG-(1-4)NAG interactsWith CHI3L1
+NAG interactsWith CHI3L1
+NAG-(1-4)NAG-(1-4)NAG-(1-4)NAG interactsWith CHI3L1
+NAG-(1-4)NAG-(1-4)NAG-(1-4)NAG-(1-4)NAG-(1-4)NAG interactsWith CHI3L1
+NAG-(4-1)NAG interactsWith CHI3L1
+NAG-(1-4)NAG-(1-4)NAG-(1-4)NAG-(1-4)NAG interactsWith CHI3L1
+HYC interactsWith Type_1_17_Beta-Hydroxysteroid_Dehydrogenase
+BHP interactsWith PLA2G2A
+BHP interactsWith PLA2G2A
+DBH interactsWith LCN2
+DBH interactsWith LCN2
+DBS interactsWith LCN2
+DBH interactsWith LCN2
+APO interactsWith PSPH
+APO interactsWith PSPH
+L-Serine interactsWith PSPH
+SER-PO4 interactsWith PSPH
+NAG-(4-1)NAG-(4-1)MAN-(3-1)MAN-(3,6-1)MAN-(3,4-1)MAN interactsWith BMP7
+NAG interactsWith BMP6
+DTM interactsWith DHFR
+Mg2+ interactsWith Hypothetical_Protein_Flj11149
+ADP interactsWith Hypothetical_Protein_Flj11149
+riboflavin interactsWith Hypothetical_Protein_Flj11149
+Zn2+ interactsWith UBE1C
+Trehalose interactsWith HMOX1
+158-159 interactsWith CASP3
+158-159 interactsWith CASP3
+SFM interactsWith PPIA
+SFM interactsWith PPIA
+160 interactsWith CASP3
+161 interactsWith CASP3
+FDM interactsWith Similar_To_Thymidylate_Kinase_(Dtmp_Kinase)
+NYM interactsWith Similar_To_Thymidylate_Kinase_(Dtmp_Kinase)
+2DT interactsWith Similar_To_Deoxythymidylate_Kinase_(Thymidylate_Kinase)
+NAG interactsWith EGFR
+NAG-(4-1)NAG-(4-1)ASO interactsWith EGFR
+NAG interactsWith EGFR
+NAG interactsWith EGFR
+NAG-(4-1)NAG interactsWith EGFR
+NAG interactsWith EGFR
+SAM interactsWith Histone_Methyltransferase_Dot1l
+Zn2+ interactsWith BIRC4
+MO6 interactsWith PTPN1
+964 interactsWith PTPN1
+NAG-(4-1)NDG-(4-1)BMA-(6-1)MAN-(6-1)MAN-(3,3-1)MAN-(4,3-1)MAN interactsWith Sialic_Acid_Binding_Ig-Like_Lectin_7
+MYR interactsWith AFP
+MYR interactsWith AFP
+heme interactsWith AFP
+Fe3+ interactsWith TF
+NAG-(1-2)MAN-(1-6)MAN-(1-4)NAG-(1-4)NAG-(6-1)FUC-(3,3-1)MAN-(2-1)NAG interactsWith Immunoglobulin_Gamma-1_Heavy_Chain_Constant_Region
+NAG-(1-2)MAN-(1-6)MAN-(1-4)NAG-(1-4)NAG-(6-1)FUC-(3,3-1)MAN-(2-1)NAG interactsWith Immunoglobulin_Gamma-1_Heavy_Chain_Constant_Region
+MAN-(1-6)MAN-(1-4)NAG-(1-4)NAG-(6-1)FUC-(2,3-1)MAN interactsWith Immunoglobulin_Gamma-1_Heavy_Chain_Constant_Region
+NAG interactsWith Sialic_Acid_Binding_Ig-Like_Lectin_7
+DCY interactsWith Sialic_Acid_Binding_Ig-Like_Lectin_7
+GSH interactsWith PGDS
+GSH interactsWith PGDS
+Mg2+ interactsWith RAC1
+GNP interactsWith RAC1
+Ca2+ interactsWith Fibrillin_1
+Ca2+ interactsWith Fibrillin_1
+Zn2+ interactsWith ESRRB
+Zn2+ interactsWith ESRRB
+Citrate interactsWith SH2D1A
+Citrate interactsWith Signaling_Lymphocytic_Activation_Molecule
+BLN interactsWith CTSS
+ADN interactsWith PLK4
+PFA interactsWith THRB
+486 interactsWith NR3C1
+989 interactsWith PTPN2
+515 interactsWith PTPN2
+794 interactsWith PTPN2
+IFG interactsWith HEXB
+C1P interactsWith CTSS
+C4P interactsWith CTSS
+Mg2+ interactsWith TGM6
+4HY interactsWith THRB
+UCN interactsWith CHEK1
+staurosporine interactsWith CHEK1
+UCM interactsWith CHEK1
+FG1 interactsWith PTPN1
+MYR interactsWith ABL1
+P16 interactsWith ABL1
+GDP interactsWith ARHGAP1
+MGF interactsWith RHOA
+MGF interactsWith ARHGAP1
+CDG interactsWith APCS
+OXL interactsWith ME2
+OXL interactsWith ME2
+L-Thyroxine interactsWith AFP
+L-Thyroxine interactsWith ALB
+L-Thyroxine interactsWith AFP
+L-Thyroxine interactsWith ALB
+L-Thyroxine interactsWith ALB
+L-Thyroxine interactsWith ALB
+L-Thyroxine interactsWith ALB
+MYR interactsWith AFP
+MYR interactsWith AFP
+L-Thyroxine interactsWith AFP
+MYR interactsWith ALB
+SUB interactsWith FKBP1B
+TST interactsWith FKBP1B
+NOC interactsWith AHCY
+IMA interactsWith F10
+CBB interactsWith F10
+CMB interactsWith F10
+CMI interactsWith F10
+Ca2+ interactsWith PSPH
+NMN interactsWith NMNAT1
+DND interactsWith NMNAT1
+AMPCPP interactsWith NMNAT1
+AMPCPP interactsWith NMNAT1
+NAD+ interactsWith NMNAT1
+901 interactsWith PTPN2
+696 interactsWith F2
+588 interactsWith PTPN2
+968 interactsWith PTPN2
+KOS interactsWith HSPCB
+K+ interactsWith NR4A2
+K+ interactsWith NR4A2
+K+ interactsWith NR4A2
+NAG interactsWith FCAR
+NAG-(4-1)NAG interactsWith FCAR
+NAG interactsWith FCAR
+NAG interactsWith FCAR
+FUC-(1-6)NAG-(4-1)NAG-(4-1)MAN-(6-1)MAN-(2-1)NAG-(4-1)GAL-(3-2)SIA interactsWith Ig_Alpha-1_Chain_C_Region
+NAG-(4-1)NAG-(4-1)MAN-(6-1)MAN-(3,3-1)MAN interactsWith FCAR
+NAG-(4-1)NAG-(4-1)MAN-(6-1)MAN-(2-1)MAN-(4-1)MAN interactsWith FCAR
+NAG-(4-1)NAG-(4-1)MAN-(6-1)MAN interactsWith RTN4R
+NAG-(4-1)NAG-(4-1)MAN interactsWith RTN4R
+FMN interactsWith Riboflavin_Kinase
+NAG interactsWith RTN4R
+NAG interactsWith RTN4R
+benzoate interactsWith HRSP12
+benzoate interactsWith HRSP12
+benzoate interactsWith HRSP12
+benzoate interactsWith HRSP12
+benzoate interactsWith HRSP12
+MBP interactsWith CDK5
+PLP interactsWith AGXT
+o-(carboxymethyl)hydroxylamine interactsWith AGXT
+UN4 interactsWith CDK2
+207 interactsWith CDK2
+ITS interactsWith AKT1
+CPR interactsWith IMPDH1
+Testosterone interactsWith 17_Beta-Hydroxysteroid_Dehydrogenase_Type_1
+BNE interactsWith FNTB
+BNE interactsWith FNTA
+MYR interactsWith AFP
+MYR interactsWith AFP
+MYR interactsWith AFP
+MYR interactsWith AFP
+MYR interactsWith AFP
+heme interactsWith AFP
+IH5 interactsWith THRA
+IH5 interactsWith THRA
+Mg2+ interactsWith PDHA1
+K+ interactsWith PDHB
+thiamin_diphosphate interactsWith PDHB
+thiamin_diphosphate interactsWith PDHA1
+Zn2+ interactsWith LIMS2
+Zn2+ interactsWith LIMS2
+Ca2+ interactsWith C1S
+Mg2+ interactsWith C1S
+NAD+ interactsWith ALDH2
+NAD+ interactsWith ALDH2
+CRD interactsWith ALDH2
+Cu2+ interactsWith S100A12
+DPN-PRO-MAI interactsWith GZMA
+FSN interactsWith F2
+4,5,6,7-tetrabromobenzotriazole interactsWith CDK2
+MO3 interactsWith DCK
+Cytarabine interactsWith DCK
+2'-Deoxycytidine interactsWith DCK
+GEO interactsWith DCK
+Dexamethasone interactsWith NR3C1
+Ca2+ interactsWith Neurogenic_Locus_Notch_Homolog_Protein_1
+AMP-PNP interactsWith CSNK2A1
+UCN interactsWith CDK2
+PTI interactsWith ESR1
+NAG interactsWith Chorionic_Gonadotropin
+MBO interactsWith CA2
+SUA interactsWith CA2
+984 interactsWith MAPK10
+AMP-PNP interactsWith MAPK10
+880 interactsWith MAPK10
+9HP interactsWith MAPK10
+537 interactsWith MAPK10
+Zn2+ interactsWith ALAD
+PB1 interactsWith ALAD
+FAP interactsWith CDK3
+FCP interactsWith CDK3
+FAL interactsWith CDK3
+FBL interactsWith CDK3
+MFP interactsWith CDK3
+MFQ interactsWith CDK3
+BYP interactsWith CDK3
+BWP interactsWith CDK3
+NLE interactsWith TPH1
+HDU interactsWith CDK3
+HDY interactsWith CDK3
+HDT interactsWith CDK2
+L86 interactsWith F2
+T76 interactsWith F2
+655 interactsWith PLAU
+ST8 interactsWith CDK2
+SGM interactsWith CCNA2
+084 interactsWith MAPK14
+094 interactsWith MAPK14
+358 interactsWith MAPK14
+NAG interactsWith PPT2
+Mg2+ interactsWith CSF1R
+ADP interactsWith CSF1R
+ADP interactsWith CSF1R
+Zn2+ interactsWith PDE4D
+ROL interactsWith PDE4D
+ROL interactsWith PDE4D
+ROL interactsWith PDE4D
+Mn2+ interactsWith BCKDHA
+ESA-ESA-ESA interactsWith Connective_Tissue_Activating_Peptide-Iii
+4ND interactsWith F2
+NAG-(1-4)NAG interactsWith CHI3L1
+NAG interactsWith CHI3L1
+NAG interactsWith CHI3L1
+NAG-(1-4)NAG-(1-4)NAG-(1-4)NAG-(1-4)NAG interactsWith Chitinase-3_Like_Protein_1
+Zn2+ interactsWith BIRC7
+P33 interactsWith BIRC7
+Mg2+ interactsWith F10
+Mg2+ interactsWith F10
+Mg2+ interactsWith F10
+1PB interactsWith MAOB
+ISN interactsWith MAOB
+FAD-1LP interactsWith MAOB
+LAZ interactsWith MAOB
+LDA interactsWith MAOB
+SRL interactsWith NR1I2
+SRL interactsWith NR1I2
+ATP interactsWith Camp-Dependent_Protein_Kinase_Inhibitor,_Alpha_Form
+dUDP interactsWith DUT
+dUDP interactsWith DUT
+dUDP interactsWith DUT
+ADZ interactsWith GSK3B
+NAG interactsWith STS
+NAG interactsWith STS
+Ca2+ interactsWith STS
+Mn2+ interactsWith ARG2
+Mn2+ interactsWith ARG2
+S2C interactsWith ARG2
+Ca2+ interactsWith MBL2
+Ca2+ interactsWith MBL2
+Ca2+ interactsWith MBL2
+SNA interactsWith PTPN2
+NAG interactsWith MASP2
+NPO interactsWith SULT1A1
+NPO interactsWith SULT1A1
+NAG-(1-4)NAG-(6-1)FUC interactsWith BCHE
+NAG-(1-4)NAG-(6-1)FUC interactsWith BCHE
+NAG interactsWith BCHE
+NAG interactsWith BCHE
+NAG interactsWith BCHE
+Butyric_acid interactsWith BCHE
+Choline interactsWith BCHE
+BCH interactsWith BCHE
+GLC-(1-4)GLC interactsWith MBL2
+alpha-D-Glucose interactsWith MBL2
+418 interactsWith PTPN2
+3',5'-ADP interactsWith SULT1E1
+PCQ interactsWith SULT1E1
+HNI interactsWith HBB
+heme interactsWith HBA2
+HNI interactsWith HBA2
+Zn2+ interactsWith Mi2-Beta
+Zn2+ interactsWith Mi2-Beta
+Zn2+ interactsWith Mi2-Beta(Chromodomain_Helicase-Dna-Binding_Protein_4)_And_Transcription_Factor_Wstf
+Zn2+ interactsWith Mi2-Beta(Chromodomain_Helicase-Dna-Binding_Protein_4)_And_Transcription_Factor_Wstf
+Zn2+ interactsWith Znf265
+DFP interactsWith F2
+ATP interactsWith PRKX
+HEC interactsWith CYP2C9
+SWF interactsWith CYP2C9
+Ca2+ interactsWith TNNC1
+Ca2+ interactsWith TNNC1
+Ca2+ interactsWith TNNC1
+Dexamethasone interactsWith NR3C1
+MYP-MYP interactsWith CTSF
+MYP interactsWith CTSF
+DRF interactsWith PPARG
+MAN interactsWith Fab_2g12,_Heavy_Chain
+benzoate interactsWith Fab_2g12,_Light_Chain
+NAG-(4-1)NAG-(4-1)MAN-(6-1)MAN-(6-1)MAN-(3,3-1)MAN interactsWith Fab_2g12,_Heavy_Chain
+NAG-(4-1)NAG-(4-1)MAN-(6-1)MAN-(6-1)MAN-(2-1)MAN-(3,3-1)MAN interactsWith Fab_2g12,_Heavy_Chain
+5BN interactsWith CDK2
+167 interactsWith F2
+GR1 interactsWith F2
+GAL-(1-4)NAG-(1-2)MAN-(1-3)MAN-(6-1)MAN-(2-1)NAG-(4-1)GAL-(4,1-4)NAG-(1-4)NAG interactsWith Chorionic_Gonadotropin
+HNI interactsWith HBA2
+HNI interactsWith HBB
+HNI interactsWith HBB
+XMA interactsWith F10
+XMB interactsWith F10
+XMD interactsWith F10
+XME interactsWith F10
+XMF interactsWith F10
+XMG interactsWith F10
+XMH interactsWith F10
+XMI interactsWith F10
+XMJ interactsWith F10
+XMK interactsWith F10
+XMC interactsWith F10
+MTM interactsWith MTAP
+MYR interactsWith CALM2
+TSX interactsWith Phosphoenolpyruvate_Carboxykinase,_Cytosolic
+ADP interactsWith PTK2
+Mg2+ interactsWith AURKB
+Mg2+ interactsWith AURKB
+ADP interactsWith AURKB
+AMP-PNP interactsWith EPHA5
+AMP-PNP interactsWith EPHA5
+Progesterone interactsWith AKR1C2
+Trehalose interactsWith GNPDA1
+16G interactsWith GNPDA1
+16G interactsWith GNPDA1
+AGP interactsWith GNPDA1
+AGP interactsWith GNPDA1
+AGP interactsWith GNPDA1
+NAG-(4-1)NAG interactsWith SERPINC1
+heme interactsWith NGB
+heme interactsWith NGB
+FEX interactsWith Bile_Acid_Receptor
+497 interactsWith PLAU
+675 interactsWith PLAU
+239 interactsWith PLAU
+426 interactsWith PLAU
+155 interactsWith PLAU
+303 interactsWith PLAU
+FPH interactsWith MAPK14
+Ca2+ interactsWith TNNC1
+Zn2+ interactsWith MOBK1B
+MLT interactsWith ME2
+TAP interactsWith NNT
+941 interactsWith PTPN2
+234 interactsWith PTPN2
+alpha-D-Glucose interactsWith NUDT9
+335 interactsWith PTPN1
+P27 interactsWith PTPN1
+P90 interactsWith PTPN1
+P90 interactsWith PTPN1
+P90 interactsWith PTPN1
+213 interactsWith PTPN1
+213 interactsWith PTPN1
+213 interactsWith PTPN1
+213 interactsWith PTPN1
+214 interactsWith PTPN1
+214 interactsWith PTPN1
+214 interactsWith PTPN1
+600 interactsWith PTPN1
+600 interactsWith PTPN1
+600 interactsWith PTPN1
+600 interactsWith PTPN1
+RP5 interactsWith NUDT9
+FU2 interactsWith HBA2
+FU2 interactsWith HBA2
+FUX interactsWith HBA2
+FUX interactsWith HBA2
+KSA interactsWith MET
+MBN interactsWith HBA2
+MBN interactsWith HBA2
+Ca2+ interactsWith NME1
+ADP interactsWith NME1
+Zn2+ interactsWith CDA
+BRD interactsWith CDA
+BRD interactsWith CDA
+staurosporine interactsWith MAPKAPK2
+ADP interactsWith MAPKAPK2
+162 interactsWith F2
+163 interactsWith F2
+Palmitate interactsWith SEC14L2
+Palmitate interactsWith SEC14L2
+Palmitate interactsWith SEC14L2
+GDL interactsWith HEXB
+NAG interactsWith HEXB
+NAG interactsWith HEXB
+NAG interactsWith HEXA
+ADP interactsWith STK6
+Mg2+ interactsWith PLK4
+ATP interactsWith AURKB
+ADP interactsWith PLK4
+Ca2+ interactsWith GSN
+Mg2+ interactsWith GSK3B
+AMP-PNP interactsWith GSK3B
+staurosporine interactsWith GSK3B
+ATU interactsWith GSK3B
+IXM interactsWith GSK3B
+679 interactsWith GSK3B
+429 interactsWith PTPN2
+GMM interactsWith CD1B
+MCR-DPN-PRO-ARM interactsWith F2
+MCR-DPN-PRO-ARM interactsWith F2
+AFL-(1-6)NAG-(4-1)NAG-(4-1)BMA-(6-1)MAN-(2-1)NAG-(4,3-1)MAN-(2-1)NAG interactsWith Ig_Gamma-1_Chain_C_Region
+AFL-(1-6)NAG-(4-1)NAG-(4-1)BMA-(6-1)MAN-(2-1)NAG-(4,3-1)MAN-(2-1)NDG interactsWith Ig_Gamma-1_Chain_C_Region
+o-(carboxymethyl)hydroxylamine interactsWith AGXT
+BR4 interactsWith PLA2G2D
+Cu1+ interactsWith Copper-Transporting_Atpase_1
+Zn2+ interactsWith GMEB1
+NADH interactsWith ME2
+NADH interactsWith ME2
+NADH interactsWith ME2
+NADH interactsWith ME2
+NADH interactsWith ME2
+Pyruvate interactsWith ME2
+A5MP interactsWith PDE4D
+A5MP interactsWith PDE4D
+A5MP interactsWith PDE4D
+3',5'-ADP interactsWith SULT2B1
+Na+ interactsWith SULT2B1
+3',5'-ADP interactsWith SULT2B1
+Pregnenolone interactsWith SULT2B1
+Na+ interactsWith SULT2B1
+AND interactsWith SULT2B1
+Zn2+ interactsWith T-Cell_Surface_Glycoprotein_Cd4
+Zn2+ interactsWith Proto-Oncogene_Tyrosine-Protein_Kinase_Lck
+Zn2+ interactsWith T-Cell_Surface_Glycoprotein_Cd8_Alpha_Chain
+TDE interactsWith Methionine_Aminopeptidase_2
+VIV interactsWith TTPA
+IPH interactsWith Insulin
+GTP interactsWith ARL1
+Mg2+ interactsWith ARL1
+Ca2+ interactsWith F13A1
+PGO interactsWith F13A1
+PGO interactsWith F13A1
+PGO interactsWith F13A1
+PGO interactsWith F13A1
+PGO interactsWith F13A1
+AMP-PNP interactsWith GSK3B
+ADP interactsWith GSK3B
+Fe2+ interactsWith Pirin
+Zn2+ interactsWith Methionine_Aminopeptidase_2
+Zn2+ interactsWith Methionine_Aminopeptidase_2
+MED interactsWith Methionine_Aminopeptidase_2
+TBU interactsWith Methionine_Aminopeptidase_2
+L-Methionine interactsWith Methionine_Aminopeptidase_2
+NAG-(4-1)NAG interactsWith ARSA
+NAG interactsWith ARSA
+Ca2+ interactsWith ARSA
+LY1 interactsWith PNMT
+IDI interactsWith PNMT
+CIR-CIR-LEU-ILE-PFF-NH2 interactsWith CCNA1
+CIR-CIR-LEU-ILE-PFF-NH2 interactsWith CCNA1
+CO4 interactsWith Dihydrofolate_Reductase
+SU9 interactsWith CDK3
+CK1 interactsWith CDK2
+CK2 interactsWith CDK2
+CK3 interactsWith CDK2
+CK4 interactsWith CDK2
+TYB interactsWith Tyrosyl-Trna_Synthetase
+GSH interactsWith TREM1
+FMN interactsWith Hypothetical_Protein_Flj11149
+Zn2+ interactsWith UBE1C
+ATP interactsWith UBE1C
+ATP interactsWith APPBP1
+ATP interactsWith Ubiquitin-Like_Protein_Nedd8
+TYM interactsWith WARS
+TYM interactsWith WARS
+GDP interactsWith ARF6
+Brefeldin_A interactsWith ARF6
+Brefeldin_A interactsWith GBF1
+Citiric_acid interactsWith ARF6
+isobutyl-(3)-1-methylxanthine interactsWith PDE4C
+isobutyl-(3)-1-methylxanthine interactsWith PDE4C
+isobutyl-(3)-1-methylxanthine interactsWith PDE4C
+isobutyl-(3)-1-methylxanthine interactsWith PDE4C
+GSP interactsWith TGM6
+Mn2+ interactsWith INSR
+Lactose interactsWith LGALS2
+Lactose interactsWith Galectin-1
+Zn2+ interactsWith Monocytic_Leukemia_Zinc_Finger_Protein
+K+ interactsWith IMPDH1
+Ribavirin_5'-monophosphate interactsWith IMPDH1
+MYD interactsWith IMPDH1
+UNK interactsWith IMPDH1
+UNK interactsWith IMPDH1
+NAD+ interactsWith IMPDH1
+Ca2+ interactsWith Factor_Ix
+Ca2+ interactsWith Factor_Ix
+Ca2+ interactsWith Factor_Ix
+Ca2+ interactsWith Factor_Ix
+Ca2+ interactsWith Factor_Ix
+Ca2+ interactsWith Factor_Ix
+HMC-(1-4)AGL-(1-4)GLC interactsWith AMY1A
+AGL-(1-4)GLC interactsWith AMY1A
+alpha-D-Glucose interactsWith AMY1A
+VIT interactsWith TTPA
+GDP interactsWith RAB11A
+GSP interactsWith RAB25
+CR4 interactsWith TMPRSS3
+heme interactsWith CYP2C18
+Palmitate interactsWith CYP2C18
+Palmitate interactsWith CYP2C18
+heme interactsWith CYP2C18
+Palmitate interactsWith CYP2C18
+FRB interactsWith Interleukin-2
+Zn2+ interactsWith IL2
+FRH interactsWith IL2
+G24 interactsWith THRA
+G24 interactsWith THRA
+Zn2+ interactsWith ACY1
+Zn2+ interactsWith ACY1
+glycine interactsWith ACY1
+glycine interactsWith ACY1
+NAG interactsWith ACE2
+NAG interactsWith ACE2
+XX5 interactsWith ACE2
+FMD interactsWith CDK2
+Brefeldin_A interactsWith PSCD2
+GDP interactsWith PSCD2
+Inosine interactsWith Purine_Nucleoside_Phosphorylase
+B3P interactsWith FLT1
+B3P interactsWith VEGF
+GDP interactsWith RAC2
+GNP interactsWith RAC2
+SUC interactsWith Fab_412d_Light_Chain
+SUC interactsWith Fab_412d_Light_Chain
+SUC interactsWith Fab_412d_Heavy_Chain
+SUC interactsWith Fab_412d_Light_Chain
+SUC interactsWith Fab_412d_Light_Chain
+SUC interactsWith Fab_412d_Heavy_Chain
+Na+ interactsWith HSPA1B
+152 interactsWith CRAT
+FRM interactsWith PARP1
+FRM interactsWith PARP1
+CMU interactsWith ECGF1
+Zn2+ interactsWith REG3G
+Zn2+ interactsWith REG3G
+BRW interactsWith GSK3B
+Guanine interactsWith Purine_Nucleoside_Phosphorylase
+Didanosine interactsWith Purine_Nucleoside_Phosphorylase
+ANG interactsWith OGG1
+ANG interactsWith 1M3Q_C
+300 interactsWith SRC
+843 interactsWith SRC
+821 interactsWith SRC
+852 interactsWith SRC
+687 interactsWith SRC
+903 interactsWith SRC
+822 interactsWith SRC
+853 interactsWith SRC
+493 interactsWith SRC
+197 interactsWith SRC
+876 interactsWith SRC
+262 interactsWith SRC
+299 interactsWith SRC
+790 interactsWith YES1
+I59 interactsWith YES1
+772 interactsWith SRC
+219 interactsWith SRC
+IS2 interactsWith SRC
+PSN interactsWith SRC
+Citiric_acid interactsWith SRC
+Malonic_acid interactsWith SRC
+Oxalic_acid interactsWith SRC
+HPS interactsWith SRC
+HPS interactsWith SRC
+791 interactsWith SRC
+256 interactsWith SRC
+787 interactsWith SRC
+benzoate interactsWith PRDX5
+benzoate interactsWith PRDX5
+Androsterone interactsWith SULT2B1
+K+ interactsWith ATIC
+XMP interactsWith ATIC
+Zn2+ interactsWith SORD
+NAD+ interactsWith SORD
+572 interactsWith SORD
+BFI interactsWith AKR1B1
+DPN-PRO-ARM interactsWith F2
+DPN-PRO-ARM interactsWith F2
+DLG-(2-1)FUC interactsWith GBGT1
+DLG-(2-1)FUC interactsWith GBGT1
+AIG-(2-1)FUC interactsWith GBGT1
+AIG-(2-1)FUC interactsWith GBGT1
+AIG-(2-1)FUC interactsWith GBGT1
+UD1 interactsWith GBGT1
+AOG-(2-1)FUC interactsWith GBGT1
+UDP-D-Galactose interactsWith GBGT1
+SPM interactsWith TDP1
+OTR interactsWith TDP1
+Zn2+ interactsWith ZFP36L1
+Zn2+ interactsWith ZFP36L1
+Na+ interactsWith POLL
+Na+ interactsWith POLL
+Cholesterol_sulfate interactsWith RORA
+GDP interactsWith TGM3
+GDP interactsWith TGM3
+Ni2+ interactsWith POLB
+glycine interactsWith HLA-DQA1
+Zn2+ interactsWith CHIT1
+Zn2+ interactsWith CHIT1
+CDA interactsWith F2
+CDB interactsWith F2
+CDD interactsWith F2
+A5MP interactsWith APRT
+Zn2+ interactsWith SMAD3
+AICAR interactsWith ATIC
+AICAR interactsWith ATIC
+Acyclovir interactsWith Purine_Nucleoside_Phosphorylase
+Zn2+ interactsWith MMP10
+Zn2+ interactsWith MMP10
+Ca2+ interactsWith MMP10
+Ca2+ interactsWith MMP10
+Ca2+ interactsWith MMP10
+TAM interactsWith AMY1A
+TCO interactsWith CTSL2
+FMN interactsWith Hypothetical_Protein_Mds018
+Zn2+ interactsWith MMP14
+Zn2+ interactsWith MMP14
+Ca2+ interactsWith MMP14
+Ca2+ interactsWith MMP14
+BAT interactsWith MMP14
+Ca2+ interactsWith Apyrase
+GP2 interactsWith Apyrase
+GP2 interactsWith Apyrase
+Zn2+ interactsWith KCND3
+NADP+ interactsWith AKR1C3
+Indomethacin interactsWith AKR1C3
+flufenamic_acid interactsWith AKR1C3
+flufenamic_acid interactsWith AKR1C3
+Cu1+ interactsWith Copper-Transporting_Atpase_1
+Ca2+ interactsWith Calmodulin
+BI2 interactsWith PRKACB
+bisindolylmaleimide_i interactsWith PRKACB
+Ca2+ interactsWith THBS1
+Ca2+ interactsWith THBS1
+Ca2+ interactsWith THBS1
+Ca2+ interactsWith THBS1
+Ca2+ interactsWith THBS1
+Ca2+ interactsWith THBS1
+Ca2+ interactsWith THBS1
+Ca2+ interactsWith THBS1
+Ca2+ interactsWith THBS1
+Ca2+ interactsWith THBS1
+Ca2+ interactsWith THBS1
+Ca2+ interactsWith THBS1
+Ca2+ interactsWith THBS1
+Ca2+ interactsWith THBS1
+Ca2+ interactsWith THBS1
+alpha-D-Glucose interactsWith GCK
+CXS interactsWith Immunoglobulin_Heavy_Chain
+Mg2+ interactsWith ITGA1
+DRM interactsWith 5(3)-Deoxyribonucleotidase
+Zn2+ interactsWith DGKD
+Zn2+ interactsWith DGKD
+FAD interactsWith ACAD8
+FAD interactsWith ACAD8
+FAD interactsWith ACAD8
+EB1 interactsWith VDR
+MC9 interactsWith VDR
+Cu2+ interactsWith UBA52
+Mg2+ interactsWith ANTXR2
+UI1 interactsWith PLAU
+UI2 interactsWith PLAU
+UI3 interactsWith PLAU
+GTG interactsWith DCPS
+GTG interactsWith DCPS
+GTG interactsWith DCPS
+GTA interactsWith DCPS
+GTA interactsWith DCPS
+GTA interactsWith DCPS
+Fe3+ interactsWith TF
+CTP interactsWith UCK2
+UTP interactsWith UCK2
+Mg2+ interactsWith UCK2
+5'-CMP interactsWith UCK2
+ADP interactsWith UCK2
+Zn2+ interactsWith CPM
+Ca2+ interactsWith FBN2
+Ca2+ interactsWith FBN2
+Ca2+ interactsWith Ldl-Receptor_Class_A_3
+TAR interactsWith Atp-Dependent_Rna_Helicase_P54
+Mg2+ interactsWith EPHX2
+n-cyclohexyl-n'-(4-iodophenyl)urea interactsWith EPHX2
+dTTP interactsWith POLB
+IMH interactsWith NP
+PZN interactsWith CASP3
+PZN interactsWith Caspase-3
+PZN interactsWith Caspase-3
+Ca2+ interactsWith PVALB
+Ca2+ interactsWith PVALB
+Zn2+ interactsWith Transcription_Initiation_Factor_Iib
+OXL interactsWith TF
+JAN interactsWith FNTB
+165 interactsWith F2
+FMC interactsWith MTAP
+MTH interactsWith MTAP
+Mg2+ interactsWith PDE3A
+HG9 interactsWith PDE3A
+HG9 interactsWith PDE3A
+666 interactsWith PDE3A
+isobutyl-(3)-1-methylxanthine interactsWith PDE3A
+isobutyl-(3)-1-methylxanthine interactsWith PDE3A
+NDP interactsWith GMDS
+NDP interactsWith GMDS
+GDP interactsWith GMDS
+NAD+ interactsWith LDHB
+OXQ interactsWith LDHB
+NAD+ interactsWith LDHB
+176 interactsWith F2
+177 interactsWith F2
+VIA interactsWith PDE5A
+CIA interactsWith PDE5A
+CIA interactsWith PDE5A
+444 interactsWith NR1H3
+MEI interactsWith RXRG
+Zn2+ interactsWith Potential_Transcriptional_Repressor_Not4hp
+Zn2+ interactsWith Potential_Transcriptional_Repressor_Not4hp
+NDP interactsWith AKR1B1
+LDT interactsWith AKR1B1
+Citiric_acid interactsWith AKR1B1
+FC6 interactsWith CYGB
+FC6 interactsWith CYGB
+Benzamidine interactsWith BCKDHA
+3FP interactsWith CDK3
+Zn2+ interactsWith ABLIM2
+Zn2+ interactsWith ABLIM2
+TAR interactsWith B3GAT1
+Mn2+ interactsWith B3GAT1
+UDP interactsWith B3GAT1
+GAL-(1-4)NAG interactsWith B3GAT1
+GAL-(1-4)NAG interactsWith B3GAT1
+GTT interactsWith GSTA1
+ABY interactsWith GSTA1
+ABY interactsWith GSTA1
+2SP interactsWith Gm2-Activator_Protein
+MO2 interactsWith FTL
+MO1 interactsWith FTL
+MO6 interactsWith FTL
+MO6 interactsWith FTL
+MO4 interactsWith FTL
+NAG-(6-1)FUC interactsWith DPP4
+NAG-(4-1)NAG-(4-1)MAN-(4-1)(6-1)MAN interactsWith DPP4
+heme interactsWith CYP2C9
+Flurbiprofen interactsWith CYP2C9
+TTG interactsWith 1RR8_A
+TTG interactsWith TOP1
+TTG interactsWith 1RR8_B
+TTC interactsWith 1RR8_A
+TTC interactsWith 1RR8_B
+Mn2+ interactsWith PPP1CB
+Mn2+ interactsWith PPP1CB
+2IN interactsWith PLAU
+MAN-(6-1)MAN-(3-1)MAN-(2,6-1)MAN interactsWith Mdc-Sign1b_Type_I_Isoform
+GAL-(1-4)NAG-(3-1)FUC-(2,1-3)GAL interactsWith Mdc-Sign1b_Type_I_Isoform
+Ca2+ interactsWith Mdc-Sign1b_Type_I_Isoform
+Ca2+ interactsWith Mdc-Sign1b_Type_I_Isoform
+Mg2+ interactsWith Mdc-Sign1b_Type_I_Isoform
+GAL-(1-4)NAG-(3-1)FUC interactsWith CLEC4M
+GLB interactsWith CLEC4M
+NAG interactsWith CLEC4M
+GAL-(1-4)NAG-(3-1)FUC interactsWith CLEC4M
+Ca2+ interactsWith CLEC4M
+Ca2+ interactsWith CLEC4M
+Ca2+ interactsWith CLEC4M
+Ca2+ interactsWith CLEC4M
+Ca2+ interactsWith CLEC4M
+(R,R)-2,3_Butanediol interactsWith Camp-Dependent_Protein_Kinase_Inhibitor,_Alpha_Form
+(R,R)-2,3_Butanediol interactsWith Camp-Dependent_Protein_Kinase_Inhibitor,_Alpha_Form
+MYE interactsWith CTSL2
+Ca2+ interactsWith MASP2
+Ca2+ interactsWith MASP2
+NADP+ interactsWith IDH1
+NADP+ interactsWith IDH1
+ICT interactsWith IDH1
+ICT interactsWith IDH1
+Zn2+ interactsWith PDE9A
+Mg2+ interactsWith PDE9A
+isobutyl-(3)-1-methylxanthine interactsWith PDE9A
+isobutyl-(3)-1-methylxanthine interactsWith PDE9A
+DFP interactsWith FAP
+PU3 interactsWith HSPCB
+PU4 interactsWith HSPCB
+PU5 interactsWith HSPCB
+PU6 interactsWith HSPCB
+PU7 interactsWith HSPCB
+PU8 interactsWith HSPCB
+PU9 interactsWith HSPCB
+PU1 interactsWith HSPCB
+PU2 interactsWith HSPCB
+PU0 interactsWith HSPCB
+PUX interactsWith HSPCB
+4-iodobenzo[b]thiophene-2-carboxamidine interactsWith PROC
+alpha-D-Glucose interactsWith Factor_Viia_Light_Chain
+Mg2+ interactsWith Cyclin_A2
+staurosporine interactsWith PRKACB
+UCN interactsWith PRKACB
+Na+ interactsWith MASP2
+5alpha-Androstane-3,17-dione interactsWith Estradiol_17_Beta-Dehydrogenase_1
+NADP+ interactsWith Estradiol_17_Beta-Dehydrogenase_1
+4-Androstene-3,17-dione interactsWith Estradiol_17_Beta-Dehydrogenase_1
+NAD+ interactsWith Deoxyhypusine_Synthase
+NAG-(4-1)NAG-(4-1)NAG interactsWith High_Affinity_Immunoglobulin_Epsilon_Receptor_Alpha-Subunit_Precursor
+NAG-(4-1)NAG-(4-1)NAG interactsWith Peptide_E131
+NAG-(4-1)NAG-(4-1)MAN interactsWith High_Affinity_Immunoglobulin_Epsilon_Receptor_Alpha-Subunit_Precursor
+NAG interactsWith High_Affinity_Immunoglobulin_Epsilon_Receptor_Alpha-Subunit_Precursor
+NAG interactsWith Peptide_E131
+NAG interactsWith Peptide_E131
+NAG-(4-1)NAG interactsWith High_Affinity_Immunoglobulin_Epsilon_Receptor_Alpha-Subunit_Precursor
+NAG interactsWith High_Affinity_Immunoglobulin_Epsilon_Receptor_Alpha-Subunit_Precursor
+NAG interactsWith High_Affinity_Immunoglobulin_Epsilon_Receptor_Alpha-Subunit_Precursor
+Citiric_acid interactsWith High_Affinity_Immunoglobulin_Epsilon_Receptor_Alpha-Subunit_Precursor
+Citiric_acid interactsWith High_Affinity_Immunoglobulin_Epsilon_Receptor_Alpha-Subunit_Precursor
+GC7 interactsWith Deoxyhypusine_Synthase
+FUC-(1-2)GAL-(1-4)NAG-(3-1)FUC interactsWith Hu3s193_Fab_Fragment,_Light_Chain
+FUC-(1-2)GAL-(1-4)NAG-(3-1)FUC interactsWith Hu3s193_Fab_Fragment,_Heavy_Chain
+Zn2+ interactsWith NLN
+778 interactsWith Protein_Farnesyltransferase_Beta_Subunit
+BLA interactsWith Heme_Oxygenase_1
+Na+ interactsWith PGLYRP3
+170 interactsWith Thrombin
+staurosporine interactsWith Tyrosine-Protein_Kinase_ItkTSK
+NDR interactsWith Progesterone_Receptor
+ID5 interactsWith AKR1B1
+BB3 interactsWith PTPN9
+892 interactsWith PTPN9
+FRJ interactsWith PTPN9
+Zn2+ interactsWith HDAC8
+Na+ interactsWith Histone_Deacetylase_8
+Na+ interactsWith Histone_Deacetylase_8
+Na+ interactsWith Histone_Deacetylase_8
+Trichostatin_A interactsWith Histone_Deacetylase_8
+Trichostatin_A interactsWith Histone_Deacetylase_8
+B3N interactsWith HDAC8
+suberoylanilide_hydroxamic_acid interactsWith HDAC8
+WSK interactsWith WAS
+Citric_acid interactsWith PDE5A
+Zn2+ interactsWith Cgmp-Specific_3',5'-Cyclic_Phosphodiesterase
+Mg2+ interactsWith Cgmp-Specific_3',5'-Cyclic_Phosphodiesterase
+CPG interactsWith Cgmp-Specific_3',5'-Cyclic_Phosphodiesterase
+CPG interactsWith Cgmp-Specific_3',5'-Cyclic_Phosphodiesterase
+Zn2+ interactsWith PDE1B
+Mg2+ interactsWith PDE1B
+AMP interactsWith Camp-Specific_3',5'-Cyclic_Phosphodiesterase_4b
+A5MP interactsWith Camp-Specific_3',5'-Cyclic_Phosphodiesterase_4d
+B3P interactsWith Camp-Specific_3',5'-Cyclic_Phosphodiesterase_4d
+ROL interactsWith Camp-Specific_3',5'-Cyclic_Phosphodiesterase_4d
+VIA interactsWith PDE5A
+Zn2+ interactsWith Prothrombin
+heme interactsWith CYP3A43
+VDN interactsWith PDE5A
+MCO interactsWith ACE
+CRI interactsWith Histone_Deacetylase_8
+CRI interactsWith Histone_Deacetylase_8
+Progesterone interactsWith CYP3A43
+metyrapone interactsWith CYP3A43
+Zn2+ interactsWith ARIH1
+Ca2+ interactsWith PADI4
+Ca2+ interactsWith PADI4
+Ca2+ interactsWith PADI4
+Ca2+ interactsWith PADI4
+BAG interactsWith PADI4
+Zn2+ interactsWith ACE
+glycine interactsWith ACE
+EAL interactsWith ACE
+VTQ interactsWith SEC14L2
+VTQ interactsWith SEC14L2
+VTQ interactsWith SEC14L2
+TMU interactsWith GSK3B
+2FH interactsWith Heme_Oxygenase_1
+Mn2+ interactsWith PPEF1
+Mn2+ interactsWith PPEF1
+Malonate_(2-) interactsWith CASP1
+Malonate_(2-) interactsWith CASP1
+NXN interactsWith CASP7
+FXN interactsWith CASP7
+FXN interactsWith CASP7
+FXN interactsWith CASP7
+NT1 interactsWith SERPINB4
+NT2 interactsWith F2
+HEX interactsWith GLTP
+LAT-(1-1)SPH-(2-1)OLA interactsWith GLTP
+OCT interactsWith GLTP
+1FH interactsWith HMOX2
+1FH interactsWith HMOX2
+Citrate interactsWith DDX39
+3',5'-ADP interactsWith HS3ST3B1
+Citiric_acid interactsWith HS3ST3B1
+UAP-(1-4)SGN interactsWith HS3ST3B1
+IDS interactsWith HS3ST3B1
+SGN interactsWith HS3ST3B1
+Na+ interactsWith HS3ST3B1
+Mg2+ interactsWith CTDSP1
+Citiric_acid interactsWith CTDSP1
+Mg2+ interactsWith CTDSP1
+GU4-(1-4)GU6-(1-4)GU0-(1-4)GU5-(1-4)GU8-(1-4)GU9-(1-4)GU8-(1-4)GU9-(1-4)GU8-(1-4)GU9-(1-4)GU8-(1-4)GU5-(1-4)GU1-(1-4)GU6 interactsWith F2
+GU4-(1-4)GU6-(1-4)GU0-(1-4)GU5-(1-4)GU8-(1-4)GU9-(1-4)GU8-(1-4)GU9-(1-4)GU8-(1-4)GU9-(1-4)GU8-(1-4)GU5-(1-4)GU1-(1-4)GU6 interactsWith SERPINB4
+GU2-(1-4)GU3 interactsWith SERPINB4
+NAG-(1-4)NAG-(6-1)FUC interactsWith F2
+NAG-(4-1)NAG-(4-1)MAN-(6-1)MAN-(3,3-1)MAN interactsWith SERPINB4
+B1V interactsWith PMP2
+CRZ interactsWith PMP2
+OKA interactsWith PPP1CC
+staurosporine interactsWith ZAP70
+K+ interactsWith 1U6B_B
+K+ interactsWith 1U6B_C
+K+ interactsWith 1U6B_B
+K+ interactsWith 1U6B_D
+Mg2+ interactsWith 1U6B_B
+Mg2+ interactsWith 1U6B_B
+Mg2+ interactsWith 1U6B_B
+Mg2+ interactsWith 1U6B_B
+Mg2+ interactsWith 1U6B_B
+Mg2+ interactsWith 1U6B_B
+Mg2+ interactsWith 1U6B_B
+Mg2+ interactsWith 1U6B_B
+Mg2+ interactsWith 1U6B_B
+537 interactsWith MAPK8
+PU3 interactsWith HSPCB
+460 interactsWith ACVR1C
+Rev pp XPO1
+Rev-RRE-XPO1 interactsWith Ran-GTP
+Rev-RRE interactsWith XPO1
+Vif pp MAPK1
+Vpr pp GTF2B
+VP16 pp GTF2B
+Gag pp SGTA
+Vpu pp SGTA
+HAdVFgp23 pp PPP2R2A
+Vpr pp POM121
+NAG-(4-1)NAG interactsWith HLA-DRB1
+NAG-(1-4)NAG-(6-1)FUC interactsWith LTF
+NAG-(4-1)NAG interactsWith MPO
+NAG-(4-1)NAG interactsWith 7API_B
+SGN-(1-4)IDU interactsWith FGF2
+NAG-(4-1)NAG interactsWith 1ZXQ
+NAG-(4-1)NAG interactsWith 1ZXQ
+NAG-(4-1)NAG interactsWith 1ZXQ
+ILG-TNB-GLY interactsWith GSTP1
+IDS-(4-1)SGN interactsWith Acidic_Fibroblast_Growth_Factor
+ACE-PTR-GLU-DIY interactsWith SRC
+NAG-(4-1)NAG interactsWith Fibrin
+NAG-(4-1)NAG-(3-1)MAN-(6-1)MAN-(3-1)MAN-(2-1)MAN-(3,3-1)MAN-(2-1)MAN interactsWith MCP
+NAG-(4-1)NAG interactsWith Beta2-Glycoprotein-I
+NAG-(4-1)NAG-(4-1)MAN-(3-1)MAN interactsWith SERPINC1
+NAG-(4-1)NAG-(4-1)MAN interactsWith FCGR1A
+AFL-(1-6)NAG-(4-1)NAG-(4-1)BMA interactsWith FCER1A
+NAG-(1-4)NAG-(6-1)FUC interactsWith FCER1A
+SGN-(1-4)IDU interactsWith FGFR1
+SGN-(1-4)IDU interactsWith FGFR1
+NAG-(4-1)NAG-(4-1)MAN interactsWith SERPINC1
+GAL-(1-3)GAL interactsWith B3GAT3
+NAG-(4-1)NAG interactsWith Heparin-Binding_Protein
+SGN-(4-1)IDS interactsWith HGF
+FUC-(1-6)NAG-(4-1)NAG interactsWith CSF2RB
+NAG-(4-1)NDG interactsWith HLA-DRB5
+NAG-(4-1)NAG interactsWith SERPINA5
+NAG-(4-1)NAG interactsWith Plasma_Serine_Protease_Inhibitor
+NAG-(4-1)NAG-(4-1)ASO interactsWith EGFR
+NAG-(4-1)NAG-(4-1)MAN-(6-1)MAN-(3,3-1)MAN interactsWith Ig_Alpha-1_Chain_C_Region
+NAG-(4-1)NAG-(4-1)MAN interactsWith FCAR
+NAG-(6-1)FUC interactsWith B2M
+NAG-(4-1)NAG-(4-1)MAN-(6-1)MAN-(3,3-1)MAN interactsWith F2
+NAG-(4-1)NAG-(4-1)MAN-(6-1)MAN-(6-1)MAN-(3,3-1)MAN interactsWith Fab_2g12,_Light_Chain
+NAG-(4-1)NAG interactsWith EGFR
+NAG-(4-1)NAG interactsWith EGFR
+NAG-(4-1)NAG interactsWith EGFR
+NAG-(4-1)NAG interactsWith LTF
+NAG-(4-1)NAG interactsWith LTF
+Gag_dimer interactsWith PPIA
+EBNA1 pp USP7
+EBNA1 interactsWith Unknown
+Unknown interactsWith TAFI_beta
+Unknown interactsWith TAFI_alpha
+Unknown interactsWith CK2_alpha
+Unknown interactsWith Importin_alpha
+FNBPA pp FN1
+Vpr pp Sp1
+Vpr pp TP53
+TAR interactsWith RNGTT
+Tat pp RNGTT
+Tat pp THRA
+HIV-1_genome interactsWith THRA
+Hdv_Ribozyme interactsWith SNRPA
+p9 pp PDCD6IP
+p6 pp PDCD6IP
+p9 pp PDCD6IP
+Cl- interactsWith LTF
+Cl- interactsWith CA2
+Cl- interactsWith AMY1A
+Cl- interactsWith MMP10
+Cl- interactsWith MMP10
+Cl- interactsWith MMP3
+Cl- interactsWith ARSJ
+Cl- interactsWith LTF
+Cl- interactsWith MCP
+Co_(2+) interactsWith 1BN5
+Co_(2+) interactsWith 1BN5
+Cl- interactsWith MMP2
+Cl- interactsWith ADK
+Cl- interactsWith Heat-Shock_70kd_Protein
+Co_(2+) interactsWith ITGA2
+Cl- interactsWith PTPN1
+Cl- interactsWith PTPN1
+Cl- interactsWith CA1
+Cl- interactsWith RAD51
+Cl- interactsWith ANK3
+Cl- interactsWith ACE
+Cl- interactsWith ACE
+Cl- interactsWith TGM6
+Cl- interactsWith L-3-Phosphoserine_Phosphatase
+Cl- interactsWith HADH2
+E1A pp EP300
+E1A pp RB1
+BR interactsWith CA13
+BR interactsWith MPO
+BR interactsWith MPO
+BR interactsWith LYPLA1
+BR interactsWith LYPLA1
+BR interactsWith LYPLA1
+BR interactsWith LYPLA1
+BR interactsWith LYPLA1
+BR interactsWith LYPLA1
+BR interactsWith LYPLA1
+BR interactsWith LYPLA1
+BR interactsWith LYPLA1
+BR interactsWith LYPLA1
+BR interactsWith LYPLA1
+BR interactsWith Beta-Defensin_1
+BR interactsWith Beta-Defensin_1
+BR interactsWith MPO
+BR interactsWith IGF2R
+BR interactsWith IGF2R
+BR interactsWith IGF2R
+BR interactsWith TGM6
+BR interactsWith TGM6
+BR interactsWith TGM6
+BR interactsWith NR4A2
+BR interactsWith NR4A2
+BR interactsWith NR4A2
+BR interactsWith NR4A2
+BR interactsWith NR4A2
+E1A pp EP400
+Unknown interactsWith WNT4
+Unknown interactsWith ARHGAP26
+Unknown interactsWith G3BP2
+Unknown interactsWith Card6
+Unknown interactsWith GAS2L2
+Unknown interactsWith TP53BP2
+Unknown interactsWith CASP8
+Unknown interactsWith CENPC1
+Unknown interactsWith DRF1
+Unknown interactsWith RBBP7
+Unknown interactsWith CCNE2
+Unknown interactsWith HNRPC
+Unknown interactsWith ribosomal_protein_L14
+Unknown interactsWith GPR113
+Unknown interactsWith INHBE
+Unknown interactsWith SLIT2
+Unknown interactsWith GFRA2
+Unknown interactsWith RPH3AL
+Unknown interactsWith CFHL4
+Unknown interactsWith monocyte_chemotactic_protein
+Unknown interactsWith SYNE1
+Unknown interactsWith L1CAM
+Unknown interactsWith SMTN
+Unknown interactsWith KRT14
+Unknown interactsWith PDLIM5
+Unknown interactsWith AMHR2
+Unknown interactsWith IRS4
+Unknown interactsWith TRPM7
+Unknown interactsWith CHKA
+Unknown interactsWith PTK2B
+Unknown interactsWith TTBK2
+Unknown interactsWith CRKL
+Unknown interactsWith MAP2K6
+Unknown interactsWith PKN2
+Unknown interactsWith PAK6
+Unknown interactsWith PINK1
+Unknown interactsWith CSNK2A1
+Unknown interactsWith FBLN2
+Unknown interactsWith MIB2
+Unknown interactsWith OR10H2
+Unknown interactsWith SC65
+Unknown interactsWith Slc5a12
+Unknown interactsWith STAB2
+Unknown interactsWith ADIPOR1
+Unknown interactsWith PTPN14
+Unknown interactsWith MED12
+Unknown interactsWith ZNF655
+Unknown interactsWith NPAS3
+Unknown interactsWith MLR1
+Unknown interactsWith LOC126208
+Unknown interactsWith HOXA3
+Unknown interactsWith PRDM15
+Unknown interactsWith ZNF278
+Unknown interactsWith Jumonji_protein
+Unknown interactsWith TCEB3C
+Unknown interactsWith TLX3
+Unknown interactsWith RBBP6
+Unknown interactsWith USP18
+Unknown interactsWith LOC131572
+Unknown interactsWith WWP2
+Unknown interactsWith PPBPL2
+Unknown interactsWith GPR103
+gH interactsWith alphavbeta3_complex
+NS5A pp FBL2
+NS5A pp FBL2
+NS5B pp FBL2
+FK506 interactsWith BAD18781
+FK506 interactsWith BAB15266
+FK506 interactsWith BAB15220
+FK506 interactsWith BAC03954
+DEVD interactsWith Caspase3
+FK506 interactsWith FKBP12
+FK506 interactsWith FKBP52
+FK506 interactsWith FKBP25
+FK506 interactsWith FKBP13
+FK506 interactsWith FKBP12.6
+FK506 interactsWith FKBP54
+Shepherdin interactsWith Hsp90
+ATP interactsWith Hsp90
+Tat pp Dicer
+Tax pp BAF57
+Tax pp BAF155
+Tax pp BRG1
+Tax pp Gelsolin
+Tax pp Rad51
+Tax pp Cdk2
+Tax pp GAP1m
+unknown interactsWith Ring2
+unknown interactsWith RbBP5
+unknown interactsWith MLL
+unknown interactsWith WRD5
+unknown interactsWith menin
+unknown interactsWith RbBP5
+unknown interactsWith MLL
+unknown interactsWith MOF
+Tax pp Actin
+Tax pp Annexin_VI
+Tax pp PAK3
+Tax pp PCTAIRE-1
+Tax pp RAG2
+Tax pp Cdc42
+Tax pp Rac1
+Tax pp RhoA
+MIR1 pp HLA.B7
+Unknown interactsWith p65(RelA)
+FK506 interactsWith FKBP65
+696 interactsWith PLAU
+4-iodobenzo[b]thiophene-2-carboxamidine interactsWith PLAU
+Citric_acid interactsWith PLAU
+CR9 interactsWith PLAU
+CR9 interactsWith F7
+132 interactsWith HPN
+CR9 interactsWith HPN
+CR9 interactsWith F2
+BIR interactsWith MME
+TI1 interactsWith MME
+OIR interactsWith MME
+Exogenous_Tripeptide_Formyl-(Nle)lf pp SERPINC1
+NAG interactsWith SERPINC1
+Citric_acid interactsWith Glycine_N-Methyltransferase
+Ny-Eso-1_Peptide pp Hla_Class_I_Histocompatibility_Antigen,_A-2_Alpha_Chain
+Ny-Eso-1_Peptide_Analogue_S9a pp Hla_Class_I_Histocompatibility_Antigen,_A-2_Alpha_Chain
+Ny-Eso-1_Peptide_Analogue_S9s pp Hla_Class_I_Histocompatibility_Antigen,_A-2_Alpha_Chain
+FAD interactsWith GCDH
+NBC interactsWith GCDH
+TAR interactsWith TREM1
+TAR interactsWith TREM1
+Ca2+ interactsWith GSN
+GAL-(1-4)NAG-(1-2)MAN-(1-6)MAN-(1-4)NAG-(1-4)NAG-(6-1)FUC-(4,3-1)MAN interactsWith Igg1
+NAG-(1-2)MAN-(1-6)MAN-(1-4)NAG-(1-4)NAG-(6-1)FUC-(3,3-1)MAN-(2-1)NAG interactsWith Igg1
+HG2 interactsWith Igg1
+GAL-(1-4)NAG-(1-2)MAN-(1-6)MAN-(1-4)NAG-(1-4)NAG-(6-1)FUC-(4,3-1)MAN interactsWith Recombinant_Igg1_Heavy_Chain
+NAG-(1-2)MAN-(1-6)MAN-(1-4)NAG-(1-4)NAG-(6-1)FUC-(3,3-1)MAN-(2-1)NAG interactsWith Recombinant_Igg1_Heavy_Chain
+Mg2+ interactsWith ENO2
+Mg2+ interactsWith ENO2
+Peptostreptococcal_Albumin-Binding_Protein pp ALB
+decanoate interactsWith ALB
+decanoate interactsWith ALB
+decanoate interactsWith ALB
+Citric_acid interactsWith ALB
+998 interactsWith BIRC4
+Envelope_Glycoprotein_Gp41 pp Anti-Hiv-1_Antibody_2f5_Light_Chain
+Envelope_Glycoprotein_Gp41 pp Anti-Hiv-1_Antibody_2f5_Heavy_Chain
+Envelope_Glycoprotein_Gp41 pp Anti-Hiv-1_Antibody_2f5_Light_Chain
+Envelope_Glycoprotein_Gp41 pp Anti-Hiv-1_Antibody_2f5_Heavy_Chain
+Zn2+ interactsWith UBE1C
+667 interactsWith CA2
+Co_(2+) interactsWith RAB5A
+GDP interactsWith RAB5A
+FSP interactsWith CTSK
+FSP interactsWith CTSK
+Mg2+ interactsWith RABGEF1
+1U1K_B pd HNRPA1
+GOX interactsWith AMY2A
+LAG interactsWith AMY2A
+GOX interactsWith AMY2A
+LM2 interactsWith AMY2A
+TDT interactsWith HADH2
+NAD+ interactsWith HADH2
+Mg2+ interactsWith ARF1
+GDP interactsWith ARF1
+Gp41_Peptide pp Antibody_2f5_(Heavy_Chain)
+Gp41_Peptide pp Antibody_2f5_(Light_Chain)
+Gp41_Peptide pp Antibody_2f5_(Heavy_Chain)
+Gp41_Peptide pp Antibody_2f5_(Light_Chain)
+Gp41_Peptide pp Antibody_2f5_(Heavy_Chain)
+Gp41_Peptide pp Antibody_2f5_(Heavy_Chain)
+Gp41_Peptide pp Antibody_2f5_(Light_Chain)
+Gp41_Peptide pp Antibody_2f5_(Heavy_Chain)
+Gp41_Peptide pp Antibody_2f5_(Light_Chain)
+Gp41_Peptide pp Antibody_2f5_(Heavy_Chain)
+Gp41_Peptide pp Antibody_2f5_(Light_Chain)
+Gp41_Peptide pp Antibody_2f5_(Light_Chain)
+Gp41_Peptide pp Antibody_2f5_(Heavy_Chain)
+Gp41_Peptide pp Antibody_2f5_(Heavy_Chain)
+Gp41_Peptide pp Antibody_2f5_(Light_Chain)
+Gp41_Peptide pp Antibody_2f5_(Heavy_Chain)
+Gp41_Peptide pp Antibody_2f5_(Light_Chain)
+Gp41_Peptide_Analog pp Antibody_2f5_(Heavy_Chain)
+Gp41_Peptide_Analog pp Antibody_2f5_(Light_Chain)
+Gp41_Peptide_Analog pp Antibody_2f5_(Heavy_Chain)
+Gp41_Peptide_Analog pp Antibody_2f5_(Light_Chain)
+Gp41_Peptide_Analog pp Antibody_2f5_(Heavy_Chain)
+Gp41_Peptide_Analog pp Antibody_2f5_(Light_Chain)
+Gp41_Peptide pp Antibody_2f5_(Heavy_Chain)
+Gp41_Peptide pp Antibody_2f5_(Light_Chain)
+FRQ interactsWith PARP1
+FRQ interactsWith PARP1
+heme interactsWith CYGB
+benzoate interactsWith PRDX5
+GSH interactsWith GSTA1
+GSH interactsWith GSTA1
+Cl- interactsWith GSTA1
+K+ interactsWith GSTA1
+Zn2+ interactsWith SNRPC
+Mn2+ interactsWith ITGA2
+Zn2+ interactsWith GTF2E1
+Mg2+ interactsWith THEX1
+Mg2+ interactsWith THEX1
+AMP interactsWith THEX1
+NAG-(1-4)NAG-(6-1)AFL interactsWith DPP4
+NAG-(4-1)NAG-(4-1)BMA-(3-1)MAN interactsWith DPP4
+NAG interactsWith DPP4
+NDG interactsWith DPP4
+NAG-(6-1)AFL interactsWith DPP4
+NAG-(4-1)NAG interactsWith DPP4
+NAG interactsWith DPP4
+NAG-(4-1)NAG interactsWith DPP4
+K+ interactsWith HDAC8
+K+ interactsWith HDAC8
+NHB interactsWith HDAC8
+NHB interactsWith HDAC8
+AMP-PNP interactsWith ITPKA
+IP3 interactsWith ITPKA
+Mn2+ interactsWith ITPKA
+ADP interactsWith ITPKA
+ITS interactsWith ITPKA
+Ca2+ interactsWith OGT
+L01 interactsWith BACE1
+ALC interactsWith Kynurenine--Oxoglutarate_Transaminase_I
+pyridoxamine_phosphate interactsWith Kynurenine--Oxoglutarate_Transaminase_I
+1P3 interactsWith PPIA
+E1P interactsWith PPIA
+25A interactsWith RNASEL
+14-Mer_From_Nuclear_Receptor_Coactivator_2 pp PPARG
+PLB interactsWith PPARG
+GDP interactsWith RAB9B
+Citric_acid interactsWith Aldose_Reductase
+FIR interactsWith Aldose_Reductase
+FIS interactsWith Aldose_Reductase
+Peroxisome_Proliferator_Activated_Receptor_Gamma_Coactivator_1_Alpha pp ESRRA
+AAY interactsWith ITGAL
+AAY interactsWith ITGAL
+AAY interactsWith ITGAL
+AB8 interactsWith ITGAL
+AB8 interactsWith ITGAL
+AB8 interactsWith ITGAL
+NADP+ interactsWith Arpg836
+NADP+ interactsWith Arpg836
+AA2 interactsWith FGFR2
+Citrate interactsWith GSK3B
+Citrate interactsWith GSK3B
+DFN interactsWith GSK3B
+NAG-(4-1)NAG interactsWith ADAM33
+Zn2+ interactsWith ADAM33
+Ca2+ interactsWith ADAM33
+NAG-(4-1)NAG-(4-1)BMA-(6-1)BMA-(3,3-1)BMA interactsWith ADAM33
+097 interactsWith ADAM33
+Mn2+ interactsWith Methionine_Aminopeptidase_2
+Mn2+ interactsWith Methionine_Aminopeptidase_2
+AO5 interactsWith Methionine_Aminopeptidase_2
+AO1 interactsWith Methionine_Aminopeptidase_2
+AO2 interactsWith Methionine_Aminopeptidase_2
+Prostaglandin_D2 interactsWith Aldo-Keto_Reductase_Family_1_Member_C3
+NDP interactsWith Aldo-Keto_Reductase_Family_1_Member_C3
+RUT interactsWith Aldo-Keto_Reductase_Family_1_Member_C3
+Mg2+ interactsWith FAHD1
+Mg2+ interactsWith FAHD1
+Mg2+ interactsWith FAHD1
+Fe3+ interactsWith HBD
+Fe3+ interactsWith Hemoglobin_Alpha_Chain
+heme interactsWith HBD
+heme interactsWith HBA2
+Sorting_Nexin_5 pp Leukocyte_Antigen_(Hla)_Class_I_Molecule
+Major_Histocompatibility_Complex,_Class_Ii,_Dr_Alpha pp Mhc_Class_I_Antigen
+Peptide_Derived_From_The_C-Terminus_Of_Rap2a pp FNTB
+Peptide_Derived_From_The_C-Terminus_Of_Rap2a pp FNTA
+FII interactsWith FNTB
+FII interactsWith FNTA
+Peptide_Derived_From_The_C-Terminus_Of_H-Ras pp FNTB
+FII interactsWith FNTA
+diethylstilbestrol interactsWith TTR
+Zn2+ interactsWith BIRC7
+148 interactsWith BIRC7
+NAG interactsWith ITGB3
+NAG-(4-1)NAG-(4-1)BMA-(6-1)BMA-(3,3-1)BMA interactsWith ITGB3
+NAG-(4-1)NAG-(4-1)MAN-(6-1)MAN-(3-1)MAN-(3,3-1)MAN-(4,6-1)MAN interactsWith ITGB3
+Mg2+ interactsWith ITGB3
+Ca2+ interactsWith ITGB3
+Ca2+ interactsWith ITGB3
+AGG interactsWith ITGB3
+Eptifibatide pp ITGB3
+180 interactsWith ITGB3
+NAG-(4-1)NAG-(4-1)MAN-(3-1)MAN interactsWith ITGB3
+CCB interactsWith ADH1A
+CCB interactsWith ADH1A
+NAD+ interactsWith ADH1B
+BNF interactsWith ADH1B
+HPL interactsWith ADH1B
+HPL interactsWith ADH1B
+FXY interactsWith ADH1A
+FXY interactsWith ADH1A
+FXY interactsWith ADH1A
+745 interactsWith PLAU
+FAD interactsWith DIA1
+ITS interactsWith PLEKHA4
+444 interactsWith NR1H2
+Peptide_Inhibitor pp CCNA2
+DAN interactsWith NEU2
+GLB interactsWith LGALS1
+GLB interactsWith LGALS1
+Lactose interactsWith LGALS1
+Lactose interactsWith LGALS1
+NAG-(4-1)GAL interactsWith LGALS1
+NAG-(4-1)GAL interactsWith LGALS1
+NADP+ interactsWith DECR1
+Hexanoyl-CoA interactsWith DECR1
+Hexanoyl-CoA interactsWith DECR1
+Hexanoyl-CoA interactsWith DECR1
+Hexanoyl-CoA interactsWith DECR1
+NADP+ interactsWith DECR1
+Hexanoyl-CoA interactsWith DECR1
+Hexanoyl-CoA interactsWith DECR1
+Diablo_Homolog,_Mitochondrial pp Baculoviral_Iap_Repeat-Containing_Protein_8
+Zn2+ interactsWith Baculoviral_Iap_Repeat-Containing_Protein_8
+Zn2+ interactsWith Baculoviral_Iap_Repeat-Containing_Protein_8
+Zn2+ interactsWith Baculoviral_Iap_Repeat-Containing_Protein_8
+STI interactsWith SYK
+staurosporine interactsWith SYK
+IX1 interactsWith PTPN1
+4-Androstene-3,17-dione interactsWith Aldo-Keto_Reductase_Family_1_Member_C3
+Ca2+ interactsWith LDLR
+Ca2+ interactsWith LDLR
+staurosporine interactsWith PRKCQ
+Na+ interactsWith C6orf82
+Zn2+ interactsWith LCN1
+Cl- interactsWith LCN1
+Cl- interactsWith LCN1
+NDP interactsWith HSD11B1
+GW5 interactsWith ESR1
+L79 interactsWith RXRA
+Hirudin_Iib pp F2
+NAG interactsWith F2
+OSC interactsWith F2
+OSC interactsWith F2
+Mg2+ interactsWith MAP2K2
+ATP interactsWith MAP2K2
+5EA interactsWith MAP2K2
+5EA interactsWith MAP2K2
+Mg2+ interactsWith MAP2K2
+ATP interactsWith MAP2K2
+BBM interactsWith MAP2K2
+H2B interactsWith PAH
+32P interactsWith BACE1
+1TV9_T pd POLB
+1TVA_P pd POLB
+1TVA_D pd POLB
+1TVA_T pd POLB
+Ca2+ interactsWith Loc51668_Protein
+H1S interactsWith CCL5
+H3S interactsWith CCL5
+ALH interactsWith CDK5
+ALH interactsWith CDK5
+IXM interactsWith CDK5
+RRC interactsWith CDK5
+Gene_Terminal_Protein_(Membrane_Protein_Lmp-2aLMP-2b) pp Hla_Class_I_Histocompatibility_Antigen_B-27_Alpha_Chain
+D76 interactsWith F10
+O16 interactsWith PGDS
+ITS interactsWith PDPK1
+4PT interactsWith PDPK1
+R71 interactsWith LSS
+C14 interactsWith LSS
+Lanosterol interactsWith Lanosterol_Synthase
+Zn2+ interactsWith ABLIM2
+Zn2+ interactsWith ABLIM2
+Zn2+ interactsWith Kiaa1045_Protein
+Zn2+ interactsWith Kiaa1045_Protein
+Zn2+ interactsWith RNF144
+Zn2+ interactsWith RNF144
+Zn2+ interactsWith ZNF295
+Zn2+ interactsWith ZNF295
+Zn2+ interactsWith ZNF295
+1X9N_B pd LIG1
+1X9N_C pd LIG1
+1X9N_D pd LIG1
+AMP interactsWith LIG1
+Zn2+ interactsWith Beta2-Chimaerin
+Zn2+ interactsWith Beta2-Chimaerin
+TTB interactsWith RARB
+Na+ interactsWith CLEC4M
+Na+ interactsWith CLEC4M
+Mg2+ interactsWith UCHL3
+Mg2+ interactsWith UCHL3
+Mg2+ interactsWith UCHL3
+GVE interactsWith UCHL3
+GVE interactsWith RPS27A
+Mg2+ interactsWith PIGR
+Ca2+ interactsWith ANXA2
+Ca2+ interactsWith ANXA2
+Ca2+ interactsWith ANXA2
+Ca2+ interactsWith ANXA2
+Ca2+ interactsWith ANXA2
+SGN-(1-4)IDS interactsWith F2
+SGN interactsWith F2
+SGN interactsWith F2
+SGN-(1-4)IDS interactsWith F2
+SGN-(1-4)IDS interactsWith F2
+NAG-(4-1)NAG interactsWith F2
+NAG-(4-1)NAG interactsWith F2
+NAG-(4-1)NAG-(4-1)BMA-(6-1)BMA-(3,3-1)BMA interactsWith F2
+R1881 interactsWith AR
+S-Adenosylhomocysteine interactsWith 9-Mer_Peptide_From_Tumor_Protein_P53
+S-Adenosylhomocysteine interactsWith 9-Mer_Peptide_From_Tumor_Protein_P53
+AMP-PNP interactsWith PIM1
+Zn2+ interactsWith Zinc_Finger_Y-Chromosomal_Protein
+3',5'-ADP interactsWith SULT1B1
+GSH interactsWith GSTM2
+GSH interactsWith GSTM2
+bisindolylmaleimide_i interactsWith PIM1
+NAG interactsWith F11
+Na+ interactsWith F11
+Na+ interactsWith F11
+heme interactsWith HBA2
+heme interactsWith Hemoglobin_Beta_Chain
+GMP interactsWith NP
+Mn2+ interactsWith PDE4B
+ROL interactsWith PDE4B
+8BR interactsWith PDE4B
+8BR interactsWith PDE4B
+AMP interactsWith PDE4B
+Co_(2+) interactsWith BF
+Mg2+ interactsWith BF
+DFP interactsWith BF
+GBS interactsWith BF
+158 interactsWith CASP1
+158 interactsWith CASP1
+Q2Y interactsWith CASP1
+Q2Y interactsWith CASP1
+4QB interactsWith CASP1
+4QB interactsWith CASP1
+BTH interactsWith CASP1
+BTH interactsWith CASP1
+HQC interactsWith CASP1
+HQC interactsWith CASP1
+NAG interactsWith DPP4
+5AP interactsWith DPP4
+5AP interactsWith DPP4
+5PH interactsWith CASP1
+5PH interactsWith CASP1
+OQB interactsWith CASP1
+OQB interactsWith CASP1
+YBH interactsWith CASP1
+YBH interactsWith CASP1
+Ca2+ interactsWith MMP1
+Ca2+ interactsWith MMP1
+Ca2+ interactsWith MMP1
+Ca2+ interactsWith MMP1
+Ca2+ interactsWith MMP1
+Cl- interactsWith MMP1
+Cl- interactsWith MMP1
+Na+ interactsWith MMP1
+Zn2+ interactsWith MMP1
+Zn2+ interactsWith MMP1
+PFS interactsWith GM2A
+PFS interactsWith GM2A
+PFS interactsWith GM2A
+LPE interactsWith GM2A
+LPE interactsWith GM2A
+LPE interactsWith GM2A
+lauric_acid interactsWith GM2A
+Histone_Deacetylase_9 pp MEF2B
+Histone_Deacetylase_9 pp MEF2B
+1TQE_C pd MEF2B
+1TQE_C pd MEF2B
+1TQE_D pd MEF2B
+1TQE_D pd MEF2B
+AMU-ALA-GMA-LYS-NH2 interactsWith PGLYRP3
+Zn2+ interactsWith RBX1
+Zn2+ interactsWith RBX1
+Zn2+ interactsWith RBX1
+NAG interactsWith ITGAV
+NAG interactsWith ITGAV
+NAG-(4-1)NAG interactsWith ITGAV
+ATP interactsWith CDK7
+ATP interactsWith CDK7
+heme interactsWith CYGB
+heme interactsWith CYGB
+AZG interactsWith NP
+3DG interactsWith NP
+1W0T_C pd TERF1
+1W0T_C pd TERF1
+1W0T_D pd TERF1
+1W0T_D pd TERF1
+1W0U_C pd TERF2
+1W0U_C pd TERF2
+1W0U_D pd TERF2
+1W0U_D pd TERF2
+Mn2+ interactsWith ISG20
+Mn2+ interactsWith ISG20
+5'-UMP interactsWith ISG20
+UDP interactsWith ABO
+DLG-(2-1)FUC interactsWith ABO
+BHG-(2-1)FUC interactsWith ABO
+GLB interactsWith GALK1
+Mg2+ interactsWith GALK1
+Mg2+ interactsWith GALK1
+AMP-PNP interactsWith GALK1
+AMP-PNP interactsWith GALK1
+AMP-PNP interactsWith GALK1
+Zn2+ interactsWith TK1
+Mg2+ interactsWith TK1
+dTTP interactsWith TK1
+3SA interactsWith AMY2A
+IAB interactsWith AMY2A
+5SA interactsWith AMY2A
+6SA interactsWith AMY2A
+Zn2+ interactsWith Wilms'_Tumor_Protein
+FMM interactsWith EGFR
+TCD interactsWith NR1I3
+CIO interactsWith PDE4B
+FIL interactsWith PDE4B
+FIL interactsWith PDE4B
+PIL interactsWith PDE4B
+5RM interactsWith PDE4B
+ROF interactsWith PDE4B
+4RR interactsWith PDE4B
+4RR interactsWith PDE4B
+4RR interactsWith PDE4B
+4SR interactsWith PDE4B
+Ca2+ interactsWith CIB1
+Ca2+ interactsWith CIB1
+CIO interactsWith PDE4D
+PIL interactsWith PDE4D
+ROF interactsWith PDE4D
+ZAR interactsWith PDE4D
+VIA interactsWith PDE4B
+VDN interactsWith PDE4B
+CIA interactsWith PDE5A
+VDN interactsWith PDE5A
+AIH interactsWith ESR1
+AIU interactsWith ESR1
+AIJ interactsWith ESR1
+AIT interactsWith ESR1
+MMI interactsWith BACE1
+ATP interactsWith Bis(5'-Nucleosyl)-Tetraphosphatase
+Cl- interactsWith DHRS8
+Androsterone interactsWith DHRS8
+Androsterone interactsWith DHRS8
+Androsterone interactsWith DHRS8
+Cl- interactsWith CRYZ
+Cl- interactsWith CRYZ
+NADP+ interactsWith CRYZ
+NADP+ interactsWith HSD11B1
+CBO interactsWith HSD11B1
+PUZ interactsWith HSPCA
+580 interactsWith TGFBR1
+Ca2+ interactsWith KCNIP1
+Ca2+ interactsWith KCNIP1
+resveratrol interactsWith NQO2
+resveratrol interactsWith NQO2
+resveratrol interactsWith NQO2
+n-octonyl-CoA interactsWith DCI
+Guanine_Nucleotide-Binding_Protein_Galpha(13)_:galpha(I1)_Chimera pp ARHGEF1
+NAG interactsWith KLK1
+Ca2+ interactsWith KLK1
+Palmitate interactsWith Trafficking_Protein_Particle_Complex_Subunit_3
+Stanolone interactsWith AR
+GSH interactsWith GSTA3
+GSH interactsWith GSTA3
+Ca2+ interactsWith Oncomodulin
+Ca2+ interactsWith Oncomodulin
+MXA interactsWith DHFR
+Small_Peptide_Savlqkkitdyfhpkk pp PCNA
+Small_Peptide_Savlqkkitdyfhpkk pp PCNA
+Small_Peptide_Savlqkkitdyfhpkk pp PCNA
+olomoucine interactsWith CDK2
+771 interactsWith F7
+LO1 interactsWith PTPN1
+L02 interactsWith F2
+Hirugen pp F2
+L03 interactsWith F2
+2CH interactsWith MAPK14
+CIG interactsWith CDK2
+NAG-(4-1)NAG interactsWith DPP4
+715 interactsWith DPP4
+DB1 interactsWith LCN2
+DB1 interactsWith LCN2
+DB1 interactsWith LCN2
+CM1 interactsWith LCN2
+CM2 interactsWith LCN2
+Rac3_Derived_Peptide pp AR
+NAG-(1-4)NAG-(6-1)FUC interactsWith BCHE
+NAG-(4-1)NAG interactsWith BCHE
+MIP interactsWith BCHE
+NAG interactsWith BCHE
+NAG interactsWith BCHE
+EFS interactsWith BCHE
+NAG-(6-1)FUC interactsWith BCHE
+DEP interactsWith BCHE
+Zn2+ interactsWith BIRC5
+AEJ interactsWith ESR1
+AEJ interactsWith ESR1
+AEJ interactsWith ESR1
+AEJ interactsWith ESR1
+1XSL_N pd POLL
+1XSL_O pd POLL
+1XSN_T pd POLL
+1XSN_P pd POLL
+1XSN_D pd POLL
+Mg2+ interactsWith POLL
+D3T interactsWith POLL
+1XSP_T pd POLL
+1XSP_P pd POLL
+PPV interactsWith POLL
+NAG interactsWith FSHB
+NAG interactsWith CGA
+NAG interactsWith FSHB
+NAG interactsWith FSHB
+NAG-(4-1)NAG interactsWith FSHR
+NAG-(4-1)NAG-(4-1)MAN interactsWith FSHR
+Zn2+ interactsWith AIRE
+Zn2+ interactsWith AIRE
+Zn2+ interactsWith UBA2
+ATP interactsWith SAE1
+ATP interactsWith UBA2
+ATP interactsWith SUMO1
+905 interactsWith F7
+ZNH interactsWith Hemoglobin_Alpha_Chain
+ZNH interactsWith Hemoglobin_Alpha_Chain
+staurosporine interactsWith PIM1
+ADN interactsWith PIM1
+GSH interactsWith GSTM1
+GSH interactsWith GSTM1
+GSSG interactsWith GSTM2
+GSSG interactsWith GSTM2
+Tat_Protein pp DPP4
+AFL-(1-6)NAG-(4-1)NAG interactsWith DPP4
+NAG-(4-1)NAG-(4-1)BMA interactsWith DPP4
+NAG-(4-1)NAG interactsWith DPP4
+Nuclear_Receptor_Coactivator_1_Isoform_1 pp RXRA
+Nuclear_Receptor_Coactivator_1_Isoform_1 pp NR1I3
+Nuclear_Receptor_Coactivator_1_Isoform_1 pp RXRA
+Nuclear_Receptor_Coactivator_1_Isoform_1 pp NR1I3
+5beta-Pregnan-_3,20-dione interactsWith NR1I3
+F15 interactsWith RXRA
+Nuclear_Receptor_Coactivator_1_Isoform_1 pp RXRA
+Nuclear_Receptor_Coactivator_1_Isoform_1 pp NR1I3
+Nuclear_Receptor_Coactivator_1_Isoform_1 pp RXRA
+Nuclear_Receptor_Coactivator_1_Isoform_1 pp NR1I3
+CID interactsWith NR1I3
+Zn2+ interactsWith RFFL
+Zn2+ interactsWith RFFL
+GDB interactsWith GSTM1
+GDB interactsWith GSTM1
+heme interactsWith HBA2
+CHK interactsWith HBA2
+Mg2+ interactsWith BAT1
+ADP interactsWith BAT1
+heme interactsWith HBB
+Triiodothyronine interactsWith THRB
+L-Thyroxine interactsWith THRB
+442 interactsWith THRB
+IMH interactsWith NP
+OHH interactsWith CMA1
+OHH interactsWith CTSG
+Envelope_Polyprotein_Gp160 pp Fab_4e10
+Envelope_Polyprotein_Gp160 pp Fab_4e10
+397 interactsWith ESR2
+Mg2+ interactsWith FEN1
+Mg2+ interactsWith FEN1
+Mg2+ interactsWith FEN1
+Mg2+ interactsWith FEN1
+Cu2+ interactsWith AOC3
+Ca2+ interactsWith AOC3
+NAG-(4-1)NAG interactsWith AOC3
+NAG interactsWith AOC3
+Ca2+ interactsWith AOC3
+Zn2+ interactsWith Transcription_Factor_Sp1
+dTTP interactsWith TK1
+Zn2+ interactsWith TK1
+DTU interactsWith TK1
+DTU interactsWith TK1
+3IP interactsWith MAPK14
+L10 interactsWith MAPK14
+L11 interactsWith MAPK14
+L12 interactsWith MAPK14
+IPH interactsWith Insulin_B-Chain
+IPH interactsWith Insulin_B-Chain
+IPH interactsWith Insulin_B-Chain
+Mn2+ interactsWith PPP5C
+Mn2+ interactsWith PPP5C
+RIG interactsWith CHIT1
+RAG interactsWith CHIT1
+CoA interactsWith ACAT2
+697 interactsWith ESR2
+697 interactsWith ESR2
+244 interactsWith ESR2
+244 interactsWith ESR2
+041 interactsWith ESR2
+041 interactsWith ESR2
+244 interactsWith ESR1
+GEN interactsWith ESR2
+GEN interactsWith ESR1
+Ca2+ interactsWith MAN1B1
+SMD interactsWith MAN1B1
+BU1 interactsWith MAN1B1
+FSE interactsWith CDK4
+AMP-PNP interactsWith HSPA1B
+DEE interactsWith PDE4D
+3DE interactsWith PDE4D
+4DE interactsWith PDE4D
+4DE interactsWith PDE4D
+5DE interactsWith PDE4D
+6DE interactsWith PDE4B
+7DE interactsWith PDE4B
+7DE interactsWith PDE4B
+7DE interactsWith PDE4D
+NAG-(1-4)NAG-(6-1)FUC interactsWith SUMF2
+NAG-(4-1)NAG interactsWith SUMF2
+Ca2+ interactsWith SUMF2
+Ca2+ interactsWith SUMF2
+Ca2+ interactsWith CALM2
+Ca2+ interactsWith CALM2
+Ca2+ interactsWith CALM2
+Ca2+ interactsWith CALM2
+TBU interactsWith CALM2
+CT7 interactsWith CDK2
+CT9 interactsWith CDK2
+NAG interactsWith HGFAC
+4BC interactsWith HSPCA
+43P interactsWith HSPCA
+T-Cell_Receptor_Cd3_Zeta_Itam-1 pp PTPRC
+Polyoma_Middle_T_Antigen pp PTPRC
+NAG interactsWith CD28
+NAG interactsWith CD28
+NAG interactsWith CD28
+AMP-PNP interactsWith CSNK2A1
+1YNW_C pd VDR
+1YNW_C pd RXRA
+1YNW_D pd RXRA
+1YNW_D pd VDR
+Zn2+ interactsWith RXRA
+Zn2+ interactsWith RXRA
+RIS interactsWith FDPS
+EPH interactsWith NR5A2
+EPH interactsWith NR5A2
+EPH interactsWith NR5A2
+Sythetic_Optimal_Phosphopeptide_(Mode-1) pp SFN
+Sythetic_Optimal_Phosphopeptide_(Mode-1) pp SFN
+Ca2+ interactsWith SFN
+ATP interactsWith PDPK1
+Peptide_Antagonist pp ESR1
+Peptide_Antagonist pp ESR1
+OHT interactsWith ESR1
+farnesol interactsWith MAOB
+ISN interactsWith MAOB
+NDP interactsWith Tat-Interacting_Protein_Tip30
+PE8 interactsWith Tat-Interacting_Protein_Tip30
+GEN interactsWith ESR2
+FRI interactsWith Interleukin-2
+FRI interactsWith Interleukin-2
+Neuropeptide_Y pp DPP4
+Rifampicin interactsWith NR1I2
+NAG interactsWith ICAM3
+NAG interactsWith ICAM3
+Mg2+ interactsWith ITGAL
+Hirudin_Iiia pp F2
+81A interactsWith F2
+14A interactsWith F2
+FME interactsWith CLPP
+FME interactsWith CLPP
+CRS interactsWith Insulin
+UZ9 interactsWith Insulin
+Zn2+ interactsWith Creb_Binding_Protein
+Zn2+ interactsWith Creb_Binding_Protein
+Zn2+ interactsWith Creb_Binding_Protein
+Zn2+ interactsWith Creb_Binding_Protein
+Zn2+ interactsWith Creb_Binding_Protein
+CNQ interactsWith PARP1
+CNQ interactsWith PARP1
+1WTB_B pd HNRPD
+1X0F_B pd HNRPD
+Cl- interactsWith PAPSS1
+fluorescein interactsWith 4m5.3_Anti-Fluorescein_Single_Chain_Antibody_Fragment
+MH2 interactsWith SOD2
+M7G interactsWith DCPS
+M7G interactsWith DCPS
+G7M interactsWith DCPS
+G7M interactsWith DCPS
+Om03-4 pp BACE1
+Peptidic_Inhibitor pp BACE1
+Mg2+ interactsWith RHEB
+GDP interactsWith RHEB
+GNP interactsWith RHEB
+GTP interactsWith RHEB
+331 interactsWith PPARD
+B7G interactsWith PPARD
+Cu2+ interactsWith Copper-Transporting_Atpase_1
+Histone_2a_Peptide pp HLA-G
+NBL interactsWith CTSK
+SFA interactsWith PPIA
+SFA interactsWith PPIA
+PFD interactsWith MMP13
+1YQK_B pd OGG1
+1YQK_C pd OGG1
+1YQM_B pd OGG1
+1YQL_C pd OGG1
+1YQM_C pd OGG1
+1YQR_C pd OGG1
+13-Mer_Fragment_Of_Sh2_And_Ph_Domain-Containing_Adapter_Protein_Aps pp CBL
+Mg2+ interactsWith CBL
+Adenine interactsWith PECR
+Epstein-Barr_Nuclear_Antigen-1 pp USP7
+Na+ interactsWith USP7
+GDP interactsWith ARL8
+MBN interactsWith Hemoglobin_Alpha_Chain
+MBN interactsWith Hemoglobin_Alpha_Chain
+Acetyl-CoA interactsWith GCN5L2
+GDP interactsWith ARL5
+NADP+ interactsWith SPR
+BRY interactsWith CDK2
+RYU interactsWith CDK2
+PM2 interactsWith TPSAB1
+PM2 interactsWith TPSAB1
+MPY interactsWith STK6
+AFL-(1-6)NAG-(4-1)NAG-(4-1)MAN-(6-1)MAN-(2-1)NDG-(4-1)GLA-(4,3-1)MAN-(2-1)NAG interactsWith Ig_Gamma-1_Chain_C_Region
+AFL-(1-6)NAG-(4-1)NAG-(4-1)BMA-(6-1)MAN-(2-1)NAG-(4-1)GLA-(4,3-1)MAN-(2-1)NAG interactsWith Ig_Gamma-1_Chain_C_Region
+Zn2+ interactsWith 4ZNF
+GAL-(1-4)NAG interactsWith LGALS3
+BEK interactsWith LGALS3
+NAG interactsWith AOC3
+Co_(2+) interactsWith NMT1
+1SC7_C pd TOP1
+M38 interactsWith TOP1
+SA3 interactsWith TOP1
+997 interactsWith BIRC4
+Epitope_Of_Melanocyte_Protein_Pmel_17 pp Hla_Class_I_Histocompatibility_Antigen,_A-2_Alpha_Chain
+Epitope_Of_Melanocyte_Protein_Pmel_17 pp Hla_Class_I_Histocompatibility_Antigen,_A-2_Alpha_Chain
+Synthetic_Peptide pp F2
+AB3 interactsWith CBR1
+AB3 interactsWith CBR1
+NDP interactsWith CBR1
+PE5 interactsWith CBR1
+P33 interactsWith CBR1
+DTF interactsWith GRB2
+Ca2+ interactsWith CALM2
+288 interactsWith PYGM
+288 interactsWith PYGM
+Ca2+ interactsWith CLEC4M
+Ebna-3_Nuclear_Protein pp Hla_Class_I_Histocompatibility_Antigen,_B-15_Alpha_Chain
+Urea interactsWith Hla_Class_I_Histocompatibility_Antigen,_B-15_Alpha_Chain
+Ubiquitin-Conjugating_Enzyme_E2_E1 pp Hla_Class_I_Histocompatibility_Antigen,_B-15_Alpha_Chain
+Urea interactsWith B2M
+Urea interactsWith Hla_Class_I_Histocompatibility_Antigen,_B-15_Alpha_Chain
+GSH interactsWith CIB1
+Protein_Associated_To_Tight_Junctions pp Maguk_P55_Subfamily_Member_5
+inositol interactsWith GBA
+Mbp_Peptide pp HLA-DRA
+Mbp_Peptide pp Hla_Class_Ii_Histocompatibility_Antigen,_Dr_Beta_Chain
+6NP interactsWith MAPK14
+L47 interactsWith KIF11
+Formin pp Formin-Binding_Protein_3
+IMD interactsWith PIM1
+AMP-PNP interactsWith PIM1
+AMP interactsWith PIM1
+AMP interactsWith PIM1
+LI6 interactsWith PIM1
+LI7 interactsWith PIM1
+Cetuximab_Fab_Light_Chain pp EGFR
+Cetuximab_Fab_Heavy_Chain pp EGFR
+NAG-(4-1)NAG-(4-1)MAN-(6-1)MAN-(6-1)MAN-(2-1)MAN-(3,3-1)MAN-(3-1)MAN-(4,3-1)MAN interactsWith EGFR
+NAG-(4-1)NAG interactsWith EGFR
+NAG interactsWith EGFR
+NAG-(4-1)NAG interactsWith EGFR
+NAG interactsWith EGFR
+NAG-(4-1)NAG interactsWith EGFR
+1YZ8_B pd PITX3
+1YZ8_A pd PITX3
+DBQ interactsWith CLK1
+LI8 interactsWith PDPK1
+Zn2+ interactsWith GTF2H2
+Zn2+ interactsWith GTF2H2
+NAG interactsWith FAP
+NAG-(4-1)NAG interactsWith FAP
+NAG-(3-1)NAG interactsWith FAP
+NAG interactsWith FAP
+NAG interactsWith FAP
+NAG interactsWith FAP
+NAG interactsWith FAP
+Mg2+ interactsWith F7
+PY3 interactsWith F7
+ADP interactsWith APAF1
+Zn2+ interactsWith UHRF2
+Zn2+ interactsWith UHRF2
+Mg2+ interactsWith ARF4
+GDP interactsWith ARF4
+Zn2+ interactsWith AK1
+Zn2+ interactsWith AK1
+AP5 interactsWith AK1
+Ace-Lys-Gln-Leu-Arg-Chloromethylketone_With_Chloromethylketone_Replaced_By_A_Methylene_Group pp HPN
+NAG-(4-1)NAG interactsWith FOLH1
+NAG-(4-1)NAG interactsWith FOLH1
+NAG-(4-1)NAG interactsWith FOLH1
+NAG-(4-1)NAG interactsWith FOLH1
+NAG-(4-1)NAG interactsWith FOLH1
+NAG interactsWith FOLH1
+NAG interactsWith FOLH1
+NAG interactsWith FOLH1
+Zn2+ interactsWith FOLH1
+Zn2+ interactsWith FOLH1
+198 interactsWith AR
+NAD+ interactsWith HSD17B4
+Na+ interactsWith UBE2S
+SAM interactsWith SRM
+PAP interactsWith SULT1C1
+GDP interactsWith RAB4A
+GNP interactsWith RAB4A
+Mg2+ interactsWith RAB4A
+Mono-Adp-Ribosyltransferase_C3 pp RALA
+GDP interactsWith RALA
+Mg2+ interactsWith RALA
+537 interactsWith MAPK8
+MAK interactsWith RNH1
+NAG interactsWith CPA4
+L-Valine interactsWith CPA4
+Zn2+ interactsWith CPA4
+Peptide_Inhibitor pp F2
+ALC-PRO-MMO interactsWith F2
+GFB-204 interactsWith VEGF
+GFB-204 interactsWith PDGF
+myristate interactsWith c-Src
+NS3 pp PKA
+NS3 pp MBP
+NS3 pp Protamine
+NS3 pp H4
+NS3 pp H2B
+1R-Chl_polyamide interactsWith H4c
+1R_polyamide interactsWith H4c
+vammin pp KDR
+NS3 pp p53
+VEGF-E_NZ2 pp VEGFR-2
+VEGF-E_NZ7 pp VEGFR-2
+NS3 pp H2B
+NS3 pp PKA
+ILY pp CD59
+Vpr pp p300
+Vpr pp TFIIB
+Vpr pp GR-alpha
+IP7 interactsWith TCOF1
+Vpr pp NUPL1
+Vpr pp NUP54
+SV40_large_T_antigen interactsWith Unknown
+Vpr pp NUP153
+MA interactsWith Unknown
+Vif pp Sp140
+Rev pp CK2
+Rev pp MAP_kinase_p42
+Rev pp CDC2
+NS5A pp AHNAK
+NS5A pp SFRP4
+NS5A pp NDRG1
+NS5A pp MGP
+NS5A pp CRABP-1
+NS5A pp FTH1
+NS5A pp Translokin
+NS5A pp MGC2574
+NS5A pp TACSTD2
+NS5A pp PI4K
+NS5A pp PTMA
+NS5A pp CENT-delta-2
+NS5A pp C9_ORF6
+Tax pp IKK-gamma
+Tax pp Int6
+EIAV_p9 pp AIP1
+HIV-1_p6 pp AIP1
+Vif pp Triad3
+Vif pp SAT
+MA pp hPAK65
+Vpr pp LysRS
+NS2 pp CIDE-B
+Rev pp PTMA
+H5R pp hnRNPA2
+Rex pp PTMA
+Matrix pp Rae1
+Matrix pp Nup98
+Gag pp BANF1
+Matrix pp BANF1
+E1A pp CtBP
+MA pp K-alpha
+Vpr pp K-alpha
+TAg pp K-alpha
+p17 pp calmodulin
+Gag pp calmodulin
+A2L pp hnRNPA2
+A2L pp RBM3
+Gag pp ABCE1
+Tat pp EEF1D
+Tat-1 pp GLI-2
+Tat pp cyclin_T1
+Tat pp MDM2
+Tat pp MDM2
+RTA pp IRF7
+LANA pp Sin3A
+LANA pp SAP30
+LANA pp CIR
+CIR pp SAP30
+Wortmannin interactsWith PRKDC
+18E6 pd p21
+11E6-p53-p300_complex interactsWith p21
+Unknown interactsWith E6AP
+Unknown interactsWith p300
+Unknown interactsWith p53
+16E6 interactsWith Unknown
+18E6 interactsWith unknown
+11E6 interactsWith unknown
+Wortmannin interactsWith PIK3CG
+CKII interactsWith PC4
+Tat pp PC4
+delta-Ag pp DIP
+Wortmannin interactsWith PLK1
+Unknown interactsWith E6AP
+Unknown interactsWith p300
+Unknown interactsWith p53
+Unknown interactsWith p300
+Unknown interactsWith p53
+16E6 interactsWith Unknown
+Unknown interactsWith E6AP
+Unknown interactsWith p300
+Unknown interactsWith p53
+Tat pp LRP1
+Tat pp SART3
+Tat pp Sp1
+Tax pp Sp1
+Tat interactsWith NF-kappa-B
+Tat pp Oct
+Tat interactsWith Sp1
+Tat pp Sp1
+Tat interactsWith DNA-PK
+Rev pp PRKCA
+Tat pp TCF-4
+Vpr pp NUPL2
+Tat pp GRIP1
+Tat pp Cyclin_T1
+Tat pp SRC1a
+Unknown interactsWith ABIN2
+Unknown interactsWith PAPOLA
+Unknown interactsWith RelA
+Unknown interactsWith Cot/Tpl2
+Unknown interactsWith PAPOLA
+Unknown interactsWith RelA
+Unknown interactsWith ABIN2
+Unknown interactsWith NF-kB1/p105
+Unknown interactsWith NF-kB2/p100
+Unknown interactsWith NF-kB2/p52
+Unknown interactsWith RelA
+Unknown interactsWith TRAF2
+Unknown interactsWith TRAF3
+Unknown interactsWith c-Rel
+Unknown interactsWith IkBbeta
+Unknown interactsWith IKBKAP
+Unknown interactsWith IKKalpha
+Unknown interactsWith IKKbeta
+Unknown interactsWith IKKgamma
+Unknown interactsWith MCM5
+Unknown interactsWith MCM7
+Unknown interactsWith NF-kB2/p100
+Unknown interactsWith RelA
+Unknown interactsWith beta-TrCP
+Unknown interactsWith c-Rel
+Unknown interactsWith CUL1
+Unknown interactsWith IkBbeta
+Unknown interactsWith IKBKAP
+Unknown interactsWith IKKalpha
+Unknown interactsWith IKKbeta
+Unknown interactsWith IKKgamma
+Unknown interactsWith NF-kB2/p100
+Unknown interactsWith RelA
+Unknown interactsWith SKP1A
+Unknown interactsWith ASE_1
+Unknown interactsWith c-Rel
+Unknown interactsWith IKKalpha
+Unknown interactsWith IKKbeta
+Unknown interactsWith IKKgamma
+Unknown interactsWith IQGAP2
+Unknown interactsWith KPNA2
+Unknown interactsWith LRPPRC
+Unknown interactsWith MCC1
+Unknown interactsWith MTIF2
+Unknown interactsWith NF-kB1/p105
+Unknown interactsWith NF-kB2/p100
+Unknown interactsWith PAF53
+Unknown interactsWith PDCD2
+Unknown interactsWith POLR1A
+Unknown interactsWith POLR1B
+Unknown interactsWith POLR1D
+Unknown interactsWith POLR2H
+Unknown interactsWith POLR2L
+Unknown interactsWith RelA
+Unknown interactsWith RPA5
+Unknown interactsWith ASE_1
+Unknown interactsWith beta-TrCP
+Unknown interactsWith c-Rel
+Unknown interactsWith CUL1
+Unknown interactsWith IKKalpha
+Unknown interactsWith IKKbeta
+Unknown interactsWith IKKgamma
+Unknown interactsWith IQGAP2
+Unknown interactsWith KPNA2
+Unknown interactsWith LRPPRC
+Unknown interactsWith MCC1
+Unknown interactsWith MTIF2
+Unknown interactsWith NF-kB1/p105
+Unknown interactsWith NF-kB2/p100
+Unknown interactsWith NGAP
+Unknown interactsWith PAF53
+Unknown interactsWith PDCD2
+Unknown interactsWith POLR1A
+Unknown interactsWith POLR1B
+Unknown interactsWith POLR1D
+Unknown interactsWith POLR2H
+Unknown interactsWith POLR2L
+Unknown interactsWith RelA
+Unknown interactsWith RPA5
+Unknown interactsWith SKP1A
+Unknown interactsWith c-Rel
+Unknown interactsWith FLJ20288
+Unknown interactsWith IKKalpha
+Unknown interactsWith KIAA0379
+Unknown interactsWith KIAA0685
+Unknown interactsWith KIAA1115
+Unknown interactsWith NF-kB2/p100
+Unknown interactsWith PPP6c
+Unknown interactsWith RelA
+Unknown interactsWith beta-TrCP
+Unknown interactsWith c-Rel
+Unknown interactsWith CUL1
+Unknown interactsWith FLJ20288
+Unknown interactsWith IKKalpha
+Unknown interactsWith KIAA0379
+Unknown interactsWith KIAA0685
+Unknown interactsWith KIAA1115
+Unknown interactsWith NF-kB2/p100
+Unknown interactsWith PPP6c
+Unknown interactsWith RelA
+Unknown interactsWith SKP1A
+Unknown interactsWith IKKbeta
+Unknown interactsWith CDC37
+Unknown interactsWith FKBP51
+Unknown interactsWith HSP90_alpha
+Unknown interactsWith HSP90_beta
+Unknown interactsWith IKKbeta
+Unknown interactsWith CDC37
+Unknown interactsWith HSP90_alpha
+Unknown interactsWith HSP90_beta
+Unknown interactsWith KIAA1967
+Unknown interactsWith CDC37
+Unknown interactsWith FKBP51
+Unknown interactsWith HSP90_alpha
+Unknown interactsWith HSP90_beta
+Unknown interactsWith CDC37
+Unknown interactsWith FKBP51
+Unknown interactsWith HSP90_alpha
+Unknown interactsWith HSP90_beta
+Unknown interactsWith KTN1
+Unknown interactsWith CDC37
+Unknown interactsWith DIS
+Unknown interactsWith FLJ22677
+Unknown interactsWith HSP90_alpha
+Unknown interactsWith HSP90_beta
+Unknown interactsWith IKKalpha
+Unknown interactsWith IKKbeta
+Unknown interactsWith Taxilin
+Unknown interactsWith TBK1
+Unknown interactsWith CDC37
+Unknown interactsWith FKBP51
+Unknown interactsWith HAN11
+Unknown interactsWith HSP90_alpha
+Unknown interactsWith HSP90_beta
+Unknown interactsWith RPL30
+Unknown interactsWith RPL4
+Unknown interactsWith RPS13
+Unknown interactsWith 14-3-3_zeta
+Unknown interactsWith 14-3-3beta
+Unknown interactsWith 14-3-3epsilon
+Unknown interactsWith 14-3-3eta
+Unknown interactsWith 14-3-3gamma
+Unknown interactsWith 14-3-3tau
+Unknown interactsWith CDC37
+Unknown interactsWith HSP70
+Unknown interactsWith HSP90_alpha
+Unknown interactsWith HSP90_beta
+Unknown interactsWith MARK2
+Unknown interactsWith MEK5b
+Unknown interactsWith PFDN2
+Unknown interactsWith TRAF7
+Unknown interactsWith 14-3-3_zeta
+Unknown interactsWith 14-3-3beta
+Unknown interactsWith 14-3-3epsilon
+Unknown interactsWith 14-3-3eta
+Unknown interactsWith 14-3-3gamma
+Unknown interactsWith 14-3-3tau
+Unknown interactsWith C20orf126
+Unknown interactsWith CDC37
+Unknown interactsWith HSP70
+Unknown interactsWith HSP90_alpha
+Unknown interactsWith HSP90_beta
+Unknown interactsWith MARK2
+Unknown interactsWith MEK5b
+Unknown interactsWith PFDN2
+Unknown interactsWith TRAF7
+Unknown interactsWith ABIN
+Unknown interactsWith ABIN2
+Unknown interactsWith COPB2
+Unknown interactsWith c-Rel
+Unknown interactsWith IkBalpha
+Unknown interactsWith IkBepsilon
+Unknown interactsWith IKKalpha
+Unknown interactsWith IKKgamma
+Unknown interactsWith JLP
+Unknown interactsWith NF-kB2/p100
+Unknown interactsWith RelA
+Unknown interactsWith ABIN2
+Unknown interactsWith c-Rel
+Unknown interactsWith IkBalpha
+Unknown interactsWith IkBbeta
+Unknown interactsWith IkBepsilon
+Unknown interactsWith IKKalpha
+Unknown interactsWith IKKgamma
+Unknown interactsWith NF-kB1/p105
+Unknown interactsWith NF-kB2/p100
+Unknown interactsWith RelA
+Unknown interactsWith RelB
+Unknown interactsWith ABIN2
+Unknown interactsWith c-Rel
+Unknown interactsWith IkBalpha
+Unknown interactsWith IkBbeta
+Unknown interactsWith IkBepsilon
+Unknown interactsWith IKKalpha
+Unknown interactsWith IKKgamma
+Unknown interactsWith KPNA3
+Unknown interactsWith NF-kB1/p105
+Unknown interactsWith NF-kB2/p100
+Unknown interactsWith RelA
+Unknown interactsWith RelB
+Unknown interactsWith c-Rel
+Unknown interactsWith NIK
+Unknown interactsWith RelA
+Unknown interactsWith CDC4
+Unknown interactsWith c-Rel
+Unknown interactsWith KIAA0310
+Unknown interactsWith NIK
+Unknown interactsWith RelA
+Unknown interactsWith USP9
+Unknown interactsWith IKKalpha
+Unknown interactsWith IKKbeta
+Unknown interactsWith IKKgamma
+Unknown interactsWith ABIN2
+Unknown interactsWith Cot/Tpl2
+Unknown interactsWith c-Rel
+Unknown interactsWith DDX3
+Unknown interactsWith GLG1
+Unknown interactsWith GTFII-I
+Unknown interactsWith IkBalpha
+Unknown interactsWith IkBbeta
+Unknown interactsWith IKKalpha
+Unknown interactsWith IKKgamma
+Unknown interactsWith NF-kB1/p105
+Unknown interactsWith NF-kB2/p100
+Unknown interactsWith RelA
+Unknown interactsWith RelB
+Unknown interactsWith RPL30
+Unknown interactsWith RPL6
+Unknown interactsWith RPS13
+Unknown interactsWith ABIN2
+Unknown interactsWith c-Rel
+Unknown interactsWith DDX3
+Unknown interactsWith GLG1
+Unknown interactsWith GTFII-I
+Unknown interactsWith IkBbeta
+Unknown interactsWith IKKalpha
+Unknown interactsWith NF-kB1/p105
+Unknown interactsWith NF-kB2/p100
+Unknown interactsWith RelA
+Unknown interactsWith RelB
+Unknown interactsWith RPL30
+Unknown interactsWith RPL6
+Unknown interactsWith RPS13
+Unknown interactsWith CDC37
+Unknown interactsWith FBL
+Unknown interactsWith HSP90_alpha
+Unknown interactsWith HSP90_beta
+Unknown interactsWith IKKalpha
+Unknown interactsWith IKKbeta
+Unknown interactsWith IKKgamma
+Unknown interactsWith RPL30
+Unknown interactsWith RPL4
+Unknown interactsWith RPL6
+Unknown interactsWith RPL8
+Unknown interactsWith RPS11
+Unknown interactsWith RPS13
+Unknown interactsWith ABIN2
+Unknown interactsWith IKKalpha
+Unknown interactsWith IQGAP2
+Unknown interactsWith nAKAP95
+Unknown interactsWith BAF53a
+Unknown interactsWith HDAC6
+Unknown interactsWith KPNA2
+Unknown interactsWith KPNA6
+Unknown interactsWith NF-kB1/p105
+Unknown interactsWith NF-kB2/p100
+Unknown interactsWith RelA
+Unknown interactsWith REQ
+Unknown interactsWith SMARCA4
+Unknown interactsWith SMARCC1
+Unknown interactsWith SMARCC2
+Unknown interactsWith SMARCE1
+Unknown interactsWith SNF5
+Unknown interactsWith USP11
+Unknown interactsWith BAF53a
+Unknown interactsWith BCL7A
+Unknown interactsWith HDAC6
+Unknown interactsWith KPNA2
+Unknown interactsWith KPNA6
+Unknown interactsWith NF-kB1/p105
+Unknown interactsWith NF-kB2/p100
+Unknown interactsWith RelA
+Unknown interactsWith REQ
+Unknown interactsWith SMARCA4
+Unknown interactsWith SMARCC1
+Unknown interactsWith SMARCC2
+Unknown interactsWith SMARCE1
+Unknown interactsWith SNF5
+Unknown interactsWith USP11
+Unknown interactsWith TRAF2
+Unknown interactsWith CS
+Unknown interactsWith TAB1
+Unknown interactsWith CDC37
+Unknown interactsWith FKBP51
+Unknown interactsWith HSP90_alpha
+Unknown interactsWith HSP90_beta
+Unknown interactsWith TAB1
+Unknown interactsWith TAB2
+Unknown interactsWith TAB2paralog
+Unknown interactsWith CDC37
+Unknown interactsWith HSP90_alpha
+Unknown interactsWith HSP90_beta
+Unknown interactsWith I-TRAF
+Unknown interactsWith TBKBP1
+Unknown interactsWith TBKBP2
+Unknown interactsWith TRAF2
+Unknown interactsWith FANCD2
+Unknown interactsWith FANCD2
+Unknown interactsWith TNF
+Unknown interactsWith DJ1057D18.1
+Unknown interactsWith FANCD2
+Unknown interactsWith TRAF2
+Unknown interactsWith DJ1057D18.1
+Unknown interactsWith FANCD2
+Unknown interactsWith TNF
+Unknown interactsWith TRAF2
+Unknown interactsWith TRAF2
+Unknown interactsWith TRAF2
+Unknown interactsWith Hypo1
+Unknown interactsWith KCNQ1
+Unknown interactsWith PSD6
+Unknown interactsWith PSMB5
+Unknown interactsWith PSMC1
+Unknown interactsWith PSMC2
+Unknown interactsWith PSMC3
+Unknown interactsWith PSMD1
+Unknown interactsWith PSMD12
+Unknown interactsWith PSMD13
+Unknown interactsWith PSMD3
+Unknown interactsWith PSMD7
+Tat pp CD10/Nep
+IN pp LEDGF
+gag_MA pp Fes
+gag_MA pp Hck
+Integrase pp LEDGF/p75
+Matrix pp EED
+Rev pp Nup214
+Tat pp granulin
+Tat interactsWith P-TEFb
+Unknown interactsWith ACTG1
+Unknown interactsWith CBR1
+Unknown interactsWith EGFR
+Unknown interactsWith SHC
+Unknown interactsWith PLEC1
+Unknown interactsWith MYH9
+Unknown interactsWith KRT8
+Unknown interactsWith KRT17
+Unknown interactsWith TUBB2
+Unknown interactsWith KRT7
+Unknown interactsWith CORO1C
+Unknown interactsWith DBN1
+Unknown interactsWith VIM
+Unknown interactsWith GSTM3
+Unknown interactsWith KRT18
+Unknown interactsWith ACTR3
+Unknown interactsWith ATP5A1
+Unknown interactsWith EPPK1
+Unknown interactsWith LMO7
+Unknown interactsWith SPTAN1
+Unknown interactsWith EEF1G
+Unknown interactsWith MRLC2
+Unknown interactsWith EPLIN
+Unknown interactsWith MYL9
+Unknown interactsWith GSN
+Unknown interactsWith ACTN4
+Unknown interactsWith SVIL
+Unknown interactsWith FLII
+Unknown interactsWith GSTM1
+Unknown interactsWith PTPN11
+Unknown interactsWith M-RIP
+Unknown interactsWith MYO1C
+Unknown interactsWith IQGAP1
+Unknown interactsWith FLNA
+Unknown interactsWith SPTBN1
+Unknown interactsWith MYO18A
+Unknown interactsWith HNRPH1
+Unknown interactsWith ABLIM
+Unknown interactsWith ACTG2
+Unknown interactsWith ACTR2
+Unknown interactsWith MYL6
+Unknown interactsWith FAM55B
+Unknown interactsWith NEXN
+Unknown interactsWith RACGAP1
+Unknown interactsWith ACTN1
+Unknown interactsWith RAI14
+Unknown interactsWith PPP1R12A
+Unknown interactsWith LUZP1
+Unknown interactsWith HCMOGT-1
+Unknown interactsWith AP2A1
+Unknown interactsWith DST
+Unknown interactsWith MYH10
+Unknown interactsWith PAWR
+Unknown interactsWith TUBA1
+Unknown interactsWith PHGDH
+Unknown interactsWith SLC25A5
+Unknown interactsWith RPS8
+Unknown interactsWith ARPC3
+Unknown interactsWith ARPC4
+Unknown interactsWith Cd59
+Unknown interactsWith RPS13
+Unknown interactsWith HSPA5
+Unknown interactsWith CTTN
+Unknown interactsWith HSPA9B
+Unknown interactsWith HSPA8
+Unknown interactsWith WDR1
+Unknown interactsWith LMNA
+Unknown interactsWith DDX5
+Unknown interactsWith ATAD3A
+Unknown interactsWith PABPC1
+Unknown interactsWith HNRPM
+Unknown interactsWith KIAA0376
+Unknown interactsWith MYO1B
+Unknown interactsWith DHX9
+Unknown interactsWith AP2B1
+Unknown interactsWith HNRPU
+Unknown interactsWith IPO7
+Unknown interactsWith MYO1B
+Unknown interactsWith CBLB
+Unknown interactsWith THRAP3
+Unknown interactsWith DNA-PK-cs
+Unknown interactsWith FLNB
+Unknown interactsWith EEF1A1
+Unknown interactsWith DAPK3
+Unknown interactsWith EIF4A1
+Unknown interactsWith RPL3
+Unknown interactsWith BAT1
+Unknown interactsWith RBBP7
+Unknown interactsWith RPL4
+Unknown interactsWith HADHB
+Unknown interactsWith PRSS11
+Unknown interactsWith CORO1B
+Unknown interactsWith ACTC
+Unknown interactsWith PPP1CB
+Unknown interactsWith TPM1
+Unknown interactsWith ARPC2
+Unknown interactsWith RPS3
+Unknown interactsWith RPS3A
+Unknown interactsWith CAPZB
+Unknown interactsWith Glutathione_S-Transferase
+Unknown interactsWith RPS9
+Unknown interactsWith RPL10
+Unknown interactsWith RPL26
+Unknown interactsWith HIST1H2BH
+Unknown interactsWith CFL2
+Unknown interactsWith RPS16
+Unknown interactsWith RPS15A
+Unknown interactsWith RPS11
+Unknown interactsWith SMU1
+Unknown interactsWith HSPD1
+Unknown interactsWith DDX3
+Unknown interactsWith ANXA6
+Unknown interactsWith KIAA0843
+Unknown interactsWith TD-60
+Unknown interactsWith NCL
+Unknown interactsWith PPP1R9B
+Unknown interactsWith EEF2
+Unknown interactsWith HSPCB
+Unknown interactsWith ILF3
+Unknown interactsWith BCLAF1
+Unknown interactsWith VAV2
+Unknown interactsWith OGDH
+Unknown interactsWith SMARCA5
+Unknown interactsWith MATR3
+Unknown interactsWith ITPR3
+Unknown interactsWith MYH14
+Unknown interactsWith FSCN1
+Unknown interactsWith TMOD3
+Unknown interactsWith TUBB5
+Unknown interactsWith TUBB3
+Unknown interactsWith GRWD1
+Unknown interactsWith DLST
+Unknown interactsWith CAMK2D
+Unknown interactsWith ANXA2
+Unknown interactsWith TPM2
+Unknown interactsWith HNRPA1
+Unknown interactsWith RPL7
+Unknown interactsWith HSPB1
+Unknown interactsWith RPL18
+Unknown interactsWith CFL1
+Unknown interactsWith HIST2H4
+Unknown interactsWith PPIA
+Unknown interactsWith RPL12
+Unknown interactsWith RPL27
+Unknown interactsWith RPS14
+Unknown interactsWith RPLP2
+Unknown interactsWith HIST1H3A
+Unknown interactsWith HNRPH2
+Unknown interactsWith TAOK2
+Unknown interactsWith LUC7L2
+Unknown interactsWith SAFB2
+Unknown interactsWith S100A6
+Unknown interactsWith PLS3
+Unknown interactsWith SHMT2
+Unknown interactsWith PDCD6
+Unknown interactsWith PPP3CA
+Unknown interactsWith translation_initiation_factor_eIF-4A2_homolog
+Unknown interactsWith SYNPO
+Unknown interactsWith RUVBL2
+Unknown interactsWith ARPC1A
+Unknown interactsWith DNAJA2
+Unknown interactsWith ARPC5
+Unknown interactsWith HNRPF
+Unknown interactsWith Sos1
+Unknown interactsWith SNRPD2
+Unknown interactsWith GMFB
+Unknown interactsWith DDX6
+Unknown interactsWith UGDH
+Unknown interactsWith RPS28
+Unknown interactsWith RPS25
+Unknown interactsWith RPS23
+Unknown interactsWith RPS20
+Unknown interactsWith RPL30
+Unknown interactsWith RPL24
+Unknown interactsWith DNCL1
+Unknown interactsWith SLC25A3
+Unknown interactsWith PRDX1
+Unknown interactsWith HIST2H2AA
+Unknown interactsWith GRB2
+Unknown interactsWith G22P1
+Unknown interactsWith DUT
+Unknown interactsWith RPL23A
+Unknown interactsWith VAV3
+Unknown interactsWith MYO1A
+Unknown interactsWith ribosomal_protein_L23
+Unknown interactsWith Human_Mitochondrial_Single-Stranded_DNA_Binding_Protein
+Unknown interactsWith PCMT1
+Unknown interactsWith TUFM
+Unknown interactsWith dystonin_isoform_1__(fragment)
+Unknown interactsWith MYO3B
+Unknown interactsWith SERPINH1
+Unknown interactsWith AP2M1
+Unknown interactsWith RPL21
+Unknown interactsWith C20orf160
+Unknown interactsWith RPL31
+Unknown interactsWith NPM1
+Unknown interactsWith RPL36
+Unknown interactsWith KIAA0864
+Unknown interactsWith FUSIP1
+Unknown interactsWith PTBP1
+Unknown interactsWith HNRPA1
+Unknown interactsWith RPS5
+Unknown interactsWith C11orf23
+Unknown interactsWith MYO6
+Unknown interactsWith DLD
+Unknown interactsWith RPL35A
+Unknown interactsWith NONO
+Unknown interactsWith IMPDH2
+Unknown interactsWith UACA
+Unknown interactsWith PDLIM7
+Unknown interactsWith RPL18A
+Unknown interactsWith AP2S1
+Unknown interactsWith ribosomal_protein_S26;_cytosolic
+Unknown interactsWith Alu_RNA-binding_protein
+Gag pp KARS
+CA pp CypA
+Vpr pp CypA
+rhodocetin interactsWith alpha-2-beta-1_integrin
+Tat pp RBL2
+Vpr pp VprBP
+Vpr pp VprBP
+Unknown interactsWith EGFR
+Unknown interactsWith SHC
+Unknown interactsWith PLEC1
+Unknown interactsWith KRT8
+Unknown interactsWith KRT17
+Unknown interactsWith KRT7
+Unknown interactsWith KRT18
+Unknown interactsWith EPPK1
+Unknown interactsWith PTPN11
+Unknown interactsWith IQGAP1
+Unknown interactsWith ACTG2
+Unknown interactsWith RACGAP1
+Unknown interactsWith AP2A1
+Unknown interactsWith Cd59
+Unknown interactsWith AP2B1
+Unknown interactsWith CBLB
+Unknown interactsWith SMU1
+Unknown interactsWith VAV2
+Unknown interactsWith HIST1H3A
+Unknown interactsWith Sos1
+Unknown interactsWith SNRPD2
+Unknown interactsWith GRB2
+Unknown interactsWith VAV3
+Unknown interactsWith AP2M1
+Unknown interactsWith KIAA0864
+Unknown interactsWith AP2S1
+Tat-1 pp B23
+Tat-2 pp B23
+Tat pp pRb2/p130
+SifA pp SKIP
+Tat pp THBS1
+Tax pp MBD2
+Rev pp KPNB1
+tax pp CDK4
+Rev pp C1QBP
+Rev pp KPNA2
+tax pp CDK6
+UL56 pp KIF1A
+Gag pp AP-3_delta
+Gag pp TSG101
+MA pp AP-3_delta
+E2 interactsWith GPR30
+Tat pp CDK9
+Rev pp KPNB1
+Rev pp XPO1
+E1A pp CDKN1B
+Ca2+ interactsWith ANXA5
+Ca2+ interactsWith ANXA5
+Ca2+ interactsWith ANXA5
+Ca2+ interactsWith ANXA5
+Ca2+ interactsWith ANXA5
+Ca2+ interactsWith ANXA5
+Zn2+ interactsWith CA1
+acetazolamide interactsWith CA13
+Zn2+ interactsWith HIVEP1
+Zn2+ interactsWith HIVEP1
+FMS interactsWith CA13
+MZM interactsWith CA13
+Zn2+ interactsWith CA2
+RE9 interactsWith CRABP1
+Zn2+ interactsWith MMP1
+Zn2+ interactsWith MMP1
+Ca2+ interactsWith MMP1
+Ca2+ interactsWith MMP1
+Ca2+ interactsWith MMP1
+ETS interactsWith CA2
+PTS interactsWith CA2
+MTS interactsWith CA2
+Zn2+ interactsWith CA2
+TRI interactsWith CA13
+Trifluoperazine interactsWith TNNC1
+Zn2+ interactsWith CA2
+Zn2+ interactsWith CA2
+Zn2+ interactsWith CA2
+Benzamidine interactsWith F2
+MIT interactsWith F2
+MID interactsWith F2
+Ca2+ interactsWith SELL
+Ca2+ interactsWith SELL
+Ca2+ interactsWith SELL
+MAN interactsWith 1FC2_D
+Fe3+ interactsWith FTMT
+Rapamycin interactsWith FKBP1B
+FK506 interactsWith FKBP1A
+SB3 interactsWith FKBP1B
+SBX interactsWith FKBP1B
+SB1 interactsWith FKBP1A
+SB1 interactsWith FKBP1A
+FAD interactsWith 1GRH
+NAD+ interactsWith 1GRB
+GSH interactsWith 1GRE
+GSH interactsWith 1GRE
+Acetamide interactsWith 1GRF
+CEC interactsWith 1GRG
+GSB interactsWith GSTA1
+GSB interactsWith GSTA1
+NAD+ interactsWith QDPR
+Zn2+ interactsWith ADH1C
+Zn2+ interactsWith ADH1C
+NAD+ interactsWith ADH1C
+CXL interactsWith ADH1C
+CXL interactsWith ADH1C
+NAD+ interactsWith ADH1B
+PYZ interactsWith ADH1B
+NAD+ interactsWith ADH1B
+HAP interactsWith MMP3
+Lactose interactsWith LGALS2
+Ca2+ interactsWith LALBA
+Zn2+ interactsWith LALBA
+GDB interactsWith GSTM2
+GDB interactsWith GSTM2
+GDB interactsWith GSTM2
+GDB interactsWith GSTM2
+GDB interactsWith GSTM2
+GDB interactsWith GSTM2
+GDB interactsWith GSTM2
+Zn2+ interactsWith 1HRA
+Zn2+ interactsWith 1HRA
+Phosphoglycolate interactsWith TPI1
+Ca2+ interactsWith ANXA5
+IPD interactsWith IMPA1
+LIP interactsWith IMPA1
+Mn2+ interactsWith IMPA1
+Mn2+ interactsWith IMPA1
+Ca2+ interactsWith IMPA1
+Cu2+ interactsWith LTF
+Cu2+ interactsWith LTF
+OXL interactsWith LTF
+BNG interactsWith PNLIP
+Ca2+ interactsWith PNLIP
+PLC interactsWith PNLIP
+Acetaldehyde interactsWith IGLL1
+Acetaldehyde interactsWith IGLL1
+HAP interactsWith MMP8
+Ca2+ interactsWith MPO
+Ca2+ interactsWith MPO
+IP6 interactsWith HBB
+CAG interactsWith HRAS
+Ca2+ interactsWith PLA2G2A
+Ca2+ interactsWith PLA2G2A
+GEL interactsWith PLA2G2A
+MAN interactsWith ELA2
+alpha-D-Glucose interactsWith ELA2
+MAN interactsWith ELA2
+C60 interactsWith REN
+Cu2+ interactsWith CA2
+Mn2+ interactsWith CA13
+Ni2+ interactsWith CA13
+PO3 interactsWith SRC
+Zn2+ interactsWith 1TFI
+Acetaminophen interactsWith 1TYL_D
+Acetaminophen interactsWith 1TYL_C
+Guanine interactsWith NP
+acetazolamide interactsWith CA2
+acetazolamide interactsWith CA2
+acetazolamide interactsWith CA2
+MNC interactsWith HBA2
+MNC interactsWith HBB
+NBN interactsWith HBA2
+NBN interactsWith HBB
+NPN interactsWith HBA2
+NPN interactsWith HBB
+aminocaproic_acid interactsWith 2PK4
+AMS interactsWith CA2
+Ca2+ interactsWith LYZ
+Zn2+ interactsWith 4ZNF
+Zn2+ interactsWith 5ZNF
+Zn2+ interactsWith 7ZNF
+INH interactsWith MMP27
+Zn2+ interactsWith MMP3
+Zn2+ interactsWith MMP27
+GDP interactsWith ARF1
+GDP interactsWith ARF1
+Oleic_Acid interactsWith 1HMS
+monoethanolamine interactsWith 1HMR
+MTX interactsWith DHFR
+MXA interactsWith DHFR
+PO3 interactsWith SRC
+ethacrynate interactsWith GSTA1
+ethacrynate interactsWith GSTA1
+CAG interactsWith HRAS
+CAG interactsWith HRAS
+AGN interactsWith HRAS
+INB interactsWith PLA2G2A
+INB interactsWith PLA2G2A
+Zn2+ interactsWith TP53
+Mn2+ interactsWith ITGAL
+Zn2+ interactsWith ESR2
+Zn2+ interactsWith ESR2
+Zn2+ interactsWith ESR1
+Zn2+ interactsWith ESR1
+A5MP interactsWith FBP1
+EG3 interactsWith CA2
+EG2 interactsWith CA2
+EG1 interactsWith CA2
+Ca2+ interactsWith 1HUP
+Ca2+ interactsWith 1HUP
+Na+ interactsWith LYZ
+Na+ interactsWith LYZ
+GDP interactsWith NME2
+GDP interactsWith NME2
+Zn2+ interactsWith MMP7
+Zn2+ interactsWith MMP7
+Ca2+ interactsWith MMP7
+Ca2+ interactsWith MMP7
+SRS interactsWith MMP20
+RRS interactsWith MMP20
+RSS interactsWith MMP7
+aminocaproic_acid interactsWith PLG
+aminocaproic_acid interactsWith PLG
+RO4 interactsWith MMP3
+Zn2+ interactsWith MMP3
+Ca2+ interactsWith 1SRA
+Ca2+ interactsWith 1SRA
+Acetaldehyde interactsWith LCK
+Ca2+ interactsWith ANXA3
+Ca2+ interactsWith ANXA3
+Ca2+ interactsWith ANXA3
+Ca2+ interactsWith ANXA3
+Ca2+ interactsWith ANXA3
+acetazolamide interactsWith CA2
+FAD interactsWith 1XAN
+HXP interactsWith 1XAN
+HBD interactsWith Human_Insulin
+HBD interactsWith Human_Insulin
+HBD interactsWith Human_Insulin
+IPH interactsWith Insulin
+IPH interactsWith Insulin
+Ca2+ interactsWith MMP10
+Ca2+ interactsWith MMP10
+Rapamycin interactsWith FKBP3
+BAT interactsWith MMP1
+Ca2+ interactsWith Factor_Ix
+Na+ interactsWith MMP10
+HEC interactsWith 1GRH
+MIN interactsWith F2
+Zn2+ interactsWith Retinoic_Acid_Receptor
+Zn2+ interactsWith Retinoic_Acid_Receptor
+Zn2+ interactsWith THRA
+Zn2+ interactsWith THRA
+Ethanolamine interactsWith ANXA3
+aminocaproic_acid interactsWith 1HPK
+Cu2+ interactsWith CP
+Cu2+ interactsWith CP
+Cu2+ interactsWith CP
+Cu2+ interactsWith CP
+Cu2+ interactsWith CP
+Cu2+ interactsWith CP
+Cu2+ interactsWith CP
+Cu2+ interactsWith CP
+NAG-(1-4)NAG-(1-1)GOL interactsWith LYZL2
+GAL-(1-4)NAG-(1-1)GOL interactsWith LYZL2
+17beta-estradiol interactsWith HSD17B1
+17beta-estradiol interactsWith 1FDT
+NADP+ interactsWith 1FDT
+Zn2+ interactsWith 1FAQ
+Zn2+ interactsWith 1FAQ
+ATP interactsWith CDK2
+ATP interactsWith CDK2
+Benzamidine interactsWith PLAT
+GNP interactsWith RAP1A
+Mg2+ interactsWith RAP1A
+Ca2+ interactsWith RAF1
+Mn2+ interactsWith ITGAX
+ATP interactsWith CDK2
+ATP interactsWith CDK2
+Mn2+ interactsWith CDK2
+MNS interactsWith CA2
+SAB interactsWith CA2
+STB interactsWith CA2
+Zn2+ interactsWith YY1
+Zn2+ interactsWith YY1
+Zn2+ interactsWith YY1
+Zn2+ interactsWith YY1
+NAG interactsWith AGA
+NAG interactsWith AGA
+NAG-(4-1)NAG-(4-1)MAN interactsWith AGA
+Ca2+ interactsWith 1EMN
+Ca2+ interactsWith 1EMN
+Zn2+ interactsWith MMP27
+Zn2+ interactsWith MMP27
+Ca2+ interactsWith MMP27
+Ca2+ interactsWith MMP27
+INH interactsWith MMP27
+SCC interactsWith SERPINA1
+PPM interactsWith LCK
+BM2 interactsWith F2
+BM9 interactsWith F2
+dCTP interactsWith POLB
+Zn2+ interactsWith POLB
+DCT interactsWith POLB
+dATP interactsWith POLB
+Mn2+ interactsWith POLB
+DCT interactsWith POLB
+dTTP interactsWith POLB
+ATP interactsWith POLB
+ATP interactsWith POLB
+AZT interactsWith POLB
+DAD interactsWith POLB
+STP interactsWith POLB
+dATP interactsWith POLB
+dATP interactsWith POLB
+K+ interactsWith POLB
+K+ interactsWith POLB
+Mn2+ interactsWith POLB
+IN2 interactsWith F2
+IN2 interactsWith F2
+DI2 interactsWith F2
+DI3 interactsWith F2
+DI4 interactsWith F2
+DI5 interactsWith F2
+DP7 interactsWith F2
+NAG interactsWith 1GYA
+NAG interactsWith 1GYA
+MAN-(1-2)MAN-(1-3)MAN-(6-1)MAN-(6-1)MAN-(2-1)MAN-(4,3-1)MAN interactsWith 1GYA
+OXL interactsWith LTF
+P28 interactsWith TTR
+P28 interactsWith TTR
+L-Thyroxine interactsWith TTR
+L-Thyroxine interactsWith TTR
+Zn2+ interactsWith 1SP2
+Zn2+ interactsWith 1SP1
+NAG-(4-1)NAG interactsWith PPGB
+NAG interactsWith PPGB
+Zn2+ interactsWith 1BOR
+Zn2+ interactsWith 1BOR
+AMP-PNP interactsWith HCK
+Ca2+ interactsWith HCK
+Ca2+ interactsWith HCK
+IPH interactsWith Fatty_Acid_Acylated_Insulin
+MYR interactsWith Fatty_Acid_Acylated_Insulin
+MYR interactsWith Fatty_Acid_Acylated_Insulin
+OAP interactsWith PLA2G2A
+17beta-estradiol interactsWith 1IOL
+NAG interactsWith SERPINB4
+NAG interactsWith SERPINC1
+GSB interactsWith GLO1
+GSB interactsWith GLO1
+Zn2+ interactsWith GLO1
+GSB interactsWith GLO1
+FAD interactsWith ACADS
+FAD interactsWith ACADS
+FAD interactsWith ACADS
+DCT interactsWith POLB
+GTO interactsWith HRAS
+Mn2+ interactsWith HRAS
+Rapamycin interactsWith FRAP1
+Quercetin interactsWith HCK
+Quercetin interactsWith HCK
+DPN-PRO-MAI interactsWith PROC
+TS4 interactsWith TXNRD2
+GSSG interactsWith TXNRD2
+TS2 interactsWith TXNRD2
+GCG interactsWith TXNRD2
+HLE-RIN interactsWith MMP8
+Zn2+ interactsWith CA4
+Zn2+ interactsWith CA2
+Zn2+ interactsWith CA2
+acetazolamide interactsWith CA2
+Zn2+ interactsWith CA2
+Zn2+ interactsWith CA2
+NAG-(4-1)NAG-(4-1)MAN-(6-1)MAN-(6-1)MAN-(2-1)MAN-(3,3-1)MAN-(2-1)MAN-(4,3-1)MAN interactsWith GUSB
+NAG-(4-1)NAG-(4-1)MAN-(6-1)MAN-(6-1)MAN-(2-1)MAN-(3,3-1)MAN-(2-1)MAN-(4,3-1)MAN interactsWith GUSB
+Zn2+ interactsWith BTK
+NAG-(4-1)NAG interactsWith 1ZXQ
+NAG-(4-1)NAG interactsWith 1ZXQ
+NAG-(4-1)NAG interactsWith 1ZXQ
+GPR interactsWith GSTP1
+GPR interactsWith GSTP1
+GTX interactsWith GSTP1
+GTX interactsWith GSTP1
+PC interactsWith BPI
+PC interactsWith BPI
+ethacrynate interactsWith GSTP1
+REA interactsWith RARB
+GTT interactsWith GSTP1
+GTT interactsWith GSTP1
+ethacrynate interactsWith GSTP1
+n-octonyl-CoA interactsWith ACADM
+n-octonyl-CoA interactsWith ACADM
+n-octonyl-CoA interactsWith ACADM
+n-octonyl-CoA interactsWith ACADM
+n-octonyl-CoA interactsWith ACADM
+CIN interactsWith HBB
+NDD interactsWith HBB
+Zn2+ interactsWith Insulin_B-Chain
+IPH interactsWith R6_Insulin_Hexamer
+IPH interactsWith R6_Insulin_Hexamer
+staurosporine interactsWith CDK2
+MDL interactsWith F2
+DX9 interactsWith F10
+Ca2+ interactsWith SPARC
+Ca2+ interactsWith SPARC
+NAG-(4-1)NAG interactsWith SPARC
+T42 interactsWith F2
+T19 interactsWith F2
+AMP-PNP interactsWith INSR
+Mg2+ interactsWith INSR
+ILG-PBB-GLY interactsWith GSTP1
+ILG-PBB-GLY interactsWith GSTP1
+HSM interactsWith CA13
+GDP interactsWith RAP2B
+Mg2+ interactsWith RAP2B
+APM interactsWith APCS
+Ca2+ interactsWith 1HTN
+Ca2+ interactsWith 1HTN
+AZL interactsWith F2
+ALZ interactsWith F2
+I11 interactsWith F2
+Zn2+ interactsWith TP53
+FRU interactsWith 2FIT
+A interactsWith Fragile_Histidine_Protein
+Ca2+ interactsWith PPP3R1
+Ca2+ interactsWith PPP3R1
+Ca2+ interactsWith PPP3R1
+Ca2+ interactsWith PPP3R1
+Zn2+ interactsWith PPP3CA
+Fe3+ interactsWith PPP3CA
+L04 interactsWith MMP27
+E64 interactsWith CTSL2
+NAG-(4-1)NAG interactsWith ARSJ
+NAG-(4-1)NAG interactsWith ARSJ
+Ca2+ interactsWith ARSJ
+ORN interactsWith GATM
+NADP+ interactsWith DHFR
+COE interactsWith DHFR
+COE interactsWith DHFR
+COE interactsWith 1HFR
+GNP interactsWith RAC1
+Mg2+ interactsWith RAC2
+phosphotyrosine interactsWith PTPN1
+phosphotyrosine interactsWith PTPN1
+MO6 interactsWith PTPN1
+BZP-LEU-NFP-BNS interactsWith CTSL2
+Ca2+ interactsWith IMPA1
+ILG-TNB-GLY interactsWith GSTP1
+alrestatin interactsWith AKR1B1
+alrestatin interactsWith AKR1B1
+Citiric_acid interactsWith AKR1B1
+GDP interactsWith RAC1
+Mg2+ interactsWith RAC1
+RPX interactsWith FKBP1A
+RPX interactsWith FRAP1
+NAG interactsWith 1A7S
+NAG interactsWith Heparin-Binding_Protein
+BPM interactsWith PTPN1
+BPM interactsWith PTPN1
+Mg2+ interactsWith ARSA
+NAG-(4-1)NAG interactsWith ARSA
+DFP interactsWith GZMM
+NAD+ interactsWith DHPS
+Ca2+ interactsWith PLA2G4A
+Ca2+ interactsWith PLA2G4A
+SGN interactsWith Acidic_Fibroblast_Growth_Factor
+IDS-(4-1)SGN interactsWith Acidic_Fibroblast_Growth_Factor
+IDS-(4-1)SGN interactsWith Acidic_Fibroblast_Growth_Factor
+IDS-(4-1)SGN interactsWith Acidic_Fibroblast_Growth_Factor
+IDS interactsWith Acidic_Fibroblast_Growth_Factor
+IDS interactsWith Acidic_Fibroblast_Growth_Factor
+Geldanamycin interactsWith HSPCB
+SGN interactsWith Acidic_Fibroblast_Growth_Factor
+IDS interactsWith Acidic_Fibroblast_Growth_Factor
+IDS interactsWith Acidic_Fibroblast_Growth_Factor
+SGN interactsWith Acidic_Fibroblast_Growth_Factor
+SGN interactsWith Acidic_Fibroblast_Growth_Factor
+SGN interactsWith Acidic_Fibroblast_Growth_Factor
+NAG-(4-1)NAG-(4-1)MAN interactsWith CTLA4
+FUC-(1-6)NAG-(4-1)NAG-(4-1)BMA interactsWith CTLA4
+SU1 interactsWith FGFR1
+ACE-PTR-GLU-DIP interactsWith SRC
+ACE-FTY-GLU-DIP interactsWith SRC
+ACE-PTH-GLU-DIP interactsWith SRC
+ACE-PTH-GLU-DIP interactsWith SRC
+ACE-PTH-GLU-DIP interactsWith SRC
+ACE-PTR-GLU-DIP interactsWith SRC
+ACE-PTR-GLU-DIX interactsWith SRC
+ACE-PTR-GLU-DIX interactsWith SRC
+ACE-PTR-GLU-DIY interactsWith SRC
+ADW interactsWith HINT1
+ADW interactsWith HINT1
+A5MP interactsWith HINT2
+A12 interactsWith 5FIT
+AMW interactsWith FHIT
+SU2 interactsWith FGFR1
+A12 interactsWith HINT1
+CH3-DPN-PRO-ARG-BOT interactsWith F2
+BCC-ARG-THZ interactsWith F2
+FAD interactsWith TXNRD2
+GTT interactsWith TXNRD2
+NADP+ interactsWith Estradiol_17_Beta-Dehydrogenase_1
+17beta-estradiol interactsWith HSD17B1
+17beta-estradiol interactsWith HSD17B1
+NAD+ interactsWith HSD17B1
+NAD+ interactsWith HSD17B1
+17beta-estradiol interactsWith 1FDW
+FAD interactsWith TXNRD2
+COP interactsWith 1OHJ
+BIC-ARG-EOA interactsWith F2
+Mn2+ interactsWith PPM1A
+Mn2+ interactsWith PPM1A
+17beta-estradiol interactsWith 1A27
+NADP+ interactsWith 1A27
+RNG-BCY-LYS-OHO interactsWith F2
+FAD interactsWith IVD
+FAD interactsWith IVD
+FAD interactsWith IVD
+COS interactsWith IVD
+COS interactsWith IVD
+COS interactsWith IVD
+Ca2+ interactsWith 1TN3
+Ca2+ interactsWith 1TN3
+D13 interactsWith MAPK14
+D13 interactsWith MAPK14
+ANS-ARG-2EP-KTH interactsWith F2
+NAG interactsWith ICAM3
+MO6 interactsWith SREBF1
+OPH-LEU-RPH-OAR interactsWith F2
+acetohydroxamic_acid interactsWith CA2
+IB2 interactsWith FHIT
+GTP interactsWith RAP2B
+IB2 interactsWith FHIT
+NAG interactsWith Intercellular_Adhesion_Molecule-1
+NAG interactsWith Intercellular_Adhesion_Molecule-1
+NAG interactsWith Intercellular_Adhesion_Molecule-1
+NAG-(4-1)NAG interactsWith Intercellular_Adhesion_Molecule-1
+NAG interactsWith Intercellular_Adhesion_Molecule-1
+NAG interactsWith Intercellular_Adhesion_Molecule-1
+NAG-(4-1)NAG interactsWith Intercellular_Adhesion_Molecule-1
+NAG-(4-1)NAG interactsWith Intercellular_Adhesion_Molecule-1
+NAG interactsWith IL1R1
+NAG interactsWith IL1R1
+NAG interactsWith IL1R1
+NAG interactsWith IL1R1
+FKA interactsWith FKBP1A
+FKA interactsWith FKBP1A
+Fe3+ interactsWith TF
+PME interactsWith IGLL1
+PME interactsWith IGLL1
+PME interactsWith IGLL1
+PME interactsWith IGLL1
+heme interactsWith HBE1
+FUC-(1-6)GLC-(4-1)GLC-(4-1)MAN-(3-1)MAN-(2-1)GLC-(4-1)GAL interactsWith IFNB1
+GLC-(6-1)FUC interactsWith IFNB1
+GSP interactsWith RHOA
+Mg2+ interactsWith RAC1
+MOL-ARG-LOM interactsWith F2
+TAR interactsWith IL6
+GBC-PLP interactsWith OAT
+GBC-PLP interactsWith OAT
+alpha-D-Glucose interactsWith HK3
+G6P interactsWith HK3
+alpha-D-Glucose interactsWith HK3
+G6P interactsWith HK3
+Ca2+ interactsWith HK1
+Ca2+ interactsWith HK1
+CAN-PLP interactsWith OAT
+CAN-PLP interactsWith OAT
+MNO interactsWith CASP1
+MNO interactsWith CASP1
+GNP interactsWith CDC42
+Mg2+ interactsWith CDC42
+Ca2+ interactsWith 1AP4
+BMT-VAL-SAR-MLE-VAL-MLE-ALA-DAL-MLE-MLE-MVA interactsWith PPIA
+BMT-ABA-DSE-MLE-VAL-MLE-ALA-DAL-MLE-MLE-MVA interactsWith PPIA
+TMD-VAL-MSA-MLE-VAL-MLE-ALA-DAL-MLE-MLE-MVA interactsWith PPIA
+BMT-ABA-MGY-MHL-VAL-MLE-ALA-DAL-MLE-MLE-MVA interactsWith PPIA
+TMB-ABA-SAR-IML-VAL-MLE-ALA-DAL-MLE-MLE-MVA interactsWith PPIA
+MAN-(1-4)NAG-(1-3)HP3 interactsWith LYZL2
+GDP interactsWith RASA1
+IPH interactsWith Insulin
+IPH interactsWith Insulin
+IPH interactsWith Insulin
+GAL-(1-4)NAG interactsWith 1A3K
+AP1 interactsWith FKBP1A
+TBM-VAL-MSA-MLE-VAL-MLE-ALA-DAL-MLE-MLE-MNV interactsWith PPIA
+BMT-VAL-MAA-MLE-VAL-MLE-ALA-DAL-MLE-MLE-MVA interactsWith PPIA
+BMT-THR-SAR-MLE-LEU-MLE-ALA-VAD-MLE-LEU-MVA interactsWith PPIA
+CTO interactsWith LYZ
+Ca2+ interactsWith 1AJJ
+GDP interactsWith RHOA
+GDP interactsWith ARHGAP1
+Mg2+ interactsWith RHOA
+NAG interactsWith 2FN2
+NAG interactsWith ACPP
+NAG interactsWith ACPP
+NAG-(4-1)NAG interactsWith ACPP
+NAG interactsWith ACPP
+NAG-(4-1)NAG-(4-1)MAN interactsWith ACPP
+PT3 interactsWith ACPP
+17beta-estradiol interactsWith ESR1
+17beta-estradiol interactsWith ESR1
+Cu1+ interactsWith SOD1
+BMT-THR-SAR-MLE-VAL-MLE-ALA-DAL-MLE-MLE-MVA interactsWith PPIA
+GLU-BCS-PGY interactsWith GSTP1
+NAG-(4-1)NAG-(4-1)MAN-(6-1)MAN-(2-1)NAG-(3,3-1)MAN interactsWith FGA
+Ca2+ interactsWith FGA
+NAG-(4-1)NAG interactsWith FGA
+NAG-(4-1)NAG interactsWith FGA
+NAG interactsWith FGA
+NAG interactsWith FGA
+NAG interactsWith FGA
+NAG interactsWith FGA
+Urea interactsWith CA13
+K+ interactsWith HK1
+K+ interactsWith HK1
+naphthalene_trisulfonate interactsWith FGF1
+Zn2+ interactsWith RXRA
+Zn2+ interactsWith RXRA
+1GN interactsWith LGALS7
+Lactose interactsWith LGALS7
+NAG-(4-1)GAL interactsWith LGALS7
+GLB interactsWith LGALS7
+GTX interactsWith GLO1
+GTX interactsWith GLO1
+Zn2+ interactsWith GLO1
+GTX interactsWith GLO1
+GTX interactsWith GLO1
+R56 interactsWith F2
+R56 interactsWith F2
+MYR interactsWith AFP
+MYR interactsWith AFP
+GR3 interactsWith F2
+Zn2+ interactsWith NR1D1
+Zn2+ interactsWith NR1D1
+ADP interactsWith KIF5A
+Mg2+ interactsWith KIF5A
+PRL interactsWith F2
+INP interactsWith CTSL2
+SDK interactsWith CTSL2
+POS interactsWith CTSL2
+PCM interactsWith CTSL2
+raloxifene interactsWith ESR1
+Ca2+ interactsWith SPARC
+Ca2+ interactsWith SPARC
+NAG-(4-1)NAG interactsWith SPARC
+IN9 interactsWith MMP27
+IN8 interactsWith MMP27
+PFM interactsWith OAT
+PFM interactsWith OAT
+CRS interactsWith Insulin
+CRS interactsWith Insulin
+CRS interactsWith Insulin
+CRS interactsWith Insulin
+CRS interactsWith Insulin
+CRS interactsWith Insulin
+CRS interactsWith Insulin
+Mg2+ interactsWith ITGA2
+INA interactsWith CTSL2
+IN3 interactsWith CTSL2
+Ca2+ interactsWith 1BCI
+Ca2+ interactsWith 1BCI
+Zn2+ interactsWith COL18A1
+GR4 interactsWith F2
+ATT interactsWith MMP20
+sulfasalazine interactsWith GSTP1
+sulfasalazine interactsWith Sulfasalazine
+sulfasalazine interactsWith Sulfasalazine
+Fe3+ interactsWith TPH1
+B3I interactsWith AFP
+B3I interactsWith AFP
+NTP interactsWith SERPINC1
+GDP interactsWith CDC42
+Zn2+ interactsWith CPA1
+GDB interactsWith GSTP1
+GDB interactsWith GSTP1
+PMS interactsWith GZMB
+IN6 interactsWith CTSL2
+395 interactsWith RARB
+Uracil interactsWith UNG
+DDH interactsWith HBA2
+2,3-Bisphosphoglycerate interactsWith HBB
+K21 interactsWith ANXA5
+CAT interactsWith PTPN11
+NDP interactsWith MTHFD1
+CBD interactsWith GSTP1
+Citiric_acid interactsWith Angiogenin
+Ca2+ interactsWith LALBA
+2FU interactsWith HBB
+BNN-CUC-TRG-LEU-PRO interactsWith F2
+APA interactsWith TPSAB1
+CBZ interactsWith CA2
+MAN-(1-6)NGA-(4-1)NGA interactsWith SERPINE1
+NGA interactsWith SERPINE1
+NAG-(4-1)NAG interactsWith 1A7S
+GTT interactsWith GSTT2
+GTT interactsWith GSTT2
+4PP interactsWith F10
+chlorambucil interactsWith GSTP1
+chlorambucil interactsWith GSTP1
+GGL interactsWith GSTT2
+GGL interactsWith GSTT2
+NAG interactsWith 1BIK
+Ca2+ interactsWith 1A4V
+BBA interactsWith PLAT
+NAD+ interactsWith AHCY
+NAD+ interactsWith AHCY
+ADC interactsWith AHCY
+HMI-ASN-BNN interactsWith MMP1
+HMI-ASP-BNN interactsWith MMP1
+577 interactsWith MAPK14
+AOP interactsWith CCL5
+AOP interactsWith CCL5
+CPR interactsWith IMPDH1
+CPR interactsWith IMPDH1
+SAE interactsWith IMPDH1
+PMS-RON-GLY-3GA interactsWith F2
+Tat pp SMAD4
+Tat pp SMAD3
+NAG interactsWith Cd58
+NAG interactsWith Cd58
+NAG interactsWith Cd58
+Gag pp PPIA
+IN pp PSIP1
+PLP-TRS interactsWith BCAT2
+MAN-(1-6)NAG-(1-2)MAN-(1-6)MAN-(1-4)NAG-(1-4)NAG-(6-1)MAN-(4,3-1)MAN interactsWith FCGR3A
+UD1 interactsWith Udp-Galactose_4-Epimerase
+UD1 interactsWith GALE
+UDP-D-Galactose interactsWith GALE
+Cholic_acid interactsWith FECH
+Cholic_acid interactsWith FECH
+Cholic_acid interactsWith FECH
+2Fe-2S interactsWith FECH
+Citrate interactsWith NCF2
+Zn2+ interactsWith CBL
+Zn2+ interactsWith CBL
+FUC-(1-6)NAG-(4-1)NAG-(4-1)MAN-(6-1)MAN-(2-1)NAG-(4-1)GAL-(4,3-1)MAN-(2-1)NAG interactsWith FCGR3A
+AMP-PNP interactsWith MAPK12
+TMA interactsWith GALE
+TMA interactsWith GALE
+TMA interactsWith GALE
+UDP-D-Glucose interactsWith GALE
+NADH interactsWith GALE
+NAD+ interactsWith GALE
+ACE-HAC-ARG-ALA-ODA-SER-CLE interactsWith HLA-DRA
+ACE-HAC-ARG-MAA-HAQ-SEL interactsWith HLA-DRA
+Zn2+ interactsWith Apoptosis_Inhibitor_Survivin
+IN0 interactsWith FDFT1
+IN0 interactsWith FDFT1
+NAG-(4-1)NAG interactsWith ERBB3
+NAG interactsWith ERBB3
+NAG interactsWith ERBB3
+NAG interactsWith ERBB3
+NAG interactsWith ERBB3
+NAG interactsWith ERBB3
+NAG interactsWith ERBB3
+NAG interactsWith ERBB3
+NAG interactsWith ERBB3
+NAG-(4-1)NAG interactsWith FAP
+NAG-(4-1)NAG interactsWith FAP
+NAG interactsWith FAP
+NAG interactsWith FAP
+NAG interactsWith FAP
+NAG interactsWith FAP
+NAG-(6-1)FUC interactsWith FAP
+NDG interactsWith HLA-DRA
+NAG-(4-1)NDG interactsWith HLA-DRA
+Fe2+ interactsWith Factor_Inhibiting_Hif1
+pyridoxamine_phosphate interactsWith BCAT2
+2-Oxo-Isovalerate interactsWith BCAT2
+2-Oxo-Isovalerate interactsWith BCAT2
+ILP interactsWith BCAT2
+ILP interactsWith BCAT2
+ITP interactsWith EEA1
+ITP interactsWith EEA1
+Zn2+ interactsWith EEA1
+Zn2+ interactsWith EEA1
+Zn2+ interactsWith EEA1
+Zn2+ interactsWith EEA1
+Vitamin_A interactsWith RBP4
+Vitamin_A interactsWith RBP4
+Vitamin_A interactsWith RBP4
+Vitamin_A interactsWith RBP4
+Zn2+ interactsWith EP300
+Zn2+ interactsWith EP300
+Zn2+ interactsWith EP300
+MN3 interactsWith SOD2
+Ca2+ interactsWith CRP
+Ca2+ interactsWith CRP
+Mn2+ interactsWith SOD2
+NAG-(4-1)NAG interactsWith HLA-DRA
+PC interactsWith CRP
+NAG interactsWith HLA-DRA
+NAG interactsWith HLA-DRA
+NAG interactsWith HLA-DRA
+Ca2+ interactsWith CBL
+NAG interactsWith AMY2A
+Na+ interactsWith ATXN1
+Na+ interactsWith ATXN1
+NLX interactsWith Liver_Carboxylesterase_I
+NLX interactsWith Liver_Carboxylesterase_I
+NLX interactsWith Liver_Carboxylesterase_I
+HTQ interactsWith Liver_Carboxylesterase_I
+HTQ interactsWith Liver_Carboxylesterase_I
+HTQ interactsWith Liver_Carboxylesterase_I
+HTQ interactsWith Liver_Carboxylesterase_I
+HTQ interactsWith Liver_Carboxylesterase_I
+9-amino-1,2,3,4-tetrahydroacridine interactsWith Liver_Carboxylesterase_I
+9-amino-1,2,3,4-tetrahydroacridine interactsWith Liver_Carboxylesterase_I
+9-amino-1,2,3,4-tetrahydroacridine interactsWith Liver_Carboxylesterase_I
+9-amino-1,2,3,4-tetrahydroacridine interactsWith Liver_Carboxylesterase_I
+9-amino-1,2,3,4-tetrahydroacridine interactsWith Liver_Carboxylesterase_I
+NAG-(4-1)NAG interactsWith Liver_Carboxylesterase_I
+Mg2+ interactsWith Camp-Specific_3',5'-Cyclic_Phosphodiesterase_4d
+Zn2+ interactsWith Camp-Specific_3',5'-Cyclic_Phosphodiesterase_4d
+NAG interactsWith ERBB2
+NAG interactsWith ERBB2
+44B interactsWith NR1H2
+BNS interactsWith NR1H2
+BNS interactsWith NR1H2
+BNS interactsWith NR1H2
+965 interactsWith NR1H2
+965 interactsWith NR1H2
+965 interactsWith NR1H2
+444 interactsWith NR1H2
+444 interactsWith NR1H2
+NAG-(4-1)NAG interactsWith GBA
+NDG interactsWith GBA
+CO1 interactsWith NR1H2
+DBQ interactsWith TNK2
+ACP interactsWith TNK2
+ACP interactsWith TNK2
+Mg2+ interactsWith TNK2
+Mg2+ interactsWith TNK2
+Zn2+ interactsWith Prothrombin
+Mn2+ interactsWith BF
+MH2 interactsWith SOD2
+MH2 interactsWith SOD2
+1DLH_C pp HLA-DRA
+1DLH_F pp HLA-DRA
+1QBJ_F pd Double-Stranded_Rna_Specific_Adenosine_Deaminase_(Adar1)
+Ha_Peptide pp HLA-DRA
+sep pp HLA-DRA
+Myelin_Basic_Protein pp HLA-DRA
+Hemagglutinin_Ha1_Peptide_Chain pp HLA-DRA
+1EC6_C interactsWith NOVA2
+1DP7_D pd RFX1
+Peptidomimetic_Inhibitor pp HLA-DRA
+Zap-70_Peptide pp CBL
+Peptide_Inhibitor pp HLA-DRA
+sec4 pp HLA-DRA
+sec4 pp HLA-DRA
+sec4 pp HLA-DRA
+sec4 pp HLA-DRA
+sec4 pp HLA-DRA
+sec4 pp HLA-DRA
+Hemagglutinin_Ha_Peptide pp HLA-DRA
+Dna_Polymerase pp HLA-DRA
+Triosephosphate_Isomerase_Peptide pp HLA-DRA
+sec3 pp HLA-DRA
+Triosephosphate_Isomerase_Peptide pp HLA-DRA
+MW0051 pp HLA-DRA
+Hemagglutinin pp HLA-DRA
+Cl- interactsWith GALE
+NAG-(4-1)NAG interactsWith DPP4
+NAG-(4-1)NAG interactsWith DPP4
+NAG-(4-1)NAG interactsWith DPP4
+NAG-(4-1)NAG interactsWith DPP4
+NAG interactsWith DPP4
+NAG interactsWith DPP4
+NAG interactsWith DPP4
+1SEU_D pd TOP1
+1SEU_C pd TOP1
+1SEU_B pd TOP1
+NDF interactsWith Hypoxia-Inducible_Factor_1_Alpha_Inhibitor
+NDF interactsWith Hypoxia-Inducible_Factor_1_Alpha_Inhibitor
+SAM interactsWith HSA9761
+GTP interactsWith TUBG1
+GSP interactsWith TUBG1
+GLC-(1-4)HMC-(1-4)AGL interactsWith AMY1A
+NAG interactsWith SUMF1
+EHD interactsWith TOP1
+GDP interactsWith ARL10B
+Mg2+ interactsWith ARL10B
+L17 interactsWith F2
+isobutyl-(3)-1-methylxanthine interactsWith PDE4D
+isobutyl-(3)-1-methylxanthine interactsWith PDE4D
+isobutyl-(3)-1-methylxanthine interactsWith PDE4D
+Citrate interactsWith AKR7A2
+NDP interactsWith AKR7A2
+DF2 interactsWith CHEK1
+DF1 interactsWith CHEK1
+DFZ interactsWith CHEK1
+DFW interactsWith CHEK1
+DFY interactsWith CHEK1
+PFQ interactsWith CHEK1
+PFP interactsWith CHEK1
+NAG-(4-1)NAG-(4-1)BMA-(6-1)BMA-(3,3-1)BMA interactsWith PLAUR
+Citric_acid interactsWith PGAM1
+NAG-(4-1)NAG interactsWith PLAUR
+NAG-(4-1)NAG interactsWith PLAUR
+NAG-(6-1)FUC interactsWith PLAUR
+NAG-(6-1)FUC interactsWith PLAUR
+NAG-(6-1)FUC interactsWith PLAUR
+NAG interactsWith PLAUR
+NAG interactsWith PLAUR
+NAG interactsWith PLAUR
+NAG-(1-4)NAG-(6-1)FUC interactsWith PLAUR
+NAG-(1-4)NAG-(6-1)FUC interactsWith PLAUR
+NAG-(1-4)NAG-(6-1)FUC interactsWith PLAUR
+HPO interactsWith MASA
+T1D interactsWith PTPN1
+T2D interactsWith PTPN1
+SA3 interactsWith TOP1
+GAH interactsWith F2
+GNP interactsWith HRAS
+GNP interactsWith HRAS
+TX5 interactsWith VDR
+Mg2+ interactsWith RHOC
+GNP interactsWith RHOC
+P0E interactsWith NR5A1
+4ST interactsWith JAK3
+1CA interactsWith NR3C2
+P3A interactsWith NR5A2
+PEF interactsWith NR5A1
+PEF interactsWith NR5A1
+ATP interactsWith PDK3
+ADP interactsWith PDK3
+AAO interactsWith AMY2A
+ARE interactsWith AMY2A
+Mg2+ interactsWith PDK3
+LPA interactsWith PDK3
+LPA interactsWith PDK3
+LPA interactsWith DLAT
+K+ interactsWith PDK3
+K+ interactsWith PDK3
+K+ interactsWith PDK3
+ADP interactsWith SRXN1
+GTP interactsWith RAB7
+Mg2+ interactsWith RAB7
+4TR interactsWith CA2
+4TZ interactsWith CA2
+SV40gp6 pp RPA2
+OprF pp IFN-gamma
+Unknown interactsWith XIAP
+Unknown interactsWith TRAP230
+Unknown interactsWith TRAP170
+Unknown interactsWith Cdk9
+Unknown interactsWith TRAP100
+Unknown interactsWith TRAP80
+NADP+ interactsWith AKR1C1
+Na+ interactsWith ALDH2
+hydroxymethylglutathione interactsWith Alcohol_Dehydrogenase_Class_Iii_Chi_Chain
+hydroxymethylglutathione interactsWith Alcohol_Dehydrogenase_Class_Iii_Chi_Chain
+KEU interactsWith GART
+lauric_acid interactsWith Glutathione-Dependent_Formaldehyde_Dehydrogenase
+lauric_acid interactsWith Glutathione-Dependent_Formaldehyde_Dehydrogenase
+lauric_acid interactsWith Glutathione-Dependent_Formaldehyde_Dehydrogenase
+Ca2+ interactsWith Annexin_Vi
+Ca2+ interactsWith Annexin_Vi
+Ca2+ interactsWith Annexin_Vi
+Ca2+ interactsWith Annexin_Vi
+Ca2+ interactsWith Annexin_Vi
+12H interactsWith Glutathione-Dependent_Formaldehyde_Dehydrogenase
+12H interactsWith Glutathione-Dependent_Formaldehyde_Dehydrogenase
+K+ interactsWith Alcohol_Dehydrogenase_Class_Iii_Chi_Chain
+alpha-L-fucose interactsWith THBS2
+alpha-L-fucose interactsWith THBS2
+GTX interactsWith GSTA1
+GTX interactsWith GSTA1
+NAG-(1-4)NAG-(6-1)FUC interactsWith Fibrinogen_Beta_Chain
+NAG interactsWith Fibrinogen
+AMP interactsWith ETFB
+FAD interactsWith ETFB
+alpha-L-fucose interactsWith PLAU
+NAD+ interactsWith Human_Sigma_Alcohol_Dehydrogenase
+NAD+ interactsWith Human_Sigma_Alcohol_Dehydrogenase
+Zn2+ interactsWith Human_Sigma_Alcohol_Dehydrogenase
+Zn2+ interactsWith Human_Sigma_Alcohol_Dehydrogenase
+NAD+ interactsWith Alcohol_Dehydrogenase_Class_Iii_Chi_Chain
+Zn2+ interactsWith Alcohol_Dehydrogenase_Class_Iii_Chi_Chain
+Zn2+ interactsWith Alcohol_Dehydrogenase_Class_Iii_Chi_Chain
+Zn2+ interactsWith Neutral_Endopeptidase
+NAG interactsWith Neutral_Endopeptidase
+NAG interactsWith Neutral_Endopeptidase
+NAG interactsWith Neutral_Endopeptidase
+PLP interactsWith PYGM
+Zn2+ interactsWith Alcohol_Dehydrogenase_Class_Iv_Sigma_Chain
+Ca2+ interactsWith Fibrinogen
+Ca2+ interactsWith Fibrinogen
+alpha-L-fucose interactsWith Blood_Coagulation_Factor_Vii
+Ca2+ interactsWith Fibrinogen
+Ca2+ interactsWith FGL1
+Ca2+ interactsWith FGL1
+Ca2+ interactsWith Fibrinogen
+NAG-(3-2)(4-1)NAG interactsWith Fibrinogen
+NAG-(4-1)NAG interactsWith Fibrinogen
+alpha-L-fucose interactsWith 1FC2_D
+GNP interactsWith RALA
+Mg2+ interactsWith RALA
+Coproporphyrinogen_III interactsWith Uroporphyrinogen_Decarboxylase
+Coproporphyrinogen_III interactsWith Uroporphyrinogen_Decarboxylase
+Coproporphyrinogen_III interactsWith Uroporphyrinogen_Decarboxylase
+Coproporphyrinogen_I interactsWith Uroporphyrinogen_Decarboxylase
+Coproporphyrinogen_I interactsWith Uroporphyrinogen_Decarboxylase
+alpha-L-fucose interactsWith CLEC4M
+alpha-L-fucose interactsWith Factor_Viia_Light_Chain
+Gly-Pro-Arg-Pro pp Fibrinogen
+Ghrp_Peptide pp Fibrinogen_Gamma_Chain
+1K4T_B pd TOP1
+Mg2+ interactsWith FDPS
+Mg2+ interactsWith FDPS
+LY_294002 interactsWith PIM1
+1TL8_D pd Dna_Topoisomerase_I
+1TL8_C pd Dna_Topoisomerase_I
+1S9K_B pd Nuclear_Factor_Of_Activated_T-Cells,_Cytoplasmic_2
+1S9K_B pd Transcription_Factor_Ap-1
+1S9K_B pd Proto-Oncogene_Protein_C-Fos
+1S9K_A pd Proto-Oncogene_Protein_C-Fos
+1S9K_A pd Transcription_Factor_Ap-1
+1S9K_A pd Nuclear_Factor_Of_Activated_T-Cells,_Cytoplasmic_2
+Ubiquitin pp Adp-Ribosylation_Factor_Binding_Protein_Gga3
+Ubiquitin pp Adp-Ribosylation_Factor_Binding_Protein_Gga3
+Ubiquitin pp Adp-Ribosylation_Factor_Binding_Protein_Gga3
+Ubiquitin pp Adp-Ribosylation_Factor_Binding_Protein_Gga3
+Ubiquitin pp Adp-Ribosylation_Factor_Binding_Protein_Gga3
+Ubiquitin pp Adp-Ribosylation_Factor_Binding_Protein_Gga3
+Ubiquitin pp Adp-Ribosylation_Factor_Binding_Protein_Gga3
+Tneykv_Peptide pp Syntenin_1
+Hirudin_Variant-2 pp Thrombin_Heavy
+824 interactsWith Wee1-Like_Protein_Kinase
+Mg2+ interactsWith Wee1-Like_Protein_Kinase
+Mg2+ interactsWith Wee1-Like_Protein_Kinase
+TPG interactsWith Snurportin-1
+Citric_acid interactsWith Aldo-Keto_Reductase_Family_1_Member_C2
+GTA interactsWith Eukaryotic_Translation_Initiation_Factor_4e
+380 interactsWith Blood_Coagulation_Factor_Viia
+Mg2+ interactsWith Ubiquitin-Like_Protein_Smt3c
+Mg2+ interactsWith GT_MISMATCH-Specific_Thymine_Dna_Glycosylase
+Mg2+ interactsWith GT_MISMATCH-Specific_Thymine_Dna_Glycosylase
+SHY interactsWith Thrombin_Heavy
+Compound_2 interactsWith Proto-Oncogene_Tyrosine-Protein_Kinase_Src
+4EB interactsWith Serum_Albumin
+43B interactsWith Apoptosis_Regulator_Bcl-2
+43B interactsWith Apoptosis_Regulator_Bcl-X
+N3B interactsWith Apoptosis_Regulator_Bcl-X
+TN1 interactsWith Apoptosis_Regulator_Bcl-X
+4FC interactsWith Apoptosis_Regulator_Bcl-X
+Mg2+ interactsWith Cgmp-Dependent_3',5'-Cyclic_Phosphodiesterase
+Zn2+ interactsWith Cgmp-Dependent_3',5'-Cyclic_Phosphodiesterase
+GTX interactsWith Glutathione_S-Transferase_A1
+STS interactsWith Neprilysin
+AAX interactsWith Vascular_Endothelial_Growth_Factor_Receptor_2
+AAZ interactsWith Vascular_Endothelial_Growth_Factor_Receptor_2
+KT3 interactsWith Phosphoribosylglycinamide_Formyltransferase
+GAR interactsWith Phosphoribosylglycinamide_Formyltransferase
+KT5 interactsWith Phosphoribosylglycinamide_Formyltransferase
+KT5 interactsWith Phosphoribosylglycinamide_Formyltransferase
+KT5 interactsWith Phosphoribosylglycinamide_Formyltransferase
+ADP interactsWith Centromeric_Protein_E
+Mg2+ interactsWith Centromeric_Protein_E
+Mg2+ interactsWith MASA
+BGC interactsWith F7
+benzoate interactsWith Syntenin_1
+P2C interactsWith Transthyretin
+AI3 interactsWith Dna_Topoisomerase_I
+VER interactsWith Heme_Oxygenase_1
+AMP-PNP interactsWith N-Acetylgalactosamine_Kinase
+NGA interactsWith N-Acetylgalactosamine_Kinase
+FAD interactsWith Electron_Transfer_Flavoprotein_Alpha-Subunit,_Mitochondrial_Precursor
+FAD interactsWith ETFA
+FAD interactsWith Acyl-Coa_Dehydrogenase,_Medium-Chain_Specific,_Mitochondrial_Precursor
+FAD interactsWith ACADM
+FAD interactsWith Acyl-Coa_Dehydrogenase,_Medium-Chain_Specific,_Mitochondrial_Precursor
+FAD interactsWith Acyl-Coa_Dehydrogenase,_Medium-Chain_Specific,_Mitochondrial_Precursor
+FAD interactsWith Acyl-Coa_Dehydrogenase,_Medium-Chain_Specific,_Mitochondrial_Precursor
+FAD interactsWith Acyl-Coa_Dehydrogenase,_Medium-Chain_Specific,_Mitochondrial_Precursor
+S-Adenosylhomocysteine interactsWith Indolethylamine_N-Methyltransferase
+IPR interactsWith Farnesyl_Diphosphate_Synthase
+T98 interactsWith Progesterone_Receptor
+NADP+ interactsWith Voltage-Gated_Potassium_Channel_Beta-2_Subunit
+Cl- interactsWith Nadp-Dependent_Leukotriene_B4_12-_Hydroxydehydrogenase
+Cl- interactsWith Nadp-Dependent_Leukotriene_B4_12-_Hydroxydehydrogenase
+ZOL interactsWith Farnesyl_Diphosphate_Synthase
+S-Adenosylhomocysteine interactsWith Guanidinoacetate_N-Methyltransferase
+ADP interactsWith Nucleoside_Diphosphate_Kinase_3
+CT5 interactsWith Heat_Shock_Protein_Hsp90-Alpha
+BSM interactsWith Heat_Shock_Protein_Hsp90-Alpha
+784 interactsWith Coagulation_Factor_X_Synonym:_Factor_Xa,_Stuart_Factor
+Na+ interactsWith Coagulation_Factor_X_Synonym:_Factor_Xa,_Stuart_Factor
+GNP interactsWith Ras-Related_Protein_Ral-A
+Phenylalanine interactsWith Alkaline_Phosphatase
+PHE-PO3 interactsWith Alkaline_Phosphatase
+PNP interactsWith Alkaline_Phosphatase
+PNP interactsWith Alkaline_Phosphatase
+PO3 interactsWith Alkaline_Phosphatase
+Ca2+ interactsWith Alkaline_Phosphatase
+Mg2+ interactsWith Alkaline_Phosphatase
+Zn2+ interactsWith Alkaline_Phosphatase
+Zn2+ interactsWith Alkaline_Phosphatase
+NAG interactsWith Alkaline_Phosphatase
+NAG interactsWith Alkaline_Phosphatase
+heme interactsWith Hemoglobin_Alpha_Chain
+heme interactsWith HBA2
+heme interactsWith Hemoglobin_Alpha_Chain
+Citric_acid interactsWith Ribonuclease_Inhibitor
+Citric_acid interactsWith Ribonuclease_I
+T4A interactsWith Transthyretin
+T4A interactsWith Transthyretin
+Ca2+ interactsWith Vitamin_K-Dependent_Protein_S
+Ca2+ interactsWith Vitamin_K-Dependent_Protein_S
+Zn2+ interactsWith Carboxypeptidase_B
+isobutyl-(3)-1-methylxanthine interactsWith High-Affinity_Camp-Specific_3',5'-Cyclic_Phosphodiesterase_7a
+Mg2+ interactsWith High-Affinity_Camp-Specific_3',5'-Cyclic_Phosphodiesterase_7a
+NAD+ interactsWith Dihydrolipoyl_Dehydrogenase
+NAD+ interactsWith Dihydrolipoyl_Dehydrogenase
+3',5'-ADP interactsWith Heparan_Sulfate_Glucosamine_3-O-Sulfotransferase_1
+062 interactsWith Thrombin
+Zn2+ interactsWith Zinc_Finger_Protein_593
+NADH interactsWith Dihydrolipoyl_Dehydrogenase
+NADH interactsWith Dihydrolipoyl_Dehydrogenase
+Zn2+ interactsWith High-Affinity_Camp-Specific_3',5'-Cyclic_Phosphodiesterase_7a
+NAG-(4-1)NAG interactsWith Toll-Like_Receptor_3
+NAG-(4-1)NAG interactsWith Toll-Like_Receptor_3
+NAG-(4-1)NAG interactsWith Toll-Like_Receptor_3
+NAG-(4-1)NAG interactsWith Toll-Like_Receptor_3
+NAG interactsWith Toll-Like_Receptor_3
+NAG interactsWith Toll-Like_Receptor_3
+NAG interactsWith Toll-Like_Receptor_3
+NAG interactsWith Toll-Like_Receptor_3
+Ca2+ interactsWith Calpain_9
+Ca2+ interactsWith Calpain_9
+G3D interactsWith Adp-Ribosylation_Factor-Like_Protein_5
+S-Adenosylhomocysteine interactsWith Set8_Protein
+Consensus_Peptide_For_14-3-3_Proteins pp 14-3-3_Protein_Tau
+Histone_H4 pp Set8_Protein
+Peptide_Corresponding_To_Residues_15-24_Of_Histone_H4 pp Histone-Lysine_N-Methyltransferase,_H4_Lysine-20_Specific
+Carboxypeptidase_Inhibitor pp Carboxypeptidase_B
+Exocyst_Complex_Protein_Exo84 pp Ras-Related_Protein_Ral-A
+Exocyst_Complex_Protein_Exo84 pp Ras-Related_Protein_Ral-A
+Bzlf1_Trans-Activator_Protein pp Hla_Class_I_Histocompatibility_Antigen,_B-35_Alpha_Chain
+11-Peptide_Hirudin_Fragment pp Thrombin
+NAG interactsWith MME
+Ca2+ interactsWith F7
+2CV5_I pd Histone_H4
+2CV5_I pd Histone_H4
+2CV5_I pd Histone_H3.1
+2CV5_I pd Histone_H3.1
+2CV5_I pd Histone_H2a.A
+2CV5_I pd Histone_H2a.A
+2CV5_I pd Histone_H2b_K
+2CV5_I pd Histone_H2b_K
+2CV5_J pd Histone_H4
+2CV5_J pd Histone_H4
+2CV5_J pd Histone_H3.1
+2CV5_J pd Histone_H3.1
+2CV5_J pd Histone_H2a.A
+2CV5_J pd Histone_H2a.A
+2CV5_J pd Histone_H2b_K
+2CV5_J pd Histone_H2b_K
+Unknown interactsWith Cyclin_T2
+GTP interactsWith RAB5B
+lmo0320 pp TRA1
+ATP interactsWith FANCM
+Wortmannin interactsWith PIK3CA
+Wortmannin interactsWith PIK3CB
+Unknown interactsWith 14-3-3-gamma
+Unknown interactsWith CaM
+Unknown interactsWith NSF
+Unknown interactsWith CaM
+Unknown interactsWith SPTAN1
+UL36USP pp Ub
+Unknown interactsWith KA2
+Unknown interactsWith F3-contactin
+Unknown interactsWith Dyn1
+Unknown interactsWith Dynamitin
+Unknown interactsWith Profilin_II
+Unknown interactsWith VILIP-1
+Unknown interactsWith VILIP-3
+GDP interactsWith GNAI3
+NAN interactsWith Liver_Carboxylesterase_I
+NAN interactsWith Liver_Carboxylesterase_I
+NAN interactsWith Liver_Carboxylesterase_I
+NAN interactsWith Liver_Carboxylesterase_I
+NAN interactsWith Liver_Carboxylesterase_I
+NAN interactsWith Liver_Carboxylesterase_I
+NAG interactsWith Liver_Carboxylesterase_I
+NAG interactsWith Liver_Carboxylesterase_I
+BRL interactsWith PPARG
+BRL interactsWith PPARG
+TAR interactsWith Phosphoinositide_Phosphotase_Pten
+Ca2+ interactsWith APCS
+Ca2+ interactsWith APCS
+dTTP interactsWith Polymerase_(Dna_Directed)_Iota
+Mg2+ interactsWith Polymerase_(Dna_Directed)_Iota
+Zn2+ interactsWith Dna_Ligase_Iii
+CXS interactsWith SUMF1
+NAG-(4-1)NAG interactsWith SUMF1
+NADP+ interactsWith DCXR
+NADP+ interactsWith DCXR
+NAG interactsWith ACP5
+Fe3+ interactsWith ACP5
+Fe3+ interactsWith ACP5
+EEE interactsWith CES1
+EEE interactsWith CES1
+SMB interactsWith CES1
+SMB interactsWith CES1
+MVB interactsWith CES1
+MVB interactsWith CES1
+MAN-(1-6)MAN-(1-4)NAG-(1-4)NAG-(6-1)FUC interactsWith IL22
+MAN-(1-6)MAN-(1-4)NAG-(1-4)NAG-(6-1)FUC interactsWith IL22
+NAG interactsWith IL22
+NAG interactsWith IL22
+FUC-(1-6)NAG-(4-1)NAG interactsWith IL22
+FUC-(1-6)NAG-(4-1)NAG interactsWith IL22
+T2M interactsWith CTSK
+CM3 interactsWith ESR1
+CM4 interactsWith ESR1
+benzoate interactsWith CES1
+benzoate interactsWith CES1
+benzoate interactsWith CES1
+CTX interactsWith CES1
+CTX interactsWith CES1
+CTX interactsWith CES1
+CTX interactsWith CES1
+NAG interactsWith CES1
+NAG interactsWith CES1
+FHI interactsWith TTR
+NAN interactsWith CES1
+NAN interactsWith CES1
+NAN interactsWith CES1
+NAN interactsWith CES1
+NAN interactsWith CES1
+NAN interactsWith CES1
+Ni2+ interactsWith ADAR
+797 interactsWith ESR2
+797 interactsWith ESR2
+338 interactsWith ESR2
+272 interactsWith ESR2
+272 interactsWith ESR2
+272 interactsWith ESR2
+K+ interactsWith PKM2
+Mg2+ interactsWith PKM2
+OXL interactsWith PKM2
+B-D-Fructose-1,6-DP interactsWith PKM2
+CPG interactsWith GMPR
+CPK interactsWith APCS
+CPJ interactsWith APCS
+Corticosterone interactsWith NR3C2
+ADP interactsWith GALK2
+Mg2+ interactsWith GALK2
+NG1 interactsWith GALK2
+POH interactsWith 2A5R_A
+GDP interactsWith RAB2B
+Mg2+ interactsWith RAB2B
+K+ interactsWith F2
+K+ interactsWith F2
+SO4-(3-3)NAG-(4-1)NAG-(2,6-1)FUC interactsWith TLR3
+alpha-D-Glucose interactsWith TLR3
+alpha-D-Glucose interactsWith TLR3
+NAG-(1-4)NAG-(6-1)FUC interactsWith TLR3
+NAG-(4-1)NAG-(4-1)BMA-(6-1)BMA-(3,3-1)BMA interactsWith TLR3
+NAG-(4-1)NAG-(4-1)MAN interactsWith TLR3
+NAG interactsWith TLR3
+NAG-(4-1)NAG interactsWith TLR3
+NAG-(4-1)NAG interactsWith TLR3
+NAG-(4-1)NAG interactsWith TLR3
+NAG-(4-1)NAG interactsWith TLR3
+NAG-(4-1)NAG interactsWith TLR3
+NAG-(4-1)NAG interactsWith TLR3
+staurosporine interactsWith STK16
+staurosporine interactsWith STK16
+staurosporine interactsWith STK16
+K+ interactsWith GMPR
+AMP interactsWith AK5
+Na+ interactsWith F10
+784 interactsWith F10
+SNL interactsWith NR3C2
+PDN interactsWith NR3C2
+Progesterone interactsWith NR3C2
+Progesterone interactsWith NR3C2
+Progesterone interactsWith NR3C2
+Progesterone interactsWith NR3C2
+Aldosterone interactsWith NR3C2
+IP3 interactsWith ITPKC
+NAG-(4-1)NAG interactsWith ERBB2
+Citric_acid interactsWith CPOX
+Mg2+ interactsWith Ras-Related_Protein_Rab-14
+GSM interactsWith GSTM2
+GSM interactsWith GSTM2
+NAG interactsWith ERBB2
+NAG interactsWith ERBB2
+3'-TMP interactsWith NT5M
+GDP interactsWith RAB2
+GDP interactsWith RAB2
+Mg2+ interactsWith RAB2
+Mg2+ interactsWith RAB2
+GNP interactsWith RAB21
+GNP interactsWith RAB21
+GNP interactsWith RAB21
+Mg2+ interactsWith RAB21
+Mg2+ interactsWith RAB21
+Mg2+ interactsWith RAB21
+Mg2+ interactsWith RAB21
+U2P interactsWith NT5M
+dUMP interactsWith NT5M
+Mg2+ interactsWith NT5M
+Mg2+ interactsWith NT5M
+GTP interactsWith RAB4A
+GDP interactsWith RAB21
+GDP interactsWith Ras-Related_Protein_Rab-14
+GNP interactsWith RAB6A
+Mg2+ interactsWith RAB6A
+3FC interactsWith CTSK
+P6L interactsWith NR5A2
+Mg2+ interactsWith RAB4A
+Mg2+ interactsWith RAB4A
+GNP interactsWith RAB4A
+GNP interactsWith RAB11A
+Mg2+ interactsWith RAB11A
+Mg2+ interactsWith RAB25
+NAG-(4-1)NAG interactsWith IL22
+NAG-(4-1)NAG interactsWith IL22
+NAG-(4-1)NAG interactsWith IL22
+alpha-galactosyl_ceramide interactsWith CD1D
+alpha-galactosyl_ceramide interactsWith CD1D
+DGP interactsWith NT5M
+5'-UMP interactsWith NT5M
+Cl- interactsWith TTR
+5'-TMP interactsWith NT5M
+Sars_Nucleocapsid_Peptide pp HLA-A
+Steroid_Receptor_Coactivator-1 pp ESR2
+Steroid_Receptor_Coactivator-1 pp ESR2
+Pvyi pp APBA1
+Hypothetical_28.7_Kda_Protein_In_Dhfr_3'region_(Orf1) pp LYN
+Nuclear_Receptor_Coactivator_2 pp NR5A2
+23-Mer_Peptide_From_Pelb-Igg_Kappa_Light_Chain_Fusion_Protein pp Activation_Peptide_From_Cathepsin_E
+Nuclear_Receptor_Subfamily_0,_Group_B,_Member_2 pp PPARG
+1ZET_P pd POLI
+1ZET_T pd POLI
+Latent_Membrane_Protein_1 pp TRAF3
+17-Mer_Peptide_P1-Xpc_From_Dna-Repair_Protein_Complementing_Xp-C_Cells pp Centrin_2
+Nuclear_Receptor_Coactivator_1,_Residues_1430-_1441 pp NR3C2
+Gag pp Hla_Class_I_Histocompatibility_Antigen
+Gag_Protein pp Hla_Class_I_Histocompatibility_Antigen,_A-2_Alpha_Chain
+Influenza_Nucleoprotein pp Hla_Class_I_Histocompatibility_Antigen,_B-27_Alpha_Chain_Precursor
+Hiv_Peptide pp Hla_Class_I_Histocompatibility_Antigen_B-27_Alpha_Chain
+Epstein-Barr_Nuclear_Antigen-6 pp Hla_Class_I_Histocompatibility_Antigen,_B-27_Alpha_Chain_Precursor
+1T8I_D pd TOP1
+1T8I_C pd TOP1
+Diprotin_A pp DPP4
+Hirudin_Iiib' pp F2
+1Z8I_I pp F2
+1Z8J_I pp F2
+Antagonist_Peptide pp PLAUR
+Antagonist_Peptide pp PLAUR
+Antagonist_Peptide pp PLAUR
+Antagonist_Peptide pp PLAUR
+Antagonist_Peptide pp PLAUR
+Zn2+ interactsWith Prothrombin
+Zn2+ interactsWith Prothrombin
+Unknown interactsWith alpha-PIX
+Unknown interactsWith ILK
+IN pp p300
+HVS_cyclin pp cdk6
+HVS_cyclin pp Fbxo7
+NAG interactsWith Heparin_Cofactor_Ii
+NAG interactsWith Heparin_Cofactor_Ii
+NAG interactsWith Heparin_Cofactor_Ii
+NAG-(4-1)NAG-(4-1)MAN interactsWith Heparin_Cofactor_Ii
+STN-BUM interactsWith MMP9
+Zn2+ interactsWith MMP9
+Zn2+ interactsWith MMP9
+Zn2+ interactsWith MMP2
+Zn2+ interactsWith MMP2
+BUM-STN interactsWith MMP9
+Ca2+ interactsWith MMP9
+Ca2+ interactsWith MMP9
+Ca2+ interactsWith MMP9
+Ca2+ interactsWith MMP9
+Ca2+ interactsWith MMP2
+Ca2+ interactsWith MMP2
+CGS interactsWith MMP12
+MAN-(1-2)MAN interactsWith Fab_2g12,_Light_Chain
+MAN-(1-2)MAN interactsWith Fab_2g12,_Heavy_Chain
+acetohydroxamic_acid interactsWith MMP12
+INN interactsWith Tumor_Necrosis_Factor-Alpha-Converting_Enzyme
+Zn2+ interactsWith Tumor_Necrosis_Factor-Alpha-Converting_Enzyme
+Zn2+ interactsWith NQO2
+PLP interactsWith BCAT2
+Guanylhydrazone_dihydrochloride interactsWith AMD1
+Guanylhydrazone_dihydrochloride interactsWith AMD1
+SMM interactsWith AMD1
+SMM interactsWith AMD1
+MHZ interactsWith AMD1
+MHZ interactsWith AMD1
+MAO interactsWith AMD1
+MAO interactsWith AMD1
+CG interactsWith AMD1
+CG interactsWith AMD1
+Putrescine interactsWith AMD1
+Putrescine interactsWith AMD1
+Putrescine interactsWith AMD1
+Putrescine interactsWith AMD1
+BAT interactsWith MMP12
+Zn2+ interactsWith MMP12
+Zn2+ interactsWith MMP12
+R1881 interactsWith NR3C1
+Na+ interactsWith POLB
+Na+ interactsWith POLB
+Na+ interactsWith POLB
+Fe3+ interactsWith LTF
+Fe3+ interactsWith LTF
+Fe3+ interactsWith LTF
+1MQ3_D pd POLB
+Mg2+ interactsWith POLB
+Mg2+ interactsWith POLB
+Mg2+ interactsWith POLB
+1MQ2_P pd POLB
+NAD+ interactsWith GAPDH
+NAD+ interactsWith GAPD
+NAD+ interactsWith GAPD
+Gag_Peptide pp Hla_Class_I_Histocompatibility_Antigen,_A-2_Alpha_Chain
+Gag_Peptide pp Hla_Class_I_Histocompatibility_Antigen,_A-2_Alpha_Chain
+Gag_Peptide pp Hla_Class_I_Histocompatibility_Antigen,_A-2_Alpha_Chain
+Gag_Peptide pp Hla_Class_I_Histocompatibility_Antigen,_A-2_Alpha_Chain
+Gag_Peptide pp Hla_Class_I_Histocompatibility_Antigen,_A-2_Alpha_Chain
+Gag_Peptide pp Hla_Class_I_Histocompatibility_Antigen,_A-2_Alpha_Chain
+Gag_Peptide pp Hla_Class_I_Histocompatibility_Antigen,_A-2_Alpha_Chain
+IHJ interactsWith Cathepsin_K
+IHI interactsWith Cathepsin_K
+IHE interactsWith Cathepsin_K
+Citric_acid interactsWith Sh3_Domain-Binding_Glutamic_Acid-Rich-Like_Protein
+FAD interactsWith Nrh_Dehydrogenase_[quinone]_2
+FAD interactsWith NQO2
+FAD interactsWith NQO2
+NGH interactsWith MMP12
+DEO interactsWith MMP12
+CP8 interactsWith MMP12
+CB1 interactsWith Nrh_Dehydrogenase_[quinone]_2
+CB1 interactsWith Nrh_Dehydrogenase_[quinone]_2
+CB1 interactsWith Nrh_Dehydrogenase_[quinone]_2
+ADP interactsWith PAPSS1
+PF3 interactsWith MMP12
+PF3 interactsWith MMP12
+PF3 interactsWith MMP12
+PF3 interactsWith MMP12
+PF3 interactsWith MMP12
+Ca2+ interactsWith MMP12
+Ca2+ interactsWith MMP12
+Ca2+ interactsWith MMP12
+Ca2+ interactsWith MMP12
+Ca2+ interactsWith MMP12
+ADP interactsWith Bifunctional_3'-Phosphoadenosine_5'-_Phosphosulfate_Synthethase_1
+Zn2+ interactsWith Skeletal_Muscle_Lim-Protein_2
+Zn2+ interactsWith Skeletal_Muscle_Lim-Protein_2
+Zn2+ interactsWith Nrh_Dehydrogenase_[quinone]_2
+NP2 interactsWith Histone_Acetylatransferase_Pcaf
+NP1 interactsWith Histone_Acetylatransferase_Pcaf
+THH interactsWith Aminomethyltransferase
+APS interactsWith Bifunctional_3'-Phosphoadenosine_5'-_Phosphosulfate_Synthethase_1
+Mg2+ interactsWith Peptidyl-Prolyl_Cis-Trans_Isomerase_A
+GDP interactsWith Adp-Ribosylation_Factor-Like_10c
+Mg2+ interactsWith Adp-Ribosylation_Factor-Like_10c
+AMP-PNP interactsWith Pyridoxal_Kinase
+AMP-PNP interactsWith Pyridoxal_Kinase
+Ca2+ interactsWith Calpain-1_Catalytic_Subunit
+Ca2+ interactsWith Calpain-1_Catalytic_Subunit
+glycine interactsWith Phosphomannomutase_2
+glycine interactsWith Phosphomannomutase_2
+glycine interactsWith Phosphomannomutase_2
+NAD+ interactsWith DehydrogenaseREDUCTASE_(SDR_FAMILY)_MEMBER_6
+NVI interactsWith Glutaminyl-Peptide_Cyclotransferase
+1BN interactsWith Glutaminyl-Peptide_Cyclotransferase
+AHN interactsWith Glutaminyl-Peptide_Cyclotransferase
+BGT interactsWith Glutaminyl-Peptide_Cyclotransferase
+BGT interactsWith Glutaminyl-Peptide_Cyclotransferase
+Zn2+ interactsWith Glutaminyl-Peptide_Cyclotransferase
+Zn2+ interactsWith Glutaminyl-Peptide_Cyclotransferase
+Zn2+ interactsWith Glutaminyl-Peptide_Cyclotransferase
+BR interactsWith Hspc223
+BR interactsWith Hspc223
+BR interactsWith Hspc223
+FAD-DPK interactsWith MAOB
+FAD interactsWith MAOA
+MLG interactsWith MAOA
+GBN interactsWith Branched_Chain_Aminotransferase_1,_Cytosolic
+GBN interactsWith Branched_Chain_Aminotransferase_1,_Cytosolic
+4MV interactsWith Branched_Chain_Aminotransferase_1,_Cytosolic
+4MV interactsWith Branched_Chain_Aminotransferase_1,_Cytosolic
+4MV interactsWith Branched_Chain_Aminotransferase_1,_Cytosolic
+PLP interactsWith Branched_Chain_Aminotransferase_1,_Cytosolic
+B3P interactsWith Thiopurine_S-Methyltransferase
+S-Adenosylhomocysteine interactsWith Thiopurine_S-Methyltransferase
+NAG interactsWith Lactotransferrin
+NAG interactsWith Lactotransferrin
+DGT interactsWith POLB
+DGT interactsWith POLB
+DGT interactsWith POLB
+8MO interactsWith Cytochrome_P450,_Family_2,_Subfamily_A,_Polypeptide_6
+COU interactsWith Cytochrome_P450,_Family_2,_Subfamily_A,_Polypeptide_6
+heme interactsWith Cytochrome_P450,_Family_2,_Subfamily_A,_Polypeptide_6
+LIF interactsWith Vascular_Endothelial_Growth_Factor_Receptor_2
+Zn2+ interactsWith Carbonic_Anhydrase_Iii
+APS interactsWith Bifunctional_3'-Phosphoadenosine_5'-_Phosphosulfate_Synthethase_1
+Mg2+ interactsWith ARF6
+Mg2+ interactsWith ARF6
+dopamine interactsWith SULT1A3
+3',5'-ADP interactsWith SULT1A3
+CXS interactsWith Calcyclin-Binding_Protein
+Zn2+ interactsWith Ubiquitin_Ligase_Siah1
+2-Oxoglutaric_acid interactsWith Phytanoyl-Coa_Dioxygenase
+Fe2+ interactsWith Phytanoyl-Coa_Dioxygenase
+GBN interactsWith Branched_Chain_Aminotransferase
+GBN interactsWith Branched_Chain_Aminotransferase
+GTP interactsWith Adp-Ribosylation_Factor_6
+AB5 interactsWith ARG1
+Ca2+ interactsWith Calmodulin
+Ca2+ interactsWith Calmodulin
+DQB interactsWith Phosphoribosylglycinamide_Formyltransferase
+GRF interactsWith Phosphoribosylglycinamide_Formyltransferase
+MAN-(1-2)MAN-(1-2)MAN-(1-3)MAN-(6-1)MAN-(3-1)MAN-(5,6-1)MAN interactsWith Fab_2g12,_Light_Chain
+MAN-(1-2)MAN-(1-2)MAN-(1-3)MAN-(6-1)MAN-(3-1)MAN-(5,6-1)MAN interactsWith Fab_2g12,_Heavy_Chain
+MAN-(1-2)MAN-(1-6)MAN-(3-1)MAN-(2-1)MAN interactsWith Fab_2g12,_Light_Chain
+MAN-(1-2)MAN-(1-6)MAN-(3-1)MAN-(2-1)MAN interactsWith Fab_2g12,_Heavy_Chain
+MAN-(1-2)MAN-(1-2)MAN-(1-3)MAN interactsWith Fab_2g12,_Light_Chain
+MAN-(1-2)MAN-(1-2)MAN-(1-3)MAN interactsWith Fab_2g12,_Heavy_Chain
+ADP interactsWith Dna_Topoisomerase_Ii,_Alpha_Isozyme
+ADP interactsWith Dna_Topoisomerase_Ii,_Alpha_Isozyme
+AMP-PNP interactsWith Dna_Topoisomerase_Ii,_Alpha_Isozyme
+Mg2+ interactsWith Dna_Topoisomerase_Ii,_Alpha_Isozyme
+Na+ interactsWith Smad_Ubiquitination_Regulatory_Factor_2
+1ZJN_T pd POLB
+1ZJM_D pd POLB
+1ZJM_P pd POLB
+1ZJM_T pd POLB
+14-Mer_Fragment_Of_Nuclear_Receptor_Coactivator_2 pp Androgen_Receptor
+1ZZJ_D pd Heterogeneous_Nuclear_Ribonucleoprotein_K
+1ZZJ_D pd Heterogeneous_Nuclear_Ribonucleoprotein_K
+1ZZI_C pd Heterogeneous_Nuclear_Ribonucleoprotein_K
+1ZZN_B interactsWith U1_Small_Nuclear_Ribonucleoprotein_A_Rna_Binding_Domain
+Cholera_Enterotoxin,_A_Chain pp Adp-Ribosylation_Factor_6
+Cholera_Enterotoxin,_A_Chain pp ARF6
+Cholera_Enterotoxin,_A_Chain pp ARF6
+Gp42_Protein pp HLA-DRB1
+Phage-Derived_Peptide_Antagonist pp Vascular_Endothelial_Growth_Factor
+Phage-Derived_Peptide_Antagonist pp Vascular_Endothelial_Growth_Factor
+Peptide_V108 pp Vascular_Endothelial_Growth_Factor
+Peptide_V108 pp Vascular_Endothelial_Growth_Factor
+Peptide_V108 pp Vascular_Endothelial_Growth_Factor
+Heavy_Chain_Of_Neutralizing_Antibody pp Vascular_Endothelial_Growth_Factor
+Fab_Fragment pp Vascular_Endothelial_Growth_Factor
+9-Mer_Peptide pp SRPK1
+Myelin_Basic_Protein pp T_Cell_Receptor_Beta_Chain
+Myelin_Basic_Protein pp T_Cell_Receptor_Beta_Chain
+Myelin_Basic_Protein pp HLA-DRB5
+Myelin_Basic_Protein pp HLA-DRB5
+Myelin_Basic_Protein pp HLA-DRA
+Myelin_Basic_Protein pp HLA-DRA
+Myelin_Basic_Protein pp HLA-DRA
+Myelin_Basic_Protein pp HLA-DRA
+2BZF_C pd BANF1
+2BZF_B pd BANF1
+Hiv-P24 pp Hla_Class_I_Histocompatibility_Antigen,_B-57_Alpha_Chain
+Gag_Protein pp Hla_Class_I_Histocompatibility_Antigen,_B-57_Alpha_Chain
+Hiv-P24 pp Hla_Class_I_Histocompatibility_Antigen,_B-57_Alpha_Chain
+2AXY_H pd PCBP2
+2AXY_F pd PCBP2
+2AXY_E pd PCBP2
+Exoenzyme_S_Peptide pp YWHAB
+Cellular_Tumor_Antigen_P53 pp RPA1
+Signal_Transduction_Protein_Cbl-B pp SH3KBP1
+Signal_Transduction_Protein_Cbl-B pp SH3KBP1
+2ACJ_F pd ADAR
+2ACJ_F pd ADAR
+2ACJ_F pd ADAR
+2ACJ_E pd ADAR
+2ACJ_E pd ADAR
+2ACJ_E pd ADAR
+Ebv_Peptide_Lpeplpqgqltay pp Hla-B35_Variant
+Ebv_Peptide_Lpeplpqgqltay pp Hla-B35_Variant
+Mono-Adp-Ribosyltransferase_C3 pp RALA
+Trans-Activating_Transcriptional_Regulatory_Peptide pp Hla_Class_I_Histocompatibility_Antigen,_A-2_Alpha_Chain
+Trans-Activating_Transcriptional_Regulatory_Peptide pp Hla_Class_I_Histocompatibility_Antigen,_A-2_Alpha_Chain
+Cyclin-Dependent_Kinase_Inhibitor_1b pp CKS1B
+Cyclin-Dependent_Kinase_Inhibitor_1b pp SKP2
+Peptide pp YWHAG
+2ALZ_P pd POLI
+2ALZ_T pd POLI
+S pp ACE2
+Spike pp ACE2
+2AD9_B interactsWith PTBP1
+2ADB_B interactsWith PTBP1
+2ADC_C interactsWith PTBP1
+2ADC_B interactsWith PTBP1
+Hirudin pp F2
+Hirugen pp F2
+Hirugen pp F2
+FL9 interactsWith TTR
+FL9 interactsWith TTR
+T2 interactsWith TTR
+MIL interactsWith TTR
+CIT interactsWith AKR1B1
+CIT interactsWith AKR1B1
+AG6P interactsWith AKR1B1
+NAG-(4-1)NAG interactsWith SERPINA3
+NAG-(4-1)NAG-(4-1)MAN interactsWith SERPINA3
+N-Acetyl-D-Glucosamine interactsWith REN
+SPS interactsWith GAPD
+HEM interactsWith 2MM1
+Palmitate interactsWith 2HMB
+DZF interactsWith DHFR
+DZF interactsWith DHFR
+ENC interactsWith HBB
+ENC interactsWith HBA2
+FUC-(1-6)NAG-(3-1)(4-2)NAG interactsWith LTF
+NAG-(6-1)FUC interactsWith LTF
+NAG-(6-1)FUC interactsWith LTF
+GAL-(1-4)NAG-(1-2)MAN-(1-3)MAN-(1-4)NAG-(1-4)NAG-(6-1)FUC-(4,6-1)MAN-(2-1)NAG interactsWith LTF
+N-Acetyl-D-Glucosamine interactsWith LTF
+N-Acetyl-D-Glucosamine interactsWith CTSD
+NAG-(4-1)NAG-(4-1)MAN-(6-1)MAN interactsWith CTSD
+NAG-(4-1)NAG-(4-1)MAN-(6-1)MAN interactsWith CTSD
+FUC-(1-6)NAG-(4-1)NAG-(4-1)MAN-(6-1)MAN-(2-1)NAG-(4-1)GAL-(3-2)SIA-(4,3-1)MAN-(2-1)NAG interactsWith 1MCO_H
+ interactsWith LYZ
+MUP interactsWith PNLIP
+GTT interactsWith LYZ
+N-Acetyl-D-Glucosamine interactsWith 1HNF
+N-Acetyl-D-Glucosamine interactsWith 1HNF
+N-Acetyl-D-Glucosamine interactsWith 1HNF
+NAG-(4-1)NAG interactsWith CGB
+NAG-(4-1)NAG interactsWith CGA
+NAG-(4-1)NAG interactsWith CGA
+aminocaproic_acid interactsWith 1PK2
+N-Acetyl-D-Glucosamine interactsWith ELA2
+N-Acetyl-D-Glucosamine interactsWith ELA2
+NAG-(6-1)FUC interactsWith ELA2
+FUC-(1-6)NAG-(4-1)NAG interactsWith ELA2
+FUC-(1-6)NAG-(4-1)NAG-(4-1)BMA interactsWith ELA2
+FUC-(1-6)NAG-(4-1)NAG-(4-1)BMA interactsWith ELA2
+HEM interactsWith MPO
+HEM interactsWith MPO
+NAG-(4-1)NAG interactsWith MPO
+NAG-(4-1)NAG interactsWith MPO
+NAG-(4-1)NAG interactsWith MPO
+HNI interactsWith HBA2
+SGN interactsWith FGF2
+UAP-(1-4)SGN-(1-4)IDU interactsWith FGF2
+AMH interactsWith PLG
+APA interactsWith F2
+EOX-EPO interactsWith CTSB
+EOX-EPO interactsWith CTSB
+EOX-EPO interactsWith Cathepsin_B
+V7O interactsWith CKS1B
+BMT-DHN-SAR-MLE-VAL-MLE-ALA-DAL-MLE-MLE-MVA interactsWith PPIA
+HAE-MOP-LEU-PHE-NH2 interactsWith MMP27
+HAE-MOP-LEU-PHE-NH2 interactsWith MMP27
+DEC interactsWith HBB
+TMM interactsWith HBB
+BTP-ASP-GM1 interactsWith MMP1
+HMP-ASP-GM1 interactsWith MMP1
+NAG-(6-1)FUC interactsWith Pr3
+NAG-(4-1)NAG-(4-1)MAN interactsWith SERPINA1
+NAG-(4-1)NAG interactsWith SERPINA1
+NAG-(4-1)NAG interactsWith SERPINA1
+N-Acetyl-D-Glucosamine interactsWith SERPINA1
+NAG-(4-1)NAG-(4-1)BMA-(6-1)BMA-(3,3-1)BMA interactsWith SERPINA1
+ISP interactsWith PRSS1
+RGS interactsWith 4GR1
+GTT interactsWith GSTA1
+GTT interactsWith GSTA1
+MAN-(1-3)MAN-(1-4)NAG-(1-4)NAG-(6-1)FUC-(2,6-1)MAN interactsWith MPO
+MAN-(1-3)MAN-(1-4)NAG-(1-4)NAG-(6-1)FUC-(2,6-1)MAN interactsWith MPO
+MAN-(1-3)MAN-(1-4)NAG-(1-4)NAG-(6-1)FUC-(2,6-1)MAN interactsWith MPO
+N-Acetyl-D-Glucosamine interactsWith MPO
+N-Acetyl-D-Glucosamine interactsWith MPO
+DMF-PHC-HII-CHA-IP3 interactsWith REN
+DMF-PHC-HII-CHA-IP3 interactsWith REN
+DMF-PHC-HII-CHA-IP4 interactsWith REN
+DMF-PHC-HII-CHA-IP4 interactsWith REN
+BMT-ABA-SAR-MLE-VAL-MLE-ALA-ALA-MLE-MLE-MVA interactsWith PPIA
+BMT-ABA-SAR-MLE-VAL-MLE-ALA-ALA-MLE-MLE-MVA interactsWith PPIA
+BMT-ABA-SAR-MLE-VAL-MLE-ALA-ALA-MLE-MLE-MVA interactsWith PPIA
+DMT-ABA-SAR-MLE-VAL-MLE-ALA-ALA-MLE-MLE-MVA interactsWith PPIA
+DMT-ABA-SAR-MLE-VAL-MLE-ALA-ALA-MLE-MLE-MVA interactsWith PPIA
+DMT-ABA-SAR-MLE-VAL-MLE-ALA-ALA-MLE-MLE-MVA interactsWith PPIA
+BMT-ABA-SAR-MNL-VAL-MLE-ALA-DAL-MLE-MLE-MVA interactsWith PPIA
+Stearic_acid interactsWith 1HMT
+GMP interactsWith HPRT1
+PPP-CPP-CHA-IP3 interactsWith REN
+RA interactsWith TTR
+RA interactsWith TTR
+ interactsWith LYZ
+NAG-(1-4)NAG-(1-4)NAG-(1-4)NAG interactsWith LYZ
+NDP interactsWith Dihydrofolate_Reductase
+COH interactsWith HBB
+N-Acetyl-D-Glucosamine interactsWith HLA-DRB1
+NAG-(4-1)NAG interactsWith HLA-DRA
+N-Acetyl-D-Glucosamine interactsWith HLA-DRA
+Folic_acid interactsWith DHFR
+Sulfanilamide interactsWith CA13
+NAG-(4-1)NAG interactsWith CD59
+NAG-(1-4)NAG-(6-1)FUC interactsWith CD59
+CBZ-ABU-LEU-PHE-EMR interactsWith MMP1
+CBZ-ABU-LEU-PHE-EMR interactsWith MMP1
+RA interactsWith CRABP1
+N-Acetyl-D-Glucosamine interactsWith CGB
+N-Acetyl-D-Glucosamine interactsWith CGB
+N-Acetyl-D-Glucosamine interactsWith CGB
+N-Acetyl-D-Glucosamine interactsWith CGA
+N-Acetyl-D-Glucosamine interactsWith CGA
+GSSG interactsWith 1GRA
+NDP interactsWith 1GRA
+NDP interactsWith 1GRB
+N-Acetyl-D-Glucosamine interactsWith F2
+N-Acetyl-D-Glucosamine interactsWith F2
+HEM interactsWith HBG2
+ANS-ARG-EPI interactsWith F2
+818 interactsWith FKBP1B
+NAG-(4-1)MAN-(6-1)MAN-(2-1)NAG-(4-1)GAL interactsWith 1FC2_D
+NAG-(4-1)MAN-(6-1)MAN-(2-1)NAG-(4-1)GAL-(2,3-1)MAN interactsWith 1FC1_B
+N-Acetyl-D-Glucosamine interactsWith 1FC1_B
+N-Acetyl-D-Glucosamine interactsWith 1FC1_B
+N-Acetyl-D-Glucosamine interactsWith 1FC2_D
+FUC-(1-6)NAG-(4-1)NAG-(4-1)MAN-(6-1)MAN-(2-1)NAG-(4-1)GAL-(4,3-1)MAN-(2-1)NAG interactsWith 1FC1_A
+T4 interactsWith TTR
+T4 interactsWith TTR
+NDP interactsWith AKR1B1
+GMPPNP interactsWith HRAS
+GppCp interactsWith HRAS
+GppCp interactsWith HRAS
+FUC-(1-6)NAG-(4-1)NAG interactsWith F2
+FUC-(1-6)NAG-(4-1)NAG-(4-1)MAN-(6-1)MAN interactsWith F2
+DPB interactsWith 5(3)-Deoxyribonucleotidase
+NAG-(4-1)NAG interactsWith EGFR
+N-Acetyl-D-Glucosamine interactsWith EGFR
+E4D interactsWith ESRRA
+GMP interactsWith TGM3
+NAG-(4-1)NAG-(4-1)MAN interactsWith EGFR
+Methacrylyl-CoA interactsWith ACAD8
+MRK interactsWith GCK
+BAX interactsWith BRAF
+PIE interactsWith PITPNA
+BI8 interactsWith PRKX
+CK8 interactsWith CDK2
+CK7 interactsWith CDK2
+CK6 interactsWith CDK2
+CK5 interactsWith CDK2
+BW2 interactsWith ATIC
+BW2 interactsWith ATIC
+N-Acetyl-D-Glucosamine interactsWith ICAM3
+N-Acetyl-D-Glucosamine interactsWith ICAM3
+N-Acetyl-D-Glucosamine interactsWith ICAM3
+myristic_acid interactsWith HNF4A
+DZN interactsWith ALDH1A2
+PLP interactsWith L-Serine_Dehydratase
+3CY interactsWith Caspase-3
+CNE interactsWith Caspase-3
+CNE interactsWith Caspase-3
+PTF interactsWith Caspase-3
+PTF interactsWith Caspase-3
+BOP interactsWith Caspase-3
+NA4 interactsWith Casp-3
+NA4 interactsWith Casp-3
+FPR interactsWith Caspase-3
+3CY interactsWith Caspase-3
+NA3 interactsWith Caspase-3
+NA3 interactsWith Caspase-3
+NAG-(4-1)NAG interactsWith CPM
+I1P interactsWith CDK3
+CIT interactsWith UCK2
+CTN interactsWith UCK2
+HEC interactsWith CYCS
+Celecoxib interactsWith CA2
+N2M interactsWith Heparin-Binding_Growth_Factor_1
+NAA-(1-4)NAA-(1-4)ALI interactsWith CHIT1
+ interactsWith CHIT1
+ interactsWith CHIT1
+NA1-(1-4)NAA-(1-4)AMI interactsWith CHIT1
+NA1-(1-4)NAG-(1-4)ALI interactsWith CHIT1
+FUC-(1-6)NAG-(4-1)NAG-(4-1)BMA interactsWith HLA-DQB1
+N-Acetyl-D-Glucosamine interactsWith HLA-DQA1
+N-Acetyl-D-Glucosamine interactsWith HLA-DQA1
+NGH interactsWith MMP10
+NGH interactsWith MMP10
+NGH interactsWith MMP10
+NGH interactsWith MMP10
+NGH interactsWith MMP10
+354 interactsWith ATIC
+354 interactsWith ATIC
+TQT interactsWith Dihydrofolate_Reductase
+TQD interactsWith Dihydrofolate_Reductase
+TQD interactsWith Dihydrofolate_Reductase
+FAD-RHP interactsWith MAOB
+FAD-RMA interactsWith MAOB
+FAD-RAS interactsWith MAOB
+FAD-RAS interactsWith MAOB
+LY4 interactsWith PRKACB
+ interactsWith GALM
+ interactsWith GALM
+ interactsWith GALM
+IBMX interactsWith PDE5A
+L08 interactsWith ITGAL
+L08 interactsWith ITGAL
+L08 interactsWith ITGAL
+NAG-(4-1)NAG-(4-1)MAN interactsWith Alpha-Galactosidase_A
+NAG-(4-1)NAG-(4-1)BMA-(3-1)MAN interactsWith Alpha-Galactosidase_A
+NAG-(4-1)NAG interactsWith Alpha-Galactosidase_A
+NAG-(4-1)NAG interactsWith Alpha-Galactosidase_A
+N-Acetyl-D-Glucosamine interactsWith Alpha-Galactosidase_A
+MAN-(1-3)MAN-(1-4)NAG-(1-4)NAG-(6-1)FUC-(2,6-1)MAN interactsWith Alpha-Galactosidase_A
+MAN-(1-3)MAN-(1-4)NAG-(1-4)NAG-(6-1)FUC-(2,6-1)MAN interactsWith Alpha-Galactosidase_A
+NAG-(4-1)NAG-(4-1)BMA-(6-1)BMA-(3,3-1)BMA interactsWith Alpha-Galactosidase_A
+NAG-(4-1)NAG-(4-1)BMA-(6-1)BMA-(3,3-1)BMA interactsWith Alpha-Galactosidase_A
+ interactsWith Alpha-Galactosidase_A
+DPN-PHE-ARM interactsWith Factor_Viia_Heavy_Chain
+N5B interactsWith CDK2
+292 interactsWith CDK2
+7IN interactsWith PLAU
+5IN interactsWith PLAU
+N-Acetyl-D-Glucosamine interactsWith Factor_Viia_Heavy_Chain
+N41 interactsWith Cell_Division_Protein_Kinase_2
+N76 interactsWith Cell_Division_Protein_Kinase_2
+N76 interactsWith Cell_Division_Protein_Kinase_2
+N20 interactsWith Cell_Division_Protein_Kinase_2
+PY1 interactsWith ACVR1B
+PM1 interactsWith CDK2
+Imatinib interactsWith KIT
+FTB interactsWith Phosphoenolpyruvate_Carboxykinase,_Cytosolic
+NAG-(4-1)NAG interactsWith EGFR
+N-Acetyl-D-Glucosamine interactsWith EGFR
+FUC-(1-6)NAG-(4-1)NAG-(4-1)BMA interactsWith EGFR
+NAG-(4-1)NAG-(4-1)BMA-(3-1)MAN interactsWith EGFR
+FUC-(1-6)NAG-(4-1)NAG interactsWith EGFR
+NAG-(4-1)NAG-(4-1)BMA-(3-1)MAN interactsWith GP1BA
+FUC-(1-6)NAG-(4-1)NAG-(4-1)BMA interactsWith C1R
+CIT interactsWith Tandem_Ph_Domain_Containing_Protein-1
+GTT interactsWith CLIC1
+N-Acetyl-D-Glucosamine interactsWith HLA-DQA2
+4HY interactsWith THRB
+4HY interactsWith THRB
+ interactsWith HEXB
+RA interactsWith RARB
+DHEA interactsWith Estrogenic_17-Beta_Hydroxysteroid_Dehydrogenase
+N-Acetyl-D-Glucosamine interactsWith CP
+N-Acetyl-D-Glucosamine interactsWith CP
+NW1 interactsWith CDK3
+CMG interactsWith CDK3
+FBI interactsWith HMGCR
+FBI interactsWith HMGCR
+Ca2+ interactsWith 1SMD
+NADP+ interactsWith AKR1B1
+NADP+ interactsWith AKR1B1
+CIT interactsWith AKR1B1
+Zn2+ interactsWith ACE2
+N-Acetyl-D-Glucosamine interactsWith ACE2
+GSH interactsWith GSTP1
+GSH interactsWith GSTP1
+Mg2+ interactsWith ITGAL
+Mg2+ interactsWith ITGAL
+PLP interactsWith OAT
+PLP interactsWith OAT
+myristic_acid interactsWith AFP
+myristic_acid interactsWith AFP
+myristic_acid interactsWith AFP
+myristic_acid interactsWith AFP
+myristic_acid interactsWith AFP
+myristic_acid interactsWith AFP
+myristic_acid interactsWith AFP
+myristic_acid interactsWith AFP
+myristic_acid interactsWith ALB
+S2C interactsWith Arginase_1
+Mn2+ interactsWith ARG1
+Mn2+ interactsWith ARG1
+Ebv-Peptide_Lpeplpqgqltay pp Hla_Class_I_Histocompatibility_Antigen,_B-35_Alpha_Chain
+Ebv-Peptide_Lpeplpqgqltay pp Hla_Class_I_Histocompatibility_Antigen,_B-35_Alpha_Chain
+Cl- interactsWith AMY2A
+Cl- interactsWith AKR1B1
+Cl- interactsWith ACE2
+Co_(2+) interactsWith Methionine_Aminopeptidase
+Co_(2+) interactsWith Methionine_Aminopeptidase
+1YFH_G pd Methylated-Dna--Protein-Cysteine_Methyltransferase
+1YFH_G pd Methylated-Dna--Protein-Cysteine_Methyltransferase
+1YFH_F pd Methylated-Dna--Protein-Cysteine_Methyltransferase
+1YFH_E pd Methylated-Dna--Protein-Cysteine_Methyltransferase
+1YFH_F pd Methylated-Dna--Protein-Cysteine_Methyltransferase
+2A1R_C interactsWith PARN
+Lctpsra_Peptide_From_Arylsulfatase_A pp SUMF1
+Ctpsr_Peptide_From_Arylsulfatase_A pp SUMF1
+Elastase-1 pp Alpha-1-Antitrypsin
+Consensus_Peptide_Mode_1_For_14-3-3_Proteins pp 14-3-3_Protein_Eta
+Voltage-Dependent_L-Type_Calcium_Channel_Alpha-_1c_Subunit pp CALM1
+Voltage-Dependent_L-Type_Calcium_Channel_Alpha-_1c_Subunit pp CALM1
+Ca2+ interactsWith CALM2
+Ca2+ interactsWith CALM2
+Ca2+ interactsWith CALM2
+Ca2+ interactsWith CALM2
+alpha-D-Glucose interactsWith F7
+alpha-D-Glucose interactsWith F7
+alpha-D-Glucose interactsWith F7
+Ca2+ interactsWith F7
+Ca2+ interactsWith F7
+Ca2+ interactsWith F7
+Ca2+ interactsWith F7
+Ca2+ interactsWith F7
+Ca2+ interactsWith F7
+Ca2+ interactsWith F7
+Ca2+ interactsWith F7
+Ca2+ interactsWith F7
+Ca2+ interactsWith F7
+Ca2+ interactsWith F7
+Ca2+ interactsWith F7
+Ca2+ interactsWith F7
+Ca2+ interactsWith F7
+Ca2+ interactsWith F7
+Cu2+ interactsWith SOD1
+alpha-L-fucose interactsWith Tissue_Factor
+Monastrol interactsWith KIF11
+N-Acetyl-D-Glucosamine interactsWith FAP
+UDP interactsWith GBGT1
+Mn2+ interactsWith GBGT1
+alpha-L-fucose interactsWith F7
+alpha-L-fucose interactsWith F7
+alpha-L-fucose interactsWith F7
+alpha-L-fucose interactsWith F7
+alpha-L-fucose interactsWith F7
+alpha-L-fucose interactsWith F7
+alpha-L-fucose interactsWith F7
+alpha-L-fucose interactsWith F7
+N-Acetyl-D-Glucosamine interactsWith DPP4
+NAG-(4-1)NAG interactsWith GBA
+NAG-(4-1)NAG-(4-1)MAN-(4-1)MAN interactsWith DPP10
+NAG-(4-1)NAG-(4-1)MAN-(4-1)MAN interactsWith DPP10
+NAG-(4-1)NAG-(4-1)MAN-(4-1)MAN interactsWith DPP10
+NAG-(4-1)NAG-(4-1)MAN-(4-1)MAN interactsWith DPP10
+NAG-(4-1)NAG-(4-1)MAN interactsWith DPP10
+NAG-(4-1)NAG-(4-1)MAN interactsWith DPP10
+NAG-(4-1)NAG-(4-1)MAN interactsWith DPP10
+NAG-(4-1)NAG-(4-1)MAN interactsWith DPP10
+NAG-(4-1)NAG-(4-1)MAN interactsWith DPP10
+NAG-(4-1)NAG-(4-1)MAN interactsWith DPP10
+NAG-(4-1)NAG interactsWith DPP10
+NAG-(4-1)NAG interactsWith DPP10
+NAG-(4-1)NAG interactsWith DPP10
+NAG-(4-1)NAG interactsWith DPP10
+HEM interactsWith HMOX1
+D91 interactsWith Coagulation_Factor_X,_Heavy_Chain
+3BP interactsWith F7
+3CB interactsWith F7
+Zn2 interactsWith Skeletal_Muscle_Lim-Protein_3
+Zn2 interactsWith Skeletal_Muscle_Lim-Protein_3
+Zn2 interactsWith Skeletal_Muscle_Lim-Protein_3
+Zn2 interactsWith Skeletal_Muscle_Lim-Protein_3
+Zn2 interactsWith Ring_Finger_Protein_38
+Zn2 interactsWith Ring_Finger_Protein_38
+Zn2 interactsWith Inhibitor_Of_Growth_Protein_3
+Zn2 interactsWith Inhibitor_Of_Growth_Protein_3
+GMPPNP interactsWith Ras-Related_Protein_Rab-18
+Mg2 interactsWith Ras-Related_Protein_Rab-18
+Zn2 interactsWith Leupaxin
+Zn2 interactsWith Leupaxin
+Zn2 interactsWith Zinc_Finger_Protein_292
+LI4 interactsWith MAPK14
+LI3 interactsWith MAPK14
+WBT interactsWith MAPK14
+LI2 interactsWith MAPK14
+L09 interactsWith MAPK14
+Zn2 interactsWith Zinc_Finger_Hit_Domain_Containing_Protein_2
+Zn2 interactsWith Zinc_Finger_Hit_Domain_Containing_Protein_2
+HEM interactsWith Heme_Oxygenase_1
+HEM interactsWith Heme_Oxygenase_1
+TRR interactsWith Dihydrofolate_Reductase
+NDP interactsWith Dihydrofolate_Reductase
+Zn2 interactsWith Skeletal_Muscle_Lim-Protein_1
+Zn2 interactsWith Skeletal_Muscle_Lim-Protein_1
+Zn2 interactsWith C-Terminal_Lim_Domain_Protein_1
+Zn2 interactsWith C-Terminal_Lim_Domain_Protein_1
+Zn2 interactsWith Thyroid_Receptor_Interacting_Protein_6
+Zn2 interactsWith Thyroid_Receptor_Interacting_Protein_6
+Zn2 interactsWith Zinc_Finger_Protein_64,_Isoforms_1
+Zn2 interactsWith Zinc_Finger_Protein_64,_Isoforms_1
+Zn2 interactsWith Hypothetical_Protein_Flj13222
+Zn2 interactsWith Hypothetical_Protein_Flj13222
+Zn2 interactsWith Hypothetical_Protein_Loc130617
+Zn2 interactsWith Hypothetical_Protein_Loc130617
+Zn2 interactsWith Fhl5_Protein
+Zn2 interactsWith Fhl5_Protein
+Zn2 interactsWith Transcriptional_Repressor_Ctcf
+Zn2 interactsWith Transcriptional_Repressor_Ctcf
+Zn2 interactsWith Zinc_Finger_Protein_462
+Zn2 interactsWith Zinc_Finger_Protein_24
+Zn2 interactsWith Zinc_Finger_Protein_24
+Zn2 interactsWith Lim_Domain_Kinase_2
+Zn2 interactsWith Lim_Domain_Kinase_2
+Zn2 interactsWith Zinc_Finger,_Fyve_Domain_Containing_27_Isoform_B
+Zn2 interactsWith Zinc_Finger,_Fyve_Domain_Containing_27_Isoform_B
+DR5 interactsWith ABO
+GAL interactsWith ABO
+Mn2 interactsWith ABO
+UDP interactsWith ABO
+DR4 interactsWith ABO
+DR4 interactsWith ABO
+NLC interactsWith ABO
+NLC interactsWith ABO
+Lactose interactsWith ABO
+DR3 interactsWith ABO
+DR3 interactsWith ABO
+NAG-(4-1)GAL-(2-1)FUC interactsWith ABO
+NAG-(4-1)GAL-(2-1)FUC interactsWith ABO
+NAG-(4-1)NAG interactsWith SUMF1
+Acetamide interactsWith SUMF1
+Ca2 interactsWith SUMF1
+Ca2+ interactsWith SUMF1
+Ca2+ interactsWith SUMF1
+Ca2 interactsWith SUMF1
+S-Adenosylhomocysteine interactsWith Adrenal_Gland_Protein_Ad-003
+GMPPNP interactsWith Ras-Related_Protein_Rab-30
+Mg2 interactsWith Ras-Related_Protein_Rab-30
+HEX interactsWith Glycolipid_Transfer_Protein
+CoA interactsWith Acetyl-Coa_Acetyltransferase,_Mitochondrial
+NADP interactsWith DECR1
+CoA interactsWith Acetyl-Coa_Acetyltransferase,_Mitochondrial
+CoA interactsWith Acetyl-Coa_Acetyltransferase,_Mitochondrial
+Mg2 interactsWith Hydroxymethylglutaryl-Coa_Lyase,_Mitochondrial
+Y27632 interactsWith Rho-Associated_Protein_Kinase_1
+H52 interactsWith Rho-Associated_Protein_Kinase_1
+HFS interactsWith Rho-Associated_Protein_Kinase_1
+3',5'-ADP interactsWith Sulfotransferase_1c1
+HA1077 interactsWith Rho-Associated_Protein_Kinase_1
+GDP interactsWith Ras-Related_Protein_R-Ras2
+Mg2 interactsWith Ras-Related_Protein_R-Ras2
+Zn2 interactsWith Methylated-Dna--Protein-Cysteine_Methyltransferase
+Cu1 interactsWith ATP7A
+P5B interactsWith F7
+alpha-D-Glucose interactsWith F7
+HEM interactsWith Heme_Oxygenase_1
+F29 interactsWith Mitogen-Activated_Protein_Kinase_1
+5PI interactsWith F7
+Hexanoyl-CoA interactsWith DECR1
+Hexanoyl-CoA interactsWith DECR1
+Hexanoyl-CoA interactsWith DECR1
+Hexanoyl-CoA interactsWith DECR1
+Hexanoyl-CoA interactsWith DECR1
+Ca2 interactsWith PPIC
+BMT-ABA-SAR-MLE-VAL-MLE-ALA-ALA-MLE-MLE-MVA interactsWith PPIC
+BMT-ABA-SAR-MLE-VAL-MLE-ALA-ALA-MLE-MLE-MVA interactsWith PPIA
+BMT-ABA-SAR-MLE-VAL-MLE-ALA-ALA-MLE-MLE-MVA interactsWith PPIC
+BMT-ABA-SAR-MLE-VAL-MLE-ALA-ALA-MLE-MLE-MVA interactsWith PPIC
+4SP interactsWith CDK2
+DT4 interactsWith CDK2
+DT2 interactsWith CDK2
+DT1 interactsWith CDK2
+CT8 interactsWith CDK2
+CT6 interactsWith CDK2
+NAG-(4-1)NAG interactsWith GAS6
+NAG-(4-1)NAG interactsWith GAS6
+Ca2 interactsWith GAS6
+DT5 interactsWith CDK2
+DT5 interactsWith CDK2
+Zn2 interactsWith SOD1
+Zn2+ interactsWith SOD1
+Zn2+ interactsWith SOD1
+44C interactsWith TTR
+44C interactsWith TTR
+1C2 interactsWith PTPN1
+N-Acetyl-D-Glucosamine interactsWith GBA
+23D interactsWith PAK7
+ZIP interactsWith CDK2
+SK2 interactsWith PTPN1
+UN3 interactsWith PTPN1
+ENT interactsWith PTPN1
+HEM interactsWith CYP2D6
+205 interactsWith TTR
+Malonic_acid interactsWith GPX1
+GDP interactsWith RAB27B
+26C interactsWith TTR
+UN7 interactsWith PTPN1
+UN5 interactsWith PTPN1
+Na+ interactsWith F2
+Na+ interactsWith F2
+Na+ interactsWith F2
+Na+ interactsWith F2
+Mg2+ interactsWith 1IDO
+ADP interactsWith DCK
+FAD interactsWith MAOB
+Mg2+ interactsWith Integrin_Alpha-M
+Mg2+ interactsWith Cd11b
+N-Acetyl-D-Glucosamine interactsWith FAP
+N-Acetyl-D-Glucosamine interactsWith FAP
+N-Acetyl-D-Glucosamine interactsWith FAP
+Ca2+ interactsWith Integrin_Alpha-M
+Mn2+ interactsWith PPP1CC
+Mn2+ interactsWith PPP1CC
+Mn2+ interactsWith PPP1CC
+Mn2+ interactsWith PPP1CC
+FAD interactsWith Dihydrolipoyl_Dehydrogenase
+FAD interactsWith Dihydrolipoyl_Dehydrogenase
+Ca2 interactsWith Calmodulin
+Ca2 interactsWith Calmodulin
+Mg2 interactsWith Deoxycytidine_Kinase
+UDP interactsWith Deoxycytidine_Kinase
+2'-Deoxycytidine interactsWith Deoxycytidine_Kinase
+MO3 interactsWith Deoxycytidine_Kinase
+MO3 interactsWith Deoxycytidine_Kinase
+CK9 interactsWith Cell_Division_Protein_Kinase_2
+Mg2 interactsWith Forkhead_Box_Protein_P2
+Mg2 interactsWith Forkhead_Box_Protein_P2
+CFB interactsWith Deoxycytidine_Kinase
+GMP interactsWith Gmp_Reductase_2
+3PI interactsWith Myotubularin-Related_Protein_2
+MSG interactsWith Purine_Nucleoside_Phosphorylase
+RA4 interactsWith Thrombin_Heavy_Chain
+RA8 interactsWith Thrombin_Heavy_Chain
+CCR interactsWith Prothrombin_Heavy_Chain
+UIB interactsWith Thrombin_Heavy_Chain
+UIR interactsWith Thrombin_Heavy_Chain
+UIP interactsWith Thrombin_Heavy_Chain
+P01 interactsWith Proto-Oncogene_Tyrosine-Protein_Kinase_Src
+S03 interactsWith Proto-Oncogene_Tyrosine-Protein_Kinase_Src
+PIB interactsWith Myotubularin-Related_Protein_2
+C1N interactsWith Calpain_1,_Large_[catalytic]_Subunit
+Ca2 interactsWith Calpain_1,_Large_[catalytic]_Subunit
+Ca2 interactsWith Calpain_1,_Large_[catalytic]_Subunit
+S03 interactsWith Proto-Oncogene_Tyrosine-Protein_Kinase_Src
+CoA interactsWith Diamine_Acetyltransferase_1
+CoA interactsWith Diamine_Acetyltransferase_1
+FS4 interactsWith Iron-Responsive_Element_Binding_Protein_1
+Acetyl-CoA interactsWith Diamine_Acetyltransferase_1
+B7G interactsWith PPARD
+NDG interactsWith DPP4
+AMK interactsWith Beta-Secretase_1
+AMK interactsWith Beta-Secretase_1
+AMK interactsWith Beta-Secretase_1
+AUA interactsWith Beta-Secretase_1
+628 interactsWith Cell_Division_Protein_Kinase_2
+Trifluoperazine interactsWith Troponin_C,_Slow_Skeletal_And_Cardiac_Muscles
+Trifluoperazine interactsWith Troponin_C,_Slow_Skeletal_And_Cardiac_Muscles
+Trifluoperazine interactsWith Troponin_C,_Slow_Skeletal_And_Cardiac_Muscles
+Trifluoperazine interactsWith Troponin_C,_Slow_Skeletal_And_Cardiac_Muscles
+Ca2 interactsWith Troponin_C,_Slow_Skeletal_And_Cardiac_Muscles
+B33 interactsWith Diamine_Acetyltransferase_1
+S-Adenosylhomocysteine interactsWith Histone-Lysine_N-Methyltransferase,_H3_Lysine-4_Specific_Set7
+VX6 interactsWith Proto-Oncogene_Tyrosine-Protein_Kinase_Abl1
+PIM interactsWith Indoleamine_2,3-Dioxygenase
+HEM interactsWith Indoleamine_2,3-Dioxygenase
+073 interactsWith Tyrosine-Protein_Phosphatase,_Non-Receptor_Type_1
+073 interactsWith Tyrosine-Protein_Phosphatase,_Non-Receptor_Type_1
+073 interactsWith Tyrosine-Protein_Phosphatase,_Non-Receptor_Type_1
+GSH interactsWith Glutaredoxin-2
+Mg2 interactsWith Ras-Related_Protein_R-Ras
+GDP interactsWith Ras-Related_Protein_Rab-1a
+Mg2 interactsWith Ras-Related_Protein_Rab-1a
+GDP interactsWith Ras-Related_Protein_R-Ras
+Zn2 interactsWith Cellular_Tumor_Antigen_P53
+FRP interactsWith Beta-Secretase_1
+(R,R)-2,3_Butanediol interactsWith Tryptase_Alpha-1
+FUC-(1-3)NAG interactsWith Tryptase_Alpha-1
+N-Acetyl-D-Glucosamine interactsWith Tryptase_Alpha-1
+NAG-(1-4)NAG-(3-1)FUC interactsWith Tryptase_Alpha-1
+(R,R)-2,3_Butanediol interactsWith Alpha_I_Tryptase
+(R,R)-2,3_Butanediol interactsWith Alpha_I_Tryptase
+N-Acetyl-D-Glucosamine interactsWith Alpha_I_Tryptase
+FUC-(1-3)NAG-(6-1)FUC-(2,4-1)NAG interactsWith Alpha_I_Tryptase
+GMPPNP interactsWith Ras-Related_Protein_Rab-31
+Mg2 interactsWith Ras-Related_Protein_Rab-31
+UDP interactsWith Polypeptide_N-Acetylgalactosaminyltransferase_2
+NDG interactsWith Dipeptidyl_Peptidase_4
+FPB interactsWith Dipeptidyl_Peptidase_4
+N-Acetyl-D-Glucosamine interactsWith Dipeptidyl_Peptidase_4
+IZA interactsWith Tyrosine-Protein_Kinase_Jak2
+CoA interactsWith Diamine_Acetyltransferase_1
+DLQ interactsWith SerineTHREONINE_PROTEIN_PHOSPHATASE_PP1-Gamma_Catalytic_Subunit
+MOQ interactsWith SerineTHREONINE_PROTEIN_PHOSPHATASE_PP1-Gamma_Catalytic_Subunit
+cis-Vaccenate interactsWith Peroxisome_Proliferator_Activated_Receptor_Delta
+cis-Vaccenate interactsWith Peroxisome_Proliferator_Activated_Receptor_Delta
+B7G interactsWith Peroxisome_Proliferator_Activated_Receptor_Delta
+B7G interactsWith Peroxisome_Proliferator_Activated_Receptor_Delta
+B7G interactsWith Peroxisome_Proliferator_Activated_Receptor_Delta
+B33 interactsWith Diamine_Acetyltransferase_1
+B4P interactsWith Adenylate_Kinase_Isoenzyme_2,_Mitochondrial
+Na interactsWith Receptor-Type_Tyrosine-Protein_Phosphatase_Mu
+Na interactsWith Receptor-Type_Tyrosine-Protein_Phosphatase_Mu
+N-Acetyl-D-Glucosamine interactsWith Receptor-Type_Tyrosine-Protein_Phosphatase_Mu
+NDG-(1-4)NAG-(6-1)AFL interactsWith Receptor-Type_Tyrosine-Protein_Phosphatase_Mu
+NAG-(4-1)NAG-(4-1)BMA-(3-1)MAN interactsWith Receptor-Type_Tyrosine-Protein_Phosphatase_Mu
+HPM interactsWith SerineTHREONINE-Protein_Kinase_6
+HPM interactsWith SerineTHREONINE-Protein_Kinase_6
+AMP-PNP interactsWith SerineTHREONINE-Protein_Kinase_6
+Zn2 interactsWith Ubiquitin-Protein_Ligase_E3_Mdm2
+RM1 interactsWith Amine_Oxidase_(Flavin-Containing)_B
+ADP interactsWith Nonsecretory_Ribonuclease
+ATP interactsWith Nonsecretory_Ribonuclease
+FAD-RM2 interactsWith Amine_Oxidase_(Flavin-Containing)_B
+FAD-MA0 interactsWith Amine_Oxidase_(Flavin-Containing)_B
+IMZ interactsWith Ubiquitin-Protein_Ligase_E3_Mdm2
+IMZ interactsWith Ubiquitin-Protein_Ligase_E3_Mdm2
+IMZ interactsWith Ubiquitin-Protein_Ligase_E3_Mdm2
+IMZ interactsWith Ubiquitin-Protein_Ligase_E3_Mdm2
+IMZ interactsWith Ubiquitin-Protein_Ligase_E3_Mdm2
+Acetoacetyl-CoA interactsWith 3-Hydroxyacyl-Coa_Dehydrogenase
+Acetoacetyl-CoA interactsWith 3-Hydroxyacyl-Coa_Dehydrogenase
+Acetoacetyl-CoA interactsWith 3-Hydroxyacyl-Coa_Dehydrogenase
+Acetoacetyl-CoA interactsWith 3-Hydroxyacyl-Coa_Dehydrogenase
+Acetoacetyl-CoA interactsWith 3-Hydroxyacyl-Coa_Dehydrogenase
+NADH interactsWith L-3-Hydroxyacyl-Coa_Dehydrogenase
+3HC interactsWith L-3-Hydroxyacyl-Coa_Dehydrogenase
+3HC interactsWith L-3-Hydroxyacyl-Coa_Dehydrogenase
+Zn2+ interactsWith Hydroxyacylglutathione_Hydrolase
+Zn2+ interactsWith Hydroxyacylglutathione_Hydrolase
+GBP interactsWith Hydroxyacylglutathione_Hydrolase
+GTT interactsWith Hydroxyacylglutathione_Hydrolase
+Mn2+ interactsWith Hydroxyacylglutathione_Hydrolase
+NAD+ interactsWith L-3-Hydroxyacyl_Coa_Dehydrogenase
+NAD+ interactsWith 3-Hydroxyacyl-Coa_Dehydrogenase
+NAD+ interactsWith 3-Hydroxyacyl-Coa_Dehydrogenase
+NAD+ interactsWith 3-Hydroxyacyl-Coa_Dehydrogenase
+NAD+ interactsWith 3-Hydroxyacyl-Coa_Dehydrogenase
+AMP-PNP interactsWith Death-Associated_Protein_Kinase
+AMP-PNP interactsWith Death-Associated_Protein_Kinase
+Mn2+ interactsWith Death-Associated_Protein_Kinase
+NAG-(6-1)FUC interactsWith Von_Willebrand_Factor
+Flavocytochrome_B558_Alpha_Polypeptide pp Neutrophil_Cytosol_Factor_1
+Flavocytochrome_B558_Alpha_Polypeptide pp Neutrophil_Cytosol_Factor_1
+Botrocetin pp Von_Willebrand_Factor
+Botrocetin pp Von_Willebrand_Factor
+N-Acetyl-D-Glucosamine interactsWith ITGB2
+N-Acetyl-D-Glucosamine interactsWith ITGB2
+N-Acetyl-D-Glucosamine interactsWith ITGB2
+DIZ interactsWith Ubiquitin-Protein_Ligase_E3_Mdm2
+Mg2+ interactsWith Cystic_Fibrosis_Transmembrane_Conductance_Regulator
+AGG interactsWith Integrin_Alpha-Iib
+NAG-(4-1)NAG-(4-1)BMA-(6-1)BMA-(3,3-1)BMA interactsWith Integrin_Alpha-Iib
+N-Acetyl-D-Glucosamine interactsWith Integrin_Alpha-Iib
+N-Acetyl-D-Glucosamine interactsWith Integrin_Alpha-Iib
+NAG-(4-1)NAG-(4-1)BMA-(3-1)MAN interactsWith Integrin_Alpha-Iib
+DRG interactsWith Death-Associated_Protein_Kinase_1
+Ca2+ interactsWith Annexin_A8
+ATP interactsWith CFTR
+ATP interactsWith CFTR
+180 interactsWith Integrin_Alpha-Iib
+Ca2+ interactsWith Integrin_Alpha-Iib
+Ca2+ interactsWith Integrin_Alpha-Iib
+Ca2+ interactsWith Integrin_Alpha-Iib
+Ca2+ interactsWith Integrin_Alpha-Iib
+Optimized_P53_Peptide pp Ubiquitin-Protein_Ligase_E3_Mdm2
+Eptifibatide pp Integrin_Alpha-Iib
+ATP interactsWith Cystic_Fibrosis_Transmembrane_Conductance_Regulator
+PAX6_BRARE pp PKNX1_HUMAN
+PAX6_BRARE pp HXB1_HUMAN
+PAX6_BRARE pp PROX1_HUMAN
+LHX3_MOUSE pp ISL1_HUMAN
+LHX3_MOUSE pp ISL1_HUMAN
+PBX1_MOUSE pp PKNX1_HUMAN
+Zn2+ interactsWith MMP8
+Zn2+ interactsWith MMP8
+HEM interactsWith HBB
+HEM interactsWith HBB
+HEM interactsWith HBB
+HEM interactsWith HBA2
+HEM interactsWith HBA2
+GDP interactsWith HRAS
+GDP interactsWith HRAS
+GDP interactsWith HRAS
+Zn2+ interactsWith CA13
+Mg2+ interactsWith HRAS
+Mg2+ interactsWith HRAS
+Ca2+ interactsWith MMP13
+Ca2+ interactsWith MMP13
+Ca2+ interactsWith MMP13
+Zn2+ interactsWith MMP13
+Zn2+ interactsWith MMP13
+Zn2+ interactsWith MMP13
+Zn2+ interactsWith MMP13
+Mg2+ interactsWith CDK3
+ATP interactsWith CDK3
+Ca2+ interactsWith MMP8
+Ca2+ interactsWith MMP8
+HEM interactsWith CYGB
+NAG-(4-1)NAG interactsWith HEXB
+AFL-(1-6)NAG-(4-1)NAG-(4-1)BMA-(6-1)BMA-(2-1)NAG-(4-1)GAL-(4,3-1)BMA interactsWith Ig_Gamma-1_Chain_C_Region
+NGT interactsWith HEXB
+3',5'-ADP interactsWith SULT1A1
+Mg2+ interactsWith PDE5A
+Zn2+ interactsWith PDE5A
+Zn2+ interactsWith PDE5A
+Ca2+ interactsWith F10
+Ca2+ interactsWith F10
+Ca2+ interactsWith F10
+Ca2+ interactsWith F10
+Ca2+ interactsWith MMP3
+Ca2+ interactsWith MMP3
+Ca2+ interactsWith MMP3
+Ca2+ interactsWith MMP3
+Ca2+ interactsWith MMP3
+Ca2+ interactsWith MMP3
+FAD interactsWith NQO1
+FAD interactsWith NQO1
+GTP interactsWith HRAS
+GTP interactsWith HRAS
+GTP interactsWith HRAS
+Glycolic_acid interactsWith Glucose-6-Phosphate_1-Dehydrogenase
+Glycolic_acid interactsWith Glucose-6-Phosphate_1-Dehydrogenase
+N-Acetyl-D-Glucosamine interactsWith SERPINC1
+N-Acetyl-D-Glucosamine interactsWith SERPINC1
+N-Acetyl-D-Glucosamine interactsWith SERPINC1
+NAG-(4-1)NAG interactsWith SERPINC1
+NAG-(4-1)NAG interactsWith SERPINC1
+NAG-(4-1)NAG interactsWith SERPINC1
+ADP interactsWith KIF11
+ADP interactsWith KIF11
+Mg2+ interactsWith KIF11
+GDP interactsWith GNAI1
+Ca2+ interactsWith ANGPT2
+Cl- interactsWith TASP1
+DIH interactsWith NP
+1ZTG_Z pd Poly(Rc)-Binding_Protein_1
+Hirudin_I pp Thrombin
+Nuclear_Receptor_Coactivator_2 pp Estrogen_Receptor
+Glucocorticoid_Receptor_Interacting_Protein_1 pp ESR1
+Glucocorticoid_Receptor_Interacting_Protein_1 pp ESR1
+Steroid_Receptor_Coactivator-3 pp ESR1
+Oncoprotein pp Retinoblastoma_Protein
+Collybistin_Ii pp Cell_Division_Cycle_42_Isoform_1
+phosphotyrosine interactsWith Human_Protein_Tyrosine_Phosphatase_Ptpn5
+GSK interactsWith Activated_Factor_Xa_Heavy_Chain
+093 interactsWith Phosphatidylinositol-4,5-Bisphosphate_3-Kinase_Catalytic_Subunit_Gamma_Isoform
+GMPPNP interactsWith Gtpase_Hras
+XY2 interactsWith Gtpase_Hras
+Mg2 interactsWith Rho-Related_Gtp-Binding_Protein_Rho6
+GTP interactsWith Rho-Related_Gtp-Binding_Protein_Rho6
+STU interactsWith Mitogen-Activated_Protein_Kinase_Kinase_Kinase_5
+NDP interactsWith Aflatoxin_B1_Aldehyde_Reductase_Member_3
+Mg2 interactsWith Gtpase_Hras
+CAG interactsWith Gtpase_Hras
+090 interactsWith Phosphatidylinositol-4,5-Bisphosphate_3-Kinase_Catalytic_Subunit_Gamma_Isoform
+039 interactsWith Phosphatidylinositol-4,5-Bisphosphate_3-Kinase_Catalytic_Subunit_Gamma_Isoform
+ATP interactsWith Multidrug_Resistance-Associated_Protein_1
+Mg2 interactsWith Multidrug_Resistance-Associated_Protein_1
+ATP interactsWith Cell_Division_Protein_Kinase_2
+ATP interactsWith Cell_Division_Protein_Kinase_2
+TXF interactsWith Estrogen-Related_Receptor_Gamma
+CAG interactsWith Gtpase_Hras
+MBN interactsWith Hemoglobin_Alpha_Subunit
+TXF interactsWith Estrogen-Related_Receptor_Gamma
+TGG interactsWith Aldose_Reductase
+NDP interactsWith Aldose_Reductase
+FAD interactsWith Nad(P)h_Dehydrogenase_[quinone]_1
+FAD interactsWith Nad(P)h_Dehydrogenase_[quinone]_1
+DTC interactsWith Nad(P)h_Dehydrogenase_[quinone]_1
+DTC interactsWith Nad(P)h_Dehydrogenase_[quinone]_1
+624 interactsWith Coagulation_Factor_Xi
+421 interactsWith Coagulation_Factor_Xi
+709 interactsWith Coagulation_Factor_Xi
+MIB interactsWith Histone_Acetyltransferase_Pcaf
+367 interactsWith Coagulation_Factor_Xi
+BUK interactsWith Coagulation_Factor_Xi
+632 interactsWith Coagulation_Factor_Xi
+62A interactsWith Coagulation_Factor_Xi
+Ca2 interactsWith Collagenase_3
+FIN interactsWith Neutrophil_Collagenase
+033 interactsWith Collagenase_3
+339 interactsWith Coagulation_Factor_Xi
+427 interactsWith Coagulation_Factor_Xi
+412 interactsWith Coagulation_Factor_Xi
+Zn2 interactsWith Carbonic_Anhydrase_Ii
+MIU interactsWith Thrombin
+FUN interactsWith Carbonic_Anhydrase_Ii
+NR2 interactsWith Carbonic_Anhydrase_Ii
+NR2 interactsWith Carbonic_Anhydrase_Ii
+HDB interactsWith Coagulation_Factor_Xi
+368 interactsWith Coagulation_Factor_Xi
+689 interactsWith Estrogen_Receptor
+689 interactsWith Estrogen_Receptor
+MPX interactsWith Carbonic_Anhydrase_Ii
+TRU interactsWith Carbonic_Anhydrase_Ii
+SDA interactsWith Carbonic_Anhydrase_Ii
+ZEC interactsWith Carbonic_Anhydrase_Ii
+ZEC interactsWith Carbonic_Anhydrase_Ii
+17H interactsWith Androgen_Receptor
+Stanolone interactsWith Androgen_Receptor
+Testosterone interactsWith Androgen_Receptor
+GSN interactsWith Glutathione_S-Transferase_P
+GSN interactsWith Glutathione_S-Transferase_P
+DIH interactsWith Purine_Nucleoside_Phosphorylase
+NAG-(4-1)NAG-(4-1)BMA-(3-1)MAN interactsWith Hla_Class_Ii_Histocompatibility_Antigen,_Dm_Beta_Chain
+NAG-(4-1)NAG-(4-1)BMA-(3-1)MAN interactsWith Hla_Class_Ii_Histocompatibility_Antigen,_Dm_Alpha_Chain
+458 interactsWith Estrogen_Receptor
+458 interactsWith Estrogen_Receptor
+DIH interactsWith Purine_Nucleoside_Phosphorylase
+Mg2 interactsWith Kinesin-Like_Protein_Kif2
+ADP interactsWith Kinesin-Like_Protein_Kif2
+Ca2 interactsWith Dihydropyrimidinase-Related_Protein_2
+672 interactsWith Suppressor_Of_Tumorigenicity_14
+730 interactsWith Suppressor_Of_Tumorigenicity_14
+Mg2 interactsWith Guanine_Nucleotide-Binding_Protein_G(I),_Alpha-1_Subunit
+Cu1 interactsWith Sco1_Protein_Homolog,_Mitochondrial
+Ni2 interactsWith Sco1_Protein_Homolog,_Mitochondrial
+877 interactsWith Mitogen-Activated_Protein_Kinase_8
+2-Oxoglutaric_acid interactsWith Jumonji_Domain-Containing_Protein_2a
+Fe3 interactsWith Jumonji_Domain-Containing_Protein_2a
+Zn2 interactsWith Jumonji_Domain-Containing_Protein_2a
+Mg2 interactsWith Cgmp-Specific_3',5'-Cyclic_Phosphodiesterase
+VIA interactsWith Cgmp-Specific_3',5'-Cyclic_Phosphodiesterase
+VIA interactsWith Cgmp-Specific_3',5'-Cyclic_Phosphodiesterase
+VIA interactsWith Cgmp-Specific_3',5'-Cyclic_Phosphodiesterase
+F3G interactsWith Caspase_1,_Isoform_Gamma
+F3G interactsWith Caspase_1,_Isoform_Gamma
+7CA interactsWith Cgmp-Specific_3',5'-Cyclic_Phosphodiesterase
+PCP interactsWith Sulfotransferase_1c2
+3',5'-ADP interactsWith Sulfotransferase_1c2
+N-Acetyl-D-Glucosamine interactsWith Angiopoietin-1_Receptor
+N-Acetyl-D-Glucosamine interactsWith Angiopoietin-1_Receptor
+N-Acetyl-D-Glucosamine interactsWith Angiopoietin-1_Receptor
+N-Acetyl-D-Glucosamine interactsWith Angiopoietin-1_Receptor
+NAG-(4-1)NAG-(4-1)NAG-(4-1)NAG interactsWith Angiopoietin-1_Receptor
+Zn2 interactsWith Ubiquitin_Ligase_Protein_Ring2
+Zn2 interactsWith Ubiquitin_Ligase_Protein_Ring2
+Zn2 interactsWith B_Lymphoma_Mo-Mlv_Insertion_Region
+Zn2 interactsWith B_Lymphoma_Mo-Mlv_Insertion_Region
+OVA interactsWith Methionine_Aminopeptidase_1
+Co_(2+) interactsWith Methionine_Aminopeptidase_1
+NAG-(4-1)NAG interactsWith Angiopoietin-1_Receptor
+NAG-(4-1)NAG interactsWith Angiopoietin-1_Receptor
+F2G interactsWith Caspase-1
+F2G interactsWith Caspase-1
+F1G interactsWith Caspase-1
+F1G interactsWith Caspase-1
+DPN interactsWith Carbonic_Anhydrase_2
+Phenylalanine interactsWith Carbonic_Anhydrase_2
+459 interactsWith Estrogen_Receptor
+459 interactsWith Estrogen_Receptor
+N-Acetyl-D-Glucosamine interactsWith Coagulation_Factor_Xi
+N-Acetyl-D-Glucosamine interactsWith Coagulation_Factor_Xi
+Ca2 interactsWith Low-Density_Lipoprotein_Receptor
+Ca2 interactsWith Low-Density_Lipoprotein_Receptor
+Na interactsWith Low-Density_Lipoprotein_Receptor
+Zn2 interactsWith Midline-1
+Zn2 interactsWith Midline-1
+3SP interactsWith Thrombin_Heavy_Chain
+NAG-(4-1)NAG interactsWith Coagulation_Factor_Xi
+F2G interactsWith Caspase-1
+NTO interactsWith Antithrombin-Iii
+NAG-(4-1)NAG-(4-1)BMA-(3-1)MAN-(2-1)MAN-(3,6-1)MAN interactsWith Antithrombin-Iii
+NU5 interactsWith Cell_Division_Protein_Kinase_2
+Ni2 interactsWith Sco1_Protein_Homolog,_Mitochondrial
+NGT interactsWith Beta-Hexosaminidase_Beta_Chain
+NGT interactsWith Beta-Hexosaminidase_Beta_Chain
+NGT interactsWith Beta-Hexosaminidase_Alpha_Chain
+NAG-(4-1)NAG-(4-1)MAN interactsWith Beta-Hexosaminidase_Alpha_Chain
+NAG-(4-1)NAG interactsWith Beta-Hexosaminidase_Alpha_Chain
+NAG-(4-1)NAG interactsWith Beta-Hexosaminidase_Alpha_Chain
+NAG-(4-1)NAG interactsWith Beta-Hexosaminidase_Alpha_Chain
+NAG-(4-1)NAG-(4-1)MAN interactsWith Beta-Hexosaminidase_Beta_Chain
+NAG-(4-1)NAG-(4-1)MAN interactsWith Beta-Hexosaminidase_Alpha_Chain
+NAG-(4-1)NAG-(4-1)MAN interactsWith Beta-Hexosaminidase_Alpha_Chain
+Ca2 interactsWith Guanylyl_Cyclase-Activating_Protein_3
+Ca2 interactsWith Guanylyl_Cyclase-Activating_Protein_3
+Ca2 interactsWith Guanylyl_Cyclase-Activating_Protein_3
+SP3 interactsWith Peroxisome_Proliferator-Activated_Receptor_Gamma
+SP0 interactsWith Peroxisome_Proliferator-Activated_Receptor_Gamma
+RO0 interactsWith Peroxisome_Proliferator-Activated_Receptor_Gamma
+F2G interactsWith Caspase-1
+SP3 interactsWith Peroxisome_Proliferator-Activated_Receptor_Gamma
+Mg2 interactsWith Ras-Related_C3_Botulinum_Toxin_Substrate_3
+GDP interactsWith Ras-Related_C3_Botulinum_Toxin_Substrate_3
+ADP interactsWith Abl_Tyrosine_Kinase
+P16 interactsWith Abl_Tyrosine
+AGS interactsWith Abl_Kinase
+112 interactsWith Abl_Kinase
+112 interactsWith Proto-Oncogene_Tyrosine-Protein_Kinase_Abl1
+Mg2 interactsWith Proto-Oncogene_Tyrosine-Protein_Kinase_Abl1
+Glycoprotein_E pp Ig_Gamma-1_Chain_C_Region
+Glycoprotein_E pp Ig_Gamma-1_Chain_C_Region
+C-Jun-Amino-Terminal_Kinase-Interacting_Protein_1 pp Mitogen-Activated_Protein_Kinase_8
+Cyclin-A2 pp Cell_Division_Protein_Kinase_2
+Atp-Peptide_Conjugate pp Abl_Tyrosine_Kinase
+Atp-Peptide_Conjugate pp Abl_Tyrosine_Kinase
+Atp-Peptide_Conjugate pp Abl_Kinase
+Activin_Receptor_Type_2a pp Bone_Morphogenetic_Protein_2
+Decapeptide_Hirudin_Analogue pp Thrombin_Heavy_Chain
+Nuclear_Receptor_Coactivator_2 pp Estrogen_Receptor
+Nuclear_Receptor_Coactivator_2 pp Estrogen_Receptor
+Histone_H2a_Type_1 pp Histone_H3.1
+Core_Histone_Macro-H2a.1 pp Histone_H3.1
+Core_Histone_Macro-H2a.1 pp Histone_H3.1
+Histone_H4 pp Histone_H3.1
+Histone_H4 pp Histone_H3.1
+716 interactsWith Coagulation_Factor_Xi
+C4A interactsWith Tryptase_Beta-2
+C3A interactsWith Tryptase_Beta-2
+270 interactsWith Tryptase_Beta-2
+270 interactsWith Tryptase_Beta-2
+Zn2 interactsWith Deformed_Epidermal_Autoregulatory_Factor_1_Homolog
+Zn2 interactsWith Deformed_Epidermal_Autoregulatory_Factor_1_Homolog
+995 interactsWith Coagulation_Factor_Xi
+GMPPNP interactsWith RAB11B
+GDP interactsWith RAB11B
+Mg2 interactsWith RAB11B
+3QC interactsWith Kinesin-Like_Protein_Kif11
+682 interactsWith Coagulation_Factor_Xi
+Ca2 interactsWith Fibrillin-1
+ADN interactsWith Tak1_Kinase_-_Tab1_Chimera_Fusion_Protein
+3D3 interactsWith SerineTHREONINE-Protein_Kinase_Chk1
+3C3 interactsWith SerineTHREONINE-Protein_Kinase_Chk1
+3B3 interactsWith SerineTHREONINE-Protein_Kinase_Chk1
+3A3 interactsWith SerineTHREONINE-Protein_Kinase_Chk1
+MBN interactsWith Hemoglobin_Alpha_Chain
+Adenine interactsWith PYGM
+AMP interactsWith PYGM
+AMP interactsWith PYGM
+alpha-D-Glucose interactsWith PYGM
+alpha-D-Glucose interactsWith PYGM
+G6P interactsWith Glucose-6-Phosphate_1-Dehydrogenase
+NADP+ interactsWith Glucose-6-Phosphate_1-Dehydrogenase
+NADP+ interactsWith Glucose-6-Phosphate_1-Dehydrogenase
+NADP+ interactsWith Glucose-6-Phosphate_1-Dehydrogenase
+K interactsWith Methionine_Aminopeptidase_1
+Co_(2+) interactsWith Methionine_Aminopeptidase_1
+Co_(2+) interactsWith Methionine_Aminopeptidase_1
+Progesterone interactsWith PGR
+MOF interactsWith PGR
+SLF interactsWith CD1A
+SLF interactsWith CD1A
+N-Acetyl-D-Glucosamine interactsWith CD1A
+alpha-L-fucose interactsWith CD1A
+NAG-(4-1)NAG interactsWith CD1A
+NAG-(4-1)NAG interactsWith CD1A
+R1881 interactsWith PGR
+JH0 interactsWith CD1A
+JH0 interactsWith CD1A
+NAG-(6-1)FUC interactsWith CD1A
+NAG-(6-1)FUC interactsWith CD1A
+NAG-(1-4)NAG-(6-1)FUC interactsWith CD1A
diff --git a/distribution/src/main/sampleData/BINDyeast.sif b/distribution/src/main/sampleData/BINDyeast.sif
new file mode 100644
index 0000000..f2ee782
--- /dev/null
+++ b/distribution/src/main/sampleData/BINDyeast.sif
@@ -0,0 +1,71307 @@
+Rpb1 pp Rpb5
+Rpo31 pp Rpb5
+Rpo21 pp Rpb8
+Rpo31 pp Rpb8
+Rpa190 pp Rpb5
+Rpa190 pp Rpb8
+Rpo21 pp Rpb10
+Rpb2 pp Rpb10
+Rpa135 pp Rpa12
+Ret1 pp Rpc11
+Rpb3 pp Rpb11
+Rpc40 pp Rpc19
+Rpc31 pp Rpc82
+Rpc31 pp Rpc34
+Rpc34 pp Rpc82
+Prp3 pp Prp4
+Clf1 pp Mud2
+Clf1 pp Prp40
+Cet1 pp Ceg1
+Prp9 pp Prp21
+Prp11 pp Prp21
+Rad53 pp Rad9
+Yku70 pp Yku80
+Ade2 pp Ade2
+Ade2 pp Rad18
+Ade2 pp Sed4
+Ade2 pp Ybr134w
+Ade6 pp Ylr386w
+Ade8 pp Med4
+Ade8 pp Soh1
+Ade8 pp Ycr063w
+Adh2 pp Yfl042c
+Ahc1 pp Ycr082w
+Aip1 pp Apc9
+Alr1 pp Gcd7
+Alr1 pp Pgd1
+Alr1 pp Ygl024w
+Alr1 pp Ynl086w
+Apg12 pp Aut1
+Apg12 pp Apg16
+Apg13 pp Apg1
+Apg13 pp Pup2
+Apg13 pp Sec35
+Apg13 pp Ynl086w
+Apg5 pp Apg12
+Apg5 pp Apg16
+Apg7 pp Apg12
+Apg7 pp Aut1
+Apg7 pp Aut7
+Apm1 pp Apl2
+Apm2 pp Apl2
+Arh1 pp Cdc39
+Arh1 pp Gif1
+Arp10 pp Arp1
+Atp20 pp She2
+Bem4 pp Scs3
+Bem4 pp Yil163c
+Bem4 pp Ylr049c
+Bmh2 pp Bop3
+Bmh2 pp Ecm13
+Bub2 pp Ddi1
+Bub2 pp Gic1
+Bub2 pp Tos10
+Bub2 pp Ynl335w
+Bub3 pp Mad3
+Bud6 pp Ygl015c
+Caf20 pp Cdc33
+Car1 pp Car1
+Car2 pp Snf6
+Car2 pp Ygr010w
+Car2 pp Ylr328w
+Cdc13 pp Stn1
+Cdc20 pp Mad2
+Cdc42 pp Bem4
+Cdc42 pp Rdi1
+Cdc43 pp Ram2
+Cdc53 pp Cdc7
+Cdc53 pp Skp1
+Cdc53 pp Erg27
+Cdc53 pp Ylr128w
+Cdc53 pp Ylr368w
+Cdc53 pp Zip2
+Cdc7 pp Arg3
+Cdc7 pp Dhh1
+Cdc7 pp Ptm1
+Cdc7 pp Tel2
+Cdc7 pp Ycr022c
+Cdc7 pp Ycr050c
+Cdc7 pp Yel023c
+Cdc7 pp Yfr057w
+Cdc7 pp Ynr048w
+Cdc7 pp Yor006c
+Cdd1 pp Cdd1
+Chk1 pp Gfd1
+Chk1 pp Gsy2
+Cin4 pp Gyp1
+Cin4 pp Ybr284w
+Cit2 pp Cit2
+Cit2 pp Mhp1
+Cka2 pp Ckb2
+Clb1 pp Cks1
+Clb2 pp Cks1
+Clb2 pp Fpr1
+Clb2 pp Mus81
+Clb2 pp Ydr412w
+Clb2 pp Yhr035w
+Clb2 pp Ynr022c
+Clb3 pp Cks1
+Cln3 pp Mad3
+Cna1 pp Ynl047c
+Cnb1 pp Ymr211w
+Cns1 pp Stp1
+Cof1 pp Act1
+Cpa1 pp Ckb2
+Cpr6 pp Hyr1
+Crn1 pp Skp1
+Cse2 pp Med4
+Ctf13 pp Aqy2
+Ctf13 pp Yor359w
+Cyp2 pp Jsn1
+Cys4 pp Ycr086w
+Dal3 pp Dal3
+Dal82 pp Dal82
+Dam1 pp Duo1
+Dcp2 pp Dcp1
+Dcp2 pp Yel015w
+Dhh1 pp Dcp1
+Dhh1 pp Yel015w
+Dib1 pp Prp6
+Dig1 pp Dig2
+Dmc1 pp Dmc1
+Dna43 pp Mcm6
+Duo1 pp Bim1
+Duo1 pp Dad1
+Ebs1 pp Dcp1
+Ebs1 pp Gal83
+Ebs1 pp Mad2
+Ebs1 pp Mum2
+Ebs1 pp Std1
+Dci1 pp Eci1
+Ecm19 pp Taf61
+Ecm31 pp Ecm31
+Ent3 pp Yor111w
+Est1 pp Mcm6
+Est1 pp Spt23
+Est1 pp Ure2
+Est1 pp Yal028w
+Est1 pp Fyv13
+Est1 pp Yjl019w
+Est1 pp Ymd8
+Fap1 pp Mre11
+Fap1 pp She2
+Far3 pp Yfr008w
+Fmn1 pp Ydr398w
+Fol2 pp Fol2
+Fpr1 pp Hom3
+Fpr1 pp Ymr087w
+Fui1 pp Rpn3
+Prp45 pp Ylr345w
+Prp45 pp Prp46
+Fur1 pp Apg13
+Fzf1 pp Ckb2
+Fzf1 pp Pho12
+Fzf1 pp Tfc4
+Gcd7 pp Ypl070w
+Gcn3 pp Gcn3
+Gcn5 pp Ada2
+Gdh1 pp Lsm1
+Gfd1 pp Nab2
+Gim5 pp Yke2
+Gis4 pp Cup2
+Glc7 pp Bdf2
+Glc7 pp Bni4
+Glc7 pp Gip1
+Glc7 pp Mhp1
+Glc7 pp Pan1
+Glc7 pp Ref2
+Glc7 pp Scd5
+Glc7 pp Fin1
+Glc7 pp Ydr412w
+Glc7 pp Yhr100c
+Glc7 pp Yor315w
+Glg2 pp Glg2
+Glk1 pp Arg81
+Glk1 pp Fig1
+Gpd2 pp Gna1
+Grx3 pp Rcs1
+Grx5 pp Yil105c
+Grx5 pp Ynl047c
+Gsg1 pp Yhb1
+Gsp1 pp Mog1
+Gsp2 pp Mog1
+Gtr1 pp Gtr1
+Gzf3 pp Hda1
+Hap2 pp Hap3
+Hap2 pp Hap5
+Hap3 pp Hap5
+Hex3 pp Smt3
+Hex3 pp Yer116c
+His3 pp His3
+Hor2 pp Ypl201c
+Hpr5 pp Gds1
+Hpr5 pp Mel1
+Hpr5 pp Ydr078c
+Hrp1 pp Nab2
+Hrr25 pp Ady1
+Hrt1 pp Yak1
+Hrt1 pp Yil001w
+Hrt1 pp Yjl200c
+Hsh49 pp Sif2
+Hst3 pp Sfp1
+Hta1 pp Nap1
+Htz1 pp Yjl019w
+Ime4 pp Mum2
+Ino4 pp Apl2
+Ino4 pp Hcs1
+Ino4 pp Ino2
+Ino4 pp Ymr317w
+Ino4 pp Prm1
+Ino80 pp Gds1
+Ino80 pp Nhp10
+Ipk1 pp Rps28b
+Ipk1 pp Ste24
+Ipk1 pp Ylr323c
+Ipk1 pp Bud21
+Ire1 pp Kre28
+Isa1 pp Rps26a
+Isa1 pp Rps26b
+Isc10 pp Trp5
+Isu2 pp Ypl088w
+Kap104 pp Ynr069c
+Kar4 pp Mum2
+Kcs1 pp Bmh2
+Kel1 pp Caf17
+Kel1 pp Std1
+Kel1 pp Ymr181c
+Kgd2 pp Smt3
+Kin1 pp Yol082w
+Krr1 pp Mcm6
+Kss1 pp Ste7
+Lap4 pp Lap4
+Lap4 pp Yol082w
+Lcp5 pp Bfr2
+Leu4 pp Ykl183w
+Los1 pp Rpc25
+Lpp1 pp She2
+Lrs4 pp Ycr086w
+Lsm2 pp Dcp1
+Lsm2 pp Dhh1
+Lsm2 pp Lsm1
+Lsm2 pp Lsm5
+Lsm2 pp Lsm6
+Lsm2 pp Lsm7
+Lsm2 pp Mtr3
+Lsm2 pp Rps28a
+Lsm2 pp Rps28b
+Lsm2 pp Smd2
+Lsm4 pp Ckb2
+Lsm4 pp Dcp1
+Lsm4 pp Lsm1
+Lsm4 pp Lsm6
+Lsm4 pp Lsm7
+Lsm4 pp Lsm8
+Lsm4 pp Rps28a
+Lsm4 pp Rps28b
+Lsm4 pp Ylr269c
+Lsm8 pp Dcp1
+Lsm8 pp Dss4
+Lsm8 pp Hsh49
+Lsm8 pp Lsm2
+Lsm8 pp Lsm5
+Lsm8 pp Lsm6
+Lsm8 pp Lsm7
+Lsm8 pp Mtr3
+Lsm8 pp Rps28a
+Lsm8 pp Rps28b
+Lsm8 pp Yel015w
+Lsm8 pp Ylr269c
+Lst7 pp Put3
+Lys5 pp Fzf1
+Mak3 pp Mak10
+Mak31 pp Mak10
+Mcm16 pp Mcm22
+Mec3 pp Apg16
+Med11 pp Srb6
+Med7 pp Med4
+Mer1 pp Mrp8
+Met18 pp Med11
+Met30 pp Hdr1
+Met30 pp Mns1
+Met30 pp Srl2
+Met30 pp Ybr270c
+Met30 pp Yel015w
+Met30 pp Yjl058c
+Met31 pp Gcn4
+Mig1 pp Ypl025c
+Mkk2 pp Slt2
+Mob2 pp Yol036w
+Mpd2 pp Msr1
+Mpd2 pp Ylr312c
+Mrp8 pp Mrp8
+Mrp8 pp Smp2
+Msb2 pp Cdc36
+Msb2 pp Mad2
+Msb2 pp Mad3
+Msb2 pp Nip7
+Msb2 pp Tid3
+Msh5 pp Hsl7
+Msh5 pp Mre11
+Msh5 pp Pgd1
+Msh5 pp Tid3
+Msh5 pp Ygl170c
+Msn5 pp Hmo1
+Msn5 pp Sec9
+Msn5 pp Swi5
+Msn5 pp Yor359w
+Msn5 pp Ypr008w
+Mtw1 pp Lap4
+Mtw1 pp Nup49
+Mtw1 pp Sec35
+Nab2 pp Gcn3
+Ndc1 pp Asm4
+Ndc1 pp Nup53
+Nhp10 pp Yer092w
+Nic96 pp Nup53
+Nic96 pp Sec35
+Nif3 pp Nif3
+Nip1 pp Sui1
+Nip1 pp Ynl047c
+Nip1 pp Yor284w
+Nip100 pp Arp1
+Nip100 pp Tid3
+Nip100 pp Yjl184w
+Npl4 pp Ufd1
+Npl6 pp Rsc8
+Nth1 pp Ylr270w
+Nuf2 pp Prs2
+Nup157 pp Mad2
+Nup157 pp Nup53
+Nup157 pp Yel015w
+Nup2 pp Hsp10
+Nup57 pp Nsp1
+Nup57 pp Nup49
+Nup57 pp Taf17
+Pac1 pp Ylr254c
+Pcf11 pp Ada2
+Pcf11 pp Clp1
+Pcf11 pp Rna14
+Pcf11 pp Rna15
+Pcf11 pp Apg17
+Pcf11 pp Ylr424w
+Pcf11 pp Cvt9
+Pcl10 pp Pho85
+Pcl2 pp Swi5
+Pcl6 pp Yjl084c
+Pcl6 pp Ylr190w
+Pdb1 pp Ylr345w
+Pdr11 pp Hmo1
+Pex7 pp Pex18
+Pex7 pp Pex21
+Pex7 pp Pot1
+Pfk1 pp Ubp8
+Pho85 pp Clg1
+Pho85 pp Pcl2
+Pho85 pp Pcl6
+Pho85 pp Pcl7
+Pho85 pp Pcl8
+Pho85 pp Pcl9
+Pho85 pp Sor1
+Pho85 pp Ydl246c
+Pho85 pp Ynl201c
+Pib1 pp Ypl133c
+Pkc1 pp Zds2
+Pkh1 pp Yhr207c
+Pkh1 pp Yir044c
+Pkh1 pp Yrf1-4
+Pom152 pp Iks1
+Pom152 pp Nup53
+Ppa2 pp Gcn3
+Ppg1 pp Cpr6
+Ppg1 pp Hsc82
+Ppg1 pp Ppt1
+Ppt1 pp Adr1
+Pre10 pp Gna1
+Pre3 pp Ylr386w
+Pre5 pp She2
+Pro3 pp Pro3
+Prp11 pp Prp21
+Prp5 pp Snf11
+Prp6 pp Ubc9
+Prs5 pp Prs2
+Pse1 pp Apl2
+Pse1 pp Hsp10
+Pse1 pp Kgd2
+Pse1 pp Nup57
+Pse1 pp Sor1
+Pse1 pp Wtm2
+Pse1 pp Ydl246c
+Pse1 pp Yer045c
+Pse1 pp Yir025w
+Pse1 pp Ymr048w
+Pse1 pp Ypl133c
+Ptc1 pp Nbp2
+Ptc2 pp Ydr071c
+Put4 pp Mtf1
+Put4 pp Ycr045c
+Put4 pp Yjl084c
+Put4 pp Ylr294c
+Rad10 pp Gcd1
+Rad10 pp Ycr086w
+Rad17 pp Mec3
+Rad4 pp Rad23
+Rad4 pp Rps31
+Rad51 pp Sap1
+Rad51 pp Ubc9
+Rad51 pp Ymr233w
+Rad51 pp Ypl238c
+Rad51 pp Ypr011c
+Rad55 pp Rad51
+Rad6 pp Rad18
+Ram1 pp Ram2
+Rck1 pp Hog1
+Rga1 pp Yhl042w
+Rga1 pp Yjl185c
+Rgr1 pp Pex19
+Rho1 pp Bem4
+Rho4 pp Bem4
+Rim101 pp Zap1
+Rim11 pp Ime1
+Rlf2 pp Msi1
+Rnp1 pp Yfr047c
+Rpb10 pp Cup2
+Rpc19 pp Gtr1
+Rpc19 pp Yfr011c
+Rpc19 pp Yhl018w
+Rpc19 pp Ylr266c
+Rpc40 pp Rpc19
+Rpc40 pp Ylr238w
+Rpc53 pp Rpc37
+Rpn11 pp Rpn8
+Rpn12 pp Xpt1
+Rpn12 pp Ydr273w
+Rpn5 pp Spc19
+Rpn5 pp Ydr179c
+Rpn6 pp Gcn4
+Rpp0 pp Rpp1a
+Rps26a pp Ylr435w
+Rps26b pp Ylr435w
+Rps28b pp Dcp1
+Rps28b pp Ybr094w
+Rps8b pp Cks1
+Rps8b pp Gna1
+Rpt3 pp Ame1
+Rpt3 pp Rpt3
+Rpt3 pp Rpt4
+Rpt3 pp Rpt5
+Rpt3 pp Nas6
+Rrn10 pp Ydl113c
+Rrn7 pp Rrn6
+Rrn9 pp Rrn10
+Rsg1 pp Yol083w
+Rta1 pp Wss1
+Rvs161 pp Rvs167
+Rvs161 pp Ybr108w
+Sae2 pp Sae2
+Sae2 pp Ycr086w
+Sap4 pp Mad2
+Sap4 pp Mad3
+Sap4 pp Pgi1
+Sap4 pp Yjl178c
+Sap4 pp Yjl211c
+Sap4 pp Ymr181c
+Sap4 pp Yor062c
+Sap4 pp Ypr040w
+Sec14 pp Ydl001w
+Sec21 pp Ybr281c
+Sed1 pp Hem13
+Shr3 pp Gnp1
+Sin4 pp Cdc34
+Sin4 pp Cse1
+Sin4 pp Gds1
+Sin4 pp Mad2
+Sin4 pp Mad3
+Sin4 pp Pet191
+Sin4 pp Prp40
+Sin4 pp Qcr6
+Sin4 pp Ygr046w
+Sin4 pp Ygr117c
+Sip2 pp Snf4
+Skp1 pp Bdf1
+Skp1 pp Cdc4
+Skp1 pp Ctf13
+Skp1 pp Grr1
+Skp1 pp Met30
+Skp1 pp Rub1
+Skp1 pp Sgt1
+Skp1 pp Ylr097c
+Skp1 pp Ylr224w
+Skp1 pp Ylr352w
+Skp1 pp Ylr368w
+Slu7 pp Ydl144c
+Sme1 pp Smx3
+Smi1 pp Bas1
+Smk1 pp Cak1
+Smt3 pp Ubc9
+Smx3 pp Smd2
+Snf1 pp Gal83
+Snf1 pp Sip2
+Snf1 pp Ynl218w
+Snf4 pp Coq5
+Snf4 pp Gal83
+Snf4 pp Ydl214c
+Snf4 pp Yjl114w
+Snf4 pp Yjr083c
+Snf4 pp Ymr291w
+Sno1 pp Snz1
+Sno1 pp Snz2
+Sno3 pp Snz1
+Sno3 pp Snz2
+Snp1 pp Kin3
+Snu23 pp Prp38
+Spc19 pp Tid3
+Spc34 pp Jsn1
+Spc34 pp Spc19
+Spo1 pp Ybr250w
+Spo11 pp Ski8
+Spo12 pp Ycr086w
+Spo13 pp Ady1
+Spr28 pp Cdc11
+Spt2 pp Fob1
+Spt2 pp Mcm6
+Srb5 pp Med8
+Srb7 pp Med4
+Srb7 pp Med7
+Srl2 pp Srl2
+Srp1 pp Arg1
+Srp1 pp Car1
+Srp1 pp Dut1
+Srp1 pp Fcy1
+Srp1 pp Icl1
+Srp1 pp Met17
+Srp1 pp Nif3
+Srp1 pp Pho13
+Srp1 pp She2
+Srp1 pp Sor1
+Srp1 pp Thi6
+Srp1 pp Tsa1
+Srp1 pp Xpt1
+Srp1 pp Yap3
+Srp1 pp Yfl061w
+Srp1 pp Ygr024c
+Srp1 pp Ymr226c
+Srp101 pp Ymr163c
+Ssp1 pp Ssp1
+Ste11 pp Ste50
+Ste12 pp Dig2
+Ste18 pp Ste4
+Stm1 pp Yjr072c
+Stt4 pp Gds1
+Stt4 pp Std1
+Sxm1 pp Ydr132c
+Sxm1 pp Yol070c
+Syf1 pp Isy1
+Syf1 pp Ntc20
+Syf1 pp Syf2
+Clf1 pp Ntc20
+Taf40 pp Hmo1
+Taf40 pp Taf25
+Taf60 pp Gfd1
+Taf60 pp Taf17
+Tah18 pp Gcr2
+Tah18 pp Gdh2
+Tah18 pp Gds1
+Tah18 pp Med1
+Tem1 pp Dig1
+Tem1 pp Dmc1
+Tem1 pp Eci1
+Tem1 pp Fil1
+Tem1 pp Fob1
+Tem1 pp Hmo1
+Tem1 pp Hsp10
+Tem1 pp Kin3
+Tem1 pp Lac1
+Tem1 pp Mns1
+Tem1 pp Sec66
+Tem1 pp Smx3
+Tem1 pp Snz2
+Tem1 pp Sor1
+Tem1 pp Wtm2
+Tem1 pp Ycr087w
+Tem1 pp Ydl246c
+Tem1 pp Yel015w
+Tem1 pp Yhr198c
+Tem1 pp Yjl058c
+Tem1 pp Yjr056c
+Tem1 pp Apg17
+Tem1 pp Ynl218w
+Tem1 pp Prm3
+Tfa1 pp Tfa2
+Tfa1 pp Tfb1
+Tfb1 pp Lap4
+Tfb1 pp Sec35
+Tfb1 pp Yol082w
+Thi4 pp Thi4
+Thi6 pp Thi6
+Tif35 pp Gna1
+Top1 pp Ymr233w
+Tpk3 pp Bcy1
+Tpk3 pp Tpk3
+Tpo1 pp Cup2
+Tps2 pp Sbh2
+Tps2 pp Yar066w
+Trs31 pp Bet3
+Trs31 pp Trs20
+Trs33 pp Yol082w
+Sub1 pp Ymr316cb
+Ubc6 pp Mir1
+Ubc6 pp Ypl229w
+Ubc9 pp Ubc9
+Ubp5 pp Akl1
+Ula1 pp Uba3
+Ume6 pp Gds1
+Ume6 pp Yol082w
+Ura3 pp Ura3
+Urk1 pp Ydr020c
+Vam7 pp Ktr3
+Vam7 pp Sec10
+Vam7 pp Spc72
+Vam7 pp Stb2
+Vam7 pp Vam3
+Vam7 pp Ygl104c
+Vam7 pp Ygl161c
+Vam7 pp Yif1
+Vam7 pp Yjl151c
+Vam7 pp Apg17
+Vam7 pp Ymr071c
+Vam7 pp Yol129w
+Vam7 pp Yor292c
+Vam7 pp Ypl246c
+Vam7 pp Ypt7
+Vik1 pp Ymr051c
+Vma22 pp Vma6
+Vma22 pp Ydr469w
+Vps17 pp Vps5
+Vps27 pp Yhl002w
+Vps35 pp Cup2
+Vps36 pp Snf8
+Vps4 pp Snf7
+Wsc3 pp Pex14
+Fun11 pp Ydr152w
+Yap5 pp Rcs1
+Yar003w pp Ybr175w
+Yar003w pp Fyv9
+Bud14 pp Glc7
+Prm9 pp Apg12
+Prm9 pp Ycr030c
+Ybl101wa pp Ecm13
+Ybl101wa pp Ure2
+Ybl101wa pp Yfl002wa
+Ybl101wa pp Yjl162c
+Uga2 pp Rpp2b
+Uga2 pp Ykl023w
+Ybr052c pp Pst2
+Ybr077c pp Mvp1
+Sif2 pp Yil112w
+Ybr141c pp Nbp35
+Ybr141c pp Ydr372c
+Ybr190w pp Clf1
+Ybr228w pp Ylr135w
+Gpx2 pp Clf1
+Ybr270c pp Gcn3
+Ybr270c pp Taf17
+Ybr270c pp Yil105c
+Yck1 pp Dun1
+Yck1 pp Yer079w
+Yck1 pp Ynl116w
+Yck2 pp Adp1
+Yck2 pp Ctl1
+Yck2 pp Gds1
+Yck2 pp Ppa2
+Yck2 pp Spb1
+Yck2 pp Yer079w
+Yck2 pp Eap1
+Ycl020w pp Yfl002wa
+Kcc4 pp Nap1
+Ycl046w pp Snf4
+Ycp4 pp Pst2
+Ycr086w pp Tat2
+Ydl012c pp Cth1
+Ydl012c pp Gds1
+Ydl012c pp Yfr047c
+Ydl012c pp Yhr032w
+Ydl012c pp Yhr140w
+Ydl012c pp Yil172c
+Ydl012c pp Yjl065c
+Ydl063c pp Rpl5
+Ydl063c pp Yra1
+Ydl071c pp Gna1
+Ydl071c pp Plp1
+Ydl071c pp Yel068c
+Ydl071c pp Ygr269w
+Ydl071c pp Ynl155w
+Ydl076c pp Cha4
+Ydl089w pp Ydl089w
+Ydl089w pp Ylr324w
+Ydl089w pp Ymr316cb
+Ydl110c pp Put3
+Ydl110c pp Bud21
+Ydl113c pp Snx4
+Ydl133w pp Ydl001w
+Ydl146w pp Ykl070w
+Ydl203c pp Ndd1
+Ydl203c pp Ygr058w
+Fyv14 pp Yfr032c
+Rri1 pp Ymr025w
+Ydl239c pp Cha4
+Ydl239c pp Spo21
+Ydl239c pp Ssp1
+Ydl246c pp Sor1
+Ydl246c pp Ydl246c
+Ydr013w pp Ydr489w
+Ydr026c pp Fob1
+Pst2 pp Ste50
+Pst2 pp Pst2
+Ydr051c pp Ydr051c
+Ydr061w pp Ycr086w
+Ydr063w pp Arc19
+Ydr063w pp Ygl239c
+Ydr070c pp Gna1
+Ydr071c pp Ptc4
+Ydr084c pp Ygl161c
+Ydr084c pp Ygl198w
+Ydr115w pp Mrp8
+Ydr128w pp Sec13
+Ydr132c pp Nmd3
+Ydr132c pp Yjl218w
+Ydr179c pp Ymr025w
+Ydr200c pp Far3
+Ydr200c pp Ynl127w
+Ydr214w pp Mad2
+Ydr215c pp Dbp7
+Ydr215c pp Spt14
+Ydr255c pp Rpc25
+Ydr267c pp Yhr122w
+Ydr279w pp Ylr154c
+Ydr326c pp Yer007ca
+Ydr326c pp Yil105c
+Ydr348c pp Ymr295c
+Ydr357c pp Smx3
+Urh1 pp Yil071c
+Ydr482c pp Caf20
+Ydr482c pp Scw11
+Yel023c pp Ydl011c
+Yfr042w pp Kre6
+Yfr043c pp Ydr489w
+Yfr047c pp Yfr047c
+Ygl051w pp Yar033w
+Tos8 pp Hsh49
+Ygl161c pp Ygl198w
+Ygl214w pp Ylr435w
+Ygl230c pp Kti12
+Ygl230c pp Uga4
+Ygl230c pp Yor161c
+Ygl242c pp Bas1
+Ygr010w pp Ygr010w
+Ygr010w pp Ylr328w
+Ygr017w pp Sfp1
+Ygr017w pp Ylr072w
+Ygr024c pp Ygr024c
+Ygr058w pp Hog1
+Ygr058w pp Ygr058w
+Ygr058w pp Ygr136w
+Ygr058w pp Ynl047c
+Ygr068c pp Ckb1
+Ygr068c pp Sft2
+Ygr122w pp Snf7
+Ygr154c pp Pwp2
+Ygr173w pp Ydr152w
+Ygr250c pp Sgn1
+Ygr278w pp Scm4
+Ygr294w pp Yhl018w
+Yhl002w pp Ynr005c
+Shu1 pp Hda1
+Shu1 pp Ydr078c
+Yhl018w pp Yhl018w
+Yhl046c pp Gds1
+Yhr022c pp Yil028w
+Yhr022c pp Ynr005c
+Yhr039c pp Dig2
+Yhr083w pp Spc19
+Yhr083w pp Ynl092w
+Yhr105w pp Akr2
+Yhr105w pp Ktr3
+Yhr105w pp Ygl161c
+Yhr105w pp Yif1
+Yhr105w pp Ypl246c
+Yhr111w pp Yhr111w
+Yhr115c pp Yel041w
+Yhr115c pp Cdc123
+Yhr145c pp Gcn4
+Yhr188c pp Yjr015w
+Yhr197w pp Apg17
+Htm1 pp Rpl30
+Htm1 pp Kre32
+Yil007c pp Ady1
+Urm1 pp Yhr111w
+Yil011w pp Rad14
+Fis1 pp Jsn1
+Fis1 pp Sfh1
+Ser33 pp Ser3
+Ser33 pp Ser33
+Yil082w pp Ygr024c
+Yil105c pp Dmc1
+Yil105c pp She2
+Yil105c pp Ynl047c
+Yil113w pp Kns1
+Yil113w pp Slt2
+Yil132c pp Sfh1
+Yil132c pp Ylr322w
+Yil132c pp Ylr376c
+Yil151c pp Ybl051c
+Yil151c pp Fyv9
+Yil151c pp Yps3
+Ist3 pp Spt15
+Ist3 pp Bud13
+Ist3 pp Ymr057c
+Yjl048c pp She2
+Mdv1 pp Dnm1
+Yjl160c pp Yil071c
+Yjr024c pp Yjr024c
+Yjr072c pp Ylr243w
+Yjr072c pp Yor262w
+Yjr136c pp Ykl033w
+Yju2 pp Syf1
+Yju2 pp Ure2
+Yke2 pp Far3
+Ykl002w pp Spc24
+Ykl090w pp Tbf1
+Ykl090w pp Ygr024c
+Ykl116c pp Ask10
+Ykl116c pp Ste23
+Ykr007w pp Ybr077c
+Tos5 pp Cup2
+Ykr022c pp Ybl010c
+Ykr022c pp Ylr424w
+Ykr060w pp Ydr179c
+Ykr083c pp Ask1
+Ykr096w pp Ybl051c
+Ykr104w pp Rib4
+Yll049w pp Ynr069c
+Yll057c pp Yll057c
+Mht1 pp Rib4
+Bre2 pp Ydr469w
+Ylr046c pp Shu1
+Ylr065c pp Apg9
+Cdc123 pp Ylr386w
+Ylr238w pp Ydr200c
+Ylr315w pp Ydr383c
+Ylr328w pp Ylr328w
+Ylr345w pp Mtr3
+Ylr345w pp Sfh1
+Ylr368w pp Imp2
+Ylr368w pp Trr2
+Ylr368w pp Ppe1
+Ylr368w pp Yjl048c
+Ylr368w pp Ymr048w
+Ylr368w pp Ypr078c
+Ylr368w pp Ypr093c
+Ylr392c pp Jsn1
+Apg17 pp Sec35
+Imd3 pp Gcn3
+Imd3 pp Gdh2
+Imd3 pp Taf25
+Imd3 pp Ydr469w
+Ylr465c pp Amd1
+Yml053c pp Tdh2
+Yml068w pp Snf11
+Ufo1 pp Skp1
+Taf65 pp Taf25
+Yml119w pp Yll032c
+Ymr025w pp Pop2
+Ymr068w pp Yil105c
+Ymr075ca pp Ycr023c
+Vps20 pp Ask1
+Ymr093w pp Ydr398w
+Ymr102c pp Ynl218w
+Ymr210w pp Mrp8
+Ymr269w pp Gcn3
+Ymr312w pp Iki1
+Ymr322c pp Snz1
+Ymr322c pp Snz2
+Ymr322c pp Snz3
+Ynk1 pp Ynk1
+Ynl056w pp Siw14
+Ynl056w pp Ynl099c
+Ynl078w pp Nap1
+Ynl086w pp Ykl061w
+Ynl091w pp Gds1
+Ynl091w pp Ykl075c
+Ynl091w pp Ynl164c
+Ynl091w pp Caf40
+Ynl091w pp Ypl229w
+Ynl094w pp Ssn8
+Ynl094w pp Yal049c
+Ynl122c pp Ykl061w
+Ynl127w pp Rho4
+Ynl127w pp Tpd3
+Ynl157w pp Ace2
+Ynl157w pp Yjl075c
+Ynl171c pp Ycr106w
+Ynl201c pp Aad6
+Ynl201c pp Gds1
+Ynl201c pp Std1
+Ynl201c pp Ypr115w
+Ynl218w pp Mad2
+Ynl218w pp Ynl218w
+Ynl311c pp Met14
+Ynl311c pp Ser33
+Ynr004w pp Ypl157w
+Ynr025c pp Sec35
+Ynr029c pp Yjl064w
+Ynr029c pp Yjl065c
+Ynr068c pp Ynr069c
+Yol034w pp Spc24
+Yol070c pp Ynl078w
+Yol106w pp Smx3
+Yol111c pp Sgt2
+Yor138c pp Npr2
+Yor138c pp Ygr268c
+Yor215c pp Yhr115c
+Yor220w pp Cup2
+Yor264w pp Ycr086w
+Yor264w pp Ygr058w
+Yor353c pp Kic1
+Yor353c pp Sec35
+Yor353c pp Yol082w
+Vtc3 pp Vma22
+Ypl110c pp Ygr024c
+Prp46 pp Pep12
+Prm3 pp Prm3
+Ypl222w pp Ufd1
+Ypl260w pp Tid3
+Ypr105c pp Pex14
+Ypr105c pp Sec35
+Ypr105c pp Tip20
+Ypr105c pp Vma22
+Ypr105c pp Ylr315w
+Ypr105c pp Ymr181c
+Ypr105c pp Yor164c
+Ypr105c pp Yor331c
+Ypr152c pp Ybr194w
+Ypt1 pp Bos1
+Ypt1 pp Ktr3
+Ypt1 pp Pep12
+Ypt1 pp Ypl246c
+Ypt31 pp Pep12
+Ypt31 pp Ykr030w
+Ypt31 pp Ynl146w
+Ypt31 pp Prm3
+Ypt53 pp Siw14
+Yrb1 pp Nap1
+Ysc84 pp Gfd1
+Ysc84 pp Sla1
+Ysc84 pp Ygr268c
+Ysc84 pp Ylr243w
+Yth1 pp Fip1
+Yth1 pp Ktr3
+Zrc1 pp Mrp8
+Yar027w pp Yar027w
+Yar030c pp Yar027w
+Yar033w pp Yar033w
+Pop8 pp Srb2
+Ybl044w pp Hsp150
+Aut7 pp Aut1
+Ybr064w pp Hsp150
+Ybr077c pp Ykr007w
+She3 pp She3
+Cks1 pp Yar027w
+Cks1 pp Cdc28
+Ybr137w pp Ybr137w
+Sec66 pp Srb2
+Trs20 pp Srb2
+Trs20 pp Bet3
+Ilv6 pp Pup3
+Ycl046w pp Snf4
+Ycl056c pp Ydl157c
+Ycl056c pp Ynl100w
+Ycr099c pp Ybl059w
+Ycr099c pp Sec13
+Ydl023c pp Hsp150
+Srp14 pp Srp21
+Ydl110c pp Ylr125w
+Rdi1 pp Rho4
+Cdc36 pp Ylr125w
+Dad1 pp Duo1
+Dad1 pp Spc34
+Ydr020c pp Ydr020c
+Ydr078c pp Yil152w
+Grx3 pp Ygl220w
+Ydr100w pp Ydr100w
+Ydr100w pp Ygl161c
+Ydr100w pp Bet1
+Ydr100w pp Pep12
+Rub1 pp Ubc12
+Fyv9 pp Ynr046w
+Rpa14 pp Rpa12
+Nbp2 pp Ptc1
+Taf25 pp Taf19
+Hmo1 pp Taf19
+Spc19 pp Spc34
+Spc19 pp Ykr083c
+Ydr267c pp Yhr122w
+Rpp2b pp Rpp1b
+Apt2 pp Apt1
+Tlg1 pp Yip3
+Trs31 pp Bet3
+Ydr492w pp Yae1
+Smt3 pp Ycr087ca
+Smt3 pp Ubc9
+Smt3 pp Ecm11
+Smt3 pp Smt3
+Qcr7 pp Duo1
+Yel017w pp Yel017w
+Hpa3 pp Hpa3
+Lsm5 pp Lsm6
+Lsm5 pp Lsm7
+Spi1 pp Ycl063w
+Bur6 pp Ncb2
+Mob2 pp Yir016w
+Snz3 pp Rad59
+Snz3 pp Snz3
+Snz3 pp Sno1
+Snz3 pp Snz2
+Snz3 pp Sno2
+Yfr047c pp Yfr047c
+Pnc1 pp Pnc1
+Prm8 pp Ylr065c
+Ygl057c pp Yjl135w
+Ygl060w pp Nup145
+Duo1 pp Spc34
+Bud13 pp Ist3
+Fzf1 pp Lys5
+Vma7 pp Vma22
+Scm4 pp Rad59
+Spt4 pp Rad10
+Smd1 pp Ykl183w
+Ygr115c pp Ste18
+Yip1 pp Ybl049w
+Yip1 pp Ycr033w
+Yip1 pp Tlg1
+Yip1 pp Ygl161c
+Yip1 pp Yif1
+Ser2 pp Ykl177w
+Fol2 pp Fol2
+Ygr268c pp Ygr268c
+Shu1 pp Ydr078c
+Yhl018w pp Yhl018w
+Yhl023c pp Ycl016c
+Yhl044w pp Ykr035c
+Yhl045w pp Mrpl13
+Thr1 pp Thr1
+Med6 pp Ycl016c
+Vma22 pp Dal80
+Yng2 pp Ykr020w
+Yhr113w pp Yhr113w
+Ady1 pp Spo13
+Ady1 pp Yil007c
+Egd2 pp Btt1
+Rpn10 pp Rrn10
+Cap2 pp Ybl049w
+Arc15 pp Arc19
+Yil141w pp Rrn10
+Gtt1 pp Gtt1
+Gtt1 pp Yjl097w
+Ctk2 pp Ctk3
+Yjl043w pp Ycl063w
+Yjl064w pp Tim17
+Rfa3 pp Ycl063w
+Pfd1 pp Duo1
+Yjl199c pp Yjl199c
+Yjl199c pp Ylr198c
+Prp21 pp Prp11
+Yjl218w pp Yjl218w
+Yjr056c pp Yjr056c
+Rpa12 pp Rsm7
+Yjr087w pp Rrn10
+Ykl023w pp Srp40
+Ask1 pp Ykr083c
+Ykl056c pp Ylr285w
+Ynk1 pp Ynk1
+Cyt2 pp Ylr285w
+Lap4 pp Lap4
+She2 pp Yjl048c
+She2 pp She2
+Ykl160w pp Ykl036c
+Ypt52 pp Tem1
+Ykr030w pp Arl3
+Yll059c pp Yml011c
+Ylr008c pp Ylr125w
+Ppr1 pp Ppr1
+Snf7 pp Snf7
+Ylr036c pp Ykr065c
+Ylr053c pp Ylr285w
+Srn2 pp Ylr051c
+Ylr123c pp Ycl016c
+Ylr124w pp Erv25
+Rpl37a pp Ssp1
+Qri5 pp Ymr299c
+Cdd1 pp Cdd1
+Ylr261c pp Ssn8
+Kre34 pp Ynl140c
+Ylr322w pp Ssn8
+Ylr327c pp Ymr312w
+Ylr328w pp Ylr328w
+Ylr358c pp Ssn8
+Ylr358c pp Mfa2
+Ylr366w pp Rpl20a
+Ylr376c pp Ydr078c
+Ylr376c pp Yil132c
+Ylr376c pp Dal80
+Gtr1 pp Bzz1
+Gtr1 pp Ykr007w
+Sno1 pp Snz2
+Apg16 pp Apg16
+Vti1 pp Pep12
+Siw14 pp Ynl056w
+Yip3 pp Pib1
+Yip3 pp Yip1
+Yip3 pp Yip3
+Yip3 pp Yif1
+Aad14 pp Aad14
+Snz2 pp Snz2
+Snz2 pp Sno2
+Dcp1 pp Rps28a
+Cin5 pp Lys5
+Cin5 pp Clc1
+Pep12 pp Sec17
+Pep12 pp Ygl161c
+Yor111w pp Yor111w
+Cdc4 pp Gcn4
+Cdc4 pp Cdc16
+Mak16 pp Yjr044c
+Drs2 pp Ypl146c
+Prp45 pp Syf1
+Prp45 pp Ylr345w
+Prp45 pp Apg17
+Prp45 pp Pep12
+Pop5 pp Yjr115w
+Fun12 pp Ylr241w
+Fun11 pp Pex19
+Fun11 pp Ynr022c
+Erv46 pp Ydl239c
+Yal064w pp Tos5
+Rfa1 pp Rfa3
+Sen34 pp Ybl051c
+Kin3 pp Kin3
+Yar027w pp Yar027w
+Yar027w pp Yar030c
+Yar027w pp Cks1
+Yar033w pp Yar033w
+Yat1 pp Ygr069w
+Ecm15 pp Smt3
+Ecm15 pp Yer067w
+Htb2 pp Hmlalpha1
+Ybl006c pp Ydr489w
+Fus3 pp Ydr469w
+Fus3 pp Dig2
+Fus3 pp Yhr168w
+Fus3 pp Yil169c
+Fus3 pp Dig1
+Apn2 pp Gcn4
+Mcm2 pp Lip5
+Ncl1 pp Ygr237c
+Rrn10 pp Rpn10
+Rrn10 pp Yil141w
+Rrn10 pp Yjr087w
+Lsm2 pp Pat1
+Ybl032w pp Yfr012w
+Rib1 pp Ynl105w
+Rib1 pp Ypr172w
+Stu1 pp Ydr330w
+Mrpl16 pp Ygr033c
+Ura7 pp Ura8
+Cor1 pp Xdj1
+Cor1 pp Qcr2
+Ybl049w pp Yip1
+Ybl049w pp Cap2
+Sec17 pp Pep12
+Ybl053w pp Hxt13
+Ybl053w pp Rho1
+Ptc3 pp Ydr071c
+Ptc3 pp Hsp10
+Ybl059w pp Ycr099c
+Sef1 pp Bmh2
+Sef1 pp Ygr117c
+Prs4 pp Prs5
+Ybl071c pp Orc5
+Ybl077w pp Ybl077w
+Aut7 pp Yol083w
+Ybl086c pp Gef1
+Ybl089w pp Rpl38
+Ybl089w pp Yor082c
+Sft2 pp Thi5
+Pkc1 pp Gip1
+Ybl107c pp Atr1
+Ybr004c pp Srl2
+Ybr013c pp Mal12
+Gal10 pp Yol150c
+Fur4 pp Ade2
+Ybr025c pp Ynl207w
+Ybr033w pp Ynl228w
+Ybr043c pp Fbp26
+Yro2 pp Rvb1
+Ubp14 pp Gpd2
+Ubp14 pp Met22
+Ubp14 pp Skm1
+Ubp14 pp Yol132w
+Ubp14 pp Hxt11
+Ubp14 pp Leo1
+Akl1 pp Akl1
+Ybr061c pp Ybr300c
+Ybr061c pp Ydr383c
+Ybr061c pp Mfa1
+Ybr061c pp Yer028c
+Ybr061c pp Ygr182c
+Ybr061c pp Ski6
+Ybr061c pp Ygr201c
+Ybr061c pp Ygr219w
+Ybr061c pp Ygr235c
+Ybr061c pp Ygr277c
+Ybr061c pp Prs3
+Ybr061c pp Sod2
+Ybr061c pp Yhr022c
+Ybr061c pp Ppa1
+Ybr061c pp Med6
+Ybr061c pp Fyv4
+Ybr061c pp Yjl017w
+Ybr061c pp Yjl097w
+Ybr061c pp Rpb4
+Ybr061c pp Qcr8
+Ybr064w pp Faa1
+Tip1 pp Ytp1
+Tip1 pp Mep3
+Bap2 pp Eft1
+Tat1 pp Zeo1
+Ybr074w pp Adh3
+Ybr077c pp Ygr201c
+Ybr077c pp Ykr007w
+Ybr077c pp Tom6
+Rfc5 pp Rfc2
+Rfc5 pp Ecm19
+Ybr090c pp Yer158c
+Pho5 pp Ykr106w
+Pho5 pp Bet5
+Ybr094w pp Dcp1
+Ybr101c pp Ybr014c
+Ybr101c pp Yhl021c
+Ybr101c pp Pho86
+Ybr101c pp Ykl171w
+Ybr101c pp Mht1
+Ybr101c pp Bud20
+Ybr101c pp Ylr194c
+Ybr101c pp Aip1
+Ybr101c pp Ddr48
+Ybr101c pp Plb3
+Ybr101c pp Ypl136w
+Sif2 pp Pat1
+Sif2 pp Yil112w
+Sif2 pp Yjr141w
+Sif2 pp Rna14
+Ybr108w pp Rvs167
+Ybr108w pp Ygr136w
+Vma2 pp Ygr117c
+She3 pp She3
+Hsl7 pp Yer087w
+Hsl7 pp Swe1
+Cks1 pp Cdc28
+Cks1 pp Dut1
+Cks1 pp Ydr078c
+Cks1 pp Clb1
+Cks1 pp Clb4
+Ybr137w pp Ybr137w
+Ybr139w pp Fre3
+Mrps9 pp Mam33
+Ara1 pp Ydl211c
+Ara1 pp Tep1
+Rpb5 pp Fyv11
+Cst13 pp Ydr111c
+Tos1 pp Ybl095w
+Tos1 pp Rim2
+Tos1 pp Mga1
+Tos1 pp Ynl217w
+Tos1 pp Yap7
+Tos1 pp Nca2
+Ysy6 pp Kre27
+Ysy6 pp Xdj1
+Ysy6 pp Yml108w
+Npl4 pp Cdc48
+Npl4 pp Yap6
+Npl4 pp Ufd1
+Sec66 pp Prd1
+Ybr175w pp Mga1
+Ybr175w pp Yhr177w
+Ybr175w pp Pot1
+Ybr175w pp Std1
+Ybr178w pp Yhr122w
+Ybr184w pp Cnm67
+Ybr187w pp Ppg1
+Ntc20 pp Syf1
+Rim2 pp Yer078c
+Msi1 pp Nem1
+Msi1 pp Cdc73
+Taf90 pp Yap6
+Taf90 pp Taf60
+Taf90 pp Aro9
+Taf90 pp Pif1
+Ybr203w pp Sft1
+Fth1 pp Rsr1
+Met8 pp Ymr206w
+Ybr216c pp Nup100
+Ybr216c pp Yap1
+Apg12 pp Apg17
+Apg12 pp Apg16
+Ybr223c pp Smt3
+Ybr228w pp Ylr135w
+Ybr230c pp Rts1
+Pbp2 pp Ddr48
+Ybr239c pp Faa1
+Ybr239c pp Ypl133c
+Ybr246w pp Ydr520c
+Ybr250w pp Ymd8
+Dut1 pp Yll037w
+Trs20 pp Trs31
+Trs20 pp Yjr116w
+Trs20 pp Bet3
+Rgd1 pp Yjl058c
+Rgd1 pp Hof1
+Ybr261c pp Rmt2
+Shm1 pp Yml018c
+Ypt10 pp Mrs6
+Ybr266c pp Ypr031w
+Ybr270c pp Pat1
+Ybr270c pp Yap6
+Ybr270c pp Yer093c
+Ybr270c pp Yfl047w
+Ybr270c pp Mga1
+Ybr270c pp Yil105c
+Ybr270c pp Nup192
+Ybr270c pp Gcn3
+Ybr270c pp Apg17
+Ybr270c pp Ylr424w
+Ybr270c pp Hrb1
+Ybr270c pp Ynl018c
+Ybr270c pp Ynl047c
+Ybr270c pp Std1
+Ybr270c pp Nip29
+Ybr270c pp Bbp1
+Hsm3 pp Hyp2
+Hsm3 pp Bre2
+Dpb3 pp Ada2
+Dpb3 pp Yil006w
+Dpb3 pp Cce1
+Dpb3 pp Has1
+Ybr281c pp Ynl191w
+Mrpl27 pp Hgh1
+Ssh1 pp Ylr311c
+Ybr285w pp Ypr156c
+Apm3 pp Ybr014c
+Apm3 pp Apl6
+Pho89 pp Yhr188c
+Pho89 pp Ylr137w
+Pho89 pp Yml089c
+Bud3 pp Yil104c
+Bud3 pp Bud4
+Ycl016c pp Yhl023c
+Ycl016c pp Med6
+Ycl016c pp Ylr123c
+Ycl019w pp Ydr261wa
+Ycl019w pp Ydr261wb
+Ycl019w pp Yhr189w
+Ycl019w pp Yol030w
+Ycl020w pp Ydr261wa
+Ycl020w pp Ydr261wb
+Ycl020w pp Smt3
+Ycl022c pp Chs2
+Agp1 pp Gtt1
+Bik1 pp Bim1
+Rrp7 pp Yol082w
+Ste50 pp Akl1
+Ste50 pp Ste11
+Ste50 pp Apg17
+Ste50 pp Ypr076w
+Ycl038c pp Ymr009w
+Glk1 pp Glk1
+Glk1 pp Ydr516c
+Pdi1 pp Yer189w
+Pdi1 pp Tal1
+Ycl046w pp Snf4
+Kar4 pp Mtc2
+Kar4 pp Ime4
+Kar4 pp Ymr147w
+Kar4 pp Slz1
+Fyv5 pp Cbp3
+Ycl063w pp Spi1
+Ycl063w pp Yjl043w
+Ycl063w pp Rfa3
+Ycl063w pp Apg17
+Hmlalpha2 pp Top1
+Ycl076w pp Npt1
+Ycr001w pp Met7
+Mrpl32 pp Yps6
+Pgk1 pp Ade2
+Pol4 pp Gzf3
+Hsp30 pp Yjl068c
+Ycr030c pp Yjr126c
+Ycr030c pp Ymr132c
+Ycr033w pp Yip1
+Rbk1 pp Pex14
+Bud5 pp Fun11
+Bud5 pp Pex19
+Bud5 pp Kre28
+Bud5 pp Cin8
+Bud5 pp Set1
+Ycr041w pp Hcm1
+Ycr041w pp Rho3
+Ycr041w pp Bet4
+Img1 pp Knh1
+Bud23 pp Pop3
+Are1 pp Frm2
+Rsc6 pp Rsc8
+Rsc6 pp Sds3
+Rsc6 pp Sps19
+Rsc6 pp Mge1
+Ycr060w pp Yhr034c
+Sed4 pp Ynl171c
+Cvt17 pp Isc1
+Ycr079w pp Fcp1
+Ycr082w pp Ygr161cc
+Ycr086w pp Ykl077w
+Ycr086w pp Plp2
+Ycr087ca pp Smt3
+Abp1 pp Yor284w
+Ycr095c pp Yhl029c
+Ycr095c pp Ynl099c
+Ycr095c pp Ypl027w
+Ycr099c pp Ygr203w
+Ycr099c pp Ygr205w
+Ycr099c pp Ygr262c
+Ycr099c pp Imp3
+Ycr099c pp Yil059c
+Ycr100c pp Yil110w
+Ycr106w pp Pet112
+Ycr106w pp Mrpl49
+Aad3 pp Tsc10
+Aad3 pp Yor114w
+Ydl001w pp Ume6
+Ptc1 pp Nbp2
+Hex3 pp Ecm7
+Dia3 pp Yel017w
+Kre26 pp Mph1
+Prp11 pp Prp21
+Mtf2 pp Prp9
+Mtf2 pp Psp1
+Mtf2 pp Ilv1
+Mtf2 pp Fre6
+Mtf2 pp Ylr386w
+Knh1 pp Ybr226c
+Knh1 pp Ymr289w
+Knh1 pp Hsd1
+Rad59 pp Snz3
+Rad59 pp Scm4
+Ubc9 pp Smt3
+Bdf2 pp Pus2
+Ydl085w pp Ygr139w
+Ydl089w pp Ycr086w
+Ydl089w pp Ydl089w
+Ydl089w pp Ydr233c
+Ydl089w pp Gtt1
+Ydl089w pp Ylr324w
+Ydl089w pp Erg6
+Ydl089w pp Yip2
+Ydl091c pp Tim44
+Pmt5 pp Ole1
+Ydl100c pp Yap6
+Ydl100c pp Gcr2
+Ydl100c pp Yor164c
+Ydl100c pp Yah1
+Qri7 pp Mal12
+Kin28 pp Pcl10
+Ydl113c pp Ylr424w
+Ydl113c pp Nip100
+Ydl114w pp Ydl123w
+Ydl114w pp Ylr040c
+Nup84 pp Ycl044c
+Nup84 pp Lre1
+Nup84 pp Ycl069w
+Nup84 pp Hmlalpha2
+Nup84 pp Mtf2
+Nup84 pp Pds1
+Nup84 pp Nup145
+Nup84 pp Tos3
+Nup84 pp Cos12
+Nup84 pp Mrp4
+Nup84 pp Yhr033w
+Nup84 pp Dpb11
+Nup84 pp Yol014w
+Nup84 pp Dci1
+Nup84 pp Rrs1
+Nup84 pp Glr1
+Nup84 pp Nip29
+Ydl121c pp Ydl100c
+Ydl121c pp Scw10
+Vcx1 pp Ykl102c
+Rpp1b pp Rad59
+Rpp1b pp Ydr367w
+Rpp1b pp Rpp2b
+Rpp1b pp Hpt1
+Rpp1b pp Rfa3
+Rpp1b pp Nuc1
+Rpp1b pp Pex2
+Rpp1b pp Yjr012c
+Rpp1b pp Abm1
+Rpp1b pp Mgm101
+Rpp1b pp Ykl002w
+Rpp1b pp Ylr051c
+Scm3 pp Pat1
+Scm3 pp Pex14
+Rpo21 pp Ynl266w
+Rpn5 pp Ydr341c
+Rpn5 pp Nam7
+Sas10 pp Fat1
+Sas10 pp Ybr281c
+Sas10 pp Hsp30
+Sas10 pp Med2
+Sas10 pp Gcs1
+Sas10 pp Ena1
+Sas10 pp Ydr269c
+Sas10 pp Ydr307w
+Sas10 pp Sip1
+Sas10 pp Deg1
+Sas10 pp Prp43
+Sas10 pp Ygl185c
+Sas10 pp Ygl198w
+Sas10 pp Ygl250w
+Sas10 pp Fyv13
+Sas10 pp Ygr290w
+Sas10 pp Net1
+Sas10 pp Yjl175w
+Sas10 pp Mpp10
+Sas10 pp Rps4a
+Sas10 pp Ssk1
+Sas10 pp Esbp6
+Sas10 pp Rap1
+Sas10 pp Erg24
+Sas10 pp Yol118c
+Sas10 pp Yor252w
+Sas10 pp Yor309c
+Sas10 pp Yor314w
+Sas10 pp Pmt3
+Sas10 pp Sks1
+Sas10 pp Gpi2
+Sas10 pp Apl4
+Clb3 pp Nip29
+Ydl157c pp Ycl056c
+Ste7 pp Kss1
+Dhh1 pp Pat1
+Dhh1 pp Yel015w
+Dhh1 pp Rsp5
+Dhh1 pp Pbp1
+Dhh1 pp Dcp1
+Ydl166c pp Ylr222c
+Nrp1 pp Ybl081w
+Nrp1 pp Ngr1
+Ydl175c pp Pat1
+Ydl175c pp Ynr073c
+Pcl9 pp Ymr147w
+Ydl186w pp Erg20
+Arf1 pp Ygr130c
+Ydl193w pp Cox18
+Ydl196w pp Ydl094c
+Ydl196w pp Yer071c
+Ydl203c pp Rsp5
+Ydl203c pp Ygr058w
+Ydl203c pp Gzf3
+Ydl203c pp Nip29
+Nhp2 pp Ynl124w
+Ydl209c pp Ylr426w
+Ydl214c pp Ycr086w
+Ydl214c pp Vac8
+Rri1 pp Pat1
+Cdc13 pp Stn1
+Gcs1 pp Ybl098w
+Gcs1 pp Yel064c
+Gcs1 pp Sho1
+Gcs1 pp Ygl161c
+Gcs1 pp Ygl198w
+Gcs1 pp Yip1
+Gcs1 pp Yjl151c
+Gcs1 pp Ypk1
+Gcs1 pp Ykr088c
+Gcs1 pp Yol129w
+Gcs1 pp Snc2
+Gcs1 pp Pis1
+Gcs1 pp Dpm1
+Bre4 pp Ycr016w
+Ydl237w pp Arp6
+Ydl238c pp Ybr284w
+Ydl239c pp Yal028w
+Ydl239c pp Kin3
+Ydl239c pp Hsp26
+Ydl239c pp Prp9
+Ydl239c pp Kgd2
+Ydl239c pp Ydr273w
+Ydl239c pp Ilv1
+Ydl239c pp Ygr268c
+Ydl239c pp Ssp1
+Ydl239c pp Ykl023w
+Ydl239c pp Lap4
+Ydl239c pp Ylr072w
+Ydl239c pp Arv1
+Ydl239c pp Apg17
+Ydl239c pp Cat2
+Ydl239c pp Ymr124w
+Ydl239c pp Urk1
+Ydl239c pp Yol083w
+Ydl239c pp Spo21
+Ydl239c pp Yor284w
+Ydl239c pp Yor324c
+Ydl239c pp Dig1
+Ydl239c pp Ypl070w
+Ydl239c pp Nip29
+Ydl239c pp Bbp1
+Aad4 pp Aad14
+Nth1 pp Ylr270w
+Rad57 pp Pet130
+Sok1 pp Gac1
+Ydr013w pp Ydr489w
+Ydr018c pp Ydr479c
+Ydr020c pp Ydr020c
+Ydr020c pp Urk1
+Ydr026c pp Rpl32
+Ydr026c pp Prp9
+Ydr026c pp Srp40
+Rad28 pp Ynl124w
+Lys14 pp Rfa1
+Lys14 pp Mum2
+Lys14 pp Ybr144c
+Lys14 pp Adh5
+Lys14 pp Dtr1
+Lys14 pp Pwp2
+Lys14 pp Ycr095c
+Lys14 pp Pex19
+Lys14 pp Ydl085w
+Lys14 pp Rgt2
+Lys14 pp Clb3
+Lys14 pp Ydl247w
+Lys14 pp Ses1
+Lys14 pp Ydr131c
+Lys14 pp Yap6
+Lys14 pp Mth1
+Lys14 pp Hxt7
+Lys14 pp Ydr417c
+Lys14 pp Ydr438w
+Lys14 pp Ydr449c
+Lys14 pp Nhx1
+Lys14 pp Kre29
+Lys14 pp Sah1
+Lys14 pp Bud18
+Lys14 pp Yer064c
+Lys14 pp Yfr021w
+Lys14 pp Yfr046c
+Lys14 pp Yfr055w
+Lys14 pp Met13
+Lys14 pp Sua5
+Lys14 pp Gts1
+Lys14 pp Ygl223c
+Lys14 pp Ygr111w
+Lys14 pp Dam1
+Lys14 pp Asn2
+Lys14 pp Crh1
+Lys14 pp Cos6
+Lys14 pp Mrp4
+Lys14 pp Vma22
+Lys14 pp Pig2
+Lys14 pp Pan6
+Lys14 pp Yvh1
+Lys14 pp Ost1
+Lys14 pp Yjl185c
+Lys14 pp Hoc1
+Lys14 pp Nup100
+Lys14 pp Nap1
+Lys14 pp Ylr063w
+Lys14 pp Cha4
+Lys14 pp Sen2
+Lys14 pp Pex13
+Lys14 pp Ylr328w
+Lys14 pp Atr1
+Lys14 pp Aep1
+Lys14 pp Ctf13
+Lys14 pp Ymr187c
+Lys14 pp Yor009w
+Lys14 pp Kre24
+Lys14 pp Ypl114w
+Lys14 pp Ypl138c
+Lys14 pp Cbc2
+Lys14 pp Fyv15
+Lys14 pp Rpo26
+Ydr042c pp Ylr413w
+Dbf4 pp Apg17
+Dbf4 pp Gac1
+Rad55 pp Rad51
+Ydr078c pp Shu1
+Ydr078c pp Yil152w
+Ydr078c pp Ylr376c
+Ydr084c pp Ygl198w
+Slu7 pp Nas6
+Rli1 pp Ygl185c
+Rli1 pp Hcr1
+Ydr100w pp Ydr100w
+Ydr105c pp Ygp1
+Ydr107c pp Ipt1
+Fob1 pp Ioc2
+Trm1 pp Gbp2
+Trm1 pp Yel017w
+Trm1 pp Gtt1
+Trm1 pp Mlh2
+Ydr136c pp Spo21
+Pex7 pp Pex21
+Pex7 pp Pex18
+Ydr154c pp Rvs161
+Cph1 pp Ykr105c
+Hom2 pp Ycr030c
+Sup35 pp Tim18
+Ngg1 pp Ycl010c
+Ngg1 pp Ycr041w
+Ngg1 pp Ydl239c
+Ngg1 pp Ada2
+Ngg1 pp Tid3
+Ngg1 pp Yjr080c
+Ngg1 pp Apg17
+Sly1 pp Dia1
+Rvb1 pp Rvb2
+Nup42 pp Bag7
+Spc19 pp Spc34
+Spc19 pp Ykr083c
+Msc2 pp Zrg17
+Adk1 pp Hem15
+Pcf11 pp Clp1
+Ydr229w pp Ygl066w
+Ydr229w pp Yjl017w
+Ydr249c pp Hmt1
+Pam1 pp Sur1
+Btt1 pp Caf130
+Btt1 pp Egd2
+Cta1 pp Pex14
+Cta1 pp Pre5
+Yap6 pp Fir1
+Yap6 pp Nap1
+Yap6 pp Apg17
+Ydr261wa pp Ydr261wa
+Ydr261wa pp Ydr261wb
+Ydr262w pp Guk1
+Din7 pp Yor214c
+Ydr267c pp Yhr122w
+Msw1 pp Snu66
+Ydr271c pp Ydr509w
+Ydr271c pp Ade2
+Ydr271c pp Esa1
+Ydr275w pp Esc2
+Ydr279w pp Cak1
+Ydr279w pp Fkh1
+Pro1 pp Sup35
+Cyp5 pp Ydl100c
+Ydr307w pp Nup53
+Gic2 pp Ydr116c
+Tfb1 pp Pta1
+Tfb1 pp Ape3
+Tfb1 pp Cos2
+Tfb1 pp Yap6
+Tfb1 pp Ilv1
+Tfb1 pp Ygl198w
+Tfb1 pp Ygr033c
+Tfb1 pp Sec35
+Tfb1 pp Yhr113w
+Tfb1 pp Yil071c
+Tfb1 pp Tid3
+Tfb1 pp Lap4
+Tfb1 pp Gfa1
+Tfb1 pp Trk2
+Tfb1 pp Mec3
+Tfb1 pp Apg17
+Tfb1 pp Jnm1
+Tfb1 pp Yol082w
+Tfb1 pp Vps21
+Tfb1 pp Yor197w
+Tfb1 pp Nce4
+Tfb1 pp Ypl170w
+Tfb1 pp Dpm1
+Pib1 pp Yip3
+Mcm21 pp Ydl026w
+Mcm21 pp Kre26
+Mcm21 pp Ydl046w
+Mcm21 pp Ydl050c
+Mcm21 pp Ydl053c
+Mcm21 pp Rps29b
+Mcm21 pp Cox9
+Mcm21 pp Ydl096c
+Mcm21 pp Snu23
+Mcm21 pp Ydl110c
+Mcm21 pp Ydl118w
+Mcm21 pp Ydl162c
+Mcm21 pp Inh1
+Mcm21 pp Ydr455c
+Mcm21 pp Snm1
+Mcm21 pp Ydr542w
+Mcm21 pp Yel068c
+Mcm21 pp Smb1
+Mcm21 pp Edc2
+Mcm21 pp Yer084w
+Mcm21 pp Yfl015c
+Mcm21 pp Yfr054c
+Mcm21 pp Ygl239c
+Mcm21 pp Ygr018c
+Mcm21 pp Cax4
+Mcm21 pp Ygr146c
+Mcm21 pp Yhl042w
+Mcm21 pp Chs7
+Mcm21 pp Spo12
+Mcm21 pp Yhr189w
+Mcm21 pp Yil141w
+Mcm21 pp Yll033w
+Mcm21 pp Yll037w
+Asp1 pp Asp1
+Asp1 pp Vps45
+Pep7 pp Ypt52
+Skp1 pp Ynl311c
+Skp1 pp Sgt1
+Pex3 pp Pex19
+Pex3 pp Ylr002c
+Ydr332w pp Ymr074c
+Msn5 pp Nup100
+Ydr346c pp Ylr077w
+Ydr348c pp Ydl114w
+Yps7 pp Ict1
+Yps7 pp Sgt2
+Tcm10 pp Spc98
+Sbe2 pp Apl1
+Ydr357c pp Ygl079w
+Ydr357c pp Apg17
+Ydr365c pp Lcb1
+Ydr370c pp Yfl049w
+Ydr371w pp Gtt1
+Ydr372c pp Pep8
+Ydr372c pp Ylr352w
+Frq1 pp Idh2
+Lsm6 pp Lsm5
+Ydr380w pp Ena5
+Ydr380w pp Yor382w
+Eft2 pp Ret2
+Mus81 pp Ypl108w
+Rvs167 pp Rvs161
+Rpt3 pp Nas6
+Ncb2 pp Bur6
+Ydr398w pp Rpl32
+Dit1 pp Ysr3
+Ydr415c pp Ydl100c
+Ydr415c pp Bir1
+Ydr425w pp Ygl161c
+Ydr425w pp Ygl198w
+Ydr425w pp Yip1
+Ydr425w pp Snx4
+Ydr425w pp Yjr110w
+Ydr425w pp Ypt52
+Rpn9 pp Mnt4
+Tif35 pp Ypl105c
+Ydr431w pp Ydl100c
+Kre22 pp Ynl116w
+Lrs4 pp Ycr086w
+Apt2 pp Ydr084c
+Ydr442w pp Ydr084c
+Ydr445c pp Yer071c
+Ecm11 pp Smt3
+Rmt2 pp Apg12
+Rmt2 pp Rec107
+Tlg1 pp Yip1
+Prp3 pp Apg17
+Prp3 pp Pho85
+Prp3 pp Prp4
+Snf1 pp Gal83
+Ydr479c pp Ylr324w
+Sac2 pp Yap6
+Sac2 pp Sda1
+Pac11 pp Yil135c
+Pac11 pp Nip100
+Pkh1 pp Ygr086c
+Pkh1 pp Ypl004c
+Ydr506c pp Ybr230c
+Gnp1 pp Leo1
+Gnp1 pp Ccl1
+Smt3 pp Smt3
+Ttr1 pp Ydl100c
+Ydr514c pp Mdg1
+Age1 pp Yor066w
+Ydr534c pp Qcr2
+Stl1 pp Yil135c
+Ydr541c pp Snf7
+Vab2 pp Ydr469w
+Vab2 pp Ygl079w
+Vab2 pp Ygr107w
+Vab2 pp Nup82
+Vab2 pp Ynl086w
+Vac8 pp Ykl061w
+Vac8 pp Ylr254c
+Yel015w pp Yel015w
+Yel015w pp Rps28b
+Yel015w pp Dcp1
+Yel016c pp Far1
+Yel016c pp Yol150c
+Yel017w pp Yel017w
+Yel017w pp Gtt1
+Yel018w pp Ade2
+Yel020c pp Rho3
+Anp1 pp Yhr080c
+Anp1 pp Pre6
+Rad23 pp Rps1a
+Yel041w pp Utr1
+Yel041w pp Mrt4
+Yel041w pp Yor315w
+Gda1 pp Yel017w
+Gda1 pp Ald5
+Gda1 pp Yjl152w
+Gda1 pp Ssp120
+Gda1 pp Hpa2
+Yel043w pp Yor164c
+Yel047c pp Aro4
+Yel048c pp Kss1
+Yel048c pp Slt2
+Yel048c pp Om45
+Yel048c pp Ynl227c
+Rpl12a pp Ydr084c
+Npr2 pp Bbp1
+Can1 pp Lst7
+Can1 pp Ume1
+Yel064c pp Lys1
+Yel064c pp Bio3
+Yel064c pp Ssp2
+Hpa3 pp Hpa3
+Hpa3 pp Srb2
+Hpa3 pp Ypl112c
+Yel068c pp Ylr225c
+Hxt13 pp Rpc40
+Yel070w pp Bio3
+Yel077c pp Chl4
+Yel077c pp Hxk1
+Pac2 pp Yjl120w
+Pac2 pp Yol082w
+Ntf2 pp Mrpl11
+Ntf2 pp Yer004w
+Tir1 pp Ydr084c
+Afg3 pp Hmt1
+Isc1 pp Rtt105
+Isc1 pp Rox1
+Srb4 pp Ybl065w
+Srb4 pp Coq1
+Srb4 pp Ybr047w
+Srb4 pp Med8
+Srb4 pp Arc40
+Srb4 pp Ycr082w
+Srb4 pp Mrpl11
+Srb4 pp Doa4
+Srb4 pp Hta1
+Srb4 pp Yap6
+Srb4 pp Kre28
+Srb4 pp Ubc8
+Srb4 pp Isc1
+Srb4 pp Rsc8
+Srb4 pp Yfr038w
+Srb4 pp Cwh41
+Srb4 pp Rsm23
+Srb4 pp Ygl261c
+Srb4 pp Ygr090w
+Srb4 pp Crm1
+Srb4 pp Ygr243w
+Srb4 pp Yhl005c
+Srb4 pp Yhl044w
+Srb4 pp Yhl045w
+Srb4 pp Med6
+Srb4 pp Yhr116w
+Srb4 pp Spo12
+Srb4 pp Rpn10
+Srb4 pp Tim44
+Srb4 pp Ths1
+Srb4 pp Yil141w
+Srb4 pp Gtt1
+Srb4 pp Yjl142c
+Srb4 pp Ime1
+Srb4 pp Yjr126c
+Srb4 pp Bat2
+Srb4 pp Ykl051w
+Srb4 pp Ykl063c
+Srb4 pp Sdh3
+Srb4 pp Ltv1
+Srb4 pp Ptr2
+Srb4 pp Yll020c
+Srb4 pp Gin11
+Srb4 pp Cbf5
+Srb4 pp Mec3
+Srb4 pp Ylr331c
+Srb4 pp Yap1
+Srb4 pp Apt1
+Srb4 pp Spc2
+Srb4 pp Yml082w
+Srb4 pp Sub1
+Srb4 pp Arg80
+Srb4 pp Mcm1
+Srb4 pp Fet3
+Srb4 pp Ymr087w
+Srb4 pp Med11
+Srb4 pp Ymr114c
+Srb4 pp Ymr118c
+Srb4 pp Rim11
+Srb4 pp Ymr181c
+Srb4 pp Ymr244w
+Srb4 pp Ymr293c
+Srb4 pp Lst8
+Srb4 pp Msk1
+Srb4 pp End3
+Srb4 pp Ynl159c
+Srb4 pp Mer1
+Srb4 pp Ynl211c
+Srb4 pp Ynl235c
+Srb4 pp Hch1
+Srb4 pp Pop3
+Srb4 pp Caf40
+Srb4 pp Rpl18b
+Srb4 pp Cit1
+Srb4 pp Urk1
+Srb4 pp Pop2
+Srb4 pp Ynr071c
+Srb4 pp Yol022c
+Srb4 pp Ngl1
+Srb4 pp Yol106w
+Srb4 pp Med7
+Srb4 pp Cin5
+Srb4 pp Ckb2
+Srb4 pp Yor072w
+Srb4 pp Idh2
+Srb4 pp Thi80
+Srb4 pp Tuf1
+Srb4 pp Yor197w
+Srb4 pp Cpa1
+Srb4 pp Mrs2
+Srb4 pp Kre5
+Srb4 pp Fdh1
+Srb4 pp Taf47
+Srb4 pp Ktr6
+Srb4 pp Ypl098c
+Gcd11 pp Rrp40
+Cho1 pp Nup53
+Fir1 pp Yjr110w
+Kre30 pp Ygr206w
+Kre29 pp Yml023c
+Hvg1 pp Ymr119w
+Caj1 pp Hxt7
+Caj1 pp Ypl205c
+Caj1 pp Atp20
+Yer049w pp Lpp1
+Yer051w pp Ser3
+Yer051w pp Yps3
+Yer051w pp Ymr310c
+Hom3 pp Phm8
+Hom3 pp Yir014w
+Hom3 pp Yap5
+Hom3 pp Ykr079c
+Hom3 pp Ymr263w
+Yer053c pp Ylr326w
+Pcl6 pp Ybr141c
+Pcl6 pp Whi4
+Pcl6 pp Yer156c
+Pcl6 pp Yor392w
+Cem1 pp Ypl073c
+Tho1 pp Sub2
+Tho1 pp Ymr048w
+Yer064c pp Ynl157w
+Yer064c pp Pus1
+Yer064c pp Ypr125w
+Yer066w pp Rim13
+Yer067w pp Ypl180w
+Arg5 pp Fre1
+Yer071c pp Rpb5
+Yer071c pp Cwh36
+Yer071c pp Ydr366c
+Yer071c pp Yke2
+Yer071c pp Ymr048w
+Yer071c pp Svl3
+Ald5 pp Ypl257w
+Yer077c pp Gsy1
+Yer077c pp Yil110w
+Yer078c pp Prp31
+Ser3 pp Yal011w
+Ser3 pp Yal060w
+Ser3 pp Yar003w
+Ser3 pp Gal7
+Ser3 pp Gal1
+Ser3 pp Ybr042c
+Ser3 pp Ecm2
+Ser3 pp Ybr074w
+Ser3 pp Iml3
+Ser3 pp Apg14
+Ser3 pp Sup45
+Ser3 pp Cns1
+Ser3 pp Ybr168w
+Ser3 pp Npl4
+Ser3 pp Pdb1
+Ser3 pp Thi2
+Ser3 pp Ybr241c
+Ser3 pp Alg7
+Ser3 pp Aro4
+Ser3 pp Chk1
+Ser3 pp Ycl038c
+Ser3 pp Ycr072c
+Ser3 pp Qri2
+Ser3 pp Dhh1
+Ser3 pp Sfa1
+Ser3 pp Maf1
+Ser3 pp Rpl4b
+Ser3 pp Ydr105c
+Ser3 pp Pex7
+Ser3 pp Cph1
+Ser3 pp Nup42
+Ser3 pp Mss116
+Ser3 pp Ydr266c
+Ser3 pp Ydr306c
+Ser3 pp Ydr307w
+Ser3 pp Gpi8
+Ser3 pp Hxt6
+Ser3 pp Rpt3
+Ser3 pp Ydr479c
+Ser3 pp Kre2
+Ser3 pp Ydr512c
+Ser3 pp Age1
+Ser3 pp Hlr1
+Ser3 pp Ydr531w
+Ser3 pp Yer078c
+Ser3 pp Ser3
+Ser3 pp Ftr1
+Ser3 pp Mdj1
+Ser3 pp Tub2
+Ser3 pp Yfr017c
+Ser3 pp Hxk1
+Ser3 pp Yfr055w
+Ser3 pp Ygl039w
+Ser3 pp Tos8
+Ser3 pp Ygl110c
+Ser3 pp Rpl1b
+Ser3 pp Gts1
+Ser3 pp Vma7
+Ser3 pp Mrp13
+Ser3 pp Rnr4
+Ser3 pp Ygr210c
+Ser3 pp Ygr293c
+Ser3 pp Age2
+Ser3 pp Ser33
+Ser3 pp Abm1
+Ser3 pp Ykr073c
+Ser3 pp Pcd1
+Ser3 pp Ynr042w
+Ser3 pp Mrpl23
+Ser3 pp Rps28a
+Ser3 pp Yor189w
+Ser3 pp Odc2
+Ser3 pp Yor246c
+Ser3 pp Yor258w
+Ser3 pp Yor263c
+Ser3 pp Yor300w
+Ser3 pp Yor318c
+Ser3 pp Pre10
+Ser3 pp Yor387c
+Ser3 pp Fdh1
+Ser3 pp Yor392w
+Ser3 pp Ypl205c
+Ser3 pp Lea1
+Ser3 pp Ypl229w
+Ser3 pp Ypl233w
+Ser3 pp Tfp3
+Ser3 pp Tif6
+Ser3 pp Ypr038w
+Ser3 pp Mcm16
+Ser3 pp Ypr059c
+Ser3 pp Ypr126c
+Ser3 pp Mss18
+Ser3 pp Fyv15
+Ser3 pp Nce102
+Kre31 pp Yjl135w
+Kre31 pp Pus1
+Yer083c pp Kre32
+Yer083c pp Dpb2
+Ilv1 pp Ilv1
+Yer087w pp Ydl036c
+Yer093c pp Yjl058c
+Yer093c pp Clb4
+Pup3 pp Ilv6
+Rad51 pp Rad51
+Prs2 pp Prs1
+Prs2 pp Prs5
+Rps8b pp Ydr459c
+Ssa4 pp Dos2
+Ssa4 pp Alg2
+Mam1 pp Ycr086w
+Gle2 pp Mrf1
+Gle2 pp Yhl008c
+Sho1 pp Clb3
+Sho1 pp Ydl204w
+Sho1 pp Sho1
+Yer119c pp Oar1
+Glo3 pp Ecm32
+Yer124c pp Yhr003c
+Rsp5 pp Rpa43
+Lcp5 pp Bfr2
+Lcp5 pp Apg17
+Yer128w pp Vps4
+Pak1 pp Tid3
+Pak1 pp Ura4
+Glc7 pp Ybr099c
+Gdi1 pp Msl1
+Gdi1 pp Aos1
+Yer140w pp Ydl054c
+Yer140w pp Dhh1
+Yer140w pp Ykl056c
+Ddi1 pp Yjr141w
+Ddi1 pp Ynr071c
+Ubp5 pp Akl1
+Ubp5 pp Mtf2
+Ubp5 pp Hof1
+Ubp5 pp Akr2
+Ftr1 pp Ydr307w
+Ftr1 pp Yil056w
+Ftr1 pp Pre3
+Pea2 pp Ydl233w
+Pea2 pp Yil040w
+Pea2 pp Ykl034w
+Pea2 pp Yor315w
+Yer152c pp Yjl107c
+Pet122 pp Asg7
+Oxa1 pp Rpc34
+Oxa1 pp Yor121c
+Yer156c pp Ypt1
+Sec34 pp Sec35
+Yer158c pp Oac1
+Rph1 pp Ypl071c
+Pda1 pp Smi1
+Pda1 pp Ssh4
+Dmc1 pp Dmc1
+Dmc1 pp Rpl11b
+Dmc1 pp Gcd14
+Yer186c pp Gcn3
+Spb4 pp Yjr082c
+Yfl002wb pp Ydr261wa
+Msh4 pp Msh5
+Hxt10 pp Mvp1
+Mdj1 pp Yhl045w
+Mdj1 pp Hym1
+Lpd1 pp Osm1
+Lpd1 pp Dci1
+Pau5 pp Upf3
+Pau5 pp Ymd8
+Gat1 pp Scl1
+Frs2 pp Ydl193w
+Frs2 pp Ygr169c
+Fyv11 pp Nfs1
+Fyv11 pp Glc7
+Fyv11 pp Yke2
+Fyv11 pp Ylr243w
+Ste2 pp Ysc84
+Ste2 pp Ssp2
+Yfl027c pp Yer078c
+Yfl027c pp Yhr115c
+Yfl027c pp Ykl195w
+Yfl030w pp Yil077c
+Yfl030w pp Ykr007w
+Rpo41 pp Dfg5
+Yfl040w pp Ppm1
+Yfl040w pp Ylr349w
+Yfl051c pp Gpx1
+Yfl052w pp Gcd14
+Yfl052w pp Yor366w
+Snz3 pp Snz3
+Yfl065c pp Ylr415c
+Nic96 pp Nup53
+Yfr003c pp Yor147w
+Yfr003c pp Ypr050c
+Yfr007w pp Ybr056w
+Yfr008w pp Nup82
+Yfr008w pp Cox8
+Yfr008w pp Apg17
+Yfr008w pp Far3
+Yfr008w pp Med7
+Yfr008w pp Mcm16
+Yfr011c pp Yjl021c
+Ioc3 pp Ioc2
+Gsy1 pp Yap6
+Gsy1 pp Gsy1
+Gsy1 pp Sod2
+Gsy1 pp Glg2
+Gsy1 pp Gsy2
+Gsy1 pp Std1
+Cdc26 pp Fre6
+Rsc8 pp Sfh1
+Yfr042w pp Ynr025c
+Yfr047c pp Yfr047c
+Ymr31 pp Kgd2
+Ymr31 pp Ymr147w
+Ymr31 pp Apm4
+Ymr31 pp Yol082w
+Ymr31 pp Yol083w
+Ymr31 pp Std1
+Ymr31 pp Yor049c
+Ymr31 pp Dig1
+Ymr31 pp Bbp1
+Rpn12 pp Ydl156w
+Rpn12 pp Ydr273w
+Ygl005c pp Nup57
+Ygl010w pp Ypl257w
+Pdr1 pp Pdr1
+Ygl014w pp Pdr16
+Cwh41 pp Tim44
+Cgr1 pp Sla2
+Aga2 pp Ygr257c
+Pnc1 pp Pnc1
+Hem2 pp Hem2
+Rna15 pp Ydl218w
+Rna15 pp Maf1
+Rna15 pp Dad1
+Rna15 pp Ydr084c
+Rna15 pp Grx3
+Rna15 pp Plp1
+Rna15 pp Pad1
+Rna15 pp Ddi1
+Rna15 pp Ygr004w
+Rna15 pp Rsm7
+Rna15 pp Nup2
+Rna15 pp Nup53
+Rna15 pp Rrn9
+Rna15 pp Ynl013c
+Rna15 pp Yip3
+Rna15 pp Ynl157w
+Ygl052w pp Cdc24
+Erv14 pp Fps1
+Ygl057c pp Fus3
+Rad6 pp Rex4
+Rad6 pp Toa1
+Ygl060w pp Rvs167
+Duo1 pp Dad1
+Duo1 pp Qcr7
+Duo1 pp Bim1
+Duo1 pp Dam1
+Duo1 pp Pfd1
+Duo1 pp Spc34
+Pus2 pp Lpd1
+Rpb9 pp Yar064w
+Rpb9 pp Ybr089w
+Rpb9 pp Pho88
+Rpb9 pp Iml3
+Rpb9 pp Ics2
+Rpb9 pp Pop7
+Rpb9 pp Ecm31
+Rpb9 pp Ntc20
+Rpb9 pp Der1
+Rpb9 pp Aor1
+Rpb9 pp Ydl053c
+Rpb9 pp Ydl183c
+Rpb9 pp Ydl219w
+Rpb9 pp Cis1
+Rpb9 pp Cdc34
+Rpb9 pp Ydr056c
+Rpb9 pp Ydr067c
+Rpb9 pp Pet100
+Rpb9 pp Ydr115w
+Rpb9 pp Ydr136c
+Rpb9 pp Atc1
+Rpb9 pp Ydr199w
+Rpb9 pp Swm1
+Rpb9 pp Ydr286c
+Rpb9 pp Ydr340w
+Rpb9 pp Smb1
+Rpb9 pp Hvg1
+Rpb9 pp Yer053c
+Rpb9 pp Flo8
+Rpb9 pp Spr6
+Rpb9 pp Isc10
+Rpb9 pp Yer181c
+Rpb9 pp Gna1
+Rpb9 pp Mob2
+Rpb9 pp Ypt1
+Rpb9 pp Asg7
+Rpb9 pp Yjl182c
+Rpb9 pp Rps22a
+Rpb9 pp Yjr162c
+Rpb9 pp Ykl036c
+Rpb9 pp Ykl086w
+Rpb9 pp Sdh3
+Rpb9 pp Mcr1
+Rpb9 pp Cnb1
+Ygl074c pp Rpt3
+Mps2 pp Bdf2
+Lif1 pp Cdc50
+Lif1 pp Nej1
+Lif1 pp Ylr424w
+Nup145 pp Ygl060w
+Srm1 pp Yor364w
+Ygl098w pp Yel017w
+Ygl102c pp Yhr194w
+Ygl104c pp Nup53
+Taf60 pp Luc7
+Taf60 pp Rim13
+Taf60 pp Taf17
+Taf60 pp Pub1
+Sld3 pp Opt2
+Snf4 pp Gal83
+Snf4 pp Sip2
+Nab2 pp Psp1
+Nab2 pp Nab2
+Nab2 pp Gar1
+Nab2 pp Pub1
+Mon1 pp Pan3
+Soh1 pp Cdc24
+Soh1 pp Ybl009w
+Soh1 pp Ybl051c
+Soh1 pp Ecm31
+Soh1 pp Pch2
+Soh1 pp Med8
+Soh1 pp Ycr030c
+Soh1 pp Rrp43
+Soh1 pp Fad1
+Soh1 pp Rpn5
+Soh1 pp Cdc36
+Soh1 pp Ydr084c
+Soh1 pp Ubc13
+Soh1 pp Ydr095c
+Soh1 pp Fob1
+Soh1 pp Hta1
+Soh1 pp Yap6
+Soh1 pp Srb7
+Soh1 pp Ydr479c
+Soh1 pp Smt3
+Soh1 pp Ydr534c
+Soh1 pp Utr4
+Soh1 pp Yel048c
+Soh1 pp Srb4
+Soh1 pp Yer119c
+Soh1 pp Pea2
+Soh1 pp Yer184c
+Soh1 pp Yfr026c
+Soh1 pp Ckb1
+Soh1 pp Pex14
+Soh1 pp Ygl157w
+Soh1 pp Ygl250w
+Soh1 pp Ygr139w
+Soh1 pp Med6
+Soh1 pp Yhr130c
+Soh1 pp Yil025c
+Soh1 pp Ulp2
+Soh1 pp Met28
+Soh1 pp Yjl032w
+Soh1 pp Ham1
+Soh1 pp Ykl137w
+Soh1 pp Sir1
+Soh1 pp Gin11
+Soh1 pp Psr2
+Soh1 pp Ylr108c
+Soh1 pp Ylr222c
+Soh1 pp Ylr311c
+Soh1 pp Sfh1
+Soh1 pp Apg17
+Soh1 pp Yml133c
+Soh1 pp Stv1
+Soh1 pp Abf2
+Soh1 pp Erg2
+Soh1 pp Cse2
+Soh1 pp Cpr8
+Soh1 pp Cmk2
+Soh1 pp Tlg2
+Soh1 pp Med7
+Soh1 pp Std1
+Soh1 pp Ade2
+Soh1 pp Yrr1
+Soh1 pp Med4
+Soh1 pp Yor263c
+Soh1 pp Yor289w
+Soh1 pp Atf1
+Soh1 pp Ypl064c
+Soh1 pp Nut2
+Ygl132w pp Fun26
+Ygl139w pp Tir2
+Tip20 pp Ynl258c
+Lys5 pp Fzf1
+Lys5 pp Cin5
+Lys5 pp Ade2
+Ams1 pp Yol082w
+Ams1 pp Yol083w
+Ygl157w pp Ynr064c
+Ygl161c pp Ydr084c
+Ygl161c pp Ydr100w
+Ygl161c pp Ygl198w
+Ygl161c pp Yip1
+Ygl161c pp Pep12
+Ygl177w pp Tim54
+Apg1 pp Ctk3
+Gts1 pp Ycr072c
+Gts1 pp Ydl233w
+Gts1 pp Yap6
+Gts1 pp Tho1
+Gts1 pp Ald5
+Gts1 pp Spt2
+Gts1 pp Yhr177w
+Gts1 pp Dot5
+Gts1 pp Rpl34b
+Gts1 pp Yil057c
+Gts1 pp Yil122w
+Gts1 pp Ynr068c
+Gts1 pp Sfl1
+Gts1 pp Yor331c
+Gts1 pp Yor333c
+Gts1 pp Ypl013c
+Gts1 pp Ktr6
+Gts1 pp Prm4
+Gts1 pp Pos5
+Cox4 pp Ski8
+Cox4 pp Cat2
+Ygl198w pp Yip1
+Ski8 pp Akl1
+Ski8 pp Rdh54
+Ski8 pp Frm2
+Ygl220w pp Grx3
+Gog5 pp Gtt1
+Mto1 pp Yil057c
+Mto1 pp Ppq1
+Hap2 pp Hap3
+Hap2 pp Mth1
+Hap2 pp Ygr146c
+Hap2 pp Apg17
+Hap2 pp Nup53
+Hap2 pp Std1
+Hap2 pp Hap5
+Ygl245w pp Opi1
+Zip2 pp Hxt13
+Cos12 pp Yjr020w
+Ygr003w pp Ylr297w
+Ygr004w pp Ylr324w
+Ygr004w pp Yip2
+Ygr010w pp Ylr328w
+Ygr010w pp Ynl218w
+Snu71 pp Faa3
+Snu71 pp Prp40
+Ygr016w pp Ylr135w
+Vma7 pp Vma22
+Mtl1 pp Ylr460c
+Ygr026w pp Ylr324w
+Ygr033c pp Ylr135w
+Ygr035c pp Crs5
+Ygr035c pp Yor118w
+Kss1 pp Dig1
+Bud9 pp Bud9
+Bud9 pp Ypl251w
+Ygr045c pp Yor271c
+Ufd1 pp Vma10
+Ygr052w pp Yjl086c
+Ygr052w pp Ypl060w
+Ygr054w pp Ydr366c
+Rsc1 pp Mtf2
+Lst7 pp Put3
+Ygr058w pp Ygr058w
+Ygr058w pp Ygr136w
+Ygr058w pp Ynl047c
+Ygr058w pp Yor097c
+Vht1 pp Yjl199c
+Ygr066c pp Yap6
+Ygr066c pp Ylr386w
+Ygr068c pp Rsp5
+Ygr069w pp Rpl19b
+Ygr071c pp Yjl058c
+Ygr071c pp Tbf1
+Upf3 pp Urm1
+Ygr073c pp Yml119w
+Ygr079w pp Ynl081c
+Ygr079w pp Urk1
+Tom20 pp Frq1
+Mrp13 pp Ygr251w
+Ygr086c pp Mrp8
+Dbf2 pp Mob1
+Dbf2 pp Ykl061w
+Dbf2 pp Ylr424w
+Ask10 pp Ask10
+Ask10 pp Apg16
+Ygr101w pp Yjl213w
+Vma21 pp Yfr018c
+Clb1 pp Nip29
+Dam1 pp Dad1
+Dam1 pp Ygl079w
+Dam1 pp Tid3
+Dam1 pp Yjl064w
+Dam1 pp Spc34
+Dam1 pp Rec102
+Dam1 pp Apg17
+Dam1 pp Ylr424w
+Dam1 pp Ypr045c
+Dam1 pp Mcm16
+Dam1 pp Cvt9
+Rps23a pp Rpl17a
+Nup57 pp Pex19
+Nup57 pp Syf1
+Nup57 pp Yel043w
+Nup57 pp Ygl170c
+Nup57 pp Nup49
+Nup57 pp Sec35
+Nup57 pp Nsp1
+Nup57 pp Ykl061w
+Nup57 pp Lap4
+Nup57 pp Apg17
+Nup57 pp Rim11
+Nup57 pp Jnm1
+Nup57 pp Mcm16
+Nup57 pp Ypr083w
+Mep1 pp Yel017w
+Mep1 pp Gtt1
+Ygr122w pp Snf7
+Ppt1 pp Yer113c
+Ppt1 pp Ygl138c
+Ppt1 pp Mac1
+Ppt1 pp Hem15
+Asn2 pp Ykl137w
+Syf2 pp Syf1
+Ygr141w pp Ste2
+Ygr141w pp Ymr265c
+Btn2 pp Aah1
+Btn2 pp Mge1
+Thi4 pp Thi4
+Thi4 pp Mac1
+Ygr145w pp Bfr2
+Ygr149w pp Gtt1
+Ygr151c pp Ydr413c
+Mtr3 pp Ylr345w
+Nsr1 pp Msg5
+Fyv13 pp Arl3
+Ygr165w pp Hmt1
+Ygr165w pp Mlh2
+Ygr165w pp Dip5
+Kre11 pp Yor197w
+Clc1 pp Cin5
+Ygr168c pp Yap5
+Ygr169c pp Ydr516c
+Yip1 pp Slf1
+Yip1 pp Ylr324w
+Yip1 pp Yip3
+Ygr173w pp Ydl054c
+Ygr173w pp Ydr152w
+Ygr173w pp Suc2
+Ygr173w pp Fet4
+Atf2 pp Yip1
+Pbp1 pp Nup145
+Pbp1 pp Yhr121w
+Pbp1 pp Tad2
+Ygr179c pp Ame1
+Tim13 pp Hmt1
+Tys1 pp Ypl013c
+Crh1 pp Ydl100c
+Hip1 pp Gtt1
+Hip1 pp Ylr283w
+Pdx1 pp Tom70
+Fyv8 pp Rgd1
+Fyv8 pp Pup2
+Pmt6 pp Akl1
+Ygr205w pp Clb4
+Ygr207c pp Gic2
+Ser2 pp Taf47
+Trx2 pp Rpp1a
+Trx2 pp Ulp1
+Zpr1 pp Hch1
+Zpr1 pp Hrt1
+Zpr1 pp Cin5
+Rps0a pp Faa3
+Crm1 pp She1
+Crm1 pp Pat1
+Crm1 pp Pex19
+Crm1 pp Dad1
+Crm1 pp Ydr102c
+Crm1 pp Nup42
+Crm1 pp Ydr229w
+Crm1 pp Yel015w
+Crm1 pp Yer004w
+Crm1 pp Hor2
+Crm1 pp Yfl068w
+Crm1 pp Ygl149w
+Crm1 pp Ygl170c
+Crm1 pp Nup57
+Crm1 pp Pbp1
+Crm1 pp Pex2
+Crm1 pp Yjr083c
+Crm1 pp Sgm1
+Crm1 pp Nup100
+Crm1 pp Ltv1
+Crm1 pp Pcd1
+Crm1 pp Ecm30
+Crm1 pp Yap1
+Crm1 pp Ndi1
+Crm1 pp Ymr124w
+Crm1 pp Ynl164c
+Crm1 pp Dcp1
+Crm1 pp Yor147w
+Crm1 pp Yor177c
+Crm1 pp Ser1
+Crm1 pp Scd5
+Crm1 pp Ypl056c
+Crm1 pp Vps30
+Ygr223c pp Vps21
+Smi1 pp Rpc40
+Spg1 pp Hap5
+Ygr237c pp Ylr128w
+Pex21 pp Sif2
+Pex21 pp Yap6
+Pex21 pp Mga1
+Pex21 pp Top3
+Pex21 pp Ymr192w
+Pex21 pp Ppa2
+Pex21 pp Yor389w
+Ygr242w pp Pex19
+Ygr247w pp Yer045c
+Ygr247w pp Snc2
+Ygr250c pp Fun11
+Ygr250c pp Hof1
+Gcn5 pp Yor225w
+Eno1 pp Ynr036c
+Ygr263c pp Sun4
+Ygr263c pp Dci1
+Fol2 pp Fol2
+Ygr268c pp Cdc24
+Ygr268c pp Ubp14
+Ygr268c pp Rvs167
+Ygr268c pp Rsp5
+Ygr268c pp Ygr268c
+Ygr271w pp Yer049w
+Rnh70 pp Smm1
+Ygr280c pp Ymr102c
+Ygr283c pp Hch1
+Zuo1 pp Cps1
+Mal11 pp Ydr413c
+Mal12 pp Ylr054c
+Rpl14b pp Hta1
+Yhl002w pp Yap6
+Yhl002w pp Ygr268c
+Yhl002w pp Vps27
+Lag1 pp Lac1
+Mrp4 pp Rrn6
+Mrp4 pp Sif2
+Mrp4 pp Ydl100c
+Mrp4 pp Fob1
+Mrp4 pp Ilv1
+Mrp4 pp Mga1
+Mrp4 pp Apg17
+Mrp4 pp Nup53
+Mrp4 pp Ste4
+Mrp4 pp Bbp1
+Shu1 pp Hap3
+Shu1 pp Pdc5
+Shu1 pp Ylr376c
+Shu1 pp Bbp1
+Rps20 pp Gpi13
+Yhl018w pp Yhl018w
+Apm2 pp Gal10
+Apm2 pp Yfr045w
+Apm2 pp Apl2
+Apm2 pp Apl4
+Yhl021c pp Ygr101w
+Yhl021c pp Rgs2
+Yhl026c pp Met22
+Rim101 pp Fkh1
+Mup3 pp Tif3
+Gpa1 pp Ydl100c
+Gpa1 pp Ste4
+Yhr009c pp Yor359w
+Dia4 pp Ypr004c
+Spo13 pp Ady1
+Ded81 pp Mlc1
+Ded81 pp Htm1
+Thr1 pp Thr1
+Slt2 pp Smd3
+Slt2 pp Ypt6
+Slt2 pp Sec22
+Slt2 pp Ylr346c
+Slt2 pp Ylr350w
+Yhr035w pp Yll013c
+Yhr036w pp Nup145
+Yhr040w pp Rtt106
+Srb2 pp Acs1
+Srb2 pp Pop8
+Srb2 pp Sec66
+Srb2 pp Fzo1
+Srb2 pp Med8
+Srb2 pp Trs20
+Srb2 pp Pgk1
+Srb2 pp Ydr154c
+Srb2 pp Yer066w
+Srb2 pp Yjl015c
+Srb2 pp Yjl086c
+Srb2 pp Ylr164w
+Srb2 pp Imh1
+Srb2 pp Rpl26a
+Srb2 pp Sno2
+Srb2 pp Yor073w
+Srb2 pp Ypr203w
+Dog2 pp Apg17
+Yhr045w pp Ade2
+Smf2 pp Ykr089c
+Yhr056c pp Yfl067w
+Yhr056c pp Dps1
+Cyp2 pp Ydl100c
+Vma22 pp Vma6
+Rpp1 pp Hem15
+Pan5 pp Aos1
+Rrp3 pp Ydr367w
+Dys1 pp Apl2
+Qns1 pp Qns1
+Hxt1 pp Yhr122w
+Hxt5 pp Yll020c
+Sfb3 pp Yjl199c
+Sfb3 pp Cyc1
+Sfb3 pp Sec23
+Kic1 pp Tim22
+Kic1 pp Ydr229w
+Kic1 pp Rpn11
+Kic1 pp Hym1
+Kic1 pp Ylr315w
+Kic1 pp Ylr365w
+Kic1 pp Ctf19
+Cdc12 pp Shs1
+Cdc12 pp Cdc11
+Ctm1 pp Ygr071c
+Yhr111w pp Urm1
+Yhr111w pp Yil132c
+Yhr113w pp Yhr113w
+Yhr113w pp Yol082w
+Bzz1 pp Yal064w
+Bzz1 pp Ybl109w
+Bzz1 pp Rim2
+Bzz1 pp Rrp43
+Bzz1 pp Per1
+Bzz1 pp Ydl015c
+Bzz1 pp Ydl037c
+Bzz1 pp Ydl100c
+Bzz1 pp Pph21
+Bzz1 pp Ydl172c
+Bzz1 pp Fyv14
+Bzz1 pp Tim22
+Bzz1 pp Ydr042c
+Bzz1 pp Ydr056c
+Bzz1 pp Doa4
+Bzz1 pp Kgd2
+Bzz1 pp Ydr319c
+Bzz1 pp Syf1
+Bzz1 pp Sip1
+Bzz1 pp Slf1
+Bzz1 pp Qcr7
+Bzz1 pp Yel017w
+Bzz1 pp Yer079w
+Bzz1 pp Shc1
+Bzz1 pp Rpl23b
+Bzz1 pp Rsp5
+Bzz1 pp Bur6
+Bzz1 pp Yfl012w
+Bzz1 pp Lpd1
+Bzz1 pp Eco1
+Bzz1 pp Jac1
+Bzz1 pp Rpl30
+Bzz1 pp Pnc1
+Bzz1 pp Rsm23
+Bzz1 pp Rps26a
+Bzz1 pp Edc1
+Bzz1 pp Gog5
+Bzz1 pp Mto1
+Bzz1 pp Ygr031w
+Bzz1 pp Ygr110w
+Bzz1 pp Rsm27
+Bzz1 pp Yhl044w
+Bzz1 pp Yhr133c
+Bzz1 pp Urm1
+Bzz1 pp Pig2
+Bzz1 pp Yil132c
+Bzz1 pp Mrs1
+Bzz1 pp Vtc4
+Bzz1 pp Rtt101
+Bzz1 pp Yjl065c
+Bzz1 pp Yjl086c
+Bzz1 pp Pho86
+Bzz1 pp Yjl152w
+Bzz1 pp Hsp150
+Bzz1 pp Kre9
+Bzz1 pp Atp12
+Bzz1 pp Prp21
+Bzz1 pp Abm1
+Bzz1 pp Cap1
+Bzz1 pp Ape2
+Bzz1 pp Zrt3
+Bzz1 pp Ykl177w
+Bzz1 pp Ykr032w
+Bzz1 pp Yll054c
+Bzz1 pp Sen2
+Bzz1 pp Ylr112w
+Bzz1 pp Tis11
+Bzz1 pp Imh1
+Bzz1 pp Pau4
+Bzz1 pp Erg6
+Bzz1 pp Pre8
+Bzz1 pp Gtr1
+Bzz1 pp Yml131w
+Bzz1 pp Ynl092w
+Bzz1 pp Erg24
+Bzz1 pp Aut1
+Bzz1 pp Arc35
+Bzz1 pp Yol002c
+Bzz1 pp Tlg2
+Bzz1 pp Yol082w
+Bzz1 pp Yor059c
+Bzz1 pp Yor175c
+Bzz1 pp Rpb8
+Bzz1 pp Plp2
+Bzz1 pp Sur1
+Bzz1 pp Car1
+Bzz1 pp Nip29
+Bzz1 pp Rrd2
+Bzz1 pp Nip100
+Bzz1 pp Ypr094w
+Yhr115c pp Ybr042c
+Tom71 pp Tfc7
+Yhr122w pp Uga4
+Ept1 pp Chs2
+Ept1 pp Yel017w
+Ept1 pp Gtt1
+Fur1 pp Ydl100c
+Fur1 pp Urk1
+Arp1 pp Jnm1
+Yhr130c pp Mrp7
+Ecm14 pp Mid1
+Yck1 pp Akr1
+Aro9 pp Yim1
+Chs7 pp Pgm1
+Rpc10 pp Yil025c
+Yhr145c pp Spo1
+Mrpl6 pp Yer066w
+Imp3 pp Glo3
+Yhr151c pp Ynl193w
+Yhr156c pp Met3
+Sol3 pp Ydr287w
+Cdc23 pp Ybr270c
+Cdc23 pp Ada2
+Cdc23 pp Leu3
+Cdc23 pp Nip29
+Yhr168w pp Yer147c
+Dbp8 pp Ykl075c
+Apg7 pp Apg12
+Apg7 pp Aut1
+Eno2 pp Yil091c
+Eno2 pp Ypr053c
+Stb5 pp Ycl038c
+Stb5 pp Cdc9
+Stb5 pp Ydr070c
+Stb5 pp Yhr121w
+Stb5 pp Sui2
+Stb5 pp Fms1
+Stb5 pp Mrpl17
+Stb5 pp Lcb4
+Stb5 pp Mek1
+Stb5 pp Atf1
+Stb5 pp Gpi2
+Oye2 pp Dpb11
+Yhr180w pp Ydl100c
+Ssp1 pp Rpl37a
+Erg9 pp Gtt1
+Erg9 pp Nup53
+Yhr197w pp Apg17
+Yhr198c pp Ykr029c
+Ppx1 pp Tfb4
+Htm1 pp Pep8
+Yhr207c pp Thi21
+Imd2 pp Nup49
+Bet1 pp Ydr100w
+Yil007c pp Ady1
+Yil007c pp Rpt5
+Urm1 pp Sik1
+Snl1 pp Ymr222c
+Yil023c pp Gtt1
+Yil023c pp Ypk2
+Yil023c pp Cpr8
+Yil025c pp Yor352w
+Irr1 pp Ymr313c
+Cap2 pp Yal014c
+Cap2 pp Ybr096w
+Cap2 pp Mud1
+Cap2 pp Ump1
+Cap2 pp Ntc20
+Cap2 pp Der1
+Cap2 pp Ypt10
+Cap2 pp Ybr277c
+Cap2 pp Ctp1
+Cap2 pp Ilv6
+Cap2 pp Ycl022c
+Cap2 pp Grx1
+Cap2 pp Ycl056c
+Cap2 pp Cdc36
+Yil039w pp Ydr453c
+Yil040w pp Ssa2
+Pig2 pp Gac1
+Met30 pp Ynl182c
+Dfg10 pp Ybr285w
+Pcl7 pp Whi4
+Pcl7 pp Ylr190w
+Pcl7 pp Fpr4
+Pcl7 pp Ynl218w
+Pcl7 pp Pho85
+Rhr2 pp Ptp2
+Rhr2 pp Ypl201c
+Fyv2 pp Ylr386w
+Snp1 pp Hmt1
+Yil064w pp Yfr003c
+Sec6 pp Ppq1
+Ser33 pp Ser33
+Ser33 pp Ylr053c
+Ser33 pp Erg3
+Yil092w pp Nab2
+Yil092w pp Qns1
+Yil092w pp Cpr8
+Yil092w pp Ynr040w
+Fyv10 pp Alg5
+Fmc1 pp Aos1
+Yil103w pp Dph2
+Yil104c pp Lcb1
+Yil104c pp Ynl124w
+Yil104c pp Ynl326c
+Mob1 pp Ybr255w
+Mob1 pp Yil169c
+Mob1 pp Cbk1
+Yil108w pp Ygr136w
+Yil108w pp Hms1
+Sec24 pp Lst7
+Sec24 pp Sec23
+Cox5b pp Chl4
+Prm5 pp Msn1
+Rho3 pp Yhr087w
+Yil121w pp Ygr145w
+Fkh1 pp Bop3
+Yil132c pp Ylr376c
+Flx1 pp Kre28
+Rrd1 pp Pex15
+Imp2' pp Pat1
+Yil158w pp Mph1
+Suc2 pp Ydl100c
+Yil169c pp Ynr074c
+Ist3 pp Bud13
+Yir016w pp Mob2
+Yir016w pp Cbk1
+Met28 pp Ydr306c
+Met28 pp Apg17
+Met28 pp Pub1
+Sec11 pp Tif3
+Lys1 pp Pex14
+Gtt1 pp Gtt1
+Yir040c pp Gsg1
+Yjl010c pp Ctm1
+Yjl015c pp Idh2
+Yjl018w pp Ybr070c
+Rnr2 pp Alg5
+Snx4 pp Apg17
+Nup192 pp Akl1
+Nup192 pp Hof1
+Nup192 pp Nup53
+Nsp1 pp Apg17
+Rtt101 pp Snz3
+Yjl048c pp She2
+Iks1 pp Nup53
+Iks1 pp Cin5
+Nup82 pp Nsp1
+Nup82 pp Ykl061w
+Nup82 pp Apg17
+Mrpl8 pp Rim4
+Yjl070c pp Ybl100c
+Yjl070c pp Ydr250c
+Yjl070c pp Ydr374c
+Yjl070c pp Rpb7
+Yjl070c pp Tif35
+Yjl070c pp Ydr504c
+Yjl070c pp Yps5
+Arg2 pp She3
+Yjl072c pp Ydr489w
+Yjl075c pp Ydl100c
+Pry3 pp Ape2
+Yjl091c pp Sbh1
+Mrpl49 pp Dph2
+Mrpl49 pp Yol075c
+Yjl097w pp Gtt1
+Chs6 pp Pet100
+Chs6 pp Ylr424w
+Mef2 pp Gat4
+Gzf3 pp Hda1
+Pho86 pp Apg17
+Pho86 pp Nup53
+Lsm1 pp Pat1
+Pbs2 pp Ybr047w
+Yjl131c pp Chs7
+Lcb3 pp Prm8
+Yjl135w pp Ygl057c
+Glg2 pp Gsy2
+Glg2 pp Efr3
+Yak1 pp Yor197w
+Tim17 pp Yjl064w
+Yjl152w pp Plp2
+Ino1 pp Ydl100c
+Hsp150 pp Ybl044w
+Hsp150 pp Ybr064w
+Hsp150 pp Ydl023c
+Tpk1 pp Bcy1
+Kre9 pp Toa1
+Pfd1 pp Yor380w
+Yjl184w pp Git1
+Yjl184w pp Rpt5
+Rps22a pp Ino1
+Rps14b pp Ynl041c
+Yjl199c pp Yjl199c
+Yjl202c pp Erg25
+Nuc1 pp Ykl222c
+Opt1 pp Yfr017c
+Yjl218w pp Ydr132c
+Yjl218w pp Yjl218w
+Sag1 pp Sqt1
+Hys2 pp Pol32
+Yjr008w pp Arp1
+Met3 pp Met3
+Yjr011c pp Ynr069c
+Yjr011c pp Std1
+Yjr015w pp Ydr179c
+Rec107 pp Srp1
+Lsm8 pp Pat1
+Bna1 pp Yml108w
+Yjr030c pp Ygl042c
+Yjr030c pp Cis3
+Gea1 pp Rsc8
+Yjr037w pp Ydl246c
+Isy1 pp Syf1
+Isy1 pp Ylr297w
+Hit1 pp Btt1
+Hit1 pp Rsa1
+Yjr056c pp Yjr056c
+Aps2 pp Ymr119w
+Rpa12 pp Yal045c
+Rpa12 pp Yar047c
+Rpa12 pp Sec17
+Rpa12 pp Ybr099c
+Rpa12 pp Ybr116c
+Rpa12 pp Mba1
+Rpa12 pp Ybr187w
+Rpa12 pp Ybr219c
+Rpa12 pp Ybr220c
+Rpa12 pp Ybr228w
+Rpa12 pp Ydl129w
+Rpa12 pp Pet100
+Rpa12 pp Rpa14
+Rpa12 pp Sdh4
+Rpa12 pp Ydr196c
+Yae1 pp Ydr492w
+Yae1 pp Rpl31b
+Ham1 pp Nup42
+Cdc11 pp Spr28
+Yjr080c pp Ssa2
+Yjr082c pp Cbp6
+Yjr082c pp Msh5
+Yjr082c pp Ydr066c
+Yjr082c pp Gat1
+Yjr082c pp Yjr001w
+Yjr082c pp Ylr217w
+Yjr082c pp Hrb1
+Yjr082c pp Ynl051w
+Yjr082c pp Ynl094w
+Yjr082c pp Cpr8
+Yjr082c pp Yol129w
+Yjr082c pp Ypr096c
+Yjr082c pp Vps4
+Yjr083c pp Nip7
+Ste18 pp Yar061w
+Ste18 pp Ygr115c
+Ste18 pp Ste4
+Grr1 pp Ybr284w
+Grr1 pp Hof1
+Grr1 pp Ypr158wb
+Jsn1 pp Cys3
+Jsn1 pp Mtw1
+Jsn1 pp Yal066w
+Jsn1 pp Erp1
+Jsn1 pp Sen34
+Jsn1 pp Yar030c
+Jsn1 pp Prm9
+Jsn1 pp Ybl049w
+Jsn1 pp Ybl053w
+Jsn1 pp Ybl059w
+Jsn1 pp Ybl089w
+Jsn1 pp Ybl094c
+Jsn1 pp Ybr014c
+Jsn1 pp Yro2
+Jsn1 pp Nrg2
+Jsn1 pp Tip1
+Jsn1 pp Ybr074w
+Jsn1 pp Ecm8
+Jsn1 pp Mrpl36
+Jsn1 pp Spp381
+Jsn1 pp Cns1
+Jsn1 pp Ybr161w
+Jsn1 pp Ybr174c
+Jsn1 pp Ybr184w
+Jsn1 pp Aor1
+Jsn1 pp Ybr271w
+Jsn1 pp Dpb3
+Jsn1 pp Ybr293w
+Jsn1 pp Ycl005w
+Jsn1 pp Bud3
+Jsn1 pp Ycl045c
+Jsn1 pp Apa1
+Jsn1 pp Ycl063w
+Jsn1 pp Hmlalpha1
+Jsn1 pp Ycr041w
+Jsn1 pp Yil071c
+Jsn1 pp Ycr087ca
+Jsn1 pp Cdc50
+Jsn1 pp Hex3
+Jsn1 pp Ydl046w
+Jsn1 pp Slc1
+Jsn1 pp Rpl31a
+Jsn1 pp Hnt1
+Jsn1 pp Rpn5
+Jsn1 pp Nhp2
+Jsn1 pp Ptp1
+Jsn1 pp Maf1
+Jsn1 pp Ydr008c
+Jsn1 pp Ydr010c
+Jsn1 pp Ydr031w
+Jsn1 pp YDR134C
+Jsn1 pp Ydr152w
+Jsn1 pp Rpa14
+Jsn1 pp Taf25
+Jsn1 pp Rsm24
+Jsn1 pp Ydr193w
+Jsn1 pp Ydr203w
+Jsn1 pp Adk1
+Jsn1 pp Msw1
+Jsn1 pp Ydr269c
+Jsn1 pp Ydr271c
+Jsn1 pp Pib1
+Jsn1 pp Bcp1
+Jsn1 pp Sac7
+Jsn1 pp Ydr438w
+Jsn1 pp Lrs4
+Jsn1 pp Ydr474c
+Jsn1 pp Ydr482c
+Jsn1 pp Rpl37b
+Jsn1 pp Smt3
+Jsn1 pp Ydr516c
+Jsn1 pp Ydr526c
+Jsn1 pp Ydr527w
+Jsn1 pp Ydr533c
+Jsn1 pp Yel008w
+Jsn1 pp Vac8
+Jsn1 pp Yel068c
+Jsn1 pp Yel070w
+Jsn1 pp Yel075c
+Jsn1 pp Sbh2
+Jsn1 pp Smb1
+Jsn1 pp Kre30
+Jsn1 pp Pet117
+Jsn1 pp Tho1
+Jsn1 pp Boi2
+Jsn1 pp Rsp5
+Jsn1 pp Pda1
+Jsn1 pp Yfl047w
+Jsn1 pp Cdc14
+Jsn1 pp Cdc26
+Jsn1 pp Ygl046w
+Jsn1 pp Ygl069c
+Jsn1 pp Gup1
+Jsn1 pp Abc1
+Jsn1 pp Rpl1b
+Jsn1 pp Ygl157w
+Jsn1 pp Rok1
+Jsn1 pp Ygl198w
+Jsn1 pp Ygl204c
+Jsn1 pp Ygl217c
+Jsn1 pp Edc1
+Jsn1 pp Gog5
+Jsn1 pp Sap4
+Jsn1 pp Ygr018c
+Jsn1 pp Ygr042w
+Jsn1 pp Scm4
+Jsn1 pp Ygr064w
+Jsn1 pp Tom20
+Jsn1 pp Thi4
+Jsn1 pp Kre11
+Jsn1 pp Yip1
+Jsn1 pp Ygr182c
+Jsn1 pp Hgh1
+Jsn1 pp Yap1802
+Jsn1 pp Ygr262c
+Jsn1 pp Ygr263c
+Jsn1 pp Ygr269w
+Jsn1 pp Ygr294w
+Jsn1 pp Yhl026c
+Jsn1 pp Rpl8a
+Jsn1 pp Yhr003c
+Jsn1 pp Ppa1
+Jsn1 pp Yhr049w
+Jsn1 pp Vma22
+Jsn1 pp Sae3
+Jsn1 pp Arp1
+Jsn1 pp Yhr130c
+Jsn1 pp Yhr156c
+Jsn1 pp Spc97
+Jsn1 pp Egd2
+Jsn1 pp Flo5
+Jsn1 pp Yil060w
+Jsn1 pp Yrb2
+Jsn1 pp Sec28
+Jsn1 pp Yil096c
+Jsn1 pp Yil137c
+Jsn1 pp Yil174w
+Jsn1 pp Yir003w
+Jsn1 pp Yir025w
+Jsn1 pp Kar2
+Jsn1 pp Rtt101
+Jsn1 pp Ime2
+Jsn1 pp Yjl107c
+Jsn1 pp Gzf3
+Jsn1 pp Rpb4
+Jsn1 pp Yjl192c
+Jsn1 pp Yjl199c
+Jsn1 pp Spc1
+Jsn1 pp Yjr038c
+Jsn1 pp Isy1
+Jsn1 pp Aps2
+Jsn1 pp Yjr087w
+Jsn1 pp Yjr119c
+Jsn1 pp Rps5
+Jsn1 pp Xpt1
+Jsn1 pp Ykl002w
+Jsn1 pp Ykl076c
+Jsn1 pp Ykl111c
+Jsn1 pp Rad27
+Jsn1 pp Sba1
+Jsn1 pp Mrpl31
+Jsn1 pp Rpc25
+Jsn1 pp Ykl146w
+Jsn1 pp Ykl160w
+Jsn1 pp Ykl224c
+Jsn1 pp Ykr040c
+Jsn1 pp Ykr087c
+Jsn1 pp Ykr105c
+Jsn1 pp Cox17
+Jsn1 pp Yll030c
+Jsn1 pp Apg10
+Jsn1 pp Gin11
+Jsn1 pp Ylr009w
+Jsn1 pp Mlh2
+Jsn1 pp Ylr037c
+Jsn1 pp Ylr051c
+Jsn1 pp Rex2
+Jsn1 pp Spc3
+Jsn1 pp Fyv7
+Jsn1 pp Sul2
+Jsn1 pp Ylr104w
+Jsn1 pp Ylr118c
+Jsn1 pp Acs2
+Jsn1 pp Ylr156w
+Jsn1 pp Dph5
+Jsn1 pp Pex13
+Jsn1 pp Ylr205c
+Jsn1 pp Ylr230w
+Jsn1 pp Ylr236c
+Jsn1 pp Rck2
+Jsn1 pp Ylr269c
+Jsn1 pp Ylr283w
+Jsn1 pp Sec72
+Jsn1 pp Gsp1
+Jsn1 pp Ylr322w
+Jsn1 pp Ylr324w
+Jsn1 pp Rps25b
+Jsn1 pp Arc18
+Jsn1 pp Ylr379w
+Jsn1 pp Ylr386w
+Jsn1 pp Afg2
+Jsn1 pp Ylr413w
+Jsn1 pp Ura4
+Jsn1 pp Yml013w
+Jsn1 pp Taf40
+Jsn1 pp Yml018c
+Jsn1 pp Yml041c
+Jsn1 pp Cat2
+Jsn1 pp Pho84
+Jsn1 pp Erg13
+Jsn1 pp Erb1
+Jsn1 pp Far3
+Jsn1 pp Ymr067c
+Jsn1 pp Ypk2
+Jsn1 pp Ymr160w
+Jsn1 pp Ymr187c
+Jsn1 pp Vti1
+Jsn1 pp Cln1
+Jsn1 pp Erg2
+Jsn1 pp Ymr253c
+Jsn1 pp Ymr263w
+Jsn1 pp Ymr278w
+Jsn1 pp Msu1
+Jsn1 pp Ymr293c
+Jsn1 pp Ynl008c
+Jsn1 pp Ynl024c
+Jsn1 pp Siw14
+Jsn1 pp Ynl092w
+Jsn1 pp Ynl105w
+Jsn1 pp Ynl109w
+Jsn1 pp Ynl144c
+Jsn1 pp Ynl146w
+Jsn1 pp Ynl171c
+Jsn1 pp Ynl176c
+Jsn1 pp Pex17
+Jsn1 pp Ynl215w
+Jsn1 pp Ela1
+Jsn1 pp Zwf1
+Jsn1 pp Ynl266w
+Jsn1 pp Ynl285w
+Jsn1 pp Rsm19
+Jsn1 pp Ynr048w
+Jsn1 pp Ynr071c
+Jsn1 pp Thp1
+Jsn1 pp Yol101c
+Jsn1 pp Ctr9
+Jsn1 pp Slg1
+Jsn1 pp Rts1
+Jsn1 pp Dhs1
+Jsn1 pp Yor097c
+Jsn1 pp Yor114w
+Jsn1 pp Rpo31
+Jsn1 pp Pfy1
+Jsn1 pp Rps28a
+Jsn1 pp Yor189w
+Jsn1 pp Yor197w
+Jsn1 pp Npt1
+Jsn1 pp Rbl2
+Jsn1 pp Cpa1
+Jsn1 pp Yor314w
+Jsn1 pp Faa1
+Jsn1 pp Yor379c
+Jsn1 pp Ypl004c
+Jsn1 pp Svl3
+Jsn1 pp Ypl052w
+Jsn1 pp Ypl088w
+Jsn1 pp Ssu1
+Jsn1 pp Mkk2
+Jsn1 pp Ypl158c
+Jsn1 pp Ypl159c
+Jsn1 pp Pcl8
+Jsn1 pp Mdl2
+Jsn1 pp Atp15
+Jsn1 pp Ypr003c
+Jsn1 pp Msf1
+Jsn1 pp Ypr050c
+Jsn1 pp Ypr096c
+Jsn1 pp Ypr114w
+Jsn1 pp Clb5
+Jsn1 pp Ypr126c
+Jsn1 pp Ypr130c
+Jsn1 pp Ypr148c
+Jsn1 pp Prp4
+Jsn1 pp Mlc2
+Yuh1 pp Prs1
+Yuh1 pp Std1
+Vps25 pp Vps36
+Vps25 pp Snf8
+Ura8 pp Ydr133c
+Ura8 pp Ura8
+Rsm7 pp Rpa12
+Atp2 pp Ybr271w
+Ent3 pp Yor111w
+Str2 pp Yel059w
+Mcm22 pp Mcm16
+Ykl002w pp Mrs5
+Ykl002w pp Pho88
+Ykl002w pp Ybr197c
+Ykl002w pp Ame1
+Ykl002w pp Ybr242w
+Ykl002w pp Ybr262c
+Ykl002w pp Ycl049c
+Ykl002w pp Pcl2
+Ykl002w pp Ydl162c
+Ykl002w pp Cdc36
+Ykl002w pp Dad1
+Ykl002w pp Ydr063w
+Ykl002w pp Ydr290w
+Ykl002w pp Ade8
+Ykl002w pp Pau2
+Ykl002w pp Yel057c
+Ykl002w pp Yel068c
+Ykl002w pp Yel074w
+Ykl002w pp Tir1
+Ykl002w pp Ypt31
+Ykl002w pp Hvg1
+Ykl002w pp Bud18
+Ykl002w pp Yer079w
+Ykl002w pp Yer084w
+Ykl002w pp Yer092w
+Ykl002w pp Rtt105
+Ykl002w pp Yer121w
+Ykl002w pp Adk2
+Ykl002w pp Mob2
+Ykl002w pp Ygl258w
+Ykl002w pp Yps5
+Ykl002w pp Vma7
+Ykl002w pp Ygr035c
+Ykl002w pp Ylr108c
+Ykl002w pp Apg17
+Ykl002w pp Std1
+Ykl002w pp Yor284w
+Cap1 pp Yil086c
+Lac1 pp Ymr298w
+Ufd4 pp Kgd2
+Cce1 pp Axl1
+Prp40 pp Ada2
+Arc19 pp Arc15
+Ykl023w pp Ycl010c
+Ykl023w pp Cup1-1
+Ykl023w pp Cyp2
+Ykl023w pp Med6
+Ugp1 pp Ugp1
+Ykl036c pp Ypk1
+Ykl036c pp Ykl160w
+Phd1 pp Smt3
+Ykl050c pp Apg17
+Ykl056c pp Tho1
+Nup120 pp Ilv1
+Nup120 pp Nup145
+Nup120 pp Ygr161cc
+Nup120 pp Mga1
+Nup120 pp Urk1
+Nup120 pp Yor142wa
+Ykl063c pp Yel017w
+Ynk1 pp Ynk1
+Smy1 pp Cos8
+Ykl098w pp Ygl245w
+Lap4 pp Lap4
+Lap4 pp Yol082w
+Srp21 pp Srp14
+She2 pp Cdc24
+She2 pp Ybr027c
+She2 pp Sse2
+She2 pp Ycl033c
+She2 pp Ycr087w
+She2 pp Hmo1
+She2 pp Ygr066c
+She2 pp She2
+She2 pp Ykr022c
+She2 pp Ylr037c
+She2 pp Ufo1
+She2 pp Ura5
+She2 pp Yol073c
+Dbr1 pp Upf3
+Ape2 pp Nut2
+Tpk3 pp Bcy1
+Ykl174c pp Yar033w
+Ykl177w pp Ser2
+Prs1 pp Prs3
+Ykl183w pp Smd1
+Mtr2 pp Ypl138c
+Acp1 pp Ydl239c
+Acp1 pp Ydr084c
+Mst1 pp Kre28
+Uba1 pp Rhk1
+Mrpl13 pp Yhl045w
+Ykr007w pp Gtr2
+Ykr007w pp Gtr1
+Tof2 pp Ycr086w
+Ypt52 pp Sec1
+Irs4 pp Yhr212c
+Ykr020w pp Yng2
+Ykr022c pp Ybl010c
+Ykr022c pp Ylr424w
+Gcn3 pp Yjl215c
+Gcn3 pp Tes1
+Gcn3 pp Cce1
+Gcn3 pp Gcn3
+Gcn3 pp Gal2
+Gcn3 pp Mac1
+Gcn3 pp Std1
+Gcn3 pp Ade2
+Gcn3 pp Spr1
+Sap190 pp Gts1
+Sap190 pp Ypr040w
+Dal80 pp Ydr520c
+Dal80 pp Sap1
+Dal80 pp Vma22
+Dal80 pp Ylr376c
+Dal80 pp Hda1
+Ykr035c pp Yhl044w
+Spc34 pp Dad1
+Spc34 pp Apg17
+Ykr043c pp Ybr238c
+Ykr044w pp Yhr159w
+Rho4 pp Rdi1
+Ykr065c pp Ylr036c
+Bet3 pp Trs31
+Met1 pp Pre6
+Nup133 pp Nup84
+Ykr083c pp Ybr137w
+Ykr083c pp Trr1
+Ykr083c pp Ask1
+Ykr083c pp Apg17
+Srl3 pp Stb1
+Srp40 pp Ycr087ca
+Srp40 pp Hmo1
+Srp40 pp Ygr280c
+Srp40 pp Ykl023w
+Srp40 pp Yor060c
+Bas1 pp Shm2
+Ykr100c pp Ydl100c
+Hsp104 pp Ygr205w
+Apg10 pp Apg12
+Rnp1 pp Ydr455c
+Yll047w pp Ymr069w
+Yll049w pp Apg17
+Yll049w pp Jnm1
+Yll049w pp Ynr069c
+Ylr002c pp Ygr079w
+Ylr012c pp Kkq8
+Ppr1 pp Iml2
+Ppr1 pp Apl1
+Ppr1 pp Yjr119c
+Ppr1 pp Stb6
+Ppr1 pp Ppr1
+Ppr1 pp Cat2
+Bre2 pp Ydr469w
+Snf7 pp Snf7
+Sed5 pp Sly1
+Sed5 pp Gtt1
+Ylr030w pp Tcp1
+Ylr030w pp Ykl224c
+Ylr030w pp Ynl326c
+Ylr031w pp Apg12
+Ylr042c pp Ylr434c
+Stu2 pp Bik1
+Ylr049c pp Acs1
+Ylr051c pp Srn2
+Ylr052w pp Ame1
+Ylr052w pp Pgs1
+Ylr052w pp Nhp10
+Ylr052w pp Yer092w
+Ylr052w pp Ygl220w
+Ylr052w pp Ylr424w
+Erg3 pp Fur1
+Ylr063w pp Pex19
+Ylr063w pp Ygr126w
+Ylr065c pp Apg9
+Ylr065c pp Prm8
+Fyv7 pp Gat1
+Ylr070c pp Ylr070c
+Bos1 pp Rpl9a
+Bos1 pp Bfa1
+Bos1 pp Spc2
+Srl2 pp Srl2
+Srl2 pp Rna14
+Emp70 pp Ydr383c
+Gaa1 pp Pho12
+Gaa1 pp Gtt1
+Cdc45 pp Dot6
+Sen2 pp Bio3
+Ylr108c pp Ylr108c
+Ylr108c pp Apg17
+Efr4 pp Rho3
+Msl5 pp Ybr012wb
+Msl5 pp Swm1
+Msl5 pp Yor142wa
+Msl5 pp Ypl105c
+Msl5 pp Ypl257wa
+Ylr124w pp Yml041c
+Ylr125w pp Ydl110c
+Ylr125w pp Cdc36
+Ylr125w pp Ylr008c
+Ylr125w pp Ymr030w
+Cki1 pp Alk1
+Pdc5 pp Ylr261c
+Pdc5 pp Yor390w
+Ylr140w pp Rps8a
+Ylr143w pp Yml023c
+Ylr145w pp Yhr214w
+Spe4 pp Adh4
+Smd3 pp Ura8
+Smd3 pp Hxt17
+Smd3 pp Ypr014c
+Pcd1 pp Uba3
+Asp3-1 pp Tom7
+Ylr157ca pp Ybr012wb
+Asp3-1 pp Yer175c
+Ylr159w pp Yor342c
+Ylr159w pp Ypl280w
+Ylr161w pp Cpr8
+Sec10 pp Sec15
+Sec10 pp Ymr002w
+Sec10 pp Sec8
+Aps1 pp Apl4
+Dph5 pp Sme1
+Ylr173w pp Ydr455c
+Cbf5 pp Ynl124w
+Ylr177w pp Frm2
+Ylr177w pp Tpk2
+Ylr181c pp Dpb3
+Tos4 pp Ylr037c
+Ylr190w pp Tif35
+Pex13 pp Ylr049c
+Ylr193c pp Yjl094c
+Pwp1 pp Esbp6
+Sik1 pp Cpa1
+Ylr198c pp Yjl199c
+Ylr198c pp Sec62
+Ylr199c pp Ymr263w
+Yke2 pp Fyv8
+Ylr202c pp Yir010w
+Mss51 pp Vtc3
+Sec13 pp Ycr099c
+Sec13 pp Ydl166c
+Sec13 pp Sec31
+Sec13 pp Nup145
+Ylr218c pp Pdb1
+Ylr221c pp Ypr115w
+Ylr222c pp Lap3
+Ylr222c pp Coq2
+Ifh1 pp Srl1
+Ylr224w pp Sgt1
+Bur2 pp Cis3
+Ylr227c pp Yml133c
+Ylr227c pp Vps21
+Ylr235c pp Yfr055w
+Ylr236c pp Car2
+Thi7 pp Dos2
+Ylr239c pp Ypl073c
+Ylr241w pp Yhr034c
+Ylr241w pp Ykr065c
+Cdd1 pp Cdd1
+Erf2 pp Yjr146w
+Ylr253w pp Ycp4
+Ylr255c pp Tsc10
+Ylr257w pp Tfc4
+Ylr257w pp Ylr054c
+Gsy2 pp Gsy2
+Red1 pp Smt3
+Red1 pp Ylr064w
+Nej1 pp Ycr087ca
+Nej1 pp Eno2
+Nej1 pp Yip3
+Bop2 pp Gdh3
+Bop2 pp Phm6
+Sec22 pp Rad57
+Ylr270w pp Gal2
+Smd2 pp Smx3
+Dbp9 pp Ybr269c
+Ysh1 pp Ydl062w
+Ysh1 pp Rpc11
+Ysh1 pp Ylr437c
+Eci1 pp Pex14
+Ylr285w pp Ykl056c
+Ylr285w pp Cyt2
+Ylr285w pp Ylr053c
+Ylr287c pp Rpp1b
+Ylr287c pp Rpp0
+Mec3 pp Mrs5
+Mec3 pp Ybr124w
+Mec3 pp Opy1
+Mec3 pp Ybr197c
+Mec3 pp Der1
+Mec3 pp Ilv6
+Mec3 pp Hmlalpha1
+Mec3 pp Hmlalpha2
+Mec3 pp Ycr007c
+Mec3 pp Ycr016w
+Mec3 pp Cis1
+Mec3 pp Ygl168w
+Mec3 pp Rps26a
+Mec3 pp Rpl11b
+Mec3 pp Mtr3
+Mec3 pp Ctr2
+Mec3 pp Yhr180w
+Mec3 pp Urm1
+Mec3 pp Dot5
+Mec3 pp Msl1
+Mec3 pp Yhc3
+Mec3 pp Yjl199c
+Mec3 pp Pex2
+Mec3 pp Bna1
+Mec3 pp Cyc1
+Mec3 pp Rpa12
+Mec3 pp Mir1
+Mec3 pp Yjr083c
+Mec3 pp Nnf1
+Mec3 pp Yjr146w
+Mec3 pp Yjr157w
+Mec3 pp Met14
+Mec3 pp Ura6
+Mec3 pp Ykl044w
+Mec3 pp Ask1
+Mec3 pp Toa2
+Mec3 pp Ykl107w
+Mec3 pp Srp102
+Mec3 pp Pir3
+Mec3 pp Ykl183w
+Mec3 pp Mrs4
+Mec3 pp Srl3
+Mec3 pp Yll023c
+Mec3 pp Ylr003c
+Mec3 pp Ylr009w
+Mec3 pp Ylr011w
+Mec3 pp Ylr021w
+Mec3 pp Ylr050c
+Mec3 pp Ylr051c
+Mec3 pp Ylr104w
+Mec3 pp Srn2
+Mec3 pp Ylr124w
+Mec3 pp Ylr125w
+Mec3 pp Stm1
+Mec3 pp Yke2
+Mec3 pp Ylr202c
+Mec3 pp Ylr239c
+Mec3 pp Ylr252w
+Mec3 pp Ylr254c
+Mec3 pp Ylr290c
+Mec3 pp Apg16
+Mec3 pp Ymr295c
+Mec3 pp Ynl013c
+Mec3 pp Ynl110c
+Mec3 pp Tom22
+Mec3 pp Ynl158w
+Mec3 pp Ynl190w
+Mec3 pp Rpl18b
+Mec3 pp Htz1
+Mec3 pp Yol046c
+Mec3 pp Yol093w
+Mec3 pp Yol131w
+Mec3 pp Cdc33
+Mec3 pp Yor087w
+Mec3 pp Yor104w
+Gcd7 pp Ecm31
+Gcd7 pp Ycr076c
+Gcd7 pp Ycr086w
+Gcd7 pp Syf1
+Gcd7 pp Ydr444w
+Gcd7 pp Ada2
+Gcd7 pp Sac2
+Gcd7 pp Yfr008w
+Gcd7 pp Gts1
+Gcd7 pp Ygr024c
+Gcd7 pp Gcd2
+Gcd7 pp Yhl018w
+Gcd7 pp Yjl199c
+Gcd7 pp Gcn3
+Gcd7 pp Cdd1
+Gcd7 pp Ylr386w
+Gcd7 pp Apg17
+Gcd7 pp Far3
+Gcd7 pp Yor284w
+Gcd7 pp Yor380w
+Gcd7 pp Ypl070w
+Gcd7 pp Nip29
+Ylr294c pp Spr1
+Atp14 pp Yat1
+Atp14 pp Med8
+Atp14 pp Fad1
+Atp14 pp Rpp1a
+Atp14 pp Ydl118w
+Atp14 pp Ydl148c
+Atp14 pp Ydl172c
+Atp14 pp Ydl233w
+Atp14 pp Trp1
+Atp14 pp Ydr319c
+Atp14 pp Lsm6
+Atp14 pp Ydr445c
+Atp14 pp Ydr455c
+Atp14 pp Smt3
+Atp14 pp Apa2
+Atp14 pp Yer116c
+Atp14 pp Sec34
+Atp14 pp Sno3
+Atp14 pp Yfr017c
+Atp14 pp Yfr043c
+Atp14 pp Ygl010w
+Atp14 pp Ygl047w
+Atp14 pp Rpt6
+Atp14 pp Ygl226w
+Atp14 pp Ygl250w
+Atp14 pp Sec9
+Atp14 pp Ygr035c
+Atp14 pp Ygr081c
+Atp14 pp Ygr122w
+Atp14 pp Rpl24b
+Atp14 pp Tos10
+Atp14 pp Pbp1
+Atp14 pp Hgh1
+Atp14 pp Zuo1
+Atp14 pp Hsn1
+Atp14 pp Fur1
+Atp14 pp Yhr138c
+Atp14 pp Yhr140w
+Atp14 pp Egd2
+Atp14 pp Yhr212c
+Atp14 pp Bet1
+Atp14 pp Yil005w
+Atp14 pp His6
+Atp14 pp Yil032c
+Atp14 pp Pcl7
+Atp14 pp Mmd1
+Atp14 pp Rhr2
+Atp14 pp Yil059c
+Atp14 pp Sec28
+Atp14 pp Yil110w
+Atp14 pp Cox5b
+Atp14 pp Prm5
+Atp14 pp Ayr1
+Atp14 pp Ssl2
+Atp14 pp Yil157c
+Atp14 pp Yir036c
+Atp14 pp Yir040c
+Atp14 pp Pre3
+Atp14 pp Gyp6
+Atp14 pp Yjl058c
+Atp14 pp Yjl067w
+Atp14 pp Pry3
+Atp14 pp Yjl100w
+Atp14 pp Rpb4
+Atp14 pp Qcr8
+Atp14 pp Atp12
+Atp14 pp Yjl225c
+Atp14 pp Tdh2
+Atp14 pp Yjr037w
+Atp14 pp Yjr083c
+Atp14 pp Yjr100c
+Atp14 pp Vps25
+Atp14 pp Yjr120w
+Atp14 pp Xpt1
+Atp14 pp Yjr141w
+Atp14 pp Yjr154w
+Atp14 pp Ykl002w
+Atp14 pp Fba1
+Atp14 pp Vma5
+Atp14 pp Ykl088w
+Atp14 pp Lap4
+Atp14 pp Pgm1
+Atp14 pp Ltv1
+Atp14 pp Emp70
+Atp14 pp Gis3
+Atp14 pp Rrn5
+Atp14 pp Asp3-1
+Atp14 pp Msf1'
+Atp14 pp Cdc123
+Atp14 pp Ylr455w
+Atp14 pp Ylr460c
+Atp14 pp Yap1
+Atp14 pp Src1
+Atp14 pp Sml1
+Atp14 pp Yml079w
+Atp14 pp Gtr1
+Atp14 pp Ymr003w
+Atp14 pp Sub1
+Atp14 pp Ymr090w
+Atp14 pp Cin4
+Atp14 pp Ymr141c
+Atp14 pp Ymr144w
+Atp14 pp Yim1
+Atp14 pp Nup53
+Atp14 pp Mmt1
+Atp14 pp Ymr181c
+Atp14 pp Dfg5
+Atp14 pp Idp3
+Atp14 pp Sun4
+Atp14 pp Ynl194c
+Atp14 pp Ynl205c
+Atp14 pp Yif1
+Atp14 pp Ynl324w
+Atp14 pp Mdj2
+Atp14 pp Yol008w
+Atp14 pp Yol050c
+Atp14 pp Yor145c
+Atp14 pp Ser1
+Atp14 pp Yor324c
+Atp14 pp Nip29
+Atp14 pp Ypr118w
+Atp14 pp Tif3
+Atp14 pp Smx3
+Ylr297w pp Ypr156c
+Ecm38 pp Yol137w
+Ylr301w pp Ado1
+Aco1 pp Chs1
+Ubc12 pp Rub1
+Cda2 pp Gup1
+Bud6 pp Ygl015c
+Ylr322w pp Ybl086c
+Ylr324w pp Ylr324w
+Rpl38 pp Ktr7
+Rpl38 pp Snc2
+Ylr328w pp Ylr328w
+Ylr328w pp Mid2
+Rec102 pp Apm1
+Kre21 pp Prp45
+Kre21 pp Sft2
+Ylr339c pp Bud23
+Ylr339c pp Yfl043c
+Ylr339c pp Yfl044c
+Ylr339c pp Pau4
+Rpp0 pp Rpp1a
+Rpp0 pp Rpp1b
+Rpp0 pp Rpp2b
+Ylr343w pp Sec53
+Ylr345w pp Ykl174c
+Ylr345w pp Sfh1
+Kap95 pp Ecm31
+Kap95 pp Psa1
+Kap95 pp Cta1
+Kap95 pp Asp1
+Kap95 pp Trr1
+Kap95 pp Rpl12b
+Kap95 pp Hpa3
+Kap95 pp Pro3
+Kap95 pp Yfr047c
+Kap95 pp Pnc1
+Kap95 pp Hem2
+Kap95 pp Sae2
+Kap95 pp Thi4
+Kap95 pp Fol2
+Kap95 pp Imd2
+Kap95 pp Bcy1
+Kap95 pp Ynk1
+Kap95 pp Nap1
+Kap95 pp Ylr328w
+Kap95 pp Fbp1
+Kap95 pp Yap1
+Kap95 pp Apg16
+Kap95 pp Yip3
+Kap95 pp Aad14
+Kap95 pp Rib4
+Kap95 pp Car1
+Kap95 pp Nip29
+Dic1 pp Ybl113c
+Nit3 pp Snc2
+Bud8 pp Ybr027c
+Ylr356w pp Yhr085w
+Ylr358c pp Mtf1
+Rom2 pp Ydl203c
+Vid22 pp Brn1
+Vid22 pp Ybr012wb
+Vid22 pp Pch2
+Vid22 pp Ycl063w
+Vid22 pp Pph21
+Vid22 pp Dhh1
+Vid22 pp Mth1
+Vid22 pp Ydr317w
+Vid22 pp Trr1
+Vid22 pp Gnp1
+Vid22 pp Yel006w
+Vid22 pp Tip20
+Vid22 pp Cdc55
+Vid22 pp Cyp2
+Vid22 pp Dfg10
+Vid22 pp Yjl058c
+Vid22 pp Ykl050c
+Vid22 pp Ade16
+Vid22 pp Ylr057w
+Vid22 pp Ymr048w
+Vid22 pp Ymr140w
+Vid22 pp Rim13
+Vid22 pp Coq2
+Vid22 pp Cin5
+Vid22 pp Faa1
+Vid22 pp Rad17
+Vid22 pp Ypl060w
+Vid22 pp Ypl107w
+Vid22 pp Ypl257wa
+Vid22 pp Ccl1
+Vid22 pp Rox1
+Ylr374c pp Ycl065w
+Fbp1 pp Fbp1
+Ylr381w pp Yat1
+Iki3 pp Mfa1
+Ylr385c pp Ylr424w
+Ylr386w pp Ylr386w
+Rps29a pp Ykr016w
+Ssr1 pp Apg5
+Ylr392c pp Bbp1
+Atp10 pp Ymr279c
+Ylr407w pp Ygl235w
+Ylr409c pp Yjl069c
+Ylr414c pp Yor013w
+Ylr416c pp Ctf4
+Rpn13 pp Rpn2
+Apg17 pp Ycr082w
+Apg17 pp Cis1
+Apg17 pp Kgd2
+Apg17 pp Ydr383c
+Apg17 pp Yer092w
+Apg17 pp Sec35
+Apg17 pp Yjr024c
+Apg17 pp Apg17
+Apg17 pp Ymr124w
+Apg17 pp Ynl078w
+Apg17 pp Ynl182c
+Apg17 pp Mge1
+Apg17 pp Nip29
+Apg17 pp Plo1
+Tus1 pp Yor053w
+Ylr427w pp Lys21
+Ylr437c pp Met28
+Ylr446w pp Prp6
+Ylr446w pp Yap6
+Ylr446w pp Mga1
+Ylr446w pp Slt2
+Ylr446w pp Ykr074w
+Ylr446w pp Ylr211c
+Ylr446w pp Cin5
+Ylr446w pp Std1
+Vma6 pp Yat1
+Vma6 pp Ybr028c
+Vma6 pp Tkl2
+Vma6 pp Mrpl36
+Vma6 pp Tyr1
+Vma6 pp Git1
+Vma6 pp Ydl193w
+Vma6 pp Ydl221w
+Vma6 pp Ydl233w
+Vma6 pp Ydl241w
+Vma6 pp Tps2
+Vma6 pp Rrp1
+Vma6 pp Dpb4
+Vma6 pp Yap6
+Vma6 pp Mth1
+Vma6 pp Hnt2
+Vma6 pp Sac2
+Vma6 pp Yer064c
+Vma6 pp Tos8
+Vma6 pp Ygr086c
+Vma6 pp Yhr009c
+Vma6 pp Set1
+Vma6 pp Ecm14
+Vma6 pp Yhr177w
+Vma6 pp Ayr1
+Vma6 pp Pan6
+Vma6 pp Yir035c
+Vma6 pp Nup192
+Vma6 pp Yjl058c
+Vma6 pp Trl1
+Vma6 pp Ime2
+Vma6 pp Pfd1
+Vma6 pp Yjl199c
+Vma6 pp Hxt9
+Vma6 pp Hys2
+Vma6 pp Spc1
+Vma6 pp Yjr141w
+Vma6 pp Sor1
+Vma6 pp Pan3
+Vma6 pp Mae1
+Vma6 pp Aat1
+Vma6 pp Rad27
+Vma6 pp Pir1
+Vma6 pp Ykr005c
+Vma6 pp Ykr100c
+Vma6 pp Yll033w
+Vma6 pp Ylr011w
+Vma6 pp Snf7
+Vma6 pp Pdc5
+Vma6 pp Mss51
+Vma6 pp Cdc123
+Vma6 pp Pig1
+Vma6 pp Ylr352w
+Vma6 pp Ylr426w
+Vma6 pp Ylr465c
+Vma6 pp Apt1
+Vma6 pp Yml041c
+Vma6 pp Ymr071c
+Vma6 pp Sas2
+Vma6 pp Rim13
+Vma6 pp Ynl028w
+Vma6 pp Ynl134c
+Vma6 pp Psd1
+Vma6 pp Nop13
+Vma6 pp Ynl182c
+Vma6 pp Slz1
+Vma6 pp Lem3
+Vma6 pp Cit1
+Vma6 pp Plb3
+Vma6 pp Yol036w
+Vma6 pp Cin5
+Vma6 pp Pep12
+Vma6 pp Std1
+Vma6 pp Yor053w
+Vma6 pp Spr1
+Vma6 pp Mkk1
+Vma6 pp Abp140
+Vma6 pp Gcd1
+Vma6 pp Yor315w
+Vma6 pp Vma4
+Vma6 pp Ald4
+Vma6 pp Yor379c
+Vma6 pp Ula1
+Vma6 pp Mnn9
+Vma6 pp Rrd2
+Vma6 pp Icl2
+Vma6 pp Ypr078c
+Rpl6b pp Yhr149c
+Fpr4 pp Pet130
+Rif2 pp Pho11
+Rif2 pp Ybl095w
+Rif2 pp Sft2
+Rif2 pp Rdh54
+Rif2 pp Hpc2
+Rif2 pp Arc40
+Rif2 pp Ycl023c
+Rif2 pp Hsp30
+Rif2 pp Sir2
+Rif2 pp Pcl2
+Rif2 pp Uga4
+Rif2 pp Bmh2
+Rif2 pp Mkc7
+Rif2 pp Ydr203w
+Rif2 pp Msw1
+Rif2 pp Sip1
+Rif2 pp Kre22
+Rif2 pp Ydr489w
+Rif2 pp Cin8
+Rif2 pp Yel076wc
+Rif2 pp Srb4
+Rif2 pp Yfl013c
+Rif2 pp Alr2
+Rif2 pp Ygl005c
+Rif2 pp Ygr073c
+Rif2 pp Mdr1
+Rif2 pp Yhl017w
+Rif2 pp Kel1
+Rif2 pp Erg9
+Rif2 pp Pho12
+Rif2 pp Yil039w
+Rif2 pp Yil174w
+Rif2 pp Pri1
+Rif2 pp Yjl015c
+Rif2 pp Pep8
+Rif2 pp Tif2
+Rif2 pp Swi3
+Rif2 pp Atp2
+Rif2 pp Rad27
+Rif2 pp Cof1
+Rif2 pp Ylr016c
+Rif2 pp Gis3
+Rif2 pp Ylr110c
+Rif2 pp Yps3
+Rif2 pp Ylr251w
+Rif2 pp Ylr301w
+Rif2 pp Ylr315w
+Rif2 pp Ylr426w
+Rif2 pp Cna1
+Rif2 pp Fpr4
+Rif2 pp Yox1
+Rif2 pp Ymd8
+Rif2 pp Far3
+Rif2 pp Ymr147w
+Rif2 pp Ynl013c
+Rif2 pp Rnh35
+Rif2 pp Fyv6
+Rif2 pp Ytp1
+Rif2 pp Ynl260c
+Rif2 pp Ynr009w
+Rif2 pp Ynr013c
+Rif2 pp Lys9
+Rif2 pp Ynr066c
+Rif2 pp Ynr071c
+Rif2 pp Top1
+Rif2 pp Rrp6
+Rif2 pp Slk19
+Rif2 pp Bfr1
+Rif2 pp Yor206w
+Rif2 pp Yor220w
+Rif2 pp Wtm1
+Rif2 pp Yor314w
+Rif2 pp Ypl034w
+Rif2 pp Sur1
+Rif2 pp Ypl098c
+Rif2 pp Pep4
+Rif2 pp Rpc40
+Rif2 pp Ypr144c
+Ylr456w pp Ypr172w
+Nbp1 pp Ydl001w
+Nbp1 pp Gis4
+Cdc91 pp Ssa2
+Cdc91 pp Rpl18b
+Ypt7 pp Ydr003w
+Erg6 pp Ycl023c
+Yml011c pp Ydl214c
+Yml011c pp Ydr314c
+Yml011c pp Yll059c
+Yml011c pp Std1
+Yml011c pp Ade2
+Erv25 pp Ylr124w
+Yml014w pp Akl1
+Yml014w pp Arg81
+Apt1 pp Apt2
+Yml023c pp Yol128c
+Tsa1 pp Ypl208w
+Ndc1 pp Ygr010w
+Ndc1 pp Nup53
+Ndc1 pp Yor284w
+Src1 pp Ydr489w
+Ymd8 pp Ylr054c
+Yml041c pp Apg17
+Cat2 pp Cat2
+Cat2 pp Lys7
+Cat2 pp Ynl046w
+Rrn11 pp Ykl137w
+Gsf2 pp Gtt1
+Yml053c pp Tdh2
+Spc2 pp Apg12
+Spc2 pp Cmk2
+Cmp2 pp Ynl047c
+Ogg1 pp Rcl1
+Mft1 pp Pho23
+Tem1 pp Hsp26
+Tem1 pp Ybr137w
+Tem1 pp Ecm31
+Tem1 pp Ycr076c
+Tem1 pp Ycr087ca
+Tem1 pp Whi4
+Tem1 pp Asp1
+Tem1 pp Yel015w
+Tem1 pp Hpa3
+Tem1 pp Pro3
+Tem1 pp Dmc1
+Tem1 pp Yfl010c
+Tem1 pp Yfl054c
+Tem1 pp Hem2
+Tem1 pp Nif3
+Tem1 pp Ygr058w
+Tem1 pp Thi4
+Tem1 pp Fol2
+Tem1 pp Ygr268c
+Tem1 pp Thr1
+Tem1 pp Yhr111w
+Tem1 pp Yhr112c
+Tem1 pp Yhr113w
+Tem1 pp Ssp1
+Tem1 pp Yjl199c
+Tem1 pp Yjl218w
+Tem1 pp Yjr056c
+Tem1 pp Sor1
+Tem1 pp Ugp1
+Tem1 pp Ynk1
+Tem1 pp Lap4
+Tem1 pp Ypt52
+Tem1 pp Ylr070c
+Tem1 pp Srl2
+Tem1 pp Hcr1
+Tem1 pp Cdd1
+Tem1 pp Sfh1
+Tem1 pp Ylr328w
+Tem1 pp Fbp1
+Tem1 pp Apg17
+Tem1 pp Yip3
+Tem1 pp Aad14
+Tem1 pp Urk1
+Tem1 pp Hsp10
+Tem1 pp Ade2
+Tem1 pp Mge1
+Tem1 pp Yor284w
+Tem1 pp Yor380w
+Tem1 pp Ypl070w
+Tem1 pp Car1
+Tem1 pp Nip29
+Tem1 pp Bbp1
+Tem1 pp Qcr2
+Tem1 pp Hpa2
+Dak1 pp Pnt1
+Hmg1 pp Ynr009w
+Hmg1 pp Yor102w
+Bet5 pp Trs31
+Pre8 pp Ygl149w
+Pre8 pp Cup2
+Pre8 pp Snf6
+Pre8 pp Yil132c
+Pre8 pp Yjl199c
+Pre8 pp Apc9
+Pre8 pp Ylr345w
+Pre8 pp Ylr386w
+Pre8 pp Yol082w
+Pre8 pp Hsp10
+Pre8 pp Bbp1
+Pre8 pp Ypr126c
+Rad10 pp Spt4
+Vps9 pp Ram2
+Taf19 pp Taf25
+Taf19 pp Hmo1
+Taf19 pp Yjl058c
+Taf19 pp Taf40
+Yml101c pp Ydl100c
+Yml101c pp Vps25
+Cac2 pp Ydl099w
+Cac2 pp Rlf2
+Mdm1 pp Ypr099c
+Sec65 pp Ybl032w
+Yml107c pp Ylr435w
+Zds2 pp Cdc55
+Zds2 pp Rpl39
+Ctk3 pp Ctk2
+Van1 pp Rtt102
+Yml119w pp Yll032c
+Gtr1 pp Gtr2
+Gtr1 pp Fbp1
+Yml125c pp Cox12
+Yml125c pp Nup53
+Yml127w pp Rsc8
+Yml127w pp Str3
+Ero1 pp Fal1
+Cdc5 pp Yjl019w
+Ymr003w pp Kar3
+Ymr009w pp Ydr384c
+Ymr010w pp Ydr533c
+Spo20 pp Apg17
+Ymr018w pp Tlg1
+Ymr025w pp Yer137c
+Ymr025w pp Sec35
+Ymr025w pp Apg17
+Hof1 pp Ydr203w
+Hof1 pp Apg17
+Lys7 pp Yer083c
+Ymr041c pp Rpl5
+Arg80 pp Arg81
+Mcm1 pp Srl2
+Nup116 pp Spc72
+Nup116 pp Swh1
+Nup116 pp Yar066w
+Nup116 pp Cor1
+Nup116 pp Rps8a
+Nup116 pp Ybl094c
+Nup116 pp Flr1
+Nup116 pp Ybr027c
+Nup116 pp Vid24
+Nup116 pp She3
+Nup116 pp Ybr137w
+Nup116 pp Ybr144c
+Nup116 pp Adh5
+Nup116 pp Med8
+Nup116 pp Ybr216c
+Nup116 pp Apg12
+Nup116 pp Ybr273c
+Nup116 pp Ybr301w
+Nup116 pp Fus1
+Nup116 pp Ycl039w
+Nup116 pp Sat4
+Nup116 pp Pex19
+Nup116 pp Idp1
+Nup116 pp Rpp1a
+Nup116 pp Ena1
+Nup116 pp Rli1
+Nup116 pp Kgd2
+Nup116 pp Ume6
+Nup116 pp Ydr229w
+Nup116 pp Ydr271c
+Nup116 pp Ydr372c
+Nup116 pp Cad1
+Nup116 pp Rmt2
+Nup116 pp Pkh1
+Nup116 pp Smt3
+Nup116 pp Gle2
+Nup116 pp Yer119c
+Nup116 pp Gdi1
+Nup116 pp Ygl170c
+Nup116 pp Clg1
+Nup116 pp Sap4
+Nup116 pp Mto1
+Nup116 pp Sec9
+Nup116 pp Twf1
+Nup116 pp Ygr139w
+Nup116 pp Ygr151c
+Nup116 pp Pet54
+Nup116 pp Lag1
+Nup116 pp Yap3
+Nup116 pp Ecm34
+Nup116 pp Yhl049c
+Nup116 pp Fil1
+Nup116 pp Gar1
+Nup116 pp Iki1
+Nup116 pp Yhr209w
+Nup116 pp Yil055c
+Nup116 pp Ser33
+Nup116 pp Hyr1
+Nup116 pp Nup82
+Nup116 pp Yjl091c
+Nup116 pp Tes1
+Nup116 pp Utr1
+Nup116 pp Yjr079w
+Nup116 pp Sgm1
+Nup116 pp Yjr136c
+Nup116 pp Yjr141w
+Nup116 pp Ykl061w
+Nup116 pp Nup100
+Nup116 pp Smy1
+Nup116 pp Ykl088w
+Nup116 pp Ltv1
+Nup116 pp Ykl221w
+Nup116 pp Ylr077w
+Nup116 pp Bos1
+Nup116 pp Xdj1
+Nup116 pp Gis3
+Nup116 pp Cbf5
+Nup116 pp Pwp1
+Nup116 pp Ylr294c
+Nup116 pp Ylr312c
+Nup116 pp Bud8
+Nup116 pp Afg2
+Nup116 pp Ylr401c
+Nup116 pp Ylr434c
+Nup116 pp Yap1
+Nup116 pp Pre8
+Nup116 pp Yim1
+Nup116 pp Ymr157c
+Nup116 pp Ymr206w
+Nup116 pp Jnm1
+Nup116 pp Gas1
+Nup116 pp Ynl078w
+Nup116 pp Ynl194c
+Nup116 pp Sps18
+Nup116 pp Tos6
+Nup116 pp Ynl319w
+Nup116 pp Aut1
+Nup116 pp Ynr040w
+Nup116 pp Ynr061c
+Nup116 pp Ynr074c
+Nup116 pp Yol111c
+Nup116 pp Yol146w
+Nup116 pp Dcp1
+Nup116 pp Yol154w
+Nup116 pp Hsp10
+Nup116 pp Yor060c
+Nup116 pp Yor062c
+Nup116 pp Yng1
+Nup116 pp Yor102w
+Nup116 pp Yor104w
+Nup116 pp Yor112w
+Nup116 pp Yor121c
+Nup116 pp Pup1
+Nup116 pp Sas5
+Nup116 pp Yor251c
+Nup116 pp Yor286w
+Nup116 pp Yor289w
+Nup116 pp Yor302w
+Nup116 pp Yor314w
+Nup116 pp Scd5
+Nup116 pp Tye7
+Nup116 pp Pre10
+Nup116 pp Ypl013c
+Nup116 pp Sen54
+Nup116 pp Ypr172w
+Far3 pp Ydl133w
+Stv1 pp Cct2
+Bub2 pp Ddi1
+Aac1 pp Yll013c
+Rim9 pp Pif1
+Ymr068w pp Ygl250w
+Ymr068w pp Apg17
+Ymr068w pp Ynl047c
+Vps20 pp Vps25
+Vps20 pp Vps36
+Vps20 pp Taf40
+Adh3 pp Ylr080w
+Ymr090w pp Mae1
+Ymr093w pp Fir1
+Sno1 pp Snz3
+Sno1 pp Snz1
+Sno1 pp Snz2
+Snz1 pp Snz3
+Snz1 pp Snz2
+Ymr097c pp Pep4
+Srt1 pp Cys3
+Ypk2 pp Yor154w
+Ymr110c pp Ydl204w
+Ymr119w pp Gtt1
+Pkr1 pp Mex67
+Ymr124w pp Ylr031w
+Sto1 pp Cbc2
+Ymr134w pp Cpa1
+Rim11 pp Ime1
+Ymr144w pp Akl1
+Ymr144w pp Ybr239c
+Tif34 pp Tif35
+Tif34 pp Ypl105c
+Swp1 pp Yal064w
+Swp1 pp Yor279c
+Yim2 pp Ydr221w
+Nup53 pp Asm4
+Nup53 pp Sho1
+Nup53 pp Nup145
+Nup53 pp Ygl170c
+Nup53 pp Ylr324w
+Nup53 pp Nup53
+Nup53 pp Yol129w
+Rim13 pp Snf7
+Ymr155w pp Pex19
+Apg16 pp Smt3
+Apg16 pp Yfl040w
+Apg16 pp Yfl068w
+Apg16 pp Ymr048w
+Apg16 pp Apg16
+Apg16 pp Ste4
+Apg16 pp Apg5
+Ymr163c pp Pex19
+Ddr48 pp Ypr096c
+Rgm1 pp Pta1
+Rgm1 pp Yar061w
+Hsc82 pp Bud6
+Ymr187c pp Ylr221c
+Cln1 pp Zpr1
+Cln1 pp Bbp1
+Rot1 pp Yil007c
+Tom40 pp Yhr003c
+Tom40 pp Yjr038c
+Ymr204c pp Yjl185c
+Ymr204c pp Apg17
+Pfk2 pp Pfk1
+Ymr206w pp Mlh2
+Ymr209c pp Ygl204c
+Ymr211w pp Smt3
+Ymr211w pp Pex4
+Cef1 pp Syf1
+Cef1 pp Apg17
+Ymr215w pp Ygl198w
+Ymr226c pp Tfc6
+Pep5 pp Vam6
+Fus2 pp Rvs161
+Fus2 pp Ecm34
+Rna1 pp Yhr156c
+Rna1 pp Yim2
+Taf17 pp Sik1
+Taf17 pp Kri1
+Taf17 pp Std1
+Taf17 pp Ade2
+Cus1 pp Rpt5
+Cus1 pp Leo1
+Rpl20a pp Ylr366w
+Zrc1 pp Rps7b
+Faa4 pp Spl2
+Ymr258c pp Yil019w
+Tif11 pp Ygr156w
+Cue1 pp Scy1
+Dsk2 pp Hch1
+Cat8 pp Std1
+Has1 pp Lap4
+Jnm1 pp Nup49
+Jnm1 pp Ygr294w
+Jnm1 pp Hch1
+Jnm1 pp Nip100
+Jnm1 pp Ypr126c
+Ymr298w pp Cdc24
+Ymr298w pp Lag1
+Ymr298w pp Nup53
+Ymr299c pp Qri5
+Gas1 pp Ape2
+Ymr312w pp Iki1
+Ymr312w pp Ylr327c
+Pre5 pp She2
+Dia1 pp Rsp5
+Ymr325w pp Arr1
+Sis1 pp Yir040c
+Pbi2 pp Yhl002w
+Ynl018c pp Tom20
+Ynl018c pp Yol075c
+Ynl019c pp Ylr001c
+Ark1 pp Yap6
+Ark1 pp Yap1802
+Ynl024c pp Mus81
+Ssn8 pp Ylr261c
+Ssn8 pp Ylr322w
+Ssn8 pp Ylr358c
+Ynl034w pp Rps4a
+Nce103 pp Prs5
+Idh1 pp Yol082w
+Idh1 pp Idh2
+Tfc5 pp Ygl250w
+Ynl041c pp Ydr115w
+Ynl041c pp Ydr229w
+Ynl041c pp Nup49
+Ynl041c pp Ygl223c
+Ynl041c pp Sec35
+Ynl041c pp Tid3
+Ynl041c pp Ylr386w
+Yip3 pp Tlg1
+Yip3 pp Yip3
+Ynl045w pp Ynl028w
+Sfb2 pp Sec23
+Vac7 pp Ybl104c
+Ynl056w pp Siw14
+Ynl056w pp Ynl099c
+Ynl058c pp Gup1
+Sun4 pp Ylr440c
+Tom7 pp Sbe2
+Tom7 pp Lsm6
+Imp4 pp Mpp10
+Ynl078w pp Hmt1
+Ynl078w pp Nap1
+Ynl078w pp Rim11
+End3 pp Nip100
+Ynl086w pp Nup49
+Ynl086w pp Sec35
+Ynl086w pp Ykl061w
+Ynl086w pp Med4
+Top2 pp Smt3
+Top2 pp Faa4
+Top2 pp Tir2
+Ynl092w pp Kgd2
+Ynl092w pp Nup42
+Ynl092w pp Yap6
+Ynl092w pp Tfg2
+Ynl092w pp Crh1
+Ynl092w pp Yap1802
+Ynl092w pp Mga1
+Ynl092w pp Yhr081w
+Ynl092w pp Yhr188c
+Ynl092w pp Yil024c
+Ynl092w pp Yjl058c
+Ynl092w pp Yjr020w
+Ynl092w pp Yjr070c
+Ynl092w pp Fip1
+Ynl092w pp Yjr097w
+Ynl092w pp Sft1
+Ynl092w pp Pan3
+Ynl092w pp Ykl153w
+Ynl092w pp Ylr124w
+Ynl092w pp Ylr287c
+Ynl092w pp Yml037c
+Ynl092w pp Cdc5
+Ynl092w pp Yor004w
+Ynl092w pp Cin5
+Ynl092w pp Glo4
+Ynl092w pp Scd5
+Ynl095c pp Yhr199c
+Ynl099c pp Taf17
+Ynl099c pp Siw14
+Ynl100w pp Ycl056c
+Yaf9 pp Lac1
+Ynl116w pp Thi4
+Ynl116w pp Cdc123
+Ynl116w pp Sml1
+Ynl124w pp Gpa2
+Ynl140c pp Kre34
+Aah1 pp Ykl086w
+Aah1 pp Ylr225c
+Mep2 pp Kre30
+Mfa2 pp Ylr358c
+Lsm7 pp Lsm5
+Ynl152w pp Hof1
+Gim3 pp Ume6
+Yck2 pp Akr1
+Ynl155w pp Yor364w
+Ynl159c pp Ynl159c
+Ynl159c pp Ade2
+Ynl165w pp Msl1
+Bni5 pp Ydr136c
+Bni5 pp Ypr1
+Mdg1 pp Hsp10
+Nop13 pp Yhr180w
+Ynl176c pp Rdi1
+Ynl176c pp Apc9
+Rps3 pp Ltv1
+Rps3 pp Ylr301w
+Rho5 pp Ynl099c
+Npr1 pp Yap1802
+Srp1 pp Prp45
+Srp1 pp Acs1
+Srp1 pp Gdh3
+Srp1 pp Ecm15
+Srp1 pp Pdx3
+Srp1 pp Hsp26
+Srp1 pp Ybr137w
+Srp1 pp Ecm31
+Srp1 pp Gbp2
+Srp1 pp Frm2
+Srp1 pp Rnq1
+Srp1 pp Glk1
+Srp1 pp Ycr076c
+Srp1 pp Psa1
+Srp1 pp Whi4
+Srp1 pp Ydl246c
+Srp1 pp Hem13
+Srp1 pp Snf11
+Srp1 pp Ydr100w
+Srp1 pp Kgd2
+Srp1 pp Hmo1
+Srp1 pp Spc19
+Srp1 pp Cta1
+Srp1 pp Mcm21
+Srp1 pp Trr1
+Srp1 pp Ydr383c
+Srp1 pp Hpt1
+Srp1 pp Ydr428c
+Srp1 pp Ydr453c
+Srp1 pp Rib3
+Srp1 pp Smt3
+Srp1 pp Hlr1
+Srp1 pp Ydr533c
+Srp1 pp Yel015w
+Srp1 pp Gly1
+Srp1 pp Hpa3
+Srp1 pp Yer010c
+Srp1 pp Pro3
+Srp1 pp Hig1
+Srp1 pp Rad51
+Srp1 pp Bmh1
+Srp1 pp Dmc1
+Srp1 pp Yfl010c
+Srp1 pp Gna1
+Srp1 pp Sec53
+Srp1 pp Snz3
+Srp1 pp Yfr047c
+Srp1 pp Pnc1
+Srp1 pp Hem2
+Srp1 pp Cup2
+Srp1 pp Sae2
+Srp1 pp Nif3
+Srp1 pp Fzf1
+Srp1 pp Ygr010w
+Srp1 pp Ygr024c
+Srp1 pp Ctt1
+Srp1 pp Ygr136w
+Srp1 pp Thi4
+Srp1 pp Cys4
+Srp1 pp Tdh3
+Srp1 pp Mga1
+Srp1 pp Fol2
+Srp1 pp Ygr280c
+Srp1 pp Yap3
+Srp1 pp Yhl009wa
+Srp1 pp Prs3
+Srp1 pp Yhl018w
+Srp1 pp Arg4
+Srp1 pp Thr1
+Srp1 pp Dys1
+Srp1 pp Yhr112c
+Srp1 pp Imd2
+Srp1 pp Urm1
+Srp1 pp Bcy1
+Srp1 pp Yil132c
+Srp1 pp Tdh1
+Srp1 pp Yjl058c
+Srp1 pp Yjl199c
+Srp1 pp Yjl218w
+Srp1 pp Tdh2
+Srp1 pp Met3
+Srp1 pp Yjr037w
+Srp1 pp Yjr056c
+Srp1 pp Xpt1
+Srp1 pp Sor1
+Srp1 pp Ykl023w
+Srp1 pp Ynk1
+Srp1 pp Ykl069w
+Srp1 pp Lap4
+Srp1 pp She2
+Srp1 pp Apl2
+Srp1 pp Shm2
+Srp1 pp Srl2
+Srp1 pp Pnp1
+Srp1 pp Ylr211c
+Srp1 pp Cdd1
+Srp1 pp Eci1
+Srp1 pp Ylr324w
+Srp1 pp Ylr328w
+Srp1 pp Ylr345w
+Srp1 pp Fbp1
+Srp1 pp Cat2
+Srp1 pp Rnt1
+Srp1 pp Yip3
+Srp1 pp Ynl047c
+Srp1 pp Ynl182c
+Srp1 pp Aad14
+Srp1 pp Snz2
+Srp1 pp Ynl335w
+Srp1 pp Ynr069c
+Srp1 pp Yol082w
+Srp1 pp Hsp10
+Srp1 pp Idh2
+Srp1 pp Yor155c
+Srp1 pp Yor284w
+Srp1 pp Dig1
+Srp1 pp Ypl088w
+Srp1 pp Car1
+Srp1 pp Smx3
+Srp1 pp Qcr2
+Srp1 pp Hpa2
+Ynl201c pp Ybl046w
+Ynl201c pp Ydl239c
+Ynl201c pp Mth1
+Ynl201c pp Zip1
+Ynl201c pp Erv14
+Ynl201c pp Yjl058c
+Ynl201c pp Snt309
+Sps19 pp Ymr102c
+Rtt106 pp Hlr1
+Vid27 pp Apg7
+Rap1 pp Rif2
+Alg9 pp Ygr149w
+Ade12 pp Gly1
+Pop1 pp Ctr3
+Pop1 pp Ylr435w
+Ynl226w pp Nip7
+Ynl228w pp Ynl228w
+Ela1 pp Apg17
+Ynl234w pp Gtt1
+Ynl234w pp Nup53
+Sla2 pp Nup100
+Sui1 pp Ydr128w
+Mrpl17 pp Dal1
+Mrpl17 pp Tye7
+Ynl258c pp Sas3
+Ynl258c pp Gat1
+Ynl258c pp Yhr056c
+Ynl258c pp Ykr022c
+Ynl258c pp Ylr440c
+Ynl258c pp Nbp1
+Ynl260c pp Yhr168w
+Ynl260c pp Ymr322c
+Yif1 pp Yip1
+Yif1 pp Yip3
+Yif1 pp Yip2
+Tof1 pp Ymr048w
+Met2 pp Mud1
+Met2 pp Tfa1
+Ynl285w pp Ypl245w
+Kri1 pp Yil105c
+Ynl311c pp Met14
+Dal82 pp Std1
+Pha2 pp Yfl051c
+Ynl321w pp Hsp150
+Egt2 pp Ubi4
+Aad14 pp Aad14
+Snz2 pp Snz3
+Snz2 pp Snz2
+Sno2 pp Snz3
+Sno2 pp Cyc1
+Sno2 pp Snz2
+Aut1 pp Aut7
+Aut1 pp Apg12
+Urk1 pp Smt3
+Urk1 pp Yjr056c
+Urk1 pp Ynl078w
+Urk1 pp Urk1
+Ynr013c pp Chk1
+Ynr024w pp Srb4
+Cpr8 pp Yjl045w
+Cpr8 pp Ynl187w
+Ecm39 pp Aor1
+Rsm19 pp Ybr197c
+Ynr046w pp Fyv9
+Lys9 pp Pus4
+Bre5 pp Ydr126w
+Bre5 pp Yap6
+Bre5 pp Ubp3
+Pop2 pp Yap6
+Pop2 pp Std1
+Ynr065c pp Idp2
+Ynr068c pp Ynr069c
+Ynr074c pp Lpp1
+Cos10 pp Yll012w
+Yol003c pp Spr6
+Top1 pp Ymr233w
+Top1 pp Ynl099c
+Yol014w pp Ykr021w
+Yol015w pp Ydr107c
+Yol015w pp Yhr167w
+Yol015w pp Ypr171w
+Cmk2 pp Sgt2
+Tlg2 pp Aad6
+Tlg2 pp Nup53
+Tat2 pp Yel017w
+Tat2 pp Pho23
+Yol030w pp Yjr003c
+Yol030w pp Hit1
+Yol031c pp Ylr412w
+Yol034w pp Yor324c
+Rpp2a pp Yol014w
+Ngl1 pp Dph5
+Spe2 pp Ydr214w
+Gpm3 pp Ylr387c
+Prs5 pp Yer163c
+Yol063c pp Mga1
+Inp54 pp Ydl204w
+Inp54 pp Gtt1
+Nuf2 pp Hyp2
+Nuf2 pp Nup57
+Nuf2 pp Kel2
+Nuf2 pp Tid3
+Nuf2 pp Cdc42
+Nuf2 pp Jnm1
+Nuf2 pp Ynl086w
+Yol075c pp Cat2
+Yol085c pp Pol4
+Spo21 pp Ynl086w
+Rfc4 pp Rfc3
+Hmi1 pp Mdl2
+Yol099c pp Yhl049c
+Yol099c pp Erg3
+Tpt1 pp His7
+Ndj1 pp Ydr383c
+Ndj1 pp Yjl019w
+Wsc3 pp Yjr082c
+Wsc3 pp Plb3
+Yol106w pp Yfl010c
+Yol107w pp Prm8
+Yol107w pp Aro2
+Yol111c pp Ydl100c
+Skm1 pp Ygl185c
+Trf4 pp Cbp4
+Trf4 pp Nvj1
+Trf4 pp Yil079c
+Trf4 pp Tfc5
+Yol117w pp Yil071c
+Hrp1 pp Lpd1
+Hrp1 pp Nab2
+Mdh2 pp Ydl100c
+Alr1 pp Faa3
+Yol131w pp Bdf2
+Yol131w pp Nup84
+Yol131w pp Ydr527w
+Yol131w pp Ylr080w
+Yol131w pp Swi6
+Yol131w pp Ymr048w
+Yol131w pp Dfg5
+Yol131w pp Ynl266w
+Yol131w pp Ynr040w
+Yol131w pp Std1
+Yol131w pp Ypl249c
+Yol132w pp Ssr1
+Cdc33 pp Caf20
+Nop8 pp Gtr1
+Ctr9 pp Vps29
+Gre2 pp Ygr111w
+Gre2 pp Pwp1
+Fre7 pp Yfl049w
+Yol154w pp Bud14
+Yol159c pp Ydl100c
+Ysp3 pp Mnn4
+Yor006c pp Yil025c
+Sgt2 pp Ybr137w
+Sgt2 pp Yol111c
+Sgt2 pp Yor164c
+Slg1 pp Ymr002w
+Tir2 pp Yfr016c
+Rts1 pp Seh1
+Rts1 pp Bop3
+Rod1 pp Ymr178w
+Hsp10 pp Hsp10
+Ahc1 pp Ycr082w
+Ahc1 pp Ylr424w
+Ahc1 pp Mdm12
+Bub3 pp Bub1
+She4 pp Yer156c
+She4 pp Nup57
+She4 pp Ypl200w
+Pep12 pp Sft2
+Pep12 pp Ydr100w
+Pep12 pp Vti1
+Cyc2 pp Ycl056c
+Cyc2 pp Rps18a
+Glo4 pp Yro2
+Whi2 pp Ydr061w
+Whi2 pp Akr1
+Whi2 pp Pre9
+Whi2 pp Psr1
+Whi2 pp Psr2
+Dbp5 pp Ybr027c
+Dbp5 pp Ydl011c
+Std1 pp Hxt3
+Std1 pp Bub1
+Std1 pp Yjl048c
+Std1 pp Rgt1
+Std1 pp Ynl201c
+Yor049c pp Fen1
+Yor050c pp Aro4
+Yor054c pp Ygl132w
+Sgt1 pp Smf2
+Sgt1 pp Yil152w
+Yor059c pp Yer045c
+Yor059c pp Prm8
+Yor059c pp Rta1
+Yor059c pp Icy1
+Yor060c pp Mth1
+Yor060c pp Ssa2
+Cka2 pp Ckb2
+Cyt1 pp Yol073c
+Yor068c pp Fth1
+Vps5 pp Smf3
+Yor073w pp Lys12
+Ufe1 pp Fms1
+Ufe1 pp Ypr040w
+Yor076c pp Agp3
+Yor076c pp Pex15
+Bud21 pp Ynl320w
+Yor087w pp Ydr203w
+Yor088w pp Mcm1
+Rki1 pp Yll012w
+Rps7a pp Ymr075w
+Yor097c pp Erg6
+Crc1 pp Pfk1
+Ras1 pp Akr1
+Yor108w pp Ydr455c
+Tfc7 pp Pgk1
+Tfc7 pp Cox14
+Yor111w pp Ent1
+Yor111w pp Yor111w
+Yor112w pp Mmm1
+Trs33 pp Yol082w
+Rpt5 pp Rpt3
+Rpt5 pp Fyv10
+Rpt5 pp Cct8
+Rpt5 pp Rpt4
+Rio1 pp Rps1a
+Leo1 pp Nhx1
+Leo1 pp Yol131w
+Ubp2 pp Ygr268c
+Rga1 pp Ybr137w
+Rga1 pp Ydl239c
+Yor131c pp Ypl034w
+Yor142wa pp Pan6
+Yor142wa pp Yol103wb
+Yor146w pp Ddc1
+Spp2 pp Ykl075c
+Yor155c pp Trp2
+Yor155c pp Yor155c
+Pup1 pp Ydr428c
+Pup1 pp Pup3
+Pet123 pp Rrn6
+Pet123 pp Sec35
+Pet123 pp Swi6
+Pet123 pp Apg17
+Pet123 pp Ylr424w
+Sme1 pp Ydr383c
+Sme1 pp Pau2
+Sme1 pp Ygr269w
+Sme1 pp Swi6
+Sme1 pp Smx3
+Yor164c pp Apg17
+Rps28a pp Kin3
+Rps28a pp Ybl081w
+Rps28a pp Ybr094w
+Rps28a pp Yel015w
+Rps28a pp Hcs1
+Rps28a pp Erg3
+Rps28a pp Ylr135w
+Rps28a pp Dcp1
+Rps28a pp Std1
+Lcb4 pp Yer071c
+Lcb4 pp Akr2
+Lcb4 pp Gsp2
+Yor173w pp Spo12
+Hem15 pp Yer071c
+Yor177c pp Nmd5
+Dci1 pp Pex14
+Dci1 pp Eci1
+Las17 pp Rvs167
+Las17 pp Ygr136w
+Las17 pp Yjl100w
+Tuf1 pp Ydr542w
+Ris1 pp Smt3
+Lip5 pp Ydr344c
+Bfr1 pp Ykr030w
+Bfr1 pp Ylr128w
+Rpb10 pp Ydr527w
+Yor220w pp Taf60
+Mct1 pp Ykl221w
+Isu2 pp Cdc19
+Wtm2 pp Rpp1a
+Mkk1 pp Mnt3
+Mge1 pp Ymr147w
+Dfr1 pp Cne1
+Abp140 pp Mbr1
+Abp140 pp Yor172w
+Abp140 pp Mge1
+Ssp2 pp Trp1
+Esa1 pp Ykr021w
+Yor245c pp Prm8
+Yor245c pp Ygr228w
+Yor245c pp Yor097c
+Yor252w pp Ypr152c
+Cdc31 pp Kar1
+Gcd1 pp Gcd6
+Yor264w pp Med8
+Yor264w pp Ycr086w
+Yor264w pp Ydr115w
+Yor264w pp Yfl013c
+Yor264w pp Yfr022w
+Yor264w pp Pex14
+Yor264w pp Ygl220w
+Yor264w pp Yhr039c
+Yor264w pp Yhr067w
+Yor264w pp Yil060w
+Yor264w pp Msl1
+Yor264w pp Yjl055w
+Yor264w pp Yjl215c
+Yor264w pp Apn1
+Yor264w pp Ykl146w
+Yor264w pp Ykr090w
+Yor264w pp Yef3
+Yor264w pp Ylr334c
+Yor264w pp Bud22
+Yor264w pp Ymr192w
+Yor264w pp Smm1
+Yor264w pp Ynr068c
+Yor264w pp Ntg2
+Yor264w pp Yor324c
+Yor264w pp Clb2
+Rbl2 pp Yor177c
+Pnt1 pp Mms21
+Pac1 pp Pgm1
+Pac1 pp Ylr254c
+Yor273c pp Yel072w
+Mod5 pp Yer010c
+Yor275c pp Snf7
+Yor275c pp Vps4
+Yor282w pp Dps1
+Yor284w pp Sbe2
+Yor284w pp Yor284w
+Yor285w pp Rps11a
+Yor285w pp Ydr233c
+Yor285w pp Yel015w
+Yor285w pp Dmc1
+Yor285w pp Spl2
+Yor285w pp Ynl208w
+Yor285w pp Dpm1
+Mpd1 pp Ypr085c
+Yor292c pp Ydr387c
+Yor292c pp Pob3
+Rrs1 pp Ykr017c
+Yor298w pp Ade5
+Bud7 pp Kin28
+Bud7 pp Spg1
+Bud7 pp Ygr294w
+Bud7 pp Yjr116w
+Bud7 pp Ykr070w
+Bud7 pp Ylr108c
+Bud7 pp Yml041c
+Bud7 pp Ynl246w
+Bud7 pp Kri1
+Bud7 pp Ynr069c
+Bud7 pp Met22
+Bud7 pp Hxt11
+Bud7 pp Cyc2
+Bud7 pp Std1
+Bud7 pp Yor049c
+Rax1 pp Ygr259c
+Yor302w pp Ygr268c
+Yor302w pp Lap4
+Yor302w pp Yol082w
+Yor302w pp Std1
+Yor302w pp Yor049c
+Cpa1 pp Nce103
+Yor305w pp Ydr415c
+Sly41 pp Prm8
+Yor315w pp Ydr492w
+Yor315w pp Yol035c
+Hsh49 pp Rtf1
+Yor324c pp Hof1
+Yor325w pp Kar3
+Yor333c pp Tho1
+Mrs2 pp YDR134C
+Yor345c pp Can1
+Mne1 pp Rps20
+Mne1 pp Ura10
+Yor353c pp Kic1
+Yor354c pp Yjr082c
+Hap5 pp Hap3
+Hap5 pp Mth1
+Hap5 pp Hap4
+Hap5 pp Std1
+Pde2 pp Flo5
+Ald4 pp Ppa1
+Yor378w pp Ydr327w
+Yor380w pp Yor380w
+Fre3 pp Are2
+Yor383c pp Ilv1
+Yor385w pp Rsp5
+Err1 pp Ade2
+Snf8 pp Ydr383c
+Snf8 pp Vps36
+Ula1 pp Fol2
+Ula1 pp Uba3
+Ypl005w pp Ycl063w
+Ypl005w pp Rpp1a
+Chl1 pp Yol150c
+Ulp1 pp Chs2
+Ulp1 pp Ycr007c
+Ulp1 pp Ydr100w
+Ulp1 pp Dig2
+Ulp1 pp Gtt1
+Ulp1 pp Yjl067w
+Ulp1 pp Erg6
+Rad1 pp Ylr135w
+Nce4 pp Ydr060w
+Pho85 pp Pcl6
+Pho85 pp Pcl10
+Pho85 pp Pcl8
+Pma2 pp Ykl174c
+Pma2 pp Ypl136w
+Ism1 pp Yjl100w
+Nop4 pp Sup45
+Dig1 pp Dig2
+Dig1 pp Dig1
+Arl3 pp Ykr030w
+Grx5 pp Yfl010c
+Grx5 pp Yil105c
+Grx5 pp Yjl162c
+Grx5 pp Hof1
+Ald6 pp Tfc5
+Ypl066w pp Ygr182c
+Ypl068c pp Ecm15
+Ypl070w pp Ura7
+Ypl070w pp Ecm31
+Ypl070w pp Dut1
+Ypl070w pp Kgd2
+Ypl070w pp Asp1
+Ypl070w pp Rpt3
+Ypl070w pp Sam2
+Ypl070w pp Hpa3
+Ypl070w pp Pro3
+Ypl070w pp Ilv1
+Ypl070w pp Ygr010w
+Ypl070w pp Yhl018w
+Ypl070w pp Dcd1
+Ypl070w pp Yjl199c
+Ypl070w pp Yjl218w
+Ypl070w pp Cdd1
+Ypl070w pp Eci1
+Ypl070w pp Sfh1
+Ypl070w pp Apg16
+Ypl070w pp Yip3
+Ypl070w pp Aad14
+Ypl070w pp Yol082w
+Ypl070w pp Yor155c
+Ypl070w pp Yor284w
+Ypl070w pp Nip29
+Ypl070w pp Hpa2
+Ypl073c pp Set2
+Yta6 pp Ypl004c
+Gpi2 pp Sur4
+Ypl077c pp Syf1
+Ypl077c pp Ydr489w
+Ypl077c pp Yap1801
+Ypl077c pp Apg17
+Ypl088w pp Ypl088w
+Glr1 pp Yol082w
+Sec62 pp Pwp2
+Ypl095c pp Ydr100w
+Ypl095c pp Ygl161c
+Ypl095c pp Ygl198w
+Ypl095c pp Yip1
+Png1 pp Ybr204c
+Ypl105c pp Cos2
+Car1 pp Yfl012w
+Car1 pp Ygr136w
+Car1 pp Car1
+Ypl114w pp Rec114
+Mrp51 pp Ydr333c
+Mrp51 pp Lsc2
+Kap120 pp Sam2
+Kap120 pp Spt2
+Nan1 pp Ydl072c
+Spo19 pp Ykl047w
+Spo19 pp Cha4
+Apg5 pp Apg12
+Ypl150w pp Ynl253w
+Prp46 pp Prp45
+Prp46 pp Ylr326w
+Prp46 pp Ylr386w
+Prp46 pp Pep12
+Rad53 pp Stn1
+Kip2 pp Soh1
+Ypl157w pp Ypl004c
+Ypl158c pp Rim11
+Ypl159c pp Apg17
+Svs1 pp Acp1
+Mex67 pp Hsp26
+Mex67 pp Pro3
+Mex67 pp Pan3
+Mex67 pp Fbp1
+Mex67 pp Met2
+Mex67 pp Ade2
+Cox10 pp Tho1
+Nab3 pp Yll020c
+Prm3 pp Fps1
+Apl5 pp Aps3
+Ypl196w pp Prs5
+Ypl200w pp Ape3
+Ypl201c pp Hor2
+Tpk2 pp Bcy1
+Hrr25 pp Rad51
+Hrr25 pp Ady1
+Hrr25 pp Dcp1
+Ypl207w pp Gyp6
+Ypl208w pp Ycl046w
+Ypl208w pp Sas5
+Thi6 pp Erb1
+Cbp3 pp Yar069c
+Ypl216w pp Ydr398w
+Sar1 pp Sac2
+Bop1 pp Ybr012c
+Ypl222w pp Ymr009w
+Ypl222w pp Mge1
+Mmt2 pp Rrn5
+Hsp82 pp Yir042c
+Cin2 pp Cdc12
+Cin2 pp Prp2
+Hut1 pp Yel017w
+Hut1 pp Fms1
+Ypl245w pp Cit2
+Ypl249c pp Ynl191w
+Vik1 pp Sec61
+Vik1 pp Ynr042w
+Apm1 pp Apl2
+Kel3 pp Aip1
+Dim1 pp Pry3
+Ypl276w pp Ydr494w
+Ypl276w pp Nut2
+Ypl280w pp Ydr425w
+Yrf1-7 pp Cce1
+Cit3 pp Ssa4
+Rlf2 pp Msi1
+Rlf2 pp Mec3
+Ccl1 pp Tfb3
+Yip2 pp Ylr324w
+Apl4 pp Yfr043c
+Apl4 pp Apl2
+Csr2 pp Pdc6
+Hts1 pp Rpn11
+Hts1 pp Cof1
+Hts1 pp Spr1
+Ypr037c pp Ydl100c
+Ypr037c pp Ypr156c
+Ypr040w pp Pph21
+Ypr040w pp Pph22
+Ypr040w pp Pph3
+Ypr040w pp Ppg1
+Ypr040w pp Yor380w
+Tif5 pp Htb1
+Ypr045c pp Ade2
+Mcm16 pp Prp24
+Msf1 pp Ymr147w
+Ypr050c pp Ylr456w
+Mak3 pp Mak10
+Smk1 pp Yfl010c
+Smk1 pp Yll030c
+Smk1 pp Ade2
+Smk1 pp Qcr2
+Ymc1 pp Ynl246w
+Ypr063c pp Cos2
+Ypr071w pp Ylr465c
+Ypr071w pp Ypr071w
+Not5 pp Nop4
+Ypr078c pp Rpp1a
+Ypr078c pp Sip1
+Ypr083w pp Jnm1
+Ypr084w pp Mrps28
+Ypr084w pp Rsp5
+Ypr084w pp Ade2
+Ypr085c pp Ade2
+Sua7 pp Rft1
+Sua7 pp Ybr014c
+Sua7 pp Ybr175w
+Sua7 pp Med8
+Sua7 pp Ybr209w
+Sua7 pp Bud3
+Sua7 pp Frm2
+Sua7 pp Lre1
+Sua7 pp Bre1
+Sua7 pp Rpp1a
+Sua7 pp Ydl086w
+Sua7 pp Ydl158c
+Sua7 pp Ydr102c
+Sua7 pp Ydr133c
+Sua7 pp Ngg1
+Sua7 pp Ydr271c
+Sua7 pp Phm5
+Sua7 pp Glc3
+Sua7 pp Ald5
+Sua7 pp Yer076c
+Sua7 pp Oxa1
+Sua7 pp Yfl013c
+Sua7 pp Ypt1
+Sua7 pp Yfl042c
+Sua7 pp Tip20
+Sua7 pp Tfg2
+Sua7 pp Ygr053c
+Sua7 pp Tel2
+Sua7 pp Ade3
+Sua7 pp Ygr205w
+Sua7 pp Ygr207c
+Sua7 pp Nas6
+Sua7 pp Rtt102
+Sua7 pp Ygr291c
+Sua7 pp Ygr294w
+Sua7 pp Yhl044w
+Sua7 pp Yhl045w
+Sua7 pp Fil1
+Sua7 pp Yhr040w
+Sua7 pp Med6
+Sua7 pp Sae3
+Sua7 pp Spc97
+Sua7 pp Yhr214w
+Sua7 pp Yil005w
+Sua7 pp Bcy1
+Sua7 pp Rnr3
+Sua7 pp Mpm1
+Sua7 pp Yjl072c
+Sua7 pp Pry1
+Sua7 pp Ess1
+Sua7 pp Arp3
+Sua7 pp Oct1
+Sua7 pp Cbt1
+Sua7 pp Hif1
+Sua7 pp Stu2
+Sua7 pp Ylr201c
+Sua7 pp Ylr294c
+Sua7 pp Atp14
+Sua7 pp Ylr455w
+Sua7 pp Nbp1
+Sua7 pp Ost6
+Sua7 pp Sec65
+Sua7 pp Yml108w
+Sua7 pp Ymr184w
+Sua7 pp Mrpl24
+Sua7 pp Ymr263w
+Sua7 pp Scw10
+Sua7 pp Ymr315w
+Sua7 pp Pbi2
+Sua7 pp Gcd10
+Sua7 pp Rps7b
+Sua7 pp Caf40
+Sua7 pp Rib2
+Sua7 pp Yol070c
+Sua7 pp Yol111c
+Sua7 pp Pex11
+Sua7 pp Spt20
+Sua7 pp Yol150c
+Sua7 pp Fre7
+Sua7 pp Cyc2
+Sua7 pp Tom6
+Sua7 pp Yor049c
+Sua7 pp Yng1
+Sua7 pp Cdc21
+Sua7 pp Atx2
+Sua7 pp Yor082c
+Sua7 pp Tfc7
+Sua7 pp Yor114w
+Sua7 pp Yor154w
+Sua7 pp Yor271c
+Sua7 pp Snf8
+Sua7 pp Arl3
+Sua7 pp Sec62
+Sua7 pp Msy1
+Sua7 pp Atp20
+Sua7 pp Sro7
+Sua7 pp Uba3
+Sua7 pp Nca2
+Sua7 pp Ypr157w
+Srp54 pp Ade2
+Ypr094w pp Ypr133c
+Pre2 pp Std1
+Fhl1 pp Hmo1
+Fhl1 pp Smt3
+Ypr105c pp Sec35
+Ypr105c pp Tid3
+Ypr105c pp Apg17
+Ypr105c pp Qcr2
+Isr1 pp Chs2
+Isr1 pp Tif3
+Yth1 pp Fip1
+Rpn7 pp Rpn3
+Dbf20 pp Nup145
+Dbf20 pp Ade2
+Pis1 pp Erg6
+Clb2 pp Sco2
+Clb2 pp Cks1
+Clb2 pp Rps11a
+Ypr123c pp Ypl034w
+Ypr126c pp Yal064wb
+Asn1 pp Yhr113w
+Ypr148c pp Ydl237w
+Ypr158wa pp Yer159ca
+Ypr158wa pp Yor142wa
+Ypr158wa pp Ypr158wa
+Tif3 pp Asp3-1
+Ypr169w pp Ras1
+Ypr171w pp Ybr187w
+Ypr172w pp Tof2
+Vps4 pp Snf7
+Ypr174c pp Yel017w
+Ypr174c pp Rpi1
+Ypr174c pp Vps21
+Dpb2 pp Sno2
+Prp4 pp Yap1802
+Gdb1 pp Yfr017c
+Arr3 pp Ylr171w
+Smc1 pp Smc2
+Smc1 pp Smc3
+Kel1 pp Kel1
+Met4 pp Met4
+Met4 pp Met28
+Spc42 pp Spc42
+Rpn4 pp Rpn2
+Abp1 pp App1
+Abp1 pp Yor284w
+Abp1 pp Prk1
+Abp1 pp Ark1
+Abp1 pp Srv2
+Abp1 pp Inp52
+Bbc1 pp Ydl129w
+Bbc1 pp Pkc1
+Bbc1 pp Yir003w
+Bbc1 pp Las17
+Bbc1 pp Vrp1
+Bbc1 pp Myo5
+Bbc1 pp App1
+Bbc1 pp Fir1
+Bbc1 pp Nfi1
+Bbc1 pp Ufd1
+Bbc1 pp Fap1
+Bbc1 pp Siz1
+Bbc1 pp Yor081c
+Bbc1 pp Gdb1
+Bem1 pp Yel043w
+Bem1 pp Caf130
+Boi1 pp Afr1
+Boi1 pp Hof1
+Boi1 pp Dse1
+Boi1 pp Yer158c
+Boi1 pp Yjr056c
+Boi1 pp Zds2
+Boi1 pp Nis1
+Boi2 pp Dse1
+Bzz1 pp Ylr064w
+Bzz1 pp App1
+Bzz1 pp Las17
+Bzz1 pp Myo3
+Bzz1 pp Myo5
+Bzz1 pp Vps73
+Bzz1 pp Ypl246c
+Bzz1 pp Ypr171w
+Bzz1 pp Fir1
+Bzz1 pp Ubp7
+Bzz1 pp Ydl146w
+Bzz1 pp Nis1
+Bzz1 pp Sen2
+Bzz1 pp Grr1
+Bzz1 pp Ktr3
+Bzz1 pp Sna3
+Bzz1 pp Bos1
+Bzz1 pp Ymr253c
+Bzz1 pp Ykr030w
+Cdc25 pp Bnr1
+Cdc25 pp Nfi1
+Cdc25 pp She3
+Cdc25 pp Rsm19
+Fus1 pp Pea2
+Fus1 pp Sho1
+Fus1 pp Bni1
+Fus1 pp Bnr1
+Fus1 pp Fun31
+Fus1 pp Pkc1
+Fus1 pp Rom1
+Fus1 pp Bud2
+Fus1 pp Fir1
+Fus1 pp Fun21
+Fus1 pp Ykl105c
+Fus1 pp Vac7
+Fus1 pp Sir1
+Fus1 pp Haa1
+Fus1 pp Ynl058c
+Fus1 pp Pet127
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+Sho1 pp Adr1
+Sho1 pp Gln3
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+Sla1 pp Ynl152w
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+Unknown interactsWith Yhr033w
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+Unknown interactsWith Mdh1
+Unknown interactsWith Cor1
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+Unknown interactsWith Prp19
+Unknown interactsWith Qcr2
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+Unknown interactsWith Yhb1
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+Unknown interactsWith Rpn1
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+Unknown interactsWith Rpn9
+Unknown interactsWith Rpt1
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+Ela1 interactsWith Unknown
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+Unknown interactsWith Cic1
+Unknown interactsWith Yra1
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+Unknown interactsWith Reg1
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+Unknown interactsWith Ric1
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+Unknown interactsWith Myo5
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+Unknown interactsWith Uba1
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+Unknown interactsWith Vps13
+Unknown interactsWith Ynk1
+Unknown interactsWith Ynl311c
+Yhr115c interactsWith Unknown
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+Unknown interactsWith Ssz1
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+Unknown interactsWith Ydr341c
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+Unknown interactsWith Hom3
+Unknown interactsWith Hsh49
+Arf1 interactsWith Unknown
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+Dss4 interactsWith Unknown
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+Nop13 interactsWith Unknown
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+Unknown interactsWith Imd3
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+Unknown interactsWith Rrp5
+Unknown interactsWith Rrp13
+Unknown interactsWith Cic1
+Hsh49 interactsWith Unknown
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+Unknown interactsWith Rse1
+Ubc1 interactsWith Unknown
+Unknown interactsWith Adk1
+Rad10 interactsWith Unknown
+Unknown interactsWith Rad1
+Unknown interactsWith Sod2
+Est1 interactsWith Unknown
+Unknown interactsWith Cbf5
+Unknown interactsWith Dbp7
+Unknown interactsWith Hsh49
+Unknown interactsWith Kre33
+Unknown interactsWith Mss116
+Unknown interactsWith Pdi1
+Unknown interactsWith Pet56
+Unknown interactsWith Puf6
+Unknown interactsWith Pwp1
+Unknown interactsWith Rrp1
+Unknown interactsWith Yer077c
+Unknown interactsWith Yjl109c
+Unknown interactsWith Ykl014c
+Unknown interactsWith Rpf2
+Unknown interactsWith Rrp12
+Met30 interactsWith Unknown
+Unknown interactsWith Cdc53
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+Unknown interactsWith Met4
+Unknown interactsWith Rub1
+Unknown interactsWith Sis1
+Unknown interactsWith Skp1
+Unknown interactsWith Tef4
+Dmc1 interactsWith Unknown
+Unknown interactsWith Por1
+Cdc11 interactsWith Unknown
+Unknown interactsWith Cdc10
+Unknown interactsWith Cdc12
+Unknown interactsWith Cdc3
+Unknown interactsWith Pdi1
+Unknown interactsWith Tif4631
+Unknown interactsWith Tif4632
+Lsm4 interactsWith Unknown
+Unknown interactsWith Pat1
+Unknown interactsWith Tps1
+Unknown interactsWith Ubp15
+Unknown interactsWith Arf2
+Unknown interactsWith His4
+Ygr052w interactsWith Unknown
+Rpc40 interactsWith Unknown
+Unknown interactsWith Arf1
+Unknown interactsWith Arf2
+Unknown interactsWith Kri1
+Unknown interactsWith Rpa135
+Unknown interactsWith Rpa190
+Unknown interactsWith Rpc19
+Hrt1 interactsWith Unknown
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+Unknown interactsWith Idh1
+Unknown interactsWith Rpn8
+Unknown interactsWith Rtt101
+Unknown interactsWith Sec27
+Unknown interactsWith Yll034c
+Spt2 interactsWith Unknown
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+Unknown interactsWith Cka2
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+Unknown interactsWith Imd2
+Unknown interactsWith Nop1
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+Gpi16 interactsWith Unknown
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+Ctf13 interactsWith Unknown
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+Sgn1 interactsWith Unknown
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+Unknown interactsWith Ygr250c
+Ubc12 interactsWith Unknown
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+Unknown interactsWith Sti1
+Ynl311c interactsWith Unknown
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+Unknown interactsWith Skp1
+Tpk3 interactsWith Unknown
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+Unknown interactsWith Rpn10
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+Clb2 interactsWith Unknown
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+Snp1 interactsWith Unknown
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+Unknown interactsWith Cor1
+Unknown interactsWith Qcr2
+Dia2 interactsWith Unknown
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+Gdi1 interactsWith Unknown
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+Unknown interactsWith Ypt1
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+Unknown interactsWith Ypt32
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+Unknown interactsWith Tif4632
+Unknown interactsWith Tif4631
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+Cdc42 pp Bem3
+Cdc42 pp Bni1
+Pbs2 pp Hog1
+Bud6 pp Bni1
+Pfy1 pp Bni1
+Act1 pp Bni1
+Pbs2 pp Ste11
+Chc1 pp YAP1801
+Clc1 pp YAP1801
+Clc1 pp Yap1802
+Chc1 pp YAP1802
+Pan1 pp YOL101c
+Pan1 pp YOR105w
+Pan1 pp YAP1802
+Pan1 pp Yap1801
+Cdc42 pp Gic1
+Cdc42 pp Gic2
+Cdc42 pp Ste20
+Cdc42 pp Cla4
+Bni1 pp Tef1
+Bni1 pp Tef2
+Pan1 pp End3
+Sla1 pp End3
+Hof1 pp Bni1
+Spa2 pp Bni1
+Rho3 pp Bni1
+Pan1 pp Sla1
+Bni1 pp Rho1
+Cdc42 pp Rga1
+Bni1 pp Num1
+Rsr1 pp Rga1
+Rho1 pp Rga1
+Pan1 pp Prk1
+Kar9 pp Num1
+Tub3 pp Num1
+Prk1 pp Sla1
+Ark1 pp Sla1
+Ark1 pp Pan1
+Pan1 pp YDL161w
+Pan1 interactsWith Arp2/3-complex
+Ent1 pp Chc1
+Prk1 pp Scd5
+Akl1 pp Scd5
+Sla1 pp Sla2
+Sla1 pp Sed5
+Sla1 pp Rad52
+Hcm1 pd itI(AAU)I1
+Hcm1 pd itL(CAA)G1
+Hcm1 pd itR(UCU)G2
+Hcm1 pd itT(AGU)N1
+Hcm1 pd itV(AAC)G3-0
+Hcm1 pd itV(AAC)L
+Hcm1 pd iYAL040C
+Hcm1 pd iYAR009C
+Hcm1 pd iYAR019C-0
+Hcm1 pd iYAR019C-1
+Hcm1 pd iYAR035W
+Hcm1 pd iYAR062W
+Hcm1 pd iYBL023C
+Hcm1 pd iYBL033C
+Hcm1 pd iYBL071C
+Hcm1 pd iYBL093C
+Hcm1 pd iYBR007C-0
+Hcm1 pd iYBR035C
+Hcm1 pd iYBR107C
+Hcm1 pd iYBR231C
+Hcm1 pd iYCL044C
+Hcm1 pd iYCL052C
+Hcm1 pd iYCL058C
+Hcm1 pd iYCR018C-A
+Hcm1 pd iYCR027C
+Hcm1 pd iYDL012C
+Hcm1 pd iYDL025C
+Hcm1 pd iYDL032W
+Hcm1 pd iYDL088C
+Hcm1 pd iYDL108W
+Hcm1 pd iYDL110C
+Hcm1 pd iYDL130W-A
+Hcm1 pd iYDL142C
+Hcm1 pd iYDL160C
+Hcm1 pd iYDL169C
+Hcm1 pd iYDL175C
+Hcm1 pd iYDL181W
+Hcm1 pd iYDL186W
+Hcm1 pd iYDL215C
+Hcm1 pd iYDL223C
+Hcm1 pd iYDL245C-1
+Hcm1 pd iYDL248W-0
+Hcm1 pd iYDR026C
+Hcm1 pd iYDR038C
+Hcm1 pd iYDR039C
+Hcm1 pd iYDR070C
+Hcm1 pd iYDR082W
+Hcm1 pd iYDR088C
+Hcm1 pd iYDR132C
+Hcm1 pd iYDR143C
+Hcm1 pd iYDR160W
+Hcm1 pd iYDR245W
+Hcm1 pd iYDR267C
+Hcm1 pd iYDR277C
+Hcm1 pd iYDR286C
+Hcm1 pd iYDR411C
+Hcm1 pd iYDR523C
+Hcm1 pd iYDR527W-0
+Hcm1 pd iYEL059W
+Hcm1 pd iYEL061C
+Hcm1 pd iYER022W
+Hcm1 pd iYER107C
+Hcm1 pd iYGL034C-1
+Hcm1 pd iYGL124C
+Hcm1 pd iYGL147C
+Hcm1 pd iYGL157W
+Hcm1 pd iYGL161C
+Hcm1 pd iYGL194C
+Hcm1 pd iYGL210W
+Hcm1 pd iYGL211W
+Hcm1 pd iYGL215W
+Hcm1 pd iYGL223C
+Hcm1 pd iYGR075C
+Hcm1 pd iYGR148C
+Hcm1 pd iYGR156W
+Hcm1 pd iYGR165W
+Hcm1 pd iYGR250C-1
+Hcm1 pd iYGR287C
+Hcm1 pd iYHL010C
+Hcm1 pd iYHL025W
+Hcm1 pd iYHL040C
+Hcm1 pd iYHL046C
+Hcm1 pd iYHL049C-0
+Hcm1 pd iYHL050C
+Hcm1 pd iYHR062C
+Hcm1 pd iYHR107C
+Hcm1 pd iYHR108W
+Hcm1 pd iYHR113W
+Hcm1 pd iYHR132C
+Hcm1 pd iYHR138C
+Hcm1 pd iYHR139C-A
+Hcm1 pd iYHR149C
+Hcm1 pd iYIL090W
+Hcm1 pd iYIL091C
+Hcm1 pd iYIL112W
+Hcm1 pd iYIL119C-1
+Hcm1 pd iYIL124W
+Hcm1 pd iYIL145C
+Hcm1 pd iYIL164C-0
+Hcm1 pd iYIL177C-0
+Hcm1 pd iYIR028W
+Hcm1 pd iYIR040C
+Hcm1 pd iYJL107C
+Hcm1 pd iYJL155C
+Hcm1 pd iYJL199C
+Hcm1 pd iYJR156C
+Hcm1 pd iYKL070W
+Hcm1 pd iYKL148C
+Hcm1 pd iYKL162C-A-0
+Hcm1 pd iYKR095W
+Hcm1 pd iYLL066C-0
+Hcm1 pd iYLL066C-1
+Hcm1 pd iYLL067C-1
+Hcm1 pd iYLR004C
+Hcm1 pd iYLR035C-A-1
+Hcm1 pd iYLR037C-0
+Hcm1 pd iYLR089C
+Hcm1 pd iYLR160C-1
+Hcm1 pd iYLR192C
+Hcm1 pd iYLR205C
+Hcm1 pd iYLR228C-0
+Hcm1 pd iYLR460C-0
+Hcm1 pd iYLR460C-1
+Hcm1 pd iYML067C
+Hcm1 pd iYML133C-0
+Hcm1 pd iYML133C-1
+Hcm1 pd iYMR165C
+Hcm1 pd iYMR171C
+Hcm1 pd iYMR201C
+Hcm1 pd iYMR230W
+Hcm1 pd iYMR233W
+Hcm1 pd iYMR247C
+Hcm1 pd iYMR308C
+Hcm1 pd iYMR324C
+Hcm1 pd iYNL013C
+Hcm1 pd iYNL041C
+Hcm1 pd iYNL079C
+Hcm1 pd iYNL094W
+Hcm1 pd iYNL108C
+Hcm1 pd iYNL113W
+Hcm1 pd iYNL129W
+Hcm1 pd iYNL134C
+Hcm1 pd iYNL271C
+Hcm1 pd iYNL294C
+Hcm1 pd iYNL311C
+Hcm1 pd iYNL338W
+Hcm1 pd iYNL339C
+Hcm1 pd iYNR016C-0
+Hcm1 pd iYNR054C-1
+Hcm1 pd iYNR058W
+Hcm1 pd iYNR071C
+Hcm1 pd iYNR075W
+Hcm1 pd iYOL015W
+Hcm1 pd iYOL060C
+Hcm1 pd iYOL119C
+Hcm1 pd iYOL136C
+Hcm1 pd iYOL152W
+Hcm1 pd iYOLWtau1-1
+Hcm1 pd iYOR008C
+Hcm1 pd iYOR018W
+Hcm1 pd iYOR058C-0
+Hcm1 pd iYOR065W
+Hcm1 pd iYOR067C
+Hcm1 pd iYOR070C-1
+Hcm1 pd iYOR071C
+Hcm1 pd iYOR076C
+Hcm1 pd iYOR133W
+Hcm1 pd iYOR144C
+Hcm1 pd iYOR226C
+Hcm1 pd iYOR254C
+Hcm1 pd iYOR307C
+Hcm1 pd iYOR354C-0
+Hcm1 pd iYPL029W
+Hcm1 pd iYPL052W
+Hcm1 pd iYPL056C
+Hcm1 pd iYPL156C
+Hcm1 pd iYPL161C
+Hcm1 pd iYPL171C
+Hcm1 pd iYPL217C
+Hcm1 pd iYPL277C
+Hcm1 pd iYPL281C
+Hcm1 pd iYPL282C
+Hcm1 pd iYPL283C-0
+Hcm1 pd iYPL283C-1
+Hcm1 pd iYPR002C-A
+Hcm1 pd iYPR010C
+Hcm1 pd iYPR013C-0
+Hcm1 pd iYPR035W
+Hcm1 pd iYPR045C
+Hcm1 pd iYPR049C
+Hcm1 pd iYPR074C
+Hcm1 pd iYPR083W
+Hcm1 pd iYPR108W
+Plm2 pd iSNR68
+Plm2 pd itG(GCC)D1
+Plm2 pd itN(GUU)G
+Plm2 pd itN(GUU)N1
+Plm2 pd itT(UGU)P
+Plm2 pd itV(AAC)E1
+Plm2 pd itV(AAC)L
+Plm2 pd iYAL039C-0
+Plm2 pd iYAL044C
+Plm2 pd iYAL058C-A
+Plm2 pd iYAR009C
+Plm2 pd iYAR035W
+Plm2 pd iYBL020W
+Plm2 pd iYBL026W
+Plm2 pd iYBL034C
+Plm2 pd iYBR042C
+Plm2 pd iYBR072W
+Plm2 pd iYBR103W
+Plm2 pd iYBR160W
+Plm2 pd iYBR221C
+Plm2 pd iYBR229C
+Plm2 pd iYBR261C
+Plm2 pd iYBR273C
+Plm2 pd iYBR285W
+Plm2 pd iYBR286W
+Plm2 pd iYBR293W
+Plm2 pd iYCR030C
+Plm2 pd iYDL083C
+Plm2 pd iYDL090C
+Plm2 pd iYDL108W
+Plm2 pd iYDL113C
+Plm2 pd iYDL128W
+Plm2 pd iYDL142C
+Plm2 pd iYDL150W
+Plm2 pd iYDL160C
+Plm2 pd iYDL175C
+Plm2 pd iYDL177C
+Plm2 pd iYDL197C
+Plm2 pd iYDL216C
+Plm2 pd iYDL231C
+Plm2 pd iYDR030C
+Plm2 pd iYDR062W
+Plm2 pd iYDR167W
+Plm2 pd iYDR185C
+Plm2 pd iYDR213W
+Plm2 pd iYDR219C
+Plm2 pd iYDR228C
+Plm2 pd iYDR234W
+Plm2 pd iYDR283C
+Plm2 pd iYDR286C
+Plm2 pd iYDR300C
+Plm2 pd iYDR303C
+Plm2 pd iYDR311W
+Plm2 pd iYDR328C
+Plm2 pd iYDR378C
+Plm2 pd iYDR423C
+Plm2 pd iYDR473C-0
+Plm2 pd iYDR544C
+Plm2 pd iYEL009C
+Plm2 pd iYEL059W
+Plm2 pd iYER006W
+Plm2 pd iYER034W
+Plm2 pd iYER044C
+Plm2 pd iYER082C
+Plm2 pd iYER089C
+Plm2 pd iYER099C
+Plm2 pd iYER101C
+Plm2 pd iYER103W
+Plm2 pd iYER139C
+Plm2 pd iYER162C
+Plm2 pd iYER178W
+Plm2 pd iYFL012W
+Plm2 pd iYFL034C-A
+Plm2 pd iYFR029W
+Plm2 pd iYFR048W
+Plm2 pd iYFR055W-0
+Plm2 pd iYGL051W
+Plm2 pd iYGL114W
+Plm2 pd iYGL115W
+Plm2 pd iYGL160W
+Plm2 pd iYGL186C
+Plm2 pd iYGL192W
+Plm2 pd iYGL196W
+Plm2 pd iYGLWomega1-0
+Plm2 pd iYGR036C
+Plm2 pd iYGR048W
+Plm2 pd iYGR069W
+Plm2 pd iYGR098C
+Plm2 pd iYGR111W
+Plm2 pd iYGR147C
+Plm2 pd iYGR156W
+Plm2 pd iYGR158C
+Plm2 pd iYGR197C
+Plm2 pd iYGR246C
+Plm2 pd iYGR247W
+Plm2 pd iYGR261C
+Plm2 pd iYHL009C
+Plm2 pd iYHL018W
+Plm2 pd iYHL025W
+Plm2 pd iYHR001W-A
+Plm2 pd iYHR058C
+Plm2 pd iYHR136C
+Plm2 pd iYHR147C
+Plm2 pd iYIL020C
+Plm2 pd iYIL049W
+Plm2 pd iYIL123W
+Plm2 pd iYIL131C
+Plm2 pd iYIR031C
+Plm2 pd iYJL031C
+Plm2 pd iYJL050W
+Plm2 pd iYJL175W
+Plm2 pd iYJR041C
+Plm2 pd iYJR059W
+Plm2 pd iYKL087C
+Plm2 pd iYKL109W
+Plm2 pd iYLL067C-1
+Plm2 pd iYLR035C-A-1
+Plm2 pd iYLR038C
+Plm2 pd iYLR089C
+Plm2 pd iYLR114C
+Plm2 pd iYML133C-1
+Plm2 pd iYMR110C
+Plm2 pd iYMR230W
+Plm2 pd iYNL113W
+Plm2 pd iYNL262W
+Plm2 pd iYNL337W
+Plm2 pd iYNR031C
+Plm2 pd iYNR039C
+Plm2 pd iYNR057C
+Plm2 pd iYNR061C
+Plm2 pd iYOL159C
+Plm2 pd iYOL161C-1
+Plm2 pd iYOR030W
+Plm2 pd iYOR327C
+Plm2 pd iYOR350C
+Plm2 pd iYPL031C
+Plm2 pd iYPL139C
+Plm2 pd iYPL189W
+Plm2 pd iYPL244C
+Plm2 pd iYPR035W
+Plm2 pd iYPR045C
+Plm2 pd iYPR046W
+Plm2 pd iYPR071W
+Plm2 pd iYPR128C
+Plm2 pd iYPR130C
+Plm2 pd iYPR133C
+Pog1 pd iCEN8
+Pog1 pd iYBL007C
+Pog1 pd iYBL022C
+Pog1 pd iYBL099W
+Pog1 pd iYBR017C
+Pog1 pd iYBR019C
+Pog1 pd iYBR020W
+Pog1 pd iYBR039W
+Pog1 pd iYBR096W
+Pog1 pd iYBR134W
+Pog1 pd iYBR160W
+Pog1 pd iYBR247C
+Pog1 pd iYBR272C
+Pog1 pd iYBR284W
+Pog1 pd iYCR035C
+Pog1 pd iYDL083C
+Pog1 pd iYDL217C
+Pog1 pd iYDR010C
+Pog1 pd iYDR104C
+Pog1 pd iYDR131C
+Pog1 pd iYDR200C
+Pog1 pd iYDR250C
+Pog1 pd iYDR255C
+Pog1 pd iYDR272W
+Pog1 pd iYDR473C-0
+Pog1 pd iYDR522C
+Pog1 pd iYFL007W
+Pog1 pd iYFL039C
+Pog1 pd iYGL015C
+Pog1 pd iYGL094C
+Pog1 pd iYGL101W
+Pog1 pd iYGL249W
+Pog1 pd iYGR015C
+Pog1 pd iYGR098C
+Pog1 pd iYGR123C
+Pog1 pd iYGR156W
+Pog1 pd iYGR161C-1
+Pog1 pd iYGR165W
+Pog1 pd iYGR184C
+Pog1 pd iYGR188C
+Pog1 pd iYGR196C
+Pog1 pd iYHL022C
+Pog1 pd iYHR004C
+Pog1 pd iYHR090C
+Pog1 pd iYIL016W
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+Pog1 pd iYIL037C
+Pog1 pd iYIL070C
+Pog1 pd iYIR004W
+Pog1 pd iYIR024C
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+Pog1 pd iYJL081C
+Pog1 pd iYKL048C
+Pog1 pd iYKL057C
+Pog1 pd iYKL090W
+Pog1 pd iYKR010C
+Pog1 pd iYKR024C
+Pog1 pd iYLR106C
+Pog1 pd iYLR392C
+Pog1 pd iYML069W
+Pog1 pd iYNL134C
+Pog1 pd iYNL260C
+Pog1 pd iYOL021C
+Pog1 pd iYOL035C
+Pog1 pd iYOL096C
+Pog1 pd iYOL105C
+Pog1 pd iYOL138C
+Pog1 pd iYOR283W
+Pog1 pd iYPL174C
+Pog1 pd iYPL233W
+Pog1 pd iYPL269W
+Pog1 pd iYPR104C
+Pog1 pd iYPR107C
+Tos4 pd iSNR42
+Tos4 pd itE(UUC)E1
+Tos4 pd itG(GCC)C
+Tos4 pd itH(GUG)H
+Tos4 pd itI(AAU)N2
+Tos4 pd itL(UAA)B2
+Tos4 pd itQ(UUG)E2
+Tos4 pd itR(UCU)G2
+Tos4 pd iYAL039C-1
+Tos4 pd iYAL043C
+Tos4 pd iYAL063C-0
+Tos4 pd iYAR060C
+Tos4 pd iYBL001C
+Tos4 pd iYBL003C
+Tos4 pd iYBL022C
+Tos4 pd iYBL082C
+Tos4 pd iYBL093C
+Tos4 pd iYBR042C
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+Tos8 pd iLSR1
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+Rox1 pd iSNR54
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+Mot3 pd iSNR56
+Abf1 pd iSNR57
+Gcr2 pd iSNR57
+Hal9 pd iSNR57
+Hms1 pd iSNR57
+Rlm1 pd iSNR57
+Smp1 pd iSNR57
+Yap1 pd iSNR57
+Yap6 pd iSNR57
+Cup9 pd iSNR59
+Gcr1 pd iSNR6
+Rfx1 pd iSNR6
+Rox1 pd iSNR6
+Rph1 pd iSNR6
+Arg80 pd iSNR61
+Dal81 pd iSNR61
+Hir2 pd iSNR61
+Leu3 pd iSNR61
+Fhl1 pd iSNR63
+Arg80 pd iSNR67
+Hms1 pd iSNR67
+Leu3 pd iSNR67
+Rtg3 pd iSNR67
+Stp2 pd iSNR67
+Cup9 pd iSNR71
+Hal9 pd iSNR71
+Leu3 pd iSNR71
+Met31 pd iSNR71
+Put3 pd iSNR8
+Reb1 pd iSNR8
+Rap1 pd itA(AGC)G
+Mbp1 pd itD(GUC)J2
+Pho2 pd itE(CUC)D-0
+Ino2 pd itE(CUC)D-0
+Ino4 pd itE(CUC)D-0
+Mot3 pd itE(CUC)D-0
+Swi6 pd itE(CUC)D-1
+Rph1 pd itE(UUC)E3
+Pho2 pd itE(UUC)J
+Hap4 pd itF(GAA)B
+Dig1 pd itF(GAA)D
+Ste12 pd itF(GAA)D
+Pho2 pd itG(GCC)J1
+Mot3 pd itG(GCC)J1
+Cin5 pd itG(UCC)G
+Hir2 pd itH(GUG)E1
+Sum1 pd itH(GUG)E1
+Zap1 pd itH(GUG)E1
+Ste12 pd itH(GUG)G2
+Ixr1 pd itH(GUG)K
+Mac1 pd itI(AAU)N2
+Met4 pd itI(AAU)N2
+Abf1 pd itK(CUU)D1
+Mot3 pd itK(CUU)J
+Swi4 pd itK(UUU)D
+Ste12 pd itL(CAA)A
+Ste12 pd itL(CAA)D
+Rlm1 pd itL(CAA)G1
+Skn7 pd itL(GAG)G
+Rph1 pd itL(UAA)B1
+Dig1 pd itL(UAA)K
+Ste12 pd itL(UAA)K
+Dig1 pd itM(CAU)D
+Cin5 pd itM(CAU)J1
+Put3 pd itM(CAU)O2
+Gcn4 pd itM(CAU)P
+Stp2 pd itN(GUU)F
+Dig1 pd itN(GUU)N1
+Pdr1 pd itP(UGG)O1
+Smp1 pd itP(UGG)O1
+Yap5 pd itP(UGG)O1
+Fkh2 pd itP(UGG)O2
+Mata1 pd itQ(CUG)M
+Stp2 pd itQ(CUG)M
+Dig1 pd itQ(UUG)D2
+Ste12 pd itQ(UUG)D2
+Dig1 pd itQ(UUG)E1
+Reb1 pd itQ(UUG)E2
+Gcr1 pd itR(ACG)K
+Fhl1 pd itR(CCG)L
+Rap1 pd itR(CCG)L
+Smp1 pd itS(AGA)D3
+Mot3 pd itS(UGA)P
+Rme1 pd itT(AGU)I2
+Dal81 pd itT(AGU)J
+Dig1 pd itT(AGU)J
+Fzf1 pd itT(AGU)J
+Gcr2 pd itT(AGU)J
+Hap2 pd itT(AGU)J
+Rcs1 pd itT(AGU)J
+Rme1 pd itT(AGU)J
+Mac1 pd itT(UGU)G2
+Rox1 pd itT(UGU)G2
+Sum1 pd itT(UGU)G2
+Hms1 pd itV(AAC)E1
+Dig1 pd itV(AAC)K2
+Ste12 pd itV(AAC)K2
+Pho2 pd itV(CAC)D
+Pho2 pd itV(UAC)D
+Dig1 pd itW(CCA)G1
+Rox1 pd itW(CCA)G1
+Hir1 pd itW(CCA)J
+Rfx1 pd itW(CCA)J
+Rox1 pd itW(CCA)J
+Rtg1 pd itW(CCA)K-1
+Rtg3 pd itW(CCA)K-1
+Dig1 pd itW(CCA)M
+Swi4 pd itY(GUA)O
+Yfl044c pd iYAL010C
+Mig1 pd iYAL012W
+Met31 pd iYAL013W
+Met4 pd iYAL013W
+Rox1 pd iYAL016W
+Fzf1 pd iYAL018C
+Ime4 pd iYAL018C
+Nrg1 pd iYAL018C
+Rcs1 pd iYAL018C
+Swi5 pd iYAL018C
+Adr1 pd iYAL022C
+Fzf1 pd iYAL022C
+Ime4 pd iYAL022C
+Nrg1 pd iYAL022C
+Pdr1 pd iYAL022C
+Sfp1 pd iYAL022C
+Smp1 pd iYAL022C
+Yfl044c pd iYAL022C
+Abf1 pd iYAL023C
+Sum1 pd iYAL023C
+Fkh2 pd iYAL024C
+Cbf1 pd iYAL026C
+Fkh2 pd iYAL029C
+Reb1 pd iYAL031C
+Rap1 pd iYAL034C
+Cin5 pd iYAL038W
+Abf1 pd iYAL042W
+Abf1 pd iYAL043C
+Bas1 pd iYAL044C
+Bas1 pd iYAL045C
+Abf1 pd iYAL054C
+Cin5 pd iYAL063C-0
+Phd1 pd iYAL063C-0
+Yap6 pd iYAL063C-0
+Ace2 pd iYAL063C-2
+Mbp1 pd iYAL063C-2
+Ndd1 pd iYAL063C-2
+Skn7 pd iYAL063C-2
+Swi5 pd iYAL063C-2
+Gts1 pd iYAL064C-A-4
+Rim101 pd iYAL064C-A-4
+Ixr1 pd iYAL064C-A-5
+Nrg1 pd iYAL064C-A-5
+Cin5 pd iYALWdelta1
+Mac1 pd iYALWdelta1
+Rox1 pd iYALWdelta1
+Yap6 pd iYALWdelta1
+Dot6 pd iYAR007C
+Mbp1 pd iYAR007C
+Dig1 pd iYAR009C
+Mac1 pd iYAR009C
+Rox1 pd iYAR009C
+Fkh2 pd iYAR018C
+Mcm1 pd iYAR018C
+Ndd1 pd iYAR018C
+Slf1 pd iYAR023C
+Phd1 pd iYAR033W
+Phd1 pd iYAR044W-1
+Sok2 pd iYAR044W-1
+Yjl206c pd iYAR044W-2
+Rph1 pd iYAR044W-3
+Dig1 pd iYAR047C-1
+Gcn4 pd iYAR047C-1
+Rme1 pd iYAR047C-1
+Skn7 pd iYAR047C-1
+Gln3 pd iYAR053W
+Hap3 pd iYAR053W
+Gts1 pd iYARCdelta8-2
+Rph1 pd iYARCdelta8-3
+Hap4 pd iYBL001C
+Smp1 pd iYBL001C
+Hal9 pd iYBL002W
+Hir2 pd iYBL004W
+Abf1 pd iYBL007C
+Cad1 pd iYBL009W
+Reb1 pd iYBL014C
+Dig1 pd iYBL017C
+Yfl044c pd iYBL020W
+Rap1 pd iYBL022C
+Mbp1 pd iYBL023C
+Phd1 pd iYBL026W
+Yap6 pd iYBL028C
+Arg81 pd iYBL029W
+Hal9 pd iYBL029W
+Cin5 pd iYBL030C-0
+Phd1 pd iYBL030C-0
+Yap6 pd iYBL030C-0
+Cin5 pd iYBL030C-1
+Cup9 pd iYBL030C-1
+Ixr1 pd iYBL030C-1
+Nrg1 pd iYBL030C-1
+Rox1 pd iYBL030C-1
+Skn7 pd iYBL030C-1
+Sok2 pd iYBL030C-1
+Yap6 pd iYBL030C-1
+Fkh2 pd iYBL033C
+Hsf1 pd iYBL033C
+Smp1 pd iYBL038W
+Abf1 pd iYBL039C
+Msn1 pd iYBL042C
+Yap5 pd iYBL043W
+Cin5 pd iYBL044W
+Cup9 pd iYBL044W
+Hap4 pd iYBL045C
+Crz1 pd iYBL057C
+Reb1 pd iYBL059W
+Fhl1 pd iYBL072C
+Mss11 pd iYBL073W
+Rgt1 pd iYBL073W
+Gcn4 pd iYBL076C
+Rtg3 pd iYBL079W
+Abf1 pd iYBL080C
+Fkh1 pd iYBL082C
+Fhl1 pd iYBL087C
+Ixr1 pd iYBL087C
+Mss11 pd iYBL087C
+Pdr1 pd iYBL087C
+Rap1 pd iYBL087C
+Fhl1 pd iYBL093C
+Fkh2 pd iYBL098W
+Rtg1 pd iYBL098W
+Msn4 pd iYBL108W
+Phd1 pd iYBL108W
+Swi5 pd iYBL108W
+Gal4 pd iYBL109W-0
+Gat3 pd iYBL109W-0
+Hap4 pd iYBL109W-0
+Pdr1 pd iYBL109W-0
+Phd1 pd iYBL109W-0
+Rgm1 pd iYBL109W-0
+Yap5 pd iYBL109W-0
+Zap1 pd iYBL109W-0
+Swi5 pd iYBL109W-1
+Gal4 pd iYBL111C
+Gat3 pd iYBL111C
+Pdr1 pd iYBL111C
+Rgm1 pd iYBL111C
+Yap5 pd iYBL111C
+Haa1 pd iYBLWdelta3
+Mot3 pd iYBLWtau1
+Dal82 pd iYBR002C
+Cin5 pd iYBR007C-0
+Ixr1 pd iYBR007C-0
+Cin5 pd iYBR008C
+Hir2 pd iYBR009C
+Abf1 pd iYBR011C
+Met4 pd iYBR011C
+Yfl044c pd iYBR013C
+Gal4 pd iYBR017C
+Sum1 pd iYBR017C
+Gal4 pd iYBR020W
+Hap2 pd iYBR025C
+Abf1 pd iYBR029C
+Fkh1 pd iYBR029C
+Ino4 pd iYBR029C
+Rph1 pd iYBR032W
+Fkh2 pd iYBR037C
+Ndd1 pd iYBR037C
+Hap3 pd iYBR038W
+Hap4 pd iYBR038W
+Pdr1 pd iYBR039W
+Rcs1 pd iYBR039W
+Stp2 pd iYBR039W
+Rfx1 pd iYBR042C
+Gcn4 pd iYBR043C
+Pho2 pd iYBR044C
+Msn1 pd iYBR047W
+Cbf1 pd iYBR049C
+Hsf1 pd iYBR049C
+Hir2 pd iYBR053C-0
+Cin5 pd iYBR053C-1
+Gcr1 pd iYBR056W
+Ime4 pd iYBR057C
+Pdr1 pd iYBR057C
+Rlm1 pd iYBR057C
+Yap5 pd iYBR057C
+Gal4 pd iYBR060C-0
+Hir2 pd iYBR060C-1
+Msn2 pd iYBR060C-1
+Skn7 pd iYBR066C
+Dal81 pd iYBR069C
+Cin5 pd iYBR070C
+Mbp1 pd iYBR070C
+Swi4 pd iYBR070C
+Msn4 pd iYBR073W
+Sum1 pd iYBR075W
+Cin5 pd iYBR076W
+Swi4 pd iYBR076W
+Abf1 pd iYBR077C
+Fkh2 pd iYBR077C
+Mbp1 pd iYBR077C
+Ndd1 pd iYBR077C
+Swi4 pd iYBR077C
+Swi6 pd iYBR077C
+Abf1 pd iYBR080C
+Stp2 pd iYBR080C
+Hsf1 pd iYBR082C-0
+Dig1 pd iYBR082C-1
+Fhl1 pd iYBR084C-A
+Cbf1 pd iYBR090C
+Fkh2 pd iYBR092C
+Ndd1 pd iYBR092C
+Hir1 pd iYBR095C
+Hir1 pd iYBR096W
+Mot3 pd iYBR096W
+Arg81 pd iYBR100W
+Abf1 pd iYBR101C
+Cad1 pd iYBR102C
+Ime4 pd iYBR102C
+Yap5 pd iYBR102C
+Fkh1 pd iYBR103W
+Rtg1 pd iYBR108W
+Fkh1 pd iYBR109C
+Rfx1 pd iYBR109C
+Gcn4 pd iYBR115C
+Fhl1 pd iYBR117C
+Gcn4 pd iYBR118W
+Mig1 pd iYBR121C
+Fhl1 pd iYBR126C
+Fkh2 pd iYBR134W
+Hms1 pd iYBR134W
+Fkh1 pd iYBR138C
+Fkh2 pd iYBR138C
+Ndd1 pd iYBR138C
+Abf1 pd iYBR145W
+Sum1 pd iYBR147W
+Dot6 pd iYBR156C
+Cin5 pd iYBR157C-0
+Phd1 pd iYBR157C-0
+Ace2 pd iYBR157C-1
+Phd1 pd iYBR157C-1
+Swi5 pd iYBR157C-1
+Mot3 pd iYBR158W
+Phd1 pd iYBR158W
+Pho2 pd iYBR160W
+Swi4 pd iYBR162C
+Fkh1 pd iYBR162W-A
+Hir1 pd iYBR163W
+Hap5 pd iYBR167C
+Sum1 pd iYBR179C
+Fhl1 pd iYBR181C
+Rap1 pd iYBR181C
+Fhl1 pd iYBR188C
+Gal4 pd iYBR188C
+Rap1 pd iYBR188C
+Fhl1 pd iYBR189W
+Rap1 pd iYBR189W
+Stp2 pd iYBR192W
+Dal81 pd iYBR195C
+Fzf1 pd iYBR203W
+Gcr2 pd iYBR203W
+Pdr1 pd iYBR203W
+Yfl044c pd iYBR207W
+Abf1 pd iYBR211C
+Hap3 pd iYBR216C
+Cbf1 pd iYBR222C
+Ace2 pd iYBR229C
+Yjl206c pd iYBR234C
+Reb1 pd iYBR236C
+Pho2 pd iYBR238C
+Hap2 pd iYBR243C
+Cbf1 pd iYBR249C
+Gcn4 pd iYBR249C
+Mot3 pd iYBR253W
+Zap1 pd iYBR254C
+Zms1 pd iYBR264C
+Sip4 pd iYBR267W
+Hal9 pd iYBR274W
+Hap5 pd iYBR275C
+Mot3 pd iYBR275C
+Uga3 pd iYBR281C
+Abf1 pd iYBR283C
+Smp1 pd iYBR294W
+Hap3 pd iYBRCdelta18
+Rtg1 pd iYBRWdelta16
+Abf1 pd iYCL011C
+Cin5 pd iYCL025C
+Stp1 pd iYCL025C
+Cad1 pd iYCL026C-A
+Ste12 pd iYCL026C-A
+Abf1 pd iYCL031C
+Pho4 pd iYCL035C
+Phd1 pd iYCL046W
+Cin5 pd iYCL047C
+Sum1 pd iYCL049C
+Hsf1 pd iYCL050C
+Ace2 pd iYCL055W-0
+Fkh1 pd iYCL055W-0
+Fkh2 pd iYCL055W-0
+Mbp1 pd iYCL055W-0
+Ndd1 pd iYCL055W-0
+Phd1 pd iYCL055W-0
+Ste12 pd iYCL055W-0
+Swi4 pd iYCL055W-0
+Dig1 pd iYCL056C
+Ste12 pd iYCL056C
+Yfl044c pd iYCL063W
+Fkh1 pd iYCL064C
+Gal4 pd iYCL065W-0
+Gat3 pd iYCL065W-0
+Hap4 pd iYCL065W-0
+Hir1 pd iYCL065W-0
+Hir2 pd iYCL065W-0
+Hms1 pd iYCL065W-0
+Pdr1 pd iYCL065W-0
+Rcs1 pd iYCL065W-0
+Smp1 pd iYCL065W-0
+Yap5 pd iYCL065W-0
+Zap1 pd iYCL065W-0
+Gal4 pd iYCL065W-1
+Hir2 pd iYCL065W-1
+Pdr1 pd iYCL065W-1
+Rph1 pd iYCL065W-1
+Rtg3 pd iYCL065W-1
+Aro80 pd iYCL067C
+Gal4 pd iYCL067C
+Gat3 pd iYCL067C
+Hap4 pd iYCL067C
+Yap5 pd iYCL067C
+Fkh1 pd iYCL069W
+Rme1 pd iYCL069W
+Gat3 pd iYCL074W
+Slf1 pd iYCL074W
+Sip4 pd iYCL074W
+Gat3 pd iYCL075W
+Dal81 pd iYCLWdelta5
+Ste12 pd iYCR017C
+Arg80 pd iYCR018C-A
+Bas1 pd iYCR018C-A
+Hms1 pd iYCR018C-A
+Leu3 pd iYCR018C-A
+Rlm1 pd iYCR018C-A
+Rtg1 pd iYCR018C-A
+Rtg3 pd iYCR018C-A
+Ste12 pd iYCR018C-A
+Yfl044c pd iYCR020C-A
+Bas1 pd iYCR020W-B
+Rtg3 pd iYCR020W-B
+Yfl044c pd iYCR021C
+Gcr2 pd iYCR024C
+Ndd1 pd iYCR024C-A
+Rap1 pd iYCR024C-A
+Mac1 pd iYCR025C
+Rap1 pd iYCR025C
+Hap3 pd iYCR028C
+Gat3 pd iYCR039C
+Hap4 pd iYCR039C
+Mata1 pd iYCR039C
+Stp2 pd iYCR039C
+Yap5 pd iYCR039C
+Zap1 pd iYCR039C
+Yfl044c pd iYCR044C
+Abf1 pd iYCR052W
+Mbp1 pd iYCR063W
+Phd1 pd iYCR063W
+Swi4 pd iYCR063W
+Pho4 pd iYCR065W
+Smp1 pd iYCR073C
+Fkh1 pd iYCR075C
+Abf1 pd iYCR081W
+Dig1 pd iYCR088W
+Ste12 pd iYCR088W
+Fkh1 pd iYCR092C
+Fzf1 pd iYCR094W
+Pho4 pd iYCR095C-1
+Stp1 pd iYCR095C-1
+Gat3 pd iYCR096C
+Rtg3 pd iYCR096C
+Gat3 pd iYCR097W
+Phd1 pd iYCR098C-0
+Phd1 pd iYCR100C
+Hal9 pd iYCR102C
+Crz1 pd iYCR104W
+Gal4 pd iYCR104W
+Gln3 pd iYCR104W
+Hap4 pd iYCR104W
+Ime4 pd iYCR104W
+Pdr1 pd iYCR104W
+Yap5 pd iYCR104W
+Zap1 pd iYCR104W
+Crz1 pd iYCR105W
+Gal4 pd iYCR105W
+Crz1 pd iYCR106W
+Gal4 pd iYCR106W
+Yap5 pd iYCR106W
+Rtg3 pd iYCRWdelta12
+Swi5 pd iYCRWdelta8
+Arg81 pd iYDL001W
+Aro80 pd iYDL001W
+Bas1 pd iYDL001W
+Crz1 pd iYDL001W
+Hap5 pd iYDL001W
+Hir1 pd iYDL001W
+Hir2 pd iYDL001W
+Ime4 pd iYDL001W
+Leu3 pd iYDL001W
+Pdr1 pd iYDL001W
+Sum1 pd iYDL001W
+Cin5 pd iYDL003W
+Mbp1 pd iYDL004W
+Abf1 pd iYDL012C
+Fkh2 pd iYDL018C
+Mbp1 pd iYDL018C
+Swi6 pd iYDL018C
+Hsf1 pd iYDL020C
+Yap1 pd iYDL020C
+Sum1 pd iYDL028C
+Skn7 pd iYDL031W
+Abf1 pd iYDL034W
+Swi5 pd iYDL034W
+Azf1 pd iYDL037C-0
+Cin5 pd iYDL037C-0
+Yap6 pd iYDL037C-0
+Cin5 pd iYDL037C-1
+Yap6 pd iYDL037C-1
+Dal82 pd iYDL038C
+Mcm1 pd iYDL044C
+Hms1 pd iYDL056W
+Pho2 pd iYDL059C
+Met4 pd iYDL059C
+Yap5 pd iYDL060W
+Fhl1 pd iYDL061C
+Hap4 pd iYDL067C
+Arg81 pd iYDL070W
+Hal9 pd iYDL070W
+Hir2 pd iYDL070W
+Cup9 pd iYDL075W
+Fhl1 pd iYDL075W
+Gcr2 pd iYDL075W
+Hal9 pd iYDL075W
+Hir2 pd iYDL075W
+Hms1 pd iYDL075W
+Leu3 pd iYDL075W
+Zap1 pd iYDL075W
+Fhl1 pd iYDL076C
+Rap1 pd iYDL076C
+Fhl1 pd iYDL083C
+Gat3 pd iYDL083C
+Pdr1 pd iYDL083C
+Yap5 pd iYDL083C
+Hal9 pd iYDL084W
+Hap2 pd iYDL084W
+Fkh1 pd iYDL085W
+Gts1 pd iYDL098C
+Mbp1 pd iYDL101C
+Swi6 pd iYDL101C
+Gts1 pd iYDL102W
+Abf1 pd iYDL106C
+Stp2 pd iYDL112W
+Gat3 pd iYDL115C
+Yap5 pd iYDL115C
+Hms1 pd iYDL116W
+Stp1 pd iYDL116W
+Stp2 pd iYDL116W
+Abf1 pd iYDL117W
+Abf1 pd iYDL123W
+Dig1 pd iYDL128W
+Ste12 pd iYDL128W
+Swi4 pd iYDL128W
+Swi6 pd iYDL128W
+Cin5 pd iYDL130W
+Rfx1 pd iYDL130W
+Fhl1 pd iYDL130W-A
+Abf1 pd iYDL131W
+Fhl1 pd iYDL133C-A
+Rap1 pd iYDL133C-A
+Fhl1 pd iYDL137W
+Rap1 pd iYDL137W
+Rgt1 pd iYDL138W
+Swi6 pd iYDL142C
+Hir2 pd iYDL143W
+Abf1 pd iYDL145C
+Stp1 pd iYDL147W
+Pdr1 pd iYDL148C
+Arg80 pd iYDL149W
+Cup9 pd iYDL149W
+Hal9 pd iYDL149W
+Hap3 pd iYDL149W
+Mcm1 pd iYDL149W
+Yfl044c pd iYDL149W
+Zap1 pd iYDL149W
+Crz1 pd iYDL156W
+Abf1 pd iYDL160C
+Cin5 pd iYDL169C
+Swi5 pd iYDL174C
+Arg80 pd iYDL176W
+Hap5 pd iYDL176W
+Rph1 pd iYDL176W
+Mata1 pd iYDL179W
+Hap4 pd iYDL182W
+Dal81 pd iYDL183C-1
+Gcn4 pd iYDL183C-1
+Fhl1 pd iYDL184C
+Rap1 pd iYDL184C
+Gcr1 pd iYDL185W
+Rox1 pd iYDL185W
+Rap1 pd iYDL188C
+Reb1 pd iYDL188C
+Sum1 pd iYDL188C
+Stp2 pd iYDL189W
+Abf1 pd iYDL190C
+Met31 pd iYDL191W
+Fhl1 pd iYDL192W
+Rap1 pd iYDL192W
+Gcr2 pd iYDL193W
+Abf1 pd iYDL194W
+Gcn4 pd iYDL198C
+Rph1 pd iYDL206W
+Abf1 pd iYDL209C
+Reb1 pd iYDL213C
+Phd1 pd iYDL214C
+Swi5 pd iYDL223C
+Yap5 pd iYDL224C
+Pho2 pd iYDL226C
+Reb1 pd iYDL226C
+Swi5 pd iYDL226C
+Swi6 pd iYDL227C-0
+Swi4 pd iYDL227C-1
+Swi5 pd iYDL227C-1
+Swi6 pd iYDL227C-1
+Swi4 pd iYDL227C-2
+Leu3 pd iYDL228C
+Rfx1 pd iYDL230W
+Cad1 pd iYDL239C
+Phd1 pd iYDL245C-0
+Rlm1 pd iYDL245C-0
+Rox1 pd iYDL245C-0
+Sok2 pd iYDL245C-0
+Yap6 pd iYDL245C-0
+Cup9 pd iYDL246C-0
+Nrg1 pd iYDL246C-0
+Rlm1 pd iYDL246C-0
+Rox1 pd iYDL246C-0
+Yap6 pd iYDL246C-0
+Rlm1 pd iYDL247W
+Ixr1 pd iYDL248W-1
+Fkh1 pd iYDR002W
+Gcr2 pd iYDR002W
+Fzf1 pd iYDR004W
+Hsf1 pd iYDR010C
+Yap1 pd iYDR010C
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+Yap5 pd iYJL188C
+Fhl1 pd iYJL190C
+Gat3 pd iYJL190C
+Rap1 pd iYJL190C
+Yap5 pd iYJL190C
+Fhl1 pd iYJL192C
+Met31 pd iYJL192C
+Rap1 pd iYJL192C
+Swi4 pd iYJL196C
+Gcn4 pd iYJL200C
+Pho4 pd iYJL200C
+Gcr2 pd iYJL204C
+Thi2 pd iYJL204C
+Rfx1 pd iYJL209W
+Yfl044c pd iYJL209W
+Cbf1 pd iYJL210W
+Dal81 pd iYJL212C
+Met31 pd iYJL212C
+Met4 pd iYJL212C
+Nrg1 pd iYJL216C
+Sok2 pd iYJL216C
+Yap6 pd iYJL216C
+Phd1 pd iYJL218W
+Yap6 pd iYJL218W
+Phd1 pd iYJL219W
+Cin5 pd iYJL220W
+Nrg1 pd iYJL220W
+Phd1 pd iYJL220W
+Yap6 pd iYJL220W
+Gat3 pd iYJL225C-0
+Yap5 pd iYJL225C-0
+Gal4 pd iYJL225C-1
+Gat3 pd iYJL225C-1
+Hap4 pd iYJL225C-1
+Pdr1 pd iYJL225C-1
+Rgm1 pd iYJL225C-1
+Smp1 pd iYJL225C-1
+Yap5 pd iYJL225C-1
+Ste12 pd iYJLCdelta3
+Arg80 pd iYJLWdelta9
+Fzf1 pd iYJLWdelta9
+Hms1 pd iYJLWdelta9
+Mcm1 pd iYJLWdelta9
+Yap1 pd iYJLWdelta9
+Fzf1 pd iYJLWtau4
+Gcr2 pd iYJLWtau4
+Nrg1 pd iYJLWtau4
+Zap1 pd iYJLWtau4
+Cin5 pd iYJR003C
+Pho4 pd iYJR004C
+Hir1 pd iYJR006W
+Cin5 pd iYJR011C
+Stp1 pd iYJR011C
+Stp2 pd iYJR015W
+Gcn4 pd iYJR025C
+Sum1 pd iYJR025C
+Mbp1 pd iYJR030C
+Swi6 pd iYJR030C
+Mss11 pd iYJR041C
+Ace2 pd iYJR044C
+Cad1 pd iYJR044C
+Fzf1 pd iYJR044C
+Gcr2 pd iYJR044C
+Ime4 pd iYJR044C
+Mbp1 pd iYJR044C
+Ndd1 pd iYJR044C
+Pdr1 pd iYJR044C
+Smp1 pd iYJR044C
+Swi5 pd iYJR044C
+Yap5 pd iYJR044C
+Ace2 pd iYJR046W
+Mac1 pd iYJR049C
+Swi4 pd iYJR053W
+Swi6 pd iYJR053W
+Rap1 pd iYJR058C
+Cin5 pd iYJR060W
+Gat3 pd iYJR067C
+Gat3 pd iYJR068W
+Hap4 pd iYJR077C
+Skn7 pd iYJR077C
+Sum1 pd iYJR077C
+Hap3 pd iYJR082C
+Reb1 pd iYJR090C
+Fkh1 pd iYJR091C
+Fkh2 pd iYJR091C
+Mcm1 pd iYJR091C
+Ndd1 pd iYJR091C
+Cin5 pd iYJR094C-0
+Nrg1 pd iYJR094C-0
+Phd1 pd iYJR094C-0
+Yap6 pd iYJR094C-0
+Yap6 pd iYJR094C-1
+Pho4 pd iYJR098C
+Reb1 pd iYJR098C
+Cup9 pd iYJR100C
+Ixr1 pd iYJR100C
+Mac1 pd iYJR100C
+Met31 pd iYJR100C
+Reb1 pd iYJR100C
+Rox1 pd iYJR100C
+Rtg1 pd iYJR100C
+Cin5 pd iYJR102C
+Abf1 pd iYJR104C
+Ino4 pd iYJR104C
+Fkh2 pd iYJR109C
+Gcn4 pd iYJR109C
+Yap1 pd iYJR109C
+Gcn4 pd iYJR111C
+Abf1 pd iYJR115W
+Hap4 pd iYJR120W
+Fhl1 pd iYJR122W
+Fkh2 pd iYJR128W
+Ndd1 pd iYJR128W
+Phd1 pd iYJR128W
+Cin5 pd iYJR131W
+Ime4 pd iYJR135C
+Abf1 pd iYJR137C
+Met31 pd iYJR137C
+Hms1 pd iYJR139C
+Ace2 pd iYJR144W
+Cha4 pd iYJR144W
+Fzf1 pd iYJR144W
+Gal4 pd iYJR144W
+Ime4 pd iYJR144W
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+Sfp1 pd iYJR144W
+Swi5 pd iYJR144W
+Ace2 pd iYJR145C
+Cin5 pd iYJR145C
+Fhl1 pd iYJR145C
+Yap6 pd iYJR145C
+Skn7 pd iYJR147W
+Swi4 pd iYJR147W
+Ace2 pd iYJR148W
+Pho4 pd iYJR150C-0
+Nrg1 pd iYJR157W-0
+Phd1 pd iYJR157W-0
+Cup9 pd iYJR157W-1
+Phd1 pd iYJR157W-1
+Rlm1 pd iYJR157W-1
+Rox1 pd iYJR157W-1
+Sok2 pd iYJR157W-1
+Yap6 pd iYJR157W-1
+Phd1 pd iYJR158W-0
+Cup9 pd iYJR158W-1
+Mot3 pd iYJR158W-1
+Phd1 pd iYJR158W-1
+Rox1 pd iYJR158W-1
+Sok2 pd iYJR158W-1
+Yap6 pd iYJR158W-1
+Rlm1 pd iYJR159W
+Ixr1 pd iYJR160C-0
+Gat3 pd iYJR161C
+Rgm1 pd iYJR161C
+Yap5 pd iYJR161C
+Gat3 pd iYKL001C
+Abf1 pd iYKL005C
+Fhl1 pd iYKL006C-A
+Rap1 pd iYKL006C-A
+Abf1 pd iYKL008C
+Cbf1 pd iYKL008C
+Mss11 pd iYKL008C
+Swi4 pd iYKL008C
+Abf1 pd iYKL014C
+Abf1 pd iYKL016C
+Hap4 pd iYKL016C
+Abf1 pd iYKL029C
+Dig1 pd iYKL033W
+Ste12 pd iYKL033W
+Rph1 pd iYKL033W-A
+Cad1 pd iYKL040C
+Cin5 pd iYKL045W
+Ixr1 pd iYKL045W
+Nrg1 pd iYKL045W
+Sok2 pd iYKL045W
+Yap6 pd iYKL045W
+Yap5 pd iYKL049C
+Hsf1 pd iYKL052C
+Mcm1 pd iYKL059C
+Reb1 pd iYKL059C
+Abf1 pd iYKL060C
+Ixr1 pd iYKL061W
+Phd1 pd iYKL061W
+Phd1 pd iYKL063C-0
+Hal9 pd iYKL063C-1
+Phd1 pd iYKL063C-1
+Fkh2 pd iYKL066W
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+Arg81 pd iYKL073W
+Aro80 pd iYKL073W
+Yjl206c pd iYKL073W
+Arg80 pd iYKL077W
+Reb1 pd iYKL082C
+Ace2 pd iYKL085W
+Mbp1 pd iYKL085W
+Ime4 pd iYKL086W
+Cad1 pd iYKL087C
+Dig1 pd iYKL096W
+Ste12 pd iYKL096W
+Fkh2 pd iYKL097C
+Mbp1 pd iYKL097C
+Ndd1 pd iYKL097C
+Skn7 pd iYKL097C
+Swi4 pd iYKL097C
+Smp1 pd iYKL097W-A-1
+Ste12 pd iYKL097W-A-1
+Swi4 pd iYKL097W-A-1
+Phd1 pd iYKL098W
+Cad1 pd iYKL102C
+Cad1 pd iYKL103C
+Cin5 pd iYKL103C
+Swi4 pd iYKL103C
+Reb1 pd iYKL104C
+Pho2 pd iYKL107W
+Cin5 pd iYKL108W
+Mata1 pd iYKL108W
+Cin5 pd iYKL110C-0
+Hir2 pd iYKL110C-0
+Phd1 pd iYKL110C-0
+Yap6 pd iYKL110C-0
+Phd1 pd iYKL110C-1
+Mbp1 pd iYKL113C
+Swi6 pd iYKL113C
+Dal81 pd iYKL120W
+Leu3 pd iYKL120W
+Leu3 pd iYKL121W
+Cin5 pd iYKL131W
+Abf1 pd iYKL135C
+Fzf1 pd iYKL139W
+Gln3 pd iYKL139W
+Pho4 pd iYKL139W
+Mbp1 pd iYKL143W
+Skn7 pd iYKL143W
+Abf1 pd iYKL144C
+Reb1 pd iYKL148C
+Ace2 pd iYKL151C
+Hsf1 pd iYKL152C
+Cad1 pd iYKL155C
+Fhl1 pd iYKL157W
+Fkh1 pd iYKL158W
+Swi6 pd iYKL161C-0
+Nrg1 pd iYKL162C-A-1
+Phd1 pd iYKL162C-A-1
+Sok2 pd iYKL162C-A-1
+Swi5 pd iYKL163W
+Mcm1 pd iYKL164C-0
+Smp1 pd iYKL164C-0
+Swi5 pd iYKL164C-0
+Mcm1 pd iYKL164C-1
+Swi5 pd iYKL164C-1
+Abf1 pd iYKL167C
+Ixr1 pd iYKL167C
+Abf1 pd iYKL173W
+Sum1 pd iYKL177W
+Abf1 pd iYKL179C
+Nrg1 pd iYKL179C
+Zap1 pd iYKL179C
+Fhl1 pd iYKL181W
+Rap1 pd iYKL181W
+Cin5 pd iYKL183W
+Rap1 pd iYKL183W
+Smp1 pd iYKL186C
+Abf1 pd iYKL191W
+Cbf1 pd iYKL192C
+Abf1 pd iYKL196C
+Zms1 pd iYKL197C
+Uga3 pd iYKL201C
+Hir1 pd iYKL203C
+Crz1 pd iYKL211C
+Swi6 pd iYKL214C
+Bas1 pd iYKL218C-1
+Bas1 pd iYKL218C-2
+Pho2 pd iYKL220C-1
+Gts1 pd iYKL220C-1
+Mcm1 pd iYKL220C-1
+Phd1 pd iYKL221W-0
+Swi4 pd iYKL221W-0
+Swi6 pd iYKL221W-0
+Gal4 pd iYKL225W
+Gat3 pd iYKL225W
+Pdr1 pd iYKL225W
+Phd1 pd iYKL225W
+Yap5 pd iYKL225W
+Msn1 pd iYKLCdelta2
+Fzf1 pd iYKLCdelta5
+Gcr1 pd iYKLCdelta5
+Rox1 pd iYKLCdelta5
+Rph1 pd iYKLCdelta5
+Hms1 pd iYKLCdelta6
+Rtg3 pd iYKLCdelta6
+Bas1 pd iYKR010C
+Swi4 pd iYKR011C
+Swi6 pd iYKR011C
+Uga3 pd iYKR014C
+Rcs1 pd iYKR026C
+Rfx1 pd iYKR026C
+Abf1 pd iYKR029C
+Sum1 pd iYKR034W
+Dal81 pd iYKR038C
+Msn1 pd iYKR038C
+Ace2 pd iYKR041W
+Dal81 pd iYKR041W
+Fkh2 pd iYKR041W
+Mcm1 pd iYKR041W
+Ndd1 pd iYKR041W
+Skn7 pd iYKR041W
+Swi4 pd iYKR041W
+Ndd1 pd iYKR043C
+Skn7 pd iYKR043C
+Skn7 pd iYKR045C
+Cad1 pd iYKR052C
+Yap1 pd iYKR052C
+Fkh1 pd iYKR054C
+Abf1 pd iYKR055W
+Fhl1 pd iYKR056W
+Abf1 pd iYKR058W
+Fkh1 pd iYKR058W
+Hms1 pd iYKR062W
+Cin5 pd iYKR066C
+Yjl206c pd iYKR066C
+Reb1 pd iYKR068C
+Cad1 pd iYKR071C
+Yap1 pd iYKR071C
+Phd1 pd iYKR074W
+Ixr1 pd iYKR075C-0
+Leu3 pd iYKR078W
+Bas1 pd iYKR079C
+Bas1 pd iYKR080W
+Abf1 pd iYKR081C
+Pho4 pd iYKR084C
+Fhl1 pd iYKR086W
+Rlm1 pd iYKR090W
+Ste12 pd iYKR090W
+Skn7 pd iYKR092C-1
+Swi4 pd iYKR092C-1
+Hal9 pd iYKR093W
+Fhl1 pd iYKR094C
+Sip4 pd iYKR096W
+Skn7 pd iYKR096W
+Rtg1 pd iYKR098C
+Nrg1 pd iYKR101W-2
+Phd1 pd iYKR101W-2
+Smp1 pd iYKR101W-2
+Yap6 pd iYKR101W-2
+Pho4 pd iYKR102W-1
+Rlm1 pd iYKR102W-2
+Swi6 pd iYKR102W-2
+Smp1 pd iYKR105C
+Gat3 pd iYKR106W-0
+Gat3 pd iYKR106W-1
+Pdr1 pd iYKR106W-1
+Cin5 pd iYKRCdelta11
+Arg80 pd iYLL001W
+Hap4 pd iYLL001W
+Hir1 pd iYLL001W
+Hms1 pd iYLL001W
+Sum1 pd iYLL005C
+Cin5 pd iYLL007C
+Cbf1 pd iYLL009C
+Cbf1 pd iYLL010C
+Abf1 pd iYLL012W
+Skn7 pd iYLL018C
+Skn7 pd iYLL018C-A
+Skn7 pd iYLL019C
+Fkh1 pd iYLL026W
+Hap3 pd iYLL026W
+Hap5 pd iYLL026W
+Hap2 pd iYLL028W
+Hap3 pd iYLL028W
+Hap5 pd iYLL028W
+Gcr2 pd iYLL032C
+Abf1 pd iYLL034C
+Ixr1 pd iYLL034C
+Reb1 pd iYLL034C
+Rap1 pd iYLL039C
+Reb1 pd iYLL040C
+Ixr1 pd iYLL041C
+Fhl1 pd iYLL044W
+Cin5 pd iYLL052C
+Yap6 pd iYLL052C
+Cin5 pd iYLL054C
+Cbf1 pd iYLL056C-0
+Cbf1 pd iYLL056C-1
+Cad1 pd iYLL060C
+Yap1 pd iYLL060C
+Cin5 pd iYLL062C
+Phd1 pd iYLL063C
+Gal4 pd iYLL065W
+Gat3 pd iYLL065W
+Phd1 pd iYLL065W
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+Yap5 pd iYLL065W
+Yap5 pd iYLL066C-0
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+Gat3 pd iYLL066C-1
+Pdr1 pd iYLL066C-1
+Rgm1 pd iYLL066C-1
+Smp1 pd iYLL066C-1
+Yap5 pd iYLL066C-1
+Yap5 pd iYLL067C-0
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+Gat3 pd iYLL067C-1
+Hap4 pd iYLL067C-1
+Msn4 pd iYLL067C-1
+Pdr1 pd iYLL067C-1
+Rap1 pd iYLL067C-1
+Rgm1 pd iYLL067C-1
+Smp1 pd iYLL067C-1
+Swi5 pd iYLL067C-1
+Yap5 pd iYLL067C-1
+Cin5 pd iYLR001C
+Hir1 pd iYLR002C
+Rcs1 pd iYLR002C
+Nrg1 pd iYLR012C
+Swi5 pd iYLR012C
+Yfl044c pd iYLR016C
+Abf1 pd iYLR024C
+Fhl1 pd iYLR029C
+Dal81 pd iYLR030W
+Mata1 pd iYLR033W
+Cin5 pd iYLR034C
+Rfx1 pd iYLR034C
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+Gcr1 pd iYLR035C-A-1
+Gcr2 pd iYLR035C-A-1
+Ste12 pd iYLR035C-A-1
+Hap4 pd iYLR038C
+Fhl1 pd iYLR047C
+Rap1 pd iYLR047C
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+Abf1 pd iYLR055C
+Swi4 pd iYLR055C
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+Fhl1 pd iYLR060W
+Hir1 pd iYLR060W
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+Dal81 pd iYLR062C
+Rme1 pd iYLR065C
+Fhl1 pd iYLR074C
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+Yap1 pd iYLR077W
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+Yap6 pd iYLR080W
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+Fkh2 pd iYLR084C
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+Abf1 pd iYLR095C
+Dal81 pd iYLR096W
+Mss11 pd iYLR098C
+Mbp1 pd iYLR103C
+Swi6 pd iYLR103C
+Met31 pd iYLR105C
+Ndd1 pd iYLR105C
+Ste12 pd iYLR105C
+Yap1 pd iYLR105C
+Rtg3 pd iYLR107W
+Cad1 pd iYLR108C
+Rlm1 pd iYLR110C
+Skn7 pd iYLR110C
+Dal81 pd iYLR111W
+Fkh1 pd iYLR113W
+Cin5 pd iYLR121C
+Yap6 pd iYLR121C
+Zap1 pd iYLR129W
+Ndd1 pd iYLR131C
+Put3 pd iYLR142W
+Pho2 pd iYLR152C
+Pho4 pd iYLR152C
+Crz1 pd iYLR162W-0
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+Msn4 pd iYLR162W-0
+Pdr1 pd iYLR162W-0
+Smp1 pd iYLR162W-0
+Yap5 pd iYLR162W-0
+Msn4 pd iYLR164W
+Fhl1 pd iYLR166C
+Ixr1 pd iYLR166C
+Sfp1 pd iYLR166C
+Hap4 pd iYLR168C
+Abf1 pd iYLR173W
+Cbf1 pd iYLR173W
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+Met4 pd iYLR179C
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+Fhl1 pd iYLR184W
+Fkh2 pd iYLR189C
+Mcm1 pd iYLR189C
+Ndd1 pd iYLR189C
+Fkh2 pd iYLR191W
+Mcm1 pd iYLR191W
+Ndd1 pd iYLR191W
+Swi5 pd iYLR194C
+Pdr1 pd iYLR206W
+Swi5 pd iYLR206W
+Fkh1 pd iYLR209C
+Ime4 pd iYLR210W
+Nrg1 pd iYLR210W
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+Hap2 pd iYLR219W
+Hap3 pd iYLR219W
+Hap5 pd iYLR219W
+Abf1 pd iYLR222C
+Reb1 pd iYLR223C
+Azf1 pd iYLR224W
+Cin5 pd iYLR228C-0
+Dal81 pd iYLR238W
+Dal81 pd iYLR246W
+Stp2 pd iYLR246W
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+Gcr2 pd iYLR262C
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+Abf1 pd iYLR263W
+Fhl1 pd iYLR263W
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+Pho4 pd iYLR266C
+Rtg3 pd iYLR276C
+Swi5 pd iYLR276C
+Fzf1 pd iYLR277C
+Fkh2 pd iYLR286C
+Rfx1 pd iYLR286C
+Ixr1 pd iYLR287C
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+Fhl1 pd iYLR287C-A
+Rap1 pd iYLR287C-A
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+Hap4 pd iYLR295C
+Yap6 pd iYLR295C
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+Fkh2 pd iYLR301W
+Mbp1 pd iYLR301W
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+Fhl1 pd iYLR325C
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+Gcn4 pd iYLR358C
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+Smp1 pd iYLR392C
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+Skn7 pd iYLR397C
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+Yfl044c pd iYLR422W
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+Fhl1 pd iYLR441C
+Rap1 pd iYLR441C
+Fhl1 pd iYLR447C
+Rap1 pd iYLR447C
+Zms1 pd iYLR450W
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+Gat3 pd iYLR461W-0
+Pdr1 pd iYLR461W-0
+Yap5 pd iYLR461W-0
+Gat3 pd iYLR461W-1
+Msn4 pd iYLR461W-1
+Yap5 pd iYLR461W-1
+Gat3 pd iYLR466W
+Hap4 pd iYLR466W
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+Rgm1 pd iYLR466W
+Smp1 pd iYLR466W
+Yap5 pd iYLR466W
+Dal81 pd iYLRCdelta5
+Stp2 pd iYLRCdelta5
+Skn7 pd iYLRWdelta15
+Rtg3 pd iYLRWdelta17
+Rlm1 pd iYLRWdelta6-0
+Reb1 pd iYML002W
+Aro80 pd iYML007W
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+Abf1 pd iYML013C-A
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+Fhl1 pd iYML026C
+Rap1 pd iYML026C
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+Swi6 pd iYML028W
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+Fkh2 pd iYML051W
+Ndd1 pd iYML051W
+Fkh2 pd iYML053C
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+Gcn4 pd iYOR304W
+Cin5 pd iYOR306C
+Put3 pd iYOR306C
+Pdr1 pd iYOR307C
+Abf1 pd iYOR310C
+Cin5 pd iYOR311C
+Fhl1 pd iYOR312C
+Rap1 pd iYOR312C
+Sum1 pd iYOR313C
+Cin5 pd iYOR314W
+Fkh2 pd iYOR314W
+Ixr1 pd iYOR314W
+Mcm1 pd iYOR314W
+Ndd1 pd iYOR314W
+Nrg1 pd iYOR314W
+Rlm1 pd iYOR314W
+Rox1 pd iYOR314W
+Skn7 pd iYOR314W
+Swi4 pd iYOR314W
+Yap6 pd iYOR314W
+Ndd1 pd iYOR316C-0
+Rap1 pd iYOR316C-1
+Gal4 pd iYOR318C
+Pdr1 pd iYOR318C
+Reb1 pd iYOR318C
+Rgm1 pd iYOR318C
+Yap5 pd iYOR318C
+Abf1 pd iYOR322C
+Reb1 pd iYOR335C
+Gcn4 pd iYOR336W
+Pho4 pd iYOR336W
+Rap1 pd iYOR337W
+Rap1 pd iYOR342C
+Dig1 pd iYOR343C
+Rap1 pd iYOR343C
+Ste12 pd iYOR343C
+Hsf1 pd iYOR344C-0
+Swi4 pd iYOR344C-0
+Cin5 pd iYOR344C-1
+Fhl1 pd iYOR354C-1
+Rap1 pd iYOR358W
+Mcm1 pd iYOR360C
+Rap1 pd iYOR366W
+Sum1 pd iYOR366W
+Dal81 pd iYOR368W
+Fhl1 pd iYOR369C
+Swi4 pd iYOR372C
+Swi6 pd iYOR372C
+Rfx1 pd iYOR377W-1
+Cin5 pd iYOR380W-0
+Cin5 pd iYOR380W-1
+Pdr1 pd iYOR380W-1
+Mcm1 pd iYOR388C
+Yjl206c pd iYOR388C
+Ste12 pd iYORWdelta14
+Ste12 pd iYORWdelta22
+Stp2 pd iYORWtau3
+Stp2 pd iYPL008W
+Dal82 pd iYPL011C
+Abf1 pd iYPL013C
+Yjl206c pd iYPL015C
+Rap1 pd iYPL017C
+Bas1 pd iYPL019C
+Hap2 pd iYPL019C
+Hir1 pd iYPL019C
+Rcs1 pd iYPL019C
+Ace2 pd iYPL025C
+Skn7 pd iYPL025C
+Swi4 pd iYPL025C
+Fkh1 pd iYPL032C
+Crz1 pd iYPL036W
+Fzf1 pd iYPL036W
+Gal4 pd iYPL036W
+Ime4 pd iYPL036W
+Nrg1 pd iYPL036W
+Rcs1 pd iYPL036W
+Sfp1 pd iYPL036W
+Yfl044c pd iYPL036W
+Yjl206c pd iYPL036W
+Abf1 pd iYPL037C
+Ime4 pd iYPL050C
+Swi5 pd iYPL050C
+Mbp1 pd iYPL056C
+Stb1 pd iYPL056C
+Swi4 pd iYPL056C
+Hir2 pd iYPL061W
+Cin5 pd iYPL062W
+Cin5 pd iYPL063W
+Sum1 pd iYPL076W-0
+Fhl1 pd iYPL080C
+Rap1 pd iYPL080C
+Mbp1 pd iYPL082C
+Dal81 pd iYPL084W
+Sfp1 pd iYPL086C
+Fhl1 pd iYPL090C
+Yap5 pd iYPL090C
+Fkh2 pd iYPL117C
+Dal81 pd iYPL123C
+Fzf1 pd iYPL123C
+Dal81 pd iYPL125W
+Rtg3 pd iYPL125W
+Swi4 pd iYPL125W
+Swi4 pd iYPL127C
+Swi6 pd iYPL127C
+Sum1 pd iYPL130W
+Fhl1 pd iYPL132W
+Pho4 pd iYPL133C
+Fkh1 pd iYPL139C
+Fkh2 pd iYPL139C
+Fkh1 pd iYPL140C
+Fkh1 pd iYPL141C
+Ndd1 pd iYPL141C
+Fhl1 pd iYPL144W
+Rap1 pd iYPL144W
+Rap1 pd iYPL145C
+Msn4 pd iYPL151C
+Fkh2 pd iYPL155C
+Ste12 pd iYPL156C
+Swi5 pd iYPL158C
+Abf1 pd iYPL159C
+Swi4 pd iYPL163C
+Swi6 pd iYPL163C
+Cin5 pd iYPL165C
+Mata1 pd iYPL173W
+Smp1 pd iYPL176C
+Mac1 pd iYPL177C-0
+Phd1 pd iYPL177C-0
+Fkh2 pd iYPL177C-1
+Cad1 pd iYPL178W
+Reb1 pd iYPL181W
+Sfp1 pd iYPL184C
+Rfx1 pd iYPL189W
+Fhl1 pd iYPL199C
+Reb1 pd iYPL206C
+Hap2 pd iYPL208W
+Hap3 pd iYPL208W
+Hap5 pd iYPL208W
+Crz1 pd iYPL213W
+Abf1 pd iYPL229W
+Swi5 pd iYPL235W
+Abf1 pd iYPL242C
+Ndd1 pd iYPL242C
+Adr1 pd iYPL249C-A
+Fhl1 pd iYPL249C-A
+Hir1 pd iYPL249C-A
+Ime4 pd iYPL249C-A
+Pdr1 pd iYPL249C-A
+Rap1 pd iYPL249C-A
+Rcs1 pd iYPL249C-A
+Smp1 pd iYPL249C-A
+Adr1 pd iYPL253C
+Aro80 pd iYPL253C
+Bas1 pd iYPL253C
+Gcr2 pd iYPL253C
+Hir1 pd iYPL253C
+Ime4 pd iYPL253C
+Nrg1 pd iYPL253C
+Pdr1 pd iYPL253C
+Pho4 pd iYPL253C
+Rcs1 pd iYPL253C
+Arg80 pd iYPL266W
+Arg81 pd iYPL266W
+Dal81 pd iYPL266W
+Phd1 pd iYPL266W
+Stp1 pd iYPL266W
+Swi4 pd iYPL268W
+Swi6 pd iYPL268W
+Hap4 pd iYPL271W
+Hap4 pd iYPL272C-1
+Mcm1 pd iYPL277C
+Yjl206c pd iYPL277C
+Gal4 pd iYPL283C-0
+Gat3 pd iYPL283C-0
+Msn4 pd iYPL283C-0
+Pdr1 pd iYPL283C-0
+Rgm1 pd iYPL283C-0
+Swi5 pd iYPL283C-0
+Yap5 pd iYPL283C-0
+Gal4 pd iYPL283C-1
+Gat3 pd iYPL283C-1
+Pdr1 pd iYPL283C-1
+Rgm1 pd iYPL283C-1
+Yap5 pd iYPL283C-1
+Zap1 pd iYPL283C-1
+Smp1 pd iYPLCtau2
+Ste12 pd iYPR002C-A
+Skn7 pd iYPR008W
+Swi4 pd iYPR008W
+Ino4 pd iYPR013C-0
+Nrg1 pd iYPR013C-0
+Phd1 pd iYPR013C-0
+Yap6 pd iYPR013C-0
+Yjl206c pd iYPR013C-0
+Cin5 pd iYPR013C-1
+Nrg1 pd iYPR013C-1
+Phd1 pd iYPR013C-1
+Sok2 pd iYPR013C-1
+Yap6 pd iYPR013C-1
+Cin5 pd iYPR014C-0
+Abf1 pd iYPR017C
+Hap4 pd iYPR019W
+Reb1 pd iYPR025C
+Rap1 pd iYPR029C
+Dot6 pd iYPR031W
+Fkh2 pd iYPR034W
+Msn1 pd iYPR034W
+Stp2 pd iYPR041W
+Fhl1 pd iYPR042C
+Cad1 pd iYPR047W
+Yap1 pd iYPR047W
+Reb1 pd iYPR054W
+Yfl044c pd iYPR055W
+Mig1 pd iYPR057W
+Dig1 pd iYPR060C
+Cin5 pd iYPR064W
+Skn7 pd iYPR064W
+Yap1 pd iYPR064W
+Yap6 pd iYPR064W
+Reb1 pd iYPR066W
+Reb1 pd iYPR074C
+Mbp1 pd iYPR076W
+Fhl1 pd iYPR079W
+Rap1 pd iYPR079W
+Yap5 pd iYPR079W
+Dal81 pd iYPR080W
+Mss11 pd iYPR082C
+Abf1 pd iYPR104C
+Msn4 pd iYPR104C
+Rox1 pd iYPR108W
+Arg81 pd iYPR109W
+Mac1 pd iYPR110C
+Mcm1 pd iYPR112C
+Ime4 pd iYPR114W
+Mcm1 pd iYPR121W-0
+Cin5 pd iYPR122W
+Smp1 pd iYPR122W
+Mac1 pd iYPR124W
+Abf1 pd iYPR128C
+Fhl1 pd iYPR131C
+Rap1 pd iYPR131C
+Yap5 pd iYPR131C
+Mss11 pd iYPR133C
+Mss11 pd iYPR133W-A
+Cha4 pd iYPR139C
+Yap6 pd iYPR148C-0
+Fkh2 pd iYPR148C-1
+Ndd1 pd iYPR148C-1
+Rap1 pd iYPR148C-1
+Yap6 pd iYPR148C-1
+Ndd1 pd iYPR151C
+Skn7 pd iYPR151C
+Hsf1 pd iYPR157W
+Gcr1 pd iYPR158W
+Reb1 pd iYPR163C
+Met31 pd iYPR167C
+Abf1 pd iYPR176C
+Reb1 pd iYPR181C
+Swi5 pd iYPR182W
+Msn4 pd iYPR185W
+Pho2 pd iYPR194C
+Fkh1 pd iYPR195C-0
+Hir1 pd iYPR195C-0
+Hir2 pd iYPR195C-0
+Crz1 pd iYPR201W-0
+Gal4 pd iYPR201W-1
+Gat3 pd iYPR201W-1
+Pdr1 pd iYPR201W-1
+Phd1 pd iYPR201W-1
+Rgm1 pd iYPR201W-1
+Yap5 pd iYPR201W-1
+Gcr2 pd iYPRWdelta14
+Mbp1 pd iYPRWdelta14
+Ndd1 pd iYPRWsigma2-0
+Reb1 pd iYPRWsigma2-0
+Reb1 pd iYPRWsigma2-1
+Swi4 pd iYPRWsigma2-1
+Mot3 pd iYPRWsigma4
+Ste12 pd iYPRWsigma4
+Dig1 pd iYPRWtau4
+Smp1 pd iYPRWtau4
+Ste12 pd iYPRWtau4
+Nrg1 pd Q0005
+Skn7 pd Q0005
+Swi5 pd Q0025
+Yap5 pd Q0075
+Reb1 pd Q0100
+Pdr1 pd Q0115
+Pdr1 pd Q0120
+Pdr1 pd Q0125
+Yap5 pd Q0125
+Pdr1 pd Q0140
+Yap5 pd Q0155
+Phd1 pd Q0183B
+Phd1 pd Q0185A
+Pdr1 pd Q0190A
+Stp2 pd Q0190A
+Yap5 pd Q0280A
+Msn4 pd RDN37-1A
+Pdr1 pd RDN37-1A
+Smp1 pd RDN37-1A
+Yap5 pd RDN37-1A
+Crz1 pd RDN37-1B
+Gal4 pd RDN37-1B
+Msn4 pd RDN37-1B
+Pdr1 pd RDN37-1B
+Smp1 pd RDN37-1B
+Yap5 pd RDN37-1B
+Gat3 pd TEL15R-2
+Hap4 pd TEL15R-2
+Pdr1 pd TEL15R-2
+Rap1 pd TEL15R-2
+Rgm1 pd TEL15R-2
+Yap5 pd TEL15R-2
+Mal13 pd TEL15R-4
+Msn4 pd TEL15R-4
+Phd1 pd TEL15R-4
+Swi5 pd TEL15R-4
+Gat3 pd TEL15R-6
+Pdr1 pd TEL15R-6
+Smp1 pd TEL15R-6
+Yap5 pd TEL15R-6
+Dig1 pd YBLCsigma1
+Ste12 pd YBLCsigma1
+Gcr1 pd YBLWdelta1
+Dig1 pd YBLWdelta10
+Gcr1 pd YBLWdelta10
+Ste12 pd YBLWdelta10
+Mot3 pd YBLWtau1
+Gcr2 pd YBLWTy2-1A
+Arg80 pd YDRCTy1-2A
+Dig1 pd YDRCTy1-2A
+Leu3 pd YDRCTy1-2A
+Phd1 pd YDRCTy1-2A
+Rlm1 pd YDRCTy1-2A
+Gcr1 pd YDRCTy1-2D
+Gcr2 pd YDRCTy1-2D
+Gcr1 pd YDRWdelta12
+Gcr2 pd YDRWdelta12
+Ste12 pd YDRWdelta12
+Dig1 pd YDRWdelta23
+Gcr1 pd YDRWdelta23
+Dig1 pd YELCdelta4
+Gcr1 pd YELCdelta4
+Ste12 pd YELCdelta4
+Dig1 pd YERWdelta21
+Dig1 pd YERWdelta9
+Phd1 pd YERWdelta9
+Arg80 pd YGRCTy1-2A
+Dig1 pd YGRCTy1-2A
+Hap5 pd YGRCTy1-2A
+Leu3 pd YGRCTy1-2A
+Ste12 pd YGRCTy1-2A
+Ste12 pd YGRCTy1-2B
+Dig1 pd YGRCTy1-2D
+Gcr1 pd YGRCTy1-2D
+Gcr2 pd YGRCTy1-2D
+Ste12 pd YGRCTy1-2D
+Gcr1 pd YILCdelta2
+Ste12 pd YILWTy3-1A
+Gcr1 pd YJLWdelta16
+Gcr1 pd YKRCdelta11
+Msn4 pd YMRCdelta11
+Gcr1 pd YMRCtau1
+Pdr1 pd YMRCtau1
+Gcr2 pd YOLCdelta2
+Mot3 pd YPLCtau1
+Phd1 pd YPLCTy4-1B
+Rlm1 pd YPLCTy4-1E
+Rtg3 pd YPLCTy4-1E
+Ste12 pd YPLCTy4-1E
+Phd1 pd YPRWdelta14
+Swi4 pd iCEN5
+Hsf1 pd iYAL004W
+Gcr1 pd iYAL039C-1
+Hir1 pd iYBR009C
+Dal81 pd iYBR068C
+Leu3 pd iYBR068C
+Ste12 pd iYBR082C-1
+Rap1 pd iYBR084C-A
+Gcn4 pd iYBR113W
+Gcr1 pd iYBR196C
+Gcr2 pd iYBR196C
+Dal81 pd iYCL025C
+Bas1 pd iYCL030C
+Gcn4 pd iYCL030C
+Pho2 pd iYCL030C
+Swi5 pd iYDL128W
+Gln3 pd iYDL171C
+Swi5 pd iYDL180W
+Stp1 pd iYDR046C
+Rlm1 pd iYDR076W
+Hir2 pd iYDR224C
+Aro80 pd iYDR379W
+Bas1 pd iYDR408C
+Mcm1 pd iYDR460W
+Ino2 pd iYDR497C
+Ino4 pd iYDR497C
+Hap4 pd iYDR529C
+Ino4 pd iYER026C
+Sip4 pd iYER065C
+Arg80 pd iYER068W
+Arg81 pd iYER068W
+Mbp1 pd iYER069W
+Swi6 pd iYER069W
+Msn4 pd iYER102W
+Mcm1 pd iYER111C
+Swi6 pd iYER111C
+Yap1 pd iYFL056C-0
+Cbf1 pd iYFR029W
+Leu3 pd iYGL009C
+Skn7 pd iYGL038C
+Swi4 pd iYGL038C
+Zap1 pd iYGL256W-3
+Abf1 pd iYGR058W
+Bas1 pd iYGR061C
+Ino4 pd iYGR156W
+Rfx1 pd iYGR180C
+Rlm1 pd iYGR189C
+Gcr1 pd iYGR192C
+Bas1 pd iYGR203W
+Put3 pd iYHR036W
+Aro80 pd iYHR136C
+Rfx1 pd iYIL066C
+Rap1 pd iYIL133C
+Met4 pd iYIR017C
+Arg80 pd iYJL088W
+Arg81 pd iYJL089W
+Met4 pd iYJL101C
+Yap1 pd iYJL101C
+Rlm1 pd iYJL158C
+Rlm1 pd iYJL160C-1
+Mbp1 pd iYJL196C
+Mcm1 pd iYJL196C
+Mac1 pd iYJL218W
+Gcr2 pd iYJR009C-0
+Cbf1 pd iYJR009C-1
+Hsf1 pd iYJR045C
+Met4 pd iYKL001C
+Gcr2 pd iYKL060C
+Rlm1 pd iYKL097W-A-1
+Zap1 pd iYKL176C
+Ino2 pd iYKL183W
+Ino4 pd iYKL183W
+Swi5 pd iYKL186C
+Mcm1 pd iYKL209C
+Dal81 pd iYKR092C-1
+Hsf1 pd iYLL024C
+Hsf1 pd iYLL027W
+Msn4 pd iYLL027W
+Hsf1 pd iYLL039C
+Swi5 pd iYLR078C
+Cbf1 pd iYLR080W
+Yap1 pd iYLR108C
+Zap1 pd iYLR130C
+Fkh2 pd iYLR131C
+Mcm1 pd iYLR131C
+Put3 pd iYLR141W
+Mac1 pd iYLR213C
+Hsf1 pd iYLR217W
+Mcm1 pd iYLR273C
+Rlm1 pd iYLR341W
+Swi4 pd iYLR341W
+Bas1 pd iYLR358C
+Dal82 pd iYLR437C
+Skn7 pd iYML029W
+Yap1 pd iYML029W
+Yap1 pd iYML117W-A
+Bas1 pd iYMR120C
+Ste12 pd iYMR198W
+Swi4 pd iYMR198W
+Swi6 pd iYMR198W
+Bas1 pd iYMR300C
+Swi4 pd iYMR306C-A
+Hir1 pd iYNL031C
+Leu3 pd iYNL104C
+Mcm1 pd iYNL146W
+Ste12 pd iYNL146W
+Zap1 pd iYNL254C
+Cbf1 pd iYNL278W
+Met4 pd iYNL278W
+Swi4 pd iYNL290W
+Ace2 pd iYNL328C
+Swi5 pd iYNL328C
+Reb1 pd iYOL005C
+Reb1 pd iYOL006C
+Rap1 pd iYOL128C
+Mac1 pd iYOL153C-1
+Bas1 pd iYOR128C
+Ino2 pd iYPL232W
+Ino4 pd iYPL232W
+Gln3 pd iYPR034W
+Mbp1 pd iYPR120C
+Mac1 pd iYPR122W
+Abf1 pd iYPR186C
+Hap4 pd iYPR190C
+Fkh2 pd iYPRWsigma2-1
+Mcm1 pd iYPRWsigma2-1
+Ndd1 pd iYPRWsigma2-1
+Mcm1 pd iYAL040C
+Gal4 pd iYBR018C
+Gal4 pd iYBR019C
+Smp1 pd iYBR182C
+Dig1 pd iYCL028W
+Ste12 pd iYCL028W
+Rap1 pd iYCL030C
+Gcn4 pd iYDL171C
+Swi4 pd iYDL227C-0
+Nrg1 pd iYDL245C-0
+Gal4 pd iYDR008C
+Nrg1 pd iYDR043C-0
+Fkh2 pd iYDR146C
+Mcm1 pd iYDR146C
+Ndd1 pd iYDR146C
+Yap6 pd iYDR259C
+Sum1 pd iYDR310C
+Aro80 pd iYDR420W
+Stb1 pd iYDR500C
+Rap1 pd iYDR544C
+Fhl1 pd iYEL009C
+Swi4 pd iYER111C
+Rap1 pd iYFL015C
+Mcm1 pd iYFL027C
+Ste12 pd iYFL027C
+Rap1 pd iYFR031C-A
+Fkh2 pd iYGL117W
+Mcm1 pd iYGL117W
+Fhl1 pd iYGL124C
+Rap1 pd iYGL124C
+Stb1 pd iYHR061C
+Ste12 pd iYHR083W
+Fhl1 pd iYIL069C
+Nrg1 pd iYIL100W
+Nrg1 pd iYIL119C-0
+Nrg1 pd iYIR013C
+Nrg1 pd iYIR020C
+Zap1 pd iYJL056C
+Nrg1 pd iYJR157W-1
+Nrg1 pd iYJR158W-1
+Gcn4 pd iYKL016C
+Rap1 pd iYKL063C-1
+Stb1 pd iYKL097C
+Cup9 pd iYKR092C-1
+Gal4 pd iYLR080W
+Ace2 pd iYLR286C
+Stb1 pd iYLR341W
+Rap1 pd iYLR399C
+Gal4 pd iYML052W
+Fhl1 pd iYNL068C
+Gcn4 pd iYNL104C
+Rap1 pd iYNL217W
+Stb1 pd iYNL290W
+Rap1 pd iYNL339C
+Rap1 pd iYOL083W-1
+Mbp1 pd iYOR074C
+Swi6 pd iYOR074C
+Stb1 pd iYOR138C
+Stb1 pd iYOR246C
+Rap1 pd iYOR344C-0
+Stb1 pd iYOR372C
+Stb1 pd iYPL256C
+Fhl1 pd iYPR102C
+Rap1 pd iYPR102C
+Rsp5 pp Sla2
+Rsp5 pp actin
+Swi4 pp Swi6
+Mbp1 pp Swi6
+Rif2 pp Rap1
+Gcr1 pp Gcr1
+Gcr1 pp Gcr2
+Swi6 pp Hrr25
+Kss1 pp Ste12
+Rap1 pp Sir3
+Sir4 pp Rap1
+Sir3 pp Sir4
+Sir3 pp Sir3
+Sir1 pp Orc1
+Sir1 pp Sir4
+Rgd1 pp Rho3
+Cdc24 pp Cla4
+Rad53 pp Asf1
+Asf1 pp Hht1
+Rgd1 pp Rho4
+Asf1 pp Hhf1
+Rif2 pp Rif1
+Rif1 pp Rap1
+SBF interactsWith iYOR246C
+SBF interactsWith iYNL290W
+SBF interactsWith iYPL256C
+SBF interactsWith iYDR525W
+SBF interactsWith iYPL163C
+SBF interactsWith iYKL102C
+SBF interactsWith iYOL007C
+SBF interactsWith iYGR221C
+SBF interactsWith iYNL301C
+SBF interactsWith iYMR198W
+SBF interactsWith iYDL128W
+SBF interactsWith iYIL124W
+SBF interactsWith iYLR110C
+SBF interactsWith iYDR309C
+SBF interactsWith iYDR451C
+SBF interactsWith iYHR061C
+SBF interactsWith iYGR189C
+SBF interactsWith iYKL097C
+SBF interactsWith iYJL187C
+SBF interactsWith iYOR372C
+SBF interactsWith iYDR500C
+SBF interactsWith iYBR077C
+SBF interactsWith iYGL179C-0
+SBF interactsWith iYIL142W
+SBF interactsWith iYLR341W
+SBF interactsWith iYMR016C-1
+SBF interactsWith iYMR306C-A
+SBF interactsWith iYML028W
+SBF interactsWith iYBR162C
+SBF interactsWith iYLR330W
+SBF interactsWith iYJL158C
+SBF interactsWith iYPL056C
+SBF interactsWith iYKR011C
+SBF interactsWith iYEL041W
+SBF interactsWith iYLR111W
+SBF interactsWith iYPL057C
+SBF interactsWith iYGR279C
+SBF interactsWith iYOR377W-1
+SBF interactsWith iYMR016C-0
+SBF interactsWith iYOR342C
+SBF interactsWith iYLR084C
+SBF interactsWith YDR525W-A
+SBF interactsWith iYOL114C
+SBF interactsWith iYLR183C
+SBF interactsWith iYOR314W
+SBF interactsWith iYOR248W
+SBF interactsWith iYJL225C-0
+SBF interactsWith itY(GUA)O
+SBF interactsWith iYKL008C
+SBF interactsWith iYGR152C
+SBF interactsWith iYBR070C
+SBF interactsWith iYNL231C
+SBF interactsWith iYKL098W
+SBF interactsWith iYGR040W
+SBF interactsWith iYKR041W
+SBF interactsWith iYGL179C-1
+SBF interactsWith iYDR221W
+SBF interactsWith iYNL299W
+SBF interactsWith iYJR053W
+SBF interactsWith iYDR076W
+SBF interactsWith iYPRWsigma2-1
+SBF interactsWith iYDR525W-A
+SBF interactsWith iYJL079C
+SBF interactsWith TEL15R-1
+SBF interactsWith iYDR134C
+SBF interactsWith iYPL127C
+SBF interactsWith iYHR216W
+SBF interactsWith iYOR344C-0
+SBF interactsWith iYKL221W-0
+SBF interactsWith iYGR013W
+SBF interactsWith iYPR201W-1
+SBF interactsWith iYBR162W-A
+SBF interactsWith iYOR343C
+SBF interactsWith iYARWdelta7
+SBF interactsWith iYFL064C
+SBF interactsWith iYAL024C
+SBF interactsWith iYKL097W-A-1
+SBF interactsWith iYLR121C
+SBF interactsWith iYJL093C
+SBF interactsWith iYIR018W-0
+SBF interactsWith iYAL040C
+SBF interactsWith TEL15R-6
+SBF interactsWith TEL15R-2
+SBF interactsWith iYGL007W-0
+SBF interactsWith TEL1R
+SBF interactsWith iYOL110W
+SBF interactsWith iYOL156W-1
+SBF interactsWith iYOR113W
+SBF interactsWith iYDR524C
+SBF interactsWith iYGL097W-1
+SBF interactsWith iYHR093W
+SBF interactsWith iYGL097W-0
+SBF interactsWith iYOR245C
+SBF interactsWith iYCL025C
+SBF interactsWith iYCL055W-0
+SBF interactsWith iYGR139W
+SBF interactsWith iYPL283C-1
+SBF interactsWith iYPR203W
+SBF interactsWith iYDR072C
+SBF interactsWith iYDR542W
+SBF interactsWith iYPL222W
+SBF interactsWith iYGL013C
+SBF interactsWith iYLR184W
+SBF interactsWith iYIL123W
+SBF interactsWith iYMR135W-A
+SBF interactsWith iYBL030C-1
+SBF interactsWith iYLR112W
+SBF interactsWith itA(AGC)P
+SBF interactsWith iYKL104C
+SBF interactsWith iYDL227C-0
+SBF interactsWith iYNL338W
+SBF interactsWith iYGR086C
+SBF interactsWith iYDR345C-0
+SBF interactsWith iYHR007C
+SBF interactsWith iYKL045W
+SBF interactsWith iYDL183C-1
+SBF interactsWith iYEL075C
+SBF interactsWith iYOL012C
+SBF interactsWith iYNL066W
+SBF interactsWith iYEL008W
+SBF interactsWith iYCR063W
+SBF interactsWith iYNL283C
+SBF interactsWith iYMR305C
+SBF interactsWith iYDL055C-0
+SBF interactsWith iYLR299W
+SBF interactsWith iYDL004W
+SBF interactsWith iYER111C
+SBF interactsWith iYLL066C-1
+SBF interactsWith iYDR544C
+SBF interactsWith iYBL111C
+SBF interactsWith iYBL109W-0
+SBF interactsWith iYER069W
+SBF interactsWith iYJL196C
+SBF interactsWith iYLR461W-1
+SBF interactsWith iYML133C-0
+SBF interactsWith iYDR507C
+SBF interactsWith iYDR441C
+SBF interactsWith iYERWomega2-1
+SBF interactsWith iYNR008W
+SBF interactsWith iYDR543C
+SBF interactsWith iYKL103C
+SBF interactsWith iYNL279W
+SBF interactsWith iYPL283C-0
+SBF interactsWith iYGR107W
+SBF interactsWith iYHL049C-0
+SBF interactsWith iYGR295C-1
+SBF interactsWith iYML133C-1
+SBF interactsWith iYLL067C-1
+SBF interactsWith iYGL008C
+SBF interactsWith iYLR461W-0
+SBF interactsWith iYNL031C
+SBF interactsWith iYDR296W
+SBF interactsWith iYLR466W
+SBF interactsWith iYGR109C
+SBF interactsWith TEL9L
+SBF interactsWith iYHR217C
+SBF interactsWith iYMR178W
+SBF interactsWith iYERWomega2-0
+SBF interactsWith iYHR219W
+SBF interactsWith iYIL177C-0
+SBF interactsWith iYJL225C-1
+SBF interactsWith iYIL177C-1
+SBF interactsWith iYNL339C
+MBF interactsWith iYCR063W
+MBF interactsWith iYNL283C
+MBF interactsWith iYMR305C
+MBF interactsWith iYDL055C-0
+MBF interactsWith iYLR299W
+MBF interactsWith iYDL004W
+MBF interactsWith iYER111C
+MBF interactsWith iYLL066C-1
+MBF interactsWith iYDR544C
+MBF interactsWith iYBL111C
+MBF interactsWith iYBL109W-0
+MBF interactsWith iYER069W
+MBF interactsWith iYJL196C
+MBF interactsWith iYLR461W-1
+MBF interactsWith iYML133C-0
+MBF interactsWith iYDR507C
+MBF interactsWith iYDR441C
+MBF interactsWith iYERWomega2-1
+MBF interactsWith iYNR008W
+MBF interactsWith iYDR543C
+MBF interactsWith iYKL103C
+MBF interactsWith iYNL279W
+MBF interactsWith iYPL283C-0
+MBF interactsWith iYGR107W
+MBF interactsWith iYHL049C-0
+MBF interactsWith iYGR295C-1
+MBF interactsWith iYML133C-1
+MBF interactsWith iYLL067C-1
+MBF interactsWith iYGL008C
+MBF interactsWith iYLR461W-0
+MBF interactsWith iYNL031C
+MBF interactsWith iYDR296W
+MBF interactsWith iYLR466W
+MBF interactsWith iYGR109C
+MBF interactsWith TEL9L
+MBF interactsWith iYHR217C
+MBF interactsWith iYMR178W
+MBF interactsWith iYERWomega2-0
+MBF interactsWith iYHR219W
+MBF interactsWith iYIL177C-0
+MBF interactsWith iYJL225C-1
+MBF interactsWith iYIL177C-1
+MBF interactsWith iYNL339C
+MBF interactsWith iYDR263C
+MBF interactsWith iYHR149C
+MBF interactsWith iYER094C
+MBF interactsWith iYNL337W
+MBF interactsWith iYDL101C
+MBF interactsWith iYAL069W
+MBF interactsWith iYBR297W
+MBF interactsWith iYKL113C
+MBF interactsWith iYDL018C
+MBF interactsWith iRDN5-1
+MBF interactsWith iYNL313C
+MBF interactsWith iYPR076W
+MBF interactsWith iYNL103W
+MBF interactsWith iYERWdelta7
+MBF interactsWith iYMR214W
+MBF interactsWith iYBL022C
+MBF interactsWith iYPR078C
+MBF interactsWith tS(CGA)C
+MBF interactsWith SNR63
+MBF interactsWith iYLR103C
+MBF interactsWith iYEL002C
+MBF interactsWith iYHR142W
+MBF interactsWith iYOL010W
+MBF interactsWith iYAL003W
+MBF interactsWith iYDR138W
+MBF interactsWith itL(CAA)A
+MBF interactsWith iYFL063W
+MBF interactsWith iYER124C
+MBF interactsWith itG(GCC)E
+MBF interactsWith iYKL114C
+MBF interactsWith iYPR155C
+MBF interactsWith iYOR074C
+MBF interactsWith iYCR062W
+MBF interactsWith iYKL185W
+MBF interactsWith iYKL039W
+MBF interactsWith itE(UUC)E2
+MBF interactsWith iSNR7-S
+MBF interactsWith iYJR030C
+MBF interactsWith iYLR449W
+MBF interactsWith iYDR189W
+MBF interactsWith iYEL074W
+MBF interactsWith iYBL003C
+MBF interactsWith iYBLWtau1
+MBF interactsWith iYOR229W
+Asf1 pp Hht2
+Asf1 pp Hhf2
+Ste18 pp Akr1
+Ste4 pp Akr1
+Akr1 pp Akr1
+Sla1 pp Abp1
+Sla1 pp Las17
+Srv2 pp Abp1
+TAF1 pp Not1
+Cdc7 pp Cdc7
+Cdc7 pp Dbf4
+Cdc5 pp Dbf4
+Rad53 pp Dbf4
+Cdc36 pp Cdc39
+Mot2 pp Cdc39
+Not5 pp Cdc39
+Fus3 pp Ste11
+Kss1 pp Ste11
+Ste5 pp Ste11
+Ste5 pp Ste7
+Cdc7/Dbf4 interactsWith Rad53
+Unknown interactsWith RSC9
+Unknown interactsWith RTT102
+Unknown interactsWith STH1
+Unknown interactsWith ARP7
+Unknown interactsWith ARP9
+Unknown interactsWith NPL6
+Unknown interactsWith PIM1
+Unknown interactsWith RSC3
+Unknown interactsWith RSC4
+Unknown interactsWith RSC58
+RSC6 interactsWith Unknown
+Unknown interactsWith RSC8
+Unknown interactsWith RTT102
+Unknown interactsWith SFH1
+Unknown interactsWith SSB1
+Unknown interactsWith STH1
+Unknown interactsWith ARP7
+Unknown interactsWith ARP9
+Unknown interactsWith HSC82
+Unknown interactsWith HSP104
+Unknown interactsWith HTL1
+Unknown interactsWith NFI1
+Unknown interactsWith NPL6
+Unknown interactsWith RSC2
+Unknown interactsWith RSC3
+Unknown interactsWith RSC30
+Unknown interactsWith RSC4
+Unknown interactsWith RSC58
+Unknown interactsWith RSC6
+RSC8 interactsWith Unknown
+Unknown interactsWith RSC9
+Unknown interactsWith RTT102
+Unknown interactsWith SFH1
+Unknown interactsWith SPT16
+Unknown interactsWith SSA1
+Unknown interactsWith SSB1
+Unknown interactsWith SSE1
+Unknown interactsWith STH1
+Unknown interactsWith ARP7
+Unknown interactsWith ARP9
+Unknown interactsWith HTA2
+Unknown interactsWith HTL1
+Unknown interactsWith NPL6
+Unknown interactsWith RSC2
+Unknown interactsWith RSC4
+Unknown interactsWith RSC58
+Unknown interactsWith RSC6
+Unknown interactsWith RSC8
+Unknown interactsWith RSC9
+RTT102 interactsWith Unknown
+Unknown interactsWith SFH1
+Unknown interactsWith STH1
+CSE4 pd CEN1
+CSE4 pd CEN3
+CTF3 pd CEN1
+CTF3 pd CEN3
+NDC10 pd CEN1
+NDC10 pd CEN3
+CTF13 interactsWith ARC18
+CTF13 interactsWith BUD19
+CTF13 interactsWith CLA4
+CTF13 interactsWith CTF19
+CTF13 interactsWith DBF2
+CTF13 interactsWith DEF1
+CTF13 interactsWith EAP1
+CTF13 interactsWith GIC2
+CTF13 interactsWith GPG1
+CTF13 interactsWith HTZ1
+CTF13 interactsWith IRA2
+CTF13 interactsWith MCK1
+CTF13 interactsWith NDJ1
+CTF13 interactsWith NTC20
+CTF13 interactsWith NUP133
+CTF13 interactsWith PAC10
+CTF13 interactsWith PAC11
+CTF13 interactsWith RIM21
+CTF13 interactsWith RPS9B
+CTF13 interactsWith RSA1
+CTF13 interactsWith SAT4
+CTF13 interactsWith SCJ1
+CTF13 interactsWith SIT4
+CTF13 interactsWith UBP13
+CTF13 interactsWith YIL165C
+CTF13 interactsWith YMR252C
+CTF13 interactsWith YOR296W
+CTF13 interactsWith CTF13
+NDC10 interactsWith FYV8
+NDC10 interactsWith RAD51
+SKP1 interactsWith CTF13
+SKP1 interactsWith FYV8
+SKP1 interactsWith PAC10
+SKP1 interactsWith RSC2
+RSC1 interactsWith CSE4
+RSC1 interactsWith CTF14
+RSC1 interactsWith CTF18
+RSC1 interactsWith CTF19
+RSC1 interactsWith CTF3
+RSC1 interactsWith CTF8
+RSC1 interactsWith MCM22
+RSC1 interactsWith OKP1
+RSC1 interactsWith SCC1
+RSC1 interactsWith SCC2
+RSC2 interactsWith CSE4
+RSC2 interactsWith CTF14
+RSC2 interactsWith CTF18
+RSC2 interactsWith CTF19
+RSC2 interactsWith CTF3
+RSC2 interactsWith CTF7
+RSC2 interactsWith CTF8
+RSC2 interactsWith MCM22
+RSC2 interactsWith OKP1
+RSC2 interactsWith SCC1
+RSC2 interactsWith SCC2
+RSC2 interactsWith SMC3
+NDC10 interactsWith CTF8
+NDC10 interactsWith GIM5
+NDC10 interactsWith NIS1
+NDC10 interactsWith RSC1
+NDC10 interactsWith RSC2
+NDC10 interactsWith VID21
+CTF13 interactsWith CTF8
+CTF13 interactsWith FYV8
+CTF13 interactsWith GIM5
+CTF13 interactsWith NIS1
+CTF13 interactsWith NST1
+CTF13 interactsWith RAD51
+CTF13 interactsWith RSC1
+CTF13 interactsWith RSC2
+CTF13 interactsWith SPO74
+CTF13 interactsWith VID21
+Rsr1 pp Cdc42
+Rps28B interactsWith Rps28B_3'UTR
+Rgt2 pp Std1
+Rgt2 pp Mth1
+Rgt2 pp Yck1
+Spt15 pd Pho5_promoter
+Bdf1 pd Pho5_promoter
+Swi4 pp Swi6
+Mbp1 pp Swi6
+Whi5 interactsWith SBF
+Whi5/SBF_Complex interactsWith CLN2
+Whi5 pp Cdc28
+Whi5 interactsWith SBF
+Whi5 pp Cdc28
+Whi5/SBF_Complex interactsWith CLN2
+Whi5/SBF_Complex interactsWith PCL1
+Cln2 interactsWith Unknown
+Unknown interactsWith Bem3
+Unknown interactsWith Bmh2
+Unknown interactsWith Cdc28
+Unknown interactsWith Cdc4
+Unknown interactsWith Cdc48
+Unknown interactsWith Cdc53
+Unknown interactsWith Cdh1
+Unknown interactsWith Cks1
+Unknown interactsWith Far1
+Unknown interactsWith Grr1
+Unknown interactsWith Rga1
+Unknown interactsWith Sin3
+Unknown interactsWith Skp1
+Unknown interactsWith Srl3
+Unknown interactsWith Ste20
+Unknown interactsWith Ubi4
+Unknown interactsWith Ypl014
+Unknown interactsWith Ypl267
+Clb2 interactsWith Unknown
+Unknown interactsWith Bud3
+Unknown interactsWith Cdc28
+Unknown interactsWith Cdc6
+Unknown interactsWith Cks1
+Unknown interactsWith Cue5
+Unknown interactsWith Kap60
+Unknown interactsWith Kel1
+Unknown interactsWith Lte1
+Unknown interactsWith Nap1
+Unknown interactsWith Sic1
+Clb3 interactsWith Unknown
+Unknown interactsWith Ace2
+Unknown interactsWith Bik1
+Unknown interactsWith Cbk1
+Unknown interactsWith Cdc25
+Unknown interactsWith Cdc28
+Unknown interactsWith Cdc4
+Unknown interactsWith Cdc53
+Unknown interactsWith Cdh1
+Unknown interactsWith Cks1
+Unknown interactsWith Dbf2
+Unknown interactsWith Mds3
+Unknown interactsWith Mob1
+Unknown interactsWith Sic1
+Unknown interactsWith Ypl267
+Clb5 interactsWith Unknown
+Unknown interactsWith Cdc28
+Unknown interactsWith Cks1
+Unknown interactsWith Far1
+Unknown interactsWith Orc1
+Unknown interactsWith Sic1
+Unknown interactsWith Spc42
+Cdc48 interactsWith Unknown
+Unknown interactsWith Cdc53
+Unknown interactsWith Sel1
+Unknown interactsWith Npl4
+Unknown interactsWith Shp1
+Unknown interactsWith Ufd1
+Ace2 interactsWith Unknown
+Unknown interactsWith Clb2
+Unknown interactsWith Clb3
+Unknown interactsWith Cln2
+Bem3 interactsWith Unknown
+Unknown interactsWith Cln2
+Bud3 interactsWith Unknown
+Unknown interactsWith Clb2
+Unknown interactsWith Cln2
+Cdc25 interactsWith Unknown
+Unknown interactsWith Clb3
+Unknown interactsWith Cln2
+Cdc48 interactsWith Unknown
+Unknown interactsWith Cln2
+Cdc6 interactsWith Unknown
+Unknown interactsWith Clb2
+Dbf2 interactsWith Unknown
+Unknown interactsWith Clb2
+Unknown interactsWith Clb3
+Far1 interactsWith Unknown
+Unknown interactsWith Clb5
+Unknown interactsWith Cln2
+Grr1 interactsWith Unknown
+Unknown interactsWith Cln2
+Orc6 interactsWith Unknown
+Unknown interactsWith Clb5
+Rga1 interactsWith Unknown
+Unknown interactsWith Cln2
+Sic1 interactsWith Unknown
+Unknown interactsWith Clb2
+Unknown interactsWith Clb3
+Unknown interactsWith Clb5
+Sld2 interactsWith Unknown
+Unknown interactsWith Clb5
+Swi5 interactsWith Unknown
+Unknown interactsWith Clb3
+Unknown interactsWith Cps35
+Unknown interactsWith Cps40
+Unknown interactsWith Cps50
+Snf1 pp Srb10
+Snf1 pp Srb11
+Snf1 pp Sin4
+Tub1 pp Bim1
+Tub3 pp Bim1
+Rfa2 pd RNR2_URS2
+Rfa2 pd RAD51_URS2
+unknown interactsWith Tlg1
+unknown interactsWith Tlg2
+unknown interactsWith Snc1
+Vsm1 interactsWith Unknown
+Vsm1 pp Sso1
+Met4 pp Ubi4
+Srb9 pp Tpk1
+eRF1 pp Mlc1
+Pre1 interactsWith Unknown
+Unknown interactsWith Pre2
+Unknown interactsWith Pre3
+Unknown interactsWith Pre4
+Unknown interactsWith Pre5
+Unknown interactsWith Pre7
+Unknown interactsWith Pre6
+Unknown interactsWith Pre8
+Unknown interactsWith Pre9
+Unknown interactsWith Pre10
+Unknown interactsWith Pup1
+Unknown interactsWith Pup2
+Unknown interactsWith Pup3
+Unknown interactsWith Scl1
+Unknown interactsWith Rpn1
+Unknown interactsWith Rpn2
+Unknown interactsWith Rpn3
+Unknown interactsWith Rpn5
+Unknown interactsWith Rpn6
+Unknown interactsWith Rpn7
+Unknown interactsWith Rpn8
+Unknown interactsWith Rpn9
+Unknown interactsWith Rpn10
+Unknown interactsWith Rpn12
+Unknown interactsWith Rpn11
+Unknown interactsWith Rpn13
+Unknown interactsWith Rpt1
+Unknown interactsWith Rpt2
+Unknown interactsWith Rpt3
+Unknown interactsWith Rpt4
+Unknown interactsWith Rpt5
+Unknown interactsWith Rpt6
+Unknown interactsWith Rad23
+Unknown interactsWith Ubp6
+Ubiquitinated_Sic1 interactsWith 26S_Proteasome
+Ubiquitinated_Sic1 pp Rad23
+Ubiquitinated_Sic1 pp Rpn10
+Ubiquitinated_Sic1 pp Dsk2
+unknown interactsWith Snc2
+Rrn11 pp Rrn6
+eRF1 pp eRF3
+Vps4 pp Vps32
+Vps22 pp Vps28
+Vps20 pp Vps28
+Vps20 pp Vps36
+Vps20 pp Vps22
+Rrn7 pp Rrn6
+Rrn11 pp Rrn7
+Rap1 pd HIS4_intergenic_region
+Cdc31 pp Sac3
+Cdc31 pp Sus1
+Sus1 pp Sac3
+Cdc31 pp Thp1
+Cdc31 pp Sfi1
+Vps23 pp Hse1
+Vps25 pp Vps36
+Vps32 pp Vps32
+Ste12 pd iYNL278W
+Ste12 pd iYNL280C
+Ste12 pd iYDRCdelta9-0
+Ste12 pd itQ(UUG)D2
+Ste12 pd itV(AAC)K2
+Ste12 pd iYCR088W
+Ste12 pd iYCR027C
+Ste12 pd iYBL017C
+Ste12 pd iYCL028W
+Ste12 pd iYDRWdelta10
+Ste12 pd iYDR106W
+Ste12 pd iYBLWdelta10
+Ste12 pd iYHR083W
+Ste12 pd iYDRWdelta26
+Ste12 pd iYDL126C
+Ste12 pd iYDL128W
+Ste12 pd iYOL155C-0
+Ste12 pd iYOL156W-0
+Ste12 pd iYNR070W
+Ste12 pd iYNR067C
+Ste12 pd iYNR064C
+Ste12 pd iYNR053C
+Ste12 pd iYNR051C
+Ste12 pd iYNR049C
+Ste12 pd iYNR047W
+Ste12 pd iYNR045W
+Ste12 pd iYNR043W
+Ste12 pd iYKR041W
+Ste12 pd iYKR039W
+Ste12 pd iYOR344C-0
+Ste12 pd iYORWdelta24
+Ste12 pd iYOR343C
+Ste12 pd iYOR289W
+Ste12 pd iYNL193W
+Ste12 pd iYOL155C-1
+Ste12 pd iYOL156W-1
+Ste12 pd YBLCsigma1
+Ste12 pd iYPRWsigma4
+Ste12 pd iYPLWdelta7
+Ste12 pd iYPL192C
+Ste12 pd iYNL043C
+Ste12 pd iYMR064W
+Ste12 pd itN(GUU)N1
+Ste12 pd iYLR332W-1
+Ste12 pd iYPRCdelta22
+Ste12 pd iYKL097C
+Ste12 pd iYMR197C
+Ste12 pd iYOR129C
+Ste12 pd iYNL105W
+Ste12 pd iYMR164C
+Ste12 pd iYIL083C
+Ste12 pd iYDR099W
+Ste12 pd iYKL025C
+Ste12 pd iYKL027W
+Ste12 pd iYDRCsigma1
+Ste12 pd iYIL169C-0
+Ste12 pd iYIL170W-0
+Ste12 pd itL(UAA)K
+Ste12 pd itQ(UUG)E1
+Ste12 pd iYGR233C-0
+Ste12 pd iYERCsigma3
+Ste12 pd itF(GAA)D
+Ste12 pd itL(CAA)A
+Ste12 pd iYIL037C
+Ste12 pd iYERCdelta24
+Ste12 pd iYDR085C
+Ste12 pd iYBR041W
+Ste12 pd iYBR039W
+Ste12 pd iYIL015W
+Ste12 pd iYHRCsigma2
+Ste12 pd itR(UCU)G1
+Ste12 pd iYCL074W
+Ste12 pd iYJL157C
+Ste12 pd iYDR281C
+Ste12 pd itK(CUU)K
+Ste12 pd iYHR204W
+Ste12 pd iYGR189C
+Ste12 pd iYER018C
+Ste12 pd iYDR309C
+Ste12 pd itG(GCC)E
+Ste12 pd iYCRWdelta11
+Ste12 pd iYCL022C
+Ste12 pd iYIL119C-0
+Ste12 pd iYDR543C
+Ste12 pd iYBR084W
+Ste12 pd iYBR082C-1
+Ste12 pd itD(GUC)B
+Ste12 pd iYDR471W
+Ste12 pd iYBL004W
+Ste12 pd iYFL039C
+Ste12 pd iYJLCdelta6
+Ste12 pd itV(CAC)H
+Ste12 pd itG(GCC)G2
+Ste12 pd iYJL149W
+Ste12 pd iYHR113W
+Ste12 pd iYHR111W
+Ste12 pd iYHR109W
+Ste12 pd iYHR093W
+Ste12 pd iYHR091C
+Ste12 pd iYHR089C
+Ste12 pd iYHR087W
+Ste12 pd iYHR085W
+Ste12 pd iYEL011W
+Ste12 pd itA(UGC)E
+Ste12 pd iYER063W
+Gal4 pd iYBR021W
+Gal4 pd iYLR080W
+Gal4 pd iYDR008C
+Gal4 pd iYBR019C
+Gal4 pd iYDR543C
+Gal4 pd iYJR044C
+Gal4 pd iYNL338W
+Gal4 pd iYNL336W-0
+Gal4 pd iYBL109W-0
+Gal4 pd iYERWomega2-0
+Gal4 pd iYNL335W
+Gal4 pd iYJR144W
+Gal4 pd iYNL337W
+Gal4 pd iYDR544C
+Gal4 pd iYBR018C
+Gal4 pd iYLR094C
+Gal4 pd iYBR020W
+Gal4 pd iYOR119C
+Gal4 pd iYBR035C
+Gal4 pd iYDR277C
+Gal4 pd iYLR102C
+Gal4 pd iYML052W
+Gal4 pd iYBR057C
+Gal4 pd iYDR010C
+Gal4 pd iYDR012W
+Gal4 pd iYBR036C
+Gal4 pd iYDR011W
+Gal4 pd iYLR098C
+Gal4 pd iYOR122C
+Gal4 pd iYGL133W
+Gal4 pd iYGL135W
+Gal4 pd iYDR016C
+Gal4 pd iYBR037C
+Gal4 pd iYLR096W
+Gal4 pd iTLC1
+Gal4 pd iYLL067C-1
+Gal4 pd iYLR104W
+Gal4 pd iYNL339C
+Gal4 pd iYDR014W-1
+Gal4 pd iYPL282C
+Gal4 pd iYLR466W
+Gal4 pd iYPR201W-1
+Gal4 pd iYPL280W
+Gal4 pd iYDR014W-0
+Gal4 pd iYPL283C-0
+Gal4 pd iYPL277C
+Gal4 pd iYBL111C
+Gal4 pd iYML133C-1
+Gal4 pd iYER073W
+Gal4 pd iYJL225C-1
+Gal4 pd iYHR091C
+Hph1 pp Hph2
+Hph1 pp Cna1
+Hph1 pp Cna2
+Vps27 pp Hse1
+Gcn5 pp Ada2
+Rvs167 pp Sla1
+Inp52 pp Sla1
+Rsp5 pp Sla1
+Inp51 pp Sla1
+Rap1 pd Rps11b_promoter
+Sko1 pd Gre2_promoter
+Sko1 pd Ahp1_promoter
+Spt15 pd Pgk1_promoter
+Spt15 pd Act1_promoter
+Spt15 pd Stl1_promoter
+Rap1 pd Rpl2b_promoter
+Gal4 pd Gal2_promoter
+Gal4 pd Gal10_promoter
+Pcl1 pp Epa1
+Pcl1 pp Hms1
+Pcl1 pp Ncp1
+Glc7 pp Reg1
+Cpr6 pp Hsp90
+Vps1 pp Sla1
+Sti1 pp Hsp90
+UbSic1 interactsWith 26S_Proteasome
+UbSic1 pp Rpn10
+UbSic1 pp Rad23
+Rpb3 pd Pgk1_promoter
+Rpb3 pd Act1_promoter
+Spt15 pd Gre2_promoter
+Spt15 pd Ctt1_promoter
+Hhf2 pd Pol1_gene
+Rpb3 pd Pma1_gene
+Hog1 pp Nha1
+Hog1 pp Tok1
+Mex67 pp Mtr2
+Yra1 interactsWith Mex67/Mtr2
+Yra1 pp Sub2
+Yra1 pp Mex67
+Prp9 pp Prp9
+RNA_Pol_II interactsWith Fcp1
+Yap1 pp Yap1
+Vps22 pp Vps36
+Vps4 pp Rim20
+Vps25 pp Vps20
+Vps25 pp Vps22
+Vps28 pp Vps37
+Vps24 pp Vps32
+Vps31 pp Vps32
+Vps32 pp Vps32
+Vps32 pp Rim20
+Mcm7 interactsWith Unknown
+Unknown interactsWith Mcm4
+Unknown interactsWith Mcm6
+Mcm4/6/7_trimer interactsWith Mcm4/6/7_trimer
+Mcm4,6,7_helicase interactsWith Four-way_junction_DNA
+Mcm4,6,7_helicase interactsWith Helicase-bound_four-way_junction_DNA
+SOD1 pp SOD1
+Hog1 pp Sic1
+Vps46 pp Vps46
+Vta1 pp Vps32
+Doa4 pp Vps32
+Arl1 pp Imh1
+Arl3 pp Slo1
+Ctf18 pp Rfc2
+Ctf18 pp Rfc3
+Ctf18 pp Rfc4
+Ctf18 pp Rfc5
+Stu2 pp Spc72
+Arr1 pp Arr1
+Arr1 pp Yap4
+Yap4 pp Yap4
+Yap2 pp Yap2
+Yap5 pp Yap5
+Met28 pp Yap5
+Met4 pp Yap5
+Yap7 pp Yap7
+Met28 pp Met4
+Gcn4 pp Gcn4
+Met4 pp Met4
+Taf25 pp Taf47
+Taf25 pp Taf65
+Taf25 pp Spt7
+Upf1 pp Nmd2
+Upf3 pp Nmd2
+Spc72 pp Spc72
+SLN1 pp Ypd1p
+SLN1 pp Ypd1p
+Chorismate_Synthase pp Chorismate_Synthase
+Chorismate_Synthase pp Chorismate_Synthase
+Chorismate_Synthase pp Chorismate_Synthase
+Chorismate_Synthase pp Chorismate_Synthase
+TIF4631 pp CDC33
+ARO4 pp ARO4
+ECI1 pp ECI1
+ECI1 pp ECI1
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+AHA1 pp HSP82
+AHA1 pp HSP82
+DCP1 pp DCP1
+RPB9 pp RPB2
+RPB9 pp RPO21
+RPB2 pp RPO21
+RPB5 pp RPO21
+RPO26 pp RPO21
+RPB8 pp RPO21
+RPB9 pp RPB2
+RPB9 pp RPO21
+RPB10 pp RPB3
+RPB10 pp RPB2
+RPB11 pp RPO21
+RPB11 pp RPB3
+RPB11 pp RPB8
+RPC10 pp RPB2
+RPC10 pp RPB3
+DAL2 pp DAL2
+Ydr533c_Protein pp Ydr533c_Protein
+Acetyl-Coa_Carboxylase pp Acetyl-Coa_Carboxylase
+Acetyl-Coa_Carboxylase pp Acetyl-Coa_Carboxylase
+1UYT_C pp Acetyl-Coa_Carboxylase
+ACC1 pp ACC1
+RPL40A pp STP22
+ARO4 pp ARO4
+ARO4 pp ARO4
+KRE2 pp KRE2
+KRE2 pp KRE2
+ARO4 pp ARO4
+ARO4 pp ARO4
+SIR4 pp SIR4
+CDD1 pp CDD1
+CDD1 pp CDD1
+CDD1 pp CDD1
+CDD1 pp CDD1
+CDD1 pp CDD1
+INO1 pp INO1
+EFT1 interactsWith 1S1H_A
+RPS0B interactsWith 1S1H_A
+RPS3 interactsWith 1S1H_A
+RPS9A interactsWith 1S1H_A
+RPS2 interactsWith 1S1H_A
+RPS2 pp RPS0B
+RPS2 pp RPS9A
+RPS5 interactsWith 1S1H_A
+RPS22A interactsWith 1S1H_A
+RPS22A pp RPS0B
+RPS22A pp RPS2
+40s_Ribosomal_Protein_S16 interactsWith 1S1H_A
+40s_Ribosomal_Protein_S16 pp RPS5
+RPS20 interactsWith 1S1H_A
+RPS20 pp RPS3
+RPS14A interactsWith 1S1H_A
+RPS14A pp RPS5
+40s_Ribosomal_Protein_S23 interactsWith 1S1H_A
+40s_Ribosomal_Protein_S23 pp EFT1
+40s_Ribosomal_Protein_S18 interactsWith 1S1H_A
+40s_Ribosomal_Protein_S29-B pp RPS20
+40s_Ribosomal_Protein_S29-B pp RPS3
+40s_Ribosomal_Protein_S29-B interactsWith 1S1H_A
+RPS13 interactsWith 1S1H_A
+RPS11B interactsWith 1S1H_A
+RPS15 interactsWith 1S1H_A
+RPS15 pp 40s_Ribosomal_Protein_S18
+1S1I_4 interactsWith 1S1I_3
+RPL1B interactsWith 1S1I_3
+60s_Ribosomal_Protein_L2 interactsWith 1S1I_3
+60s_Ribosomal_Protein_L3 interactsWith 1S1I_3
+RPL4A interactsWith 1S1I_3
+RPL5 interactsWith 1S1I_4
+RPL5 interactsWith 1S1I_3
+RPL7A interactsWith 1S1I_3
+RPL7A interactsWith 1S1I_4
+RPL8B interactsWith 1S1I_3
+RPL9A interactsWith 1S1I_3
+RPL10 interactsWith 1S1I_3
+60s_Ribosomal_Protein_L11 interactsWith 1S1I_3
+60s_Ribosomal_Protein_L11 interactsWith 1S1I_4
+60s_Ribosomal_Protein_L12 interactsWith 1S1I_3
+RPL15A interactsWith 1S1I_3
+RPL15A pp RPL8B
+RPL16A interactsWith 1S1I_3
+RPL16A pp 60s_Ribosomal_Protein_L3
+RPL16A pp RPL9A
+60s_Ribosomal_Protein_L17-A interactsWith 1S1I_3
+RPL18B interactsWith 1S1I_3
+RPL18B pp RPL4A
+60s_Ribosomal_Protein_L19 interactsWith 1S1I_3
+60s_Ribosomal_Protein_L21-A interactsWith 1S1I_3
+60s_Ribosomal_Protein_L21-A pp RPL5
+60s_Ribosomal_Protein_L21-A interactsWith 1S1I_4
+RPL23B interactsWith 1S1I_3
+RPL23B pp 60s_Ribosomal_Protein_L3
+60s_Ribosomal_Protein_L24-A pp 60s_Ribosomal_Protein_L3
+60s_Ribosomal_Protein_L24-A pp RPL23B
+60s_Ribosomal_Protein_L24-A interactsWith 1S1I_3
+60s_Ribosomal_Protein_L25 interactsWith 1S1I_3
+RPL26A interactsWith 1S1I_3
+RPL28 interactsWith 1S1I_3
+RPL32 interactsWith 1S1I_3
+RPL31B interactsWith 1S1I_3
+RPL35B interactsWith 1S1I_3
+RPL37A interactsWith 1S1I_3
+RPL37A pp RPL4A
+60s_Ribosomal_Protein_L42 interactsWith 1S1I_3
+60s_Ribosomal_Protein_L42 pp RPL15A
+RPL43B interactsWith 1S1I_3
+RPL43B pp 60s_Ribosomal_Protein_L2
+ARO4 pp ARO4
+YNL168C pp YNL168C
+RFC4 pp RFC1
+RFC3 pp RFC4
+RFC3 pp RFC1
+RFC2 pp RFC3
+RFC5 pp RFC1
+RFC5 pp RFC2
+POL30 pp RFC3
+POL30 pp RFC1
+POL30 pp POL30
+POL30 pp RFC4
+POL30 pp POL30
+POL30 pp POL30
+Histone_H4_Peptide pp HST2
+Histone_H4_Peptide pp HST2
+LOT6 pp LOT6
+Pcf11_Protein pp Pcf11_Protein
+Pcf11_Protein pp Pcf11_Protein
+Pcf11_Protein pp Pcf11_Protein
+Cytochrome_B2,_Mitochondrial pp Cytochrome_B2,_Mitochondrial
+Cytochrome_B2,_Mitochondrial pp Cytochrome_B2,_Mitochondrial
+Cytochrome_B2,_Mitochondrial pp Cytochrome_B2,_Mitochondrial
+Dna_Repair_Protein_Rad51 pp Dna_Repair_Protein_Rad51
+Coproporphyrinogen_Iii_Oxidase pp Coproporphyrinogen_Iii_Oxidase
+Coproporphyrinogen_Iii_Oxidase pp Coproporphyrinogen_Iii_Oxidase
+Homoserine_Dehydrogenase pp Homoserine_Dehydrogenase
+5-Methylthioribose-1-Phosphate_Isomerase pp 5-Methylthioribose-1-Phosphate_Isomerase
+5-Methylthioribose-1-Phosphate_Isomerase pp 5-Methylthioribose-1-Phosphate_Isomerase
+5-Methylthioribose-1-Phosphate_Isomerase pp 5-Methylthioribose-1-Phosphate_Isomerase
+5-Methylthioribose-1-Phosphate_Isomerase pp 5-Methylthioribose-1-Phosphate_Isomerase
+Rad24 interactsWith Unknown
+Unknown interactsWith Rfc2
+Unknown interactsWith Rfc3
+Unknown interactsWith Rfc4
+ABF1 pd ACS1|YAL053W
+ABF1 pd PTA1|ERV46
+ABF1 pd ERV46|CDC24
+ABF1 pd PMT2|FUN26
+ABF1 pd PET112|NUP170
+ABF1 pd URA7|MRPL16
+ABF1 pd SLA1|YBL006C
+ABF1 pd IPP1|YBR012W-A
+ABF1 pd CDS1|YBR030W
+ABF1 pd YBR077C|ECM33
+ABF1 pd SEC18|SPT7
+ABF1 pd YBR101C|EXO84
+ABF1 pd CMD1|ALG1
+ABF1 pd OPY1|SHE3
+ABF1 pd ADH5|MRPS9
+ABF1 pd AME1|NGR1
+ABF1 pd SSH1|YBR284W
+ABF1 pd RRP7|HIS4
+ABF1 pd GBP2|SGF29
+ABF1 pd RSC6|THR4
+ABF1 pd SRB8|YCR082W
+ABF1 pd CWC2|NHP2
+ABF1 pd SNF3|YDL193W
+ABF1 pd UFD2|YDL189W
+ABF1 pd COP1|YDL144C
+ABF1 pd LYS21|STF1
+ABF1 pd SNA4|UBP1
+ABF1 pd CYK3|NUP84
+ABF1 pd PHO2|QRI2
+ABF1 pd GPR1|YDL033C
+ABF1 pd YDL012C|YDL010W
+ABF1 pd REG1|RAD28
+ABF1 pd FIN1|YDR131C
+ABF1 pd MSS116|YDR194W-A
+ABF1 pd YDR194W-A|REF2
+ABF1 pd YDR233C|LYS4
+ABF1 pd PEX5|MNN10
+ABF1 pd YDR279W|RRP45
+ABF1 pd GCN2|DPP1
+ABF1 pd PLO2|MHR1
+ABF1 pd TFB1|SSF2
+ABF1 pd YDR326C|SKP1
+ABF1 pd PEX3|YDR330W
+ABF1 pd YDR339C|tX(XXX)D
+ABF1 pd BCP1|TFC6
+ABF1 pd tK(CUU)D1|SEM1
+ABF1 pd YDR384C|EFT2
+ABF1 pd RPB7|MRP20
+ABF1 pd SIP1|CAD1
+ABF1 pd GUK1|NHX1
+ABF1 pd YIL134C-A|snR68
+ABF1 pd DFG10|NEO1
+ABF1 pd PRM2|CST6
+ABF1 pd BCY1|ULP2
+ABF1 pd MSL1|DSN1
+ABF1 pd SEC11|DAL81
+ABF1 pd RAD23|ANP1
+ABF1 pd PMP2|YEL017W
+ABF1 pd snR14|SEC3
+ABF1 pd EMP47|RGD2
+ABF1 pd LPD1|SMX2
+ABF1 pd SAP4|SHE10
+ABF1 pd EDC1|NIF3
+ABF1 pd YGL196W|GCN1
+ABF1 pd HOS2|IME4
+ABF1 pd YGL107C|MLC1
+ABF1 pd MUP1|RSC1
+ABF1 pd YGR058W|SPR3
+ABF1 pd NUP57|SEC35
+ABF1 pd UTP8|SYF2
+ABF1 pd QCR9|UBR1
+ABF1 pd TYS1|TFG1
+ABF1 pd PHB2|NAS6
+ABF1 pd PUP2|ENO1
+ABF1 pd YGR268C|YTA7
+ABF1 pd YHL029C|WSC4
+ABF1 pd WSC4|RIM101
+ABF1 pd SMF2|YHR050W-A
+ABF1 pd SSZ1|RRP3
+ABF1 pd NMD2|YHR078W
+ABF1 pd YNG2|MSR1
+ABF1 pd YHR115C|YHR116W
+ABF1 pd YAP1801|YHR162W
+ABF1 pd YHR199C|RPN10
+ABF1 pd YJL184W|MNN11
+ABF1 pd SWI3|KRE9
+ABF1 pd MDV1|CCT7
+ABF1 pd MRPL8|YJL062W-A
+ABF1 pd CCT8|tM(CAU)J2
+ABF1 pd NTA1|RPA12
+ABF1 pd FIP1|IME1
+ABF1 pd YJR115W|YJR116W
+ABF1 pd ECM17|IML1
+ABF1 pd YKT6|YKL195W
+ABF1 pd DPH2|CNB1
+ABF1 pd SNU114|EBP2
+ABF1 pd MRP49|TPK3
+ABF1 pd RPC25|LTV1
+ABF1 pd APL2|OCT1
+ABF1 pd SMY1|DHR2
+ABF1 pd FBA1|MPE1
+ABF1 pd MAE1|TFA1
+ABF1 pd ATP7|PUT3
+ABF1 pd YKL014C|ARC19
+ABF1 pd LAC1|CAP1
+ABF1 pd YKL005C|AUR1
+ABF1 pd SET3|MSG1
+ABF1 pd GLG1|TIF1
+ABF1 pd RPF2|NUP133
+ABF1 pd YLL034C|YLL033W
+ABF1 pd UBR2|SNF7
+ABF1 pd SPT8|ERG3
+ABF1 pd IOC2|KIN2
+ABF1 pd UTP13|IFH1
+ABF1 pd CDC42|tI(UAU)L
+ABF1 pd GSP1|ATP14
+ABF1 pd REC102|CHS5
+ABF1 pd snR57|RPS25B
+ABF1 pd VPS33|AFG2
+ABF1 pd ATP18|YML081W
+ABF1 pd MVP1|TAF4
+ABF1 pd YMR030W-A|ARP9
+ABF1 pd TOM37|RNA14
+ABF1 pd AIP1|UTP15
+ABF1 pd ECM16|POM152
+ABF1 pd VTI1|CIK1
+ABF1 pd CLN1|ROT1
+ABF1 pd TIF11|TPS3
+ABF1 pd LCB1|PRC1
+ABF1 pd KRE1|YNL321W
+ABF1 pd YNL313C|RFA2
+ABF1 pd MCK1|MRPS18
+ABF1 pd CAF40|SEC21
+ABF1 pd LYP1|PIK1
+ABF1 pd DSL1|SIP3
+ABF1 pd GIS2|YNL254C
+ABF1 pd SUI1|SLA2
+ABF1 pd YNL213C|VID27
+ABF1 pd YNL190W|SRP1
+ABF1 pd NPR1|YNL182C
+ABF1 pd TOM70|YNL119W
+ABF1 pd DCP2|MLS1
+ABF1 pd MLS1|YNL116W
+ABF1 pd YNL086W|MKT1
+ABF1 pd ARP5|YNL058C
+ABF1 pd IDH1|NCE103
+ABF1 pd RSM19|DBP6
+ABF1 pd PET494|YNR046W
+ABF1 pd RRI2|MSN1
+ABF1 pd BRX1|MDM20
+ABF1 pd HST1|RTG1
+ABF1 pd PRE6|YOL036W
+ABF1 pd YOR044W|TOM6
+ABF1 pd NOB1|SGT1
+ABF1 pd RPO31|RPT5
+ABF1 pd YOR205C|NOC2
+ABF1 pd RPN8|YOR262W
+ABF1 pd NOP58|HSD1
+ABF1 pd IQG1|CIN2
+ABF1 pd NSL1|SSO1
+ABF1 pd YPL229W|CET1
+ABF1 pd YPL159C|YPL158C
+ABF1 pd EGD1|PMA2
+ABF1 pd YPL013C|RRP12
+ABF1 pd DSS4|RLF2
+ABF1 pd FHL1|COD1
+ABF1 pd ANT1|SCD6
+ABF1 pd BET2|PRP4
+ABF1 pd PZF1|RPO26
+ACE2 pd YAL064W|YAL063C-A
+ACE2 pd FLO9|GDH3
+ACE2 pd ICS2|CST13
+ACE2 pd KAR4|SPB1
+ACE2 pd VCX1|PCL2
+ACE2 pd GCN4|TOS9
+ACE2 pd DSE1|RSP5
+ACE2 pd AAD6|AGP3
+ACE2 pd FRS2|GAT1
+ACE2 pd SCW11|CWH41
+ACE2 pd YGL007C-A|YGL006W-A
+ACE2 pd KSS1|BUD9
+ACE2 pd CHS7|DSE2
+ACE2 pd YJL160C|HSP150
+ACE2 pd YJL077W-B|ICS3
+ACE2 pd YKL151C|MCR1
+ACE2 pd CTS1|YLR287C
+ACE2 pd YML007C-A|YAP1
+ACE2 pd GLO1|YML003W
+ACE2 pd MDJ2|EGT2
+ACE2 pd TPM1|NIS1
+ADR1 pd FUN26|CCR4
+ADR1 pd RIB5|POP4
+ADR1 pd YDL241W|LRG1
+ADR1 pd YDL159W-A|STE7
+ADR1 pd YDL119C|CYK3
+ADR1 pd YDL091C|RAM1
+ADR1 pd ERP3|CDC7
+ADR1 pd REG1|RAD28
+ADR1 pd ECM37|PAN6
+ADR1 pd PAU2|YEL048C
+ADR1 pd snR52|GLC7
+ADR1 pd YFR008W|tG(GCC)F1
+ADR1 pd YFR044C|YFR045W
+ADR1 pd ESP1|TEL2
+ADR1 pd DAP2|YHR029C
+ADR1 pd PET130|BBC1
+ADR1 pd OSM1|tG(GCC)J2
+ADR1 pd HIR3|YJR141W
+ADR1 pd tW(CCA)K|YKL071W
+ADR1 pd ATP7|PUT3
+ADR1 pd YPS3|YLR125W
+ADR1 pd YLR364W|RPS22B
+ADR1 pd YNL101W|YNL100W
+ADR1 pd YNR004W|VPS27
+ADR1 pd AAD15|YOL164W-A
+ADR1 pd PPT2|PXA1
+ADR1 pd YPR108W-A|tT(UGU)P
+AFT2 pd YBR077C|ECM33
+AFT2 pd AGP2|HSL7
+AFT2 pd YBR204C|KTR3
+AFT2 pd KTR3|FTH1
+AFT2 pd PHO89|YBR296C-A
+AFT2 pd PAU3|YCR105W
+AFT2 pd RDS1|AAD3
+AFT2 pd IWR1|YDL114W
+AFT2 pd RAM1|YDL089W
+AFT2 pd GPR1|YDL033C
+AFT2 pd CTH1|YDR152W
+AFT2 pd MSW1|CCC2
+AFT2 pd APT2|SSN2
+AFT2 pd PRP3|YDR474C
+AFT2 pd JIP4|YDR476C
+AFT2 pd FIT1|STL1
+AFT2 pd XBP1|SGA1
+AFT2 pd MAM33|RPS24B
+AFT2 pd YPS6|YIR041W
+AFT2 pd DLD3|YEL070W
+AFT2 pd PRB1|SOM1
+AFT2 pd tQ(UUG)E2|UBC8
+AFT2 pd tQ(UUG)E1|YER048W-A
+AFT2 pd YER078C|YER078W-A
+AFT2 pd snR52|GLC7
+AFT2 pd FTR1|LSM5
+AFT2 pd ECM32|BMH1
+AFT2 pd YER188C-A|YER189W
+AFT2 pd YFL042C|YFL041W-A
+AFT2 pd YFL041W-A|FET5
+AFT2 pd tF(GAA)F|YFR007W
+AFT2 pd YFR017C|YFR018C
+AFT2 pd LSB3|HIS2
+AFT2 pd YGL261C|YPS5
+AFT2 pd MND1|GTS1
+AFT2 pd HSF1|RCS1
+AFT2 pd SDS23|OLE1
+AFT2 pd SEC9|NMA2
+AFT2 pd YGR130C|YGR131W
+AFT2 pd SKN1|tG(UCC)G
+AFT2 pd YHL046C|YHL044W
+AFT2 pd SOD2|YHR009C
+AFT2 pd YHR032W|YHR033W
+AFT2 pd YHR115C|YHR116W
+AFT2 pd YHR194W|NVJ1
+AFT2 pd YJL205C|RCY1
+AFT2 pd PRY1|PRY3
+AFT2 pd YJL068C|MPM1
+AFT2 pd YJR005C-A|HYS2
+AFT2 pd VPS55|SSC1
+AFT2 pd YKL224C|YKL222C
+AFT2 pd LAP4|HSL1
+AFT2 pd DEF1|YKL053C-A
+AFT2 pd MRS4|YSR3
+AFT2 pd YLL064C|AYT1
+AFT2 pd DPS1|BPT1
+AFT2 pd PSR1|COX17
+AFT2 pd SMF3|MLH2
+AFT2 pd YPS1|YPS3
+AFT2 pd TIS11|YLR137W
+AFT2 pd NHA1|SLS1
+AFT2 pd HCR1|YLR193C
+AFT2 pd HMX1|ENT2
+AFT2 pd CLB4|YLR211C
+AFT2 pd CRR1|FRE1
+AFT2 pd ECI1|YLR285W
+AFT2 pd SUR4|VID22
+AFT2 pd LSM3|MRPL4
+AFT2 pd YLR460C|PAU4
+AFT2 pd GTR1|NDI1
+AFT2 pd YMR034C|IMP2
+AFT2 pd YMR041C|tF(GAA)M
+AFT2 pd AAC1|FET3
+AFT2 pd YMR086W|YMR087W
+AFT2 pd YMR134W|DCR1
+AFT2 pd ECM5|MMT1
+AFT2 pd RNH1|RNA1
+AFT2 pd YMR265C|RSN1
+AFT2 pd YMR279C|CAT8
+AFT2 pd YRF1-6|COS1
+AFT2 pd YNL269W|LYP1
+AFT2 pd ATX1|DSL1
+AFT2 pd ZWF1|NAR1
+AFT2 pd YNL194C|YNL193W
+AFT2 pd NST1|RHO2
+AFT2 pd BUD17|CPR8
+AFT2 pd PDR18|YNR071C
+AFT2 pd COS10|YNR075C-A
+AFT2 pd YNR075C-A|PAU6
+AFT2 pd YOL161C|YOL159C-A
+AFT2 pd ENB1|YOL157C
+AFT2 pd YOL155W-A|YOL155C
+AFT2 pd ISU2|YOR227W
+AFT2 pd RAX1|YOR302W
+AFT2 pd COT1|YOR316C-A
+AFT2 pd YOR316C-A|FAA1
+AFT2 pd MIP1|VMA4
+AFT2 pd FIT3|FRE5
+AFT2 pd VIK1|YAH1
+AFT2 pd PRM4|KIP2
+AFT2 pd YPL137C|ISU1
+AFT2 pd PMA2|YPL034W
+AFT2 pd tF(GAA)P1|YPR003C
+AFT2 pd tK(UUU)P|CLB2
+AFT2 pd YPR151C|YPR152C
+ARR1 pd HMLALPHA1|CHA1
+ARR1 pd MGM101|RPS4A
+ARR1 pd COS9|SRY1
+ARR1 pd tP(UGG)L|YLL025W
+ARR1 pd YLR022C|YLR023C
+ARR1 pd SRL2|EMP70
+ARR1 pd YLR162W-A|MAS1
+ASH1 pd YBR070C|YBR071W
+ASH1 pd HXT6|HXT3
+ASH1 pd YHP1|PPN1
+ASH1 pd XBP1|SGA1
+ASH1 pd PIR1|PIR3
+ASH1 pd GAP1|tA(AGC)K2
+ASH1 pd YKR096W|PCK1
+ASH1 pd ECM38|EXG1
+ASH1 pd RPL15B|YMR122W-A
+ASH1 pd YOL114C|SKM1
+ASH1 pd SKS1|NCE4
+AZF1 pd YBL029C-A|YBL029W
+AZF1 pd YDL037C|YDL036C
+AZF1 pd YDR042C|snR47
+AZF1 pd RPL27B|snR13
+AZF1 pd XBP1|SGA1
+AZF1 pd MUC1|MRS1
+AZF1 pd CAN1|NPR2
+AZF1 pd YHL042W|ARN1
+AZF1 pd KNS1|COX19
+AZF1 pd YLR023C|UBR2
+AZF1 pd ERG6|YML007C-A
+AZF1 pd snR49|BRE5
+BAS1 pd GCV3|PTA1
+BAS1 pd IST2|RFC5
+BAS1 pd YBR216C|APG12
+BAS1 pd HIS4|BIK1
+BAS1 pd GCV1|YDR020C
+BAS1 pd ADE8|SIZ1
+BAS1 pd DRE3|YIL002W-A
+BAS1 pd CEM1|HOR2
+BAS1 pd MET6|IES5
+BAS1 pd MTO1|ADE5,7
+BAS1 pd YGL186C|YGL185C
+BAS1 pd STR3|MND1
+BAS1 pd ADE6|COX18
+BAS1 pd YGR203W|ADE3
+BAS1 pd ECM25|YJL200C
+BAS1 pd SRY1|JEN1
+BAS1 pd COY1|STE3
+BAS1 pd YKR079C|MTD1
+BAS1 pd SHM2|REX2
+BAS1 pd RSC2|ADE13
+BAS1 pd ADE17|RPL15B
+BAS1 pd YMR188C|GCV2
+BAS1 pd ZRC1|YMR244W
+BAS1 pd ADE4|ATM1
+BAS1 pd ADE2|YOR129C
+BAS1 pd YOR267C|PAC1
+BAS1 pd VTC3|CTF19
+CAD1 pd YBL009W|YBL008W-A
+CAD1 pd FRM2|AGP1
+CAD1 pd YDR132C|YCF1
+CAD1 pd YDR533C|FIT1
+CAD1 pd GLY1|IES6
+CAD1 pd PHO81|YHB1
+CAD1 pd ARN1|YHL039W
+CAD1 pd SOD2|YHR009C
+CAD1 pd GSH1|LSB6
+CAD1 pd LAP4|HSL1
+CAD1 pd CYT2|YKL086W
+CAD1 pd tW(CCA)K|YKL071W
+CAD1 pd NFU1|PTM1
+CAD1 pd MRS4|YSR3
+CAD1 pd DRE2|SIS2
+CAD1 pd GTT2|YLL058W
+CAD1 pd YLR108C|AHP1
+CAD1 pd YML117W|ATR1
+CAD1 pd LYS7|SUB1
+CAD1 pd MCH4|RRI2
+CAD1 pd YOR172W|YOR173W
+CAD1 pd MSF1|TAH18
+CBF1 pd ACS1|YAL053W
+CBF1 pd DRS2|MAK16
+CBF1 pd YAL018C|FUN31
+CBF1 pd DEP1|CYS3
+CBF1 pd CHS2|ATP3
+CBF1 pd REB1|REG2
+CBF1 pd ARO4|YBR250W
+CBF1 pd YBR255C-A|RIB5
+CBF1 pd APE3|YBR287W
+CBF1 pd YCR087C-A|ABP1
+CBF1 pd MSH3|CDC39
+CBF1 pd BRE1|YDL073W
+CBF1 pd RAD59|USO1
+CBF1 pd RPN4|OSH2
+CBF1 pd RPT2|PTC1
+CBF1 pd snR47|NRG1
+CBF1 pd CDC34|PST1
+CBF1 pd DOP1|PEX7
+CBF1 pd RVB1|HST4
+CBF1 pd YDR267C|MSW1
+CBF1 pd MHR1|SUR2
+CBF1 pd GNP1|SMT3
+CBF1 pd APA2|YDR531W
+CBF1 pd YIL127C|STH1
+CBF1 pd RPI1|RHO3
+CBF1 pd YIL088C|YIL087C
+CBF1 pd SER33|SPO22
+CBF1 pd BCY1|ULP2
+CBF1 pd MET28|YAP5
+CBF1 pd GLY1|IES6
+CBF1 pd IES6|YEL043W
+CBF1 pd SRI1|RIP1
+CBF1 pd SAH1|ERG28
+CBF1 pd HIS1|FCY2
+CBF1 pd FCY21|FCY22
+CBF1 pd YER071C|VTC1
+CBF1 pd RPS24A|YER074W-A
+CBF1 pd MET6|IES5
+CBF1 pd PRS2|UBC6
+CBF1 pd GLE2|FLO8
+CBF1 pd SWI4|LSM4
+CBF1 pd BOI2|SPR6
+CBF1 pd DSE1|RSP5
+CBF1 pd ECM32|BMH1
+CBF1 pd RIM15|HAC1
+CBF1 pd EPL1|FYV11
+CBF1 pd LPD1|SMX2
+CBF1 pd PTR3|MET10
+CBF1 pd YFR048W|YMR31
+CBF1 pd SIP2|SPT16
+CBF1 pd SDS23|OLE1
+CBF1 pd SCM4|YGR052W
+CBF1 pd snR48|ERG25
+CBF1 pd YGR109W-B|YGR110W
+CBF1 pd SYF2|YGR130C
+CBF1 pd YGR154C|CYS4
+CBF1 pd ELP2|YGR201C
+CBF1 pd YGR203W|ADE3
+CBF1 pd YGR223C|AZR1
+CBF1 pd SMI1|BNS1
+CBF1 pd PHO81|YHB1
+CBF1 pd OSH7|QCR10
+CBF1 pd YHR032W|YHR033W
+CBF1 pd SRB2|NCP1
+CBF1 pd KSP1|YHR083W
+CBF1 pd GAR1|YNG2
+CBF1 pd SFB3|TRA1
+CBF1 pd YHR112C|YHR113W
+CBF1 pd SPL2|ARO9
+CBF1 pd PEX2|CBP1
+CBF1 pd SWE1|MNN5
+CBF1 pd SET2|ERG20
+CBF1 pd ERG20|QCR8
+CBF1 pd CIS3|FAR1
+CBF1 pd SNA3|YJL149W
+CBF1 pd YJL133C-A|MRS3
+CBF1 pd YJL118W|PHO86
+CBF1 pd GSH1|LSB6
+CBF1 pd NUP82|BNA3
+CBF1 pd VTC4|RPC17
+CBF1 pd TDH2|MET3
+CBF1 pd PTK2|CBF1
+CBF1 pd RPL43B|SFC1
+CBF1 pd ECM17|IML1
+CBF1 pd RPS4A|HMS2
+CBF1 pd ACP1|DPH2
+CBF1 pd ATP7|PUT3
+CBF1 pd LAC1|CAP1
+CBF1 pd SIS2|tK(UUU)K
+CBF1 pd YLL056C|YLL055W
+CBF1 pd PSR1|COX17
+CBF1 pd EMP46|GAL2
+CBF1 pd YLR091W|SUL2
+CBF1 pd snR6|YLR108C
+CBF1 pd YLR149C|STM1
+CBF1 pd PDR8|BOP2
+CBF1 pd EXG1|YLR301W
+CBF1 pd UTP21|VIP1
+CBF1 pd PHO84|GTR1
+CBF1 pd NDI1|YML119W
+CBF1 pd YML018C|PSP2
+CBF1 pd MSN2|LYS7
+CBF1 pd YMR194C-B|ICY1
+CBF1 pd ICY1|YMR196W
+CBF1 pd SKY1|GUA1
+CBF1 pd ATM1|PRP12
+CBF1 pd PSE1|NIP1
+CBF1 pd WSC2|POP3
+CBF1 pd YNL277W-A|MET2
+CBF1 pd ATX1|DSL1
+CBF1 pd BNI4|CSL4
+CBF1 pd POP1|ADE12
+CBF1 pd LEU4|MET4
+CBF1 pd YNL095C|APP1
+CBF1 pd YNL080C|TPM1
+CBF1 pd YDJ1|YNL063W
+CBF1 pd IDH1|NCE103
+CBF1 pd DOM34|CIT1
+CBF1 pd PHO91|YNR014W
+CBF1 pd BRE5|POP2
+CBF1 pd PFK27|MED7
+CBF1 pd YOL101C|PKH2
+CBF1 pd MET22|YOL063C
+CBF1 pd YOR054C|NOB1
+CBF1 pd YNG1|CYT1
+CBF1 pd NUP1|KTR1
+CBF1 pd YRR1|DDP1
+CBF1 pd VPH1|YOR271C
+CBF1 pd MBF1|BUD7
+CBF1 pd RAX1|YOR302W
+CBF1 pd SNC2|PDR10
+CBF1 pd TYE7|tP(UGG)O3
+CBF1 pd YOR365C|SCP1
+CBF1 pd BBP1|HFI1
+CBF1 pd ICY2|RPL36B
+CBF1 pd YPL236C|RVB2
+CBF1 pd YPL206C|HRR25
+CBF1 pd OYE3|YPL170W
+CBF1 pd VTC3|CTF19
+CBF1 pd RPL11A|PRE2
+CBF1 pd YPR158W-B|YPR158C-D
+CIN5 pd FLO9|GDH3
+CIN5 pd CDC19|YAL037C-A
+CIN5 pd YAL037C-A|YAL037W
+CIN5 pd PET9|YBL029C-A
+CIN5 pd YBR007C|FLR1
+CIN5 pd FLR1|HHF1
+CIN5 pd YBR053C|YRO2
+CIN5 pd YBR070C|YBR071W
+CIN5 pd YBR071W|HSP26
+CIN5 pd ECM8|YBR077C
+CIN5 pd BEM1|YBR200W-A
+CIN5 pd SUL1|PCA1
+CIN5 pd AGP1|KCC4
+CIN5 pd HSP30|YCR023C
+CIN5 pd YCR102C|PAU3
+CIN5 pd PRR2|FYV14
+CIN5 pd UGX2|SFA1
+CIN5 pd RPP1B|YDL129W
+CIN5 pd YDL037C|YDL036C
+CIN5 pd MCD1|NHP10
+CIN5 pd MRH1|LYS14
+CIN5 pd YDR042C|snR47
+CIN5 pd RAD55|SED1
+CIN5 pd tR(ACG)D|YDR089W
+CIN5 pd PRO1|CFT1
+CIN5 pd YDR338C|YDR339C
+CIN5 pd HXT3|SGI1
+CIN5 pd APT2|SSN2
+CIN5 pd GNP1|SMT3
+CIN5 pd RPI1|RHO3
+CIN5 pd MET30|PIG2
+CIN5 pd SGN1|MPH1
+CIN5 pd YIR018C-A|MUC1
+CIN5 pd MUC1|MRS1
+CIN5 pd MAK10|AFG1
+CIN5 pd YER028C|SMB1
+CIN5 pd KRE29|HVG1
+CIN5 pd ACA1|SPO73
+CIN5 pd VTC1|ALD5
+CIN5 pd SEC4|VTC2
+CIN5 pd tG(GCC)F2|YFR017C
+CIN5 pd YFR055W|YFR057W
+CIN5 pd FZF1|HXK2
+CIN5 pd YGL007C-A|YGL006W-A
+CIN5 pd MUQ1|STF2
+CIN5 pd SEC9|NMA2
+CIN5 pd ASK10|ESP1
+CIN5 pd PEX4|CAF130
+CIN5 pd THI4|YGR145W
+CIN5 pd MSM1|YIP1
+CIN5 pd PBP1|OKP1
+CIN5 pd TDH3|PDX1
+CIN5 pd TRX2|YGR210C
+CIN5 pd PHO81|YHB1
+CIN5 pd KEL2|PEX21
+CIN5 pd YGR243W|LSC2
+CIN5 pd SOL4|MGA1
+CIN5 pd MGA1|YGR250C
+CIN5 pd YGR250C|YGR251W
+CIN5 pd YHL046C|YHL044W
+CIN5 pd YHL042W|ARN1
+CIN5 pd SBP1|RPL8A
+CIN5 pd YHR048W|FSH1
+CIN5 pd STB5|OYE2
+CIN5 pd MIA1|snR37
+CIN5 pd BET4|MAD2
+CIN5 pd tM(CAU)J1|YJL027C
+CIN5 pd CYR1|SYS1
+CIN5 pd YJR003C|SAG1
+CIN5 pd YJR011C|YJR013W
+CIN5 pd IME1|RPL43B
+CIN5 pd NMD5|XPT1
+CIN5 pd RPS4A|HMS2
+CIN5 pd PGU1|YJR154W
+CIN5 pd YKL224C|YKL222C
+CIN5 pd LOT5|FAS1
+CIN5 pd KTI12|HAP4
+CIN5 pd SLD2|YKL107W
+CIN5 pd LAP4|HSL1
+CIN5 pd PRI2|PHD1
+CIN5 pd GPX1|PAN3
+CIN5 pd tD(GUC)K|GAP1
+CIN5 pd CCP1|GPT2
+CIN5 pd SIR1|FLO10
+CIN5 pd YKR104W|YKR105C
+CIN5 pd MHT1|MMP1
+CIN5 pd YLL054C|YLL053C
+CIN5 pd YLR001C|NOC3
+CIN5 pd RPL15A|YLR030W
+CIN5 pd EMP46|GAL2
+CIN5 pd YPS3|YLR125W
+CIN5 pd ECM22|CDC42
+CIN5 pd YLR264C-A|NEJ1
+CIN5 pd ACO1|STT4
+CIN5 pd STE11|NMD4
+CIN5 pd YLR412W|YLR412C-A
+CIN5 pd YLR460C|PAU4
+CIN5 pd COS3|YML131W
+CIN5 pd YML117W|ATR1
+CIN5 pd LYS7|SUB1
+CIN5 pd ISF1|ADH3
+CIN5 pd YTA12|YMR090W
+CIN5 pd MSS11|SMP2
+CIN5 pd HOT1|DDR48
+CIN5 pd ECM5|MMT1
+CIN5 pd ERG8|YMR221C
+CIN5 pd YMR244C-A|FAA4
+CIN5 pd PPA2|PRP24
+CIN5 pd RIT1|tY(GUA)M2
+CIN5 pd FET4|YMR321C
+CIN5 pd RHO5|RPS3
+CIN5 pd RPS3|YNL177C
+CIN5 pd TOP2|YNL087W
+CIN5 pd AAD15|YOL164W-A
+CIN5 pd YOL164W-A|YOL164W
+CIN5 pd YOL157C|HXT11
+CIN5 pd FRE7|GRE2
+CIN5 pd MED7|HRT1
+CIN5 pd RRI2|MSN1
+CIN5 pd SHR5|YOL109W
+CIN5 pd MAM3|GPD2
+CIN5 pd DDR2|SPE2
+CIN5 pd ROD1|YOR019W
+CIN5 pd STI1|CIN5
+CIN5 pd CIN5|DFG16
+CIN5 pd YOR049C|YOR051C
+CIN5 pd GAC1|YOR179C
+CIN5 pd WTM2|WTM1
+CIN5 pd HSD1|RPL20B
+CIN5 pd SPS4|YOR315W
+CIN5 pd YOR316C-A|FAA1
+CIN5 pd TYE7|tP(UGG)O3
+CIN5 pd RDR1|FRE3
+CIN5 pd YPL277C|SAM3
+CIN5 pd YPL063W|ALD6
+CIN5 pd YPR013C|YPR015C
+CIN5 pd YPR022C|EAF3
+CIN5 pd ARP7|GLN1
+CIN5 pd YPR063C|ROX1
+CIN5 pd THI22|AXL1
+CIN5 pd AXL1|CTR1
+CIN5 pd DPM1|GDB1
+DAL80 pd MAK16|LTE1
+DAL80 pd YBL059C-A|YBL059W
+DAL80 pd POP8|PEP1
+DAL80 pd TYR1|POP7
+DAL80 pd YBR203W|YBR204C
+DAL80 pd HMLALPHA1|CHA1
+DAL80 pd PAU3|YCR105W
+DAL80 pd KNH1|STP4
+DAL80 pd YDR042C|snR47
+DAL80 pd YDR067C|DOS2
+DAL80 pd PSL10|ARO1
+DAL80 pd PRP3|YDR474C
+DAL80 pd YDR542W|YRF1-1
+DAL80 pd TIR1|tE(UUC)E1
+DAL80 pd YER188C-A|YER189W
+DAL80 pd VTC2|MSH4
+DAL80 pd PRP38|MRPL25
+DAL80 pd MSR1|HXT4
+DAL80 pd LIN1|REC104
+DAL80 pd FAR1|SSY5
+DAL80 pd CCT8|tM(CAU)J2
+DAL80 pd CSE4|ELM1
+DAL80 pd SRL2|EMP70
+DAL80 pd LSM3|MRPL4
+DAL80 pd HXT2|tE(UUC)M
+DAL80 pd PET111|YMR258C
+DAL80 pd NTG2|NGL1
+DAL80 pd YOL024W|IFM1
+DAL80 pd YOR093C|ARF3
+DAL80 pd YOR173W|MED4
+DAL80 pd FAA1|HSH49
+DAL80 pd tC(GCA)P2|THI22
+DAL81 pd YGR017W|UGA1
+DAL82 pd YAL064C-A|YAL064W
+DAL82 pd FLO9|GDH3
+DAL82 pd SWD1|RFA1
+DAL82 pd YBL059C-A|YBL059W
+DAL82 pd RER2|COQ1
+DAL82 pd DUR1,2|tC(GCA)B
+DAL82 pd tC(GCA)B|tE(UUC)B
+DAL82 pd LRG1|ADY3
+DAL82 pd YDL238C|YDL237W
+DAL82 pd GLT1|UGA3
+DAL82 pd PST2|MRH1
+DAL82 pd YDR042C|snR47
+DAL82 pd YDR090C|RLI1
+DAL82 pd MKC7|TAF12
+DAL82 pd YVH1|DAL1
+DAL82 pd DAL1|DAL4
+DAL82 pd DAL4|DAL2
+DAL82 pd DCG1|DAL7
+DAL82 pd DAL7|DAL3
+DAL82 pd DAL3|MGA2
+DAL82 pd YPS6|YIR041W
+DAL82 pd PRE1|PRP22
+DAL82 pd ACA1|SPO73
+DAL82 pd snR52|GLC7
+DAL82 pd FRS2|GAT1
+DAL82 pd PRP38|MRPL25
+DAL82 pd SLH1|YGR271C-A
+DAL82 pd YGR273C|TAF1
+DAL82 pd ARN2|YHL046C
+DAL82 pd tM(CAU)J1|YJL027C
+DAL82 pd tW(CCA)J|YJL010C
+DAL82 pd YJR011C|YJR013W
+DAL82 pd YKL098W|YKL096C-B
+DAL82 pd STB6|tW(CCA)K
+DAL82 pd SFT1|RPL14A
+DAL82 pd SRL2|EMP70
+DAL82 pd CKI1|PDC5
+DAL82 pd ATP14|YLR297W
+DAL82 pd CRN1|SEN1
+DAL82 pd ECM30|YLR437C
+DAL82 pd LSM3|MRPL4
+DAL82 pd YMR251W|HOR7
+DAL82 pd PET111|YMR258C
+DAL82 pd tQ(CUG)M|SCS7
+DAL82 pd SCS7|YMR272W-B
+DAL82 pd YRF1-6|COS1
+DAL82 pd ERG24|PRM1
+DAL82 pd MRP7|HRB1
+DAL82 pd ZPS1|FRE7
+DAL82 pd PPM2|ARG8
+DAL82 pd YOL075C|YOL073C
+DAL82 pd DIS3|TAT2
+DAL82 pd THI80|ELG1
+DAL82 pd GPI2|GCR1
+DAL82 pd tC(GCA)P2|THI22
+DAL82 pd snR45|ASN1
+DIG1 pd tA(UGC)A|BUD14
+DIG1 pd BUD14|ADE1
+DIG1 pd tL(CAA)A|tS(AGA)A
+DIG1 pd PRM9|YAR033W
+DIG1 pd SKT5|YBL060W
+DIG1 pd PEP1|FUS3
+DIG1 pd tG(GCC)B|RRN6
+DIG1 pd tS(AGA)B|UTP20
+DIG1 pd IPP1|YBR012W-A
+DIG1 pd ATP3|FIG1
+DIG1 pd FIG1|FAT1
+DIG1 pd ORC2|TRM7
+DIG1 pd tD(GUC)B|UBC4
+DIG1 pd UBC4|TEC1
+DIG1 pd YCL056C|KAR4
+DIG1 pd RNQ1|FUS1
+DIG1 pd CWH43|SRD1
+DIG1 pd YCR023C|YCR024C
+DIG1 pd YCR026C|RHB1
+DIG1 pd ABP1|FIG2
+DIG1 pd RDI1|PPH21
+DIG1 pd YDL129W|VCX1
+DIG1 pd VCX1|PCL2
+DIG1 pd AFR1|SSS1
+DIG1 pd tQ(UUG)D2|YDR098C-B
+DIG1 pd STB3|YDR169C-A
+DIG1 pd YDR169C-A|SEC7
+DIG1 pd YDR170W-A|HSP42
+DIG1 pd YDR210W-B|YDR210C-D
+DIG1 pd SNU56|tY(GUA)D
+DIG1 pd PHM6|YDR282C
+DIG1 pd GIC2|SUM1
+DIG1 pd TFB1|SSF2
+DIG1 pd tF(GAA)D|YDR316W-A
+DIG1 pd tX(XXX)D|YDR341C
+DIG1 pd tM(CAU)D|TCM10
+DIG1 pd YDR370C|CTS2
+DIG1 pd LSM6|RGA2
+DIG1 pd TOM1|YDR458C
+DIG1 pd RMT2|YDR466W
+DIG1 pd tL(CAA)D|GIN4
+DIG1 pd AYR1|SIM1
+DIG1 pd YIL083C|YIL082W-A
+DIG1 pd PRM2|CST6
+DIG1 pd SNL1|BAR1
+DIG1 pd YEL041W|UTR2
+DIG1 pd CAJ1|tQ(UUG)E1
+DIG1 pd tQ(UUG)E1|YER048W-A
+DIG1 pd YER064C|ICL1
+DIG1 pd PUP3|RAD51
+DIG1 pd SHO1|YER119C
+DIG1 pd GLC7|tH(GUG)E2
+DIG1 pd tH(GUG)E2|tK(CUU)E2
+DIG1 pd YER159C-A|SPT2
+DIG1 pd YER187W|YER188C-A
+DIG1 pd GYP8|STE2
+DIG1 pd YFR022W|PES4
+DIG1 pd tA(AGC)F|YFR026C
+DIG1 pd GCN1|HOS2
+DIG1 pd tW(CCA)G1|YGL117W
+DIG1 pd YGL117W|CDC20
+DIG1 pd tH(GUG)G2|SRM1
+DIG1 pd TOS8|tE(UUC)G1
+DIG1 pd AGA2|RPL24A
+DIG1 pd tF(GAA)G|SCW11
+DIG1 pd SNU71|MSB2
+DIG1 pd tK(UUU)G2|CLB1
+DIG1 pd tR(UCU)G2|YGR165W
+DIG1 pd YGR173W|tG(GCC)G1
+DIG1 pd CRH1|tW(CCA)G2
+DIG1 pd PHO81|YHB1
+DIG1 pd YHB1|YGR235C
+DIG1 pd COS8|ARN2
+DIG1 pd GPA1|MRS11
+DIG1 pd tA(AGC)H|RPS27B
+DIG1 pd YHR083W|STE12
+DIG1 pd YHR085W|NAM8
+DIG1 pd RPL42B|CHS7
+DIG1 pd MNL1|SCH9
+DIG1 pd tT(AGU)J|PHO90
+DIG1 pd SWE1|MNN5
+DIG1 pd ASG7|SET2
+DIG1 pd snR190|RPA34
+DIG1 pd YJL113W|tD(GUC)J1
+DIG1 pd PRY3|YJL077W-B
+DIG1 pd YJL077W-B|ICS3
+DIG1 pd MOG1|HOC1
+DIG1 pd PGU1|YJR154W
+DIG1 pd tL(UAA)K|HYM1
+DIG1 pd GFA1|LAP4
+DIG1 pd CWP2|CWP1
+DIG1 pd CWP1|YJU2
+DIG1 pd YKL033W|tV(AAC)K2
+DIG1 pd tV(AAC)K2|IXR1
+DIG1 pd TOS5|PRY2
+DIG1 pd PXL1|SRL3
+DIG1 pd YLL057C|YLL056C
+DIG1 pd RAX2|ARP6
+DIG1 pd HOG1|tR(ACG)L
+DIG1 pd YLR114C|CFT2
+DIG1 pd ECM22|CDC42
+DIG1 pd THI7|YLR238W
+DIG1 pd CDC46|SMD2
+DIG1 pd CHS5|MID2
+DIG1 pd MID2|tD(GUC)L2
+DIG1 pd tD(GUC)L2|snR61
+DIG1 pd YLR352W|BUD8
+DIG1 pd tN(GUU)L|TUS1
+DIG1 pd SST2|RIF2
+DIG1 pd RIF2|YLR454W
+DIG1 pd TUB3|PHO84
+DIG1 pd PRM6|PRP39
+DIG1 pd AEP1|KAR5
+DIG1 pd tL(CAA)M|ASI1
+DIG1 pd MSS11|SMP2
+DIG1 pd VTI1|CIK1
+DIG1 pd FSH2|UBP8
+DIG1 pd PEP5|FUS2
+DIG1 pd RNA1|TAF9
+DIG1 pd SCW10|FKS3
+DIG1 pd TRF5|CLA4
+DIG1 pd RFC3|PCL1
+DIG1 pd tN(GUU)N1|MRPL10
+DIG1 pd tT(AGU)N1|WSC2
+DIG1 pd ERG24|PRM1
+DIG1 pd SEC2|BNI1
+DIG1 pd YNL193W|CHS1
+DIG1 pd INP52|LEU4
+DIG1 pd VAC7|MSG5
+DIG1 pd YIP3|tP(UGG)N1
+DIG1 pd tI(AAU)N1|YNL034W
+DIG1 pd snR66|YNL024C-A
+DIG1 pd YNL024C-A|YNL024C
+DIG1 pd BUD17|CPR8
+DIG1 pd YNR054C|tL(UAA)N
+DIG1 pd tL(UAA)N|HOL1
+DIG1 pd AAD15|YOL164W-A
+DIG1 pd YOL083W|CVT19
+DIG1 pd YOR129C|ORT1
+DIG1 pd ORT1|tD(GUC)O
+DIG1 pd tA(UGC)O|SNF2
+DIG1 pd PRM3|YPL191C
+DIG1 pd CUP9|YPL176C
+DIG1 pd SVS1|YPL162C
+DIG1 pd PRM4|KIP2
+DIG1 pd HAL1|ICL2
+DIG1 pd ARO7|YPR061C
+DIG1 pd OPY2|YPR078C
+DIG1 pd tK(UUU)P|CLB2
+DIG1 pd MSS18|CTF4
+DIG1 pd NCA2|TPO3
+DIG1 pd tI(AAU)P2|YPR171W
+DIG1 pd YPR196W|SGE1
+FHL1 pd ROX3|RPL32
+FHL1 pd RPL23A|YBL086C
+FHL1 pd YBL071C-B|KTI11
+FHL1 pd YBL028C|RPL19B
+FHL1 pd YBR047W|RPS11B
+FHL1 pd RPL19A|AAC3
+FHL1 pd TKL2|TEF2
+FHL1 pd RPS6B|SMP1
+FHL1 pd NTC20|RPS9B
+FHL1 pd RPS9B|RPL21A
+FHL1 pd SRO9|GFD2
+FHL1 pd ARF1|RPL35A
+FHL1 pd RPL41A|YDL183C
+FHL1 pd ARF2|RPL35B
+FHL1 pd RPL41B|YDL133W
+FHL1 pd STF1|RPP1B
+FHL1 pd RPS16B|RPL13A
+FHL1 pd RXT3|RPL31A
+FHL1 pd RPS29B|TSR1
+FHL1 pd YDR063W|RPS13
+FHL1 pd SYF1|RPL12B
+FHL1 pd RPS17B|ADA2
+FHL1 pd UTP6|RPS18A
+FHL1 pd UGO1|RPL27B
+FHL1 pd RPL37B|PLM2
+FHL1 pd MLP2|RPL40A
+FHL1 pd RPL16A|CSM2
+FHL1 pd RPS24B|SEC6
+FHL1 pd YIL055C|RHR2
+FHL1 pd YIL019W|RPL2B
+FHL1 pd RPL12A|MAK10
+FHL1 pd GCN4|TOS9
+FHL1 pd RPL34A|HMF1
+FHL1 pd ALD5|RPS24A
+FHL1 pd DOT6|PTC2
+FHL1 pd AST2|RPS8B
+FHL1 pd SLX8|RPL23B
+FHL1 pd YER130C|RPS26B
+FHL1 pd RPL22B|YFL034W
+FHL1 pd RPL2A|YFR032C
+FHL1 pd YFR032C-B|QCR6
+FHL1 pd YGL188C-A|COX4
+FHL1 pd RPL9A|YGL146C
+FHL1 pd MRM2|RPL1B
+FHL1 pd MON1|RPS2
+FHL1 pd VPS73|RPL28
+FHL1 pd RPL24A|RPL30
+FHL1 pd RPS25A|YGR027W-A
+FHL1 pd YGR033C|RPL26B
+FHL1 pd RPL11B|YGR086C
+FHL1 pd YGR117C|RPS23A
+FHL1 pd RPL24B|YGR149W
+FHL1 pd RTA1|RPS0A
+FHL1 pd RPL8A|GUT1
+FHL1 pd YHL015W-A|RPS20
+FHL1 pd DED81|YHR020W
+FHL1 pd RPS27B|ECM12
+FHL1 pd RPL42B|CHS7
+FHL1 pd RPS4B|MNL1
+FHL1 pd RPS22A|RPL39
+FHL1 pd YJL178C|RPL17B
+FHL1 pd RPS21B|LCB3
+FHL1 pd CAF17|RPS5
+FHL1 pd RPS4A|HMS2
+FHL1 pd PRS1|RPL17A
+FHL1 pd APE2|RPS27A
+FHL1 pd SFT1|RPL14A
+FHL1 pd TRM2|RPS21A
+FHL1 pd RPL40B|MLP1
+FHL1 pd RPL8B|FPS1
+FHL1 pd HSP104|tP(UGG)L
+FHL1 pd RPL15A|YLR030W
+FHL1 pd YLR047C|RPS0B
+FHL1 pd FRS1|RPL22A
+FHL1 pd BUD20|RPL10
+FHL1 pd SEC10|RPS31
+FHL1 pd YLR264C-A|NEJ1
+FHL1 pd RPS30A|MEC3
+FHL1 pd RPL38|YLR326W
+FHL1 pd RPS25B|tE(UUC)L
+FHL1 pd VRP1|RPP0
+FHL1 pd tR(CCG)L|RPL26A
+FHL1 pd RPS1A|SIR3
+FHL1 pd VMA6|RPL6B
+FHL1 pd RPL6A|YML072C
+FHL1 pd TEM1|RPS1B
+FHL1 pd RPS18B|YML025C
+FHL1 pd YML025C|RPS17A
+FHL1 pd SEC59|snR78
+FHL1 pd ASC1|SPC24
+FHL1 pd RPL13B|RPS16A
+FHL1 pd MRPL24|RPL36A
+FHL1 pd RRP5|RPS10B
+FHL1 pd YMR242W-A|ZRC1
+FHL1 pd RPS19B|RPL18B
+FHL1 pd RHO5|RPS3
+FHL1 pd YNL162W-A|RPL42A
+FHL1 pd RPS7B|YNL095C
+FHL1 pd RPL16B|FKH2
+FHL1 pd ACC1|MAS6
+FHL1 pd YGK3|RPL25
+FHL1 pd RPS19A|RPL18A
+FHL1 pd RPL18A|MCH4
+FHL1 pd RPS15|RPP2A
+FHL1 pd RKI1|RPS7A
+FHL1 pd YOR161C-C|YRR1
+FHL1 pd RPL33B|snR17a
+FHL1 pd YOR292C|RPS10A
+FHL1 pd RPL20B|SPS4
+FHL1 pd MSC6|GDS1
+FHL1 pd RPS12|MRS6
+FHL1 pd RPL36B|GYP5
+FHL1 pd YPL199C|RPL7B
+FHL1 pd snR17b|RPL33A
+FHL1 pd COX11|RPL5
+FHL1 pd RPS6A|RLM1
+FHL1 pd MOT1|RPS9A
+FHL1 pd PUF2|RPL43A
+FHL1 pd MRL1|TEF1
+FHL1 pd RPL11A|PRE2
+FKH1 pd RHK1|YBL081W
+FKH1 pd YBL057C|PTC3
+FKH1 pd CDS1|YBR030W
+FKH1 pd YBR077C|ECM33
+FKH1 pd SIF2|YMC2
+FKH1 pd HDR1|YBR139W
+FKH1 pd YSY6|DEM1
+FKH1 pd CHA1|YCL063W
+FKH1 pd ERS1|YCR075W-A
+FKH1 pd YCR075W-A|YCR076C
+FKH1 pd MSH3|CDC39
+FKH1 pd CDC50|YCR095C
+FKH1 pd NDE2|SUB2
+FKH1 pd ERP3|CDC7
+FKH1 pd YRB1|YDR003W
+FKH1 pd LUV1|REG1
+FKH1 pd AFR1|SSS1
+FKH1 pd YDR107C|GSG1
+FKH1 pd DIN7|AKR1
+FKH1 pd UTP4|YCG1
+FKH1 pd YHP1|PPN1
+FKH1 pd YIL077C|SEC28
+FKH1 pd YEL016C|YEL015W
+FKH1 pd YPT31|FIR1
+FKH1 pd THO1|YER064C
+FKH1 pd ARG5,6|RNR1
+FKH1 pd GLO3|YCK3
+FKH1 pd DSE1|RSP5
+FKH1 pd YPT1|TUB2
+FKH1 pd YFR003C|RPN11
+FKH1 pd YFR018C|FAB1
+FKH1 pd YFR022W|PES4
+FKH1 pd RET2|RPN12
+FKH1 pd MNT2|ADH4
+FKH1 pd ADH4|ZRT1
+FKH1 pd SPC105|NUP145
+FKH1 pd SCW11|CWH41
+FKH1 pd KSS1|BUD9
+FKH1 pd SCM4|YGR052W
+FKH1 pd PRP31|DBF2
+FKH1 pd ESP1|TEL2
+FKH1 pd MSM1|YIP1
+FKH1 pd BUB1|tK(CUU)G3
+FKH1 pd YGR268C|YTA7
+FKH1 pd YHR083W|STE12
+FKH1 pd HXT1|HXT5
+FKH1 pd YHR116W|TOM71
+FKH1 pd ORC6|SET1
+FKH1 pd CHS7|DSE2
+FKH1 pd YHR182W|GND1
+FKH1 pd YHR199C|RPN10
+FKH1 pd RPS22A|RPL39
+FKH1 pd JSN1|BUD4
+FKH1 pd YJR097W|YJR098C
+FKH1 pd YKL098W|YKL096C-B
+FKH1 pd YKL070W|YKL069W
+FKH1 pd YKL069W|tV(AAC)K1
+FKH1 pd DYN1|RHO4
+FKH1 pd GLG1|TIF1
+FKH1 pd ACE2|YLR132C
+FKH1 pd PNP1|CLB4
+FKH1 pd ECM38|EXG1
+FKH1 pd YLR352W|BUD8
+FKH1 pd BDF1|YLR401C
+FKH1 pd RPL31B|YLR406C-A
+FKH1 pd YLR406C-A|YLR407W
+FKH1 pd PDS5|tV(AAC)M2
+FKH1 pd CTF18|SEC14
+FKH1 pd SPC24|YMR118C
+FKH1 pd RPS16A|YMR144W
+FKH1 pd SSO2|YMR184W
+FKH1 pd VTI1|CIK1
+FKH1 pd SCJ1|GAS3
+FKH1 pd tT(AGU)N1|WSC2
+FKH1 pd YNL176C|NOP13
+FKH1 pd YNL146W|MFA2
+FKH1 pd APP1|YPT53
+FKH1 pd YNL092W|NST1
+FKH1 pd YOL114C|SKM1
+FKH1 pd YOL031C|GAS5
+FKH1 pd YOL024W|IFM1
+FKH1 pd RPL20B|SPS4
+FKH1 pd SPS4|YOR315W
+FKH1 pd GRD19|HAP5
+FKH1 pd ALG5|NEW1
+FKH1 pd CUP9|YPL176C
+FKH1 pd KIP2|PEP4
+FKH1 pd YPL141C|MKK2
+FKH1 pd MKK2|UME1
+FKH1 pd IDI1|HOS3
+FKH1 pd SVL3|PHO85
+FKH1 pd ARP7|GLN1
+FKH1 pd OPY2|YPR078C
+FKH1 pd FHL1|COD1
+FKH1 pd tK(UUU)P|CLB2
+FKH1 pd OPT2|YPR196W
+FKH2 pd ACS1|YAL053W
+FKH2 pd MYO4|YAL028W
+FKH2 pd LTE1|PMT2
+FKH2 pd KIN3|CDC15
+FKH2 pd BNA4|BRN1
+FKH2 pd HHF1|HHT1
+FKH2 pd SCO1|CHS2
+FKH2 pd YBR053C|YRO2
+FKH2 pd YBR077C|ECM33
+FKH2 pd PHO3|PHO5
+FKH2 pd PHO5|YBR094W
+FKH2 pd SIF2|YMC2
+FKH2 pd HDR1|YBR139W
+FKH2 pd ICS2|CST13
+FKH2 pd KAR4|SPB1
+FKH2 pd DUN1|ARR4
+FKH2 pd ARP2|MPS1
+FKH2 pd PST2|MRH1
+FKH2 pd RAD55|SED1
+FKH2 pd SWI5|EKI1
+FKH2 pd KGD2|NUM1
+FKH2 pd YDR221W|YDR222W
+FKH2 pd YAP6|SWM1
+FKH2 pd DIN7|AKR1
+FKH2 pd TFB1|SSF2
+FKH2 pd UTP4|YCG1
+FKH2 pd YHP1|PPN1
+FKH2 pd RPL37B|PLM2
+FKH2 pd FKH1|GIN1
+FKH2 pd AYR1|SIM1
+FKH2 pd ARG5,6|RNR1
+FKH2 pd PUP3|RAD51
+FKH2 pd DSE1|RSP5
+FKH2 pd FRS2|GAT1
+FKH2 pd YFR022W|PES4
+FKH2 pd MNT2|ADH4
+FKH2 pd YGL117W|CDC20
+FKH2 pd STT3|ALK1
+FKH2 pd YGL007C-A|YGL006W-A
+FKH2 pd ERG26|YGR001C
+FKH2 pd SCM4|YGR052W
+FKH2 pd PRP31|DBF2
+FKH2 pd tK(UUU)G2|CLB1
+FKH2 pd UBR1|TYS1
+FKH2 pd SMI1|BNS1
+FKH2 pd YHL029C|WSC4
+FKH2 pd SNF6|RIM4
+FKH2 pd RPL14B|OSH7
+FKH2 pd RRM3|YHR032W
+FKH2 pd GIC1|RPP1
+FKH2 pd CHS7|DSE2
+FKH2 pd YHR151C|SPO12
+FKH2 pd CIS3|FAR1
+FKH2 pd TDH1|YJL051W
+FKH2 pd JSN1|BUD4
+FKH2 pd ZMS1|snR3
+FKH2 pd YKL098W|YKL096C-B
+FKH2 pd YKR041W|UTH1
+FKH2 pd GLG1|TIF1
+FKH2 pd SRP40|PTR2
+FKH2 pd DPS1|BPT1
+FKH2 pd ACE2|YLR132C
+FKH2 pd UGT51|YLR190W
+FKH2 pd CTS1|YLR287C
+FKH2 pd ECM38|EXG1
+FKH2 pd BDF1|YLR401C
+FKH2 pd TEM1|RPS1B
+FKH2 pd YML053C|SUR7
+FKH2 pd YMR031C|HOF1
+FKH2 pd SPC24|YMR118C
+FKH2 pd RPS16A|YMR144W
+FKH2 pd SSO2|YMR184W
+FKH2 pd VTI1|CIK1
+FKH2 pd CIK1|CLN1
+FKH2 pd SCJ1|GAS3
+FKH2 pd YNL176C|NOP13
+FKH2 pd MDG1|APC1
+FKH2 pd YNL058C|YNL056W
+FKH2 pd snR66|YNL024C-A
+FKH2 pd YNL024C-A|YNL024C
+FKH2 pd YOL114C|SKM1
+FKH2 pd ASE1|tK(UUU)O
+FKH2 pd WTM2|WTM1
+FKH2 pd YOR238W|ABP140
+FKH2 pd YOR246C|SRL1
+FKH2 pd SPS4|YOR315W
+FKH2 pd IQG1|CIN2
+FKH2 pd KIP2|PEP4
+FKH2 pd YPL141C|MKK2
+FKH2 pd IDI1|HOS3
+FKH2 pd SKS1|NCE4
+FKH2 pd ARP7|GLN1
+FKH2 pd tK(UUU)P|CLB2
+FKH2 pd YPR148C|NCE102
+FKH2 pd OPT2|YPR196W
+GAL4 pd KAP104|GAL7
+GAL4 pd GAL7|GAL10
+GAL4 pd GAL10|GAL1
+GAL4 pd PAU3|YCR105W
+GAL4 pd TRP1|GAL3
+GAL4 pd MTH1|tE(CUC)D
+GAL4 pd YEL057C|HAT2
+GAL4 pd RPL1B|PCL10
+GAL4 pd EMP46|GAL2
+GAL4 pd YLR356W|RSC2
+GAL4 pd SUR7|GAL80
+GAL4 pd MLF3|MSK1
+GAL4 pd RIO1|GCY1
+GAL4 pd YOR138C|SFL1
+GAL4 pd OPT2|YPR196W
+GAL80 pd GAL10|GAL1
+GAT1 pd YCR095C|HMRA2
+GAT1 pd HMRA2|HMRA1
+GAT1 pd YDL238C|YDL237W
+GAT1 pd ENA1|RSM10
+GAT1 pd YDR316W-B|YDR317W
+GAT1 pd DJP1|IST3
+GAT1 pd DAL4|DAL2
+GAT1 pd CAN1|NPR2
+GAT1 pd tK(CUU)E1|tR(UCU)E
+GAT1 pd MNN1|NOP16
+GAT1 pd CAJ1|tQ(UUG)E1
+GAT1 pd YGR038C-A|KSS1
+GAT1 pd SKN1|tG(UCC)G
+GAT1 pd RNR4|tL(CAA)G3
+GAT1 pd YHR029C|SLT2
+GAT1 pd OPT1|PEX2
+GAT1 pd GZF3|UTP10
+GAT1 pd YJR011C|YJR013W
+GAT1 pd CPA2|YJR110W
+GAT1 pd MCH2|FRE2
+GAT1 pd COS9|SRY1
+GAT1 pd SRP40|PTR2
+GAT1 pd YLR023C|UBR2
+GAT1 pd YLR047C|RPS0B
+GAT1 pd ARG81|TAF13
+GAT1 pd YMR098C|tD(GUC)M
+GAT1 pd YMR118C|tL(CAA)M
+GAT1 pd YNL144C|MEP2
+GAT1 pd YOL159C|ENB1
+GAT1 pd ECM23|ULP1
+GCN4 pd RTG3|SFT2
+GCN4 pd ILS1|SSA3
+GCN4 pd AQR2|TCM62
+GCN4 pd ZTA1|YBR047W
+GCN4 pd BAP2|TAT1
+GCN4 pd SIF2|YMC2
+GCN4 pd CYC8|RAD16
+GCN4 pd LYS2|TKL2
+GCN4 pd SUP45|ADH5
+GCN4 pd MRPS9|YBR147W
+GCN4 pd TOS1|YSY6
+GCN4 pd HIS7|ARO4
+GCN4 pd ARO4|YBR250W
+GCN4 pd TRS20|YBR255W
+GCN4 pd RIB5|POP4
+GCN4 pd HIS4|BIK1
+GCN4 pd YCR023C|YCR024C
+GCN4 pd RSC6|THR4
+GCN4 pd YHM1|ASF2
+GCN4 pd ASF2|SEC31
+GCN4 pd YDL183C|LYS20
+GCN4 pd GLT1|UGA3
+GCN4 pd COX9|IDP1
+GCN4 pd MCH1|YDL053C
+GCN4 pd LYS14|YDR034C-D
+GCN4 pd YDR034W-B|ARO3
+GCN4 pd ECM18|PSL10
+GCN4 pd PSL10|ARO1
+GCN4 pd PRP28|PEX5
+GCN4 pd HSP78|YAP6
+GCN4 pd YDR341C|HXT7
+GCN4 pd TRR1|TRP4
+GCN4 pd VPS60|RIB3
+GCN4 pd GNP1|SMT3
+GCN4 pd NIT1|SUC2
+GCN4 pd PRM5|HIS5
+GCN4 pd tS(UGA)I|YIL056W
+GCN4 pd LYS1|YIR035C
+GCN4 pd CAN1|NPR2
+GCN4 pd GLC3|tK(CUU)E1
+GCN4 pd tK(CUU)E1|tR(UCU)E
+GCN4 pd YER039C-A|GLN3
+GCN4 pd HOM3|YER053C
+GCN4 pd HIS1|FCY2
+GCN4 pd MOT2|ARG5,6
+GCN4 pd VTC1|ALD5
+GCN4 pd YER085C|ILV1
+GCN4 pd PTC2|TRP2
+GCN4 pd TMT1|YER175W-A
+GCN4 pd YER175W-A|ECM32
+GCN4 pd CAF16|GYP8
+GCN4 pd FRS2|GAT1
+GCN4 pd YFR055W|YFR057W
+GCN4 pd tK(UUU)G1|ARO8
+GCN4 pd YGL186C|YGL185C
+GCN4 pd STR3|MND1
+GCN4 pd GTS1|APG1
+GCN4 pd SCS3|MET13
+GCN4 pd SGF73|ALG2
+GCN4 pd YGL060W|YGL059W
+GCN4 pd YGR067C|YGR068C
+GCN4 pd YGR093W|VAS1
+GCN4 pd YGR161C|YGR161W-A
+GCN4 pd YGR203W|ADE3
+GCN4 pd FOL2|YGR268C
+GCN4 pd SLH1|YGR271C-A
+GCN4 pd WSC4|RIM101
+GCN4 pd ARG4|DED81
+GCN4 pd DED81|YHR020W
+GCN4 pd YHR022C|YHR022C-A
+GCN4 pd YHR022C-A|MYO1
+GCN4 pd MAS2|THR1
+GCN4 pd YHR029C|SLT2
+GCN4 pd TRM5|PCL5
+GCN4 pd YHR121W|YHR122W
+GCN4 pd YAP1801|YHR162W
+GCN4 pd OPT1|PEX2
+GCN4 pd YJL200C|tT(AGU)J
+GCN4 pd tT(AGU)J|PHO90
+GCN4 pd URA2|TRK1
+GCN4 pd SIP4|ARG3
+GCN4 pd YJL072C|ARG2
+GCN4 pd tW(CCA)J|YJL010C
+GCN4 pd ILV3|ESS1
+GCN4 pd BNA1|YJR026W
+GCN4 pd CPA2|YJR110W
+GCN4 pd YJR111C|NNF1
+GCN4 pd RPS4A|HMS2
+GCN4 pd TRP3|snR64
+GCN4 pd PIR3|YKL162C
+GCN4 pd LAP4|HSL1
+GCN4 pd TUL1|YKL033W-A
+GCN4 pd ATP7|PUT3
+GCN4 pd YKR096W|PCK1
+GCN4 pd SPO75|ORC3
+GCN4 pd DNM1|YLR001C
+GCN4 pd YLR152C|ACS2
+GCN4 pd PDR8|BOP2
+GCN4 pd ILV5|YLR356W
+GCN4 pd HMG2|LEU3
+GCN4 pd YML117W|ATR1
+GCN4 pd WAR1|HMG1
+GCN4 pd YMR018W|STB4
+GCN4 pd ECM40|RIM9
+GCN4 pd SNO1|SNZ1
+GCN4 pd DCR1|GAT2
+GCN4 pd YMR188C|GCV2
+GCN4 pd YMR194C-B|ICY1
+GCN4 pd YNL311C|YNL310C
+GCN4 pd NAR1|LAP3
+GCN4 pd NPR1|YNL182C
+GCN4 pd CPT1|YNL130C-A
+GCN4 pd ESBP6|NAF1
+GCN4 pd LEU4|MET4
+GCN4 pd SUN4|AQR1
+GCN4 pd IDH1|NCE103
+GCN4 pd MRP7|HRB1
+GCN4 pd LYS9|snR49
+GCN4 pd YNR069C|PDR18
+GCN4 pd ZPS1|FRE7
+GCN4 pd PPM2|ARG8
+GCN4 pd MCH4|RRI2
+GCN4 pd MET22|YOL063C
+GCN4 pd GPD2|ARG1
+GCN4 pd RGS2|YOR108W
+GCN4 pd ORT1|tD(GUC)O
+GCN4 pd PET56|HIS3
+GCN4 pd MCT1|ODC2
+GCN4 pd RAX1|YOR302W
+GCN4 pd KRE5|TEA1
+GCN4 pd SAM3|SAM4
+GCN4 pd YPL264C|KEL3
+GCN4 pd YAH1|ICY2
+GCN4 pd ICY2|RPL36B
+GCN4 pd YPL137C|ISU1
+GCN4 pd tM(CAU)P|CAR1
+GCN4 pd VMA13|YPR036W-A
+GCN4 pd BRR1|YMC1
+GCN4 pd RPC40|DBF20
+GCN4 pd snR45|ASN1
+GCN4 pd MET16|NUT2
+GCR1 pd CYC3|CDC19
+GCR1 pd YBR196C-A|YBR196C-B
+GCR1 pd YBR196C-B|YBR197C
+GCR1 pd tF(GAA)D|YDR316W-A
+GCR1 pd SNP1|YIL057C
+GCR1 pd tK(CUU)E1|tR(UCU)E
+GCR1 pd ECM32|BMH1
+GCR1 pd TDH3|PDX1
+GCR1 pd SBP1|RPL8A
+GCR1 pd PDC1|STU2
+GLN3 pd EXO84|SIF2
+GLN3 pd CHA1|YCL063W
+GLN3 pd KAR4|SPB1
+GLN3 pd HIS4|BIK1
+GLN3 pd tK(CUU)C|MAK32
+GLN3 pd YCR095C|HMRA2
+GLN3 pd GDH2|PRR2
+GLN3 pd GLT1|UGA3
+GLN3 pd COX9|IDP1
+GLN3 pd YDL001W|NTH1
+GLN3 pd RAD28|YDR031W
+GLN3 pd ENA1|RSM10
+GLN3 pd YDR090C|RLI1
+GLN3 pd GNP1|SMT3
+GLN3 pd RPI1|RHO3
+GLN3 pd DJP1|IST3
+GLN3 pd DAL1|DAL4
+GLN3 pd DAL4|DAL2
+GLN3 pd DCG1|DAL7
+GLN3 pd DAL7|DAL3
+GLN3 pd DAL3|MGA2
+GLN3 pd tK(CUU)E1|tR(UCU)E
+GLN3 pd GCN4|TOS9
+GLN3 pd MNN1|NOP16
+GLN3 pd CAJ1|tQ(UUG)E1
+GLN3 pd TMT1|YER175W-A
+GLN3 pd YER188C-A|YER189W
+GLN3 pd FRS2|GAT1
+GLN3 pd ADH4|ZRT1
+GLN3 pd YGL007C-A|YGL006W-A
+GLN3 pd YGR038C-A|KSS1
+GLN3 pd QCR9|UBR1
+GLN3 pd PHO81|YHB1
+GLN3 pd YHL029C|WSC4
+GLN3 pd DUR3|YHL015W-A
+GLN3 pd YHL015W-A|RPS20
+GLN3 pd ERG11|YHR007C-A
+GLN3 pd YSC83|ARG4
+GLN3 pd ARG4|DED81
+GLN3 pd YHR029C|SLT2
+GLN3 pd RFA3|CPS1
+GLN3 pd HSP150|CIS3
+GLN3 pd PET130|BBC1
+GLN3 pd CTK2|tL(UAA)J
+GLN3 pd CPA2|YJR110W
+GLN3 pd HMS2|BAT2
+GLN3 pd YJR151W-A|DAL5
+GLN3 pd COS9|SRY1
+GLN3 pd STB6|tW(CCA)K
+GLN3 pd tH(GUG)K|YNK1
+GLN3 pd SRP40|PTR2
+GLN3 pd DPS1|BPT1
+GLN3 pd YLR023C|UBR2
+GLN3 pd LSM3|MRPL4
+GLN3 pd YPT7|CDC5
+GLN3 pd SOK2|SPO20
+GLN3 pd YMR088C|YTA12
+GLN3 pd YMR118C|tL(CAA)M
+GLN3 pd YNL144C|MEP2
+GLN3 pd MEP2|AAH1
+GLN3 pd YOL159C|ENB1
+GLN3 pd YOL155W-A|YOL155C
+GLN3 pd MCH4|RRI2
+GLN3 pd SHR5|YOL109W
+GLN3 pd GPD2|ARG1
+GLN3 pd WTM2|WTM1
+GLN3 pd SPS4|YOR315W
+GLN3 pd DIM1|DIP5
+GLN3 pd YPL056C|LGE1
+GLN3 pd ARP7|GLN1
+GLN3 pd snR45|ASN1
+GLN3 pd OPT2|YPR196W
+GZF3 pd YBL111C|YBL108C-A
+GZF3 pd YCR095C|HMRA2
+GZF3 pd HMRA2|HMRA1
+GZF3 pd PAU3|YCR105W
+GZF3 pd YDL001W|NTH1
+GZF3 pd ENA1|RSM10
+GZF3 pd TOM1|YDR458C
+GZF3 pd YDR542W|YRF1-1
+GZF3 pd tK(CUU)E1|tR(UCU)E
+GZF3 pd MNN1|NOP16
+GZF3 pd YER187W|YER188C-A
+GZF3 pd YER188C-A|YER189W
+GZF3 pd YGR038C-A|KSS1
+GZF3 pd COS9|SRY1
+GZF3 pd YLL066C|YLL064C
+GZF3 pd YBT1|RNP1
+GZF3 pd YLR023C|UBR2
+GZF3 pd YMR098C|tD(GUC)M
+GZF3 pd YMR118C|tL(CAA)M
+GZF3 pd tI(AAU)P2|YPR171W
+HAC1 pd TAD2|KAR2
+HAP1 pd CYC3|CDC19
+HAP1 pd COR1|YBL044W
+HAP1 pd MNN2|YBR016W
+HAP1 pd DLD1|YDL173W
+HAP1 pd YDR233C|LYS4
+HAP1 pd YDR542W|YRF1-1
+HAP1 pd CAJ1|tQ(UUG)E1
+HAP1 pd FTR1|LSM5
+HAP1 pd QCR6|PHO4
+HAP1 pd IME4|COX13
+HAP1 pd COX4|YGL186C
+HAP1 pd SDS23|OLE1
+HAP1 pd ERG26|YGR001C
+HAP1 pd YGR035W-A|CAX4
+HAP1 pd UFD1|SCM4
+HAP1 pd PDC6|CTT1
+HAP1 pd YGR109W-B|YGR110W
+HAP1 pd OSH7|QCR10
+HAP1 pd ERG11|YHR007C-A
+HAP1 pd SMF2|YHR050W-A
+HAP1 pd MSR1|HXT4
+HAP1 pd YHR189W|ERG9
+HAP1 pd ANB1|CYC1
+HAP1 pd SOD1|ADO1
+HAP1 pd CNB1|tL(UAA)K
+HAP1 pd LOT5|FAS1
+HAP1 pd YKL098W|YKL096C-B
+HAP1 pd ASK1|YKL051W
+HAP1 pd PTM1|snR69
+HAP1 pd SPT23|RAM2
+HAP1 pd YLR108C|AHP1
+HAP1 pd RRN5|PUT1
+HAP1 pd ACS2|YLR154C
+HAP1 pd YLR154C|tQ(UUG)L
+HAP1 pd tQ(UUG)L|RDN37-1
+HAP1 pd HMX1|ENT2
+HAP1 pd YLR254C|HAP1
+HAP1 pd ERG13|YML125C
+HAP1 pd CYB2|YML054C-A
+HAP1 pd USA1|TSA1
+HAP1 pd ERG5|SOK2
+HAP1 pd MSN2|LYS7
+HAP1 pd AAC1|FET3
+HAP1 pd YMR069W|MOT3
+HAP1 pd REC114|YMR134W
+HAP1 pd NDE1|TIF34
+HAP1 pd CYB5|NOP15
+HAP1 pd COQ2|MVD1
+HAP1 pd MNT4|FRE4
+HAP1 pd YOL114C|SKM1
+HAP1 pd YOL027C|YOL026C
+HAP1 pd YNG1|CYT1
+HAP1 pd YOR316C-A|FAA1
+HAP1 pd PUT4|CIN1
+HAP1 pd tC(GCA)P2|THI22
+HAP2 pd tS(AGA)A|UIP3
+HAP2 pd HMLALPHA1|CHA1
+HAP2 pd KAR4|SPB1
+HAP2 pd YCR095C|HMRA2
+HAP2 pd GLT1|UGA3
+HAP2 pd SUB2|RPS16B
+HAP2 pd YDL001W|NTH1
+HAP2 pd ENA1|RSM10
+HAP2 pd YDR316W-B|YDR317W
+HAP2 pd ARH1|ATP17
+HAP2 pd QCR7|APA2
+HAP2 pd DAL4|DAL2
+HAP2 pd DCG1|DAL7
+HAP2 pd DAL3|MGA2
+HAP2 pd RIP1|YEL023C
+HAP2 pd GCN4|TOS9
+HAP2 pd MNN1|NOP16
+HAP2 pd GRX4|TMT1
+HAP2 pd FRS2|GAT1
+HAP2 pd QCR6|PHO4
+HAP2 pd COX4|YGL186C
+HAP2 pd YGR017W|UGA1
+HAP2 pd MEP1|YGR121W-A
+HAP2 pd QCR9|UBR1
+HAP2 pd PHO81|YHB1
+HAP2 pd RPS20|YLF2
+HAP2 pd OSH7|QCR10
+HAP2 pd SMF2|YHR050W-A
+HAP2 pd tT(AGU)J|PHO90
+HAP2 pd RPS14B|RPS22A
+HAP2 pd snR190|RPA34
+HAP2 pd MIR1|BNA2
+HAP2 pd STB6|tW(CCA)K
+HAP2 pd TPO1|ISA1
+HAP2 pd DPS1|BPT1
+HAP2 pd REX3|snR6
+HAP2 pd MSC3|CCC1
+HAP2 pd YPT7|CDC5
+HAP2 pd YMR118C|tL(CAA)M
+HAP2 pd snR40|CAF40
+HAP2 pd AVO1|ATP19
+HAP2 pd YOR267C|PAC1
+HAP2 pd GDH1|YOR376W-A
+HAP2 pd DIM1|DIP5
+HAP2 pd DIP5|YPL264C
+HAP2 pd YPL208W|YPL207W
+HAP2 pd RPL5|SPO19
+HAP2 pd VTC3|CTF19
+HAP2 pd snR45|ASN1
+HAP3 pd CHS2|ATP3
+HAP3 pd tC(GCA)B|tE(UUC)B
+HAP3 pd FEN2|RIM1
+HAP3 pd GLT1|UGA3
+HAP3 pd APG9|NOP14
+HAP3 pd YDL001W|NTH1
+HAP3 pd PLP1|ATC1
+HAP3 pd GRX4|TMT1
+HAP3 pd TMT1|YER175W-A
+HAP3 pd YER175W-A|ECM32
+HAP3 pd YFR022W|PES4
+HAP3 pd YGL196W|GCN1
+HAP3 pd COX4|YGL186C
+HAP3 pd OSH7|QCR10
+HAP3 pd SMF2|YHR050W-A
+HAP3 pd IDS2|SFH5
+HAP3 pd MIR1|BNA2
+HAP3 pd LHS1|STB6
+HAP3 pd TPO1|ISA1
+HAP3 pd MSC3|CCC1
+HAP3 pd NDI1|YML119W
+HAP3 pd AEP1|KAR5
+HAP3 pd YNL010W|IDP3
+HAP3 pd YPL208W|YPL207W
+HAP4 pd YBL111C|YBL108C-A
+HAP4 pd tF(GAA)B|ATP1
+HAP4 pd COR1|YBL044W
+HAP4 pd PET9|YBL029C-A
+HAP4 pd ECM15|NTH2
+HAP4 pd CHS2|ATP3
+HAP4 pd YCR102C|PAU3
+HAP4 pd LYS20|INH1
+HAP4 pd COX9|IDP1
+HAP4 pd MED2|ATP16
+HAP4 pd YDL001W|NTH1
+HAP4 pd ATP5|BFR2
+HAP4 pd TIM11|PEP7
+HAP4 pd ARH1|ATP17
+HAP4 pd PRP3|YDR474C
+HAP4 pd QCR7|APA2
+HAP4 pd DRE3|YIL002W-A
+HAP4 pd SRI1|RIP1
+HAP4 pd YEL001C|MNN1
+HAP4 pd YER007C-A|snR14
+HAP4 pd CAJ1|tQ(UUG)E1
+HAP4 pd YER187W|YER188C-A
+HAP4 pd YER188C-A|YER189W
+HAP4 pd IME4|COX13
+HAP4 pd tD(GUC)G2|snR46
+HAP4 pd VMA21|YGR106C
+HAP4 pd QCR9|UBR1
+HAP4 pd RPL14B|OSH7
+HAP4 pd SMF2|YHR050W-A
+HAP4 pd tP(UGG)H|CRP1
+HAP4 pd YJL058C|IKS1
+HAP4 pd MIR1|BNA2
+HAP4 pd YJR096W|YJR097W
+HAP4 pd ATP7|PUT3
+HAP4 pd YLL066C|YLL064C
+HAP4 pd COX12|RIC1
+HAP4 pd ATP14|YLR297W
+HAP4 pd snR61|snR55
+HAP4 pd COX8|VPS33
+HAP4 pd YPT7|CDC5
+HAP4 pd COX7|PET111
+HAP4 pd YRF1-6|COS1
+HAP4 pd POR1|tD(GUC)N
+HAP4 pd MSG5|COX5A
+HAP4 pd IRA2|REX4
+HAP4 pd AVO1|ATP19
+HAP4 pd YPL272C|ATP15
+HAP4 pd YPL112C|tM(CAU)P
+HAP4 pd tM(CAU)P|CAR1
+HAP4 pd tK(CUU)P|YPR011C
+HAP4 pd CDC54|ATP20
+HAP5 pd tF(GAA)B|ATP1
+HAP5 pd YDL001W|NTH1
+HAP5 pd LYS14|YDR034C-D
+HAP5 pd RAD55|SED1
+HAP5 pd YDR384C|EFT2
+HAP5 pd LPP1|PSP1
+HAP5 pd QCR7|APA2
+HAP5 pd PDR11|TIR3
+HAP5 pd tK(CUU)E1|tR(UCU)E
+HAP5 pd ACA1|SPO73
+HAP5 pd GRX4|TMT1
+HAP5 pd GYP8|STE2
+HAP5 pd ADH4|ZRT1
+HAP5 pd COX4|YGL186C
+HAP5 pd TOS8|tE(UUC)G1
+HAP5 pd SCM4|YGR052W
+HAP5 pd QCR9|UBR1
+HAP5 pd PHO81|YHB1
+HAP5 pd tT(AGU)H|STP2
+HAP5 pd SMF2|YHR050W-A
+HAP5 pd snR37|YJL103C
+HAP5 pd tM(CAU)J1|YJL027C
+HAP5 pd MIR1|BNA2
+HAP5 pd LOT5|FAS1
+HAP5 pd STB6|tW(CCA)K
+HAP5 pd YKL063C|MSN4
+HAP5 pd TPO1|ISA1
+HAP5 pd MSC3|CCC1
+HAP5 pd BDF1|YLR401C
+HAP5 pd YPT7|CDC5
+HAP5 pd YMR194C-B|ICY1
+HAP5 pd snR40|CAF40
+HAP5 pd TYE7|tP(UGG)O3
+HAP5 pd YPL208W|YPL207W
+HAP5 pd snR45|ASN1
+HSF1 pd SSA1|EFB1
+HSF1 pd SSA3|AAR2
+HSF1 pd REB1|REG2
+HSF1 pd ORC2|TRM7
+HSF1 pd YBR071W|HSP26
+HSF1 pd UBC4|TEC1
+HSF1 pd YBR085C-A|IST2
+HSF1 pd YBR101C|EXO84
+HSF1 pd TKL2|TEF2
+HSF1 pd SSE2|NPL4
+HSF1 pd KTR3|FTH1
+HSF1 pd RIF1|PPS1
+HSF1 pd KRR1|FYV5
+HSF1 pd APA1|YCL049C
+HSF1 pd HSP30|YCR023C
+HSF1 pd INH1|YDL180W
+HSF1 pd RPN4|OSH2
+HSF1 pd GAL3|SNQ2
+HSF1 pd YDR071C|IPT1
+HSF1 pd GSG1|YDR109C
+HSF1 pd INO2|YDR124W
+HSF1 pd CTH1|YDR152W
+HSF1 pd CPR1|RPA14
+HSF1 pd YDR170W-A|HSP42
+HSF1 pd UPC2|AHA1
+HSF1 pd HSP78|YAP6
+HSF1 pd PIB1|YDR314C
+HSF1 pd ARH1|ATP17
+HSF1 pd GTT1|YPS6
+HSF1 pd YER034W|EDC2
+HSF1 pd KRE30|PHM8
+HSF1 pd RPS8B|SSA4
+HSF1 pd ACT1|YPT1
+HSF1 pd MDJ1|HSP12
+HSF1 pd PNC1|YGL036W
+HSF1 pd PMA1|YGL007C-A
+HSF1 pd YGL007C-A|YGL006W-A
+HSF1 pd VPS62|BTN2
+HSF1 pd YGR146C-A|NAT2
+HSF1 pd PTI1|CHO2
+HSF1 pd YGR161C|YGR161W-A
+HSF1 pd TDH3|PDX1
+HSF1 pd SNG1|YGR198W
+HSF1 pd YGR210C|ZPR1
+HSF1 pd SOL4|MGA1
+HSF1 pd YHR048W|FSH1
+HSF1 pd KSP1|YHR083W
+HSF1 pd SBE22|GRE3
+HSF1 pd YJL083W|IML2
+HSF1 pd SMC3|JEM1
+HSF1 pd TAD2|KAR2
+HSF1 pd SSC1|TAH11
+HSF1 pd YJR116W|STE24
+HSF1 pd GPM1|YKL151C
+HSF1 pd RGT1|UGP1
+HSF1 pd UFD4|MRT4
+HSF1 pd DRE2|SIS2
+HSF1 pd UBI4|ENT4
+HSF1 pd YLR042C|TRX1
+HSF1 pd YLR063W|YLR064W
+HSF1 pd YLR108C|AHP1
+HSF1 pd CPR6|YLR218C
+HSF1 pd HSP60|LCB5
+HSF1 pd GSP1|ATP14
+HSF1 pd YLR327C|tS(GCU)L
+HSF1 pd KAP95|DIC1
+HSF1 pd ERO1|COX14
+HSF1 pd YML100W-A|TSL1
+HSF1 pd AVO2|YMR069W
+HSF1 pd ISF1|ADH3
+HSF1 pd YMR107W|ILV2
+HSF1 pd ECM5|MMT1
+HSF1 pd YMR185W|HSC82
+HSF1 pd YMR251W|HOR7
+HSF1 pd POP3|HCH1
+HSF1 pd ESBP6|NAF1
+HSF1 pd NIS1|YNL077W
+HSF1 pd YDJ1|YNL063W
+HSF1 pd SIS1|LST8
+HSF1 pd YNR009W|CSE2
+HSF1 pd YNR069C|PDR18
+HSF1 pd YOL138C|YOL137W
+HSF1 pd CVT19|IRA2
+HSF1 pd SGT2|tR(ACG)O
+HSF1 pd tR(ACG)O|SLG1
+HSF1 pd BUB3|STI1
+HSF1 pd YOR267C|PAC1
+HSF1 pd YOR298W|MBF1
+HSF1 pd MBF1|BUD7
+HSF1 pd TYE7|tP(UGG)O3
+HSF1 pd ICY2|RPL36B
+HSF1 pd HSP82|YAR1
+HSF1 pd SSE1|YPL105C
+HSF1 pd SVL3|PHO85
+HSF1 pd NCR1|YPL005W
+HSF1 pd VMA13|YPR036W-A
+HSF1 pd YPR036W-A|ERV2
+HSF1 pd YPR153W|PIN3
+HSF1 pd YPR157W|YPR158W
+HSF1 pd YPR174C|DPB2
+HSF1 pd OPT2|YPR196W
+INO2 pd CDS1|YBR030W
+INO2 pd PWP2|YIH1
+INO2 pd GIT1|YCR099C
+INO2 pd KNH1|STP4
+INO2 pd SWI5|EKI1
+INO2 pd STB3|YDR169C-A
+INO2 pd YDR169C-A|SEC7
+INO2 pd DON1|YDR275W
+INO2 pd tE(CUC)D|YDR279W
+INO2 pd TFB1|SSF2
+INO2 pd HXT3|SGI1
+INO2 pd ITR1|SEC20
+INO2 pd KEL2|PEX21
+INO2 pd PUP2|ENO1
+INO2 pd OPI1|APM2
+INO2 pd INO1|SNA3
+INO2 pd YAK1|RPB4
+INO2 pd YJL118W|PHO86
+INO2 pd SOD1|ADO1
+INO2 pd LOT5|FAS1
+INO2 pd VMA6|RPL6B
+INO2 pd HMG1|FPR3
+INO2 pd NOP13|MDG1
+INO2 pd PSD1|YNL168C
+INO2 pd CPT1|YNL130C-A
+INO2 pd ACC1|MAS6
+INO2 pd WTM2|WTM1
+INO2 pd RPL33B|snR17a
+INO2 pd YOR316C-A|FAA1
+INO2 pd SSO1|FAS2
+INO4 pd ACS1|YAL053W
+INO4 pd SRO77|PKC1
+INO4 pd CDS1|YBR030W
+INO4 pd TPI1|YDR051C
+INO4 pd SAC6|FIN1
+INO4 pd SWI5|EKI1
+INO4 pd tE(CUC)D|YDR279W
+INO4 pd HXT3|SGI1
+INO4 pd ITR1|SEC20
+INO4 pd YEL041W|UTR2
+INO4 pd CHO1|GAL83
+INO4 pd SAH1|ERG28
+INO4 pd PTI1|CHO2
+INO4 pd KEL2|PEX21
+INO4 pd YHR122W|EPT1
+INO4 pd SET2|ERG20
+INO4 pd YJL048C|YJL047C-A
+INO4 pd SOD1|ADO1
+INO4 pd LOT5|FAS1
+INO4 pd ADH3|YMR084W
+INO4 pd PSD1|YNL168C
+INO4 pd YNL045W|YIP3
+INO4 pd ACC1|MAS6
+INO4 pd YOR316C-A|FAA1
+INO4 pd SSO1|FAS2
+INO4 pd YPR013C|YPR015C
+LEU3 pd BAP2|TAT1
+LEU3 pd tL(CAA)C|LEU2
+LEU3 pd YDR524C-B|SNA2
+LEU3 pd VTC1|ALD5
+LEU3 pd LEU1|PMA1
+LEU3 pd SET5|BAT1
+LEU3 pd ILV3|ESS1
+LEU3 pd YKL121W|OAC1
+LEU3 pd snR69|RGT1
+LEU3 pd ILV5|YLR356W
+LEU3 pd YMR107W|ILV2
+LEU3 pd LEU4|MET4
+LEU3 pd RGS2|YOR108W
+LEU3 pd ISU2|YOR227W
+LEU3 pd YOR271C|snR8
+MAC1 pd PMP1|YCR026C
+MAC1 pd PRM5|HIS5
+MAC1 pd FTR1|LSM5
+MAC1 pd UTR1|ISY1
+MAC1 pd CRR1|FRE1
+MAC1 pd VIP1|YLR410W-A
+MAC1 pd FET4|YMR321C
+MAC1 pd NRD1|RAD50
+MAC1 pd ZPS1|FRE7
+MAC1 pd CUP9|YPL176C
+MAC1 pd AXL1|CTR1
+MAC1 pd KRE6|YPR159C-A
+MAC1 pd tG(GCC)P2|GPH1
+MBP1 pd RFA1|SEN34
+MBP1 pd POL12|STU1
+MBP1 pd MCM2|PIM1
+MBP1 pd HTA2|HTB2
+MBP1 pd YBR007C|FLR1
+MBP1 pd YBR070C|YBR071W
+MBP1 pd YBR077C|ECM33
+MBP1 pd MRC1|KRR1
+MBP1 pd KAR4|SPB1
+MBP1 pd BUD31|HCM1
+MBP1 pd HO|GCS1
+MBP1 pd DUN1|ARR4
+MBP1 pd ERP3|CDC7
+MBP1 pd ATP16|MCD1
+MBP1 pd YDR049W|TPI1
+MBP1 pd UBC13|DNF2
+MBP1 pd MSH6|GRX3
+MBP1 pd PDS1|YDR115W
+MBP1 pd MKC7|TAF12
+MBP1 pd tI(UAU)D|GCD6
+MBP1 pd DIN7|AKR1
+MBP1 pd PEX10|YDR266C
+MBP1 pd tE(CUC)D|YDR279W
+MBP1 pd MHR1|SUR2
+MBP1 pd GIC2|SUM1
+MBP1 pd YHP1|PPN1
+MBP1 pd RPL37B|PLM2
+MBP1 pd GIN4|GNP1
+MBP1 pd YDR524C-B|SNA2
+MBP1 pd RUF1|HLR1
+MBP1 pd CCT2|AXL2
+MBP1 pd IRR1|YIL024C
+MBP1 pd YEL001C|MNN1
+MBP1 pd ACA1|SPO73
+MBP1 pd ARG5,6|RNR1
+MBP1 pd PUP3|RAD51
+MBP1 pd SWI4|LSM4
+MBP1 pd SHO1|YER119C
+MBP1 pd YFL012W|HXT10
+MBP1 pd CDC4|SMC1
+MBP1 pd OCH1|PNC1
+MBP1 pd PDR1|ERG4
+MBP1 pd KSS1|BUD9
+MBP1 pd PAC10|YGR079W
+MBP1 pd CLB6|tC(GCA)G
+MBP1 pd RNR4|tL(CAA)G3
+MBP1 pd BUB1|tK(CUU)G3
+MBP1 pd CRH1|tW(CCA)G2
+MBP1 pd TOS2|snR7-L
+MBP1 pd GIC1|RPP1
+MBP1 pd CTM1|ERP5
+MBP1 pd SPO16|RTT107
+MBP1 pd ELO1|CDC6
+MBP1 pd SWE1|MNN5
+MBP1 pd NCA3|ASF1
+MBP1 pd SMC3|JEM1
+MBP1 pd PRE3|YJR001W
+MBP1 pd YJR030C|GEA1
+MBP1 pd POL32|tM(CAU)J3
+MBP1 pd PTK1|PEX1
+MBP1 pd PIR3|YKL162C
+MBP1 pd RAD27|ABF1
+MBP1 pd LAP4|HSL1
+MBP1 pd tH(GUG)K|YNK1
+MBP1 pd LAC1|CAP1
+MBP1 pd ECM4|YKR077W
+MBP1 pd YLR047C|RPS0B
+MBP1 pd CDC45|YLR104W
+MBP1 pd TUB4|CRR1
+MBP1 pd ATP14|YLR297W
+MBP1 pd ECM38|EXG1
+MBP1 pd SPO77|FKS1
+MBP1 pd TAL1|ILV5
+MBP1 pd YLR364W|RPS22B
+MBP1 pd YLR385C|VAC14
+MBP1 pd CRN1|SEN1
+MBP1 pd LSM3|MRPL4
+MBP1 pd TSA1|YOX1
+MBP1 pd SEL1|ERV25
+MBP1 pd YMR069W|MOT3
+MBP1 pd PDS5|tV(AAC)M2
+MBP1 pd CTF18|SEC14
+MBP1 pd RPS16A|YMR144W
+MBP1 pd YMR178W|SPT21
+MBP1 pd CIK1|CLN1
+MBP1 pd YMR279C|CAT8
+MBP1 pd SCW10|FKS3
+MBP1 pd FKS3|GAS1
+MBP1 pd YNL313C|RFA2
+MBP1 pd TRF5|CLA4
+MBP1 pd RFC3|PCL1
+MBP1 pd YNL274C|TOF1
+MBP1 pd PDR16|ELA1
+MBP1 pd ALG9|MGS1
+MBP1 pd YNL193W|CHS1
+MBP1 pd MET4|POL1
+MBP1 pd TPM1|NIS1
+MBP1 pd NIS1|YNL077W
+MBP1 pd HHT2|HHF2
+MBP1 pd LRO1|YNR009W
+MBP1 pd TLG2|ESC8
+MBP1 pd CYT1|YOR066W
+MBP1 pd CDC21|UFE1
+MBP1 pd YOR246C|SRL1
+MBP1 pd YOR342C|YOR343W-A
+MBP1 pd PLC1|YPL267W
+MBP1 pd CIN2|HSP82
+MBP1 pd RAD53|YPL152W-A
+MBP1 pd MOT1|RPS9A
+MBP1 pd HST2|YPL014W
+MBP1 pd OPY2|YPR078C
+MBP1 pd CLB5|tC(GCA)P2
+MBP1 pd RUF6|tA(AGC)P
+MBP1 pd YPR174C|DPB2
+MCM1 pd CLN3|CYC3
+MCM1 pd KIN3|CDC15
+MCM1 pd HDR1|YBR139W
+MCM1 pd RAM1|YDL089W
+MCM1 pd SWI5|EKI1
+MCM1 pd RVB1|HST4
+MCM1 pd RVS167|SAC7
+MCM1 pd YHP1|PPN1
+MCM1 pd TFB3|MFA1
+MCM1 pd RUF1|HLR1
+MCM1 pd AYR1|SIM1
+MCM1 pd SIM1|POG1
+MCM1 pd YIL077C|SEC28
+MCM1 pd RPS24B|SEC6
+MCM1 pd YEL041W|UTR2
+MCM1 pd SWI4|LSM4
+MCM1 pd YER158C|BUR6
+MCM1 pd GYP8|STE2
+MCM1 pd MCM6|tK(CUU)G1
+MCM1 pd AGA2|RPL24A
+MCM1 pd STT3|ALK1
+MCM1 pd TFC4|UFD1
+MCM1 pd PRP31|DBF2
+MCM1 pd GPA1|MRS11
+MCM1 pd SFB3|TRA1
+MCM1 pd YHR151C|SPO12
+MCM1 pd ELO1|CDC6
+MCM1 pd YJL160C|HSP150
+MCM1 pd CIS3|FAR1
+MCM1 pd FAR1|SSY5
+MCM1 pd PBS2|YJL127C-B
+MCM1 pd YJL127C-B|SPT10
+MCM1 pd PRY1|PRY3
+MCM1 pd TDH1|YJL051W
+MCM1 pd JSN1|BUD4
+MCM1 pd STE6|tT(CGU)K
+MCM1 pd PIR1|PIR3
+MCM1 pd MPE1|TOA2
+MCM1 pd YKR041W|UTH1
+MCM1 pd YKR096W|PCK1
+MCM1 pd RAX2|ARP6
+MCM1 pd UGT51|YLR190W
+MCM1 pd PIG1|CDC46
+MCM1 pd COQ5|ZDS2
+MCM1 pd YML053C|SUR7
+MCM1 pd YMR001C-A|YMR002W
+MCM1 pd YMR031C|HOF1
+MCM1 pd YMR253C|GFD1
+MCM1 pd TRF5|CLA4
+MCM1 pd RFC3|PCL1
+MCM1 pd CBK1|YGP1
+MCM1 pd YNL146W|MFA2
+MCM1 pd YNL058C|YNL056W
+MCM1 pd VAC7|MSG5
+MCM1 pd BUD17|CPR8
+MCM1 pd YNR062C|YNR063W
+MCM1 pd CYT1|YOR066W
+MCM1 pd SPS4|YOR315W
+MCM1 pd YPL277C|SAM3
+MCM1 pd MRD1|PIS1
+MCM1 pd tK(UUU)P|CLB2
+MET31 pd DEP1|CYS3
+MET31 pd YEL073C|YEL072W
+MET31 pd MET6|IES5
+MET31 pd STR3|MND1
+MET31 pd PDR1|ERG4
+MET31 pd YLR179C|SAM1
+MET31 pd YNL277W-A|MET2
+MET31 pd RPS19A|RPL18A
+MET32 pd DEP1|CYS3
+MET32 pd NGR1|MET8
+MET32 pd RAD59|USO1
+MET32 pd tT(AGU)D|tS(AGA)D1
+MET32 pd YEL073C|YEL072W
+MET32 pd MET6|IES5
+MET32 pd YER134C|tV(AAC)E1
+MET32 pd STR3|MND1
+MET32 pd YGR054W|MUP1
+MET32 pd BUB1|tK(CUU)G3
+MET32 pd NUP82|BNA3
+MET32 pd TDH2|MET3
+MET32 pd MET14|VPS1
+MET32 pd YLR091W|SUL2
+MET32 pd YLR179C|SAM1
+MET32 pd RPS16A|YMR144W
+MET32 pd YNL277W-A|MET2
+MET32 pd YNL275W|YNL274C
+MET32 pd tF(GAA)P1|YPR003C
+MET4 pd DEP1|CYS3
+MET4 pd YEL047C|GLY1
+MET4 pd MET6|IES5
+MET4 pd STR3|MND1
+MET4 pd YGR054W|MUP1
+MET4 pd tP(UGG)L|YLL025W
+MET4 pd YLR179C|SAM1
+MET4 pd RPS22B|snR44
+MET4 pd YNL277W-A|MET2
+MOT3 pd YBR013C|tT(AGU)B
+MOT3 pd MIS1|RPL19A
+MOT3 pd YBR096W|VPS15
+MOT3 pd HSP30|YCR023C
+MOT3 pd RPS13|YDR065W
+MOT3 pd RAD55|SED1
+MOT3 pd RAD30|tS(AGA)D3
+MOT3 pd RPI1|RHO3
+MOT3 pd XBP1|SGA1
+MOT3 pd tT(AGU)I2|MNT3
+MOT3 pd MUC1|MRS1
+MOT3 pd DLD3|YEL070W
+MOT3 pd PRB1|SOM1
+MOT3 pd RPR1|YEL020C
+MOT3 pd GLC7|tH(GUG)E2
+MOT3 pd PAU5|tP(UGG)F
+MOT3 pd ADH4|ZRT1
+MOT3 pd ABC1|tW(CCA)G1
+MOT3 pd VPS62|BTN2
+MOT3 pd DUR3|YHL015W-A
+MOT3 pd YHL015W-A|RPS20
+MOT3 pd tK(CUU)J|tW(CCA)J
+MOT3 pd PAP1|OSH6
+MOT3 pd YKR041W|UTH1
+MOT3 pd ZRT2|ACE2
+MOT3 pd YKU80|tK(CUU)M
+MOT3 pd YMR118C|tL(CAA)M
+MOT3 pd YMR185W|HSC82
+MOT3 pd tQ(CUG)M|SCS7
+MOT3 pd IDH1|NCE103
+MOT3 pd ADH1|PHM7
+MOT3 pd SPS4|YOR315W
+MOT3 pd YPL137C|ISU1
+MSN2 pd YAL061W|BDH1
+MSN2 pd SSA1|EFB1
+MSN2 pd YBR085C-A|IST2
+MSN2 pd ADP1|PGK1
+MSN2 pd THI13|AAD4
+MSN2 pd GAL3|SNQ2
+MSN2 pd PST2|MRH1
+MSN2 pd TPI1|YDR051C
+MSN2 pd YDR098C-A|BMH2
+MSN2 pd YDR132C|YCF1
+MSN2 pd YDR170W-A|HSP42
+MSN2 pd YDR352W|TRR1
+MSN2 pd TRR1|TRP4
+MSN2 pd tG(CCC)D|YDR391C
+MSN2 pd TSA2|GUK1
+MSN2 pd UBC8|GLC3
+MSN2 pd GCN4|TOS9
+MSN2 pd ECM32|BMH1
+MSN2 pd SRM1|TOS8
+MSN2 pd PDC6|CTT1
+MSN2 pd SKN1|tG(UCC)G
+MSN2 pd TDH3|PDX1
+MSN2 pd SOL4|MGA1
+MSN2 pd MGA1|YGR250C
+MSN2 pd tT(UGU)G2|GND2
+MSN2 pd SOD2|YHR009C
+MSN2 pd TPK1|YJL163C
+MSN2 pd SSC1|TAH11
+MSN2 pd YKL086W|MDH1
+MSN2 pd YKL071W|YKL070W
+MSN2 pd YKL063C|MSN4
+MSN2 pd CCP1|GPT2
+MSN2 pd ISA1|HSP104
+MSN2 pd SSA2|YLL023C
+MSN2 pd YLR053C|YLR054C
+MSN2 pd YLR108C|AHP1
+MSN2 pd MAS1|YLR164W
+MSN2 pd YLR257W|GSY2
+MSN2 pd YML100W-A|TSL1
+MSN2 pd YMR086W|YMR087W
+MSN2 pd DCR1|GAT2
+MSN2 pd HOT1|DDR48
+MSN2 pd CBK1|YGP1
+MSN2 pd YGP1|ASI2
+MSN2 pd YNL134C|FYV6
+MSN2 pd YOL159C|ENB1
+MSN2 pd YOL114C|SKM1
+MSN2 pd DDR2|SPE2
+MSN2 pd STI1|CIN5
+MSN2 pd ISU2|YOR227W
+MSN2 pd TYE7|tP(UGG)O3
+MSN2 pd tG(GCC)P2|GPH1
+MSN4 pd SSA1|EFB1
+MSN4 pd YBR071W|HSP26
+MSN4 pd HMLALPHA1|CHA1
+MSN4 pd YCR095C|HMRA2
+MSN4 pd AFR1|SSS1
+MSN4 pd YDR098C-A|BMH2
+MSN4 pd HSP78|YAP6
+MSN4 pd EXG2|tS(AGA)D2
+MSN4 pd tG(CCC)D|YDR391C
+MSN4 pd TSA2|GUK1
+MSN4 pd MMF1|PCL7
+MSN4 pd tK(CUU)E1|tR(UCU)E
+MSN4 pd RPS8B|SSA4
+MSN4 pd YER188C-A|YER189W
+MSN4 pd VTC2|MSH4
+MSN4 pd RPL2A|YFR032C
+MSN4 pd YGR038C-A|KSS1
+MSN4 pd YGR046W|TFC4
+MSN4 pd SCM4|YGR052W
+MSN4 pd PDC6|CTT1
+MSN4 pd SKN1|tG(UCC)G
+MSN4 pd TDH3|PDX1
+MSN4 pd SOD2|YHR009C
+MSN4 pd YHR086W-A|YHR087W
+MSN4 pd HSP150|CIS3
+MSN4 pd CCT8|tM(CAU)J2
+MSN4 pd MCH2|FRE2
+MSN4 pd YKL086W|MDH1
+MSN4 pd CCP1|GPT2
+MSN4 pd AYT1|MHT1
+MSN4 pd ISA1|HSP104
+MSN4 pd YLR053C|YLR054C
+MSN4 pd YLR108C|AHP1
+MSN4 pd AHP1|CCW12
+MSN4 pd YLR162W-A|MAS1
+MSN4 pd LSM3|MRPL4
+MSN4 pd COS3|YML131W
+MSN4 pd YML100W-A|TSL1
+MSN4 pd YML007C-A|YAP1
+MSN4 pd YMR050C|tW(CCA)M
+MSN4 pd tL(CAA)M|ASI1
+MSN4 pd HOT1|DDR48
+MSN4 pd YMR251W|HOR7
+MSN4 pd PRE5|YMR315W
+MSN4 pd ZWF1|NAR1
+MSN4 pd CBK1|YGP1
+MSN4 pd YGP1|ASI2
+MSN4 pd YNL134C|FYV6
+MSN4 pd DDR2|SPE2
+MSN4 pd PET127|ROD1
+MSN4 pd STI1|CIN5
+MSN4 pd ISU2|YOR227W
+MSN4 pd YPR063C|ROX1
+MSN4 pd ARR3|YPR202W
+NDD1 pd KIN3|CDC15
+NDD1 pd BUD31|HCM1
+NDD1 pd PST2|MRH1
+NDD1 pd SWI5|EKI1
+NDD1 pd YHP1|PPN1
+NDD1 pd RUF1|HLR1
+NDD1 pd BNR1|YIL158W
+NDD1 pd YER188C-A|YER189W
+NDD1 pd YGL117W|CDC20
+NDD1 pd STT3|ALK1
+NDD1 pd YGL007C-A|YGL006W-A
+NDD1 pd snR48|ERG25
+NDD1 pd PRP31|DBF2
+NDD1 pd tA(AGC)G|SKN1
+NDD1 pd SMI1|BNS1
+NDD1 pd YHL029C|WSC4
+NDD1 pd SFB3|TRA1
+NDD1 pd YHR151C|SPO12
+NDD1 pd CIS3|FAR1
+NDD1 pd GSH1|LSB6
+NDD1 pd PRY1|PRY3
+NDD1 pd TDH1|YJL051W
+NDD1 pd JSN1|BUD4
+NDD1 pd YKR041W|UTH1
+NDD1 pd RAX2|ARP6
+NDD1 pd snR79|MDN1
+NDD1 pd UGT51|YLR190W
+NDD1 pd GTR1|NDI1
+NDD1 pd YML053C|SUR7
+NDD1 pd YMR001C-A|YMR002W
+NDD1 pd CIK1|CLN1
+NDD1 pd YNL146W|MFA2
+NDD1 pd YNL058C|YNL056W
+NDD1 pd YOR246C|SRL1
+NDD1 pd SPS4|YOR315W
+NDD1 pd snR17b|RPL33A
+NDD1 pd tK(UUU)P|CLB2
+NDD1 pd YPR148C|NCE102
+NRG1 pd FLO9|GDH3
+NRG1 pd YAL061W|BDH1
+NRG1 pd OSH1|FLO1
+NRG1 pd YBL029C-A|YBL029W
+NRG1 pd GAL7|GAL10
+NRG1 pd NRG2|TIP1
+NRG1 pd ECM8|YBR077C
+NRG1 pd TBS1|APD1
+NRG1 pd ICS2|CST13
+NRG1 pd PHO89|YBR296C-A
+NRG1 pd tK(CUU)C|MAK32
+NRG1 pd PAU3|YCR105W
+NRG1 pd RAM1|YDL089W
+NRG1 pd OSH2|ERP3
+NRG1 pd ENA1|RSM10
+NRG1 pd NRG1|HEM13
+NRG1 pd RAD55|SED1
+NRG1 pd YDR111C|PDS1
+NRG1 pd YDR132C|YCF1
+NRG1 pd PPM1|PPZ2
+NRG1 pd SPP41|RMT2
+NRG1 pd GNP1|SMT3
+NRG1 pd FIT1|STL1
+NRG1 pd RPI1|RHO3
+NRG1 pd XBP1|SGA1
+NRG1 pd HIS6|YIL019W
+NRG1 pd GAT4|YIR014W
+NRG1 pd MUC1|MRS1
+NRG1 pd GTT1|YPS6
+NRG1 pd YEL041W|UTR2
+NRG1 pd GEA2|URA3
+NRG1 pd YER010C|TIR1
+NRG1 pd YER028C|SMB1
+NRG1 pd CAJ1|tQ(UUG)E1
+NRG1 pd MET6|IES5
+NRG1 pd RAD51|SHC1
+NRG1 pd FTR1|LSM5
+NRG1 pd AGP3|YFL054C
+NRG1 pd GSY1|YFR016C
+NRG1 pd PDR1|ERG4
+NRG1 pd ERG26|YGR001C
+NRG1 pd SCM4|YGR052W
+NRG1 pd tA(AGC)G|SKN1
+NRG1 pd YGR237C|KEL2
+NRG1 pd MGA1|YGR250C
+NRG1 pd YHL042W|ARN1
+NRG1 pd YHR032W|YHR033W
+NRG1 pd ELO1|CDC6
+NRG1 pd YJL107C|IME2
+NRG1 pd YJL077W-B|ICS3
+NRG1 pd IME1|RPL43B
+NRG1 pd RPL43B|SFC1
+NRG1 pd KTI12|HAP4
+NRG1 pd CWP2|CWP1
+NRG1 pd PRI2|PHD1
+NRG1 pd CCP1|GPT2
+NRG1 pd YKR075C|ECM4
+NRG1 pd SIR1|FLO10
+NRG1 pd YLR012C|GAT3
+NRG1 pd YPS3|YLR125W
+NRG1 pd EMG1|YLR187W
+NRG1 pd COS3|YML131W
+NRG1 pd PHO84|GTR1
+NRG1 pd YMR010W|HXT2
+NRG1 pd SOK2|SPO20
+NRG1 pd AAC1|FET3
+NRG1 pd YMR069W|MOT3
+NRG1 pd ADH3|YMR084W
+NRG1 pd DCR1|GAT2
+NRG1 pd YMR194C-B|ICY1
+NRG1 pd YMR251W|HOR7
+NRG1 pd FET4|YMR321C
+NRG1 pd PDR16|ELA1
+NRG1 pd MGS1|YNL217W
+NRG1 pd SUN4|AQR1
+NRG1 pd MNT4|FRE4
+NRG1 pd YNR069C|PDR18
+NRG1 pd ENB1|YOL157C
+NRG1 pd SMF1|RPS19A
+NRG1 pd YAP7|YOL027C
+NRG1 pd CIN5|DFG16
+NRG1 pd BAG7|IDH2
+NRG1 pd YOR138C|SFL1
+NRG1 pd YOR152C|PDR5
+NRG1 pd YOR179C|DCI1
+NRG1 pd ISU2|YOR227W
+NRG1 pd RDR1|FRE3
+NRG1 pd DIM1|DIP5
+NRG1 pd FAS2|YPL230W
+NRG1 pd PDR12|SUR1
+NRG1 pd SKS1|NCE4
+NRG1 pd YPR013C|YPR015C
+NRG1 pd ATH1|YPR027C
+NRG1 pd YPR061C|FCY1
+NRG1 pd YPR157W|YPR158W
+OPI1 pd YCR007C|tN(GUU)C
+OPI1 pd RPS22B|snR44
+OPI1 pd tA(AGC)P|RUF6
+OPI1 pd RUF6|tA(AGC)P
+PDR1 pd YBL111C|YBL108C-A
+PDR1 pd HMLALPHA1|CHA1
+PDR1 pd PAU3|YCR105W
+PDR1 pd YDL001W|NTH1
+PDR1 pd RAD61|DAD1
+PDR1 pd YDR542W|YRF1-1
+PDR1 pd YER188C-A|YER189W
+PDR1 pd EGD2|YHR194W
+PDR1 pd YLL066C|YLL064C
+PDR1 pd YLR162W-A|MAS1
+PDR1 pd ENT2|HRD3
+PDR1 pd PAU4|YLR462W
+PDR1 pd TAF13|VPS9
+PDR1 pd SMP2|YMR166C
+PDR1 pd YOR138C|SFL1
+PDR1 pd FAA1|HSH49
+PDR1 pd RDR1|FRE3
+PDR1 pd snR17b|RPL33A
+PDR1 pd VTC3|CTF19
+PDR1 pd tI(AAU)P2|YPR171W
+PDR3 pd YBL006C|PDR3
+PHD1 pd FLO9|GDH3
+PHD1 pd CLN3|CYC3
+PHD1 pd OSH1|FLO1
+PHD1 pd YBL111C|YBL108C-A
+PHD1 pd YBL108C-A|tL(UAA)B1
+PHD1 pd YBL029C-A|YBL029W
+PHD1 pd TIP1|BAP2
+PHD1 pd BAP2|TAT1
+PHD1 pd TAT1|YBR070C
+PHD1 pd CYC8|RAD16
+PHD1 pd ICS2|CST13
+PHD1 pd GIT1|YCR099C
+PHD1 pd STP4|SIT4
+PHD1 pd GAL3|SNQ2
+PHD1 pd EXG2|tS(AGA)D2
+PHD1 pd GIC2|SUM1
+PHD1 pd HXT6|HXT3
+PHD1 pd HXT3|SGI1
+PHD1 pd YHP1|PPN1
+PHD1 pd YDR524C-B|SNA2
+PHD1 pd YIL172C|YIL169C
+PHD1 pd RPI1|RHO3
+PHD1 pd XBP1|SGA1
+PHD1 pd tS(UGA)I|YIL056W
+PHD1 pd PDR11|TIR3
+PHD1 pd MUC1|MRS1
+PHD1 pd YEL075C|YEL073C
+PHD1 pd DLD3|YEL070W
+PHD1 pd HXT13|HPA3
+PHD1 pd CYC7|UTR4
+PHD1 pd GCN4|TOS9
+PHD1 pd ZRG8|YER034W
+PHD1 pd ACA1|SPO73
+PHD1 pd FTR1|LSM5
+PHD1 pd SRM1|TOS8
+PHD1 pd SOL4|MGA1
+PHD1 pd MGA1|YGR250C
+PHD1 pd YGR250C|YGR251W
+PHD1 pd SCW4|PXR1
+PHD1 pd ERG11|YHR007C-A
+PHD1 pd YJL218W|YJL217W
+PHD1 pd HSP150|CIS3
+PHD1 pd CIS3|FAR1
+PHD1 pd PBS2|YJL127C-B
+PHD1 pd YJL127C-B|SPT10
+PHD1 pd IME2|SET4
+PHD1 pd PRY1|PRY3
+PHD1 pd IME1|RPL43B
+PHD1 pd ZMS1|snR3
+PHD1 pd PIR3|YKL162C
+PHD1 pd KTI12|HAP4
+PHD1 pd YKL063C|MSN4
+PHD1 pd SIR1|FLO10
+PHD1 pd COS3|YML131W
+PHD1 pd YML117W|ATR1
+PHD1 pd YMR010W|HXT2
+PHD1 pd ERG5|SOK2
+PHD1 pd SOK2|SPO20
+PHD1 pd SPO20|YMR018W
+PHD1 pd DCR1|GAT2
+PHD1 pd PSO2|CIN4
+PHD1 pd YMR194C-B|ICY1
+PHD1 pd FET4|YMR321C
+PHD1 pd RFC3|PCL1
+PHD1 pd RHO5|RPS3
+PHD1 pd YOL155W-A|YOL155C
+PHD1 pd STI1|CIN5
+PHD1 pd CIN5|DFG16
+PHD1 pd VAM3|RGS2
+PHD1 pd GAC1|YOR179C
+PHD1 pd YOR179C|DCI1
+PHD1 pd MSC6|GDS1
+PHD1 pd DIM1|DIP5
+PHD1 pd FAS2|YPL230W
+PHD1 pd CUP9|YPL176C
+PHD1 pd SKS1|NCE4
+PHD1 pd YPL017C|SWI1
+PHD1 pd YPR013C|YPR015C
+PHD1 pd tC(GCA)P2|THI22
+PHD1 pd ARR3|YPR202W
+PHO2 pd GIT1|YCR099C
+PHO2 pd RDS1|AAD3
+PHO2 pd YER034W|EDC2
+PHO2 pd SPL2|ARO9
+PHO2 pd LSM3|MRPL4
+PHO2 pd IDH1|NCE103
+PHO4 pd CDC15|PAU7
+PHO4 pd PHO89|YBR296C-A
+PHO4 pd GRX1|LSB5
+PHO4 pd YCR095C|HMRA2
+PHO4 pd GIT1|YCR099C
+PHO4 pd SEC1|TRM82
+PHO4 pd PHM6|YDR282C
+PHO4 pd GCN2|DPP1
+PHO4 pd HXT7|HXT6
+PHO4 pd APT2|SSN2
+PHO4 pd YEL001C|MNN1
+PHO4 pd RPS24A|YER074W-A
+PHO4 pd YER078C|YER078W-A
+PHO4 pd YFR026C|ECO1
+PHO4 pd YFR044C|YFR045W
+PHO4 pd PCL10|ITC1
+PHO4 pd PUP2|ENO1
+PHO4 pd YGR273C|TAF1
+PHO4 pd SPL2|ARO9
+PHO4 pd YJL118W|PHO86
+PHO4 pd TDH1|YJL051W
+PHO4 pd SAG1|APL1
+PHO4 pd APS2|PTK2
+PHO4 pd HBS1|MRPL20
+PHO4 pd YLR152C|ACS2
+PHO4 pd PDR8|BOP2
+PHO4 pd PHO84|GTR1
+PHO4 pd YNL311C|YNL310C
+PHO4 pd YGP1|ASI2
+PHO4 pd KTR5|CRZ1
+PHO4 pd PFK27|MED7
+PHO4 pd YRR1|DDP1
+PHO4 pd VTC3|CTF19
+PUT3 pd YBL064C|KIP1
+PUT3 pd RPL16A|CSM2
+PUT3 pd YHR036W|PUT2
+PUT3 pd RRN5|PUT1
+PUT3 pd YLR312C|MRPL15
+PUT3 pd RAX1|YOR302W
+PUT3 pd MCH5|SLY41
+PUT3 pd VMA13|YPR036W-A
+RAP1 pd FUN19|POP5
+RAP1 pd RPL23A|YBL086C
+RAP1 pd PIM1|HAP3
+RAP1 pd RPL19A|AAC3
+RAP1 pd RPS6B|SMP1
+RAP1 pd NTC20|RPS9B
+RAP1 pd RPS9B|RPL21A
+RAP1 pd ARF1|RPL35A
+RAP1 pd PPH22|YDL186W
+RAP1 pd RPL41A|YDL183C
+RAP1 pd ARF2|RPL35B
+RAP1 pd RPL41B|YDL133W
+RAP1 pd RPS16B|RPL13A
+RAP1 pd RXT3|RPL31A
+RAP1 pd YDR063W|RPS13
+RAP1 pd YDR186C|CCT6
+RAP1 pd SYF1|RPL12B
+RAP1 pd UTP6|RPS18A
+RAP1 pd UGO1|RPL27B
+RAP1 pd RPL37B|PLM2
+RAP1 pd MLP2|RPL40A
+RAP1 pd RPL16A|CSM2
+RAP1 pd POG1|YIL121W
+RAP1 pd YIL019W|RPL2B
+RAP1 pd YEL075C|YEL073C
+RAP1 pd RPL12A|MAK10
+RAP1 pd YEL023C|GEA2
+RAP1 pd YPT31|FIR1
+RAP1 pd ALD5|RPS24A
+RAP1 pd SLX8|RPL23B
+RAP1 pd RPL22B|YFL034W
+RAP1 pd FRS2|GAT1
+RAP1 pd RPL2A|YFR032C
+RAP1 pd YGL188C-A|COX4
+RAP1 pd MON1|RPS2
+RAP1 pd VPS73|RPL28
+RAP1 pd RPL24A|RPL30
+RAP1 pd YGR033C|RPL26B
+RAP1 pd YGR117C|RPS23A
+RAP1 pd RPL24B|YGR149W
+RAP1 pd RPS27B|ECM12
+RAP1 pd YHR032W|YHR033W
+RAP1 pd HXT5|YHR097C
+RAP1 pd RPL42B|CHS7
+RAP1 pd RPS4B|MNL1
+RAP1 pd YJL192C|RPS14B
+RAP1 pd RPS22A|RPL39
+RAP1 pd YJL178C|RPL17B
+RAP1 pd RPS21B|LCB3
+RAP1 pd DPB11|SIP4
+RAP1 pd APS2|PTK2
+RAP1 pd PRS1|RPL17A
+RAP1 pd YKL063C|MSN4
+RAP1 pd SFT1|RPL14A
+RAP1 pd UBI4|ENT4
+RAP1 pd PDC1|STU2
+RAP1 pd YLR047C|RPS0B
+RAP1 pd RPS30A|MEC3
+RAP1 pd RPS25B|tE(UUC)L
+RAP1 pd tR(CCG)L|RPL26A
+RAP1 pd YLR387C|RPS29A
+RAP1 pd BDF1|YLR401C
+RAP1 pd VMA6|RPL6B
+RAP1 pd RPL6A|YML072C
+RAP1 pd TEM1|RPS1B
+RAP1 pd RPS18B|YML025C
+RAP1 pd YML025C|RPS17A
+RAP1 pd ERG5|SOK2
+RAP1 pd RPL13B|RPS16A
+RAP1 pd YMR242W-A|ZRC1
+RAP1 pd RPS19B|RPL18B
+RAP1 pd YNL162W-A|RPL42A
+RAP1 pd YNL144C|MEP2
+RAP1 pd RPS7B|YNL095C
+RAP1 pd RPL16B|FKH2
+RAP1 pd PFK27|MED7
+RAP1 pd YGK3|RPL25
+RAP1 pd SHR5|YOL109W
+RAP1 pd YOL083W|CVT19
+RAP1 pd MAM3|GPD2
+RAP1 pd DDR2|SPE2
+RAP1 pd RPS15|RPP2A
+RAP1 pd RKI1|RPS7A
+RAP1 pd YOR179C|DCI1
+RAP1 pd RPL33B|snR17a
+RAP1 pd YOR292C|RPS10A
+RAP1 pd RAX1|YOR302W
+RAP1 pd RPL20B|SPS4
+RAP1 pd YOR342C|YOR343W-A
+RAP1 pd YOR365C|SCP1
+RAP1 pd RPL36B|GYP5
+RAP1 pd KES1|YPL144W
+RAP1 pd snR17b|RPL33A
+RAP1 pd COX11|RPL5
+RAP1 pd YPL017C|SWI1
+RAP1 pd APL4|CSR2
+RAP1 pd MRL1|TEF1
+RAP1 pd RPL11A|PRE2
+RCS1 pd POP7|YBR168W
+RCS1 pd KTR3|FTH1
+RCS1 pd HSP30|YCR023C
+RCS1 pd YCR095C|HMRA2
+RCS1 pd PAU3|YCR105W
+RCS1 pd RDS1|AAD3
+RCS1 pd CTH1|YDR152W
+RCS1 pd AKR1|PEX10
+RCS1 pd MSW1|CCC2
+RCS1 pd YDR541C|YDR542W
+RCS1 pd DLD3|YEL070W
+RCS1 pd HPA3|SIT1
+RCS1 pd PRB1|SOM1
+RCS1 pd snR52|GLC7
+RCS1 pd FTR1|LSM5
+RCS1 pd LSB3|HIS2
+RCS1 pd MND1|GTS1
+RCS1 pd YGL159W|tL(CAA)G1
+RCS1 pd HSF1|RCS1
+RCS1 pd SDS23|OLE1
+RCS1 pd SEC9|NMA2
+RCS1 pd tK(UUU)G2|CLB1
+RCS1 pd KEL2|PEX21
+RCS1 pd YGR250C|YGR251W
+RCS1 pd YGR257C|RAD2
+RCS1 pd ARN2|YHL046C
+RCS1 pd ARN1|YHL039W
+RCS1 pd YHL035C|SBP1
+RCS1 pd YHR199C|RPN10
+RCS1 pd RPA34|YJL147C
+RCS1 pd tY(GUA)J2|CDC8
+RCS1 pd MCH2|FRE2
+RCS1 pd LST4|ZRT3
+RCS1 pd LAP4|HSL1
+RCS1 pd MET14|VPS1
+RCS1 pd MRS4|YSR3
+RCS1 pd FRE6|COF1
+RCS1 pd tP(UGG)L|YLL025W
+RCS1 pd YLR108C|AHP1
+RCS1 pd TIS11|YLR137W
+RCS1 pd HMX1|ENT2
+RCS1 pd TUB4|CRR1
+RCS1 pd CRR1|FRE1
+RCS1 pd AFG2|SKI2
+RCS1 pd VIP1|YLR410W-A
+RCS1 pd YML117W|ATR1
+RCS1 pd YMD8|YML037C
+RCS1 pd SOK2|SPO20
+RCS1 pd YMR041C|tF(GAA)M
+RCS1 pd ECM5|MMT1
+RCS1 pd YMR253C|GFD1
+RCS1 pd FET4|YMR321C
+RCS1 pd YNL269W|LYP1
+RCS1 pd ATX1|DSL1
+RCS1 pd ZWF1|NAR1
+RCS1 pd RPC19|DBP2
+RCS1 pd MNT4|FRE4
+RCS1 pd YOL161C|YOL159C-A
+RCS1 pd ENB1|YOL157C
+RCS1 pd YOR296W|TIM18
+RCS1 pd RDR1|FRE3
+RCS1 pd YOR381W-A|FIT2
+RCS1 pd FIT3|FRE5
+RCS1 pd PRM4|KIP2
+RCS1 pd YPL137C|ISU1
+RCS1 pd tF(GAA)P1|YPR003C
+RCS1 pd AXL1|CTR1
+RCS1 pd YPR151C|YPR152C
+RDS1 pd MNN2|YBR016W
+RDS1 pd PAU3|YCR105W
+RDS1 pd YCR105W|RDS1
+RDS1 pd RDS1|AAD3
+RDS1 pd YER048W-A|YER049W
+RDS1 pd EPL1|FYV11
+RDS1 pd RCK1|YGL157W
+RDS1 pd TEL2|MDR1
+RDS1 pd LSM1|YJL123C
+RDS1 pd ZWF1|NAR1
+RDS1 pd MDH2|YOL125W
+RDS1 pd YOR316C-A|FAA1
+RDS1 pd YPR125W|YPR127W
+REB1 pd FUN21|SNC1
+REB1 pd YBL059W|SHP1
+REB1 pd PIN4|SEC17
+REB1 pd EDE1|YBL046W
+REB1 pd YBL036C|POL12
+REB1 pd RRN6|FMT1
+REB1 pd SPT7|tR(UCU)B
+REB1 pd RXT2|YBR096W
+REB1 pd SHE3|CCZ1
+REB1 pd ARL1|UBS1
+REB1 pd NPL4|SEC66
+REB1 pd FZO1|DTR1
+REB1 pd ABD1|PRP5
+REB1 pd snR189|BPH1
+REB1 pd TAF2|YCR043C
+REB1 pd SED4|CVT17
+REB1 pd CDC39|CDC50
+REB1 pd GCS1|SHS1
+REB1 pd FYV14|SHR3
+REB1 pd CWC2|NHP2
+REB1 pd PPH22|YDL186W
+REB1 pd DLD1|YDL173W
+REB1 pd YDL156W|CLB3
+REB1 pd RPO21|SCM3
+REB1 pd RGT2|ARF2
+REB1 pd YDL046W|MRP10
+REB1 pd tS(AGA)D1|RPT2
+REB1 pd YRB1|YDR003W
+REB1 pd REG1|RAD28
+REB1 pd YDR036C|KRS1
+REB1 pd CPR1|RPA14
+REB1 pd ARG82|HMO1
+REB1 pd RVB1|HST4
+REB1 pd RMS1|HSP78
+REB1 pd PIB1|YDR314C
+REB1 pd PEP7|UTP4
+REB1 pd YCG1|YDR326C
+REB1 pd SKP1|PEX3
+REB1 pd NHX1|TOM1
+REB1 pd RMT2|YDR466W
+REB1 pd YDR542W|YRF1-1
+REB1 pd MLP2|RPL40A
+REB1 pd STH1|KGD1
+REB1 pd SDP1|YIL112W
+REB1 pd SEC24|YIL108W
+REB1 pd YIL105C|SHQ1
+REB1 pd tE(CUC)I|YIL088C
+REB1 pd RPN2|SER33
+REB1 pd YIL023C|TIM44
+REB1 pd MPH1|YIR003W
+REB1 pd tM(CAU)E|CUP5
+REB1 pd YEL023C|GEA2
+REB1 pd tQ(UUG)E2|UBC8
+REB1 pd PRE1|PRP22
+REB1 pd YAT2|GCD11
+REB1 pd YER039C-A|GLN3
+REB1 pd tQ(UUG)E1|YER048W-A
+REB1 pd YER067W|MOT2
+REB1 pd NUP157|MAM1
+REB1 pd YER156C|SEC34
+REB1 pd EPL1|FYV11
+REB1 pd YFL006W|SEC4
+REB1 pd ZIP2|PDE1
+REB1 pd YGL245W|RTF1
+REB1 pd HAP2|MTO1
+REB1 pd EMP24|YGL198W
+REB1 pd IME4|COX13
+REB1 pd MND1|GTS1
+REB1 pd YGL161C|YGL160W
+REB1 pd PEX14|NUT1
+REB1 pd PRP43|ABC1
+REB1 pd MF(ALPHA)2|snR10
+REB1 pd RPB9|YGL068W
+REB1 pd NMA2|YGR012W
+REB1 pd PAC10|YGR079W
+REB1 pd PHB1|PEX4
+REB1 pd NAT2|RPL24B
+REB1 pd OKP1|RNR4
+REB1 pd UBR1|TYS1
+REB1 pd tG(GCC)G2|CRM1
+REB1 pd PHB2|NAS6
+REB1 pd YGR235C|SPG1
+REB1 pd YAP1802|YGR243W
+REB1 pd GOS1|ECM29
+REB1 pd THR1|PPA1
+REB1 pd VMA10|YHR040W
+REB1 pd tP(UGG)H|CRP1
+REB1 pd DBP8|NMD3
+REB1 pd ELO1|CDC6
+REB1 pd IME2|SET4
+REB1 pd snR37|YJL103C
+REB1 pd GYP6|YJL043W
+REB1 pd OST1|PRE3
+REB1 pd HYS2|SUI2
+REB1 pd YJR085C|STE18
+REB1 pd GRR1|JSN1
+REB1 pd YJR096W|YJR097W
+REB1 pd YJR098C|YUH1
+REB1 pd ATP2|CAF17
+REB1 pd ZMS1|snR3
+REB1 pd ECM17|IML1
+REB1 pd YKL146W|RPT1
+REB1 pd GFA1|LAP4
+REB1 pd YKL082C|TEF4
+REB1 pd LHS1|STB6
+REB1 pd MPE1|TOA2
+REB1 pd ASK1|YKL051W
+REB1 pd PAN3|URA6
+REB1 pd YKR015C|YKR016W
+REB1 pd BET3|MET1
+REB1 pd COF1|YLL049W
+REB1 pd VPS13|UBI4
+REB1 pd CCW12|HOG1
+REB1 pd APS1|DPH5
+REB1 pd IFH1|YLR224W
+REB1 pd YPT6|YLR262C-A
+REB1 pd IMH1|CDC25
+REB1 pd SEC61|CSR1
+REB1 pd ECM19|CCW14
+REB1 pd COX14|MSC1
+REB1 pd TUB3|PHO84
+REB1 pd NDI1|YML119W
+REB1 pd ATP18|YML081W
+REB1 pd YML002W|YPT7
+REB1 pd SUB1|YMR040W
+REB1 pd NUP116|CSM3
+REB1 pd SPC24|YMR118C
+REB1 pd RPL15B|YMR122W-A
+REB1 pd YMR182W-A|RUF3
+REB1 pd YMR185W|HSC82
+REB1 pd YMR188C|GCV2
+REB1 pd CEF1|SCJ1
+REB1 pd YMR221C|FSH2
+REB1 pd CAT8|GPI12
+REB1 pd YRF1-6|COS1
+REB1 pd KRI1|MCK1
+REB1 pd MRPL10|tT(AGU)N1
+REB1 pd ERG24|PRM1
+REB1 pd YIF1|POL2
+REB1 pd SUI1|SLA2
+REB1 pd PSD1|YNL168C
+REB1 pd RPL42A|CBK1
+REB1 pd DCP2|MLS1
+REB1 pd YNL115C|RPC19
+REB1 pd CYB5|NOP15
+REB1 pd YNL092W|NST1
+REB1 pd NST1|RHO2
+REB1 pd ASI3|SIS1
+REB1 pd PRP2|URK1
+REB1 pd PHO91|YNR014W
+REB1 pd ZRG17|YNR040W
+REB1 pd CTR9|NOP8
+REB1 pd TOP1|RPB11
+REB1 pd RPB11|SIN3
+REB1 pd YOR021C|YOR022C
+REB1 pd WHI2|YOR044W
+REB1 pd RAT1|YOR049C
+REB1 pd CDC21|UFE1
+REB1 pd YOR093C|ARF3
+REB1 pd RPO31|RPT5
+REB1 pd PFY1|LEO1
+REB1 pd ADE2|YOR129C
+REB1 pd SPP2|SMP3
+REB1 pd SMP3|MRPL23
+REB1 pd RPB2|YOR152C
+REB1 pd PUP1|PET123
+REB1 pd YOR186W|TUF1
+REB1 pd snR8|YTM1
+REB1 pd YOR287C|MPD1
+REB1 pd FAA1|HSH49
+REB1 pd YOR324C|MYO2
+REB1 pd ALA1|KRE5
+REB1 pd YOR353C|MSC6
+REB1 pd PUS1|NIP7
+REB1 pd YPL206C|HRR25
+REB1 pd RXT1|YPL180W
+REB1 pd MEI5|VPS30
+REB1 pd CCL1|ATH1
+REB1 pd SMK1|SEC8
+REB1 pd TKL1|OPY2
+REB1 pd snR41|YPR093C
+REB1 pd YPR100W|SNT309
+REB1 pd tK(UUU)P|CLB2
+REB1 pd TIF3|MMS1
+REB1 pd SEC23|SMX3
+RFX1 pd PTP1|SSB1
+RFX1 pd RPP1B|YDL129W
+RFX1 pd STE14|YDR411C
+RFX1 pd RNR3|FIS1
+RFX1 pd SHC1|tE(UUC)E2
+RFX1 pd RNR4|tL(CAA)G3
+RFX1 pd RPS21B|LCB3
+RFX1 pd CTS1|YLR287C
+RFX1 pd ECM5|MMT1
+RFX1 pd YOR267C|PAC1
+RFX1 pd FSH3|PLP2
+RGT1 pd YER028C|SMB1
+RGT1 pd HXT1|HXT5
+RGT1 pd YKR075C|ECM4
+RIM101 pd PRP3|YDR474C
+RIM101 pd YEL072W|DLD3
+RIM101 pd YLR047C|RPS0B
+RLM1 pd YDL247W|YDL246C
+RLM1 pd IPT1|SNF11
+RLM1 pd RAD55|SED1
+RLM1 pd AFR1|SSS1
+RLM1 pd AGE1|YDR524W-A
+RLM1 pd SIM1|POG1
+RLM1 pd YEL001C|MNN1
+RLM1 pd tL(CAA)G1|RCK1
+RLM1 pd YHL042W|ARN1
+RLM1 pd DSE2|RPC10
+RLM1 pd EGD2|YHR194W
+RLM1 pd YJL160C|HSP150
+RLM1 pd YJL107C|IME2
+RLM1 pd SOR1|YJR160C
+RLM1 pd CWP2|CWP1
+RLM1 pd PXL1|SRL3
+RLM1 pd FLO10|YKR103W
+RLM1 pd CHS5|MID2
+RLM1 pd ECM19|CCW14
+RLM1 pd snR40|CAF40
+RLM1 pd RPL9B|SUN4
+RLM1 pd ASE1|tK(UUU)O
+RLR1 pd MAK5|SUP45
+RLR1 pd MBP1|PSA1
+RLR1 pd MRH1|LYS14
+RLR1 pd YDR042C|snR47
+RLR1 pd YIL169C|YIL166C
+RLR1 pd STE2|BST1
+RLR1 pd YFL002W-A|SPB4
+RLR1 pd YGR071C|UPF3
+RLR1 pd ENO2|CTR2
+RLR1 pd HSP150|CIS3
+RLR1 pd YUR1|TIF2
+RLR1 pd tW(CCA)J|YJL010C
+RLR1 pd OAC1|VPH2
+RLR1 pd STB6|tW(CCA)K
+RLR1 pd YPT7|CDC5
+RLR1 pd MTF1|RRP5
+RLR1 pd AQR1|YDJ1
+RLR1 pd YOL155C|ZPS1
+RLR1 pd DED1|YOR205C
+RLR1 pd RPL5|SPO19
+ROX1 pd FLO9|GDH3
+ROX1 pd CYC3|CDC19
+ROX1 pd OSH1|FLO1
+ROX1 pd YBL029C-A|YBL029W
+ROX1 pd tG(GCC)B|RRN6
+ROX1 pd TAT1|YBR070C
+ROX1 pd YBR071W|HSP26
+ROX1 pd ECM8|YBR077C
+ROX1 pd tD(GUC)B|UBC4
+ROX1 pd ICS2|CST13
+ROX1 pd tC(GCA)B|tE(UUC)B
+ROX1 pd BUD31|HCM1
+ROX1 pd GIT1|YCR099C
+ROX1 pd YCR102C|PAU3
+ROX1 pd YDL156W|CLB3
+ROX1 pd RAD55|SED1
+ROX1 pd YDR132C|YCF1
+ROX1 pd tE(CUC)D|YDR279W
+ROX1 pd RPI1|RHO3
+ROX1 pd DLD3|YEL070W
+ROX1 pd VAC8|tQ(UUG)E2
+ROX1 pd ICL1|tS(UGA)E
+ROX1 pd VTC1|ALD5
+ROX1 pd tF(GAA)F|YFR007W
+ROX1 pd tH(GUG)G2|SRM1
+ROX1 pd TOS8|tE(UUC)G1
+ROX1 pd PDR1|ERG4
+ROX1 pd YGL007C-A|YGL006W-A
+ROX1 pd COD5|YGL004C
+ROX1 pd tI(AAU)G|ASN2
+ROX1 pd YGR146C|YGR146C-A
+ROX1 pd tG(GCC)G2|CRM1
+ROX1 pd YJL046W|tY(GUA)J1
+ROX1 pd tK(CUU)J|tW(CCA)J
+ROX1 pd KTI12|HAP4
+ROX1 pd TPO1|ISA1
+ROX1 pd tS(AGA)L|LOT6
+ROX1 pd AHP1|CCW12
+ROX1 pd YPS3|YLR125W
+ROX1 pd YLR412W|YLR412C-A
+ROX1 pd YLR412C-A|YLR413W
+ROX1 pd DOR1|tR(UCU)M2
+ROX1 pd SOK2|SPO20
+ROX1 pd DCR1|GAT2
+ROX1 pd FET4|YMR321C
+ROX1 pd snR40|CAF40
+ROX1 pd IDH1|NCE103
+ROX1 pd MNT4|FRE4
+ROX1 pd YOL157C|HXT11
+ROX1 pd RPS19A|RPL18A
+ROX1 pd YOL026C|tS(GCU)O
+ROX1 pd MCH5|SLY41
+ROX1 pd SPS4|YOR315W
+ROX1 pd DIM1|DIP5
+ROX1 pd FAS2|YPL230W
+ROX1 pd tF(GAA)P1|YPR003C
+ROX1 pd YPR013C|YPR015C
+ROX1 pd YPR108W-A|YPR109W
+RPH1 pd CPR1|RPA14
+RPH1 pd DPS1|BPT1
+RPN4 pd PIM1|HAP3
+RPN4 pd REB1|REG2
+RPN4 pd LSR1|AOR1
+RPN4 pd SSH1|YBR284W
+RPN4 pd YCR060W|YCR061W
+RPN4 pd SRB8|YCR082W
+RPN4 pd MSH3|CDC39
+RPN4 pd YDL183C|LYS20
+RPN4 pd YDL144C|CCT4
+RPN4 pd RPO21|SCM3
+RPN4 pd RPN6|PMT1
+RPN4 pd YDL037C|YDL036C
+RPN4 pd tS(AGA)D1|RPT2
+RPN4 pd CTH1|YDR152W
+RPN4 pd MSW1|CCC2
+RPN4 pd tK(CUU)D1|SEM1
+RPN4 pd SHE9|RPT3
+RPN4 pd YDR425W|RPN9
+RPN4 pd RPN2|SER33
+RPN4 pd DLD3|YEL070W
+RPN4 pd RAD23|ANP1
+RPN4 pd TIR1|tE(UUC)E1
+RPN4 pd tE(UUC)E1|PRE1
+RPN4 pd GPA2|RPN3
+RPN4 pd PUP3|RAD51
+RPN4 pd MAG1|DDI1
+RPN4 pd YER163C|CHD1
+RPN4 pd ECM32|BMH1
+RPN4 pd AAD6|AGP3
+RPN4 pd EPL1|FYV11
+RPN4 pd YFR003C|RPN11
+RPN4 pd GCN20|UBP6
+RPN4 pd PRE4|RET2
+RPN4 pd KEM1|NUP49
+RPN4 pd NAB2|GPG1
+RPN4 pd RPT6|YGL047W
+RPN4 pd PDR1|ERG4
+RPN4 pd SCL1|YGL010W
+RPN4 pd TFC4|UFD1
+RPN4 pd CAF130|PRE9
+RPN4 pd VPS62|BTN2
+RPN4 pd PUP2|ENO1
+RPN4 pd OST1|PRE3
+RPN4 pd YJR005C-A|HYS2
+RPN4 pd snR64|UBA1
+RPN4 pd YKL146W|RPT1
+RPN4 pd DEF1|YKL053C-A
+RPN4 pd ATP7|PUT3
+RPN4 pd YKR104W|YKR105C
+RPN4 pd UBI4|ENT4
+RPN4 pd RPS30A|MEC3
+RPN4 pd RPN13|YLR422W
+RPN4 pd PRE8|RPM2
+RPN4 pd YML007C-A|YAP1
+RPN4 pd NRD1|RAD50
+RPN4 pd YNL156C|YNL155W
+RPN4 pd YOL038C-A|PRE6
+RPN4 pd SGT2|tR(ACG)O
+RPN4 pd YOR052C|YOR054C
+RPN4 pd PUP1|PET123
+RPN4 pd RPT4|GCD1
+RPN4 pd RPN8|YOR262W
+RPN4 pd YTH1|RPN7
+RTG3 pd FLO9|GDH3
+RTG3 pd HMLALPHA1|CHA1
+RTG3 pd COX9|IDP1
+RTG3 pd YDL001W|NTH1
+RTG3 pd YEL072W|DLD3
+RTG3 pd tK(CUU)E1|tR(UCU)E
+RTG3 pd YER128W|PAK1
+RTG3 pd ADH4|ZRT1
+RTG3 pd tG(GCC)G2|CRM1
+RTG3 pd SIP4|ARG3
+RTG3 pd CCT8|tM(CAU)J2
+RTG3 pd CPA2|YJR110W
+RTG3 pd HMS2|BAT2
+RTG3 pd COS9|SRY1
+RTG3 pd tW(CCA)K|YKL071W
+RTG3 pd tH(GUG)K|YNK1
+RTG3 pd DPS1|BPT1
+RTG3 pd ACO1|STT4
+RTG3 pd YMR098C|tD(GUC)M
+RTG3 pd IDH1|NCE103
+RTG3 pd YPR196W|SGE1
+SFP1 pd RPL23A|YBL086C
+SFP1 pd YBR047W|RPS11B
+SFP1 pd NTC20|RPS9B
+SFP1 pd RPS9B|RPL21A
+SFP1 pd RPL41A|YDL183C
+SFP1 pd RPL41B|YDL133W
+SFP1 pd STF1|RPP1B
+SFP1 pd RPS16B|RPL13A
+SFP1 pd YDR063W|RPS13
+SFP1 pd RGP1|HPR1
+SFP1 pd RPL16A|CSM2
+SFP1 pd ALD5|RPS24A
+SFP1 pd MPT5|YGL176C
+SFP1 pd MRM2|RPL1B
+SFP1 pd VPS73|RPL28
+SFP1 pd YGR117C|RPS23A
+SFP1 pd tW(CCA)G2|HIP1
+SFP1 pd RPS27B|ECM12
+SFP1 pd SPS100|YHR140W
+SFP1 pd RPS21B|LCB3
+SFP1 pd CAF17|RPS5
+SFP1 pd FLO10|YKR103W
+SFP1 pd FRS1|RPL22A
+SFP1 pd RPL6A|YML072C
+SFP1 pd RPS18B|YML025C
+SFP1 pd YML025C|RPS17A
+SFP1 pd RPL13B|RPS16A
+SFP1 pd YNL162W-A|RPL42A
+SFP1 pd RPL16B|FKH2
+SFP1 pd RPS19A|RPL18A
+SFP1 pd GYP1|YOR071C
+SFP1 pd tV(AAC)O|MPC54
+SFP1 pd RPL33B|snR17a
+SFP1 pd RPL20B|SPS4
+SFP1 pd SPS4|YOR315W
+SFP1 pd RPS6A|RLM1
+SFP1 pd RPL11A|PRE2
+SIG1 pd tK(CUU)C|MAK32
+SIG1 pd PAU3|YCR105W
+SIG1 pd RDS1|AAD3
+SIG1 pd CLB3|MSH5
+SIG1 pd tE(CUC)D|YDR279W
+SIG1 pd TOM1|YDR458C
+SIG1 pd ERG28|MEI4
+SIG1 pd SHC1|tE(UUC)E2
+SIG1 pd NUP157|MAM1
+SIG1 pd tF(GAA)F|YFR007W
+SIG1 pd YGR165W|KRE11
+SIG1 pd LIN1|REC104
+SIG1 pd PET130|BBC1
+SIG1 pd OCT1|YKL133C
+SIP4 pd ICL1|tS(UGA)E
+SIP4 pd YER188C-A|YER189W
+SIP4 pd RPL43B|SFC1
+SIP4 pd YKR096W|PCK1
+SIP4 pd YLR307C-A|CDA2
+SIP4 pd tQ(CUG)M|SCS7
+SIP4 pd DCP2|MLS1
+SIP4 pd MDH2|YOL125W
+SIP4 pd RKI1|RPS7A
+SKN7 pd tF(GAA)B|ATP1
+SKN7 pd YBL029C-A|YBL029W
+SKN7 pd YBR053C|YRO2
+SKN7 pd NRG2|TIP1
+SKN7 pd YBR077C|ECM33
+SKN7 pd YBR085C-A|IST2
+SKN7 pd ICS2|CST13
+SKN7 pd ALG7|GPX2
+SKN7 pd tK(CUU)C|MAK32
+SKN7 pd SSK22|SOL2
+SKN7 pd YDL183C|LYS20
+SKN7 pd KNH1|STP4
+SKN7 pd DIA3|tA(AGC)D
+SKN7 pd RPT2|PTC1
+SKN7 pd YDL001W|NTH1
+SKN7 pd snR47|NRG1
+SKN7 pd NRG1|HEM13
+SKN7 pd CPR1|RPA14
+SKN7 pd YDR170W-A|HSP42
+SKN7 pd GIC2|SUM1
+SKN7 pd TSA2|GUK1
+SKN7 pd YDR524C-B|SNA2
+SKN7 pd RPI1|RHO3
+SKN7 pd POR2|SDP1
+SKN7 pd YIR018C-A|MUC1
+SKN7 pd GTT1|YPS6
+SKN7 pd GLY1|IES6
+SKN7 pd PMP2|YEL017W
+SKN7 pd YEL001C|MNN1
+SKN7 pd YER010C|TIR1
+SKN7 pd PEA2|SPI1
+SKN7 pd PET122|OXA1
+SKN7 pd YFL054C|DAK2
+SKN7 pd FRS2|GAT1
+SKN7 pd LSB3|HIS2
+SKN7 pd SDS23|OLE1
+SKN7 pd OCH1|PNC1
+SKN7 pd YGL007C-A|YGL006W-A
+SKN7 pd SNU71|MSB2
+SKN7 pd YGR015C|YGR016W
+SKN7 pd SCM4|YGR052W
+SKN7 pd YGR086C|PDC6
+SKN7 pd PDC6|CTT1
+SKN7 pd TPO2|CBF2
+SKN7 pd SOL4|MGA1
+SKN7 pd MGA1|YGR250C
+SKN7 pd SCW4|PXR1
+SKN7 pd NEM1|GPA1
+SKN7 pd CIS3|FAR1
+SKN7 pd NCA3|ASF1
+SKN7 pd MIR1|BNA2
+SKN7 pd HMS2|BAT2
+SKN7 pd KTI12|HAP4
+SKN7 pd CYT2|YKL086W
+SKN7 pd YKL063C|MSN4
+SKN7 pd PRI2|PHD1
+SKN7 pd YKR041W|UTH1
+SKN7 pd YKR075C|ECM4
+SKN7 pd SRP40|PTR2
+SKN7 pd YKR096W|PCK1
+SKN7 pd KNS1|COX19
+SKN7 pd COX19|DPS1
+SKN7 pd CRR1|FRE1
+SKN7 pd tA(AGC)L|YLR257W
+SKN7 pd YLR257W|GSY2
+SKN7 pd ATP14|YLR297W
+SKN7 pd ECM38|EXG1
+SKN7 pd ACO1|STT4
+SKN7 pd RPL6A|YML072C
+SKN7 pd YML053C|SUR7
+SKN7 pd YML007C-A|YAP1
+SKN7 pd SOK2|SPO20
+SKN7 pd MSN2|LYS7
+SKN7 pd YMR069W|MOT3
+SKN7 pd DCR1|GAT2
+SKN7 pd NDE1|TIF34
+SKN7 pd SMP2|YMR166C
+SKN7 pd HOT1|DDR48
+SKN7 pd YMR251W|HOR7
+SKN7 pd SCW10|FKS3
+SKN7 pd YNL193W|CHS1
+SKN7 pd RHO5|RPS3
+SKN7 pd MDG1|APC1
+SKN7 pd YNL097C-A|PHO23
+SKN7 pd TOP2|YNL087W
+SKN7 pd RNH35|LAT1
+SKN7 pd PBI2|HEF3
+SKN7 pd MAS6|YNR018W
+SKN7 pd YOL155W-A|YOL155C
+SKN7 pd MDH2|YOL125W
+SKN7 pd GPD2|ARG1
+SKN7 pd DDR2|SPE2
+SKN7 pd RPS15|RPP2A
+SKN7 pd STI1|CIN5
+SKN7 pd BAG7|IDH2
+SKN7 pd ISU2|YOR227W
+SKN7 pd TPO4|MOD5
+SKN7 pd SPS4|YOR315W
+SKN7 pd PUT4|CIN1
+SKN7 pd FAS2|YPL230W
+SKN7 pd YPL137C|ISU1
+SKN7 pd YPL041C|ISM1
+SKN7 pd SKS1|NCE4
+SKN7 pd YPR013C|YPR015C
+SKN7 pd YPR063C|ROX1
+SKN7 pd YPR148C|NCE102
+SKN7 pd tG(GCC)P2|GPH1
+SKO1 pd RAD55|SED1
+SKO1 pd FIT1|STL1
+SKO1 pd GAT1|PAU5
+SKO1 pd YHL042W|ARN1
+SKO1 pd YHR032W|YHR033W
+SKO1 pd YHR048W|FSH1
+SKO1 pd HXT5|YHR097C
+SKO1 pd PIR3|YKL162C
+SKO1 pd CWP2|CWP1
+SKO1 pd SOK2|SPO20
+SKO1 pd HOT1|DDR48
+SKO1 pd YOR316C-A|FAA1
+SKO1 pd YPR013C|YPR015C
+SMP1 pd tS(AGA)D3|HKR1
+SMP1 pd GLC7|tH(GUG)E2
+SMP1 pd ECM19|CCW14
+SNT2 pd CYC3|CDC19
+SNT2 pd SSA3|AAR2
+SNT2 pd HDR1|YBR139W
+SNT2 pd SUP45|ADH5
+SNT2 pd tL(CAA)C|LEU2
+SNT2 pd YCR090C|KIN82
+SNT2 pd POT1|BNR1
+SNT2 pd YHR138C|SPS100
+SNT2 pd TOK1|HPR5
+SNT2 pd EBP2|YKL171W
+SNT2 pd YLR149C|STM1
+SNT2 pd tQ(UUG)L|RDN37-1
+SNT2 pd RFX1|YLR177W
+SNT2 pd ECM22|CDC42
+SNT2 pd YNL182C|YNL181W
+SNT2 pd FHL1|COD1
+SNT2 pd CLB5|tC(GCA)P2
+SNT2 pd YPR157W|YPR158W
+SNT2 pd DPM1|GDB1
+SOK2 pd GDH3|YAL061W
+SOK2 pd COR1|YBL044W
+SOK2 pd YBL044W|ECM13
+SOK2 pd YBL029C-A|YBL029W
+SOK2 pd ECM8|YBR077C
+SOK2 pd RDS1|AAD3
+SOK2 pd ENA1|RSM10
+SOK2 pd RAD55|SED1
+SOK2 pd YAP6|SWM1
+SOK2 pd GIC2|SUM1
+SOK2 pd HXT6|HXT3
+SOK2 pd APT2|SSN2
+SOK2 pd YHP1|PPN1
+SOK2 pd YDR524C-B|SNA2
+SOK2 pd RPI1|RHO3
+SOK2 pd XBP1|SGA1
+SOK2 pd DLD3|YEL070W
+SOK2 pd HXT13|HPA3
+SOK2 pd YEL041W|UTR2
+SOK2 pd YEL001C|MNN1
+SOK2 pd YER028C|SMB1
+SOK2 pd ZRG8|YER034W
+SOK2 pd ACA1|SPO73
+SOK2 pd tL(CAA)G1|RCK1
+SOK2 pd KEL2|PEX21
+SOK2 pd SOL4|MGA1
+SOK2 pd MGA1|YGR250C
+SOK2 pd YHL042W|ARN1
+SOK2 pd IME2|SET4
+SOK2 pd tM(CAU)J1|YJL027C
+SOK2 pd ZMS1|snR3
+SOK2 pd PIR1|PIR3
+SOK2 pd PIR3|YKL162C
+SOK2 pd KTI12|HAP4
+SOK2 pd YKL098W|YKL096C-B
+SOK2 pd YKL063C|MSN4
+SOK2 pd SIR1|FLO10
+SOK2 pd YLR023C|UBR2
+SOK2 pd ECM38|EXG1
+SOK2 pd SPO77|FKS1
+SOK2 pd AAC1|FET3
+SOK2 pd RPL15B|YMR122W-A
+SOK2 pd DCR1|GAT2
+SOK2 pd BUD17|CPR8
+SOK2 pd YOL155W-A|YOL155C
+SOK2 pd STI1|CIN5
+SOK2 pd YOR049C|YOR051C
+SOK2 pd WHI5|YOR084W
+SOK2 pd YOR152C|PDR5
+SOK2 pd GAC1|YOR179C
+SOK2 pd YOR316C-A|FAA1
+SOK2 pd PDR12|SUR1
+SOK2 pd SKS1|NCE4
+SPT2 pd CDC19|YAL037C-A
+SPT2 pd CST13|YBR159W
+SPT2 pd LSR1|AOR1
+SPT2 pd RPL31A|snR63
+SPT2 pd MBP1|PSA1
+SPT2 pd MRH1|LYS14
+SPT2 pd YDR042C|snR47
+SPT2 pd SED1|SHU2
+SPT2 pd AGE1|YDR524W-A
+SPT2 pd YDR524W-A|YDR524C-B
+SPT2 pd YIL169C|YIL166C
+SPT2 pd YEL047C|GLY1
+SPT2 pd HIP1|TDH3
+SPT2 pd YHB1|YGR235C
+SPT2 pd ENO2|CTR2
+SPT2 pd snR190|RPA34
+SPT2 pd tE(UUC)K|PIR1
+SPT2 pd CWP2|CWP1
+SPT2 pd snR69|RGT1
+SPT2 pd TAL1|ILV5
+SPT2 pd TUB3|PHO84
+SPT2 pd SIW14|HHT2
+SPT2 pd YOL087C|YOL086W-A
+SPT2 pd RPL3|YNG1
+SPT2 pd snR17a|DFR1
+SPT2 pd SRL1|APC5
+SPT2 pd YAH1|ICY2
+SPT2 pd TEF1|YPR081C
+SPT23 pd MMS4|YBR101C
+SPT23 pd YBR203W|YBR204C
+SPT23 pd YCL069W|YCL068C
+SPT23 pd HMLALPHA1|CHA1
+SPT23 pd tK(CUU)C|MAK32
+SPT23 pd HTL1|HSP30
+SPT23 pd HMRA2|HMRA1
+SPT23 pd AAD3|YCR108C
+SPT23 pd SHS1|WHI4
+SPT23 pd ENA1|RSM10
+SPT23 pd YDR084C|AFR1
+SPT23 pd VPS3|PUF6
+SPT23 pd snR67|snR53
+SPT23 pd YFL002W-A|SPB4
+SPT23 pd LOC1|NIC96
+SPT23 pd YGL159W|tL(CAA)G1
+SPT23 pd ERG26|YGR001C
+SPT23 pd SLH1|YGR271C-A
+SPT23 pd tS(AGA)H|tQ(UUG)H
+SPT23 pd RCY1|PRP21
+SPT23 pd RPL17B|SWI3
+SPT23 pd snR37|YJL103C
+SPT23 pd tW(CCA)J|YJL010C
+SPT23 pd PRE3|YJR001W
+SPT23 pd YJR011C|YJR013W
+SPT23 pd ISY1|OSM1
+SPT23 pd STB6|tW(CCA)K
+SPT23 pd YLR023C|UBR2
+SPT23 pd YLR047C|RPS0B
+SPT23 pd RPS0B|YLR049C
+SPT23 pd tQ(UUG)L|RDN37-1
+SPT23 pd YPT7|CDC5
+SPT23 pd YMR118C|tL(CAA)M
+SPT23 pd YMR192W|MRPL24
+SPT23 pd YMR258C|YMR259C
+SPT23 pd RLP7|DOM34
+SPT23 pd MSN1|TRF4
+SPT23 pd PHO80|RRP6
+SPT23 pd ASE1|tK(UUU)O
+SPT23 pd SPP2|SMP3
+SPT23 pd YPL052W|ARL3
+STB1 pd FUN26|CCR4
+STB1 pd BUD31|HCM1
+STB1 pd RPL37B|PLM2
+STB1 pd YDR524C-B|SNA2
+STB1 pd CLB6|tC(GCA)G
+STB1 pd TOS2|snR7-L
+STB1 pd YGR277C|CWC22
+STB1 pd GIC1|RPP1
+STB1 pd YKL098W|YKL096C-B
+STB1 pd SPO77|FKS1
+STB1 pd FKS3|GAS1
+STB1 pd RFC3|PCL1
+STB1 pd YOL007C|TOP1
+STB1 pd YOR246C|SRL1
+STB1 pd NDD1|NUD1
+STB1 pd CLN2|BBP1
+STB4 pd ZTA1|YBR047W
+STB4 pd FAT2|TDP1
+STB4 pd YIL166C|YIL165C
+STB4 pd YEL020C|MMS21
+STB4 pd DCP2|MLS1
+STB4 pd ANT1|SCD6
+STB5 pd KNH1|STP4
+STB5 pd COX20|HEM1
+STB5 pd YDR248C|YDR249C
+STB5 pd POT1|BNR1
+STB5 pd GDA1|YEL041W
+STB5 pd AGP3|YFL054C
+STB5 pd tG(GCC)G2|CRM1
+STB5 pd YAP1801|YHR162W
+STB5 pd YHR162W|SOL3
+STB5 pd YHR177W|STB5
+STB5 pd YHR182W|GND1
+STB5 pd COY1|STE3
+STB5 pd YLR152C|ACS2
+STB5 pd TAL1|ILV5
+STB5 pd PRE5|YMR315W
+STB5 pd YNL274C|TOF1
+STB5 pd YNL127W|SPC98
+STB5 pd YPL063W|ALD6
+STB5 pd TIF6|DSS4
+STB5 pd TKL1|OPY2
+STE12 pd CYC3|CDC19
+STE12 pd MYO4|YAL028W
+STE12 pd tA(UGC)A|BUD14
+STE12 pd BUD14|ADE1
+STE12 pd PAU7|YAR023C
+STE12 pd tL(CAA)A|tS(AGA)A
+STE12 pd YAR068W|PHO11
+STE12 pd SKT5|YBL060W
+STE12 pd PEP1|FUS3
+STE12 pd tG(GCC)B|RRN6
+STE12 pd YBL005W-B|tS(AGA)B
+STE12 pd tS(AGA)B|UTP20
+STE12 pd YBR007C|FLR1
+STE12 pd IPP1|YBR012W-A
+STE12 pd CHS3|SCO2
+STE12 pd ATP3|FIG1
+STE12 pd ORC2|TRM7
+STE12 pd NRG2|TIP1
+STE12 pd UBC4|TEC1
+STE12 pd TEC1|MIS1
+STE12 pd SLI15|ICS2
+STE12 pd ICS2|CST13
+STE12 pd YBR168W|SSE2
+STE12 pd KTR4|BEM1
+STE12 pd YCL056C|KAR4
+STE12 pd RNQ1|FUS1
+STE12 pd FRM2|AGP1
+STE12 pd tK(CUU)C|MAK32
+STE12 pd YCR023C|YCR024C
+STE12 pd RHB1|tQ(UUG)C
+STE12 pd ABP1|FIG2
+STE12 pd YDL241W|LRG1
+STE12 pd RDI1|PPH21
+STE12 pd VCX1|PCL2
+STE12 pd YDL001W|NTH1
+STE12 pd AFR1|SSS1
+STE12 pd SSS1|RRP1
+STE12 pd tQ(UUG)D2|YDR098C-B
+STE12 pd MKC7|TAF12
+STE12 pd SWI5|EKI1
+STE12 pd YDR169C-A|SEC7
+STE12 pd YDR170W-A|HSP42
+STE12 pd YDR210W-B|YDR210C-D
+STE12 pd SNU56|tY(GUA)D
+STE12 pd YDR249C|PAM1
+STE12 pd PHM6|YDR282C
+STE12 pd GIC2|SUM1
+STE12 pd SUM1|TFB1
+STE12 pd TFB1|SSF2
+STE12 pd tF(GAA)D|YDR316W-A
+STE12 pd tX(XXX)D|YDR341C
+STE12 pd YPS7|tM(CAU)D
+STE12 pd LSM6|RGA2
+STE12 pd TOM1|YDR458C
+STE12 pd TFB3|MFA1
+STE12 pd tL(CAA)D|GIN4
+STE12 pd APA2|YDR531W
+STE12 pd YDR533C|FIT1
+STE12 pd AYR1|SIM1
+STE12 pd PRM2|CST6
+STE12 pd SNL1|BAR1
+STE12 pd YIL014C-A|tT(AGU)I2
+STE12 pd MUC1|MRS1
+STE12 pd YEL041W|UTR2
+STE12 pd tK(CUU)E1|tR(UCU)E
+STE12 pd MEI4|ACA1
+STE12 pd CAJ1|tQ(UUG)E1
+STE12 pd tQ(UUG)E1|YER048W-A
+STE12 pd YER064C|ICL1
+STE12 pd PUP3|RAD51
+STE12 pd SHO1|YER119C
+STE12 pd GLC7|tH(GUG)E2
+STE12 pd tH(GUG)E2|tK(CUU)E2
+STE12 pd tV(AAC)E1|GDI1
+STE12 pd BEM2|YER156C
+STE12 pd YER159C-A|SPT2
+STE12 pd YER184C|YER185W
+STE12 pd YER187W|YER188C-A
+STE12 pd ACT1|YPT1
+STE12 pd GYP8|STE2
+STE12 pd PAU5|tP(UGG)F
+STE12 pd GCN1|HOS2
+STE12 pd RAD54|SUT1
+STE12 pd tL(CAA)G1|RCK1
+STE12 pd tW(CCA)G1|YGL117W
+STE12 pd YGL117W|CDC20
+STE12 pd tH(GUG)G2|SRM1
+STE12 pd OLE1|ERV14
+STE12 pd tR(UCU)G1|YGL050W
+STE12 pd AGA2|RPL24A
+STE12 pd SCW11|CWH41
+STE12 pd SNU71|MSB2
+STE12 pd YGR031W|GSC2
+STE12 pd ASK10|ESP1
+STE12 pd YGR173W|tG(GCC)G1
+STE12 pd CRH1|tW(CCA)G2
+STE12 pd TOS2|snR7-L
+STE12 pd PHO81|YHB1
+STE12 pd MGA1|YGR250C
+STE12 pd MAL12|YGR294W
+STE12 pd COS8|ARN2
+STE12 pd GPA1|MRS11
+STE12 pd tA(AGC)H|RPS27B
+STE12 pd FYV4|VMA22
+STE12 pd KSP1|YHR083W
+STE12 pd YHR083W|STE12
+STE12 pd YHR085W|NAM8
+STE12 pd RPL42B|CHS7
+STE12 pd YHR151C|SPO12
+STE12 pd MNL1|SCH9
+STE12 pd ELO1|CDC6
+STE12 pd SWE1|MNN5
+STE12 pd ASG7|SET2
+STE12 pd YJL163C|YJL162C
+STE12 pd YJL162C|tE(UUC)J
+STE12 pd FAR1|SSY5
+STE12 pd IDS2|SFH5
+STE12 pd YJL113W|tD(GUC)J1
+STE12 pd PRY3|YJL077W-B
+STE12 pd YJL077W-B|ICS3
+STE12 pd BFA1|YJR054W
+STE12 pd YJR054W|tR(CCU)J
+STE12 pd PGU1|YJR154W
+STE12 pd MCH2|FRE2
+STE12 pd STE6|tT(CGU)K
+STE12 pd tL(UAA)K|HYM1
+STE12 pd COY1|STE3
+STE12 pd GFA1|LAP4
+STE12 pd CWP2|CWP1
+STE12 pd CWP1|YJU2
+STE12 pd YKL033W|tV(AAC)K2
+STE12 pd tV(AAC)K2|IXR1
+STE12 pd MRP17|DID4
+STE12 pd TOS5|PRY2
+STE12 pd YKR016W|YKR017C
+STE12 pd GAP1|tA(AGC)K2
+STE12 pd YKR041W|UTH1
+STE12 pd YKR060W|KTR2
+STE12 pd YKR075C|ECM4
+STE12 pd PXL1|SRL3
+STE12 pd YLL057C|YLL056C
+STE12 pd RAX2|ARP6
+STE12 pd SEN2|snR79
+STE12 pd snR79|MDN1
+STE12 pd HOG1|tR(ACG)L
+STE12 pd CPR6|YLR218C
+STE12 pd ECM22|CDC42
+STE12 pd CDC46|SMD2
+STE12 pd CHS5|MID2
+STE12 pd MID2|tD(GUC)L2
+STE12 pd YLR352W|BUD8
+STE12 pd YLR412W|YLR412C-A
+STE12 pd YLR412C-A|YLR413W
+STE12 pd SST2|RIF2
+STE12 pd RIF2|YLR454W
+STE12 pd PRM6|PRP39
+STE12 pd tS(AGA)M|YML005W
+STE12 pd snR77|snR76
+STE12 pd AEP1|KAR5
+STE12 pd DCR1|GAT2
+STE12 pd MSS11|SMP2
+STE12 pd VTI1|CIK1
+STE12 pd FSH2|UBP8
+STE12 pd PEP5|FUS2
+STE12 pd RNA1|TAF9
+STE12 pd tR(UCU)M1|RNT1
+STE12 pd YMR244C-A|FAA4
+STE12 pd SCW10|FKS3
+STE12 pd TRF5|CLA4
+STE12 pd RFC3|PCL1
+STE12 pd tN(GUU)N1|MRPL10
+STE12 pd ERG24|PRM1
+STE12 pd SEC2|BNI1
+STE12 pd YNL217W|RAP1
+STE12 pd SSB2|YNL208W
+STE12 pd YNL193W|CHS1
+STE12 pd RHO5|RPS3
+STE12 pd CBK1|YGP1
+STE12 pd YNL146W|MFA2
+STE12 pd INP52|LEU4
+STE12 pd TOP2|YNL087W
+STE12 pd VAC7|MSG5
+STE12 pd YIP3|tP(UGG)N1
+STE12 pd snR66|YNL024C-A
+STE12 pd YNL024C-A|YNL024C
+STE12 pd BUD17|CPR8
+STE12 pd MVD1|AGA1
+STE12 pd YNR054C|tL(UAA)N
+STE12 pd tL(UAA)N|HOL1
+STE12 pd AAD15|YOL164W-A
+STE12 pd YOL159C|ENB1
+STE12 pd YOL155W-A|YOL155C
+STE12 pd ZPS1|FRE7
+STE12 pd WSC3|NDJ1
+STE12 pd YOL083W|CVT19
+STE12 pd YOL031C|GAS5
+STE12 pd YOR086C|tN(GUU)O2
+STE12 pd YOR091W|ECM3
+STE12 pd YOR093C|ARF3
+STE12 pd RKI1|RPS7A
+STE12 pd YOR129C|ORT1
+STE12 pd ORT1|tD(GUC)O
+STE12 pd YOR246C|SRL1
+STE12 pd tA(UGC)O|SNF2
+STE12 pd SPS4|YOR315W
+STE12 pd YOR342C|YOR343W-A
+STE12 pd TYE7|tP(UGG)O3
+STE12 pd FRE3|YOR381W-A
+STE12 pd YOR381W-A|FIT2
+STE12 pd PRM3|YPL191C
+STE12 pd CUP9|YPL176C
+STE12 pd SVS1|YPL162C
+STE12 pd PRM4|KIP2
+STE12 pd DIG1|CAM1
+STE12 pd tF(GAA)P1|YPR003C
+STE12 pd HAL1|ICL2
+STE12 pd OPY2|YPR078C
+STE12 pd tK(UUU)P|CLB2
+STE12 pd tC(GCA)P2|THI22
+STE12 pd THI22|AXL1
+STE12 pd MSS18|CTF4
+STE12 pd YPR143W|tI(AAU)P1
+STE12 pd NCA2|TPO3
+STE12 pd YPR158W-B|YPR158C-D
+STE12 pd MMS1|RHO1
+STE12 pd tI(AAU)P2|YPR171W
+STP1 pd GLY1|IES6
+STP1 pd YGR054W|MUP1
+STP1 pd GIS3|IOC2
+STP1 pd MDH2|YOL125W
+STP1 pd DIM1|DIP5
+SUM1 pd PMT2|FUN26
+SUM1 pd KAP104|GAL7
+SUM1 pd FIG1|FAT1
+SUM1 pd YBR147W|YSW1
+SUM1 pd FZO1|DTR1
+SUM1 pd YCL049C|YCL048W
+SUM1 pd PPH22|YDL186W
+SUM1 pd YDL001W|NTH1
+SUM1 pd YDR042C|snR47
+SUM1 pd PHM6|YDR282C
+SUM1 pd SUM1|TFB1
+SUM1 pd ASP1|MRPL35
+SUM1 pd DIT2|DIT1
+SUM1 pd SPS2|SPS1
+SUM1 pd SPS1|AGE1
+SUM1 pd YDR542W|YRF1-1
+SUM1 pd DAL1|DAL4
+SUM1 pd tH(GUG)E1|CHO1
+SUM1 pd FET5|YFL040W
+SUM1 pd HXT10|AUA1
+SUM1 pd YFR022W|PES4
+SUM1 pd YFR032C|RPL29
+SUM1 pd SPO74|tK(CUU)G2
+SUM1 pd YGL138C|SEC27
+SUM1 pd YGR058W|SPR3
+SUM1 pd tT(UGU)G2|GND2
+SUM1 pd RAD2|TNA1
+SUM1 pd GND1|SSP1
+SUM1 pd PFS1|tV(CAC)H
+SUM1 pd snR37|YJL103C
+SUM1 pd GYP6|YJL043W
+SUM1 pd BNA1|YJR026W
+SUM1 pd MIR1|BNA2
+SUM1 pd DAL80|DID2
+SUM1 pd SRL2|EMP70
+SUM1 pd SCS7|YMR272W-B
+SUM1 pd HXT14|PFS2
+SUM1 pd TPT1|YOL101C
+SUM1 pd AUS1|tT(AGU)O2
+SUM1 pd YOR071C|tP(UGG)O2
+SUM1 pd SAS5|YOR214C
+SUM1 pd SEC63|YOR255W
+SUM1 pd YOR365C|SCP1
+SUM1 pd SPO19|TAF14
+SUM1 pd GPI2|GCR1
+SUT1 pd FLO9|GDH3
+SUT1 pd YBL029C-A|YBL029W
+SUT1 pd TAT1|YBR070C
+SUT1 pd PRR2|FYV14
+SUT1 pd YDL037C|YDL036C
+SUT1 pd YDR132C|YCF1
+SUT1 pd HXT6|HXT3
+SUT1 pd APT2|SSN2
+SUT1 pd RPI1|RHO3
+SUT1 pd HXT13|HPA3
+SUT1 pd ERG28|MEI4
+SUT1 pd FTR1|LSM5
+SUT1 pd AGP3|YFL054C
+SUT1 pd RAD54|SUT1
+SUT1 pd tL(CAA)G1|RCK1
+SUT1 pd SDS23|OLE1
+SUT1 pd YGR067C|YGR068C
+SUT1 pd SOL4|MGA1
+SUT1 pd YHR080C|YHR081W
+SUT1 pd KTI12|HAP4
+SUT1 pd CWP2|CWP1
+SUT1 pd YKL063C|MSN4
+SUT1 pd YKR075C|ECM4
+SUT1 pd YKR096W|PCK1
+SUT1 pd ACS2|YLR154C
+SUT1 pd tQ(UUG)L|RDN37-1
+SUT1 pd ACO1|STT4
+SUT1 pd SOK2|SPO20
+SUT1 pd YMR069W|MOT3
+SUT1 pd DCR1|GAT2
+SUT1 pd RHO5|RPS3
+SUT1 pd VAM3|RGS2
+SUT1 pd GAC1|YOR179C
+SUT1 pd CUP9|YPL176C
+SUT1 pd PRM4|KIP2
+SUT1 pd ICL2|SPO69
+SUT1 pd YPR148C|NCE102
+SWI4 pd YBR070C|YBR071W
+SWI4 pd CYC8|RAD16
+SWI4 pd CDC28|YBR161W
+SWI4 pd TOS1|YSY6
+SWI4 pd KAR4|SPB1
+SWI4 pd BUD31|HCM1
+SWI4 pd HO|GCS1
+SWI4 pd VCX1|PCL2
+SWI4 pd PSA1|tK(UUU)D
+SWI4 pd HTB1|HTA1
+SWI4 pd GIC2|SUM1
+SWI4 pd APT2|SSN2
+SWI4 pd TSA2|GUK1
+SWI4 pd RPL37B|PLM2
+SWI4 pd GIN4|GNP1
+SWI4 pd GNP1|SMT3
+SWI4 pd YDR524C-B|SNA2
+SWI4 pd RUF1|HLR1
+SWI4 pd AYR1|SIM1
+SWI4 pd YAP5|YIR018C-A
+SWI4 pd YIR018C-A|MUC1
+SWI4 pd MUC1|MRS1
+SWI4 pd YEL041W|UTR2
+SWI4 pd YEL001C|MNN1
+SWI4 pd YER010C|TIR1
+SWI4 pd ARG5,6|RNR1
+SWI4 pd SWI4|LSM4
+SWI4 pd FZF1|HXK2
+SWI4 pd TOS3|MPT5
+SWI4 pd OCH1|PNC1
+SWI4 pd SNU71|MSB2
+SWI4 pd KSS1|BUD9
+SWI4 pd CLB6|tC(GCA)G
+SWI4 pd RSR1|TOS10
+SWI4 pd CRH1|tW(CCA)G2
+SWI4 pd TOS2|snR7-L
+SWI4 pd SOL4|MGA1
+SWI4 pd SCW4|PXR1
+SWI4 pd GIC1|RPP1
+SWI4 pd YHR149C|YHR150W
+SWI4 pd SWE1|MNN5
+SWI4 pd YJL185C|YJL184W
+SWI4 pd CIS3|FAR1
+SWI4 pd BFA1|YJR054W
+SWI4 pd HMS2|BAT2
+SWI4 pd MCH2|FRE2
+SWI4 pd LAP4|HSL1
+SWI4 pd YKL098W|YKL096C-B
+SWI4 pd CWP2|CWP1
+SWI4 pd PRI2|PHD1
+SWI4 pd LAC1|CAP1
+SWI4 pd TOS5|PRY2
+SWI4 pd PDC1|STU2
+SWI4 pd SPT8|ERG3
+SWI4 pd RAX2|ARP6
+SWI4 pd CHS5|MID2
+SWI4 pd GTR1|NDI1
+SWI4 pd TSA1|YOX1
+SWI4 pd SOK2|SPO20
+SWI4 pd RPS16A|YMR144W
+SWI4 pd YMR178W|SPT21
+SWI4 pd CIK1|CLN1
+SWI4 pd YMR279C|CAT8
+SWI4 pd SCW10|FKS3
+SWI4 pd FKS3|GAS1
+SWI4 pd RPL18B|TOS6
+SWI4 pd TRF5|CLA4
+SWI4 pd RFC3|PCL1
+SWI4 pd PDR16|ELA1
+SWI4 pd RHO5|RPS3
+SWI4 pd YOL114C|SKM1
+SWI4 pd HTZ1|PLB3
+SWI4 pd YOR246C|SRL1
+SWI4 pd SPS4|YOR315W
+SWI4 pd TYE7|tP(UGG)O3
+SWI4 pd NDD1|NUD1
+SWI4 pd PLC1|YPL267W
+SWI4 pd SVS1|YPL162C
+SWI4 pd HHO1|NAN1
+SWI4 pd HAA1|SUT2
+SWI4 pd YPR013C|YPR015C
+SWI4 pd tK(UUU)P|CLB2
+SWI4 pd RUF6|tA(AGC)P
+SWI5 pd YBL108C-A|tL(UAA)B1
+SWI5 pd ICS2|CST13
+SWI5 pd HO|GCS1
+SWI5 pd GCS1|SHS1
+SWI5 pd HBT1|YDL222C
+SWI5 pd DLD1|YDL173W
+SWI5 pd VCX1|PCL2
+SWI5 pd YDL119C|CYK3
+SWI5 pd IWR1|YDL114W
+SWI5 pd GPR1|YDL033C
+SWI5 pd DBP10|PRP9
+SWI5 pd HXT3|SGI1
+SWI5 pd NCB2|UTP5
+SWI5 pd tD(GUC)I2|FAA3
+SWI5 pd YER078W-A|YER079W
+SWI5 pd YER188C-A|YER189W
+SWI5 pd FRS2|GAT1
+SWI5 pd YFR017C|YFR018C
+SWI5 pd RPL2A|YFR032C
+SWI5 pd SHE10|VID30
+SWI5 pd YGL140C|YGL139W
+SWI5 pd YGL108C|YGL107C
+SWI5 pd SCW11|CWH41
+SWI5 pd KSS1|BUD9
+SWI5 pd snR48|ERG25
+SWI5 pd YGR086C|PDC6
+SWI5 pd CRH1|tW(CCA)G2
+SWI5 pd PUP2|ENO1
+SWI5 pd FUR1|ARP1
+SWI5 pd YJL160C|HSP150
+SWI5 pd SCP160|PRY1
+SWI5 pd YJL077W-B|ICS3
+SWI5 pd MTR2|ASH1
+SWI5 pd PIR1|PIR3
+SWI5 pd YLR012C|GAT3
+SWI5 pd YLR162W|YLR162W-A
+SWI5 pd YLR162W-A|MAS1
+SWI5 pd YLR194C|NMT1
+SWI5 pd ENT2|HRD3
+SWI5 pd CTS1|YLR287C
+SWI5 pd YLR346C|KAP95
+SWI5 pd RPL31B|YLR406C-A
+SWI5 pd YLR406C-A|YLR407W
+SWI5 pd LSM3|MRPL4
+SWI5 pd COS3|YML131W
+SWI5 pd CTK3|BUL2
+SWI5 pd HOT1|DDR48
+SWI5 pd YMR251W|HOR7
+SWI5 pd TPS3|YMR262W
+SWI5 pd MDJ2|EGT2
+SWI5 pd LAP3|KEX2
+SWI5 pd YNL193W|CHS1
+SWI5 pd CBK1|YGP1
+SWI5 pd TPM1|NIS1
+SWI5 pd YPL158C|YPL157W
+SWI5 pd tC(GCA)P1|GRX5
+SWI6 pd YBL029C-A|YBL029W
+SWI6 pd YBR077C|ECM33
+SWI6 pd BUD31|HCM1
+SWI6 pd HO|GCS1
+SWI6 pd VCX1|PCL2
+SWI6 pd DUN1|ARR4
+SWI6 pd PSA1|tK(UUU)D
+SWI6 pd ERP3|CDC7
+SWI6 pd ATP16|MCD1
+SWI6 pd PDS1|YDR115W
+SWI6 pd YDR132C|YCF1
+SWI6 pd HTB1|HTA1
+SWI6 pd DIN7|AKR1
+SWI6 pd GIC2|SUM1
+SWI6 pd YHP1|PPN1
+SWI6 pd RPL37B|PLM2
+SWI6 pd GIN4|GNP1
+SWI6 pd YDR524C-B|SNA2
+SWI6 pd RUF1|HLR1
+SWI6 pd AYR1|SIM1
+SWI6 pd tS(UGA)I|YIL056W
+SWI6 pd IRR1|YIL024C
+SWI6 pd YEL041W|UTR2
+SWI6 pd YEL001C|MNN1
+SWI6 pd ARG5,6|RNR1
+SWI6 pd PUP3|RAD51
+SWI6 pd SWI4|LSM4
+SWI6 pd YFR017C|YFR018C
+SWI6 pd FZF1|HXK2
+SWI6 pd TOS3|MPT5
+SWI6 pd OCH1|PNC1
+SWI6 pd SNU71|MSB2
+SWI6 pd KSS1|BUD9
+SWI6 pd CLB6|tC(GCA)G
+SWI6 pd YGR109W-B|YGR110W
+SWI6 pd RNR4|tL(CAA)G3
+SWI6 pd CRH1|tW(CCA)G2
+SWI6 pd TOS2|snR7-L
+SWI6 pd SCW4|PXR1
+SWI6 pd GIC1|RPP1
+SWI6 pd YHR149C|YHR150W
+SWI6 pd EGD2|YHR194W
+SWI6 pd ELO1|CDC6
+SWI6 pd SWE1|MNN5
+SWI6 pd YJL185C|YJL184W
+SWI6 pd CIS3|FAR1
+SWI6 pd NCA3|ASF1
+SWI6 pd TOK1|HPR5
+SWI6 pd BFA1|YJR054W
+SWI6 pd MCH2|FRE2
+SWI6 pd RAD27|ABF1
+SWI6 pd YKL098W|YKL096C-B
+SWI6 pd CWP2|CWP1
+SWI6 pd TOS5|PRY2
+SWI6 pd YKR041W|UTH1
+SWI6 pd SPT8|ERG3
+SWI6 pd CDC45|YLR104W
+SWI6 pd ECM38|EXG1
+SWI6 pd CHS5|MID2
+SWI6 pd SPO77|FKS1
+SWI6 pd YLR437C|CAR2
+SWI6 pd LSM3|MRPL4
+SWI6 pd GTR1|NDI1
+SWI6 pd TSA1|YOX1
+SWI6 pd SOK2|SPO20
+SWI6 pd YMR069W|MOT3
+SWI6 pd PDS5|tV(AAC)M2
+SWI6 pd YMR122W-A|PKR1
+SWI6 pd DCR1|GAT2
+SWI6 pd RPS16A|YMR144W
+SWI6 pd SMP2|YMR166C
+SWI6 pd YMR178W|SPT21
+SWI6 pd CIK1|CLN1
+SWI6 pd SCJ1|GAS3
+SWI6 pd TPS3|YMR262W
+SWI6 pd YMR279C|CAT8
+SWI6 pd SCW10|FKS3
+SWI6 pd FKS3|GAS1
+SWI6 pd RPL18B|TOS6
+SWI6 pd RFC3|PCL1
+SWI6 pd YNL274C|TOF1
+SWI6 pd ZWF1|NAR1
+SWI6 pd PDR16|ELA1
+SWI6 pd LRO1|YNR009W
+SWI6 pd YOL114C|SKM1
+SWI6 pd CDC21|UFE1
+SWI6 pd YOR246C|SRL1
+SWI6 pd SPS4|YOR315W
+SWI6 pd TYE7|tP(UGG)O3
+SWI6 pd NDD1|NUD1
+SWI6 pd ATF1|YOR378W
+SWI6 pd SVS1|YPL162C
+SWI6 pd HHO1|NAN1
+SWI6 pd OPY2|YPR078C
+SWI6 pd tK(UUU)P|CLB2
+SWI6 pd CLB5|tC(GCA)P2
+SWI6 pd RUF6|tA(AGC)P
+SWI6 pd GDB1|APG13
+TEC1 pd YAR010C|tA(UGC)A
+TEC1 pd BUD14|ADE1
+TEC1 pd PEP1|FUS3
+TEC1 pd tG(GCC)B|RRN6
+TEC1 pd UTP20|HTA2
+TEC1 pd IPP1|YBR012W-A
+TEC1 pd ATP3|FIG1
+TEC1 pd UBC4|TEC1
+TEC1 pd YCL069W|YCL068C
+TEC1 pd RNQ1|FUS1
+TEC1 pd ABP1|FIG2
+TEC1 pd VCX1|PCL2
+TEC1 pd tQ(UUG)D2|YDR098C-B
+TEC1 pd YDR098C-A|BMH2
+TEC1 pd tI(AAU)D|YDR107C
+TEC1 pd MSS4|YDR210W
+TEC1 pd YDR210W-B|YDR210C-D
+TEC1 pd GIC2|SUM1
+TEC1 pd tF(GAA)D|YDR316W-A
+TEC1 pd YDR316W-B|YDR317W
+TEC1 pd tX(XXX)D|YDR341C
+TEC1 pd TOM1|YDR458C
+TEC1 pd MRPL28|STP1
+TEC1 pd SPS2|SPS1
+TEC1 pd AYR1|SIM1
+TEC1 pd RPI1|RHO3
+TEC1 pd SNP1|YIL057C
+TEC1 pd YEL041W|UTR2
+TEC1 pd tK(CUU)E1|tR(UCU)E
+TEC1 pd CAJ1|tQ(UUG)E1
+TEC1 pd SHO1|YER119C
+TEC1 pd tH(GUG)E2|tK(CUU)E2
+TEC1 pd YER188C-A|YER189W
+TEC1 pd ACT1|YPT1
+TEC1 pd STE2|BST1
+TEC1 pd YGL098W|tH(GUG)G2
+TEC1 pd PUS2|PYC1
+TEC1 pd AGA2|RPL24A
+TEC1 pd tF(GAA)G|SCW11
+TEC1 pd SNU71|MSB2
+TEC1 pd YGR038C-A|KSS1
+TEC1 pd TOS2|snR7-L
+TEC1 pd COS8|ARN2
+TEC1 pd tS(AGA)H|tQ(UUG)H
+TEC1 pd tA(AGC)H|RPS27B
+TEC1 pd YHR083W|STE12
+TEC1 pd RPL42B|CHS7
+TEC1 pd SWE1|MNN5
+TEC1 pd GFA1|LAP4
+TEC1 pd YKL098W|YKL096C-B
+TEC1 pd YKL096C-B|CWP2
+TEC1 pd CWP1|YJU2
+TEC1 pd tD(GUC)K|GAP1
+TEC1 pd GAP1|tA(AGC)K2
+TEC1 pd PXL1|SRL3
+TEC1 pd DPS1|BPT1
+TEC1 pd RAX2|ARP6
+TEC1 pd snR61|snR55
+TEC1 pd AEP1|KAR5
+TEC1 pd DCR1|GAT2
+TEC1 pd MSS11|SMP2
+TEC1 pd PEP5|FUS2
+TEC1 pd YRF1-6|COS1
+TEC1 pd RFC3|PCL1
+TEC1 pd WSC2|POP3
+TEC1 pd ERG24|PRM1
+TEC1 pd VAC7|MSG5
+TEC1 pd YOL159C|ENB1
+TEC1 pd WSC3|NDJ1
+TEC1 pd YOR129C|ORT1
+TEC1 pd MRPL23|RPB2
+TEC1 pd SPS4|YOR315W
+TEC1 pd tE(UUC)P|CBC2
+TEC1 pd SVS1|YPL162C
+TEC1 pd YPR158W|YPR158W-A
+THI2 pd ECM15|NTH2
+THI2 pd PHO3|PHO5
+THI2 pd THI3|MRK1
+THI2 pd YDR049W|TPI1
+THI2 pd YDR437W|YDR438W
+THI2 pd YDR438W|LRS4
+THI2 pd RML2|snR67
+THI2 pd FCY21|FCY22
+THI2 pd YGR271C-A|YGR272C
+THI2 pd ARN2|YHL046C
+THI2 pd SRP40|PTR2
+THI2 pd YLR004C|SSL1
+THI2 pd YAP1|GIS4
+THI2 pd THI20|tG(GCC)O1
+THI2 pd THI80|ELG1
+THI2 pd THI21|tW(CCA)P
+THI2 pd THI6|LEA1
+THI2 pd tC(GCA)P2|THI22
+TYE7 pd CYC3|CDC19
+TYE7 pd ERP2|tP(UGG)A
+TYE7 pd SHE1|PET9
+TYE7 pd PEP1|FUS3
+TYE7 pd CHS2|ATP3
+TYE7 pd HSL7|CKS1
+TYE7 pd tC(GCA)B|tE(UUC)B
+TYE7 pd ADP1|PGK1
+TYE7 pd YCR087C-A|ABP1
+TYE7 pd YCR095C|HMRA2
+TYE7 pd SLC1|LHP1
+TYE7 pd tK(CUU)E1|tR(UCU)E
+TYE7 pd CAJ1|tQ(UUG)E1
+TYE7 pd FCY21|FCY22
+TYE7 pd RPS24A|YER074W-A
+TYE7 pd BOI2|SPR6
+TYE7 pd ECM32|BMH1
+TYE7 pd PTR3|MET10
+TYE7 pd MNT2|ADH4
+TYE7 pd ERG26|YGR001C
+TYE7 pd SYF2|YGR130C
+TYE7 pd YGR223C|AZR1
+TYE7 pd SRB2|NCP1
+TYE7 pd GAR1|YNG2
+TYE7 pd TDH2|MET3
+TYE7 pd YJR088C|BIR1
+TYE7 pd ECM17|IML1
+TYE7 pd ATP7|PUT3
+TYE7 pd YPS3|YLR125W
+TYE7 pd CCC1|RSA3
+TYE7 pd MSN2|LYS7
+TYE7 pd ICY1|YMR196W
+TYE7 pd ATM1|PRP12
+TYE7 pd BNI4|CSL4
+TYE7 pd BRE5|POP2
+TYE7 pd MET22|YOL063C
+TYE7 pd YOR192C|YOR192C-C
+TYE7 pd YPL206C|HRR25
+UGA3 pd SED1|SHU2
+UGA3 pd ZWF1|NAR1
+UME1 pd YBR047W|RPS11B
+UME1 pd YCL069W|YCL068C
+UME1 pd HMLALPHA1|CHA1
+UME1 pd HTL1|HSP30
+UME1 pd YCR095C|HMRA2
+UME1 pd HMRA2|HMRA1
+UME1 pd YDR084C|AFR1
+UME1 pd YEL072W|DLD3
+UME1 pd tK(CUU)E1|tR(UCU)E
+UME1 pd MEI4|ACA1
+UME1 pd YER188C-A|YER189W
+UME1 pd ERG26|YGR001C
+UME1 pd YGR038C-A|KSS1
+UME1 pd tG(GCC)G2|CRM1
+UME1 pd snR37|YJL103C
+UME1 pd tH(GUG)K|YNK1
+UME1 pd YMR192W|MRPL24
+UME1 pd YMR258C|YMR259C
+UME1 pd NDJ1|YOL103W-A
+UME1 pd PHO80|RRP6
+UME1 pd ASE1|tK(UUU)O
+UME1 pd SNF2|YOR291W
+UME1 pd THI22|AXL1
+UME1 pd YPR125W|YPR127W
+UME6 pd ACS1|YAL053W
+UME6 pd YBL064C|KIP1
+UME6 pd FUS3|ACH1
+UME6 pd CYC8|RAD16
+UME6 pd YPC1|YBR184W
+UME6 pd YBR196C-B|YBR197C
+UME6 pd SSH1|YBR284W
+UME6 pd YCL057C-A|PRD1
+UME6 pd AGP1|KCC4
+UME6 pd YCR060W|YCR061W
+UME6 pd GDH2|PRR2
+UME6 pd tG(GCC)D1|UGA4
+UME6 pd SNF3|YDL193W
+UME6 pd YDR034W-B|ARO3
+UME6 pd CDC34|PST1
+UME6 pd RLI1|UBC13
+UME6 pd CTA1|RMS1
+UME6 pd DPP1|ZIP1
+UME6 pd GNP1|SMT3
+UME6 pd SRI1|RIP1
+UME6 pd MEI4|ACA1
+UME6 pd SWI4|LSM4
+UME6 pd YER130C|RPS26B
+UME6 pd PDA1|DMC1
+UME6 pd FRS2|GAT1
+UME6 pd GSY1|YFR016C
+UME6 pd tG(GCC)F2|YFR017C
+UME6 pd HFM1|YGL250W
+UME6 pd STR3|MND1
+UME6 pd YGR067C|YGR068C
+UME6 pd MES1|YGR266W
+UME6 pd YGR268C|YTA7
+UME6 pd PXR1|YOR1
+UME6 pd GOS1|ECM29
+UME6 pd SAE3|YHR080C
+UME6 pd EPT1|NDT80
+UME6 pd SPL2|ARO9
+UME6 pd YHR138C|SPS100
+UME6 pd SPO16|RTT107
+UME6 pd INO1|SNA3
+UME6 pd YJL103C|MEF2
+UME6 pd DPB11|SIP4
+UME6 pd TDH1|YJL051W
+UME6 pd tD(GUC)J2|YJL045W
+UME6 pd RPL43B|SFC1
+UME6 pd SMY1|DHR2
+UME6 pd PTM1|snR69
+UME6 pd FOX2|tL(CAA)K
+UME6 pd RNP1|RPL8B
+UME6 pd UBI4|ENT4
+UME6 pd GPI13|YLL029W
+UME6 pd KNS1|COX19
+UME6 pd YLR012C|GAT3
+UME6 pd YLR114C|CFT2
+UME6 pd HSP60|LCB5
+UME6 pd YLR262C-A|RED1
+UME6 pd ATP14|YLR297W
+UME6 pd CDC3|TAD3
+UME6 pd RRN11|CAT2
+UME6 pd SUB1|YMR040W
+UME6 pd PDS5|tV(AAC)M2
+UME6 pd SRT1|YMR102C
+UME6 pd YMR107W|ILV2
+UME6 pd YMR185W|HSC82
+UME6 pd CAT8|GPI12
+UME6 pd HAS1|YMR291W
+UME6 pd CHS1|YNL191W
+UME6 pd GAS4|YOL131W
+UME6 pd YOL124C|HRP1
+UME6 pd NDJ1|YOL103W-A
+UME6 pd YOL101C|PKH2
+UME6 pd YOL093W|YOL092W
+UME6 pd DDR2|SPE2
+UME6 pd CRC1|RAS1
+UME6 pd SNF2|YOR291W
+UME6 pd TEA1|YOR338W
+UME6 pd MSC6|GDS1
+UME6 pd YPL201C|CSM4
+UME6 pd BEM4|CDC60
+UME6 pd YPL017C|SWI1
+UME6 pd ICL2|SPO69
+UME6 pd APL4|CSR2
+UME6 pd TIF3|MMS1
+XBP1 pd HMLALPHA1|CHA1
+XBP1 pd RPI1|RHO3
+XBP1 pd MUC1|MRS1
+XBP1 pd SOL4|MGA1
+XBP1 pd HXT8|YJL213W
+XBP1 pd IME1|RPL43B
+XBP1 pd PRI2|PHD1
+XBP1 pd SCW10|FKS3
+XBP1 pd TOP2|YNL087W
+YAP1 pd RIB1|HEK2
+YAP1 pd tK(CUU)C|MAK32
+YAP1 pd YCR095C|HMRA2
+YAP1 pd YCR102C|PAU3
+YAP1 pd YDL183C|LYS20
+YAP1 pd ENA1|RSM10
+YAP1 pd YDR084C|AFR1
+YAP1 pd YDR132C|YCF1
+YAP1 pd YAP6|SWM1
+YAP1 pd YDR533C|FIT1
+YAP1 pd GLY1|IES6
+YAP1 pd tK(CUU)E1|tR(UCU)E
+YAP1 pd AAD6|AGP3
+YAP1 pd MRM2|RPL1B
+YAP1 pd TRX2|YGR210C
+YAP1 pd STB5|OYE2
+YAP1 pd GSH1|LSB6
+YAP1 pd SOD1|ADO1
+YAP1 pd CPA2|YJR110W
+YAP1 pd CYT2|YKL086W
+YAP1 pd tH(GUG)K|YNK1
+YAP1 pd MRS4|YSR3
+YAP1 pd GTT2|YLL058W
+YAP1 pd BUD20|RPL10
+YAP1 pd YLR460C|PAU4
+YAP1 pd COS3|YML131W
+YAP1 pd ERO1|COX14
+YAP1 pd YML117W|ATR1
+YAP1 pd USA1|TSA1
+YAP1 pd LYS7|SUB1
+YAP1 pd HOT1|DDR48
+YAP1 pd ECM5|MMT1
+YAP1 pd YMR192W|MRPL24
+YAP1 pd FAA4|YMR247C
+YAP1 pd YNL134C|FYV6
+YAP1 pd TOP2|YNL087W
+YAP1 pd MCH4|RRI2
+YAP1 pd AFT2|YPL201C
+YAP3 pd MUM2|UBP14
+YAP3 pd MGM101|RPS4A
+YAP3 pd YLL055W|YLL054C
+YAP3 pd YMR192W|MRPL24
+YAP5 pd MUM2|UBP14
+YAP5 pd PAU3|YCR105W
+YAP5 pd RPL16A|CSM2
+YAP5 pd YLR162W-A|MAS1
+YAP5 pd TAF13|VPS9
+YAP5 pd YNR029C|ECM39
+YAP5 pd tC(GCA)P1|GRX5
+YAP5 pd ARR3|YPR202W
+YAP6 pd OSH1|FLO1
+YAP6 pd tK(CUU)C|MAK32
+YAP6 pd HSP30|YCR023C
+YAP6 pd YCR102C|PAU3
+YAP6 pd PAU3|YCR105W
+YAP6 pd YCR105W|RDS1
+YAP6 pd ENA1|RSM10
+YAP6 pd YDR042C|snR47
+YAP6 pd YIL172C|YIL169C
+YAP6 pd YIR018C-A|MUC1
+YAP6 pd MUC1|MRS1
+YAP6 pd GTT1|YPS6
+YAP6 pd tK(CUU)E1|tR(UCU)E
+YAP6 pd GCN4|TOS9
+YAP6 pd AGP3|YFL054C
+YAP6 pd PHO81|YHB1
+YAP6 pd STB5|OYE2
+YAP6 pd HXT9|YJL218W
+YAP6 pd IME1|RPL43B
+YAP6 pd RPL43B|SFC1
+YAP6 pd KTI12|HAP4
+YAP6 pd SIR1|FLO10
+YAP6 pd AQY2|FRE6
+YAP6 pd ATP14|YLR297W
+YAP6 pd YLR460C|PAU4
+YAP6 pd YML117W|ATR1
+YAP6 pd VAN1|TAF8
+YAP6 pd ECM5|MMT1
+YAP6 pd YMR192W|MRPL24
+YAP6 pd YMR258C|YMR259C
+YAP6 pd FET4|YMR321C
+YAP6 pd YNL134C|FYV6
+YAP6 pd RPL9B|SUN4
+YAP6 pd YOL159C|ENB1
+YAP6 pd YOL155W-A|YOL155C
+YAP6 pd STI1|CIN5
+YAP6 pd CIN5|DFG16
+YAP6 pd STD1|RAT1
+YAP6 pd TYE7|tP(UGG)O3
+YAP6 pd ARR3|YPR202W
+YAP7 pd DEP1|CYS3
+YAP7 pd YBL028C|RPL19B
+YAP7 pd FLR1|HHF1
+YAP7 pd ZTA1|YBR047W
+YAP7 pd BAP2|TAT1
+YAP7 pd SWD3|ECM31
+YAP7 pd FZO1|DTR1
+YAP7 pd TRS20|YBR255W
+YAP7 pd FRM2|AGP1
+YAP7 pd tK(CUU)C|MAK32
+YAP7 pd HTL1|HSP30
+YAP7 pd YCR102C|PAU3
+YAP7 pd AAD4|YDL241W
+YAP7 pd ADY3|YDL238C
+YAP7 pd HEM3|YDL204W
+YAP7 pd HNT1|YDL124W
+YAP7 pd YDL121C|YFH1
+YAP7 pd RPN4|OSH2
+YAP7 pd RAD57|MAF1
+YAP7 pd GAL3|SNQ2
+YAP7 pd ENA1|RSM10
+YAP7 pd YDR042C|snR47
+YAP7 pd YDR132C|YCF1
+YAP7 pd YDR223W|HTB1
+YAP7 pd tE(CUC)D|YDR279W
+YAP7 pd MRPS28|YDR338C
+YAP7 pd YDR341C|HXT7
+YAP7 pd YDR533C|FIT1
+YAP7 pd DJP1|IST3
+YAP7 pd DAL7|DAL3
+YAP7 pd RML2|snR67
+YAP7 pd tK(CUU)E1|tR(UCU)E
+YAP7 pd PTC2|TRP2
+YAP7 pd YER140W|COX15
+YAP7 pd SCC4|SPT15
+YAP7 pd YER184C|YER185W
+YAP7 pd AAD6|AGP3
+YAP7 pd QCR6|PHO4
+YAP7 pd RTG2|HFM1
+YAP7 pd SNF4|YGL114W
+YAP7 pd SEC9|NMA2
+YAP7 pd UGA1|VMA7
+YAP7 pd YGR038C-A|KSS1
+YAP7 pd TRX2|YGR210C
+YAP7 pd YGR223C|AZR1
+YAP7 pd PHO81|YHB1
+YAP7 pd ERG11|YHR007C-A
+YAP7 pd SOD2|YHR009C
+YAP7 pd YHR029C|SLT2
+YAP7 pd ERP5|YHR111W
+YAP7 pd STB5|OYE2
+YAP7 pd CTF8|YHR192W
+YAP7 pd YHR199C|RPN10
+YAP7 pd GSH1|LSB6
+YAP7 pd SIP4|ARG3
+YAP7 pd PEP8|YJL052C-A
+YAP7 pd BET4|MAD2
+YAP7 pd SOD1|ADO1
+YAP7 pd CPA2|YJR110W
+YAP7 pd ATP2|CAF17
+YAP7 pd MGM101|RPS4A
+YAP7 pd COS9|SRY1
+YAP7 pd LAP4|HSL1
+YAP7 pd CYT2|YKL086W
+YAP7 pd tW(CCA)K|YKL071W
+YAP7 pd tH(GUG)K|YNK1
+YAP7 pd NFU1|PTM1
+YAP7 pd YKL033W|tV(AAC)K2
+YAP7 pd YKR043C|UIP5
+YAP7 pd MRS4|YSR3
+YAP7 pd YKR060W|KTR2
+YAP7 pd DRE2|SIS2
+YAP7 pd UBP11|BAS1
+YAP7 pd GTT2|YLL058W
+YAP7 pd AQY2|FRE6
+YAP7 pd YLR047C|RPS0B
+YAP7 pd BUD20|RPL10
+YAP7 pd YLR108C|AHP1
+YAP7 pd YLR193C|YLR194C
+YAP7 pd YLR254C|HAP1
+YAP7 pd ATP14|YLR297W
+YAP7 pd YHC1|ECM38
+YAP7 pd YLR460C|PAU4
+YAP7 pd COS3|YML131W
+YAP7 pd YML117W|ATR1
+YAP7 pd ALO1|TUB1
+YAP7 pd YPT7|CDC5
+YAP7 pd LYS7|SUB1
+YAP7 pd tL(CAA)M|ASI1
+YAP7 pd ECM5|MMT1
+YAP7 pd YMR192W|MRPL24
+YAP7 pd YMR258C|YMR259C
+YAP7 pd ADH6|FET4
+YAP7 pd YNL260C|ATX1
+YAP7 pd MPA43|RPA49
+YAP7 pd NAR1|LAP3
+YAP7 pd YNL213C|VID27
+YAP7 pd YNL176C|NOP13
+YAP7 pd YNL134C|FYV6
+YAP7 pd TOP2|YNL087W
+YAP7 pd FRE7|GRE2
+YAP7 pd MCH4|RRI2
+YAP7 pd GPD2|ARG1
+YAP7 pd YAP7|YOL027C
+YAP7 pd SLG1|TIR4
+YAP7 pd ECM3|YOR093C
+YAP7 pd YRR1|DDP1
+YAP7 pd YOR172W|YOR173W
+YAP7 pd ISU2|YOR227W
+YAP7 pd OYE3|YPL170W
+YAP7 pd SSU1|GLR1
+YAP7 pd MSF1|TAH18
+YAP7 pd YPR085C|SUA7
+YAP7 pd YPR117W|YPR118W
+YAP7 pd MET16|NUT2
+YAP7 pd ARR2|ARR3
+YDR026c pd PDX3|TLC1
+YDR026c pd FZO1|DTR1
+YDR026c pd ROT2|YBR230C
+YDR026c pd YDL085C-A|NDE2
+YDR026c pd SEC20|LCD1
+YDR026c pd DRE3|YIL002W-A
+YDR026c pd POL5|RPL12A
+YDR026c pd YFL006W|SEC4
+YDR026c pd PEX14|NUT1
+YDR026c pd YGR093W|VAS1
+YDR026c pd NBP1|CDC91
+YDR026c pd tF(GAA)N|KRE33
+YDR026c pd PRP2|URK1
+YHP1 pd KIN3|CDC15
+YHP1 pd tC(GCA)B|tE(UUC)B
+YHP1 pd REG1|RAD28
+YHP1 pd RVB1|HST4
+YHP1 pd tE(CUC)D|YDR279W
+YHP1 pd COY1|STE3
+YHP1 pd YLR312C|MRPL15
+YHP1 pd REC102|CHS5
+YHP1 pd tV(AAC)O|MPC54
+YHP1 pd YPL159C|YPL158C
+YOX1 pd KIN3|CDC15
+YOX1 pd KAR4|SPB1
+YOX1 pd AAD3|YCR108C
+YOX1 pd ENA1|RSM10
+YOX1 pd MKC7|TAF12
+YOX1 pd RVB1|HST4
+YOX1 pd tE(CUC)D|YDR279W
+YOX1 pd tK(CUU)E1|tR(UCU)E
+YOX1 pd YFL002W-A|SPB4
+YOX1 pd YGL159W|tL(CAA)G1
+YOX1 pd tH(GUG)G2|SRM1
+YOX1 pd ERG26|YGR001C
+YOX1 pd tG(GCC)G2|CRM1
+YOX1 pd YHR151C|SPO12
+YOX1 pd YHR181W|YHR182W
+YOX1 pd tT(AGU)J|PHO90
+YOX1 pd snR37|YJL103C
+YOX1 pd tW(CCA)J|YJL010C
+YOX1 pd CCT8|tM(CAU)J2
+YOX1 pd tH(GUG)K|YNK1
+YOX1 pd YLR023C|UBR2
+YOX1 pd YLR047C|RPS0B
+YOX1 pd RPS0B|YLR049C
+YOX1 pd snR61|snR55
+YOX1 pd YPT7|CDC5
+YOX1 pd YMR118C|tL(CAA)M
+YOX1 pd YMR192W|MRPL24
+YOX1 pd PHO80|RRP6
+YOX1 pd ASE1|tK(UUU)O
+YOX1 pd tC(GCA)P1|GRX5
+YOX1 pd ECM23|ULP1
+ZAP1 pd ADH4|ZRT1
+ZAP1 pd ZAP1|YJL055W
+ZAP1 pd LST4|ZRT3
+ZAP1 pd ZRT2|ACE2
+ZAP1 pd YNL254C|YNL253W
+Unknown interactsWith Rfc5
+Vps38 pp Vps34
+VPS30 pp VPS38
+DBF2 interactsWith SPO12
+SSB1 interactsWith HBS1
+SSB1 interactsWith SSB2
+HBS1 interactsWith SSB2
+SEC24 pp SEC23
+SEC6 interactsWith SEC8
+CDC25 pp RAS2
+CDC7 interactsWith DBF4
+CDC25 pp RAS2
+MAD2 interactsWith KAR3
+RPB3 pp RPB2
+EFT2 interactsWith EFT1
+ACT1 pp ACT1
+BEM2 interactsWith MSB1
+SNF3 interactsWith HXT1
+CBF1 interactsWith MIF2
+BIK1 interactsWith TUB1
+BIK1 interactsWith TUB2
+CIN4 interactsWith CIN1
+ACT1 interactsWith SAC1
+HSC82 interactsWith HSP82
+CDC24 interactsWith RSR1
+CDC24 interactsWith CDC42
+CDC24 interactsWith MSB1
+CDC42 interactsWith MSB1
+LEU2 interactsWith AAT1
+CKS1 interactsWith CDC28
+CDC28 interactsWith CLN1
+CDC28 interactsWith LSC1
+CDC28 interactsWith CLN2
+GRF10 interactsWith PHO4
+PHO2 interactsWith PHO4
+ABP1 pp ACT1
+NUM1 interactsWith TUB2
+CDC28 interactsWith ELM1
+GRR1 interactsWith ELM1
+BEM1 pp STE5
+BEM1 pp STE20
+BEM1 pp ACT1
+FKS1 interactsWith CNA1
+FKS1 interactsWith CMP2
+GCD10 pp PRT1
+SLT2 interactsWith FKS1
+CNB1 interactsWith FKS1
+PTC1 interactsWith PTP1
+PTP1 interactsWith PTP2
+NSP1 pp NUP82
+GSC2 interactsWith FKS1
+CBF2 interactsWith MIF2
+SAC6 interactsWith BEM2
+BEM2 interactsWith MYO1
+BEM2 interactsWith TPM1
+BEM2 interactsWith MYO2
+BEM2 interactsWith ACT1
+BEM2 interactsWith TUB2
+RHK1 interactsWith WBP1
+WBP1 interactsWith STT3
+WBP1 interactsWith ALG5
+SYG1 pp STE4
+SEC16 pp SEC23
+SED4 interactsWith SAR1
+SED4 pp SEC16
+SFT1 interactsWith SED5
+NAP1 pp CLB2
+SNF11 pp SNF2
+SWI3 pp SNF2
+RAD57 interactsWith RAD51
+RAD55 interactsWith RAD51
+RAD55 pp RAD51
+RAD57 interactsWith RAD52
+RAD55 interactsWith RAD52
+SHO1 pp PBS2
+SSK22 pp SSK1
+SSK1 pp SSK2
+XRS2 pp MRE11
+MRE11 pp MRE11
+MRE11 interactsWith RAD50
+MRE11 pp RAD50
+TUB2 pp RBL2
+CCR4 interactsWith RAD52
+RGR1 pp SIN4
+STE20 interactsWith CLA4
+CLN1 interactsWith CLA4
+CLA4 interactsWith CLN2
+STE20 pp CDC42
+STE5 pp STE4
+NIC96 pp NUP49
+NIC96 pp NUP57
+NIC96 pp NSP1
+NUP49 pp NSP1
+TOM37 interactsWith TOM70
+TOM20 pp TOM22
+ABP1 pp RVS167
+RVS167 pp ACT1
+FIP1 pp RNA14
+RNA14 pp HRP1
+CKB1 interactsWith CKA1
+CKA1 interactsWith CKB2
+CKB1 interactsWith CKA2
+CKA1 interactsWith CKA2
+CKB2 interactsWith CKA2
+KEM1 interactsWith SKI3
+RFA1 pp RFA3
+HSC82 interactsWith YDJ1
+YDJ1 interactsWith HSP82
+MRE11 pp RAD50
+TFC1 interactsWith TFC4
+TFC4 interactsWith BRF1
+SPT15 pp BRF1
+TFC4 pp BRF1
+SIP1 pp SNF1
+SNF1 pp SIP2
+AST1 interactsWith PMA1
+PMT2 interactsWith PMT1
+NGG1 pp ADA2
+ADA2 pp GCN5
+REF2 pp FIR1
+SIR4 pp RAP1
+RPT6 pp GAL4
+KAR1 pp CDC31
+NMD5 pp NAM7
+NMD4 pp NAM7
+NAM7 pp DCP2
+NAM7 pp DBP2
+DCP2 pp DCP1
+ACT1 pp SRV2
+HSP60 pp HSP10
+CCT4 interactsWith TCP1
+CCT4 interactsWith CCT2
+CCT1 interactsWith CCT2
+TCP1 interactsWith CCT2
+CCT4 interactsWith CCT3
+CCT1 interactsWith CCT3
+TCP1 interactsWith CCT3
+CCT2 interactsWith CCT3
+CCT4 interactsWith ACT1
+CMD1 pp NUF1
+CMD1 pp DST1
+CMD1 pp CNA1
+CMD1 pp CMP2
+CMD1 pp CMK2
+CMD1 pp CMK1
+SEC65 pp SRP54
+RAD6 pp UBR1
+ARF2 interactsWith SEC27
+ARF1 interactsWith SEC27
+ARF2 interactsWith SEC21
+ARF1 interactsWith SEC21
+PKC1 interactsWith PPZ2
+PKC1 interactsWith KRE6
+CDC15 interactsWith DBF2
+SNC1 pp SEC9
+SEC9 pp SSO2
+SEC9 pp SNC2
+SEC9 pp SSO1
+PKC1 interactsWith SKN7
+SIR4 pp RAP1
+SIR3 pp RAP1
+SIT4 interactsWith BEM2
+CDC55 interactsWith GRR1
+CDC24 interactsWith BEM1
+CDC24 pp BEM1
+BEM1 interactsWith BEM2
+BUB1 pp BUB3
+BOS1 pp SEC22
+RNA15 interactsWith PAP1
+PCF11 interactsWith RNA14
+PAP1 interactsWith RNA14
+KIN28 pp RPO21
+KIN28 pp RPB2
+PRP6 interactsWith REG1
+PRP5 interactsWith REG1
+REG1 interactsWith PRP3
+REG1 interactsWith PRP8
+REG1 interactsWith RNA1
+REG1 interactsWith PRP2
+REG1 interactsWith PRP4
+CCR4 interactsWith SPT10
+GLC7 interactsWith IPL1
+NOP1 interactsWith NOP4
+NUP2 pp SRP1
+SRP1 pp NUP1
+ATS1 interactsWith TUB1
+PTC1 interactsWith SLN1
+MBR1 interactsWith ISF1
+SEC31 pp SEC13
+ABP1 interactsWith ACT1
+TPM1 interactsWith ANC1
+ACT1 pp PFY1
+DRS2 interactsWith CAM1
+CMD1 interactsWith NUF1
+CMD1 pp NUF1
+NUF1 pp SPC42
+CLN3 interactsWith BUD2
+CLN3 interactsWith CLN1
+CLN3 interactsWith CLN2
+CLN1 interactsWith CLN2
+PKC1 interactsWith STT4
+PET122 pp PET54
+PET54 pp PET494
+REG1 interactsWith GAL83
+SAC6 interactsWith MNN10
+SAC6 interactsWith DYN2
+MNN10 interactsWith CAP2
+DYN2 interactsWith CAP2
+KAR2 interactsWith SEC63
+DBF2 interactsWith DBF20
+ABP1 interactsWith SAC6
+SAC6 interactsWith CAP1
+SLA1 interactsWith ABP1
+ABP1 interactsWith SLA2
+TIF4632 interactsWith TIF4631
+TIF4631 pp CDC33
+TIF4631 pp CAF20
+CDC33 pp CAF20
+PRE1 interactsWith PRE4
+MTH1 pp SNF3
+MTH1 pp RTG2
+CKB1 pp CKA1
+CKB1 pp TOP2
+CKA1 pp TOP2
+CKB1 pp CKB2
+CKA1 pp CKB2
+TOP2 pp CKB2
+CKB1 pp CKA2
+CKA1 pp CKA2
+TOP2 pp CKA2
+CKB2 pp CKA2
+PTC1 interactsWith PTP2
+CDC55 interactsWith ELM1
+CLN3 pp FAR1
+SWI4 pp CLB2
+PRP5 interactsWith PRP11
+PRP9 interactsWith PRP11
+PRP5 interactsWith PRP9
+PRP5 interactsWith PRP21
+PRP9 interactsWith PRP21
+PRP11 interactsWith PRP21
+PRP21 interactsWith PRP4
+SNF3 interactsWith HXT3
+SNF3 interactsWith HXT4
+SNF3 interactsWith HXT2
+ACT1 pp COF1
+ALPHA2 pp MCM1
+PRI1 interactsWith PRI2
+YPK1 interactsWith YPK2
+TPS1 interactsWith HXK2
+RVS161 interactsWith FEN1
+RVS161 interactsWith SUR2
+RVS161 interactsWith SUR4
+RVS161 interactsWith SUR1
+RAD6 pp UBR1
+RAP1 pp GCR1
+RPN4 interactsWith SEC63
+RPC19 pp RPC40
+NUP170 interactsWith NUP157
+NIC96 interactsWith POM152
+NUP188 interactsWith POM152
+MET30 pp MET4
+BEM1 interactsWith AKR1
+AKR1 pp STE4
+BMH1 interactsWith CHC1
+DPB11 interactsWith POL2
+PYC2 interactsWith ICL1
+ICL1 interactsWith PYC1
+PYC2 interactsWith MLS1
+PYC1 interactsWith MLS1
+ABP1 pp SRV2
+SLT2 interactsWith BRO1
+BCK1 interactsWith BRO1
+CWH41 interactsWith KRE6
+HSP42 pp HSP42
+PMT1 interactsWith PMT4
+PMT1 interactsWith PMT3
+PMT4 interactsWith PMT3
+SEC17 interactsWith BET3
+SEC18 interactsWith BET3
+SEC4 interactsWith BET3
+YPT1 interactsWith BET3
+BET1 interactsWith BET3
+BET3 interactsWith SEC22
+BET3 interactsWith SEC21
+BET3 interactsWith SEC2
+SSD1 interactsWith TOR1
+SLT2 pp MKK1
+SLT2 pp MKK2
+PTC1 interactsWith SLT2
+SUB1 interactsWith SUA7
+SUB1 pp SUA7
+TFC5 interactsWith TFC3
+TFC5 pp TFC4
+ADA2 pp SPT15
+SNF1 pp SIP4
+NUP170 interactsWith NUP82
+NUP157 interactsWith NUP82
+NUP170 interactsWith NUP2
+NUP170 interactsWith NUP1
+NUP170 pp NUP1
+RNA1 interactsWith NUP1
+UME6 pp IME1
+TOM20 pp TOM40
+TOM40 pp TOM22
+TOM7 pp TOM22
+TOM20 pp TOM70
+TOM40 pp TOM70
+TOM7 pp TOM70
+TOM20 pp TOM7
+TOM40 pp TOM7
+TOM40 pp TOM6
+TOM7 interactsWith TOM6
+ROM1 interactsWith ROM2
+ROM2 pp RHO1
+EFB1 interactsWith TEF2
+FEN1 interactsWith SUR4
+FEN1 interactsWith ERG2
+CLN3 interactsWith SIT4
+SIT4 interactsWith SAP4
+CLN3 interactsWith SAP185
+SIT4 interactsWith SAP185
+SIT4 pp SAP185
+BEM2 interactsWith SAP185
+SAP155 interactsWith SAP185
+CLN3 interactsWith SAP190
+SIT4 interactsWith SAP190
+SIT4 pp SAP190
+BEM2 interactsWith SAP190
+SAP155 interactsWith SAP190
+SAP185 interactsWith SAP190
+SIT4 interactsWith SIS2
+SAP155 interactsWith SIS2
+SAP185 interactsWith SIS2
+SAP190 interactsWith SIS2
+CLN3 interactsWith SAP155
+SIT4 interactsWith SAP155
+SIT4 pp SAP155
+BEM2 interactsWith SAP155
+REG1 interactsWith CYR1
+SAP1 pp SPT2
+SPT2 pp CDC23
+DOA4 interactsWith UBI4
+TAF90 pp TAF25
+TSM1 pp TAF25
+TAF25 pp TAF25
+TAF25 pp SPT15
+TAF25 pp TAF60
+TAF25 pp TAF145
+TAF25 pp ANC1
+HDA3 pp HDA1
+CBF2 pp MCK1
+CBF5 pp MCK1
+PRI1 interactsWith MEC3
+PXA2 pp PXA1
+TUB4 interactsWith SPC98
+TUB4 pp SPC98
+AFG3 pp YTA12
+GCR3 pp CBC2
+NUP188 pp POM152
+RAD23 interactsWith DSK2
+RFC5 interactsWith POL30
+SCO2 interactsWith COX17
+SCO1 interactsWith COX17
+TUB4 interactsWith BUB2
+BUB2 interactsWith BUB2
+SMC1 interactsWith TRF4
+TRF5 interactsWith TRF4
+CDC24 interactsWith BEM4
+RHO1 pp BEM4
+CLN2 pp CDC28
+CLB2 pp CDC28
+SIT4 pp TAP42
+PPH21 pp TAP42
+PPH22 pp TAP42
+BET4 pp BET2
+CLN3 interactsWith CDC53
+CLN3 pp CDC53
+CDC53 pp CLN1
+CKS1 pp CLN2
+CDC53 interactsWith CLN2
+CDC53 pp CLN2
+CDC34 interactsWith CLN2
+STE50 pp STE11
+GPA1 pp STE11
+SIR4 pp SIR3
+MSH3 pp MLH1
+MSH3 pp MSH2
+MLH1 pp MSH2
+PMS1 pp MSH2
+MSH3 pp PMS1
+MLH1 pp PMS1
+PMS1 pp PMS1
+YPD1 pp SLN1
+YPD1 interactsWith PBS2
+YPD1 interactsWith SSK1
+YPD1 pp SSK1
+YPD1 interactsWith HOG1
+YPD1 interactsWith SSK2
+YPD1 interactsWith PTP2
+KNH1 interactsWith KRE9
+GCS1 interactsWith YCK1
+GCS1 interactsWith YCK2
+YCK1 interactsWith YCK2
+GCS1 interactsWith YCK3
+NAM7 pp NAM7
+HPR1 interactsWith STO1
+GLE1 pp GLE1
+GLE1 pp NUP42
+GLE1 pp RIP1
+RIP1 pp GLE2
+KAP104 pp NUP57
+SRP1 pp CBC2
+SRP1 pp MUD13
+SEC26 pp RET2
+PEX5 pp PEX13
+CMD1 pp NUF1
+VPS13 interactsWith KEX2
+GPA1 pp STE4
+RRN6 pp RRN11
+RRN7 pp RRN11
+KAR2 interactsWith LHS1
+CDC48 pp DOA1
+SEO1 interactsWith MUP1
+ARC1 interactsWith MES1
+ARC1 pp MES1
+ARC1 interactsWith LOS1
+ARC1 interactsWith YGL245w
+ARC1 pp YGL245w
+SMC1 pp TRF4
+SMC2 pp TRF4
+TOP1 interactsWith TRF4
+GSP1 pp DIS3
+GLE1 interactsWith NUP159
+EMP24 pp ERV25
+YHM1 interactsWith ABF2
+TPS2 interactsWith PMU1
+RAD51 pp RAD52
+CDC34 interactsWith UBI4
+CDC34 pp UBI4
+CDC28 pp CDC6
+SEC16 pp SEC23
+HAC1 pp HAC1
+CPR7 pp RPD3
+CPR6 pp RPD3
+CPR6 pp HSP82
+STE5 pp STE5
+CYC8 interactsWith SNF3
+RGT2 interactsWith SNF3
+SNF3 interactsWith RGT1
+SNF3 interactsWith SKS1
+GLE1 interactsWith GLE2
+NUP42 pp GLE2
+RIP1 pp GLE2
+GLE2 interactsWith NUP145
+GLE1 interactsWith NUP100
+GLE2 interactsWith NUP100
+GLE1 interactsWith NUP116
+GLE2 pp NUP116
+NUP100 interactsWith NUP116
+GLE2 pp SRP1
+PTA1 interactsWith SPT3
+SPT3 interactsWith TOA2
+SPT3 interactsWith TOA1
+SPT3 interactsWith MOT1
+TOA1 interactsWith MOT1
+STI1 pp HSP82
+ADA2 pp GCN5
+CLN3 interactsWith BUD2
+CLN3 interactsWith CTR9
+SSA1 interactsWith UBP3
+RAD6 pp UBR1
+UBC8 pp QRI8
+RPT6 interactsWith RPT4
+PKC1 interactsWith GAS1
+GAS1 interactsWith KRE6
+PAB1 pp TIF4632
+PAB1 pp TIF4631
+SWI5 interactsWith DBF2
+DBF2 interactsWith SIC1
+STE50 pp STE4
+PCF11 interactsWith RNA15
+PCF11 interactsWith RNA14
+RTG3 pp RTG1
+YBR270c pp NMD2
+ADA2 pp GCN5
+NGG1 pp ADA2
+CDC13 interactsWith STN1
+CDC13 pp STN1
+TIF2 interactsWith TIF1
+TIF2 interactsWith DED1
+TIF1 interactsWith DED1
+CDC33 interactsWith DED1
+PIG2 pp GSY2
+GSY2 pp PIG1
+RSP5 interactsWith PAN1
+RSP5 interactsWith VRP1
+PKC1 interactsWith HOC1
+ABP1 pp RVS167
+MPS1 interactsWith CDC37
+TPM1 interactsWith Dec-01
+MDM20 interactsWith MYO2
+RSC8 pp STH1
+RPA34 interactsWith TOP1
+YRB2 interactsWith RNA1
+SPC97 pp TUB4
+STT3 interactsWith ALG5
+TIF4631 interactsWith TIF1
+TIF1 interactsWith TIF3
+NUP145 pp KAP95
+GLE2 pp NUP116
+GLY1 pp GLY1
+SLU7 pp PRP18
+ADA2 pp GCN5
+PPH21 pp RTS1
+STH1 pp SFH1
+ROK1 interactsWith GAR1
+SSC1 pp MGE1
+SLY1 pp SED5
+YPT1 pp SED5
+SED5 pp SEC22
+SBP1 pp GAR1
+SNM1 pp POP1
+KAP123 pp GSP1
+BNR1 pp RHO4
+BNR1 pp PFY1
+SEC31 interactsWith SEC16
+SEC31 interactsWith SEC23
+TPS2 pp TPS2
+TPS2 pp TSL1
+TSL1 pp TSL1
+TPS2 pp TPS3
+TSL1 pp TPS3
+TPS3 pp TPS3
+KAR2 pp SEC63
+SEC4 pp SEC2
+VTI1 pp PEP12
+PCF11 pp PAB1
+PCF11 pp RNA15
+PAB1 pp RNA15
+PAB1 pp RNA14
+RNA15 pp RNA14
+RNA14 pp RNA14
+AFR1 pp CDC12
+CIN8 interactsWith KAR3
+CIN8 interactsWith CDC20
+CIN8 interactsWith MAD1
+CIN8 interactsWith PAC10
+CIN8 interactsWith BUB1
+CIN8 interactsWith ARP1
+CIN8 interactsWith MAD2
+CIN8 interactsWith MAD3
+CIN8 interactsWith BUB2
+CIN8 interactsWith JNM1
+CIN8 interactsWith BUB3
+CIN8 interactsWith PAC1
+CIN8 interactsWith IPL1
+CIN8 interactsWith NIP100
+MPS1 interactsWith CIN8
+NUM1 interactsWith CIN8
+PAC11 interactsWith CIN8
+PUP3 interactsWith PUP1
+SPT15 pp SPT15
+SEC1 pp MSO1
+MSH2 pp DHS1
+MSH2 pp EXO1
+CDC19 interactsWith MCK1
+CDC19 pp MCK1
+ARP2 pp ARP3
+ARC15 pp ARP3
+ARP3 pp ARC19
+ARP3 pp ARC18
+ARP3 pp ARC35
+GOS1 pp YKT6
+MSN5 pp GSP1
+KAP123 pp GSP1
+CSE1 pp GSP1
+GSP1 pp PSE1
+SEC20 pp SEC22
+TIP20 pp SEC22
+SEC20 pp UFE1
+TIP20 pp UFE1
+SEC22 pp UFE1
+SEC20 pp TIP20
+MIP6 pp MEX67
+NUP85 interactsWith MEX67
+CIN8 interactsWith PAC2
+PAC2 interactsWith TUB3
+PAC2 interactsWith TUB1
+CIN8 interactsWith CIN4
+TUB1 interactsWith CIN4
+CIN8 interactsWith CIN1
+TUB1 interactsWith CIN1
+TUB3 interactsWith CIN1
+CIN8 interactsWith CIN2
+TUB1 interactsWith CIN2
+TOM40 pp TOM5
+TOM7 interactsWith TOM5
+YPT31 pp DSS4
+SEC4 interactsWith DSS4
+SEC4 pp DSS4
+YPT1 pp DSS4
+GDI1 pp SEC4
+ARP2 interactsWith SRP1
+ARP2 pp SRP1
+ARP1 interactsWith SRP1
+ARP1 pp SRP1
+ARP2 interactsWith NUP1
+ARP1 interactsWith NUP1
+MLH1 pp PMS1
+GCN20 pp GCN1
+MGA2 interactsWith SPT23
+RPD3 pp SIN3
+FIR1 pp PAB1
+UBA2 pp UFD1
+UBA2 pp PAP1
+FIR1 pp PAP1
+UFD1 pp PAP1
+KAP123 interactsWith PSE1
+RDI1 pp CDC42
+RDI1 pp RHO1
+ARP2 interactsWith SLA2
+ARP2 interactsWith END3
+VPS33 pp VAM3
+BUD6 pp BUD6
+APM3 interactsWith YCK1
+APM3 interactsWith SLA2
+APM3 interactsWith YCK2
+APM3 interactsWith END3
+PAB1 interactsWith CDC33
+TIF4631 interactsWith CDC33
+CDC2 interactsWith HUS2
+MBR1 interactsWith SAC1
+SOK1 interactsWith MBR1
+RAD16 pp RAD7
+NMD2 pp NAM7
+UPF3 pp NMD2
+SQT1 pp RPL10
+TFA1 pp TFA2
+SIR4 pp HDF1
+SIR4 pp YKU70
+KIP3 interactsWith DYN1
+KIP3 interactsWith KAR3
+DYN1 interactsWith KAR3
+CIN8 interactsWith DYN1
+CIN8 interactsWith KIP2
+DYN1 interactsWith KAR3
+SIC1 pp CLB5
+VPS5 pp VPS17
+HOP1 interactsWith MEK1
+RED1 interactsWith MEK1
+CDC24 interactsWith VMA5
+RAD18 pp RAD6
+CDH1 interactsWith SIC1
+CDC28 interactsWith CDC7
+CDC28 interactsWith HSF1
+CDC28 interactsWith SLT2
+CDC28 interactsWith YDJ1
+PDI1 interactsWith EUG1
+PIM1 interactsWith SSS1
+SSS1 interactsWith SEC61
+SSS1 pp SEC61
+STE5 pp STE4
+PRI1 interactsWith DDC1
+DBF2 pp POP2
+TOM37 pp TOM70
+TOM40 pp TOM5
+PEX5 pp PEX14
+PEX14 pp PEX14
+PEX14 pp PEX13
+UBA2 pp AOS1
+SKP1 pp GRR1
+CDC53 interactsWith CDC6
+CDC34 interactsWith CDC6
+CDC4 interactsWith CDC6
+CDC4 pp CDC6
+MCM3 pp CDC46
+CDC45 pp CDC46
+SPP41 pp FPR1
+HOM3 pp FPR1
+DUN1 interactsWith RNR4
+RNR4 pp RNR2
+RNR4 interactsWith RAD53
+CSG2 interactsWith CCC2
+SEC31 pp SEC24
+SEC31 pp SEC16
+SEC31 pp SEC23
+SEC23 pp SEC23
+CDC53 interactsWith SIC1
+CDC34 interactsWith SIC1
+SKP1 interactsWith SIC1
+CDC4 interactsWith SIC1
+RNA15 interactsWith HRP1
+RNA15 pp HRP1
+RNA14 interactsWith HRP1
+RNA14 pp HRP1
+MCD1 interactsWith SMC1
+MCD1 pp SMC1
+SNF5 interactsWith GCN5
+GCN5 interactsWith SRB2
+SPT7 interactsWith SIN4
+GCN5 interactsWith SIN4
+SNF5 interactsWith SPT20
+SPT15 pp SPT20
+SRB5 interactsWith SPT20
+SRB2 interactsWith SPT20
+RGR1 interactsWith SPT20
+SIN4 interactsWith SPT20
+GAL11 interactsWith SPT20
+SPT7 interactsWith GAL11
+SPT7 interactsWith SNF2
+GCN5 interactsWith SNF2
+SRB2 interactsWith SNF2
+SIN4 interactsWith SNF2
+GAL11 interactsWith SNF2
+SPT20 interactsWith SNF2
+GCN5 interactsWith SWI1
+SRB2 interactsWith SWI1
+RGR1 interactsWith SWI1
+SIN4 interactsWith SWI1
+GAL11 interactsWith SWI1
+SPT20 interactsWith SWI1
+SWI5 pp DMC1
+DMC1 pp TID3
+DMC1 pp PDC1
+DMC1 pp PET309
+RAD51 pp APC2
+DMC1 pp APC2
+DMC1 pp PDC5
+DMC1 pp ACC1
+DMC1 pp RIS1
+UBC9 pp SMT3
+CEG1 pp CET1
+CCC2 pp ATX1
+TFP1 interactsWith CYS4
+CIS1 interactsWith CIK1
+NIC96 pp NUP49
+NIC96 pp NUP57
+NUP49 pp NSP1
+GLE1 interactsWith GLE1
+GLE1 interactsWith NUP42
+GLE1 interactsWith RIP1
+MDJ1 pp SSC1
+SLA2 pp SLA2
+PEP3 pp VPS33
+PEP3 pp PEP5
+VPS33 pp PEP5
+PEP3 pp VPS16
+VPS33 pp VPS16
+TIF35 pp TIF34
+TIF35 pp PRT1
+SUI1 pp PRT1
+MAP2 interactsWith MAP1
+CSG2 interactsWith SUR2
+CSG2 interactsWith SCS7
+CSG2 interactsWith SUR1
+SCS7 interactsWith SUR1
+KAP104 pp NUP42
+KAP104 pp NUP49
+KAP104 pp NUP1
+SPT15 interactsWith SUA7
+HAP3 pp HAP4
+HAP2 pp HAP4
+HAP4 pp HAP5
+NOP1 interactsWith SIK1
+NOP1 pp SIK1
+NOP1 interactsWith NOP5
+NOP1 pp NOP5
+NOP1 interactsWith NOP58
+NOP1 pp NOP58
+SIK1 pp NOP5
+SIK1 pp NOP58
+NOP1 interactsWith NOP4
+UME6 pp RIM11
+CYB2 pp MAS6
+CYB2 pp TIM23
+TUB2 interactsWith STU2
+SRO9 interactsWith TPM1
+SRO9 interactsWith ACT1
+CMD1 pp NUF1
+NUF1 pp NUF1
+NUF1 interactsWith SPC97
+NUF1 pp SPC97
+NUF1 interactsWith SPC98
+NUF1 pp SPC98
+NUF1 pp SPC42
+TUB4 pp SPC98
+GPA2 interactsWith RAS2
+RRP43 pp RRP42
+RRP43 pp SKI6
+RRP42 pp SKI6
+RRP43 pp RRP4
+RRP42 pp RRP4
+SKI6 pp RRP4
+RRP43 pp DIS3
+RRP42 pp DIS3
+SKI6 pp DIS3
+RRP4 pp DIS3
+SKP1 pp CTF13
+SUP35 pp HSP104
+STB3 pp SIN3
+STB5 pp SIN3
+STB4 pp SIN3
+STB2 pp SIN3
+STB1 pp SIN3
+SRM1 interactsWith YRB2
+SRM1 pp YRB2
+YRB2 pp GSP1
+SEC17 pp VTI1
+YKT6 pp VTI1
+BIK1 interactsWith BIM1
+NUM1 interactsWith BIM1
+BIM1 pp TUB3
+BIK1 pp TUB1
+BIM1 pp TUB1
+TUB2 pp TUB1
+TUB1 pp ADH1
+BIK1 interactsWith BUB3
+BIM1 interactsWith BUB3
+RPO21 interactsWith CEG1
+RPO21 pp CEG1
+MCM2 pp CDC7
+MCM2 interactsWith DBF4
+MCM2 pp DBF4
+DBF4 pp DBF4
+THR4 interactsWith SEC13
+LST7 interactsWith SEC13
+SER2 interactsWith SEC13
+HOM6 interactsWith SEC13
+LST4 interactsWith SEC13
+SEC13 interactsWith LST8
+SLT2 interactsWith TPM1
+BEM2 interactsWith TPM1
+SAC6 interactsWith ACT1
+NUP159 pp KAP95
+GSP1 pp KAP95
+NUP2 pp KAP95
+KAP95 pp SRP1
+NUP2 pp SRP1
+KAP95 pp NUP1
+NPL3 pp MTR10
+NUP159 pp MTR10
+GSP1 pp MTR10
+NUP1 pp MTR10
+LHP1 pp SXM1
+SXM1 pp NUP159
+SXM1 pp NSP1
+SXM1 pp RPL25
+SXM1 pp NUP1
+TIM22 interactsWith TIM54
+TIM22 pp TIM54
+TIM54 pp MMM1
+TIM54 pp TIM18
+TIM44 pp TIM23
+PEX19 pp PEX3
+MED8 pp MED2
+MED8 pp SRB4
+MED2 pp SRB4
+MED8 pp RPB3
+MED2 pp RPB3
+PGD1 pp RPB3
+MED8 pp MED7
+MED2 pp MED7
+SRB4 pp MED7
+PGD1 pp MED7
+RPB3 pp MED7
+SIN4 pp GAL11
+MED8 pp MED4
+MED2 pp MED4
+SRB4 pp MED4
+PGD1 pp MED4
+RPB3 pp MED4
+MED7 pp MED4
+MED8 pp PGD1
+MED2 pp PGD1
+SRB4 pp PGD1
+CDC2 interactsWith HUS2
+CDC2 pp HUS2
+CDC2 interactsWith HYS2
+ATP6 pp ATP4
+ATP17 pp ATP4
+PEX5 pp PEX17
+PEX14 pp PEX17
+NYV1 pp VAM3
+SNC1 pp TLG1
+SEC17 pp TLG1
+GOS1 pp SED5
+SFT1 pp SED5
+TLG1 pp VTI1
+YKT6 pp VTI1
+SED5 pp VTI1
+SEC17 pp TLG2
+VTI1 pp TLG2
+VTI1 pp VAM3
+EMP24 pp SEC24
+HIP1 pp SEC24
+BET1 pp SEC24
+SEC24 pp SEC22
+EMP24 pp SAR1
+HIP1 pp SAR1
+SEC22 pp SAR1
+EMP24 pp SEC23
+HIP1 pp SEC23
+BET1 pp SEC23
+SEC22 pp SEC23
+CDC24 pp STE4
+MRS5 interactsWith TIM22
+TIM12 interactsWith TIM22
+MRS5 pp TIM10
+TIM12 pp MRS11
+TIM22 pp MRS11
+TIM22 pp TIM10
+MRS11 pp AAC1
+TIM10 pp AAC1
+GSC2 interactsWith KAR2
+CDC23 interactsWith APC2
+SIC1 interactsWith APC2
+ANP1 pp HOC1
+ANP1 pp MNN9
+HOC1 pp MNN9
+VAN1 pp MNN9
+MRE11 interactsWith RAD50
+WBP1 pp STT3
+STT3 pp OST1
+STT3 pp SWP1
+OST4 interactsWith OST3
+CDC2 interactsWith RAD24
+RAD24 interactsWith POL1
+RAD24 interactsWith RFC1
+MOB1 interactsWith CDC5
+LTE1 interactsWith MOB1
+CDC15 interactsWith MOB1
+MPS1 pp MOB1
+DBF2 pp MOB1
+VPS41 interactsWith VPS21
+SAC6 interactsWith VPS21
+RVS167 interactsWith VPS21
+VAN1 interactsWith VPS21
+ARP1 interactsWith KAR9
+DYN1 interactsWith KAR9
+JNM1 interactsWith KAR9
+NIC96 pp NUP188
+SPT15 pp TAF145
+TAF145 interactsWith TOA2
+TAF145 interactsWith TOA1
+CMD1 pp MYO5
+NSP1 pp GSP1
+GIM4 pp PAC10
+GIM4 interactsWith CCT2
+GIM4 interactsWith CCT3
+GIM4 pp YKE2
+TUB2 interactsWith YKE2
+PAC10 pp YKE2
+CCT2 interactsWith YKE2
+CCT3 interactsWith YKE2
+GIM4 interactsWith TUB4
+GIM4 pp TUB4
+PAC10 interactsWith TUB4
+PAC10 pp TUB4
+YKE2 interactsWith TUB4
+YKE2 pp TUB4
+GIM4 pp GIM5
+PAC10 pp GIM5
+YKE2 pp GIM5
+TUB4 interactsWith GIM5
+TUB4 pp GIM5
+GIM5 pp GIM5
+YKE2 interactsWith TUB1
+GIM4 pp GIM3
+PAC10 pp GIM3
+YKE2 pp GIM3
+TUB4 interactsWith GIM3
+TUB4 pp GIM3
+GIM5 pp GIM3
+YKE2 interactsWith SPC98
+PAC10 interactsWith RBL2
+YKE2 interactsWith RBL2
+GIM3 interactsWith RBL2
+GLE2 pp NUP116
+RRP4 interactsWith MTR4
+APC11 pp APC4
+APC11 pp CDC23
+APC4 pp CDC23
+CDC26 pp CDC23
+DOC1 pp CDC23
+APC11 pp CDC16
+APC4 pp CDC16
+DOC1 pp CDC16
+CDC23 pp CDC16
+APC11 pp APC9
+APC4 pp APC9
+CDC26 pp APC9
+DOC1 pp APC9
+CDC23 pp APC9
+CDC16 pp APC9
+APC11 pp APC2
+APC4 pp APC2
+DOC1 pp APC2
+APC9 pp APC2
+APC11 pp APC1
+APC4 pp APC1
+DOC1 pp APC1
+CDC16 pp APC1
+APC9 pp APC1
+APC2 pp APC1
+APC11 pp APC5
+APC4 pp APC5
+CDC26 pp APC5
+DOC1 pp APC5
+CDC23 pp APC5
+CDC16 pp APC5
+APC9 pp APC5
+APC2 pp APC5
+APC1 pp APC5
+APC11 pp CDC26
+APC4 pp CDC26
+APC11 pp DOC1
+APC4 pp DOC1
+CDC26 pp DOC1
+SEC4 interactsWith SMY1
+MYO1 interactsWith SMY1
+SMY1 interactsWith SEC2
+CMD1 interactsWith MYO2
+SEC5 interactsWith MYO2
+SEC4 interactsWith MYO2
+SEC15 interactsWith MYO2
+SEC9 interactsWith MYO2
+MYO1 interactsWith MYO2
+SMY1 interactsWith MYO2
+SEC10 interactsWith MYO2
+TPM1 interactsWith MYO2
+SEC2 interactsWith MYO2
+MYO2 interactsWith SEC8
+BFR2 interactsWith SEC13
+BFR2 interactsWith SEC16
+BFR2 interactsWith SEC23
+BFR2 interactsWith YPT1
+PKC1 interactsWith TOR2
+SUB2 interactsWith BRR1
+NIC96 pp NUP188
+KEM1 interactsWith SKI8
+KEM1 interactsWith SKI2
+SKI8 interactsWith DCP1
+SKI2 interactsWith DCP1
+DCP1 interactsWith SKI3
+EGD2 interactsWith MFT1
+SUP45 pp SUP35
+SEF1 interactsWith RPM2
+FUI1 interactsWith FUR4
+TAF90 pp ADA2
+RAD23 pp PRE1
+RAD23 pp RAD4
+RAD23 pp RPT6
+RAD23 pp RPT1
+RAD23 pp PUP1
+VAC8 pp ACT1
+CDC34 interactsWith SKP1
+CDC34 interactsWith GRR1
+SKP1 pp GRR1
+TIM22 pp MRS11
+CDC53 interactsWith CDC34
+CDC53 interactsWith SKP1
+CDC53 pp SKP1
+CDC34 pp SKP1
+CDC53 pp MET30
+CDC53 pp GRR1
+SKP1 pp GRR1
+CDC53 interactsWith CDC4
+CDC53 pp CDC4
+CDC34 interactsWith CDC4
+SKP1 pp CDC4
+SIR4 pp UBP3
+CSM1 interactsWith TUB1
+SPO86 interactsWith TUB1
+CDC39 pp NOT3
+MOT2 pp NOT3
+CDC39 pp NOT5
+MOT2 interactsWith NOT5
+MOT2 pp NOT5
+NOT3 pp NOT5
+RPN4 interactsWith RPN10
+RPN4 interactsWith RPN12
+STE50 pp SPC24
+SSK22 pp SPC24
+PRP9 pp SPC24
+SPO71 pp SPC24
+SPC25 pp SPC24
+FIR1 pp SPC24
+YFR046c pp SPC24
+MDS3 pp SPC24
+TID3 pp SPC24
+BUD6 pp SPC24
+YLR419w pp SPC24
+RSE1 pp SPC24
+SPC24 pp MRE11
+SPC24 pp YOL034w
+SPC24 pp TLG2
+SPC24 pp NOC2
+SPC24 pp RPA135
+SPC24 pp ASN1
+CDC28 pp CLB3
+CDC28 pp CLB1
+CDC28 pp CLB6
+CTK2 pp CTK1
+CDC28 pp CLB4
+CTK1 pp CTK3
+CDC28 pp CLN1
+SSN8 pp SRB10
+PCL2 pp PHO85
+CLG1 pp PHO85
+PCL1 pp PHO85
+KIN28 pp CCL1
+CDC28 pp CLB2
+CDC28 pp CLB5
+MOB1 pp CAF17
+MOB1 pp POP2
+MOB1 pp DBF20
+CAF16 pp MOB1
+DBF2 interactsWith MOB1
+DBF2 pp MOB1
+SPC97 pp SPC98
+TUB4 pp SPC98
+NUP85 interactsWith MTR10
+GSP1 pp MTR10
+HRB1 pp MTR10
+CDC34 interactsWith UBC12
+CDC34 interactsWith ULA1
+CDC34 interactsWith UBA3
+CDC34 interactsWith RUB1
+ROT2 interactsWith SAC7
+ROT2 interactsWith BIG1
+SAC7 interactsWith ROT1
+BIG1 interactsWith ROT1
+TOR2 interactsWith ROT1
+ROT2 interactsWith TOR2
+RPB7 pp RPB4
+MAM33 pp CYB2
+CSG2 interactsWith SUR2
+CSG2 interactsWith SCS7
+CSG2 interactsWith SUR1
+SCS7 interactsWith SUR1
+INP51 interactsWith INP52
+INP51 interactsWith INP53
+INP52 interactsWith INP53
+COS16 interactsWith CDC1
+PER1 interactsWith CDC1
+ARF1 interactsWith CDC1
+CDC13 interactsWith HDF2
+HDF2 pp YKU70
+YKU80 pp HDF1
+BOS1 interactsWith SEC22
+USO1 interactsWith BET5
+ANP1 interactsWith BET5
+YPT1 interactsWith BET5
+BET1 interactsWith BET5
+BOS1 interactsWith BET5
+SEC22 interactsWith BET5
+BET5 interactsWith DSS4
+BET3 interactsWith BET5
+BET3 pp BET5
+TLG2 pp SNC2
+DBP7 interactsWith DBP6
+RTF1 interactsWith CBF1
+CBF2 interactsWith CBF1
+CBF1 interactsWith CEP3
+CBF1 interactsWith CSL4
+CBF1 interactsWith CSE4
+VPS24 pp SNF7
+USO1 interactsWith SEC35
+YPT1 interactsWith SEC35
+SPC72 pp SPC72
+SPC72 pp STU2
+STU2 pp STU2
+TRS20 pp TRS23
+TRS20 interactsWith BET3
+TRS20 pp BET3
+SLY1 interactsWith BET3
+TRS23 interactsWith BET3
+TRS23 pp BET3
+BET3 interactsWith SED5
+TRS20 pp BET5
+TRS23 pp BET5
+BET3 interactsWith BET5
+BET3 pp BET5
+TRS20 pp TRS33
+TRS23 pp TRS33
+BET3 interactsWith TRS33
+BET3 pp TRS33
+BET5 pp TRS33
+SIT4 interactsWith DBF2
+SIT4 interactsWith DBF20
+CDC14 pp CDC14
+BCK1 interactsWith SLG1
+SUP45 pp NAM7
+SUP35 pp NAM7
+POP7 pp RPP1
+SNM1 pp POP1
+BEM1 interactsWith ARP1
+BIM1 interactsWith DYN1
+ARP1 interactsWith STT4
+DYN1 interactsWith STT4
+BIM1 interactsWith JNM1
+STT4 interactsWith JNM1
+SBA1 pp HSP82
+SRM1 pp CRM1
+CRM1 interactsWith YRB2
+CRM1 pp YRB2
+CRM1 pp GSP1
+STE5 pp PMD1
+STE5 pp OKP1
+STE5 pp YGR179c
+YCK3 pp STE11
+SYGP-ORF48 pp STE11
+AUT7 interactsWith AUT2
+AUT7 pp AUT2
+TUB2 pp AUT2
+TUB1 pp AUT2
+PBN1 pp PRB1
+SAP30 pp RPD3
+MPT5 interactsWith MTO1
+PIB2 interactsWith MPT5
+SEC1 interactsWith SEC10
+SEC5 interactsWith SEC10
+SEC3 interactsWith SEC10
+SEC4 interactsWith SEC10
+SEC15 interactsWith SEC10
+SEC15 pp SEC10
+SEC9 interactsWith SEC10
+SEC6 interactsWith SEC10
+SEC10 interactsWith SEC8
+ARP1 pp JNM1
+ARP1 pp NIP100
+JNM1 pp NIP100
+SAC6 pp ACT1
+TIF35 pp TIF34
+RPG1 pp NIP1
+TIF34 pp NIP1
+GCD14 pp GCD10
+RPG1 pp PRT1
+TIF35 pp PRT1
+TIF34 pp PRT1
+VMA22 pp VPH2
+VMA22 pp VPH1
+VPH2 pp VPH1
+CDC13 interactsWith HDF1
+CDC13 interactsWith YKU70
+GAL3 pp GAL80
+GAL80 pp GAL4
+LIF1 pp DNL4
+MEC3 pp DDC1
+GPA1 pp STE4
+NUT1 interactsWith NUT2
+CDC2 interactsWith RFC2
+RFC2 interactsWith POL2
+RFC2 interactsWith RFC1
+TIF35 pp TIF34
+NIP1 pp PRT1
+SUI1 pp PRT1
+NIP1 pp TIF5
+PRT1 pp TIF5
+SRP101 pp SRP102
+GCS1 pp AKR1
+AFR1 interactsWith IQG1
+AFR1 pp IQG1
+AKR1 interactsWith IQG1
+AKR1 pp IQG1
+ACT1 pp IQG1
+CDC42 pp IQG1
+MAK31 interactsWith RSC8
+RSC6 pp RSC8
+MYO1 pp SRO7
+NUF1 interactsWith SPC97
+NUF1 pp SPC97
+NUF1 interactsWith SPC98
+NUF1 pp SPC98
+VPS29 interactsWith VPS35
+VPS29 pp VPS35
+VPS35 pp VPS17
+VPS35 pp VPS5
+MLC1 pp MYO2
+ACT1 pp TWF1
+TWF1 interactsWith COF1
+PAB1 pp PAB1
+PAB1 pp TIF4631
+PAB1 pp CDC33
+TIF4631 pp CDC33
+VAM7 interactsWith VAM3
+VAM7 pp VAM3
+SRB4 interactsWith MED6
+RAD24 pp RAD24
+RAD24 pp RFC2
+YPT1 interactsWith YPT6
+YPT31 pp YIP1
+YPT1 pp YIP1
+RAD27 interactsWith RAD17
+DST1 interactsWith RPB2
+DPB11 pp SLD2
+VRP1 pp LAS17
+CDC28 interactsWith STE20
+STE20 interactsWith CDC42
+CSE1 pp GSP1
+SAC6 interactsWith SWE1
+SWE1 interactsWith TPM1
+SWE1 interactsWith PFY1
+SWE1 interactsWith MYO2
+NMT1 interactsWith FAA4
+NGG1 pp TOM1
+ARF1 interactsWith CHC1
+SEC17 pp GOS1
+TAF90 pp NGG1
+TAF61 pp NGG1
+TAF25 pp NGG1
+TAF61 pp ADA2
+TAF25 pp ADA2
+NGG1 pp TAF60
+SPT7 pp TRA1
+TAF90 pp TRA1
+TAF61 pp TRA1
+TAF25 pp TRA1
+NGG1 pp TRA1
+SPT3 pp TRA1
+ADA2 pp TRA1
+TAF60 pp TRA1
+GCN5 pp TRA1
+TRA1 pp SPT8
+NGG1 pp TAF17
+TRA1 pp TAF17
+TRA1 pp SPT20
+TAF90 pp TAF25
+TAF90 pp ADA2
+TAF25 pp TAF60
+CDC20 pp MAD2
+HOP1 interactsWith RED1
+HOP1 interactsWith MEK1
+RED1 interactsWith MEK1
+VMA2 interactsWith TLG2
+PIB2 pp MSS1
+MTO1 pp MSS1
+CYR1 pp SRV2
+RNR1 pp SML1
+PKC1 interactsWith PSA1
+PSA1 interactsWith PDE2
+MAK21 interactsWith SKI6
+MAK21 interactsWith SKI2
+GZF3 pp GZF3
+GZF3 pp DAL80
+DAL80 pp DAL80
+GTT1 pp GTT2
+MRE11 pp MRE11
+SPT6 interactsWith STH1
+STH1 interactsWith HHT2
+STH1 interactsWith HHF2
+STE11 pp HSC82
+STE11 pp HSP82
+CSG2 interactsWith TSC10
+CSG2 interactsWith TSC13
+CSG2 interactsWith LCB2
+CSG2 interactsWith MSS4
+CSG2 interactsWith YER093c
+CSG2 interactsWith LCB1
+CSG2 interactsWith RPD3
+CSG2 interactsWith SIN3
+CSG2 interactsWith FAS2
+CSG2 interactsWith TOR2
+CSG2 interactsWith SUR2
+SFL1 pp TPK2
+MGA1 pp TPK2
+JAC1 interactsWith SOD1
+SOD1 interactsWith SSQ1
+SEP7 pp GIN4
+SHS1 pp GIN4
+GIN4 pp CDC12
+GIN4 pp CDC11
+SEP7 pp CDC12
+SHS1 pp CDC12
+SEP7 pp CDC11
+SHS1 pp CDC11
+CDC12 pp CDC11
+SEP7 pp CDC3
+SHS1 pp CDC3
+CDC12 pp CDC3
+CDC11 pp CDC3
+KIC1 pp HSC82
+NRK1 pp HSC82
+KIC1 interactsWith CDC31
+KIC1 pp CDC31
+NRK1 interactsWith CDC31
+NRK1 pp CDC31
+FAL1 interactsWith FAL1
+FAL1 interactsWith LCP5
+LCP5 interactsWith PAP1
+RSE1 interactsWith SAR1
+PRP2 interactsWith SAR1
+PAB1 interactsWith PBP1
+PAB1 pp PBP1
+PAB1 pp SIM1
+PAB1 pp KRE1
+MRS5 interactsWith TIM9
+TIM9 interactsWith MRS11
+TIM9 pp MRS11
+CDC36 pp ADA2
+TCM62 pp SDH1
+TCM62 pp SDH3
+TCM62 pp SDH2
+FUR4 interactsWith URA3
+SEM1 interactsWith SUV3
+MSU1 interactsWith SUV3
+PRS5 interactsWith PRS3
+PRS5 interactsWith PRPS1
+PRS3 interactsWith PRPS5
+PRPS5 interactsWith PRS1
+NHP2 pp GAR1
+NOP10 pp GAR1
+NHP2 pp NOP10
+ROK1 interactsWith FMI1
+ROK1 interactsWith RRP5
+PRP8 pp SNU114
+DST1 pp NMD5
+NUP159 pp NMD5
+NMD5 pp NUP2
+NMD5 pp NUP1
+CSE1 interactsWith SRP1
+CSE1 pp SRP1
+KAP123 pp YAP1
+CRM1 pp YAP1
+CRM1 interactsWith RNA1
+SPP381 pp PRP38
+YPT6 interactsWith IMH1
+IMH1 pp IMH1
+SPT7 pp TAF90
+SPT7 pp TAF61
+TAF90 pp TAF61
+SPT7 pp TAF25
+TAF61 pp TAF25
+TAF90 pp NGG1
+TAF61 pp NGG1
+TAF25 pp NGG1
+TAF90 pp SPT3
+TAF61 pp SPT3
+TAF25 pp SPT3
+TAF61 pp ADA2
+TAF25 pp ADA2
+SPT7 pp TAF60
+TAF90 pp TAF60
+TAF61 pp TAF60
+TAF25 pp TAF60
+NGG1 pp TAF60
+SPT3 pp TAF60
+ADA2 pp TAF60
+TAF90 pp GCN5
+TAF61 pp GCN5
+TAF25 pp GCN5
+TAF60 pp GCN5
+SPT7 pp TRA1
+TAF90 pp TRA1
+TAF61 pp TRA1
+TAF25 pp TRA1
+TAF60 pp TRA1
+GCN5 pp TRA1
+TAF90 pp SPT8
+TAF61 pp SPT8
+TAF25 pp SPT8
+TAF60 pp SPT8
+TRA1 pp SPT8
+SPT7 pp TAF17
+TAF90 pp TAF17
+TAF61 pp TAF17
+TAF25 pp TAF17
+NGG1 pp TAF17
+SPT3 pp TAF17
+ADA2 pp TAF17
+TAF60 pp TAF17
+GCN5 pp TAF17
+TRA1 pp TAF17
+SPT8 pp TAF17
+TAF90 pp SPT20
+TAF61 pp SPT20
+TAF25 pp SPT20
+TAF60 pp SPT20
+TRA1 pp SPT20
+TAF17 pp SPT20
+SPT7 pp HFI1
+TAF90 pp HFI1
+TAF61 pp HFI1
+TAF25 pp HFI1
+SPT3 pp HFI1
+TAF60 pp HFI1
+TRA1 pp HFI1
+SPT8 pp HFI1
+TAF17 pp HFI1
+TAF90 pp TAF25
+NGG1 pp TRA1
+SPT3 pp TRA1
+ADA2 pp TRA1
+TAF90 pp ADA2
+AHP1 pp AHP1
+ATP5 pp ATP4
+ATP6 pp ATP4
+ATP17 pp ATP4
+LUV1 interactsWith RBL2
+RFA1 interactsWith RAD1
+SEM1 interactsWith SEC15
+POL32 pp POL1
+TLG1 pp TLG2
+VPS45 pp TLG2
+VPS45 pp PEP12
+KEM1 interactsWith NMD3
+NMD3 interactsWith RPL10
+NMD3 pp NAM7
+REX2 interactsWith ILV5
+YNT20 interactsWith ILV5
+REX2 interactsWith PRP12
+YNT20 interactsWith PRP12
+REX2 interactsWith YME1
+YNT20 interactsWith YME1
+PRP12 interactsWith YME1
+SIN4 interactsWith PDR5
+INP52 interactsWith INP53
+Sua7p pp ADR1
+Pho4 pp SUA7
+CDC48 pp UFD2
+CTF13 interactsWith SKP1
+CTF13 interactsWith NDC10
+CTF19 interactsWith NDC10
+CTF13 interactsWith CEP3
+CTF13 interactsWith CTF19
+SSC1 pp MGE1
+MCM21 pp SKP1
+OKP1 pp CBF2
+CTF19 pp OKP1
+MCM21 pp OKP1
+MCM21 pp CBF1
+MCM21 pp MIF2
+OKP1 pp CEP3
+CBF2 pp CTF19
+CEP3 pp CTF19
+MCM21 pp CTF19
+CTF19 pp CSE4
+MCM21 pp MCM21
+SMD3 pp SNU66
+SMC1 pp TID3
+SMC2 pp TID3
+IMP3 pp MPP10
+MPP10 pp IMP4
+HOG1 pp HOT1
+TOM20 pp TOM40
+SLK19 interactsWith KAR3
+NIC96 pp NUP192
+LSM6 pp LSM4
+LSM6 pp LSM5
+LSM4 pp LSM5
+LSM6 pp LSM1
+LSM4 pp LSM1
+LSM5 pp LSM1
+LSM6 pp LSM3
+LSM4 pp LSM3
+LSM5 pp LSM3
+LSM1 pp LSM3
+LSM8 pp LSM3
+LSM6 pp LSM7
+LSM4 pp LSM7
+LSM5 pp LSM7
+LSM1 pp LSM7
+LSM3 pp LSM7
+ARP4 pp HTA1
+EXO84 pp SEC5
+EXO84 pp SEC10
+SNF1 pp HIR2
+SNU66 pp PRP4
+TIF4631 pp TIF2
+TIF4631 pp TIF1
+DCP2 pp DCP1
+SEC34 pp SEC35
+plc1 pp gpr1
+GPR1 pp GPA2
+GLE1 pp GFD1
+NUP42 pp GFD1
+GFD1 pp DBP5
+GAL80 pp GAL4
+KAP122 pp TOA2
+KAP122 pp NUP2
+KAP122 pp NUP1
+KAP122 pp TOA1
+SPT15 pp KAP114
+OCH1 interactsWith STE11
+TAD2 pp TAD3
+TAD2 pp TIS11
+SKP1 pp BIR1
+CBF2 pp BIR1
+FRQ1 pp PIK1
+USO1 interactsWith SEC34
+SLY1 interactsWith SEC34
+SEC34 interactsWith BET1
+SEC34 interactsWith YKT6
+SEC34 interactsWith SEC22
+SEC34 interactsWith RUD3
+SEC34 interactsWith YPT1
+SEC34 pp SEC35
+YDR267c pp SPO12
+FIR1 pp SPO12
+CDH1 interactsWith SPO12
+OSH3 pp SPO12
+FUR1 pp SPO12
+SPO12 pp SET2
+SPO12 pp BAT2
+SPO12 pp YLR016c
+SPO12 pp YLR132c
+SPO12 pp MEC3
+SPO12 pp YPR118w
+SPO12 pp YPR152c
+TFC8 pp SPT15
+MLH1 pp MLH2
+MLH1 pp MLH3
+MLH1 pp PMS1
+RAD6 pp UBR1
+RPC17 pp RPC11
+RPC17 pp BRF1
+RPC17 pp RPC31
+TIM22 interactsWith TIM18
+TIM22 pp TIM18
+TIM54 interactsWith TIM18
+TIM54 pp TIM18
+LUV1 pp VPS54
+LUV1 pp VPS52
+VPS54 pp SAC2
+VPS54 pp VPS53
+SAC2 pp VPS53
+VPS52 pp VPS53
+RNT1 pp RNT1
+TIM10 interactsWith TIM18
+STE2 pp GPA1
+CTS1 pp GPA1
+GPA1 pp STE4
+STE2 pp STE4
+CTS1 pp STE4
+GSG1 pp TRS23
+TRS85 pp TRS23
+GSG1 pp TRS120
+TRS85 pp TRS120
+TRS23 pp TRS120
+GSG1 pp TRS31
+TRS85 pp TRS31
+TRS23 pp TRS31
+TRS120 pp TRS31
+GSG1 pp TRS65
+TRS85 pp KRE11
+TRS23 pp KRE11
+TRS23 pp TRS65
+TRS120 pp KRE11
+TRS120 pp TRS65
+TRS31 pp KRE11
+TRS31 pp TRS65
+GSG1 pp BET3
+TRS85 pp BET3
+TRS120 pp BET3
+TRS31 pp BET3
+KRE11 pp BET3
+TRS65 pp BET3
+GSG1 pp BET5
+TRS85 pp BET5
+TRS120 pp BET5
+TRS31 pp BET5
+KRE11 pp BET5
+TRS65 pp BET5
+GSG1 pp TRS130
+TRS85 pp TRS130
+TRS23 pp TRS130
+TRS120 pp TRS130
+TRS31 pp TRS130
+KRE11 pp TRS130
+TRS65 pp TRS130
+BET3 pp TRS130
+BET5 pp TRS130
+GSG1 pp TRS33
+TRS85 pp TRS33
+TRS120 pp TRS33
+TRS31 pp TRS33
+KRE11 pp TRS33
+TRS65 pp TRS33
+TRS130 pp TRS33
+PAT1 pp KEM1
+LSM6 pp KEM1
+LSM4 pp KEM1
+LSM5 pp KEM1
+KEM1 pp LSM1
+KEM1 pp LSM3
+LSM8 pp LSM3
+KEM1 pp LSM7
+PAT1 pp DCP1
+KEM1 pp DCP1
+LSM4 pp LSM8
+SWI4 interactsWith SWI6
+PAT1 pp LSM6
+PAT1 pp LSM4
+PAT1 pp LSM5
+KEM1 pp LSM1
+PAT1 pp LSM3
+PAT1 pp LSM7
+PAT1 pp DCP1
+LSM6 pp DCP1
+LSM4 pp DCP1
+LSM5 pp DCP1
+LSM1 pp DCP1
+LSM3 pp DCP1
+LSM7 pp DCP1
+PAB1 pp TAO3
+PAB1 pp SGN1
+BDF2 interactsWith BDF1
+GLC7 pp RED1
+YNG2 pp TRA1
+SIR2 pp NET1
+TOP3 pp SGS1
+SRB10 pp SNF1
+SSN8 pp SNF1
+SIN4 pp SNF1
+CDC4 pp HRT1
+CRR1 pp HRT1
+VAB2 pp VAC8
+VAC8 pp NVJ1
+VAC8 pp APG13
+UME6 pp MCK1
+PAB1 interactsWith SPB8
+STS1 pp SRP1
+STS1 pp RPN11
+DDC2 interactsWith RNR1
+LCD1 interactsWith RNR1
+DDC2 interactsWith SML1
+LCD1 interactsWith SML1
+KAR9 pp BIM1
+KAR9 pp STU2
+KAR9 pp KAR9
+BUR2 pp SGV1
+EIF-1A pp EIF-5B
+CRM1 pp GPE1
+ARV1 interactsWith ARE2
+ATC1 pp BUD6
+CBF1 pp CBF2
+CBF1 pp MIF2
+CBF1 pp CTF13
+CBF1 pp CEP3
+ARF1 interactsWith SWA2
+SWA2 pp CLC1
+SCO1 pp COX2
+HSC82 pp CNA2
+NUP100 pp MEX67
+NUP116 pp MEX67
+WSC1 pp ROM2
+MID2 pp ROM2
+DUO1 pp DAM1
+VPS30 pp VPS34
+SPC24 pp SPC25
+SPC25 pp SPC25
+NDC80 pp SPC25
+SPC24 interactsWith NDC80
+SPC25 interactsWith NDC80
+SPC24 pp SPC24
+MCM21 pp SPC24
+SPC24 interactsWith NUF2
+SPC25 interactsWith NUF2
+SPC24 pp NUF2
+SPC25 pp NUF2
+NDC80 pp NUF2
+SPC24 interactsWith MCM21
+NPR1 pp CAC3
+CAC1 pp CAC3
+GOS1 pp YKT6
+SFT1 pp YKT6
+GOS1 pp SFT1
+YKT6 pp SED5
+NDC80 interactsWith NDC10
+NUF2 interactsWith NDC10
+SPC25 interactsWith NDC10
+SPC24 interactsWith NDC10
+ERG26 pp ERG25
+RPG1 pp SLA2
+STE50 pp STE11
+STE5 pp STE11
+SSN6 pp SFL1
+SSY5 pp PTR3
+PTR3 pp PTR3
+TAF25 pp SPT7
+TAF25 pp UME6
+TAF25 pp YAP6
+TAF25 pp PRP22
+TAF25 pp ASK10
+TAF25 pp TAO3
+TAF25 pp PRP40
+TAF25 pp ECM22
+TAF25 pp RAP1
+TAF25 pp CLP1
+TAF25 pp RLM1
+TAF25 pp YPR115w
+TAF25 pp RIM15
+DNM1 pp DNM1
+NOP7 pp MAK16
+NOP7 pp SPB1
+NOP7 pp RRP1
+NOP7 pp NOP16
+NOP7 pp NSA2
+NOP7 pp NSA1
+NOP7 pp CIC1
+NOP7 pp RPF1
+NOP7 pp EBP2
+NOP7 pp MRT4
+NOP7 pp DRS1
+NOP7 pp YLR009w
+NOP7 pp ERB1
+NOP7 pp HAS1
+NOP7 pp YNL110c
+NOP7 pp RRP7
+NOP7 pp BRX1
+NOP7 pp YTM1
+NOP7 pp NIP7
+NOP7 pp NOG1
+NOP7 pp TIF6
+NOP7 pp LOC1
+NUG1 pp SPB1
+NUG1 pp DBP10
+NUG1 pp ARX1
+NUG1 pp NOP7
+NUG1 pp SDA1
+NUG1 pp CIC1
+NUG1 pp YHR197w
+NUG1 pp YKL009W
+NUG1 pp NOC3
+NUG1 pp YLR106c
+NUG1 pp ERB1
+NUG1 pp HAS1
+NUG1 pp NOP2
+NUG1 pp RLP7
+NUG1 pp NOC2
+NUG1 pp NIP7
+NUG1 pp YPL146c
+NUG1 pp NOG1
+NUG1 pp YCR072c
+CCZ1 pp YPT7
+RIM20 pp RIM101
+RHO1 pp LRG
+Tap42 pp TIP41
+DAM1 interactsWith BIK1
+DAM1 interactsWith CHL4
+DAM1 interactsWith MCM22
+DAM1 interactsWith STU2
+DAM1 interactsWith MCM16
+DAM1 interactsWith MCM21
+CTF13 interactsWith CHL4
+CTF13 interactsWith IRR1
+CTF3 pp MCM22
+MCM16 pp MCM22
+MCM22 pp SPC34
+CTF13 interactsWith CTF3
+CTF13 interactsWith MCM16
+CTF3 pp MCM16
+CTF13 interactsWith SMC1
+CTF13 interactsWith MCM21
+Gln3 pp SNF1
+Mps1 pp Spc42
+SSF1 pp MAK16
+SSF1 pp RRP1
+SSF1 pp NOP16
+SSF1 pp NSA1
+SSF1 pp NOP7
+SSF1 pp SSF1
+SSF1 pp RPF1
+SSF1 pp EBP2
+SSF1 pp YKL082c
+SSF1 pp YKR081c
+SSF1 pp DRS1
+SSF1 pp DBP9
+SSF1 pp ERB1
+SSF1 pp HAS1
+SSF1 pp NOP2
+SSF1 pp RLP7
+SSF1 pp BRX1
+SSF1 pp YTM1
+SSF1 pp NIP7
+SSF1 pp NOG1
+SSF1 pp NOP4
+SSF1 pp TIF6
+MND1 pp HOP2
+DUN1 pp PAN3
+Bfa1 pp Tem1
+Bub2 pp Tem1
+PKC1 pp RHO1
+Med8 pp Hxk2
+_PLC1 pp SGD1
+PHO85 interactsWith SPT7
+PHO85 interactsWith BEM1
+PHO85 interactsWith RGD1
+PHO85 interactsWith SRB8
+PHO85 interactsWith BRE1
+PHO85 interactsWith NUM1
+PHO85 interactsWith UME6
+PHO85 interactsWith MNN10
+PHO85 interactsWith ERD1
+PHO85 interactsWith SSN2
+PHO85 interactsWith NHX1
+PHO85 interactsWith ANP1
+PHO85 interactsWith YER049W
+PHO85 interactsWith SHC1
+PHO85 interactsWith SWI4
+PHO85 interactsWith BEM2
+PHO85 interactsWith PMR1
+PHO85 interactsWith YGL015C
+PHO85 interactsWith PAC10
+PHO85 interactsWith SRB5
+PHO85 interactsWith CHO2
+PHO85 interactsWith YGR161C
+PHO85 interactsWith WSC4
+PHO85 interactsWith VPS29
+PHO85 interactsWith SLT2
+PHO85 interactsWith PAN5
+PHO85 interactsWith VPS35
+PHO85 interactsWith GSH1
+PHO85 interactsWith BCK1
+PHO85 interactsWith OPI3
+PHO85 interactsWith HOC1
+PHO85 interactsWith YJR142W
+PHO85 interactsWith YKE2
+PHO85 interactsWith FKS1
+PHO85 interactsWith VPS38
+PHO85 interactsWith ROM2
+PHO85 interactsWith SUR4
+PHO85 interactsWith TUS1
+PHO85 interactsWith YML122C
+PHO85 interactsWith VAN1
+PHO85 interactsWith EFR3
+PHO85 interactsWith FKS3
+PHO85 interactsWith LEM3
+PHO85 interactsWith CLA4
+PHO85 interactsWith BNI1
+PHO85 interactsWith GCR2
+PHO85 interactsWith TPM1
+PHO85 interactsWith SMF1
+PHO85 interactsWith MCH4
+PHO85 interactsWith TAT2
+PHO85 interactsWith SLG1
+PHO85 interactsWith RTS1
+PHO85 interactsWith VAM3
+PHO85 interactsWith SFL1
+PHO85 interactsWith HFI1
+PHO85 interactsWith VIK1
+PHO85 interactsWith BEM4
+PHO85 interactsWith GCR1
+ERG25 pp ERG28
+ERG25 pp ERG27
+ERG28 pp ERG27
+PHO80 pp PHO85
+Pex7 pp Pex13
+Bub1 pp Mad1
+ERF4 pp erf2
+CGP1 interactsWith CBF1
+COY1 interactsWith GOS1
+SYN8 pp Snc1
+TLG1 pp Ykt6
+SYN8 pp Vti1
+TLG1 pp Vti1
+SYN8 pp Pep12
+TLG1 pp Pep12
+RGA1 pp RSR1
+RGA2 pp RSR1
+STE20 pp CDC42
+RGA1 pp CDC42
+RGA2 pp CDC42
+BEM3 pp CDC42
+MPS3 pp CDC31
+MPS3 interactsWith CDC31
+GPA2 pp GPB1
+GPA2 pp GPB2
+YPD1 pp SSK1
+FAR3 pp FAR9
+FAR7 pp FAR9
+FAR3 pp FAR10
+FAR3 pp FAR8
+FAR7 pp FAR8
+FAR3 pp FAR11
+FAR3 pp FAR7
+CHL4 pp IML3
+CHL4 interactsWith NDC10
+CHL4 interactsWith MIF2
+CHL4 pp MIF2
+CHL4 pp CTF3
+CHL4 interactsWith CTF13
+CHL4 interactsWith CEP3
+CHL4 pp CTF19
+IML3 pp CTF19
+Apg1 pp Apg1
+IMH1 pp ARL1
+ARL1 pp VPS54
+ARL3 pp SLO1
+CLA4 interactsWith RPL23A
+CLA4 interactsWith YBL062W
+CLA4 interactsWith SKT5
+CLA4 interactsWith EDE1
+CLA4 interactsWith CHS3
+CLA4 interactsWith RPL19A
+CLA4 interactsWith SWD3
+CLA4 interactsWith YBR174C
+CLA4 interactsWith BEM1
+CLA4 interactsWith SHS1
+CLA4 interactsWith RPL35A
+CLA4 interactsWith SEM1
+CLA4 interactsWith DYN2
+CLA4 interactsWith SWI4
+CLA4 interactsWith PEA2
+CLA4 interactsWith BEM2
+CLA4 interactsWith RAD54
+CLA4 interactsWith ITC1
+CLA4 interactsWith SSF73
+CLA4 interactsWith RPL24A
+CLA4 interactsWith PRE9
+CLA4 interactsWith ELP2
+CLA4 interactsWith SMI1
+CLA4 interactsWith STE20
+CLA4 interactsWith SLT2
+CLA4 interactsWith UBA4
+CLA4 interactsWith CHS7
+CLA4 interactsWith SPO12
+CLA4 interactsWith CTF8
+CLA4 interactsWith RPN10
+CLA4 interactsWith HOS4
+CLA4 interactsWith MGA2
+CLA4 interactsWith RPS21B
+CLA4 interactsWith ASF1
+CLA4 interactsWith CHS6
+CLA4 interactsWith BCK1
+CLA4 interactsWith RTT101
+CLA4 interactsWith IXR1
+CLA4 interactsWith SPA2
+CLA4 interactsWith APC9
+CLA4 interactsWith BUD6
+CLA4 interactsWith CHS5
+CLA4 interactsWith VAC14
+CLA4 interactsWith GIM5
+CLA4 interactsWith YML095C-A
+CLA4 interactsWith CTF18
+CLA4 interactsWith UBP8
+CLA4 interactsWith SAP30
+CLA4 interactsWith ELP6
+CLA4 interactsWith BNI1
+CLA4 interactsWith URE2
+CLA4 interactsWith RTT106
+CLA4 interactsWith GIM3
+CLA4 interactsWith FKH2
+CLA4 interactsWith SLK19
+CLA4 interactsWith RIM20
+CLA4 interactsWith NIP100
+CLA4 interactsWith BEM4
+CLA4 interactsWith YPL047W
+CLA4 interactsWith CTF4
+CLA4 interactsWith DCC1
+CLA4 interactsWith FAB1
+CLA4 interactsWith RXT2
+PSF3 interactsWith PSF1
+SLD5 interactsWith PSF1
+ERI1 pp RAS2
+GPA1 pp SCP160
+BYE1 interactsWith Rpb1
+BYE1 interactsWith ESS1
+TOR1 pp KOG1
+SSD1 interactsWith TOR1
+TOR1 pp LST8
+SSD1 interactsWith TCO89
+TOR1 pp TOR2
+AAC3 interactsWith AAC1
+AAC3 interactsWith PET9
+AMN1 interactsWith LTE1
+AMN1 interactsWith CDC15
+AMN1 interactsWith MOB1
+AMN1 interactsWith CDC5
+AMN1 interactsWith SLK19
+AMN1 interactsWith ESP1
+AMN1 interactsWith TEM1
+AMN1 interactsWith DBF2
+CDC50 interactsWith CDC39
+CDC50 interactsWith YNR048W
+DNM1 interactsWith FZO1
+ECM1 interactsWith MTR2
+ERP4 interactsWith ERP2
+ERP6 interactsWith ERP1
+EUG1 interactsWith PDI1
+GBP2 interactsWith CDC13
+GIN4 interactsWith REI1
+LEM3 interactsWith CDC50
+MDV1 interactsWith FZO1
+MID2 interactsWith PKC1
+MID2 interactsWith RHO1
+MID2 interactsWith SLG1
+MPD1 interactsWith PDI1
+MPD2 interactsWith PDI1
+PCL10 interactsWith SNF1
+PCL6 interactsWith PCL10
+PCL6 interactsWith SNF1
+PCL7 interactsWith PCL6
+PCL7 interactsWith SNF1
+PCL7 interactsWith PCL10
+PCL8 interactsWith PCL6
+PCL8 interactsWith SNF1
+PCL8 interactsWith PCL7
+PET8 interactsWith SAM1
+PET9 interactsWith AAC3
+PKH3 interactsWith PKH2
+PKH3 interactsWith PKH1
+REH1 interactsWith NAP1
+REI1 interactsWith NAP1
+REI1 interactsWith SWE1
+REX4 interactsWith RRP5
+SCM4 interactsWith CDC4
+SCS22 interactsWith SCS2
+SEY1 interactsWith YOP1
+SPL2 interactsWith PLC1
+SSU72 interactsWith RPB2
+TYE7 interactsWith GCR2
+URB1 interactsWith RSA3
+VTS1 interactsWith VTI1
+WSS1 interactsWith SMT3
+AHA1 pp HSP82
+ALF1 pp TUB1
+AME1 pp CTF19
+AME1 pp OKP1
+AME1 pp MCM21
+AVO1 pp AVO2
+BZZ1 pp LAS17
+BZZ1 pp MYO5
+CDC4 pp CDC6
+CWC25 pp PRP19
+DBP2 pp NAM7
+DBP9 pp DBP6
+DHH1 pp PAT1
+DHH1 pp LSM1
+DHH1 pp DCP1
+EDC3 pp DCP2
+EDC3 pp LSM1
+EDC3 pp DCP1
+EDC3 pp KEM1
+EDC3 pp DHH1
+ENP1 pp NOP1
+ENP2 pp UTP9
+ENT3 pp GGA2
+ESS1 pp RPO21
+FIN1 pp BMH1
+FIN1 pp BMH2
+FIN1 pp FIN1
+FIN1 pp GLC7
+FIN1 pp FIN1
+FIN1 pp BMH2
+FIN1 pp REB1
+FIN1 pp FIN1
+FIN1 pp FIR1
+FIN1 pp WSS1
+FMP15 pp KAP123
+FMP15 pp TOM40
+GIM3 pp PAC10
+GIM4 pp PAC10
+GIM5 pp GIM4
+GIM5 pp GIM3
+GMH1 pp GEA2
+GMH1 pp GEA1
+HCH1 pp HSP82
+HRT1 pp CDC53
+HRT1 pp CUL3
+HRT1 pp APC2
+HYP2 pp DYS1
+HYR1 pp YAP1
+IOC2 pp ISW1
+IOC3 pp ISW1
+IOC4 pp ISW1
+JIP5 pp BRE1
+LIA1 pp HYP2
+LIN1 pp WSS1
+LIN1 pp PRP8
+LIN1 pp NFI1
+LIN1 pp YJL149W
+LIN1 pp HEX3
+LIN1 pp RFC1
+LIN1 pp IRR1
+LRP1 pp RRP6
+MDV1 pp DNM1
+MLC2 pp MYO1
+MLH2 pp MLH1
+MLH3 pp MLH1
+MLH3 pp PMS1
+MYO5 pp BZZ1
+NPA3 pp YKL014C
+PAC10 pp GIM5
+PAC2 pp TUB1
+PEX27 pp PEX25
+PTI1 pp PTA1
+PTI1 pp RNA14
+PTI1 pp PCF11
+RNH202 pp RNH201
+RNH203 pp RNH201
+RTT101 pp HRT1
+RTT101 pp HRT1
+SAC3 pp MTR2
+SAC3 pp NUP116
+SAC3 pp MEX67
+SAC3 pp NSP1
+SAC3 pp DBP5
+SAC3 pp NUP1
+SAC3 pp MEX67
+SHQ1 pp RNT1
+SNZ1 pp YHR198C
+SNZ1 pp SNO1
+SNZ1 pp SNZ2
+SNZ1 pp SNZ1
+STB1 pp SIN3
+STB2 pp SIN3
+SUB2 pp SAC3
+SWC4 pp ESA1
+SWI6 pp MSN5
+SYN8 pp VTI1
+SYN8 pp PEP12
+THI11 pp SNZ2
+THP1 pp SAC3
+TOR1 pp KOG1
+TOR1 pp LST8
+TOR2 pp AVO1
+TOR2 pp LST8
+TOR2 pp AVO2
+TRM82 pp TRM8
+TSC11 pp TOR2
+URB2 pp YKL014C
+VPS51 pp TLG1
+VPS52 pp YPT6
+YGR046W pp HSP60
+YGR198W pp STT4
+YIP4 pp YPT1
+YIP5 pp YPT1
+YJR136C pp RSM23
+YKE2 pp GIM5
+YKE2 pp PAC10
+YKL088W pp SIS2
+YKL088W pp VHS3
+YKR022C pp PRP8
+YKR022C pp CWC2
+YLR132C pp COR1
+YLR132C pp PRP19
+YML023C pp SMC5
+YML023C pp RHC18
+YNL313C pp KAR2
+Cdc16 interactsWith Unknown
+Unknown interactsWith Apc1
+Unknown interactsWith Apc2
+Unknown interactsWith Cdc27
+Unknown interactsWith Apc4
+Unknown interactsWith Apc5
+Unknown interactsWith Cdc23
+Unknown interactsWith Cdc26
+Unknown interactsWith Apc9
+Unknown interactsWith Apc10
+Unknown interactsWith Apc11
+Unknown interactsWith Apc13
+ADA2 pp GCN5
+ADA2 pp TRA1
+ADA2 pp ADA3
+ADR1 pp ADH2
+ADR1 pp GAL4
+AFR1 pp STE2
+ARK1 interactsWith PRK1
+ARP4 pp ACT3
+BEM2 interactsWith MYO2
+BEM2 interactsWith RHO1
+BEM2 interactsWith TPM1
+BEM2 interactsWith SAC6
+BST1 interactsWith BST1
+BUR6 interactsWith YDR1
+CBP1 interactsWith CBP1
+CBP1 interactsWith COB
+CCC1 interactsWith FET3
+CCC1 interactsWith CSG1
+CDC14 interactsWith CLB2
+CDC14 interactsWith NET1
+CDC14 interactsWith SIC1
+CDC14 interactsWith TEM1
+CDC14 interactsWith SIC1
+CDC14 interactsWith SIR2
+CDC24 pp CDC28
+CDC24 pp CDC42
+CDC24 pp FAR1
+CDC4 interactsWith SIC1
+CDC4 interactsWith SIC1
+CDC42 interactsWith Ste20
+CDC45 pp CDC6
+CDC45 pp MCM7
+CEG1 pp CET1
+CHA4 pp CHA1
+CKA1 pp CKA2
+CKA1 pp CKB2
+CKA1 pp CKB1
+CKA2 pp CKB1
+CKA2 pp CKB2
+CKB1 pp CKB2
+CLB1 interactsWith CLB2
+CLB1 interactsWith CLB4
+CLB1 interactsWith CLN1
+CLB1 interactsWith CDC13
+CLB1 interactsWith CLB3
+CLB3 interactsWith CLB2
+CLB3 interactsWith CLB4
+CLB3 interactsWith CLN1
+CLB4 interactsWith CLB2
+CLB4 interactsWith CLN1
+CLB5 interactsWith CDC28
+CLB5 interactsWith CLB1
+CLB5 interactsWith CLB4
+CLB5 interactsWith CLB6
+CLB6 interactsWith CLB2
+CLB6 interactsWith CLB4
+CLB6 interactsWith CLB5
+CLB6 interactsWith CLN1
+CLB6 interactsWith CLN2
+CLB6 interactsWith CDC28
+CLB6 interactsWith CLB1
+CLB6 interactsWith CLB3
+CLB6 interactsWith CLN3
+CLB6 interactsWith CLB4
+CLB6 interactsWith CDC28
+CLB6 interactsWith CLB1
+CLN2 interactsWith CLN1
+CLN2 interactsWith CLN3
+CLN2 interactsWith STE20
+CNA1 interactsWith CNA2
+COT1 interactsWith ZRC1
+CPR6 pp HSP90
+CPR7 pp HSP90
+CPR7 interactsWith HSP90
+CSE1 interactsWith SRP1
+CSE1 interactsWith SRP1
+DAL1 interactsWith DAL5
+DAL1 interactsWith DAL7
+DAL1 interactsWith DAL80
+DBF20 interactsWith CDC28
+DBF20 interactsWith DBF2
+DCP1 pp DCP2
+DCP2 pp DCP1
+DNA2 interactsWith POL1
+DUO1 pp ASK1
+DUO1 pp SPC34
+ECM10 interactsWith MGE1
+ECM10 interactsWith SSC1
+ECM10 interactsWith SSQ1
+ELP3 pp ELP4
+ELP3 pp ELP6
+ELP4 pp ELP1
+ELP4 pp ELP6
+ELP6 pp ELP1
+EXO1 pp MLH1
+EXO1 pp MSH2
+EXO1 pp MSH3
+EXO1 pp MSH6
+EXO1 pp PMS1
+FAA1 interactsWith FAA4
+FAA1 interactsWith Faa2
+FAA1 interactsWith NMT1
+FAA2 interactsWith Faa1
+FAA4 interactsWith Faa1
+FAA4 interactsWith NMT1
+FKH1 interactsWith CLB2
+FKH1 interactsWith FKH2
+FKH1 interactsWith ACE2
+FKH1 interactsWith CLB2
+FKH1 interactsWith FKH2
+FKH1 interactsWith SWI5
+FKH2 interactsWith CLB2
+FKH2 interactsWith FKH1
+FKH2 interactsWith CLB2
+FKH2 interactsWith ACE2
+FKH2 interactsWith SWI5
+FLO5 interactsWith FLO1
+GAC1 pp GLC7
+GAC1 pp GLC7
+GCN1 pp GCN2
+GCN1 pp GCN4
+GCN5 pp TRA1
+GCN5 pp ADA3
+GCS1 pp GLO3
+GDH3 interactsWith GDH1
+GEA1 pp SEC7
+GIN4 interactsWith HSL1
+GIN4 interactsWith SWE1
+GIN4 interactsWith CDC28
+GIN4 interactsWith KCC4
+GLC7 pp RED1
+GLN3 pp DAL3
+GLN3 pp GLN1
+GLN3 pp GDH2
+GPI2 interactsWith GPI1
+GPI2 interactsWith SPT14
+GPR1 pp GPA2
+GSY1 interactsWith GSY2
+GTR1 pp GTR2
+HAL5 interactsWith TRK1
+HAL5 interactsWith TRK2
+HCR1 pp NIP1
+HCR1 pp PRT1
+HCR1 pp TIF34
+HCR1 pp TIF35
+HOT1 interactsWith MSN2
+HOT1 interactsWith MSN4
+HPR1 pp MFT1
+HPR1 pp RLR1
+HPR1 pp THP2
+HSL1 interactsWith CDC28
+HSL1 interactsWith GIN4
+HSL1 interactsWith KCC4
+HSL1 interactsWith SWE1
+HSL7 interactsWith SWE1
+HST1 interactsWith HST1
+HST1 interactsWith SUM1
+HST3 interactsWith HST1
+HST3 interactsWith HST4
+HST3 interactsWith SIR2
+HST4 interactsWith HST1
+HST4 interactsWith SIR2
+INO2 pp INO1
+INO4 pp INO1
+INO4 pp INO2
+INP51 interactsWith SAC1
+IRA1 pp CYR1
+IRA1 pp RAS1
+IRA1 pp RAS2
+ISA1 interactsWith ISA2
+ISA2 interactsWith ISA1
+IXR1 pp ROX1
+KAP104 pp NAB2
+KAP104 pp NAB2
+KCC4 interactsWith HSL1
+KCC4 interactsWith SWE1
+KCC4 interactsWith CDC28
+KES1 interactsWith Sec14
+KIP3 interactsWith KIP2
+LRG1 interactsWith BEM2
+LRG1 interactsWith PKC1
+MBP1 pp SWI4
+MBP1 pp SWI6
+MBP1 pp CDC28
+MCM10 pp MCM2
+MEC1 interactsWith RAD53
+MFT1 pp RLR1
+MFT1 pp MFT1
+MFT1 pp THP2
+MID2 interactsWith MTL1
+MIH1 interactsWith CDC25
+MMS2 interactsWith RAD6
+MMS2 interactsWith REV3
+MMS2 interactsWith POL30
+MMS2 interactsWith RAD18
+MMS4 interactsWith MUS81
+MMS4 interactsWith RAD1
+MMS4 interactsWith RAD10
+MRE11 pp RAD50
+MRE11 pp XRS2
+MRS11 pp MRS5
+MRS11 pp TIM22
+MRS4 interactsWith MRS3
+MRS5 pp MRS11
+MRS5 pp TIM22
+MSH3 pp MSH2
+MTH1 interactsWith RGT2
+MTH1 interactsWith SNF3
+MTR10 pp Npl3
+MUS81 interactsWith RAD1
+MUS81 interactsWith RAD10
+NET1 pp SIC1
+NET1 pp NET1
+NET1 pp SIC1
+NET1 pp SIR2
+NET1 pp NET1
+NET1 pp SIR2
+NHP6A pp HMG1
+NHP6A interactsWith HMG1
+NHP6A interactsWith NHP6B
+NHP6A interactsWith HO
+NHP6A interactsWith NHP6B
+NHP6A interactsWith SCEI
+NHP6B interactsWith HMG1
+NTF2 pp RAN
+OAF1 pp POX1
+OAF1 pp Oaf1
+OAF1 pp POX1
+OAF1 interactsWith Pip2
+OAF1 interactsWith Oaf1
+OAF1 interactsWith Pip2
+OST2 pp OST3
+OST2 pp Ost1
+OST2 pp Ost5
+OST2 pp Swp1
+OST2 pp Wbp1
+OST3 pp Ost2
+OST3 pp Ost1
+OST3 pp Ost5
+OST3 pp Swp1
+OST3 pp Wbp1
+OST5 pp OST3
+OST5 pp Ost1
+OST5 pp Ost2
+OST5 pp Swp1
+OST5 pp Wbp1
+PAN2 pp Pab1
+PCL10 interactsWith PCL8
+PDR1 pp PDR5
+PDR1 pp PDR3
+PDR3 pp PDR1
+PDR3 pp PDR5
+PET309 interactsWith COX1
+PEX13 interactsWith PEX14
+PEX13 interactsWith PTS1
+PEX14 pp PEX13
+PEX14 pp PTS1
+PEX18 pp PEX21
+PEX18 pp Pex7
+PEX21 pp PEX18
+PEX21 pp Pex7
+PHB1 pp PHB2
+PHB2 pp PHB1
+PHO2 interactsWith PHO4
+PHO2 interactsWith PHO5
+PHO2 pp SWI5
+PHO2 pp HO
+PHO2 pp PHO5
+PHO85 interactsWith CDC28
+PHO85 interactsWith GLC7
+PHO85 interactsWith GSY2
+PHO85 interactsWith PHO5
+PHO85 interactsWith Gsy2
+PHO85 interactsWith SNF1
+PHO85 pp GSY2
+PHO85 pp PHO4
+PHO85 pp PHO80
+PIP2 pp Pip2
+POR2 interactsWith POR1
+PPH21 pp SIT4
+PPH21 pp TAP42
+PPH21 pp PPH22
+PPH22 pp CDC55
+PPH22 pp SIT4
+PPH22 pp TAP42
+PPZ1 interactsWith BCK1
+PPZ1 interactsWith ENA1
+PPZ1 interactsWith PPZ2
+PPZ1 interactsWith SLT2
+PPZ2 interactsWith BCK1
+PPZ2 interactsWith SLT2
+PPZ2 interactsWith ENA1
+PRO1 interactsWith PRO2
+PTC1 interactsWith PTC2
+PTP3 pp HOG1
+PTP3 pp PTP2
+PTR3 interactsWith PTR2
+PTR3 interactsWith SSY1
+RAD24 pp RFC2
+RAD24 pp RFC3
+RAD24 pp RFC4
+RAD24 pp MATA1
+RAD24 pp RFC5
+RAD50 pp XRS2
+RAD52 interactsWith RAD59
+RAD53 interactsWith MEC1
+RAD55 pp RAD51
+RAD55 pp RAD57
+RAD57 pp MRE11
+RAD57 pp RAD51
+RAD57 pp MSH5
+RAD57 pp RAD51
+RAD6 pp UBR1
+RAD6 pp RAD18
+RAD9 interactsWith CDC9
+RCS1 pp FET3
+RCS1 pp FRE1
+RCS1 pp FRE2
+RCS1 pp FTR1
+RDH54 interactsWith RAD54
+RDH54 interactsWith RAD52
+RDH54 interactsWith RAD54
+RDH54 interactsWith SNF2
+RED1 pp HOP1
+RLR1 pp HPR1
+RLR1 pp MFT1
+RLR1 pp THP2
+RNR4 interactsWith RNR2
+RNR4 interactsWith RNR3
+RNR4 interactsWith RNR1
+ROX1 pp SSN6
+ROX1 pp TUP1
+RTG1 interactsWith CIT2
+SAM1 interactsWith SAM2
+SAP30 pp RPD3
+SAP30 pp SIN3
+SAP30 pp HMR
+SBA1 pp HSP90
+SCH9 interactsWith CDC25
+SCH9 interactsWith CYR1
+SEC1 pp SEC4
+SEC10 interactsWith SEC8
+SEC10 interactsWith SEC15
+SEC10 interactsWith SEC3
+SEC10 interactsWith SEC5
+SEC10 interactsWith SEC6
+SEC10 pp SEC15
+SEC15 pp SEC6
+SEC15 pp SEC8
+SEC15 pp SEC3
+SEC15 pp SEC5
+SEC15 pp SEC10
+SEC15 pp SEC6
+SEC15 pp SEC8
+SEC16 pp SEC23
+SEC27 interactsWith SEC21
+SEC27 interactsWith SEC22
+SEC3 interactsWith SEC6
+SEC3 interactsWith SEC8
+SEC3 interactsWith SEC5
+SEC3 pp SEC8
+SEC5 interactsWith SEC6
+SEC5 interactsWith SEC8
+SEC6 pp SEC8
+SEC6 pp SEC8
+SEC6 pp SEC15
+SEC8 pp SEC15
+SEC8 pp SEC3
+SEC8 pp SEC6
+SFT1 interactsWith SED5
+SGD1 interactsWith GPD1
+SHR3 interactsWith Gap1
+SHR3 interactsWith SEC12
+SIC1 pp CLB1
+SIC1 pp CLB5
+SIC1 pp CLN1
+SIC1 pp RBX1
+SIC1 pp CDC28
+SIC1 pp CDC34
+SIC1 pp CLB1
+SIC1 pp SIC1
+SIM1 interactsWith NCA3
+SIM1 interactsWith UTH1
+SIM1 interactsWith SIM1
+SIN3 pp GCN5
+SIN3 pp HMR
+SIN3 pp RPD3
+SIN3 pp SAP30
+SIN3 interactsWith RPD3
+SIP4 pp CAT8
+SIP4 pp GAL4
+SIP4 pp SNF1
+SIR1 interactsWith HM
+SIR1 interactsWith MATA1
+SIR2 pp RAP1
+SIR2 pp SIR3
+SIR2 pp SIR4
+SIT4 interactsWith SSD1
+SKI8 pp SKI2
+SKI8 pp SKI3
+SKN7 pp YAP1
+SKN7 pp TRX2
+SKO1 pp MIG1
+SLI15 pp IPL1
+SLK19 interactsWith SCC1
+SMF2 interactsWith SMF1
+SNF4 interactsWith SNF1
+SOM1 interactsWith IMP1
+SPC1 interactsWith Sec11
+SPC2 interactsWith Spc1
+SPC2 interactsWith Spc1
+SPC3 interactsWith Spc2
+SPC3 interactsWith Spc1
+SPC34 pp ASK1
+SPC34 pp DUO1
+SPC97 pp Spc98
+SPC97 pp Tub4
+SPC98 pp Spc97
+SPT20 interactsWith GAL4
+SPT20 interactsWith ADA2
+SPT20 interactsWith ADA3
+SPT20 interactsWith GCN5
+SPT20 interactsWith SPT15
+SPT20 interactsWith SPT7
+SPT8 pp ADA1
+SPT8 pp HIS3
+SPT8 pp SPT20
+SPT8 pp ADA2
+SPT8 pp ADA3
+SPT8 pp GCN5
+SPT8 pp SPT3
+SPT8 pp SPT7
+SPT8 pp TBP
+SSA3 interactsWith SSA2
+SSA3 interactsWith SSA4
+SSA3 interactsWith SSA1
+SSF1 interactsWith SSF1
+SSF1 interactsWith SSF2
+SSM4 interactsWith RNA14
+SSY1 interactsWith CAR1
+SSY1 interactsWith GAP1
+SSY1 interactsWith PTR2
+SSY1 interactsWith PTR3
+SSY5 interactsWith PTR3
+SSY5 interactsWith SSY1
+STD1 pp SNF4
+STE12 pp STE2
+STE50 pp FUS1
+STE50 pp STE11
+STE50 pp STE11
+STE50 pp STE11
+STE50 pp STE5
+STI1 interactsWith HSP90
+STP1 interactsWith STP2
+STP1 interactsWith BAP3
+STP2 interactsWith BAP3
+STP2 interactsWith STP1
+STT3 pp Ost4
+STT3 pp Ost1
+STT3 pp Swp1
+STT3 pp Wbp1
+SUB2 pp HPR1
+SUB2 pp MFT1
+SUB2 pp RLR1
+SUB2 pp THP2
+SUB2 pp YRA1
+SWE1 interactsWith CDC28
+SWI6 interactsWith MBP1
+SWP1 pp OST3
+SWP1 pp Ost2
+SWP1 pp Ost1
+SWP1 pp Ost5
+SWP1 pp STT3
+SWP1 pp Wbp1
+THP2 pp RLR1
+TIM13 pp Tim10
+TIM13 pp Tim8
+TIM13 pp Tim12
+TIM13 pp Tim8
+TIM13 pp TIM9
+TIM22 pp Tim54
+TIM22 pp Tim12
+TIM8 pp Tim10
+TIM8 pp Tim12
+TIM8 pp Tim13
+TIM8 pp TIM9
+TIM8 pp Tim13
+TIM9 pp Tim13
+TIM9 pp Tim8
+TIM9 pp TIM22
+TIM9 interactsWith Tim54
+TKL2 interactsWith TKL1
+TOM22 pp TOM5
+TOM22 pp TOM6
+TOM22 pp TOM7
+TOM22 pp TOM70
+TOM22 pp TOM40
+TOM40 pp TOM5
+TOM40 pp TOM6
+TOM40 pp TOM7
+TOM40 pp TOM70
+TOM5 pp TOM20
+TOM5 pp TOM22
+TOM5 pp TOM40
+TOM5 pp TOM6
+TOM5 pp TOM7
+TOM5 pp TOM70
+TOM6 pp TOM22
+TOM6 pp TOM40
+TOM6 pp TOM5
+TOM6 pp TOM7
+TOM6 pp TOM70
+TOM7 pp TOM5
+TOM7 pp TOM70
+TOP3 interactsWith RAD1
+TOP3 interactsWith TOP1
+TOP3 interactsWith TOP2
+TUB4 pp Spc97
+TUP1 pp MCM1
+TUP1 pp SSN6
+URA8 interactsWith URA7
+URE2 pp GLN3
+VIK1 pp KAR3
+VIK1 pp CIK1
+VMA22 interactsWith VMA12
+VPS35 pp VPS10
+WBP1 pp OST3
+WBP1 pp Ost1
+WBP1 pp Ost2
+WBP1 pp Ost5
+WBP1 pp STT3
+WBP1 pp Swp1
+XBP1 pp CLN1
+XBP1 pp MBP1
+XBP1 pp SWI4
+YAP3 pp YAP3
+YDJ1 interactsWith HSP90
+YFH1 interactsWith FET3
+YPT31 pp YPT1
+YPT31 interactsWith YPT1
+YPT31 interactsWith YPT32
+YPT32 interactsWith SEC4
+YPT32 interactsWith YPT1
+YPT32 interactsWith YPT31
+YRA1 interactsWith MFT1
+YRA1 interactsWith RLR1
+YRA1 interactsWith THP2
+YRA1 interactsWith HPR1
+ZDS1 interactsWith ZDS2
+Mcm7 pd YAL069W
+Orc_complex interactsWith YAL069W
+Mcm3 pd YAL069W
+Orc1 pd YAL069W
+Mcm4 pd YAL069W
+Mcm7 pd YAL067C
+Mcm3 pd YAL067C
+Mcm4 pd YAL067C
+Mcm7 pd YAL066W
+Mcm3 pd YAL066W
+Mcm4 pd YAL066W
+Mcm4 pd YAL064W
+Orc_complex interactsWith iYAL063C-2
+Mcm3 pd iYAL063C-2
+Orc1 pd iYAL063C-2
+Mcm7 pd iYAL056W
+Mcm3 pd iYAL056W
+Orc1 pd iYAL056W
+Mcm4 pd iYAL056W
+Mcm7 pd YAL055W
+Orc_complex interactsWith YAL055W
+Mcm3 pd YAL055W
+Orc1 pd YAL055W
+Mcm4 pd YAL055W
+Orc_complex interactsWith iYAL039C-0
+Orc1 pd iYAL039C-0
+Mcm4 pd iYAL039C-0
+Mcm4 pd iYAL038W
+Mcm7 pd iYAL017W
+Orc_complex interactsWith iYAL017W
+Mcm3 pd iYAL017W
+Orc1 pd iYAL017W
+Mcm4 pd iYAL017W
+Mcm4 pd YAL005C
+Mcm7 pd YAL002W
+Mcm3 pd YAL002W
+Mcm4 pd YAL002W
+Mcm7 pd iYAL002W
+Mcm3 pd iYAL002W
+Mcm4 pd iYAL002W
+Mcm7 pd YAL001C
+Mcm3 pd YAL001C
+Orc1 pd YAL001C
+Orc_complex interactsWith YAR008W
+Mcm3 pd YAR008W
+Orc_complex interactsWith iYAR008W
+Mcm3 pd iYAR008W
+Orc1 pd iYAR008W
+Mcm4 pd iYAR008W
+Orc1 pd YAR019C
+Mcm3 pd iYAR019C-1
+Orc1 pd YARCdelta8
+Mcm7 pd iYARCdelta8-3
+Orc_complex interactsWith iYARCdelta8-3
+Orc1 pd iYARCdelta8-3
+Mcm4 pd iYARCdelta8-3
+Mcm4 pd iYAR068W
+Mcm7 pd YBL109W
+Orc_complex interactsWith YBL109W
+Mcm3 pd YBL109W
+Mcm4 pd YBL109W
+Mcm7 pd iYBL109W-0
+Orc_complex interactsWith iYBL109W-0
+Mcm3 pd iYBL109W-0
+Orc1 pd iYBL109W-0
+Mcm4 pd iYBL109W-0
+Orc_complex interactsWith iYBL109W-1
+Mcm7 pd iYBL108W
+Orc_complex interactsWith iYBL108W
+Mcm4 pd iYBL108W
+Orc1 pd YBL100C
+Mcm4 pd YBL099W
+Orc1 pd YBL098W
+Orc1 pd YBL094C
+Mcm7 pd iYBL086C
+Orc_complex interactsWith iYBL086C
+Mcm3 pd iYBL086C
+Orc1 pd iYBL086C
+Mcm4 pd iYBL086C
+Mcm4 pd iYBL069W
+Mcm7 pd YBL068W
+Orc1 pd YBL068W
+Mcm4 pd YBL068W
+Mcm7 pd iYBL068W
+Orc_complex interactsWith iYBL068W
+Mcm3 pd iYBL068W
+Orc1 pd iYBL068W
+Mcm4 pd iYBL068W
+Mcm7 pd YBL067C
+Mcm3 pd YBL067C
+Mcm7 pd iYBL067C
+Mcm4 pd iYBL067C
+Mcm7 pd iYBL065W
+Mcm3 pd iYBL065W
+Mcm4 pd iYBL065W
+Mcm7 pd YBL064C
+Orc1 pd YBL064C
+Orc_complex interactsWith iYBL041W
+Orc1 pd iYBL041W
+Mcm7 pd iYBL040C
+Orc_complex interactsWith iYBL040C
+Mcm3 pd iYBL040C
+Orc1 pd iYBL040C
+Mcm4 pd iYBL040C
+Orc_complex interactsWith YBL039C
+Orc_complex interactsWith YBL027W
+Mcm4 pd YBL027W
+Mcm7 pd iYBL027W
+Orc_complex interactsWith iYBL027W
+Mcm3 pd iYBL027W
+Orc1 pd iYBL027W
+Mcm4 pd iYBL027W
+Mcm7 pd iYBL023C
+Mcm4 pd iYBL023C
+Orc_complex interactsWith YBL017C
+Mcm4 pd iYBLCsigma1
+Mcm4 pd iYBL009W
+Mcm7 pd YBL006C
+Mcm3 pd YBL001C
+Mcm4 pd YBL001C
+Mcm7 pd iYBL001C
+Orc_complex interactsWith iYBL001C
+Mcm3 pd iYBL001C
+Orc1 pd iYBL001C
+Mcm4 pd iYBL001C
+Mcm7 pd iYBR008C
+Orc_complex interactsWith iYBR008C
+Mcm3 pd iYBR008C
+Orc1 pd iYBR008C
+Mcm4 pd iYBR008C
+Orc_complex interactsWith YBR009C
+Mcm7 pd iYBRCdelta11
+Mcm3 pd iYBRCdelta11
+Mcm4 pd iYBRCdelta11
+Orc1 pd YBR013C
+Mcm7 pd iYBRCdelta14
+Mcm4 pd iYBRCdelta14
+Orc1 pd YBR027C
+Mcm3 pd YBR044C
+Mcm7 pd iYBR044C
+Mcm3 pd iYBR044C
+Mcm4 pd iYBR044C
+Orc_complex interactsWith YBR048W
+Orc_complex interactsWith iYBR057C
+Orc1 pd YBR063C
+Orc1 pd YBR066C
+Mcm7 pd YBR070C
+Mcm3 pd YBR070C
+Mcm4 pd YBR070C
+Mcm7 pd YBR075W
+Mcm3 pd YBR075W
+Mcm4 pd YBR075W
+Mcm7 pd iYBR075W
+Mcm3 pd iYBR075W
+Mcm4 pd iYBR075W
+Orc1 pd YBR077C
+Mcm7 pd iYBR082C-0
+Orc_complex interactsWith iYBR082C-0
+Mcm3 pd iYBR082C-0
+Orc1 pd iYBR082C-0
+Mcm4 pd iYBR082C-0
+Mcm4 pd iYBR083W
+Mcm7 pd iYBR085W-0
+Orc_complex interactsWith iYBR085W-0
+Mcm3 pd iYBR085W-0
+Orc1 pd iYBR085W-0
+Mcm4 pd iYBR085W-0
+Mcm7 pd iYBR085W-1
+Mcm3 pd iYBR085W-1
+Mcm4 pd iYBR085W-1
+Mcm7 pd YBR089W
+Mcm7 pd iYBR100W
+Orc1 pd YBR106W
+Mcm7 pd YBR108W
+Mcm3 pd YBR108W
+Orc_complex interactsWith YBR120C
+Mcm3 pd YBR123C
+Mcm7 pd YBR124W
+Orc_complex interactsWith YBR124W
+Mcm3 pd YBR124W
+Orc1 pd YBR124W
+Mcm4 pd YBR124W
+Orc_complex interactsWith iYBR124W
+Mcm3 pd iYBR124W
+Orc1 pd iYBR124W
+Orc_complex interactsWith YBR125C
+Orc_complex interactsWith YBR131W
+Mcm4 pd iYBR131W
+Mcm7 pd YBR134W
+Mcm3 pd YBR134W
+Mcm4 pd YBR134W
+Mcm7 pd iYBR139W
+Mcm3 pd iYBR139W
+Mcm4 pd iYBR139W
+Mcm7 pd YBR148W
+Mcm3 pd YBR148W
+Mcm4 pd YBR148W
+Mcm7 pd iYBR148W
+Mcm3 pd iYBR148W
+Mcm4 pd iYBR148W
+Mcm3 pd YBR149W
+Mcm4 pd YBR149W
+Mcm3 pd YBR154C
+Mcm7 pd YBR180W
+Orc_complex interactsWith YBR180W
+Mcm3 pd YBR180W
+Orc1 pd YBR180W
+Mcm4 pd YBR180W
+Orc_complex interactsWith YBR181C
+Orc_complex interactsWith iYBR200W
+Orc1 pd iYBR200W
+Orc1 pd iYBR201W-1
+Mcm7 pd iYBR203W
+Mcm3 pd iYBR203W
+Mcm4 pd iYBR203W
+Mcm3 pd YBR204C
+Mcm7 pd YBR228W
+Mcm4 pd YBR228W
+Mcm7 pd YBR241C
+Mcm3 pd YBR241C
+Mcm7 pd iYBR241C
+Orc1 pd iYBR241C
+Mcm4 pd iYBR241C
+Mcm3 pd YBR242W
+Mcm3 pd YBR243C
+Mcm4 pd YBR244W
+Mcm7 pd YBR250W
+Mcm3 pd YBR250W
+Mcm4 pd YBR250W
+Mcm3 pd iYBR250W
+Mcm4 pd iYBR250W
+Mcm3 pd YBR258C
+Orc_complex interactsWith YBR267W
+Orc_complex interactsWith iYBR267W
+Mcm7 pd iYBR268W
+Orc_complex interactsWith iYBR268W
+Mcm3 pd iYBR268W
+Orc1 pd iYBR268W
+Mcm4 pd iYBR268W
+Mcm7 pd YBR269C
+Orc_complex interactsWith YBR269C
+Mcm3 pd YBR269C
+Orc1 pd YBR269C
+Mcm4 pd YBR269C
+Orc_complex interactsWith iYBR270C
+Mcm3 pd iYBR270C
+Orc1 pd iYBR270C
+Mcm4 pd iYBR270C
+Mcm4 pd iYBR274W
+Mcm7 pd iYBR275C
+Mcm3 pd iYBR275C
+Orc1 pd iYBR275C
+Mcm4 pd iYBR275C
+Mcm7 pd YBR276C
+Mcm3 pd YBR276C
+Mcm4 pd YBR276C
+Mcm7 pd YBR277C
+Mcm7 pd iYBR278W
+Mcm3 pd iYBR278W
+Mcm4 pd iYBR278W
+Mcm4 pd YBR284W
+Mcm7 pd iYBR284W
+Mcm3 pd iYBR284W
+Mcm4 pd iYBR284W
+Mcm7 pd YBR285W
+Mcm3 pd YBR285W
+Mcm4 pd YBR285W
+Mcm7 pd YBR286W
+Mcm3 pd YBR294W
+Orc_complex interactsWith iYBR294W
+Orc1 pd iYBR294W
+Mcm4 pd iYBR294W
+Mcm4 pd iYBR295W
+Mcm3 pd YBR297W
+Mcm7 pd iYBR297W
+Mcm3 pd iYBR297W
+Mcm4 pd iYBR297W
+Mcm3 pd YBR298C
+Mcm4 pd YBR298C
+Mcm7 pd YCL076W
+Orc_complex interactsWith YCL076W
+Orc1 pd YCL076W
+Orc_complex interactsWith YCL075W
+Orc1 pd YCL075W
+Orc1 pd YCL074W
+Orc1 pd iYCL074W
+Mcm7 pd iYCLWomega2-0
+Orc_complex interactsWith iYCLWomega2-0
+Mcm3 pd iYCLWomega2-0
+Orc1 pd iYCLWomega2-0
+Mcm4 pd iYCLWomega2-0
+Mcm7 pd iYCL069W
+Orc_complex interactsWith iYCL069W
+Mcm3 pd iYCL069W
+Orc1 pd iYCL069W
+Mcm4 pd iYCL069W
+Orc_complex interactsWith iYCL068C
+Orc1 pd iYCL068C
+Orc_complex interactsWith YCL067C
+Orc1 pd YCL067C
+Mcm7 pd iYCL067C
+Orc_complex interactsWith iYCL067C
+Mcm3 pd iYCL067C
+Orc1 pd iYCL067C
+Orc_complex interactsWith YCL066W
+Orc1 pd YCL066W
+Orc_complex interactsWith YCL065W
+Mcm3 pd YCL065W
+Orc1 pd YCL065W
+Mcm7 pd iYCL065W-0
+Orc_complex interactsWith iYCL065W-0
+Mcm3 pd iYCL065W-0
+Orc1 pd iYCL065W-0
+Mcm4 pd iYCL065W-0
+Mcm7 pd iYCL065W-1
+Orc_complex interactsWith iYCL065W-1
+Mcm3 pd iYCL065W-1
+Orc1 pd iYCL065W-1
+Mcm4 pd iYCL065W-1
+Mcm3 pd YCL064C
+Orc1 pd YCL064C
+Orc1 pd iYCL064C
+Mcm4 pd iYCL064C
+Mcm7 pd iYCL063W
+Mcm3 pd iYCL063W
+Orc1 pd iYCL063W
+Mcm4 pd iYCL063W
+Orc1 pd YCL050C
+Mcm7 pd iYCL050C
+Orc_complex interactsWith iYCL050C
+Mcm3 pd iYCL050C
+Orc1 pd iYCL050C
+Mcm4 pd iYCL050C
+Orc_complex interactsWith YCL049C
+Orc1 pd YCL049C
+Orc1 pd YCL048W
+Mcm7 pd iYCL048W
+Orc_complex interactsWith iYCL048W
+Mcm3 pd iYCL048W
+Orc1 pd iYCL048W
+Mcm4 pd iYCL048W
+Orc1 pd iYCL038C
+Mcm3 pd iYCL028W
+Mcm7 pd YCL004W
+Mcm3 pd YCL004W
+Mcm4 pd YCL004W
+Orc1 pd YCL001W
+Mcm7 pd YCR010C
+Orc_complex interactsWith YCR010C
+Mcm3 pd YCR010C
+Orc1 pd YCR010C
+Mcm4 pd YCR010C
+Orc1 pd YCR013C
+Orc1 pd iYCR020W-B
+Mcm3 pd YCR026C
+Mcm3 pd iYCR026C
+Orc1 pd iYCR026C
+Mcm4 pd iYCR026C
+Orc1 pd iSNR65
+Orc_complex interactsWith YCR036W
+Mcm4 pd YCR036W
+Mcm7 pd iYCR036W
+Orc_complex interactsWith iYCR036W
+Orc1 pd iYCR036W
+Mcm4 pd iYCR036W
+Mcm7 pd YCR038C
+Orc_complex interactsWith YCR038C
+Mcm3 pd YCR038C
+Orc1 pd YCR038C
+Mcm4 pd YCR038C
+Orc_complex interactsWith iYCR038C
+Orc1 pd iYCR038C
+Orc_complex interactsWith YCR039C
+Orc1 pd YCR039C
+Orc_complex interactsWith iYCR039C
+Orc1 pd iYCR039C
+Orc_complex interactsWith YCR040W
+Orc1 pd YCR040W
+Orc_complex interactsWith YCR041W
+Orc1 pd YCR041W
+Mcm4 pd YCR041W
+Mcm7 pd YCR057C
+Orc_complex interactsWith YCR057C
+Mcm3 pd YCR057C
+Orc1 pd YCR057C
+Mcm4 pd YCR057C
+Mcm3 pd YCR060W
+Orc1 pd YCR060W
+Mcm4 pd YCR060W
+Mcm7 pd iYCR060W
+Mcm3 pd iYCR060W
+Orc1 pd iYCR060W
+Mcm4 pd iYCR060W
+Orc1 pd YCR084C
+Mcm7 pd YCR087W
+Mcm3 pd YCR090C
+Mcm4 pd YCR090C
+Mcm7 pd iYCR090C-0
+Mcm3 pd iYCR090C-0
+Orc1 pd iYCR090C-0
+Mcm4 pd iYCR090C-0
+Orc1 pd iYCR095C-1
+Orc1 pd iYCRWdelta12
+Mcm7 pd YCR096C
+Orc_complex interactsWith YCR096C
+Mcm3 pd YCR096C
+Orc1 pd YCR096C
+Orc1 pd iYCR096C
+Mcm3 pd YCR097W
+Orc1 pd YCR097W
+Orc_complex interactsWith iYCR097W
+Mcm3 pd iYCR097W
+Orc1 pd iYCR097W
+Mcm4 pd iYCR097W
+Orc1 pd iYCRWdelta13
+Orc_complex interactsWith itT(AGU)C
+Orc1 pd itT(AGU)C
+Orc1 pd YCR104W
+Mcm4 pd YCR104W
+Orc_complex interactsWith YDL248W
+Mcm7 pd iYDL247W
+Mcm3 pd iYDL247W
+Mcm4 pd iYDL247W
+Mcm7 pd iYDL246C-1
+Mcm3 pd iYDL246C-1
+Mcm4 pd iYDL246C-1
+Mcm7 pd iYDL245C-1
+Mcm3 pd iYDL245C-1
+Mcm4 pd iYDL245C-1
+Mcm3 pd YDL244W
+Mcm7 pd YDL241W
+Mcm7 pd iYDL228C
+Orc_complex interactsWith iYDL228C
+Mcm3 pd iYDL228C
+Orc1 pd iYDL228C
+Mcm4 pd iYDL228C
+Mcm7 pd YDL227C
+Mcm3 pd YDL227C
+Orc1 pd YDL227C
+Mcm7 pd YDL210W
+Mcm3 pd YDL210W
+Mcm4 pd YDL210W
+Orc_complex interactsWith iYDL210W
+Mcm3 pd iYDL210W
+Orc1 pd iYDL210W
+Mcm4 pd iYDL210W
+Orc_complex interactsWith YDL209C
+Mcm7 pd iYDL189W
+Mcm3 pd iYDL189W
+Orc1 pd iYDL189W
+Mcm4 pd iYDL189W
+Mcm7 pd YDL187C
+Orc1 pd YDL187C
+Mcm7 pd YDL180W
+Mcm7 pd iYDL180W
+Mcm3 pd iYDL180W
+Mcm4 pd iYDL180W
+Mcm7 pd iYDL178W
+Mcm4 pd iYDL178W
+Mcm7 pd iYDL170W
+Mcm7 pd YDL169C
+Mcm3 pd YDL169C
+Mcm4 pd YDL169C
+Orc1 pd YDL158C
+Orc_complex interactsWith YDL154W
+Orc1 pd YDL150W
+Mcm3 pd YDL139C
+Mcm7 pd iYDL139C
+Orc_complex interactsWith iYDL139C
+Mcm3 pd iYDL139C
+Orc1 pd iYDL139C
+Mcm4 pd iYDL139C
+Mcm7 pd YDL136W
+Mcm3 pd YDL116W
+Orc1 pd YDL116W
+Mcm4 pd YDL116W
+Mcm7 pd iYDL116W
+Orc_complex interactsWith iYDL116W
+Mcm3 pd iYDL116W
+Orc1 pd iYDL116W
+Mcm4 pd iYDL116W
+Mcm7 pd YDL115C
+Orc_complex interactsWith YDL115C
+Mcm3 pd YDL115C
+Orc1 pd YDL115C
+Mcm4 pd YDL115C
+Mcm7 pd iYDL114W
+Orc_complex interactsWith iYDL114W
+Orc1 pd iYDL114W
+Mcm4 pd iYDL114W
+Orc1 pd YDL095W
+Orc_complex interactsWith YDL081C
+Orc1 pd YDL079C
+Mcm4 pd YDL079C
+Mcm3 pd YDL078C
+Mcm7 pd iYDL078C
+Mcm3 pd iYDL078C
+Orc1 pd iYDL078C
+Mcm4 pd iYDL078C
+Mcm7 pd YDL077C
+Orc_complex interactsWith YDL077C
+Mcm3 pd YDL077C
+Mcm4 pd YDL077C
+Mcm3 pd iYDL073W
+Orc1 pd iYDL073W
+Mcm4 pd iYDL073W
+Orc_complex interactsWith YDL072C
+Mcm3 pd YDL072C
+Mcm4 pd YDL072C
+Orc1 pd YDL064W
+Mcm7 pd YDL055C
+Mcm7 pd YDL042C
+Orc_complex interactsWith YDL042C
+Mcm3 pd YDL042C
+Mcm4 pd YDL042C
+Orc1 pd YDL031W
+Mcm3 pd iYDL025C
+Orc_complex interactsWith YDL024C
+Mcm3 pd YDL024C
+Mcm3 pd itA(AGC)D
+Orc1 pd YDL022W
+Orc1 pd iYDL019C
+Orc_complex interactsWith iYDLCdelta1-0
+Orc1 pd iYDLCdelta1-0
+Orc1 pd iYDLWtau1
+Mcm4 pd iYDL004W
+Mcm4 pd YDL003W
+Mcm7 pd YDR007W
+Orc_complex interactsWith YDR007W
+Orc1 pd YDR007W
+Mcm4 pd YDR007W
+Mcm7 pd YDR008C
+Orc_complex interactsWith YDR008C
+Mcm3 pd YDR008C
+Orc1 pd YDR008C
+Mcm4 pd YDR008C
+Mcm7 pd iYDR008C
+Orc_complex interactsWith iYDR008C
+Mcm3 pd iYDR008C
+Orc1 pd iYDR008C
+Mcm4 pd iYDR008C
+Mcm7 pd YDR018C
+Mcm3 pd YDR018C
+Mcm4 pd YDR018C
+Mcm7 pd iYDR018C
+Orc_complex interactsWith iYDR018C
+Mcm3 pd iYDR018C
+Orc1 pd iYDR018C
+Mcm4 pd iYDR018C
+Orc_complex interactsWith YDR019C
+Mcm7 pd iYDR032C-0
+Mcm3 pd iYDR032C-0
+Mcm7 pd YDR048C
+Mcm4 pd YDR048C
+Mcm7 pd YDR049W
+Orc_complex interactsWith YDR049W
+Mcm3 pd YDR049W
+Orc1 pd YDR049W
+Mcm4 pd YDR049W
+Mcm7 pd iYDR049W
+Orc_complex interactsWith iYDR049W
+Mcm3 pd iYDR049W
+Orc1 pd iYDR049W
+Mcm4 pd iYDR049W
+Mcm3 pd YDR050C
+Mcm3 pd iYDR051C
+Mcm7 pd iYDR057W
+Mcm4 pd iYDR057W
+Mcm7 pd YDR058C
+Mcm3 pd YDR058C
+Mcm4 pd YDR058C
+Mcm3 pd iYDR058C
+Orc1 pd itD(GUC)D
+Orc_complex interactsWith YDR070C
+Mcm7 pd iYDR091C
+Mcm4 pd iYDR091C
+Mcm3 pd YDR092W
+Mcm7 pd YDR094W
+Orc1 pd YDR094W
+Mcm7 pd iYDR096W
+Mcm3 pd iYDR096W
+Mcm4 pd iYDR096W
+Orc_complex interactsWith itQ(UUG)D2
+Orc1 pd itQ(UUG)D2
+Orc_complex interactsWith YDR124W
+Mcm3 pd YDR124W
+Mcm4 pd YDR124W
+Mcm7 pd YDR125C
+Orc_complex interactsWith YDR125C
+Mcm3 pd YDR125C
+Orc1 pd YDR125C
+Mcm4 pd YDR125C
+Mcm7 pd iYDR125C
+Orc_complex interactsWith iYDR125C
+Mcm3 pd iYDR125C
+Orc1 pd iYDR125C
+Mcm4 pd iYDR125C
+Mcm7 pd YDR126W
+Orc_complex interactsWith YDR126W
+Mcm3 pd YDR126W
+Orc1 pd YDR126W
+Mcm4 pd YDR126W
+Mcm4 pd iYDR132C
+Orc1 pd YDR141C
+Mcm7 pd YDR147W
+Orc_complex interactsWith YDR147W
+Mcm3 pd YDR147W
+Orc1 pd YDR147W
+Mcm4 pd YDR147W
+Mcm7 pd iYDR147W
+Orc_complex interactsWith iYDR147W
+Mcm3 pd iYDR147W
+Orc1 pd iYDR147W
+Mcm4 pd iYDR147W
+Orc_complex interactsWith YDR148C
+Orc1 pd YDR149C
+Orc1 pd iYDR150W
+Mcm7 pd iYDR152W
+Orc1 pd YDR156W
+Mcm7 pd iYDR170W-A-1
+Orc_complex interactsWith iYDR170W-A-1
+Mcm3 pd iYDR170W-A-1
+Orc1 pd iYDR170W-A-1
+Mcm4 pd iYDR170W-A-1
+Mcm7 pd YDR171W
+Mcm3 pd YDR171W
+Mcm4 pd YDR171W
+Mcm7 pd iYDR172W
+Mcm4 pd iYDR172W
+Mcm7 pd YDR186C
+Orc_complex interactsWith YDR186C
+Mcm3 pd YDR186C
+Orc1 pd YDR186C
+Mcm4 pd YDR186C
+Mcm7 pd YDR216W
+Mcm3 pd YDR216W
+Mcm4 pd YDR216W
+Mcm7 pd iYDR216W
+Mcm3 pd iYDR216W
+Mcm4 pd iYDR216W
+Orc1 pd YDR223W
+Mcm7 pd iYDR223W
+Orc_complex interactsWith iYDR223W
+Mcm3 pd iYDR223W
+Orc1 pd iYDR223W
+Mcm4 pd iYDR223W
+Orc1 pd iYDR225W
+Mcm7 pd iYDR227W
+Mcm3 pd iYDR227W
+Mcm4 pd iYDR227W
+Mcm7 pd iYDR229W
+Mcm3 pd iYDR229W
+Orc1 pd YDR235W
+Mcm4 pd YDR241W
+Orc_complex interactsWith YDR242W
+Mcm3 pd YDR243C
+Orc1 pd YDR258C
+Mcm7 pd iYDR277C
+Mcm3 pd iYDR277C
+Mcm4 pd iYDR277C
+Mcm7 pd YDR278C
+Mcm3 pd YDR278C
+Orc1 pd YDR278C
+Mcm4 pd YDR278C
+Mcm3 pd YDR285W
+Mcm4 pd YDR285W
+Mcm7 pd iYDR297W
+Orc_complex interactsWith iYDR297W
+Mcm3 pd iYDR297W
+Orc1 pd iYDR297W
+Mcm4 pd iYDR297W
+Orc_complex interactsWith YDR298C
+Mcm3 pd iYDR299W
+Orc1 pd iYDR299W
+Mcm4 pd iYDR299W
+Mcm3 pd YDRWdelta23
+Mcm7 pd iYDR321W
+Mcm3 pd iYDR321W
+Mcm7 pd iYDR342C-2
+Mcm3 pd iYDR342C-2
+Mcm4 pd iYDR342C-2
+Mcm3 pd YDR366C
+Mcm3 pd YDR381W
+Mcm7 pd YDR383C
+Orc_complex interactsWith YDR383C
+Mcm3 pd YDR383C
+Orc1 pd YDR383C
+Mcm4 pd YDR383C
+Mcm7 pd iYDR383C
+Orc_complex interactsWith iYDR383C
+Mcm3 pd iYDR383C
+Orc1 pd iYDR383C
+Mcm4 pd iYDR383C
+Orc1 pd iYDR385W
+Mcm7 pd YDR398W
+Mcm3 pd YDR398W
+Mcm4 pd YDR398W
+Mcm7 pd YDR403W
+Mcm7 pd iYDR403W
+Orc_complex interactsWith iYDR403W
+Mcm3 pd iYDR403W
+Orc1 pd iYDR403W
+Mcm4 pd iYDR403W
+Mcm7 pd iYDR418W
+Orc_complex interactsWith iYDR418W
+Mcm3 pd iYDR418W
+Orc1 pd iYDR418W
+Mcm4 pd iYDR418W
+Orc_complex interactsWith itS(AGA)D3
+Mcm3 pd itS(AGA)D3
+Orc1 pd itS(AGA)D3
+Mcm3 pd iYDR421W
+Mcm7 pd iYDR423C
+Mcm3 pd iYDR423C
+Mcm4 pd iYDR423C
+Mcm7 pd iYDRWdelta30
+Orc_complex interactsWith iYDRWdelta30
+Mcm3 pd iYDRWdelta30
+Orc1 pd iYDRWdelta30
+Mcm4 pd iYDRWdelta30
+Mcm7 pd YDR446W
+Orc_complex interactsWith YDR446W
+Mcm3 pd YDR446W
+Orc1 pd YDR446W
+Mcm4 pd YDR446W
+Orc_complex interactsWith iYDR447C
+Orc1 pd iYDR447C
+Mcm3 pd iYDR448W
+Mcm7 pd iYDR457W
+Mcm3 pd iYDR457W
+Mcm4 pd iYDR457W
+Mcm7 pd iYDR472W
+Orc_complex interactsWith iYDR472W
+Mcm3 pd iYDR472W
+Orc1 pd iYDR472W
+Mcm4 pd iYDR472W
+Mcm7 pd YDR473C
+Orc_complex interactsWith YDR473C
+Mcm3 pd YDR473C
+Mcm4 pd YDR473C
+Orc1 pd YDR498C
+Mcm7 pd iYDR498C
+Orc_complex interactsWith iYDR498C
+Mcm3 pd iYDR498C
+Orc1 pd iYDR498C
+Mcm4 pd iYDR498C
+Orc_complex interactsWith YDR499W
+Orc1 pd YDR499W
+Mcm7 pd iYDR502C
+Orc_complex interactsWith iYDR502C
+Mcm3 pd iYDR502C
+Orc1 pd iYDR502C
+Mcm4 pd iYDR502C
+Mcm7 pd itL(CAA)D
+Orc_complex interactsWith itL(CAA)D
+Mcm3 pd itL(CAA)D
+Orc1 pd itL(CAA)D
+Mcm4 pd itL(CAA)D
+Orc_complex interactsWith YDR507C
+Mcm3 pd YDR507C
+Orc1 pd YDR507C
+Mcm7 pd iYDR509W
+Mcm3 pd iYDR509W
+Orc1 pd iYDR509W
+Mcm4 pd iYDR509W
+Mcm7 pd iYDR511W
+Mcm3 pd iYDR511W
+Mcm4 pd iYDR511W
+Mcm7 pd YDR523C
+Mcm3 pd YDR523C
+Mcm4 pd YDR523C
+Mcm7 pd iYDR523C
+Orc1 pd iYDR523C
+Mcm4 pd iYDR523C
+Mcm7 pd YDR526C
+Mcm3 pd YDR526C
+Mcm3 pd YDR533C
+Mcm7 pd iYDR533C
+Orc_complex interactsWith iYDR533C
+Mcm3 pd iYDR533C
+Orc1 pd iYDR533C
+Mcm4 pd iYDR533C
+Mcm7 pd iYDR534C-1
+Orc_complex interactsWith iYDR534C-1
+Mcm3 pd iYDR534C-1
+Orc1 pd iYDR534C-1
+Mcm4 pd iYDR534C-1
+Mcm7 pd iYDR542W
+Orc_complex interactsWith iYDR542W
+Mcm3 pd iYDR542W
+Orc1 pd iYDR542W
+Mcm4 pd iYDR542W
+Mcm7 pd iYDR543C
+Orc_complex interactsWith iYDR543C
+Mcm3 pd iYDR543C
+Orc1 pd iYDR543C
+Mcm4 pd iYDR543C
+Mcm7 pd YDR544C
+Orc_complex interactsWith YDR544C
+Mcm3 pd YDR544C
+Orc1 pd YDR544C
+Mcm4 pd YDR544C
+Orc_complex interactsWith iYDR544C
+Mcm7 pd YDR545W
+Mcm3 pd YDR545W
+Mcm4 pd YDR545W
+Orc_complex interactsWith iYEL077C
+Orc1 pd iYEL077C
+Mcm7 pd YEL074W
+Orc_complex interactsWith YEL074W
+Mcm3 pd YEL074W
+Mcm7 pd iYEL074W
+Orc_complex interactsWith iYEL074W
+Mcm3 pd iYEL074W
+Orc1 pd iYEL074W
+Mcm4 pd iYEL074W
+Mcm4 pd YEL073C
+Mcm7 pd iYEL073C-1
+Orc_complex interactsWith iYEL073C-1
+Mcm3 pd iYEL073C-1
+Orc1 pd iYEL073C-1
+Mcm4 pd iYEL073C-1
+Mcm7 pd iYEL073C-3
+Orc_complex interactsWith iYEL073C-3
+Mcm3 pd iYEL073C-3
+Orc1 pd iYEL073C-3
+Mcm4 pd iYEL073C-3
+Mcm7 pd iYEL071W-0
+Mcm3 pd iYEL071W-0
+Mcm4 pd iYEL071W-0
+Mcm7 pd iYEL070W
+Mcm4 pd iYEL070W
+Orc_complex interactsWith YEL054C
+Mcm7 pd iYEL051W
+Orc_complex interactsWith iYEL051W
+Mcm3 pd iYEL051W
+Orc1 pd iYEL051W
+Mcm4 pd iYEL051W
+Mcm7 pd iSNR67
+Mcm7 pd itG(GCC)E
+Mcm7 pd YEL046C
+Mcm7 pd iYEL031W
+Orc_complex interactsWith iYEL031W
+Mcm3 pd iYEL031W
+Orc1 pd iYEL031W
+Mcm4 pd iYEL031W
+Mcm7 pd YEL023C
+Mcm3 pd YEL023C
+Mcm4 pd YEL023C
+Orc1 pd iYEL022W
+Orc1 pd YEL021W
+Mcm3 pd YEL006W
+Mcm7 pd iYEL006W
+Orc_complex interactsWith iYEL006W
+Mcm3 pd iYEL006W
+Orc1 pd iYEL006W
+Mcm4 pd iYEL006W
+Mcm7 pd YEL005C
+Mcm3 pd YEL005C
+Orc1 pd YEL005C
+Mcm4 pd YEL005C
+Orc1 pd YEL001C
+Mcm7 pd iYER010C-0
+Orc_complex interactsWith iYER010C-0
+Mcm3 pd iYER010C-0
+Orc1 pd iYER010C-0
+Mcm4 pd iYER010C-0
+Mcm7 pd iYER028C
+Orc_complex interactsWith iYER028C
+Mcm3 pd iYER028C
+Orc1 pd iYER028C
+Mcm4 pd iYER028C
+Mcm7 pd YER029C
+Orc_complex interactsWith YER029C
+Mcm3 pd YER029C
+Orc1 pd YER029C
+Mcm4 pd YER029C
+Mcm7 pd iYER030W
+Orc_complex interactsWith iYER030W
+Orc1 pd iYER030W
+Mcm4 pd iYER030W
+Orc_complex interactsWith iYER036C
+Mcm7 pd YER060W
+Mcm4 pd YER060W
+Mcm4 pd iYER060W
+Mcm7 pd iYER065C
+Orc_complex interactsWith iYER065C
+Orc1 pd iYER065C
+Mcm4 pd iYER065C
+Mcm3 pd iYERCdelta10
+Mcm4 pd YER071C
+Orc1 pd iYER077C
+Mcm4 pd iYER077C
+Mcm7 pd iYER096W
+Orc_complex interactsWith iYER096W
+Mcm3 pd iYER096W
+Orc1 pd iYER096W
+Mcm7 pd iYERWdelta12
+Orc_complex interactsWith iYERWdelta12
+Orc1 pd iYERWdelta12
+Mcm4 pd iYERWdelta12
+Orc1 pd YER119C
+Mcm4 pd YER123W
+Mcm7 pd iYER123W
+Mcm3 pd iYER123W
+Orc1 pd iYER123W
+Mcm4 pd iYER123W
+Mcm3 pd YER124C
+Mcm7 pd YER131W
+Mcm7 pd itV(AAC)E1
+Orc_complex interactsWith itV(AAC)E1
+Mcm3 pd itV(AAC)E1
+Orc1 pd itV(AAC)E1
+Mcm4 pd itV(AAC)E1
+Mcm4 pd YER136W
+Mcm3 pd YER137C
+Mcm7 pd iSCR1
+Orc_complex interactsWith iSCR1
+Mcm3 pd iSCR1
+Orc1 pd iSCR1
+Mcm4 pd iSCR1
+Mcm7 pd itI(AAU)E1
+Mcm3 pd itI(AAU)E1
+Mcm4 pd itI(AAU)E1
+Mcm7 pd YER154W
+Mcm7 pd iYERCdelta24
+Orc_complex interactsWith iYERCdelta24
+Mcm3 pd iYERCdelta24
+Orc1 pd iYERCdelta24
+Mcm4 pd iYERCdelta24
+Orc1 pd iYER162C
+Mcm3 pd iYER178W
+Mcm7 pd YER179W
+Mcm3 pd YER179W
+Mcm4 pd YER179W
+Mcm7 pd iYER179W
+Orc_complex interactsWith iYER179W
+Mcm3 pd iYER179W
+Orc1 pd iYER179W
+Mcm4 pd iYER179W
+Mcm7 pd YER180C
+Mcm4 pd YER180C
+Mcm3 pd YER181C
+Orc1 pd YER184C
+Mcm7 pd iYERWomega2-0
+Orc_complex interactsWith iYERWomega2-0
+Mcm3 pd iYERWomega2-0
+Orc1 pd iYERWomega2-0
+Mcm4 pd iYERWomega2-0
+Orc_complex interactsWith iYERWomega2-1
+Orc_complex interactsWith iYFL064C
+Mcm7 pd YFL063W
+Orc_complex interactsWith YFL063W
+Mcm3 pd YFL063W
+Orc1 pd YFL063W
+Mcm4 pd YFL063W
+Orc_complex interactsWith iYFL063W
+Orc1 pd iYFL063W
+Mcm3 pd iYFL059W
+Mcm4 pd iYFL059W
+Mcm3 pd YFL058W
+Mcm3 pd iYFL055W-0
+Mcm4 pd iYFL055W-0
+Mcm7 pd iYFL055W-1
+Orc_complex interactsWith iYFL055W-1
+Mcm3 pd iYFL055W-1
+Orc1 pd iYFL055W-1
+Mcm4 pd iYFL055W-1
+Orc1 pd iYFL051C-0
+Mcm7 pd iYFL051C-1
+Orc_complex interactsWith iYFL051C-1
+Mcm3 pd iYFL051C-1
+Orc1 pd iYFL051C-1
+Mcm4 pd iYFL051C-1
+Mcm7 pd iYFL049W
+Orc_complex interactsWith iYFL049W
+Mcm3 pd iYFL049W
+Orc1 pd iYFL049W
+Mcm4 pd iYFL049W
+Mcm7 pd iYFL047W
+Mcm3 pd iYFL047W
+Orc1 pd iYFL047W
+Mcm7 pd YFL041W
+Orc_complex interactsWith YFL041W
+Mcm4 pd YFL041W
+Mcm7 pd iYFL034W
+Mcm3 pd iYFL034W
+Mcm4 pd iYFL034W
+Mcm7 pd iYFL009W
+Orc_complex interactsWith iYFL009W
+Mcm3 pd iYFL009W
+Orc1 pd iYFL009W
+Mcm7 pd YFL003C
+Orc_complex interactsWith YFL003C
+Mcm3 pd YFL003C
+Orc1 pd YFL003C
+Mcm4 pd YFL003C
+Orc_complex interactsWith iYFL003C
+Mcm7 pd itY(GUA)F1
+Mcm3 pd itY(GUA)F1
+Orc1 pd itY(GUA)F1
+Mcm4 pd itY(GUA)F1
+Mcm7 pd YFR012W
+Mcm3 pd YFR012W
+Orc1 pd YFR012W
+Mcm4 pd YFR012W
+Orc_complex interactsWith YFR022W
+Mcm3 pd YFR022W
+Mcm7 pd iYFR022W
+Orc_complex interactsWith iYFR022W
+Mcm3 pd iYFR022W
+Orc1 pd iYFR022W
+Mcm4 pd iYFR022W
+Mcm7 pd YFR023W
+Orc1 pd YFR023W
+Mcm4 pd YFR023W
+Mcm7 pd iYFR024C-A
+Orc_complex interactsWith iYFR024C-A
+Orc1 pd iYFR024C-A
+Orc_complex interactsWith iYFR053C-0
+Orc1 pd iYFR053C-0
+Mcm7 pd iYFR053C-1
+Orc_complex interactsWith iYFR053C-1
+Mcm3 pd iYFR053C-1
+Orc1 pd iYFR053C-1
+Mcm4 pd iYFR053C-1
+Mcm3 pd YFR054C
+Mcm3 pd iYFR054C-0
+Mcm7 pd YFR057W
+Orc_complex interactsWith YFR057W
+Mcm3 pd YFR057W
+Orc1 pd YFR057W
+Mcm4 pd YFR057W
+Orc_complex interactsWith iYGL256W-0
+Mcm4 pd YGL250W
+Mcm4 pd iYGL250W
+Mcm7 pd YGL230C
+Orc_complex interactsWith YGL230C
+Mcm3 pd YGL230C
+Mcm4 pd YGL230C
+Mcm7 pd iYGL230C
+Orc_complex interactsWith iYGL230C
+Mcm3 pd iYGL230C
+Orc1 pd iYGL230C
+Mcm4 pd iYGL230C
+Orc_complex interactsWith YGL229C
+Orc1 pd YGL229C
+Mcm7 pd iYGL228W
+Orc_complex interactsWith iYGL228W
+Mcm3 pd iYGL228W
+Mcm4 pd iYGL228W
+Mcm4 pd iYGL226C-A
+Mcm7 pd YGL204C
+Orc_complex interactsWith YGL204C
+Mcm3 pd YGL204C
+Orc1 pd YGL204C
+Mcm4 pd YGL204C
+Mcm7 pd iYGL204C
+Orc_complex interactsWith iYGL204C
+Mcm3 pd iYGL204C
+Orc1 pd iYGL204C
+Mcm4 pd iYGL204C
+Mcm3 pd YGL203C
+Mcm3 pd iYGL203C
+Mcm4 pd iYGL203C
+Mcm7 pd iYGLWdelta3
+Orc_complex interactsWith iYGLWdelta3
+Mcm3 pd iYGLWdelta3
+Orc1 pd iYGLWdelta3
+Mcm4 pd iYGLWdelta3
+Mcm7 pd iYGL202W
+Mcm3 pd iYGL202W
+Mcm4 pd iYGL202W
+Mcm7 pd itK(CUU)G1
+Mcm3 pd itK(CUU)G1
+Orc_complex interactsWith iYGL180W
+Orc1 pd iYGL180W
+Orc_complex interactsWith YGL179C
+Mcm3 pd YGL179C
+Orc1 pd iYGL179C-1
+Mcm4 pd YGL169W
+Mcm4 pd iYGL169W
+Mcm7 pd YGL168W
+Mcm3 pd YGL168W
+Mcm4 pd YGL168W
+Mcm7 pd YGL159W
+Mcm3 pd YGL159W
+Mcm7 pd iYGL159W
+Mcm3 pd iYGL159W
+Mcm4 pd iYGL159W
+Mcm4 pd YGL145W
+Mcm7 pd iYGL145W
+Mcm7 pd iYGL141W
+Mcm3 pd iYGL141W
+Mcm4 pd iYGL141W
+Orc_complex interactsWith YGL130W
+Mcm7 pd YGL128C
+Orc_complex interactsWith YGL128C
+Mcm3 pd YGL128C
+Mcm4 pd YGL128C
+Orc_complex interactsWith YGL119W
+Mcm3 pd YGL119W
+Orc1 pd YGL119W
+Mcm7 pd iYGL119W
+Orc_complex interactsWith iYGL119W
+Mcm3 pd iYGL119W
+Orc1 pd iYGL119W
+Mcm4 pd iYGL119W
+Orc_complex interactsWith iYGL118C
+Mcm3 pd iYGL118C
+Orc1 pd iYGL118C
+Mcm4 pd iYGL118C
+Mcm7 pd iYGL084C
+Orc_complex interactsWith iYGL084C
+Mcm3 pd iYGL084C
+Orc1 pd iYGL084C
+Mcm4 pd iYGL084C
+Mcm3 pd YGL083W
+Mcm3 pd iYGL062W
+Mcm4 pd iYGL062W
+Mcm7 pd YGL061C
+Mcm3 pd YGL061C
+Mcm4 pd YGL061C
+Mcm7 pd iYGL040C-0
+Orc_complex interactsWith iYGL040C-0
+Mcm3 pd iYGL040C-0
+Orc1 pd iYGL040C-0
+Mcm4 pd iYGL040C-0
+Orc_complex interactsWith iYGL007W-0
+Mcm7 pd iYGL007W-1
+Mcm3 pd iYGL007W-1
+Orc1 pd iYGL007W-1
+Mcm4 pd iYGL007W-1
+Orc_complex interactsWith iYGL005C
+Mcm7 pd YGR004W
+Mcm7 pd iYGR008C
+Orc_complex interactsWith iYGR008C
+Mcm3 pd iYGR008C
+Orc1 pd iYGR008C
+Mcm4 pd iYGR008C
+Mcm4 pd YGR032W
+Mcm3 pd YGR034W
+Mcm7 pd iYGRCdelta16
+Mcm3 pd iYGRCdelta16
+Mcm4 pd iYGRCdelta16
+Orc_complex interactsWith iYGRCdelta18
+Orc1 pd iYGRCdelta18
+Mcm7 pd YGR039W
+Orc_complex interactsWith YGR039W
+Orc1 pd YGR039W
+Mcm4 pd YGR039W
+Mcm7 pd iYGR039W
+Mcm4 pd iYGR039W
+Mcm7 pd YGR040W
+Mcm4 pd YGR040W
+Mcm4 pd iYGR042W
+Orc_complex interactsWith iYGR043C-0
+Orc1 pd iYGR043C-0
+Mcm7 pd YGR069W
+Mcm3 pd YGR069W
+Mcm4 pd YGR069W
+Mcm7 pd YGR087C
+Orc_complex interactsWith YGR087C
+Mcm3 pd YGR087C
+Orc1 pd YGR087C
+Mcm4 pd YGR087C
+Mcm7 pd iYGR087C-0
+Mcm3 pd iYGR087C-0
+Mcm4 pd iYGR087C-0
+Mcm7 pd iYGR087C-1
+Mcm3 pd iYGR087C-1
+Mcm4 pd iYGR087C-1
+Mcm7 pd iYGR089W-0
+Orc_complex interactsWith iYGR089W-0
+Mcm3 pd iYGR089W-0
+Orc1 pd iYGR089W-0
+Mcm4 pd iYGR089W-0
+Mcm3 pd itT(UGU)G1
+Mcm3 pd iYGR090W
+Mcm3 pd YGR110W
+Mcm3 pd iYGR110W
+Orc1 pd iYGR110W
+Orc1 pd YGR125W
+Mcm4 pd YGR139W
+Mcm7 pd iYGR143W
+Mcm3 pd iYGR143W
+Mcm4 pd iYGR143W
+Mcm7 pd YGR152C
+Orc_complex interactsWith YGR152C
+Mcm3 pd YGR152C
+Orc1 pd YGR152C
+Mcm4 pd YGR152C
+Mcm7 pd YGR157W
+Mcm4 pd YGR160W
+Orc1 pd YGR164W
+Mcm4 pd YGR164W
+Mcm7 pd YGR168C
+Mcm3 pd YGR168C
+Mcm4 pd YGR168C
+Mcm7 pd iYGR168C
+Orc_complex interactsWith iYGR168C
+Mcm3 pd iYGR168C
+Orc1 pd iYGR168C
+Mcm4 pd iYGR168C
+Mcm7 pd YGR169C
+Orc_complex interactsWith YGR169C
+Orc1 pd YGR169C
+Mcm4 pd YGR169C
+Mcm7 pd YGR182C
+Orc1 pd YGR182C
+Mcm3 pd iYGR194C
+Orc1 pd iYGR194C
+Mcm4 pd iYGR211W
+Mcm7 pd YGR212W
+Mcm3 pd YGR212W
+Mcm4 pd YGR212W
+Orc_complex interactsWith YGR232W
+Mcm7 pd YGR243W
+Orc_complex interactsWith YGR243W
+Mcm3 pd YGR243W
+Mcm4 pd YGR243W
+Mcm7 pd iYGR243W
+Orc_complex interactsWith iYGR243W
+Mcm3 pd iYGR243W
+Orc1 pd iYGR243W
+Mcm4 pd iYGR243W
+Orc_complex interactsWith YGR246C
+Orc1 pd YGR246C
+Mcm4 pd YGR246C
+Mcm7 pd iYGR253C-0
+Orc_complex interactsWith iYGR253C-0
+Mcm3 pd iYGR253C-0
+Orc1 pd iYGR253C-0
+Mcm4 pd iYGR253C-0
+Mcm7 pd iYGR254W
+Mcm3 pd iYGR254W
+Mcm4 pd iYGR254W
+Mcm3 pd YGR286C
+Orc_complex interactsWith YGR294W
+Mcm7 pd iYGR295C-1
+Orc_complex interactsWith iYGR295C-1
+Mcm3 pd iYGR295C-1
+Orc1 pd iYGR295C-1
+Mcm4 pd iYGR295C-1
+Mcm7 pd iYHL049C-0
+Orc_complex interactsWith iYHL049C-0
+Mcm3 pd iYHL049C-0
+Orc1 pd iYHL049C-0
+Mcm4 pd iYHL049C-0
+Mcm7 pd iYHL049C-1
+Orc_complex interactsWith iYHL049C-1
+Mcm3 pd iYHL049C-1
+Orc1 pd iYHL049C-1
+Mcm4 pd iYHL049C-1
+Orc_complex interactsWith YHL048W
+Mcm7 pd iYHL048W
+Orc_complex interactsWith iYHL048W
+Mcm3 pd iYHL048W
+Orc1 pd iYHL048W
+Mcm4 pd iYHL048W
+Orc_complex interactsWith YHLComega1
+Orc1 pd YHLComega1
+Mcm7 pd iYHLComega1
+Orc_complex interactsWith iYHLComega1
+Mcm3 pd iYHLComega1
+Orc1 pd iYHLComega1
+Mcm4 pd iYHLComega1
+Mcm7 pd iYHL047C-0
+Orc_complex interactsWith iYHL047C-0
+Mcm3 pd iYHL047C-0
+Orc1 pd iYHL047C-0
+Mcm4 pd iYHL047C-0
+Orc_complex interactsWith iYHL047C-1
+Orc1 pd iYHL047C-1
+Mcm4 pd iYHL047C-1
+Orc_complex interactsWith YHL046C
+Mcm7 pd YHL043W
+Orc1 pd YHL037C
+Mcm7 pd YHL030W
+Mcm3 pd YHL030W
+Mcm7 pd iYHL030W
+Orc_complex interactsWith iYHL030W
+Mcm3 pd iYHL030W
+Mcm4 pd iYHL030W
+Mcm7 pd YHL029C
+Mcm7 pd YHL022C
+Orc_complex interactsWith YHL022C
+Mcm3 pd YHL022C
+Orc1 pd YHL022C
+Mcm4 pd YHL022C
+Mcm7 pd iYHL022C
+Orc_complex interactsWith iYHL022C
+Mcm3 pd iYHL022C
+Orc1 pd iYHL022C
+Mcm4 pd iYHL022C
+Mcm7 pd YHL021C
+Mcm3 pd YHL021C
+Orc1 pd YHL016C
+Orc_complex interactsWith iYHL011C
+Orc1 pd iYHL011C
+Orc_complex interactsWith iYHL009C
+Orc1 pd YHL006C
+Mcm3 pd YHR003C
+Mcm7 pd itT(AGU)H
+Orc_complex interactsWith itT(AGU)H
+Mcm3 pd itT(AGU)H
+Orc1 pd itT(AGU)H
+Mcm4 pd itT(AGU)H
+Orc1 pd YHR008C
+Orc1 pd iYHRCdelta5
+Mcm7 pd iYHRWdelta7
+Orc1 pd iYHRWdelta7
+Mcm4 pd iYHRWdelta7
+Mcm7 pd itQ(UUG)H
+Orc_complex interactsWith itQ(UUG)H
+Mcm3 pd itQ(UUG)H
+Orc1 pd itQ(UUG)H
+Mcm4 pd itQ(UUG)H
+Mcm3 pd YHR015W
+Mcm7 pd YHR029C
+Mcm3 pd YHR029C
+Orc1 pd YHR029C
+Mcm4 pd YHR029C
+Mcm7 pd iYHR029C
+Orc_complex interactsWith iYHR029C
+Orc1 pd iYHR029C
+Mcm4 pd iYHR029C
+Mcm7 pd YHR030C
+Orc1 pd YHR031C
+Orc_complex interactsWith YHR041C
+Mcm7 pd iYHR053C
+Mcm3 pd iYHR053C
+Mcm4 pd iYHR053C
+Mcm7 pd YHR054C
+Mcm3 pd YHR054C
+Orc1 pd YHR054C
+Mcm4 pd YHR054C
+Mcm7 pd iYHR055C
+Mcm3 pd iYHR055C
+Mcm4 pd iYHR055C
+Mcm3 pd YHR056C
+Mcm7 pd iYHR057C
+Mcm3 pd iYHR057C
+Mcm4 pd iYHR057C
+Mcm3 pd iYHR059W
+Mcm4 pd iYHR059W
+Mcm7 pd YHR060W
+Mcm7 pd iYHR072W
+Orc_complex interactsWith iYHR072W
+Orc1 pd iYHR072W
+Orc_complex interactsWith YHR073W
+Mcm3 pd YHR073W
+Orc1 pd YHR073W
+Mcm4 pd YHR073W
+Mcm7 pd iYHR073W
+Orc_complex interactsWith iYHR073W
+Mcm3 pd iYHR073W
+Orc1 pd iYHR073W
+Mcm4 pd iYHR073W
+Orc_complex interactsWith iYHR091C
+Orc1 pd iYHR091C
+Mcm7 pd iYHR096C
+Orc_complex interactsWith iYHR096C
+Mcm3 pd iYHR096C
+Orc1 pd iYHR096C
+Mcm4 pd iYHR096C
+Mcm7 pd YHR125W
+Mcm3 pd YHR125W
+Orc1 pd YHR125W
+Mcm4 pd YHR125W
+Mcm7 pd iYHRWdelta9
+Mcm3 pd iYHRWdelta9
+Orc1 pd iYHRWdelta9
+Mcm4 pd iYHRWdelta9
+Mcm7 pd YHR126C
+Orc_complex interactsWith YHR126C
+Mcm3 pd YHR126C
+Mcm4 pd YHR126C
+Mcm7 pd YHR130C
+Mcm4 pd YHR139C
+Mcm3 pd iYHR139C-A
+Mcm7 pd YHR140W
+Mcm3 pd YHR140W
+Mcm4 pd YHR140W
+Mcm4 pd iYHR140W
+Mcm7 pd iYHR146W
+Orc_complex interactsWith iYHR146W
+Mcm3 pd iYHR146W
+Orc1 pd iYHR146W
+Mcm4 pd iYHR146W
+Mcm3 pd YHR147C
+Orc1 pd YHR153C
+Mcm7 pd YHR171W
+Orc_complex interactsWith YHR171W
+Mcm3 pd YHR171W
+Orc1 pd YHR171W
+Orc1 pd YHR181W
+Mcm3 pd YHR184W
+Mcm7 pd iYHR184W
+Mcm3 pd iYHR184W
+Mcm4 pd iYHR184W
+Mcm7 pd YHR185C
+Mcm3 pd YHR185C
+Mcm4 pd YHR185C
+Mcm7 pd iYHR201C
+Orc_complex interactsWith iYHR201C
+Mcm3 pd iYHR201C
+Mcm4 pd iYHR201C
+Mcm3 pd YHR208W
+Mcm7 pd YHR209W
+Mcm3 pd YHR209W
+Mcm4 pd YHR209W
+Mcm3 pd YHR210C
+Orc_complex interactsWith YHR216W
+Mcm3 pd YHR216W
+Mcm7 pd YHR217C
+Orc_complex interactsWith YHR217C
+Mcm3 pd YHR217C
+Orc1 pd YHR217C
+Mcm4 pd YHR217C
+Mcm7 pd YHR219W
+Mcm3 pd YHR219W
+Mcm3 pd YIL177C
+Orc_complex interactsWith iYIL177C-0
+Mcm7 pd iYIL177C-1
+Orc_complex interactsWith iYIL177C-1
+Mcm3 pd iYIL177C-1
+Orc1 pd iYIL177C-1
+Mcm4 pd iYIL177C-1
+Orc_complex interactsWith YIL176C
+Orc_complex interactsWith iYIL174W-0
+Mcm7 pd iYIL174W-1
+Orc_complex interactsWith iYIL174W-1
+Mcm3 pd iYIL174W-1
+Orc1 pd iYIL174W-1
+Mcm4 pd iYIL174W-1
+Mcm7 pd iYIL173W
+Mcm3 pd iYIL173W
+Mcm4 pd iYIL173W
+Mcm3 pd iYIL167W
+Mcm4 pd iYIL167W
+Mcm7 pd iYIL166C
+Orc_complex interactsWith iYIL166C
+Mcm3 pd iYIL166C
+Orc1 pd iYIL166C
+Mcm4 pd iYIL166C
+Mcm7 pd YIL165C
+Orc_complex interactsWith YIL165C
+Mcm4 pd YIL165C
+Mcm7 pd iYIL156W
+Orc1 pd iYIL156W
+Mcm4 pd iYIL156W
+Mcm7 pd iYIL153W
+Mcm7 pd iYIL147C
+Orc_complex interactsWith iYIL147C
+Mcm3 pd iYIL147C
+Orc1 pd iYIL147C
+Mcm4 pd iYIL147C
+Mcm7 pd iYIL144W
+Mcm3 pd iYIL144W
+Mcm4 pd iYIL144W
+Mcm3 pd iYIL142W
+Mcm7 pd iYIL130W
+Mcm3 pd iYIL130W
+Mcm4 pd iYIL130W
+Mcm7 pd iYIL129C
+Mcm4 pd iYIL129C
+Mcm7 pd iYIL120W
+Orc_complex interactsWith iYIL120W
+Mcm3 pd iYIL120W
+Orc1 pd iYIL120W
+Mcm4 pd iYIL120W
+Mcm7 pd YIL101C
+Orc_complex interactsWith YIL101C
+Orc1 pd YIL101C
+Mcm4 pd YIL101C
+Mcm4 pd YIL092W
+Mcm7 pd iYIL078W
+Orc_complex interactsWith iYIL078W
+Mcm3 pd iYIL078W
+Orc1 pd iYIL078W
+Mcm4 pd iYIL078W
+Mcm7 pd YIL077C
+Mcm4 pd YIL077C
+Mcm4 pd YIL075C
+Mcm7 pd YIL073C
+Mcm3 pd YIL073C
+Orc_complex interactsWith YIL061C
+Orc1 pd YIL061C
+Orc_complex interactsWith iYIL061C
+Mcm3 pd iYIL061C
+Orc1 pd iYIL061C
+Orc1 pd YIL059C
+Mcm7 pd iYIL058W
+Orc_complex interactsWith iYIL058W
+Mcm3 pd iYIL058W
+Orc1 pd iYIL058W
+Mcm4 pd iYIL058W
+Mcm7 pd YIL057C
+Orc_complex interactsWith YIL057C
+Mcm3 pd YIL057C
+Orc1 pd YIL057C
+Mcm4 pd YIL057C
+Mcm7 pd iYIL057C
+Mcm3 pd iYIL057C
+Mcm4 pd iYIL057C
+Orc_complex interactsWith YIL027C
+Mcm7 pd YIL025C
+Mcm3 pd YIL025C
+Mcm4 pd YIL025C
+Mcm7 pd YIL024C
+Mcm3 pd YIL024C
+Mcm4 pd YIL024C
+Mcm7 pd YIL023C
+Mcm4 pd YIL023C
+Mcm7 pd iYIL023C
+Orc_complex interactsWith iYIL023C
+Orc1 pd iYIL023C
+Mcm4 pd iYIL023C
+Mcm7 pd iYIL021W
+Orc_complex interactsWith iYIL021W
+Orc1 pd iYIL021W
+Mcm4 pd iYIL021W
+Mcm4 pd iYIL017C
+Mcm7 pd iYIL009W
+Orc_complex interactsWith iYIL009W
+Mcm3 pd iYIL009W
+Orc1 pd iYIL009W
+Mcm4 pd iYIL009W
+Mcm3 pd YIR001C
+Mcm4 pd YIR001C
+Mcm7 pd iYIR001C
+Mcm3 pd iYIR001C
+Orc1 pd iYIR001C
+Mcm4 pd iYIR001C
+Mcm3 pd YIR002C
+Mcm7 pd iYIR003W
+Orc_complex interactsWith iYIR003W
+Mcm3 pd iYIR003W
+Mcm4 pd iYIR003W
+Orc1 pd YIR009W
+Orc_complex interactsWith YIR027C
+Mcm3 pd YIR027C
+Mcm4 pd YIR027C
+Mcm7 pd YIR029W
+Orc_complex interactsWith YIR029W
+Mcm3 pd YIR029W
+Mcm4 pd YIR029W
+Mcm7 pd iYIR029W
+Orc_complex interactsWith iYIR029W
+Mcm3 pd iYIR029W
+Orc1 pd iYIR029W
+Mcm4 pd iYIR029W
+Mcm7 pd YIR030C
+Orc_complex interactsWith YIR030C
+Mcm3 pd YIR030C
+Orc1 pd YIR030C
+Mcm4 pd YIR030C
+Mcm7 pd YJL225C
+Mcm3 pd YJL225C
+Mcm4 pd YJL225C
+Orc_complex interactsWith iYJL225C-0
+Orc1 pd iYJL225C-0
+Mcm7 pd iYJL225C-1
+Orc_complex interactsWith iYJL225C-1
+Mcm3 pd iYJL225C-1
+Orc1 pd iYJL225C-1
+Mcm4 pd iYJL225C-1
+Orc_complex interactsWith YJL223C
+Mcm7 pd iYJL222W
+Mcm3 pd iYJL222W
+Mcm4 pd iYJL222W
+Mcm7 pd YJL217W
+Mcm3 pd YJL217W
+Mcm4 pd YJL217W
+Mcm7 pd iYJL217W
+Orc_complex interactsWith iYJL217W
+Mcm3 pd iYJL217W
+Orc1 pd iYJL217W
+Mcm4 pd iYJL217W
+Mcm7 pd iYJL215C
+Orc_complex interactsWith iYJL215C
+Mcm3 pd iYJL215C
+Orc1 pd iYJL215C
+Mcm4 pd iYJL215C
+Orc_complex interactsWith YJL210W
+Mcm7 pd iYJL197W
+Orc_complex interactsWith iYJL197W
+Orc1 pd iYJL197W
+Mcm4 pd iYJL197W
+Mcm7 pd YJL196C
+Mcm3 pd YJL196C
+Orc1 pd YJL196C
+Mcm4 pd YJL196C
+Orc_complex interactsWith iYJL172W
+Mcm3 pd iYJL172W
+Orc1 pd iYJL172W
+Orc1 pd YJL171C
+Orc1 pd YJL168C
+Orc_complex interactsWith YJL163C
+Mcm7 pd iYJL163C
+Orc_complex interactsWith iYJL163C
+Mcm3 pd iYJL163C
+Orc1 pd iYJL163C
+Orc_complex interactsWith itE(UUC)J
+Mcm7 pd YJL151C
+Mcm7 pd YJL132W
+Mcm4 pd YJL128C
+Mcm7 pd YJL124C
+Orc_complex interactsWith YJL124C
+Mcm3 pd YJL124C
+Orc1 pd YJL124C
+Orc_complex interactsWith itD(GUC)J1
+Orc1 pd itD(GUC)J1
+Mcm3 pd YJL104W
+Mcm7 pd isnR37
+Orc_complex interactsWith isnR37
+Mcm3 pd isnR37
+Orc1 pd isnR37
+Mcm4 pd isnR37
+Mcm3 pd YJL103C
+Orc1 pd YJL103C
+Mcm4 pd YJL103C
+Mcm7 pd YJL099W
+Mcm7 pd iYJL098W
+Mcm7 pd YJL075C
+Mcm4 pd YJL075C
+Mcm7 pd iYJL075C
+Mcm3 pd iYJL075C
+Mcm3 pd YJL074C
+Orc_complex interactsWith YJL062W
+Mcm7 pd YJL053W
+Orc_complex interactsWith YJL053W
+Mcm3 pd YJL053W
+Mcm7 pd iYJL053W
+Orc_complex interactsWith iYJL053W
+Mcm3 pd iYJL053W
+Orc1 pd iYJL053W
+Mcm4 pd iYJL053W
+Mcm3 pd iYJL051W
+Orc1 pd iYJL051W
+Mcm4 pd iYJL051W
+Mcm4 pd iYJL046W
+Mcm4 pd itY(GUA)J1
+Mcm7 pd itR(UCU)J2
+Orc_complex interactsWith itR(UCU)J2
+Mcm3 pd itR(UCU)J2
+Orc1 pd itR(UCU)J2
+Mcm4 pd itR(UCU)J2
+Mcm7 pd iYJLCdelta6
+Mcm3 pd iYJLCdelta6
+Mcm4 pd iYJLCdelta6
+Mcm7 pd YJL038C
+Orc_complex interactsWith YJL038C
+Mcm3 pd YJL038C
+Orc1 pd YJL038C
+Mcm4 pd YJL038C
+Mcm3 pd iYJL038C
+Orc1 pd iYJL038C
+Mcm4 pd iYJL038C
+Orc_complex interactsWith iYJL036W
+Orc1 pd itM(CAU)J1
+Orc_complex interactsWith iYJL013C
+Orc1 pd iYJL013C
+Mcm4 pd YJLWdelta9
+Mcm7 pd iYJLWdelta9
+Orc_complex interactsWith iYJLWdelta9
+Mcm3 pd iYJLWdelta9
+Orc1 pd iYJLWdelta9
+Mcm4 pd iYJLWdelta9
+Mcm7 pd YJL010C
+Orc_complex interactsWith YJL010C
+Mcm7 pd iYJL008C
+Mcm3 pd iYJL008C
+Orc1 pd iYJL008C
+Mcm7 pd itM(CAU)J2
+Orc_complex interactsWith YJR003C
+Mcm3 pd YJR003C
+Mcm4 pd YJR003C
+Mcm7 pd iYJR003C
+Orc_complex interactsWith iYJR003C
+Mcm3 pd iYJR003C
+Orc1 pd iYJR003C
+Mcm4 pd iYJR003C
+Orc_complex interactsWith YJR004C
+Orc1 pd iYJR009C-0
+Mcm4 pd iYJR009C-0
+Mcm3 pd YJR011C
+Mcm4 pd iYJR011C
+Mcm4 pd iYJR015W
+Orc_complex interactsWith YJR020W
+Orc1 pd YJR021C
+Orc_complex interactsWith YJR044C
+Mcm7 pd iYJR044C
+Orc_complex interactsWith iYJR044C
+Mcm3 pd iYJR044C
+Mcm4 pd iYJR044C
+Mcm7 pd iYJR046W
+Orc_complex interactsWith itS(AGA)J
+Orc1 pd itS(AGA)J
+Mcm7 pd iYJR055W
+Orc_complex interactsWith iYJR055W
+Mcm3 pd iYJR055W
+Orc1 pd iYJR055W
+Mcm4 pd iYJR055W
+Mcm7 pd itD(GUC)J4
+Mcm3 pd itD(GUC)J4
+Orc1 pd itD(GUC)J4
+Mcm4 pd iYJR094W-A
+Mcm7 pd YJR097W
+Orc_complex interactsWith YJR097W
+Mcm3 pd YJR097W
+Orc1 pd YJR097W
+Mcm7 pd iYJR097W
+Orc_complex interactsWith iYJR097W
+Mcm3 pd iYJR097W
+Orc1 pd iYJR097W
+Mcm4 pd iYJR097W
+Mcm7 pd YJR115W
+Mcm3 pd YJR115W
+Mcm4 pd YJR115W
+Mcm3 pd YJR118C
+Mcm4 pd YJR118C
+Mcm7 pd iYJR118C
+Mcm4 pd iYJR118C
+Mcm4 pd YJR119C
+Mcm3 pd YJR124C
+Mcm3 pd iYJR124C
+Mcm7 pd iYJR137C
+Orc_complex interactsWith iYJR137C
+Mcm3 pd iYJR137C
+Orc1 pd iYJR137C
+Mcm4 pd iYJR137C
+Mcm7 pd iYJR139C
+Orc_complex interactsWith iYJR139C
+Mcm3 pd iYJR139C
+Orc1 pd iYJR139C
+Mcm4 pd iYJR139C
+Mcm7 pd iYJR144W
+Orc_complex interactsWith iYJR144W
+Mcm3 pd iYJR144W
+Mcm4 pd iYJR144W
+Orc1 pd YJR147W
+Mcm7 pd iYJR150C-1
+Mcm3 pd iYJR150C-1
+Mcm4 pd iYJR150C-1
+Mcm3 pd YJR156C
+Mcm4 pd YJR156C
+Mcm7 pd iYJR156C
+Mcm3 pd iYJR156C
+Mcm4 pd iYJR156C
+Mcm7 pd YJR157W
+Mcm3 pd YJR157W
+Mcm4 pd YJR157W
+Mcm7 pd iYJR159W
+Mcm3 pd iYJR159W
+Mcm4 pd iYJR159W
+Mcm4 pd iYJR160C-1
+Orc_complex interactsWith YJR161C
+Mcm7 pd iYJR161C
+Orc_complex interactsWith iYJR161C
+Mcm3 pd iYJR161C
+Orc1 pd iYJR161C
+Mcm4 pd iYJR161C
+Mcm7 pd YJR162C
+Orc_complex interactsWith YJR162C
+Mcm3 pd YJR162C
+Mcm7 pd YKL225W
+Orc_complex interactsWith YKL225W
+Mcm3 pd YKL225W
+Orc1 pd YKL225W
+Mcm4 pd YKL225W
+Mcm7 pd iYKL225W
+Orc_complex interactsWith iYKL225W
+Mcm3 pd iYKL225W
+Orc1 pd iYKL225W
+Mcm4 pd iYKL225W
+Orc_complex interactsWith iYKL224C
+Mcm3 pd iYKL224C
+Orc1 pd iYKL224C
+Mcm7 pd iYKL223W
+Orc_complex interactsWith iYKL223W
+Mcm3 pd iYKL223W
+Orc1 pd iYKL223W
+Mcm4 pd iYKL223W
+Mcm7 pd iYKL221W-0
+Mcm3 pd iYKL221W-0
+Mcm4 pd iYKL221W-0
+Mcm7 pd iYKL221W-1
+Mcm4 pd iYKL221W-1
+Mcm3 pd YKL219W
+Mcm7 pd YKL212W
+Orc_complex interactsWith iYKL204W
+Orc1 pd iYKL204W
+Mcm7 pd YKL203C
+Orc_complex interactsWith YKL203C
+Mcm3 pd YKL203C
+Mcm4 pd YKL203C
+Mcm3 pd iYKL189W
+Orc1 pd iYKL189W
+Mcm7 pd iYKL188C
+Mcm3 pd iYKL188C
+Mcm4 pd iYKL188C
+Orc_complex interactsWith YKL184W
+Mcm3 pd YKL183W
+Mcm7 pd YKL178C
+Mcm3 pd YKL178C
+Mcm4 pd YKL178C
+Orc_complex interactsWith YKL177W
+Mcm4 pd YKL177W
+Orc1 pd YKL169C
+Mcm7 pd YKL160W
+Orc_complex interactsWith YKL160W
+Mcm3 pd YKL160W
+Orc1 pd YKL160W
+Mcm4 pd YKL160W
+Mcm3 pd YKL159C
+Mcm7 pd YKL153W
+Mcm3 pd YKL152C
+Mcm7 pd YKL144C
+Orc1 pd YKL139W
+Mcm4 pd YKL136W
+Mcm3 pd YKL131W
+Orc_complex interactsWith YKL123W
+Mcm4 pd iYKL123W
+Mcm3 pd YKL122C
+Mcm4 pd YKL107W
+Orc1 pd YKL104C
+Mcm7 pd iYKL104C
+Mcm7 pd YKL098W
+Orc_complex interactsWith YKL098W
+Mcm3 pd YKL098W
+Orc1 pd YKL098W
+Mcm4 pd YKL098W
+Orc_complex interactsWith iYKL098W
+Orc1 pd iYKL098W
+Mcm4 pd iYKL084W
+Orc_complex interactsWith iYKLWdelta7
+Orc1 pd iYKLWdelta7
+Orc1 pd YKL066W
+Orc1 pd YKL062W
+Mcm7 pd iYKL059C
+Orc_complex interactsWith iYKL059C
+Mcm3 pd iYKL059C
+Orc1 pd iYKL059C
+Mcm4 pd iYKL059C
+Mcm3 pd YKL058W
+Orc1 pd YKL058W
+Mcm4 pd YKL058W
+Mcm7 pd iYKL057C
+Orc_complex interactsWith iYKL057C
+Mcm3 pd iYKL057C
+Orc1 pd iYKL057C
+Mcm4 pd iYKL057C
+Mcm7 pd YKL031W
+Orc_complex interactsWith YKL031W
+Mcm3 pd YKL031W
+Orc1 pd YKL031W
+Mcm4 pd YKL031W
+Mcm7 pd YKL029C
+Orc1 pd YKL027W
+Mcm7 pd iYKL027W
+Orc_complex interactsWith iYKL027W
+Mcm3 pd iYKL027W
+Orc1 pd iYKL027W
+Mcm4 pd iYKL027W
+Mcm7 pd YKL026C
+Mcm3 pd YKL026C
+Orc1 pd YKL026C
+Mcm4 pd YKL026C
+Orc1 pd YKL025C
+Orc_complex interactsWith iYKL025C
+Mcm3 pd iYKL015W
+Mcm4 pd iYKL015W
+Orc_complex interactsWith iYKL014C
+Orc1 pd iYKL014C
+Mcm7 pd YKL013C
+Orc_complex interactsWith YKL013C
+Mcm3 pd YKL013C
+Orc1 pd YKL013C
+Mcm4 pd YKL013C
+Orc_complex interactsWith YKR004C
+Mcm3 pd YKR004C
+Orc_complex interactsWith iYKR004C
+Orc1 pd iYKR004C
+Orc_complex interactsWith YKR005C
+Orc1 pd YKR005C
+Orc1 pd iYKR006C
+Mcm4 pd iYKR008W
+Mcm7 pd iYKRCdelta8
+Orc_complex interactsWith iYKR011C
+Orc1 pd iYKR011C
+Mcm4 pd YKR030W
+Orc_complex interactsWith iYKR039W
+Orc1 pd iYKR039W
+Orc_complex interactsWith YKR040C
+Mcm3 pd iYKR042W
+Mcm7 pd YKR050W
+Orc_complex interactsWith YKR050W
+Mcm4 pd YKR050W
+Mcm7 pd iYKR050W
+Mcm3 pd iYKR050W
+Mcm4 pd iYKR050W
+Mcm7 pd YKR051W
+Mcm3 pd YKR051W
+Orc_complex interactsWith iYKR075C-1
+Orc1 pd iYKR075C-1
+Orc_complex interactsWith YKR076W
+Mcm3 pd YKR076W
+Mcm4 pd YKR076W
+Mcm4 pd iYKR076W
+Orc_complex interactsWith iYKR077W
+Orc1 pd iYKR077W
+Mcm7 pd iYKR082W
+Mcm3 pd iYKR082W
+Mcm4 pd iYKR082W
+Mcm7 pd YKR091W
+Orc_complex interactsWith YKR091W
+Mcm3 pd YKR091W
+Orc_complex interactsWith iYKR091W
+Orc1 pd iYKR091W
+Mcm7 pd iYKR093W
+Mcm4 pd iYKR093W
+Mcm7 pd YKR098C
+Mcm4 pd YKR098C
+Orc_complex interactsWith YKR101W
+Orc_complex interactsWith iYKR101W-0
+Orc1 pd iYKR101W-0
+Orc1 pd iYKR104W
+Orc_complex interactsWith YKR105C
+Orc1 pd YKR105C
+Orc_complex interactsWith iYKR106W-0
+Mcm3 pd iYKR106W-1
+Orc_complex interactsWith iYLL067C-1
+Mcm7 pd YLL065W
+Orc_complex interactsWith YLL065W
+Mcm3 pd YLL065W
+Orc1 pd YLL065W
+Mcm4 pd YLL065W
+Orc_complex interactsWith iYLL065W
+Orc_complex interactsWith iYLL063C
+Orc1 pd iYLL063C
+Orc_complex interactsWith YLL055W
+Mcm3 pd YLL055W
+Orc1 pd YLL055W
+Orc1 pd YLL046C
+Mcm4 pd YLL044W
+Mcm7 pd iYLL043W
+Mcm7 pd YLL042C
+Mcm3 pd YLL042C
+Mcm4 pd YLL042C
+Mcm7 pd YLL034C
+Orc_complex interactsWith YLL034C
+Mcm3 pd YLL034C
+Orc1 pd YLL034C
+Mcm4 pd YLL034C
+Mcm7 pd iYLL032C
+Mcm3 pd iYLL032C
+Mcm4 pd iYLL032C
+Orc1 pd YLL030C
+Mcm7 pd iYLL026W
+Orc_complex interactsWith iYLL026W
+Mcm3 pd iYLL026W
+Orc1 pd iYLL026W
+Mcm4 pd iYLL026W
+Mcm3 pd itP(UGG)L-0
+Mcm4 pd itP(UGG)L-0
+Mcm3 pd itP(UGG)L-1
+Orc1 pd YLL007C
+Mcm7 pd YLL005C
+Mcm3 pd YLL005C
+Mcm4 pd YLL005C
+Mcm3 pd YLR002C
+Mcm7 pd iYLR002C
+Orc_complex interactsWith iYLR002C
+Mcm3 pd iYLR002C
+Orc1 pd iYLR002C
+Mcm4 pd iYLR002C
+Mcm7 pd YLR003C
+Mcm3 pd YLR003C
+Mcm4 pd YLR003C
+Mcm4 pd YLR013W
+Mcm7 pd YLR036C
+Mcm3 pd YLR036C
+Mcm4 pd YLR036C
+Mcm7 pd iYLR036C
+Mcm4 pd iYLR036C
+Mcm7 pd iYLR042C
+Mcm3 pd iYLR042C
+Orc_complex interactsWith YLR043C
+Mcm3 pd YLR043C
+Mcm4 pd YLR043C
+Mcm3 pd YLR044C
+Orc_complex interactsWith YLR049C
+Mcm7 pd iYLR060W
+Mcm4 pd YLR076C
+Mcm7 pd YLR080W
+Orc_complex interactsWith YLR080W
+Mcm3 pd YLR080W
+Orc1 pd YLR080W
+Mcm4 pd YLR080W
+Mcm7 pd iYLR080W
+Orc_complex interactsWith iYLR080W
+Mcm3 pd iYLR080W
+Orc1 pd iYLR080W
+Mcm4 pd iYLR080W
+Mcm4 pd YLR101C
+Mcm4 pd YLR110C
+Mcm7 pd iYLR113W
+Mcm3 pd iYLR113W
+Orc1 pd iYLR113W
+Mcm4 pd iYLR113W
+Orc_complex interactsWith iYLR117C
+Orc1 pd iYLR117C
+Mcm7 pd iYLR134W
+Orc_complex interactsWith iYLR134W
+Mcm3 pd iYLR134W
+Orc1 pd iYLR134W
+Mcm4 pd iYLR134W
+Orc_complex interactsWith iYLR136C
+Mcm3 pd iYLR136C
+Orc1 pd iYLR136C
+Orc_complex interactsWith iYLRWdelta6-0
+Orc1 pd iYLRWdelta6-0
+Orc_complex interactsWith YLR155C
+Orc_complex interactsWith YLR162W
+Mcm3 pd YLR177W
+Orc1 pd YLR177W
+Mcm3 pd iYLR177W
+Orc_complex interactsWith YLR178C
+Mcm3 pd YLR178C
+Mcm7 pd iYLR228C-0
+Mcm3 pd iYLR228C-0
+Mcm4 pd iYLR228C-0
+Orc_complex interactsWith iYLR228C-1
+Orc1 pd iYLR228C-1
+Mcm4 pd YLR232W
+Mcm7 pd iYLR241W
+Mcm4 pd iYLR241W
+Mcm7 pd YLR242C
+Mcm3 pd YLR242C
+Mcm4 pd YLR242C
+Mcm7 pd iYLR244C
+Mcm3 pd iYLR244C
+Mcm3 pd iYLR246W
+Mcm4 pd iYLR246W
+Orc_complex interactsWith YLR257W
+Orc1 pd YLR257W
+Mcm7 pd iYLR257W
+Orc_complex interactsWith iYLR257W
+Mcm3 pd iYLR257W
+Orc1 pd iYLR257W
+Mcm4 pd iYLR257W
+Mcm4 pd iYLR272C
+Mcm4 pd iYLRWdelta17
+Orc1 pd YLR287C
+Mcm4 pd YLR287C
+Mcm7 pd YLR293C
+Orc_complex interactsWith YLR293C
+Mcm4 pd YLR293C
+Orc_complex interactsWith YLR300W
+Mcm7 pd iYLR300W
+Orc_complex interactsWith iYLR300W
+Mcm3 pd iYLR300W
+Orc1 pd iYLR300W
+Mcm4 pd iYLR300W
+Mcm7 pd YLR301W
+Mcm3 pd YLR301W
+Mcm4 pd YLR301W
+Mcm7 pd iYLRCdelta18
+Orc1 pd iYLRCdelta18
+Mcm7 pd YLR306W
+Mcm3 pd YLR306W
+Mcm4 pd YLR306W
+Mcm7 pd iYLR306W
+Orc_complex interactsWith iYLR306W
+Mcm3 pd iYLR306W
+Orc1 pd iYLR306W
+Mcm4 pd iYLR306W
+Orc1 pd YLR307W
+Mcm7 pd iYLR308W
+Mcm3 pd iYLR308W
+Mcm4 pd iYLR308W
+Mcm7 pd YLR319C
+Orc_complex interactsWith YLR319C
+Mcm3 pd YLR319C
+Mcm4 pd YLR328W
+Mcm7 pd iYLR328W
+Mcm4 pd iYLR328W
+Mcm4 pd YLR329W
+Mcm7 pd itD(GUC)L2
+Orc_complex interactsWith itD(GUC)L2
+Mcm3 pd itD(GUC)L2
+Orc1 pd itD(GUC)L2
+Mcm4 pd itD(GUC)L2
+Orc_complex interactsWith iSNR55
+Mcm3 pd iSNR55
+Orc1 pd iSNR55
+Mcm4 pd iSNR55
+Mcm4 pd YLR342W
+Mcm7 pd iYLR345W
+Orc_complex interactsWith iYLR345W
+Mcm3 pd iYLR345W
+Orc1 pd iYLR345W
+Mcm4 pd iYLR345W
+Mcm7 pd iYLR346C
+Mcm3 pd iYLR346C
+Mcm4 pd iYLR346C
+Orc_complex interactsWith iYLR354C
+Mcm3 pd YLR355C
+Mcm7 pd YLR383W
+Mcm3 pd YLR383W
+Orc_complex interactsWith YLR384C
+Mcm7 pd YLR399C
+Orc_complex interactsWith YLR399C
+Mcm3 pd YLR399C
+Mcm4 pd YLR399C
+Mcm7 pd iYLR403W
+Orc_complex interactsWith iYLR403W
+Mcm3 pd iYLR403W
+Orc1 pd iYLR403W
+Mcm4 pd iYLR403W
+Mcm3 pd YLR404W
+Orc_complex interactsWith YLR405W
+Mcm7 pd iYLR405W
+Mcm3 pd iYLR405W
+Mcm4 pd iYLR405W
+Orc1 pd YLR406C
+Mcm7 pd YLR408C
+Mcm7 pd YLR411W
+Mcm3 pd YLR411W
+Mcm4 pd YLR411W
+Mcm7 pd iYLR411W
+Mcm3 pd iYLR411W
+Mcm4 pd iYLR411W
+Mcm7 pd YLR412W
+Mcm3 pd YLR412W
+Mcm4 pd YLR412W
+Mcm3 pd iYLR412W-0
+Orc1 pd YLR414C
+Orc1 pd YLR434C
+Mcm7 pd iYLR435W
+Mcm3 pd iYLR435W
+Orc1 pd iYLR435W
+Mcm4 pd iYLR435W
+Mcm7 pd YLR438W
+Mcm4 pd YLR438W
+Mcm7 pd iYLR444C
+Orc_complex interactsWith iYLR444C
+Mcm3 pd iYLR444C
+Orc1 pd iYLR444C
+Mcm7 pd YLR445W
+Orc_complex interactsWith YLR445W
+Mcm3 pd YLR445W
+Orc1 pd YLR445W
+Mcm4 pd YLR445W
+Orc_complex interactsWith iYLR445W
+Orc1 pd iYLR445W
+Mcm3 pd YLR452C
+Mcm7 pd YLR453C
+Mcm7 pd iYLR459W
+Mcm3 pd iYLR459W
+Mcm4 pd iYLR459W
+Mcm7 pd iYLR461W-0
+Orc_complex interactsWith iYLR461W-0
+Mcm3 pd iYLR461W-0
+Orc1 pd iYLR461W-0
+Mcm4 pd iYLR461W-0
+Orc_complex interactsWith iYLR461W-1
+Orc1 pd iYLR461W-1
+Mcm7 pd iYLR466W
+Mcm3 pd iYLR466W
+Mcm4 pd iYLR466W
+Orc_complex interactsWith iYML133C-0
+Mcm7 pd iYML133C-1
+Orc_complex interactsWith iYML133C-1
+Mcm3 pd iYML133C-1
+Orc1 pd iYML133C-1
+Mcm4 pd iYML133C-1
+Orc_complex interactsWith YML132W
+Orc_complex interactsWith iYML132W-0
+Orc_complex interactsWith iYML132W-1
+Mcm3 pd iYML132W-1
+Mcm3 pd iYML130C
+Mcm7 pd YML119W
+Orc_complex interactsWith YML119W
+Mcm3 pd YML119W
+Mcm4 pd YML119W
+Mcm7 pd iYML119W
+Orc_complex interactsWith iYML119W
+Mcm3 pd iYML119W
+Orc1 pd iYML119W
+Mcm4 pd iYML119W
+Mcm7 pd iYML116W
+Orc_complex interactsWith iYML116W
+Mcm3 pd iYML116W
+Mcm4 pd iYML116W
+Mcm7 pd YML115C
+Mcm4 pd YML115C
+Mcm7 pd iYML105C
+Mcm3 pd iYML105C
+Mcm7 pd iYML100W
+Mcm4 pd iYML100W
+Mcm4 pd YML091C
+Mcm7 pd YML087C
+Mcm3 pd YML087C
+Mcm4 pd YML087C
+Orc_complex interactsWith YML082W
+Orc_complex interactsWith YML077W
+Orc_complex interactsWith iYML077W
+Orc1 pd iYML077W
+Orc_complex interactsWith YML069W
+Mcm7 pd iYML069W
+Orc_complex interactsWith iYML069W
+Mcm3 pd iYML069W
+Orc1 pd iYML069W
+Mcm4 pd iYML069W
+Mcm3 pd YML068W
+Orc1 pd iYML066C
+Orc1 pd YML065W
+Orc_complex interactsWith iYML059C
+Orc1 pd iYML059C
+Mcm7 pd YML058W
+Orc1 pd YML058W
+Mcm4 pd YML058W
+Orc_complex interactsWith YML056C
+Mcm3 pd YML056C
+Mcm4 pd YML056C
+Orc_complex interactsWith iYML046W
+Orc1 pd iYML046W
+Mcm7 pd itG(GCC)M
+Mcm3 pd itG(GCC)M
+Orc1 pd itG(GCC)M
+Orc_complex interactsWith iYMLWdelta4
+Orc1 pd iYMLWdelta4
+Mcm7 pd iYML042W
+Mcm3 pd itP(UGG)M
+Mcm4 pd itP(UGG)M
+Mcm7 pd YML032C
+Orc1 pd YML032C
+Orc_complex interactsWith YML012W
+Orc1 pd YML012W
+Orc_complex interactsWith YML007W
+Mcm7 pd iYML004C
+Orc_complex interactsWith iYML004C
+Orc1 pd iYML004C
+Mcm4 pd iYML004C
+Mcm7 pd YML003W
+Mcm3 pd YML003W
+Mcm4 pd YML003W
+Mcm4 pd iCEN13
+Mcm7 pd iYMR010W-0
+Orc_complex interactsWith iYMR010W-0
+Mcm3 pd iYMR010W-0
+Orc1 pd iYMR010W-0
+Mcm4 pd iYMR010W-0
+Mcm7 pd iYMR011W
+Mcm3 pd iYMR011W
+Orc1 pd iYMR011W
+Mcm7 pd iYMR015C
+Mcm3 pd iYMR015C
+Mcm4 pd iYMR015C
+Orc1 pd YMR029C
+Orc_complex interactsWith YMR034C
+Mcm7 pd iYMR035W
+Mcm4 pd iYMR035W
+Orc_complex interactsWith YMR044W
+Mcm3 pd iYMR046W-A
+Mcm7 pd iYMR049C-0
+Orc_complex interactsWith iYMR049C-0
+Mcm3 pd iYMR049C-0
+Orc1 pd iYMR049C-0
+Mcm4 pd iYMR049C-0
+Mcm7 pd itV(AAC)M1
+Orc_complex interactsWith itV(AAC)M1
+Mcm3 pd itV(AAC)M1
+Orc1 pd itV(AAC)M1
+Mcm4 pd itV(AAC)M1
+Mcm3 pd iYMRWdelta12
+Mcm7 pd YMR076C
+Mcm4 pd YMR076C
+Mcm7 pd itV(AAC)M2
+Mcm4 pd itV(AAC)M2
+Mcm7 pd iYMR082C-0
+Mcm3 pd iYMR082C-0
+Orc1 pd iYMR082C-0
+Mcm4 pd iYMR082C-0
+Mcm7 pd iYMR090W
+Mcm4 pd iYMR090W
+Mcm3 pd YMR098C
+Orc1 pd YMR098C
+Mcm7 pd iYMR100W
+Mcm3 pd iYMR100W
+Mcm4 pd iYMR100W
+Mcm7 pd YMR101C
+Mcm4 pd YMR101C
+Mcm7 pd iYMR105C
+Orc_complex interactsWith iYMR105C
+Mcm3 pd iYMR105C
+Orc1 pd iYMR105C
+Mcm4 pd iYMR105C
+Mcm7 pd YMR107W
+Mcm7 pd YMR110C
+Orc_complex interactsWith YMR110C
+Mcm3 pd YMR110C
+Orc1 pd YMR110C
+Mcm4 pd YMR110C
+Orc_complex interactsWith YMR118C
+Orc_complex interactsWith iYMR118C
+Mcm7 pd iYMRWdelta16
+Orc_complex interactsWith iYMRWdelta16
+Mcm3 pd iYMRWdelta16
+Orc1 pd iYMRWdelta16
+Mcm4 pd iYMRWdelta16
+Mcm3 pd iYMRWtau2
+Orc1 pd iYMRWtau2
+Mcm7 pd iYMRWdelta17
+Orc_complex interactsWith iYMRWdelta17
+Mcm3 pd iYMRWdelta17
+Orc1 pd iYMRWdelta17
+Mcm7 pd YMR132C
+Orc_complex interactsWith YMR132C
+Mcm3 pd YMR132C
+Orc1 pd YMR132C
+Mcm4 pd YMR132C
+Mcm7 pd iYMR132C
+Orc_complex interactsWith iYMR132C
+Mcm3 pd iYMR132C
+Orc1 pd iYMR132C
+Mcm4 pd iYMR132C
+Orc_complex interactsWith YMR133W
+Mcm3 pd YMR133W
+Orc1 pd YMR133W
+Mcm4 pd iYMR134W
+Mcm7 pd iYMR136W
+Mcm3 pd iYMR136W
+Mcm4 pd iYMR136W
+Orc_complex interactsWith YMR141C
+Mcm7 pd YMR144W
+Orc_complex interactsWith YMR144W
+Mcm3 pd YMR144W
+Mcm4 pd YMR144W
+Mcm3 pd iYMR144W
+Orc1 pd iYMR144W
+Mcm7 pd itM(CAU)M
+Mcm4 pd YMR174C
+Mcm3 pd iYMR174C
+Mcm7 pd YMR175W
+Mcm3 pd YMR175W
+Orc1 pd YMR175W
+Mcm4 pd YMR175W
+Mcm7 pd iYMR175W
+Orc_complex interactsWith iYMR175W
+Mcm3 pd iYMR175W
+Orc1 pd iYMR175W
+Mcm4 pd iYMR175W
+Mcm7 pd iYMR186W
+Mcm4 pd iYMR186W
+Mcm7 pd YMR187C
+Mcm3 pd YMR187C
+Mcm4 pd YMR187C
+Mcm7 pd iYMR192W
+Mcm3 pd iYMR192W
+Orc1 pd iYMR192W
+Mcm4 pd iYMR192W
+Orc1 pd YMR193W
+Mcm3 pd iYMR194W
+Mcm4 pd YMR205C
+Mcm7 pd YMR210W
+Mcm3 pd YMR210W
+Mcm4 pd YMR210W
+Mcm7 pd iYMR210W
+Orc_complex interactsWith iYMR210W
+Mcm3 pd iYMR210W
+Orc1 pd iYMR210W
+Mcm4 pd iYMR210W
+Mcm3 pd YMR211W
+Mcm4 pd iYMR223W
+Mcm3 pd iYMR243C
+Mcm7 pd YMR244W
+Mcm3 pd YMR244W
+Mcm4 pd YMR244W
+Orc_complex interactsWith iYMR244W
+Mcm3 pd iYMR244W
+Orc_complex interactsWith YMR245W
+Mcm4 pd YMR245W
+Mcm7 pd iYMR250W
+Mcm3 pd iYMR250W
+Mcm4 pd iYMR250W
+Mcm7 pd YMR251W
+Mcm4 pd YMR251W
+Mcm3 pd YMR269W
+Mcm7 pd iYMR269W
+Orc1 pd iYMR269W
+Mcm4 pd iYMR269W
+Mcm7 pd YMR270C
+Mcm7 pd YMR274C
+Mcm3 pd YMR274C
+Mcm4 pd YMR274C
+Mcm7 pd iYMR274C
+Mcm3 pd iYMR274C
+Orc1 pd iYMR274C
+Mcm4 pd iYMR274C
+Mcm3 pd iYMR283C
+Mcm7 pd iYMRWdelta21
+Mcm4 pd iYMRWdelta21
+Mcm3 pd itY(GUA)M2
+Mcm4 pd itY(GUA)M2
+Mcm7 pd YMR311C
+Orc_complex interactsWith YMR311C
+Mcm3 pd YMR311C
+Mcm7 pd iYMR311C
+Orc_complex interactsWith iYMR311C
+Mcm3 pd iYMR311C
+Orc1 pd iYMR311C
+Mcm4 pd iYMR311C
+Orc_complex interactsWith YMR312W
+Mcm3 pd YMR312W
+Mcm7 pd YMR320W
+Orc1 pd YMR320W
+Mcm4 pd YMR320W
+Orc_complex interactsWith iYMR320W
+Mcm7 pd iYMR321C
+Mcm3 pd iYMR321C
+Mcm4 pd iYMR321C
+Mcm7 pd YMR322C
+Mcm3 pd YMR322C
+Mcm4 pd YMR322C
+Mcm7 pd YMR323W
+Orc_complex interactsWith YMR323W
+Mcm3 pd YMR323W
+Mcm4 pd YMR323W
+Mcm7 pd iYMR325W
+Orc_complex interactsWith iYMR325W
+Mcm3 pd iYMR325W
+Orc1 pd iYMR325W
+Mcm7 pd YNL339C
+Mcm3 pd YNL339C
+Orc_complex interactsWith iYNL339C
+Mcm7 pd iYNL338W
+Orc_complex interactsWith iYNL338W
+Mcm3 pd iYNL338W
+Orc1 pd iYNL338W
+Mcm4 pd iYNL338W
+Mcm7 pd YNL337W
+Orc_complex interactsWith YNL337W
+Mcm3 pd YNL337W
+Orc1 pd YNL337W
+Mcm4 pd YNL337W
+Mcm7 pd iYNL337W
+Orc_complex interactsWith iYNL337W
+Mcm3 pd iYNL337W
+Orc1 pd iYNL337W
+Mcm4 pd iYNL337W
+Mcm7 pd iYNL336W-0
+Orc_complex interactsWith iYNL336W-0
+Mcm3 pd iYNL336W-0
+Orc1 pd iYNL336W-0
+Mcm7 pd iYNL336W-1
+Orc_complex interactsWith iYNL336W-1
+Mcm3 pd iYNL336W-1
+Orc1 pd iYNL336W-1
+Mcm7 pd iYNL335W
+Orc_complex interactsWith iYNL335W
+Mcm3 pd iYNL335W
+Orc1 pd iYNL335W
+Mcm3 pd iYNL333W
+Mcm4 pd iYNL333W
+Mcm3 pd YNL332W
+Mcm4 pd YNL332W
+Mcm7 pd YNL326C
+Mcm3 pd YNL326C
+Mcm3 pd iYNL314W
+Mcm3 pd iYNL312W
+Mcm7 pd YNL304W
+Orc_complex interactsWith YNL304W
+Mcm3 pd YNL304W
+Orc1 pd YNL304W
+Mcm4 pd YNL304W
+Mcm7 pd YNL303W
+Orc_complex interactsWith YNL303W
+Mcm3 pd YNL303W
+Orc1 pd YNL303W
+Mcm4 pd YNL303W
+Orc1 pd iYNL303W
+Mcm4 pd YNL297C
+Orc_complex interactsWith iYNL295W
+Mcm7 pd iYNL289W-0
+Mcm3 pd iYNL289W-0
+Mcm4 pd iYNL289W-0
+Mcm7 pd iYNL289W-1
+Orc_complex interactsWith iYNL289W-1
+Mcm3 pd iYNL289W-1
+Orc1 pd iYNL289W-1
+Mcm4 pd iYNL289W-1
+Mcm7 pd iYNL287W
+Orc1 pd iYNL287W
+Mcm4 pd iYNL287W
+Orc_complex interactsWith YNL285W
+Orc1 pd YNL285W
+Mcm4 pd YNL285W
+Mcm4 pd itG(UCC)N
+Mcm7 pd YNL273W
+Mcm3 pd YNL273W
+Mcm7 pd iYNL273W
+Mcm3 pd iYNL273W
+Mcm4 pd iYNL273W
+Mcm7 pd YNL272C
+Mcm3 pd YNL272C
+Mcm4 pd YNL272C
+Orc1 pd YNL269W
+Mcm4 pd YNL266W
+Mcm4 pd iYNL261W
+Mcm7 pd YNL256W
+Mcm3 pd YNL256W
+Mcm7 pd iYNL254C
+Orc_complex interactsWith iYNL254C
+Mcm3 pd iYNL254C
+Orc1 pd iYNL254C
+Mcm4 pd iYNL254C
+Mcm7 pd YNL253W
+Mcm3 pd YNL253W
+Mcm4 pd YNL253W
+Mcm7 pd iYNL242W
+Mcm3 pd iYNL242W
+Orc1 pd iYNL242W
+Mcm4 pd iYNL242W
+Mcm7 pd YNL241C
+Orc_complex interactsWith YNL241C
+Orc_complex interactsWith YNL215W
+Mcm3 pd iYNL212W
+Mcm4 pd iYNL212W
+Mcm7 pd iYNL211C
+Orc_complex interactsWith iYNL211C
+Mcm3 pd iYNL211C
+Orc1 pd iYNL211C
+Mcm4 pd iYNL211C
+Mcm4 pd iYNL209W
+Orc_complex interactsWith iYNL192W
+Orc1 pd iYNL192W
+Mcm3 pd YNL191W
+Orc_complex interactsWith YNL190W
+Mcm3 pd YNL190W
+Orc_complex interactsWith iYNL190W
+Orc1 pd YNL171C
+Mcm7 pd iYNL167C
+Orc_complex interactsWith iYNL167C
+Mcm3 pd iYNL167C
+Orc1 pd iYNL167C
+Mcm4 pd iYNL167C
+Mcm3 pd YNL166C
+Mcm7 pd iYNL165W
+Orc_complex interactsWith iYNL165W
+Mcm3 pd iYNL165W
+Orc1 pd iYNL165W
+Mcm4 pd iYNL165W
+Mcm7 pd YNL143C
+Mcm3 pd YNL143C
+Mcm4 pd YNL135C
+Orc1 pd YNL122C
+Mcm7 pd iYNL115C
+Orc_complex interactsWith iYNL115C
+Mcm3 pd iYNL115C
+Orc1 pd iYNL115C
+Mcm4 pd iYNL115C
+Mcm7 pd YNL114C
+Orc_complex interactsWith YNL114C
+Mcm3 pd YNL114C
+Orc1 pd YNL114C
+Mcm4 pd YNL114C
+Mcm7 pd YNL113W
+Orc_complex interactsWith YNL113W
+Orc1 pd YNL113W
+Orc_complex interactsWith iYNL113W
+Mcm3 pd iYNL113W
+Mcm7 pd iYNL112W
+Mcm3 pd iYNL112W
+Orc1 pd iYNL112W
+Mcm4 pd iYNL112W
+Orc_complex interactsWith YNL094W
+Orc1 pd YNL094W
+Mcm7 pd iYNL094W
+Orc_complex interactsWith iYNL094W
+Mcm3 pd iYNL094W
+Orc1 pd iYNL094W
+Mcm4 pd iYNL094W
+Mcm7 pd YNL093W
+Orc_complex interactsWith YNL093W
+Mcm3 pd YNL093W
+Orc1 pd YNL093W
+Mcm4 pd YNL093W
+Mcm7 pd iYNL068C
+Orc_complex interactsWith iYNL068C
+Mcm3 pd iYNL068C
+Orc1 pd iYNL068C
+Mcm4 pd iYNL068C
+Orc_complex interactsWith YNL067W
+Mcm7 pd YNL045W
+Orc_complex interactsWith YNL045W
+Mcm3 pd YNL045W
+Orc1 pd YNL045W
+Orc_complex interactsWith YNL044W
+Mcm4 pd YNL044W
+Orc_complex interactsWith YNL043C
+Mcm4 pd YNL043C
+Orc_complex interactsWith iYNL043C
+Orc1 pd iYNL043C
+Mcm7 pd iYNL036W
+Orc_complex interactsWith iYNL036W
+Mcm7 pd itT(AGU)N2
+Orc_complex interactsWith itT(AGU)N2
+Mcm3 pd itT(AGU)N2
+Orc1 pd itT(AGU)N2
+Mcm4 pd itT(AGU)N2
+Orc_complex interactsWith itP(UGG)N2
+Mcm3 pd itP(UGG)N2
+Orc1 pd itP(UGG)N2
+Mcm7 pd YNL013C
+Orc_complex interactsWith YNL013C
+Mcm3 pd YNL013C
+Mcm4 pd YNL013C
+Mcm7 pd iYNL013C
+Mcm3 pd iYNL013C
+Mcm4 pd iYNL013C
+Mcm7 pd YNL008C
+Orc_complex interactsWith YNL008C
+Mcm3 pd YNL008C
+Orc1 pd YNL008C
+Mcm4 pd YNL008C
+Mcm3 pd YNR003C
+Mcm7 pd iYNR003C
+Orc_complex interactsWith iYNR003C
+Mcm3 pd iYNR003C
+Orc1 pd iYNR003C
+Mcm4 pd iYNR003C
+Mcm7 pd YNR004W
+Orc_complex interactsWith YNR004W
+Mcm3 pd YNR004W
+Orc1 pd YNR004W
+Mcm4 pd YNR004W
+Orc_complex interactsWith iYNR006W
+Mcm3 pd iYNR006W
+Mcm7 pd YNR034W
+Mcm7 pd iYNR034W-0
+Orc1 pd iYNR034W-0
+Mcm4 pd iYNR034W-0
+Mcm3 pd iYNR034W-1
+Mcm3 pd iYNR036C
+Mcm7 pd YNR049C
+Mcm3 pd YNR049C
+Mcm4 pd YNR049C
+Mcm7 pd iYNR049C
+Mcm4 pd iYNR049C
+Orc1 pd YNR059W
+Mcm7 pd iYNR059W
+Orc1 pd iYNR059W
+Mcm4 pd iYNR059W
+Mcm7 pd iYNR069C-1
+Orc_complex interactsWith iYNR069C-1
+Orc1 pd iYNR069C-1
+Mcm4 pd iYNR069C-1
+Mcm4 pd YNR074C
+Mcm7 pd iYNR076W
+Orc_complex interactsWith iYNR076W
+Mcm3 pd iYNR076W
+Orc1 pd iYNR076W
+Mcm4 pd iYNR076W
+Mcm7 pd YOL166C
+Orc_complex interactsWith YOL166C
+Mcm3 pd YOL166C
+Orc1 pd YOL166C
+Mcm4 pd YOL166C
+Orc_complex interactsWith iYOL166C
+Orc1 pd iYOL166C
+Mcm7 pd iYOL165C
+Orc_complex interactsWith iYOL165C
+Mcm3 pd iYOL165C
+Orc1 pd iYOL165C
+Mcm4 pd iYOL165C
+Mcm4 pd iYOL164W
+Mcm7 pd YOL162W
+Orc_complex interactsWith YOL162W
+Mcm3 pd YOL162W
+Orc1 pd YOL162W
+Mcm4 pd YOL162W
+Mcm7 pd iYOL162W
+Orc_complex interactsWith iYOL162W
+Mcm3 pd iYOL162W
+Orc1 pd iYOL162W
+Mcm4 pd iYOL162W
+Orc_complex interactsWith iYOL161C-1
+Orc1 pd iYOL161C-1
+Mcm7 pd iYOLCdelta2
+Mcm3 pd iYOLCdelta2
+Mcm4 pd iYOLCdelta2
+Mcm3 pd iYOL154W
+Mcm4 pd iYOL154W
+Mcm3 pd YOL153C
+Orc_complex interactsWith YOL143C
+Mcm7 pd YOL132W
+Orc_complex interactsWith YOL132W
+Mcm3 pd YOL132W
+Orc1 pd YOL132W
+Mcm4 pd YOL132W
+Orc_complex interactsWith iYOL132W
+Orc1 pd iYOL132W
+Mcm4 pd iYOL132W
+Orc_complex interactsWith YOL131W
+Mcm3 pd YOL131W
+Mcm4 pd YOL131W
+Mcm7 pd iYOL125W
+Orc_complex interactsWith iYOL125W
+Mcm3 pd iYOL125W
+Orc1 pd iYOL125W
+Mcm4 pd iYOL125W
+Mcm3 pd YOL124C
+Mcm7 pd iYOL123W
+Mcm4 pd YOL114C
+Mcm3 pd YOL106W
+Mcm7 pd iYOLCdelta3
+Mcm4 pd iYOLCdelta3
+Mcm7 pd itT(AGU)O1
+Orc_complex interactsWith itT(AGU)O1
+Mcm3 pd itT(AGU)O1
+Orc1 pd itT(AGU)O1
+Mcm4 pd itT(AGU)O1
+Mcm7 pd iYOL104C
+Mcm4 pd iYOL104C
+Mcm7 pd iYOL088C
+Mcm4 pd iYOL088C
+Mcm7 pd YOL083W
+Orc_complex interactsWith YOL083W
+Mcm3 pd YOL083W
+Orc1 pd YOL083W
+Mcm7 pd iYOL083W-0
+Orc_complex interactsWith iYOL083W-0
+Mcm3 pd iYOL083W-0
+Orc1 pd iYOL083W-0
+Mcm4 pd iYOL083W-0
+Orc_complex interactsWith YOL061W
+Mcm7 pd iYOLWdelta6
+Mcm3 pd iYOLWdelta6
+Mcm3 pd itN(GUU)O1
+Mcm7 pd YOL024W
+Orc_complex interactsWith YOL024W
+Mcm3 pd YOL024W
+Orc1 pd YOL024W
+Mcm4 pd YOL024W
+Mcm7 pd iYOL024W
+Orc_complex interactsWith iYOL024W
+Mcm3 pd iYOL024W
+Orc1 pd iYOL024W
+Mcm4 pd iYOL024W
+Orc1 pd YOL020W
+Orc_complex interactsWith YOL009C
+Mcm3 pd YOL009C
+Orc1 pd YOL009C
+Mcm4 pd YOL009C
+Mcm7 pd iYOR005C
+Orc_complex interactsWith iYOR005C
+Mcm3 pd iYOR005C
+Orc1 pd iYOR005C
+Mcm4 pd iYOR005C
+Orc_complex interactsWith YOR006C
+Orc1 pd YOR006C
+Mcm3 pd iYOR007C
+Orc1 pd YOR013W
+Mcm7 pd iYOR015W
+Mcm7 pd YOR050C
+Orc1 pd YOR050C
+Mcm4 pd YOR050C
+Mcm7 pd iYOR058C-0
+Mcm3 pd iYOR058C-0
+Mcm7 pd iYORCdelta11
+Mcm3 pd iYORCdelta11
+Orc1 pd YOR068C
+Mcm3 pd iYOR072W-1
+Mcm4 pd iYOR072W-1
+Mcm7 pd itP(UGG)O2
+Mcm7 pd iYOR091W
+Orc_complex interactsWith iYOR091W
+Mcm3 pd iYOR091W
+Orc1 pd iYOR091W
+Mcm4 pd iYOR091W
+Orc_complex interactsWith iYOR092W
+Mcm3 pd iYOR092W
+Mcm4 pd iYOR092W
+Orc1 pd YOR114W
+Mcm3 pd YOR128C
+Mcm7 pd iYOR128C
+Orc_complex interactsWith iYOR128C
+Mcm3 pd iYOR128C
+Orc1 pd iYOR128C
+Mcm4 pd iYOR128C
+Mcm7 pd iYORWdelta14
+Orc_complex interactsWith iYORWdelta14
+Mcm3 pd iYORWdelta14
+Orc1 pd iYORWdelta14
+Mcm4 pd iYORWdelta14
+Mcm3 pd YOR143C
+Orc1 pd YOR144C
+Mcm7 pd iYOR144C
+Mcm3 pd iYOR144C
+Orc1 pd iYOR144C
+Mcm4 pd iYOR144C
+Orc1 pd iYOR147W
+Mcm7 pd iYOR151C
+Mcm4 pd iYOR151C
+Mcm7 pd YOR152C
+Mcm4 pd YOR152C
+Mcm4 pd iYOR152C-1
+Mcm4 pd iYOR154W
+Mcm7 pd iYOR156C
+Mcm4 pd iYOR156C
+Orc_complex interactsWith YOR172W
+Orc1 pd YOR172W
+Mcm7 pd iYOR172W
+Orc_complex interactsWith iYOR172W
+Mcm3 pd iYOR172W
+Orc1 pd iYOR172W
+Mcm4 pd iYOR172W
+Mcm3 pd YOR173W
+Mcm4 pd YOR173W
+Mcm4 pd iYOR178C-0
+Mcm7 pd YOR182C
+Mcm7 pd YOR183W
+Orc_complex interactsWith iYOR184W
+Orc1 pd iYOR184W
+Mcm7 pd YOR185C
+Orc_complex interactsWith YOR185C
+Mcm3 pd YOR185C
+Orc1 pd YOR185C
+Mcm4 pd YOR185C
+Mcm7 pd YOR204W
+Mcm7 pd YOR206W
+Mcm3 pd YOR206W
+Mcm4 pd YOR206W
+Mcm7 pd iYOR206W
+Mcm3 pd iYOR206W
+Mcm4 pd iYOR206W
+Mcm4 pd YOR225W
+Orc1 pd YOR226C
+Mcm7 pd iYOR227W
+Mcm3 pd iYOR227W
+Orc1 pd iYOR227W
+Mcm4 pd iYOR227W
+Mcm7 pd YOR228C
+Mcm3 pd YOR228C
+Mcm4 pd YOR228C
+Mcm7 pd iYOR229W
+Mcm4 pd iYOR229W
+Mcm7 pd YOR234C
+Mcm7 pd YOR235W
+Mcm3 pd YOR235W
+Orc_complex interactsWith YOR237W
+Mcm3 pd YOR237W
+Orc1 pd YOR237W
+Mcm4 pd YOR237W
+Orc_complex interactsWith iYOR237W
+Mcm3 pd iYOR237W
+Orc1 pd iYOR237W
+Mcm4 pd iYOR237W
+Mcm7 pd YOR238W
+Orc_complex interactsWith YOR238W
+Mcm3 pd YOR238W
+Mcm4 pd YOR238W
+Orc_complex interactsWith iYOR240W
+Orc_complex interactsWith iYORWsigma3
+Orc1 pd iYORWsigma3
+Mcm4 pd iYORWsigma3
+Mcm3 pd YOR290C
+Mcm4 pd YOR290C
+Mcm7 pd iYOR296W
+Orc_complex interactsWith iYOR296W
+Mcm3 pd iYOR296W
+Orc1 pd iYOR296W
+Mcm4 pd iYOR296W
+Mcm3 pd YOR297C
+Orc1 pd YOR299W
+Orc1 pd YOR300W
+Orc1 pd YOR311C
+Mcm3 pd iYOR311C
+Mcm7 pd YOR313C
+Mcm3 pd YOR313C
+Mcm4 pd YOR313C
+Mcm7 pd iYOR316C-0
+Orc_complex interactsWith iYOR316C-0
+Mcm3 pd iYOR316C-0
+Orc1 pd iYOR316C-0
+Mcm4 pd iYOR316C-0
+Mcm7 pd iYOR316C-1
+Orc_complex interactsWith iYOR316C-1
+Mcm3 pd iYOR316C-1
+Orc1 pd iYOR316C-1
+Mcm4 pd iYOR316C-1
+Mcm7 pd iYOR317W
+Orc_complex interactsWith iYOR317W
+Orc1 pd iYOR317W
+Mcm4 pd iYOR317W
+Mcm7 pd YOR345C
+Mcm3 pd YOR345C
+Mcm4 pd YOR345C
+Mcm7 pd iYOR376W-1
+Orc1 pd iYOR376W-1
+Mcm4 pd iYOR376W-1
+Mcm7 pd iYOR380W-0
+Mcm3 pd iYOR380W-0
+Mcm4 pd iYOR380W-0
+Mcm7 pd YOR388C
+Mcm4 pd YOR388C
+Mcm7 pd iYOR390W
+Mcm3 pd iYOR390W
+Mcm4 pd iYOR390W
+Mcm7 pd YOR391C
+Mcm3 pd YOR391C
+Mcm4 pd YOR391C
+Orc_complex interactsWith YOR392W
+Mcm7 pd iYPL283C-0
+Orc_complex interactsWith iYPL283C-0
+Mcm3 pd iYPL283C-0
+Orc1 pd iYPL283C-0
+Mcm4 pd iYPL283C-0
+Mcm7 pd iYPL283C-1
+Orc_complex interactsWith iYPL283C-1
+Mcm3 pd iYPL283C-1
+Orc1 pd iYPL283C-1
+Mcm4 pd iYPL283C-1
+Mcm3 pd iYPL282C
+Mcm3 pd iYPL281C
+Mcm7 pd YPL280W
+Mcm3 pd YPL280W
+Mcm4 pd YPL280W
+Mcm7 pd iYPL280W
+Mcm3 pd iYPL280W
+Mcm4 pd iYPL280W
+Mcm3 pd iYPL279C
+Mcm3 pd iYPL277C
+Mcm7 pd YPL275W
+Mcm3 pd YPL275W
+Mcm4 pd YPL275W
+Mcm4 pd YPL271W
+Mcm3 pd YPL265W
+Mcm7 pd iYPL265W
+Orc_complex interactsWith iYPL265W
+Orc1 pd iYPL265W
+Mcm4 pd iYPL265W
+Mcm7 pd YPL264C
+Orc_complex interactsWith YPL264C
+Mcm3 pd YPL264C
+Orc1 pd YPL264C
+Mcm4 pd YPL264C
+Mcm7 pd iYPL264C
+Orc_complex interactsWith YPL253C
+Mcm3 pd YPL253C
+Mcm7 pd iYPL253C
+Mcm3 pd iYPL253C
+Orc1 pd iYPL253C
+Mcm4 pd iYPL253C
+Orc_complex interactsWith YPL252C
+Orc1 pd YPL252C
+Mcm7 pd iYPL243W
+Mcm3 pd iYPL243W
+Mcm4 pd iYPL243W
+Orc_complex interactsWith YPL230W
+Mcm7 pd iYPL230W
+Orc_complex interactsWith iYPL230W
+Mcm3 pd iYPL230W
+Orc1 pd iYPL230W
+Mcm4 pd iYPL230W
+Mcm3 pd YPL229W
+Orc_complex interactsWith YPL207W
+Mcm4 pd YPL207W
+Mcm7 pd iYPL207W
+Mcm7 pd YPL206C
+Orc_complex interactsWith YPL199C
+Mcm4 pd YPL192C
+Mcm7 pd YPL189W
+Mcm4 pd YPL189W
+Mcm4 pd iYPL189W
+Mcm4 pd YPL185W
+Mcm3 pd iYPL179W
+Mcm4 pd iYPL179W
+Mcm7 pd iYPLWdelta7
+Orc_complex interactsWith iYPLWdelta7
+Mcm3 pd iYPLWdelta7
+Orc1 pd iYPLWdelta7
+Mcm4 pd iYPLWdelta7
+Mcm7 pd iYPL178W
+Mcm3 pd iYPL178W
+Mcm4 pd iYPL178W
+Mcm7 pd iYPL177C-1
+Orc_complex interactsWith iYPL177C-1
+Mcm3 pd iYPL177C-1
+Orc1 pd iYPL177C-1
+Mcm4 pd iYPL177C-1
+Mcm7 pd iYPL175W
+Mcm3 pd iYPL175W
+Mcm4 pd iYPL175W
+Mcm4 pd iYPL173W
+Mcm7 pd iYPL164C
+Mcm4 pd iYPL164C
+Mcm4 pd YPL157W
+Mcm7 pd iYPL154C
+Mcm3 pd iYPL154C
+Mcm4 pd iYPL154C
+Mcm7 pd iYPL152W
+Mcm3 pd iYPL152W
+Mcm4 pd iYPL152W
+Mcm3 pd YPL140C
+Mcm7 pd iYPL140C
+Orc_complex interactsWith iYPL140C
+Mcm3 pd iYPL140C
+Orc1 pd iYPL140C
+Mcm4 pd iYPL140C
+Orc_complex interactsWith YPL139C
+Mcm4 pd YPL139C
+Mcm4 pd YPL134C
+Mcm7 pd iYPL131W
+Mcm3 pd iYPL131W
+Mcm4 pd iYPL131W
+Mcm7 pd YPL130W
+Mcm3 pd YPL130W
+Mcm4 pd YPL130W
+Mcm7 pd iYPL129W
+Mcm4 pd iYPL129W
+Mcm7 pd YPL124W
+Mcm3 pd YPL124W
+Mcm4 pd YPL124W
+Mcm4 pd YPL123C
+Mcm7 pd iYPL116W
+Mcm3 pd iYPL116W
+Mcm4 pd iYPL116W
+Orc_complex interactsWith YPL087W
+Mcm3 pd YPL087W
+Orc1 pd YPL087W
+Mcm4 pd YPL087W
+Mcm7 pd iYPL087W
+Orc_complex interactsWith iYPL087W
+Mcm3 pd iYPL087W
+Orc1 pd iYPL087W
+Mcm4 pd iYPL087W
+Mcm4 pd iYPL081W
+Mcm4 pd YPL080C
+Mcm3 pd YPL074W
+Mcm7 pd iYPL074W
+Mcm3 pd iYPL074W
+Orc1 pd iYPL074W
+Mcm4 pd iYPL074W
+Mcm7 pd YPL073C
+Orc_complex interactsWith YPL073C
+Mcm3 pd YPL073C
+Mcm4 pd YPL073C
+Mcm7 pd YPL072W
+Orc_complex interactsWith YPL072W
+Mcm3 pd YPL072W
+Orc_complex interactsWith YPL071C
+Mcm7 pd iYPL070W
+Mcm4 pd iYPL070W
+Mcm7 pd iYPL068C
+Mcm4 pd iYPL068C
+Mcm4 pd iYPL066W
+Mcm4 pd YPL065W
+Mcm7 pd YPLWdelta11
+Mcm3 pd YPLWdelta11
+Mcm4 pd YPLWdelta11
+Orc_complex interactsWith YPL055C
+Orc1 pd iYPL054W
+Mcm4 pd iYPL054W
+Mcm3 pd YPL053C
+Mcm3 pd iYPL036W
+Orc1 pd YPL027W
+Mcm4 pd YPL027W
+Orc_complex interactsWith iYPL022W
+Orc1 pd iYPL022W
+Mcm7 pd YPL021W
+Orc_complex interactsWith YPL021W
+Mcm3 pd YPL021W
+Orc1 pd YPL021W
+Mcm4 pd YPL021W
+Mcm7 pd iYPL021W
+Orc_complex interactsWith iYPL021W
+Mcm3 pd iYPL021W
+Orc1 pd iYPL021W
+Mcm4 pd iYPL021W
+Mcm4 pd YPL008W
+Mcm7 pd iYPL003W
+Mcm4 pd iYPL003W
+Mcm4 pd YPL002C
+Mcm7 pd YPR003C
+Mcm3 pd YPR003C
+Mcm4 pd YPR003C
+Mcm7 pd iYPR003C
+Orc_complex interactsWith iYPR003C
+Mcm3 pd iYPR003C
+Orc1 pd iYPR003C
+Mcm4 pd iYPR003C
+Orc_complex interactsWith YPR004C
+Orc1 pd YPR004C
+Mcm3 pd iYPR004C
+Mcm3 pd YPR011C
+Mcm4 pd YPR020W
+Mcm7 pd iYPR031W
+Orc_complex interactsWith iYPR031W
+Mcm3 pd iYPR031W
+Orc1 pd iYPR031W
+Mcm4 pd iYPR031W
+Mcm7 pd YPR044C
+Mcm7 pd YPR045C
+Mcm7 pd YPR068C
+Mcm3 pd YPR068C
+Mcm4 pd YPR068C
+Mcm7 pd iYPR068C
+Mcm3 pd iYPR068C
+Mcm4 pd iYPR068C
+Mcm7 pd iYPR074C
+Orc_complex interactsWith iYPR074C
+Mcm3 pd iYPR074C
+Orc1 pd iYPR074C
+Mcm4 pd iYPR074C
+Mcm7 pd YPR075C
+Mcm3 pd YPR075C
+Mcm4 pd YPR075C
+Mcm7 pd YPR077C
+Orc_complex interactsWith YPR077C
+Orc1 pd YPR077C
+Mcm7 pd iYPR080W
+Mcm4 pd iYPR093C
+Mcm7 pd YPR094W
+Mcm4 pd YPR098C
+Mcm7 pd iYPR111W
+Mcm4 pd iYPR111W
+Orc1 pd iYPR121W-1
+Orc1 pd YPR130C
+Mcm7 pd iYPR143W
+Orc_complex interactsWith iYPR143W
+Mcm3 pd iYPR143W
+Orc1 pd iYPR143W
+Mcm4 pd iYPR143W
+Orc1 pd iYPR144C
+Mcm3 pd YPR157W
+Mcm7 pd iYPR157W
+Mcm3 pd iYPR157W
+Orc1 pd iYPR157W
+Mcm4 pd iYPR157W
+Mcm7 pd iYPRCdelta22
+Mcm3 pd iYPRCdelta22
+Mcm4 pd iYPRCdelta22
+Mcm7 pd YPR166C
+Orc1 pd YPR166C
+Mcm7 pd iYPRWsigma4
+Orc_complex interactsWith iYPRWsigma4
+Mcm3 pd iYPRWsigma4
+Orc1 pd iYPRWsigma4
+Mcm4 pd iYPRWsigma4
+Mcm7 pd YPR170C
+Mcm7 pd iYPR196W
+Mcm3 pd iYPR196W
+Mcm4 pd iYPR196W
+Mcm7 pd iYPRWtau4
+Mcm3 pd iYPRWtau4
+Orc1 pd iYPRWtau4
+Mcm4 pd iYPRWtau4
+Mcm7 pd iYPR201W-0
+Orc_complex interactsWith iYPR201W-0
+Mcm3 pd iYPR201W-0
+Orc1 pd iYPR201W-0
+Mcm7 pd iYPR201W-1
+Orc_complex interactsWith iYPR201W-1
+Mcm3 pd iYPR201W-1
+Orc1 pd iYPR201W-1
+Mcm4 pd iYPR201W-1
+Mcm7 pd YPR204W
+Pom152 interactsWith Unknown
+Unknown interactsWith Nic96
+Unknown interactsWith Nup188
+Snf1 pp Sip1
+Snf1 pp Sip2
+Snf1 pp Gal83
+Snf4 pp Sip1
+Snf4 pp Sip2
+Snf4 pp Gal83
+Rpn1 pp Rad23
+Rpn1 pp Sui1
+Rpn1 pp Ssk22
+Rpn1 pp Ykl171w
+Rpt3 pp Ame1
+Rpt3 pp Rpt3
+Rpt3 pp Rpt4
+Rpt3 pp Rpt5
+Rpt3 pp Sky1
+Rpt3 pp Rpt6
+Rpt6 pp Sui1
+Rpn5 pp Doa4
+Rpn5 pp Snf11
+Rpn5 pp Ydr179c
+Rpn5 pp Sha3
+Rpn9 pp Rpt3
+Rpn9 pp Sui1
+Rpn9 pp Ygr067c
+Rpn9 pp Ylr386w
+Rpn11 pp Rpn8
+Rpn12 pp Rpn8
+Pre5 pp Sub2
+Pre8 pp Nup49
+Pre9 pp Sui1
+Pre10 pp Pup2
+Pre10 pp Rim13
+Pre10 pp Sui1
+Pre10 pp Ylr076c
+Scl1 pp Ump1
+Pre1 pp Pre2
+Pre1 pp Pre4
+Pre2 pp Pre3
+Pre2 pp Pup3
+Pre2 pp Ump1
+Pre3 pp Aos1
+Pre3 pp Pup1
+Pre4 pp Bim1
+Pre4 pp Nup157
+Pre4 pp Rtt101
+Pre4 pp Ybr270c
+Pre4 pp Ygr067c
+Pre4 pp Ynl253w
+Pre7 pp Nup157
+Pre7 pp Rpn4
+Pre7 pp Ssk22
+Pre7 pp Yil007c
+Pup1 pp Pup3
+Pup1 pp Ubp5
+Yaf9 pp Swc4
+Swi2 pp Gcn4
+Swi1 pp Gcn4
+Snf5 pp Gcn4
+Taf13 interactsWith Unknown
+Abp1 pp SCP1
+Abp1 pp ARK1
+Abp1 pp YDR266C
+Abp1 pp ARK1
+Abp1 pp YIR003W
+Abp1 pp PAC11
+Abp1 pp PRK1
+Abp1 pp LSG1
+Abp1 pp CDC9
+Abp1 pp YIR003W
+Abp1 pp SRV2
+Boi1 pp MSI1
+Boi1 pp SRM1
+Boi1 pp RSM7
+Boi1 pp YLR169W
+Boi1 pp ACF2
+Boi1 pp YDL156W
+Boi1 pp YER158C
+Boi1 pp SMC4
+Boi1 pp YOL070C
+Boi1 pp YDR239C
+Boi1 pp BSP1
+Boi1 pp RPC53
+Boi1 pp DAL2
+Boi2 pp YER158C
+Boi2 pp BBP1
+Boi2 pp YDR239C
+Myo5 pp PKH3
+Myo5 pp ZRG17
+Myo5 pp BCK1
+Myo5 pp UBP7
+Myo5 pp YKL097C
+Myo5 pp CLA4
+Myo5 pp BBC1
+Myo5 pp YOR389W
+Myo5 pp APP1
+Myo5 pp YIR003W
+Myo5 pp VRP1
+Myo5 pp ACF2
+Myo5 pp YDR132C
+Myo5 pp SCD5
+Myo5 pp VRP1
+Myo5 pp VRP1
+Myo5 pp BNR1
+Myo5 pp RGM1
+Myo5 pp ZRG8
+Myo5 pp OSH2
+Myo5 pp UBP7
+Myo5 pp LSG1
+Myo5 pp BNI1
+Myo5 pp BNI1
+Myo5 pp BNI1
+Myo5 pp LAS17
+Rvs167 pp DEM1
+Rvs167 pp YNL152W
+Rvs167 pp YPR091C
+Rvs167 pp YPL009C
+Rvs167 pp LAS17
+Rvs167 pp PSK1
+Rvs167 pp MRS3
+Rvs167 pp ACF2
+Rvs167 pp SML1
+Rvs167 pp ABP1
+Rvs167 pp YGL085W
+Rvs167 pp YBR108W
+Rvs167 pp APP2
+Rvs167 pp YDL156W
+Rvs167 pp YBR239C
+Rvs167 pp APP2
+Rvs167 pp SNP1
+Rvs167 pp CUE5
+Rvs167 pp BBP1
+Rvs167 pp ACF4
+Rvs167 pp APP1
+Rvs167 pp YDR239C
+Rvs167 pp GYP5
+Rvs167 pp BSP1
+Rvs167 pp GTS1
+Rvs167 pp LAS17
+Rvs167 pp RIM101
+Yfr024c-a pp DEM1
+Yfr024c-a pp YNL152W
+Yfr024c-a pp YPR091C
+Yfr024c-a pp YAP5
+Yfr024c-a pp LAS17
+Yfr024c-a pp PSK1
+Yfr024c-a pp MRS3
+Yfr024c-a pp ACF2
+Yfr024c-a pp SML1
+Yfr024c-a pp GYP5
+Yfr024c-a pp YBR108W
+Yfr024c-a pp CUE5
+Yfr024c-a pp UBP7
+Yfr024c-a pp YLL023C
+Yfr024c-a pp SHS1
+Yfr024c-a pp ABP1
+Yfr024c-a pp YCR087W
+Yfr024c-a pp ABP1
+Yfr024c-a pp SEC8
+Yfr024c-a pp BSP1
+Yfr024c-a pp AGP2
+Yfr024c-a pp YAP5
+Yfr024c-a pp YBR108W
+Yfr024c-a pp UBP7
+Yfr024c-a pp AVO2
+Yfr024c-a pp YBR108W
+Yfr024c-a pp APP2
+Yfr024c-a pp RSM7
+Yfr024c-a pp YHR182W
+Yfr024c-a pp YDL156W
+Yfr024c-a pp YBR108W
+Yfr024c-a pp YIR003W
+Yfr024c-a pp YBR239C
+Yfr024c-a pp SNP1
+Yfr024c-a pp YNL047C
+Yfr024c-a pp MVP1
+Yfr024c-a pp HUA1
+Yfr024c-a pp CUE5
+Yfr024c-a pp WSC4
+Yfr024c-a pp YAR068W
+Yfr024c-a pp YER158C
+Yfr024c-a pp PMD1
+Yfr024c-a pp NCR1
+Yfr024c-a pp YBP2
+Yfr024c-a pp SLA1
+Yfr024c-a pp MRPL36
+Yfr024c-a pp CUE5
+Yfr024c-a pp ACF4
+Yfr024c-a pp STP22
+Yfr024c-a pp APP1
+Yfr024c-a pp CDC1
+Yfr024c-a pp YOR086C
+Yfr024c-a pp ABP1
+Yfr024c-a pp PHO2
+Yfr024c-a pp APP2
+Yfr024c-a pp RGT1
+Yfr024c-a pp PUS1
+Yfr024c-a pp TIP41
+Yfr024c-a pp YRA2
+Yfr024c-a pp YMR221C
+Yfr024c-a pp SAP190
+Yfr024c-a pp ZAP1
+Yfr024c-a pp ROG1
+Yfr024c-a pp YIR003W
+Yfr024c-a pp BSP1
+Yfr024c-a pp GTS1
+Yfr024c-a pp RPC53
+Yfr024c-a pp RIM101
+Yfr024c-a pp SCW11
+Yfr024c-a pp PRK1
+Yfr024c-a pp CDC6
+Yfr024c-a pp ACF2
+Yhr016c pp DEM1
+Yhr016c pp YNL152W
+Yhr016c pp LAS17
+Yhr016c pp MRS3
+Yhr016c pp ACF2
+Yhr016c pp YBR108W
+Yhr016c pp YOL070C
+Yhr016c pp GYP5
+Yhr016c pp CUE5
+Yhr016c pp YLL023C
+Yhr016c pp PEX14
+Yhr016c pp SHS1
+Yhr016c pp ABP1
+Yhr016c pp YCR087W
+Yhr016c pp ABP1
+Yhr016c pp SEC8
+Yhr016c pp BSP1
+Yhr016c pp AGP2
+Yhr016c pp YBR108W
+Yhr016c pp AVO2
+Yhr016c pp YBR108W
+Yhr016c pp APP2
+Yhr016c pp YHR182W
+Yhr016c pp YDL156W
+Yhr016c pp YBR108W
+Yhr016c pp YBR239C
+Yhr016c pp APP2
+Yhr016c pp SNP1
+Yhr016c pp CUE5
+Yhr016c pp WSC4
+Yhr016c pp NCR1
+Yhr016c pp SLA1
+Yhr016c pp MRPL36
+Yhr016c pp ACF4
+Yhr016c pp APP1
+Yhr016c pp ABP1
+Yhr016c pp GYP5
+Yhr016c pp APP2
+Yhr016c pp PUS1
+Yhr016c pp TIP41
+Yhr016c pp YRA2
+Yhr016c pp SAP190
+Yhr016c pp ROG1
+Yhr016c pp BSP1
+Yhr016c pp GTS1
+Yhr016c pp RIM101
+Yhr016c pp SCW11
+Yhr016c pp ACF2
+Sho1 pp GIP2
+Sho1 pp LAS17
+Sho1 pp PCF11
+Sho1 pp YPR151C
+Sho1 pp DSN1
+Sho1 pp TUS1
+Sho1 pp ASF2
+Sho1 pp MDM1
+Sho1 pp YGL085W
+Sho1 pp SRX1
+Sho1 pp RHO4
+Sho1 pp FUS1
+Sho1 pp PBS2
+Sho1 pp YKR027W
+Sho1 pp RGA1
+Sho1 pp YGL085W
+Smc1 pp Scc1
+Snf5 pp Hap4
+Swi2 pp Hap4
+Swi1 pp Hap4
+Swi1 pp Pho4
+Swi2 pp Pho4
+Snf5 pp Pho4
+Unknown interactsWith Taf2
+Unknown interactsWith TBP
+Unknown interactsWith Taf14
+Unknown interactsWith Taf12
+Unknown interactsWith Taf3
+Unknown interactsWith Taf11
+Unknown interactsWith Taf4
+Unknown interactsWith Taf6
+Unknown interactsWith Taf7
+Unknown interactsWith Taf8
+Unknown interactsWith Taf9
+Unknown interactsWith Taf10
+Swi1 pp Swi5
+Swi2 pp Swi5
+Snf5 pp Swi5
+ADH6 pp ADH6
+RNR2 pp RNR2
+RNR4 pp RNR4
+YAP1 pp Ap-1_Like_Transcription_Factor_Yap1
+Unknown interactsWith Taf1
+Unknown interactsWith Taf5
+Unknown interactsWith Bre5
+Unknown interactsWith Cka2
+Unknown interactsWith Cka1
+TFIID interactsWith Unknown
+Unknown interactsWith Bul1
+Unknown interactsWith Rsp5
+Spt15 pd Gal10_locus
+Spt15 pd Gal7_locus
+Spt15 pd Gal1_locus
+Vps22 pp Vps37
+Vps23 pp Vps27
+Vps4 pp Vps46
+Est1 interactsWith Unknown
+Unknown interactsWith Cdc13
+Est2 interactsWith Unknown
+Unknown interactsWith Ubp3
+Spt7 interactsWith Unknown
+Unknown interactsWith Taf5
+Unknown interactsWith Taf6
+Unknown interactsWith Taf9
+Unknown interactsWith Taf10
+Unknown interactsWith Taf12
+Unknown interactsWith Tra1
+Tub4 pp Spc97
+Tub4 pp Spc98
+Spc97 pp Spc98
+Mf-alpha-1 pp Erv29
+Rpb3 pd HSP104
+Arg5 pd 15S_rRNA2
+Arg5 pd Q0180
+Arg5 pd Q0185A
+Arg5 pd Q0183A
+Arg5 pd Q0190A
+Arg5 pd Q0195
+Arg5 pd Q0185D
+Arg5 pd Q0185E
+Arg5 pd Q0185F
+Arg5 pd IntQ0185G
+Arg5 pd Q0185H
+Arg5 pd Q0280A
+Arg5 pd IntQ0280D
+Arg5 pd Q0280F
+Arg5 pd Q0115
+Arg5 pd iYDL245C-1
+Arg5 pd iYGLWdelta10
+Arg5 pd iYGL015C
+Arg5 pd iYHL046C
+Arg5 pd iYLL064C
+Arg5 pd iYNL097C
+Arg5 pd iYOR351C
+Arg5 pd COX1
+Tom37 interactsWith Unknown
+Unknown interactsWith Sam35
+Unknown interactsWith Sam50
+RPA interactsWith MAT_locus
+Rad51 pd MAT_locus
+Mre11 pd MAT_locus
+Rad51 pd HML_locus
+TFIIB pp Rpb1
+TFIIB pp Rpb2
+TFIIB pp Tfg1
+Unknown interactsWith Gcn5
+Unknown interactsWith Ada2
+Unknown interactsWith Ada1
+Unknown interactsWith Spt3
+Unknown interactsWith Spt20
+Unknown interactsWith Spt8
+Unknown interactsWith Ada3
+Pex5 pp Pex13
+Mcm10 pd ARS305
+Mcm10 pd ARS603
+Mcm10 pd ARS1004
+Mcm10 pd ARS1
+Clb2-Cdc28_complex interactsWith Cdc6
+Cdc6 pp Cdc4
+Cdc6 pp Clb3
+Clb2 pp Cdc28
+Clb3 pp Cdc28
+Clb5-Cdc28_complex interactsWith Cdc6
+Pex13 pp Pex14
+Pex5 pp Pex14
+Pex5 pp Pex8
+Pex5 pp Mdh3
+Ssc1 pp Tim44
+Tfb4 interactsWith Unknown
+Unknown interactsWith Tfb1
+Unknown interactsWith Tfb2
+Unknown interactsWith Rad3
+Unknown interactsWith Ssl1
+Tfb3 interactsWith Unknown
+Unknown interactsWith Ccl1
+Unknown interactsWith Kin28
+Pab1 pp Sup35
+Ino80 pd PHO84_promoter
+Ino80 pd PHO5_promoter
+TBP pd PHO84_promoter
+TBP pd PHO5_promoter
+Med1 pp Med4
+Med1 pp Med7
+Unknown interactsWith Swr1
+Unknown interactsWith Arp4
+Rvb2 pp Rvb1
+Unknown interactsWith Swc3
+Unknown interactsWith Swc4
+Unknown interactsWith Arp6
+Unknown interactsWith Swc5
+Unknown interactsWith Act1
+Unknown interactsWith Vps72
+Unknown interactsWith Arp4
+Rad16 pp Sgs1
+Rvb1/Rvb2 interactsWith Unknown
+Ino80 interactsWith Unknown
+Unknown interactsWith Act1
+Unknown interactsWith Ies1
+Unknown interactsWith Ies3
+Unknown interactsWith Arp8
+Unknown interactsWith Rvb1/Rvb2
+Unknown interactsWith Arp5
+Unknown interactsWith Nhp10
+Rvb1/Rvb2 interactsWith Pih1
+Cse4 pd CEN3
+Med4 pp Med7
+Cak1 pp Cdc28
+Med4 pp Med9
+Srb7 pp Med10
+Srb7 pp Med7
+Srb4 pp Med11
+Srb5 pp Med8
+Srb4 pp Rox3
+Lhp1 interactsWith iYAL012W_RNA
+Lhp1 interactsWith iYAL013W_RNA
+Lhp1 interactsWith iYAL014C_RNA
+Lhp1 interactsWith iYAL068C-2_RNA
+Lhp1 interactsWith iYAR007C_RNA
+Lhp1 interactsWith iYAR009C_RNA
+Lhp1 interactsWith iYAR033W_RNA
+Lhp1 interactsWith iYAR047C-0_RNA
+Lhp1 interactsWith iYARCdelta8-0_RNA
+Lhp1 interactsWith YAL003W_RNA
+Lhp1 interactsWith YAL004W_RNA
+Lhp1 interactsWith YAL005C_RNA
+Lhp1 interactsWith YAL012W_RNA
+Lhp1 interactsWith YAL015C_RNA
+Lhp1 interactsWith YAL017W_RNA
+Lhp1 interactsWith YAL023C_RNA
+Lhp1 interactsWith YAL026C_RNA
+Lhp1 interactsWith YAL028W_RNA
+Lhp1 interactsWith YAL035W_RNA
+Lhp1 interactsWith YAL038W_RNA
+Lhp1 interactsWith YAL039C_RNA
+Lhp1 interactsWith YAL060W_RNA
+Lhp1 interactsWith YAL063C_RNA
+Lhp1 interactsWith YAR002C-A_RNA
+Lhp1 interactsWith YAR009C_RNA
+Lhp1 interactsWith YAR031W_RNA
+Lhp1 interactsWith YAR073W_RNA
+Lhp1 interactsWith YAR075W_RNA
+Lhp1 interactsWith iYBL099W_RNA
+Lhp1 interactsWith iYBR013C_RNA
+Lhp1 interactsWith iYBR044C_RNA
+Lhp1 interactsWith iYBR054W_RNA
+Lhp1 interactsWith iYBR070C_RNA
+Lhp1 interactsWith iYBR161W_RNA
+Lhp1 interactsWith iYBR203W_RNA
+Lhp1 interactsWith iYBR237W_RNA
+Lhp1 interactsWith iYBR270C_RNA
+Lhp1 interactsWith iYBRCdelta18_RNA
+Lhp1 interactsWith LSR1_RNA
+Lhp1 interactsWith tV(UAC)B_RNA
+Lhp1 interactsWith YBL002W_RNA
+Lhp1 interactsWith YBL005W-A_RNA
+Lhp1 interactsWith YBL007C_RNA
+Lhp1 interactsWith YBL027W_RNA
+Lhp1 interactsWith YBL030C_RNA
+Lhp1 interactsWith YBL032W_RNA
+Lhp1 interactsWith YBL036C_RNA
+Lhp1 interactsWith YBL041W_RNA
+Lhp1 interactsWith YBL045C_RNA
+Lhp1 interactsWith YBL066C_RNA
+Lhp1 interactsWith YBL068W_RNA
+Lhp1 interactsWith YBL072C_RNA
+Lhp1 interactsWith YBL075C_RNA
+Lhp1 interactsWith YBL076C_RNA
+Lhp1 interactsWith YBL092W_RNA
+Lhp1 interactsWith YBL101W-A_RNA
+Lhp1 interactsWith YBR012W-A_RNA
+Lhp1 interactsWith YBR054W_RNA
+Lhp1 interactsWith YBR068C_RNA
+Lhp1 interactsWith YBR069C_RNA
+Lhp1 interactsWith YBR078W_RNA
+Lhp1 interactsWith YBR084C-A_RNA
+Lhp1 interactsWith YBR084W_RNA
+Lhp1 interactsWith YBR085W_RNA
+Lhp1 interactsWith YBR086C_RNA
+Lhp1 interactsWith YBR088C_RNA
+Lhp1 interactsWith YBR115C_RNA
+Lhp1 interactsWith YBR118W_RNA
+Lhp1 interactsWith YBR121C_RNA
+Lhp1 interactsWith YBR143C_RNA
+Lhp1 interactsWith YBR145W_RNA
+Lhp1 interactsWith YBR149W_RNA
+Lhp1 interactsWith YBR150C_RNA
+Lhp1 interactsWith YBR151W_RNA
+Lhp1 interactsWith YBR156C_RNA
+Lhp1 interactsWith YBR181C_RNA
+Lhp1 interactsWith YBR189W_RNA
+Lhp1 interactsWith YBR191W_RNA
+Lhp1 interactsWith YBR196C_RNA
+Lhp1 interactsWith YBR221C_RNA
+Lhp1 interactsWith YBR246W_RNA
+Lhp1 interactsWith YBR249C_RNA
+Lhp1 interactsWith YBR279W_RNA
+Lhp1 interactsWith YBR283C_RNA
+Lhp1 interactsWith YBR286W_RNA
+Lhp1 interactsWith YBR287W_RNA
+Lhp1 interactsWith YBR300C_RNA
+Lhp1 interactsWith itM(CAU)C_RNA
+Lhp1 interactsWith iYCL073C_RNA
+Lhp1 interactsWith iYCR010C_RNA
+Lhp1 interactsWith iYCR024C_RNA
+Lhp1 interactsWith iYCR024C-A_RNA
+Lhp1 interactsWith SNR189_RNA
+Lhp1 interactsWith SNR33_RNA
+Lhp1 interactsWith tE(UUC)C_RNA
+Lhp1 interactsWith tL(CAA)C_RNA
+Lhp1 interactsWith tN(GUU)C_RNA
+Lhp1 interactsWith tP(AGG)C_RNA
+Lhp1 interactsWith tS(CGA)C_RNA
+Lhp1 interactsWith YCL005W_RNA
+Lhp1 interactsWith YCL006C_RNA
+Lhp1 interactsWith YCL008C_RNA
+Lhp1 interactsWith YCL009C_RNA
+Lhp1 interactsWith YCL019W_RNA
+Lhp1 interactsWith YCL020W_RNA
+Lhp1 interactsWith YCL025C_RNA
+Lhp1 interactsWith YCL030C_RNA
+Lhp1 interactsWith YCL031C_RNA
+Lhp1 interactsWith YCL037C_RNA
+Lhp1 interactsWith YCL039W_RNA
+Lhp1 interactsWith YCL040W_RNA
+Lhp1 interactsWith YCL041C_RNA
+Lhp1 interactsWith YCL043C_RNA
+Lhp1 interactsWith YCL073C_RNA
+Lhp1 interactsWith YCR012W_RNA
+Lhp1 interactsWith YCR013C_RNA
+Lhp1 interactsWith YCR021C_RNA
+Lhp1 interactsWith YCR024C-A_RNA
+Lhp1 interactsWith YCR048W_RNA
+Lhp1 interactsWith YCR077C_RNA
+Lhp1 interactsWith YCR081W_RNA
+Lhp1 interactsWith iYDL038C_RNA
+Lhp1 interactsWith iYDL047W_RNA
+Lhp1 interactsWith iYDL073W_RNA
+Lhp1 interactsWith iYDL185W_RNA
+Lhp1 interactsWith iYDR033W_RNA
+Lhp1 interactsWith iYDR067C_RNA
+Lhp1 interactsWith iYDR077W_RNA
+Lhp1 interactsWith iYDR117C_RNA
+Lhp1 interactsWith iYDR164C_RNA
+Lhp1 interactsWith iYDR170W-A-0_RNA
+Lhp1 interactsWith iYDR231C_RNA
+Lhp1 interactsWith iYDR342C-0_RNA
+Lhp1 interactsWith iYDR345C-0_RNA
+Lhp1 interactsWith iYDR357C_RNA
+Lhp1 interactsWith iYDR381W_RNA
+Lhp1 interactsWith iYDR382W_RNA
+Lhp1 interactsWith iYDR419W_RNA
+Lhp1 interactsWith iYDR420W_RNA
+Lhp1 interactsWith iYDR439W-0_RNA
+Lhp1 interactsWith iYDR447C_RNA
+Lhp1 interactsWith iYDR506C_RNA
+Lhp1 interactsWith iYDR524C_RNA
+Lhp1 interactsWith iYDR527W-0_RNA
+Lhp1 interactsWith iYDR530C_RNA
+Lhp1 interactsWith SNR13_RNA
+Lhp1 interactsWith tV(CAC)D_RNA
+Lhp1 interactsWith YDL014W_RNA
+Lhp1 interactsWith YDL015C_RNA
+Lhp1 interactsWith YDL025C_RNA
+Lhp1 interactsWith YDL048C_RNA
+Lhp1 interactsWith YDL051W_RNA
+Lhp1 interactsWith YDL055C_RNA
+Lhp1 interactsWith YDL081C_RNA
+Lhp1 interactsWith YDL082W_RNA
+Lhp1 interactsWith YDL083C_RNA
+Lhp1 interactsWith YDL119C_RNA
+Lhp1 interactsWith YDL124W_RNA
+Lhp1 interactsWith YDL125C_RNA
+Lhp1 interactsWith YDL130W_RNA
+Lhp1 interactsWith YDL131W_RNA
+Lhp1 interactsWith YDL137W_RNA
+Lhp1 interactsWith YDL140C_RNA
+Lhp1 interactsWith YDL141W_RNA
+Lhp1 interactsWith YDL145C_RNA
+Lhp1 interactsWith YDL161W_RNA
+Lhp1 interactsWith YDL172C_RNA
+Lhp1 interactsWith YDL174C_RNA
+Lhp1 interactsWith YDL182W_RNA
+Lhp1 interactsWith YDL184C_RNA
+Lhp1 interactsWith YDL185W_RNA
+Lhp1 interactsWith YDL191W_RNA
+Lhp1 interactsWith YDL194W_RNA
+Lhp1 interactsWith YDL195W_RNA
+Lhp1 interactsWith YDL203C_RNA
+Lhp1 interactsWith YDL228C_RNA
+Lhp1 interactsWith YDR012W_RNA
+Lhp1 interactsWith YDR025W_RNA
+Lhp1 interactsWith YDR035W_RNA
+Lhp1 interactsWith YDR044W_RNA
+Lhp1 interactsWith YDR050C_RNA
+Lhp1 interactsWith YDR056C_RNA
+Lhp1 interactsWith YDR072C_RNA
+Lhp1 interactsWith YDR074W_RNA
+Lhp1 interactsWith YDR077W_RNA
+Lhp1 interactsWith YDR086C_RNA
+Lhp1 interactsWith YDR099W_RNA
+Lhp1 interactsWith YDR104C_RNA
+Lhp1 interactsWith YDR116C_RNA
+Lhp1 interactsWith YDR119W_RNA
+Lhp1 interactsWith YDR134C_RNA
+Lhp1 interactsWith YDR154C_RNA
+Lhp1 interactsWith YDR158W_RNA
+Lhp1 interactsWith YDR162C_RNA
+Lhp1 interactsWith YDR165W_RNA
+Lhp1 interactsWith YDR168W_RNA
+Lhp1 interactsWith YDR170W-A_RNA
+Lhp1 interactsWith YDR170W-A_RNA
+Lhp1 interactsWith YDR188W_RNA
+Lhp1 interactsWith YDR214W_RNA
+Lhp1 interactsWith YDR216W_RNA
+Lhp1 interactsWith YDR224C_RNA
+Lhp1 interactsWith YDR225W_RNA
+Lhp1 interactsWith YDR233C_RNA
+Lhp1 interactsWith YDR248C_RNA
+Lhp1 interactsWith YDR278C_RNA
+Lhp1 interactsWith YDR340W_RNA
+Lhp1 interactsWith YDR345C_RNA
+Lhp1 interactsWith YDR353W_RNA
+Lhp1 interactsWith YDR366C_RNA
+Lhp1 interactsWith YDR368W_RNA
+Lhp1 interactsWith YDR382W_RNA
+Lhp1 interactsWith YDR385W_RNA
+Lhp1 interactsWith YDR406W_RNA
+Lhp1 interactsWith YDR408C_RNA
+Lhp1 interactsWith YDR417C_RNA
+Lhp1 interactsWith YDR441C_RNA
+Lhp1 interactsWith YDR450W_RNA
+Lhp1 interactsWith YDR471W_RNA
+Lhp1 interactsWith YDR481C_RNA
+Lhp1 interactsWith YDR538W_RNA
+Lhp1 interactsWith YDRCTy1-2A_RNA
+Lhp1 interactsWith YDRCTy1-2C_RNA
+Lhp1 interactsWith YDRCTy1-2D_RNA
+Lhp1 interactsWith YDRWdelta12_RNA
+Lhp1 interactsWith irpr1_RNA
+Lhp1 interactsWith iSCR1_RNA
+Lhp1 interactsWith iSNR52_RNA
+Lhp1 interactsWith iSNR67_RNA
+Lhp1 interactsWith itE(UUC)E1_RNA
+Lhp1 interactsWith iYEL008W_RNA
+Lhp1 interactsWith iYEL009C_RNA
+Lhp1 interactsWith iYEL018W_RNA
+Lhp1 interactsWith iYEL024W_RNA
+Lhp1 interactsWith iYEL025C_RNA
+Lhp1 interactsWith iYEL035C_RNA
+Lhp1 interactsWith iYEL047C_RNA
+Lhp1 interactsWith iYEL050C_RNA
+Lhp1 interactsWith iYEL055C_RNA
+Lhp1 interactsWith iYEL060C_RNA
+Lhp1 interactsWith iYEL069C-0_RNA
+Lhp1 interactsWith iYEL071W-0_RNA
+Lhp1 interactsWith iYEL072W-1_RNA
+Lhp1 interactsWith iYEL073C-2_RNA
+Lhp1 interactsWith iYEL074W_RNA
+Lhp1 interactsWith iYEL075C_RNA
+Lhp1 interactsWith iYELWdelta5_RNA
+Lhp1 interactsWith iYER004W_RNA
+Lhp1 interactsWith iYER007C-A_RNA
+Lhp1 interactsWith iYER012W_RNA
+Lhp1 interactsWith iYER015W_RNA
+Lhp1 interactsWith iYER019C-A_RNA
+Lhp1 interactsWith iYER026C_RNA
+Lhp1 interactsWith iYER030W_RNA
+Lhp1 interactsWith iYER039C-A_RNA
+Lhp1 interactsWith iYER042W_RNA
+Lhp1 interactsWith iYER043C_RNA
+Lhp1 interactsWith iYER048W-A_RNA
+Lhp1 interactsWith iYER054C_RNA
+Lhp1 interactsWith iYER059W_RNA
+Lhp1 interactsWith iYER063W_RNA
+Lhp1 interactsWith iYER102W_RNA
+Lhp1 interactsWith iYER109C_RNA
+Lhp1 interactsWith iYER161C_RNA
+Lhp1 interactsWith iYERComega1-0_RNA
+Lhp1 interactsWith iYERWdelta21-0_RNA
+Lhp1 interactsWith iYERWdelta21-1_RNA
+Lhp1 interactsWith iYERWdelta21-2_RNA
+Lhp1 interactsWith iYERWdelta22_RNA
+Lhp1 interactsWith snR14_RNA
+Lhp1 interactsWith SNR4_RNA
+Lhp1 interactsWith SNR52_RNA
+Lhp1 interactsWith YEL027W_RNA
+Lhp1 interactsWith YEL034W_RNA
+Lhp1 interactsWith YEL054C_RNA
+Lhp1 interactsWith YELCdelta4_RNA
+Lhp1 interactsWith YER011W_RNA
+Lhp1 interactsWith YER055C_RNA
+Lhp1 interactsWith YER056C-A_RNA
+Lhp1 interactsWith YER110C_RNA
+Lhp1 interactsWith YER120W_RNA
+Lhp1 interactsWith YER124C_RNA
+Lhp1 interactsWith YER131W_RNA
+Lhp1 interactsWith YER165W_RNA
+Lhp1 interactsWith YER178W_RNA
+Lhp1 interactsWith YER187W_RNA
+Lhp1 interactsWith YERCdelta8_RNA
+Lhp1 interactsWith YERWdelta17_RNA
+Lhp1 interactsWith iYFL031W_RNA
+Lhp1 interactsWith iYFL040W_RNA
+Lhp1 interactsWith YFL022C_RNA
+Lhp1 interactsWith YFL026W_RNA
+Lhp1 interactsWith YFL031W_RNA
+Lhp1 interactsWith YFL037W_RNA
+Lhp1 interactsWith YFL039C_RNA
+Lhp1 interactsWith YFL045C_RNA
+Lhp1 interactsWith YFL057C_RNA
+Lhp1 interactsWith YFL066C_RNA
+Lhp1 interactsWith YFLWdelta1_RNA
+Lhp1 interactsWith YFR009W_RNA
+Lhp1 interactsWith YFR011C_RNA
+Lhp1 interactsWith YFR015C_RNA
+Lhp1 interactsWith YFR031C-A_RNA
+Lhp1 interactsWith YFR032C-A_RNA
+Lhp1 interactsWith YFR032C-A_RNA
+Lhp1 interactsWith YFR046C_RNA
+Lhp1 interactsWith YFR050C_RNA
+Lhp1 interactsWith YFR051C_RNA
+Lhp1 interactsWith YFR053C_RNA
+Lhp1 interactsWith itH(GUG)G2_RNA
+Lhp1 interactsWith iYGL007W-1_RNA
+Lhp1 interactsWith iYGL009C_RNA
+Lhp1 interactsWith iYGL076C_RNA
+Lhp1 interactsWith iYGL099W_RNA
+Lhp1 interactsWith iYGL224C_RNA
+Lhp1 interactsWith iYGR020C_RNA
+Lhp1 interactsWith iYGR031W_RNA
+Lhp1 interactsWith iYGR124W_RNA
+Lhp1 interactsWith iYGR157W_RNA
+Lhp1 interactsWith iYGR249W-1_RNA
+Lhp1 interactsWith iYGR267C_RNA
+Lhp1 interactsWith iYGR287C_RNA
+Lhp1 interactsWith SNR46_RNA
+Lhp1 interactsWith SNR7-L_RNA
+Lhp1 interactsWith SNR7-S_RNA
+Lhp1 interactsWith tL(GAG)G_RNA
+Lhp1 interactsWith YGL008C_RNA
+Lhp1 interactsWith YGL009C_RNA
+Lhp1 interactsWith YGL026C_RNA
+Lhp1 interactsWith YGL030W_RNA
+Lhp1 interactsWith YGL031C_RNA
+Lhp1 interactsWith YGL036W_RNA
+Lhp1 interactsWith YGL050W_RNA
+Lhp1 interactsWith YGL055W_RNA
+Lhp1 interactsWith YGL067W_RNA
+Lhp1 interactsWith YGL088W_RNA
+Lhp1 interactsWith YGL103W_RNA
+Lhp1 interactsWith YGL123W_RNA
+Lhp1 interactsWith YGL135W_RNA
+Lhp1 interactsWith YGL147C_RNA
+Lhp1 interactsWith YGL189C_RNA
+Lhp1 interactsWith YGL200C_RNA
+Lhp1 interactsWith YGL202W_RNA
+Lhp1 interactsWith YGL215W_RNA
+Lhp1 interactsWith YGL233W_RNA
+Lhp1 interactsWith YGL234W_RNA
+Lhp1 interactsWith YGL245W_RNA
+Lhp1 interactsWith YGL248W_RNA
+Lhp1 interactsWith YGL253W_RNA
+Lhp1 interactsWith YGL254W_RNA
+Lhp1 interactsWith YGR014W_RNA
+Lhp1 interactsWith YGR019W_RNA
+Lhp1 interactsWith YGR020C_RNA
+Lhp1 interactsWith YGR027C_RNA
+Lhp1 interactsWith YGR034W_RNA
+Lhp1 interactsWith YGR055W_RNA
+Lhp1 interactsWith YGR071C_RNA
+Lhp1 interactsWith YGR075C_RNA
+Lhp1 interactsWith YGR079W_RNA
+Lhp1 interactsWith YGR085C_RNA
+Lhp1 interactsWith YGR086C_RNA
+Lhp1 interactsWith YGR087C_RNA
+Lhp1 interactsWith YGR094W_RNA
+Lhp1 interactsWith YGR098C_RNA
+Lhp1 interactsWith YGR118W_RNA
+Lhp1 interactsWith YGR124W_RNA
+Lhp1 interactsWith YGR134W_RNA
+Lhp1 interactsWith YGR138C_RNA
+Lhp1 interactsWith YGR148C_RNA
+Lhp1 interactsWith YGR155W_RNA
+Lhp1 interactsWith YGR164W_RNA
+Lhp1 interactsWith YGR173W_RNA
+Lhp1 interactsWith YGR175C_RNA
+Lhp1 interactsWith YGR178C_RNA
+Lhp1 interactsWith YGR192C_RNA
+Lhp1 interactsWith YGR209C_RNA
+Lhp1 interactsWith YGR214W_RNA
+Lhp1 interactsWith YGR224W_RNA
+Lhp1 interactsWith YGR234W_RNA
+Lhp1 interactsWith YGR240C_RNA
+Lhp1 interactsWith YGR241C_RNA
+Lhp1 interactsWith YGR243W_RNA
+Lhp1 interactsWith YGR254W_RNA
+Lhp1 interactsWith YGR264C_RNA
+Lhp1 interactsWith YGR274C_RNA
+Lhp1 interactsWith YGR275W_RNA
+Lhp1 interactsWith YGR282C_RNA
+Lhp1 interactsWith YGR285C_RNA
+Lhp1 interactsWith YGR293C_RNA
+Lhp1 interactsWith YGRCTy1-2A_RNA
+Lhp1 interactsWith YGRCTy1-2B_RNA
+Lhp1 interactsWith YGRCTy1-2C_RNA
+Lhp1 interactsWith YGRCTy1-2D_RNA
+Lhp1 interactsWith iCEN8_RNA
+Lhp1 interactsWith iYHLWdelta2_RNA
+Lhp1 interactsWith iYHR140W_RNA
+Lhp1 interactsWith iYHR199C_RNA
+Lhp1 interactsWith iYHR202W_RNA
+Lhp1 interactsWith YHL001W_RNA
+Lhp1 interactsWith YHL011C_RNA
+Lhp1 interactsWith YHL015W_RNA
+Lhp1 interactsWith YHL019C_RNA
+Lhp1 interactsWith YHL020C_RNA
+Lhp1 interactsWith YHL033C_RNA
+Lhp1 interactsWith YHR007C_RNA
+Lhp1 interactsWith YHR010W_RNA
+Lhp1 interactsWith YHR014W_RNA
+Lhp1 interactsWith YHR017W_RNA
+Lhp1 interactsWith YHR018C_RNA
+Lhp1 interactsWith YHR019C_RNA
+Lhp1 interactsWith YHR020W_RNA
+Lhp1 interactsWith YHR023W_RNA
+Lhp1 interactsWith YHR080C_RNA
+Lhp1 interactsWith YHR085W_RNA
+Lhp1 interactsWith YHR103W_RNA
+Lhp1 interactsWith YHR109W_RNA
+Lhp1 interactsWith YHR114W_RNA
+Lhp1 interactsWith YHR117W_RNA
+Lhp1 interactsWith YHR140W_RNA
+Lhp1 interactsWith YHR186C_RNA
+Lhp1 interactsWith YHR214C-B_RNA
+Lhp1 interactsWith YHR216W_RNA
+Lhp1 interactsWith iYIL174W-0_RNA
+Lhp1 interactsWith iYIR008C_RNA
+Lhp1 interactsWith iYIR018W-1_RNA
+Lhp1 interactsWith iYIR025W_RNA
+Lhp1 interactsWith YIL011W_RNA
+Lhp1 interactsWith YIL015W_RNA
+Lhp1 interactsWith YIL018W_RNA
+Lhp1 interactsWith YIL039W_RNA
+Lhp1 interactsWith YIL047C_RNA
+Lhp1 interactsWith YIL051C_RNA
+Lhp1 interactsWith YIL052C_RNA
+Lhp1 interactsWith YIL053W_RNA
+Lhp1 interactsWith YIL066C_RNA
+Lhp1 interactsWith YIL069C_RNA
+Lhp1 interactsWith YIL074C_RNA
+Lhp1 interactsWith YIL078W_RNA
+Lhp1 interactsWith YIL085C_RNA
+Lhp1 interactsWith YIL086C_RNA
+Lhp1 interactsWith YIL104C_RNA
+Lhp1 interactsWith YIL105C_RNA
+Lhp1 interactsWith YIL109C_RNA
+Lhp1 interactsWith YIL123W_RNA
+Lhp1 interactsWith YIL133C_RNA
+Lhp1 interactsWith YIL142W_RNA
+Lhp1 interactsWith YIL143C_RNA
+Lhp1 interactsWith YIL148W_RNA
+Lhp1 interactsWith YIL151C_RNA
+Lhp1 interactsWith YILCdelta2_RNA
+Lhp1 interactsWith YIR029W_RNA
+Lhp1 interactsWith YIR030C_RNA
+Lhp1 interactsWith YIR033W_RNA
+Lhp1 interactsWith YIR035C_RNA
+Lhp1 interactsWith iYJL104W_RNA
+Lhp1 interactsWith iYJL179W_RNA
+Lhp1 interactsWith iYJR005W_RNA
+Lhp1 interactsWith iYJR045C_RNA
+Lhp1 interactsWith iYJR075W_RNA
+Lhp1 interactsWith iYJR094W-A_RNA
+Lhp1 interactsWith iYJR105W_RNA
+Lhp1 interactsWith iYJR109C_RNA
+Lhp1 interactsWith iYJR114W_RNA
+Lhp1 interactsWith iYJR120W_RNA
+Lhp1 interactsWith iYJR121W_RNA
+Lhp1 interactsWith iYJR126C_RNA
+Lhp1 interactsWith iYJR147W_RNA
+Lhp1 interactsWith iYJR148W_RNA
+Lhp1 interactsWith iYJR150C-1_RNA
+Lhp1 interactsWith iYJR151C-0_RNA
+Lhp1 interactsWith iYJR156C_RNA
+Lhp1 interactsWith iYJR160C-1_RNA
+Lhp1 interactsWith iYJRWdelta17_RNA
+Lhp1 interactsWith snR128_RNA
+Lhp1 interactsWith SNR190_RNA
+Lhp1 interactsWith snR3_RNA
+Lhp1 interactsWith YJL002C_RNA
+Lhp1 interactsWith YJL010C_RNA
+Lhp1 interactsWith YJL012C_RNA
+Lhp1 interactsWith YJL014W_RNA
+Lhp1 interactsWith YJL020C_RNA
+Lhp1 interactsWith YJL026W_RNA
+Lhp1 interactsWith YJL034W_RNA
+Lhp1 interactsWith YJL052W_RNA
+Lhp1 interactsWith YJL054W_RNA
+Lhp1 interactsWith YJL076W_RNA
+Lhp1 interactsWith YJL078C_RNA
+Lhp1 interactsWith YJL089W_RNA
+Lhp1 interactsWith YJL109C_RNA
+Lhp1 interactsWith YJL121C_RNA
+Lhp1 interactsWith YJL138C_RNA
+Lhp1 interactsWith YJL141C_RNA
+Lhp1 interactsWith YJL145W_RNA
+Lhp1 interactsWith YJL172W_RNA
+Lhp1 interactsWith YJL177W_RNA
+Lhp1 interactsWith YJL188C_RNA
+Lhp1 interactsWith YJL190C_RNA
+Lhp1 interactsWith YJLWdelta9_RNA
+Lhp1 interactsWith YJR009C_RNA
+Lhp1 interactsWith YJR013W_RNA
+Lhp1 interactsWith YJR016C_RNA
+Lhp1 interactsWith YJR019C_RNA
+Lhp1 interactsWith YJR024C_RNA
+Lhp1 interactsWith YJR027W_RNA
+Lhp1 interactsWith YJR028W_RNA
+Lhp1 interactsWith YJR029W_RNA
+Lhp1 interactsWith YJR051W_RNA
+Lhp1 interactsWith YJR059W_RNA
+Lhp1 interactsWith YJR064W_RNA
+Lhp1 interactsWith YJR096W_RNA
+Lhp1 interactsWith YJR104C_RNA
+Lhp1 interactsWith YJR123W_RNA
+Lhp1 interactsWith YJR143C_RNA
+Lhp1 interactsWith YJR145C_RNA
+Lhp1 interactsWith YJR150C_RNA
+Lhp1 interactsWith iYKL220C-0_RNA
+Lhp1 interactsWith iYKR079C_RNA
+Lhp1 interactsWith SNR42_RNA
+Lhp1 interactsWith SNR69_RNA
+Lhp1 interactsWith YKL033W-A_RNA
+Lhp1 interactsWith YKL033W-A_RNA
+Lhp1 interactsWith YKL056C_RNA
+Lhp1 interactsWith YKL060C_RNA
+Lhp1 interactsWith YKL080W_RNA
+Lhp1 interactsWith YKL086W_RNA
+Lhp1 interactsWith YKL096W_RNA
+Lhp1 interactsWith YKL103C_RNA
+Lhp1 interactsWith YKL153W_RNA
+Lhp1 interactsWith YKL162C_RNA
+Lhp1 interactsWith YKL180W_RNA
+Lhp1 interactsWith YKL181W_RNA
+Lhp1 interactsWith YKLCdelta2_RNA
+Lhp1 interactsWith YKR002W_RNA
+Lhp1 interactsWith YKR042W_RNA
+Lhp1 interactsWith YKR057W_RNA
+Lhp1 interactsWith YKR059W_RNA
+Lhp1 interactsWith YKR071C_RNA
+Lhp1 interactsWith YKR075C_RNA
+Lhp1 interactsWith YKR082W_RNA
+Lhp1 interactsWith YKR094C_RNA
+Lhp1 interactsWith YKRCdelta11_RNA
+Lhp1 interactsWith iYLL046C_RNA
+Lhp1 interactsWith iYLL048C_RNA
+Lhp1 interactsWith iYLR027C_RNA
+Lhp1 interactsWith iYLR035C-A-0_RNA
+Lhp1 interactsWith iYLR035C-A-1_RNA
+Lhp1 interactsWith iYLR146C_RNA
+Lhp1 interactsWith iYLR159W_RNA
+Lhp1 interactsWith iYLR162W-0_RNA
+Lhp1 interactsWith iYLR162W-A_RNA
+Lhp1 interactsWith iYLR166C_RNA
+Lhp1 interactsWith iYLRCdelta19_RNA
+Lhp1 interactsWith iYLRCdelta8_RNA
+Lhp1 interactsWith RDN18-1A_RNA
+Lhp1 interactsWith RDN37-1_RNA
+Lhp1 interactsWith RDN37-1A_RNA
+Lhp1 interactsWith RDN37-1B_RNA
+Lhp1 interactsWith RDN5-1_RNA
+Lhp1 interactsWith RDN58-1_RNA
+Lhp1 interactsWith SNR34_RNA
+Lhp1 interactsWith SNR44_RNA
+Lhp1 interactsWith SNR55_RNA
+Lhp1 interactsWith SNR57_RNA
+Lhp1 interactsWith SNR6_RNA
+Lhp1 interactsWith SNR61_RNA
+Lhp1 interactsWith tI(UAU)L_RNA
+Lhp1 interactsWith tL(UAG)L2_RNA
+Lhp1 interactsWith tQ(UUG)L_RNA
+Lhp1 interactsWith tR(CCG)L_RNA
+Lhp1 interactsWith tS(GCU)L_RNA
+Lhp1 interactsWith YLL018C_RNA
+Lhp1 interactsWith YLL021W_RNA
+Lhp1 interactsWith YLL024C_RNA
+Lhp1 interactsWith YLL026W_RNA
+Lhp1 interactsWith YLL035W_RNA
+Lhp1 interactsWith YLL039C_RNA
+Lhp1 interactsWith YLL041C_RNA
+Lhp1 interactsWith YLL044W_RNA
+Lhp1 interactsWith YLL045C_RNA
+Lhp1 interactsWith YLL048C_RNA
+Lhp1 interactsWith YLR001C_RNA
+Lhp1 interactsWith YLR006C_RNA
+Lhp1 interactsWith YLR027C_RNA
+Lhp1 interactsWith YLR029C_RNA
+Lhp1 interactsWith YLR044C_RNA
+Lhp1 interactsWith YLR048W_RNA
+Lhp1 interactsWith YLR059C_RNA
+Lhp1 interactsWith YLR060W_RNA
+Lhp1 interactsWith YLR062C_RNA
+Lhp1 interactsWith YLR075W_RNA
+Lhp1 interactsWith YLR076C_RNA
+Lhp1 interactsWith YLR089C_RNA
+Lhp1 interactsWith YLR098C_RNA
+Lhp1 interactsWith YLR109W_RNA
+Lhp1 interactsWith YLR110C_RNA
+Lhp1 interactsWith YLR121C_RNA
+Lhp1 interactsWith YLR123C_RNA
+Lhp1 interactsWith YLR131C_RNA
+Lhp1 interactsWith YLR134W_RNA
+Lhp1 interactsWith YLR141W_RNA
+Lhp1 interactsWith YLR150W_RNA
+Lhp1 interactsWith YLR152C_RNA
+Lhp1 interactsWith YLR157C_RNA
+Lhp1 interactsWith YLR161W_RNA
+Lhp1 interactsWith YLR166C_RNA
+Lhp1 interactsWith YLR167W_RNA
+Lhp1 interactsWith YLR170C_RNA
+Lhp1 interactsWith YLR175W_RNA
+Lhp1 interactsWith YLR187W_RNA
+Lhp1 interactsWith YLR188W_RNA
+Lhp1 interactsWith YLR190W_RNA
+Lhp1 interactsWith YLR193C_RNA
+Lhp1 interactsWith YLR196W_RNA
+Lhp1 interactsWith YLR202C_RNA
+Lhp1 interactsWith YLR205C_RNA
+Lhp1 interactsWith YLR206W_RNA
+Lhp1 interactsWith YLR244C_RNA
+Lhp1 interactsWith YLR249W_RNA
+Lhp1 interactsWith YLR257W_RNA
+Lhp1 interactsWith YLR258W_RNA
+Lhp1 interactsWith YLR259C_RNA
+Lhp1 interactsWith YLR262C-A_RNA
+Lhp1 interactsWith YLR262C-A_RNA
+Lhp1 interactsWith YLR264W_RNA
+Lhp1 interactsWith YLR267W_RNA
+Lhp1 interactsWith YLR286C_RNA
+Lhp1 interactsWith YLR287C-A_RNA
+Lhp1 interactsWith YLR291C_RNA
+Lhp1 interactsWith YLR293C_RNA
+Lhp1 interactsWith YLR300W_RNA
+Lhp1 interactsWith YLR301W_RNA
+Lhp1 interactsWith YLR304C_RNA
+Lhp1 interactsWith YLR325C_RNA
+Lhp1 interactsWith YLR333C_RNA
+Lhp1 interactsWith YLR339C_RNA
+Lhp1 interactsWith YLR340W_RNA
+Lhp1 interactsWith YLR350W_RNA
+Lhp1 interactsWith YLR355C_RNA
+Lhp1 interactsWith YLR367W_RNA
+Lhp1 interactsWith YLR388W_RNA
+Lhp1 interactsWith YLR389C_RNA
+Lhp1 interactsWith YLR398C_RNA
+Lhp1 interactsWith YLR413W_RNA
+Lhp1 interactsWith YLR432W_RNA
+Lhp1 interactsWith YLR441C_RNA
+Lhp1 interactsWith YLR448W_RNA
+Lhp1 interactsWith YLR450W_RNA
+Lhp1 interactsWith YLR451W_RNA
+Lhp1 interactsWith YLRWdelta15_RNA
+Lhp1 interactsWith iYML118W_RNA
+Lhp1 interactsWith iYML125C_RNA
+Lhp1 interactsWith iYMR122C-0_RNA
+Lhp1 interactsWith iYMR165C_RNA
+Lhp1 interactsWith iYMR182C-1_RNA
+Lhp1 interactsWith iYMR194W_RNA
+Lhp1 interactsWith iYMR240C_RNA
+Lhp1 interactsWith iYMR246W_RNA
+Lhp1 interactsWith iYMR271C_RNA
+Lhp1 interactsWith iYMR309C_RNA
+Lhp1 interactsWith iYMRWdelta12_RNA
+Lhp1 interactsWith tH(GUG)M_RNA
+Lhp1 interactsWith tP(UGG)M_RNA
+Lhp1 interactsWith tR(UCU)M2_RNA
+Lhp1 interactsWith tV(AAC)M3_RNA
+Lhp1 interactsWith tY(GUA)M2_RNA
+Lhp1 interactsWith YML007W_RNA
+Lhp1 interactsWith YML014W_RNA
+Lhp1 interactsWith YML018C_RNA
+Lhp1 interactsWith YML024W_RNA
+Lhp1 interactsWith YML026C_RNA
+Lhp1 interactsWith YML028W_RNA
+Lhp1 interactsWith YML033W_RNA
+Lhp1 interactsWith YML035C_RNA
+Lhp1 interactsWith YML039W_RNA
+Lhp1 interactsWith YML040W_RNA
+Lhp1 interactsWith YML045W_RNA
+Lhp1 interactsWith YML052W_RNA
+Lhp1 interactsWith YML056C_RNA
+Lhp1 interactsWith YML063W_RNA
+Lhp1 interactsWith YML073C_RNA
+Lhp1 interactsWith YML075C_RNA
+Lhp1 interactsWith YML091C_RNA
+Lhp1 interactsWith YML107C_RNA
+Lhp1 interactsWith YML116W_RNA
+Lhp1 interactsWith YML123C_RNA
+Lhp1 interactsWith YML125C_RNA
+Lhp1 interactsWith YML126C_RNA
+Lhp1 interactsWith YML130C_RNA
+Lhp1 interactsWith YML132W_RNA
+Lhp1 interactsWith YMLCdelta1_RNA
+Lhp1 interactsWith YMR008C_RNA
+Lhp1 interactsWith YMR011W_RNA
+Lhp1 interactsWith YMR045C_RNA
+Lhp1 interactsWith YMR046C_RNA
+Lhp1 interactsWith YMR061W_RNA
+Lhp1 interactsWith YMR075W_RNA
+Lhp1 interactsWith YMR083W_RNA
+Lhp1 interactsWith YMR085W_RNA
+Lhp1 interactsWith YMR088C_RNA
+Lhp1 interactsWith YMR090W_RNA
+Lhp1 interactsWith YMR108W_RNA
+Lhp1 interactsWith YMR109W_RNA
+Lhp1 interactsWith YMR116C_RNA
+Lhp1 interactsWith YMR120C_RNA
+Lhp1 interactsWith YMR121C_RNA
+Lhp1 interactsWith YMR123W_RNA
+Lhp1 interactsWith YMR125W_RNA
+Lhp1 interactsWith YMR126C_RNA
+Lhp1 interactsWith YMR142C_RNA
+Lhp1 interactsWith YMR143W_RNA
+Lhp1 interactsWith YMR145C_RNA
+Lhp1 interactsWith YMR146C_RNA
+Lhp1 interactsWith YMR152W_RNA
+Lhp1 interactsWith YMR154C_RNA
+Lhp1 interactsWith YMR159C_RNA
+Lhp1 interactsWith YMR173W_RNA
+Lhp1 interactsWith YMR173W-A_RNA
+Lhp1 interactsWith YMR181C_RNA
+Lhp1 interactsWith YMR182C_RNA
+Lhp1 interactsWith YMR186W_RNA
+Lhp1 interactsWith YMR205C_RNA
+Lhp1 interactsWith YMR208W_RNA
+Lhp1 interactsWith YMR230W_RNA
+Lhp1 interactsWith YMR279C_RNA
+Lhp1 interactsWith YMR295C_RNA
+Lhp1 interactsWith YMR297W_RNA
+Lhp1 interactsWith YMR301C_RNA
+Lhp1 interactsWith YMR303C_RNA
+Lhp1 interactsWith YMR305C_RNA
+Lhp1 interactsWith YMR306W_RNA
+Lhp1 interactsWith YMR309C_RNA
+Lhp1 interactsWith YMR315W_RNA
+Lhp1 interactsWith YMR318C_RNA
+Lhp1 interactsWith IntYNR053C_RNA
+Lhp1 interactsWith iYNL006W_RNA
+Lhp1 interactsWith iYNL190W_RNA
+Lhp1 interactsWith iYNL222W_RNA
+Lhp1 interactsWith iYNL226W_RNA
+Lhp1 interactsWith iYNLCdelta1-0_RNA
+Lhp1 interactsWith iYNLCdelta1-1_RNA
+Lhp1 interactsWith iYNLCdelta1-2_RNA
+Lhp1 interactsWith iYNLCdelta1-3_RNA
+Lhp1 interactsWith iYNR045W_RNA
+Lhp1 interactsWith iYNR050C_RNA
+Lhp1 interactsWith tL(CAA)N_RNA
+Lhp1 interactsWith tL(UAA)N_RNA
+Lhp1 interactsWith YNL006W_RNA
+Lhp1 interactsWith YNL010W_RNA
+Lhp1 interactsWith YNL013C_RNA
+Lhp1 interactsWith YNL017C_RNA
+Lhp1 interactsWith YNL041C_RNA
+Lhp1 interactsWith YNL045W_RNA
+Lhp1 interactsWith YNL055C_RNA
+Lhp1 interactsWith YNL066W_RNA
+Lhp1 interactsWith YNL067W_RNA
+Lhp1 interactsWith YNL068C_RNA
+Lhp1 interactsWith YNL069C_RNA
+Lhp1 interactsWith YNL070W_RNA
+Lhp1 interactsWith YNL071W_RNA
+Lhp1 interactsWith YNL096C_RNA
+Lhp1 interactsWith YNL104C_RNA
+Lhp1 interactsWith YNL106C_RNA
+Lhp1 interactsWith YNL112W_RNA
+Lhp1 interactsWith YNL119W_RNA
+Lhp1 interactsWith YNL131W_RNA
+Lhp1 interactsWith YNL134C_RNA
+Lhp1 interactsWith YNL135C_RNA
+Lhp1 interactsWith YNL138W_RNA
+Lhp1 interactsWith YNL154C_RNA
+Lhp1 interactsWith YNL160W_RNA
+Lhp1 interactsWith YNL168C_RNA
+Lhp1 interactsWith YNL169C_RNA
+Lhp1 interactsWith YNL172W_RNA
+Lhp1 interactsWith YNL178W_RNA
+Lhp1 interactsWith YNL190W_RNA
+Lhp1 interactsWith YNL192W_RNA
+Lhp1 interactsWith YNL209W_RNA
+Lhp1 interactsWith YNL220W_RNA
+Lhp1 interactsWith YNL228W_RNA
+Lhp1 interactsWith YNL231C_RNA
+Lhp1 interactsWith YNL241C_RNA
+Lhp1 interactsWith YNL255C_RNA
+Lhp1 interactsWith YNL287W_RNA
+Lhp1 interactsWith YNL288W_RNA
+Lhp1 interactsWith YNL289W_RNA
+Lhp1 interactsWith YNL297C_RNA
+Lhp1 interactsWith YNL300W_RNA
+Lhp1 interactsWith YNL301C_RNA
+Lhp1 interactsWith YNL302C_RNA
+Lhp1 interactsWith YNL307C_RNA
+Lhp1 interactsWith YNL327W_RNA
+Lhp1 interactsWith YNL330C_RNA
+Lhp1 interactsWith YNR050C_RNA
+Lhp1 interactsWith YNR053C_RNA
+Lhp1 interactsWith iYOL052C_RNA
+Lhp1 interactsWith iYOR040W_RNA
+Lhp1 interactsWith iYOR062C_RNA
+Lhp1 interactsWith iYOR072W-1_RNA
+Lhp1 interactsWith iYOR103C_RNA
+Lhp1 interactsWith iYOR181W_RNA
+Lhp1 interactsWith iYOR207C_RNA
+Lhp1 interactsWith iYOR222W_RNA
+Lhp1 interactsWith iYOR235W_RNA
+Lhp1 interactsWith iYOR277C_RNA
+Lhp1 interactsWith iYOR307C_RNA
+Lhp1 interactsWith iYOR348C_RNA
+Lhp1 interactsWith iYOR377W-1_RNA
+Lhp1 interactsWith SNR8_RNA
+Lhp1 interactsWith tM(CAU)O2_RNA
+Lhp1 interactsWith tR(ACG)O_RNA
+Lhp1 interactsWith YOL005C_RNA
+Lhp1 interactsWith YOL036W_RNA
+Lhp1 interactsWith YOL039W_RNA
+Lhp1 interactsWith YOL040C_RNA
+Lhp1 interactsWith YOL059W_RNA
+Lhp1 interactsWith YOL072W_RNA
+Lhp1 interactsWith YOL075C_RNA
+Lhp1 interactsWith YOL077C_RNA
+Lhp1 interactsWith YOL086C_RNA
+Lhp1 interactsWith YOL098C_RNA
+Lhp1 interactsWith YOL100W_RNA
+Lhp1 interactsWith YOL102C_RNA
+Lhp1 interactsWith YOL103W_RNA
+Lhp1 interactsWith YOL106W_RNA
+Lhp1 interactsWith YOL109W_RNA
+Lhp1 interactsWith YOL120C_RNA
+Lhp1 interactsWith YOL121C_RNA
+Lhp1 interactsWith YOL139C_RNA
+Lhp1 interactsWith YOLCdelta2_RNA
+Lhp1 interactsWith YOLWdelta6_RNA
+Lhp1 interactsWith YOR063W_RNA
+Lhp1 interactsWith YOR065W_RNA
+Lhp1 interactsWith YOR067C_RNA
+Lhp1 interactsWith YOR068C_RNA
+Lhp1 interactsWith YOR071C_RNA
+Lhp1 interactsWith YOR075W_RNA
+Lhp1 interactsWith YOR095C_RNA
+Lhp1 interactsWith YOR096W_RNA
+Lhp1 interactsWith YOR098C_RNA
+Lhp1 interactsWith YOR099W_RNA
+Lhp1 interactsWith YOR102W_RNA
+Lhp1 interactsWith YOR103C_RNA
+Lhp1 interactsWith YOR108W_RNA
+Lhp1 interactsWith YOR122C_RNA
+Lhp1 interactsWith YOR127W_RNA
+Lhp1 interactsWith YOR129C_RNA
+Lhp1 interactsWith YOR132W_RNA
+Lhp1 interactsWith YOR133W_RNA
+Lhp1 interactsWith YOR136W_RNA
+Lhp1 interactsWith YOR153W_RNA
+Lhp1 interactsWith YOR155C_RNA
+Lhp1 interactsWith YOR167C_RNA
+Lhp1 interactsWith YOR168W_RNA
+Lhp1 interactsWith YOR175C_RNA
+Lhp1 interactsWith YOR185C_RNA
+Lhp1 interactsWith YOR187W_RNA
+Lhp1 interactsWith YOR191W_RNA
+Lhp1 interactsWith YOR194C_RNA
+Lhp1 interactsWith YOR197W_RNA
+Lhp1 interactsWith YOR198C_RNA
+Lhp1 interactsWith YOR204W_RNA
+Lhp1 interactsWith YOR217W_RNA
+Lhp1 interactsWith YOR219C_RNA
+Lhp1 interactsWith YOR221C_RNA
+Lhp1 interactsWith YOR230W_RNA
+Lhp1 interactsWith YOR232W_RNA
+Lhp1 interactsWith YOR254C_RNA
+Lhp1 interactsWith YOR257W_RNA
+Lhp1 interactsWith YOR260W_RNA
+Lhp1 interactsWith YOR261C_RNA
+Lhp1 interactsWith YOR264W_RNA
+Lhp1 interactsWith YOR270C_RNA
+Lhp1 interactsWith YOR286W_RNA
+Lhp1 interactsWith YOR293W_RNA
+Lhp1 interactsWith YOR312C_RNA
+Lhp1 interactsWith YOR315W_RNA
+Lhp1 interactsWith YOR317W_RNA
+Lhp1 interactsWith YOR323C_RNA
+Lhp1 interactsWith YOR326W_RNA
+Lhp1 interactsWith YOR331C_RNA
+Lhp1 interactsWith YOR352W_RNA
+Lhp1 interactsWith YOR353C_RNA
+Lhp1 interactsWith YOR369C_RNA
+Lhp1 interactsWith YOR372C_RNA
+Lhp1 interactsWith YOR385W_RNA
+Lhp1 interactsWith iSNR59_RNA
+Lhp1 interactsWith iSNR70_RNA
+Lhp1 interactsWith iYPL063W_RNA
+Lhp1 interactsWith iYPL087W_RNA
+Lhp1 interactsWith iYPL135W_RNA
+Lhp1 interactsWith iYPL144W_RNA
+Lhp1 interactsWith iYPL146C_RNA
+Lhp1 interactsWith iYPL155C_RNA
+Lhp1 interactsWith iYPL162C_RNA
+Lhp1 interactsWith iYPL163C_RNA
+Lhp1 interactsWith iYPL183W-A_RNA
+Lhp1 interactsWith iYPL190C_RNA
+Lhp1 interactsWith iYPL192C_RNA
+Lhp1 interactsWith iYPL218W_RNA
+Lhp1 interactsWith iYPL226W_RNA
+Lhp1 interactsWith iYPL242C_RNA
+Lhp1 interactsWith iYPR027C_RNA
+Lhp1 interactsWith iYPR030W_RNA
+Lhp1 interactsWith iYPR045C_RNA
+Lhp1 interactsWith iYPR046W_RNA
+Lhp1 interactsWith iYPR079W_RNA
+Lhp1 interactsWith iYPRCdelta13_RNA
+Lhp1 interactsWith SNR45_RNA
+Lhp1 interactsWith SNR70_RNA
+Lhp1 interactsWith tC(GCA)P2_RNA
+Lhp1 interactsWith tE(UUC)P_RNA
+Lhp1 interactsWith tF(GAA)P2_RNA
+Lhp1 interactsWith tI(AAU)P2_RNA
+Lhp1 interactsWith tK(CUU)P_RNA
+Lhp1 interactsWith tK(UUU)P_RNA
+Lhp1 interactsWith tM(CAU)P_RNA
+Lhp1 interactsWith tN(GUU)P_RNA
+Lhp1 interactsWith tS(UGA)P_RNA
+Lhp1 interactsWith tT(UGU)P_RNA
+Lhp1 interactsWith tW(CCA)P_RNA
+Lhp1 interactsWith YPL014W_RNA
+Lhp1 interactsWith YPL028W_RNA
+Lhp1 interactsWith YPL032C_RNA
+Lhp1 interactsWith YPL037C_RNA
+Lhp1 interactsWith YPL046C_RNA
+Lhp1 interactsWith YPL048W_RNA
+Lhp1 interactsWith YPL058C_RNA
+Lhp1 interactsWith YPL061W_RNA
+Lhp1 interactsWith YPL081W_RNA
+Lhp1 interactsWith YPL082C_RNA
+Lhp1 interactsWith YPL084W_RNA
+Lhp1 interactsWith YPL090C_RNA
+Lhp1 interactsWith YPL094C_RNA
+Lhp1 interactsWith YPL106C_RNA
+Lhp1 interactsWith YPL110C_RNA
+Lhp1 interactsWith YPL112C_RNA
+Lhp1 interactsWith YPL116W_RNA
+Lhp1 interactsWith YPL117C_RNA
+Lhp1 interactsWith YPL131W_RNA
+Lhp1 interactsWith YPL142C_RNA
+Lhp1 interactsWith YPL155C_RNA
+Lhp1 interactsWith YPL178W_RNA
+Lhp1 interactsWith YPL183C_RNA
+Lhp1 interactsWith YPL190C_RNA
+Lhp1 interactsWith YPL197C_RNA
+Lhp1 interactsWith YPL198W_RNA
+Lhp1 interactsWith YPL217C_RNA
+Lhp1 interactsWith YPL218W_RNA
+Lhp1 interactsWith YPL220W_RNA
+Lhp1 interactsWith YPL221W_RNA
+Lhp1 interactsWith YPL240C_RNA
+Lhp1 interactsWith YPL246C_RNA
+Lhp1 interactsWith YPL248C_RNA
+Lhp1 interactsWith YPL250C_RNA
+Lhp1 interactsWith YPL271W_RNA
+Lhp1 interactsWith YPL281C_RNA
+Lhp1 interactsWith YPR021C_RNA
+Lhp1 interactsWith YPR022C_RNA
+Lhp1 interactsWith YPR028W_RNA
+Lhp1 interactsWith YPR029C_RNA
+Lhp1 interactsWith YPR035W_RNA
+Lhp1 interactsWith YPR036W_RNA
+Lhp1 interactsWith YPR043W_RNA
+Lhp1 interactsWith YPR062W_RNA
+Lhp1 interactsWith YPR065W_RNA
+Lhp1 interactsWith YPR074C_RNA
+Lhp1 interactsWith YPR080W_RNA
+Lhp1 interactsWith YPR090W_RNA
+Lhp1 interactsWith YPR091C_RNA
+Lhp1 interactsWith YPR097W_RNA
+Lhp1 interactsWith YPR102C_RNA
+Lhp1 interactsWith YPR122W_RNA
+Lhp1 interactsWith YPR125W_RNA
+Lhp1 interactsWith YPR132W_RNA
+Lhp1 interactsWith YPR145W_RNA
+Lhp1 interactsWith YPR148C_RNA
+Lhp1 interactsWith YPR149W_RNA
+Lhp1 interactsWith YPR156C_RNA
+Lhp1 interactsWith YPR159W_RNA
+Lhp1 interactsWith YPR161C_RNA
+Lhp1 interactsWith YPR163C_RNA
+Lhp1 interactsWith YPR165W_RNA
+Lhp1 interactsWith YPR181C_RNA
+Lhp1 interactsWith YPR183W_RNA
+Lhp1 interactsWith YPR185W_RNA
+Lhp1 interactsWith YPR204W_RNA
+Lhp1 interactsWith Q0125_RNA
+Lhp1 interactsWith Q0183A_RNA
+Lhp1 interactsWith Q0183B_RNA
+Lhp1 interactsWith Q0185D_RNA
+Lhp1 interactsWith Q0190A_RNA
+Lhp1 interactsWith Q0190B_RNA
+Lhp1 interactsWith Q0280A_RNA
+Lhp1 interactsWith Q0280D_RNA
+Lhp1 interactsWith Q0310_RNA
+Lhp1 interactsWith Q0350_RNA
+Unknown interactsWith Srb2
+Unknown interactsWith Srb6
+Unknown interactsWith Med6
+Pol2-Dpb2 interactsWith Pol2-Dpb2
+Dpb2 pp Dpb4
+Dpb2 pp Dpb3
+Pol2 pp Dpb2
+Dpb3 pp Dpb4
+Dpb2 pp Dpb2
+Rtt103 interactsWith Unknown
+Unknown interactsWith Rai1
+Unknown interactsWith Rat1
+Unknown interactsWith RNApII
+Rtt103 pp Rpo21
+Tfc4 pp Brf1
+Spt15 pp Brf1
+Rpc17 pp Brf1
+Rpc17 pp Rpc11
+Rpc17 pp Rpc31
+Unknown interactsWith Rpo31
+Unknown interactsWith Ret1
+Unknown interactsWith Rpc82
+Unknown interactsWith Rpc53
+Unknown interactsWith Rpc40
+Unknown interactsWith Rpc37
+Unknown interactsWith Rpc34
+Unknown interactsWith Rpb5
+Unknown interactsWith Rpc25
+Unknown interactsWith Rpo26
+Unknown interactsWith Rpc19
+Unknown interactsWith Rpb8
+Unknown interactsWith Rpc10
+Unknown interactsWith Rpb10
+Vam3 pp Vps1
+Vam3 pp Vam3
+Vam3 pp Vti1
+Vam3 pp Sec17
+Dad2 interactsWith Unknown
+Unknown interactsWith Dam1
+Unknown interactsWith Spc19
+Unknown interactsWith Ask1
+Unknown interactsWith Spc34
+Unknown interactsWith Duo1
+Unknown interactsWith Dad1
+Ndc80 interactsWith Unknown
+Unknown interactsWith Nuf2
+Unknown interactsWith Spc24
+Srb4_subcomplex interactsWith Med9/10_module
+Ost1 pp Ost2
+Ost1 pp Ost3
+Ost1 pp Ost4
+Ost1 pp Ost5
+Ost1 pp Ost6
+Ost1 pp Wbp1
+Ost1 pp Stt3
+Rpc34 pp Brf1
+Std1 pp Snf1
+Rpb10 pp Rpa135
+Rpc10 pp Rpa135
+Swp1 pp Wbp1
+Swp1 pp Stt3
+Wbp1 pp Stt3
+Ost1 pp Swp1
+Wbp1 pp Ost2
+Stt3 pp Ost5
+Wbp1 pp Ost5
+SCC1 pd 3_312_595_at
+SCC1 pd 3_312_595_x_at
+SCC1 pd 3_919_1183_at
+SCC1 pd 3_1206_1500_at
+SCC1 pd 3_1206_1500_s_at
+SCC1 pd 3_7226_7472_at
+SCC1 pd 3_7226_7472_x_at
+SCC1 pd 3_7801_8078_at
+SCC1 pd 3_8478_8700_at
+SCC1 pd 3_8478_8700_x_at
+SCC1 pd 3_8701_8998_at
+SCC1 pd 3_8701_8998_x_at
+SCC1 pd 3_11401_11520_s_at
+SCC1 pd 3_14006_14100_s_at
+SCC1 pd 3_15301_15600_at
+SCC1 pd 3_15601_15900_at
+SCC1 pd 3_15901_16200_at
+SCC1 pd 3_16201_16500_at
+SCC1 pd 3_16501_16800_at
+SCC1 pd 3_16801_17100_at
+SCC1 pd 3_19801_20100_at
+SCC1 pd 3_20101_20400_at
+SCC1 pd 3_20401_20700_at
+SCC1 pd 3_20701_21000_at
+SCC1 pd 3_21001_21300_at
+SCC1 pd 3_21301_21600_at
+SCC1 pd 3_27001_27300_at
+SCC1 pd 3_27301_27600_at
+SCC1 pd 3_29101_29400_at
+SCC1 pd 3_29401_29700_at
+SCC1 pd 3_32401_32700_at
+SCC1 pd 3_32701_33000_at
+SCC1 pd 3_33001_33300_at
+SCC1 pd 3_33301_33600_at
+SCC1 pd 3_33601_33900_at
+SCC1 pd 3_33901_34200_at
+SCC1 pd 3_34201_34500_at
+SCC1 pd 3_34501_34800_at
+SCC1 pd 3_34801_35100_at
+SCC1 pd 3_35101_35400_at
+SCC1 pd 3_35401_35700_at
+SCC1 pd 3_36001_36300_at
+SCC1 pd 3_36301_36600_at
+SCC1 pd 3_36601_36900_at
+SCC1 pd 3_36901_37200_at
+SCC1 pd 3_37201_37500_at
+SCC1 pd 3_37501_37800_at
+SCC1 pd 3_37801_38100_at
+SCC1 pd 3_38101_38400_at
+SCC1 pd 3_38401_38700_at
+SCC1 pd 3_38701_39000_at
+SCC1 pd 3_48001_48300_at
+SCC1 pd 3_52801_53100_at
+SCC1 pd 3_53101_53400_at
+SCC1 pd 3_53401_53700_at
+SCC1 pd 3_53701_54000_at
+SCC1 pd 3_54001_54300_at
+SCC1 pd 3_54301_54600_at
+SCC1 pd 3_54601_54900_at
+SCC1 pd 3_54901_55200_at
+SCC1 pd 3_55201_55500_at
+SCC1 pd 3_55501_55800_at
+SCC1 pd 3_55801_56100_at
+SCC1 pd 3_56101_56400_at
+SCC1 pd 3_56401_56700_at
+SCC1 pd 3_62101_62400_at
+SCC1 pd 3_62701_63000_at
+SCC1 pd 3_63001_63300_at
+SCC1 pd 3_63301_63600_at
+SCC1 pd 3_63601_63900_at
+SCC1 pd 3_63901_64200_at
+SCC1 pd 3_64201_64500_at
+SCC1 pd 3_64501_64800_at
+SCC1 pd 3_64801_65100_at
+SCC1 pd 3_72001_72300_at
+SCC1 pd 3_72301_72600_at
+SCC1 pd 3_72601_72900_at
+SCC1 pd 3_72901_73200_at
+SCC1 pd 3_73201_73500_at
+SCC1 pd 3_73501_73800_at
+SCC1 pd 3_80701_81000_at
+SCC1 pd 3_81001_81300_at
+SCC1 pd 3_81301_81600_at
+SCC1 pd 3_81601_81900_at
+SCC1 pd 3_81901_82200_at
+SCC1 pd 3_91501_91800_at
+SCC1 pd 3_91801_92100_at
+SCC1 pd 3_92101_92400_at
+SCC1 pd 3_92401_92700_at
+SCC1 pd 3_92701_93000_at
+SCC1 pd 3_93001_93300_at
+SCC1 pd 3_93301_93600_at
+SCC1 pd 3_93601_93900_at
+SCC1 pd 3_93901_94200_at
+SCC1 pd 3_97201_97500_at
+SCC1 pd 3_98101_98400_at
+SCC1 pd 3_98401_98700_at
+SCC1 pd 3_98701_99000_at
+SCC1 pd 3_99001_99300_at
+SCC1 pd 3_99301_99600_at
+SCC1 pd 3_99601_99900_at
+SCC1 pd 3_99901_100200_at
+SCC1 pd 3_100201_100500_at
+SCC1 pd 3_100501_100800_at
+SCC1 pd 3_100801_101100_at
+SCC1 pd 3_101101_101400_at
+SCC1 pd 3_101401_101700_at
+SCC1 pd 3_101701_102000_at
+SCC1 pd 3_102001_102300_at
+SCC1 pd 3_102301_102600_at
+SCC1 pd 3_102601_102900_at
+SCC1 pd 3_102901_103200_at
+SCC1 pd 3_103201_103500_at
+SCC1 pd 3_103501_103800_at
+SCC1 pd 3_103801_104100_at
+SCC1 pd 3_104101_104400_at
+SCC1 pd 3_105601_105900_at
+SCC1 pd 3_105901_106200_at
+SCC1 pd 3_106201_106500_at
+SCC1 pd 3_108901_109200_at
+SCC1 pd 3_109201_109500_at
+SCC1 pd 3_109501_109800_at
+SCC1 pd 3_109801_110100_at
+SCC1 pd 3_110101_110400_at
+SCC1 pd 3_110401_110700_at
+SCC1 pd 3_110701_111000_at
+SCC1 pd 3_111001_111300_at
+SCC1 pd 3_111301_111600_at
+SCC1 pd 3_111601_111900_at
+SCC1 pd 3_111901_112200_at
+SCC1 pd 3_112201_112500_at
+SCC1 pd 3_112501_112800_at
+SCC1 pd 3_112801_113100_at
+SCC1 pd 3_113101_113400_at
+SCC1 pd 3_113401_113700_at
+SCC1 pd 3_113701_114000_at
+SCC1 pd 3_114001_114300_at
+SCC1 pd 3_114301_114600_at
+SCC1 pd 3_114601_114900_at
+SCC1 pd 3_114901_115200_at
+SCC1 pd 3_115201_115500_at
+SCC1 pd 3_115501_115800_at
+SCC1 pd 3_115801_116100_at
+SCC1 pd 3_116101_116400_at
+SCC1 pd 3_116401_116700_at
+SCC1 pd 3_116701_117000_at
+SCC1 pd 3_117001_117300_at
+SCC1 pd 3_117301_117600_at
+SCC1 pd 3_117601_117900_at
+SCC1 pd 3_118801_119100_at
+SCC1 pd 3_120301_120600_at
+SCC1 pd 3_120901_121200_at
+SCC1 pd 3_121201_121500_at
+SCC1 pd 3_121501_121800_at
+SCC1 pd 3_121801_122100_at
+SCC1 pd 3_128101_128400_at
+SCC1 pd 3_128401_128700_at
+SCC1 pd 3_128701_129000_at
+SCC1 pd 3_129001_129300_at
+SCC1 pd 3_129301_129600_at
+SCC1 pd 3_129601_129900_at
+SCC1 pd 3_129901_130200_at
+SCC1 pd 3_130201_130500_at
+SCC1 pd 3_130501_130800_at
+SCC1 pd 3_130801_131100_at
+SCC1 pd 3_131101_131400_at
+SCC1 pd 3_131401_131700_at
+SCC1 pd 3_131701_132000_at
+SCC1 pd 3_132001_132300_at
+SCC1 pd 3_132301_132600_at
+SCC1 pd 3_132601_132900_at
+SCC1 pd 3_132901_133200_at
+SCC1 pd 3_133201_133500_at
+SCC1 pd 3_133501_133800_at
+SCC1 pd 3_133801_134100_at
+SCC1 pd 3_134101_134400_at
+SCC1 pd 3_134401_134700_at
+SCC1 pd 3_134701_135000_at
+SCC1 pd 3_135301_135600_at
+SCC1 pd 3_135601_135900_at
+SCC1 pd 3_139201_139500_at
+SCC1 pd 3_139501_139800_at
+SCC1 pd 3_139801_140100_at
+SCC1 pd 3_140101_140400_at
+SCC1 pd 3_140401_140700_at
+SCC1 pd 3_140701_141000_at
+SCC1 pd 3_143401_143700_at
+SCC1 pd 3_143701_144000_at
+SCC1 pd 3_144001_144300_at
+SCC1 pd 3_144301_144600_at
+SCC1 pd 3_144601_144900_at
+SCC1 pd 3_144901_145200_at
+SCC1 pd 3_145201_145500_at
+SCC1 pd 3_151820_152100_at
+SCC1 pd 3_152101_152400_at
+SCC1 pd 3_152401_152700_at
+SCC1 pd 3_152701_153000_at
+SCC1 pd 3_153001_153300_at
+SCC1 pd 3_153301_153600_at
+SCC1 pd 3_153601_153900_at
+SCC1 pd 3_153901_154200_at
+SCC1 pd 3_154201_154500_at
+SCC1 pd 3_154801_155100_at
+SCC1 pd 3_156301_156600_at
+SCC1 pd 3_156601_156900_at
+SCC1 pd 3_156901_157200_at
+SCC1 pd 3_157201_157500_at
+SCC1 pd 3_157501_157800_at
+SCC1 pd 3_158401_158700_at
+SCC1 pd 3_159901_160200_at
+SCC1 pd 3_169528_169800_at
+SCC1 pd 3_169801_170100_at
+SCC1 pd 3_170101_170400_at
+SCC1 pd 3_170401_170700_at
+SCC1 pd 3_170701_171000_at
+SCC1 pd 3_171001_171300_at
+SCC1 pd 3_174301_174600_at
+SCC1 pd 3_174601_174900_at
+SCC1 pd 3_187201_187500_at
+SCC1 pd 3_187501_187800_at
+SCC1 pd 3_187801_188100_at
+SCC1 pd 3_188101_188400_at
+SCC1 pd 3_188401_188700_at
+SCC1 pd 3_188701_189000_at
+SCC1 pd 3_190201_190500_at
+SCC1 pd 3_190501_190800_at
+SCC1 pd 3_190801_191100_at
+SCC1 pd 3_191101_191400_at
+SCC1 pd 3_191401_191700_at
+SCC1 pd 3_191701_192000_at
+SCC1 pd 3_192001_192300_at
+SCC1 pd 3_192301_192600_at
+SCC1 pd 3_192601_192900_at
+SCC1 pd 3_192901_193200_at
+SCC1 pd 3_193501_193800_at
+SCC1 pd 3_193801_194100_at
+SCC1 pd 3_194101_194400_at
+SCC1 pd 3_194401_194700_at
+SCC1 pd 3_194701_195000_at
+SCC1 pd 3_195001_195300_at
+SCC1 pd 3_198501_198600_at
+SCC1 pd 3_198701_198800-m_at
+SCC1 pd 3_198701_198800-m-r_at
+SCC1 pd 3_198801_198900-m_at
+SCC1 pd 3_198801_198900-m-r_at
+SCC1 pd 3_198901_199000-m_at
+SCC1 pd 3_198901_199000-m-r_at
+SCC1 pd 3_199001_199100-m_at
+SCC1 pd 3_199001_199100-m-r_at
+SCC1 pd 3_199101_199200-m_at
+SCC1 pd 3_199101_199200-m-r_at
+SCC1 pd 3_199201_199300-m_at
+SCC1 pd 3_199201_199300-m-r_at
+SCC1 pd 3_199301_199400-m_at
+SCC1 pd 3_199301_199400-m-r_at
+SCC1 pd 3_199401_199500-m_at
+SCC1 pd 3_199401_199500-m-r_at
+SCC1 pd 3_199501_199600-m_s_at
+SCC1 pd 3_199601_199700-m_s_at
+SCC1 pd 3_199601_199700-m-r_at
+SCC1 pd 3_199701_199800-m_s_at
+SCC1 pd 3_199701_199800-m-r_at
+SCC1 pd 3_199801_199900-m_s_at
+SCC1 pd 3_199801_199900-m-r_at
+SCC1 pd 3_199901_200000-m_s_at
+SCC1 pd 3_199901_200000-m-r_at
+SCC1 pd 3_200001_200100-m_s_at
+SCC1 pd 3_200001_200100-m-r_at
+SCC1 pd 3_200101_200200-m_at
+SCC1 pd 3_200101_200200-m-r_at
+SCC1 pd 3_200201_200300-m_at
+SCC1 pd 3_200201_200300-m-r_at
+SCC1 pd 3_200301_200400-m_at
+SCC1 pd 3_200301_200400-m-r_at
+SCC1 pd 3_200401_200500-m_at
+SCC1 pd 3_200501_200600-m_at
+SCC1 pd 3_200601_200700-m_at
+SCC1 pd 3_200701_200800-m_at
+SCC1 pd 3_200701_200800-m-r_at
+SCC1 pd 3_200801_200900-m_at
+SCC1 pd 3_200801_200900-m-r_at
+SCC1 pd 3_200901_201000-m-r_at
+SCC1 pd 3_201001_201100-m-r_at
+SCC1 pd 3_201101_201200-m_at
+SCC1 pd 3_201101_201200-m-r_at
+SCC1 pd 3_201301_201400_at
+SCC1 pd 3_201401_201500-r_at
+SCC1 pd 3_201501_201600_at
+SCC1 pd 3_201601_201700_at
+SCC1 pd 3_201601_201700-r_at
+SCC1 pd 3_201701_201800_at
+SCC1 pd 3_201701_201800-r_at
+SCC1 pd 3_218401_218700_at
+SCC1 pd 3_218701_219000_at
+SCC1 pd 3_219001_219300_at
+SCC1 pd 3_219301_219600_at
+SCC1 pd 3_220201_220500_at
+SCC1 pd 3_230101_230400_at
+SCC1 pd 3_230401_230700_at
+SCC1 pd 3_230701_230997_at
+SCC1 pd 3_231027_231300_at
+SCC1 pd 3_231301_231600_at
+SCC1 pd 3_231601_231900_at
+SCC1 pd 3_231901_232200_at
+SCC1 pd 3_232201_232500_at
+SCC1 pd 3_232501_232800_at
+SCC1 pd 3_232801_233100_at
+SCC1 pd 3_233101_233400_at
+SCC1 pd 3_233401_233700_at
+SCC1 pd 3_233701_234000_at
+SCC1 pd 3_234001_234300_at
+SCC1 pd 3_234301_234600_at
+SCC1 pd 3_239101_239400_at
+SCC1 pd 3_239401_239700_at
+SCC1 pd 3_240001_240300_at
+SCC1 pd 3_240301_240600_at
+SCC1 pd 3_240601_240900_at
+SCC1 pd 3_240901_241200_at
+SCC1 pd 3_241201_241500_at
+SCC1 pd 3_241501_241800_at
+SCC1 pd 3_247801_248100_at
+SCC1 pd 3_248101_248400_at
+SCC1 pd 3_248701_249000_at
+SCC1 pd 3_249001_249300_at
+SCC1 pd 3_259201_259500_at
+SCC1 pd 3_259501_259800_at
+SCC1 pd 3_259801_260100_at
+SCC1 pd 3_260101_260400_at
+SCC1 pd 3_260401_260700_at
+SCC1 pd 3_260701_261000_at
+SCC1 pd 3_261001_261300_at
+SCC1 pd 3_261301_261600_at
+SCC1 pd 3_261601_261900_at
+SCC1 pd 3_261901_262200_at
+SCC1 pd 3_270601_270900_at
+SCC1 pd 3_270901_271200_at
+SCC1 pd 3_271201_271500_at
+SCC1 pd 3_271501_271800_at
+SCC1 pd 3_271801_272100_at
+SCC1 pd 3_272101_272400_at
+SCC1 pd 3_273601_273900_at
+SCC1 pd 3_274501_274800_at
+SCC1 pd 3_274801_275100_at
+SCC1 pd 3_275101_275400_at
+SCC1 pd 3_275401_275700_at
+SCC1 pd 3_275701_276000_at
+SCC1 pd 3_276001_276300_at
+SCC1 pd 3_276901_277200_at
+SCC1 pd 3_277201_277500_at
+SCC1 pd 3_277501_277800_at
+SCC1 pd 3_277801_278100_at
+SCC1 pd 3_291601_291900_at
+SCC1 pd 3_291901_292200_at
+SCC1 pd 3_292501_292800_at
+SCC1 pd 3_293101_293400-m_at
+SCC1 pd 3_293101_293400-m_x_at
+SCC1 pd 3_293401_293700-m_at
+SCC1 pd 3_293401_293700-m_x_at
+SCC1 pd 3_293730_294000_at
+SCC1 pd 3_294001_294300_at
+SCC1 pd 3_294301_294600_at
+SCC1 pd 3_294601_294900_at
+SCC1 pd 3_294901_295200_at
+SCC1 pd 3_295801_296100_at
+SCC1 pd 3_296101_296400_at
+SCC1 pd 3_296401_296700_at
+SCC1 pd 3_296701_297000_at
+SCC1 pd 3_297001_297300_at
+SCC1 pd 3_297301_297600_at
+SCC1 pd 3_297601_297900_at
+SCC1 pd 3_297901_298200_at
+SCC1 pd 3_304801_305100_at
+SCC1 pd 3_304801_305100_x_at
+SCC1 pd 3_307829_308048_at
+SCC1 pd 3_308117_308400_at
+SCC1 pd 3_308401_308700_at
+SCC1 pd 3_309001_309300_at
+SCC1 pd 3_309301_309600_at
+SCC1 pd 3_315301_315550_s_at
+SCC1 pd 3_315658_315889_s_at
+SCC1 pd 4_16515_16743_at
+SCC1 pd 4_16515_16743_s_at
+SCC1 pd 4_17101_17400_x_at
+SCC1 pd 4_24001_24300_at
+SCC1 pd 4_24301_24600_at
+SCC1 pd 4_24601_24900_at
+SCC1 pd 4_25501_25800_at
+SCC1 pd 4_25801_26100_at
+SCC1 pd 4_26101_26400_at
+SCC1 pd 4_26401_26700_at
+SCC1 pd 4_26701_27000_at
+SCC1 pd 4_27001_27300_at
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+SCC1 pd 5_427201_427500_at
+SCC1 pd 5_433801_434100_at
+SCC1 pd 5_434101_434400_at
+SCC1 pd 5_434401_434636_s_at
+SCC1 pd 5_441601_441900_at
+SCC1 pd 5_442501_442789_at
+SCC1 pd 5_442801_443100_s_at
+SCC1 pd 5_443101_443364_at
+SCC1 pd 5_453301_453600_at
+SCC1 pd 5_453601_453900_at
+SCC1 pd 5_453901_454200_at
+SCC1 pd 5_454201_454500_at
+SCC1 pd 5_455101_455400_at
+SCC1 pd 5_455401_455700_at
+SCC1 pd 5_455701_456000_at
+SCC1 pd 5_456001_456300_at
+SCC1 pd 5_456301_456600_at
+SCC1 pd 5_456601_456900_at
+SCC1 pd 5_456901_457200_at
+SCC1 pd 5_457201_457500_at
+SCC1 pd 5_457501_457800_at
+SCC1 pd 5_457801_458100_at
+SCC1 pd 5_458101_458400_at
+SCC1 pd 5_458401_458700_at
+SCC1 pd 5_458701_459000_at
+SCC1 pd 5_465601_465900_s_at
+SCC1 pd 5_465901_466200_s_at
+SCC1 pd 5_466201_466500_at
+SCC1 pd 5_466501_466800_at
+SCC1 pd 5_466801_467100_at
+SCC1 pd 5_467101_467400_at
+SCC1 pd 5_468301_468600_at
+SCC1 pd 5_468601_468900_at
+SCC1 pd 5_468901_469200_at
+SCC1 pd 5_469201_469449_at
+SCC1 pd 5_469533_469800_at
+SCC1 pd 5_469801_470100_at
+SCC1 pd 5_470101_470400_at
+SCC1 pd 5_470401_470700_at
+SCC1 pd 5_470701_471000_at
+SCC1 pd 5_471601_471900_at
+SCC1 pd 5_471901_472200_at
+SCC1 pd 5_475501_475800_at
+SCC1 pd 5_475801_476100_at
+SCC1 pd 5_476101_476400_at
+SCC1 pd 5_476701_477000_at
+SCC1 pd 5_477001_477300_at
+SCC1 pd 5_488164_488400_at
+SCC1 pd 5_489601_489900_at
+SCC1 pd 5_489901_490200_at
+SCC1 pd 5_491701_492000_at
+SCC1 pd 5_499501_499800_at
+SCC1 pd 5_499801_500100_at
+SCC1 pd 5_500101_500400_at
+SCC1 pd 5_509101_509400_at
+SCC1 pd 5_518401_518700_at
+SCC1 pd 5_518701_519000_at
+SCC1 pd 5_519001_519300_at
+SCC1 pd 5_519301_519600_at
+SCC1 pd 5_519601_519900_at
+SCC1 pd 5_519901_520200_at
+SCC1 pd 5_520201_520500_at
+SCC1 pd 5_520501_520800_at
+SCC1 pd 5_520801_521100_at
+SCC1 pd 5_521101_521400_at
+SCC1 pd 5_521401_521700_at
+SCC1 pd 5_521701_522000_at
+SCC1 pd 5_522001_522300_at
+SCC1 pd 5_522301_522600_at
+SCC1 pd 5_528301_528600_at
+SCC1 pd 5_528601_528900_at
+SCC1 pd 5_528901_529200_at
+SCC1 pd 5_529201_529500_at
+SCC1 pd 5_529801_530100_at
+SCC1 pd 5_530101_530400_at
+SCC1 pd 5_537601_537900_at
+SCC1 pd 5_542401_542700_at
+SCC1 pd 5_542701_543000_at
+SCC1 pd 5_547501_547800_at
+SCC1 pd 5_547801_548100_at
+SCC1 pd 5_548101_548400_at
+SCC1 pd 5_548401_548700_at
+SCC1 pd 5_548701_549000_at
+SCC1 pd 5_549001_549300_at
+SCC1 pd 5_549301_549600_at
+SCC1 pd 5_555001_555300_at
+SCC1 pd 5_555301_555600_at
+SCC1 pd 5_555601_555900_at
+SCC1 pd 5_556501_556800_at
+SCC1 pd 5_556801_557100_at
+SCC1 pd 5_557101_557400_at
+SCC1 pd 5_557401_557700_at
+SCC1 pd 5_557701_558000_at
+SCC1 pd 5_558001_558300_at
+SCC1 pd 5_566701_567000_at
+SCC1 pd 5_569401_569700_at
+SCC1 pd 5_569401_569700_s_at
+SCC1 pd 5_570022_570300_s_at
+SCC1 pd 6_147001_147300-r_at
+SCC1 pd 6_147301_147600-r_at
+SCC1 pd 6_147601_147900-r_at
+SCC1 pd 6_147901_148200-r_at
+SCC1 pd 6_148201_148500-r_at
+SCC1 pd 6_148501_148800-r_at
+SCC1 pd 6_148801_149100-r_at
+SCC1 pd 6_149101_149400-r_at
+SCC1 pd 6_149401_149700-r_at
+SCC1 pd 6_149701_150000-r_at
+SCC1 pd 6_150001_150300-r_at
+SCC1 pd 6_150301_150600-r_at
+SCC1 pd 6_150601_150900-r_at
+SCC1 pd 6_150901_151200-r_at
+SCC1 pd 6_151201_151500-r_at
+SCC1 pd 6_151501_151800-r_at
+SCC1 pd 6_151801_152100-r_at
+SCC1 pd 6_152101_152400-r_at
+SCC1 pd 6_152401_152700-r_at
+SCC1 pd 6_152701_153000-r_at
+SCC1 pd 6_153001_153300-r_at
+SCC1 pd 6_153301_153600-r_at
+SCC1 pd 6_153601_153900-r_at
+SCC1 pd 6_153901_154200-r_at
+SCC1 pd 6_154201_154500-r_at
+SCC1 pd 6_154501_154800-r_at
+SCC1 pd 6_154801_155100-r_at
+SCC1 pd 6_155101_155400-r_at
+SCC1 pd 6_156001_156300-r_at
+SCC1 pd 6_157501_157800-r_at
+SCC1 pd 6_157801_158100-r_at
+SCC1 pd 6_158101_158400-r_at
+SCC1 pd 6_158401_158700-r_at
+SCC1 pd 6_158701_159000-r_at
+SCC1 pd 6_159601_159900-r_at
+SCC1 pd 6_159901_160200-r_at
+SCC1 pd 6_160201_160500-r_at
+SCC1 pd 6_160501_160800-r_at
+SCC1 pd 6_160801_161100-r_at
+SCC1 pd 6_161101_161400-r_at
+SCC1 pd 6_162045_162300-r_s_at
+SCC1 pd 6_165001_165300-r_at
+SCC1 pd 6_165301_165600-r_at
+SCC1 pd 6_165601_165900-r_at
+SCC1 pd 6_165901_166200-r_at
+SCC1 pd 6_166201_166500-r_at
+SCC1 pd 6_168001_168300-r_at
+SCC1 pd 6_168301_168600-r_at
+SCC1 pd 6_168601_168900-r_at
+SCC1 pd 6_168901_169200-r_at
+SCC1 pd 6_169201_169500-r_at
+SCC1 pd 6_169501_169800-r_at
+SCC1 pd 6_170101_170400-r_at
+SCC1 pd 6_170701_171000-r_at
+SCC1 pd 6_171001_171300-r_at
+SCC1 pd 6_171301_171600-r_at
+SCC1 pd 6_171601_171900-r_at
+SCC1 pd 6_171901_172200-r_at
+SCC1 pd 6_172201_172500-r_at
+SCC1 pd 6_172501_172800-r_at
+SCC1 pd 6_172801_173100-r_at
+SCC1 pd 6_173101_173400-r_at
+SCC1 pd 6_173401_173700-r_at
+SCC1 pd 6_173701_174000-r_at
+SCC1 pd 6_177001_177300-r_at
+SCC1 pd 6_177301_177600-r_at
+SCC1 pd 6_177601_177900-r_at
+SCC1 pd 6_177901_178168-r_at
+SCC1 pd 6_177901_178168-r_s_at
+SCC1 pd 6_178228_178500-r_at
+SCC1 pd 6_178801_179100-r_at
+SCC1 pd 6_179101_179400-r_at
+SCC1 pd 6_179401_179700-r_at
+SCC1 pd 6_189001_189300-r_at
+SCC1 pd 6_189301_189600-r_at
+SCC1 pd 6_192301_192600-r_at
+SCC1 pd 6_192601_192900-r_at
+SCC1 pd 6_192901_193200-r_at
+SCC1 pd 6_197701_198000-r_at
+SCC1 pd 6_199501_199800-r_at
+SCC1 pd 6_199801_200100-r_at
+SCC1 pd 6_200101_200400-r_at
+SCC1 pd 6_200401_200700-r_at
+SCC1 pd 6_200701_201000-r_at
+SCC1 pd 6_201001_201300-r_at
+SCC1 pd 6_201301_201600-r_at
+SCC1 pd 6_201901_202200-r_at
+SCC1 pd 6_202201_202500-r_at
+SCC1 pd 6_202501_202800-r_at
+SCC1 pd 6_207301_207600-r_at
+SCC1 pd 6_207601_207900-r_at
+SCC1 pd 6_207901_208200-r_at
+SCC1 pd 6_211501_211800-r_at
+SCC1 pd 6_211801_212100-r_at
+SCC1 pd 6_212101_212400-r_at
+SCC1 pd 6_215101_215400-r_at
+SCC1 pd 6_215401_215700-r_at
+SCC1 pd 6_215701_216000-r_at
+SCC1 pd 6_216001_216300-r_at
+SCC1 pd 6_216301_216600-r_at
+SCC1 pd 6_216601_216900-r_at
+SCC1 pd 6_216901_217200-r_at
+SCC1 pd 6_217201_217500-r_at
+SCC1 pd 6_217501_217800-r_at
+SCC1 pd 6_217801_218100-r_at
+SCC1 pd 6_218101_218400-r_at
+SCC1 pd 6_218401_218700-r_at
+SCC1 pd 6_231001_231300-r_at
+SCC1 pd 6_231301_231600-r_at
+SCC1 pd 6_231601_231900-r_at
+SCC1 pd 6_235801_236100-r_at
+SCC1 pd 6_236101_236400-r_at
+SCC1 pd 6_236401_236700-r_at
+SCC1 pd 6_236701_237000-r_at
+SCC1 pd 6_237301_237600-r_at
+SCC1 pd 6_237601_237900-r_at
+SCC1 pd 6_237901_238200-r_at
+SCC1 pd 6_238201_238500-r_at
+SCC1 pd 6_238501_238800-r_at
+SCC1 pd 6_238801_239100-r_at
+SCC1 pd 6_239101_239400-r_at
+SCC1 pd 6_239401_239700-r_at
+SCC1 pd 6_239701_240000-r_at
+SCC1 pd 6_243301_243600-r_at
+SCC1 pd 6_243601_243900-r_at
+SCC1 pd 6_247201_247500-r_at
+SCC1 pd 6_247801_248100-r_at
+SCC1 pd 6_248101_248400-r_at
+SCC1 pd 6_248401_248700-r_at
+SCC1 pd 6_248701_249000-r_at
+SCC1 pd 6_249001_249300-r_at
+SCC1 pd 6_249301_249600-r_at
+SCC1 pd 6_249601_249900-r_at
+SCC1 pd 6_249901_250200-r_at
+SCC1 pd 6_250201_250500-r_at
+SCC1 pd 6_250501_250800-r_at
+SCC1 pd 6_257101_257400-r_at
+SCC1 pd 6_257401_257700-r_at
+SCC1 pd 6_257701_258000-r_at
+SCC1 pd 6_258601_258900-r_at
+SCC1 pd 6_269701_270000-r_at
+SCC1 pd 6_270001_270148-r_s_at
+SCC1 pd 3_204501_204600_s_at
+SCC1 pd 3_204501_204600-r_at
+SCC1 pd 3_204601_204700_s_at
+SCC1 pd 3_204601_204700-r_at
+SCC1 pd 3_204701_204800_s_at
+SCC1 pd 3_204801_204900_s_at
+SCC1 pd 3_204801_204900-r_at
+SCC1 pd 3_204901_205000_s_at
+SCC1 pd 3_204901_205000-r_at
+SCL1 pp PRE9
+PUP3 pp PUP1
+PRE2 pp PRE1
+PRE4 pp PRE10
+PRE3 pp PUP1
+PRE3 pp SCL1
+PRE3 pp PRE10
+PRE3 pp PRE4
+PUP1 pp PRE7
+PUP1 pp PRE4
+PUP3 pp PRE2
+PRE1 pp PRE2
+PRE2 pp PUP3
+PRE2 pp PRE1
+PRE2 pp PUP1
+PRE7 pp PUP1
+PRE4 pp PRE3
+PRE4 pp PUP1
+PRE3 pp PRE4
+PRE3 pp PRE3
+H4_Peptide pp GCN5
+Gaf pp Gaf
+PRE7 pp PUP2
+PRE4 pp PRE10
+PRE4 pp PRE5
+PRE4 pp PRE7
+PRE3 pp PRE4
+PUP1 pp PRE7
+PUP1 pp PRE4
+PUP3 pp PRE7
+PRE7 pp PUP1
+PRE7 pp PUP3
+PRE4 pp PRE3
+PRE4 pp PUP1
+PRE3 pp PRE4
+Cyp1(Hap1-Pc7)_Activatory_Protein pp Cyp1(Hap1-Pc7)_Activatory_Protein
+Cyp1(Hap1-Pc7)_Activatory_Protein pp Cyp1(Hap1-Pc7)_Activatory_Protein
+Cyp1(Hap1-Pc7)_Activatory_Protein pp Cyp1(Hap1-Pc7)_Activatory_Protein
+RAD53 pp RAD53
+SEC4 pp SEC4
+SEC4 pp SEC4
+HMT1 pp HMT1
+HMT1 pp HMT1
+HMT1 pp HMT1
+HMT1 pp HMT1
+HMT1 pp HMT1
+HMT1 pp HMT1
+HMT1 pp HMT1
+HMT1 pp HMT1
+RIB4 pp RIB4
+RIB4 pp RIB4
+RIB4 pp RIB4
+RIB4 pp RIB4
+URE2 pp URE2
+URE2 pp URE2
+URE2 pp URE2
+IPP1 pp IPP1
+QCR2 pp COR1
+COB pp COR1
+CYT1 pp COB
+RIP1 pp COR1
+RIP1 pp CYT1
+RIP1 pp COB
+QCR6 pp CYT1
+QCR7 pp COB
+QCR7 pp CYT1
+QCR8 pp COB
+QCR8 pp QCR7
+QCR8 pp COR1
+QCR8 pp CYT1
+QCR8 pp RIP1
+QCR8 pp QCR6
+Ubiquinol-Cytochrome_C_Reductase_Complex_7.3_Kd_Protein pp RIP1
+Ubiquinol-Cytochrome_C_Reductase_Complex_7.3_Kd_Protein pp COR1
+Ubiquinol-Cytochrome_C_Reductase_Complex_7.3_Kd_Protein pp CYT1
+GNA1 pp GNA1
+GNA1 pp GNA1
+Regulatory_Protein_Gal4 pp Regulatory_Protein_Gal4
+RPB2 pp RPO21
+RPB3 pp RPB2
+RPB3 pp RPO21
+RPB5 pp RPO21
+RPO26 pp RPO21
+RPB8 pp RPO21
+RPB8 pp RPB3
+RPB9 pp RPB2
+RPB9 pp RPO21
+RPB10 pp RPB2
+RPB10 pp RPB3
+RPB11 pp RPO21
+RPB11 pp RPB3
+RPB11 pp RPB8
+RPC10 pp RPB2
+RPC10 pp RPB3
+RPB2 pp RPO21
+RPB3 pp RPB2
+RPB5 pp RPO21
+RPO26 pp RPO21
+RPB8 pp RPO21
+RPB9 pp RPB2
+RPB9 pp RPO21
+RPB10 pp RPB3
+RPB10 pp RPB2
+RPB11 pp RPO21
+RPB11 pp RPB3
+RPC10 pp RPB2
+RPC10 pp RPB3
+RPB2 pp RPO21
+RPB3 pp RPB2
+RPB3 pp RPO21
+RPB5 pp RPO21
+RPO26 pp RPO21
+RPO26 pp RPB2
+RPB8 pp RPO21
+RPB9 pp RPB2
+RPB9 pp RPO21
+RPB10 pp RPB2
+RPB10 pp RPB3
+RPB11 pp RPO21
+RPB11 pp RPB3
+RPC10 pp RPB3
+Protease_A_Inhibitor_3 pp PEP4
+PRE3 pp SCL1
+PRE3 pp PRE10
+PUP1 pp PRE3
+PUP3 pp PUP1
+PRE2 pp PRE6
+PRE2 pp PRE1
+PRE7 pp PUP2
+PRE4 pp PRE7
+PRE4 pp PRE3
+PRE4 pp PRE10
+SCL1 pp PRE4
+PRE3 pp PRE4
+PRE3 pp PRE3
+PUP1 pp PRE7
+PUP1 pp PRE4
+PUP3 pp PRE2
+PUP3 pp PRE7
+PRE1 pp PRE2
+PRE2 pp PUP3
+PRE2 pp PRE6
+PRE2 pp PRE1
+PRE7 pp PUP1
+PRE7 pp PUP3
+PRE4 pp PRE3
+PRE4 pp PUP1
+HMF1 pp HMF1
+HMF1 pp HMF1
+HMF1 pp HMF1
+1F7U_B interactsWith Arginyl-Trna_Synthetase
+1F7V_B interactsWith Arginyl-Trna_Synthetase
+THI80 pp THI80
+MMS2 pp UBC13
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+MAS1 pp MAS2
+MAS1 pp MAS2
+MAS1 pp MAS2
+Cytochrome_C_Oxidase_Polypeptide_Iv pp MAS1
+MAS1 pp MAS2
+MAS2 pp MAS2
+LPD1 pp LPD1
+RNR4 pp RNR2
+LYS7 pp SOD1
+SOD1 pp LYS7
+SOD1 pp SOD1
+LYS7 pp SOD1
+LYS7 pp LYS7
+HHF1 pp HHT1
+HTB2 pp HTA1
+HTB2 pp HHF1
+HHT1 pp HTA1
+HHT1 pp HHT1
+HHF1 pp HHT1
+HHF1 pp HTA1
+HHF1 pp HTB2
+HTA1 pp HTA1
+HTA1 pp HHT1
+HTA1 pp HHF1
+HTB2 pp HTA1
+HTB2 pp HHF1
+Hypothetical_27.5_Kda_Protein_In_Spx19-Gcr2_Intergenic_Region pp Hypothetical_27.5_Kda_Protein_In_Spx19-Gcr2_Intergenic_Region
+RPL40A pp UBC1
+NIT3 pp NIT3
+Dna_Repair_Protein_Rad9 pp RAD53
+Dna_Repair_Protein_Rad9 pp RAD53
+Dna_Repair_Protein_Rad9 pp RAD53
+Dna_Repair_Protein_Rad9 pp RAD53
+Dna_Repair_Protein_Rad9 pp RAD53
+Dna_Repair_Protein_Rad9 pp RAD53
+Dna_Repair_Protein_Rad9 pp RAD53
+APT1 pp APT1
+ERV2 pp ERV2
+ERV2 pp ERV2
+URE2 pp URE2
+ILV2 pp ILV2
+Doc1APC10 pp Doc1APC10
+PUP3 pp PUP1
+PRE4 pp PRE7
+PRE3 pp PRE4
+PUP1 pp PRE7
+PUP1 pp PRE4
+PUP3 pp PRE2
+PRE2 pp PUP3
+PRE7 pp PUP1
+PRE4 pp PRE3
+PRE4 pp PUP1
+PRE6 pp PRE2
+PUP2 pp PRE7
+PRE5 pp PRE4
+PRE10 pp PRE4
+PRE10 pp PRE3
+SCL1 pp PRE3
+SCL1 pp PUP1
+RPB8 pp RPO21
+RPB10 pp RPB2
+RPB10 pp RPB3
+RPC10 pp RPB3
+Alpha_Amanitin pp RPO21
+Alpha_Amanitin pp RPB2
+CYB2 pp CYB2
+CYB2 pp CYB2
+QCR2 pp COR1
+CYT1 pp COB
+RIP1 pp COB
+QCR6 pp CYT1
+QCR7 pp COB
+QCR8 pp COB
+QCR8 pp CYT1
+Ubiquinol-Cytochrome_C_Reductase_Complex_7.3_Kd_Protein pp RIP1
+Ubiquinol-Cytochrome_C_Reductase_Complex_7.3_Kd_Protein pp COR1
+Ubiquinol-Cytochrome_C_Reductase_Complex_7.3_Kd_Protein pp CYT1
+Heavy_Chain_(Vh)_Of_Fv-Fragment pp RIP1
+Light_Chain_(Vl)_Of_Fv-Fragment pp Heavy_Chain_(Vh)_Of_Fv-Fragment
+Light_Chain_(Vl)_Of_Fv-Fragment pp RIP1
+COR1 pp QCR7
+QCR2 pp COR1
+QCR2 pp QCR2
+QCR2 pp QCR7
+COB pp QCR8
+COB pp COB
+COB pp RIP1
+CYT1 pp COB
+CYT1 pp CYT1
+RIP1 pp COR1
+RIP1 pp COB
+QCR7 pp COB
+QCR7 pp QCR2
+QCR7 pp CYT1
+QCR7 pp COR1
+QCR8 pp QCR8
+QCR8 pp COB
+QCR8 pp COB
+Ubiquinol-Cytochrome_C_Reductase_Complex_7.3_Kd_Protein pp RIP1
+Light_Chain_(Vl)_Of_Fv-Fragment pp Heavy_Chain_(Vh)_Of_Fv-Fragment
+CYC1 pp CYT1
+Myo-Inositol-1-Phosphate_Synthase pp Myo-Inositol-1-Phosphate_Synthase
+Myo-Inositol-1-Phosphate_Synthase pp Myo-Inositol-1-Phosphate_Synthase
+Myo-Inositol-1-Phosphate_Synthase pp Myo-Inositol-1-Phosphate_Synthase
+Inositol-3-Phosphate_Synthase pp Inositol-3-Phosphate_Synthase
+Myo-Inositol-1-Phosphate_Synthase pp Myo-Inositol-1-Phosphate_Synthase
+Myo-Inositol-1-Phosphate_Synthase pp Myo-Inositol-1-Phosphate_Synthase
+Myo-Inositol-1-Phosphate_Synthase pp Myo-Inositol-1-Phosphate_Synthase
+Myo-Inositol-1-Phosphate_Synthase pp Myo-Inositol-1-Phosphate_Synthase
+MET8 pp MET8
+MET8 pp MET8
+APC2 pp APC2
+APC2 pp APC2
+APC2 pp APC2
+APC2 pp APC2
+HMRA2 pp Mating-Type_Protein_A-1
+NTF2 pp NTF2
+NTF2 pp NTF2
+NTF2 pp NTF2
+TFP1 pp TFP1
+Heavy_Chain_(Vh)_Of_Fv-Fragment pp RIP1
+Light_Chain_(Vl)_Of_Fv-Fragment pp RIP1
+1LWS_B pd TFP1
+1LWS_C pd TFP1
+1LWT_B pd TFP1
+1LWT_C pd TFP1
+SAR1 pp SEC23
+ORC1 pp ORC1
+HEM15 pp HEM15
+1LMV_B interactsWith 1LMV_A
+Iq4_Motif_From_Myo2p,_A_Class_V_Myosin pp MLC1
+Integral_Membrane_Protein_Sed5 pp SLY1
+CYS3 pp CYS3
+CYS3 pp CYS3
+CYS3 pp CYS3
+CYS3 pp CYS3
+CYS3 pp CYS3
+CYS3 pp CYS3
+HMRA2 pp HMRA2
+1K61_E pd HMRA2
+1K61_E pd HMRA2
+1K61_E pd HMRA2
+1K61_E pd HMRA2
+1K61_F pd HMRA2
+1K61_F pd HMRA2
+1K61_F pd HMRA2
+GSH2 pp GSH2
+GSH2 pp GSH2
+14-Mer_Peptide_From_Peroxisomal_Membrane_Protein_Pex14 pp PEX13
+SMX3 pp SMX3
+SMX3 pp SMX3
+SMX3 pp SMX3
+SMX3 pp SMX3
+SMX3 pp SMX3
+SMX3 pp SMX3
+SMX3 pp SMX3
+SMX3 pp SMX3
+SMX3 pp SMX3
+SMX3 pp SMX3
+SMX3 pp SMX3
+SMX3 pp SMX3
+ARO4 pp ARO4
+Flp_Recombinase pp Flp_Recombinase
+Flp_Recombinase pp Flp_Recombinase
+Flp_Recombinase pp Flp_Recombinase
+Flp_Recombinase pp Flp_Recombinase
+ILV2 pp ILV2
+TPI1 pp TPI1
+Iq2_Motif_From_Myo2p,_A_Class_V_Myosin pp MLC1
+CDC4 pp SKP1
+Gll(Tpo)ppqsg pp CDC4
+Transcription_Factor_Iiib_Brf1_Subunit pp SPT15
+SRP102 pp SRP101
+ACC1 pp ACC1
+ACC1 pp ACC1
+Recombinase_Flp_Protein pp Recombinase_Flp_Protein
+Recombinase_Flp_Protein pp Recombinase_Flp_Protein
+Recombinase_Flp_Protein pp Recombinase_Flp_Protein
+Recombinase_Flp_Protein pp Recombinase_Flp_Protein
+MET3 pp MET3
+MTR2 pp MEX67
+RPL40A pp Protein_Cue2
+Inositol-3-Phosphate_Synthase pp Inositol-3-Phosphate_Synthase
+Inositol-3-Phosphate_Synthase pp Inositol-3-Phosphate_Synthase
+Inositol-3-Phosphate_Synthase pp Inositol-3-Phosphate_Synthase
+Inositol-3-Phosphate_Synthase pp Inositol-3-Phosphate_Synthase
+Inositol-3-Phosphate_Synthase pp Inositol-3-Phosphate_Synthase
+Inositol-3-Phosphate_Synthase pp Inositol-3-Phosphate_Synthase
+Inositol-3-Phosphate_Synthase pp Inositol-3-Phosphate_Synthase
+Inositol-3-Phosphate_Synthase pp Inositol-3-Phosphate_Synthase
+Vacuolar_Protein_Sorting-Associated_Protein_Vps9 pp Vacuolar_Protein_Sorting-Associated_Protein_Vps9
+RPL40A pp Vacuolar_Protein_Sorting-Associated_Protein_Vps9
+RPL40A pp Vacuolar_Protein_Sorting-Associated_Protein_Vps9
+TOP2 pp TOP2
+Copii-Binding_Peptide_Of_The_Protein_Transport_Protein_Bet1 pp SEC24
+Copii-Binding_Peptide_Of_The_Integral_Membrane_Protein_Sed5 pp SEC24
+Dxe_Cargo_Sorting_Signal_Peptide_Of_Yeast_Sys1_Protein pp SEC24
+DST1 pp RPO21
+ECI1 pp ECI1
+ECI1 pp ECI1
+QCR2 pp COR1
+CYT1 pp COB
+RIP1 pp COB
+QCR8 pp QCR7
+Heavy_Chain_(Vh)_Of_Fv-Fragment pp RIP1
+Light_Chain_(Vl)_Of_Fv-Fragment pp Heavy_Chain_(Vh)_Of_Fv-Fragment
+Light_Chain_(Vl)_Of_Fv-Fragment pp RIP1
+RPL40A pp Vacuolar_Protein_Sorting-Associated_Protein_Vps27
+TOP2 pp TOP2
+Iq2_And_Iq3_Motifs_From_Myo2p,_A_Class_V_Myosin pp MLC1
+Iq2_And_Iq3_Motifs_From_Myo2p,_A_Class_V_Myosin pp MLC1
+TOA2 pp Transcription_Initiation_Factor_Iia_Large_Chain
+HOM6 pp HOM6
+SRP1 pp SRP1
+Nucleoporin_Nup2 pp SRP1
+HST2 pp HST2
+HST2 pp HST2
+HST2 pp HST2
+Cyc8 pp Tup1
+Rfx1 pd RNR3_Promoter
+Rfx1 pp Rfx1
+Rfx1 pp Ssn6
+Rfx1 pp Tup1
+Rfx1 pd CRT1_Promoter
+Rfx1 interactsWith Ssn6-Tup1
+elg1 pp Rfc4
+elg1 pp Rfc3
+Rfx1 pd RNR2_Promoter
+Mer1 pp Prp11
+Sin3 pp Opi1
+Ino2 pp Opi1
+Ino2 pp Ino4
+Ume6 pp Arg80
+Ume6 pp Arg81
+elg1 pp Rfc5
+elg1 pp Rfc2
+Cdc13 pd Telomeric_DNA
+Cdc28 pp Pho2
+Rfm1 interactsWith Unknown
+Sum1 pp Hst1
+Glc7 pp Scd5
+Glc7 pp Gac1
+Glc7 pp Red1
+CMK1 pp Cmd1
+YAR064W pp Cmd1
+YBR011C pp Cmd1
+YBR050C pp Cmd1
+YBR213W pp Cmd1
+YBR229C pp Cmd1
+YDR195W pp Cmd1
+YDR231C pp Cmd1
+YDR292C pp Cmd1
+YER023W pp Cmd1
+YFL003C pp Cmd1
+YFL010W-A pp Cmd1
+YFR004W pp Cmd1
+YFR054C pp Cmd1
+YGL063W pp Cmd1
+YGL229C pp Cmd1
+YGR034W pp Cmd1
+YGR050C pp Cmd1
+YGR144W pp Cmd1
+YGR253C pp Cmd1
+YHR028C pp Cmd1
+YHR179W pp Cmd1
+YIL021W pp Cmd1
+YJR073C pp Cmd1
+YKL175W pp Cmd1
+YKR025W pp Cmd1
+YLL051C pp Cmd1
+YLR443W pp Cmd1
+YML057W pp Cmd1
+YMR200W pp Cmd1
+YNL066W pp Cmd1
+YNL079C pp Cmd1
+YNL202W pp Cmd1
+YNR035C pp Cmd1
+YOL016C pp Cmd1
+YOR029W pp Cmd1
+YOR358W pp Cmd1
+Ace2 pd iYAL040C
+Ace2 pd iYAL063C-2
+Ace2 pd iYBR057C
+Ace2 pd iYBR157C-0
+Ace2 pd iYBR157C-1
+Ace2 pd iYBR229C
+Ace2 pd iYBR230C
+Ace2 pd iYDL055C-0
+Ace2 pd iYDL128W
+Ace2 pd iYDR010C
+Ace2 pd iYDR155C
+Ace2 pd iYDR525W
+Ace2 pd iYEL008W
+Ace2 pd iYER078C
+Ace2 pd iYER080W
+Ace2 pd iYER087C-A
+Ace2 pd iYER088C
+Ace2 pd iYER124C
+Ace2 pd iYER126C
+Ace2 pd iYER176W
+Ace2 pd iYERWomega2-1
+Ace2 pd iYFL014W
+Ace2 pd iYFL022C
+Ace2 pd iYFL056C-0
+Ace2 pd iYFR017C
+Ace2 pd iYFR031C-A
+Ace2 pd iYGL008C
+Ace2 pd iYGL028C
+Ace2 pd iYGL228W
+Ace2 pd iYGL229C
+Ace2 pd iYGR040W
+Ace2 pd iYGR050C
+Ace2 pd iSNR48
+Ace2 pd iYGR124W
+Ace2 pd iYGR233C-1
+Ace2 pd iYHL029C
+Ace2 pd iYHR091C
+Ace2 pd iYHR142W
+Ace2 pd iYHR193C
+Ace2 pd iYHR194W
+Ace2 pd iYIL100W
+Ace2 pd iYJL048C
+Ace2 pd iYJL075C
+Ace2 pd iYJL078C
+Ace2 pd iYJL080C
+Ace2 pd iYJL160C-1
+Ace2 pd iYJR044C
+Ace2 pd iYJR145C
+Ace2 pd iYJR147W
+Ace2 pd iYJR148W
+Ace2 pd iYKL085W
+Ace2 pd iYKL097C
+Ace2 pd iYKL143W
+Ace2 pd iYKL151C
+Ace2 pd iYKR041W
+Ace2 pd iYLR112W
+Ace2 pd iYLR206W
+Ace2 pd iYLR255C
+Ace2 pd iYLR286C
+Ace2 pd iYLR287C-A
+Ace2 pd iYLR299W
+Ace2 pd iYLR346C
+Ace2 pd iYLR397C
+Ace2 pd iYLR399C
+Ace2 pd iYLR438C-A
+Ace2 pd iYLR440C
+Ace2 pd iYML008C
+Ace2 pd iYML101C
+Ace2 pd iYMR135W-A
+Ace2 pd iYMR134W
+Ace2 pd iYMR165C
+Ace2 pd iYMR251W
+Ace2 pd iYNL154C
+Ace2 pd iYNL179C-1
+Ace2 pd iYNL241C
+Ace2 pd iYNL328C
+Ace2 pd iYNR017W
+Ace2 pd iYOR138C
+Ace2 pd iYOR314W
+Ace2 pd iYOR344C-0
+Ace2 pd iYPL019C
+Ace2 pd iYPL025C
+Ace2 pd iYPL231W
+Ace2 pd iYPL253C
+Ace2 pd iYPL283C-0
+Fkh1 pd iYBL082C
+Fkh1 pd iYBR029C
+Fkh1 pd iYBR070C
+Fkh1 pd iYBR077C
+Fkh1 pd iYBR103W
+Fkh1 pd iYBR138C
+Fkh1 pd iYBR157C-1
+Fkh1 pd iYCL064C
+Fkh1 pd iYCR075C
+Fkh1 pd iYCR092C
+Fkh1 pd iYDL085W
+Fkh1 pd iYDR259C
+Fkh1 pd iYDR263C
+Fkh1 pd iYDR324C
+Fkh1 pd iYDR451C
+Fkh1 pd iYDR500C
+Fkh1 pd iYEL016C
+Fkh1 pd iYEL017C-A
+Fkh1 pd iYER124C
+Fkh1 pd iYER176W
+Fkh1 pd iYFL022C
+Fkh1 pd iYFR003C
+Fkh1 pd iYFR018C
+Fkh1 pd iYGL093W
+Fkh1 pd iYGR050C
+Fkh1 pd iYHR048W
+Fkh1 pd iYHR142W
+Fkh1 pd iYHR182W
+Fkh1 pd iYJL190C
+Fkh1 pd iYJR044C
+Fkh1 pd iYJR091C
+Fkh1 pd iYJR094C-0
+Fkh1 pd iYKL063C-0
+Fkh1 pd iYKR054C
+Fkh1 pd iYLR044C
+Fkh1 pd iYLR112W
+Fkh1 pd iYLR209C
+Fkh1 pd iYLR286C
+Fkh1 pd iYLR352W
+Fkh1 pd iYLR406C
+Fkh1 pd iYML064C
+Fkh1 pd iYML101C
+Fkh1 pd iYMR015C
+Fkh1 pd iYMR078C
+Fkh1 pd iYMR085W
+Fkh1 pd iYMR143W
+Fkh1 pd iYMR183C
+Fkh1 pd iYMR198W
+Fkh1 pd iYMR214W
+Fkh1 pd iYNL104C
+Fkh1 pd iYNL241C
+Fkh1 pd iYOL024W
+Fkh1 pd iYOL031C
+Fkh1 pd iYPL032C
+Fkh1 pd iYPL117C
+Fkh1 pd iYPL139C
+Fkh1 pd iYPL140C
+Fkh1 pd iYPL141C
+Fkh1 pd iYPL231W
+Fkh1 pd iYPR013C-0
+Fkh1 pd iYPR033C
+Fkh1 pd iYPR034W
+Fkh1 pd iYPRWsigma2-1
+Fkh1 pd iYPR195C-0
+Fkh2 pd iYAL024C
+Fkh2 pd iYAL029C
+Fkh2 pd iYBL033C
+Fkh2 pd iYBR077C
+Fkh2 pd iYBR134W
+Fkh2 pd iYBR157C-1
+Fkh2 pd iYDR146C
+Fkh2 pd iYDR259C
+Fkh2 pd iYDR263C
+Fkh2 pd iYDR324C
+Fkh2 pd iYDR451C
+Fkh2 pd iYDR500C
+Fkh2 pd iYDR525W
+Fkh2 pd iYDR543C
+Fkh2 pd iYEL008W
+Fkh2 pd iYEL041W
+Fkh2 pd iYER069W
+Fkh2 pd iYER078C
+Fkh2 pd iYER094C
+Fkh2 pd iYER124C
+Fkh2 pd iYERWomega2-1
+Fkh2 pd iYFL022C
+Fkh2 pd iYFR017C
+Fkh2 pd iYGL008C
+Fkh2 pd iYGL115W
+Fkh2 pd iYGL117W
+Fkh2 pd iYGL228W
+Fkh2 pd iYGR050C
+Fkh2 pd iSNR48
+Fkh2 pd iYGR109C
+Fkh2 pd iYGR180C
+Fkh2 pd iYGR248W
+Fkh2 pd iYGR253C-1
+Fkh2 pd iYGR295C-1
+Fkh2 pd iYHL023C
+Fkh2 pd iYHL025W
+Fkh2 pd iYHR061C
+Fkh2 pd iYHR142W
+Fkh2 pd iYHR151C
+Fkh2 pd iYHR193C
+Fkh2 pd itS(UGA)I
+Fkh2 pd iYIL124W
+Fkh2 pd iYIL159W
+Fkh2 pd iYIL169C-0
+Fkh2 pd iYJL052W
+Fkh2 pd iYJL078C
+Fkh2 pd iYJL158C
+Fkh2 pd iYJR044C
+Fkh2 pd iYJR091C
+Fkh2 pd iYJR109C
+Fkh2 pd iYJR128W
+Fkh2 pd iYJR145C
+Fkh2 pd iYJR147W
+Fkh2 pd iYKL045W
+Fkh2 pd iYKL097W-A-1
+Fkh2 pd iYKL097C
+Fkh2 pd iYKR041W
+Fkh2 pd iYLR084C
+Fkh2 pd iYLR131C
+Fkh2 pd iYLR189C
+Fkh2 pd iYLR206W
+Fkh2 pd iYLR255C
+Fkh2 pd iYLR286C
+Fkh2 pd iYLR299W
+Fkh2 pd iYLR346C
+Fkh2 pd iYLR399C
+Fkh2 pd iYLR437C
+Fkh2 pd iYLR438C-A
+Fkh2 pd iYML028W
+Fkh2 pd iYML053C
+Fkh2 pd iYML064C
+Fkh2 pd iYMR016C-1
+Fkh2 pd iYMR069W
+Fkh2 pd iYMR076C
+Fkh2 pd iYMR135W-A
+Fkh2 pd iYMR143W
+Fkh2 pd iYMR198W
+Fkh2 pd iYMR214W
+Fkh2 pd itI(AAU)N1
+Fkh2 pd iYNL241C
+Fkh2 pd iYNL290W
+Fkh2 pd iYNL338W
+Fkh2 pd iYNR017W
+Fkh2 pd itP(UGG)O2
+Fkh2 pd iYOR235W
+Fkh2 pd iYOR246C
+Fkh2 pd iYOR273C
+Fkh2 pd iYOR312C
+Fkh2 pd iYOR314W
+Fkh2 pd iYOR344C-0
+Fkh2 pd iYOR369C
+Fkh2 pd iYPL025C
+Fkh2 pd iYPL155C
+Fkh2 pd iYPR034W
+Fkh2 pd iYPRWsigma2-1
+Fkh2 pd iSNR45
+Fkh2 pd iYPR148C-1
+Mbp1 pd iYAL063C-2
+Mbp1 pd iYBL023C
+Mbp1 pd iYBR057C
+Mbp1 pd iYBR070C
+Mbp1 pd iYBR077C
+Mbp1 pd iYBR189W
+Mbp1 pd iYCR063W
+Mbp1 pd iYDL004W
+Mbp1 pd iYDL018C
+Mbp1 pd iYDL101C
+Mbp1 pd iYDR263C
+Mbp1 pd iYDR309C
+Mbp1 pd iYDR451C
+Mbp1 pd iYDR500C
+Mbp1 pd iYDR525W
+Mbp1 pd iYDR543C
+Mbp1 pd iYER069W
+Mbp1 pd iYER078C
+Mbp1 pd iYER087C-A
+Mbp1 pd iYER094C
+Mbp1 pd iYER111C
+Mbp1 pd iYERWomega2-1
+Mbp1 pd iYFL014W
+Mbp1 pd iYFR017C
+Mbp1 pd iYFR033C
+Mbp1 pd iYGL147C
+Mbp1 pd iYGL228W
+Mbp1 pd iYGR109C
+Mbp1 pd iYGRCdelta20
+Mbp1 pd itR(UCU)G2
+Mbp1 pd iYGR180C
+Mbp1 pd iYGR189C
+Mbp1 pd iYHR091C
+Mbp1 pd iYHR149C
+Mbp1 pd iYHR151C
+Mbp1 pd iYHR174W
+Mbp1 pd iYHR193C
+Mbp1 pd iYHR194W
+Mbp1 pd iYIL026C
+Mbp1 pd itD(GUC)J2
+Mbp1 pd iYJL048C
+Mbp1 pd iYJL080C
+Mbp1 pd iSNR190
+Mbp1 pd iYJL187C
+Mbp1 pd iYJL196C
+Mbp1 pd iYJR030C
+Mbp1 pd iYJR044C
+Mbp1 pd iYKL085W
+Mbp1 pd iYKL097C
+Mbp1 pd iYKL113C
+Mbp1 pd iYKL143W
+Mbp1 pd iYKR041W
+Mbp1 pd iYLR103C
+Mbp1 pd iYLR206W
+Mbp1 pd iYLR299W
+Mbp1 pd iYLR354C
+Mbp1 pd iYLR366W
+Mbp1 pd itK(UUU)L
+Mbp1 pd iYLR397C
+Mbp1 pd iYLR437C
+Mbp1 pd iYLR438C-A
+Mbp1 pd iYML028W
+Mbp1 pd iYML029W
+Mbp1 pd iYML101C
+Mbp1 pd iYMR069W
+Mbp1 pd iYMR076C
+Mbp1 pd iYMR143W
+Mbp1 pd iYMR165C
+Mbp1 pd iYMR178W
+Mbp1 pd iYMR198W
+Mbp1 pd iYMR214W
+Mbp1 pd iYNL154C
+Mbp1 pd iYNL241C
+Mbp1 pd iYNL290W
+Mbp1 pd iYNL302C
+Mbp1 pd iYNL338W
+Mbp1 pd iYNR008W
+Mbp1 pd iYNR017W
+Mbp1 pd iYNR043W
+Mbp1 pd iYOR074C
+Mbp1 pd iYOR235W
+Mbp1 pd iYOR246C
+Mbp1 pd iYOR268C
+Mbp1 pd iYPL019C
+Mbp1 pd iYPL056C
+Mbp1 pd iYPL082C
+Mbp1 pd iSNR59
+Mbp1 pd iYPL231W
+Mbp1 pd iYPL253C
+Mbp1 pd iYPL283C-0
+Mbp1 pd itG(GCC)P1
+Mbp1 pd iYPR076W
+Mbp1 pd iYPR079W
+Mbp1 pd iYPR120C
+Mcm1 pd iYAL040C
+Mcm1 pd iYDR146C
+Mcm1 pd iYDR179C
+Mcm1 pd itE(CUC)D-0
+Mcm1 pd iYDR388W
+Mcm1 pd iYDR451C
+Mcm1 pd iYDR460W
+Mcm1 pd iYDR507C
+Mcm1 pd iYDR525W
+Mcm1 pd iYDR527W-1
+Mcm1 pd itS(AGA)E
+Mcm1 pd iYEL041W
+Mcm1 pd iYEL045C
+Mcm1 pd iYER078C
+Mcm1 pd iYER111C
+Mcm1 pd iYER158C
+Mcm1 pd iYERCdelta24
+Mcm1 pd iYFL027C
+Mcm1 pd iYGL022W
+Mcm1 pd iYGL032C
+Mcm1 pd iYGL117W
+Mcm1 pd iYGL201C
+Mcm1 pd itK(UUU)G1
+Mcm1 pd iYGR040W
+Mcm1 pd iYGR047C
+Mcm1 pd iYGR091W
+Mcm1 pd itA(AGC)G
+Mcm1 pd iYGR191W
+Mcm1 pd iYHR098C
+Mcm1 pd iYHR151C
+Mcm1 pd iYIL016W
+Mcm1 pd iYIL069C
+Mcm1 pd iYIL077C
+Mcm1 pd iYIL124W
+Mcm1 pd iYIL159W
+Mcm1 pd iYJL052W
+Mcm1 pd iYJL079C
+Mcm1 pd iSNR190
+Mcm1 pd iYJL155C
+Mcm1 pd iYJL157C
+Mcm1 pd iYJL160C-0
+Mcm1 pd iYJL196C
+Mcm1 pd iYJR044C
+Mcm1 pd iYJR091C
+Mcm1 pd iYJR128W
+Mcm1 pd iYKL164C-1
+Mcm1 pd iYKL164C-0
+Mcm1 pd iYKL209C
+Mcm1 pd iYKR041W
+Mcm1 pd iYKR096W
+Mcm1 pd iYLR084C
+Mcm1 pd iYLR131C
+Mcm1 pd iYLR189C
+Mcm1 pd iYLR273C
+Mcm1 pd iYML053C
+Mcm1 pd iYMR143W
+Mcm1 pd iYMR230W
+Mcm1 pd iYNL054W
+Mcm1 pd iYNL146W
+Mcm1 pd itG(UCC)N
+Mcm1 pd iYNL290W
+Mcm1 pd iYNL296W
+Mcm1 pd iYNL299W
+Mcm1 pd iYNL339C
+Mcm1 pd iYNR017W
+Mcm1 pd iYNR027W
+Mcm1 pd iYNR043W
+Mcm1 pd iYNR062C-0
+Mcm1 pd iYNR062C-1
+Mcm1 pd iYOL152W
+Mcm1 pd iYOR065W
+Mcm1 pd iYOR235W
+Mcm1 pd iYOR246C
+Mcm1 pd iYOR314W
+Mcm1 pd iYOR388C
+Mcm1 pd iYPL277C
+Mcm1 pd itT(UGU)P
+Mcm1 pd iYPR112C
+Mcm1 pd iYPRWsigma2-1
+Ndd1 pd iYAR018C
+Ndd1 pd iYBR037C
+Ndd1 pd iYBR077C
+Ndd1 pd iYBR138C
+Ndd1 pd iYCR024C-A
+Ndd1 pd iYCR063W
+Ndd1 pd iYDR032C-2
+Ndd1 pd iYDR146C
+Ndd1 pd iYDR148C
+Ndd1 pd iYDR451C
+Ndd1 pd iYDR525W
+Ndd1 pd iYDR543C
+Ndd1 pd iYEL008W
+Ndd1 pd iYER078C
+Ndd1 pd iYERWomega2-1
+Ndd1 pd iYFR017C
+Ndd1 pd iYGL008C
+Ndd1 pd iYGL117W
+Ndd1 pd iYGL228W
+Ndd1 pd iSNR48
+Ndd1 pd iYGR229C
+Ndd1 pd iYHL029C
+Ndd1 pd iYHR091C
+Ndd1 pd iYHR151C
+Ndd1 pd iYIL159W
+Ndd1 pd iYJL048C
+Ndd1 pd iYJL052W
+Ndd1 pd iYJL079C
+Ndd1 pd iYJL101C
+Ndd1 pd iSNR190
+Ndd1 pd iYJL158C
+Ndd1 pd iYJR044C
+Ndd1 pd iYJR091C
+Ndd1 pd iYJR128W
+Ndd1 pd iYJR145C
+Ndd1 pd iYKL097C
+Ndd1 pd iYKR041W
+Ndd1 pd iYLR084C
+Ndd1 pd iYLR110C
+Ndd1 pd iYLR131C
+Ndd1 pd iYLR189C
+Ndd1 pd iYLR438C-A
+Ndd1 pd iYML029W
+Ndd1 pd iYML051W
+Ndd1 pd iYML053C
+Ndd1 pd iYMR001C
+Ndd1 pd iYMR013C-0
+Ndd1 pd iYMR013C-1
+Ndd1 pd iYMR016C-1
+Ndd1 pd iYMR135W-A
+Ndd1 pd iYMR134W
+Ndd1 pd iYMR143W
+Ndd1 pd iYMR165C
+Ndd1 pd iYMR198W
+Ndd1 pd iYMR251W
+Ndd1 pd iYNL057W
+Ndd1 pd iYNL146W
+Ndd1 pd iYNL241C
+Ndd1 pd iYNL338W
+Ndd1 pd iYNR017W
+Ndd1 pd iYOR235W
+Ndd1 pd iYOR246C
+Ndd1 pd iYOR314W
+Ndd1 pd iYPRWsigma2-1
+Ndd1 pd iYPR148C-1
+Swi4 pd iYBL003C
+Swi4 pd iYBL030C-1
+Swi4 pd iYBR057C
+Swi4 pd iYBR070C
+Swi4 pd iYBR077C
+Swi4 pd iYBR113W
+Swi4 pd iYBR162C
+Swi4 pd iYCR063W
+Swi4 pd iYDL055C-0
+Swi4 pd iYDL128W
+Swi4 pd iYDL227C-0
+Swi4 pd iYDR010C
+Swi4 pd iYDR134C
+Swi4 pd iYDR224C
+Swi4 pd iYDR309C
+Swi4 pd iYDR441C
+Swi4 pd iYDR451C
+Swi4 pd iYDR500C
+Swi4 pd iYDR507C
+Swi4 pd iYDR509W
+Swi4 pd iYDR524C
+Swi4 pd iYDR525W
+Swi4 pd iYDR527W-0
+Swi4 pd iYDR544C
+Swi4 pd iYEL041W
+Swi4 pd iCEN5
+Swi4 pd iYER010C-1
+Swi4 pd iYER069W
+Swi4 pd iYER078C
+Swi4 pd iYER111C
+Swi4 pd iYER145C
+Swi4 pd iYER176W
+Swi4 pd iYERWomega2-1
+Swi4 pd iYFR017C
+Swi4 pd iYGL038C
+Swi4 pd iYGL179C-0
+Swi4 pd iYGL228W
+Swi4 pd iYGL254W
+Swi4 pd iYGR012W
+Swi4 pd iYGR013W
+Swi4 pd iYGR040W
+Swi4 pd iYGR050C
+Swi4 pd iSNR48
+Swi4 pd iYGR109C
+Swi4 pd iYGR152C
+Swi4 pd iYGR189C
+Swi4 pd iYGR191W
+Swi4 pd iYGR221C
+Swi4 pd iYGR248W
+Swi4 pd iYGR279C
+Swi4 pd iYHR061C
+Swi4 pd iYHR063C
+Swi4 pd iYHR091C
+Swi4 pd iYHR149C
+Swi4 pd iYHR193C
+Swi4 pd itS(UGA)I
+Swi4 pd iYIL124W
+Swi4 pd iYIR020C
+Swi4 pd iYJL158C
+Swi4 pd iYJL187C
+Swi4 pd iYJL196C
+Swi4 pd iYJR044C
+Swi4 pd iYJR145C
+Swi4 pd iYJR147W
+Swi4 pd iYKL008C
+Swi4 pd iYKL045W
+Swi4 pd iYKL097W-A-1
+Swi4 pd iYKL097C
+Swi4 pd iYKL103C
+Swi4 pd iYKL181W
+Swi4 pd iYKR011C
+Swi4 pd iYKR041W
+Swi4 pd iYKR092C-1
+Swi4 pd iYLR044C
+Swi4 pd iYLR055C
+Swi4 pd iYLR084C
+Swi4 pd iYLR110C
+Swi4 pd iYLR255C
+Swi4 pd iYLR299W
+Swi4 pd iYLR330W
+Swi4 pd iYLR341W
+Swi4 pd iYLR437C
+Swi4 pd iYLR438C-A
+Swi4 pd iYML026C
+Swi4 pd iYML028W
+Swi4 pd iYML101C
+Swi4 pd iYMR016C-0
+Swi4 pd iYMR016C-1
+Swi4 pd iYMR069W
+Swi4 pd iYMR135W-A
+Swi4 pd iYMR134W
+Swi4 pd iYMR143W
+Swi4 pd iYMR145C
+Swi4 pd iYMR178W
+Swi4 pd iYMR198W
+Swi4 pd iYMR251W
+Swi4 pd iYMR305C
+Swi4 pd iYMR306C-A
+Swi4 pd iYNL179C-1
+Swi4 pd iYNL231C
+Swi4 pd iYNL241C
+Swi4 pd iYNL290W
+Swi4 pd iYNL299W
+Swi4 pd iYNL301C
+Swi4 pd iYNL339C
+Swi4 pd iYNR017W
+Swi4 pd iYNR043W
+Swi4 pd iYOL012C
+Swi4 pd iYOL114C
+Swi4 pd iYOR138C
+Swi4 pd iYOR178C-0
+Swi4 pd iYOR246C
+Swi4 pd iYOR314W
+Swi4 pd iYOR344C-0
+Swi4 pd iYOR372C
+Swi4 pd iYOR377W-1
+Swi4 pd iYPL025C
+Swi4 pd iYPL056C
+Swi4 pd iYPL127C
+Swi4 pd iYPL163C
+Swi4 pd iYPL231W
+Swi4 pd iYPL253C
+Swi4 pd iYPR008W
+Swi4 pd iYPR013C-0
+Swi4 pd iYPR034W
+Swi4 pd iYPRWsigma2-1
+Swi4 pd iYPR148C-1
+Swi5 pd iYAL018C
+Swi5 pd iYAL022C
+Swi5 pd iYAL063C-2
+Swi5 pd iYBL109W-1
+Swi5 pd iYBL111C
+Swi5 pd iYBR057C
+Swi5 pd iYBR082C-1
+Swi5 pd iYBR157C-0
+Swi5 pd iYBR157C-1
+Swi5 pd iYBR189W
+Swi5 pd iYDL034W
+Swi5 pd iYDL083C
+Swi5 pd iYDL128W
+Swi5 pd iYDL174C
+Swi5 pd iYDL180W
+Swi5 pd iYDL223C
+Swi5 pd iYDL224C
+Swi5 pd iYDL226C
+Swi5 pd iYDR054C
+Swi5 pd iYDR110W
+Swi5 pd iYDR345C-0
+Swi5 pd iYDR525W
+Swi5 pd iYDR543C
+Swi5 pd iYDR544C
+Swi5 pd iYEL008W
+Swi5 pd iYEL045C
+Swi5 pd iYEL077C
+Swi5 pd iYER073W
+Swi5 pd iYER078C
+Swi5 pd iYER176W
+Swi5 pd iYERWomega2-1
+Swi5 pd iYFL014W
+Swi5 pd iYFL022C
+Swi5 pd iYFL064C
+Swi5 pd iYFR017C
+Swi5 pd iYFR031C-A
+Swi5 pd iYGL028C
+Swi5 pd iYGL108C
+Swi5 pd iYGL189C
+Swi5 pd iYGL228W
+Swi5 pd iYGR040W
+Swi5 pd iSNR48
+Swi5 pd iYGR086C
+Swi5 pd iYGR189C
+Swi5 pd iYGR233C-1
+Swi5 pd iYGR253C-1
+Swi5 pd iYGR295C-1
+Swi5 pd iYHR032W
+Swi5 pd iYHR086W
+Swi5 pd iYHR091C
+Swi5 pd iYHR138C
+Swi5 pd iYHR193C
+Swi5 pd iYILCdelta5-1
+Swi5 pd iYIL019W
+Swi5 pd iYIL051C
+Swi5 pd iYIL129C
+Swi5 pd iYIL177C-1
+Swi5 pd iYIL177C-0
+Swi5 pd iYJL043W
+Swi5 pd iYJL078C
+Swi5 pd iYJL080C
+Swi5 pd iSNR190
+Swi5 pd iYJL160C-1
+Swi5 pd iYJL160C-0
+Swi5 pd iYJL188C
+Swi5 pd iYJL225C-0
+Swi5 pd iYJR044C
+Swi5 pd iYJR145C
+Swi5 pd iYKL045W
+Swi5 pd iYKL164C-1
+Swi5 pd iYKL164C-0
+Swi5 pd iYKL186C
+Swi5 pd iYKR041W
+Swi5 pd iYLL066C-1
+Swi5 pd iYLR012C
+Swi5 pd iYLR078C
+Swi5 pd iYLR194C
+Swi5 pd iYLR206W
+Swi5 pd iYLR286C
+Swi5 pd iYLR299W
+Swi5 pd iYLR346C
+Swi5 pd iYLR406C
+Swi5 pd iYLR438C-A
+Swi5 pd iYLR461W-1
+Swi5 pd iYLR466W
+Swi5 pd iYML101C
+Swi5 pd iYML112W
+Swi5 pd iYML125C
+Swi5 pd iYML132W-1
+Swi5 pd iYML133C-1
+Swi5 pd iYML133C-0
+Swi5 pd iYMR013C-1
+Swi5 pd iYMR122C-0
+Swi5 pd iYMR134W
+Swi5 pd iYMR165C
+Swi5 pd iYMR251W
+Swi5 pd iYMR261C
+Swi5 pd iYNL146W
+Swi5 pd iYNL193W
+Swi5 pd iYNL241C
+Swi5 pd iYNL271C
+Swi5 pd iYNL328C
+Swi5 pd iYNL337W
+Swi5 pd iYNL338W
+Swi5 pd iYNL339C
+Swi5 pd iYNR017W
+Swi5 pd iYOR138C
+Swi5 pd iYOR235W
+Swi5 pd iYOR273C
+Swi5 pd iYOR348C
+Swi5 pd iYOR369C
+Swi5 pd iYPL019C
+Swi5 pd iYPL050C
+Swi5 pd iYPL056C
+Swi5 pd iYPL158C
+Swi5 pd iYPL283C-0
+Swi5 pd iYPR182W
+Swi6 pd iYBL030C-1
+Swi6 pd iYBR077C
+Swi6 pd iYDL004W
+Swi6 pd iYDL034W
+Swi6 pd iYDL055C-0
+Swi6 pd iYDL128W
+Swi6 pd iYDL227C-0
+Swi6 pd iYDR010C
+Swi6 pd iYDR134C
+Swi6 pd iYDR263C
+Swi6 pd iYDR309C
+Swi6 pd iYDR451C
+Swi6 pd iYDR500C
+Swi6 pd iYDR524C
+Swi6 pd iYDR525W
+Swi6 pd iYDR527W-0
+Swi6 pd iYEL008W
+Swi6 pd iYEL041W
+Swi6 pd iCEN5
+Swi6 pd iYER069W
+Swi6 pd iYER078C
+Swi6 pd iYER094C
+Swi6 pd iYER111C
+Swi6 pd iYER176W
+Swi6 pd iYERWomega2-1
+Swi6 pd iYFL014W
+Swi6 pd iYFL022C
+Swi6 pd iYFR017C
+Swi6 pd iYGL038C
+Swi6 pd iYGL179C-0
+Swi6 pd iYGL228W
+Swi6 pd iYGR012W
+Swi6 pd iYGR013W
+Swi6 pd iYGR040W
+Swi6 pd iYGR050C
+Swi6 pd iSNR48
+Swi6 pd iYGR109C
+Swi6 pd iYGRCdelta20
+Swi6 pd iYGR180C
+Swi6 pd iYGR189C
+Swi6 pd iYGR221C
+Swi6 pd iYGR248W
+Swi6 pd iYGR279C
+Swi6 pd iYHL029C
+Swi6 pd iYHR061C
+Swi6 pd iYHR091C
+Swi6 pd iYHR149C
+Swi6 pd iYHR151C
+Swi6 pd iYHR193C
+Swi6 pd itS(UGA)I
+Swi6 pd iYIL124W
+Swi6 pd itD(GUC)J2
+Swi6 pd iYJL048C
+Swi6 pd iSNR190
+Swi6 pd iYJL158C
+Swi6 pd iYJL187C
+Swi6 pd iYJL196C
+Swi6 pd iYJR044C
+Swi6 pd iYJR145C
+Swi6 pd iYJR147W
+Swi6 pd iYKL045W
+Swi6 pd iYKL097W-A-1
+Swi6 pd iYKL097C
+Swi6 pd iYKL113C
+Swi6 pd iYKR011C
+Swi6 pd iYKR041W
+Swi6 pd iYLR055C
+Swi6 pd iYLR103C
+Swi6 pd iYLR110C
+Swi6 pd iYLR299W
+Swi6 pd iYLR330W
+Swi6 pd iYLR341W
+Swi6 pd iYLR354C
+Swi6 pd iYLR437C
+Swi6 pd iYLR438C-A
+Swi6 pd iYML008C
+Swi6 pd iYML028W
+Swi6 pd iYML101C
+Swi6 pd iYMR016C-0
+Swi6 pd iYMR016C-1
+Swi6 pd iYMR069W
+Swi6 pd iYMR076C
+Swi6 pd iYMR122C-0
+Swi6 pd iYMR135W-A
+Swi6 pd iYMR143W
+Swi6 pd iYMR165C
+Swi6 pd iYMR178W
+Swi6 pd iYMR198W
+Swi6 pd iYMR214W
+Swi6 pd iYMR251W
+Swi6 pd iYMR305C
+Swi6 pd iYMR306C-A
+Swi6 pd iYNL179C-1
+Swi6 pd iYNL231C
+Swi6 pd iYNL241C
+Swi6 pd iYNL274C
+Swi6 pd iYNL290W
+Swi6 pd iYNL299W
+Swi6 pd iYNL301C
+Swi6 pd iYNL338W
+Swi6 pd iYNL339C
+Swi6 pd iYNR008W
+Swi6 pd iYNR017W
+Swi6 pd iYNR043W
+Swi6 pd iYOL114C
+Swi6 pd iYOR235W
+Swi6 pd iYOR246C
+Swi6 pd iYOR314W
+Swi6 pd iYOR344C-0
+Swi6 pd iYOR372C
+Swi6 pd iYOR377W-1
+Swi6 pd iYPL025C
+Swi6 pd iYPL056C
+Swi6 pd iYPL127C
+Swi6 pd iYPL144W
+Swi6 pd iYPL163C
+Swi6 pd iYPL231W
+Swi6 pd iYPL256C
+Swi6 pd iYPL283C-0
+Swi6 pd itG(GCC)P1
+Swi6 pd iYPR076W
+Swi6 pd iYPR079W
+Swi6 pd iYPRWsigma2-1
+Swi6 pd iYPR120C
+Swi6 pd iSNR45
+Swi6 pd itA(AGC)P
+PRP22 pp YNL274C
+PRP22 pp PMI40
+PRP22 pp DBP7
+PRP22 pp PRP45
+PRP22 pp SYF3
+PRP45 pp DOP1
+PRP45 pp FIR1
+PRP45 pp YGR198W
+PRP45 pp YTA7
+PRP45 pp UBR2
+PRP45 pp VAC14
+PRP45 pp SGS1
+PRP45 pp CDC27
+PRP45 pp YLR424W
+PRP45 pp YMR031C
+PRP45 pp VPS75
+PRP45 pp AHC1
+PRP45 pp PKC1
+PRP45 pp SYF1
+PRP45 pp ADE6
+PRP45 pp YGR071C
+PRP45 pp SEC6
+PRP45 pp APL1
+PRP45 pp YJR061W
+PRP45 pp DYN1
+PRP45 pp MMS22
+PRP45 pp NUP188
+PRP45 pp ECM5
+PRP45 pp SLA2
+PRP45 pp SKI3
+PRP45 pp RAD16
+PRP45 pp RMD1
+PRP45 pp NUP84
+PRP45 pp NGG1
+PRP45 pp TRP5
+PRP45 pp YAP1801
+PRP45 pp YJL103C
+PRP45 pp YJL149W
+PRP45 pp YLR187W
+PRP45 pp NIS1
+PRP45 pp BNI1
+PRP45 pp MNT4
+PRP45 pp NFI1
+PRP45 pp EAF3
+PRP45 pp PRP46
+PRP45 pp SYF3
+PRP46 pp HFM1
+PRP46 pp PKC1
+PRP46 pp YLR426W
+PRP46 pp VAP1
+PRP46 pp PEP12
+PRP46 pp SYF3
+LSM1 pp AAC1
+LSM1 pp AIR2
+LSM1 pp BRO1
+LSM1 pp CHK1
+LSM1 pp FUN30
+LSM1 pp GAD1
+LSM1 pp GCN3
+LSM1 pp GDH1
+LSM1 pp GNT1
+LSM1 pp HEX3
+LSM1 pp INP53
+LSM1 pp LSM3
+LSM1 pp LSM6
+LSM1 pp MDM32
+LSM1 pp MIG3
+LSM1 pp MTR3
+LSM1 pp NEO1
+LSM1 pp PAT1
+LSM1 pp PMT4
+LSM1 pp PRB1
+LSM1 pp RIA1
+LSM1 pp RRD2
+LSM1 pp SDS24
+LSM1 pp SIP1
+LSM1 pp SIW14
+LSM1 pp SNU114
+LSM1 pp SPT16
+LSM1 pp STE11
+LSM1 pp SWI1
+LSM1 pp UFO1
+LSM1 pp YCR024C
+LSM1 pp YIL042C
+LSM1 pp YLR003C
+LSM1 pp YNL276C
+LSM1 pp YRB1
+LSM2 pp AIR2
+LSM2 pp BEM3
+LSM2 pp CSM2
+LSM2 pp DBP1
+LSM2 pp DOT1
+LSM2 pp FAR1
+LSM2 pp GCD11
+LSM2 pp GDB1
+LSM2 pp HFA1
+LSM2 pp KEM1
+LSM2 pp LSM3
+LSM2 pp MAK31
+LSM2 pp NEO1
+LSM2 pp PAT1
+LSM2 pp PDR17
+LSM2 pp PEX8
+LSM2 pp PRP24
+LSM2 pp PSU1
+LSM2 pp RAD18
+LSM2 pp RIC1
+LSM2 pp RIS1
+LSM2 pp RNR3
+LSM2 pp SEC21
+LSM2 pp SEC5
+LSM2 pp SEF1
+LSM2 pp SMD2
+LSM2 pp SOV1
+LSM2 pp SRO7
+LSM2 pp SSN3
+LSM2 pp SWD1
+LSM2 pp TPT1
+LSM2 pp WHI2
+LSM2 pp YEL015W
+LSM2 pp YGL185C
+LSM2 pp YLR126C
+LSM2 pp YLR128W
+LSM2 pp YMR237W
+LSM2 pp YOL163W
+LSM3 pp BAS1
+LSM3 pp BRO1
+LSM3 pp HEX3
+LSM3 pp IML1
+LSM3 pp LRG1
+LSM3 pp PAT1
+LSM3 pp PET309
+LSM3 pp RAD18
+LSM3 pp RPL13B
+LSM3 pp RPS7A
+LSM3 pp YBR108W
+LSM3 pp YLR281C
+LSM4 pp COP1
+LSM4 pp DCP1
+LSM4 pp DSE1
+LSM4 pp FBP26
+LSM4 pp GCR2
+LSM4 pp GZF3
+LSM4 pp IML1
+LSM4 pp KEM1
+LSM4 pp MUS81
+LSM4 pp NST1
+LSM4 pp PAT1
+LSM4 pp PPN1
+LSM4 pp PRP11
+LSM4 pp PSU1
+LSM4 pp RTT103
+LSM4 pp SIN3
+LSM4 pp SLK19
+LSM4 pp SMD2
+LSM4 pp SNF5
+LSM4 pp STE13
+LSM4 pp STE6
+LSM4 pp STN1
+LSM4 pp VAC14
+LSM4 pp VPS72
+LSM4 pp YIL029C
+LSM4 pp YLL032C
+LSM5 pp FOB1
+LSM5 pp GCD11
+LSM5 pp GCN3
+LSM5 pp GDB1
+LSM5 pp GNT1
+LSM5 pp IML1
+LSM5 pp LSM1
+LSM5 pp LSM2
+LSM5 pp LSM3
+LSM5 pp LSM4
+LSM5 pp LSM6
+LSM5 pp LSM7
+LSM5 pp NEO1
+LSM5 pp NOT3
+LSM5 pp PAT1
+LSM5 pp PET56
+LSM5 pp PRP24
+LSM5 pp RPA135
+LSM5 pp RPS26B
+LSM5 pp RPS6A
+LSM5 pp RRD2
+LSM5 pp SHM2
+LSM5 pp SMD2
+LSM5 pp STE6
+LSM5 pp TRM3
+LSM5 pp YCR024C
+LSM5 pp YFL066C
+LSM5 pp YGR210C
+LSM5 pp YHL008C
+LSM5 pp YJL084C
+LSM6 pp GNT1
+LSM6 pp HFM1
+LSM6 pp LSM2
+LSM6 pp LSM3
+LSM6 pp LSM4
+LSM6 pp LSM7
+LSM6 pp PAT1
+LSM6 pp PRP24
+LSM6 pp SMD2
+LSM6 pp YLR053C
+LSM6 pp YMR221C
+LSM6 pp YUR1
+LSM7 pp HOS4
+LSM7 pp LSM3
+LSM7 pp PAT1
+LSM7 pp PRP24
+LSM7 pp PRP4
+LSM7 pp VAM6
+LSM7 pp YFL066C
+LSM8 pp AAD3
+LSM8 pp ARG8
+LSM8 pp ARO1
+LSM8 pp ATC1
+LSM8 pp ATG2
+LSM8 pp BBC1
+LSM8 pp BPT1
+LSM8 pp CKI1
+LSM8 pp COQ1
+LSM8 pp HMT1
+LSM8 pp KEM1
+LSM8 pp LSM5
+LSM8 pp LYS9
+LSM8 pp MAK31
+LSM8 pp MTH1
+LSM8 pp NFT1
+LSM8 pp NOG2
+LSM8 pp PEX6
+LSM8 pp PFK2
+LSM8 pp PRP24
+LSM8 pp PRP4
+LSM8 pp PSU1
+LSM8 pp SCW11
+LSM8 pp SEN1
+LSM8 pp SIL1
+LSM8 pp SYS1
+LSM8 pp TCM62
+LSM8 pp VTH1
+LSM8 pp YCF1
+LSM8 pp YEL015W
+LSM8 pp YEL023C
+LSM8 pp YHR034C
+LSM8 pp YKR021W
+LSM8 pp YLR143W
+LSM8 pp YNL050C
+LSM8 pp YNL227C
+PSU1 pp AHC1
+PSU1 pp APL3
+PSU1 pp ARG81
+PSU1 pp COR1
+PSU1 pp CTK3
+PSU1 pp DNM1
+PSU1 pp DYN1
+PSU1 pp GPH1
+PSU1 pp GRE2
+PSU1 pp KEM1
+PSU1 pp KOG1
+PSU1 pp LEU3
+PSU1 pp NUP84
+PSU1 pp PUF4
+PSU1 pp SPO14
+PSU1 pp SPT6
+PSU1 pp STU1
+PSU1 pp TIF4632
+PSU1 pp TRS31
+PSU1 pp UBP2
+PSU1 pp YAR009C
+PSU1 pp YBL054W
+PSU1 pp YCR076C
+PSU1 pp YIR014W
+PSU1 pp YIR024C
+PSU1 pp YJR023C
+PSU1 pp YKL133C
+PSU1 pp YOR093C
+YEL015W pp DSE1
+YEL015W pp FIR1
+YEL015W pp HIR3
+YEL015W pp KEM1
+YEL015W pp SEF1
+YEL015W pp SKT5
+YEL015W pp SPT6
+YEL015W pp SRL2
+YEL015W pp YEL015W
+PAT1 pp DOP1
+PAT1 pp SAC7
+PAT1 pp SPR6
+PAT1 pp MRF1
+PAT1 pp ZDS2
+PAT1 pp YMR002W
+PAT1 pp HSH155
+PAT1 pp PSU1
+PAT1 pp BUD17
+PAT1 pp NOG2
+LSM2 pp YPS1
+LSM2 pp PET127
+LSM2 pp GYP5
+LSM8 pp PCF11
+LSM8 pp TOS8
+LSM8 pp MTR3
+LSM8 pp YHR035W
+LSM8 pp SKI7
+LSM8 pp HSH49
+LSM8 pp PAT1
+LSM1 pp LSM2
+LSM3 pp LSM8
+LSM4 pp LSM8
+LSM6 pp LSM8
+YEL015W pp PSU1
+LSM8 pp LSM2
+Mer1 pp Snu56
+Mer1 pp Snu71
+Ppz1 pp Red1
+Ppz1 pp Gip2
+Ppz1 pp Yta6
+Spt15 pd Pgk1_promoter
+Spt15 pd Arg1_promoter
+Ume6 pd Spo13_promoter
+Ume6 pd Ino1_promoter
+Ume6 pd Sip4_promoter
+Unknown interactsWith Tup1-Ssn6
+Hos1 interactsWith Unknown
+Pol32 pp Pol32
+Pol30 pp Pol30
+Ppz1 pp Yol091w
+Ppz1 pp Yfr003c
+End3 pp Yap1802
+Ede1 pp Yap1802
+Kex2 pp Sla1
+Gcn5 pd Arg1_promoter
+Hos2 interactsWith Tup1-Ssn6
+Rpd3 interactsWith Tup1-Ssn6
+Rpd3 pp Tup1
+Rpd3 pp Cyc8
+Hos2 pp Cyc8
+CNB1 interactsWith RMD7
+CNB1 interactsWith VPS1
+CNB1 interactsWith OPI3
+CNB1 interactsWith YPT6
+CNB1 interactsWith KRE1
+CNB1 interactsWith GAS1
+CNB1 interactsWith VAN1
+CNB1 interactsWith VPS63
+CNB1 interactsWith CSF1
+CNB1 interactsWith SAC1
+CNB1 interactsWith VPS24
+CNB1 interactsWith MNN11
+CNB1 interactsWith VMA22
+CNB1 interactsWith VMA10
+CNB1 interactsWith PPA1
+CNB1 interactsWith SMI1
+CNB1 interactsWith CHO2
+CNB1 interactsWith BUD25
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+CNB1 interactsWith PMT2
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+CNB1 interactsWith BTS1
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+CNB1 interactsWith VPH2
+CNB1 interactsWith YKL118W
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+CNB1 interactsWith VMA2
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+TUB2 interactsWith HCM1
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+Pho4 pp Pse1
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+Unknown interactsWith EMP24
+Unknown interactsWith ERV25
+PFD2 interactsWith Unknown
+Unknown interactsWith PFD3
+Unknown interactsWith PFD1
+Unknown interactsWith PFD6
+Unknown interactsWith PFD5
+Unknown interactsWith PFD4
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+Unknown interactsWith CCT2
+Unknown interactsWith CCT8
+Unknown interactsWith CCT3
+Unknown interactsWith CCT7
+Unknown interactsWith CCT5
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+Unknown interactsWith PLP2
+ISW1 interactsWith Unknown
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+Unknown interactsWith RSC3
+Unknown interactsWith RSC8
+Unknown interactsWith RSC1
+Unknown interactsWith RSC30
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+Unknown interactsWith RSC4
+Unknown interactsWith RSC58
+Unknown interactsWith SFH1
+Unknown interactsWith RSC2
+Unknown interactsWith RSC9
+Unknown interactsWith ARP9
+Unknown interactsWith NPL6
+Unknown interactsWith ARP7
+SCC1 interactsWith Unknown
+Unknown interactsWith SMC1
+Unknown interactsWith SCC3
+Unknown interactsWith SMC3
+MCM19 interactsWith Unknown
+Unknown interactsWith MCM21
+Unknown interactsWith OKP1
+Unknown interactsWith MCM22
+Unknown interactsWith CTF3
+Unknown interactsWith MCM18
+Unknown interactsWith MCM16
+SPC97 interactsWith Unknown
+Unknown interactsWith TUB4
+Unknown interactsWith SPC98
+CAC3 interactsWith Unknown
+Unknown interactsWith CAC2
+Unknown interactsWith CAC1
+SPC25 interactsWith Unknown
+Unknown interactsWith NDC80
+Unknown interactsWith SPC24
+Unknown interactsWith NUF2
+BRN1 interactsWith Unknown
+Unknown interactsWith YCS5
+Unknown interactsWith SMC2
+Unknown interactsWith SMC4
+Unknown interactsWith YCS4
+VPS29 interactsWith Unknown
+Unknown interactsWith VPS26
+Unknown interactsWith VPS35
+Unknown interactsWith VPS5
+Unknown interactsWith VPS17
+CHC1 interactsWith Unknown
+Unknown interactsWith CLC1
+CDC10 interactsWith Unknown
+Unknown interactsWith SHS1
+Unknown interactsWith CDC12
+Unknown interactsWith CDC11
+Unknown interactsWith CDC3
+CAP2 interactsWith Unknown
+Unknown interactsWith YIR003W
+Unknown interactsWith CAP1
+VPS54 interactsWith Unknown
+Unknown interactsWith VPS52
+Unknown interactsWith VPS53
+Unknown interactsWith VPS51
+TRS20 interactsWith Unknown
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+Unknown interactsWith TRS31
+Unknown interactsWith BET3
+Unknown interactsWith BET5
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+HSE1 interactsWith Unknown
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+Unknown interactsWith VPS41
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+Unknown interactsWith VPS33
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+Unknown interactsWith VPS16
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+Unknown interactsWith APS3
+Unknown interactsWith APL5
+TOS1 interactsWith Unknown
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+Unknown interactsWith ARF1
+Unknown interactsWith SEC26
+Unknown interactsWith GLO3
+Unknown interactsWith RET2
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+Unknown interactsWith ARC15
+Unknown interactsWith ARP3
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+Unknown interactsWith ARC18
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+EXO84 interactsWith Unknown
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+Unknown interactsWith EXO70
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+Unknown interactsWith APM1
+Unknown interactsWith APL4
+COG3 interactsWith Unknown
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+Unknown interactsWith COG1
+Unknown interactsWith COG2
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+Unknown interactsWith COG6
+Unknown interactsWith COG5
+Unknown interactsWith COG4
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+Unknown interactsWith APL1
+Unknown interactsWith APS2
+Unknown interactsWith APM4
+VPS15 interactsWith Unknown
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+Unknown interactsWith VPS38
+Unknown interactsWith VPS30
+DPB3 interactsWith Unknown
+Unknown interactsWith DPB4
+Unknown interactsWith POL2
+Unknown interactsWith DPB2
+ORC2 interactsWith Unknown
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+Unknown interactsWith ORC3
+Unknown interactsWith ORC1
+Unknown interactsWith ORC5
+Unknown interactsWith ORC4
+POL12 interactsWith Unknown
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+Unknown interactsWith PRI2
+Unknown interactsWith POL1
+Unknown interactsWith POP2
+BAT1 interactsWith Unknown
+Unknown interactsWith BAT2
+SER3 interactsWith Unknown
+Unknown interactsWith PHO12
+Unknown interactsWith SER33
+BET4 interactsWith Unknown
+Unknown interactsWith BET2
+TPS1 interactsWith Unknown
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+Unknown interactsWith TSL1
+Unknown interactsWith TPS3
+TRP2 interactsWith Unknown
+Unknown interactsWith TRP3
+KGD2 interactsWith Unknown
+Unknown interactsWith LPD1
+Unknown interactsWith KGD1
+LCB2 interactsWith Unknown
+Unknown interactsWith LCB1
+PDB1 interactsWith Unknown
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+Unknown interactsWith PDA1
+Unknown interactsWith LPD1
+Unknown interactsWith PDX1
+Unknown interactsWith LAT1
+OST4 interactsWith Unknown
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+Unknown interactsWith STT3
+Unknown interactsWith OST5
+Unknown interactsWith OST1
+Unknown interactsWith OST6
+Unknown interactsWith SWP1
+Unknown interactsWith OST3
+Unknown interactsWith OST2
+QCR1 interactsWith Unknown
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+Unknown interactsWith RBS1
+Unknown interactsWith QCR2
+LYS2 interactsWith Unknown
+Unknown interactsWith LYS5
+PFK1 interactsWith Unknown
+Unknown interactsWith PFK2
+PHO88 interactsWith Unknown
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+Unknown interactsWith MNN8
+Unknown interactsWith OLE1
+Unknown interactsWith PMR1
+Unknown interactsWith PHB2
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+Unknown interactsWith HOC1
+Unknown interactsWith MNN9
+GLE2 interactsWith Unknown
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+Unknown interactsWith NSP1
+Unknown interactsWith NUP82
+Unknown interactsWith NUP116
+NUP84 interactsWith Unknown
+Unknown interactsWith NUP145
+Unknown interactsWith SEH1
+Unknown interactsWith NUP85
+Unknown interactsWith NUP120
+Unknown interactsWith SEC13
+NIC96 interactsWith Unknown
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+Unknown interactsWith NUP57
+Unknown interactsWith NSP1
+CSN5 interactsWith Unknown
+Unknown interactsWith CSN9
+Unknown interactsWith CSN11
+Unknown interactsWith CSI1
+Unknown interactsWith CSN10
+ULA1 interactsWith Unknown
+Unknown interactsWith UBA3
+CDC27 interactsWith Unknown
+Unknown interactsWith APC11
+Unknown interactsWith APC4
+Unknown interactsWith CDC26
+Unknown interactsWith APC10
+Unknown interactsWith CDC23
+Unknown interactsWith CDC16
+Unknown interactsWith APC9
+Unknown interactsWith APC2
+Unknown interactsWith APC1
+Unknown interactsWith APC5
+PRE7 interactsWith Unknown
+Unknown interactsWith PRE1
+Unknown interactsWith PUP3
+Unknown interactsWith PRE4
+Unknown interactsWith SCL1
+Unknown interactsWith PRE9
+Unknown interactsWith PUP2
+Unknown interactsWith PRE3
+Unknown interactsWith PRE8
+Unknown interactsWith PSE1
+Unknown interactsWith PRE5
+Unknown interactsWith PRE6
+Unknown interactsWith PUP1
+Unknown interactsWith PRE10
+Unknown interactsWith PRE2
+RPT2 interactsWith Unknown
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+Unknown interactsWith RPN6
+Unknown interactsWith RPN5
+Unknown interactsWith RPT3
+Unknown interactsWith RPN9
+Unknown interactsWith RPN3
+Unknown interactsWith RPN11
+Unknown interactsWith UBP6
+Unknown interactsWith RPN12
+Unknown interactsWith RPT6
+Unknown interactsWith HUL5
+Unknown interactsWith ECM29
+Unknown interactsWith RPN1
+Unknown interactsWith RPN10
+Unknown interactsWith RPN2
+Unknown interactsWith RPT1
+Unknown interactsWith RPN13
+Unknown interactsWith RPT5
+Unknown interactsWith RPT4
+Unknown interactsWith RPN8
+Unknown interactsWith RPN7
+YTA10 interactsWith Unknown
+Unknown interactsWith HMG2
+Unknown interactsWith YTA12
+CEG1 interactsWith Unknown
+Unknown interactsWith CET1
+SEC66 interactsWith Unknown
+Unknown interactsWith SSS1
+Unknown interactsWith SBH1
+Unknown interactsWith SEC67
+Unknown interactsWith SEC61
+Unknown interactsWith SEC63
+Unknown interactsWith SEC62
+PAF1 interactsWith Unknown
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+Unknown interactsWith SPT16
+Unknown interactsWith RTF1
+Unknown interactsWith CDC73
+Unknown interactsWith SPT5
+Unknown interactsWith POB3
+Unknown interactsWith CTR9
+Unknown interactsWith LEO1
+ROX3 interactsWith Unknown
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+Unknown interactsWith SRB6
+Unknown interactsWith SRB8
+Unknown interactsWith MED2
+Unknown interactsWith SRB7
+Unknown interactsWith SRB9
+Unknown interactsWith SRB4
+Unknown interactsWith HRS1
+Unknown interactsWith SOH1
+Unknown interactsWith NUT1
+Unknown interactsWith SRB5
+Unknown interactsWith SRB2
+Unknown interactsWith MED6
+Unknown interactsWith RGR1
+Unknown interactsWith MED11
+Unknown interactsWith SRB11
+Unknown interactsWith SIN4
+Unknown interactsWith MED9
+Unknown interactsWith GAL11
+Unknown interactsWith MED7
+Unknown interactsWith MED4
+Unknown interactsWith SRB10
+Unknown interactsWith MED1
+Unknown interactsWith MED10
+RPB5 interactsWith Unknown
+Unknown interactsWith RPB1
+Unknown interactsWith RPB7
+Unknown interactsWith RPB9
+Unknown interactsWith TFG2
+Unknown interactsWith RPC10
+Unknown interactsWith RPB3
+Unknown interactsWith RPB4
+Unknown interactsWith SPT5
+Unknown interactsWith RPB11
+Unknown interactsWith RPB2
+Unknown interactsWith RPB10
+Unknown interactsWith RPB8
+Unknown interactsWith RPB6
+PRP9 interactsWith Unknown
+Unknown interactsWith PRP11
+Unknown interactsWith SMB1
+Unknown interactsWith SMX2
+Unknown interactsWith SMD1
+Unknown interactsWith IST3
+Unknown interactsWith MSL1
+Unknown interactsWith PRP21
+Unknown interactsWith SMD3
+Unknown interactsWith SMD2
+Unknown interactsWith RSE1
+Unknown interactsWith HRT2
+Unknown interactsWith CUS1
+Unknown interactsWith HSH155
+Unknown interactsWith CUS2
+Unknown interactsWith SME1
+Unknown interactsWith HSH49
+Unknown interactsWith LEA1
+Unknown interactsWith SMX3
+MUD1 interactsWith Unknown
+Unknown interactsWith LUC7
+Unknown interactsWith PRP42
+Unknown interactsWith SNU56
+Unknown interactsWith SMB1
+Unknown interactsWith SMX2
+Unknown interactsWith SNU71
+Unknown interactsWith SMD1
+Unknown interactsWith NAM8
+Unknown interactsWith SNP1
+Unknown interactsWith PRP40
+Unknown interactsWith SMD3
+Unknown interactsWith SMD2
+Unknown interactsWith YHC1
+Unknown interactsWith PRP39
+Unknown interactsWith SME1
+Unknown interactsWith SMX3
+CTK2 interactsWith Unknown
+Unknown interactsWith CTK1
+Unknown interactsWith CTK3
+EDC3 interactsWith Unknown
+Unknown interactsWith DCP2
+Unknown interactsWith DCP1
+PAN2 interactsWith Unknown
+Unknown interactsWith PAN3
+POP5 interactsWith Unknown
+Unknown interactsWith POP8
+Unknown interactsWith POP7
+Unknown interactsWith POP4
+Unknown interactsWith POP6
+Unknown interactsWith RPP1
+Unknown interactsWith POP1
+Unknown interactsWith POP3
+SKI8 interactsWith Unknown
+Unknown interactsWith SKI2
+Unknown interactsWith SKI3
+CCR4 interactsWith Unknown
+Unknown interactsWith NOT1
+Unknown interactsWith NOT2
+Unknown interactsWith NOT4
+Unknown interactsWith CAF130
+Unknown interactsWith NOT3
+Unknown interactsWith CAF40
+Unknown interactsWith POP2
+Unknown interactsWith NOT5
+RRP46 interactsWith Unknown
+Unknown interactsWith RRP43
+Unknown interactsWith MTR3
+Unknown interactsWith RRP41
+Unknown interactsWith RRP42
+Unknown interactsWith RRP45
+Unknown interactsWith RRP4
+Unknown interactsWith RRP40
+Unknown interactsWith CSL4
+Unknown interactsWith RRP44
+Unknown interactsWith RRP6
+BCY1 interactsWith Unknown
+Unknown interactsWith TPK1
+Unknown interactsWith TPK2
+YKU80 interactsWith Unknown
+Unknown interactsWith YKU70
+TFC3 interactsWith Unknown
+Unknown interactsWith TFC1
+Unknown interactsWith TFC6
+Unknown interactsWith TFC4
+Unknown interactsWith TFC7
+Unknown interactsWith TFC8
+TOA2 interactsWith Unknown
+Unknown interactsWith TOA1
+EPL1 interactsWith Unknown
+Unknown interactsWith ACT1
+Unknown interactsWith YNG2
+Unknown interactsWith TRA1
+Unknown interactsWith ARP4
+Unknown interactsWith YAP1
+Unknown interactsWith CRZ1
+Unknown interactsWith ESA1
+Unknown interactsWith EAF3
+SNF1 interactsWith Unknown
+Unknown interactsWith SNF4
+Unknown interactsWith SIP2
+SNF5 interactsWith Unknown
+Unknown interactsWith SNF11
+Unknown interactsWith SNF6
+Unknown interactsWith SWI3
+Unknown interactsWith YAP1
+Unknown interactsWith ARP9
+Unknown interactsWith CRZ1
+Unknown interactsWith SNF12
+Unknown interactsWith SWI2
+Unknown interactsWith SWI1
+Unknown interactsWith TAF30
+Unknown interactsWith ARP7
+CPS50 interactsWith Unknown
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+Unknown interactsWith CPS25
+Unknown interactsWith SET1
+Unknown interactsWith CPS35
+Unknown interactsWith CPS60
+Unknown interactsWith CPS40
+CDC27 interactsWith Unknown
+Unknown interactsWith KIN28
+Unknown interactsWith TFB1
+Unknown interactsWith TFB3
+Unknown interactsWith RAD3
+Unknown interactsWith SSL2
+Unknown interactsWith SSL1
+Unknown interactsWith FPR1
+Unknown interactsWith TFB2
+Unknown interactsWith CCL1
+Unknown interactsWith TFB4
+SPT7 interactsWith Unknown
+Unknown interactsWith TAF90
+Unknown interactsWith SGF29
+Unknown interactsWith TAF61
+Unknown interactsWith TAF25
+Unknown interactsWith SWI7
+Unknown interactsWith SPT3
+Unknown interactsWith SWI8
+Unknown interactsWith SGF73
+Unknown interactsWith TAF60
+Unknown interactsWith SWI9
+Unknown interactsWith TRA1
+Unknown interactsWith SPT8
+Unknown interactsWith TAF17
+Unknown interactsWith SPT20
+Unknown interactsWith HFI1
+RXT3 interactsWith Unknown
+Unknown interactsWith SDS3
+Unknown interactsWith RCO1
+Unknown interactsWith ECM16
+Unknown interactsWith SAP30
+Unknown interactsWith PHO23
+Unknown interactsWith SDS6
+Unknown interactsWith SDS16
+Unknown interactsWith UME1
+Unknown interactsWith RXT1
+Unknown interactsWith EAF3
+FUN19 interactsWith Unknown
+Unknown interactsWith TAF90
+Unknown interactsWith TAF150
+Unknown interactsWith TAF61
+Unknown interactsWith TAF25
+Unknown interactsWith TFIID
+Unknown interactsWith TAF60
+Unknown interactsWith TAF130
+Unknown interactsWith TAF40
+Unknown interactsWith TAF19
+Unknown interactsWith TAF65
+Unknown interactsWith TAF48
+Unknown interactsWith TAF67
+Unknown interactsWith TAF17
+Unknown interactsWith TAF47
+Unknown interactsWith TAF30
+ELP2 interactsWith Unknown
+Unknown interactsWith ELP5
+Unknown interactsWith ELP1
+Unknown interactsWith ELP6
+Unknown interactsWith ELP3
+Unknown interactsWith ELP4
+ITC1 interactsWith Unknown
+Unknown interactsWith ADH1
+Unknown interactsWith ISW2
+MAK31 interactsWith Unknown
+Unknown interactsWith MAK10
+Unknown interactsWith MAK3
+SRP101 interactsWith Unknown
+Unknown interactsWith SRP102
+SRP14 interactsWith Unknown
+Unknown interactsWith SRP21
+Unknown interactsWith SEC65
+Unknown interactsWith SRP72
+Unknown interactsWith SRP68
+Unknown interactsWith SRP54
+VAR1 interactsWith Unknown
+Unknown interactsWith MRP21
+Unknown interactsWith MRPS9
+Unknown interactsWith MRPS5
+Unknown interactsWith MRP10
+Unknown interactsWith EHD3
+Unknown interactsWith RSM10
+Unknown interactsWith RSM24
+Unknown interactsWith MRPS28
+Unknown interactsWith MRP1
+Unknown interactsWith RSM18
+Unknown interactsWith YMR31
+Unknown interactsWith RSM23
+Unknown interactsWith MRP13
+Unknown interactsWith MRPS35
+Unknown interactsWith RSM27
+Unknown interactsWith MRP4
+Unknown interactsWith MRPS2
+Unknown interactsWith RSM25
+Unknown interactsWith RSM26
+Unknown interactsWith RSM7
+Unknown interactsWith MRP17
+Unknown interactsWith RSM22
+Unknown interactsWith MRPS8
+Unknown interactsWith MRPS17
+Unknown interactsWith SWS2
+Unknown interactsWith NAM9
+Unknown interactsWith MRPS18
+Unknown interactsWith YNR036C
+Unknown interactsWith RSM19
+Unknown interactsWith PET123
+Unknown interactsWith MRPS16
+Unknown interactsWith MRP51
+Unknown interactsWith MRP2
+YBR159W interactsWith Unknown
+Unknown interactsWith GCD6
+Unknown interactsWith GCD11
+Unknown interactsWith GCD2
+Unknown interactsWith SUI2
+Unknown interactsWith GCN3
+Unknown interactsWith GCD7
+Unknown interactsWith IST1
+Unknown interactsWith RAS1
+Unknown interactsWith GCD1
+Unknown interactsWith SUI3
+TIF32 interactsWith Unknown
+Unknown interactsWith TIF35
+Unknown interactsWith HCR1
+Unknown interactsWith TIF34
+Unknown interactsWith NIP1
+Unknown interactsWith SUI1
+Unknown interactsWith PRT1
+Unknown interactsWith TIF5
+Unknown interactsWith SUA7
+FRS2 interactsWith Unknown
+Unknown interactsWith FRS1
+ARC1 interactsWith Unknown
+Unknown interactsWith MES1
+NUC1 interactsWith Unknown
+Unknown interactsWith YKR079C
+YNR046W interactsWith Unknown
+Unknown interactsWith YOL124C
+YER007C-A interactsWith Unknown
+Unknown interactsWith YJR014W
+YBL046W interactsWith Unknown
+Unknown interactsWith PPH3
+Unknown interactsWith PSY2
+ENP1 interactsWith Unknown
+Unknown interactsWith TSR1
+Unknown interactsWith SLX9
+Unknown interactsWith RIO2
+Unknown interactsWith NOB1
+PLO2 interactsWith Unknown
+Unknown interactsWith HDA1
+Unknown interactsWith PLO1
+IPP1 interactsWith Unknown
+Unknown interactsWith YDL203C
+Unknown interactsWith ROM2
+Unknown interactsWith TUS1
+LTE1 interactsWith Unknown
+Unknown interactsWith KEL1
+PTC4 interactsWith Unknown
+Unknown interactsWith YDR186C
+Rad51 interactsWith DNA
+RPA_Complex interactsWith DNA
+Glc7 pp Glc8
+Ste20 pp Ste20
+Ste4 pp Ste20
+Ste4 pp Ste5
+Ste20 pp Bem1
+Pho4 pp Pho4
+Ssn3 pp Ssn8
+Ste4 pp Cla4
+Ssn3-Ssn8 interactsWith Ste12
+Sec27 pp Sec28
+Orc6 pp Dbf4
+Sec27 pp Ret1
+Dsl1 pp Tip20
+Ret1 pp Sec28
+Dsl1 pp Ret2
+Dsl1 pp Ret1
+Orc3 pp Dbf4
+Orc2 pp Dbf4
+Orc5 pp Dbf4
+GAL4 pp GAL80
+Kre6 pp Las17
+Kre6 pp Sla1
+Ste12 pp Dig2
+Ste12 pp Dig1
+Skp1 pp Cdc4
+Cdc28 pp Clb6
+Cdc28 pp Clb5
+Cdc28 pp Clb4
+Cdc28 pp Clb1
+Unknown interactsWith Orc5
+Unknown interactsWith Cdc34
+Unknown interactsWith Cdc53
+Orc1 interactsWith Unknown
+Unknown interactsWith Orc2
+Unknown interactsWith Orc3
+Unknown interactsWith Orc4
+Unknown interactsWith Orc6
+Cdc4 interactsWith Unknown
+Sec26 pp Ret1
+Sec21 pp Sec27
+Sec26 pp Sec27
+Sjl3 pp Bsp1
+Pab1 pp Sup35
+Rai1 interactsWith Unknown
+Sjl2 pp Bsp1
+Unknown interactsWith Rat1
+Unknown interactsWith Las1
+Unknown interactsWith Grc3
+Unknown interactsWith Ste5
+Unknown interactsWith Ste7
+Fus3 interactsWith Unknown
+Fus3/Ste5/Ste7 interactsWith Ste12
+Fus3/Ste7 interactsWith Dig1
+Fus3/Ste7 interactsWith Dig2
+Fus3/Ste5/Ste7 interactsWith Dig2
+Fus3/Ste5/Ste7 interactsWith Dig1
+Fus3/Ste7 interactsWith Ste12
+Rad53 pp Rad9
+Ste12 pp Kap121
+Unknown interactsWith Ste11
+Kss1 interactsWith Unknown
+Unknown interactsWith Ste5
+Unknown interactsWith Ste7
+Ufo1 pp Ho
+Ufo1 pp Skp1
+Ufo1 pp Cdc53
+Kss1/Ste5/Ste7/Ste11 interactsWith Ste12
+Kss1/Ste5/Ste7/Ste11 interactsWith Rst1
+Kss1/Ste5/Ste7/Ste11 interactsWith Rst2
+Kss1/Ste7/Ste11 interactsWith Ste12
+Kss1/Ste7/Ste11 interactsWith Rst1
+Kss1/Ste7/Ste11 interactsWith Rst2
+Nup2 interactsWith Unknown
+Unknown interactsWith Kap95
+Unknown interactsWith Srp1
+Nup2p/Srp1p/Kap95p_complex interactsWith Nup60
+SUC2_promoter pd Mig1
+SUC2_promoter pd MIG3
+SUC2_promoter pd RGT1
+Snp1 pd SNR19
+Eap1 pp Cdc33
+unknown interactsWith Scc3
+unknown interactsWith Smc1
+unknown interactsWith Smc3
+Scc1 interactsWith Unknown
+Vik1 pp Kar3
+Tof1 pp Csm3
+TBP1 pd iYAL001C
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+TBP1 pd itS(AGA)B
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+TBP1 pd iYBR014C
+TBP1 pd iYBR017C
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+TBP1 pd iYOR155C
+TBP1 pd iYOR156C
+TBP1 pd iYOR161C
+TBP1 pd iYOR166C
+TBP1 pd iYOR172W
+TBP1 pd iYOR173W
+TBP1 pd iYOR177C
+TBP1 pd iYOR178C-0
+TBP1 pd iYOR179C-0
+TBP1 pd iYOR183W
+TBP1 pd iYOR186W
+TBP1 pd iYOR187W
+TBP1 pd iYOR188W
+TBP1 pd iYOR189W
+TBP1 pd iYOR190W
+TBP1 pd iYOR192C-0
+TBP1 pd iYOR198C
+TBP1 pd iYOR213C
+TBP1 pd iYOR214C
+TBP1 pd iYOR215C
+TBP1 pd iYOR222W
+TBP1 pd iYOR224C
+TBP1 pd iYOR229W
+TBP1 pd iYOR230W
+TBP1 pd iYOR231W
+TBP1 pd iYOR232W
+TBP1 pd iYOR236W
+TBP1 pd iYOR237W
+TBP1 pd iYOR238W
+TBP1 pd iYOR240W
+TBP1 pd iYOR242C
+TBP1 pd iYOR245C
+TBP1 pd iYOR249C
+TBP1 pd iYOR250C
+TBP1 pd iYOR252W
+TBP1 pd iYOR257W
+TBP1 pd iYOR262W
+TBP1 pd iYOR265W
+TBP1 pd iYOR270C
+TBP1 pd iYOR279C
+TBP1 pd iYOR280C
+TBP1 pd iYOR283W
+TBP1 pd iYOR284W
+TBP1 pd iYOR285W
+TBP1 pd iYOR287C
+TBP1 pd iYOR292C
+TBP1 pd iYOR293W
+TBP1 pd iYOR294W
+TBP1 pd iYOR295W
+TBP1 pd iYOR298C-A
+TBP1 pd iYOR300W
+TBP1 pd iYOR301W
+TBP1 pd iYOR306C
+TBP1 pd iYOR307C
+TBP1 pd iYOR308C
+TBP1 pd iYOR311C
+TBP1 pd iYOR312C
+TBP1 pd iYOR316C-0
+TBP1 pd iYOR322C
+TBP1 pd iYOR323C
+TBP1 pd iYOR329C
+TBP1 pd iYOR336W
+TBP1 pd iYOR337W
+TBP1 pd iYOR339C
+TBP1 pd iYOR342C
+TBP1 pd iYOR347C
+TBP1 pd iYOR350C
+TBP1 pd iYOR353C
+TBP1 pd iYOR355W
+TBP1 pd iYOR358W
+TBP1 pd iYOR360C
+TBP1 pd iYOR361C
+TBP1 pd iYOR362C
+TBP1 pd iYOR363C
+TBP1 pd iYOR367W
+TBP1 pd iYOR369C
+TBP1 pd iYOR370C
+TBP1 pd iYOR371C
+TBP1 pd iYOR373W
+TBP1 pd iYOR376W-1
+TBP1 pd iYOR377W-1
+TBP1 pd iYOR380W-1
+TBP1 pd iYOR381W-1
+TBP1 pd iYOR384W
+TBP1 pd iYOR385W
+TBP1 pd iYOR387C-0
+TBP1 pd iYOR389W
+TBP1 pd iYPL006W
+TBP1 pd iYPL020C
+TBP1 pd iYPL022W
+TBP1 pd iYPL028W
+TBP1 pd iYPL029W
+TBP1 pd iYPL030W
+TBP1 pd iYPL032C
+TBP1 pd iYPL033C
+TBP1 pd iYPL036W
+TBP1 pd iYPL039W
+TBP1 pd iYPL041C
+TBP1 pd iYPL042C
+TBP1 pd iYPL045W
+TBP1 pd iYPL048W
+TBP1 pd iYPL050C
+TBP1 pd iYPL052W
+TBP1 pd iYPL056C
+TBP1 pd iYPL057C
+TBP1 pd iYPL058C-0
+TBP1 pd iYPLCtau2
+TBP1 pd iYPL061W
+TBP1 pd iYPL062W
+TBP1 pd iYPL066W
+TBP1 pd iYPL068C
+TBP1 pd iYPL069C
+TBP1 pd iYPL074W
+TBP1 pd iYPL075W
+TBP1 pd iYPL076W-1
+TBP1 pd iYPL078C
+TBP1 pd iYPL080C
+TBP1 pd iYPL083C
+TBP1 pd iYPL085W
+TBP1 pd iYPL088W
+TBP1 pd iYPL090C
+TBP1 pd iYPL092W
+TBP1 pd iYPL093W
+TBP1 pd iYPL095C
+TBP1 pd iYPL097W
+TBP1 pd iYPL099C
+TBP1 pd iYPL101W
+TBP1 pd iYPL106C
+TBP1 pd iYPL109C
+TBP1 pd iYPL110C
+TBP1 pd iYPL113C
+TBP1 pd iYPL119C
+TBP1 pd iYPL125W
+TBP1 pd iYPL126W
+TBP1 pd iYPL128C
+TBP1 pd iYPL130W
+TBP1 pd iYPL131W
+TBP1 pd iYPL132W
+TBP1 pd iYPL134C
+TBP1 pd iYPL139C
+TBP1 pd iYPL140C
+TBP1 pd iYPL141C
+TBP1 pd iYPL144W
+TBP1 pd iYPL146C
+TBP1 pd iYPL150W
+TBP1 pd iYPL153C
+TBP1 pd iYPL154C
+TBP1 pd iYPL155C
+TBP1 pd iYPL156C
+TBP1 pd iYPL159C
+TBP1 pd iYPL162C
+TBP1 pd iYPL163C
+TBP1 pd iYPL164C
+TBP1 pd iYPL165C
+TBP1 pd iYPL172C
+TBP1 pd iYPL177C-0
+TBP1 pd iYPLWdelta8
+TBP1 pd iYPL180W
+TBP1 pd iYPL181W
+TBP1 pd iYPL185W
+TBP1 pd iYPL188W
+TBP1 pd iYPL192C
+TBP1 pd iYPL194W
+TBP1 pd iYPL195W
+TBP1 pd iYPL196W
+TBP1 pd iYPL197C
+TBP1 pd iYPL202C
+TBP1 pd iYPL204W
+TBP1 pd iYPL208W
+TBP1 pd iYPL210C
+TBP1 pd iYPL216W
+TBP1 pd iYPL219W
+TBP1 pd iYPL220W
+TBP1 pd iYPL221W
+TBP1 pd iYPL222W
+TBP1 pd iYPL224C
+TBP1 pd iYPL226W
+TBP1 pd iYPL229W
+TBP1 pd iYPL230W
+TBP1 pd iYPL231W
+TBP1 pd iYPL232W
+TBP1 pd iYPL233W
+TBP1 pd iYPL239W
+TBP1 pd iYPL241C
+TBP1 pd iYPL242C
+TBP1 pd iYPL247C
+TBP1 pd iYPL248C
+TBP1 pd iYPL249C
+TBP1 pd iYPL250C
+TBP1 pd iYPL251W
+TBP1 pd iYPL255W
+TBP1 pd iYPL259C
+TBP1 pd iYPL262W
+TBP1 pd iYPL264C
+TBP1 pd iYPL266W
+TBP1 pd iYPL267W
+TBP1 pd iYPL268W
+TBP1 pd iYPL269W
+TBP1 pd iYPL270W
+TBP1 pd iYPL271W
+TBP1 pd iYPL274W
+TBP1 pd iYPL275W-2
+TBP1 pd iYPL277C
+TBP1 pd iYPL279C
+TBP1 pd iYPL282C
+TBP1 pd iYPL283C-0
+TBP1 pd iCEN16
+TBP1 pd iYPR001W
+TBP1 pd iYPR003C
+TBP1 pd iYPR004C
+TBP1 pd iYPR005C
+TBP1 pd iYPR006C
+TBP1 pd iYPR008W
+TBP1 pd iYPR010C
+TBP1 pd iYPR011C
+TBP1 pd iYPR013C-0
+TBP1 pd iYPR015C
+TBP1 pd iYPR016C
+TBP1 pd iYPR018W
+TBP1 pd iYPR019W
+TBP1 pd iYPR021C
+TBP1 pd iYPR022C
+TBP1 pd iYPR030W
+TBP1 pd iYPR031W
+TBP1 pd iYPR034W
+TBP1 pd iYPR035W
+TBP1 pd iYPR046W
+TBP1 pd iYPR047W
+TBP1 pd iYPR055W
+TBP1 pd iYPR056W
+TBP1 pd iYPR057W
+TBP1 pd iYPR060C
+TBP1 pd iYPR065W
+TBP1 pd iYPR066W
+TBP1 pd iYPR068C
+TBP1 pd iYPR070W
+TBP1 pd itS(UGA)P
+TBP1 pd iYPR073C
+TBP1 pd iYPR074C
+TBP1 pd iYPR076W
+TBP1 pd iYPR079W
+TBP1 pd iYPR081C
+TBP1 pd iYPR083W
+TBP1 pd iYPR086W
+TBP1 pd iSNR51
+TBP1 pd iYPR104C
+TBP1 pd itT(UGU)P
+TBP1 pd iYPR113W
+TBP1 pd iYPR114W
+TBP1 pd iYPR115W
+TBP1 pd iYPR116W
+TBP1 pd iYPR117W
+TBP1 pd iYPRWsigma2-1
+TBP1 pd iYPR121W-1
+TBP1 pd iYPR122W
+TBP1 pd iYPR133W-A
+TBP1 pd iYPR134W
+TBP1 pd iYPR135W
+TBP1 pd iYPR138C
+TBP1 pd iYPR151C
+TBP1 pd iYPR153W
+TBP1 pd iYPR155C
+TBP1 pd iYPR157W
+TBP1 pd itG(GCC)P2
+TBP1 pd iYPR161C
+TBP1 pd iYPR162C
+TBP1 pd iYPR164W
+TBP1 pd iYPR166C
+TBP1 pd iYPR168W
+TBP1 pd iYPR171W
+TBP1 pd iYPR173C
+TBP1 pd iYPR182W
+TBP1 pd iYPR183W
+TBP1 pd iYPR184W
+TBP1 pd iYPR191W
+TBP1 pd iYPR193C
+TBP1 pd iYPRWtau4
+TBP1 pd iYPR199C
+TBP1 pd iYPR201W-1
+TBP1 pd iYPR203W
+Sen2 pp Sen54
+Sen34 pp Sen15
+Prp45 pp Prp46
+Cdc28 pp Mpt5
+Vps4 pp Vps20
+Vps4 pp Vta1
+Vta1 pp Vps60
+Unknown interactsWith Ste11
+Kss1/Ste5/Ste7 interactsWith Rst1
+Kss1/Ste7 interactsWith Rst1
+Kss1/Ste7 interactsWith Ste12
+Kss1/Ste5/Ste7 interactsWith Ste12
+Unknown interactsWith Smc2
+Unknown interactsWith Ycs4
+Ycs5 interactsWith Unknown
+Unknown interactsWith Brn1
+Unknown interactsWith Smc4
+Fus3/Ste5/Ste7/Ste11 interactsWith Rst1
+Fus3/Ste5/Ste7/Ste11 interactsWith Rst2
+Kss1/Ste5/Ste7 interactsWith Rst2
+Kss1/Ste7 interactsWith Rst2
+Fus3/Ste5/Ste7/Ste11 interactsWith Ste12
+Abp1 pp App1
+Abp1 pp Cla4
+Abp1 pp Hua2
+Abp1 pp Rvs167
+Abp1 pp Srv2
+Acf2 pp Rvs167
+Act1 pp Cof1
+Act1 pp Las17
+Act1 pp Pfy1
+Act1 pp Rvs167
+Act1 pp Srv2
+Aip1 pp Srv2
+Air1 pp Cdc24
+Arp1 pp Nip100
+Atg17 pp Atg17
+Atg17 pp Dad2
+Atg17 pp Exo84
+Atg17 pp Myo1
+Atg17 pp Nip100
+Atg17 pp Rho1
+Atg17 pp Rho2
+Atg17 pp Sro77
+Sso2 pp Atg7
+Bcy1 pp Sro77
+Bem1 pp Boi2
+Bem1 pp Cdc24
+Bem1 pp Cdc42
+Bem1 pp Far1
+Bem1 pp Sec15
+Bem1 pp Ste20
+Bem1 pp Swe1
+Bem3 pp Bem4
+Bem3 pp Cla4
+Bem3 pp Zds1
+Bem3 pp Zds2
+Bem4 pp Cdc11
+Bem4 pp Cdc12
+Bem4 pp Cdc24
+Bem4 pp Cdc42
+Bem4 pp Gic1
+Bem4 pp Nfi1
+Bem4 pp Rho1
+Bem4 pp Rho2
+Bem4 pp Rho4
+Bem4 pp Rsr1
+Bem4 pp Spr28
+Bni1 pp Msb3
+Bni1 pp Pfy1
+Bni1 pp Rho1
+Bni1 pp Zds2
+Msb2 pp Bni4
+Bnr1 pp Pfy1
+Boi1 pp Dse1
+Boi1 pp Ste20
+Boi1 pp Zds2
+Boi2 pp Cdc42
+Boi2 pp Cla4
+Boi2 pp Dse1
+Boi2 pp Mrs6
+Boi2 pp Msb1
+Boi2 pp Ste20
+Boi2 pp Zds2
+Bub2 pp Gic1
+Bud2 pp Cln2
+Bud8 pp Ste20
+Bud8 pp Ykl082c
+Cap1 pp Bsp1
+Cap1 pp Cap2
+Cap1 pp Gic2
+Cdc11 pp Cdc12
+Cdc11 pp Nfi1
+Cdc11 pp Spr28
+Cdc11 pp Yor084w
+Cdc11 pp Zds2
+Cdc12 pp Cdc12
+Cdc12 pp Cla4
+Cdc12 pp Gic1
+Cdc12 pp Gic2
+Cdc12 pp She3
+Cdc24 pp Cdc42
+Cdc24 pp Ent2
+Cdc24 pp Far1
+Cdc24 pp Rsr1
+Cdc24 pp Sec15
+Cdc24 pp Ste20
+Cdc24 pp Swe1
+Cdc24 pp Ygr221c
+Cdc42 pp Cla4
+Cdc42 pp Gic1
+Cdc42 pp Gic2
+Cdc42 pp Rga1
+Cdc42 pp Ste20
+Cka1 pp Rho3
+Cka2 pp Rho3
+Ckb1 pp Rho3
+Cla4 pp Gic1
+Cla4 pp Gic2
+Msb2 pp Cla4
+Cla4 pp Rga1
+Cla4 pp Sla2
+Cla4 pp Zds2
+Crn1 pp App1
+Crn1 pp Svl3
+Dfg5 pp Gic1
+Dse1 pp Zds2
+Ent2 pp Sro77
+Exo84 pp Sec15
+Gic1 pp Csm1
+Gic1 pp Gic1
+Gic1 pp Gic2
+Gic1 pp Hof1
+Gic1 pp Ste50
+Gic1 pp Ykl082c
+Gic1 pp Zds1
+Gic1 pp Zds2
+Gic2 pp Csm1
+Gic2 pp Rga1
+Gic2 pp Ste50
+Gic2 pp Ykl082c
+Gic2 pp Zds1
+Gic2 pp Zds2
+Hsl7 pp App1
+Kin3 pp Sro77
+Las17 pp Rbd2
+Las17 pp Rvs167
+Las17 pp Sla1
+Las17 pp Yhr133c
+Msb3 pp Spa2
+Msb4 pp Spa2
+Myo1 pp Spr3
+Myo1 pp Ypr188c
+Nfi1 pp Nip100
+Nip100 pp Nip100
+Nip100 pp Pac11
+Nip100 pp Rho1
+Nip100 pp Rho2
+Nip100 pp Sro77
+Pfs1 pp Nas2
+Pfy1 pp Srv2
+Pkc1 pp Rho1
+Pkc1 pp Ygr221c
+Pkc1 pp Zds2
+Rga1 pp Rho1
+Rho1 pp Nas2
+Rho1 pp Shc1
+Rho1 pp Zds2
+Rho4 pp Nas2
+Rpn4 pp Nas2
+Rsr1 pp Sec15
+Rvs161 pp Rvs167
+Rvs167 pp Acf4
+Rvs167 pp App1
+Rvs167 pp Bsp1
+Rvs167 pp Hua1
+Rvs167 pp Hua2
+Rvs167 pp Rvs167
+Rvs167 pp Sla1
+Rvs167 pp Sla2
+Rvs167 pp Srv2
+Rvs167 pp Ybr108w
+Rvs167 pp Ynl086w
+Rvs167 pp Ysc84
+Skt5 pp Nas2
+Sla1 pp App1
+Sla1 pp Bsp1
+Sla1 pp Hua1
+Sla1 pp Srv2
+Sla1 pp Ysc84
+Sla2 pp App1
+Sla2 pp Hua2
+Sla2 pp Ysc84
+Spr6 pp Zds2
+Sro77 pp App1
+Sro77 pp Mca1
+Sro77 pp Yap1801
+Sro77 pp Yip1
+Srv2 pp Srv2
+Srv2 pp Trm5
+Sso1 pp Yap1801
+Sso2 pp Yap1801
+Ste20 pp Bem4
+Swe1 pp App1
+Yal004w pp Zds2
+Yel023c pp Zds2
+Yhr149c pp Zds1
+Yhr149c pp Zds2
+Ykl082c pp Zds2
+Zds1 pp Zds2
+Zds2 pp Zds2
+Glc7 pp Reg2
+H4 pd ura4
+H3 pd ura4
+Rpo21 interactsWith Unknown
+Naf1 pp Nhp2
+Naf1 pp Cbf5
+Unknown interactsWith Naf1
+Nop58 interactsWith U14
+Unknown interactsWith Rpl3
+Unknown interactsWith Rpl4a
+Unknown interactsWith Rpl6a
+Unknown interactsWith Rpl6b
+Unknown interactsWith Rpl7a
+Unknown interactsWith Rpl9a
+Fus3/Ste5/Ste7/Ste11 interactsWith Far1
+Kss1/Ste5/Ste7/Ste11 interactsWith Far1
+Fus3/Ste7/Ste11 interactsWith Rst1
+Fus3/Ste7/Ste11 interactsWith Rst2
+Fus3/Ste7/Ste11 interactsWith Ste12
+Nop58 interactsWith snR190
+Nop58 interactsWith snR4
+Nop58 interactsWith U18
+Unknown interactsWith Rpa135
+Unknown interactsWith Rpa190
+Unknown interactsWith Rpa34
+Unknown interactsWith Rpa43
+Unknown interactsWith Rpa49
+Unknown interactsWith Rpb10
+Unknown interactsWith Rpb5
+Unknown interactsWith Rpb8
+Unknown interactsWith Rpc19
+Unknown interactsWith Rpc40
+Unknown interactsWith Rpo26
+Rpa12 interactsWith Unknown
+Cbp20 pp Cbp80
+RNAPII interactsWith Gal1_mRNA
+MCD1 pd CEN3
+Mcd1 pd HMR-GIT1_region
+Mcd1 pd rDNA
+Unknown interactsWith Rpc10
+Unknown interactsWith Rpa14
+Ycs4 pp Smt3
+RNAPII interactsWith Arp2_mRNA
+CBC interactsWith 18S_rRNA
+CBC interactsWith Gal1_mRNA
+Rfa2 pd TEL6
+Rfa3 pd TEL6
+Rfa3 pd TEL15
+Cdc13 pd TEL6
+Mec1 pd TEL6
+Tel1 pd TEL6
+Rfa2 pd TEL15
+Cdc13 pd TEL15
+Mec1 pd TEL15
+Tel1 pd TEL15
+RNAPII interactsWith 18S_rRNA
+RNAPII interactsWith Act1_mRNA
+RNAPI interactsWith 18S_rRNA
+Pcf11 pp Rna14
+Pcf11 pp Rna15
+Pcf11 pp Clp1
+CF_IA interactsWith Hrp1
+NUP53 pp NIC96
+NUP53 pp Kap95
+Sen1 pp Rpo21
+Sen1 pp Rad2
+Sen1 pp Rnt1
+Sen1 pp Gcr2
+Sen1 pp Nup49
+Sen1 pp Pyc2
+Sen1 pp Prs3
+Sen1 pp Ypr148c
+Nop58 interactsWith U24
+Nop58 interactsWith snR13
+Unknown interactsWith PGK1_promoter
+Unknown interactsWith RPS11B_promoter
+Mot1 interactsWith Unknown
+Unknown interactsWith Tbp1
+Mot1 interactsWith Unknown
+Unknown interactsWith Tbp1
+Unknown interactsWith Tbp1
+Mot1 interactsWith Unknown
+Unknown interactsWith PYK1_promoter
+Unknown interactsWith RPL2B_promoter
+Mot1 interactsWith Unknown
+Unknown interactsWith Tbp1
+Sec21 pp Sec28
+Unknown interactsWith Rps15
+Unknown interactsWith Rps6a
+Gpi2 interactsWith Unknown
+Unknown interactsWith Eri1
+Unknown interactsWith Rps8a
+Unknown interactsWith Rps11a
+Unknown interactsWith Gpi2
+Ras2-GTP interactsWith Unknown
+Cse1 pd EFB1
+Cse1 pd SSA1
+Cse1 pd CYS3
+Cse1 pd CDC19
+Cse1 pd CLN3
+Cse1 pd YAL049C
+Cse1 pd ACS1
+Cse1 pd YAL069W
+Cse1 pd YAR066W
+Cse1 pd ECM15
+Cse1 pd HTB2
+Cse1 pd HTA2
+Cse1 pd ACH1
+Cse1 pd RPL19B
+Cse1 pd PET9
+Cse1 pd COR1
+Cse1 pd RPS8A
+Cse1 pd RPL32
+Cse1 pd ATP1
+Cse1 pd YBL100C
+Cse1 pd YBL109W
+Cse1 pd HHF1
+Cse1 pd HHT1
+Cse1 pd KAP104
+Cse1 pd GAL7
+Cse1 pd GAL10
+Cse1 pd GAL1
+Cse1 pd RPL4A
+Cse1 pd PDX3
+Cse1 pd YBR042C
+Cse1 pd RPS11B
+Cse1 pd YRO2
+Cse1 pd BAP2
+Cse1 pd ECM33
+Cse1 pd UBC4
+Cse1 pd RPL19A
+Cse1 pd YBR100W
+Cse1 pd TEF2
+Cse1 pd AMN1
+Cse1 pd YBR162C
+Cse1 pd UMP1
+Cse1 pd RPS6B
+Cse1 pd RPS9B
+Cse1 pd RPL21A
+Cse1 pd PGI1
+Cse1 pd CDC47
+Cse1 pd PYC2
+Cse1 pd SSH1
+Cse1 pd DAN3
+Cse1 pd SGF29
+Cse1 pd AGP1
+Cse1 pd GRX1
+Cse1 pd GLK1
+Cse1 pd PDI1
+Cse1 pd YCL044C
+Cse1 pd YCL046W
+Cse1 pd YCL075W
+Cse1 pd YCLX09W
+Cse1 pd YCLX10C
+Cse1 pd YCLX11W
+Cse1 pd CIT2
+Cse1 pd PGK1
+Cse1 pd YCR013C
+Cse1 pd PMP1
+Cse1 pd RPS14A
+Cse1 pd MATALPHA1
+Cse1 pd YCR045C
+Cse1 pd TUP1
+Cse1 pd PAU3
+Cse1 pd YCRX06W
+Cse1 pd NOP1
+Cse1 pd RPN4
+Cse1 pd GPD1
+Cse1 pd YDL023C
+Cse1 pd YDL053C
+Cse1 pd PSA1
+Cse1 pd RPS29B
+Cse1 pd BDF2
+Cse1 pd BRE1
+Cse1 pd RPL31A
+Cse1 pd RPP1A
+Cse1 pd RPL13A
+Cse1 pd YDL086W
+Cse1 pd YDL096C
+Cse1 pd SNA4
+Cse1 pd HNT1
+Cse1 pd RPP1B
+Cse1 pd LYS21
+Cse1 pd ARF2
+Cse1 pd DHH1
+Cse1 pd TFP1
+Cse1 pd RPL35A
+Cse1 pd ARF1
+Cse1 pd NHP2
+Cse1 pd NOP6
+Cse1 pd BRE4
+Cse1 pd NTH1
+Cse1 pd YDR003W
+Cse1 pd GAL3
+Cse1 pd SNQ2
+Cse1 pd RPL4B
+Cse1 pd RPS11A
+Cse1 pd PST2
+Cse1 pd MRH1
+Cse1 pd LYS14
+Cse1 pd ARO3
+Cse1 pd KRS1
+Cse1 pd BAP3
+Cse1 pd TPI1
+Cse1 pd RPS13
+Cse1 pd SED1
+Cse1 pd BMH2
+Cse1 pd ARO1
+Cse1 pd YDR133C
+Cse1 pd YDR134C
+Cse1 pd YDR154C
+Cse1 pd CPR1
+Cse1 pd HOM2
+Cse1 pd SUP35
+Cse1 pd CCT6
+Cse1 pd RVB1
+Cse1 pd HTA1
+Cse1 pd ADK1
+Cse1 pd COX20
+Cse1 pd RTN1
+Cse1 pd SVF1
+Cse1 pd TRP4
+Cse1 pd ARO10
+Cse1 pd YRA1
+Cse1 pd RPP2B
+Cse1 pd EFT2
+Cse1 pd UTP5
+Cse1 pd HPT1
+Cse1 pd MRP20
+Cse1 pd YDR417C
+Cse1 pd RPL12B
+Cse1 pd NPL3
+Cse1 pd YDR433W
+Cse1 pd YDR445C
+Cse1 pd RPS18A
+Cse1 pd RPL27B
+Cse1 pd RIB3
+Cse1 pd ITR1
+Cse1 pd GNP1
+Cse1 pd YDR542W
+Cse1 pd GCN4
+Cse1 pd URA3
+Cse1 pd SNU13
+Cse1 pd CUP5
+Cse1 pd YEL033W
+Cse1 pd HYP2
+Cse1 pd UTR2
+Cse1 pd GLY1
+Cse1 pd RPL12A
+Cse1 pd SOM1
+Cse1 pd PRB1
+Cse1 pd DLD3
+Cse1 pd CAJ1
+Cse1 pd HOM3
+Cse1 pd PIC2
+Cse1 pd HIS1
+Cse1 pd FCY2
+Cse1 pd YER064C
+Cse1 pd YER067W
+Cse1 pd VTC1
+Cse1 pd ALD5
+Cse1 pd RPS24A
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+Mlp2 pd YCL076W
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+Prp20 pd MKK2
+Prp20 pd YPL141C
+Prp20 pd YPL146C
+Prp20 pd PXA1
+Prp20 pd ATG5
+Prp20 pd PRP46
+Prp20 pd RRD2
+Prp20 pd RAD53
+Prp20 pd PEP4
+Prp20 pd KIP2
+Prp20 pd PRM4
+Prp20 pd TGS1
+Prp20 pd REV3
+Prp20 pd MEX67
+Prp20 pd DAP1
+Prp20 pd NIP100
+Prp20 pd SPT14
+Prp20 pd YPL183C
+Prp20 pd YPL184C
+Prp20 pd UIP4
+Prp20 pd MF(ALPHA)1
+Prp20 pd YPL191C
+Prp20 pd PRM3
+Prp20 pd APL5
+Prp20 pd OXR1
+Prp20 pd YPL197C
+Prp20 pd RPL7B
+Prp20 pd CSM4
+Prp20 pd YPL201C
+Prp20 pd YPL207W
+Prp20 pd YPL208W
+Prp20 pd IPL1
+Prp20 pd PUS1
+Prp20 pd CBP3
+Prp20 pd YPL216W
+Prp20 pd BMS1
+Prp20 pd RPL1A
+Prp20 pd YPL222W
+Prp20 pd CET1
+Prp20 pd YPL229W
+Prp20 pd TFP3
+Prp20 pd HSP82
+Prp20 pd SRP68
+Prp20 pd GAL4
+Prp20 pd GYP5
+Prp20 pd VIK1
+Prp20 pd BBP1
+Prp20 pd CLN2
+Prp20 pd APM1
+Prp20 pd YPL260W
+Prp20 pd FUM1
+Prp20 pd KEL3
+Prp20 pd PLC1
+Prp20 pd KAR9
+Prp20 pd YPL272C
+Prp20 pd SAM3
+Prp20 pd FDH2
+Prp20 pd FDH2
+Prp20 pd YPL277C
+Prp20 pd YPL278C
+Prp20 pd HSP32
+Prp20 pd ERR2
+Prp20 pd YPL282C
+Prp20 pd CIT3
+Prp20 pd PDH1
+Prp20 pd YPR003C
+Prp20 pd REC8
+Prp20 pd YPR012W
+Prp20 pd YPR015C
+Prp20 pd AGC1
+Prp20 pd YPR027C
+Prp20 pd APL4
+Prp20 pd SRO7
+Prp20 pd HTS1
+Prp20 pd TIP41
+Prp20 pd PUF2
+Prp20 pd MSF1
+Prp20 pd ATG11
+Prp20 pd NHP6A
+Prp20 pd SEC8
+Prp20 pd TFB4
+Prp20 pd BRR1
+Prp20 pd YMC1
+Prp20 pd JID1
+Prp20 pd MED1
+Prp20 pd YPR076W
+Prp20 pd YPR077C
+Prp20 pd YPR078C
+Prp20 pd GRS2
+Prp20 pd YPR097W
+Prp20 pd RPL11A
+Prp20 pd FHL1
+Prp20 pd COG4
+Prp20 pd YTH1
+Prp20 pd YPR109W
+Prp20 pd DBF20
+Prp20 pd MRD1
+Prp20 pd YPR118W
+Prp20 pd CLB2
+Prp20 pd THI22
+Prp20 pd YPR125W
+Prp20 pd YPR127W
+Prp20 pd ANT1
+Prp20 pd SCD6
+Prp20 pd YPR136C
+Prp20 pd RRP9
+Prp20 pd YPR143W
+Prp20 pd NOC4
+Prp20 pd YPR148C
+Prp20 pd YPR150W
+Prp20 pd YPR152C
+Prp20 pd NCA2
+Prp20 pd TPO3
+Prp20 pd GPH1
+Prp20 pd SGV1
+Prp20 pd ORC4
+Prp20 pd MMS1
+Prp20 pd VPS4
+Prp20 pd YPR174C
+Prp20 pd DPB2
+Prp20 pd AOS1
+Prp20 pd SEC23
+Prp20 pd GDB1
+Prp20 pd PZF1
+Prp20 pd SKI3
+Prp20 pd RPC82
+Prp20 pd AQY1
+Prp20 pd OPT2
+Prp20 pd ARR3
+Prp20 pd YPR202W
+Xpo1 pd TFC3
+Xpo1 pd EFB1
+Xpo1 pd SSA1
+Xpo1 pd ERP2
+Xpo1 pd CYS3
+Xpo1 pd CDC19
+Xpo1 pd CLN3
+Xpo1 pd YAL045C
+Xpo1 pd YAL068C
+Xpo1 pd YAL069W
+Xpo1 pd YAR066W
+Xpo1 pd YAR074C
+Xpo1 pd HTB2
+Xpo1 pd HTA2
+Xpo1 pd PIM1
+Xpo1 pd RPL19B
+Xpo1 pd YBL028C
+Xpo1 pd YBL029W
+Xpo1 pd PET9
+Xpo1 pd SHE1
+Xpo1 pd POL12
+Xpo1 pd COR1
+Xpo1 pd EDE1
+Xpo1 pd RPS8A
+Xpo1 pd AAR2
+Xpo1 pd ILS1
+Xpo1 pd YBL086C
+Xpo1 pd RPL23A
+Xpo1 pd RPL32
+Xpo1 pd ATP1
+Xpo1 pd YBL109W
+Xpo1 pd HHF1
+Xpo1 pd HHT1
+Xpo1 pd KAP104
+Xpo1 pd GAL7
+Xpo1 pd GAL10
+Xpo1 pd GAL1
+Xpo1 pd YBR025C
+Xpo1 pd RPL4A
+Xpo1 pd YBR052C
+Xpo1 pd BAP2
+Xpo1 pd TAT1
+Xpo1 pd YBR071W
+Xpo1 pd HSP26
+Xpo1 pd ECM33
+Xpo1 pd RPL19A
+Xpo1 pd TEF2
+Xpo1 pd APD1
+Xpo1 pd ICS2
+Xpo1 pd AMN1
+Xpo1 pd RPS6B
+Xpo1 pd RPS9B
+Xpo1 pd PGI1
+Xpo1 pd DUR1,2
+Xpo1 pd HIS7
+Xpo1 pd SSH1
+Xpo1 pd MAL33
+Xpo1 pd DAN3
+Xpo1 pd RER1
+Xpo1 pd SGF29
+Xpo1 pd LEU2
+Xpo1 pd YCL019W
+Xpo1 pd YCL021W
+Xpo1 pd AGP1
+Xpo1 pd HIS4
+Xpo1 pd GRX1
+Xpo1 pd GLK1
+Xpo1 pd PDI1
+Xpo1 pd YCL076W
+Xpo1 pd YCLX09W
+Xpo1 pd YCLX10C
+Xpo1 pd CIT2
+Xpo1 pd PGK1
+Xpo1 pd YCR013C
+Xpo1 pd RPS14A
+Xpo1 pd CDC39
+Xpo1 pd YCR097WB
+Xpo1 pd PAU3
+Xpo1 pd AAD3
+Xpo1 pd YCRX12W
+Xpo1 pd YDL023C
+Xpo1 pd YDL026W
+Xpo1 pd GPR1
+Xpo1 pd PSA1
+Xpo1 pd RPS29B
+Xpo1 pd YDL062W
+Xpo1 pd IDP1
+Xpo1 pd CBS1
+Xpo1 pd BDF2
+Xpo1 pd RPL31A
+Xpo1 pd YDL099W
+Xpo1 pd ARR4
+Xpo1 pd UBP1
+Xpo1 pd YDL124W
+Xpo1 pd HNT1
+Xpo1 pd CDC48
+Xpo1 pd RPP1B
+Xpo1 pd RPL35B
+Xpo1 pd RGT2
+Xpo1 pd YDL163W
+Xpo1 pd RPL35A
+Xpo1 pd ARF1
+Xpo1 pd YDL203C
+Xpo1 pd GDH2
+Xpo1 pd SSB1
+Xpo1 pd YRB1
+Xpo1 pd GAL3
+Xpo1 pd YDR010C
+Xpo1 pd SNQ2
+Xpo1 pd RPL4B
+Xpo1 pd CIS1
+Xpo1 pd SES1
+Xpo1 pd MRH1
+Xpo1 pd BAP3
+Xpo1 pd TPI1
+Xpo1 pd PST1
+Xpo1 pd MAK21
+Xpo1 pd RPS13
+Xpo1 pd SED1
+Xpo1 pd YDR094W
+Xpo1 pd YDR133C
+Xpo1 pd YDR134C
+Xpo1 pd YCF1
+Xpo1 pd CPR1
+Xpo1 pd YDR179W-A
+Xpo1 pd CDC1
+Xpo1 pd MSS4
+Xpo1 pd HTB1
+Xpo1 pd HTA1
+Xpo1 pd SIR4
+Xpo1 pd HEM1
+Xpo1 pd RTN1
+Xpo1 pd SEC26
+Xpo1 pd YDR248C
+Xpo1 pd MET32
+Xpo1 pd DIN7
+Xpo1 pd BSC2
+Xpo1 pd ATP5
+Xpo1 pd GIC2
+Xpo1 pd YDR327W
+Xpo1 pd YDR340W
+Xpo1 pd HXT6
+Xpo1 pd HXT3
+Xpo1 pd MRP1
+Xpo1 pd YPS7
+Xpo1 pd YDR366C
+Xpo1 pd YRA1
+Xpo1 pd EFT2
+Xpo1 pd SHE9
+Xpo1 pd HPT1
+Xpo1 pd RPL12B
+Xpo1 pd YDR426C
+Xpo1 pd NPL3
+Xpo1 pd YDR433W
+Xpo1 pd RPL27B
+Xpo1 pd PHO8
+Xpo1 pd RPL37B
+Xpo1 pd SAM2
+Xpo1 pd YDR527W
+Xpo1 pd YDR542W
+Xpo1 pd YDR543C
+Xpo1 pd YDR544C
+Xpo1 pd YRF1-1
+Xpo1 pd GCN4
+Xpo1 pd URA3
+Xpo1 pd YEL033W
+Xpo1 pd HYP2
+Xpo1 pd UTR2
+Xpo1 pd GLY1
+Xpo1 pd RPL12A
+Xpo1 pd PRB1
+Xpo1 pd DLD3
+Xpo1 pd NOP16
+Xpo1 pd RPN3
+Xpo1 pd EDC2
+Xpo1 pd PHM8
+Xpo1 pd MXR1
+Xpo1 pd HOM3
+Xpo1 pd HIS1
+Xpo1 pd FCY2
+Xpo1 pd RPL34A
+Xpo1 pd HMF1
+Xpo1 pd PET117
+Xpo1 pd THO1
+Xpo1 pd YER064C
+Xpo1 pd YER067W
+Xpo1 pd RNR1
+Xpo1 pd YER071C
+Xpo1 pd ALD5
+Xpo1 pd RPS24A
+Xpo1 pd SER3
+Xpo1 pd MET6
+Xpo1 pd RPS8B
+Xpo1 pd SSA4
+Xpo1 pd RPL23B
+Xpo1 pd SCS2
+Xpo1 pd DSE1
+Xpo1 pd RPS26B
+Xpo1 pd YER156C
+Xpo1 pd CCA1
+Xpo1 pd BRR2
+Xpo1 pd YER189W
+Xpo1 pd VTC2
+Xpo1 pd HSP12
+Xpo1 pd PAU5
+Xpo1 pd GAT1
+Xpo1 pd STE2
+Xpo1 pd HAC1
+Xpo1 pd YFL035C-A
+Xpo1 pd TUB2
+Xpo1 pd YPT1
+Xpo1 pd ACT1
+Xpo1 pd AAD6
+Xpo1 pd AAD16
+Xpo1 pd YFL063W
+Xpo1 pd RPL2A
+Xpo1 pd QCR6
+Xpo1 pd HXK1
+Xpo1 pd YFR055W
+Xpo1 pd YFR056C
+Xpo1 pd PMA1
+Xpo1 pd LEU1
+Xpo1 pd YGL015C
+Xpo1 pd SCW11
+Xpo1 pd CGR1
+Xpo1 pd RPL30
+Xpo1 pd RPL24A
+Xpo1 pd PNC1
+Xpo1 pd PYC1
+Xpo1 pd RPL7A
+Xpo1 pd YGL102C
+Xpo1 pd RPL28
+Xpo1 pd MLC1
+Xpo1 pd NAB2
+Xpo1 pd RPS2
+Xpo1 pd RPL1B
+Xpo1 pd YGL140C
+Xpo1 pd RPL9A
+Xpo1 pd INO80
+Xpo1 pd MIG2
+Xpo1 pd HXK2
+Xpo1 pd ZRT1
+Xpo1 pd YGL261C
+Xpo1 pd SWC4
+Xpo1 pd MSB2
+Xpo1 pd RPS25A
+Xpo1 pd MSP1
+Xpo1 pd GSC2
+Xpo1 pd YGR033C
+Xpo1 pd RPL26B
+Xpo1 pd YGR035C
+Xpo1 pd RME1
+Xpo1 pd MUP1
+Xpo1 pd RPL11B
+Xpo1 pd PIL1
+Xpo1 pd CTT1
+Xpo1 pd PHB1
+Xpo1 pd TPO2
+Xpo1 pd YGR145W
+Xpo1 pd YGR146C
+Xpo1 pd RPL24B
+Xpo1 pd CYS4
+Xpo1 pd CHO2
+Xpo1 pd NSR1
+Xpo1 pd YGR164W
+Xpo1 pd ERG1
+Xpo1 pd QCR9
+Xpo1 pd CRH1
+Xpo1 pd TDH3
+Xpo1 pd RPS0A
+Xpo1 pd AMA1
+Xpo1 pd YHB1
+Xpo1 pd YGR235C
+Xpo1 pd PFK1
+Xpo1 pd ENO1
+Xpo1 pd SCW4
+Xpo1 pd BGL2
+Xpo1 pd ZUO1
+Xpo1 pd YGR294W
+Xpo1 pd RPL14B
+Xpo1 pd RPS20
+Xpo1 pd RPL8A
+Xpo1 pd YHL046C
+Xpo1 pd ERG11
+Xpo1 pd ARG4
+Xpo1 pd YHR020W
+Xpo1 pd SSZ1
+Xpo1 pd PCL5
+Xpo1 pd YHR087W
+Xpo1 pd TOM71
+Xpo1 pd FUR1
+Xpo1 pd SPL2
+Xpo1 pd YHR138C
+Xpo1 pd RPL42B
+Xpo1 pd DSE2
+Xpo1 pd YHR145C
+Xpo1 pd ENO2
+Xpo1 pd CTR2
+Xpo1 pd OYE2
+Xpo1 pd GND1
+Xpo1 pd BAT1
+Xpo1 pd YHR214C-B
+Xpo1 pd YHR214W
+Xpo1 pd IMD2
+Xpo1 pd RPL2B
+Xpo1 pd CKA1
+Xpo1 pd MMF1
+Xpo1 pd RPL34B
+Xpo1 pd RHR2
+Xpo1 pd YIL060W
+Xpo1 pd RPS24B
+Xpo1 pd THS1
+Xpo1 pd SIM1
+Xpo1 pd RPL16A
+Xpo1 pd YIL169C
+Xpo1 pd YIL176C
+Xpo1 pd YIL177C
+Xpo1 pd YIR016W
+Xpo1 pd CYR1
+Xpo1 pd CTK2
+Xpo1 pd YJL007C
+Xpo1 pd RNR2
+Xpo1 pd KAR2
+Xpo1 pd TDH1
+Xpo1 pd GSH1
+Xpo1 pd UTP10
+Xpo1 pd YJL122W
+Xpo1 pd URA2
+Xpo1 pd TIF2
+Xpo1 pd CIS3
+Xpo1 pd HSP150
+Xpo1 pd RPL17B
+Xpo1 pd RPL39
+Xpo1 pd RPS22A
+Xpo1 pd RPS14B
+Xpo1 pd SOP4
+Xpo1 pd YJL200C
+Xpo1 pd OPT1
+Xpo1 pd MPP10
+Xpo1 pd SUI2
+Xpo1 pd TDH2
+Xpo1 pd ILV3
+Xpo1 pd YJR027W
+Xpo1 pd SSC1
+Xpo1 pd ANB1
+Xpo1 pd RPA12
+Xpo1 pd TOR1
+Xpo1 pd LIA1
+Xpo1 pd YJR080C
+Xpo1 pd SOD1
+Xpo1 pd ATP2
+Xpo1 pd RPS5
+Xpo1 pd YJR129C
+Xpo1 pd NMD5
+Xpo1 pd RPS4A
+Xpo1 pd YJR162C
+Xpo1 pd SFT1
+Xpo1 pd RPL14A
+Xpo1 pd UGP1
+Xpo1 pd PTM1
+Xpo1 pd YKL047W
+Xpo1 pd YKL056C
+Xpo1 pd NUP120
+Xpo1 pd FBA1
+Xpo1 pd YNK1
+Xpo1 pd NUP100
+Xpo1 pd LHS1
+Xpo1 pd TEF4
+Xpo1 pd CWP1
+Xpo1 pd YKL097W-A
+Xpo1 pd UTP11
+Xpo1 pd GFA1
+Xpo1 pd HAP4
+Xpo1 pd MRP8
+Xpo1 pd GPM1
+Xpo1 pd YKL153W
+Xpo1 pd RPS27A
+Xpo1 pd PIR3
+Xpo1 pd PIR1
+Xpo1 pd RPL17A
+Xpo1 pd FAS1
+Xpo1 pd YKL199C
+Xpo1 pd YKL225W
+Xpo1 pd YKR023W
+Xpo1 pd DAL80
+Xpo1 pd CAF4
+Xpo1 pd GAP1
+Xpo1 pd UTH1
+Xpo1 pd YKR049C
+Xpo1 pd DYN1
+Xpo1 pd RHO4
+Xpo1 pd DRE2
+Xpo1 pd PTR2
+Xpo1 pd YKR100C
+Xpo1 pd YKR106W
+Xpo1 pd DRS1
+Xpo1 pd SSA2
+Xpo1 pd YLL029W
+Xpo1 pd UBI4
+Xpo1 pd YLL044W
+Xpo1 pd RPL8B
+Xpo1 pd YLL049W
+Xpo1 pd YLL064C
+Xpo1 pd YLR016C
+Xpo1 pd MEU1
+Xpo1 pd RPL15A
+Xpo1 pd PDC1
+Xpo1 pd RPS0B
+Xpo1 pd RPL22A
+Xpo1 pd BUD28
+Xpo1 pd RPL10
+Xpo1 pd YLR076C
+Xpo1 pd GAL2
+Xpo1 pd SMC4
+Xpo1 pd YLR089C
+Xpo1 pd AHP1
+Xpo1 pd CCW12
+Xpo1 pd PDC5
+Xpo1 pd STM1
+Xpo1 pd ACS2
+Xpo1 pd YLR156W
+Xpo1 pd YLR159W
+Xpo1 pd YLR161W
+Xpo1 pd RPS31
+Xpo1 pd TFS1
+Xpo1 pd SAM1
+Xpo1 pd RPL37A
+Xpo1 pd HCR1
+Xpo1 pd YLR194C
+Xpo1 pd FRE1
+Xpo1 pd YLR217W
+Xpo1 pd YEF3
+Xpo1 pd HSP60
+Xpo1 pd CTS1
+Xpo1 pd RPS30A
+Xpo1 pd ATP14
+Xpo1 pd EXG1
+Xpo1 pd MET17
+Xpo1 pd ACO1
+Xpo1 pd YLR331C
+Xpo1 pd MID2
+Xpo1 pd RPS25B
+Xpo1 pd YLR334C
+Xpo1 pd YLR339C
+Xpo1 pd RPP0
+Xpo1 pd FKS1
+Xpo1 pd RPL26A
+Xpo1 pd TAL1
+Xpo1 pd ILV5
+Xpo1 pd RPS22B
+Xpo1 pd RPS29A
+Xpo1 pd YLR391W
+Xpo1 pd BDF1
+Xpo1 pd SFP1
+Xpo1 pd YLR413W
+Xpo1 pd VMA6
+Xpo1 pd RPL6B
+Xpo1 pd YML003W
+Xpo1 pd MRPL39
+Xpo1 pd ERV25
+Xpo1 pd TSA1
+Xpo1 pd GAL80
+Xpo1 pd SUR7
+Xpo1 pd IMD4
+Xpo1 pd SML1
+Xpo1 pd RPS1B
+Xpo1 pd FPR3
+Xpo1 pd RPM2
+Xpo1 pd COQ5
+Xpo1 pd ATR1
+Xpo1 pd NDI1
+Xpo1 pd PHO84
+Xpo1 pd ERG13
+Xpo1 pd ERO1
+Xpo1 pd YML133C
+Xpo1 pd YMR002W
+Xpo1 pd YMR003W
+Xpo1 pd CLU1
+Xpo1 pd VPS20
+Xpo1 pd YMR090W
+Xpo1 pd MYO5
+Xpo1 pd ASC1
+Xpo1 pd RPL15B
+Xpo1 pd STO1
+Xpo1 pd YMR141C
+Xpo1 pd RPL13B
+Xpo1 pd RPS16A
+Xpo1 pd YMR163C
+Xpo1 pd HSC82
+Xpo1 pd RPL36A
+Xpo1 pd YMR196W
+Xpo1 pd RRP5
+Xpo1 pd RPS10B
+Xpo1 pd PEP5
+Xpo1 pd RNA1
+Xpo1 pd RPL20A
+Xpo1 pd FAA4
+Xpo1 pd YMR252C
+Xpo1 pd ADH2
+Xpo1 pd YMR304C-A
+Xpo1 pd NIP1
+Xpo1 pd YMR321C
+Xpo1 pd YMR326C
+Xpo1 pd SIS1
+Xpo1 pd YNL017C
+Xpo1 pd HHF2
+Xpo1 pd HHT2
+Xpo1 pd NCE103
+Xpo1 pd YNL043C
+Xpo1 pd POR1
+Xpo1 pd YDJ1
+Xpo1 pd SUN4
+Xpo1 pd RPL9B
+Xpo1 pd RPL16B
+Xpo1 pd LEU4
+Xpo1 pd DBP2
+Xpo1 pd YNL134C
+Xpo1 pd MEP2
+Xpo1 pd MFA2
+Xpo1 pd RPS3
+Xpo1 pd NPR1
+Xpo1 pd UBP10
+Xpo1 pd YNL190W
+Xpo1 pd SSB2
+Xpo1 pd ADE12
+Xpo1 pd PDR16
+Xpo1 pd NAR1
+Xpo1 pd NRD1
+Xpo1 pd YNL285W
+Xpo1 pd SEC21
+Xpo1 pd YNL300W
+Xpo1 pd RPL18B
+Xpo1 pd RPS19B
+Xpo1 pd EGT2
+Xpo1 pd YNL337W
+Xpo1 pd YNL338W
+Xpo1 pd CIT1
+Xpo1 pd NOG2
+Xpo1 pd DSE4
+Xpo1 pd YNR077C
+Xpo1 pd SIN3
+Xpo1 pd PLB3
+Xpo1 pd DIS3
+Xpo1 pd YOL046C
+Xpo1 pd YOL053C-A
+Xpo1 pd GPD2
+Xpo1 pd ADH1
+Xpo1 pd ITR2
+Xpo1 pd YOL106W
+Xpo1 pd ZEO1
+Xpo1 pd RPL18A
+Xpo1 pd YOL124C
+Xpo1 pd RPL25
+Xpo1 pd YOL155C
+Xpo1 pd AAD15
+Xpo1 pd YOL166C
+Xpo1 pd TOM6
+Xpo1 pd YOR052C
+Xpo1 pd RPL3
+Xpo1 pd RPS7A
+Xpo1 pd YOR121C
+Xpo1 pd PFY1
+Xpo1 pd EFT1
+Xpo1 pd PDR5
+Xpo1 pd GLN4
+Xpo1 pd RPS30B
+Xpo1 pd MSB1
+Xpo1 pd BFR1
+Xpo1 pd DED1
+Xpo1 pd YOR225W
+Xpo1 pd WTM1
+Xpo1 pd YOR235W
+Xpo1 pd DFR1
+Xpo1 pd SRL1
+Xpo1 pd YOR248W
+Xpo1 pd SEC63
+Xpo1 pd GCD1
+Xpo1 pd YTM1
+Xpo1 pd TPO4
+Xpo1 pd CAF20
+Xpo1 pd CPA1
+Xpo1 pd YOR309C
+Xpo1 pd RPL20B
+Xpo1 pd SPS4
+Xpo1 pd RPA190
+Xpo1 pd TYE7
+Xpo1 pd REV1
+Xpo1 pd GDS1
+Xpo1 pd PRE10
+Xpo1 pd RPS12
+Xpo1 pd GDH1
+Xpo1 pd SMA1
+Xpo1 pd PMA2
+Xpo1 pd EGD1
+Xpo1 pd SUR1
+Xpo1 pd ALD6
+Xpo1 pd YPL066W
+Xpo1 pd GCR1
+Xpo1 pd RPL21B
+Xpo1 pd RPS9A
+Xpo1 pd MOT1
+Xpo1 pd RPS6A
+Xpo1 pd MRP51
+Xpo1 pd RPL5
+Xpo1 pd YPL137C
+Xpo1 pd RPL33A
+Xpo1 pd OYE3
+Xpo1 pd CUP9
+Xpo1 pd PPQ1
+Xpo1 pd RPL7B
+Xpo1 pd CSM4
+Xpo1 pd BMS1
+Xpo1 pd RPL1A
+Xpo1 pd YPL221W
+Xpo1 pd HSP82
+Xpo1 pd YPL251W
+Xpo1 pd YPL267W
+Xpo1 pd YRF1-7
+Xpo1 pd HAA1
+Xpo1 pd YPR027C
+Xpo1 pd GLN1
+Xpo1 pd RPL43A
+Xpo1 pd YPR044C
+Xpo1 pd TKL1
+Xpo1 pd YPR076W
+Xpo1 pd TEF1
+Xpo1 pd YPR092W
+Xpo1 pd RPL11A
+Xpo1 pd MRD1
+Xpo1 pd YPR117W
+Xpo1 pd YPR123C
+Xpo1 pd ASN1
+Xpo1 pd NCE102
+Xpo1 pd YPR151C
+Xpo1 pd TPO3
+Xpo1 pd GDB1
+Xpo1 pd QCR2
+Xpo1 pd OPT2
+Xpo1 pd ARR1
+Unknown interactsWith Mpe1
+Unknown interactsWith Pap1
+Unknown interactsWith Yth1
+Pfs2 pp Fip1
+Pfs2 interactsWith Unknown
+Cft1 interactsWith Unknown
+Unknown interactsWith Cft2
+Unknown interactsWith Pta1
+Unknown interactsWith Brr5
+Unknown interactsWith CF_II
+SRG1_locus pd Tbp1
+SRG1_locus interactsWith Pol_II
+SER3_locus interactsWith Pol_II
+Glc7 pp Gip1
+Glc7 pp Gip2
+Glc7 pp Yta6
+Sla1 pp Ppz1
+Glc7 pp Yol091w
+Glc7 pp Yfr003c
+Glc7 pp Yal014c
+Ndt80 pd SPS4_promoter
+Ndt80 pd SMK1_promoter
+Sum1 pd SMK1_promoter
+Wbp1 pp Ost1
+Ref2 interactsWith Unknown
+Unknown interactsWith Glc7
+Unknown interactsWith Core-CPF_complex
+Unknown interactsWith Syc1
+Unknown interactsWith Pti1
+Unknown interactsWith Swd2
+Unknown interactsWith Ssu72
+Rna14 pp Rna15
+Pfs2 pp Rna14
+Ppz1 pp Glc8
+Sec26 pp Ret2
+Sec21 pp Ret3
+Arf1 pp Sec26
+Arf1 pp Glo3
+Arf1 pp Gcs1
+Glo3 pp Sec27
+Glo3 pp Sec21
+Arf1 pp Sec28
+Prp38 pp Spp381
+Cus1 pp Hsh49
+Hac1 pp Gcn5
+Ire1 pp Ada2
+Ire1 pp Ada5
+Pho85/Pcl5 interactsWith Gcn4
+Histone_H3 pd YBR094W_locus
+Histone_H3 pd PHO8_promoter
+Histone_H3 pd GAL1_promoter
+Histone_H3 pd PHO5_promoter
+Histone_H3 pd PGK1_gene
+Pho4 pd PHO5_promoter
+Histone_Octamer interactsWith PHO5_promoter
+Unknown interactsWith Rps5
+Unknown interactsWith Rps3
+Unknown interactsWith Rps4a
+Unknown interactsWith Rps13
+Unknown interactsWith Rpp0
+Unknown interactsWith Rpl8a
+Unknown interactsWith Rpl36a
+Unknown interactsWith Rpl30
+Unknown interactsWith Rpl27a
+Unknown interactsWith Rpl21a
+Unknown interactsWith Rpl20a
+Unknown interactsWith Rpl18a
+Unknown interactsWith Rpl19a
+Unknown interactsWith Rpl17a
+Unknown interactsWith Rpl16b
+Unknown interactsWith Rpl16a
+Unknown interactsWith Rpl15a
+Unknown interactsWith Rpl13a
+Unknown interactsWith Rpl12a
+Unknown interactsWith Rpl10
+Rai1 pp Rat1
+Hsp104_hexamer interactsWith Sup35
+Hsp104 pp Hsp104
+Htb2 pd Pho5_promoter
+Rsp5 pp Rvs167
+Ref2 pp Glc7
+Sen1 interactsWith snR13
+Sen1 interactsWith snR45
+Sen1 interactsWith snR5
+Sen1 interactsWith snR10
+Sen1 interactsWith snR11
+Sen1 interactsWith snR30
+Sen1 interactsWith snR31
+Sen1 interactsWith snR42
+Syc1 interactsWith Unknown
+Unknown interactsWith Swd2
+Pti1 pp Pta1
+Pti1 pp Ssu72
+Pti1 pp Clp1
+Nab3 pd PYK1_promoter
+APT interactsWith PYK1_3prime-end_region
+APT interactsWith SNR13
+Nab3 pd PMA1_promoter
+APT interactsWith PMA1_3prime-end_region
+Sho1 pp Pbs2
+Pbs2 pp Ste11
+Sho1 pp Ste11
+Cdc14 pp Net1
+Clb2/Cdc28 interactsWith Net1
+Yfh1 pp Aco1
+Myo5 pp Vrp1
+Myo3 pp Vrp1
+Tao3 pp Cbk1
+Tao3 pp Kic1
+Ctf8 interactsWith Unknown
+Unknown interactsWith Rfc4
+Unknown interactsWith Rfc3
+Unknown interactsWith Rfc2
+Unknown interactsWith Ctf18
+Unknown interactsWith Rfc5
+Unknown interactsWith Dcc1
+Fus2 pp Fus2
+Fus2 pp Bni1
+Fus2 pp Rvs161
+Fus2 pp Chs5
+Fus2 pp Cdc24
+Fus2 pp Bnr1
+Fus1 pp Ste5
+Mpe1 pd PMA1_3prime-end_region
+Nab3 pd SNR13
+APT interactsWith SNR71
+Nab3 pd SNR71
+Unknown interactsWith Arl3
+Sys1 interactsWith Unknown
+Act1 pp Bni1
+Cps60 interactsWith Unknown
+Unknown interactsWith Set1
+Unknown interactsWith Cps15
+Unknown interactsWith Cps25
+Unknown interactsWith Cps30
+She4 pp Myo3
+Cbk1 pp Yor353c
+Cbk1 pp Mob2
+Cbk1 pp Kic1
+Cbk1 pp Cbk1
+Hym1 pp Yor353c
+Unknown interactsWith ARP7
+Unknown interactsWith ARP9
+Unknown interactsWith COG6
+Unknown interactsWith HSC82
+Unknown interactsWith HSP104
+Unknown interactsWith HTL1
+NPL6 interactsWith Unknown
+Unknown interactsWith PIM1
+Unknown interactsWith RSC2
+Unknown interactsWith RSC3
+Unknown interactsWith RSC4
+Unknown interactsWith RSC58
+Unknown interactsWith RSC6
+Unknown interactsWith RSC8
+Unknown interactsWith RSC9
+Unknown interactsWith SFH1
+Unknown interactsWith SSA1
+Unknown interactsWith SSA2
+Unknown interactsWith STH1
+Unknown interactsWith ARP7
+Unknown interactsWith ARP9
+Unknown interactsWith HSP104
+Unknown interactsWith NPL6
+RSC2 interactsWith Unknown
+Unknown interactsWith RSC3
+Unknown interactsWith RSC30
+Unknown interactsWith RSC4
+Unknown interactsWith RSC58
+Unknown interactsWith RSC6
+Unknown interactsWith RSC8
+Unknown interactsWith RSC9
+Unknown interactsWith SFH1
+Unknown interactsWith SPT16
+Unknown interactsWith SSA1
+Unknown interactsWith SSA2
+Unknown interactsWith STH1
+Unknown interactsWith ARP7
+Unknown interactsWith ARP9
+Unknown interactsWith COG6
+Unknown interactsWith HSC82
+Unknown interactsWith HSP104
+Unknown interactsWith NFI1
+Unknown interactsWith NPL6
+Unknown interactsWith RSC2
+RSC3 interactsWith Unknown
+Unknown interactsWith RSC4
+Unknown interactsWith RSC58
+Unknown interactsWith RSC6
+Unknown interactsWith RSC8
+Unknown interactsWith RSC9
+Unknown interactsWith RTT102
+Unknown interactsWith SFH1
+Unknown interactsWith SSA1
+Unknown interactsWith SSA2
+Unknown interactsWith SSE1
+Unknown interactsWith STH1
+Unknown interactsWith ARP7
+Unknown interactsWith ARP9
+Unknown interactsWith NPL6
+Unknown interactsWith RSC2
+RSC4 interactsWith Unknown
+Unknown interactsWith RSC58
+Unknown interactsWith RSC6
+Unknown interactsWith RSC8
+Unknown interactsWith RSC9
+Unknown interactsWith SFH1
+Unknown interactsWith SPT16
+Unknown interactsWith STH1
+Unknown interactsWith ARP7
+Unknown interactsWith ARP9
+Unknown interactsWith HTA2
+Unknown interactsWith HTL1
+Unknown interactsWith NFI1
+Unknown interactsWith NPL6
+Unknown interactsWith RSC2
+Unknown interactsWith RSC3
+Unknown interactsWith RSC4
+RSC58 interactsWith Unknown
+Unknown interactsWith RSC6
+Unknown interactsWith RSC8
+Pol30_homotrimer interactsWith MSH2-MSH6_complex
+Mec3 pp Set1
+Pol30 pp Rad27
+Pol30 pp Cac1
+Cdc7/Dbf4 interactsWith Mcm2
+Cdc7/Dbf4 interactsWith Mcm3
+Cdc7/Dbf4 interactsWith Mcm4
+Cdc7/Dbf4 interactsWith Mcm5
+Cdc7/Dbf4 interactsWith Mcm6
+Cdc7/Dbf4 interactsWith Mcm7
+Cdc7/Dbf4 interactsWith Mcm10
+Cdc7/Dbf4 interactsWith Rfa1
+Cdc7/Dbf4 interactsWith Rfa2
+Cdc7/Dbf4 interactsWith Rfa3
+Fus3 pp Mpt5
+Rad9 pp Rad9
+Kss1 pp Mpt5
+Taf1 pp TBP1
+Taf1 pp Taf8
+Taf1 pp Taf4
+Taf1 pp Taf3
+Taf1 pp Taf10
+Sst2 pp Mpt5
+Prk1 pp Pan1
+Pan1 pp Sla1
+Pan1 pp End3
+Fus3 pp Gpa1
+Pol30 pp Elg1
+Cdc42 pp Bem1
+Cla4 pp Bem1
+Pat1 pp Top2
+Rad53 pp Dun1
+Fus3 pp Ptp3
+Swi6 pp Stb1
+Rfc2 pp Elg1
+Sph1 pp Mkk1
+Rfc3 pp Elg1
+Rfc4 pp Elg1
+Rad53 pp Rad53
+Rfc5 pp Elg1
+Far1 pp Bem1
+Rad27 pp Elg1
+Far1 pp Ste4
+Eco1 pp Ctf18
+Eco1 pp Rfc2
+Eco1 pp Rfc3
+Eco1 pp Rfc4
+Eco1 pp Rfc5
+Eco1 pp Rfc1
+Eco1 pp Rad24
+Fus3 pp Rst1
+Fus3 pp Rst2
+Rad53 pp Hho1
+Sec3 pp Cdc42
+Srx1 pp Tsa1
+Srx1 pp Tsa2
+Srx1 pp Ahp1
+Rfc1 interactsWith Unknown
+Rfc5 interactsWith Unknown
+Rfc2 interactsWith Unknown
+Rfc3 interactsWith Unknown
+Rfc4 interactsWith Unknown
+Sec3 pp Rho1
+Ste12 pp Rst1
+PCNA interactsWith RFC
+Ste12 pp Rst2
+Swi6 pp Slt2
+Cdc42 pp Skm1
+PCNA-RFC_complex interactsWith ATP
+Pol30 interactsWith Unknown
+Mec1 pp Pie1
+Rad53 pp Ptc2
+Rad53 pp Swi6
+Dun1 pp Rad9
+Dun1 pp Pan3
+Cdc5 pp Bfa1
+Tem1 pp Bfa1
+Rnr1 pp Sml1
+Swi4 pp Slt2
+Fus3/Rst1/Rst2-complex interactsWith Ste12
+Swi4 interactsWith Clb2/Cdc28
+Mbp1 interactsWith Clb2/Cdc28
+Fus3 pp Far1
+Swi6 interactsWith Clb2/Cdc28
+Dun1 pp Sml1
+Mec1 pp Rfa2
+Rad17 pp Mec3
+Ddc1 pp Rad17
+Ddc1 pp Mec3
+Ddc1 interactsWith Rad17/Mec3
+Swi5 interactsWith Unknown
+Unknown interactsWith Snf2
+Unknown interactsWith Gal11
+Pol3 pp Pol31
+Pol30 interactsWith DNA_Polymerase_delta
+Swi5 pp Gal11
+Pol30 pp Pol32
+Rad17 pp Rad17
+Chk1 pp Pds1
+Rad24 pp Ddc1
+Rad24 pp Sae1
+Rad24 pp Sae3
+Rad24 pp Msh5
+Rad24 pp Rad57
+BNI1 interactsWith PCL1
+BNI1 interactsWith SWE1
+BNI1 interactsWith SWI4
+BNI1 interactsWith BBC1
+BNI1 interactsWith BEM1
+BNI1 interactsWith BEM2
+BNI1 interactsWith BEM4
+BNI1 interactsWith BUD6
+BNI1 interactsWith CLA4
+BNI1 interactsWith ELM1
+BNI1 interactsWith GIN4
+BNI1 interactsWith NAP1
+BNI1 interactsWith NBP2
+BNI1 interactsWith SLA1
+BNI1 interactsWith ATS1
+BNI1 interactsWith SAC3
+BNI1 interactsWith YKE2
+BNI1 interactsWith BCK1
+BNI1 interactsWith CHS3
+BNI1 interactsWith CHS5
+BNI1 interactsWith CHS7
+BNI1 interactsWith SKT5
+BNI1 interactsWith SLT2
+BNI1 interactsWith SMI1
+BNI1 interactsWith BNI4
+BNI1 interactsWith BNR1
+BNI1 interactsWith CYK3
+BNI1 interactsWith SHS1
+BNI1 interactsWith ERG2
+BNI1 interactsWith ERG3
+BNI1 interactsWith FAB1
+BNI1 interactsWith MDM20
+BNI1 interactsWith ARP1
+BNI1 interactsWith ASE1
+BNI1 interactsWith DYN1
+BNI1 interactsWith DYN2
+BNI1 interactsWith JNM1
+BNI1 interactsWith NIP100
+BNI1 interactsWith NUM1
+BNI1 interactsWith PAC1
+BNI1 interactsWith PAC11
+BNI1 interactsWith ELP2
+BNI1 interactsWith ELP3
+BNI1 interactsWith ELP4
+BNI1 interactsWith ELP6
+BNI1 interactsWith UBA4
+BNI1 interactsWith PIN4
+BNI1 interactsWith TIP41
+BNI1 interactsWith KRE24
+BNI1 interactsWith MMR1
+BNI1 interactsWith TUS1
+BNI1 interactsWith YBL062W
+BNI1 interactsWith YDR149C
+BNI1 interactsWith YGR228W
+BNI1 interactsWith YKR047W
+BNI1 interactsWith YLL049W
+BNI1 interactsWith YMR299C
+BNI1 interactsWith YNL119W
+BNI1 interactsWith YOR322C
+BNI1 interactsWith VID22
+BNI1 interactsWith VPS67
+BNI1 interactsWith DRS2
+BNI1 interactsWith SNC2
+BNI1 interactsWith VPS28
+BNI1 interactsWith YPT6
+BBC1 interactsWith CAP1
+BBC1 interactsWith CAP2
+BBC1 interactsWith PAC10
+BBC1 interactsWith GIM3
+BBC1 interactsWith GIM5
+BBC1 interactsWith SAC6
+BBC1 interactsWith BEM1
+BBC1 interactsWith BEM4
+BBC1 interactsWith SLA1
+BBC1 interactsWith CHS5
+BBC1 interactsWith RAS2
+BBC1 interactsWith ELP2
+BBC1 interactsWith ELP3
+BBC1 interactsWith SDS3
+BBC1 interactsWith YLR235C
+BBC1 interactsWith YML095C-A
+NBP2 interactsWith BIM1
+NBP2 interactsWith CIN2
+NBP2 interactsWith KAR9
+NBP2 interactsWith KIP3
+NBP2 interactsWith PAC10
+NBP2 interactsWith GIM5
+NBP2 interactsWith CAP1
+NBP2 interactsWith CAP2
+NBP2 interactsWith FAB1
+NBP2 interactsWith SMI1
+NBP2 interactsWith VAM7
+NBP2 interactsWith VPS29
+NBP2 interactsWith RPL16A
+NBP2 interactsWith RPS18B
+NBP2 interactsWith RPS23A
+NBP2 interactsWith CPR6
+NBP2 interactsWith FPR1
+NBP2 interactsWith CLB4
+NBP2 interactsWith RTT109
+NBP2 interactsWith RTG2
+NBP2 interactsWith RTG3
+NBP2 interactsWith MON1
+NBP2 interactsWith YDL063C
+NBP2 interactsWith YGL211W
+NBP2 interactsWith YGL217C
+NBP2 interactsWith YML095C-A
+BIM1 interactsWith DEP1
+BIM1 interactsWith RXT2
+BIM1 interactsWith IML3
+BIM1 interactsWith BEM1
+BIM1 interactsWith AOR1
+BIM1 interactsWith DCC1
+BIM1 interactsWith BIK1
+BIM1 interactsWith MRC1
+BIM1 interactsWith CYK3
+BIM1 interactsWith SHS1
+BIM1 interactsWith RAD61
+BIM1 interactsWith YDR149C
+BIM1 interactsWith NUM1
+BIM1 interactsWith SAC3
+BIM1 interactsWith CHL4
+BIM1 interactsWith RTT103
+BIM1 interactsWith IPK1
+BIM1 interactsWith MCM21
+BIM1 interactsWith MSN5
+BIM1 interactsWith VID21
+BIM1 interactsWith YDR360W
+BIM1 interactsWith NKP1
+BIM1 interactsWith DYN2
+BIM1 interactsWith PAC11
+BIM1 interactsWith GIM4
+BIM1 interactsWith CIN8
+BIM1 interactsWith FAB1
+BIM1 interactsWith MAD1
+BIM1 interactsWith RAD54
+BIM1 interactsWith KEM1
+BIM1 interactsWith YGL211W
+BIM1 interactsWith KIP3
+BIM1 interactsWith YGL217C
+BIM1 interactsWith PAC10
+BIM1 interactsWith BUB1_
+BIM1 interactsWith ELP2
+BIM1 interactsWith YGR228W
+BIM1 interactsWith SMI1
+BIM1 interactsWith YTA7
+BIM1 interactsWith UBA4
+BIM1 interactsWith ARP1
+BIM1 interactsWith CTF8
+BIM1 interactsWith MAD3
+BIM1 interactsWith MAD2
+BIM1 interactsWith LSM1
+BIM1 interactsWith BFA1
+BIM1 interactsWith MCM22
+BIM1 interactsWith ELM1
+BIM1 interactsWith KTI12
+BIM1 interactsWith DYN1
+BIM1 interactsWith YLL049W
+BIM1 interactsWith ARP6
+BIM1 interactsWith MMR1
+BIM1 interactsWith YKE2
+BIM1 interactsWith YPT6
+BIM1 interactsWith NKP2
+BIM1 interactsWith VID22
+BIM1 interactsWith CTF3
+BIM1 interactsWith IKI3
+BIM1 interactsWith VAC14
+BIM1 interactsWith PPZ1
+BIM1 interactsWith RAD52
+BIM1 interactsWith YML094C-A
+BIM1 interactsWith GIM5
+BIM1 interactsWith TUB3
+BIM1 interactsWith CSM3
+BIM1 interactsWith BUB2
+BIM1 interactsWith CTF18
+BIM1 interactsWith MRE11
+BIM1 interactsWith SAP30
+BIM1 interactsWith JNM1
+BIM1 interactsWith YMR299C
+BIM1 interactsWith ELP6
+BIM1 interactsWith PHO23
+BIM1 interactsWith INP52
+BIM1 interactsWith YNL136W
+BIM1 interactsWith GIM3
+BIM1 interactsWith YNL170W
+BIM1 interactsWith YNL201C
+BIM1 interactsWith IES2
+BIM1 interactsWith TOF1
+BIM1 interactsWith CLA4
+BIM1 interactsWith MCK1
+BIM1 interactsWith BRE5
+BIM1 interactsWith HTZ1
+BIM1 interactsWith BUB3
+BIM1 interactsWith ASE1
+BIM1 interactsWith SLK19
+BIM1 interactsWith PAC1
+BIM1 interactsWith CIN1
+BIM1 interactsWith CHL1
+BIM1 interactsWith YPL017C
+BIM1 interactsWith CTF19
+BIM1 interactsWith ELP3
+BIM1 interactsWith ELP4
+BIM1 interactsWith KRE24
+BIM1 interactsWith KIP2
+BIM1 interactsWith NIP100
+BIM1 interactsWith MCM16
+BIM1 interactsWith CTF4
+BIM1 interactsWith MMS1
+ARC40 interactsWith BCK1
+ARC40 interactsWith BNI4
+ARC40 interactsWith CHS3
+ARC40 interactsWith SKT5
+ARC40 interactsWith CHS5
+ARC40 interactsWith CHS6
+ARC40 interactsWith CHS7
+ARC40 interactsWith HOC1
+ARC40 interactsWith KRE1
+ARC40 interactsWith SLT2
+ARC40 interactsWith SPF1
+ARC40 interactsWith RMD7
+ARC40 interactsWith ARC18
+ARC40 interactsWith BEM1
+ARC40 interactsWith BEM2
+ARC40 interactsWith CLA4
+ARC40 interactsWith MYO5
+ARC40 interactsWith PEA2
+ARC40 interactsWith VRP1
+ARC40 interactsWith YKE2
+ARC40 interactsWith GIM3
+ARC40 interactsWith GIM4
+ARC40 interactsWith SAC6
+ARC40 interactsWith GLO3
+ARC40 interactsWith SAP155
+ARC40 interactsWith SEC66
+ARC40 interactsWith ILM1
+ARC40 interactsWith MNN11
+ARC40 interactsWith STE24
+ARC40 interactsWith CIK1
+ARC40 interactsWith RIM101
+ARC40 interactsWith RUD3
+ARC40 interactsWith SEC22
+ARC40 interactsWith TFP3
+ARC40 interactsWith CPR7
+ARC40 interactsWith SHE4
+ARC40 interactsWith SUM1
+ARC40 interactsWith YBL062W
+ARC40 interactsWith YLR111W
+ARP2 interactsWith BCK1
+ARP2 interactsWith BNI4
+ARP2 interactsWith CHS3
+ARP2 interactsWith SKT5
+ARP2 interactsWith CHS5
+ARP2 interactsWith CHS6
+ARP2 interactsWith CHS7
+ARP2 interactsWith HOC1
+ARP2 interactsWith KRE1
+ARP2 interactsWith SLT2
+ARP2 interactsWith SPF1
+ARP2 interactsWith RMD7
+ARP2 interactsWith BEM1
+ARP2 interactsWith BEM2
+ARP2 interactsWith CLA4
+ARP2 interactsWith PEA2
+ARP2 interactsWith PRK1
+ARP2 interactsWith RGD1
+ARP2 interactsWith RVS161
+ARP2 interactsWith RVS167
+ARP2 interactsWith VRP1
+ARP2 interactsWith YKE2
+ARP2 interactsWith PAC10
+ARP2 interactsWith GIM3
+ARP2 interactsWith GIM4
+ARP2 interactsWith SAC6
+ARP2 interactsWith SAC7
+ARP2 interactsWith ILM1
+ARP2 interactsWith SAP155
+ARP2 interactsWith SEC66
+ARP2 interactsWith MNN11
+ARP2 interactsWith STE24
+ARP2 interactsWith BTS1
+ARP2 interactsWith RUD3
+ARP2 interactsWith CPR7
+ARP2 interactsWith SHE4
+ARP2 interactsWith SUM1
+ARP2 interactsWith SRO9
+ARP2 interactsWith UTH1
+ARP2 interactsWith DEP1
+ARP2 interactsWith YBL062W
+ARP2 interactsWith YDR018C
+ARP2 interactsWith YGL250W
+ARP2 interactsWith YLR111W
+SGS1 interactsWith MMS4
+SGS1 interactsWith MUS81
+SGS1 interactsWith SAE2
+SGS1 interactsWith RAD50
+SGS1 interactsWith HPR5
+SGS1 interactsWith ASF1
+SGS1 interactsWith RAD27
+SGS1 interactsWith SLX1
+SGS1 interactsWith SLX4
+SGS1 interactsWith WSS1
+SGS1 interactsWith POL32
+SGS1 interactsWith RNR1
+SGS1 interactsWith RRM3
+SGS1 interactsWith MGS1
+SGS1 interactsWith CSM3
+SGS1 interactsWith ESC2
+SGS1 interactsWith RTT107
+SGS1 interactsWith TOP1
+SGS1 interactsWith SWE1
+SGS1 interactsWith PUB1
+SGS1 interactsWith RPL24A
+SGS1 interactsWith SIS2
+SGS1 interactsWith SOD1
+SGS1 interactsWith YBR094W
+SGS1 interactsWith CTF18
+RAD27 interactsWith MMS4
+RAD27 interactsWith MUS81
+RAD27 interactsWith SAE2
+RAD27 interactsWith RAD50
+RAD27 interactsWith HPR5
+RAD27 interactsWith DDC1
+RAD27 interactsWith CAC2
+RAD27 interactsWith EXO1
+RAD27 interactsWith MRE11
+RAD27 interactsWith RAD9
+RAD27 interactsWith RAD17
+RAD27 interactsWith RAD24
+RAD27 interactsWith RAD51
+RAD27 interactsWith RAD52
+RAD27 interactsWith RAD54
+RAD27 interactsWith RAD55
+RAD27 interactsWith RAD57
+RAD27 interactsWith XRS2
+RAD27 interactsWith CTF4
+RAD27 interactsWith RPL27A
+RAD27 interactsWith RPS30B
+RAD27 interactsWith DOC1
+RAD27 interactsWith ESC2
+RAD27 interactsWith HST1
+RAD27 interactsWith HPC2
+RAD27 interactsWith CSM3
+RAD27 interactsWith LYS7
+RAD27 interactsWith SIS2
+RAD27 interactsWith SOD1
+RAD27 interactsWith YDJ1
+RAD27 interactsWith HST3
+RAD27 interactsWith FYV11
+RAD27 interactsWith YLR352W
+RAD27 interactsWith YNL171C
+RAD27 interactsWith YPR116W
+RAD27 interactsWith CTF18
+CLA4 interactsWith EDE1
+CLA4 interactsWith SKT5
+CLA4 interactsWith YBL062W
+CLA4 interactsWith RPL23A
+CLA4 interactsWith CHS3
+CLA4 interactsWith RPL19A
+CLA4 interactsWith RXT2
+CLA4 interactsWith YBR174C
+CLA4 interactsWith SWD3
+CLA4 interactsWith BEM1
+CLA4 interactsWith DCC1
+CLA4 interactsWith RPL35A
+CLA4 interactsWith SHS1
+CLA4 interactsWith SEM1
+CLA4 interactsWith DYN2
+CLA4 interactsWith SWI4
+CLA4 interactsWith PEA2
+CLA4 interactsWith BEM2
+CLA4 interactsWith FAB1
+CLA4 interactsWith RPL24A
+CLA4 interactsWith SSF73
+CLA4 interactsWith ITC1
+CLA4 interactsWith RAD54
+CLA4 interactsWith PRE9
+CLA4 interactsWith ELP2
+CLA4 interactsWith SMI1
+CLA4 interactsWith STE20
+CLA4 interactsWith SLT2
+CLA4 interactsWith UBA4
+CLA4 interactsWith CHS7
+CLA4 interactsWith SPO12
+CLA4 interactsWith CTF8
+CLA4 interactsWith RPN10
+CLA4 interactsWith HOS4
+CLA4 interactsWith MGA2
+CLA4 interactsWith RTT101
+CLA4 interactsWith BCK1
+CLA4 interactsWith CHS6
+CLA4 interactsWith ASF1
+CLA4 interactsWith RPS21B
+CLA4 interactsWith IXR1
+CLA4 interactsWith SPA2
+CLA4 interactsWith APC9
+CLA4 interactsWith BUD6
+CLA4 interactsWith CHS5
+CLA4 interactsWith VAC14
+CLA4 interactsWith GIM5
+CLA4 interactsWith YML095C-A
+CLA4 interactsWith CTF18
+CLA4 interactsWith UBP8
+CLA4 interactsWith SAP30
+CLA4 interactsWith ELP6
+CLA4 interactsWith FKH2
+CLA4 interactsWith GIM3
+CLA4 interactsWith RTT106
+CLA4 interactsWith URE2
+CLA4 interactsWith SLK19
+CLA4 interactsWith RIM20
+CLA4 interactsWith YPL047W
+CLA4 interactsWith BEM4
+CLA4 interactsWith NIP100
+CLA4 interactsWith CTF4
+SHS1 interactsWith CYK3
+SHS1 interactsWith SWI4
+SHS1 interactsWith BEM2
+SHS1 interactsWith BNI4
+SMY1 interactsWith DRS2
+SMY1 interactsWith SLA1
+SMY1 interactsWith SKT5
+SMY1 interactsWith CHS3
+SMY1 interactsWith BEM1
+SMY1 interactsWith SHS1
+SMY1 interactsWith SWI4
+SMY1 interactsWith BEM2
+SMY1 interactsWith BUB1
+SMY1 interactsWith CHS7
+SMY1 interactsWith BNI4
+SMY1 interactsWith CLA4
+SLT2 interactsWith EDE1
+SLT2 interactsWith CHS3
+SLT2 interactsWith ECM33
+SLT2 interactsWith SEC66
+SLT2 interactsWith ROT2
+SLT2 interactsWith SWI5
+SLT2 interactsWith MNN10
+SLT2 interactsWith YPS7
+SLT2 interactsWith ERD1
+SLT2 interactsWith SWI4
+SLT2 interactsWith BEM2
+SLT2 interactsWith CWH41
+SLT2 interactsWith RIM8
+SLT2 interactsWith HUR1
+SLT2 interactsWith KRE11
+SLT2 interactsWith SMI1
+SLT2 interactsWith GCN5
+SLT2 interactsWith GGA2
+SLT2 interactsWith YUR1
+SLT2 interactsWith HOC1
+SLT2 interactsWith YKL037W
+SLT2 interactsWith FPS1
+SLT2 interactsWith CHS5
+SLT2 interactsWith FKS1
+SLT2 interactsWith RIM13
+SLT2 interactsWith TPM1
+SLT2 interactsWith BNI4
+SLT2 interactsWith IRA2
+SLT2 interactsWith RIM20
+SLT2 interactsWith YPL158C
+BNI4 interactsWith EDE1
+BNI4 interactsWith RGD1
+BNI4 interactsWith RVS161
+BNI4 interactsWith CYK3
+BNI4 interactsWith NBP2
+BNI4 interactsWith RVS167
+BNI4 interactsWith SMI1
+BNI4 interactsWith BCK1
+BNI4 interactsWith ILM1
+BNI4 interactsWith IXR1
+BNI4 interactsWith SPA2
+BNI4 interactsWith VRP1
+BNI4 interactsWith FKS1
+BNI4 interactsWith VAN1
+BNI4 interactsWith BRE5
+BNI4 interactsWith YPL066W
+PHO85 interactsWith SPT7
+PHO85 interactsWith BEM1
+PHO85 interactsWith RGD1
+PHO85 interactsWith SRB8
+PHO85 interactsWith BRE1
+PHO85 interactsWith NUM1
+PHO85 interactsWith UME6
+PHO85 interactsWith MNN10
+PHO85 interactsWith ERD1
+PHO85 interactsWith SSN2
+PHO85 interactsWith NHX1
+PHO85 interactsWith ANP1
+PHO85 interactsWith YER049W
+PHO85 interactsWith SHC1
+PHO85 interactsWith SWI4
+PHO85 interactsWith BEM2
+PHO85 interactsWith YGL015C
+PHO85 interactsWith PMR1
+PHO85 interactsWith PAC10
+PHO85 interactsWith SRB5
+PHO85 interactsWith CHO2
+PHO85 interactsWith YGR161C
+PHO85 interactsWith WSC4
+PHO85 interactsWith VPS29
+PHO85 interactsWith SLT2
+PHO85 interactsWith PAN5
+PHO85 interactsWith BCK1
+PHO85 interactsWith GSH1
+PHO85 interactsWith VPS35
+PHO85 interactsWith OPI3
+PHO85 interactsWith HOC1
+PHO85 interactsWith YJR142W
+PHO85 interactsWith YKE2
+PHO85 interactsWith FKS1
+PHO85 interactsWith VPS38
+PHO85 interactsWith ROM2
+PHO85 interactsWith SUR4
+PHO85 interactsWith TUS1
+PHO85 interactsWith VAN1
+PHO85 interactsWith YML122C
+PHO85 interactsWith EFR3
+PHO85 interactsWith FKS3
+PHO85 interactsWith TPM1
+PHO85 interactsWith GCR2
+PHO85 interactsWith BNI1
+PHO85 interactsWith CLA4
+PHO85 interactsWith LEM3
+PHO85 interactsWith TAT2
+PHO85 interactsWith MCH4
+PHO85 interactsWith SMF1
+PHO85 interactsWith SLG1
+PHO85 interactsWith RTS1
+PHO85 interactsWith VAM3
+PHO85 interactsWith SFL1
+PHO85 interactsWith GCR1
+PHO85 interactsWith BEM4
+PHO85 interactsWith VIK1
+PHO85 interactsWith HFI1
+ARL3 interactsWith VAM6
+ARL3 interactsWith ARF1
+ARL3 interactsWith GSS1
+ARL3 interactsWith VPS61
+ARL3 interactsWith RGP1
+ARL3 interactsWith SUM1
+ARL3 interactsWith SWA2
+ARL3 interactsWith GDA1
+ARL3 interactsWith GLO3
+ARL3 interactsWith COG7
+ARL3 interactsWith SWF3
+ARL3 interactsWith GOS1
+ARL3 interactsWith CPR7
+ARL3 interactsWith YKL118W
+ARL3 interactsWith VPS67
+ARL3 interactsWith RIC1
+ARL3 interactsWith VPS63
+ARL3 interactsWith YPT6
+ARL3 interactsWith COG8
+ARL3 interactsWith COG6
+ARL3 interactsWith COG5
+ARL3 interactsWith MON2
+ARL3 interactsWith TLG2
+ARL3 interactsWith VAM10
+ARL3 interactsWith VPS5
+ARL3 interactsWith GYP1
+ARL3 interactsWith VAM3
+ARL3 interactsWith VPS17
+GYP1 interactsWith CSS2
+GYP1 interactsWith VMA2
+GYP1 interactsWith ARL1
+GYP1 interactsWith VPS61
+GYP1 interactsWith NBP2
+GYP1 interactsWith SUM1
+GYP1 interactsWith ERD1
+GYP1 interactsWith RMD7
+GYP1 interactsWith COG7
+GYP1 interactsWith CHO2
+GYP1 interactsWith GOS1
+GYP1 interactsWith SYS1
+GYP1 interactsWith MNN11
+GYP1 interactsWith CPR7
+GYP1 interactsWith CBF1
+GYP1 interactsWith RIC1
+GYP1 interactsWith VPS63
+GYP1 interactsWith YPT6
+GYP1 interactsWith SEC22
+GYP1 interactsWith COG8
+GYP1 interactsWith SCS7
+GYP1 interactsWith COG6
+GYP1 interactsWith COG5
+GYP1 interactsWith RUD3
+GYP1 interactsWith LGE1
+GYP1 interactsWith SUR1
+GYP1 interactsWith VMA13
+RIC1 interactsWith VPS8
+RIC1 interactsWith SWC1
+RIC1 interactsWith FUN30
+RIC1 interactsWith PMT2
+RIC1 interactsWith DRS2
+RIC1 interactsWith BUD14
+RIC1 interactsWith FUI1
+RIC1 interactsWith SFT2
+RIC1 interactsWith ARL1
+RIC1 interactsWith RER1
+RIC1 interactsWith SRO9
+RIC1 interactsWith MAK31
+RIC1 interactsWith PER1
+RIC1 interactsWith PTC1
+RIC1 interactsWith BRE1
+RIC1 interactsWith VAM6
+RIC1 interactsWith ARR4
+RIC1 interactsWith RPL35A
+RIC1 interactsWith VPS41
+RIC1 interactsWith YDR107C
+RIC1 interactsWith GSS1
+RIC1 interactsWith ENT5
+RIC1 interactsWith NBP2
+RIC1 interactsWith RAV2
+RIC1 interactsWith YDR203W
+RIC1 interactsWith UME6
+RIC1 interactsWith SWA2
+RIC1 interactsWith SWR1
+RIC1 interactsWith VPS74
+RIC1 interactsWith SPF1
+RIC1 interactsWith YEL043W
+RIC1 interactsWith VMA8
+RIC1 interactsWith MAK10
+RIC1 interactsWith RMD7
+RIC1 interactsWith YER084W
+RIC1 interactsWith SCS2
+RIC1 interactsWith GLO3
+RIC1 interactsWith RAD4
+RIC1 interactsWith BST1
+RIC1 interactsWith RIM15
+RIC1 interactsWith RPL2A
+RIC1 interactsWith COG7
+RIC1 interactsWith SWF3
+RIC1 interactsWith ERV14
+RIC1 interactsWith GUP1
+RIC1 interactsWith SNF4
+RIC1 interactsWith KEM1
+RIC1 interactsWith RTF1
+RIC1 interactsWith UPF3
+RIC1 interactsWith VMA21
+RIC1 interactsWith SMI1
+RIC1 interactsWith APL6
+RIC1 interactsWith GOS1
+RIC1 interactsWith NEM1
+RIC1 interactsWith VPS29
+RIC1 interactsWith VMA22
+RIC1 interactsWith YIL039W
+RIC1 interactsWith SEC28
+RIC1 interactsWith SYS1
+RIC1 interactsWith VPS35
+RIC1 interactsWith RAV1
+RIC1 interactsWith GEF1
+RIC1 interactsWith CBF1
+RIC1 interactsWith OPI3
+RIC1 interactsWith TEF4
+RIC1 interactsWith CNB1
+RIC1 interactsWith VPS1
+RIC1 interactsWith VPS67
+RIC1 interactsWith GMH1
+RIC1 interactsWith RPL40B
+RIC1 interactsWith ENT4
+RIC1 interactsWith VPS13
+RIC1 interactsWith BRE2
+RIC1 interactsWith EMP70
+RIC1 interactsWith ARP6
+RIC1 interactsWith CSF1
+RIC1 interactsWith IMH1
+RIC1 interactsWith EST2
+RIC1 interactsWith VPS38
+RIC1 interactsWith DCR2
+RIC1 interactsWith YPT7
+RIC1 interactsWith YMD8
+RIC1 interactsWith VPS71
+RIC1 interactsWith COG8
+RIC1 interactsWith MVP1
+RIC1 interactsWith YMR010W
+RIC1 interactsWith STV1
+RIC1 interactsWith PKR1
+RIC1 interactsWith SKY1
+RIC1 interactsWith SCS7
+RIC1 interactsWith RCE1
+RIC1 interactsWith GAS1
+RIC1 interactsWith COG6
+RIC1 interactsWith COG5
+RIC1 interactsWith RPL16B
+RIC1 interactsWith FAR11
+RIC1 interactsWith YNL136W
+RIC1 interactsWith PSD1
+RIC1 interactsWith KEX2
+RIC1 interactsWith MID1
+RIC1 interactsWith KRE25
+RIC1 interactsWith MON2
+RIC1 interactsWith TRF5
+RIC1 interactsWith PPG1
+RIC1 interactsWith BRE5
+RIC1 interactsWith HTZ1
+RIC1 interactsWith ESC8
+RIC1 interactsWith TLG2
+RIC1 interactsWith VAM10
+RIC1 interactsWith VPS5
+RIC1 interactsWith VPS21
+RIC1 interactsWith INP53
+RIC1 interactsWith YOR112W
+RIC1 interactsWith RGA1
+RIC1 interactsWith VPS17
+RIC1 interactsWith RUD3
+RIC1 interactsWith SNC2
+RIC1 interactsWith EGD1
+RIC1 interactsWith LGE1
+RIC1 interactsWith YPL105C
+RIC1 interactsWith VPS30
+RIC1 interactsWith BEM4
+RIC1 interactsWith APL5
+RIC1 interactsWith OXR1
+RIC1 interactsWith TFP3
+RIC1 interactsWith DSS4
+RIC1 interactsWith SRO7
+RIC1 interactsWith YPR050C
+RIC1 interactsWith MAK3
+RIC1 interactsWith MRL1
+RIC1 interactsWith YPR084W
+RIC1 interactsWith YPR197C
+YPT6 interactsWith VPS8
+YPT6 interactsWith SWC1
+YPT6 interactsWith FUN30
+YPT6 interactsWith BUD14
+YPT6 interactsWith YBL083C
+YPT6 interactsWith SFT2
+YPT6 interactsWith ARL1
+YPT6 interactsWith APM3
+YPT6 interactsWith RER1
+YPT6 interactsWith SRO9
+YPT6 interactsWith MAK31
+YPT6 interactsWith PER1
+YPT6 interactsWith RAD18
+YPT6 interactsWith PTC1
+YPT6 interactsWith BRE1
+YPT6 interactsWith VAM6
+YPT6 interactsWith ARR4
+YPT6 interactsWith RPL35A
+YPT6 interactsWith VPS41
+YPT6 interactsWith YDR107C
+YPT6 interactsWith GSS1
+YPT6 interactsWith SWF1
+YPT6 interactsWith ENT5
+YPT6 interactsWith NBP2
+YPT6 interactsWith RAV2
+YPT6 interactsWith YDR203W
+YPT6 interactsWith SUM1
+YPT6 interactsWith SWA2
+YPT6 interactsWith SWR1
+YPT6 interactsWith VID21
+YPT6 interactsWith VPS74
+YPT6 interactsWith YEL043W
+YPT6 interactsWith VMA8
+YPT6 interactsWith MAK10
+YPT6 interactsWith YER084W
+YPT6 interactsWith SBH1
+YPT6 interactsWith SCS2
+YPT6 interactsWith GLO3
+YPT6 interactsWith RAD4
+YPT6 interactsWith BST1
+YPT6 interactsWith RIM15
+YPT6 interactsWith RPL2A
+YPT6 interactsWith COG7
+YPT6 interactsWith SWF3
+YPT6 interactsWith ERV14
+YPT6 interactsWith GUP1
+YPT6 interactsWith SNF4
+YPT6 interactsWith VAM7
+YPT6 interactsWith RTF1
+YPT6 interactsWith ZRT1
+YPT6 interactsWith VMA7
+YPT6 interactsWith UPF3
+YPT6 interactsWith VMA21
+YPT6 interactsWith SMI1
+YPT6 interactsWith APL6
+YPT6 interactsWith OPI1
+YPT6 interactsWith GOS1
+YPT6 interactsWith NEM1
+YPT6 interactsWith VPS29
+YPT6 interactsWith VMA10
+YPT6 interactsWith VMA22
+YPT6 interactsWith YIL039W
+YPT6 interactsWith SEC28
+YPT6 interactsWith SYS1
+YPT6 interactsWith SNX4
+YPT6 interactsWith PEP8
+YPT6 interactsWith YJL123C
+YPT6 interactsWith VPS35
+YPT6 interactsWith RAV1
+YPT6 interactsWith GEF1
+YPT6 interactsWith CBF1
+YPT6 interactsWith OPI3
+YPT6 interactsWith TEF4
+YPT6 interactsWith CNB1
+YPT6 interactsWith IRS4
+YPT6 interactsWith VPS67
+YPT6 interactsWith GMH1
+YPT6 interactsWith ENT4
+YPT6 interactsWith BRE2
+YPT6 interactsWith EMP70
+YPT6 interactsWith ARP6
+YPT6 interactsWith CSF1
+YPT6 interactsWith IMH1
+YPT6 interactsWith EST2
+YPT6 interactsWith VPS38
+YPT6 interactsWith DCR2
+YPT6 interactsWith YPT7
+YPT6 interactsWith VPS71
+YPT6 interactsWith COG8
+YPT6 interactsWith MVP1
+YPT6 interactsWith YMR010W
+YPT6 interactsWith STV1
+YPT6 interactsWith PKR1
+YPT6 interactsWith SKY1
+YPT6 interactsWith RSN1
+YPT6 interactsWith RCE1
+YPT6 interactsWith GAS1
+YPT6 interactsWith COG6
+YPT6 interactsWith COG5
+YPT6 interactsWith RPL16B
+YPT6 interactsWith YNL136W
+YPT6 interactsWith PSD1
+YPT6 interactsWith KRE25
+YPT6 interactsWith MON2
+YPT6 interactsWith PPG1
+YPT6 interactsWith BRE5
+YPT6 interactsWith HTZ1
+YPT6 interactsWith ESC8
+YPT6 interactsWith TLG2
+YPT6 interactsWith INO4
+YPT6 interactsWith VAM10
+YPT6 interactsWith VPS5
+YPT6 interactsWith VPS21
+YPT6 interactsWith VAM3
+YPT6 interactsWith INP53
+YPT6 interactsWith YOR112W
+YPT6 interactsWith VPS17
+YPT6 interactsWith RUD3
+YPT6 interactsWith EGD1
+YPT6 interactsWith LGE1
+YPT6 interactsWith VPS30
+YPT6 interactsWith BEM4
+YPT6 interactsWith APL5
+YPT6 interactsWith OXR1
+YPT6 interactsWith TFP3
+YPT6 interactsWith DSS4
+YPT6 interactsWith SRO7
+YPT6 interactsWith YPR050C
+YPT6 interactsWith MAK3
+YPT6 interactsWith MRL1
+YPT6 interactsWith YPR084W
+YPT6 interactsWith YPR197C
+CDC73 interactsWith VPS8
+CDC73 interactsWith SWC1
+CDC73 interactsWith DEP1
+CDC73 interactsWith NUP60
+CDC73 interactsWith ECM8
+CDC73 interactsWith RXT2
+CDC73 interactsWith SIF2
+CDC73 interactsWith SOY
+CDC73 interactsWith HPC2
+CDC73 interactsWith PDB1
+CDC73 interactsWith AOR1
+CDC73 interactsWith SRO9
+CDC73 interactsWith PAT1
+CDC73 interactsWith NHP10
+CDC73 interactsWith YDL033C
+CDC73 interactsWith RGP1
+CDC73 interactsWith MNN10
+CDC73 interactsWith RTT103
+CDC73 interactsWith SWR1
+CDC73 interactsWith MSN5
+CDC73 interactsWith SEM1
+CDC73 interactsWith XRS2
+CDC73 interactsWith LSM6
+CDC73 interactsWith DOT1
+CDC73 interactsWith VPS72
+CDC73 interactsWith VAC8
+CDC73 interactsWith SPF1
+CDC73 interactsWith YEL033W
+CDC73 interactsWith CIN8
+CDC73 interactsWith YER084W
+CDC73 interactsWith SWI4
+CDC73 interactsWith GLO3
+CDC73 interactsWith YER139C
+CDC73 interactsWith SPT2
+CDC73 interactsWith PDA1
+CDC73 interactsWith UBP6
+CDC73 interactsWith SWF3
+CDC73 interactsWith DST1
+CDC73 interactsWith KEM1
+CDC73 interactsWith BUD13
+CDC73 interactsWith VID30
+CDC73 interactsWith RTF1
+CDC73 interactsWith YTA7
+CDC73 interactsWith GOS1
+CDC73 interactsWith THP2
+CDC73 interactsWith APQ12
+CDC73 interactsWith SEC28
+CDC73 interactsWith MET18
+CDC73 interactsWith IST3
+CDC73 interactsWith LSM1
+CDC73 interactsWith SET2
+CDC73 interactsWith HIR3
+CDC73 interactsWith YKL053C-A
+CDC73 interactsWith CTK1
+CDC73 interactsWith ELF1
+CDC73 interactsWith LST4
+CDC73 interactsWith DOA1
+CDC73 interactsWith RTT109
+CDC73 interactsWith RIC1
+CDC73 interactsWith PET309
+CDC73 interactsWith ARP6
+CDC73 interactsWith YLR168C
+CDC73 interactsWith SWI6
+CDC73 interactsWith MMR1
+CDC73 interactsWith QRI5
+CDC73 interactsWith LIP2
+CDC73 interactsWith YPT6
+CDC73 interactsWith SEC22
+CDC73 interactsWith YLR269C
+CDC73 interactsWith NKP2
+CDC73 interactsWith ORM2
+CDC73 interactsWith VID22
+CDC73 interactsWith IKI3
+CDC73 interactsWith YML012C-A
+CDC73 interactsWith RAD52
+CDC73 interactsWith VPS71
+CDC73 interactsWith LYS7
+CDC73 interactsWith RIM13
+CDC73 interactsWith MRPS8
+CDC73 interactsWith SAP30
+CDC73 interactsWith RCE1
+CDC73 interactsWith BUL1
+CDC73 interactsWith SSN8
+CDC73 interactsWith PHO23
+CDC73 interactsWith YNL140C
+CDC73 interactsWith YNL198C
+CDC73 interactsWith GCR2
+CDC73 interactsWith IES2
+CDC73 interactsWith RIM21
+CDC73 interactsWith SIN3
+CDC73 interactsWith HTZ1
+CDC73 interactsWith MDM38
+CDC73 interactsWith THP1
+CDC73 interactsWith RRP6
+CDC73 interactsWith DFG16
+CDC73 interactsWith HIR2
+CDC73 interactsWith DIA2
+CDC73 interactsWith VPS21
+CDC73 interactsWith LEO1
+CDC73 interactsWith UBP2
+CDC73 interactsWith RUD3
+CDC73 interactsWith TIM18
+CDC73 interactsWith SNU66
+CDC73 interactsWith PDE2
+CDC73 interactsWith SSN3
+CDC73 interactsWith SUR1
+CDC73 interactsWith BTS1
+CDC73 interactsWith CTI6
+CDC73 interactsWith YPL182C
+CDC73 interactsWith MED1
+CDC73 interactsWith YPR084W
+SET2 interactsWith SWC1
+SET2 interactsWith DEP1
+SET2 interactsWith SIF2
+SET2 interactsWith SWD3
+SET2 interactsWith DCC1
+SET2 interactsWith SNT1
+SET2 interactsWith YDL033C
+SET2 interactsWith BRE1
+SET2 interactsWith SWR1
+SET2 interactsWith VID21
+SET2 interactsWith SDC1
+SET2 interactsWith RIM8
+SET2 interactsWith RIM8
+SET2 interactsWith SOH1
+SET2 interactsWith RTF1
+SET2 interactsWith SHY1
+SET2 interactsWith HOS4
+SET2 interactsWith SET3
+SET2 interactsWith BRE2
+SET2 interactsWith ARP6
+SET2 interactsWith SEC22
+SET2 interactsWith VAC14
+SET2 interactsWith VPS71
+SET2 interactsWith GIM5
+SET2 interactsWith MSC1
+SET2 interactsWith GIM3
+SET2 interactsWith RIM21
+SET2 interactsWith MON2
+SET2 interactsWith BRE5
+SET2 interactsWith HTZ1
+SET2 interactsWith VAM3
+SET2 interactsWith LEO1
+SET2 interactsWith LGE1
+SET2 interactsWith BEM4
+SET2 interactsWith YPR014C
+LIA1 interactsWith SRO9
+LIA1 interactsWith ARF1
+LIA1 interactsWith PRB1
+LIA1 interactsWith RMD9
+LIA1 interactsWith SOH1
+LIA1 interactsWith RTF1
+LIA1 interactsWith SRB2
+LIA1 interactsWith YMR269W
+LIA1 interactsWith AAH1
+LIA1 interactsWith YOR309C
+ARP1 interactsWith HCM1
+ARP1 interactsWith GIM4
+ARP1 interactsWith CIN8
+ARP1 interactsWith RPL34A
+ARP1 interactsWith BOI2
+ARP1 interactsWith MON1
+ARP1 interactsWith KIP3
+ARP1 interactsWith YGL217C
+ARP1 interactsWith PAC10
+ARP1 interactsWith SMI1
+ARP1 interactsWith VPS29
+ARP1 interactsWith YKE2
+ARP1 interactsWith CLB4
+ARP1 interactsWith VID22
+ARP1 interactsWith GIM5
+ARP1 interactsWith CIK1
+ARP1 interactsWith GIM3
+ARP1 interactsWith BRE5
+ARP1 interactsWith CIN1
+ARP1 interactsWith KAR9
+ARP1 interactsWith KAR3
+JNM1 interactsWith LTE1
+JNM1 interactsWith HCM1
+JNM1 interactsWith PAT1
+JNM1 interactsWith GIM4
+JNM1 interactsWith CIN8
+JNM1 interactsWith PAC2
+JNM1 interactsWith BOI2
+JNM1 interactsWith KIP3
+JNM1 interactsWith YGL217C
+JNM1 interactsWith PAC10
+JNM1 interactsWith SMI1
+JNM1 interactsWith VPS35
+JNM1 interactsWith CAP1
+JNM1 interactsWith YKE2
+JNM1 interactsWith CLB4
+JNM1 interactsWith CPR6
+JNM1 interactsWith YLR217W
+JNM1 interactsWith GIM5
+JNM1 interactsWith TUB3
+JNM1 interactsWith RPL16B
+JNM1 interactsWith GIM3
+JNM1 interactsWith CIN1
+JNM1 interactsWith CIN2
+JNM1 interactsWith KAR9
+JNM1 interactsWith KAR3
+NIP100 interactsWith DEP1
+NIP100 interactsWith CRD1
+NIP100 interactsWith MRPL1
+NIP100 interactsWith EMI1
+NIP100 interactsWith GIM4
+NIP100 interactsWith CIN8
+NIP100 interactsWith PAC2
+NIP100 interactsWith BOI2
+NIP100 interactsWith MON1
+NIP100 interactsWith KIP3
+NIP100 interactsWith YGL217C
+NIP100 interactsWith PAC10
+NIP100 interactsWith CAP2
+NIP100 interactsWith CAP1
+NIP100 interactsWith BRE2
+NIP100 interactsWith YKE2
+NIP100 interactsWith CLB4
+NIP100 interactsWith CPR6
+NIP100 interactsWith YLR217W
+NIP100 interactsWith ATP10
+NIP100 interactsWith GIM5
+NIP100 interactsWith CIN4
+NIP100 interactsWith SAP30
+NIP100 interactsWith GAS1
+NIP100 interactsWith GIM3
+NIP100 interactsWith MCK1
+NIP100 interactsWith CIN1
+NIP100 interactsWith YPL205C
+NIP100 interactsWith CIN2
+NIP100 interactsWith KAR9
+NIP100 interactsWith KAR3
+DYN1 interactsWith LTE1
+DYN1 interactsWith HCM1
+DYN1 interactsWith GIM4
+DYN1 interactsWith CIN8
+DYN1 interactsWith BOI2
+DYN1 interactsWith MON1
+DYN1 interactsWith KIP3
+DYN1 interactsWith YGL217C
+DYN1 interactsWith PAC10
+DYN1 interactsWith YKE2
+DYN1 interactsWith GIM5
+DYN1 interactsWith GIM3
+DYN1 interactsWith CIN1
+DYN1 interactsWith KAR9
+DYN1 interactsWith KAR3
+DYN2 interactsWith GIM4
+DYN2 interactsWith CIN8
+DYN2 interactsWith MON1
+DYN2 interactsWith KIP3
+DYN2 interactsWith YGL217C
+DYN2 interactsWith PAC10
+DYN2 interactsWith YKE2
+DYN2 interactsWith GIM5
+DYN2 interactsWith GIM3
+DYN2 interactsWith CIN1
+DYN2 interactsWith KAR9
+PAC11 interactsWith GIM4
+PAC11 interactsWith CIN8
+PAC11 interactsWith BOI2
+PAC11 interactsWith KIP3
+PAC11 interactsWith YGL217C
+PAC11 interactsWith PAC10
+PAC11 interactsWith YKE2
+PAC11 interactsWith CLB4
+PAC11 interactsWith GIM5
+PAC11 interactsWith GIM3
+PAC11 interactsWith CIN1
+PAC11 interactsWith KAR9
+YMR299c interactsWith GIM4
+YMR299c interactsWith CIN8
+YMR299c interactsWith PAC2
+YMR299c interactsWith MON1
+YMR299c interactsWith KIP3
+YMR299c interactsWith YGL217C
+YMR299c interactsWith PAC10
+YMR299c interactsWith YKE2
+YMR299c interactsWith CLB4
+YMR299c interactsWith GIM5
+YMR299c interactsWith GIM3
+YMR299c interactsWith CIN1
+YMR299c interactsWith CIN2
+YMR299c interactsWith KAR9
+YMR299c interactsWith KAR3
+PAC1 interactsWith GIM4
+PAC1 interactsWith CIN8
+PAC1 interactsWith BEM2
+PAC1 interactsWith FAB1
+PAC1 interactsWith KIP3
+PAC1 interactsWith YGL217C
+PAC1 interactsWith PAC10
+PAC1 interactsWith YHR168W
+PAC1 interactsWith CAP1
+PAC1 interactsWith YKE2
+PAC1 interactsWith GIM5
+PAC1 interactsWith GIM3
+PAC1 interactsWith YOR296W
+PAC1 interactsWith YOR300W
+PAC1 interactsWith KAR9
+PAC1 interactsWith KAR3
+NUM1 interactsWith LTE1
+NUM1 interactsWith CCZ1
+NUM1 interactsWith AOR1
+NUM1 interactsWith HCM1
+NUM1 interactsWith PAT1
+NUM1 interactsWith GIM4
+NUM1 interactsWith CIN8
+NUM1 interactsWith FAB1
+NUM1 interactsWith MAD1
+NUM1 interactsWith MON1
+NUM1 interactsWith KIP3
+NUM1 interactsWith YGL217C
+NUM1 interactsWith PAC10
+NUM1 interactsWith SMI1
+NUM1 interactsWith CAP2
+NUM1 interactsWith VPS35
+NUM1 interactsWith BFA1
+NUM1 interactsWith CAP1
+NUM1 interactsWith DNM1
+NUM1 interactsWith YKE2
+NUM1 interactsWith CLB4
+NUM1 interactsWith CPR6
+NUM1 interactsWith YLR217W
+NUM1 interactsWith BUD6
+NUM1 interactsWith YPT7
+NUM1 interactsWith GIM5
+NUM1 interactsWith BUB2
+NUM1 interactsWith TPM1
+NUM1 interactsWith GIM3
+NUM1 interactsWith ASE1
+NUM1 interactsWith YOR322C
+NUM1 interactsWith CIN1
+NUM1 interactsWith YPL205C
+NUM1 interactsWith KAR9
+NUM1 interactsWith KAR3
+BFA1 interactsWith BIK1
+BFA1 interactsWith GIM4
+BFA1 interactsWith PAC10
+BFA1 interactsWith YKE2
+BFA1 interactsWith GIM5
+BFA1 interactsWith GIM3
+BFA1 interactsWith RAD50
+BFA1 interactsWith BUB3
+BFA1 interactsWith KAR9
+BFA1 interactsWith CTF4
+BFA1 interactsWith KAR3
+BIK1 interactsWith RPL19B
+BIK1 interactsWith HCM1
+BIK1 interactsWith PAT1
+BIK1 interactsWith RTT103
+BIK1 interactsWith YDR360W
+BIK1 interactsWith GIM4
+BIK1 interactsWith CIN8
+BIK1 interactsWith PAC2
+BIK1 interactsWith SHC1
+BIK1 interactsWith FAB1
+BIK1 interactsWith RPL24A
+BIK1 interactsWith MAD1
+BIK1 interactsWith KEM1
+BIK1 interactsWith PAC10
+BIK1 interactsWith DBF2
+BIK1 interactsWith BUB1
+BIK1 interactsWith MSL1
+BIK1 interactsWith MAD2
+BIK1 interactsWith RPA34
+BIK1 interactsWith RIC1
+BIK1 interactsWith YKE2
+BIK1 interactsWith GIM5
+BIK1 interactsWith YML095C-A
+BIK1 interactsWith TUB3
+BIK1 interactsWith BUB2
+BIK1 interactsWith CIN4
+BIK1 interactsWith INP52
+BIK1 interactsWith GIM3
+BIK1 interactsWith HTZ1
+BIK1 interactsWith BUB3
+BIK1 interactsWith ASE1
+BIK1 interactsWith RBL2
+BIK1 interactsWith CIN1
+BIK1 interactsWith CIN2
+BIK1 interactsWith KAR9
+ARP6 interactsWith DEP1
+ARP6 interactsWith CSS2
+ARP6 interactsWith AKL1
+ARP6 interactsWith CBP6
+ARP6 interactsWith SWD3
+ARP6 interactsWith MRC1
+ARP6 interactsWith HCM1
+ARP6 interactsWith YDL033C
+ARP6 interactsWith BRE1
+ARP6 interactsWith GSS1
+ARP6 interactsWith RGP1
+ARP6 interactsWith YDR360W
+ARP6 interactsWith GIM4
+ARP6 interactsWith PAC2
+ARP6 interactsWith GLO3
+ARP6 interactsWith DEG1
+ARP6 interactsWith MAD1
+ARP6 interactsWith BUD13
+ARP6 interactsWith RTF1
+ARP6 interactsWith YGR071C
+ARP6 interactsWith PAC10
+ARP6 interactsWith BUB1
+ARP6 interactsWith MGM101
+ARP6 interactsWith BRE2
+ARP6 interactsWith SPT8
+ARP6 interactsWith PET309
+ARP6 interactsWith HOG1
+ARP6 interactsWith SEC22
+ARP6 interactsWith EST2
+ARP6 interactsWith YLR374C
+ARP6 interactsWith YML090W
+ARP6 interactsWith GIM5
+ARP6 interactsWith TUB3
+ARP6 interactsWith COG6
+ARP6 interactsWith PHO23
+ARP6 interactsWith GIM3
+ARP6 interactsWith KRE25
+ARP6 interactsWith MET22
+ARP6 interactsWith WHI2
+ARP6 interactsWith LEO1
+ARP6 interactsWith SER1
+ARP6 interactsWith RUD3
+ARP6 interactsWith SNU66
+ARP6 interactsWith CIN1
+ARP6 interactsWith LGE1
+ARP6 interactsWith CTI6
+ARP6 interactsWith YPL182C
+ARP6 interactsWith THI6
+ARP6 interactsWith CIN2
+ASE1 interactsWith CSM1
+ASE1 interactsWith FIN1
+ASE1 interactsWith YDR149C
+ASE1 interactsWith DYN2
+ASE1 interactsWith PAC11
+ASE1 interactsWith GIM4
+ASE1 interactsWith CIN8
+ASE1 interactsWith BEM2
+ASE1 interactsWith PAC10
+ASE1 interactsWith ARP1
+ASE1 interactsWith ELM1
+ASE1 interactsWith DYN1
+ASE1 interactsWith YLL049W
+ASE1 interactsWith YLR254C
+ASE1 interactsWith VAC14
+ASE1 interactsWith GIM5
+ASE1 interactsWith JNM1
+ASE1 interactsWith YMR299C
+ASE1 interactsWith GIM3
+ASE1 interactsWith PAC1
+ASE1 interactsWith KIP2
+ASE1 interactsWith NIP100
+ASE1 interactsWith CLB2
+ASE1 interactsWith KAR3
+KAR9 interactsWith YDR149C
+KAR9 interactsWith GIM4
+KAR9 interactsWith PAC10
+KAR9 interactsWith IXR1
+KAR9 interactsWith YLL049W
+KAR9 interactsWith YKE2
+KAR9 interactsWith GIM5
+KAR9 interactsWith BUB2
+KAR9 interactsWith GIM3
+KAR9 interactsWith KIN4
+KAR9 interactsWith KIP2
+KAR9 interactsWith MCM16
+MYO2 interactsWith SKT5
+MYO2 interactsWith YBL062W
+MYO2 interactsWith CHS3
+MYO2 interactsWith BEM1
+MYO2 interactsWith BIK1
+MYO2 interactsWith PTC1
+MYO2 interactsWith SHS1
+MYO2 interactsWith YDR149C
+MYO2 interactsWith NUM1
+MYO2 interactsWith DYN2
+MYO2 interactsWith PAC11
+MYO2 interactsWith BEM2
+MYO2 interactsWith FAB1
+MYO2 interactsWith CKB1
+MYO2 interactsWith YGL211W
+MYO2 interactsWith ELP2
+MYO2 interactsWith YGR228W
+MYO2 interactsWith SMI1
+MYO2 interactsWith SLT2
+MYO2 interactsWith UBA4
+MYO2 interactsWith ARP1
+MYO2 interactsWith CHS7
+MYO2 interactsWith URM1
+MYO2 interactsWith BCK1
+MYO2 interactsWith BFA1
+MYO2 interactsWith RPS4A
+MYO2 interactsWith ELM1
+MYO2 interactsWith DYN1
+MYO2 interactsWith YKR074W
+MYO2 interactsWith YLL049W
+MYO2 interactsWith CHS5
+MYO2 interactsWith FLM1
+MYO2 interactsWith VAC14
+MYO2 interactsWith BUB2
+MYO2 interactsWith TPM1
+MYO2 interactsWith YNL119W
+MYO2 interactsWith YNL120C
+MYO2 interactsWith BNI4
+MYO2 interactsWith CLA4
+MYO2 interactsWith CKB2
+MYO2 interactsWith PAC1
+MYO2 interactsWith ELP3
+MYO2 interactsWith ELP4
+MYO2 interactsWith KIP2
+MYO2 interactsWith NIP100
+CLB4 interactsWith PAC10
+CLB4 interactsWith YLL049W
+CLB4 interactsWith CTF18
+CLB4 interactsWith KAR3
+KIP2 interactsWith DRS2
+KIP2 interactsWith GIM4
+KIP2 interactsWith CIN8
+KIP2 interactsWith PAC2
+KIP2 interactsWith PAC10
+KIP2 interactsWith DBF2
+KIP2 interactsWith YKE2
+KIP2 interactsWith GIM5
+KIP2 interactsWith TUB3
+KIP2 interactsWith GIM3
+KIP2 interactsWith CIN1
+KIP2 interactsWith CIN2
+KIP3 interactsWith SHE1
+KIP3 interactsWith DCC1
+KIP3 interactsWith YDR149C
+KIP3 interactsWith YGL152C
+KIP3 interactsWith KEM1
+KIP3 interactsWith CTF8
+KIP3 interactsWith YLL049W
+KIP3 interactsWith CTF18
+KIP3 interactsWith SLK19
+KIP3 interactsWith CTF4
+KIP3 interactsWith KAR3
+CIN8 interactsWith KIP1
+CIN8 interactsWith IML3
+CIN8 interactsWith MRPL36
+CIN8 interactsWith DCC1
+CIN8 interactsWith CSM1
+CIN8 interactsWith YDR149C
+CIN8 interactsWith CHL4
+CIN8 interactsWith MCM21
+CIN8 interactsWith PPM1
+CIN8 interactsWith GIM4
+CIN8 interactsWith PAC2
+CIN8 interactsWith BEM2
+CIN8 interactsWith BMH1
+CIN8 interactsWith MAD1
+CIN8 interactsWith HUR1
+CIN8 interactsWith PAC10
+CIN8 interactsWith BUB1
+CIN8 interactsWith SMI1
+CIN8 interactsWith MAD3
+CIN8 interactsWith MAD2
+CIN8 interactsWith BFA1
+CIN8 interactsWith MCM22
+CIN8 interactsWith ELM1
+CIN8 interactsWith YLL049W
+CIN8 interactsWith YKE2
+CIN8 interactsWith CLB4
+CIN8 interactsWith CTF3
+CIN8 interactsWith GIM5
+CIN8 interactsWith TUB3
+CIN8 interactsWith CSM3
+CIN8 interactsWith BUB2
+CIN8 interactsWith CTF18
+CIN8 interactsWith CIN4
+CIN8 interactsWith GIM3
+CIN8 interactsWith TOF1
+CIN8 interactsWith CLA4
+CIN8 interactsWith RTS1
+CIN8 interactsWith SLK19
+CIN8 interactsWith RBL2
+CIN8 interactsWith CIN1
+CIN8 interactsWith CHL1
+CIN8 interactsWith CTF19
+CIN8 interactsWith RRD2
+CIN8 interactsWith CIN2
+CIN8 interactsWith MCM16
+CIN8 interactsWith CLB2
+CIN8 interactsWith CTF4
+KAR3 interactsWith LTE1
+KAR3 interactsWith NUP60
+KAR3 interactsWith BUD14
+KAR3 interactsWith MUM2
+KAR3 interactsWith SIF2
+KAR3 interactsWith IML3
+KAR3 interactsWith MRC1
+KAR3 interactsWith RAD61
+KAR3 interactsWith CHL4
+KAR3 interactsWith SWM1
+KAR3 interactsWith MCM21
+KAR3 interactsWith SEM1
+KAR3 interactsWith XRS2
+KAR3 interactsWith PAC11
+KAR3 interactsWith GIM4
+KAR3 interactsWith BEM2
+KAR3 interactsWith BMH1
+KAR3 interactsWith UBP6
+KAR3 interactsWith CDC26
+KAR3 interactsWith MAD1
+KAR3 interactsWith PMR1
+KAR3 interactsWith HUR1
+KAR3 interactsWith KEM1
+KAR3 interactsWith PAC10
+KAR3 interactsWith DBF2
+KAR3 interactsWith PRE9
+KAR3 interactsWith BUB1
+KAR3 interactsWith ARD1
+KAR3 interactsWith CTF8
+KAR3 interactsWith YHR194W
+KAR3 interactsWith RPN10
+KAR3 interactsWith YIL090W
+KAR3 interactsWith MAD3
+KAR3 interactsWith MAD2
+KAR3 interactsWith ASF1
+KAR3 interactsWith SOD1
+KAR3 interactsWith MCM22
+KAR3 interactsWith RTT109
+KAR3 interactsWith YLL049W
+KAR3 interactsWith ARP6
+KAR3 interactsWith YKE2
+KAR3 interactsWith CPR6
+KAR3 interactsWith YLR217W
+KAR3 interactsWith CTF3
+KAR3 interactsWith RAD52
+KAR3 interactsWith GIM5
+KAR3 interactsWith CSM3
+KAR3 interactsWith BUB2
+KAR3 interactsWith GIM3
+KAR3 interactsWith TOF1
+KAR3 interactsWith MCK1
+KAR3 interactsWith PSH1
+KAR3 interactsWith BUB3
+KAR3 interactsWith SLK19
+KAR3 interactsWith CHL1
+KAR3 interactsWith CTF19
+KAR3 interactsWith RRD2
+KAR3 interactsWith MCM16
+YDR332w interactsWith SHP1
+YDR332w interactsWith HHF1
+YDR332w interactsWith RAD61
+YDR332w interactsWith HTA1
+YDR332w interactsWith PEX5
+YDR332w interactsWith PEX10
+YDR332w interactsWith BIM1
+YDR332w interactsWith HOP2
+YDR332w interactsWith MAD1
+YDR332w interactsWith UBR1
+YDR332w interactsWith BUB1
+YDR332w interactsWith CTF8
+YDR332w interactsWith MAD3
+YDR332w interactsWith MAD2
+YDR332w interactsWith GIM5
+YDR332w interactsWith YML095C-A
+YDR332w interactsWith CIK1
+YDR332w interactsWith INP52
+YDR332w interactsWith GIM3
+YDR332w interactsWith HTZ1
+YDR332w interactsWith BUB3
+YDR332w interactsWith CHL1
+YDR332w interactsWith CTF4
+YDR332w interactsWith KAR3
+TUB3 interactsWith SWC1
+TUB3 interactsWith GIM4
+TUB3 interactsWith PAC2
+TUB3 interactsWith MAD1
+TUB3 interactsWith PAC10
+TUB3 interactsWith ARP1
+TUB3 interactsWith MAD3
+TUB3 interactsWith YKE2
+TUB3 interactsWith VPS71
+TUB3 interactsWith GIM5
+TUB3 interactsWith CIN4
+TUB3 interactsWith GIM3
+TUB3 interactsWith HTZ1
+TUB3 interactsWith DSE3
+TUB3 interactsWith RBL2
+TUB3 interactsWith PNT1
+TUB3 interactsWith CIN1
+TUB3 interactsWith NIP100
+TUB3 interactsWith CIN2
+RBL2 interactsWith GIM4
+RBL2 interactsWith PAC2
+RBL2 interactsWith PAC10
+RBL2 interactsWith YKE2
+RBL2 interactsWith GIM5
+RBL2 interactsWith CIN4
+RBL2 interactsWith GIM3
+RBL2 interactsWith BUB3
+RBL2 interactsWith CIN1
+RBL2 interactsWith CIN2
+PAC2 interactsWith MAD1
+PAC2 interactsWith PAC10
+PAC2 interactsWith BUB1
+PAC2 interactsWith MAD2
+PAC2 interactsWith YKE2
+PAC2 interactsWith GIM5
+PAC2 interactsWith CTF18
+PAC2 interactsWith GIM3
+CIN2 interactsWith GIM4
+CIN2 interactsWith MAD1
+CIN2 interactsWith PAC10
+CIN2 interactsWith BUB1
+CIN2 interactsWith MAD3
+CIN2 interactsWith MAD2
+CIN2 interactsWith BFA1
+CIN2 interactsWith YKE2
+CIN2 interactsWith GIM5
+CIN2 interactsWith BUB2
+CIN2 interactsWith CTF18
+CIN2 interactsWith GIM3
+CIN2 interactsWith CIN1
+CIN4 interactsWith GIM4
+CIN4 interactsWith PAC10
+CIN4 interactsWith YKE2
+CIN4 interactsWith GIM5
+CIN4 interactsWith GIM3
+CIN4 interactsWith CIN1
+CTF4 interactsWith NUP60
+CTF4 interactsWith SWD1
+CTF4 interactsWith SLA1
+CTF4 interactsWith MUM2
+CTF4 interactsWith MMS4
+CTF4 interactsWith IML3
+CTF4 interactsWith AOR1
+CTF4 interactsWith DCC1
+CTF4 interactsWith MRC1
+CTF4 interactsWith MRC1
+CTF4 interactsWith HEX3
+CTF4 interactsWith RPN4
+CTF4 interactsWith CLB3
+CTF4 interactsWith SHS1
+CTF4 interactsWith RAD57
+CTF4 interactsWith RAD61
+CTF4 interactsWith RAD55
+CTF4 interactsWith HTA1
+CTF4 interactsWith CHL4
+CTF4 interactsWith PMP3
+CTF4 interactsWith MCM21
+CTF4 interactsWith GIM4
+CTF4 interactsWith RAD23
+CTF4 interactsWith ISC1
+CTF4 interactsWith RMD7
+CTF4 interactsWith RAD51
+CTF4 interactsWith SLX8
+CTF4 interactsWith CHD1
+CTF4 interactsWith RAD24
+CTF4 interactsWith UBP6
+CTF4 interactsWith CDC26
+CTF4 interactsWith SSF73
+CTF4 interactsWith MAD1
+CTF4 interactsWith MMS2
+CTF4 interactsWith SOH1
+CTF4 interactsWith RAD54
+CTF4 interactsWith HUR1
+CTF4 interactsWith KEM1
+CTF4 interactsWith RTF1
+CTF4 interactsWith PAC10
+CTF4 interactsWith UBR1
+CTF4 interactsWith BUB1
+CTF4 interactsWith SMI1
+CTF4 interactsWith ARD1
+CTF4 interactsWith RRM3
+CTF4 interactsWith CTF8
+CTF4 interactsWith RPN10
+CTF4 interactsWith MAD3
+CTF4 interactsWith MAD2
+CTF4 interactsWith HPR5
+CTF4 interactsWith POL32
+CTF4 interactsWith SOD1
+CTF4 interactsWith MCM22
+CTF4 interactsWith RPS4A
+CTF4 interactsWith HSL1
+CTF4 interactsWith RAD5
+CTF4 interactsWith ARP6
+CTF4 interactsWith STM1
+CTF4 interactsWith TOP3
+CTF4 interactsWith YLR235C
+CTF4 interactsWith SEC22
+CTF4 interactsWith CTF3
+CTF4 interactsWith TSA1
+CTF4 interactsWith RAD52
+CTF4 interactsWith GIM5
+CTF4 interactsWith LYS7
+CTF4 interactsWith CSM3
+CTF4 interactsWith BUB2
+CTF4 interactsWith CTF18
+CTF4 interactsWith SGS1
+CTF4 interactsWith MRE11
+CTF4 interactsWith GIM3
+CTF4 interactsWith RAD50
+CTF4 interactsWith TOF1
+CTF4 interactsWith MID1
+CTF4 interactsWith MCK1
+CTF4 interactsWith BRE5
+CTF4 interactsWith HTZ1
+CTF4 interactsWith RTS1
+CTF4 interactsWith BUB3
+CTF4 interactsWith ELG1
+CTF4 interactsWith SLK19
+CTF4 interactsWith YPL017C
+CTF4 interactsWith CTF19
+CTF4 interactsWith NCE4
+CTF4 interactsWith LGE1
+CTF4 interactsWith SUR1
+CTF4 interactsWith YPL144W
+CTF4 interactsWith DDC1
+CTF4 interactsWith VIK1
+CTF4 interactsWith YPR015C
+CTF4 interactsWith RLF2
+CTF4 interactsWith MCM16
+CTF4 interactsWith CLB2
+CTF4 interactsWith CLB5
+CTF8 interactsWith MRC1
+CTF8 interactsWith MRC1
+CTF8 interactsWith RAD57
+CTF8 interactsWith RAD55
+CTF8 interactsWith RAD9
+CTF8 interactsWith HTA1
+CTF8 interactsWith MSN5
+CTF8 interactsWith GIM4
+CTF8 interactsWith CIN8
+CTF8 interactsWith SLX8
+CTF8 interactsWith CDC26
+CTF8 interactsWith SSF73
+CTF8 interactsWith MAD1
+CTF8 interactsWith SOH1
+CTF8 interactsWith RAD54
+CTF8 interactsWith PMR1
+CTF8 interactsWith HUR1
+CTF8 interactsWith KEM1
+CTF8 interactsWith RTF1
+CTF8 interactsWith PAC10
+CTF8 interactsWith UBR1
+CTF8 interactsWith SMI1
+CTF8 interactsWith RRM3
+CTF8 interactsWith MAD2
+CTF8 interactsWith HPR5
+CTF8 interactsWith RAD5
+CTF8 interactsWith ARP6
+CTF8 interactsWith TOP3
+CTF8 interactsWith YLR235C
+CTF8 interactsWith RAD52
+CTF8 interactsWith GIM5
+CTF8 interactsWith LYS7
+CTF8 interactsWith CSM3
+CTF8 interactsWith BUB2
+CTF8 interactsWith GIM3
+CTF8 interactsWith RAD50
+CTF8 interactsWith TOF1
+CTF8 interactsWith HTZ1
+CTF8 interactsWith ASE1
+CTF8 interactsWith SLK19
+CTF8 interactsWith RAD17
+CTF8 interactsWith CHL1
+CTF8 interactsWith LGE1
+CTF8 interactsWith DDC1
+CTF8 interactsWith VIK1
+CTF8 interactsWith YPR045C
+CTF8 interactsWith CLB2
+CTF18 interactsWith LTE1
+CTF18 interactsWith NUP60
+CTF18 interactsWith MUM2
+CTF18 interactsWith UBC4
+CTF18 interactsWith MRPL36
+CTF18 interactsWith MRC1
+CTF18 interactsWith MRC1
+CTF18 interactsWith RAD57
+CTF18 interactsWith RAD55
+CTF18 interactsWith RAD9
+CTF18 interactsWith GIM4
+CTF18 interactsWith RAD23
+CTF18 interactsWith RAD51
+CTF18 interactsWith SLX8
+CTF18 interactsWith RAD24
+CTF18 interactsWith CDC26
+CTF18 interactsWith MAD1
+CTF18 interactsWith SOH1
+CTF18 interactsWith RAD54
+CTF18 interactsWith YGL217C
+CTF18 interactsWith PAC10
+CTF18 interactsWith BUB1
+CTF18 interactsWith MAD3
+CTF18 interactsWith MAD2
+CTF18 interactsWith HPR5
+CTF18 interactsWith POL32
+CTF18 interactsWith RPS4A
+CTF18 interactsWith ELM1
+CTF18 interactsWith HSL1
+CTF18 interactsWith RAD5
+CTF18 interactsWith ARP6
+CTF18 interactsWith TOP3
+CTF18 interactsWith VPS63
+CTF18 interactsWith RAD52
+CTF18 interactsWith GIM5
+CTF18 interactsWith LYS7
+CTF18 interactsWith CSM3
+CTF18 interactsWith CIK1
+CTF18 interactsWith MRE11
+CTF18 interactsWith GIM3
+CTF18 interactsWith RAD50
+CTF18 interactsWith TOF1
+CTF18 interactsWith MCK1
+CTF18 interactsWith HTZ1
+CTF18 interactsWith BUB3
+CTF18 interactsWith SLK19
+CTF18 interactsWith CIN1
+CTF18 interactsWith CHL1
+CTF18 interactsWith DDC1
+CTF18 interactsWith YPL205C
+CTF18 interactsWith VIK1
+CTF18 interactsWith CLB2
+DCC1 interactsWith LTE1
+DCC1 interactsWith NUP60
+DCC1 interactsWith AOR1
+DCC1 interactsWith MRC1
+DCC1 interactsWith MRC1
+DCC1 interactsWith HEX3
+DCC1 interactsWith RPN4
+DCC1 interactsWith RAD57
+DCC1 interactsWith UME6
+DCC1 interactsWith RAD9
+DCC1 interactsWith RAD23
+DCC1 interactsWith PAC2
+DCC1 interactsWith ISC1
+DCC1 interactsWith RAD51
+DCC1 interactsWith CHD1
+DCC1 interactsWith SSF73
+DCC1 interactsWith MAD1
+DCC1 interactsWith RAD54
+DCC1 interactsWith KEM1
+DCC1 interactsWith RTF1
+DCC1 interactsWith UBR1
+DCC1 interactsWith BUB1
+DCC1 interactsWith RRM3
+DCC1 interactsWith RPN10
+DCC1 interactsWith MAD3
+DCC1 interactsWith MAD2
+DCC1 interactsWith HPR5
+DCC1 interactsWith POL32
+DCC1 interactsWith RPS4A
+DCC1 interactsWith HSL1
+DCC1 interactsWith RAD27
+DCC1 interactsWith YLR235C
+DCC1 interactsWith TSA1
+DCC1 interactsWith RAD52
+DCC1 interactsWith GIM5
+DCC1 interactsWith LYS7
+DCC1 interactsWith CSM3
+DCC1 interactsWith SPT21
+DCC1 interactsWith SGS1
+DCC1 interactsWith CIK1
+DCC1 interactsWith MRE11
+DCC1 interactsWith GIM3
+DCC1 interactsWith RTT106
+DCC1 interactsWith RAD50
+DCC1 interactsWith TOF1
+DCC1 interactsWith HTZ1
+DCC1 interactsWith SLK19
+DCC1 interactsWith CIN1
+DCC1 interactsWith CHL1
+DCC1 interactsWith DDC1
+DCC1 interactsWith CIN2
+DCC1 interactsWith VMA13
+DCC1 interactsWith CLB2
+DCC1 interactsWith CLB5
+DCC1 interactsWith KAR3
+SCC1 interactsWith DCC1
+SCC1 interactsWith MRC1
+SCC1 interactsWith CHL4
+SCC1 interactsWith MCM21
+SCC1 interactsWith CIN8
+SCC1 interactsWith BIM1
+SCC1 interactsWith YGL250W
+SCC1 interactsWith BUB1
+SCC1 interactsWith CTF8
+SCC1 interactsWith MCM22
+SCC1 interactsWith CTF3
+SCC1 interactsWith GIM5
+SCC1 interactsWith CSM3
+SCC1 interactsWith CTF18
+SCC1 interactsWith GIM3
+SCC1 interactsWith TOF1
+SCC1 interactsWith BUB3
+SCC1 interactsWith CHL1
+SCC1 interactsWith YPL017C
+SCC1 interactsWith CTF19
+SCC1 interactsWith MCM16
+SCC1 interactsWith CTF4
+SCC1 interactsWith KAR3
+CHL1 interactsWith MRC1
+CHL1 interactsWith RAD61
+CHL1 interactsWith CHL4
+CHL1 interactsWith MCM21
+CHL1 interactsWith MAD1
+CHL1 interactsWith BUB1
+CHL1 interactsWith MAD3
+CHL1 interactsWith MAD2
+CHL1 interactsWith HPR5
+CHL1 interactsWith MCM22
+CHL1 interactsWith RAD27
+CHL1 interactsWith YKE2
+CHL1 interactsWith NKP2
+CHL1 interactsWith CTF3
+CHL1 interactsWith GIM5
+CHL1 interactsWith GIM3
+CHL1 interactsWith RTS1
+CHL1 interactsWith ELG1
+CHL1 interactsWith CTF19
+CHL1 interactsWith MCM16
+CHL1 interactsWith CLB2
+MAD2 interactsWith IML3
+MAD2 interactsWith SOY
+MAD2 interactsWith HCM1
+MAD2 interactsWith CHL4
+MAD2 interactsWith MCM21
+MAD2 interactsWith VID21
+MAD2 interactsWith GIM4
+MAD2 interactsWith YGL060W
+MAD2 interactsWith PAC10
+MAD2 interactsWith YJL064W
+MAD2 interactsWith MCM22
+MAD2 interactsWith YKE2
+MAD2 interactsWith CTF3
+MAD2 interactsWith GIM5
+MAD2 interactsWith YML095C-A
+MAD2 interactsWith RAS2
+MAD2 interactsWith GIM3
+MAD2 interactsWith HTZ1
+MAD2 interactsWith SLK19
+MAD2 interactsWith CIN1
+MAD2 interactsWith YPL017C
+MAD2 interactsWith CTF19
+MAD2 interactsWith MCM16
+YKE2 interactsWith VPS8
+YKE2 interactsWith SSA1
+YKE2 interactsWith SWC1
+YKE2 interactsWith YAL042C-a
+YKE2 interactsWith SLA1
+YKE2 interactsWith HAP3
+YKE2 interactsWith NCL1
+YKE2 interactsWith PIN4
+YKE2 interactsWith SIF2
+YKE2 interactsWith IML3
+YKE2 interactsWith RAD16
+YKE2 interactsWith CBP6
+YKE2 interactsWith SEC66
+YKE2 interactsWith PCH2
+YKE2 interactsWith BEM1
+YKE2 interactsWith AOR1
+YKE2 interactsWith YBR255W
+YKE2 interactsWith DCC1
+YKE2 interactsWith SNT1
+YKE2 interactsWith CSM1
+YKE2 interactsWith RPN4
+YKE2 interactsWith YDL033C
+YKE2 interactsWith CLB3
+YKE2 interactsWith MKC7
+YKE2 interactsWith YDR149C
+YKE2 interactsWith CPR1
+YKE2 interactsWith PLP1
+YKE2 interactsWith CHL4
+YKE2 interactsWith PMP3
+YKE2 interactsWith RTT103
+YKE2 interactsWith SSD1
+YKE2 interactsWith SUM1
+YKE2 interactsWith MCM21
+YKE2 interactsWith SWR1
+YKE2 interactsWith YDR360W
+YKE2 interactsWith VPS72
+YKE2 interactsWith SPF1
+YKE2 interactsWith YEL041W
+YKE2 interactsWith MAK10
+YKE2 interactsWith HAT2
+YKE2 interactsWith ISC1
+YKE2 interactsWith BEM2
+YKE2 interactsWith FAB1
+YKE2 interactsWith MAD1
+YKE2 interactsWith MMS2
+YKE2 interactsWith KEM1
+YKE2 interactsWith HOS2
+YKE2 interactsWith HAP2
+YKE2 interactsWith YGL242C
+YKE2 interactsWith HXK2
+YKE2 interactsWith UGA1
+YKE2 interactsWith SHY1
+YKE2 interactsWith BUB1
+YKE2 interactsWith YTA7
+YKE2 interactsWith VPS29
+YKE2 interactsWith SLT2
+YKE2 interactsWith UBA4
+YKE2 interactsWith WSS1
+YKE2 interactsWith STB5
+YKE2 interactsWith CTF8
+YKE2 interactsWith URM1
+YKE2 interactsWith CAP2
+YKE2 interactsWith SDS3
+YKE2 interactsWith PRK1
+YKE2 interactsWith MAD3
+YKE2 interactsWith BBC1
+YKE2 interactsWith BCK1
+YKE2 interactsWith MNN11
+YKE2 interactsWith RPS22A
+YKE2 interactsWith CPR7
+YKE2 interactsWith HOC1
+YKE2 interactsWith STE24
+YKE2 interactsWith MCM22
+YKE2 interactsWith PAN3
+YKE2 interactsWith ELM1
+YKE2 interactsWith YKL118W
+YKE2 interactsWith YLL049W
+YKE2 interactsWith ARP6
+YKE2 interactsWith YLR089C
+YKE2 interactsWith EST1
+YKE2 interactsWith TOP3
+YKE2 interactsWith SEC72
+YKE2 interactsWith VRP1
+YKE2 interactsWith CTF3
+YKE2 interactsWith VAC14
+YKE2 interactsWith PPZ1
+YKE2 interactsWith RAD52
+YKE2 interactsWith VPS71
+YKE2 interactsWith MAC1
+YKE2 interactsWith BUB2
+YKE2 interactsWith CTF18
+YKE2 interactsWith MYO5
+YKE2 interactsWith RIM13
+YKE2 interactsWith RSN1
+YKE2 interactsWith ELP6
+YKE2 interactsWith PET8
+YKE2 interactsWith YNL140C
+YKE2 interactsWith CAF40
+YKE2 interactsWith RIM21
+YKE2 interactsWith CLA4
+YKE2 interactsWith HTZ1
+YKE2 interactsWith AHC1
+YKE2 interactsWith BUB3
+YKE2 interactsWith ASE1
+YKE2 interactsWith RGA1
+YKE2 interactsWith RUD3
+YKE2 interactsWith DSE3
+YKE2 interactsWith PNT1
+YKE2 interactsWith YOR296W
+YKE2 interactsWith CIN1
+YKE2 interactsWith MNE1
+YKE2 interactsWith HAP5
+YKE2 interactsWith YPL017C
+YKE2 interactsWith CTF19
+YKE2 interactsWith SET6
+YKE2 interactsWith CBP3
+YKE2 interactsWith VIK1
+YKE2 interactsWith EAF3
+YKE2 interactsWith MCM16
+YKE2 interactsWith MED1
+YKE2 interactsWith CTF4
+PAC10 interactsWith VPS8
+PAC10 interactsWith SWC1
+PAC10 interactsWith DRS2
+PAC10 interactsWith BUD14
+PAC10 interactsWith SLA1
+PAC10 interactsWith NCL1
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+PAC10 interactsWith YBR108W
+PAC10 interactsWith RAD16
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+PAC10 interactsWith AOR1
+PAC10 interactsWith YBR255W
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+PAC10 interactsWith CSM1
+PAC10 interactsWith RPN4
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+PAC10 interactsWith YDR360W
+PAC10 interactsWith VPS72
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+PAC10 interactsWith STE24
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+GIM3 interactsWith PLP1
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+GIM3 interactsWith SSD1
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+GIM3 interactsWith STB5
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+GIM3 interactsWith PAN3
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+GIM3 interactsWith RIM13
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+GIM3 interactsWith CIN1
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+GIM3 interactsWith YPL017C
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+GIM3 interactsWith VIK1
+GIM3 interactsWith EAF3
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+GIM4 interactsWith SWC1
+GIM4 interactsWith SLA1
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+GIM4 interactsWith PIN4
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+GIM4 interactsWith IML3
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+GIM4 interactsWith AOR1
+GIM4 interactsWith DCC1
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+GIM4 interactsWith CSM1
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+GIM4 interactsWith CLB3
+GIM4 interactsWith YDR149C
+GIM4 interactsWith CPR1
+GIM4 interactsWith CHL4
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+GIM4 interactsWith ISC1
+GIM4 interactsWith PEA2
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+GIM4 interactsWith BUB1
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+GIM4 interactsWith HSE1
+GIM4 interactsWith VPS29
+GIM4 interactsWith UBA4
+GIM4 interactsWith CAP2
+GIM4 interactsWith SDS3
+GIM4 interactsWith PRK1
+GIM4 interactsWith MAD3
+GIM4 interactsWith BBC1
+GIM4 interactsWith MNN11
+GIM4 interactsWith RPS22A
+GIM4 interactsWith CPR7
+GIM4 interactsWith HOC1
+GIM4 interactsWith STE24
+GIM4 interactsWith YJR129C
+GIM4 interactsWith MCM22
+GIM4 interactsWith PAN3
+GIM4 interactsWith ELM1
+GIM4 interactsWith YKL118W
+GIM4 interactsWith DNM1
+GIM4 interactsWith MMM1
+GIM4 interactsWith YLL007C
+GIM4 interactsWith YLL049W
+GIM4 interactsWith YLR089C
+GIM4 interactsWith SEC72
+GIM4 interactsWith VRP1
+GIM4 interactsWith CTF3
+GIM4 interactsWith VAC14
+GIM4 interactsWith VMA6
+GIM4 interactsWith RAD52
+GIM4 interactsWith VPS71
+GIM4 interactsWith RAD10
+GIM4 interactsWith MSC1
+GIM4 interactsWith BUB2
+GIM4 interactsWith MYO5
+GIM4 interactsWith RIM13
+GIM4 interactsWith ELP6
+GIM4 interactsWith YNL140C
+GIM4 interactsWith RIM21
+GIM4 interactsWith CLA4
+GIM4 interactsWith HTZ1
+GIM4 interactsWith MSN1
+GIM4 interactsWith AHC1
+GIM4 interactsWith BUB3
+GIM4 interactsWith RGA1
+GIM4 interactsWith RUD3
+GIM4 interactsWith DSE3
+GIM4 interactsWith PNT1
+GIM4 interactsWith CIN1
+GIM4 interactsWith HAP5
+GIM4 interactsWith CHL1
+GIM4 interactsWith YPL017C
+GIM4 interactsWith CTF19
+GIM4 interactsWith BEM4
+GIM4 interactsWith MMT2
+GIM4 interactsWith VIK1
+GIM4 interactsWith EAF3
+GIM4 interactsWith MCM16
+GIM4 interactsWith YPR050C
+GIM4 interactsWith MED1
+GIM5 interactsWith VPS8
+GIM5 interactsWith SWC1
+GIM5 interactsWith DRS2
+GIM5 interactsWith SLA1
+GIM5 interactsWith NCL1
+GIM5 interactsWith PIN4
+GIM5 interactsWith SIF2
+GIM5 interactsWith IML3
+GIM5 interactsWith YBR108W
+GIM5 interactsWith SEC66
+GIM5 interactsWith AOR1
+GIM5 interactsWith YBR255W
+GIM5 interactsWith BSD2
+GIM5 interactsWith CSM1
+GIM5 interactsWith RPN4
+GIM5 interactsWith CLB3
+GIM5 interactsWith MKC7
+GIM5 interactsWith YDR149C
+GIM5 interactsWith PLP1
+GIM5 interactsWith CHL4
+GIM5 interactsWith PMP3
+GIM5 interactsWith SSD1
+GIM5 interactsWith SUM1
+GIM5 interactsWith MCM21
+GIM5 interactsWith SWR1
+GIM5 interactsWith YDR360W
+GIM5 interactsWith VPS72
+GIM5 interactsWith SPF1
+GIM5 interactsWith MAK10
+GIM5 interactsWith KAP123
+GIM5 interactsWith BEM2
+GIM5 interactsWith BMH1
+GIM5 interactsWith FAB1
+GIM5 interactsWith MAD1
+GIM5 interactsWith MMS2
+GIM5 interactsWith MON1
+GIM5 interactsWith NUT1
+GIM5 interactsWith KEM1
+GIM5 interactsWith HOS2
+GIM5 interactsWith HXK2
+GIM5 interactsWith UGA1
+GIM5 interactsWith YGR054W
+GIM5 interactsWith BUB1
+GIM5 interactsWith SMI1
+GIM5 interactsWith YTA7
+GIM5 interactsWith YHL029C
+GIM5 interactsWith VPS29
+GIM5 interactsWith SLT2
+GIM5 interactsWith UBA4
+GIM5 interactsWith BZZ1
+GIM5 interactsWith WSS1
+GIM5 interactsWith STB5
+GIM5 interactsWith URM1
+GIM5 interactsWith CAP2
+GIM5 interactsWith PRK1
+GIM5 interactsWith MAD3
+GIM5 interactsWith BCK1
+GIM5 interactsWith VPS35
+GIM5 interactsWith RPS22A
+GIM5 interactsWith CPR7
+GIM5 interactsWith HOC1
+GIM5 interactsWith STE24
+GIM5 interactsWith MCM22
+GIM5 interactsWith PAN3
+GIM5 interactsWith ELM1
+GIM5 interactsWith YKL118W
+GIM5 interactsWith DNM1
+GIM5 interactsWith MMM1
+GIM5 interactsWith YLL007C
+GIM5 interactsWith YLL049W
+GIM5 interactsWith YLR089C
+GIM5 interactsWith SEC72
+GIM5 interactsWith VRP1
+GIM5 interactsWith VPS38
+GIM5 interactsWith CTF3
+GIM5 interactsWith VAC14
+GIM5 interactsWith VMA6
+GIM5 interactsWith RAD52
+GIM5 interactsWith VPS71
+GIM5 interactsWith GSF2
+GIM5 interactsWith MSC1
+GIM5 interactsWith MAC1
+GIM5 interactsWith BUB2
+GIM5 interactsWith MYO5
+GIM5 interactsWith SAS2
+GIM5 interactsWith RIM13
+GIM5 interactsWith HOT1
+GIM5 interactsWith RSN1
+GIM5 interactsWith ELP6
+GIM5 interactsWith YNL140C
+GIM5 interactsWith BNI5
+GIM5 interactsWith CAF40
+GIM5 interactsWith RIM21
+GIM5 interactsWith HTZ1
+GIM5 interactsWith RTG1
+GIM5 interactsWith MSN1
+GIM5 interactsWith AHC1
+GIM5 interactsWith BUB3
+GIM5 interactsWith VPS17
+GIM5 interactsWith RUD3
+GIM5 interactsWith DSE3
+GIM5 interactsWith PNT1
+GIM5 interactsWith CIN1
+GIM5 interactsWith YPL017C
+GIM5 interactsWith CTF19
+GIM5 interactsWith BEM3
+GIM5 interactsWith YPL176C
+GIM5 interactsWith VIK1
+GIM5 interactsWith EAF3
+GIM5 interactsWith MCM16
+GIM5 interactsWith YPR050C
+GIM5 interactsWith MAK3
+GIM5 interactsWith MED1
+CSM3 interactsWith MRC1
+CSM3 interactsWith RAD57
+CSM3 interactsWith RAD9
+CSM3 interactsWith GIM4
+CSM3 interactsWith ISC1
+CSM3 interactsWith SLX8
+CSM3 interactsWith RAD4
+CSM3 interactsWith RAD24
+CSM3 interactsWith CDH1
+CSM3 interactsWith MAD1
+CSM3 interactsWith PAC10
+CSM3 interactsWith BUB1
+CSM3 interactsWith APQ12
+CSM3 interactsWith HPR5
+CSM3 interactsWith POL32
+CSM3 interactsWith CSN12
+CSM3 interactsWith RAD5
+CSM3 interactsWith YKE2
+CSM3 interactsWith TOP3
+CSM3 interactsWith MEC3
+CSM3 interactsWith SEL1
+CSM3 interactsWith GIM5
+CSM3 interactsWith YMR010W
+CSM3 interactsWith BUB2
+CSM3 interactsWith GIM3
+CSM3 interactsWith MON2
+CSM3 interactsWith BRE5
+CSM3 interactsWith ELG1
+CSM3 interactsWith RAD17
+CSM3 interactsWith YPL077C
+CSM3 interactsWith GUP2
+CSM3 interactsWith DDC1
+MRC1 interactsWith NUP60
+MRC1 interactsWith PHO5
+MRC1 interactsWith RAD9
+MRC1 interactsWith XRS2
+MRC1 interactsWith RAD51
+MRC1 interactsWith RAD24
+MRC1 interactsWith SOH1
+MRC1 interactsWith RRM3
+MRC1 interactsWith HPR5
+MRC1 interactsWith POL32
+MRC1 interactsWith RAD27
+MRC1 interactsWith RAD52
+MRC1 interactsWith CSM3
+MRC1 interactsWith SGS1
+MRC1 interactsWith CIK1
+MRC1 interactsWith RAD50
+MRC1 interactsWith TOF1
+MRC1 interactsWith HTZ1
+MRC1 interactsWith YOR024W
+MRC1 interactsWith HST3
+MRC1 interactsWith ELG1
+MRC1 interactsWith RAD17
+MRC1 interactsWith DDC1
+TOF1 interactsWith NUP60
+TOF1 interactsWith UMP1
+TOF1 interactsWith RAD55
+TOF1 interactsWith RAD9
+TOF1 interactsWith IPK1
+TOF1 interactsWith RAD23
+TOF1 interactsWith RAD24
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+TOF1 interactsWith RAD5
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+ELG1 interactsWith YBR094W
+ELG1 interactsWith MMS4
+ELG1 interactsWith YBR099C
+ELG1 interactsWith MMS4
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+ELG1 interactsWith HPR5
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+ELG1 interactsWith RAD52
+ELG1 interactsWith SGS1
+ELG1 interactsWith MRE11
+ELG1 interactsWith RAD50
+ELG1 interactsWith MID1
+ELG1 interactsWith BRE5
+ELG1 interactsWith KAR3
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+POL32 interactsWith MRC1
+POL32 interactsWith RAD55
+POL32 interactsWith RAD9
+POL32 interactsWith MNN10
+POL32 interactsWith VID21
+POL32 interactsWith XRS2
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+POL32 interactsWith UBP3
+POL32 interactsWith RAD24
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+POL32 interactsWith ARC18
+POL32 interactsWith RAD52
+POL32 interactsWith YDJ1
+POL32 interactsWith RAD50
+POL32 interactsWith RAD17
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+POL32 interactsWith DDC1
+TOP1 interactsWith MMS4
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+TOP1 interactsWith YDR249C
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+TOP1 interactsWith MRE11
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+TOP1 interactsWith HMS1
+TOP1 interactsWith EXO1
+TOP1 interactsWith YOR044W
+TOP1 interactsWith TOM6
+TOP1 interactsWith NCE4
+TOP1 interactsWith MCM16
+CDC2 interactsWith YBR094W
+CDC2 interactsWith MMS4
+CDC2 interactsWith MRC1
+CDC2 interactsWith RAD57
+CDC2 interactsWith RAD24
+CDC2 interactsWith UBP6
+CDC2 interactsWith POL32
+CDC2 interactsWith CSM3
+CDC2 interactsWith YMR075C-A
+CDC2 interactsWith GAS1
+CDC2 interactsWith TOF1
+CDC2 interactsWith MID1
+CDC2 interactsWith MCK1
+CDC2 interactsWith TRM10
+CDC2 interactsWith RAD17
+CDC2 interactsWith DDC1
+CDC45 interactsWith LTE1
+CDC45 interactsWith HIR1
+CDC45 interactsWith CSS2
+CDC45 interactsWith MMS4
+CDC45 interactsWith MSI1
+CDC45 interactsWith HPC2
+CDC45 interactsWith AOR1
+CDC45 interactsWith CHK1
+CDC45 interactsWith YBR277C
+CDC45 interactsWith DPB3
+CDC45 interactsWith DCC1
+CDC45 interactsWith MRC1
+CDC45 interactsWith PAT1
+CDC45 interactsWith CSM1
+CDC45 interactsWith NHP10
+CDC45 interactsWith FYV3
+CDC45 interactsWith RAD57
+CDC45 interactsWith DPB4
+CDC45 interactsWith SWI5
+CDC45 interactsWith RAD9
+CDC45 interactsWith RTT103
+CDC45 interactsWith XRS2
+CDC45 interactsWith VPS72
+CDC45 interactsWith GIM4
+CDC45 interactsWith HAT2
+CDC45 interactsWith NPR2
+CDC45 interactsWith SWI4
+CDC45 interactsWith SPT2
+CDC45 interactsWith RAD24
+CDC45 interactsWith FAB1
+CDC45 interactsWith MAD1
+CDC45 interactsWith SOH1
+CDC45 interactsWith ARO2
+CDC45 interactsWith NUT1
+CDC45 interactsWith RAD54
+CDC45 interactsWith KEM1
+CDC45 interactsWith RTF1
+CDC45 interactsWith RMD11
+CDC45 interactsWith RRM3
+CDC45 interactsWith VMA10
+CDC45 interactsWith STB5
+CDC45 interactsWith CTF8
+CDC45 interactsWith APQ12
+CDC45 interactsWith IMP2'
+CDC45 interactsWith MAD2
+CDC45 interactsWith HPR5
+CDC45 interactsWith ASF1
+CDC45 interactsWith LSM1
+CDC45 interactsWith POL32
+CDC45 interactsWith BFA1
+CDC45 interactsWith YJR070C
+CDC45 interactsWith SOD1
+CDC45 interactsWith HIR3
+CDC45 interactsWith SIS2
+CDC45 interactsWith RTT109
+CDC45 interactsWith SPT8
+CDC45 interactsWith TOP3
+CDC45 interactsWith YLR235C
+CDC45 interactsWith SEC22
+CDC45 interactsWith MEC3
+CDC45 interactsWith RAD52
+CDC45 interactsWith GIM5
+CDC45 interactsWith SUB1
+CDC45 interactsWith CSM3
+CDC45 interactsWith BUB2
+CDC45 interactsWith CTF18
+CDC45 interactsWith YMR166C
+CDC45 interactsWith SCS7
+CDC45 interactsWith IES2
+CDC45 interactsWith TOF1
+CDC45 interactsWith RIM21
+CDC45 interactsWith TRF5
+CDC45 interactsWith TOP1
+CDC45 interactsWith HTZ1
+CDC45 interactsWith MET22
+CDC45 interactsWith YOR024W
+CDC45 interactsWith HST3
+CDC45 interactsWith DFG16
+CDC45 interactsWith HIR2
+CDC45 interactsWith WHI2
+CDC45 interactsWith LEO1
+CDC45 interactsWith RAD17
+CDC45 interactsWith HAT1
+CDC45 interactsWith NCE4
+CDC45 interactsWith LGE1
+CDC45 interactsWith GON5
+CDC45 interactsWith DDC1
+CDC45 interactsWith BRR1
+CDC45 interactsWith MED1
+CDC45 interactsWith CLB5
+CDC45 interactsWith CTF4
+CDC45 interactsWith KAR3
+CDC7 interactsWith HIR1
+CDC7 interactsWith CHK1
+CDC7 interactsWith DCC1
+CDC7 interactsWith RPS14A
+CDC7 interactsWith FEN1
+CDC7 interactsWith FYV3
+CDC7 interactsWith RAD9
+CDC7 interactsWith ESC2
+CDC7 interactsWith RAD24
+CDC7 interactsWith CKB1
+CDC7 interactsWith MAD1
+CDC7 interactsWith YGL250W
+CDC7 interactsWith RTT107
+CDC7 interactsWith CTF8
+CDC7 interactsWith CKA1
+CDC7 interactsWith MAD2
+CDC7 interactsWith LAS21
+CDC7 interactsWith TIF2
+CDC7 interactsWith CPR7
+CDC7 interactsWith BFA1
+CDC7 interactsWith YJR070C
+CDC7 interactsWith HIR3
+CDC7 interactsWith YKL056C
+CDC7 interactsWith HSL1
+CDC7 interactsWith TIF1
+CDC7 interactsWith SPT8
+CDC7 interactsWith TOP3
+CDC7 interactsWith YLR235C
+CDC7 interactsWith MEC3
+CDC7 interactsWith ORM2
+CDC7 interactsWith TSR2
+CDC7 interactsWith PPZ1
+CDC7 interactsWith RAD52
+CDC7 interactsWith BUB2
+CDC7 interactsWith CTF18
+CDC7 interactsWith MUB1
+CDC7 interactsWith MLH1
+CDC7 interactsWith SGS1
+CDC7 interactsWith IRA2
+CDC7 interactsWith STI1
+CDC7 interactsWith CKB2
+CDC7 interactsWith PDE2
+CDC7 interactsWith RAD17
+CDC7 interactsWith DDC1
+CDC7 interactsWith CLB2
+DBF4 interactsWith HIR1
+DBF4 interactsWith HPC2
+DBF4 interactsWith CHK1
+DBF4 interactsWith DCC1
+DBF4 interactsWith RPS14A
+DBF4 interactsWith YDL062W
+DBF4 interactsWith RAD9
+DBF4 interactsWith ESC2
+DBF4 interactsWith RAD24
+DBF4 interactsWith BMH1
+DBF4 interactsWith RSM23
+DBF4 interactsWith KEM1
+DBF4 interactsWith PAC10
+DBF4 interactsWith BUB1
+DBF4 interactsWith RTT107
+DBF4 interactsWith STB5
+DBF4 interactsWith CTF8
+DBF4 interactsWith MET18
+DBF4 interactsWith HIR3
+DBF4 interactsWith TIF1
+DBF4 interactsWith TOP3
+DBF4 interactsWith YLR235C
+DBF4 interactsWith MEC3
+DBF4 interactsWith MMS22
+DBF4 interactsWith GIM5
+DBF4 interactsWith VAN1
+DBF4 interactsWith GIM3
+DBF4 interactsWith IRA2
+DBF4 interactsWith STI1
+DBF4 interactsWith RAD17
+DBF4 interactsWith NCE4
+DBF4 interactsWith CTF4
+DDC1 interactsWith YDL033C
+DDC1 interactsWith HTA1
+DDC1 interactsWith LYS7
+DDC1 interactsWith CLA4
+DDC1 interactsWith HXT17
+DDC1 interactsWith YME1
+DDC1 interactsWith KAR3
+RAD9 interactsWith MRC1
+RAD9 interactsWith YDL162C
+RAD9 interactsWith YHL029C
+RAD9 interactsWith SEC22
+RAD9 interactsWith GIM3
+RAD24 interactsWith MRC1
+RAD24 interactsWith SOD1
+RAD24 interactsWith DOA1
+RAD50 interactsWith DEP1
+RAD50 interactsWith NUP60
+RAD50 interactsWith SWD1
+RAD50 interactsWith SWD3
+RAD50 interactsWith DCC1
+RAD50 interactsWith MRC1
+RAD50 interactsWith CSM1
+RAD50 interactsWith BRE1
+RAD50 interactsWith YDL162C
+RAD50 interactsWith SWM1
+RAD50 interactsWith RNH202
+RAD50 interactsWith ESC2
+RAD50 interactsWith NPR2
+RAD50 interactsWith BIM1
+RAD50 interactsWith UBP6
+RAD50 interactsWith SLT2
+RAD50 interactsWith RRM3
+RAD50 interactsWith RTT107
+RAD50 interactsWith RTT101
+RAD50 interactsWith BCK1
+RAD50 interactsWith ASF1
+RAD50 interactsWith HSL1
+RAD50 interactsWith BRE2
+RAD50 interactsWith RAD5
+RAD50 interactsWith VID22
+RAD50 interactsWith TSA1
+RAD50 interactsWith YML095C-A
+RAD50 interactsWith VAN1
+RAD50 interactsWith LYS7
+RAD50 interactsWith MLS1
+RAD50 interactsWith MID1
+RAD50 interactsWith CLA4
+RAD50 interactsWith RLF2
+RAD50 interactsWith CLB2
+RAD50 interactsWith CTF4
+RAD52 interactsWith UMP1
+RAD52 interactsWith SIT4
+RAD52 interactsWith YDL162C
+RAD52 interactsWith PMR1
+RAD52 interactsWith HUR1
+RAD52 interactsWith KEM1
+RAD52 interactsWith LYS7
+CDC8 interactsWith MMS4
+CDC8 interactsWith MRC1
+CDC8 interactsWith CSM1
+CDC8 interactsWith YDR438W
+CDC8 interactsWith ECM11
+CDC8 interactsWith PPN1
+CDC8 interactsWith TSA2
+CDC8 interactsWith YDR458C
+CDC8 interactsWith PKH1
+CDC8 interactsWith BCK2
+CDC8 interactsWith RAD24
+CDC8 interactsWith SWF3
+CDC8 interactsWith KEM1
+CDC8 interactsWith STB5
+CDC8 interactsWith PET191
+CDC8 interactsWith IXR1
+CDC8 interactsWith YKL098W
+CDC8 interactsWith RAD27
+CDC8 interactsWith APN1
+CDC8 interactsWith TOP3
+CDC8 interactsWith YLR235C
+CDC8 interactsWith SEC22
+CDC8 interactsWith SGS1
+CDC8 interactsWith CIK1
+CDC8 interactsWith MGS1
+CDC8 interactsWith URE2
+CDC8 interactsWith ZWF1
+CDC8 interactsWith TRF5
+CDC8 interactsWith ISW2
+CDC8 interactsWith DDC1
+MMS4 interactsWith ESC2
+MMS4 interactsWith XRS2
+MMS4 interactsWith RAD27
+MMS4 interactsWith TOP3
+MMS4 interactsWith YLR235C
+MMS4 interactsWith VID22
+MMS4 interactsWith NCE4
+MUS81 interactsWith RAD27
+MUS81 interactsWith TOP3
+MUS81 interactsWith YLR235C
+MUS81 interactsWith VID22
+MUS81 interactsWith NCE4
+YBR094w interactsWith SOY
+YBR094w interactsWith CSM1
+YBR094w interactsWith YDL162C
+YBR094w interactsWith ESC2
+YBR094w interactsWith ISC1
+YBR094w interactsWith YEN1
+YBR094w interactsWith SOH1
+YBR094w interactsWith ASF1
+YBR094w interactsWith POL32
+YBR094w interactsWith TOP3
+YBR094w interactsWith VID22
+YBR094w interactsWith TSA1
+YBR094w interactsWith LYS7
+YBR094w interactsWith GIM3
+YBR094w interactsWith MON2
+YBR094w interactsWith RRP6
+YBR094w interactsWith NCE4
+HST1 interactsWith ESC2
+HST1 interactsWith WHI2
+HST3 interactsWith MRC1
+HST3 interactsWith HST4
+HST3 interactsWith POL32
+HST3 interactsWith YLR235C
+HST3 interactsWith YML095C-A
+HST3 interactsWith SGS1
+HST3 interactsWith CIK1
+HST3 interactsWith YOR082C
+ESC2 interactsWith NUP60
+ESC2 interactsWith SWD1
+ESC2 interactsWith YBR099C
+ESC2 interactsWith YBR174C
+ESC2 interactsWith SLX1
+ESC2 interactsWith SRO9
+ESC2 interactsWith RPN4
+ESC2 interactsWith RNH202
+ESC2 interactsWith MUS81
+ESC2 interactsWith UBP6
+ESC2 interactsWith YGR071C
+ESC2 interactsWith UPF3
+ESC2 interactsWith RRM3
+ESC2 interactsWith NMD2
+ESC2 interactsWith WSS1
+ESC2 interactsWith THP2
+ESC2 interactsWith RPL34B
+ESC2 interactsWith HPR5
+ESC2 interactsWith SWI3
+ESC2 interactsWith POL32
+ESC2 interactsWith HIR3
+ESC2 interactsWith SLX4
+ESC2 interactsWith RNH203
+ESC2 interactsWith YLR235C
+ESC2 interactsWith VID22
+ESC2 interactsWith YLR374C
+ESC2 interactsWith MSC1
+ESC2 interactsWith NAM7
+ESC2 interactsWith RNH35
+ESC2 interactsWith INP52
+ESC2 interactsWith MGS1
+ESC2 interactsWith TOP1
+ESC2 interactsWith SKI7
+ESC2 interactsWith LEO1
+ESC2 interactsWith RIS1
+ESC2 interactsWith PUS7
+ESC2 interactsWith NCE4
+ESC2 interactsWith SUR1
+ESC2 interactsWith RPL21B
+RTT107 interactsWith RMD7
+RTT107 interactsWith PMR1
+RTT107 interactsWith HUR1
+RTT107 interactsWith RRM3
+RTT107 interactsWith ZAP1
+RTT107 interactsWith SOD1
+RTT107 interactsWith TOP3
+RTT107 interactsWith YLR235C
+RTT107 interactsWith VID22
+RTT107 interactsWith IMP2
+RTT107 interactsWith GAL11
+RTT107 interactsWith NCE4
+RAS2 interactsWith PDR17
+RAS2 interactsWith RAS1
+RAS2 interactsWith YNL063W
+RAS2 interactsWith COX16
+ALG6 interactsWith PMT2
+ALG6 interactsWith PMT1
+ALG6 interactsWith YDL096C
+ALG6 interactsWith RPO41
+ALG6 interactsWith OST5
+ALG6 interactsWith OST3
+CHS1 interactsWith DEP1
+CHS1 interactsWith PEX22
+CHS1 interactsWith ECM21
+CHS1 interactsWith PHO5
+CHS1 interactsWith GRS1
+CHS1 interactsWith TYR1
+CHS1 interactsWith YBR209W
+CHS1 interactsWith FIG2
+CHS1 interactsWith YDL206W
+CHS1 interactsWith HBT1
+CHS1 interactsWith YDR248C
+CHS1 interactsWith PMP3
+CHS1 interactsWith YDR314C
+CHS1 interactsWith IPK1
+CHS1 interactsWith SPF1
+CHS1 interactsWith YEL033W
+CHS1 interactsWith PEA2
+CHS1 interactsWith PDA1
+CHS1 interactsWith YFR045W
+CHS1 interactsWith YGL081W
+CHS1 interactsWith CUE3
+CHS1 interactsWith EMP24
+CHS1 interactsWith HAP2
+CHS1 interactsWith VPS29
+CHS1 interactsWith YIL110W
+CHS1 interactsWith BCK1
+CHS1 interactsWith RPE1
+CHS1 interactsWith RPA34
+CHS1 interactsWith VPS35
+CHS1 interactsWith ELO1
+CHS1 interactsWith NUC1
+CHS1 interactsWith HXT8
+CHS1 interactsWith HIT1
+CHS1 interactsWith CNB1
+CHS1 interactsWith UTH1
+CHS1 interactsWith FPS1
+CHS1 interactsWith PDC1
+CHS1 interactsWith BUD20
+CHS1 interactsWith ARC18
+CHS1 interactsWith SKI2
+CHS1 interactsWith YMR003W
+CHS1 interactsWith PKR1
+CHS1 interactsWith PFK2
+CHS1 interactsWith MRE11
+CHS1 interactsWith YNL087W
+CHS1 interactsWith YNL171C
+CHS1 interactsWith YNL179C
+CHS1 interactsWith YNL200C
+CHS1 interactsWith PSY2
+CHS1 interactsWith SPS19
+CHS1 interactsWith YNL203C
+CHS1 interactsWith SPS18
+CHS1 interactsWith YNL228W
+CHS1 interactsWith PDR16
+CHS1 interactsWith YNL235C
+CHS1 interactsWith PEX6
+CHS1 interactsWith MDM38
+CHS1 interactsWith WHI2
+CHS1 interactsWith VPS5
+CHS1 interactsWith VPS17
+CHS1 interactsWith YOR322C
+CHS1 interactsWith LGE1
+CHS1 interactsWith BEM4
+CHS1 interactsWith PRM3
+CHS1 interactsWith LEA1
+CHS1 interactsWith CLN2
+CHS1 interactsWith YPL261C
+CHS1 interactsWith YME1
+CHS1 interactsWith YPR053C
+CHS3 interactsWith SLA1
+CHS3 interactsWith EDE1
+CHS3 interactsWith RPS8A
+CHS3 interactsWith MNN2
+CHS3 interactsWith MUM2
+CHS3 interactsWith YBR077C
+CHS3 interactsWith YDL032W
+CHS3 interactsWith YDL033C
+CHS3 interactsWith HBT1
+CHS3 interactsWith SAC6
+CHS3 interactsWith MNN10
+CHS3 interactsWith RVS167
+CHS3 interactsWith IES6
+CHS3 interactsWith SWI4
+CHS3 interactsWith FAB1
+CHS3 interactsWith CDC26
+CHS3 interactsWith GUP1
+CHS3 interactsWith EMP24
+CHS3 interactsWith VAM7
+CHS3 interactsWith DOC1
+CHS3 interactsWith PRE9
+CHS3 interactsWith SMI1
+CHS3 interactsWith BCK1
+CHS3 interactsWith RPA34
+CHS3 interactsWith OPI3
+CHS3 interactsWith ILM1
+CHS3 interactsWith VPS24
+CHS3 interactsWith MST1
+CHS3 interactsWith VPS67
+CHS3 interactsWith UBI4
+CHS3 interactsWith CSF1
+CHS3 interactsWith CCW12
+CHS3 interactsWith YLR111W
+CHS3 interactsWith VRP1
+CHS3 interactsWith KRE21
+CHS3 interactsWith FKS1
+CHS3 interactsWith ARC18
+CHS3 interactsWith VAN1
+CHS3 interactsWith TOM37
+CHS3 interactsWith YTA12
+CHS3 interactsWith ASC1
+CHS3 interactsWith GAS1
+CHS3 interactsWith TPM1
+CHS3 interactsWith YNL171C
+CHS3 interactsWith BRE5
+CHS3 interactsWith SHE4
+CHS3 interactsWith RPL20B
+CHS3 interactsWith LGE1
+CHS3 interactsWith BTS1
+CHS5 interactsWith SLA1
+CHS5 interactsWith EDE1
+CHS5 interactsWith RPS8A
+CHS5 interactsWith ECM21
+CHS5 interactsWith GRS1
+CHS5 interactsWith AOR1
+CHS5 interactsWith DAN3
+CHS5 interactsWith RVS161
+CHS5 interactsWith PAT1
+CHS5 interactsWith YDL033C
+CHS5 interactsWith BRE1
+CHS5 interactsWith CLB3
+CHS5 interactsWith YDL206W
+CHS5 interactsWith SAC6
+CHS5 interactsWith MNN10
+CHS5 interactsWith LSM6
+CHS5 interactsWith SHE9
+CHS5 interactsWith DOT1
+CHS5 interactsWith SWI4
+CHS5 interactsWith PEA2
+CHS5 interactsWith FAB1
+CHS5 interactsWith YFR045W
+CHS5 interactsWith YGL081W
+CHS5 interactsWith GUP1
+CHS5 interactsWith YGL152C
+CHS5 interactsWith PEX14
+CHS5 interactsWith EMP24
+CHS5 interactsWith PRE9
+CHS5 interactsWith SMI1
+CHS5 interactsWith HSE1
+CHS5 interactsWith CTK2
+CHS5 interactsWith BCK1
+CHS5 interactsWith RPA34
+CHS5 interactsWith SWI3
+CHS5 interactsWith MNN11
+CHS5 interactsWith RPL14A
+CHS5 interactsWith UFD4
+CHS5 interactsWith IXR1
+CHS5 interactsWith VPS24
+CHS5 interactsWith SMY1
+CHS5 interactsWith VPS67
+CHS5 interactsWith NUP133
+CHS5 interactsWith UBI4
+CHS5 interactsWith FPS1
+CHS5 interactsWith CSF1
+CHS5 interactsWith CCW12
+CHS5 interactsWith YLR111W
+CHS5 interactsWith SEC22
+CHS5 interactsWith FKS1
+CHS5 interactsWith ARC18
+CHS5 interactsWith TUS1
+CHS5 interactsWith VAN1
+CHS5 interactsWith ASC1
+CHS5 interactsWith MRE11
+CHS5 interactsWith GAS1
+CHS5 interactsWith PET8
+CHS5 interactsWith LAT1
+CHS5 interactsWith TPM1
+CHS5 interactsWith YNL171C
+CHS5 interactsWith COQ2
+CHS5 interactsWith MDM12
+CHS5 interactsWith IRA2
+CHS5 interactsWith VPS21
+CHS5 interactsWith PDE2
+CHS5 interactsWith LGE1
+CHS5 interactsWith COX11
+CHS5 interactsWith BEM4
+CHS5 interactsWith LEA1
+CHS6 interactsWith MUM2
+CHS6 interactsWith UME6
+CHS6 interactsWith MSN5
+CHS6 interactsWith RVS167
+CHS6 interactsWith RPO41
+CHS6 interactsWith GUP1
+CHS6 interactsWith SMI1
+CHS6 interactsWith SLT2
+CHS6 interactsWith IST3
+CHS6 interactsWith LAS21
+CHS6 interactsWith BCK1
+CHS6 interactsWith MNN11
+CHS6 interactsWith ILM1
+CHS6 interactsWith NUP133
+CHS6 interactsWith UBI4
+CHS6 interactsWith VRP1
+CHS6 interactsWith KRE21
+CHS6 interactsWith FKS1
+CHS6 interactsWith ARC18
+CHS6 interactsWith VAN1
+CHS6 interactsWith YNL235C
+CHS6 interactsWith IRA2
+CHS7 interactsWith SLA1
+CHS7 interactsWith EDE1
+CHS7 interactsWith CYK3
+CHS7 interactsWith SAC6
+CHS7 interactsWith MNN10
+CHS7 interactsWith RVS167
+CHS7 interactsWith RPO41
+CHS7 interactsWith PRE9
+CHS7 interactsWith SMI1
+CHS7 interactsWith SLT2
+CHS7 interactsWith QDR2
+CHS7 interactsWith BCK1
+CHS7 interactsWith RPA34
+CHS7 interactsWith OPI3
+CHS7 interactsWith NUP133
+CHS7 interactsWith CCW12
+CHS7 interactsWith YLR111W
+CHS7 interactsWith VRP1
+CHS7 interactsWith FKS1
+CHS7 interactsWith TUS1
+CHS7 interactsWith VAN1
+CHS7 interactsWith TPM1
+CHS7 interactsWith PEX6
+CHS7 interactsWith SHE4
+CNE1 interactsWith GUP1
+CNE1 interactsWith MST1
+CNE1 interactsWith PEX1
+CNE1 interactsWith YDJ1
+CNE1 interactsWith YNL171C
+CNE1 interactsWith YNR036C
+CTS1 interactsWith PEX6
+DIE2 interactsWith RPO41
+DIE2 interactsWith OST5
+DIE2 interactsWith YGR064W
+DIE2 interactsWith MDM12
+DIE2 interactsWith OST3
+ECM15 interactsWith TOM37
+ERV29 interactsWith TOM37
+FKS1 interactsWith SLA1
+FKS1 interactsWith EDE1
+FKS1 interactsWith SKT5
+FKS1 interactsWith YBL062W
+FKS1 interactsWith UBC4
+FKS1 interactsWith GRS1
+FKS1 interactsWith FEN1
+FKS1 interactsWith PTC1
+FKS1 interactsWith HBT1
+FKS1 interactsWith RGP1
+FKS1 interactsWith LSM6
+FKS1 interactsWith RVS167
+FKS1 interactsWith SNF1
+FKS1 interactsWith GNP1
+FKS1 interactsWith SWI4
+FKS1 interactsWith UBP3
+FKS1 interactsWith BEM2
+FKS1 interactsWith RIM8
+FKS1 interactsWith YGL081W
+FKS1 interactsWith CUE3
+FKS1 interactsWith YGL196W
+FKS1 interactsWith DOC1
+FKS1 interactsWith GSC2
+FKS1 interactsWith PEX4
+FKS1 interactsWith PRE9
+FKS1 interactsWith CCH1
+FKS1 interactsWith RPN10
+FKS1 interactsWith IMP2'
+FKS1 interactsWith YJL046W
+FKS1 interactsWith LSM1
+FKS1 interactsWith RPS21B
+FKS1 interactsWith MNN11
+FKS1 interactsWith NUC1
+FKS1 interactsWith HIT1
+FKS1 interactsWith ILM1
+FKS1 interactsWith IXR1
+FKS1 interactsWith ELM1
+FKS1 interactsWith CNB1
+FKS1 interactsWith VPS67
+FKS1 interactsWith DBP7
+FKS1 interactsWith SPA2
+FKS1 interactsWith FPS1
+FKS1 interactsWith YLR021W
+FKS1 interactsWith QRI5
+FKS1 interactsWith MMS22
+FKS1 interactsWith MID2
+FKS1 interactsWith KRE21
+FKS1 interactsWith ROM2
+FKS1 interactsWith PSP2
+FKS1 interactsWith YMR073C
+FKS1 interactsWith CRZ1
+FKS1 interactsWith YDJ1
+FKS1 interactsWith RPL16B
+FKS1 interactsWith YNL171C
+FKS1 interactsWith BNI1
+FKS1 interactsWith RIM21
+FKS1 interactsWith BRE5
+FKS1 interactsWith YOL003C
+FKS1 interactsWith TOP1
+FKS1 interactsWith DFG16
+FKS1 interactsWith SHE4
+FKS1 interactsWith RIM20
+FKS1 interactsWith RPL20B
+FKS1 interactsWith YPL041C
+FKS1 interactsWith RLM1
+FKS1 interactsWith YPL144W
+FKS1 interactsWith BEM4
+FKS1 interactsWith YPL261C
+FKS1 interactsWith CSR2
+GAS1 interactsWith YAL053W
+GAS1 interactsWith ROT2
+GAS1 interactsWith IMG1
+GAS1 interactsWith PTC1
+GAS1 interactsWith AAD4
+GAS1 interactsWith VPS61
+GAS1 interactsWith RGP1
+GAS1 interactsWith NBP2
+GAS1 interactsWith SSD1
+GAS1 interactsWith DOT1
+GAS1 interactsWith GNP1
+GAS1 interactsWith SWI4
+GAS1 interactsWith BEM2
+GAS1 interactsWith CWH41
+GAS1 interactsWith CUE3
+GAS1 interactsWith EMP24
+GAS1 interactsWith KRE11
+GAS1 interactsWith SMI1
+GAS1 interactsWith NEM1
+GAS1 interactsWith SLT2
+GAS1 interactsWith QDR2
+GAS1 interactsWith BCK1
+GAS1 interactsWith BUD19
+GAS1 interactsWith OPI3
+GAS1 interactsWith CNB1
+GAS1 interactsWith SIS2
+GAS1 interactsWith VPS63
+GAS1 interactsWith RSC2
+GAS1 interactsWith ROM2
+GAS1 interactsWith ECM7
+GAS1 interactsWith NAB6
+GAS1 interactsWith TGL3
+GAS1 interactsWith YMR316C-A
+GAS1 interactsWith YMR317W
+GAS1 interactsWith ADH6
+GAS1 interactsWith YMR326C
+GAS1 interactsWith RIM21
+GAS1 interactsWith KRE1
+GAS1 interactsWith SLG1
+GAS1 interactsWith HAP5
+GAS1 interactsWith PHO85
+GAS1 interactsWith YPL041C
+GAS1 interactsWith RLM1
+GAS1 interactsWith BEM4
+HKR1 interactsWith MNN10
+HKR1 interactsWith DOT1
+HKR1 interactsWith CDC26
+HKR1 interactsWith EMP24
+HKR1 interactsWith NSR1
+HKR1 interactsWith BCK1
+HKR1 interactsWith VPS24
+HKR1 interactsWith TOM37
+HKR1 interactsWith YTA12
+HKR1 interactsWith PKR1
+HKR1 interactsWith YDJ1
+HKR1 interactsWith YNL171C
+HKR1 interactsWith IFM1
+HKR1 interactsWith ARP8
+HKR1 interactsWith GDH1
+HKR1 interactsWith BEM4
+HOC1 interactsWith VPS8
+HOC1 interactsWith SLA1
+HOC1 interactsWith EDE1
+HOC1 interactsWith UBC4
+HOC1 interactsWith RPS6B
+HOC1 interactsWith SAC6
+HOC1 interactsWith RVS167
+HOC1 interactsWith SPF1
+HOC1 interactsWith RPL1B
+HOC1 interactsWith PEX4
+HOC1 interactsWith ARD1
+HOC1 interactsWith BCK1
+HOC1 interactsWith RPA34
+HOC1 interactsWith SWI3
+HOC1 interactsWith POL32
+HOC1 interactsWith CSN12
+HOC1 interactsWith RPS4A
+HOC1 interactsWith YPT52
+HOC1 interactsWith VPS67
+HOC1 interactsWith NUP133
+HOC1 interactsWith RPL22A
+HOC1 interactsWith CSF1
+HOC1 interactsWith HCR1
+HOC1 interactsWith ATP14
+HOC1 interactsWith VRP1
+HOC1 interactsWith KRE21
+HOC1 interactsWith VPS38
+HOC1 interactsWith COG8
+HOC1 interactsWith VPS9
+HOC1 interactsWith VAN1
+HOC1 interactsWith TOM37
+HOC1 interactsWith CIK1
+HOC1 interactsWith KRE1
+HOC1 interactsWith YNR005C
+HOC1 interactsWith BRE5
+HOC1 interactsWith SHE4
+HOC1 interactsWith VPS21
+HOC1 interactsWith COX10
+HOG1 interactsWith YBL083C
+HOG1 interactsWith SOY
+HOG1 interactsWith SEM1
+HOG1 interactsWith ERD1
+HOG1 interactsWith ITR1
+HOG1 interactsWith EMP24
+HOG1 interactsWith DBF2
+HOG1 interactsWith MNN11
+HOG1 interactsWith VPS24
+HOG1 interactsWith MST1
+HOG1 interactsWith YLR358C
+HOG1 interactsWith SKI2
+HOG1 interactsWith VPS9
+HOG1 interactsWith YTA12
+HOG1 interactsWith CIK1
+HOG1 interactsWith SCS7
+HOG1 interactsWith YNL171C
+HOG1 interactsWith IES2
+HOG1 interactsWith PDR17
+HOG1 interactsWith KRE25
+HOG1 interactsWith LEO1
+HOG1 interactsWith BIT89
+HOG1 interactsWith YPR045C
+KNH1 interactsWith VPS8
+KNH1 interactsWith EDS1
+KNH1 interactsWith RPN4
+KNH1 interactsWith YDL033C
+KNH1 interactsWith PEX19
+KNH1 interactsWith PEX5
+KNH1 interactsWith YDR249C
+KNH1 interactsWith PEX3
+KNH1 interactsWith PTP3
+KNH1 interactsWith DST1
+KNH1 interactsWith YGR064W
+KNH1 interactsWith PEX4
+KNH1 interactsWith PRE9
+KNH1 interactsWith NSR1
+KNH1 interactsWith PSD2
+KNH1 interactsWith YGR206W
+KNH1 interactsWith RPS0A
+KNH1 interactsWith YHL005C
+KNH1 interactsWith ARD1
+KNH1 interactsWith YHR034C
+KNH1 interactsWith RPS4B
+KNH1 interactsWith QDR2
+KNH1 interactsWith RPA34
+KNH1 interactsWith VPS35
+KNH1 interactsWith KRE9
+KNH1 interactsWith IXR1
+KNH1 interactsWith YPK1
+KNH1 interactsWith PEX13
+KNH1 interactsWith YLR282C
+KNH1 interactsWith CHS5
+KNH1 interactsWith ORM2
+KNH1 interactsWith VPS38
+KNH1 interactsWith COG8
+KNH1 interactsWith IMP2
+KNH1 interactsWith TOM37
+KNH1 interactsWith RPS10B
+KNH1 interactsWith YNL171C
+KNH1 interactsWith PEX6
+KNH1 interactsWith VPS5
+KNH1 interactsWith GYP1
+KNH1 interactsWith YPR197C
+KRE11 interactsWith RRN10
+KRE11 interactsWith ECM21
+KRE11 interactsWith MUM2
+KRE11 interactsWith FYV5
+KRE11 interactsWith PER1
+KRE11 interactsWith DOT1
+KRE11 interactsWith YEL048C
+KRE11 interactsWith GUP1
+KRE11 interactsWith MMM2
+KRE11 interactsWith CHO2
+KRE11 interactsWith SMI1
+KRE11 interactsWith ARD1
+KRE11 interactsWith BCK1
+KRE11 interactsWith KRE9
+KRE11 interactsWith SWI3
+KRE11 interactsWith ILM1
+KRE11 interactsWith VPS24
+KRE11 interactsWith CTK1
+KRE11 interactsWith VPS67
+KRE11 interactsWith VID22
+KRE11 interactsWith TOM37
+KRE11 interactsWith YTA12
+KRE11 interactsWith ASC1
+KRE11 interactsWith YNL171C
+KRE11 interactsWith KRE1
+KRE11 interactsWith PEX6
+KRE11 interactsWith TRS33
+KRE11 interactsWith RPL20B
+KRE11 interactsWith BTS1
+KRE6 interactsWith PEX22
+KRE6 interactsWith YBL053W
+KRE6 interactsWith YBR042C
+KRE6 interactsWith YDL206W
+KRE6 interactsWith RGP1
+KRE6 interactsWith RTN1
+KRE6 interactsWith YDR248C
+KRE6 interactsWith GGA1
+KRE6 interactsWith EFT2
+KRE6 interactsWith YEL047C
+KRE6 interactsWith RPO41
+KRE6 interactsWith YGL081W
+KRE6 interactsWith RPL1B
+KRE6 interactsWith YGL196W
+KRE6 interactsWith EMP24
+KRE6 interactsWith CLG1
+KRE6 interactsWith RTF1
+KRE6 interactsWith VMA21
+KRE6 interactsWith RPL34B
+KRE6 interactsWith SWI3
+KRE6 interactsWith VPS24
+KRE6 interactsWith OAC1
+KRE6 interactsWith FPS1
+KRE6 interactsWith POM34
+KRE6 interactsWith ACE2
+KRE6 interactsWith PUS5
+KRE6 interactsWith VAN1
+KRE6 interactsWith VAM10
+KRE6 interactsWith DIA2
+KRE6 interactsWith PRM3
+KRE9 interactsWith QCR8
+KRE9 interactsWith YJR011C
+KRE9 interactsWith BAT2
+KRE9 interactsWith YKL177W
+KRE9 interactsWith STM1
+KRE9 interactsWith MRE11
+KRE9 interactsWith ARK1
+KRE9 interactsWith KRE1
+KRE9 interactsWith PRM3
+KTR3 interactsWith KRE21
+KTR3 interactsWith TOM37
+LAS21 interactsWith FUI1
+LAS21 interactsWith ECM21
+LAS21 interactsWith YBL104C
+LAS21 interactsWith ECM8
+LAS21 interactsWith AGP1
+LAS21 interactsWith PEX19
+LAS21 interactsWith YDL096C
+LAS21 interactsWith SEM1
+LAS21 interactsWith RPL9A
+LAS21 interactsWith ARD1
+LAS21 interactsWith IMP2'
+LAS21 interactsWith BCK1
+LAS21 interactsWith RPA34
+LAS21 interactsWith CSF1
+LAS21 interactsWith PEX15
+LAS21 interactsWith RPL21B
+LAS21 interactsWith YPL080C
+LAS21 interactsWith LEA1
+LAS21 interactsWith YPR045C
+LRE1 interactsWith IMP2
+MID2 interactsWith SAC6
+MID2 interactsWith SMI1
+MID2 interactsWith ILM1
+MID2 interactsWith FPS1
+MID2 interactsWith CCW12
+MID2 interactsWith YLR111W
+MID2 interactsWith KRE21
+MID2 interactsWith ROM2
+MID2 interactsWith VAN1
+MID2 interactsWith SLG1
+MNL1 interactsWith RPL20B
+MNS1 interactsWith CKB1
+SKN1 interactsWith RRN10
+SKN1 interactsWith PEX5
+SKN1 interactsWith PEX4
+SKN1 interactsWith PRE9
+SKN1 interactsWith LST4
+SKN1 interactsWith IFM1
+SKT5 interactsWith SLA1
+SKT5 interactsWith EDE1
+SKT5 interactsWith UBP13
+SKT5 interactsWith AST1
+SKT5 interactsWith RPS8A
+SKT5 interactsWith SAC6
+SKT5 interactsWith UME6
+SKT5 interactsWith MNN10
+SKT5 interactsWith ATP17
+SKT5 interactsWith RVS167
+SKT5 interactsWith SPF1
+SKT5 interactsWith SWI4
+SKT5 interactsWith RPO41
+SKT5 interactsWith FAB1
+SKT5 interactsWith GUP1
+SKT5 interactsWith SMI1
+SKT5 interactsWith SLT2
+SKT5 interactsWith BCK1
+SKT5 interactsWith RPA34
+SKT5 interactsWith OPI3
+SKT5 interactsWith ILM1
+SKT5 interactsWith YPK1
+SKT5 interactsWith LST4
+SKT5 interactsWith FPS1
+SKT5 interactsWith CSF1
+SKT5 interactsWith CCW12
+SKT5 interactsWith YLR111W
+SKT5 interactsWith SEC22
+SKT5 interactsWith VRP1
+SKT5 interactsWith KRE21
+SKT5 interactsWith ARC18
+SKT5 interactsWith TUS1
+SKT5 interactsWith VAN1
+SKT5 interactsWith YTA12
+SKT5 interactsWith TPM1
+SKT5 interactsWith BRE5
+SKT5 interactsWith SHE4
+SKT5 interactsWith RSA1
+SMI1 interactsWith SLA1
+SMI1 interactsWith ECM21
+SMI1 interactsWith FAT1
+SMI1 interactsWith UBC4
+SMI1 interactsWith CCZ1
+SMI1 interactsWith TYR1
+SMI1 interactsWith BEM1
+SMI1 interactsWith PTC1
+SMI1 interactsWith RPA14
+SMI1 interactsWith MNN10
+SMI1 interactsWith SBE2
+SMI1 interactsWith RVS167
+SMI1 interactsWith SPF1
+SMI1 interactsWith SWI4
+SMI1 interactsWith UBP3
+SMI1 interactsWith BEM2
+SMI1 interactsWith PDA1
+SMI1 interactsWith RPL29
+SMI1 interactsWith RIM8
+SMI1 interactsWith DOC1
+SMI1 interactsWith PRE9
+SMI1 interactsWith RPS0A
+SMI1 interactsWith CCH1
+SMI1 interactsWith YGR237C
+SMI1 interactsWith RPN10
+SMI1 interactsWith BCK1
+SMI1 interactsWith PHO86
+SMI1 interactsWith MNN11
+SMI1 interactsWith BUD19
+SMI1 interactsWith ILM1
+SMI1 interactsWith ELM1
+SMI1 interactsWith CNB1
+SMI1 interactsWith VPS67
+SMI1 interactsWith SPA2
+SMI1 interactsWith FPS1
+SMI1 interactsWith MMS22
+SMI1 interactsWith YLR358C
+SMI1 interactsWith ROM2
+SMI1 interactsWith IKI3
+SMI1 interactsWith VAN1
+SMI1 interactsWith NAB6
+SMI1 interactsWith LYS7
+SMI1 interactsWith ASC1
+SMI1 interactsWith PFK2
+SMI1 interactsWith YNL171C
+SMI1 interactsWith KRE1
+SMI1 interactsWith BRE5
+SMI1 interactsWith YOL003C
+SMI1 interactsWith DFG16
+SMI1 interactsWith RIM20
+SMI1 interactsWith PHO85
+SMI1 interactsWith YPL077C
+SMI1 interactsWith RLM1
+SVP26 interactsWith BUD25
+SVP26 interactsWith EMP24
+SVP26 interactsWith MST1
+SVP26 interactsWith VPS38
+SVP26 interactsWith BDF1
+SVP26 interactsWith AEP2
+SVP26 interactsWith YDJ1
+SVP26 interactsWith HTZ1
+YKL037W interactsWith PTC1
+YKL037W interactsWith UBP3
+YKL037W interactsWith BCK1
+YKL037W interactsWith FPS1
+YKL037W interactsWith ABF2
+YLR057W interactsWith EMP24
+YLR057W interactsWith PEX6
+YUR1 interactsWith BCK1
+YUR1 interactsWith UBI4
+YUR1 interactsWith PEX15
+RVS161 interactsWith DEP1
+RVS161 interactsWith SLA1
+RVS161 interactsWith SKT5
+RVS161 interactsWith MNN2
+RVS161 interactsWith CHS3
+RVS161 interactsWith RXT2
+RVS161 interactsWith TPS1
+RVS161 interactsWith YBR255W
+RVS161 interactsWith CYK3
+RVS161 interactsWith MNN10
+RVS161 interactsWith SUM1
+RVS161 interactsWith GIM4
+RVS161 interactsWith SPF1
+RVS161 interactsWith SWI4
+RVS161 interactsWith GUP1
+RVS161 interactsWith PAC10
+RVS161 interactsWith SLT2
+RVS161 interactsWith CHS7
+RVS161 interactsWith CAP2
+RVS161 interactsWith SDS3
+RVS161 interactsWith YIB3
+RVS161 interactsWith BBC1
+RVS161 interactsWith BCK1
+RVS161 interactsWith CHS6
+RVS161 interactsWith HOC1
+RVS161 interactsWith CAP1
+RVS161 interactsWith EAP1
+RVS161 interactsWith DOA1
+RVS161 interactsWith CSF1
+RVS161 interactsWith CCW12
+RVS161 interactsWith YLR111W
+RVS161 interactsWith YKE2
+RVS161 interactsWith SEC22
+RVS161 interactsWith GIM5
+RVS161 interactsWith MYO5
+RVS161 interactsWith SAP30
+RVS161 interactsWith END3
+RVS161 interactsWith PHO23
+RVS161 interactsWith GIM3
+RVS161 interactsWith CLA4
+RVS161 interactsWith KRE1
+RVS161 interactsWith SIN3
+RVS161 interactsWith VPS21
+RVS161 interactsWith RUD3
+RVS161 interactsWith MNN9
+RVS167 interactsWith DEP1
+RVS167 interactsWith SLA1
+RVS167 interactsWith MNN2
+RVS167 interactsWith RXT2
+RVS167 interactsWith TPS1
+RVS167 interactsWith YBR255W
+RVS167 interactsWith CYK3
+RVS167 interactsWith MNN10
+RVS167 interactsWith SUM1
+RVS167 interactsWith GIM4
+RVS167 interactsWith SPF1
+RVS167 interactsWith SWI4
+RVS167 interactsWith GUP1
+RVS167 interactsWith PAC10
+RVS167 interactsWith SLT2
+RVS167 interactsWith CAP2
+RVS167 interactsWith SDS3
+RVS167 interactsWith YIB3
+RVS167 interactsWith BBC1
+RVS167 interactsWith BCK1
+RVS167 interactsWith CAP1
+RVS167 interactsWith EAP1
+RVS167 interactsWith DOA1
+RVS167 interactsWith CSF1
+RVS167 interactsWith CCW12
+RVS167 interactsWith YLR111W
+RVS167 interactsWith YKE2
+RVS167 interactsWith SEC22
+RVS167 interactsWith CHS5
+RVS167 interactsWith GIM5
+RVS167 interactsWith MYO5
+RVS167 interactsWith SAP30
+RVS167 interactsWith END3
+RVS167 interactsWith PHO23
+RVS167 interactsWith GIM3
+RVS167 interactsWith CLA4
+RVS167 interactsWith KRE1
+RVS167 interactsWith SIN3
+RVS167 interactsWith VPS21
+RVS167 interactsWith RUD3
+RVS167 interactsWith MNN9
+ARL1 interactsWith PER1
+ARL1 interactsWith VAM6
+ARL1 interactsWith ARR4
+ARL1 interactsWith ARF1
+ARL1 interactsWith GSS1
+ARL1 interactsWith VPS61
+ARL1 interactsWith RGP1
+ARL1 interactsWith NBP2
+ARL1 interactsWith RAV2
+ARL1 interactsWith YDR203W
+ARL1 interactsWith RMD7
+ARL1 interactsWith GLO3
+ARL1 interactsWith COG7
+ARL1 interactsWith VMA21
+ARL1 interactsWith GOS1
+ARL1 interactsWith VPS29
+ARL1 interactsWith VPS35
+ARL1 interactsWith CPR7
+ARL1 interactsWith RAV1
+ARL1 interactsWith YKL118W
+ARL1 interactsWith VPH2
+ARL1 interactsWith VPS1
+ARL1 interactsWith VPS67
+ARL1 interactsWith ARV1
+ARL1 interactsWith VPS63
+ARL1 interactsWith VMA6
+ARL1 interactsWith COG8
+ARL1 interactsWith MVP1
+ARL1 interactsWith STV1
+ARL1 interactsWith PKR1
+ARL1 interactsWith COG6
+ARL1 interactsWith YNL043C
+ARL1 interactsWith YIP3
+ARL1 interactsWith COG5
+ARL1 interactsWith KEX2
+ARL1 interactsWith KRE25
+ARL1 interactsWith MON2
+ARL1 interactsWith TLG2
+ARL1 interactsWith VAM10
+ARL1 interactsWith VPS5
+ARL1 interactsWith VPS17
+HPR5 interactsWith MMS4
+HPR5 interactsWith YBR099C
+HPR5 interactsWith MRC1
+HPR5 interactsWith XRS2
+HPR5 interactsWith MUS81
+HPR5 interactsWith RAD54
+HPR5 interactsWith RRM3
+HPR5 interactsWith RTT107
+HPR5 interactsWith MPH1
+HPR5 interactsWith POL32
+HPR5 interactsWith TOP3
+HPR5 interactsWith YLR235C
+HPR5 interactsWith MMS22
+HPR5 interactsWith RAD50
+HPR5 interactsWith TOF1
+HPR5 interactsWith NCE4
+HPR5 interactsWith MMS1
+RRM3 interactsWith PPH3
+RRM3 interactsWith PMR1
+RRM3 interactsWith HUR1
+RRM3 interactsWith SAE2
+RRM3 interactsWith SOD2
+RRM3 interactsWith RTT101
+RRM3 interactsWith TOP3
+RRM3 interactsWith RAD52
+RRM3 interactsWith MRE11
+RRM3 interactsWith NCE4
+RRM3 interactsWith MMS1
+KRE1 interactsWith DRS2
+KRE1 interactsWith YAL053W
+KRE1 interactsWith KRE20
+KRE1 interactsWith CNE1
+KRE1 interactsWith BUD14
+KRE1 interactsWith SKT5
+KRE1 interactsWith RHK1
+KRE1 interactsWith YBL083C
+KRE1 interactsWith CHS3
+KRE1 interactsWith ROT2
+KRE1 interactsWith PER1
+KRE1 interactsWith PTC1
+KRE1 interactsWith SAC6
+KRE1 interactsWith NBP2
+KRE1 interactsWith SAC7
+KRE1 interactsWith ERD1
+KRE1 interactsWith ERG28
+KRE1 interactsWith BEM2
+KRE1 interactsWith FAB1
+KRE1 interactsWith CWH41
+KRE1 interactsWith GUP1
+KRE1 interactsWith HUR1
+KRE1 interactsWith KEX1
+KRE1 interactsWith SLT2
+KRE1 interactsWith YUR1
+KRE1 interactsWith MNN11
+KRE1 interactsWith OPI3
+KRE1 interactsWith STE24
+KRE1 interactsWith ILM1
+KRE1 interactsWith CNB1
+KRE1 interactsWith VPS67
+KRE1 interactsWith CHS5
+KRE1 interactsWith TOM37
+KRE1 interactsWith DFG5
+KRE1 interactsWith KEX2
+KRE1 interactsWith SHE4
+KRE1 interactsWith VPS28
+CIN1 interactsWith CHL4
+CIN1 interactsWith MCM21
+CIN1 interactsWith MAD1
+CIN1 interactsWith BUB1
+CIN1 interactsWith CTF8
+CIN1 interactsWith MAD3
+CIN1 interactsWith HTZ1
+CIN1 interactsWith CTF19
+CIN1 interactsWith KAR9
+CIN1 interactsWith CTF4
+ROT2 interactsWith PDB1
+ROT2 interactsWith RPO41
+ROT2 interactsWith GUP1
+ROT2 interactsWith CHO2
+ROT2 interactsWith GGA2
+ROT2 interactsWith BCK1
+ROT2 interactsWith CSF1
+ROT2 interactsWith VAM10
+ROT2 interactsWith VPS5
+ROT2 interactsWith GYP1
+CWH41 interactsWith YBR235W
+CWH41 interactsWith PER1
+CWH41 interactsWith PTC1
+CWH41 interactsWith SWF3
+CWH41 interactsWith GUP1
+CWH41 interactsWith SNF4
+CWH41 interactsWith EMP24
+CWH41 interactsWith BCK1
+CWH41 interactsWith CSF1
+CWH41 interactsWith SCJ1
+CWH41 interactsWith LEA1
+ALG8 interactsWith PER1
+ALG8 interactsWith TPS2
+ALG8 interactsWith RPO41
+ALG8 interactsWith OST5
+ALG8 interactsWith SLT2
+ALG8 interactsWith BCK1
+ALG8 interactsWith CSF1
+ALG8 interactsWith YLR358C
+ALG8 interactsWith SHE4
+ALG8 interactsWith DIA2
+ALG8 interactsWith OST3
+DEP1 interactsWith HIR1
+DEP1 interactsWith RPL19B
+DEP1 interactsWith SIF2
+DEP1 interactsWith SEC66
+DEP1 interactsWith SNT1
+DEP1 interactsWith NHP10
+DEP1 interactsWith BRE1
+DEP1 interactsWith THI3
+DEP1 interactsWith SWI5
+DEP1 interactsWith SAS4
+DEP1 interactsWith SWR1
+DEP1 interactsWith SEM1
+DEP1 interactsWith SPT3
+DEP1 interactsWith VPS72
+DEP1 interactsWith SWI4
+DEP1 interactsWith YER139C
+DEP1 interactsWith UBP6
+DEP1 interactsWith SOH1
+DEP1 interactsWith ITC1
+DEP1 interactsWith YGL149W
+DEP1 interactsWith YIP5
+DEP1 interactsWith PMR1
+DEP1 interactsWith HOS2
+DEP1 interactsWith RTF1
+DEP1 interactsWith VMA21
+DEP1 interactsWith TIM13
+DEP1 interactsWith YGR182C
+DEP1 interactsWith ELP2
+DEP1 interactsWith YTA7
+DEP1 interactsWith SRB2
+DEP1 interactsWith VMA22
+DEP1 interactsWith STB5
+DEP1 interactsWith RPN10
+DEP1 interactsWith ASF1
+DEP1 interactsWith OPI3
+DEP1 interactsWith HIR3
+DEP1 interactsWith YKL118W
+DEP1 interactsWith SET3
+DEP1 interactsWith SPT8
+DEP1 interactsWith CSF1
+DEP1 interactsWith YLR111W
+DEP1 interactsWith SEC22
+DEP1 interactsWith IKI3
+DEP1 interactsWith VPS71
+DEP1 interactsWith PRM6
+DEP1 interactsWith TOM37
+DEP1 interactsWith ELP6
+DEP1 interactsWith YNL140C
+DEP1 interactsWith IES2
+DEP1 interactsWith CLA4
+DEP1 interactsWith HTZ1
+DEP1 interactsWith VPS21
+DEP1 interactsWith LEO1
+DEP1 interactsWith SAS5
+DEP1 interactsWith ISW2
+DEP1 interactsWith LGE1
+DEP1 interactsWith ELP3
+DEP1 interactsWith ELP4
+DEP1 interactsWith KRE24
+DEP1 interactsWith YPL144W
+DEP1 interactsWith EAF3
+CTI6 interactsWith SWC1
+CTI6 interactsWith SIF2
+CTI6 interactsWith AOR1
+CTI6 interactsWith THI3
+CTI6 interactsWith SWR1
+CTI6 interactsWith VPS72
+CTI6 interactsWith HOS2
+CTI6 interactsWith PAC10
+CTI6 interactsWith TIM13
+CTI6 interactsWith YGR182C
+CTI6 interactsWith VPS71
+CTI6 interactsWith PRM6
+CTI6 interactsWith HTZ1
+CTI6 interactsWith LEO1
+SAP30 interactsWith VPS8
+SAP30 interactsWith SWC1
+SAP30 interactsWith LTE1
+SAP30 interactsWith SIF2
+SAP30 interactsWith AOR1
+SAP30 interactsWith NHP10
+SAP30 interactsWith YDL033C
+SAP30 interactsWith BRE1
+SAP30 interactsWith THI3
+SAP30 interactsWith SWR1
+SAP30 interactsWith SPT3
+SAP30 interactsWith VPS72
+SAP30 interactsWith RMD7
+SAP30 interactsWith IES5
+SAP30 interactsWith SWI4
+SAP30 interactsWith YER139C
+SAP30 interactsWith SOH1
+SAP30 interactsWith YIP5
+SAP30 interactsWith HOS2
+SAP30 interactsWith RTF1
+SAP30 interactsWith TIM13
+SAP30 interactsWith YGR182C
+SAP30 interactsWith STB5
+SAP30 interactsWith RPN10
+SAP30 interactsWith ASF1
+SAP30 interactsWith SET2
+SAP30 interactsWith SET3
+SAP30 interactsWith SPT8
+SAP30 interactsWith ARP6
+SAP30 interactsWith SEC22
+SAP30 interactsWith VRP1
+SAP30 interactsWith VPS71
+SAP30 interactsWith PRM6
+SAP30 interactsWith VPS9
+SAP30 interactsWith MRE11
+SAP30 interactsWith TOM70
+SAP30 interactsWith YNL140C
+SAP30 interactsWith YNL171C
+SAP30 interactsWith IES2
+SAP30 interactsWith HTZ1
+SAP30 interactsWith LEO1
+SAP30 interactsWith SAS5
+SAP30 interactsWith SNU66
+SAP30 interactsWith LGE1
+SAP30 interactsWith ELP3
+CDC42 interactsWith LTE1
+CDC42 interactsWith YBR077C
+CDC42 interactsWith SEC66
+CDC42 interactsWith BEM1
+CDC42 interactsWith PAT1
+CDC42 interactsWith SWF1
+CDC42 interactsWith SSD1
+CDC42 interactsWith GIC2
+CDC42 interactsWith SUM1
+CDC42 interactsWith SWI4
+CDC42 interactsWith PEA2
+CDC42 interactsWith PMR1
+CDC42 interactsWith HUR1
+CDC42 interactsWith YGL211W
+CDC42 interactsWith YGR151C
+CDC42 interactsWith RSR1
+CDC42 interactsWith ELP2
+CDC42 interactsWith UBA4
+CDC42 interactsWith CAP2
+CDC42 interactsWith CAP1
+CDC42 interactsWith SPA2
+CDC42 interactsWith BUD6
+CDC42 interactsWith ELP6
+CDC42 interactsWith BNI1
+CDC42 interactsWith MSB3
+CDC42 interactsWith CLA4
+CDC42 interactsWith MSB1
+CDC42 interactsWith ELP3
+CDC42 interactsWith ELP4
+CDC42 interactsWith BEM4
+SWF1 interactsWith ARL1
+SWF1 interactsWith PER1
+SWF1 interactsWith YDL133W
+SWF1 interactsWith CUP5
+SWF1 interactsWith SPF1
+SWF1 interactsWith RMD7
+SWF1 interactsWith COG7
+SWF1 interactsWith YGL007W
+SWF1 interactsWith VMA21
+SWF1 interactsWith YGR228W
+SWF1 interactsWith SMI1
+SWF1 interactsWith GOS1
+SWF1 interactsWith YHR151C
+SWF1 interactsWith SYS1
+SWF1 interactsWith SNX4
+SWF1 interactsWith BCK1
+SWF1 interactsWith KTI12
+SWF1 interactsWith YKL118W
+SWF1 interactsWith VPS1
+SWF1 interactsWith SPO14
+SWF1 interactsWith YKR033C
+SWF1 interactsWith RIC1
+SWF1 interactsWith VID22
+SWF1 interactsWith YLR374C
+SWF1 interactsWith IKI3
+SWF1 interactsWith COG8
+SWF1 interactsWith HSC82
+SWF1 interactsWith ELP6
+SWF1 interactsWith COG6
+SWF1 interactsWith COG5
+SWF1 interactsWith PDR17
+SWF1 interactsWith MSO1
+SWF1 interactsWith TLG2
+SWF1 interactsWith MSB4
+SWF1 interactsWith OST3
+SWF1 interactsWith SNC2
+SWF1 interactsWith ARL3
+SWF1 interactsWith BTS1
+Mlh1 pp Pms1
+Msh2-Msh6 interactsWith Mlh1-Pms1
+Pol30 pp Msh3
+Pol30 pp Msh6
+Swi5 pp Pho2
+Pho85 pp Pcl1
+Pho85 pp Pcl2
+Pho85 pp Pcl8
+Pho85 pp Pcl9
+Pho85 pp Pcl10
+Pho80 pp Pho85
+Pfy1 pp Act1
+Pho81 pp Pho80
+Pho81 pp Pcl7
+Rvs167 pp Pcl2
+Rvs167 pp Pcl9
+Pcl10 pp Gsy2
+Pho80 pp Pho4
+Pho2 pp Pho4
+Pho81 pp Pho4
+Bas1 pp Bas2
+Pol31 pp Pol32
+Pho80-Pho85 interactsWith Pho4
+Gsy2 pp Glg2
+Pho80-Pho85 interactsWith Pho81
+Pho85-Pcl10 interactsWith Gsy2
+Cdc28 pp Cln1
+Cdc28 pp Cln2
+Cdc28 pp Cln3
+Prp19 pp Cef1
+Ntc30 pp Ntc30
+Slu7 pp Prp18
+Prp8 pp Upc2
+Msl5 pp Mud2
+Ste4 pp Ste18
+Ste4/Ste18 interactsWith Akr1
+Stb1 interactsWith Cln1-Cdc28
+Stb1 interactsWith Cln2-Cdc28
+Stb1 interactsWith Clb2-Cdc28
+Cdc28 pp Clb2
+Cdc28 pp Clb3
+Cdc37 pp Cdc28
+Cdc37 pp Cak1
+Cdc37 pp Mps1
+Cdc37 pd Cdc5
+Cdc37 pp Cdc7
+Cdc37 pp Ste11
+Bem1 pp Ste5
+Bem1 interactsWith Ste5/Ste11/Ste7/Fus3-complex
+Rvs167 pp Rvs167
+Rvs167 pp Rvs161
+Rvs167 pp Abp1
+cTPx_II pp cTPx_II
+cTPx_II-cTPxII interactsWith SFH2
+Orc2 pp Cdc7
+Orc2 pp Orc3
+Asf1 pp Bdf1
+Asf1 pp Bdf2
+Asf1 pp TAFII67
+Asf1 pp TAFII145
+Asf1 pp Tbp1
+Ste5 pp Kss1
+Kss1 pp Dig1
+Cyr1 pp Cdc25
+Kss1 pp Dig2
+Yfl023w pp Rpb5
+Yfl023w pp Pfd6
+Nhp6a interactsWith CP
+Sph1 pp Mkk2
+Sph1 pp Ste7
+Msh2 pp Msh3
+Sph1 pp Ste11
+Abp1 pp Myo5
+Abp1 pp Yir003w
+Abp1 pp App1
+Pob3 pp Spt16
+Abp1 pp Inp52
+Pol30 interactsWith Msh2-Msh3_heterodimer
+Cac1 pp Cac3
+Kss1 pp Sst2
+Pob3/Spt16 interactsWith Pol-alpha
+QCR2 pp COR1
+COB pp COR1
+CYT1 pp COB
+RIP1 pp COR1
+RIP1 pp CYT1
+RIP1 pp COB
+QCR6 pp CYT1
+QCR7 pp COB
+QCR7 pp CYT1
+QCR8 pp COB
+QCR8 pp QCR7
+QCR8 pp COR1
+QCR8 pp CYT1
+QCR8 pp RIP1
+QCR8 pp QCR6
+QCR9 pp RIP1
+QCR9 pp COR1
+QCR9 pp CYT1
+Spt5 pp Spt4
+Top1 pp Tof1
+Top1 pp Tof2
+Sgs1 pp Top3
+Far1 pp Msn5
+Slt2 pp Smi1
+Sgs1 pp Top2
+Top1 pp Top1
+Top1 pp Nsr1
+Rlm1 pp Mlp1
+Sdp1 pp Slt2
+Slt2 pp Rlm1
+Paf1 pp Ctr9
+Leo1 interactsWith Unknown
+Rtf1 interactsWith Unknown
+Asf1 pp Cac2
+Sas2 pp Sas2
+Asf1 pp Hir1
+Abp1 pp Prk1
+Asf1 pp Hir2
+Abp1 pp Ark1
+Cdc28-Cln2 interactsWith Far1
+Paf1_complex interactsWith CP
+Paf1 interactsWith DSIF
+Slt2 pp Sir3
+Far1 pp Cdc48
+Cdc24/Far1 interactsWith Ste4
+Unknown interactsWith Sas2
+Unknown interactsWith Sas4
+Unknown interactsWith Sas5
+Asf1 pp Sas4
+Cyr1 pp Srv2
+Abp1 interactsWith Cyr1-Srv2_complex.
+SAS_complex interactsWith Asf1
+VPS36 pp Sst2
+TLG2 pp Sst2
+PCNA_homotrimer interactsWith Rad30
+Slt2 pp Mkk1
+Slt2 pp Mkk2
+Spt4 pp Hir1
+Sas2 pp Sas4
+Sas2 pp Cac1
+Sas2 pp Asf1
+Sas4 pp Sas4
+Cln2 pp Grr1
+Spa2 pp Pea2
+Spa2 pp Bud6
+Spa2 pp Ste11
+Complex_Cyr1/Srv2 interactsWith Unknown
+Cdc25 interactsWith Unknown
+Ras2 interactsWith Unknown
+Hhf1 pp Hht1
+Htb2 pp Hta1
+Htb2 pp Hhf1
+Hht1 pp Hta1
+Hht1 pp Hht1
+Hhf1 pp Hht1
+Hhf1 pp Hta1
+Hhf1 pp Htb2
+Hta1 pp Hta1
+Hta1 pp Hht1
+Hta1 pp Hhf1
+Htb2 pp Hta1
+Htb2 pp Hhf1
+Htb2 pp Hhf1
+Vph1 pp Vma13
+Sas4 pp Cac1
+Sas4 pp Sas5
+Sas5 pp Cac1
+Sas5 pp Asf1
+Dpb11 pp Drc1
+Pep12 pp Sst2
+Kel1 pp Sst2
+Eco1 pp Scc1
+Spa2 pp Ste7
+Eco1 pp Scc3
+Ark1 pp Sho1
+Pex13 pp Pex14
+Pex14 pp Abp1
+Pex14 pp Rvs167
+Pex14 pp Sho1
+Pex14 pp Sla1
+Pex14 pp Yar014c
+Pex14 pp Yfr024c-a
+Pex14 pp Ysc84
+Spa2 pp Mkk1
+Spa2 pp Mkk2
+Bud6 pp Ste11
+Las17 pp Rvs167
+Las17 pp Vrp1
+Mck1 pp Hsl1
+Las17 pp Lsb1
+Esp1 interactsWith Unknown
+Pds1 interactsWith Unknown
+Hht1 interactsWith Unknown
+Hhf1 interactsWith Unknown
+Uaf30 interactsWith Unknown
+Rrn5 interactsWith Unknown
+Rrn9 interactsWith Unknown
+Rrn10 interactsWith Unknown
+Las17 pp Lsb2
+Ptp3 pp Slt2
+Las17 pp Lsb3
+Las17 pp Lsb4
+Las17 interactsWith Arp2/3_complex
+Cdc73 interactsWith Paf1/Ctr9
+PCNA pp Rrm3
+Paf1/Ctr9 interactsWith Unknown
+Ptp2 pp Mpk1
+Bck1 pp Bck1
+Bck1 pp Mkk2
+Dhh1 pp Pop2
+Ppz1 pp Hal3
+Gin4 pp Cdc3
+Kar2 pp Lhs1
+Kar2 pp Sil1
+Bck1 pp Mkk1
+Abp1 interactsWith Unknown
+Ste7 pp Kss1
+Cdc14 pp Sli15
+Las17 pp Act1
+Rad52 pp Rfa2
+Rad52 pp Rfa3
+Rad52 pp Rad51
+Rad52 pp Rad52
+Rad52 pp Rad59
+Rfa1 interactsWith Unknown
+Rfa2 interactsWith Unknown
+Rfa3 interactsWith Unknown
+Ty1_RNA interactsWith Ty1_RNA
+RPA_Complex interactsWith DNA
+Cdc13 pp Stn1
+Cdc13 pp Ten1
+Stn1 pp Ten1
+Dbr1 interactsWith Ty1_RNA_lariat
+Dbr1 interactsWith ACT1_intron_lariat
+Hsl1 pp Hsl7
+Hsl7 pp Swe1
+Hsl7 pp Hsl7
+Hsl1 pp Hsl1
+Ino80 interactsWith Unknown
+Unknown interactsWith Ies2
+Unknown interactsWith Arp4
+Unknown interactsWith Rvb2
+Unknown interactsWith Rvb1
+Unknown interactsWith Act1
+Unknown interactsWith Ies3
+Unknown interactsWith Nhp10
+Unknown interactsWith Ies4
+Unknown interactsWith Ies5
+Unknown interactsWith Ies6
+Unknown interactsWith Arp8
+Unknown interactsWith Ies1
+Unknown interactsWith Arp5
+Unknown interactsWith Taf14
+Unknown interactsWith Htz1-Htb2
+Unknown interactsWith Htb2
+Unknown interactsWith Htz1
+Unknown interactsWith Vps72
+Swr1 interactsWith Unknown
+Unknown interactsWith Htz1-Htb2
+Unknown interactsWith Htb2
+Unknown interactsWith Nap1
+Htz1 interactsWith Unknown
+Htz1 pp Htb2
+Unknown interactsWith Yaf9
+Unknown interactsWith Vps71
+Unknown interactsWith Aor1
+Unknown interactsWith Act1
+Unknown interactsWith Arp6
+Unknown interactsWith God1
+Unknown interactsWith Rvb1
+Unknown interactsWith Rvb2
+Unknown interactsWith Arp4
+Unknown interactsWith Swc1
+Htz1 pd CAR2
+Htz1 pd RDS1_promoter
+Htz1 pd LSM3
+Htz1 pd ADE17_promoter
+Rpd3 pp Sin3
+DNA interactsWith Hht1
+DNA interactsWith Htb2
+DNA interactsWith Hta1
+DNA interactsWith Hht1
+DNA interactsWith Hhf1
+DNA interactsWith Hhf1
+DNA interactsWith Hta1
+DNA interactsWith Htb2
+DNA interactsWith Hht1
+DNA interactsWith Htb2
+DNA interactsWith Hta1
+DNA interactsWith Hhf1
+DNA interactsWith Hht1
+DNA interactsWith Hhf1
+DNA interactsWith Hta1
+DNA interactsWith Htb2
+Sin3 interactsWith Unknown
+Hog1 interactsWith Unknown
+Rpd3 pd GRE2_promoter
+Rpd3 pd CTT1_promoter
+Rpd3 pd ALD3_promoter
+Sin3 pd CTT1_promoter
+Rpb1 pd STL1_promoter
+Sin3 pd STL1_promoter
+Hhf1 pd HSP12_promoter
+Sin3 pd HSP12_promoter
+Rpb1 pd GRE2_promoter
+Rpb1 pd HSP12_promoter
+Rpd3 pd HSP12_promoter
+Rpd3 pd RPB11_promoter
+Hog1 interactsWith Sin3-Rpd3_Complex
+Rpd3 pd STL1_promoter
+Rpd3 pd YKR033C_promoter
+Hog1 pp Rpd3
+Mid2 pp Zeo1
+RAP1 pd YAR075W
+RAP1 pd YAL069W
+RAP1 pd iYAL069W
+RAP1 pd iYBL111C
+RAP1 pd YBL109W
+RAP1 pd iYBL109W-0
+RAP1 pd iYBL109W-1
+RAP1 pd YBL108W
+RAP1 pd YCLWOMEGA1
+RAP1 pd YCLWTY5-1A
+RAP1 pd YCL076W
+RAP1 pd YCL075W
+RAP1 pd YCLWTY5-1B
+RAP1 pd iYCL075W
+RAP1 pd YCL074W
+RAP1 pd YCLWTY5-1C
+RAP1 pd YCL069W
+RAP1 pd iYCL069W
+RAP1 pd YCL068C
+RAP1 pd YCL067C
+RAP1 pd iYCL067C
+RAP1 pd YCL066W
+RAP1 pd YCL065W
+RAP1 pd iYCL065W-0
+RAP1 pd YCR039C
+RAP1 pd iYCR039C
+RAP1 pd YCR040W
+RAP1 pd YCR041W
+RAP1 pd iYCRWDELTA12
+RAP1 pd YCRWOMEGA3
+RAP1 pd iYCRWOMEGA3
+RAP1 pd iYCR096C
+RAP1 pd YCR097W
+RAP1 pd YCR097W-A
+RAP1 pd iNTYCR097W-A2
+RAP1 pd iYCR097W
+RAP1 pd iYDR542W
+RAP1 pd YDR543C
+RAP1 pd iYDR543C
+RAP1 pd iYDR544C
+RAP1 pd iYEL074W
+RAP1 pd iYERWOMEGA2-0
+RAP1 pd iYERWOMEGA2-1
+RAP1 pd iYFL064C
+RAP1 pd YFL063W
+RAP1 pd iYFL063W
+RAP1 pd TEL6R
+RAP1 pd iYGR295C-0
+RAP1 pd iYGR295C-1
+RAP1 pd iYHL049C-0
+RAP1 pd iYHL049C-1
+RAP1 pd YHL001W
+RAP1 pd YHR216W
+RAP1 pd iYHR216W
+RAP1 pd YHR217C
+RAP1 pd TEL9L
+RAP1 pd iYiL177C-0
+RAP1 pd iYiL177C-1
+RAP1 pd iYJL225C-0
+RAP1 pd iYJL225C-1
+RAP1 pd iYJR144W
+RAP1 pd iYJR161C
+RAP1 pd YJR162C
+RAP1 pd YKL225W
+RAP1 pd iYKR106W-0
+RAP1 pd iYKR106W-1
+RAP1 pd iYLL067C-1
+RAP1 pd iYLL066C-1
+RAP1 pd YLL065W
+RAP1 pd iYLL065W
+RAP1 pd iYLR461W-0
+RAP1 pd iYLR461W-1
+RAP1 pd iYLR466W
+RAP1 pd iYML133C-0
+RAP1 pd iYML133C-1
+RAP1 pd YMR326C
+RAP1 pd YNL338W
+RAP1 pd iYNL338W
+RAP1 pd iYNL337W
+RAP1 pd YNL326C
+RAP1 pd YNL325C
+RAP1 pd iYNR076W
+RAP1 pd YOL166C
+RAP1 pd iYOL166C
+RAP1 pd iYOL162W
+RAP1 pd TEL15R-1
+RAP1 pd TEL15R-2
+RAP1 pd iYPL283C-0
+RAP1 pd iYPL283C-1
+RAP1 pd YAR073W
+RAP1 pd YBL113C
+RAP1 pd iYBL108W
+RAP1 pd iYCL074W
+RAP1 pd iYCLWOMEGA2-0
+RAP1 pd iYCL068C
+RAP1 pd iYCL065W-1
+RAP1 pd YCL064C
+RAP1 pd iYCR038C
+RAP1 pd YCR096C
+RAP1 pd YDR449C
+RAP1 pd iYDR541C-1
+RAP1 pd YDR542W
+RAP1 pd iYEL075C
+RAP1 pd YEL074W
+RAP1 pd YEL009C
+RAP1 pd YER189W
+RAP1 pd YER190W
+RAP1 pd YFL068W
+RAP1 pd YFL065C
+RAP1 pd YFL064C
+RAP1 pd YFL062W
+RAP1 pd YGR294W
+RAP1 pd YHL048W
+RAP1 pd iYHR091C
+RAP1 pd iYHR217C
+RAP1 pd YHR219W
+RAP1 pd iYHR219W
+RAP1 pd YIL177C
+RAP1 pd YIL176C
+RAP1 pd YIL175W
+RAP1 pd YJL223C
+RAP1 pd YJR161C
+RAP1 pd YKL224C
+RAP1 pd iYKL224C
+RAP1 pd YKL223W
+RAP1 pd YKR105C
+RAP1 pd iYKR105C
+RAP1 pd YKR106W
+RAP1 pd YLL066C
+RAP1 pd iYLL066C-0
+RAP1 pd YLL064C
+RAP1 pd iYLL064C
+RAP1 pd YLR448W
+RAP1 pd iYLR460C-1
+RAP1 pd YLR461W
+RAP1 pd iYML076C
+RAP1 pd iYMR324C
+RAP1 pd iYMR325W
+RAP1 pd iYNL339C
+RAP1 pd YNL096C
+RAP1 pd YNR076W
+RAP1 pd YOR394W
+RAP1 pd TEL15R-6
+RAP1 pd YPL282C
+RAP1 pd iYPL282C
+RAP1 pd YPR202W
+RAP1 pd YPR204W
+RAP1 pd YDR064W
+RAP1 pd YDR544C
+RAP1 pd iYFL014W
+RAP1 pd YGL030W
+RAP1 pd YHR022C
+RAP1 pd iYKL225W
+RAP1 pd YOL120C
+RAP1 pd iYPR201W-1
+RAP1 pd iYAL053W
+RAP1 pd iYAL039C-1
+RAP1 pd YAL038W
+RAP1 pd YAL034C
+RAP1 pd iYAL034C
+RAP1 pd TEL1R
+RAP1 pd YBL111C
+RAP1 pd YBL094C
+RAP1 pd iYBL094C
+RAP1 pd YBL093C
+RAP1 pd iYBL093C
+RAP1 pd YBL087C
+RAP1 pd iYBL087C
+RAP1 pd YBL086C
+RAP1 pd iYBL082C
+RAP1 pd iSNR56
+RAP1 pd iYBL072C
+RAP1 pd iYBL071C
+RAP1 pd iYBL061C
+RAP1 pd iYBL030C-1
+RAP1 pd YBL028C
+RAP1 pd iYBL028C
+RAP1 pd YBL027W
+RAP1 pd YBL022C
+RAP1 pd iYBL022C
+RAP1 pd YBL021C
+RAP1 pd iYBL021C
+RAP1 pd iYBR046C
+RAP1 pd YBR047W
+RAP1 pd iYBR047W
+RAP1 pd YBR048W
+RAP1 pd YBR084C-A
+RAP1 pd iYBR084C-A
+RAP1 pd YBR085W
+RAP1 pd iYBR117C
+RAP1 pd YBR118W
+RAP1 pd YBR176W
+RAP1 pd iYBR179C
+RAP1 pd YBR181C
+RAP1 pd iYBR181C
+RAP1 pd YBR182C
+RAP1 pd YBR187W
+RAP1 pd YBR188C
+RAP1 pd iYBR188C
+RAP1 pd YBR189W
+RAP1 pd iYBR189W
+RAP1 pd YBR190W
+RAP1 pd YBR191W
+RAP1 pd YBR196C
+RAP1 pd iLSR1
+RAP1 pd YBR302C
+RAP1 pd YCL037C
+RAP1 pd iYCL037C
+RAP1 pd YCL036W
+RAP1 pd iYCL030C
+RAP1 pd iYCL025C
+RAP1 pd iYCRCDELTA6-B
+RAP1 pd iYCR024C-A
+RAP1 pd YCR025C
+RAP1 pd iYCR025C
+RAP1 pd YCR031C
+RAP1 pd SNR189
+RAP1 pd YCR038C
+RAP1 pd YCR104W
+RAP1 pd iYDL230W
+RAP1 pd YDL192W
+RAP1 pd iYDL192W
+RAP1 pd YDL191W
+RAP1 pd iYDL188C
+RAP1 pd YDL186W
+RAP1 pd iYDL185W
+RAP1 pd iYDL184C
+RAP1 pd YDL183C
+RAP1 pd iYDL169C
+RAP1 pd YDL168W
+RAP1 pd YDL137W
+RAP1 pd iYDL137W
+RAP1 pd YDL136W
+RAP1 pd YDL133C-A
+RAP1 pd iYDL133C-A
+RAP1 pd YDL133W
+RAP1 pd YDL131W
+RAP1 pd iYDL131W
+RAP1 pd YDL130W-A
+RAP1 pd iYDL130W-A
+RAP1 pd YDL083C
+RAP1 pd iYDL083C
+RAP1 pd YDL082W
+RAP1 pd iYDL076C
+RAP1 pd YDL075W
+RAP1 pd iYDL061C
+RAP1 pd iYDL055C-0
+RAP1 pd iYDL055C-1
+RAP1 pd iYDL034W
+RAP1 pd iTA(AGC)D
+RAP1 pd iYDL022W
+RAP1 pd YDL021W
+RAP1 pd iYDR023W
+RAP1 pd YDR024W
+RAP1 pd iYDR036C
+RAP1 pd YDR037W
+RAP1 pd iYDR040C
+RAP1 pd iSNR47
+RAP1 pd iYDR062W
+RAP1 pd YDR063W
+RAP1 pd iYDR063W
+RAP1 pd iYDR186C
+RAP1 pd YDR188W
+RAP1 pd YDR276C
+RAP1 pd iYDR276C
+RAP1 pd YDR300C
+RAP1 pd iYDR300C
+RAP1 pd YDR324C
+RAP1 pd iYDR324C
+RAP1 pd YDR382W
+RAP1 pd iYDR392W
+RAP1 pd iYDR408C
+RAP1 pd iYDR416W
+RAP1 pd YDR417C
+RAP1 pd YDR418W
+RAP1 pd YDR447C
+RAP1 pd iYDR447C
+RAP1 pd YDR448W
+RAP1 pd iYDR449C
+RAP1 pd YDR450W
+RAP1 pd YDR470C
+RAP1 pd iYDR470C
+RAP1 pd YDR471W
+RAP1 pd YDR500C
+RAP1 pd iYDR500C
+RAP1 pd YDR501W
+RAP1 pd YDR545W
+RAP1 pd YEL076C-A
+RAP1 pd YEL073C
+RAP1 pd iYEL073C-0
+RAP1 pd iYEL073C-4
+RAP1 pd YEL072W
+RAP1 pd iYEL072W-0
+RAP1 pd iYEL057C
+RAP1 pd YEL054C
+RAP1 pd iYEL054C
+RAP1 pd YEL053C
+RAP1 pd YEL046C
+RAP1 pd iYEL036C
+RAP1 pd YEL035C
+RAP1 pd iYEL035C
+RAP1 pd YEL034W
+RAP1 pd iYEL023C
+RAP1 pd iYEL009C
+RAP1 pd YEL008W
+RAP1 pd iYEL008W
+RAP1 pd YER031C
+RAP1 pd iYER031C
+RAP1 pd YER032W
+RAP1 pd iYER033C
+RAP1 pd YER034W
+RAP1 pd iYER045C-0
+RAP1 pd iYER045C-1
+RAP1 pd iYER056C-A
+RAP1 pd YER057C
+RAP1 pd YER073W
+RAP1 pd iYER073W
+RAP1 pd YER074W
+RAP1 pd YER081W
+RAP1 pd YER101C
+RAP1 pd iYER101C
+RAP1 pd YER116C
+RAP1 pd iYER116C
+RAP1 pd YER117W
+RAP1 pd YER168C
+RAP1 pd iYER168C
+RAP1 pd YFL066C
+RAP1 pd iYFL066C
+RAP1 pd iYFL051C-1
+RAP1 pd iYFL034C-A
+RAP1 pd iYFL016C
+RAP1 pd YFL015C
+RAP1 pd iYFL015C
+RAP1 pd YFL014W
+RAP1 pd YFR031C-A
+RAP1 pd iYFR031C-A
+RAP1 pd YFR032C
+RAP1 pd iYGLWOMEGA1-0
+RAP1 pd YGL263W
+RAP1 pd iYGL259W-0
+RAP1 pd YGL258W
+RAP1 pd iYGL189C
+RAP1 pd YGL188C
+RAP1 pd iYGL188C
+RAP1 pd YGL187C
+RAP1 pd YGL147C
+RAP1 pd YGL146C
+RAP1 pd iYGL142C
+RAP1 pd YGL136C
+RAP1 pd iYGL136C
+RAP1 pd YGL135W
+RAP1 pd iYGL124C
+RAP1 pd YGL123W
+RAP1 pd iYGL116W
+RAP1 pd YGL115W
+RAP1 pd YGL104C
+RAP1 pd iYGL104C
+RAP1 pd iYGL084C
+RAP1 pd YGL076C
+RAP1 pd iYGL076C
+RAP1 pd YGL075C
+RAP1 pd iYGL075C
+RAP1 pd YGL072C
+RAP1 pd iYGL072C
+RAP1 pd YGL031C
+RAP1 pd iYGL031C
+RAP1 pd YGL007W
+RAP1 pd YGR027C
+RAP1 pd iYGR027C
+RAP1 pd iYGR033C
+RAP1 pd YGR034W
+RAP1 pd iYGR084C
+RAP1 pd YGR085C
+RAP1 pd iYGR085C
+RAP1 pd YGR086C
+RAP1 pd YGR117C
+RAP1 pd iYGR117C
+RAP1 pd YGR118W
+RAP1 pd YGR148C
+RAP1 pd iYGR148C
+RAP1 pd YGR149W
+RAP1 pd iYGR160W
+RAP1 pd YGR177C
+RAP1 pd iYGR180C
+RAP1 pd YGR192C
+RAP1 pd iYGR192C
+RAP1 pd YGR213C
+RAP1 pd iYGR213C
+RAP1 pd YGR214W
+RAP1 pd YGR234W
+RAP1 pd iYGR258C-0
+RAP1 pd YGR283C
+RAP1 pd iYGR283C
+RAP1 pd YGR295C
+RAP1 pd YHR021W-A
+RAP1 pd YHL050C
+RAP1 pd iYHL050C
+RAP1 pd YHL049C
+RAP1 pd YHL045W
+RAP1 pd YHL038C
+RAP1 pd YHL037C
+RAP1 pd YHL033C
+RAP1 pd iYHL033C
+RAP1 pd YHL032C
+RAP1 pd iYHL016C
+RAP1 pd YHL015W
+RAP1 pd YHL002W
+RAP1 pd iYHL002W
+RAP1 pd iYHR009C
+RAP1 pd YHR010W
+RAP1 pd YHR021C
+RAP1 pd iYHR021C
+RAP1 pd iYHR032W
+RAP1 pd iYHR096C
+RAP1 pd iYHR121W
+RAP1 pd YHR122W
+RAP1 pd YHR141C
+RAP1 pd YHR142W
+RAP1 pd YHR174W
+RAP1 pd YHR203C
+RAP1 pd iYHR203C
+RAP1 pd YHR204W
+RAP1 pd YHR218W
+RAP1 pd YIL174W
+RAP1 pd iYiL149C
+RAP1 pd YIL148W
+RAP1 pd YIL133C
+RAP1 pd iYiL133C
+RAP1 pd YIL132C
+RAP1 pd iYiL122W
+RAP1 pd iYiL055C
+RAP1 pd YIL054W
+RAP1 pd YIL052C
+RAP1 pd iYiL052C
+RAP1 pd YIL051C
+RAP1 pd YIL019W
+RAP1 pd iYiL019W
+RAP1 pd YIL018W
+RAP1 pd YIR014W
+RAP1 pd iYiR015W
+RAP1 pd YJL225C
+RAP1 pd YJL192C
+RAP1 pd iYJL192C
+RAP1 pd YJL191W
+RAP1 pd iYJL191W
+RAP1 pd YJL190C
+RAP1 pd iYJL190C
+RAP1 pd YJL189W
+RAP1 pd YJL178C
+RAP1 pd iYJL178C
+RAP1 pd YJL177W
+RAP1 pd iYJL136C
+RAP1 pd YJL135W
+RAP1 pd iYJL134W
+RAP1 pd YJL096W
+RAP1 pd iYJL090C
+RAP1 pd iYJL050W
+RAP1 pd iTM(CAU)J1
+RAP1 pd YJL028W
+RAP1 pd iYJL028W
+RAP1 pd iYJL027C
+RAP1 pd YJL026W
+RAP1 pd YJR045C
+RAP1 pd YJR047C
+RAP1 pd YJR058C
+RAP1 pd iYJR058C
+RAP1 pd iYJR094C-1
+RAP1 pd YJR094W-A
+RAP1 pd YJR122W
+RAP1 pd iYJR122W
+RAP1 pd YJR123W
+RAP1 pd iYJR131W
+RAP1 pd iYJR134C
+RAP1 pd YJR135C
+RAP1 pd YJR139C
+RAP1 pd iYJR139C
+RAP1 pd YJR145C
+RAP1 pd iYJR145C
+RAP1 pd YJR146W
+RAP1 pd YKL181W
+RAP1 pd iYKL181W
+RAP1 pd YKL180W
+RAP1 pd YKL178C
+RAP1 pd iYKL177W
+RAP1 pd YKL176C
+RAP1 pd iYKL176C
+RAP1 pd YKL175W
+RAP1 pd YKL157W
+RAP1 pd iYKL157W
+RAP1 pd YKL156W
+RAP1 pd YKL152C
+RAP1 pd YKL151C
+RAP1 pd iYKL098W
+RAP1 pd YKL060C
+RAP1 pd iYKL040C
+RAP1 pd YKL031W
+RAP1 pd iYKL006C-A
+RAP1 pd YKL006W
+RAP1 pd iYKR056W
+RAP1 pd YKR057W
+RAP1 pd iYKR092C-0
+RAP1 pd YKR094C
+RAP1 pd iYKR094C
+RAP1 pd iYKR101W-0
+RAP1 pd YLR390W-A
+RAP1 pd YLR287C-A
+RAP1 pd YLL067C
+RAP1 pd iYLL067C-0
+RAP1 pd YLL045C
+RAP1 pd iYLL044W
+RAP1 pd iYLL039C
+RAP1 pd YLR003C
+RAP1 pd YLR004C
+RAP1 pd iYLR044C
+RAP1 pd iYLR047C
+RAP1 pd YLR048W
+RAP1 pd YLR060W
+RAP1 pd iYLR060W
+RAP1 pd YLR061W
+RAP1 pd YLR074C
+RAP1 pd iYLR074C
+RAP1 pd YLR075W
+RAP1 pd iYLR103C
+RAP1 pd YLR104W
+RAP1 pd iYLR104W
+RAP1 pd YLR110C
+RAP1 pd YLR111W
+RAP1 pd YLR112W
+RAP1 pd iYLR166C
+RAP1 pd YLR167W
+RAP1 pd iYLR183C
+RAP1 pd YLR184W
+RAP1 pd iYLR184W
+RAP1 pd YLR185W
+RAP1 pd YLR255C
+RAP1 pd iYLR255C
+RAP1 pd iYLR264W
+RAP1 pd YLR286C
+RAP1 pd iYLR286C
+RAP1 pd YLR287C
+RAP1 pd iYLR287C
+RAP1 pd iYLR287C-A
+RAP1 pd YLR288C
+RAP1 pd iYLR310C
+RAP1 pd YLR325C
+RAP1 pd YLR326W
+RAP1 pd YLR333C
+RAP1 pd iYLR333C
+RAP1 pd YLR334C
+RAP1 pd iYLRWDELTA20
+RAP1 pd iYLR338W
+RAP1 pd YLR340W
+RAP1 pd iYLRCDELTA21
+RAP1 pd TR(CCG)L
+RAP1 pd iTR(CCG)L
+RAP1 pd YLR344W
+RAP1 pd YLR367W
+RAP1 pd iSNR44
+RAP1 pd YLR387C
+RAP1 pd iYLR387C
+RAP1 pd iYLR389C
+RAP1 pd YLR390W
+RAP1 pd iYLR390W
+RAP1 pd iYLR399C
+RAP1 pd YLR400W
+RAP1 pd iYLR400W
+RAP1 pd YLR401C
+RAP1 pd iYLR401C
+RAP1 pd YLR402W
+RAP1 pd iYLR402W
+RAP1 pd iYLR406C
+RAP1 pd YLR407W
+RAP1 pd iYLR407W
+RAP1 pd iYLR437C
+RAP1 pd YLR438W
+RAP1 pd iYLR441C
+RAP1 pd YLR447C
+RAP1 pd iYLR447C
+RAP1 pd YLR452C
+RAP1 pd iYLR452C
+RAP1 pd YLR453C
+RAP1 pd YLR462W
+RAP1 pd YLR463C
+RAP1 pd YLR465C
+RAP1 pd YLR466W
+RAP1 pd YLR467W
+RAP1 pd YML132W
+RAP1 pd iYML089C
+RAP1 pd YML073C
+RAP1 pd iYML073C
+RAP1 pd iYML065W
+RAP1 pd YML064C
+RAP1 pd iYML064C
+RAP1 pd YML063W
+RAP1 pd YML026C
+RAP1 pd iYML026C
+RAP1 pd YML025C
+RAP1 pd iYML025C
+RAP1 pd YML024W
+RAP1 pd YMR013C
+RAP1 pd iYMR013C-0
+RAP1 pd iYMR013C-1
+RAP1 pd YMR014W
+RAP1 pd iYMR015C
+RAP1 pd iYMR082C-1
+RAP1 pd iYMR099C
+RAP1 pd iYMR116C
+RAP1 pd YMR142C
+RAP1 pd iYMR142C
+RAP1 pd YMR143W
+RAP1 pd iYMR143W
+RAP1 pd YMR144W
+RAP1 pd iYMR193W
+RAP1 pd YMR193C-A
+RAP1 pd YMR194W
+RAP1 pd iYMR224C
+RAP1 pd iYMR229C
+RAP1 pd YMR230W
+RAP1 pd iYMR230W
+RAP1 pd YMR242C
+RAP1 pd iYMR242C
+RAP1 pd YMR243C
+RAP1 pd iYMR243C
+RAP1 pd iYMR265C
+RAP1 pd iYMR323W
+RAP1 pd iYNL329C
+RAP1 pd YNL310C
+RAP1 pd iYNL302C
+RAP1 pd YNL301C
+RAP1 pd iYNL289W-0
+RAP1 pd iYNL289W-1
+RAP1 pd YNL288W
+RAP1 pd iYNL254C
+RAP1 pd iYNL217W
+RAP1 pd YNL216W
+RAP1 pd iYNL201C
+RAP1 pd iYNL191W
+RAP1 pd iYNL179C-1
+RAP1 pd YNL178W
+RAP1 pd iYNL163C
+RAP1 pd YNL162W
+RAP1 pd iYNL154C
+RAP1 pd iYNL102W
+RAP1 pd iYNL096C
+RAP1 pd YNL069C
+RAP1 pd iYNL069C
+RAP1 pd YNL068C
+RAP1 pd iYNL068C
+RAP1 pd YNL067W
+RAP1 pd iYNL067W
+RAP1 pd iSNR66
+RAP1 pd YNL011C
+RAP1 pd iYNL011C
+RAP1 pd YNL010W
+RAP1 pd iYNR069C-0
+RAP1 pd YOL165C
+RAP1 pd iYOL136C
+RAP1 pd YOL128C
+RAP1 pd iYOL128C
+RAP1 pd YOL127W
+RAP1 pd YOL121C
+RAP1 pd iYOL121C
+RAP1 pd YOL119C
+RAP1 pd iYOL110W
+RAP1 pd YOL109W
+RAP1 pd iYOL086C
+RAP1 pd iYOL083W-0
+RAP1 pd iYOL083W-1
+RAP1 pd YOL082W
+RAP1 pd iYOL060C
+RAP1 pd iYOL040C
+RAP1 pd YOL039W
+RAP1 pd iSNR62
+RAP1 pd iYOR056C
+RAP1 pd iYOR095C
+RAP1 pd YOR096W
+RAP1 pd YOR100C
+RAP1 pd iYOR100C
+RAP1 pd iYOR124C
+RAP1 pd iYOR161C
+RAP1 pd iYOR179C-1
+RAP1 pd YOR182C
+RAP1 pd YOR183W
+RAP1 pd YOR184W
+RAP1 pd YOR234C
+RAP1 pd iYOR234C
+RAP1 pd YOR235W
+RAP1 pd iYOR235W
+RAP1 pd YOR292C
+RAP1 pd iYOR292C
+RAP1 pd YOR293W
+RAP1 pd iYOR301W
+RAP1 pd iYOR312C
+RAP1 pd iYOR340C
+RAP1 pd YOR343C
+RAP1 pd iYOR343C
+RAP1 pd iYOR344C-0
+RAP1 pd iYOR354C-0
+RAP1 pd iYOR354C-1
+RAP1 pd iYOR358W
+RAP1 pd iYOR366W
+RAP1 pd YOR367W
+RAP1 pd iYOR369C
+RAP1 pd iYOR387C-0
+RAP1 pd iYOR387C-1
+RAP1 pd iYOR393W
+RAP1 pd TEL15R-3
+RAP1 pd TEL15R-4
+RAP1 pd YPL249C-A
+RAP1 pd iYPL249C-A
+RAP1 pd iYPL227C
+RAP1 pd iYPL221W
+RAP1 pd YPL220W
+RAP1 pd YPL199C
+RAP1 pd iYPL199C
+RAP1 pd iYPL190C
+RAP1 pd YPL162C
+RAP1 pd iYPL162C
+RAP1 pd iYPL145C
+RAP1 pd YPL143W
+RAP1 pd YPL132W
+RAP1 pd iYPL132W
+RAP1 pd YPL111W
+RAP1 pd iYPL095C
+RAP1 pd iYPL090C
+RAP1 pd iYPL082C
+RAP1 pd YPL081W
+RAP1 pd iYPL081W
+RAP1 pd YPL080C
+RAP1 pd iYPL080C
+RAP1 pd YPL017C
+RAP1 pd iYPL017C
+RAP1 pd iYPR029C
+RAP1 pd iYPR042C
+RAP1 pd YPR043W
+RAP1 pd iYPR079W
+RAP1 pd YPR080W
+RAP1 pd YPR102C
+RAP1 pd iYPR102C
+RAP1 pd YPR103W
+RAP1 pd iYPR105C
+RAP1 pd YPR106W
+RAP1 pd iYPR110C
+RAP1 pd YPR131C
+RAP1 pd iYPR131C
+RAP1 pd YPR132W
+RAP1 pd iYPR161C
+RAP1 pd YPR203W
+RAP1 pd iYPR203W
+SIR2 pd YAR075W
+SIR3 pd YAR075W
+SIR4 pd YAR075W
+SIR2 pd YAL069W
+SIR3 pd YAL069W
+SIR4 pd YAL069W
+SIR2 pd iYAL069W
+SIR3 pd iYAL069W
+SIR4 pd iYAL069W
+SIR2 pd iYBL111C
+SIR3 pd iYBL111C
+SIR4 pd iYBL111C
+SIR2 pd YBL109W
+SIR3 pd YBL109W
+SIR4 pd YBL109W
+SIR2 pd iYBL109W-0
+SIR3 pd iYBL109W-0
+SIR4 pd iYBL109W-0
+SIR2 pd iYBL109W-1
+SIR3 pd iYBL109W-1
+SIR4 pd iYBL109W-1
+SIR2 pd YBL108W
+SIR3 pd YBL108W
+SIR4 pd YBL108W
+SIR2 pd YCLWOMEGA1
+SIR3 pd YCLWOMEGA1
+SIR4 pd YCLWOMEGA1
+SIR2 pd YCLWTY5-1A
+SIR3 pd YCLWTY5-1A
+SIR4 pd YCLWTY5-1A
+SIR2 pd YCL076W
+SIR3 pd YCL076W
+SIR4 pd YCL076W
+SIR2 pd YCL075W
+SIR3 pd YCL075W
+SIR4 pd YCL075W
+SIR2 pd YCLWTY5-1B
+SIR3 pd YCLWTY5-1B
+SIR4 pd YCLWTY5-1B
+SIR2 pd iYCL075W
+SIR3 pd iYCL075W
+SIR4 pd iYCL075W
+SIR2 pd YCL074W
+SIR3 pd YCL074W
+SIR4 pd YCL074W
+SIR2 pd YCLWTY5-1C
+SIR3 pd YCLWTY5-1C
+SIR4 pd YCLWTY5-1C
+SIR2 pd YCL069W
+SIR3 pd YCL069W
+SIR4 pd YCL069W
+SIR2 pd iYCL069W
+SIR3 pd iYCL069W
+SIR4 pd iYCL069W
+SIR2 pd YCL068C
+SIR3 pd YCL068C
+SIR4 pd YCL068C
+SIR2 pd YCL067C
+SIR3 pd YCL067C
+SIR4 pd YCL067C
+SIR2 pd iYCL067C
+SIR3 pd iYCL067C
+SIR4 pd iYCL067C
+SIR2 pd YCL066W
+SIR3 pd YCL066W
+SIR4 pd YCL066W
+SIR2 pd YCL065W
+SIR3 pd YCL065W
+SIR4 pd YCL065W
+SIR2 pd iYCL065W-0
+SIR3 pd iYCL065W-0
+SIR4 pd iYCL065W-0
+SIR2 pd YCR039C
+SIR3 pd YCR039C
+SIR4 pd YCR039C
+SIR2 pd iYCR039C
+SIR3 pd iYCR039C
+SIR4 pd iYCR039C
+SIR2 pd YCR040W
+SIR3 pd YCR040W
+SIR4 pd YCR040W
+SIR2 pd YCR041W
+SIR3 pd YCR041W
+SIR4 pd YCR041W
+SIR2 pd iYCRWDELTA12
+SIR3 pd iYCRWDELTA12
+SIR4 pd iYCRWDELTA12
+SIR2 pd YCRWOMEGA3
+SIR3 pd YCRWOMEGA3
+SIR4 pd YCRWOMEGA3
+SIR2 pd iYCRWOMEGA3
+SIR3 pd iYCRWOMEGA3
+SIR4 pd iYCRWOMEGA3
+SIR2 pd iYCR096C
+SIR3 pd iYCR096C
+SIR4 pd iYCR096C
+SIR2 pd YCR097W
+SIR3 pd YCR097W
+SIR4 pd YCR097W
+SIR2 pd YCR097W-A
+SIR3 pd YCR097W-A
+SIR4 pd YCR097W-A
+SIR2 pd iNTYCR097W-A2
+SIR3 pd iNTYCR097W-A2
+SIR2 pd iYCR097W
+SIR3 pd iYCR097W
+SIR4 pd iYCR097W
+SIR2 pd iYDR542W
+SIR3 pd iYDR542W
+SIR4 pd iYDR542W
+SIR2 pd YDR543C
+SIR3 pd YDR543C
+SIR4 pd YDR543C
+SIR2 pd iYDR543C
+SIR3 pd iYDR543C
+SIR4 pd iYDR543C
+SIR2 pd iYDR544C
+SIR3 pd iYDR544C
+SIR4 pd iYDR544C
+SIR2 pd iYEL074W
+SIR3 pd iYEL074W
+SIR4 pd iYEL074W
+SIR2 pd iYERWOMEGA2-0
+SIR3 pd iYERWOMEGA2-0
+SIR4 pd iYERWOMEGA2-0
+SIR2 pd iYERWOMEGA2-1
+SIR3 pd iYERWOMEGA2-1
+SIR4 pd iYERWOMEGA2-1
+SIR2 pd iYFL064C
+SIR3 pd iYFL064C
+SIR4 pd iYFL064C
+SIR2 pd YFL063W
+SIR3 pd YFL063W
+SIR4 pd YFL063W
+SIR2 pd iYFL063W
+SIR3 pd iYFL063W
+SIR4 pd iYFL063W
+SIR2 pd TEL6R
+SIR3 pd TEL6R
+SIR4 pd TEL6R
+SIR2 pd iYGR295C-0
+SIR3 pd iYGR295C-0
+SIR4 pd iYGR295C-0
+SIR2 pd iYGR295C-1
+SIR3 pd iYGR295C-1
+SIR4 pd iYGR295C-1
+SIR2 pd iYHL049C-0
+SIR3 pd iYHL049C-0
+SIR4 pd iYHL049C-0
+SIR2 pd iYHL049C-1
+SIR3 pd iYHL049C-1
+SIR4 pd iYHL049C-1
+SIR2 pd YHL001W
+SIR3 pd YHL001W
+SIR2 pd YHR216W
+SIR3 pd YHR216W
+SIR4 pd YHR216W
+SIR2 pd iYHR216W
+SIR3 pd iYHR216W
+SIR4 pd iYHR216W
+SIR2 pd YHR217C
+SIR3 pd YHR217C
+SIR4 pd YHR217C
+SIR2 pd TEL9L
+SIR3 pd TEL9L
+SIR4 pd TEL9L
+SIR2 pd iYiL177C-0
+SIR3 pd iYiL177C-0
+SIR4 pd iYiL177C-0
+SIR2 pd iYiL177C-1
+SIR3 pd iYiL177C-1
+SIR4 pd iYiL177C-1
+SIR2 pd iYJL225C-0
+SIR3 pd iYJL225C-0
+SIR4 pd iYJL225C-0
+SIR2 pd iYJL225C-1
+SIR3 pd iYJL225C-1
+SIR4 pd iYJL225C-1
+SIR2 pd iYJR144W
+SIR3 pd iYJR144W
+SIR4 pd iYJR144W
+SIR2 pd iYJR161C
+SIR3 pd iYJR161C
+SIR4 pd iYJR161C
+SIR2 pd YJR162C
+SIR3 pd YJR162C
+SIR4 pd YJR162C
+SIR2 pd YKL225W
+SIR3 pd YKL225W
+SIR4 pd YKL225W
+SIR2 pd iYKR106W-0
+SIR3 pd iYKR106W-0
+SIR4 pd iYKR106W-0
+SIR2 pd iYKR106W-1
+SIR3 pd iYKR106W-1
+SIR4 pd iYKR106W-1
+SIR2 pd iYLL067C-1
+SIR3 pd iYLL067C-1
+SIR4 pd iYLL067C-1
+SIR2 pd iYLL066C-1
+SIR3 pd iYLL066C-1
+SIR4 pd iYLL066C-1
+SIR2 pd YLL065W
+SIR3 pd YLL065W
+SIR4 pd YLL065W
+SIR2 pd iYLL065W
+SIR3 pd iYLL065W
+SIR4 pd iYLL065W
+SIR2 pd iYLR461W-0
+SIR3 pd iYLR461W-0
+SIR4 pd iYLR461W-0
+SIR2 pd iYLR461W-1
+SIR3 pd iYLR461W-1
+SIR4 pd iYLR461W-1
+SIR2 pd iYLR466W
+SIR3 pd iYLR466W
+SIR4 pd iYLR466W
+SIR2 pd iYML133C-0
+SIR3 pd iYML133C-0
+SIR4 pd iYML133C-0
+SIR2 pd iYML133C-1
+SIR3 pd iYML133C-1
+SIR4 pd iYML133C-1
+SIR2 pd YMR326C
+SIR3 pd YMR326C
+SIR4 pd YMR326C
+SIR2 pd YNL338W
+SIR3 pd YNL338W
+SIR4 pd YNL338W
+SIR2 pd iYNL338W
+SIR3 pd iYNL338W
+SIR4 pd iYNL338W
+SIR2 pd iYNL337W
+SIR3 pd iYNL337W
+SIR4 pd iYNL337W
+SIR2 pd YNL326C
+SIR3 pd YNL326C
+SIR4 pd YNL326C
+SIR2 pd YNL325C
+SIR3 pd YNL325C
+SIR4 pd YNL325C
+SIR2 pd iYNR076W
+SIR3 pd iYNR076W
+SIR4 pd iYNR076W
+SIR2 pd YOL166C
+SIR3 pd YOL166C
+SIR4 pd YOL166C
+SIR2 pd iYOL166C
+SIR3 pd iYOL166C
+SIR4 pd iYOL166C
+SIR2 pd iYOL162W
+SIR3 pd iYOL162W
+SIR4 pd iYOL162W
+SIR2 pd TEL15R-1
+SIR3 pd TEL15R-1
+SIR4 pd TEL15R-1
+SIR2 pd TEL15R-2
+SIR3 pd TEL15R-2
+SIR4 pd TEL15R-2
+SIR2 pd iYPL283C-0
+SIR3 pd iYPL283C-0
+SIR4 pd iYPL283C-0
+SIR2 pd iYPL283C-1
+SIR3 pd iYPL283C-1
+SIR4 pd iYPL283C-1
+SIR2 pd YAR073W
+SIR4 pd YAR073W
+SIR2 pd YBL113C
+SIR4 pd YBL113C
+SIR2 pd iYBL108W
+SIR4 pd iYBL108W
+SIR2 pd iYCL074W
+SIR4 pd iYCL074W
+SIR2 pd iYCLWOMEGA2-0
+SIR4 pd iYCLWOMEGA2-0
+SIR2 pd iYCL068C
+SIR4 pd iYCL068C
+SIR2 pd iYCL065W-1
+SIR4 pd iYCL065W-1
+SIR2 pd YCL064C
+SIR4 pd YCL064C
+SIR2 pd iYCR038C
+SIR4 pd iYCR038C
+SIR2 pd YCR096C
+SIR4 pd YCR096C
+SIR2 pd YDR449C
+SIR2 pd iYDR541C-1
+SIR2 pd YDR542W
+SIR4 pd YDR542W
+SIR2 pd iYEL075C
+SIR4 pd iYEL075C
+SIR2 pd YEL074W
+SIR4 pd YEL074W
+SIR2 pd YEL009C
+SIR2 pd YER189W
+SIR4 pd YER189W
+SIR2 pd YER190W
+SIR2 pd YFL068W
+SIR2 pd YFL065C
+SIR2 pd YFL064C
+SIR4 pd YFL064C
+SIR2 pd YFL062W
+SIR2 pd YGR294W
+SIR2 pd YHL048W
+SIR2 pd iYHR091C
+SIR2 pd iYHR217C
+SIR4 pd iYHR217C
+SIR2 pd YHR219W
+SIR2 pd iYHR219W
+SIR2 pd YIL177C
+SIR2 pd YIL176C
+SIR2 pd YIL175W
+SIR4 pd YIL175W
+SIR2 pd YJL223C
+SIR4 pd YJL223C
+SIR2 pd YJR161C
+SIR2 pd YKL224C
+SIR2 pd iYKL224C
+SIR2 pd YKL223W
+SIR2 pd YKR105C
+SIR4 pd YKR105C
+SIR2 pd iYKR105C
+SIR4 pd iYKR105C
+SIR2 pd YKR106W
+SIR4 pd YKR106W
+SIR2 pd YLL066C
+SIR2 pd iYLL066C-0
+SIR4 pd iYLL066C-0
+SIR2 pd YLL064C
+SIR2 pd iYLL064C
+SIR4 pd iYLL064C
+SIR2 pd YLR448W
+SIR2 pd iYLR460C-1
+SIR4 pd iYLR460C-1
+SIR2 pd YLR461W
+SIR4 pd YLR461W
+SIR2 pd iYML076C
+SIR2 pd iYMR324C
+SIR4 pd iYMR324C
+SIR2 pd iYMR325W
+SIR2 pd iYNL339C
+SIR4 pd iYNL339C
+SIR2 pd YNL096C
+SIR2 pd YNR076W
+SIR4 pd YNR076W
+SIR2 pd YOR394W
+SIR2 pd TEL15R-6
+SIR4 pd TEL15R-6
+SIR2 pd YPL282C
+SIR2 pd iYPL282C
+SIR2 pd YPR202W
+SIR2 pd YPR204W
+SIR3 pd YDR064W
+SIR3 pd YDR544C
+SIR4 pd YDR544C
+SIR3 pd iYFL014W
+SIR3 pd YGL030W
+SIR3 pd YHR022C
+SIR3 pd iYKL225W
+SIR4 pd iYKL225W
+SIR3 pd YOL120C
+SIR3 pd iYPR201W-1
+SIR4 pd iYPR201W-1
+SIR4 pd YBL111C
+SIR4 pd YFL066C
+SIR4 pd YGR295C
+SIR4 pd YHL049C
+SIR4 pd YLR167W
+SIR4 pd YLR462W
+SIR4 pd YLR463C
+SIR4 pd iYOR235W
+SIR2 pd YFL040W
+SIR3 pd YFL040W
+SIR4 pd YFL040W
+SIR2 pd YFR055W
+SIR3 pd YFR055W
+SIR2 pd YJL113W
+SIR3 pd YJL113W
+SIR4 pd YJL113W
+SIR2 pd iYLRWDELTA6-B
+SIR3 pd iYLRWDELTA6-B
+SIR2 pd RDN25-1A
+SIR3 pd RDN25-1A
+SIR2 pd iYLR162W-0
+SIR3 pd iYLR162W-0
+SIR2 pd YNR072W
+SIR3 pd YNR072W
+SIR4 pd YNR072W
+SIR2 pd YNR077C
+SIR3 pd YNR077C
+SIR4 pd YNR077C
+SIR2 pd YPL197C
+SIR3 pd YPL197C
+SIR2 pd YPR052C
+SIR3 pd YPR052C
+SIR4 pd YPR052C
+SIR2 pd YAL068C
+SIR4 pd YAL068C
+SIR2 pd iYAL068C-0
+SIR2 pd CEN1
+SIR2 pd iYBLWDELTA3
+SIR2 pd iYBR048W
+SIR2 pd YBR301W
+SIR2 pd YCL073C
+SIR4 pd YCL073C
+SIR2 pd iYCL073C
+SIR4 pd iYCL073C
+SIR2 pd iYCR095C-1
+SIR2 pd YCRWDELTA12
+SIR2 pd iNTYCR097W-A1
+SIR2 pd YDL227C
+SIR2 pd iYDL021W
+SIR2 pd iYDR345C-1
+SIR2 pd iYDR541C-0
+SIR2 pd YEL022W
+SIR2 pd YER188W
+SIR2 pd YFR057W
+SIR4 pd YFR057W
+SIR2 pd YGR004W
+SIR2 pd YHLCOMEGA1
+SIR2 pd iYHR086W
+SIR2 pd iYHR162W
+SIR4 pd iYHR162W
+SIR2 pd iYHR215W
+SIR2 pd iYJL223C-0
+SIR2 pd iYJLWDELTA8
+SIR2 pd iYKR104W
+SIR2 pd RDN25-1B
+SIR2 pd RDN37-1A
+SIR2 pd RDN58-1
+SIR2 pd RDN37-1B
+SIR2 pd RDN18-1
+SIR2 pd RDN18-1A
+SIR2 pd RDN18-1B
+SIR2 pd RDN37-1C
+SIR2 pd iRDN37-1
+SIR2 pd RDN5-1
+SIR2 pd iRDN5-1
+SIR2 pd iYLR161W
+SIR2 pd YLR162W
+SIR2 pd iYLR162W-A
+SIR2 pd YLRWDELTA12
+SIR2 pd YLR399C
+SIR2 pd YMR325W
+SIR2 pd iYMR012W
+SIR2 pd YNL339C
+SIR2 pd iYOL165C
+SIR4 pd iYOL165C
+SIR2 pd YOLWTAU1
+SIR4 pd YOLWTAU1
+SIR2 pd iYPL177C-1
+SIR2 pd YPL046C
+SIR3 pd YAL041W
+SIR4 pd YAL041W
+SIR3 pd YBR010W
+SIR3 pd YBR014C
+SIR3 pd YBR023C
+SIR3 pd YBR030W
+SIR3 pd iYBR115C
+SIR3 pd iYCL054W
+SIR3 pd iCEN3
+SIR3 pd iYCR073W-A
+SIR3 pd YDL120W
+SIR3 pd YDL055C
+SIR3 pd iYDL001W
+SIR3 pd iYDR041W
+SIR3 pd iYDR191W
+SIR3 pd iYDRCTY1-2
+SIR3 pd YDR225W
+SIR3 pd iYDR311W
+SIR3 pd YDR385W
+SIR3 pd iYDR406W
+SIR3 pd iYDR431W
+SIR3 pd iYDR434W
+SIR3 pd YEL068C
+SIR3 pd iYELCTAU1
+SIR3 pd iYER055C
+SIR3 pd iYER072W
+SIR3 pd YER146W
+SIR3 pd YER157W
+SIR3 pd YGL012W
+SIR3 pd YGL011C
+SIR3 pd YGL008C
+SIR3 pd iYGR222W
+SIR3 pd iYGR233C-0
+SIR3 pd iYGR243W
+SIR3 pd YHR144C
+SIR3 pd iYiL094C
+SIR3 pd YILCDELTA2
+SIR3 pd iYiLCDELTA5-0
+SIR3 pd iYiR034C
+SIR3 pd YIR035C
+SIR3 pd iSNR60
+SIR3 pd iYJL045W
+SIR3 pd YJR096W
+SIR3 pd YKL214C
+SIR3 pd YKL102C
+SIR3 pd iYKL029C
+SIR3 pd iCEN11
+SIR3 pd YKR060W
+SIR3 pd YKR080W
+SIR3 pd iSNR61
+SIR3 pd iYLR412W-0
+SIR3 pd YMR307W
+SIR3 pd iYML087C
+SIR3 pd YML001W
+SIR3 pd iYMR034C
+SIR3 pd iYMR079W
+SIR4 pd iYMR079W
+SIR3 pd iYMR221C
+SIR3 pd iYNL197C
+SIR3 pd iYNR050C
+SIR3 pd YOR143C
+SIR4 pd YOR143C
+SIR3 pd iYOR356W
+SIR3 pd YPR121W
+SIR4 pd YPR121W
+SIR4 pd iTL(CAA)A
+SIR4 pd YBLWDELTA3
+SIR4 pd YBR072W
+SIR4 pd iYBR134W
+SIR4 pd iYCR100C
+SIR4 pd YDL240W
+SIR4 pd iYDL226C
+SIR4 pd YDL125C
+SIR4 pd iYDRCSiGMA1
+SIR4 pd YDR350C
+SIR4 pd iTH(GUG)G1
+SIR4 pd YGL079W
+SIR4 pd iYHR175W
+SIR4 pd iYHR196W
+SIR4 pd YIL102C
+SIR4 pd iYJR084W
+SIR4 pd iYKL137W
+SIR4 pd iYMR217W
+SIR4 pd iYORCDELTA11
+Sla1 pp Lsb5
+Sla1 pp Sup35
+SWF1 interactsWith ELP4
+SWF1 interactsWith KRE24
+SWF1 interactsWith BEM4
+SWF1 interactsWith SSO1
+Eno2 pp Sup35
+Eft2 pp Sup35
+Reg1 pp Sup35
+Sla1 pp Glc7
+Hsl1 pp Cdh1
+Met30 pp Cdc53
+Clb2 pp Cdh1
+Clb2 pp Cdc20
+Hsl1 pp Cdc20
+Met30 pp Swe1
+Met30 pp Cdc34
+Met30 pp Skp1
+Ste4 pp Fus3
+Ste5 pp Fus1
+Ste5 pp Fus3
+Ste7 pp Fus3
+Ste11 pp Fus2
+Ste11 pp Fus3
+Kss1 pp Fus1
+Kss1 pp Fus3
+Fus3 pp Fus1
+Fus3 pp Fus3
+Fus1 pp Fus1
+Fus1 pp Fus2
+Fus1 pp Fus3
+Fus1 pp Bni1
+Fus1 pp Chs5
+Fus1 pp Cdc42
+Fus1 pp Pea2
+Fus2 pp Fus1
+Fus2 pp Fus2
+Fus2 pp Fus3
+Fus2 pp Bni1
+Fus2 pp Pea2
+Fus2 pp Rvs161
+Fus2 pp Cdc42
+Bni1 pp Fus1
+Bni1 pp Fus2
+Bni1 pp Cdc42
+Bni1 pp Bni1
+Spa2 pp Bni1
+Pea2 pp Fus1
+Rvs161 pp Fus2
+Chs5 pp Fus1
+Chs5 pp Fus2
+Chs5 pp Pea2
+Cdc42 pp Fus1
+Cdc42 pp Bni1
+Cdc24 pp Fus2
+Cdc24 pp Rvs161
+Rga1 pp Cdc42
+Far1 pp Fus1
+Far1 pp Bni1
+Far1 pp Cdc42
+Bud6 pp Bni1
+Bnr1 pp Fus1
+Bnr1 pp Fus2
+Bnr1 pp Cdc42
+Bnr1 pp Pea2
+Bnr1 pp Bni1
+Bnr1 pp Pea2
+Act1 pp Fus1
+Act1 pp Bni1
+Bnr1 pp Fus1
+Bni1 pp Fus1
+Fus1 pp Fus1
+Ste5 pp Fus1
+Bnr1 pp Bni1
+Bnr1 pp Bni1
+Spa2 pp Bni1
+Bni1 pp Bni1
+Bni1 pp Bni1
+Bni1 pp Bni1
+Bni1 pp Bni1
+Fus2 pp Bni1
+Bnr1 pp Bni1
+Fus1 pp Pea2
+Yil112w pp Hst1
+Set3 interactsWith Unknown
+Cpr1 interactsWith Unknown
+Sif2 pp Snt1
+Hos2 interactsWith Unknown
+Kel1 pp Kel1
+Kel1 pp Kel2
+Swe1 pp Cdc5
+Swe1 pp Clb2
+Pea2 pp Gic2
+Fus1 pp Sho1
+Fus1 pp Bni1
+Shs1 pp Spa2
+Hda2 pp Hda3
+Hda1 pp Hda3
+Hda1 pp Hda1
+Shs1 pp Cdc12
+Bud6 pp Gic2
+Unknown interactsWith Rpc10
+Unknown interactsWith Rpb11
+Unknown interactsWith Rpb10
+Unknown interactsWith Rpb9
+Unknown interactsWith Rpb8
+Unknown interactsWith Rpb7
+Unknown interactsWith Rpo26
+Unknown interactsWith Rpb5
+Unknown interactsWith Rpb4
+Unknown interactsWith Rpb3
+Unknown interactsWith Rpb2
+Rpo21 interactsWith Unknown
+Ppz1 pp Scd5
+Set2 interactsWith RNAPII
+1D66_B pp 1D66_A
+CYB2 pp CYB2
+CYB2 pp CYB2
+POT1 pp POT1
+PPR1 pp PPR1
+SOD1 pp SOD1
+SOD1 pp SOD1
+SOD1 pp SOD1
+SOD1 pp SOD1
+SPT15 pp SPT15
+TKL1 pp TKL1
+TKL1 pp TKL1
+TKL1 pp TKL1
+TPI1 pp TPI1
+1YSA_B interactsWith 1YSA_A
+1YSA_C pd 1YSA_A
+1YSA_C pd 1YSA_B
+1YSA_D pd 1YSA_B
+1YSA_D pd 1YSA_A
+1YSA_D pp 1YSA_C
+1YTB_D pd SPT15
+TPI1 pp TPI1
+2ZTA_B pp 2ZTA_A
+TPI1 pp TPI1
+TPI1 pp TPI1
+CYB2 pp CYB2
+1GCL_B pp 1GCL_A
+1GCL_C pp 1GCL_B
+1GCL_D pp 1GCL_C
+1GCL_D pp 1GCL_A
+1ASZ_R interactsWith DPS1
+DPS1 pp DPS1
+1ASZ_S interactsWith DPS1
+1ASY_R interactsWith DPS1
+DPS1 pp DPS1
+1ASY_S interactsWith DPS1
+CYB2 pp CYB2
+ARO7 pp ARO7
+PDC1 pp PDC1
+HMRA2 pp HMRA1
+1YRN_C pd HMRA2
+1YRN_C pd HMRA1
+Gcn4p-Ii pp Gcn4p-Ii
+Gcn4p-Ii pp Gcn4p-Ii
+Gcn4p-Ii pp Gcn4p-Ii
+ADK1 pp ADK1
+2DGC_B pd GCN4
+TOA1 pp Yeast_Transcription_Factor_Iia
+TOA2 pp Yeast_Transcription_Factor_Iia
+1YTF_E pd TOA1
+1YTF_E pd SPT15
+1YTF_F pd SPT15
+L-Tyrosine pp ARO7
+1TTT_E interactsWith 1TTT_D
+1TTT_F interactsWith 1TTT_D
+GPH1 pp GPH1
+IPP1 pp IPP1
+Gcn4p1 pp Gcn4p1
+Gcn4p1 pp Gcn4p1
+Gcn4p1 pp Gcn4p1
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+POT1 pp POT1
+PUT3 pp PUT3
+GPM1 pp GPM1
+GPM1 pp GPM1
+GPM1 pp GPM1
+GPM1 pp GPM1
+HSP82 pp HSP82
+ARO7 pp ARO7
+ARO7 pp ARO7
+PHO4 pp PHO4
+MCM1 pp MCM1
+HMRA2 pp MCM1
+HMRA2 pp MCM1
+1MNM_E pd HMRA2
+1MNM_E pd MCM1
+1MNM_E pd MCM1
+1MNM_E pd HMRA2
+1MNM_F pd HMRA2
+1MNM_F pd MCM1
+1MNM_F pd MCM1
+1MNM_F pd HMRA2
+PRE9 pp SCL1
+PRE6 pp PRE8
+PUP2 pp PRE9
+PUP2 pp PRE8
+PRE5 pp PRE9
+PRE10 pp PRE9
+PRE10 pp PRE8
+PRE3 pp SCL1
+PRE3 pp PRE10
+PUP1 pp SCL1
+PUP1 pp PRE3
+PUP3 pp PUP1
+PRE2 pp PRE6
+PRE2 pp PRE1
+PRE7 pp PUP2
+PRE4 pp PRE3
+PRE4 pp PRE10
+PRE4 pp PRE5
+PRE4 pp PRE7
+PRE3 pp PRE4
+PRE3 pp PRE3
+PUP1 pp PRE7
+PUP1 pp PRE4
+PUP1 pp PRE2
+PUP3 pp PRE2
+PUP3 pp PRE7
+PRE1 pp PRE2
+PRE2 pp PUP3
+PRE2 pp PRE1
+PRE7 pp PUP1
+PRE7 pp PUP3
+PRE4 pp PRE3
+PRE4 pp PUP1
+PRE4 pp SCL1
+IPP1 pp IPP1
+TFP1 pp TFP1
+HMRA2 pp HMRA1
+CDC8 pp CDC8
+CDC8 pp CDC8
+Aspartate_Aminotransferase pp Aspartate_Aminotransferase
+PUT3 pd 1ZME_A
+PUT3 pd 1ZME_A
+PUT3 pp PUT3
+SRP1 pp SRP1
+SRP1 pp SRP1
+CDC8 pp CDC8
+Gcn4-Pmse pp Gcn4-Pmse
+Gcn4-Pmse pp Gcn4-Pmse
+Gcn4-Pmse pp Gcn4-Pmse
+Gcn4-Pmse pp Gcn4-Pmse
+Gcn4-Pmse pp Gcn4-Pmse
+HAP1 pd 1HWT_A
+HAP1 pd 1HWT_B
+HAP1 pd 1HWT_B
+HAP1 pd 1HWT_A
+HAP1 pp HAP1
+1HWT_E pd HAP1
+1HWT_F pd HAP1
+HAP1 pd 1HWT_E
+HAP1 pd 1HWT_F
+HAP1 pd 1HWT_A
+HAP1 pd 1HWT_B
+HAP1 pp HAP1
+HAP1 pp HAP1
+HAP1 pp HAP1
+HAP1 pp HAP1
+HAP1 pd 1HWT_A
+CYB2 pp CYB2
+HAP1 pd 2HAP_B
+HAP1 pd 2HAP_A
+HAP1 pd 2HAP_B
+HAP1 pp HAP1
+GPM1 pp GPM1
+CTA1 pp CTA1
+CTA1 pp CTA1
+CTA1 pp CTA1
+CTA1 pp CTA1
+RPL40A pp YUH1
+YUH1 pp YUH1
+YUH1 pp RPL40A
+RPL40A pp YUH1
+RPL40A pp YUH1
+SWI6 pp SWI6
+PDX3 pp PDX3
+1CN8_B interactsWith RPL30
+RBL2 pp RBL2
+HPA2 pp HPA2
+HPA2 pp HPA2
+HPA2 pp HPA2
+HPA2 pp HPA2
+HPA2 pp HPA2
+GPM1 pp GPM1
+GPM1 pp GPM1
+GPM1 pp GPM1
+GPM1 pp GPM1
+GPM1 pp GPM1
+GPM1 pp GPM1
+GPM1 pp GPM1
+CET1 pp CET1
+CET1 pp CET1
+CET1 pp CET1
+YPD1 pp YPD1
+YPD1 pp YPD1
+LTP1 pp LTP1
+LTP1 pp LTP1
+HOM6 pp HOM6
+HOM6 pp HOM6
+LTP1 pp LTP1
+PDC6 pp PDC6
+URA3 pp URA3
+URA3 pp URA3
+RPL30 interactsWith 1CK5_A
+PAI3 pp PEP4
+Proteinase_Inhibitor_Ia3_Peptide pp PEP4
+SMT3 pp ULP1
+EFB1 pp TEF2
+TFP1 pp TFP1
+Flp_Recombinase pp Flp_Recombinase
+Flp_Recombinase pp Flp_Recombinase
+Flp_Recombinase pp Flp_Recombinase
+Flp_Recombinase pp Flp_Recombinase
+CKS1 pp CKS1
+CKS1 pp CKS1
+CKS1 pp CKS1
+1FCW_B interactsWith 1FCW_A
+1FCW_C interactsWith 1FCW_B
+1FCW_C interactsWith 1FCW_A
+1FCW_E interactsWith 1FCW_D
+Med22 pp Med11
+Med22 pp Med17
+Med1 pp Med14
+Bre2 interactsWith Unknown
+Unknown interactsWith Set1
+Unknown interactsWith Swd1
+Unknown interactsWith Spp1
+Unknown interactsWith Swd2
+Unknown interactsWith Swd3
+Unknown interactsWith Sdc1
+Ssu72 pp Rpb2
+Ssu72 pp Pta1
+Pta1 pp Pcf11
+Cft1 pp Clp1
+Cft2 pp Ydl094c
+Cft1 pp Pcf11
+Cft1 pp Rna14
+Ysh1 pp Pcf11
+Ysh1 pp Clp1
+Cft2 pp Pcf11
+Cft2 pp Ssu72
+Cft2 pp Pfs2
+Cft2 pp Pta1
+Cft2 pp Ysh1
+Cft2 pp Cft1
+Cft2 pp Cft2
+Pcf11 pp Rpo21
+Cft1 pp Rpo21
+Cft2 pp Rpo21
+Sec2 pp Sec4
+Sec2 pp Elp1
+RPN1 interactsWith Unknown
+Unknown interactsWith RPN10
+Unknown interactsWith RPN11
+Unknown interactsWith RPN12
+Unknown interactsWith RPN2
+Unknown interactsWith RPN3
+Unknown interactsWith RPN5
+Unknown interactsWith RPN6
+Unknown interactsWith RPN8
+Unknown interactsWith RPN9
+Unknown interactsWith RPT1
+Unknown interactsWith RPT2
+Unknown interactsWith RPT3
+Unknown interactsWith RPT6
+Unknown interactsWith UBP6
+Unknown interactsWith RPN7
+Unknown interactsWith YDL025C
+PRE2 interactsWith Unknown
+Unknown interactsWith PRE1
+Unknown interactsWith PRE10
+Unknown interactsWith PRE3
+Unknown interactsWith PRE5
+Unknown interactsWith PRE6
+Unknown interactsWith PRE7
+Unknown interactsWith PRE8
+Unknown interactsWith PRE9
+Unknown interactsWith PUP1
+Unknown interactsWith PUP2
+Unknown interactsWith SCL1
+Unknown interactsWith VPS13
+ARX1 interactsWith Unknown
+Unknown interactsWith RPL20B
+Unknown interactsWith RPL4A
+Unknown interactsWith RPL8B
+Unknown interactsWith YJL122W
+BCP1 interactsWith Unknown
+Unknown interactsWith RPL23A
+Unknown interactsWith YPL208W
+SPT16 interactsWith Unknown
+Unknown interactsWith CKA1
+Unknown interactsWith CKA2
+Unknown interactsWith CKB1
+Unknown interactsWith CKB2
+STO1 interactsWith Unknown
+Unknown interactsWith CBC2
+CDC39 interactsWith Unknown
+Unknown interactsWith CCR4
+Unknown interactsWith POP2
+DBP3 interactsWith Unknown
+Unknown interactsWith BMH1
+Unknown interactsWith NSR1
+DBP7 interactsWith Unknown
+Unknown interactsWith FUN12
+Unknown interactsWith MAK21
+Unknown interactsWith RRP5
+HGH1 interactsWith Unknown
+Unknown interactsWith EFT2
+PRT1 interactsWith Unknown
+Unknown interactsWith NIP1
+Unknown interactsWith RPG1
+Unknown interactsWith TIF5
+Unknown interactsWith HCR1
+Unknown interactsWith TIF34
+Unknown interactsWith TIF35
+RRP46 interactsWith Unknown
+Unknown interactsWith CSL4
+Unknown interactsWith DIS3
+Unknown interactsWith RRP4
+Unknown interactsWith RRP40
+Unknown interactsWith RRP42
+Unknown interactsWith RRP45
+Unknown interactsWith RRP6
+Unknown interactsWith SKI6
+Unknown interactsWith SKI7
+Unknown interactsWith LRP1
+Unknown interactsWith RRP43
+GAR1 interactsWith Unknown
+Unknown interactsWith CBF5
+Unknown interactsWith NHP2
+Unknown interactsWith NOP6
+Unknown interactsWith YGR283C
+Unknown interactsWith YMR310C
+GIR2 interactsWith Unknown
+Unknown interactsWith GIR1
+IMD3 interactsWith Unknown
+Unknown interactsWith IMD2
+Unknown interactsWith IMD4
+IPI1 interactsWith Unknown
+Unknown interactsWith IPI2
+Unknown interactsWith IPI3
+SRP1 interactsWith Unknown
+Unknown interactsWith KAP95
+NAT3 interactsWith Unknown
+Unknown interactsWith MDM20
+SRB5 interactsWith Unknown
+Unknown interactsWith MED4
+Unknown interactsWith NUT1
+Unknown interactsWith SIN4
+Unknown interactsWith SRB4
+Unknown interactsWith SRB2
+Unknown interactsWith MED7
+Unknown interactsWith RGR1
+MES1 interactsWith Unknown
+Unknown interactsWith ARC1
+Unknown interactsWith YGL245W
+TIF4631 interactsWith Unknown
+Unknown interactsWith IML1
+Unknown interactsWith CDC33
+Unknown interactsWith CDC48
+Unknown interactsWith KAP123
+Unknown interactsWith TIF2
+Unknown interactsWith TOP1
+Unknown interactsWith YEF3
+PTA1 interactsWith Unknown
+Unknown interactsWith CFT2
+Unknown interactsWith YSH1
+Unknown interactsWith CFT1
+Unknown interactsWith GLC7
+Unknown interactsWith MPE1
+Unknown interactsWith PAP1
+Unknown interactsWith PFS2
+Unknown interactsWith REF2
+Unknown interactsWith SSU72
+MTR4 interactsWith Unknown
+Unknown interactsWith AIR2
+Unknown interactsWith TRF4
+NAB2 interactsWith Unknown
+Unknown interactsWith KAP104
+YKR079C interactsWith Unknown
+Unknown interactsWith NAP1
+Unknown interactsWith YBR267W
+NOC3 interactsWith Unknown
+Unknown interactsWith NOC2
+Unknown interactsWith PUS7
+NOP58 interactsWith Unknown
+Unknown interactsWith SIK1
+Unknown interactsWith RVB2
+NOP7 interactsWith Unknown
+Unknown interactsWith ERB1
+Unknown interactsWith YTM1
+PRP19 interactsWith Unknown
+Unknown interactsWith CDC40
+Unknown interactsWith CEF1
+Unknown interactsWith CLF1
+NOP12 interactsWith Unknown
+Unknown interactsWith BRX1
+Unknown interactsWith PWP1
+RCL1 interactsWith Unknown
+Unknown interactsWith BMS1
+RLI1 interactsWith Unknown
+Unknown interactsWith RPP0
+Unknown interactsWith YNL260C
+RPA34 interactsWith Unknown
+Unknown interactsWith RPA49
+Unknown interactsWith RPA135
+Unknown interactsWith RPA190
+Unknown interactsWith RPA43
+Unknown interactsWith RPC40
+Unknown interactsWith YER004W
+RPO21 interactsWith Unknown
+Unknown interactsWith RPB5
+Unknown interactsWith RPO26
+Unknown interactsWith RPB2
+Unknown interactsWith RPB3
+Unknown interactsWith RPB4
+Unknown interactsWith RPB7
+Unknown interactsWith TAF14
+Unknown interactsWith TFG1
+Unknown interactsWith TFG2
+Unknown interactsWith SPT5
+Unknown interactsWith SPT6
+RPC25 interactsWith Unknown
+Unknown interactsWith RPC19
+Unknown interactsWith RPC53
+Unknown interactsWith RET1
+Unknown interactsWith RPC17
+Unknown interactsWith RPC34
+Unknown interactsWith RPC37
+Unknown interactsWith RPC82
+Unknown interactsWith RPO31
+Unknown interactsWith PSY2
+Unknown interactsWith RPC31
+Unknown interactsWith STU1
+POP3 interactsWith Unknown
+Unknown interactsWith POP1
+Unknown interactsWith POP4
+Unknown interactsWith RPP1
+RRB1 interactsWith Unknown
+Unknown interactsWith RPL3
+RSC58 interactsWith Unknown
+Unknown interactsWith STH1
+Unknown interactsWith ARP7
+Unknown interactsWith ARP9
+Unknown interactsWith NPL6
+Unknown interactsWith RSC2
+Unknown interactsWith RSC3
+Unknown interactsWith RSC4
+Unknown interactsWith RSC6
+Unknown interactsWith RSC8
+Unknown interactsWith RSC9
+Unknown interactsWith SFH1
+Unknown interactsWith RTT102
+SIT4 interactsWith Unknown
+Unknown interactsWith RAT1
+Unknown interactsWith SAP185
+Unknown interactsWith RCK2
+Unknown interactsWith SAP155
+Unknown interactsWith SAP190
+SPT16 interactsWith Unknown
+Unknown interactsWith CDC73
+Unknown interactsWith CTR9
+Unknown interactsWith LEO1
+Unknown interactsWith PAF1
+Unknown interactsWith RTF1
+Unknown interactsWith CHD1
+Unknown interactsWith POB3
+LHP1 interactsWith Unknown
+Unknown interactsWith SRP68
+Unknown interactsWith SRP72
+TFC1 interactsWith Unknown
+Unknown interactsWith ILS1
+Unknown interactsWith TFC4
+Unknown interactsWith TFC7
+GCD6 interactsWith Unknown
+Unknown interactsWith GCD1
+Unknown interactsWith GCD11
+Unknown interactsWith GCD2
+Unknown interactsWith GCD7
+Unknown interactsWith SUI3
+Unknown interactsWith ACT1
+SUP35 interactsWith Unknown
+Unknown interactsWith SUP45
+THP2 interactsWith Unknown
+Unknown interactsWith HPR1
+Unknown interactsWith MFT1
+Unknown interactsWith RLR1
+Unknown interactsWith YNL253W
+TRM1 interactsWith Unknown
+Unknown interactsWith NSA1
+YPL183C interactsWith Unknown
+Unknown interactsWith TRM7
+SNU56 interactsWith Unknown
+Unknown interactsWith MUD1
+Unknown interactsWith PRP39
+Unknown interactsWith PRP40
+Unknown interactsWith SNU71
+Unknown interactsWith PRP42
+Unknown interactsWith SNP1
+Unknown interactsWith TRA1
+BRR2 interactsWith Unknown
+Unknown interactsWith PRP8
+LSM3 interactsWith Unknown
+Unknown interactsWith PRP4
+Unknown interactsWith SNU114
+Unknown interactsWith KEM1
+Unknown interactsWith LSM1
+Unknown interactsWith PAT1
+Unknown interactsWith YGR054W
+Unknown interactsWith LSM6
+Unknown interactsWith PRP24
+Unknown interactsWith PRP3
+Unknown interactsWith PRP6
+Unknown interactsWith SWR1
+Unknown interactsWith STT4
+UTP9 interactsWith Unknown
+Unknown interactsWith POL5
+Unknown interactsWith NAN1
+Unknown interactsWith UTP10
+Unknown interactsWith UTP15
+Unknown interactsWith UTP4
+Unknown interactsWith UTP5
+Unknown interactsWith UTP8
+UTP21 interactsWith Unknown
+Unknown interactsWith DIP2
+Unknown interactsWith UTP13
+Unknown interactsWith UTP18
+Unknown interactsWith UTP6
+Unknown interactsWith PWP2
+UTP22 interactsWith Unknown
+Unknown interactsWith RRP7
+YDR117C interactsWith Unknown
+Unknown interactsWith RPS4B
+YKL088W interactsWith Unknown
+Unknown interactsWith SIS2
+Unknown interactsWith YOR054C
+Unknown interactsWith Swm1
+Unknown interactsWith Cdc26
+Unknown interactsWith Apc1
+Unknown interactsWith Apc11
+Unknown interactsWith Doc1
+Unknown interactsWith Apc9
+Unknown interactsWith Mnd2
+Unknown interactsWith Cdc23
+Unknown interactsWith Apc5
+Unknown interactsWith Apc4
+Unknown interactsWith Cdc27
+Unknown interactsWith Apc2
+Cdc16 interactsWith Unknown
+Apc2 interactsWith Unknown
+Unknown interactsWith Cdc16
+Unknown interactsWith Apc4
+Unknown interactsWith Cdc23
+Unknown interactsWith Doc1
+Unknown interactsWith Apc11
+APC/C_complex interactsWith Ama1
+APC/C_complex interactsWith Pds1
+COMPASS_complex interactsWith Hht1
+Hem15 pp Hem15
+Ykg9 pp Ykg9
+Bur1 pd GAL1/10_UAS
+Cet1 pd GAL1
+RNA_Pol_II pd ADH1
+Cet1 pd GAL1/10_UAS
+Dsg1 pd GAL1/10_UAS
+Bur1 pd GAL1
+RNA_Pol_II pd ADH1_promoter
+Tim23 interactsWith Unknown
+Unknown interactsWith Pam16
+Unknown interactsWith Tim44
+Unknown interactsWith mtHSP70
+Unknown interactsWith Tim17
+Unknown interactsWith Tom40
+Unknown interactsWith Tom5
+Unknown interactsWith Tom22
+Unknown interactsWith Tom70
+Unknown interactsWith Tom22
+Tim21 interactsWith Tom22-Tom40
+Unknown interactsWith Tom40
+Tim21 pp Tim23
+Tim21 interactsWith TIM23core-PAM_complex
+Tim21 interactsWith Unknown
+Tim21 interactsWith Tom70-Tom40-Tom22-Tom5_complex
+Tim23 pp Tim50
+Tim21 pp Tom22
+Pam18 pp Tim17
+TEL1 pp Xrs2
+Clb2-Cdk1 interactsWith Ace2
+Clb2-Cdk1 interactsWith Ady3
+Clb2-Cdk1 interactsWith Arg1
+Clb2-Cdk1 interactsWith Ase1
+Clb2-Cdk1 interactsWith Ash1
+Clb2-Cdk1 interactsWith Atg20
+Clb2-Cdk1 interactsWith Axl2
+Clb2-Cdk1 interactsWith Bbp1
+Clb2-Cdk1 interactsWith Bck2
+Clb2-Cdk1 interactsWith Bem1
+Clb2-Cdk1 interactsWith Bem3
+Clb2-Cdk1 interactsWith Bna3
+Clb2-Cdk1 interactsWith Bni1
+Clb2-Cdk1 interactsWith Bsp1
+Clb2-Cdk1 interactsWith Bud4
+Clb2-Cdk1 interactsWith Bud6
+Clb2-Cdk1 interactsWith Caf120
+Clb2-Cdk1 interactsWith Cdc20
+Clb2-Cdk1 interactsWith Cdc5
+Clb2-Cdk1 interactsWith Cdc6
+Clb2-Cdk1 interactsWith Cdh1
+Clb2-Cdk1 interactsWith Chs2
+Clb2-Cdk1 interactsWith Cnn1
+Clb2-Cdk1 interactsWith Csr2
+Clb2-Cdk1 interactsWith Cst9
+Clb2-Cdk1 interactsWith Cyc2
+Clb2-Cdk1 interactsWith Dbf2
+Clb2-Cdk1 interactsWith Dbf20
+Clb2-Cdk1 interactsWith Dbf4
+Clb2-Cdk1 interactsWith Ddc1
+Clb2-Cdk1 interactsWith Dna2
+Clb2-Cdk1 interactsWith Dna43
+Clb2-Cdk1 interactsWith Dnf2
+Clb2-Cdk1 interactsWith Dpb2
+Clb2-Cdk1 interactsWith Eco1
+Clb2-Cdk1 interactsWith Elm1
+Clb2-Cdk1 interactsWith Far1
+Clb2-Cdk1 interactsWith Fin1
+Clb2-Cdk1 interactsWith Fkh2
+Clb2-Cdk1 interactsWith Fmt1
+Clb2-Cdk1 interactsWith Frt2
+Clb2-Cdk1 interactsWith Fun21
+Clb2-Cdk1 interactsWith Fun30
+Clb2-Cdk1 interactsWith Fus1
+Clb2-Cdk1 interactsWith Gin4
+Clb2-Cdk1 interactsWith Hcm1
+Clb2-Cdk1 interactsWith Hdr1
+Clb2-Cdk1 interactsWith Hos4
+Clb2-Cdk1 interactsWith Icy2
+Clb2-Cdk1 interactsWith Ifh1
+Clb2-Cdk1 interactsWith Ino2
+Clb2-Cdk1 interactsWith Ipl1
+Clb2-Cdk1 interactsWith Jsn1
+Clb2-Cdk1 interactsWith Kar3
+Clb2-Cdk1 interactsWith Kar9
+Clb2-Cdk1 interactsWith Kel1
+Clb2-Cdk1 interactsWith Kel2
+Clb2-Cdk1 interactsWith Kip2
+Clb2-Cdk1 interactsWith Kip3
+Clb2-Cdk1 interactsWith Lre1
+Clb2-Cdk1 interactsWith Lrs4
+Clb2-Cdk1 interactsWith Lte1
+Clb2-Cdk1 interactsWith Luv1
+Clb2-Cdk1 interactsWith Mcm2
+Clb2-Cdk1 interactsWith Mcm3
+Clb2-Cdk1 interactsWith Mcm6
+Clb2-Cdk1 interactsWith Mih1
+Clb2-Cdk1 interactsWith Mlp1
+Clb2-Cdk1 interactsWith Mmr1
+Clb2-Cdk1 interactsWith Mms4
+Clb2-Cdk1 interactsWith Mob1
+Clb2-Cdk1 interactsWith Mpc54
+Clb2-Cdk1 interactsWith Mps2
+Clb2-Cdk1 interactsWith Mpt1
+Clb2-Cdk1 interactsWith Msb1
+Clb2-Cdk1 interactsWith Msh6
+Clb2-Cdk1 interactsWith Nbp1
+Clb2-Cdk1 interactsWith Ndd1
+Clb2-Cdk1 interactsWith Net1
+Clb2-Cdk1 interactsWith Nth1
+Clb2-Cdk1 interactsWith Nup1
+Clb2-Cdk1 interactsWith Nup60
+Clb2-Cdk1 interactsWith Orc1
+Clb2-Cdk1 interactsWith Orc2
+Clb2-Cdk1 interactsWith Orc6
+Clb2-Cdk1 interactsWith Pak1
+Clb2-Cdk1 interactsWith Pcl7
+Clb2-Cdk1 interactsWith Pin2
+Clb2-Cdk1 interactsWith Pkh2
+Clb2-Cdk1 interactsWith Plm2
+Clb2-Cdk1 interactsWith Pol1
+Clb2-Cdk1 interactsWith Pom152
+Clb2-Cdk1 interactsWith Ptk2
+Clb2-Cdk1 interactsWith Pxl1
+Clb2-Cdk1 interactsWith Rad9
+Clb2-Cdk1 interactsWith Rav1
+Clb2-Cdk1 interactsWith Rbs1
+Clb2-Cdk1 interactsWith Rfc1
+Clb2-Cdk1 interactsWith Rlf2
+Clb2-Cdk1 interactsWith Rrp6
+Clb2-Cdk1 interactsWith Rts1
+Clb2-Cdk1 interactsWith Sac7
+Clb2-Cdk1 interactsWith Sec3
+Clb2-Cdk1 interactsWith Sfb3
+Clb2-Cdk1 interactsWith Sld2
+Clb2-Cdk1 interactsWith Sld3
+Clb2-Cdk1 interactsWith Slk19
+Clb2-Cdk1 interactsWith Smc4
+Clb2-Cdk1 interactsWith Spa2
+Clb2-Cdk1 interactsWith Spc110
+Clb2-Cdk1 interactsWith Src1
+Clb2-Cdk1 interactsWith Srm1
+Clb2-Cdk1 interactsWith Ssk1
+Clb2-Cdk1 interactsWith Stb1
+Clb2-Cdk1 interactsWith Stu2
+Clb2-Cdk1 interactsWith Swi5
+Clb2-Cdk1 interactsWith Swi6
+Clb2-Cdk1 interactsWith Tfg1
+Clb2-Cdk1 interactsWith Tus1
+Clb2-Cdk1 interactsWith Ufe1
+Clb2-Cdk1 interactsWith Ulp2
+Clb2-Cdk1 interactsWith Whi5
+Clb2-Cdk1 interactsWith Xbp1
+Clb2-Cdk1 interactsWith YDL025C
+Clb2-Cdk1 interactsWith YDL089W
+Clb2-Cdk1 interactsWith YDR348C
+Clb2-Cdk1 interactsWith Yen1
+Clb2-Cdk1 interactsWith YER158C
+Clb2-Cdk1 interactsWith YGR035C
+Clb2-Cdk1 interactsWith YHL035C
+Clb2-Cdk1 interactsWith YHR149C
+Clb2-Cdk1 interactsWith YJL084C
+Clb2-Cdk1 interactsWith YJR054W
+Clb2-Cdk1 interactsWith YKR078W
+Clb2-Cdk1 interactsWith YLR187W
+Clb2-Cdk1 interactsWith YLR278C
+Clb2-Cdk1 interactsWith YML119W
+Clb2-Cdk1 interactsWith YNL058C
+Clb2-Cdk1 interactsWith YNL321W
+Clb2-Cdk1 interactsWith YNR047W
+Clb2-Cdk1 interactsWith YOL036W
+Clb2-Cdk1 interactsWith YOL070C
+Clb2-Cdk1 interactsWith YOR066W
+Clb2-Cdk1 interactsWith YOR315W
+Clb2-Cdk1 interactsWith YPL267W
+Clb2-Cdk1 interactsWith Yrf1-3
+Clb2-Cdk1 interactsWith Yrf1-6
+Clb2-Cdk1 interactsWith Yta7
+Clb2-Cdk1 interactsWith Zip1
+Clb5-Cdk1 interactsWith Ace2
+Clb5-Cdk1 interactsWith Ady3
+Clb5-Cdk1 interactsWith Arg1
+Clb5-Cdk1 interactsWith Ase1
+Clb5-Cdk1 interactsWith Ash1
+Clb5-Cdk1 interactsWith Atg20
+Clb5-Cdk1 interactsWith Axl2
+Clb5-Cdk1 interactsWith Bbp1
+Clb5-Cdk1 interactsWith Bck2
+Clb5-Cdk1 interactsWith Bem1
+Clb5-Cdk1 interactsWith Bem3
+Clb5-Cdk1 interactsWith Bna3
+Clb5-Cdk1 interactsWith Bni1
+Clb5-Cdk1 interactsWith Bsp1
+Clb5-Cdk1 interactsWith Bud4
+Clb5-Cdk1 interactsWith Bud6
+Clb5-Cdk1 interactsWith Caf120
+Clb5-Cdk1 interactsWith Cdc20
+Clb5-Cdk1 interactsWith Cdc5
+Clb5-Cdk1 interactsWith Cdc6
+Clb5-Cdk1 interactsWith Cdh1
+Clb5-Cdk1 interactsWith Chs2
+Clb5-Cdk1 interactsWith Cnn1
+Clb5-Cdk1 interactsWith Csr2
+Clb5-Cdk1 interactsWith Cst9
+Clb5-Cdk1 interactsWith Cyc2
+Clb5-Cdk1 interactsWith Dbf2
+Clb5-Cdk1 interactsWith Dbf20
+Clb5-Cdk1 interactsWith Dbf4
+Clb5-Cdk1 interactsWith Ddc1
+Clb5-Cdk1 interactsWith Dna2
+Clb5-Cdk1 interactsWith Dna43
+Clb5-Cdk1 interactsWith Dnf2
+Clb5-Cdk1 interactsWith Dpb2
+Clb5-Cdk1 interactsWith Eco1
+Clb5-Cdk1 interactsWith Elm1
+Clb5-Cdk1 interactsWith Far1
+Clb5-Cdk1 interactsWith Fin1
+Clb5-Cdk1 interactsWith Fkh2
+Clb5-Cdk1 interactsWith Fmt1
+Clb5-Cdk1 interactsWith Frt2
+Clb5-Cdk1 interactsWith Fun21
+Clb5-Cdk1 interactsWith Fun30
+Clb5-Cdk1 interactsWith Fus1
+Clb5-Cdk1 interactsWith Gin4
+Clb5-Cdk1 interactsWith Hcm1
+Clb5-Cdk1 interactsWith Hdr1
+Clb5-Cdk1 interactsWith Hos4
+Clb5-Cdk1 interactsWith Icy2
+Clb5-Cdk1 interactsWith Ifh1
+Clb5-Cdk1 interactsWith Ino2
+Clb5-Cdk1 interactsWith Ipl1
+Clb5-Cdk1 interactsWith Jsn1
+Clb5-Cdk1 interactsWith Kar3
+Clb5-Cdk1 interactsWith Kar9
+Clb5-Cdk1 interactsWith Kel1
+Clb5-Cdk1 interactsWith Kel2
+Clb5-Cdk1 interactsWith Kip2
+Clb5-Cdk1 interactsWith Kip3
+Clb5-Cdk1 interactsWith Lre1
+Clb5-Cdk1 interactsWith Lrs4
+Clb5-Cdk1 interactsWith Lte1
+Clb5-Cdk1 interactsWith Luv1
+Clb5-Cdk1 interactsWith Mcm2
+Clb5-Cdk1 interactsWith Mcm3
+Clb5-Cdk1 interactsWith Mcm6
+Clb5-Cdk1 interactsWith Mih1
+Clb5-Cdk1 interactsWith Mlp1
+Clb5-Cdk1 interactsWith Mmr1
+Clb5-Cdk1 interactsWith Mms4
+Clb5-Cdk1 interactsWith Mob1
+Clb5-Cdk1 interactsWith Mpc54
+Clb5-Cdk1 interactsWith Mps2
+Clb5-Cdk1 interactsWith Mpt1
+Clb5-Cdk1 interactsWith Msb1
+Clb5-Cdk1 interactsWith Msh6
+Clb5-Cdk1 interactsWith Nbp1
+Clb5-Cdk1 interactsWith Ndd1
+Clb5-Cdk1 interactsWith Net1
+Clb5-Cdk1 interactsWith Nth1
+Clb5-Cdk1 interactsWith Nup1
+Clb5-Cdk1 interactsWith Nup60
+Clb5-Cdk1 interactsWith Orc1
+Clb5-Cdk1 interactsWith Orc2
+Clb5-Cdk1 interactsWith Orc6
+Clb5-Cdk1 interactsWith Pak1
+Clb5-Cdk1 interactsWith Pcl7
+Clb5-Cdk1 interactsWith Pin2
+Clb5-Cdk1 interactsWith Pkh2
+Clb5-Cdk1 interactsWith Plm2
+Clb5-Cdk1 interactsWith Pol1
+Clb5-Cdk1 interactsWith Pom152
+Clb5-Cdk1 interactsWith Ptk2
+Clb5-Cdk1 interactsWith Pxl1
+Clb5-Cdk1 interactsWith Rad9
+Clb5-Cdk1 interactsWith Rav1
+Clb5-Cdk1 interactsWith Rbs1
+Clb5-Cdk1 interactsWith Rfc1
+Clb5-Cdk1 interactsWith Rlf2
+Clb5-Cdk1 interactsWith Rrp6
+Clb5-Cdk1 interactsWith Rts1
+Clb5-Cdk1 interactsWith Sac7
+Clb5-Cdk1 interactsWith Sec3
+Clb5-Cdk1 interactsWith Sfb3
+Clb5-Cdk1 interactsWith Sld2
+Clb5-Cdk1 interactsWith Sld3
+Clb5-Cdk1 interactsWith Slk19
+Clb5-Cdk1 interactsWith Smc4
+Clb5-Cdk1 interactsWith Spa2
+Clb5-Cdk1 interactsWith Spc110
+Clb5-Cdk1 interactsWith Src1
+Clb5-Cdk1 interactsWith Srm1
+Clb5-Cdk1 interactsWith Ssk1
+Clb5-Cdk1 interactsWith Stb1
+Clb5-Cdk1 interactsWith Stu2
+Clb5-Cdk1 interactsWith Swe1
+Clb5-Cdk1 interactsWith Swi5
+Clb5-Cdk1 interactsWith Swi6
+Clb5-Cdk1 interactsWith Tfg1
+Clb5-Cdk1 interactsWith Tus1
+Clb5-Cdk1 interactsWith Ufe1
+Clb5-Cdk1 interactsWith Ulp2
+Clb5-Cdk1 interactsWith Whi5
+Clb5-Cdk1 interactsWith Xbp1
+Clb5-Cdk1 interactsWith YDL025C
+Clb5-Cdk1 interactsWith YDL089W
+Clb5-Cdk1 interactsWith YDR348C
+Clb5-Cdk1 interactsWith Yen1
+Clb5-Cdk1 interactsWith YER158C
+Clb5-Cdk1 interactsWith YGR035C
+Clb5-Cdk1 interactsWith YHL035C
+Clb5-Cdk1 interactsWith YHR149C
+Clb5-Cdk1 interactsWith YJL084C
+Clb5-Cdk1 interactsWith YJR054W
+Clb5-Cdk1 interactsWith YKR078W
+Clb5-Cdk1 interactsWith YLR187W
+Clb5-Cdk1 interactsWith YLR278C
+Clb5-Cdk1 interactsWith YML119W
+Clb5-Cdk1 interactsWith YNL058C
+Clb5-Cdk1 interactsWith YNL321W
+Clb5-Cdk1 interactsWith YNR047W
+Clb5-Cdk1 interactsWith YOL036W
+Clb5-Cdk1 interactsWith YOL070C
+Clb5-Cdk1 interactsWith YOR066W
+Clb5-Cdk1 interactsWith YOR315W
+Clb5-Cdk1 interactsWith YPL267W
+Clb5-Cdk1 interactsWith Yrf1-3
+Clb5-Cdk1 interactsWith Yrf1-6
+Clb5-Cdk1 interactsWith Yta7
+Clb5-Cdk1 interactsWith Zip1
+Grr1 pp Hof1
+Vrp1 pp Hof1
+Hrr25 pp Hrr25
+Unknown interactsWith Tfb4
+Unknown interactsWith Ssl1
+Unknown interactsWith Tfb2
+Unknown interactsWith Rad3
+Tfb1 interactsWith Unknown
+Prp9 interactsWith Unknown
+Unknown interactsWith Prp21
+Unknown interactsWith Prp11
+PBS2 interactsWith DIG2
+PBS2 interactsWith TEC1
+PBS2 interactsWith FLO1
+PBS2 interactsWith DSE1
+PBS2 interactsWith GPR1
+PBS2 interactsWith PCL1
+PBS2 interactsWith TPK1
+PBS2 interactsWith CLN1
+PBS2 interactsWith FKH1
+PBS2 interactsWith CTS1
+PBS2 interactsWith FKH2
+PBS2 interactsWith MEP2
+PBS2 interactsWith MUC1
+PBS2 interactsWith RGS2
+PBS2 interactsWith ASH1
+PBS2 interactsWith EGT2
+PBS2 interactsWith RAS2
+PBS2 interactsWith SOK2
+PBS2 interactsWith FLO10
+PBS2 interactsWith URE2
+PBS2 interactsWith MSN1
+PBS2 interactsWith SIP4
+PBS2 interactsWith IPK1
+PBS2 interactsWith PRY2
+PBS2 interactsWith SFL1
+PBS2 interactsWith SNO1
+PBS2 interactsWith PRY3
+PBS2 interactsWith CLA4
+PBS2 interactsWith RCS1
+PBS2 interactsWith ROX1
+PBS2 interactsWith DFG16
+PBS2 interactsWith AGA1
+PBS2 interactsWith MSN5
+PBS2 interactsWith MSS11
+PBS2 interactsWith ENT1
+PBS2 interactsWith ISW1
+PBS2 interactsWith HMS1
+PBS2 interactsWith GAT4
+PBS2 interactsWith BMH1
+PBS2 interactsWith RIM9
+PBS2 interactsWith DIA3
+PBS2 interactsWith BUD6
+PBS2 interactsWith BNI1
+PBS2 interactsWith RSC1
+PBS2 interactsWith MEP3
+PBS2 interactsWith MEP1
+PBS2 interactsWith DIA1
+PBS2 interactsWith PGU1
+PBS2 interactsWith CNA1
+PBS2 interactsWith BUD8
+PBS2 interactsWith YPL114W
+PBS2 interactsWith KTR2
+PBS2 interactsWith TPK2
+PBS2 interactsWith YLR042C
+PBS2 interactsWith YOR225W
+PBS2 interactsWith YEL033W
+PBS2 interactsWith SPO12
+PBS2 interactsWith YPS1
+PBS2 interactsWith COG5
+PBS2 interactsWith RIM8
+PBS2 interactsWith YGR149W
+PBS2 interactsWith YAP1
+PBS2 interactsWith YLR414C
+PBS2 interactsWith PAM1
+PBS2 interactsWith WHI3
+PBS2 interactsWith RPS0A
+PBS2 interactsWith WHI2
+PBS2 interactsWith SUT1
+PBS2 interactsWith CAR2
+PBS2 interactsWith ASI2
+PBS2 interactsWith BUD4
+PBS2 interactsWith DFG5
+PBS2 interactsWith IME2
+PBS2 interactsWith YOL155C
+PBS2 interactsWith KSS1
+PBS2 interactsWith MID2
+PBS2 interactsWith MGA1
+PBS2 interactsWith FMP45
+PBS2 interactsWith YOR248W
+PBS2 interactsWith LIN1
+PBS2 interactsWith YJL017W
+IPK1 interactsWith DIG2
+IPK1 interactsWith TEC1
+IPK1 interactsWith FLO1
+IPK1 interactsWith CLB1
+IPK1 interactsWith DSE1
+IPK1 interactsWith GPR1
+IPK1 interactsWith PCL1
+IPK1 interactsWith XBP1
+IPK1 interactsWith YAK1
+IPK1 interactsWith TPK1
+IPK1 interactsWith CLN1
+IPK1 interactsWith TPK3
+IPK1 interactsWith FKH1
+IPK1 interactsWith CTS1
+IPK1 interactsWith FKH2
+IPK1 interactsWith MEP2
+IPK1 interactsWith ASH1
+IPK1 interactsWith EGT2
+IPK1 interactsWith RAS2
+IPK1 interactsWith PDE1
+IPK1 interactsWith SOK2
+IPK1 interactsWith FLO10
+IPK1 interactsWith CLN2
+IPK1 interactsWith URE2
+IPK1 interactsWith MSN1
+IPK1 interactsWith SIP4
+IPK1 interactsWith PRY2
+IPK1 interactsWith PBS2
+IPK1 interactsWith SNO1
+IPK1 interactsWith ACE2
+IPK1 interactsWith PRY3
+IPK1 interactsWith CLA4
+IPK1 interactsWith RCS1
+IPK1 interactsWith CLB2
+IPK1 interactsWith ROX1
+IPK1 interactsWith DFG16
+IPK1 interactsWith MSN5
+IPK1 interactsWith MSS11
+IPK1 interactsWith CNB1
+IPK1 interactsWith ENT1
+IPK1 interactsWith ISW1
+IPK1 interactsWith HMS1
+IPK1 interactsWith GAT4
+IPK1 interactsWith BMH1
+IPK1 interactsWith HSL1
+IPK1 interactsWith RIM9
+IPK1 interactsWith MRP21
+IPK1 interactsWith DIA3
+IPK1 interactsWith BUD6
+IPK1 interactsWith BNI1
+IPK1 interactsWith RSC1
+IPK1 interactsWith MEP3
+IPK1 interactsWith MEP1
+IPK1 interactsWith HOG1
+IPK1 interactsWith DIA1
+IPK1 interactsWith PGU1
+IPK1 interactsWith CNA1
+IPK1 interactsWith BUD8
+IPK1 interactsWith RIM13
+IPK1 interactsWith YPL114W
+IPK1 interactsWith KTR2
+IPK1 interactsWith TPK2
+IPK1 interactsWith YJL142C
+IPK1 interactsWith YLR042C
+IPK1 interactsWith YOR225W
+IPK1 interactsWith YEL033W
+IPK1 interactsWith SPO12
+IPK1 interactsWith RIM8
+IPK1 interactsWith YGR149W
+IPK1 interactsWith YAP1
+IPK1 interactsWith YLR414C
+IPK1 interactsWith SSA4
+IPK1 interactsWith PAM1
+IPK1 interactsWith WHI3
+IPK1 interactsWith YGR045C
+IPK1 interactsWith RPS0A
+IPK1 interactsWith WHI2
+IPK1 interactsWith MKS1
+IPK1 interactsWith SUT1
+IPK1 interactsWith CAR2
+IPK1 interactsWith SPH1
+IPK1 interactsWith DSE2
+IPK1 interactsWith ASI2
+IPK1 interactsWith BUD4
+IPK1 interactsWith DFG5
+IPK1 interactsWith IME2
+IPK1 interactsWith YOL155C
+IPK1 interactsWith KSS1
+IPK1 interactsWith MID2
+IPK1 interactsWith MGA1
+IPK1 interactsWith FMP45
+IPK1 interactsWith YOR248W
+IPK1 interactsWith SRL1
+IPK1 interactsWith MIH1
+IPK1 interactsWith LIN1
+IPK1 interactsWith YJL017W
+IRA2 interactsWith TEC1
+IRA2 interactsWith FLO1
+IRA2 interactsWith DSE1
+IRA2 interactsWith GPR1
+IRA2 interactsWith PCL1
+IRA2 interactsWith TPK1
+IRA2 interactsWith CLN1
+IRA2 interactsWith TPK3
+IRA2 interactsWith FKH1
+IRA2 interactsWith FKH2
+IRA2 interactsWith MUC1
+IRA2 interactsWith ASH1
+IRA2 interactsWith EGT2
+IRA2 interactsWith PDE1
+IRA2 interactsWith SOK2
+IRA2 interactsWith URE2
+IRA2 interactsWith MSN1
+IRA2 interactsWith SIP4
+IRA2 interactsWith PRY2
+IRA2 interactsWith SNO1
+IRA2 interactsWith CLA4
+IRA2 interactsWith CLB2
+IRA2 interactsWith ROX1
+IRA2 interactsWith DFG16
+IRA2 interactsWith MSN5
+IRA2 interactsWith MSS11
+IRA2 interactsWith ISW1
+IRA2 interactsWith HMS1
+IRA2 interactsWith GAT4
+IRA2 interactsWith RIM9
+IRA2 interactsWith MRP21
+IRA2 interactsWith DIA3
+IRA2 interactsWith BUD6
+IRA2 interactsWith BNI1
+IRA2 interactsWith SFP1
+IRA2 interactsWith HMI1
+IRA2 interactsWith MEP1
+IRA2 interactsWith HOG1
+IRA2 interactsWith DIA1
+IRA2 interactsWith RIM13
+IRA2 interactsWith TPK2
+IRA2 interactsWith YJL142C
+IRA2 interactsWith YLR042C
+IRA2 interactsWith YOR225W
+IRA2 interactsWith SPO12
+IRA2 interactsWith YPS1
+IRA2 interactsWith RIM8
+IRA2 interactsWith YGR149W
+IRA2 interactsWith YAP1
+IRA2 interactsWith YLR414C
+IRA2 interactsWith SSA4
+IRA2 interactsWith PAM1
+IRA2 interactsWith WHI3
+IRA2 interactsWith YGR045C
+IRA2 interactsWith RPS0A
+IRA2 interactsWith WHI2
+IRA2 interactsWith MKS1
+IRA2 interactsWith SUT1
+IRA2 interactsWith MSM1
+IRA2 interactsWith SPH1
+IRA2 interactsWith DSE2
+IRA2 interactsWith ASI2
+IRA2 interactsWith KSS1
+IRA2 interactsWith MID2
+IRA2 interactsWith MGA1
+IRA2 interactsWith FMP45
+IRA2 interactsWith LIN1
+HOG1 interactsWith DIG2
+HOG1 interactsWith CLB1
+HOG1 interactsWith DSE1
+HOG1 interactsWith GPR1
+HOG1 interactsWith PCL1
+HOG1 interactsWith TPK1
+HOG1 interactsWith CLN1
+HOG1 interactsWith TPK3
+HOG1 interactsWith FKH1
+HOG1 interactsWith CTS1
+HOG1 interactsWith FKH2
+HOG1 interactsWith MEP2
+HOG1 interactsWith RGS2
+HOG1 interactsWith ASH1
+HOG1 interactsWith EGT2
+HOG1 interactsWith RAS2
+HOG1 interactsWith PDE1
+HOG1 interactsWith SOK2
+HOG1 interactsWith FLO10
+HOG1 interactsWith CLN2
+HOG1 interactsWith SIP4
+HOG1 interactsWith IPK1
+HOG1 interactsWith PRY2
+HOG1 interactsWith SNO1
+HOG1 interactsWith PRY3
+HOG1 interactsWith CLA4
+HOG1 interactsWith RCS1
+HOG1 interactsWith CLB2
+HOG1 interactsWith ROX1
+HOG1 interactsWith AGA1
+HOG1 interactsWith MSN5
+HOG1 interactsWith PDE2
+HOG1 interactsWith ENT1
+HOG1 interactsWith ISW1
+HOG1 interactsWith HMS1
+HOG1 interactsWith GAT4
+HOG1 interactsWith HSL1
+HOG1 interactsWith BUD6
+HOG1 interactsWith BNI1
+HOG1 interactsWith RSC1
+HOG1 interactsWith MEP3
+HOG1 interactsWith MEP1
+HOG1 interactsWith DIA1
+HOG1 interactsWith PGU1
+HOG1 interactsWith CNA1
+HOG1 interactsWith RIM13
+HOG1 interactsWith YPL114W
+HOG1 interactsWith KTR2
+HOG1 interactsWith YJL142C
+HOG1 interactsWith YLR042C
+HOG1 interactsWith YOR225W
+HOG1 interactsWith YEL033W
+HOG1 interactsWith SPO12
+HOG1 interactsWith YPS1
+HOG1 interactsWith COG5
+HOG1 interactsWith RIM8
+HOG1 interactsWith YGR149W
+HOG1 interactsWith YAP1
+HOG1 interactsWith YLR414C
+HOG1 interactsWith PAM1
+HOG1 interactsWith YGR045C
+HOG1 interactsWith RPS0A
+HOG1 interactsWith SUT1
+HOG1 interactsWith DFG5
+HOG1 interactsWith IME2
+HOG1 interactsWith YOL155C
+HOG1 interactsWith KSS1
+HOG1 interactsWith MID2
+HOG1 interactsWith MGA1
+HOG1 interactsWith YOR248W
+HOG1 interactsWith LIN1
+HSL1 interactsWith DIG2
+HSL1 interactsWith TEC1
+HSL1 interactsWith FLO1
+HSL1 interactsWith DSE1
+HSL1 interactsWith SNF1
+HSL1 interactsWith GPR1
+HSL1 interactsWith XBP1
+HSL1 interactsWith TPK1
+HSL1 interactsWith CLN1
+HSL1 interactsWith TPK3
+HSL1 interactsWith FKH1
+HSL1 interactsWith CTS1
+HSL1 interactsWith MEP2
+HSL1 interactsWith MUC1
+HSL1 interactsWith RGS2
+HSL1 interactsWith ASH1
+HSL1 interactsWith EGT2
+HSL1 interactsWith RAS2
+HSL1 interactsWith PDE1
+HSL1 interactsWith CLN2
+HSL1 interactsWith URE2
+HSL1 interactsWith MSN1
+HSL1 interactsWith SIP4
+HSL1 interactsWith PRY2
+HSL1 interactsWith PBS2
+HSL1 interactsWith SNO1
+HSL1 interactsWith ACE2
+HSL1 interactsWith PRY3
+HSL1 interactsWith RCS1
+HSL1 interactsWith ELM1
+HSL1 interactsWith ROX1
+HSL1 interactsWith DFG16
+HSL1 interactsWith AGA1
+HSL1 interactsWith MSS11
+HSL1 interactsWith CNB1
+HSL1 interactsWith ENT1
+HSL1 interactsWith ISW1
+HSL1 interactsWith GAT4
+HSL1 interactsWith BMH1
+HSL1 interactsWith RIM9
+HSL1 interactsWith DIA3
+HSL1 interactsWith BUD6
+HSL1 interactsWith RSC1
+HSL1 interactsWith MEP3
+HSL1 interactsWith HMI1
+HSL1 interactsWith MEP1
+HSL1 interactsWith DIA1
+HSL1 interactsWith PGU1
+HSL1 interactsWith CNA1
+HSL1 interactsWith BUD8
+HSL1 interactsWith RIM13
+HSL1 interactsWith KTR2
+HSL1 interactsWith TPK2
+HSL1 interactsWith YLR042C
+HSL1 interactsWith YOR225W
+HSL1 interactsWith YEL033W
+HSL1 interactsWith SPO12
+HSL1 interactsWith COG5
+HSL1 interactsWith RIM8
+HSL1 interactsWith YAP1
+HSL1 interactsWith PAM1
+HSL1 interactsWith RPS0A
+HSL1 interactsWith MKS1
+HSL1 interactsWith SUT1
+HSL1 interactsWith DSE2
+HSL1 interactsWith ASI2
+HSL1 interactsWith BUD4
+HSL1 interactsWith IME2
+HSL1 interactsWith YOL155C
+HSL1 interactsWith MID2
+HSL1 interactsWith YOR248W
+HSL1 interactsWith SRL1
+HSL1 interactsWith LIN1
+HSL1 interactsWith YJL017W
+SFL1 interactsWith DIG2
+SFL1 interactsWith TEC1
+SFL1 interactsWith FLO1
+SFL1 interactsWith CLB1
+SFL1 interactsWith DSE1
+SFL1 interactsWith GPR1
+SFL1 interactsWith XBP1
+SFL1 interactsWith TPK1
+SFL1 interactsWith CLN1
+SFL1 interactsWith TPK3
+SFL1 interactsWith FKH1
+SFL1 interactsWith FKH2
+SFL1 interactsWith MEP2
+SFL1 interactsWith MUC1
+SFL1 interactsWith RGS2
+SFL1 interactsWith EGT2
+SFL1 interactsWith RAS2
+SFL1 interactsWith PDE1
+SFL1 interactsWith FLO10
+SFL1 interactsWith URE2
+SFL1 interactsWith MSN1
+SFL1 interactsWith SIP4
+SFL1 interactsWith IPK1
+SFL1 interactsWith PRY2
+SFL1 interactsWith SNO1
+SFL1 interactsWith CLB2
+SFL1 interactsWith ROX1
+SFL1 interactsWith DFG16
+SFL1 interactsWith MSS11
+SFL1 interactsWith PDE2
+SFL1 interactsWith ENT1
+SFL1 interactsWith ISW1
+SFL1 interactsWith HMS1
+SFL1 interactsWith GAT4
+SFL1 interactsWith RIM9
+SFL1 interactsWith DIA3
+SFL1 interactsWith BUD6
+SFL1 interactsWith BNI1
+SFL1 interactsWith RSC1
+SFL1 interactsWith MEP3
+SFL1 interactsWith MEP1
+SFL1 interactsWith DIA1
+SFL1 interactsWith PGU1
+SFL1 interactsWith CNA1
+SFL1 interactsWith BUD8
+SFL1 interactsWith YPL114W
+SFL1 interactsWith KTR2
+SFL1 interactsWith YOR225W
+SFL1 interactsWith YEL033W
+SFL1 interactsWith SPO12
+SFL1 interactsWith YPS1
+SFL1 interactsWith COG5
+SFL1 interactsWith RIM8
+SFL1 interactsWith YAP1
+SFL1 interactsWith YLR414C
+SFL1 interactsWith PAM1
+SFL1 interactsWith WHI3
+SFL1 interactsWith SUT1
+SFL1 interactsWith CAR2
+SFL1 interactsWith SPH1
+SFL1 interactsWith ASI2
+SFL1 interactsWith BUD4
+SFL1 interactsWith DFG5
+SFL1 interactsWith IME2
+SFL1 interactsWith YOL155C
+SFL1 interactsWith MGA1
+SFL1 interactsWith FMP45
+SFL1 interactsWith YOR248W
+SFL1 interactsWith SRL1
+SFL1 interactsWith MIH1
+SFL1 interactsWith YJL017W
+YAK1 interactsWith RAS2
+YAK1 interactsWith RSR1
+PRY2 interactsWith RAS2
+ROX1 interactsWith RAS2
+TEC1 interactsWith RAS2
+CLB1 interactsWith RAS2
+CLB1 interactsWith RSR1
+WHI3 interactsWith RSR1
+SSA4 interactsWith RAS2
+YGR149W interactsWith RSR1
+YLR414C interactsWith RAS2
+PAM1 interactsWith RSR1
+CAR2 interactsWith RAS2
+WHI2 interactsWith RSR1
+YJL017W interactsWith RAS2
+BUD4 interactsWith RAS2
+RAS2 interactsWith RSR1
+PBS2 interactsWith RAS2
+SUT1 interactsWith RSR1
+YAP1 interactsWith RSR1
+YGR045C interactsWith RSR1
+RPS0A interactsWith RAS2
+DFG5 interactsWith RAS2
+YOL155C interactsWith RAS2
+IME2 interactsWith RAS2
+SFL1 interactsWith RSR1
+LIN1 interactsWith RAS2
+FKH2 interactsWith RSR1
+MEP2 interactsWith RSR1
+YOR248W interactsWith RAS2
+CLN1 interactsWith RAS2
+RCS1 interactsWith RAS2
+PRY3 interactsWith RAS2
+PRY3 interactsWith RSR1
+SNO1 interactsWith RAS2
+PDE2 interactsWith RAS2
+ISW1 interactsWith RAS2
+DFG16 interactsWith RAS2
+GAT4 interactsWith RAS2
+BUD8 interactsWith RAS2
+BUD8 interactsWith RSR1
+KTR2 interactsWith RAS2
+TPK2 interactsWith RAS2
+TPK2 interactsWith RSR1
+SFP1 interactsWith RSR1
+RSC1 interactsWith RAS2
+RSC1 interactsWith RSR1
+YEL033W interactsWith RAS2
+YPS1 interactsWith RAS2
+YPS1 interactsWith RSR1
+AKR1 interactsWith RAS2
+AKR1 interactsWith RSR1
+YJL142C interactsWith RAS2
+YAK1 interactsWith FLO8
+YAK1 interactsWith STE20
+YAK1 interactsWith STE12
+YAK1 interactsWith PHD1
+YAK1 interactsWith MSN1
+YAK1 interactsWith GLN3
+YAK1 interactsWith BEM1
+YAK1 interactsWith TEC1
+FKH2 interactsWith TEC1
+FLO10 interactsWith FLO8
+FLO10 interactsWith STE20
+FLO10 interactsWith STE12
+FLO10 interactsWith PHD1
+FLO10 interactsWith MSN1
+FLO10 interactsWith GLN3
+FLO10 interactsWith BEM1
+MIH1 interactsWith TEC1
+MKS1 interactsWith FLO8
+MKS1 interactsWith STE20
+MKS1 interactsWith STE12
+MKS1 interactsWith PHD1
+MKS1 interactsWith MSN1
+MKS1 interactsWith GLN3
+MKS1 interactsWith BEM1
+FLO10 interactsWith TEC1
+MUC1 interactsWith FLO8
+MUC1 interactsWith PHD1
+MUC1 interactsWith MSN1
+MUC1 interactsWith GLN3
+MUC1 interactsWith BEM1
+PRY2 interactsWith FLO8
+PRY2 interactsWith STE20
+PRY2 interactsWith STE12
+PRY2 interactsWith PHD1
+PRY2 interactsWith MSN1
+PRY2 interactsWith GLN3
+PRY2 interactsWith BEM1
+SPH1 interactsWith PHD1
+SPH1 interactsWith MSN1
+ROX1 interactsWith PHD1
+ROX1 interactsWith MSN1
+ROX1 interactsWith GLN3
+TEC1 interactsWith FLO8
+TEC1 interactsWith STE20
+TEC1 interactsWith STE12
+TEC1 interactsWith PHD1
+TEC1 interactsWith MSN1
+TEC1 interactsWith GLN3
+TEC1 interactsWith BEM1
+CLB1 interactsWith FLO8
+CLB1 interactsWith STE20
+CLB1 interactsWith STE12
+CLB1 interactsWith PHD1
+CLB1 interactsWith MSN1
+CLB1 interactsWith GLN3
+CLB1 interactsWith BEM1
+WHI3 interactsWith FLO8
+WHI3 interactsWith STE20
+WHI3 interactsWith STE12
+WHI3 interactsWith PHD1
+WHI3 interactsWith MSN1
+WHI3 interactsWith GLN3
+SNF1 interactsWith FLO8
+SNF1 interactsWith STE20
+SNF1 interactsWith STE12
+SNF1 interactsWith PHD1
+SNF1 interactsWith MSN1
+SNF1 interactsWith GLN3
+SNF1 interactsWith TEC1
+SSA4 interactsWith FLO8
+SSA4 interactsWith STE20
+SSA4 interactsWith STE12
+SSA4 interactsWith PHD1
+SSA4 interactsWith MSN1
+SSA4 interactsWith GLN3
+SSA4 interactsWith BEM1
+SSA4 interactsWith TEC1
+PCL1 interactsWith FLO8
+PCL1 interactsWith STE20
+PCL1 interactsWith STE12
+PCL1 interactsWith PHD1
+PCL1 interactsWith MSN1
+PCL1 interactsWith GLN3
+PCL1 interactsWith BEM1
+PCL1 interactsWith TEC1
+YGR149W interactsWith FLO8
+YGR149W interactsWith STE20
+YGR149W interactsWith STE12
+YGR149W interactsWith PHD1
+YGR149W interactsWith MSN1
+YGR149W interactsWith GLN3
+YGR149W interactsWith BEM1
+YGR149W interactsWith TEC1
+DIG2 interactsWith FLO8
+DIG2 interactsWith STE20
+DIG2 interactsWith STE12
+DIG2 interactsWith PHD1
+DIG2 interactsWith MSN1
+DIG2 interactsWith GLN3
+DIG2 interactsWith BEM1
+RIM8 interactsWith FLO8
+RIM8 interactsWith STE20
+RIM8 interactsWith STE12
+RIM8 interactsWith PHD1
+RIM8 interactsWith MSN1
+RIM8 interactsWith GLN3
+TPK1 interactsWith FLO8
+TPK1 interactsWith STE20
+TPK1 interactsWith STE12
+TPK1 interactsWith PHD1
+TPK1 interactsWith MSN1
+TPK1 interactsWith GLN3
+TPK1 interactsWith TEC1
+YLR414C interactsWith FLO8
+YLR414C interactsWith STE20
+YLR414C interactsWith STE12
+YLR414C interactsWith PHD1
+YLR414C interactsWith MSN1
+YLR414C interactsWith GLN3
+YLR414C interactsWith BEM1
+YLR414C interactsWith TEC1
+PAM1 interactsWith FLO8
+PAM1 interactsWith STE20
+PAM1 interactsWith STE12
+PAM1 interactsWith PHD1
+PAM1 interactsWith MSN1
+XBP1 interactsWith FLO8
+XBP1 interactsWith PHD1
+XBP1 interactsWith MSN1
+XBP1 interactsWith GLN3
+BUD8 interactsWith TEC1
+CAR2 interactsWith STE12
+CAR2 interactsWith PHD1
+CAR2 interactsWith GLN3
+DSE1 interactsWith FLO8
+DSE1 interactsWith STE20
+DSE1 interactsWith STE12
+DSE1 interactsWith PHD1
+DSE1 interactsWith MSN1
+DSE1 interactsWith GLN3
+DSE1 interactsWith TEC1
+IME2 interactsWith TEC1
+IPK1 interactsWith FLO8
+IPK1 interactsWith STE20
+IPK1 interactsWith STE12
+IPK1 interactsWith PHD1
+IPK1 interactsWith MSN1
+IPK1 interactsWith GLN3
+WHI2 interactsWith FLO8
+WHI2 interactsWith PHD1
+WHI2 interactsWith MSN1
+CLN1 interactsWith TEC1
+CLN2 interactsWith FLO8
+CLN2 interactsWith STE20
+CLN2 interactsWith STE12
+CLN2 interactsWith PHD1
+CLN2 interactsWith MSN1
+CLN2 interactsWith GLN3
+YJL017W interactsWith STE12
+YJL017W interactsWith PHD1
+YJL017W interactsWith MSN1
+YJL017W interactsWith GLN3
+BUD4 interactsWith FLO8
+BUD4 interactsWith PHD1
+BUD4 interactsWith MSN1
+BUD4 interactsWith GLN3
+RAS2 interactsWith FLO8
+RAS2 interactsWith STE20
+RAS2 interactsWith STE12
+RAS2 interactsWith PHD1
+RAS2 interactsWith MSN1
+RAS2 interactsWith GLN3
+RAS2 interactsWith BEM1
+RAS2 interactsWith TEC1
+ASI2 interactsWith FLO8
+ASI2 interactsWith PHD1
+ASI2 interactsWith MSN1
+PBS2 interactsWith FLO8
+PBS2 interactsWith STE20
+PBS2 interactsWith STE12
+PBS2 interactsWith PHD1
+PBS2 interactsWith GLN3
+PBS2 interactsWith TEC1
+SUT1 interactsWith FLO8
+SUT1 interactsWith PHD1
+SUT1 interactsWith MSN1
+SUT1 interactsWith GLN3
+SUT1 interactsWith BEM1
+SUT1 interactsWith TEC1
+SNF4 interactsWith FLO8
+SNF4 interactsWith STE20
+SNF4 interactsWith STE12
+SNF4 interactsWith PHD1
+SNF4 interactsWith MSN1
+SNF4 interactsWith GLN3
+SNF4 interactsWith BEM1
+SNF4 interactsWith TEC1
+YAP1 interactsWith FLO8
+YAP1 interactsWith PHD1
+YAP1 interactsWith MSN1
+MSN1 interactsWith FLO8
+MSN1 interactsWith STE20
+MSN1 interactsWith STE12
+MSN1 interactsWith PHD1
+MSN1 interactsWith GLN3
+YGR045C interactsWith FLO8
+YGR045C interactsWith STE20
+YGR045C interactsWith STE12
+YGR045C interactsWith PHD1
+YGR045C interactsWith MSN1
+YGR045C interactsWith GLN3
+YGR045C interactsWith BEM1
+YGR045C interactsWith TEC1
+RPS0A interactsWith FLO8
+RPS0A interactsWith STE20
+RPS0A interactsWith STE12
+RPS0A interactsWith PHD1
+RPS0A interactsWith MSN1
+RPS0A interactsWith GLN3
+RPS0A interactsWith BEM1
+RPS0A interactsWith TEC1
+URE2 interactsWith FLO8
+URE2 interactsWith STE20
+URE2 interactsWith STE12
+URE2 interactsWith PHD1
+URE2 interactsWith MSN1
+URE2 interactsWith GLN3
+URE2 interactsWith BEM1
+URE2 interactsWith TEC1
+DFG5 interactsWith FLO8
+DFG5 interactsWith STE20
+DFG5 interactsWith STE12
+DFG5 interactsWith PHD1
+DFG5 interactsWith MSN1
+DFG5 interactsWith GLN3
+DFG5 interactsWith BEM1
+SIP4 interactsWith FLO8
+SIP4 interactsWith STE20
+SIP4 interactsWith STE12
+SIP4 interactsWith PHD1
+SIP4 interactsWith MSN1
+SIP4 interactsWith GLN3
+SIP4 interactsWith BEM1
+SIP4 interactsWith TEC1
+ASH1 interactsWith STE20
+ASH1 interactsWith PHD1
+ASH1 interactsWith MSN1
+YOL155C interactsWith FLO8
+YOL155C interactsWith STE20
+YOL155C interactsWith STE12
+YOL155C interactsWith PHD1
+YOL155C interactsWith MSN1
+YOL155C interactsWith GLN3
+DIG2 interactsWith TEC1
+EGT2 interactsWith FLO8
+EGT2 interactsWith STE20
+EGT2 interactsWith STE12
+EGT2 interactsWith PHD1
+EGT2 interactsWith MSN1
+EGT2 interactsWith GLN3
+EGT2 interactsWith BEM1
+IME2 interactsWith FLO8
+IME2 interactsWith STE20
+IME2 interactsWith STE12
+IME2 interactsWith PHD1
+IME2 interactsWith MSN1
+IME2 interactsWith GLN3
+IME2 interactsWith BEM1
+RGS2 interactsWith FLO8
+RGS2 interactsWith STE20
+RGS2 interactsWith STE12
+RGS2 interactsWith PHD1
+RGS2 interactsWith MSN1
+RGS2 interactsWith GLN3
+RGS2 interactsWith BEM1
+RGS2 interactsWith TEC1
+SRL1 interactsWith FLO8
+SRL1 interactsWith STE20
+SRL1 interactsWith STE12
+SRL1 interactsWith PHD1
+SRL1 interactsWith MSN1
+SRL1 interactsWith GLN3
+MID2 interactsWith TEC1
+MIH1 interactsWith FLO8
+MIH1 interactsWith STE20
+MIH1 interactsWith STE12
+MIH1 interactsWith PHD1
+MIH1 interactsWith MSN1
+PDE1 interactsWith FLO8
+PDE1 interactsWith STE20
+PDE1 interactsWith STE12
+PDE1 interactsWith PHD1
+PDE1 interactsWith BEM1
+PDE1 interactsWith TEC1
+TPK3 interactsWith FLO8
+TPK3 interactsWith STE12
+TPK3 interactsWith PHD1
+TPK3 interactsWith MSN1
+SFL1 interactsWith PHD1
+SFL1 interactsWith TEC1
+SOK2 interactsWith FLO8
+SOK2 interactsWith STE20
+SOK2 interactsWith STE12
+SOK2 interactsWith PHD1
+SOK2 interactsWith MSN1
+SOK2 interactsWith GLN3
+SOK2 interactsWith BEM1
+SOK2 interactsWith TEC1
+LIN1 interactsWith FLO8
+LIN1 interactsWith STE20
+LIN1 interactsWith STE12
+LIN1 interactsWith PHD1
+LIN1 interactsWith MSN1
+LIN1 interactsWith GLN3
+LIN1 interactsWith BEM1
+LIN1 interactsWith TEC1
+FKH1 interactsWith TEC1
+FKH2 interactsWith FLO8
+FKH2 interactsWith STE20
+FKH2 interactsWith STE12
+FKH2 interactsWith PHD1
+FKH2 interactsWith MSN1
+FKH2 interactsWith GLN3
+FKH2 interactsWith BEM1
+MGA1 interactsWith FLO8
+MGA1 interactsWith STE20
+MGA1 interactsWith STE12
+MGA1 interactsWith PHD1
+MGA1 interactsWith MSN1
+MGA1 interactsWith GLN3
+MGA1 interactsWith BEM1
+MEP2 interactsWith FLO8
+MEP2 interactsWith STE12
+MEP2 interactsWith PHD1
+MEP2 interactsWith MSN1
+MEP2 interactsWith GLN3
+MEP2 interactsWith BEM1
+FMP45 interactsWith FLO8
+FMP45 interactsWith STE20
+FMP45 interactsWith STE12
+FMP45 interactsWith PHD1
+FMP45 interactsWith MSN1
+FMP45 interactsWith GLN3
+YOR248W interactsWith FLO8
+YOR248W interactsWith STE20
+YOR248W interactsWith STE12
+YOR248W interactsWith PHD1
+YOR248W interactsWith MSN1
+YOR248W interactsWith GLN3
+GPR1 interactsWith FLO8
+GPR1 interactsWith STE12
+GPR1 interactsWith PHD1
+GPR1 interactsWith MSN1
+GPR1 interactsWith GLN3
+GPR1 interactsWith BEM1
+KSS1 interactsWith FLO8
+KSS1 interactsWith STE20
+KSS1 interactsWith STE12
+KSS1 interactsWith PHD1
+KSS1 interactsWith MSN1
+KSS1 interactsWith GLN3
+CLN1 interactsWith FLO8
+CLN1 interactsWith STE20
+CLN1 interactsWith STE12
+CLN1 interactsWith PHD1
+CLN1 interactsWith MSN1
+CLN1 interactsWith GLN3
+CLN1 interactsWith BEM1
+MGA1 interactsWith TEC1
+MID2 interactsWith FLO8
+MID2 interactsWith STE20
+MID2 interactsWith STE12
+MID2 interactsWith PHD1
+MID2 interactsWith MSN1
+MID2 interactsWith GLN3
+MID2 interactsWith BEM1
+CTS1 interactsWith FLO8
+CTS1 interactsWith STE20
+CTS1 interactsWith STE12
+CTS1 interactsWith PHD1
+CTS1 interactsWith MSN1
+CTS1 interactsWith GLN3
+CTS1 interactsWith BEM1
+DSE2 interactsWith FLO8
+DSE2 interactsWith PHD1
+DSE2 interactsWith MSN1
+DSE2 interactsWith GLN3
+DSE2 interactsWith BEM1
+DSE2 interactsWith TEC1
+ENT1 interactsWith TEC1
+FKH1 interactsWith FLO8
+FKH1 interactsWith STE20
+FKH1 interactsWith STE12
+FKH1 interactsWith PHD1
+FKH1 interactsWith MSN1
+FKH1 interactsWith GLN3
+FKH1 interactsWith BEM1
+CLN3 interactsWith FLO8
+CLN3 interactsWith STE20
+CLN3 interactsWith STE12
+CLN3 interactsWith PHD1
+CLN3 interactsWith MSN1
+CLN3 interactsWith GLN3
+CLN3 interactsWith BEM1
+RCS1 interactsWith FLO8
+RCS1 interactsWith STE20
+RCS1 interactsWith STE12
+RCS1 interactsWith PHD1
+RCS1 interactsWith MSN1
+RCS1 interactsWith GLN3
+RCS1 interactsWith BEM1
+RCS1 interactsWith TEC1
+IPK1 interactsWith TEC1
+ACE2 interactsWith FLO8
+ACE2 interactsWith STE20
+ACE2 interactsWith STE12
+ACE2 interactsWith PHD1
+ACE2 interactsWith MSN1
+ACE2 interactsWith GLN3
+ACE2 interactsWith BEM1
+PRY3 interactsWith STE20
+PRY3 interactsWith PHD1
+PRY3 interactsWith MSN1
+PRY3 interactsWith GLN3
+CLA4 interactsWith FLO8
+CLA4 interactsWith STE20
+CLA4 interactsWith STE12
+CLA4 interactsWith PHD1
+CLA4 interactsWith MSN1
+CLA4 interactsWith GLN3
+SNO1 interactsWith FLO8
+SNO1 interactsWith STE20
+SNO1 interactsWith STE12
+SNO1 interactsWith PHD1
+SNO1 interactsWith MSN1
+SNO1 interactsWith GLN3
+SNO1 interactsWith BEM1
+SNO1 interactsWith TEC1
+EGT2 interactsWith TEC1
+ELM1 interactsWith STE20
+CLB1 interactsWith TEC1
+CLB2 interactsWith FLO8
+CLB2 interactsWith STE20
+CLB2 interactsWith STE12
+CLB2 interactsWith PHD1
+CLB2 interactsWith MSN1
+CLB2 interactsWith GLN3
+CLB2 interactsWith BEM1
+MSN5 interactsWith FLO8
+MSN5 interactsWith STE20
+MSN5 interactsWith STE12
+MSN5 interactsWith PHD1
+MSN5 interactsWith MSN1
+MSN5 interactsWith GLN3
+MSN5 interactsWith BEM1
+BMH1 interactsWith FLO8
+BMH1 interactsWith STE20
+BMH1 interactsWith STE12
+BMH1 interactsWith PHD1
+BMH1 interactsWith MSN1
+BMH1 interactsWith GLN3
+BMH1 interactsWith BEM1
+AGA1 interactsWith FLO8
+AGA1 interactsWith STE20
+AGA1 interactsWith STE12
+AGA1 interactsWith PHD1
+AGA1 interactsWith MSN1
+AGA1 interactsWith GLN3
+AGA1 interactsWith BEM1
+CNB1 interactsWith FLO8
+CNB1 interactsWith STE20
+CNB1 interactsWith STE12
+CNB1 interactsWith PHD1
+CNB1 interactsWith GLN3
+PDE2 interactsWith FLO8
+PDE2 interactsWith STE20
+PDE2 interactsWith STE12
+PDE2 interactsWith PHD1
+PDE2 interactsWith MSN1
+PDE2 interactsWith GLN3
+PDE2 interactsWith BEM1
+PDE2 interactsWith TEC1
+ENT1 interactsWith FLO8
+ENT1 interactsWith STE20
+ENT1 interactsWith STE12
+ENT1 interactsWith PHD1
+ENT1 interactsWith MSN1
+ENT1 interactsWith GLN3
+ENT1 interactsWith BEM1
+ISW1 interactsWith FLO8
+ISW1 interactsWith PHD1
+ISW1 interactsWith MSN1
+DFG16 interactsWith FLO8
+DFG16 interactsWith STE20
+DFG16 interactsWith STE12
+DFG16 interactsWith PHD1
+DFG16 interactsWith MSN1
+DFG16 interactsWith GLN3
+MSN5 interactsWith TEC1
+MSS11 interactsWith FLO8
+MSS11 interactsWith STE20
+MSS11 interactsWith STE12
+MSS11 interactsWith PHD1
+MSS11 interactsWith MSN1
+MSS11 interactsWith GLN3
+MSS11 interactsWith BEM1
+HMS1 interactsWith FLO8
+HMS1 interactsWith STE20
+HMS1 interactsWith STE12
+HMS1 interactsWith PHD1
+HMS1 interactsWith MSN1
+HMS1 interactsWith GLN3
+HMS1 interactsWith BEM1
+GAT4 interactsWith FLO8
+GAT4 interactsWith STE20
+GAT4 interactsWith STE12
+GAT4 interactsWith PHD1
+GAT4 interactsWith MSN1
+GAT4 interactsWith GLN3
+DIA2 interactsWith FLO8
+DIA2 interactsWith PHD1
+DIA2 interactsWith MSN1
+DIA2 interactsWith GLN3
+DFG5 interactsWith TEC1
+BMH1 interactsWith TEC1
+DIA3 interactsWith FLO8
+DIA3 interactsWith PHD1
+DIA3 interactsWith MSN1
+DIA3 interactsWith GLN3
+RIM9 interactsWith FLO8
+RIM9 interactsWith STE20
+RIM9 interactsWith STE12
+RIM9 interactsWith PHD1
+RIM9 interactsWith MSN1
+RIM9 interactsWith GLN3
+HOG1 interactsWith TEC1
+HSL1 interactsWith FLO8
+HSL1 interactsWith PHD1
+HSL1 interactsWith MSN1
+MKS1 interactsWith TEC1
+CLN3 interactsWith TEC1
+BUD8 interactsWith FLO8
+BUD8 interactsWith STE20
+BUD8 interactsWith STE12
+BUD8 interactsWith PHD1
+BUD8 interactsWith MSN1
+BUD8 interactsWith GLN3
+BUD8 interactsWith BEM1
+KSS1 interactsWith TEC1
+KTR2 interactsWith FLO8
+KTR2 interactsWith STE20
+KTR2 interactsWith STE12
+KTR2 interactsWith PHD1
+KTR2 interactsWith MSN1
+KTR2 interactsWith GLN3
+KTR2 interactsWith BEM1
+TPK2 interactsWith FLO8
+TPK2 interactsWith STE20
+TPK2 interactsWith STE12
+TPK2 interactsWith PHD1
+TPK2 interactsWith MSN1
+TPK2 interactsWith GLN3
+TPK2 interactsWith BEM1
+TPK2 interactsWith TEC1
+YLR042C interactsWith FLO8
+YLR042C interactsWith STE20
+YLR042C interactsWith STE12
+YLR042C interactsWith PHD1
+YLR042C interactsWith MSN1
+YLR042C interactsWith GLN3
+YLR042C interactsWith TEC1
+RIM13 interactsWith FLO8
+RIM13 interactsWith PHD1
+KTR2 interactsWith TEC1
+MEP1 interactsWith FLO8
+MEP1 interactsWith STE20
+MEP1 interactsWith STE12
+MEP1 interactsWith PHD1
+MEP1 interactsWith MSN1
+MEP1 interactsWith GLN3
+MEP1 interactsWith BEM1
+HMS1 interactsWith TEC1
+HOG1 interactsWith FLO8
+HOG1 interactsWith STE20
+HOG1 interactsWith STE12
+HOG1 interactsWith MSN1
+HOG1 interactsWith GLN3
+SFP1 interactsWith FLO8
+SFP1 interactsWith STE20
+SFP1 interactsWith STE12
+SFP1 interactsWith PHD1
+SFP1 interactsWith MSN1
+SFP1 interactsWith GLN3
+RSC1 interactsWith FLO8
+RSC1 interactsWith STE20
+RSC1 interactsWith STE12
+RSC1 interactsWith PHD1
+RSC1 interactsWith MSN1
+RSC1 interactsWith GLN3
+RSC1 interactsWith BEM1
+RSC1 interactsWith TEC1
+VPS25 interactsWith FLO8
+VPS25 interactsWith STE20
+VPS25 interactsWith STE12
+VPS25 interactsWith PHD1
+VPS25 interactsWith MSN1
+VPS25 interactsWith GLN3
+VPS25 interactsWith BEM1
+VPS25 interactsWith TEC1
+YPL114W interactsWith FLO8
+YPL114W interactsWith PHD1
+YPL114W interactsWith MSN1
+YOR225W interactsWith FLO8
+YOR225W interactsWith STE20
+YOR225W interactsWith STE12
+YOR225W interactsWith PHD1
+YOR225W interactsWith MSN1
+YOR225W interactsWith GLN3
+YOR225W interactsWith BEM1
+YOR225W interactsWith TEC1
+YEL033W interactsWith FLO8
+YEL033W interactsWith STE20
+YEL033W interactsWith STE12
+YEL033W interactsWith PHD1
+YEL033W interactsWith MSN1
+YEL033W interactsWith GLN3
+YEL033W interactsWith BEM1
+SPO12 interactsWith FLO8
+SPO12 interactsWith PHD1
+SPO12 interactsWith MSN1
+SPO12 interactsWith GLN3
+YPS1 interactsWith FLO8
+YPS1 interactsWith STE20
+YPS1 interactsWith STE12
+YPS1 interactsWith PHD1
+YPS1 interactsWith MSN1
+YPS1 interactsWith GLN3
+YPS1 interactsWith BEM1
+COG5 interactsWith PHD1
+COG5 interactsWith MSN1
+AGA1 interactsWith TEC1
+YJL142C interactsWith FLO8
+YJL142C interactsWith STE20
+YJL142C interactsWith PHD1
+YJL142C interactsWith MSN1
+YJL142C interactsWith GLN3
+YJL142C interactsWith BEM1
+YJL142C interactsWith TEC1
+YAK1 interactsWith KSS1
+FLO10 interactsWith KSS1
+PRY2 interactsWith KSS1
+TEC1 interactsWith KSS1
+WHI3 interactsWith KSS1
+TPK1 interactsWith KSS1
+CAR2 interactsWith KSS1
+IPK1 interactsWith KSS1
+WHI2 interactsWith KSS1
+BUD4 interactsWith KSS1
+RAS2 interactsWith KSS1
+SNF4 interactsWith KSS1
+MSN1 interactsWith KSS1
+DFG5 interactsWith KSS1
+IME2 interactsWith KSS1
+TPK3 interactsWith KSS1
+MGA1 interactsWith KSS1
+FMP45 interactsWith KSS1
+SKI3 interactsWith KSS1
+ELM1 interactsWith KSS1
+CLB2 interactsWith KSS1
+AGA1 interactsWith KSS1
+DFG16 interactsWith KSS1
+RIM9 interactsWith KSS1
+YLR042C interactsWith KSS1
+HOG1 interactsWith KSS1
+SFP1 interactsWith KSS1
+RSC1 interactsWith KSS1
+SPO12 interactsWith KSS1
+YJL142C interactsWith KSS1
+Med21 pp Med4
+Med31 pp Med21
+Med31 pp Med10
+Med17 pp Med8
+Med10 pp Med7
+Mak31 interactsWith Unknown
+Unknown interactsWith Mak10
+Unknown interactsWith Mak3
+Cbc2 pp Sto1
+Tye7 pp Ino4
+YNR064C pp Ino4
+Rtg1 pp Ino4
+Rtg3 pp Ino4
+YLR422W pp Ino4
+Pho4 pp Ino4
+Rse1 interactsWith Unknown
+Unknown interactsWith Hsh155
+Unknown interactsWith Cus1
+Unknown interactsWith Hsh49
+Unknown interactsWith Rds3
+Unknown interactsWith Rcp10
+Ist3 interactsWith Unknown
+Unknown interactsWith Bud13
+Unknown interactsWith Pml1
+Tfg3 pd ADH1
+Tfg2 pd ADH1
+Tfg1 pd ADH1
+Vma10 pp Tfp1
+Vma10 pp Vma2
+Vma10 pp Vma4
+Vma10 pp Vma6
+Vma10 pp Vma10
+Vma5 pp Vma4
+Mud1 pp Rrp3
+Mud1 pp Ynl227c
+Mud1 pp Ylr449w
+Mud1 pp Ydr110w
+Mud1 pp Ppz1
+Snp1 pp Yal047c
+Snp1 pp Ycr101c
+Snp1 pp Yfr039c
+Snp1 pp Ygr203w
+Snp1 pp Ylr017w
+Snp1 pp Ylr213c
+Snp1 pp Ymr009w
+Snp1 pp Ymr044w
+Snp1 pp Yor275c
+Snp1 pp Acs2
+Snp1 pp Fas3
+Snp1 pp Gcr2
+Snp1 pp Ire1
+Snp1 pp Kip1
+Snp1 pp Mdj1
+Snp1 pp Mrpl4
+Snp1 pp Myo1
+Snp1 pp Nup157
+Snp1 pp Rev1
+Snp1 pp Sin3
+Snp1 pp Tkl2
+Snp1 pp Ppz1
+Snp1 pp Ydr110w
+Snp1 pp Cbp3
+Snp1 pp Hex3
+Snp1 pp Brr2
+Mud2 pp Ylr357w
+Mud2 pp Prp39
+Mud2 pp Ylr116w
+Mud2 pp Smy2
+Mud2 pp Ypl105c
+Ylr116w pp Prp22
+Ylr116w pp Tor1
+Ylr116w pp Yap80
+Ylr116w pp Ydl156w
+Ylr116w pp Ydl161w
+Ylr116w pp Yil130w
+Ylr116w pp Ymr065w
+Smd1 pp Los1
+Smd1 pp Sac7
+Smd1 pp Slu7
+Smd1 pp Ybr043c
+Smd1 pp Ygl202w
+Smd1 pp Yjr033c
+Smd1 pp Ykl188c
+Smd1 pp Ylr440c
+Smd3 pp Cdc12
+Smd3 pp Mtd1
+Smd3 pp Rev7
+Smd3 pp Sen1
+Smd3 pp Spa2
+Smd3 pp Yer029c
+Smd3 pp Ygr290w
+Smd3 pp Yhr178w
+Smd3 pp Ymr088c
+Smd3 pp Cna1
+Smd3 pp Rad16
+Yer029c pp Sip1
+Yer029c pp Ccc1
+Yer029c pp Ynl187w
+Yer029c pp Ynr053c
+Yir009w pp Pet127
+Yir009w pp Pet309
+Yir009w pp Bas1
+Yir009w pp Gin10
+Yir009w pp Lte1
+Yir009w pp Mec1
+Yir009w pp Nce3
+Yir009w pp Srs2
+Yir009w pp Ssl2
+Yir009w pp Ydl001w
+Yir009w pp Ydr184c
+Yir009w pp Yhr099w
+Yir009w pp Yhr197w
+Yir009w pp Ynl091w
+Yir009w pp Yor011w
+Yir009w pp Ylr456w
+Yir009w pp Cna1
+Yir009w pp Rad16
+Ylr456w pp Hbs1
+Ylr456w pp Ynr053c
+Ylr456w pp Yer032w
+Ylr456w pp Yil144w
+Prp9 pp Mdm1
+Prp9 pp Mpt1
+Prp9 pp Ycl060c
+Prp9 pp Ycl061c
+Prp9 pp Ydr421w
+Prp9 pp Ydr485c
+Prp9 pp Yml049c
+Prp9 pp Yor023c
+Prp9 pp Yor191w
+Prp9 pp Ypl146c
+Prp9 pp Hex3
+Prp9 pp Ynr053c
+Prp9 pp Prp21
+Prp21 pp Prp11
+Prp21 pp Ynr053c
+Prp21 pp Pfk27
+Prp21 pp Sec7
+Prp21 pp Srb8
+Prp21 pp Ste20
+Prp21 pp Ubp13
+Prp21 pp Ybl101c
+Prp21 pp Ykr090w
+Prp21 pp Ymr285c
+Prp21 pp Yol091w
+Prp21 pp Pet309
+Prp11 pp Ids2
+Prp11 pp Rna12
+Prp11 pp Tif4631
+Prp11 pp Tif4632
+Prp11 pp Ybr113w
+Prp11 pp Ydr131c
+Prp11 pp Ydr180w
+Prp11 pp Ydr386w
+Prp11 pp Ydr409w
+Prp11 pp Yer113c
+Prp11 pp Ykl155c
+Prp11 pp Yll014w
+Prp11 pp Ymr117c
+Prp11 pp Ynl023c
+Prp11 pp Ynr053c
+Prp11 pp Cbp3
+Cus1 pp Ylr090w
+Cus1 pp Brr2
+Cus1 pp Yor319w
+Yor319w pp Ygr056w
+Yor319w pp Yhr209w
+Yor319w pp Yjr022w
+Yjr022w pp Ybl026w
+Yjr022w pp Ycr077c
+Yjr022w pp Ydr228c
+Yjr022w pp Yel015w
+Yjr022w pp Ygl096w
+Yjr022w pp Yhr034c
+Yjr022w pp Yhr035w
+Yjr022w pp Yil173w
+Yjr022w pp Ynl050c
+Yjr022w pp Yor076c
+Yjr022w pp Coq1
+Yjr022w pp Kem1
+Yjr022w pp Lys9
+Yjr022w pp Mth1
+Yjr022w pp Mtr3
+Yjr022w pp Psu1
+Yjr022w pp Uss1
+Ylr116w pp Prp39
+Ylr116w pp Smy2
+Ylr116w pp Ypl105c
+Prp9 pp Pet127
+Kar3 pd CEN3
+Kar3 pd CEN6
+Gcn4 pp Tra1
+Gcn4 pp Gal11
+importin-alpha interactsWith Unknown
+Unknown interactsWith ran
+Unknown interactsWith cse1
+TBP pd RDN5-1_promoter
+TBP pd SCR1_promoter
+TBP pd TA(AGC)K1_promoter
+TBP pd TD(GUC)J1_promoter
+TBP pd TD(GUC)L1_promoter
+TBP pd TE(UUC)J_promoter
+TBP pd TF(GAA)B_promoter
+TBP pd TG(CCC)D_promoter
+TBP pd TG(GCC)O2_promoter
+TBP pd TG(UCC)G_promoter
+TBP pd TH(GUG)E1_promoter
+TBP pd TH(GUG)H_promoter
+TBP pd TI(AAU)I2_promoter
+TBP pd TK(CUU)E1_promoter
+TBP pd TK(CUU)E2_promoter
+TBP pd TL(CAA)A_promoter
+TBP pd TN(GUU)L_promoter
+TBP pd TN(GUU)N2_promoter
+TBP pd TN(GUU)O2_promoter
+TBP pd TP(AGG)N_promoter
+TBP pd TP(UGG)O2_promoter
+TBP pd TR(ACG)K_promoter
+TBP pd TR(UCU)B_promoter
+TBP pd TR(UCU)G2_promoter
+TBP pd TR(UCU)G3_promoter
+TBP pd TS(AGA)B_promoter
+TBP pd TS(CGA)C_promoter
+TBP pd TT(AGU)I2_promoter
+TBP pd TT(AGU)J_promoter
+TBP pd TT(AGU)N2_promoter
+TBP pd TT(AGU)O1_promoter
+TBP pd TV(AAC)E2_promoter
+TBP pd TV(AAC)G1_promoter
+TBP pd TV(AAC)G2_promoter
+TBP pd TV(AAC)G3_promoter
+TBP pd TV(AAC)K1_promoter
+TBP pd TV(AAC)M1_promoter
+TBP pd TV(UAC)D_promoter
+TBP pd TW(CCA)G1_promoter
+TBP pd TW(CCA)K_promoter
+TBP pd TY(GUA)F1_promoter
+TBP pd TY(GUA)F2_promoter
+TBP pd TY(GUA)J2_promoter
+TBP pd YELCTAU1_promoter
+TBP pd YGL080W_promoter
+TBP pd YGRWSIGMA5_promoter
+TBP pd YJL005W_promoter
+TBP pd YPL029W_promoter
+TBP pd YPRCDELTA22_promoter
+Btn2 pp Ist2
+Smc5 pp Sap1
+Smc5 pp Yal028w
+Wss1 pp Psy2
+Wss1 pp Tof1
+Cdc53 pp Hrt1
+Cdc53 pp Yjl149
+Cdc53 pp Ylr352
+Skp1 pp Rcy1
+Rav1 pp Skp1
+Cdc53 pp Ybr280
+Skp1 pp Ybr280
+Rav2 pp Vma1
+Rav2 pp Vma2
+Rav2 pp Vma4
+Rav2 pp Vma8
+Rav1 pp Vma4
+Rav1 pp Vma2
+Rav1 pp Vma8
+Rav1 pp Vma1
+Spt10 pd CRF1-HTB1_IGR
+Spt10 pd HTB1
+Snf5 pd HTA1_promoter
+Spt10 pd HTA1
+Snf5 pd HTA1
+Spt10 pd HTB1-HTA1_IGR
+Spt10 pd SIW14-HHT2
+Spt10 pd KTR5
+Spt10 pd HHF2
+Spt10 pd HHT2
+Spt10 pd HHF1-HHT1_IGR
+Spt10 pd HHT2-HHF2_IGR
+Spt10 pd HHT1-IPP1_IGR
+Spt10 pd HHT1
+Spt10 pd HHF1
+Spt10 pd FLR1-HHF1_IGR
+Spt10 pd HTB2-ECM15_IGR
+Spt10 pd HTA2-HTB2_IGR
+Spt10 pd HTB2
+Spt10 pd UTP20
+Spt10 pd HTA2
+Spt10 pd HTA1-ADK1_IGR
+Ino4 pd INO1_Promoter
+Ino2 pd INO1_Promoter
+Mot1 pd HSP26_Promoter
+Sua7 pd HSP26_Promoter
+Taf1 pd BNA1_Promoter
+Spt15 pd HSP26_Promoter
+RPO21 pd URA1_Promoter
+RPO21 pd BNA1_Promoter
+RPO21 pd INO1_Promoter
+Mot1 pd INO1_Promoter
+Spt15 pd INO1_Promoter
+Spt15 pd BNA1_Promoter
+Spt15 pd URA1_Promoter
+Mot1 pd URA1_Promoter
+Mot1 pd BNA1_Promoter
+Taf4 pd BNA1_Promoter
+Taf4 pd URA1_Promoter
+Taf1 pd URA1_Promoter
+Rad50 pp Rad50
+Rad50 pp Mre11
+Unknown interactsWith Vps11
+Unknown interactsWith Vps16
+Unknown interactsWith Vps18
+Unknown interactsWith Vps41
+Unknown interactsWith Ykt6
+Unknown interactsWith Nyv1
+Sec17 interactsWith SNARE_Complex
+Vps39 interactsWith Unknown
+Vti1 interactsWith Unknown
+Vam3 interactsWith Unknown
+Vps33 interactsWith Unknown
+HOPS interactsWith SNARE
+Skp1 pp Ylr097
+Skp1 pp Ymr258
+Skp1 pp Yjl149
+Skp1 pp Ylr352
+Skp1 pp Grr1
+Skp1 pp Hrt1
+Skp1 pp EF-2
+Skp1 pp Cep3
+Sir2 pp Sir4
+Sir3 interactsWith Sir2/Sir4
+Sir3 pp Sir3
+Sir3 pp Sir4
+Sir3 pp Sir2
+Caf4 pp Srb10
+Not2 pp Srb10
+Caf4 pp Srb9
+Caf4 pp Dbf2
+Caf4 pp Not1
+Caf4 pp Ccr4
+Vma4 pp Vma13
+APC/C_complex interactsWith Cdc20
+APC/C_complex interactsWith Cdh1
+Unknown interactsWith Cdc23
+Unknown interactsWith Apc2
+Unknown interactsWith Apc5
+Unknown interactsWith Cdc27
+Unknown interactsWith Cdc16
+Apc4 interactsWith Unknown
+Unknown interactsWith Apc1
+Unknown interactsWith Vph1
+Unknown interactsWith Vma6
+Unknown interactsWith Vma16
+Unknown interactsWith Vma3
+Unknown interactsWith Vma11
+Ccr4 pp Srb9
+Dbf2 pp Srb10
+Srb9 pp Srb10
+Unknown interactsWith Srb4
+Not1 pp Srb10
+Not2 pp Srb9
+Caf1 pp Srb9
+Caf16 pp Srb9
+Caf16 pp Ccr4
+Caf16 pp Caf16
+Rmi1 pp Top3
+Sgs1 pp Rmi1
+Sgs1 pp Top3
+Mtr4 pp Trf5
+Mtr4 pp Trf4
+Mtr4 pp Air2
+Hsp82 pp Gnd1
+Hsp82 pp Bna3
+Hsp82 pp Yal049c
+Hsp82 pp Agt1
+Hsp82 pp Prm2
+Hsp82 pp Ynl326c
+Hsp82 pp Vma4
+Hsp82 pp Ydr412w
+Hsp82 pp Ydl199c
+Hsp82 pp Hog1
+Hsp82 pp Sft1
+Hsp82 pp Ykl069w
+Hsp82 pp Grx5
+Hsp82 pp Put2
+Hsp82 pp Ynl194c
+Hsp82 pp Srt1
+Hsp82 pp Sma2
+Hsp82 pp Atg14
+Hsp82 pp Ubc6
+Hsp82 pp Hxt10
+Hsp82 pp Ugp1
+Hsp82 pp Mup1
+Hsp82 pp Yip5
+Hsp82 pp Bap3
+Hsp82 pp Ste11
+Hsp82 pp Xyl2
+Hsp82 pp Ydj1
+Hsp82 pp Hsp60
+Hsp82 pp Pho86
+Hsp82 pp She4
+Hsp82 pp Tsc13
+Hsp82 pp Hap1
+Hsp82 pp Put4
+Hsp82 pp Ydr051c
+Hsp82 pp Ybr227c
+Hsp82 pp Lac1
+Hsp82 pp Yhr036w
+Hsp82 pp Tpm1
+Hsp82 pp Ymr155w
+Hsp82 pp Dps1
+Hsp82 pp Hsp42
+Hsp82 pp Vps55
+Hsp82 pp Cdc12
+Hsp82 pp Rds1
+Hsp82 pp Bos1
+Hsp82 pp Sho1
+Hsp82 pp Lyp1
+Hsp82 pp Mnt3
+Hsp82 pp Wtm2
+Hsp82 pp Ant1
+Hsp82 pp Sap30
+Hsp82 pp Rbd2
+Hsp82 pp Whi5
+Hsp82 pp Hts1
+Hsp82 pp Cdc37
+Hsp82 pp Ypl257w
+Hsp82 pp RPL18A
+Hsp82 pp Yer156c
+Hsp82 pp Ubx7
+Hsp82 pp Cos7
+Hsp82 pp Mup3
+Hsp82 pp Ole1
+Hsp82 pp Gda1
+Hsp82 pp Ycl056c
+Hsp82 pp Are2
+Hsp82 pp Dal5
+Hsp82 pp Ecm37
+Hsp82 pp Tlg2
+Hsp82 pp Are1
+Hsp82 pp Nmd5
+Hsp82 pp Sse1
+Hsp82 pp Bsp1
+Hsp82 pp Ypr003c
+Hsp82 pp Acf4
+Hsp82 pp Can1
+Hsp82 pp Sts1
+Hsp82 pp Pdx3
+Hsp82 pp Aha1
+Hsp82 pp Mim1
+Hsp82 pp Yjr134c
+Hsp82 pp Tvp23
+Hsp82 pp Ykl174c
+Hsp82 pp Yjl114w
+Hsp82 pp Uip5
+Hsp82 pp Slt2
+Hsp82 pp Ypl199c
+Hsp82 pp Cos6
+Hsp82 pp Asg7
+Hsp82 pp Gcn2
+Hsp82 pp Ylr036c
+Hsp82 pp Ydl133w
+Hsp82 pp Rrd2
+Hsp82 pp Cns1
+Hsp82 pp Ynl100w
+Hsp82 pp Bsd2
+Hsp82 pp Ras1
+Hsp82 pp Ylr404w
+Hsp82 pp Pos5
+Hsp82 pp Sir2
+Hsp82 pp Yml131w
+Hsp82 pp Avt6
+Hsp82 pp Cfd1
+Hsp82 pp Act1
+Hsp82 pp Inp54
+Hsp82 pp Bsc6
+Hsp82 pp Ycr101c
+Hsp82 pp Ykr067w
+Hsp82 pp Lys21
+Hsp82 pp Ydl180w
+Hsp82 pp Ypt53
+Hsp82 pp Sap18
+Hsp82 pp Nup57
+Hsp82 pp Nop15
+Hsp82 pp Yil120w
+Hsp82 pp Ydl012c
+Hsp82 pp Agp2
+Hsp82 pp Cos3
+Hsp82 pp Htb1
+Hsp82 pp Cct4
+Hsp82 pp Pex11
+Hsp82 pp Arr3
+Hsp82 pp Sba1
+Hsp82 pp Met14
+Hsp82 pp Hxt17
+Hsp82 pp Ddr2
+Hsp82 pp Dcg1
+Hsp82 pp Ept1
+Hsp82 pp Yor097c
+Hsp82 pp Pep12
+Hsp82 pp Mph2
+Hsp82 pp Hxt1
+Hsp82 pp Phm6
+Hsp82 pp Hnt1
+Hsp82 pp Sor1
+Hsp82 pp Ypl014w
+Hsp82 pp Kss1
+Hsp82 pp Esbp6
+Hsp82 pp Aqr1
+Hsp82 pp Frs2
+Hsp82 pp Hsp10
+Hsp82 pp Ypl109c
+Hsp82 pp Uip4
+Hsp82 pp Ehd1
+Hsp82 pp Ypr148c
+Hsp82 pp Ypt7
+Hsp82 pp Yir042c
+Hsp82 pp Ypt31
+Hsp82 pp Ybr220c
+Hsp82 pp Car2
+Hsp82 pp Mdh3
+Hsp82 pp Izh4
+Hsp82 pp Esc5
+Hsp82 pp Tef3
+Hsp82 pp Gmh1
+Hsp82 pp Ykr064w
+Hsp82 pp Tah1
+Hsp82 pp Ypr115w
+Hsp82 pp Rim1
+Hsp82 pp Yck1
+Hsp82 pp Ypr089w
+Hsp82 pp She3
+Hsp82 pp Sti1
+Hsp82 pp Arg4
+Hsp82 pp Sor2
+Hsp82 pp Tom22
+Hsp82 pp Yil041w
+Hsp82 pp Fun26
+Hsp82 pp Thi13
+Hsp82 pp Pdr3
+Hsp82 pp Ypl264c
+Hsp82 pp Mog1
+Hsp82 pp Ypr127w
+Hsp82 pp Ydr319c
+Hsp82 pp Hxt5
+Hsp82 pp Pyk2
+Hsp82 pp Erv46
+Hsp82 pp Ham1
+Cdh1 pp Hsl1
+Cdh1 pp Clb2
+Unknown interactsWith Cdc16
+Cdh1 interactsWith Unknown
+Cdh1 interactsWith Unknown
+Unknown interactsWith Doc1
+Hsl1 interactsWith Unknown
+Unknown interactsWith Apc4
+Clb2 interactsWith Unknown
+Unknown interactsWith Apc4
+Pac1 pp Pac1
+Pac1 pp Ndl1
+Ndl1 pp Ndl1
+Kap95 pp Srp1
+Rpb1 pd NEL025C
+Unknown interactsWith Trf4
+Unknown interactsWith Trf4
+Air2 interactsWith Unknown
+Air1 interactsWith Unknown
+Unknown interactsWith Air2
+Unknown interactsWith Air1
+Trf4 interactsWith Unknown
+Unknown interactsWith Mtr4
+Unknown interactsWith Ccr4
+Unknown interactsWith Not1
+Unknown interactsWith Not2
+Srb11 interactsWith Unknown
+Bro1 pp Snf7
+Sup35 pp Sup35
+Vrp1 pp Hof1
+Vrp1 pp Myo3
+Isw1 pd MET16_promoter
+Isw1 pd MET16
+Rpb3 pd MET16
+Rpb3 pd MET16_promoter
+Esa1 pd RPS11B_promoter
+Esa1 pd MET16_promoter
+Rpb1 pd MET16
+Rpb1 pd MET16_promoter
+Isw1 pd RPS11B
+Spo7 pp Nem1
+Nem1-Spo7 interactsWith Smp2
+Hhf2 pd PHO5_promoter
+Hhf2 pd PHO5
+Hhf2 pd PET56
+Hhf2 pd HIS3
+Unknown interactsWith Not1
+Tho2 pd PMA1
+Tho2 pd GAL1
+Mps1 pp Mps1
+RNAPII interactsWith Ssu72
+CTDK1 interactsWith RNAPII
+TFIIK interactsWith RNAPII
+Unknown interactsWith Ctk3
+Unknown interactsWith Ctk2
+Ctk1 interactsWith Unknown
+Unknown interactsWith Kin28
+Unknown interactsWith Ccl1
+Tfb3 interactsWith Unknown
+Rsp5 interactsWith RNAPII
+Cdc5 pp Swe1
+Cdc28/Cln1 interactsWith Swe1
+Cdc28/Clb5 interactsWith Swe1
+Cla4 pp Swe1
+Ego1 pp Gtr2
+Ego1 pp Ego3
+Sec9 pp Sro7
+Sro7 pp Myo2
+TDP1 pp TDP1
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+VPS36 pp SNF8
+VPS25 pp SNF8
+VPS25 pp VPS36
+VPS25 pp VPS36
+CYC1 pp CCP1
+CYC1 pp CCP1
+CCP1 pp CCP1
+YPT1 pp GDI1
+TFP1 pp TFP1
+SMC1 pp SMC1
+MCD1 pp SMC1
+MCD1 pp SMC1
+ACC1 pp ACC1
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+VPS25 pp SNF8
+VPS36 pp SNF8
+VPS36 pp VPS25
+VPS36 pp VPS25
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+YJL068C pp YJL068C
+RPB3 pp RPO21
+RPB8 pp RPO21
+RPB9 pp RPO21
+RPB11 pp RPB3
+RPB2 pp RPO21
+RPB5 pp RPO21
+RPO26 pp RPB2
+RPO26 pp RPB5
+RPO26 pp RPO21
+RPB8 pp RPO21
+RPB9 pp RPB2
+RPB10 pp RPB3
+RPB10 pp RPB2
+RPB11 pp RPO21
+RPB11 pp RPB3
+RPB11 pp RPB2
+RPB11 pp RPB8
+RPC10 pp RPB2
+RPC10 pp RPB3
+RPB8 pp RPO21
+RPB9 pp RPO21
+RPC10 pp RPB2
+RPB2 pp RPO21
+RPB5 pp RPB2
+RPO26 pp RPO21
+RPB8 pp RPO21
+RPB9 pp RPB2
+RPB10 pp RPB3
+RPB10 pp RPB2
+RPB11 pp RPB2
+RPB11 pp RPB3
+RPC10 pp RPB2
+RPB2 pp RPO21
+RPB3 pp RPB2
+RPB8 pp RPO21
+RPB9 pp RPB2
+RPB11 pp RPB3
+RPC10 pp RPB2
+RPB8 pp RPO21
+RPB11 pp RPB3
+HEM13 pp HEM13
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+SHE2 pp SHE2
+SRP1 pp GSP1
+CSE1 pp GSP1
+CSE1 pp SRP1
+RPB2 pp RPO21
+RPB4 pp RPB2
+RPB5 pp RPO21
+RPO26 pp RPO21
+RPB7 pp RPB4
+RPB7 pp RPO26
+RPB7 pp RPO21
+RPB8 pp RPO21
+RPB9 pp RPB2
+RPB9 pp RPO21
+RPB10 pp RPB3
+RPB10 pp RPB2
+RPB11 pp RPO21
+RPB11 pp RPB3
+RPB11 pp RPB8
+RPC10 pp RPB2
+RPC10 pp RPB3
+YML079W pp YML079W
+YML079W pp YML079W
+YML079W pp YML079W
+RPB3 pp RPB2
+RPB4 pp RPB2
+RPB7 pp RPB4
+RPB7 pp RPO26
+RPB8 pp RPO21
+RPB11 pp RPB8
+RPC10 pp RPB10
+RPB7 pp RPB4
+RPB2 pp RPO21
+RPB3 pp RPB2
+RPB5 pp RPO21
+RPO26 pp RPO21
+RPB7 pp RPB4
+RPB7 pp RPO26
+RPB7 pp RPB2
+RPB8 pp RPO21
+RPB9 pp RPB2
+RPB9 pp RPO21
+RPB10 pp RPB3
+RPB10 pp RPB2
+RPB11 pp RPO21
+RPB11 pp RPB3
+RPC10 pp RPB2
+DST1 pp RPO21
+DST1 pp RPB2
+RPB2 pp RPO21
+RPB7 pp RPB4
+RPB7 pp RPB4
+RPB7 pp RPB7
+LPD1 pp LPD1
+Carboxypeptidase_Y_Inhibitor pp PRC1
+SRB7 pp MED7
+SRB7 pp MED7
+RFC4 pp RFC1
+RFC3 pp RFC4
+RFC3 pp RFC1
+RFC2 pp RFC3
+RFC5 pp RFC1
+RFC5 pp RFC2
+POL30 pp RFC3
+POL30 pp RFC1
+POL30 pp POL30
+POL30 pp RFC4
+Proliferating_Cell_Nuclear_Antigen pp POL30
+POL30 pp POL30
+VPS25 pp VPS25
+VPS25 pp VPS25
+VPS25 pp VPS25
+VPS25 pp VPS25
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+Ubiquitin-Like_Protein_Dsk2 pp Ubiquitin
+YDJ1 pp YDJ1
+U1C pd ACT1
+Prp8 pd ACT1
+Lea1 pd ACT1
+Dcn1 pp Ubi4
+Dcn1 pp Rub1
+Dcn1 pp Cdc53
+Trf4 pp Air1
+Trf4 pp Prp16
+Unknown interactsWith Mtr4
+Trf4 interactsWith Unknown
+Trf5 pp Mtr4
+Unknown interactsWith Hul4
+Trf4 pp Air2
+Rnt1 interactsWith FIT2
+Rnt1 interactsWith ARN2
+Sch9 pp piD261
+SCC4 pd c6-7_s_at
+SCC4 pd c6-17_at
+SCC4 pd c6-19_s_at
+SCC4 pd c6-253_at
+SCC4 pd c6-476_s_at
+SCC4 pd c6-477_s_at
+SCC4 pd c6-654_at
+SCC4 pd c6-755_at
+SCC4 pd c6-899_at
+SCC4 pd c6-901_at
+SCC4 pd c6-3_s_at
+SCC4 pd c6-189_at
+SCC4 pd c6-254_at
+SCC4 pd c6-467_s_at
+SCC4 pd c6-613_at
+SCC4 pd c6-736_at
+SCC4 pd c6-756_at
+SCC4 pd c6-758_at
+SCC4 pd c6-479_s_at
+SCC4 pd c6-612_at
+SCC4 pd c6-900_at
+SCC4 pd c6-737_at
+SCC4 pd c6-11_s_at
+SCC4 pd c6-610_at
+SCC4 pd c6-18_at
+SCC4 pd c6-468_s_at
+SCC4 pd c6-752_at
+SCC4 pd c6-179_at
+SCC4 pd c6-556_at
+SCC4 pd c6-563_at
+SCC4 pd c6-898_at
+SCC4 pd c6-671_at
+SCC4 pd c6-482_at
+SCC4 pd c6-492_at
+SCC4 pd c6-662_at
+SCC4 pd c6-564_at
+SCC4 pd c6-674_at
+SCC4 pd c6-548_at
+SCC4 pd c6-1_s_at
+SCC4 pd c6-897_at
+SCC4 pd c6-447_at
+SCC4 pd c6-320_at
+SCC4 pd c6-753_at
+SCC4 pd c6-9_s_at
+SCC4 pd c6-180_at
+SCC4 pd c6-178_at
+SCC4 pd c6-338_at
+SCC4 pd c6-13_s_at
+SCC4 pd c6-508_at
+SCC4 pd c6-757_at
+SCC4 pd c6-473_s_at
+SCC4 pd c6-356_at
+SCC4 pd c6-465_s_at
+SCC4 pd c6-491_at
+SCC4 pd c6-614_at
+SCC4 pd c6-319_at
+SCC4 pd c6-466_s_at
+SCC4 pd c6-546_at
+SCC4 pd c6-351_at
+SCC4 pd c6-509_at
+SCC4 pd c6-312_at
+SCC4 pd c6-525_at
+SCC4 pd c6-848_at
+SCC4 pd c6-481_at
+SCC4 pd c6-259_at
+SCC4 pd c6-735_at
+SCC4 pd c6-557_at
+SCC4 pd c6-609_at
+SCC4 pd c6-673_at
+SCC4 pd c6-759_at
+SCC4 pd c6-260_at
+SCC4 pd c6-559_at
+SCC4 pd c6-519_at
+SCC4 pd c6-656_at
+SCC4 pd c6-747_at
+SCC4 pd c6-258_at
+SCC4 pd c6-469_s_at
+SCC4 pd c6-555_at
+SCC4 pd c6-754_at
+SCC4 pd c6-611_at
+SCC4 pd c6-207_at
+SCC4 pd c6-448_at
+SCC4 pd c6-657_at
+SCC4 pd c6-639_at
+SCC4 pd c6-670_at
+SCC4 pd c6-896_at
+SCC4 pd c6-139_at
+SCC4 pd c6-252_at
+SCC4 pd c6-255_at
+SCC4 pd c6-704_at
+SCC4 pd c6-527_at
+SCC4 pd c6-545_at
+SCC4 pd c6-661_at
+SCC4 pd c6-638_at
+SCC4 pd c6-355_at
+SCC4 pd c6-446_at
+SCC4 pd c6-393_at
+SCC4 pd c6-566_at
+SCC4 pd c6-703_at
+SCC4 pd c6-74_at
+SCC4 pd c6-357_at
+SCC4 pd c6-433_at
+SCC4 pd c6-526_at
+SCC4 pd c6-575_at
+SCC4 pd c6-343_at
+SCC4 pd c6-311_at
+SCC4 pd c6-182_at
+SCC4 pd c6-528_at
+SCC4 pd c6-744_at
+SCC4 pd c6-845_at
+SCC4 pd c6-553_at
+SCC4 pd c6-684_at
+SCC4 pd c6-721_at
+SCC4 pd c6-683_at
+SCC4 pd c6-831_at
+SCC4 pd c6-181_at
+SCC4 pd c6-250_at
+SCC4 pd c6-516_at
+SCC4 pd c6-541_at
+SCC4 pd c6-449_at
+SCC4 pd c6-853_at
+SCC4 pd c6-718_at
+SCC4 pd c6-434_at
+SCC4 pd c6-190_at
+SCC4 pd c6-438_at
+SCC4 pd c6-682_at
+SCC4 pd c6-517_at
+SCC4 pd c6-303_at
+SCC4 pd c6-507_at
+SCC4 pd c6-773_at
+SCC4 pd c6-569_at
+SCC4 pd c6-676_at
+SCC4 pd c6-25_s_at
+SCC4 pd c6-518_at
+SCC4 pd c6-646_at
+SCC4 pd c6-653_at
+SCC4 pd c6-463_s_at
+SCC2 pd c6-3_s_at
+SCC2 pd c6-7_s_at
+SCC2 pd c6-9_s_at
+SCC2 pd c6-13_s_at
+SCC2 pd c6-17_at
+SCC2 pd c6-19_s_at
+SCC2 pd c6-21_at
+SCC2 pd c6-252_at
+SCC2 pd c6-253_at
+SCC2 pd c6-462_s_at
+SCC2 pd c6-465_s_at
+SCC2 pd c6-466_s_at
+SCC2 pd c6-467_s_at
+SCC2 pd c6-468_s_at
+SCC2 pd c6-469_s_at
+SCC2 pd c6-477_s_at
+SCC2 pd c6-478_s_at
+SCC2 pd c6-479_s_at
+SCC2 pd c6-554_at
+SCC2 pd c6-663_at
+SCC2 pd c6-664_at
+SCC2 pd c6-666_at
+SCC2 pd c6-736_at
+SCC2 pd c6-897_at
+SCC2 pd c6-900_at
+SCC2 pd c6-901_at
+SCC2 pd c6-11_s_at
+SCC2 pd c6-20_at
+SCC2 pd c6-179_at
+SCC2 pd c6-186_at
+SCC2 pd c6-187_at
+SCC2 pd c6-447_at
+SCC2 pd c6-470_s_at
+SCC2 pd c6-476_s_at
+SCC2 pd c6-491_at
+SCC2 pd c6-496_at
+SCC2 pd c6-553_at
+SCC2 pd c6-737_at
+SCC2 pd c6-899_at
+SCC2 pd c6-668_at
+SCC2 pd c6-898_at
+SCC2 pd c6-18_at
+SCC2 pd c6-25_s_at
+SCC2 pd c6-180_at
+SCC2 pd c6-563_at
+SCC2 pd c6-338_at
+SCC2 pd c6-459_at
+SCC2 pd c6-473_s_at
+SCC2 pd c6-559_at
+SCC2 pd c6-665_at
+SCC2 pd c6-667_at
+SCC2 pd c6-148_at
+SCC2 pd c6-185_at
+SCC2 pd c6-551_at
+SCC2 pd c6-682_at
+SCC2 pd c6-833_at
+SCC2 pd c6-192_at
+SCC2 pd c6-662_at
+SCC2 pd c6-895_at
+SCC2 pd c6-552_at
+SCC2 pd c6-681_at
+SCC2 pd c6-178_at
+SCC2 pd c6-557_at
+SCC2 pd c6-498_at
+SCC2 pd c6-564_at
+SCC2 pd c6-475_s_at
+SCC2 pd c6-340_at
+SCC2 pd c6-1_s_at
+SCC2 pd c6-464_s_at
+SCC2 pd c6-680_at
+SCC2 pd c6-490_at
+SCC2 pd c6-454_at
+SCC2 pd c6-450_at
+SCC2 pd c6-558_at
+SCC2 pd c6-482_at
+SCC2 pd c6-23_at
+SCC2 pd c6-683_at
+SCC2 pd c6-882_at
+SCC2 pd c6-497_at
+SCC2 pd c6-147_at
+SCC2 pd c6-463_s_at
+SCC2 pd c6-474_s_at
+SCC2 pd c6-734_at
+SCC2 pd c6-752_at
+SCC2 pd c6-455_at
+SCC2 pd c6-254_at
+SCC2 pd c6-352_at
+SCC2 pd c6-896_at
+SCC2 pd c6-489_at
+SCC2 pd c6-495_at
+SCC2 pd c6-567_at
+SCC2 pd c6-255_at
+SCC2 pd c6-456_at
+SCC2 pd c6-735_at
+SCC2 pd c6-448_at
+SCC2 pd c6-684_at
+SCC2 pd c6-353_at
+SCC2 pd c6-566_at
+SCC2 pd c6-320_at
+SCC2 pd c6-453_at
+SCC2 pd c6-181_at
+SCC2 pd c6-612_at
+SCC2 pd c6-556_at
+SCC2 pd c6-560_at
+SCC2 pd c6-341_at
+SCC2 pd c6-452_at
+SCC2 pd c6-146_at
+SCC2 pd c6-653_at
+SCC2 pd c6-449_at
+SCC2 pd c6-669_at
+SCC2 pd c6-832_at
+SCC2 pd c6-613_at
+SCC2 pd c6-526_at
+SCC2 pd c6-562_at
+SCC2 pd c6-657_at
+SCC2 pd c6-446_at
+SCC2 pd c6-488_at
+SCC2 pd c6-831_at
+SCC2 pd c6-251_at
+SCC2 pd c6-673_at
+SCC2 pd c6-565_at
+SCC2 pd c6-441_at
+SCC2 pd c6-654_at
+SCC2 pd c6-256_at
+SCC2 pd c6-486_at
+SCC2 pd c6-607_at
+SCC2 pd c6-679_at
+SCC2 pd c6-494_at
+SCC2 pd c6-614_at
+SCC2 pd c6-661_at
+SCC2 pd c6-658_at
+SCC2 pd c6-739_at
+SCC2 pd c6-738_at
+Unknown interactsWith Utp1
+Unknown interactsWith Utp2
+Unknown interactsWith Utp3
+Unknown interactsWith Utp4
+Unknown interactsWith Utp5
+Unknown interactsWith Utp6
+Unknown interactsWith Utp7
+Unknown interactsWith Utp8
+Unknown interactsWith Utp9
+Unknown interactsWith Utp10
+Unknown interactsWith Utp11
+Unknown interactsWith Utp12
+Gpi14 pp Ypl192c
+Ypi1 pp Ylr090w
+Ylr424w pp Ygl090w
+Gic2 pp Ykl082c
+Ylr424w pp Yil149c
+Sam35 pp Yil033c
+Ykl088w pp Ylr094c
+Sam35 pp Ynl092w
+Thg1 pp Ygr024c
+Ykr022c pp Ynl107w
+Yjl097w pp Yjl019w
+Ylr424w pp Yjr056c
+Naf1 pp Yil091c
+Yhr122w pp Yor145c
+Naf1 pp Yhr043c
+Ydr288w pp Yor358w
+Npa3 pp Yfl068w
+Yor287c pp Yer032w
+Ynr054c pp Ydr532c
+Naf1 pp Ybr078w
+Yor287c pp Yor016c
+Yor287c pp Ydl013w
+Ydr267c pp Ydl030w
+Ypi1 pp Yml016c
+Psf1 pp Ypr135w
+Npa3 pp Ygr131w
+Ynl158w pp Ydr197w
+Ygr046w pp Yjr068w
+Frq1 pp Ygl098w
+Gpi14 pp Ybr023c
+Ydr267c pp Ydr017c
+Npa3 pp Yil029c
+Yjl097w pp Ydl133w
+Pam18 pp Ycl056c
+Gpi14 pp Yir038c
+Zim17 pp Yhr129c
+Npa3 pp Yil020c
+Ylr424w pp Yol091w
+Yhr122w pp Ypl090c
+Hmt1 pp Yil091c
+Thp2 pp Ygl098w
+Ygr046w pp Ykl115c
+Ydr267c pp Yer184c
+Swc4 pp Ylr424w
+Met30 pp Ynl245c
+Ylr424w pp Ycr073c
+Gpi14 pp Ydr046c
+Ylr424w pp Yhr056c
+Ylr424w pp Ypl174c
+Ydr531w pp Ydr151c
+Ydr267c pp Ymr111c
+Ydr267c pp Yor358w
+Gpi14 pp Ycl025c
+Ypi1 pp Ykl193c
+Psf2 pp Ydr489w
+Qri8 pp Ynr046w
+Yjl147c pp Ypl233w
+Yml023c pp Ydl088c
+Sam35 pp Ykl135c
+Yjl097w pp Ymr110c
+Gpi14 pp Yir033w
+Ylr424w pp Yer127w
+Yml023c pp Ydl013w
+Naf1 pp Yjl030w
+Yhr122w pp Yor283w
+Npa3 pp Ygr183c
+Naf1 pp Ydl173w
+Ylr424w pp Ykr034w
+Ygr046w pp Yhl011c
+Npa3 pp Yal044c
+Zds2 pp Ykl082c
+Npa3 pp Ygl218w
+Ipi1 pp Yor156c
+Ydr413c pp Ykl115c
+Ylr424w pp Ygr280c
+Ydr531w pp Ypr043w
+Ydr437w pp Ydr046c
+Npa3 pp Ydr073w
+Gpi14 pp Ypl130w
+Thg1 pp Yml083c
+Ipi3 pp Yer115c
+Pam18 pp Ydr289c
+Ydr288w pp Ylr007w
+Psf1 pp Ydr489w
+Ylr424w pp Yol036w
+Dsn1 pp Ypl233w
+Psf2 pp Ylr235c
+Yml023c pp Yer038c
+Ylr424w pp Ydl239c
+Ykl088w pp Yil005w
+Yjl097w pp Ybl005w
+Gpi14 pp Ycr007c
+Npa3 pp Yhr059w
+Yol022c pp Yor018w
+Yml023c pp Ybr164c
+Vps5 pp Ykl082c
+Psf1 pp Yor162c
+Sog2 pp Ypl233w
+Mig2 pp Yfr042w
+Ydr288w pp Ydl105w
+Psf2 pp Ydr013w
+Ydr413c pp Yll038c
+Npa3 pp Yor262w
+Ydr196c pp Ynr035c
+Ylr424w pp Ybl010c
+Ykl088w pp Ycl020w
+Ykl088w pp Ydl224c
+Zim17 pp Ybr126c
+Ydr267c pp Ynl023c
+Yor287c pp Yol091w
+Thg1 pp Yhr112c
+Yhr122w pp Ygl166w
+Ydr531w pp Ydr531w
+Npa3 pp Yil070c
+Ygr277c pp Ygr041w
+Ipi1 pp Ydr303c
+Psf1 pp Ygr029w
+Zim17 pp Ypl004c
+Ydr267c pp Ygl071w
+Vps5 pp Ykr022c
+Ylr022c pp Ynl023c
+Ygr046w pp Ydl176w
+Yol022c pp Ygr102c
+Zim17 pp Ymr075w
+Ykl088w pp Ymr294w
+Ypi1 pp Ygl208w
+Ylr424w pp Yal032c
+Ydr267c pp Ydr026c
+Sam35 pp Ykl200c
+Ykl088w pp Ypr049c
+Psf1 pp Yll028w
+Yml023c pp Ydr318w
+Bud7 pp Ykl082c
+Psf1 pp Ypr175w
+Swc4 pp Ynl092w
+Gpi14 pp Yil146c
+Tim50 pp Yor223w
+Yor287c pp Ydr026c
+Ynl158w pp Ynr039c
+Bcd1 pp Ynl206c
+Npa3 pp Ygr269w
+Ylr424w pp Yfl002c
+Cdc28 pp Ykl014c
+Hmt1 pp Ypl063w
+Gpi14 pp Ynl115c
+Esf1 pp Ynr054c
+Src1 pp Ydr489w
+Yml023c pp Ymr053c
+Ylr424w pp Ylr031w
+Ylr424w pp Ycr077c
+Pcf11 pp Ylr424w
+Ykl088w pp Yjr068w
+Psf2 pp Ybl074c
+Yjl097w pp Ydr479c
+Naf1 pp Ydr288w
+Yjl097w pp Ygl055w
+Ydr267c pp Ygr221c
+Thg1 pp Ygl134w
+Yjl097w pp Yjr010c-a
+Psf2 pp Yjr083c
+Ydr267c pp Yor032c
+Yml023c pp Ydr260c
+Swc4 pp Ydr359c
+Ylr424w pp Ybr138c
+Npa3 pp Ygl152c
+Npa3 pp Ygl166w
+Swc4 pp Yol091w
+Tim50 pp Yml038c
+Gpi14 pp Ycr048w
+Ykl088w pp Yml058w
+Ypi1 pp Ypl184c
+Ylr424w pp Ykl012w
+Yjl097w pp Ygr149w
+Ynr054c pp Yhr169w
+Nsl1 pp Ylr346c
+Psf3 pp Yor358w
+Psf1 pp Yjl072c
+Yhr122w pp Ydr267c
+Yml023c pp Yor156c
+Npa3 pp Ydr436w
+Ylr424w pp Yfl024c
+Pcf11 pp Ypl233w
+Qri1 pp Ydr288w
+Yjl097w pp Yjl057c
+Mpe1 pp Yjr141w
+Yjl097w pp Ynr039c
+Ylr424w pp Ypl121c
+Yjr023c pp Yer019c-a
+Ypi1 pp Ygr016w
+Gic1 pp Ykl082c
+Ygr046w pp Ycr056w
+Npa3 pp Yor207c
+Psf2 pp Ypr135w
+Thg1 pp Yer116c
+Ykr022c pp Ykl061w
+Ydr267c pp Yol116w
+Gpi14 pp Ygl161c
+Gpi14 pp Ymr110c
+Cnb1 pp Ymr211w
+Yml023c pp Ygr048w
+Qri2 pp Ydr288w
+Ylr424w pp Yil150c
+Ydr437w pp Yjr015w
+Naf1 pp Yll007c
+Ydr413c pp Ydr436w
+Cwc2 pp Yhr102w
+Gpi14 pp Ydr508c
+Yjl097w pp Ypl192c
+Npa3 pp Yjr132w
+Bcd1 pp Ynl165w
+Yhr122w pp Ykr034w
+Gpi14 pp Yor107w
+Ypi1 pp Ybl032w
+Ydr267c pp Yir021w
+Ygr046w pp Ygl095c
+Ylr424w pp Ygl120c
+Apc9 pp Yll034c
+Zim17 pp Ygl205w
+Gpi14 pp Yal028w
+Hrt1 pp Yjl010c
+Yml023c pp Ydr510w
+Yml023c pp Yor269w
+Ynr054c pp Ydr026c
+Ydr267c pp Yil103w
+Ynr054c pp Ydr365c
+Psf2 pp Ylr320w
+Psf1 pp Ycr077c
+Psf3 pp Ycl056c
+Swc4 pp Ypl174c
+Gpi14 pp Ykr039w
+Ydr288w pp Ylr453c
+Ylr424w pp Yfr013w
+Ipi3 pp Ypr022c
+Tim50 pp Ydl100c
+Rix1 pp Ynl182c
+Yor287c pp Ypl146c
+Npa3 pp Yfl010c
+Ylr424w pp Ylr385c
+Hsh49 pp Yjr141w
+Ylr424w pp Ygl172w
+Ylr424w pp Yal034w-a
+Ykr022c pp Ydr110w
+Ykl088w pp Ynr045w
+Ypi1 pp Yer133w
+Ylr424w pp Ykr022c
+Npa3 pp Ygl187c
+Ylr424w pp Ygr187c
+Npa3 pp Ynr045w
+Npa3 pp Ygr030c
+Ypi1 pp Ymr091c
+Ygr198w pp Ybr138c
+Gpi14 pp Ydl173w
+Ynl158w pp Ynr045w
+Cwc2 pp Yll036c
+Ydr267c pp Ynl240c
+Gpi14 pp Ynr039c
+Rio2 pp Yml063w
+Ypi1 pp Yir016w
+Rgd2 pp Ydr367w
+Exo84 pp Ynr046w
+Ylr424w pp Ypl133c
+Ykl088w pp Ydr436w
+Ylr424w pp Ycr086w
+Ylr424w pp Ybr055c
+Gpi14 pp Ydr160w
+Ydr437w pp Ydl100c
+Npa3 pp Ygl189c
+Npa3 pp Ygl191w
+Psf1 pp Ylr320w
+Npa3 pp Yhr110w
+Ylr424w pp Ydl013w
+Sam35 pp Ydr073w
+Gpi14 pp Ypr159w
+Npa3 pp Yfl056c
+Atg12 pp Ylr424w
+Ykr022c pp Yjr132w
+Yml023c pp Ydl064w
+Gpi14 pp Yor156c
+Ylr424w pp Ydr473c
+Ypi1 interactsWith unknown
+unknown interactsWith Sds22
+unknown interactsWith Glc7
+Dsn1 interactsWith unknown
+unknown interactsWith Ame1
+unknown interactsWith Chl4
+unknown interactsWith Ctf3
+unknown interactsWith Ctf19
+unknown interactsWith Mcm22
+unknown interactsWith Yal034w
+unknown interactsWith Okp1
+unknown interactsWith Yal034w
+unknown interactsWith Nnf1
+unknown interactsWith Nsl1
+Ykl088w interactsWith unknown
+unknown interactsWith Sis2
+unknown interactsWith Vhs3
+Ykr079c interactsWith unknown
+unknown interactsWith Nuc1
+Psf2 interactsWith unknown
+unknown interactsWith Sld5
+unknown interactsWith Psf3
+unknown interactsWith Psf1
+Ydr288w interactsWith unknown
+unknown interactsWith Rhc18
+unknown interactsWith Smc5
+unknown interactsWith Qri2
+unknown interactsWith Nse1
+unknown interactsWith Mms21
+Yml023c interactsWith unknown
+unknown interactsWith Rhc18
+unknown interactsWith Smc5
+unknown interactsWith Kre29
+unknown interactsWith Mms21
+unknown interactsWith Qri2
+Swc4 interactsWith unknown
+unknown interactsWith Tra1
+unknown interactsWith Swr1
+unknown interactsWith Vid21
+unknown interactsWith Epl1
+unknown interactsWith Yjl081c
+unknown interactsWith Esa1
+unknown interactsWith Rvb2
+unknown interactsWith Yaf9
+unknown interactsWith Yng2
+unknown interactsWith Rvb1
+Ygr198w interactsWith unknown
+unknown interactsWith Stt4
+Tim50 interactsWith unknown
+unknown interactsWith Tom40
+Ygr046w interactsWith unknown
+unknown interactsWith Hsp60
+Cwc2 interactsWith unknown
+unknown interactsWith Brr2
+unknown interactsWith Cdc40
+unknown interactsWith Cef1
+unknown interactsWith Clf1
+unknown interactsWith Ygr278w
+unknown interactsWith Cwc23
+unknown interactsWith Ecm2
+unknown interactsWith Yjr050w
+unknown interactsWith Lea1
+unknown interactsWith Prp8
+unknown interactsWith Prp19
+unknown interactsWith Prp43
+unknown interactsWith Prp45
+unknown interactsWith Prp46
+unknown interactsWith Smb1
+unknown interactsWith Smd1
+unknown interactsWith Smd3
+unknown interactsWith Snt309
+unknown interactsWith Snu114
+unknown interactsWith Syf1
+unknown interactsWith Syf2
+unknown interactsWith Ykl095w
+unknown interactsWith Ykr022c
+unknown interactsWith Ylr424w
+Ylr424w interactsWith unknown
+unknown interactsWith Brr2
+unknown interactsWith Cdc40
+unknown interactsWith Cef1
+unknown interactsWith Clf1
+unknown interactsWith Cwc23
+unknown interactsWith Ecm2
+unknown interactsWith Prp8
+unknown interactsWith Prp19
+unknown interactsWith Prp43
+unknown interactsWith Prp45
+unknown interactsWith Prp46
+unknown interactsWith Smb1
+unknown interactsWith Ypr182w
+unknown interactsWith Smd3
+unknown interactsWith Snt309
+unknown interactsWith Snu114
+unknown interactsWith Syf1
+unknown interactsWith Ykr022c
+unknown interactsWith Cwc2
+Ylr132c interactsWith unknown
+unknown interactsWith Prp19
+unknown interactsWith Snt309
+Cwc25 interactsWith unknown
+unknown interactsWith Prp8
+unknown interactsWith Snu114
+unknown interactsWith Prp19
+unknown interactsWith Clf1
+Ynl313c interactsWith unknown
+unknown interactsWith Grs1
+unknown interactsWith Kar2
+unknown interactsWith Tub3
+Rix7 interactsWith unknown
+unknown interactsWith Amn1
+unknown interactsWith Axl2
+unknown interactsWith Imh1
+unknown interactsWith Pex19
+unknown interactsWith Pfk27
+unknown interactsWith Rgt2
+unknown interactsWith Ric1
+unknown interactsWith Rpa190
+unknown interactsWith Sst2
+unknown interactsWith Trx1
+unknown interactsWith Trx2
+unknown interactsWith Ylr035c
+unknown interactsWith Rax2
+Yjr136c interactsWith unknown
+unknown interactsWith Rsm23
+Ypr169w interactsWith unknown
+unknown interactsWith Bre1
+Mia40 interactsWith unknown
+unknown interactsWith Tom40
+unknown interactsWith Kap123
+unknown interactsWith Adh1
+Kae1 interactsWith unknown
+unknown interactsWith Gon7
+Naf1 interactsWith unknown
+unknown interactsWith Cbf5
+Yjl010c interactsWith unknown
+unknown interactsWith Nsr1
+unknown interactsWith Gcd6
+unknown interactsWith Snu13
+Esf1 interactsWith unknown
+unknown interactsWith Hca4
+unknown interactsWith Ygr145w
+unknown interactsWith Bfr2
+unknown interactsWith Lcp5
+unknown interactsWith Nop58
+unknown interactsWith Utp4
+Gwt1 interactsWith unknown
+unknown interactsWith Ded81
+unknown interactsWith Mrc1
+unknown interactsWith Sec7
+unknown interactsWith Sec63
+Yjr012c interactsWith unknown
+unknown interactsWith Hol1
+unknown interactsWith Mmp1
+unknown interactsWith Pex7
+unknown interactsWith Plb1
+Ylr145w interactsWith unknown
+unknown interactsWith Pop1
+unknown interactsWith Pop4
+unknown interactsWith Rpp1
+unknown interactsWith Pop3
+unknown interactsWith Snm1
+unknown interactsWith Pop5
+unknown interactsWith Pop6
+unknown interactsWith Pop8
+Ipi1 interactsWith unknown
+unknown interactsWith Rix1
+unknown interactsWith Ipi3
+Ynl260c interactsWith unknown
+unknown interactsWith Yae1
+Ykr079c interactsWith unknown
+unknown interactsWith Ymr099c
+Ylr132c interactsWith unknown
+unknown interactsWith Cor1
+Bem1 pp Cdc24
+Grd19 pp Adh1
+Grd19 pp Akr2
+Grd19 pp Apg17
+Grd19 pp Rbd2
+Grd19 pp Rvs167
+Grd19 pp Sec15
+Grd19 pp Yif1
+Grd19 pp Yip1
+Grd19 pp Yip5
+Grd19 pp Ylr031w
+Grd19 pp Ylr424w
+Grd19 pp Ypt53
+Mvp1 pp Std1
+Mvp1 pp Yra2
+Snx4 pp Apg17
+Snx4 pp Ask10
+Snx4 pp Cog2
+Snx4 pp Cog6
+Snx4 pp Dam1
+Snx4 pp Ecm11
+Snx4 pp Lcp5
+Snx4 pp Nip100
+Snx4 pp Sds3
+Snx4 pp Sec15
+Snx4 pp Sgt1
+Snx4 pp Snx41
+Snx4 pp Swf3
+Snx4 pp Vma8
+Snx4 pp Vps17
+Snx4 pp Ylr031w
+Snx4 pp Ylr424w
+Snx4 pp Ynl086w
+Snx4 pp Ypl201c
+Snx42 pp Rrn10
+Snx42 pp Snx4
+Snx42 pp Yip1
+Vam7 pp Akr2
+Vam7 pp Avt2
+Vam7 pp Bsp1
+Vam7 pp Ecm11
+Vam7 pp Rbd2
+Vam7 pp Rpt5
+Vam7 pp Spc72
+Vam7 pp Vps21
+Vam7 pp Ygr223c
+Vam7 pp Yif1
+Vam7 pp Yip1
+Vam7 pp Yip5
+Vps5 pp Bub1
+Vps5 pp Vps35
+Vps5 pp Ynl086w
+Vps17 pp Akr2
+Vps17 pp Bsp1
+Vps17 pp Vps5
+Vps17 pp Yif1
+Vps17 pp Yip1
+Vps17 pp Ypt53
+Ypt35 pp Akr2
+Ypt35 pp Atr1
+Ypt35 pp Bet1
+Ypt35 pp Bos1
+Ypt35 pp Ktr3
+Ypt35 pp Pep12
+Ypt35 pp Rbd2
+Ypt35 pp Sps18
+Ypt35 pp Tvp23
+Ypt35 pp Yif1
+Ypt35 pp Yip1
+Ypt35 pp Yip4
+Ypt35 pp Yip5
+Ypt35 pp Ymd8
+Ypt35 pp Yor292c
+Vps5 pp Yif1
+Vps5 pp Yip1
+Snx4 pp Yip4
+Snx42 pp Yif1
+Vps17 pp Yip4
+Bdp1 pp Tfc4
+Ku interactsWith TLC1
+Cdc13 pd Telomere_VII-L
+Est1 pd Telomere_VII-L
+Est2 pd Telomere_VII-L
+Ku interactsWith Telomere_VII-L
+Ku interactsWith Subtelomere_VII-L
+Ku interactsWith Telomere_VI-R
+Est2 pd Telomere_VI-R
+Est1 pd Telomere_VI-R
+Cdc13 pd Telomere_VI-R
+Fus3 pp Ste12
+MFalpha2 pp Ste2
+MFalpha1 pp Ste2
+Ste20 pp Ste11
+Ste50 pp Ste11
+Ste11 pp Ste11
+Fus3 pp Sst2
+Sst2 pp Gpa1
+Ste2 pp Gpa1
+Gpa1 pp Ste4
+Isw2 pp Itc1
+Abf1 pd iYAL054C
+Abf1 pd iYAL043C
+Abf1 pd iYAL023C
+Abf1 pd TEL1R
+Abf1 pd iYBL064C
+Abf1 pd iYBL057C
+Abf1 pd iYBL046W
+Abf1 pd iYBL039C
+Abf1 pd iYBL007C
+Abf1 pd iYBR030W
+Abf1 pd iYBR058C
+Abf1 pd iYBR101C
+Abf1 pd iYBR109C
+Abf1 pd iYBR145W
+Abf1 pd iYBR162C
+Abf1 pd iYBR169C
+Abf1 pd iYBR278W
+Abf1 pd iYBR283C
+Abf1 pd iYBR289W
+Abf1 pd iYCL046W
+Abf1 pd iYCL044C
+Abf1 pd iYCL031C
+Abf1 pd iYCL011C
+Abf1 pd iYCR052W
+Abf1 pd iYCR063W
+Abf1 pd iYCR081W
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+Abf1 pd iYDL230W
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+Abf1 pd iYDL106C
+Abf1 pd iYDL085W
+Abf1 pd iYDL081C
+Abf1 pd iYDL053C
+Abf1 pd iYDL034W
+Abf1 pd iYDL028C
+Abf1 pd iYDR003W
+Abf1 pd iYDR005C
+Abf1 pd iYDR029W
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+Abf1 pd iYDR137W
+Abf1 pd iYDR194C
+Abf1 pd iYDR205W
+Abf1 pd iYDR214W
+Abf1 pd iYDR221W
+Abf1 pd iYDR233C
+Abf1 pd iYDR279W
+Abf1 pd iYDR283C
+Abf1 pd iYDR326C
+Abf1 pd iYDR360W
+Abf1 pd iYDR361C
+Abf1 pd iYDR384C
+Abf1 pd iYDR393W
+Abf1 pd iYDR404C
+Abf1 pd iYDR407C
+Abf1 pd iYDR461W
+Abf1 pd iYDR463W
+Abf1 pd iYEL017C-A
+Abf1 pd isnR14
+Abf1 pd iYER026C
+Abf1 pd iYER071C
+Abf1 pd iYER089C
+Abf1 pd iYER122C
+Abf1 pd iYER140W
+Abf1 pd iYER161C
+Abf1 pd iYER171W
+Abf1 pd iYERWomega2-0
+Abf1 pd iYFL048C
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+Abf1 pd iYFL024C
+Abf1 pd iYFL018C
+Abf1 pd TEL6R
+Abf1 pd iYGL235W
+Abf1 pd iYGL222C
+Abf1 pd iYGL196W
+Abf1 pd iYGL194C
+Abf1 pd iYGL122C
+Abf1 pd iYGL107C
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+Abf1 pd iYGL037C
+Abf1 pd iYGL024W
+Abf1 pd iYGL011C
+Abf1 pd iYGR006W
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+Abf1 pd iYHR005C-A
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+Abf1 pd iYHR065C
+Abf1 pd iYHR077C
+Abf1 pd iYHR079C-B
+Abf1 pd iYHR080C
+Abf1 pd iYHR115C
+Abf1 pd iYIL135C
+Abf1 pd iYIL055C
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+Abf1 pd iYJL008C
+Abf1 pd iYJL004C
+Abf1 pd iYJR062C
+Abf1 pd iYJR088C
+Abf1 pd iYJR110W
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+Abf1 pd iSNR64
+Abf1 pd iYKL196C
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+Abf1 pd iYMRWdelta12
+Abf1 pd iYMR060C
+Abf1 pd iYMR065W
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+Abf1 pd iYNL190W
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+Abf1 pd iYNL113W
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+Abf1 pd iYNR045W
+Abf1 pd iYOL117W
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+Abf1 pd iYOR146W
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+Abf1 pd iYOR209C
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+Abf1 pd iYOR254C
+Abf1 pd iYOR261C
+Abf1 pd iYPL242C
+Abf1 pd iYPL212C
+Abf1 pd iYPL138C
+Abf1 pd iYPR181C
+Mig1 pd iYBR031W
+Mig1 pd iYBR051W
+Mig1 pd iYBR298C
+Mig1 pd YCLWTy5-1C
+Mig1 pd tP(AGG)C
+Mig1 pd iYDL246C-0
+Mig1 pd iYDL236W
+Mig1 pd iYDL214C
+Mig1 pd iYDL095W
+Mig1 pd iYDL079C
+Mig1 pd iYDR109C
+Mig1 pd iYDR342C-0
+Mig1 pd iYDR343C
+Mig1 pd iYDR516C
+Mig1 pd iYER120W
+Mig1 pd iYER173W
+Mig1 pd iYFL055W-0
+Mig1 pd iYFL054C
+Mig1 pd iYFR017C
+Mig1 pd iYFR053C-0
+Mig1 pd iYGL254W
+Mig1 pd iYGL122C
+Mig1 pd iYGR067C
+Mig1 pd iYGR242W
+Mig1 pd iYGR292W-0
+Mig1 pd iYHL032C
+Mig1 pd iYHR032W
+Mig1 pd iYHR043C
+Mig1 pd iYHR057C
+Mig1 pd iYHR094C
+Mig1 pd iYIL057C
+Mig1 pd iYIL024C
+Mig1 pd iYIR015W
+Mig1 pd iYJR056C
+Mig1 pd iYJR158W-1
+Mig1 pd iYKL218C-2
+Mig1 pd iYKL190W
+Mig1 pd iYKL063C-1
+Mig1 pd iYKL055C
+Mig1 pd iYKR039W
+Mig1 pd iYKR075C-0
+Mig1 pd iYKR098C
+Mig1 pd iYKR103W
+Mig1 pd iYLR023C
+Mig1 pd iYLR036C
+Mig1 pd iYLR069C
+Mig1 pd iYLR071C
+Mig1 pd iYLR089C
+Mig1 pd iYLR151C
+Mig1 pd iYLR190W
+Mig1 pd iYLR273C
+Mig1 pd iYLR377C
+Mig1 pd iYML107C
+Mig1 pd iYML049C
+Mig1 pd iYML009C
+Mig1 pd iYMR010W-1
+Mig1 pd iYMRWdelta12
+Mig1 pd YMR194C-A
+Mig1 pd iYMR205C
+Mig1 pd iYMR272C
+Mig1 pd iYMR307W
+Mig1 pd iYNL300W
+Mig1 pd iYNL184C
+Mig1 pd iYNL105W
+Mig1 pd iYNL081C
+Mig1 pd iYNL032W
+Mig1 pd iYNR002C
+Mig1 pd iYNR071C
+Mig1 pd iYOL157C
+Mig1 pd iYOL053C-A
+Mig1 pd iYOR180C
+Mig1 pd YOR235W
+Mig1 pd iYOR355W
+Mig1 pd iYPL248C
+Mig1 pd iYPL201C
+Mig1 pd iYPL134C
+Mig1 pd iYPR026W
+Mig1 pd iYPR051W
+Mig1 pd tI(AAU)P2
+Rap1 pd iYAL053W
+Rap1 pd iYAL034C
+Rap1 pd iYBL087C
+Rap1 pd iYBL072C
+Rap1 pd iYBL061C
+Rap1 pd iYBL050W
+Rap1 pd iYBL030C-1
+Rap1 pd iYBL028C
+Rap1 pd iYBL022C
+Rap1 pd iYBR047W
+Rap1 pd iYBR052C
+Rap1 pd iYBR060C-0
+Rap1 pd iYBR084C-A
+Rap1 pd iYBR117C
+Rap1 pd iYBR148W
+Rap1 pd iYBR179C
+Rap1 pd iYBR181C
+Rap1 pd iYBR188C
+Rap1 pd iYBR189W
+Rap1 pd iYBR196C
+Rap1 pd iYBR204C
+Rap1 pd iLSR1
+Rap1 pd iYBR294W
+Rap1 pd iYCL067C
+Rap1 pd iYCR039C
+Rap1 pd iYCL037C
+Rap1 pd iYCL030C
+Rap1 pd iYCL025C
+Rap1 pd iYCRCdelta6-B
+Rap1 pd iYCR011C
+Rap1 pd iYDL235C
+Rap1 pd iYDL230W
+Rap1 pd iYDL192W
+Rap1 pd iYDL188C
+Rap1 pd iYDL184C
+Rap1 pd iYDL169C
+Rap1 pd iYDL137W
+Rap1 pd iYDL133C-A
+Rap1 pd iYDL130W-A
+Rap1 pd iYDL083C
+Rap1 pd iYDL076C
+Rap1 pd iYDL061C
+Rap1 pd iYDL055C-1
+Rap1 pd itA(AGC)D
+Rap1 pd iYDR036C
+Rap1 pd iYDR050C
+Rap1 pd iYDR063W
+Rap1 pd iYDR070C
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+Rap1 pd iYDR249C
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+Rap1 pd iYDR300C
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+Rap1 pd iYEL023C
+Rap1 pd iYEL021W
+Rap1 pd iYEL008W
+Rap1 pd iYER031C
+Rap1 pd iYER033C
+Rap1 pd iYER045C-1
+Rap1 pd iYER047C
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+Rap1 pd itS(UGA)E-0
+Rap1 pd iYER073W
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+Rap1 pd YKLCdelta2
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+Rap1 pd itR(CCG)L
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+Rap1 pd iYOL121C
+Rap1 pd iYOL120C
+Rap1 pd iYOL110W
+Rap1 pd iYOLWdelta5
+Rap1 pd iYOL083W-1
+Rap1 pd iYOL060C
+Rap1 pd iYOL053C-A
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+Rap1 pd iYOR179C-1
+Rap1 pd iYOR212W
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+Rap1 pd YOR235W
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+Rap1 pd iYOR301W
+Rap1 pd iYOR312C
+Rap1 pd iYOR337W
+Rap1 pd iYOR340C
+Rap1 pd iYOR354C-1
+Rap1 pd iYOR358W
+Rap1 pd iYOR366W
+Rap1 pd iYOR369C
+Rap1 pd iYPL249C-A
+Rap1 pd iYPL230W
+Rap1 pd iYPL221W
+Rap1 pd iYPL199C
+Rap1 pd iYPL162C
+Rap1 pd iYPL144W
+Rap1 pd iYPL132W
+Rap1 pd iYPL090C
+Rap1 pd iYPL082C
+Rap1 pd iYPL076W-0
+Rap1 pd iYPL055C
+Rap1 pd iYPL037C
+Rap1 pd iYPL017C
+Rap1 pd iYPR029C
+Rap1 pd iYPR042C
+Rap1 pd iYPR056W
+Rap1 pd iYPR079W
+Rap1 pd iYPR102C
+Rap1 pd iYPR105C
+Rap1 pd iYPR110C
+Rap1 pd iYPR134W
+Rap1 pd iYPR160W
+Rap1 pd iYPR161C
+Unknown interactsWith Htb2
+Unknown interactsWith Htb1
+Unknown interactsWith Hta2
+Unknown interactsWith Hta1
+Unknown interactsWith Hht2
+Unknown interactsWith Hht1
+Unknown interactsWith Hhf1
+Unknown interactsWith Nhp10
+Unknown interactsWith Taf14
+Unknown interactsWith Act1
+Unknown interactsWith Rvb2
+Unknown interactsWith Arp4
+Unknown interactsWith Arp8
+Unknown interactsWith Arp5
+Unknown interactsWith Ies3
+Ino80 interactsWith Unknown
+Unknown interactsWith Htb1
+Unknown interactsWith Hta2
+Unknown interactsWith Hta1
+Unknown interactsWith Hht2
+Unknown interactsWith Hht1
+Unknown interactsWith Hhf2
+Unknown interactsWith Hhf1
+Unknown interactsWith Htb2
+Unknown interactsWith Act1
+Unknown interactsWith Rvb2
+Unknown interactsWith Rvb1
+Unknown interactsWith Arp4
+Unknown interactsWith Rvb1
+Unknown interactsWith Ino80
+Unknown interactsWith Hta2
+Unknown interactsWith Arp4
+Unknown interactsWith Act1
+Unknown interactsWith Ies5
+Unknown interactsWith Ies1
+Unknown interactsWith Ies3
+Unknown interactsWith Arp5
+Unknown interactsWith Rvb2
+Unknown interactsWith Rvb1
+Nhp10 interactsWith Unknown
+Unknown interactsWith Orc6
+Unknown interactsWith Orc5
+Unknown interactsWith Orc4
+Unknown interactsWith Orc3
+Orc1 interactsWith Unknown
+Unknown interactsWith Orc2
+Unknown interactsWith Ino80
+Unknown interactsWith Nhp10
+Unknown interactsWith Act1
+Unknown interactsWith Rvb2
+Unknown interactsWith Rvb1
+Unknown interactsWith Arp4
+Unknown interactsWith Taf14
+Unknown interactsWith Ies3
+Arp8 interactsWith Unknown
+Unknown interactsWith Hhf2
+Swr1 interactsWith Unknown
+Unknown interactsWith Arp8
+Rpc10 pp Tfc4
+Sua7 pp Sub1
+Ino80_Complex interactsWith MAT_locus_DSB
+Ino80_Complex interactsWith MAT_locus_DSB
+ORC interactsWith ARS1
+Cdc13 pp Zds2
+Cdc13 pp Imp4
+Pol1 pp Sir4
+Sir4 pp Zds2
+Cdc13 pp Sir4
+Cdc13 pp Pol1
+Pol1 pp Imp4
+Cdc6 pd ARS1
+Fhl1 pd itR(CCG)L
+Fhl1 pd iYBL028C
+Fhl1 pd iYBR047W
+Fhl1 pd iYDL076C
+Fhl1 pd iYDL083C
+Fhl1 pd iYDL133C-A
+Fhl1 pd iYDL192W
+Fhl1 pd iYDR470C
+Fhl1 pd iYEL008W
+Fhl1 pd iYEL054C
+Fhl1 pd iYER073W
+Fhl1 pd iYER101C
+Fhl1 pd iYER116C
+Fhl1 pd iYER130C
+Fhl1 pd iYFL034C-A
+Fhl1 pd iYFR031C-A
+Fhl1 pd iYFR032C
+Fhl1 pd iYFR032C-A
+Fhl1 pd iYGL031C
+Fhl1 pd iYGL104C
+Fhl1 pd iYGL124C
+Fhl1 pd iYGL136C
+Fhl1 pd iYGL147C
+Fhl1 pd iYGL189C
+Fhl1 pd iYGR033C
+Fhl1 pd iYGR117C
+Fhl1 pd iYGR118W
+Fhl1 pd iYGR148C
+Fhl1 pd iYHL002W
+Fhl1 pd iYHL033C
+Fhl1 pd iYHR141C
+Fhl1 pd iYHR203C
+Fhl1 pd iYIL019W
+Fhl1 pd iYIL069C
+Fhl1 pd iYIL132C
+Fhl1 pd iYIL133C
+Fhl1 pd iYIL149C
+Fhl1 pd iYJL136C
+Fhl1 pd iYJL178C
+Fhl1 pd iYJL190C
+Fhl1 pd iYJL191W
+Fhl1 pd iYJL192C
+Fhl1 pd iYJR122W
+Fhl1 pd iYJR123W
+Fhl1 pd iYJR145C
+Fhl1 pd iYKL006C-A
+Fhl1 pd iYKL157W
+Fhl1 pd iYKL181W
+Fhl1 pd iYKR056W
+Fhl1 pd iYKR094C
+Fhl1 pd iYLR047C
+Fhl1 pd iYLR074C
+Fhl1 pd iYLR166C
+Fhl1 pd iYLR264W
+Fhl1 pd iYLR287C-A
+Fhl1 pd iYLR325C
+Fhl1 pd iYLR333C
+Fhl1 pd iYLR366W
+Fhl1 pd iYLR387C
+Fhl1 pd iYLR399C
+Fhl1 pd iYLR406C
+Fhl1 pd iYLR441C
+Fhl1 pd iYLR447C
+Fhl1 pd iYML025C
+Fhl1 pd iYML026C
+Fhl1 pd iYML064C
+Fhl1 pd iYML073C
+Fhl1 pd iYMR013C-0
+Fhl1 pd iYMR013C-1
+Fhl1 pd iYMR229C
+Fhl1 pd iYMR242C
+Fhl1 pd iYNL179C-1
+Fhl1 pd iYNL302C
+Fhl1 pd iYOL040C
+Fhl1 pd iYOL121C
+Fhl1 pd iYOL128C
+Fhl1 pd iYOR095C
+Fhl1 pd iYOR234C
+Fhl1 pd iYOR292C
+Fhl1 pd iYOR312C
+Fhl1 pd iYOR369C
+Fhl1 pd iYPL144W
+Fhl1 pd iYPL249C-A
+Ifh1 pd itR(CCG)L
+Ifh1 pd iYDL076C
+Ifh1 pd iYDL083C
+Ifh1 pd iYDL133C-A
+Ifh1 pd iYDL192W
+Ifh1 pd iYDR470C
+Ifh1 pd iYEL054C
+Ifh1 pd iYER073W
+Ifh1 pd iYER116C
+Ifh1 pd iYFR031C-A
+Ifh1 pd iYFR032C-A
+Ifh1 pd iYGL031C
+Ifh1 pd iYGL104C
+Ifh1 pd iYGL124C
+Ifh1 pd iYGL136C
+Ifh1 pd iYGL147C
+Ifh1 pd iYGR085C
+Ifh1 pd iYHL002W
+Ifh1 pd iYHL033C
+Ifh1 pd iYHR141C
+Ifh1 pd iYIL019W
+Ifh1 pd iYIL069C
+Ifh1 pd iYIL149C
+Ifh1 pd iYJL136C
+Ifh1 pd iYJL178C
+Ifh1 pd iYJL190C
+Ifh1 pd iYJL192C
+Ifh1 pd iYJR122W
+Ifh1 pd iYJR123W
+Ifh1 pd iYKR094C
+Ifh1 pd iYLR047C
+Ifh1 pd iYLR149C
+Ifh1 pd iYLR166C
+Ifh1 pd iYLR184W
+Ifh1 pd iYLR264W
+Ifh1 pd iYLR287C-A
+Ifh1 pd iYLR325C
+Ifh1 pd iYLR333C
+Ifh1 pd iYLR366W
+Ifh1 pd iYLR406C
+Ifh1 pd iYLR441C
+Ifh1 pd iYLR447C
+Ifh1 pd iYML025C
+Ifh1 pd iYML026C
+Ifh1 pd iYML064C
+Ifh1 pd iYMR013C-0
+Ifh1 pd iYMR013C-1
+Ifh1 pd iYMR229C
+Ifh1 pd iYNL097C
+Ifh1 pd iYOL026C
+Ifh1 pd iYOL040C
+Ifh1 pd iYOL121C
+Ifh1 pd iYOR095C
+Ifh1 pd iYOR234C
+Ifh1 pd iYOR312C
+Ifh1 pd iYOR354C-0
+Ifh1 pd iYPL079W
+Ifh1 pd iYPL249C-A
+Ifh1 pd iYPR131C
+Fhl1 pd iTR(CCG)L
+Fhl1 pd iYBL028C
+Fhl1 pd iYBL093C
+Fhl1 pd iYBR047W
+Fhl1 pd iYBR061C
+Fhl1 pd iYBR084C-A
+Fhl1 pd iYBR181C
+Fhl1 pd iYBR188C
+Fhl1 pd iYBR189W
+Fhl1 pd iYBR208C
+Fhl1 pd iYBR213W
+Fhl1 pd iYBR284W
+Fhl1 pd iYDL061C
+Fhl1 pd iYDL076C
+Fhl1 pd iYDL083C
+Fhl1 pd iYDL100C
+Fhl1 pd iYDL130W-A
+Fhl1 pd iYDL133C-A
+Fhl1 pd iYDL184C
+Fhl1 pd iYDL192W
+Fhl1 pd iYDR063W
+Fhl1 pd iYDR416W
+Fhl1 pd iYDR449C
+Fhl1 pd iYDR470C
+Fhl1 pd iYDR480W
+Fhl1 pd iYEL054C
+Fhl1 pd iYER044C-A
+Fhl1 pd iYER056C-A
+Fhl1 pd iYER073W
+Fhl1 pd iYER101C
+Fhl1 pd iYER116C
+Fhl1 pd iYER134C
+Fhl1 pd iYFR031C-A
+Fhl1 pd iYGL057C
+Fhl1 pd iYGL104C
+Fhl1 pd iYGL136C
+Fhl1 pd iYGL147C
+Fhl1 pd iYGL189C
+Fhl1 pd iYGR033C
+Fhl1 pd iYGR081C
+Fhl1 pd iYGR086C
+Fhl1 pd iYGR117C
+Fhl1 pd iYGR148C
+Fhl1 pd iYGR179C
+Fhl1 pd iYGR192C
+Fhl1 pd iYHL002W
+Fhl1 pd iYHL033C
+Fhl1 pd iYHR009C
+Fhl1 pd iYHR021C
+Fhl1 pd iYHR141C
+Fhl1 pd iYHR203C
+Fhl1 pd iYIL019W
+Fhl1 pd iYIL069C
+Fhl1 pd iYIL131C
+Fhl1 pd iYIL133C
+Fhl1 pd iYIL149C
+Fhl1 pd iYJL110C
+Fhl1 pd iYJL136C
+Fhl1 pd iYJL178C
+Fhl1 pd iYJL190C
+Fhl1 pd iYJL192C
+Fhl1 pd iYJR122W
+Fhl1 pd iYJR145C
+Fhl1 pd iYKL006C-A
+Fhl1 pd iYKL065C
+Fhl1 pd iYKL157W
+Fhl1 pd iYKL181W
+Fhl1 pd iYKL222C
+Fhl1 pd iYKR075C-0
+Fhl1 pd iYLR023C
+Fhl1 pd iYLR029C
+Fhl1 pd iYLR047C
+Fhl1 pd iYLR060W
+Fhl1 pd iYLR074C
+Fhl1 pd iYLR166C
+Fhl1 pd iYLR184W
+Fhl1 pd iYLR264W
+Fhl1 pd iYLR390W
+Fhl1 pd iYLR406C
+Fhl1 pd iYLR441C
+Fhl1 pd iYLR447C
+Fhl1 pd iYML025C
+Fhl1 pd iYML026C
+Fhl1 pd iYML064C
+Fhl1 pd iYML073C
+Fhl1 pd iYMR102C
+Fhl1 pd iYMR142C
+Fhl1 pd iYMR242C
+Fhl1 pd iYMRWDELTA16
+Fhl1 pd iYNL069C
+Fhl1 pd iYNL096C
+Fhl1 pd iYNL163C
+Fhl1 pd iYNL307C
+Fhl1 pd iYOL040C
+Fhl1 pd iYOL120C
+Fhl1 pd iYOL128C
+Fhl1 pd iYOR095C
+Fhl1 pd iYOR182C
+Fhl1 pd iYOR234C
+Fhl1 pd iYOR292C
+Fhl1 pd iYOR312C
+Fhl1 pd iYPL071C
+Fhl1 pd iYPL090C
+Fhl1 pd iYPL249C-A
+Fhl1 pd iYPL265W
+Fhl1 pd iYPR042C
+Fhl1 pd iYPR102C
+Fhl1 pd iYPR131C
+Fhl1 pd iYPRCDELTA19
+Fhl1 pd YDL133C-A
+Fhl1 pd YOR235W
+Ifh1 pd iCEN12
+Ifh1 pd iCEN14
+Ifh1 pd INTYCR097W-A2
+Ifh1 pd INTYPL081W
+Ifh1 pd iTK(CUU)F
+Ifh1 pd iTK(UUU)L
+Ifh1 pd iTM(CAU)J2
+Ifh1 pd iYBL028C
+Ifh1 pd iYBL093C
+Ifh1 pd iYBR084C-A
+Ifh1 pd iYBR117C
+Ifh1 pd iYBR189W
+Ifh1 pd iYBR217W
+Ifh1 pd iYCR021C
+Ifh1 pd iYDL083C
+Ifh1 pd iYDL157C
+Ifh1 pd iYDL184C
+Ifh1 pd iYDR033W
+Ifh1 pd iYDR060W
+Ifh1 pd iYDR112W
+Ifh1 pd iYDR125C
+Ifh1 pd iYDR168W
+Ifh1 pd iYDR372C
+Ifh1 pd iYDR416W
+Ifh1 pd iYDR470C
+Ifh1 pd iYER056C-A
+Ifh1 pd iYER116C
+Ifh1 pd iYER155C
+Ifh1 pd iYFR031C-A
+Ifh1 pd iYGL031C
+Ifh1 pd iYGL104C
+Ifh1 pd iYGL136C
+Ifh1 pd iYGL189C
+Ifh1 pd iYGR033C
+Ifh1 pd iYGR048W
+Ifh1 pd iYGR075C
+Ifh1 pd iYGR081C
+Ifh1 pd iYGR117C
+Ifh1 pd iYGR120C
+Ifh1 pd iYGR148C
+Ifh1 pd iYHL033C
+Ifh1 pd iYHR009C
+Ifh1 pd iYHR021C
+Ifh1 pd iYHR039C
+Ifh1 pd iYHR107C
+Ifh1 pd iYHR136C
+Ifh1 pd iYHR141C
+Ifh1 pd iYHR203C
+Ifh1 pd iYIL019W
+Ifh1 pd iYIL052C
+Ifh1 pd iYIL069C
+Ifh1 pd iYIL133C
+Ifh1 pd iYIL149C
+Ifh1 pd iYJL088W
+Ifh1 pd iYJL136C
+Ifh1 pd iYJL137C
+Ifh1 pd iYJL178C
+Ifh1 pd iYJL180C
+Ifh1 pd iYJL190C
+Ifh1 pd iYJR122W
+Ifh1 pd iYJR145C
+Ifh1 pd iYKL006C-A
+Ifh1 pd iYKL047W
+Ifh1 pd iYKL181W
+Ifh1 pd iYLL024C
+Ifh1 pd iYLR023C
+Ifh1 pd iYLR029C
+Ifh1 pd iYLR047C
+Ifh1 pd iYLR406C
+Ifh1 pd iYML025C
+Ifh1 pd iYML026C
+Ifh1 pd iYML064C
+Ifh1 pd iYML069W
+Ifh1 pd iYML073C
+Ifh1 pd iYMR142C
+Ifh1 pd iYNL069C
+Ifh1 pd iYNL096C
+Ifh1 pd iYNL102W
+Ifh1 pd iYNL104C
+Ifh1 pd iYNL161W-0
+Ifh1 pd iYNL302C
+Ifh1 pd iYOL040C
+Ifh1 pd iYOL128C
+Ifh1 pd iYOR178C-1
+Ifh1 pd iYOR183W
+Ifh1 pd iYOR234C
+Ifh1 pd iYOR292C
+Ifh1 pd iYOR312C
+Ifh1 pd iYPL144W
+Ifh1 pd iYPL196W
+Ifh1 pd iYPL214C
+Ifh1 pd iYPL265W
+Ifh1 pd iYPL273W
+Ifh1 pd iYPR079W
+Ifh1 pd iYPR102C
+Ifh1 pd iYPR126C
+Ifh1 pd iYPR131C
+Ifh1 pd TEL9L
+Ifh1 pd YLRCdelta24
+Ifh1 pd YOR235W
+Tec1 pp Fus3
+Tec1 pp Cdc4
+Lrs4 pd CEN3
+Spo13 pd CEN6
+Unknown interactsWith Rpn13
+Unknown interactsWith Rpn11
+Unknown interactsWith Rpt5
+Unknown interactsWith Rpt3
+Unknown interactsWith Rpt2
+Unknown interactsWith Rpn3
+Unknown interactsWith Rpt4
+Unknown interactsWith Rpt1
+Sem1 interactsWith Unknown
+Fus3 pp Tec1
+Reg1 pp Bmh2
+Taf1 pp Taf6
+Dmc1 pp Mei5
+Mei5 pp Sae3
+Mei5 pd HIS4-LEU2
+Dmc1 pd HIS4-LEU2
+Rad51 pd HIS4-LEU2
+Unknown interactsWith Yaf9
+Unknown interactsWith Eaf5
+Unknown interactsWith Yng2
+Unknown interactsWith Act1
+Unknown interactsWith Eaf3
+Unknown interactsWith Esa1
+Unknown interactsWith Eaf2
+Unknown interactsWith Epl1
+Unknown interactsWith Eaf1
+Unknown interactsWith Tra1
+Arp4 interactsWith Unknown
+Unknown interactsWith Rpn1
+Unknown interactsWith Rpn2
+Unknown interactsWith Rpn5
+Unknown interactsWith Rpn6
+Unknown interactsWith Rpn7
+Unknown interactsWith Rpn8
+Unknown interactsWith Rpn9
+Unknown interactsWith Rpn10
+Unknown interactsWith Rpn12
+Unknown interactsWith Rpt6
+Unknown interactsWith Ubp6
+Rpn4 pp Ubr2
+Arn3 pp Sed1
+Snu66 pp Hub1
+Unknown interactsWith Utp17
+Unknown interactsWith Utp16
+Unknown interactsWith Utp15
+Unknown interactsWith Utp14
+Unknown interactsWith Utp13
+Unknown interactsWith Rrp5
+Unknown interactsWith Sof1
+Unknown interactsWith Rrp9
+Unknown interactsWith Dhr1
+Unknown interactsWith Snu13
+Unknown interactsWith Nop58
+Unknown interactsWith Nop56
+Tfa1 pp Tfa2
+Spt15 interactsWith TFIIA
+Tfg1 pp Fcp1
+Ifh1 pd RPL37A_URS
+Fhl1 pd RPL30_URS
+Ifh1 pd RPL9A_URS
+Rap1 pd PGK1_URS
+Rap1 pd RPL37A_URS
+Rap1 pd RPL30_URS
+Rap1 pd RPL9A_URS
+Sec8 interactsWith Unknown
+Unknown interactsWith Sec6
+Unknown interactsWith Sec15
+Bmh2 interactsWith Unknown
+Unknown interactsWith Glc7
+Fhl1 pp Crf1
+Fhl1 pp Ifh1
+Yak1 pp Crf1
+Fhl1 pd Rpl30_promoter
+Yak1 pp Yak1
+Tbp1 pd MATa_Locus
+Ppr1 pd Silenced_Gene_Promoters
+Ste20 pp Htb1
+Ste20 pp Htb2
+Unknown interactsWith Tom5
+Unknown interactsWith Tom6
+Unknown interactsWith Tom7
+Unknown interactsWith Tom22
+Unknown interactsWith Tom40
+Unknown interactsWith Stt3
+Unknown interactsWith Ost3
+Unknown interactsWith Ost4
+Ubr2 pp Rad6
+Cks1 pd GAL1
+Cdc28 pd GAL1
+Rpt1 pd GAL1
+Gal4 pd GAL1
+Exo1 pd ARS305
+DNA_polymerase_alpha interactsWith ARS305
+Ufd2 pp Cdc48
+Ufd2 pp Spt23
+Rad23 pp Ufd2
+Cdc48 pp Rad23
+Dsk2 pp Ufd2
+Unknown interactsWith U3_snoRNA
+Unknown interactsWith Imp4
+Unknown interactsWith Imp3
+Mpp10 interactsWith Unknown
+Unknown interactsWith Nop1
+Unknown interactsWith Swm1
+Unknown interactsWith Cdc26
+Unknown interactsWith Apc11
+Unknown interactsWith Doc1
+Unknown interactsWith Apc9
+Unknown interactsWith Mnd2
+Unknown interactsWith Cdc23
+Unknown interactsWith Apc4
+Unknown interactsWith Apc5
+Unknown interactsWith Cdc27
+Unknown interactsWith Apc2
+Unknown interactsWith Apc1
+Cdc16 interactsWith Unknown
+Srb4 interactsWith Sua7
+Med9/10 interactsWith Sua7
+Srb4 interactsWith TBP
+Med9/10 interactsWith TBP
+Med9/10 interactsWith Rpb1
+Srb4 interactsWith Rpb1
+Red1 pp Hop1
+Tbp1 pd MATalpha_Locus
+Ssa2 pp Sti1
+Ipl1 pp Hht2
+Ipl1 pp Hht1
+Pan1 pp End3
+Pan1 pp Pan1
+Prk1 pp Pan1
+Ssa1 pp Sti1
+Hsp90 pp Sti1
+Tap42 pp Pph22
+Tap42 pp Pph21
+Tap42 pp Sit4
+Tap42 pp Pph3
+Tap42 pp Ppg1
+Rrd2 pp Pph22
+Rrd2 pp Pph21
+Rrd1 pp Sit4
+Rrd1 pp Pph3
+Rrd1 pp Ppg1
+TFC1 pd iYIL103W-1
+TFC1 pd iYMR194C-A
+TFC1 pd iYGL056C
+TFC1 pd iYDR072C
+TFC1 pd iYDR379W
+TFC1 pd iYDL130W
+TFC1 pd iYDR277C
+TFC1 pd iYLR096W
+TFC1 pd iYKL187C
+TFC1 pd iYMR077C
+TFC1 pd iYPR036W
+TFC1 pd iYJRWDELTA17
+TFC1 pd iYGR255C
+TFC1 pd iYOR144C
+TFC1 pd iYJL049W
+TFC1 pd iYDR246W
+TFC1 pd iYAL007C
+TFC1 pd iYJLCDELTA6
+TFC1 pd iYBRWDELTA17
+TFC1 pd iYER138W-A
+TFC1 pd iTP(AGG)C
+TFC1 pd iYKLCDELTA6
+TFC1 pd iYNL135C
+TFC1 pd iTV(AAC)L
+TFC1 pd iTL(UAG)J
+TFC1 pd iYOL023W
+TFC1 pd iYJL096W
+TFC1 pd iYLRCSiGMA1
+TFC1 pd iYBR030W
+TFC1 pd iYNL043C
+TFC1 pd iYHL036W
+TFC1 pd iYPR002C-A
+TFC1 pd iYKL190W
+TFC1 pd iYORWTAU3
+TFC1 pd iYDRWDELTA25
+TFC1 pd iYGR122W
+TFC1 pd iYLR246W
+TFC1 pd iTK(UUU)D
+TFC1 pd iTL(GAG)G
+TFC1 pd iYOLWSiGMA2
+TFC1 pd iYGL084C
+TFC1 pd iYAR023C
+TFC1 pd iYBL005W
+TFC1 pd iYLRCDELTA21
+TFC1 pd iYKR038C
+TFC1 pd iTG(CCC)O
+TFC1 pd iTF(GAA)H1
+TFC1 pd iYMR103C
+TFC1 pd iYNR054C-1
+TFC1 pd iTQ(UUG)B
+TFC1 pd iYMLCDELTA2
+TFC1 pd iYNL055C
+TFC1 pd iTP(AGG)N
+TFC1 pd iYMR046W-A
+TFC1 pd iYOR007C
+TFC1 pd iYDR468C
+TFC1 pd iTY(GUA)O
+TFC1 pd iYOR289W
+TFC1 pd iSCR1
+TFC1 pd iYBLWDELTA3
+TFC1 pd iTW(CCA)K-0
+TFC1 pd iYOLCDELTA3
+TFC1 pd iYORWSiGMA3
+TFC1 pd iYBR209W
+TFC1 pd iYER075C
+TFC1 pd iYCR007C
+TFC1 pd iTA(AGC)M1
+TFC1 pd iYGR142W
+TFC1 pd iTA(AGC)K1
+TFC1 pd iTG(GCC)M
+TFC1 pd iYNLCDELTA2
+TFC1 pd iTG(GCC)E
+TFC1 pd iYMR238W
+TFC1 pd iYIR006C
+TFC1 pd iTP(UGG)N1
+TFC1 pd iYMLWDELTA6
+TFC1 pd iYMLWDELTA4
+TFC1 pd iYBRCDELTA14
+TFC1 pd iYJR051W
+TFC1 pd iYOR288C
+TFC1 pd iYCL022C
+TFC1 pd iTV(CAC)H
+TFC1 pd iSNR67
+TFC1 pd iTS(AGA)D2
+TFC1 pd iTM(CAU)D
+TFC1 pd iTA(AGC)P
+TFC1 pd iYJLCDELTA7
+TFC1 pd iYJRWDELTA14
+TFC1 pd iYJLWDELTA19
+TFC1 pd iYDR390C
+TFC1 pd iYERCTAU2
+TFC1 pd iYFR035C
+TFC1 pd iTN(GUU)F
+TFC1 pd iTK(CUU)E1
+TFC1 pd iTA(AGC)M2
+TFC1 pd iTS(AGA)M
+TFC1 pd iTI(AAU)E2
+TFC1 pd iYBLWTAU1
+TFC1 pd iTW(CCA)G2
+TFC1 pd iYJR056C
+TFC1 pd iYDLWTAU1
+TFC1 pd iYNL286W
+TFC1 pd iYMR271C
+TFC1 pd iYDR408C
+TFC1 pd iYLR154C
+TFC1 pd iYHL023C
+TFC1 pd iTN(GUU)G
+TFC1 pd iTV(AAC)G3-0
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+BRF1 pd iTQ(UUG)D2
+BRF1 pd iTV(AAC)G2
+BRF1 pd iYJL024C
+BRF1 pd iTM(CAU)M
+BRF1 pd iTV(AAC)K1-0
+BRF1 pd iYERCDELTA10
+BRF1 pd iYGR038W
+BRF1 pd iYMRWDELTA17
+BRF1 pd iTL(UAA)K
+BRF1 pd iYGL029W
+BRF1 pd iYLRWDELTA14
+BRF1 pd iYGR123C
+BRF1 pd iYJR043C
+BRF1 pd iYJL029C
+BRF1 pd iTM(CAU)J1
+BRF1 pd iTA(AGC)F
+BRF1 pd iYGR217W
+BRF1 pd iTT(AGU)N2
+BRF1 pd iTG(UCC)G
+BRF1 pd iTE(UUC)B
+BRF1 pd iTT(AGU)C
+BRF1 pd iTS(AGA)E
+BRF1 pd iTK(UUU)K
+BRF1 pd iYIL015W
+BRF1 pd iYBRCDELTA19
+BRF1 pd iTQ(UUG)H
+BRF1 pd iTI(AAU)i1
+BRF1 pd iTI(AAU)i2
+BRF1 pd iTS(UGA)E-0
+BRF1 pd iTF(GAA)P1
+BRF1 pd iYER157W
+BRF1 pd iYER150W
+BRF1 pd iYLR230W
+BRF1 pd iYDRWDELTA26
+BRF1 pd iYGR106C
+BRF1 pd iTM(CAU)O1
+BRF1 pd iTS(AGA)J
+BRF1 pd iTG(CCC)D
+BRF1 pd iTM(CAU)O2
+BRF1 pd iYMR158W
+BRF1 pd iYOLCDELTA7
+BRF1 pd iTH(GUG)M
+BRF1 pd iYFL003C
+BRF1 pd iYDR170C
+BRF1 pd iTI(UAU)L
+BRF1 pd iYKLCDELTA4
+BRF1 pd iYPR143W
+BRF1 pd iYGL170C
+BRF1 pd iTH(GUG)H
+BRF1 pd iTR(ACG)J
+BRF1 pd iTP(UGG)N2
+BRF1 pd iYNL036W
+BRF1 pd iTK(UUU)L
+BRF1 pd iTG(GCC)P2
+BRF1 pd iYMR041C
+BRF1 pd iTD(GUC)J2
+BRF1 pd iYPL112C
+BRF1 pd iYJL102W
+BRF1 pd iYER180C
+BRF1 pd iYHR020W
+BRF1 pd iYPR118W
+BRF1 pd iTM(CAU)J2
+BRF1 pd iYGRCDELTA25
+BRF1 pd iTA(UGC)A
+BRF1 pd iTD(GUC)G2
+BRF1 pd iTE(UUC)P
+BRF1 pd iYKRWDELTA10
+BRF1 pd iYDL211C-2
+BRF1 pd iYERCDELTA15
+BRF1 pd iTD(GUC)M
+BRF1 pd iYMRCTAU1
+BRF1 pd iTN(GUU)P
+BRF1 pd iTA(UGC)E
+BRF1 pd iTQ(UUG)D3
+BRF1 pd iYBR081C
+BRF1 pd iYNL035C
+BRF1 pd iYJL115W
+BRF1 pd iTS(AGA)D3
+BRF1 pd iTK(CUU)D2
+BRF1 pd iYDR419W
+BRF1 pd iTF(GAA)F
+BRF1 pd iYFLWDELTA1
+BRF1 pd iSNR6
+BRF1 pd iYKRCDELTA12
+BRF1 pd iYHR005C-A
+BRF1 pd iTD(GUC)B
+BRF1 pd iTF(GAA)D
+BRF1 pd iTT(AGU)i1
+BRF1 pd iYNRCTAU3
+BRF1 pd iYGR120C
+BRF1 pd iTQ(UUG)E1
+BRF1 pd iTA(UGC)L
+BRF1 pd iYKL069W
+BRF1 pd iTG(GCC)J2
+BRF1 pd iYFR019W
+BRF1 pd iTN(GUU)N2
+BRF1 pd iYDR058C
+BRF1 pd iTK(CUU)F
+BRF1 pd iYKL154W
+BRF1 pd iTL(CAA)D
+BRF1 pd iTV(UAC)D
+BRF1 pd iYFR016C
+BRF1 pd iYGRCDELTA30
+BRF1 pd iYGRWDELTA14
+BRF1 pd iYOL026C
+BRF1 pd iTE(UUC)G3
+BRF1 pd iYJLWDELTA15
+BRF1 pd iYLR142W
+BRF1 pd iYIL057C
+BRF1 pd iTT(AGU)J
+BRF1 pd iTD(GUC)L1
+BRF1 pd iYIL096C
+BRF1 pd iYLLCDELTA1
+BRF1 pd iYDRCTY1-2
+BRF1 pd iTL(UAA)L
+BRF1 pd iTR(UCU)G1
+BRF1 pd iTV(UAC)B
+BRF1 pd iYLR454W
+BRF1 pd iTI(UAU)D
+BRF1 pd iTR(UCU)G3
+BRF1 pd iTG(GCC)G2
+BRF1 pd iTS(AGA)B
+BRF1 pd iTR(UCU)K
+BRF1 pd iYML089C
+BRF1 pd iTD(GUC)D
+BRF1 pd iYDR306C
+BRF1 pd iTR(UCU)J2
+BRF1 pd iYEL013W
+BRF1 pd iYERWDELTA7
+BRF1 pd iYKL165C
+BRF1 pd iTG(GCC)D2
+BRF1 pd iTE(UUC)M
+BRF1 pd iYJL006C
+BRF1 pd iYGL055W
+BRF1 pd iTV(CAC)D
+BRF1 pd iTV(AAC)K2
+BRF1 pd iTI(AAU)L2
+BRF1 pd iTT(UGU)G2
+BRF1 pd iTE(UUC)K
+Cth2 interactsWith SDH4_mRNA
+Cth2 interactsWith ACO1_mRNA
+Med9/10 interactsWith Srb10/11
+Srb4_subcomplex interactsWith Srb10/11
+Arf2 pp Gga2
+Arf2 pp Gga1
+Arf1 pp Gga2
+Arf1 pp Gga1
+Med9/10 interactsWith Tfa1
+Unknown interactsWith Ioc4
+Unknown interactsWith Ioc2
+Unknown interactsWith Isw1
+Std1 pp Spt15
+Rvs167 pp Gyp5
+Rvs167 pp App1
+Rvs167 pp Gyl1
+Rvs167 pp Sec8
+Rvs167 pp Msu1
+Rvs167 pp Hse1
+Rvs167 pp Slf1
+Rvs167 pp Lcp5
+Rvs167 pp Ybp2
+Rvs167 pp Tfc6
+Rvs167 pp Cti6
+Rvs167 pp Ivy1
+Rvs167 pp Gfd2
+Rvs167 pp Kap122
+Unknown interactsWith Tfc7
+Unknown interactsWith Tfc8
+Unknown interactsWith Tfc6
+Unknown interactsWith Tfc1
+Unknown interactsWith Tfc4
+Unknown interactsWith Tfc3
+Rnt1 interactsWith MIG2_mRNA
+Tfc1 pp Tfc7
+Tfc1 pp Tfc6
+Tfc1 pp Tfc3
+Tfc8 pp Spt15
+TAF1 pp TAF5
+TAF1 pp TAF9
+TAF1 pp TAF7
+TAF1 pp TAF11
+TAF2 pp TAF3
+TAF2 pp TAF4
+TAF2 pp TAF8
+TAF3 pp TAF10
+TAF4 pp TAF10
+TAF4 pp TAF12
+TAF5 pp TAF4
+TAF5 pp TAF10
+TAF5 pp TAF12
+TAF6 pp TAF10
+TAF6 pp TAF11
+TAF6 pp TAF12
+TAF7 pp TAF2
+TAF7 pp TAF4
+TAF7 pp TAF7
+TAF7 pp TAF8
+TAF7 pp TAF11
+TAF7 pp TBP
+TAF8 pp TAF4
+TAF8 pp TAF5
+TAF8 pp TAF12
+TAF9 pp TAF4
+TAF9 pp TAF6
+TAF9 pp TAF12
+TAF10 pp TAF2
+TAF10 pp TAF8
+TAF10 pp TAF9
+TAF10 pp TAF10
+TAF10 pp TAF11
+TAF10 pp TAF12
+TAF10 pp TAF13
+TAF11 pp TAF4
+TAF11 pp TAF12
+TAF11 pp TAF13
+TAF12 pp TAF12
+Ssa3 pp Sti1
+Ssa4 pp Sti1
+Apc11 pp Ubc4
+Chd1 interactsWith Unknown
+Unknown interactsWith Taf5
+Unknown interactsWith Taf12
+Unknown interactsWith Taf6
+Unknown interactsWith Taf10
+Unknown interactsWith Taf9
+Unknown interactsWith Ada3
+Unknown interactsWith Ada5
+Unknown interactsWith Ada1
+Unknown interactsWith Gcn5
+Unknown interactsWith Ada2
+Unknown interactsWith Spt7
+Unknown interactsWith Spt3
+Unknown interactsWith Tra1
+Unknown interactsWith Rtg2
+Unknown interactsWith Ubp8
+Unknown interactsWith Sgf29
+Chd1 pp Hht1
+Hht1 pd GAL1_locus
+Hht1 pd ACT1_locus
+SLIK interactsWith Hht1
+SAGA interactsWith Hht1
+SLIK interactsWith Hhf1
+SAGA interactsWith Hhf1
+Unknown interactsWith Cdc27
+Unknown interactsWith Cdc16
+Apc11 interactsWith Unknown
+Rad53 pp Sgs1
+mtDNA pd Cha1
+mtDNA pd Ilv6
+mtDNA pd Ilv5
+mtDNA pd Pdb1
+mtDNA pd Pda1
+mtDNA pd Lsc1
+mtDNA pd Kgd2
+mtDNA pd Idh1
+mtDNA pd Lpd1
+mtDNA pd Idp1
+mtDNA pd Ald4
+mtDNA pd Kgd1
+mtDNA pd mtHsp60
+mtDNA pd mtHsp10
+mtDNA pd mtHsp70
+mtDNA pd Atp1
+mtDNA pd Aco1
+mtDNA pd Abf2
+mtDNA pd Mgm101
+mtDNA pd Rpo41
+mtDNA pd Sls1
+mtDNA pd Rim1
+Rli1 interactsWith Unknown
+Unknown interactsWith Rpl3
+Unknown interactsWith Rpl4a
+Unknown interactsWith Rpl4b
+Unknown interactsWith Rpl2b
+Unknown interactsWith Rpl10
+Unknown interactsWith Rps1b
+Unknown interactsWith Rps1a
+Unknown interactsWith Rps4b
+Unknown interactsWith Rps4a
+Unknown interactsWith Rpl8b
+Unknown interactsWith Rpl7a
+Unknown interactsWith Rpl7b
+Unknown interactsWith Rpl16a
+Unknown interactsWith Rps8a
+Unknown interactsWith Rps8b
+Unknown interactsWith Rpl13b
+Unknown interactsWith Rpl13a
+Unknown interactsWith Rps17a
+Unknown interactsWith Rps16b
+Unknown interactsWith Rps24a
+Unknown interactsWith Elp3
+Unknown interactsWith Elp2
+Elp1 interactsWith Unknown
+Met4 pd MET3
+Met4 pd MET14
+Met4 pd MET16
+Met4 pd MET17
+Met4 pd GSH1
+Met4 pd PGK1
+Met30 pp Skp1
+Cdc53 pp Skp1
+Sec23 pp Sec24
+Unknown interactsWith Bet1
+Unknown interactsWith Sec22
+Unknown interactsWith Sar1
+Sec23/24 interactsWith Unknown
+Sec12 pp Sar1
+Taf1 pp Taf4
+Rap1 pd RPL30_promoter
+Rap1 pd RPL28_promoter
+Rap1 pd RPL11A_promoter
+Ifh1 pd RPL11A_promoter
+Ifh1 pd RPS6A_promoter
+Ifh1 pd RPL30_promoter
+Ifh1 pd RPL28_promoter
+Ifh1 pd RPL7A_promoter
+Ifh1 pd RPL3_promoter
+Fhl1 pd RPL11A_promoter
+Fhl1 pd RPS6A_promoter
+Fhl1 pd RPL30_promoter
+Fhl1 pd RPL28_promoter
+Fhl1 pd RPL7A_promoter
+Fhl1 pd RPL3_promoter
+Fhl1 pp Ifh1
+Rap1 pp Ifh1
+Unknown interactsWith Dam1
+Unknown interactsWith Dad4
+Unknown interactsWith Dad3
+Unknown interactsWith Ask1
+Unknown interactsWith Spc19
+Unknown interactsWith Dad2
+Unknown interactsWith Dad1
+Unknown interactsWith Duo1
+Spc34 interactsWith Unknown
+Unknown interactsWith Hsk3
+Unknown interactsWith Ufe1
+Elp1-Elp2-Elp3 interactsWith Elp4-Elp5-Elp6
+Unknown interactsWith Elp6
+Unknown interactsWith Elp5
+Elp4 interactsWith Unknown
+Unknown interactsWith Rpl10
+Rli1 interactsWith Unknown
+Unknown interactsWith Rps3
+Rli1 pp Hcr1
+Ret2 interactsWith Unknown
+Unknown interactsWith Cop1
+Unknown interactsWith Sec26
+Unknown interactsWith Sec21
+Unknown interactsWith Sec27
+Unknown interactsWith Sec28
+Unknown interactsWith Ret3
+Hcr1 pp Prt1
+Hcr1 pp Rpg1
+Rpg1 pp Prt1
+Tif34 pp Prt1
+Tif35 pp Prt1
+Mps2 pp Spc24
+Tid3 pp Spc25
+Nip1 pp Rpg1
+Rli1 interactsWith eIF3_complex
+Unknown interactsWith Rpp1
+Unknown interactsWith Snm1
+Unknown interactsWith Pop8
+Unknown interactsWith Pop7
+Unknown interactsWith Pop6
+Unknown interactsWith Pop5
+Unknown interactsWith Pop3
+Nip1 pp Tif5
+Ubp10 pd 25S_rDNA
+Ubp10 pd 5S_rDNA
+Ubp10 pd ChrVI-R_telomere
+Ubp8 pd ChrVI-R_telomere
+H2B pd ChrVI-R_telomere
+Ubp10 pp ubiquitinated_H2B
+Sir2 pd ChrVI-R_telomere
+Tif34 pp Tif35
+Gcd10 pp Gcd14
+Nip1 pp Sui1
+Hta1 pp Arp4
+Hta1 pd MAT_locus
+Pop4 interactsWith Unknown
+Unknown interactsWith NME1
+Unknown interactsWith Rmp1
+Unknown interactsWith Rpr2
+Unknown interactsWith Pop1
+Med18 pp Med20
+Unknown interactsWith Fip1
+Unknown interactsWith Mpe1
+Unknown interactsWith Pap1
+Unknown interactsWith Pta1
+Unknown interactsWith Ysh1
+Unknown interactsWith Cft2
+Unknown interactsWith Cft1
+Pfs2 interactsWith Unknown
+MLC1 pp MYO2
+MLC1 pp IQG1
+MLC1 pp MYO1
+MLC2 pp MYO1
+Sir2 pp Histone_H4
+Smc6 pd Telomeric_DNA
+Smc6 pd NTS1
+Smc6 pd NTS2
+Lac1 pp Lag1
+Lac1 pp Ymr298w
+Lag1 pp Ymr298w
+Ymr298w pp Ymr298w
+TIM23 interactsWith Cox5a
+Unknown interactsWith Yra1
+Unknown interactsWith Mex67
+Mlp1 pp Nab2
+Ste12 pd iYAL039C-0
+Ste12 pd iYARWdelta6
+Ste12 pd iYBL003C
+Ste12 pd itS(AGA)B
+Ste12 pd iYBR039W
+Ste12 pd iYBR077C
+Ste12 pd iYBR157C-1
+Ste12 pd iYBR222C
+Ste12 pd iYBR239C
+Ste12 pd iYBR241C
+Ste12 pd iYCL028W
+Ste12 pd iYCR088W
+Ste12 pd iYDL123W
+Ste12 pd iYDL135C
+Ste12 pd iYDL181W
+Ste12 pd iYDL241W-1
+Ste12 pd iYDR034C-A
+Ste12 pd iYDR085C
+Ste12 pd iYDR139C
+Ste12 pd iYDR144C
+Ste12 pd iYDR146C
+Mcm1 pd iYDR146C
+Ste12 pd itS(AGA)D2
+Ste12 pd iYDR281C
+Ste12 pd iYDR309C
+Ste12 pd iYDR310C
+Ste12 pd iYDR311W
+Ste12 pd iYDR530C
+Ste12 pd iYER018C
+Ste12 pd iYER044C-A
+Ste12 pd itQ(UUG)E1
+Ste12 pd iYER094C
+Ste12 pd itV(AAC)E1
+Mcm1 pd iYERCdelta24
+Ste12 pd iYERCdelta24
+Ste12 pd iYER184C
+Ste12 pd iYER187W
+Ste12 pd iYGL024W
+Ste12 pd iYGL028C
+Ste12 pd itR(UCU)G1
+Ste12 pd iYGL192W
+Ste12 pd itR(UCU)G2
+Ste12 pd iYGR189C
+Ste12 pd iYGR233C-0
+Ste12 pd iYGR267C
+Ste12 pd itQ(UUG)H
+Ste12 pd iYHR059W
+Ste12 pd iYHR151C
+Mcm1 pd iYHR151C
+Ste12 pd itT(UGU)H
+Ste12 pd iYHR204W
+Ste12 pd itT(AGU)I2
+Ste12 pd iYIL015C-A
+Ste12 pd iYIL037C
+Ste12 pd iYIL083C
+Ste12 pd iYJL048C
+Ste12 pd iYJL107C
+Ste12 pd iYJL115W
+Ste12 pd iYJL157C
+Mcm1 pd iYJL157C
+Ste12 pd itE(UUC)J
+Ste12 pd iYJL162C
+Ste12 pd iYJL163C
+Ste12 pd iYJL170C
+Ste12 pd iYJR053W
+Ste12 pd iYKL029C
+Ste12 pd itL(UAA)K
+Mcm1 pd iYKR041W
+Ste12 pd iYKR041W
+Ste12 pd iYKRCdelta12
+Tec1 pd iYKRCdelta12
+Ste12 pd iYKR092C-1
+Ste12 pd iYLRCsigma1
+Ste12 pd iYLR044C
+Ste12 pd iYLR102C
+Ste12 pd iYLR120C
+Ste12 pd iYLR217W
+Ste12 pd iYLR274W
+Ste12 pd iYLR299W
+Ste12 pd iYLR453C
+Ste12 pd itS(AGA)M
+Ste12 pd itG(GCC)M
+Ste12 pd iYML047C
+Ste12 pd itA(AGC)M1
+Ste12 pd iYMR046W-A
+Ste12 pd iYMR064W
+Ste12 pd iYMRWdelta15
+Ste12 pd iYMR164C
+Ste12 pd iYMR182C-0
+Ste12 pd iYMR197C
+Ste12 pd iYMR216C
+Ste12 pd iYMR231W
+Ste12 pd iYMR305C
+Ste12 pd iYNL019C
+Ste12 pd iYNL034W
+Ste12 pd iYNL043C
+Ste12 pd iYNL105W
+Ste12 pd iYNL146W
+Mcm1 pd iYNL146W
+Ste12 pd iYNL179C-1
+Ste12 pd iYNL193W
+Ste12 pd iYNL209W
+Ste12 pd iYNL217W
+Ste12 pd iYNL239W
+Ste12 pd iYNL272C
+Ste12 pd iYNL280C
+Ste12 pd iYNR043W
+Mcm1 pd iYNR043W
+Ste12 pd iYOL040C
+Ste12 pd iYOL083W-1
+Mcm1 pd iYOL083W-1
+Ste12 pd iYOL159C
+Ste12 pd iYOR093C
+Ste12 pd iYOR095C
+Ste12 pd iYOR129C
+Ste12 pd iYOR130C
+Ste12 pd iYOR134W
+Ste12 pd iYOR336W
+Ste12 pd iYOR343C
+Ste12 pd iYOR344C-0
+Ste12 pd iYPL156C
+Ste12 pd iYPL177C-0
+Ste12 pd iYPL192C
+Ste12 pd iYPR027C
+Ste12 pd iYPR134W
+Ste12 pd iYPR143W
+Ste12 pd iSNR45
+Ste12 pd iYAR014C
+Ste12 pd iYAR020C-0
+Ste12 pd iYBL061C
+Ste12 pd iYBR007C-0
+Ste12 pd iYBR060C-0
+Mcm1 pd iYBR060C-0
+Ste12 pd iYBR082C-0
+Tec1 pd iYBR082C-0
+Ste12 pd iYBR082C-1
+Tec1 pd iYBR082C-1
+Ste12 pd iYBR199W
+Ste12 pd iYCR023C
+Ste12 pd iYDL129W
+Ste12 pd iYDR169C-0
+Ste12 pd iYDR274C
+Ste12 pd iYDR378C
+Mcm1 pd iYDR378C
+Ste12 pd iYDR451C
+Mcm1 pd iYDR451C
+Ste12 pd iYER064C
+Tec1 pd iYER064C
+Ste12 pd iYER118C
+Tec1 pd iYER118C
+Ste12 pd iYER155C
+Tec1 pd iYER155C
+Ste12 pd iYER176W
+Ste12 pd iYFL020C
+Ste12 pd iYFL039C
+Tec1 pd iYFL039C
+Ste12 pd iYFR053C-0
+Ste12 pd iYGL032C
+Mcm1 pd iYGL032C
+Ste12 pd iYGL117W
+Mcm1 pd iYGL117W
+Ste12 pd itL(CAA)G1
+Ste12 pd iYGL163C-1
+Ste12 pd iYGL163C-0
+Ste12 pd iYGR012W
+Ste12 pd iYGR013W
+Tec1 pd iYGR013W
+Ste12 pd iCEN8
+Ste12 pd iYHR005C
+Mcm1 pd iYHR005C
+Ste12 pd iYHR141C
+Tec1 pd iYHR141C
+Ste12 pd iYIL124W
+Mcm1 pd iYIL124W
+Ste12 pd iYIR020W-B-1
+Ste12 pd iYJL146W
+Ste12 pd iYJL196C
+Tec1 pd iYJL196C
+Mcm1 pd iYJL196C
+Ste12 pd iYKL096W
+Tec1 pd iYKL096W
+Ste12 pd iYKL097W-A-1
+Tec1 pd iYKL097W-A-1
+Ste12 pd iYKL209C
+Mcm1 pd iYKL209C
+Ste12 pd iYKR011C
+Tec1 pd iYKR011C
+Ste12 pd iYKR060W
+Tec1 pd iYKR060W
+Ste12 pd iYKR090W
+Ste12 pd iYLL057C
+Ste12 pd iYLR084C
+Tec1 pd iYLR084C
+Mcm1 pd iYLR084C
+Ste12 pd iYLR114C
+Ste12 pd iYLR228C-1
+Ste12 pd iYLR352W
+Tec1 pd iYLR352W
+Ste12 pd iYLR412W-1
+Tec1 pd iYLR412W-1
+Ste12 pd iYMR198W
+Tec1 pd iYMR198W
+Ste12 pd iYMR222C
+Ste12 pd iYMR235C
+Tec1 pd iYMR235C
+Ste12 pd iYMR245W
+Ste12 pd iYNL088W
+Tec1 pd iYNL088W
+Ste12 pd iYNL161W-1
+Ste12 pd iYNL290W
+Tec1 pd iYNL290W
+Mcm1 pd iYNL290W
+Ste12 pd iYNL296W
+Mcm1 pd iYNL296W
+Ste12 pd iYNL299W
+Tec1 pd iYNL299W
+Mcm1 pd iYNL299W
+Ste12 pd iYNL322C
+Ste12 pd iYNR017W
+Ste12 pd iYNR027W
+Mcm1 pd iYNR027W
+Ste12 pd iYOL105C
+Tec1 pd iYOL105C
+Ste12 pd iYOR050C
+Ste12 pd iYOR086C
+Tec1 pd iYOR086C
+Ste12 pd iYOR187W
+Ste12 pd iYOR295W
+Ste12 pd iYPL163C
+Tec1 pd iYPL163C
+Ste12 pd iYPR005C
+Ste12 pd iYPR076W
+Ste12 pd iYPR155C
+Mcm1 pd iYPR155C
+Ste12 pd iYPR158W
+Tec1 pd iYPR158W
+Tec1 pd iYBR057C
+Tec1 pd iYCR104W
+Tec1 pd iYCR106W
+Tec1 pd iYDR543C
+Tec1 pd iYDR544C
+Tec1 pd iYERWomega2-1
+Tec1 pd iYHR091C
+Ste12 pd iYHR091C
+Tec1 pd iYLL066C-1
+Tec1 pd iYLR466W
+Tec1 pd iYNL338W
+Tec1 pd iYNL339C
+Ste12 pd iYBL017C
+Tec1 pd iYBL017C
+Ste12 pd YBLWdelta1
+Tec1 pd YBLWdelta1
+Ste12 pd YDRWdelta23
+Tec1 pd YDRWdelta23
+Ste12 pd iYDRWdelta24
+Tec1 pd iYDRWdelta24
+Ste12 pd iYERCdelta20
+Tec1 pd iYERCdelta20
+Ste12 pd iYGL063W
+Tec1 pd iYGL063W
+Ste12 pd iYGRCdelta18
+Tec1 pd iYGRCdelta18
+Ste12 pd iYHR083W
+Tec1 pd iYHR083W
+Ste12 pd iYIL016W
+Tec1 pd iYIL016W
+Ste12 pd iYIL119C-0
+Tec1 pd iYIL119C-0
+Ste12 pd iYIL142W
+Tec1 pd iYIL142W
+Ste12 pd iYKL097C
+Tec1 pd iYKL097C
+Ste12 pd iYKL104C
+Tec1 pd iYKL104C
+Ste12 pd iYMR135W-A
+Tec1 pd iYMR135W-A
+Ste12 pd iYNL054W
+Tec1 pd iYNL054W
+Ste12 pd iYNL283C
+Tec1 pd iYNL283C
+Ste12 pd iYOL007C
+Tec1 pd iYOL007C
+Ste12 pd iYPR002C-A
+Tec1 pd iYPR002C-A
+Ste12 pd iYBR067C
+Ste12 pd iYDR210W
+Ste12 pd YDRCTy1-2D
+Ste12 pd YDRWdelta12
+Ste12 pd YGRCTy1-2D
+Ste12 pd iYGRWdelta19
+Ste12 pd iYGR146C
+Ste12 pd iYJL078C
+Ste12 pd iYKL045W
+Ste12 pd iYLR414C
+Ste12 pd iYBR162C
+Ste12 pd iYCL055W-1
+Ste12 pd iYCR025C
+Ste12 pd iYCR063W
+Ste12 pd iYDR076W
+Ste12 pd iYDR525W
+Ste12 pd iYGR198W
+Ste12 pd iYHR082C
+Ste12 pd iYILCdelta5-1
+Ste12 pd itS(UGA)I
+Ste12 pd iYIR003W
+Ste12 pd iYLR111W
+Ste12 pd iYML028W
+Ste12 pd iYML041C
+Ste12 pd iYMR056C
+Ste12 pd iYMR306C-A
+Ste12 pd iYMR314W
+Ste12 pd iYPL056C
+Ste12 pd iYPL256C
+Ste12 pd iYEL041W
+Ste12 pd iYGLCtau3
+Ste12 pd itY(GUA)O
+Ste12 pd iYGR064W
+Ste12 pd iYIL102C
+Ste12 pd iYKLCdelta4
+Ste12 pd iYLR452C
+Ste12 pd itK(CUU)K
+Ste12 pd iYOR246C
+Ste12 pd iYDL128W
+Ste12 pd iYDL126C
+Ste12 pd iYDRWdelta26
+Ste12 pd itA(UGC)E
+Ste12 pd iYHR085W
+Ste12 pd iYHR087W
+Ste12 pd iYHR089C
+Ste12 pd iYBLWdelta10
+Ste12 pd iYDR106W
+Ste12 pd iYCL022C
+Ste12 pd iYCR027C
+Ste12 pd iYOR357C
+Ste12 pd iYIL015W
+Ste12 pd iYERCsigma3
+Ste12 pd iYIL170W-0
+Ste12 pd iYDRCsigma1
+Ste12 pd itQ(UUG)D2
+Ste12 pd iYDRCdelta9-0
+Ste12 pd iYPRCdelta22
+Ste12 pd iYLR332W-1
+Ste12 pd iYOL156W-1
+Ste12 pd iYOR289W
+Ste12 pd iYKR039W
+Ste12 pd iYNR045W
+Ste12 pd iYNR047W
+Ste12 pd iYNR049C
+Ste12 pd iYNR051C
+Ste12 pd iYNR053C
+Ste12 pd iYOL156W-0
+Spc24 pp Mcm21
+Spc25 pp Spc25
+Spc24 pp Spc24
+Spc25 pp Nuf2
+Spc24 pp Spc25
+Tid3 pp Spc24
+Nuf2 pp Spc24
+Tid3 pp Nuf2
+Unknown interactsWith Rpr2
+Unknown interactsWith Pop8
+Unknown interactsWith Pop7
+Unknown interactsWith Pop6
+Unknown interactsWith Pop5
+Unknown interactsWith Pop4
+Unknown interactsWith Pop3
+Unknown interactsWith Pop1
+Zds1 pp Rip1
+Gfd1 pp Gfd1
+Gfd1 pp Dbp5
+Unknown interactsWith Spt15
+Unknown interactsWith Toa2
+Unknown interactsWith Toa1
+Unknown interactsWith Tfg1
+Unknown interactsWith Sua7
+Unknown interactsWith Mot1
+Unknown interactsWith Tfg2
+Unknown interactsWith Med1
+Unknown interactsWith Kin28
+Unknown interactsWith Rgr1
+Unknown interactsWith Rpb4
+Unknown interactsWith Nut1
+Unknown interactsWith Sin4
+Unknown interactsWith Med2
+Unknown interactsWith Srb6
+Unknown interactsWith Tfa2
+Unknown interactsWith Tfb3
+Unknown interactsWith Rpb3
+Unknown interactsWith Rpb7
+Unknown interactsWith Rpb2
+Unknown interactsWith Srb2
+Unknown interactsWith Ccl1
+Unknown interactsWith Rpb9
+Unknown interactsWith Med4
+Unknown interactsWith Rpo21
+Unknown interactsWith Gal11
+Unknown interactsWith Med7
+Unknown interactsWith Rpb11
+Unknown interactsWith Srb4
+Unknown interactsWith Tfa1
+Unknown interactsWith Taf7
+Unknown interactsWith Taf12
+Unknown interactsWith Rad3
+Unknown interactsWith Tfb1
+Unknown interactsWith Ssl2
+Unknown interactsWith Tfb4
+Unknown interactsWith Ssl1
+Unknown interactsWith Tfb2
+Unknown interactsWith TAF4/MPT1
+Unknown interactsWith Taf9
+Unknown interactsWith Taf5
+Unknown interactsWith Srb8
+Unknown interactsWith Taf1
+Unknown interactsWith Taf2
+Unknown interactsWith Taf6
+Unknown interactsWith Bdf1
+Pih1 pp Rrp43
+Mlp2 pp Nab2
+Unknown interactsWith Mex67
+Unknown interactsWith Yra1
+Spt15 pd Gal1_promoter
+ESA1 pd iYLL026W
+ESA1 pd iYBR101C
+ESA1 pd iYBL028C
+ESA1 pd iYPL090C
+ESA1 pd iYMR185W
+ESA1 pd iYIL133C
+ESA1 pd iYJL035C
+ESA1 pd iYHR021C
+ESA1 pd iYLR184W
+ESA1 pd iYGR117C
+ESA1 pd iYOR234C
+ESA1 pd iYFR031C-A
+ESA1 pd iYBR047W
+GCN5 pd iYLL026W
+GCN5 pd iYBL028C
+GCN5 pd iYJL190C
+GCN5 pd iYMR185W
+GCN5 pd iYGL136C
+GCN5 pd iYIL133C
+GCN5 pd iYEL035C
+GCN5 pd iYOR234C
+GCN5 pd iYBR047W
+HST1 pd iYHR138C
+HST1 pd iYMR124W
+HST1 pd iYBR017C
+HST1 pd iYHR183W
+HST1 pd iYHR185C
+HST1 pd iYDR281C
+HST1 pd itV(CAC)H
+HST1 pd iYOL162W
+HST1 pd iYDR523C
+HST1 pd iYFL041W
+HST1 pd iYOR254C
+HST1 pd iYGR258C-0
+HST1 pd itW(CCA)J
+HST1 pd iYJR044C
+HST1 pd iYNR076W
+HST1 pd iYDR522C
+HST1 pd iYJR077C
+HST1 pd iYNL204C
+HST1 pd iYGL228W
+HST1 pd iYMR134W
+HST1 pd iYOR366W
+HST1 pd iYLR027C
+HST1 pd iYGL138C
+HST1 pd iYERWomega2-1
+HST1 pd iYKR015C
+HST1 pd iYPL076W-1
+HST1 pd iYHRWdelta7
+HST1 pd iYJR144W
+HST1 pd iYOR313C
+HST1 pd iYERComega1-1
+HST1 pd iYOR209C
+HST1 pd iYOR213C
+HST1 pd iYPL076W-0
+HST1 pd itQ(UUG)H
+HST1 pd iYIR027C
+HST1 pd iYBR179C
+HST1 pd iYPL262W
+HST1 pd iYDR402C
+HST1 pd iYGL170C
+HST1 pd iYJL038C
+HST1 pd iYLR082C
+HST1 pd iYDR310C
+HST1 pd iYPL256C
+HST1 pd iYBR040W
+HST1 pd iYKR034W
+HST1 pd iYMR325W
+HST1 pd iYBR083W
+HST1 pd iYFL011W
+HST1 pd iYOL102C
+HST1 pd iYFR022W
+HST1 pd iYOL047C
+HST1 pd iYOR326W
+HST1 pd iYAL023C
+HST1 pd iYHR123W
+HST1 pd iYLR046C
+HST1 pd iYGL015C
+HST1 pd iYJR025C
+HST1 pd iYBR147W
+HST1 pd iYKL225W
+HST1 pd iYNL318C
+HST1 pd iYFR032C
+HST1 pd iYLR342W
+SUM1 pd iYKL179C
+SUM1 pd iYMR124W
+SUM1 pd iYLRCdelta5
+SUM1 pd iYPR158W
+SUM1 pd iYKL177W
+SUM1 pd iYDR370C
+SUM1 pd iYGR168C
+SUM1 pd iSNR6
+SUM1 pd iYOL162W
+SUM1 pd iYGR258C-0
+SUM1 pd iYDR183W
+SUM1 pd itT(AGU)J
+SUM1 pd iYOR366W
+SUM1 pd iYIL049W
+SUM1 pd iSNR190
+SUM1 pd iYOR313C
+SUM1 pd iYOR209C
+SUM1 pd iYPL071C
+SUM1 pd iYIR027C
+SUM1 pd iYJR100C
+SUM1 pd iYOR314W
+SUM1 pd iYMR193W
+SUM1 pd iYDR402C
+SUM1 pd iYGL170C
+SUM1 pd iYLR129W
+SUM1 pd iYAL038W
+SUM1 pd iYER007C-A
+SUM1 pd iYBR040W
+SUM1 pd iYKR034W
+SUM1 pd iYNRCdelta8
+SUM1 pd iYORWdelta16
+SUM1 pd iSNR57
+SUM1 pd iYOL102C
+SUM1 pd iYKL139W
+SUM1 pd iYOR296W
+SUM1 pd iYNL318C
+SUM1 pd iYKL220C-1
+SUM1 pd iYLR342W
+SUM1 pd iYOR297C
+HST1 pd iYLRCsigma1
+HST1 pd iYKL084W
+HST1 pd iYAR047C-1
+HST1 pd iYAR053W
+HST1 pd iCEN4
+HST1 pd iYGR170W
+HST1 pd iYGR260W
+HST1 pd iYJR088C
+HST1 pd iYMR179W
+HST1 pd iYAR009C
+HST1 pd iYDL075W
+HST1 pd YERWdelta21
+HST1 pd iYHL016C
+RPD3 pd iYHR136C
+RPD3 pd iYBL075C
+RPD3 pd iYMR214W
+RPD3 pd iYDL101C
+RPD3 pd iYHR142W
+RPD3 pd iYKL219W-0
+RPD3 pd iYIL160C
+RPD3 pd isnR37
+RPD3 pd iYMR258C
+RPD3 pd iYCR018C-A
+RPD3 pd iYDR042C
+RPD3 pd iYDR084C
+RPD3 pd iCEN13
+RPD3 pd iYOL117W
+RPD3 pd iYCL055W-0
+RPD3 pd iYGL184C
+RPD3 pd iYJL093C
+RPD3 pd iYELWdelta5
+RPD3 pd iSNR190
+RPD3 pd iYBL064C
+RPD3 pd iYER069W
+RPD3 pd iYER111C
+RPD3 pd iYKLCdelta6
+RPD3 pd iYPL217C
+RPD3 pd iYCR024C
+RPD3 pd iSNR67
+RPD3 pd iYEL050C
+RPD3 pd iYGL001C
+RPD3 pd iYLR037C-1
+RPD3 pd iYER044C-A
+RPD3 pd iYMR192W
+RPD3 pd iYCL037C
+RPD3 pd iYER124C
+RPD3 pd iYCR090C-1
+RPD3 pd iSNR61
+RPD3 pd iYNL182C
+RPD3 pd iYAL039C-0
+RPD3 pd iYDR499W
+RPD3 pd iSNR55
+RPD3 pd iYDR263C
+RPD3 pd iYOL001W
+RPD3 pd iYCL025C
+RPD3 pd iYAL024C
+RPD3 pd iYLR047C
+RPD3 pd iYLR051C
+RPD3 pd iYFLWdelta5
+SIN3 pd iYHR136C
+SIN3 pd iYLRCsigma1
+SIN3 pd iSNR56
+SIN3 pd iYMR214W
+SIN3 pd iYDL101C
+SIN3 pd iYER025W
+SIN3 pd iYHR142W
+SIN3 pd iYJL153C
+SIN3 pd iYJL149W
+SIN3 pd iYLL027W
+SIN3 pd iYJL052W
+SIN3 pd iYOR063W
+SIN3 pd iYCR063W
+SIN3 pd iYDR042C
+SIN3 pd iYDR471W
+SIN3 pd iYLR264W
+SIN3 pd itT(AGU)J
+SIN3 pd iYMR185W
+SIN3 pd iYCL055W-0
+SIN3 pd iYGL184C
+SIN3 pd iYPRWsigma2-1
+SIN3 pd iYBL064C
+SIN3 pd iYER069W
+SIN3 pd iYER111C
+SIN3 pd iYGR271W
+SIN3 pd iYIL100W
+SIN3 pd iYLR167W
+SIN3 pd iSNR67
+SIN3 pd iYOL109W
+SIN3 pd iYGR109C
+SIN3 pd iYLR037C-1
+SIN3 pd iYPR080W
+SIN3 pd iYDL075W
+SIN3 pd iYER124C
+SIN3 pd iYCR094W
+SIN3 pd iYNL289W-0
+SIN3 pd iYBR077C
+SIN3 pd iYLR286C
+SIN3 pd iYDR451C
+SIN3 pd iYDR499W
+SIN3 pd iYHL016C
+SIN3 pd iYMR013C-1
+SIN3 pd iYHR061C
+SIN3 pd iSNR55
+SIN3 pd iYAL039C-1
+SIN3 pd iYDL062W
+SIN3 pd iYDR263C
+SIN3 pd iYHR127W
+SIN3 pd iYNL125C
+SIN3 pd iYNL113W
+SIN3 pd iYNL067W
+SIN3 pd iYCL025C
+SIN3 pd iYCLWdelta5
+SIN3 pd iYER091C-A
+SIN3 pd iYGL102C
+SIN3 pd iYAL024C
+SIN3 pd iYGR118W
+SIN3 pd iYLR051C
+SIN3 pd iYER091C
+SIN3 pd iYGR067C
+SIN3 pd iYKR041W
+SIN3 pd iYOR246C
+SIN3 pd iYLL046C
+SIN3 pd iYLR299W
+SIN3 pd iYMR076C
+RPD3 pd iYBL075C
+RPD3 pd iYJL159W
+RPD3 pd iYJL149W
+RPD3 pd iYIL160C
+RPD3 pd iYDR042C
+RPD3 pd iYOL117W
+RPD3 pd iYGL184C
+RPD3 pd iYGL135W
+RPD3 pd iYJL093C
+RPD3 pd iYER111C
+RPD3 pd iSNR67
+RPD3 pd iYJL137C
+RPD3 pd iYLR037C-1
+RPD3 pd iYDL075W
+RPD3 pd iYCR090C-1
+RPD3 pd iYNL182C
+RPD3 pd iYAL039C-0
+RPD3 pd iYCL025C
+RPD3 pd iYLR149C
+RPD3 pd iYPR183W
+RPD3 pd iYMR076C
+ESA1 pd YEL045C
+ESA1 pd YPL056C
+ESA1 pd YCR025C
+ESA1 pd YOR302W
+ESA1 pd YDR010C
+ESA1 pd YBR012W-A
+ESA1 pd YIL060W
+ESA1 pd YDR366C
+ESA1 pd YOR343C
+ESA1 pd YML122C
+ESA1 pd NAT4
+ESA1 pd LGE1
+ESA1 pd RPL41A
+ESA1 pd BUD31
+ESA1 pd HSP12
+ESA1 pd PMP3
+ESA1 pd YDR445C
+ESA1 pd FYV1
+ESA1 pd YLR255C
+ESA1 pd API2
+ESA1 pd YOR050C
+ESA1 pd UTR5
+ESA1 pd YFL002W-B
+ESA1 pd SPC25
+ESA1 pd SHR5
+ESA1 pd YBL005W-A
+ESA1 pd YCR064C
+ESA1 pd MAS6
+ESA1 pd YAT1
+ESA1 pd TIP1
+ESA1 pd YHR162W
+ESA1 pd YGL007W
+ESA1 pd CCW14
+ESA1 pd YMR075C-A
+ESA1 pd SHU1
+ESA1 pd RPA14
+ESA1 pd SBP1
+ESA1 pd RPL27A
+ESA1 pd CCW12
+ESA1 pd OLE1
+ESA1 pd YML089C
+ESA1 pd YKL097C
+ESA1 pd YPL062W
+ESA1 pd YMR046C
+ESA1 pd YDL023C
+ESA1 pd YKL031W
+ESA1 pd YLR184W
+ESA1 pd ISC1
+ESA1 pd SWC5
+ESA1 pd AGP1
+ESA1 pd HIS1
+ESA1 pd YLR280C
+ESA1 pd PRY1
+ESA1 pd BDF1
+ESA1 pd COF1
+ESA1 pd FYV12
+ESA1 pd YPR064W
+ESA1 pd YNL134C
+ESA1 pd YOL118C
+ESA1 pd YCR018C-A
+ESA1 pd SRD1
+ESA1 pd YNL284C-A
+ESA1 pd YMR135W-A
+ESA1 pd YLR334C
+ESA1 pd YLR415C
+ESA1 pd CYC8
+ESA1 pd EBP2
+ESA1 pd SMM1
+ESA1 pd ASF1
+ESA1 pd YHR145C
+ESA1 pd ICY1
+ESA1 pd YKR041W
+ESA1 pd YDR170W-A
+ESA1 pd YMR046W-A
+ESA1 pd ECM15
+ESA1 pd YBL107W-A
+ESA1 pd YLR281C
+ESA1 pd YFR018C
+ESA1 pd YPR002C-A
+ESA1 pd YBL028C
+ESA1 pd YMR122C
+ESA1 pd YHR214C-C
+ESA1 pd SNA2
+ESA1 pd YOR235W
+ESA1 pd YDL071C
+ESA1 pd YLR366W
+ESA1 pd YLR112W
+ESA1 pd YBR134W
+ESA1 pd YGR107W
+ESA1 pd YKT9
+ESA1 pd YFL015C
+GCN5 pd BDF2
+GCN5 pd YGR269W
+GCN5 pd NAT4
+GCN5 pd RPL41A
+GCN5 pd CDC33
+GCN5 pd PMP3
+GCN5 pd API2
+GCN5 pd YPL182C
+GCN5 pd SPC25
+GCN5 pd FYV7
+GCN5 pd SHR5
+GCN5 pd MAS6
+GCN5 pd YAT1
+GCN5 pd TIP1
+GCN5 pd BAG7
+GCN5 pd CAR1
+GCN5 pd SHU1
+GCN5 pd RPA14
+GCN5 pd YKL083W
+GCN5 pd SBP1
+GCN5 pd CCW12
+GCN5 pd SRL1
+GCN5 pd YGL188C
+GCN5 pd YKL097C
+GCN5 pd MAP2
+GCN5 pd RPL17B
+GCN5 pd YLR184W
+GCN5 pd SWC5
+GCN5 pd STM1
+GCN5 pd FYV12
+GCN5 pd MRP2
+GCN5 pd YCR085W
+GCN5 pd ANP1
+GCN5 pd YLR415C
+GCN5 pd EBP2
+GCN5 pd ASF1
+GCN5 pd YLR281C
+GCN5 pd WHI5
+GCN5 pd YFR018C
+GCN5 pd YBL028C
+GCN5 pd YOR235W
+GCN5 pd YDL071C
+GCN5 pd YBR134W
+GCN5 pd OXA1
+GCN5 pd YKT9
+Sub1 pd PMA1
+Rna15 pd RPS5
+Rna15 pd CDC19
+Rna15 pd ADH1
+Sub1 pd ADH1
+Fcp1 pd ADH1
+RNAP_II interactsWith ACT1
+Fcp1 pd ACT1
+Rna15 pd ACT1
+Sub1 pd ACT1
+Kin28 pd ACT1
+Rpb3 pd ACT1
+Zds1 pp Gfd1
+Zds1 pp Dbp5
+Pih1 pp Nop58
+Sik1 pp Nop1
+Sik1 pp Snu13
+Nop58 pp Snu13
+Nop1 pp Snu13
+Unknown interactsWith Pam18
+Unknown interactsWith Pam16
+Unknown interactsWith Tim44
+Unknown interactsWith Mas6
+Tim17 interactsWith Unknown
+Ssc1 pp Zim17
+Ssc1 pp Mge1
+Ssc1 pp Tim44
+Zds2 pp Gfd1
+Gle1 pp Gfd1
+Sub1 pp Rna15
+Mas6 interactsWith Unknown
+Unknown interactsWith Tim50
+Unknown interactsWith Tim44
+Unknown interactsWith Tim17
+Unknown interactsWith Pam16
+Unknown interactsWith Pam18
+Snf1 interactsWith Unknown
+Unknown interactsWith Snf4
+Unknown interactsWith Sip1
+Unknown interactsWith Sip2
+Unknown interactsWith Gal83
+Unknown interactsWith RPR1
+Rpp1 interactsWith Unknown
+Snf1_complex interactsWith Gal1_promoter
+SAGA_complex interactsWith Gal1_promoter
+Hht1 pd Gal1_promoter
+Snf1 pd Ino1_promoter
+Snf1_complex interactsWith Ino1_promoter
+SAGA_complex interactsWith Ino1_promoter
+Hht1 pd Ino1_promoter
+Spt15 pd Ino1_promoter
+Spt15 pd Gal1_promoter
+SAGA_complex interactsWith Gal4
+SAGA_complex interactsWith Gcn4
+Snf1_complex interactsWith Gal4
+Snf1_complex interactsWith Ino2
+Med9 pp Med1
+Med9 pp Med7
+Med10 pp Med4
+Med8 pp Med20
+Stb5 pp Pdr1
+Yrr1 pp Yrr1
+Stb5 pd Snq2_promoter
+Stb5/Pdr1 interactsWith Snq2_promoter
+Pih1 pp Rvb2
+Tah1 pp Rvb2
+Pih1 pp Rvb1
+Tah1 pp Rvb1
+Hsp82 pp Tah1
+Tah1 pp Pih1
+Okp1 pd CEN3
+Mcm21 pd CEN3
+Tid3 pd CEN3
+Spc24 pd CEN3
+Spc25 pd CEN3
+Nuf2 pd CEN3
+Nop58 interactsWith U14
+Unknown interactsWith Rvb1
+Unknown interactsWith Rvb2
+Unknown interactsWith Act1
+Ies2 interactsWith unknown
+Unknown interactsWith Ies1
+Unknown interactsWith Swr1
+Unknown interactsWith Tdh3
+Unknown interactsWith Arp8
+Unknown interactsWith Ino80
+Hsp82 pp Ssa1
+Hsc82 pp Ssa1
+Hsp82 pp Ade1
+Hsp82 pp Cdc15
+Hsp82 pp Pol12
+Hsc82 pp Pin4
+Hsp82 pp Rtg3
+Hsc82 pp Ybl104c
+Hsc82 pp Ybr030w
+Hsp82 pp Ybr089w
+Hsp82 pp Ybr094w
+Hsp82 pp Pho88
+Hsp82 pp She3
+Hsp82 pp Ira1
+Hsp82 pp Cns1
+Hsc82 pp Cns1
+Hsp82 pp Smy2
+Hsp82 pp Ktr4
+Hsp82 pp Bsd2
+Hsc82 pp Bud3
+Hsp82 pp Kcc4
+Hsp82 pp Grx1
+Hsp82 pp Ycl048w
+Hsp82 pp Vac17
+Hsc82 pp Pgk1
+Hsp82 pp Pwp2
+Hsp82 pp Tah1
+Hsp82 pp Hcm1
+Hsp82 pp Pat1
+Hsc82 pp Pat1
+Hsc82 pp Ydl025c
+Hsc82 pp Nop14
+Hsc82 pp Ufd2
+Hsp82 pp Ydl193w
+Hsc82 pp Ydl193w
+Hsp82 pp Asf2
+Hsp82 pp Ydl199c
+Hsp82 pp Ydl203c
+Hsp82 pp Ssb1
+Hsc82 pp Ssb1
+Hsp82 pp Ady3
+Hsp82 pp Sor2
+Hsc82 pp Nth1
+Hsc82 pp Aro1
+Hsp82 pp Ydr131c
+Hsp82 pp Cwc15
+Hsp82 pp Cdc37
+Hsc82 pp Cdc37
+Hsc82 pp Rvb1
+Hsp82 pp Cbs2
+Hsp82 pp Aha1
+Hsc82 pp Aha1
+Hsp82 pp Adr1
+Hsp82 pp Exg2
+Hsp82 pp Pex10
+Hsp82 pp Mth1
+Hsp82 pp Pro1
+Hsp82 pp Cft1
+Hsp82 pp Pep7
+Hsc82 pp Tom1
+Hsp82 pp Pkh1
+Hsp82 pp Hlr1
+Hsp82 pp Ydr533c
+Hsc82 pp Ydr533c
+Hsc82 pp Nug1
+Hsp82 pp Yer028c
+Hsc82 pp Ilv1
+Hsp82 pp Met6
+Hsc82 pp Spt15
+Hsc82 pp Bem2
+Hsp82 pp Hxt10
+Hsc82 pp Ies1
+Hsc82 pp Gat1
+Hsc82 pp Lsb3
+Hsc82 pp Leu1
+Hsp82 pp Ckb1
+Hsp82 pp Stt3
+Hsp82 pp Mig1
+Hsp82 pp Hnm1
+Hsp82 pp Arc1
+Hsp82 pp Mon1
+Hsp82 pp Sec27
+Hsp82 pp Lys5
+Hsp82 pp Sec15
+Hsp82 pp Ygr067c
+Hsp82 pp Slx9
+Hsp82 pp Ygr117c
+Hsp82 pp Ppt1
+Hsc82 pp Ppt1
+Hsp82 pp Rnr4
+Hsp82 pp Tdh3
+Hsp82 pp Ygr294w
+Hsp82 pp Yap3
+Hsp82 pp Rpn1
+Hsp82 pp Slt2
+Hsp82 pp Pih1
+Hsp82 pp Ncp1
+Hsp82 pp Ssz1
+Hsp82 pp Trm5
+Hsc82 pp Yhr080c
+Hsp82 pp Yhr121w
+Hsp82 pp Rpl42b
+Hsp82 pp Dbp8
+Hsp82 pp Fmo
+Hsp82 pp Yhr181w
+Hsp82 pp Yhr202w
+Hsc82 pp Pdr11
+Hsc82 pp Rpb3
+Hsp82 pp Yil086c
+Hsp82 pp Kgd1
+Hsp82 pp Yil141w
+Hsc82 pp Rpl40a
+Hsp82 pp Bnr1
+Hsp82 pp Yil167w
+Hsp82 pp Gtt1
+Hsp82 pp Ctk2
+Hsp82 pp Cct8
+Hsp82 pp Nsp1
+Hsp82 pp Smc3
+Hsc82 pp Gwt1
+Hsc82 pp Tif2
+Hsc82 pp Rpa34
+Hsp82 pp Cps1
+Hsp82 pp Yjl182c
+Hsp82 pp Mpp10
+Hsp82 pp Tdh2
+Hsp82 pp Cpr7
+Hsc82 pp Cpr7
+Hsp82 pp Gef1
+Hsc82 pp Iml1
+Hsp82 pp Apl2
+Hsp82 pp Osh6
+Hsp82 pp Bet3
+Hsc82 pp Bet3
+Hsp82 pp Yll007c
+Hsp82 pp Sof1
+Hsp82 pp Ssa2
+Hsp82 pp Yll029w
+Hsc82 pp Rpl22a
+Hsc82 pp Mef1
+Hsp82 pp Emp70
+Hsp82 pp Csf1
+Hsp82 pp Rrn5
+Hsp82 pp Cbf5
+Hsp82 pp Ylr201c
+Hsp82 pp Cpr6
+Hsc82 pp Cpr6
+Hsc82 pp Ypt6
+Hsp82 pp Ysh1
+Hsp82 pp Vps36
+Hsp82 pp Atg17
+Hsc82 pp Rad52
+Hsp82 pp Cat2
+Hsp82 pp Rpl6a
+Hsc82 pp Fpr3
+Hsc82 pp Cue4
+Hsp82 pp Bud22
+Hsc82 pp Bud22
+Hsp82 pp Mot3
+Hsc82 pp Ymr075w
+Hsp82 pp Npl6
+Hsp82 pp Ymr111c
+Hsc82 pp Ecm16
+Hsc82 pp App2
+Hsp82 pp Fcp1
+Hsc82 pp Aep2
+Hsp82 pp Msu1
+Hsp82 pp Gas1
+Hsp82 pp Rps7b
+Hsp82 pp Ubp10
+Hsc82 pp Ubp10
+Hsc82 pp Srp1
+Hsp82 pp Bni4
+Hsp82 pp Hch1
+Hsc82 pp Hch1
+Hsc82 pp Mck1
+Hsp82 pp Prp2
+Hsc82 pp Acc1
+Hsc82 pp Mrpl50
+Hsp82 pp Ssk2
+Hsc82 pp Ssk2
+Hsp82 pp Ynr071c
+Hsc82 pp Htz1
+Hsp82 pp Rpl25
+Hsp82 pp Med7
+Hsp82 pp Tir4
+Hsp82 pp Aus1
+Hsp82 pp Sti1
+Hsc82 pp Sti1
+Hsp82 pp Exo1
+Hsp82 pp Yor053w
+Hsc82 pp Sgt1
+Hsp82 pp Ptc5
+Hsp82 pp Yor192c
+Hsp82 pp Yor218c
+Hsp82 pp Yor227w
+Hsc82 pp Pnt1
+Hsc82 pp Snu66
+Hsc82 pp Vma4
+Hsp82 pp Atf1
+Hsp82 pp Chl1
+Hsp82 pp Swi1
+Hsp82 pp Bts1
+Hsp82 pp Sse1
+Hsp82 pp Ypl141c
+Hsp82 pp Ypl207w
+Hsp82 pp Pdh1
+Hsc82 pp Apl4
+Hsp82 pp Smk1
+Hsc82 pp Ypr089w
+Hsp82 pp Mrd1
+Hsp82 pp Ctf4
+Hsc82 pp Sec23
+Hsp82 pp Ski3
+Hsp82 pp Arr3
+HSP90 interactsWith DEP1
+HSP90 interactsWith PMT2
+HSP90 interactsWith LTE1
+HSP90 interactsWith LDB7
+HSP90 interactsWith RRN10
+HSP90 interactsWith SHP1
+HSP90 interactsWith YBL083C
+HSP90 interactsWith RTG3
+HSP90 interactsWith YBL107C
+HSP90 interactsWith GAL10
+HSP90 interactsWith YBR030W
+HSP90 interactsWith CSG2
+HSP90 interactsWith SCO1
+HSP90 interactsWith YBR047W
+HSP90 interactsWith YBR108W
+HSP90 interactsWith YSA1
+HSP90 interactsWith SEC66
+HSP90 interactsWith UMP1
+HSP90 interactsWith BEM1
+HSP90 interactsWith ATG12
+HSP90 interactsWith PDB1
+HSP90 interactsWith YBR280C
+HSP90 interactsWith ILV6
+HSP90 interactsWith YCL056C
+HSP90 interactsWith FEN2
+HSP90 interactsWith THR4
+HSP90 interactsWith FIG2
+HSP90 interactsWith YCR090C
+HSP90 interactsWith COX9
+HSP90 interactsWith YDL068W
+HSP90 interactsWith VAM6
+HSP90 interactsWith RPS16B
+HSP90 interactsWith ARR4
+HSP90 interactsWith RPL41A
+HSP90 interactsWith RPL35A
+HSP90 interactsWith ARF1
+HSP90 interactsWith YDL206W
+HSP90 interactsWith HBT1
+HSP90 interactsWith SHS1
+HSP90 interactsWith AAD4
+HSP90 interactsWith KCS1
+HSP90 interactsWith RGP1
+HSP90 interactsWith NUM1
+HSP90 interactsWith UME6
+HSP90 interactsWith EXG2
+HSP90 interactsWith PMP3
+HSP90 interactsWith GGA1
+HSP90 interactsWith SHE9
+HSP90 interactsWith MRPL28
+HSP90 interactsWith SNF1
+HSP90 interactsWith EMI1
+HSP90 interactsWith YDR521W
+HSP90 interactsWith YDR535C
+HSP90 interactsWith GIM4
+HSP90 interactsWith YEL048C
+HSP90 interactsWith YEL059W
+HSP90 interactsWith PRB1
+HSP90 interactsWith CIN8
+HSP90 interactsWith NPR2
+HSP90 interactsWith AVT2
+HSP90 interactsWith SIT1
+HSP90 interactsWith HPA3
+HSP90 interactsWith YEL068C
+HSP90 interactsWith GLN3
+HSP90 interactsWith ERG28
+HSP90 interactsWith RMD7
+HSP90 interactsWith SLX8
+HSP90 interactsWith YER121W
+HSP90 interactsWith GLO3
+HSP90 interactsWith YER139C
+HSP90 interactsWith UBP5
+HSP90 interactsWith PEA2
+HSP90 interactsWith BEM2
+HSP90 interactsWith RAD4
+HSP90 interactsWith PDA1
+HSP90 interactsWith YER187W
+HSP90 interactsWith BUD27
+HSP90 interactsWith RPO41
+HSP90 interactsWith YFL054C
+HSP90 interactsWith UBP6
+HSP90 interactsWith FAB1
+HSP90 interactsWith RPL2A
+HSP90 interactsWith CDH1
+HSP90 interactsWith HOP2
+HSP90 interactsWith YGL072C
+HSP90 interactsWith DBP3
+HSP90 interactsWith YGL081W
+HSP90 interactsWith CUE3
+HSP90 interactsWith SNF4
+HSP90 interactsWith SOH1
+HSP90 interactsWith RPL9A
+HSP90 interactsWith HUR1
+HSP90 interactsWith YGL214W
+HSP90 interactsWith YGL220W
+HSP90 interactsWith ZRT1
+HSP90 interactsWith DBF2
+HSP90 interactsWith PDX1
+HSP90 interactsWith YGR237C
+HSP90 interactsWith MGA1
+HSP90 interactsWith PPA1
+HSP90 interactsWith VMA10
+HSP90 interactsWith SRB2
+HSP90 interactsWith VMA22
+HSP90 interactsWith LRP1
+HSP90 interactsWith YHR116W
+HSP90 interactsWith TOM71
+HSP90 interactsWith LIN1
+HSP90 interactsWith YIL006W
+HSP90 interactsWith RHR2
+HSP90 interactsWith FIS1
+HSP90 interactsWith SEC28
+HSP90 interactsWith MET18
+HSP90 interactsWith YIL157C
+HSP90 interactsWith BNR1
+HSP90 interactsWith YIL163C
+HSP90 interactsWith YIL166C
+HSP90 interactsWith SDL1
+HSP90 interactsWith HXT12
+HSP90 interactsWith MRS1
+HSP90 interactsWith DAL2
+HSP90 interactsWith MAD2
+HSP90 interactsWith YJL046W
+HSP90 interactsWith BCK1
+HSP90 interactsWith YJL123C
+HSP90 interactsWith YJL147C
+HSP90 interactsWith CPS1
+HSP90 interactsWith MNN11
+HSP90 interactsWith NUC1
+HSP90 interactsWith CPR7
+HSP90 interactsWith YJR038C
+HSP90 interactsWith YJR056C
+HSP90 interactsWith OPI3
+HSP90 interactsWith HOC1
+HSP90 interactsWith MIR1
+HSP90 interactsWith CSN12
+HSP90 interactsWith YJR088C
+HSP90 interactsWith YJR120W
+HSP90 interactsWith STR2
+HSP90 interactsWith CCE1
+HSP90 interactsWith YKL031W
+HSP90 interactsWith YKL037W
+HSP90 interactsWith ELM1
+HSP90 interactsWith YKL102C
+HSP90 interactsWith PRR1
+HSP90 interactsWith CTK1
+HSP90 interactsWith YKL162C
+HSP90 interactsWith YKR027W
+HSP90 interactsWith YKR035C
+HSP90 interactsWith DID2
+HSP90 interactsWith UTH1
+HSP90 interactsWith BAS1
+HSP90 interactsWith MMM1
+HSP90 interactsWith RIC1
+HSP90 interactsWith YLR046C
+HSP90 interactsWith YLR089C
+HSP90 interactsWith XDJ1
+HSP90 interactsWith YLR091W
+HSP90 interactsWith SUL2
+HSP90 interactsWith NYV1
+HSP90 interactsWith GIS3
+HSP90 interactsWith IOC2
+HSP90 interactsWith CHA4
+HSP90 interactsWith ICT1
+HSP90 interactsWith YLR111W
+HSP90 interactsWith SAM1
+HSP90 interactsWith RPL37A
+HSP90 interactsWith MMR1
+HSP90 interactsWith HCR1
+HSP90 interactsWith LIP2
+HSP90 interactsWith ARV1
+HSP90 interactsWith YPT6
+HSP90 interactsWith SEC22
+HSP90 interactsWith YLR269C
+HSP90 interactsWith RPS30A
+HSP90 interactsWith MMS22
+HSP90 interactsWith VPS65
+HSP90 interactsWith REC102
+HSP90 interactsWith ARC18
+HSP90 interactsWith ATP10
+HSP90 interactsWith SKI2
+HSP90 interactsWith YLR428C
+HSP90 interactsWith RPS1A
+HSP90 interactsWith SST2
+HSP90 interactsWith YML012C-A
+HSP90 interactsWith TRM9
+HSP90 interactsWith YML090W
+HSP90 interactsWith VAN1
+HSP90 interactsWith YMR003W
+HSP90 interactsWith SOK2
+HSP90 interactsWith PEX12
+HSP90 interactsWith YMR052C-A
+HSP90 interactsWith TOM37
+HSP90 interactsWith YMR119W-A
+HSP90 interactsWith REC114
+HSP90 interactsWith RPL13B
+HSP90 interactsWith YIM1
+HSP90 interactsWith NUP53
+HSP90 interactsWith YMR157C
+HSP90 interactsWith YMR158C-A
+HSP90 interactsWith SCJ1
+HSP90 interactsWith GAS3
+HSP90 interactsWith MRE11
+HSP90 interactsWith RPS10B
+HSP90 interactsWith SAP30
+HSP90 interactsWith SCS7
+HSP90 interactsWith AEP2
+HSP90 interactsWith GAS1
+HSP90 interactsWith GLC8
+HSP90 interactsWith YNL058C
+HSP90 interactsWith LAT1
+HSP90 interactsWith MKS1
+HSP90 interactsWith YNL087W
+HSP90 interactsWith GIM3
+HSP90 interactsWith YNL171C
+HSP90 interactsWith KEX2
+HSP90 interactsWith GIS2
+HSP90 interactsWith CLA4
+HSP90 interactsWith MCK1
+HSP90 interactsWith YNL324W
+HSP90 interactsWith FIG4
+HSP90 interactsWith YNR020C
+HSP90 interactsWith COQ2
+HSP90 interactsWith HXT17
+HSP90 interactsWith MET22
+HSP90 interactsWith YOL111C
+HSP90 interactsWith RPS19A
+HSP90 interactsWith YOL138C
+HSP90 interactsWith SHE4
+HSP90 interactsWith WHI2
+HSP90 interactsWith CYT1
+HSP90 interactsWith YOR066W
+HSP90 interactsWith SNF2
+HSP90 interactsWith HSD1
+HSP90 interactsWith TEA1
+HSP90 interactsWith YPL024W
+HSP90 interactsWith EGD1
+HSP90 interactsWith YPL041C
+HSP90 interactsWith SUR1
+HSP90 interactsWith YPL137C
+HSP90 interactsWith YPL182C
+HSP90 interactsWith GUP2
+HSP90 interactsWith YPL197C
+HSP90 interactsWith YPL201C
+HSP90 interactsWith AFT2
+HSP90 interactsWith CSR2
+HSP90 interactsWith VMA13
+HSP90 interactsWith MCM16
+HSP90 interactsWith MRPL51
+HSP90 interactsWith KAR3
+HSP90 interactsWith NCA2
+HSP90 interactsWith TPO3
+HSP90 interactsWith VPS8
+HSP90 interactsWith DRS2
+HSP90 interactsWith NCL1
+HSP90 interactsWith RPL19B
+HSP90 interactsWith PIN4
+HSP90 interactsWith UBP13
+HSP90 interactsWith RPS8A
+HSP90 interactsWith CCZ1
+HSP90 interactsWith ARL1
+HSP90 interactsWith RPL21A
+HSP90 interactsWith YBR231C
+HSP90 interactsWith YBR246W
+HSP90 interactsWith APM3
+HSP90 interactsWith BSD2
+HSP90 interactsWith STP22
+HSP90 interactsWith CDC10
+HSP90 interactsWith FEN1
+HSP90 interactsWith TUP1
+HSP90 interactsWith CDC50
+HSP90 interactsWith MED2
+HSP90 interactsWith CYK3
+HSP90 interactsWith YDL119C
+HSP90 interactsWith RDI1
+HSP90 interactsWith YDR067C
+HSP90 interactsWith SNF11
+HSP90 interactsWith VPS41
+HSP90 interactsWith VPS61
+HSP90 interactsWith RAV2
+HSP90 interactsWith YDR203W
+HSP90 interactsWith HDA2
+HSP90 interactsWith SUR2
+HSP90 interactsWith SWA2
+HSP90 interactsWith PEP7
+HSP90 interactsWith YDR334W
+HSP90 interactsWith MSN5
+HSP90 interactsWith RVS167
+HSP90 interactsWith SAC7
+HSP90 interactsWith RPL12B
+HSP90 interactsWith YDR442W
+HSP90 interactsWith YDR445C
+HSP90 interactsWith ADA2
+HSP90 interactsWith MFA1
+HSP90 interactsWith VAC8
+HSP90 interactsWith YEL057C
+HSP90 interactsWith FCY2
+HSP90 interactsWith BMH1
+HSP90 interactsWith HSP12
+HSP90 interactsWith BST1
+HSP90 interactsWith PHO4
+HSP90 interactsWith COG7
+HSP90 interactsWith PDR1
+HSP90 interactsWith CKB1
+HSP90 interactsWith MIG1
+HSP90 interactsWith DST1
+HSP90 interactsWith RIM8
+HSP90 interactsWith NUT1
+HSP90 interactsWith HXK2
+HSP90 interactsWith YGR064W
+HSP90 interactsWith YGR106C
+HSP90 interactsWith YGR122W
+HSP90 interactsWith PBP1
+HSP90 interactsWith HGH1
+HSP90 interactsWith BUB1
+HSP90 interactsWith GCN5
+HSP90 interactsWith APL6
+HSP90 interactsWith PRS3
+HSP90 interactsWith RIM101
+HSP90 interactsWith VPS29
+HSP90 interactsWith THP2
+HSP90 interactsWith CST6
+HSP90 interactsWith SYS1
+HSP90 interactsWith APS3
+HSP90 interactsWith PEP8
+HSP90 interactsWith PHO86
+HSP90 interactsWith RPE1
+HSP90 interactsWith VPS35
+HSP90 interactsWith YJL175W
+HSP90 interactsWith RCY1
+HSP90 interactsWith RAV1
+HSP90 interactsWith GEF1
+HSP90 interactsWith VPS25
+HSP90 interactsWith CAF17
+HSP90 interactsWith VPS24
+HSP90 interactsWith YKL077W
+HSP90 interactsWith APL2
+HSP90 interactsWith RSM22
+HSP90 interactsWith TPK3
+HSP90 interactsWith LST4
+HSP90 interactsWith LOS1
+HSP90 interactsWith VPS1
+HSP90 interactsWith YKR007W
+HSP90 interactsWith IRS4
+HSP90 interactsWith RHO4
+HSP90 interactsWith SNF7
+HSP90 interactsWith CPR6
+HSP90 interactsWith CHS5
+HSP90 interactsWith YLR334C
+HSP90 interactsWith SUR4
+HSP90 interactsWith YLR407W
+HSP90 interactsWith VPS36
+HSP90 interactsWith ERG6
+HSP90 interactsWith PSP2
+HSP90 interactsWith YML036W
+HSP90 interactsWith VPS71
+HSP90 interactsWith MFT1
+HSP90 interactsWith VPS9
+HSP90 interactsWith GTR1
+HSP90 interactsWith PHO84
+HSP90 interactsWith ERG5
+HSP90 interactsWith YMR031W-A
+HSP90 interactsWith ERG2
+HSP90 interactsWith SSN8
+HSP90 interactsWith IDH1
+HSP90 interactsWith COG5
+HSP90 interactsWith YDJ1
+HSP90 interactsWith END3
+HSP90 interactsWith CYB5
+HSP90 interactsWith WHI3
+HSP90 interactsWith URE2
+HSP90 interactsWith YNL235C
+HSP90 interactsWith CAF40
+HSP90 interactsWith RIM21
+HSP90 interactsWith MON2
+HSP90 interactsWith LEM3
+HSP90 interactsWith YNR005C
+HSP90 interactsWith VPS27
+HSP90 interactsWith TOP1
+HSP90 interactsWith TLG2
+HSP90 interactsWith YOL050C
+HSP90 interactsWith GAL11
+HSP90 interactsWith PRS5
+HSP90 interactsWith PEP12
+HSP90 interactsWith CKA2
+HSP90 interactsWith VAM10
+HSP90 interactsWith VPS21
+HSP90 interactsWith VAM3
+HSP90 interactsWith PDR5
+HSP90 interactsWith PUS7
+HSP90 interactsWith RIM20
+HSP90 interactsWith MCH5
+HSP90 interactsWith SNF8
+HSP90 interactsWith SSN3
+HSP90 interactsWith BRO1
+HSP90 interactsWith ISU1
+HSP90 interactsWith YPL225W
+HSP90 interactsWith YPR050C
+HSP90 interactsWith GPH1
+HSP90 interactsWith YPR170C
+HSP90 interactsWith VPS4
+HSP90 interactsWith HDA3
+HSP90 interactsWith OPT2
+HSP90 interactsWith SLA1
+HSP90 interactsWith TPS1
+HSP90 interactsWith ISW1
+HSP90 interactsWith RVS161
+HSP90 interactsWith PER1
+HSP90 interactsWith YHM1
+HSP90 interactsWith SWF1
+HSP90 interactsWith SUM1
+HSP90 interactsWith SPT3
+HSP90 interactsWith YDR417C
+HSP90 interactsWith SSN2
+HSP90 interactsWith VPS52
+HSP90 interactsWith MAK10
+HSP90 interactsWith UBP3
+HSP90 interactsWith CDC26
+HSP90 interactsWith MDM39
+HSP90 interactsWith PGD1
+HSP90 interactsWith GUP1
+HSP90 interactsWith MON1
+HSP90 interactsWith VAM7
+HSP90 interactsWith SPT4
+HSP90 interactsWith GTR2
+HSP90 interactsWith SMI1
+HSP90 interactsWith RPL34B
+HSP90 interactsWith YJR011C
+HSP90 interactsWith ILM1
+HSP90 interactsWith YPK1
+HSP90 interactsWith SAC1
+HSP90 interactsWith SRN2
+HSP90 interactsWith VPS63
+HSP90 interactsWith ROM2
+HSP90 interactsWith VAC14
+HSP90 interactsWith YPT7
+HSP90 interactsWith COG8
+HSP90 interactsWith SNO1
+HSP90 interactsWith RIM13
+HSP90 interactsWith SIW14
+HSP90 interactsWith COG6
+HSP90 interactsWith RAS2
+HSP90 interactsWith BRE5
+HSP90 interactsWith SIN3
+HSP90 interactsWith IRA2
+HSP90 interactsWith STI1
+HSP90 interactsWith RUD3
+HSP90 interactsWith VPH1
+HSP90 interactsWith SNC2
+HSP90 interactsWith BEM4
+HSP90 interactsWith APL5
+HSP90 interactsWith YME1
+Rpl40a pp Aha1
+Aha1 pp Ssa1
+Aha1 pp Ssb1
+Aha1 pp Tdh3
+Aha1 pp Ypr089w
+Cdc37 pp Mck1
+Msu1 pp Cdc37
+Cdc37 pp Ssa1
+Ssb1 pp Cdc37
+Cdc37 pp Tdh3
+Bud3 pp Cns1
+Cns1 pp Fpr3
+Cns1 pp Pgk1
+Cns1 pp Rpl22a
+Cns1 pp Ssa1
+Cns1 pp Tdh3
+Ubp10 pp Cns1
+Cns1 pp Vma4
+Aha1 pp Cpr6
+Cpr6 pp Fpr3
+Cpr6 pp Rpl22a
+Cpr6 pp Ssa1
+Cpr6 pp Ssb1
+Cpr6 pp Tdh3
+Cpr6 pp Vma4
+Cpr7 pp Fpr3
+Cpr7 pp Rpl22a
+Cpr7 pp Ssa1
+Cpr7 pp Ssb1
+Cpr7 pp Tdh3
+Cpr7 pp Vma4
+Hch1 pp Rpl22a
+Hch1 pp Ssa1
+Hch1 pp Ssb1
+Hch1 pp Tdh3
+Rvb1 pp Pih1
+Ppt1 pp Mef1
+Ppt1 pp Ssa1
+Ppt1 pp Ssb1
+Ppt1 pp Tdh3
+Ade1 pp Ssa1
+Adr1 pp Ssa1
+Aep2 pp Ssa1
+Apl4 pp Ssa1
+Aro1 pp Ssa1
+Asf2 pp Ssa1
+Atf1 pp Ssa1
+Bet3 pp Ssa1
+Bni4 pp Ssa1
+Bnr1 pp Ssa1
+Bsd2 pp Ssa1
+Bud22 pp Ssa1
+Bud3 pp Ssa1
+Cft1 pp Ssa1
+Dbp8 pp Ssa1
+Ecm16 pp Ssa1
+Exg2 pp Ssa1
+Exo1 pp Ssa1
+Fmo pp Ssa1
+Fpr3 pp Ssa1
+Htz1 pp Ssa1
+Ies1 pp Ssa1
+Ilv1 pp Ssa1
+Iml1 pp Ssa1
+Med7 pp Ssa1
+Mef1 pp Ssa1
+Met6 pp Ssa1
+Mig1 pp Ssa1
+Mon1 pp Ssa1
+Ncp1 pp Ssa1
+Nop14 pp Ssa1
+Npl6 pp Ssa1
+Nsp1 pp Ssa1
+Nth1 pp Ssa1
+Nug1 pp Ssa1
+Pdh1 pp Ssa1
+Ssa1 pp Pgk1
+Pkh1 pp Ssa1
+Pol12 pp Ssa1
+Prp2 pp Ssa1
+Rnr4 pp Ssa1
+Rpb3 pp Ssa1
+Rpl40a pp Ssa1
+Rpn1 pp Ssa1
+Rtg3 pp Ssa1
+Rvb1 pp Ssa1
+Sec27 pp Ssa1
+Sgt1 pp Ssa1
+Smy2 pp Ssa1
+Spt15 pp Ssa1
+Swi1 pp Ssa1
+Ssa1 pp Tdh3
+Tif2 pp Ssa1
+Tir4 pp Ssa1
+Tom1 pp Ssa1
+Ubp10 pp Ssa1
+Ufd2 pp Ssa1
+Ssa1 pp Vma4
+Ybr030w pp Ssa1
+Ydl025c pp Ssa1
+Ydl203c pp Ssa1
+Ygr294w pp Ssa1
+Yhr080c pp Ssa1
+Yhr121w pp Ssa1
+Yhr181w pp Ssa1
+Yhr202w pp Ssa1
+Yll007c pp Ssa1
+Ymr075w pp Ssa1
+Yor218c pp Ssa1
+Ypl141c pp Ssa1
+Ypl207w pp Ssa1
+Ypr089w pp Ssa1
+Ypt6 pp Ssa1
+Ysh1 pp Ssa1
+Ade1 pp Ssa2
+Adr1 pp Ssa2
+Asf2 pp Ssa2
+Bni4 pp Ssa2
+Bud3 pp Ssa2
+Cft1 pp Ssa2
+Chl1 pp Ssa2
+Cpr7 pp Ssa2
+Exo1 pp Ssa2
+Fpr3 pp Ssa2
+Ies1 pp Ssa2
+Iml1 pp Ssa2
+Mck1 pp Ssa2
+Met6 pp Ssa2
+Mig1 pp Ssa2
+Ncp1 pp Ssa2
+Ssa2 pp Nop14
+Npl6 pp Ssa2
+Nsp1 pp Ssa2
+Nth1 pp Ssa2
+Nug1 pp Ssa2
+Ppt1 pp Ssa2
+Rpl40a pp Ssa2
+Rtg3 pp Ssa2
+Sgt1 pp Ssa2
+Smy2 pp Ssa2
+Spt15 pp Ssa2
+Ssa1 pp Ssa2
+Ssb1 pp Ssa2
+Ssz1 pp Ssa2
+Tdh3 pp Ssa2
+Tif2 pp Ssa2
+Tir4 pp Ssa2
+Tom1 pp Ssa2
+Ubp10 pp Ssa2
+Ydl203c pp Ssa2
+Ypl207w pp Ssa2
+Ypt6 pp Ssa2
+Ade1 pp Ssb1
+Adr1 pp Ssb1
+Aep2 pp Ssb1
+Apl4 pp Ssb1
+Ssb1 pp Aro1
+Asf2 pp Ssb1
+Atf1 pp Ssb1
+Bet3 pp Ssb1
+Bni4 pp Ssb1
+Bnr1 pp Ssb1
+Bsd2 pp Ssb1
+Bud22 pp Ssb1
+Bud3 pp Ssb1
+Cft1 pp Ssb1
+Chl1 pp Ssb1
+Cns1 pp Ssb1
+Dbp8 pp Ssb1
+Ecm16 pp Ssb1
+Exg2 pp Ssb1
+Exo1 pp Ssb1
+Fmo pp Ssb1
+Ssb1 pp Fpr3
+Htz1 pp Ssb1
+Ies1 pp Ssb1
+Ilv1 pp Ssb1
+Iml1 pp Ssb1
+Med7 pp Ssb1
+Mef1 pp Ssb1
+Met6 pp Ssb1
+Mig1 pp Ssb1
+Mon1 pp Ssb1
+Mrd1 pp Ssb1
+Msu1 pp Ssb1
+Ncp1 pp Ssb1
+Nop14 pp Ssb1
+Npl6 pp Ssb1
+Nug1 pp Ssb1
+Pdh1 pp Ssb1
+Pgk1 pp Ssb1
+Pkh1 pp Ssb1
+Pol12 pp Ssb1
+Prp2 pp Ssb1
+Rnr4 pp Ssb1
+Rpb3 pp Ssb1
+Rpl40a pp Ssb1
+Rpn1 pp Ssb1
+Rtg3 pp Ssb1
+Rvb1 pp Ssb1
+Sec27 pp Ssb1
+Sgt1 pp Ssb1
+Slx9 pp Ssb1
+Smy2 pp Ssb1
+Spt15 pp Ssb1
+Ssa1 pp Ssb1
+Swi1 pp Ssb1
+Ssb1 pp Tdh3
+Tif2 pp Ssb1
+Tir4 pp Ssb1
+Tom1 pp Ssb1
+Ubp10 pp Ssb1
+Ufd2 pp Ssb1
+Ybl104c pp Ssb1
+Ybr030w pp Ssb1
+Ydl025c pp Ssb1
+Ydl203c pp Ssb1
+Ygr294w pp Ssb1
+Yhr080c pp Ssb1
+Yhr121w pp Ssb1
+Yhr181w pp Ssb1
+Yhr202w pp Ssb1
+Yll007c pp Ssb1
+Ymr075w pp Ssb1
+Ymr111c pp Ssb1
+Yor218c pp Ssb1
+Ypl141c pp Ssb1
+Ypl207w pp Ssb1
+Ssb1 pp Ypr089w
+Ypt6 pp Ssb1
+Ysh1 pp Ssb1
+Aha1 pp Sse1
+Sse1 pp Bnr1
+Sse1 pp Bud3
+Cft1 pp Sse1
+Cns1 pp Sse1
+Cpr6 pp Sse1
+Ecm16 pp Sse1
+Sse1 pp Fpr3
+Sse1 pp Hcm1
+Htz1 pp Sse1
+Iml1 pp Sse1
+Med7 pp Sse1
+Mef1 pp Sse1
+Ncp1 pp Sse1
+Pdh1 pp Sse1
+Pkh1 pp Sse1
+Pol12 pp Sse1
+Ppt1 pp Sse1
+Sse1 pp Rpl22a
+Sgt1 pp Sse1
+Spt15 pp Sse1
+Ssa1 pp Sse1
+Sse1 pp Ssa2
+Ssb1 pp Sse1
+Swi1 pp Sse1
+Sse1 pp Tdh3
+Tir4 pp Sse1
+Ubp10 pp Sse1
+Sse1 pp Vma4
+Ybl104c pp Sse1
+Ybr030w pp Sse1
+Yor218c pp Sse1
+Ypl207w pp Sse1
+Ypt6 pp Sse1
+Bud3 pp Ssz1
+Ies1 pp Ssz1
+Mef1 pp Ssz1
+Ssz1 pp Ssa1
+Ssb1 pp Ssz1
+Ssz1 pp Tdh3
+Tom1 pp Ssz1
+Ypl141c pp Ssz1
+Ypt6 pp Ssz1
+Sti1 pp Bni4
+Sti1 pp Cpr6
+Sti1 pp Pgk1
+Sti1 pp Ppt1
+Sti1 pp Ssa1
+Sti1 pp Ssa2
+Sti1 pp Ssb1
+Sti1 pp Tdh3
+Pih1 pp Tah1
+Tah1 pp Rvb1
+Nop58 interactsWith U3
+Sua7 pp Ssu72
+Gle1 pp Dbp5
+Pol_II interactsWith SAC6_gene
+Msl1 pd ECM33_gene
+Bbp pd ECM33_gene
+Lea1 pd ECM33_gene
+Mud2 pd ECM33_gene
+Bbp pd DBP2_gene
+Mud2 pd DBP2_gene
+Prp42 pd DBP2_gene
+Pol_II interactsWith DBP2_gene
+Snu114 pd DBP2_gene
+Brr2 pd DBP2_gene
+Prp19 pd DBP2_gene
+Msl1 pd DBP2_gene
+Prp19 pd ECM33_gene
+Brr2 pd ECM33_gene
+Prp42 pd ECM33_gene
+Bbp pd SAC6_gene
+Mud2 pd SAC6_gene
+Prp42 pd SAC6_gene
+Lea1 pd DBP2_gene
+Bbp pd PDR5_gene
+Pol_II interactsWith PDR5_gene
+RNAP_II interactsWith ADH1
+Pol_II interactsWith PDR5_promoter
+Mud2 pd PDR5_gene
+Mud2 pd PDR5_promoter
+Pol_II interactsWith ECM33_gene
+Pol_II interactsWith GAL1
+Prp8 pd ECM33_gene
+Snu114 pd ECM33_gene
+Rpn11 interactsWith Unknown
+Unknown interactsWith Rpt5
+Unknown interactsWith Sec61
+Unknown interactsWith Sbh1
+Unknown interactsWith Sbh2
+Unknown interactsWith Sss1
+Rpt1 pp Rpt5
+Pol_II pd GAL1
+RNA_Pol_II pd GAL10
+RNA_Pol_II pd GAL1/10_UAS
+RNA_Pol_II pd GAL1
+RNA_Pol_II pd GAL7
+RNA_Pol_II pd GAL7_promoter
+RPO21 pd HSP26_Promoter
+Rpb1 pd RPS11B
+Rpb1 pd RPS11B_promoter
+Pol_II pd ASC1
+Rpb1 pd ALD3_promoter
+Pol_II pd PMA1
+Rpb1 pd CTT1_promoter
+Rup1 pp Rsp5
+Rup1 pp Ubp2
+Bul1 pp Rsp5
+BUL1 pp RSP5
+Mec1 pp Mdt1
+Gar1 interactsWith unknown
+unknown interactsWith Cbf5
+unknown interactsWith Nhp2
+unknown interactsWith Nop10
+unknown interactsWith snR81
+Box_H/ACA_sno/scaRNPs interactsWith U2_snRNA
+Pep8 pp Vps35
+PEP8 pp VPS35
+VPS35 pp Vps26
+Ski6 pp Rrp45
+Ski6 pp Rrp45
+Rrp45 pp Ski6
+Rrp42 pp Mtr3
+Rrp42 pp Mtr3
+Mtr3 pp Rrp42
+Mtr3 pp Rrp42
+Prp8 pd DBP2_gene
+RLF2 pp HHT1
+Scs2 pp Opi1
+Opi1 pp Scs2
+Ubc9 pp Srs2
+Rad18 pp Srs2
+Smt3 pp Srs2
+Hpr5 pp Smt3
+Rad5 pp Srs2
+Rad51 pp Srs2
+Pex6 pp Pex1
+Pex6 pp Pex1
+Pex1 interactsWith Unknown
+Unknown interactsWith Pex5
+Unknown interactsWith Pex6
+Unknown interactsWith Pex15
+FCY1 pp FCY1
+FCY1 pp FCY1
+BBC1 pp BBC1
+KAP95 pp KAP95
+PCNA pp Srs2
+PCNA pp Srs2
+Stp2 pd AGP2_promoter
+Kar3 pp Cik1
+Cik1 pp Kar3
+CIK1 pp KAR3
+Mec1 pp Rad53
+Mec1 pp Rad53
+Clb2-Cdc28 interactsWith Swe1
+Cdc28/Clb2 interactsWith Swe1
+Clb2-Cdk1 interactsWith Swe1
+Cdc28/Clb2 interactsWith Swe1
+Msh2/Msh6_heterodimer interactsWith G/C-containing_dsDNA
+Uv_Excision_Repair_Protein_Rad23 pp Peptide:n-Glycanase
+Uv_Excision_Repair_Protein_Rad23 pp Peptide:n-Glycanase
+Regulatory_Protein_Sir1 pp Origin_Recognition_Complex_Subunit_1
+Regulatory_Protein_Sir1 pp Origin_Recognition_Complex_Subunit_1
+Ubp3-Associated_Protein_Bre5 pp Ubp3-Associated_Protein_Bre5
+SerineTHREONINE-Protein_Kinase_Gcn2 pp SerineTHREONINE-Protein_Kinase_Gcn2
+SerineTHREONINE-Protein_Kinase pp SerineTHREONINE-Protein_Kinase
+Snf1 pp Snf4
+Snf1 pp Snf4
+SNF1 pp SNF4
+eEF1A pp Actin
+bI3_maturase interactsWith bI3_intron
+TOA2 pp SPT15
+TOA2 pp SPT15
+SPT15 pp TOA2
+TOA1 pp TOA2
+Toa1 pp Toa2
+TOA2 pp TOA1
+TOA2 pp TOA1
+TOA1 pp SPT15
+TOA1 pp SPT15
+TOA1 pp SPT15
+SPT15 pp TOA1
+Nucleoporin_Nup1 pp KAP95
+Rtf1 pd Pma1_gene
+Rtf1 pd Pma1_promoter
+Leo1 pd Pma1_gene
+Leo1 pd Pma1_promoter
+Rtf1 pd Fir1_gene
+Rtf1 pd Fir1_promoter
+Swi2 pd Tel_0.5
+Swi2 pd GIT1
+Ada2 pd GIT1
+Ada2 pd HMR-I
+Ada2 pd t-RNA-THR
+Spt7 pd GIT1
+Spt7 pd t-RNA-THR
+Spt7 pd HMR-I
+Rsc8 pd GIT1
+Glc7 pp Bud27
+Glc7 pp Yfl023w
+Bem2 pp Bud14
+Glc7 pp Bud14
+Sir3 pd t-RNA-THR
+Sir3 pd HMR-I
+Sir3 pd GIT1
+Sir3 pd MATa1
+Sir3 pd Tel_0.5
+Ada2 pd Tel_7.5
+Ada2 pd Tel_0.5
+Spt7 pd Tel_7.5
+Spt7 pd Tel_0.5
+Rsc8 pd Tel_0.5
+Cdc45 pd ARS607
+Glc7 pp Pti1
+Glc7 pp Cft1
+Glc7 pp Cft2
+Glc7 pp Pta1
+Glc7 pp Brr5
+Dam1 pp Set1
+Ipl1 pp Dam1
+Osh6 pp Vps4
+Osh7 pp Vps4
+Gcn4 pd YPL264C_promoter
+Gcn4 pd PYC2_promoter
+Gcn4 pd PHO8_promoter
+Gcn4 pd ORT1_promoter
+Gcn4 pd ODC2_promoter
+Gcn4 pd NCE103_promoter
+Gcn4 pd MET22_promoter
+Gcn4 pd MET13_promoter
+Gcn4 pd LYS2_promoter
+Gcn4 pd LYS14_promoter
+Gcn4 pd LYS1_promoter
+Gcn4 pd LEU4_promoter
+Gcn4 pd LEU3_promoter
+Gcn4 pd ISU1_promoter
+Gcn4 pd ILV3_promoter
+Gcn4 pd SFT2_promoter
+Gcn4 pd STR3_promoter
+Gcn4 pd YMR135C_promoter
+Gcn4 pd YMC2_promoter
+Gcn4 pd YMC1_promoter
+Gcn4 pd YLR152C_promoter
+Gcn4 pd YJL200C_promoter
+Gcn4 pd YIL056W_promoter
+Gcn4 pd YHR162W_promoter
+Gcn4 pd YGL117W_promoter
+Gcn4 pd YBR147W_promoter
+Gcn4 pd YBR043C_promoter
+Gcn4 pd UGA3_promoter
+Gcn4 pd TRP4_promoter
+Gcn4 pd TRP2_promoter
+Gcn4 pd TEA1_promoter
+Gcn4 pd IDP1_promoter
+Gcn4 pd ICY2_promoter
+Gcn4 pd BAP2_promoter
+Gcn4 pd ARO4_promoter
+Gcn4 pd ARO1_promoter
+Gcn4 pd ARG8_promoter
+Gcn4 pd ARG5_promoter
+Gcn4 pd ARG4_promoter
+Gcn4 pd ARG3_promoter
+Gcn4 pd ARG1_promoter
+Gcn4 pd ALD5_promoter
+Gcn4 pd ADH5_promoter
+Gcn4 pd ADE3_promoter
+Gcn4 pd BNA1_promoter
+Gcn4 pd CPA1_promoter
+Gcn4 pd HSP78_promoter
+Gcn4 pd HRB1_promoter
+Gcn4 pd HOM3_promoter
+Gcn4 pd PET56_promoter
+Gcn4 pd HIS3_promoter
+Gcn4 pd HIS1_promoter
+Gcn4 pd GAT1_promoter
+Gcn4 pd FOL2_promoter
+Gcn4 pd YNL124W_promoter
+Gcn4 pd ESBP6_promoter
+Gcn4 pd ECM40_promoter
+Gcn4 pd DED81_promoter
+Gcn4 pd YJR110W_promoter
+Gcn4 pd CPA2_promoter
+PHO85 interactsWith ROM2
+PHO85 interactsWith CLA4
+PHO85 interactsWith BEM4
+PHO85 interactsWith BEM2
+PHO85 interactsWith BEM1
+PHO85 interactsWith LEM3
+PHO85 interactsWith YML122C
+PHO85 interactsWith YJR142W
+PHO85 interactsWith YGR161C
+PHO85 interactsWith YGL015C
+PHO85 interactsWith BRE1
+PHO85 interactsWith GSH1
+PHO85 interactsWith VIK1
+PHO85 interactsWith RTS1
+PHO85 interactsWith SUR4
+PHO85 interactsWith BNI1
+PHO85 interactsWith PAC10
+PHO85 interactsWith WSC4
+PHO85 interactsWith WSC1
+PHO85 interactsWith ERD1
+PHO85 interactsWith SHC1
+PHO85 interactsWith FKS3
+PHO85 interactsWith FKS1
+PHO85 interactsWith PMR1
+PHO85 interactsWith VAN1
+PHO85 interactsWith HOC1
+PHO85 interactsWith MNN10
+PHO85 interactsWith ANP1
+PHO85 interactsWith TPM1
+PHO85 interactsWith NUM1
+PHO85 interactsWith YKE2
+PHO85 interactsWith OPI3
+PHO85 interactsWith CHO2
+PHO85 interactsWith UME6
+PHO85 interactsWith VAM3
+PHO85 interactsWith VPS44
+PHO85 interactsWith VPS38
+PHO85 interactsWith VPS35
+PHO85 interactsWith VPS29
+PHO85 interactsWith YOL119C
+PHO85 interactsWith SMF1
+PHO85 interactsWith TAT2
+PHO85 interactsWith GCR2
+PHO85 interactsWith YER049W
+PHO85 interactsWith SPT4
+PHO85 interactsWith SFL1
+PHO85 interactsWith SRB8
+PHO85 interactsWith SRB9
+PHO85 interactsWith SWI4
+PHO85 interactsWith SLT2
+PHO85 interactsWith BCK1
+PHO85 interactsWith RGD1
+PHO85 interactsWith SOP10
+Set1 pd Adh1_promoter
+Set1 pd Early_body_of_PMA1_gene
+PUP1 pp PRE8
+PRE8 pp PUP1
+Pre8 pp Pup1
+PUP3 pp PRE9
+PUP3 pp PRE9
+PUP3 pp PRE9
+PUP3 pp PRE9
+PRE9 pp PUP3
+PRE7 pp PRE5
+PRE7 pp PRE5
+PRE7 pp PRE5
+PRE7 pp PRE5
+PRE5 pp PRE7
+PRE7 pp PRE2
+PRE7 pp PRE2
+PRE7 pp PRE2
+PUP3 pp PRE8
+PUP3 pp PRE8
+PRE8 pp PUP3
+PRE2 pp PUP2
+PRE2 pp PUP2
+PRE2 pp PUP2
+PRE2 pp PUP2
+PUP2 pp PRE2
+Potential_Proteasome_Component_C5 pp PRE5
+Proteasome_Component_Pre4 pp Potential_Proteasome_Component_C5
+Potential_Proteasome_Component_C5 pp Proteasome_Component_Pre2
+Potential_Proteasome_Component_C5 pp PUP2
+Proteasome_Component_Pre2 pp PRE6
+PRE1 pp PUP3
+PRE1 pp PUP3
+PUP3 pp Proteasome_Component_Pup1
+Proteasome_Component_Pup1 pp Proteasome_Component_Pre3
+Proteasome_Component_Pup1 pp SCL1
+Proteasome_Component_Pre3 pp PRE10
+Proteasome_Component_Pre3 pp SCL1
+Proteasome_Component_Pre4 pp PRE10
+Proteasome_Component_Pre4 pp PRE5
+PRE1 pp Proteasome_Component_Pre2
+Proteasome_Component_Pre2 pp PRE1
+Proteasome_Component_Pre2 pp PRE1
+PRE1 pp PRE9
+PRE1 pp PRE9
+PRE1 pp PRE9
+PRE1 pp PRE9
+PRE9 pp PRE1
+PRE1 pp PRE6
+PRE1 pp PRE6
+PRE1 pp PRE6
+PRE1 pp PRE6
+PRE6 pp PRE1
+PRE1 pp PRE1
+PRE1 pp PRE1
+PRE1 pp PRE1
+PUP3 pp Proteasome_Component_Pre2
+Proteasome_Component_Pre2 pp PUP3
+Proteasome_Component_Pup1 pp PRE8
+Proteasome_Component_Pup1 pp Potential_Proteasome_Component_C5
+Potential_Proteasome_Component_C5 pp Proteasome_Component_Pup1
+Proteasome_Component_Pre3 pp Proteasome_Component_Pre3
+Proteasome_Component_Pre3 pp Proteasome_Component_Pre4
+Proteasome_Component_Pre4 pp Proteasome_Component_Pre3
+PRE10 pp PRE5
+PRE10 pp PRE5
+PRE10 pp PRE5
+PRE10 pp PRE5
+PRE10 pp PRE5
+PRE10 pp PRE5
+PRE10 pp PRE5
+PRE10 pp PRE5
+Pre10 pp Pre5
+PRE10 pp SCL1
+PRE10 pp SCL1
+PRE10 pp SCL1
+Pre10 pp Scl1
+SCL1 pp PRE10
+PRE5 pp PUP2
+PRE5 pp PUP2
+PRE5 pp PUP2
+PRE5 pp PUP2
+PRE5 pp PUP2
+PRE5 pp PUP2
+PRE5 pp PUP2
+PUP2 pp PRE6
+PUP2 pp PRE6
+PUP2 pp PRE6
+PUP2 pp PRE6
+PUP2 pp PRE6
+PUP2 pp PRE6
+PUP2 pp PRE6
+PRE6 pp PRE9
+PRE6 pp PRE9
+PRE6 pp PRE9
+PRE6 pp PRE9
+PRE6 pp PRE9
+PRE6 pp PRE9
+PRE6 pp PRE9
+PRE6 pp PRE9
+PRE6 pp PRE9
+PRE9 pp PRE8
+PRE9 pp PRE8
+PRE9 pp PRE8
+PRE9 pp PRE8
+PRE9 pp PRE8
+PRE9 pp PRE8
+PRE9 pp PRE8
+PRE9 pp PRE8
+Pre8 pp Pre9
+PRE8 pp SCL1
+PRE8 pp SCL1
+PRE8 pp SCL1
+SCL1 pp PRE8
+SCL1 pp PRE8
+SCL1 pp PRE8
+Potential_Proteasome_Component_C5 pp PUP3
+PUP3 pp Potential_Proteasome_Component_C5
+Proteasome_Component_Pre4 pp Proteasome_Component_Pup1
+Proteasome_Component_Pup1 pp Proteasome_Component_Pre4
+Kes1_Protein pp Kes1_Protein
+Kes1_Protein pp Kes1_Protein
+Proteasome_Component_Pre4 pp Proteasome_Component_Pre3
+SerineTHREONINE-Protein_Kinase_Ste11 pp SerineTHREONINE-Protein_Kinase_Ste11
+Unknown interactsWith Cdc48
+Unknown interactsWith Ubc6
+Unknown interactsWith Ubc7
+Unknown interactsWith Cue1
+Doa10 interactsWith Unknown
+Unknown interactsWith Hrd1
+Unknown interactsWith Hrd3
+Unknown interactsWith Cdc48
+Npl4 interactsWith Unknown
+Ubx2 interactsWith Unknown
+Unknown interactsWith Doa10
+Unknown interactsWith Hrd1
+Unknown interactsWith Cdc48
+Ufd1 interactsWith unknown
+unknown interactsWith Ubx2
+unknown interactsWith Cdc48
+unknown interactsWith Npl4
+Hmg2 interactsWith unknown
+unknown interactsWith Ubx2
+unknown interactsWith Cdc48
+CPY pp Ubx2
+unknown interactsWith Ubx2
+Dfm1 interactsWith unknown
+unknown interactsWith Cdc48
+unknown interactsWith Ufd1
+Doa10 interactsWith unknown
+unknown interactsWith Ubx2
+unknown interactsWith Cdc48
+unknown interactsWith Ufd1
+Hrd1 interactsWith unknown
+unknown interactsWith Ubx2
+unknown interactsWith Cdc48
+unknown interactsWith Ufd1
+Der1 interactsWith unknown
+unknown interactsWith Ubx2
+unknown interactsWith Cdc48
+unknown interactsWith Ufd1
+CCP1 pp CCP1
+CCP1 pp CCP1
+TES1 pp TES1
+TES1 pp TES1
+TES1 pp TES1
+TES1 pp TES1
+FMS1 pp FMS1
+FMS1 pp FMS1
+FMS1 pp FMS1
+FMS1 pp FMS1
+CYC1 pp CCP1
+CYC1 pp CCP1
+CYC1 pp CCP1
+CYC1 pp CCP1
+CYC1 pp CCP1
+CYC1 pp CCP1
+CCP1 pp CYC1
+RPB11 pp RPB2
+RPB11 pp RPB2
+RPB11 pp RPB2
+RPB11 pp RPB2
+RPO26 pp RPB5
+Rraa-Like_Protein_Yer010c pp Rraa-Like_Protein_Yer010c
+Rraa-Like_Protein_Yer010c pp Rraa-Like_Protein_Yer010c
+Nucleoporin_Nup2 pp Importin_Alpha_Subunit
+SNF1 pp SNF1
+Cyclin-Dependent_Kinase_Inhibitor_Far1 pp FUS3
+Tyrosine-Protein_Phosphatase_Msg5 pp FUS3
+SerineTHREONINE-Protein_Kinase_Ste7 pp FUS3
+IRE1 pp IRE1
+Hypothetical_73.8_Kda_Protein_In_Sas3-Sec17_Intergenic_Region,_Residues_301-310 pp SerineTHREONINE-Protein_Kinase_Rad53
+ENO1 pp ENO1
+ENO1 pp ENO1
+ENO1 pp ENO1
+ENO1 pp ENO1
+General_Control_Protein_Gcn4 pp General_Control_Protein_Gcn4
+3-Hydroxyanthranilate_3,4-Dioxygenase pp 3-Hydroxyanthranilate_3,4-Dioxygenase
+Nbp2p pp Nbp2p
+Nbp2p pp Nbp2p
+Nbp2p pp Nbp2p
+Nbp2p pp Nbp2p
+Signal_Recognition_Particle_Receptor_Beta_Subunit pp Signal_Recognition_Particle_Receptor_Beta_Subunit
+Ypl069c pp Ypl069c
+Ubiquitin pp Protein_Ybl047c
+Seven_Residue_Peptide pp YDJ1
+1SFO_R interactsWith RPB2
+1SFO_R interactsWith RPO21
+1SFO_T pd RPO21
+1SFO_T pd RPB2
+Ac-Arg-Glu-Lys-Boroarg_Peptide_Inhibitor pp KEX2
+1S40_B pd CDC13
+Ctd-Peptide pp Pcf11_Protein
+1T0K_C interactsWith 60s_Ribosomal_Protein_L30
+1T0K_D interactsWith 60s_Ribosomal_Protein_L30
+PpV interactsWith Sit4
+cdc2 interactsWith Cdc28
+UbcD6 interactsWith rad6
+eIF-2alpha interactsWith NULL
+lwr interactsWith Ubc9
+eff interactsWith Ubc5
+eff interactsWith Ubc4
+UbcD2 interactsWith Ubc5
+UbcD2 interactsWith Ubc4
+Dna_Repair_Protein_Rad9 pp RAD53
+Ser-Leu-Glu-Val-Tpo-Glu-Ala-Aspala-Thr-Phe-Ala-_Lys pp RAD53
+Ser-Leu-Glu-Val-Tpo-Glu-Ala-Aspala-Thr-Phe-Ala-_Lys pp RAD53
+Heavy_Chain_(Vh)_Of_Fv-Fragment pp RIP1
+Light_Chain_(Vl)_Of_Fv-Fragment pp RIP1
+Octapeptide_Glyaskla pp NMT1
+1I6H_D pd RPO21
+1I6H_D pd RPB2
+1I6H_R interactsWith RPO21
+1I6H_R interactsWith RPB2
+Proteasome_Activator_Protein_Pa26 pp PRE8
+Proteasome_Activator_Protein_Pa26 pp PRE9
+Proteasome_Activator_Protein_Pa26 pp SCL1
+Proteasome_Activator_Protein_Pa26 pp PRE8
+Proteasome_Activator_Protein_Pa26 pp PRE10
+Proteasome_Activator_Protein_Pa26 pp SCL1
+Proteasome_Activator_Protein_Pa26 pp PRE5
+Proteasome_Activator_Protein_Pa26 pp PRE10
+Proteasome_Activator_Protein_Pa26 pp PUP2
+Proteasome_Activator_Protein_Pa26 pp PRE5
+Proteasome_Activator_Protein_Pa26 pp PRE6
+Proteasome_Activator_Protein_Pa26 pp PUP2
+Proteasome_Activator_Protein_Pa26 pp PRE9
+Proteasome_Activator_Protein_Pa26 pp PRE6
+1GIX_1 interactsWith 1GIX_C
+1GIX_1 interactsWith 1GIX_B
+30s_Ribosomal_Protein_S7 interactsWith 1GIX_D
+rpsM interactsWith 1GIX_C
+1ID3_I pd HHT1
+1ID3_I pd HTB2
+1ID3_I pd HTA1
+1ID3_I pd HHT1
+1ID3_I pd HHF1
+1ID3_I pd HHF1
+1ID3_I pd HTA1
+1ID3_I pd HTB2
+1ID3_J pd HHT1
+1ID3_J pd HTB2
+1ID3_J pd HTA1
+1ID3_J pd HHF1
+1ID3_J pd HHT1
+1ID3_J pd HHF1
+1ID3_J pd HTB2
+Von_Hippel-Lindau_Disease_Tumor_Suppressor pp ELC1
+Nucleoplasmin pp SRP1
+1LE8_C pd HMRA2
+1LE8_C pd Mating-Type_Protein_A-1
+1LE8_D pd Mating-Type_Protein_A-1
+1LE8_D pd HMRA2
+1J5N_B pd NHP6A
+1J5N_C pd NHP6A
+1MNN_B pd NDT80
+1MNN_C pd NDT80
+1M6X_E pd Flp_Recombinase
+1M6X_F pd Flp_Recombinase
+1M6X_I pd Flp_Recombinase
+1P4E_J pd Recombinase_Flp_Protein
+1M6X_G pd Flp_Recombinase
+1P4E_H pd Recombinase_Flp_Protein
+1M6X_H pd Flp_Recombinase
+1NGM_G pd SPT15
+1NGM_H pd SPT15
+1P4E_E pd Recombinase_Flp_Protein
+1P4E_F pd Recombinase_Flp_Protein
+1P4E_G pd Recombinase_Flp_Protein
+1P4E_J pd Recombinase_Flp_Protein
+Ac-Ala-Lys-Boroarg_N-Acetylated_Boronic_Acid_Peptide_Inhibitor pp KEX2
+1NH2_E pd TOA1
+1NH2_E pd SPT15
+1NH2_F pd SPT15
+1NH2_F pd TOA1
+Histone_H4 pp HST2
+Unknown interactsWith Srb4
+Heme_b(L) interactsWith COB
+Heme_b(H) interactsWith COB
+Heme_c1 interactsWith CYT1
+2Fe-2S interactsWith RIP1
+UQ6 interactsWith COB
+1DGC_B pd GCN4
+1PYI_D pd PPR1
+1PYI_D pd PPR1
+1PYI_E pd PPR1
+1PYI_E pd PPR1
+1CSM_M pp ARO7
+1CSM_L pp ARO7
+L-Tyrosine pp ARO7
+L-Tyrosine pp ARO7
+1A0A_C pd PHO4
+1A0A_C pd PHO4
+1A0A_D pd PHO4
+1A0A_D pd PHO4
+1AKH_C pd HMRA2
+1AKH_C pd HMRA1
+1ZME_B interactsWith 1ZME_A
+Large_T_Antigen pp SRP1
+486D_D interactsWith 486D_C
+1FLO_K pd Flp_Recombinase
+1P4E_J pd Recombinase_Flp_Protein
+1M6X_J pd Flp_Recombinase
+1FLO_H pd Flp_Recombinase
+PLP interactsWith YBL036C
+Zn2+ interactsWith HAP1
+Zn2+ interactsWith HAP1
+FNS interactsWith CYB2
+Zn2+ interactsWith VPS27
+Zn2+ interactsWith VPS27
+RDC interactsWith HSP82
+3PG interactsWith GPM1
+heme interactsWith CTA1
+ARG interactsWith YDR341C
+CoA interactsWith Histone_H3
+PLP interactsWith Yeast_Hypothetical_Protein,_Selenomet
+FMN interactsWith PDX3
+FMN interactsWith PDX3
+ATP interactsWith ACT1
+NEN interactsWith Sec18p_(Residues_22_-_210)
+NEN interactsWith Sec18p_(Residues_22_-_210)
+Acetyl-CoA interactsWith HPA2
+Benzamidine interactsWith ATX1
+Benzamidine interactsWith ATX1
+HGU interactsWith CCP1
+IP6 interactsWith GPM1
+IP6 interactsWith GPM1
+benzene_hexacarboxylic_acid interactsWith GPM1
+Mn2+ interactsWith CCP1
+heme interactsWith CCP1
+Mn2+ interactsWith CET1
+4NP interactsWith LTP1
+Na+ interactsWith HOM6
+NAD+ interactsWith HOM6
+NDA interactsWith HOM6
+L-homoserine interactsWith HOM6
+Adenine interactsWith LTP1
+SHF interactsWith HEM2
+Mg2+ interactsWith MET22
+A5MP interactsWith MET22
+thiamin_diphosphate interactsWith PDC6
+thiamin_diphosphate interactsWith PDC6
+Mg2+ interactsWith PDC6
+PYM interactsWith PDC6
+PYM interactsWith PDC6
+ATP interactsWith ACT1
+BMP interactsWith URA3
+BMP interactsWith URA3
+MAN-(1-6)MAN-(1-6)MAN-(3-1)MAN-(2-1)MAN-(2-1)MAN-(3,1-4)NAG-(1-4)NAG-(4,6-1)MAN interactsWith PEP4
+MAN-(1-2)MAN-(1-2)MAN-(1-3)MAN-(1-4)NAG-(1-4)NAG-(3,6-1)MAN-(2-1)MAN-(4,6-1)MAN interactsWith PEP4
+Mg2+ interactsWith YPT52
+GNP interactsWith YPT52
+GDP interactsWith YPT52
+Zn2+ interactsWith TFP1
+Zn2+ interactsWith TFP1
+Mn2+ interactsWith PAP1
+3AT interactsWith PAP1
+3AT interactsWith PAP1
+Cordycepin interactsWith PAP1
+Mg2+ interactsWith 1EHZ_A
+O4M interactsWith 1EHZ_A
+MO5 interactsWith 1EHZ_A
+MN5 interactsWith 1EHZ_A
+MO3 interactsWith 1EHZ_A
+MO6 interactsWith 1EHZ_A
+MO1 interactsWith 1EHZ_A
+MN5 interactsWith 1EHZ_A
+MAN-(1-2)MAN-(1-3)MAN-(1-4)NAG-(1-4)NAG interactsWith PEP4
+EMR-PCE-SMC-TRM interactsWith PEP4
+STA-LEU-TRJ-(c1)GLU-NPD-NPY interactsWith PEP4
+GCL-GSC-PHE-SOT interactsWith PEP4
+NME-CAL-HIS-PHE-BOC interactsWith PEP4
+MOR-PHE-NLE interactsWith PEP4
+CFS interactsWith PEP4
+NAG-(4-1)NAG-(4-1)MAN-(6-1)MAN-(3-1)MAN-(3,3-1)MAN-(4,6-1)MAN interactsWith MNS1
+NAG-(4-1)NAG-(4-1)MAN interactsWith MNS1
+NAG interactsWith MNS1
+Ca2+ interactsWith MNS1
+CoA interactsWith ESA1
+EPX interactsWith PRE7
+EPX interactsWith PRE2
+EPX interactsWith PRE2
+Mg2+ interactsWith PRE7
+Mg2+ interactsWith PRE7
+Mg2+ interactsWith SCL1
+Zn2+ interactsWith SSO1
+Zn2+ interactsWith Cyp1(Hap1-Pc7)_Activatory_Protein
+Zn2+ interactsWith Cyp1(Hap1-Pc7)_Activatory_Protein
+GDP interactsWith SEC4
+Mg2+ interactsWith SEC4
+GNP interactsWith SEC4
+NAD+ interactsWith MTD1
+CPG interactsWith TEF2
+Ca2+ interactsWith FRQ1
+Ca2+ interactsWith FRQ1
+Ca2+ interactsWith FRQ1
+INJ interactsWith RIB4
+INJ interactsWith RIB4
+Cu1+ interactsWith Atx1_Copper_Chaperone
+Cu2+ interactsWith Copper-Transporting_Atpase
+heme interactsWith COB
+heme interactsWith COB
+heme interactsWith CYT1
+2Fe-2S interactsWith RIP1
+SMA interactsWith COB
+UQ6 interactsWith COB
+Acetyl-CoA interactsWith GNA1
+Acetyl-CoA interactsWith GNA1
+IMD interactsWith GNA1
+IMD interactsWith GNA1
+16G interactsWith GNA1
+16G interactsWith GNA1
+CoA interactsWith GNA1
+CoA interactsWith GNA1
+GDP interactsWith TEF2
+GDP interactsWith TEF2
+MYA interactsWith Peptide_N-Myristoyltransferase
+NHM interactsWith NMT1
+Mn2+ interactsWith RPO21
+MAN-(1-2)MAN-(1-2)MAN-(1-3)MAN-(1-4)NAG-(1-4)NAG-(3,6-1)MAN-(2-1)MAN interactsWith PEP4
+NAG interactsWith PEP4
+Mg2+ interactsWith PRE2
+Mg2+ interactsWith PUP3
+Mg2+ interactsWith 1I9V_A
+Mg2+ interactsWith 1I9V_A
+NMY interactsWith 1I9V_A
+Ca2+ interactsWith MET3
+Mg2+ interactsWith MET3
+Ca2+ interactsWith MET3
+Na+ interactsWith Sulfate_Adenylyltransferase
+Na+ interactsWith MET3
+Na+ interactsWith MET3
+APS interactsWith MET3
+Na+ interactsWith Sulfate_Adenylyltransferase
+ARG interactsWith 1F7U_B
+K+ interactsWith CCP1
+thiamine interactsWith THI80
+thiamine interactsWith THI80
+ADP interactsWith KAR3
+4OX interactsWith 5-Aminolaevulinic_Acid_Dehydratase
+4OX interactsWith 5-Aminolaevulinic_Acid_Dehydratase
+KAH interactsWith HEM2
+SHU interactsWith HEM2
+Zn2+ interactsWith MAS1
+FAD interactsWith LPD1
+FAD interactsWith LPD1
+DAV interactsWith 5-Aminolaevulinic_Acid_Dehydratase
+Zn2+ interactsWith RNR2
+REO interactsWith ECI1
+REO interactsWith ECI1
+Mn2+ interactsWith HTA1
+Mn2+ interactsWith HTB2
+AMO interactsWith 1IL2_C
+HBA interactsWith OYE2
+Mg2+ interactsWith MET22
+Zn2+ interactsWith MET22
+Zn2+ interactsWith MET22
+Zn2+ interactsWith MET22
+Zn2+ interactsWith MET22
+Zn2+ interactsWith MET22
+Zn2+ interactsWith MET22
+Na+ interactsWith MET22
+Ca2+ interactsWith MET22
+3',5'-ADP interactsWith MET22
+Na+ interactsWith Sulfate_Adenylyltransferase
+ADP interactsWith Sulfate_Adenylyltransferase
+THJ interactsWith Sulfate_Adenylyltransferase
+SHF interactsWith HEM2
+FAD interactsWith ERV2
+FAD interactsWith ERV2
+GTT interactsWith URE2
+GTX interactsWith URE2
+GTB interactsWith URE2
+K+ interactsWith CCP1
+K+ interactsWith ILV2
+Mg2+ interactsWith ILV2
+thiamin_diphosphate interactsWith ILV2
+thiamin_diphosphate interactsWith ILV2
+FAD interactsWith ILV2
+FAD interactsWith ILV2
+FAD interactsWith ILV2
+THD interactsWith TKL1
+THD interactsWith TKL1
+Ca2+ interactsWith TKL1
+K+ interactsWith CCP1
+95A interactsWith PUP1
+95A interactsWith PUP3
+FMN interactsWith CYB2
+heme interactsWith COB
+heme interactsWith CYT1
+2Fe-2S interactsWith RIP1
+SMA interactsWith COB
+SMA interactsWith RIP1
+heme interactsWith CYT1
+NAD+ interactsWith INO1
+NAD+ interactsWith INO1
+DG6 interactsWith INO1
+DG6 interactsWith INO1
+NADH interactsWith INO1
+PLP interactsWith Threonine_Synthase
+NAD+ interactsWith INO1
+Mg2+ interactsWith YPT31
+GNP interactsWith YPT31
+GDP interactsWith YPT31
+NAD+ interactsWith MET8
+MAN interactsWith Saccharopepsin
+NAG interactsWith Saccharopepsin
+UQ6 interactsWith COB
+PIE interactsWith CYT1
+PIE interactsWith RIP1
+PIE interactsWith COB
+PEF interactsWith QCR8
+PEF interactsWith QCR7
+PEF interactsWith COB
+CDL interactsWith COB
+CDL interactsWith CYT1
+CDL interactsWith QCR7
+PEF interactsWith COB
+UMQ interactsWith COR1
+UMQ interactsWith Ubiquinol-Cytochrome_C_Reductase_Complex_7.3_Kd_Protein
+UMQ interactsWith RIP1
+PCF interactsWith COB
+PCF interactsWith COR1
+PCF interactsWith RIP1
+HIF interactsWith Cytochrome_C_Peroxidase
+Ca2+ interactsWith TFP1
+Zn2+ interactsWith SEC23
+Mg2+ interactsWith SAR1
+GNP interactsWith SEC23
+GNP interactsWith SAR1
+Zn2+ interactsWith SEC24
+Acetyl-CoA interactsWith ESA1
+GDP interactsWith ARL1
+G3D interactsWith ARF2
+PLP interactsWith CYS3
+PLP interactsWith CYS3
+PLP interactsWith CYS3
+PLP interactsWith CYS3
+Cu2+ interactsWith Copper-Zinc_Superoxide_Dismutase
+Mg2+ interactsWith GSH2
+AMP-PNP interactsWith GSH2
+gamma-Glutamyl_cysteine interactsWith GSH2
+phosphoenolpyruvate interactsWith ARO4
+K+ interactsWith ILV2
+Mg2+ interactsWith ILV2
+CIE interactsWith ILV2
+CIE interactsWith ILV2
+AYD interactsWith ILV2
+AYD interactsWith ILV2
+FAD interactsWith ILV2
+FAD interactsWith ILV2
+thiamin_diphosphate interactsWith ILV2
+thiamin_diphosphate interactsWith ILV2
+Glycerone-P interactsWith TPI1
+IMD interactsWith CYC1
+HEC interactsWith CYC1
+SO1 interactsWith EFT2
+HEC interactsWith CYC1
+Mg2+ interactsWith SRP102
+GTP interactsWith SRP102
+ATP interactsWith Phosphoribosylamidoimidazole-_Succinocarboxamide_Synthase
+Mg2+ interactsWith Phosphoribosylamidoimidazole-_Succinocarboxamide_Synthase
+A5MP interactsWith Phosphoribosylamidoimidazole-_Succinocarboxamide_Synthase
+ATP interactsWith Phosphoribosylamidoimidazole-_Succinocarboxamide_Synthase
+Mg2+ interactsWith Phosphoribosylamidoimidazole-_Succinocarboxamide_Synthase
+ZEM interactsWith CCP1
+Acetyl-CoA interactsWith ACC1
+Acetyl-CoA interactsWith ACC1
+Adenine interactsWith ACC1
+5,6-Dihydrouracil interactsWith FCY1
+NAG-(4-1)NAG-(4-1)MAN-(6-1)MAN-(6-1)MAN-(3,3-1)MAN-(4,3-1)MAN interactsWith MNS1
+NAG interactsWith MNS1
+NAG-(4-1)NAG-(4-1)MAN-(6-1)MAN-(3,3-1)MAN interactsWith MNS1
+Ca2+ interactsWith MNS1
+DMJ interactsWith MNS1
+PBG interactsWith HEM2
+NAG interactsWith KEX2
+NAG-(4-1)NAG interactsWith KEX2
+Ca2+ interactsWith KEX2
+Ca2+ interactsWith KEX2
+Ca2+ interactsWith KEX2
+Ni2+ interactsWith HIS7
+1PR interactsWith HIS7
+Mg2+ interactsWith TOP2
+AMP-PNP interactsWith TOP2
+HPY interactsWith FCY1
+Zn2+ interactsWith SEC24
+n-octonyl-CoA interactsWith ECI1
+n-octonyl-CoA interactsWith ECI1
+n-octonyl-CoA interactsWith ECI1
+DBT interactsWith COB
+UQ6 interactsWith COB
+3PE interactsWith QCR8
+3PE interactsWith QCR7
+3PE interactsWith COB
+3PE interactsWith COB
+3PH interactsWith COR1
+3PH interactsWith COB
+3PH interactsWith RIP1
+3PH interactsWith CYT1
+3PH interactsWith RIP1
+PC1 interactsWith CYT1
+PC1 interactsWith COB
+CDL interactsWith COB
+Ca2+ interactsWith CMD1
+Ca2+ interactsWith CMD1
+Zn2+ interactsWith AIP1
+NAG-(4-1)NAG-(4-1)MAN-(6-1)MAN-(6-1)MAN-(2-1)MAN-(3,3-1)MAN-(2-1)MAN-(4,3-1)MAN-(2-1)MAN interactsWith EXG1
+NAG-(4-1)NAG-(4-1)BMA-(6-1)BMA-(3,3-1)BMA interactsWith EXG1
+NAG-(4-1)NAG-(4-1)MAN-(3-1)MAN-(2-1)MAN-(3,6-1)MAN-(6-1)MAN-(6,3-1)MAN interactsWith EXG1
+NAG-(4-1)NAG-(4-1)MAN-(3-1)MAN-(2-1)MAN-(3,6-1)MAN-(6-1)MAN-(6,3-1)MAN interactsWith EXG1
+CoA interactsWith Histone_H3
+CoA interactsWith Histone_H3
+Zn2+ interactsWith HST2
+Mg2+ interactsWith SKY1
+ADP interactsWith SKY1
+Adenine interactsWith SKY1
+Ni2+ interactsWith SKY1
+ATP interactsWith SKY1
+ADN interactsWith SKY1
+AMP-PNP interactsWith SKY1
+CDX interactsWith TOP2
+NHO interactsWith HOM6
+Zn2+ interactsWith HST2
+APR interactsWith HST2
+OAD interactsWith HST2
+SAM interactsWith PPM1
+S-Adenosylhomocysteine interactsWith PPM1
+Ca2+ interactsWith POP2
+PIB interactsWith GRD19
+MTN interactsWith CDC33
+MTN interactsWith TIF4631
+MTN interactsWith CDC33
+MTN interactsWith CDC33
+MTN interactsWith CDC33
+Zn2+ interactsWith YDJ1
+Zn2+ interactsWith YDJ1
+Mn2+ interactsWith ARO4
+K+ interactsWith General_Control_Protein_Gcn4
+K+ interactsWith General_Control_Protein_Gcn4
+K+ interactsWith General_Control_Protein_Gcn4
+K+ interactsWith KEX2
+K+ interactsWith KEX2
+K+ interactsWith KEX2
+K+ interactsWith KEX2
+K+ interactsWith KEX2
+148 interactsWith KEX2
+148 interactsWith KEX2
+A5MP interactsWith ACS1
+Mn2+ interactsWith KRE2
+GDP interactsWith KRE2
+MAM interactsWith KRE2
+MAM interactsWith KRE2
+G3P interactsWith ARO4
+Phosphoglycolate interactsWith ARO4
+Phosphoglycolate interactsWith ARO4
+Phenylalanine interactsWith ARO4
+Phenylalanine interactsWith ARO4
+Zn2+ interactsWith CDD1
+D6P interactsWith INO1
+NEN interactsWith ERO1
+FAD interactsWith ERO1
+FAD interactsWith ERO1
+TYR interactsWith ARO4
+TYR interactsWith ARO4
+TYR interactsWith ARO4
+Ca2+ interactsWith FMP41
+Zn2+ interactsWith ADH6
+Zn2+ interactsWith ADH6
+NADP+ interactsWith ADH6
+Mg2+ interactsWith RFC1
+Mg2+ interactsWith RFC4
+Mg2+ interactsWith RFC3
+Mg2+ interactsWith RFC2
+AGS interactsWith RFC1
+AGS interactsWith RFC4
+AGS interactsWith RFC4
+AGS interactsWith RFC3
+AGS interactsWith RFC3
+AGS interactsWith RFC2
+AGS interactsWith RFC5
+ADP interactsWith RFC5
+APR interactsWith HST2
+APR interactsWith Histone_H4_Peptide
+Ca2+ interactsWith LOT6
+FMN interactsWith LOT6
+FMN interactsWith LOT6
+173 interactsWith Cytochrome_B2,_Mitochondrial
+173 interactsWith Cytochrome_B2,_Mitochondrial
+FMN interactsWith Cytochrome_B2,_Mitochondrial
+FNS interactsWith Cytochrome_B2,_Mitochondrial
+178 interactsWith Homoserine_Dehydrogenase
+Ribitol interactsWith YMR087W
+NADP+ interactsWith ADH6
+NAG-(4-1)NDG interactsWith EXG1
+GPA2 interactsWith RSR1
+MPH1 interactsWith FLO8
+MPH1 interactsWith STE20
+MPH1 interactsWith STE12
+MPH1 interactsWith PHD1
+MPH1 interactsWith MSN1
+MPH1 interactsWith GLN3
+MPH1 interactsWith BEM1
+DBR1 interactsWith FLO8
+DBR1 interactsWith STE20
+DBR1 interactsWith PHD1
+DBR1 interactsWith MSN1
+DBR1 interactsWith GLN3
+DBR1 interactsWith BEM1
+GPA2 interactsWith TEC1
+GPA2 interactsWith FLO8
+GPA2 interactsWith STE20
+GPA2 interactsWith STE12
+GPA2 interactsWith PHD1
+GPA2 interactsWith MSN1
+GPA2 interactsWith GLN3
+GPA2 interactsWith BEM1
+DBR1 interactsWith TEC1
+MPH1 interactsWith KSS1
+DBR1 interactsWith KSS1
+Unknown interactsWith SNR19
+Unknown interactsWith Smd3
+Unknown interactsWith Smd2
+Unknown interactsWith Smd1
+Unknown interactsWith Yhc1
+Unknown interactsWith Snu71
+Unknown interactsWith Snu56
+Unknown interactsWith Snp1
+Unknown interactsWith Prp42
+Unknown interactsWith Prp40
+Unknown interactsWith Prp39
+Unknown interactsWith Mud1
+Unknown interactsWith Luc7
+Co_(2+) interactsWith SEC4
+Co_(2+) interactsWith IPP1
+Co_(2+) interactsWith IPP1
+Co_(2+) interactsWith ARO4
+BR interactsWith YKL069W
+BR interactsWith YKL069W
+BR interactsWith DOC1
+BR interactsWith DOC1
+BR interactsWith ASF1
+BR interactsWith ASF1
+1TRJ_C interactsWith ASC1
+GDP interactsWith EFT2
+S-Adenosylhomocysteine interactsWith DOT1
+Cu1+ interactsWith COX17
+GER interactsWith YPT1
+GER interactsWith GDI1
+Mg2+ interactsWith SMC1
+AGS interactsWith SMC1
+AGS interactsWith SMC1
+RCP interactsWith ACC1
+RCP interactsWith ACC1
+RCP interactsWith ACC1
+1R7M_C pd SCEI
+1R7M_D pd SCEI
+PIH interactsWith General_Control_Protein_Gcn4
+PIH interactsWith General_Control_Protein_Gcn4
+1R9S_R interactsWith RPB2
+1R9S_R interactsWith RPO21
+1R9S_T pd RPO21
+1R9S_T pd RPB2
+UTP interactsWith RPO21
+UTP interactsWith RPB2
+1R9T_R interactsWith RPB2
+1R9T_R interactsWith RPO21
+1R9T_T pd RPB5
+1R9T_T pd RPO21
+1R9T_T pd RPB2
+1R9T_N pd RPO21
+1R9T_N pd RPB5
+ATP interactsWith RPB2
+ATP interactsWith RPO21
+ATP interactsWith RPO21
+ATP interactsWith RPB2
+GTP interactsWith RPO21
+GTP interactsWith RPB2
+UTP interactsWith RPB2
+UTP interactsWith RPO21
+CTP interactsWith RPB2
+CTP interactsWith RPO21
+APR interactsWith YMR087W
+Na+ interactsWith YMR087W
+ADP interactsWith YMR087W
+TAR interactsWith VMA5
+Cu1+ interactsWith Metallothionein
+Cu1+ interactsWith Metallothionein
+Cu1+ interactsWith Metallothionein
+Cu1+ interactsWith Metallothionein
+Cu1+ interactsWith Metallothionein
+Cu1+ interactsWith Metallothionein
+Cu1+ interactsWith Metallothionein
+Cu1+ interactsWith Metallothionein
+1TB interactsWith ILV2
+1TB interactsWith ILV2
+P23 interactsWith ILV2
+YF3 interactsWith ILV2
+YF3 interactsWith ILV2
+YF4 interactsWith ILV2
+YF4 interactsWith ILV2
+1CS interactsWith ILV2
+1CS interactsWith ILV2
+P25 interactsWith ILV2
+NSP interactsWith ILV2
+NSP interactsWith ILV2
+P22 interactsWith ILV2
+1MM interactsWith ILV2
+1MM interactsWith ILV2
+YF1 interactsWith ILV2
+YF1 interactsWith ILV2
+1MM interactsWith ILV2
+GTP interactsWith CSE1
+S1A interactsWith ACC1
+Guanine interactsWith YML079W
+Adenine interactsWith YML079W
+Citric_acid interactsWith YML079W
+Citric_acid interactsWith YML079W
+Ca2+ interactsWith BUB3
+Ca2+ interactsWith BUB3
+Ca2+ interactsWith PCF11
+1Y1W_T pd RPO21
+1Y1W_T pd RPB2
+1Y1W_N pd RPB2
+1Y77_P interactsWith RPO21
+1Y77_P interactsWith RPB2
+1Y77_T pd RPO21
+1Y77_T pd RPB2
+G2P interactsWith RPB2
+G2P interactsWith RPO21
+Zn2+ interactsWith DST1
+FAD interactsWith FMS1
+IMD interactsWith MYO3
+NAD+ interactsWith LPD1
+Mg2+ interactsWith RFC1
+Mg2+ interactsWith RFC4
+Mg2+ interactsWith RFC3
+Mg2+ interactsWith RFC2
+AGS interactsWith RFC1
+AGS interactsWith RFC4
+AGS interactsWith RFC4
+AGS interactsWith RFC3
+AGS interactsWith RFC3
+AGS interactsWith RFC2
+AGS interactsWith RFC5
+ADP interactsWith RFC5
+Zn2+ interactsWith KTI11
+FAD interactsWith FMS1
+GLB interactsWith GAL10
+NAD+ interactsWith GAL10
+UDP-D-Glucose interactsWith GAL10
+12-Mer_Peptide_From_Cytoskeleton_Assembly_Control_Protein_Sla1 pp LSB3
+SPM interactsWith FMS1
+SPM interactsWith FMS1
+SPM interactsWith FMS1
+heme interactsWith CCP1
+IP7 interactsWith NSR1
+IP7 interactsWith YGR130c
+IP7 interactsWith SRP40
+IP7 interactsWith NAB4
+Unknown interactsWith Spc34
+Unknown interactsWith Ask1
+Unknown interactsWith Dam1
+Unknown interactsWith Duo1
+Unknown interactsWith Spc19
+Unknown interactsWith Dad2
+Unknown interactsWith Dad1
+Unknown interactsWith Dad3
+Unknown interactsWith Dad4
+Zn2+ interactsWith 1ARD
+Zn2+ interactsWith 1ARE
+Zn2+ interactsWith 1ARF
+IMD interactsWith CCP1
+TML interactsWith CYC1
+DMI interactsWith CCP1
+K+ interactsWith CCP1
+K+ interactsWith CCP1
+Mn2+ interactsWith ENO1
+PAH interactsWith ENO1
+Mn2+ interactsWith ENO1
+FMN interactsWith CYB2
+Pyruvate interactsWith Cytochrome_B2,_Mitochondrial
+Zn2+ interactsWith 1PAA
+Zn2+ interactsWith PPR1
+Zn2+ interactsWith PPR1
+TML interactsWith CYC1
+Cu2+ interactsWith Copper-Zinc_Superoxide_Dismutase
+Zn2+ interactsWith Copper-Zinc_Superoxide_Dismutase
+N3T interactsWith TKL1
+N3T interactsWith TKL1
+Ca2+ interactsWith TKL1
+N1T interactsWith TKL1
+N1T interactsWith TKL1
+M6T interactsWith TKL1
+M6T interactsWith TKL1
+M6T interactsWith TKL1
+Mg2+ interactsWith 4TNA
+Mg2+ interactsWith 1TRA
+thiamin_diphosphate interactsWith TKL1
+thiamin_diphosphate interactsWith TKL1
+ADP interactsWith 1UKZ
+ADP interactsWith 1UKY
+A5MP interactsWith 1UKZ
+FK506 interactsWith 1YAT
+TML interactsWith CYC7
+TML interactsWith CYC7
+MO6 interactsWith 2TRA
+OTG interactsWith HXK2
+Phosphoglycolate interactsWith TPI1
+ATP interactsWith PGK1
+3PG interactsWith PGK1
+3PG interactsWith GPM1
+Zn2+ interactsWith ENO1
+MO5 interactsWith 4TRA
+MO4 interactsWith 4TRA
+MO6 interactsWith 1EHZ_A
+MO5 interactsWith 4TRA
+Ca2+ interactsWith ENO1
+Pyruvate interactsWith CYB2
+ATP interactsWith DPS1
+ATP interactsWith 1ASZ_R
+ATP interactsWith DPS1
+PAH interactsWith ENO1
+Phenylpyruvate interactsWith CYB2
+Phenylpyruvate interactsWith CYB2
+thiamin_diphosphate interactsWith PDC1
+thiamin_diphosphate interactsWith PDC1
+Mg2+ interactsWith PDC1
+AP5 interactsWith ADK1
+IMD interactsWith ADK1
+ATF interactsWith ADK1
+ATF interactsWith ADK1
+ATF interactsWith ADK1
+Cu1+ interactsWith 2JCW
+MAP interactsWith PGK1
+3PG interactsWith PGK1
+Zn2+ interactsWith 1NCS
+Zn2+ interactsWith 1ZFD
+Zn2+ interactsWith 1PYC
+Zn2+ interactsWith 1PYC
+HEC interactsWith CYC1
+E4P interactsWith TKL1
+E4P interactsWith TKL1
+PLP interactsWith GPH1
+Mn2+ interactsWith IPP1
+Mn2+ interactsWith IPP1
+Mn2+ interactsWith IPP1
+BZI interactsWith CCP1
+NAG interactsWith 1AC5
+NAG-(4-1)NAG interactsWith 1AC5
+DMI interactsWith CCP1
+HEC interactsWith CYC1
+Zn2+ interactsWith PUT3
+Zn2+ interactsWith PUT3
+25T interactsWith CCP1
+2AP interactsWith CCP1
+2EZ interactsWith CCP1
+IMD interactsWith CCP1
+1MZ interactsWith CCP1
+2MZ interactsWith CCP1
+aminothiazole interactsWith CCP1
+2MA interactsWith CCP1
+ANL interactsWith CCP1
+3AP interactsWith CCP1
+4AP interactsWith CCP1
+24T interactsWith CCP1
+NVI interactsWith CCP1
+IDM interactsWith CCP1
+MPI interactsWith CCP1
+TMT interactsWith CCP1
+TMZ interactsWith CCP1
+3MT interactsWith CCP1
+MOR-PHE-NLE-CHF-NME interactsWith PEP4
+MAN-(1-2)MAN-(1-3)MAN-(1-4)NAG-(1-4)NAG interactsWith PEP4
+NAG interactsWith Saccharopepsin
+Cu1+ interactsWith 1AQR
+Cu1+ interactsWith 1AQR
+Cu1+ interactsWith 1AQR
+Cu1+ interactsWith 1AQR
+Cu1+ interactsWith 1AQR
+Cu1+ interactsWith 1AQR
+Cu1+ interactsWith 1AQR
+Cu1+ interactsWith 1AQS
+Cu1+ interactsWith 1AQS
+Cu1+ interactsWith 1AQS
+Cu1+ interactsWith 1AQS
+Cu1+ interactsWith 1AQS
+Cu1+ interactsWith 1AQS
+Cu1+ interactsWith 1AQS
+M7G interactsWith CDC33
+BAR interactsWith ARO7
+Mg2+ interactsWith SCL1
+Mg2+ interactsWith PRE7
+Mg2+ interactsWith PRE7
+Mg2+ interactsWith PUP3
+Mg2+ interactsWith PRE3
+Mg2+ interactsWith PUP1
+Mg2+ interactsWith PRE2
+Mg2+ interactsWith PUP1
+Mg2+ interactsWith IPP1
+Mn2+ interactsWith CDC19
+K+ interactsWith CDC19
+Phosphoglycolate interactsWith CDC19
+B-D-Fructose-1,6-DP interactsWith CDC19
+Mg2+ interactsWith KAR3
+ADP interactsWith KAR3
+ADP interactsWith 1AM1
+ADP interactsWith 1AMW
+ATM interactsWith CDC8
+Zn2+ interactsWith ADR1
+Zn2+ interactsWith ADR1
+5'-TMP interactsWith CDC8
+Geldanamycin interactsWith HSP82
+Maleic_acid interactsWith AAT2
+Maleic_acid interactsWith AAT2
+PLP interactsWith AAT2
+PLP interactsWith AAT2
+Maleic_acid interactsWith AAT2
+FMN interactsWith OYE2
+FMN interactsWith OYE2
+MHM interactsWith CCP1
+CCH interactsWith CCP1
+MIM interactsWith Myristoyl-Coa:protein_N-Myristoyltransferase
+T5A interactsWith CDC8
+Acetyl-CoA interactsWith 1BOB
+Zn2+ interactsWith FCY1
+APR interactsWith EFT2
+LI5 interactsWith FSH1
+Mg2+ interactsWith CSE1
+TAD interactsWith EFT2
+Exotoxin_A pp EFT2
+Exotoxin_A pp EFT2
+Exotoxin_A pp EFT2
+Caspofungin interactsWith YHR085W
+Caspofungin interactsWith CCT5
+Caspofungin interactsWith CCT2
+Caspofungin interactsWith SMI1
+Caspofungin interactsWith SIT4
+Caspofungin interactsWith MNN10
+Caspofungin interactsWith FKS1
+Caspofungin interactsWith CHS7
+Caspofungin interactsWith CHS6
+Caspofungin interactsWith CHS5
+Caspofungin interactsWith CHS4
+Caspofungin interactsWith CHS3
+Caspofungin interactsWith RCY1
+Caspofungin interactsWith SLA1
+Caspofungin interactsWith VPS66
+Caspofungin interactsWith ZUO1
+Caspofungin interactsWith THP1
+Caspofungin interactsWith SWI6
+Caspofungin interactsWith SPT10
+Caspofungin interactsWith SNF2
+Caspofungin interactsWith RSM27
+Caspofungin interactsWith RRN6
+Caspofungin interactsWith RPB3
+Caspofungin interactsWith NPL3
+Caspofungin interactsWith CDC40
+Caspofungin interactsWith ARG82
+Caspofungin interactsWith ARD1
+Caspofungin interactsWith AFG3
+Caspofungin interactsWith SUR1
+Caspofungin interactsWith LEM3
+Caspofungin interactsWith RPL18B
+Caspofungin interactsWith YNL080C
+Caspofungin interactsWith CRZ1
+Caspofungin interactsWith TUS1
+Caspofungin interactsWith YLR338W
+Caspofungin interactsWith PGU1
+Caspofungin interactsWith RAV1
+Caspofungin interactsWith YJR024C
+Caspofungin interactsWith YIL110W
+Caspofungin interactsWith SMF2
+Caspofungin interactsWith NEM1
+Caspofungin interactsWith FKS2
+Caspofungin interactsWith SSK2
+Caspofungin interactsWith SLG1
+Caspofungin interactsWith YOR024W
+Caspofungin interactsWith YPL056C
+Caspofungin interactsWith MCT1
+Caspofungin interactsWith CKA2
+Caspofungin interactsWith SUR4
+Caspofungin interactsWith YGR283C
+Caspofungin interactsWith ERV14
+Caspofungin interactsWith FEN1
+Caspofungin interactsWith CWH43
+Caspofungin interactsWith YBR147W
+Caspofungin interactsWith YBR144C
+Caspofungin interactsWith CSG2
+Caspofungin interactsWith MCA1
+Caspofungin interactsWith YOR118W
+Caspofungin interactsWith HLR1
+Caspofungin interactsWith YDR479C
+Caspofungin interactsWith YDR326C
+Caspofungin interactsWith SPT20
+Caspofungin interactsWith SPC72
+Caspofungin interactsWith SNF7
+Caspofungin interactsWith SLT2
+Caspofungin interactsWith PPA1
+Caspofungin interactsWith GPH1
+Caspofungin interactsWith ERG6
+Caspofungin interactsWith CCR4
+Caspofungin interactsWith VMA21
+Caspofungin interactsWith SPC98
+Caspofungin interactsWith ILM1
+Caspofungin interactsWith GLY1
+Caspofungin interactsWith DBF4
+Caspofungin interactsWith STP22
+Caspofungin interactsWith TFP3
+Caspofungin interactsWith VMA2
+Caspofungin interactsWith DNF2
+Caspofungin interactsWith MRK1
+Caspofungin interactsWith YCR087C-A
+Caspofungin interactsWith SEC66
+Caspofungin interactsWith VID24
+Caspofungin interactsWith YAT1
+Caspofungin interactsWith VPH2
+Caspofungin interactsWith VMA22
+Caspofungin interactsWith VMA13
+Caspofungin interactsWith VMA10
+Caspofungin interactsWith VMA7
+Caspofungin interactsWith VMA5
+Caspofungin interactsWith VMA4
+Caspofungin interactsWith CUP5
+Peptide_Val-Ala-Asp pp Peptide:n-Glycanase
+(Ace)aapa(Mcm) pp Cyclophilin_A
+Zn2+ interactsWith Peptide:n-Glycanase
+SUC interactsWith Peptide:n-Glycanase
+SUC interactsWith Peptide:n-Glycanase
+SUC interactsWith Peptide:n-Glycanase
+protoporphyrin_disodium interactsWith Cytochrome_C_Peroxidase,_Mitochondrial
+ATP interactsWith SerineTHREONINE-Protein_Kinase_Gcn2
+Mg2+ interactsWith SerineTHREONINE-Protein_Kinase_Gcn2
+AMP-PNP interactsWith SerineTHREONINE-Protein_Kinase_Gcn2
+Sulfometuron_Methyl interactsWith ILV2
+Sulfometuron_Methyl interactsWith ILV2
+FMI interactsWith Cytochrome_C_Peroxidase,_Mitochondrial
+GNP interactsWith YPT1
+1RM1_E pd TOA1
+1RM1_E pd SPT15
+1RM1_D pd SPT15
+Zn2+ interactsWith HEM2
+Zn2+ interactsWith HEM2
+SHO interactsWith HEM2
+AMP-PNP interactsWith Galactokinase
+Cl- interactsWith Galactokinase
+Mg2+ interactsWith Galactokinase
+GLA interactsWith Galactokinase
+ERG interactsWith Kes1_Protein
+Cholesterol interactsWith Kes1_Protein
+HC3 interactsWith Kes1_Protein
+HC2 interactsWith Kes1_Protein
+7_Beta-_Hydroxycholesterol interactsWith Kes1_Protein
+Proteasome_Activator_Protein_Pa26 pp PRE10
+Proteasome_Activator_Protein_Pa26 pp PRE10
+Proteasome_Activator_Protein_Pa26 pp PRE5
+Proteasome_Activator_Protein_Pa26 pp PRE5
+Proteasome_Activator_Protein_Pa26 pp PUP2
+Proteasome_Activator_Protein_Pa26 pp PUP2
+Proteasome_Activator_Protein_Pa26 pp PRE6
+Proteasome_Activator_Protein_Pa26 pp PRE6
+Proteasome_Activator_Protein_Pa26 pp SCL1
+Proteasome_Activator_Protein_Pa26 pp SCL1
+Proteasome_Activator_Protein_Pa26 pp PRE9
+Proteasome_Activator_Protein_Pa26 pp PRE9
+Proteasome_Activator_Protein_Pa26 pp PRE9
+Proteasome_Activator_Protein_Pa26 pp PRE8
+Proteasome_Activator_Protein_Pa26 pp PRE8
+Spermine interactsWith 1TN2
+N-Acetyl-D-Glucosamine interactsWith PRC1
+N-Acetyl-D-Glucosamine interactsWith PRC1
+N-Acetyl-D-Glucosamine interactsWith PRC1
+HEM interactsWith 1YEA
+Spermine interactsWith 2TRA
+FMN-SO3 interactsWith CYB2
+HEM interactsWith CYC7
+HEM interactsWith CYC7
+SO1 interactsWith GPM1
+phosphoglycolohydroxamate interactsWith TPI1
+phosphoglycolohydroxamate interactsWith TPI1
+Phosphoglycolate interactsWith ENO1
+2PG interactsWith ENO1
+2PG interactsWith ENO1
+GMP interactsWith 1GKY
+HEM interactsWith CYB2
+NAG-(4-1)NAG interactsWith KRE2
+NAG-(4-1)NAG-(4-1)MAN-(3-1)MAN-(2-1)MAN-(3,6-1)MAN-(3-1)MAN-(6,6-1)MAN interactsWith KRE2
+H1L interactsWith Acetyl-Coa_Carboxylase
+H1L interactsWith Acetyl-Coa_Carboxylase
+H1L interactsWith Acetyl-Coa_Carboxylase
+D1L interactsWith Acetyl-Coa_Carboxylase
+D1L interactsWith Acetyl-Coa_Carboxylase
+N-Acetyl-D-Glucosamine interactsWith KEX2
+N-Acetyl-D-Glucosamine interactsWith KEX2
+CNA interactsWith Histone_H4_Peptide
+CNA interactsWith HST2
+ interactsWith PEP4
+MAN-(1-4)NAG-(1-4)NAG interactsWith PEP4
+N-Acetyl-D-Glucosamine interactsWith Saccharopepsin
+DDH interactsWith CCP1
+NHM interactsWith Myristoyl-Coa:protein_N-Myristoyltransferase
+HEM interactsWith CYC1
+HEM interactsWith CYC1
+HEM interactsWith CYC1
+HEM interactsWith CYC1
+HEM interactsWith CYC1
+HEM interactsWith CCP1
+HEM interactsWith CCP1
+HEM interactsWith CCP1
+HEM interactsWith CCP1
+ZNH interactsWith CCP1
+Peptide pp IRE1
+Zn2+ interactsWith RPB10
+Zn2+ interactsWith RPB3
+Mg2+ interactsWith RPO21
+Zn2+ interactsWith RPB2
+Zn2+ interactsWith RPO21
+Zn2+ interactsWith RPO21
+Zn2+ interactsWith RPO21
+Zn2+ interactsWith RPC10
+Zn2+ interactsWith RPB9
+Zn2+ interactsWith RPB9
+Zn2+ interactsWith RPB9
+Zn2+ interactsWith RPB9
+Zn2+ interactsWith RPB9
+Zn2+ interactsWith RPB9
+Mg2+ interactsWith ENO1
+Mg2+ interactsWith ENO1
+2PG interactsWith ENO1
+2PG interactsWith ENO1
+phosphoenolpyruvate interactsWith ENO1
+K interactsWith Emp46p
+K interactsWith Emp46p
+K interactsWith Emp46p
+Zn2 interactsWith Zinc-Responsive_Transcriptional_Regulator_Zap1
+Zn2 interactsWith Zinc-Responsive_Transcriptional_Regulator_Zap1
+Na interactsWith General_Control_Protein_Gcn4
+2PG interactsWith Enolase_1
+Mg2 interactsWith Enolase_1
+K interactsWith Enolase_1
+K interactsWith Enolase_1
+GDP interactsWith YPT1
+Mg2+ interactsWith YPT1
+Mg2+ interactsWith YPT1
+PMM interactsWith Folic_Acid_Synthesis_Protein_Fol1
+PMM interactsWith Folic_Acid_Synthesis_Protein_Fol1
+FMN interactsWith Nadph-Cytochrome_P450_Reductase
+NADP interactsWith Nadph-Cytochrome_P450_Reductase
+FMN interactsWith Nadph-Cytochrome_P450_Reductase
+FMN interactsWith Nadph-Cytochrome_P450_Reductase
+FAD interactsWith Nadph-Cytochrome_P450_Reductase
+TTH interactsWith Secretory_Pathway_Gdp_Dissociation_Inhibitor
+TTH interactsWith Secretory_Pathway_Gdp_Dissociation_Inhibitor
+Ni2 interactsWith 3-Hydroxyanthranilate_3,4-Dioxygenase
+Ni2 interactsWith 3-Hydroxyanthranilate_3,4-Dioxygenase
+Mg2 interactsWith BTS1
+Cu2 interactsWith Sco1_Protein
+Cu2 interactsWith Sco1_Protein
+Cdc4 pp Cyclin_E1
+Ub interactsWith Ubistatin_A
+Ub interactsWith Ubistatin_B
+RNT1 interactsWith 1T4L_A
+60s_Ribosomal_Protein_L30 pp Maltose-Binding_Periplasmic_Protein
+Smc1/Scc1_dimer interactsWith ATP
+Unknown interactsWith subtelomeric_DNA
+Unknown interactsWith subtelomeric_DNA
+Ypt35 interactsWith PtdIns3P
+1IL2_C interactsWith Aspartyl-Trna_Synthetase
+1IL2_D interactsWith Aspartyl-Trna_Synthetase
+Cell_Division_Control_Protein_Kar1 pp Caltractin
+Histone_H3 pp Hat_A1
+Histone_H3 pp Hat_A1
+Nucleoporin_Nsp1 pp KPNB1
+YBR028C interactsWith PI[3,4,5]P3_ammonium
+YBR057C interactsWith PI[3,4,5]P3_ammonium
+YBR059C interactsWith PI[3,4,5]P3_ammonium
+YBR079C interactsWith PI[3,4,5]P3_ammonium
+YBR084W interactsWith PI[3,4,5]P3_ammonium
+YBR213W interactsWith PI[3,4,5]P3_ammonium
+YCL024W interactsWith PI[3,4,5]P3_ammonium
+YCL026C-A interactsWith PI[3,4,5]P3_ammonium
+YCR025C interactsWith PI[3,4,5]P3_ammonium
+YCR077C interactsWith PI[3,4,5]P3_ammonium
+YDL028C interactsWith PI[3,4,5]P3_ammonium
+YDL141W interactsWith PI[3,4,5]P3_ammonium
+YDL229W interactsWith PI[3,4,5]P3_ammonium
+YDR070C interactsWith PI[3,4,5]P3_ammonium
+YDR106W interactsWith PI[3,4,5]P3_ammonium
+YDR149C interactsWith PI[3,4,5]P3_ammonium
+YDR231C interactsWith PI[3,4,5]P3_ammonium
+YDR283C interactsWith PI[3,4,5]P3_ammonium
+YDR288W interactsWith PI[3,4,5]P3_ammonium
+YDR477W interactsWith PI[3,4,5]P3_ammonium
+YDR523C interactsWith PI[3,4,5]P3_ammonium
+YEL048C interactsWith PI[3,4,5]P3_ammonium
+YER014W interactsWith PI[3,4,5]P3_ammonium
+YER059W interactsWith PI[3,4,5]P3_ammonium
+YER142C interactsWith PI[3,4,5]P3_ammonium
+YER152C interactsWith PI[3,4,5]P3_ammonium
+YFL029C interactsWith PI[3,4,5]P3_ammonium
+YFL033C interactsWith PI[3,4,5]P3_ammonium
+YFL068W interactsWith PI[3,4,5]P3_ammonium
+YFR014C interactsWith PI[3,4,5]P3_ammonium
+YFR053C interactsWith PI[3,4,5]P3_ammonium
+YGL059W interactsWith PI[3,4,5]P3_ammonium
+YGL179C interactsWith PI[3,4,5]P3_ammonium
+YGL180W interactsWith PI[3,4,5]P3_ammonium
+YGR052W interactsWith PI[3,4,5]P3_ammonium
+YGR101W interactsWith PI[3,4,5]P3_ammonium
+YGR133W interactsWith PI[3,4,5]P3_ammonium
+YGR242W interactsWith PI[3,4,5]P3_ammonium
+YGR262C interactsWith PI[3,4,5]P3_ammonium
+YHR030C interactsWith PI[3,4,5]P3_ammonium
+YHR174W interactsWith PI[3,4,5]P3_ammonium
+YIL099W interactsWith PI[3,4,5]P3_ammonium
+YIR034C interactsWith PI[3,4,5]P3_ammonium
+YIR041W interactsWith PI[3,4,5]P3_ammonium
+YJL185C interactsWith PI[3,4,5]P3_ammonium
+YJR006W interactsWith PI[3,4,5]P3_ammonium
+YJR058C interactsWith PI[3,4,5]P3_ammonium
+YJR080C interactsWith PI[3,4,5]P3_ammonium
+YLL008W interactsWith PI[3,4,5]P3_ammonium
+YLL018C interactsWith PI[3,4,5]P3_ammonium
+YLL023C interactsWith PI[3,4,5]P3_ammonium
+YLR020C interactsWith PI[3,4,5]P3_ammonium
+YLR022C interactsWith PI[3,4,5]P3_ammonium
+YML058C-A interactsWith PI[3,4,5]P3_ammonium
+YMR172C-A interactsWith PI[3,4,5]P3_ammonium
+YMR238W interactsWith PI[3,4,5]P3_ammonium
+YMR255W interactsWith PI[3,4,5]P3_ammonium
+YNL300W interactsWith PI[3,4,5]P3_ammonium
+YNR069C interactsWith PI[3,4,5]P3_ammonium
+YOL053W interactsWith PI[3,4,5]P3_ammonium
+YOL056W interactsWith PI[3,4,5]P3_ammonium
+YOL097C interactsWith PI[3,4,5]P3_ammonium
+YOL117W interactsWith PI[3,4,5]P3_ammonium
+YPL150W interactsWith PI[3,4,5]P3_ammonium
+YPL280W interactsWith PI[3,4,5]P3_ammonium
+YAL029C interactsWith PI(3,4)P2_ammonium
+YBL052C interactsWith PI(3,4)P2_ammonium
+YBL107W-A interactsWith PI(3,4)P2_ammonium
+YBR025C interactsWith PI(3,4)P2_ammonium
+YBR028C interactsWith PI(3,4)P2_ammonium
+YBR057C interactsWith PI(3,4)P2_ammonium
+YBR059C interactsWith PI(3,4)P2_ammonium
+YBR077C interactsWith PI(3,4)P2_ammonium
+YBR079C interactsWith PI(3,4)P2_ammonium
+YBR129C interactsWith PI(3,4)P2_ammonium
+YBR213W interactsWith PI(3,4)P2_ammonium
+YBR226C interactsWith PI(3,4)P2_ammonium
+YCL024W interactsWith PI(3,4)P2_ammonium
+YCL075W interactsWith PI(3,4)P2_ammonium
+YCR025C interactsWith PI(3,4)P2_ammonium
+YCR097W interactsWith PI(3,4)P2_ammonium
+YDL028C interactsWith PI(3,4)P2_ammonium
+YDL229W interactsWith PI(3,4)P2_ammonium
+YDL244W interactsWith PI(3,4)P2_ammonium
+YDR070C interactsWith PI(3,4)P2_ammonium
+YDR106W interactsWith PI(3,4)P2_ammonium
+YDR167W interactsWith PI(3,4)P2_ammonium
+YDR231C interactsWith PI(3,4)P2_ammonium
+YDR283C interactsWith PI(3,4)P2_ammonium
+YDR288W interactsWith PI(3,4)P2_ammonium
+YDR477W interactsWith PI(3,4)P2_ammonium
+YDR523C interactsWith PI(3,4)P2_ammonium
+YER020W interactsWith PI(3,4)P2_ammonium
+YER059W interactsWith PI(3,4)P2_ammonium
+YER152C interactsWith PI(3,4)P2_ammonium
+YER169W interactsWith PI(3,4)P2_ammonium
+YFL029C interactsWith PI(3,4)P2_ammonium
+YFL033C interactsWith PI(3,4)P2_ammonium
+YFL068W interactsWith PI(3,4)P2_ammonium
+YFR014C interactsWith PI(3,4)P2_ammonium
+YFR053C interactsWith PI(3,4)P2_ammonium
+YGL059W interactsWith PI(3,4)P2_ammonium
+YGL179C interactsWith PI(3,4)P2_ammonium
+YGL180W interactsWith PI(3,4)P2_ammonium
+YGR040W interactsWith PI(3,4)P2_ammonium
+YGR052W interactsWith PI(3,4)P2_ammonium
+YGR101W interactsWith PI(3,4)P2_ammonium
+YGR262C interactsWith PI(3,4)P2_ammonium
+YHR128W interactsWith PI(3,4)P2_ammonium
+YHR174W interactsWith PI(3,4)P2_ammonium
+YIL003W interactsWith PI(3,4)P2_ammonium
+YIL099W interactsWith PI(3,4)P2_ammonium
+YIR034C interactsWith PI(3,4)P2_ammonium
+YIR041W interactsWith PI(3,4)P2_ammonium
+YJL173C interactsWith PI(3,4)P2_ammonium
+YJL185C interactsWith PI(3,4)P2_ammonium
+YJR058C interactsWith PI(3,4)P2_ammonium
+YKL104C interactsWith PI(3,4)P2_ammonium
+YLL008W interactsWith PI(3,4)P2_ammonium
+YLL018C interactsWith PI(3,4)P2_ammonium
+YLL023C interactsWith PI(3,4)P2_ammonium
+YLR020C interactsWith PI(3,4)P2_ammonium
+YLR022C interactsWith PI(3,4)P2_ammonium
+YLR139C interactsWith PI(3,4)P2_ammonium
+YML058C-A interactsWith PI(3,4)P2_ammonium
+YMR148W interactsWith PI(3,4)P2_ammonium
+YMR172C-A interactsWith PI(3,4)P2_ammonium
+YMR200W interactsWith PI(3,4)P2_ammonium
+YMR229C interactsWith PI(3,4)P2_ammonium
+YMR238W interactsWith PI(3,4)P2_ammonium
+YOL020W interactsWith PI(3,4)P2_ammonium
+YOL056W interactsWith PI(3,4)P2_ammonium
+YOL073C interactsWith PI(3,4)P2_ammonium
+YOL097C interactsWith PI(3,4)P2_ammonium
+YOL117W interactsWith PI(3,4)P2_ammonium
+YPR036W interactsWith PI(3,4)P2_ammonium
+YBL107C interactsWith PI[3]P_ammonium
+YBR057C interactsWith PI[3]P_ammonium
+YBR059C interactsWith PI[3]P_ammonium
+YBR180W interactsWith PI[3]P_ammonium
+YBR213W interactsWith PI[3]P_ammonium
+YBR249C interactsWith PI[3]P_ammonium
+YCL008C interactsWith PI[3]P_ammonium
+YCL024W interactsWith PI[3]P_ammonium
+YCR025C interactsWith PI[3]P_ammonium
+YDL028C interactsWith PI[3]P_ammonium
+YDL229W interactsWith PI[3]P_ammonium
+YDL237W interactsWith PI[3]P_ammonium
+YDR106W interactsWith PI[3]P_ammonium
+YDR231C interactsWith PI[3]P_ammonium
+YDR283C interactsWith PI[3]P_ammonium
+YDR347W interactsWith PI[3]P_ammonium
+YDR348C interactsWith PI[3]P_ammonium
+YDR460W interactsWith PI[3]P_ammonium
+YDR477W interactsWith PI[3]P_ammonium
+YDR522C interactsWith PI[3]P_ammonium
+YDR523C interactsWith PI[3]P_ammonium
+YER059W interactsWith PI[3]P_ammonium
+YER152C interactsWith PI[3]P_ammonium
+YFL029C interactsWith PI[3]P_ammonium
+YFL033C interactsWith PI[3]P_ammonium
+YFL068W interactsWith PI[3]P_ammonium
+YFR053C interactsWith PI[3]P_ammonium
+YGL059W interactsWith PI[3]P_ammonium
+YGL179C interactsWith PI[3]P_ammonium
+YGL180W interactsWith PI[3]P_ammonium
+YGR029W interactsWith PI[3]P_ammonium
+YGR101W interactsWith PI[3]P_ammonium
+YGR262C interactsWith PI[3]P_ammonium
+YHR128W interactsWith PI[3]P_ammonium
+YHR174W interactsWith PI[3]P_ammonium
+YJL115W interactsWith PI[3]P_ammonium
+YJR058C interactsWith PI[3]P_ammonium
+YKL121W interactsWith PI[3]P_ammonium
+YLL008W interactsWith PI[3]P_ammonium
+YLL023C interactsWith PI[3]P_ammonium
+YLR022C interactsWith PI[3]P_ammonium
+YMR148W interactsWith PI[3]P_ammonium
+YMR238W interactsWith PI[3]P_ammonium
+YMR250W interactsWith PI[3]P_ammonium
+YOL020W interactsWith PI[3]P_ammonium
+YOL056W interactsWith PI[3]P_ammonium
+YOL058W interactsWith PI[3]P_ammonium
+YOL073C interactsWith PI[3]P_ammonium
+YOL097C interactsWith PI[3]P_ammonium
+YOL119C interactsWith PI[3]P_ammonium
+YPL150W interactsWith PI[3]P_ammonium
+YBL030C interactsWith PI[4,5]P2_ammonium
+YBL099W interactsWith PI[4,5]P2_ammonium
+YBL103C interactsWith PI[4,5]P2_ammonium
+YBR057C interactsWith PI[4,5]P2_ammonium
+YBR059C interactsWith PI[4,5]P2_ammonium
+YBR213W interactsWith PI[4,5]P2_ammonium
+YBR226C interactsWith PI[4,5]P2_ammonium
+YCL024W interactsWith PI[4,5]P2_ammonium
+YCL075W interactsWith PI[4,5]P2_ammonium
+YCR025C interactsWith PI[4,5]P2_ammonium
+YCR077C interactsWith PI[4,5]P2_ammonium
+YCR097W interactsWith PI[4,5]P2_ammonium
+YDL028C interactsWith PI[4,5]P2_ammonium
+YDL229W interactsWith PI[4,5]P2_ammonium
+YDL244W interactsWith PI[4,5]P2_ammonium
+YDR067C interactsWith PI[4,5]P2_ammonium
+YDR070C interactsWith PI[4,5]P2_ammonium
+YDR106W interactsWith PI[4,5]P2_ammonium
+YDR167W interactsWith PI[4,5]P2_ammonium
+YDR231C interactsWith PI[4,5]P2_ammonium
+YDR283C interactsWith PI[4,5]P2_ammonium
+YDR395W interactsWith PI[4,5]P2_ammonium
+YDR477W interactsWith PI[4,5]P2_ammonium
+YDR523C interactsWith PI[4,5]P2_ammonium
+YEL064C interactsWith PI[4,5]P2_ammonium
+YER014W interactsWith PI[4,5]P2_ammonium
+YER059W interactsWith PI[4,5]P2_ammonium
+YER152C interactsWith PI[4,5]P2_ammonium
+YFL029C interactsWith PI[4,5]P2_ammonium
+YFL033C interactsWith PI[4,5]P2_ammonium
+YFL068W interactsWith PI[4,5]P2_ammonium
+YFR014C interactsWith PI[4,5]P2_ammonium
+YFR053C interactsWith PI[4,5]P2_ammonium
+YGL059W interactsWith PI[4,5]P2_ammonium
+YGL165C interactsWith PI[4,5]P2_ammonium
+YGL179C interactsWith PI[4,5]P2_ammonium
+YGL180W interactsWith PI[4,5]P2_ammonium
+YGR052W interactsWith PI[4,5]P2_ammonium
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+RPL13B interactsWith Caffeine
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+ARV1 interactsWith Fluconazole
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+EAP1 interactsWith Hydroxyurea
+ERG28 interactsWith Hydroxyurea
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+MOT2 interactsWith Rapamycin
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+MSO1 interactsWith Rapamycin
+MSS11 interactsWith Rapamycin
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+RPS16A interactsWith Rapamycin
+RPS17A interactsWith Rapamycin
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+VPS36 interactsWith Rapamycin
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+YOR322C interactsWith Rapamycin
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+GAL11 interactsWith Sulfometuron_Methyl
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+GCN2 interactsWith Sulfometuron_Methyl
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+GCN3 interactsWith Sulfometuron_Methyl
+GCN4 interactsWith Sulfometuron_Methyl
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+HOC1 interactsWith Sulfometuron_Methyl
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+MOG1 interactsWith Sulfometuron_Methyl
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+RPL20B interactsWith Sulfometuron_Methyl
+RPL34B interactsWith Sulfometuron_Methyl
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+RPL8B interactsWith Sulfometuron_Methyl
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+SNF5 interactsWith Sulfometuron_Methyl
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+RPL13B interactsWith Tunicamycin_Mix
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+VAM7 interactsWith Tunicamycin_Mix
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+VMA22 interactsWith Tunicamycin_Mix
+VMA4 interactsWith Tunicamycin_Mix
+VMA5 interactsWith Tunicamycin_Mix
+VMA6 interactsWith Tunicamycin_Mix
+VMA7 interactsWith Tunicamycin_Mix
+VMA8 interactsWith Tunicamycin_Mix
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+VPS25 interactsWith Tunicamycin_Mix
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+VTS1 interactsWith Tunicamycin_Mix
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+YGL168W interactsWith Tunicamycin_Mix
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+YLR047C interactsWith Tunicamycin_Mix
+YLR218C interactsWith Tunicamycin_Mix
+YLR426W interactsWith Tunicamycin_Mix
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+YMR007W interactsWith Tunicamycin_Mix
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+YNL081C interactsWith Tunicamycin_Mix
+YOL093W interactsWith Tunicamycin_Mix
+YOR199W interactsWith Tunicamycin_Mix
+YOR246C interactsWith Tunicamycin_Mix
+YPR170C interactsWith Tunicamycin_Mix
+YPT11 interactsWith Tunicamycin_Mix
+CDC10 interactsWith Rapamycin
+CLB5 interactsWith Rapamycin
+KRE6 interactsWith Rapamycin
+NPL3 interactsWith Rapamycin
+PRE9 interactsWith Rapamycin
+RPS27B interactsWith Rapamycin
+SIC1 interactsWith Rapamycin
+SRB2 interactsWith Rapamycin
+SWI6 interactsWith Rapamycin
+URE2 interactsWith Rapamycin
+TFP3 interactsWith Rapamycin
+YDR348C interactsWith Rapamycin
+RLM1 interactsWith Rapamycin
+YPK1 interactsWith Rapamycin
+BEM1 interactsWith Rapamycin
+CIK1 interactsWith Rapamycin
+NBP2 interactsWith Rapamycin
+RPL12B interactsWith Rapamycin
+STP22 interactsWith Rapamycin
+PAC10 interactsWith Rapamycin
+SSD1 interactsWith Rapamycin
+SIS2 interactsWith Rapamycin
+Nrk1 interactsWith Nicotinamide_Riboside
+Nrk1 interactsWith Tiazofurin
+Ras2 interactsWith GDP
+Ras2 interactsWith GTP
+Opi1 interactsWith PA
+Pol12 interactsWith Unknown
+Pol1 interactsWith Unknown
+Pri1 interactsWith Unknown
+Pri2 interactsWith Unknown
+Cdc73 interactsWith Unknown
+Ire1 interactsWith ADP
+HMRA2 pd 1APL_A
+HMRA2 pd 1APL_B
+HMRA2 pd 1APL_B
+HMRA2 pd 1APL_A
+1D66_A pd 1D66_E
+1D66_A pd 1D66_D
+1D66_B pd 1D66_D
+1D66_B pd 1D66_E
+Yeast_Alpha-Glucosidase pp Mhc_Class_I_H-2kb_Heavy_Chain
+RAP1 pd 1IGN_C
+RAP1 pd 1IGN_D
+1TTT_D interactsWith tufA
+1TTT_D interactsWith tufA
+1TTT_E interactsWith tufA
+1TTT_E interactsWith tufA
+1TTT_F interactsWith tufA
+PUT3 pd 1ZME_B
+PUT3 pd 1ZME_B
+SPT15 pp Transcription_Initiation_Factor_Iid_230k_Chain
+486D_C interactsWith 486D_A
+Histone_H3 pp Tgcn5_Histone_Acetyl_Transferase
+Fxfg_Nucleoporin_Repeats pp KPNB1
+PBS2 interactsWith DBR1
+PBS2 interactsWith GPA2
+IPK1 interactsWith DBR1
+IPK1 interactsWith GPA2
+IRA2 interactsWith DBR1
+IRA2 interactsWith GPA2
+HOG1 interactsWith GPA2
+HSL1 interactsWith DBR1
+HSL1 interactsWith GPA2
+SFL1 interactsWith DBR1
+YAK1 interactsWith CDC42
+FLO10 interactsWith CDC42
+MKS1 interactsWith CDC42
+MUC1 interactsWith CDC42
+TEC1 interactsWith CDC42
+WHI3 interactsWith CDC42
+SNF1 interactsWith CDC42
+SSA4 interactsWith CDC42
+PCL1 interactsWith CDC42
+YGR149W interactsWith CDC42
+DIG2 interactsWith CDC42
+RIM8 interactsWith CDC42
+TPK1 interactsWith CDC42
+YLR414C interactsWith CDC42
+PAM1 interactsWith CDC42
+IPK1 interactsWith CDC42
+CLN2 interactsWith CDC42
+RAS2 interactsWith CDC42
+PBS2 interactsWith CDC42
+SUT1 interactsWith CDC42
+SNF4 interactsWith CDC42
+MSN1 interactsWith CDC42
+YGR045C interactsWith CDC42
+RPS0A interactsWith CDC42
+URE2 interactsWith CDC42
+DFG5 interactsWith CDC42
+SIP4 interactsWith CDC42
+YOL155C interactsWith CDC42
+EGT2 interactsWith CDC42
+IME2 interactsWith CDC42
+RGS2 interactsWith CDC42
+SRL1 interactsWith CDC42
+PDE1 interactsWith CDC42
+TPK3 interactsWith CDC42
+SOK2 interactsWith CDC42
+LIN1 interactsWith CDC42
+FKH2 interactsWith CDC42
+MGA1 interactsWith CDC42
+MEP2 interactsWith CDC42
+FMP45 interactsWith CDC42
+YOR248W interactsWith CDC42
+GPR1 interactsWith CDC42
+KSS1 interactsWith CDC42
+CLN1 interactsWith CDC42
+MID2 interactsWith CDC42
+CTS1 interactsWith CDC42
+DSE2 interactsWith CDC42
+FKH1 interactsWith CDC42
+CLN3 interactsWith CDC42
+RCS1 interactsWith CDC42
+ACE2 interactsWith CDC42
+CLA4 interactsWith CDC42
+SNO1 interactsWith CDC42
+CLB2 interactsWith CDC42
+MSN5 interactsWith CDC42
+BMH1 interactsWith CDC42
+AGA1 interactsWith CDC42
+PDE2 interactsWith CDC42
+ENT1 interactsWith CDC42
+ISW1 interactsWith CDC42
+DFG16 interactsWith CDC42
+MSS11 interactsWith CDC42
+HMS1 interactsWith CDC42
+RIM9 interactsWith CDC42
+BUD8 interactsWith CDC42
+KTR2 interactsWith CDC42
+TPK2 interactsWith CDC42
+MEP1 interactsWith CDC42
+HOG1 interactsWith CDC42
+SFP1 interactsWith CDC42
+RSC1 interactsWith CDC42
+VPS25 interactsWith CDC42
+YOR225W interactsWith CDC42
+YEL033W interactsWith CDC42
+YPS1 interactsWith CDC42
+YJL142C interactsWith CDC42
+GLN3 interactsWith STE11
+YAK1 interactsWith STE11
+FLO10 interactsWith STE11
+MKS1 interactsWith STE11
+PRY2 interactsWith STE11
+SPH1 interactsWith STE11
+TEC1 interactsWith STE11
+CLB1 interactsWith STE11
+WHI3 interactsWith STE11
+SNF1 interactsWith STE11
+SSA4 interactsWith STE11
+PCL1 interactsWith STE11
+YGR149W interactsWith STE11
+DIG2 interactsWith STE11
+TPK1 interactsWith STE11
+YLR414C interactsWith STE11
+PAM1 interactsWith STE11
+CAR2 interactsWith STE11
+YJL017W interactsWith STE11
+BUD4 interactsWith STE11
+RAS2 interactsWith STE11
+PBS2 interactsWith STE11
+SUT1 interactsWith STE11
+YAP1 interactsWith STE11
+MSN1 interactsWith STE11
+YGR045C interactsWith STE11
+DFG5 interactsWith STE11
+YOL155C interactsWith STE11
+PDE1 interactsWith STE11
+TPK3 interactsWith STE11
+SOK2 interactsWith STE11
+LIN1 interactsWith STE11
+FKH2 interactsWith STE11
+MGA1 interactsWith STE11
+MEP2 interactsWith STE11
+FMP45 interactsWith STE11
+YOR248W interactsWith STE11
+GPR1 interactsWith STE11
+CLN1 interactsWith STE11
+MID2 interactsWith STE11
+DSE2 interactsWith STE11
+RCS1 interactsWith STE11
+PRY3 interactsWith STE11
+MSN5 interactsWith STE11
+AGA1 interactsWith STE11
+ISW1 interactsWith STE11
+MSS11 interactsWith STE11
+DIA2 interactsWith STE11
+DIA3 interactsWith STE11
+BUD8 interactsWith STE11
+TPK2 interactsWith STE11
+MEP1 interactsWith STE11
+HOG1 interactsWith STE11
+SFP1 interactsWith STE11
+RSC1 interactsWith STE11
+VPS25 interactsWith STE11
+YEL033W interactsWith STE11
+AKR1 interactsWith STE11
+YJL142C interactsWith STE11
+Nam8 interactsWith Unknown
+yCD interactsWith Cytosine
+Ssa1 interactsWith ATP
+Vam7 interactsWith Unknown
+POA1 interactsWith ADP-ribose
+Adh2 interactsWith EtOH
+Adh3 interactsWith Acetaldehyde
+Adh1 interactsWith Acetaldehyde
+DIPP interactsWith IP7
+ORC interactsWith ATP
+Orc4 interactsWith ATP
+Orc5 interactsWith ATP
+Orc1 interactsWith ATP
+YPng1 interactsWith Biotin-VAD-fmk
+Hsk3 interactsWith Unknown
+PHO36 pp Osmotin
+Ceramide_synthase interactsWith Sphinganine
+Ceramide_synthase interactsWith Sphinganine
+Ceramide_synthase interactsWith Sphinganine
+Ssc1 interactsWith ATP
+ARN1 interactsWith FC
+Ssb1 interactsWith ATP
+Ssb1 interactsWith ATP
+Ssz1 interactsWith ATP
+Kar3 interactsWith ATP
+Kar3Cik1 interactsWith ATP
+Sar1 interactsWith GTP
+RSA1 interactsWith UV
+YBL036C interactsWith UV
+YAR031W interactsWith UV
+YAP1 interactsWith t-BuOOH
+SKN7 interactsWith t-BuOOH
+HFI1 interactsWith t-BuOOH
+VPS33 interactsWith t-BuOOH
+YDL009C interactsWith t-BuOOH
+YER044C interactsWith t-BuOOH
+TOP1 interactsWith t-BuOOH
+VMA22 interactsWith t-BuOOH
+VPS16 interactsWith t-BuOOH
+YLR109W interactsWith t-BuOOH
+YEL045C interactsWith t-BuOOH
+YBR260C interactsWith UV
+CWH36 interactsWith UV
+MTF2 interactsWith UV
+SNR17B interactsWith UV
+MSE1 interactsWith UV
+YNL296W interactsWith UV
+YLR324W interactsWith UV
+YLR190W interactsWith UV
+PEP3 interactsWith UV
+SAC1 interactsWith UV
+10/1/1999 interactsWith UV
+VPH2 interactsWith UV
+YGR001C interactsWith UV
+PEA2 interactsWith UV
+YDR512C interactsWith UV
+NUP42 interactsWith UV
+HSP42 interactsWith UV
+SPT7 interactsWith t-BuOOH
+VMA4 interactsWith t-BuOOH
+YKL118W interactsWith t-BuOOH
+AAT2 interactsWith t-BuOOH
+SNF7 interactsWith t-BuOOH
+YKR027W interactsWith t-BuOOH
+SAC1 interactsWith t-BuOOH
+HYR1 interactsWith t-BuOOH
+VPS3 interactsWith t-BuOOH
+RVS167 interactsWith t-BuOOH
+PMP1 interactsWith t-BuOOH
+STP22 interactsWith t-BuOOH
+WHI2 interactsWith t-BuOOH
+YNL323W interactsWith t-BuOOH
+KEX2 interactsWith t-BuOOH
+PEP3 interactsWith t-BuOOH
+CHC1 interactsWith t-BuOOH
+YLR062C interactsWith t-BuOOH
+PHO85 interactsWith t-BuOOH
+YPL059W interactsWith t-BuOOH
+VPS45 interactsWith t-BuOOH
+YPR099C interactsWith t-BuOOH
+VPH1 interactsWith t-BuOOH
+FMC1 interactsWith t-BuOOH
+PPA1 interactsWith t-BuOOH
+VMA8 interactsWith t-BuOOH
+YDR482C interactsWith t-BuOOH
+VPS8 interactsWith t-BuOOH
+BEM4 interactsWith t-BuOOH
+ERG3 interactsWith t-BuOOH
+SNF6 interactsWith t-BuOOH
+CUP5 interactsWith t-BuOOH
+YBR101C interactsWith t-BuOOH
+POS5 interactsWith t-BuOOH
+GLY1 interactsWith t-BuOOH
+COX6 interactsWith UV
+ARP5 interactsWith UV
+POR1 interactsWith UV
+CIK1 interactsWith UV
+ERG6 interactsWith UV
+RIC1 interactsWith UV
+MRT4 interactsWith UV
+SPT10 interactsWith UV
+YHR168W interactsWith UV
+KEL1 interactsWith UV
+REC104 interactsWith UV
+YHR142W interactsWith UV
+YHR138C interactsWith UV
+SNF6 interactsWith UV
+YGR223C interactsWith UV
+MSK1 interactsWith UV
+YNL206C interactsWith UV
+SNT309 interactsWith UV
+YHL023C interactsWith UV
+YGR272C interactsWith UV
+COX18 interactsWith UV
+ARC1 interactsWith UV
+RPB9 interactsWith UV
+RNR1 interactsWith UV
+YDR532C interactsWith UV
+YDR417C interactsWith UV
+MSS116 interactsWith UV
+RAD57 interactsWith UV
+YBR266C interactsWith UV
+FZO1 interactsWith UV
+YPR131C interactsWith UV
+CTR1 interactsWith UV
+YGL218W interactsWith UV
+SPS1 interactsWith UV
+YDR496C interactsWith UV
+YMR206W interactsWith UV
+SGS1 interactsWith UV
+CTK3 interactsWith UV
+YML081W interactsWith UV
+YJR120W interactsWith UV
+GRR1 interactsWith UV
+YJL184W interactsWith UV
+YJL027C interactsWith UV
+YHL021C interactsWith UV
+RPS0A interactsWith UV
+YGL232W interactsWith UV
+QCR6 interactsWith UV
+NRP1 interactsWith UV
+YCR024C interactsWith UV
+MRPL44 interactsWith UV
+LAT1 interactsWith UV
+SKM1 interactsWith UV
+SAC2 interactsWith UV
+RPL12B interactsWith UV
+ATP17 interactsWith UV
+MSN5 interactsWith UV
+PEP7 interactsWith UV
+CPH1 interactsWith UV
+YDL223C interactsWith UV
+RPL35B interactsWith UV
+COX9 interactsWith UV
+YDL045W-A interactsWith UV
+YBR246W interactsWith UV
+YBR231C interactsWith UV
+YBR194W interactsWith UV
+YBR030W interactsWith UV
+OSH1 interactsWith UV
+YBR269C interactsWith t-BuOOH
+YIL028W interactsWith t-BuOOH
+YPL101W interactsWith t-BuOOH
+YOR306C interactsWith t-BuOOH
+YOL163W interactsWith t-BuOOH
+PHO80 interactsWith t-BuOOH
+YNL294C interactsWith t-BuOOH
+CYB5 interactsWith t-BuOOH
+END3 interactsWith t-BuOOH
+HDF1 interactsWith t-BuOOH
+DSK2 interactsWith t-BuOOH
+YMR237W interactsWith t-BuOOH
+SCJ1 interactsWith t-BuOOH
+SIP18 interactsWith t-BuOOH
+YMR099C interactsWith t-BuOOH
+STB4 interactsWith t-BuOOH
+BEM3 interactsWith t-BuOOH
+YPL123C interactsWith t-BuOOH
+YPL250C interactsWith t-BuOOH
+PDR13 interactsWith t-BuOOH
+YHL013C interactsWith t-BuOOH
+OCH1 interactsWith t-BuOOH
+BST1 interactsWith t-BuOOH
+RUB1 interactsWith t-BuOOH
+SAC6 interactsWith t-BuOOH
+SIT4 interactsWith t-BuOOH
+RPN4 interactsWith t-BuOOH
+TUP1 interactsWith t-BuOOH
+YCR061W interactsWith t-BuOOH
+YCR026C interactsWith t-BuOOH
+YBR246W interactsWith t-BuOOH
+VPS15 interactsWith t-BuOOH
+RTG3 interactsWith t-BuOOH
+YMR007W interactsWith t-BuOOH
+PLB2 interactsWith t-BuOOH
+PPZ1 interactsWith t-BuOOH
+WSC4 interactsWith t-BuOOH
+RIM101 interactsWith t-BuOOH
+YHL023C interactsWith t-BuOOH
+YLF2 interactsWith t-BuOOH
+PRS3 interactsWith t-BuOOH
+YGR169C interactsWith t-BuOOH
+CYS4 interactsWith t-BuOOH
+YGR089W interactsWith t-BuOOH
+YER080W interactsWith t-BuOOH
+YER002W interactsWith t-BuOOH
+SAC2 interactsWith t-BuOOH
+YDR130C interactsWith t-BuOOH
+YDR098C interactsWith t-BuOOH
+OST4 interactsWith t-BuOOH
+GOS1 interactsWith t-BuOOH
+YHL042W interactsWith t-BuOOH
+YHL044W interactsWith t-BuOOH
+ERG6 interactsWith t-BuOOH
+YPT7 interactsWith t-BuOOH
+HOG1 interactsWith t-BuOOH
+RPS0B interactsWith t-BuOOH
+RIC1 interactsWith t-BuOOH
+KTI12 interactsWith t-BuOOH
+YKL037W interactsWith t-BuOOH
+YJL206C interactsWith t-BuOOH
+CPS1 interactsWith t-BuOOH
+SPL2 interactsWith t-BuOOH
+YHR121W interactsWith t-BuOOH
+TOM71 interactsWith t-BuOOH
+KSP1 interactsWith t-BuOOH
+VPS29 interactsWith t-BuOOH
+YDL118W interactsWith t-BuOOH
+RRN10 interactsWith t-BuOOH
+YLR192C interactsWith t-BuOOH
+HBS1 interactsWith t-BuOOH
+VPH2 interactsWith t-BuOOH
+YJR102C interactsWith t-BuOOH
+GRR1 interactsWith t-BuOOH
+RPL39 interactsWith t-BuOOH
+YJL188C interactsWith t-BuOOH
+SWI3 interactsWith t-BuOOH
+YJL175W interactsWith t-BuOOH
+YAK1 interactsWith t-BuOOH
+PHO86 interactsWith t-BuOOH
+TRX2 interactsWith t-BuOOH
+YGR206W interactsWith t-BuOOH
+ERG4 interactsWith t-BuOOH
+CHS5 interactsWith t-BuOOH
+YLR414C interactsWith t-BuOOH
+VPS9 interactsWith t-BuOOH
+DDC1 interactsWith t-BuOOH
+RSA1 interactsWith t-BuOOH
+YPL176C interactsWith t-BuOOH
+OYE3 interactsWith t-BuOOH
+KES1 interactsWith t-BuOOH
+VPS30 interactsWith t-BuOOH
+YPL105C interactsWith t-BuOOH
+IRA2 interactsWith t-BuOOH
+YNR014W interactsWith t-BuOOH
+YMR307W interactsWith t-BuOOH
+RIM13 interactsWith t-BuOOH
+YMR077C interactsWith t-BuOOH
+RIM9 interactsWith t-BuOOH
+ERG5 interactsWith t-BuOOH
+YER083C interactsWith t-BuOOH
+REG1 interactsWith t-BuOOH
+PDE2 interactsWith t-BuOOH
+VAM3 interactsWith t-BuOOH
+YOR021C interactsWith t-BuOOH
+SPT20 interactsWith t-BuOOH
+ADH1 interactsWith t-BuOOH
+SSK2 interactsWith t-BuOOH
+MCK1 interactsWith t-BuOOH
+ADE12 interactsWith t-BuOOH
+DOM34 interactsWith t-BuOOH
+CIK1 interactsWith t-BuOOH
+YMR196W interactsWith t-BuOOH
+YMR191W interactsWith t-BuOOH
+RPB4 interactsWith t-BuOOH
+RPS21B interactsWith t-BuOOH
+ISU1 interactsWith t-BuOOH
+YPL136W interactsWith t-BuOOH
+YPL168W interactsWith t-BuOOH
+YCR087C-A interactsWith t-BuOOH
+YCR068W interactsWith t-BuOOH
+YCR047C interactsWith t-BuOOH
+YCR045C interactsWith t-BuOOH
+YCR027C interactsWith t-BuOOH
+YCR025C interactsWith t-BuOOH
+YCR050C interactsWith t-BuOOH
+YCR085W interactsWith t-BuOOH
+YCR087W interactsWith t-BuOOH
+CWH36 interactsWith t-BuOOH
+MAL33 interactsWith t-BuOOH
+CTP1 interactsWith t-BuOOH
+APE3 interactsWith t-BuOOH
+YBR216C interactsWith t-BuOOH
+YPL183W-A interactsWith t-BuOOH
+YPL181W interactsWith t-BuOOH
+YIL092W interactsWith t-BuOOH
+RAD1 interactsWith UV
+RAD16 interactsWith UV
+RAD17 interactsWith UV
+YOR200W interactsWith UV
+RAD7 interactsWith UV
+YGL220W interactsWith UV
+HPR1 interactsWith UV
+YDR115W interactsWith UV
+NUP84 interactsWith UV
+YNL215W interactsWith UV
+YLR322W interactsWith UV
+YHR100C interactsWith UV
+RAD9 interactsWith UV
+ADE1 interactsWith UV
+DDC1 interactsWith UV
+MMS2 interactsWith UV
+RAD23 interactsWith UV
+MOT2 interactsWith UV
+MKK1 interactsWith UV
+YML096W interactsWith UV
+MET18 interactsWith UV
+RAD18 interactsWith UV
+RAD10 interactsWith UV
+RAD4 interactsWith UV
+RAD2 interactsWith UV
+NPL6 interactsWith UV
+RAD5 interactsWith UV
+YBR101C interactsWith UV
+YGL007W interactsWith UV
+RAD14 interactsWith UV
+VMA21 interactsWith UV
+NPL3 interactsWith UV
+YKE2 interactsWith UV
+RNR4 interactsWith UV
+YDJ1 interactsWith UV
+UBC13 interactsWith UV
+AAD4 interactsWith UV
+YDL072C interactsWith UV
+YBL100C interactsWith UV
+RRN10 interactsWith UV
+MGM1 interactsWith UV
+CYT1 interactsWith UV
+ADH1 interactsWith UV
+RSC2 interactsWith UV
+YLR312W-A interactsWith UV
+MEC3 interactsWith UV
+AAT2 interactsWith UV
+NUP133 interactsWith UV
+YHR134W interactsWith UV
+"ADE5,7" interactsWith UV
+CTK2 interactsWith UV
+SFP1 interactsWith UV
+PET8 interactsWith UV
+ADE4 interactsWith UV
+BDF1 interactsWith UV
+BUR2 interactsWith UV
+ATP12 interactsWith UV
+REF2 interactsWith UV
+YNR020C interactsWith UV
+YLR315W interactsWith UV
+CTK1 interactsWith UV
+YKL054C interactsWith UV
+FLX1 interactsWith UV
+YSA1 interactsWith UV
+MCT1 interactsWith UV
+RRP6 interactsWith UV
+SRB5 interactsWith UV
+YGR182C interactsWith 4NQO
+YCL060C interactsWith 4NQO
+YBR242W interactsWith 4NQO
+OSH1 interactsWith 4NQO
+YAR031W interactsWith 4NQO
+YPL098C interactsWith 4NQO
+ALD6 interactsWith 4NQO
+SKS1 interactsWith 4NQO
+RPS30B interactsWith 4NQO
+YOR078W interactsWith 4NQO
+YNL101W interactsWith 4NQO
+POR1 interactsWith 4NQO
+MOG1 interactsWith 4NQO
+SDS3 interactsWith 4NQO
+RPS4B interactsWith 4NQO
+YDL173W interactsWith 4NQO
+TRM1 interactsWith 4NQO
+YDR229W interactsWith 4NQO
+YGR169C interactsWith 4NQO
+YGR160W interactsWith 4NQO
+SYF2 interactsWith 4NQO
+BUD9 interactsWith 4NQO
+YGR022C interactsWith 4NQO
+YGL196W interactsWith 4NQO
+ARO2 interactsWith 4NQO
+YGL124C interactsWith 4NQO
+YGL088W interactsWith 4NQO
+YFL030W interactsWith 4NQO
+YDR506C interactsWith 4NQO
+RPL37B interactsWith 4NQO
+RTT103 interactsWith 4NQO
+YDR248C interactsWith 4NQO
+YGR018C interactsWith 4NQO
+YDR260C interactsWith 4NQO
+AMD2 interactsWith 4NQO
+YMR119W interactsWith 4NQO
+YLR110C interactsWith 4NQO
+YLR023C interactsWith 4NQO
+MLP1 interactsWith 4NQO
+TIF1 interactsWith 4NQO
+YKL030W interactsWith 4NQO
+MAE1 interactsWith 4NQO
+RPL39 interactsWith 4NQO
+YIL165C interactsWith 4NQO
+YIL093C interactsWith 4NQO
+RPL34B interactsWith 4NQO
+ARD1 interactsWith 4NQO
+YGR224W interactsWith 4NQO
+GIM4 interactsWith 4NQO
+IMP1 interactsWith 4NQO
+YNL212W interactsWith 4NQO
+YNL227C interactsWith 4NQO
+YDL157C interactsWith 4NQO
+RPL35B interactsWith 4NQO
+UME1 interactsWith 4NQO
+RPS6A interactsWith 4NQO
+YPL014W interactsWith 4NQO
+PIP2 interactsWith 4NQO
+YOR304C-A interactsWith 4NQO
+RPS10A interactsWith 4NQO
+PET56 interactsWith 4NQO
+BFR1 interactsWith 4NQO
+YRR1 interactsWith 4NQO
+YOR115C interactsWith 4NQO
+YOR111W interactsWith 4NQO
+YNR036C interactsWith 4NQO
+MRPL32 interactsWith 4NQO
+ADE6 interactsWith UV
+OXA1 interactsWith UV
+NEM1 interactsWith UV
+RIM101 interactsWith UV
+YGR262C interactsWith UV
+PRE9 interactsWith UV
+RAD54 interactsWith UV
+RPL1B interactsWith UV
+DBP3 interactsWith UV
+RPL7A interactsWith UV
+RML2 interactsWith UV
+YEL044W interactsWith UV
+RAD30 interactsWith UV
+YDR348C interactsWith UV
+ADK1 interactsWith UV
+CLB3 interactsWith UV
+SRB2 interactsWith UV
+NUP120 interactsWith UV
+MMM1 interactsWith UV
+PET122 interactsWith UV
+MRP20 interactsWith UV
+DUN1 interactsWith UV
+KAR3 interactsWith UV
+ANC1 interactsWith UV
+MIP1 interactsWith UV
+VAM3 interactsWith UV
+YOR083W interactsWith UV
+YOR054C interactsWith UV
+YOL072W interactsWith UV
+YNR037C interactsWith UV
+ATP11 interactsWith UV
+YLR358C interactsWith UV
+YLR261C interactsWith UV
+MSS2 interactsWith UV
+NAT1 interactsWith UV
+YBL089W interactsWith UV
+YGL101W interactsWith UV
+YER116C interactsWith UV
+ADA2 interactsWith UV
+ADE8 interactsWith UV
+SHE9 interactsWith UV
+RPA14 interactsWith UV
+SIT4 interactsWith UV
+YAR029W interactsWith UV
+TPD3 interactsWith UV
+YPR096C interactsWith UV
+YPR070W interactsWith UV
+CKB2 interactsWith UV
+PEP12 interactsWith UV
+DFG16 interactsWith UV
+VMA7 interactsWith UV
+ARD1 interactsWith UV
+YIL110W interactsWith UV
+POS5 interactsWith UV
+YOR295W interactsWith UV
+BUB3 interactsWith UV
+SLG1 interactsWith UV
+IFM1 interactsWith UV
+YNR036C interactsWith UV
+YNL224C interactsWith UV
+YNL213C interactsWith UV
+RPL20A interactsWith UV
+SPT21 interactsWith UV
+YML010W-A interactsWith UV
+MEF1 interactsWith UV
+ERG3 interactsWith UV
+REV7 interactsWith UV
+YLR089C interactsWith UV
+ADH4 interactsWith UV
+YHR067W interactsWith UV
+RAD6 interactsWith UV
+QCR7 interactsWith UV
+HAP3 interactsWith UV
+YPL041C interactsWith UV
+YNL136W interactsWith UV
+YMR326C interactsWith UV
+YML081C-A interactsWith UV
+RAD52 interactsWith UV
+ATP10 interactsWith UV
+YGL110C interactsWith UV
+CDC26 interactsWith UV
+YFL054C interactsWith UV
+YPR133W-A interactsWith UV
+CYT2 interactsWith UV
+YML011C interactsWith UV
+CTF18 interactsWith UV
+HAP2 interactsWith UV
+YFR045W interactsWith UV
+RAD24 interactsWith UV
+COQ4 interactsWith UV
+NBP2 interactsWith UV
+RPL31A interactsWith UV
+TUP1 interactsWith UV
+YCR020W-B interactsWith UV
+YME1 interactsWith UV
+PHO85 interactsWith UV
+UBP2 interactsWith UV
+POP2 interactsWith UV
+YNR014W interactsWith UV
+YNR013C interactsWith UV
+BEM4 interactsWith UV
+YOR241W interactsWith UV
+12/1/1999 interactsWith UV
+ATP1 interactsWith UV
+RPS8A interactsWith UV
+YAR002W interactsWith UV
+COX10 interactsWith UV
+YOR304C-A interactsWith UV
+YOR297C interactsWith UV
+YOR082C interactsWith UV
+SUR4 interactsWith UV
+MGM101 interactsWith UV
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+HOP2 interactsWith MMS
+YGL029W interactsWith MMS
+CKB1 interactsWith MMS
+PDR6 interactsWith MMS
+CDH1 interactsWith MMS
+YFR048W interactsWith MMS
+YFR045W interactsWith MMS
+YFR038W interactsWith MMS
+CDC26 interactsWith MMS
+YFR024C interactsWith MMS
+YFR021W interactsWith MMS
+YFR020W interactsWith MMS
+FAB1 interactsWith MMS
+MIG1 interactsWith MMS
+OCH1 interactsWith MMS
+RCK1 interactsWith MMS
+NUT1 interactsWith MMS
+ARO2 interactsWith MMS
+YGL124C interactsWith MMS
+VPS45 interactsWith MMS
+MMS2 interactsWith MMS
+YGL084C interactsWith MMS
+RPB9 interactsWith MMS
+YGL066W interactsWith MMS
+RAD6 interactsWith MMS
+YGL046W interactsWith MMS
+YGL045W interactsWith MMS
+YFR018C interactsWith MMS
+ECM4 interactsWith MMS
+NAP1 interactsWith MMS
+YKR046C interactsWith MMS
+GAP1 interactsWith MMS
+YKR035C interactsWith MMS
+SPO14 interactsWith MMS
+YKR030W interactsWith MMS
+YKR029C interactsWith MMS
+SAP190 interactsWith MMS
+GCN3 interactsWith MMS
+DBP7 interactsWith MMS
+YKR021W interactsWith MMS
+YKR020W interactsWith MMS
+IRS4 interactsWith MMS
+YKR015C interactsWith MMS
+YKR049C interactsWith MMS
+TRK2 interactsWith MMS
+YKR051W interactsWith MMS
+YKR075C interactsWith MMS
+YKR073C interactsWith MMS
+SIS2 interactsWith MMS
+YKR067W interactsWith MMS
+CCP1 interactsWith MMS
+YKR065C interactsWith MMS
+YKR064W interactsWith MMS
+KTR2 interactsWith MMS
+YKR060W interactsWith MMS
+GLG1 interactsWith MMS
+RPS21A interactsWith MMS
+RHO4 interactsWith MMS
+DYN1 interactsWith MMS
+MRS4 interactsWith MMS
+YPT52 interactsWith MMS
+PRY2 interactsWith MMS
+YKR012C interactsWith MMS
+ASH1 interactsWith MMS
+MRP49 interactsWith MMS
+CTK1 interactsWith MMS
+YKL121W interactsWith MMS
+YKL118W interactsWith MMS
+YKL115C interactsWith MMS
+APN1 interactsWith MMS
+RAD27 interactsWith MMS
+KTI12 interactsWith MMS
+AAT1 interactsWith MMS
+HSL1 interactsWith MMS
+YKL098W interactsWith MMS
+YJU3 interactsWith MMS
+YKL076C interactsWith MMS
+YKL204W interactsWith MMS
+YKL207W interactsWith MMS
+CBT1 interactsWith MMS
+FOX2 interactsWith MMS
+YKR007W interactsWith MMS
+YKR005C interactsWith MMS
+YKR003W interactsWith MMS
+VPS1 interactsWith MMS
+YKL221W interactsWith MMS
+FRE2 interactsWith MMS
+YKL218C interactsWith MMS
+JEN1 interactsWith MMS
+URA1 interactsWith MMS
+YKL214C interactsWith MMS
+DOA1 interactsWith MMS
+SAC1 interactsWith MMS
+TRP3 interactsWith MMS
+LHS1 interactsWith MMS
+MTD1 interactsWith MMS
+YLR218C interactsWith MMS
+YLR118C interactsWith MMS
+HOG1 interactsWith MMS
+APC9 interactsWith MMS
+YLR099C interactsWith MMS
+YLR095C interactsWith MMS
+GIS3 interactsWith MMS
+XDJ1 interactsWith MMS
+YLR089C interactsWith MMS
+YLR087C interactsWith MMS
+SIC1 interactsWith MMS
+YLR057W interactsWith MMS
+SRN2 interactsWith MMS
+YLR124W interactsWith MMS
+CPR6 interactsWith MMS
+MSS51 interactsWith MMS
+YKE2 interactsWith MMS
+PEX13 interactsWith MMS
+YLR190W interactsWith MMS
+MDL1 interactsWith MMS
+SWI6 interactsWith MMS
+YLR177W interactsWith MMS
+PEP3 interactsWith MMS
+YLR125W interactsWith MMS
+RIC1 interactsWith MMS
+KIM2 interactsWith MMS
+FLO10 interactsWith MMS
+SIR1 interactsWith MMS
+UBP11 interactsWith MMS
+PCK1 interactsWith MMS
+YKR096W interactsWith MMS
+PTR2 interactsWith MMS
+SRL3 interactsWith MMS
+YKR090W interactsWith MMS
+YKR089C interactsWith MMS
+YKR087C interactsWith MMS
+YLL018C-A interactsWith MMS
+YLR036C interactsWith MMS
+RAD5 interactsWith MMS
+YLR030W interactsWith MMS
+SNF7 interactsWith MMS
+YLR015W interactsWith MMS
+PPR1 interactsWith MMS
+YLR012C interactsWith MMS
+SSK1 interactsWith MMS
+YLL059C interactsWith MMS
+YBT1 interactsWith MMS
+FPS1 interactsWith MMS
+VPS13 interactsWith MMS
+NUP133 interactsWith MMS
+YJL103C interactsWith MMS
+HYR1 interactsWith MMS
+YIR035C interactsWith MMS
+LYS1 interactsWith MMS
+DCG1 interactsWith MMS
+DAL4 interactsWith MMS
+DAL1 interactsWith MMS
+GIF1 interactsWith MMS
+DAL81 interactsWith MMS
+YIR020W-B interactsWith MMS
+YIR002C interactsWith MMS
+YIL166C interactsWith MMS
+YIL165C interactsWith MMS
+ECM37 interactsWith MMS
+YIL145C interactsWith MMS
+CTK2 interactsWith MMS
+YJL007C interactsWith MMS
+YJL036W interactsWith MMS
+BCK1 interactsWith MMS
+HPR5 interactsWith MMS
+YJL082W interactsWith MMS
+SCP160 interactsWith MMS
+YJL077C interactsWith MMS
+JEM1 interactsWith MMS
+YJL060W interactsWith MMS
+YJL058C interactsWith MMS
+IKS1 interactsWith MMS
+TDH1 interactsWith MMS
+RTT101 interactsWith MMS
+YJL046W interactsWith MMS
+YJL038C interactsWith MMS
+YJL037W interactsWith MMS
+REV7 interactsWith MMS
+FLX1 interactsWith MMS
+YIL132C interactsWith MMS
+YIL057C interactsWith MMS
+YIL055C interactsWith MMS
+RHR2 interactsWith MMS
+RPL34B interactsWith MMS
+PCL7 interactsWith MMS
+PIG2 interactsWith MMS
+CBR1 interactsWith MMS
+YIL042C interactsWith MMS
+YIL041W interactsWith MMS
+YIL040W interactsWith MMS
+YIL039W interactsWith MMS
+NOT3 interactsWith MMS
+YIL037C interactsWith MMS
+YIL036W interactsWith MMS
+YIL060W interactsWith MMS
+YIL064W interactsWith MMS
+YIL065C interactsWith MMS
+MET18 interactsWith MMS
+YIL110W interactsWith MMS
+FMC1 interactsWith MMS
+PRK1 interactsWith MMS
+REV1 pd 2AQ4_P
+REV1 pd 2AQ4_T
diff --git a/distribution/src/main/sampleData/README_SAMPLE_DATA.txt b/distribution/src/main/sampleData/README_SAMPLE_DATA.txt
new file mode 100644
index 0000000..15da04f
--- /dev/null
+++ b/distribution/src/main/sampleData/README_SAMPLE_DATA.txt
@@ -0,0 +1,70 @@
+README.txt:
+
+ This directory contains sample data for Cytoscape. It includes the
+ following data sets:
+
+----------------------------------------------------------------------------
+
+galFiltered.sif
+galFiltered.gml
+galFiltered.xgmml
+galExpData.pvals
+
+galFiltered.cys
+
+These files contain an interaction network and expression data from
+the paper:
+
+Ideker, T., Thorsson V, Ranish JA, Christmas R, Buhler J, Eng JK, Bumgarner R,
+Goodlett DR, Aebersold R, Hood L. Integrated genomic and proteomic analyses of
+a systematically perturbed metabolic network. Science, 292, 929-34 (2001).
+
+The 'galExpData.pvals' file contains 20 experimental conditions involving
+systematic perturbations of the galactose utilization pathway in yeast.
+The 'galFiltered.*' files contain an interaction network of 331 genes that
+were significantly differentially expressed in at least one of the 20
+experimental conditions. The two network files are identical networks in
+different formats; the '.sif' is in the simple interactions format,
+the '.gml' is in GML format, and '.xgmml' is in XGMML format.
+
+The 'galFiltered.cys' is a CYtoscape Session file contains network data,
+attributes, and desktop states.
+
+----------------------------------------------------------------------------
+
+BINDyeast.sif
+
+This is a Cytoscape network containing all of the yeast interactions known
+to the BIND database (http://www.bind.ca) circa 10/10/2006.
+
+----------------------------------------------------------------------------
+
+BINDhuman.sif
+
+This is a Cytoscape network containing all of the human interactions known
+to the BIND database (http://www.bind.ca) circa 10/10/2006.
+
+----------------------------------------------------------------------------
+
+yeastHighQuality.sif
+
+This is a Cytoscape network combining two public data sets of high quality
+interactions in yeast. It includes:
+
+2455 high-confidence protein-protein interactions from the paper
+
+von Mering C, Krause R, Snel B, Cornell M, Oliver SG, Fields S, Bork P.
+Comparative assessment of large-scale data sets of protein-protein
+interactions. Nature, 417, 399-403, May 2002.
+
+and 4433 high confidence protein-dna interactions (p-values < 0.001) from
+the paper
+
+Lee, T.I., Rinaldi, N.J., Robert, F., Odom, D.T., Bar-Joseph, Z., Gerber, G.K.,
+Hannett, N.M., Harbison, C.R., Thompson, C.M., Simon I., Zeitlinger J.,
+Jennings, E.G., Murray, H.L., Gordon, D.B., Ren, B., Wyrick, J.J., Tagne, J.,
+Volkert T.L., Fraenkel, E., Gifford D.K., and Young, R.A.
+Transcriptional regulatory networks in Saccharomyces cerevisiae.
+Science, 298: 799-804 (2002).
+http://web.wi.mit.edu/young/regulator_network/
+
diff --git a/distribution/src/main/sampleData/Sample.nnf b/distribution/src/main/sampleData/Sample.nnf
new file mode 100644
index 0000000..30c7a7c
--- /dev/null
+++ b/distribution/src/main/sampleData/Sample.nnf
@@ -0,0 +1,142 @@
+# A simple 3-level nested network example file.
+#
+# The top-level network is called "Overview", below that are "Level1.x" and below that "Level2.x".
+
+# Top-level network
+Overview Level1.1 interact Level1.2
+Overview Level1.2 interact Level1.3
+Overview Level1.4
+Overview Level1.5 interact Level1.1
+
+# First level-1 network
+Level1.1 SimpleNode1 interact Level2.1 # Note that "SimpleNode1" does not have a nested network because there is
+Level1.1 SimpleNode2 interact Level2.2 # no network named "SimpleNode1", i.e. "SimpleNode1" does not appear in the
+Level1.1 Level2.1 interact Level2.8 # first column anywhere in this file.
+
+# Second level-1 network
+Level1.2 Level2.7 interact Level2.2
+Level1.2 Level2.5 interact SimpleNode3
+Level1.2 Level2.4 interact Level2.2
+Level1.2 Level2.2 interact SimpleNode4
+Level1.2 Level2.2 interact Level2.4
+Level1.2 Level2.1 interact Level2.7
+Level1.2 Level2.5 interact Level2.4
+
+# Third level-1 network
+Level1.3 Level2.4 interact Level2.5
+Level1.3 Level2.6 interact Level2.4
+Level1.3 Level2.6 interact Level2.5
+
+# Fourth level-1 network
+Level1.4 Level2.1 interact Level2.8
+Level1.4 SimpleNode2 interact Level2.
+Level1.4 Level2.5 interact Level2.3
+Level1.4 Level2.2 interact SimpleNode5
+Level1.4 Level2.5 interact Level2.2
+Level1.4 SimpleNode6 interact Level2.7
+
+# Fifth level-1 network
+Level1.5 Level2.4 interact Level2.2
+Level1.5 SimpleNode7 interact Level2.1
+Level1.5 Level2.9 interact Level2.
+Level1.5 Level2.3 interact Level2.5
+Level1.5 Level2.2 interact Level2.2
+
+# First level-2 network
+Level2.1 Node1 interact Node2
+Level2.1 Node2 interact Node1
+Level2.1 Node4 interact Node4
+Level2.1 Node5 interact Node6
+Level2.1 Node3 interact Node8
+Level2.1 Node5 interact Node2
+Level2.1 Node8 interact Node5
+Level2.1 Node2 interact Node6
+Level2.1 Node5 interact Node7
+
+# Second level-2 network
+Level2.2 Node6 interact Node9
+Level2.2 Node8 interact Node11
+Level2.2 Node3 interact Node12
+Level2.2 Node6 interact Node3
+Level2.2 Node20 interact Node4
+Level2.2 Node11 interact Node7
+Level2.2 Node4 interact Node13
+Level2.2 Node8 interact Node20
+Level2.2 Node12 interact Node3
+
+# Third level-2 network
+Level2.3 Node5 interact Node4
+Level2.3 Node4 interact Node1
+Level2.3 Node8 interact Node2
+Level2.3 Node12 interact Node8
+Level2.3 Node11 interact Node13
+Level2.3 Node9 interact Node12
+Level2.3 Node7 interact Node4
+Level2.3 Node3 interact Node20
+Level2.3 Node12 interact Node7
+
+# Fourth level-2 network
+Level2.3 Node11 interact Node13
+Level2.4 Node1 interact Node2
+Level2.4 Node3 interact Node8
+Level2.4 Node2 interact Node10
+Level2.4 Node14 interact Node19
+Level2.4 Node9 interact Node7
+Level2.4 Node8 interact Node6
+Level2.4 Node10 interact Node5
+Level2.4 Node11 interact Node1
+
+# Fifth level-2 network
+Level2.5 Node16 interact Node15
+Level2.5 Node15 interact Node10
+Level2.5 Node2 interact Node8
+Level2.5 Node9 interact Node9
+Level2.5 Node8 interact Node2
+Level2.5 Node12 interact Node3
+Level2.5 Node15 interact Node11
+Level2.5 Node16 interact Node10
+Level2.5 Node7 interact Node8
+
+# Sixth level-2 network
+Level2.6 Node10 interact Node4
+Level2.6 Node20 interact Node2
+Level2.6 Node4 interact Node8
+Level2.6 Node8 interact Node17
+Level2.6 Node16 interact Node20
+Level2.6 Node20 interact Node8
+Level2.6 Node8 interact Node6
+Level2.6 Node6 interact Node4
+Level2.6 Node5 interact Node17
+
+# Seventh level-2 network
+Level2.7 Node2 interact Node5
+Level2.7 Node4 interact Node7
+Level2.7 Node6 interact Node4
+Level2.7 Node4 interact Node3
+Level2.7 Node3 interact Node2
+Level2.7 Node13 interact Node18
+Level2.7 Node6 interact Node13
+Level2.7 Node5 interact Node20
+Level2.7 Node4 interact Node5
+
+# Eighth level-2 network
+Level2.8 Node4 interact Node6
+Level2.8 Node15 interact Node16
+Level2.8 Node6 interact Node15
+Level2.8 Node12 interact Node4
+Level2.8 Node4 interact Node6
+Level2.8 Node2 interact Node7
+Level2.8 Node11 interact Node9
+Level2.8 Node9 interact Node10
+Level2.8 Node8 interact Node12
+
+# Ninth level-2 network
+Level2.9 Node3 interact Node6
+Level2.9 Node4 interact Node6
+Level2.9 Node9 interact Node12
+Level2.9 Node17 interact Node12
+Level2.9 Node8 interact Node9
+Level2.9 Node4 interact Node16
+Level2.9 Node17 interact Node8
+Level2.9 Node2 interact Node4
+Level2.9 Node17 interact Node2
diff --git a/distribution/src/main/sampleData/gal.probeset.na b/distribution/src/main/sampleData/gal.probeset.na
new file mode 100644
index 0000000..5883aab
--- /dev/null
+++ b/distribution/src/main/sampleData/gal.probeset.na
@@ -0,0 +1,5936 @@
+Probeset
+YHR051W = probeset2
+YHR124W = probeset3
+YKL181W = probeset4
+YGR072W = probeset5
+YHL020C = probeset6
+YGR145W = probeset7
+YGL041C = probeset8
+YGR218W = probeset9
+YOR202W = probeset10
+YCR005C = probeset11
+YER187W = probeset12
+YBR026C = probeset13
+YMR244W = probeset14
+YMR317W = probeset15
+YAR047C = probeset16
+YIR031C = probeset17
+YDL177C = probeset18
+YLR338W = probeset19
+YGR073C = probeset20
+YGR146C = probeset21
+YOR130C = probeset22
+YLR193C = probeset23
+YMR318C = probeset24
+YLR266C = probeset25
+YGL114W = probeset26
+YLR339C = probeset27
+YFL062W = probeset28
+YJR010W = probeset29
+YHR052W = probeset30
+YKL182W = probeset31
+YHR125W = probeset32
+YHL021C = probeset33
+YGR219W = probeset34
+YGL042C = probeset35
+YOR203W = probeset36
+YCR006C = probeset37
+YER188W = probeset38
+YMR172W = probeset39
+YNL120C = probeset40
+YBR027C = probeset41
+YMR245W = probeset42
+YJR011C = probeset43
+YIR032C = probeset44
+YHR053C = probeset45
+YHR126C = probeset46
+YPR110C = probeset47
+YGR147C = probeset48
+YOR131C = probeset49
+YAL016W = probeset50
+YLR194C = probeset51
+YMR319C = probeset52
+YGL115W = probeset53
+YFL063W = probeset54
+YDL178W = probeset55
+YKL183W = probeset56
+YGR074W = probeset57
+YHL022C = probeset58
+YDR493W = probeset59
+YOR204W = probeset60
+YCR007C = probeset61
+YFL064C = probeset62
+YER189W = probeset63
+YNL121C = probeset64
+YBR028C = probeset65
+YMR173W = probeset66
+YMR246W = probeset67
+YJR012C = probeset68
+YLR267W = probeset69
+YHR054C = probeset70
+YGR075C = probeset71
+YGR148C = probeset72
+YOR205C = probeset73
+YAL017W = probeset74
+YIL001W = probeset75
+YMR174C = probeset76
+YLR195C = probeset77
+YGL043W = probeset78
+YGL116W = probeset79
+YOL100W = probeset80
+YLR287C-A = probeset81
+YDL179W = probeset82
+YIR033W = probeset83
+YAL018C = probeset84
+YIL002C = probeset85
+YHR127W = probeset86
+YKL184W = probeset87
+YHL023C = probeset88
+YPR111W = probeset89
+YDR494W = probeset90
+YGL044C = probeset91
+YOR132W = probeset92
+YFL065C = probeset93
+YOL101C = probeset94
+YBR029C = probeset95
+YNL122C = probeset96
+YIR034C = probeset97
+YLR268W = probeset98
+YHR055C = probeset99
+YPR112C = probeset100
+YGR076C = probeset101
+YOR060C = probeset102
+YDR495C = probeset103
+YLR269C = probeset104
+YGL117W = probeset105
+YCR008W = probeset106
+YJR013W = probeset107
+YML070W = probeset108
+YHR128W = probeset109
+YKL185W = probeset110
+YBR240C = probeset111
+YGR149W = probeset112
+YOR133W = probeset113
+YOR206W = probeset114
+YGL118C = probeset115
+YFL066C = probeset116
+YOL102C = probeset117
+YCR009C = probeset118
+YNL050C = probeset119
+YMR175W = probeset120
+YLR196W = probeset121
+YIR035C = probeset122
+YHR056C = probeset123
+YKL186C = probeset124
+YHR129C = probeset125
+YGR077C = probeset126
+YDR496C = probeset127
+YOR207C = probeset128
+YAL019W = probeset129
+YIL003W = probeset130
+YHL024W = probeset131
+YGL045W = probeset132
+YNL123W = probeset133
+YJR014W = probeset134
+YIL004C = probeset135
+YPR040W = probeset136
+YBR241C = probeset137
+YPR113W = probeset138
+YOR061W = probeset139
+YOR134W = probeset140
+YML072C = probeset141
+YLR197W = probeset142
+YIR036C = probeset143
+YHR057C = probeset144
+YKL187C = probeset145
+YGR078C = probeset146
+YOR062C = probeset147
+YOR135C = probeset148
+YDR497C = probeset149
+YHL025W = probeset150
+YLR198C = probeset151
+YGL046W = probeset152
+YGL119W = probeset153
+YOL030W = probeset154
+YFL067W = probeset155
+YOL103W = probeset156
+YNL124W = probeset157
+YJR015W = probeset158
+YDR200C = probeset159
+YPR041W = probeset160
+YHL026C = probeset161
+YPR114W = probeset162
+YOR208W = probeset163
+YOL031C = probeset164
+YOL104C = probeset165
+YNL125C = probeset166
+YMR177W = probeset167
+YJR016C = probeset168
+YML073C = probeset169
+YHR058C = probeset170
+YKL188C = probeset171
+YDR498C = probeset172
+YOR209C = probeset173
+YIL005W = probeset174
+YBR242W = probeset175
+YLR199C = probeset176
+YPL010W = probeset177
+YGL047W = probeset178
+YFL068W = probeset179
+YNL052W = probeset180
+YIR037W = probeset181
+YBR170C = probeset182
+YGR079W = probeset183
+YPR115W = probeset184
+YBR243C = probeset185
+YPL011C = probeset186
+YOR063W = probeset187
+YGL048C = probeset188
+YOR136W = probeset189
+YOL105C = probeset190
+YMR178W = probeset191
+YML074C = probeset192
+YJR017C = probeset193
+YIR038C = probeset194
+YOR064C = probeset195
+YOR137C = probeset196
+YDR201W = probeset197
+YIL006W = probeset198
+YHL027W = probeset199
+YOL032W = probeset200
+YNL053W = probeset201
+YNL126W = probeset202
+YGR290W = probeset203
+YDR202C = probeset204
+YIL007C = probeset205
+YHR059W = probeset206
+YMR251W-A = probeset207
+YKL189W = probeset208
+YPR043W = probeset209
+YPR116W = probeset210
+YDR499W = probeset211
+YGL049C = probeset212
+YMR179W = probeset213
+YML075C = probeset214
+YGR291C = probeset215
+YIR039C = probeset216
+YOR138C = probeset217
+YBR171W = probeset218
+YBR244W = probeset219
+YHL028W = probeset220
+YPL012W = probeset221
+YOL033W = probeset222
+YOL106W = probeset223
+YNL054W = probeset224
+YNL127W = probeset225
+YJR018W = probeset226
+YDR130C = probeset227
+YBR172C = probeset228
+YBR245C = probeset229
+YHL029C = probeset230
+YPR117W = probeset231
+YPL013C = probeset232
+YOR065W = probeset233
+YNL055C = probeset234
+YJR019C = probeset235
+YML076C = probeset236
+YPR045C = probeset237
+YOR139C = probeset238
+YGL260W = probeset239
+YIL008W = probeset240
+YOL034W = probeset241
+YOL107W = probeset242
+YER110C = probeset243
+YNL128W = probeset244
+YGR292W = probeset245
+YDR131C = probeset246
+YGL261C = probeset247
+YBR173C = probeset248
+YPR118W = probeset249
+YOR066W = probeset250
+YOL035C = probeset251
+YOL108C = probeset252
+YGR293C = probeset253
+YOR350C = probeset254
+YOR067C = probeset255
+YDR204W = probeset256
+YDL100C = probeset257
+YIL009W = probeset258
+YBR246W = probeset259
+YPL014W = probeset260
+YNL056W = probeset261
+YER111C = probeset262
+YNL129W = probeset263
+YML077W = probeset264
+YDR132C = probeset265
+YJR010C-A = probeset266
+YPR046W = probeset267
+YBR174C = probeset268
+YBR247C = probeset269
+YPR119W = probeset270
+YPL015C = probeset271
+YER093C-A = probeset272
+YOR351C = probeset273
+YOR068C = probeset274
+YDR205W = probeset275
+YGL262W = probeset276
+YDL101C = probeset277
+YBL070C = probeset278
+YJL200C = probeset279
+YOL036W = probeset280
+YOL109W = probeset281
+YNL057W = probeset282
+YML078W = probeset283
+YGR294W = probeset284
+YDR133C = probeset285
+YGL190C = probeset286
+YPR047W = probeset287
+YBR248C = probeset288
+YOL037C = probeset289
+YNL058C = probeset290
+YGR295C = probeset291
+YER112W = probeset292
+YDR060W = probeset293
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+YGR296W = probeset326
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+YOR281C = probeset333
+YOR354C = probeset334
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+YLR120C = probeset352
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+YJL203W = probeset359
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+YGR001C = probeset366
+YJL131C = probeset367
+YJL204C = probeset368
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+YCR085W = probeset389
+YDL106C = probeset390
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+YBL075C = probeset392
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+YOR283W = probeset396
+YOR356W = probeset397
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+YEL012W = probeset400
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+YOR357C = probeset403
+YJL132W = probeset404
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+YIL153W = probeset407
+YER117W = probeset408
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+YDR138W = probeset411
+YCR086W = probeset412
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+YNL273W = probeset414
+YBL076C = probeset415
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+YJL206C = probeset417
+YFR024C = probeset418
+YIL154C = probeset419
+YER045C = probeset420
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+YDR066C = probeset422
+YMR102C = probeset423
+YLR050C = probeset424
+YOR284W = probeset425
+YDR139C = probeset426
+YLR123C = probeset427
+YKR071C = probeset428
+YNL274C = probeset429
+YEL013W = probeset430
+YDL034W = probeset431
+YDL107W = probeset432
+YCL055W = probeset433
+YKL112W = probeset434
+YHR001W-A = probeset435
+YGR003W = probeset436
+YJL060W = probeset437
+YJL133W = probeset438
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+YPL232W = probeset440
+YGL196W = probeset441
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+YCL056C = probeset444
+YKL040C = probeset445
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+YDR350C = probeset448
+YDR423C = probeset449
+YJL207C = probeset450
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+YIL155C = probeset452
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+YDR067C = probeset455
+YMR103C = probeset456
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+YOR285W = probeset458
+YOR358W = probeset459
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+YPL233W = probeset470
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+YNL275W = probeset477
+YBL078C = probeset478
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+YGR005C = probeset480
+YJL208C = probeset481
+YDR424C = probeset482
+YIL083C = probeset483
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+YER047C = probeset485
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+YPL161C = probeset488
+YMR104C = probeset489
+YOR286W = probeset490
+YPL234C = probeset491
+YOR359W = probeset492
+YKR073C = probeset493
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+YNL276C = probeset495
+YEL015W = probeset496
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+YCL057W = probeset498
+YKL041W = probeset499
+YOR287C = probeset500
+YJL062W = probeset501
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+YDR351W = probeset503
+YIL156W = probeset504
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+YLR125W = probeset511
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+YJL063C = probeset514
+YJL136C = probeset515
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+YIL157C = probeset518
+YER048C = probeset519
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+YDR069C = probeset521
+YMR105C = probeset522
+YLR053C = probeset523
+YGL199C = probeset524
+YLR126C = probeset525
+YLL021W = probeset526
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+YBL079W = probeset529
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+YMR032W = probeset536
+YPL235W = probeset537
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+YCL059C = probeset540
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+YJL137C = probeset544
+YFR028C = probeset545
+YIL085C = probeset546
+YPL090C = probeset547
+YMR106C = probeset548
+YPL163C = probeset549
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+YLR054C = probeset551
+YLR127C = probeset552
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+YEL017W = probeset554
+YML001W = probeset555
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+YKL043W = probeset557
+YDR280W = probeset558
+YJL064W = probeset559
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+YDR353W = probeset561
+YIL158W = probeset562
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+YMR033W = probeset566
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+YNL278W = probeset569
+YJR096W = probeset570
+YDR281C = probeset571
+YJL065C = probeset572
+YGR008C = probeset573
+YJL138C = probeset574
+YIL086C = probeset575
+YNR013C = probeset576
+YMR034C = probeset577
+YPL164C = probeset578
+YLR055C = probeset579
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+YIL159W = probeset587
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+YBR084C-A = probeset599
+YGR009C = probeset600
+YDR282C = probeset601
+YJL066C = probeset602
+YDR355C = probeset603
+YJL139C = probeset604
+YDR428C = probeset605
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+YPL238C = probeset609
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+YLR056W = probeset619
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+YLR129W = probeset621
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+YKL119C = probeset624
+YDR283C = probeset625
+YDR429C = probeset626
+YIL088C = probeset627
+YMR036C = probeset628
+YBR100W = probeset629
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+YJL067W = probeset632
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+YNR015W = probeset635
+YLR413W = probeset636
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+YMR109W = probeset638
+YPL166W = probeset639
+YPL239W = probeset640
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+YLR057W = probeset642
+YKR078W = probeset643
+YJR099W = probeset644
+YJL068C = probeset645
+YDR284C = probeset646
+YDR357C = probeset647
+YNR016C = probeset648
+YLR414C = probeset649
+YPR198W = probeset650
+YMR037C = probeset651
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+YPL167C = probeset653
+YLR058C = probeset654
+YKR079C = probeset655
+YHR200W = probeset656
+YML005W = probeset657
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+YKL047W = probeset660
+YBR102C = probeset661
+YMR320W = probeset662
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+YLR341W = probeset664
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+YKL048C = probeset667
+YJL069C = probeset668
+YMR321C = probeset669
+YLR415C = probeset670
+YMR038C = probeset671
+YPL095C = probeset672
+YLR059C = probeset673
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+YGR222W = probeset676
+YLL027W = probeset677
+YDR285W = probeset678
+YDR358W = probeset679
+YLR342W = probeset680
+YNR017W = probeset681
+YGR150C = probeset682
+YPL168W = probeset683
+YGR223C = probeset684
+YKL049C = probeset685
+YDR286C = probeset686
+YMR322C = probeset687
+YDR359C = probeset688
+YLR416C = probeset689
+YMR039C = probeset690
+YBR030W = probeset691
+YBR103W = probeset692
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+YDL181W = probeset694
+YAL020C = probeset695
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+YCR010C = probeset698
+YLL028W = probeset699
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+YNR018W = probeset702
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+YPL096W = probeset704
+YHR203C = probeset705
+YGR151C = probeset706
+YML008C = probeset707
+YBR031W = probeset708
+YBR104W = probeset709
+YDL182W = probeset710
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+YGR224W = probeset712
+YGL120C = probeset713
+YLL029W = probeset714
+YCR011C = probeset715
+YBR105C = probeset716
+YMR250W = probeset717
+YDR287W = probeset718
+YMR323W = probeset719
+YDL183C = probeset720
+YLR271W = probeset721
+YLR344W = probeset722
+YNR019W = probeset723
+YLR417W = probeset724
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+YGR152C = probeset727
+YML009C = probeset728
+YMR324C = probeset729
+YLR272C = probeset730
+YLR418C = probeset731
+YPL098C = probeset732
+YBR032W = probeset733
+YBL001C = probeset734
+YAR053W = probeset735
+YAL022C = probeset736
+YHR204W = probeset737
+YGR225W = probeset738
+YGL121C = probeset739
+YMR251W = probeset740
+YDR288W = probeset741
+YDL184C = probeset742
+YLR345W = probeset743
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+YGR226C = probeset745
+YMR252C = probeset746
+YDR289C = probeset747
+YLR273C = probeset748
+YLR346C = probeset749
+YCR012W = probeset750
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+YBR106W = probeset753
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+YHR205W = probeset755
+YGR080W = probeset756
+YGR153W = probeset757
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+YCR013C = probeset760
+YBR034C = probeset761
+YNL200C = probeset762
+YBR107C = probeset763
+YLR419W = probeset764
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+YGR081C = probeset766
+YGR154C = probeset767
+YBL002W = probeset768
+YOR211C = probeset769
+YMR180C = probeset770
+YMR253C = probeset771
+YMR326C = probeset772
+YLR347C = probeset773
+YBL003C = probeset774
+YDL185W = probeset775
+YAL024C = probeset776
+YHR060W = probeset777
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+YBR035C = probeset782
+YNL201C = probeset783
+YLR274W = probeset784
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+YHR061C = probeset786
+YHR207C = probeset787
+YMR181C = probeset788
+YMR254C = probeset789
+YGL050W = probeset790
+YLR348C = probeset791
+YGL123W = probeset792
+YBR108W = probeset793
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+YGR228W = probeset800
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+YBR109C = probeset805
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+YLR275W = probeset807
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+YHR135C = probeset809
+YKL192C = probeset810
+YGR083C = probeset811
+YGR229C = probeset812
+YBL004W = probeset813
+YOR213C = probeset814
+YMR182C = probeset815
+YHL030W = probeset816
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+YIR041W = probeset821
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+YHR208W = probeset823
+YGR156W = probeset824
+YOR140W = probeset825
+YFL034C-B = probeset826
+YBR037C = probeset827
+YNL130C = probeset828
+YNL203C = probeset829
+YMR255W = probeset830
+YJR021C = probeset831
+YIR042C = probeset832
+YDL188C = probeset833
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+YHR136C = probeset836
+YKL193C = probeset837
+YPR120C = probeset838
+YGR084C = probeset839
+YBL005W = probeset840
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+YMR256C = probeset845
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+YGL052W = probeset847
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+YBL006C = probeset850
+YCR020C-A = probeset851
+YHL032C = probeset852
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+YGR157W = probeset854
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+YHR064C = probeset857
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+YGR158C = probeset860
+YOR215C = probeset861
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+YLR278C = probeset865
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+YOR142W = probeset877
+YGL054C = probeset878
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+YOL111C = probeset880
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+YHR065C = probeset885
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+YGR086C = probeset887
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+YOR143C = probeset890
+YOR216C = probeset891
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+YIL013C = probeset900
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+YNL133C = probeset905
+YMR185W = probeset906
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+YJR024C = probeset908
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+YGR087C = probeset913
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+YOR144C = probeset915
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+YHR066W = probeset923
+YHL035C = probeset924
+YGL056C = probeset925
+YGL129C = probeset926
+YOR217W = probeset927
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+YOL114C = probeset950
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+YKR005C = probeset952
+YNL135C = probeset953
+YML083C = probeset954
+YKL198C = probeset955
+YOR219C = probeset956
+YDR210W = probeset957
+YIL015W = probeset958
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+YBR252W = probeset960
+YHL036W = probeset961
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+YPR125W = probeset964
+YGR089W = probeset965
+YHL037C = probeset966
+YOR073W = probeset967
+YOR146W = probeset968
+YKR006C = probeset969
+YHR069C = probeset970
+YKL199C = probeset971
+YPR126C = probeset972
+YOR074C = probeset973
+YDR211W = probeset974
+YIL016W = probeset975
+YBR180W = probeset976
+YBR253W = probeset977
+YPL021W = probeset978
+YGL058W = probeset979
+YOL042W = probeset980
+YOL115W = probeset981
+YNL063W = probeset982
+YNL136W = probeset983
+YML084W = probeset984
+YNL209W = probeset985
+YBR181C = probeset986
+YBR254C = probeset987
+YHL038C = probeset988
+YOR147W = probeset989
+YOL043C = probeset990
+YNL064C = probeset991
+YNL137C = probeset992
+YMR189W = probeset993
+YML085C = probeset994
+YOR148C = probeset995
+YDR212W = probeset996
+YPL022W = probeset997
+YGL059W = probeset998
+YOL116W = probeset999
+YKR007W = probeset1000
+YPR054W = probeset1001
+YBR182C = probeset1002
+YPR127W = probeset1003
+YOR075W = probeset1004
+YPL023C = probeset1005
+YML086C = probeset1006
+YPR128C = probeset1007
+YOR076C = probeset1008
+YDR140W = probeset1009
+YOR149C = probeset1010
+YDR213W = probeset1011
+YIL018W = probeset1012
+YBR255W = probeset1013
+YHL039W = probeset1014
+YOL044W = probeset1015
+YOL117W = probeset1016
+YKR008W = probeset1017
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+YJL216C = probeset1190
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+YOR161C = probeset2383
+YOR234C = probeset2384
+YOR307C = probeset2385
+YIL103W = probeset2386
+YGL145W = probeset2387
+YGL218W = probeset2388
+YCR036W = probeset2389
+YKR020W = probeset2390
+YNL150W = probeset2391
+YNL223W = probeset2392
+YJR114W = probeset2393
+YJL010C = probeset2394
+YAL047C = probeset2395
+YHR083W = probeset2396
+YIL104C = probeset2397
+YPR140W = probeset2398
+YDR016C = probeset2399
+YGL146C = probeset2400
+YCR037C = probeset2401
+YGL219C = probeset2402
+YNL151C = probeset2403
+YBR058C = probeset2404
+YNL224C = probeset2405
+YMR276W = probeset2406
+YLR297W = probeset2407
+YPR141C = probeset2408
+YCL005W = probeset2409
+YGR178C = probeset2410
+YOR162C = probeset2411
+YBL026W = probeset2412
+YOR308C = probeset2413
+YIL031W = probeset2414
+YLR298C = probeset2415
+YGL073W = probeset2416
+YOL130W = probeset2417
+YKR021W = probeset2418
+YCL006C = probeset2419
+YJR115W = probeset2420
+YJL011C = probeset2421
+YDR300C = probeset2422
+YAL048C = probeset2423
+YIL032C = probeset2424
+YHR084W = probeset2425
+YIL105C = probeset2426
+YHR157W = probeset2427
+YDR017C = probeset2428
+YPL110C = probeset2429
+YGL074C = probeset2430
+YLR001C = probeset2431
+YGL147C = probeset2432
+YCR038C = probeset2433
+YKR022C = probeset2434
+YBR059C = probeset2435
+YNL225C = probeset2436
+YJR043C = probeset2437
+YMR277W = probeset2438
+YHR158C = probeset2439
+YPR142C = probeset2440
+YGR179C = probeset2441
+YOR090C = probeset2442
+YBL027W = probeset2443
+YOR309C = probeset2444
+YOL131W = probeset2445
+YNL152W = probeset2446
+YCL007C = probeset2447
+YBL028C = probeset2448
+YJR116W = probeset2449
+YJL012C = probeset2450
+YAL049C = probeset2451
+YHR085W = probeset2452
+YIL033C = probeset2453
+YBR270C = probeset2454
+YDR018C = probeset2455
+YGL075C = probeset2456
+YOR163W = probeset2457
+YLR002C = probeset2458
+YOR236W = probeset2459
+YCR039C = probeset2460
+YNL080C = probeset2461
+YNL153C = probeset2462
+YJR044C = probeset2463
+YMR278W = probeset2464
+YLR299W = probeset2465
+YOR164C = probeset2466
+YDR301W = probeset2467
+YIL106W = probeset2468
+YMR279C = probeset2469
+YPL111W = probeset2470
+YGL148W = probeset2471
+YOL132W = probeset2472
+YKR023W = probeset2473
+YCL008C = probeset2474
+YNL226W = probeset2475
+YJR117W = probeset2476
+YJL013C = probeset2477
+YHR086W = probeset2478
+YIL034C = probeset2479
+YPR070W = probeset2480
+YIL107C = probeset2481
+YHR159W = probeset2482
+YPR143W = probeset2483
+YOR091W = probeset2484
+YPL112C = probeset2485
+YGL076C = probeset2486
+YDR019C = probeset2487
+YOL060C = probeset2488
+YLR003C = probeset2489
+YOR237W = probeset2490
+YKR024C = probeset2491
+YNL081C = probeset2492
+YNL154C = probeset2493
+YNL227C = probeset2494
+YJR045C = probeset2495
+YJR118C = probeset2496
+YPR144C = probeset2497
+YDR302W = probeset2498
+YBR271W = probeset2499
+YGL149W = probeset2500
+YOL133W = probeset2501
+YCL009C = probeset2502
+YDR303C = probeset2503
+YIL035C = probeset2504
+YHR087W = probeset2505
+YPR071W = probeset2506
+YBR272C = probeset2507
+YPL040C = probeset2508
+YOR092W = probeset2509
+YPL113C = probeset2510
+YOR165W = probeset2511
+YGL077C = probeset2512
+YLR004C = probeset2513
+YOR238W = probeset2514
+YOL134C = probeset2515
+YJR119C = probeset2516
+YOR093C = probeset2517
+YOR166C = probeset2518
+YJL014W = probeset2519
+YIL108W = probeset2520
+YOL061W = probeset2521
+YNL082W = probeset2522
+YKR025W = probeset2523
+YNL155W = probeset2524
+YJR046W = probeset2525
+YNL228W = probeset2526
+YDR231C = probeset2527
+YJL015C = probeset2528
+YDR304C = probeset2529
+YHR088W = probeset2530
+YPR072W = probeset2531
+YIL109C = probeset2532
+YBR273C = probeset2533
+YPR145W = probeset2534
+YPL041C = probeset2535
+YGL078C = probeset2536
+YOR239W = probeset2537
+YOL062C = probeset2538
+YOL135C = probeset2539
+YKR026C = probeset2540
+YNL156C = probeset2541
+YNL229C = probeset2542
+YJR047C = probeset2543
+YHR089C = probeset2544
+YPR073C = probeset2545
+YPR146C = probeset2546
+YOR167C = probeset2547
+YDL200C = probeset2548
+YIL036W = probeset2549
+YPL114W = probeset2550
+YLR005W = probeset2551
+YNL083W = probeset2552
+YDR305C = probeset2553
+YIL037C = probeset2554
+YOR094W = probeset2555
+YPL042C = probeset2556
+YPL115C = probeset2557
+YOL063C = probeset2558
+YLR006C = probeset2559
+YOL136C = probeset2560
+YNL084C = probeset2561
+YPR074C = probeset2562
+YPR147C = probeset2563
+YOR095C = probeset2564
+YDR232W = probeset2565
+YJL016W = probeset2566
+YBR274W = probeset2567
+YGL079W = probeset2568
+YKR027W = probeset2569
+YNL157W = probeset2570
+YJR048W = probeset2571
+YDR233C = probeset2572
+YDR306C = probeset2573
+YIL038C = probeset2574
+YBR275C = probeset2575
+YOR168W = probeset2576
+YOL064C = probeset2577
+YDL201W = probeset2578
+YJR049C = probeset2579
+YPR075C = probeset2580
+YPR148C = probeset2581
+YOR169C = probeset2582
+YDR160W = probeset2583
+YJL017W = probeset2584
+YPL043W = probeset2585
+YPL116W = probeset2586
+YLR007W = probeset2587
+YOL137W = probeset2588
+YKR028W = probeset2589
+YNL085W = probeset2590
+YNL158W = probeset2591
+YBR276C = probeset2592
+YPL044C = probeset2593
+YOR096W = probeset2594
+YPL117C = probeset2595
+YOL065C = probeset2596
+YLR008C = probeset2597
+YOL138C = probeset2598
+YKR029C = probeset2599
+YDL202W = probeset2600
+YNL159C = probeset2601
+YER140W = probeset2602
+YOR097C = probeset2603
+YDR161W = probeset2604
+YDR234W = probeset2605
+YJL018W = probeset2606
+YDR307W = probeset2607
+YDL203C = probeset2608
+YIL039W = probeset2609
+YNL086W = probeset2610
+YDR162C = probeset2611
+YOR380W = probeset2612
+YDR308C = probeset2613
+YPR076W = probeset2614
+YBR277C = probeset2615
+YPR149W = probeset2616
+YOL066C = probeset2617
+YDL130W = probeset2618
+YOL139C = probeset2619
+YPR077C = probeset2620
+YER141W = probeset2621
+YOR098C = probeset2622
+YJL019W = probeset2623
+YDR235W = probeset2624
+YPL045W = probeset2625
+YPL118W = probeset2626
+YLR009W = probeset2627
+YNL087W = probeset2628
+YER142C = probeset2629
+YDR090C = probeset2630
+YOR381W = probeset2631
+YDR236C = probeset2632
+YDR309C = probeset2633
+YPL119C = probeset2634
+YOL067C = probeset2635
+YDL131W = probeset2636
+YDL204W = probeset2637
+YGR100W = probeset2638
+YPR078C = probeset2639
+YDR163W = probeset2640
+YLR220W = probeset2641
+YDL205C = probeset2642
+YBR278W = probeset2643
+YDR520C = probeset2644
+YNL088W = probeset2645
+YDR091C = probeset2646
+YDR164C = probeset2647
+YOR382W = probeset2648
+YLR221C = probeset2649
+YOR099W = probeset2650
+YAR002W = probeset2651
+YOL068C = probeset2652
+YDL132W = probeset2653
+YNL089C = probeset2654
+YKL210W = probeset2655
+YOR383C = probeset2656
+YGR101W = probeset2657
+YER070W = probeset2658
+YER143W = probeset2659
+YDR237W = probeset2660
+YBR279W = probeset2661
+YKL211C = probeset2662
+YGR102C = probeset2663
+YFR050C = probeset2664
+YER071C = probeset2665
+YER144C = probeset2666
+YMR201C = probeset2667
+YDR238C = probeset2668
+YLR222C = probeset2669
+YPR079W = probeset2670
+YDL060W = probeset2671
+YAR003W = probeset2672
+YDL133W = probeset2673
+YDL206W = probeset2674
+YDR521W = probeset2675
+YDR092W = probeset2676
+YDR165W = probeset2677
+YDL061C = probeset2678
+YDL134C = probeset2679
+YGR030C = probeset2680
+YPL048W = probeset2681
+YJL160C = probeset2682
+YOL069W = probeset2683
+YFR051C = probeset2684
+YDR522C = probeset2685
+YER145C = probeset2686
+YDR166C = probeset2687
+YOR384W = probeset2688
+YDR239C = probeset2689
+YLR223C = probeset2690
+YPL049C = probeset2691
+YEL040W = probeset2692
+YDL207W = probeset2693
+YKL212W = probeset2694
+YGR103W = probeset2695
+YER072W = probeset2696
+YFL020C = probeset2697
+YDR093W = probeset2698
+YMR202W = probeset2699
+YLR150W = probeset2700
+YDL135C = probeset2701
+YKL213C = probeset2702
+YGR104C = probeset2703
+YDR523C = probeset2704
+YLR151C = probeset2705
+YOR385W = probeset2706
+YEL041W = probeset2707
+YDL062W = probeset2708
+YDL208W = probeset2709
+YHR010W = probeset2710
+YKL140W = probeset2711
+YGR031W = probeset2712
+YJL161W = probeset2713
+YFR052W = probeset2714
+YDR450W = probeset2715
+YER073W = probeset2716
+YER146W = probeset2717
+YMR130W = probeset2718
+YDR167W = probeset2719
+YPL260W = probeset2720
+YMR203W = probeset2721
+YDL063C = probeset2722
+YLR224W = probeset2723
+YDL209C = probeset2724
+YKL214C = probeset2725
+YJL162C = probeset2726
+YDR451C = probeset2727
+YFR053C = probeset2728
+YDR524C = probeset2729
+YER147C = probeset2730
+YMR131C = probeset2731
+YDR095C = probeset2732
+YPL261C = probeset2733
+YMR204C = probeset2734
+YLR152C = probeset2735
+YOR386W = probeset2736
+YLR225C = probeset2737
+YFL021W = probeset2738
+YEL042W = probeset2739
+YDL136W = probeset2740
+YHR011W = probeset2741
+YKL141W = probeset2742
+YGR032W = probeset2743
+YOR387C = probeset2744
+YGR105W = probeset2745
+YGL001C = probeset2746
+YER074W = probeset2747
+YFL022C = probeset2748
+YDR168W = probeset2749
+YAR007C = probeset2750
+YGR033C = probeset2751
+YJL090C = probeset2752
+YKL215C = probeset2753
+YGR106C = probeset2754
+YJL163C = probeset2755
+YFR054C = probeset2756
+YER075C = probeset2757
+YDR169C = probeset2758
+YMR205C = probeset2759
+YLR153C = probeset2760
+YEL043W = probeset2761
+YDL064W = probeset2762
+YML100W = probeset2763
+YDL137W = probeset2764
+YHR012W = probeset2765
+YKL142W = probeset2766
+YOR388C = probeset2767
+YDR452W = probeset2768
+YDR525W = probeset2769
+YER148W = probeset2770
+YDR096W = probeset2771
+YPL262W = probeset2772
+YLR080W = probeset2773
+YDL065C = probeset2774
+YML101C = probeset2775
+YLR226W = probeset2776
+YHR013C = probeset2777
+YJL091C = probeset2778
+YJL164C = probeset2779
+YDR453C = probeset2780
+YDR526C = probeset2781
+YER076C = probeset2782
+YMR060C = probeset2783
+YER149C = probeset2784
+YDR097C = probeset2785
+YPL190C = probeset2786
+YPL263C = probeset2787
+YLR154C = probeset2788
+YLR227C = probeset2789
+YGL002W = probeset2790
+YFL023W = probeset2791
+YEL044W = probeset2792
+YAR008W = probeset2793
+YDL138W = probeset2794
+YKL070W = probeset2795
+YKL143W = probeset2796
+YKL216W = probeset2797
+YGR034W = probeset2798
+YDR380W = probeset2799
+YGR107W = probeset2800
+YGL003C = probeset2801
+YFR055W = probeset2802
+YFL024C = probeset2803
+YEL045C = probeset2804
+YMR133W = probeset2805
+YMR206W = probeset2806
+YLR081W = probeset2807
+YAR009C = probeset2808
+YDL139C = probeset2809
+YLL050C = probeset2810
+YKL144C = probeset2811
+YGR035C = probeset2812
+YJL165C = probeset2813
+YFR056C = probeset2814
+YDR454C = probeset2815
+YER077C = probeset2816
+YDR098C = probeset2817
+YPL191C = probeset2818
+YLR082C = probeset2819
+YPL264C = probeset2820
+YOR389W = probeset2821
+YLR155C = probeset2822
+YLR228C = probeset2823
+YML102W = probeset2824
+YDL066W = probeset2825
+YKL071W = probeset2826
+YHR014W = probeset2827
+YKL217W = probeset2828
+YJL092W = probeset2829
+YDR381W = probeset2830
+YGR108W = probeset2831
+YGL004C = probeset2832
+YDR527W = probeset2833
+YNR040W = probeset2834
+YFL025C = probeset2835
+YMR061W = probeset2836
+YMR134W = probeset2837
+YEL046C = probeset2838
+YDL067C = probeset2839
+YML103C = probeset2840
+YLL051C = probeset2841
+YJL093C = probeset2842
+YKL218C = probeset2843
+YGR036C = probeset2844
+YOR020C = probeset2845
+YGR109C = probeset2846
+YDR455C = probeset2847
+YNR041C = probeset2848
+YER078C = probeset2849
+YMR062C = probeset2850
+YPL192C = probeset2851
+YMR135C = probeset2852
+YLR083C = probeset2853
+YLR229C = probeset2854
+YML030W = probeset2855
+YHR015W = probeset2856
+YKL072W = probeset2857
+YKL145W = probeset2858
+YJL166W = probeset2859
+YDR382W = probeset2860
+YFR057W = probeset2861
+YGL005C = probeset2862
+YDR528W = probeset2863
+YDR099W = probeset2864
+YEL047C = probeset2865
+YPL265W = probeset2866
+YMR208W = probeset2867
+YLR156W = probeset2868
+YML104C = probeset2869
+YLL052C = probeset2870
+YHR016C = probeset2871
+YJL094C = probeset2872
+YGR037C = probeset2873
+YDR383C = probeset2874
+YOR021C = probeset2875
+YLR440C = probeset2876
+YDR529C = probeset2877
+YBR200W = probeset2878
+YMR209C = probeset2879
+YLR084C = probeset2880
+YLR157C = probeset2881
+YFL026W = probeset2882
+YNL010W = probeset2883
+YML031W = probeset2884
+YDL068W = probeset2885
+YKL073W = probeset2886
+YKL146W = probeset2887
+YKL219W = probeset2888
+YJL167W = probeset2889
+YDR456W = probeset2890
+YNR042W = probeset2891
+YFL027C = probeset2892
+YER079W = probeset2893
+YNL011C = probeset2894
+YMR063W = probeset2895
+YPL193W = probeset2896
+YMR136W = probeset2897
+YEL048C = probeset2898
+YML032C = probeset2899
+YPL266W = probeset2900
+YDL069C = probeset2901
+YML105C = probeset2902
+YKL074C = probeset2903
+YKL147C = probeset2904
+YDR384C = probeset2905
+YJL168C = probeset2906
+YOR022C = probeset2907
+YLR441C = probeset2908
+YMR137C = probeset2909
+YLR085C = probeset2910
+YBR201W = probeset2911
+YLR158C = probeset2912
+YGL006W = probeset2913
+YHR017W = probeset2914
+YPR001W = probeset2915
+YJL095W = probeset2916
+YGR038W = probeset2917
+YDR457W = probeset2918
+YNR043W = probeset2919
+YFL028C = probeset2920
+YMR064W = probeset2921
+YPL194W = probeset2922
+YPL267W = probeset2923
+YLL054C = probeset2924
+YKL075C = probeset2925
+YHR018C = probeset2926
+YKL148C = probeset2927
+YOR023C = probeset2928
+YDR458C = probeset2929
+YLR442C = probeset2930
+YBR202W = probeset2931
+YGL007W = probeset2932
+YNL012W = probeset2933
+YEL049W = probeset2934
+YML106W = probeset2935
+YPR002W = probeset2936
+YBR130C = probeset2937
+YJL096W = probeset2938
+YGR039W = probeset2939
+YDR385W = probeset2940
+YJL169W = probeset2941
+YGL008C = probeset2942
+YNR044W = probeset2943
+YFL029C = probeset2944
+YMR065W = probeset2945
+YNL013C = probeset2946
+YMR138W = probeset2947
+YPL195W = probeset2948
+YLR086W = probeset2949
+YPL268W = probeset2950
+YGR250C = probeset2951
+YML107C = probeset2952
+YLR159W = probeset2953
+YKL076C = probeset2954
+YHR019C = probeset2955
+YKL149C = probeset2956
+YPR003C = probeset2957
+YLR370C = probeset2958
+YDR459C = probeset2959
+YLR087C = probeset2960
+YBR203W = probeset2961
+YML034W = probeset2962
+YLL055W = probeset2963
+YBR204C = probeset2964
+YJL097W = probeset2965
+YDR386W = probeset2966
+YOR024W = probeset2967
+YGL009C = probeset2968
+YNR045W = probeset2969
+YLR443W = probeset2970
+YMR066W = probeset2971
+YMR139W = probeset2972
+YPL196W = probeset2973
+YML035C = probeset2974
+YPL269W = probeset2975
+YLL056C = probeset2976
+YPR004C = probeset2977
+YDR387C = probeset2978
+YLR444C = probeset2979
+YMR067C = probeset2980
+YBR131W = probeset2981
+YBL100C = probeset2982
+YNL014W = probeset2983
+YGR251W = probeset2984
+YML108W = probeset2985
+YKL077W = probeset2986
+YBR132C = probeset2987
+YJL098W = probeset2988
+YOR025W = probeset2989
+YLR371W = probeset2990
+YNR046W = probeset2991
+YLR088W = probeset2992
+YLL057C = probeset2993
+YPR005C = probeset2994
+YGL220W = probeset2995
+YBR205W = probeset2996
+YLR089C = probeset2997
+YBL101C = probeset2998
+YNL015W = probeset2999
+YGR252W = probeset3000
+YML036W = probeset3001
+YML109W = probeset3002
+YGL221C = probeset3003
+YKL078W = probeset3004
+YBR060C = probeset3005
+YBR133C = probeset3006
+YJL099W = probeset3007
+YOR026W = probeset3008
+YDR388W = probeset3009
+YLR372W = probeset3010
+YLR445W = probeset3011
+YNR047W = probeset3012
+YMR068W = probeset3013
+YPL198W = probeset3014
+YGR180C = probeset3015
+YML037C = probeset3016
+YGR253C = probeset3017
+YOR310C = probeset3018
+YPR006C = probeset3019
+YLR373C = probeset3020
+YPL199C = probeset3021
+YBR206W = probeset3022
+YNL016W = probeset3023
+YLL058W = probeset3024
+YGL222C = probeset3025
+YKL079W = probeset3026
+YBR061C = probeset3027
+YOR027W = probeset3028
+YDR389W = probeset3029
+YNR048W = probeset3030
+YLR446W = probeset3031
+YHR160C = probeset3032
+YNL017C = probeset3033
+YMR069W = probeset3034
+YER119C-A = probeset3035
+YML038C = probeset3036
+YBL102W = probeset3037
+YOR311C = probeset3038
+YLL059C = probeset3039
+YMR280C = probeset3040
+YPR007C = probeset3041
+YOR028C = probeset3042
+YLR374C = probeset3043
+YLR447C = probeset3044
+YCR040W = probeset3045
+YNR049C = probeset3046
+YBR134W = probeset3047
+YBL030C = probeset3048
+YBR207W = probeset3049
+YNL300W = probeset3050
+YBL103C = probeset3051
+YGR181W = probeset3052
+YGR254W = probeset3053
+YDR020C = probeset3054
+YGL150C = probeset3055
+YGL223C = probeset3056
+YBR062C = probeset3057
+YNL301C = probeset3058
+YBR208C = probeset3059
+YHR161C = probeset3060
+YNL018C = probeset3061
+YGR182C = probeset3062
+YGR255C = probeset3063
+YOR312C = probeset3064
+YAL051W = probeset3065
+YCR041W = probeset3066
+YCL010C = probeset3067
+YBR135W = probeset3068
+YBL104C = probeset3069
+YGL224C = probeset3070
+YCR042C = probeset3071
+YBR063C = probeset3072
+YPR008W = probeset3073
+YMR281W = probeset3074
+YOR029W = probeset3075
+YLR375W = probeset3076
+YLR448W = probeset3077
+YNL019C = probeset3078
+YGR183C = probeset3079
+YBL031W = probeset3080
+YOR313C = probeset3081
+YMR282C = probeset3082
+YDR021W = probeset3083
+YLR376C = probeset3084
+YGL151W = probeset3085
+YCL011C = probeset3086
+YBR136W = probeset3087
+YBR209W = probeset3088
+YJR120W = probeset3089
+YBL105C = probeset3090
+YHR162W = probeset3091
+YGR256W = probeset3092
+YDR022C = probeset3093
+YOR240W = probeset3094
+YGL152C = probeset3095
+YCR043C = probeset3096
+YKR100C = probeset3097
+YPR009W = probeset3098
+YNL230C = probeset3099
+YHR090C = probeset3100
+YLR449W = probeset3101
+YGR184C = probeset3102
+YGR257C = probeset3103
+YBL032W = probeset3104
+YAL053W = probeset3105
+YIL110W = probeset3106
+YMR283C = probeset3107
+YER001W = probeset3108
+YLR377C = probeset3109
+YGL225W = probeset3110
+YBR064W = probeset3111
+YBR137W = probeset3112
+YBL033C = probeset3113
+YNL303W = probeset3114
+YJR121W = probeset3115
+YBL106C = probeset3116
+YAL054C = probeset3117
+YHR163W = probeset3118
+YOR241W = probeset3119
+YCR044C = probeset3120
+YOR314W = probeset3121
+YBR065C = probeset3122
+YBR138C = probeset3123
+YNL231C = probeset3124
+YHR091C = probeset3125
+YHR164C = probeset3126
+YCL012W = probeset3127
+YGR185C = probeset3128
+YGR258C = probeset3129
+YOR242C = probeset3130
+YIL111W = probeset3131
+YER002W = probeset3132
+YGL080W = probeset3133
+YDR023W = probeset3134
+YGL153W = probeset3135
+YLR378C = probeset3136
+YGL226W = probeset3137
+YKR101W = probeset3138
+YBL034C = probeset3139
+YNL304W = probeset3140
+YJR122W = probeset3141
+YBL107C = probeset3142
+YER003C = probeset3143
+YGL154C = probeset3144
+YCR045C = probeset3145
+YOR315W = probeset3146
+YBR066C = probeset3147
+YMR284W = probeset3148
+YNL305C = probeset3149
+YHR092C = probeset3150
+YHR165C = probeset3151
+YGR259C = probeset3152
+YOR243C = probeset3153
+YOR316C = probeset3154
+YAL055W = probeset3155
+YIL112W = probeset3156
+YMR285C = probeset3157
+YDR024W = probeset3158
+YGL081W = probeset3159
+YGL227W = probeset3160
+YKR102W = probeset3161
+YJR050W = probeset3162
+YNL232W = probeset3163
+YBR139W = probeset3164
+YBL035C = probeset3165
+YJR123W = probeset3166
+YGR186W = probeset3167
+YOR170W = probeset3168
+YCR046C = probeset3169
+YJR124C = probeset3170
+YLR379W = probeset3171
+YHR166C = probeset3172
+YCL014W = probeset3173
+YGR187C = probeset3174
+YOR171C = probeset3175
+YBL108W = probeset3176
+YAL056W = probeset3177
+YIL040W = probeset3178
+YIL113W = probeset3179
+YER004W = probeset3180
+YDR025W = probeset3181
+YGL082W = probeset3182
+YGL155W = probeset3183
+YGL228W = probeset3184
+YKR030W = probeset3185
+YKR103W = probeset3186
+YNL160W = probeset3187
+YNL233W = probeset3188
+YJR051W = probeset3189
+YNL306W = probeset3190
+YBL036C = probeset3191
+YJL020C = probeset3192
+YHR093W = probeset3193
+YIL114C = probeset3194
+YPR150W = probeset3195
+YDR026C = probeset3196
+YOR244W = probeset3197
+YLR010C = probeset3198
+YCR047C = probeset3199
+YGL229C = probeset3200
+YOR317W = probeset3201
+YKR031C = probeset3202
+YBR068C = probeset3203
+YMR286W = probeset3204
+YJR125C = probeset3205
+YNL307C = probeset3206
+YHR094C = probeset3207
+YPR151C = probeset3208
+YGR188C = probeset3209
+YOR245C = probeset3210
+YOR318C = probeset3211
+YIL041W = probeset3212
+YMR287C = probeset3213
+YER005W = probeset3214
+YGL083W = probeset3215
+YGL156W = probeset3216
+YOL140W = probeset3217
+YKR104W = probeset3218
+YCL016C = probeset3219
+YNL161W = probeset3220
+YNL234W = probeset3221
+YJR052W = probeset3222
+YJL021C = probeset3223
+YDR310C = probeset3224
+YIL042C = probeset3225
+YIL115C = probeset3226
+YHR167W = probeset3227
+YOR172W = probeset3228
+YGL084C = probeset3229
+YDR027C = probeset3230
+YBR069C = probeset3231
+YKR105C = probeset3232
+YNL235C = probeset3233
+YNL308C = probeset3234
+YJR126C = probeset3235
+YPR152C = probeset3236
+YGR189C = probeset3237
+YBL037W = probeset3238
+YOR246C = probeset3239
+YAL058W = probeset3240
+YER006W = probeset3241
+YPL120W = probeset3242
+YGL157W = probeset3243
+YLR011W = probeset3244
+YOL141W = probeset3245
+YCR048W = probeset3246
+YKR032W = probeset3247
+YNL162W = probeset3248
+YCL017C = probeset3249
+YJR053W = probeset3250
+YKL001C = probeset3251
+YIL043C = probeset3252
+YHR095W = probeset3253
+YHR168W = probeset3254
+YBR280C = probeset3255
+YDR028C = probeset3256
+YOR173W = probeset3257
+YPL121C = probeset3258
+YLR012C = probeset3259
+YOR319W = probeset3260
+YCR049C = probeset3261
+YKR033C = probeset3262
+YNL163C = probeset3263
+YMR288W = probeset3264
+YJR127C = probeset3265
+YHR096C = probeset3266
+YBL038W = probeset3267
+YJL022W = probeset3268
+YDR311W = probeset3269
+YAL059W = probeset3270
+YIL116W = probeset3271
+YER007W = probeset3272
+YGL085W = probeset3273
+YGL158W = probeset3274
+YOL142W = probeset3275
+YNL090W = probeset3276
+YKR106W = probeset3277
+YNL236W = probeset3278
+YJR054W = probeset3279
+YNL309W = probeset3280
+YBL039C = probeset3281
+YJL023C = probeset3282
+YIL044C = probeset3283
+YIL117C = probeset3284
+YPR080W = probeset3285
+YHR169W = probeset3286
+YER008C = probeset3287
+YPR153W = probeset3288
+YBR281C = probeset3289
+YOR174W = probeset3290
+YPL122C = probeset3291
+YOL070C = probeset3292
+YOR247W = probeset3293
+YOL143C = probeset3294
+YNL164C = probeset3295
+YHR097C = probeset3296
+YPR081C = probeset3297
+YCL018W = probeset3298
+YKL002W = probeset3299
+YOR175C = probeset3300
+YDR312W = probeset3301
+YCR073W-A = probeset3302
+YGL086W = probeset3303
+YDR029W = probeset3304
+YLR013W = probeset3305
+YGL159W = probeset3306
+YNL091W = probeset3307
+YKR034W = probeset3308
+YNL237W = probeset3309
+YJR055W = probeset3310
+YKL003C = probeset3311
+YJR128W = probeset3312
+YJL024C = probeset3313
+YDR240C = probeset3314
+YDR313C = probeset3315
+YPR154W = probeset3316
+YPL050C = probeset3317
+YPL123C = probeset3318
+YGL087C = probeset3319
+YLR014C = probeset3320
+YOR248W = probeset3321
+YKR035C = probeset3322
+YJR056C = probeset3323
+YJR129C = probeset3324
+YHR098C = probeset3325
+YPR082C = probeset3326
+YPR155C = probeset3327
+YOR249C = probeset3328
+YIL045W = probeset3329
+YIL118W = probeset3330
+YER009W = probeset3331
+YBR282W = probeset3332
+YOL071W = probeset3333
+YOL144W = probeset3334
+YNL092W = probeset3335
+YNL165W = probeset3336
+YNL238W = probeset3337
+YDR314C = probeset3338
+YIL119C = probeset3339
+YBR283C = probeset3340
+YOR176W = probeset3341
+YOL145C = probeset3342
+YKR036C = probeset3343
+YNL166C = probeset3344
+YPR156C = probeset3345
+YKL004W = probeset3346
+YOR177C = probeset3347
+YDR241W = probeset3348
+YJL025W = probeset3349
+YIL046W = probeset3350
+YPL051W = probeset3351
+YGL088W = probeset3352
+YPL124W = probeset3353
+YLR015W = probeset3354
+YOL072W = probeset3355
+YNL093W = probeset3356
+YNL239W = probeset3357
+YKL005C = probeset3358
+YJR057W = probeset3359
+YDR315C = probeset3360
+YIL047C = probeset3361
+YPR083W = probeset3362
+YGL089C = probeset3363
+YOL073C = probeset3364
+YLR016C = probeset3365
+YDL210W = probeset3366
+YKR037C = probeset3367
+YNL167C = probeset3368
+YJR058C = probeset3369
+YOR178C = probeset3370
+YJL026W = probeset3371
+YER060W-A = probeset3372
+YDR242W = probeset3373
+YDL211C = probeset3374
+YBR284W = probeset3375
+YPL052W = probeset3376
+YPL125W = probeset3377
+YOL146W = probeset3378
+YNL094W = probeset3379
+YDR170C = probeset3380
+YDR243C = probeset3381
+YJL027C = probeset3382
+YPR084W = probeset3383
+YPR157W = probeset3384
+YPL053C = probeset3385
+YOL147C = probeset3386
+YNL095C = probeset3387
+YKR038C = probeset3388
+YNL168C = probeset3389
+YPR085C = probeset3390
+YKL006W = probeset3391
+YOR179C = probeset3392
+YDR316W = probeset3393
+YLR300W = probeset3394
+YIL048W = probeset3395
+YBR285W = probeset3396
+YPL126W = probeset3397
+YLR017W = probeset3398
+YJR059W = probeset3399
+YPR158W = probeset3400
+YPL127C = probeset3401
+YLR018C = probeset3402
+YOL075C = probeset3403
+YOL148C = probeset3404
+YNL096C = probeset3405
+YDL212W = probeset3406
+YNL169C = probeset3407
+YER150W = probeset3408
+YKL007W = probeset3409
+YDR171W = probeset3410
+YDR244W = probeset3411
+YJL028W = probeset3412
+YDR317W = probeset3413
+YDL140C = probeset3414
+YDL213C = probeset3415
+YIL049W = probeset3416
+YLR301W = probeset3417
+YBR286W = probeset3418
+YPL054W = probeset3419
+YKR039W = probeset3420
+YER151C = probeset3421
+YKL008C = probeset3422
+YOR390W = probeset3423
+YJL029C = probeset3424
+YLR302C = probeset3425
+YPR086W = probeset3426
+YPR159W = probeset3427
+YPL055C = probeset3428
+YPL128C = probeset3429
+YNL097C = probeset3430
+YOR391C = probeset3431
+YDR172W = probeset3432
+YDR245W = probeset3433
+YDR318W = probeset3434
+YDL214C = probeset3435
+YBR287W = probeset3436
+YLR019W = probeset3437
+YOL076W = probeset3438
+YOL149W = probeset3439
+YER152C = probeset3440
+YDR173C = probeset3441
+YDR319C = probeset3442
+YPR087W = probeset3443
+YBR288C = probeset3444
+YPL056C = probeset3445
+YOL077C = probeset3446
+YDL141W = probeset3447
+YNL098C = probeset3448
+YGR110W = probeset3449
+YPR088C = probeset3450
+YKL009W = probeset3451
+YDR246W = probeset3452
+YDL142C = probeset3453
+YDL215C = probeset3454
+YLR303W = probeset3455
+YKL220C = probeset3456
+YPL129W = probeset3457
+YDR530C = probeset3458
+YER153C = probeset3459
+YOR392W = probeset3460
+YLR231C = probeset3461
+YLR304C = probeset3462
+YPL057C = probeset3463
+YNL099C = probeset3464
+YGR111W = probeset3465
+YER080W = probeset3466
+YDR174W = probeset3467
+YMR210W = probeset3468
+YDR247W = probeset3469
+YDL216C = probeset3470
+YBR289W = probeset3471
+YOL078W = probeset3472
+YDR175C = probeset3473
+YDR248C = probeset3474
+YOR393W = probeset3475
+YLR305C = probeset3476
+YPR089W = probeset3477
+YPL058C = probeset3478
+YDL070W = probeset3479
+YDL143W = probeset3480
+YKL221W = probeset3481
+YGR112W = probeset3482
+YDR531W = probeset3483
+YER081W = probeset3484
+YER154W = probeset3485
+YEL050C = probeset3486
+YMR211W = probeset3487
+YDL071C = probeset3488
+YAR014C = probeset3489
+YDL144C = probeset3490
+YLR232W = probeset3491
+YDL217C = probeset3492
+YKL222C = probeset3493
+YJL170C = probeset3494
+YOL079W = probeset3495
+YDR532C = probeset3496
+YER082C = probeset3497
+YER155C = probeset3498
+YMR212C = probeset3499
+YDR249C = probeset3500
+YOR394W = probeset3501
+YLR160C = probeset3502
+YLR233C = probeset3503
+YGR040W = probeset3504
+YGR113W = probeset3505
+YDR176W = probeset3506
+YDL072C = probeset3507
+YDL145C = probeset3508
+YLR306W = probeset3509
+YPL059W = probeset3510
+YGR114C = probeset3511
+YJL171C = probeset3512
+YDR533C = probeset3513
+YER083C = probeset3514
+YER156C = probeset3515
+YFL030W = probeset3516
+YEL051W = probeset3517
+YAR015W = probeset3518
+YDL218W = probeset3519
+YHR020W = probeset3520
+YKL150W = probeset3521
+YKL223W = probeset3522
+YGR041W = probeset3523
+YDR460W = probeset3524
+YMR140W = probeset3525
+YMR213W = probeset3526
+YDR177W = probeset3527
+YPL270W = probeset3528
+YLR161W = probeset3529
+YLR234W = probeset3530
+YLR307W = probeset3531
+YHR021C = probeset3532
+YKL151C = probeset3533
+YKL224C = probeset3534
+YGR115C = probeset3535
+YDR534C = probeset3536
+YMR141C = probeset3537
+YGL010W = probeset3538
+YFL031W = probeset3539
+YEL052W = probeset3540
+YDL073W = probeset3541
+YDL146W = probeset3542
+YDL219W = probeset3543
+YGR042W = probeset3544
+YJL172W = probeset3545
+YDR461W = probeset3546
+YGL011C = probeset3547
+YER084W = probeset3548
+YER157W = probeset3549
+YEL053C = probeset3550
+YMR214W = probeset3551
+YPL271W = probeset3552
+YDR178W = probeset3553
+YDL074C = probeset3554
+YML110C = probeset3555
+YLR162W = probeset3556
+YIR001C = probeset3557
+YLR308W = probeset3558
+YHR022C = probeset3559
+YKL152C = probeset3560
+YGR043C = probeset3561
+YJL173C = probeset3562
+YOR100C = probeset3563
+YDR535C = probeset3564
+YER085C = probeset3565
+YER158C = probeset3566
+YMR142C = probeset3567
+YDR179C = probeset3568
+YPL272C = probeset3569
+YLR163C = probeset3570
+YHR049C-A = probeset3571
+YLR309C = probeset3572
+YFL032W = probeset3573
+YDL147W = probeset3574
+YKL225W = probeset3575
+YGR116W = probeset3576
+YDR462W = probeset3577
+YFL033C = probeset3578
+YEL054C = probeset3579
+YLR090W = probeset3580
+YMR215W = probeset3581
+YAR018C = probeset3582
+YDL148C = probeset3583
+YIR002C = probeset3584
+YGR044C = probeset3585
+YDR390C = probeset3586
+YGR117C = probeset3587
+YER159C = probeset3588
+YMR216C = probeset3589
+YGL012W = probeset3590
+YDL075W = probeset3591
+YML111W = probeset3592
+YHR023W = probeset3593
+YKL080W = probeset3594
+YKL153W = probeset3595
+YJL174W = probeset3596
+YDR463W = probeset3597
+YGL013C = probeset3598
+YOR101W = probeset3599
+YDR536W = probeset3600
+YER086W = probeset3601
+YMR070W = probeset3602
+YEL055C = probeset3603
+YMR143W = probeset3604
+YPL273W = probeset3605
+YLR091W = probeset3606
+YLR164W = probeset3607
+YDL076C = probeset3608
+YAR019C = probeset3609
+YLL060C = probeset3610
+YLR237W = probeset3611
+YHR024C = probeset3612
+YGR045C = probeset3613
+YDR391C = probeset3614
+YNR050C = probeset3615
+YDR537C = probeset3616
+YMR071C = probeset3617
+YLR165C = probeset3618
+YFL034W = probeset3619
+YML112W = probeset3620
+YIR003W = probeset3621
+YDL149W = probeset3622
+YKL081W = probeset3623
+YKL154W = probeset3624
+YJL175W = probeset3625
+YGR118W = probeset3626
+YDR464W = probeset3627
+YOR102W = probeset3628
+YER087W = probeset3629
+YMR144W = probeset3630
+YPL274W = probeset3631
+YLR092W = probeset3632
+YMR217W = probeset3633
+YDL077C = probeset3634
+YLR238W = probeset3635
+YKL082C = probeset3636
+YKL155C = probeset3637
+YJL176C = probeset3638
+YGR119C = probeset3639
+YOR103C = probeset3640
+YDR465C = probeset3641
+YNR051C = probeset3642
+YER088C = probeset3643
+YMR145C = probeset3644
+YMR218C = probeset3645
+YLR093C = probeset3646
+YLR166C = probeset3647
+YGL014W = probeset3648
+YLR239C = probeset3649
+YEL056W = probeset3650
+YML113W = probeset3651
+YLL061W = probeset3652
+YIR004W = probeset3653
+YHR025W = probeset3654
+YGR046W = probeset3655
+YDR392W = probeset3656
+YOR030W = probeset3657
+YGL015C = probeset3658
+YDR538W = probeset3659
+YNL020C = probeset3660
+YMR072W = probeset3661
+YEL057C = probeset3662
+YPL275W = probeset3663
+YML041C = probeset3664
+YML114C = probeset3665
+YDL078C = probeset3666
+YLL062C = probeset3667
+YPR010C = probeset3668
+YGR047C = probeset3669
+YNR052C = probeset3670
+YER089C = probeset3671
+YMR073C = probeset3672
+YMR146C = probeset3673
+YBR210W = probeset3674
+YLR094C = probeset3675
+YFL036W = probeset3676
+YIR005W = probeset3677
+YHR026W = probeset3678
+YKL156W = probeset3679
+YBR211C = probeset3680
+YOR031W = probeset3681
+YJL177W = probeset3682
+YDR466W = probeset3683
+YOR104W = probeset3684
+YLR450W = probeset3685
+YDR539W = probeset3686
+YPL276W = probeset3687
+YDL079C = probeset3688
+YLR167W = probeset3689
+YML115C = probeset3690
+YIR006C = probeset3691
+YLL063C = probeset3692
+YHR027C = probeset3693
+YPR011C = probeset3694
+YOR032C = probeset3695
+YJL178C = probeset3696
+YDR467C = probeset3697
+YNR053C = probeset3698
+YMR074C = probeset3699
+YPL277C = probeset3700
+YLR095C = probeset3701
+YLR168C = probeset3702
+YGL016W = probeset3703
+YFL037W = probeset3704
+YNL021W = probeset3705
+YEL058W = probeset3706
+YML042W = probeset3707
+YKL084W = probeset3708
+YKL157W = probeset3709
+YGR048W = probeset3710
+YDR394W = probeset3711
+YOR105W = probeset3712
+YLR451W = probeset3713
+YFL038C = probeset3714
+YNL022C = probeset3715
+YMR147W = probeset3716
+YML043C = probeset3717
+YLL064C = probeset3718
+YHR028C = probeset3719
+YOR033C = probeset3720
+YDR468C = probeset3721
+YNR054C = probeset3722
+YLR452C = probeset3723
+YBR212W = probeset3724
+YPL278C = probeset3725
+YGL017W = probeset3726
+YOL001W = probeset3727
+YEL059W = probeset3728
+YML116W = probeset3729
+YIR007W = probeset3730
+YKL085W = probeset3731
+YKL158W = probeset3732
+YBR140C = probeset3733
+YGR049W = probeset3734
+YJL179W = probeset3735
+YDR395W = probeset3736
+YOR106W = probeset3737
+YGL018C = probeset3738
+YOL002C = probeset3739
+YFL039C = probeset3740
+YNL023C = probeset3741
+YMR075W = probeset3742
+YMR148W = probeset3743
+YLR096W = probeset3744
+YLR169W = probeset3745
+YIR008C = probeset3746
+YHR029C = probeset3747
+YKL159C = probeset3748
+YPR013C = probeset3749
+YOR034C = probeset3750
+YNR055C = probeset3751
+YLR453C = probeset3752
+YBR213W = probeset3753
+YPL279C = probeset3754
+YLR097C = probeset3755
+YGR260W = probeset3756
+YML117W = probeset3757
+YLL065W = probeset3758
+YBR141C = probeset3759
+YDR396W = probeset3760
+YDR469W = probeset3761
+YLR380W = probeset3762
+YOR107W = probeset3763
+YOL003C = probeset3764
+YNL024C = probeset3765
+YMR149W = probeset3766
+YGR261C = probeset3767
+YKL087C = probeset3768
+YPR014C = probeset3769
+YDR397C = probeset3770
+YOR035C = probeset3771
+YNR056C = probeset3772
+YMR077C = probeset3773
+YBR214W = probeset3774
+YLR098C = probeset3775
+YGL019W = probeset3776
+YML118W = probeset3777
+YIR009W = probeset3778
+YGL230C = probeset3779
+YLR381W = probeset3780
+YOR108W = probeset3781
+YLR454W = probeset3782
+YNL025C = probeset3783
+YGR262C = probeset3784
+YPR015C = probeset3785
+YLR382C = probeset3786
+YDR100W = probeset3787
+YNR057C = probeset3788
+YMR078C = probeset3789
+YBR142W = probeset3790
+YBR215W = probeset3791
+YLR099C = probeset3792
+YOL004W = probeset3793
+YML046W = probeset3794
+YML119W = probeset3795
+YDR101C = probeset3796
+YGL231C = probeset3797
+YKL088W = probeset3798
+YBR070C = probeset3799
+YBR143C = probeset3800
+YBR216C = probeset3801
+YDR398W = probeset3802
+YOR036W = probeset3803
+YOR109W = probeset3804
+YLR455W = probeset3805
+YOL005C = probeset3806
+YGR190C = probeset3807
+YGR263C = probeset3808
+YML047C = probeset3809
+YOR320C = probeset3810
+YPR016C = probeset3811
+YNL026W = probeset3812
+YDR102C = probeset3813
+YCR050C = probeset3814
+YKL089W = probeset3815
+YBR144C = probeset3816
+YNL310C = probeset3817
+YOR037W = probeset3818
+YDR399W = probeset3819
+YLR383W = probeset3820
+YOL006C = probeset3821
+YLR456W = probeset3822
+YNR058W = probeset3823
+YMR079W = probeset3824
+YGR264C = probeset3825
+YAL060W = probeset3826
+YMR290C = probeset3827
+YPR017C = probeset3828
+YOR038C = probeset3829
+YLR384C = probeset3830
+YGL232W = probeset3831
+YLR457C = probeset3832
+YBR071W = probeset3833
+YBR217W = probeset3834
+YBL040C = probeset3835
+YHR170W = probeset3836
+YNL027W = probeset3837
+YGR191W = probeset3838
+YDR030C = probeset3839
+YML048W = probeset3840
+YOR321W = probeset3841
+YNL311C = probeset3842
+YBR218C = probeset3843
+YNR059W = probeset3844
+YOL007C = probeset3845
+YGR192C = probeset3846
+YML049C = probeset3847
+YOR322C = probeset3848
+YAL061W = probeset3849
+YLR385C = probeset3850
+YGL160W = probeset3851
+YDR103W = probeset3852
+YCR051W = probeset3853
+YGL233W = probeset3854
+YBR072W = probeset3855
+YBR145W = probeset3856
+YHR171W = probeset3857
+YNL028W = probeset3858
+YER010C = probeset3859
+YGR265W = probeset3860
+YDR104C = probeset3861
+YGL161C = probeset3862
+YPR018W = probeset3863
+YMR291W = probeset3864
+YJR130C = probeset3865
+YOR039W = probeset3866
+YNL029C = probeset3867
+YGR193C = probeset3868
+YBL041W = probeset3869
+YOR250C = probeset3870
+YAL062W = probeset3871
+YOR323C = probeset3872
+YDR031W = probeset3873
+YGL234W = probeset3874
+YCR052W = probeset3875
+YBR073W = probeset3876
+YBR146W = probeset3877
+YNL312W = probeset3878
+YBL042C = probeset3879
+YAL063C = probeset3880
+YOL008W = probeset3881
+YHR172W = probeset3882
+YGR266W = probeset3883
+YDR032C = probeset3884
+YDR105C = probeset3885
+YNL240C = probeset3886
+YMR292W = probeset3887
+YPR019W = probeset3888
+YNL313C = probeset3889
+YLR386W = probeset3890
+YLR459W = probeset3891
+YOL009C = probeset3892
+YHR173C = probeset3893
+YGR194C = probeset3894
+YGR267C = probeset3895
+YOR251C = probeset3896
+YOR324C = probeset3897
+YIL120W = probeset3898
+YER011W = probeset3899
+YMR293C = probeset3900
+YLR387C = probeset3901
+YGL162W = probeset3902
+YCR053W = probeset3903
+YGL235W = probeset3904
+YBR074W = probeset3905
+YCL022C = probeset3906
+YBR147W = probeset3907
+YJR131W = probeset3908
+YGL163C = probeset3909
+YGL236C = probeset3910
+YCR054C = probeset3911
+YNL241C = probeset3912
+YDL001W = probeset3913
+YBL043W = probeset3914
+YGR268C = probeset3915
+YAL064W = probeset3916
+YJL100W = probeset3917
+YIL121W = probeset3918
+YER012W = probeset3919
+YDR033W = probeset3920
+YGL090W = probeset3921
+YDR106W = probeset3922
+YDL002C = probeset3923
+YBR075W = probeset3924
+YCL023C = probeset3925
+YBR148W = probeset3926
+YJR132W = probeset3927
+YNL314W = probeset3928
+YJL101C = probeset3929
+YHR174W = probeset3930
+YGR195W = probeset3931
+YGL091C = probeset3932
+YDR034C = probeset3933
+YGL164C = probeset3934
+YOR252W = probeset3935
+YDR107C = probeset3936
+YGL237C = probeset3937
+YOR325W = probeset3938
+YMR294W = probeset3939
+YNL315C = probeset3940
+YLR388W = probeset3941
+YGR196C = probeset3942
+YOR180C = probeset3943
+YBL044W = probeset3944
+YIL122W = probeset3945
+YER013W = probeset3946
+YMR295C = probeset3947
+YPL200W = probeset3948
+YLR389C = probeset3949
+YBR076W = probeset3950
+YJR060W = probeset3951
+YBR149W = probeset3952
+YNL242W = probeset3953
+YBL045C = probeset3954
+YJR133W = probeset3955
+YHR175W = probeset3956
+YGR269W = probeset3957
+YPL201C = probeset3958
+YOR253W = probeset3959
+YGL165C = probeset3960
+YOR326W = probeset3961
+YKR040C = probeset3962
+YBR077C = probeset3963
+YJR134C = probeset3964
+YNL316C = probeset3965
+YDL003W = probeset3966
+YCL024W = probeset3967
+YGR197C = probeset3968
+YOR254C = probeset3969
+YAL066W = probeset3970
+YOR327C = probeset3971
+YJL102W = probeset3972
+YIL050W = probeset3973
+YIL123W = probeset3974
+YMR296C = probeset3975
+YER014W = probeset3976
+YGL092W = probeset3977
+YDR035W = probeset3978
+YDR108W = probeset3979
+YGL238W = probeset3980
+YCL025C = probeset3981
+YNL170W = probeset3982
+YJR061W = probeset3983
+YNL243W = probeset3984
+YJL103C = probeset3985
+YAL067C = probeset3986
+YIL051C = probeset3987
+YCR024C-A = probeset3988
+YHR176W = probeset3989
+YPR160W = probeset3990
+YDR036C = probeset3991
+YOR181W = probeset3992
+YPL202C = probeset3993
+YLR020C = probeset3994
+YDR109C = probeset3995
+YCR057C = probeset3996
+YOL150C = probeset3997
+YGL239C = probeset3998
+YNL171C = probeset3999
+YNL244C = probeset4000
+YJR062C = probeset4001
+YJR135C = probeset4002
+YDL004W = probeset4003
+YPR161C = probeset4004
+YBL046W = probeset4005
+YOR182C = probeset4006
+YJL030W = probeset4007
+YIL124W = probeset4008
+YER015W = probeset4009
+YGL093W = probeset4010
+YGL166W = probeset4011
+YDL005C = probeset4012
+YKR041W = probeset4013
+YBR078W = probeset4014
+YKL010C = probeset4015
+YNL317W = probeset4016
+YBL047C = probeset4017
+YJL031C = probeset4018
+YAL068C = probeset4019
+YDR320C = probeset4020
+YIL052C = probeset4021
+YHR177W = probeset4022
+YGR198W = probeset4023
+YEL059C-A = probeset4024
+YGL094C = probeset4025
+YGL167C = probeset4026
+YOR255W = probeset4027
+YOR328W = probeset4028
+YBR079C = probeset4029
+YMR297W = probeset4030
+YNL318C = probeset4031
+YJR136C = probeset4032
+YPR162C = probeset4033
+YOR256C = probeset4034
+YJL104W = probeset4035
+YOR329C = probeset4036
+YIL125W = probeset4037
+YER016W = probeset4038
+YDR037W = probeset4039
+YPL130W = probeset4040
+YLR021W = probeset4041
+YPL203W = probeset4042
+YOL151W = probeset4043
+YKR042W = probeset4044
+YNL172W = probeset4045
+YJR063W = probeset4046
+YKL011C = probeset4047
+YHR178W = probeset4048
+YER017C = probeset4049
+YGR199W = probeset4050
+YMR001C = probeset4051
+YGL095C = probeset4052
+YDR038C = probeset4053
+YOR183W = probeset4054
+YLR022C = probeset4055
+YCR059C = probeset4056
+YKR043C = probeset4057
+YNL173C = probeset4058
+YMR298W = probeset4059
+YJR137C = probeset4060
+YDL006W = probeset4061
+YCL027W = probeset4062
+YPR163C = probeset4063
+YBL048W = probeset4064
+YJL032W = probeset4065
+YDR321W = probeset4066
+YJL105W = probeset4067
+YAL069W = probeset4068
+YIL053W = probeset4069
+YIL126W = probeset4070
+YBR290W = probeset4071
+YPL131W = probeset4072
+YPL204W = probeset4073
+YGL168W = probeset4074
+YOL152W = probeset4075
+YJR064W = probeset4076
+YNL246W = probeset4077
+YNL319W = probeset4078
+YHR179W = probeset4079
+YIL127C = probeset4080
+YPR090W = probeset4081
+YBR291C = probeset4082
+YER018C = probeset4083
+YDR039C = probeset4084
+YOR184W = probeset4085
+YLR023C = probeset4086
+YOR257W = probeset4087
+YOL080C = probeset4088
+YPL205C = probeset4089
+YJR065C = probeset4090
+YDL007W = probeset4091
+YPR091C = probeset4092
+YCL028W = probeset4093
+YKL012W = probeset4094
+YBL049W = probeset4095
+YOR185C = probeset4096
+YJL033W = probeset4097
+YDR322W = probeset4098
+YJL106W = probeset4099
+YIL054W = probeset4100
+YMR002W = probeset4101
+YGL096W = probeset4102
+YPL132W = probeset4103
+YGL169W = probeset4104
+YKR044W = probeset4105
+YNL174W = probeset4106
+YCL029C = probeset4107
+YKL013C = probeset4108
+YNL247W = probeset4109
+YJR138W = probeset4110
+YDR250C = probeset4111
+YDR323C = probeset4111
+YJL107C = probeset4113
+YIL055C = probeset4114
+YBR292C = probeset4115
+YPR164W = probeset4116
+YPL133C = probeset4117
+YLR024C = probeset4118
+YPL206C = probeset4119
+YOR258W = probeset4120
+YKR045C = probeset4121
+YNL175C = probeset4122
+YNL248C = probeset4123
+YJR139C = probeset4124
+YDL008W = probeset4125
+YOR259C = probeset4126
+YJL034W = probeset4127
+YIL128W = probeset4128
+YER019W = probeset4129
+YMR003W = probeset4130
+YPL060W = probeset4131
+YGL097W = probeset4132
+YOL081W = probeset4133
+YDL009C = probeset4134
+YOL154W = probeset4135
+YJR066W = probeset4136
+YKL014C = probeset4137
+YJL035C = probeset4138
+YDR324C = probeset4139
+YJL108C = probeset4140
+YPR092W = probeset4141
+YPR165W = probeset4142
+YPL134C = probeset4143
+YOR186W = probeset4144
+YOL155C = probeset4145
+YKR046C = probeset4146
+YNL176C = probeset4147
+YJR067C = probeset4148
+YNL249C = probeset4149
+YPR093C = probeset4150
+YPR166C = probeset4151
+YDR251W = probeset4152
+YIL056W = probeset4153
+YDL220C = probeset4154
+YBR293W = probeset4155
+YPL061W = probeset4156
+YMR004W = probeset4157
+YGL098W = probeset4158
+YLR025W = probeset4159
+YPL207W = probeset4160
+YOL082W = probeset4161
+YIL057C = probeset4162
+YOR187W = probeset4163
+YLR026C = probeset4164
+YNL177C = probeset4165
+YPR167C = probeset4166
+YKL015W = probeset4167
+YDR252W = probeset4168
+YJL036W = probeset4169
+YDR325W = probeset4170
+YBR294W = probeset4171
+YMR005W = probeset4172
+YPL062W = probeset4173
+YPL135W = probeset4174
+YGL099W = probeset4175
+YOL083W = probeset4176
+YPL208W = probeset4177
+YOL156W = probeset4178
+YKR047W = probeset4179
+YKL016C = probeset4180
+YJR068W = probeset4181
+YDR253C = probeset4182
+YDR326C = probeset4183
+YLR310C = probeset4184
+YPR094W = probeset4185
+YMR006C = probeset4186
+YOR188W = probeset4187
+YPL209C = probeset4188
+YLR027C = probeset4189
+YOL157C = probeset4190
+YDL221W = probeset4191
+YKR048C = probeset4192
+YJR069C = probeset4193
+YPR095C = probeset4194
+YDR180W = probeset4195
+YJL037W = probeset4196
+YDL222C = probeset4197
+YIL058W = probeset4198
+YBR295W = probeset4199
+YPL063W = probeset4200
+YPL136W = probeset4201
+YOL084W = probeset4202
+YNL178W = probeset4203
+YKL017C = probeset4204
+YDR181C = probeset4205
+YJL038C = probeset4206
+YIL059C = probeset4207
+YLR311C = probeset4208
+YBR296C = probeset4209
+YPR168W = probeset4210
+YPL064C = probeset4211
+YPL137C = probeset4212
+YOR189W = probeset4213
+YLR028C = probeset4214
+YOL085C = probeset4215
+YOL158C = probeset4216
+YKR049C = probeset4217
+YNL179C = probeset4218
+YPR096C = probeset4219
+YAR020C = probeset4220
+YDR254W = probeset4221
+YDR327W = probeset4222
+YDL223C = probeset4223
+YMR007W = probeset4224
+YER161C = probeset4225
+YJL039C = probeset4226
+YDR255C = probeset4227
+YDR328C = probeset4228
+YLR312C = probeset4229
+YPR169W = probeset4230
+YMR008C = probeset4231
+YPL138C = probeset4232
+YLR029C = probeset4233
+YOL086C = probeset4234
+YDL150W = probeset4235
+YOL159C = probeset4236
+YKL018W = probeset4237
+YDR182W = probeset4238
+YDL151C = probeset4239
+YDL224C = probeset4240
+YBR297W = probeset4241
+YPL065W = probeset4242
+YGR120C = probeset4243
+YER162C = probeset4244
+YDR256C = probeset4245
+YDR329C = probeset4246
+YLR313C = probeset4247
+YPR097W = probeset4248
+YBR298C = probeset4249
+YPL139C = probeset4250
+YOL087C = probeset4251
+YPR098C = probeset4252
+YBR001C = probeset4253
+YKL019W = probeset4254
+YDR183W = probeset4255
+YLR240W = probeset4256
+YHR100C = probeset4257
+YPL066W = probeset4258
+YMR009W = probeset4259
+YGR121C = probeset4260
+YDR540C = probeset4261
+YER163C = probeset4262
+YDR184C = probeset4263
+YDR257C = probeset4264
+YLR314C = probeset4265
+YPL067C = probeset4266
+YOL088C = probeset4267
+YDL152W = probeset4268
+YDL225W = probeset4269
+YPR099C = probeset4270
+YER090W = probeset4271
+YBR002C = probeset4272
+YMR220W = probeset4273
+YDL080C = probeset4274
+YAR023C = probeset4275
+YDL153C = probeset4276
+YLR241W = probeset4277
+YDL226C = probeset4278
+YBR299W = probeset4279
+YHR101C = probeset4280
+YDR541C = probeset4281
+YER091C = probeset4282
+YDR185C = probeset4283
+YMR221C = probeset4284
+YDR258C = probeset4285
+YLR242C = probeset4286
+YPL068C = probeset4287
+YOL089C = probeset4288
+YGR122W = probeset4289
+YER164W = probeset4290
+YEL060C = probeset4291
+YDL081C = probeset4292
+YDL227C = probeset4293
+YLR315W = probeset4294
+YGR050C = probeset4295
+YGR123C = probeset4296
+YJL180C = probeset4297
+YMR222C = probeset4298
+YDR186C = probeset4299
+YLR170C = probeset4300
+YDR259C = probeset4301
+YLR316C = probeset4302
+YAL034W-A = probeset4303
+YBR003W = probeset4304
+YPL069C = probeset4305
+YDL154W = probeset4306
+YHR102W = probeset4307
+YER092W = probeset4308
+YER165W = probeset4309
+YEL061C = probeset4310
+YBR004C = probeset4311
+YLR243W = probeset4312
+YHR030C = probeset4313
+YGR051C = probeset4314
+YDR470C = probeset4315
+YDR543C = probeset4316
+YER093C = probeset4317
+YMR150C = probeset4318
+YLR244C = probeset4319
+YFL040W = probeset4320
+YDL082W = probeset4321
+YDL155W = probeset4322
+YKL160W = probeset4323
+YHR103W = probeset4324
+YGR124W = probeset4325
+YJL181W = probeset4326
+YGL020C = probeset4327
+YER166W = probeset4328
+YPL280W = probeset4329
+YMR223W = probeset4330
+YLR171W = probeset4331
+YDL083C = probeset4332
+YLR317W = probeset4333
+YHR031C = probeset4334
+YKL161C = probeset4335
+YJL182C = probeset4336
+YDR544C = probeset4337
+YOL052C-A = probeset4338
+YER094C = probeset4339
+YPL281C = probeset4340
+YMR224C = probeset4341
+YLR172C = probeset4342
+YLR245C = probeset4343
+YFL041W = probeset4344
+YBR005W = probeset4345
+YEL062W = probeset4346
+YDL156W = probeset4347
+YIR010W = probeset4348
+YHR104W = probeset4349
+YGR052W = probeset4350
+YGR125W = probeset4351
+YDR471W = probeset4352
+YFL042C = probeset4353
+YER167W = probeset4354
+YMR151W = probeset4355
+YEL063C = probeset4356
+YDR188W = probeset4357
+YML120C = probeset4358
+YIR011C = probeset4359
+YDL157C = probeset4360
+YKL006C-A = probeset4361
+YKL162C = probeset4362
+YGR053C = probeset4363
+YER168C = probeset4364
+YPL282C = probeset4365
+YMR225C = probeset4366
+YGL021W = probeset4367
+YLR319C = probeset4368
+YBR006W = probeset4369
+YAR027W = probeset4370
+YDL084W = probeset4371
+YHR032W = probeset4372
+YHR105W = probeset4373
+YGR126W = probeset4374
+YJL183W = probeset4375
+YDR472W = probeset4376
+YOR110W = probeset4377
+YER095W = probeset4378
+YBR007C = probeset4379
+YMR152W = probeset4380
+YEL064C = probeset4381
+YDR189W = probeset4382
+YLR173W = probeset4383
+YLR246W = probeset4384
+YDL158C = probeset4385
+YDR473C = probeset4386
+YMR080C = probeset4387
+YHL001W = probeset4388
+YMR226C = probeset4389
+YPL283C = probeset4390
+YLR247C = probeset4391
+YGL022W = probeset4392
+YNL100W = probeset4393
+YDL085W = probeset4394
+YAR028W = probeset4395
+YML121W = probeset4396
+YIR012W = probeset4397
+YHR033W = probeset4398
+YKL090W = probeset4399
+YKL163W = probeset4400
+YHR106W = probeset4401
+YGR054W = probeset4402
+YGR127W = probeset4403
+YJL184W = probeset4404
+YGL023C = probeset4405
+YOR111W = probeset4406
+YER096W = probeset4407
+YFL044C = probeset4408
+YER169W = probeset4409
+YMR153W = probeset4410
+YBR008C = probeset4411
+YLR174W = probeset4412
+YML122C = probeset4413
+YIR013C = probeset4414
+YKL091C = probeset4415
+YHR034C = probeset4416
+YHR107C = probeset4417
+YKL164C = probeset4418
+YJL185C = probeset4419
+YGR128C = probeset4420
+YDR474C = probeset4421
+YMR081C = probeset4422
+YMR154C = probeset4423
+YMR227C = probeset4424
+YHL002W = probeset4425
+YEL065W = probeset4426
+YNL101W = probeset4427
+YAR029W = probeset4428
+YDL086W = probeset4429
+YDL159W = probeset4430
+YGR055W = probeset4431
+YHL003C = probeset4432
+YOR112W = probeset4433
+YNR060W = probeset4434
+YFL045C = probeset4435
+YER097W = probeset4436
+YBR009C = probeset4437
+YML123C = probeset4438
+YLR175W = probeset4439
+YDL087C = probeset4440
+YLR248W = probeset4441
+YKL092C = probeset4442
+YER019C-A = probeset4443
+YKL165C = probeset4444
+YNR061C = probeset4445
+YMR082C = probeset4446
+YLR176C = probeset4447
+YGL024W = probeset4448
+YEL066W = probeset4449
+YNL102W = probeset4450
+YML050W = probeset4451
+YIR014W = probeset4452
+YHR035W = probeset4453
+YHR108W = probeset4454
+YGR056W = probeset4455
+YBR220C = probeset4456
+YOR040W = probeset4457
+YJL186W = probeset4458
+YGR129W = probeset4459
+YOR113W = probeset4460
+YGL025C = probeset4461
+YER098W = probeset4462
+YEL067C = probeset4463
+YMR155W = probeset4464
+YMR228W = probeset4465
+YML124C = probeset4466
+YDL088C = probeset4467
+YLR249W = probeset4468
+YKL166C = probeset4469
+YGR057C = probeset4470
+YOR041C = probeset4471
+YJL187C = probeset4472
+YDR476C = probeset4473
+YNR062C = probeset4474
+YLR460C = probeset4475
+YER099C = probeset4476
+YMR156C = probeset4477
+YMR229C = probeset4478
+YHL004W = probeset4479
+YFL046W = probeset4480
+YNL030W = probeset4481
+YNL103W = probeset4482
+YML051W = probeset4483
+YIR015W = probeset4484
+YHR036W = probeset4485
+YKL093W = probeset4486
+YPR020W = probeset4487
+YHR109W = probeset4488
+YBR221C = probeset4489
+YHL005C = probeset4490
+YGL026C = probeset4491
+YOR114W = probeset4492
+YNL031C = probeset4493
+YMR083W = probeset4494
+YNL104C = probeset4495
+YEL068C = probeset4496
+YLR177W = probeset4497
+YML125C = probeset4498
+YPR021C = probeset4499
+YKL167C = probeset4500
+YJL188C = probeset4501
+YOR115C = probeset4502
+YMR157C = probeset4503
+YLR178C = probeset4504
+YOL010W = probeset4505
+YFL047W = probeset4506
+YML052W = probeset4507
+YDL089W = probeset4508
+YIR016W = probeset4509
+YHR037W = probeset4510
+YKL094W = probeset4511
+YHL006C = probeset4512
+YBR222C = probeset4513
+YGR058W = probeset4514
+YOR042W = probeset4515
+YGL027C = probeset4516
+YDR477W = probeset4517
+YNR063W = probeset4518
+YLR461W = probeset4519
+YFL048C = probeset4520
+YMR084W = probeset4521
+YEL069C = probeset4522
+YML053C = probeset4523
+YML126C = probeset4524
+YIR017C = probeset4525
+YKL168C = probeset4526
+YPR022C = probeset4527
+YOR116C = probeset4528
+YNR064C = probeset4529
+YLR179C = probeset4530
+YOL011W = probeset4531
+YNL032W = probeset4532
+YNL105W = probeset4533
+YHR038W = probeset4534
+YKL095W = probeset4535
+YBR150C = probeset4536
+YHL007C = probeset4537
+YGR059W = probeset4538
+YBR223C = probeset4539
+YJL189W = probeset4540
+YOR043W = probeset4541
+YGL028C = probeset4542
+YDR478W = probeset4543
+YLR462W = probeset4544
+YOL012C = probeset4545
+YNL106C = probeset4546
+YMR158W = probeset4547
+YML054C = probeset4548
+YHR039C = probeset4549
+YPR023C = probeset4550
+YKL169C = probeset4551
+YDR479C = probeset4552
+YHR079C-A = probeset4553
+YNR065C = probeset4554
+YLR463C = probeset4555
+YMR159C = probeset4556
+YFL049W = probeset4557
+YNL033W = probeset4558
+YGR270W = probeset4559
+YML127W = probeset4560
+YIR018W = probeset4561
+YKL096W = probeset4562
+YHL008C = probeset4563
+YOR044W = probeset4564
+YLR390W = probeset4565
+YOR117W = probeset4566
+YOL013C = probeset4567
+YMR086W = probeset4568
+YML128C = probeset4569
+YKL097C = probeset4570
+YNR066C = probeset4571
+YBR151W = probeset4572
+YBR224W = probeset4573
+YGL029W = probeset4574
+YNL034W = probeset4575
+YNL107W = probeset4576
+YML055W = probeset4577
+YGR271W = probeset4578
+YPR024W = probeset4579
+YHL009C = probeset4580
+YOR045W = probeset4581
+YOR118W = probeset4582
+YMR087W = probeset4583
+YNL035C = probeset4584
+YNL108C = probeset4585
+YML056C = probeset4586
+YGR272C = probeset4587
+YML129C = probeset4588
+YPR025C = probeset4589
+YOR046C = probeset4590
+YDR110W = probeset4591
+YLR392C = probeset4592
+YOR119C = probeset4593
+YNR067C = probeset4594
+YLR465C = probeset4595
+YGL240W = probeset4596
+YMR088C = probeset4597
+YBR152W = probeset4598
+YBR225W = probeset4599
+YOL014W = probeset4600
+YDR111C = probeset4601
+YBR080C = probeset4602
+YKL098W = probeset4603
+YGR273C = probeset4604
+YOR330C = probeset4605
+YKL099C = probeset4606
+YOR047C = probeset4607
+YGL241W = probeset4608
+YNR068C = probeset4609
+YMR089C = probeset4610
+YBR153W = probeset4611
+YOL015W = probeset4612
+YNL036W = probeset4613
+YNL109W = probeset4614
+YML057W = probeset4615
+YGL242C = probeset4616
+YBR081C = probeset4617
+YBR154C = probeset4618
+YPR026W = probeset4619
+YBR227C = probeset4620
+YLR393W = probeset4621
+YOL016C = probeset4622
+YLR466W = probeset4623
+YNL037C = probeset4624
+YGR274C = probeset4625
+YOR331C = probeset4626
+YPR027C = probeset4627
+YOR048C = probeset4628
+YCR060W = probeset4629
+YNR069C = probeset4630
+YNL320W = probeset4631
+YHR180W = probeset4632
+YDR040C = probeset4633
+YML058W = probeset4634
+YDR113C = probeset4635
+YGL170C = probeset4636
+YBR082C = probeset4637
+YLR394W = probeset4638
+YBL050W = probeset4639
+YML059C = probeset4640
+YOR049C = probeset4641
+YLR395C = probeset4642
+YGL243W = probeset4643
+YCR061W = probeset4644
+YCL030C = probeset4645
+YBR155W = probeset4646
+YBR228W = probeset4647
+YNL321W = probeset4648
+YBL051C = probeset4649
+YOL017W = probeset4650
+YHR181W = probeset4651
+YNL038W = probeset4652
+YGR275W = probeset4653
+YDR114C = probeset4654
+YOR332W = probeset4655
+YBR156C = probeset4656
+YPR028W = probeset4657
+YBR229C = probeset4658
+YNL322C = probeset4659
+YJR140C = probeset4660
+YOL018C = probeset4661
+YGR276C = probeset4662
+YOR333C = probeset4663
+YPR029C = probeset4664
+YER020W = probeset4665
+YDR041W = probeset4666
+YGL171W = probeset4667
+YLR396C = probeset4668
+YGL244W = probeset4669
+YCR062W = probeset4670
+YCL031C = probeset4671
+YBR083W = probeset4672
+YBL052C = probeset4673
+YHR182W = probeset4674
+YNL039W = probeset4675
+YDR042C = probeset4676
+YOR260W = probeset4677
+YBR157C = probeset4678
+YDL010W = probeset4679
+YGR277C = probeset4680
+YOR261C = probeset4681
+YIL130W = probeset4682
+YER021W = probeset4683
+YGL172W = probeset4684
+YDR115W = probeset4685
+YLR397C = probeset4686
+YDL011C = probeset4687
+YCR063W = probeset4688
+YGL245W = probeset4689
+YBR084W = probeset4690
+YNL250W = probeset4691
+YJR141W = probeset4692
+YNL323W = probeset4693
+YJL110C = probeset4694
+YOL019W = probeset4695
+YHR183W = probeset4696
+YIL131C = probeset4697
+YDR043C = probeset4698
+YDR116C = probeset4699
+YGL173C = probeset4700
+YCR064C = probeset4701
+YOR334W = probeset4702
+YGL246C = probeset4703
+YCL032W = probeset4704
+YBL053W = probeset4705
+YOR335C = probeset4706
+YFR001W = probeset4707
+YER022W = probeset4708
+YLR398C = probeset4709
+YLR100W = probeset4710
+YDL012C = probeset4711
+YBR085W = probeset4712
+YCL033C = probeset4713
+YBR158W = probeset4714
+YNL324W = probeset4715
+YJR142W = probeset4716
+YIL132C = probeset4717
+YHR184W = probeset4718
+YGR278W = probeset4719
+YPL210C = probeset4720
+YDR117C = probeset4721
+YOR262W = probeset4722
+YLR101C = probeset4723
+YBR086C = probeset4724
+YJR070C = probeset4725
+YNL252C = probeset4726
+YNL325C = probeset4727
+YJR143C = probeset4728
+YHR185C = probeset4729
+YBL054W = probeset4730
+YGR279C = probeset4731
+YOR263C = probeset4732
+YJL111W = probeset4733
+YFR002W = probeset4734
+YDR400W = probeset4735
+YER023W = probeset4736
+YDR044W = probeset4737
+YLR399C = probeset4738
+YGL174W = probeset4739
+YGL247W = probeset4740
+YCR065W = probeset4741
+YBR159W = probeset4742
+YBL055C = probeset4743
+YFR003C = probeset4744
+YIL133C = probeset4745
+YOR190W = probeset4746
+YDR045C = probeset4747
+YGL175C = probeset4748
+YOR336W = probeset4749
+YLR102C = probeset4750
+YNL180C = probeset4751
+YNL326C = probeset4752
+YDL013W = probeset4753
+YHR186C = probeset4754
+YCL034W = probeset4755
+YJL112W = probeset4756
+YDR401W = probeset4757
+YIL060W = probeset4758
+YER024W = probeset4759
+YDR118W = probeset4760
+YPL211W = probeset4761
+YCR066W = probeset4762
+YGL248W = probeset4763
+YKR050W = probeset4764
+YBR087W = probeset4765
+YCL035C = probeset4766
+YJR071W = probeset4767
+YNL253W = probeset4768
+YJR144W = probeset4769
+YIL061C = probeset4770
+YDR402C = probeset4771
+YDR046C = probeset4772
+YOR191W = probeset4773
+YOR264W = probeset4774
+YGL176C = probeset4775
+YPL212C = probeset4776
+YOR337W = probeset4777
+YCR067C = probeset4778
+YLR103C = probeset4779
+YBR088C = probeset4780
+YJR072C = probeset4781
+YNL254C = probeset4782
+YJR145C = probeset4783
+YDL014W = probeset4784
+YOR192C = probeset4785
+YBL056W = probeset4786
+YFR004W = probeset4787
+YIL134W = probeset4788
+YER025W = probeset4789
+YDR119W = probeset4790
+YLR030W = probeset4791
+YOL160W = probeset4792
+YGL249W = probeset4793
+YDL015C = probeset4794
+YKR051W = probeset4795
+YNL181W = probeset4796
+YKL020C = probeset4797
+YNL327W = probeset4798
+YBL057C = probeset4799
+YFR005C = probeset4800
+YIL062C = probeset4801
+YHR187W = probeset4802
+YIL135C = probeset4803
+YPR171W = probeset4804
+YER026C = probeset4805
+YPL140C = probeset4806
+YOR265W = probeset4807
+YOR338W = probeset4808
+YOL161C = probeset4809
+YKR052C = probeset4810
+YNL182C = probeset4811
+YNL255C = probeset4812
+YJR073C = probeset4813
+YNL328C = probeset4814
+YHR188C = probeset4815
+YCL036W = probeset4816
+YJL041W = probeset4817
+YOR339C = probeset4818
+YDR330W = probeset4819
+YDR403W = probeset4820
+YMR010W = probeset4821
+YDR047W = probeset4822
+YPL213W = probeset4823
+YLR031W = probeset4824
+YDL016C = probeset4825
+YCR068W = probeset4826
+YLR104W = probeset4827
+YCL037C = probeset4828
+YBR089W = probeset4829
+YKL021C = probeset4830
+YJR146W = probeset4831
+YIL063C = probeset4832
+YDR404C = probeset4833
+YPR172W = probeset4834
+YER027C = probeset4835
+YOR193W = probeset4836
+YPL141C = probeset4837
+YOR266W = probeset4838
+YPL214C = probeset4839
+YLR105C = probeset4840
+YKR053C = probeset4841
+YNL183C = probeset4842
+YNL329C = probeset4843
+YPR173C = probeset4844
+YOR194C = probeset4845
+YBL058W = probeset4846
+YOR267C = probeset4847
+YJL042W = probeset4848
+YJL115W = probeset4849
+YDR331W = probeset4850
+YFR006W = probeset4851
+YIL136W = probeset4852
+YMR011W = probeset4853
+YLR032W = probeset4854
+YGL178W = probeset4855
+YCR069W = probeset4856
+YOL162W = probeset4857
+YCL038C = probeset4858
+YKL022C = probeset4859
+YJR074W = probeset4860
+YNL256W = probeset4861
+YJR147W = probeset4862
+YJL116C = probeset4863
+YHR189W = probeset4864
+YIL137C = probeset4865
+YER028C = probeset4866
+YPL142C = probeset4867
+YGL179C = probeset4868
+YKR054C = probeset4869
+YNL184C = probeset4870
+YNL257C = probeset4871
+YDL017W = probeset4872
+YLL001W = probeset4873
+YPR174C = probeset4874
+YBL059W = probeset4875
+YOR268C = probeset4876
+YJL043W = probeset4877
+YDR332W = probeset4878
+YDR405W = probeset4879
+YIL064W = probeset4880
+YFR007W = probeset4881
+YMR012W = probeset4882
+YDR049W = probeset4883
+YLR033W = probeset4884
+YOL090W = probeset4885
+YPL215W = probeset4886
+YOL163W = probeset4887
+YDL018C = probeset4888
+YJR075W = probeset4889
+YJR148W = probeset4890
+YDR260C = probeset4891
+YJL044C = probeset4892
+YDR333C = probeset4893
+YIL065C = probeset4894
+YIL138C = probeset4895
+YER029C = probeset4896
+YMR013C = probeset4897
+YOR195W = probeset4898
+YLR034C = probeset4899
+YNL185C = probeset4900
+YJR076C = probeset4901
+YNL258C = probeset4902
+YLL002W = probeset4903
+YKL023W = probeset4904
+YOR196C = probeset4905
+YJL117W = probeset4906
+YFR008W = probeset4907
+YDR406W = probeset4908
+YPL070W = probeset4909
+YPL143W = probeset4910
+YOL091W = probeset4911
+YPL216W = probeset4912
+YOL164W = probeset4913
+YLR107W = probeset4914
+YDL019C = probeset4915
+YKR055W = probeset4916
+YKL024C = probeset4917
+YJR149W = probeset4918
+YDR261C = probeset4919
+YDR407C = probeset4920
+YIL066C = probeset4921
+YIL139C = probeset4922
+YPR175W = probeset4923
+YPL071C = probeset4924
+YOR269W = probeset4925
+YPL217C = probeset4926
+YLR108C = probeset4927
+YOL165C = probeset4928
+YJR077C = probeset4929
+YNL259C = probeset4930
+YLL003W = probeset4931
+YPR176C = probeset4932
+YJL045W = probeset4933
+YDR334W = probeset4934
+YJL118W = probeset4935
+YFR009W = probeset4936
+YMR014W = probeset4937
+YOL092W = probeset4938
+YKR056W = probeset4939
+YNL186W = probeset4940
+YKL025C = probeset4941
+YJL119C = probeset4942
+YIL067C = probeset4943
+YDR408C = probeset4944
+YMR015C = probeset4945
+YOR197W = probeset4946
+YPL145C = probeset4947
+YLR036C = probeset4948
+YOL166C = probeset4949
+YDL230W = probeset4950
+YLL004W = probeset4951
+YPR177C = probeset4952
+YOR198C = probeset4953
+YJL046W = probeset4954
+YDR335W = probeset4955
+YDL231C = probeset4956
+YPL072W = probeset4957
+YOL093W = probeset4958
+YGR200C = probeset4959
+YPL218W = probeset4960
+YLR109W = probeset4961
+YLL005C = probeset4962
+YKR057W = probeset4963
+YNL187W = probeset4964
+YJR078W = probeset4965
+YKL026C = probeset4966
+YDR190C = probeset4967
+YDR263C = probeset4968
+YJL047C = probeset4969
+YIL068C = probeset4970
+YPL073C = probeset4971
+YMR016C = probeset4972
+YPL146C = probeset4973
+YLR037C = probeset4974
+YOL094C = probeset4975
+YDR336W = probeset4976
+YLR320W = probeset4977
+YDR409W = probeset4978
+YPL219W = probeset4979
+YKR058W = probeset4980
+YNL188W = probeset4981
+YJR079W = probeset4982
+YMR300C = probeset4983
+YJL048C = probeset4984
+YDR264C = probeset4985
+YLR321C = probeset4986
+YIL069C = probeset4987
+YPR178W = probeset4988
+YOR199W = probeset4989
+YLR038C = probeset4990
+YOL095C = probeset4991
+YDL232W = probeset4992
+YLL006W = probeset4993
+YPR179C = probeset4994
+YER170W = probeset4995
+YKL027W = probeset4996
+YDR191W = probeset4997
+YAR030C = probeset4998
+YDR337W = probeset4999
+YDL160C = probeset5000
+YPL074W = probeset5001
+YMR017W = probeset5002
+YPL147W = probeset5003
+YGR202C = probeset5004
+YKR059W = probeset5005
+YLL007C = probeset5006
+YNL189W = probeset5007
+YDR192C = probeset5008
+YMR301C = probeset5009
+YDR338C = probeset5010
+YPL148C = probeset5011
+YLR039C = probeset5012
+YOL096C = probeset5013
+YDL233W = probeset5014
+YER171W = probeset5015
+YKL028W = probeset5016
+YJL049W = probeset5017
+YDR265W = probeset5018
+YLR322W = probeset5019
+YDL234C = probeset5020
+YMR018W = probeset5021
+YPL075W = probeset5022
+YGR130C = probeset5023
+YER172C = probeset5024
+YKL029C = probeset5025
+YMR302C = probeset5026
+YDR266C = probeset5027
+YDR339C = probeset5028
+YLR323C = probeset5029
+YBR010W = probeset5030
+YAR031W = probeset5031
+YOL097C = probeset5032
+YDL161W = probeset5033
+YGR203W = probeset5034
+YLL008W = probeset5035
+YBR011C = probeset5036
+YLR250W = probeset5037
+YDL162C = probeset5038
+YDL235C = probeset5039
+YPL076W = probeset5040
+YMR019W = probeset5041
+YPL149W = probeset5042
+YLL009C = probeset5043
+YDR194C = probeset5044
+YMR303C = probeset5045
+YDR267C = probeset5046
+YPL077C = probeset5047
+YOL098C = probeset5048
+YAL001C = probeset5049
+YHR110W = probeset5050
+YGR131W = probeset5051
+YGR204W = probeset5052
+YER173W = probeset5053
+YBR012C = probeset5054
+YMR230W = probeset5055
+YDL090C = probeset5056
+YLR251W = probeset5057
+YLR324W = probeset5058
+YGR132C = probeset5059
+YER174C = probeset5060
+YLR325C = probeset5061
+YGL100W = probeset5062
+YPL078C = probeset5063
+YOL099C = probeset5064
+YAR033W = probeset5065
+YDL163W = probeset5066
+YDL236W = probeset5067
+YHR111W = probeset5068
+YGR205W = probeset5069
+YBR013C = probeset5070
+YDR195W = probeset5071
+YMR231W = probeset5072
+YMR304W = probeset5073
+YDL091C = probeset5074
+YDR268W = probeset5075
+YDL164C = probeset5076
+YLR252W = probeset5077
+YHR112C = probeset5078
+YJL190C = probeset5079
+YAL002W = probeset5080
+YER175C = probeset5081
+YDR196C = probeset5082
+YMR305C = probeset5083
+YDR269C = probeset5084
+YGL101W = probeset5085
+YEL070W = probeset5086
+YDL237W = probeset5087
+YGR060W = probeset5088
+YGR133W = probeset5089
+YGR206W = probeset5090
+YGL102C = probeset5091
+YFL050C = probeset5092
+YBR014C = probeset5093
+YMR232W = probeset5094
+YLR180W = probeset5095
+YLR253W = probeset5096
+YDL238C = probeset5097
+YLR326W = probeset5098
+YPL079W = probeset5099
+YGR061C = probeset5100
+YGR207C = probeset5101
+YAL003W = probeset5102
+YLR181C = probeset5103
+YLR254C = probeset5104
+YLR327C = probeset5105
+YEL071W = probeset5106
+YAR035W = probeset5107
+YDL092W = probeset5108
+YDL165W = probeset5109
+YHR040W = probeset5110
+YKL170W = probeset5111
+YHR113W = probeset5112
+YJL191W = probeset5113
+YGR134W = probeset5114
+YDR480W = probeset5115
+YFL051C = probeset5116
+YER176W = probeset5117
+YEL017C-A = probeset5118
+YBR015C = probeset5119
+YMR160W = probeset5120
+YDR197W = probeset5121
+YMR233W = probeset5122
+YMR306W = probeset5123
+YDL166C = probeset5124
+YIR020C = probeset5125
+YDL239C = probeset5126
+YHR041C = probeset5127
+YGR062C = probeset5128
+YJL192C = probeset5129
+YDR481C = probeset5130
+YDR198C = probeset5131
+YGL030W = probeset5132
+YLR255C = probeset5133
+YGL103W = probeset5134
+YEL072W = probeset5135
+YDL093W = probeset5136
+YHR114W = probeset5137
+YKL171W = probeset5138
+YHL010C = probeset5139
+YGR135W = probeset5140
+YGL031C = probeset5141
+YGR208W = probeset5142
+YGL104C = probeset5143
+YER177W = probeset5144
+YEL073C = probeset5145
+YMR161W = probeset5146
+YMR234W = probeset5147
+YLR182W = probeset5148
+YML130C = probeset5149
+YDL094C = probeset5150
+YDL167C = probeset5151
+YLR328W = probeset5152
+YHR115C = probeset5153
+YGR063C = probeset5154
+YDR482C = probeset5155
+YGR209C = probeset5156
+YMR162C = probeset5157
+YMR235C = probeset5158
+YLR183C = probeset5159
+YMR308C = probeset5160
+YFL052W = probeset5161
+YBR016W = probeset5162
+YIR021W = probeset5163
+YHR042W = probeset5164
+YKL172W = probeset5165
+YHL011C = probeset5166
+YBR300C = probeset5167
+YGR136W = probeset5168
+YJL193W = probeset5169
+YOR120W = probeset5170
+YGL032C = probeset5171
+YER178W = probeset5172
+YNL110C = probeset5173
+YBR017C = probeset5174
+YLR256W = probeset5175
+YLR329W = probeset5176
+YHR043C = probeset5177
+YOR121C = probeset5178
+YMR163C = probeset5179
+YMR309C = probeset5180
+YGL105W = probeset5181
+YFL053W = probeset5182
+YEL074W = probeset5183
+YJR001W = probeset5184
+YML131W = probeset5185
+YDL095W = probeset5186
+YDL168W = probeset5187
+YIR022W = probeset5188
+YAL007C = probeset5189
+YKL173W = probeset5190
+YHR116W = probeset5191
+YPR100W = probeset5192
+YGR064W = probeset5193
+YGR137W = probeset5194
+YJL194W = probeset5195
+YDR483W = probeset5196
+YFL054C = probeset5197
+YMR090W = probeset5198
+YER179W = probeset5199
+YBR018C = probeset5200
+YNL111C = probeset5201
+YEL075C = probeset5202
+YMR236W = probeset5203
+YLR184W = probeset5204
+YDL096C = probeset5205
+YDL169C = probeset5206
+YLR257W = probeset5207
+YHR044C = probeset5208
+YKL174C = probeset5209
+YGR065C = probeset5210
+YGR138C = probeset5211
+YJL195C = probeset5212
+YOR122C = probeset5213
+YMR091C = probeset5214
+YHL012W = probeset5215
+YBR301W = probeset5216
+YGL033W = probeset5217
+YGL106W = probeset5218
+YJR002W = probeset5219
+YML132W = probeset5220
+YIR023W = probeset5221
+YHR117W = probeset5222
+YHL013C = probeset5223
+YPR101W = probeset5224
+YDR484W = probeset5225
+YGL034C = probeset5226
+YNR070W = probeset5227
+YGL107C = probeset5228
+YEL076C = probeset5229
+YBR019C = probeset5230
+YJR003C = probeset5231
+YMR237W = probeset5232
+YDL097C = probeset5233
+YLR185W = probeset5234
+YML133C = probeset5235
+YIR024C = probeset5236
+YLR258W = probeset5237
+YHR118C = probeset5238
+YGR066C = probeset5239
+YPR102C = probeset5240
+YJL196C = probeset5241
+YOR050C = probeset5242
+YOR123C = probeset5243
+YDR485C = probeset5244
+YNR071C = probeset5245
+YML095C-A = probeset5246
+YAL008W = probeset5247
+YMR092C = probeset5248
+YMR165C = probeset5249
+YLR259C = probeset5250
+YFL055W = probeset5251
+YNL112W = probeset5252
+YML060W = probeset5253
+YHR045W = probeset5254
+YKL175W = probeset5255
+YBR230C = probeset5256
+YHL014C = probeset5257
+YGL035C = probeset5258
+YGL108C = probeset5259
+YFL056C = probeset5260
+YML061C = probeset5261
+YMR238W = probeset5262
+YJR004C = probeset5263
+YDL098C = probeset5264
+YLR186W = probeset5265
+YHR046C = probeset5266
+YKL176C = probeset5267
+YGR067C = probeset5268
+YOR051C = probeset5269
+YDR486C = probeset5270
+YOR124C = probeset5271
+YAL009W = probeset5272
+YMR166C = probeset5273
+YMR239C = probeset5274
+YNL040W = probeset5275
+YNL113W = probeset5276
+YIR025W = probeset5277
+YPR030W = probeset5278
+YHR119W = probeset5279
+YBR231C = probeset5280
+YPR103W = probeset5281
+YJL197W = probeset5282
+YNR072W = probeset5283
+YFL057C = probeset5284
+YNL041C = probeset5285
+YMR093W = probeset5286
+YNL114C = probeset5287
+YML062C = probeset5288
+YLR187W = probeset5289
+YIR026C = probeset5290
+YHR047C = probeset5291
+YPR104C = probeset5292
+YGR068C = probeset5293
+YOR052C = probeset5294
+YOR125C = probeset5295
+YDR487C = probeset5296
+YNR073C = probeset5297
+YHL015W = probeset5298
+YGL036W = probeset5299
+YOL020W = probeset5300
+YGL109W = probeset5301
+YJR005W = probeset5302
+YDL099W = probeset5303
+YPR031W = probeset5304
+YKL177W = probeset5305
+YHL016C = probeset5306
+YBR232C = probeset5307
+YJL198W = probeset5308
+YGL037C = probeset5309
+YOL021C = probeset5310
+YMR094W = probeset5311
+YNL115C = probeset5312
+YMR167W = probeset5313
+YLR188W = probeset5314
+YIR027C = probeset5315
+YKL178C = probeset5316
+YPR105C = probeset5317
+YJL199C = probeset5318
+YDR488C = probeset5319
+YOR126C = probeset5320
+YNR074C = probeset5321
+YMR095C = probeset5322
+YMR168C = probeset5323
+YLR189C = probeset5324
+YFL058W = probeset5325
+YNL042W = probeset5326
+YJR006W = probeset5327
+YML063W = probeset5328
+YHR048W = probeset5329
+YPR032W = probeset5330
+YGR069W = probeset5331
+YOR053W = probeset5332
+YGL038C = probeset5333
+YOL022C = probeset5334
+YNL043C = probeset5335
+YGR280C = probeset5336
+YER056C-A = probeset5337
+YML064C = probeset5338
+YKL179C = probeset5339
+YPR033C = probeset5340
+YOR054C = probeset5341
+YMR169C = probeset5342
+YBR160W = probeset5343
+YBR233W = probeset5344
+YHL017W = probeset5345
+YPL001W = probeset5346
+YFL059W = probeset5347
+YNL116W = probeset5348
+YJR007W = probeset5349
+YIR028W = probeset5350
+YHR049W = probeset5351
+YBR234C = probeset5352
+YPR106W = probeset5353
+YPL002C = probeset5354
+YOR127W = probeset5355
+YDR489W = probeset5356
+YNR075W = probeset5357
+YMR096W = probeset5358
+YPR107C = probeset5359
+YOR128C = probeset5360
+YMR097C = probeset5361
+YBR161W = probeset5362
+YHL018W = probeset5363
+YBR162W-A = probeset5364
+YGL039W = probeset5365
+YOL023W = probeset5366
+YNL044W = probeset5367
+YNL117W = probeset5368
+YGR281W = probeset5369
+YJR008W = probeset5370
+YML065W = probeset5371
+YDR120C = probeset5372
+YIR029W = probeset5373
+YPR034W = probeset5374
+YBR162C = probeset5375
+YHL019C = probeset5376
+YOR055W = probeset5377
+YNR076W = probeset5378
+YNL118C = probeset5379
+YGR282C = probeset5380
+YML066C = probeset5381
+YJR009C = probeset5382
+YOR056C = probeset5383
+YOR129C = probeset5384
+YNR077C = probeset5385
+YGL250W = probeset5386
+YMR098C = probeset5387
+YBR235W = probeset5388
+YPL003W = probeset5389
+YOL024W = probeset5390
+YNL045W = probeset5391
+YGL251C = probeset5392
+YBR090C = probeset5393
+YPR035W = probeset5394
+YBR236C = probeset5395
+YPR108W = probeset5396
+YPL004C = probeset5397
+YGR283C = probeset5398
+YML067C = probeset5399
+YOR340C = probeset5400
+YER100W = probeset5401
+YDR121W = probeset5402
+YMR099C = probeset5403
+YBR163W = probeset5404
+YOL025W = probeset5405
+YNL046W = probeset5406
+YNL119W = probeset5407
+YER101C = probeset5408
+YGL252C = probeset5409
+YBR091C = probeset5410
+YPR036W = probeset5411
+YBR164C = probeset5412
+YPR109W = probeset5413
+YNL330C = probeset5414
+YOR057W = probeset5415
+YOL026C = probeset5416
+YNL047C = probeset5417
+YGR284C = probeset5418
+YFL010W-A = probeset5419
+YPR037C = probeset5420
+YOR058C = probeset5421
+YDR122W = probeset5422
+YBR237W = probeset5423
+YPL005W = probeset5424
+YHR190W = probeset5425
+YML068W = probeset5426
+YDR050C = probeset5427
+YDR123C = probeset5428
+YOR341W = probeset5429
+YCR071C = probeset5430
+YBR092C = probeset5431
+YNL331C = probeset5432
+YBR238C = probeset5433
+YOL027C = probeset5434
+YHR191C = probeset5435
+YGR285C = probeset5436
+YBL060W = probeset5437
+YOR342C = probeset5438
+YER102W = probeset5439
+YOR059C = probeset5440
+YGL180W = probeset5441
+YGL253W = probeset5442
+YBR165W = probeset5443
+YBL061C = probeset5444
+YNL048W = probeset5445
+YML069W = probeset5446
+YDR051C = probeset5447
+YCR072C = probeset5448
+YBR093C = probeset5449
+YBR166C = probeset5450
+YJR150C = probeset5451
+YBR239C = probeset5452
+YPL007C = probeset5453
+YOL028C = probeset5454
+YCL040W = probeset5455
+YNL049C = probeset5456
+YGR286C = probeset5457
+YOR270C = probeset5458
+YOR343C = probeset5459
+YER030W = probeset5460
+YER103W = probeset5461
+YGL181W = probeset5462
+YDR124W = probeset5463
+YDL020C = probeset5464
+YGL254W = probeset5465
+YCL041C = probeset5466
+YNL332W = probeset5467
+YHR192W = probeset5468
+YER031C = probeset5469
+YDR052C = probeset5470
+YDR125C = probeset5471
+YGL182C = probeset5472
+YCR073C = probeset5473
+YNL260C = probeset5474
+YBR167C = probeset5475
+YJR151C = probeset5476
+YOL029C = probeset5477
+YHR193C = probeset5478
+YBL062W = probeset5479
+YGR287C = probeset5480
+YOR271C = probeset5481
+YOR344C = probeset5482
+YFR010W = probeset5483
+YIL140W = probeset5484
+YER104W = probeset5485
+YGL255W = probeset5486
+YBR094W = probeset5487
+YNL333W = probeset5488
+YPL008W = probeset5489
+YFR011C = probeset5490
+YER105C = probeset5491
+YGL183C = probeset5492
+YLR110C = probeset5493
+YBR095C = probeset5494
+YNL334C = probeset5495
+YPL009C = probeset5496
+YDL021W = probeset5497
+YCL042W = probeset5498
+YBL063W = probeset5499
+YOR345C = probeset5500
+YJL120W = probeset5501
+YIL141W = probeset5502
+YER032W = probeset5503
+YEL001C = probeset5504
+YDR053W = probeset5505
+YGL256W = probeset5506
+YCL043C = probeset5507
+YNL261W = probeset5508
+YBR168W = probeset5509
+YBL064C = probeset5510
+YKL100C = probeset5511
+YJR152W = probeset5512
+YJL121C = probeset5513
+YDR410C = probeset5514
+YHR194W = probeset5515
+YER033C = probeset5516
+YDR054C = probeset5517
+YGR288W = probeset5518
+YOR272W = probeset5519
+YGL184C = probeset5520
+YCR075C = probeset5521
+YGL257C = probeset5522
+YJR080C = probeset5523
+YBR169C = probeset5524
+YDL022W = probeset5525
+YGR289C = probeset5526
+YOR273C = probeset5527
+YFR012W = probeset5528
+YIL142W = probeset5529
+YER106W = probeset5530
+YEL002C = probeset5531
+YDR127W = probeset5532
+YPL220W = probeset5533
+YLR111W = probeset5534
+YDL023C = probeset5535
+YBR096W = probeset5536
+YCL044C = probeset5537
+YNL262W = probeset5538
+YJR153W = probeset5539
+YNL335W = probeset5540
+YDR411C = probeset5541
+YIL070C = probeset5542
+YHR195W = probeset5543
+YIL143C = probeset5544
+YER107C = probeset5545
+YGL185C = probeset5546
+YOR346W = probeset5547
+YCR076C = probeset5548
+YNL263C = probeset5549
+YBL065W = probeset5550
+YKL101W = probeset5551
+YJL122W = probeset5552
+YOR347C = probeset5553
+YFR013W = probeset5554
+YER034W = probeset5555
+YDR055W = probeset5556
+YDR128W = probeset5557
+YPL221W = probeset5558
+YGL258W = probeset5559
+YLR112W = probeset5560
+YDL024C = probeset5561
+YKR060W = probeset5562
+YBR097W = probeset5563
+YCL045C = probeset5564
+YNL190W = probeset5565
+YNL336W = probeset5566
+YJR154W = probeset5567
+YKL102C = probeset5568
+YBL066C = probeset5569
+YJL123C = probeset5570
+YFR014C = probeset5571
+YIL071C = probeset5572
+YHR196W = probeset5573
+YPR180W = probeset5574
+YER108C = probeset5575
+YDR056C = probeset5576
+YOR274W = probeset5577
+YLR040C = probeset5578
+YGL186C = probeset5579
+YDR129C = probeset5580
+YCR077C = probeset5581
+YNL264C = probeset5582
+YJR082C = probeset5583
+YEL003W = probeset5584
+YPR181C = probeset5585
+YJL050W = probeset5586
+YOR275C = probeset5587
+YOR348C = probeset5588
+YDR412W = probeset5589
+YIL144W = probeset5590
+YER035W = probeset5591
+YPL222W = probeset5592
+YGL259W = probeset5593
+YLR113W = probeset5594
+YDL025C = probeset5595
+YKR061W = probeset5596
+YNL191W = probeset5597
+YBR098W = probeset5598
+YBL067C = probeset5599
+YJR155W = probeset5600
+YKL103C = probeset5601
+YNL337W = probeset5602
+YJL124C = probeset5603
+YDR413C = probeset5604
+YFR015C = probeset5605
+YHR197W = probeset5606
+YIL145C = probeset5607
+YER036C = probeset5608
+YPL223C = probeset5609
+YGL187C = probeset5610
+YLR114C = probeset5611
+YBR099C = probeset5612
+YNL265C = probeset5613
+YJR083C = probeset5614
+YJR156C = probeset5615
+YEL004W = probeset5616
+YHR198C = probeset5617
+YCL046W = probeset5618
+YKL030W = probeset5619
+YJL051W = probeset5620
+YDR340W = probeset5621
+YIL072W = probeset5622
+YMR020W = probeset5623
+YPL150W = probeset5624
+YEL005C = probeset5625
+YDR057W = probeset5626
+YLR041W = probeset5627
+YKR062W = probeset5628
+YLL010C = probeset5629
+YCL047C = probeset5630
+YNL192W = probeset5631
+YKL104C = probeset5632
+YJL125C = probeset5633
+YDR341C = probeset5634
+YIL073C = probeset5635
+YFR016C = probeset5636
+YDR414C = probeset5637
+YIL146C = probeset5638
+YPR182W = probeset5639
+YMR021C = probeset5640
+YPL151C = probeset5641
+YDR058C = probeset5642
+YOR276W = probeset5643
+YPL224C = probeset5644
+YLR042C = probeset5645
+YGL188C = probeset5646
+YOR349W = probeset5647
+YKR063C = probeset5648
+YNL339C = probeset5649
+YDL026W = probeset5650
+YHR199C = probeset5651
+YKL031W = probeset5652
+YBL068W = probeset5653
+YJL052W = probeset5654
+YOR277C = probeset5655
+YER037W = probeset5656
+YLR115W = probeset5657
+YDL027C = probeset5658
+YCR079W = probeset5659
+YAL058C-A = probeset5660
+YNL193W = probeset5661
+YNL266W = probeset5662
+YJR084W = probeset5663
+YKL032C = probeset5664
+YKL105C = probeset5665
+YJR157W = probeset5666
+YDR342C = probeset5667
+YDR415C = probeset5668
+YIL074C = probeset5669
+YFR017C = probeset5670
+YNR001C = probeset5671
+YIL147C = probeset5672
+YPR183W = probeset5673
+YER038C = probeset5674
+YDR059C = probeset5675
+YGL189C = probeset5676
+YLR043C = probeset5677
+YNL194C = probeset5678
+YJR085C = probeset5679
+YLL011W = probeset5680
+YCL048W = probeset5681
+YBL069W = probeset5682
+YJL053W = probeset5683
+YJL126W = probeset5684
+YMR022W = probeset5685
+YPL152W = probeset5686
+YPL225W = probeset5687
+YDL028C = probeset5688
+YLR116W = probeset5689
+YKR064W = probeset5690
+YCL049C = probeset5691
+YNL267W = probeset5692
+YJR158W = probeset5693
+YDR343C = probeset5694
+YJL127C = probeset5695
+YFR018C = probeset5696
+YIL075C = probeset5697
+YNR002C = probeset5698
+YPR184W = probeset5699
+YER039C = probeset5700
+YPL080C = probeset5701
+YMR023C = probeset5702
+YPL153C = probeset5703
+YOR278W = probeset5704
+YLR044C = probeset5705
+YLR117C = probeset5706
+YKR065C = probeset5707
+YNL195C = probeset5708
+YEL007W = probeset5709
+YLL012W = probeset5710
+YKL033W = probeset5711
+YKL106W = probeset5712
+YDR270W = probeset5713
+YOR279C = probeset5714
+YJL054W = probeset5715
+YDR416W = probeset5716
+YLR400W = probeset5717
+YIL148W = probeset5718
+YPL226W = probeset5719
+YLL013C = probeset5720
+YNL268W = probeset5721
+YJR086W = probeset5722
+YJR159W = probeset5723
+YDR271C = probeset5724
+YDR344C = probeset5725
+YJL128C = probeset5726
+YDR417C = probeset5727
+YLR401C = probeset5728
+YIL149C = probeset5729
+YNR003C = probeset5730
+YPR185W = probeset5731
+YPL154C = probeset5732
+YLR045C = probeset5733
+YPL227C = probeset5734
+YLR118C = probeset5735
+YKR066C = probeset5736
+YNL196C = probeset5737
+YEL008W = probeset5738
+YDL029W = probeset5739
+YPR186C = probeset5740
+YKL034W = probeset5741
+YKL107W = probeset5742
+YJL055W = probeset5743
+YIL076W = probeset5744
+YPL081W = probeset5745
+YMR024W = probeset5746
+YEL009C = probeset5747
+YJR087W = probeset5748
+YNL269W = probeset5749
+YJL056C = probeset5750
+YDR345C = probeset5751
+YJL129C = probeset5752
+YIL077C = probeset5753
+YPL082C = probeset5754
+YPL155C = probeset5755
+YLR046C = probeset5756
+YDL240W = probeset5757
+YNL197C = probeset5758
+YJR088C = probeset5759
+YLL014W = probeset5760
+YKL035W = probeset5761
+YKL108W = probeset5762
+YDR272W = probeset5763
+YDR418W = probeset5764
+YLR402W = probeset5765
+YNR004W = probeset5766
+YMR025W = probeset5767
+YPL228W = probeset5768
+YGR210C = probeset5769
+YLR119W = probeset5770
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+YMR241W = probeset5880
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+YMR242C = probeset5887
+YGL111W = probeset5888
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+YGR143W = probeset5896
+YOR200W = probeset5897
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+YDL175C = probeset5904
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+YGR071C = probeset5906
+YDR490C = probeset5907
+YOR201C = probeset5908
+YAL013W = probeset5909
+YER186C = probeset5910
+YMR170C = probeset5911
+YMR243C = probeset5912
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+YDL248W = probeset5915
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+YHR050W = probeset5917
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+YHR123W = probeset5919
+YGR144W = probeset5920
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+YGR217W = probeset5922
+YCR004C = probeset5923
+YBR025C = probeset5924
+YLR191W = probeset5925
+YMR316W = probeset5926
+YLR264W = probeset5927
+YIR030C = probeset5928
+YDR491C = probeset5929
+YLR192C = probeset5930
+YLR265C = probeset5931
+YGL113W = probeset5932
+YFL061W = probeset5933
+YDL176W = probeset5934
+YAL015C = probeset5935
+NumSigGenes: = probeset5936
diff --git a/distribution/src/main/sampleData/galExpData.csv b/distribution/src/main/sampleData/galExpData.csv
new file mode 100644
index 0000000..1b9f7ce
--- /dev/null
+++ b/distribution/src/main/sampleData/galExpData.csv
@@ -0,0 +1,5935 @@
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+YGR142W,BTN2,0.215,-0.012,-0.387,2.60120e-03,9.05810e-01,5.17860e-03
+YGR215W,YGR215W,-0.204,-0.281,0.134,6.53210e-03,8.58750e-03,5.07440e-01
+YCR002C,CDC10,-0.159,-0.179,-0.426,1.32870e-04,2.44140e-03,9.50470e-09
+YBR023C,CHS3,-0.276,0.000,0.000,1.34900e-06,9.99999e-01,9.99999e-01
+YMR241W,YHM2,-0.062,-0.451,-0.248,1.21540e-01,3.24610e-05,1.89660e-02
+YMR314W,PRE5,-0.002,-0.003,0.059,9.53960e-01,9.41780e-01,3.61700e-01
+YDL174C,DLD1,0.564,0.560,-0.024,7.48610e-08,5.05530e-09,6.90390e-01
+YLR335W,NUP2,0.217,-0.284,0.164,1.87060e-05,1.57810e-04,8.22100e-02
+YPL088W,YPL088W,-0.319,-0.243,0.683,1.94000e-07,7.46860e-03,9.66090e-06
+YGR216C,GPI1,-0.175,-0.093,-0.143,3.33770e-04,1.16230e-01,2.61520e-01
+YAL012W,CYS3,-0.205,-0.634,0.152,1.70780e-04,1.65890e-07,4.67050e-02
+YMR242C,RPL20A,-0.334,-0.432,-0.118,1.42650e-06,6.50880e-07,3.03150e-02
+YGL111W,YGL111W,0.206,-0.325,0.460,1.89950e-04,5.98920e-04,3.91100e-03
+YLR336C,SGD1,-0.164,-0.356,0.071,1.18110e-04,3.28010e-06,2.89350e-01
+YLR409C,YLR409C,0.189,-1.051,0.339,7.67040e-04,4.46360e-06,8.98350e-02
+YPL089C,RLM1,-0.060,-0.037,0.209,1.45130e-01,4.76010e-01,2.64910e-03
+YAR044W,OSH1,0.077,-0.019,0.100,5.95940e-02,7.25450e-01,2.22220e-01
+YDL247W,YDL247W,-0.066,0.239,-0.231,1.07680e-01,1.05700e-04,1.82710e-02
+YHR122W,YHR122W,0.026,-0.230,0.183,5.89370e-01,4.01870e-03,1.94920e-01
+YGR070W,ROM1,-0.225,0.343,-0.134,1.89760e-03,8.03800e-05,3.48200e-01
+YGR143W,SKN1,-0.284,0.261,-0.161,1.47420e-06,4.12760e-06,1.03090e-02
+YOR200W,YOR200W,-0.149,-0.348,0.412,5.93310e-02,1.07370e-03,1.09280e-01
+YGL112C,TAF60,0.006,-0.146,0.144,8.80330e-01,8.93720e-03,9.19820e-02
+YFL060C,SNO3,0.033,-0.093,0.184,5.71210e-01,2.91210e-01,1.87390e-01
+YER185W,YER185W,-0.140,-0.198,0.511,1.17280e-01,2.58890e-01,6.06350e-03
+YDR279W,YDR279W,0.199,0.049,-0.181,2.65410e-04,4.91460e-01,7.23300e-02
+YMR315W,YMR315W,-0.112,0.016,0.030,6.73870e-03,7.94270e-01,6.54720e-01
+YLR190W,YLR190W,0.083,-0.095,-0.022,4.39630e-02,5.37000e-02,7.42430e-01
+YDL175C,YDL175C,0.149,0.037,0.202,1.09090e-02,6.94110e-01,1.98960e-01
+YLR263W,RED1,-0.377,0.277,-0.404,1.19290e-05,2.05490e-02,5.28080e-02
+YGR071C,YGR071C,0.013,-0.156,0.363,8.33850e-01,1.09690e-01,2.41570e-02
+YDR490C,PKH1,0.170,0.083,0.312,6.26680e-02,6.57970e-01,1.43880e-01
+YOR201C,PET56,-0.145,-0.282,-0.054,1.02860e-03,3.99080e-03,5.57910e-01
+YAL013W,DEP1,0.182,0.011,0.325,4.52960e-04,8.60990e-01,8.08750e-03
+YER186C,YER186C,-0.048,0.039,-0.220,2.56910e-01,4.51050e-01,3.43470e-02
+YMR170C,ALD2,-0.000,0.000,0.000,9.01450e-01,9.99999e-01,9.99999e-01
+YMR243C,ZRC1,-0.124,-0.063,-0.160,3.84420e-03,3.00040e-01,5.04830e-02
+YCR003W,MRPL32,0.149,-0.089,0.069,5.35340e-03,1.76760e-01,6.24690e-01
+YBR024W,SCO2,-0.054,0.094,-0.105,2.15510e-01,6.68250e-02,3.47290e-01
+YDL248W,COS7,-0.148,0.126,-0.661,4.28110e-04,5.99210e-03,2.54970e-15
+YAL014C,YAL014C,-0.090,0.002,-0.077,6.92800e-02,9.79400e-01,3.87320e-01
+YHR050W,SMF2,0.162,0.331,-0.300,6.71450e-04,3.02500e-06,2.48930e-05
+YKL180W,RPL17A,0.104,0.011,0.347,8.04730e-02,8.58030e-01,9.03450e-03
+YHR123W,EPT1,-0.288,-0.313,-0.156,2.52090e-05,1.96950e-04,3.78570e-01
+YGR144W,THI4,-0.069,-0.238,-0.125,6.18490e-01,4.01000e-01,6.18960e-01
+YGL040C,HEM2,0.065,0.138,-0.342,1.17670e-01,2.89490e-02,2.83570e-06
+YGR217W,CCH1,-0.012,-0.109,0.045,9.53960e-01,4.22990e-01,8.19620e-01
+YCR004C,YCP4,0.195,0.166,0.004,2.22600e-04,1.57850e-03,9.45540e-01
+YBR025C,YBR025C,-0.101,-0.060,-0.387,1.42630e-02,1.95550e-01,1.75110e-08
+YLR191W,PEX13,0.178,-0.056,0.222,7.69250e-04,5.83050e-01,9.79870e-02
+YMR316W,YMR316W,-0.388,-0.128,0.666,2.06000e-07,3.52570e-02,2.78090e-08
+YLR264W,RPS28B,-0.259,-0.299,-0.170,1.60860e-04,2.06320e-04,2.10590e-01
+YIR030C,DCG1,0.089,-0.221,-0.098,3.38350e-01,1.75660e-01,7.44740e-01
+YDR491C,YDR491C,0.014,-0.421,0.274,7.93290e-01,8.68960e-05,5.86440e-02
+YLR192C,HCR1,-0.331,-0.136,0.529,1.01330e-06,6.14260e-03,4.05600e-09
+YLR265C,YLR265C,0.001,-0.204,0.055,9.79400e-01,3.24910e-03,6.28570e-01
+YGL113W,YGL113W,0.102,-0.666,0.593,3.56360e-01,7.26330e-03,1.41500e-02
+YFL061W,YFL061W,0.090,0.025,0.143,2.64700e-01,8.38900e-01,3.51880e-01
+YDL176W,YDL176W,0.142,0.225,0.455,1.57070e-02,6.12890e-03,3.34810e-03
+YAL015C,NTG1,-0.350,-0.115,-0.150,1.55410e-03,6.92520e-02,1.27770e-01
diff --git a/distribution/src/main/sampleData/galExpData.probeset.pvals b/distribution/src/main/sampleData/galExpData.probeset.pvals
new file mode 100644
index 0000000..6b1ac38
--- /dev/null
+++ b/distribution/src/main/sampleData/galExpData.probeset.pvals
@@ -0,0 +1,11866 @@
+GENE COMMON gal1RG gal4RG gal80R gal1RG gal4RG gal80R
+YHR051W COX6 -0.034 0.111 -0.304 3.75720e-01 1.56240e-02 7.91340e-06
+probeset2 COX6 -0.034 0.111 -0.304 3.75720e-01 1.56240e-02 7.91340e-06
+probeset3 NDT80 -0.090 0.007 -0.348 2.71460e-01 9.64330e-01 3.44760e-01
+probeset4 PRS1 -0.167 -0.233 0.112 6.27120e-03 7.89400e-04 1.44060e-01
+probeset5 UPF3 0.245 -0.471 0.787 4.10450e-04 7.51780e-04 1.37130e-05
+probeset6 OPI1 0.174 -0.015 0.151 1.40160e-04 7.19120e-01 1.53950e-02
+probeset7 YGR145W 0.387 -0.577 -0.088 5.37920e-03 8.27330e-03 7.64180e-01
+
+probeset8 YGL041C 0.285 -0.086 0.103 4.46050e-04 4.50790e-01 7.03040e-01
+
+probeset9 CRM1 -0.018 -0.001 -0.018 6.13810e-01 9.79400e-01 8.09690e-01
+
+probeset10 HIS3 -0.432 -0.710 0.239 1.09790e-02 1.79790e-04 5.48950e-03
+
+probeset11 CIT2 0.085 0.392 0.464 4.18980e-02 1.53050e-06 2.74360e-06
+
+probeset12 KHS1 0.159 0.139 -0.045 8.51260e-04 4.17830e-03 6.18020e-01
+
+probeset13 YBR026C 0.276 0.189 0.291 3.63320e-05 6.15230e-04 1.24430e-03
+
+probeset14 YMR244W 0.078 -0.239 -0.072 5.76050e-01 3.55240e-01 8.85690e-01
+
+probeset15 YMR317W -0.181 0.086 -0.453 5.94980e-02 3.03060e-01 7.60020e-03
+
+probeset16 YAR047C -0.234 -0.109 0.155 2.46640e-02 4.96380e-01 4.83330e-01
+
+probeset17 DAL7 0.289 -0.161 1.085 3.04210e-05 8.90570e-02 2.51800e-07
+
+probeset18 YDL177C -0.002 -0.367 0.633 9.79400e-01 1.42900e-02 6.05450e-03
+
+probeset19 YLR338W -0.216 0.096 -0.238 2.15180e-05 5.11510e-02 9.32590e-03
+
+probeset20 YGR073C -0.125 -0.126 -0.051 5.55560e-02 1.71320e-01 7.89410e-01
+
+probeset21 YGR146C -0.189 -0.067 0.341 3.72480e-03 2.88770e-01 4.61960e-03
+
+probeset22 ORT1 -0.025 -0.322 0.172 5.92360e-01 6.13670e-05 2.37790e-02
+
+probeset23 YLR193C 0.124 0.057 -0.052 8.16620e-03 2.30570e-01 6.30040e-01
+
+probeset24 YMR318C 0.068 -0.716 0.558 1.10340e-01 1.49790e-08 5.55910e-08
+
+probeset25 YLR266C -0.058 0.066 -0.136 1.31160e-01 1.39630e-01 6.49860e-02
+
+probeset26 YGL114W -0.009 -0.076 0.224 8.59500e-01 2.32420e-01 1.42010e-01
+
+probeset27 YLR339C -0.239 -0.072 -0.362 2.57470e-06 2.60270e-01 5.80940e-06
+
+probeset28 COS4 -0.192 0.213 -0.561 3.44560e-05 1.62290e-04 3.31070e-13
+
+probeset29 MET3 -0.253 -0.136 -0.017 2.91960e-06 1.71460e-02 8.56570e-01
+
+probeset30 YHR052W 0.101 -0.324 0.126 1.39850e-02 3.82030e-05 1.95990e-01
+
+probeset31 FAS1 -0.140 -0.183 -0.415 9.08500e-04 1.19420e-03 2.43900e-08
+
+probeset32 YHR125W -0.513 -0.052 -0.036 2.40260e-04 1.01320e-01 7.78200e-01
+
+probeset33 YHL021C -0.130 0.544 -0.757 4.44280e-03 1.84500e-06 6.01690e-18
+
+probeset34 YGR219W -0.070 -0.188 -0.206 1.66960e-01 2.29010e-02 1.58970e-01
+
+probeset35 YGL042C -0.075 -0.408 0.028 2.69230e-01 3.02660e-03 8.95260e-01
+
+probeset36 YOR203W -0.492 -0.561 0.359 6.48760e-09 1.80630e-05 1.86630e-01
+
+probeset37 YCR006C -0.067 0.055 0.410 4.05710e-01 6.63470e-01 8.10030e-02
+
+probeset38 YER188W -0.322 -0.285 -0.089 4.03760e-02 1.85790e-01 7.21210e-01
+
+probeset39 HOT1 0.162 -0.332 0.489 3.39870e-02 1.31310e-03 1.96070e-03
+
+probeset40 YNL120C -0.053 -0.800 0.428 5.64090e-01 5.14230e-04 7.51560e-02
+
+probeset41 YBR027C -0.210 -0.110 0.307 8.47300e-03 4.27360e-01 7.58960e-02
+
+probeset42 YMR245W 0.095 -0.187 0.213 5.49810e-02 3.40940e-02 8.66970e-02
+
+probeset43 YJR011C -0.112 -0.545 0.142 1.85960e-01 2.52110e-02 6.59060e-01
+
+probeset44 DAL3 0.181 -0.148 -0.004 8.14360e-02 5.29160e-01 9.99999e-01
+
+probeset45 CUP1A -0.656 -0.750 0.795 1.67310e-04 8.46380e-04 1.51870e-10
+
+probeset46 YHR126C -0.238 0.193 -0.071 2.36540e-04 9.74530e-04 5.56390e-01
+
+probeset47 RPC40 -0.120 -0.339 -0.026 1.96070e-03 1.27430e-05 7.05640e-01
+
+probeset48 NAT2 0.158 -0.074 0.295 7.17510e-04 1.83220e-01 7.18280e-03
+
+probeset49 YOR131C -0.037 -0.135 -0.113 3.43680e-01 1.20150e-02 1.28600e-01
+
+probeset50 TPD3 0.053 0.198 -0.055 2.11860e-01 6.89500e-04 4.22030e-01
+
+probeset51 YLR194C 0.046 -0.383 0.251 2.86640e-01 1.46600e-04 2.82510e-02
+
+probeset52 FET4 -0.182 -0.327 -0.360 7.00470e-04 1.09890e-04 3.48440e-07
+
+probeset53 SNF4 -0.111 0.112 -0.221 5.85410e-03 1.12340e-02 2.75350e-03
+
+probeset54 YFL063W 0.128 -0.152 -0.001 6.69880e-02 2.89770e-01 9.99999e-01
+
+probeset55 AIP2 -0.131 -0.091 -0.693 1.80100e-03 7.77810e-02 2.14570e-12
+
+probeset56 YKL183W -0.116 -0.151 -0.045 7.62850e-03 2.51430e-02 6.30540e-01
+
+probeset57 SMD1 -0.074 -0.133 0.029 1.19390e-01 8.22100e-02 8.07550e-01
+
+probeset58 SPO11 -0.402 -0.499 0.176 4.71620e-04 1.19080e-01 4.21550e-01
+
+probeset59 YDR493W 0.062 -0.077 -0.204 3.18440e-01 2.37620e-01 1.61090e-01
+
+probeset60 DED1 -0.033 -0.056 -0.910 3.99440e-01 3.12680e-01 8.34900e-16
+
+probeset61 YCR007C -0.019 0.003 0.387 7.66740e-01 9.79400e-01 5.61670e-03
+
+probeset62 YFL064C 0.032 -0.011 -0.261 4.65490e-01 8.20760e-01 5.18620e-03
+
+probeset63 YER189W 0.211 0.082 -0.026 3.03140e-05 8.04400e-02 7.10280e-01
+
+probeset64 TOM70 0.162 0.024 -0.514 1.21720e-03 6.32020e-01 3.14050e-07
+
+probeset65 YBR028C 0.004 -0.323 0.219 9.31760e-01 1.38290e-04 1.30940e-01
+
+probeset66 DDR48 -0.873 0.096 -0.692 1.48840e-11 3.03670e-01 3.52770e-15
+
+probeset67 FAA4 -0.001 -0.499 0.600 9.79400e-01 2.25910e-05 1.27350e-07
+
+probeset68 YJR012C 0.124 0.085 0.015 8.92050e-02 3.41710e-01 8.95260e-01
+
+probeset69 BOP2 0.199 0.403 0.640 4.53770e-04 2.42730e-05 1.19290e-05
+
+probeset70 YHR054C -0.071 0.055 -0.015 9.88090e-02 1.89090e-01 8.46790e-01
+
+probeset71 PRP38 -0.075 -0.227 0.081 1.84370e-01 9.43450e-03 6.19910e-01
+
+probeset72 RPL24B -0.202 -0.423 -0.126 9.95090e-05 1.33550e-06 3.88370e-02
+
+probeset73 YOR205C 0.069 0.030 0.389 2.15510e-01 7.80940e-01 2.63030e-02
+
+probeset74 YAL017W -0.122 -0.019 -0.251 2.55330e-03 7.02390e-01 2.65410e-04
+
+probeset75 YIL001W -0.044 -0.096 -0.032 3.27520e-01 1.65560e-01 7.71950e-01
+
+probeset76 PAI3 -0.070 -0.088 -0.190 6.66630e-02 1.25930e-01 3.17050e-03
+
+probeset77 NMT1 -0.003 -0.316 -0.012 9.41780e-01 5.11950e-05 9.12770e-01
+
+probeset78 DST1 0.156 -0.466 0.568 4.35230e-03 2.93520e-05 1.07510e-04
+
+probeset79 CDC20 0.006 -0.066 0.294 9.20340e-01 5.34760e-01 3.89590e-02
+
+probeset80 PKH2 -0.119 -0.049 0.160 6.34510e-01 8.28970e-01 4.70840e-01
+
+probeset81 RPS30A -0.289 -0.288 -0.095 6.11880e-06 3.13860e-05 9.16400e-02
+
+probeset82 PCL9 0.189 0.012 -0.028 6.98210e-04 8.33850e-01 7.75500e-01
+
+probeset83 MGA2 0.079 -0.142 0.051 1.26790e-01 8.03350e-03 5.16940e-01
+
+probeset84 YAL018C -0.227 -0.000 -0.000 5.64090e-01 4.65210e-01 7.47870e-01
+
+probeset85 INP51 -0.013 -0.194 -0.021 7.93290e-01 3.12900e-03 8.41480e-01
+
+probeset86 HSN1 0.159 -0.413 0.532 8.85090e-03 3.96450e-03 2.18090e-03
+
+probeset87 SPE1 -0.030 -0.071 -0.055 5.02650e-01 1.65710e-01 4.99810e-01
+
+probeset88 YHL023C 0.127 -0.183 0.132 1.31160e-02 3.08130e-02 2.09430e-01
+
+probeset89 DBF20 0.148 0.137 0.077 7.18020e-03 4.64460e-02 5.45930e-01
+
+probeset90 YDR494W 0.193 0.010 0.199 5.37600e-05 8.46790e-01 1.09830e-02
+
+probeset91 RNA15 0.162 -0.211 0.281 1.36390e-03 4.09020e-03 5.74480e-03
+
+probeset92 VPS17 0.079 0.085 0.150 5.93070e-02 8.09700e-02 5.66330e-02
+
+probeset93 YFL065C 0.003 -0.061 -0.118 9.58820e-01 3.53180e-01 3.32280e-01
+
+probeset94 YOL101C -0.081 -0.111 -0.032 3.58970e-02 2.04630e-02 6.01550e-01
+
+probeset95 CDS1 -0.032 -0.028 -0.007 5.48140e-01 6.29550e-01 9.45540e-01
+
+probeset96 YNL122C -0.074 0.026 -0.045 1.30380e-01 6.23720e-01 6.87930e-01
+
+probeset97 LYS1 -0.085 -0.272 0.278 3.83370e-02 1.80940e-04 2.17220e-03
+
+probeset98 SEC22 -0.123 -0.009 -0.541 7.22570e-03 9.03610e-01 6.23470e-05
+
+probeset99 CUP1B -0.867 -0.416 0.802 2.88130e-06 2.67530e-02 1.96960e-12
+
+probeset100 YPR112C 0.227 0.286 0.547 2.47900e-03 3.23240e-04 9.10460e-04
+
+probeset101 MRPL25 0.145 0.000 0.046 6.24340e-03 9.99999e-01 7.01740e-01
+
+probeset102 YOR060C -0.022 -0.126 0.246 6.36010e-01 6.44630e-02 5.29760e-02
+
+probeset103 VPS3 -0.011 -0.216 0.251 9.79400e-01 7.42430e-01 3.71690e-02
+
+probeset104 YLR269C 0.015 0.214 0.089 8.95260e-01 1.19540e-01 5.16600e-01
+
+probeset105 YGL117W -0.356 -0.740 0.262 3.27050e-08 7.34450e-06 5.06850e-02
+
+probeset106 SAT4 0.151 0.005 0.135 1.63140e-02 9.64330e-01 3.82500e-01
+
+probeset107 YJR013W -0.048 0.064 -0.205 2.99740e-01 2.36720e-01 9.14120e-02
+
+probeset108 DAK1 -0.053 0.171 -0.373 3.31080e-01 9.25650e-04 5.84920e-07
+
+probeset109 FUR1 -0.091 -0.398 -0.046 1.32070e-01 3.47610e-04 6.87930e-01
+
+probeset110 ASH1 -0.076 0.215 -0.016 3.69370e-02 8.23600e-05 7.88450e-01
+
+probeset111 THI2 0.009 -0.054 0.294 9.23040e-01 6.60710e-01 1.43380e-01
+
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+probeset5930 HCR1 -0.331 -0.136 0.529 1.01330e-06 6.14260e-03 4.05600e-09
+
+probeset5931 YLR265C 0.001 -0.204 0.055 9.79400e-01 3.24910e-03 6.28570e-01
+
+probeset5932 YGL113W 0.102 -0.666 0.593 3.56360e-01 7.26330e-03 1.41500e-02
+
+probeset5933 YFL061W 0.090 0.025 0.143 2.64700e-01 8.38900e-01 3.51880e-01
+
+probeset5934 YDL176W 0.142 0.225 0.455 1.57070e-02 6.12890e-03 3.34810e-03
+
+probeset5935 NTG1 -0.350 -0.115 -0.150 1.55410e-03 6.92520e-02 1.27770e-01
+
+
diff --git a/distribution/src/main/sampleData/galExpData.pvals b/distribution/src/main/sampleData/galExpData.pvals
new file mode 100644
index 0000000..b8c9c58
--- /dev/null
+++ b/distribution/src/main/sampleData/galExpData.pvals
@@ -0,0 +1,5936 @@
+GENE COMMON gal1RG gal4RG gal80R gal1RG gal4RG gal80R
+YHR051W COX6 -0.034 0.111 -0.304 3.75720e-01 1.56240e-02 7.91340e-06
+YHR124W NDT80 -0.090 0.007 -0.348 2.71460e-01 9.64330e-01 3.44760e-01
+YKL181W PRS1 -0.167 -0.233 0.112 6.27120e-03 7.89400e-04 1.44060e-01
+YGR072W UPF3 0.245 -0.471 0.787 4.10450e-04 7.51780e-04 1.37130e-05
+YHL020C OPI1 0.174 -0.015 0.151 1.40160e-04 7.19120e-01 1.53950e-02
+YGR145W YGR145W 0.387 -0.577 -0.088 5.37920e-03 8.27330e-03 7.64180e-01
+YGL041C YGL041C 0.285 -0.086 0.103 4.46050e-04 4.50790e-01 7.03040e-01
+YGR218W CRM1 -0.018 -0.001 -0.018 6.13810e-01 9.79400e-01 8.09690e-01
+YOR202W HIS3 -0.432 -0.710 0.239 1.09790e-02 1.79790e-04 5.48950e-03
+YCR005C CIT2 0.085 0.392 0.464 4.18980e-02 1.53050e-06 2.74360e-06
+YER187W KHS1 0.159 0.139 -0.045 8.51260e-04 4.17830e-03 6.18020e-01
+YBR026C YBR026C 0.276 0.189 0.291 3.63320e-05 6.15230e-04 1.24430e-03
+YMR244W YMR244W 0.078 -0.239 -0.072 5.76050e-01 3.55240e-01 8.85690e-01
+YMR317W YMR317W -0.181 0.086 -0.453 5.94980e-02 3.03060e-01 7.60020e-03
+YAR047C YAR047C -0.234 -0.109 0.155 2.46640e-02 4.96380e-01 4.83330e-01
+YIR031C DAL7 0.289 -0.161 1.085 3.04210e-05 8.90570e-02 2.51800e-07
+YDL177C YDL177C -0.002 -0.367 0.633 9.79400e-01 1.42900e-02 6.05450e-03
+YLR338W YLR338W -0.216 0.096 -0.238 2.15180e-05 5.11510e-02 9.32590e-03
+YGR073C YGR073C -0.125 -0.126 -0.051 5.55560e-02 1.71320e-01 7.89410e-01
+YGR146C YGR146C -0.189 -0.067 0.341 3.72480e-03 2.88770e-01 4.61960e-03
+YOR130C ORT1 -0.025 -0.322 0.172 5.92360e-01 6.13670e-05 2.37790e-02
+YLR193C YLR193C 0.124 0.057 -0.052 8.16620e-03 2.30570e-01 6.30040e-01
+YMR318C YMR318C 0.068 -0.716 0.558 1.10340e-01 1.49790e-08 5.55910e-08
+YLR266C YLR266C -0.058 0.066 -0.136 1.31160e-01 1.39630e-01 6.49860e-02
+YGL114W YGL114W -0.009 -0.076 0.224 8.59500e-01 2.32420e-01 1.42010e-01
+YLR339C YLR339C -0.239 -0.072 -0.362 2.57470e-06 2.60270e-01 5.80940e-06
+YFL062W COS4 -0.192 0.213 -0.561 3.44560e-05 1.62290e-04 3.31070e-13
+YJR010W MET3 -0.253 -0.136 -0.017 2.91960e-06 1.71460e-02 8.56570e-01
+YHR052W YHR052W 0.101 -0.324 0.126 1.39850e-02 3.82030e-05 1.95990e-01
+YKL182W FAS1 -0.140 -0.183 -0.415 9.08500e-04 1.19420e-03 2.43900e-08
+YHR125W YHR125W -0.513 -0.052 -0.036 2.40260e-04 1.01320e-01 7.78200e-01
+YHL021C YHL021C -0.130 0.544 -0.757 4.44280e-03 1.84500e-06 6.01690e-18
+YGR219W YGR219W -0.070 -0.188 -0.206 1.66960e-01 2.29010e-02 1.58970e-01
+YGL042C YGL042C -0.075 -0.408 0.028 2.69230e-01 3.02660e-03 8.95260e-01
+YOR203W YOR203W -0.492 -0.561 0.359 6.48760e-09 1.80630e-05 1.86630e-01
+YCR006C YCR006C -0.067 0.055 0.410 4.05710e-01 6.63470e-01 8.10030e-02
+YER188W YER188W -0.322 -0.285 -0.089 4.03760e-02 1.85790e-01 7.21210e-01
+YMR172W HOT1 0.162 -0.332 0.489 3.39870e-02 1.31310e-03 1.96070e-03
+YNL120C YNL120C -0.053 -0.800 0.428 5.64090e-01 5.14230e-04 7.51560e-02
+YBR027C YBR027C -0.210 -0.110 0.307 8.47300e-03 4.27360e-01 7.58960e-02
+YMR245W YMR245W 0.095 -0.187 0.213 5.49810e-02 3.40940e-02 8.66970e-02
+YJR011C YJR011C -0.112 -0.545 0.142 1.85960e-01 2.52110e-02 6.59060e-01
+YIR032C DAL3 0.181 -0.148 -0.004 8.14360e-02 5.29160e-01 9.99999e-01
+YHR053C CUP1A -0.656 -0.750 0.795 1.67310e-04 8.46380e-04 1.51870e-10
+YHR126C YHR126C -0.238 0.193 -0.071 2.36540e-04 9.74530e-04 5.56390e-01
+YPR110C RPC40 -0.120 -0.339 -0.026 1.96070e-03 1.27430e-05 7.05640e-01
+YGR147C NAT2 0.158 -0.074 0.295 7.17510e-04 1.83220e-01 7.18280e-03
+YOR131C YOR131C -0.037 -0.135 -0.113 3.43680e-01 1.20150e-02 1.28600e-01
+YAL016W TPD3 0.053 0.198 -0.055 2.11860e-01 6.89500e-04 4.22030e-01
+YLR194C YLR194C 0.046 -0.383 0.251 2.86640e-01 1.46600e-04 2.82510e-02
+YMR319C FET4 -0.182 -0.327 -0.360 7.00470e-04 1.09890e-04 3.48440e-07
+YGL115W SNF4 -0.111 0.112 -0.221 5.85410e-03 1.12340e-02 2.75350e-03
+YFL063W YFL063W 0.128 -0.152 -0.001 6.69880e-02 2.89770e-01 9.99999e-01
+YDL178W AIP2 -0.131 -0.091 -0.693 1.80100e-03 7.77810e-02 2.14570e-12
+YKL183W YKL183W -0.116 -0.151 -0.045 7.62850e-03 2.51430e-02 6.30540e-01
+YGR074W SMD1 -0.074 -0.133 0.029 1.19390e-01 8.22100e-02 8.07550e-01
+YHL022C SPO11 -0.402 -0.499 0.176 4.71620e-04 1.19080e-01 4.21550e-01
+YDR493W YDR493W 0.062 -0.077 -0.204 3.18440e-01 2.37620e-01 1.61090e-01
+YOR204W DED1 -0.033 -0.056 -0.910 3.99440e-01 3.12680e-01 8.34900e-16
+YCR007C YCR007C -0.019 0.003 0.387 7.66740e-01 9.79400e-01 5.61670e-03
+YFL064C YFL064C 0.032 -0.011 -0.261 4.65490e-01 8.20760e-01 5.18620e-03
+YER189W YER189W 0.211 0.082 -0.026 3.03140e-05 8.04400e-02 7.10280e-01
+YNL121C TOM70 0.162 0.024 -0.514 1.21720e-03 6.32020e-01 3.14050e-07
+YBR028C YBR028C 0.004 -0.323 0.219 9.31760e-01 1.38290e-04 1.30940e-01
+YMR173W DDR48 -0.873 0.096 -0.692 1.48840e-11 3.03670e-01 3.52770e-15
+YMR246W FAA4 -0.001 -0.499 0.600 9.79400e-01 2.25910e-05 1.27350e-07
+YJR012C YJR012C 0.124 0.085 0.015 8.92050e-02 3.41710e-01 8.95260e-01
+YLR267W BOP2 0.199 0.403 0.640 4.53770e-04 2.42730e-05 1.19290e-05
+YHR054C YHR054C -0.071 0.055 -0.015 9.88090e-02 1.89090e-01 8.46790e-01
+YGR075C PRP38 -0.075 -0.227 0.081 1.84370e-01 9.43450e-03 6.19910e-01
+YGR148C RPL24B -0.202 -0.423 -0.126 9.95090e-05 1.33550e-06 3.88370e-02
+YOR205C YOR205C 0.069 0.030 0.389 2.15510e-01 7.80940e-01 2.63030e-02
+YAL017W YAL017W -0.122 -0.019 -0.251 2.55330e-03 7.02390e-01 2.65410e-04
+YIL001W YIL001W -0.044 -0.096 -0.032 3.27520e-01 1.65560e-01 7.71950e-01
+YMR174C PAI3 -0.070 -0.088 -0.190 6.66630e-02 1.25930e-01 3.17050e-03
+YLR195C NMT1 -0.003 -0.316 -0.012 9.41780e-01 5.11950e-05 9.12770e-01
+YGL043W DST1 0.156 -0.466 0.568 4.35230e-03 2.93520e-05 1.07510e-04
+YGL116W CDC20 0.006 -0.066 0.294 9.20340e-01 5.34760e-01 3.89590e-02
+YOL100W PKH2 -0.119 -0.049 0.160 6.34510e-01 8.28970e-01 4.70840e-01
+YLR287C-A RPS30A -0.289 -0.288 -0.095 6.11880e-06 3.13860e-05 9.16400e-02
+YDL179W PCL9 0.189 0.012 -0.028 6.98210e-04 8.33850e-01 7.75500e-01
+YIR033W MGA2 0.079 -0.142 0.051 1.26790e-01 8.03350e-03 5.16940e-01
+YAL018C YAL018C -0.227 -0.000 -0.000 5.64090e-01 4.65210e-01 7.47870e-01
+YIL002C INP51 -0.013 -0.194 -0.021 7.93290e-01 3.12900e-03 8.41480e-01
+YHR127W HSN1 0.159 -0.413 0.532 8.85090e-03 3.96450e-03 2.18090e-03
+YKL184W SPE1 -0.030 -0.071 -0.055 5.02650e-01 1.65710e-01 4.99810e-01
+YHL023C YHL023C 0.127 -0.183 0.132 1.31160e-02 3.08130e-02 2.09430e-01
+YPR111W DBF20 0.148 0.137 0.077 7.18020e-03 4.64460e-02 5.45930e-01
+YDR494W YDR494W 0.193 0.010 0.199 5.37600e-05 8.46790e-01 1.09830e-02
+YGL044C RNA15 0.162 -0.211 0.281 1.36390e-03 4.09020e-03 5.74480e-03
+YOR132W VPS17 0.079 0.085 0.150 5.93070e-02 8.09700e-02 5.66330e-02
+YFL065C YFL065C 0.003 -0.061 -0.118 9.58820e-01 3.53180e-01 3.32280e-01
+YOL101C YOL101C -0.081 -0.111 -0.032 3.58970e-02 2.04630e-02 6.01550e-01
+YBR029C CDS1 -0.032 -0.028 -0.007 5.48140e-01 6.29550e-01 9.45540e-01
+YNL122C YNL122C -0.074 0.026 -0.045 1.30380e-01 6.23720e-01 6.87930e-01
+YIR034C LYS1 -0.085 -0.272 0.278 3.83370e-02 1.80940e-04 2.17220e-03
+YLR268W SEC22 -0.123 -0.009 -0.541 7.22570e-03 9.03610e-01 6.23470e-05
+YHR055C CUP1B -0.867 -0.416 0.802 2.88130e-06 2.67530e-02 1.96960e-12
+YPR112C YPR112C 0.227 0.286 0.547 2.47900e-03 3.23240e-04 9.10460e-04
+YGR076C MRPL25 0.145 0.000 0.046 6.24340e-03 9.99999e-01 7.01740e-01
+YOR060C YOR060C -0.022 -0.126 0.246 6.36010e-01 6.44630e-02 5.29760e-02
+YDR495C VPS3 -0.011 -0.216 0.251 9.79400e-01 7.42430e-01 3.71690e-02
+YLR269C YLR269C 0.015 0.214 0.089 8.95260e-01 1.19540e-01 5.16600e-01
+YGL117W YGL117W -0.356 -0.740 0.262 3.27050e-08 7.34450e-06 5.06850e-02
+YCR008W SAT4 0.151 0.005 0.135 1.63140e-02 9.64330e-01 3.82500e-01
+YJR013W YJR013W -0.048 0.064 -0.205 2.99740e-01 2.36720e-01 9.14120e-02
+YML070W DAK1 -0.053 0.171 -0.373 3.31080e-01 9.25650e-04 5.84920e-07
+YHR128W FUR1 -0.091 -0.398 -0.046 1.32070e-01 3.47610e-04 6.87930e-01
+YKL185W ASH1 -0.076 0.215 -0.016 3.69370e-02 8.23600e-05 7.88450e-01
+YBR240C THI2 0.009 -0.054 0.294 9.23040e-01 6.60710e-01 1.43380e-01
+YGR149W YGR149W -0.610 0.044 -0.364 1.42050e-10 4.73700e-01 3.71270e-08
+YOR133W EFT1 -0.260 -0.053 -0.584 2.95720e-04 2.86080e-01 3.41550e-10
+YOR206W YOR206W 0.145 -0.451 0.325 4.86040e-03 1.20380e-04 1.28960e-02
+YGL118C YGL118C 0.069 -0.184 0.548 4.13750e-01 2.30250e-01 1.87860e-02
+YFL066C YFL066C 0.042 -0.025 -0.357 3.09380e-01 6.07390e-01 7.82560e-06
+YOL102C TPT1 -0.017 -0.181 0.151 7.09610e-01 3.61500e-02 1.67850e-01
+YCR009C RVS161 -0.145 -0.148 0.151 9.60260e-04 9.07840e-03 1.59170e-02
+YNL050C YNL050C 0.301 -0.448 0.594 1.42500e-05 3.19260e-03 7.51240e-04
+YMR175W SIP18 0.018 -0.317 -0.334 6.41590e-01 4.27300e-03 1.79500e-05
+YLR196W PWP1 0.130 -1.068 0.996 9.45220e-03 1.25350e-07 2.86900e-05
+YIR035C YIR035C -0.464 -0.383 0.005 1.39470e-08 3.58160e-06 9.41780e-01
+YHR056C YHR056C -0.112 -0.338 0.142 3.27520e-01 4.04810e-01 8.12930e-01
+YKL186C MTR2 0.157 0.035 0.338 7.51310e-03 5.55630e-01 5.61460e-03
+YHR129C ARP1 -0.270 -0.255 0.160 2.40260e-03 3.02210e-02 3.06580e-01
+YGR077C PEX8 -0.064 0.309 -0.177 1.17720e-01 4.87440e-06 7.74640e-02
+YDR496C YDR496C 0.208 -0.295 0.386 7.80620e-05 2.79540e-01 1.48180e-02
+YOR207C RET1 -0.044 0.253 0.242 4.18690e-01 3.91270e-02 2.05150e-01
+YAL019W YAL019W 0.070 -0.000 0.000 9.12230e-02 8.83870e-01 9.99999e-01
+YIL003W YIL003W -0.071 -0.139 0.131 1.33500e-01 4.94110e-02 2.98400e-01
+YHL024W NOS1 0.154 0.119 -0.136 4.44770e-03 1.57440e-01 2.78720e-01
+YGL045W YGL045W -0.279 0.097 -0.290 1.36790e-06 5.37860e-02 9.81230e-03
+YNL123W YNL123W -0.049 -0.206 -0.021 3.41890e-01 7.82600e-02 8.62490e-01
+YJR014W YJR014W 0.070 -0.158 0.090 1.25230e-01 3.77260e-02 3.38880e-01
+YIL004C BET1 -0.093 -0.542 -0.310 1.51940e-01 2.42060e-04 1.15740e-01
+YPR040W YPR040W 0.210 0.070 0.461 7.04270e-05 2.64450e-01 1.11930e-04
+YBR241C YBR241C -0.056 0.529 -0.121 1.79150e-01 4.64080e-08 5.80590e-02
+YPR113W PIS1 -0.495 0.025 -0.890 1.04560e-09 5.45930e-01 5.62020e-18
+YOR061W CKA2 0.080 -0.124 0.158 5.06040e-02 5.45210e-02 4.93520e-02
+YOR134W BAG7 -0.363 -0.017 0.493 2.86230e-08 7.57500e-01 1.31050e-04
+YML072C YML072C -0.034 0.298 0.404 4.66330e-01 2.72020e-05 2.97720e-04
+YLR197W SIK1 0.020 -0.521 0.490 7.01740e-01 1.08140e-05 3.38140e-08
+YIR036C YIR036C 0.047 0.286 -0.099 3.02150e-01 1.33720e-05 2.44580e-01
+YHR057C CYP2 0.166 0.026 0.290 8.23870e-04 6.53650e-01 2.28400e-02
+YKL187C YKL187C 0.999 1.222 0.206 7.45680e-11 2.38260e-10 6.22650e-02
+YGR078C PAC10 -0.004 -0.564 0.442 9.28730e-01 8.21280e-05 1.73100e-02
+YOR062C YOR062C 0.168 -0.041 0.391 9.70280e-03 7.47870e-01 1.12720e-02
+YOR135C YOR135C -0.092 -0.078 -0.816 2.06040e-02 1.00100e-01 5.38730e-16
+YDR497C ITR1 -0.117 -0.068 -0.057 4.17370e-03 1.58480e-01 4.15390e-01
+YHL025W SNF6 -0.001 -0.039 0.133 9.79400e-01 4.12820e-01 1.05750e-01
+YLR198C YLR198C 0.104 -0.598 0.352 7.48800e-02 5.40760e-07 8.48220e-02
+YGL046W YGL046W -0.123 -0.057 -0.040 1.38370e-01 6.32020e-01 7.78200e-01
+YGL119W ABC1 -0.072 -0.015 -0.030 1.17030e-01 7.78200e-01 7.50240e-01
+YOL030W YOL030W -0.070 0.093 -0.581 6.59390e-02 5.74330e-02 7.62910e-13
+YFL067W YFL067W 0.053 -0.058 -0.293 1.79630e-01 2.05620e-01 2.52950e-06
+YOL103W ITR2 -0.075 -0.175 -0.282 6.31750e-02 1.26650e-03 2.64440e-06
+YNL124W YNL124W 0.161 -0.220 0.144 2.33450e-03 1.54790e-03 1.97330e-01
+YJR015W YJR015W -0.149 0.141 -0.345 9.44830e-04 1.87170e-03 5.30400e-07
+YDR200C YDR200C 0.006 -0.236 0.150 8.85690e-01 5.19000e-03 7.77490e-02
+YPR041W TIF5 -0.059 -0.243 -0.177 1.12030e-01 6.19970e-03 1.17380e-02
+YHL026C YHL026C -0.016 -0.305 0.278 7.99270e-01 2.70020e-02 9.57270e-02
+YPR114W YPR114W -0.137 -0.063 -0.232 1.21680e-03 1.78030e-01 1.47700e-04
+YOR208W PTP2 -0.274 -0.131 0.210 2.10220e-06 2.93440e-02 5.66470e-03
+YOL031C YOL031C -0.414 -0.147 -0.424 2.17020e-08 1.21600e-02 1.29710e-04
+YOL104C NDJ1 -0.258 -0.068 -0.554 5.84390e-06 1.47040e-01 3.13410e-08
+YNL125C ESBP6 0.496 0.413 -0.299 5.62760e-09 2.88880e-07 1.31460e-04
+YMR177W MMT1 -0.154 -0.548 -0.151 4.28160e-02 1.47850e-04 6.50980e-01
+YJR016C ILV3 -0.083 0.069 -0.411 5.13550e-02 1.08860e-01 1.21610e-07
+YML073C RPL6A -0.408 -0.513 -0.563 1.88660e-07 4.20910e-07 9.69810e-08
+YHR058C MED6 0.122 -0.282 0.315 1.47840e-02 3.14050e-03 3.11260e-02
+YKL188C PXA2 0.245 0.182 0.460 1.51890e-04 6.58320e-02 2.83920e-03
+YDR498C SEC20 0.075 0.087 -0.672 8.35390e-02 2.73060e-01 7.22970e-09
+YOR209C NPT1 -0.160 -0.306 -0.027 1.79220e-04 3.19010e-04 6.83090e-01
+YIL005W YIL005W 0.077 -0.235 0.014 5.04880e-01 4.78620e-01 2.67410e-01
+YBR242W YBR242W 0.021 -0.339 0.377 6.58510e-01 1.67070e-04 8.27640e-03
+YLR199C YLR199C 0.078 -0.048 -0.038 1.02770e-01 6.06930e-01 7.52630e-01
+YPL010W RET3 -0.226 -0.075 -0.172 9.94130e-06 1.30710e-01 5.68770e-03
+YGL047W YGL047W -0.158 0.011 -0.062 1.89420e-03 8.65550e-01 5.58290e-01
+YFL068W YFL068W 0.026 -0.053 -0.112 5.26750e-01 2.45860e-01 1.19590e-01
+YNL052W COX5A 0.103 0.172 -0.222 1.89660e-02 5.14780e-04 7.49870e-05
+YIR037W HYR1 -0.158 0.233 -0.164 2.45880e-04 3.82460e-04 2.86320e-03
+YBR170C NPL4 0.128 -0.134 0.429 7.82980e-03 1.34540e-01 1.61840e-03
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+YGL122C NAB2 0.174 0.020 0.187 8.72950e-04 6.17070e-01 5.99660e-03
+YOR210W RPB10 0.012 -0.452 0.341 8.21910e-01 1.87850e-05 1.53370e-02
+YCR013C YCR013C -0.614 0.399 -1.060 5.59880e-09 7.85670e-07 1.26880e-17
+YBR034C HMT1 0.183 -0.711 0.697 2.31470e-04 6.44930e-06 1.86690e-06
+YNL200C YNL200C -0.316 0.431 -0.301 2.07390e-06 2.17910e-05 3.84350e-07
+YBR107C MCM19 -0.177 -0.110 0.086 2.25760e-03 1.49890e-01 4.56150e-01
+YLR419W YLR419W 0.198 0.232 0.000 5.32650e-01 5.26400e-01 3.19580e-01
+YHR133C YHR133C -0.277 -0.197 -0.044 6.21840e-07 1.24160e-03 5.87250e-01
+YGR081C YGR081C 0.116 -0.774 0.705 8.11360e-02 1.04050e-03 1.21100e-02
+YGR154C YGR154C -0.034 -0.145 0.696 6.63470e-01 2.42960e-01 2.72160e-03
+YBL002W HTB2 0.218 0.164 -0.071 8.98900e-05 8.96490e-04 2.06950e-01
+YOR211C MGM1 0.179 0.995 0.371 2.01430e-01 8.16800e-04 1.86580e-02
+YMR180C CTL1 -0.102 0.030 0.094 2.13830e-01 7.65880e-01 4.88720e-01
+YMR253C YMR253C -0.089 0.098 0.030 4.50880e-02 6.56990e-02 7.65880e-01
+YMR326C YMR326C -0.507 -0.036 -0.069 2.36790e-02 9.38260e-01 8.62490e-01
+YLR347C KAP95 0.021 0.035 0.088 5.57530e-01 4.37310e-01 3.53930e-01
+YBL003C HTA2 0.138 0.224 0.007 3.13250e-03 4.99500e-05 8.99340e-01
+YDL185W VMA1 -0.055 0.483 0.000 2.38070e-01 1.85940e-02 9.99999e-01
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+YHR060W VMA22 0.099 -0.431 -0.005 1.80440e-01 1.49290e-03 9.79400e-01
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+YHR206W SKN7 0.092 -0.184 0.167 3.08970e-02 3.82450e-03 1.24220e-01
+YGR227W DIE2 -0.064 -0.013 -0.382 2.03370e-01 8.56570e-01 4.02020e-03
+YCR014C POL4 0.054 -0.562 0.009 4.62990e-01 1.91260e-02 9.64330e-01
+YBR035C PDX3 -0.034 -0.025 -0.073 4.38830e-01 6.08750e-01 2.83130e-01
+YNL201C YNL201C 0.269 0.349 -0.372 2.99340e-05 5.51560e-06 3.02550e-03
+YLR274W CDC46 0.012 -0.087 -0.127 7.68460e-01 8.55590e-02 1.29930e-01
+YIR040C YIR040C -0.269 -0.396 0.212 4.07980e-01 2.39530e-01 5.54490e-01
+YHR061C GIC1 -0.076 -0.031 -0.005 1.43440e-01 7.46300e-01 9.79400e-01
+YHR207C YHR207C 0.139 -0.249 0.054 5.94360e-03 2.81450e-03 6.45720e-01
+YMR181C YMR181C -0.210 0.333 -0.071 2.34540e-05 3.68970e-05 3.92020e-01
+YMR254C YMR254C 0.243 -0.066 0.555 1.69880e-01 7.01740e-01 9.91190e-03
+YGL050W YGL050W 0.054 -0.240 0.094 3.40470e-01 1.73170e-02 5.16940e-01
+YLR348C DIC1 0.540 0.001 0.389 1.83860e-08 9.99999e-01 1.39330e-03
+YGL123W RPS2 -0.306 -0.172 -0.301 1.14150e-06 1.34240e-03 7.62630e-06
+YBR108W YBR108W -0.001 -0.006 0.068 9.79400e-01 8.91330e-01 2.76680e-01
+YDL186W YDL186W 0.087 -0.028 0.033 2.83610e-02 5.20280e-01 6.06480e-01
+YAL025C MAK16 0.295 -0.935 1.033 6.46950e-05 1.01380e-05 7.39470e-04
+YKL191W DPH2 0.121 -0.183 0.534 2.75180e-02 6.46460e-02 1.96350e-03
+YHR134W YHR134W -0.152 -0.263 0.268 9.48050e-03 5.44920e-03 5.74560e-02
+YGR082W TOM20 -0.092 0.032 -0.211 2.51040e-02 4.89330e-01 7.46580e-03
+YGR155W CYS4 0.040 -0.153 -0.004 2.66370e-01 5.04470e-03 9.53960e-01
+YGR228W YGR228W 0.176 -0.469 -0.067 9.53370e-04 5.88060e-06 6.84290e-01
+YGL124C YGL124C -0.043 0.106 -0.142 3.99440e-01 1.45070e-01 2.67020e-01
+YOR212W STE4 -0.189 -0.256 -0.158 4.18700e-05 1.01350e-03 2.31840e-02
+YCR015C YCR015C -0.007 -0.549 0.123 8.99340e-01 8.17970e-04 5.76860e-01
+YBR036C CSG2 -0.142 0.258 -0.019 1.13660e-03 7.41980e-05 7.61650e-01
+YBR109C CMD1 -0.089 0.074 -0.163 2.49890e-02 1.36940e-01 9.20820e-03
+YDL187C YDL187C -0.025 -0.232 0.193 8.36350e-01 3.25850e-01 5.05520e-01
+YLR275W SMD2 0.099 -0.461 0.306 6.44170e-01 8.84330e-02 2.63810e-01
+YHR062C RPP1 0.061 -0.498 0.641 3.46930e-01 8.97140e-04 1.58870e-02
+YHR135C YCK1 0.082 -0.049 0.119 3.72850e-02 2.39990e-01 3.72270e-02
+YKL192C ACP1 -0.075 0.207 -0.247 2.25240e-01 1.11060e-04 6.35070e-03
+YGR083C GCD2 0.163 -0.386 0.417 7.39470e-04 1.41260e-05 4.31790e-04
+YGR229C SMI1 0.275 -0.445 -0.047 2.28720e-06 1.71100e-05 6.41590e-01
+YBL004W YBL004W 0.015 -0.000 -0.563 7.70200e-01 2.13330e-01 7.84530e-02
+YOR213C SAS5 0.045 -0.105 0.329 2.80780e-01 7.31000e-02 1.00430e-02
+YMR182C RGM1 -0.099 -0.046 -0.080 8.83240e-02 6.01550e-01 5.43370e-01
+YHL030W ECM29 -0.134 0.040 -0.344 1.06170e-03 3.54860e-01 4.08020e-07
+YLR276C DBP9 0.288 -0.675 0.949 5.23050e-05 9.47720e-06 5.35340e-05
+YGL051W YGL051W -0.111 0.105 -0.093 1.13910e-02 3.28040e-02 2.97950e-01
+YNL202W SPS19 0.917 0.392 0.730 9.23870e-10 1.80140e-06 1.20080e-06
+YJR020W YJR020W 0.474 0.367 0.007 9.81950e-09 8.18420e-07 9.49570e-01
+YIR041W YIR041W -0.110 0.034 -0.189 1.42040e-02 5.15610e-01 1.52440e-02
+YHL031C GOS1 0.074 0.167 -0.161 1.07540e-01 3.01670e-03 8.86900e-02
+YHR208W BAT1 -0.129 -0.486 0.070 1.99880e-03 1.59940e-06 2.47980e-01
+YGR156W YGR156W -0.009 -0.172 0.056 8.52300e-01 5.87380e-02 6.43130e-01
+YOR140W SFL1 0.190 -0.184 0.507 1.50340e-04 1.29790e-02 4.41880e-06
+YFL034C-B MOB2 -0.228 0.276 0.051 1.71630e-03 3.39410e-01 7.94270e-01
+YBR037C SCO1 0.105 0.474 -0.367 5.15390e-02 1.22910e-07 1.16520e-03
+YNL130C CPT1 -0.117 -0.024 -0.329 4.31250e-03 6.16140e-01 6.55210e-05
+YNL203C YNL203C 0.820 0.356 0.663 1.79600e-09 9.44750e-06 3.31170e-05
+YMR255W GFD1 0.211 -0.159 0.397 2.21420e-04 1.17420e-01 2.90740e-03
+YJR021C REC107 -0.044 -0.072 0.037 4.03230e-01 4.40620e-01 7.49440e-01
+YIR042C YIR042C -0.074 -0.143 0.376 6.00220e-01 6.50980e-01 2.33510e-01
+YDL188C PPH22 -0.088 0.042 -0.113 2.27870e-02 3.80010e-01 7.39390e-02
+YLR349W YLR349W 0.499 -0.131 0.840 2.34200e-07 6.24690e-01 2.46320e-04
+YHR063C YHR063C 0.030 -0.444 -0.032 4.26140e-01 2.69170e-06 7.29030e-01
+YHR136C SPL2 -0.023 0.114 0.123 7.43970e-01 3.62850e-01 3.67920e-01
+YKL193C SDS22 -0.161 0.198 -0.143 3.75930e-02 4.97640e-03 5.53780e-02
+YPR120C CLB5 0.180 0.229 -0.317 2.60500e-03 1.52790e-03 5.14980e-02
+YGR084C MRP13 0.101 -0.213 0.225 1.97940e-02 3.31880e-03 4.50710e-02
+YBL005W PDR3 -0.000 0.000 0.000 6.43130e-01 9.99999e-01 9.99999e-01
+YOR141C ARP8 0.347 0.076 0.628 3.09850e-07 4.49730e-01 1.52590e-04
+YOR214C YOR214C -0.274 -0.161 0.364 1.13130e-01 4.67170e-01 1.44060e-01
+YIL010W DOT5 -0.109 -0.097 -0.218 3.95750e-02 1.69730e-01 8.40910e-02
+YMR183C SSO2 -0.822 0.256 -0.825 2.17410e-11 2.11460e-03 1.03060e-16
+YMR256C COX7 0.116 0.198 -0.091 1.59470e-02 2.50260e-03 5.02340e-01
+YLR277C YSH1 0.047 -0.175 0.204 3.04890e-01 1.71400e-02 7.27440e-02
+YGL052W YGL052W -0.182 0.066 -0.364 5.72360e-03 4.89940e-01 3.25870e-02
+YGL125W MET13 -0.064 0.199 0.000 1.77310e-01 1.03980e-03 9.99999e-01
+YCR016W YCR016W 0.216 -0.838 0.790 1.30540e-04 9.35570e-06 5.63130e-03
+YBL006C YBL006C -0.072 -0.066 0.042 9.15640e-02 2.03000e-01 7.04340e-01
+YCR020C-A MAK31 -0.223 -0.361 0.304 2.71280e-02 2.15630e-02 1.94750e-01
+YHL032C GUT1 0.572 0.520 0.032 2.13840e-08 2.76380e-08 7.63330e-01
+YHR209W YHR209W -0.509 0.022 0.176 2.29990e-08 8.83870e-01 5.56450e-02
+YGR157W CHO2 -0.193 -0.068 -0.241 7.45910e-05 1.21590e-01 6.51760e-04
+YKR001C VPS1 0.028 -0.001 -0.162 4.27360e-01 9.79400e-01 4.62810e-03
+YNL204C SPS18 -0.024 -0.075 -0.365 8.25400e-01 7.37880e-01 1.06640e-01
+YHR064C PDR13 -0.207 -0.312 0.004 4.03400e-05 3.92220e-05 9.58820e-01
+YKL194C MST1 -0.141 -0.033 -0.592 5.07450e-02 7.96250e-01 3.25090e-04
+YGR085C RPL11B -0.188 -0.425 -0.084 2.63900e-04 7.40280e-07 1.61300e-01
+YGR158C MTR3 0.034 -0.720 0.200 5.10360e-01 4.16790e-05 2.18830e-01
+YOR215C YOR215C 0.151 0.137 0.335 7.07790e-04 1.08810e-02 1.27300e-04
+YAL027W YAL027W -0.278 -0.040 0.017 1.13990e-01 6.49920e-01 8.87540e-01
+YIL011W YIL011W -0.068 0.054 -0.022 1.25070e-01 2.67150e-01 8.18490e-01
+YMR257C PET111 -0.076 -0.110 -0.148 1.52810e-01 2.07140e-01 2.33180e-01
+YLR278C YLR278C 0.033 0.070 -0.195 5.64870e-01 3.61890e-01 2.60140e-01
+YGL053W YGL053W -0.129 0.179 -0.156 2.10540e-03 3.21490e-03 5.20760e-02
+YGL126W SCS3 -0.284 0.064 -0.191 4.39810e-05 2.06090e-01 1.13030e-01
+YOL110W SHR5 0.157 0.171 0.416 2.79810e-03 6.74120e-03 1.19550e-03
+YNL131W TOM22 -0.043 0.009 0.036 3.52990e-01 8.31390e-01 5.85560e-01
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+YJR022W LSM8 0.059 -0.435 0.294 6.01100e-01 7.07010e-02 1.43440e-01
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+YDL189W YDL189W -0.005 -0.150 0.126 9.10390e-01 2.46800e-01 3.29550e-01
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+YGL054C ERV14 -0.028 0.119 -0.265 4.62430e-01 8.21190e-03 1.11030e-03
+YGL127C SOH1 -0.138 -0.250 0.186 2.50850e-02 3.96160e-03 3.68320e-01
+YOL111C YOL111C -0.018 0.085 -0.118 6.58510e-01 5.99540e-02 6.75600e-02
+YMR184W YMR184W -0.238 -0.263 0.102 1.66060e-03 6.76870e-03 5.04240e-01
+YJR023C YJR023C -0.005 -0.411 0.144 9.70870e-01 2.17420e-01 7.44740e-01
+YNL205C YNL205C -0.377 -0.269 -0.203 1.39330e-02 3.17150e-01 5.90650e-01
+YIR044C YIR044C -0.170 0.222 -0.421 4.73140e-04 7.36020e-04 9.37850e-06
+YHR065C RRP3 0.247 -0.916 0.734 1.69310e-05 6.46960e-06 3.21600e-03
+YHR138C YHR138C -0.248 0.381 0.454 3.05030e-06 4.68930e-04 1.74070e-03
+YGR086C YGR086C 0.153 0.330 -0.189 5.38520e-04 1.06220e-06 1.00160e-03
+YOR070C GYP1 -0.013 0.144 -0.013 7.40140e-01 4.85140e-03 8.58030e-01
+YGR159C NSR1 -0.124 -0.302 -0.198 5.23430e-03 3.92220e-05 4.41030e-03
+YOR143C THI80 0.114 -0.567 0.427 3.34490e-02 4.62000e-05 4.43630e-03
+YOR216C RUD3 0.259 -0.200 0.303 4.20920e-05 1.73860e-01 4.66680e-02
+YAL028W YAL028W -0.292 0.041 -0.044 1.24090e-05 5.48880e-01 6.49390e-01
+YIL012W YIL012W -0.382 -0.316 -0.362 7.56500e-05 2.92190e-02 2.99440e-01
+YMR258C YMR258C -0.231 0.021 0.089 2.12040e-05 7.08280e-01 3.67730e-01
+YKR002W PAP1 0.300 -0.016 -0.023 1.08780e-05 7.80940e-01 8.10760e-01
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+YNL132W YNL132W -0.049 -0.019 -0.119 7.69330e-01 9.34930e-01 7.34890e-01
+YML080W YML080W 0.244 -0.784 0.676 9.36790e-05 3.79570e-06 7.34200e-03
+YAL029C MYO4 0.013 0.533 0.169 8.19620e-01 1.89420e-03 2.05900e-01
+YIL013C PDR11 -0.396 0.503 0.000 2.01800e-01 1.03850e-01 9.99999e-01
+YKL195W YKL195W 0.076 -0.017 0.282 1.19290e-01 7.08940e-01 1.08440e-02
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+YPR122W AXL1 -0.107 -0.366 -0.055 2.84670e-01 1.55920e-01 8.48150e-01
+YGL128C YGL128C -0.062 0.026 0.119 2.44810e-01 7.52630e-01 3.24680e-01
+YNL133C YNL133C 0.264 -0.381 0.412 1.66540e-04 3.61640e-02 1.53490e-02
+YMR185W YMR185W 0.267 0.031 0.210 3.31510e-05 8.12930e-01 1.50810e-01
+YNL206C YNL206C 0.175 -0.273 0.144 2.47630e-04 1.17710e-03 1.61580e-01
+YJR024C YJR024C -0.065 -0.031 -0.051 9.39510e-02 5.36530e-01 4.54530e-01
+YLR279W YLR279W -0.128 0.065 -0.080 3.16510e-01 7.89410e-01 5.61760e-01
+YKL196C YKT6 -0.109 -0.198 0.246 2.46070e-02 2.98490e-03 6.95200e-03
+YHR139C SPS100 -0.594 0.221 1.262 8.10900e-06 8.59840e-02 1.27270e-07
+YPR123C YPR123C 0.515 0.024 -0.317 9.75840e-08 7.75500e-01 2.89060e-01
+YGR087C PDC6 -0.671 0.050 -0.435 1.85640e-11 2.44000e-01 1.44090e-08
+YOR071C YOR071C -0.099 -0.089 -0.173 1.20870e-02 9.03570e-02 1.35800e-02
+YOR144C EFD1 0.278 -0.072 -0.213 1.01980e-03 6.04230e-01 4.86320e-01
+YBL008W HIR1 0.153 -0.268 0.000 1.87390e-01 8.34020e-02 9.17740e-01
+YBR250W YBR250W 0.025 0.010 -0.030 5.59440e-01 8.33850e-01 7.52630e-01
+YGL055W OLE1 -0.168 0.086 0.072 9.81480e-05 3.37500e-02 2.35940e-01
+YOL112W MSB4 0.057 -0.239 0.025 2.30570e-01 5.24390e-03 8.30180e-01
+YCR019W MAK32 -0.064 -0.064 -0.114 2.89350e-01 4.77750e-01 3.75920e-01
+YKR003W YKR003W -0.130 -0.085 -0.106 2.41750e-03 1.54970e-01 1.67710e-01
+YML081W YML081W 0.004 -0.202 0.414 9.49570e-01 7.18610e-02 1.49510e-03
+YHR066W SSF1 0.447 -0.932 0.836 2.56880e-08 5.22410e-06 2.54870e-03
+YHL035C YHL035C 0.286 -0.325 0.064 1.75510e-06 3.05450e-04 5.66840e-01
+YGL056C SDS23 0.564 0.218 0.337 5.59640e-10 1.40710e-04 1.60460e-04
+YGL129C YGL129C 0.105 0.079 -0.123 1.19430e-02 6.56460e-02 7.98150e-02
+YOR217W RFC1 -0.032 0.309 0.027 5.84300e-01 1.70710e-01 8.73540e-01
+YKR004C ECM9 0.010 0.091 -0.144 8.33850e-01 7.10470e-02 1.81580e-01
+YMR186W HSC82 -0.032 -0.032 -0.608 5.24690e-01 4.99500e-01 1.68330e-14
+YNL134C YNL134C -0.485 0.339 -0.477 2.38940e-07 7.15500e-06 1.38880e-10
+YJR025C BNA1 -0.148 -0.185 -0.079 1.02450e-03 1.87230e-03 1.62510e-01
+YKL197C PEX1 0.069 0.092 -0.135 2.13430e-01 6.25650e-01 2.60390e-01
+YOR145C YOR145C 0.394 -0.572 0.777 6.42320e-08 2.58240e-04 1.47010e-06
+YBL009W YBL009W 0.125 -0.291 -0.180 4.08440e-01 2.53240e-01 1.68080e-01
+YOR218C YOR218C -0.103 -0.274 0.140 1.43750e-01 1.45680e-02 4.48670e-01
+YIL014W YIL014W -0.085 -0.182 -0.041 3.62350e-02 4.13240e-02 6.78340e-01
+YMR187C YMR187C -0.001 -0.215 0.445 9.99999e-01 1.28160e-01 9.27110e-02
+YBR251W MRPS5 0.237 0.007 0.262 4.12860e-05 9.03610e-01 4.40320e-02
+YOL113W SKM1 -0.161 -0.090 0.040 6.74100e-04 1.76600e-01 6.57970e-01
+YNL061W NOP2 0.107 -0.193 0.370 1.95380e-02 5.99660e-03 3.19010e-04
+YNL207W YNL207W 0.150 -0.583 0.515 7.12180e-03 8.81080e-06 6.14570e-04
+YML082W YML082W 0.144 -0.461 0.525 2.34380e-03 3.56250e-05 2.65780e-03
+YHR067W YHR067W -0.022 -0.075 0.008 6.49920e-01 3.92020e-01 9.49570e-01
+YPR051W MAK3 0.078 -0.453 0.632 7.84530e-02 2.05100e-05 2.84200e-05
+YPR124W CTR1 0.760 0.469 -0.462 8.42180e-11 2.41890e-08 8.38210e-06
+YGR088W CTT1 -0.910 0.596 -0.394 1.68230e-10 1.98280e-04 3.07260e-06
+YPL020C ULP1 0.254 0.530 0.645 7.08500e-05 6.73370e-03 2.42240e-04
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+YPL240C HSP82 0.222 -0.201 -0.661 1.85820e-05 2.41570e-03 6.76880e-11
+YCR095C YCR095C -0.067 -0.479 0.390 2.28310e-01 5.72500e-04 1.36720e-02
+YLR131C ACE2 -0.087 -0.029 0.138 1.74480e-01 6.78930e-01 1.88330e-01
+YEL021W URA3 -0.388 -0.332 -0.000 7.08740e-02 1.03290e-01 1.56540e-01
+YCL063W YCL063W -0.121 -0.164 -0.255 6.02200e-02 1.97240e-01 1.93690e-01
+YKL120W OAC1 0.324 -0.755 0.262 3.33870e-06 1.71070e-06 4.11780e-02
+YGR011W YGR011W -0.060 -0.131 -0.350 5.50360e-01 3.61700e-01 3.58410e-02
+YJL214W HXT8 0.340 0.815 -0.361 7.10040e-06 8.49960e-11 2.67870e-04
+YIL162W SUC2 -0.318 0.688 -1.131 4.14420e-07 1.78620e-09 1.74030e-20
+YDR074W TPS2 -0.439 0.030 -0.215 3.54650e-09 4.87220e-01 2.46910e-03
+YDR147W EKI1 0.044 -0.461 0.345 5.28820e-01 1.05350e-01 1.64570e-02
+YDL043C PRP11 -0.051 -0.334 0.170 2.94710e-01 3.12270e-04 2.05620e-01
+YLR204W QRI5 0.024 -0.027 -0.159 7.74600e-01 7.96250e-01 4.85120e-01
+YCL064C CHA1 0.462 0.077 0.954 1.74510e-08 4.96070e-01 2.23680e-08
+YNL282W POP3 -0.005 -0.764 0.447 9.41780e-01 6.29200e-05 1.61580e-01
+YBR189W RPS9B -0.274 -0.421 -0.106 5.89110e-05 1.10800e-06 5.51350e-02
+YJL142C YJL142C -0.220 0.254 -0.235 1.24780e-05 8.45470e-04 1.18310e-02
+YJL215C YJL215C 0.088 -0.407 -0.000 7.26880e-01 1.05080e-01 9.99999e-01
+YFR033C QCR6 -0.147 0.064 -0.084 3.73960e-04 1.27390e-01 1.46470e-01
+YDR504C YDR504C -0.020 0.064 0.051 7.12960e-01 2.20470e-01 6.66270e-01
+YIL163C YIL163C -0.407 -0.244 -0.238 1.11090e-01 3.63240e-01 4.19640e-01
+YER054C GIP2 0.057 0.206 0.247 1.69580e-01 6.20320e-04 4.36030e-03
+YMR111C YMR111C 0.051 -0.383 0.302 4.82150e-01 2.29630e-02 1.69800e-01
+YDR148C KGD2 0.161 0.037 -0.053 3.52600e-04 3.78980e-01 3.22530e-01
+YPL241C CIN2 -0.072 -0.292 0.118 1.67630e-01 1.45950e-02 5.43730e-01
+YOR293W RPS10A -0.464 -0.441 -0.038 1.05520e-06 5.94910e-07 5.22310e-01
+YOR366W YOR366W 0.138 -0.212 0.233 5.91080e-01 5.15610e-01 4.56150e-01
+YLR132C YLR132C 0.052 -0.121 0.105 3.74710e-01 2.43770e-01 4.58320e-01
+YCR096C A2 0.087 0.023 0.341 1.43690e-01 8.00280e-01 3.24610e-02
+YLR205C YLR205C 0.023 0.013 0.324 7.68460e-01 9.10390e-01 4.69830e-02
+YFL001W DEG1 0.098 -0.472 0.126 7.01010e-02 6.15180e-05 4.11890e-01
+YNL283C WSC2 -0.043 0.076 -0.414 3.18770e-01 1.02510e-01 7.48480e-10
+YEL022W GEA2 -0.056 0.179 0.063 6.78340e-01 2.65340e-01 2.62410e-01
+YDL116W NUP84 0.038 0.034 -0.034 3.80420e-01 4.96690e-01 6.87930e-01
+YBL085W BOI1 -0.070 0.723 0.165 7.40900e-01 1.45350e-02 1.57370e-01
+YKL121W YKL121W -0.056 0.201 -0.172 3.03980e-01 3.81420e-02 2.70800e-01
+YGR012W YGR012W 0.132 -0.004 -0.034 2.15470e-02 9.64330e-01 7.53440e-01
+YIL090W YIL090W 0.139 0.006 0.169 1.98000e-03 9.15220e-01 1.15060e-01
+YDR431W YDR431W -0.069 -0.178 -0.235 4.85420e-01 1.86040e-01 2.50710e-01
+YFL002C SPB4 -0.285 -0.247 -0.108 4.59440e-06 1.57960e-03 1.36650e-01
+YER127W LCP5 0.267 -0.916 0.545 9.38060e-04 3.81690e-06 6.76700e-02
+YDR075W PPH3 0.473 -0.480 0.521 6.17100e-09 6.93680e-05 3.03610e-04
+YEL023C YEL023C 0.177 -0.136 -0.210 2.18630e-01 6.23240e-01 3.04740e-01
+YDL044C MTF2 0.294 -0.288 0.096 3.02640e-04 4.25800e-02 6.93490e-01
+YKR080W MTD1 -0.673 -1.173 0.669 5.38520e-11 1.93170e-08 3.40590e-08
+YKL122C SRP21 0.196 -0.388 0.740 1.53600e-02 3.66700e-04 4.22940e-04
+YBL086C YBL086C 0.059 0.085 0.150 2.27140e-01 1.12890e-01 1.31000e-01
+YFR034C PHO4 0.121 -0.336 0.348 9.95130e-02 6.96710e-04 2.08020e-02
+YJL216C YJL216C 0.311 0.211 -0.392 1.76010e-04 2.98720e-02 3.11530e-03
+YIL091C YIL091C 0.334 -0.418 0.418 4.02610e-03 3.50380e-02 2.99000e-01
+YDR505C PSP1 0.100 0.093 -0.025 2.26820e-02 7.49720e-02 7.94270e-01
+YIL164C NIT1 -0.064 -0.053 -0.163 5.97580e-01 7.20510e-01 2.24090e-01
+YER055C HIS1 -0.475 -1.006 0.426 1.15730e-08 7.20130e-10 2.23390e-07
+YMR112C MED11 0.092 -0.452 0.132 5.63700e-01 1.18330e-01 3.16670e-01
+YOR294W RRS1 0.258 -0.953 0.961 1.00280e-04 6.57640e-06 2.08280e-05
+YPL242C IQG1 0.021 0.161 -0.354 7.03680e-01 7.05330e-03 4.85860e-03
+YOR367W SCP1 0.102 -0.206 0.177 1.74020e-02 3.44260e-03 1.72700e-01
+YKR081C YKR081C 0.169 -0.910 1.020 5.67090e-03 1.59710e-06 6.69040e-04
+YNL284C MRPL10 0.126 0.119 -0.067 3.98350e-03 7.45450e-02 3.64400e-01
+YDL117W YDL117W -0.113 0.250 0.124 1.89610e-01 1.78910e-01 7.90370e-01
+YCL065W YCL065W -0.379 -0.320 -0.547 2.13460e-03 7.20360e-02 1.78650e-02
+YGR013W SNU71 0.111 -0.316 0.575 2.27700e-02 6.59530e-03 5.71070e-04
+YJL143W TIM17 -0.088 0.087 -0.173 4.40320e-02 9.53690e-02 3.61640e-02
+YDR432W NPL3 -0.520 -0.000 0.000 4.08120e-03 5.21290e-01 9.41780e-01
+YFL003C MSH4 -0.218 -0.188 0.424 6.04380e-02 5.79320e-01 2.28630e-01
+YER128W YER128W 0.075 -0.575 0.517 4.62160e-01 3.72420e-02 3.69080e-02
+YDR076W RAD55 -0.056 -0.022 0.147 2.88490e-01 8.83870e-01 2.61150e-01
+YLR060W FRS1 -0.139 -0.276 -0.233 2.49350e-03 3.91260e-05 5.79450e-05
+YDL045C FAD1 0.121 0.028 0.082 5.46930e-03 5.91930e-01 4.22510e-01
+YLR133W CKI1 -0.122 0.054 -0.222 4.07820e-03 2.45160e-01 7.10860e-03
+YLR206W ENT2 0.074 0.084 -0.429 1.04160e-01 7.08740e-02 1.34340e-06
+YKL050C YKL050C 0.083 0.111 0.275 1.99960e-01 1.96350e-01 4.88450e-02
+YBL087C RPL23A -0.409 -0.336 -0.221 5.07480e-08 4.52940e-06 6.90490e-04
+YFR035C YFR035C 0.398 -0.730 1.113 1.98240e-06 8.47240e-07 1.04610e-07
+YDR506C YDR506C 0.002 0.080 0.137 9.70870e-01 3.34170e-01 2.23770e-01
+YIL165C YIL165C -0.138 -0.485 -0.399 6.00660e-01 4.90010e-02 9.72140e-02
+YER056C FCY2 -0.127 -0.684 0.545 4.86760e-03 1.93420e-06 1.26000e-06
+YOR295W YOR295W 0.101 -0.374 0.318 1.43810e-01 6.43830e-03 1.45510e-01
+YOR368W RAD17 0.151 -0.019 0.075 3.07670e-01 9.53960e-01 8.70280e-01
+YCR098C GIT1 0.064 -0.061 0.266 3.24510e-01 7.41670e-01 4.82480e-02
+YEL024W RIP1 0.052 0.289 -0.414 1.83630e-01 2.92570e-06 3.19980e-10
+YDL118W YDL118W -0.093 -0.074 0.389 2.25450e-01 4.60230e-01 4.94700e-02
+YCL066W ALPHA1 -0.437 -0.291 -0.262 2.62400e-04 3.86690e-01 2.00420e-01
+YKL123W YKL123W 0.245 -0.215 0.583 1.78830e-01 5.77680e-01 1.84460e-02
+YGR014W MSB2 -0.066 -0.131 -0.171 9.37170e-02 1.29400e-02 3.18360e-02
+YJL071W ARG2 -0.217 -0.395 0.270 6.58070e-03 7.59180e-05 7.81000e-02
+YDR360W YDR360W 0.033 -0.401 0.022 8.40180e-01 1.91160e-01 9.70870e-01
+YOR369C RPS12 -0.319 -0.153 -0.096 8.37630e-06 3.77980e-03 7.51560e-02
+YJL144W YJL144W -0.356 0.296 -0.509 2.12120e-06 3.00060e-04 4.43360e-04
+YJL217W YJL217W 0.729 0.346 0.133 2.39320e-10 5.93880e-07 9.50120e-02
+YDR433W YDR433W -0.001 -0.084 0.348 9.79400e-01 8.68040e-02 1.84400e-03
+YIL092W YIL092W 0.101 -0.385 0.171 3.43140e-01 1.21800e-01 6.65150e-01
+YER129W PAK1 -0.004 -0.160 0.122 9.41780e-01 1.48980e-01 3.57120e-01
+YMR040W YMR040W -0.228 0.285 0.394 1.10760e-01 1.28430e-01 6.72870e-02
+YMR113W YMR113W -0.060 -0.305 0.257 2.63170e-01 7.85020e-03 1.38670e-01
+YEL025C YEL025C -0.277 -0.073 -0.234 1.61960e-05 2.57650e-01 1.08400e-01
+YDR077W SED1 -0.313 0.397 0.042 3.15920e-06 1.87210e-04 4.99190e-01
+YPL243W SRP68 0.160 0.084 0.235 5.83260e-04 2.45630e-01 6.77880e-03
+YLR061W RPL22A -0.299 -0.357 -0.107 4.76040e-06 2.49020e-06 6.75870e-02
+YLR134W PDC5 -0.645 0.027 -0.351 1.25850e-11 5.85140e-01 1.20760e-08
+YKR082W NUP133 0.150 0.000 0.000 6.97520e-03 9.99999e-01 9.99999e-01
+YDL119C YDL119C -0.098 -0.077 0.137 4.15850e-02 1.70260e-01 2.68060e-01
+YLR207W HRD3 -0.106 -0.042 0.043 1.97030e-02 5.25370e-01 6.74830e-01
+YLL030C YLL030C -0.050 -0.000 0.000 9.12770e-01 6.17070e-01 9.70870e-01
+YCL067C ALPHA2 0.169 -0.085 0.301 1.28730e-03 1.14810e-01 2.75550e-03
+YNL285W YNL285W -0.089 0.029 0.164 3.83330e-01 8.23060e-01 3.76120e-01
+YBL088C TEL1 0.076 -0.252 0.000 1.30940e-01 3.91590e-01 9.99999e-01
+YGR015C YGR015C -0.043 -0.040 -0.023 4.54530e-01 6.80110e-01 8.52300e-01
+YJL072C YJL072C -0.114 -0.492 0.157 2.40670e-01 9.56170e-05 3.82290e-01
+YDR361C YDR361C 0.072 -0.324 0.712 2.54700e-01 1.67810e-03 2.83700e-05
+YIL093C YIL093C 0.178 -0.073 -0.133 1.64010e-02 2.27250e-01 1.97330e-01
+YDR507C GIN4 0.511 0.298 -0.434 8.59810e-05 3.61080e-02 1.72090e-01
+YNR020C YNR020C 0.077 -0.387 0.272 1.21540e-01 2.21420e-04 5.05240e-02
+YIL166C YIL166C -0.137 -0.026 -0.089 6.17160e-02 7.56680e-01 4.78620e-01
+YER057C HIG1 0.026 0.156 -0.229 5.29510e-01 1.81610e-03 2.23470e-04
+YMR041C YMR041C 0.193 0.242 0.194 1.33760e-04 5.17750e-05 6.39710e-02
+YMR114C YMR114C 0.231 0.248 0.411 5.19750e-05 1.82010e-03 1.67630e-03
+YDR078C YDR078C -0.014 0.024 -0.024 8.52300e-01 8.73540e-01 8.64010e-01
+YPL171C OYE3 -0.323 0.408 -1.000 1.34800e-07 4.78370e-06 3.97560e-08
+YOR296W YOR296W 0.050 0.172 0.031 8.20760e-01 3.04590e-01 9.23040e-01
+YLR062C YLR062C -0.303 -0.549 -0.220 2.22930e-05 5.19690e-07 1.16880e-01
+YPL244C YPL244C -0.226 -0.064 0.287 1.89500e-05 2.50350e-01 2.83390e-02
+YCR099C YCR099C -0.143 -0.288 0.186 1.34310e-01 1.59740e-01 4.99810e-01
+YKR083C YKR083C -0.364 0.016 -0.319 1.26310e-07 8.03360e-01 1.13270e-02
+YFL004W YFL004W 0.093 0.007 -0.002 2.42030e-02 8.73540e-01 9.79400e-01
+YDL046W YDL046W 0.105 0.334 -0.041 7.64270e-03 3.15680e-07 5.13630e-01
+YKL051W YKL051W -0.518 -0.159 -0.013 8.99870e-10 4.92350e-03 8.78590e-01
+YKL124W SSH4 0.234 0.028 0.319 1.51920e-05 6.74830e-01 3.60090e-02
+YOR297C TIM18 -0.027 -0.032 0.003 5.57150e-01 6.01550e-01 9.79400e-01
+YJL145W YJL145W 0.131 -0.251 0.174 6.23420e-03 1.97560e-02 1.39630e-01
+YJL218W YJL218W 0.034 -0.230 -0.054 7.37130e-01 2.63680e-01 8.37620e-01
+YFR036W CDC26 -0.015 -0.113 0.287 6.95370e-01 5.77330e-02 1.51520e-03
+YDR434W YDR434W -0.085 -0.107 -0.142 3.60660e-02 2.89150e-02 2.28310e-02
+YLR135W YLR135W 0.089 -0.135 0.313 8.47170e-02 2.12550e-01 1.50610e-02
+YLR208W SEC13 -0.120 -0.043 -0.017 1.93590e-03 3.00640e-01 7.86540e-01
+YLL031C YLL031C -0.093 0.146 -0.606 3.24480e-02 6.32250e-03 4.86340e-10
+YCL068C YCL068C 0.047 -0.255 0.110 4.89330e-01 8.85430e-02 4.07530e-01
+YNL286W CUS2 0.162 -0.194 0.301 4.22150e-03 7.75590e-02 2.97910e-02
+YKL052C YKL052C -0.065 -0.339 0.623 2.76410e-01 9.96170e-04 1.04840e-02
+YDR362C TFC6 0.286 0.156 0.228 1.78870e-05 1.06010e-01 8.11690e-02
+YFR037C RSC8 0.297 -0.226 0.350 1.50780e-06 1.38490e-02 3.55410e-03
+YIL094C LYS12 0.185 -0.224 0.527 1.45260e-04 7.93950e-04 2.38690e-06
+YDR435C YDR435C -0.120 0.070 -0.475 8.71980e-03 1.17230e-01 2.11940e-08
+YDR508C GNP1 0.319 -0.123 -0.164 7.22310e-07 4.53570e-02 1.78510e-02
+YPL172C COX10 -0.302 0.294 0.052 6.90030e-06 3.63060e-02 6.74830e-01
+YHR039C-A VMA10 -0.024 -0.295 0.141 6.01100e-01 3.60990e-04 2.37390e-01
+YLR136C TIS11 -0.035 -0.043 0.090 3.95930e-01 3.65960e-01 3.16990e-01
+YKR084C HBS1 0.033 -0.150 0.183 3.87750e-01 8.77860e-03 3.65200e-02
+YLR209C YLR209C -0.187 0.151 -0.802 3.92910e-05 1.65400e-03 2.73410e-12
+YFL005W SEC4 0.068 -0.048 -0.393 1.40480e-01 3.75520e-01 1.20810e-04
+YEL026W SNU13 -0.185 -0.807 0.253 1.87140e-02 1.39630e-07 3.21340e-02
+YML010W SPT5 0.153 -0.000 -0.430 1.84670e-03 9.03610e-01 2.88200e-01
+YDL047W SIT4 0.044 0.017 0.170 2.42040e-01 7.05640e-01 1.22380e-02
+YKL125W RRN3 0.480 -0.225 0.608 3.72200e-07 3.21090e-02 5.48430e-04
+YBL089W YBL089W -0.124 -0.123 -0.140 2.03000e-01 5.40830e-01 5.28470e-01
+YJL073W JEM1 0.020 -0.161 0.066 6.36510e-01 5.46330e-03 4.10510e-01
+YGR016W YGR016W 0.077 -0.205 -0.139 6.32510e-01 4.27110e-01 6.20860e-01
+YJL146W IDS2 0.158 0.071 0.099 7.73400e-04 1.72390e-01 3.28370e-01
+YJL219W HXT9 0.298 0.592 -0.162 5.60080e-06 1.68990e-09 9.79460e-02
+YNR021W YNR021W -0.096 -0.069 -0.167 1.50890e-02 1.53140e-01 2.52090e-03
+YER058W PET117 -0.234 -0.111 0.104 1.85370e-02 4.12590e-01 6.26620e-01
+YMR042W ARGR1 0.130 -0.171 0.060 1.66450e-01 2.10590e-01 7.76400e-01
+YMR115W YMR115W 0.266 -0.031 0.399 4.26770e-06 6.71370e-01 2.74550e-03
+YDR079W PET100 0.025 0.090 -0.286 6.25650e-01 1.01960e-01 2.57910e-02
+YLR063W YLR063W -0.157 -0.503 -0.086 8.68760e-02 4.92540e-02 6.84290e-01
+YML011C YML011C -0.104 -0.238 0.150 1.30040e-01 7.39690e-02 4.03460e-01
+YPL245W YPL245W -0.389 -0.276 -0.257 2.58760e-07 5.92830e-02 1.58200e-01
+YLL032C YLL032C 0.038 -0.068 0.106 4.97620e-01 4.80970e-01 3.76530e-01
+YNL287W SEC21 -0.113 0.036 -0.343 3.56710e-03 4.28090e-01 3.13510e-07
+YJL074C SMC3 0.299 -0.022 -0.120 1.64550e-04 8.99340e-01 8.06500e-01
+YJL147C YJL147C 0.200 -0.257 0.183 8.97400e-03 4.53030e-02 2.11760e-01
+YNR022C YNR022C -0.039 -0.196 0.043 5.14620e-01 1.12840e-02 7.80030e-01
+YMR116C ASC1 -0.278 -0.164 -0.382 1.14860e-04 2.16830e-03 3.92210e-09
+YPL246C YPL246C -0.093 -0.092 -0.198 1.23490e-02 1.18880e-01 2.14400e-03
+YOR298W YOR298W -0.154 0.322 -0.558 8.93900e-02 1.39030e-03 1.17380e-02
+YKR085C MRPL20 0.010 -0.084 -0.036 8.42790e-01 1.95460e-01 8.09690e-01
+YFL006W YFL006W -0.029 0.135 0.098 5.07120e-01 6.06350e-03 2.63810e-01
+YCL069W YCL069W -0.093 -0.220 0.043 3.04130e-01 8.10690e-02 8.11840e-01
+YKL053W YKL053W -0.016 -0.209 0.579 8.48150e-01 1.44940e-01 2.28830e-02
+YKL126W YPK1 -0.121 0.000 0.000 7.24030e-01 9.99999e-01 9.99999e-01
+YDR290W YDR290W -0.048 -0.158 0.069 8.85690e-01 4.17740e-01 8.80330e-01
+YGR017W YGR017W 0.029 -0.153 0.080 4.43190e-01 7.54950e-03 3.64990e-01
+YOR001W RRP6 0.164 -0.340 -0.033 1.05030e-03 1.78750e-01 6.11500e-01
+YDR363W ESC2 0.091 0.147 0.249 9.54480e-02 2.77900e-01 5.68830e-02
+YFR038W YFR038W 0.278 -0.526 0.499 8.22290e-06 1.39830e-03 3.15890e-03
+YDR436W PPZ2 0.081 0.337 0.060 1.27560e-01 6.18090e-06 6.01100e-01
+YIL095W PRK1 0.088 -0.211 0.000 6.19910e-01 9.24800e-02 9.99999e-01
+YDR509W YDR509W 0.340 -0.218 -0.420 3.85660e-05 1.68430e-02 5.50170e-03
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diff --git a/distribution/src/main/sampleData/galFiltered.csv b/distribution/src/main/sampleData/galFiltered.csv
new file mode 100755
index 0000000..576cbb4
--- /dev/null
+++ b/distribution/src/main/sampleData/galFiltered.csv
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+YGL073W,YOR178C,pp,TRUE,abcd12622,1.2344543
+YGL073W,YHR053C,pd,TRUE,abcd12623,1.2344543
+YGL073W,YHR055C,pd,TRUE,abcd12624,1.2344543
+YGL073W,YER103W,pd,TRUE,abcd12625,1.2344543
+YOR120W,YPL248C,pd,TRUE,abcd12626,1.2344543
+YPR041W,YOR361C,pp,TRUE,abcd12627,1.2344543
+YPR041W,YMR309C,pp,TRUE,abcd12628,1.2344543
+YNL135C,YDR174W,pp,TRUE,abcd12629,1.2344543
+YBR217W,YNR007C,pp,TRUE,abcd12630,1.2344543
+YMR255W,YGL122C,pp,TRUE,abcd12631,1.2344543
+YLR258W,YIL045W,pp,TRUE,abcd12632,1.2344543
+YLR258W,YBR274W,pp,TRUE,abcd12633,1.2344543
+YDL215C,YER040W,pd,TRUE,abcd12634,1.2344543
+YDL215C,YLR432W,pp,TRUE,abcd12635,1.2344543
+YER079W,YHR135C,pp,TRUE,abcd12636,1.2344543
+YER079W,YNL154C,pp,TRUE,abcd12637,1.2344543
+YDL030W,YDL013W,pp,TRUE,abcd12638,1.2344543
+YDL030W,YMR005W,pp,TRUE,abcd12639,1.2344543
+YLR362W,YER124C,pp,TRUE,abcd12640,1.2344543
+YLR362W,YMR186W,pp,TRUE,abcd12641,1.2344543
+YLR362W,YPL240C,pp,TRUE,abcd12642,1.2344543
+YHR084W,YMR043W,pp,TRUE,abcd12643,1.2344543
+YHR084W,YDR461W,pd,TRUE,abcd12644,1.2344543
+YHR084W,YFL026W,pd,TRUE,abcd12645,1.2344543
+YGR085C,YLR075W,pp,TRUE,abcd12646,1.2344543
+YGR085C,YDR395W,pp,TRUE,abcd12647,1.2344543
+YKL074C,YGL035C,pp,TRUE,abcd12648,1.2344543
+YGR088W,YLR256W,pd,TRUE,abcd12649,1.2344543
+YER081W,YIL074C,pp,TRUE,abcd12650,1.2344543
+YPR113W,YMR043W,pd,TRUE,abcd12651,1.2344543
+YIL070C,YML054C,pp,TRUE,abcd12652,1.2344543
+YIL061C,YDL013W,pp,TRUE,abcd12653,1.2344543
+YIL061C,YNL199C,pp,TRUE,abcd12654,1.2344543
+YIL061C,YLR153C,pp,TRUE,abcd12655,1.2344543
+YGR046W,YNL236W,pp,TRUE,abcd12656,1.2344543
+YNL091W,YNL164C,pp,TRUE,abcd12657,1.2344543
+YHR030C,YLL021W,pp,TRUE,abcd12658,1.2344543
+YHR030C,YER111C,pp,TRUE,abcd12659,1.2344543
+YPR048W,YOR355W,pp,TRUE,abcd12660,1.2344543
+YPR048W,YDL215C,pp,TRUE,abcd12661,1.2344543
+YHR005C,YLR362W,pp,TRUE,abcd12662,1.2344543
+YDR070C,YFL017C,pp,TRUE,abcd12663,1.2344543
+YJL157C,YAL040C,pp,TRUE,abcd12664,1.2344543
+YJL157C,YOR212W,pp,TRUE,abcd12665,1.2344543
+YNL036W,YIR009W,pp,TRUE,abcd12666,1.2344543
+YML114C,YDR167W,pp,TRUE,abcd12667,1.2344543
+YMR117C,YCL032W,pp,TRUE,abcd12668,1.2344543
+YMR117C,YPR010C,pp,TRUE,abcd12669,1.2344543
+YHR115C,YOR215C,pp,TRUE,abcd12670,1.2344543
+YGR009C,YAL030W,pp,TRUE,abcd12671,1.2344543
+YGR009C,YOR327C,pp,TRUE,abcd12672,1.2344543
+YGR009C,YDR335W,pp,TRUE,abcd12673,1.2344543
+YGR009C,YBL050W,pp,TRUE,abcd12674,1.2344543
+YDL088C,YER110C,pp,TRUE,abcd12675,1.2344543
+YLR197W,YDL014W,pp,TRUE,abcd12676,1.2344543
+YLR197W,YOR310C,pp,TRUE,abcd12677,1.2344543
+YGL202W,YGR074W,pp,TRUE,abcd12678,1.2344543
+YIL162W,YNL167C,pd,TRUE,abcd12679,1.2344543
+YBR170C,YGR048W,pp,TRUE,abcd12680,1.2344543
+YOR212W,YLR362W,pp,TRUE,abcd12681,1.2344543
+YDR103W,YLR362W,pp,TRUE,abcd12682,1.2344543
+YDL023C,YJL159W,pp,TRUE,abcd12683,1.2344543
+YGR136W,YGR058W,pp,TRUE,abcd12684,1.2344543
+YBR109C,YOR326W,pp,TRUE,abcd12685,1.2344543
+YBR109C,YFR014C,pp,TRUE,abcd12686,1.2344543
+YDR395W,YDL075W,pp,TRUE,abcd12687,1.2344543
+YDR395W,YIL133C,pp,TRUE,abcd12688,1.2344543
+YDR395W,YNL069C,pp,TRUE,abcd12689,1.2344543
+YDR395W,YER056CA,pp,TRUE,abcd12690,1.2344543
+YDR395W,YIL052C,pp,TRUE,abcd12691,1.2344543
+YDR395W,YOL127W,pp,TRUE,abcd12692,1.2344543
+YDR395W,YPR102C,pp,TRUE,abcd12693,1.2344543
+YLR345W,YLR321C,pp,TRUE,abcd12694,1.2344543
+YBL079W,YDL088C,pp,TRUE,abcd12695,1.2344543
+YBR045C,YIL045W,pp,TRUE,abcd12696,1.2344543
+YBR045C,YOR178C,pp,TRUE,abcd12697,1.2344543
+YER054C,YER133W,pp,TRUE,abcd12698,1.2344543
+YER054C,YBR045C,pp,TRUE,abcd12699,1.2344543
+YPR145W,YMR117C,pp,TRUE,abcd12700,1.2344543
+YNR053C,YJL203W,pp,TRUE,abcd12701,1.2344543
+YNR053C,YDL030W,pp,TRUE,abcd12702,1.2344543
+YGR074W,YBR043C,pp,TRUE,abcd12703,1.2344543
+YDR277C,YJR022W,pp,TRUE,abcd12704,1.2344543
+YDR277C,YDL194W,pp,TRUE,abcd12705,1.2344543
+YBL026W,YOR167C,pp,TRUE,abcd12706,1.2344543
diff --git a/distribution/src/main/sampleData/galFiltered.cys b/distribution/src/main/sampleData/galFiltered.cys
new file mode 100644
index 0000000..09a3438
Binary files /dev/null and b/distribution/src/main/sampleData/galFiltered.cys differ
diff --git a/distribution/src/main/sampleData/galFiltered.edgeAttrs1 b/distribution/src/main/sampleData/galFiltered.edgeAttrs1
new file mode 100644
index 0000000..35134a7
--- /dev/null
+++ b/distribution/src/main/sampleData/galFiltered.edgeAttrs1
@@ -0,0 +1,354 @@
+TestEdgeAttributes1
+YKR026C (pp) YGL122C = 1
+YGR218W (pp) YGL097W = 1
+YGL097W (pp) YOR204W = 1
+YLR249W (pp) YPR080W = 1
+YLR249W (pp) YBR118W = 1
+YLR293C (pp) YGL097W = 1
+YMR146C (pp) YDR429C = 1
+YDR429C (pp) YFL017C = 1
+YPR080W (pp) YAL003W = 2
+YBR118W (pp) YAL003W = 1
+YOL123W (pp) YGL044C = 1
+YPL211W (pp) YGR014W = 1
+YJL030W (pp) YGL229C = 1
+YJL013C (pp) YGL229C = 1
+YGL122C (pp) YOL123W = 1
+YGR014W (pp) YJL030W = 1
+YGR014W (pp) YJL013C = 1
+YGR203W (pp) YIL061C = 1
+YCR084C (pp) YBR112C = 1
+YCR084C (pp) YCL067C = 1
+YER112W (pp) YOR167C = 1
+YJR022W (pp) YNR050C = 1
+YJR022W (pp) YNL050C = 1
+YJR022W (pp) YEL015W = 2
+YJR022W (pp) YOR167C = 1
+YJR022W (pp) YLR264W = 2
+YJR022W (pp) YNR053C = 2
+YER116C (pp) YDL013W = 1
+YNL307C (pp) YAL038W = 1
+YNL216W (pd) YCR012W = 1
+YNL216W (pd) YGR254W = 1
+YNL216W (pd) YHR174W = 1
+YNL216W (pd) YIL133C = 1
+YNL216W (pd) YLR044C = 1
+YNL216W (pd) YOL120C = 1
+YNL216W (pd) YNL301C = 1
+YNL216W (pd) YCL030C = 1
+YNL216W (pp) YDR171W = 1
+YNL216W (pd) YBR093C = 1
+YNL216W (pd) YER074W = 1
+YNL216W (pd) YIL069C = 1
+YNL216W (pd) YAL038W = 1
+YNL216W (pd) YOL127W = 1
+YNL216W (pd) YDR050C = 1
+YNL216W (pd) YOL086C = 1
+YAL030W (pp) YER143W = 1
+YOR327C (pp) YER143W = 2
+YER062C (pp) YPL201C = 1
+YDR412W (pp) YCR086W = 2
+YDR412W (pp) YGL013C = 1
+YDR412W (pp) YLR117C = 1
+YDR412W (pp) YPR119W = 1
+YDL014W (pp) YOR310C = 1
+YER179W (pp) YLR044C = 1
+YER179W (pp) YLR134W = 1
+YER179W (pp) YIL105C = 1
+YOR361C (pp) YMR309C = 1
+YOR361C (pp) YDR429C = 1
+YOR326W (pp) YGL106W = 1
+YMR186W (pp) YBR155W = 1
+YEL009C (pd) YMR108W = 2
+YEL009C (pd) YOR202W = 1
+YEL009C (pd) YCL030C = 1
+YEL009C (pd) YBR248C = 2
+YEL009C (pd) YOL058W = 1
+YEL009C (pd) YMR300C = 1
+YMR138W (pp) YHR141C = 1
+YMR138W (pp) YLR109W = 1
+YCL032W (pp) YDR032C = 1
+YCL032W (pp) YLR362W = 1
+YCL032W (pp) YDR103W = 1
+YCR012W (pd) YJR060W = 1
+YBR019C (pd) YOL051W = 1
+YBR019C (pd) YGL035C = 1
+YOL051W (pd) YBR020W = 1
+YOL051W (pd) YLR081W = 1
+YOL051W (pp) YPL248C = 1
+YOL051W (pd) YBR018C = 1
+YIR009W (pp) YKR099W = 1
+YIR009W (pp) YIL143C = 2
+YIR009W (pp) YDR184C = 2
+YIR009W (pp) YNL091W = 1
+YNL236W (pp) YKL012W = 1
+YML032C (pp) YNL312W = 1
+YLR116W (pp) YKL012W = 1
+YCR086W (pp) YOR264W = 1
+YDR309C (pp) YLR229C = 1
+YGR058W (pp) YOR264W = 2
+YJR109C (pp) YOR303W = 1
+YLR256W (pd) YML054C = 1
+YLR256W (pd) YJR048W = 1
+YLR256W (pd) YEL039C = 1
+YGL237C (pd) YJR048W = 1
+YBL021C (pd) YJR048W = 1
+YDR311W (pp) YKL028W = 1
+YPL149W (pp) YHR171W = 1
+YPL149W (pp) YBR217W = 1
+YKL109W (pp) YGL237C = 1
+YKL109W (pp) YBL021C = 1
+YKL109W (pd) YJR048W = 1
+YKL109W (pd) YGL035C = 1
+YMR043W (pd) YIL015W = 1
+YMR043W (pd) YJL159W = 1
+YMR043W (pd) YKR097W = 1
+YMR043W (pd) YGR108W = 1
+YMR043W (pd) YDR461W = 1
+YMR043W (pd) YNL145W = 1
+YMR043W (pd) YJL157C = 1
+YMR043W (pd) YFL026W = 1
+YHR171W (pp) YDR412W = 1
+YHR171W (pp) YNR007C = 2
+YNR050C (pp) YMR138W = 1
+YJL203W (pp) YOL136C = 1
+YLL021W (pp) YLR362W = 1
+YGL013C (pd) YJL219W = 1
+YGL013C (pd) YOL156W = 1
+YKL101W (pp) YBR160W = 1
+YCL067C (pd) YIL015W = 1
+YCL067C (pp) YMR043W = 1
+YCL067C (pd) YDR461W = 1
+YCL067C (pd) YFL026W = 1
+YBL005W (pd) YJL219W = 1
+YDR323C (pp) YOR036W = 1
+YGL008C (pd) YMR043W = 1
+YER040W (pd) YPR035W = 1
+YER040W (pd) YGR019W = 1
+YNL098C (pp) YLR310C = 1
+YGL115W (pp) YGL208W = 1
+YPL089C (pp) YHR030C = 1
+YJL089W (pd) YER065C = 1
+YJL089W (pd) YKR097W = 3
+YJL089W (pd) YLR377C = 1
+YMR021C (pd) YLR214W = 1
+YDR335W (pp) YDR174W = 1
+YLL028W (pp) YGL166W = 1
+YIL143C (pp) YDR311W = 1
+YDL081C (pp) YLR340W = 1
+YKL012W (pp) YKL074C = 1
+YEL015W (pp) YML064C = 1
+YHR135C (pp) YNL116W = 1
+YMR309C (pp) YNL047C = 1
+YNL154C (pp) YKL204W = 3
+YDR382W (pp) YFL039C = 1
+YFL039C (pp) YCL040W = 1
+YFL039C (pp) YHR179W = 1
+YPL075W (pd) YCR012W = 3
+YPL075W (pd) YGR254W = 3
+YPL075W (pd) YHR174W = 3
+YPL075W (pp) YNL199C = 1
+YPL075W (pd) YDR050C = 1
+YPL075W (pd) YOL086C = 1
+YNL199C (pp) YPR048W = 1
+YCL030C (pd) YKR099W = 1
+YBL069W (pp) YGL008C = 1
+YNL189W (pp) YDL236W = 1
+YNL189W (pp) YPL111W = 1
+YNL189W (pp) YER065C = 1
+YNL189W (pp) YPR062W = 1
+YDR184C (pp) YLR319C = 2
+YNL311C (pp) YKL001C = 2
+YOL058W (pp) YNL189W = 1
+YOL016C (pp) YBR109C = 1
+YJL036W (pp) YDL113C = 1
+YEL041W (pp) YHR115C = 1
+YNL167C (pd) YOR202W = 1
+YDL063C (pp) YPL131W = 1
+YGL161C (pp) YDR100W = 1
+YMR183C (pp) YGR009C = 1
+YMR291W (pp) YGL115W = 1
+YGR048W (pp) YPL222W = 2
+YAL040C (pd) YMR043W = 3
+YFR034C (pd) YBR093C = 1
+YFR037C (pp) YOR290C = 1
+YER133W (pp) YDR412W = 1
+YER133W (pp) YOR178C = 1
+YER133W (pp) YOR315W = 1
+YER133W (pp) YMR311C = 1
+YER133W (pp) YBR050C = 1
+YGL035C (pd) YLR044C = 1
+YGL035C (pd) YLR377C = 1
+YGL035C (pd) YIL162W = 1
+YFL038C (pp) YOR036W = 1
+YOR355W (pp) YNL091W = 3
+YML074C (pp) YJL190C = 3
+YMR058W (pp) YER145C = 1
+YML123C (pd) YFR034C = 1
+YPL031C (pp) YHR071W = 1
+YAL038W (pd) YPL075W = 1
+YML051W (pp) YBR020W = 1
+YML051W (pp) YDR009W = 1
+YLL019C (pp) YIL113W = 1
+YML024W (pd) YNL216W = 1
+YOR039W (pp) YOR303W = 1
+YER111C (pd) YMR043W = 1
+YDR146C (pd) YMR043W = 1
+YDR146C (pd) YGL035C = 1
+YKL211C (pp) YER090W = 2
+YDR354W (pd) YEL009C = 1
+YNL113W (pp) YPR110C = 1
+YLR310C (pp) YER103W = 1
+YNL047C (pp) YIL105C = 1
+YBR160W (pd) YMR043W = 1
+YBR160W (pp) YGR108W = 1
+YIL113W (pp) YHR030C = 1
+YLR117C (pp) YBR190W = 1
+YFL017C (pp) YOL059W = 1
+YFL017C (pp) YER102W = 1
+YFL017C (pp) YOR362C = 1
+YMR044W (pp) YIL061C = 3
+YOL149W (pp) YOR167C = 1
+YOR036W (pp) YDR100W = 1
+YOR036W (pp) YGL161C = 1
+YLR191W (pp) YGL153W = 1
+YER110C (pp) YML007W = 1
+YBR135W (pp) YER102W = 1
+YNL214W (pp) YGL153W = 1
+YJR060W (pd) YPR167C = 1
+YOR089C (pp) YDR323C = 1
+YNL117W (pd) YJL089W = 1
+YLR175W (pp) YNL307C = 1
+YDR167W (pp) YLR432W = 1
+YGR108W (pp) YBR135W = 1
+YDR244W (pp) YLR191W = 2
+YDR244W (pp) YGL153W = 1
+YDR244W (pp) YNL214W = 1
+YDR244W (pp) YDR142C = 2
+YDR244W (pp) YDL078C = 1
+YPR119W (pd) YMR043W = 1
+YDR142C (pp) YGL153W = 3
+YDR142C (pp) YIL160C = 3
+YBR020W (pd) YGL035C = 1
+YDR009W (pd) YGL035C = 1
+YPL248C (pd) YBR019C = 1
+YPL248C (pd) YML051W = 1
+YPL248C (pp) YML051W = 1
+YPL248C (pd) YBR020W = 1
+YPL248C (pd) YLR081W = 3
+YPL248C (pd) YBR018C = 1
+YAR007C (pp) YML032C = 3
+YAR007C (pd) YPL111W = 1
+YKL161C (pp) YPL089C = 1
+YNL312W (pd) YPL111W = 1
+YLR075W (pp) YPR102C = 1
+YLR229C (pp) YJL157C = 1
+YPL240C (pp) YBR155W = 1
+YPL240C (pp) YOR036W = 1
+YOL156W (pd) YBL005W = 1
+YML064C (pp) YHR198C = 1
+YML064C (pp) YLR284C = 1
+YML064C (pp) YDR174W = 1
+YER052C (pp) YNL135C = 1
+YPR124W (pd) YMR021C = 1
+YGL166W (pd) YHR053C = 1
+YGL166W (pd) YHR055C = 1
+YGL134W (pp) YPL031C = 1
+YGL134W (pp) YLR258W = 1
+YJL194W (pd) YMR043W = 1
+YLR264W (pp) YER112W = 3
+YLR264W (pp) YOL149W = 1
+YLR264W (pp) YBL026W = 3
+YBL050W (pp) YOR036W = 1
+YNL145W (pd) YCL067C = 1
+YNL145W (pd) YHR084W = 1
+YBR274W (pp) YMR255W = 1
+YLR452C (pp) YHR005C = 1
+YDR299W (pd) YJL194W = 1
+YIL074C (pp) YNL311C = 1
+YLR319C (pp) YLR362W = 1
+YGL073W (pp) YOR178C = 3
+YGL073W (pd) YHR053C = 3
+YGL073W (pd) YHR055C = 1
+YGL073W (pd) YER103W = 1
+YOR120W (pd) YPL248C = 1
+YPR041W (pp) YOR361C = 1
+YPR041W (pp) YMR309C = 1
+YNL135C (pp) YDR174W = 1
+YBR217W (pp) YNR007C = 1
+YMR255W (pp) YGL122C = 1
+YLR258W (pp) YIL045W = 1
+YLR258W (pp) YBR274W = 1
+YDL215C (pd) YER040W = 1
+YDL215C (pp) YLR432W = 1
+YER079W (pp) YHR135C = 1
+YER079W (pp) YNL154C = 1
+YDL030W (pp) YDL013W = 1
+YDL030W (pp) YMR005W = 1
+YLR362W (pp) YER124C = 1
+YLR362W (pp) YMR186W = 1
+YLR362W (pp) YPL240C = 1
+YHR084W (pp) YMR043W = 1
+YHR084W (pd) YDR461W = 1
+YHR084W (pd) YFL026W = 1
+YGR085C (pp) YLR075W = 1
+YGR085C (pp) YDR395W = 1
+YKL074C (pp) YGL035C = 1
+YGR088W (pd) YLR256W = 1
+YER081W (pp) YIL074C = 1
+YPR113W (pd) YMR043W = 1
+YIL070C (pp) YML054C = 1
+YIL061C (pp) YDL013W = 1
+YIL061C (pp) YNL199C = 1
+YIL061C (pp) YLR153C = 1
+YGR046W (pp) YNL236W = 1
+YNL091W (pp) YNL164C = 1
+YHR030C (pp) YLL021W = 1
+YHR030C (pp) YER111C = 1
+YPR048W (pp) YOR355W = 1
+YPR048W (pp) YDL215C = 1
+YHR005C (pp) YLR362W = 1
+YDR070C (pp) YFL017C = 1
+YJL157C (pp) YAL040C = 1
+YJL157C (pp) YOR212W = 1
+YNL036W (pp) YIR009W = 1
+YML114C (pp) YDR167W = 1
+YMR117C (pp) YCL032W = 1
+YMR117C (pp) YPR010C = 1
+YHR115C (pp) YOR215C = 1
+YGR009C (pp) YAL030W = 1
+YGR009C (pp) YOR327C = 1
+YGR009C (pp) YDR335W = 1
+YGR009C (pp) YBL050W = 1
+YDL088C (pp) YER110C = 1
+YLR197W (pp) YDL014W = 1
+YLR197W (pp) YOR310C = 1
+YGL202W (pp) YGR074W = 1
+YIL162W (pd) YNL167C = 1
+YBR170C (pp) YGR048W = 1
+YOR212W (pp) YLR362W = 1
+YDR103W (pp) YLR362W = 1
+YDL023C (pp) YJL159W = 1
+YGR136W (pp) YGR058W = 1
+YBR109C (pp) YOR326W = 1
+YBR109C (pp) YFR014C = 1
+YDR395W (pp) YDL075W = 1
+YDR395W (pp) YIL133C = 1
+YDR395W (pp) YNL069C = 1
+YDR395W (pp) YER056CA = 1
+YDR395W (pp) YIL052C = 1
+YDR395W (pp) YOL127W = 1
+YDR395W (pp) YPR102C = 1
+YLR345W (pp) YLR321C = 1
+YBL079W (pp) YDL088C = 1
+YBR045C (pp) YIL045W = 1
+YBR045C (pp) YOR178C = 1
+YER054C (pp) YER133W = 1
+YER054C (pp) YBR045C = 1
+YPR145W (pp) YMR117C = 1
+YNR053C (pp) YJL203W = 1
+YNR053C (pp) YDL030W = 1
+YGR074W (pp) YBR043C = 1
+YDR277C (pp) YJR022W = 1
+YDR277C (pp) YDL194W = 1
+YBL026W (pp) YOR167C = 1
diff --git a/distribution/src/main/sampleData/galFiltered.edgeAttrs2 b/distribution/src/main/sampleData/galFiltered.edgeAttrs2
new file mode 100644
index 0000000..9afbc3d
--- /dev/null
+++ b/distribution/src/main/sampleData/galFiltered.edgeAttrs2
@@ -0,0 +1,354 @@
+TestEdgeAttribute2
+YKR026C (pp) YGL122C = 2
+YGR218W (pp) YGL097W = 2
+YGL097W (pp) YOR204W = 2
+YLR249W (pp) YPR080W = 2
+YLR249W (pp) YBR118W = 2
+YLR293C (pp) YGL097W = 2
+YMR146C (pp) YDR429C = 2
+YDR429C (pp) YFL017C = 2
+YPR080W (pp) YAL003W = 2
+YBR118W (pp) YAL003W = 2
+YOL123W (pp) YGL044C = 2
+YPL211W (pp) YGR014W = 2
+YJL030W (pp) YGL229C = 2
+YJL013C (pp) YGL229C = 2
+YGL122C (pp) YOL123W = 2
+YGR014W (pp) YJL030W = 2
+YGR014W (pp) YJL013C = 2
+YGR203W (pp) YIL061C = 2
+YCR084C (pp) YBR112C = 2
+YCR084C (pp) YCL067C = 2
+YER112W (pp) YOR167C = 2
+YJR022W (pp) YNR050C = 2
+YJR022W (pp) YNL050C = 2
+YJR022W (pp) YEL015W = 2
+YJR022W (pp) YOR167C = 2
+YJR022W (pp) YLR264W = 2
+YJR022W (pp) YNR053C = 2
+YER116C (pp) YDL013W = 2
+YNL307C (pp) YAL038W = 2
+YNL216W (pd) YCR012W = 2
+YNL216W (pd) YGR254W = 2
+YNL216W (pd) YHR174W = 2
+YNL216W (pd) YIL133C = 2
+YNL216W (pd) YLR044C = 2
+YNL216W (pd) YOL120C = 2
+YNL216W (pd) YNL301C = 2
+YNL216W (pd) YCL030C = 2
+YNL216W (pp) YDR171W = 2
+YNL216W (pd) YBR093C = 2
+YNL216W (pd) YER074W = 2
+YNL216W (pd) YIL069C = 2
+YNL216W (pd) YAL038W = 2
+YNL216W (pd) YOL127W = 2
+YNL216W (pd) YDR050C = 2
+YNL216W (pd) YOL086C = 2
+YAL030W (pp) YER143W = 2
+YOR327C (pp) YER143W = 2
+YER062C (pp) YPL201C = 2
+YDR412W (pp) YCR086W = 2
+YDR412W (pp) YGL013C = 2
+YDR412W (pp) YLR117C = 2
+YDR412W (pp) YPR119W = 2
+YDL014W (pp) YOR310C = 2
+YER179W (pp) YLR044C = 2
+YER179W (pp) YLR134W = 2
+YER179W (pp) YIL105C = 2
+YOR361C (pp) YMR309C = 2
+YOR361C (pp) YDR429C = 2
+YOR326W (pp) YGL106W = 2
+YMR186W (pp) YBR155W = 2
+YEL009C (pd) YMR108W = 2
+YEL009C (pd) YOR202W = 2
+YEL009C (pd) YCL030C = 2
+YEL009C (pd) YBR248C = 2
+YEL009C (pd) YOL058W = 2
+YEL009C (pd) YMR300C = 2
+YMR138W (pp) YHR141C = 2
+YMR138W (pp) YLR109W = 2
+YCL032W (pp) YDR032C = 2
+YCL032W (pp) YLR362W = 2
+YCL032W (pp) YDR103W = 2
+YCR012W (pd) YJR060W = 2
+YBR019C (pd) YOL051W = 2
+YBR019C (pd) YGL035C = 2
+YOL051W (pd) YBR020W = 2
+YOL051W (pd) YLR081W = 2
+YOL051W (pp) YPL248C = 2
+YOL051W (pd) YBR018C = 2
+YIR009W (pp) YKR099W = 2
+YIR009W (pp) YIL143C = 2
+YIR009W (pp) YDR184C = 2
+YIR009W (pp) YNL091W = 2
+YNL236W (pp) YKL012W = 2
+YML032C (pp) YNL312W = 2
+YLR116W (pp) YKL012W = 2
+YCR086W (pp) YOR264W = 2
+YDR309C (pp) YLR229C = 2
+YGR058W (pp) YOR264W = 2
+YJR109C (pp) YOR303W = 2
+YLR256W (pd) YML054C = 2
+YLR256W (pd) YJR048W = 2
+YLR256W (pd) YEL039C = 2
+YGL237C (pd) YJR048W = 2
+YBL021C (pd) YJR048W = 2
+YDR311W (pp) YKL028W = 2
+YPL149W (pp) YHR171W = 2
+YPL149W (pp) YBR217W = 2
+YKL109W (pp) YGL237C = 2
+YKL109W (pp) YBL021C = 2
+YKL109W (pd) YJR048W = 2
+YKL109W (pd) YGL035C = 2
+YMR043W (pd) YIL015W = 2
+YMR043W (pd) YJL159W = 2
+YMR043W (pd) YKR097W = 2
+YMR043W (pd) YGR108W = 2
+YMR043W (pd) YDR461W = 2
+YMR043W (pd) YNL145W = 2
+YMR043W (pd) YJL157C = 2
+YMR043W (pd) YFL026W = 2
+YHR171W (pp) YDR412W = 2
+YHR171W (pp) YNR007C = 2
+YNR050C (pp) YMR138W = 2
+YJL203W (pp) YOL136C = 2
+YLL021W (pp) YLR362W = 2
+YGL013C (pd) YJL219W = 2
+YGL013C (pd) YOL156W = 2
+YKL101W (pp) YBR160W = 2
+YCL067C (pd) YIL015W = 2
+YCL067C (pp) YMR043W = 2
+YCL067C (pd) YDR461W = 2
+YCL067C (pd) YFL026W = 2
+YBL005W (pd) YJL219W = 2
+YDR323C (pp) YOR036W = 2
+YGL008C (pd) YMR043W = 2
+YER040W (pd) YPR035W = 2
+YER040W (pd) YGR019W = 2
+YNL098C (pp) YLR310C = 2
+YGL115W (pp) YGL208W = 2
+YPL089C (pp) YHR030C = 2
+YJL089W (pd) YER065C = 2
+YJL089W (pd) YKR097W = 2
+YJL089W (pd) YLR377C = 2
+YMR021C (pd) YLR214W = 2
+YDR335W (pp) YDR174W = 2
+YLL028W (pp) YGL166W = 2
+YIL143C (pp) YDR311W = 2
+YDL081C (pp) YLR340W = 2
+YKL012W (pp) YKL074C = 2
+YEL015W (pp) YML064C = 2
+YHR135C (pp) YNL116W = 2
+YMR309C (pp) YNL047C = 2
+YNL154C (pp) YKL204W = 2
+YDR382W (pp) YFL029C = 3
+YFL039C (pp) YCL020W = 3
+YFL039C (pp) YHR129W = 3
+YPL075W (pd) YCR022W = 3
+YPL075W (pd) YGR224W = 3
+YPL075W (pd) YHR124W = 3
+YPL075W (pp) YNL129C = 3
+YPL075W (pd) YDR020C = 3
+YPL075W (pd) YOL026C = 3
+YNL199C (pp) YPR028W = 3
+YCL030C (pd) YKR029W = 3
+YBL069W (pp) YGL028C = 3
+YNL189W (pp) YDL226W = 3
+YNL189W (pp) YPL121W = 3
+YNL189W (pp) YER025C = 3
+YNL189W (pp) YPR022W = 3
+YDR184C (pp) YLR329C = 3
+YNL311C (pp) YKL021C = 3
+YOL058W (pp) YNL129W = 3
+YOL016C (pp) YBR129C = 3
+YJL036W (pp) YDL123C = 3
+YEL041W (pp) YHR125C = 3
+YNL167C (pd) YOR222W = 3
+YDL063C (pp) YPL121W = 3
+YGL161C (pp) YDR120W = 3
+YMR183C (pp) YGR029C = 3
+YMR291W (pp) YGL125W = 3
+YGR048W (pp) YPL222W = 3
+YAL040C (pd) YMR023W = 3
+YFR034C (pd) YBR023C = 3
+YFR037C (pp) YOR220C = 3
+YER133W (pp) YDR422W = 3
+YER133W (pp) YOR128C = 3
+YER133W (pp) YOR325W = 3
+YER133W (pp) YMR321C = 3
+YER133W (pp) YBR020C = 3
+YGL035C (pd) YLR024C = 3
+YGL035C (pd) YLR327C = 3
+YGL035C (pd) YIL122W = 3
+YFL038C (pp) YOR026W = 3
+YOR355W (pp) YNL021W = 3
+YML074C (pp) YJL120C = 3
+YMR058W (pp) YER125C = 3
+YML123C (pd) YFR024C = 3
+YPL031C (pp) YHR021W = 3
+YAL038W (pd) YPL025W = 3
+YML051W (pp) YBR020W = 3
+YML051W (pp) YDR029W = 3
+YLL019C (pp) YIL123W = 3
+YML024W (pd) YNL226W = 3
+YOR039W (pp) YOR323W = 3
+YER111C (pd) YMR023W = 3
+YDR146C (pd) YMR023W = 3
+YDR146C (pd) YGL025C = 3
+YKL211C (pp) YER020W = 3
+YDR354W (pd) YEL029C = 3
+YNL113W (pp) YPR120C = 3
+YLR310C (pp) YER123W = 3
+YNL047C (pp) YIL125C = 3
+YBR160W (pd) YMR023W = 3
+YBR160W (pp) YGR128W = 3
+YIL113W (pp) YHR020C = 3
+YLR117C (pp) YBR120W = 3
+YFL017C (pp) YOL029W = 3
+YFL017C (pp) YER122W = 3
+YFL017C (pp) YOR322C = 3
+YMR044W (pp) YIL021C = 3
+YOL149W (pp) YOR127C = 3
+YOR036W (pp) YDR120W = 3
+YOR036W (pp) YGL121C = 3
+YLR191W (pp) YGL123W = 3
+YER110C (pp) YML027W = 3
+YBR135W (pp) YER122W = 3
+YNL214W (pp) YGL123W = 3
+YJR060W (pd) YPR127C = 3
+YOR089C (pp) YDR323C = 3
+YNL117W (pd) YJL029W = 3
+YLR175W (pp) YNL327C = 3
+YDR167W (pp) YLR422W = 3
+YGR108W (pp) YBR125W = 3
+YDR244W (pp) YLR121W = 3
+YDR244W (pp) YGL123W = 3
+YDR244W (pp) YNL224W = 3
+YDR244W (pp) YDR122C = 3
+YDR244W (pp) YDL028C = 3
+YPR119W (pd) YMR023W = 3
+YDR142C (pp) YGL123W = 3
+YDR142C (pp) YIL120C = 3
+YBR020W (pd) YGL025C = 3
+YDR009W (pd) YGL025C = 3
+YPL248C (pd) YBR029C = 3
+YPL248C (pd) YML021W = 3
+YPL248C (pp) YML021W = 3
+YPL248C (pd) YBR020W = 3
+YPL248C (pd) YLR021W = 3
+YPL248C (pd) YBR028C = 3
+YAR007C (pp) YML022C = 3
+YAR007C (pd) YPL121W = 3
+YKL161C (pp) YPL029C = 3
+YNL312W (pd) YPL121W = 3
+YLR075W (pp) YPR122C = 3
+YLR229C (pp) YJL127C = 3
+YPL240C (pp) YBR125W = 3
+YPL240C (pp) YOR026W = 3
+YOL156W (pd) YBL025W = 3
+YML064C (pp) YHR128C = 3
+YML064C (pp) YLR224C = 3
+YML064C (pp) YDR124W = 3
+YER052C (pp) YNL125C = 3
+YPR124W (pd) YMR021C = 3
+YGL166W (pd) YHR023C = 3
+YGL166W (pd) YHR025C = 3
+YGL134W (pp) YPL021C = 3
+YGL134W (pp) YLR228W = 3
+YJL194W (pd) YMR023W = 3
+YLR264W (pp) YER122W = 3
+YLR264W (pp) YOL129W = 3
+YLR264W (pp) YBL026W = 3
+YBL050W (pp) YOR026W = 3
+YNL145W (pd) YCL027C = 3
+YNL145W (pd) YHR024W = 3
+YBR274W (pp) YMR225W = 3
+YLR452C (pp) YHR025C = 3
+YDR299W (pd) YJL124W = 3
+YIL074C (pp) YNL321C = 3
+YLR319C (pp) YLR322W = 3
+YGL073W (pp) YOR128C = 3
+YGL073W (pd) YHR023C = 3
+YGL073W (pd) YHR025C = 3
+YGL073W (pd) YER123W = 3
+YOR120W (pd) YPL228C = 3
+YPR041W (pp) YOR321C = 3
+YPR041W (pp) YMR329C = 3
+YNL135C (pp) YDR124W = 3
+YBR217W (pp) YNR027C = 3
+YMR255W (pp) YGL122C = 3
+YLR258W (pp) YIL025W = 3
+YLR258W (pp) YBR224W = 3
+YDL215C (pd) YER020W = 3
+YDL215C (pp) YLR422W = 3
+YER079W (pp) YHR125C = 3
+YER079W (pp) YNL124C = 3
+YDL030W (pp) YDL023W = 3
+YDL030W (pp) YMR025W = 3
+YLR362W (pp) YER124C = 3
+YLR362W (pp) YMR126W = 3
+YLR362W (pp) YPL220C = 3
+YHR084W (pp) YMR023W = 3
+YHR084W (pd) YDR421W = 3
+YHR084W (pd) YFL026W = 3
+YGR085C (pp) YLR025W = 3
+YGR085C (pp) YDR325W = 3
+YKL074C (pp) YGL025C = 3
+YGR088W (pd) YLR226W = 3
+YER081W (pp) YIL024C = 3
+YPR113W (pd) YMR023W = 3
+YIL070C (pp) YML024C = 3
+YIL061C (pp) YDL023W = 3
+YIL061C (pp) YNL129C = 3
+YIL061C (pp) YLR123C = 3
+YGR046W (pp) YNL226W = 3
+YNL091W (pp) YNL124C = 3
+YHR030C (pp) YLL021W = 3
+YHR030C (pp) YER121C = 3
+YPR048W (pp) YOR325W = 3
+YPR048W (pp) YDL225C = 3
+YHR005C (pp) YLR322W = 3
+YDR070C (pp) YFL027C = 3
+YJL157C (pp) YAL020C = 3
+YJL157C (pp) YOR222W = 3
+YNL036W (pp) YIR029W = 3
+YML114C (pp) YDR127W = 3
+YMR117C (pp) YCL022W = 3
+YMR117C (pp) YPR020C = 3
+YHR115C (pp) YOR225C = 3
+YGR009C (pp) YAL020W = 3
+YGR009C (pp) YOR327C = 3
+YGR009C (pp) YDR325W = 3
+YGR009C (pp) YBL020W = 3
+YDL088C (pp) YER120C = 3
+YLR197W (pp) YDL024W = 3
+YLR197W (pp) YOR320C = 3
+YGL202W (pp) YGR024W = 3
+YIL162W (pd) YNL127C = 3
+YBR170C (pp) YGR028W = 3
+YOR212W (pp) YLR322W = 3
+YDR103W (pp) YLR322W = 3
+YDL023C (pp) YJL129W = 3
+YGR136W (pp) YGR028W = 3
+YBR109C (pp) YOR326W = 3
+YBR109C (pp) YFR024C = 3
+YDR395W (pp) YDL025W = 3
+YDR395W (pp) YIL123C = 3
+YDR395W (pp) YNL029C = 3
+YDR395W (pp) YER026CA =3
+YDR395W (pp) YIL022C = 3
+YDR395W (pp) YOL127W = 3
+YDR395W (pp) YPR122C = 3
+YLR345W (pp) YLR321C = 3
+YBL079W (pp) YDL028C = 3
+YBR045C (pp) YIL025W = 3
+YBR045C (pp) YOR128C = 3
+YER054C (pp) YER123W = 3
+YER054C (pp) YBR025C = 3
+YPR145W (pp) YMR127C = 3
+YNR053C (pp) YJL223W = 3
+YNR053C (pp) YDL020W = 3
+YGR074W (pp) YBR023C = 3
+YDR277C (pp) YJR022W = 3
+YDR277C (pp) YDL124W = 3
+YBL026W (pp) YOR127C = 3
diff --git a/distribution/src/main/sampleData/galFiltered.gml b/distribution/src/main/sampleData/galFiltered.gml
new file mode 100644
index 0000000..e311038
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diff --git a/distribution/src/main/sampleData/galFiltered.nodeAttrTable.xls b/distribution/src/main/sampleData/galFiltered.nodeAttrTable.xls
new file mode 100755
index 0000000..986cf9f
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diff --git a/distribution/src/main/sampleData/galFiltered.nodeAttrTable.xlsx b/distribution/src/main/sampleData/galFiltered.nodeAttrTable.xlsx
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diff --git a/distribution/src/main/sampleData/galFiltered.nodeAttrs1 b/distribution/src/main/sampleData/galFiltered.nodeAttrs1
new file mode 100644
index 0000000..cfb540b
--- /dev/null
+++ b/distribution/src/main/sampleData/galFiltered.nodeAttrs1
@@ -0,0 +1,329 @@
+TestNodeAttribute1
+YKR026C = 1
+YGL122C = 1
+YMR146C = 1
+YDR429C = 1
+YFL017C = 1
+YOL123W = 1
+YGL044C = 1
+YGR203W = 1
+YIL061C = 1
+YCR084C = 1
+YBR112C = 1
+YCL067C = 1
+YER112W = 1
+YOR167C = 1
+YJR022W = 1
+YNR050C = 1
+YNL050C = 1
+YEL015W = 1
+YLR264W = 1
+YNR053C = 1
+YER116C = 1
+YDL013W = 1
+YNL307C = 1
+YAL038W = 1
+YNL216W = 1
+YCR012W = 1
+YGR254W = 1
+YHR174W = 1
+YIL133C = 1
+YLR044C = 1
+YOL120C = 1
+YNL301C = 1
+YCL030C = 1
+YDR171W = 1
+YBR093C = 1
+YER074W = 1
+YIL069C = 1
+YOL127W = 1
+YDR050C = 1
+YOL086C = 1
+YAL030W = 1
+YER143W = 1
+YOR327C = 1
+YDR412W = 1
+YCR086W = 1
+YGL013C = 1
+YLR117C = 1
+YPR119W = 1
+YER179W = 1
+YLR134W = 1
+YIL105C = 1
+YOR361C = 1
+YMR309C = 1
+YMR186W = 1
+YBR155W = 1
+YEL009C = 1
+YMR108W = 1
+YOR202W = 1
+YBR248C = 1
+YOL058W = 1
+YMR300C = 1
+YMR138W = 1
+YHR141C = 1
+YLR109W = 1
+YCL032W = 1
+YDR032C = 1
+YLR362W = 1
+YDR103W = 1
+YJR060W = 1
+YBR019C = 1
+YOL051W = 1
+YGL035C = 1
+YBR020W = 1
+YLR081W = 1
+YPL248C = 1
+YBR018C = 1
+YIR009W = 1
+YKR099W = 1
+YIL143C = 1
+YDR184C = 1
+YNL091W = 1
+YNL236W = 1
+YKL012W = 1
+YML032C = 1
+YNL312W = 1
+YLR116W = 1
+YOR264W = 1
+YDR309C = 1
+YLR229C = 1
+YGR058W = 1
+YLR256W = 1
+YML054C = 1
+YJR048W = 1
+YEL039C = 1
+YGL237C = 1
+YBL021C = 1
+YDR311W = 1
+YKL028W = 1
+YPL149W = 1
+YHR171W = 1
+YBR217W = 1
+YKL109W = 1
+YMR043W = 2
+YIL015W = 2
+YJL159W = 2
+YKR097W = 2
+YGR108W = 2
+YDR461W = 2
+YNL145W = 2
+YJL157C = 2
+YFL026W = 2
+YNR007C = 2
+YJL203W = 2
+YOL136C = 2
+YLL021W = 2
+YJL219W = 2
+YOL156W = 2
+YKL101W = 2
+YBR160W = 2
+YBL005W = 2
+YDR323C = 2
+YOR036W = 2
+YGL008C = 2
+YER040W = 2
+YPR035W = 2
+YGR019W = 2
+YNL098C = 2
+YLR310C = 2
+YPL089C = 2
+YHR030C = 2
+YJL089W = 2
+YER065C = 2
+YLR377C = 2
+YDR335W = 2
+YDR174W = 2
+YLL028W = 2
+YGL166W = 2
+YKL074C = 2
+YML064C = 2
+YNL047C = 2
+YNL199C = 2
+YPR048W = 2
+YLR321C = 2
+YBR072W = 2
+YGL073W = 2
+YBL069W = 2
+YNL189W = 2
+YDL236W = 2
+YPL111W = 2
+YPR062W = 2
+YLR319C = 2
+YNL167C = 2
+YGL161C = 2
+YDR100W = 2
+YMR183C = 2
+YGR009C = 2
+YAL040C = 2
+YFR034C = 2
+YER133W = 2
+YOR178C = 2
+YOR315W = 2
+YMR311C = 2
+YBR050C = 2
+YIL162W = 2
+YFL038C = 2
+YOR355W = 2
+YML123C = 2
+YPL031C = 2
+YHR071W = 2
+YML051W = 2
+YDR009W = 2
+YLL019C = 2
+YIL113W = 2
+YML024W = 2
+YER111C = 2
+YDR146C = 2
+YDR354W = 2
+YER103W = 2
+YBR190W = 2
+YOL059W = 2
+YER102W = 2
+YOR362C = 2
+YMR044W = 2
+YOL149W = 2
+YBR135W = 2
+YPR167C = 2
+YOR089C = 2
+YNL117W = 2
+YLR175W = 2
+YDR167W = 2
+YLR432W = 2
+YAR007C = 2
+YKL161C = 2
+YLR075W = 2
+YPR102C = 2
+YPL240C = 2
+YHR198C = 2
+YLR284C = 2
+YER052C = 2
+YNL135C = 2
+YHR053C = 3
+YHR055C = 3
+YGL134W = 3
+YLR258W = 3
+YJL194W = 3
+YBL026W = 3
+YBL050W = 3
+YHR084W = 3
+YBR274W = 3
+YMR255W = 3
+YLR452C = 3
+YHR005C = 3
+YDR299W = 3
+YOR120W = 3
+YPR041W = 3
+YIL045W = 3
+YDL215C = 3
+YDL030W = 3
+YMR005W = 3
+YER124C = 3
+YGR085C = 3
+YDR395W = 3
+YGR088W = 3
+YPR113W = 3
+YIL070C = 3
+YLR153C = 3
+YGR046W = 3
+YNL164C = 3
+YDR070C = 3
+YOR212W = 3
+YNL036W = 3
+YML114C = 3
+YMR117C = 3
+YPR010C = 3
+YDL023C = 3
+YGR136W = 3
+YDL075W = 3
+YNL069C = 3
+YER056CA = 3
+YIL052C = 3
+YLR345W = 3
+YBR045C = 3
+YER054C = 3
+YPR145W = 3
+YDR277C = 3
+YDL194W = 3
+YGR218W = 3
+YGL097W = 3
+YOR204W = 3
+YLR293C = 3
+YLR249W = 3
+YPR080W = 3
+YBR118W = 3
+YAL003W = 3
+YPL211W = 3
+YGR014W = 3
+YJL030W = 3
+YGL229C = 3
+YJL013C = 3
+YER062C = 3
+YPL201C = 3
+YDL014W = 3
+YOR310C = 3
+YLR197W = 3
+YOR326W = 3
+YGL106W = 3
+YOL016C = 3
+YBR109C = 3
+YFR014C = 3
+YJR109C = 3
+YOR303W = 3
+YOR039W = 3
+YGL115W = 3
+YGL208W = 3
+YMR291W = 3
+YMR021C = 3
+YLR214W = 3
+YPR124W = 3
+YDL081C = 3
+YLR340W = 3
+YHR135C = 3
+YNL116W = 3
+YNL154C = 3
+YKL204W = 3
+YER079W = 3
+YDR382W = 3
+YDL130W = 3
+YFL039C = 3
+YCL040W = 3
+YHR179W = 3
+YNL311C = 3
+YKL001C = 3
+YIL074C = 3
+YER081W = 3
+YJL036W = 3
+YDL113C = 3
+YEL041W = 3
+YHR115C = 3
+YOR215C = 3
+YDL063C = 3
+YPL131W = 3
+YGR048W = 3
+YPL222W = 3
+YBR170C = 3
+YFR037C = 3
+YOR290C = 3
+YML074C = 3
+YJL190C = 3
+YMR058W = 3
+YER145C = 3
+YKL211C = 3
+YER090W = 3
+YNL113W = 3
+YPR110C = 3
+YLR191W = 3
+YGL153W = 3
+YNL214W = 3
+YDR244W = 3
+YDR142C = 3
+YDL078C = 3
+YIL160C = 3
+YER110C = 3
+YML007W = 3
+YDL088C = 3
+YBL079W = 3
+YGL202W = 3
+YGR074W = 3
+YBR043C = 3
diff --git a/distribution/src/main/sampleData/galFiltered.nodeAttrs2 b/distribution/src/main/sampleData/galFiltered.nodeAttrs2
new file mode 100644
index 0000000..08094ae
--- /dev/null
+++ b/distribution/src/main/sampleData/galFiltered.nodeAttrs2
@@ -0,0 +1,329 @@
+TestNodeAttribute2
+YKR026C = 4
+YGL122C = 4
+YMR146C = 4
+YDR429C = 4
+YFL017C = 4
+YOL123W = 4
+YGL044C = 4
+YGR203W = 4
+YIL061C = 4
+YCR084C = 4
+YBR112C = 4
+YCL067C = 4
+YER112W = 4
+YOR167C = 4
+YJR022W = 4
+YNR050C = 4
+YNL050C = 4
+YEL015W = 4
+YLR264W = 4
+YNR053C = 4
+YER116C = 4
+YDL013W = 4
+YNL307C = 4
+YAL038W = 4
+YNL216W = 4
+YCR012W = 4
+YGR254W = 4
+YHR174W = 4
+YIL133C = 4
+YLR044C = 4
+YOL120C = 4
+YNL301C = 4
+YCL030C = 4
+YDR171W = 4
+YBR093C = 4
+YER074W = 4
+YIL069C = 4
+YOL127W = 4
+YDR050C = 4
+YOL086C = 4
+YAL030W = 4
+YER143W = 4
+YOR327C = 4
+YDR412W = 4
+YCR086W = 4
+YGL013C = 4
+YLR117C = 4
+YPR119W = 4
+YER179W = 4
+YLR134W = 4
+YIL105C = 4
+YOR361C = 4
+YMR309C = 4
+YMR186W = 4
+YBR155W = 4
+YEL009C = 4
+YMR108W = 4
+YOR202W = 4
+YBR248C = 4
+YOL058W = 4
+YMR300C = 4
+YMR138W = 4
+YHR141C = 4
+YLR109W = 4
+YCL032W = 4
+YDR032C = 4
+YLR362W = 4
+YDR103W = 4
+YJR060W = 4
+YBR019C = 4
+YOL051W = 4
+YGL035C = 4
+YBR020W = 4
+YLR081W = 4
+YPL248C = 4
+YBR018C = 4
+YIR009W = 4
+YKR099W = 4
+YIL143C = 4
+YDR184C = 4
+YNL091W = 4
+YNL236W = 4
+YKL012W = 4
+YML032C = 4
+YNL312W = 4
+YLR116W = 4
+YOR264W = 4
+YDR309C = 4
+YLR229C = 4
+YGR058W = 4
+YLR256W = 4
+YML054C = 4
+YJR048W = 4
+YEL039C = 4
+YGL237C = 4
+YBL021C = 4
+YDR311W = 4
+YKL028W = 4
+YPL149W = 4
+YHR171W = 4
+YBR217W = 4
+YKL109W = 4
+YMR043W = 5
+YIL015W = 5
+YJL159W = 5
+YKR097W = 5
+YGR108W = 5
+YDR461W = 5
+YNL145W = 5
+YJL157C = 5
+YFL026W = 5
+YNR007C = 5
+YJL203W = 5
+YOL136C = 5
+YLL021W = 5
+YJL219W = 5
+YOL156W = 5
+YKL101W = 5
+YBR160W = 5
+YBL005W = 5
+YDR323C = 5
+YOR036W = 5
+YGL008C = 5
+YER040W = 5
+YPR035W = 5
+YGR019W = 5
+YNL098C = 5
+YLR310C = 5
+YPL089C = 5
+YHR030C = 5
+YJL089W = 5
+YER065C = 5
+YLR377C = 5
+YDR335W = 5
+YDR174W = 5
+YLL028W = 5
+YGL166W = 5
+YKL074C = 5
+YML064C = 5
+YNL047C = 5
+YNL199C = 5
+YPR048W = 5
+YLR321C = 5
+YBR072W = 5
+YGL073W = 5
+YBL069W = 5
+YNL189W = 5
+YDL236W = 5
+YPL111W = 5
+YPR062W = 5
+YLR319C = 5
+YNL167C = 5
+YGL161C = 5
+YDR100W = 5
+YMR183C = 5
+YGR009C = 5
+YAL040C = 5
+YFR034C = 5
+YER133W = 5
+YOR178C = 5
+YOR315W = 5
+YMR311C = 5
+YBR050C = 5
+YIL162W = 5
+YFL038C = 5
+YOR355W = 5
+YML123C = 5
+YPL031C = 5
+YHR071W = 5
+YML051W = 5
+YDR009W = 5
+YLL019C = 5
+YIL113W = 5
+YML024W = 5
+YER111C = 5
+YDR146C = 5
+YDR354W = 5
+YER103W = 5
+YBR190W = 5
+YOL059W = 5
+YER102W = 5
+YOR362C = 5
+YMR044W = 5
+YOL149W = 5
+YBR135W = 5
+YPR167C = 5
+YOR089C = 5
+YNL117W = 5
+YLR175W = 5
+YDR167W = 5
+YLR432W = 5
+YAR007C = 5
+YKL161C = 5
+YLR075W = 5
+YPR102C = 5
+YPL240C = 5
+YHR198C = 5
+YLR284C = 5
+YER052C = 5
+YNL135C = 5
+YHR053C = 5
+YHR055C = 5
+YGL134W = 5
+YLR258W = 6
+YJL194W = 6
+YBL026W = 6
+YBL050W = 6
+YHR084W = 6
+YBR274W = 6
+YMR255W = 6
+YLR452C = 6
+YHR005C = 6
+YDR299W = 6
+YOR120W = 6
+YPR041W = 6
+YIL045W = 6
+YDL215C = 6
+YDL030W = 6
+YMR005W = 6
+YER124C = 6
+YGR085C = 6
+YDR395W = 6
+YGR088W = 6
+YPR113W = 6
+YIL070C = 6
+YLR153C = 6
+YGR046W = 6
+YNL164C = 6
+YDR070C = 6
+YOR212W = 6
+YNL036W = 6
+YML114C = 6
+YMR117C = 6
+YPR010C = 6
+YDL023C = 6
+YGR136W = 6
+YDL075W = 6
+YNL069C = 6
+YER056CA =63
+YIL052C = 6
+YLR345W = 6
+YBR045C = 6
+YER054C = 6
+YPR145W = 6
+YDR277C = 6
+YDL194W = 6
+YGR218W = 6
+YGL097W = 6
+YOR204W = 6
+YLR293C = 6
+YLR249W = 6
+YPR080W = 6
+YBR118W = 6
+YAL003W = 6
+YPL211W = 6
+YGR014W = 6
+YJL030W = 6
+YGL229C = 6
+YJL013C = 6
+YER062C = 6
+YPL201C = 6
+YDL014W = 6
+YOR310C = 6
+YLR197W = 6
+YOR326W = 6
+YGL106W = 6
+YOL016C = 6
+YBR109C = 6
+YFR014C = 6
+YJR109C = 6
+YOR303W = 6
+YOR039W = 6
+YGL115W = 6
+YGL208W = 6
+YMR291W = 6
+YMR021C = 6
+YLR214W = 6
+YPR124W = 6
+YDL081C = 6
+YLR340W = 6
+YHR135C = 6
+YNL116W = 6
+YNL154C = 6
+YKL204W = 6
+YER079W = 6
+YDR382W = 6
+YDL130W = 6
+YFL039C = 6
+YCL040W = 6
+YHR179W = 6
+YNL311C = 6
+YKL001C = 6
+YIL074C = 6
+YER081W = 6
+YJL036W = 6
+YDL113C = 6
+YEL041W = 6
+YHR115C = 6
+YOR215C = 6
+YDL063C = 6
+YPL131W = 6
+YGR048W = 6
+YPL222W = 6
+YBR170C = 6
+YFR037C = 6
+YOR290C = 6
+YML074C = 6
+YJL190C = 6
+YMR058W = 6
+YER145C = 6
+YKL211C = 6
+YER090W = 6
+YNL113W = 6
+YPR110C = 6
+YLR191W = 6
+YGL153W = 6
+YNL214W = 6
+YDR244W = 6
+YDR142C = 6
+YDL078C = 6
+YIL160C = 6
+YER110C = 6
+YML007W = 6
+YDL088C = 6
+YBL079W = 6
+YGL202W = 6
+YGR074W = 6
+YBR043C = 6
diff --git a/distribution/src/main/sampleData/galFiltered.nodeAttrs3 b/distribution/src/main/sampleData/galFiltered.nodeAttrs3
new file mode 100644
index 0000000..2a50ee0
--- /dev/null
+++ b/distribution/src/main/sampleData/galFiltered.nodeAttrs3
@@ -0,0 +1,329 @@
+TestNodeAttribute3
+YKR026C = homer
+YGL122C = homer
+YMR146C = homer
+YDR429C = homer
+YFL017C = homer
+YOL123W = homer
+YGL044C = homer
+YGR203W = homer
+YIL061C = homer
+YCR084C = homer
+YBR112C = homer
+YCL067C = homer
+YER112W = homer
+YOR167C = homer
+YJR022W = homer
+YNR050C = homer
+YNL050C = homer
+YEL015W = homer
+YLR264W = homer
+YNR053C = homer
+YER116C = homer
+YDL013W = homer
+YNL307C = homer
+YAL038W = homer
+YNL216W = homer
+YCR012W = homer
+YGR254W = homer
+YHR174W = homer
+YIL133C = homer
+YLR044C = homer
+YOL120C = homer
+YNL301C = homer
+YCL030C = homer
+YDR171W = homer
+YBR093C = homer
+YER074W = homer
+YIL069C = homer
+YOL127W = homer
+YDR050C = homer
+YOL086C = homer
+YAL030W = homer
+YER143W = homer
+YOR327C = homer
+YDR412W = homer
+YCR086W = homer
+YGL013C = homer
+YLR117C = homer
+YPR119W = homer
+YER179W = homer
+YLR134W = homer
+YIL105C = homer
+YOR361C = homer
+YMR309C = homer
+YMR186W = homer
+YBR155W = homer
+YEL009C = homer
+YMR108W = homer
+YOR202W = homer
+YBR248C = homer
+YOL058W = homer
+YMR300C = homer
+YMR138W = homer
+YHR141C = homer
+YLR109W = homer
+YCL032W = homer
+YDR032C = homer
+YLR362W = homer
+YDR103W = homer
+YJR060W = homer
+YBR019C = homer
+YOL051W = homer
+YGL035C = homer
+YBR020W = homer
+YLR081W = homer
+YPL248C = homer
+YBR018C = homer
+YIR009W = homer
+YKR099W = homer
+YIL143C = homer
+YDR184C = homer
+YNL091W = homer
+YNL236W = homer
+YKL012W = homer
+YML032C = homer
+YNL312W = homer
+YLR116W = homer
+YOR264W = homer
+YDR309C = homer
+YLR229C = homer
+YGR058W = homer
+YLR256W = homer
+YML054C = homer
+YJR048W = homer
+YEL039C = homer
+YGL237C = homer
+YBL021C = homer
+YDR311W = homer
+YKL028W = homer
+YPL149W = homer
+YHR171W = homer
+YBR217W = homer
+YKL109W = homer
+YMR043W = marge
+YIL015W = marge
+YJL159W = marge
+YKR097W = marge
+YGR108W = marge
+YDR461W = marge
+YNL145W = marge
+YJL157C = marge
+YFL026W = marge
+YNR007C = marge
+YJL203W = marge
+YOL136C = marge
+YLL021W = marge
+YJL219W = marge
+YOL156W = marge
+YKL101W = marge
+YBR160W = marge
+YBL005W = marge
+YDR323C = marge
+YOR036W = marge
+YGL008C = marge
+YER040W = marge
+YPR035W = marge
+YGR019W = marge
+YNL098C = marge
+YLR310C = marge
+YPL089C = marge
+YHR030C = marge
+YJL089W = marge
+YER065C = marge
+YLR377C = marge
+YDR335W = marge
+YDR174W = marge
+YLL028W = marge
+YGL166W = marge
+YKL074C = marge
+YML064C = marge
+YNL047C = marge
+YNL199C = marge
+YPR048W = marge
+YLR321C = marge
+YBR072W = marge
+YGL073W = marge
+YBL069W = marge
+YNL189W = marge
+YDL236W = marge
+YPL111W = marge
+YPR062W = marge
+YLR319C = marge
+YNL167C = marge
+YGL161C = marge
+YDR100W = marge
+YMR183C = marge
+YGR009C = marge
+YAL040C = marge
+YFR034C = marge
+YER133W = marge
+YOR178C = marge
+YOR315W = marge
+YMR311C = marge
+YBR050C = marge
+YIL162W = marge
+YFL038C = marge
+YOR355W = marge
+YML123C = marge
+YPL031C = marge
+YHR071W = marge
+YML051W = marge
+YDR009W = marge
+YLL019C = marge
+YIL113W = marge
+YML024W = marge
+YER111C = marge
+YDR146C = marge
+YDR354W = marge
+YER103W = marge
+YBR190W = marge
+YOL059W = marge
+YER102W = marge
+YOR362C = marge
+YMR044W = marge
+YOL149W = marge
+YBR135W = marge
+YPR167C = marge
+YOR089C = marge
+YNL117W = marge
+YLR175W = marge
+YDR167W = marge
+YLR432W = marge
+YAR007C = marge
+YKL161C = marge
+YLR075W = marge
+YPR102C = marge
+YPL240C = marge
+YHR198C = marge
+YLR284C = marge
+YER052C = marge
+YNL135C = marge
+YHR053C = bart
+YHR055C = bart
+YGL134W = bart
+YLR258W = bart
+YJL194W = bart
+YBL026W = bart
+YBL050W = bart
+YHR084W = bart
+YBR274W = bart
+YMR255W = bart
+YLR452C = bart
+YHR005C = bart
+YDR299W = bart
+YOR120W = bart
+YPR041W = bart
+YIL045W = bart
+YDL215C = bart
+YDL030W = bart
+YMR005W = bart
+YER124C = bart
+YGR085C = bart
+YDR395W = bart
+YGR088W = bart
+YPR113W = bart
+YIL070C = bart
+YLR153C = bart
+YGR046W = bart
+YNL164C = bart
+YDR070C = bart
+YOR212W = bart
+YNL036W = bart
+YML114C = bart
+YMR117C = bart
+YPR010C = bart
+YDL023C = bart
+YGR136W = bart
+YDL075W = bart
+YNL069C = bart
+YER056CA = bart
+YIL052C = bart
+YLR345W = bart
+YBR045C = bart
+YER054C = bart
+YPR145W = bart
+YDR277C = bart
+YDL194W = bart
+YGR218W = bart
+YGL097W = bart
+YOR204W = bart
+YLR293C = bart
+YLR249W = bart
+YPR080W = bart
+YBR118W = bart
+YAL003W = bart
+YPL211W = bart
+YGR014W = bart
+YJL030W = bart
+YGL229C = bart
+YJL013C = bart
+YER062C = bart
+YPL201C = bart
+YDL014W = bart
+YOR310C = bart
+YLR197W = bart
+YOR326W = bart
+YGL106W = bart
+YOL016C = bart
+YBR109C = bart
+YFR014C = bart
+YJR109C = bart
+YOR303W = bart
+YOR039W = bart
+YGL115W = bart
+YGL208W = bart
+YMR291W = bart
+YMR021C = bart
+YLR214W = bart
+YPR124W = bart
+YDL081C = bart
+YLR340W = bart
+YHR135C = bart
+YNL116W = bart
+YNL154C = bart
+YKL204W = bart
+YER079W = bart
+YDR382W = bart
+YDL130W = bart
+YFL039C = bart
+YCL040W = bart
+YHR179W = bart
+YNL311C = bart
+YKL001C = bart
+YIL074C = bart
+YER081W = bart
+YJL036W = bart
+YDL113C = bart
+YEL041W = bart
+YHR115C = bart
+YOR215C = bart
+YDL063C = bart
+YPL131W = bart
+YGR048W = bart
+YPL222W = bart
+YBR170C = bart
+YFR037C = bart
+YOR290C = bart
+YML074C = bart
+YJL190C = bart
+YMR058W = bart
+YER145C = bart
+YKL211C = bart
+YER090W = bart
+YNL113W = bart
+YPR110C = bart
+YLR191W = bart
+YGL153W = bart
+YNL214W = bart
+YDR244W = bart
+YDR142C = bart
+YDL078C = bart
+YIL160C = bart
+YER110C = bart
+YML007W = bart
+YDL088C = bart
+YBL079W = bart
+YGL202W = bart
+YGR074W = bart
+YBR043C = bart
diff --git a/distribution/src/main/sampleData/galFiltered.select.from.file.txt b/distribution/src/main/sampleData/galFiltered.select.from.file.txt
new file mode 100644
index 0000000..6a5dbf0
--- /dev/null
+++ b/distribution/src/main/sampleData/galFiltered.select.from.file.txt
@@ -0,0 +1,10 @@
+YKR026C
+YGR218W
+YGL097W
+YLR249W
+YLR293C
+YDR429C
+YBR118W
+YOL123W
+YPL211W
+YJL030W
diff --git a/distribution/src/main/sampleData/galFiltered.sif b/distribution/src/main/sampleData/galFiltered.sif
new file mode 100644
index 0000000..9e71eb5
--- /dev/null
+++ b/distribution/src/main/sampleData/galFiltered.sif
@@ -0,0 +1,362 @@
+YKR026C pp YGL122C
+YGR218W pp YGL097W
+YGL097W pp YOR204W
+YLR249W pp YPR080W
+YLR249W pp YBR118W
+YLR293C pp YGL097W
+YMR146C pp YDR429C
+YDR429C pp YFL017C
+YPR080W pp YAL003W
+YBR118W pp YAL003W
+YOL123W pp YGL044C
+YPL211W pp YGR014W
+YJL030W pp YGL229C
+YJL013C pp YGL229C
+YGL122C pp YOL123W
+YGR014W pp YJL030W
+YGR014W pp YJL013C
+YGR203W pp YIL061C
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diff --git a/distribution/src/main/sampleData/galFiltered.txt b/distribution/src/main/sampleData/galFiltered.txt
new file mode 100755
index 0000000..ef47648
--- /dev/null
+++ b/distribution/src/main/sampleData/galFiltered.txt
@@ -0,0 +1,362 @@
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+YER133W YMR311C pp TRUE abcd12527 1.2344543
+YER133W YBR050C pp TRUE abcd12528 1.2344543
+YGL035C YLR044C pd TRUE abcd12529 1.2344543
+YGL035C YLR377C pd TRUE abcd12530 1.2344543
+YGL035C YIL162W pd TRUE abcd12531 1.2344543
+YFL038C YOR036W pp TRUE abcd12532 1.2344543
+YOR355W YNL091W pp TRUE abcd12533 1.2344543
+YML074C YJL190C pp TRUE abcd12534 1.2344543
+YMR058W YER145C pp TRUE abcd12535 1.2344543
+YML123C YFR034C pd TRUE abcd12536 1.2344543
+YPL031C YHR071W pp TRUE abcd12537 1.2344543
+YAL038W YPL075W pd TRUE abcd12538 1.2344543
+YML051W YBR020W pp TRUE abcd12539 1.2344543
+YML051W YDR009W pp TRUE abcd12540 1.2344543
+YLL019C YIL113W pp TRUE abcd12541 1.2344543
+YML024W YNL216W pd TRUE abcd12542 1.2344543
+YOR039W YOR303W pp TRUE abcd12543 1.2344543
+YER111C YMR043W pd TRUE abcd12544 1.2344543
+YDR146C YMR043W pd TRUE abcd12545 1.2344543
+YDR146C YGL035C pd TRUE abcd12546 1.2344543
+YKL211C YER090W pp TRUE abcd12547 1.2344543
+YDR354W YEL009C pd TRUE abcd12548 1.2344543
+YNL113W YPR110C pp TRUE abcd12549 1.2344543
+YLR310C YER103W pp TRUE abcd12550 1.2344543
+YNL047C YIL105C pp TRUE abcd12551 1.2344543
+YBR160W YMR043W pd TRUE abcd12552 1.2344543
+YBR160W YGR108W pp TRUE abcd12553 1.2344543
+YIL113W YHR030C pp TRUE abcd12554 1.2344543
+YLR117C YBR190W pp TRUE abcd12555 1.2344543
+YFL017C YOL059W pp TRUE abcd12556 1.2344543
+YFL017C YER102W pp TRUE abcd12557 1.2344543
+YFL017C YOR362C pp TRUE abcd12558 1.2344543
+YMR044W YIL061C pp TRUE abcd12559 1.2344543
+YOL149W YOR167C pp TRUE abcd12560 1.2344543
+YOR036W YDR100W pp TRUE abcd12561 1.2344543
+YOR036W YGL161C pp TRUE abcd12562 1.2344543
+YLR191W YGL153W pp TRUE abcd12563 1.2344543
+YER110C YML007W pp TRUE abcd12564 1.2344543
+YBR135W YER102W pp TRUE abcd12565 1.2344543
+YNL214W YGL153W pp TRUE abcd12566 1.2344543
+YJR060W YPR167C pd TRUE abcd12567 1.2344543
+YOR089C YDR323C pp TRUE abcd12568 1.2344543
+YNL117W YJL089W pd TRUE abcd12569 1.2344543
+YLR175W YNL307C pp TRUE abcd12570 1.2344543
+YDR167W YLR432W pp TRUE abcd12571 1.2344543
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+YDR244W YLR191W pp TRUE abcd12573 1.2344543
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+YDR142C YIL160C pp TRUE abcd12580 1.2344543
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+YDR009W YGL035C pd TRUE abcd12582 1.2344543
+YPL248C YBR019C pd TRUE abcd12583 1.2344543
+YPL248C ? pd TRUE abcd12584 1.2344543
+YPL248C YJR048W pd TRUE abcd12585 1.2344543
+YPL248C YGL035C pd TRUE abcd12586 1.2344543
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+YPL248C YLR081W pd TRUE abcd12590 1.2344543
+YPL248C YBR018C pd TRUE abcd12591 1.2344543
+YAR007C YML032C pp TRUE abcd12592 1.2344543
+YAR007C YPL111W pd TRUE abcd12593 1.2344543
+YKL161C YPL089C pp TRUE abcd12594 1.2344543
+YNL312W YPL111W pd TRUE abcd12595 1.2344543
+YLR075W YPR102C pp TRUE abcd12596 1.2344543
+YLR229C YJL157C pp TRUE abcd12597 1.2344543
+YPL240C YBR155W pp TRUE abcd12598 1.2344543
+YPL240C YOR036W pp TRUE abcd12599 1.2344543
+YOL156W YBL005W pd TRUE abcd12600 1.2344543
+YML064C YHR198C pp TRUE abcd12601 1.2344543
+YML064C YLR284C pp TRUE abcd12602 1.2344543
+YML064C YDR174W pp TRUE abcd12603 1.2344543
+YER052C YNL135C pp TRUE abcd12604 1.2344543
+YPR124W YMR021C pd TRUE abcd12605 1.2344543
+YGL166W YHR053C pd TRUE abcd12606 1.2344543
+YGL166W YHR055C pd TRUE abcd12607 1.2344543
+YGL134W YPL031C pp TRUE abcd12608 1.2344543
+YGL134W YLR258W pp TRUE abcd12609 1.2344543
+YJL194W YMR043W pd TRUE abcd12610 1.2344543
+YLR264W YER112W pp TRUE abcd12611 1.2344543
+YLR264W YOL149W pp TRUE abcd12612 1.2344543
+YLR264W YBL026W pp TRUE abcd12613 1.2344543
+YBL050W YOR036W pp TRUE abcd12614 1.2344543
+YNL145W YCL067C pd TRUE abcd12615 1.2344543
+YNL145W YHR084W pd TRUE abcd12616 1.2344543
+YBR274W YMR255W pp TRUE abcd12617 1.2344543
+YLR452C YHR005C pp TRUE abcd12618 1.2344543
+YDR299W YJL194W pd TRUE abcd12619 1.2344543
+YIL074C YNL311C pp TRUE abcd12620 1.2344543
+YLR319C YLR362W pp TRUE abcd12621 1.2344543
+YGL073W YOR178C pp TRUE abcd12622 1.2344543
+YGL073W YHR053C pd TRUE abcd12623 1.2344543
+YGL073W YHR055C pd TRUE abcd12624 1.2344543
+YGL073W YER103W pd TRUE abcd12625 1.2344543
+YOR120W YPL248C pd TRUE abcd12626 1.2344543
+YPR041W YOR361C pp TRUE abcd12627 1.2344543
+YPR041W YMR309C pp TRUE abcd12628 1.2344543
+YNL135C YDR174W pp TRUE abcd12629 1.2344543
+YBR217W YNR007C pp TRUE abcd12630 1.2344543
+YMR255W YGL122C pp TRUE abcd12631 1.2344543
+YLR258W YIL045W pp TRUE abcd12632 1.2344543
+YLR258W YBR274W pp TRUE abcd12633 1.2344543
+YDL215C YER040W pd TRUE abcd12634 1.2344543
+YDL215C YLR432W pp TRUE abcd12635 1.2344543
+YER079W YHR135C pp TRUE abcd12636 1.2344543
+YER079W YNL154C pp TRUE abcd12637 1.2344543
+YDL030W YDL013W pp TRUE abcd12638 1.2344543
+YDL030W YMR005W pp TRUE abcd12639 1.2344543
+YLR362W YER124C pp TRUE abcd12640 1.2344543
+YLR362W YMR186W pp TRUE abcd12641 1.2344543
+YLR362W YPL240C pp TRUE abcd12642 1.2344543
+YHR084W YMR043W pp TRUE abcd12643 1.2344543
+YHR084W YDR461W pd TRUE abcd12644 1.2344543
+YHR084W YFL026W pd TRUE abcd12645 1.2344543
+YGR085C YLR075W pp TRUE abcd12646 1.2344543
+YGR085C YDR395W pp TRUE abcd12647 1.2344543
+YKL074C YGL035C pp TRUE abcd12648 1.2344543
+YGR088W YLR256W pd TRUE abcd12649 1.2344543
+YER081W YIL074C pp TRUE abcd12650 1.2344543
+YPR113W YMR043W pd TRUE abcd12651 1.2344543
+YIL070C YML054C pp TRUE abcd12652 1.2344543
+YIL061C YDL013W pp TRUE abcd12653 1.2344543
+YIL061C YNL199C pp TRUE abcd12654 1.2344543
+YIL061C YLR153C pp TRUE abcd12655 1.2344543
+YGR046W YNL236W pp TRUE abcd12656 1.2344543
+YNL091W YNL164C pp TRUE abcd12657 1.2344543
+YHR030C YLL021W pp TRUE abcd12658 1.2344543
+YHR030C YER111C pp TRUE abcd12659 1.2344543
+YPR048W YOR355W pp TRUE abcd12660 1.2344543
+YPR048W YDL215C pp TRUE abcd12661 1.2344543
+YHR005C YLR362W pp TRUE abcd12662 1.2344543
+YDR070C YFL017C pp TRUE abcd12663 1.2344543
+YJL157C YAL040C pp TRUE abcd12664 1.2344543
+YJL157C YOR212W pp TRUE abcd12665 1.2344543
+YNL036W YIR009W pp TRUE abcd12666 1.2344543
+YML114C YDR167W pp TRUE abcd12667 1.2344543
+YMR117C YCL032W pp TRUE abcd12668 1.2344543
+YMR117C YPR010C pp TRUE abcd12669 1.2344543
+YHR115C YOR215C pp TRUE abcd12670 1.2344543
+YGR009C YAL030W pp TRUE abcd12671 1.2344543
+YGR009C YOR327C pp TRUE abcd12672 1.2344543
+YGR009C YDR335W pp TRUE abcd12673 1.2344543
+YGR009C YBL050W pp TRUE abcd12674 1.2344543
+YDL088C YER110C pp TRUE abcd12675 1.2344543
+YLR197W YDL014W pp TRUE abcd12676 1.2344543
+YLR197W YOR310C pp TRUE abcd12677 1.2344543
+YGL202W YGR074W pp TRUE abcd12678 1.2344543
+YIL162W YNL167C pd TRUE abcd12679 1.2344543
+YBR170C YGR048W pp TRUE abcd12680 1.2344543
+YOR212W YLR362W pp TRUE abcd12681 1.2344543
+YDR103W YLR362W pp TRUE abcd12682 1.2344543
+YDL023C YJL159W pp TRUE abcd12683 1.2344543
+YGR136W YGR058W pp TRUE abcd12684 1.2344543
+YBR109C YOR326W pp TRUE abcd12685 1.2344543
+YBR109C YFR014C pp TRUE abcd12686 1.2344543
+YDR395W YDL075W pp TRUE abcd12687 1.2344543
+YDR395W YIL133C pp TRUE abcd12688 1.2344543
+YDR395W YNL069C pp TRUE abcd12689 1.2344543
+YDR395W YER056CA pp TRUE abcd12690 1.2344543
+YDR395W YIL052C pp TRUE abcd12691 1.2344543
+YDR395W YOL127W pp TRUE abcd12692 1.2344543
+YDR395W YPR102C pp TRUE abcd12693 1.2344543
+YLR345W YLR321C pp TRUE abcd12694 1.2344543
+YBL079W YDL088C pp TRUE abcd12695 1.2344543
+YBR045C YIL045W pp TRUE abcd12696 1.2344543
+YBR045C YOR178C pp TRUE abcd12697 1.2344543
+YER054C YER133W pp TRUE abcd12698 1.2344543
+YER054C YBR045C pp TRUE abcd12699 1.2344543
+YPR145W YMR117C pp TRUE abcd12700 1.2344543
+YNR053C YJL203W pp TRUE abcd12701 1.2344543
+YNR053C YDL030W pp TRUE abcd12702 1.2344543
+YGR074W YBR043C pp TRUE abcd12703 1.2344543
+YDR277C YJR022W pp TRUE abcd12704 1.2344543
+YDR277C YDL194W pp TRUE abcd12705 1.2344543
+YBL026W YOR167C pp TRUE abcd12706 1.2344543
diff --git a/distribution/src/main/sampleData/galFiltered.xgmml b/distribution/src/main/sampleData/galFiltered.xgmml
new file mode 100644
index 0000000..1f75e8d
--- /dev/null
+++ b/distribution/src/main/sampleData/galFiltered.xgmml
@@ -0,0 +1,27388 @@
+<?xml version='1.0'?>
+<graph id="Yeast Network (galFiltered.gml)" label="Yeast Network (galFiltered.gml)" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:ns1="http://www.w3.org/1999/xlink" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns="http://www.cs.rpi.edu/XGMML">
+ <att name="documentVersion" value="1.0"/>
+ <att name="networkMetadata">
+ <rdf:RDF>
+ <rdf:Description rdf:about="http://www.cytoscape.org/">
+ <dc:type>Protein-Protein Interaction</dc:type>
+ <dc:description>This XGMML file is created from the following data sets:
+
+<Network>
+galFiltered.gml
+
+<Attributes>
+galExpData.pvals
+gene_ontology.obo
+gene_association.sgd
+
+
+These files contain an interaction network and expression data from the paper:
+
+Ideker, T., Thorsson V, Ranish JA, Christmas R, Buhler J, Eng JK, Bumgarner R,
+Goodlett DR, Aebersold R, Hood L. Integrated genomic and proteomic analyses of
+a systematically perturbed metabolic network. Science, 292, 929-34 (2001).
+
+The 'galExpData.pvals' file contains 20 experimental conditions involving
+systematic perturbations of the galactose utilization pathway in yeast.
+The 'galFiltered.*' files contain an interaction network of 331 genes that
+were significantly differentially expressed in at least one of the 20
+experimental conditions.</dc:description>
+ <dc:date>2006-05-31 15:02:11</dc:date>
+ <dc:identifier>N/A</dc:identifier>
+ <dc:title>Yeast Network (galFiltered.gml)</dc:title>
+ <dc:source>http://chianti.ucsd.edu/idekerlab/</dc:source>
+ <dc:format>Cytoscape-XGMML</dc:format>
+ </rdf:Description>
+ </rdf:RDF>
+ </att>
+ <att name="backgroundColor" value="#9999ff"/>
+ <att label="documentVersion" name="documentVersion" value="1.0" type="string"/>
+ <att label="GRAPH_VIEW_ZOOM" name="GRAPH_VIEW_ZOOM" value="1.0604413437252773" type="real"/>
+ <att label="GRAPH_VIEW_CENTER_X" name="GRAPH_VIEW_CENTER_X" value="2741.2107899524485" type="real"/>
+ <att label="GRAPH_VIEW_CENTER_Y" name="GRAPH_VIEW_CENTER_Y" value="1866.0783074060714" type="real"/>
+ <node id="-331" label="YBR043C" name="base">
+ <att label="gal1RGexp" name="gal1RGexp" value="0.454" type="real"/>
+ <att label="gal4RGexp" name="gal4RGexp" value="0.023" type="real"/>
+ <att label="gal1RGsig" name="gal1RGsig" value="5.373E-8" type="real"/>
+ <att label="gal80Rexp" name="gal80Rexp" value="0.0" type="real"/>
+ <att label="canonicalName" name="canonicalName" value="YBR043C" type="string"/>
+ <att label="gal4RGsig" name="gal4RGsig" value="0.94178" type="real"/>
+ <att label="GO Aliases" name="GO Aliases" type="list">
+ <att value="AQR2" type="string"/>
+ <att value="QDR3" type="string"/>
+ </att>
+ <att label="GO Cellular Component" name="GO Cellular Component" type="list">
+ <att value="cell" type="string"/>
+ <att value="cell part" type="string"/>
+ <att value="integral to membrane" type="string"/>
+ <att value="integral to plasma membrane" type="string"/>
+ <att value="intrinsic to membrane" type="string"/>
+ <att value="intrinsic to plasma membrane" type="string"/>
+ <att value="membrane" type="string"/>
+ <att value="membrane part" type="string"/>
+ <att value="plasma membrane" type="string"/>
+ <att value="plasma membrane part" type="string"/>
+ </att>
+ <att label="gal80Rsig" name="gal80Rsig" value="0.999999" type="real"/>
+ <att label="GO Biological Process" name="GO Biological Process" type="list">
+ <att value="cellular physiological process" type="string"/>
+ <att value="cellular process" type="string"/>
+ <att value="drug transport" type="string"/>
+ <att value="establishment of localization" type="string"/>
+ <att value="localization" type="string"/>
+ <att value="multidrug transport" type="string"/>
+ <att value="physiological process" type="string"/>
+ <att value="response to abiotic stimulus" type="string"/>
+ <att value="response to chemical stimulus" type="string"/>
+ <att value="response to drug" type="string"/>
+ <att value="response to stimulus" type="string"/>
+ <att value="transport" type="string"/>
+ </att>
+ <att label="GO Common Name" name="GO Common Name" value="QDR3" type="string"/>
+ <att label="GO Molecular Function" name="GO Molecular Function" type="list">
+ <att value="drug transporter activity" type="string"/>
+ <att value="multidrug efflux pump activity" type="string"/>
+ <att value="multidrug transporter activity" type="string"/>
+ <att value="transporter activity" type="string"/>
+ </att>
+ <att label="species" name="species" value="Saccharomyces cerevisiae" type="string"/>
+ <graphics width="1" fill="#fcfffd" outline="#000000" x="1265.0" y="4817.0" h="40.0" w="40.0">
+ <att name="cytoscapeNodeGraphicsAttributes">
+ <att name="nodeTransparency" value="1.0"/>
+ <att name="nodeLabelFont" value="Default-0-12"/>
+ <att name="borderLineType" value="solid"/>
+ </att>
+ </graphics>
+ </node>
+ <node id="-330" label="YGR074W" name="base">
+ <att label="gal1RGexp" name="gal1RGexp" value="-0.074" type="real"/>
+ <att label="gal4RGexp" name="gal4RGexp" value="-0.133" type="real"/>
+ <att label="gal1RGsig" name="gal1RGsig" value="0.11939" type="real"/>
+ <att label="gal80Rexp" name="gal80Rexp" value="0.029" type="real"/>
+ <att label="canonicalName" name="canonicalName" value="YGR074W" type="string"/>
+ <att label="gal4RGsig" name="gal4RGsig" value="0.08221" type="real"/>
+ <att label="GO Aliases" name="GO Aliases" type="list">
+ <att value="D1" type="string"/>
+ <att value="SMD1" type="string"/>
+ <att value="SPP92" type="string"/>
+ <att value="Sm" type="string"/>
+ </att>
+ <att label="GO Cellular Component" name="GO Cellular Component" type="list">
+ <att value="U4/U6 x U5 tri-snRNP complex" type="string"/>
+ <att value="cell" type="string"/>
+ <att value="cell part" type="string"/>
+ <att value="commitment complex" type="string"/>
+ <att value="intracellular" type="string"/>
+ <att value="intracellular membrane-bound organelle" type="string"/>
+ <att value="intracellular organelle" type="string"/>
+ <att value="intracellular organelle part" type="string"/>
+ <att value="intracellular part" type="string"/>
+ <att value="major (U2-dependent) spliceosome" type="string"/>
+ <att value="membrane-bound organelle" type="string"/>
+ <att value="minor (U12-dependent) spliceosome complex" type="string"/>
+ <att value="nuclear part" type="string"/>
+ <att value="nucleus" type="string"/>
+ <att value="organelle" type="string"/>
+ <att value="organelle part" type="string"/>
+ <att value="protein complex" type="string"/>
+ <att value="ribonucleoprotein complex" type="string"/>
+ <att value="small nuclear ribonucleoprotein complex" type="string"/>
+ <att value="snRNP U1" type="string"/>
+ <att value="snRNP U5" type="string"/>
+ <att value="spliceosome complex" type="string"/>
+ </att>
+ <att label="gal80Rsig" name="gal80Rsig" value="0.80755" type="real"/>
+ <att label="GO Biological Process" name="GO Biological Process" type="list">
+ <att value="RNA metabolism" type="string"/>
+ <att value="RNA processing" type="string"/>
+ <att value="RNA splicing" type="string"/>
+ <att value="RNA splicing, via transesterification reactions" type="string"/>
+ <att value="RNA splicing, via transesterification reactions with bulged adenosine as nucleophile" type="string"/>
+ <att value="biopolymer metabolism" type="string"/>
+ <att value="cellular metabolism" type="string"/>
+ <att value="cellular physiological process" type="string"/>
+ <att value="cellular process" type="string"/>
+ <att value="mRNA metabolism" type="string"/>
+ <att value="mRNA processing" type="string"/>
+ <att value="macromolecule metabolism" type="string"/>
+ <att value="metabolism" type="string"/>
+ <att value="nuclear mRNA splicing, via spliceosome" type="string"/>
+ <att value="nucleobase, nucleoside, nucleotide and nucleic acid metabolism" type="string"/>
+ <att value="physiological process" type="string"/>
+ <att value="primary metabolism" type="string"/>
+ </att>
+ <att label="GO Common Name" name="GO Common Name" value="SMD1" type="string"/>
+ <att label="GO Molecular Function" name="GO Molecular Function" type="list">
+ <att value="RNA binding" type="string"/>
+ <att value="RNA splicing factor activity, transesterification mechanism" type="string"/>
+ <att value="binding" type="string"/>
+ <att value="mRNA binding" type="string"/>
+ <att value="nucleic acid binding" type="string"/>
+ </att>
+ <att label="species" name="species" value="Saccharomyces cerevisiae" type="string"/>
+ <graphics width="1" fill="#fff1f1" outline="#000000" x="1428.0" y="4753.0" h="40.0" w="40.0">
+ <att name="cytoscapeNodeGraphicsAttributes">
+ <att name="nodeTransparency" value="1.0"/>
+ <att name="nodeLabelFont" value="Default-0-12"/>
+ <att name="borderLineType" value="solid"/>
+ </att>
+ </graphics>
+ </node>
+ <node id="-329" label="YGL202W" name="base">
+ <att label="gal1RGexp" name="gal1RGexp" value="-0.305" type="real"/>
+ <att label="gal4RGexp" name="gal4RGexp" value="-0.286" type="real"/>
+ <att label="gal1RGsig" name="gal1RGsig" value="4.2677E-7" type="real"/>
+ <att label="gal80Rexp" name="gal80Rexp" value="-0.536" type="real"/>
+ <att label="canonicalName" name="canonicalName" value="YGL202W" type="string"/>
+ <att label="gal4RGsig" name="gal4RGsig" value="4.2373E-5" type="real"/>
+ <att label="GO Aliases" name="GO Aliases" type="list">
+ <att value="ARO8" type="string"/>
+ </att>
+ <att label="GO Cellular Component" name="GO Cellular Component" type="list">
+ <att value="cell" type="string"/>
+ <att value="cell part" type="string"/>
+ <att value="cytoplasm" type="string"/>
+ <att value="intracellular" type="string"/>
+ <att value="intracellular part" type="string"/>
+ </att>
+ <att label="gal80Rsig" name="gal80Rsig" value="3.8938E-13" type="real"/>
+ <att label="GO Biological Process" name="GO Biological Process" type="list">
+ <att value="amine metabolism" type="string"/>
+ <att value="amino acid and derivative metabolism" type="string"/>
+ <att value="amino acid metabolism" type="string"/>
+ <att value="aromatic amino acid family metabolism" type="string"/>
+ <att value="aromatic compound metabolism" type="string"/>
+ <att value="carboxylic acid metabolism" type="string"/>
+ <att value="cellular metabolism" type="string"/>
+ <att value="cellular physiological process" type="string"/>
+ <att value="cellular process" type="string"/>
+ <att value="metabolism" type="string"/>
+ <att value="nitrogen compound metabolism" type="string"/>
+ <att value="organic acid metabolism" type="string"/>
+ <att value="physiological process" type="string"/>
+ <att value="primary metabolism" type="string"/>
+ </att>
+ <att label="GO Common Name" name="GO Common Name" value="ARO8" type="string"/>
+ <att label="GO Molecular Function" name="GO Molecular Function" type="list">
+ <att value="aromatic-amino-acid transaminase activity" type="string"/>
+ <att value="catalytic activity" type="string"/>
+ <att value="transaminase activity" type="string"/>
+ <att value="transferase activity" type="string"/>
+ <att value="transferase activity, transferring nitrogenous groups" type="string"/>
+ </att>
+ <att label="species" name="species" value="Saccharomyces cerevisiae" type="string"/>
+ <graphics width="1" fill="#ffe2e2" outline="#000000" x="1484.0" y="4680.0" h="40.0" w="40.0">
+ <att name="cytoscapeNodeGraphicsAttributes">
+ <att name="nodeTransparency" value="1.0"/>
+ <att name="nodeLabelFont" value="Default-0-12"/>
+ <att name="borderLineType" value="solid"/>
+ </att>
+ </graphics>
+ </node>
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diff --git a/distribution/src/main/sampleData/galFiltered.xls b/distribution/src/main/sampleData/galFiltered.xls
new file mode 100755
index 0000000..a32578a
Binary files /dev/null and b/distribution/src/main/sampleData/galFiltered.xls differ
diff --git a/distribution/src/main/sampleData/galFiltered2.xgmml b/distribution/src/main/sampleData/galFiltered2.xgmml
new file mode 100644
index 0000000..0629648
--- /dev/null
+++ b/distribution/src/main/sampleData/galFiltered2.xgmml
@@ -0,0 +1,17902 @@
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+ <dc:description>N/A</dc:description>
+ <dc:date>2006-02-17 16:39:29</dc:date>
+ <dc:identifier>N/A</dc:identifier>
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diff --git a/distribution/src/main/sampleData/galFiltered25.cys b/distribution/src/main/sampleData/galFiltered25.cys
new file mode 100644
index 0000000..e3bba48
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diff --git a/distribution/src/main/sampleData/galFilteredAnnotated.xgmml b/distribution/src/main/sampleData/galFilteredAnnotated.xgmml
new file mode 100644
index 0000000..186685e
--- /dev/null
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+ <att value="YFL017C (pp) YOR362C" label="string" name="canonicalName"/>
+ <graphics width="2" fill="#0000e1">
+ <att name="cytoscapeEdgeGraphicsAttributes">
+ <att value="0" name="sourceArrow"/>
+ <att value="0" name="targetArrow"/>
+ <att value="Default-0-10" name="edgeLabelFont"/>
+ <att value="2" name="edgeLineType"/>
+ </att>
+ </graphics>
+ </edge>
+ <edge id="YFL017C (pp) YER102W" label="YFL017C (pp) YER102W" source="-5" target="-184">
+ <att value="pp" label="string" name="interaction"/>
+ <att value="YFL017C (pp) YER102W" label="string" name="canonicalName"/>
+ <graphics width="2" fill="#0000e1">
+ <att name="cytoscapeEdgeGraphicsAttributes">
+ <att value="0" name="sourceArrow"/>
+ <att value="0" name="targetArrow"/>
+ <att value="Default-0-10" name="edgeLabelFont"/>
+ <att value="2" name="edgeLineType"/>
+ </att>
+ </graphics>
+ </edge>
+ <edge id="YFL017C (pp) YOL059W" label="YFL017C (pp) YOL059W" source="-5" target="-183">
+ <att value="pp" label="string" name="interaction"/>
+ <att value="YFL017C (pp) YOL059W" label="string" name="canonicalName"/>
+ <graphics width="2" fill="#0000e1">
+ <att name="cytoscapeEdgeGraphicsAttributes">
+ <att value="0" name="sourceArrow"/>
+ <att value="0" name="targetArrow"/>
+ <att value="Default-0-10" name="edgeLabelFont"/>
+ <att value="2" name="edgeLineType"/>
+ </att>
+ </graphics>
+ </edge>
+ <edge id="YDR429C (pp) YFL017C" label="YDR429C (pp) YFL017C" source="-4" target="-5">
+ <att value="pp" label="string" name="interaction"/>
+ <att value="YDR429C (pp) YFL017C" label="string" name="canonicalName"/>
+ <graphics width="2" fill="#0000e1">
+ <att name="cytoscapeEdgeGraphicsAttributes">
+ <att value="0" name="sourceArrow"/>
+ <att value="0" name="targetArrow"/>
+ <att value="Default-0-10" name="edgeLabelFont"/>
+ <att value="2" name="edgeLineType"/>
+ </att>
+ </graphics>
+ </edge>
+ <edge id="YMR146C (pp) YDR429C" label="YMR146C (pp) YDR429C" source="-3" target="-4">
+ <att value="pp" label="string" name="interaction"/>
+ <att value="YMR146C (pp) YDR429C" label="string" name="canonicalName"/>
+ <graphics width="2" fill="#0000e1">
+ <att name="cytoscapeEdgeGraphicsAttributes">
+ <att value="0" name="sourceArrow"/>
+ <att value="0" name="targetArrow"/>
+ <att value="Default-0-10" name="edgeLabelFont"/>
+ <att value="2" name="edgeLineType"/>
+ </att>
+ </graphics>
+ </edge>
+ <edge id="YGL122C (pp) YOL123W" label="YGL122C (pp) YOL123W" source="-2" target="-6">
+ <att value="pp" label="string" name="interaction"/>
+ <att value="YGL122C (pp) YOL123W" label="string" name="canonicalName"/>
+ <graphics width="2" fill="#0000e1">
+ <att name="cytoscapeEdgeGraphicsAttributes">
+ <att value="0" name="sourceArrow"/>
+ <att value="0" name="targetArrow"/>
+ <att value="Default-0-10" name="edgeLabelFont"/>
+ <att value="2" name="edgeLineType"/>
+ </att>
+ </graphics>
+ </edge>
+ <edge id="YKR026C (pp) YGL122C" label="YKR026C (pp) YGL122C" source="-1" target="-2">
+ <att value="pp" label="string" name="interaction"/>
+ <att value="YKR026C (pp) YGL122C" label="string" name="canonicalName"/>
+ <graphics width="2" fill="#0000e1">
+ <att name="cytoscapeEdgeGraphicsAttributes">
+ <att value="0" name="sourceArrow"/>
+ <att value="0" name="targetArrow"/>
+ <att value="Default-0-10" name="edgeLabelFont"/>
+ <att value="2" name="edgeLineType"/>
+ </att>
+ </graphics>
+ </edge>
+</graph>
+
diff --git a/distribution/src/main/sampleData/galFiltered_int_edge_attr.ea b/distribution/src/main/sampleData/galFiltered_int_edge_attr.ea
new file mode 100644
index 0000000..fc913a2
--- /dev/null
+++ b/distribution/src/main/sampleData/galFiltered_int_edge_attr.ea
@@ -0,0 +1,363 @@
+Continuous edge Attr1
+YFL017C (pp) YER102W = 38
+YBR160W (pd) YMR043W = 205
+YGR058W (pp) YOR264W = 147
+YGL097W (pp) YOR204W = 202
+YLR256W (pd) YML054C = 297
+YPR113W (pd) YMR043W = 352
+YBR045C (pp) YOR178C = 280
+YMR043W (pd) YJL157C = 91
+YIL162W (pd) YNL167C = 218
+YLR256W (pd) YJR048W = 153
+YDL081C (pp) YLR340W = 124
+YJL194W (pd) YMR043W = 45
+YPL248C (pd) ? = 48
+YNL216W (pd) YLR044C = 21
+YDR395W (pp) YIL052C = 66
+YLR258W (pp) YIL045W = 361
+YBR217W (pp) YNR007C = 152
+YKL109W (pp) YBL021C = 114
+YNL145W (pd) YHR084W = 163
+YNL216W (pd) YNL301C = 71
+YER040W (pd) YPR035W = 58
+YCL067C (pd) YFL026W = 196
+YLR321C (pp) YDR412W = 133
+YJR066W (pp) YLR116W = 116
+YPL075W (pd) YGR254W = 354
+YFR034C (pd) YBR093C = 174
+YPL248C (pd) YLR081W = 233
+YCL067C (pd) YIL015W = 284
+YDL030W (pp) YMR005W = 94
+YCL067C (pp) YMR043W = 136
+YCL032W (pp) YDR032C = 93
+YDR412W (pp) YPR119W = 15
+YML032C (pp) YNL312W = 135
+YBL079W (pp) YDL088C = 171
+YNR053C (pp) YJL203W = 127
+YPL075W (pp) YNL199C = 56
+YMR043W (pd) YFL026W = 265
+YOR089C (pp) YDR323C = 290
+YML064C (pp) YLR284C = 172
+YOR355W (pp) YNL091W = 69
+YDL063C (pp) YPL131W = 167
+YDR299W (pd) YJL194W = 204
+YMR043W (pd) YIL015W = 27
+YBR170C (pp) YGR048W = 132
+YNL098C (pp) YLR310C = 229
+YKL109W (pd) YGL035C = 176
+YBL069W (pp) YGL008C = 341
+YHR030C (pp) YER111C = 353
+YOL051W (pd) YBR020W = 134
+YNL216W (pp) YDR171W = 103
+YEL009C (pd) YOL058W = 96
+YER111C (pd) YMR043W = 32
+YEL009C (pd) YCL030C = 128
+YGL013C (pd) YOL156W = 340
+YDR167W (pp) YLR432W = 177
+YNL199C (pp) YPR048W = 339
+YNL113W (pp) YPR110C = 62
+YMR044W (pp) YIL061C = 113
+YML051W (pp) YBR020W = 285
+YGR085C (pp) YLR075W = 211
+YBR160W (pp) YGR108W = 68
+YDR323C (pp) YOR036W = 191
+YGL134W (pp) YPL031C = 131
+YGR014W (pp) YJL013C = 292
+YPL248C (pp) YML051W = 175
+YMR117C (pp) YCL032W = 173
+YIL143C (pp) YDR311W = 320
+YCR084C (pp) YBR112C = 145
+YPL075W (pd) YHR174W = 201
+YDR244W (pp) YGL153W = 97
+YLR310C (pp) YER103W = 107
+YDR395W (pp) YNL069C = 4
+YEL009C (pd) YBR248C = 241
+YOL149W (pp) YOR167C = 358
+YNL117W (pd) YJL089W = 344
+YFL038C (pp) YOR036W = 243
+YPL089C (pp) YHR030C = 67
+YIR009W (pp) YIL143C = 264
+YOR036W (pp) YDR100W = 146
+YMR186W (pp) YBR155W = 273
+YCL067C (pd) YDR461W = 350
+YOR327C (pp) YER143W = 109
+YML024W (pd) YNL216W = 348
+YGL073W (pp) YOR178C = 238
+YGL035C (pd) YIL162W = 81
+YNL216W (pd) YIL133C = 5
+YLR116W (pp) YKL012W = 70
+YNL189W (pp) YPL111W = 180
+YJR022W (pp) YEL015W = 92
+YJL089W (pd) YLR377C = 215
+YGL073W (pd) YHR055C = 313
+YPR119W (pd) YMR043W = 303
+YHR005C (pp) YLR362W = 169
+YMR043W (pd) YDR461W = 85
+YJR109C (pp) YOR303W = 318
+YLR293C (pp) YGL097W = 25
+YLR362W (pp) YER124C = 18
+YGR203W (pp) YIL061C = 190
+YDR244W (pp) YNL214W = 311
+YGL035C (pd) YLR377C = 275
+YOR120W (pd) YPL248C = 55
+YNR050C (pp) YMR138W = 52
+YDR395W (pp) YOL127W = 267
+YJL203W (pp) YOL136C = 159
+YJR022W (pp) YNL050C = 236
+YDR244W (pp) YDL078C = 11
+YPL031C (pp) YHR071W = 36
+YGR218W (pp) YGL097W = 203
+YFL017C (pp) YOR362C = 252
+YNL047C (pp) YIL105C = 331
+YER112W (pp) YOR167C = 170
+YER133W (pp) YMR311C = 306
+YMR309C (pp) YNL047C = 120
+YOL058W (pp) YNL189W = 155
+YLR319C (pp) YLR362W = 294
+YER110C (pp) YML007W = 84
+YNL216W (pd) YGR254W = 106
+YGL134W (pp) YLR258W = 332
+YBR135W (pp) YER102W = 317
+YPL075W (pd) YCR012W = 138
+YML123C (pd) YFR034C = 49
+YPL248C (pd) YGL035C = 130
+YAL040C (pd) YMR043W = 228
+YGR085C (pp) YDR395W = 117
+YJL089W (pd) YKR097W = 6
+YLR264W (pp) YOL149W = 342
+YPR048W (pp) YDL215C = 309
+YJL157C (pp) YAL040C = 31
+YPL211W (pp) YGR014W = 319
+YER052C (pp) YNL135C = 225
+YBR109C (pp) YOR326W = 198
+YDR412W (pp) YCR086W = 104
+YBR045C (pp) YIL045W = 63
+YOR212W (pp) YLR362W = 212
+YDL088C (pp) YER110C = 73
+YOR326W (pp) YGL106W = 269
+YER133W (pp) YOR178C = 89
+YLR452C (pp) YHR005C = 325
+YPR041W (pp) YMR309C = 1
+YLR362W (pp) YMR186W = 230
+YER040W (pd) YGR019W = 276
+YCL032W (pp) YLR362W = 308
+YGL073W (pd) YHR053C = 99
+YCL030C (pd) YKR099W = 8
+YFL039C (pp) YHR179W = 160
+YDR142C (pp) YIL160C = 302
+YIL070C (pp) YML054C = 214
+YMR291W (pp) YGL115W = 312
+? (pd) YKR099W = 185
+YER133W (pp) YOR315W = 305
+YLR345W (pp) YLR321C = 194
+YNL312W (pd) YPL111W = 139
+YGL122C (pp) YOL123W = 270
+YDR184C (pp) YLR319C = 199
+YNL135C (pp) YDR174W = 119
+YML064C (pp) YHR198C = 321
+YNL091W (pp) YNL164C = 251
+YLR075W (pp) YPR102C = 355
+YNL216W (pd) YIL069C = 219
+YNL216W (pd) YHR174W = 262
+YMR146C (pp) YDR429C = 349
+YCL032W (pp) YDR103W = 154
+YNL216W (pd) YOL120C = 224
+YEL009C (pd) YMR108W = 53
+YOR361C (pp) YDR429C = 322
+YDR429C (pp) YFL017C = 231
+YIL113W (pp) YHR030C = 221
+YOL156W (pd) YBL005W = 282
+YBR274W (pp) YMR255W = 296
+YJL036W (pp) YDL113C = 242
+YER054C (pp) YER133W = 14
+YNL216W (pd) YCL030C = 272
+YGL073W (pd) YER103W = 162
+YGR108W (pp) YBR135W = 226
+YDL023C (pp) YJL159W = 260
+YPR145W (pp) YMR117C = 83
+YNL189W (pp) YPR062W = 217
+YER062C (pp) YPL201C = 323
+YIR009W (pp) YKR099W = 44
+YLR197W (pp) YOR310C = 289
+YDR412W (pp) YLR117C = 166
+YLR229C (pp) YJL157C = 165
+YLR264W (pp) YBL026W = 188
+YPL248C (pd) YBR020W = 24
+YGL115W (pp) YGL208W = 50
+YER179W (pp) YLR134W = 268
+YPL240C (pp) YOR036W = 210
+YOR036W (pp) YGL161C = 345
+YPL149W (pp) YBR217W = 335
+YIL061C (pp) YDL013W = 100
+YGR046W (pp) YNL236W = 288
+YDL215C (pd) YER040W = 61
+YLR117C (pp) YBR190W = 10
+YIR009W (pp) YNL091W = 329
+YLL021W (pp) YLR362W = 3
+YNL036W (pp) YIR009W = 19
+YNL216W (pd) YER074W = 23
+YMR117C (pp) YPR010C = 240
+YNL216W (pd) YCR012W = 249
+YOL051W (pd) YBR018C = 43
+YBR072W (pd) YGL073W = 41
+YDR395W (pp) YIL133C = 151
+YER179W (pp) YIL105C = 123
+YGR014W (pp) YJL030W = 77
+YJL013C (pp) YGL229C = 338
+YDR395W (pp) YPR102C = 110
+YGR009C (pp) YDR335W = 261
+YNL216W (pd) YAL038W = 42
+YDR309C (pp) YLR229C = 140
+YDR146C (pd) YMR043W = 314
+YKL109W (pd) YJR048W = 327
+YDR382W (pp) YDL130W = 181
+YAR007C (pp) YML032C = 34
+YKL161C (pp) YPL089C = 156
+YJL157C (pp) YOR212W = 26
+YOR361C (pp) YMR309C = 111
+YDR277C (pp) YDL194W = 315
+YEL009C (pd) YMR300C = 307
+YDR244W (pp) YDR142C = 161
+YNL214W (pp) YGL153W = 125
+YJR022W (pp) YNR053C = 351
+YDR335W (pp) YDR174W = 253
+YGR088W (pd) YLR256W = 333
+YML064C (pp) YDR174W = 28
+YGR136W (pp) YGR058W = 22
+YKR026C (pp) YGL122C = 39
+YER054C (pp) YBR045C = 235
+YHR084W (pd) YFL026W = 102
+YAL030W (pp) YER143W = 200
+YDR382W (pp) YFL039C = 37
+YDR395W (pp) YDL075W = 299
+YDL030W (pp) YDL013W = 232
+YMR183C (pp) YGR009C = 82
+YHR084W (pp) YMR043W = 29
+YGL161C (pp) YDR100W = 246
+YDL215C (pp) YLR432W = 279
+YBL050W (pp) YOR036W = 178
+YDR311W (pp) YKL028W = 30
+YKL012W (pp) YKL074C = 283
+YDR277C (pp) YJR022W = 98
+YGL035C (pd) YLR044C = 54
+YPL075W (pd) YDR050C = 256
+YDR142C (pp) YGL153W = 88
+YEL041W (pp) YHR115C = 115
+YPL240C (pp) YBR155W = 359
+YNL311C (pp) YKL001C = 12
+YLR362W (pp) YPL240C = 78
+YPR048W (pp) YOR355W = 295
+YBR118W (pp) YAL003W = 208
+YBL005W (pd) YJL219W = 197
+YKL074C (pp) YGL035C = 20
+YER079W (pp) YNL154C = 207
+YLR197W (pp) YDL014W = 74
+YIR009W (pp) YDR184C = 121
+YMR138W (pp) YLR109W = 40
+? (pd) YGL035C = 57
+YMR021C (pd) YLR214W = 239
+YHR171W (pp) YDR412W = 79
+YOL051W (pd) YLR081W = 346
+YDR395W (pp) YER056CA = 209
+YIL074C (pp) YNL311C = 122
+YER116C (pp) YDL013W = 108
+YMR043W (pd) YGR108W = 247
+YDL014W (pp) YOR310C = 80
+YER079W (pp) YHR135C = 357
+YHR030C (pp) YLL021W = 137
+YNL189W (pp) YDL236W = 46
+YGL237C (pd) YJR048W = 72
+YNL145W (pd) YCL067C = 310
+YDR146C (pd) YGL035C = 164
+YNL167C (pd) YOR202W = 168
+YBR109C (pp) YFR014C = 60
+YMR043W (pd) YNL145W = 258
+YFR037C (pp) YOR290C = 271
+YML051W (pp) YDR009W = 141
+YDR244W (pp) YLR191W = 237
+YER081W (pp) YIL074C = 35
+YNL189W (pp) YER065C = 64
+YPL075W (pd) YOL086C = 105
+YMR058W (pp) YER145C = 347
+YGR048W (pp) YPL222W = 75
+YLR258W (pp) YBR274W = 216
+YPL248C (pd) YJR048W = 278
+YOL016C (pp) YBR109C = 326
+YFL017C (pp) YOL059W = 189
+YHR084W (pd) YDR461W = 245
+YJR022W (pp) YNR050C = 16
+YGL202W (pp) YGR074W = 293
+YKL211C (pp) YER090W = 149
+YEL015W (pp) YML064C = 360
+YLR249W (pp) YBR118W = 87
+YGL008C (pd) YMR043W = 263
+YGR009C (pp) YBL050W = 112
+YFL039C (pp) YCL040W = 158
+YGL166W (pd) YHR055C = 213
+YDR103W (pp) YLR362W = 330
+YER133W (pp) YDR412W = 356
+YLL019C (pp) YIL113W = 277
+YBL021C (pd) YJR048W = 179
+YHR115C (pp) YOR215C = 101
+YNL216W (pd) YBR093C = 192
+YGL013C (pd) YJL219W = 126
+YER133W (pp) YBR050C = 157
+YMR043W (pd) YKR097W = 65
+YDR354W (pd) YEL009C = 324
+YLL028W (pp) YGL166W = 337
+YML074C (pp) YJL190C = 143
+YER179W (pp) YLR044C = 47
+YBL026W (pp) YOR167C = 148
+YNL307C (pp) YAL038W = 291
+YHR135C (pp) YNL116W = 186
+YAL038W (pd) YPL075W = 266
+YMR043W (pd) YJL159W = 227
+YJL030W (pp) YGL229C = 7
+YGR009C (pp) YAL030W = 193
+YOR039W (pp) YOR303W = 90
+YIL061C (pp) YLR153C = 17
+YPR124W (pd) YMR021C = 287
+YPL248C (pd) YBR019C = 187
+YJR022W (pp) YLR264W = 142
+YPR080W (pp) YAL003W = 248
+YLR191W (pp) YGL153W = 362
+YNR053C (pp) YDL030W = 257
+YBR019C (pd) YOL051W = 220
+YLR175W (pp) YNL307C = 244
+YDR009W (pd) YGL035C = 328
+YKL101W (pp) YBR160W = 304
+YIL061C (pp) YNL199C = 250
+YCR084C (pp) YCL067C = 2
+YKL109W (pp) YGL237C = 254
+YNL216W (pd) YDR050C = 59
+YGR074W (pp) YBR043C = 300
+YPL248C (pd) YML051W = 334
+YCR012W (pd) YJR060W = 259
+YDR070C (pp) YFL017C = 182
+YJR060W (pd) YPR167C = 13
+YBR020W (pd) YGL035C = 301
+YBR019C (pd) YGL035C = 86
+YGL166W (pd) YHR053C = 223
+YPL248C (pd) YBR018C = 76
+YHR171W (pp) YNR007C = 286
+YGR009C (pp) YOR327C = 51
+YPL149W (pp) YHR171W = 118
+YMR138W (pp) YHR141C = 183
+YLR256W (pd) YEL039C = 9
+YOL123W (pp) YGL044C = 95
+YCR086W (pp) YOR264W = 281
+YNL154C (pp) YKL204W = 184
+YAR007C (pd) YPL111W = 255
+YMR255W (pp) YGL122C = 336
+YNL216W (pd) YOL127W = 234
+YPR041W (pp) YOR361C = 144
+YLR249W (pp) YPR080W = 222
+YNL236W (pp) YKL012W = 206
+YDR412W (pp) YGL013C = 316
+YLR264W (pp) YER112W = 129
+YML114C (pp) YDR167W = 33
+YJR022W (pp) YOR167C = 298
+YJL089W (pd) YER065C = 150
+YOL051W (pp) YPL248C = 195
+YEL009C (pd) YOR202W = 274
+YNL216W (pd) YOL086C = 343
diff --git a/distribution/src/main/sampleData/galFiltered_list_edge_attr.ea b/distribution/src/main/sampleData/galFiltered_list_edge_attr.ea
new file mode 100644
index 0000000..65c8f96
--- /dev/null
+++ b/distribution/src/main/sampleData/galFiltered_list_edge_attr.ea
@@ -0,0 +1,15 @@
+List edge Attr1 (class=Integer)
+YFL017C (pp) YER102W = (38::38)
+YBR160W (pd) YMR043W = (205::205)
+YGR058W (pp) YOR264W = (147::147)
+YGL097W (pp) YOR204W = (202::203)
+YLR256W (pd) YML054C = (297::297)
+YPR113W (pd) YMR043W = (352::352)
+YBR045C (pp) YOR178C = (280::281)
+YMR043W (pd) YJL157C = (91::92)
+YIL162W (pd) YNL167C = (218::219)
+YLR256W (pd) YJR048W = (153::154)
+YDL081C (pp) YLR340W = (124::125)
+YJL194W (pd) YMR043W = (45::46)
+YPL248C (pd) ? = (48::49)
+YNL216W (pd) YLR044C = (21::22)
diff --git a/distribution/src/main/sampleData/galFilteredintAttr.xls b/distribution/src/main/sampleData/galFilteredintAttr.xls
new file mode 100755
index 0000000..28c7b57
Binary files /dev/null and b/distribution/src/main/sampleData/galFilteredintAttr.xls differ
diff --git a/distribution/src/main/sampleData/human_interactome_may07_small.tab.gz b/distribution/src/main/sampleData/human_interactome_may07_small.tab.gz
new file mode 100644
index 0000000..56f9055
Binary files /dev/null and b/distribution/src/main/sampleData/human_interactome_may07_small.tab.gz differ
diff --git a/distribution/src/main/sampleData/sampleStyles.props b/distribution/src/main/sampleData/sampleStyles.props
new file mode 100644
index 0000000..1ce3bb3
--- /dev/null
+++ b/distribution/src/main/sampleData/sampleStyles.props
@@ -0,0 +1,1063 @@
+#This file specifies visual mappings for Cytoscape and has been automatically generated.
+# WARNING: any changes you make to this file while Cytoscape is running may be overwritten.
+# Any changes may make these visual mappings unreadable.
+# Please make sure you know what you are doing before modifying this file by hand.
+#
+#Thu Dec 10 14:23:26 PST 2009
+edgeAppearanceCalculator.Aqua.defaultEdgeColor=0,0,0
+edgeAppearanceCalculator.Aqua.defaultEdgeFont=SanSerif,plain,10
+edgeAppearanceCalculator.Aqua.defaultEdgeFontSize=10.0
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+edgeAppearanceCalculator.default.defaultNodeLineWidth=1.0
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+edgeAppearanceCalculator.default.defaultNodeShape=rect
+edgeAppearanceCalculator.default.defaultNodeSize=35.0
+edgeAppearanceCalculator.default.defaultNodeToolTip=
+edgeAppearanceCalculator.default.defaultNodeWidth=70.0
+edgeAppearanceCalculator.default.edgeLabelCalculator=default-Edge Label-Passthrough Mapper
+edgeAppearanceCalculator.default.nodeSizeLocked=true
+edgeColorCalculator.BasicDiscrete.mapping.controller=interaction
+edgeColorCalculator.BasicDiscrete.mapping.controllerType=4
+edgeColorCalculator.BasicDiscrete.mapping.map.pd=255,0,51
+edgeColorCalculator.BasicDiscrete.mapping.map.pp=0,204,0
+edgeColorCalculator.BasicDiscrete.mapping.type=DiscreteMapping
+edgeColorCalculator.BasicDiscrete.visualPropertyType=EDGE_COLOR
+edgeLabelCalculator.EdgeLabel.mapping.controller=interaction
+edgeLabelCalculator.EdgeLabel.mapping.type=PassThroughMapping
+edgeLabelCalculator.EdgeLabel.visualPropertyType=EDGE_LABEL
+edgeLabelCalculator.Solid-Edge\ Label-Passthrough\ Mapper.mapping.controller=interaction
+edgeLabelCalculator.Solid-Edge\ Label-Passthrough\ Mapper.mapping.type=PassThroughMapping
+edgeLabelCalculator.Solid-Edge\ Label-Passthrough\ Mapper.visualPropertyType=EDGE_LABEL
+edgeLabelCalculator.default-Edge\ Label-Passthrough\ Mapper.mapping.controller=interaction
+edgeLabelCalculator.default-Edge\ Label-Passthrough\ Mapper.mapping.type=PassThroughMapping
+edgeLabelCalculator.default-Edge\ Label-Passthrough\ Mapper.visualPropertyType=EDGE_LABEL
+edgeLineStyleCalculator.Sample1-Edge\ Line\ Style-Discrete\ Mapper.mapping.controller=interaction
+edgeLineStyleCalculator.Sample1-Edge\ Line\ Style-Discrete\ Mapper.mapping.controllerType=4
+edgeLineStyleCalculator.Sample1-Edge\ Line\ Style-Discrete\ Mapper.mapping.map.pd=LONG_DASH
+edgeLineStyleCalculator.Sample1-Edge\ Line\ Style-Discrete\ Mapper.mapping.map.pp=SOLID
+edgeLineStyleCalculator.Sample1-Edge\ Line\ Style-Discrete\ Mapper.mapping.type=DiscreteMapping
+edgeLineStyleCalculator.Sample1-Edge\ Line\ Style-Discrete\ Mapper.visualPropertyType=EDGE_LINE_STYLE
+globalAppearanceCalculator.Aqua.defaultBackgroundColor=255,255,255
+globalAppearanceCalculator.Aqua.defaultEdgeReverseSelectionColor=0,255,0
+globalAppearanceCalculator.Aqua.defaultEdgeSelectionColor=255,0,0
+globalAppearanceCalculator.Aqua.defaultNodeReverseSelectionColor=0,255,0
+globalAppearanceCalculator.Aqua.defaultNodeSelectionColor=255,255,0
+globalAppearanceCalculator.Cloud.defaultBackgroundColor=255,255,255
+globalAppearanceCalculator.Cloud.defaultEdgeReverseSelectionColor=0,255,0
+globalAppearanceCalculator.Cloud.defaultEdgeSelectionColor=255,0,0
+globalAppearanceCalculator.Cloud.defaultNodeReverseSelectionColor=0,255,0
+globalAppearanceCalculator.Cloud.defaultNodeSelectionColor=255,255,0
+globalAppearanceCalculator.Metro.defaultBackgroundColor=255,255,255
+globalAppearanceCalculator.Metro.defaultEdgeReverseSelectionColor=0,255,0
+globalAppearanceCalculator.Metro.defaultEdgeSelectionColor=255,0,0
+globalAppearanceCalculator.Metro.defaultNodeReverseSelectionColor=0,255,0
+globalAppearanceCalculator.Metro.defaultNodeSelectionColor=255,255,0
+globalAppearanceCalculator.Nested\ Network\ Style.defaultBackgroundColor=255,255,255
+globalAppearanceCalculator.Nested\ Network\ Style.defaultEdgeReverseSelectionColor=0,255,0
+globalAppearanceCalculator.Nested\ Network\ Style.defaultEdgeSelectionColor=255,0,0
+globalAppearanceCalculator.Nested\ Network\ Style.defaultNodeReverseSelectionColor=0,255,0
+globalAppearanceCalculator.Nested\ Network\ Style.defaultNodeSelectionColor=255,255,0
+globalAppearanceCalculator.Ripple.defaultBackgroundColor=255,255,255
+globalAppearanceCalculator.Ripple.defaultEdgeReverseSelectionColor=0,255,0
+globalAppearanceCalculator.Ripple.defaultEdgeSelectionColor=255,0,0
+globalAppearanceCalculator.Ripple.defaultNodeReverseSelectionColor=0,255,0
+globalAppearanceCalculator.Ripple.defaultNodeSelectionColor=255,255,0
+globalAppearanceCalculator.Sample1.defaultBackgroundColor=255,255,255
+globalAppearanceCalculator.Sample1.defaultEdgeReverseSelectionColor=0,255,0
+globalAppearanceCalculator.Sample1.defaultEdgeSelectionColor=255,0,0
+globalAppearanceCalculator.Sample1.defaultNodeReverseSelectionColor=0,255,0
+globalAppearanceCalculator.Sample1.defaultNodeSelectionColor=255,255,0
+globalAppearanceCalculator.Skeleton.defaultBackgroundColor=0,0,0
+globalAppearanceCalculator.Skeleton.defaultEdgeReverseSelectionColor=0,255,0
+globalAppearanceCalculator.Skeleton.defaultEdgeSelectionColor=255,0,0
+globalAppearanceCalculator.Skeleton.defaultNodeReverseSelectionColor=0,255,0
+globalAppearanceCalculator.Skeleton.defaultNodeSelectionColor=255,255,0
+globalAppearanceCalculator.Solid.defaultBackgroundColor=255,255,255
+globalAppearanceCalculator.Solid.defaultEdgeReverseSelectionColor=0,255,0
+globalAppearanceCalculator.Solid.defaultEdgeSelectionColor=255,0,0
+globalAppearanceCalculator.Solid.defaultNodeReverseSelectionColor=0,255,0
+globalAppearanceCalculator.Solid.defaultNodeSelectionColor=255,255,0
+globalAppearanceCalculator.Tube.defaultBackgroundColor=255,255,255
+globalAppearanceCalculator.Tube.defaultEdgeReverseSelectionColor=0,255,0
+globalAppearanceCalculator.Tube.defaultEdgeSelectionColor=255,0,0
+globalAppearanceCalculator.Tube.defaultNodeReverseSelectionColor=0,255,0
+globalAppearanceCalculator.Tube.defaultNodeSelectionColor=255,255,0
+globalAppearanceCalculator.Universe.defaultBackgroundColor=0,0,0
+globalAppearanceCalculator.Universe.defaultEdgeReverseSelectionColor=0,255,0
+globalAppearanceCalculator.Universe.defaultEdgeSelectionColor=255,0,0
+globalAppearanceCalculator.Universe.defaultNodeReverseSelectionColor=0,255,0
+globalAppearanceCalculator.Universe.defaultNodeSelectionColor=255,255,0
+globalAppearanceCalculator.default.defaultBackgroundColor=204,204,255
+globalAppearanceCalculator.default.defaultEdgeReverseSelectionColor=0,255,0
+globalAppearanceCalculator.default.defaultEdgeSelectionColor=255,0,0
+globalAppearanceCalculator.default.defaultNodeReverseSelectionColor=0,255,0
+globalAppearanceCalculator.default.defaultNodeSelectionColor=255,255,0
+nodeAppearanceCalculator.Aqua.defaultEdgeColor=0,0,0
+nodeAppearanceCalculator.Aqua.defaultEdgeFont=SanSerif,plain,10
+nodeAppearanceCalculator.Aqua.defaultEdgeFontSize=10.0
+nodeAppearanceCalculator.Aqua.defaultEdgeLabel=
+nodeAppearanceCalculator.Aqua.defaultEdgeLabelColor=0,0,0
+nodeAppearanceCalculator.Aqua.defaultEdgeLabelOpacity=255
+nodeAppearanceCalculator.Aqua.defaultEdgeLabelPosition=C,C,c,0,0
+nodeAppearanceCalculator.Aqua.defaultEdgeLabelWidth=100.0
+nodeAppearanceCalculator.Aqua.defaultEdgeLineStyle=SOLID
+nodeAppearanceCalculator.Aqua.defaultEdgeLineWidth=1.0
+nodeAppearanceCalculator.Aqua.defaultEdgeOpacity=255
+nodeAppearanceCalculator.Aqua.defaultEdgeSourceArrowColor=0,0,0
+nodeAppearanceCalculator.Aqua.defaultEdgeSourceArrowOpacity=255
+nodeAppearanceCalculator.Aqua.defaultEdgeSourceArrowShape=NONE
+nodeAppearanceCalculator.Aqua.defaultEdgeTargetArrowColor=0,0,0
+nodeAppearanceCalculator.Aqua.defaultEdgeTargetArrowOpacity=255
+nodeAppearanceCalculator.Aqua.defaultEdgeTargetArrowShape=NONE
+nodeAppearanceCalculator.Aqua.defaultEdgeToolTip=
+nodeAppearanceCalculator.Aqua.defaultNodeBorderColor=0,0,0
+nodeAppearanceCalculator.Aqua.defaultNodeBorderOpacity=255
+nodeAppearanceCalculator.Aqua.defaultNodeFillColor=102,204,255
+nodeAppearanceCalculator.Aqua.defaultNodeFont=Nimbus Sans L Bold,plain,12
+nodeAppearanceCalculator.Aqua.defaultNodeFontSize=12.0
+nodeAppearanceCalculator.Aqua.defaultNodeHight=40.0
+nodeAppearanceCalculator.Aqua.defaultNodeLabel=
+nodeAppearanceCalculator.Aqua.defaultNodeLabelColor=255,255,255
+nodeAppearanceCalculator.Aqua.defaultNodeLabelOpacity=200
+nodeAppearanceCalculator.Aqua.defaultNodeLabelPosition=C,C,c,0,0
+nodeAppearanceCalculator.Aqua.defaultNodeLabelWidth=100.0
+nodeAppearanceCalculator.Aqua.defaultNodeLineStyle=SOLID
+nodeAppearanceCalculator.Aqua.defaultNodeLineWidth=0.0
+nodeAppearanceCalculator.Aqua.defaultNodeOpacity=170
+nodeAppearanceCalculator.Aqua.defaultNodeShape=ellipse
+nodeAppearanceCalculator.Aqua.defaultNodeSize=35.0
+nodeAppearanceCalculator.Aqua.defaultNodeToolTip=
+nodeAppearanceCalculator.Aqua.defaultNodeWidth=75.0
+nodeAppearanceCalculator.Aqua.nodeLabelCalculator=Aqua-Node Label-Passthrough Mapper
+nodeAppearanceCalculator.Aqua.nodeSizeLocked=false
+nodeAppearanceCalculator.Cloud.defaultEdgeColor=0,0,0
+nodeAppearanceCalculator.Cloud.defaultEdgeFont=SanSerif,plain,10
+nodeAppearanceCalculator.Cloud.defaultEdgeFontSize=10.0
+nodeAppearanceCalculator.Cloud.defaultEdgeLabel=
+nodeAppearanceCalculator.Cloud.defaultEdgeLabelColor=0,0,0
+nodeAppearanceCalculator.Cloud.defaultEdgeLabelOpacity=255
+nodeAppearanceCalculator.Cloud.defaultEdgeLabelPosition=C,C,c,0,0
+nodeAppearanceCalculator.Cloud.defaultEdgeLabelWidth=100.0
+nodeAppearanceCalculator.Cloud.defaultEdgeLineStyle=SOLID
+nodeAppearanceCalculator.Cloud.defaultEdgeLineWidth=1.0
+nodeAppearanceCalculator.Cloud.defaultEdgeOpacity=255
+nodeAppearanceCalculator.Cloud.defaultEdgeSourceArrowColor=0,0,0
+nodeAppearanceCalculator.Cloud.defaultEdgeSourceArrowOpacity=255
+nodeAppearanceCalculator.Cloud.defaultEdgeSourceArrowShape=NONE
+nodeAppearanceCalculator.Cloud.defaultEdgeTargetArrowColor=0,0,0
+nodeAppearanceCalculator.Cloud.defaultEdgeTargetArrowOpacity=255
+nodeAppearanceCalculator.Cloud.defaultEdgeTargetArrowShape=NONE
+nodeAppearanceCalculator.Cloud.defaultEdgeToolTip=
+nodeAppearanceCalculator.Cloud.defaultNodeBorderColor=255,255,255
+nodeAppearanceCalculator.Cloud.defaultNodeBorderOpacity=0
+nodeAppearanceCalculator.Cloud.defaultNodeFillColor=255,255,255
+nodeAppearanceCalculator.Cloud.defaultNodeFont=Century Schoolbook L Bold,plain,12
+nodeAppearanceCalculator.Cloud.defaultNodeFontSize=12.0
+nodeAppearanceCalculator.Cloud.defaultNodeHight=30.0
+nodeAppearanceCalculator.Cloud.defaultNodeLabel=
+nodeAppearanceCalculator.Cloud.defaultNodeLabelColor=0,0,0
+nodeAppearanceCalculator.Cloud.defaultNodeLabelOpacity=200
+nodeAppearanceCalculator.Cloud.defaultNodeLabelPosition=C,C,c,0,0
+nodeAppearanceCalculator.Cloud.defaultNodeLabelWidth=100.0
+nodeAppearanceCalculator.Cloud.defaultNodeLineStyle=SOLID
+nodeAppearanceCalculator.Cloud.defaultNodeLineWidth=1.0
+nodeAppearanceCalculator.Cloud.defaultNodeOpacity=0
+nodeAppearanceCalculator.Cloud.defaultNodeShape=rect
+nodeAppearanceCalculator.Cloud.defaultNodeSize=25.0
+nodeAppearanceCalculator.Cloud.defaultNodeToolTip=
+nodeAppearanceCalculator.Cloud.defaultNodeWidth=70.0
+nodeAppearanceCalculator.Cloud.nodeFontSizeCalculator=Cloud-Node Font Size-Continuous Mapper
+nodeAppearanceCalculator.Cloud.nodeLabelCalculator=Cloud-Node Label-Passthrough Mapper
+nodeAppearanceCalculator.Cloud.nodeSizeLocked=true
+nodeAppearanceCalculator.Metro.defaultEdgeColor=0,0,0
+nodeAppearanceCalculator.Metro.defaultEdgeFont=SanSerif,plain,10
+nodeAppearanceCalculator.Metro.defaultEdgeFontSize=10.0
+nodeAppearanceCalculator.Metro.defaultEdgeLabel=
+nodeAppearanceCalculator.Metro.defaultEdgeLabelColor=0,0,0
+nodeAppearanceCalculator.Metro.defaultEdgeLabelOpacity=255
+nodeAppearanceCalculator.Metro.defaultEdgeLabelPosition=C,C,c,0,0
+nodeAppearanceCalculator.Metro.defaultEdgeLabelWidth=100.0
+nodeAppearanceCalculator.Metro.defaultEdgeLineStyle=SOLID
+nodeAppearanceCalculator.Metro.defaultEdgeLineWidth=1.0
+nodeAppearanceCalculator.Metro.defaultEdgeOpacity=255
+nodeAppearanceCalculator.Metro.defaultEdgeSourceArrowColor=0,0,0
+nodeAppearanceCalculator.Metro.defaultEdgeSourceArrowOpacity=255
+nodeAppearanceCalculator.Metro.defaultEdgeSourceArrowShape=NONE
+nodeAppearanceCalculator.Metro.defaultEdgeTargetArrowColor=0,0,0
+nodeAppearanceCalculator.Metro.defaultEdgeTargetArrowOpacity=255
+nodeAppearanceCalculator.Metro.defaultEdgeTargetArrowShape=NONE
+nodeAppearanceCalculator.Metro.defaultEdgeToolTip=
+nodeAppearanceCalculator.Metro.defaultNodeBorderColor=0,0,255
+nodeAppearanceCalculator.Metro.defaultNodeBorderOpacity=150
+nodeAppearanceCalculator.Metro.defaultNodeFillColor=255,255,255
+nodeAppearanceCalculator.Metro.defaultNodeFont=SansSerif.bold,plain,12
+nodeAppearanceCalculator.Metro.defaultNodeFontSize=25.0
+nodeAppearanceCalculator.Metro.defaultNodeHight=55.0
+nodeAppearanceCalculator.Metro.defaultNodeLabel=
+nodeAppearanceCalculator.Metro.defaultNodeLabelColor=0,0,0
+nodeAppearanceCalculator.Metro.defaultNodeLabelOpacity=255
+nodeAppearanceCalculator.Metro.defaultNodeLabelPosition=E,NW,c,6,0
+nodeAppearanceCalculator.Metro.defaultNodeLabelWidth=100.0
+nodeAppearanceCalculator.Metro.defaultNodeLineStyle=SOLID
+nodeAppearanceCalculator.Metro.defaultNodeLineWidth=11.0
+nodeAppearanceCalculator.Metro.defaultNodeOpacity=0
+nodeAppearanceCalculator.Metro.defaultNodeShape=rect
+nodeAppearanceCalculator.Metro.defaultNodeSize=35.0
+nodeAppearanceCalculator.Metro.defaultNodeToolTip=
+nodeAppearanceCalculator.Metro.defaultNodeWidth=80.0
+nodeAppearanceCalculator.Metro.nodeLabelCalculator=Subway-Node Label-Passthrough Mapper
+nodeAppearanceCalculator.Metro.nodeSizeLocked=false
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultEdgeColor=0,0,0
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultEdgeFont=SanSerif,plain,10
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultEdgeFontSize=10.0
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultEdgeLabel=
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultEdgeLabelColor=0,0,0
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultEdgeLabelOpacity=255
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultEdgeLabelPosition=C,C,c,0,0
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultEdgeLabelWidth=100.0
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultEdgeLineStyle=SOLID
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultEdgeLineWidth=1.0
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultEdgeOpacity=255
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultEdgeSourceArrowColor=0,0,0
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultEdgeSourceArrowOpacity=255
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultEdgeSourceArrowShape=NONE
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultEdgeTargetArrowColor=0,0,0
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultEdgeTargetArrowOpacity=255
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultEdgeTargetArrowShape=NONE
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultEdgeToolTip=
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultNodeBorderColor=0,153,0
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultNodeBorderOpacity=190
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultNodeFillColor=153,255,153
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultNodeFont=SansSerif,plain,12
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultNodeFontSize=13.0
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultNodeHight=30.0
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultNodeLabel=
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultNodeLabelColor=0,0,0
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultNodeLabelOpacity=255
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultNodeLabelPosition=C,C,c,0,0
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultNodeLabelWidth=100.0
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultNodeLineStyle=SOLID
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultNodeLineWidth=2.0
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultNodeOpacity=150
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultNodeShape=ellipse
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultNodeSize=40.0
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultNodeToolTip=
+nodeAppearanceCalculator.Nested\ Network\ Style.defaultNodeWidth=70.0
+nodeAppearanceCalculator.Nested\ Network\ Style.nodeBorderColorCalculator=Nested Network Style-Node Border Color-Discrete Mapper
+nodeAppearanceCalculator.Nested\ Network\ Style.nodeFillColorCalculator=Nested Network Style-Node Color-Discrete Mapper
+nodeAppearanceCalculator.Nested\ Network\ Style.nodeLabelCalculator=Nested Network Style-Node Label-Passthrough Mapper
+nodeAppearanceCalculator.Nested\ Network\ Style.nodeLabelColor=Nested Network Style-Node Label Color-Discrete Mapper
+nodeAppearanceCalculator.Nested\ Network\ Style.nodeLabelPositionCalculator=Nested Network Style-Node Label Position-Discrete Mapper
+nodeAppearanceCalculator.Nested\ Network\ Style.nodeLineWidthCalculator=Nested Network Style-Node Line Width-Discrete Mapper
+nodeAppearanceCalculator.Nested\ Network\ Style.nodeShapeCalculator=Nested Network Style-Node Shape-Discrete Mapper
+nodeAppearanceCalculator.Nested\ Network\ Style.nodeSizeLocked=true
+nodeAppearanceCalculator.Nested\ Network\ Style.nodeUniformSizeCalculator=Nested Network Style-Node Size-Discrete Mapper
+nodeAppearanceCalculator.Ripple.defaultEdgeColor=0,0,0
+nodeAppearanceCalculator.Ripple.defaultEdgeFont=SanSerif,plain,10
+nodeAppearanceCalculator.Ripple.defaultEdgeFontSize=10.0
+nodeAppearanceCalculator.Ripple.defaultEdgeLabel=
+nodeAppearanceCalculator.Ripple.defaultEdgeLabelColor=0,0,0
+nodeAppearanceCalculator.Ripple.defaultEdgeLabelOpacity=255
+nodeAppearanceCalculator.Ripple.defaultEdgeLabelPosition=C,C,c,0,0
+nodeAppearanceCalculator.Ripple.defaultEdgeLabelWidth=100.0
+nodeAppearanceCalculator.Ripple.defaultEdgeLineStyle=SOLID
+nodeAppearanceCalculator.Ripple.defaultEdgeLineWidth=1.0
+nodeAppearanceCalculator.Ripple.defaultEdgeOpacity=255
+nodeAppearanceCalculator.Ripple.defaultEdgeSourceArrowColor=0,0,0
+nodeAppearanceCalculator.Ripple.defaultEdgeSourceArrowOpacity=255
+nodeAppearanceCalculator.Ripple.defaultEdgeSourceArrowShape=NONE
+nodeAppearanceCalculator.Ripple.defaultEdgeTargetArrowColor=0,0,0
+nodeAppearanceCalculator.Ripple.defaultEdgeTargetArrowOpacity=255
+nodeAppearanceCalculator.Ripple.defaultEdgeTargetArrowShape=NONE
+nodeAppearanceCalculator.Ripple.defaultEdgeToolTip=
+nodeAppearanceCalculator.Ripple.defaultNodeBorderColor=0,0,0
+nodeAppearanceCalculator.Ripple.defaultNodeBorderOpacity=255
+nodeAppearanceCalculator.Ripple.defaultNodeFillColor=153,204,255
+nodeAppearanceCalculator.Ripple.defaultNodeFont=SansSerif.bold,plain,12
+nodeAppearanceCalculator.Ripple.defaultNodeFontSize=12.0
+nodeAppearanceCalculator.Ripple.defaultNodeHight=30.0
+nodeAppearanceCalculator.Ripple.defaultNodeLabel=
+nodeAppearanceCalculator.Ripple.defaultNodeLabelColor=0,0,0
+nodeAppearanceCalculator.Ripple.defaultNodeLabelOpacity=220
+nodeAppearanceCalculator.Ripple.defaultNodeLabelPosition=C,C,c,0,0
+nodeAppearanceCalculator.Ripple.defaultNodeLabelWidth=100.0
+nodeAppearanceCalculator.Ripple.defaultNodeLineStyle=SOLID
+nodeAppearanceCalculator.Ripple.defaultNodeLineWidth=0.0
+nodeAppearanceCalculator.Ripple.defaultNodeOpacity=170
+nodeAppearanceCalculator.Ripple.defaultNodeShape=ellipse
+nodeAppearanceCalculator.Ripple.defaultNodeSize=55.0
+nodeAppearanceCalculator.Ripple.defaultNodeToolTip=
+nodeAppearanceCalculator.Ripple.defaultNodeWidth=70.0
+nodeAppearanceCalculator.Ripple.nodeLabelCalculator=Ripple-Node Label-Passthrough Mapper
+nodeAppearanceCalculator.Ripple.nodeSizeLocked=true
+nodeAppearanceCalculator.Ripple.nodeUniformSizeCalculator=Ripple-Node Size-Continuous Mapper
+nodeAppearanceCalculator.Sample1.defaultEdgeColor=0,0,0
+nodeAppearanceCalculator.Sample1.defaultEdgeFont=SanSerif,plain,10
+nodeAppearanceCalculator.Sample1.defaultEdgeFontSize=10.0
+nodeAppearanceCalculator.Sample1.defaultEdgeLabel=
+nodeAppearanceCalculator.Sample1.defaultEdgeLabelColor=0,0,0
+nodeAppearanceCalculator.Sample1.defaultEdgeLabelOpacity=255
+nodeAppearanceCalculator.Sample1.defaultEdgeLabelPosition=C,C,c,0,0
+nodeAppearanceCalculator.Sample1.defaultEdgeLabelWidth=100.0
+nodeAppearanceCalculator.Sample1.defaultEdgeLineStyle=SOLID
+nodeAppearanceCalculator.Sample1.defaultEdgeLineWidth=1.0
+nodeAppearanceCalculator.Sample1.defaultEdgeOpacity=255
+nodeAppearanceCalculator.Sample1.defaultEdgeSourceArrowColor=0,0,0
+nodeAppearanceCalculator.Sample1.defaultEdgeSourceArrowOpacity=255
+nodeAppearanceCalculator.Sample1.defaultEdgeSourceArrowShape=NONE
+nodeAppearanceCalculator.Sample1.defaultEdgeTargetArrowColor=0,0,0
+nodeAppearanceCalculator.Sample1.defaultEdgeTargetArrowOpacity=255
+nodeAppearanceCalculator.Sample1.defaultEdgeTargetArrowShape=NONE
+nodeAppearanceCalculator.Sample1.defaultEdgeToolTip=
+nodeAppearanceCalculator.Sample1.defaultNodeBorderColor=0,0,0
+nodeAppearanceCalculator.Sample1.defaultNodeBorderOpacity=255
+nodeAppearanceCalculator.Sample1.defaultNodeFillColor=204,204,255
+nodeAppearanceCalculator.Sample1.defaultNodeFont=Dialog.bold,plain,12
+nodeAppearanceCalculator.Sample1.defaultNodeFontSize=12.0
+nodeAppearanceCalculator.Sample1.defaultNodeHight=30.0
+nodeAppearanceCalculator.Sample1.defaultNodeLabel=
+nodeAppearanceCalculator.Sample1.defaultNodeLabelColor=0,0,0
+nodeAppearanceCalculator.Sample1.defaultNodeLabelOpacity=255
+nodeAppearanceCalculator.Sample1.defaultNodeLabelPosition=C,C,c,0,0
+nodeAppearanceCalculator.Sample1.defaultNodeLabelWidth=100.0
+nodeAppearanceCalculator.Sample1.defaultNodeLineStyle=SOLID
+nodeAppearanceCalculator.Sample1.defaultNodeLineWidth=0.0
+nodeAppearanceCalculator.Sample1.defaultNodeOpacity=255
+nodeAppearanceCalculator.Sample1.defaultNodeShape=ellipse
+nodeAppearanceCalculator.Sample1.defaultNodeSize=40.0
+nodeAppearanceCalculator.Sample1.defaultNodeToolTip=
+nodeAppearanceCalculator.Sample1.defaultNodeWidth=70.0
+nodeAppearanceCalculator.Sample1.nodeLabelCalculator=NodeLabel
+nodeAppearanceCalculator.Sample1.nodeSizeLocked=true
+nodeAppearanceCalculator.Skeleton.defaultEdgeColor=0,0,0
+nodeAppearanceCalculator.Skeleton.defaultEdgeFont=SanSerif,plain,10
+nodeAppearanceCalculator.Skeleton.defaultEdgeFontSize=10.0
+nodeAppearanceCalculator.Skeleton.defaultEdgeLabel=
+nodeAppearanceCalculator.Skeleton.defaultEdgeLabelColor=0,0,0
+nodeAppearanceCalculator.Skeleton.defaultEdgeLabelOpacity=255
+nodeAppearanceCalculator.Skeleton.defaultEdgeLabelPosition=C,C,c,0,0
+nodeAppearanceCalculator.Skeleton.defaultEdgeLabelWidth=100.0
+nodeAppearanceCalculator.Skeleton.defaultEdgeLineStyle=SOLID
+nodeAppearanceCalculator.Skeleton.defaultEdgeLineWidth=1.0
+nodeAppearanceCalculator.Skeleton.defaultEdgeOpacity=255
+nodeAppearanceCalculator.Skeleton.defaultEdgeSourceArrowColor=0,0,0
+nodeAppearanceCalculator.Skeleton.defaultEdgeSourceArrowOpacity=255
+nodeAppearanceCalculator.Skeleton.defaultEdgeSourceArrowShape=NONE
+nodeAppearanceCalculator.Skeleton.defaultEdgeTargetArrowColor=0,0,0
+nodeAppearanceCalculator.Skeleton.defaultEdgeTargetArrowOpacity=255
+nodeAppearanceCalculator.Skeleton.defaultEdgeTargetArrowShape=NONE
+nodeAppearanceCalculator.Skeleton.defaultEdgeToolTip=
+nodeAppearanceCalculator.Skeleton.defaultNodeBorderColor=255,255,255
+nodeAppearanceCalculator.Skeleton.defaultNodeBorderOpacity=255
+nodeAppearanceCalculator.Skeleton.defaultNodeFillColor=255,255,255
+nodeAppearanceCalculator.Skeleton.defaultNodeFont=Default,plain,12
+nodeAppearanceCalculator.Skeleton.defaultNodeFontSize=15.0
+nodeAppearanceCalculator.Skeleton.defaultNodeHight=40.0
+nodeAppearanceCalculator.Skeleton.defaultNodeLabel=
+nodeAppearanceCalculator.Skeleton.defaultNodeLabelColor=255,255,255
+nodeAppearanceCalculator.Skeleton.defaultNodeLabelOpacity=255
+nodeAppearanceCalculator.Skeleton.defaultNodeLabelPosition=C,C,c,0,0
+nodeAppearanceCalculator.Skeleton.defaultNodeLabelWidth=100.0
+nodeAppearanceCalculator.Skeleton.defaultNodeLineStyle=SOLID
+nodeAppearanceCalculator.Skeleton.defaultNodeLineWidth=3.0
+nodeAppearanceCalculator.Skeleton.defaultNodeOpacity=0
+nodeAppearanceCalculator.Skeleton.defaultNodeShape=ellipse
+nodeAppearanceCalculator.Skeleton.defaultNodeSize=35.0
+nodeAppearanceCalculator.Skeleton.defaultNodeToolTip=
+nodeAppearanceCalculator.Skeleton.defaultNodeWidth=90.0
+nodeAppearanceCalculator.Skeleton.nodeLabelCalculator=Skeleton-Node Label-Passthrough Mapper
+nodeAppearanceCalculator.Skeleton.nodeSizeLocked=false
+nodeAppearanceCalculator.Solid.defaultEdgeColor=0,0,0
+nodeAppearanceCalculator.Solid.defaultEdgeFont=SanSerif,plain,10
+nodeAppearanceCalculator.Solid.defaultEdgeFontSize=10.0
+nodeAppearanceCalculator.Solid.defaultEdgeLabel=
+nodeAppearanceCalculator.Solid.defaultEdgeLabelColor=0,0,0
+nodeAppearanceCalculator.Solid.defaultEdgeLabelOpacity=255
+nodeAppearanceCalculator.Solid.defaultEdgeLabelPosition=C,C,c,0,0
+nodeAppearanceCalculator.Solid.defaultEdgeLabelWidth=100.0
+nodeAppearanceCalculator.Solid.defaultEdgeLineStyle=SOLID
+nodeAppearanceCalculator.Solid.defaultEdgeLineWidth=1.0
+nodeAppearanceCalculator.Solid.defaultEdgeOpacity=255
+nodeAppearanceCalculator.Solid.defaultEdgeSourceArrowColor=0,0,0
+nodeAppearanceCalculator.Solid.defaultEdgeSourceArrowOpacity=255
+nodeAppearanceCalculator.Solid.defaultEdgeSourceArrowShape=NONE
+nodeAppearanceCalculator.Solid.defaultEdgeTargetArrowColor=0,0,0
+nodeAppearanceCalculator.Solid.defaultEdgeTargetArrowOpacity=255
+nodeAppearanceCalculator.Solid.defaultEdgeTargetArrowShape=NONE
+nodeAppearanceCalculator.Solid.defaultEdgeToolTip=
+nodeAppearanceCalculator.Solid.defaultNodeBorderColor=0,0,0
+nodeAppearanceCalculator.Solid.defaultNodeBorderOpacity=255
+nodeAppearanceCalculator.Solid.defaultNodeFillColor=102,102,102
+nodeAppearanceCalculator.Solid.defaultNodeFont=Courier 10 Pitch Bold,plain,12
+nodeAppearanceCalculator.Solid.defaultNodeFontSize=18.0
+nodeAppearanceCalculator.Solid.defaultNodeHight=30.0
+nodeAppearanceCalculator.Solid.defaultNodeLabel=
+nodeAppearanceCalculator.Solid.defaultNodeLabelColor=0,0,0
+nodeAppearanceCalculator.Solid.defaultNodeLabelOpacity=160
+nodeAppearanceCalculator.Solid.defaultNodeLabelPosition=S,NW,c,0,5
+nodeAppearanceCalculator.Solid.defaultNodeLabelWidth=100.0
+nodeAppearanceCalculator.Solid.defaultNodeLineStyle=SOLID
+nodeAppearanceCalculator.Solid.defaultNodeLineWidth=0.0
+nodeAppearanceCalculator.Solid.defaultNodeOpacity=255
+nodeAppearanceCalculator.Solid.defaultNodeShape=ellipse
+nodeAppearanceCalculator.Solid.defaultNodeSize=45.0
+nodeAppearanceCalculator.Solid.defaultNodeToolTip=
+nodeAppearanceCalculator.Solid.defaultNodeWidth=70.0
+nodeAppearanceCalculator.Solid.nodeLabelCalculator=Solid-Node Label-Passthrough Mapper
+nodeAppearanceCalculator.Solid.nodeSizeLocked=true
+nodeAppearanceCalculator.Tube.defaultEdgeColor=0,0,0
+nodeAppearanceCalculator.Tube.defaultEdgeFont=SanSerif,plain,10
+nodeAppearanceCalculator.Tube.defaultEdgeFontSize=10.0
+nodeAppearanceCalculator.Tube.defaultEdgeLabel=
+nodeAppearanceCalculator.Tube.defaultEdgeLabelColor=0,0,0
+nodeAppearanceCalculator.Tube.defaultEdgeLabelOpacity=255
+nodeAppearanceCalculator.Tube.defaultEdgeLabelPosition=C,C,c,0,0
+nodeAppearanceCalculator.Tube.defaultEdgeLabelWidth=100.0
+nodeAppearanceCalculator.Tube.defaultEdgeLineStyle=SOLID
+nodeAppearanceCalculator.Tube.defaultEdgeLineWidth=1.0
+nodeAppearanceCalculator.Tube.defaultEdgeOpacity=255
+nodeAppearanceCalculator.Tube.defaultEdgeSourceArrowColor=0,0,0
+nodeAppearanceCalculator.Tube.defaultEdgeSourceArrowOpacity=255
+nodeAppearanceCalculator.Tube.defaultEdgeSourceArrowShape=NONE
+nodeAppearanceCalculator.Tube.defaultEdgeTargetArrowColor=0,0,0
+nodeAppearanceCalculator.Tube.defaultEdgeTargetArrowOpacity=255
+nodeAppearanceCalculator.Tube.defaultEdgeTargetArrowShape=NONE
+nodeAppearanceCalculator.Tube.defaultEdgeToolTip=
+nodeAppearanceCalculator.Tube.defaultNodeBorderColor=0,0,0
+nodeAppearanceCalculator.Tube.defaultNodeBorderOpacity=255
+nodeAppearanceCalculator.Tube.defaultNodeFillColor=0,0,0
+nodeAppearanceCalculator.Tube.defaultNodeFont=Monospaced.bold,plain,12
+nodeAppearanceCalculator.Tube.defaultNodeFontSize=12.0
+nodeAppearanceCalculator.Tube.defaultNodeHight=30.0
+nodeAppearanceCalculator.Tube.defaultNodeLabel=
+nodeAppearanceCalculator.Tube.defaultNodeLabelColor=204,204,255
+nodeAppearanceCalculator.Tube.defaultNodeLabelOpacity=255
+nodeAppearanceCalculator.Tube.defaultNodeLabelPosition=C,C,c,0,0
+nodeAppearanceCalculator.Tube.defaultNodeLabelWidth=100.0
+nodeAppearanceCalculator.Tube.defaultNodeLineStyle=SOLID
+nodeAppearanceCalculator.Tube.defaultNodeLineWidth=0.0
+nodeAppearanceCalculator.Tube.defaultNodeOpacity=0
+nodeAppearanceCalculator.Tube.defaultNodeShape=rect
+nodeAppearanceCalculator.Tube.defaultNodeSize=20.0
+nodeAppearanceCalculator.Tube.defaultNodeToolTip=
+nodeAppearanceCalculator.Tube.defaultNodeWidth=70.0
+nodeAppearanceCalculator.Tube.nodeLabelCalculator=Pipe-Node Label-Passthrough Mapper
+nodeAppearanceCalculator.Tube.nodeSizeLocked=true
+nodeAppearanceCalculator.Universe.defaultEdgeColor=0,0,0
+nodeAppearanceCalculator.Universe.defaultEdgeFont=SanSerif,plain,10
+nodeAppearanceCalculator.Universe.defaultEdgeFontSize=10.0
+nodeAppearanceCalculator.Universe.defaultEdgeLabel=
+nodeAppearanceCalculator.Universe.defaultEdgeLabelColor=0,0,0
+nodeAppearanceCalculator.Universe.defaultEdgeLabelOpacity=255
+nodeAppearanceCalculator.Universe.defaultEdgeLabelPosition=C,C,c,0,0
+nodeAppearanceCalculator.Universe.defaultEdgeLabelWidth=100.0
+nodeAppearanceCalculator.Universe.defaultEdgeLineStyle=SOLID
+nodeAppearanceCalculator.Universe.defaultEdgeLineWidth=1.0
+nodeAppearanceCalculator.Universe.defaultEdgeOpacity=255
+nodeAppearanceCalculator.Universe.defaultEdgeSourceArrowColor=0,0,0
+nodeAppearanceCalculator.Universe.defaultEdgeSourceArrowOpacity=255
+nodeAppearanceCalculator.Universe.defaultEdgeSourceArrowShape=NONE
+nodeAppearanceCalculator.Universe.defaultEdgeTargetArrowColor=0,0,0
+nodeAppearanceCalculator.Universe.defaultEdgeTargetArrowOpacity=255
+nodeAppearanceCalculator.Universe.defaultEdgeTargetArrowShape=NONE
+nodeAppearanceCalculator.Universe.defaultEdgeToolTip=
+nodeAppearanceCalculator.Universe.defaultNodeBorderColor=0,0,0
+nodeAppearanceCalculator.Universe.defaultNodeBorderOpacity=255
+nodeAppearanceCalculator.Universe.defaultNodeFillColor=0,0,0
+nodeAppearanceCalculator.Universe.defaultNodeFont=Monospaced.bold,plain,12
+nodeAppearanceCalculator.Universe.defaultNodeFontSize=20.0
+nodeAppearanceCalculator.Universe.defaultNodeHight=30.0
+nodeAppearanceCalculator.Universe.defaultNodeLabel=
+nodeAppearanceCalculator.Universe.defaultNodeLabelColor=255,255,204
+nodeAppearanceCalculator.Universe.defaultNodeLabelOpacity=180
+nodeAppearanceCalculator.Universe.defaultNodeLabelPosition=C,C,c,0,0
+nodeAppearanceCalculator.Universe.defaultNodeLabelWidth=100.0
+nodeAppearanceCalculator.Universe.defaultNodeLineStyle=SOLID
+nodeAppearanceCalculator.Universe.defaultNodeLineWidth=0.0
+nodeAppearanceCalculator.Universe.defaultNodeOpacity=0
+nodeAppearanceCalculator.Universe.defaultNodeShape=ellipse
+nodeAppearanceCalculator.Universe.defaultNodeSize=60.0
+nodeAppearanceCalculator.Universe.defaultNodeToolTip=
+nodeAppearanceCalculator.Universe.defaultNodeWidth=100.0
+nodeAppearanceCalculator.Universe.nodeLabelCalculator=Universe-Node Label-Passthrough Mapper
+nodeAppearanceCalculator.Universe.nodeSizeLocked=true
+nodeAppearanceCalculator.default.defaultEdgeColor=0,0,0
+nodeAppearanceCalculator.default.defaultEdgeFont=SanSerif,plain,10
+nodeAppearanceCalculator.default.defaultEdgeFontSize=10.0
+nodeAppearanceCalculator.default.defaultEdgeLabel=
+nodeAppearanceCalculator.default.defaultEdgeLabelColor=0,0,0
+nodeAppearanceCalculator.default.defaultEdgeLabelOpacity=255
+nodeAppearanceCalculator.default.defaultEdgeLabelPosition=C,C,c,0,0
+nodeAppearanceCalculator.default.defaultEdgeLabelWidth=100.0
+nodeAppearanceCalculator.default.defaultEdgeLineStyle=SOLID
+nodeAppearanceCalculator.default.defaultEdgeLineWidth=1.0
+nodeAppearanceCalculator.default.defaultEdgeOpacity=255
+nodeAppearanceCalculator.default.defaultEdgeSourceArrowColor=0,0,0
+nodeAppearanceCalculator.default.defaultEdgeSourceArrowOpacity=255
+nodeAppearanceCalculator.default.defaultEdgeSourceArrowShape=NONE
+nodeAppearanceCalculator.default.defaultEdgeTargetArrowColor=0,0,0
+nodeAppearanceCalculator.default.defaultEdgeTargetArrowOpacity=255
+nodeAppearanceCalculator.default.defaultEdgeTargetArrowShape=NONE
+nodeAppearanceCalculator.default.defaultEdgeToolTip=
+nodeAppearanceCalculator.default.defaultNodeBorderColor=204,204,204
+nodeAppearanceCalculator.default.defaultNodeBorderOpacity=255
+nodeAppearanceCalculator.default.defaultNodeFillColor=204,204,204
+nodeAppearanceCalculator.default.defaultNodeFont=SansSerif.bold,plain,12
+nodeAppearanceCalculator.default.defaultNodeFontSize=12.0
+nodeAppearanceCalculator.default.defaultNodeHight=30.0
+nodeAppearanceCalculator.default.defaultNodeLabel=
+nodeAppearanceCalculator.default.defaultNodeLabelColor=0,0,0
+nodeAppearanceCalculator.default.defaultNodeLabelOpacity=255
+nodeAppearanceCalculator.default.defaultNodeLabelPosition=C,C,c,0,0
+nodeAppearanceCalculator.default.defaultNodeLabelWidth=100.0
+nodeAppearanceCalculator.default.defaultNodeLineStyle=SOLID
+nodeAppearanceCalculator.default.defaultNodeLineWidth=0.0
+nodeAppearanceCalculator.default.defaultNodeOpacity=255
+nodeAppearanceCalculator.default.defaultNodeShape=ellipse
+nodeAppearanceCalculator.default.defaultNodeSize=40.0
+nodeAppearanceCalculator.default.defaultNodeToolTip=
+nodeAppearanceCalculator.default.defaultNodeWidth=70.0
+nodeAppearanceCalculator.default.nodeLabelCalculator=NodeLabel
+nodeAppearanceCalculator.default.nodeSizeLocked=true
+nodeBorderColorCalculator.Nested\ Network\ Style-Node\ Border\ Color-Discrete\ Mapper.mapping.controller=has_nested_network
+nodeBorderColorCalculator.Nested\ Network\ Style-Node\ Border\ Color-Discrete\ Mapper.mapping.controllerType=-1
+nodeBorderColorCalculator.Nested\ Network\ Style-Node\ Border\ Color-Discrete\ Mapper.mapping.map.yes=0,102,204
+nodeBorderColorCalculator.Nested\ Network\ Style-Node\ Border\ Color-Discrete\ Mapper.mapping.type=DiscreteMapping
+nodeBorderColorCalculator.Nested\ Network\ Style-Node\ Border\ Color-Discrete\ Mapper.visualPropertyType=NODE_BORDER_COLOR
+nodeFillColorCalculator.Nested\ Network\ Style-Node\ Color-Discrete\ Mapper.mapping.controller=has_nested_network
+nodeFillColorCalculator.Nested\ Network\ Style-Node\ Color-Discrete\ Mapper.mapping.controllerType=-1
+nodeFillColorCalculator.Nested\ Network\ Style-Node\ Color-Discrete\ Mapper.mapping.map.yes=255,255,255
+nodeFillColorCalculator.Nested\ Network\ Style-Node\ Color-Discrete\ Mapper.mapping.type=DiscreteMapping
+nodeFillColorCalculator.Nested\ Network\ Style-Node\ Color-Discrete\ Mapper.visualPropertyType=NODE_FILL_COLOR
+nodeFontSizeCalculator.Cloud-Node\ Font\ Size-Continuous\ Mapper.mapping.boundaryvalues=2
+nodeFontSizeCalculator.Cloud-Node\ Font\ Size-Continuous\ Mapper.mapping.bv0.domainvalue=1.0
+nodeFontSizeCalculator.Cloud-Node\ Font\ Size-Continuous\ Mapper.mapping.bv0.equal=12.0
+nodeFontSizeCalculator.Cloud-Node\ Font\ Size-Continuous\ Mapper.mapping.bv0.greater=12.0
+nodeFontSizeCalculator.Cloud-Node\ Font\ Size-Continuous\ Mapper.mapping.bv0.lesser=1.0
+nodeFontSizeCalculator.Cloud-Node\ Font\ Size-Continuous\ Mapper.mapping.bv1.domainvalue=64.0
+nodeFontSizeCalculator.Cloud-Node\ Font\ Size-Continuous\ Mapper.mapping.bv1.equal=300.0
+nodeFontSizeCalculator.Cloud-Node\ Font\ Size-Continuous\ Mapper.mapping.bv1.greater=1.0
+nodeFontSizeCalculator.Cloud-Node\ Font\ Size-Continuous\ Mapper.mapping.bv1.lesser=300.0
+nodeFontSizeCalculator.Cloud-Node\ Font\ Size-Continuous\ Mapper.mapping.controller=Degree
+nodeFontSizeCalculator.Cloud-Node\ Font\ Size-Continuous\ Mapper.mapping.interpolator=LinearNumberToNumberInterpolator
+nodeFontSizeCalculator.Cloud-Node\ Font\ Size-Continuous\ Mapper.mapping.type=ContinuousMapping
+nodeFontSizeCalculator.Cloud-Node\ Font\ Size-Continuous\ Mapper.visualPropertyType=NODE_FONT_SIZE
+nodeFontSizeCalculator.Cloud-Node\ Font\ Size-Discrete\ Mapper.mapping.controller=Degree
+nodeFontSizeCalculator.Cloud-Node\ Font\ Size-Discrete\ Mapper.mapping.controllerType=-1
+nodeFontSizeCalculator.Cloud-Node\ Font\ Size-Discrete\ Mapper.mapping.map.10=30.0
+nodeFontSizeCalculator.Cloud-Node\ Font\ Size-Discrete\ Mapper.mapping.map.11=32.0
+nodeFontSizeCalculator.Cloud-Node\ Font\ Size-Discrete\ Mapper.mapping.map.12=34.0
+nodeFontSizeCalculator.Cloud-Node\ Font\ Size-Discrete\ Mapper.mapping.map.13=36.0
+nodeFontSizeCalculator.Cloud-Node\ Font\ Size-Discrete\ Mapper.mapping.map.14=38.0
+nodeFontSizeCalculator.Cloud-Node\ Font\ Size-Discrete\ Mapper.mapping.map.15=40.0
+nodeFontSizeCalculator.Cloud-Node\ Font\ Size-Discrete\ Mapper.mapping.map.17=42.0
+nodeFontSizeCalculator.Cloud-Node\ Font\ Size-Discrete\ Mapper.mapping.map.18=44.0
+nodeFontSizeCalculator.Cloud-Node\ Font\ Size-Discrete\ Mapper.mapping.map.19=46.0
+nodeFontSizeCalculator.Cloud-Node\ Font\ Size-Discrete\ Mapper.mapping.map.1=12.0
+nodeFontSizeCalculator.Cloud-Node\ Font\ Size-Discrete\ Mapper.mapping.map.20=48.0
+nodeFontSizeCalculator.Cloud-Node\ Font\ Size-Discrete\ Mapper.mapping.map.22=50.0
+nodeFontSizeCalculator.Cloud-Node\ Font\ Size-Discrete\ Mapper.mapping.map.24=52.0
+nodeFontSizeCalculator.Cloud-Node\ Font\ Size-Discrete\ Mapper.mapping.map.27=54.0
+nodeFontSizeCalculator.Cloud-Node\ Font\ Size-Discrete\ Mapper.mapping.map.29=56.0
+nodeFontSizeCalculator.Cloud-Node\ Font\ Size-Discrete\ Mapper.mapping.map.2=14.0
+nodeFontSizeCalculator.Cloud-Node\ Font\ Size-Discrete\ Mapper.mapping.map.30=58.0
+nodeFontSizeCalculator.Cloud-Node\ Font\ Size-Discrete\ Mapper.mapping.map.39=60.0
+nodeFontSizeCalculator.Cloud-Node\ Font\ Size-Discrete\ Mapper.mapping.map.3=16.0
+nodeFontSizeCalculator.Cloud-Node\ Font\ Size-Discrete\ Mapper.mapping.map.44=62.0
+nodeFontSizeCalculator.Cloud-Node\ Font\ Size-Discrete\ Mapper.mapping.map.4=18.0
+nodeFontSizeCalculator.Cloud-Node\ Font\ Size-Discrete\ Mapper.mapping.map.5=20.0
+nodeFontSizeCalculator.Cloud-Node\ Font\ Size-Discrete\ Mapper.mapping.map.64=64.0
+nodeFontSizeCalculator.Cloud-Node\ Font\ Size-Discrete\ Mapper.mapping.map.6=22.0
+nodeFontSizeCalculator.Cloud-Node\ Font\ Size-Discrete\ Mapper.mapping.map.7=24.0
+nodeFontSizeCalculator.Cloud-Node\ Font\ Size-Discrete\ Mapper.mapping.map.8=26.0
+nodeFontSizeCalculator.Cloud-Node\ Font\ Size-Discrete\ Mapper.mapping.map.9=28.0
+nodeFontSizeCalculator.Cloud-Node\ Font\ Size-Discrete\ Mapper.mapping.type=DiscreteMapping
+nodeFontSizeCalculator.Cloud-Node\ Font\ Size-Discrete\ Mapper.visualPropertyType=NODE_FONT_SIZE
+nodeFontSizeCalculator.Node\ Font\ Size-Continuous\ Mapper.mapping.boundaryvalues=0
+nodeFontSizeCalculator.Node\ Font\ Size-Continuous\ Mapper.mapping.controller=Degree
+nodeFontSizeCalculator.Node\ Font\ Size-Continuous\ Mapper.mapping.interpolator=LinearNumberToNumberInterpolator
+nodeFontSizeCalculator.Node\ Font\ Size-Continuous\ Mapper.mapping.type=ContinuousMapping
+nodeFontSizeCalculator.Node\ Font\ Size-Continuous\ Mapper.visualPropertyType=NODE_FONT_SIZE
+nodeFontSizeCalculator.Node\ Font\ Size-Discrete\ Mapper.mapping.controller=Degree
+nodeFontSizeCalculator.Node\ Font\ Size-Discrete\ Mapper.mapping.controllerType=-1
+nodeFontSizeCalculator.Node\ Font\ Size-Discrete\ Mapper.mapping.type=DiscreteMapping
+nodeFontSizeCalculator.Node\ Font\ Size-Discrete\ Mapper.visualPropertyType=NODE_FONT_SIZE
+nodeLabelCalculator.Aqua-Node\ Label-Passthrough\ Mapper.mapping.controller=ID
+nodeLabelCalculator.Aqua-Node\ Label-Passthrough\ Mapper.mapping.type=PassThroughMapping
+nodeLabelCalculator.Aqua-Node\ Label-Passthrough\ Mapper.visualPropertyType=NODE_LABEL
+nodeLabelCalculator.BasicPassThrough.mapping.controller=label
+nodeLabelCalculator.BasicPassThrough.mapping.type=PassThroughMapping
+nodeLabelCalculator.BasicPassThrough.visualPropertyType=NODE_LABEL
+nodeLabelCalculator.Cloud-Node\ Label-Passthrough\ Mapper.mapping.controller=ID
+nodeLabelCalculator.Cloud-Node\ Label-Passthrough\ Mapper.mapping.type=PassThroughMapping
+nodeLabelCalculator.Cloud-Node\ Label-Passthrough\ Mapper.visualPropertyType=NODE_LABEL
+nodeLabelCalculator.Nested\ Network\ Style-Node\ Label-Passthrough\ Mapper.mapping.controller=ID
+nodeLabelCalculator.Nested\ Network\ Style-Node\ Label-Passthrough\ Mapper.mapping.type=PassThroughMapping
+nodeLabelCalculator.Nested\ Network\ Style-Node\ Label-Passthrough\ Mapper.visualPropertyType=NODE_LABEL
+nodeLabelCalculator.NodeLabel.mapping.controller=ID
+nodeLabelCalculator.NodeLabel.mapping.type=PassThroughMapping
+nodeLabelCalculator.NodeLabel.visualPropertyType=NODE_LABEL
+nodeLabelCalculator.Pipe-Node\ Label-Passthrough\ Mapper.mapping.controller=ID
+nodeLabelCalculator.Pipe-Node\ Label-Passthrough\ Mapper.mapping.type=PassThroughMapping
+nodeLabelCalculator.Pipe-Node\ Label-Passthrough\ Mapper.visualPropertyType=NODE_LABEL
+nodeLabelCalculator.Ripple-Node\ Label-Passthrough\ Mapper.mapping.controller=ID
+nodeLabelCalculator.Ripple-Node\ Label-Passthrough\ Mapper.mapping.type=PassThroughMapping
+nodeLabelCalculator.Ripple-Node\ Label-Passthrough\ Mapper.visualPropertyType=NODE_LABEL
+nodeLabelCalculator.Skeleton-Node\ Label-Passthrough\ Mapper.mapping.controller=ID
+nodeLabelCalculator.Skeleton-Node\ Label-Passthrough\ Mapper.mapping.type=PassThroughMapping
+nodeLabelCalculator.Skeleton-Node\ Label-Passthrough\ Mapper.visualPropertyType=NODE_LABEL
+nodeLabelCalculator.Solid-Node\ Label-Passthrough\ Mapper.mapping.controller=ID
+nodeLabelCalculator.Solid-Node\ Label-Passthrough\ Mapper.mapping.type=PassThroughMapping
+nodeLabelCalculator.Solid-Node\ Label-Passthrough\ Mapper.visualPropertyType=NODE_LABEL
+nodeLabelCalculator.Subway-Node\ Label-Passthrough\ Mapper.mapping.controller=ID
+nodeLabelCalculator.Subway-Node\ Label-Passthrough\ Mapper.mapping.type=PassThroughMapping
+nodeLabelCalculator.Subway-Node\ Label-Passthrough\ Mapper.visualPropertyType=NODE_LABEL
+nodeLabelCalculator.Universe-Node\ Label-Passthrough\ Mapper.mapping.controller=ID
+nodeLabelCalculator.Universe-Node\ Label-Passthrough\ Mapper.mapping.type=PassThroughMapping
+nodeLabelCalculator.Universe-Node\ Label-Passthrough\ Mapper.visualPropertyType=NODE_LABEL
+nodeLabelCalculator.id\ as\ node\ labels.mapping.controller=ID
+nodeLabelCalculator.id\ as\ node\ labels.mapping.type=PassThroughMapping
+nodeLabelCalculator.id\ as\ node\ labels.visualPropertyType=NODE_LABEL
+nodeLabelColor.Nested\ Network\ Style-Node\ Label\ Color-Discrete\ Mapper.mapping.controller=has_nested_network
+nodeLabelColor.Nested\ Network\ Style-Node\ Label\ Color-Discrete\ Mapper.mapping.controllerType=-1
+nodeLabelColor.Nested\ Network\ Style-Node\ Label\ Color-Discrete\ Mapper.mapping.map.yes=0,102,204
+nodeLabelColor.Nested\ Network\ Style-Node\ Label\ Color-Discrete\ Mapper.mapping.type=DiscreteMapping
+nodeLabelColor.Nested\ Network\ Style-Node\ Label\ Color-Discrete\ Mapper.visualPropertyType=NODE_LABEL_COLOR
+nodeLabelPositionCalculator.Nested\ Network\ Style-Node\ Label\ Position-Discrete\ Mapper.mapping.controller=has_nested_network
+nodeLabelPositionCalculator.Nested\ Network\ Style-Node\ Label\ Position-Discrete\ Mapper.mapping.controllerType=-1
+nodeLabelPositionCalculator.Nested\ Network\ Style-Node\ Label\ Position-Discrete\ Mapper.mapping.map.yes=SE,NW,c,0,0
+nodeLabelPositionCalculator.Nested\ Network\ Style-Node\ Label\ Position-Discrete\ Mapper.mapping.type=DiscreteMapping
+nodeLabelPositionCalculator.Nested\ Network\ Style-Node\ Label\ Position-Discrete\ Mapper.visualPropertyType=NODE_LABEL_POSITION
+nodeLineWidthCalculator.Nested\ Network\ Style-Node\ Line\ Width-Discrete\ Mapper.mapping.controller=has_nested_network
+nodeLineWidthCalculator.Nested\ Network\ Style-Node\ Line\ Width-Discrete\ Mapper.mapping.controllerType=-1
+nodeLineWidthCalculator.Nested\ Network\ Style-Node\ Line\ Width-Discrete\ Mapper.mapping.map.yes=5.0
+nodeLineWidthCalculator.Nested\ Network\ Style-Node\ Line\ Width-Discrete\ Mapper.mapping.type=DiscreteMapping
+nodeLineWidthCalculator.Nested\ Network\ Style-Node\ Line\ Width-Discrete\ Mapper.visualPropertyType=NODE_LINE_WIDTH
+nodeShapeCalculator.Nested\ Network\ Style-Node\ Shape-Discrete\ Mapper.mapping.controller=has_nested_network
+nodeShapeCalculator.Nested\ Network\ Style-Node\ Shape-Discrete\ Mapper.mapping.controllerType=-1
+nodeShapeCalculator.Nested\ Network\ Style-Node\ Shape-Discrete\ Mapper.mapping.map.yes=rect
+nodeShapeCalculator.Nested\ Network\ Style-Node\ Shape-Discrete\ Mapper.mapping.type=DiscreteMapping
+nodeShapeCalculator.Nested\ Network\ Style-Node\ Shape-Discrete\ Mapper.visualPropertyType=NODE_SHAPE
+nodeUniformSizeCalculator.Nested\ Network\ Style-Node\ Size-Discrete\ Mapper.mapping.controller=has_nested_network
+nodeUniformSizeCalculator.Nested\ Network\ Style-Node\ Size-Discrete\ Mapper.mapping.controllerType=-1
+nodeUniformSizeCalculator.Nested\ Network\ Style-Node\ Size-Discrete\ Mapper.mapping.map.yes=60.0
+nodeUniformSizeCalculator.Nested\ Network\ Style-Node\ Size-Discrete\ Mapper.mapping.type=DiscreteMapping
+nodeUniformSizeCalculator.Nested\ Network\ Style-Node\ Size-Discrete\ Mapper.visualPropertyType=NODE_SIZE
+nodeUniformSizeCalculator.Node\ Size-Continuous\ Mapper.mapping.boundaryvalues=0
+nodeUniformSizeCalculator.Node\ Size-Continuous\ Mapper.mapping.controller=Degree
+nodeUniformSizeCalculator.Node\ Size-Continuous\ Mapper.mapping.interpolator=LinearNumberToNumberInterpolator
+nodeUniformSizeCalculator.Node\ Size-Continuous\ Mapper.mapping.type=ContinuousMapping
+nodeUniformSizeCalculator.Node\ Size-Continuous\ Mapper.visualPropertyType=NODE_SIZE
+nodeUniformSizeCalculator.Ripple-Node\ Size-Continuous\ Mapper.mapping.boundaryvalues=2
+nodeUniformSizeCalculator.Ripple-Node\ Size-Continuous\ Mapper.mapping.bv0.domainvalue=1.0
+nodeUniformSizeCalculator.Ripple-Node\ Size-Continuous\ Mapper.mapping.bv0.equal=30.0
+nodeUniformSizeCalculator.Ripple-Node\ Size-Continuous\ Mapper.mapping.bv0.greater=30.0
+nodeUniformSizeCalculator.Ripple-Node\ Size-Continuous\ Mapper.mapping.bv0.lesser=1.0
+nodeUniformSizeCalculator.Ripple-Node\ Size-Continuous\ Mapper.mapping.bv1.domainvalue=99.9999994635582
+nodeUniformSizeCalculator.Ripple-Node\ Size-Continuous\ Mapper.mapping.bv1.equal=1000.0
+nodeUniformSizeCalculator.Ripple-Node\ Size-Continuous\ Mapper.mapping.bv1.greater=1000.0
+nodeUniformSizeCalculator.Ripple-Node\ Size-Continuous\ Mapper.mapping.bv1.lesser=1000.0
+nodeUniformSizeCalculator.Ripple-Node\ Size-Continuous\ Mapper.mapping.controller=Degree
+nodeUniformSizeCalculator.Ripple-Node\ Size-Continuous\ Mapper.mapping.interpolator=LinearNumberToNumberInterpolator
+nodeUniformSizeCalculator.Ripple-Node\ Size-Continuous\ Mapper.mapping.type=ContinuousMapping
+nodeUniformSizeCalculator.Ripple-Node\ Size-Continuous\ Mapper.visualPropertyType=NODE_SIZE
diff --git a/distribution/src/main/sampleData/yeastHighQuality.sif b/distribution/src/main/sampleData/yeastHighQuality.sif
new file mode 100644
index 0000000..e678982
--- /dev/null
+++ b/distribution/src/main/sampleData/yeastHighQuality.sif
@@ -0,0 +1,6888 @@
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+YMR021C pd YPR110C
+YMR021C pd YPR111W
+YMR043W pd YPR112C
+YMR043W pd YPR113W
+YGL192W pd YPR115W
+YNL068C pd YPR119W
+YMR043W pd YPR119W
+YOR372C pd YPR119W
+YBR049C pd YPR119W
+YER111C pd YPR119W
+YDL056W pd YPR120C
+YMR021C pd YPR123C
+YOR028C pd YPR124W
+YMR021C pd YPR124W
+YBR182C pd YPR124W
+YMR021C pd YPR125W
+YKL112W pd YPR128C
+YKL112W pd YPR129W
+YPR104C pd YPR131C
+YNL216W pd YPR131C
+YIR018W pd YPR131C
+YPR104C pd YPR132W
+YNL216W pd YPR132W
+YIR018W pd YPR132W
+YMR164C pd YPR133C
+YMR164C pd YPR133W-A
+YMR164C pd YPR134W
+YLR098C pd YPR139C
+YLR098C pd YPR140W
+YIR023W pd YPR145W
+YEL009C pd YPR145W
+YER040W pd YPR145W
+YDR259C pd YPR148C
+YNL068C pd YPR149W
+YOR372C pd YPR149W
+YNL216W pd YPR149W
+YDR259C pd YPR149W
+YOR372C pd YPR151C
+YHR206W pd YPR151C
+YGL073W pd YPR158W
+YPL075W pd YPR158W-A
+YPL075W pd YPR158W-B
+YBR049C pd YPR163C
+YBR049C pd YPR164W
+YPL038W pd YPR167C
+YPL038W pd YPR168W
+YKL112W pd YPR176C
+YKL112W pd YPR178W
+YBR049C pd YPR181C
+YBR049C pd YPR182W
+YDR146C pd YPR183W
+YKL112W pd YPR186C
+YKL112W pd YPR187W
+YKL109W pd YPR190C
+YKL109W pd YPR191W
+YDL106C pd YPR194C
+YIL131C pd YPR195C
+YBL008W pd YPR195C
+YOR038C pd YPR195C
+YPL049C pd YPR198W
+YBR182C pd YPR198W
+YHR084W pd YPR198W
+YPL248C pd YPR202W
+YLR013W pd YPR202W
+YGL013C pd YPR202W
+YKL043W pd YPR202W
+YMR182C pd YPR202W
+YIR018W pd YPR202W
+YPL248C pd YPR203W
+YLR013W pd YPR203W
+YGL013C pd YPR203W
+YKL043W pd YPR203W
+YMR182C pd YPR203W
+YIR018W pd YPR203W
diff --git a/javadoc/pom.xml b/javadoc/pom.xml
new file mode 100644
index 0000000..b3f7164
--- /dev/null
+++ b/javadoc/pom.xml
@@ -0,0 +1,177 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+
+ <parent>
+ <groupId>cytoscape</groupId>
+ <artifactId>parent</artifactId>
+ <version>2.8.4-SNAPSHOT</version>
+ </parent>
+
+ <groupId>cytoscape</groupId>
+ <artifactId>javadoc</artifactId>
+ <packaging>jar</packaging>
+ <name>Cytoscape Javadoc Distribution</name>
+
+ <build>
+ <plugins>
+ <plugin>
+ <artifactId>maven-javadoc-plugin</artifactId>
+ <version>2.7</version>
+ <configuration>
+ <encoding>UTF-8</encoding>
+ <locale>en</locale>
+ <javadocVersion>1.5</javadocVersion>
+ <links>
+ <link>http://download.oracle.com/javase/1.5.0/docs/api/</link>
+ </links>
+ <footer>Cytoscape ${project.version} API</footer>
+ <header>Cytoscape ${project.version} API</header>
+ <bottom>Copyright 2010 Cytoscape Consortium. All rights reserved.</bottom>
+ <maxmemory>2g</maxmemory>
+ <additionalJOption>-J-Xmx2g</additionalJOption>
+ <includeDependencySources>true</includeDependencySources>
+ <dependencySourceIncludes>
+ <dependencySourceInclude>cytoscape:*</dependencySourceInclude>
+ <dependencySourceInclude>cytoscape.corelibs:*</dependencySourceInclude>
+ </dependencySourceIncludes>
+
+ <!--
+ <excludePackageNames>archive:browser:com.nerius.*:coreCommands:coreCommands.*:csplugins.*:cytoscape.editor:cytoscape.editor.*:cytoscape.filters:cytoscape.filters.*:cytoscape.graph.layout:cytoscape.graph.layout.*:ding.view.test:edu.ucsd.*:fing.model.test:linkout:ManualLayout:ManualLayout.*:org.apache.*:org.cytoscape.coreplugin.*:org.cytoscape.EquationFunctions:org.cytoscape.EquationFunctions.*:org.jgraph:org.jgraph.*:prefuse.*:sbmlreader:cruft.obo.*:</excludePackageNames>
+ -->
+ </configuration>
+ <executions>
+ <execution>
+ <id>javadoc-jar</id>
+ <phase>package</phase>
+ <goals>
+ <goal>aggregate-jar</goal>
+ </goals>
+ </execution>
+ </executions>
+ </plugin>
+ </plugins>
+ </build>
+
+ <!-- bootstrap for cytoscape dependencies, namely the parent POM snapshots -->
+ <repositories>
+ <repository>
+ <id>cytoscape_snapshots</id>
+ <snapshots>
+ <enabled>true</enabled>
+ </snapshots>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <name>Cytoscape Snapshots</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/</url>
+ </repository>
+ <repository>
+ <id>cytoscape_releases</id>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ <name>Cytoscape Releases</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/releases/</url>
+ </repository>
+ </repositories>
+
+ <dependencies>
+ <!-- the application -->
+ <dependency>
+ <groupId>cytoscape</groupId>
+ <artifactId>application</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+
+ <!-- corelibs -->
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>util-intr</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>graph-dynamic</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>graph-fixed</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>giny</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>render-immed</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>render-stateful</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>render-export</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>fing</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>phoebe-dnd</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>geom-spacial</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>geom-rtree</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>undo-support</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>equations</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>task</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>ding</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>obo</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.corelibs</groupId>
+ <artifactId>commons-cli-1-x-cytocape-custom</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ </dependencies>
+</project>
+
diff --git a/legacy/build.xml b/legacy/build.xml
new file mode 100644
index 0000000..5ea7973
--- /dev/null
+++ b/legacy/build.xml
@@ -0,0 +1,1122 @@
+<?xml version="1.0"?>
+<!-- ======================================================= -->
+<!-- ======================================================= -->
+<!-- Build file for Cytoscape -->
+<!-- Created by Ethan Cerami, cerami at cbio.mskcc.org -->
+<!-- To get a quick listing of all ant targets, type: -->
+<!-- ant -projecthelp -->
+<!-- ======================================================= -->
+<!-- ======================================================= -->
+
+<project name="Cytoscape" default="jar" basedir=".">
+
+ <!-- =========================================================== -->
+ <!-- Define Directories and other environment variables -->
+ <!-- =========================================================== -->
+
+ <!-- Property file for any local build variables like the local webhost -->
+ <property file="build.properties" />
+
+ <!-- The directory containing library jar files -->
+ <property name="lib.dir" value="${basedir}/lib" />
+
+ <!-- Read in the system environment variables -->
+ <property environment="env"/>
+
+ <!-- The directory containing library jar files only for -->
+ <!-- testing and building. These files should not be in the -->
+ <!-- release lib directory. -->
+ <property name="buildlib.dir" value="${lib.dir}/build-libs" />
+
+ <!-- The directory containing source code -->
+ <property name="src.dir" value="${basedir}/src" />
+
+ <!-- The directory containing unit test source code -->
+ <property name="tests.dir" value="${basedir}/tests" />
+
+ <!-- The directory containing resources -->
+ <property name="resources.dir" value="${basedir}/resources" />
+
+ <!-- Temporary build directory -->
+ <!-- Any file generated by a build target should go in the build dir. -->
+ <property name="build.dir" value="${basedir}/build" />
+
+ <!-- JUnit report directory -->
+ <property name="junit.report.dir" value="${build.dir}/junit-reports" />
+
+ <!-- Temporary compiled classes directory -->
+ <property name="build.classes" value="${build.dir}/classes" />
+
+ <!-- Global "magic" property for <javac> -->
+ <property name="build.compiler" value="modern" />
+
+ <!-- Location of the corelibs sources (for javadocs) -->
+ <property name="corelibs.dir" value="${basedir}/../corelibs/" />
+
+ <!-- Release number -->
+ <!-- You should use version wherever you need to reference the
+ version for something. Note that version.num is ONLY a number.
+ This is primarily to support windows versioning. Do NOT add
+ letters, "beta", etc. to version.num.
+ Extra information can, however, be added to version. -->
+ <property name="version.num" value="2.8.0" />
+ <property name="version" value="${version.num}-alpha1" />
+ <property name="dirname.release.dir" value="cytoscape-v${version}" />
+ <property name="java.target_version" value="1.5" />
+
+ <!-- Web Start Directory -->
+ <property name="webstart.dir" value="${build.dir}/webstart" />
+
+ <!-- Temporary Release Directory -->
+ <property name="release.dir" value="${build.dir}/${dirname.release.dir}" />
+
+ <!-- Temporary directory for all distribution files -->
+ <property name="dist.dir" value="${build.dir}/dist" />
+
+ <!-- Manifest file name -->
+ <property name="manifest.file" value="${build.dir}/Cytoscape.manifest" />
+
+ <!-- Javadoc directories -->
+ <property name="javadoc.dir" value="${build.dir}/API" />
+
+ <!-- The XML Schema Directory used by JAXB -->
+ <property name="schema.dir" value="${basedir}/resources/schema" />
+
+ <!-- XML Schema files used by JAXB -->
+ <property name="xgmml.schema" value="xgmml.xsd" />
+ <property name="cysession.schema" value="cysession.xsd" />
+ <property name="bookmark.schema" value="bookmarks.xsd" />
+
+ <!-- Auto generated package name -->
+ <property name="package" value="cytoscape.generated" />
+
+ <!-- Check to see if install4j is available -->
+ <available property="install4j.available"
+ file="${env.INSTALL4J_HOME}/bin/install4j.jar"/>
+
+ <!-- ======================================================= -->
+ <!-- Cytoscape ClassPath definition -->
+ <!-- ======================================================= -->
+
+ <!-- Classpath with all lib JAR Files -->
+ <path id="classpath">
+ <pathelement path="${build.classes}" />
+ <!-- <pathelement path="${basedir}"/> -->
+ <fileset dir="${lib.dir}">
+ <include name="**/*.jar" />
+ </fileset>
+ <fileset dir="${buildlib.dir}">
+ <include name="**/*.jar" />
+ </fileset>
+ </path>
+
+ <!-- ======================================================= -->
+ <!-- For XJC compiler task -->
+ <!-- ======================================================= -->
+ <taskdef name="xjc" classname="com.sun.tools.xjc.XJCTask">
+ <classpath refid="classpath" />
+ </taskdef>
+
+ <!-- ======================================================= -->
+ <!-- For converting SVG files to PNGs. Specifically for -->
+ <!-- creating the splash screen. -->
+ <!-- ======================================================= -->
+ <taskdef name="rasterize"
+ classname="org.apache.tools.ant.taskdefs.optional.RasterizerTask">
+ <classpath refid="classpath" />
+ </taskdef>
+
+
+ <!-- ======================================================= -->
+ <!-- Clean generated packages -->
+ <!-- ======================================================= -->
+ <target name="clean-generated" description="Delete XJC generated packages.">
+
+ <!-- Clean up generated packages -->
+ <delete dir="${src.dir}/cytoscape/generated" />
+ <delete dir="${src.dir}/cytoscape/generated2" />
+ <delete dir="${src.dir}/cytoscape/bookmarks" />
+ </target>
+
+ <!-- ======================================================= -->
+ <!-- Generate package using XJC compiler -->
+ <!-- ======================================================= -->
+ <target name="bind" description="Run XJC to generate new packages.">
+
+ <xjc schema="${schema.dir}/${cysession.schema}"
+ destdir="${src.dir}"
+ package="${package}">
+ <produces dir="${src.dir}/cytoscape/generated"
+ includes="* impl/*" />
+ </xjc>
+ <!--
+ <xjc schema="${schema.dir}/${xgmml.schema}"
+ destdir="${src.dir}"
+ package="${package}2"
+ extension="true"
+ binding="${schema.dir}/binding.xjb">
+ <arg value="-nv" />
+ <produces dir="${src.dir}/cytoscape/generated2" includes="* impl/*" />
+ </xjc>
+ -->
+
+ <xjc schema="${schema.dir}/${bookmark.schema}"
+ destdir="${src.dir}"
+ package="cytoscape.bookmarks">
+ <arg value="-nv" />
+ <produces dir="${src.dir}/cytoscape/bookmarks" includes="* impl/*" />
+ </xjc>
+
+ <!-- copy prop file into build dir -->
+ <echo>Copying jaxb.properties from ${src.dir}/cytoscape/generated to build dir...</echo>
+ <copy todir="${build.classes}/cytoscape/generated">
+ <fileset dir="${src.dir}/cytoscape/generated" includes="*.properties" />
+ </copy>
+
+ <copy todir="${build.classes}/cytoscape/bookmarks">
+ <fileset dir="${src.dir}/cytoscape/bookmarks" includes="*.properties" />
+ </copy>
+ </target>
+
+
+ <!-- ======================================================= -->
+ <!-- Environment Information -->
+ <!-- ======================================================= -->
+
+ <!-- Outputs Current compilation classpath -->
+ <target name="show_cp">
+ <property name="temp" refid="classpath" />
+ <echo message="Classpath: ${temp}" />
+ </target>
+
+ <!-- ======================================================= -->
+ <!-- Create Build directories and copy images -->
+ <!-- ======================================================= -->
+
+ <!-- Target to create the build directories prior to compilation -->
+ <target name="prepare">
+ <mkdir dir="${build.dir}" />
+ <mkdir dir="${build.classes}" />
+
+ <!-- copy over images -->
+ <copy todir="${build.classes}/cytoscape/images">
+ <fileset dir="${basedir}/images" />
+ </copy>
+
+
+ <copy todir="${build.classes}">
+ <fileset dir="${src.dir}" includes="**/*.xml" />
+ </copy>
+ <copy todir="${build.classes}">
+ <fileset dir="${tests.dir}" includes="**/*.xml" />
+ </copy>
+
+ <antcall target="splash" />
+
+ </target>
+
+ <!-- ======================================================= -->
+ <!-- Create the PNG splash screen from the SVG file with the -->
+ <!-- proper version number substituted in. -->
+ <!-- ======================================================= -->
+ <target name="splash">
+ <filter token="version" value="${version}"/>
+ <echo>
+ ---------------------------------------
+ Creating splash and about screens
+ ---------------------------------------
+ </echo>
+ <copy file="images/CytoscapeSplashScreen.svg"
+ tofile="${build.classes}/cytoscape/images/CytoscapeSplashScreen.svg"
+ filtering="true"
+ overwrite="true"/>
+ <filter token="version" value="${version}"/>
+ <copy file="images/CytoscapeCredits.svg"
+ tofile="${build.classes}/cytoscape/images/CytoscapeCredits.svg"
+ filtering="true"
+ overwrite="true"/>
+ <available property="splashUpToDate"
+ file="${build.classes}/cytoscape/images/CytoscapeSplashScreen.png"/>
+ <antcall target="createSplash" />
+ </target>
+ <target name="createSplash" unless="splashUpToDate" >
+ <rasterize src="${build.classes}/cytoscape/images/CytoscapeSplashScreen.svg"
+ dest="${build.classes}/cytoscape/images/CytoscapeSplashScreen.png" />
+ <rasterize src="${build.classes}/cytoscape/images/CytoscapeCredits.svg"
+ dest="${build.classes}/cytoscape/images/CytoscapeCredits.png" />
+ </target>
+
+ <!-- ======================================================= -->
+ <!-- Clean the build environment -->
+ <!-- ======================================================= -->
+
+ <!-- Target to clean out all directories -->
+ <target name="clean" depends="clean-generated" description="Removes all generated files.">
+ <delete dir="${build.dir}" />
+ <delete file="${basedir}/cytoscape.jar" />
+ </target>
+
+ <!-- ======================================================= -->
+ <!-- Compile Cytoscape -->
+ <!-- ======================================================= -->
+ <!-- Target to compile all code -->
+ <target name="compile"
+ depends="prepare, bind"
+ description="Compiles all source code.">
+ <javac
+ destdir="${build.classes}"
+ nowarn="off"
+ debug="true"
+ source="${java.target_version}"
+ target="${java.target_version}"
+ optimize="on"
+ includeAntRuntime="false"
+ deprecation="yes">
+ <classpath refid="classpath" />
+ <include name="cytoscape/**" />
+ <src path="${src.dir}" />
+ <src path="${tests.dir}" />
+ <compilerarg line="-Xmaxwarns 10000" />
+ </javac>
+
+ <!-- Run RMIC for BioDataServer -->
+ <rmic classname="cytoscape.data.servers.BioDataServerRmi"
+ base="${build.classes}"
+ classpathref="classpath" />
+
+ <!-- copy resources/ directory to build area -->
+ <echo>Copying resources/ directory to build</echo>
+ <copy todir="${build.classes}/cytoscape/resources">
+ <fileset dir="${basedir}/resources" />
+ </copy>
+
+
+ <!-- build help system -->
+ <antcall target="help" />
+
+ </target>
+
+ <!-- ======================================================= -->
+ <!-- Generates cytoscape manual - see build file in docs -->
+ <!-- dir for details. -->
+ <!-- ======================================================= -->
+ <target name="manual">
+ <ant dir="docs" target="all"/>
+ </target>
+
+ <!-- ======================================================= -->
+ <!-- Build Cytoscape Help - Index html source files etc. -->
+ <!-- ======================================================= -->
+ <target name="help"
+ description="Builds Help system files (full text search db, etc).">
+ <!-- Check to see if the help files need to be indexed... -->
+ <uptodate property="helpIsUpToDate"
+ targetfile="${build.classes}/cytoscape/help/JavaHelpSearch/SCHEMA">
+ <srcfiles dir="${basedir}/docs/help" includes="**/*" />
+ </uptodate>
+ <antcall target="buildHelp" />
+ </target>
+
+ <target name="buildHelp"
+ unless="helpIsUpToDate">
+ <!-- Copy the JavaHelp system files and html source over to build area -->
+ <echo>Copying javahelp files: helpset, html files, images</echo>
+ <copy todir="${build.classes}/cytoscape/help">
+ <fileset dir="${basedir}/docs/help" />
+ </copy>
+ <mkdir dir="${build.classes}/cytoscape/help/images"/>
+ <copy todir="${build.classes}/cytoscape/help/images">
+ <fileset dir="${basedir}/docs/images" />
+ </copy>
+
+ <!-- then index the help files in the build area -->
+ <echo>Indexing help files and creating search db</echo>
+ <java classname="com.sun.java.help.search.Indexer"
+ classpathref="classpath"
+ dir="${build.classes}/cytoscape/help"
+ fork="true">
+ <arg value="-db" />
+ <arg value="JavaHelpSearch" />
+ <arg value="${build.classes}/cytoscape/help" />
+ </java>
+ </target>
+
+
+ <!-- ======================================================= -->
+ <!-- Run Cytoscape -->
+ <!-- ======================================================= -->
+
+ <!-- Target to Run Cytoscape -->
+ <target name="run" depends="test" description="Runs Cytoscape.">
+ <java jar="${basedir}/cytoscape.jar" fork="true">
+ <arg value="-p" />
+ <arg value="plugins/core" />
+ </java>
+ </target>
+
+ <!-- ========================================================= -->
+ <!-- Make the Full JavaDocs for Cytoscape (including key libs) -->
+ <!-- ========================================================= -->
+ <target name="doc" description="Runs JavaDoc.">
+ <javadoc destdir="${javadoc.dir}"
+ source="1.5"
+ breakiterator="true"
+ Windowtitle="Cytoscape ${version} API"
+ header="Cytoscape ${version} (c) 2006,2007 ISB, MSKCC, UCSD"
+ footer="www.cytoscape.org"
+ classpathref="classpath"
+ access="public">
+
+ <packageset dir="${src.dir}">
+ <include name="cytoscape/**" />
+ <!-- exclude xjc generated code -->
+ <exclude name="cytoscape/generated/" />
+ <exclude name="cytoscape/generated2/" />
+ <exclude name="cytoscape/bookmarks/" />
+ </packageset>
+ <packageset dir="${corelibs.dir}/ding/src">
+ <include name="**" />
+ <exclude name="ding/view/test/" />
+ </packageset>
+ <packageset dir="${corelibs.dir}/fing/src">
+ <include name="**" />
+ <exclude name="fing/model/test/" />
+ </packageset>
+ <packageset dir="${corelibs.dir}/giny/src">
+ <include name="**" />
+ </packageset>
+ <packageset dir="${corelibs.dir}/task/src">
+ <include name="cytoscape/**" />
+ </packageset>
+ <packageset dir="${corelibs.dir}/undo.support/src">
+ <include name="undo/**" />
+ </packageset>
+ <packageset dir="${corelibs.dir}/util.intr/src">
+ <include name="cytoscape/**" />
+ <exclude name="cytoscape/util/intr/test/" />
+ </packageset>
+
+ <link href="http://java.sun.com/j2se/1.5/docs/api/" />
+ <!-- link href="http://csbi.sourceforge.net/API/" / -->
+ </javadoc>
+ </target>
+
+ <!-- ======================================================= -->
+ <!-- Make the JavaDocs for cytoscape jar ONLY -->
+ <!-- ======================================================= -->
+ <target name="doc-simple" description="Runs JavaDoc.">
+ <javadoc destdir="${javadoc.dir}"
+ source="1.5"
+ breakiterator="true"
+ Windowtitle="Cytoscape ${version} API"
+ header="Cytoscape ${version} (c) 2006-2010 ISB, MSKCC, UCSD"
+ footer="www.cytoscape.org"
+ classpathref="classpath"
+ access="public">
+
+ <packageset dir="${src.dir}">
+ <include name="cytoscape/**" />
+ <!-- exclude xjc generated code -->
+ <exclude name="cytoscape/generated/" />
+ <exclude name="cytoscape/generated2/" />
+ <exclude name="cytoscape/bookmarks/" />
+ </packageset>
+
+ <link href="http://java.sun.com/j2se/1.5/docs/api/" />
+ </javadoc>
+ </target>
+
+ <!-- ======================================================= -->
+ <!-- Manfiest Target -->
+ <!-- Automatically creates Cytoscape Manifest File, based on -->
+ <!-- JAR Files located in cytoscape.lib -->
+ <!-- ======================================================= -->
+ <target name="generate_manifest" depends="prepare">
+ <echo>
+ ***********************************************
+ Creating Cytoscape Manifest File
+ ***********************************************
+ </echo>
+ <path id="manifest.classpath">
+ <fileset dir="${lib.dir}">
+ <include name="*.jar" />
+ </fileset>
+ </path>
+ <pathconvert property="manifest.classpath.string"
+ pathsep=" ">
+ <path refid="manifest.classpath" />
+ <chainedmapper>
+ <flattenmapper/>
+ <globmapper from="*" to="lib/*" handledirsep="yes" />
+ </chainedmapper>
+ </pathconvert>
+ <manifest file="${manifest.file}">
+ <attribute name="Main-Class" value="cytoscape.CyMain" />
+ <attribute name="Class-Path" value="${manifest.classpath.string}" />
+ <attribute name="Java-Version" value="${java.target_version}" />
+ </manifest>
+ </target>
+
+ <!-- ======================================================= -->
+ <!-- Create the Cytoscape Jar file -->
+ <!-- ======================================================= -->
+
+ <!-- Target to Create Cytoscape Jar File -->
+ <target name="jar"
+ depends="compile, generate_manifest"
+ description="Creates Cytoscape Jar File.">
+
+ <echo>
+ ***********************************************
+ Creating Cytoscape JAR File
+ ***********************************************
+ </echo>
+
+ <copy file="${basedir}/resources/javax.imageio.spi.ImageWriterSpi"
+ todir="${build.dir}/temp/META-INF/services" />
+ <copy file="${basedir}/resources/org.freehep.util.export.ExportFileType"
+ todir="${build.dir}/temp/META-INF/services" />
+ <copy file="${basedir}/resources/props/vizmap.props"
+ todir="${build.classes}" />
+
+ <filter token="version" value="${version.num}"/>
+ <copy file="${basedir}/resources/props/cytoscape.props"
+ todir="${build.classes}"
+ filtering="true"
+ overwrite="true"/>
+
+ <jar destfile="${basedir}/cytoscape.jar"
+ manifest="${manifest.file}">
+ <fileset dir="${build.classes}" />
+ <fileset dir="${build.dir}/temp" />
+ </jar>
+ </target>
+
+ <!-- =================================================================== -->
+ <!-- Runs the tests in the project jar quickly, and sets a property -->
+ <!-- if a test fails. -->
+ <!-- =================================================================== -->
+ <target name="test" depends="jar">
+
+ <echo>
+ ***********************************************
+ Running all unit tests (quickly).
+ ***********************************************
+ </echo>
+ <mkdir dir="${junit.report.dir}" />
+ <mkdir dir="${junit.report.dir}/fast" />
+ <junit printsummary="yes"
+ haltonfailure="no"
+ maxmemory="512m">
+ <!-- We need a new classpath so that AllTests is read from
+ the cytoscape.jar file instead of the build dir which
+ allows it reflect on the jar file and find other tests. -->
+ <classpath>
+ <fileset dir="${basedir}">
+ <include name="*.jar" />
+ </fileset>
+ <fileset dir="${lib.dir}">
+ <include name="*.jar" />
+ </fileset>
+ </classpath>
+ <formatter type="plain" usefile="true" />
+ <formatter type="xml" usefile="true" />
+ <test name="cytoscape.AllTests"
+ fork="yes"
+ todir="${junit.report.dir}/fast"
+ failureProperty="junit.test.failure"
+ errorProperty="junit.test.failure">
+ </test>
+ </junit>
+ <junitreport todir="${junit.report.dir}/fast">
+ <fileset dir="${junit.report.dir}/fast">
+ <include name="TEST-*.xml" />
+ </fileset>
+ <report format="frames" todir="${junit.report.dir}/fast" />
+ </junitreport>
+ <fail message="JUnit Tests failed! Check ${junit.report.dir}/fast/index.html for details. Run 'ant test-slow' for more useful output."
+ if="junit.test.failure" />
+ </target>
+
+
+ <!-- ======================================================= -->
+ <!-- Run All of the Cytoscape Unit Tests without gui -->
+ <!-- and generates an html report. This task is only run -->
+ <!-- if the test-fast case fails. -->
+ <!-- ======================================================= -->
+ <target name="test-slow" depends="jar">
+ <echo>
+ ***********************************************
+ Running all unit tests individually.
+ ***********************************************
+ </echo>
+ <mkdir dir="${junit.report.dir}" />
+ <junit printsummary="yes"
+ haltonfailure="no"
+ maxmemory="512m">
+ <classpath refid="classpath" />
+ <formatter type="plain" usefile="true" />
+ <formatter type="xml" usefile="true" />
+ <batchtest fork="yes"
+ todir="${junit.report.dir}"
+ failureProperty="junit.test.failure">
+ <fileset dir="${src.dir}"
+ includes="**/*Test.java"
+ excludes="**/AllTests.java" />
+ <fileset dir="${tests.dir}"
+ includes="**/*Test.java"
+ excludes="**/AllTests.java" />
+ </batchtest>
+ </junit>
+
+ <junitreport todir="${junit.report.dir}">
+ <fileset dir="${junit.report.dir}">
+ <include name="TEST-*.xml" />
+ </fileset>
+ <report format="frames" todir="${junit.report.dir}" />
+ </junitreport>
+
+ <fail message="JUnit Tests failed! Check ${junit.report.dir}/index.html for details."
+ if="junit.test.failure" />
+
+ </target>
+
+ <!-- ======================================================= -->
+ <!-- Run All of the Cytoscape Unit Tests -->
+ <!-- ======================================================= -->
+ <target name="test-gui"
+ depends="jar"
+ description="Runs all Cytoscape Unit Tests.">
+
+ <!-- Create a new classpath so that we're running from a jar file
+ which is needed by AllTests. -->
+ <path id="junit.classpath">
+ <fileset dir="${lib.dir}">
+ <include name="**/*.jar" />
+ </fileset>
+ <fileset dir="${basedir}">
+ <include name="**/*.jar" />
+ </fileset>
+ </path>
+
+ <java classname="cytoscape.AllTests"
+ classpathref="junit.classpath"
+ fork="true"
+ maxmemory="512m">
+ <arg line="-ui" />
+ </java>
+ </target>
+
+ <!-- ======================================================= -->
+ <!-- Run all of the Swing Unit Tests -->
+ <!-- ======================================================= -->
+ <target name="test-swing" depends="jar">
+ <mkdir dir="${junit.report.dir}" />
+ <junit printsummary="yes"
+ haltonfailure="no"
+ maxmemory="512m" showoutput="on">
+ <classpath refid="classpath" />
+ <formatter type="plain" usefile="true" />
+ <formatter type="xml" usefile="true" />
+ <batchtest fork="yes"
+ todir="${junit.report.dir}"
+ failureProperty="junit.test.failure">
+ <fileset dir="${tests.dir}"
+ includes="**/*TestSwing.java" />
+ </batchtest>
+ </junit>
+
+ <junitreport todir="${junit.report.dir}">
+ <fileset dir="${junit.report.dir}">
+ <include name="TEST-*.xml" />
+ </fileset>
+ <report format="frames" todir="${junit.report.dir}" />
+ </junitreport>
+
+ <fail message="JUnit Tests failed! Check ${junit.report.dir}/index.html for details."
+ if="junit.test.failure" />
+
+ </target>
+
+ <!-- ======================================================= -->
+ <!-- Run all of the JFC Unit Tests -->
+ <!-- ======================================================= -->
+ <target name="test-jfc" depends="jar">
+ <mkdir dir="${junit.report.dir}" />
+ <junit printsummary="yes"
+ haltonfailure="no"
+ maxmemory="512m">
+ <classpath refid="classpath" />
+ <formatter type="plain" usefile="true" />
+ <formatter type="xml" usefile="true" />
+ <batchtest fork="yes"
+ todir="${junit.report.dir}"
+ failureProperty="junit.test.failure">
+ <fileset dir="${tests.dir}"
+ includes="**/*TestJFC.java" />
+ </batchtest>
+ </junit>
+
+ <junitreport todir="${junit.report.dir}">
+ <fileset dir="${junit.report.dir}">
+ <include name="TEST-*.xml" />
+ </fileset>
+ <report format="frames" todir="${junit.report.dir}" />
+ </junitreport>
+
+ <fail message="JUnit Tests failed! Check ${junit.report.dir}/index.html for details."
+ if="junit.test.failure" />
+
+ </target>
+
+ <!-- ======================================================= -->
+ <!-- Creates the release files used for the distribution -->
+ <!-- -->
+ <!-- Use the "dist" target to create a Cytoscape release. -->
+ <!-- -->
+ <!-- ======================================================= -->
+ <target name="release"
+ depends="jar, test"
+ description="Creates Cytoscape Release">
+
+ <echo>
+ ***********************************************
+ Creating Cytoscape Release
+ ***********************************************
+ </echo>
+
+ <!-- Create Release Directory -->
+ <mkdir dir="${release.dir}" />
+ <mkdir dir="${release.dir}/plugins" />
+ <mkdir dir="${release.dir}/sampleData" />
+
+ <echo>
+ ---------------------------------------
+ Copying over all necessary JAR files.
+ ---------------------------------------
+ </echo>
+
+ <copy file="${basedir}/cytoscape.jar" tofile="${release.dir}/cytoscape.jar" />
+
+ <copy toDir="${release.dir}/lib">
+ <fileset dir="${lib.dir}" includes="*.jar" />
+ </copy>
+
+
+ <echo>
+ ---------------------------------------
+ Copying over all OS-specific scripts.
+ ---------------------------------------
+ </echo>
+ <copy file="resources/bin/cytoscape.bat" todir="${release.dir}" />
+ <copy file="resources/bin/cytoscape.sh" todir="${release.dir}" />
+ <copy file="resources/bin/gen_vmoptions.sh" todir="${release.dir}" />
+ <copy file="resources/bin/gen_vmoptions.bat" todir="${release.dir}" />
+ <chmod perm="+x" file="${release.dir}/cytoscape.sh" />
+ <chmod perm="+x" file="${release.dir}/gen_vmoptions.sh" />
+
+
+ <echo>
+ ------------------------------------------------------
+ Copying over user documentation and Cytoscape License.
+ ------------------------------------------------------
+ </echo>
+ <copy file="docs/LICENSE.txt" todir="${release.dir}" />
+ <copy file="docs/LICENSE.html" todir="${release.dir}" />
+ <mkdir dir="${release.dir}/docs"/>
+ <filter token="version" value="${version}"/>
+ <copy file="docs/INSTALL.txt" todir="${release.dir}/docs" filtering="true"/>
+ <copy todir="${release.dir}/docs">
+ <fileset dir="docs/pdf">
+ <include name="*.pdf"/>
+ </fileset>
+ <fileset dir="docs/html">
+ <include name="*.html"/>
+ </fileset>
+ </copy>
+ <mkdir dir="${release.dir}/docs/images"/>
+ <copy todir="${release.dir}/docs/images">
+ <fileset dir="docs/images"/>
+ </copy>
+
+
+ <echo>
+ ---------------------------------------
+ Copying over sample data files.
+ ---------------------------------------
+ </echo>
+ <copy file="testData/README_SAMPLE_DATA.txt" todir="${release.dir}/sampleData" />
+ <copy file="testData/BINDyeast.sif" todir="${release.dir}/sampleData" />
+ <copy file="testData/BINDhuman.sif" todir="${release.dir}/sampleData" />
+ <copy file="testData/galExpData.pvals" todir="${release.dir}/sampleData" />
+ <copy file="testData/galFiltered.gml" todir="${release.dir}/sampleData" />
+ <copy file="testData/galFiltered.xgmml" todir="${release.dir}/sampleData" />
+ <copy file="testData/galFiltered.sif" todir="${release.dir}/sampleData" />
+ <copy file="testData/galFiltered.cys" todir="${release.dir}/sampleData" />
+ <copy file="testData/yeastHighQuality.sif" todir="${release.dir}/sampleData" />
+ <copy file="testData/galFiltered.edgeAttrs1" todir="${release.dir}/sampleData" />
+ <copy file="testData/galFiltered.edgeAttrs2" todir="${release.dir}/sampleData" />
+ <copy file="testData/galFiltered.nodeAttrs1" todir="${release.dir}/sampleData" />
+ <copy file="testData/galFiltered.nodeAttrs2" todir="${release.dir}/sampleData" />
+ <copy file="testData/galFiltered.nodeAttrTable.xls" todir="${release.dir}/sampleData" />
+ <copy file="testData/galExpData.pvals" todir="${release.dir}/sampleData" />
+ <copy file="testData/galExpData.probeset.pvals" todir="${release.dir}/sampleData" />
+ <copy file="testData/gal.probeset.na" todir="${release.dir}/sampleData" />
+ <copy file="testData/human_interactome_may07_small.tab.gz" todir="${release.dir}/sampleData" />
+ <copy file="testData/Apoptosis_BioPAX.xml" todir="${release.dir}/sampleData" />
+ <copy file="testData/sampleStyles.props" todir="${release.dir}/sampleData" />
+ <copy file="testData/NNFData/Sample.nnf" todir="${release.dir}/sampleData" />
+
+ <!-- Copy over Third Party Licenses -->
+ <echo>
+ ---------------------------------------
+ Copying over third party licenses.
+ ---------------------------------------
+ </echo>
+ <mkdir dir="${release.dir}/licenses" />
+ <copy todir="${release.dir}/licenses">
+ <fileset dir="licenses">
+ <include name="*.txt" />
+ <include name="*.htm*" />
+ </fileset>
+ </copy>
+
+ <!-- Copy over Release PlugIns -->
+ <echo>
+ ---------------------------------------
+ Copying over PlugIns.
+ ---------------------------------------
+ </echo>
+ <copy todir="${release.dir}/plugins">
+ <fileset dir="plugins/core">
+ <include name="*.jar" />
+ </fileset>
+ </copy>
+ </target>
+
+ <target name="all" depends="release" />
+
+ <target name="release-extras"
+ depends="release"
+ description="add extra plugins into release">
+ <echo>
+ ---------------------------------------
+ Copying over extra PlugIns.
+ ---------------------------------------
+ </echo>
+ <copy todir="${release.dir}/plugins">
+ <fileset dir="plugins/extras">
+ <include name="*.jar" />
+ </fileset>
+ </copy>
+ </target>
+
+
+ <!-- ======================================================= -->
+ <!-- Creates a distribution based on the nightly build. -->
+ <!-- ======================================================= -->
+ <target name="nightly-release" depends="release">
+ <tstamp>
+ <format property="todays.date"
+ pattern="yyyy-MM-dd_hhmmaa" />
+ </tstamp>
+ <mkdir dir="${dist.dir}" />
+ <zip destfile="${dist.dir}/cytoscape-${todays.date}.zip"
+ basedir="${build.dir}"
+ includes="${dirname.release.dir}/**" />
+ </target>
+
+ <!-- ======================================================= -->
+ <!-- Create Zip files for distribution -->
+ <!-- Final releases are made available in zip_release/ dir -->
+ <!-- Questions? email: cerami at cbio.mskcc.org -->
+ <!-- -->
+ <!-- Use the "dist" target to create a Cytoscape release. -->
+ <!-- -->
+ <!-- ======================================================= -->
+ <target name="zip_release"
+ depends="release"
+ description="Creates Zipped Cytoscape Release Bundles">
+
+ <echo>
+ ---------------------------------------
+ Creating zip/tar.gz release bundles.
+ ---------------------------------------
+ </echo>
+ <mkdir dir="${dist.dir}" />
+
+ <!-- Create Windows Zip Distribution -->
+ <zip destfile="${dist.dir}/cytoscape-v${version}.zip"
+ basedir="${build.dir}"
+ includes="${dirname.release.dir}/**" />
+ <!-- Stupid Ant does not preserve execute permissions. -->
+
+ <!-- Create Unix/Linux/MaxOS X tar.gz Distribution -->
+ <!-- Include Executable Permissions -->
+ <tar tarfile="${dist.dir}/cytoscape-v${version}.tar">
+ <tarfileset dir="${build.dir}" mode="755">
+ <!-- Stupid Ant. -->
+ <include name="${dirname.release.dir}/*.sh" />
+ <include name="${dirname.release.dir}/*.bat" />
+ </tarfileset>
+ <!-- Stupid Ant makes this so hard when it's not. -->
+ <tarfileset dir="${build.dir}">
+ <!-- It's Java's fault. -->
+ <include name="${dirname.release.dir}/**" />
+ <exclude name="${dirname.release.dir}/*.sh" />
+ <exclude name="${dirname.release.dir}/*.bat" />
+ </tarfileset>
+ </tar>
+ <gzip src="${dist.dir}/cytoscape-v${version}.tar"
+ zipfile="${dist.dir}/cytoscape-v${version}.tar.gz" />
+ <delete file="${dist.dir}/cytoscape-v${version}.tar" />
+
+ </target>
+
+ <!-- Create tar.gz release of source code -->
+ <!-- Note that the source tar because does not preserve -->
+ <!-- individual permissions of files. This is a bug in Ant/Java. -->
+ <target name="source"
+ description="Generates a release .tar.gz of all source code">
+ <tar tarfile="${dist.dir}/cytoscapeSource-v${version}.tar">
+ <tarfileset dir="${basedir}">
+ <exclude name="build/**" />
+ <exclude name="CVS/**" />
+ <exclude name=".svn/**" />
+ <exclude name="*.log" />
+ </tarfileset>
+ </tar>
+ <gzip src="${dist.dir}/cytoscapeSource-v${version}.tar"
+ zipfile="${dist.dir}/cytoscapeSource-v${version}.tar.gz" />
+ <delete file="${dist.dir}/cytoscapeSource-v${version}.tar" />
+ </target>
+
+ <!-- ======================================================= -->
+ <!-- Creates the install bundles that users will use to -->
+ <!-- actually install cytoscape. -->
+ <!-- NOTE - you MUST have install4j installed on your system -->
+ <!-- with the environment variable INSTALL4J_HOME set and -->
+ <!-- pointing to said installation. -->
+ <!-- The cytoscape team has a floating license, contact us -->
+ <!-- for access. -->
+ <!-- -->
+ <!-- Use the "dist" target to create a Cytoscape release. -->
+ <!-- -->
+ <!-- ======================================================= -->
+ <taskdef name="install4j"
+ classname="com.install4j.Install4JTask"
+ classpath="${env.INSTALL4J_HOME}/bin/ant.jar"
+ onerror="ignore"/>
+
+ <target name="install-bundles"
+ if="install4j.available" >
+ <echo>
+ ${env.INSTALL4J_HOME}
+ ---------------------------------------
+ Creating install4j bundles
+ ---------------------------------------
+ </echo>
+ <filter token="version" value="${version}"/>
+ <filter token="windows_version" value="${version.num}"/>
+ <copy file="tools/Cytoscape.install4j"
+ tofile="build/Cytoscape.install4j"
+ filtering="true"
+ overwrite="true"/>
+ <install4j projectfile="build/Cytoscape.install4j"/>
+ </target>
+
+ <!-- ======================================================= -->
+ <!-- Creates all of the necessary installation files -->
+ <!-- Use this target when you're ready to create a cytoscape -->
+ <!-- release. -->
+ <!-- ======================================================= -->
+ <target name="dist"
+ depends="zip_release,doc,install-bundles,source">
+ <copy toDir="${dist.dir}/javadoc">
+ <fileset dir="${javadoc.dir}" includes="**"/>
+ </copy>
+ </target>
+
+
+ <!-- ======================================================= -->
+ <!-- Create Cytoscape WebStart Distribution -->
+ <!-- Questions? email: cerami at cbio.mskcc.org -->
+ <!-- ======================================================= -->
+
+ <target name="jnlp.jar" depends="compile">
+ <jar destfile="${basedir}/resources/JnlpWriter.jar">
+ <fileset dir="${build.dir}/classes">
+ <include name="cytoscape/util/JnlpWriterUtil.class"/>
+ </fileset>
+ <manifest>
+ <attribute name="Main-Class" value="cytoscape.util.JnlpWriterUtil"/>
+ <attribute name="Class-Path" value="../lib/jdom-1.0.jar"/>
+ </manifest>
+ </jar>
+ </target>
+
+
+ <target name="jnlp" depends="release, jnlp.jar" description="Creates jnlp for webstart">
+ <fail message="You must specify a webstartURL argument when executing this task: ant -DwebstartURL=http://yourdomain.com [ant target]">
+ <condition>
+ <not> <isset property="webstartURL"/> </not>
+ </condition>
+ </fail>
+
+ <java jar="${basedir}/resources/JnlpWriter.jar" fork="true" failonerror="true">
+ <arg value="-filename"/>
+ <arg value="cy1.jnlp" />
+ <arg value="-cyto_dir" />
+ <arg value="${release.dir}" />
+ <arg value="-url" />
+ <arg value="${webstartURL}" />
+ <arg value="-save_dir" />
+ <arg value="${basedir}/resources/webstart" />
+ </java>
+ </target>
+
+ <target name="webstart" depends="jnlp" description="Creates Cytoscape Webstart Release">
+
+ <echo>
+ ***********************************************
+ Creating Cytoscape Webstart Release
+ * NOTE: If this is your first time using Webstart:
+ * you must create a keystore:
+ * keytool -genkey -alias cytoscape -keypass secret
+ * enter "secret" for the password.
+ ***********************************************
+ </echo>
+
+ <!-- Create Webstart Directory -->
+ <mkdir dir="${webstart.dir}" />
+ <mkdir dir="${webstart.dir}/plugins" />
+
+ <echo>
+ ---------------------------------------
+ Copying over all necessary JAR files.
+ ---------------------------------------
+ </echo>
+
+ <copy file="${basedir}/resources/webstart/cy1.jnlp" todir="${webstart.dir}" />
+
+ <copy todir="${webstart.dir}">
+ <fileset dir="${basedir}/resources/webstart">
+ <exclude name="*.jsp"/>
+ </fileset>
+ </copy>
+
+
+
+
+ <copy file="${basedir}/cytoscape.jar" tofile="${webstart.dir}/cytoscape.jar" />
+ <signjar jar="${webstart.dir}/cytoscape.jar" alias="cytoscape" storepass="secret" />
+
+ <copy toDir="${webstart.dir}/lib">
+ <fileset dir="${lib.dir}" includes="*.jar" />
+ </copy>
+
+ <signjar alias="cytoscape" storepass="secret">
+ <fileset dir="${webstart.dir}/lib" includes="*.jar" />
+ </signjar>
+
+
+
+ <!-- Copy over props files -->
+ <echo>
+ ---------------------------------------
+ Copying over all property files.
+ ---------------------------------------
+ </echo>
+ <copy file="${basedir}/resources/props/cytoscape.props" tofile="${webstart.dir}/cytoscape.props" />
+ <copy file="${basedir}/resources/props/vizmap.props" tofile="${webstart.dir}/vizmap.props" />
+
+ <!-- Copy over Webstart PlugIns -->
+ <echo>
+ ---------------------------------------
+ Copying over PlugIns.
+ ---------------------------------------
+ </echo>
+ <copy todir="${webstart.dir}/plugins">
+ <fileset dir="plugins/core">
+ <include name="*.jar" />
+ </fileset>
+ </copy>
+ <copy todir="${webstart.dir}/plugins">
+ <fileset dir="plugins">
+ <include name="*.jar" />
+ </fileset>
+ </copy>
+
+ <signjar alias="cytoscape" storepass="secret">
+ <fileset dir="${webstart.dir}/plugins" includes="*.jar" />
+ </signjar>
+ </target>
+
+
+ <target name="webstart-extras"
+ description="add extra plugins into webstart">
+ <echo>
+ ---------------------------------------
+ Copying over extra PlugIns.
+ ---------------------------------------
+ </echo>
+ <copy todir="${webstart.dir}/plugins">
+ <fileset dir="plugins/extras">
+ <include name="*.jar" />
+ </fileset>
+ </copy>
+
+ <antcall target="webstart" />
+
+ </target>
+
+ <!-- ======================================================= -->
+ <!-- Create Cytoscape WebStart WAR file Distribution -->
+ <!-- ======================================================= -->
+ <target name="war" depends="webstart" description="Create war package for webstart distribution">
+ <!-- Using jar rather that war task because we don't have a webxml file -->
+ <jar destfile="${build.dir}/Cytoscape.war">
+ <fileset dir="${build.dir}/webstart">
+ <include name="**/**"/>
+ </fileset>
+ <fileset dir="${basedir}/resources/webstart"/>
+ </jar>
+ </target>
+
+
+ <property name="dir.jalopy" value="/mystuff/jalopy/bin" />
+ <property name="dir.lib" value="${basedir}/ext/lib" />
+ <property name="dir.compile" value="${basedir}/tmp~/build/classes" />
+ <property name="dir.src.java" value="${basedir}/src/java" />
+
+ <!-- ==================================================================== -->
+ <!-- Defines the Jalopy task -->
+ <!-- ==================================================================== -->
+ <taskdef name="jalopy"
+ classname="de.hunsicker.jalopy.plugin.ant.AntPlugin">
+ <classpath>
+ <fileset dir="${buildlib.dir}/jalopy">
+ <include name="*.jar" />
+ </fileset>
+ </classpath>
+ </taskdef>
+
+
+ <!-- ==================================================================== -->
+ <!-- Formats all source files -->
+ <!-- ==================================================================== -->
+ <target name="format" description="jalopy formatting">
+ <jalopy convention="${resources.dir}/cytoscape_jalopy_code_convention.xml"
+ classpathref="classpath">
+ <fileset dir="${src.dir}">
+ <include name="**/*.java" />
+ <exclude name="generated/" />
+ <exclude name="generated2/" />
+ <exclude name="bookmarks/" />
+ </fileset>
+ <fileset dir="${tests.dir}">
+ <include name="**/*.java" />
+ </fileset>
+ </jalopy>
+ </target>
+</project>
diff --git a/legacy/resources/Gene_Ontology_Wizard.html b/legacy/resources/Gene_Ontology_Wizard.html
new file mode 100644
index 0000000..52ab586
--- /dev/null
+++ b/legacy/resources/Gene_Ontology_Wizard.html
@@ -0,0 +1,90 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html>
+<head>
+
+
+
+ <meta content="text/html; charset=ISO-8859-1" http-equiv="content-type">
+
+
+ <title>Gene Ontology Wizard</title>
+</head>
+
+
+<body style="color: rgb(0, 0, 0); background-color: rgb(204, 204, 204);" alink="#000099" link="#000099" vlink="#990099">
+
+
+<div style="text-decoration: underline; font-weight: bold; text-align: left; font-family: sans-serif;">Supported
+File Formats<br>
+
+
+</div>
+
+
+<span style="font-family: sans-serif;">
+Cytoscape supports the following file formats:</span><br style="font-family: sans-serif;">
+
+
+<ul style="font-family: sans-serif;">
+
+
+ <li>Cytoscape BioDataServer Format</li>
+
+
+
+ <ul>
+
+
+ <li>.Onto, .syno and .anno files.</li>
+
+
+ <li>Manifest file required.</li>
+
+
+
+ </ul>
+
+
+ <li>GO Annotation and Ontology Format </li>
+
+
+
+ <ul>
+
+
+ <li>OBO and Gene Association files.</li>
+
+
+ <li>Latest data is available at <a style="font-weight: bold;" href="http://www.geneontology.org/GO.downloads.shtml">Open
+Biomedical Ontologies</a></li>
+
+
+
+ </ul>
+
+
+</ul>
+
+<span style="font-family: sans-serif; font-weight: bold; text-decoration: underline;">Taxonomy Table</span><br style="font-family: sans-serif;">
+
+<span style="font-family: sans-serif;">Taxonomy table is obtained from NCBI:</span><br style="font-family: sans-serif;">
+
+<div style="margin-left: 40px;"><a style="font-family: sans-serif;" href="http://0-www.ncbi.nlm.nih.gov.csulib.ctstateu.edu/Taxonomy/TaxIdentifier/tax_identifier.cgi"><b><b>NCBI
+Taxonomy name/id Status Report Page</b></b></a><br>
+
+<br>
+
+<br style="font-family: sans-serif;">
+
+</div>
+
+
+<div style="margin-left: 40px; font-family: sans-serif;">
+<br>
+
+
+</div>
+
+
+</body>
+</html>
diff --git a/legacy/resources/cytoscape_jalopy_code_convention.xml b/legacy/resources/cytoscape_jalopy_code_convention.xml
new file mode 100644
index 0000000..cb8e89c
--- /dev/null
+++ b/legacy/resources/cytoscape_jalopy_code_convention.xml
@@ -0,0 +1,434 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<jalopy>
+ <general>
+ <compliance>
+ <version>15</version>
+ </compliance>
+ <style>
+ <description>Sun Java Coding Convention</description>
+ <name>Sun</name>
+ </style>
+ </general>
+ <inspector>
+ <enable>false</enable>
+ <naming>
+ <classes>
+ <abstract>[A-Z][a-zA-Z0-9]+</abstract>
+ <general>[A-Z][a-zA-Z0-9]+</general>
+ </classes>
+ <fields>
+ <default>[a-z][\w]+</default>
+ <defaultStatic>[a-z][\w]+</defaultStatic>
+ <defaultStaticFinal>[a-zA-Z][\w]+</defaultStaticFinal>
+ <private>[a-z][\w]+</private>
+ <privateStatic>[a-z][\w]+</privateStatic>
+ <privateStaticFinal>[a-zA-Z][\w]+</privateStaticFinal>
+ <protected>[a-z][\w]+</protected>
+ <protectedStatic>[a-z][\w]+</protectedStatic>
+ <protectedStaticFinal>[a-zA-Z][\w]+</protectedStaticFinal>
+ <public>[a-z][\w]+</public>
+ <publicStatic>[a-z][\w]+</publicStatic>
+ <publicStaticFinal>[a-zA-Z][\w]+</publicStaticFinal>
+ </fields>
+ <interfaces>[A-Z][a-zA-Z0-9]+</interfaces>
+ <labels>\w+</labels>
+ <methods>
+ <default>[a-z][\w]+</default>
+ <defaultStatic>[a-z][\w]+</defaultStatic>
+ <defaultStaticFinal>[a-z][\w]+</defaultStaticFinal>
+ <private>[a-z][\w]+</private>
+ <privateStatic>[a-z][\w]+</privateStatic>
+ <privateStaticFinal>[a-z][\w]+</privateStaticFinal>
+ <protected>[a-z][\w]+</protected>
+ <protectedStatic>[a-z][\w]+</protectedStatic>
+ <protectedStaticFinal>[a-z][\w]+</protectedStaticFinal>
+ <public>[a-z][\w]+</public>
+ <publicStatic>[a-z][\w]+</publicStatic>
+ <publicStaticFinal>[a-z][\w]+</publicStaticFinal>
+ </methods>
+ <packages>[a-z]+(?:\.[a-z]+)*</packages>
+ <parameters>
+ <default>[a-z][\w]+</default>
+ <final>[a-z][\w]+</final>
+ </parameters>
+ <variables>[a-z][\w]*</variables>
+ </naming>
+ <tips>
+ <adhereToNamingConvention>false</adhereToNamingConvention>
+ <alwaysOverrideHashCode>false</alwaysOverrideHashCode>
+ <avoidThreadGroups>false</avoidThreadGroups>
+ <declareCollectionComment>false</declareCollectionComment>
+ <dontIgnoreExceptions>false</dontIgnoreExceptions>
+ <dontSubstituteObjectEquals>false</dontSubstituteObjectEquals>
+ <neverDeclareException>false</neverDeclareException>
+ <neverDeclareThrowable>false</neverDeclareThrowable>
+ <neverInvokeWaitOutsideLoop>false</neverInvokeWaitOutsideLoop>
+ <neverReturnZeroArrays>false</neverReturnZeroArrays>
+ <neverUseEmptyFinally>false</neverUseEmptyFinally>
+ <obeyContractEquals>false</obeyContractEquals>
+ <overrideToString>false</overrideToString>
+ <referToObjectsByInterface>false</referToObjectsByInterface>
+ <replaceStructureWithClass>false</replaceStructureWithClass>
+ <stringLiterallI18n>false</stringLiterallI18n>
+ <useInterfaceOnlyForTypes>false</useInterfaceOnlyForTypes>
+ <wrongCollectionComment>false</wrongCollectionComment>
+ </tips>
+ </inspector>
+ <internal>
+ <version>6</version>
+ </internal>
+ <messages>
+ <priority>
+ <general>30000</general>
+ <parser>30000</parser>
+ <parserJavadoc>30000</parserJavadoc>
+ <printer>30000</printer>
+ <printerJavadoc>30000</printerJavadoc>
+ <transform>30000</transform>
+ </priority>
+ <showErrorStackTrace>true</showErrorStackTrace>
+ </messages>
+ <misc>
+ <threadCount>1</threadCount>
+ </misc>
+ <printer>
+ <alignment>
+ <methodCallChain>true</methodCallChain>
+ <parameterMethodDeclaration>false</parameterMethodDeclaration>
+ <ternaryOperator>true</ternaryOperator>
+ <variableAssignment>false</variableAssignment>
+ <variableDeclAssignment>false</variableDeclAssignment>
+ <variableIdentifier>false</variableIdentifier>
+ </alignment>
+ <backup>
+ <directory>bak</directory>
+ <level>0</level>
+ </backup>
+ <blanklines>
+ <after>
+ <block>1</block>
+ <braceLeft>0</braceLeft>
+ <class>1</class>
+ <declaration>0</declaration>
+ <footer>1</footer>
+ <header>1</header>
+ <interface>1</interface>
+ <lastImport>2</lastImport>
+ <method>1</method>
+ <package>1</package>
+ </after>
+ <before>
+ <block>1</block>
+ <braceRight>0</braceRight>
+ <caseBlock>1</caseBlock>
+ <comment>
+ <javadoc>1</javadoc>
+ <multiline>1</multiline>
+ <singleline>1</singleline>
+ </comment>
+ <controlStatement>1</controlStatement>
+ <declaration>1</declaration>
+ <footer>0</footer>
+ <header>1</header>
+ </before>
+ <keepUpTo>1</keepUpTo>
+ </blanklines>
+ <brace>
+ <comment>false</comment>
+ </brace>
+ <braces>
+ <empty>
+ <cuddle>false</cuddle>
+ <insertStatement>false</insertStatement>
+ </empty>
+ <insert>
+ <dowhile>false</dowhile>
+ <for>false</for>
+ <ifelse>false</ifelse>
+ <while>false</while>
+ </insert>
+ <remove>
+ <block>true</block>
+ <dowhile>false</dowhile>
+ <for>false</for>
+ <ifelse>false</ifelse>
+ <while>false</while>
+ </remove>
+ <treatDifferent>
+ <methodClass>false</methodClass>
+ <methodClassIfWrapped>false</methodClassIfWrapped>
+ </treatDifferent>
+ </braces>
+ <chunks>
+ <blanklines>true</blanklines>
+ <comments>true</comments>
+ </chunks>
+ <comments>
+ <format>
+ <multiline>false</multiline>
+ </format>
+ <javadoc>
+ <check>
+ <innerclass>false</innerclass>
+ <tags>false</tags>
+ <throwsTags>false</throwsTags>
+ </check>
+ <fieldsShort>true</fieldsShort>
+ <generate>
+ <class>1</class>
+ <constructor>1</constructor>
+ <field>1</field>
+ <method>1</method>
+ </generate>
+ <parseComments>false</parseComments>
+ <parseDescription>false</parseDescription>
+ <skip>
+ <ifml>false</ifml>
+ </skip>
+ <tags>
+ <in-line></in-line>
+ <standard></standard>
+ </tags>
+ <templates>
+ <class>/**| *|*/</class>
+ <constructor>
+ <bottom> */</bottom>
+ <exception> * @throws $exceptionType$ DOCUMENT ME!</exception>
+ <param> * @param $paramType$ DOCUMENT ME!</param>
+ <top>/**| * Creates a new $objectType$ object.</top>
+ </constructor>
+ <interface>/**| * | */</interface>
+ <method>
+ <bottom> */</bottom>
+ <exception> * @throws $exceptionType$ DOCUMENT ME!</exception>
+ <param> * @param $paramType$ DOCUMENT ME!</param>
+ <return> * @return DOCUMENT ME!</return>
+ <top>/**| * DOCUMENT ME!</top>
+ </method>
+ <variable>/**| * | */</variable>
+ </templates>
+ </javadoc>
+ <remove>
+ <javadoc>false</javadoc>
+ <multiline>false</multiline>
+ <singleline>false</singleline>
+ </remove>
+ <separator>
+ <fillCharacter>-</fillCharacter>
+ <insert>false</insert>
+ <insertRecursive>false</insertRecursive>
+ <text>
+ <annotation>Annotations</annotation>
+ <class>Inner Classes</class>
+ <constructor>Constructors</constructor>
+ <enum>Enumerations</enum>
+ <field>Instance fields</field>
+ <initializer>Instance initializers</initializer>
+ <interface>Inner Interfaces</interface>
+ <method>Methods</method>
+ <static>Static fields/initializers</static>
+ </text>
+ </separator>
+ </comments>
+ <environment></environment>
+ <footer>
+ <ignoreIfExists>false</ignoreIfExists>
+ <keys></keys>
+ <smartMode>0</smartMode>
+ <use>false</use>
+ </footer>
+ <header>
+ <ignoreIfExists>true</ignoreIfExists>
+ <keys>Cytoscape Consortium</keys>
+ <smartMode>0</smartMode>
+ <text>/*| Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)|| The Cytoscape Consortium is:| - Institute for Systems Biology| - University of California San Diego| - Memorial Sloan-Kettering Cancer Center| - Institut Pasteur| - Agilent Technologies|| This library is free software; you can redistribute it and/or modify it| under the terms of the GNU Lesser General Public License as published| by the Free Software Foundation; either version 2.1 of the License, or| an [...]
+ <use>true</use>
+ </header>
+ <history>
+ <policy>disabled</policy>
+ </history>
+ <imports>
+ <grouping>
+ <defaultDepth>3</defaultDepth>
+ <packages>*:0|gnu:2|java:2|javax:2</packages>
+ </grouping>
+ <policy>disabled</policy>
+ <sort>true</sort>
+ </imports>
+ <indentation>
+ <caseFromSwitch>true</caseFromSwitch>
+ <continuation>
+ <block>false</block>
+ <operator>false</operator>
+ </continuation>
+ <firstColumnComments>true</firstColumnComments>
+ <label>false</label>
+ <policy>
+ <deep>true</deep>
+ </policy>
+ <sizes>
+ <braceCuddled>1</braceCuddled>
+ <braceLeft>1</braceLeft>
+ <braceRight>0</braceRight>
+ <braceRightAfter>1</braceRightAfter>
+ <continuation>4</continuation>
+ <deep>75</deep>
+ <extends>4</extends>
+ <general>4</general>
+ <implements>4</implements>
+ <leading>0</leading>
+ <tabs>4</tabs>
+ <throws>4</throws>
+ <trailingComment>1</trailingComment>
+ </sizes>
+ <tabs>
+ <enable>true</enable>
+ <onlyLeading>true</onlyLeading>
+ </tabs>
+ </indentation>
+ <misc>
+ <arrayBracketsAfterIdent>false</arrayBracketsAfterIdent>
+ <forceFinalModifier>false</forceFinalModifier>
+ <forceFormatting>false</forceFormatting>
+ <insertExpressionParentheses>true</insertExpressionParentheses>
+ <insertLoggingConditional>false</insertLoggingConditional>
+ <insertTrailingNewline>true</insertTrailingNewline>
+ <insertUID>false</insertUID>
+ <method>
+ <forceFinalModifier>false</forceFinalModifier>
+ </method>
+ </misc>
+ <sorting>
+ <declaration>
+ <annotation>false</annotation>
+ <class>false</class>
+ <constructor>false</constructor>
+ <enable>false</enable>
+ <enum>false</enum>
+ <interface>false</interface>
+ <method>false<bean>false</bean>
+ </method>
+ <order>static|field|initializer|constructor|method|interface|class|annotation|enum</order>
+ <variable>false</variable>
+ </declaration>
+ <modifier>
+ <enable>false</enable>
+ <order>public=true|protected=true|private=true|abstract=true|static=true|final=true|synchronized=true|transient=true|volatile=true|native=true|strictfp=true</order>
+ </modifier>
+ </sorting>
+ <whitespace>
+ <after>
+ <comma>true</comma>
+ <semicolon>true</semicolon>
+ <typeCast>true</typeCast>
+ </after>
+ <before>
+ <braces>true</braces>
+ <brackets>false</brackets>
+ <bracketsTypes>false</bracketsTypes>
+ <caseColon>false</caseColon>
+ <operator>
+ <not>false</not>
+ </operator>
+ <parentheses>
+ <methodCall>false</methodCall>
+ <methodDeclaration>false</methodDeclaration>
+ <statement>true</statement>
+ </parentheses>
+ </before>
+ <padding>
+ <braces>true</braces>
+ <brackets>false</brackets>
+ <operator>
+ <assignment>true</assignment>
+ <bitwise>true</bitwise>
+ <logical>true</logical>
+ <mathematical>true</mathematical>
+ <relational>true</relational>
+ <shift>true</shift>
+ </operator>
+ <parenthesis>false</parenthesis>
+ <typeCast>false</typeCast>
+ </padding>
+ </whitespace>
+ <wrapping>
+ <always>
+ <after>
+ <arrayElement>0</arrayElement>
+ <braceRight>false</braceRight>
+ <extendsTypes>false</extendsTypes>
+ <implementsTypes>false</implementsTypes>
+ <label>true</label>
+ <methodCallChained>false</methodCallChained>
+ <ternaryOperator>
+ <first>false</first>
+ <second>false</second>
+ </ternaryOperator>
+ <throwsTypes>false</throwsTypes>
+ </after>
+ <before>
+ <braceLeft>false</braceLeft>
+ <extends>false</extends>
+ <implements>false</implements>
+ <throws>false</throws>
+ </before>
+ <parameter>
+ <methodCall>false</methodCall>
+ <methodCallNested>false</methodCallNested>
+ <methodDeclaration>false</methodDeclaration>
+ </parameter>
+ </always>
+ <anon>
+ <align>
+ <after>2147483647</after>
+ </align>
+ <lcurly>
+ <newline>true</newline>
+ </lcurly>
+ </anon>
+ <anondef>
+ <align>
+ <after>2147483647</after>
+ </align>
+ <lcurly>
+ <nonewline>true</nonewline>
+ </lcurly>
+ </anondef>
+ <enum>
+ <align>
+ <after>1</after>
+ </align>
+ <lcurly>
+ <nonewline>false</nonewline>
+ </lcurly>
+ </enum>
+ <general>
+ <beforeOperator>true</beforeOperator>
+ <enable>true</enable>
+ <lineLength>100</lineLength>
+ </general>
+ <ondemand>
+ <after>
+ <assignment>false</assignment>
+ <leftParenthesis>false</leftParenthesis>
+ <parameter>false</parameter>
+ <types>
+ <extends>false</extends>
+ <implements>false</implements>
+ <throws>false</throws>
+ </types>
+ </after>
+ <before>
+ <rightParenthesis>false</rightParenthesis>
+ </before>
+ <deep>
+ <parameter>true</parameter>
+ </deep>
+ <groupingParentheses>false</groupingParentheses>
+ <hard>
+ <parameter>false</parameter>
+ </hard>
+ </ondemand>
+ </wrapping>
+ </printer>
+</jalopy>
diff --git a/legacy/resources/javax.imageio.spi.ImageWriterSpi b/legacy/resources/javax.imageio.spi.ImageWriterSpi
new file mode 100644
index 0000000..565cf0c
--- /dev/null
+++ b/legacy/resources/javax.imageio.spi.ImageWriterSpi
@@ -0,0 +1 @@
+org.freehep.graphicsio.raw.RawImageWriterSpi
\ No newline at end of file
diff --git a/legacy/resources/org.freehep.util.export.ExportFileType b/legacy/resources/org.freehep.util.export.ExportFileType
new file mode 100644
index 0000000..f0a8faf
--- /dev/null
+++ b/legacy/resources/org.freehep.util.export.ExportFileType
@@ -0,0 +1,5 @@
+org.freehep.graphicsio.exportchooser.ImageIOExportFileType
+org.freehep.graphicsio.pdf.PDFExportFileType
+org.freehep.graphicsio.ps.EPSExportFileType
+org.freehep.graphicsio.ps.PSExportFileType
+org.freehep.graphicsio.svg.SVGExportFileType
\ No newline at end of file
diff --git a/legacy/resources/plugin_website/CyPluginDB_schema.sql b/legacy/resources/plugin_website/CyPluginDB_schema.sql
new file mode 100644
index 0000000..b5e2d8d
--- /dev/null
+++ b/legacy/resources/plugin_website/CyPluginDB_schema.sql
@@ -0,0 +1,135 @@
+DROP DATABASE IF EXISTS cyplugindb;
+CREATE DATABASE cyplugindb;
+
+USE cyplugindb;
+
+CREATE TABLE authors (
+ author_auto_id int(11) NOT NULL auto_increment,
+ names varchar(150) default NULL,
+ email varchar(90) default NULL,
+ affiliation varchar(150) default NULL,
+ affiliationURL varchar(200) default NULL,
+ PRIMARY KEY (author_auto_id)
+);
+
+
+
+CREATE TABLE categories (
+ category_id int(11) NOT NULL,
+ name varchar(50) NOT NULL,
+ description varchar(100) default NULL,
+ PRIMARY KEY (category_id)
+);
+
+INSERT INTO categories VALUES
+(1,'Core','Cytoscape core'),
+(2,'Analysis','Used for analyzing existing networks'),
+(3,'Network and Attribute I/O','Used for importing networks and attributes in different file formats'),
+(4,'Network Inference','Used for inferring new networks'),
+(5,'Functional Enrichment','Used for functional enrichment of networks'),
+(6,'Communication/Scripting','Used for communicating with or scripting Cytoscape'),
+(7,'Other','None of the above');
+
+
+CREATE TABLE plugin_author (
+ plugin_version_id int(11) default NULL,
+ author_id int(11) default NULL,
+ authorship_seq int(11) default NULL
+);
+
+
+CREATE TABLE plugin_files (
+ plugin_file_auto_id int(11) NOT NULL auto_increment,
+ file_data longblob,
+ file_type enum('jar','zip') default NULL,
+ file_name varchar(100) default NULL,
+ md5 varchar(40),
+ PRIMARY KEY (plugin_file_auto_id)
+);
+
+
+CREATE TABLE plugin_list (
+ plugin_auto_id int(11) NOT NULL auto_increment,
+ name varchar(100) NOT NULL,
+ unique_id int,
+ description text,
+ license text,
+ license_required varchar(3) default NULL,
+ project_url varchar(100) default NULL,
+ category_id int(11) default NULL,
+ sysdat date default NULL,
+ PRIMARY KEY (plugin_auto_id)
+);
+
+
+CREATE TABLE plugin_version (
+ version_auto_id int(11) NOT NULL auto_increment,
+ plugin_id int(11) default NULL,
+ plugin_file_id int(11) default NULL,
+ cy_version set('2.0','2.1','2.2','2.3','2.4','2.5','2.5.1','2.5.2','2.6','2.6.1','2.6.2') default NULL,
+ version double default '0.1',
+ release_date date default NULL,
+ release_note text,
+ release_note_url varchar(100) default NULL,
+ minimum_java_version varchar(10),
+ comment text,
+ jar_url varchar(100) default NULL,
+ source_url varchar(100) default NULL,
+ status varchar(20) default NULL,
+ reference text,
+ theme_only ENUM('yes', 'no') DEFAULT 'no',
+ sysdat date default NULL,
+ PRIMARY KEY (version_auto_id)
+);
+
+
+CREATE TABLE usagelog (
+ log_auto_id int not null auto_increment,
+ plugin_version_id int(11) NOT NULL,
+ remote_host varchar(60) default NULL,
+ ip_address varchar(20) default NULL,
+ refer_page varchar(99),
+ sysdat date default NULL,
+ PRIMARY KEY (log_auto_id)
+);
+
+
+CREATE TABLE contacts (
+ contact_auto_id int not null auto_increment,
+ name varchar(99),
+ email varchar(99),
+ plugin_version_id int,
+ sysdat date default NULL,
+ PRIMARY KEY (contact_auto_id)
+);
+
+CREATE TABLE theme_list (
+ theme_auto_id int(11) NOT NULL auto_increment,
+ name varchar(100) NOT NULL,
+ unique_id int,
+ description text,
+ sysdat date,
+ PRIMARY KEY (theme_auto_id)
+);
+
+
+
+CREATE TABLE theme_version (
+ version_auto_id int(11) NOT NULL auto_increment,
+ theme_id int(11) NOT NULL,
+ cy_version set('2.6','2.7 ','2.8') default NULL,
+ version double default '0.1',
+ release_date date default NULL,
+ status varchar(20) default NULL,
+ sysdat date default NULL,
+ PRIMARY KEY (version_auto_id)
+);
+
+
+
+CREATE TABLE theme_plugin (
+ theme_plugin_auto_id int(11) NOT NULL auto_increment,
+ theme_version_id int(11),
+ plugin_version_id int(11),
+ PRIMARY KEY (theme_plugin_auto_id)
+);
diff --git a/legacy/resources/plugin_website/generate_plugin_xml.pl b/legacy/resources/plugin_website/generate_plugin_xml.pl
new file mode 100644
index 0000000..2cca00a
--- /dev/null
+++ b/legacy/resources/plugin_website/generate_plugin_xml.pl
@@ -0,0 +1,501 @@
+# This script takes the information in the cyplugindb database and creates the plugins.xml file
+# in a web-accessible location for the Cytoscape Plugin Manager to read.
+# Call generate_plugin_xml.pl -help for information on usage.
+
+use strict;
+#use warnings;
+
+use Encode 'encode';
+use Data::Dumper;
+use XML::DOM;
+use Getopt::Long;
+use DBI;
+
+# constants
+use constant CYTOSCAPE_URL => "http://cytoscape.org";
+use constant DATABASE_NAME => "cyplugindb";
+use constant PLUGIN_DL_SCRIPT => "pluginjardownload.php";
+
+
+#Globals
+my %xmlEl = (
+ 'id' => "uniqueID",
+ 'name' => "name",
+ 'desc' => "description",
+ 'license' => "license",
+ 'cy_vers' => "cytoscapeVersions",
+ 'version' => "version",
+ 'pl_vers' => "pluginVersion",
+ 'th_vers' => "themeVersion",
+ 'plugin_list' => "pluginlist",
+ 'theme_list' => "themes",
+ 'url' => "url"
+);
+
+my $dbh;
+my ($BaseUrl, $XmlFileLoc, $HttpLoc, $Host, $UserName, $PassWord, $Debug, $Help);
+
+GetOptions ("loc=s" => \$XmlFileLoc,
+ "url=s" => \$BaseUrl,
+ "host=s" => \$Host,
+ "user=s" => \$UserName,
+ "passwd=s" => \$PassWord,
+ "debug" => \$Debug,
+ "help" => \$Help);
+
+
+usage("Help:") if ($Help);
+usage("ERROR: Missing required parameter:") if (!$BaseUrl || !$XmlFileLoc || !$UserName || !$PassWord);
+
+$Host = 'localhost' if (!$Host);
+my $XmlFile = $XmlFileLoc . "/plugins.xml";
+
+dbConnect();
+
+# Create the xml document
+my $Doc = XML::DOM::Document->new();
+my $XMLPi = $Doc->setXMLDecl($Doc->createXMLDecl ('1.0', 'UTF-8'));
+my $Root = $Doc->createElement("project");
+$Doc->appendChild($Root);
+addProjectInfo();
+
+# --- create the plugin list --- #
+
+my $PluginListEl = $Doc->createElement($xmlEl{'plugin_list'});
+
+my $Plugins = retrievePlugins();
+foreach my $plugin (@$Plugins)
+ {
+ my $Plugin = createPluginNode(@$plugin);
+ $PluginListEl->appendChild($Plugin) if $Plugin;
+ }
+$Root->appendChild($PluginListEl);
+
+# --- create the themes --- #
+my $ThemeListEl = $Doc->createElement($xmlEl{'theme_list'});
+
+my $themeSql = qq(
+SELECT DISTINCT L.theme_auto_id, L.name, L.unique_id, L.description,
+ V.version_auto_id, V.cy_version, V.version, V.release_date
+FROM theme_list L
+ INNER JOIN theme_version V
+ ON L.theme_auto_id = V.theme_id
+);
+
+my $Themes = $dbh->selectall_arrayref($themeSql);
+foreach my $theme (@$Themes)
+ {
+ my $Theme = createThemeNode(@$theme);
+ $ThemeListEl->appendChild($Theme) if $Theme;
+ }
+$Root->appendChild($ThemeListEl);
+
+# format the xml in some basic manner, doesn't seem to be a nice lib for pretty formatting of xml
+my $Xml = $Doc->toString();
+$Xml =~ s/></>\n</g if $Debug;
+$Xml =~ s/^\s+//;
+
+open(XMLOUT, ">$XmlFile") || die "Failed to open $XmlFile: $!";
+print XMLOUT $Xml;
+close(XMLOUT);
+
+
+
+# -------------------- SUBS --------------------- #
+
+sub retrievePlugins
+ {
+ my %args = @_;
+
+ my $ThemeOnly = $args{'theme_only'};
+ my $PluginVersionId = $args{'plugin_vers_id'};
+
+ my $pluginSql = qq(
+SELECT DISTINCT L.plugin_auto_id, L.name, L.unique_id, L.description, L.license, L.license_required,
+C.name, V.version, V.release_date, V.cy_version, V.plugin_file_id, V.version_auto_id, V.theme_only
+FROM plugin_list L
+ INNER JOIN plugin_version V
+ ON L.plugin_auto_id = V.plugin_id
+ INNER JOIN categories C
+ ON L.category_id = C.category_id
+WHERE V.status = 'published' AND V.plugin_file_id is not NULL
+);
+
+ $pluginSql .= "AND V.theme_only != 'yes' " if (!$ThemeOnly || $ThemeOnly eq 'no');
+ $pluginSql .= "AND V.version_auto_id = $PluginVersionId " if ($PluginVersionId);
+ $pluginSql .= "ORDER BY L.name";
+
+
+ my $pluginsRef = $dbh->selectall_arrayref($pluginSql);
+ #print "$pluginSql\n" . Dumper $pluginsRef if ($Debug);
+ return $pluginsRef;
+ }
+
+# set up the <project> element and the global info for the xml doc
+sub addProjectInfo
+ {
+ my $Name = $Doc->createElement($xmlEl{'name'});
+ $Name->appendChild($Doc->createTextNode("Cytoscape Plugins"));
+
+ my $Desc = $Doc->createElement($xmlEl{'desc'});
+ $Desc->appendChild($Doc->createTextNode("These plugins have been submitted to Cytoscape by their authors,
+ they may have their own licensing requirements. Please contact the plugin authors with any questions."));
+
+ my $ProjUrl = $Doc->createElement($xmlEl{'url'});
+ $ProjUrl->appendChild($Doc->createTextNode(CYTOSCAPE_URL));
+
+ $Root->appendChild($Name);
+ $Root->appendChild($Desc);
+ $Root->appendChild($ProjUrl);
+ }
+
+sub createIdNode
+ {
+ my $Id = shift;
+ my $IdEl = $Doc->createElement($xmlEl{'id'});
+ $IdEl->appendChild($Doc->createTextNode($Id));
+ return $IdEl;
+ }
+
+sub createNameNode
+ {
+ my $Name = shift;
+ $Name = fixEncoding($Name);
+ my $NameEl = $Doc->createElement($xmlEl{'name'});
+ $NameEl->appendChild($Doc->createTextNode($Name));
+ return $NameEl;
+ }
+
+sub createDescNode
+ {
+ my $Desc = shift;
+ $Desc = fixEncoding($Desc);
+ my $DescEl = $Doc->createElement($xmlEl{'desc'});
+ $DescEl->appendChild($Doc->createTextNode( stripBadHex($Desc) ));
+ return $DescEl;
+ }
+
+sub createCyVersionNode
+ {
+ my $CyVersion = shift;
+ my $CyVersionsEl = $Doc->createElement($xmlEl{'cy_vers'});
+ my @cyVersions = split(/,/, $CyVersion);
+
+ foreach my $v (@cyVersions)
+ {
+ $v = fixEncoding($v);
+ my $VersionEl = $Doc->createElement($xmlEl{'version'});
+ $VersionEl->appendChild($Doc->createTextNode($v));
+ $CyVersionsEl->appendChild($VersionEl);
+ }
+
+ return $CyVersionsEl;
+ }
+
+sub createReleaseDateNode
+ {
+ my $ReleaseDate = shift;
+ $ReleaseDate = fixEncoding($ReleaseDate);
+ my $RelDateEl = $Doc->createElement('release_date');
+ $RelDateEl->appendChild($Doc->createTextNode($ReleaseDate));
+ return $RelDateEl;
+ }
+
+sub createVersionNode
+ {
+ my $VersionElName = shift;
+ my $Version = shift;
+ $Version = fixEncoding($Version);
+ my $VersEl = $Doc->createElement($VersionElName);
+ $VersEl->appendChild($Doc->createTextNode($Version));
+ return $VersEl;
+ }
+
+sub createThemeNode
+ {
+ my @theme = @_;
+
+ my ($ThemeAutoId, $Name, $UniqueId, $Description,
+ $ThemeVersionId, $CyVersion, $ThemeVersion, $ReleaseDate) = @theme;
+
+ if (isNull($Name, $UniqueId, $CyVersion, $ThemeVersion, $ThemeVersionId))
+ {
+ warn "One of the following required parameters was null in the database, skipping this theme:
+ - Theme Name ($Name)
+ - Unique Id ($UniqueId)
+ - Theme Version ($ThemeVersion)
+ - Cytoscape Version ($CyVersion)
+ - Version Id ($ThemeVersionId)";
+ return undef;
+ }
+
+ my $ThemeEl = $Doc->createElement('theme');
+
+ $ThemeEl->appendChild( createIdNode($UniqueId) );
+ $ThemeEl->appendChild( createNameNode($Name) );
+ $ThemeEl->appendChild( createDescNode($Description) );
+ $ThemeEl->appendChild( createCyVersionNode($CyVersion) );
+
+ my $ThemeVersEl = $Doc->createElement($xmlEl{'th_vers'});
+ $ThemeVersEl->appendChild($Doc->createTextNode($ThemeVersion));
+ $ThemeEl->appendChild($ThemeVersEl);
+
+ # get plugin ids
+ my $PluginIds = $dbh->selectcol_arrayref
+ ("SELECT plugin_version_id FROM theme_plugin
+ WHERE theme_version_id = $ThemeVersionId");
+
+ my $PluginListEl = $Doc->createElement($xmlEl{'plugin_list'});
+
+ # add plugins
+ foreach my $pluginId (@$PluginIds)
+ {
+ my $Plugins = retrievePlugins('theme_only' => 1, 'plugin_vers_id' => $pluginId);
+ foreach my $plugin (@$Plugins)
+ {
+ my $PluginEl = undef;
+
+ if ($plugin->[12] eq 'yes')
+ {
+ $PluginEl = createPluginNode(@$plugin);
+ if (!$PluginEl)
+ {
+ warn "A plugin in the theme '$Name' cannot be retrieved due to a missing parameter. Skipping this theme.";
+ return undef;
+ }
+ }
+ else # create the short hand version
+ {
+ # <plugin>
+ # <uniqueID>goodZIPPlugin777</uniqueID>
+ # <pluginVersion>0.45</pluginVersion>
+ # </plugin>
+ $PluginEl = $Doc->createElement('plugin');
+ $PluginEl->appendChild( createIdNode( $plugin->[2] ) );
+ $PluginEl->appendChild( createVersionNode($xmlEl{'pl_vers'}, $plugin->[7]) );
+ }
+ $PluginListEl->appendChild($PluginEl) if $PluginEl;
+ }
+ }
+ $ThemeEl->appendChild($PluginListEl);
+ return $ThemeEl;
+ }
+
+sub isNull
+ {
+ my @pluginInfo = @_;
+ foreach my $info (@pluginInfo)
+ { # one of the parameters is null, return true
+ if (!$info) { return 1; }
+ }
+ return 0;
+ }
+
+sub createPluginNode
+ {
+ my @plugin = @_;
+
+ my ($PluginAutoId, $PluginName, $UniqueId, $Description,
+ $License, $LicenseReq, $Category, $PluginVersion,
+ $ReleaseDate, $CyVersion, $PluginFileId,
+ $PluginVersionId, $ThemeOnly) = @plugin;
+
+
+ if (isNull($PluginName, $UniqueId, $PluginVersion, $CyVersion, $PluginVersionId))
+ {
+ warn "One of the following required parameters was null in the database, skipping this plugin:
+ - Plugin Name ($PluginName)
+ - Unique Id ($UniqueId)
+ - Plugin Version ($PluginVersion)
+ - Cytoscape Version ($CyVersion)
+ - Version Id ($PluginVersionId)";
+ return undef;
+ }
+
+ my $PluginEl = $Doc->createElement('plugin');
+
+ $PluginEl->appendChild( createIdNode($UniqueId) );
+ $PluginEl->appendChild( createNameNode($PluginName) );
+ $PluginEl->appendChild( createDescNode($Description) );
+
+ my $CategoryEl = $Doc->createElement('category');
+ $CategoryEl->appendChild($Doc->createTextNode($Category));
+ $PluginEl->appendChild($CategoryEl);
+
+ $PluginEl->appendChild( createVersionNode($xmlEl{'pl_vers'}, $PluginVersion) );
+ $PluginEl->appendChild( createCyVersionNode($CyVersion) );
+
+ if ($LicenseReq eq 'yes')
+ {
+ my $LicenseEl = $Doc->createElement($xmlEl{'license'});
+ my $LicenseTextEl = $Doc->createElement('text') ;
+ $LicenseEl->appendChild($LicenseTextEl);
+ my $TextNode = $Doc->createTextNode( fixEncoding($License) );
+ $LicenseTextEl->appendChild($TextNode);
+ $PluginEl->appendChild($LicenseEl);
+ }
+
+ $PluginEl->appendChild( createReleaseDateNode($ReleaseDate) );
+
+ # add authors
+ my $Authors = addAuthors($PluginVersionId);
+ $PluginEl->appendChild($Authors) if $Authors;
+
+ # file type / download url
+ my $FileUrl = $BaseUrl . "/" . PLUGIN_DL_SCRIPT . "?id=$PluginFileId";
+ my $PluginUlrEl = $Doc->createElement('url');
+ $PluginUlrEl->appendChild($Doc->createTextNode($FileUrl));
+ $PluginEl->appendChild($PluginUlrEl);
+
+ my $FileTag = addFileInfo($PluginFileId);
+
+ if ($FileTag)
+ {
+ $PluginEl->appendChild($FileTag);
+ return $PluginEl;
+ }
+ else { return undef; }
+ }
+
+
+sub addAuthors
+ {
+ my $PluginVersionId = shift || return 0;
+
+ my $AuthorList = $Doc->createElement('authorlist');
+
+ my $sql = "SELECT names, affiliation FROM plugin_author
+ INNER JOIN authors
+ ON author_auto_id = author_id
+ WHERE plugin_version_id = $PluginVersionId
+ ORDER BY authorship_seq";
+ my $Authors = $dbh->selectall_arrayref($sql);
+
+ if (@$Authors == 0)
+ {
+ warn "No authors found for plugin_version_id $PluginVersionId";
+ return 0;
+ }
+
+ foreach my $author (@$Authors)
+ {
+ my $AuthorElement = $Doc->createElement('author');
+ my $Name = $Doc->createElement('name');
+ $author->[0] = fixEncoding($author->[0]);
+ $Name->appendChild($Doc->createTextNode($author->[0]));
+ $AuthorElement->appendChild($Name);
+
+ my $Inst = $Doc->createElement('institution');
+ $Inst->appendChild($Doc->createTextNode($author->[1]));
+ $author->[1] = fixEncoding($author->[1]);
+ $AuthorElement->appendChild($Inst);
+
+ $AuthorList->appendChild($AuthorElement);
+ }
+ return $AuthorList;
+ }
+
+
+
+# add the <filetype> and <url> elements to each <plugin>
+sub addFileInfo
+ {
+ my $PluginFileId = shift || return 0;
+
+ print "addFileInfo($PluginFileId)\n" if $Debug;
+
+ my ($FileType, $FileName) = $dbh->selectrow_array
+ ("SELECT file_type, file_name
+ FROM plugin_files
+ WHERE plugin_file_auto_id = $PluginFileId");
+
+ print "$FileType, $FileName\n" if $Debug;
+
+ if (!$FileName)
+ {
+ warn "Missing a plugin name for plugin_file_auto_id $PluginFileId";
+ return 0;
+ }
+
+ my $PluginFileType = $Doc->createElement("filetype");
+ $FileName =~ s/\s+$//; # in case they get inserted in the db with spaces at the end
+ if ($FileName =~ /.*\.(jar|zip)$/i)
+ { $FileType = $1; }
+ else
+ {
+ if (isJar($FileType))
+ { $FileType = "jar"; }
+ elsif (isZip($FileType))
+ { $FileType = "zip"; }
+ }
+ print "\tFile type: $FileType\n" if $Debug;
+
+ $PluginFileType->appendChild( $Doc->createTextNode($FileType) );
+ return $PluginFileType;
+ }
+
+
+# these are illegal for xml
+sub stripBadHex
+ {
+ my $str = shift;# || warn "No string passed to stripBadHex method";
+ $str =~ s/\x0b|\x0c|\x0d|\x0e|\x0f//g;
+ $str =~ s/([\x00-\x7f])[\x80-\xbf]/$1/g;
+ return $str;
+ }
+
+sub isZip
+ {
+ # application/x-zip-compressed
+ my $Type = shift || warn "No string passed to isZip method";
+ $Type =~ /^application\/(zip|x-zip-compressed)$/ ? return 1: return 0;
+ }
+
+sub isJar
+ {
+ # application/x-jar application/x-java-archive
+ my $Type = shift || warn "No string passed to isJar method";
+ $Type =~ /^application\/x-(jar|java-archive)/ ? return 1: return 0;
+ }
+
+
+# encode everything UTF8
+sub fixEncoding
+ {
+ my $string = shift;
+ $string = stripBadHex($string);
+ return encode("UTF8", $string);
+ }
+
+# connect to database
+sub dbConnect
+ {
+ my $DSN = "DBI:mysql:host=$Host;database=".DATABASE_NAME;
+ my $attr = {RaiseError => 1};
+ $dbh = DBI->connect($DSN, $UserName, $PassWord, $attr);
+ }
+
+# check usage
+sub usage
+ {
+ my $Msg = shift;
+ print qq($Msg
+Usage: $0 -loc <some dir> -host <db host> -user <db user name> -passwd <db password>
+
+ Parameter Description Optional/Required
+ -loc : Location to write resulting XML file to. REQUIRED
+ -url : Base url for the pluginjardownload.php REQUIRED
+ used for the plugin download url.
+ -user : Database user name. REQUIRED
+ -passwd : Database password. REQUIRED
+ -host : Database host name, OPTIONAL
+ defaults to localhost
+ [-help : See this message]
+);
+ exit(-1);
+ }
+
+
+
+
+
diff --git a/legacy/resources/plugin_website/plugin.props.example b/legacy/resources/plugin_website/plugin.props.example
new file mode 100644
index 0000000..f0f539f
--- /dev/null
+++ b/legacy/resources/plugin_website/plugin.props.example
@@ -0,0 +1,43 @@
+# This props file would be filled out and included in the plugin jar file. This props file will be used
+# to put information into the Plugin Manager about the plugin
+
+# -- The following properties are REQUIRED -- #
+
+# The plugin name that will be displayed to users
+pluginName=My Plugin
+
+# Description used to give users information about the plugin such as what it does.
+# Html tags are encouraged for formatting purposes.
+pluginDescription=Information about the plugin that will be displayed to users
+
+# Plugin version number, this must be two numbers separated by a decimlal. Ex. 0.2, 14.03
+pluginVersion=1.0
+
+# Compatible Cytoscape version
+cytoscapeVersion=2.5
+
+# Category, use one of the categories listed on the website or create your own
+pluginCategory=Scripting/Communication
+
+
+# -- The following properties are OPTIONAL -- #
+
+# URL to a website that gives more information about your plugin, Ex. http://my-lab-site.org
+projectURL=http://my-lab-site.org/myCytoscapePlugin
+
+# List of authors. Note each author and institution pair are separated by a : (colon)
+# each additional author institution pair must be separated from other pairs bye a ; (semicolon)
+pluginAuthorsInstitutions=Sarah and Victor:ISB;Mike, Kei and Peng:UCSD
+
+# Date this plugin/plugin version was released
+releaseDate=May 1, 2008
+
+
+# -- The following properties should be set ONLY BY CORE PLUGINS -- #
+
+# URL where these plugins will be found on (xml file describing all plugins)
+downloadURL=http://cytoscape.org/plugins/plugins.xml
+
+# Unique identifier, for core plugins this would come from the database and should not change, all other plugins will
+# have defined this in the download xml file and shout NOT set this property
+uniqueID=1
\ No newline at end of file
diff --git a/legacy/resources/plugin_website/plugin.xml b/legacy/resources/plugin_website/plugin.xml
new file mode 100644
index 0000000..329c30d
--- /dev/null
+++ b/legacy/resources/plugin_website/plugin.xml
@@ -0,0 +1,40 @@
+<!-- Example xml file describing plugins and where to d/l them -->
+<project>
+ <!-- global info regarding the project these plugins come from -->
+ <name> Cytoscape Plugins </name>
+ <description> Test </description>
+ <url> http://cytoscape.org </url>
+
+ <pluginlist>
+ <!-- Info specific to a plugin -->
+ <plugin>
+ <uniqueID> A string that will not change from one version to another</uniqueID>
+ <name> foobar </name>
+ <description>
+ <![CDATA[
+ Whatever you want to say about a plugin<br>Html tags are encouraged for layout<p>
+ ]]>
+ </description>
+ <pluginVersion> 1.0 </pluginVersion>
+ <cytoscapeVersions>
+ <version>2.5</version>
+ </cytoscapeVersions>
+ <filetype> jar </filetype>
+ <category> Enrichment </category>
+ <url> http://url/to/download/jar-or-zip-file.xxx </url>
+ <authorlist>
+ <author>
+ <name>Jane Doe</name>
+ <institution>UC</institution>
+ </author>
+ </authorlist>
+ <license>
+ <text><![CDATA[
+ This is some license text a user would see and have to ok in order to install a plugin.
+ <p>Html tags are encouraged for nicer formatting for user<p>
+ ]]></text>
+ </license>
+ </plugin>
+ </pluginlist>
+
+</project>
diff --git a/legacy/resources/schema/binding.xjb b/legacy/resources/schema/binding.xjb
new file mode 100644
index 0000000..f10e86a
--- /dev/null
+++ b/legacy/resources/schema/binding.xjb
@@ -0,0 +1,15 @@
+<jxb:bindings version="2.0" xmlns:jxb="http://java.sun.com/xml/ns/jaxb"
+ xmlns:xs="http://www.w3.org/2001/XMLSchema">
+
+ <!-- This file is for avoiding name conflict between RDF and Dublin Core -->
+
+ <jxb:bindings schemaLocation="rdf.xsd" node="/xs:schema">
+ <jxb:schemaBindings>
+ <jxb:package name="cytoscape.generated2"/>
+ <jxb:nameXmlTransform>
+ <jxb:elementName prefix="Rdf"/>
+ <jxb:anonymousTypeName prefix="Rdf" suffix="Type"/>
+ </jxb:nameXmlTransform>
+ </jxb:schemaBindings>
+ </jxb:bindings>
+</jxb:bindings>
diff --git a/legacy/resources/schema/dcmes-xml-dtd.xsd b/legacy/resources/schema/dcmes-xml-dtd.xsd
new file mode 100644
index 0000000..71abfce
--- /dev/null
+++ b/legacy/resources/schema/dcmes-xml-dtd.xsd
@@ -0,0 +1,200 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+ DTD 2002-04-22 for
+ Expressing Simple Dublin Core in RDF/XML
+ http://dublincore.org/documents/2002/07/31/dcmes-xml/
+
+ Public ID: "-//DUBLIN CORE//DCMES DTD 2002/07/31//EN"
+
+ Authors:
+ Dave Beckett <dave.beckett at bristol.ac.uk>
+ Eric Miller <emiller at w3.org>
+ Dan Brickley <danbri at w3.org>
+
+ Based on
+ Dublin Core Metadata Element Set, Version 1.1: Reference Description
+ http://dublincore.org/documents/1999/07/02/dces/
+
+ This DTD is for information only and NON-NORMATIVE.
+
+-->
+<!-- The namespaces for RDF and DCMES 1.1 respectively -->
+<!-- Declare convenience entities for XML namespace declarations -->
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" elementFormDefault="qualified"
+ targetNamespace="http://purl.org/dc/elements/1.1/"
+ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+ xmlns:dc="http://purl.org/dc/elements/1.1/"
+ xmlns:jxb="http://java.sun.com/xml/ns/jaxb"
+ jxb:version="1.0">
+ <xs:import namespace="http://www.w3.org/1999/02/22-rdf-syntax-ns#" schemaLocation="rdf.xsd"/>
+
+
+ <xs:import namespace="http://www.w3.org/XML/1998/namespace"
+ schemaLocation="xml.xsd"/>
+
+
+ <!-- The wrapper element -->
+ <xs:element name="dcmes" abstract="true"/>
+ <!-- The resource description container element -->
+ <xs:attributeGroup name="attlist.rdf.Description">
+ <xs:attribute ref="rdf:about"/>
+ </xs:attributeGroup>
+ <!-- The elements from DCMES 1.1 -->
+ <!-- The name given to the resource. -->
+ <xs:element name="title" substitutionGroup="dc:dcmes">
+ <xs:complexType mixed="true">
+ <xs:attributeGroup ref="dc:attlist.dc.title"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:attributeGroup name="attlist.dc.title">
+ <xs:attribute ref="xml:lang"/>
+ <xs:attribute ref="rdf:resource"/>
+ </xs:attributeGroup>
+ <!--
+ An entity primarily responsible for making the content of the
+ resource.
+ -->
+ <xs:element name="creator" substitutionGroup="dc:dcmes">
+ <xs:complexType mixed="true">
+ <xs:attributeGroup ref="dc:attlist.dc.creator"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:attributeGroup name="attlist.dc.creator">
+ <xs:attribute ref="xml:lang"/>
+ <xs:attribute ref="rdf:resource"/>
+ </xs:attributeGroup>
+ <!-- The topic of the content of the resource. -->
+ <xs:element name="subject" substitutionGroup="dc:dcmes">
+ <xs:complexType mixed="true">
+ <xs:attributeGroup ref="dc:attlist.dc.subject"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:attributeGroup name="attlist.dc.subject">
+ <xs:attribute ref="xml:lang"/>
+ <xs:attribute ref="rdf:resource"/>
+ </xs:attributeGroup>
+ <!-- An account of the content of the resource. -->
+ <xs:element name="description" substitutionGroup="dc:dcmes">
+ <xs:complexType mixed="true">
+ <xs:attributeGroup ref="dc:attlist.dc.description"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:attributeGroup name="attlist.dc.description">
+ <xs:attribute ref="xml:lang"/>
+ <xs:attribute ref="rdf:resource"/>
+ </xs:attributeGroup>
+ <!-- The entity responsible for making the resource available. -->
+ <xs:element name="publisher" substitutionGroup="dc:dcmes">
+ <xs:complexType mixed="true">
+ <xs:attributeGroup ref="dc:attlist.dc.publisher"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:attributeGroup name="attlist.dc.publisher">
+ <xs:attribute ref="xml:lang"/>
+ <xs:attribute ref="rdf:resource"/>
+ </xs:attributeGroup>
+ <!--
+ An entity responsible for making contributions to the content of
+ the resource.
+ -->
+ <xs:element name="contributor" substitutionGroup="dc:dcmes">
+ <xs:complexType mixed="true">
+ <xs:attributeGroup ref="dc:attlist.dc.contributor"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:attributeGroup name="attlist.dc.contributor">
+ <xs:attribute ref="xml:lang"/>
+ <xs:attribute ref="rdf:resource"/>
+ </xs:attributeGroup>
+ <!-- A date associated with an event in the life cycle of the resource. -->
+ <xs:element name="date" substitutionGroup="dc:dcmes">
+ <xs:complexType mixed="true">
+ <xs:attributeGroup ref="dc:attlist.dc.date"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:attributeGroup name="attlist.dc.date">
+ <xs:attribute ref="xml:lang"/>
+ <xs:attribute ref="rdf:resource"/>
+ </xs:attributeGroup>
+ <!-- The nature or genre of the content of the resource. -->
+ <xs:element name="type" substitutionGroup="dc:dcmes">
+ <xs:complexType mixed="true">
+ <xs:attributeGroup ref="dc:attlist.dc.type"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:attributeGroup name="attlist.dc.type">
+ <xs:attribute ref="xml:lang"/>
+ <xs:attribute ref="rdf:resource"/>
+ </xs:attributeGroup>
+ <!-- The physical or digital manifestation of the resource. -->
+ <xs:element name="format" substitutionGroup="dc:dcmes">
+ <xs:complexType mixed="true">
+ <xs:attributeGroup ref="dc:attlist.dc.format"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:attributeGroup name="attlist.dc.format">
+ <xs:attribute ref="xml:lang"/>
+ <xs:attribute ref="rdf:resource"/>
+ </xs:attributeGroup>
+ <!-- An unambiguous reference to the resource within a given context. -->
+ <xs:element name="identifier" substitutionGroup="dc:dcmes">
+ <xs:complexType mixed="true">
+ <xs:attributeGroup ref="dc:attlist.dc.identifier"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:attributeGroup name="attlist.dc.identifier">
+ <xs:attribute ref="xml:lang"/>
+ <xs:attribute ref="rdf:resource"/>
+ </xs:attributeGroup>
+ <!-- A Reference to a resource from which the present resource is derived. -->
+ <xs:element name="source" substitutionGroup="dc:dcmes">
+ <xs:complexType mixed="true">
+ <xs:attributeGroup ref="dc:attlist.dc.source"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:attributeGroup name="attlist.dc.source">
+ <xs:attribute ref="xml:lang"/>
+ <xs:attribute ref="rdf:resource"/>
+ </xs:attributeGroup>
+ <!-- A language of the intellectual content of the resource. -->
+ <xs:element name="language" substitutionGroup="dc:dcmes">
+ <xs:complexType mixed="true">
+ <xs:attributeGroup ref="dc:attlist.dc.language"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:attributeGroup name="attlist.dc.language">
+ <xs:attribute ref="xml:lang"/>
+ <xs:attribute ref="rdf:resource"/>
+ </xs:attributeGroup>
+ <!-- A reference to a related resource. -->
+ <xs:element name="relation" substitutionGroup="dc:dcmes">
+ <xs:complexType mixed="true">
+ <xs:attributeGroup ref="dc:attlist.dc.relation"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:attributeGroup name="attlist.dc.relation">
+ <xs:attribute ref="xml:lang"/>
+ <xs:attribute ref="rdf:resource"/>
+ </xs:attributeGroup>
+ <!-- The extent or scope of the content of the resource. -->
+ <xs:element name="coverage" substitutionGroup="dc:dcmes">
+ <xs:complexType mixed="true">
+ <xs:attributeGroup ref="dc:attlist.dc.coverage"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:attributeGroup name="attlist.dc.coverage">
+ <xs:attribute ref="xml:lang"/>
+ <xs:attribute ref="rdf:resource"/>
+ </xs:attributeGroup>
+ <!-- Information about rights held in and over the resource. -->
+ <xs:element name="rights" substitutionGroup="dc:dcmes">
+ <xs:complexType mixed="true">
+ <xs:attributeGroup ref="dc:attlist.dc.rights"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:attributeGroup name="attlist.dc.rights">
+ <xs:attribute ref="xml:lang"/>
+ <xs:attribute ref="rdf:resource"/>
+ </xs:attributeGroup>
+</xs:schema>
diff --git a/legacy/resources/schema/plugins.xsd b/legacy/resources/schema/plugins.xsd
new file mode 100644
index 0000000..ef58346
--- /dev/null
+++ b/legacy/resources/schema/plugins.xsd
@@ -0,0 +1,57 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema">
+ <xs:element name="project" type="Project" />
+
+ <xs:complexType name="Project">
+ <xs:all>
+ <xs:element name="name" type="xs:string"/>
+ <xs:element name="description" type="xs:string"/>
+ <xs:element name="url" type="xs:string"/>
+ <xs:element name="pluginlist" type="PluginList"/>
+ </xs:all>
+ </xs:complexType>
+
+ <xs:complexType name="PluginList">
+ <xs:sequence>
+ <xs:element name="plugin" type="Plugin" minOccurs="1" maxOccurs="unbounded"/>
+ </xs:sequence>
+ </xs:complexType>
+
+ <xs:complexType name="Plugin">
+ <xs:all>
+ <xs:element name="uniqueID" type="xs:string"/>
+ <xs:element name="name" type="xs:string"/>
+ <xs:element name="description" type="xs:string"/>
+ <xs:element name="pluginVersion" type="xs:double"/>
+ <xs:element name="cytoscapeVersion" type="xs:string"/>
+ <xs:element name="filetype" type="xs:string"/>
+ <xs:element name="category" type="xs:string" minOccurs="0"/>
+ <xs:element name="url" type="xs:string"/>
+ <xs:element name="license" type="License" minOccurs="0"/>
+ <xs:element name="authorlist" type="AuthorList" maxOccurs="1"/>
+ </xs:all>
+ </xs:complexType>
+
+ <xs:complexType name="License">
+ <xs:sequence>
+ <xs:choice id="license.choice">
+ <xs:element name="text" type="xs:string"/>
+ <xs:element name="url" type="xs:string"/>
+ </xs:choice>
+ </xs:sequence>
+ </xs:complexType>
+
+ <xs:complexType name="AuthorList">
+ <xs:sequence>
+ <xs:element name="author" type="Author" minOccurs="1" maxOccurs="unbounded"/>
+ </xs:sequence>
+ </xs:complexType>
+
+ <xs:complexType name="Author">
+ <xs:all>
+ <xs:element name="name" type="xs:string"/>
+ <xs:element name="institution" type="xs:string"/>
+ </xs:all>
+ </xs:complexType>
+
+</xs:schema>
\ No newline at end of file
diff --git a/legacy/resources/schema/rdf.xsd b/legacy/resources/schema/rdf.xsd
new file mode 100644
index 0000000..67be714
--- /dev/null
+++ b/legacy/resources/schema/rdf.xsd
@@ -0,0 +1,29 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" elementFormDefault="qualified"
+ targetNamespace="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+ xmlns:dc="http://purl.org/dc/elements/1.1/"
+ xmlns:jaxb="http://java.sun.com/xml/ns/jaxb"
+ xmlns:xjc="http://java.sun.com/xml/ns/jaxb/xjc"
+ jaxb:version="2.0" jaxb:extensionBindingPrefixes="xjc">
+
+ <xs:import namespace="http://purl.org/dc/elements/1.1/" schemaLocation="dcmes-xml-dtd.xsd"/>
+ <xs:element name="RDF">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element minOccurs="0" maxOccurs="unbounded" ref="rdf:Description"/>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="Description">
+
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element minOccurs="0" maxOccurs="unbounded" ref="dc:dcmes"/>
+ </xs:sequence>
+ <xs:attributeGroup ref="dc:attlist.rdf.Description"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:attribute name="about"/>
+ <xs:attribute name="resource"/>
+</xs:schema>
diff --git a/legacy/resources/schema/readme.txt b/legacy/resources/schema/readme.txt
new file mode 100644
index 0000000..5709781
--- /dev/null
+++ b/legacy/resources/schema/readme.txt
@@ -0,0 +1,15 @@
+Files in "schema" directry are used by JAXB's xjc schema compiler.
+Feel free to add new schema files here when you need to use JAXB in Cytoscape.
+
+<Schema Directory Contents>
+
+--schema/
+
+ +-- xml.xsd - for basic xml namespace.
+ +-- xlinks-2001.xsd - For xlink
+ +-- cysession.xsd - Schema for CySession.xml
+ +-- rdf.xsd - For RDF/XML
+ +-- dcmes-xml-dtd.xsd - Schema file for Dublin Core ontology
+ +-- xgmml.xsd - Cytoscape XGMML Schema. Slightly modified for JAXB's XJC Compiler.
+
+2_16_2006 Kei Ono (kono at ucsd.edu)
\ No newline at end of file
diff --git a/legacy/resources/schema/xgmml.xsd b/legacy/resources/schema/xgmml.xsd
new file mode 100644
index 0000000..f95aad7
--- /dev/null
+++ b/legacy/resources/schema/xgmml.xsd
@@ -0,0 +1,461 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!--
+ Schema File for XGMML.
+
+ This file is modifed by Keiichiro Ono to support:
+ 1. Additional Attribute Types (boolean, map, and complex)
+ 2. Support for RDF Metadata
+-->
+<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema"
+ targetNamespace="http://www.cs.rpi.edu/XGMML"
+ xmlns:xlink="http://www.w3.org/1999/xlink"
+ xmlns="http://www.cs.rpi.edu/XGMML"
+ xmlns:dc="http://purl.org/dc/elements/1.0/"
+ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+ xmlns:jxb="http://java.sun.com/xml/ns/jaxb"
+ jxb:version="2.0"
+ elementFormDefault="qualified"
+ attributeFormDefault="unqualified"
+ version="xgmml 1.0">
+
+<!-- get access to the xlink: attribute groups for xlink:type (simple) -->
+<xsd:import namespace="http://www.w3.org/1999/xlink"
+ schemaLocation="xlinks-2001.xsd"/>
+
+<!-- For metadata -->
+ <xsd:import namespace="http://purl.org/dc/elements/1.1/"
+ schemaLocation="dcmes-xml-dtd.xsd"/>
+
+<!-- Boolean type -->
+<xsd:simpleType name="boolean.type">
+ <xsd:restriction base="xsd:nonNegativeInteger">
+ <xsd:enumeration value="0"/>
+ <xsd:enumeration value="1"/>
+ </xsd:restriction>
+</xsd:simpleType>
+
+<!-- Positive number type -->
+<xsd:simpleType name="number.type">
+ <xsd:restriction base="xsd:nonNegativeInteger"/>
+</xsd:simpleType>
+
+<!-- ID type -->
+<xsd:simpleType name="id.type">
+ <xsd:restriction base="xsd:NMTOKEN"/>
+</xsd:simpleType>
+
+<xsd:simpleType name="idref.type">
+ <xsd:restriction base="xsd:NMTOKEN"/>
+</xsd:simpleType>
+
+<!-- String type -->
+<xsd:simpleType name="string.type">
+ <xsd:restriction base="xsd:string"/>
+</xsd:simpleType>
+
+<!-- URI type -->
+<xsd:simpleType name="uri.type">
+ <xsd:restriction base="xsd:anyURI"/>
+</xsd:simpleType>
+
+<!-- Anchor type -->
+<xsd:simpleType name="anchor.type">
+ <xsd:restriction base="xsd:NMTOKEN">
+ <xsd:enumeration value="c"/>
+ <xsd:enumeration value="n"/>
+ <xsd:enumeration value="ne"/>
+ <xsd:enumeration value="e"/>
+ <xsd:enumeration value="se"/>
+ <xsd:enumeration value="s"/>
+ <xsd:enumeration value="sw"/>
+ <xsd:enumeration value="w"/>
+ <xsd:enumeration value="nw"/>
+ </xsd:restriction>
+</xsd:simpleType>
+
+<!-- Graphics Type -->
+<xsd:simpleType name="type-graphics.type">
+ <xsd:restriction base="xsd:NMTOKEN">
+
+<!-- Type of Graphics (GML types) type-graphics-gml.type -->
+ <xsd:enumeration value="arc"/>
+ <xsd:enumeration value="bitmap"/>
+ <xsd:enumeration value="image"/>
+ <xsd:enumeration value="line"/>
+ <xsd:enumeration value="oval"/>
+ <xsd:enumeration value="polygon"/>
+ <xsd:enumeration value="rectangle"/>
+ <xsd:enumeration value="text"/>
+
+<!-- Type of Graphics (New types) type-graphics-app.type -->
+ <xsd:enumeration value="box"/>
+ <xsd:enumeration value="circle"/>
+ <xsd:enumeration value="ver_ellipsis"/>
+ <xsd:enumeration value="hor_ellipsis"/>
+ <xsd:enumeration value="rhombus"/>
+ <xsd:enumeration value="triangle"/>
+ <xsd:enumeration value="pentagon"/>
+ <xsd:enumeration value="hexagon"/>
+ <xsd:enumeration value="octagon"/>
+
+<!-- Type of Graphics (Cytoscape Local) -->
+ <xsd:enumeration value="ellipse"/>
+ <xsd:enumeration value="diamond"/>
+ <xsd:enumeration value="paralellogram"/>
+ </xsd:restriction>
+</xsd:simpleType>
+
+<!-- Line types -->
+<!-- Arrow type -->
+<xsd:simpleType name="arrow.type">
+ <xsd:restriction base="xsd:NMTOKEN">
+ <xsd:enumeration value="none"/>
+ <xsd:enumeration value="first"/>
+ <xsd:enumeration value="last"/>
+ <xsd:enumeration value="both"/>
+ </xsd:restriction>
+</xsd:simpleType>
+
+<!-- Capstyle type -->
+<xsd:simpleType name="capstyle.type">
+ <xsd:restriction base="xsd:NMTOKEN">
+ <xsd:enumeration value="butt"/>
+ <xsd:enumeration value="projecting"/>
+ <xsd:enumeration value="round"/>
+ </xsd:restriction>
+</xsd:simpleType>
+
+<!-- Joinstyle type -->
+<xsd:simpleType name="joinstyle.type">
+ <xsd:restriction base="xsd:NMTOKEN">
+ <xsd:enumeration value="bevel"/>
+ <xsd:enumeration value="miter"/>
+ <xsd:enumeration value="round"/>
+ </xsd:restriction>
+</xsd:simpleType>
+
+<!-- Arc style type -->
+<xsd:simpleType name="arcstyle.type">
+ <xsd:restriction base="xsd:NMTOKEN">
+ <xsd:enumeration value="pieslice"/>
+ <xsd:enumeration value="chord"/>
+ <xsd:enumeration value="arc"/>
+ </xsd:restriction>
+</xsd:simpleType>
+
+<!-- Text types -->
+<!-- Text justification type -->
+<xsd:simpleType name="justify.type">
+ <xsd:restriction base="xsd:NMTOKEN">
+ <xsd:enumeration value="left"/>
+ <xsd:enumeration value="right"/>
+ <xsd:enumeration value="center"/>
+ </xsd:restriction>
+</xsd:simpleType>
+
+<!-- Font type -->
+<xsd:simpleType name="font.type">
+ <xsd:restriction base="xsd:string"/>
+</xsd:simpleType>
+
+<!-- Color type -->
+<xsd:simpleType name="color.type">
+ <xsd:restriction base="xsd:string"/>
+</xsd:simpleType>
+
+<!-- Angle type -->
+<!-- Number followed by unit identifier (deg, grad or rad) -->
+<xsd:simpleType name="angle.type">
+ <xsd:restriction base="xsd:string">
+ <xsd:pattern value="(\+|-)?\d*(deg|grad|rad)?"/>
+ </xsd:restriction>
+</xsd:simpleType>
+
+<!-- Object type: Mod. by kono at ucsd.edu -->
+<xsd:simpleType name="object.type">
+ <xsd:restriction base="xsd:NMTOKEN">
+ <xsd:enumeration value="list"/>
+ <xsd:enumeration value="string"/>
+ <xsd:enumeration value="real"/>
+ <xsd:enumeration value="integer"/>
+
+ <xsd:enumeration value="boolean"/>
+ <xsd:enumeration value="map"/>
+ <xsd:enumeration value="complex"/>
+ </xsd:restriction>
+</xsd:simpleType>
+
+<!-- Global Attributes -->
+<xsd:attributeGroup name="global-atts">
+ <xsd:attribute name="id" type="id.type"/>
+ <xsd:attribute name="name" type="string.type"/>
+ <xsd:attribute name="label" type="string.type"/>
+ <xsd:attribute name="labelanchor" type="string.type"/>
+</xsd:attributeGroup>
+
+<!-- Standard XML Attributes -->
+<xsd:attributeGroup name="xml-atts">
+ <xsd:attribute ref="xml:lang"/>
+ <xsd:attribute ref="xml:space"/>
+</xsd:attributeGroup>
+
+<!-- Safe Graph Attributes -->
+<xsd:attributeGroup name="graph-atts-safe">
+ <xsd:attribute name="directed" type="boolean.type"
+ default="0"/>
+</xsd:attributeGroup>
+
+<!-- Unsafe Graph Attributes (GML) -->
+<xsd:attributeGroup name="graph-atts-gml-unsafe">
+ <xsd:attribute name="Vendor" type="string.type"/>
+</xsd:attributeGroup>
+
+<!-- Unsafe Graph Attributes (new attributes) (Graphics attributes) -->
+<xsd:attributeGroup name="graph-atts-app-unsafe-gr">
+ <xsd:attribute name="Scale" type="xsd:integer"/>
+ <xsd:attribute name="Layout" type="string.type"/>
+ <xsd:attribute name="Graphic" type="boolean.type"/>
+</xsd:attributeGroup>
+
+<!-- Unsafe Graph Attributes (new attributes) (Structural attributes) -->
+<xsd:attributeGroup name="graph-atts-app-unsafe-ngr">
+ <xsd:attribute name="Rootnode" type="idref.type"/>
+</xsd:attributeGroup>
+
+<!-- Simple Graph (Structural graph) -->
+<xsd:complexType name="simpleGraph">
+ <xsd:sequence>
+ <xsd:element ref="att" minOccurs="0" maxOccurs="unbounded"/>
+ <xsd:choice minOccurs="0" maxOccurs="unbounded">
+ <xsd:element ref="node"/>
+ <xsd:element ref="edge"/>
+ </xsd:choice>
+ </xsd:sequence>
+ <xsd:attributeGroup ref="global-atts"/>
+ <xsd:attributeGroup ref="xml-atts"/>
+ <xsd:attributeGroup ref="xlink:simpleLink"/>
+ <xsd:attributeGroup ref="graph-atts-safe"/>
+ <xsd:attributeGroup ref="graph-atts-gml-unsafe"/>
+ <xsd:attributeGroup ref="graph-atts-app-unsafe-ngr"/>
+</xsd:complexType>
+
+<!-- Graphical Graph "is a" Simple Graph -->
+<xsd:complexType name="graphicGraph">
+ <xsd:complexContent>
+ <xsd:extension base="simpleGraph">
+ <xsd:attributeGroup ref="graph-atts-app-unsafe-gr"/>
+ </xsd:extension>
+ </xsd:complexContent>
+</xsd:complexType>
+
+<!-- Graph Element -->
+<xsd:element name="graph" type="graphicGraph"/>
+
+<!-- Safe Node Attributes (GML) -->
+<xsd:attributeGroup name="node-atts-gml-safe">
+ <xsd:attribute name="edgeanchor" type="string.type"/>
+</xsd:attributeGroup>
+
+<!-- Safe Node Attributes (new attributes) -->
+<xsd:attributeGroup name="node-atts-app-safe">
+ <xsd:attribute name="weight" type="string.type"/>
+</xsd:attributeGroup>
+
+<!-- Simple Node (Structural Node) -->
+<xsd:complexType name="simpleNode">
+ <xsd:sequence>
+ <xsd:element ref="att" minOccurs="0" maxOccurs="unbounded"/>
+ </xsd:sequence>
+ <xsd:attributeGroup ref="global-atts"/>
+ <xsd:attributeGroup ref="xlink:simpleLink"/>
+ <xsd:attributeGroup ref="node-atts-app-safe"/>
+</xsd:complexType>
+
+<!-- Graphical Node "is a" Simple Node -->
+<xsd:complexType name="graphicNode">
+ <xsd:complexContent>
+ <xsd:extension base="simpleNode">
+ <xsd:sequence>
+ <xsd:element ref="graphics" minOccurs="0"/>
+ </xsd:sequence>
+ <xsd:attributeGroup ref="node-atts-gml-safe"/>
+ </xsd:extension>
+ </xsd:complexContent>
+</xsd:complexType>
+
+<!-- Node Element -->
+<xsd:element name="node" type="graphicNode"/>
+
+<!-- Safe Edge Attributes (GML) -->
+<xsd:attributeGroup name="edge-atts-gml-safe">
+ <xsd:attribute name="source" type="idref.type" use="required"/>
+ <xsd:attribute name="target" type="idref.type" use="required"/>
+</xsd:attributeGroup>
+
+<!-- Safe Edge Attributes (new attributes) -->
+<xsd:attributeGroup name="edge-atts-app-safe">
+ <xsd:attribute name="weight" type="string.type"/>
+</xsd:attributeGroup>
+
+<!-- Simple Edge (Structural Edge) -->
+<xsd:complexType name="simpleEdge">
+ <xsd:sequence>
+ <xsd:element ref="att" minOccurs="0" maxOccurs="unbounded"/>
+ </xsd:sequence>
+ <xsd:attributeGroup ref="global-atts"/>
+ <xsd:attributeGroup ref="xlink:simpleLink"/>
+ <xsd:attributeGroup ref="edge-atts-gml-safe"/>
+ <xsd:attributeGroup ref="edge-atts-app-safe"/>
+</xsd:complexType>
+
+<!-- Graphical Edge "is a" Simple Edge -->
+<xsd:complexType name="graphicEdge">
+ <xsd:complexContent>
+ <xsd:extension base="simpleEdge">
+ <xsd:sequence>
+ <xsd:element ref="graphics" minOccurs="0"/>
+ </xsd:sequence>
+ </xsd:extension>
+ </xsd:complexContent>
+</xsd:complexType>
+
+<!-- Edge Element -->
+<xsd:element name="edge" type="graphicEdge"/>
+
+<!-- Graphics Type -->
+<xsd:attributeGroup name="graphics-type-att">
+ <xsd:attribute name="type" type="type-graphics.type"/>
+</xsd:attributeGroup>
+
+<!-- Point Attributes (x,y,z) -->
+<xsd:attributeGroup name="point-atts">
+ <xsd:attribute name="x" type="xsd:double"/>
+ <xsd:attribute name="y" type="xsd:double"/>
+ <xsd:attribute name="z" type="xsd:double"/>
+</xsd:attributeGroup>
+
+<!-- Dimension Attributes (width,height,depth) -->
+<xsd:attributeGroup name="dimension-atts">
+ <xsd:attribute name="w" type="xsd:double"/>
+ <xsd:attribute name="h" type="xsd:double"/>
+ <xsd:attribute name="d" type="xsd:double"/>
+</xsd:attributeGroup>
+
+<!-- External Attributes (Image and Bitmap) -->
+<xsd:attributeGroup name="external-atts">
+ <xsd:attribute name="image" type="uri.type"/>
+ <xsd:attribute name="bitmap" type="uri.type"/>
+</xsd:attributeGroup>
+
+<!-- Line Attributes -->
+<xsd:attributeGroup name="line-atts">
+ <xsd:attribute name="width" type="number.type"/>
+ <xsd:attribute name="arrow" type="arrow.type"/>
+ <xsd:attribute name="capstyle" type="capstyle.type"/>
+ <xsd:attribute name="joinstyle" type="joinstyle.type"/>
+ <xsd:attribute name="smooth" type="boolean.type"/>
+ <xsd:attribute name="splinesteps" type="number.type"/>
+</xsd:attributeGroup>
+
+<!-- Text Attributes -->
+<xsd:attributeGroup name="text-atts">
+ <xsd:attribute name="justify" type="justify.type"/>
+ <xsd:attribute name="font" type="font.type"/>
+</xsd:attributeGroup>
+
+<!-- Bitmap Attributes -->
+<xsd:attributeGroup name="bitmap-atts">
+ <xsd:attribute name="background" type="color.type"/>
+ <xsd:attribute name="foreground" type="color.type"/>
+</xsd:attributeGroup>
+
+<!-- Arc Attributes -->
+<xsd:attributeGroup name="arc-atts">
+ <xsd:attribute name="extent" type="xsd:integer"/>
+ <xsd:attribute name="start" type="xsd:integer"/>
+ <xsd:attribute name="style" type="arcstyle.type"/>
+</xsd:attributeGroup>
+
+<!-- Graphical Object Attributes -->
+<xsd:attributeGroup name="object-atts">
+ <xsd:attribute name="stipple" type="string.type"/>
+ <xsd:attribute name="visible" type="boolean.type"/>
+ <xsd:attribute name="fill" type="color.type"/>
+ <xsd:attribute name="outline" type="color.type"/>
+ <xsd:attribute name="anchor" type="anchor.type"/>
+</xsd:attributeGroup>
+
+<!-- Graphics Element -->
+<xsd:element name="graphics">
+ <xsd:complexType>
+ <xsd:sequence>
+ <xsd:choice minOccurs="0" maxOccurs="1">
+ <xsd:element ref="Line"/>
+ <xsd:element ref="center"/>
+ </xsd:choice>
+ <xsd:element ref="att" minOccurs="0" maxOccurs="unbounded"/>
+ </xsd:sequence>
+ <xsd:attributeGroup ref="graphics-type-att"/>
+ <xsd:attributeGroup ref="point-atts"/>
+ <xsd:attributeGroup ref="dimension-atts"/>
+ <xsd:attributeGroup ref="external-atts"/>
+ <xsd:attributeGroup ref="line-atts"/>
+ <xsd:attributeGroup ref="text-atts"/>
+ <xsd:attributeGroup ref="bitmap-atts"/>
+ <xsd:attributeGroup ref="arc-atts"/>
+ <xsd:attributeGroup ref="object-atts"/>
+ </xsd:complexType>
+</xsd:element>
+
+<!-- Center Point Element -->
+<xsd:element name="center">
+ <xsd:complexType>
+ <xsd:attributeGroup ref="point-atts"/>
+ </xsd:complexType>
+</xsd:element>
+
+<!-- Line Element -->
+<xsd:element name="Line">
+ <xsd:complexType>
+ <xsd:sequence>
+ <xsd:element ref="point" minOccurs="2" maxOccurs="unbounded"/>
+ </xsd:sequence>
+ </xsd:complexType>
+</xsd:element>
+
+<!-- Point Element -->
+<xsd:element name="point">
+ <xsd:complexType>
+ <xsd:attributeGroup ref="point-atts"/>
+ </xsd:complexType>
+</xsd:element>
+
+<!-- Value Attribute -->
+<xsd:attributeGroup name="attribute-value">
+ <xsd:attribute name="value" type="string.type"/>
+</xsd:attributeGroup>
+
+<!-- Type Attribute -->
+<xsd:attributeGroup name="attribute-type">
+ <xsd:attribute name="type" type="object.type"/>
+</xsd:attributeGroup>
+
+<!-- Att Element -->
+<xsd:element name="att">
+ <xsd:complexType mixed="true">
+ <xsd:sequence>
+ <xsd:element ref="att" minOccurs="0" maxOccurs="unbounded"/>
+ <xsd:element ref="graph" minOccurs="0" maxOccurs="unbounded"/>
+ <xsd:element ref="rdf:RDF" minOccurs="0" maxOccurs="unbounded"/>
+ </xsd:sequence>
+ <xsd:attributeGroup ref="global-atts"/>
+ <xsd:attributeGroup ref="attribute-value"/>
+ <xsd:attributeGroup ref="attribute-type"/>
+ </xsd:complexType>
+</xsd:element>
+
+</xsd:schema>
+
+
+
+
diff --git a/legacy/resources/schema/xml.xsd b/legacy/resources/schema/xml.xsd
new file mode 100644
index 0000000..07d6934
--- /dev/null
+++ b/legacy/resources/schema/xml.xsd
@@ -0,0 +1,146 @@
+<?xml version='1.0'?>
+<xs:schema targetNamespace="http://www.w3.org/XML/1998/namespace" xmlns:xs="http://www.w3.org/2001/XMLSchema" xml:lang="en">
+
+ <xs:annotation>
+ <xs:documentation>
+ See http://www.w3.org/XML/1998/namespace.html and
+ http://www.w3.org/TR/REC-xml for information about this namespace.
+
+ This schema document describes the XML namespace, in a form
+ suitable for import by other schema documents.
+
+ Note that local names in this namespace are intended to be defined
+ only by the World Wide Web Consortium or its subgroups. The
+ following names are currently defined in this namespace and should
+ not be used with conflicting semantics by any Working Group,
+ specification, or document instance:
+
+ base (as an attribute name): denotes an attribute whose value
+ provides a URI to be used as the base for interpreting any
+ relative URIs in the scope of the element on which it
+ appears; its value is inherited. This name is reserved
+ by virtue of its definition in the XML Base specification.
+
+ id (as an attribute name): denotes an attribute whose value
+ should be interpreted as if declared to be of type ID.
+ The xml:id specification is not yet a W3C Recommendation,
+ but this attribute is included here to facilitate experimentation
+ with the mechanisms it proposes. Note that it is _not_ included
+ in the specialAttrs attribute group.
+
+ lang (as an attribute name): denotes an attribute whose value
+ is a language code for the natural language of the content of
+ any element; its value is inherited. This name is reserved
+ by virtue of its definition in the XML specification.
+
+ space (as an attribute name): denotes an attribute whose
+ value is a keyword indicating what whitespace processing
+ discipline is intended for the content of the element; its
+ value is inherited. This name is reserved by virtue of its
+ definition in the XML specification.
+
+ Father (in any context at all): denotes Jon Bosak, the chair of
+ the original XML Working Group. This name is reserved by
+ the following decision of the W3C XML Plenary and
+ XML Coordination groups:
+
+ In appreciation for his vision, leadership and dedication
+ the W3C XML Plenary on this 10th day of February, 2000
+ reserves for Jon Bosak in perpetuity the XML name
+ xml:Father
+ </xs:documentation>
+ </xs:annotation>
+
+ <xs:annotation>
+ <xs:documentation>This schema defines attributes and an attribute group
+ suitable for use by
+ schemas wishing to allow xml:base, xml:lang, xml:space or xml:id
+ attributes on elements they define.
+
+ To enable this, such a schema must import this schema
+ for the XML namespace, e.g. as follows:
+ <schema . . .>
+ . . .
+ <import namespace="http://www.w3.org/XML/1998/namespace"
+ schemaLocation="http://www.w3.org/2001/xml.xsd"/>
+
+ Subsequently, qualified reference to any of the attributes
+ or the group defined below will have the desired effect, e.g.
+
+ <type . . .>
+ . . .
+ <attributeGroup ref="xml:specialAttrs"/>
+
+ will define a type which will schema-validate an instance
+ element with any of those attributes</xs:documentation>
+ </xs:annotation>
+
+ <xs:annotation>
+ <xs:documentation>In keeping with the XML Schema WG's standard versioning
+ policy, this schema document will persist at
+ http://www.w3.org/2005/08/xml.xsd.
+ At the date of issue it can also be found at
+ http://www.w3.org/2001/xml.xsd.
+ The schema document at that URI may however change in the future,
+ in order to remain compatible with the latest version of XML Schema
+ itself, or with the XML namespace itself. In other words, if the XML
+ Schema or XML namespaces change, the version of this document at
+ http://www.w3.org/2001/xml.xsd will change
+ accordingly; the version at
+ http://www.w3.org/2005/08/xml.xsd will not change.
+ </xs:documentation>
+ </xs:annotation>
+
+ <xs:attribute name="lang">
+ <xs:annotation>
+ <xs:documentation>Attempting to install the relevant ISO 2- and 3-letter
+ codes as the enumerated possible values is probably never
+ going to be a realistic possibility. See
+ RFC 3066 at http://www.ietf.org/rfc/rfc3066.txt and the IANA registry
+ at http://www.iana.org/assignments/lang-tag-apps.htm for
+ further information.
+
+ The union allows for the 'un-declaration' of xml:lang with
+ the empty string.</xs:documentation>
+ </xs:annotation>
+ <xs:simpleType>
+ <xs:union memberTypes="xs:language">
+ <xs:simpleType>
+ <xs:restriction base="xs:string">
+ <xs:enumeration value=""/>
+ </xs:restriction>
+ </xs:simpleType>
+ </xs:union>
+ </xs:simpleType>
+ </xs:attribute>
+
+ <xs:attribute name="space">
+ <xs:simpleType>
+ <xs:restriction base="xs:NCName">
+ <xs:enumeration value="default"/>
+ <xs:enumeration value="preserve"/>
+ </xs:restriction>
+ </xs:simpleType>
+ </xs:attribute>
+
+ <xs:attribute name="base" type="xs:anyURI">
+ <xs:annotation>
+ <xs:documentation>See http://www.w3.org/TR/xmlbase/ for
+ information about this attribute.</xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+
+ <xs:attribute name="id" type="xs:ID">
+ <xs:annotation>
+ <xs:documentation>See http://www.w3.org/TR/xml-id/ for
+ information about this attribute.</xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+
+ <xs:attributeGroup name="specialAttrs">
+ <xs:attribute ref="xml:base"/>
+ <xs:attribute ref="xml:lang"/>
+ <xs:attribute ref="xml:space"/>
+ </xs:attributeGroup>
+
+</xs:schema>
diff --git a/packaging/README.txt b/packaging/README.txt
new file mode 100644
index 0000000..31c9697
--- /dev/null
+++ b/packaging/README.txt
@@ -0,0 +1,6 @@
+To build the installer bundles, edit pom.xml to change the <executable>
+for install4jc to where your install4j installation is. Then run:
+
+ mvn install4j:compile
+
+The installers will be created in the target/install4j subdirectory.
diff --git a/packaging/pom.xml b/packaging/pom.xml
new file mode 100644
index 0000000..1c60642
--- /dev/null
+++ b/packaging/pom.xml
@@ -0,0 +1,140 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+
+ <parent>
+ <groupId>cytoscape</groupId>
+ <artifactId>parent</artifactId>
+ <version>2.8.4-SNAPSHOT</version>
+ </parent>
+
+ <groupId>cytoscape</groupId>
+ <artifactId>packaging</artifactId>
+ <packaging>jar</packaging>
+ <name>Cytoscape Release Bundle Packaging</name>
+
+ <pluginRepositories>
+ <pluginRepository>
+ <id>googlecode-maven-install4j</id>
+ <name>googlecode-maven-install4j</name>
+ <url>http://maven-install4j.googlecode.com/svn/m2-repo</url>
+ </pluginRepository>
+ </pluginRepositories>
+
+ <!-- bootstrap for cytoscape dependencies, namely the parent POM snapshots -->
+ <repositories>
+ <repository>
+ <id>cytoscape_snapshots</id>
+ <snapshots>
+ <enabled>true</enabled>
+ </snapshots>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <name>Cytoscape Snapshots</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/</url>
+ </repository>
+ <repository>
+ <id>cytoscape_releases</id>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ <name>Cytoscape Releases</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/releases/</url>
+ </repository>
+ </repositories>
+
+ <build>
+ <resources>
+ <resource>
+ <directory>src/main/install4j</directory>
+ <filtering>true</filtering>
+ </resource>
+ </resources>
+ <plugins>
+ <!-- This will unpack the distribution into the target directory,
+ copy the distribution into target/install4j directory, and
+ unpack the javadoc in the target/install4j directory -->
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-dependency-plugin</artifactId>
+ <executions>
+ <execution>
+ <id>unpack-distribution</id>
+ <goals>
+ <goal>unpack-dependencies</goal>
+ </goals>
+ <configuration>
+ <outputDirectory>${project.build.directory}</outputDirectory>
+ <excludeTransitive>true</excludeTransitive>
+ <includeTypes>zip</includeTypes>
+ <excludeTypes>tar.gz</excludeTypes>
+ </configuration>
+ </execution>
+ <execution>
+ <id>unpack-javadoc</id>
+ <goals>
+ <goal>unpack-dependencies</goal>
+ </goals>
+ <configuration>
+ <outputDirectory>${project.build.directory}/install4j/javadoc</outputDirectory>
+ <excludeTransitive>true</excludeTransitive>
+ <excludeGroupIds>junit</excludeGroupIds>
+ <excludeTypes>zip</excludeTypes>
+ <excludeTypes>tar.gz</excludeTypes>
+ <includeClassifiers>javadoc</includeClassifiers>
+ </configuration>
+ </execution>
+ <execution>
+ <id>copy-distribution</id>
+ <goals>
+ <goal>copy-dependencies</goal>
+ </goals>
+ <configuration>
+ <outputDirectory>${project.build.directory}/install4j</outputDirectory>
+ <excludeTransitive>true</excludeTransitive>
+ <excludeTypes>jar</excludeTypes>
+ </configuration>
+ </execution>
+ </executions>
+ </plugin>
+ <!-- This will create the bundles -->
+ <plugin>
+ <groupId>com.google.code.maven-install4j</groupId>
+ <artifactId>maven-install4j-plugin</artifactId>
+ <version>0.1.1</version>
+ <configuration>
+ <executable>/Applications/install4j 4/bin/install4jc</executable>
+ <configFile>${project.build.outputDirectory}/Cytoscape.install4j</configFile>
+ <releaseId>${project.version}</releaseId>
+ <attach>true</attach>
+ <skipOnMissingExecutable>true</skipOnMissingExecutable>
+ </configuration>
+ </plugin>
+ </plugins>
+ </build>
+
+ <dependencies>
+ <dependency>
+ <groupId>cytoscape</groupId>
+ <artifactId>cytoscape</artifactId>
+ <version>${project.version}</version>
+ <type>zip</type>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape</groupId>
+ <artifactId>cytoscape</artifactId>
+ <version>${project.version}</version>
+ <type>tar.gz</type>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape</groupId>
+ <artifactId>javadoc</artifactId>
+ <version>${project.version}</version>
+ <classifier>javadoc</classifier>
+ </dependency>
+ </dependencies>
+</project>
+
diff --git a/packaging/src/main/images/cytoscape.icns b/packaging/src/main/images/cytoscape.icns
new file mode 100755
index 0000000..5e78bde
Binary files /dev/null and b/packaging/src/main/images/cytoscape.icns differ
diff --git a/packaging/src/main/images/cytoscape_file.icns b/packaging/src/main/images/cytoscape_file.icns
new file mode 100644
index 0000000..6b398f5
Binary files /dev/null and b/packaging/src/main/images/cytoscape_file.icns differ
diff --git a/packaging/src/main/images/gml.icns b/packaging/src/main/images/gml.icns
new file mode 100755
index 0000000..b904997
Binary files /dev/null and b/packaging/src/main/images/gml.icns differ
diff --git a/packaging/src/main/images/icon16x16.png b/packaging/src/main/images/icon16x16.png
new file mode 100755
index 0000000..eb3f5b4
Binary files /dev/null and b/packaging/src/main/images/icon16x16.png differ
diff --git a/packaging/src/main/images/icon32x32.png b/packaging/src/main/images/icon32x32.png
new file mode 100755
index 0000000..119e770
Binary files /dev/null and b/packaging/src/main/images/icon32x32.png differ
diff --git a/packaging/src/main/images/sif.icns b/packaging/src/main/images/sif.icns
new file mode 100755
index 0000000..c6de14f
Binary files /dev/null and b/packaging/src/main/images/sif.icns differ
diff --git a/packaging/src/main/install4j/Cytoscape.install4j b/packaging/src/main/install4j/Cytoscape.install4j
new file mode 100644
index 0000000..4eb51c6
--- /dev/null
+++ b/packaging/src/main/install4j/Cytoscape.install4j
@@ -0,0 +1,931 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<install4j version="4.2.8" transformSequenceNumber="2">
+ <directoryPresets config="${project.build.directory}/cytoscape-${version}" />
+ <application name="Cytoscape" distributionSourceDir="" applicationId="5211-3645-3154-2580" mediaDir="dist" mediaFilePattern="${compiler:sys.shortName}_${compiler:sys.version}_${compiler:sys.platform}" compression="6" lzmaCompression="false" pack200Compression="false" excludeSignedFromPacking="true" keepModificationTimes="false" missingFilesStrategy="warn" shortName="Cytoscape" publisher="Cytoscape Consortium" publisherWeb="http://cytoscape.org" version="${version}" allPathsRelative="tr [...]
+ <languages skipLanguageSelection="false" languageSelectionInPrincipalLanguage="false">
+ <principalLanguage id="en" customLocalizationFile="" />
+ <additionalLanguages />
+ </languages>
+ <searchSequence>
+ <registry />
+ <envVar name="JAVA_HOME" />
+ <envVar name="JDK_HOME" />
+ </searchSequence>
+ <variables>
+ <variable name="WINDOWS_VERSION" value="@windows_version@" />
+ </variables>
+ </application>
+ <files>
+ <filesets />
+ <roots />
+ <mountPoints>
+ <mountPoint id="1" root="" location="" mode="755" />
+ </mountPoints>
+ <entries>
+ <dirEntry mountPoint="1" file="${project.build.directory}/cytoscape-${version}" overwrite="4" shared="false" mode="755" uninstallMode="0" excludeSuffixes="" dirMode="777">
+ <exclude />
+ </dirEntry>
+ </entries>
+ <components />
+ </files>
+ <launchers>
+ <launcher name="Cytoscape" id="3" external="false" excludeFromMenu="false" menuName="" icnsFile="${basedir}/src/main/images/cytoscape.icns" pngIcon16File="${basedir}/src/main/images/icon16x16.png" pngIcon32File="${basedir}/src/main/images/icon32x32.png" macServiceDependencies="" swtApp="false" fileset="">
+ <executable name="Cytoscape" type="1" iconSet="true" iconFile="" executableDir="." redirectStderr="true" stderrFile="output.log" stderrMode="overwrite" redirectStdout="true" stdoutFile="output.log" stdoutMode="overwrite" failOnStderrOutput="true" executableMode="1" changeWorkingDirectory="true" workingDirectory="." singleInstance="false" serviceStartType="2" serviceDependencies="" serviceDescription="" jreLocation="" executionLevel="asInvoker" checkConsoleParameter="false" globalSi [...]
+ <versionInfo include="false" fileVersion="${compiler:WINDOWS_VERSION}" fileDescription="Cytoscape" legalCopyright="Cytoscape Consortium" internalName="${compiler:sys.shortName}" productName="" />
+ </executable>
+ <splashScreen show="false" autoOff="true" alwaysOnTop="true" width="0" height="0" bitmapFile="" java6SplashScreen="false">
+ <text>
+ <statusLine x="20" y="20" text="" font="Arial" fontSize="8" fontColor="0,0,0" fontWeight="500" />
+ <versionLine x="20" y="40" text="version ${compiler:sys.version}" font="Arial" fontSize="8" fontColor="0,0,0" fontWeight="500" />
+ </text>
+ </splashScreen>
+ <java mainClass="cytoscape.CyMain" vmParameters="-Xms10m -Xmx1550m" arguments="-p plugins" allowVMPassthroughParameters="true" preferredVM="" bundleRuntime="true">
+ <classPath>
+ <scanDirectory location="." failOnError="false" />
+ <directory location="lib" failOnError="false" />
+ </classPath>
+ <nativeLibraryDirectories />
+ </java>
+ <includedFiles />
+ <unextractableFiles />
+ <customScript mode="1" file="">
+ <scriptLines />
+ </customScript>
+ </launcher>
+ </launchers>
+ <installerGui installerType="1" suggestPreviousProgramGroup="true" addOnAppId="" suggestPreviousLocations="false">
+ <customCode useInstalledFiles="false" />
+ <applications>
+ <application name="" id="installer" beanClass="com.install4j.runtime.beans.applications.InstallerApplication" enabled="true" commentSet="false" comment="" customIcnsFile="" customIcoFile="">
+ <serializedBean>
+ <java class="java.beans.XMLDecoder">
+ <object class="com.install4j.runtime.beans.applications.InstallerApplication">
+ <void property="allowConsole">
+ <boolean>false</boolean>
+ </void>
+ <void property="allowUnattended">
+ <boolean>false</boolean>
+ </void>
+ <void property="resizable">
+ <boolean>false</boolean>
+ </void>
+ <void property="watermark">
+ <boolean>false</boolean>
+ </void>
+ </object>
+ </java>
+ </serializedBean>
+ <startup>
+ <screen name="" id="5" beanClass="com.install4j.runtime.beans.screens.StartupScreen" enabled="true" commentSet="false" comment="" rollbackBarrier="false" backButton="2" finishScreen="false">
+ <serializedBean>
+ <java class="java.beans.XMLDecoder">
+ <object class="com.install4j.runtime.beans.screens.StartupScreen" />
+ </java>
+ </serializedBean>
+ <condition />
+ <validation />
+ <preActivation />
+ <postActivation />
+ <actions />
+ <formComponents />
+ </screen>
+ </startup>
+ <screens>
+ <screen name="" id="6" beanClass="com.install4j.runtime.beans.screens.WelcomeScreen" enabled="true" commentSet="false" comment="" rollbackBarrier="false" backButton="2" finishScreen="false">
+ <serializedBean>
+ <java class="java.beans.XMLDecoder">
+ <object class="com.install4j.runtime.beans.screens.WelcomeScreen" />
+ </java>
+ </serializedBean>
+ <condition />
+ <validation />
+ <preActivation />
+ <postActivation />
+ <actions />
+ <formComponents />
+ </screen>
+ <screen name="" id="7" beanClass="com.install4j.runtime.beans.screens.LicenseScreen" enabled="true" commentSet="false" comment="" rollbackBarrier="false" backButton="2" finishScreen="false">
+ <serializedBean>
+ <java class="java.beans.XMLDecoder">
+ <object class="com.install4j.runtime.beans.screens.LicenseScreen">
+ <void property="displayedText">
+ <string><!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html><head>
+
+
+<h1>GNU Lesser General Public License</h1>
+
+<tt><!-- Insert License text here -->
+
+
+
+</tt><p><tt>Version 2.1, February 1999</tt></p>
+
+<blockquote>
+<p><tt>Copyright (C) 1991, 1999 Free Software Foundation, Inc.
+59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+Everyone is permitted to copy and distribute verbatim copies
+of this license document, but changing it is not allowed.</tt></p>
+
+<p><tt>[This is the first released version of the Lesser GPL. It also counts
+ as the successor of the GNU Library Public License, version 2, hence
+ the version number 2.1.]</tt></p></blockquote>
+
+<h3><tt>Preamble</tt></h3>
+
+<p><tt> The licenses for most software are designed to take away your
+freedom to share and change it. By contrast, the GNU General Public
+Licenses are intended to guarantee your freedom to share and change
+free software--to make sure the software is free for all its users. </tt></p>
+
+<tt> </tt><p><tt>This license, the Lesser General Public License,
+applies to some specially designated software packages--typically
+libraries--of the Free Software Foundation and other authors who decide
+to use it. You can use it too, but we suggest you first think carefully
+about whether this license or the ordinary General Public License is
+the better strategy to use in any particular case, based on the
+explanations below.
+</tt></p>
+<p><tt> When we speak of free software, we are referring to freedom of
+use, not price. Our General Public Licenses are designed to make sure
+that you have the freedom to distribute copies of free software (and
+charge for this service if you wish); that you receive source code or
+can get it if you want it; that you can change the software and use
+pieces of it in new free programs; and that you are informed that you
+can do these things.</tt></p>
+
+<tt> </tt><p><tt>To protect your rights, we need to make restrictions
+that forbid distributors to deny you these rights or to ask you to
+surrender these rights. These restrictions translate to certain
+responsibilities for you if you distribute copies of the library or if
+you modify it.
+</tt></p>
+<p><tt> For example, if you distribute copies of the library, whether
+gratis or for a fee, you must give the recipients all the rights that
+we gave you. You must make sure that they, too, receive or can get the
+source code. If you link other code with the library, you must provide
+complete object files to the recipients, so that they can relink them
+with the library after making changes to the library and recompiling
+it. And you must show them these terms so they know their rights. </tt></p>
+
+<tt> </tt><p><tt>We protect your rights with a two-step method: (1) we
+copyright the library, and (2) we offer you this license, which gives
+you legal permission to copy, distribute and/or modify the library. </tt></p>
+
+<tt> </tt><p><tt>To protect each distributor, we want to make it very
+clear that there is no warranty for the free library. Also, if the
+library is modified by someone else and passed on, the recipients
+should know that what they have is not the original version, so that
+the original author's reputation will not be affected by problems that
+might be introduced by others. </tt></p>
+<p>
+<tt> Finally, software patents pose a constant threat to the existence
+of any free program. We wish to make sure that a company cannot
+effectively restrict the users of a free program by obtaining a
+restrictive license from a patent holder. Therefore, we insist that any
+patent license obtained for a version of the library must be consistent
+with the full freedom of use specified in this license. </tt></p>
+
+<tt> </tt><p><tt>Most GNU software, including some libraries, is
+covered by the ordinary GNU General Public License. This license, the
+GNU Lesser General Public License, applies to certain designated
+libraries, and is quite different from the ordinary General Public
+License. We use this license for certain libraries in order to permit
+linking those libraries into non-free programs. </tt></p>
+
+<tt> </tt><p><tt>When a program is linked with a library, whether
+statically or using a shared library, the combination of the two is
+legally speaking a combined work, a derivative of the original library.
+The ordinary General Public License therefore permits such linking only
+if the entire combination fits its criteria of freedom. The Lesser
+General Public License permits more lax criteria for linking other code
+with the library. </tt></p>
+
+<tt> </tt><p><tt>We call this license the "Lesser" General Public
+License because it does Less to protect the user's freedom than the
+ordinary General Public License. It also provides other free software
+developers Less of an advantage over competing non-free programs. These
+disadvantages are the reason we use the ordinary General Public License
+for many libraries. However, the Lesser license provides advantages in
+certain special circumstances. </tt></p>
+
+<tt> </tt><p><tt>For example, on rare occasions, there may be a special
+need to encourage the widest possible use of a certain library, so that
+it becomes a de-facto standard. To achieve this, non-free programs must
+be allowed to use the library. A more frequent case is that a free
+library does the same job as widely used non-free libraries. In this
+case, there is little to gain by limiting the free library to free
+software only, so we use the Lesser General Public License.
+</tt></p>
+<tt> </tt><p><tt>In other cases, permission to use a particular library
+in non-free programs enables a greater number of people to use a large
+body of free software. For example, permission to use the GNU C Library
+in non-free programs enables many more people to use the whole GNU
+operating system, as well as its variant, the GNU/Linux operating
+system. </tt></p>
+
+<p><tt> Although the Lesser General Public License is Less protective
+of the users' freedom, it does ensure that the user of a program that
+is linked with the Library has the freedom and the wherewithal to run
+that program using a modified version of the Library.
+</tt></p>
+<tt> </tt><p><tt>The precise terms and conditions for copying,
+distribution and modification follow. Pay close attention to the
+difference between a "work based on the library" and a "work that uses
+the library". The former contains code derived from the library,
+whereas the latter must be combined with the library in order to run. </tt></p>
+
+<h3><tt>TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION</tt></h3>
+
+<p><tt><strong>0.</strong> This License Agreement applies to any
+software library or other program which contains a notice placed by the
+copyright holder or other authorized party saying it may be distributed
+under the terms of this Lesser General Public License (also called
+"this License"). Each licensee is addressed as "you".</tt></p>
+
+<p><tt> A "library" means a collection of software functions and/or
+data prepared so as to be conveniently linked with application programs
+(which use some of those functions and data) to form executables. </tt></p>
+
+<p><tt> The "Library", below, refers to any such software library or
+work which has been distributed under these terms. A "work based on the
+Library" means either the Library or any derivative work under
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+portion of it, either verbatim or with modifications and/or translated
+straightforwardly into another language. (Hereinafter, translation is
+included without limitation in the term "modification".) </tt></p>
+
+<p><tt> "Source code" for a work means the preferred form of the work
+for making modifications to it. For a library, complete source code
+means all the source code for all modules it contains, plus any
+associated interface definition files, plus the scripts used to control
+compilation and installation of the library.</tt></p>
+
+<tt> </tt><p><tt>Activities other than copying, distribution and
+modification are not covered by this License; they are outside its
+scope. The act of running a program using the Library is not
+restricted, and output from such a program is covered only if its
+contents constitute a work based on the Library (independent of the use
+of the Library in a tool for writing it). Whether that is true depends
+on what the Library does and what the program that uses the Library
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+
+<p><tt><strong>1.</strong> You may copy and distribute verbatim copies
+of the Library's complete source code as you receive it, in any medium,
+provided that you conspicuously and appropriately publish on each copy
+an appropriate copyright notice and disclaimer of warranty; keep intact
+all the notices that refer to this License and to the absence of any
+warranty; and distribute a copy of this License along with the Library.
+</tt></p>
+<p><tt> You may charge a fee for the physical act of transferring a
+copy, and you may at your option offer warranty protection in exchange
+for a fee. </tt></p>
+
+<p><tt><strong>2.</strong> You may modify your copy or copies of the
+Library or any portion of it, thus forming a work based on the Library,
+and copy and distribute such modifications or work under the terms of
+Section 1 above, provided that you also meet all of these conditions:
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+
+<blockquote>
+<p><tt>a) The modified work must itself be a software library. </tt></p>
+<p><tt>b) You must cause the files modified to carry prominent notices stating that you changed the files and the date of any change.</tt></p>
+<p><tt>c) You must cause the whole of the work to be licensed at no charge to all third parties under the terms of this License. </tt></p>
+<p><tt>d) If a facility in the modified Library refers to a function or
+a table of data to be supplied by an application program that uses the
+facility, other than as an argument passed when the facility is
+invoked, then you must make a good faith effort to ensure that, in the
+event an application does not supply such function or table, the
+facility still operates, and performs whatever part of its purpose
+remains meaningful. </tt></p>
+
+
+<p><tt> (For example, a function in a library to compute square roots
+has a purpose that is entirely well-defined independent of the
+application. Therefore, Subsection 2d requires that any
+application-supplied function or table used by this function must be
+optional: if the application does not supply it, the square root
+function must still compute square roots.) </tt></p>
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+
+
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+ </installerGui>
+ <mediaSets>
+ <macosFolder name="Mac OS X Folder" id="9" mediaFileName="" installDir="Cytoscape_v${compiler:sys.version}" overridePrincipalLanguage="true" requires64bit="false" jreBitType="all" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" customInstallBaseDir="" createUninstallIcon="true" contentFilesType="1" downloadURL="">
+ <excludedLaunchers />
+ <excludedComponents />
+ <excludedBeans />
+ <overriddenPrincipalLanguage id="en" customLocalizationFile="" />
+ <exclude />
+ <variables />
+ </macosFolder>
+ <win32 name="Windows 64 bit" id="11" mediaFileName="Cytoscape_${compiler:sys.version}_windows_64bit" installDir="Cytoscape_v${compiler:sys.version}" overridePrincipalLanguage="true" requires64bit="true" jreBitType="64" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" includedJRE="" manualJREEntry="false" bundleType="1" jreURL="" jreFtpURL="" jreShared="false" directDownload="false" customInstallBaseDir="" createUninstallIcon="true" contentFilesType="1" downl [...]
+ <excludedLaunchers />
+ <excludedComponents />
+ <excludedBeans>
+ <bean refId="50" />
+ </excludedBeans>
+ <overriddenPrincipalLanguage id="en" customLocalizationFile="" />
+ <exclude />
+ <variables />
+ </win32>
+ <unixInstaller name="Unix Installer" id="12" mediaFileName="" installDir="Cytoscape_v${compiler:sys.version}" overridePrincipalLanguage="true" requires64bit="false" jreBitType="all" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" includedJRE="" manualJREEntry="false" bundleType="1" jreURL="" jreFtpURL="" jreShared="false" directDownload="false" customInstallBaseDir="" createUninstallIcon="true" contentFilesType="1" downloadURL="">
+ <excludedLaunchers />
+ <excludedComponents />
+ <excludedBeans>
+ <bean refId="50" />
+ </excludedBeans>
+ <overriddenPrincipalLanguage id="en" customLocalizationFile="" />
+ <exclude />
+ <variables />
+ <installerScript mode="1" file="">
+ <scriptLines />
+ </installerScript>
+ </unixInstaller>
+ <win32 name="Windows 32 bit" id="166" mediaFileName="Cytoscape_${compiler:sys.version}_windows_32bit" installDir="Cytoscape_v${compiler:sys.version}" overridePrincipalLanguage="true" requires64bit="false" jreBitType="32" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" includedJRE="" manualJREEntry="false" bundleType="1" jreURL="" jreFtpURL="" jreShared="false" directDownload="false" customInstallBaseDir="" createUninstallIcon="true" contentFilesType="1" dow [...]
+ <excludedLaunchers />
+ <excludedComponents />
+ <excludedBeans />
+ <overriddenPrincipalLanguage id="en" customLocalizationFile="" />
+ <exclude />
+ <variables />
+ </win32>
+ </mediaSets>
+ <buildIds buildAll="true">
+ <mediaSet refId="11" />
+ </buildIds>
+</install4j>
+
diff --git a/pom.xml b/pom.xml
new file mode 100644
index 0000000..6c58156
--- /dev/null
+++ b/pom.xml
@@ -0,0 +1,225 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+
+ <groupId>cytoscape</groupId>
+ <artifactId>parent</artifactId>
+ <packaging>pom</packaging>
+ <version>2.8.4-SNAPSHOT</version>
+ <name>Cytoscape Parent POM</name>
+
+ <properties>
+ <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+ </properties>
+
+ <profiles>
+ <profile>
+ <id>work</id>
+ <activation>
+ <activeByDefault>true</activeByDefault>
+ </activation>
+ <modules>
+ <module>corelibs</module>
+ <module>application</module>
+ <module>coreplugins</module>
+ <module>distribution</module>
+ </modules>
+ </profile>
+ <profile>
+ <id>release</id>
+ <modules>
+ <module>corelibs</module>
+ <module>application</module>
+ <module>coreplugins</module>
+ <module>distribution</module>
+ <module>javadoc</module>
+ <module>packaging</module>
+ </modules>
+ </profile>
+ <profile>
+ <id>all</id>
+ <modules>
+ <module>corelibs</module>
+ <module>application</module>
+ <module>coreplugins</module>
+ <module>distribution</module>
+ <module>javadoc</module>
+ <module>packaging</module>
+ <module>webstart</module>
+ <module>archetypes</module>
+ </modules>
+ </profile>
+ </profiles>
+
+
+ <build>
+ <plugins>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-release-plugin</artifactId>
+ <version>2.1</version>
+ <configuration>
+ <tagBase>svn+ssh://grenache.ucsd.edu/cellar/common/svn/cytoscape/tags</tagBase>
+ <autoVersionSubmodules>true</autoVersionSubmodules>
+ <goals>deploy</goals>
+ <!-- we need this for corelibs/docs to be installed so that
+ application will build correctly -->
+ <preparationGoals>clean install</preparationGoals>
+ </configuration>
+ </plugin>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-compiler-plugin</artifactId>
+ <version>2.3.2</version>
+ <configuration>
+ <source>1.6</source>
+ <target>1.6</target>
+ <optimize>true</optimize>
+ <showWarnings>true</showWarnings>
+ <showDeprecation>true</showDeprecation>
+ </configuration>
+ </plugin>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-surefire-plugin</artifactId>
+ <version>2.7.1</version>
+ <configuration>
+ <argLine>-Xmx256m</argLine>
+ <redirectTestOutputToFile>true</redirectTestOutputToFile>
+ </configuration>
+ </plugin>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-javadoc-plugin</artifactId>
+ <version>2.7</version>
+ <configuration>
+ <encoding>UTF-8</encoding>
+ <locale>en</locale>
+ <javadocVersion>1.6</javadocVersion>
+ <links>
+ <link>http://download.oracle.com/javase/1.5.0/docs/api/</link>
+ </links>
+ <footer>Cytoscape ${project.version} API</footer>
+ <header>Cytoscape ${project.version} API</header>
+ <bottom>Copyright 2010 Cytoscape Consortium. All rights reserved.</bottom>
+ <maxmemory>2g</maxmemory>
+ <additionalJOption>-J-Xmx2g</additionalJOption>
+ </configuration>
+ <executions>
+ <execution>
+ <id>attach-javadocs</id>
+ <goals>
+ <goal>jar</goal>
+ </goals>
+ </execution>
+ </executions>
+ </plugin>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-source-plugin</artifactId>
+ <version>2.1.2</version>
+ <executions>
+ <execution>
+ <id>attach-sources</id>
+ <goals>
+ <goal>jar</goal>
+ </goals>
+ </execution>
+ </executions>
+ </plugin>
+ </plugins>
+ </build>
+
+ <dependencies>
+ <dependency>
+ <groupId>junit</groupId>
+ <artifactId>junit</artifactId>
+ <version>3.8.1</version>
+ <scope>test</scope>
+ </dependency>
+ </dependencies>
+
+ <!--
+ Don't add additional repositories!
+ We want everything coming from either Maven Central or our repository.
+ Remember, it's easy to add third party jars to our repository.
+ -->
+ <repositories>
+ <repository>
+ <id>cytoscape_snapshots</id>
+ <snapshots>
+ <enabled>true</enabled>
+ </snapshots>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <name>Cytoscape Snapshots</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/</url>
+ </repository>
+ <repository>
+ <id>cytoscape_releases</id>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ <name>Cytoscape Releases</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/releases/</url>
+ </repository>
+ <repository>
+ <id>cytoscape_thirdparty</id>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ <name>Cytoscape Third Party</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/thirdparty/</url>
+ </repository>
+ <repository>
+ <id>cytoscape_biopax_release</id>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ <name>Cytoscape BioPAX Release Mirror</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/biopax-release/</url>
+ </repository>
+ <repository>
+ <id>cytoscape_biopax_snapshot</id>
+ <snapshots>
+ <enabled>true</enabled>
+ </snapshots>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <name>Cytoscape BioPAX Snapshot Mirror</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/biopax-snapshot/</url>
+ </repository>
+ </repositories>
+
+ <distributionManagement>
+ <repository>
+ <id>releases</id>
+ <name>Internal Releases</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/releases</url>
+ </repository>
+ <snapshotRepository>
+ <id>snapshots</id>
+ <name>Internal Snapshots</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots</url>
+ </snapshotRepository>
+ </distributionManagement>
+
+ <scm>
+ <connection>scm:svn:http://chianti.ucsd.edu/svn/cytoscape/trunk</connection>
+ <developerConnection>scm:svn:svn+ssh://grenache.ucsd.edu/cellar/common/svn/cytoscape/trunk</developerConnection>
+ <url>http://chianti.ucsd.edu/svn/cytoscape/trunk</url>
+ </scm>
+
+
+</project>
+
diff --git a/webstart/README.txt b/webstart/README.txt
new file mode 100644
index 0000000..0e5dd91
--- /dev/null
+++ b/webstart/README.txt
@@ -0,0 +1,17 @@
+
+This project generates a JNLP file and associated jars suitable for running
+Cytoscape as a webstart. To generate things run:
+
+ mvn webstart:jnlp-inline -Dwebstart.url=http://example.com
+
+Note that the "-Dwebstart.url=http://example.com" argument is manadatory to
+provide the jnlp file with a codebase.
+
+
+If this is your first time using Webstart you must create a keystore:
+
+ keytool -genkey -alias cytoscape -keypass secret
+ enter "secret" for the password.
+
+The actual keystore file created is assumed to be in: ${user.home}/.keystore
+
diff --git a/webstart/pom.xml b/webstart/pom.xml
new file mode 100644
index 0000000..680b9a3
--- /dev/null
+++ b/webstart/pom.xml
@@ -0,0 +1,222 @@
+<!-- Test project which creates and signs a jar artifact -->
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+
+ <parent>
+ <groupId>cytoscape</groupId>
+ <artifactId>parent</artifactId>
+ <version>2.8.3-SNAPSHOT</version>
+ </parent>
+
+ <groupId>cytoscape</groupId>
+ <artifactId>webstart</artifactId>
+ <packaging>pom</packaging>
+ <name>Cytoscape Webstart</name>
+
+ <!-- This is the url used to define the codebase of the jnlp file. -->
+ <url>${webstart.url}</url>
+
+ <!-- bootstrap for cytoscape dependencies, namely the parent POM snapshots -->
+ <repositories>
+ <repository>
+ <id>cytoscape_snapshots</id>
+ <snapshots>
+ <enabled>true</enabled>
+ </snapshots>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <name>Cytoscape Snapshots</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/</url>
+ </repository>
+ <repository>
+ <id>cytoscape_releases</id>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ <name>Cytoscape Releases</name>
+ <url>http://cytoscape.wodaklab.org/nexus/content/repositories/releases/</url>
+ </repository>
+ </repositories>
+
+ <build>
+ <plugins>
+ <plugin>
+ <groupId>org.codehaus.mojo.webstart</groupId>
+ <artifactId>webstart-maven-plugin</artifactId>
+ <version>1.0-beta-1</version>
+ <executions>
+ <execution>
+ <goals>
+ <goal>jnlp-inline</goal>
+ </goals>
+ </execution>
+ </executions>
+ <configuration>
+ <excludeTransitive>true</excludeTransitive>
+ <resourcesDirectory>${project.basedir}/src/main/resources</resourcesDirectory>
+ <libPath>lib</libPath>
+ <jnlp>
+ <inputTemplateResourcePath>${project.basedir}/src/main/jnlp</inputTemplateResourcePath>
+ <inputTemplate>template.vm</inputTemplate>
+ <outputFile>cytoscape.jnlp</outputFile>
+ <mainClass>cytoscape.CyMain</mainClass>
+ </jnlp>
+ <!--
+ If this is your first time using Webstart you must create a keystore:
+ keytool -genkey -alias cytoscape -keypass secret
+ enter "secret" for the password.
+ The actual keystore file created is assumed to be in: ${user.home}/.keystore
+ -->
+ <sign>
+ <keypass>secret</keypass>
+ <storepass>secret</storepass>
+ <alias>cytoscape</alias>
+ <verify>true</verify>
+ </sign>
+ <verbose>true</verbose>
+ </configuration>
+ </plugin>
+ </plugins>
+ </build>
+
+ <dependencies>
+ <!-- the application -->
+ <dependency>
+ <groupId>cytoscape</groupId>
+ <artifactId>application</artifactId>
+ <version>${project.version}</version>
+ <classifier>jar-with-dependencies</classifier>
+ </dependency>
+ <!-- coreplugins -->
+ <dependency>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>advanced-network-merge</artifactId>
+ <version>${project.version}</version>
+ <classifier>jar-with-dependencies</classifier>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>automatic-layout</artifactId>
+ <version>${project.version}</version>
+ <classifier>jar-with-dependencies</classifier>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>biomart-client</artifactId>
+ <version>${project.version}</version>
+ <classifier>jar-with-dependencies</classifier>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>biopax</artifactId>
+ <version>${project.version}</version>
+ <classifier>jar-with-dependencies</classifier>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>editor</artifactId>
+ <version>${project.version}</version>
+ <classifier>jar-with-dependencies</classifier>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>equation-functions</artifactId>
+ <version>${project.version}</version>
+ <classifier>jar-with-dependencies</classifier>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>manual-layout</artifactId>
+ <version>${project.version}</version>
+ <classifier>jar-with-dependencies</classifier>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>ncbi-client</artifactId>
+ <version>${project.version}</version>
+ <classifier>jar-with-dependencies</classifier>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>psi-mi</artifactId>
+ <version>${project.version}</version>
+ <classifier>jar-with-dependencies</classifier>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>rfilters</artifactId>
+ <version>${project.version}</version>
+ <classifier>jar-with-dependencies</classifier>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>sbml-reader</artifactId>
+ <version>${project.version}</version>
+ <classifier>jar-with-dependencies</classifier>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>table-import</artifactId>
+ <version>${project.version}</version>
+ <classifier>jar-with-dependencies</classifier>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>attribute-browser</artifactId>
+ <version>${project.version}</version>
+ <classifier>jar-with-dependencies</classifier>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>cpath</artifactId>
+ <version>${project.version}</version>
+ <classifier>jar-with-dependencies</classifier>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>cpath2</artifactId>
+ <version>${project.version}</version>
+ <classifier>jar-with-dependencies</classifier>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>linkout</artifactId>
+ <version>${project.version}</version>
+ <classifier>jar-with-dependencies</classifier>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>quickfind</artifactId>
+ <version>${project.version}</version>
+ <classifier>jar-with-dependencies</classifier>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>filters</artifactId>
+ <version>${project.version}</version>
+ <classifier>jar-with-dependencies</classifier>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>core-commands</artifactId>
+ <version>${project.version}</version>
+ <classifier>jar-with-dependencies</classifier>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>network-analyzer</artifactId>
+ <version>${project.version}</version>
+ <classifier>jar-with-dependencies</classifier>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape-temp</groupId>
+ <artifactId>y-layouts</artifactId>
+ <version>1.0.1</version>
+ </dependency>
+ </dependencies>
+
+</project>
diff --git a/webstart/src/main/jnlp/template.vm b/webstart/src/main/jnlp/template.vm
new file mode 100644
index 0000000..ed2f831
--- /dev/null
+++ b/webstart/src/main/jnlp/template.vm
@@ -0,0 +1,57 @@
+<?xml version="1.0" encoding="utf-8"?>
+<jnlp codebase="$project.Url" href="$outputFile">
+ <information>
+ <title>Cytoscape</title>
+ <vendor>Cytoscape Consortium</vendor>
+ <homepage href="http://cytoscape.org"/>
+ <offline-allowed/>
+ </information>
+ <security>
+ <all-permissions/>
+ </security>
+ <resources>
+ <j2se version="$j2seVersion" max-heap-size="1024M"/>
+ $dependencies
+ </resources>
+ <application-desc main-class="$mainClass">
+ <argument>-p</argument>
+ <argument>csplugins.network.merge.NetworkMergePlugin</argument>
+ <argument>-p</argument>
+ <argument>csplugins.layout.LayoutPlugin</argument>
+ <argument>-p</argument>
+ <argument>edu.ucsd.bioeng.idekerlab.biomartclient.BiomartClientPlugin</argument>
+ <argument>-p</argument>
+ <argument>cytoscape.coreplugins.biopax.BiopaxPlugin</argument>
+ <argument>-p</argument>
+ <argument>browser.AttributeBrowserPlugin</argument>
+ <argument>-p</argument>
+ <argument>org.cytoscape.coreplugin.cpath.plugin.CPathPlugIn</argument>
+ <argument>-p</argument>
+ <argument>org.cytoscape.coreplugin.cpath2.plugin.CPathPlugIn2</argument>
+ <argument>-p</argument>
+ <argument>cytoscape.editor.CytoscapeEditorPlugin</argument>
+ <argument>-p</argument>
+ <argument>org.cytoscape.EquationFunctions.EquationFunctionsPlugin</argument>
+ <argument>-p</argument>
+ <argument>filter.cytoscape.CsFilter</argument>
+ <argument>-p</argument>
+ <argument>cytoscape.filters.FilterPlugin</argument>
+ <argument>-p</argument>
+ <argument>linkout.LinkOutPlugin</argument>
+ <argument>-p</argument>
+ <argument>ManualLayout.ManualLayoutPlugin</argument>
+ <argument>-p</argument>
+ <argument>edu.ucsd.bioeng.idekerlab.ncbiclient.NCBIClientPlugin</argument>
+ <argument>-p</argument>
+ <argument>org.cytoscape.coreplugin.psi_mi.plugin.PsiMiPlugIn</argument>
+ <argument>-p</argument>
+ <argument>csplugins.quickfind.plugin.QuickFindPlugIn</argument>
+ <argument>-p</argument>
+ <argument>sbmlreader.SBMLReaderPlugin</argument>
+ <argument>-p</argument>
+ <argument>edu.ucsd.bioeng.coreplugin.tableImport.TableImportPlugin</argument>
+ <argument>-p</argument>
+ <argument>yfiles.YFilesLayoutPlugin</argument>
+ </application-desc>
+</jnlp>
+
--
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